BLASTP 2.2.22 [Sep-27-2009]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


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


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

Query= gi|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


Results from round 1


>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 =  724 bits (1869), Expect = 0.0,   Method: Compositional matrix adjust.
 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|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 =  498 bits (1281), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 248/361 (68%), Positives = 295/361 (81%), Gaps = 15/361 (4%)

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   +  +  DD ++ K   S+ +G +K+K 
Sbjct: 248 LREQLGANLLKEARVNLEGLVYSSETPIRDHSKMKVK-SDDISKTKNKKSKVHGFNKKKH 306

Query: 301 LATPVHRRNLASNVWMAKGIHSSF------------LSDSG--QREENHRRSPSFPSKRS 346
           +  P+ RRN +SNVWMA+GIHSS             + D+G  +R+ +H+R+     K  
Sbjct: 307 VDFPIQRRNRSSNVWMAQGIHSSLPYEKQGEKDYQSMHDTGFKKRKYSHKRNKKLHKKSP 366

Query: 347 L 347
           L
Sbjct: 367 L 367


>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 =  357 bits (915), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 189/370 (51%), Positives = 241/370 (65%), Gaps = 28/370 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  ER
Sbjct: 46  PQRISKILSRAGVASRRDVERMIMEGRVSLNGVVLDTPVVNATLADRIEVDGHPIRGIER 105

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+SVGRLDINTEGLLLLTNDGGLAR
Sbjct: 106 TRLWLYHKPGGLVTTNADPEGRPTVFENLPEELPRVLSVGRLDINTEGLLLLTNDGGLAR 165

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELPST WLR YRVR HG++DQ+ L+ LK+GI + G+ YG ++ TLD  +GSN W+T+G
Sbjct: 166 VLELPSTGWLRRYRVRAHGEIDQEALDRLKEGIAVDGVLYGAIEATLDRVQGSNVWITMG 225

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+ +
Sbjct: 226 LREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLIAD 285

Query: 253 AQVNLDAPIYSSETLV---------RDRPNIIS--EVPDDF---------TRMKKNSSQK 292
           ++ N DAPIY+ +             D+    S  E  +D          TR       +
Sbjct: 286 SKANFDAPIYNDQPAAAEPEAEPADHDKAEWGSKREKAEDKRERALARLDTRRDDGRPSE 345

Query: 293 NGLSKQK---KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN-----HRRSPSFPSK 344
            G S+ K   + A P  RRN +SNVWMA G   +        E++      RR+P+   +
Sbjct: 346 RGRSRGKPEERPARPPVRRNRSSNVWMAPGARPTVEKKPKAAEDDLSPKGARRAPAEGKR 405

Query: 345 RSLRRTSAKK 354
           R   + +A K
Sbjct: 406 RDRPKDAAAK 415


>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 =  356 bits (914), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 166/250 (66%), Positives = 197/250 (78%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GRSTVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRSTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQD L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPATGWLRRYRVRAHGEIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L+EEA
Sbjct: 232 REGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVVEVRGRTLRDQLGPRLIEEA 291

Query: 254 QVNLDAPIYS 263
           + N DAPIY+
Sbjct: 292 KANFDAPIYN 301


>gi|150395641|ref|YP_001326108.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150027156|gb|ABR59273.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 576

 Score =  356 bits (914), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 175/336 (52%), Positives = 226/336 (67%), Gaps = 24/336 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  ER
Sbjct: 47  PQRISKILSRAGVASRRDVERMIMEGRVSLNGLVLDTPVVNATLADRIEVDGHPIRGIER 106

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+S+GRLDINTEGLLLLTNDGGLAR
Sbjct: 107 TRLWLYHKPGGLVTTNADPEGRPTVFENLPEDLPRVLSIGRLDINTEGLLLLTNDGGLAR 166

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELPST WLR YRVR HG++DQ  L+ LK+GI ++G+ YG ++ TLD  +GSN W+T+G
Sbjct: 167 VLELPSTGWLRRYRVRAHGEIDQAALDRLKEGIAVEGVLYGAIEATLDRVQGSNVWITMG 226

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+ +
Sbjct: 227 LREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLIAD 286

Query: 253 AQVNLDAPIYSSETLVRD------------------------RPNIISEVPDDFTRMKKN 288
           A+ N DAPIY+ ++   +                        R   ++ +       + N
Sbjct: 287 AKANFDAPIYNDQSTAAEPEAEPVADHGKAEWGSKREKAGDKRERALARLDTRRDDGRPN 346

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSF 324
              ++    +++ A P  RRN +SNVWMA G   + 
Sbjct: 347 DRGRSRGKAEERPARPPLRRNRSSNVWMAPGARPTV 382


>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 =  356 bits (913), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 187/373 (50%), Positives = 239/373 (64%), Gaps = 34/373 (9%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  ER
Sbjct: 46  PQRISKILSRAGVASRRDVERMIMEGRVSLNGVVLDTPVVNATLADRIEVDGHPIRGIER 105

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+SVGRLDINTEGLLLLTNDGGLAR
Sbjct: 106 TRLWLYHKPGGLVTTNADPEGRPTVFENLPEELPRVLSVGRLDINTEGLLLLTNDGGLAR 165

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELPST WLR YRVR HG++DQ+ L+ LK+GI + G+ YG ++ TLD  +GSN W+T+G
Sbjct: 166 VLELPSTGWLRRYRVRAHGEIDQEALDRLKEGIAVDGVLYGAIEATLDRVQGSNVWITMG 225

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+ +
Sbjct: 226 LREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLIAD 285

Query: 253 AQVNLDAPIYSS-----------------------ETLVRDRPNIISEVPDDFTRMKKNS 289
           ++ N DAPIY+                        E     R   ++ +    TR     
Sbjct: 286 SKANFDAPIYNDQPAAAEPEAEPADHGKAEWGSKREKAEDKRERALARL---DTRRDDGR 342

Query: 290 SQKNGLSKQK---KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN-----HRRSPSF 341
             + G S+ K   + A P  RRN +SNVWMA G   +        E++      RR+P+ 
Sbjct: 343 PSERGRSRGKPEERPARPPVRRNRSSNVWMAPGARPTVEKKPKAAEDDLSPKGARRAPAE 402

Query: 342 PSKRSLRRTSAKK 354
             +R   + +A K
Sbjct: 403 GKRRDRPKDAAAK 415


>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 =  355 bits (912), Expect = 5e-96,   Method: Compositional matrix adjust.
 Identities = 175/335 (52%), Positives = 224/335 (66%), Gaps = 26/335 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR+SK+++RAG+ASRR++ERMI + RVK+NG++LE   VN    D IEVDG P+R  ER
Sbjct: 46  PQRISKILSRAGVASRRDIERMIMEGRVKLNGVVLETPVVNATLADQIEVDGHPIRGIER 105

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLY+KP GLVTT+SDP+GR TVFDNLP    RV+SVGRLDINTEGLLLLTNDGGLAR
Sbjct: 106 TRLWLYYKPAGLVTTNSDPEGRPTVFDNLPDELPRVLSVGRLDINTEGLLLLTNDGGLAR 165

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELPST WLR YRVR HG++DQ+ L+ LK+GI + G+ YG ++ TLD  +GSN W+T+G
Sbjct: 166 ALELPSTGWLRRYRVRAHGEIDQEALDRLKEGIAVDGVLYGAIEATLDRVQGSNVWITMG 225

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LR+QLGP L+ E
Sbjct: 226 LREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPEGHVQEIRGRTLRDQLGPRLIAE 285

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPD-----DFTRMKKNSSQKNGLSK---------- 297
           ++ N DAP+Y+ +    +R       P+        R K    ++  L++          
Sbjct: 286 SKANFDAPLYNDQPAAPEREAHNEVAPEWGKERSARREKPEDKRERALARLDTQRDDSRS 345

Query: 298 -----------QKKLATPVHRRNLASNVWMAKGIH 321
                      + + A P  +R+  +NVWMA G  
Sbjct: 346 RDRRERPREKFEDRPARPPAKRSRTANVWMAPGAR 380


>gi|222085015|ref|YP_002543544.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221722463|gb|ACM25619.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 680

 Score =  355 bits (910), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 163/251 (64%), Positives = 201/251 (80%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI   RV++NG+LL+   VNV   D IEVDG+P+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMDGRVRLNGVLLDSPVVNVTLADKIEVDGMPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLARV
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARV 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQD L+ LK+GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPTTGWLRRYRVRAHGEIDQDALDKLKEGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L+E+A
Sbjct: 232 REGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGRVLEVRGRTLRDQLGPRLVEDA 291

Query: 254 QVNLDAPIYSS 264
           + N DAP+Y++
Sbjct: 292 KANFDAPLYNA 302


>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 =  355 bits (910), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 165/252 (65%), Positives = 199/252 (78%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+SK++ARAG+ASRR+VERMI + RV +NG+LL+   VN   +D IEVDG+P+R AER
Sbjct: 56  PERISKIMARAGVASRRDVERMIMEGRVSLNGVLLDTPVVNATLSDKIEVDGMPIRGAER 115

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGL+R
Sbjct: 116 TRLWLYHKPAGLVTTNSDPEGRPTVFDNLPGELPRVLSIGRLDINTEGLLLLTNDGGLSR 175

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELP+T WLR YRVR HG+VDQ  L+ LK GI + G+ YG +  TLD  +G N W+T+G
Sbjct: 176 VLELPTTGWLRRYRVRAHGEVDQAALDKLKDGIAVDGVLYGAIDATLDRTQGHNVWITMG 235

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  ++LR+QLGP L+EE
Sbjct: 236 LREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGKVLEVRGRMLRDQLGPRLIEE 295

Query: 253 AQVNLDAPIYSS 264
           A  N DAPIY++
Sbjct: 296 AGANFDAPIYNT 307


>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 =  353 bits (906), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 164/250 (65%), Positives = 196/250 (78%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R  ERT
Sbjct: 48  ERISKVMARAGVASRRDIERMIMEGRVTLNGAVLDTPVVNVTLADRIEVDGVPIRGIERT 107

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 108 RLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 167

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG +DQD L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 168 LELPATGWLRRYRVRAHGDIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 227

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L+EEA
Sbjct: 228 REGKNREIKNVMGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGRTLRDQLGPRLIEEA 287

Query: 254 QVNLDAPIYS 263
           + N DAPIY+
Sbjct: 288 KANFDAPIYN 297


>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 =  353 bits (906), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 164/251 (65%), Positives = 197/251 (78%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGRVLDTPVVNVTLADRIEVDGVPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GRSTVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 112 RLWLYHKPTGLVTTNADPEGRSTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQD L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPATGWLRRYRVRAHGEIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V       VNRLIRISYGPFQLG L      EV  + LR+QLGP L+EEA
Sbjct: 232 REGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPESHVVEVRGRTLRDQLGPRLIEEA 291

Query: 254 QVNLDAPIYSS 264
           + N DAPIY++
Sbjct: 292 KANFDAPIYNT 302


>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 =  350 bits (898), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 163/250 (65%), Positives = 196/250 (78%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGKVLDTPVVNVTLADRIEVDGVPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L+EEA
Sbjct: 232 REGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVVEVRGRTLRDQLGPRLIEEA 291

Query: 254 QVNLDAPIYS 263
           + N DAPIY+
Sbjct: 292 KANFDAPIYN 301


>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 =  349 bits (896), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 163/250 (65%), Positives = 196/250 (78%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDG+P+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGKVLETPVVNVTLADRIEVDGMPVRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L+EEA
Sbjct: 232 REGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGRTLRDQLGPRLIEEA 291

Query: 254 QVNLDAPIYS 263
           + N DAPIY+
Sbjct: 292 KANFDAPIYN 301


>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 =  349 bits (895), Expect = 4e-94,   Method: Compositional matrix adjust.
 Identities = 162/267 (60%), Positives = 201/267 (75%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+SK++ARAG+ASRR++ERMI + RV +NG+ L+   +N   +D IEVDG+P+R AER
Sbjct: 52  PERISKIMARAGVASRRDIERMIMEGRVSLNGVKLDTPVMNATLSDKIEVDGMPIRGAER 111

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGL+R
Sbjct: 112 TRLWLYHKPAGLVTTNSDPEGRPTVFDNLPGELPRVLSIGRLDINTEGLLLLTNDGGLSR 171

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELP+T WLR YRVR HG+VDQ  L+ LK+GI + G+ YG +  TLD  +G N W+T+G
Sbjct: 172 VLELPTTGWLRRYRVRAHGEVDQAALDKLKEGIAVDGVLYGAIDATLDRTQGHNVWITMG 231

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  ++LR+QLGP L+E+
Sbjct: 232 LREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGKVLEVRGRMLRDQLGPRLIEQ 291

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVP 279
           +  N DAPIY +     +  N     P
Sbjct: 292 SGANFDAPIYDAPVADDEEENTPKRAP 318


>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 =  348 bits (894), Expect = 6e-94,   Method: Compositional matrix adjust.
 Identities = 162/261 (62%), Positives = 199/261 (76%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K   ++   P+R+SK++ARAGIASRR+VERMI + RV VNG +L+   +N    D IEVD
Sbjct: 73  KTGSEDTLKPERISKLLARAGIASRRDVERMIMEGRVAVNGKVLDSPVLNATLADRIEVD 132

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P+R  ERTRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLL
Sbjct: 133 GEPIRGIERTRLWLYHKPSGLVTTNSDPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLL 192

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDGGLARVLELP+T WLR YRVR +G++DQ KL+ LK GI + G+ YG +   LD  +
Sbjct: 193 LTNDGGLARVLELPTTGWLRRYRVRAYGEIDQAKLDTLKDGIAVDGVLYGAIDAVLDRSQ 252

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N W+T+GLREGKNREIK V      +VNRLIRISYGPFQLG L     +EV  ++LR+
Sbjct: 253 GHNVWITMGLREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPESQVQEVRGRMLRD 312

Query: 244 QLGPHLLEEAQVNLDAPIYSS 264
           QLGP L+EE++ N DAP+YS+
Sbjct: 313 QLGPRLIEESKANFDAPLYSN 333


>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 =  324 bits (831), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 154/247 (62%), Positives = 189/247 (76%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +ARAGIASRR+ E MI   RVKVNG +++  A++V  TD IEVDG  L +AERTR
Sbjct: 185 RIARRLARAGIASRRDAEAMIVDGRVKVNGKIIDSPALDVKPTDRIEVDGALLPQAERTR 244

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWL+HKP G VTT+ DP+GR TVFD LP    RV+S+GRLDINTEGLLLLTNDGGL+RVL
Sbjct: 245 LWLFHKPAGTVTTNKDPEGRRTVFDMLPEDMPRVLSIGRLDINTEGLLLLTNDGGLSRVL 304

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR HG + Q KL+ L+ GI + G+ YG ++ TLD ++GSN W+T+GLR
Sbjct: 305 ELPSTGWLRRYRVRAHGSITQAKLDELRNGISVDGVFYGAIEATLDREQGSNVWITLGLR 364

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE+K V      +VNRLIR+SYGPFQLG L  GS REV  + LR+QLG  L+EEA 
Sbjct: 365 EGKNREVKNVLGALGLEVNRLIRLSYGPFQLGDLAEGSVREVKGRTLRDQLGDRLVEEAG 424

Query: 255 VNLDAPI 261
           V+ D PI
Sbjct: 425 VDFDGPI 431


>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 =  323 bits (829), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 169/326 (51%), Positives = 218/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPGV 392


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

 Score =  323 bits (829), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 169/326 (51%), Positives = 218/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPGV 392


>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 =  323 bits (829), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 152/250 (60%), Positives = 193/250 (77%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VDG PL++ E
Sbjct: 56  TGERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVDGKPLKQTE 115

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWLYHKP GLVTT+ DP+GR TVF+ LP+   RV+SVGRLDINTEGLLLLTNDGGL+
Sbjct: 116 RTRLWLYHKPAGLVTTNRDPEGRPTVFEALPAEMPRVLSVGRLDINTEGLLLLTNDGGLS 175

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++ TL+ ++G+N W+++
Sbjct: 176 RVLELPSTGWLRRYRVRAHGKVTQVQLDELKNGIAVDGVFYGSIEATLEREQGANVWISI 235

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  +ILR+QLG  L+E
Sbjct: 236 GLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRILRDQLGDKLIE 295

Query: 252 EAQVNLDAPI 261
           ++  + DAP+
Sbjct: 296 DSGADFDAPV 305


>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 =  323 bits (827), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 165/330 (50%), Positives = 219/330 (66%), Gaps = 12/330 (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 QLGPHLLEEAQVNLDAPI---YSSETLV-RDRPNIISEVPDDFTRMKKNSSQKNGLS--- 296
           QLG  L+EE+  + DAP+   +S+  +  R R  +    P+     ++   ++  +S   
Sbjct: 292 QLGDKLIEESGADFDAPVLNEFSNAAVQGRTRREMEEGQPEQDGETRRAPREREWISSRP 351

Query: 297 -----KQKKLATPVHRRNLASNVWMAKGIH 321
                ++ K      RR   +NVWMA G  
Sbjct: 352 ERRRGREDKTEKVEPRRRGNANVWMAPGAR 381


>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 =  323 bits (827), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 353 REEKTEKVEPRRRSN--ANVWMAPG 375


>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 =  323 bits (827), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRSN--ANVWMAPG 391


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

 Score =  323 bits (827), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 169/326 (51%), Positives = 218/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPGV 422


>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 =  322 bits (826), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKAEKVEPRRRGN--ANVWMAPG 391


>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 =  322 bits (826), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  322 bits (826), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 353 REEKTEKVEPRRRGN--ANVWMAPG 375


>gi|254702620|ref|ZP_05164448.1| hypothetical protein Bsuib36_01462 [Brucella suis bv. 3 str. 686]
          Length = 581

 Score =  322 bits (826), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  322 bits (825), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 353 REEKTEKVEPRRRGN--ANVWMAPG 375


>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 =  322 bits (825), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  322 bits (825), Expect = 5e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  322 bits (825), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 386 REEKTEKVEPRRRGN--ANVWMAPG 408


>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 =  322 bits (825), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 353 REEKTEKVEPRRRGN--ANVWMAPG 375


>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 =  322 bits (824), Expect = 7e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 386 REEKTEKVEPRRRGN--ANVWMAPG 408


>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 =  321 bits (823), Expect = 9e-86,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPG 421


>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 =  321 bits (823), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 168/326 (51%), Positives = 217/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRTPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPGV 392


>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 =  321 bits (823), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 169/325 (52%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPG 421


>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 =  321 bits (823), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 168/326 (51%), Positives = 217/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPGV 392


>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 =  321 bits (822), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 153/253 (60%), Positives = 190/253 (75%)

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 LLEEAQVNLDAPI 261
           L+EE+  + DAP+
Sbjct: 309 LIEESGADFDAPV 321


>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 =  321 bits (822), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 153/253 (60%), Positives = 190/253 (75%)

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 LLEEAQVNLDAPI 261
           L+EE+  + DAP+
Sbjct: 293 LIEESGADFDAPV 305


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

 Score =  320 bits (821), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/326 (51%), Positives = 217/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRTPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPGV 422


>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 =  320 bits (821), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 172/341 (50%), Positives = 219/341 (64%), Gaps = 28/341 (8%)

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 PHLLEEAQVNLDAPI---YSSETLVRDR----------PNIISEVPDDFTRMKKNSSQKN 293
             L+ +A  + DAPI   +S+  +V ++             IS    D  R ++ SS + 
Sbjct: 241 ERLIMQANADFDAPILKPFSNTAVVAEKRSHKDLTVANDGWISSHGGDLRRRQRKSSAER 300

Query: 294 G------------LSKQKKLATPVHR---RNLASNVWMAKG 319
           G            + K+K     + R   R+  SNVWMA G
Sbjct: 301 GRTRLSTKLDKKFMGKEKSEEGKIERFLPRSRHSNVWMAPG 341


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/326 (51%), Positives = 217/326 (66%), Gaps = 16/326 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGI 320
             ++ +   P  R N  +NVWMA G+
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPGV 422


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 353 REEKTEKVEPRRRGN--ANVWMAPG 375


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 153/253 (60%), Positives = 190/253 (75%)

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 LLEEAQVNLDAPI 261
           L+EE+  + DAP+
Sbjct: 339 LIEESGADFDAPV 351


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 216/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 386 REEKTEKVEPRRRGN--ANVWMAPG 408


>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 =  320 bits (820), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 369 REEKTEKVEPRRRGN--ANVWMAPG 391


>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 =  320 bits (819), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 386 REEKTEKVEPRRRGN--ANVWMAPG 408


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

 Score =  320 bits (819), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPG 421


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

 Score =  319 bits (818), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPG 421


>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 =  319 bits (818), Expect = 4e-85,   Method: Compositional matrix adjust.
 Identities = 168/325 (51%), Positives = 217/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPG 421


>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 =  318 bits (816), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 167/325 (51%), Positives = 216/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 399 REEKTEKVEPRRRGN--ANVWMAPG 421


>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 =  318 bits (815), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 150/258 (58%), Positives = 190/258 (73%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            Q +    R++K++AR G+ASRR+VERM+A+ R++VNG LL+  AV V  +D IEVDG  
Sbjct: 34  AQASAESGRIAKILARVGVASRRDVERMVAEGRIRVNGKLLDSPAVVVSLSDRIEVDGEE 93

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   ERTRLW+YHKP GLVTT+ DP+GR TVF+ LP    RV+S+GRLDINTEGLLLLTN
Sbjct: 94  VAGIERTRLWIYHKPAGLVTTNRDPEGRRTVFETLPKHLPRVLSIGRLDINTEGLLLLTN 153

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP T WLR YRVR +G +DQ++L+ LK GI + G+ YG ++ TLD ++G N
Sbjct: 154 DGGLARTLELPETGWLRRYRVRAYGDIDQNRLDTLKDGIAVDGVLYGAIEATLDRKQGHN 213

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+GLREGKNREIK V       VNRLIRIS+GPFQLG +  G   E+  + LREQLG
Sbjct: 214 VWITMGLREGKNREIKNVLSALGLDVNRLIRISFGPFQLGDVREGDVVEIKSRTLREQLG 273

Query: 247 PHLLEEAQVNLDAPIYSS 264
             L+EE+  N DAP+  S
Sbjct: 274 VRLIEESGANFDAPLNDS 291


>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 =  317 bits (812), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 177/374 (47%), Positives = 229/374 (61%), Gaps = 27/374 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V  N   +R++K +ARAGIASRR+ E MI   R+ VNG ++    +NV+ +DHI VD +P
Sbjct: 38  VYTNCDSERIAKRLARAGIASRRDAEMMIIAGRIAVNGTVVTTPVLNVIPSDHITVDEIP 97

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   ERTRLWLYHKP GLVTT+ DP+GR TVFDNLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 98  IPPIERTRLWLYHKPSGLVTTNRDPEGRPTVFDNLPKEMPRVVSVGRLDINTEGLLLLTN 157

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG++ Q +L+ LK GI I GI YG +  ++D ++GSN
Sbjct: 158 DGGLARVLELPLTGWVRKYRVRAHGKIKQSELDKLKNGIAIDGIFYGSIDASIDREQGSN 217

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK         VNRLIR+SYGPFQL  L  G+ RE+  + LR+QLG
Sbjct: 218 VWLSVALREGKNREIKNFLGALGLSVNRLIRVSYGPFQLSDLEEGAVRELKGRTLRDQLG 277

Query: 247 PHLLEEAQVNLDAPIY----SSETLVRDRPN-IISEVPDDFTRMKKNSSQKNG------- 294
             L+ +A  N DAPI     +S  +V+ + N  +S+  D++     +  Q+N        
Sbjct: 278 ERLIMQANANFDAPILKPFSNSAVVVKQQSNKKLSQANDEWISSSGHHKQRNKKDGFIEH 337

Query: 295 ----LSKQKKLATPVHRRNL--------ASNVWMAKGIHSSFLSDSGQ--REENHRRSPS 340
               LSK K    P+ +R           SNVWMA G              E+N  RS  
Sbjct: 338 NRAQLSK-KPNEQPIEQRKTERFSSRSRRSNVWMASGARPQITRKRPYYGEEDNQDRSRV 396

Query: 341 FPSKRSLRRTSAKK 354
           F  ++ L +   K+
Sbjct: 397 FAGEKFLYKNKEKQ 410


>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 =  317 bits (811), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 147/247 (59%), Positives = 191/247 (77%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +ARAGIASRR+ E MIA  RVK+NG +L+  AV V ++D IE+D  PL   ERTR
Sbjct: 70  RIAKRLARAGIASRRDAEGMIADGRVKLNGKVLDTPAVVVTASDRIEIDNAPLPAIERTR 129

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWL+HK  G VTT+ DP+GR T+FD LPS   RV++VGRLDINTEGLLLLTNDGGLAR+L
Sbjct: 130 LWLFHKAAGTVTTNRDPEGRPTIFDRLPSDMPRVLTVGRLDINTEGLLLLTNDGGLARIL 189

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP+T WLR YRVR HG + Q +L+ L++GI I G+ YG ++ T+D ++GSN W+T+GLR
Sbjct: 190 ELPATGWLRRYRVRAHGAITQARLDELRQGIAIDGVFYGAIEATMDREQGSNVWLTLGLR 249

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE+KKV      +VNRLIR+S+GPFQLG L  GS +E+  ++LR+QLG  L+EE+ 
Sbjct: 250 EGKNREVKKVLAHLGLEVNRLIRLSFGPFQLGDLKEGSVQEIKGRMLRDQLGERLIEESG 309

Query: 255 VNLDAPI 261
            + DAP+
Sbjct: 310 ADFDAPV 316


>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 =  317 bits (811), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 167/325 (51%), Positives = 215/325 (66%), Gaps = 16/325 (4%)

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 LLEEAQVNLDAPIYS--SETLVRDRPN---IISEVPDDFTR---------MKKNSSQKNG 294
           L+EE+  + DAP+ +  S   V+ R        E+P +  R         +     ++ G
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 295 LSKQKKLATPVHRRNLASNVWMAKG 319
             ++ +   P  R N  +NVWMA G
Sbjct: 386 REEKTEKVEPRRRGN--ANVWMAPG 408


>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 =  315 bits (808), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 182/381 (47%), Positives = 233/381 (61%), Gaps = 38/381 (9%)

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 PHLLEEAQVNLDAPI---YSSETLVRDRPN-----------IISEVPD-------DFT-R 284
             L+ +A  N DAPI   +S+  +V ++ N           I S + D        F+ R
Sbjct: 241 ERLIMQANANFDAPILKSFSNSVVVAEKQNHKDLAITNDGWIFSSIGDVQRRRRGGFSER 300

Query: 285 MKKNSSQKNG---LSKQKKLATPVHR---RNLASNVWMAKGIH------SSFLSDSGQRE 332
            +   S K G   + ++K       R   R+  SNVWMA G         SF S+    +
Sbjct: 301 SRARLSTKPGEKFMRQEKSEGGKAERFLPRSRRSNVWMAPGARPQSTRKKSFYSE----D 356

Query: 333 ENHRRSPSFPSKRSLRRTSAK 353
             H    +   KRSL R   K
Sbjct: 357 TPHDYKSNLAGKRSLHRGKEK 377


>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 =  315 bits (808), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 150/257 (58%), Positives = 187/257 (72%)

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 GPHLLEEAQVNLDAPIY 262
           G  L EEA  + DAPI+
Sbjct: 291 GDALAEEAGADFDAPIF 307


>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 =  313 bits (803), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 175/371 (47%), Positives = 228/371 (61%), Gaps = 45/371 (12%)

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 PHLLEEAQVNLDAPI---------------------------YSSETLVRDRPNIISEVP 279
             L+ +A  + DAPI                           +SSE ++R R N  S V 
Sbjct: 241 ERLIMQANADFDAPILKPFSNSPVIAEKQSQKDVSVANDGWVFSSERVIRRRSNDGS-VE 299

Query: 280 DDFTRMKKNSSQ--KNGLSKQKKLAT--PVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
            D  R++  S +    G S++ K     P  RR   +NVWMA           G R ++ 
Sbjct: 300 HDRARLRAKSHENMNKGKSEEGKAERFLPRSRR---ANVWMA----------PGARPQSA 346

Query: 336 RRSPSFPSKRS 346
           RR PS+  ++S
Sbjct: 347 RRKPSYNEEKS 357


>gi|218660352|ref|ZP_03516282.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium etli IE4771]
          Length = 296

 Score =  313 bits (801), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 153/245 (62%), Positives = 182/245 (74%), Gaps = 8/245 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+R  ERT
Sbjct: 39  ERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVPIRGIERT 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 99  RLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 159 LELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 218

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V       VNRLIRISYGPFQLG L  G   EV         GPH    A
Sbjct: 219 REGKNREIKNVMGALGLDVNRLIRISYGPFQLGDLPEGHVIEVR--------GPHAARSA 270

Query: 254 QVNLD 258
           +   D
Sbjct: 271 RPAPD 275


>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 =  313 bits (801), Expect = 3e-83,   Method: Compositional matrix adjust.
 Identities = 171/370 (46%), Positives = 225/370 (60%), Gaps = 43/370 (11%)

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 PHLLEEAQVNLDAPI---------------------------YSSETLVRDRPNIISEVP 279
             L+ +A  + DAPI                           +SSE  +R RP   S   
Sbjct: 241 ERLIMQANADFDAPILKPFSNSAVVAEKQSQKDLSVANDGWVFSSERAIRRRPRDGSV-- 298

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREENHR 336
            + +R + ++     + K+K       R   R+  +NVWMA           G R ++ R
Sbjct: 299 -EHSRARLSTKSHENVKKEKSEEGKAERFLPRSRRANVWMA----------PGARPQSTR 347

Query: 337 RSPSFPSKRS 346
           R PS+  ++S
Sbjct: 348 RKPSYSEEKS 357


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

 Score =  313 bits (801), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 173/376 (46%), Positives = 227/376 (60%), Gaps = 41/376 (10%)

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 REQLGPHLLEEAQVNLDAPIY--------------SSETLVRDRPNIISEVPDDFTRMKK 287
           R+QLG  L+ +A  + D+PI               S +  V     ++S V  + TR +K
Sbjct: 269 RDQLGERLIAQANADFDSPILKPFSNSVVSVKKQNSKKLFVAGDDEVVSRV--NGTRHEK 326

Query: 288 NS-------------SQKNGLSKQKKLATPVHRRNLASNVWMAKGI-----HSSFLSDSG 329
            S             S +  + K K L+     R+  SNVWMA G         F  + G
Sbjct: 327 QSGFCEGRRARLNTKSDEQSMGKTKNLSL----RSRHSNVWMAPGARPQVERKKFCYNEG 382

Query: 330 QREENHRRSPSFPSKR 345
                H RS  +  K+
Sbjct: 383 SY---HNRSSDYVGKK 395


>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 =  312 bits (800), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 173/374 (46%), Positives = 223/374 (59%), Gaps = 68/374 (18%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ASRR+ E MI   RVKVNG +L   A NV  +D IEVD  PL  AERT
Sbjct: 49  ERIAKRLARAGLASRRDAEAMIEAGRVKVNGRVLSSPAFNVRPSDRIEVDDEPLPAAERT 108

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+L+HKP G+VTT  DP+GR T+FD LP    R+I+VGRLDINTEGL+LLTNDGGLAR 
Sbjct: 109 RLFLFHKPAGVVTTTRDPEGRRTIFDTLPEGLPRLITVGRLDINTEGLILLTNDGGLARA 168

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR HG+VD   L  L+KGI + G+ YG +  +LD Q+GSNAW+T+GL
Sbjct: 169 LELPSTGWLRRYRVRVHGKVDPKALAELEKGIAVDGVFYGAITASLDRQQGSNAWLTLGL 228

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K V      +V RLIR+SYGPFQLG L  G+  EV  + LR+QLG  L+E+A
Sbjct: 229 REGKNREVKNVLGALGLEVTRLIRVSYGPFQLGDLPEGAVLEVKGRTLRDQLGERLIEQA 288

Query: 254 QVNLDAPI---YSSETL----------------------------------------VRD 270
             + +API   ++++ +                                         RD
Sbjct: 289 GADFEAPIAIPFANKPVRAERRKPEEEKRKTGLEENAGRQERKPANRRKSREEKHEEARD 348

Query: 271 RPNIISEVPDDF---------------------TRMKKNSSQK-NGLSK-QKKLATPVHR 307
           R  + ++ PDDF                      R +K+  ++ +G SK +     PV R
Sbjct: 349 R--LQTKRPDDFKGKGSAAHKGKDQRPPRISKTARPEKSGQERMSGDSKAEGPTRAPVER 406

Query: 308 RNLASNVWMAKGIH 321
           R+ ASNVWMA G  
Sbjct: 407 RSRASNVWMAPGAR 420


>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 =  311 bits (798), Expect = 7e-83,   Method: Compositional matrix adjust.
 Identities = 152/258 (58%), Positives = 187/258 (72%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            + N   +R++KV+AR G+ SRRE E  I   RV++NG LL   AV V   D + VDG P
Sbjct: 96  AEANDRGERIAKVMARVGLCSRREAEVWIENGRVELNGKLLTTPAVTVTPDDKVVVDGQP 155

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV++VGRLDINTEGLLLLTN
Sbjct: 156 LPMRERTRLWLYHKPRGLVTTNKDPEGRPTVFERLPDDLPRVLTVGRLDINTEGLLLLTN 215

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP+T WLR YRVR  G+V Q  L+ LK GI I+G+ YG ++ TLD ++G+N
Sbjct: 216 DGGLARVLELPATGWLRRYRVRAFGKVTQPDLDTLKDGIAIEGVLYGAIEATLDKEQGNN 275

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+TVGLREGKNRE+K+V E     VNRLIR+SYGPFQL  L  G  RE+  ++LR+QLG
Sbjct: 276 VWMTVGLREGKNREVKRVLEHLGLAVNRLIRLSYGPFQLMDLPEGDVREIRGRVLRDQLG 335

Query: 247 PHLLEEAQVNLDAPIYSS 264
             L EEA  + DAPI+ +
Sbjct: 336 DALAEEAGADFDAPIFHA 353


>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 =  311 bits (797), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 148/250 (59%), Positives = 184/250 (73%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ SRR+ E  I   RV VNG +LE  A+ V   D I VDG PL + ERT
Sbjct: 87  ERIAKVMARAGLCSRRDAEAWILAGRVAVNGKILESPALTVTYDDEIVVDGQPLPQKERT 146

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT  DP+GR TVFD+LP    RV++VGRLDINTEGLLLLTNDGGLARV
Sbjct: 147 RLWLYHKPRGLVTTARDPEGRPTVFDSLPKDLPRVLAVGRLDINTEGLLLLTNDGGLARV 206

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR +G+++Q +L+ L  GI I GI YG ++  LD Q+G N W+TVGL
Sbjct: 207 LELPATGWLRRYRVRAYGKIEQSQLDSLADGIAIDGILYGTIEAVLDKQQGDNVWLTVGL 266

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K+V E     VNRLIR+S+GPFQL  L  G  RE+  ++LR+QLG  L E A
Sbjct: 267 REGKNREVKRVLEHLGLSVNRLIRLSFGPFQLADLGEGEVREIRGRVLRDQLGDKLAEAA 326

Query: 254 QVNLDAPIYS 263
             + +AP+ +
Sbjct: 327 GADFEAPVLT 336


>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 =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 146/250 (58%), Positives = 186/250 (74%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K +ARAG+ SRRE E  I   RV VNG +L+  A  V   D + VDG PL   E
Sbjct: 35  TGERIAKAMARAGLCSRREAETWIEAGRVSVNGNVLDTPAFTVTQKDKVYVDGKPLPTRE 94

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWL+HKP G VTT+ DP+GR TVFD LP    RV++VGRLDINTEGLLLLTNDGGL+
Sbjct: 95  RTRLWLFHKPRGTVTTNKDPEGRKTVFDILPKDMPRVVTVGRLDINTEGLLLLTNDGGLS 154

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RV+ELP+T WLR YRVR  G+V Q++L+ LK G+ I G+ YG ++ TLDT+KG N W+T+
Sbjct: 155 RVIELPATGWLRRYRVRAFGKVTQEQLDALKDGVAIDGVLYGAIEATLDTEKGDNVWLTI 214

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNRE+K++ E  +  VNRLIRIS+GPFQLG L  G  +E+  ++LR+QLG  L+ 
Sbjct: 215 GLREGKNREVKRILEHLDLSVNRLIRISFGPFQLGDLGEGELQEIRGRVLRDQLGERLVS 274

Query: 252 EAQVNLDAPI 261
           EA ++ DAPI
Sbjct: 275 EADLDFDAPI 284


>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 =  311 bits (796), Expect = 1e-82,   Method: Compositional matrix adjust.
 Identities = 156/293 (53%), Positives = 200/293 (68%), Gaps = 12/293 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           F  +R++KV+ARAG+ SRRE E  IA  RV+VNG  L+  A+ V + D + VDG PL   
Sbjct: 13  FEGERIAKVMARAGLCSRREAETWIAAGRVEVNGKKLDTPAITVGAKDKVLVDGNPLPTR 72

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLYHKP GLVTT+ DP+GR TVFD LP    RV++VGRLDINTEGLLLLTNDGGL
Sbjct: 73  ERTRLWLYHKPRGLVTTNKDPEGRKTVFDRLPKDLPRVLTVGRLDINTEGLLLLTNDGGL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           ARVLELP+T WLR YRVR  G+V Q  L+ L  G+ I G+ YG ++ +LD ++G N W+T
Sbjct: 133 ARVLELPATGWLRRYRVRAFGKVTQADLDTLADGVAIDGVLYGGIEASLDKEQGDNVWLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           VGLREGKNRE+K+V E     VNRLIR+S+GPFQL  +  G  RE+  ++LR+QLG  L 
Sbjct: 193 VGLREGKNREVKRVLEHLGLSVNRLIRLSFGPFQLQDIAEGEVREIRGRVLRDQLGDKLA 252

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           EEA  + DAPI +                D+  + KK+  QK G S+ + +++
Sbjct: 253 EEAGADFDAPILNQPKQ------------DEQPKKKKSVGQKGGGSEARWMSS 293


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

 Score =  309 bits (791), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 154/270 (57%), Positives = 191/270 (70%), Gaps = 2/270 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V E    +R++K +ARAG+ASRR+ E MIA  R+ VNG ++   A NV  +D I VDG P
Sbjct: 34  VSEKSESERIAKRLARAGLASRRDAEMMIAAGRIVVNGAVVTTPAFNVTRSDVIMVDGKP 93

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLY+KPIG VTT+ DP GR TVFDNLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 94  LPPIERTRLWLYYKPIGFVTTNRDPQGRPTVFDNLPKGMPRVLSVGRLDINTEGLLLLTN 153

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ ++GSN
Sbjct: 154 DGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIEREQGSN 213

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LR+QLG
Sbjct: 214 VWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRMLRDQLG 273

Query: 247 PHLLEEAQVNLDAPIYS--SETLVRDRPNI 274
             L+ +A  + DAPI    S + V ++ NI
Sbjct: 274 ERLIMQANADFDAPILKPFSNSAVSEKQNI 303


>gi|218674407|ref|ZP_03524076.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium etli GR56]
          Length = 277

 Score =  309 bits (791), Expect = 5e-82,   Method: Compositional matrix adjust.
 Identities = 147/223 (65%), Positives = 175/223 (78%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGRVLDTPVVNVTLADRIEVDGVPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLAR 
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARA 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           REGKNREIK V       VNRLIRISYGPFQLG L  G   EV
Sbjct: 232 REGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVIEV 274


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

 Score =  306 bits (783), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 177/380 (46%), Positives = 227/380 (59%), Gaps = 35/380 (9%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V E    +R++K +ARAG+ASRR+ E MI   R+ VNG ++   A NV  +D I VDG P
Sbjct: 35  VSEKSESERIAKRLARAGLASRRDAEMMIVAGRIVVNGTVVTTPAFNVSRSDVIMVDGKP 94

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLY+KPIG VTT+ DP GR TVFDNLP    RV+SVGRLDINTEGLLLLTN
Sbjct: 95  LPPIERTRLWLYYKPIGFVTTNRDPQGRPTVFDNLPKGMPRVLSVGRLDINTEGLLLLTN 154

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ ++GSN
Sbjct: 155 DGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIEREQGSN 214

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LR+QLG
Sbjct: 215 VWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRMLRDQLG 274

Query: 247 PHLLEEAQVNLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK---- 299
             L+ +A  + DAPI   +S+  +V  +    S V +D   +   SS++N L  +K    
Sbjct: 275 ERLIVQANADFDAPILKPFSNSAVVAKQNITKSSVIEDSWIV---SSKENLLYGRKSRFL 331

Query: 300 -------------KLATPVHR----------RNLASNVWMAKGIHSSFL--SDSGQREEN 334
                        KL    H           R+  SNVWMA G          S   + +
Sbjct: 332 GHSQVRLSKKIDTKLRAKDHNKGGKEERAFLRSRCSNVWMAPGACPQIARKKSSSDADNH 391

Query: 335 HRRSPSFPSKRSLRRTSAKK 354
           + R  ++  KRS  R   K+
Sbjct: 392 YDRKSNWVGKRSTDRGKEKR 411


>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 =  303 bits (777), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 143/233 (61%), Positives = 175/233 (75%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ SRRE ER I   RV VNG  L   A  V   D + VDG+PL + E+T
Sbjct: 52  ERIAKRLARAGLCSRREAERWIEDGRVTVNGHRLSSPACVVGPGDIVIVDGIPLSEPEKT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DP+GR TVFD+LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 112 RLWRYHKPAGLVTTHKDPEGRPTVFDHLPEGMPRVISVGRLDLNSEGLLLLTNDGELARK 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  WLR YRVR HG+V +D L  L+ GI I G+ YG +  TLD ++G+NAW++V L
Sbjct: 172 LELPSNAWLRRYRVRVHGEVSEDALARLENGITIDGMAYGPISATLDRRQGANAWLSVSL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++V E+  W V+RLIR+SYGPFQLGTL  G+  EV+ K+LREQ+G
Sbjct: 232 REGKNREIRRVMEYLGWPVSRLIRVSYGPFQLGTLEEGAADEVAGKVLREQMG 284


>gi|46201216|ref|ZP_00208014.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 294

 Score =  302 bits (774), Expect = 5e-80,   Method: Compositional matrix adjust.
 Identities = 145/233 (62%), Positives = 175/233 (75%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ SRRE ER I   RV VNG  L+  A  V   D I VDG PL + E+T
Sbjct: 7   ERIAKRLARAGLCSRREAERWIEMGRVSVNGKTLDSPACVVGPGDIILVDGTPLSEPEKT 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DP+GR TVFD+LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 67  RLWRYHKPAGLVTTHKDPEGRPTVFDHLPEGMPRVISVGRLDLNSEGLLLLTNDGELARK 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  WLR YRVR HG+V +D L  L+ GI I G+ YG +  TLD ++G+NAW++V L
Sbjct: 127 LELPSNAWLRRYRVRVHGEVSEDALARLENGITIDGMAYGPISATLDRRQGANAWLSVSL 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++V EF  W V+RLIR+SYGPFQLGTL  G+  EV+ K+LREQ+G
Sbjct: 187 REGKNREIRRVMEFLGWPVSRLIRVSYGPFQLGTLEEGAADEVAGKVLREQMG 239


>gi|319405144|emb|CBI78750.1| Pseudouridine synthase [Bartonella sp. AR 15-3]
          Length = 459

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 173/377 (45%), Positives = 223/377 (59%), 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 PHLLEEAQVNLDAPI---YSSETLVRDRPNIISEVPDD-----------FTRMKKNSSQK 292
             L+ +A  N DAPI   +S+ T+V  + +  + V  D           + + +K S   
Sbjct: 241 ERLILQANANFDAPILKPFSNSTVVEKQNSTKAPVIKDSWIISSKESLLYGKKRKFSGHS 300

Query: 293 NG-LSKQ--KKL----------ATPVHRRNLASNVWMAKGIHSSFL--SDSGQREENHRR 337
              LSK+  +KL                R+  SNVWMA G          S     +H R
Sbjct: 301 QAQLSKKIDEKLRGKDQNKGGKEERAFLRSRCSNVWMAPGACPQITRKKSSSNANNHHDR 360

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


>gi|319898380|ref|YP_004158473.1| Pseudouridine synthase [Bartonella clarridgeiae 73]
 gi|319402344|emb|CBI75883.1| Pseudouridine synthase [Bartonella clarridgeiae 73]
          Length = 496

 Score =  300 bits (768), Expect = 2e-79,   Method: Compositional matrix adjust.
 Identities = 167/346 (48%), Positives = 212/346 (61%), Gaps = 39/346 (11%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R++K +ARAG+ASRR+ E MI   R+ VNG ++     NV  +D I VDG P
Sbjct: 34  MSEKSESERIAKRLARAGVASRRDAEMMIFAGRIVVNGAIIATPVFNVTRSDVITVDGKP 93

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP+G VTT+ DP GR TVFDNLP    RV+SVGRLD+NTEGLLLLTN
Sbjct: 94  LPPIERTRLWLYHKPVGFVTTNRDPQGRPTVFDNLPKDMPRVLSVGRLDMNTEGLLLLTN 153

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ ++GSN
Sbjct: 154 DGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIEREQGSN 213

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LR+QLG
Sbjct: 214 VWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRMLRDQLG 273

Query: 247 PHLLEEAQVNLDAPIYS--SETLVRDRPNIISEVPDDFTRMKKNS---SQKNGLSKQKKL 301
             L+ +A  + +API    S + V ++ N  S  P     + KNS   S+K  + + KK 
Sbjct: 274 ERLILQANADFNAPIIKPFSNSAVIEKQN--STKPP----VMKNSWIVSRKESILRGKKG 327

Query: 302 ATPVHR----------------------------RNLASNVWMAKG 319
             P H                             R+  SNVWMA G
Sbjct: 328 RFPGHSQVRLSKKFDEKLRVKDQNKSGKEERVFLRSRCSNVWMAPG 373


>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 =  299 bits (766), Expect = 4e-79,   Method: Compositional matrix adjust.
 Identities = 140/251 (55%), Positives = 180/251 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAGIASRR+ E MI   RV +NG +L   A+NV  +D I +DG PL   ERT
Sbjct: 26  ERIAKAIARAGIASRRDAEAMIEAGRVSLNGKILTSPAINVTESDRIAIDGEPLPARERT 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA+V
Sbjct: 86  RLWLLHKPRGVVTTARDPEGRQTVFDGLPDDLPRVVAIGRLDINTEGLLLLTNDGGLAKV 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T WLR YRVR  G + Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+GL
Sbjct: 146 IAHPDTGWLRRYRVRAFGDITQADLDRLKKGVTVDGMEYGPVEATLDRVQGDNLWLTLGL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L+EQLG  L E+A
Sbjct: 206 REGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKEQLGKSLAEQA 265

Query: 254 QVNLDAPIYSS 264
            V+ ++P+  +
Sbjct: 266 GVDFESPVREA 276


>gi|218512381|ref|ZP_03509221.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli 8C-3]
          Length = 244

 Score =  299 bits (765), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 141/213 (66%), Positives = 166/213 (77%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           VNV   D IEVDG+P+R  ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+
Sbjct: 20  VNVTLADRIEVDGMPIRGIERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSI 79

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINTEGLLLLTNDGGLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ 
Sbjct: 80  GRLDINTEGLLLLTNDGGLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVL 139

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           YG ++ TLD  +GSN W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G
Sbjct: 140 YGSIEATLDRTQGSNVWITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEG 199

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
              EV  + LR+QLGP L+EEA+ N DAPIY++
Sbjct: 200 HVIEVRGRTLRDQLGPRLIEEAKANFDAPIYNA 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 =  299 bits (765), Expect = 6e-79,   Method: Compositional matrix adjust.
 Identities = 141/253 (55%), Positives = 185/253 (73%), Gaps = 1/253 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++KV+ARAG+ASRR+ E M+ Q RV VNG ++   A++V   D I+VDG PL + E
Sbjct: 364 TGERIAKVLARAGLASRRDAEEMVTQGRVSVNGRIINSPALDVTENDEIKVDGAPLPERE 423

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL+LYHKP GL+TTHSDP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLA
Sbjct: 424 RTRLFLYHKPRGLMTTHSDPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDGGLA 483

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELP T W R YRVR HG++ Q +L+ L  G+ + G+ YG ++ TL+  +G+N W+ V
Sbjct: 484 RVLELPDTGWTRRYRVRAHGEITQGQLDQLAAGVEVDGVKYGPIEATLERDQGANVWLVV 543

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G  +EV  ++LREQLG  ++ 
Sbjct: 544 AIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELPEGEVQEVKTRVLREQLGEKVIA 603

Query: 252 EAQVNLDAPIYSS 264
           ++  +L  P  SS
Sbjct: 604 QSGADL-GPAGSS 615


>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 =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 142/253 (56%), Positives = 182/253 (71%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P+R++KV+ARAG+ASRR+ E MI + RV +NG  L   AV V   D I VDG PL 
Sbjct: 35  ETAEPERIAKVMARAGVASRRDAEAMILEGRVSLNGETLTTPAVTVGPGDRIVVDGEPLP 94

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ERTRLW++HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDG
Sbjct: 95  VRERTRLWIFHKPRGVVTTARDPEGRQTVFDILPEDLPRVVAIGRLDINTEGLLLLTNDG 154

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GLA+V+  P T WLR YRVR +G VDQ  L+ L+ G+ I G+ YG ++ ++D Q+G N W
Sbjct: 155 GLAKVIAHPETGWLRRYRVRAYGDVDQAALDRLRGGVTIDGMEYGPVEASIDRQQGDNVW 214

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  K+L+EQLG  
Sbjct: 215 LTLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTKVLKEQLGRS 274

Query: 249 LLEEAQVNLDAPI 261
           L E+A V+  +P+
Sbjct: 275 LAEQAGVDFTSPV 287


>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 =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 140/248 (56%), Positives = 178/248 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAGIASRR+ E MI   RV VNG  L   A NV   D I +DG P+   ER+
Sbjct: 86  ERIAKAMARAGIASRRDAETMIVAGRVSVNGETLTSPARNVTENDRILIDGEPMPSRERS 145

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW++HKP G+VTT  DP+GR TVFD LP    RV++VGRLDINTEGLLLLTNDGGLA+V
Sbjct: 146 RLWIFHKPRGVVTTARDPEGRQTVFDVLPEDLPRVVAVGRLDINTEGLLLLTNDGGLAKV 205

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T WLR YRVR HG  DQ +L+ L KG+ I G+ YG ++ TLD  +G N W+T+GL
Sbjct: 206 IAHPDTGWLRRYRVRAHGDTDQAQLDRLAKGVTIDGMEYGPVEATLDRVQGDNVWLTLGL 265

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  ++L++QLG  L E+A
Sbjct: 266 REGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTRVLKDQLGKSLAEQA 325

Query: 254 QVNLDAPI 261
            V+ D+P+
Sbjct: 326 GVDFDSPV 333


>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 =  298 bits (762), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 138/253 (54%), Positives = 180/253 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ASRR+ E M+ Q RV VNG ++   A+++   D + VDG PL   ERT
Sbjct: 377 ERIAKALARAGLASRRDAEEMVTQGRVAVNGRVINSPALDITPNDVVTVDGKPLPPRERT 436

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTH DP+GR TVFDNLP    R+ISVGRLD NTEGLLLLTNDGGLAR 
Sbjct: 437 RLFLYHKPRGLMTTHDDPEGRPTVFDNLPEGLPRLISVGRLDFNTEGLLLLTNDGGLART 496

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG V Q +L+ LK GI ++G+ YG +  TL+  +G+N W+   +
Sbjct: 497 LELPDTGWLRRYRVRAHGDVTQAQLDELKAGIEVEGVKYGPIDATLERDQGANVWLVFAI 556

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++LREQLG  ++E++
Sbjct: 557 REGKNREVRNVCAHLGLEVNRLIRVSYGPFQLGEVPEGQVEEIKSRVLREQLGDKVIEKS 616

Query: 254 QVNLDAPIYSSET 266
               D P  ++ T
Sbjct: 617 GAQFDVPQKAAAT 629


>gi|13476819|ref|NP_108388.1| hypothetical protein mlr8253 [Mesorhizobium loti MAFF303099]
 gi|14027580|dbj|BAB53849.1| mlr8253 [Mesorhizobium loti MAFF303099]
          Length = 546

 Score =  297 bits (760), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 141/248 (56%), Positives = 185/248 (74%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ASRR+ E +IA  RVKVNG  L   A NVM  D I +DG+ +   ERT
Sbjct: 98  ERIAKRLARAGLASRRDAEELIAAGRVKVNGRALTSPAFNVMPGDIIHLDGMEIPPIERT 157

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+L+HKP G+VTT+ DP+GR TVFD LP+   R++++GRLDINTEGLLLLTNDGGL+RV
Sbjct: 158 RLFLFHKPAGVVTTNRDPEGRKTVFDVLPAELPRLMTIGRLDINTEGLLLLTNDGGLSRV 217

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG+V++  L  L++GI + G+ YG ++ +LD ++GSNAW+T+GL
Sbjct: 218 LELPATGWLRRYRVRVHGKVEESALAGLREGIAVDGVFYGAIEASLDREQGSNAWLTIGL 277

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K +       V RLIRISYGPFQL  L  G   E+  ++LR+QLG  L+EE+
Sbjct: 278 REGKNREVKNILGALGLDVTRLIRISYGPFQLEDLPEGHVLEIKGRVLRDQLGERLVEES 337

Query: 254 QVNLDAPI 261
             N DA I
Sbjct: 338 GANFDAEI 345


>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 =  296 bits (759), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 142/248 (57%), Positives = 181/248 (72%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KVIARAG+ SRRE+E  I   RV VNG +L   A  V + D I VDG PL + ERT
Sbjct: 30  ERIAKVIARAGLGSRREIEEWITAGRVSVNGEVLASPAFTVTAEDEIRVDGEPLPERERT 89

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKPIG+VTT+ DP+GR+T+F+ LP    R++SVGRLDIN+EGLLLLTNDGGLARV
Sbjct: 90  RLFLYHKPIGVVTTNRDPEGRTTLFELLPGHLPRLVSVGRLDINSEGLLLLTNDGGLARV 149

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR  G VDQ +L+ L KGIV++G+ YG ++  LD  +G+N W+TV L
Sbjct: 150 LELPETGWLRRYRVRAKGTVDQAQLDALIKGIVVEGVEYGPIEAVLDRVQGANVWITVAL 209

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIRISYGPFQLG +  G   EV  +ILR+Q+G  +   A
Sbjct: 210 REGKNREVRNVLGALGLQVNRLIRISYGPFQLGEIAEGGVEEVRTRILRDQIGNDIAAAA 269

Query: 254 QVNLDAPI 261
             + + P+
Sbjct: 270 GADFNGPL 277


>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 =  296 bits (759), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 137/243 (56%), Positives = 181/243 (74%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRR+ E M+ Q RV VNG ++   A++V   D I+VDG PL + ERTR
Sbjct: 375 RIAKVLARAGLASRRDAEEMVTQGRVTVNGRVINSPALDVTENDVIQVDGAPLPQRERTR 434

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+LYHKP GL+TTHSDP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLARVL
Sbjct: 435 LFLYHKPRGLMTTHSDPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDGGLARVL 494

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP T W R YRVR HG++ Q +L+ L  G+ + G+ YG ++ TL+  +G+N W+ V +R
Sbjct: 495 ELPDTGWTRRYRVRAHGEITQAQLDQLAAGVEVDGVKYGPIEATLERDQGANVWLIVAIR 554

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE++ V  +   +VNRLIR+SYGPFQL  L  G  +EV  ++LREQLG  ++ ++ 
Sbjct: 555 EGKNREVRNVLAYLGLEVNRLIRVSYGPFQLLELPEGEVQEVKTRVLREQLGEKVIAQSG 614

Query: 255 VNL 257
            +L
Sbjct: 615 ADL 617


>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 =  296 bits (758), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 146/273 (53%), Positives = 196/273 (71%), Gaps = 11/273 (4%)

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 NLDAPI---YSSETLVR--------DRPNIISE 277
           N DA I   +S++ + R        +RP I+ E
Sbjct: 403 NFDAEISKPFSNKPVRRTEPRQEEAERPKIMRE 435


>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 =  296 bits (757), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 139/251 (55%), Positives = 180/251 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL   ERT
Sbjct: 22  ERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPARERT 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA+V
Sbjct: 82  RLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLAKV 141

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+GL
Sbjct: 142 IAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLTLGL 201

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L E+A
Sbjct: 202 REGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLAEQA 261

Query: 254 QVNLDAPIYSS 264
            V+ ++P+  +
Sbjct: 262 GVDFESPVRET 272


>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 =  296 bits (757), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 139/251 (55%), Positives = 180/251 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL   ERT
Sbjct: 22  ERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPARERT 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA+V
Sbjct: 82  RLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLAKV 141

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+GL
Sbjct: 142 IAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLTLGL 201

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L E+A
Sbjct: 202 REGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLAEQA 261

Query: 254 QVNLDAPIYSS 264
            V+ ++P+  +
Sbjct: 262 GVDFESPVRET 272


>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 =  295 bits (756), Expect = 5e-78,   Method: Compositional matrix adjust.
 Identities = 142/247 (57%), Positives = 181/247 (73%)

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 VNLDAPI 261
           V+  +P+
Sbjct: 276 VDFTSPV 282


>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 =  295 bits (756), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 138/244 (56%), Positives = 182/244 (74%)

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 NLDA 259
           N DA
Sbjct: 464 NFDA 467


>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 =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 139/251 (55%), Positives = 179/251 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV   D I VD  PL   ERT
Sbjct: 22  ERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDADRITVDDEPLPARERT 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA+V
Sbjct: 82  RLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLAKV 141

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+GL
Sbjct: 142 IAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLTLGL 201

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L E+A
Sbjct: 202 REGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLAEQA 261

Query: 254 QVNLDAPIYSS 264
            V+ ++P+  +
Sbjct: 262 GVDFESPVRET 272


>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 =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 147/264 (55%), Positives = 186/264 (70%), Gaps = 10/264 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRRE ERMIA+ R+ V+G +++  A+NV +   IEVDG PL   E  R
Sbjct: 13  RIAKVLARAGVASRREAERMIAEGRISVDGTVIDSPALNVTARARIEVDGRPLDAPEPAR 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLYHKP GLVTTH D  GR T+FD+LP    RV+SVGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 73  LWLYHKPPGLVTTHKDDQGRPTIFDDLPEDMPRVMSVGRLDLNSEGLLLLTNDGGIKRRL 132

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR  G      L  L++G+V+    +  MQVTLD Q+G+NAW+TVGLR
Sbjct: 133 ELPSTGWLRRYRVRVKGTPTDATLAPLREGVVVDREIFQPMQVTLDRQQGANAWLTVGLR 192

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++  E     VNRLIRISYGPFQLG L  G+  EV ++++R+QLG   L++A+
Sbjct: 193 EGKNREIRRAMESIGLSVNRLIRISYGPFQLGPLAPGAVEEVRRRVMRDQLG---LDDAE 249

Query: 255 VNLDAPIYS-------SETLVRDR 271
            +   P  S        ET  RD+
Sbjct: 250 ADAPRPKRSRAGQRTGPETKTRDK 273


>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 =  295 bits (755), Expect = 7e-78,   Method: Compositional matrix adjust.
 Identities = 139/251 (55%), Positives = 180/251 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL   ERT
Sbjct: 22  ERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPARERT 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA+V
Sbjct: 82  RLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLAKV 141

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+GL
Sbjct: 142 IAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLTLGL 201

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L E+A
Sbjct: 202 REGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLAEQA 261

Query: 254 QVNLDAPIYSS 264
            V+ ++P+  +
Sbjct: 262 GVDFESPVRET 272


>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 =  295 bits (754), Expect = 9e-78,   Method: Compositional matrix adjust.
 Identities = 139/255 (54%), Positives = 179/255 (70%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++KV+ARAG+ASRR+ E  + Q RV VNG ++   A++V S D I +DG PL + E
Sbjct: 358 TGERIAKVMARAGVASRRDAEEWVTQGRVAVNGRVINSPALDVTSRDVITIDGQPLPERE 417

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLA
Sbjct: 418 RTRLFLYHKPRGLMTTHADPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDGGLA 477

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELP T WLR YRVR HG+V Q +L+ LK G+ + G+ YG +  TL+  +G+N W+  
Sbjct: 478 RALELPDTGWLRRYRVRAHGEVTQAQLDALKNGVEVDGVKYGSIDATLERDQGANVWLVF 537

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            +REGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  +  
Sbjct: 538 AIREGKNREVRNVMAHLGLEVNRLIRVSYGPFQLAEIAEGQVEEVKTRVLREQLGDKIAA 597

Query: 252 EAQVNLDAPIYSSET 266
            A  N       +ET
Sbjct: 598 LANANFAGTAAEAET 612


>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 =  294 bits (753), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 138/233 (59%), Positives = 174/233 (74%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+K+I+RAG+ASRR+ E M+ Q RV VNG ++   A++V S D + VDG PL + ERT
Sbjct: 354 ERVAKMISRAGLASRRDAEEMVTQGRVAVNGRVINSPALDVTSRDVVTVDGQPLPERERT 413

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTH+DP+GR TVFD+LP    RVISVGRLD NTEGLLLLTNDGGLAR 
Sbjct: 414 RLFLYHKPRGLMTTHADPEGRPTVFDHLPEGLPRVISVGRLDFNTEGLLLLTNDGGLARA 473

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG+V Q +L+ LK G+ + G+ YG +  TL+  +G+N W+T  +
Sbjct: 474 LELPDTGWLRRYRVRAHGEVTQAQLDALKNGVEVDGVKYGSIDATLERDQGANVWLTFAI 533

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNRE++ V      +VNRLIRISYGPFQL  +  G   EV  ++LREQLG
Sbjct: 534 REGKNREVRNVMAHLGLEVNRLIRISYGPFQLAEIAEGEVEEVKTRVLREQLG 586


>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 =  294 bits (752), Expect = 1e-77,   Method: Compositional matrix adjust.
 Identities = 142/255 (55%), Positives = 179/255 (70%), Gaps = 3/255 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +F  +R++K +ARAG+ SRRE E+ IA+ RV VNG++L  AA NV   D I +DG P+++
Sbjct: 83  SFEGERIAKAMARAGVCSRREAEQWIAEGRVAVNGVVLPNAAFNVKEGDRITIDGAPMQE 142

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTN 126
            ERTRL+L+HKP G VTT  DP+GR TVF  L        RV+SVGRLDINTEGLLLLTN
Sbjct: 143 RERTRLFLFHKPAGYVTTAHDPEGRPTVFAFLEERHGELPRVVSVGRLDINTEGLLLLTN 202

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T W R YRVR HG  DQ +L+ L+KG+ I G+ Y  ++  L+  +G+N
Sbjct: 203 DGGLARTLELPATGWTRRYRVRVHGDTDQAQLDELRKGVTIDGVVYAPIEARLERVQGAN 262

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+ + L EGKNREIK+V       V RLIR+SYGPFQLG L  G+  EV  KILREQLG
Sbjct: 263 AWIAMSLTEGKNREIKRVMAHLGLDVTRLIRVSYGPFQLGELAEGAVEEVKLKILREQLG 322

Query: 247 PHLLEEAQVNLDAPI 261
             L E A V+  +P+
Sbjct: 323 KSLAELAGVDFSSPV 337


>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 =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 136/232 (58%), Positives = 177/232 (76%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMI + RV VNG +++  A+NV  +D I VDG PL +AE  R
Sbjct: 63  RIAKVLSRAGVASRREAERMITEGRVAVNGAVIDSPALNVTGSDRIVVDGTPLPEAEAPR 122

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVTT+SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 123 LWLYYKPTGLVTTNSDEKGRRTIFDELPEDLPRVMTVGRLDLNSEGLLLLTNDGGVKRQL 182

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+    + ++L+KG+VI G  +  M V LD Q+G+NAW+T+GLR
Sbjct: 183 ELPSTGWLRRYRVRINGRPQDHEFDVLRKGVVIDGERFQPMTVNLDRQQGANAWLTIGLR 242

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E   + VNRL+RISYGPFQLGTL  G   E+  +++R+QLG
Sbjct: 243 EGKNREIRRAMEEVGYPVNRLLRISYGPFQLGTLKEGEVEELRPRVVRDQLG 294


>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 =  293 bits (751), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 139/243 (57%), Positives = 177/243 (72%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+KVI+RAG+ASRR+ E  + Q RV VNG ++   A++V S D I VDG PL + ERT
Sbjct: 309 ERVAKVISRAGLASRRDAEEWVTQGRVAVNGRVINSPALDVTSRDVITVDGEPLPERERT 368

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTH+DP+GR TVFD+LP    R+ISVGRLD NTEGLLLLTNDGGLAR 
Sbjct: 369 RLFLYHKPRGLMTTHADPEGRPTVFDHLPDGLPRLISVGRLDFNTEGLLLLTNDGGLARA 428

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG+V Q +L+ LK G+ ++G+ YG +  TL+  +G+N W+T  +
Sbjct: 429 LELPDTGWLRRYRVRAHGEVTQPQLDALKNGVEVEGVKYGSIDATLERDQGANVWLTFAI 488

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIRISYGPFQL  +  G   EV  ++LREQ G  +   A
Sbjct: 489 REGKNREVRNVMAHLGLEVNRLIRISYGPFQLAEIAEGEVEEVKTRVLREQFGDRIAALA 548

Query: 254 QVN 256
            +N
Sbjct: 549 NMN 551


>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 =  293 bits (749), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 150/269 (55%), Positives = 191/269 (71%), Gaps = 10/269 (3%)

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 GLREGKNREIRRVMEALGFVVNRLIRISYGPFQLGALEAGEVQEVRRKVLRDQLG----- 252

Query: 252 EAQVNLDAP-IYSSETLVRDRPNIISEVP 279
              ++ DAP +  S  ++R+   I+ E P
Sbjct: 253 ---LDQDAPDLQRSRRIIRNE-KIVDETP 277


>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 =  293 bits (749), Expect = 3e-77,   Method: Compositional matrix adjust.
 Identities = 139/259 (53%), Positives = 188/259 (72%), Gaps = 4/259 (1%)

Query: 7   VQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + E   P+  R++KV++RAG+ASRRE ERMIA+ RV VNG  ++  A+NV + D I +DG
Sbjct: 28  IPEGAAPEGDRIAKVLSRAGVASRREAERMIAEGRVSVNGKKIDSPALNVTARDRISIDG 87

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL +AE  R+WLY+KPIGLVT++SD  GR T+FD LP    RV++VGRLD+N+EGLLLL
Sbjct: 88  QPLPEAEGPRMWLYYKPIGLVTSNSDEKGRKTIFDELPEDMPRVMTVGRLDLNSEGLLLL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGG+ R LELP+T WLR YRVR +G+   +    L+KG+VI+G  +  M V+LD Q+G
Sbjct: 148 TNDGGIKRKLELPATGWLRRYRVRINGRPKDEDFAPLRKGLVIEGERFQPMTVSLDRQQG 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+TVGLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+Q
Sbjct: 208 ANAWLTVGLREGKNREIRRAMEDIGFSVNRLLRVSYGPFQLGNLKPGEVEELRPRVVRDQ 267

Query: 245 LGPHLLEEAQVNLDAPIYS 263
           LG  L EE ++    P  +
Sbjct: 268 LG--LAEEEEIPAARPTRA 284


>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 =  292 bits (748), Expect = 5e-77,   Method: Compositional matrix adjust.
 Identities = 145/265 (54%), Positives = 188/265 (70%), Gaps = 9/265 (3%)

Query: 2   KDKNIV---QENFTP------QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           KDKN V   +   TP      +R++KV+ARAG+ SRRE+E  I   RV VNG +L   AV
Sbjct: 9   KDKNRVPRIKRELTPAAPKEAERIAKVVARAGLGSRREIEEWIEAGRVAVNGEVLTTPAV 68

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            V + D I VDG PL + ERTRL++YHKP G+VTT+ DP+GR+T+F+ LP    R++SVG
Sbjct: 69  TVTAEDAITVDGAPLPERERTRLFIYHKPRGVVTTNRDPEGRTTLFEILPQGLPRLVSVG 128

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD+N+EGLLLLTNDGGLARVLELP T WLR YRVR +G+V+Q +L+ L KGI + G+ Y
Sbjct: 129 RLDLNSEGLLLLTNDGGLARVLELPETGWLRRYRVRANGEVNQAQLDSLLKGITVDGVEY 188

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           G ++  LD  +G+NAW+TV LREGKNREI+ VF     +VNRLIR+SYGPFQLG +  G 
Sbjct: 189 GPIEAELDRVQGANAWITVSLREGKNREIRNVFGALGLQVNRLIRVSYGPFQLGDVPEGG 248

Query: 233 TREVSKKILREQLGPHLLEEAQVNL 257
             EV  ++LR+Q+G  L   A  + 
Sbjct: 249 IEEVRTRVLRDQIGNDLAAAAGADF 273


>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 =  290 bits (743), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 145/268 (54%), Positives = 186/268 (69%), Gaps = 8/268 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ SRR+ ER I   RVKVNG LL   A  V   D IEVD   L   ERT
Sbjct: 19  ERIAKRMARAGLCSRRDAERWIEAGRVKVNGKLLTTPAHTVTPRDRIEVDDKLLGGPERT 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL +K  GLVTT+ DP+GR+T+F+ LP    RV+SVGRLDINTEGLLLLTNDGGLARV
Sbjct: 79  RLWLLNKRSGLVTTNKDPEGRTTIFERLPDDLPRVLSVGRLDINTEGLLLLTNDGGLARV 138

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HGQ  Q++L+ L  GI + G+ YG ++  L+ Q+G+N W+T  +
Sbjct: 139 LELPTTGWLRRYRVRAHGQTTQEELDKLADGIAVDGVLYGAIEAELERQQGTNVWLTFAM 198

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE+K V      +VNRLIRISYGPFQLG L +G  +EV  ++LR+QLG  L+  +
Sbjct: 199 REGKNREVKNVLSALGLEVNRLIRISYGPFQLGDLASGEVQEVRGRMLRQQLGAKLISAS 258

Query: 254 QVNLDAPIYSS--------ETLVRDRPN 273
             + DAP+ ++        E + + RPN
Sbjct: 259 GADFDAPLAATAPKNNPVGEKIEKARPN 286


>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 =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 136/235 (57%), Positives = 176/235 (74%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++KV++RAG+ASRRE ERMIA+ R+ VNG +++  A+NV   + I VDG PL +AE
Sbjct: 67  TGDRIAKVLSRAGVASRREAERMIAEGRISVNGTVIDSPALNVTGQERILVDGAPLPQAE 126

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RLWLYHKP GLVTT+ D  GR T+FD+LP    RV++VGRLD+N+EGLLLLTNDGG+ 
Sbjct: 127 APRLWLYHKPSGLVTTNRDEKGRKTIFDDLPETLPRVMTVGRLDLNSEGLLLLTNDGGIK 186

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELPST WLR YRVR +G+  ++    L+KG+VI G  +  M V LD Q+G+NAW+TV
Sbjct: 187 RKLELPSTGWLRRYRVRINGRPKEEDFAPLRKGLVIDGERFQPMIVDLDRQQGANAWLTV 246

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  ++LR+QLG
Sbjct: 247 GLREGKNREIRRAMEDIGYNVNRLLRVSYGPFQLGDLKPGEVEELRPRVLRDQLG 301


>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 =  290 bits (742), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 144/232 (62%), Positives = 172/232 (74%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KVIARAG+ASRRE ERMI   RV VNG  ++RAA+NV   D I VDG  LR  E  R
Sbjct: 10  RIAKVIARAGLASRREAERMIEAGRVTVNGKKIDRAALNVTDKDRIAVDGRDLRAPEPQR 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLYHKP GLVTT+ D  GR T+FD LP    RV+SVGRLDIN+EGLLLLTNDGGL R L
Sbjct: 70  LWLYHKPTGLVTTNKDEQGRPTIFDELPEDLPRVMSVGRLDINSEGLLLLTNDGGLKRKL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   D    L++G+VI G  +  M VTLD Q+G+NAWVTVG+R
Sbjct: 130 ELPSTGWLRRYRVRVNGRPTDDTFAPLRQGLVIDGEKFQPMIVTLDRQQGANAWVTVGIR 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EG+NRE+++  E     VNRLIR+SYGPFQLGTL  G+  E+  +ILR+QLG
Sbjct: 190 EGRNREVRRAMEAVGLSVNRLIRVSYGPFQLGTLKPGAVEEIRPRILRDQLG 241


>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 =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 136/258 (52%), Positives = 179/258 (69%)

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 HLLEEAQVNLDAPIYSSE 265
            +   +    D P+   E
Sbjct: 604 KIATMSGAQFDKPVREDE 621


>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 =  289 bits (740), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 135/252 (53%), Positives = 177/252 (70%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ SRR+ E  I Q RV VNG ++   A++V + D I VDG PL + ERT
Sbjct: 366 ERIAKVVARAGLCSRRDAEDWIMQGRVAVNGRVIGSPALDVTARDVITVDGQPLPERERT 425

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTH DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGL+R 
Sbjct: 426 RLFLYHKPRGLMTTHDDPEGRPTVFDHLPDGLPRLISIGRLDFNTEGLLLLTNDGGLSRA 485

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LE P T WLR YRVR HG V Q +L+ LK G+ + G+ YG +  TL+  +G+N W+T  +
Sbjct: 486 LEHPDTGWLRRYRVRAHGDVTQARLDELKNGVEVDGVKYGSIDATLERDQGANVWLTFAI 545

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++LREQLG  ++  A
Sbjct: 546 REGKNREVRNVMAHLGLEVNRLIRVSYGPFQLGEIPEGQVEEIKSRVLREQLGDKIIALA 605

Query: 254 QVNLDAPIYSSE 265
               D P+   +
Sbjct: 606 GAQFDKPVQEGD 617


>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 =  289 bits (739), Expect = 5e-76,   Method: Compositional matrix adjust.
 Identities = 136/233 (58%), Positives = 172/233 (73%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K+++RAG+ASRRE ERMI   RV VNG +++  A+NV   D + VDG PL  AE  
Sbjct: 9   ERIAKILSRAGVASRREAERMIEAGRVAVNGKVIDSPALNVTERDRVTVDGAPLADAEPA 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT  D  GR T+FD+LP    RV+SVGRLD+N+EGLLLLTNDG + R 
Sbjct: 69  RLWLYHKPSGLVTTARDEKGRKTIFDDLPEDMPRVMSVGRLDLNSEGLLLLTNDGAVKRQ 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G    +    L++G+VI+G  +  M V++D Q+G+NAW+TVGL
Sbjct: 129 LELPSTGWLRRYRVRIKGTPKDEDFAPLRQGLVIEGERFQPMIVSIDRQQGANAWLTVGL 188

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++  E   + VNRLIRISYGPFQLGTL  G   EV +++LR+QLG
Sbjct: 189 REGKNREIRRAIEDIGFIVNRLIRISYGPFQLGTLAPGKVEEVRRRVLRDQLG 241


>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 =  288 bits (738), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 135/232 (58%), Positives = 176/232 (75%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMIA+ RVKVNG  ++  A+NV   D I VDG PL +AE  R
Sbjct: 42  RIAKVLSRAGVASRREAERMIAEGRVKVNGTKIDSPALNVTERDRIIVDGKPLPQAEAPR 101

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVT++SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 102 LWLYNKPTGLVTSNSDEKGRRTIFDELPEDLPRVMTVGRLDLNSEGLLLLTNDGGIKRRL 161

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   +    L+KG+VI+G  +  M V LD Q+G+NAW+T+GLR
Sbjct: 162 ELPSTGWLRRYRVRINGRPKDEDFEPLRKGMVIEGERFQPMTVALDRQQGANAWLTIGLR 221

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E   + VNRL+R+SYGPFQLG+L  G   E+  +++R+QLG
Sbjct: 222 EGKNREIRRALEDIGFNVNRLLRLSYGPFQLGSLKLGEVEELRPRVVRDQLG 273


>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 =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 138/259 (53%), Positives = 183/259 (70%), Gaps = 1/259 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V  +D I VDG PL + ERTR
Sbjct: 477 RIAKVVARAGLCSRRDAEAWIVEGRVAVNGRVIDSPALDVTYSDVITVDGKPLPERERTR 536

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLAR L
Sbjct: 537 LFLYHKPRGLMTTHADPEGRPTVFDNLPEDLPRLISIGRLDFNTEGLLLLTNDGGLARAL 596

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP T WLR YRVR HG+V Q +L+ L  G+ + G+ YG ++  L+  +G+N W+   +R
Sbjct: 597 ELPETGWLRRYRVRAHGEVTQAQLDQLASGVEVDGVKYGPIEAKLERDQGANVWLVFAIR 656

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  +++ A+
Sbjct: 657 EGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLEIEEGQVEEVKTRVLREQLGEKIIKLAE 716

Query: 255 VNLDAPIYSSETLVRDRPN 273
            +   P   SET  + RP 
Sbjct: 717 ADFGGPS-PSETRPKPRPG 734


>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 =  288 bits (737), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 135/244 (55%), Positives = 173/244 (70%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAG+ SRR+ E  I + RV VNG ++   A++V   D I VDG PL   ERT
Sbjct: 467 ERIAKVVSRAGLCSRRDAEDWITEGRVAVNGRIINSPALDVTERDVITVDGKPLPPPERT 526

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTH+DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR 
Sbjct: 527 RLFLYHKPRGLMTTHADPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGGLART 586

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG+V Q +LN LK G+ + G+ YG +  TL+  +G+N W+   +
Sbjct: 587 LELPDTGWLRRYRVRAHGEVTQAQLNELKDGVEVDGVKYGPIDATLERDQGANVWLVFAI 646

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   EV  ++LREQLG  +   A
Sbjct: 647 REGKNREVRNVLAHLGLEVNRLIRVSYGPFQLGEIEEGQVEEVKTRVLREQLGEKIALAA 706

Query: 254 QVNL 257
             N 
Sbjct: 707 GANF 710


>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 =  288 bits (737), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 136/232 (58%), Positives = 178/232 (76%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV + D I VDG PL +AE  R
Sbjct: 63  RIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVTNLDRIVVDGNPLPEAEAPR 122

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVTT SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 123 LWLYYKPNGLVTTTSDEKGRKTIFDALPEDLPRVMTVGRLDLNSEGLLLLTNDGGVKRQL 182

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+    + ++L+KG+VI G  +  M ++LD Q+G+NAW+T+GLR
Sbjct: 183 ELPSTGWLRRYRVRINGRPQDHEFDVLRKGVVIDGERFQPMTISLDRQQGANAWLTIGLR 242

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E   + VNRL+RISYGPFQLGTL  G   E+  +++R+QLG
Sbjct: 243 EGKNREIRRAMEEVGYPVNRLLRISYGPFQLGTLKEGEVEELRPRVVRDQLG 294


>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 =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 139/246 (56%), Positives = 176/246 (71%), Gaps = 3/246 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRRE E+MI   RV VNG ++ RAA+NV   D + VDG P+   E  R
Sbjct: 56  RIAKVLARAGVASRREAEKMIEMGRVAVNGEIITRAALNVTDKDKVTVDGKPVDAPEDPR 115

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLYHKP GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLTNDG + R L
Sbjct: 116 IWLYHKPAGLVTTTKDEQGRPTIYDDLPEELPRVMSVGRLDLNSEGLLLLTNDGSIKRRL 175

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   D L  L+ GIV+ G  +  M+VTLD Q+G+NAW+T+GLR
Sbjct: 176 ELPSTGWLRKYRVRVNGKPSDDMLAPLRAGIVVDGQAFQPMEVTLDRQQGANAWLTIGLR 235

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++        VNRLIR+SYGPFQLG L  G  +EV  +++R+QLG   LE A+
Sbjct: 236 EGKNREIRRAMTDIGLTVNRLIRVSYGPFQLGQLKQGEVQEVRSRVVRDQLG---LEGAK 292

Query: 255 VNLDAP 260
            N   P
Sbjct: 293 SNRPQP 298


>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 =  288 bits (736), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 133/233 (57%), Positives = 172/233 (73%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAG+ SRR+ E  + Q RV VNG ++   A++V + D I VDG PL   ERT
Sbjct: 423 ERIAKVVSRAGLCSRRDAEEWVTQGRVAVNGRIINSPALDVTTRDVITVDGKPLPLPERT 482

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL++YHKP GL+TTH+DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR 
Sbjct: 483 RLFMYHKPRGLMTTHADPEGRPTVFDHLPDGLPRLISIGRLDFNTEGLLLLTNDGGLART 542

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG+V Q +L+ LKKG+ + G+ YG +  TL+  +G+N W+   +
Sbjct: 543 LELPDTGWLRRYRVRAHGEVTQGQLDELKKGVEVDGVKYGSIDATLERDQGANVWLVFAI 602

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNRE++ V      +VNRLIR+SYGPFQLG L  G   EV  ++LREQLG
Sbjct: 603 REGKNREVRNVLAHLGLEVNRLIRVSYGPFQLGELEEGQVEEVKTRVLREQLG 655


>gi|144897623|emb|CAM74487.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 287

 Score =  287 bits (735), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 136/242 (56%), Positives = 178/242 (73%)

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 LG 246
           LG
Sbjct: 250 LG 251


>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 =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 136/232 (58%), Positives = 173/232 (74%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAGIASRRE ERMI   RV VNG  ++  A+NV  +D I VDG P+ + E  R
Sbjct: 31  RIAKVLARAGIASRREAERMIEAGRVTVNGKTIDSPALNVTPSDRITVDGKPVAEPEPAR 90

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLYHKP GLVTT+ D  GR T+FDNLP    RV+SVGRLD+N+EGLLLLTNDG + R L
Sbjct: 91  LWLYHKPTGLVTTNRDEKGRPTIFDNLPEDMPRVMSVGRLDLNSEGLLLLTNDGTIKRKL 150

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   +    L++G+VI+G  +  M VTLD Q+G+NAW+T+GLR
Sbjct: 151 ELPSTGWLRKYRVRINGRPKDEDFAPLRQGLVIEGERFQPMTVTLDRQQGANAWLTIGLR 210

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+ +++LR+QLG
Sbjct: 211 EGKNREIRRAIEDIGFTVNRLLRVSYGPFQLGNLKPGEVEEIRRRVLRDQLG 262


>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 =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 145/254 (57%), Positives = 180/254 (70%), Gaps = 5/254 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           F   R++KV+ARAG  SRR+ E  IA+ RV VNG +L+  A NV   D IEVDG PL + 
Sbjct: 38  FEGDRIAKVMARAGACSRRDAEIWIAEGRVAVNGAVLDSPAFNVREGDRIEVDGAPLAER 97

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSRVISVGRLDINTEGLLLLTN 126
           E TRL+L+HKP GLVT+  DP+GR TVF  L    P +  R++SVGRLDINTEGLLLLTN
Sbjct: 98  EPTRLFLFHKPEGLVTSAKDPEGRDTVFGFLEERHPDL-PRLVSVGRLDINTEGLLLLTN 156

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T W R YRVR HG++DQ +L+ L+KG+ +  + Y  ++  LD  +G+N
Sbjct: 157 DGGLARTLELPATGWTRRYRVRAHGEIDQARLDELRKGVTVDDVDYAPIEARLDRVQGAN 216

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+ LREGKNREIK+V E     VNRLIRIS+GPFQLG L  G+  EV  KILREQLG
Sbjct: 217 VWITMALREGKNREIKRVLEHLGLGVNRLIRISFGPFQLGELAEGAVEEVKLKILREQLG 276

Query: 247 PHLLEEAQVNLDAP 260
             L E A V+  +P
Sbjct: 277 KGLAELAGVDFSSP 290


>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 =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 140/233 (60%), Positives = 170/233 (72%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K+++R G+ASRRE ERMI   RV VNG L++  A+NV ++D I VDG P+   E  
Sbjct: 8   ERIAKILSRRGVASRREAERMIEAGRVSVNGRLIDSPALNVTTSDRILVDGKPVAAPEPP 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT  D  GR TVF  LP    RV+SVGRLDI +EGLLLLTNDG + R 
Sbjct: 68  RLWLYHKPAGLVTTERDEKGRPTVFGALPEEMPRVMSVGRLDIASEGLLLLTNDGEIKRR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG V+  KL  L++GI ++G+ Y  M VT D Q+G+NAW+TV L
Sbjct: 128 LELPATGWLRRYRVRSHGYVEDAKLEPLRRGISVEGVRYQPMSVTFDRQQGANAWMTVAL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++  E    KVNRLIRISYGPFQLG L AG   EV  K+LR+QLG
Sbjct: 188 REGKNREIRRAMEAIGIKVNRLIRISYGPFQLGNLAAGEVEEVRPKVLRDQLG 240


>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 =  286 bits (732), Expect = 3e-75,   Method: Compositional matrix adjust.
 Identities = 140/265 (52%), Positives = 188/265 (70%), Gaps = 1/265 (0%)

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 LLEEAQVNLDAPIYSSETLVRDRPN 273
           +++ A  +   P   SE   + RP 
Sbjct: 698 IIQLAGADFGGPS-PSEARPKPRPG 721


>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 =  286 bits (731), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 135/250 (54%), Positives = 179/250 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+KVIARAG+ SRRE+E  I   RV VNG +LE  A  V   D I VDG PL   ERT
Sbjct: 30  ERVAKVIARAGLGSRREIEEWILAGRVAVNGEVLESPARTVTPEDAITVDGNPLPAKERT 89

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL++YHKP G+VTT+ DP+GR T+F+ LP+   R++SVGRLD+NTEGL+LLTNDGGL+RV
Sbjct: 90  RLFMYHKPKGVVTTNYDPEGRPTLFEILPAGLPRLVSVGRLDLNTEGLILLTNDGGLSRV 149

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR  G + QDKL+ L +G+ + G+ YG ++  LD  +G+N+W+T+ L
Sbjct: 150 LELPETGWLRRYRVRAKGDITQDKLDALMEGVTVDGVHYGPIEAKLDRVQGANSWLTLAL 209

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   EV  ++L +QLG  L   A
Sbjct: 210 REGKNREVRNVLGSLGLEVNRLIRVSYGPFQLGEIPQGEVEEVRTRVLADQLGEALSAAA 269

Query: 254 QVNLDAPIYS 263
             + + P+++
Sbjct: 270 GADFEGPLFN 279


>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 =  285 bits (730), Expect = 5e-75,   Method: Compositional matrix adjust.
 Identities = 143/249 (57%), Positives = 174/249 (69%), Gaps = 2/249 (0%)

Query: 9   ENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +N TP   R++KVIARAG ASRRE ERMIA+ RV VNG +++  A+NV   D I VD  P
Sbjct: 2   DNKTPPGDRIAKVIARAGRASRREAERMIAEGRVAVNGTVIDSPALNVTDKDRITVDDTP 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E  RLWLYHK  GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 62  LDGPEEARLWLYHKSTGLVTTTKDEQGRPTIYDDLPDDLPRVMSVGRLDLNSEGLLLLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGL R LELPST WLR YRVR +G+     L  L+ G+ + G  +  M V+LD Q+G+N
Sbjct: 122 DGGLKRRLELPSTGWLRRYRVRINGRPTDPMLQPLRDGLTVDGQTFQPMIVSLDRQQGAN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIRISYGPFQLG +  G  +EV +KILR+QLG
Sbjct: 182 AWLTVGLREGKNREIRRAMADLGLSVNRLIRISYGPFQLGQMKPGEVQEVRRKILRDQLG 241

Query: 247 PHLLEEAQV 255
             L  E + 
Sbjct: 242 LGLDAEPEA 250


>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 =  285 bits (729), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 144/238 (60%), Positives = 175/238 (73%), Gaps = 3/238 (1%)

Query: 12  TPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           TP+   R++KV++RAGIASRRE ERMI   RV VNG ++   A+NV   D I+VDG  + 
Sbjct: 4   TPEKGDRIAKVLSRAGIASRREAERMIEAGRVSVNGKVIPSPALNVTPKDKIKVDGKEVG 63

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            AE  RLWLYHKP+GLVTT  D  GR TVFDNLP    RV+SVGRLDIN+EGLLLLTNDG
Sbjct: 64  DAEPARLWLYHKPVGLVTTERDEKGRDTVFDNLPDGLPRVMSVGRLDINSEGLLLLTNDG 123

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL R LELPST WLR YRVR +G V +D L  L+KG+VI G  +  M +++D Q+GSNAW
Sbjct: 124 GLKRKLELPSTGWLRKYRVRVNGIVIEDHLTPLRKGLVIDGEKFQPMNISVDRQQGSNAW 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +TVG+REGKNREI++ FE     VNRLIR+SYGPFQL  L A    E+  ++LR+QLG
Sbjct: 184 LTVGIREGKNREIRRAFETIFLPVNRLIRVSYGPFQLNDLRADEVEEIKGRVLRDQLG 241


>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 =  285 bits (728), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 138/232 (59%), Positives = 171/232 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMI   RV VNG +++  A+NV   D I VDG  + K E  R
Sbjct: 37  RIAKVLSRAGVASRREAERMIEAGRVSVNGKVIDSPALNVTPRDKITVDGTLVEKPEAPR 96

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLYHKP GLVTT  D  GR TVFD LP    RV+SVGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 97  LWLYHKPTGLVTTERDEKGRETVFDKLPEDMPRVMSVGRLDLNSEGLLLLTNDGGIKRKL 156

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST W+R YRVR +G+ ++  L  L+KGI + G  +  M VTLD Q+G+NAW+T+GLR
Sbjct: 157 ELPSTGWVRKYRVRVNGKPEEAVLEKLRKGITVDGEAFQGMSVTLDRQQGANAWLTIGLR 216

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E     VNRLIRISYGPF+LG L AG+  EV  ++LR+QLG
Sbjct: 217 EGKNREIRRAMEAVGLTVNRLIRISYGPFRLGELKAGAVEEVKGRVLRDQLG 268


>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 =  284 bits (727), Expect = 1e-74,   Method: Compositional matrix adjust.
 Identities = 143/260 (55%), Positives = 181/260 (69%), Gaps = 4/260 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAGIASRRE ERMI   RV VNG  +   A+NV   D I VDG P+ + E +R
Sbjct: 37  RIAKVLARAGIASRREAERMIEAGRVAVNGKPINSPALNVTGKDKITVDGKPVSEPEPSR 96

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLYHKP GLVTT  D  GR+T+FD LP    RV+SVGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 97  LWLYHKPPGLVTTARDEKGRTTIFDKLPENMPRVMSVGRLDLNSEGLLLLTNDGGIKRKL 156

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   +    L+KG+VI G  +  M VTLD Q+G+NAW+T+GLR
Sbjct: 157 ELPSTGWLRKYRVRVNGRPRDEDFAPLRKGLVIDGERFQPMTVTLDRQQGANAWLTIGLR 216

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+ ++++R+QLG     +A+
Sbjct: 217 EGKNREIRRAIEDIGYVVNRLLRVSYGPFQLGDLKPGEVEEIRRRVMRDQLG----LDAE 272

Query: 255 VNLDAPIYSSETLVRDRPNI 274
            +  AP        R RP I
Sbjct: 273 GDGKAPAKRPARPQRKRPAI 292


>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 =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 133/232 (57%), Positives = 172/232 (74%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMI   RV+VNG+ ++  A+NV + D+I VDG P+   E  R
Sbjct: 19  RIAKVLSRAGLASRREAERMIEAGRVRVNGVQIDSPALNVTAADNITVDGKPVGDPEPPR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLYHKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R L
Sbjct: 79  MWLYHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGDVKRKL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  WLR YRVR +G+   + L  L++GI + G  +  M VTLD Q+G+NAW+TVGLR
Sbjct: 139 ELPSNGWLRRYRVRVNGRPSDEVLEPLRRGITVDGEEFQPMTVTLDRQQGANAWLTVGLR 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG
Sbjct: 199 EGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKPGEVEELKRKVVRDQLG 250


>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 =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 135/232 (58%), Positives = 171/232 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   RV+VNG  ++  A+NV  +D I VDG P+ + E  R
Sbjct: 19  RIAKVLSRAGIASRREAERMIEAGRVRVNGAQIDSPALNVTPSDAITVDGKPVGEPEPPR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WL+HKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R L
Sbjct: 79  VWLFHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGEVKRRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  WLR YRVR +G+   D L  L+KGI + G  +  M VTLD Q+G+NAW+TVGLR
Sbjct: 139 ELPSNGWLRRYRVRVNGRPTDDMLEPLRKGITVDGEDFQPMTVTLDRQQGANAWLTVGLR 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG
Sbjct: 199 EGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKTGEVEELKRKVVRDQLG 250


>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 =  283 bits (725), Expect = 2e-74,   Method: Compositional matrix adjust.
 Identities = 135/232 (58%), Positives = 171/232 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   RV+VNG  ++  A+NV  +D I VDG P+ + E  R
Sbjct: 19  RIAKVLSRAGIASRREAERMIEAGRVRVNGAQIDSPALNVTPSDAITVDGKPVGEPEPPR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WL+HKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R L
Sbjct: 79  VWLFHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGEVKRRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  WLR YRVR +G+   D L  L+KGI + G  +  M VTLD Q+G+NAW+TVGLR
Sbjct: 139 ELPSNGWLRRYRVRVNGRPTDDMLEPLRKGITVDGEDFQPMTVTLDRQQGANAWLTVGLR 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG
Sbjct: 199 EGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKTGEVEELKRKVVRDQLG 250


>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 =  283 bits (724), Expect = 3e-74,   Method: Compositional matrix adjust.
 Identities = 148/265 (55%), Positives = 183/265 (69%), Gaps = 7/265 (2%)

Query: 12  TPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           TPQ  R++KV++RAG+ASRRE ERMI   RVKVNG  +   A+NV  TD I VDG  +  
Sbjct: 6   TPQGDRIAKVLSRAGVASRREAERMIEAGRVKVNGQHISSPALNVQGTDKITVDGKEVSP 65

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  RLWLYHKP GLVTT +D  GR T++  LP    RV+SVGRLDIN+EGLLLLTNDGG
Sbjct: 66  PEPARLWLYHKPTGLVTTDNDEKGRETIYSALPEDMPRVMSVGRLDINSEGLLLLTNDGG 125

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + R LELP+T WLR YRVR +G+     L+ L++GI  +G  +  MQ+TLD Q+G+NAW+
Sbjct: 126 VKRRLELPTTGWLRRYRVRINGRPTDATLDPLRRGISSEGENFQPMQITLDRQQGANAWL 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           TVGLREGKNREI++     +  VNRLIRISYGPFQLG L  G+  EV +KILR+QLG   
Sbjct: 186 TVGLREGKNREIRRALAELDLSVNRLIRISYGPFQLGELKPGAVEEVRRKILRDQLG--- 242

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNI 274
             E +V   AP +      R  PN+
Sbjct: 243 -LEGEVEESAPKHPDAGKKRG-PNV 265


>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 =  283 bits (723), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 137/242 (56%), Positives = 175/242 (72%)

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 LG 246
           +G
Sbjct: 252 MG 253


>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 =  283 bits (723), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 133/250 (53%), Positives = 179/250 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL + ERT
Sbjct: 410 ERIAKVVARAGLCSRRDAEAWITEGRVTVNGKVIDSPALDVKASDVITIDGKPLPERERT 469

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR 
Sbjct: 470 RLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGGLARA 529

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG ++  L+  +G+N W+   +
Sbjct: 530 LELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIEAKLERDQGANVWLVFAI 589

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG  ++  A
Sbjct: 590 REGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGEKVIALA 649

Query: 254 QVNLDAPIYS 263
             +   P  S
Sbjct: 650 GCDFAGPSPS 659


>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 =  282 bits (722), Expect = 4e-74,   Method: Compositional matrix adjust.
 Identities = 133/250 (53%), Positives = 179/250 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL + ERT
Sbjct: 405 ERIAKVVARAGLCSRRDAEAWITEGRVTVNGKVIDSPALDVKASDIITIDGKPLPERERT 464

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR 
Sbjct: 465 RLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGGLARA 524

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG ++  L+  +G+N W+   +
Sbjct: 525 LELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIEAKLERDQGANVWLVFAI 584

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG  ++  A
Sbjct: 585 REGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGEKVIALA 644

Query: 254 QVNLDAPIYS 263
             +   P  S
Sbjct: 645 GCDFAGPSPS 654


>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 =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 141/294 (47%), Positives = 190/294 (64%), Gaps = 17/294 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K +ARAG+ASRREVERMI   RVKV+G  L+  A  V  ++HIEVDG  +    
Sbjct: 7   TSERIAKFLARAGVASRREVERMIEGGRVKVDGKTLDTPAFKVTGSEHIEVDGKRIEPPA 66

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T+LW YHKP GLVTTH+DP+GR TVFD +P    RVIS+GRLD+ +EGLLLLTNDG LA
Sbjct: 67  ATKLWRYHKPDGLVTTHADPEGRETVFDAIPKDIGRVISIGRLDLTSEGLLLLTNDGALA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELPST W R YR R  G + +  L +L+ G+ ++GI YG M+V ++ + GSN W+ V
Sbjct: 127 RALELPSTGWTRRYRARAFGSISESALKILRAGVTVEGIKYGPMEVEVERETGSNIWLEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           G+REGKNRE++K  +    +VNRLIRI+YGPFQLG L  G  + V  ++L +Q G HL++
Sbjct: 187 GIREGKNREVRKALDAVGLRVNRLIRIAYGPFQLGQLEKGEIKSVPSRVLHDQCG-HLID 245

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK-NGLSKQKKLATP 304
                 D P  + + + + RP           R  +   QK +G   Q+ +  P
Sbjct: 246 MG----DTP--TGQAIAKPRP---------ANRAARKPGQKPDGKPGQRAMGGP 284


>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 =  281 bits (720), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 136/232 (58%), Positives = 171/232 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRRE E++I   RV VNG  +   A+NV   D I VDG PL + E  R
Sbjct: 24  RIAKVLARAGVASRREAEKIIEAGRVTVNGKTILTPALNVTDKDRIVVDGKPLAEPEPPR 83

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLY+KPIGLVT+  D  GR TVFD LP    RV+SVGRLDIN+EGLLLLTNDG L R +
Sbjct: 84  IWLYYKPIGLVTSERDEKGRETVFDTLPDDMPRVVSVGRLDINSEGLLLLTNDGELKRKM 143

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G + + KL+ L+ GI I G+ Y  ++V  D Q+G+NAW+T+GLR
Sbjct: 144 ELPSTGWLRRYRVRINGSLSEAKLDELRAGIQIDGVHYAPVEVKFDRQQGANAWLTMGLR 203

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI+K+ E     VNRL+RISYGPFQLGTL  G   EV ++I+R+Q+G
Sbjct: 204 EGKNREIRKLMEAMGVVVNRLLRISYGPFQLGTLKPGKVEEVKQRIVRDQMG 255


>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 =  281 bits (720), Expect = 9e-74,   Method: Compositional matrix adjust.
 Identities = 136/240 (56%), Positives = 177/240 (73%), Gaps = 2/240 (0%)

Query: 9   ENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           EN  P  QR++KV+ARAG+ASRRE ERMI   RV+VN  L+E  A+NV+ +D I VDG  
Sbjct: 6   ENTGPTGQRIAKVLARAGVASRREAERMIEAGRVRVNSKLIESPALNVVPSDRISVDGKL 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E TR+WL+HKP GL+T+  D +GR TVFD LP    RV+SVGRLD+N+EGLL+LTN
Sbjct: 66  IGDPEPTRMWLFHKPQGLITSERDEEGRETVFDVLPPEMPRVLSVGRLDLNSEGLLVLTN 125

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG + R LELPST WLR YRVR  G + + KL+ L++GI ++G+ Y  M VT D Q+G+N
Sbjct: 126 DGEVKRKLELPSTGWLRRYRVRIKGSLSEAKLDELREGITVEGVHYQPMDVTFDRQQGAN 185

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+T+G+REGKNREI++  E     VNRLIRISYGPFQLG + AG   E+  +++R+QLG
Sbjct: 186 AWLTIGIREGKNREIRRTMEALGVTVNRLIRISYGPFQLGNIKAGEVEELKSRVVRDQLG 245


>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 =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 139/246 (56%), Positives = 172/246 (69%), Gaps = 2/246 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KVIARAG+ASRRE ERM+   RV VNG  ++  A+NV  +D I VDG  L   E  R
Sbjct: 10  RIAKVIARAGLASRREAERMVEAGRVTVNGRKIDSPALNVTPSDKITVDGRALATPEPPR 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLYHKP GLVTT  D  GR T+FD LP    RV+SVGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 70  LWLYHKPTGLVTTTRDEQGRDTIFDKLPEDLPRVMSVGRLDLNSEGLLLLTNDGGIKRRL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+ +      L+KG+ ++G  +  MQVTLD Q+G+NAW+TV +R
Sbjct: 130 ELPSTGWLRRYRVRVNGRPNDATFEPLRKGVTLEGERFQPMQVTLDRQQGANAWITVAIR 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++  E     VNRLIR+SYGPFQLG L +G   E+  +++REQLG  L EE  
Sbjct: 190 EGKNREIRRAMESVGLSVNRLIRVSYGPFQLGQLKSGEVEEIRPRVMREQLG--LTEEEA 247

Query: 255 VNLDAP 260
                P
Sbjct: 248 GRTPGP 253


>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 =  281 bits (718), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 141/248 (56%), Positives = 180/248 (72%), Gaps = 5/248 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++KV+ARAG+ SRR+ E  IA+ RV VNG +L +  V+V   D I VDG  L     
Sbjct: 89  PQRIAKVMARAGLCSRRDAEAWIAEGRVSVNGTVLTQPGVSVSDEDVILVDGEKLAARGH 148

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSRVISVGRLDINTEGLLLLTNDG 128
           TRL+L+HKP GLVTT+ DP+GR TVFD L    P +  RV+S+GRLDINTEGLLLLTNDG
Sbjct: 149 TRLFLFHKPRGLVTTNHDPEGRPTVFDYLHERHPDM-PRVLSIGRLDINTEGLLLLTNDG 207

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           GL+R+LELP+T W+R YRVR  G  DQ  L+ L++GI I GI Y  M+VT D ++G+N+W
Sbjct: 208 GLSRLLELPTTGWVRRYRVRAKGTTDQAVLDQLRQGITIDGIHYAGMEVTFDREQGANSW 267

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+ LREGKNRE+K+V E    +VNRLIR+S+GPFQLG L  G   EV  ++LR+QLGP 
Sbjct: 268 LTLSLREGKNREVKRVLEQIGLEVNRLIRLSFGPFQLGDLPEGDVTEVRTRVLRDQLGPS 327

Query: 249 LLEEAQVN 256
           L   A V+
Sbjct: 328 LAAAAGVD 335


>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 =  281 bits (718), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 134/233 (57%), Positives = 172/233 (73%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KVIARAGI SRR+ E++I + RV +NG  +E  A  V ++D + VDG PL   E  
Sbjct: 6   ERIAKVIARAGICSRRDAEKLIVEGRVTLNGRKVETPATLVAASDTVTVDGKPLPALEPA 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW Y+KPIGLVT+H D  GR TVF+ LP+   RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 66  RLWRYNKPIGLVTSHRDEQGRPTVFERLPATLPRVISVGRLDLNSEGLLLLTNDGELARR 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LE PS  WLR YRVR HG  D  KL  L+KG+ ++G+ YG ++V L+ Q+G+NAW++V L
Sbjct: 126 LEHPSQGWLRRYRVRVHGAPDPVKLAALEKGVTVEGVAYGSIRVALERQQGANAWLSVSL 185

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++V E     V+RLIR++YGPFQLG L  G+  E+  KI+REQLG
Sbjct: 186 REGKNREIRRVMEHLGLPVSRLIRVAYGPFQLGQLEEGTVDEIPGKIMREQLG 238


>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 =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 139/239 (58%), Positives = 172/239 (71%), Gaps = 2/239 (0%)

Query: 10  NFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           N TPQ  R++KV++RAG+ASRR+ ERMI + RV VNG ++   A+NV   D I VDG  +
Sbjct: 3   NDTPQGDRIAKVLSRAGVASRRDAERMITEGRVSVNGKVITSPALNVTDADRIVVDGKAM 62

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  E  R+WLYHKP GLVTT  D   R TVF +LP    RV+SVGRLD+N+EGLLLLTND
Sbjct: 63  RAPEAPRIWLYHKPAGLVTTERDEKDRPTVFASLPEDMPRVMSVGRLDLNSEGLLLLTND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GG+ R LELPST WLR YRVR +G V + +L  L+ GI + GI Y  M VT D Q+G+NA
Sbjct: 123 GGVKRRLELPSTGWLRRYRVRINGSVSEARLEQLRAGITVDGIRYQPMIVTFDRQQGANA 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           W+TV LREGKNREI++  E     VNRLIR+SYGPFQLG L AG+  EV  +++R+QLG
Sbjct: 183 WLTVSLREGKNREIRRAMEAIGVTVNRLIRVSYGPFQLGNLEAGAVEEVKGRVVRDQLG 241


>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 =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 139/246 (56%), Positives = 171/246 (69%), Gaps = 3/246 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI + RV VNG  +   A+NV   D I VDG PL   E  R
Sbjct: 23  RIAKVLSRAGIASRREAERMIEEGRVTVNGETIASPALNVTDKDRITVDGKPLEAPEAPR 82

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +W+YHKP GLVTT  D  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 83  MWMYHKPAGLVTTTKDEQGRETIFDKLPEDLPRVMTVGRLDLNSEGLLLLTNDGGIKRKL 142

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+  ++ L  L+ GI + G  +  MQV LD Q+GSNAW+TVGLR
Sbjct: 143 ELPSTGWLRRYRVRVNGKPTEEMLKPLRDGITVDGQTFQPMQVELDRQQGSNAWLTVGLR 202

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++        VNRLIRISYGPFQLG +  G   E+  +I+R+QLG   LE A+
Sbjct: 203 EGKNREIRRAMSDIGLTVNRLIRISYGPFQLGQMKVGEVVELRGRIVRDQLG---LEGAK 259

Query: 255 VNLDAP 260
                P
Sbjct: 260 TTRPEP 265


>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 =  280 bits (717), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 133/233 (57%), Positives = 171/233 (73%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K ++RAG+ASRRE ERMI   RV VNG ++E  A+NV   D IEVD  PL + ER 
Sbjct: 5   ERIAKRLSRAGVASRREAERMIEAGRVSVNGAVIESPALNVTDADVIEVDNAPLPEIERP 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W+YHKP GLVT+++D  GR TVFD LP    RV+SVGRLD+N+EGLLLLTNDGG+ R 
Sbjct: 65  RVWMYHKPTGLVTSNADEKGRETVFDKLPDSLPRVMSVGRLDMNSEGLLLLTNDGGVKRK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G    +    L++GIV +G  +  M+V+LD  +G+NAW+TVGL
Sbjct: 125 LELPSTGWLRKYRVRMKGAPKDEDFAPLRRGIVAEGERFQPMEVSLDRVQGANAWITVGL 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++      ++VNRLIR+SYGPF+LG L  G   EV  ++LR+QLG
Sbjct: 185 REGKNREIRRAMAELGFEVNRLIRVSYGPFRLGELKPGEVEEVRPRVLRDQLG 237


>gi|46370355|gb|AAS89963.1| hypothetical protein [Agrobacterium vitis]
          Length = 240

 Score =  280 bits (716), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 136/217 (62%), Positives = 162/217 (74%)

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 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           RLIRISYGPFQLG L     +EV  ++LR+QLGP L+
Sbjct: 181 RLIRISYGPFQLGDLPESQVQEVRGRMLRDQLGPRLI 217


>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 =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 151/304 (49%), Positives = 188/304 (61%), Gaps = 8/304 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAG+ASRR+ ERMI   RV VNG  ++  A+NV   D I VDG PL   +  
Sbjct: 8   ERIAKVLSRAGVASRRDAERMIELGRVAVNGRTIDSPALNVGPKDRITVDGQPLAPPQPA 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLY+KP GLVT+ +D  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 68  RLWLYYKPEGLVTSAADEKGRETVFDHLPEDLPRVMSVGRLDLNSEGLLLLTNDGELKRR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G      L  L+KGI ++G  +  M VTLD  +G+NAW+TVGL
Sbjct: 128 LELPSTGWLRKYRVRVKGNPTDPDLEPLRKGITVEGERFQPMTVTLDRVQGANAWLTVGL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE- 252
           REGKNREI++        VNRLIRISYGPF+L  L  G   EV  K+LR+QLG    EE 
Sbjct: 188 REGKNREIRRAMSAIGLTVNRLIRISYGPFRLNELQPGMVEEVRPKVLRDQLGLDPREED 247

Query: 253 ------AQVNLDAPIYSSETLVRDRPNIISEVPDDFTR-MKKNSSQKNGLSKQKKLATPV 305
                 A+    A   S  +    RP+    +P D  R   K + +  G     K A P 
Sbjct: 248 GRPPKAARPPRGAGAASGRSHPGARPSGSKPLPPDEARGGSKGAPRGRGAGAAPKSAGPA 307

Query: 306 HRRN 309
            RR+
Sbjct: 308 RRRD 311


>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 =  280 bits (715), Expect = 3e-73,   Method: Compositional matrix adjust.
 Identities = 135/241 (56%), Positives = 179/241 (74%)

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 G 246
           G
Sbjct: 241 G 241


>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 =  279 bits (714), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 130/232 (56%), Positives = 171/232 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRRE ERMI   R+ V+G +++  A+NV+ T  I VDG P+   E  R
Sbjct: 10  RIAKVLARAGVASRREAERMIDAGRISVDGKIIDSPALNVLPTARISVDGKPMAAPEPPR 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +W+YHKP GLVTT SD  GR T+FD+LP    RV+SVGRLD+N+EGLLLLTNDGGL R L
Sbjct: 70  VWMYHKPTGLVTTDSDEKGRKTIFDDLPEDMPRVMSVGRLDLNSEGLLLLTNDGGLKRKL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+  ++    L+KG+ +QG  +  M V++D Q+G+NAW+TVG+R
Sbjct: 130 ELPSTGWLRKYRVRINGRPTEETFEPLRKGLNLQGEHFQPMLVSIDRQQGANAWLTVGIR 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++  E     VNRLIR+SYGPFQLG L      E+ ++ L++QLG
Sbjct: 190 EGKNREIRRAMEAIQLNVNRLIRVSYGPFQLGNLKTSGVEEIRRRALKDQLG 241


>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 =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 141/244 (57%), Positives = 176/244 (72%), Gaps = 5/244 (2%)

Query: 11  FTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            TPQ  R++KV++RAG+ASRRE ERMI   RVKVNG  +   A+NV ++D I VDG  + 
Sbjct: 5   LTPQGDRIAKVLSRAGVASRREAERMIEAGRVKVNGKPISSPALNVQASDKITVDGKDVS 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E  RLWLYHKP GLVTT +D  GR T++  LP+   RV+SVGRLDIN+EGLLLLTNDG
Sbjct: 65  PPEPARLWLYHKPTGLVTTDNDEKGRETIYSALPADLPRVMSVGRLDINSEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            + R LELP+T WLR YRVR +G+     L  L++GI  +G  +  MQVTLD Q+G+NAW
Sbjct: 125 SIKRRLELPTTGWLRRYRVRVNGRPTDATLEPLRRGISSEGENFQPMQVTLDRQQGANAW 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +T+GLREGKNREI++        VNRLIRISYGPFQLG L +G+  EV +K+LR+QLG  
Sbjct: 185 LTMGLREGKNREIRRALAELGLTVNRLIRISYGPFQLGELKSGAVEEVRRKVLRDQLG-- 242

Query: 249 LLEE 252
            LEE
Sbjct: 243 -LEE 245


>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 =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 137/241 (56%), Positives = 176/241 (73%), Gaps = 1/241 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R++KV++RAG+ASRRE ERMIA  RV+VNG +++  A+NV+   D I VDG  + + E  
Sbjct: 46  RIAKVLSRAGLASRREAERMIADGRVEVNGKVIDSPALNVVVGKDRIVVDGKQVEEPEPP 105

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT SD   R T+FD+LP    RV++VGRLD+N+EGLLLLTNDGG+ R 
Sbjct: 106 RLWLYHKPAGLVTTTSDELDRKTIFDDLPEDLPRVMTVGRLDLNSEGLLLLTNDGGIKRQ 165

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR +G+        L+KG+VI+G  +  M VTLD Q+G+NAW+TVGL
Sbjct: 166 LELPSTGWLRRYRVRINGRPQDSDFEPLRKGLVIEGEKFQPMIVTLDRQQGANAWLTVGL 225

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG    EE 
Sbjct: 226 REGKNREIRRAMEDIGFSVNRLLRLSYGPFQLGQLKPGEVEELRPRVVRDQLGLAAPEEE 285

Query: 254 Q 254
           Q
Sbjct: 286 Q 286


>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 =  279 bits (713), Expect = 5e-73,   Method: Compositional matrix adjust.
 Identities = 132/250 (52%), Positives = 177/250 (70%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL + ERT
Sbjct: 391 ERIAKVVARAGLCSRRDAEAWITEGRVAVNGKVIDSPALDVKASDVITIDGKPLPERERT 450

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLAR 
Sbjct: 451 RLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGGLARA 510

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG +   L+  + +N W+   +
Sbjct: 511 LELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIDAKLERDQSANVWLVFAI 570

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG  ++  A
Sbjct: 571 REGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGEKVIALA 630

Query: 254 QVNLDAPIYS 263
             +   P  S
Sbjct: 631 GCDFAGPSPS 640


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

 Score =  279 bits (713), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 139/243 (57%), Positives = 169/243 (69%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG PL   E  
Sbjct: 8   ERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQPLAPPEPA 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 68  RLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTNDGELKRR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+NAW+TVGL
Sbjct: 128 LELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGANAWLTVGL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--PHLLE 251
           REGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG  PH   
Sbjct: 188 REGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLGLDPHADG 247

Query: 252 EAQ 254
           EA+
Sbjct: 248 EAR 250


>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 =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 139/243 (57%), Positives = 169/243 (69%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG PL   E  
Sbjct: 8   ERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQPLAPPEPA 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 68  RLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTNDGELKRR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+NAW+TVGL
Sbjct: 128 LELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGANAWLTVGL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--PHLLE 251
           REGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG  PH   
Sbjct: 188 REGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLGLDPHADG 247

Query: 252 EAQ 254
           EA+
Sbjct: 248 EAR 250


>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 =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 139/243 (57%), Positives = 169/243 (69%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG PL   E  
Sbjct: 8   ERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQPLAPPEPA 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 68  RLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTNDGELKRR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+NAW+TVGL
Sbjct: 128 LELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGANAWLTVGL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--PHLLE 251
           REGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG  PH   
Sbjct: 188 REGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLGLDPHADG 247

Query: 252 EAQ 254
           EA+
Sbjct: 248 EAR 250


>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 =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 140/247 (56%), Positives = 173/247 (70%), Gaps = 2/247 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KVIARAGIASRRE ER+I   RV VNG  + RAA+NV   D + VDG  L   E  
Sbjct: 15  ERIAKVIARAGIASRREAERLIEAGRVTVNGQKVLRAALNVTPADKVVVDGRALDAPEPA 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT  D  GRST++D+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 75  RLWLYHKPTGLVTTTRDEQGRSTIYDDLPEDMPRVMSVGRLDLNSEGLLLLTNDGELKRK 134

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR +G+        L+KG+V+ G  +  M VTLD Q+G+NAW+TV +
Sbjct: 135 LELPSTGWLRRYRVRVNGRPTDGTFEPLRKGLVVDGEAFQPMMVTLDRQQGANAWITVSI 194

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREI++  E     VNRLIR+SYGPFQLG L  G+  E+  ++LR+QLG  + EE 
Sbjct: 195 REGKNREIRRAMEAVGLVVNRLIRLSYGPFQLGQLKPGAVEEIRPRVLRDQLG--MKEEP 252

Query: 254 QVNLDAP 260
           +     P
Sbjct: 253 EAEQPKP 259


>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 =  278 bits (711), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 140/252 (55%), Positives = 178/252 (70%), Gaps = 1/252 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +AR+G+ASRR+ ERMI + R+++NG  +   A  V + D ++VDG P+   ERT
Sbjct: 8   ERIAKWLARSGVASRRDAERMIEENRIRLNGQPVTHPATFVTNGDIVQVDGEPVSAPERT 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DP+GR TVF +LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 68  RLWRYHKPDGLVTTHKDPEGRPTVFASLPEGMPRVISVGRLDLNSEGLLLLTNDGELARR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  WLR YRVR  G VD+++L  L +G V  G+ YG +   LD++KG NAW+TV L
Sbjct: 128 LELPSNGWLRRYRVRVFGVVDEERLASLAQGSVFDGVRYGPIHAVLDSRKGDNAWLTVSL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +EGKNREI+KV    N  V+RLIR SYGPFQLGTLL     EVS ++LR+QL P   E+ 
Sbjct: 188 KEGKNREIRKVMAGMNLHVSRLIRTSYGPFQLGTLLRRELEEVSPRVLRDQL-PKATEKT 246

Query: 254 QVNLDAPIYSSE 265
                AP   ++
Sbjct: 247 PTTQRAPAKQAD 258


>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 =  278 bits (711), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 135/255 (52%), Positives = 180/255 (70%), Gaps = 4/255 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K++AR+G+ SRR+VER+IA+ RV +NG +L   AV V   D + VDG  + + E  
Sbjct: 151 ERIAKLLARSGVGSRRDVERLIAEGRVAINGQVLTTPAVKVEPGDILTVDGAVVGEPEPV 210

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R++ YHKP+GLVTTH DP GR TVF+ LP    R+ISVGRLD+N+EGLLLLTNDGGLAR 
Sbjct: 211 RVFRYHKPVGLVTTHKDPQGRPTVFEALPEGLPRLISVGRLDLNSEGLLLLTNDGGLARA 270

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----GSNAWV 189
           LELP+T  +R YR R HG++ Q++L+ LK GI ++G+ YG ++  LD  K    G+N W+
Sbjct: 271 LELPATGVVRRYRARAHGRITQERLDTLKDGITVEGVRYGAIEARLDKAKEGHQGANLWL 330

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           TV L+EGKNRE+++V E    KVNRLIR+SYGPF LGTL  G   EV  +++REQL  H+
Sbjct: 331 TVTLQEGKNREVRRVLEALGLKVNRLIRLSYGPFALGTLDVGEIEEVGPRVIREQLEGHI 390

Query: 250 LEEAQVNLDAPIYSS 264
             E     D P Y S
Sbjct: 391 PPENMPKGDRPQYRS 405


>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 =  278 bits (711), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 132/246 (53%), Positives = 172/246 (69%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMI   RV+VNG  ++  A+NV   D I VD  P+   E  R
Sbjct: 26  RIAKVLSRAGVASRREAERMIEAGRVRVNGEQIDSPALNVTPEDKITVDNTPVGAPEPPR 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLYHKP GLVTT  D  GR T+FD+LP    RV+++GRLD+N+EGLLLLTNDGG+ R L
Sbjct: 86  MWLYHKPAGLVTTARDEKGRETIFDDLPEDMPRVMTIGRLDLNSEGLLLLTNDGGVKRKL 145

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YR R +G+   + L  L++GI ++G  +  M VTLD Q+G+NAW+T+GLR
Sbjct: 146 ELPSTGWLRRYRARVNGRPTDEMLEPLRRGITVEGENFLPMDVTLDRQQGANAWLTIGLR 205

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EG+NREI++  E     VNRLIR SYGPFQLG L  G   E+ +KI+R+QLG  L +   
Sbjct: 206 EGRNREIRRAMEAVGLTVNRLIRTSYGPFQLGELKTGEVEELRRKIVRDQLGLELEDPTG 265

Query: 255 VNLDAP 260
             +  P
Sbjct: 266 TAVKKP 271


>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 =  278 bits (711), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 133/238 (55%), Positives = 173/238 (72%), Gaps = 5/238 (2%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-----SNAW 188
           LELP+T W RVYRVR  G+  Q+ L+ LK G+ ++G+ YG ++  LD  +      +N W
Sbjct: 166 LELPTTGWTRVYRVRALGRTTQEALDTLKTGVTVEGVQYGPIEAKLDKAQEKADGRANLW 225

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +TV L EGKNRE++KV +    KVNRLIR++YGPFQLG +  G   E+  +++RE LG
Sbjct: 226 ITVSLNEGKNREVRKVLDSLGLKVNRLIRLAYGPFQLGDIEPGEVEEIGPRVVRELLG 283


>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 =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 133/237 (56%), Positives = 173/237 (72%), Gaps = 5/237 (2%)

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  RLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL+L+HKP GLVTT  DP+GR TVFD +    P    R++S+GRLDINTEGLLLLTNDGG
Sbjct: 85  RLFLFHKPRGLVTTEHDPEGRPTVFDYVREHSPEA-PRLVSIGRLDINTEGLLLLTNDGG 143

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LARVLELP+T W R YRVR  G +DQ  L+ L++G+ ++G+ Y  ++ TLD  +G+N W+
Sbjct: 144 LARVLELPATGWARRYRVRAKGSIDQPTLDRLRQGVTVEGVDYAQIEATLDRIQGANCWL 203

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           T+ LREGKNREIK+V E    +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG
Sbjct: 204 TMSLREGKNREIKRVLEHLGLEVNRLIRLSYGPFQLADLEEGKVEEVRTRVLRDQLG 260


>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 =  277 bits (709), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 140/252 (55%), Positives = 178/252 (70%), Gaps = 1/252 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +AR+G+ASRR+ ERMI + R+++NG  +   A  V + D ++VDG P+   ERT
Sbjct: 8   ERIAKWLARSGVASRRDAERMIEENRIRLNGQPVTHPATFVTNGDIVQVDGEPVSAPERT 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DP+GR TVF +LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 68  RLWRYHKPDGLVTTHKDPEGRPTVFASLPEGMPRVISVGRLDLNSEGLLLLTNDGELARR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  WLR YRVR  G VD+++L  L +G V  G+ YG +   LD++KG NAW+TV L
Sbjct: 128 LELPSNGWLRRYRVRVFGVVDEERLASLAQGCVFDGVRYGPIHAVLDSRKGDNAWLTVSL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +EGKNREI+KV    N  V+RLIR SYGPFQLGTL      EVS ++LR+QL P   E+A
Sbjct: 188 KEGKNREIRKVMAGMNLHVSRLIRTSYGPFQLGTLQRRELEEVSPRVLRDQL-PKATEKA 246

Query: 254 QVNLDAPIYSSE 265
                AP   ++
Sbjct: 247 PPARRAPAKQAD 258


>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 =  276 bits (706), Expect = 3e-72,   Method: Compositional matrix adjust.
 Identities = 131/233 (56%), Positives = 168/233 (72%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+A AGIASRRE ER+I + RV VNG +L   A  VM+ D + VDG  + +   T
Sbjct: 17  ERIAKVLAHAGIASRREAERLIEKGRVSVNGEILRTPAFKVMAGDDVRVDGESIGQRPPT 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W YHKP+GL+TTHSDP GR TVF  LP    RVISVGRLD+N+EGLLLLTNDG LARV
Sbjct: 77  RVWRYHKPVGLLTTHSDPQGRDTVFQTLPQDMGRVISVGRLDLNSEGLLLLTNDGELARV 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST W R YRVR +G      L  L+ G V+ G+ YG ++VT+D + G+N W+TVG+
Sbjct: 137 LELPSTGWTRRYRVRAYGNASDKALAELENGTVVDGVVYGPVEVTVDRRTGANVWLTVGI 196

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +EGKNRE++KV +     VNRL+R++YGPFQLG+L  G   E    +LR+QLG
Sbjct: 197 KEGKNREVRKVLQSVGLTVNRLMRVAYGPFQLGSLKRGEISESKLSVLRDQLG 249


>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 =  276 bits (705), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 135/242 (55%), Positives = 170/242 (70%), Gaps = 2/242 (0%)

Query: 7   VQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + +N TP   R++KV+ARAGIASRRE ER+IA+ RV VNG  ++  A+NV   D I  DG
Sbjct: 1   MADNTTPPGDRIAKVLARAGIASRREAERLIAEGRVAVNGKTVDSPALNVTEADKITFDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+ + E  RLW YHKP+GLVTT  D  GR TVFD LP+   RV+SVGRLD+N+EGLLLL
Sbjct: 61  TPIAEPEPPRLWRYHKPVGLVTTAKDEKGRETVFDALPADLPRVMSVGRLDLNSEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG + R LELP+T WLR YRVR  G   +D L  L+ GI ++G  +  M+  LD  +G
Sbjct: 121 TNDGEIKRRLELPTTGWLRRYRVRVKGAPTEDDLAPLRAGIEVEGERFKPMEARLDRLQG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+T+GLREG+NREI++        VNRLIRISYGPF+LG L  G   E+  +ILREQ
Sbjct: 181 ANAWLTLGLREGRNREIRRAMGALGLVVNRLIRISYGPFRLGELKPGEVEEIKGRILREQ 240

Query: 245 LG 246
           LG
Sbjct: 241 LG 242


>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 =  276 bits (705), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 132/234 (56%), Positives = 172/234 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KVIARAGI SRRE E++I + RV V+G +L+  A+NV   + I VDG  L   E T+
Sbjct: 16  RIAKVIARAGICSRREAEKLIEEGRVTVDGKVLKSPALNVTGRETIIVDGKALPAQEPTK 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW YHKP GLVTT  DP+GR+TVF+ LP    RV+SVGRLDINTEGLLLLTNDG LAR+L
Sbjct: 76  LWRYHKPAGLVTTAKDPEGRTTVFEKLPDDIPRVVSVGRLDINTEGLLLLTNDGELARLL 135

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP+T W R YRVR  G++ Q  L+ LK GI ++G+ YG ++ T+D  +GSN W+T+GL+
Sbjct: 136 ELPATGWTRRYRVRAWGRITQADLDKLKNGITVEGVRYGPIEATIDKVQGSNVWLTLGLK 195

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           EGKNRE+K+V       VNRLIR+S+GPFQ+G L  G  ++V  ++L +QLG H
Sbjct: 196 EGKNREVKRVLAELGLSVNRLIRLSFGPFQIGDLEPGDIKQVPNRVLMDQLGAH 249


>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 =  275 bits (704), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 134/237 (56%), Positives = 172/237 (72%), Gaps = 5/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV+ARAG+ASRREVER+I   ++ VNG +LE  AV V S D I V+G  + KAE T
Sbjct: 53  ERIAKVLARAGLASRREVERLIGLGKIAVNGRILETPAVLVSSADIITVEGQVIGKAEPT 112

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W YHKP+GL+TTHSDP GR T+FD LP+   RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 113 RVWRYHKPVGLITTHSDPQGRPTLFDQLPTHLPRVISVGRLDLNSEGLLLLTNDGELARS 172

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKG---SNAW 188
           LE PS+ W+R YRVR  G   Q +L+ LK G  ++G+ YG M+ T+D   +K    +N W
Sbjct: 173 LEKPSSGWVRRYRVRALGHASQSRLDALKDGTTVEGVIYGPMEATIDKVAEKADGRANVW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +TV + EGKNRE++KV E    KVNRLIR++YGPFQLG L  G   EV  +++RE L
Sbjct: 233 LTVAITEGKNREVRKVLESIGLKVNRLIRLAYGPFQLGNLETGEVEEVGPRVIRELL 289


>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 =  275 bits (704), Expect = 6e-72,   Method: Compositional matrix adjust.
 Identities = 134/233 (57%), Positives = 169/233 (72%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KVIARAGIASRRE ER+I + RV VNG  + RAA+NV   D + V+G  L  AE  
Sbjct: 14  ERIAKVIARAGIASRREAERLIEEGRVTVNGQKVLRAALNVTPADKVVVNGRALEAAEPA 73

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 74  RLWLYHKPTGLVTTTRDEKGRRTIYDDLPEDMPRVMSVGRLDLNSEGLLLLTNDGELKRK 133

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR +G+        L+KG+V+ G  +  M V+LD Q+G+NAW+TV +
Sbjct: 134 LELPSTGWLRRYRVRVNGRPTDASFEPLRKGLVVDGEAFQPMIVSLDRQQGANAWITVAI 193

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++  E     VNRLIR+SYGPFQLG L  G+  E+  +++R+QLG
Sbjct: 194 REGKNREIRRAMEAVGLVVNRLIRLSYGPFQLGQLKPGAVEEIRPRVMRDQLG 246


>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 =  275 bits (702), Expect = 9e-72,   Method: Compositional matrix adjust.
 Identities = 139/243 (57%), Positives = 169/243 (69%), Gaps = 2/243 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++KV++RAGIASRR+ ERMI   R+ VNG  ++  A+NV   D I VDG PL   E  
Sbjct: 8   ERIAKVLSRAGIASRRDAERMIELGRIAVNGRTIDSPALNVGPKDRITVDGQPLAPPEPA 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLY+KP GLVT+ SD  GR TVFD+LP    RV+SVGRLD+N+EGLLLLTNDG L R 
Sbjct: 68  RLWLYYKPEGLVTSASDEKGRETVFDHLPEGMPRVMSVGRLDLNSEGLLLLTNDGELKRR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR  G      L  L+KGI ++G  +  M V+LD  +G+NAW+TVGL
Sbjct: 128 LELPSTGWLRKYRVRVKGNPTDADLEPLRKGITVEGESFQPMTVSLDRVQGANAWLTVGL 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--PHLLE 251
           REGKNREI++        VNRLIR+SYGPF+L  L  G   EV  KILR+QLG  PH   
Sbjct: 188 REGKNREIRRAMSALGLTVNRLIRVSYGPFRLNELEPGMVEEVRPKILRDQLGLDPHADG 247

Query: 252 EAQ 254
           EA+
Sbjct: 248 EAR 250


>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 =  274 bits (700), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 132/232 (56%), Positives = 167/232 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ASRR+ ERMI   RV +NG  +   A  V + D I +DG P+ +  RT
Sbjct: 11  ERIAKYLARAGVASRRDAERMIESGRVALNGTKVLHPATFVAAGDIILIDGSPVGEPSRT 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHK  GL+TTH DP+GR T+F+ +P    RV+SVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 71  RLWRYHKRAGLLTTHRDPEGRPTIFERMPPELPRVVSVGRLDLNSEGLLLLTNDGALARQ 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG VD  +L  LK GIV+ G+ YG +   +D+ KGSN+W+ VGL
Sbjct: 131 LELPTTGWLRRYRVRVHGTVDPARLAALKGGIVVDGVRYGPISAEIDSTKGSNSWLAVGL 190

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EGKNREI+KV      +  RLIRI+YGPFQLG L  G+  EV+ K+LREQL
Sbjct: 191 NEGKNREIRKVMAALGLETTRLIRIAYGPFQLGNLPRGAVAEVNPKVLREQL 242


>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 =  274 bits (700), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 130/233 (55%), Positives = 172/233 (73%), Gaps = 1/233 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV +  D I VDG P++  E  
Sbjct: 53  RIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVVLGKDRIVVDGNPMQDPEPP 112

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+YHKP GLVTT +D   R T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R 
Sbjct: 113 RLWMYHKPSGLVTTTNDELDRRTIFDALPEDMPRVMTVGRLDLNSEGLLLLTNDGGIKRQ 172

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR +G+        L++G+VI+G  +  M V LD Q+G+NAW+T+GL
Sbjct: 173 LELPSTGWLRRYRVRINGRPKDTDFEPLRQGLVIEGERFQPMTVALDRQQGANAWLTIGL 232

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG
Sbjct: 233 REGKNREIRRAIEDIGFTVNRLLRLSYGPFQLGNLKPGEVEELRPRVVRDQLG 285


>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 =  274 bits (700), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 134/253 (52%), Positives = 176/253 (69%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D      N    R++KV+ARAG+ASRRE ERMI + RV VNG  ++  A++V   D I 
Sbjct: 3   EDSPETAPNPQADRIAKVMARAGVASRREAERMILEGRVTVNGKKIDSPALDVTPADRIR 62

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL + + TRLWLY+KP+GLVT++SD  GR TVFD LP    RV++VGRLD+N+EGL
Sbjct: 63  VDGKPLEEPQETRLWLYYKPLGLVTSNSDEKGRQTVFDALPRDLPRVMTVGRLDLNSEGL 122

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG L R LELP+T WLR YRVR +GQ +      L++G+ I G  +  M++ LD+
Sbjct: 123 LLLTNDGELKRRLELPTTGWLRRYRVRVNGQPNDLTFAPLRRGVTIDGEEFAPMEINLDS 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G+NAW+TVG+REG+NREI++        VNRLIRI YGPF+L  L     REV +K+L
Sbjct: 183 QQGANAWLTVGIREGRNREIRRAMAHVGLIVNRLIRIGYGPFKLTGLEENEVREVKRKVL 242

Query: 242 REQLGPHLLEEAQ 254
           R+QLG  L  E +
Sbjct: 243 RDQLGGLLTGETE 255


>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 =  273 bits (699), Expect = 2e-71,   Method: Compositional matrix adjust.
 Identities = 128/239 (53%), Positives = 173/239 (72%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++KVIAR+G+ASRR+ E+MI   RV VNG  ++  A++V   D + +DG P+   +
Sbjct: 16  TAERIAKVIARSGVASRRDAEKMILAGRVTVNGKKVDSPALDVKPADKVAIDGKPIDAPQ 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            TRLWLY+KP+GLVTT  D  GR T+FD +P    RV++VGRLD+N+EGLLLLTNDGGL 
Sbjct: 76  ETRLWLYYKPLGLVTTEKDEQGRRTIFDEMPEEMPRVLNVGRLDLNSEGLLLLTNDGGLK 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELP T WLR YRVR +G+   +  + L++GI I G  +  M+V+LD Q+G+NAW+TV
Sbjct: 136 RRLELPETGWLRKYRVRVNGRPTTETFDPLRRGITIDGEDFQPMEVSLDRQQGANAWLTV 195

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           G+REGKNREI++        VNRLIR+SYGPF+L  +  G+  EV +K+LR+QLG  LL
Sbjct: 196 GIREGKNREIRRAMGEVGMTVNRLIRVSYGPFRLNDMEPGAVVEVKRKMLRDQLGDRLL 254


>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 =  272 bits (696), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 130/232 (56%), Positives = 167/232 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SK ++RAG+ SRR+ ER IA+ RV VNG +L+  AV V   D I VDG P+ + E T
Sbjct: 31  ERISKRLSRAGLCSRRDAERWIAEGRVSVNGRVLDTPAVTVRPGDRIVVDGQPVPEPEPT 90

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W YHKP GLVTT  D  GR TVFDNLP    RV+SVGRLD+ +EGLLLLTNDG LAR 
Sbjct: 91  RVWRYHKPDGLVTTARDEKGRPTVFDNLPPELPRVVSVGRLDLTSEGLLLLTNDGALARH 150

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP T WLR YRVR HG  D+ ++  L +GI+I+GI YG ++  +D   G+N W+TV L
Sbjct: 151 LELPVTGWLRRYRVRVHGAPDEAQIAKLAQGIIIEGIEYGPIETVVDRSVGANTWLTVSL 210

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           REG+NRE+++V E     V+RLIR++YGPFQLG L  G   EV +++LR+QL
Sbjct: 211 REGRNREVRRVMEHLGLPVSRLIRVAYGPFQLGKLEPGQVEEVPRRVLRDQL 262


>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 =  272 bits (695), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 133/247 (53%), Positives = 172/247 (69%), Gaps = 8/247 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAGIASRREVER+I   +V VNG +L   AV V   D I VDG P+  A+ T
Sbjct: 81  ERIAKAMARAGIASRREVERLIGLGKVAVNGRILATPAVLVTRDDKITVDGKPIGAAQAT 140

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W YHKP GL+T+H+DP GR TVFD LPS   RVISVGRLD+ TEGLLLLTNDG L+R 
Sbjct: 141 RVWRYHKPAGLITSHNDPAGRPTVFDALPSGLPRVISVGRLDLATEGLLLLTNDGELSRA 200

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------GS 185
           LELP T  +R YR R  G++ Q++L+ LK G+V+ G+ YG ++ T+D  K         +
Sbjct: 201 LELPETALVRQYRARARGRITQEQLDKLKDGVVVDGVRYGPVEATIDKAKEKTEGEKSSA 260

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           N W++V + EGKNRE++KV E     VNRLIR++YGPFQLGTL  GS  EV  +++RE L
Sbjct: 261 NLWLSVSITEGKNREVRKVLESIGLTVNRLIRLAYGPFQLGTLPVGSVEEVGPRVIREML 320

Query: 246 GPHLLEE 252
             H+  E
Sbjct: 321 AEHIRPE 327


>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 =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 140/254 (55%), Positives = 171/254 (67%), Gaps = 11/254 (4%)

Query: 1   MKDKNIVQENFTP---------QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA 51
           M D N   EN  P         +R++K +ARAG+ASRR++ERMI   R+K+ G ++   A
Sbjct: 1   MTDDNT--ENTAPDMETSGPKGERIAKALARAGVASRRDIERMIEDGRIKLGGQIVTHPA 58

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             V   D + VDG P+   ERTRLW YHKP GL+TTH DP GR TVFD LP    RVISV
Sbjct: 59  TFVQPGDIVLVDGKPVDSPERTRLWRYHKPDGLMTTHKDPQGRQTVFDTLPEGMPRVISV 118

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDIN+EGLLLLTNDG LAR LELP   W+R YRVR  G VD+ +L  L  G   +G+ 
Sbjct: 119 GRLDINSEGLLLLTNDGELARRLELPGNSWVRRYRVRVFGVVDEKRLASLIDGFEYEGVR 178

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           YG ++  LD+ KG N+W+TV LREGKNREI++V E  N  V+RLIR+SYGPFQLG+L A 
Sbjct: 179 YGSIEAALDSTKGDNSWLTVSLREGKNREIRRVMEGLNLHVSRLIRLSYGPFQLGSLKAR 238

Query: 232 STREVSKKILREQL 245
              EV  K LREQ+
Sbjct: 239 ELEEVPGKTLREQV 252


>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 =  271 bits (694), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 137/265 (51%), Positives = 177/265 (66%), Gaps = 12/265 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAGIASRREVER+I   +V VNG +L+  A  V   D I VDG P+  A+ T
Sbjct: 99  ERIAKAMARAGIASRREVERLIGLGKVAVNGRILDTPATLVTRDDVITVDGKPIAAAQAT 158

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+W Y+KP+GL+T+H+DP GR TVFD LPS   RVISVGRLDINTEGLLLLTNDG L+R 
Sbjct: 159 RVWRYNKPVGLLTSHNDPQGRPTVFDALPSGLPRVISVGRLDINTEGLLLLTNDGELSRA 218

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------QKGSN 186
           LELP T  +R YR R  G+V Q  L+ LK G+ + G+ YG ++ ++D         + +N
Sbjct: 219 LELPETALVRQYRARARGRVTQADLDKLKDGVTVDGVRYGPVEASIDKATTKEDGSQAAN 278

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V + EGKNRE++KV E     VNRLIR++YGPFQLGTL  GS  EV  +++RE LG
Sbjct: 279 LWISVQIAEGKNREVRKVLESVGLTVNRLIRLAYGPFQLGTLAVGSVEEVGPRVIRELLG 338

Query: 247 PH-----LLEEAQVNLDAPIYSSET 266
            H     L +   V   API    T
Sbjct: 339 EHIRPDNLPQGNTVETPAPIPGRRT 363


>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 =  270 bits (689), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 129/233 (55%), Positives = 171/233 (73%), Gaps = 1/233 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV +  D I VDG  ++  E  
Sbjct: 53  RIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVVLGKDRIVVDGNQMQDPEPP 112

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+YHKP GLVTT +D   R T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R 
Sbjct: 113 RLWMYHKPSGLVTTTNDELDRRTIFDELPEDMPRVMTVGRLDLNSEGLLLLTNDGGIKRQ 172

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR +G+        L++G+VI+G  +  M V LD Q+G+NAW+T+GL
Sbjct: 173 LELPSTGWLRRYRVRINGRPKDTDFEPLRQGLVIEGERFQPMTVALDRQQGANAWLTIGL 232

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG
Sbjct: 233 REGKNREIRRAIEDIGFTVNRLLRLSYGPFQLGNLKPGEVEELRSRVVRDQLG 285


>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 =  269 bits (688), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 131/253 (51%), Positives = 177/253 (69%), Gaps = 10/253 (3%)

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 WLTVSLSEGKNREVRRVLQHLGLTVTRLIRIAYGPFALADLPRGAVEEINAKVLREQLG- 243

Query: 248 HLLEEAQVNLDAP 260
                    LDAP
Sbjct: 244 ---------LDAP 247


>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 =  268 bits (685), Expect = 9e-70,   Method: Compositional matrix adjust.
 Identities = 135/240 (56%), Positives = 169/240 (70%), Gaps = 3/240 (1%)

Query: 10  NFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           N TP    R++KV++RAGIASRRE ERMI   RV VNG  +   A+NV + D I VDG  
Sbjct: 3   NETPPPGDRIAKVLSRAGIASRREAERMIEDGRVSVNGKTITSPALNVTADDRIVVDGKQ 62

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + + E  R+WLYHKP GLVTT  D   R TVF +LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 63  VGEPEPPRIWLYHKPAGLVTTERDEKDRPTVFASLPETMPRVMSVGRLDLNSEGLLLLTN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG + R LELPST WLR YRVR +G V + KL+ L++GI ++GI Y  M VT D Q+G+N
Sbjct: 123 DGEVKRKLELPSTGWLRRYRVRINGSVSEAKLDELREGITVEGIQYQPMVVTFDRQQGAN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TV LREGKNREI++        VNRLIR+SYGPFQL  L  G   E+ ++++R+QLG
Sbjct: 183 AWLTVSLREGKNREIRRAMGEIGVTVNRLIRVSYGPFQLAALKQGEVEELKQRVVRDQLG 242


>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 =  268 bits (684), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 132/231 (57%), Positives = 170/231 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +AR+G+ASRR+ ERMIA+ RV++NG ++   A  V + D ++V+G  +   +RTR
Sbjct: 16  RIAKWLARSGVASRRDAERMIAEGRVQLNGAVVNHPATFVGAGDIVQVNGSVVGAPDRTR 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW YHKP GLVTTH DP+GR TVF++LP    RVISVGRLD+N+EGLLLLTNDG LAR L
Sbjct: 76  LWRYHKPDGLVTTHRDPEGRPTVFESLPPGLPRVISVGRLDLNSEGLLLLTNDGELARRL 135

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  W+R YRVR  G VD+  L  L +G    G+ YG ++  LD+ KG NAW+TV LR
Sbjct: 136 ELPSNGWIRRYRVRVFGVVDERMLASLARGSEFDGVRYGPIEAHLDSAKGDNAWLTVSLR 195

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGKNRE++KV +  N  V+RLIR SYGPFQLGTL  G   EV+ K++REQ+
Sbjct: 196 EGKNREVRKVMQGLNLHVSRLIRTSYGPFQLGTLTRGELEEVTGKVIREQV 246


>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 =  266 bits (679), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 130/232 (56%), Positives = 163/232 (70%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   +V VNG ++   A+NV + D I VDG P+   E  R
Sbjct: 19  RIAKVLSRAGIASRREAERMIELGQVAVNGKVITSPALNVTAKDRITVDGKPVAAPEPAR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVT+ +D  GR T++D +P    RV++VGRLD+N+EGLLLLTNDG L R L
Sbjct: 79  LWLYYKPEGLVTSDNDEKGRETIYDQMPEDLPRVMAVGRLDLNSEGLLLLTNDGELKRRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR  G      L  L+ GI ++G  +  M V +D  +G+NAW+TVGLR
Sbjct: 139 ELPSTGWLRKYRVRIKGNPTDPDLEPLRAGITVEGERFQPMLVVIDRIQGANAWLTVGLR 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++     N  VNRLIRISYGPF+LG L  G   EV  K+LR+QLG
Sbjct: 199 EGKNREIRRAMFALNLTVNRLIRISYGPFRLGDLQPGEVAEVRGKVLRDQLG 250


>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 =  265 bits (678), Expect = 6e-69,   Method: Compositional matrix adjust.
 Identities = 132/232 (56%), Positives = 167/232 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K + R+G+ASRR+ ERMI + RV++NG ++   A  V   D ++VD   +   +RT
Sbjct: 15  DRIAKWLGRSGVASRRDAERMIEEGRVRLNGDIVRHPATFVSDGDIVQVDDKVIAAPDRT 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DPDGR TVF +LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 75  RLWRYHKPDGLVTTHRDPDGRPTVFASLPEGMPRVISVGRLDLNSEGLLLLTNDGELARK 134

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  W+R YRVR  G V++D+L  L +G V +G+ YG ++  LD+ +G NAW+TV L
Sbjct: 135 LELPSNGWIRRYRVRVFGVVNEDQLADLAQGSVFEGVHYGPIEAALDSSRGDNAWLTVSL 194

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           REGKNREI+KV    N  V+RLIR SYGPFQLGTL      EV+ K+LREQ+
Sbjct: 195 REGKNREIRKVMRGLNLHVSRLIRTSYGPFQLGTLEREELEEVTGKVLREQV 246


>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 =  265 bits (678), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 130/237 (54%), Positives = 162/237 (68%), Gaps = 5/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+K +ARAG+ASRREVER+I   RV +NG +L   AV V   D + VDG  + + E T
Sbjct: 35  ERVAKALARAGVASRREVERLIEAGRVAINGKVLTTPAVKVAPGDFLTVDGQLVAEREPT 94

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R++ YHKP GL+TTH+DP GR TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R 
Sbjct: 95  RIFRYHKPTGLMTTHNDPKGRPTVFGALPKDLPRLISVGRLDLNSEGLLLLTNDGELSRA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQKGSNAW 188
           LE PS  W+R YR R  G   Q KL+ LK G+ I+G+ YG ++  LD        G N W
Sbjct: 155 LETPSNAWVRRYRARAFGDTTQAKLDKLKDGVTIEGVTYGAIEAKLDKAHEKAGGGKNVW 214

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +TV L EGKNRE++KV E    KVNRLIR+SYGPF LGTL AG   EV  +++RE L
Sbjct: 215 ITVSLSEGKNREVRKVLESIGLKVNRLIRLSYGPFALGTLAAGQIEEVGPRVIRELL 271


>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 =  265 bits (678), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 134/237 (56%), Positives = 169/237 (71%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +AR+G+ASRR+ ER++ + RV++NG  +   A  V + D ++V+G  +   ERT
Sbjct: 21  ERIAKWLARSGVASRRDAERLVEEGRVRLNGEPVTHPATFVAAGDIVQVNGAVVEAPERT 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DP+ R TVF +LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 81  RLWRYHKPDGLVTTHRDPEKRPTVFASLPPGMPRVISVGRLDLNSEGLLLLTNDGELARR 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  WLR YRVR  G VD+ +L  L  G V +G+ YG ++  LD++KG NAW+TV L
Sbjct: 141 LELPSNGWLRRYRVRVFGVVDEARLAALAGGSVFEGVRYGPIEAGLDSRKGDNAWLTVAL 200

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ---LGP 247
           REGKNRE++KV    N  V+RLIR SYGPFQLGTL      EV  K+LREQ   LGP
Sbjct: 201 REGKNREVRKVMRGLNLHVSRLIRTSYGPFQLGTLQRSELEEVPGKVLREQVPGLGP 257


>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 =  265 bits (676), Expect = 1e-68,   Method: Compositional matrix adjust.
 Identities = 127/243 (52%), Positives = 163/243 (67%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           N  +    P R++K +ARAG+ SRRE ER IA  RV VNG LL+  A  V   D + VDG
Sbjct: 29  NTAETRDGPMRIAKAMARAGLCSRREAERWIADGRVSVNGKLLKTPACEVGPKDKVIVDG 88

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  A   +LW YHKP G+VTTHSDP GR TVF+ LP    RVIS+GRLD NTEGLLLL
Sbjct: 89  KPLPAASTPQLWRYHKPKGVVTTHSDPQGRPTVFEKLPPEMPRVISIGRLDFNTEGLLLL 148

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LAR  ELP+  W+R YRVR  G+V    L  LK G+ I G+ YG ++ ++DT +G
Sbjct: 149 TTDGALARHFELPANGWVRRYRVRAKGRVTPADLAKLKDGVEIDGVSYGPIEASVDTVQG 208

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +N+W+++ +REGKNRE++ V  +    VNRLIR+S+GPFQL  L  G+   V +++L  Q
Sbjct: 209 ANSWLSISIREGKNREVRNVLAYLGLTVNRLIRVSFGPFQLLDLAPGAVEAVRRRVLVAQ 268

Query: 245 LGP 247
           LGP
Sbjct: 269 LGP 271


>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 =  264 bits (674), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 129/248 (52%), Positives = 170/248 (68%), Gaps = 9/248 (3%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-------- 185
           LELP+T  +R YR R  G++ Q++L+ LK G+V+ G+ YG ++ TLD  K S        
Sbjct: 206 LELPATSLVRQYRARARGKITQEQLDKLKDGVVVDGVSYGPIEATLDKAKESKSEDGRAP 265

Query: 186 -NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            N W++V + EGKNRE++KV E     VNRLIR++YGPF+L  L  GS  EV  +++RE 
Sbjct: 266 ANLWISVSITEGKNREVRKVLESVGLTVNRLIRLAYGPFRLDVLPIGSVEEVGPRVIREL 325

Query: 245 LGPHLLEE 252
           L  ++  E
Sbjct: 326 LADYIRPE 333


>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 =  263 bits (671), Expect = 3e-68,   Method: Compositional matrix adjust.
 Identities = 129/239 (53%), Positives = 171/239 (71%), Gaps = 2/239 (0%)

Query: 9   ENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++ TP  +R++K +ARAG+ASRR+ E+++   RV++N  ++   A  V S D + V+G  
Sbjct: 10  DSGTPRGERIAKWLARAGVASRRDAEKLVEDGRVRLNNQVVTHPATFVGSGDLVTVNGAL 69

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   +RTRLW YHK  G++TTH DP GR TVF+ LPS   RV+SVGRLD+N+EGLLLLTN
Sbjct: 70  VEAPDRTRLWRYHKTDGVMTTHRDPQGRPTVFEKLPSSMPRVVSVGRLDLNSEGLLLLTN 129

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LAR LELP T W+R YRVR HG V Q  L+ L +G+ ++G+ YG ++  LD+ KGSN
Sbjct: 130 DGMLARRLELPQTGWIRRYRVRVHGDVTQAMLDSLARGVTVEGVRYGSIEAGLDSSKGSN 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +W+TV L+EGKNREI+KV       V RLIRI+YGPFQLG L  G   EV+ K+LREQL
Sbjct: 190 SWLTVSLKEGKNREIRKVMRHIGLHVTRLIRIAYGPFQLGQLGKGEVEEVTGKVLREQL 248


>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 =  260 bits (665), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 131/256 (51%), Positives = 167/256 (65%), Gaps = 5/256 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+K +ARAG+ASRREVER+I   RV +NG +L   A+ V   D + VDG  + + E T
Sbjct: 26  ERVAKALARAGVASRREVERLIEAGRVAINGKVLTTPAIKVKPGDFLTVDGQLVAEREPT 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R++ YHKP GL+TTH+DP GR TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R 
Sbjct: 86  RIFRYHKPTGLMTTHNDPKGRPTVFQTLPKDLPRLISVGRLDLNSEGLLLLTNDGELSRA 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQKGSNAW 188
           LE PS  W+R YR R  G   Q KL+ LK G+ I+G+ YG ++  LD        G N W
Sbjct: 146 LETPSNAWVRRYRARAFGDTTQAKLDTLKDGVTIEGVKYGSIEARLDKAHDKAGGGKNIW 205

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TV L EGKNRE++KV E    KVNRLIR+SYGPF LG L AG   EV  +++RE L   
Sbjct: 206 ITVSLSEGKNREVRKVLESVGLKVNRLIRMSYGPFALGALAAGQIEEVGPRVIRELLEGV 265

Query: 249 LLEEAQVNLDAPIYSS 264
           +  E     D P ++ 
Sbjct: 266 VPPENMPTGDRPKFAG 281


>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 =  260 bits (664), Expect = 2e-67,   Method: Compositional matrix adjust.
 Identities = 120/217 (55%), Positives = 153/217 (70%)

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 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           RLIRIS+GPF LG L  G   EV   +L++QLGP L 
Sbjct: 181 RLIRISFGPFMLGDLEPGQVEEVKTSVLKDQLGPRLA 217


>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 =  258 bits (660), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 126/234 (53%), Positives = 166/234 (70%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K +ARAG+ASRRE+ERMIA  ++ +NG  L+  AV V + D I V+G  +  AE+
Sbjct: 5   PQRIAKYLARAGVASRREIERMIAIGQINLNGKTLDTPAVKVTNKDIILVNGKQIGDAEK 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R W Y+KP GL+TT  D  GR T++D  P    RV++VGRLDIN+EGLLLLTNDGGL R
Sbjct: 65  VRFWRYYKPTGLITTDRDEKGRDTIYDYFPENMPRVMTVGRLDINSEGLLLLTNDGGLKR 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELP+T WLR YRVR +G   ++ +  L+ GIVI    +  M++ LD Q+GSNAW+TVG
Sbjct: 125 KLELPATGWLRKYRVRVNGNPTEEMVAPLRNGIVIDRERFKGMEIRLDRQQGSNAWLTVG 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           LREGKNREI++  E+   +VNRLIR SYGPF+L  L  G   E+  K +++QLG
Sbjct: 185 LREGKNREIRRAMEYVGLRVNRLIRTSYGPFKLDDLKPGDVEEIKAKTIKDQLG 238


>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 =  252 bits (644), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 127/253 (50%), Positives = 166/253 (65%), Gaps = 5/253 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV+K++ARAG+ASRR VER+I   RV +NG +L   A+ V   D + VDG  + + E TR
Sbjct: 25  RVAKMLARAGVASRRAVERLIEDGRVALNGEVLTTPAIKVRPGDILTVDGKMIDEPEATR 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++ YHKP GL+TTH+DP  R TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R L
Sbjct: 85  VFRYHKPSGLMTTHNDPKQRPTVFQALPRDLPRLISVGRLDLNSEGLLLLTNDGALSRAL 144

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNAWV 189
           E+P   W+R YR R  G   Q KL+ LK G  ++G+ YG ++  LD  +     G N W+
Sbjct: 145 EMPQNAWVRRYRARAFGDTTQAKLDKLKDGCTVEGVRYGPIEARLDKAQEKAGGGKNIWI 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ L EGKNRE+++V E    KVNRLIR+SYGPF LGTLL G   EV  +++RE L   +
Sbjct: 205 TLTLSEGKNREVRRVLESIGLKVNRLIRLSYGPFALGTLLPGQVEEVGPRVIRELLEGIV 264

Query: 250 LEEAQVNLDAPIY 262
            EE     D P +
Sbjct: 265 AEENMPKGDKPQF 277


>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 =  251 bits (642), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 123/233 (52%), Positives = 161/233 (69%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAG+ SRRE E  I + RVKVNG ++    +NV  TD I VDG  L   E  
Sbjct: 16  ERIAKRIARAGVCSRREAEARINEGRVKVNGKVITSPVLNVSDTDRINVDGQALPHREPA 75

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +LW Y+KP GLV +  D   R T+FD+LP+   RV++VGRLDI++EGLLLLTNDG LAR 
Sbjct: 76  KLWRYYKPRGLVVSDRDEKDRETIFDHLPASLPRVMTVGRLDIDSEGLLLLTNDGDLARH 135

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T W R YRVR  G V++  L  L+KGI I G+ YG +   LD Q  SNAW+TV +
Sbjct: 136 LELPATGWSRKYRVRVQGHVNEAALAPLEKGITIDGVRYGRIVANLDRQMQSNAWLTVAI 195

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           REGKNRE++++ E    KV+RLIR+SYGPFQLG +  G   ++  ++L +QLG
Sbjct: 196 REGKNREVRRIMEHLGHKVSRLIRVSYGPFQLGDMSDGDVEQIRARVLSDQLG 248


>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 =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 114/236 (48%), Positives = 158/236 (66%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +   +  QR++K+++RAGIASRR +E MI + R+ ++G+ +E+ A  + S D + VDG P
Sbjct: 264 IPREYGEQRIAKLLSRAGIASRRMIEAMIEEGRIAIDGVTVEKPATLLTSLDGVTVDGKP 323

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +     TRL+LYHK  GL+TT  DP+GR T++D LP+   RV+ VGRLD+NTEGLLLLT 
Sbjct: 324 VNAPTETRLFLYHKATGLLTTERDPEGRKTIYDRLPADLPRVMPVGRLDMNTEGLLLLTT 383

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGG  R+LELP+T   R YR R  G V QD+L  L +G+ I GI YG +   L+ + G N
Sbjct: 384 DGGFKRMLELPATHIERCYRARVFGDVSQDQLEELIEGVTIDGIHYGSIDANLERRTGRN 443

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            WV + L EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+
Sbjct: 444 GWVEMKLHEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLK 499


>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 =  244 bits (624), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 114/229 (49%), Positives = 156/229 (68%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+
Sbjct: 452 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLK 500


>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 =  244 bits (623), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 114/229 (49%), Positives = 156/229 (68%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+
Sbjct: 452 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLK 500


>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 =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 130/236 (55%), Positives = 166/236 (70%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           +EGKNREI+KV E    +VNRLIR++YGPFQLG L  G+  EV K+++REQ+ P  
Sbjct: 202 KEGKNREIRKVMESLGLQVNRLIRVAYGPFQLGKLEEGAVEEVPKRVVREQIAPFF 257


>gi|148555617|ref|YP_001263199.1| pseudouridine synthase [Sphingomonas wittichii RW1]
 gi|148500807|gb|ABQ69061.1| pseudouridine synthase [Sphingomonas wittichii RW1]
          Length = 286

 Score =  243 bits (621), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 116/229 (50%), Positives = 160/229 (69%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K++ARAGIASRRE+ERMIA+ RV ++G  ++  A  + S   + VDG P+   E 
Sbjct: 46  PQRIAKLLARAGIASRREIERMIAEGRVAIDGAAIDTPATLLTSLKGVTVDGKPVAAPEA 105

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL+L+HKP GL+TT  DP GR T++D LP+   RV+ VGRLD+NTEGLLLLT DG   R
Sbjct: 106 TRLFLFHKPKGLLTTERDPKGRPTIYDRLPAGLPRVMPVGRLDLNTEGLLLLTTDGEFKR 165

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            LELPST   R+YR R +G V Q++L  L +GI I G+ YG +   ++ + G+N W+ + 
Sbjct: 166 QLELPSTGVERIYRARCYGTVHQEQLEALIEGIEIDGVRYGSIDANMERRTGANVWIEMK 225

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           LREGKNRE+++V E    +V+RLIRI+YG F+LG L  G   E+++  L
Sbjct: 226 LREGKNREVRRVLEHLGLEVSRLIRIAYGAFELGDLQPGEVGEIAQHQL 274


>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 =  241 bits (616), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 131/240 (54%), Positives = 167/240 (69%)

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


>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 =  238 bits (608), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 114/223 (51%), Positives = 152/223 (68%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K++ARAG+ASRREVERMIA+ R+ +NG  ++  A  + S D + VDG P+   E T
Sbjct: 5   HRIAKLLARAGVASRREVERMIAEGRIALNGTTIDTPATLLSSLDGVTVDGNPVDAPEPT 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+LY+KP GL+ T  DP GR T++D LP    R++ VGRLD+NTEGLLLLT DGG  R 
Sbjct: 65  RLFLYNKPNGLLVTERDPKGRPTIYDRLPEGLPRLMPVGRLDLNTEGLLLLTTDGGFKRQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T   R YR R +G + Q +L  L  GI I GI YG +   L+ + G+N W+ + L
Sbjct: 125 LELPATGVERTYRARAYGDITQAQLEELIHGIEIDGIRYGQIDANLERRTGANVWIELTL 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           REGKNRE+++V E+   +V+RLIR+ YGPF LG L  G   EV
Sbjct: 185 REGKNREVRRVLEYLGLQVSRLIRLRYGPFVLGDLPVGEIGEV 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 =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 114/233 (48%), Positives = 158/233 (67%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +A AG+ SRRE ER+I +  V VNG +L+ AA  V   + I V+G  +   ++T
Sbjct: 34  ERIAKWLAAAGVCSRREAERLIEEGLVAVNGQVLDSAAFKVTGNEKITVEGKRVGGPDKT 93

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW +HKP GLVTT+SDP+GR TVF++LP    RV+++GRLD+NTEGLLLLTNDG LAR 
Sbjct: 94  RLWRFHKPKGLVTTNSDPEGRPTVFEHLPKKLPRVMTIGRLDLNTEGLLLLTNDGELART 153

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T   R YR R  G++ Q +L+ L++G++ +G+ Y  +  TLD  KG N W+ + L
Sbjct: 154 LELPTTGLKRCYRARAFGKITQAELDKLQEGVLFEGVVYRSIIATLDKTKGDNNWIDMTL 213

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGK RE ++  E     VNRLIR+SYGPF+LG L+ G   E+    L  + G
Sbjct: 214 TEGKKREARRALESVGLIVNRLIRVSYGPFELGDLVEGGVAEIPAGELLSEFG 266


>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 =  236 bits (603), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 113/229 (49%), Positives = 152/229 (66%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K++ARAG+ASRRE+ERMIA  R+ ++G  ++  A  + S   + VDGV +     
Sbjct: 75  PQRIAKLLARAGVASRREIERMIADGRIALDGAPVDTPATLLTSLHGVTVDGVAIAAPAP 134

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRL+L+HKP G +TT  DP GR T++D LP    RV+ +GRLD+NTEGLLLLT DGG  R
Sbjct: 135 TRLFLFHKPTGCLTTERDPAGRPTIYDRLPDGLPRVMPIGRLDMNTEGLLLLTTDGGFKR 194

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +ELP+T   R YR R  G+V Q +L  L  G+ I GI YG ++  L+ + G N W+ + 
Sbjct: 195 QMELPATGVPRTYRARAFGEVSQQQLEDLFDGLEIDGIRYGQIEANLERRTGRNQWIEMT 254

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L EGKNRE+++V E    KVNRLIR +YGPF LG L  G+  EV +  L
Sbjct: 255 LTEGKNREVRRVLEHLGLKVNRLIRTAYGPFSLGELAVGTVEEVRQHDL 303


>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 =  231 bits (588), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 117/239 (48%), Positives = 159/239 (66%), Gaps = 7/239 (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  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTE 119
           G P+ +AE TRL+ +HKP GL+T   DP GR T++    + LP    RV+ 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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   G N W+ + LREGKNRE+++V E F  +VNRL+RI YGPF LG L  G   E+ +
Sbjct: 181 ERGSGRNRWIEMTLREGKNREVRRVLEHFGLEVNRLLRIGYGPFHLGDLPRGQAVELKQ 239


>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 =  229 bits (585), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 112/229 (48%), Positives = 150/229 (65%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K++ARAG+ASRREVERMI + R+ +NG  +   A  + S   + VDG P+     
Sbjct: 65  PQRIAKLLARAGVASRREVERMIEEGRITLNGEAVSTPATLLSSLHGVAVDGNPVAAPAP 124

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RL+L+HKP G +TT  DP GR T++D LP    RV+ +GRLD+ TEGLLLLT DG   R
Sbjct: 125 ARLFLFHKPSGFLTTERDPRGRPTIYDKLPPDLPRVMPIGRLDMMTEGLLLLTTDGEFKR 184

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +ELPST   R YR R  G+V Q++L  L  G+ I GI YG ++  L+ + G N W+ + 
Sbjct: 185 QMELPSTGVPRTYRARAFGEVSQNQLEDLFDGLEIDGIRYGRIEANLERRTGRNQWIEMT 244

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L EGKNRE+++V E    +VNRLIR SYGPF LG L +G+  EV +  L
Sbjct: 245 LTEGKNREVRRVLEHLGLQVNRLIRTSYGPFHLGELASGAVEEVRQHDL 293


>gi|296282690|ref|ZP_06860688.1| hypothetical protein CbatJ_03660 [Citromicrobium bathyomarinum
           JL354]
          Length = 252

 Score =  226 bits (575), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 109/228 (47%), Positives = 151/228 (66%), Gaps = 4/228 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++ARAG+ASRREVERMIA +R+ ++G  +E  A  + +   + VDG P+ K E TR
Sbjct: 10  RIAKLLARAGVASRREVERMIADKRIAIDGKTVETPATLLETLRGVTVDGKPVAKPEPTR 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L+ +HKP GL+T   DP GR T++D    +LP    RV+ +GRLD NTEGLLLLTNDG  
Sbjct: 70  LFAFHKPTGLITAEHDPRGRPTIYDALRNSLPKDAPRVMPIGRLDFNTEGLLLLTNDGEF 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R+LELP+    R YR R HG V Q +L  L +GI I G+ YG +   L+ + G+N W+ 
Sbjct: 130 KRMLELPANAVERTYRARAHGGVTQAQLEELSEGITIDGVHYGPINANLERRTGANQWIE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V + EGKNRE+++V E    +VNRL+R+++GP  LG L  G   E+ K
Sbjct: 190 VTITEGKNREVRRVLEHLGLEVNRLVRVAFGPVALGDLPRGQAMEIRK 237


>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 =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 116/233 (49%), Positives = 160/233 (68%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AGI SRR+ E++IA+ +VKV+GI +   A NV  ++ IEV G+ + +++  
Sbjct: 2   HRLAKIISNAGICSRRDAEKLIAEGQVKVDGITILSPATNVDISNQIEVSGILINQSQTP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+  P+   RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQ-PTGLPRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  SN+W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDI----LLKSNYKNLEIDGIFYNPHSIKLLKQNKSNSWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V L EGKNREI+++FE+F  KVN+LIRI YG F +G L  G  +E++ KIL +
Sbjct: 177 VVLFEGKNREIRRIFEYFGLKVNKLIRIQYGSFTIGNLKPGDYKEINNKILEK 229


>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 =  224 bits (571), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 114/233 (48%), Positives = 161/233 (69%), Gaps = 8/233 (3%)

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 S+  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEDLTSL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS +  RVY VR +G  D     LLK   K + I GI Y    + L     +NAW  
Sbjct: 121 FELPSNKLKRVYHVRAYGNPDI----LLKSEYKNLEIDGILYNPYSIKLLRGNNTNAWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L EGKNREI+++FE+F  KVN+LIR+ YG F +G L  G  +E++ KIL +
Sbjct: 177 IVLFEGKNREIRRIFEYFGLKVNKLIRVQYGSFTIGNLKPGDYKEINNKILEK 229


>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 =  222 bits (566), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 115/233 (49%), Positives = 160/233 (68%), Gaps = 8/233 (3%)

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  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS +  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  SN+W  
Sbjct: 121 FELPSNRLKRVYHVRAYGKSDI----LLKSDYKNLEIDGIFYNPHSIKLFKQNKSNSWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V L EGKNREI+++FE+F  KVN+LIRI YG F +  L  G+ +E++ KIL +
Sbjct: 177 VVLFEGKNREIRRIFEYFGLKVNKLIRIQYGSFTIDNLKPGAYKEINNKILEK 229


>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 =  221 bits (564), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 116/233 (49%), Positives = 159/233 (68%), Gaps = 8/233 (3%)

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  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS +  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  SN+W  
Sbjct: 121 FELPSNRLKRVYHVRAYGKSDI----LLKSDYKNLEIDGIFYNPHSIKLLKQNKSNSWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V L EGKNREI+++FE+F  KV++LIRI YG F +  L  G+ +E++ KIL E
Sbjct: 177 VVLFEGKNREIRRIFEYFGLKVHKLIRIQYGSFTIDNLKPGAYKEINNKILAE 229


>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 =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 113/235 (48%), Positives = 156/235 (66%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++ARAG+ASRREVERMI   RV ++G  +E  A  + S   + VDG P+ KAE TR
Sbjct: 20  RIAKLLARAGVASRREVERMITDGRVALHGKPVETPATFLESLRGVTVDGKPVGKAEPTR 79

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L+ ++KP GL+T  +DP GR+T++D     LP    RV+ +GRLD NTEGLLLLTNDGGL
Sbjct: 80  LFAFNKPTGLLTAENDPKGRATIYDALKNALPKDAGRVMPIGRLDFNTEGLLLLTNDGGL 139

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSN 186
            R +ELPS+   R YR R  G + Q++L  L +GI I G+ YG +   L+    +  G N
Sbjct: 140 KRRMELPSSGIPRTYRARAFGDITQEQLESLIEGIEIDGVRYGRIDANLEQKTKSAGGRN 199

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            W+ + + EGKNRE+++V E F  +V+RL+R++YGPFQLG L  G   E+ K  L
Sbjct: 200 QWIEMTITEGKNREVRRVLEHFGLEVSRLMRVAYGPFQLGDLPRGQAVEIRKGDL 254


>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 =  218 bits (556), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 113/232 (48%), Positives = 158/232 (68%), Gaps = 8/232 (3%)

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  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNNGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G  D     LLK   K + I GI Y    + L  +  +N+W+ 
Sbjct: 121 FELPSSKLKRVYHVRAYGNPDP----LLKSNYKNLEIDGIFYNPQSIKLLRKNSTNSWLE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V L EGKNREI+++FE F  KVN+LIR  YG F+L  L     REV+KK+ +
Sbjct: 177 VILFEGKNREIRRIFEHFGLKVNKLIRTEYGDFKLDNLKPNEYREVTKKLYK 228


>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 =  218 bits (556), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 108/230 (46%), Positives = 150/230 (65%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++ARAG+ASRRE+ERMIA  R+ +N  ++E  A  + S   + VDG P+ K E  +
Sbjct: 16  RIAKLLARAGVASRREIERMIADGRITLNDKVVETPATFLTSLQGVAVDGKPVAKPEPAQ 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L+ +HKP GL+T   DP GR+T++    + LP    R++ +GRLD+NTEGLLLLTNDGGL
Sbjct: 76  LYAFHKPTGLITAERDPAGRATIYAALRNALPKDTPRLMPIGRLDLNTEGLLLLTNDGGL 135

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
            R +ELPS+   R YR R  G V Q++L  L +G+ I G+ YG +   L+     G N W
Sbjct: 136 KRQMELPSSGIPRTYRARAFGDVSQEQLEALIEGVEIDGVRYGSIDANLERGGAGGKNQW 195

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V + + EGKNRE+++V E+   KVNRLIR +YGPF LG L  G    + K
Sbjct: 196 VEMTITEGKNREVRRVLEYLGLKVNRLIRTAYGPFGLGDLPRGQAVRIRK 245


>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 =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 112/233 (48%), Positives = 154/233 (66%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I + +VKV+GI +   A NV  ++ IEV G  +    + 
Sbjct: 2   HRLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPATNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +   VIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PHVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  SN+W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDI----LLKSHYKNLEIDGIFYNPHSIKLLKQNKSNSWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V L EGKNREI+++FE+F  KVN+LIRI YG F +  L  G  +E++ KIL +
Sbjct: 177 VVLFEGKNREIRRIFEYFGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILEK 229


>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 =  213 bits (541), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 106/228 (46%), Positives = 144/228 (63%), Gaps = 4/228 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++ARAGIASRREVERMI + RVK+   ++   A  + S   + VDG P+      R
Sbjct: 30  RIAKLLARAGIASRREVERMIEEGRVKIGDEVVTTPATLLTSLKGVSVDGKPVAPMAPPR 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L+ +HKP GL+T   DP GR T++    + LP    RV+ VGRLD+NTEGLLL+TNDG L
Sbjct: 90  LFRFHKPSGLITAERDPTGRPTIYTALRNALPQGTPRVMPVGRLDVNTEGLLLMTNDGEL 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R LELPST   R YR R  G + Q +L  L +GI I G+ YG +   L+   G N W+ 
Sbjct: 150 KRALELPSTGIPRTYRARTFGDISQARLEELMEGIEIDGVRYGSINANLERSAGRNKWIE 209

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L EGKNRE+++V E    +V+RL+R  YGPF+L  L  G+  E+ +
Sbjct: 210 LTLTEGKNREVRRVLEHLGLQVSRLLRTKYGPFELADLPRGAAEEIPQ 257


>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 =  212 bits (539), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 110/234 (47%), Positives = 156/234 (66%), Gaps = 8/234 (3%)

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  LWIYYKPVGLITTHKDPLSRKTVFEQLIGL-PRVISIGRLDLNSEGLLLLTNSGDLAHQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           E+P+++  RVY VR +G  +     LLK   K + I GI Y    + L  Q  SN+W  V
Sbjct: 122 EMPASKLKRVYNVRAYGNPNI----LLKNNYKNLKIDGIFYNPHSIKLLRQNKSNSWFEV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L EGKNREI+++FE+F  +VN+LIRI YG  ++G L  G+ +E+S KIL +QL
Sbjct: 178 VLFEGKNREIRRIFEYFGLQVNKLIRIQYGALKIGNLKPGNYQEISNKILEKQL 231


>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 =  211 bits (538), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 109/238 (45%), Positives = 156/238 (65%), Gaps = 8/238 (3%)

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  LWIYYKPIGLITTHKDPLSRKTVFEQLIGL-PRVISIGRLDLNSEGLLLLTNSGDLAHQF 121

Query: 135 ELPSTQWLRVYRVRFHGQVD---QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           E+PS++  RVY VR +G  +   ++  N LK    I GI Y    + L  Q  +N+W  V
Sbjct: 122 EMPSSKLKRVYNVRAYGNANFLLKNNYNNLK----IDGIFYNPYSIKLLRQNKNNSWFEV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            L EGKNREI+++FE+F  KVN+LIR+ YG  ++G L  G  +E+S KIL++ +   L
Sbjct: 178 VLFEGKNREIRRIFEYFGLKVNKLIRVQYGALKIGNLKPGDYKEISNKILKKIISNKL 235


>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 =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 104/227 (45%), Positives = 149/227 (65%), Gaps = 4/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K++ARAGIASRR+VERMI + R+K+N  L+   A  +++   + VD  P+      
Sbjct: 76  ERIAKLLARAGIASRRDVERMIGEGRIKLNDELVTTPATLLLNLKGVTVDDKPVAAPAPA 135

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL+ +HKP GL+T   DP GR T+++ L    P+   RV+ VGRLD+NTEGLLLLTNDG 
Sbjct: 136 RLFRFHKPEGLITAERDPAGRPTIYNALRNALPAGTPRVMPVGRLDLNTEGLLLLTNDGE 195

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L R +ELP++   R YR R  G + QD+L  L +G+ I+GI YG +   ++ + G N W+
Sbjct: 196 LKRAMELPASGIPRTYRARTFGDISQDQLEALIEGVEIEGIRYGSIDANMERRTGRNQWI 255

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + L EGKNRE+++V E    +V+RLIR +YGPF L  L  G+  EV
Sbjct: 256 EMTLTEGKNREVRRVLEHLGLQVSRLIRTAYGPFMLLDLPRGAADEV 302


>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 =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 151/231 (65%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + 
Sbjct: 2   HRLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  +N W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDV----LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL
Sbjct: 177 VVLFEGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKIL 227


>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 =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 151/231 (65%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + 
Sbjct: 2   NRLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  +N W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDV----LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL
Sbjct: 177 VVLFEGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKIL 227


>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 =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 151/231 (65%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + 
Sbjct: 2   HRLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  +N W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKYDI----LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL
Sbjct: 177 VVLFEGKNREIRRIFEYCGLKVNKLIRIQYGNFTIDNLKPGDYKEINNKIL 227


>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 =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 151/231 (65%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I + +VKV+GI +     NV  ++ IEV G  +    + 
Sbjct: 2   HRLAKIISNAGVCSRRDAEKLIVEGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  +N W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDI----LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL
Sbjct: 177 VVLFEGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKIL 227


>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 =  211 bits (536), Expect = 2e-52,   Method: Compositional matrix adjust.
 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|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 =  210 bits (534), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 109/234 (46%), Positives = 151/234 (64%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I + +VKV+G+ +     NV  ++ IEV G  +    + 
Sbjct: 2   HRLAKIISNAGVCSRRDAEKLIVEGQVKVDGVTILSPTTNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  +N W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDI----LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V L EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL   
Sbjct: 177 VVLFEGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILENH 230


>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 =  209 bits (533), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 110/231 (47%), Positives = 150/231 (64%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+I+ AG+ SRR+ E++I   +VKV+GI +     NV  ++ IEV G  +    + 
Sbjct: 2   HRLAKIISNAGVCSRRDAEKLIVAGQVKVDGITILSPTTNVDISNQIEVSGTLINNIHKP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW+Y+KP+GL+TTH DP  R TVF+ L  +  RVIS+GRLD+N+EGLLLLTN G LAR 
Sbjct: 62  RLWIYYKPVGLITTHKDPLSRKTVFEQLTGL-PRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            ELPS++  RVY VR +G+ D     LLK   K + I GI Y    + L  Q  +N W  
Sbjct: 121 FELPSSRLKRVYHVRAYGKSDI----LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL
Sbjct: 177 VVLFEGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKIL 227


>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 =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 112/229 (48%), Positives = 151/229 (65%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K++ARAG+ASRREVERMI + R+ +NG  +   A  + S   + VDG P+     
Sbjct: 28  PQRIAKLLARAGVASRREVERMIEEGRITLNGEAITTPATLLASLHGVAVDGAPVAAPAP 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RL+L+HKP G +TT  DP GR T++D LP+   RV+ +GRLD+ TEGLLLLT DG   R
Sbjct: 88  ARLFLFHKPSGFLTTERDPRGRPTIYDKLPADLPRVMPIGRLDMTTEGLLLLTTDGEFKR 147

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +ELPST   R YR R  G V Q++L  L +GI I GI YG ++  L+ + G N W+ + 
Sbjct: 148 QMELPSTGVPRTYRARAFGDVSQNQLEDLFEGIEIDGIRYGQIEANLERRTGRNQWIEMT 207

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L EGKNRE+++V E    +V+RLIR SYGPF LG L +G+  EV +  L
Sbjct: 208 LTEGKNREVRRVLEHLGLQVSRLIRTSYGPFHLGELPSGAVEEVRQHDL 256


>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 =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 115/233 (49%), Positives = 149/233 (63%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ASRREVER+I    V VNG  L   A  V   + I+V    ++  + +
Sbjct: 38  ERIAKYLARAGVASRREVERLIEAGEVTVNGQKLTSPAFKVTGREAIKVGRKVIQAPDAS 97

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GL+TT +DP GR T+FD LP    R ++VGRLD+ TEGLLLLTNDG LAR 
Sbjct: 98  RLWRYHKPSGLITTTNDPAGRRTIFDELPKSLPRTVTVGRLDLTTEGLLLLTNDGELARF 157

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP +   R YRVR  G V Q K++ L  GI ++G+ Y  ++   D + G+N+W+TV L
Sbjct: 158 LELPKSALERTYRVRAKGTVTQLKIDELASGITVEGVKYQPIKAVFDREMGANSWLTVTL 217

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNRE++K  E     VNRLIR+SYGPF L  L  G   EV   +L   L 
Sbjct: 218 TEGKNREVRKALESVGLTVNRLIRVSYGPFLLADLKPGQVDEVPPDLLETALA 270


>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 =  192 bits (488), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 97/227 (42%), Positives = 154/227 (67%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R++KV++R+G+ASRR+ + MI + RVKVNG++      + +S  D +EVDG  ++K   
Sbjct: 110 ERLNKVLSRSGVASRRKADEMIREGRVKVNGVVTTLENDHFVSIIDEVEVDGKIIKKP-M 168

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R+W++ K   ++ THS+ +GR ++   L  +  +  +I+VGRLD  +EGL+LLTNDG L
Sbjct: 169 PRMWMHFKKPKVLVTHSEVEGRESLVPILKKVLKKDHLITVGRLDYYSEGLILLTNDGNL 228

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +R LE P  ++ R YRVR  G++ Q+  ++  KGIVI  I Y  ++V +D +  +N+WV 
Sbjct: 229 SRYLEHPDNEFERTYRVRIFGKITQEMQDIFTKGIVIDNIKYKPIEVIVDKESKNNSWVV 288

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
           + ++EGKNREI+K+ E+FN KV RLIR+ YGP++L  +L  G T E+
Sbjct: 289 IKIKEGKNREIRKILEYFNIKVLRLIRVGYGPYELPESLKHGETIEI 335


>gi|23007931|ref|ZP_00049587.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 179

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 94/157 (59%), Positives = 114/157 (72%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VDG PL   ERT
Sbjct: 22  ERIAKAIARAGIASRRDAEALIEAGRVTLNGQVLTSPAINVTDSDRITVDGEPLPARERT 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA+V
Sbjct: 82  RLWLLHKPRGVVTTARDPEGRQTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLAKV 141

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +  P T WLR YRVR  G V Q  L+ LKKG+ + G+
Sbjct: 142 IAHPDTGWLRRYRVRAFGDVTQADLDKLKKGVTVDGM 178


>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 =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 95/233 (40%), Positives = 152/233 (65%), Gaps = 13/233 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPL 67
           +R+SK ++R+G+ SRR+ E+MI    +KV+G +   + + V   ++IE+         P+
Sbjct: 176 ERLSKYLSRSGVCSRRQAEKMIKDGLIKVDGKVAT-SNLPVTPKNNIEIFTQRGEKFAPV 234

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGLLL 123
           +  +  ++W+++KP G++ +H DP  R +VF+    N       +I+VGRLD N+EGL+L
Sbjct: 235 K--QNAKIWIFYKPRGMICSHDDPLKRPSVFNYIYNNTKIKEPHIIAVGRLDYNSEGLIL 292

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG +A+ LE P +   R YRVR  G++D+ KL  L++G VI G+ YG   V +D ++
Sbjct: 293 LTNDGDIAQCLEQPESNIYRQYRVRVQGELDERKLLKLRQGTVINGVQYGPFNVEIDKRQ 352

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            SN W+TVGL  GKNREI+KV + F+ +V+RL R+SYGP+++G++L G   E 
Sbjct: 353 SSNTWLTVGLYTGKNREIRKVMQKFDLRVSRLKRLSYGPYKIGSMLPGQIFET 405


>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 =  189 bits (479), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 96/244 (39%), Positives = 155/244 (63%), Gaps = 19/244 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +N++Q    P R+SK +A+  + SRRE E+MI    + V+G  +E + + V S + I+V 
Sbjct: 28  QNLIQPE--PMRLSKYLAQTSVCSRREAEKMIESGMILVDGKKVE-SNIPVTSENKIQVF 84

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--------VISVG 112
             +G  +   + T++W+++KP+G++ +H+DP  R + +D     F++        +ISVG
Sbjct: 85  TKNGEKMPTKQSTKVWIFYKPVGMICSHNDPFKRPSFYD-----FAKLRLKTDQHIISVG 139

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD N+EGL+++TNDG LAR +ELP T+  R+YRVR +G   ++KL  ++ GI I G+ Y
Sbjct: 140 RLDFNSEGLIVVTNDGELARCMELPETKLQRIYRVRVYGTFTEEKLKKIRNGITIAGVNY 199

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           G   V ++ ++  N W+ + L +GKNREI+KV + F+ +VNRLIR SYGP++L  L  G 
Sbjct: 200 GPYWVNVENRQSRNTWLIMRLEQGKNREIRKVMQKFDLRVNRLIRQSYGPYKLMGLKPGD 259

Query: 233 TREV 236
             E 
Sbjct: 260 FYEA 263


>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 =  185 bits (469), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 95/243 (39%), Positives = 154/243 (63%), Gaps = 19/243 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +N++Q    P R+SK +A+  + SRRE E+MI    + V+G  ++ + + V S + I+V 
Sbjct: 28  QNLIQSE--PMRLSKYLAQTSVCSRREAEKMIESGMILVDGKKVD-SNIPVTSENKIQVF 84

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--------VISVG 112
             +G  +   + T++W+++KPIG++ +H+DP  R + +D     F++        +ISVG
Sbjct: 85  TKNGERMPVKQSTKVWIFYKPIGMICSHNDPFKRPSFYD-----FAKLRLKTDQHIISVG 139

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD N+EGL+++TNDG LAR +ELP T+  R+YRVR +G   ++KL  ++ G+ I G+ Y
Sbjct: 140 RLDFNSEGLIVVTNDGELARCMELPETKLQRIYRVRVYGTFTEEKLKKIRNGLTIAGVNY 199

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           G   V ++ ++  N W+ + L  GKNREI+KV + F+ +VNRLIR SYGP++L  L  G 
Sbjct: 200 GPYWVNVENRQSRNTWLIMRLESGKNREIRKVMQKFDLRVNRLIRQSYGPYKLMGLKPGD 259

Query: 233 TRE 235
             E
Sbjct: 260 FYE 262


>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 =  185 bits (469), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 102/242 (42%), Positives = 151/242 (62%), Gaps = 13/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++ARAGIASRR+ E +I   RVKVNG +++   + V   D I VD  P+ K ++ 
Sbjct: 138 ERIQKILARAGIASRRKAEELIIDGRVKVNGKIIKMEEILVKPHDIITVDDKPI-KVDKP 196

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-----FSRVISVGRLDINTEGLLLLTNDG 128
           ++W++ K   ++T+  DPDGR  +   LP I        +ISVGRLD  TEGL+L TNDG
Sbjct: 197 KIWMHFKNPQVLTSEYDPDGRDCL---LPIIRKVIGIDHLISVGRLDYYTEGLILFTNDG 253

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LAR L LP   + RVY+VR  G+   +    L KG+VI  + Y  + V ++++  SN W
Sbjct: 254 ELARYLTLPQNLFFRVYKVRIFGKFTDEMKFSLAKGMVINEVFYRPVSVQVESETDSNTW 313

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           + + L+EGK REI+ + E+FN KV RLIR++YGP+ L  +L  G T EV    ++++L P
Sbjct: 314 LRITLQEGKKREIRTLLEYFNVKVLRLIRVAYGPYVLPNSLKHGETIEVP---IKDELKP 370

Query: 248 HL 249
            +
Sbjct: 371 FI 372


>gi|291001465|ref|XP_002683299.1| predicted protein [Naegleria gruberi]
 gi|284096928|gb|EFC50555.1| predicted protein [Naegleria gruberi]
          Length = 362

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 99/230 (43%), Positives = 142/230 (61%), Gaps = 9/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA-- 70
           +RVSK +AR G+ S+++   +I   +VKVNGIL+  +   +    D + V GV + K   
Sbjct: 83  ERVSKFLARVGVCSKQQGVDLIKAGQVKVNGILITESGQKMNPFYDVVTVKGVNITKKDV 142

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
               E  +L+ YHKP G++ +  D  G R T++  L  + 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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +W+ V L EGKNREI+K+F+  N  V+R++RI YGP++L  +  G  +
Sbjct: 263 KTSWIKVILHEGKNREIRKIFQQLNLPVSRIMRIQYGPYKLENIQKGQIK 312


>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 =  178 bits (451), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 106/225 (47%), Positives = 143/225 (63%), Gaps = 12/225 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
           +++ K++A AG+ SRRE+E+ I   RV VNG    L ERA       D I VDG  + + 
Sbjct: 3   EKLQKILANAGLGSRREIEKWIEGGRVSVNGSIAKLGERAT----DKDTIRVDGRIISII 58

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
            AE T  R+  Y+KP+G V+T  DP+GR+TVFDNLP+  F R IS+GRLDINT GLLL T
Sbjct: 59  SAEETYTRVLAYNKPLGEVSTKKDPEGRATVFDNLPNTSFGRWISIGRLDINTTGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  PS Q  R Y VR HG+V  + ++ L KG++I+G       V     +G+
Sbjct: 119 NNGELAHRLMHPSYQVERKYAVRVHGEVTPEMISNLTKGVLIEGDTCQFTYVQDKGGEGA 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           N W  VGL EGKNRE++K++E    +V+RL+R+ YGP  L T L+
Sbjct: 179 NHWYEVGLAEGKNREVRKLWESQGVEVSRLMRVQYGPISLPTRLS 223


>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 =  175 bits (444), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 88/229 (38%), Positives = 137/229 (59%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +A   + SRRE+ERMI   R+ +NG +L      V  TD I++DG  L   +  +
Sbjct: 10  RISKFLASYNVGSRREIERMIENGRIYLNGEILTTPVHFVNKTDSIKLDGKLLLFKKFKQ 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++ ++KP   + + +  D R  V+D LP  F   I  GRLD+N+EGLL++TNDG +AR L
Sbjct: 70  IYKFYKPTDCICSKNKQDERKIVYDLLPKRFKNFIFAGRLDVNSEGLLIVTNDGEVARSL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP  +++R YRVR +G  ++ K++ L KG  I GI Y      L  +   N W+ + L+
Sbjct: 130 ELPKNKFVRKYRVRVYGVCEEQKIDNLSKGRKIDGIQYRPFNYKLFNKDKKNFWIEMELK 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           EGKNREI+++    + +VN+L R+ +GPF++  L  G  +    K +R+
Sbjct: 190 EGKNREIRELMRSIDLRVNKLTRLEFGPFKISNLKPGEIKTAEPKEIRQ 238


>gi|299115182|emb|CBN74013.1| RNA pseudouridylate synthase domain-containing protein (C-terminal)
           RNA pseudouridylate synthase dom [Ectocarpus
           siliculosus]
          Length = 490

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 105/257 (40%), Positives = 145/257 (56%), Gaps = 29/257 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+S+ IAR+GIASRRE ERM+    V VNG  ++  A+NV   D ++V+           
Sbjct: 114 RLSRRIARSGIASRREAERMVEAGVVMVNGATVQTPALNVGPRDIVKVNVGLFQQPGNGT 173

Query: 64  -------GVPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVG 112
                  G  L + E    +LW+ HK    + T  DP+GR TVFD L  +     ++ VG
Sbjct: 174 DCFTFVQGKVLERPESHTPKLWMVHKMRNELVTRHDPEGRPTVFDRLTKLKLPDTLMPVG 233

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD NTEGLLLLTNDG LAR +ELPS+  +R Y VR +G + ++KL  ++ G  I G+ Y
Sbjct: 234 RLDYNTEGLLLLTNDGDLARKMELPSSNIVRTYSVRVYGNITEEKLRAMRSGCTIDGVRY 293

Query: 173 GDM-----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
             M           ++G NAW+T+   EGKNR+I+K+ ++    VNRL R  YGPF LG 
Sbjct: 294 KGMFVRVEGGGGKGREGRNAWLTIECTEGKNRQIRKICKYLCLTVNRLARTRYGPFSLGK 353

Query: 228 LLAGSTR--EVSKKILR 242
           + AG     E+ K  +R
Sbjct: 354 VRAGGVAAVEIPKAFMR 370


>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 =  171 bits (433), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 102/236 (43%), Positives = 144/236 (61%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +++ KV+ARAG  SRRE+ER I + RVKVNG++       V  +D I+VD   +R    +
Sbjct: 11  EKLQKVLARAGQGSRREMERAITEGRVKVNGVVAT-LGDRVTESDKIQVDDQYIRVKKGE 69

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           A+ TR+ LY+KP G + + +DP+GR TV+DNLP + S R ISVGRLD NT GLLL TNDG
Sbjct: 70  ADTTRVILYNKPEGQICSRNDPEGRPTVYDNLPRLKSGRWISVGRLDFNTSGLLLFTNDG 129

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS+   R Y VR  G+VD D L  L+ G++++        +    Q+GSN W
Sbjct: 130 ELAHKLMHPSSNIDREYLVRVQGEVDGDMLQRLRDGVLLEDGLAKFTDIVPGAQEGSNRW 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKKILRE 243
               + EGKNRE+++++E    +V+RL R+ YG  F    +  G   E+  K L+E
Sbjct: 190 FYCVVMEGKNREVRRLWESQECRVSRLKRVRYGNIFIPSNVRVGQWIELEDKELKE 245


>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 =  169 bits (429), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 134/225 (59%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE E++I   RV VNG ++ E  +     +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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+ R+++++ E     V RL R  YG  ++G L  G  RE+S
Sbjct: 183 IHEGRYRQVRRMCEAVGLTVVRLKRSRYGFLEIGELKPGQYRELS 227


>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 =  167 bits (423), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 92/225 (40%), Positives = 134/225 (59%), Gaps = 3/225 (1%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKP 81
           +G+ SRRE E+ I    V VNG ++   A  V    D + VDG  L K ++T++W+ +K 
Sbjct: 2   SGLCSRREAEKRIQSFDVTVNGHVVADVATKVDAEKDVVAVDGRVLSKTQKTKVWMAYKM 61

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 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 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           E++K        V +LIR+ YGP++L  L +G+  EV  K L ++
Sbjct: 182 EVRKALAHVRLVVKQLIRVQYGPYRLADLPSGAVLEVRPKSLEKK 226


>gi|325193088|emb|CCA27453.1| RNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 285

 Score =  166 bits (420), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 99/250 (39%), Positives = 139/250 (55%), Gaps = 10/250 (4%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVD 63
           NI        R+SK IA AGI SRR+ E+ I   +V +NG +L     ++    D + VD
Sbjct: 28  NIESSTDQKMRISKWIAMAGICSRRQAEKKILSNQVVLNGNVLRDVGQSINPKVDRVTVD 87

Query: 64  GVPL--RKAERT-----RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRL 114
           G+ L  RK E       +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|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 =  165 bits (417), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 98/218 (44%), Positives = 135/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I + RV V+G L      V VM    I VDG  V +R++
Sbjct: 3   EKLQKVLARAGHGSRREIEALIKEGRVSVDGKLATLGDRVEVMPNMKIRVDGRVVSIRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E+   R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 63  EQEICRVLAYYKPEGELCTRRDPEGRPTVFDRLPRLRGSRWIAVGRLDINTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+DKL  L++G+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDEDKLRQLRRGVQLEDGPASFKSISFQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLPL 220


>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 =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 99/240 (41%), Positives = 144/240 (60%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG+ SRRE+E  I   RV++ G    +        DH+E+DG  +++  R 
Sbjct: 12  EKLQKVLARAGLGSRREMEAAIQAGRVRIEG-RTAKLGDRARPRDHVELDGRTVQRVHRE 70

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R+ LY+KP G VTT SDP+GRSTVF+ LP    R I+VGRLDIN++GLLL TNDG L
Sbjct: 71  PPRRVLLYNKPEGEVTTRSDPEGRSTVFERLPRTPGRWIAVGRLDINSQGLLLFTNDGEL 130

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQKG 184
           A  L  PST   R Y  R HG+V ++ ++ L  G+ ++       +    M V  + Q+G
Sbjct: 131 ANALMHPSTGVEREYACRIHGEVTEEMVHRLVDGVELEDGPAHFEVVESGMPVD-EPQEG 189

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           +NAW  V + EG+ RE+++++E     V+RLIR+ YGP  +   L  G  RE+ +   RE
Sbjct: 190 TNAWYHVIVTEGRRREVRRLWESQGVTVSRLIRVRYGPMVMPRDLRRGQLRELDEAGKRE 249


>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 =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 108/256 (42%), Positives = 154/256 (60%), Gaps = 12/256 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV +   + +DG  + L +A
Sbjct: 41  EKLQKVLARAGQGSRREIEAIIAENRVSVDGKIATLGDRINVYAGVKVRIDGHLINLTQA 100

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+ +Y+KP G + T  DP+GR+TVFD LP +  +R I+VGRLDINT GLLL T D
Sbjct: 101 QKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDINTSGLLLFTTD 160

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       ++ +    G N 
Sbjct: 161 GELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGSANFKEIKVVGGVGMNQ 220

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+       LRE
Sbjct: 221 WFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMELADVNYLRE 280

Query: 244 QLGPHLLEEAQVNLDA 259
            +G  L  EA+  L A
Sbjct: 281 LVG--LPPEAETKLGA 294


>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 =  164 bits (416), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/235 (40%), Positives = 134/235 (57%), Gaps = 1/235 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + EG+NR+++++ E  +  V RL R+ YG  ++  L  G  R +++   R  L P
Sbjct: 183 IHEGRNRQVRRMCEAVSLSVVRLKRVRYGALEMRGLKPGQHRLLTEAEARALLTP 237


>gi|56478942|ref|YP_160531.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
 gi|56314985|emb|CAI09630.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
          Length = 317

 Score =  164 bits (415), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 92/221 (41%), Positives = 134/221 (60%), Gaps = 5/221 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A+ G+ SRRE+E  +   R+ VNG+  E     +   D ++ +G  +PLR  
Sbjct: 54  PERLQKVLAQIGLGSRREIEEWVVAGRISVNGLPAE-LGQKIGPGDRVKYNGKLIPLRFT 112

Query: 71  ERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
            RT R+ +YHKP G + +  DP+GR TVF+ LP +   R I+VGRLD NT GLLL TNDG
Sbjct: 113 VRTPRVLIYHKPEGEIVSREDPEGRPTVFERLPILRKGRWIAVGRLDFNTSGLLLFTNDG 172

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  R Y VR  GQ+D ++L  LK GI ++        ++ +  +G+N W
Sbjct: 173 TLANRLMHPRYELEREYAVRLLGQLDDEQLESLKTGIQLEDGLARFTSISDEGGEGANHW 232

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V L EG+NRE++++FE     V+RL+R+ YGP  L + L
Sbjct: 233 YRVTLSEGRNREVRRMFEAVGLTVSRLMRVRYGPVTLSSRL 273


>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 =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 94/213 (44%), Positives = 133/213 (62%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +++ KV+ARAG+ SRRE+ER+I+  +V VNG    R    V + D IE DG  ++ A   
Sbjct: 11  EKLQKVLARAGLGSRREMERLISLGKVSVNGATA-RLGDRVGAEDKIEYDGKRIQAAPVV 69

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
            +RTR+ LY+KP G + + +DP+GR TV+DNLP I  SR ISVGRLD NT GLLL TNDG
Sbjct: 70  KQRTRVILYNKPEGQICSRNDPEGRPTVYDNLPKIAQSRWISVGRLDFNTSGLLLFTNDG 129

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PST   R Y VR  G+VD D L  L+ G++++        +    ++  N W
Sbjct: 130 ELANKLMHPSTGIDREYLVRIQGEVDNDMLQRLRDGVLLEDGIARFTDIVEGQKESKNRW 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
               + EG+NRE+++++E    +V+RL R+ YG
Sbjct: 190 FYCVVMEGRNREVRRLWESQEVRVSRLKRVRYG 222


>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 =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 95/220 (43%), Positives = 137/220 (62%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I Q RV V+G    L +R  V+V  +  I +DG  +P+ 
Sbjct: 3   EKLQKVLARAGHGSRREIEAIIQQGRVSVDGKVATLGDR--VDVTPSTKIRLDGRILPIT 60

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           ++E    R+  Y+KP G + T SDPDGR TVFD LP +  SR ++VGRLD+NT GLLL T
Sbjct: 61  ESEEAVCRVLAYYKPEGELCTRSDPDGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQ+D +K+ LL +G+ ++        ++    +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGQIDDEKIKLLSRGVQLEDGPAAFRTISFQGGEGL 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 220


>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 =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 128/225 (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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+NR+++++ E     V+RL RI Y    LG L  G  R++S+
Sbjct: 183 HEGRNRQVRRMCEAVGCPVSRLKRIRYAFLDLGDLRPGQHRQLSR 227


>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 =  164 bits (414), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 144/229 (62%), Gaps = 7/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ SRRE E  I + RV +NG ++    V V   D + VDG  L   +R+R
Sbjct: 71  RLQKWLAEQGLCSRREGEVWIQEGRVSINGEVVTELGVKVAKRDRVAVDG-QLVTPQRSR 129

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + HKP  ++ T SDP GR T+FD + +   SR+I+VGRLDIN+EGL++LT+DG LA
Sbjct: 130 DTAIILHKPKSIICTRSDPQGRRTIFDLIENHGSSRLITVGRLDINSEGLIILTSDGQLA 189

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDT--QKGSNAW 188
             L  PS +  RVYRV+ HG +   +L  ++  G+ ++    G +++ LD   ++G+N+W
Sbjct: 190 HGLMHPSREVPRVYRVKTHGILLASQLEQIRTVGVRLEDGPTGPLEIVLDRGREQGNNSW 249

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            T+ LREG+NRE++++F+ F  +V RL+R+ YG   LG L  G+ R V+
Sbjct: 250 YTITLREGRNREVRRIFDHFGLQVARLLRVGYGGISLGNLEPGAWRPVT 298


>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 =  163 bits (413), Expect = 3e-38,   Method: Compositional matrix adjust.
 Identities = 96/217 (44%), Positives = 136/217 (62%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG+ SRR++E  I   R++VNG  + R    V     I VDG PLR+   +
Sbjct: 5   EKLQKVLARAGMGSRRQMEHWIRDGRIRVNG-RIARLGERVAPRMQITVDGRPLRRRSLS 63

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
              R+ LYHKP+G+VTT SDP GR TVF +LP I   R I+VGRLDINT GLLL T DG 
Sbjct: 64  GLPRMLLYHKPVGVVTTRSDPAGRPTVFQHLPRIKKGRWIAVGRLDINTCGLLLFTTDGE 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  PS + +R Y VR +G+V  + +  L++G+ ++ G    D    L   + +N W
Sbjct: 124 LANRLMHPSFRLVREYAVRVYGEVTAEMITRLQQGVELEDGRGAFDRIEVLCEAQAANGW 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+ RE+++++E    +V+RLIR+ YGP +L
Sbjct: 184 YRVSLAEGRRREVRRLWESQGVRVSRLIRLRYGPVRL 220


>gi|260893153|ref|YP_003239250.1| pseudouridine synthase [Ammonifex degensii KC4]
 gi|260865294|gb|ACX52400.1| pseudouridine synthase [Ammonifex degensii KC4]
          Length = 251

 Score =  163 bits (413), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 95/227 (41%), Positives = 137/227 (60%), Gaps = 1/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +REG+ R+I+++ +    +V RL R++ GP +LG L  G  R ++ +
Sbjct: 184 IREGRKRQIRRMLKALGCEVLRLKRVAVGPVRLGPLRPGEYRHLTPR 230


>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 =  163 bits (413), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 95/213 (44%), Positives = 132/213 (61%), Gaps = 8/213 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +++ KV+AR+G+ SRRE+ER I Q+RV ++G    R    V++   IEVDG PL     E
Sbjct: 20  EKLQKVLARSGLGSRREMERWIEQERVTIDGKAA-RLGDRVVAAQRIEVDGRPLVASDGE 78

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           +TR  LYHKP G V +  DP+GR TVF+ LP + S R IS+GRLD NT GLLL T DG L
Sbjct: 79  KTRCLLYHKPTGEVCSRKDPEGRRTVFERLPKVKSGRWISIGRLDYNTSGLLLFTTDGEL 138

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSNAW 188
           A  L  PS    R Y VR  G V +D L  + +G++++ G+  + D+Q       G N+W
Sbjct: 139 ANALMHPSANIEREYMVRVMGDVTEDHLKAMLEGVMLEDGVARFTDIQSG--GGDGINSW 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V L EG+NRE+++++E     V+RL R+ YG
Sbjct: 197 YYVVLMEGRNREVRRLWESQGLTVSRLKRVRYG 229


>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 =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 100/265 (37%), Positives = 148/265 (55%), Gaps = 8/265 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++ARAG+ASRR  E +IA  RV V+G ++ +        T  I +DG P+ +AE 
Sbjct: 4   ERLQKILARAGVASRRAAEELIAAGRVAVDGQIVRQPGHKADPDTQSIAIDGKPIARAEA 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              WL HKP G V+T  DP GR  V D LP  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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLGPH 248
            LREG+ REIK +++     V RL+R+  GP +LG L  G+ R +S    + LR Q   H
Sbjct: 184 VLREGRKREIKLMWKARGLNVIRLVRVGLGPLRLGDLPPGAVRRLSPAEIQALRRQC--H 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPN 273
            L   + + D  +  S    R+ P+
Sbjct: 242 ALSGCKDSADG-VQKSARGARNAPS 265


>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 =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 96/235 (40%), Positives = 140/235 (59%), Gaps = 14/235 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D   + E    +++ KV+ARAG+ SRR++E  IA+ RVKVNG + +     V + D ++V
Sbjct: 4   DNTAMSEQANTEKLQKVLARAGVGSRRQMEAWIAEGRVKVNGHVAQ-LGDRVTAEDRLQV 62

Query: 63  DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           DG P+ +     ER R+ LY+KP G V T  DP+GR TVF+NLP    R + VGRLD+N+
Sbjct: 63  DGRPVARRKLQPER-RVLLYYKPEGQVCTRDDPEGRPTVFENLPEADGRWVVVGRLDLNS 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQ 176
           +GLLL T DG LA  L  PS+   R Y VR +G+V  + L  L++G+ +      +  + 
Sbjct: 122 QGLLLFTTDGELANRLMHPSSGIEREYAVRVYGEVTPEILRRLQQGVTLDDGEAAFTRIT 181

Query: 177 VTLDTQK------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +D +         N W  V LREG+NRE+++++E    KV+RLIR+ YGP  L
Sbjct: 182 PVVDYRALGYEAPPGNEWYQVTLREGRNREVRRLWESQGLKVSRLIRVRYGPVSL 236


>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 =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 97/218 (44%), Positives = 134/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I + RV V+G L      V V +   I VDG  V +R++
Sbjct: 3   EKLQKVLARAGHGSRREIEALIKEGRVSVDGKLATLGDRVEVTANMKIRVDGRVVSIRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E+   R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 63  EQEICRVLAYYKPEGELCTRRDPEGRPTVFDRLPRLRGSRWIAVGRLDINTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+DKL  L +G+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDEDKLRQLSRGVQLEDGPASFKSISFQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLTL 220


>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 =  162 bits (410), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 103/236 (43%), Positives = 143/236 (60%), Gaps = 14/236 (5%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNV 54
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G   IL +R  ++V
Sbjct: 60  KAKPVVKASNQPKIEGEKLQKVLARAGQGSRREIETMIASGRVSVEGKIAILGDR--IDV 117

Query: 55  MSTDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVI 109
            S   + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I
Sbjct: 118 HSGVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWI 177

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           +VGRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++ 
Sbjct: 178 AVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLED 237

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 238 GPANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  162 bits (409), Expect = 8e-38,   Method: Compositional matrix adjust.
 Identities = 102/253 (40%), Positives = 152/253 (60%), Gaps = 14/253 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG----VPL 67
           +++ KV+AR G+ SRRE++ +IA  RV+VNG +   AAV   V     +++DG     PL
Sbjct: 3   EKLQKVLARQGLGSRRELDALIAAGRVEVNGKV---AAVGDRVEGPLTVKIDGKVVLTPL 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            +  + R+ +Y+KP G VTT+ DP+ R TVFD+LP     R I VGRLD+NT GLLL T 
Sbjct: 60  SEKPKCRVLMYYKPEGEVTTYKDPEDRPTVFDHLPRPDGGRWIYVGRLDLNTSGLLLFTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  RVY  R +G+V   ++  LK+G++++       +V     +G N
Sbjct: 120 DGELANALMHPSKEIERVYAARIYGEVTDKQIAALKQGVMLEDGKASFDKVVFVGGEGRN 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS-KKI--LR 242
            W  V L+EG+NRE+++++E    +V+RLIRI Y    L   L AG  RE++  +I  LR
Sbjct: 180 QWYHVSLKEGRNREVRRLWEAVGLQVSRLIRIRYAGVDLDNKLRAGKYRELTLSEINNLR 239

Query: 243 EQLGPHLLEEAQV 255
             +G   LE +++
Sbjct: 240 AAVGLKALESSEI 252


>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 =  162 bits (409), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 136/225 (60%), Gaps = 8/225 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 65  ---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
              +P++K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT G
Sbjct: 124 ISLIPVQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSG 182

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+   
Sbjct: 183 LLLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTV 242

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 243 GGTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 287


>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 =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 136/225 (60%), Gaps = 8/225 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 65  ---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
              +P++K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT G
Sbjct: 124 ISLIPVQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSG 182

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+   
Sbjct: 183 LLLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTV 242

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 243 GGTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 287


>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 =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 136/225 (60%), Gaps = 8/225 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 65  ---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
              +P++K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT G
Sbjct: 124 ISLIPVQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSG 182

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+   
Sbjct: 183 LLLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTV 242

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 243 GGTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 287


>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 =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 136/225 (60%), Gaps = 8/225 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 65  ---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
              +P++K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT G
Sbjct: 124 ISLIPVQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSG 182

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+   
Sbjct: 183 LLLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTV 242

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 243 GGTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 287


>gi|240948952|ref|ZP_04753308.1| pseudouridine synthase [Actinobacillus minor NM305]
 gi|240296767|gb|EER47378.1| pseudouridine synthase [Actinobacillus minor NM305]
          Length = 340

 Score =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 98/228 (42%), Positives = 136/228 (59%), Gaps = 8/228 (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  G-----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           G     +P +K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  SR ++VGRLDIN
Sbjct: 112 GHLINLIPTQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWVAVGRLDIN 170

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  G VD+  L  L+KG+ ++       Q+
Sbjct: 171 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGNVDEAMLQRLRKGVQLEDGPANFKQI 230

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 231 KAVGGTGINQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 278


>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 =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/218 (44%), Positives = 133/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V S   + +DG  V L  A
Sbjct: 77  EKLQKVLARAGQGSRREIEAMIAENRVSVDGKMATLGDRIDVRSGVKVRIDGHIVNLMHA 136

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+ +Y+KP G + T  DP+GR+TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 137 QKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTD 196

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       ++      G N 
Sbjct: 197 GELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGPANFKEIKFAGGVGMNQ 256

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR  YG   L
Sbjct: 257 WFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISL 294


>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 =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 96/225 (42%), Positives = 136/225 (60%), Gaps = 8/225 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 88  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 147

Query: 65  ---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
              +P++K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT G
Sbjct: 148 ISLIPVQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSG 206

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+   
Sbjct: 207 LLLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTV 266

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 267 GGTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 311


>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 =  161 bits (408), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 97/232 (41%), Positives = 140/232 (60%), Gaps = 8/232 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDH 59
           ++ +N   +    +++ K++ARAG  SRRE+E +IA  RV V+G I +    V V S+  
Sbjct: 48  IETENKANDKIVGEKLQKILARAGQGSRREIEEVIAAGRVSVDGKIAMLGDRVQVSSSTK 107

Query: 60  IEVDG-----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGR 113
           I +DG     +P +K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+VGR
Sbjct: 108 IRIDGNLVSLIPTQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGR 166

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDINT GLLL T DG LA  L  PS +  R Y VR  G+V+   +  L+KG+ ++     
Sbjct: 167 LDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGEVNDAMIQRLRKGVQLEDGPAN 226

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             Q+      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 227 FKQIKAVGGTGINQWFDVTLTEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 278


>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 =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 100/234 (42%), Positives = 141/234 (60%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K++V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KVKSVVKASNQPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSHEVEREYSVRVFGQVDDAMLARLRKGVQLEDGL 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>gi|301156161|emb|CBW15632.1| 23S rRNA pseudouridylate synthase [Haemophilus parainfluenzae T3T1]
          Length = 336

 Score =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 96/224 (42%), Positives = 137/224 (61%), Gaps = 6/224 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           Q     +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V S   + +DG  
Sbjct: 49  QSTVEGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKMATLGDRIDVHSGVKVRIDGRI 108

Query: 65  VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGL 121
           + L++A++   R+ +Y+KP G + T SDP+GR TVFD LP +  +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 225
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 229 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 272


>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 =  161 bits (407), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 140/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G I      ++V S
Sbjct: 60  KAKPVVRASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGS 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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: Compositional matrix adjust.
 Identities = 97/224 (43%), Positives = 134/224 (59%), Gaps = 6/224 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QSKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 65  VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGL 121
           + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  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 225
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>gi|148828349|ref|YP_001293102.1| methyltransferase [Haemophilus influenzae PittGG]
 gi|148719591|gb|ABR00719.1| predicted methyltransferase [Haemophilus influenzae PittGG]
          Length = 357

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K IV+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPIVKASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPHLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGS 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFAGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 95/225 (42%), Positives = 136/225 (60%), Gaps = 6/225 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG- 64
            Q     +++ KV+ARAG  SRRE+E MIA  RV V+G +      ++V S   + +DG 
Sbjct: 48  CQSTVEGEKLQKVLARAGQGSRREIEAMIADNRVSVDGKMATLGDRIDVHSGVKVRIDGR 107

Query: 65  -VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEG 120
            + L++A++   R+ +Y+KP G + T SDP+GR TVFD LP +  +R I+VGRLDINT G
Sbjct: 108 IINLQQAQKEVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRLNGARWIAVGRLDINTSG 167

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  GQVD   L  L++G+ ++       ++   
Sbjct: 168 LLLFTTDGELANCLMHPSREVEREYSVRVFGQVDDAMLARLRRGVQLEDGPANFKEIKFA 227

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 228 GGIGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 272


>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 =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 100/234 (42%), Positives = 141/234 (60%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K++V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KVKSVVKASNQPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 100/234 (42%), Positives = 141/234 (60%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K++V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KVKSVVKASNQPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>gi|257465549|ref|ZP_05629920.1| pseudouridine synthase [Actinobacillus minor 202]
 gi|257451209|gb|EEV25252.1| pseudouridine synthase [Actinobacillus minor 202]
          Length = 340

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 97/228 (42%), Positives = 136/228 (59%), Gaps = 8/228 (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  G-----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           G     +P +K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R ++VGRLDIN
Sbjct: 112 GHLINLIPTQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWVAVGRLDIN 170

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  G VD+  L  L+KG+ ++       Q+
Sbjct: 171 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGNVDEAMLQRLRKGVQLEDGPANFKQI 230

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 231 KAVGGTGINQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 278


>gi|145635048|ref|ZP_01790754.1| predicted methyltransferase [Haemophilus influenzae PittAA]
 gi|145267656|gb|EDK07654.1| predicted methyltransferase [Haemophilus influenzae PittAA]
          Length = 357

 Score =  160 bits (405), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 140/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G I      ++V S
Sbjct: 60  KAKPVVKASNQPKIEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 140/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G I      ++V S
Sbjct: 60  KAKPVVRASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 100/234 (42%), Positives = 140/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPVVRASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 140/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G I      ++V S
Sbjct: 60  KAKPVVRASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (404), Expect = 3e-37,   Method: Compositional matrix adjust.
 Identities = 95/218 (43%), Positives = 133/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR---- 68
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V+V +T  I +DG  +     
Sbjct: 75  EKLQKILARAGQGSRRELEEVIAAGRVSVDGKIASLGDRVHVNATTKIRIDGTLINLVTA 134

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           + E  R+ +Y+KP G + T +DP+GR+TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 135 QKEICRVLMYYKPEGELCTRADPEGRATVFDRLPRLSGSRWIAVGRLDINTSGLLLFTTD 194

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       Q+      G N 
Sbjct: 195 GDLANRLMHPSHEVEREYSVRVFGQVDDAMLQRLRKGVQLEDGPANFKQIKAVGGTGLNQ 254

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 255 WFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 292


>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 (404), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K IV+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPIVKASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (404), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 95/225 (42%), Positives = 136/225 (60%), Gaps = 8/225 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 65  ---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
              +P++K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT G
Sbjct: 124 ISLIPVQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWIAVGRLDINTSG 182

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL T DG LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+   
Sbjct: 183 LLLFTTDGELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTV 242

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N W  V L +G+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 243 GGTGLNQWFDVTLTKGRNREVRRLWESQGVEVSRLIRIRYGNIKL 287


>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: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K IV+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPIVKASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  160 bits (404), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 97/232 (41%), Positives = 139/232 (59%), Gaps = 8/232 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDH 59
           ++ +N   +    +++ K++ARAG  SRRE+E +IA  RV V+G I      V V S+  
Sbjct: 48  IETENKANDKIVGEKLQKILARAGQGSRREIEEVIAAGRVSVDGKIATLGDRVQVSSSTK 107

Query: 60  IEVDG-----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGR 113
           I +DG     +P +K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+VGR
Sbjct: 108 IRIDGNLVNLIPTQK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGR 166

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDINT GLLL T DG LA  L  PS +  R Y VR  G+V+   +  L+KG+ ++     
Sbjct: 167 LDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGEVNDAMIQRLRKGVQLEDGPAN 226

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             Q+      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 227 FKQIKAVGGTGINQWFDVTLTEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 278


>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 =  160 bits (404), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 98/234 (41%), Positives = 143/234 (61%), Gaps = 5/234 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
             + +R+ KV+A+AG  SRRE+ER I   RV+VNG +  +    V   D + +DG  +  
Sbjct: 2   TMSEERIQKVLAKAGQGSRREMERAIESGRVQVNGEVA-KLGDKVSEKDELRLDGKKISV 60

Query: 69  KAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
           +AE+ R + +Y+KP G + T  DP+GR TVFD LP I   R I+VGRLDINT GLLL TN
Sbjct: 61  EAEKVRRVLIYNKPEGEICTRKDPEGRHTVFDRLPRIPGERWIAVGRLDINTSGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS Q  R Y VR  G V Q+ ++ + +G+ ++        V     KGSN
Sbjct: 121 DGELANRLMHPSHQIEREYAVRVLGDVQQENIDAMCEGVELEDGPAKFTDVQFFDGKGSN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            W  V + EG+NRE+++++E   ++V+RL R+ YG   L + + AG+ +E++KK
Sbjct: 181 LWFHVVIMEGRNREVRRLWESQGFQVSRLKRVRYGSVFLDSDVRAGTWQEMAKK 234


>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 (403), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 89/221 (40%), Positives = 135/221 (61%), Gaps = 5/221 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A+AG+ASRRE+E ++   R+ VNG L       +   D ++++G  +PLR +
Sbjct: 90  PERLQKVLAQAGVASRREIEELVVAGRISVNG-LPASLGQKIGPGDRVKLNGKLIPLRFS 148

Query: 71  ERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
           +R+ R+ +YHKP G + +  DP+GR TVF+ LP +   R ++VGRLD NT GLLL TNDG
Sbjct: 149 QRSPRVLVYHKPEGEIVSRDDPEGRPTVFERLPLLRKGRWLAVGRLDFNTSGLLLFTNDG 208

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  R Y VR  GQ+ +++   L  GI ++      + +     +G N W
Sbjct: 209 DLANRLMHPRYELTREYAVRLLGQLTEEQGQSLVDGIQLEDGPARFLSLVDAGGEGVNHW 268

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V L EG+NRE++++FE     V+RL+R+ YGP +L   L
Sbjct: 269 YRVTLAEGRNREVRRMFEAVGLTVSRLMRVRYGPVELPARL 309


>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 =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 97/224 (43%), Positives = 133/224 (59%), Gaps = 6/224 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QSKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 65  VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGL 121
           + L  A++   R+ +Y+KP G + T SDP GR+TVFD LP +  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 225
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 250 GVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 99/234 (42%), Positives = 138/234 (58%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPVVRASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG    +   + E  R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHTQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGL 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>gi|254361758|ref|ZP_04977893.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093293|gb|EDN74289.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 355

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 96/219 (43%), Positives = 134/219 (61%), Gaps = 8/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-----VPL 67
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  I +DG     +P 
Sbjct: 78  EKLQKILARAGQGSRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLMPA 137

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           +K E  R+ +Y+KP G + T SDP+GRSTVFD LP +  +R I+VGRLDINT GLLL T 
Sbjct: 138 QK-EICRVLMYYKPEGELCTRSDPEGRSTVFDRLPRLSGARWIAVGRLDINTSGLLLFTT 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 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 257 QWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 295


>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 =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 100/234 (42%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K IV+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPIVKASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  + L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDITLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 94/222 (42%), Positives = 134/222 (60%), Gaps = 6/222 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+RV K++ARAG+ SRREVE  I   R+ VNG+ ++       ++D  E+DG  L  +  
Sbjct: 21  PERVQKLLARAGVGSRREVEGWIEAGRLLVNGVPVQ-PGQKASTSDRFELDGKLLDVSSA 79

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VT+  DP+GR TVFD LP +   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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L + L
Sbjct: 200 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRL 241


>gi|309973338|gb|ADO96539.1| 23S rRNA pseudouridylate synthase RluB [Haemophilus influenzae
           R2846]
          Length = 357

 Score =  159 bits (403), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 101/234 (43%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMS 56
           K K IV+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G I      ++V S
Sbjct: 60  KAKPIVKASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  + L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDITLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 95/218 (43%), Positives = 135/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV S   + +DG  + L +A
Sbjct: 47  EKLQKVLARAGQGSRREIESIIAENRVSVDGKIATLGDRINVNSGVKVRIDGNLINLTQA 106

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+ +Y+KP G + T  DP+GR+TVFD LP +  +R I+VGRLDINT GLLL T D
Sbjct: 107 QKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDINTSGLLLFTTD 166

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G VD   LN LKKG+ ++       ++      G N 
Sbjct: 167 GELANRLMHPSREVEREYSVRVFGAVDDAMLNRLKKGVQLEDGPANFKEIKFVGGVGMNQ 226

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 227 WFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 264


>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 =  159 bits (402), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 88/221 (39%), Positives = 132/221 (59%), Gaps = 5/221 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---K 69
           PQR+ K++A AG  SRRE+E +IA  R+ +NG   E  A +V+ +D + +D  PLR   +
Sbjct: 28  PQRLHKLLALAGFGSRREMETLIASGRITINGKTAEVGA-SVVPSDVVRLDSRPLRLPFE 86

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E  ++ LYHKP G + +H DP+ R++VFD LP I + + I++GRLD+NT GLL+ T  G
Sbjct: 87  PELPQVLLYHKPEGEIVSHDDPENRASVFDKLPRIRNGKWIAIGRLDMNTSGLLIFTTSG 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA     P  +  R Y VR  G++ + ++  L  GI +         +     +G+N W
Sbjct: 147 ELANRFMHPRYEVEREYAVRIFGELTEGEMAQLTYGIELDDGPANFDSIRPQGGEGANHW 206

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V LREG+NRE++++FE F   V+RLIR+ +GP  L   L
Sbjct: 207 YEVILREGRNREVRRLFEAFQKPVSRLIRVRFGPVNLPPRL 247


>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 =  159 bits (401), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 93/220 (42%), Positives = 132/220 (60%), Gaps = 4/220 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR- 68
            +P+R+ KV+A AGIASRR+ E +IA  RV VNG ++      V +  D + VDG PLR 
Sbjct: 1   MSPERLQKVLASAGIASRRDCEELIAAGRVTVNGRVVTVPGTRVDLEHDEVLVDGQPLRM 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A+RT + + HKP G+V+T  DP GR TV D L  + +RV  VGRLD+++EGL+LLT+DG
Sbjct: 61  PAKRTYI-MLHKPAGVVSTAEDPHGRPTVVD-LVDVPARVFPVGRLDLDSEGLILLTDDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  + YRV     +  D L   + G++++G       V L        W
Sbjct: 119 ELAYALTHPSFEVEKEYRVLLDRALTPDALRSWRNGVLLEGEMTAPAWVELLETTPEGVW 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           V + LREG+ R+I+ V +   ++V RL+R+  GP QLG L
Sbjct: 179 VRIVLREGRKRQIRAVAKLLGYEVRRLVRVREGPLQLGDL 218


>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 =  159 bits (401), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 85/226 (37%), Positives = 136/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       QV + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQVKIISWDKRKETAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE+S
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELS 226


>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 =  158 bits (400), Expect = 9e-37,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 135/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V ++  I +DG  + ++++
Sbjct: 3   EKLQKVLARAGHGSRREIETIIEAGRVSVDGKVAKLGDRVEVTASMKIRLDGHVLSIKES 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E T  R+  Y+KP G + T SDP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EETVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L KG+ ++        +T    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQIDDEKVKQLSKGVQLEDGPAAFRTITFQGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDL 220


>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 =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 95/219 (43%), Positives = 134/219 (61%), Gaps = 8/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-----VPL 67
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  I +DG     +P 
Sbjct: 78  EKLQKILARAGQGSRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLMPA 137

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           +K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R I+VGRLDINT GLLL T 
Sbjct: 138 QK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLSGARWIAVGRLDINTSGLLLFTT 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 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 257 QWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 295


>gi|253996068|ref|YP_003048132.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982747|gb|ACT47605.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 374

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 89/232 (38%), Positives = 135/232 (58%), Gaps = 17/232 (7%)

Query: 10  NFTP------------QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           NFTP            QR+ K++A AG+ SRR++E +IA  RV VNG + E  A  V   
Sbjct: 21  NFTPLAVDPDAPAAPTQRLHKLLALAGLGSRRDMEELIASGRVTVNGKVAEVGA-GVTEH 79

Query: 58  DHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGR 113
           D + +D  PLR   + E  ++ +YHKP G + +  DP+GR++VFD LP +   + I++GR
Sbjct: 80  DVVRLDSRPLRLPFEPELPQVLIYHKPEGEIVSQDDPEGRASVFDKLPKVKHGKWIAIGR 139

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD+NT GLL+ T  G LA     P  +  R Y VR  G++ + ++  LK+GI ++     
Sbjct: 140 LDMNTSGLLIFTTSGELANRFMHPRYEVEREYAVRIFGELTEGQIAQLKEGIELEDGPAN 199

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              +     +G+N W  V LREG+NRE++++FE F   V+RL+R+ +GP  L
Sbjct: 200 FDSIIPQGGEGANHWYQVILREGRNREVRRLFEAFQLPVSRLMRVRFGPVNL 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 =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +++ KV+ARAG  SRR +E MI Q+R+ ++G I      V+V  +  I +DG  L   E 
Sbjct: 3   EKLQKVLARAGHGSRRAIETMIMQRRISLDGKIATLGDRVDVRQSTKIRLDGRVLAITES 62

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 63  NAAICRVLAYYKPEGELCTLHDPQGRPTVFDRLPKLRTSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  GQ+D+DK+  L KGI ++       +++    +G N 
Sbjct: 123 GELANRLMHPRHEVEREYAVRVFGQIDEDKIKQLNKGIQLEDGPASFHKISFQGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E  + KVNRLIRI YG   L
Sbjct: 183 WYHVTLTEGRNREVRRLWEAVDVKVNRLIRIRYGDINL 220


>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 =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 107/255 (41%), Positives = 149/255 (58%), Gaps = 12/255 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MIA+ RV V+G I      ++V +   I +DG  + L  A
Sbjct: 64  EKLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDGHLINLLHA 123

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+ +Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 124 QKEVCRVLMYYKPEGELCTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTD 183

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+  L+ LKKG+ ++       ++      G N 
Sbjct: 184 GELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGVQLEDGPANFKEIKFAGGVGMNQ 243

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKILRE 243
           W  V L EG+NRE+++++E    +V+RLIR  YG   L  +L  G   E+   +   LRE
Sbjct: 244 WFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDLTNVNYLRE 303

Query: 244 QLGPHLLEEAQVNLD 258
            +G  L  E +  LD
Sbjct: 304 LVG--LPAEVETKLD 316


>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 =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 96/218 (44%), Positives = 132/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+AR+G  SRRE+E +I Q RV V+G I      V+V     I +DG  V +R+ 
Sbjct: 3   EKLQKVLARSGHGSRREIESIIQQGRVSVDGKIATLGDRVDVTRATKIRIDGHVVTVRET 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E T  R+ +Y+KP G + T SDP+GR TVFD LP I  +R I+VGRLD+NT GLLL T D
Sbjct: 63  EETVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGARWIAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V  DK+  L KG+ +         +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLDDGPAAFRSIRHQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG  QL
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQL 220


>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 =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 134/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  + ++++
Sbjct: 29  EKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIKES 88

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 89  EENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 148

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N 
Sbjct: 149 GELANCLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGINQ 208

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 209 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 246


>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 =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 93/213 (43%), Positives = 131/213 (61%), Gaps = 8/213 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
           +++ KV+AR+G+ SRRE+ER I Q RV ++G         V++   IEVDG PL     E
Sbjct: 20  EKLQKVLARSGLGSRREMERWIEQDRVTIDGKPAS-LGDRVVAGQRIEVDGRPLAAGDGE 78

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           +TR  LYHKP G V +  DP+GR TVF+ LP + S R IS+GRLD NT GLLL T DG L
Sbjct: 79  KTRCLLYHKPTGEVCSRKDPEGRRTVFERLPKVKSGRWISIGRLDYNTSGLLLFTTDGEL 138

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSNAW 188
           A  L  PS    R Y VR  G V ++ ++ + +G++++ G+  + D+Q       G NAW
Sbjct: 139 ANALMHPSANIEREYMVRVMGDVTEENISAMLEGVMLEDGVARFTDIQSG--GGDGINAW 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V L EG+NRE+++++E     V+RL R+ YG
Sbjct: 197 YYVVLMEGRNREVRRLWESQGLTVSRLKRVRYG 229


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

 Score =  158 bits (400), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 96/254 (37%), Positives = 140/254 (55%), Gaps = 1/254 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K+I+ AGI SRR  E MI   RV VNG ++ E  +    + 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 AQVNLDAPIYSSET 266
            +  + AP+ SS T
Sbjct: 243 REQRMAAPVKSSTT 256


>gi|52425093|ref|YP_088230.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52307145|gb|AAU37645.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 402

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 110/255 (43%), Positives = 146/255 (57%), Gaps = 12/255 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I Q RV V+G I      V V     I +DG  V L  A
Sbjct: 120 EKLQKVLARAGQGSRREIESIIEQGRVSVDGKIATLGDRVTVHDGLKIRIDGHLVNLTAA 179

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +R   R+ +Y+KP G + T  DP+GR+TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 180 QREVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTD 239

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD   ++ L+KG+ ++        +      G N 
Sbjct: 240 GELANRLMHPSQEVEREYSVRVFGQVDDAMIHRLRKGVQLEDGPANFKAIKAVGGTGLNQ 299

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  QL  TL  G   E+       LRE
Sbjct: 300 WFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIQLMKTLPRGGWEEMDLAKVNYLRE 359

Query: 244 QLGPHLLEEAQVNLD 258
            +G  L  E +  LD
Sbjct: 360 LVG--LPPETETKLD 372


>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 (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 131/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI   R+ V+G I      V V     I +DG  V +R+ 
Sbjct: 3   EKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRET 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
           E +  R+ +Y+KP G + T SDP+GR TVFD LP I   R ++VGRLD+NT GLLL T D
Sbjct: 63  EESVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGYRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFRSIRYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E  + +V+RLIR+ YG  QL
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVDVQVSRLIRVRYGDIQL 220


>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 (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/219 (42%), Positives = 133/219 (60%), Gaps = 8/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-----VPL 67
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG     +P 
Sbjct: 68  EKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLIPA 127

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           +K E  R+ +Y+KP G + T SDP+GR+TVFD LP +  +R ++VGRLDINT GLLL T 
Sbjct: 128 QK-EICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWVAVGRLDINTSGLLLFTT 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 225
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 247 QWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKL 285


>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 =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 97/219 (44%), Positives = 130/219 (59%), Gaps = 11/219 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLR-- 68
           +++ KV+ARAG+ SRRE+E  I + RV VNG    L +R  +     D IE+DG P+   
Sbjct: 3   EKLQKVLARAGLGSRREMENRIREGRVVVNGEVATLGDRVGLE----DQIELDGYPVSVS 58

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
              +  R+ +Y+KP G V T  DP+GR TVFD LP +   R I+VGRLDINT GLLL T 
Sbjct: 59  GAGQNRRVIIYNKPEGEVCTRKDPEGRPTVFDRLPKLRGERWIAVGRLDINTSGLLLFTT 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PST+  R Y VR  GQV  + +  LKKG+++         V     +G N
Sbjct: 119 DGELANRLMHPSTEIDREYLVRVMGQVTDEHIATLKKGVLLDDGMASFSDVVDGGGEGIN 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+NRE+++++E    KVNRL R+ +GP  L
Sbjct: 179 HWFYVCLMEGRNREVRRLWESQGLKVNRLKRVRFGPVFL 217


>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 =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 99/234 (42%), Positives = 139/234 (59%), Gaps = 10/234 (4%)

Query: 2   KDKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMS 56
           K K +V+ +  P    +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S
Sbjct: 60  KAKPVVRASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHS 119

Query: 57  TDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
              + +DG  + L  A++   R+ +Y+KP G + T SDP+GR+TVFD LP +  SR I+V
Sbjct: 120 GVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAV 179

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+ G+ ++   
Sbjct: 180 GRLDINTSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRNGVQLEDGP 239

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               ++      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 ANFKEIKFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 293


>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 =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 96/233 (41%), Positives = 143/233 (61%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPL---R 68
           +++ KV+AR+G+ SRRE+ER I + RV+VNG +       +   D +EVDG   PL    
Sbjct: 4   EKLHKVLARSGVGSRREMERWIKEGRVQVNGQVAT-LGDRISEGDQVEVDGRKTPLIFDN 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           +AER R+ +Y+KP+G + T  DP+GR TVF +LP +   R I++GRLDINT GLLL T D
Sbjct: 63  QAER-RVLIYNKPVGEICTRHDPEGRPTVFRHLPPLKEGRWIAIGRLDINTSGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS Q  R Y VR  G VD+  L  LK G++++        V     +G+N 
Sbjct: 122 GELANALMHPSAQIDREYAVRVLGDVDEAMLQRLKDGVLLEDGMARFTDVQFFDGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
           W    + EG+NRE+++++E    +VNRL R+ +GP  L + + +G+ +E++ K
Sbjct: 182 WYHCVVMEGRNREVRRLWESQEIQVNRLKRVRFGPLFLPSDVRSGTWKELTVK 234


>gi|326692499|ref|ZP_08229504.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           argentinum KCTC 3773]
          Length = 249

 Score =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 134/226 (59%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KVIA+AG+ASRR  E +I Q RV+VNG  ++   + VM  D ++VDG P+   E+ 
Sbjct: 6   QRLQKVIAQAGLASRRGAEELITQGRVQVNGETVKTLGIKVMPHDTVQVDGAPIEGREKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT+SD  GR TV D L  +  RV  VGRLD +T G+LLLTNDG +A  
Sbjct: 66  VYYLMNKPRGVVTTNSDDKGRQTVLDVLEDVPQRVYPVGRLDYDTTGVLLLTNDGVIANQ 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P ++  +VY  +  G    +KL  LK+G+VIQG      +V+++   +    + V V
Sbjct: 126 LMHPKSRVDKVYMAKVEGIATDEKLAPLKRGVVIQGRKTAPARVSVERVDKDKKTSMVRV 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+N ++K + +     V +L R  Y  F L  L +G  R+++
Sbjct: 186 IIHEGRNHQVKNMLQKVGLPVAKLTREQYAFFDLTGLQSGEYRKLT 231


>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 =  158 bits (399), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 131/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG  V +++ 
Sbjct: 3   EKLQKVLARAGHGSRREIESIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKET 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E T  R+ +Y+KP G + T +DPDGR TVFD LP I  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EETVCRVLVYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSHEVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPASFRTICYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITL 220


>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 =  158 bits (399), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 133/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI   RV V+G + +    V V+    I +DG  V ++++
Sbjct: 3   EKLQKVLARAGHGSRREIETMIEAGRVSVDGKIAKLGDRVEVVQGMKIRLDGHVVSIKES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T SDP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EEAVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQIDDDKVKQLSRGVQLEDGPAAFRTISFQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 220


>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 =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 97/235 (41%), Positives = 139/235 (59%), Gaps = 7/235 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ K++ARAG+ SRREVE  I   R+ +NG  +E     V   D I++DG  L  A  
Sbjct: 22  PERIQKLLARAGVGSRREVESWIEAGRLSINGKPVE-PGQKVTVNDRIDLDGKRLDIAAG 80

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VTT  DP+GR TVFD+LP +   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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L + L+ G   E+ +K +
Sbjct: 201 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLSVGKWEELDQKAV 255


>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 =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 135/225 (60%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE ERMI   RV VNG  ++E  A    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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+ R+++++ E  +  V RL R+ YG   +G L  G+ R ++
Sbjct: 183 IHEGRYRQVRRMCEAVSLSVVRLRRVRYGALSMGDLKIGAYRHLT 227


>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 =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 107/256 (41%), Positives = 152/256 (59%), Gaps = 12/256 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +IA+ RV V+G I      +NV +   + +DG  + L +A
Sbjct: 41  EKLQKVLARAGQGSRREIEAIIAENRVSVDGKIATLGDRINVYAGVKLRIDGHLINLTQA 100

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+ +Y+K  G + T  DP+GR+TVFD LP +  +R I+VGRLDINT GLLL T D
Sbjct: 101 QKEVCRVVMYYKAEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDINTSGLLLFTTD 160

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       ++ +    G N 
Sbjct: 161 GELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGPANFKEIKVVGGVGMNQ 220

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+       LRE
Sbjct: 221 WFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMELADVNYLRE 280

Query: 244 QLGPHLLEEAQVNLDA 259
            +G  L  E +  L A
Sbjct: 281 LVG--LPPETETKLGA 294


>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 =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 93/218 (42%), Positives = 131/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI   RV V+G + +    V V     I +DG  V ++++
Sbjct: 3   EKLQKVLARAGHGSRREIEAMIDAGRVSVDGKIAKLGDRVEVNPAMKIRMDGHVVSVKES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + THSDP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EEAVCRVLAYYKPEGELCTHSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P+ +  R Y VR  GQ D D +  LKKG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPNREVEREYAVRVFGQTDDDSVKQLKKGVQLEDGPAAFRTIDFQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIAL 220


>gi|229058206|ref|ZP_04196594.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228720070|gb|EEL71654.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 136/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  DK+ +L++G+ ++       QV + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGDKIRMLERGVALEDGKTAPAQVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELT 226


>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 =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 134/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V ++  I +DG  V ++++
Sbjct: 3   EKLQKVLARAGHGSRREIETIIEAGRVSVDGKIAKLGDRVEVTASMKIRLDGHVVSIKES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T SDP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EEEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L KG+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSKGVQLEDGPAAFRTISFQGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDL 220


>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 =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 95/241 (39%), Positives = 141/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG    +   +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKP-AKLGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKSKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLAKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L+ G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/217 (42%), Positives = 131/217 (60%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +R+ K++AR G+ SRRE+E  I   RV+VNG+  +     V   D + +DG P+     +
Sbjct: 3   ERLQKILARGGLGSRREIEAWIKAGRVRVNGVPAQ-LGDKVSVKDRVTIDGRPISPKRLQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
              +++ +YHKP G V +  DP+GR  VF +LP     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 225
             V LREG+NRE+++++E    +V+RLIRI +GP +L
Sbjct: 182 YHVILREGRNREVRRLWESQGVRVSRLIRIRFGPIRL 218


>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 =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 134/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  + ++++
Sbjct: 29  EKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIKES 88

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 89  EENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 148

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N 
Sbjct: 149 GELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGINQ 208

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 209 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 246


>gi|271500649|ref|YP_003333674.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344204|gb|ACZ76969.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 296

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI   R+ V+G I      V V     I +DG  V +R+ 
Sbjct: 3   EKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRET 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
           E    R+ +Y+KP G + T SDP+GR TVFD LP I   R ++VGRLD+NT GLLL T D
Sbjct: 63  EEAVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGYRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFRAIRYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG  QL
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQL 220


>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 =  157 bits (397), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/241 (39%), Positives = 141/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG    +   +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKP-AKLGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLAKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L+ G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 90/240 (37%), Positives = 139/240 (57%), Gaps = 5/240 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--- 64
           +EN    R+ K IA +G+ASRR  E M+ + RVKVNG+++    + V  TD IEVDG   
Sbjct: 19  EENQIRMRLQKAIALSGLASRRRAEEMMTEGRVKVNGVVVTELGMKVCGTDTIEVDGKTV 78

Query: 65  --VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             + ++  E    ++ +KP+G++T+  DP GR TV D L  +  RV  VGRLD +T G+L
Sbjct: 79  QSLEVKGKENKVYYMLNKPVGVITSLRDPQGRKTVRDLLGDVKERVYPVGRLDYDTSGIL 138

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG LA  L  P     ++YRV+   ++    +  L+KG++++       +V    Q
Sbjct: 139 LLTNDGDLAYRLTHPKFGVSKIYRVQTGSRIPPKSIEQLEKGLLLEDGWTAPAKVHRLPQ 198

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             ++  V + + EG+NR+I+++FE   + V RL R S+GP   G L  G  R +S+K +R
Sbjct: 199 GQNDHIVEITIHEGRNRQIRRMFERIGYPVQRLHRKSFGPLFTGELAPGGHRRLSQKEIR 258


>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 =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/241 (39%), Positives = 141/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG    +   +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKP-AKLGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQEALNNLLKGVMLDDGLAKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L+ G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLAMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>gi|332993790|gb|AEF03845.1| pseudouridine synthase [Alteromonas sp. SN2]
          Length = 298

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 96/222 (43%), Positives = 130/222 (58%), Gaps = 11/222 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAER 72
           +++ KV+A  G+ SRRE+ER I Q RV VNG L       V  T  I VDG  L R+ E+
Sbjct: 3   EKLQKVLANQGLGSRREMERWIEQGRVSVNGTLAT-LGDRVDETGQIRVDGHLLSRQTEQ 61

Query: 73  --TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
              R+ +Y+KP G + +  DP+GR TVFD LP+I   R I+VGRLD+NT GLLL TNDG 
Sbjct: 62  PVCRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRMGRWIAVGRLDMNTSGLLLFTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQK 183
           LA  L  P  +  R Y VR  G V    LN LKKG+ ++          G +      ++
Sbjct: 122 LANRLMHPKCEVEREYAVRVFGDVTHQTLNTLKKGVQLEDGEAKFLSISGKVAPPGSEEE 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             N W  V L+EG+NRE+++++E    +V+RLIR+ YGP  L
Sbjct: 182 SMNRWFNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPMDL 223


>gi|322833321|ref|YP_004213348.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321168522|gb|ADW74221.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 439

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/220 (43%), Positives = 128/220 (58%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRREVE MI   RV V+G    L +R  V V     I +DG  L   
Sbjct: 151 EKLQKVLARAGHGSRREVEAMIQAGRVSVDGKISTLGDR--VEVTGGTKIRLDGHVLSVM 208

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T
Sbjct: 209 ESQDTVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKMRGSRWIAVGRLDVNTSGLLLFT 268

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        +     +G 
Sbjct: 269 TDGELANRLMHPSREVEREYAVRVFGQVDDEKIKQLSRGVQLEDGPAAFRSIKFQGGEGL 328

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 329 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLNL 368


>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 =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 133/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  + ++++
Sbjct: 32  EKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKES 91

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E T  R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 92  EETVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 151

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +     +G N 
Sbjct: 152 GELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTIKFQGGEGINQ 211

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 212 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 249


>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 =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 134/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  + ++++
Sbjct: 29  EKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIKES 88

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 89  EENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 148

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N 
Sbjct: 149 GELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGINQ 208

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 209 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 246


>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 =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 95/221 (42%), Positives = 131/221 (59%), Gaps = 6/221 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+ARAG+ SRRE+E +I++ RV VNG +       V + D I VDG    VP   
Sbjct: 3   EKLQKVLARAGVGSRREMETVISEGRVSVNGKVAT-LGDRVEAKDVIRVDGHQISVPTLN 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G V T  DP+GR TVFD LP I  SR ++VGRLD+NT GLLL T DG
Sbjct: 62  DVICRVLAYHKPEGEVCTRHDPEGRPTVFDRLPRIKDSRWVAVGRLDVNTSGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V +  L  L+ G+ ++       ++T    +G N W
Sbjct: 122 ELANRLMHPSHEVEREYAVRVFGEVTEGMLQKLRHGVQLEDGPAKFDKITAGGGEGLNQW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V L EG+NRE+++++E    +V+RL+RI YG  +L   L
Sbjct: 182 FNVTLCEGRNREVRRLWESLEVQVSRLMRIRYGDIKLDKTL 222


>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 =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 92/220 (41%), Positives = 128/220 (58%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKA 70
           +++ KV+AR G+ SRR++E  I   RV++N    +R A     V S D + VDG PLR  
Sbjct: 3   EKLQKVLARHGLGSRRQMEAWIRAGRVQIN----DRPATIGDRVTSRDRLSVDGKPLRVP 58

Query: 71  E----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
                R R+  YHKP G + T  DP+GR TVFD LP +  SR ++VGRLD+NTEGLLL T
Sbjct: 59  SWVRPRLRVLRYHKPAGELATRQDPEGRPTVFDRLPRLRGSRWVAVGRLDLNTEGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P  +  RVY VR  G +  ++   L  G+ ++      + +     +GS
Sbjct: 119 NDGDLANALMHPRAELERVYAVRVLGSLSDEQKAALLAGVELEDGPARFLAIEEAGGEGS 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE++++    +  V+RLIRI YGP  +
Sbjct: 179 NRWYHVSLAEGRNREVRRLLAAVHLSVSRLIRIRYGPIDM 218


>gi|327480926|gb|AEA84236.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 375

 Score =  157 bits (396), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 102/244 (41%), Positives = 146/244 (59%), Gaps = 13/244 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+AR GIASRR+VE+ I + RVKVNG +       V S D I VDG  L++ E +
Sbjct: 15  EKLQKVLARLGIASRRDVEKWIVEGRVKVNGAVAT-LGQRVDSHDAIAVDGRLLKREETS 73

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + T +DP+GR TVFD LP     R I++GRLDINT GLLL T DG
Sbjct: 74  QVVRRVLIYNKPDGEICTRNDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDG 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS +  R Y VR  G+VD + +  LK G++++     + D+Q     + G N
Sbjct: 134 ELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKTGVMLEDGPARFTDIQEAPGGE-GFN 192

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSK---KILR 242
            W    + EG+NRE+++++E     V+RL R+ +GP F    L  G  RE+S+    IL 
Sbjct: 193 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLPMGRWREMSQAEVDILS 252

Query: 243 EQLG 246
           E++G
Sbjct: 253 EEVG 256


>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 =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 90/215 (41%), Positives = 125/215 (58%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           ++ KV+A  G+ SRR++E +I Q RV VNG L       +  TD + ++G P+ +  +T 
Sbjct: 198 KLHKVLADVGMGSRRDMEDLIIQGRVSVNG-LPAHIGQRIGPTDQVRINGKPVHRKIQTK 256

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
             R+ +YHKP G + + SDP+GR TVFD LP     R I+VGRLD NTEGLLL T  G L
Sbjct: 257 PPRVIMYHKPAGEIVSQSDPEGRPTVFDRLPKPRQGRWIAVGRLDFNTEGLLLFTTSGEL 316

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     R Y VR  G + Q+   LLK GI +       +++ +   +G+N W  
Sbjct: 317 ANRLMHPRYGVEREYAVRILGDLSQENTALLKSGITLDDGQAKFLRLAMGGGEGANRWYH 376

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V L EG+NRE++++FE     V+RLIR  YG F L
Sbjct: 377 VALSEGRNREVRRMFEAVGHTVSRLIRTRYGIFLL 411


>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 =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 132/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI+  RV V+G L      V   ++  I +DG  VP+ ++
Sbjct: 3   EKLQKVLARAGHGSRREIETMISAGRVSVDGKLATLGDRVEPAASLKIRIDGHVVPVSES 62

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  ISEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G VD DK+ LL +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGAVDDDKIKLLSRGVQLEDGPAAFKTLKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRIRYGDIDL 220


>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 =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 95/241 (39%), Positives = 141/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG    +   +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKP-AKLGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLGKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L+ G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/235 (40%), Positives = 144/235 (61%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ K +A  G+ SRR +E +I Q+++ VN   ++   + V   + I ++G  +  + AE
Sbjct: 15  ERIQKFLANMGMGSRRSIEELIKQKKITVNQKPIDLGHM-VYGNEIIHINGRRIYFKNAE 73

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           +  +RL +YHKP G + +HSDP  + TVF  LP + + + IS+GRLDINT GLLL+TNDG
Sbjct: 74  KRESRLIIYHKPEGEIVSHSDPKHQKTVFQKLPKVKNGKWISIGRLDINTSGLLLITNDG 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  +  PS Q  R Y VR  G+V ++ +N ++KG+ +  G+ + D        +G+N 
Sbjct: 134 KLANHMMHPSQQIDREYSVRILGEVTEEIINNIRKGVKLDDGVAHVDT-FEHTGGEGANQ 192

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           W  + L+EG+NREI+++ E  N KV+RLIR  YGP  L + L  G   E+ KK L
Sbjct: 193 WFRIILKEGRNREIRRLVESQNLKVSRLIRTRYGPLNLPSHLKRGQFMELEKKNL 247


>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 =  156 bits (395), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E MI+  RV V+G L      V+   +  I VDG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIETMISAGRVSVDGKLATLGDRVDSSPSIKIRVDGHLVSVAES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
            AE  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  TAEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G +D DK+  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGAIDDDKIRQLSRGVQLEDGPASFKTLKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W TV L EG+NRE+++++E    +V+RLIR  YG  QL
Sbjct: 183 WYTVTLTEGRNREVRRLWESVGVQVSRLIRTRYGDIQL 220


>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 =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 95/220 (43%), Positives = 133/220 (60%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G    L +R  V V     I +DG  V ++
Sbjct: 3   EKLQKVLARAGHGSRREIEGIIQAGRVSVDGKVATLGDR--VEVTKATKIRIDGHVVTVK 60

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           + E T  R+ +Y+KP G + T +DPDGR TVFD LP I  SR ++VGRLD+NT GLLL T
Sbjct: 61  ETEETVCRVLVYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPAAFRTIRYQGGEGL 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITL 220


>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 =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 133/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  + ++++
Sbjct: 35  EKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKES 94

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 95  EEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 154

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +T    +G N 
Sbjct: 155 GELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTITFQGGEGINQ 214

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 215 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 252


>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 =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 134/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  + ++++
Sbjct: 3   EKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIKES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 220


>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 =  156 bits (394), Expect = 5e-36,   Method: Compositional matrix adjust.
 Identities = 88/225 (39%), Positives = 132/225 (58%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE ER I + RV VNG ++ E  +      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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+ R+++++ E  +  V RL R+ YG   LG L  G  R +S
Sbjct: 183 IHEGRYRQVRRMCEAVSLSVVRLRRVRYGAVSLGDLKPGEYRPLS 227


>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 =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI   R+ V+G I      V V     I +DG  V +R+ 
Sbjct: 3   EKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRET 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
           E    R+ +Y+KP G + T SDP+GR TVFD LP I   R ++VGRLD+NT GLLL T D
Sbjct: 63  EEAVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRIQGYRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V  DK+  L KG+ +         +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLDDGPAAFRSIRYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG  QL
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQL 220


>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 =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 93/218 (42%), Positives = 131/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  V +++ 
Sbjct: 3   EKLQKVLARAGHGSRREIEGIIQAGRVSVDGKVATLGDRVEVTKATKIRIDGHVVTVKET 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E T  R+ +Y+KP G + T +DPDGR TVFD LP I  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EETVCRVLVYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPASFRTIRYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITL 220


>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 =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 92/216 (42%), Positives = 131/216 (60%), Gaps = 4/216 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VP 66
           E    +++ KVIAR G+ASRRE E  I+  RV+VNG +       V + D I VDG  + 
Sbjct: 7   EKAQGEKLQKVIARQGLASRREAEEWISGGRVRVNGKVAH-LGDRVTAEDKISVDGHKIA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           +  AE T + +Y+KP G VT+  DP+GR TVF  LP + S 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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           N W  V L+EG+NRE+++++E     V+RL R+ YG
Sbjct: 186 NRWFHVVLQEGRNREVRRLWESQGVTVSRLKRVRYG 221


>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 =  155 bits (393), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 95/218 (43%), Positives = 132/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG+ SRREVE +IA  RV VNG +      V V +   I VDG  V L  A
Sbjct: 17  EKLQKVLARAGVGSRREVETIIAAGRVSVNGKIASLGDRVEVKNDTKIRVDGGLVSLIAA 76

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
            +   R+ +Y+KP G + T  DP+GR+TVF+ LP I  +R +SVGRLDINT GLLL T D
Sbjct: 77  RKDICRVLMYYKPEGELCTRHDPEGRATVFERLPQISNARWVSVGRLDINTSGLLLFTTD 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G V +  L  L+KG+ ++       +++    +G N 
Sbjct: 137 GELANRLMHPSKEVEREYSVRVFGHVTEQMLAKLRKGVQLEDGPASFKKISAQGGQGMNQ 196

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W +V L EG+NRE+++++E    +V+RLIR  YG   L
Sbjct: 197 WFSVTLTEGRNREVRRLWESQGIQVSRLIRTRYGNIDL 234


>gi|227326052|ref|ZP_03830076.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 294

 Score =  155 bits (393), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 116/302 (38%), Positives = 165/302 (54%), Gaps = 17/302 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG  V +++ 
Sbjct: 3   EKLQKVLARAGHGSRREIEVIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKET 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E +  R+ +Y+KP G + T +DPDGR TVFD LP I  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EESVCRVLMYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD +K+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLEDGPASFRTIRYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W  V L EG+NRE+++++E    +V+RLIR+ YG     TL  G  R    ++  EQL  
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDI---TLPKGIPRGGWTEMPLEQL-- 237

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           + L E  V L A   S   + R+R  + +   +   R  K  SQ N  S   +  +P  +
Sbjct: 238 NYLREL-VQLPAETVSKLPVERERRRVKA---NQIRRAVKRHSQIN--SAPARRTSPKPK 291

Query: 308 RN 309
           RN
Sbjct: 292 RN 293


>gi|52143877|ref|YP_082953.1| pseudouridylate synthase [Bacillus cereus E33L]
 gi|51977346|gb|AAU18896.1| pseudouridylate synthase [Bacillus cereus E33L]
          Length = 242

 Score =  155 bits (393), Expect = 7e-36,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 137/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G++++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>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 =  155 bits (393), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 135/226 (59%), Gaps = 3/226 (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 KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++        V + +  ++   A V +
Sbjct: 121 LMHPKYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAHVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>gi|229160522|ref|ZP_04288517.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622932|gb|EEK79763.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 136/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLERGVALEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>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 =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 137/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G++++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>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 =  155 bits (392), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+A AG  SRRE+E MI + RV V+G L      V V     I VDG  V +R++
Sbjct: 3   EKLQKVLANAGHGSRREIEAMIKEGRVSVDGKLATLGDRVEVTPAMKIRVDGRVVSIRES 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLDINT GLLL T D
Sbjct: 63  TESVCRVLAYYKPEGELCTRRDPEGRPTVFDRLPKLRGSRWIAVGRLDINTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDEKIRQLSRGVQLEDGPASFKTISFQGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLPL 220


>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 =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 97/228 (42%), Positives = 135/228 (59%), Gaps = 16/228 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+A AG+ SRRE+E+ I+  RV VNG    L +RAA +    D I VDG  + + 
Sbjct: 3   EKLQKVLATAGLGSRRELEKWISAGRVSVNGSIAKLGDRAAAD----DRILVDGRLIKIV 58

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             +  R+ +Y KP G V T SDPDGR TVFD LP +   R I++GRLDINT GLLL TN 
Sbjct: 59  TDDSPRVLMYSKPEGEVCTTSDPDGRPTVFDRLPRLSRGRWIAIGRLDINTSGLLLFTNH 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G LA  L  PS +  R Y  R HG+VD+  +  L  G+V++        V     +    
Sbjct: 119 GELANRLMHPSYEVQREYMARIHGEVDEAMIKRLTDGVVLEDGLASFKSVKAQHARSSED 178

Query: 184 --GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             G N W  V L EG+ RE+++++E  + +VNRL RISYGP +L +++
Sbjct: 179 LGGRNRWFKVILAEGRTREVRRLWESQDVEVNRLKRISYGPIELPSIV 226


>gi|300121522|emb|CBK22041.2| Pseudouridine synthase [Blastocystis hominis]
          Length = 271

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 93/228 (40%), Positives = 129/228 (56%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IAR+G+ SRRE ER I   RV +NG ++   A+NV   D I VD  PL   +RTR
Sbjct: 12  RIAKRIARSGVCSRREAERWIEMGRVTLNGKVITSPAINVTQQDIIHVDNKPLSPIQRTR 71

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + +K  G + T SD   R T+FD L    +   ++ VG+LD +TEGLLLLTNDG  AR
Sbjct: 72  VIIANKLDGELVTTSDSQHRLTIFDRLRKTGLECHIMPVGQLDFHTEGLLLLTNDGDYAR 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NA---W 188
            LE PS    R YR + +G+ D  ++  L    +I G  Y    V  D  + S NA   W
Sbjct: 132 YLEHPSNAIPRRYRAKVYGRWDDSRVLALSHSNIIDGKRYKGCLVKRDLDRSSANAMEHW 191

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            T+ + EGK  E+K +  F    V +L+R ++G + LG L+ G  REV
Sbjct: 192 CTIQVTEGKYHEVKNLLGFVGLNVEKLVRTNFGAYSLGNLVPGEFREV 239


>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 =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 134/226 (59%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K E  
Sbjct: 4   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVNNIPLEKEEPI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G++++ SD  GR  V D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 64  YFLLY-KPTGVISSVSDDKGRKVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANI 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG+V++       +V + +  ++   A V +
Sbjct: 123 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVVLEDGKTAPARVKILSWDKRKEMAIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    KV +L R  Y   ++G+L  G  RE+S
Sbjct: 183 TIHEGRNRQVRRMFEALGCKVMKLKRERYAFLEVGSLRPGDARELS 228


>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 =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 94/218 (43%), Positives = 132/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI+  RV V+G L      V   ++  I +DG  VP+ ++
Sbjct: 3   EKLQKVLARAGHGSRREIETMISAGRVSVDGKLATLGDRVEPGASLKIRIDGHVVPVSES 62

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T SDP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  ISEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G VD +K+ LL +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGAVDDEKIKLLSRGVQLEDGPAAFKTLKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRIRYGDIDL 220


>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 =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 136/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>gi|221134960|ref|ZP_03561263.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Glaciecola sp. HTCC2999]
          Length = 331

 Score =  155 bits (392), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 93/217 (42%), Positives = 133/217 (61%), Gaps = 7/217 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           ++ KV+A  G+ SRRE+E  I Q R+ VNG +       V  +D I VDG  L+   KA 
Sbjct: 4   KLQKVLANQGVGSRREMETWIEQGRISVNGTIAT-LGDRVEPSDQIRVDGHLLKRDQKAP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
             R+ +Y+KP G + + +DP GR TVFD LP+I S R I+VGRLD+NT GLLL TNDG L
Sbjct: 63  VCRVLMYNKPEGELCSRTDPLGRQTVFDRLPNIQSGRWIAVGRLDLNTAGLLLFTNDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSNAW 188
           A  L  P  +  R Y VR  G+V+   L LL+ G+ ++ G+  +  +    + ++  NAW
Sbjct: 123 ANRLMHPRHEVEREYAVRVFGEVEPKTLKLLESGVELEDGLAKFTKIIARPNEEESINAW 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE+++++E    +V+RLIR+ YGP  L
Sbjct: 183 YNVSLSEGRNREVRRLWESQGVQVSRLIRLRYGPLSL 219


>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 =  155 bits (392), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 76/224 (33%), Positives = 128/224 (57%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++A     SRRE+E +I+ Q++K+N  ++   A  V   D I ++G  +   ++  
Sbjct: 7   RIAKLLASYNYGSRREIENLISNQKIKLNNKIILTPATFVNEEDKITINGKKVLFKKKIS 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   +KP  ++ + +  D R  +++ L S +   I  GRLD  +EGL++LTND  L R L
Sbjct: 67  ILKLYKPKNVICSKNKQDKREIIYEILDSKYKNFIFAGRLDFKSEGLIILTNDSSLTRNL 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP  ++ R Y VR  G  + +KL +  +G  I GI Y      + ++   N  + + L+
Sbjct: 127 ELPKNKFERKYEVRIFGDFNVEKLKIKSRGTKINGIQYKPFDFKIKSKIKKNTLIEMNLK 186

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           EGK  EI+ +F+  N +VN+L R+SYGPF+L  +L G  ++ SK
Sbjct: 187 EGKKNEIRNIFKELNLQVNKLKRVSYGPFKLDNMLPGDLKKPSK 230


>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 =  155 bits (392), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 100/249 (40%), Positives = 146/249 (58%), Gaps = 13/249 (5%)

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  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAITVDGKLIKRVEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD D ++ LK G++++    
Sbjct: 120 RLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDDMVDRLKAGVMLEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ +GP  L + L 
Sbjct: 180 KFTDIQKAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGVVVSRLKRVRFGPVFLNSDLP 238

Query: 230 AGSTREVSK 238
            G  RE+S+
Sbjct: 239 MGRWREMSQ 247


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 97/236 (41%), Positives = 136/236 (57%), Gaps = 12/236 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR 68
           F  +++ KV+A AGI SRR++E  IA+ R+ VNG   E A V   V  +D I  DG  +R
Sbjct: 51  FANEKLHKVLADAGIGSRRDMEERIAEGRISVNG---EPAHVGQRVTPSDVIRFDGRIVR 107

Query: 69  KA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLL 122
           ++     +  ++ +YHKP G + +  DP+GR TVFD+LP I  +R I+VGRLD NTEGLL
Sbjct: 108 RSALENNDVPKVLIYHKPAGEIVSKDDPEGRPTVFDHLPRIGGARWIAVGRLDFNTEGLL 167

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T+ G LA  L  P  +  R Y VR  G +  +  + L KGI +         +     
Sbjct: 168 LFTDSGNLANFLMHPRHEIEREYAVRVQGTMSPEAKDKLLKGIKLDDGIAKFTTLEEGGG 227

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           KG N W  V L EG+NRE++++FE     V+RLIR+ YG  +L + L  G TR +S
Sbjct: 228 KGFNRWYNVTLSEGRNREVRRMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMS 283


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/220 (41%), Positives = 130/220 (59%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E +I Q RV V+G    L +R  V V     I +DG  L   
Sbjct: 28  EKLQKVLARAGHGSRREIETIIQQGRVSVDGKISTLGDR--VEVTQATKIRLDGHLLSIT 85

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP +  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 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 206 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 245


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 136/226 (60%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   KRLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 95/219 (43%), Positives = 131/219 (59%), Gaps = 11/219 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E  I + RV VNG    L +R  V    TD I++DG  ++  
Sbjct: 3   EKLQKVLARAGQGSRREMENRIREGRVLVNGDVATLGDRVKV----TDTIKLDGYEVKVT 58

Query: 71  ERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
           E     R+ +Y+KP G V T  DP+GR TVFD LP +   R I+VGRLDINT GLLL T 
Sbjct: 59  EAGASRRVIIYNKPEGEVCTRKDPEGRPTVFDKLPKLRGERWIAVGRLDINTSGLLLFTT 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PST+  R Y VR  G+++ D +  LKKG+++         +     +G N
Sbjct: 119 DGELANKLMHPSTEIDREYLVRVMGEINDDHIETLKKGVLLDDGMANFTDIVDGGGEGIN 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V + EG+NRE+++++E    KVNRL R+ +GP  L
Sbjct: 179 RWFYVCVMEGRNREVRRLWESQGVKVNRLKRVRFGPVFL 217


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/215 (41%), Positives = 126/215 (58%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           ++ KV+A  G+ SRR++E +I Q RV VNG L      ++  TD + ++G P+ +  +T 
Sbjct: 30  KLHKVLADVGMGSRRDMEDLIIQGRVSVNG-LPAHIGQSIGPTDQVRINGKPVHRKIQTK 88

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
             R+ +YHKP G + + SDP+GR TVFD LP     R I+VGRLD NTEGLLL T  G L
Sbjct: 89  PPRVIMYHKPAGEIVSQSDPEGRPTVFDRLPKPRQGRWIAVGRLDFNTEGLLLFTTSGEL 148

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     R Y VR  G + Q+   LLK GI +       +++ +   +G+N W  
Sbjct: 149 ANRLMHPRYGVEREYAVRILGDLSQENTVLLKSGITLDDGQAKFLRLAIGGGEGANRWYH 208

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V L EG+NRE++++FE     V+RLIR  YG F L
Sbjct: 209 VALSEGRNREVRRMFEAVGHTVSRLIRTRYGIFLL 243


>gi|217970106|ref|YP_002355340.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217507433|gb|ACK54444.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 379

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 90/224 (40%), Positives = 136/224 (60%), Gaps = 11/224 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A+AG+ASRRE+E  +   R+ VNG L       +   D ++V+G  VPLR  
Sbjct: 116 PERLQKVLAQAGVASRREIEEWVVAGRISVNG-LPASLGQKIGPGDRVKVNGKLVPLRFT 174

Query: 71  ERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
           +R+ R+ +YHKP G + +  DP+GR TVF+ LP +   R ++VGRLD NT GLLL TNDG
Sbjct: 175 QRSPRVLIYHKPEGEIVSRDDPEGRPTVFERLPILRKGRWLAVGRLDFNTSGLLLFTNDG 234

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGS 185
            LA  L  P  +  R Y VR  G++ ++++  L  GI ++    G  +  L   +  +G+
Sbjct: 235 DLANKLMHPRYELEREYAVRILGELTEEQVKSLTDGIQLED---GPAKFNLLRDEGGEGA 291

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           N W  V + EG+NRE++++FE     V+RL+R+ YG  +L   L
Sbjct: 292 NHWYRVTISEGRNREVRRMFEAVGLTVSRLMRVRYGSVELPARL 335


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/217 (42%), Positives = 134/217 (61%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +++ KV+ARAG+ SRRE+E+ I   RV VNG +  +    V  TD I VDG  ++   KA
Sbjct: 7   EKLQKVLARAGVGSRREMEKYIDANRVSVNGKVA-KLGDRVEETDSIRVDGHTVKIEEKA 65

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ +Y+KP G ++T  DP+GR TVFD LP I   R I+VGRLDINT GL+L TNDG
Sbjct: 66  DRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGERWIAVGRLDINTAGLMLFTNDG 125

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y  R  G+V ++ +  L +G+ ++      + V     +G N W
Sbjct: 126 ELANRLMHPSYEVEREYSARVFGEVTKETIKNLTRGVELEDGPAKFLTVNPMGGEGINRW 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE++++++    +V+RLIRI YG  +L
Sbjct: 186 YNVTLNEGRNREVRRLWQSQEVEVSRLIRIRYGKLEL 222


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/220 (41%), Positives = 130/220 (59%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E +I Q RV V+G    L +R  V V     I +DG  L   
Sbjct: 28  EKLQKVLARAGHGSRREIEAIIQQGRVSVDGKISTLGDR--VEVTQATKIRLDGHLLSIT 85

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP +  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 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 206 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 245


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 97/221 (43%), Positives = 131/221 (59%), Gaps = 6/221 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+AR G+ SRR +E  IA  RV VNG  + +    V + D I VDG  LR     
Sbjct: 3   EKLQKVLARFGLGSRRLMEEWIAAGRVVVNG-QIAKLGDRVTAQDKIAVDGETLRIPSWV 61

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
             R R+  YHKP G +TT +DP GR TVFD LP +  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V L EG+NRE++++FE     V+RLIR+ YG  ++  LL
Sbjct: 182 YHVTLAEGRNREVRRLFEAVGLTVSRLIRVRYGVVEMPRLL 222


>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 =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 132/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  + ++++
Sbjct: 28  EKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKES 87

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 88  EEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 147

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +     +G N 
Sbjct: 148 GELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTIKFQGGEGINQ 207

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 208 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 245


>gi|297538013|ref|YP_003673782.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257360|gb|ADI29205.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 374

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 138/233 (59%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---A 70
           QR+ K++A AG+ SRR++E +I+  RV VNG    +    V   D + +D  P++    A
Sbjct: 37  QRLHKLLALAGLGSRRDMETLISSGRVTVNGAPATQGQ-GVTQFDTVRLDSRPVKLPFIA 95

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
           E  ++ +YHKP G + +  DP+GR++VFD LP + + + I++GRLD+NT GLL+ T  G 
Sbjct: 96  ELPQVLIYHKPEGEIVSQDDPEGRASVFDKLPKVKNGKWIAIGRLDMNTSGLLIFTTSGE 155

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA     P  +  R Y VR  G++ + ++  LK+GI ++        ++    +G+N W 
Sbjct: 156 LANRFMHPRYEVEREYAVRIFGELTEGQMTQLKEGIELEDGPANFDSISAQGGEGANHWY 215

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL------GTLLAGSTREV 236
            V LREG+NRE++++FE F   V+RL+R+ +GP  L      GT+L    +EV
Sbjct: 216 QVILREGRNREVRRLFEAFQLPVSRLMRVRFGPVNLPPRVKRGTMLKLEQKEV 268


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

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 86/232 (37%), Positives = 132/232 (56%), Gaps = 1/232 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
           T +R+ KV+A  G+ASRRE E  I   RV+VNG ++    + V    D I+VDG PL   
Sbjct: 9   TAERLQKVLAAHGLASRREAEDWIRAGRVQVNGTVVTELGLRVEEGKDVIQVDGKPLTVR 68

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ER + +L +KP G VTT  DP+GR TV D L  + +R+  VGRLD +TEGLLLLTNDG L
Sbjct: 69  ERHQYFLLYKPRGFVTTRKDPEGRPTVIDLLKDVPARIYPVGRLDQDTEGLLLLTNDGEL 128

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y  R  G V    +    +G++++       +V +  ++G   W+ 
Sbjct: 129 AYRLTHPKYGVEKTYHARMRGNVPDPVIKAFAEGVMLEDGLTAPAKVKVLDREGGATWIE 188

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++++ +   + V  L R+S+GP  +  L  G+ R +  + +R
Sbjct: 189 LTIHEGRNRQVRRMGDAVGYPVVHLTRVSFGPLTISGLKPGAYRPLKPQEVR 240


>gi|187923621|ref|YP_001895263.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187714815|gb|ACD16039.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 626

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 135/228 (59%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 202 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRIMPTDQVR 258

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR++VFDNLP +  ++ ++VGRLD N
Sbjct: 259 INGKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRASVFDNLPPMKTAKWLAVGRLDFN 318

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ ++      +++
Sbjct: 319 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELEDGPANFLRI 378

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 379 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 426


>gi|227111426|ref|ZP_03825082.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 294

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 93/218 (42%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG  V +++ 
Sbjct: 3   EKLQKVLARAGHGSRREIEGIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKET 62

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E +  R+ +Y+KP G + T +DPDGR TVFD LP I  SR ++VGRLD+NT GLLL T D
Sbjct: 63  EESVCRVLMYYKPEGELCTRNDPDGRPTVFDRLPKIQGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD +K+  L KG+ +         +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVDDEKIKQLSKGVQLDDGPASFRTIRYQGGEGLNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITL 220


>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 =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/229 (39%), Positives = 137/229 (59%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AGIASRR  E +I Q RVKVNG ++      V+STD I VDG  L   +  
Sbjct: 14  ERLQKVLAQAGIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRIVVDGRLLSIPQND 73

Query: 74  R-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L HKP G +T+ +DP GR TV + +P I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 74  YAYYLLHKPTGYITSVTDPQGRKTVMELMPKIPRRVYPVGRLDYDTSGLLLLTNDGDLAH 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-- 190
            L  PS    + YRV    ++ +  L  L+KG++++       ++   + KG  +  T  
Sbjct: 134 RLMHPSYGVEKTYRVEVGEKIPEQALKRLEKGVLLEDGKTAPARIREVSPKGRGSLPTYE 193

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           + + EG+NR+++++F+   + ++ L R+ +GP +L   LA G+ R +SK
Sbjct: 194 ITIHEGRNRQVRRMFKAVGFPLSTLKRLRFGPLELDPSLAPGAFRTLSK 242


>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 =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/229 (39%), Positives = 137/229 (59%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AGIASRR  E +I Q RVKVNG ++      V+STD I VDG  L   +  
Sbjct: 16  ERLQKVLAQAGIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRIVVDGRLLSIPQND 75

Query: 74  R-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L HKP G +T+ +DP GR TV + +P I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 76  YAYYLLHKPTGYITSVTDPQGRKTVMELMPKIPRRVYPVGRLDYDTSGLLLLTNDGDLAH 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-- 190
            L  PS    + YRV    ++ +  L  L+KG++++       ++   + KG  +  T  
Sbjct: 136 RLMHPSYGVEKTYRVEVGEKIPEQALKRLEKGVLLEDGKTAPARIREVSPKGRGSLPTYE 195

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           + + EG+NR+++++F+   + ++ L R+ +GP +L   LA G+ R +SK
Sbjct: 196 ITIHEGRNRQVRRMFKAVGFPLSTLKRLRFGPLELDPSLAPGAFRTLSK 244


>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 =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 89/228 (39%), Positives = 132/228 (57%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R+ K+IA+AG+ASRR+ E+ +   RV+VNG  +        S D IEVDG  L +AE
Sbjct: 3   TVERLQKLIAQAGLASRRQAEQWLKDGRVRVNGRSVTLGDKADPSVDRIEVDGKALPRAE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    L +KP+G VTT  DP GR T+   L  I  RV  VGRLD+N+EGLLLLTNDG L 
Sbjct: 63  QKLYLLLNKPLGYVTTLKDPQGRPTIRRFLKGIPQRVYPVGRLDVNSEGLLLLTNDGALT 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + L  P  Q  + YRV+ +G++       L++G+ ++        V        N+W  +
Sbjct: 123 QHLLHPRHQVSKTYRVKVNGRISPQACRQLEQGVELEDGVTAPAVVRNVHHSPRNSWFDL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +REG+NR+++++     ++V+ L RI  G  +LGTL  G  R ++ K
Sbjct: 183 EIREGRNRQVRRMCRGVGFEVSALKRIRIGSLELGTLAKGQCRSLTSK 230


>gi|304396082|ref|ZP_07377964.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356451|gb|EFM20816.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 296

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/218 (42%), Positives = 127/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E MIA  RV V+G I      V    +  I +DG    +   
Sbjct: 3   EKLQKVLARAGHGSRREIESMIAAGRVSVDGKIATLGDRVESSKSLKIRIDGHLVSIAES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T SDP+GR TVFD LP +  SR I+VGRLD+NT GL+L T D
Sbjct: 63  ATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLKFGGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RL+R+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITL 220


>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 =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 97/236 (41%), Positives = 136/236 (57%), Gaps = 12/236 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR 68
           F  +++ KV+A AGI SRR++E  IA+ R+ VNG   E A V   V  +D I  DG  +R
Sbjct: 9   FANEKLHKVLADAGIGSRRDMEERIAEGRISVNG---EPAHVGQRVTPSDVIRFDGRIVR 65

Query: 69  KA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLL 122
           ++     +  ++ +YHKP G + +  DP+GR TVFD+LP I  +R I+VGRLD NTEGLL
Sbjct: 66  RSALENNDVPKVLIYHKPAGEIVSKDDPEGRPTVFDHLPRIGGARWIAVGRLDFNTEGLL 125

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T+ G LA  L  P  +  R Y VR  G +  +  + L KGI +         +     
Sbjct: 126 LFTDSGNLANFLMHPRHEIEREYAVRVQGTMSPEAKDKLLKGIKLDDGIAKFTTLEEGGG 185

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           KG N W  V L EG+NRE++++FE     V+RLIR+ YG  +L + L  G TR +S
Sbjct: 186 KGFNRWYNVTLSEGRNREVRRMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMS 241


>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 =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/218 (42%), Positives = 127/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E MIA  RV V+G I      V    +  I +DG    +   
Sbjct: 3   EKLQKVLARAGHGSRREIESMIAAGRVSVDGKIATLGDRVESSKSLKIRIDGHLVSIAES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T SDP+GR TVFD LP +  SR I+VGRLD+NT GL+L T D
Sbjct: 63  ATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLKFGGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RL+R+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITL 220


>gi|218506664|ref|ZP_03504542.1| pseudouridylate synthase, subunit B protein [Rhizobium etli Brasil
           5]
          Length = 157

 Score =  154 bits (390), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 72/106 (67%), Positives = 87/106 (82%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGKVLETPVVNVTLADRIEVDGVPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           RLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTE
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTE 157


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/220 (41%), Positives = 134/220 (60%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I Q RV V+G    L +R  V V     I +DG  + ++
Sbjct: 35  EKLQKVLARAGHGSRREIETIIQQGRVSVDGKISTLGDR--VEVTQATKIRLDGHLLSIK 92

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           ++E T  R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T
Sbjct: 93  ESEETVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFT 152

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G +D +K+  L +G+ ++        ++    +G 
Sbjct: 153 TDGELANRLMHPSREVEREYAVRVFGLIDDEKIKQLSRGVQLEDGPAAFRTISFQGGEGI 212

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 213 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 252


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 133/218 (61%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  + ++++
Sbjct: 10  EKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKES 69

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T D
Sbjct: 70  EEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 129

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++    +G N 
Sbjct: 130 GELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQGGEGINQ 189

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 190 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 227


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 135/226 (59%), Gaps = 3/226 (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 KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +  ++   A V +
Sbjct: 121 LMHPRYKIEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELT 226


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 133/218 (61%), Gaps = 7/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+A AG+ SRRE+E+ IA  R+ VNG +       V   D + VDG  +  A ++
Sbjct: 3   EKLQKVLANAGVGSRREMEKWIASGRISVNGKVAT-LGDRVEPLDQLRVDGNLITAAAKS 61

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
              R+ +Y+KP G + +  DP GR TVFD LP I + R I+VGRLDINT GLLL TNDG 
Sbjct: 62  TICRVLMYNKPEGELCSRKDPQGRPTVFDRLPKIQNGRWIAVGRLDINTSGLLLFTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSNA 187
           LA  L  P  +  R Y VR  G+VD D +  LKKG+ ++ G+  + +++      +  N+
Sbjct: 122 LANRLMHPKHEIEREYAVRVFGEVDDDMIKRLKKGVELEDGVSKFTEVRKRPGDDESLNS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EGKNRE+++++E    +V+RLIR+ YG   L
Sbjct: 182 WYNVSLSEGKNREVRRLWESQGLQVSRLIRVRYGTLNL 219


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 93/217 (42%), Positives = 134/217 (61%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +++ KV+ARAG+ SRRE+E+ I   RV VNG +  +    V  TD I VDG  ++   KA
Sbjct: 6   EKLQKVLARAGVGSRREMEKYIDANRVSVNGKVA-KLGDRVEETDLIRVDGHTVKIEEKA 64

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ +Y+KP G ++T  DP+GR TVFD LP I   R I+VGRLD+NT GL+L TNDG
Sbjct: 65  DRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLFTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y  R  G+V  + +  L +G+ ++        VT    +G N W
Sbjct: 125 ELANRLMHPSYEVEREYSARVFGEVTNETVKNLLRGVELEDGPAKFTTVTPMGGEGVNRW 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE++++++  + +V+RLIRI YG  +L
Sbjct: 185 FNVTLNEGRNREVRRLWQSQDAEVSRLIRIRYGKLEL 221


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 134/226 (59%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA++G+ SRR+ E +I + +V VNG  +      V  +D IEV+G+PL   E+ 
Sbjct: 6   ERLQKVIAKSGVTSRRKAEVLITEGKVTVNGQTVTELGTKVKPSDIIEVEGIPLENPEKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP G++T+ SD  GR  V D  P +  R+  VGRLD +T GLLLLTNDG  A  
Sbjct: 66  YI-LFHKPTGVITSVSDEKGRKVVTDYFPGLNLRIFPVGRLDYDTSGLLLLTNDGDFANQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  + Y  +  G + ++++  L+KGI+++        V + +Q  + +   V +
Sbjct: 125 MTHPKYKMKKKYVAKLKGFLLREQVKQLEKGIMLEDGKTAPALVKVKSQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++F  F  +V +L RI YGP  L  L AG  RE++
Sbjct: 185 TIYEGRNRQVRRMFAHFGHEVVKLSRIEYGPLTLKGLNAGDARELT 230


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 96/219 (43%), Positives = 128/219 (58%), Gaps = 11/219 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG---VPL 67
           +++ KV+ARAG  SRRE+E  I + RV VNG    L +R +V     D I +DG   +  
Sbjct: 3   EKLQKVLARAGQGSRREMETRIREGRVLVNGEVATLGDRVSVK----DTITIDGYSIIAT 58

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
              E  R+ +Y+KP G V T  DP+GR TVFD LP +   R I+VGRLDINT GLLL T 
Sbjct: 59  EAGENRRVIIYNKPEGEVCTRKDPEGRPTVFDKLPKLRGERWIAVGRLDINTSGLLLFTT 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PST+  R Y VR  G+V  + L  LKKG+++         +     +G N
Sbjct: 119 DGELANRLMHPSTEIDREYLVRVMGEVTDENLAALKKGVILDDGIAKFTDIVDGGGEGIN 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+NRE+++++E    KVNRL R+ +GP  L
Sbjct: 179 RWFYVCLMEGRNREVRRLWESQGVKVNRLKRVRFGPVFL 217


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 90/220 (40%), Positives = 133/220 (60%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ K++ARAG  SRRE+E +I Q RV V+G    L +R  V V     I +DG  + ++
Sbjct: 28  EKLQKILARAGHGSRREIETIIQQGRVSVDGKISTLGDR--VEVTQATKIRLDGHLLSIK 85

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           ++E    R+  Y+KP G + T +DP+GR TVFD LP +  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 TDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLDDGPAAFRTISFQGGEGI 205

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 206 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 245


>gi|328868084|gb|EGG16464.1| Putative synthase [Dictyostelium fasciculatum]
          Length = 444

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 91/237 (38%), Positives = 139/237 (58%), Gaps = 19/237 (8%)

Query: 7   VQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEV 62
           ++E   P   +R+ K ++R+G+ SRR+ ERMI + RV VNG +   +  + V  TD + V
Sbjct: 154 IEEKIDPNQVERLQKRLSRSGVTSRRQSERMIMEGRVCVNGKVASMKNDLFVKPTDIVTV 213

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEG 120
           D             +  + +  +    DP+ + T+   L  + ++  ++SVGRLD  +EG
Sbjct: 214 DN-----------KIIEESVPKICNLQDPE-KDTLIPILQKMLNKDHLMSVGRLDYYSEG 261

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+L+TNDG L+R LELP + + + YRVR  G+V  D    L +G+ I GI Y  M+++++
Sbjct: 262 LILITNDGELSRYLELPQSGFEKTYRVRIFGKVTPDMNMALTRGLTIDGIRYAPMKISVE 321

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
            +  SN WV   L EGKNREI+++FE FN KV R+IR  +GP+ L  TL  G T EV
Sbjct: 322 RETDSNTWVICTLTEGKNREIRRIFEHFNVKVLRIIRTQFGPYTLPETLKPGETVEV 378


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 135/226 (59%), Gaps = 3/226 (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 KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELT 226


>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 =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 133/226 (58%), Gaps = 3/226 (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 KP G++++ SD  GR  V D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRKVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG+V++       +V + +  ++   A V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVVLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    KV +L R  Y   + G+L  G  RE+S
Sbjct: 181 TIHEGRNRQVRRMFEALGCKVMKLKRERYAFLEAGSLRPGDARELS 226


>gi|65318840|ref|ZP_00391799.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
          Length = 242

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 136/226 (60%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   KRLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFSPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>gi|330889215|gb|EGH21876.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 396

 Score =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  154 bits (388), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 86/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 170 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQV 226

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 227 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 286

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  GI +       ++
Sbjct: 287 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSESARQKLLHGIELDDGPANFLR 346

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 347 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 395


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 93/224 (41%), Positives = 134/224 (59%), Gaps = 6/224 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG-- 64
           Q+    +R+ KV+ARAG  SRR +E MI+  R+ ++G +      V++ S   I +DG  
Sbjct: 39  QQKVEGERLQKVLARAGQGSRRTIEAMISANRISIDGKMATLGDRVDIHSGVKIRIDGHI 98

Query: 65  VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGL 121
           V L +A++   R+ LY+KP G + T  DP+GR+TVFD LP +  SR I+VGRLDINT GL
Sbjct: 99  VNLTQAQKEVCRVLLYYKPEGELCTRHDPEGRATVFDRLPRLNGSRWIAVGRLDINTSGL 158

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  P  +  R Y VR  G+VD   +  L+KG+ ++        +    
Sbjct: 159 LLFTTDGELANRLMHPRHEVEREYAVRVFGEVDDAMIARLRKGVQLEDGPANFTSIKATG 218

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 219 GQGMNQWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 262


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 90/231 (38%), Positives = 132/231 (57%), Gaps = 1/231 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+NR+++++ E   +KV RL R   G  +LG+L +G  R ++KK LRE
Sbjct: 183 IHEGRNRQVRRMCEHIGYKVLRLRRTRIGTLELGSLKSGEVRALTKKELRE 233


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 133/218 (61%), Gaps = 7/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+A AG+ SRRE+E+ IA  R+ VNG +       V   D + VDG  +  A ++
Sbjct: 3   EKLQKVLANAGVGSRREMEKWIASGRISVNGKVAT-LGDRVEPVDQLRVDGNLITSAAKS 61

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
              R+ +Y+KP G + +  DP GR TVFD LP I + R I+VGRLDINT GLLL TNDG 
Sbjct: 62  TMCRVLMYNKPEGELCSRKDPQGRPTVFDRLPKIQNGRWIAVGRLDINTSGLLLFTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSNA 187
           LA  L  P  +  R Y VR  G+V+ D +  LKKG+ ++ G+  + +++      +  N+
Sbjct: 122 LANRLMHPKHEIEREYAVRVFGEVEDDMIKRLKKGVELEDGVSKFTEIRKRPGDDESLNS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EGKNRE+++++E    +V+RLIR+ YG   L
Sbjct: 182 WYNVSLSEGKNREVRRLWESQGLQVSRLIRVRYGTLNL 219


>gi|310767747|gb|ADP12697.1| 23S rRNA pseudouridylate synthase B [Erwinia sp. Ejp617]
          Length = 295

 Score =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 132/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I+  RV V+G L      V   ++  I +DG  VP+ ++
Sbjct: 3   EKLQKVLARAGHGSRREIETLISAGRVSVDGKLATLGDRVEPGASLKIRIDGHVVPVSES 62

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T SDP+GR TVFD LP +  +R ++VGRLD+NT GLLL T D
Sbjct: 63  ISEVCRILAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWVAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G VD +K+ LL +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGAVDDEKIKLLSRGVQLEDGPAAFKTLKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRIRYGDIDL 220


>gi|229166414|ref|ZP_04294170.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228616988|gb|EEK74057.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 242

 Score =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 135/226 (59%), Gaps = 3/226 (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 KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 134/226 (59%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA+AG+ASRR  E +IA+ RV+VNG  +    + V   DH+EVDG P+   E+ 
Sbjct: 6   QRLQKIIAQAGLASRRGAEELIAKGRVQVNGQTITELGMKVEPNDHVEVDGSPIEGREKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT++D  GR TV D L  +  RV  +GRLD +T G+LLLTNDG +A  
Sbjct: 66  VYYLLNKPRGVVTTNNDEKGRQTVIDLLGDVSQRVYPIGRLDYDTTGVLLLTNDGVVANQ 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P ++  +VY  +  G    +KL  LK G+VI+G      +VT++   +    + V V
Sbjct: 126 LMHPKSRVDKVYVAKVEGIATDEKLAPLKHGVVIKGRKTAPARVTIERVDKDKKTSMVRV 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+N +IK + +  +  V +L R  Y  F L  L +G  R+++
Sbjct: 186 IIHEGRNHQIKNMLQKVHLPVVKLTREQYAFFDLIGLQSGEYRKLT 231


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 131/218 (60%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+AR+G  SRRE+E +I Q RV V+G +      V+V ST  I +DG  + ++  
Sbjct: 5   EKLQKVLARSGQGSRREIEAVIEQGRVSVDGKVATLGDRVDVTSTTKIRIDGRIIAIKPV 64

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T  DP+GR TVFD LP +  +R ++VGRLDINT GLLL T D
Sbjct: 65  EDAVCRVLTYYKPEGELCTRRDPEGRPTVFDRLPRLNNARWVAVGRLDINTSGLLLFTTD 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y +R  G+VD+DK   L +G+ +         +T    +G N 
Sbjct: 125 GELANRLMHPSCKIEREYALRVFGEVDEDKQRQLTRGVQLDDGPAAFRSLTFQGGEGLNQ 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 185 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDVTL 222


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 136/226 (60%), Gaps = 3/226 (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 KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRNVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       ++++    ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPANVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELT 226


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 91/226 (40%), Positives = 131/226 (57%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QRV KVIA+AG+ASRR  E +I + RV+VNG  +    V V  TD + VD +PL   E+ 
Sbjct: 6   QRVQKVIAQAGLASRRGAEELIIKGRVQVNGQTITALGVKVEPTDTVTVDSIPLEGREKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT++D  GR TV D L  +  RV  +GRLD +T G+LLLTNDG +A  
Sbjct: 66  VYYLLNKPRGVVTTNNDEKGRRTVLDILSDVNERVYPIGRLDYDTTGVLLLTNDGVIANQ 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P ++  +VY  +  G    DKL  LK G+VI+G      +VT++   +    + V V
Sbjct: 126 LMHPKSRVDKVYIAKVAGIATDDKLAPLKHGVVIKGRKTAPARVTIERIDKDKKTSMVRV 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+N ++K + +     V +L R  Y  F L  L +G  R+++
Sbjct: 186 ILHEGRNHQVKNMLQKVGLPVEKLTREQYAFFDLTGLQSGEYRKLT 231


>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 =  154 bits (388), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 86/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 170 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQV 226

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 227 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 286

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  GI +       ++
Sbjct: 287 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSESARQKLLHGIELDDGPANFLR 346

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 347 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 395


>gi|167629967|ref|YP_001680466.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
 gi|167592707|gb|ABZ84455.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
          Length = 333

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 93/243 (38%), Positives = 132/243 (54%), Gaps = 1/243 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G+ASRRE E MI   RV++NG ++    V V  + D IEVDG  L++ E  
Sbjct: 7   RLQKLLAAHGVASRREAEAMIRAGRVRINGTVVREQGVRVDGARDVIEVDGRILKRREAP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP G+VTT  DP GR TV   L  +  RV  VGRLD +TEGLLLLTNDG LA  
Sbjct: 67  LYYALYKPRGVVTTCKDPQGRQTVIGLLSGVNERVYPVGRLDRDTEGLLLLTNDGQLAFR 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + YR R  G V    L  L +G+ ++       QV L  ++G   W+ + +
Sbjct: 127 LTHPRFGVEKTYRARLRGDVSAGALKALAEGVQLEDGVTAPAQVRLLRREGDATWIEIKI 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EG+ R+I+++ +     V  L RI++GP  LG L  G  R ++   LR       ++EA
Sbjct: 187 HEGRKRQIRRMGDAIGHPVIDLERIAFGPITLGKLKPGEVRPLTSAELRALKSAAGMKEA 246

Query: 254 QVN 256
             +
Sbjct: 247 TAH 249


>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 =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 86/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 157 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQV 213

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 214 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 273

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  GI +       ++
Sbjct: 274 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSESARQKLLHGIELDDGPANFLR 333

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 334 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 382


>gi|302188863|ref|ZP_07265536.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 409

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>gi|330980378|gb|EGH78489.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 408

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>gi|330866214|gb|EGH00923.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 408

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILKDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>gi|327394043|dbj|BAK11465.1| ribosomal large subunit pseudouridine synthase B RluB [Pantoea
           ananatis AJ13355]
          Length = 294

 Score =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E MIA  RV V+G L      +       I +DG    +   
Sbjct: 3   EKLQKVLARAGHGSRREIEAMIAAGRVSVDGKLATLGDRIENSKALKIRIDGHLVSIAES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T SDP+GR TVFD LP +  SR I+VGRLD+NT GL+L T D
Sbjct: 63  ATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLRFAGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RL+R+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITL 220


>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 =  153 bits (387), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 93/221 (42%), Positives = 134/221 (60%), Gaps = 6/221 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
           N   +++ KV+ARAG+ SRRE+E+ I   RV VNG +  +    V  TD I VDG  ++ 
Sbjct: 2   NIQGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVA-KLGDRVEETDLIRVDGHTVKI 60

Query: 69  --KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
             KA+R  R+ +Y+KP G ++T  DP+GR TVFD LP I   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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            N W  V L EG+NRE++++++  + +V+RLIRI YG  +L
Sbjct: 181 INRWFNVTLNEGRNREVRRLWQSQDVEVSRLIRIRYGKLEL 221


>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 =  153 bits (387), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 229

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 230 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 289

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 290 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRI 349

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 350 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 397


>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 =  153 bits (387), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>gi|322420558|ref|YP_004199781.1| pseudouridine synthase [Geobacter sp. M18]
 gi|320126945|gb|ADW14505.1| pseudouridine synthase [Geobacter sp. M18]
          Length = 262

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 86/225 (38%), Positives = 130/225 (57%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE E +IA+ RV VNG ++          TD 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+ R+++++ E     V RL R  Y    +G +  G  R ++
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRSRYDFLVIGEMKPGDFRHLT 227


>gi|167719822|ref|ZP_02403058.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
          Length = 399

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 97  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 153

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 154 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 213

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 214 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 273

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 274 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 321


>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 =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 229

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 230 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 289

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 290 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 349

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 350 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 397


>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 =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 229

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 230 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 289

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 290 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRI 349

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 350 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 397


>gi|167894529|ref|ZP_02481931.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
          Length = 395

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 90  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 146

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 147 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 206

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 207 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 266

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 267 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 314


>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 =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 229

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 230 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 289

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 290 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 349

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 350 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 397


>gi|167919194|ref|ZP_02506285.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei BCC215]
          Length = 408

 Score =  153 bits (386), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 99  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 155

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 156 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 215

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 216 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 275

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 276 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 323


>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 =  153 bits (386), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 134/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 172 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 228

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 229 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 288

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ ++      ++
Sbjct: 289 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELEDGPANFLR 348

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 349 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 397


>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 =  153 bits (386), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 132 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 188

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 189 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 248

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 249 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 308

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 309 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 356


>gi|167845952|ref|ZP_02471460.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
          Length = 384

 Score =  153 bits (386), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 84  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 140

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 141 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 200

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 201 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRI 260

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 261 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 308


>gi|289624030|ref|ZP_06456984.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
          Length = 308

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 108/269 (40%), Positives = 153/269 (56%), Gaps = 18/269 (6%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG   + A V   V   D
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNG---KDATVGQRVDLHD 60

Query: 59  HIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGR 113
            I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++GR
Sbjct: 61  AISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGR 120

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--IC 171
           LDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++     
Sbjct: 121 LDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPAR 180

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
           + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L  
Sbjct: 181 FTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPM 239

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVN 256
           G  RE+S+    IL  ++G   + + Q+N
Sbjct: 240 GRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>gi|170717435|ref|YP_001784534.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168825564|gb|ACA30935.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 348

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 93/226 (41%), Positives = 134/226 (59%), Gaps = 6/226 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           I Q+    +R+ KV+AR G  SRR +E MI+  R+ ++G +      V++ S   I +DG
Sbjct: 60  INQQKVEGERLQKVLARVGQGSRRTIEAMISANRISIDGKMATLGDRVDIHSGVKIRIDG 119

Query: 65  --VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTE 119
             V L +A++   R+ LY+KP G + T  DP+GR+TVFD LP +  SR I+VGRLDINT 
Sbjct: 120 HIVNLTQAQKEVCRVLLYYKPEGELCTRHDPEGRATVFDRLPRLNGSRWIAVGRLDINTS 179

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  P  +  R Y VR  G+VD   +  L+KG+ ++        +  
Sbjct: 180 GLLLFTTDGELANRLMHPRHEVEREYAVRVFGEVDDTMIARLRKGVQLEDGPANFTSIKA 239

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              +G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 240 TGGQGMNQWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKL 285


>gi|295676258|ref|YP_003604782.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295436101|gb|ADG15271.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 589

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 134/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 188 KRVLSPDDDAPKLHKVLAEAGMGSRRDMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 244

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 245 INGKPVKRKLASKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWVAVGRLDFN 304

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ ++      +++
Sbjct: 305 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELEDGPANFLRI 364

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 365 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 412


>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 =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 133/226 (58%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG +++   V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVKELGVKVSGTERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G       ++V    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELS 226


>gi|167587342|ref|ZP_02379730.1| pseudouridine synthase [Burkholderia ubonensis Bu]
          Length = 389

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 66  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 122

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 123 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 182

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 183 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGNRQKLLHGVELDDGPANFLR 242

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 243 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPL 291


>gi|330966753|gb|EGH67013.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 408

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 154/272 (56%), Gaps = 24/272 (8%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQSRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILE---D 176

Query: 173 GDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT- 227
           G  + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ YGP  L + 
Sbjct: 177 GPARFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSD 236

Query: 228 LLAGSTREVSK---KILREQLGPHLLEEAQVN 256
           L  G  RE+S+    IL  ++G   + + Q+N
Sbjct: 237 LPMGRWREMSQYEVDILSAEVGLQPVAQPQMN 268


>gi|167620251|ref|ZP_02388882.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis Bt4]
          Length = 431

 Score =  152 bits (385), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 129 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 185

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 186 INGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 245

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 246 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 305

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 306 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 353


>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 =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/217 (39%), Positives = 129/217 (59%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + ++G P+++   
Sbjct: 196 KLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVRINGKPVKRKLP 252

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ +YHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD NTEGLLLLT  G
Sbjct: 253 NKPPRVLIYHKPAGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFNTEGLLLLTTSG 312

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA     P  Q  R Y VR  G++ +     L  G+ +       +++     +G+N W
Sbjct: 313 DLANRFMHPRYQVEREYAVRVIGELAESARQKLLNGVELDDGPASFLRIQDGGGEGTNRW 372

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 373 YHVALAEGRNREVRRMFEAVGLTVSRLIRTRHGPIVL 409


>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 =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 176 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 232

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 233 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 292

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 293 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLR 352

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 353 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPL 401


>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 =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 173 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 229

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 230 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 289

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 290 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLR 349

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 350 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPL 398


>gi|167824420|ref|ZP_02455891.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
          Length = 374

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 66  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 122

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 123 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 182

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 183 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFLRI 242

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 243 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 290


>gi|167738823|ref|ZP_02411597.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
          Length = 359

 Score =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 134/230 (58%), Gaps = 9/230 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDH 59
           + K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD 
Sbjct: 47  QPKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQ 103

Query: 60  IEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLD 115
           + ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD
Sbjct: 104 VRINGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLD 163

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +
Sbjct: 164 FNTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQRLLHGVELDDGPANFL 223

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 224 RIRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 273


>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 =  152 bits (385), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 31  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 87

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 88  RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 147

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 148 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLR 207

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 208 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPL 256


>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 =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 176 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 232

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 233 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 292

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 293 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLR 352

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 353 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPL 401


>gi|196248745|ref|ZP_03147445.1| pseudouridine synthase [Geobacillus sp. G11MC16]
 gi|196211621|gb|EDY06380.1| pseudouridine synthase [Geobacillus sp. G11MC16]
          Length = 243

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 132/226 (58%), Gaps = 3/226 (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
             +L +KP G++++  D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 62  -YYLLYKPRGVISSVKDEKGRKVVTDFFKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G   +++L  L+KG++++       +V L +  +K   A V +
Sbjct: 121 LMHPRYEIEKVYVAKVKGIPTREQLKQLEKGVLLEDGITAPAKVKLLSADRKKRTAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+S
Sbjct: 181 SIHEGRNRQVRRMFEAIGCEVLKLKRERYAFLDLKGLRPGEYRELS 226


>gi|330939561|gb|EGH42880.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 299

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 107/270 (39%), Positives = 154/270 (57%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 31  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 87

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 88  RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 147

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 148 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEGMRQKLLHGVELDDGPANFLR 207

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 208 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPL 256


>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 =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 88/228 (38%), Positives = 131/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + E  
Sbjct: 4   ERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVGSKDVVEVDGVPIEQ-EPH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L++ 
Sbjct: 63  VYYLFYKPRGVISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGELSQT 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G  D+ +L  L KGI I+G        ++    Q   ++ V +
Sbjct: 123 LMHPKHEVEKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTAQSSIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R +YGP  L  L  G  RE+SKK
Sbjct: 183 TIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELSKK 230


>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 =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 92/223 (41%), Positives = 129/223 (57%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE ER+I   RV VNG ++ E         D I VDG P+R  E 
Sbjct: 3   ERLQKILSQAGIASRREAERIITDGRVAVNGQVVTELGTKADAEKDRITVDGRPIR-VEA 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +L+ L +KP+G +TT  DP+GR  V D L  I  RV  VGRLD NTEGLLLLTNDG LA
Sbjct: 62  NKLYVLLYKPVGYMTTMKDPEGRPIVTDLLKGIKERVYPVGRLDYNTEGLLLLTNDGALA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS +  + Y VR  G+V   +L  L  G+ ++        V+L  +   N W+++
Sbjct: 122 NRLAHPSHEVDKGYLVRVRGKVTPAQLKHLAVGVDLEDGRTAPAVVSLVRESEQNCWISI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+ R+++++ E     V RL R  YG  ++G L  G  R
Sbjct: 182 TIHEGRYRQVRRMCEAVGLTVVRLKRSRYGFLEIGELKPGEYR 224


>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 =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 87/228 (38%), Positives = 132/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + E+ 
Sbjct: 4   ERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQ-EQH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L++ 
Sbjct: 63  VYYLFYKPRGVISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGELSQT 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G  D+ +L  L KGI I+G        ++    Q   ++ V +
Sbjct: 123 LMHPKHEVDKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTAQSSIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R +YGP  L  L  G  RE++KK
Sbjct: 183 TIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELTKK 230


>gi|167816044|ref|ZP_02447724.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
          Length = 358

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 60  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 116

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 117 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 176

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 177 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 236

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 237 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 284


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 132/226 (58%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G       ++V    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELS 226


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 100/227 (44%), Positives = 135/227 (59%), Gaps = 13/227 (5%)

Query: 4   KNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTD 58
           K  V+E+ +P  +++ KV+ARAGI SRRE+ER I + RVKVN    +R A     V  TD
Sbjct: 77  KPSVKESASPVDEKLQKVLARAGIGSRREMERAIEEGRVKVN----DRIATLGDRVTLTD 132

Query: 59  HIEVDG--VPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
            I V G  V LR +A R R+ LY+KP G + +  DP+GR TV+D+LPS+   R ISVGRL
Sbjct: 133 KIFVGGQRVVLRTEAARRRVILYNKPEGEICSRHDPEGRPTVYDSLPSLKGERWISVGRL 192

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D NT GLLL TNDG LA  L  PS+   R Y VR  G VD D    L +G+++       
Sbjct: 193 DFNTSGLLLFTNDGELANKLMHPSSVIDREYLVRIQGDVDDDMKERLLEGVLLDDGVARF 252

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             +     +G N W    + EG+NRE+++++E    KV+RL R+ Y 
Sbjct: 253 TDIVDGAGEGKNRWFYCVVMEGRNREVRRLWESQGVKVSRLKRVRYA 299


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 154/272 (56%), Gaps = 24/272 (8%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILE---D 176

Query: 173 GDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT- 227
           G  + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ YGP  L + 
Sbjct: 177 GPARFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSD 236

Query: 228 LLAGSTREVSK---KILREQLGPHLLEEAQVN 256
           L  G  RE+S+    IL  ++G   + + Q+N
Sbjct: 237 LPMGRWREMSQYEVDILSAEVGLQPVAQPQMN 268


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 174 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 230

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 231 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 290

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 291 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLR 350

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 351 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 399


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 154/272 (56%), Gaps = 24/272 (8%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILE---D 176

Query: 173 GDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT- 227
           G  + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ YGP  L + 
Sbjct: 177 GPARFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSD 236

Query: 228 LLAGSTREVSK---KILREQLGPHLLEEAQVN 256
           L  G  RE+S+    IL  ++G   + + Q+N
Sbjct: 237 LPMGRWREMSQYEVDILSAEVGLQPVAQPQMN 268


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 174 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 230

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 231 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 290

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 291 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLR 350

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 351 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 399


>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 =  152 bits (384), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 89/226 (39%), Positives = 134/226 (59%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSN-AWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V +  + K  N A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKNKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELS 226


>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 =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 94/220 (42%), Positives = 131/220 (59%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G    L +R  VN +    I VDG  +  R
Sbjct: 3   EKLQKVLARAGHGSRREMEALITAGRVSVDGKVATLGDRVEVNAV----IRVDGHQIKTR 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
            AE    R+  YHKP G + T  DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T
Sbjct: 59  AAEEVICRVLAYHKPEGEMCTRHDPEGRPTVFDRLPKMEGARWIAVGRLDVNTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G++ +  L  L+KG+ ++       ++     +G 
Sbjct: 119 TDGELANRLMHPSHEVEREYAVRVFGEITEAMLQRLRKGVQLEDGMAKFNKIKPAGGEGL 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RL+RI YG  QL
Sbjct: 179 NQWFNVTLTEGRNREVRRLWESQEVQVSRLMRIRYGDVQL 218


>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 =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 122 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 178

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 179 INGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 238

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 239 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 298

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 299 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 346


>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 =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 132/226 (58%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G       ++V    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELS 226


>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 =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 97/233 (41%), Positives = 133/233 (57%), Gaps = 15/233 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ K++AR G  SRRE+ER I +  V VNG +           D + + G  VPL  A 
Sbjct: 3   ERLQKLLARLGHGSRREIERWIEEGLVTVNGKVAS-LGDQAGPDDKVAIRGRVVPLDVAP 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           + R+  YHKP G +TT  DP+GR TVF++LP + + R I+VGRLD NT GLLL T DG L
Sbjct: 62  KPRVIAYHKPDGELTTRKDPEGRPTVFEHLPRLRNGRWIAVGRLDYNTSGLLLFTTDGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GS 185
           A  L  PS +  R Y VR  G+V  D L  L  G+ ++     D     +T +     G+
Sbjct: 122 AAKLMHPSGEVEREYAVRILGEVSPDALKQLTTGVELE-----DGPARFETLREAGGTGA 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           N W  V LREG+NRE+++++E     V+RL R+ YGP  LG  L AG  R++ 
Sbjct: 177 NRWYHVTLREGRNREVRRLWEAVGLTVSRLTRVRYGPISLGRDLRAGRWRDLE 229


>gi|325520892|gb|EGC99873.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           TJI49]
          Length = 328

 Score =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 38  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQV 94

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 95  RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 154

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 155 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELTEASRQKLLHGVELDDGPANFLR 214

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 215 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 263


>gi|330960474|gb|EGH60734.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 408

 Score =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 154/272 (56%), Gaps = 24/272 (8%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILE---D 176

Query: 173 GDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT- 227
           G  + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ YGP  L + 
Sbjct: 177 GPARFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSD 236

Query: 228 LLAGSTREVSK---KILREQLGPHLLEEAQVN 256
           L  G  RE+S+    IL  ++G   + + Q+N
Sbjct: 237 LPMGRWREMSQYEVDILSAEVGLQPVAQPQMN 268


>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 =  152 bits (383), Expect = 9e-35,   Method: Compositional matrix adjust.
 Identities = 103/262 (39%), Positives = 150/262 (57%), Gaps = 19/262 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+AR G+ASRRE+E  I + RVKVNG         V + D I +DG  L++ E T
Sbjct: 12  EKLQKVLARMGLASRREIETWIGEGRVKVNGAAAT-LGQRVDANDAIALDGRLLKREEIT 70

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLLL T DG
Sbjct: 71  GSVRRVLIYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS Q  R Y VR  G+V ++ L  LKKG++++     + D++     + G N
Sbjct: 131 ELANRLMHPSYQMDREYAVRVRGEVTEEMLENLKKGVMLEDGPAKFTDIKEAPGGE-GFN 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKK---ILR 242
            W    + EG+NRE+++++E     V+RL R+ +GP F    L  G  RE+ ++   IL 
Sbjct: 190 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSDLTMGRWREMDQREVDILS 249

Query: 243 EQLG------PHLLEEAQVNLD 258
            ++G      P + E+ +  LD
Sbjct: 250 AEVGLAPQALPAMKEKTREKLD 271


>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 =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 131/229 (57%), Gaps = 4/229 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R+ KV+A AG+ASRRE E++I   RV+VNG  +      V   D I VDG  L +  
Sbjct: 4   TKERLQKVMAAAGVASRRECEKIILAGRVQVNGKPVTELGTRVGKADRITVDGKALHRKS 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +L +KP G+VTT  DP GR TV D +  +  R+  VGRLD  TEGLLL+TNDG LA
Sbjct: 64  ARHTYLLYKPGGVVTTMKDPQGRRTVADLMAGLHQRLYPVGRLDYLTEGLLLMTNDGELA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAW 188
           + L  PS    + Y V  HG+V ++KL++L+ G+ ++        V +   D +K    +
Sbjct: 124 QHLTHPSHHVDKTYEVEVHGRVPEEKLDVLRLGVPLEDGLTAPAVVYVKKWDPEKNLTRF 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            TV + EG+NR+++++ +F  + V  L RI  G   L  +  G  RE++
Sbjct: 184 -TVTIHEGRNRQVRRMCDFIGFPVKSLKRIQVGTLTLEGMKKGEFRELT 231


>gi|313623106|gb|EFR93379.1| ribosomal large subunit pseudouridine synthase B [Listeria innocua
           FSL J1-023]
          Length = 244

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 132/226 (58%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGVTSRRKAEKLIQEGKVTVNGKVVTELGVKVTGTERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G       ++V    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLAREEYSFLNLRGLNAGERRELS 226


>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 =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 88/222 (39%), Positives = 137/222 (61%), Gaps = 7/222 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ KV+AR+G  SRRE+E MI   R++VNG + +     + +   + +DG  +  K+E 
Sbjct: 3   EKLQKVLARSGYGSRREIEAMIGAGRIRVNGKVAQ-VGERIDADASVRIDGHEVVIKSEN 61

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
           +   R+  YHKP G + T  DP+GR TV++ LP +  +R ++VGRLD+NT GLLL T DG
Sbjct: 62  SVVCRVLTYHKPEGELCTRKDPEGRPTVYERLPRMSGARWVAVGRLDVNTSGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS +  R Y VR  G+V    +N LKKG+ ++ G+ + D    +   +G N 
Sbjct: 122 ELANRLMHPSQEVEREYAVRIFGEVTDAMINRLKKGVQLEDGLAHFDTIKAVGGGEGMNR 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           W  V L+EG+NRE+++++E    +V+RLIR+ YG  +L + L
Sbjct: 182 WYHVTLKEGRNREVRRLWESQEVQVSRLIRVRYGDIKLESGL 223


>gi|167562943|ref|ZP_02355859.1| RNA pseudouridylate synthase family protein [Burkholderia
           oklahomensis EO147]
          Length = 354

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 134/230 (58%), Gaps = 9/230 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDH 59
           + K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD 
Sbjct: 46  QPKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQ 102

Query: 60  IEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLD 115
           + ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP++  ++ ++VGRLD
Sbjct: 103 VRINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPTMKTAKWLAVGRLD 162

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +
Sbjct: 163 FNTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELPEASRQKLLHGVELDDGPANFL 222

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 223 RIRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 272


>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 =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 92/217 (42%), Positives = 129/217 (59%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +R+ K++AR G+ SRREVE  I   RV++NGI   R    V   D + V+G PL     +
Sbjct: 3   ERLQKILARGGLGSRREVEEWIKAGRVRINGIP-ARLGDKVSDEDQVTVNGRPLSPRRLQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
           A  +++ LYHKP G + +  DP+GR TVF +LP     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 225
             V L EG+ RE+++++E    +V+RLIRI +GP  L
Sbjct: 182 YHVILWEGRKREVRRLWESQGIQVSRLIRIRFGPVSL 218


>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 =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 93/222 (41%), Positives = 130/222 (58%), Gaps = 11/222 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAER 72
           +++ KV+A  G+ SRRE+ER I + RV VNG +       V  T  I VDG  L R+ E+
Sbjct: 3   EKLQKVLANQGLGSRREMERWIEEGRVSVNGSVAT-LGDRVDHTAQIRVDGHLLSRQTEQ 61

Query: 73  --TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
              R+ +Y+KP G + +  DP+GR TVFD LP+I   R I+VGRLD+NT GLLL TNDG 
Sbjct: 62  PICRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRLGRWITVGRLDMNTSGLLLFTNDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQK 183
           LA  L  P  +  R Y VR  G+V    LN L+KG+ +           G        ++
Sbjct: 122 LANRLMHPKCEVEREYAVRVFGEVSTKTLNTLQKGVELDDGEAKFLTISGTPTPQHAEEE 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             N W  V L+EG+NRE+++++E    +V+RLIR+ YGP +L
Sbjct: 182 SMNRWFNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPIEL 223


>gi|167570132|ref|ZP_02363006.1| RNA pseudouridylate synthase family protein [Burkholderia
           oklahomensis C6786]
          Length = 371

 Score =  152 bits (383), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 60  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 116

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP++  ++ ++VGRLD N
Sbjct: 117 INGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPTMKTAKWLAVGRLDFN 176

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 177 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELPEASRQKLLHGVELDDGPANFLRI 236

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 237 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 284


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 132/226 (58%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGVTSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G       ++V    +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLAREEYSFLNLRGLNAGERRELS 226


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/229 (37%), Positives = 129/229 (56%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG  SRR  E  I   RV ++G++ +   V V +S   + VDG  LR  E 
Sbjct: 37  ERLQKVLASAGYGSRRACEEYIEMGRVTIDGVVAKELGVRVDLSRQKVAVDGEKLR-VEE 95

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L+HKP G++ T+SDP GR+ V D  P    R+ +VGRLD  TEGLL++TNDG LA 
Sbjct: 96  KRYFLFHKPAGVLCTNSDPAGRTRVIDCFPPNVGRLFTVGRLDDGTEGLLIVTNDGDLAE 155

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     R+YR    G    + +N L +G+      +    V     +GS   + + 
Sbjct: 156 RLTHPKFGIPRIYRAVVAGNPSTEAINQLLEGLYFAEGRFRMSSVNRVKSQGSATVLEIT 215

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +REG+NREI+++      KV +L R  +GP +LG L  G+ R++S++ L
Sbjct: 216 MREGQNREIRRLLARVGHKVMKLKRTHFGPIKLGDLERGAHRKLSEEEL 264


>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: Compositional matrix adjust.
 Identities = 88/212 (41%), Positives = 128/212 (60%), Gaps = 6/212 (2%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKAER--TR 74
           +ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  + ++++E    R
Sbjct: 1   MARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKESEEAVCR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL T DG LA  
Sbjct: 61  VLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +T    +G N W  V L
Sbjct: 121 LMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTITFQGGEGINQWYNVTL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 181 TEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 212


>gi|311694421|gb|ADP97294.1| RNA-binding S4 domain protein [marine bacterium HP15]
          Length = 327

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 92/222 (41%), Positives = 128/222 (57%), Gaps = 6/222 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ K++ARAGI SRRE+E  +   R+ VNG  +          D  E+DG  L  +  
Sbjct: 22  PERIQKLLARAGIGSRREIEGWMEAGRLLVNGQPVA-PGQKATVEDRFELDGKRLEVSGA 80

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VTT  DP+GR TVFD LP +   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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L + L
Sbjct: 201 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRL 242


>gi|257876560|ref|ZP_05656213.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257810726|gb|EEV39546.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 240

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 87/228 (38%), Positives = 132/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + E+ 
Sbjct: 4   ERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQ-EQH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L++ 
Sbjct: 63  VYYLFYKPRGVISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGELSQT 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G  D+ +L  L KGI I+G        ++    Q   ++ V +
Sbjct: 123 LMHPKHEVDKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTTQSSIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R +YGP  L  L  G  RE++KK
Sbjct: 183 TIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELTKK 230


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 207 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRIMPTDQVR 263

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 264 INGKPVKRKLASKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFN 323

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 324 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRI 383

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 384 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 431


>gi|167582090|ref|ZP_02374964.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis TXDOH]
          Length = 379

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 73  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 129

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 130 INGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 189

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 190 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 249

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 250 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 297


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 84/217 (38%), Positives = 129/217 (59%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRK--- 69
           ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + ++G P+++   
Sbjct: 10  KLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVRINGKPVKRKLP 66

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD NTEGLL+LT  G
Sbjct: 67  SKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTEGLLMLTTSG 126

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA     P     R Y VR  G++ +     L  G+ +       +++     +G+N W
Sbjct: 127 DLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRDGGGEGTNHW 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 187 YHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 223


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 107/279 (38%), Positives = 159/279 (56%), Gaps = 28/279 (10%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNV 54
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+   L +R  ++ 
Sbjct: 1   MSEQDLQDTAITPPSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVAATLGQRVDLH- 59

Query: 55  MSTDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVI 109
              D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I
Sbjct: 60  ---DAIAVDGKLIKREEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWI 116

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           ++GRLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++ 
Sbjct: 117 NIGRLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLED 176

Query: 170 ICYGDMQVTLDTQK-----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
              G  + T D QK     G N W    + EG+NRE+++++E     V+RL R+ +GP  
Sbjct: 177 ---GPAKFT-DIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVF 232

Query: 225 LGT-LLAGSTREVSK---KILREQLGPHLLEEAQVNLDA 259
           L + L  G  RE+S+    IL  ++G   +    +NL A
Sbjct: 233 LNSDLPMGRWREMSQGEIDILAAEVGLQPVALPALNLKA 271


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/227 (40%), Positives = 136/227 (59%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A+AG+ASRR  E MI + RV VNG ++    V V   D I +VDG+ ++  E+ 
Sbjct: 120 RLQKLMAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVNPADVIVQVDGMTVQTNEKL 179

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++KP G+V+T  DPDGR  + D L  S+  RV  VGRLD+ TEGLLLLTNDG LA 
Sbjct: 180 IYMAFNKPAGVVSTMEDPDGRPCIKDFLRDSMNERVFHVGRLDVETEGLLLLTNDGELAN 239

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+  G V+      LKKGI ++ G+   D    +D+  G +  + V
Sbjct: 240 RLTHPSYEVPKTYLVQVRGPVESGIGAELKKGIRLEDGVSRVDSFKLVDSAPG-HVLIEV 298

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +  GKNR ++++FE   + V +L+R+  GP ++G+   G+ R +SK
Sbjct: 299 TIHSGKNRIVRRLFEAVGYPVEKLVRVQMGPIRIGSQKQGTVRNLSK 345


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 88/216 (40%), Positives = 128/216 (59%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           R+ K++AR G+ SRRE+E MIA  RV +NG+   +        D I +DG  +R    A 
Sbjct: 35  RLQKLLARNGLGSRREIEDMIAAGRVSINGVT-AKPGDRAGPGDMIRIDGKIIRFRLAAL 93

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
             R+ +YHKP G + +  DP GR +VFD LP I  S+ I++GRLD NT GLL+ T DG L
Sbjct: 94  LPRVIIYHKPEGEIVSVRDPQGRPSVFDKLPHIRSSKWIAIGRLDFNTSGLLIFTTDGTL 153

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  Q  R Y VR  G++  +++  L  GI ++ G+   D Q+  +   G+N W 
Sbjct: 154 ANHLMHPRYQMEREYAVRIVGELTPEQITRLTTGIELEDGLAKFD-QLLDEGGTGTNHWY 212

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L+EG+NRE++++FE     V+RLIR+ +GP  L
Sbjct: 213 RIMLKEGRNREVRRMFEALGLTVSRLIRVRFGPVNL 248


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E  I Q RV V+G I      + V     I +DG  + ++++
Sbjct: 9   EKLQKILARSGHGSRREIEGYIQQGRVSVDGKIATLGDRIEVQPATKIRLDGRILSIKES 68

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T D
Sbjct: 69  QKAICRVLAYYKPEGELCTRHDPEGRPTVFDRLPKLLGSRWIAVGRLDVNTCGLLLFTTD 128

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD  KL  L KGI ++        V     +G N 
Sbjct: 129 GELANRLMHPSREVEREYAVRVFGEVDDAKLKQLAKGIQLEDGPAAFRTVAFKGGEGINQ 188

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 189 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIGL 226


>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 =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 93/220 (42%), Positives = 128/220 (58%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E MI   RV V+G    L +R  V V     I +DG  +   
Sbjct: 3   EKLQKVLARAGHGSRREIEAMIEAGRVSVDGKIATLGDR--VEVTPALKIRIDGHLISVK 60

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T SDP+GR TVFD LP +  +R I+VGRLD+NT GLLL T
Sbjct: 61  ESVEQICRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSQEVEREYAVRVFGQVDDNKVRELARGVQLEDGPAAFKTIRFSGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 131/226 (57%), Gaps = 3/226 (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 KP G+++  SD  GR  V D    I  R+  VGRLD +T G+L+LTNDG  A +
Sbjct: 62  YFLLY-KPRGVISAVSDDKGRKVVTDFFEGIKQRIYPVGRLDYDTSGILILTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  PS +  +VY  +  G   ++ +  L++G+V++       +  L +  +K   A V +
Sbjct: 121 LMHPSNEIEKVYVAKIKGIPSKEGMRSLQRGVVLEDGKTAPAKTKLLSMDKKKQTAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE     V +L R  YG   L  L AG  RE++
Sbjct: 181 SIHEGRNRQVRRMFEAIGHPVLKLKRERYGYLTLQGLSAGDARELT 226


>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 =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 120/341 (35%), Positives = 180/341 (52%), Gaps = 40/341 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+AR G+ASRRE+E  IA+ RVKVNG         V + D I +DG  L++ E T
Sbjct: 12  EKLQKVLARLGLASRREIETWIAEGRVKVNGAAAT-LGQRVDANDAIALDGRLLKREEIT 70

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLLL T DG
Sbjct: 71  GSVRRVLIYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS Q  R Y VR  G+V ++ L  LK G++++     + D++     + G N
Sbjct: 131 ELANRLMHPSYQMDREYAVRVRGEVTEEMLENLKTGVMLEDGPAKFTDIKEAPGGE-GFN 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W    + EG+NRE+++++E     V+RL R+ +GP  L       T E++    RE   
Sbjct: 190 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFL-------TSELTMARWRE--- 239

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK-QKKLATPV 305
              +++ +V+    I S+E         +   P     MK+ + +K  L + Q+K A PV
Sbjct: 240 ---MDQREVD----ILSAE---------VGLTPQALPAMKEKTREK--LDRLQRKSAKPV 281

Query: 306 HRRN--LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             R   +        G  S+  S + +R+E  +R+P  P K
Sbjct: 282 EVRGKRVLRPAKDEAGADSARPSRAPRRDEAEQRTPRGPRK 322


>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 =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/235 (38%), Positives = 142/235 (60%), Gaps = 13/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG----VP 66
           ++V KV+ARAG  SRRE+E MI++ RV ++G    L +R    +  T+ I +DG    + 
Sbjct: 71  EKVQKVLARAGKGSRREMETMISEGRVSIDGKVAFLGDR----ITGTEQIRLDGHHVKLT 126

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
            +  +  R+ +Y+KP G + T  DP+GR TVFD LP + + R ++VGRLDINT G+LL T
Sbjct: 127 AQDEDICRVLVYNKPEGEMCTRKDPEGRPTVFDRLPPLDAGRWVAVGRLDINTSGMLLFT 186

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G++++  L  L+ G+ ++       ++T    +G 
Sbjct: 187 TDGELANRLMHPSQKVEREYAVRVFGEINEAMLQTLRAGVKLEDGMARFQKITYRGGEGR 246

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
           N W  V L EG+NRE+++++E  + +V+RLIR+ YG  ++   L  G  RE++ K
Sbjct: 247 NHWFHVVLSEGRNREVRRLWESQDVQVSRLIRVRYGDMEMQRQLPMGGWRELALK 301


>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 =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/227 (40%), Positives = 136/227 (59%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A+AG+ASRR  E MI + RV VNG ++    V V   D I +VDG+ ++  E+ 
Sbjct: 120 RLQKLMAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVNPADVIVQVDGMTVQTNEKL 179

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               ++KP G+V+T  DPDGR  + D L  S+  RV  VGRLD+ TEGLLLLTNDG LA 
Sbjct: 180 IYMAFNKPAGVVSTMEDPDGRPCIKDFLRDSMNERVFHVGRLDVETEGLLLLTNDGELAN 239

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+  G V+      LKKGI ++ G+   D    +D+  G +  + V
Sbjct: 240 RLTHPSYEVPKTYLVQVRGPVESGIGAELKKGIRLEDGVSRVDSFKLVDSAPG-HVLIEV 298

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +  GKNR ++++FE   + V +L+R+  GP ++G+   G+ R +SK
Sbjct: 299 TIHSGKNRIVRRLFEAVGYPVEKLVRVQMGPIRIGSQKQGTVRNLSK 345


>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 =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 82/220 (37%), Positives = 131/220 (59%), Gaps = 5/220 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
           +  PQR+ K++A AG+ SRRE+E +I   R+ +NG + E  A  V+  D +  D  P+  
Sbjct: 25  DAVPQRLHKLLALAGLGSRREMEELILSGRITINGKVAEVGAA-VVPGDVVRFDSRPVHL 83

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
             +AE  ++ +YHKP G + +  DP+ R+TVFD LP +  ++ I++GRLDINT GLL+ T
Sbjct: 84  PFEAELAQVLIYHKPEGEIVSQDDPEKRATVFDKLPRVRGAKWIAIGRLDINTSGLLIFT 143

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             G LA     P  +  R Y VR  G++ + ++  L +GI ++        +     +G+
Sbjct: 144 TSGELANRFMHPRYEVEREYAVRIFGELTEGEMLQLTQGIELEDGPASFDSIRPQGGEGA 203

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V LREG+NRE++++F+ F   V+RL+R+ +GP  L
Sbjct: 204 NHWYQVILREGRNREVRRLFDAFQKPVSRLMRVRFGPVNL 243


>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 =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 94/220 (42%), Positives = 131/220 (59%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G    L +R  VN +    I VDG  V  R
Sbjct: 3   EKLQKVLARAGHGSRREMEALITAGRVSVDGKVATLGDRVEVNAV----IRVDGHQVKTR 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
            AE    R+  YHKP G + T  DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T
Sbjct: 59  AAEEVICRVLAYHKPEGEMCTRHDPEGRPTVFDRLPKMEGARWIAVGRLDVNTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G++ +  L  L+KG+ ++       ++     +G 
Sbjct: 119 TDGELANRLMHPSHEVEREYAVRVFGEITEAMLQRLRKGVQLEDGTAKFNKIKPAGGEGL 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RL+RI YG  +L
Sbjct: 179 NQWFNVTLTEGRNREVRRLWESQEVQVSRLMRIRYGDVKL 218


>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 =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 106/279 (37%), Positives = 159/279 (56%), Gaps = 28/279 (10%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNV 54
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+   L +R  ++ 
Sbjct: 1   MSEQDLQNTEITPPAGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEATLGQRVDLH- 59

Query: 55  MSTDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVI 109
              D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I
Sbjct: 60  ---DAIAVDGKLIKREEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWI 116

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           ++GRLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++ 
Sbjct: 117 NIGRLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLED 176

Query: 170 ICYGDMQVTLDTQK-----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
              G  + T D QK     G N W    + EG+NRE+++++E     V+RL R+ +GP  
Sbjct: 177 ---GPAKFT-DIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVF 232

Query: 225 LGT-LLAGSTREVSK---KILREQLGPHLLEEAQVNLDA 259
           L + L  G  RE+++    IL  ++G   +    +NL A
Sbjct: 233 LNSDLPMGRWREMTQGEIDILAAEVGLQPVALPAMNLKA 271


>gi|170696462|ref|ZP_02887588.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170138615|gb|EDT06817.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 639

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 213 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRIMPTDQVR 269

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 270 INGKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFN 329

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 330 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELDDGPANFLRI 389

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 390 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 437


>gi|320663977|gb|EFX31164.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 290

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +GSN 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGSNQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>gi|307730031|ref|YP_003907255.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307584566|gb|ADN57964.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 614

 Score =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 205 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRIMPTDQVR 261

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 262 INGKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFN 321

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 322 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELDDGPANFLRI 381

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 382 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 429


>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 =  151 bits (381), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 85/229 (37%), Positives = 133/229 (58%), Gaps = 9/229 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHI 60
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD +
Sbjct: 175 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQV 231

Query: 61  EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDI 116
            ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD 
Sbjct: 232 RINGKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDF 291

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       ++
Sbjct: 292 NTEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLR 351

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 352 IRDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPL 400


>gi|315126449|ref|YP_004068452.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
 gi|315014963|gb|ADT68301.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
          Length = 289

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/217 (41%), Positives = 133/217 (61%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +++ KV+ARAG+ SRRE+E+ I   RV VNG +  +    V  TD I VDG  ++   KA
Sbjct: 6   EKLQKVLARAGVGSRREMEKYIDANRVSVNGKVA-KLGDRVEETDLIRVDGHTVKIEEKA 64

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ +Y+KP G ++T  DP+GR TVFD LP I   R I+VGRLD+NT GL+L TNDG
Sbjct: 65  DRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLFTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y  R  G+V  + +  L +G+ ++        +     +G N W
Sbjct: 125 ELANRLMHPSYEVEREYSARVFGEVTDETMKNLLRGVELEDGPAKFTGIKPMGGEGINRW 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE++++++  + +V+RLIRI YG  +L
Sbjct: 185 YNVTLNEGRNREVRRLWQSQDVEVSRLIRIRYGKLEL 221


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E  I Q RV V+G I      + V     I +DG  + ++++
Sbjct: 9   EKLQKILARSGHGSRREIEGYIQQGRVSVDGKIATLGDRLEVQPATKIRLDGRILNIKES 68

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++T  R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T D
Sbjct: 69  QKTVCRVLAYYKPEGELCTRHDPEGRPTVFDRLPKLLGSRWIAVGRLDVNTCGLLLFTTD 128

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD  KL  L KGI ++        +     +G N 
Sbjct: 129 GELANRLMHPSREVEREYAVRVFGEVDDAKLKQLAKGIQLEEGPASFRTIAFKGGEGMNQ 188

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 189 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIGL 226


>gi|323525722|ref|YP_004227875.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323382724|gb|ADX54815.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 618

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 208 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRIMPTDQVR 264

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 265 INGKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFN 324

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 325 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLNGVELDDGPANFLRI 384

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 385 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 432


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 92/211 (43%), Positives = 120/211 (56%), Gaps = 4/211 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 71
           +++ KV+ARAG+ SRRE+E+ I+  RVK++G + E     V     IEVDG  L +A  E
Sbjct: 32  EKLQKVLARAGLGSRREMEKWISDGRVKLDGRIAE-LGDRVCDNAAIEVDGQALSRAPAE 90

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
             R  LYHKP G V T  DP+GR TVF+ LP +   R IS+GRLD NT GLLL T DG L
Sbjct: 91  AVRCLLYHKPTGEVCTRKDPEGRRTVFERLPKVKGGRWISIGRLDYNTSGLLLFTTDGEL 150

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS    R Y VR  G+ D D L  L  G+ +         +      G N W  
Sbjct: 151 ANALMHPSAVIEREYMVRVMGEWDTDTLQRLIHGVELDDGFARFTDIQDGGGDGINHWFY 210

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           V L EG+NRE+++++E     V+RL R+ YG
Sbjct: 211 VVLMEGRNREVRRLWESQGLTVSRLKRVRYG 241


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 93/220 (42%), Positives = 127/220 (57%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E MI   RV V+G    L +R  V V     I +DG  +   
Sbjct: 3   EKLQKVLARAGHGSRREIEAMIEAGRVSVDGKIATLGDR--VEVTPALKIRIDGHLISVK 60

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T SDP+GR TVFD LP +  +R I+VGRLD+NT GLLL T
Sbjct: 61  ESVEQICRVLAYYKPEGELCTRSDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD  K+  L +G+ ++        +     +G 
Sbjct: 121 TDGELANRLMHPSQEVEREYAVRVFGQVDDAKVRELARGVQLEDGPAAFKTIRFSGGEGI 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>gi|291617615|ref|YP_003520357.1| RluB [Pantoea ananatis LMG 20103]
 gi|291152645|gb|ADD77229.1| RluB [Pantoea ananatis LMG 20103]
          Length = 294

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 127/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E MIA  RV V+G L      +       I +DG    +   
Sbjct: 3   EKLQKVLARAGHGSRREIEAMIAAGRVSVDGKLATLGDRIENSKALKIRIDGHLVSIAES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T SDP+GR TVFD LP +  SR I+VGRLD+NT GL+L T D
Sbjct: 63  ATEVCRVLAYYKPEGELCTRSDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD DK+  L KG+ ++        +     KG  +
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDDKIRQLSKGVQLEDGPAAFKTLRFAGGKGLTS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +T+ L EG+NRE+++++E    +V+RL+R+ YG   L
Sbjct: 183 GITLTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITL 220


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + 
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNG---EPAHIGQRIMPTDQVR 229

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 230 INGKPVKRKLPSKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFN 289

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 290 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRI 349

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++ E     V+RLIR  +GP  L
Sbjct: 350 RDGGGEGTNHWYHVALAEGRNREVRRMLEAVGLMVSRLIRTRHGPIPL 397


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 92/243 (37%), Positives = 139/243 (57%), Gaps = 11/243 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR-- 68
           P R+ KV+A AG+ SRRE+E  IA  +V VNG++      +V+++D +++ G  + +R  
Sbjct: 85  PVRLQKVLAEAGVGSRREMEEWIAAGKVSVNGVVAT-VGQSVVNSDKVKIGGRLINIRFT 143

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
             +   R+ +YHKP G + +  DPDGR +VF  LP +   R I+VGRLD NT GLLL T 
Sbjct: 144 GSSRPPRVLMYHKPEGEIVSRDDPDGRPSVFAALPRMRGGRWINVGRLDFNTSGLLLFTT 203

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G LA  L  PS++ +R Y VR  G++  D    L  G+ ++        +     +G+N
Sbjct: 204 SGELANKLMHPSSELVREYAVRVLGELTLDAQQKLLHGVELEDGRANFGSLHDGGGEGAN 263

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF----QLGTLLAGSTREVSKKILR 242
            W  V + EG+NRE++++FE     V+RLIR+ YGPF    QL   +A   +E   K+L 
Sbjct: 264 HWYRVTISEGRNREVRRMFEAVGCTVSRLIRVRYGPFILPPQLKRGMARELKEAEIKMLM 323

Query: 243 EQL 245
            +L
Sbjct: 324 REL 326


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 104/272 (38%), Positives = 156/272 (57%), Gaps = 24/272 (8%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMST 57
           KD+N  QE     +++ KV+AR G+ SRR+VE  I Q+R+KVNG+   L +R  ++    
Sbjct: 4   KDQNDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQKRIKVNGVEATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVG 112
           D I +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD +P     R I++G
Sbjct: 60  DAITIDGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPKPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLED--- 176

Query: 173 GDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT- 227
           G  + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ +GP  L + 
Sbjct: 177 GPAKFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSD 236

Query: 228 LLAGSTREVSK---KILREQLGPHLLEEAQVN 256
           L  G  RE+S+    IL  ++G   +   Q+N
Sbjct: 237 LPMGRWREMSQYEVDILSAEVGLTPVAMPQMN 268


>gi|330989187|gb|EGH87290.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 408

 Score =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 106/270 (39%), Positives = 153/270 (56%), Gaps = 20/270 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VD   +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDDRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L 
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLP 238

Query: 230 AGSTREVSK---KILREQLGPHLLEEAQVN 256
            G  RE+S+    IL  ++G   + + Q+N
Sbjct: 239 MGRWREMSQYEVDILAAEVGLQPVAQPQMN 268


>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 =  150 bits (380), Expect = 2e-34,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 132/228 (57%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +M TD + 
Sbjct: 202 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRIMPTDQVR 258

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 259 INGKPVKRKLANKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFN 318

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 319 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELAEGMRQKLLHGVELDDGPANFLRI 378

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 379 RDGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISL 426


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAER 72
           +++ KV+ARAG  SRRE+E MI+  RV V+G L      +    +  I +DG  +  AE 
Sbjct: 3   EKLQKVLARAGHGSRREIETMISAGRVSVDGKLATLGDRIENDKSLKIRIDGHLVSIAES 62

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           T    R+  Y+KP G + T +DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T D
Sbjct: 63  TTEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFKTLRFAGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RL+R+ YG  QL
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDIQL 220


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 92/226 (40%), Positives = 138/226 (61%), Gaps = 14/226 (6%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K +  +  TP ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   V + D + 
Sbjct: 144 KYLNSDALTP-KLHKVLADAGVGSRREMEELIVAGRVSVNG---EPAHIGQRVGANDQVR 199

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G P+ +    +  R+ LYHKP G + +H DP+GR+TVF  LP +   + +SVGRLD+N
Sbjct: 200 VNGRPIVRPNAKKPPRIILYHKPAGEIVSHDDPEGRATVFARLPKMRVGKWLSVGRLDLN 259

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDM 175
           TEGLL+LT  G LA  L  P     R Y VR  G++ +++ + L KGI ++ G+  +G +
Sbjct: 260 TEGLLILTTSGDLANRLMHPRYGAEREYAVRVLGELGEEQQDKLLKGIQLEDGLAQFGSL 319

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +      +GSN W  V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 320 EYL--GGEGSNRWYRVTLKEGRNREVRRMFEAAGVTVSRLIRTRFG 363


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 91/215 (42%), Positives = 130/215 (60%), Gaps = 11/215 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ K++A+AG+ SRRE+ER I Q RV++NG    L ERA     + D I+VDG  +   
Sbjct: 3   EKLQKILAQAGLGSRREMERWIEQGRVELNGSPAKLGERAE----AKDQIKVDGKVIEHG 58

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
           +R   R+  Y+KP G V T  DP+GR TVFD LP +   R I+VGRLDINT GLLL T D
Sbjct: 59  QRKARRVLAYNKPEGEVCTRHDPEGRPTVFDRLPKLHGERWIAVGRLDINTSGLLLFTTD 118

Query: 128 GGLARVLELPSTQWL-RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           G LA  L  PST  + R Y VR  G+V  + +  + +G++++        V      G N
Sbjct: 119 GELANKLMHPSTNTVDREYAVRVAGEVTDEAVKAMTEGVLLEDGMAKFTDVQYFDGDGFN 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            W  V + EG+NRE+++++E   +KV+RL R+ YG
Sbjct: 179 QWYHVCIMEGRNREVRRLWESQGFKVSRLKRVRYG 213


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 97/252 (38%), Positives = 149/252 (59%), Gaps = 19/252 (7%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNV 54
           M ++++ +   TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+   L +R  ++ 
Sbjct: 1   MSEQDLKETEITPPSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEATLGQRVDLH- 59

Query: 55  MSTDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVI 109
              D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I
Sbjct: 60  ---DAIAVDGKLIKREEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWI 116

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           ++GRLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++ 
Sbjct: 117 NIGRLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLED 176

Query: 170 --ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
               + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ +GP  L +
Sbjct: 177 GPAKFTDIQKAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNS 235

Query: 228 -LLAGSTREVSK 238
            L  G  RE+++
Sbjct: 236 DLPMGRWREMTQ 247


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 98/244 (40%), Positives = 143/244 (58%), Gaps = 13/244 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+AR G+ SRR+VE  IA+ RV VNG +       V S D I VDG  +R+ E  
Sbjct: 14  EKLQKVLARLGVGSRRDVEVWIAEGRVNVNGSVAS-LGQRVDSHDAITVDGHLIRREEAA 72

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G V T  DP+GR T+FD LP + + R I+VGRLDINT GLLL T DG
Sbjct: 73  ESVRRVLIYNKPEGEVCTRDDPEGRPTIFDRLPRLRTGRWINVGRLDINTTGLLLFTTDG 132

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS +  R Y VR  G+V ++ +  L  G++++     + D+Q     + G N
Sbjct: 133 ELANRLMHPSYEMDREYAVRVRGEVTEEMIERLLNGVMLEDGPAKFSDIQQAPGGE-GFN 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKK---ILR 242
            W    + EG+NRE+++++E     V+RL R+ +GP F    L  G  RE+ ++   IL 
Sbjct: 192 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMGRYREMDQREIDILS 251

Query: 243 EQLG 246
           E++G
Sbjct: 252 EEVG 255


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 138/240 (57%), Gaps = 16/240 (6%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++N   QR+ K +A  G+ SRR++E  I + R+KV+G + E     +   + + +DG PL
Sbjct: 3   KKNDDAQRIQKYLAARGVGSRRQIETWIKEGRLKVDGRVAE-LGQKISGNERLSLDGKPL 61

Query: 68  RKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLL 122
           R A   +    + +YHKP G + T  DP+GR +VF +LP I   R +++GRLD+NT GLL
Sbjct: 62  RIAVEHKNPHMILMYHKPAGEICTRKDPEGRVSVFQHLPKISHGRWVAIGRLDLNTSGLL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDM 175
           L TNDG LA  L  PS +  R Y VR  G+V ++ L  L++GI +         IC    
Sbjct: 122 LFTNDGALANQLMHPSAEIEREYWVRVAGEVTEEMLTALRQGIPLDDGLARFTEICPLKT 181

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
               DTQ   N + +V L+EG+NRE+++++E    KV+RL RI YG   L  +L AG  R
Sbjct: 182 LHEDDTQ--FNRYFSVTLKEGRNREVRRLWEAVGCKVSRLKRIRYGTISLPPSLSAGRHR 239


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 103/258 (39%), Positives = 143/258 (55%), Gaps = 12/258 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPL 67
           P R+ K++A AG+ SRR++E  I++ RV+VNG  L +        D I VDG      P 
Sbjct: 17  PVRLQKLLAEAGLGSRRQIEGWISEGRVRVNG-QLAKLGDQATRADRIRVDGRDVTLKPK 75

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
           R +E T++ +YHKP G + T  DP+ R TVF  LP     R I+VGRLDINT GL+L T 
Sbjct: 76  RDSE-TQIIVYHKPEGELVTRRDPEERPTVFRRLPRPKQGRWIAVGRLDINTSGLILFTT 134

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  + L  L  GI +        ++T     G+N
Sbjct: 135 DGELANRLMHPSREIEREYSVRILGEVAPETLERLTAGIELDDGPAKFERITDQGGTGAN 194

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            W  V LREG+NRE+++++E     V+RLIRI YG  +LG  L  G+ R ++     E +
Sbjct: 195 HWYNVVLREGRNREVRRLWEAAGCTVSRLIRIRYGNVELGRRLFPGNWRPLTDAERAELM 254

Query: 246 ---GPHLLEEAQVNLDAP 260
              G  +LE  ++   AP
Sbjct: 255 ALAGLRVLERPRLRRPAP 272


>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 =  150 bits (379), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 98/244 (40%), Positives = 143/244 (58%), Gaps = 13/244 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+AR G+ SRR+VE  IA+ RV VNG +       V S D I VDG  +R+ E  
Sbjct: 14  EKLQKVLARLGVGSRRDVEVWIAEGRVNVNGSVAS-LGQRVDSHDAITVDGHLIRREEAA 72

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G V T  DP+GR T+FD LP + + R I+VGRLDINT GLLL T DG
Sbjct: 73  ENVRRVLIYNKPEGEVCTRDDPEGRPTIFDRLPRLRTGRWINVGRLDINTTGLLLFTTDG 132

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS +  R Y VR  G+V ++ +  L  G++++     + D+Q     + G N
Sbjct: 133 ELANRLMHPSYEMDREYAVRVRGEVSEEMIERLLDGVMLEDGPAKFSDIQQAPGGE-GFN 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKK---ILR 242
            W    + EG+NRE+++++E     V+RL R+ +GP F    L  G  RE+ ++   IL 
Sbjct: 192 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMGRYREMDQREIDILS 251

Query: 243 EQLG 246
           E++G
Sbjct: 252 EEVG 255


>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 =  150 bits (378), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 95/237 (40%), Positives = 142/237 (59%), Gaps = 16/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +R+ K +A  G+ SRRE+E  I + R++VNG L E     +   + + +DG PLR   ER
Sbjct: 6   ERIQKWLAARGLGSRREIEGWIREGRLRVNGKLAE-LGQRISGYERLSLDGKPLRVSPER 64

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               ++ +YHKP G + + +DPDGR TVF +LP +   R +S+GRLD+NT GLLL TNDG
Sbjct: 65  EAPRQILMYHKPPGEICSRNDPDGRPTVFRHLPKLRQGRWVSIGRLDLNTAGLLLFTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTL-----DT 181
            LA  L  PS +  R Y VR  G+V++D L  L+ G+ ++    C+ D+Q        DT
Sbjct: 125 ELANRLMHPSAEIEREYWVRVAGEVNEDTLQALRNGLELEDGFACFDDVQPLQALHEDDT 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           Q   N + +V L+EG+NRE+++++E    +V+RL RI +G   L   L AG  R ++
Sbjct: 185 Q--YNRYFSVVLKEGRNREVRRLWEAVGCQVSRLKRIRFGNLWLPKNLAAGRWRPLT 239


>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 =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 134/237 (56%), Gaps = 27/237 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K+IA AG+ASRR+ E ++   RV VNG +  E  +     TD I VDG PL KAE+
Sbjct: 4   ERLQKIIAAAGMASRRKAEELVTAGRVTVNGEVKNELGSKADPETDDIRVDGKPL-KAEQ 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L HKP G VTT SDP+GR TV D +  I +R+  VGRLD  +EGLLLLTNDG +A 
Sbjct: 63  LVYVLLHKPKGYVTTVSDPEGRETVMDLVKGIPARLYPVGRLDYLSEGLLLLTNDGEMAA 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGD--------------- 174
            L   ST   + Y V+  G+  ++++  L+ G+ +   QG  + D               
Sbjct: 123 KLTHASTHVPKKYLVKVSGEPTEEQIQELRNGVQLPPEQGHIHADPREGGRFGGEKRRST 182

Query: 175 ------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                  ++ L T++G N W  V L EG+NR+I+++F+F    V ++ R+ YGP +L
Sbjct: 183 AVKTAPCKIEL-TREGDNPWYEVTLNEGRNRQIRRMFDFIGHHVEKIKRVEYGPLKL 238


>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 =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 133/235 (56%), Gaps = 14/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL-- 67
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  DG  L  
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDGKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVVIYHKRAGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKFNSIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>gi|163791509|ref|ZP_02185915.1| RluB [Carnobacterium sp. AT7]
 gi|159873232|gb|EDP67330.1| RluB [Carnobacterium sp. AT7]
          Length = 244

 Score =  150 bits (378), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 84/225 (37%), Positives = 132/225 (58%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E +I++  VKVNG +++   + + ++D +EVDGVP+ + E  
Sbjct: 2   ERLQKVLAHAGVASRRKSEELISKGHVKVNGKVVKEMGIQIGNSDVVEVDGVPIYREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  ++T  SD  GR  V D  P+I  R+  VGRLD +T G L+LTNDG L+++
Sbjct: 62  -YFLLNKPRNMITAVSDDKGRPVVTDLFPNIEQRIYPVGRLDYDTTGALMLTNDGELSQL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  Q  + Y  +  G VD+  LN L+KG+V++G        ++    +      V +
Sbjct: 121 LMHPKYQINKTYVAKVKGLVDRKALNKLEKGVVVEGKKTAPAKAKILSADRAKDITMVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EG+NR++K +F+     V +L R SYG   L  L  G  RE+
Sbjct: 181 TIHEGRNRQVKNMFQAIGHPVEKLKRESYGTLNLDGLQTGEWREL 225


>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 =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 97/235 (41%), Positives = 135/235 (57%), Gaps = 12/235 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPL-- 67
           TP+R+ K++A+ GI SRR++E  I Q RV+VNG +   A +   +TD   I  DG  L  
Sbjct: 11  TPERLQKLLAKYGIGSRRKIEEFIEQGRVRVNGKV---ATIGDKATDKDKISFDGKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I +GRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVIIYHKREGEVCTSKDEKDRKTVFDSLPRLAKSRWIMIGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS +  R Y VR +GQ +  + LN LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYEIEREYAVRVYGQELSDETLNKLKEGIQLEDGMAKFNNIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGNIILPKFVSRGKTLELN 242


>gi|167836825|ref|ZP_02463708.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis MSMB43]
          Length = 358

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 83/217 (38%), Positives = 128/217 (58%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   +M TD + ++G P+++   
Sbjct: 71  KLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRIMPTDQVRINGKPVKRKLP 127

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD NTEGLL+LT  G
Sbjct: 128 NKPPRVLLYHKPTGEIVSHADPEGRPSVFDRLPPMKTAKWLAVGRLDFNTEGLLMLTTSG 187

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA     P     R Y VR  G++ +     L  G+ +       +++     +G+N W
Sbjct: 188 DLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRDGGGEGTNHW 247

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE++++F+     V+RLIR  +GP  L
Sbjct: 248 YHVALAEGRNREVRRMFDAVGLMVSRLIRTRHGPIPL 284


>gi|254496468|ref|ZP_05109345.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354324|gb|EET12982.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 252

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 91/235 (38%), Positives = 135/235 (57%), Gaps = 7/235 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG  + +   +    D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIENGWVQVNGKPV-KLGDSASGDDKITVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           L+  + TR+ LYHKP+G +++  DP    TVFD LP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKIKQNTRILLYHKPVGEISSRHDPKFEKTVFDRLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ L +L+KG+ +        ++      G+
Sbjct: 120 NNGELANQLMHPRYGLEREYAVRVHGQVTQEMLTVLQKGVELDDGPAKFSRLESRGGDGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           N W  V L EG+NRE+++++E    +V+RLIRI YG   +   L    T E++ K
Sbjct: 180 NTWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLGRAQTYELTPK 234


>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 =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 97/235 (41%), Positives = 135/235 (57%), Gaps = 12/235 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPL-- 67
           TP+R+ K++A+ GI SRR++E  I Q RV+VNG +   A +   +TD   I  DG  L  
Sbjct: 11  TPERLQKLLAKYGIGSRRKIEEFIEQGRVRVNGKV---ATLGDKATDKDKISFDGKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I +GRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVIIYHKREGEVCTSKDEKDRKTVFDSLPKLAKSRWIMIGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS +  R Y VR +GQ +  + LN LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYEIEREYAVRVYGQELSDETLNKLKEGIQLEDGMAKFNNIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>gi|226943690|ref|YP_002798763.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
 gi|226718617|gb|ACO77788.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
          Length = 382

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 95/243 (39%), Positives = 142/243 (58%), Gaps = 14/243 (5%)

Query: 8   QENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +EN  P    +++ KV+AR G+ SRR++E  IA+ RV VNG +       V   D I +D
Sbjct: 5   EENSPPAAQGEKLQKVLARMGLGSRRDIEARIAEGRVMVNGTVAT-LGQRVGRHDAIALD 63

Query: 64  GVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           G  LR+ E      R+ +Y+KP G + T +DP+GR TVFD LP +   R +++GRLDINT
Sbjct: 64  GRLLRREEGAELVRRVLIYNKPDGEICTRNDPEGRPTVFDRLPRLKEGRWVNIGRLDINT 123

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQ 176
            GLLL T DG LA  L  PS +  R Y VR  G+V ++ L  LK+G++++     + D+Q
Sbjct: 124 TGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVTEEMLETLKRGVMLEDGPARFTDIQ 183

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTRE 235
                + G N W    + EG+NRE+++++E     V+RL R+ +GP F    L  G  RE
Sbjct: 184 EAPGGE-GLNHWFHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLAMGRWRE 242

Query: 236 VSK 238
           +++
Sbjct: 243 MTQ 245


>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 =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 87/223 (39%), Positives = 134/223 (60%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++AR+G+ASRR+ E MI + RV VN  I+ E  +   +  D I VDG  L  AE 
Sbjct: 3   ERLQKILARSGVASRRKAEEMIREGRVSVNSEIVRELGSKADIERDEIRVDG-KLICAEE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           T+++ + +KP G VT  SDP  R  V   LP +  R+  VGRLD ++EGLLLLTNDGG A
Sbjct: 62  TKVYVMLNKPRGYVTALSDPQKRPLVIHLLPELGVRLFPVGRLDYDSEGLLLLTNDGGFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + ++ P  +  + YRV+  G+++  + N L+KG+ ++   +   +V L+     ++W+T+
Sbjct: 122 QRVQHPRYRISKTYRVKISGRLNAAEFNRLQKGLELEDGKFAPDEVALEEINPKSSWLTM 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR I++ FE    +V RLIR +     LG L  G  R
Sbjct: 182 KISEGRNRVIRRAFEQLGHEVLRLIRTAVADLHLGNLREGDYR 224


>gi|284007498|emb|CBA72981.1| ribosomal large subunit pseudouridine synthase B [Arsenophonus
           nasoniae]
          Length = 322

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 131/223 (58%), Gaps = 16/223 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR--KA 70
           +++ KV+AR G  SRRE+E  I   R+ V+G L      + V +   I +DG  LR  +A
Sbjct: 23  EKLQKVLARCGYGSRREIESFIQSGRISVDGQLATLGDRIEVKANTKIRLDGHLLRIKEA 82

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E++  R+  Y+KP G + TH DP+GR TVFD LP +  SR I++GRLD+NT GLLL T D
Sbjct: 83  EKSICRILAYYKPEGELCTHHDPEGRPTVFDRLPKLTGSRWIAIGRLDVNTCGLLLFTTD 142

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G LA  L  P  +  R Y VR  G+++  K+  L KG+ ++     D + +  T K    
Sbjct: 143 GELANRLMHPRHEVEREYAVRVFGEINDAKIRQLTKGVQLE-----DGEASFKTLKFRGG 197

Query: 184 -GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 198 EGMNQWFNVTLTEGRNREVRRLWEAVGIQVSRLIRVRYGDIYL 240


>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 =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 134/218 (61%), Gaps = 8/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV ++G++       + +   + +DG  V L+ A+
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSIDGVIAN-LGDRIEADAKVRIDGRAVSLKSAD 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP +  SR ++VGRLDINT GLLL T+DG
Sbjct: 62  DVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS +  R Y VR  G+V +  +  L+ G++++ G+   D  +     +G N 
Sbjct: 122 ELANRLMHPSNEVEREYAVRTFGEVPEAAVQRLRTGVMLEDGMAQFDA-IKAAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V LREG+NRE+++++E    +V+RLIR+ YG  +L
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRVRYGMVEL 218


>gi|329297659|ref|ZP_08254995.1| 23S rRNA pseudouridylate synthase B [Plautia stali symbiont]
          Length = 292

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E MI+  R+ V+G L      +    T  I +DG    +   
Sbjct: 3   EKLQKVLARAGHGSRREIEAMISAGRISVDGKLATLGDRIENDKTLKIRIDGHLVSIAES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T +DP+GR TVFD LP +  SR I+VGRLD+NT GL+L T D
Sbjct: 63  ATEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLMLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G+VD +K+  L KG+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSRAVEREYAVRVFGEVDDEKVRQLSKGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG NRE+++++E    +V+RL+R+ YG  QL
Sbjct: 183 WYNVTLTEGCNREVRRLWEAVGVQVSRLMRVRYGDIQL 220


>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 =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 100/255 (39%), Positives = 149/255 (58%), Gaps = 25/255 (9%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNV 54
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+   L +R  ++ 
Sbjct: 1   MSEQDLQDTEITPPSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEATLGQRVDLH- 59

Query: 55  MSTDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVI 109
              D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I
Sbjct: 60  ---DAIAVDGKLIKREEAAEATRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWI 116

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           ++GRLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++ 
Sbjct: 117 NIGRLDINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLED 176

Query: 170 ICYGDMQVTLDTQK-----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
              G  + T D QK     G N W    + EG+NRE+++++E     V+RL R+ +GP  
Sbjct: 177 ---GPAKFT-DIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVF 232

Query: 225 LGT-LLAGSTREVSK 238
           L + L  G  RE+++
Sbjct: 233 LNSDLPMGRWREMTQ 247


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 102/274 (37%), Positives = 156/274 (56%), Gaps = 25/274 (9%)

Query: 1   MKDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVM 55
           M D++   +   P  +++ KV+AR G+ SRR+VE  I Q+R+KVNG+   L +R  ++  
Sbjct: 1   MNDQDHKDQEIGPAGEKLQKVLARIGVGSRRDVEAWITQKRIKVNGVEATLGQRVDLH-- 58

Query: 56  STDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVIS 110
             D I +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD +P     R I+
Sbjct: 59  --DAITIDGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPKPKEGRWIN 116

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +GRLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++  
Sbjct: 117 IGRLDINTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLED- 175

Query: 171 CYGDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
             G  + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ +GP  L 
Sbjct: 176 --GPAKFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLN 233

Query: 227 T-LLAGSTREVSK---KILREQLGPHLLEEAQVN 256
           + L  G  RE+S+    IL  ++G   +   Q+N
Sbjct: 234 SDLPMGRWREMSQYEVDILSAEVGLTPVAMPQMN 267


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 131/218 (60%), Gaps = 8/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +++ K +AR G+ SRR++E +I + RV VNG +       V   D I VDG  LR     
Sbjct: 4   EKLQKALARLGLGSRRQMEDVIREGRVSVNGTVAT-IGDRVGQGDEIRVDGRLLRYTAEN 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +R R+ +Y+KP G + +  DP+GR TVF+ LP +   R + VGRLDIN+ GLLL TNDG
Sbjct: 63  EKRRRILMYYKPEGEICSAHDPEGRPTVFERLPPLNHDRWVMVGRLDINSTGLLLFTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS +  R Y VR  G+V  + +  LK+G++++ G+   D  +     +G N 
Sbjct: 123 ELAHRLMHPSNEIEREYAVRVMGEVTPEIMLNLKRGVMLEDGMAQFD-DIVEKGGEGINK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L+EG+NRE++++FE    KV+RL+RI YG   L
Sbjct: 182 WYQVKLKEGRNREVRRLFESQGLKVSRLLRIRYGSVSL 219


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E  I   RV V+G I      V ++    I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIEAKIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD DKL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 93/227 (40%), Positives = 128/227 (56%), Gaps = 22/227 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
           +++ KV+ARAG+ SRRE+E +IA+ RV VNG ++      V   D I +DG P+   +  
Sbjct: 3   EKLQKVLARAGLGSRREMEAVIAEGRVSVNGEMVT-LGTRVEEVDRIRLDGNPVSVVKEE 61

Query: 73  ---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + T  DP+GR TVFD LP + S R I++GRLDINT GLLL T DG
Sbjct: 62  DAVCRILAYHKPEGELCTRKDPEGRKTVFDRLPPLKSGRWIAIGRLDINTSGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVT 178
            LA  L  PS +  R Y  R  G+V    +  L+ G+           I+G+  G     
Sbjct: 122 ELANRLMHPSHEVEREYSCRIFGEVTPKIIQNLRMGVELEDGPAKFQKIKGVAEG----- 176

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               +G N W  V L EG+NRE+++++E    +V+RLIRI YG   L
Sbjct: 177 -TGGEGLNQWYNVLLSEGRNREVRRLWESQGIQVSRLIRIRYGSLVL 222


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E  I   RV V+G I      V ++    I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIEAKIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD DKL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>gi|253699802|ref|YP_003020991.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251774652|gb|ACT17233.1| pseudouridine synthase [Geobacter sp. M21]
          Length = 266

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 83/225 (36%), Positives = 130/225 (57%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE E +IA  RV VNG ++          TD 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+ R+++++ E     V RL R  Y   ++G +  G  R ++
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRARYDFLEIGDMKPGEYRHLA 227


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 129/217 (59%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +R+ K++AR G+ SRREVE  I   RV++NGI  +     V   D + ++G PL     +
Sbjct: 3   ERLQKILARGGLGSRREVEAWIKAGRVRINGIPAQ-LGDKVSDEDQVTINGRPLSPRRLQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
           A  +++ LYHK  G + +  DP+GR TVF +LP     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 225
             V LREG+ RE+++++E    +V+RLIRI +GP  L
Sbjct: 182 YHVILREGRKREVRRLWESQGIQVSRLIRIRFGPVSL 218


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MI+  RV V+G L      V    +  I +DG  VP+ ++
Sbjct: 3   EKLQKVLARAGHGSRREIETMISAGRVSVDGKLATLGDRVEPSVSLKIRIDGHVVPVSES 62

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T +DP+GR TVFD LP +  +R ++VGRLD+NT GLLL T D
Sbjct: 63  ISEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWVAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G VD +K+  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGAVDDEKIKQLSRGVQLEDGPAAFKTLKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDL 220


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 131/226 (57%), Gaps = 3/226 (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
             +L +KP G++++  D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 62  -YYLLYKPRGVISSVKDEKGRKVVTDFFKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G   +++L   +KG++++       +V L +  +K   A V +
Sbjct: 121 LMHPRYEIEKVYVAKVKGIPTREQLKQPEKGVLLEDGITAPAKVKLLSADRKKRAAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+S
Sbjct: 181 SIHEGRNRQVRRMFEAIGCEVLKLKRERYAFLDLKGLRPGEYRELS 226


>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 =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 134/226 (59%), Gaps = 10/226 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVD 63
           +  E+  P ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   ++ TD + ++
Sbjct: 181 LAPEDDAP-KLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRILPTDQVRIN 236

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR++VFD LP +  ++ ++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 225
              +G+N W  V L EG+NRE++++FE     V+RLIR  +G   L
Sbjct: 357 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGSIPL 402


>gi|324117539|gb|EGC11445.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 299

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 12  EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 71

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 72  AEQICRVLVYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 132 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 191

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 192 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 229


>gi|168700584|ref|ZP_02732861.1| ribosomal large subunit pseudouridine synthase B [Gemmata
           obscuriglobus UQM 2246]
          Length = 271

 Score =  149 bits (376), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 90/235 (38%), Positives = 133/235 (56%), Gaps = 12/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R++K +A AG+ SRR  +++I+  RVKVNG+ +    + +  + H I VD  P+R AE+
Sbjct: 2   ERLNKYLAHAGVGSRRHCDKLISAGRVKVNGVKVTELGLKIDPSAHQIAVDDQPVR-AEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              W  +KP+G + T+ DP GR    D LP +  RV +VGRLD  ++GLLL+TNDG LA+
Sbjct: 61  LVYWAVNKPVGHLCTNHDPAGRPRAVDLLPHVEQRVYTVGRLDEGSDGLLLMTNDGDLAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNA 187
            L  P     ++Y V   G+   D L  L     + G+   D +V   + K     G+  
Sbjct: 121 GLTHPRYGVPKMYFVLVAGRPTDDDLQKL-----MDGVWLSDGKVRAKSAKRIKAQGNGT 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           WV V L EGKNREI+++   F  KV RL R++ GP +L  L  G  R +S + L+
Sbjct: 176 WVRVVLTEGKNREIRRMLAKFGHKVMRLKRVAIGPVKLDKLPKGKARRISDEELK 230


>gi|186476490|ref|YP_001857960.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192949|gb|ACC70914.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 597

 Score =  149 bits (376), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 133/228 (58%), Gaps = 9/228 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG   E A +   ++ TD + 
Sbjct: 191 KRVLSPDDDAPKLHKVLADAGMGSRRDMEELIVAGRVSVNG---EPAHIGQRILPTDLVR 247

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G P+++   ++  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++VGRLD N
Sbjct: 248 INGKPIKRKLQSKPPRVLLYHKPTGEIVSHADPEGRPSVFDKLPPMKTAKWLAVGRLDFN 307

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++
Sbjct: 308 TEGLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELTEGNRQKLLHGVELDDGPANFLRI 367

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L
Sbjct: 368 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIAL 415


>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 =  149 bits (376), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 88/220 (40%), Positives = 133/220 (60%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
           +++ K++AR+G  SRRE+E  + + R+ ++G+   L +R   N  ST  I +DG  + +R
Sbjct: 9   EKLQKILARSGHGSRREIEGYLQEGRISIDGVKAKLGDRIDAN--STAKIRLDGRILSIR 66

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           +A++   R+  Y+KP G + T SDP GR TVF  LP + S R I+VGRLD+NT GLLL T
Sbjct: 67  EAQKDVCRVLAYYKPEGELCTRSDPQGRPTVFQRLPRLNSARWIAVGRLDVNTSGLLLFT 126

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G++D  K+  L +G+ ++        V+    +G 
Sbjct: 127 TDGELANRLMHPSREVEREYAVRVFGEIDDAKIRQLTRGVQLEDGPASFRSVSYRGGEGI 186

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 187 NQWYNVSLTEGRNREVRRMWEAVGVQVSRLIRVRYGDIDL 226


>gi|152979359|ref|YP_001344988.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841082|gb|ABR75053.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 373

 Score =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 105/255 (41%), Positives = 147/255 (57%), Gaps = 12/255 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +IA+ RV V+G +      V V S   I +DG  V L   
Sbjct: 92  EKLQKVLARAGQGSRREIEAVIAEGRVSVDGKIAALGDRVIVHSGLKIRIDGHLVNLTGV 151

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+ +Y+KP G + T  DP+GR+TVF+ LP +  SR ++VGRLDINT GLLL T D
Sbjct: 152 QKDVCRVLMYYKPEGELCTRHDPEGRATVFERLPRLTGSRWVAVGRLDINTSGLLLFTTD 211

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G VD   L  L+KG+ ++        +      G N 
Sbjct: 212 GELANRLMHPSREVEREYSVRVFGNVDDAMLARLQKGVQLEDGPANFTAIKPAGGTGMNR 271

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+  +    LRE
Sbjct: 272 WFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMDLENVNYLRE 331

Query: 244 QLGPHLLEEAQVNLD 258
            +G  L  E +  LD
Sbjct: 332 LVG--LPPETETRLD 344


>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 =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 134/218 (61%), Gaps = 8/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV ++G++       + +   + +DG  + L+ A+
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSIDGVIAN-LGDRIEADAKVRIDGRAISLKSAD 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP +  SR ++VGRLDINT GLLL T+DG
Sbjct: 62  DVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTSDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS +  R Y VR  G+V +  +  L+ G++++ G+   D  +     +G N 
Sbjct: 122 ELANRLMHPSNEVEREYAVRTFGEVPEAAVQRLRTGVMLEDGMAQFDA-IKAAGGEGMNQ 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V LREG+NRE+++++E    +V+RLIR+ YG  +L
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRVRYGMVEL 218


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 83/225 (36%), Positives = 130/225 (57%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE E +IA  RV VNG ++          TD 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+ R+++++ E     V RL R  Y   ++G +  G  R ++
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRARYDFLEIGDMKPGEYRHLA 227


>gi|62261679|gb|AAX78007.1| unknown protein [synthetic construct]
          Length = 306

 Score =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 133/235 (56%), Gaps = 14/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL-- 67
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  DG  L  
Sbjct: 38  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDGKALHS 93

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 94  YGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 153

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 154 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKFNSIKFSGGE 213

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 214 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 268


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 133/235 (56%), Gaps = 14/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL-- 67
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  DG  L  
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDGKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKFNSIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 89/219 (40%), Positives = 133/219 (60%), Gaps = 9/219 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDG--VPLR 68
           P+R+ K++A++GI SRRE+E +IA  R+ +NG   E A+V   ++  D ++V+G  V LR
Sbjct: 66  PERLHKLLAQSGIGSRREMEELIAAGRISING---ETASVGQTASAGDRVKVNGKLVQLR 122

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            ++R  R+ LYHKP G + + +DP+ R  VF ++P I + R ++VGRLD NT GLLLLT 
Sbjct: 123 FSDRLPRVILYHKPEGEIVSRNDPEHRPNVFTSMPRISAGRWVAVGRLDFNTSGLLLLTT 182

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G LA  L  P  Q +R Y VR  G++ ++    L  GI +               +G+N
Sbjct: 183 SGDLANRLMHPRYQLVREYAVRILGELTEEVRRQLLDGIDLDDGPAQFASFQEAGGEGAN 242

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+NRE++++FE     V+RL+R+ YGPF L
Sbjct: 243 RWYRVSLHEGRNREVRRMFEAVGVVVSRLMRVRYGPFAL 281


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 89/219 (40%), Positives = 134/219 (61%), Gaps = 8/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ KV+ARAG+ SRRE+E  I+  RV VNG +       V S D + VDG  ++ KAE 
Sbjct: 3   EKLQKVLARAGLGSRRELETWISDGRVSVNGTVAT-LGDRVGSEDTLRVDGRMIKVKAEE 61

Query: 73  ---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+ +YHKP G V + +DP+GR TVFDNLP +   R + VGRLDINT G++L T DG
Sbjct: 62  DTVQRVIMYHKPPGEVCSRNDPEGRPTVFDNLPRLQGMRWVQVGRLDINTTGMMLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSN 186
            LA  L  PS  ++R Y VR  G + Q+K   +  G++++ G+  +  ++     ++G+N
Sbjct: 122 ELAHRLMHPSNGFVREYAVRVRGGMTQEKRQAMLDGVLLEDGVSKFDSIEDAGGAEEGAN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L  GK RE++++F+  + +V RL+RI +G   L
Sbjct: 182 HWYKVTLTGGKYREVRRLFQSQDLEVARLMRIRFGDLNL 220


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +IA  RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIAAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRDARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 96/232 (41%), Positives = 130/232 (56%), Gaps = 8/232 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----R 68
           P+R+ K++A+ GI SRR++E  I Q RVKVNG +        +  D I  DG  L    +
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKAIEADKISFDGKALHSYGQ 70

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
              R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL T D
Sbjct: 71  PMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLFTTD 130

Query: 128 GGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           G LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +G+N
Sbjct: 131 GDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKFNSIKFSGGEGAN 190

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 191 LWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 133/235 (56%), Gaps = 14/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL-- 67
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  DG  L  
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDGKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKFNNIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 130/234 (55%), Gaps = 2/234 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y  +  G +  D +  L+ G+VI G        ++     K + + V++
Sbjct: 123 MMHPRYKVDKTYVAKVEGLITPDSIKKLRNGVVIDGKPTSRARAKIISRDAKKNTSIVSL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  ++KK+F+    KV +L R +YG   L  L +G  RE+S   +RE L
Sbjct: 183 TIHEGRYHQVKKMFDAVGHKVQKLSRTTYGTLTLDGLTSGEYRELSHNEVRELL 236


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 12  EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 71

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 72  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 132 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 191

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 192 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 229


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 85/227 (37%), Positives = 133/227 (58%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I Q RVKVNG ++      V   D IEVD VP+ ++E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIGQGRVKVNGKVVRELGTKVGPNDKIEVDEVPV-ESEAP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+++  +D  GR TV D  P +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFMLYKPRGVISAANDDKGRKTVVDFFPHVEERIYPIGRLDYDTSGLLLLTNDGEFANQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  +VY  +  G   ++K+  L++G++++       +   +++D  K   A V 
Sbjct: 121 LMHPKFEVDKVYVAKIKGIPSREKIRQLQRGVMLEDGKTAPARAKVLSIDKSK-QTAIVE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGKNR+++++F+     V +L R  YGP  L  L AG  RE++
Sbjct: 180 LTIHEGKNRQVRRMFDAIGHSVLKLKRERYGPLDLRGLNAGEARELT 226


>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 =  149 bits (375), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 88/225 (39%), Positives = 130/225 (57%), Gaps = 2/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AG+ASRR  E MI + RVKVNG  +    V V   D +EVDG P+   E+  
Sbjct: 7   RLQKVVAQAGLASRRGAETMITEGRVKVNGETVTTLGVKVGIHDTVEVDGAPIEGREKLV 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G+VTT SD  GR TV D L  I  RV  VGRLD +T G LLLTNDG +A  L
Sbjct: 67  YYLLNKPRGVVTTTSDEKGRKTVLDLLEDIDQRVYPVGRLDYDTTGALLLTNDGTIANQL 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVG 192
             P ++  ++Y  +  G    +KL  LK+G++I+G      +VT++   +    + V + 
Sbjct: 127 MHPKSRVDKIYLAKVSGIATVEKLAPLKQGVIIKGRKTAPARVTIERVDKDKKTSMVRII 186

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+N ++K + +     V++L R  Y  F L  L +G  R+++
Sbjct: 187 IHEGRNHQVKDMLQKVGLPVDKLTREQYAFFDLIGLQSGEYRKLT 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 =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 92/218 (42%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +IA  RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIAAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRDARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 130/234 (55%), Gaps = 2/234 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y  +  G +  D +  L+ G+VI G        ++     K + + V++
Sbjct: 123 MMHPRYKVDKTYVAKVEGLITPDSIKKLRNGVVIDGKPTSRARAKILSRDAKKNTSIVSL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  ++KK+F+    KV +L R +YG   L  L +G  RE+S   +RE L
Sbjct: 183 TIHEGRYHQVKKMFDAVGHKVQKLSRTTYGTLTLDGLTSGEYRELSHNEVRELL 236


>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 =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 12  EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 71

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 72  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 132 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 191

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 192 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 229


>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 =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 24  EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 83

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 84  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 143

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 144 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 203

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 204 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 241


>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 =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 132/226 (58%), Gaps = 10/226 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVD 63
           +  E+  P ++ KV+A AG+ SRRE+E +I   RV VNG   E A +   ++ TD + ++
Sbjct: 177 LAPEDDAP-KLHKVLAEAGMGSRREMEELIVAGRVSVNG---EPAHIGQRILPTDQVRIN 232

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR++VFD LP +  ++ ++VGRLD NTE
Sbjct: 233 GKPVKRKLPNKPPRVLLYHKPTGEIVSHADPEGRASVFDRLPPMKTAKWLAVGRLDFNTE 292

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA     P     R Y VR  G++ +     L  G+ +       +++  
Sbjct: 293 GLLMLTTSGDLANRFMHPRYSVEREYAVRVVGELSEASRQKLLHGVELDDGPANFLRIRD 352

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              +G+N W  V L EG+NRE++++FE     V+RLIR  +G   L
Sbjct: 353 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGSISL 398


>gi|54112711|gb|AAV28989.1| NT02FT0029 [synthetic construct]
          Length = 271

 Score =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 133/235 (56%), Gaps = 14/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL-- 67
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  DG  L  
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDGKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGMAKFNSIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>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 =  149 bits (375), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 95/240 (39%), Positives = 133/240 (55%), Gaps = 9/240 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            + +R+ KV+A AGIASRR+ E  IA  RV VNG ++      V    D I VDG P+ K
Sbjct: 1   MSAERLQKVLASAGIASRRDCEEYIAAGRVMVNGKVVRIPGTRVDPEHDEILVDGKPIGK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTND 127
                  + HKP G+V+T  DP GR TV D  NLP    R+  VGRLD ++EGLLLLT+D
Sbjct: 61  IHHRTYVMLHKPAGVVSTTDDPHGRPTVVDLVNLPQ---RLFPVGRLDYDSEGLLLLTDD 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L + L  PS Q  + Y+V  +     + L   + G+ + G+      V L  +    A
Sbjct: 118 GELTQKLTHPSYQVEKEYQVLLNDAPSPNALRAWRTGVELDGVKTAPAWVELIERTPEGA 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQ 244
           WV V L EG+ R+I++V     ++V RLIR+  GP  LG L +G+ R ++ +   +LRE 
Sbjct: 178 WVRVILHEGRKRQIREVARLLGYEVRRLIRVREGPLALGDLPSGTWRFLTDEEVDMLREH 237


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  V +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLVSVRES 62

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  VEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDTKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>gi|206889194|ref|YP_002248392.1| ribosomal large subunit pseudouridine synthase B
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206741132|gb|ACI20189.1| ribosomal large subunit pseudouridine synthase B
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 237

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 131/226 (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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EG+ R+I+K+ E     V RLIRI+    +LG L  G  R ++K+
Sbjct: 183 HEGRKRQIRKMLERVGHPVIRLIRIAIDGVKLGDLKPGQLRPLTKE 228


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/232 (38%), Positives = 135/232 (58%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLRK 69
           +R+ K++++AG+ SRRE+ER I    V+VNG  + +   +    D I V G     PL+ 
Sbjct: 4   ERLQKILSQAGLGSRREMERWIENGWVQVNGKPV-KLGDSASEEDKITVKGKLIPNPLKV 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP+G +++  DP    TVFD+LP +   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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
             V L EG+NRE+++++E    +V+RLIRI YG   +   L+ G   E++ K
Sbjct: 183 YHVTLNEGRNREVRRLWESQGLEVSRLIRIRYGTITMPRYLSRGQHYELTPK 234


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 86/226 (38%), Positives = 132/226 (58%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I + +V VNG ++    V V  ++ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAETLIKEGKVTVNGKVVTELGVKVSGSERIEVEGIQLTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +   +   A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKIRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELS 226


>gi|239993811|ref|ZP_04714335.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii ATCC 27126]
          Length = 298

 Score =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 94/229 (41%), Positives = 135/229 (58%), Gaps = 25/229 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL-RKA 70
           +++ KV+A  G+ SRRE+ER I + RV V+G    +A +   V  T  I VDG  L R+ 
Sbjct: 3   EKLQKVLANQGLGSRREMERWIEEGRVSVDGT---KATLGDRVDHTAQIRVDGHLLSRQT 59

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E+   R+ +Y+KP G + +  DP+GR TVFD LP+I   R I+VGRLD+NT GLLL TND
Sbjct: 60  EQPICRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRLGRWITVGRLDMNTSGLLLFTND 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-- 185
           G LA  L  P  +  R Y VR  G+V    L+ L+KG+ ++     D +    T  G+  
Sbjct: 120 GELANRLMHPKCEVEREYAVRVFGEVTGKTLHTLQKGVELE-----DGEAKFLTISGAPT 174

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                    N W  V L+EG+NRE+++++E    +V+RLIR+ YGP +L
Sbjct: 175 PQHAEDESMNRWYNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPIEL 223


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 89/215 (41%), Positives = 126/215 (58%), Gaps = 4/215 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQLGD-RITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+GR+TVF+ LP +   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 225
           V + EG++R +++++E    KV+RLIR+ +GP  L
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVL 216


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 89/215 (41%), Positives = 126/215 (58%), Gaps = 4/215 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQLGD-RITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+GR+TVF+ LP +   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 225
           V + EG++R +++++E    KV+RLIR+ +GP  L
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVL 216


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 92/227 (40%), Positives = 133/227 (58%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQLGD-RITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+GR+TVF+ LP +   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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLSKSLRRGAWKEL 228


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 93/234 (39%), Positives = 138/234 (58%), Gaps = 11/234 (4%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMS 56
           M DK    Q+    +++ K++ARAG  SRRE+E  I + R+ ++G    L +R  + V  
Sbjct: 1   MSDKTQKTQKTERTEKLQKILARAGHGSRREIEGYIQEGRISIDGKTATLGDR--IEVKP 58

Query: 57  TDHIEVDG--VPLRKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISV 111
           +  I +DG  + +++ ++T  R+  Y+KP G + T  DP+GR TVFD LP +  +R I+V
Sbjct: 59  SIKIRLDGRILSIKEPQKTICRVLAYYKPEGELCTRHDPEGRPTVFDRLPKMQDARWIAV 118

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLDINT GLLL T DG LA  L  PS +  R Y VR  G+VD  KL  L +G+ ++   
Sbjct: 119 GRLDINTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGEVDNAKLRQLTQGVQLEDGP 178

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                V+    +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 179 ASFKTVSFKGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDL 232


>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 =  148 bits (374), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 86/221 (38%), Positives = 132/221 (59%), Gaps = 9/221 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           ++ KV+A +G+ SRRE+E +I   RV VN    E A +   V+ TD + V+G  +++  +
Sbjct: 70  KLHKVLADSGMGSRREMEELIVAGRVSVNA---EPAHLGQRVLPTDQVRVNGKLIQRKNK 126

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           +   R+ +YHKP G + +  DP GR+TVF  LP I + + I+VGRLD NTEGLLL T+ G
Sbjct: 127 SKPPRVLIYHKPAGEIVSMDDPQGRTTVFQKLPKISNGKWIAVGRLDFNTEGLLLFTSSG 186

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  R Y VR  G++ +++   L  GI ++      + V     +G+N W
Sbjct: 187 ELANRLMHPRYEVQREYAVRILGELSEEQRQQLLTGIQLEDGPAKFLYVDAAGGEGANRW 246

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             VGL+EG+NRE++++FE  N  V+RLIR  +G   + + L
Sbjct: 247 YKVGLKEGRNREVRRMFEACNLTVSRLIRTRFGDIMMPSTL 287


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 86/232 (37%), Positives = 137/232 (59%), Gaps = 11/232 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMST 57
           +K+K        P+R+ KV+A +G+ SRRE+E  I    V+VNG    R AV    +   
Sbjct: 99  LKEKRTDLSRIEPERLQKVLAASGVGSRREMEEWINNGWVQVNG----RVAVLGEKITPE 154

Query: 58  DHIEVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGR 113
           D + V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GR
Sbjct: 155 DQVTVKGSAIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGR 214

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDINT GLL+LT  G L +    PS +  R Y VR  G++ Q+++N L +G++++     
Sbjct: 215 LDINTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELTQEQMNALSEGVMLEDGLAR 274

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             ++     +G+N W  V L+EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 275 VERIYEQGGEGANKWYNVVLKEGRNREVRRLFESQGLTVSRLVRVGFGPIGL 326


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 91/217 (41%), Positives = 131/217 (60%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRK-- 69
           +R+ KV+AR G+ SRRE+ER I + R+K+NG  +      + + DH+ ++   V   K  
Sbjct: 17  ERIQKVLARGGVGSRREIERWIDEGRLKINGKPVGLGD-RLKAGDHLLINDRVVHWEKFV 75

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            + TR+ LYHKP+G V T  DP+GR  VF  LP +  SR I+VGRLDINT GLLL+TN+G
Sbjct: 76  EQPTRVLLYHKPVGEVVTRRDPEGRPVVFTQLPKLAISRWIAVGRLDINTSGLLLVTNNG 135

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PSTQ  R Y VR  G+V    L  LK+G+ ++        +     +G+N W
Sbjct: 136 ELANRLMHPSTQVEREYAVRILGEVSDATLAKLKQGVELEDGKAKFDDIIFFGGEGANKW 195

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NR +++++E     V+RL+R+ YGP  L
Sbjct: 196 YNVIVAEGRNRLVRRLWESQELIVSRLMRVRYGPVVL 232


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V ++    I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD++KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>gi|311279823|ref|YP_003942054.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749018|gb|ADO48770.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 299

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +++ KV+ARAG  SRRE+E MI   RV V+G I      V +     I +DG  +   E 
Sbjct: 3   EKLQKVLARAGHGSRREIESMIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKES 62

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  VEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDNKVRELARGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 88/236 (37%), Positives = 135/236 (57%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +G+ SRR+ E++IA  RV VNG ++      V   D IEV+G+ L K E  
Sbjct: 2   ERLQKVIANSGVTSRRKAEQLIAAGRVTVNGEVVRELGTKVSPNDRIEVEGIELTKEEH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+V+  +D  GR TV D    I  R+  VGRLD  T GLLL+TNDG  A  
Sbjct: 61  RYFLFYKPRGVVSAVTDDKGRKTVADYFVDIPERLYPVGRLDYETSGLLLMTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G   +++L  L++G+VI G      +V L +  +    A + +
Sbjct: 121 LMHPKHEVEKQYIARVKGIPTKEQLRRLERGVVIDGRKTAPAKVKLRSADKAKEKAIIEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQ 244
            + EG+NR+++K+FE   + V +L+R +Y    +  + AG  RE+S    K+L+ Q
Sbjct: 181 TIHEGRNRQVRKMFESIGFPVQKLMREAYAFLNVAGMNAGERRELSHHEVKLLKTQ 236


>gi|295095683|emb|CBK84773.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 291

 Score =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V ++    I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD++KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (373), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>gi|297520148|ref|ZP_06938534.1| 23S rRNA pseudouridylate synthase B [Escherichia coli OP50]
          Length = 281

 Score =  148 bits (373), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  148 bits (373), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V ++    I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD++KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>gi|187928207|ref|YP_001898694.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187725097|gb|ACD26262.1| pseudouridine synthase [Ralstonia pickettii 12J]
          Length = 594

 Score =  148 bits (373), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 94/250 (37%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       +++TD + 
Sbjct: 202 KARELTSEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNG-LPAHIGQRILATDQVR 259

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD LP +   + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 380 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 439

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 440 SAEDVRTLMG 449


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 87/227 (38%), Positives = 132/227 (58%), Gaps = 5/227 (2%)

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
             +L++KP G++++  D  GR  V D    I  R+  VGRLD +T G+LLLTNDG  A +
Sbjct: 62  -YYLFYKPRGVISSVKDDKGRKVVTDFFKDIDKRIYPVGRLDYDTSGILLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVT 190
           L  P  +  +VY  +      +++L  L+KGI+++       +V L   D QK   A + 
Sbjct: 121 LMHPRYEIEKVYIAKVKKIPTREQLKQLEKGIMLEDGMTAPAKVKLLSHDKQK-QTAIIE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE     V +L R  Y    L  L  G  RE++
Sbjct: 180 IRIHEGRNRQVRRMFEAIGCNVMKLKRERYAFLDLKGLNPGEYRELT 226


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDTKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 126/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPRLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>gi|229543960|ref|ZP_04433019.1| pseudouridine synthase [Bacillus coagulans 36D1]
 gi|229325099|gb|EEN90775.1| pseudouridine synthase [Bacillus coagulans 36D1]
          Length = 245

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 135/227 (59%), Gaps = 5/227 (2%)

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
             +L++KP G+++  SD  GR TV D      +RV  VGRLD +T GLL++TNDG  A +
Sbjct: 62  -YYLFYKPRGVISAVSDDKGRKTVSDYFRDAGARVYPVGRLDYDTSGLLVVTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  R  G   + +L  L+KGI ++       +   +++D +K   A V 
Sbjct: 121 LMHPRFEIDKTYIARLSGIPSRQELKQLEKGIRLKDGMTAPARAKLLSMDKRK-KKAIVQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE   + V +L R +YG   L  L AG  RE++
Sbjct: 180 LTIHEGRNRQVRRMFEHLGYPVEKLRREAYGMLTLKGLNAGEKRELT 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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 94/250 (37%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       +++TD + 
Sbjct: 202 KARELTSEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNG-LPAHIGQRILATDQVR 259

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD LP +   + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 380 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 439

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 440 SAEDVRTLMG 449


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 90/234 (38%), Positives = 138/234 (58%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++A AG+ASRRE E++I   RV+VNG ++ E           I VDG P+ + E 
Sbjct: 3   ERLQKILAAAGVASRREAEKIITAGRVRVNGKVVTELGCKFDADKVRISVDGKPIAQ-EA 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++++KP G+VTT SDP  R ++ D + ++  RV  VGRLD NTEGLLLLTNDG LA+
Sbjct: 62  KAYYMFYKPRGVVTTMSDPQNRRSIADFVQNLPERVFPVGRLDFNTEGLLLLTNDGALAQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWV 189
            L  PS +  + Y V+  G V Q+KL+ L+ G+ ++        V L   D ++G   + 
Sbjct: 122 ALMHPSHEVNKTYFVKVPGIVPQEKLDQLRLGVKLEDGPTAPAIVNLRDYDHERGFTLF- 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EG+NR+I+++ +   + V  L RI  GP QL  L  G  R +S++ L +
Sbjct: 181 DITIHEGRNRQIRRMCDAIGFPVRDLKRIKLGPLQLQNLGRGKFRSLSEQELSQ 234


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 133/226 (58%), Gaps = 3/226 (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 KP G++++ SD  GR  V D    I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRKVVTDFFQDIPQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG++++       +V + +  ++   + V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVILEDGKTSPARVKIISWDKRKEMSIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    KV +L R  Y   ++G+L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEAIGCKVMKLKRERYAFLEVGSLRPGDARELT 226


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 129/239 (53%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I +  VKVNG +++     V  +D +EVD VP+ K E  
Sbjct: 3   ERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVDEVPISK-EVP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L   
Sbjct: 62  VYYLLYKPRGVITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDNH 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G +  D +  L+ GI I G      + T+     ++  V++ +
Sbjct: 122 LTHPKYEVDKTYVAKVKGTITNDDMKKLRTGIHIDGRKTASAKATIIRNNNNSTIVSLTI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+N ++KK+F      V +L R SYG   L  L  G  R         +L PH +EE
Sbjct: 182 HEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYR---------RLKPHEVEE 231


>gi|330911132|gb|EGH39642.1| ribosomal large subunit pseudouridine synthase B LSU [Escherichia
           coli AA86]
          Length = 291

 Score =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 88/236 (37%), Positives = 131/236 (55%), Gaps = 5/236 (2%)

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
             ++++KPIG+++   D   R  V D  P I  R+  VGRLD NT GLLLLTNDG  A  
Sbjct: 62  -YYVFYKPIGVISAVKDDKDRKVVTDFFPGIEQRIYPVGRLDYNTSGLLLLTNDGEFANT 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  +VY  +  G +  ++   L++G+ I G+     Q   +++D  K     + 
Sbjct: 121 LMHPRYEINKVYVAKVEGVITGEERKQLERGVEIDGVKTAPAQAKILSVDKDK-KTTIIE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + EG+NR+++K+ E     V +L R  YG   L  L  G +R + K  + E L 
Sbjct: 180 LVIHEGRNRQVRKMLEAVGHPVTKLKRERYGFLDLKGLKPGDSRTLLKHEIEELLA 235


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/220 (40%), Positives = 127/220 (57%), Gaps = 10/220 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR- 68
           TP ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   +   DH++V+G P+R 
Sbjct: 96  TP-KLHKVLAQAGMGSRLEMEQLIMEGRITVNN---EPAHIGQRIQFGDHVKVNGKPIRF 151

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
              A   R+  YHKP+G V TH DP  R TVF  LP +F  +  SVGRLD+NTEGLLL T
Sbjct: 152 RIDAPPARVIAYHKPVGEVVTHDDPQNRPTVFRRLPKLFQGKWQSVGRLDLNTEGLLLFT 211

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           + G LA  L  P     R Y VR  G +++D+   L  G+ +         +     +G+
Sbjct: 212 SSGELANNLMHPRFGLEREYAVRVLGALNKDEKQRLLDGVKLDDGVAQFGSIEAGGGEGA 271

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V + EG+NRE++++FE     V+RLIRI YG   L
Sbjct: 272 NCWYRVTIAEGRNREVRRMFEAVGHAVSRLIRIRYGAMML 311


>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 =  147 bits (372), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E  I +  V VNG I      V+VM +  I +DG  +P+ + 
Sbjct: 3   EKLQKILARSGYGSRREIEEKIQRGLVSVNGKISTLGDRVSVMPSTQIRLDGRILPITEP 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           ++   R+  Y+K  G + T  DP GR TVFD LP +  SR I +GRLDINT GLLL T D
Sbjct: 63  QKIPCRVLAYYKIEGEICTRKDPKGRPTVFDRLPKLHHSRWIGIGRLDINTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y  R  GQV++  +  L +GI ++       +VT    +G N 
Sbjct: 123 GELAHRLMHPSQEIEREYASRIFGQVNEPSIKQLTQGIQLEDGMAAFRRVTFGGGEGLNH 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 183 WYNVILTEGRNREVRRLWEAIGVQVSRLIRIRYGDIKL 220


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 88/222 (39%), Positives = 128/222 (57%), Gaps = 10/222 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++A AG+ASRR+ E +I   RV+VNG ++ E       ++DHI VDG  L+  E+
Sbjct: 24  ERLQKILASAGVASRRKAEELILAGRVQVNGQVVTEMGFKADAASDHIRVDGKLLQGPEK 83

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            R ++ +KP G VTT SDP+GR TV   F        R+  VGRLD  +EGLLL+TNDG 
Sbjct: 84  LRYFMLNKPKGYVTTVSDPEGRHTVMEFFHGRGKGGERLYPVGRLDYASEGLLLMTNDGA 143

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------TQK 183
           LA  L   S+   +VY V+  G+  +++L  ++ GI+I     G+ +V          + 
Sbjct: 144 LANTLTKASSHVEKVYLVKVSGRPTEEQLEQIRAGIMIDRGRPGEGRVMTAPAGVRMVRD 203

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             N W  + L EG+NREI+K+FE     V ++ RI YGP  L
Sbjct: 204 AENPWFELTLIEGRNREIRKMFEETGHFVEKIRRIGYGPLVL 245


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 110/316 (34%), Positives = 169/316 (53%), Gaps = 28/316 (8%)

Query: 1   MKDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D +   +   P  +++ KV+AR G+ SRR+VE  I+Q R+KVNG       + V   D
Sbjct: 1   MSDTDQNDQEIRPAGEKLQKVLARIGVGSRRDVESWISQGRIKVNGKEAT-LGLRVDLHD 59

Query: 59  HIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGR 113
            I +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++GR
Sbjct: 60  AISIDGKVIKREEAAESVRRVIMYNKPDGEICTRDDPEGRPTVFDKLPRPREGRWINIGR 119

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--IC 171
           LDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G++++     
Sbjct: 120 LDINTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVMLEDGPAK 179

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
           + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ +GP  L + L  
Sbjct: 180 FTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPM 238

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+S      Q    +L  A+V L  P+          P + ++  D   RM++ SS
Sbjct: 239 GRWREMS------QYEVDVL-SAEVGL-TPVAM--------PQLNAKSKDKLERMQRKSS 282

Query: 291 QKNGLSKQKKLATPVH 306
           +  G S++ +   P +
Sbjct: 283 RPVGKSERVRTLRPAN 298


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKFIAHAGVASRRKAEELIKQGLVTINGQVVTELATTVKSGDQVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLLLTNDGDFTDMM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   +D L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKDNLRPLTRGVVIDGKKTKPARYNIIRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLIVDKLSRTQFGTLDLTGLRPGEARRLNKK 227


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 87/218 (39%), Positives = 127/218 (58%), Gaps = 11/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDGVPLR--- 68
           R+ K++AR G+ SRRE+E MIA  RV +N     L +RA +     D I +DG  +R   
Sbjct: 34  RLQKLLARNGLGSRREIEAMIAAGRVSINNTTAKLGDRAGLG----DKIRIDGRIIRLSM 89

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
            A   R+ +YHKP G + +  DP GR +VFD LP I  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 225
           W  + L+EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 210 WYRIVLKEGRNREVRRMFEALGITVSRLMRVRFGPVNL 247


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV ++G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSIDGRIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKIIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  ++  P ++ K++A AG+ SRR++E +I Q RV VNG L       +++TD + 
Sbjct: 213 KTRELTSDDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNG-LPAHIGQRILATDQVR 270

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD LP +   + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 391 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 450

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 451 SAEDVRTLMG 460


>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 =  147 bits (371), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 85/220 (38%), Positives = 131/220 (59%), Gaps = 5/220 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           Q++ KV+A+AG+ SRRE+E +IA  +V +NG   +     + + D + V    V  R A 
Sbjct: 73  QKLHKVLAQAGLGSRREMEELIASGQVTINGKTAQ-VGDRIAARDVVRVGKRVVHFRSAR 131

Query: 72  R-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           R  R+ LYHKP G + +  DP GR++VFD LP +  S+ I++GRLD NT GLL+ T DG 
Sbjct: 132 RLPRVMLYHKPEGEIVSQDDPQGRTSVFDKLPQLRSSKWIAIGRLDYNTSGLLVFTTDGE 191

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  R Y VR  G++  ++  LL  G+ ++        ++ +  +GSN W 
Sbjct: 192 LANRLMHPRFEVEREYAVRIIGRLTPEQATLLTSGVELEDGAAKFDYLSDEGGEGSNHWY 251

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            V L+EG+NRE++++FE     V+RL+R+ +GP  L + L
Sbjct: 252 RVILKEGRNREVRRMFEAVGMTVSRLMRVRFGPINLPSRL 291


>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 =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 129/239 (53%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I +  VKVNG +++     V  +D +EVD VP+ K E  
Sbjct: 3   ERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVDEVPISK-EVP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L   
Sbjct: 62  VYYLLYKPRGVITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDNH 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G +  D +  L+ GI I G      + T+     ++  V++ +
Sbjct: 122 LTHPKYEVDKTYVAKVKGTITNDDMKRLRTGIHIDGRKTASAKATVIRNNNNSTIVSLTI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+N ++KK+F      V +L R SYG   L  L  G  R         +L PH +EE
Sbjct: 182 HEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYR---------RLKPHEVEE 231


>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 =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 135/224 (60%), Gaps = 20/224 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRK 69
           +++ KV+ARAG  SRRE+E  IA  RV ++G   E A++   + +   + +DG  + L+ 
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSIDG---EIASLGDRIEADAKVRIDGRSISLKS 59

Query: 70  AER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           AE    R+  YHKP G + +  DP+GR TVFD LP +  SR ++VGRLDINT GLLL T+
Sbjct: 60  AEDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--- 183
           DG LA  L  PS +  R Y VR  G++ +  +  L+ G++++     D     D+ K   
Sbjct: 120 DGELANRLMHPSNEVDREYAVRTFGEIPEATVQRLRTGVMLE-----DGPAQFDSIKPAG 174

Query: 184 --GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             G N W  V LREG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 175 GEGMNQWWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVEL 218


>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 =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 85/225 (37%), Positives = 131/225 (58%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E +I++  VKVNG +++   + + ++D +EVDGVP+ + E  
Sbjct: 8   ERLQKVLAHAGVASRRKSEELISKGHVKVNGKVVKEMGIQIGNSDVVEVDGVPIYREEPV 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  ++T  SD  GR  V D   +I  R+  VGRLD +T G L+LTNDG L+++
Sbjct: 68  -YFLLNKPRNMITAVSDDKGRPVVTDLFTNIEQRIYPVGRLDYDTTGALMLTNDGELSQL 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  Q  + Y  +  G VD+  LN L+KGIVI+G        ++    +      V +
Sbjct: 127 LMHPKYQIDKTYVAKVKGLVDRKALNKLEKGIVIEGKKTAPAKAKILSADRAKDITMVEL 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EG+NR++K +F+     V +L R SYG   L  L  G  RE+
Sbjct: 187 TIHEGRNRQVKNMFQAIGHPVEKLKRESYGTLTLDGLQTGEWREL 231


>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 =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E ++   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESILEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 135/224 (60%), Gaps = 20/224 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRK 69
           +++ KV+ARAG  SRRE+E  IA  RV ++G   E A++   + +   + +DG  + L+ 
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSIDG---EIASLGDRIEADAKVRIDGRAISLKS 59

Query: 70  AER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           AE    R+  YHKP G + +  DP+GR TVFD LP +  SR ++VGRLDINT GLLL T+
Sbjct: 60  AEDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--- 183
           DG LA  L  PS +  R Y VR  G++ +  +  L+ G++++     D     D+ K   
Sbjct: 120 DGELANRLMHPSNEVDREYAVRTFGEIPEATVQRLRTGVMLE-----DGPAQFDSIKPAG 174

Query: 184 --GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             G N W  V LREG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 175 GEGMNQWWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVEL 218


>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 =  147 bits (371), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 142/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNG-LPAHIGQRILPTDQVR 260

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++   ++  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPSKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +GI +       ++ 
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELPESDRQKLLQGIRLDDGEANFLRC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 441 SAEDVRGLMG 450


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 123/225 (54%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A AGIASRR+ E +I + RV VNG  +      V S D IEVDGVP+ + E  R
Sbjct: 3   RLQKVMAHAGIASRRKCESLITEGRVSVNGQTVRELGTQVSSKDRIEVDGVPIYR-EEPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KP  +++  SD   R  + D +  I  R+  VGRLD +T GLLLLTNDG  A  L
Sbjct: 62  YILINKPRHVISAVSDDKNRQVILDYIQGIEERIYPVGRLDYDTTGLLLLTNDGAFANQL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  Q  +VY  +  G   +  L  L+ GIV+ G      +  L +Q   N  A V + 
Sbjct: 122 MHPRHQIDKVYVAKVKGIPSEKSLARLEAGIVLDGKKTAKAKAQLLSQNLDNQTAIVELT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +REG N ++K++FE     VN+L R  Y    LG LL G  RE++
Sbjct: 182 IREGWNHQVKRMFEAVGHPVNKLKRERYAFLTLGKLLPGEWRELT 226


>gi|218461411|ref|ZP_03501502.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli Kim 5]
          Length = 153

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 68/102 (66%), Positives = 84/102 (82%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
           RLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLD
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLD 153


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 91/223 (40%), Positives = 137/223 (61%), Gaps = 15/223 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ K++AR G  SRREVE++I+Q  VKVNG    L +RA      TD ++V+   +++ 
Sbjct: 18  EKLQKILARGGFGSRREVEKLISQGLVKVNGKVATLGDRA----FPTDTLKVNDQLVKET 73

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
               + T++ LY+KP G V +  D  GR T+F +LP I  SR ISVGRLDINT GLL+LT
Sbjct: 74  RLEKQPTQVILYNKPEGQVCSRKDEKGRETIFTSLPRIINSRWISVGRLDINTSGLLILT 133

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM--QVTLDTQ 182
           N+G LA  L  PS +  R Y VR  G+V  + L+ LKKG+ ++ G    +   ++    +
Sbjct: 134 NNGELANRLMHPSYEMEREYSVRVFGEVSDEILDRLKKGVKLEDGFAKFESIGKIPQQEE 193

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              N W  V ++EG+NRE+++++E    +V+RL+R  YG F L
Sbjct: 194 DSINQWYRVVIKEGRNREVRRIWESQGVQVSRLVRTRYGQFSL 236


>gi|242242766|ref|ZP_04797211.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233902|gb|EES36214.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 245

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 132/223 (59%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA++G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIAKSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYIAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE+F  +VN+L+RI +GP  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEYFGHQVNKLVRIQFGPIDLKGLNAGEGR 227


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 88/225 (39%), Positives = 122/225 (54%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I    VKVNG  +    V V  +DH+EVDGVPL  AE+ 
Sbjct: 3   ERLQKVMAEAGIASRRKSEVLITSGHVKVNGKTVTTLGVKVEPSDHVEVDGVPLN-AEKL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+VTT  D  GR TV D    +  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 62  VYYLFYKPRGVVTTVHDEKGRKTVLDFFEDVPERIYPVGRLDYDTSGLLIMTNDGALANR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  +  G      L  L+ G+ I G      +  L     K +NA V +
Sbjct: 122 LTHPKYEVKKTYLAKVEGVPTNADLKQLRLGVEIDGRKTAPAKSNLLDSDHKKNNALVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EG N ++KK+       V +L R  YG   L +L  G  R++
Sbjct: 182 TIHEGHNHQVKKMLAAVGHPVTKLKRERYGVLDLQSLQPGEYRKL 226


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 144/270 (53%), Gaps = 47/270 (17%)

Query: 15  RVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDG--V 65
           R+SKV++      + SRRE ERMI    V + G +L    + +   D     ++V+G  V
Sbjct: 38  RLSKVLSLHTENLVISRREAERMIRSGDVTLAGNVLTSPMMMLKEEDLNDGALKVNGKVV 97

Query: 66  PLRKAE-------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
            LR ++             +TR+W+ HK  G +   +DP  R       PS+  R+I   
Sbjct: 98  NLRSSKGPRSVAGEENSVHKTRVWIAHKLPGEIVADNDPYDR-------PSLLQRLIRGG 150

Query: 110 ------------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                       SVGRLD+NTEGL+L+TNDG  AR +ELPS +  R YRVR HG +   K
Sbjct: 151 VGKVGKTRLHLKSVGRLDMNTEGLILVTNDGKYAREMELPSNKLHRTYRVRVHGLLTDHK 210

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGS---NAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           L  ++KG+ ++GI Y  M++  ++ + S   N W+ V   EGKNR+I+ VF++    V R
Sbjct: 211 LARIRKGVTVEGIRYPPMRIIPESTRQSQSTNKWLKVTCTEGKNRQIRNVFKYLGLTVTR 270

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           LIRISYG ++L T+  G   EV  K +  Q
Sbjct: 271 LIRISYGDYRLQTIPPGMAIEVPAKHIENQ 300


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 92/224 (41%), Positives = 135/224 (60%), Gaps = 20/224 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRK 69
           +++ KV+ARAG  SRRE+E  IA  RV ++G   E A++   + +   + +DG  + L+ 
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSIDG---EIASLGDRIEADAKVRIDGRAISLKS 59

Query: 70  AER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           AE    R+  YHKP G + +  DP+GR TVFD LP +  SR ++VGRLDINT GLLL T+
Sbjct: 60  AEDVICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKVRDSRWVAVGRLDINTSGLLLFTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--- 183
           DG LA  L  PS +  R Y VR  G++ +  +  L+ G++++     D     D+ K   
Sbjct: 120 DGELANRLMHPSNEVDREYAVRTFGEIPEATVQRLRTGVMLE-----DGPAQFDSIKPAG 174

Query: 184 --GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             G N W  V LREG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 175 GEGMNQWWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVEL 218


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ +         +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLGDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 94/240 (39%), Positives = 138/240 (57%), Gaps = 23/240 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL--- 67
           +R+ K+++RAG+ASRR+VE  IA  R+ VNG   +L  RA     + D I +DG PL   
Sbjct: 4   ERLQKILSRAGVASRRQVEAWIAAGRLTVNGRPAVLGTRAD---PARDVIALDGRPLAGL 60

Query: 68  -RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEG 120
             +  R R  L+HKP G+VTT  DP GR  V D     F R      +  VGRLD ++EG
Sbjct: 61  AERLSRKRYVLFHKPRGMVTTLRDPQGRPNVGD-----FCRRHGLQGLHPVGRLDFDSEG 115

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL 179
           LLLLT+DG L   L  P  +  +VY V   G +D  +L  L+ G+++  G     +   L
Sbjct: 116 LLLLTDDGELTFALTHPRHEVDKVYHVLVRGDLDPARLRRLRDGVLLDDGPARARIARVL 175

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             + G   WV V LREG+ R+++++ +   W+V RL+R++ GP +LG L AG+ R +S++
Sbjct: 176 RPRPGGG-WVEVVLREGRKRQVRRMCQAVGWQVVRLVRVAVGPLRLGRLAAGAWRPLSRQ 234


>gi|602963|gb|AAB59990.1| ORF4 [Escherichia coli str. K-12 substr. W3110]
          Length = 243

 Score =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 90/218 (41%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  + +R++
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  147 bits (370), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 93/216 (43%), Positives = 128/216 (59%), Gaps = 14/216 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRK- 69
           +++ KV+AR G+ SRRE+ER I Q RV ++G    L +R    V   + I VDG P+   
Sbjct: 21  EKLQKVLARTGLGSRREMERWIEQGRVSIDGKPATLGDR----VTHRERISVDGRPVNTT 76

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
            A+ TR  LYHKP G V +  DP GR TVF+ LP + S R IS+GRLD NT GLLL T D
Sbjct: 77  PAQETRCILYHKPTGEVCSRKDPQGRRTVFERLPKLKSGRWISIGRLDYNTSGLLLFTTD 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGS 185
           G LA  L  PS+   R Y VR  G+  +D L  L  G++++ G+  + D+Q       G 
Sbjct: 137 GDLANKLMHPSSNIEREYMVRVMGEWKEDMLQRLLDGVMLEDGVARFSDIQD--GGGDGI 194

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           N W  V + EG+NRE+++++E     V+RL R+ YG
Sbjct: 195 NHWFYVVIMEGRNREVRRLWESQGLTVSRLKRVRYG 230


>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 =  147 bits (370), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 89/220 (40%), Positives = 133/220 (60%), Gaps = 10/220 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ K++AR+G  SRRE+E  I Q R+ ++G    L +R  + V  +  I +DG  + ++
Sbjct: 6   EKLQKILARSGHGSRREIEGYIQQGRISIDGKTATLGDR--IEVKPSIKIRLDGRILNIK 63

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           + ++T  R+  Y+KP G + T  DP+GR TVFD LP +  +R I+VGRLDINT GLLL T
Sbjct: 64  EPQKTVCRVLAYYKPEGELCTRHDPEGRPTVFDRLPRMQGARWIAVGRLDINTCGLLLFT 123

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G+VD  KL  L +G+ ++        +T    +G 
Sbjct: 124 TDGELANRLMHPSQEVEREYAVRVFGEVDTAKLRQLTQGVQLEDGPASFKTITFKGGEGI 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 184 NQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINL 223


>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 =  147 bits (370), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 128/239 (53%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I +  VKVNG ++      V  +D +EVD VP+ K E  
Sbjct: 3   ERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVRELGTKVTESDEVEVDEVPISK-EVP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L   
Sbjct: 62  VYYLLYKPRGVITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDNH 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G +  D +  L+ GI I G      + T+     ++  V++ +
Sbjct: 122 LTHPKYEVDKTYVAKVKGTITNDDMKKLRTGIHIDGRKTASAKATVIRNNNNSTIVSLTI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+N ++KK+F      V +L R SYG   L  L  G  R         +L PH +EE
Sbjct: 182 HEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYR---------RLKPHEVEE 231


>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 =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 92/215 (42%), Positives = 126/215 (58%), Gaps = 6/215 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRK 69
           T +++ KV+ARAG+ SRRE+E  IA  RVKVNG +       V   D +  D  P  LR 
Sbjct: 4   TSEKLQKVLARAGLGSRREMETAIADGRVKVNGQVAT-LGDRVELRDKVAFDDRPVALRG 62

Query: 70  AERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
           A+    R+ +Y+KP G + T  DP+GR TVFD LP +   R I++GRLDINT GLLL T 
Sbjct: 63  ADEVPRRVIMYNKPEGELCTRKDPEGRRTVFDRLPRLKGERWIAIGRLDINTSGLLLFTT 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PSTQ  R Y VR  G+V  D +  + +G+++         V     +G N
Sbjct: 123 DGELANRLMHPSTQIEREYAVRVMGEVTMDHIKAMVEGVMLDDGPARFTDVQEFGGEGIN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            W  V + EG+NRE+++++E  N  V+RL R+ YG
Sbjct: 183 TWFHVVIMEGRNREVRRLWESQNLTVSRLKRVRYG 217


>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 =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 96/239 (40%), Positives = 144/239 (60%), Gaps = 13/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL---- 67
           +++ KV+ARAGI SRR +E  IA  RV VNG   ++A V   V   D + VDG  +    
Sbjct: 3   EKLQKVLARAGIGSRRSMEDWIASGRVSVNG---KKAKVGDRVERGDVLRVDGRSMDYSG 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
             ++  R+ +Y+KP G V T +DP+GR TVFD LP + + R ++VGRLD+NT+GLLL T 
Sbjct: 60  EDSDSRRMIIYYKPEGEVCTRTDPEGRPTVFDRLPRLDNERWVAVGRLDVNTQGLLLFTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGS 185
           DG LA  L  PS++  R Y  R  G+V  + L+ L+ G+ +  G  + D ++     +G 
Sbjct: 120 DGDLANRLMHPSSEIEREYAARIFGEVTPEMLHNLRTGVQLFDGPAHFD-EILHSGGEGM 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           NAW  V ++EG+ RE+++++E    +V+RLIR+ YG   L   L AG   E+S+  + E
Sbjct: 179 NAWYHVIIKEGRRREVRRMWETQGVQVSRLIRVRYGCVTLPRGLKAGRWEELSEDQISE 237


>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 =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V++   I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIETIIEAGRVSVDGKIAKLGDRVEVVAGMKIRLDGHVISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GL+L T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLMLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+VD+ KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGEVDEHKLRDLSRGVQLEDGPAAFKTIKFTGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILL 220


>gi|251771881|gb|EES52455.1| Pseudouridine synthase, Rsu [Leptospirillum ferrodiazotrophum]
          Length = 638

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 135/237 (56%), Gaps = 3/237 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IE 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  VDGRPLPREPETFLFLFYKPKGVVSTLFDPEGRPTLRDYFPGIDP-LLHIGRLDFQTEGA 133

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLD 180
           LLLTN+G L++ +  P  +  R Y V+  G +    L  + +G I + G     +++  +
Sbjct: 134 LLLTNNGDLSQRILHPRFEIPRTYLVKIQGGMSPAHLERMARGEIRLDGRPVVPLELVPE 193

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            Q  +NAW  + L EG+NRE++++FE  N+ V +L+R ++GP  L  L  G  R V+
Sbjct: 194 RQTSTNAWYRITLTEGRNREVRRLFETLNYFVLKLVRTAFGPLTLAGLEPGEYRTVT 250


>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 =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 131/217 (60%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV +NG +       V +   + +DG  V ++ A+
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSINGEIAN-LGDRVDADAKVRLDGRLVSIKSAD 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP +  +R ++VGRLDINT GLLL T+DG
Sbjct: 62  DIICRVLAYHKPEGEICSRKDPEGRPTVFDRLPKLRDARWVAVGRLDINTSGLLLFTSDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V+   +  L+ G++++        V     +G N W
Sbjct: 122 ELANRLMHPSNEVDREYAVRTFGEVNDFTIQKLRTGVMLEDGPAQFDYVKAAGGEGVNQW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             VGLREG+NRE+++++E    +V+RLIR+ YG  +L
Sbjct: 182 WHVGLREGRNREVRRLWESQEVQVSRLIRVRYGMIEL 218


>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 =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  + +R++
Sbjct: 3   EKLQKLLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRES 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 93/221 (42%), Positives = 128/221 (57%), Gaps = 6/221 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV V+G +       V S   I +DG  V +R  E
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIAS-LGDRVESDAKIRIDGRTVSIRSEE 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T+DG
Sbjct: 62  DVVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N W
Sbjct: 122 ELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRMGVTLEDGPANFDKVKAAGGEGMNKW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V L EG+NRE+++++E    +V+RLIRI YG  +L   L
Sbjct: 182 WHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKAL 222


>gi|261855955|ref|YP_003263238.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836424|gb|ACX96191.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 369

 Score =  146 bits (369), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 101/249 (40%), Positives = 141/249 (56%), Gaps = 16/249 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K++A  G+ SRR +E  I+   VK+NG++ +   V   + D ++V G  +  ++ T
Sbjct: 4   QRLQKILATQGLGSRRMIEGWISAGEVKLNGVVAQLGDV-AEAGDVLDVRGQKITVSDET 62

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
              R+ +YHKP G +T+ SDP+GR TVF +LP+I   R I+VGRLD NT GLLL TNDG 
Sbjct: 63  PIRRVIIYHKPEGEITSTSDPEGRPTVFGSLPAIRQGRWITVGRLDFNTSGLLLATNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
           LA  L  PS Q  R Y VR  G + +D++  L   + +  G  + D Q++     G N W
Sbjct: 123 LANRLMHPSHQIERTYAVRVLGGLTEDQVKQLTTEVQLDDGPAHFD-QLSDAGGTGVNRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             V LREG+NREI+++ E     V+RLIRISY    L   L         K  R Q  P 
Sbjct: 182 YHVTLREGRNREIRRMIEAVGAVVSRLIRISYAGIPLPPRL---------KPGRAQDLPP 232

Query: 249 LLEEAQVNL 257
            +E+A V L
Sbjct: 233 EMEDALVKL 241


>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 =  146 bits (369), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 97/235 (41%), Positives = 132/235 (56%), Gaps = 14/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL-- 67
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  D   L  
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDSKALHS 67

Query: 68  --RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
             +   R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGIAKFNSIKFSGGE 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           G+N W  V L EG+NRE++++FE     V+RL RI +G   L   ++ G T E++
Sbjct: 188 GANLWYYVTLSEGRNREVRRMFEAVGVTVSRLTRIRFGDIILPKFVSRGKTLELN 242


>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 =  146 bits (369), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 137/228 (60%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNG-QLLAQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNETKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  PS    + Y VR  G+V  D L ++  G+ ++ GI      V L  D   G +  V
Sbjct: 121 NLTHPSKGIEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHE-V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++
Sbjct: 180 EITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLT 227


>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 =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 128/225 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  GIASRR+ E +I + +V VNG +++     V   D +  +   ++  E+  
Sbjct: 2   RLQKYLASCGIASRRKCEELILEGKVSVNGQIIQTLGTQVEEDDEVYYNHKRVQLEEKHV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G VTT  D   R+TV D +  + +R+  VGRLD NT GLLLLT+DG L   L
Sbjct: 62  YYMLNKPAGYVTTVQDEKQRATVLDLMKGVKTRIFPVGRLDYNTSGLLLLTSDGALTYGL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+  G+V +  L++L+KG++I        +V +  Q   + W+ + + 
Sbjct: 122 THPKHHVNKTYEVKLSGKVTERSLDMLRKGVMIDHRKTYPAEVEVVKQNAKHTWLKITIH 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           EG+NR+I+K+ E   + V +L R+S G  QLG+L  G  R ++K+
Sbjct: 182 EGRNRQIRKMCEAVGYPVVQLKRLSVGSIQLGSLKVGEYRALTKE 226


>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 =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 85/231 (36%), Positives = 130/231 (56%), Gaps = 3/231 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R+ KVIA AGIASRR+ E+MI   RV+V+G L+ +    V +   I VD  P+ + 
Sbjct: 1   MTLERLQKVIAEAGIASRRKAEKMIVAGRVRVDGKLVTKLGTKVDTFSTITVDDEPIER- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L++KP G+V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG L
Sbjct: 60  ESLHTYLFYKPRGVVSTAHDDKGRKTVVDYFDDLPYRLYPVGRLDYDTSGLLLMTNDGKL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAW 188
           A +L  P  +  +VY  +  G ++ D++  LKKG+ + G       +++    QK +N  
Sbjct: 120 ANLLMHPKNEVPKVYVAKIEGILEPDQIMTLKKGVKVDGRKCAPAKVKILKTNQKKNNQI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + + EG   E+K++F+     V +L R  Y    L  L  G  RE++++
Sbjct: 180 VQLTIHEGHYHEVKRMFKAVGHPVEKLSRERYAFLDLHALTYGQYRELTRE 230


>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 =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 90/228 (39%), Positives = 130/228 (57%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +++ K +A AG+ SRRE+ER+I    V VNG    +    V + D I V+G  +R+    
Sbjct: 41  EKLQKALADAGMGSRREMERLIESGIVTVNGNPA-KLGDRVSAEDVIRVEGRLVRRLSPE 99

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
            A+  R+ LYHKP G + +  DP+GR +VF++LP +   R I+VGRLD NTEGLLL T  
Sbjct: 100 AADTPRVLLYHKPAGEIVSRDDPEGRPSVFNHLPRVPGGRWIAVGRLDFNTEGLLLFTTS 159

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G++  +    L  G+ ++        +T +  KG N 
Sbjct: 160 GSLANRLMHPRYEMEREYAVRTVGELTPEDEAKLLAGVELEDGPAKFETLTDEGGKGLNH 219

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           W  V +REG+NRE++++FE  N  V+RLIR+ YG  +L   L    RE
Sbjct: 220 WYVVTIREGRNREVRRLFESVNLTVSRLIRVRYGAVELPPGLVRGKRE 267


>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 =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 137/228 (60%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNG-QLLAQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNETKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  PS    + Y VR  G+V  D L ++  G+ ++ GI      V L  D   G +  V
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHE-V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++
Sbjct: 180 EITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLT 227


>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 =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 109/317 (34%), Positives = 168/317 (52%), Gaps = 35/317 (11%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D+N  QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG       + V   D I
Sbjct: 4   QDQNDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGLRVDMHDAI 62

Query: 61  EVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLD 115
            +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD +P     R I++GRLD
Sbjct: 63  TIDGKVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPRPKEGRWINIGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLL+ T DG LA  L  PS +  R Y VR  G+VD + +  LK G+V++    G  
Sbjct: 123 INTTGLLMFTTDGELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLE---DGPA 179

Query: 176 QVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
           + T   Q    +G N W    + EG+NRE+++++E     V+RL R+ +GP  L + L  
Sbjct: 180 RFTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD--RPNIISEVPDDFTRMKKN 288
           G  RE+S                Q  +D  I ++E  ++    P + ++  D   RM++ 
Sbjct: 240 GRWREMS----------------QYEVD--ILAAEVGLKPVAMPQMTAKSKDKLERMQRK 281

Query: 289 SSQKNGLSKQKKLATPV 305
           SS+  G +++ +   P 
Sbjct: 282 SSRPMGKTERVRTLRPA 298


>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 =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 136/227 (59%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG+ASRR  E MI + RV VNG ++    V V  S   ++VDG+ ++  ++ 
Sbjct: 141 RLQKLLAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVDPSKVTVQVDGMTVQTNDKL 200

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
               ++KP G+V+T  DP+GR  + D L S  S RV  VGRLD+ TEGLLLLTNDG LA 
Sbjct: 201 VYMAFNKPAGVVSTMEDPEGRPCISDFLRSSMSERVFHVGRLDVETEGLLLLTNDGELAN 260

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+  G ++      +KKGI ++ G+   D    +D+  G +  V V
Sbjct: 261 RLTHPSYEVPKTYLVQVPGPMEPGVGAAMKKGIRLEDGVTRVDEFKLVDSTPG-HVLVEV 319

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +  GKNR ++++F+   + V RL+R+  GP ++G+   G+ R +SK
Sbjct: 320 TIHSGKNRIVRRLFDAVGYPVERLVRVEMGPIRIGSQKQGTVRNLSK 366


>gi|327490097|gb|EGF21885.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1058]
          Length = 242

 Score =  146 bits (368), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 136/230 (59%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A+NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGKVSINGQVVRELAINVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTQPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>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 =  146 bits (368), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 101/257 (39%), Positives = 137/257 (53%), Gaps = 12/257 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V +     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--PFQLGTLLAGSTR--EVSKKILRE 243
           W  V L EG+NRE+++++E    +V+RLIR+ YG  P   G    G T         LRE
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLRE 242

Query: 244 --QLGPHLLEEAQVNLD 258
             QL P    +  V  D
Sbjct: 243 LVQLAPETTSKVAVEKD 259


>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 =  146 bits (368), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 89/218 (40%), Positives = 125/218 (57%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIARLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQVD  K+  L +G+ ++        +     +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDDAKIRDLSRGVQLEDGPAAFRTIKFSGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 220


>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 =  146 bits (368), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 88/211 (41%), Positives = 123/211 (58%), Gaps = 5/211 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           ++ KV+A++GI SRR++E+ I   +V VN  +     + +   D I VDG P+R   +  
Sbjct: 236 KLHKVLAQSGIGSRRDMEQFILDGKVTVNDEVAH-VGMRISYGDRIAVDGKPVRLRIQPG 294

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
             RL  YHKP G V T +DP+GR TVF  LP +   +  SVGRLDINTEGLLL TN G L
Sbjct: 295 PARLLAYHKPTGEVVTLNDPEGRPTVFRRLPRLQQGKWQSVGRLDINTEGLLLFTNSGEL 354

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     R Y VR  G +++++   L +G+ I G   G   +     +G+N W  
Sbjct: 355 ANQLMHPRFGVEREYAVRVLGSLNEEQRAKLLEGVEIDGQTAGFKSIEEGGGEGANRWYR 414

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           V + EG+NRE++K+F+     V+RLIRI YG
Sbjct: 415 VVITEGRNREVRKLFDKVGLAVSRLIRIRYG 445


>gi|299067338|emb|CBJ38535.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum CMR15]
          Length = 601

 Score =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 139/250 (55%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNG-LPAHIGQRILPTDQVR 260

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++   ++  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPSKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +  
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELPESDRQKLLHGIRLDDGEANFLSC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLG 246
           S   +R  +G
Sbjct: 441 SADDVRGLMG 450


>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 =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNG-LPAHIGQRILPTDQVR 260

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAESDRQKLLQGVRLDDGEANFLRC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 441 SAEEVRVLMG 450


>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 =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 125/226 (55%), Gaps = 6/226 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  E+  P ++ KV+A  G+ SRRE+E +I Q RV VNG L       ++  D + V+
Sbjct: 210 RELSAEDDAP-KLHKVLAEGGLGSRREMEELILQGRVSVNG-LPAHIGQRILPADQVRVN 267

Query: 64  GVPLRKAERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTE 119
           G  + +   T   R+ LYHKP G + + SDP+GR TVFDNLP I   + ++VGRLD NTE
Sbjct: 268 GKLIHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDNLPRIKTGKWVAVGRLDFNTE 327

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +++  
Sbjct: 328 GLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIAD 387

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              +G N W  V L EG+NRE++++FE     V+RLIR  YG F L
Sbjct: 388 GGGEGVNHWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLL 433


>gi|257482791|ref|ZP_05636832.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 241

 Score =  145 bits (367), Expect = 6e-33,   Method: Compositional matrix adjust.
 Identities = 98/239 (41%), Positives = 138/239 (57%), Gaps = 16/239 (6%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            + D+Q     + G N W    + EG+NRE+++++E     V+RL R+ YGP  L + L
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDL 237


>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 =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 88/225 (39%), Positives = 126/225 (56%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I+Q RV VNG  +      V  +D IEVD VP+   E  
Sbjct: 2   ERLQKVMAHAGIASRRKCEEIISQGRVTVNGQTVTELGFKVKQSDKIEVDQVPIY-LEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP  +++  SD  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  RYFLFYKPRNVISAVSDDKGRPVVLDYFKHIDQRIYPIGRLDFDTTGLLLLTNDGEFANQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQ-KGSNAWVTV 191
           L  P  Q  +VY  +    +D++ L  L++GI+I G      +   LDT  +   + V +
Sbjct: 121 LMHPRYQVDKVYVAKLDKILDKEALRKLERGIIIDGKKTSKARAKVLDTNLEKKMSVVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EG N ++KK+FE     V +L R  +GP  LG +  G  RE+
Sbjct: 181 TIHEGWNHQVKKMFEAVGAHVVKLKREKFGPLNLGKMQPGEYREL 225


>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 =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 91/235 (38%), Positives = 134/235 (57%), Gaps = 7/235 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ K++ARAG+ SRRE+E  +   R+ VNG  +       +S D  E+DG  L  A  
Sbjct: 56  PERIQKLLARAGVGSRREIEGWMDAGRLLVNGKPVTPGQKATVS-DVFELDGKRLEVAAA 114

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VTT  DP+GR TVFD LP +   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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           W  V L EG+NRE+++++E    +V+RL R+ YG   L + L  G   E+ +K +
Sbjct: 235 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGSIFLPSRLTVGKWEELDQKAV 289


>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 =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 86/227 (37%), Positives = 133/227 (58%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E +I Q RVKVNG +++   V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEELILQGRVKVNGRVVKELGVKVGPRDDVEVDGIPIEREEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 62  -YYLLYKPRGVISSVKDDRGRKVVTDFFKDLDKRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVT 190
           L  P  +  +VY  +  G    ++L  L++G+ ++       +V L   D +KG+ A V 
Sbjct: 121 LMHPRYEIEKVYIAKVKGIPTHEQLKRLEQGVQLEDGMTAPAKVKLLSADRKKGT-AIVE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++
Sbjct: 180 IRIHEGRNRQVRRMFEAIGCEVLKLKRERYAFLDLKGLRPGEYRELT 226


>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 =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 91/213 (42%), Positives = 120/213 (56%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AGI SRR++E+MI + R+ VNG   E A +   + + D I V G P+R    
Sbjct: 55  KLHKVLAQAGIGSRRDMEQMILEGRITVNG---EPAHIGQRIAAGDRIAVGGKPVRYRIA 111

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
              TR+  YHKP G V TH DP  R TVF  LP +   +  SVGRLDINTEGLLL TN G
Sbjct: 112 PPPTRVIAYHKPAGEVVTHDDPQQRPTVFRRLPRLHQGKWQSVGRLDINTEGLLLFTNSG 171

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +D      L +G+ I G       +     +G+N W
Sbjct: 172 ELANQLMHPRFGIEREYAVRSLGGLDDASRQKLLEGVEIDGQRCAFKSIENGGGEGANQW 231

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
               + EG+NRE++K+F+     V+RLIRI YG
Sbjct: 232 YRCVITEGRNREVRKLFDAVGHAVSRLIRIRYG 264


>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 =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 92/222 (41%), Positives = 132/222 (59%), Gaps = 16/222 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV V+G  +      V +   I +DG  V L+ A+
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSVDG-EISGLGDRVEADAKIRIDGRAVSLKSAD 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR+TVF+ LP +  +R ++VGRLDINT GLLL T DG
Sbjct: 62  DIICRVLAYHKPEGEICSRKDPEGRTTVFERLPKVRDARWVAVGRLDINTSGLLLFTCDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----- 183
            LA  L  PS +  R Y VR  G+V +  +  L+ G+ ++     D     DT K     
Sbjct: 122 ELANRLMHPSNEVEREYAVRTFGEVPEAAVQRLRTGVTLE-----DGPAQFDTIKAAGGE 176

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N W  V LREG+NRE+++++E  + +V+RLIR+ YG  +L
Sbjct: 177 GINQWWHVTLREGRNREVRRLWESQDVQVSRLIRVRYGKVEL 218


>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 =  145 bits (367), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 85/225 (37%), Positives = 124/225 (55%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +IA  RVKVNG ++      V   D I +D   L K E  
Sbjct: 2   ERLQKAIAASGYTSRRKAEDLIAAGRVKVNGEVISELGFKVKKGDMIMIDDKAL-KGENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G + + SD  GRSTV D  P +  R+  VGRLD +T G+LL++NDG  A +
Sbjct: 61  VYYVFYKPKGCICSLSDELGRSTVIDYFPEVEERIYPVGRLDYDTTGVLLMSNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWV 189
           +  PS+   +VY V   G V  + L+ L+KG+ ++G     C   ++VT    +     +
Sbjct: 121 MMHPSSHLEKVYEVSVSGLVQGETLHKLEKGVYLEGTKTLPC--KIKVTHKDVEHKTTIL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNR++KK+FE    KV RL R+  G   L  L  G  R
Sbjct: 179 MIKLVEGKNRQVKKMFEAMGHKVKRLHRLQVGTINLKGLTPGHYR 223


>gi|319400836|gb|EFV89055.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis FRI909]
          Length = 245

 Score =  145 bits (367), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 131/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA++G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIAKSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEYFGHQVNKLARIQFGPIDLKGLNAGEGR 227


>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 =  145 bits (367), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 87/236 (36%), Positives = 133/236 (56%), Gaps = 2/236 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPL 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
            K ER + ++ +KP G++ T+ DP GR+ V D       R+  VGRLD ++EGLL++TND
Sbjct: 85  -KPERLKYFVLNKPKGVLCTNHDPAGRTRVIDLFAKERVRLFPVGRLDEDSEGLLIVTND 143

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R YRV+  G    +KL  L+ GI  +   +  +      ++G +A
Sbjct: 144 GDLANQLAHPRYRIYRTYRVQVAGFPTNEKLQQLRDGIFFREGKFQVISAKFAGKQGKSA 203

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           ++ + L +G NREI+++F     KV  L RI++GP +LG    G  RE+++  L E
Sbjct: 204 FLEIVLGQGHNREIRRLFARIGHKVMSLQRIAFGPIRLGKQKVGQYRELTRNELEE 259


>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 =  145 bits (367), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 93/233 (39%), Positives = 136/233 (58%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+AR G+ SRR+VE  IA  R+KVNG       + V   D I +DG  +++ E  
Sbjct: 17  EKLQKVLARIGVGSRRDVESWIAAGRIKVNGKDAT-LGLRVDMHDAITIDGKVIKREEAA 75

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLL+ T DG
Sbjct: 76  ESVRRVIMYNKPDGEICTRDDPEGRPTVFDKLPRPKEGRWINIGRLDINTTGLLMFTTDG 135

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS +  R Y VR  G+VD + +  LK G+V++     + D+Q     + G N
Sbjct: 136 ELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKAGVVLEDGPARFTDIQQAPGGE-GFN 194

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
            W    + EG+NRE+++++E     V+RL R+ +GP  L + L  G  RE+S+
Sbjct: 195 HWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRWREMSQ 247


>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 =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 133/230 (57%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ SRR  E  I   RV V+G ++ E  A     T  IEVDG  +R   R 
Sbjct: 24  RLQKFLAATGLGSRRHCEEYIETGRVSVDGDVITELGAKIDPETQFIEVDGERVRLQPR- 82

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L +KP G + T++DP GR  V D  P+   R+ +VGRLD N+EGL+L+TNDG LA+ 
Sbjct: 83  RYYLLNKPSGFLCTNNDPAGRRRVVDLFPNDGQRLFTVGRLDENSEGLILVTNDGELAQR 142

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  R Y V+  G   ++KL+ L+KG+  +   +    +    ++G +A++ + L
Sbjct: 143 LAHPRYRVARTYHVQVVGNPPREKLDELRKGVRFKEGVFRVSGLKYLKKQGKSAFLELTL 202

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EG+NREI+++      KV +L+RI +GP  LG L  G +R +S   L++
Sbjct: 203 HEGQNREIRRMMARIGHKVIQLVRIRFGPLNLGKLKTGESRRLSDTELKK 252


>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 =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 140/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 204 KVRELTSEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNG-LPAHIGQRILPTDQVR 261

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 382 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 441

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 442 SAEEVRVLMG 451


>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 =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 136/227 (59%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG+ASRR  E MI + RV VNG ++    V V  S   ++VDG+ ++  ++ 
Sbjct: 149 RLQKLLAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVDPSKVTVQVDGMTVQTNDKL 208

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
               ++KP G+V+T  DP+GR  + D L S  S RV  VGRLD+ TEGLLLLTNDG LA 
Sbjct: 209 VYMAFNKPAGVVSTMEDPEGRPCISDFLRSSMSERVFHVGRLDVETEGLLLLTNDGELAN 268

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+  G ++      +KKGI ++ G+   D    +D+  G +  V V
Sbjct: 269 RLTHPSYEVPKTYLVQVPGPMEPGVGAAMKKGIRLEDGVTRVDEFKLVDSTPG-HVLVEV 327

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +  GKNR ++++F+   + V RL+R+  GP ++G+   G+ R +SK
Sbjct: 328 TIHSGKNRIVRRLFDAVGYPVERLVRVEMGPIRIGSQKQGTVRNLSK 374


>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 =  145 bits (366), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 94/225 (41%), Positives = 133/225 (59%), Gaps = 22/225 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E  IA  RV V+G    L +R  V+      I +DG    ++
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIATLGDRVEVDA----KIRIDGRTTSIK 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
            A+    R+  YHKP G + +  DP+GR TVF+ LP I  SR ++VGRLDINT GLLL T
Sbjct: 59  TADDMICRVLAYHKPEGEICSRKDPEGRPTVFERLPKIRDSRWVAVGRLDINTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-- 183
           +DG LA  L  PS +  R Y VR  GQV    +  L+ G++++     D     DT K  
Sbjct: 119 SDGDLANRLMHPSNEVEREYAVRTFGQVTDANVQSLRTGVMLE-----DGPAQFDTIKPA 173

Query: 184 ---GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              G N+W  V L+EG+NRE+++++E    +V+RLIR+ YG  +L
Sbjct: 174 GGEGINSWWHVTLKEGRNREVRRLWESQEIQVSRLIRVRYGMVEL 218


>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 =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 86/246 (34%), Positives = 140/246 (56%), Gaps = 11/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLGPH 248
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++    KILR     H
Sbjct: 185 TISEGRNRQVRRMFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVKILR-----H 239

Query: 249 LLEEAQ 254
           L E  +
Sbjct: 240 LAENGK 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 =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 98/263 (37%), Positives = 143/263 (54%), Gaps = 25/263 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +++ K++A AGI SRR++E +I   RV VNG L       V + D I V+G PL +    
Sbjct: 290 EKLHKILADAGIGSRRDMEELIIAGRVSVNG-LPAHVGQRVGTEDVIRVNGKPLSRKRSA 348

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
            ++  ++ LYHKP G + T  DP  R  VFD LP +  +R I+VGRLD+N+EGLL+ T  
Sbjct: 349 ASQTPQVLLYHKPTGELVTRDDPGSRPKVFDRLPRLRGARWIAVGRLDLNSEGLLIFTTS 408

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           G LA  L  P   W R Y VR  G+VD      L  G+ ++     D   TL +      
Sbjct: 409 GDLANKLMHPRYGWEREYAVRVLGRVDDGIRQQLLTGVTLE-----DGPATLQSIEDIGG 463

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP------FQLGTLLAGSTREV 236
           +G+N W  V + EG+NRE++++F+     V+RL+RI +GP       Q G L A +  EV
Sbjct: 464 EGANHWYRVVILEGRNREVRRLFDAVGLTVSRLVRIRFGPIALPPRLQRGRLHALTEAEV 523

Query: 237 SKKILREQLGPHLLEEAQVNLDA 259
             + L++Q+  H+ E      DA
Sbjct: 524 --RQLQQQMRRHVAEMTDGAADA 544


>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 =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 91/217 (41%), Positives = 127/217 (58%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV V+G +       V +   I +DG  V +R  E
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIAS-LGDRVETDAKIRIDGRTVSIRSEE 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T+DG
Sbjct: 62  DVVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N W
Sbjct: 122 ELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRMGVTLEDGPANFDKVKAAGGEGMNKW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 182 WHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIEL 218


>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 =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 109 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNG-LPAHIGQRILPTDQVR 166

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD N
Sbjct: 167 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 226

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 227 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAESDRQKLLQGVRLDDGEANFLRC 286

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 287 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 346

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 347 SAEEVRVLMG 356


>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 =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 85/221 (38%), Positives = 127/221 (57%), Gaps = 5/221 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +++      ++ KV+A+AG+ SRR++E++I + +V VNG +     + +   D I++ 
Sbjct: 280 KRVLRPEPEAPKLHKVLAQAGVGSRRDMEQLIQEGQVSVNGEVAH-IGMRIAQGDQIKIA 338

Query: 64  GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTE 119
           G P++        R+  YHKP+G V TH DP+GR TVF  LP +   + +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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
              +G N W  V + EG+NRE++++F+     V+RLIRI Y
Sbjct: 459 GGGEGINHWYRVVITEGRNREVRRLFDAVGLTVSRLIRIRY 499


>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 =  145 bits (366), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 89/230 (38%), Positives = 130/230 (56%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ K+IA +G  SRR+ E++I ++RVKVNG   +         D + VD   +  A R  
Sbjct: 14  RLQKIIAESGFCSRRKAEQLIEERRVKVNGHPAKIGDKADPRKDVVTVDDERITVARRPT 73

Query: 74  -RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + HKP G VTT SD  GR  V D +  I  R+  VGRLD+N+EGLLL TNDG LA 
Sbjct: 74  YRYVMLHKPRGYVTTMSDEKGRRCVADLVADIDERLYPVGRLDVNSEGLLLFTNDGRLAN 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + YRV     +  ++   L +G+VI G      QV + T++ +   + V 
Sbjct: 134 DIMHPSRHVTKTYRVTVRPDITDEQAARLAEGVVIDGRKTAPAQVHVLTKEPNRVVMEVV 193

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +REG+NR+I+K+ E    +V RL R S GP +LG L  G+ R+++ + L+
Sbjct: 194 IREGRNRQIRKMMEAVGLEVARLKRTSLGPIKLGMLKPGAHRDLTAEELK 243


>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 =  145 bits (366), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 131/234 (55%), Gaps = 3/234 (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
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  -YYLFYKPRGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   + +L  L KGI I G      + Q+     K  ++ V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRELLPLAKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 92/220 (41%), Positives = 128/220 (58%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G    L +R  VN +    I VDG  V  R
Sbjct: 3   EKLQKVLARAGHGSRREMEALITAGRVSVDGKVATLGDRVEVNAV----IRVDGHTVKTR 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
             E    R+  YHK  G + T  DP+GR TVFD LP + S R I+VGRLD+NT GLLL T
Sbjct: 59  AEEEMICRVLAYHKSEGEMCTRHDPEGRPTVFDRLPKLDSARWIAVGRLDVNTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G++ +  L  L+KG+ ++       ++     +G 
Sbjct: 119 TDGELANRLMHPSHEVEREYAVRVFGEITEAMLQRLRKGVQMEDGMAKFNKIKPAGGEGL 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RL+R+ YG   L
Sbjct: 179 NQWFNVTLTEGRNREVRRLWESQEVQVSRLMRVRYGDVTL 218


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

 Score =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 130/234 (55%), Gaps = 3/234 (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
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  -YYLFYKPKGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I G      + Q+     K  ++ V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRDLLPLAKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 88/215 (40%), Positives = 125/215 (58%), Gaps = 4/215 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQLGD-RITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+ R+TVF+ LP +   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 225
           V + EG++R +++++E    KV+RLIR+ +GP  L
Sbjct: 182 VVVVEGRHRLVRRLWESQGLKVSRLIRVRFGPIVL 216


>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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 90/231 (38%), Positives = 136/231 (58%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +I   RV V+G ++ +    V  S   I VDGVP+ + E+
Sbjct: 2   ERLQKVLAHAGVASRRKCEELILAGRVSVDGEIVTQLGAKVDPSRQRIAVDGVPI-ELEQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP+  ++T SDP GR TV   LP I  RV  VGRLD +T GLLL TNDG L +
Sbjct: 61  PVVLVLNKPVAYLSTVSDPLGRRTVMQLLPPIRERVYPVGRLDYDTSGLLLFTNDGELTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----DTQKGSNAW 188
            L  PS +  +VYRV   G VD++    L +G+ ++       +V +    D + G  A 
Sbjct: 121 RLLHPSREIEKVYRVSVRGIVDRETRRALMEGVELEDGVTAPAKVEVLRQADREDGV-AV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + + EG+NR+++++FE     V RL RI++GP  LG L  G  R ++++
Sbjct: 180 VHLAIHEGRNRQVRRMFERLGLPVLRLKRIAFGPVSLGHLKTGEWRALTQE 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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 90/231 (38%), Positives = 136/231 (58%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +I   RV V+G ++ +    V  S   I VDGVP+ + E+
Sbjct: 2   ERLQKVLAHAGVASRRKCEELILAGRVSVDGEIVTQLGAKVDPSRQRIAVDGVPI-ELEQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP+  ++T SDP GR TV   LP I  RV  VGRLD +T GLLL TNDG L +
Sbjct: 61  PVVLVLNKPVAYLSTVSDPLGRRTVMQLLPPIRERVYPVGRLDYDTSGLLLFTNDGELTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----DTQKGSNAW 188
            L  PS +  +VYRV   G VD++    L +G+ ++       +V +    D + G  A 
Sbjct: 121 RLLHPSREIEKVYRVSVRGIVDRETRRALMEGVELEDGVTAPAKVEVLRQADREDGV-AV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + + EG+NR+++++FE     V RL RI++GP  LG L  G  R ++++
Sbjct: 180 VHLAIHEGRNRQVRRMFERLGLPVLRLKRIAFGPVSLGHLKTGEWRALTQE 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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 130/234 (55%), Gaps = 3/234 (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
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  -YYLFYKPRGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I G      + Q+     K  ++ V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRDLLPLAKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 136/228 (59%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNG-QLLAQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG  A+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNETKRIYPIGRLDLYTEGLLLLTNDGEFAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  PS    + Y VR  G+V  D L ++  G+ ++ GI      V L  D   G +  V
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHE-V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++
Sbjct: 180 EITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLT 227


>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 =  145 bits (365), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 86/225 (38%), Positives = 131/225 (58%), Gaps = 8/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+AR+G  SRRE+E  I+  R++VNG + +     + +   + +DG  V ++  E
Sbjct: 3   EKLQKVLARSGHGSRREIETKISAGRIRVNGKVAQ-LGERIDADAKVRIDGHEVQIKPEE 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+ +YHKP G + T  DP+GR TV+D LP +  +R ++VGRLD+NT GLLL T DG
Sbjct: 62  EVICRVLIYHKPEGELCTRKDPEGRPTVYDRLPRMSGARWVAVGRLDVNTSGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G VD+  +  L+KG+ ++        +      G N W
Sbjct: 122 ELANRLMHPSQQVEREYAVRVFGDVDEAMMQRLRKGVQLEDGPAHFNSIKPAGGDGMNRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG--PFQLGTLLAG 231
             V + EG+NRE+++++E    +V+RLIR+ YG  P + G    G
Sbjct: 182 FHVTISEGRNREVRRLWESQEVQVSRLIRVRYGDIPLEPGLPQGG 226


>gi|325690957|gb|EGD32957.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK115]
          Length = 242

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTQPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>gi|118595131|ref|ZP_01552478.1| pseudouridylate synthase [Methylophilales bacterium HTCC2181]
 gi|118440909|gb|EAV47536.1| pseudouridylate synthase [Methylophilales bacterium HTCC2181]
          Length = 280

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 89/250 (35%), Positives = 142/250 (56%), Gaps = 10/250 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL---R 68
           +R+ K++A++G  SRRE+E+ I + +V VN    + A +   +  +D I  +G  +    
Sbjct: 20  ERIHKLLAQSGYGSRREIEKAILEDKVLVNN---QNAKIGQLITPSDKIIFNGKAIFLNN 76

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G + T +DP GRSTVF+ LP I   + +S+GRLD NT GLL+ T+ 
Sbjct: 77  DNNLPRVLIYHKPEGEIVTENDPGGRSTVFEKLPRIKKGKWMSIGRLDFNTSGLLIFTSY 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G++ +D++   K GI I G       +  +  +G+N 
Sbjct: 137 GELANRLMHPKYEIEREYSVRILGELSEDQIKEFKSGIDIDGGKAKFESIYFEGGEGANK 196

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           W  V L+EG+NRE++++FE+F+  V+RLIR+ +G   L + L  G   E+++  +   L 
Sbjct: 197 WYRVVLKEGRNREVRRMFEYFDLTVSRLIRVRFGIVILPSHLKRGMHTELTQAEVTRLLQ 256

Query: 247 PHLLEEAQVN 256
            H +E    N
Sbjct: 257 KHDIEPNDFN 266


>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 =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 88/215 (40%), Positives = 125/215 (58%), Gaps = 4/215 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQLGD-RITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+ R+TVF+ LP +   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 225
           V + EG++R +++++E    KV+RLIR+ +GP  L
Sbjct: 182 VVVVEGRHRLVRRLWESQGVKVSRLIRVRFGPIVL 216


>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 =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 91/217 (41%), Positives = 127/217 (58%), Gaps = 6/217 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--L 67
           N   +++ KV+ARAG  SRRE+E  IA  RVKVNG +       + + D +  D  P  L
Sbjct: 2   NTPTEKLQKVLARAGFGSRREMETAIADGRVKVNGQVAT-LGDRIETRDRVTFDERPVNL 60

Query: 68  RKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
           R AE    R+ +Y+KP G + T  DP+GR TVF+ LP +   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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            N W  V + EG+NRE+++++E     V+RL R+ YG
Sbjct: 181 INTWFHVVILEGRNREVRRLWESQGLTVSRLKRVRYG 217


>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 =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>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 =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/239 (36%), Positives = 127/239 (53%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +IA+  VKVNG +++     V   D ++VD VP+ K E  
Sbjct: 4   ERLQKVIAHAGVASRRKAEELIAKGHVKVNGEVVKELGTKVTPNDEVKVDEVPISK-EAP 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L   
Sbjct: 63  VYYLLYKPRGVITAVTDDKHRKTVVDILEEVPERIYPVGRLDYDTSGLLLLTNDGDLDNK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G V  D L  L+ G+VI+       +  L      ++ V + +
Sbjct: 123 LTHPKYEVEKTYVAKVKGIVTNDDLKHLRTGVVIEHRKTAKAKTKLIRTNKDSSIVQLTI 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
            EG+N ++K +FE   + V +L R +YG   L  L  G  R          L PH +EE
Sbjct: 183 HEGRNHQVKNMFEKIGYPVEKLSRETYGFLTLKGLQPGDYR---------PLKPHEVEE 232


>gi|322411180|gb|EFY02088.1| hypothetical protein SDD27957_02020 [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 240

 Score =  144 bits (364), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 132/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++  +A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQVITDSATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD NT G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWNTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G  +L  L  G +R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLELTGLRPGESRRLNKK 227


>gi|311030759|ref|ZP_07708849.1| pseudouridine synthase [Bacillus sp. m3-13]
          Length = 242

 Score =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 140/249 (56%), Gaps = 12/249 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E +I + +V+VN  +++   V V   D IEV+G+P+ + E+ 
Sbjct: 2   ERLQKVIAHAGIASRRKAEELIKEGKVRVNDKVVKELGVKVNPNDKIEVEGIPVER-EKP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR    D  P I  R+  VGRLD +T GLLL+TNDG  A V
Sbjct: 61  VYFLLYKPRGVISSVSDDKGRKVATDFFPYIEERIYPVGRLDYDTSGLLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWV-TV 191
           L  P+++  +VY  +  G   ++ +  L++GI ++       ++  L  ++  N  +  +
Sbjct: 121 LMHPASEVEKVYVAKLKGIPSREAIKSLERGIKLEDGKTAPARIKLLSMERTKNTSIFEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE     V +L R  YG   L  L AG  RE         L PH ++
Sbjct: 181 SIHEGRNRQVRRMFEAIGHPVMKLKRERYGFLNLHGLSAGEARE---------LTPHEVK 231

Query: 252 EAQVNLDAP 260
           + +V    P
Sbjct: 232 QLRVMATKP 240


>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 =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 84/210 (40%), Positives = 119/210 (56%), Gaps = 4/210 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAER 72
           ++ K +A+ G+ SRRE+ER I Q R+ + G    +    VM  + + +DG P  L + ER
Sbjct: 24  KLQKALAKTGLGSRREIERWIEQGRLTIGG-RKAKLGDRVMLGERVTLDGKPVELDETER 82

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  LYHKP+G V +  DP+GR TVFD+LP +   R I VGRLD NT GLLL T DG LA
Sbjct: 83  VRCLLYHKPVGEVCSRKDPEGRRTVFDSLPELQGGRWIVVGRLDFNTSGLLLFTTDGELA 142

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS+   R Y VR  G    + L+ L+ G+++         +      G N W  V
Sbjct: 143 HKMMHPSSTIEREYLVRVMGNATDEILDTLRAGVILDDGPARFTDIVDGGGDGINRWFYV 202

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EG+NRE+++++E     V+RL R+ YG
Sbjct: 203 VLMEGRNREVRRLWESQGLTVSRLKRVRYG 232


>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 =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 85/223 (38%), Positives = 125/223 (56%), Gaps = 5/223 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V EN +  ++ K++A AG+ SRR++E +I Q RV VNG+        +   D ++V+G  
Sbjct: 98  VAENSSKPKLHKILADAGVGSRRDMEDLIIQGRVSVNGVPAH-IGQRISDEDVVKVNGRI 156

Query: 67  LRKAERTRL---WLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLL 122
           + + +  R+    LYHKP G + T  DP  R+TVF  LP +  ++ +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 225
            GSN W  V + EG+NRE++++FE     V+RLIR  +G   L
Sbjct: 277 DGSNKWYRVTIEEGRNREVRRMFEALGLTVSRLIRSRFGDVHL 319


>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 =  144 bits (363), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 125/226 (55%), Gaps = 1/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + EG+NR+++++ E     V RL RI  GP  L  L  G  R +++
Sbjct: 183 IHEGRNRQVRRMCEHIGHPVLRLKRIRVGPLVLEGLKPGQFRPLTE 228


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 137/230 (59%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K IA  G+ASRR+ E +IA  +V+VNG  +    V V    D + VDG  L   E+
Sbjct: 2   ERLQKFIASCGVASRRKAEELIASGKVRVNGRKVTELGVKVDPMKDKVMVDG-QLLAVEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ +DP GR TV D + +   R+  +GRLD++TEGLLLLTNDG LA+
Sbjct: 61  PVYYLMNKPKGVITSVTDPQGRETVMDYIKNEKRRIYPIGRLDLHTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  PS    + Y VR  G+V+   L ++  G+ ++ G+      V L  D   G +  V
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVNDTDLQVIADGVPLEDGVTAPATLVDLGFDDHNGVHE-V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+NR+++++FE F ++++ L RI+YG   L  +  G  R+++++
Sbjct: 180 EITIHEGRNRQVRRMFEHFGYRIHNLKRIAYGGLTLSGVKRGGVRQLTQR 229


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 86/234 (36%), Positives = 139/234 (59%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+ AG+ SRR+ E +I + RVKVNG  + +      S  D IEV+G  ++K ER
Sbjct: 3   ERLQKIISHAGVCSRRKAEELIKEGRVKVNGHTVTKLGTEADSVRDCIEVNGKVIKK-ER 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +L++KP  ++T+ +DP GR TV D    I  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 62  LKYFLFNKPDKVITSMTDPAGRRTVSDYFSQIKERVFPVGRLDYHSEGLLLMTNDGDLDY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GI---CYGDMQVTLDTQKGSNAW 188
           +L  PS +  ++Y V   G+  +     + +G+ I  GI   C  D+++    ++ +  +
Sbjct: 122 ILTHPSHEVYKIYEVVVRGKFSERLAEKMSEGVKIDSGITAPC--DIEIISYDKEKNKTF 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + L EGKNREI+K+ E F++ V +L R+ Y    L  +  G+ R +S + +R
Sbjct: 180 LKMVLHEGKNREIRKMMEAFHFPVFKLERVGYSFLTLKGVSRGTFRSLSPEEVR 233


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 84/215 (39%), Positives = 121/215 (56%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           ++ KV+A  G+ SRRE+E +I Q RV VNG L       ++ TD + V+G  + +   T 
Sbjct: 219 KLHKVLAEGGLGSRREMEELILQGRVSVNG-LPAHIGQRILPTDQVRVNGKLIHRKVSTK 277

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
             R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD NTEGLL+ T  G +
Sbjct: 278 PPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTEGLLIFTTSGDI 337

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A     P     R Y VR  G++ +     L  GI +       +++     +G N W  
Sbjct: 338 ANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIADGGGEGVNQWYH 397

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V L EG+NRE++++FE     V+RLIR  YG F L
Sbjct: 398 VALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLL 432


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 86/219 (39%), Positives = 132/219 (60%), Gaps = 8/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG+ SRRE+E  I+  RV VNG +       V S D + VDG  + ++  E
Sbjct: 3   EKLQKVLARAGLGSRRELETWISDGRVSVNGTVAT-LGDRVGSEDTLRVDGRIIKVKTEE 61

Query: 72  RT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            T  R+ +YHKP G V + +DP+GR TVFDNLP +   R + VGRLDINT G++L T DG
Sbjct: 62  DTVQRVIMYHKPPGEVCSRNDPEGRPTVFDNLPRLQGMRWVQVGRLDINTTGMMLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC-YGDMQVTLDTQKGSN 186
            LA  L  PS  ++R Y VR  G +  +K   +  G++++ G+  +  ++     ++G+N
Sbjct: 122 ELAHRLMHPSNGFVREYAVRVRGVMTPEKRQAMLDGVLLEDGVSKFDSIEDAGGAEEGAN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W    L  GK RE++++F+  + +V RL+RI +G   L
Sbjct: 182 HWYKATLTGGKYREVRRLFQSQDLEVARLMRIRFGDLTL 220


>gi|315172332|gb|EFU16349.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
          Length = 238

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 130/234 (55%), Gaps = 3/234 (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
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 62  -YYLFYKPRGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I G      + Q+     K  ++ V +
Sbjct: 121 LTHPKHEVDKVYVAKIKGVPTKRDLLPLVKGIRIDGKRTAPANFQILSADIKTGSSVVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 81/220 (36%), Positives = 134/220 (60%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
           F P+R+ KV+A +G+ SRRE+E  I+   V VNG + +     V   DH+ V G  + L+
Sbjct: 97  FEPERLQKVLAASGVGSRREMEEWISNGWVTVNGRVAQ-LGEKVTPDDHVTVKGSIIKLK 155

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 156 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 215

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G++  +++ +L ++G++++       ++     +G+
Sbjct: 216 SGELVQRFAHPSFEVEREYAVRVLGELTTEQMRVLTEEGVMLEDGLAKVERIYEQGGEGA 275

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 276 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 315


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 81/220 (36%), Positives = 134/220 (60%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
           F P+R+ KV+A +G+ SRRE+E  I+   V VNG + +     V   DH+ V G  + L+
Sbjct: 97  FEPERLQKVLAASGVGSRREMEEWISNGWVTVNGRVAQ-LGEKVTPDDHVTVKGSIIKLK 155

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 156 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 215

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G++  +++ +L ++G++++       ++     +G+
Sbjct: 216 SGELVQRFAHPSFEVEREYAVRVLGELTTEQMRVLTEEGVMLEDGLAKVERIYEQGGEGA 275

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 276 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 315


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 88/232 (37%), Positives = 125/232 (53%), Gaps = 3/232 (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 KP G+V+T +D  GR TV D + ++  RV  VGRLD +T GLLLLTNDG LA  
Sbjct: 62  YIMLY-KPRGVVSTANDDKGRKTVVDLVENVSQRVYPVGRLDYDTSGLLLLTNDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           L  P  +  + Y  R  G    D +  L++GI + G  Y     +V         A +++
Sbjct: 121 LTHPRYEVEKTYIARVTGVPTNDAMKQLRQGITVDGETYAPAKSKVLSAADDRKTAIISL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGKN ++KK+       V +L R  YG   L  L AG  R++  + ++E
Sbjct: 181 TIHEGKNHQVKKMLAAVGCPVEKLKREQYGFLTLKGLNAGEARQLKPEEVKE 232


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 207 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNG-LPAHIGQRILPTDQVR 264

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD N
Sbjct: 265 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 324

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 325 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEFDRQKLLQGVRLDDGEANFLRC 384

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 385 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 444

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 445 SAEEVRVLMG 454


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 134/229 (58%), Gaps = 5/229 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+K        P+R+ KV+A +G+ SRRE+E  I    V+VNG  + R    +   D +
Sbjct: 90  LKEKRTDLSRIQPERLQKVLAASGVGSRREMEEWINNGWVQVNG-HVARLGEKITPNDQV 148

Query: 61  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDI 116
            + G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP +  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 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 269 IYEQGGEGVNKWYNVIIKEGRNREVRRLFESQGLTVSRLVRVGFGPIGL 317


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 137/228 (60%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNG-QLLAQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  VGRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNESKRIYPVGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  PS    + Y VR  G+V  + L ++  G+ ++ G+      V L  D   G +  V
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDEDLQVIANGVKLEDGMTAPATIVDLGFDDHNGVHE-V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++
Sbjct: 180 EITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLT 227


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 88/215 (40%), Positives = 125/215 (58%), Gaps = 4/215 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN  L +     +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVNQRLAQLGD-RITEQDLVYIDGQLSSLSVPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+ R+TVF+ LP +   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 225
           V + EG++R +++++E    KV+RLIR+ +GP  L
Sbjct: 182 VVVVEGRHRLVRRLWESQGVKVSRLIRVRFGPIVL 216


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

 Score =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 132/226 (58%), Gaps = 3/226 (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
             +L++KP G++++  D  GR  V D    +  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 62  -YYLFYKPRGVISSVKDDKGRKVVTDFFKDVDKRIYPIGRLDYDTSGILLLTNDGDFANL 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    KV +L R  Y    L  L  G  R+++
Sbjct: 181 RIHEGRNRQVRRMFEAIGCKVMKLKRERYAFLDLKGLNPGEYRKLT 226


>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 =  144 bits (362), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 92/250 (36%), Positives = 141/250 (56%), Gaps = 7/250 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG L       ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNG-LPAHIGQRILPTDQVR 260

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP +   + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEFDRQKLLQGVRLDDGEANFLRC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLG 246
           S + +R  +G
Sbjct: 441 SAEEVRVLMG 450


>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 =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQVVSDLATTVKSGDTVEVEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   +D L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKDNLRPLTRGVVIDGKKTKPARYNIIRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLNKK 227


>gi|330719107|ref|ZP_08313707.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc fallax
           KCTC 3537]
          Length = 252

 Score =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/226 (37%), Positives = 129/226 (57%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR  E +I + RV VNG  ++     V  +D + VDGVP+   ER 
Sbjct: 8   ERLQKVIAQAGLASRRGAEALIVEGRVSVNGQQVKELGTKVRRSDTVAVDGVPIEGRERL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT  D  GR+TV D L  +  RV  VGRLD +T G LLLTNDG +A  
Sbjct: 68  VYYLLNKPRGVVTTTQDEKGRATVLDILDDVSQRVYPVGRLDYDTTGALLLTNDGTIANE 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P ++  +VY  +  G   ++ L  LKKG++I+G      +V++++  +    + V +
Sbjct: 128 LMHPKSKVDKVYIAKVKGMATENDLLPLKKGVMIEGHKTQPARVSVESVDKTKKTSMVKL 187

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EGKN ++K +     + V +L R  Y    L  L  G  R+++
Sbjct: 188 IIHEGKNHQVKNMLAKVGFPVEKLKREQYAFLDLVGLQPGEYRKLT 233


>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 =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 90/220 (40%), Positives = 129/220 (58%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E  IA  R+ ++G    L +R   +V     I +DG  + ++
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRISIDGEIANLGDRIEADV----KIRIDGRAISIK 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
            AE    R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T
Sbjct: 59  SAEDLICRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG LA  L  PS +  R Y VR  G+V    +  L+ G+ ++       +V     +G 
Sbjct: 119 SDGELANRLMHPSNEVEREYAVRTFGEVTDACIQRLRTGVTLEDGPASFDKVKAAGGEGM 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 179 NKWWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGKIEL 218


>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 =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 133/228 (58%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I +  V +NG ++   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKKGLVSINGKVVTELATTVKSGDIVEVEGTPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   + +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKK 227


>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 =  143 bits (361), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 130/228 (57%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA+AG+ASRR  E +I   RV+VNG  +      V + D ++VDG P+   E+ 
Sbjct: 6   QRLQKIIAQAGLASRRGAEELIINGRVQVNGQTVTELGTKVTANDKVQVDGAPIEGREKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT+ D  GR TV D L  +  RV  VGRLD +T G+LLLTNDG +A  
Sbjct: 66  VYYLLNKPRGVVTTNDDEKGRRTVLDILEDVDQRVYPVGRLDYDTTGVLLLTNDGVVANQ 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSNAWV 189
           L  P T+  + Y  +  G   ++KL  LK+G+V++G      +V+++    T++ S   +
Sbjct: 126 LMHPKTKVDKTYVAKVEGIATEEKLAPLKRGVVLKGRKTAPARVSIERIEPTKRTSMVRL 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T+   EG+N ++K +       V +L R  Y  F +  L  G  R+++
Sbjct: 186 TI--HEGRNHQVKNMLAKVGLPVQKLKREQYAFFDVTGLQPGEYRKLT 231


>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 =  143 bits (361), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 129/226 (57%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K ++ AG+ASRR+ E++I + RVKVNG ++    V V    D +EVDG P+ K +R 
Sbjct: 5   RINKFLSEAGVASRRKAEKLILEGRVKVNGEVVRSLGVKVNPEVDIVEVDGKPV-KPQRK 63

Query: 74  RLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   +T     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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             EG+   +K+    F  KV RL RI+ GP +LG L  G  RE+++
Sbjct: 184 FHEGRKHLVKRFLGAFGHKVKRLKRIAIGPIKLGKLSPGKWRELNQ 229


>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 =  143 bits (361), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 128/227 (56%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQMVTELATTVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++  D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVRDDKGRQTVVDLLPEVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  +VY  R  G   +D L  L KGIVI G        ++    ++ + + V + 
Sbjct: 121 LHPRHEIDKVYVARVKGLASKDNLRPLTKGIVIDGKKTQPARYRIVKTDREKNRSVVELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+FE     V++L R  +G   L  L +G  R ++KK
Sbjct: 181 IHEGRNHQVKKMFEAVGLMVDKLSRTRFGTLDLSGLNSGEARRLNKK 227


>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 =  143 bits (361), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 121/215 (56%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           ++ KV+A  G+ SRRE+E +I Q RV VNG L       ++ TD + V+G  + +   T 
Sbjct: 236 KLHKVLAEGGLGSRREMEELILQGRVSVNG-LPAHIGQRILPTDQVRVNGKLIHRKVTTK 294

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
             R+ LYHKP G + + SDP+GR TVFD+LP I   + ++VGRLD NTEGLL+ T  G +
Sbjct: 295 PPRVLLYHKPSGEIVSQSDPEGRPTVFDSLPRIKNGKWVAVGRLDFNTEGLLIFTTSGDI 354

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A     P     R Y VR  G++ +     L  GI +       +++     +G N W  
Sbjct: 355 ANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIQLDDGEANFLRIADGGGEGVNQWYH 414

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V L EG+NRE++++FE     V+RLIR  YG F L
Sbjct: 415 VALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLL 449


>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 =  143 bits (361), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 83/218 (38%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E ++ + R+ V+G +      V V +T  I +DG  + +++ 
Sbjct: 17  EKLQKILARSGHGSRREIEGLLKEGRISVDGKMATLGDRVEVKATTKIRLDGRLLAIKEP 76

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E+   R+  Y+KP G + T  DP+GR TVF+ LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 77  EKEICRVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTD 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++   K+  L  G+ ++        V+    +G N 
Sbjct: 137 GELANRLMHPSREVEREYAVRVFGEITDAKIRQLTTGVQLEDGPASFKTVSYRGGEGMNQ 196

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 197 WYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDL 234


>gi|317402968|gb|EFV83508.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 469

 Score =  143 bits (361), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 85/213 (39%), Positives = 123/213 (57%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V   D + V+G P+ +A  
Sbjct: 114 KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAPNDQVRVNGKPIMRANT 170

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 171 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 230

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +A  +  P     R Y VR  G++D+ +   L  GI ++        +      GSN W
Sbjct: 231 DMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGVAAFGALDYLGGDGSNRW 290

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 291 YRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 323


>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 =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 133/228 (58%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I +  V +NG ++   A  V + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEDLIKRGLVTINGKVVTELATTVKAGDVVEVEGTPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   + +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGLATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK
Sbjct: 180 TIHEGRNHQVKKMFELVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKK 227


>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 =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 85/217 (39%), Positives = 131/217 (60%), Gaps = 13/217 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV----NVMSTDHIEVDGVPL--- 67
           ++ K+++  G  SRR +E MI   ++ +NG   E+A +    N  +   I +D   +   
Sbjct: 4   KIQKILSDLGYGSRRFIECMIKCGKISING---EKAIIGQYLNKKNPGEILIDKKKIIVK 60

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
           R     ++ +Y+KPIG V T  D   R TVFD LP +  +R +SVGRLDINT+GLLL TN
Sbjct: 61  RNKNLPKVLIYNKPIGEVCTRDDFQKRLTVFDKLPKLNLNRWVSVGRLDINTKGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQG-ICYGDMQVTLDTQKG 184
           DG LA  L  P +Q  R Y +R  G+++++K+N+L+KG+ +I G + + ++    D ++G
Sbjct: 121 DGTLANKLMHPRSQIEREYNIRIFGEMNKNKINILRKGVKIIHGYVSFKEIVPLYDKKEG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            N W    L EGKNREI+ +F+    +VN+LIR+ YG
Sbjct: 181 KNKWFKGILCEGKNREIRLMFKSIQCQVNQLIRVRYG 217


>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 =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 84/215 (39%), Positives = 120/215 (55%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           ++ KV+A  G+ SRRE+E +I Q RV VNG L       ++  D + V+G  + +   T 
Sbjct: 225 KLHKVLAEGGLGSRREMEELILQGRVSVNG-LPAHIGQRILPADQVRVNGKLIHRKVSTK 283

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
             R+ LYHKP G + + SDP+GR TVFD+LP I   + ++VGRLD NTEGLL+ T  G +
Sbjct: 284 PPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRIKTGKWVAVGRLDFNTEGLLIFTTSGDI 343

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A     P     R Y VR  G++ +     L  GI +       +++     +G N W  
Sbjct: 344 ANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIADGGGEGVNQWYH 403

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V L EG+NRE++++FE     V+RLIR  YG F L
Sbjct: 404 VALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLL 438


>gi|319638171|ref|ZP_07992934.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400444|gb|EFV81102.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 352

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 81/220 (36%), Positives = 134/220 (60%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
           F P+R+ KV+A +G+ SRRE+E  I+   V VNG + +     V   DH+ V G  + L+
Sbjct: 97  FEPERLQKVLAASGVGSRREMEEWISNGWVTVNGRVAQ-LGDKVTPDDHVTVKGSIIKLK 155

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 156 WADRLPRIILYYKQEGEIVSRDDPQGRISIFDRLPQAASSRWVAIGRLDINTSGLLILTT 215

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G++  +++ +L ++G++++       ++     +G+
Sbjct: 216 SGELVQRFAHPSFEVEREYAVRVLGELTTEQMRVLTEEGVMLEDGLAKVERIYEQGGEGA 275

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 276 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 315


>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 =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 127/217 (58%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ KV+ARAG  SRRE+E  IA  R+ V+G +       V S   + +DG  +  K+E 
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRISVDGEIAS-LGDRVESDVKVRIDGRAISIKSEE 61

Query: 73  ---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T+DG
Sbjct: 62  DVVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G N W
Sbjct: 122 ELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRMGVTLEDGPASFDKVKAAGGEGMNKW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 182 WHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIEL 218


>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 =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 86/234 (36%), Positives = 138/234 (58%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+ AG+ SRR+ E +I   RVKVNG  + +      S  D IEV+G  ++K ER
Sbjct: 3   ERLQKIISHAGVCSRRKAEELIKDGRVKVNGHTVTKLGTEADSVRDCIEVNGKVIKK-ER 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +L++KP  ++T+ +DP GR TV D    I  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 62  LKYFLFNKPDKVITSMTDPAGRRTVADYFSQIKERVFPVGRLDYHSEGLLLMTNDGDLDY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GI---CYGDMQVTLDTQKGSNAW 188
           +L  PS +  ++Y V   G+  +     + +G+ I  GI   C  D+++    ++ +  +
Sbjct: 122 ILTHPSHEVYKIYEVVVRGKFSERLAEKMSEGVKIDSGITAPC--DIEIISYDKEKNKTF 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + L EGKNREI+K+ E F++ V +L R+ Y    L  +  G+ R +S + +R
Sbjct: 180 LKMVLHEGKNREIRKMMEAFHFPVFKLERVGYSFLTLKGVSRGTFRSLSPEEVR 233


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

 Score =  143 bits (360), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 131/227 (57%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNG ++    V V   D IEVDG+PL + E  
Sbjct: 12  ERLQKVIAHAGVASRRKAEQLIVEGKVKVNGKVVTELGVKVSPQDRIEVDGIPLEREEPV 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G++++  D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 72  YYLLY-KPRGVISSVKDEKGRKVVTDFFKHVNKRIYPIGRLDYDTSGLLLLTNDGEFANI 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  +VY  +  G   ++K+  L+KG++++       +   +++D +K   A V 
Sbjct: 131 LMHPRYEIEKVYIAKVKGIPAREKVKQLEKGVMLEDGVTAPAKAKVLSIDKRK-QTAIVE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE     V +L R  Y    L  L  G  RE+S
Sbjct: 190 LRIHEGRNRQVRRMFEAIGHPVLKLKRERYAFLDLKGLNPGDYRELS 236


>gi|184201169|ref|YP_001855376.1| pseudouridine synthase [Kocuria rhizophila DC2201]
 gi|183581399|dbj|BAG29870.1| pseudouridine synthase [Kocuria rhizophila DC2201]
          Length = 368

 Score =  143 bits (360), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 132/226 (58%), Gaps = 4/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG+ASRR  E MI   RV V+G ++    V V  +   + VDG+ ++  E+ 
Sbjct: 131 RLQKLMAQAGVASRRVCEEMIQDGRVSVDGEIVTELGVRVDPALQAVHVDGMRIQTDEKL 190

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + ++KP G+V+T  DPDGR  V D L P    RV  VGRLD+ TEGLLLLTNDG L  
Sbjct: 191 VYYAFNKPAGVVSTMEDPDGRRCVSDFLDPRKHQRVFHVGRLDVETEGLLLLTNDGELTN 250

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+ HG V++   N +K+GI ++ GI   D    +D+  G +  + V
Sbjct: 251 RLTHPSYEVPKTYLVQVHGPVEKGIGNQMKQGIRLEDGIAKVDDFRLVDSTPG-HVLIEV 309

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L  G+NR ++++F+  +  V +L R   GP  +G    G+ R++S
Sbjct: 310 VLHSGRNRIVRRMFDAVDHPVEKLARTHVGPIAIGDQKQGTVRKLS 355


>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 =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>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 =  142 bits (359), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 93/243 (38%), Positives = 142/243 (58%), Gaps = 12/243 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDGV 65
           E+    ++ K++A+AG+ SRRE+E++IA +RV VNG    L +RA+    S D I VDG 
Sbjct: 5   ESPAGDKLQKLLAQAGVGSRREMEKVIADRRVTVNGKVAKLGDRAS----SRDKIAVDGK 60

Query: 66  PLRKAERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGL 121
            +  AE+    R+ +Y+KP G + + SDP+GR TVF+ LP +  SR I+VGRLD NT GL
Sbjct: 61  LVGVAEQDSAGRVLIYNKPEGEICSRSDPEGRKTVFERLPKLTGSRWIAVGRLDFNTSGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ T DG LA  L  PS++  R Y  R  G V    L  L  G++++        +    
Sbjct: 121 MIFTTDGQLANALMHPSSEIDREYLCRVLGNVSDVVLQRLSDGVLLEDGTAKFTDIVDGG 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKKI 240
            +G+N W  V L EG+NRE+++++E    +V+RL R+ +G  F    L  G  +E+  K 
Sbjct: 181 GEGANHWYYVALMEGRNREVRRLWESQEIQVSRLKRVRFGGVFLPSKLRQGQWQEMPYKE 240

Query: 241 LRE 243
           ++E
Sbjct: 241 VQE 243


>gi|332969784|gb|EGK08795.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter sp.
           1501(2011)]
          Length = 354

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 83/220 (37%), Positives = 129/220 (58%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLR-- 68
           +++ K +AR G+ SRR++E +I   RV +N    ++ A     V  +D I VDG  ++  
Sbjct: 47  EKLQKALARMGLGSRRQMEEVIKAGRVSIN----QKPATIGDRVEQSDEIRVDGRLIKYK 102

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
             + +R R+  Y+KP G + + +DP+GR+TVF+ LP +   R I VGRLDIN+ GLLL T
Sbjct: 103 SEREKRRRVLAYYKPEGEICSANDPEGRTTVFERLPKLTHDRWIMVGRLDINSTGLLLFT 162

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS + +R Y VR  G++  + +  L  G++++        +     +G 
Sbjct: 163 NDGELAHRLMHPSNEIVREYAVRILGELTPEMMRNLTDGVMLEDGLAKFEDIRQGGGEGV 222

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L+EG+NRE++++ E    KV+RL+R SYG   L
Sbjct: 223 NKWYHVKLKEGRNREVRRLIESQGLKVSRLLRTSYGSVDL 262


>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 =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 127/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQMVTELATTVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++  D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVRDDKGRQTVVDLLPEVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  +VY  R  G   +D L  L KGIVI G        ++    ++ + + V + 
Sbjct: 121 LHPRHEIDKVYVARVKGLASKDNLRPLTKGIVIDGKKTQPARYRIVKTDREKNRSVVELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 181 IHEGRNHQVKKMFEAVGLMVDKLSRTRFGTLDLSGLNPGEARRLNKK 227


>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 =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 96/265 (36%), Positives = 140/265 (52%), Gaps = 20/265 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPL--- 67
           QR+ K+++RAGIASRR+VE  IA  R+ VNG   +L  RA       D I VDG PL   
Sbjct: 4   QRLQKLLSRAGIASRRQVENWIAAGRITVNGRPAVLGTRADPE---RDVIAVDGRPLADL 60

Query: 68  -RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLT 125
            ++  R R  + HKP G+VTT  DP GR +V D       R +  VGRLD ++EGLLLLT
Sbjct: 61  RQRLARKRYVMLHKPRGMVTTLRDPQGRPSVGDFCRRAGLRGLHPVGRLDFDSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG L   L  P  +  +VY V   G ++  +L  L+ G+++           +   +  
Sbjct: 121 DDGELTFALTHPRHEVDKVYHVLVRGPLEPQRLRRLRDGVLLDDGPARARSARILRPRPG 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             WV V LREG+ R+++++     W V RL+R++ GP +LG L AG  R +S++      
Sbjct: 181 GGWVEVVLREGRKRQVRRMCRAVGWDVVRLVRVAVGPLRLGRLTAGQWRPLSRQ------ 234

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRD 270
               +E  +     PI+  E   R+
Sbjct: 235 ---EVEALRAAAGLPIHGDEPAPRE 256


>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 =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 83/218 (38%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E  + + R+ V+G +      V V ++  I +DG  + +R+ 
Sbjct: 17  EKLQKILARSGHGSRREIEGFLKEGRISVDGKMATLGDRVEVTTSTKIRLDGRLLTIREP 76

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E+   R+  Y+KP G + T  DP+GR TVF  LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 77  EKDICRVMAYYKPEGELCTRHDPEGRPTVFTRLPKLTGARWIAVGRLDVNTSGLLLFTTD 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++   K+  L  G+ ++        V+    +G N 
Sbjct: 137 GELANRLMHPSREVEREYAVRVFGEITDAKIRQLTMGVQLEDGPASFKTVSFRGGEGMNQ 196

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 197 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDL 234


>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 =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 90/256 (35%), Positives = 136/256 (53%), Gaps = 12/256 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++AR GIASRR  E++I   RV +NG  ++         D + VDG PL+  ER 
Sbjct: 3   ERVQKILARWGIASRRGAEKLILAGRVTLNGKPVQLGDQADPEGDRLCVDGKPLKATERP 62

Query: 74  RLWLY--HKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           R + Y  HKP G+V+T +DP GRSTV D LP    +   +  +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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I++V E   + V +L R++ G   LG L  G  R ++K  +++     
Sbjct: 183 IDIMLTEGRNRQIRRVAEQLGFPVVKLHRLAIGNLHLGDLQRGQARPLTKAEIKQL---- 238

Query: 249 LLEEAQVNLDAPIYSS 264
               +Q N + P +SS
Sbjct: 239 ---RSQYNSNFPFHSS 251


>gi|325687113|gb|EGD29136.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK72]
          Length = 242

 Score =  142 bits (359), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDCVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>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 =  142 bits (359), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 82/218 (37%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKA 70
           P+R+ KV+A +G  SRRE+E  IA   V+VNG   +     V   D + V G P  L+ A
Sbjct: 117 PERLQKVLAASGAGSRREMEEWIAAGLVQVNGKTAQ-LGDKVTPDDQVTVKGSPIKLKWA 175

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 176 DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 235

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G++  +++  L  +G+++        ++     +G+N 
Sbjct: 236 ELVQRFAHPSFEVEREYAVRVLGELTAEQMRELTTEGVMLDDGLAKVERIFEQGGEGANK 295

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W +V ++EG+NRE++++FE F   V+RL+R+ +GP  L
Sbjct: 296 WYSVVIKEGRNREVRRIFEHFGLTVSRLVRVGFGPIGL 333


>gi|323489657|ref|ZP_08094884.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323396788|gb|EGA89607.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 243

 Score =  142 bits (359), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 86/234 (36%), Positives = 134/234 (57%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I   +V+VNG  ++   V V ++D IEV+GV L K ++ 
Sbjct: 2   ERLQKVLAHAGVASRRKSEQLILDGKVRVNGKTIKELGVKVSNSDKIEVEGVQLEKEQKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G+++  SD   R  V D    I  R+  VGRLD +T GLL++TNDG  A +
Sbjct: 62  YHLLY-KPRGVISAVSDDKNRKVVTDFFEGIEKRIYPVGRLDYDTSGLLIMTNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           L  P  +  + Y  R  G  ++D L  L++GI ++       +V L    +K   A V +
Sbjct: 121 LTHPKFEIDKTYVARLKGIPEKDDLRKLERGIKLEDGMTAPAKVKLLSGDKKTGKAIVQI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
            + EG+NR+++++FE   + V +L R  +    L  L AG +RE+S    K+LR
Sbjct: 181 TIHEGRNRQVRRMFEAIGYPVQKLSREQFAFLTLHGLNAGESRELSAHEVKLLR 234


>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 =  142 bits (359), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 134/226 (59%), Gaps = 10/226 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG   V    A
Sbjct: 24  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQ-TGMSVKSGDKIELDGRGFVATALA 82

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP +  +R I++GRLDINT GLLL T DG 
Sbjct: 83  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAIGRLDINTTGLLLATTDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKG 184
           LA  +  PS +  R Y VR      ++K++      + +G+   D     D         
Sbjct: 143 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLARGVALEDGPAKFDEIERIGGTD 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LA
Sbjct: 203 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELA 248


>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 =  142 bits (358), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 91/225 (40%), Positives = 125/225 (55%), Gaps = 2/225 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            + +R+ KV+A AGIASRR+ E  IA  RV VNG ++      V    D I VDG P+ K
Sbjct: 1   MSAERLQKVLASAGIASRRDCEEYIAAGRVMVNGKVVRIPGTRVDPEHDEILVDGRPIGK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  + HKP G+V+T  DP GR TV D L ++  R+  VGRLD ++EGLLLLT+DG 
Sbjct: 61  IHHRTYVMLHKPAGVVSTTDDPQGRPTVID-LVNLEQRLFPVGRLDYDSEGLLLLTDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L + L  PS Q  + YRV  +       L   + G+ + G+      V L  +    AWV
Sbjct: 120 LTQKLTHPSYQVEKEYRVLLNEAPSPAALRAWRTGVELDGVKTAPAWVELIERTPDGAWV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+ R+I++V     ++V RLIR+  GP  LG L +G+ R
Sbjct: 180 RVILHEGRKRQIREVARVLGYEVRRLIRVREGPLTLGDLPSGTWR 224


>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 =  142 bits (358), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 84/223 (37%), Positives = 132/223 (59%), Gaps = 4/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++++AG++SRR+ E+++ + RV VNG ++ E  +   +  DHI+VDG  L KA +
Sbjct: 4   ERLQKILSQAGVSSRRQAEKLMQEGRVTVNGSVITELGSKADLDRDHIKVDG-RLLKAPK 62

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++++  +KP G VTT  DP+GR TV D L  +  RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 63  HQIYIALNKPKGTVTTVHDPEGRETVMDLLHRVKERVYPVGRLDYHSEGLLLLTNDGELA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   +T   + Y V+  G +  ++    + G+ + G       + L   +  N W  V
Sbjct: 123 NSIMSAATHLEKTYVVKVTGTLTAEQEEKFRTGVPLSGRRTLPAGLKL-LSRAENPWYEV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            L EG+N +I+ +F  F   V +L R+  GP +LGTL  G+ R
Sbjct: 182 KLTEGRNNQIRMMFRHFGKLVEKLKRVRIGPIELGTLKTGAFR 224


>gi|327470426|gb|EGF15882.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK330]
          Length = 242

 Score =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A N+ S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNIKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>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 =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + +
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKK 227


>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 =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 124/215 (57%), Gaps = 13/215 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V   D + V+G P+ +   
Sbjct: 118 KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAPNDQVRVNGKPIARPNA 174

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 175 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 234

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            +A  +  P     R Y VR  G++D  +   L +GI ++     +G  +       GSN
Sbjct: 235 DMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEYL--GGDGSN 292

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            W  V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 293 RWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 327


>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 =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 124/215 (57%), Gaps = 13/215 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V   D + V+G P+ +   
Sbjct: 125 KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAPNDQVRVNGKPIARPNA 181

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 182 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 241

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            +A  +  P     R Y VR  G++D  +   L +GI ++     +G  +       GSN
Sbjct: 242 DMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEYL--GGDGSN 299

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            W  V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 300 RWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 334


>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 =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 124/215 (57%), Gaps = 13/215 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V   D + V+G P+ +   
Sbjct: 125 KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAPNDQVRVNGKPIARPNA 181

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 182 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 241

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            +A  +  P     R Y VR  G++D  +   L +GI ++     +G  +       GSN
Sbjct: 242 DMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEYL--GGDGSN 299

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            W  V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 300 RWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 334


>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 =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 137/228 (60%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K IA  G+ASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKFIASCGVASRRKAEELITEGKVQVNGRKVTELGVKIDPQKDKVKVNG-QLLAQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNESKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL--DTQKGSNAWV 189
            L  PS    + Y VR  G+V  + L ++  G+ ++ G+      V L  D   G +  V
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDEDLQVIANGVKLEDGMTAPATIVDLGFDDHNGVHE-V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++
Sbjct: 180 EITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLT 227


>gi|149181685|ref|ZP_01860178.1| RluB [Bacillus sp. SG-1]
 gi|148850663|gb|EDL64820.1| RluB [Bacillus sp. SG-1]
          Length = 243

 Score =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 84/226 (37%), Positives = 127/226 (56%), Gaps = 3/226 (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 KP G+++  +D   R  V D  P I  R+  VGRLD +T GL+LLTNDG  A +
Sbjct: 62  YYLLY-KPRGVISAVTDDKDRKVVTDFFPYIQERIYPVGRLDYDTSGLILLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P     + Y  R  G   + KL  L+KGI+++        ++V    +K   + V +
Sbjct: 121 LTHPRYNIDKTYVARLKGIPPKFKLKELEKGIMLEDGKTAPAKVKVLKIEKKQDKSIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EGKNR++K++FE   ++V +L R  +    L  L AG +RE+S
Sbjct: 181 TIHEGKNRQVKRMFEAIGYQVQKLKRERFAFLDLHGLNAGESRELS 226


>gi|254525039|ref|ZP_05137094.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722630|gb|EED41155.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 546

 Score =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 90/226 (39%), Positives = 134/226 (59%), Gaps = 10/226 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG   V    A
Sbjct: 24  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQ-TGMSVKSGDKIELDGRGFVATALA 82

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP +  +R I++GRLDINT GLLL T DG 
Sbjct: 83  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAIGRLDINTTGLLLATTDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKG 184
           LA  +  PS +  R Y VR      ++K++      + +G+   D     D         
Sbjct: 143 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLSRGVALEDGPAKFDEIERIGGTD 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LA
Sbjct: 203 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELA 248


>gi|326565822|gb|EGE15984.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis BC1]
          Length = 328

 Score =  142 bits (358), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 88/214 (41%), Positives = 127/214 (59%), Gaps = 8/214 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R KAER
Sbjct: 24  EKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRLKAER 82

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + + SDP GR TVFD LP + + R + VGRLDIN+ GLLL TNDG
Sbjct: 83  EKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLFTNDG 142

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS+  +R Y VR  G+V     + L  G+ ++ G+   D  +      G N 
Sbjct: 143 ELAHRLMHPSSGIIREYAVRVLGEVTSQIASQLTAGVELEDGVAKFD-DIKEGGGIGVNK 201

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           W  V ++EG+ RE++++FE    KV+RLIR  YG
Sbjct: 202 WYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYG 235


>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 =  142 bits (358), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 92/248 (37%), Positives = 134/248 (54%), Gaps = 13/248 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRK 69
           PQR+ K++A+ G+ASRR+VE  I   RV+VNG ++ E  +      D IEV+G  +PL K
Sbjct: 4   PQRLQKLLAQQGLASRRQVEAWILAGRVRVNGKVVTELGSKADPERDCIEVNGQVIPLAK 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTN 126
                + L HKP+G+++T +DP GR TV D LP  +   +R+  VGRLD ++ G LLLTN
Sbjct: 64  DPARYVLLLHKPVGVLSTCADPWGRKTVLDLLPPSWKRQTRLYPVGRLDADSSGALLLTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG L   L  P     + YRV+  G   Q  L   + G+ ++G      +V         
Sbjct: 124 DGDLTLKLTHPRYHLPKTYRVQVQGHPSQATLQHWRDGVDLEGYTTLPAEVEFCPAPDFR 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +  + +W+ V L EG+NR+I++V E     V  L R + GP  LG L AG  R++   
Sbjct: 184 QREHPNCSWLRVVLFEGRNRQIRRVAERLGHPVLSLHREAIGPLGLGNLKAGQFRQLDPH 243

Query: 240 ILREQLGP 247
            L+  L P
Sbjct: 244 ELQALLAP 251


>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 =  142 bits (358), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 133/228 (58%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I +  V +NG ++   A  V + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEDLIKRGLVTINGKVVTELATTVKAGDVVEVEGTPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   + +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGLATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKK 227


>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 =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 90/220 (40%), Positives = 129/220 (58%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E  IA  R+ ++G    L +R   +V     I +DG  V ++
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRISIDGEIANLGDRIEADV----KIRIDGRTVSIK 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
             E    R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T
Sbjct: 59  SEEDLICRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG LA  L  PS +  R Y VR  G+V+   +  L+ G+ ++       +V     +G 
Sbjct: 119 SDGELANRLMHPSNEVEREYAVRTFGEVNDACIQRLRTGVTLEDGPASFDKVKAAGGEGM 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 179 NKWWHVTLAEGRNREVRRLWESQEVQVSRLIRIRYGKIEL 218


>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 =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  D+D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGIADKDNLRPLTRGVEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 87/222 (39%), Positives = 133/222 (59%), Gaps = 20/222 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAE 71
           +R+ KV+ARAG  SRR+VE  I + +V  NG   E A +   +   D +++D   L    
Sbjct: 3   ERIQKVLARAGYGSRRQVETWIKEGKVSCNG---ETATLGDQISEGDRLKLDNKLLSPK- 58

Query: 72  RTRLW-------LYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
             RLW       LY+KP+G V T SDP+GR T+F  LP+    R +SVGRLD+NT GL++
Sbjct: 59  --RLWQQPQQVILYNKPVGEVCTRSDPEGRRTIFQALPTPEQGRWVSVGRLDLNTSGLII 116

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDT 181
           LT DG LA  L  PS +  R Y VR  G+V  + +  L+ G++++     + D+Q +   
Sbjct: 117 LTTDGELANRLMHPSNEMDREYAVRVLGEVTPEIMQNLRDGVMLEDGEAHFADIQES--G 174

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            +G+N W  V ++EG+NRE+++++E    +V+RL+R+ YGP 
Sbjct: 175 GEGANHWYHVVIQEGRNREVRRLWESQGVQVSRLMRVRYGPI 216


>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 =  142 bits (357), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 97/245 (39%), Positives = 143/245 (58%), Gaps = 14/245 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG   V    A
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQ-TGMSVKSGDKIELDGRGFVATALA 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP +  +R I+VGRLDINT GLLL T DG 
Sbjct: 87  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAVGRLDINTTGLLLATTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKG 184
           LA  +  PS +  R Y VR      ++K++      + +G+   D     D         
Sbjct: 147 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIIDRLGRGVALEDGPAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK---KI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LA G + E+     + 
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVTLPRELARGHSVELGSAQVEA 266

Query: 241 LREQL 245
           LR QL
Sbjct: 267 LRAQL 271


>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 =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 91/229 (39%), Positives = 130/229 (56%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR  E +I   RV VNG ++ +    V+   D IEVDG PL   E 
Sbjct: 3   ERLQKVMARAGVASRRHCEALIQAGRVTVNGQVVTQLGTKVVPGKDVIEVDGRPLGTPET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G V+T  DP GR  V D L   +  RV  VGRLD +TEGLLLLTNDG LA
Sbjct: 63  KVYVMLNKPKGYVSTLYDPQGRPKVIDLLGDEVAQRVYPVGRLDFDTEGLLLLTNDGDLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVT 190
             L  PS    + Y V+  G     KL  L++GI ++       +V  LD +  ++A ++
Sbjct: 123 HGLMHPSRMVKKTYIVKVRGVPGPAKLRALQEGIELEDGPTAPAEVKMLDVRPPNSATLS 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + EG+NR+++++F     +V  L R + GP +LG L  G  R ++ +
Sbjct: 183 VRIHEGRNRQVRRMFAALGHEVIHLRRTTLGPLKLGDLSVGEWRYLTDQ 231


>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 =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/213 (39%), Positives = 124/213 (58%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARVGLGSRRYMEEVIAAGRVSVNGQVAQ-VGERIEPGDELRIDGRKVSFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD LP+I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPESRPTVFDQLPAIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V     N + KG+V+          +    +G N W
Sbjct: 122 ELANRLMHPSNEVEREYAVRVMGEVTPQIKNNMLKGVVLDDGPAKFESFSEIGGEGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 92/221 (41%), Positives = 131/221 (59%), Gaps = 14/221 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E  IA  R+ ++G    L +R   +V     I +DG  V ++
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRISIDGEIANLGDRVEADV----KIRIDGRAVSIK 58

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
             E    R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T
Sbjct: 59  SEEDLVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG 184
           +DG LA  L  PS +  R Y VR  G+V    +  L+ G+ ++ G  + D +V     +G
Sbjct: 119 SDGELANRLMHPSNEVEREYAVRTFGEVTDACIQRLRTGVTLEDGPAHFD-KVKAAGGEG 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            N W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 178 MNKWWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIEL 218


>gi|40063061|gb|AAR37917.1| RNA pseudouridylate synthase family protein [uncultured marine
           bacterium 560]
          Length = 244

 Score =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 86/219 (39%), Positives = 133/219 (60%), Gaps = 12/219 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +R+ K+IA AG  SRR  ER+I Q RV +N     L ++A +N    D + +DG  + L+
Sbjct: 3   ERLQKLIANAGYGSRRWAERLIEQGRVSLNNHDVKLGDKAVLN----DKVRIDGKLIDLK 58

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  +T  ++ + +K  G + +  DP+GR +VFD LP   SR I +GRLD+N+ GLLL TN
Sbjct: 59  RYAKTETKVLILNKQAGFICSTKDPEGRKSVFDLLPE-NSRWIMIGRLDLNSSGLLLFTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  PS Q  R Y VR  G+V ++ +  L  G+ ++       +VT    +G+N
Sbjct: 118 NGELASKLMHPSAQIDREYAVRVLGKVKEEHIKKLTNGVELEDGFAKFHKVTQGGGEGAN 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V +REG+ RE+++++EF ++KV+RLIRI +G   L
Sbjct: 178 RWYRVVIREGRKREVRRLWEFLDFKVSRLIRIRFGDICL 216


>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 =  142 bits (357), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQIITDLATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G  +L  L  G +R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLELTGLRPGESRRLNKK 227


>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 =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 83/219 (37%), Positives = 129/219 (58%), Gaps = 10/219 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR--- 68
           +++ K +AR G+ SRR++E +I   RV +N    + A++   V   D I VDG  ++   
Sbjct: 43  EKLQKALARMGLGSRRQMEEVIKAGRVSIN---QKPASIGDRVEQGDEIRVDGRLIKYKS 99

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
            + +R R+  Y+KP G + + +DP+GR+TVF+ LP +   R I VGRLDIN+ GLLL TN
Sbjct: 100 EREKRRRVLAYYKPEGEICSANDPEGRTTVFERLPKLTHDRWIMVGRLDINSTGLLLFTN 159

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS + +R Y VR  G++  + +  L  G++++        +     +G N
Sbjct: 160 DGELAHRLMHPSNEIVREYAVRILGELTPEMMRNLTDGVMLEDGLAKFEDIKQGGGEGVN 219

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L+EG+NRE++++ E    KV+RL+R SYG   L
Sbjct: 220 KWYHVKLKEGRNREVRRLIESQGLKVSRLLRTSYGSVDL 258


>gi|326564224|gb|EGE14460.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 12P80B1]
          Length = 328

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 88/214 (41%), Positives = 127/214 (59%), Gaps = 8/214 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R KAER
Sbjct: 24  EKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRLKAER 82

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + + SDP GR TVFD LP + + R + VGRLDIN+ GLLL TNDG
Sbjct: 83  EKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLFTNDG 142

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS+  +R Y VR  G+V     + L  G+ ++ G+   D  +      G N 
Sbjct: 143 ELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFD-DIKEGGGIGVNK 201

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           W  V ++EG+ RE++++FE    KV+RLIR  YG
Sbjct: 202 WYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYG 235


>gi|332359120|gb|EGJ36941.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK49]
          Length = 242

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 134/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+  P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEVEDQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDEKGRKTVVDLLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  +  G  R++SKK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTDIKPGEYRKLSKK 227


>gi|326575652|gb|EGE25575.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis CO72]
          Length = 328

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 88/214 (41%), Positives = 127/214 (59%), Gaps = 8/214 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R KAER
Sbjct: 24  EKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRLKAER 82

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + + SDP GR TVFD LP + + R + VGRLDIN+ GLLL TNDG
Sbjct: 83  EKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLFTNDG 142

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS+  +R Y VR  G+V     + L  G+ ++ G+   D  +      G N 
Sbjct: 143 ELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTTGVELEDGVAKFD-DIKEGGGIGVNK 201

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           W  V ++EG+ RE++++FE    KV+RLIR  YG
Sbjct: 202 WYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYG 235


>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 =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 88/214 (41%), Positives = 127/214 (59%), Gaps = 8/214 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R KAER
Sbjct: 24  EKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRLKAER 82

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + + SDP GR TVFD LP + + R + VGRLDIN+ GLLL TNDG
Sbjct: 83  EKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLFTNDG 142

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS+  +R Y VR  G+V     + L  G+ ++ G+   D  +      G N 
Sbjct: 143 ELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFD-DIKEGGGIGVNK 201

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           W  V ++EG+ RE++++FE    KV+RLIR  YG
Sbjct: 202 WYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYG 235


>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 =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 132/228 (57%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I +  V +NG ++   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKKGLVTINGKVVTELATTVKSGDVVEVEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDEKGRKTVVDLLPNVTERIYPVGRLDWDTTGLLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   V +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIVKVDPEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTQFGTLDLAGLRPGESRRLNKK 227


>gi|193782973|gb|ACF20459.1| pseudouridine synthase [Serratia symbiotica]
          Length = 300

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 91/221 (41%), Positives = 130/221 (58%), Gaps = 9/221 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+AR G  SRRE+E MI   RV +NG    L +R  ++ M    I+ + + ++KA
Sbjct: 3   EKLHKVLARTGYGSRREIEAMINACRVSINGKIAKLGDRIEIHPMMKIRIDGNIISIKKA 62

Query: 71  ERT--RLWLYHKPIGLVTT---HSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLL 124
           E T  R+  Y+KP G + T    S+P+GR TVFD+LP + + R +SVGRLDINT GLLL 
Sbjct: 63  EETICRVLAYYKPEGELCTISNPSNPEGRLTVFDHLPKLRNLRWVSVGRLDINTSGLLLF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T +G LA  L  PS +  R Y VR  G+   + +  LK  I ++        +T    KG
Sbjct: 123 TTNGELANRLMHPSRKIEREYAVRVFGKPSAENIKKLKHNIELEDGPAFFRTITFQGGKG 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            N W  V L EG+NRE+++++E    +V+RLIRI YG   L
Sbjct: 183 LNQWYHVTLTEGRNREVRRLWEAVGIQVSRLIRIRYGNIVL 223


>gi|269467788|gb|EEZ79546.1| 16S rRNA uridine-516 pseudouridylate synthase [uncultured SUP05
           cluster bacterium]
          Length = 241

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 85/218 (38%), Positives = 134/218 (61%), Gaps = 10/218 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVPL---- 67
           +R+ K+IA AG  SRR  ER+I Q RV+VN    + A++   +  TD +++DG  +    
Sbjct: 2   ERLQKLIATAGYGSRRWAERLIEQGRVEVNN---KTASIGDKADITDKVKIDGRTIDLSR 58

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E T++ + +K  G++ ++ D +GR + +D LP   SR + VGRLD+NT GLLL TN+
Sbjct: 59  YNEEETKVIILNKQAGVICSNKDKEGRKSAYDLLPK-ESRWVMVGRLDLNTSGLLLFTNN 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS++  R Y VR  G+V+ + L  L +GI ++       +VT+   +G+N 
Sbjct: 118 GDLANKLMHPSSEIEREYAVRVLGKVENEDLKQLTEGIDLEDGFAKFSRVTIGGGQGANR 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L+EGK RE+++++E   +KV+RLIRI +G  +L
Sbjct: 178 WYKVVLKEGKKREVRRLWEALGFKVSRLIRIRFGEIRL 215


>gi|320106004|ref|YP_004181594.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319924525|gb|ADV81600.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
          Length = 301

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 91/244 (37%), Positives = 133/244 (54%), Gaps = 28/244 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A AGIASRR+ E +I + RV+VNG ++ E         DHI VDG  L+  E  
Sbjct: 15  RLQKILADAGIASRRKSEEVILEGRVQVNGKVVTELGTRANPEKDHIRVDGKLLQGPEEH 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINTEGLLLLTND 127
           R +L +KP G VTT  DP+ R T+ D       +P +  R+  VGRLD N+EGLLL+TND
Sbjct: 75  RYYLVNKPRGYVTTMHDPEKRPTIVDLLIKDGKMPDV--RLYPVGRLDYNSEGLLLMTND 132

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G LA  L   S    + Y V+  GQ  +  ++ L++G++I+    G +Q T   ++    
Sbjct: 133 GELANALSKASNSVEKTYLVKVAGQPSEQAIDQLRRGVMIE---RGRLQETQGARRNRVM 189

Query: 184 -----------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                      G N W  V L EG+NR+++K+FE  +  V ++ RI YG   L  +  G 
Sbjct: 190 TAPAKVKLVRAGLNPWFEVSLTEGRNRQLRKMFEEIDHHVEKIRRIGYGALVL-DVAPGE 248

Query: 233 TREV 236
            RE+
Sbjct: 249 FREL 252


>gi|224004838|ref|XP_002296070.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209586102|gb|ACI64787.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 365

 Score =  141 bits (356), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 92/256 (35%), Positives = 141/256 (55%), Gaps = 16/256 (6%)

Query: 2   KDKNIVQENFTPQ----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MS 56
           K K+I   N +      R++ ++ +    SRR+ ERM+   RV + G +++  +     S
Sbjct: 63  KRKDITNTNLSNGTEGVRITTLLCKHLGLSRRQSERMVLLGRVTLFGKVVDSPSFEFSAS 122

Query: 57  TDH----IEVDGVPLRKAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----IFS 106
           TD     I+VDG  +  AE+T R+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 IQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++G     +Q T  D    +N W+ +   EGKNR+++++       V RLIRISYG + L
Sbjct: 243 VRGASGEVVQSTGKDVNGSTNTWLQITCTEGKNRQLRRILGSMGLDVTRLIRISYGDYDL 302

Query: 226 GTLLAGSTREVSKKIL 241
            ++  G   EV  K L
Sbjct: 303 NSIPPGLAIEVPVKPL 318


>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 =  141 bits (356), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 91/239 (38%), Positives = 132/239 (55%), Gaps = 8/239 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K++A+ G+ASRR  ERMIA+ RV VNG ++          D I VDG  +R+  +
Sbjct: 4   PIRLHKLLAQMGVASRRAAERMIAEGRVSVNGRIVNTPGAMASPEDEIRVDGKLVRQQPK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L +KP G+++T  D  GR TV D L    +RV  VGRLD ++EGL+LLTNDG LA+
Sbjct: 64  MRYILLNKPAGVLSTAKDERGRKTVIDLLGQ-SNRVYPVGRLDKDSEGLMLLTNDGELAQ 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYG-DMQVTLDTQKGSNAWVT 190
            +  P     + Y V   G      L  L +G+ ++ G     D ++   ++  S   +T
Sbjct: 123 RITHPRYGVHKQYMVEVEGYFSDRSLQDLLQGVELEDGFSKPLDAKIISRSRDKSKLLIT 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQLG 246
           +G  EG+ R++++      +KV RL R++ GP  LG L  G  RE+S    K LR QLG
Sbjct: 183 MG--EGRKRQVRRTLAALGYKVKRLTRVALGPLSLGNLKPGEYRELSDQEAKWLRSQLG 239


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 93/249 (37%), Positives = 136/249 (54%), Gaps = 14/249 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLR 68
           TPQR+ K++A+ G+ASRR+VE  I   R++VNG ++ E         D +EVDG  +P  
Sbjct: 3   TPQRLQKLLAQQGLASRRQVEAWILAGRIRVNGKVVTELGFKADPERDRVEVDGRVIPFG 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLT 125
              R  L L HKP+G+++T  DP GR TV D LP  ++R I    VGRLD ++ G LLLT
Sbjct: 63  DPARYVL-LLHKPLGVLSTCKDPWGRKTVLDLLPPPWNRQIRLYPVGRLDADSSGALLLT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---- 181
           NDG L   L  P     ++YRV+  G+  +  L   + G+ ++G      +V        
Sbjct: 122 NDGDLTLKLTHPRYHLPKIYRVQVQGRPSRATLQQWRDGVNLEGYTTLPAEVEFCPAPNF 181

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q  +++W+ V L EG+NR+I++V E     V RL R + GP  LG L AG  R +  
Sbjct: 182 GYRQDANSSWLRVVLFEGRNRQIRRVAEQLGHPVLRLHREAIGPLHLGNLKAGQFRLLEP 241

Query: 239 KILREQLGP 247
           + ++  L P
Sbjct: 242 QEVQALLAP 250


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 79/205 (38%), Positives = 121/205 (59%), Gaps = 2/205 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +ARAG+A+RR+ E++I   RVKVNG +++     V   D +EVDG  + K E+ 
Sbjct: 2   ERLQKYLARAGVAARRDAEQLILAGRVKVNGKVVKELGFKVSDRDVVEVDG-RIVKPEKL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP G +TT  DP GR TV   L   +  RV  VGRLD+NTEGLL+LTNDG LA 
Sbjct: 61  VYILMYKPAGYITTVDDPFGRPTVLSLLAGKVKERVFPVGRLDMNTEGLLILTNDGDLAM 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  Q  + Y     G  ++ KL  L++G++++       +V     +G N+W+ + 
Sbjct: 121 ALTHPKHQVPKTYLALVRGTPNRAKLKELERGVLLEDGYTAPAKVNFKKPEGKNSWIEIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIR 217
           + EG+ R+++++F+     V +LIR
Sbjct: 181 IHEGRKRQVRRMFKKIGHPVLKLIR 205


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/237 (34%), Positives = 132/237 (55%), Gaps = 6/237 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q+N    R+ KVI  +G ASRR  E+ I   R++VN  ++   A  V  +D + +D   L
Sbjct: 4   QKNEEAVRLVKVILESGFASRRNCEKAIMSGRIRVNNEVILDPAYRVKESDSVSIDR-KL 62

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + +R R    +KP+G+V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 63  IERQRKRYMALYKPLGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 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-----GTLLAGSTREVSKK 239
            + + + EGKNREI+K+F++  +KV  L RIS G         GTL AG  R+++KK
Sbjct: 183 KIRLTINEGKNREIRKIFDYLGYKVIDLERISVGCVSKYDETSGTLEAGHIRDLTKK 239


>gi|227498494|ref|ZP_03928640.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226903952|gb|EEH89870.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 246

 Score =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 132/230 (57%), Gaps = 11/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A +G+ASRRE E++I Q RV VNG  +      V  TD I +DG PLRK ER 
Sbjct: 7   ERLQKMMAASGVASRRECEKIILQGRVTVNGKPVIELGTKVSPTDRILIDGRPLRK-ERH 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L +KP  ++TT  DP GR TV + +     RV  VGRLD  TEGLL++TNDG LA+ 
Sbjct: 66  RYFLLNKPPAVMTTMKDPRGRRTVAELMDKERERVYPVGRLDFMTEGLLIMTNDGALAQG 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------DTQKGSNA 187
           +  PS    + Y V   G V+++KL+ L+ GI    +C G     L      D+++  + 
Sbjct: 126 MTHPSYHINKTYEVVVDGHVEEEKLDKLRTGI---RLCDGMTAPALVEVKRYDSRRDQSI 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  V + EG+NR+++++ E   + V +L R       L  +  G+ RE++
Sbjct: 183 F-EVTIHEGRNRQVRRMCEAIGYPVRKLKRTQVAFLSLQGVKKGAYRELT 231


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 92/229 (40%), Positives = 131/229 (57%), Gaps = 5/229 (2%)

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 KP G+V+T  D  GR TV D +P    RV  VGRLD NT GLLLLTNDG  + +
Sbjct: 62  YYMLY-KPTGVVSTVEDDKGRKTVVDLVPP-GHRVFPVGRLDYNTSGLLLLTNDGEFSNL 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL-DTQKGSN-AWVT 190
           L  P  +  + Y V+  G  D   +  L+KG+V+  G   G  +V + D  K  N A + 
Sbjct: 120 LLHPKYKVPKRYIVKIKGVPDYYHVKGLEKGVVLPDGFKTGKARVEMRDIDKKKNTAILE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EG NR+++++ E    +V +L R  +G   L  L +G  RE+SKK
Sbjct: 180 MVIYEGHNRQVRQMVETLGAEVIKLKREQFGFLTLAGLTSGDWRELSKK 228


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 130/228 (57%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V + D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATQVKAGDLVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      + T+   D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYTIIKVDHEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKK 227


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 129/227 (56%), Gaps = 9/227 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           ++D  +  E   P R+ K +A +G+ SRRE+E  I    + VNG   ++A +   V   D
Sbjct: 235 LRDTRVDMEQIEPVRLQKALAASGVGSRREMEEWIEAGLILVNG---KKATLGDRVGPQD 291

Query: 59  HIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
            +   G P+R        R+ LYHK  G + T  DP+GR T+FD LP    SR ++VGRL
Sbjct: 292 RVTAKGNPIRLKWPDRLPRVILYHKQEGELVTRDDPEGRVTIFDRLPQAKSSRWVAVGRL 351

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NT GLL++T  G LA  L  PS +  R Y VR  GQ++ +++  + +GI ++      
Sbjct: 352 DVNTSGLLIVTTSGELANRLMHPSFEAEREYAVRVLGQLEPEQMKEMTRGIELEDGPAHF 411

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            ++     +G N W  V ++EG+NRE++++FE F   V+RLIR+ +G
Sbjct: 412 QRIVEQGGEGVNHWYRVVIKEGRNREVRRIFEHFGLTVSRLIRVRFG 458


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + A V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRAVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/213 (39%), Positives = 122/213 (57%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V   D + V+G P+ +   
Sbjct: 111 KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAPNDQVRVNGKPIMRVNT 167

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 168 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 227

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +A  +  P     R Y VR  G++D+ +   L  GI ++        +      GSN W
Sbjct: 228 DMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGLAAFGALDYLGGDGSNRW 287

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 288 YRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 320


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 89/219 (40%), Positives = 128/219 (58%), Gaps = 10/219 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR-KA 70
           +++ KV+ARAG  SRRE+E  IA  R+ ++G   E A++   + +   I +DG  +  K+
Sbjct: 3   EKLQKVLARAGHGSRREMEAWIAAGRISIDG---EIASLGDRIEADAKIRIDGRAISIKS 59

Query: 71  ER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
           E     R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T+
Sbjct: 60  EEDIVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G V    +  L+ G+ ++       +V     +G N
Sbjct: 120 DGELANRLMHPSNEVEREYAVRTFGDVSDACIQHLRTGVTLEDGPANFDKVKAAGGEGMN 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L
Sbjct: 180 KWWHVTLSEGRNREVRRLWESQEVQVSRLIRIRYGSIEL 218


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 131/231 (56%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++A+AGIASRR+ E++I + R+++NG ++    +    + D I  DG PL   E+
Sbjct: 3   ERLQKILAKAGIASRRKAEQLILEGRIRINGHVVTGMGSKADPNRDTITCDGHPLVFEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L +KP G VTT SDP GR  V D L  I  R+  VGRLD++TEG LL+TNDG L  
Sbjct: 63  IYVLL-NKPAGYVTTLSDPQGRPMVSDLLADIPLRLFPVGRLDLDTEGALLMTNDGELGN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G    DKL  L+ GI I G+      V L  +      V + 
Sbjct: 122 AILHPRYEVNKTYEAEVSGSPSVDKLKRLESGIEIDGVMTRPAVVRLLRRHKGTTLVEIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EGK R+++K+F+  N +V  L R +YG  +LG+L  G  R +++  L++
Sbjct: 182 IHEGKKRQVRKMFQAINHRVLHLRRTAYGNLRLGSLPLGKYRVLNQNDLKK 232


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/218 (37%), Positives = 127/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E  + + R+ V+G I      + V     I +DG  + +++ 
Sbjct: 17  EKLQKILARSGHGSRREIETFLKEGRISVDGKIATLGDRIEVKPATKIRLDGRILAIKEP 76

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E+   R+  Y+KP G + T  DP+GR TVF  LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 77  EKEICRVMAYYKPEGELCTRHDPEGRPTVFTRLPKLVGARWIAVGRLDVNTSGLLLFTTD 136

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G++   K+  L +G+ ++        V+    +G N 
Sbjct: 137 GELANRLMHPSREVEREYAVRVFGEITDAKIRQLTQGVQLEDGPAAFKTVSFRGGEGMNQ 196

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 197 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDL 234


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 91/241 (37%), Positives = 140/241 (58%), Gaps = 7/241 (2%)

Query: 5   NIVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIE 61
           N  Q+   P+  R+ KV+A AG+ASRR  E MI   RV+V+G ++    + V + T  I 
Sbjct: 95  NAGQDMHDPEGVRLQKVMAAAGVASRRVCEEMIEDGRVEVDGSIVTELGLRVNVETAVIS 154

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTE 119
           VDG+ L+  E     +++KP G+V+T  DP+GR  + D L + ++  R+  VGRLD  TE
Sbjct: 155 VDGIRLQLKENMIYLVFNKPRGVVSTMDDPEGRRNISDFLKNKYAHERLFHVGRLDQATE 214

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVT 178
           GLLLLTNDG LA  L  PS +  + Y V+  G ++    N ++KGI ++ G+   D    
Sbjct: 215 GLLLLTNDGELANRLTHPSYEVPKTYLVQTKGPMETGVSNQMRKGIELEDGVTKIDAFKL 274

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +D+  G +  V V L  GKNR ++++F+   + V RL+R+  GP +LG    GS R + +
Sbjct: 275 VDSTPG-HVLVEVVLHSGKNRIVRRLFDAVGYPVERLVRLQVGPIRLGDQKQGSIRALGQ 333

Query: 239 K 239
           +
Sbjct: 334 Q 334


>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 =  141 bits (355), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 80/234 (34%), Positives = 138/234 (58%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V S+D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVKSSDTVEVEGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR+ V D   ++ +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRTVVTDYFKNLEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIQKKYVAKLKGYLMREEVKALEQGIELEDGFTQPAQVKIKNQNKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
            + EG+NR+++++FE FN  V++LIRI +G   L  L AG  R ++    KILR
Sbjct: 185 TISEGRNRQVRRMFEHFNHTVDKLIRIEFGNLNLKGLNAGEGRVLTPHEVKILR 238


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 128/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 10  RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 69  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  ++V  D    S + V
Sbjct: 129 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADK---SRSIV 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 186 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 235


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 141/246 (57%), Gaps = 11/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +V+VNG  +      V  +D + V+G+PL + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLIEEGKVQVNGKTVTELGTKVRPSDEVTVEGIPLEQEDKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFYKPAQVITSVSDDRGRKVVTDYFDDLVTRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y  +  G + ++++  L+KGI ++ G+     ++V    ++ + + V +
Sbjct: 125 MTHPRYKIPKTYVAKIEGYILREQVKQLEKGIQLEDGLTQPAKVKVKKQNKEKNTSLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLGPH 248
            + EG+NR+++++FE F + V +L R+S+GP  L  L AG  R +S    K LR     H
Sbjct: 185 TITEGRNRQVRRMFEHFGFSVQKLSRVSFGPLTLKGLGAGEGRVLSPHEVKSLR-----H 239

Query: 249 LLEEAQ 254
           L E  Q
Sbjct: 240 LAENGQ 245


>gi|206601589|gb|EDZ38072.1| Pseudouridine synthase, Rsu [Leptospirillum sp. Group II '5-way
           CG']
          Length = 583

 Score =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/225 (37%), Positives = 133/225 (59%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++A  G+ASRR  E MI    VKVNGI++      V   TD + VDG  +      
Sbjct: 19  RLQKLLAHRGLASRRNAEEMIRGGLVKVNGIVVTVPGTKVHPETDRVTVDGKNVPVEPEP 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L+L++KP G+V+T  DPDG++T+ D  P I + +I VGRLDI +EG+LLLTN+G LA+ 
Sbjct: 79  FLFLFYKPKGVVSTLHDPDGKTTLKDFFPRI-NPLIHVGRLDIQSEGVLLLTNNGDLAQR 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTVG 192
           +  P  +  R Y V+  G V  + L+ L+ G V + G     +++  +    +N+W  + 
Sbjct: 138 ILHPRYEIPRTYLVKVQGVVTPEHLDRLRSGKVRLDGRPVQPLELEQERLTETNSWYRIT 197

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+NRE++++F+  ++ V +L RI++G   L  L  G  R V+
Sbjct: 198 LTEGRNREVRRLFDALHYFVLKLTRIAFGNLDLTGLEPGEYRLVT 242


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/220 (38%), Positives = 125/220 (56%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLR-- 68
           +++ K +AR G+ SRR++E +I   RV VN     + +R    V   D I VDG  ++  
Sbjct: 4   EKLQKALARMGLGSRRQMEEVIKAGRVTVNNGPATIGDR----VEQGDEIRVDGRQIKYT 59

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
               +R R+  Y+KP G V + +DP+GR TVF+ LP +   R + VGRLDIN+ GLLL T
Sbjct: 60  AENEKRRRVLAYYKPEGEVCSANDPEGRPTVFERLPKLTHDRWVMVGRLDINSTGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +A  L  PS++  R Y VR  G V  D    +  G++++        +     +G 
Sbjct: 120 NDGEMAHRLMHPSSEVTREYAVRVLGDVTPDMARAMTTGVMLEDGMAKFEDIKEGGGEGV 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L+EG+NRE++++FE    KV+RL+R SYG   L
Sbjct: 180 NKWHHVKLKEGRNREVRRLFESQGLKVSRLLRTSYGNIAL 219


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 32  RINKYIAHAGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVEGQPIYNEEKV- 90

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP +  R+  VGRLD +T G L+LTNDG     +
Sbjct: 91  YYLLNKPRGVISSVTDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGALILTNDGDFTDEM 150

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+VI+G       Y  ++V  D  K + + V
Sbjct: 151 IHPRNEIDKVYVARVKGVANKEVLRPLTRGLVIEGKKTKPAVYEILKV--DPVK-NRSVV 207

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R +SKK
Sbjct: 208 QLTIHEGRNHQVKKMFEAVGLPVDKLSRTQFGHLDLTGLKPGEARRLSKK 257


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 81/221 (36%), Positives = 132/221 (59%), Gaps = 6/221 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPL 67
           +F P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L
Sbjct: 94  HFEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKL 152

Query: 68  RKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
           + A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT
Sbjct: 153 KWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILT 212

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKG 184
             G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G
Sbjct: 213 TSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRMLTEEGVMLEDGLAKVERIYEQGGEG 272

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 ANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 313


>gi|332358327|gb|EGJ36153.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK355]
          Length = 242

 Score =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVRELATNVKSGDRVEIEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R+++KK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLNKK 227


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 87/231 (37%), Positives = 127/231 (54%), Gaps = 2/231 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + +++++ GIASR + +  I   RV++N  L+      +    D + +D  P+ +    +
Sbjct: 3   LDRLLSKLGIASRSQAQEWIRAGRVRINRRLVRMPDTWIDWPGDAVTLDDRPIEQRP-PQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L+HKP G+VTTH D  GR T+FD LP     + +VGRLD  T GLLLLTND  L+  L
Sbjct: 62  FILFHKPKGVVTTHQDEKGRPTIFDVLPPELKGLHAVGRLDQATSGLLLLTNDSTLSSFL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  Q  R+Y V   G+V ++       G+  QG       VT+  + G  + + V L 
Sbjct: 122 TDPKQQVPRLYLVTVRGEVSEETGRAALDGVDDQGERLHCASVTIQKRSGRESHLVVTLT 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGKNREI+++F+    +V RL RI YGPF LG L  G+ RE+  +  R QL
Sbjct: 182 EGKNREIRRLFKALGHEVTRLRRIQYGPFILGDLQPGAWRELPIEAARAQL 232


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 128/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  ++V  D    S + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADK---SRSIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 227


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 125/227 (55%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I   RV+VNG ++      V   D +EVD VP+ K E  
Sbjct: 2   ERLQKVIAHAGVASRRDAEKLILAGRVRVNGQVVTELGTKVTKKDLVEVDQVPIYKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ +D  GR  V D    I  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 62  -YYLFNKPDGVISSVADDKGRKVVVDYFKEIPQRIYPIGRLDYHTTGVLLLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G    D L  L++G+VI G      +  +   K +  NA V +
Sbjct: 121 LMHPRYEIDKVYVAKVKGYPSPDALKRLEEGLVIDGQKTAKARARIRKNKAAKENATVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++K+ E     V RL R  YG      L  G  R + K
Sbjct: 181 TIHEGRNRQVRKMLEAVGHPVKRLNRERYGFLTTEGLGVGEYRPLLK 227


>gi|23099278|ref|NP_692744.1| ribosomal large subunit pseudouridylate synthase [Oceanobacillus
           iheyensis HTE831]
 gi|22777507|dbj|BAC13779.1| ribosomal large subunit pseudouridylate synthase [Oceanobacillus
           iheyensis HTE831]
          Length = 244

 Score =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 87/229 (37%), Positives = 131/229 (57%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA++G+ SRR+ E+MI   +VKVNG  ++   V V + D I VDGVPL K E  
Sbjct: 6   ERLQKVIAQSGVTSRRKAEQMILDGKVKVNGETVQEMGVKVTANDEIVVDGVPLEK-ETP 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR  V D   ++  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 65  VYFLLYKPRGVISSVKDDKGRKVVTDYFEAVEQRIFPIGRLDYDTSGVLLLTNDGDFANL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVT 190
           L  P  +  +VY  +  G  ++ +L LL+KGI         +QV L   D QK   + + 
Sbjct: 125 LMHPRHEIDKVYIAKVRGIPNKKELALLQKGIRSDKDVLKAVQVKLLSTDHQK-KTSIIE 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + L EGKNR+++++ E   + V +L R  Y    L  L AG  R ++ K
Sbjct: 184 LTLHEGKNRQVRRMLEELGYPVMKLKRERYDFIGLEGLNAGEYRSLTPK 232


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 133/234 (56%), Gaps = 6/234 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR 68
           N   +R+ K++A AG+ASRR+ E +I   +V+VNG  +         S D I V+G P+ 
Sbjct: 6   NANMERLQKILAAAGVASRRKCEELILSGKVQVNGETVTTLGTKADPSVDVITVEGKPI- 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            AE+    +++KP G++T+ SDP GR  V D L  I  RV  VGRLD +TEGLLLLTNDG
Sbjct: 65  GAEKKLYLMFNKPKGVITSASDPQGRKIVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGS 185
             A +L  P     + Y     G      L+ LK+G++++       +V    +D ++  
Sbjct: 125 EFAHLLTHPKHHVPKTYLATVKGVPHGTALDKLKQGVMLEDGMTAPAEVEYYDIDPEE-K 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            A +++ + EG+NR+++++F+  +  V RL RIS+G   LG L  G  R ++K+
Sbjct: 184 YATISITIHEGRNRQVRRMFDAISHPVTRLKRISFGDLVLGNLKRGLYRHLTKE 237


>gi|309378850|emb|CBX22555.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 349

 Score =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 81/221 (36%), Positives = 132/221 (59%), Gaps = 6/221 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPL 67
           +F P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L
Sbjct: 93  HFEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKL 151

Query: 68  RKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
           + A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT
Sbjct: 152 KWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILT 211

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKG 184
             G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G
Sbjct: 212 TSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEG 271

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 272 ANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  140 bits (354), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 84/213 (39%), Positives = 121/213 (56%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   +   D ++V+G P+R    
Sbjct: 97  KLHKVLAQAGLGSRLEMEQLILEGRISVN---AEPAHIGQRIQFGDTVKVNGKPIRVQID 153

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G V TH DP  R TVF  LP +F  +  SVGRLD+NTEGLLLLT+ G
Sbjct: 154 PPPPRVIAYHKPAGEVVTHDDPQNRPTVFRRLPKLFQGKWQSVGRLDLNTEGLLLLTSSG 213

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G ++ ++   L  G+ +         +     +G+N W
Sbjct: 214 ELANKLMHPRFGLEREYAVRVLGALNNEEKKRLLDGVTLDDGVAQFGSIEAGGGEGANCW 273

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V + EG+NRE++++FE     V+RLIRI YG
Sbjct: 274 YRVTISEGRNREVRRMFEAVGHAVSRLIRIRYG 306


>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 =  140 bits (354), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 81/233 (34%), Positives = 131/233 (56%), Gaps = 3/233 (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 E    +L++KP G++++  D  GR TV D    +  R+  VGRLD +T GLLL+TN
Sbjct: 61  IEK-ETLHTYLFYKPRGVISSVKDDKGRKTVVDYFEDVPYRLYPVGRLDYDTSGLLLMTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKG 184
           DG LA  L  P  +  +VY  +  G +  + ++ L  G+ I G       +++    +K 
Sbjct: 120 DGELANKLMHPRNEVPKVYVAKIKGLLSPEDIHSLTHGVRIDGRKSAPAKLKILKTDEKK 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   V + + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 180 NTQIVQLTIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELT 232


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 81/221 (36%), Positives = 132/221 (59%), Gaps = 6/221 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPL 67
           +F P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L
Sbjct: 94  HFEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKL 152

Query: 68  RKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
           + A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT
Sbjct: 153 KWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILT 212

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKG 184
             G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G
Sbjct: 213 TSGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEG 272

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 ANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 313


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 123/228 (53%), Gaps = 3/228 (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 KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLY-KPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G        Q+     K +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLAKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKK 228


>gi|296133130|ref|YP_003640377.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296031708|gb|ADG82476.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/225 (36%), Positives = 129/225 (57%), Gaps = 1/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K +A AG+ASRR+ E +IA  +VKVNG ++      V  S D +EV G+ +   E+
Sbjct: 4   QRLQKFMAHAGVASRRKCEELIAAGKVKVNGKVVTEMGYTVDPSVDRVEVAGLGIIVHEK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G++++ SD  GR TV D + +  +R+  VGRLD +TEGL+LLTNDG L  
Sbjct: 64  KEYILLYKPAGVLSSASDDRGRKTVVDLIKNAKTRLYPVGRLDYDTEGLILLTNDGRLTN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  +  + YR    G   +DKL  L+ GI+++       +V +  Q   N  V + 
Sbjct: 124 LLIHPRYKVDKTYRAVVQGIPGEDKLAALRNGIMLEDGPTYPARVKMLKQINGNGLVEIT 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+NR+++++F+     V +L R  +G  +LG L  G  R +S
Sbjct: 184 IHEGRNRQVRRMFDAIGHPVLKLKRTRFGFLELGNLQPGQYRALS 228


>gi|327462027|gb|EGF08356.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 135/230 (58%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q +V +NG ++   A NV S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIRQGKVSINGQVVCELATNVKSGDRVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV + LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVELLPQVKERIYPVGRLDWDTSGILILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +GI I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKV--DPAK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G  R+++KK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLNKK 227


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/213 (39%), Positives = 122/213 (57%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V   D + V+G P+ +   
Sbjct: 116 KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAPNDQVRVNGKPIMRTNT 172

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 173 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 232

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +A  +  P     R Y VR  G++D+ +   L  GI ++        +      GSN W
Sbjct: 233 DMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGVAAFGALDYLGGDGSNRW 292

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 293 YRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 325


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 129/218 (59%), Gaps = 11/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL-RKAE 71
           ++ KV+A AG+ SRR++E +I   RV VNG   E A +   ++ TD + ++G  L RK  
Sbjct: 170 KLHKVLADAGLGSRRDMEELIIAGRVSVNG---EPAHIGQRILPTDQVRINGKLLQRKVT 226

Query: 72  RT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           ++  ++ LYHKP G + +  DP+ R++VFDNLPS+  S+ ++VGRLD NTEGLLL TN+G
Sbjct: 227 KSLPKVMLYHKPAGEIVSRDDPEKRASVFDNLPSLKNSKWLAVGRLDFNTEGLLLFTNNG 286

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNA 187
            LA  L  P     R Y VR  G++++     L  G+ + G   G      D   +G N 
Sbjct: 287 DLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVDL-GDGIGQFSSIADGGGEGINK 345

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V + EG+NRE++++FE     V+RLIR  YG   L
Sbjct: 346 WYRVTIGEGRNREVRRMFESVGLTVSRLIRTRYGVITL 383


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

 Score =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 121/228 (53%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA AG+ASRR  E MI Q RV VN  +++     V + D + VDG P++  E   
Sbjct: 5   RLQKFIAHAGVASRRTAEEMIKQGRVAVNNTVVQDMGFTVSNDDFVTVDGKPVKIEEEKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP+G V+T  D  GR TV D +     R+  VGRLD +T GL+LLTNDG     L
Sbjct: 65  YIMLHKPVGYVSTSQDQFGRPTVVDLVKDAGKRLYPVGRLDYDTSGLILLTNDGDFTYRL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VY     G  +++++   + G+ I+       +  +  ++G N  V + + 
Sbjct: 125 THPKHEINKVYEAVISGFPEKNEIKSFESGLKIENYQTSPAEFVVLEKQGINTLVRITIH 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNR+++K+ E    KV  L RI  GP  L  L  G  R +S + L+
Sbjct: 185 EGKNRQVRKMCEAIGHKVLTLKRIQIGPIALDNLPVGKWRHLSLRELK 232


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/220 (38%), Positives = 125/220 (56%), Gaps = 12/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLR-- 68
           +++ K +AR G+ SRR++E +I   RV VN     + +R    V   D I VDG  ++  
Sbjct: 4   EKLQKALARMGLGSRRQMEEVIKAGRVTVNNGPATIGDR----VEQGDEIRVDGRQIKYT 59

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
               +R R+  Y+KP G V + +DP+GR TVF+ LP +   R + VGRLDIN+ GLLL T
Sbjct: 60  SENEKRRRVLAYYKPEGEVCSANDPEGRPTVFERLPKLTHDRWVMVGRLDINSTGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +A  L  PS++  R Y VR  G V  D    +  G++++        +     +G 
Sbjct: 120 NDGEMAHRLMHPSSEVTREYAVRVLGDVTPDMARAMTTGVMLEDGMAKFEDIKEGGGEGV 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L+EG+NRE++++FE    KV+RL+R SYG   L
Sbjct: 180 NKWHHVQLKEGRNREVRRLFESQGLKVSRLLRTSYGNITL 219


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 128/228 (56%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG+++           D I V G P+ K E+
Sbjct: 2   ERLQKILAQAGVASRRKCEELIQAGSVEVNGVIVTELGTKADPDQDMITVKGRPI-KTEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP+GR  V D L  +  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 61  KIYLMMNKPKGVITSASDPEGRKIVSDYLKGVKERVYPVGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  P     + Y     G     +L+ LKKGIV++       +V        G  + + 
Sbjct: 121 LLTHPKHHVPKTYVATVKGVPHGTELDKLKKGIVLEDGITAPAEVEYKDVDPNGKESVIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + + EG+NR+++++FE  +  V RL RI++G   L  L  G TR ++K
Sbjct: 181 ITIYEGRNRQVRRMFEAISHPVIRLKRIAFGDLLLQNLKRGLTRPLTK 228


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 123/228 (53%), Gaps = 3/228 (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 KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLY-KPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G        Q+     K +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLAKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKK 228


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/217 (39%), Positives = 122/217 (56%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   V   D I+V+G P+R    
Sbjct: 132 KLHKVLAQAGMGSRLEMEQLILEGRISVNN---EPAHIGQRVQFGDQIKVNGKPIRFRVA 188

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
              TR+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL T+ G
Sbjct: 189 PPPTRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTEGLLLFTSSG 248

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +  ++   L  G+ ++        +     +G+N W
Sbjct: 249 ELANKLMHPRFGLEREYAVRVLGALSDEERQRLLDGVSLEDGMAAFGSIEDGGGEGANCW 308

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE++++FE     V+RLIRI YG   L
Sbjct: 309 YRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMML 345


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/218 (38%), Positives = 128/218 (58%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG--VPLRKA 70
           +++ K++AR+G  SRRE+E  +   R+ V+G I      V V     I +DG  + +++ 
Sbjct: 43  EKLQKILARSGHGSRREIETFLQAGRISVDGKIATLGDRVEVTPATKIRLDGRLLAIKEP 102

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E+   R+  Y+KP G + T  DP+GR TVF+ LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 103 EKEICRVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTTD 162

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G+++  K+  L +G+ ++        V+    +G N 
Sbjct: 163 GELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSYRGGEGMNQ 222

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 223 WFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDL 260


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 84/213 (39%), Positives = 121/213 (56%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   +   D ++V+G P+R    
Sbjct: 98  KLHKVLAQAGLGSRLEMEQLILEGRISVNA---EPAHIGQRIQFGDTVKVNGKPIRVRID 154

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G V TH DP  R TVF  LP +F  +  SVGRLD+NTEGLLLLT+ G
Sbjct: 155 PPPPRVIAYHKPSGEVVTHDDPQNRPTVFRRLPKLFQGKWQSVGRLDLNTEGLLLLTSSG 214

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +  ++   L +G+ +         +     +G+N W
Sbjct: 215 ELANKLMHPRFGLEREYAVRVLGALSNEEKKRLLEGVTLDDGVAQFSSIEAGGGEGANCW 274

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V + EG+NRE++++FE     V+RLIRI YG
Sbjct: 275 YRVTISEGRNREVRRMFEAVGHAVSRLIRIRYG 307


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 130/228 (57%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V + D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATKVKAGDLVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   + +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARIKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKK 227


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 130/228 (57%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V + D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGMVTINGQVVNELATKVKAGDLVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   + +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKK 227


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 123/228 (53%), Gaps = 3/228 (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 KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLY-KPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G        Q+     K +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLAKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKK 228


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 128/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVNLKGLRPGEARRLNKK 227


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 127/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 10  RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 69  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  + V  D  +   + V
Sbjct: 129 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVHVEADKNR---SIV 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 186 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 235


>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 =  140 bits (353), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 128/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 10  RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 69  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  ++V  D  +   + V
Sbjct: 129 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNR---SIV 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 186 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 235


>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 =  140 bits (352), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 80/234 (34%), Positives = 137/234 (58%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V S+D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVKSSDTVEVEGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRTVVTDYFKDLEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIQKKYVAKLKGYLMREEVKSLEQGIELEDGFTQPAQVKIKNQNKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
            + EG+NR+++++FE FN  V++LIRI +G   L  L AG  R ++    KILR
Sbjct: 185 TISEGRNRQVRRMFEHFNHTVDKLIRIEFGNLNLKGLNAGEGRVLTPHEVKILR 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 =  140 bits (352), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 90/237 (37%), Positives = 137/237 (57%), Gaps = 10/237 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K+IA+AGI SRR+ E++I + RV VNG  ++       + TD I VDGVPL+K E 
Sbjct: 2   ERLQKLIAQAGITSRRKAEKLIEEGRVYVNGNQVKEVGAKADLQTDEISVDGVPLQKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++++  D  GR TV D +P  F RV  VGRLD +T GL++LTNDG  A 
Sbjct: 62  V-YYLLYKPSGVISSAGDDKGRKTVIDLVPGEF-RVFPVGRLDFDTSGLIVLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWV 189
           +L  P  +  + Y  +  G   ++ L  L +GIV++       +   +  D +KG+ A V
Sbjct: 120 LLMHPKYRIHKTYIAKVKGLPLREDLKKLDRGIVLEDGKTAPAKTKVIKTDKRKGT-AVV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILRE 243
            + + EG+NR+++++F+   + V +L R  YG   L  L AG  RE+     K LRE
Sbjct: 179 EITIHEGRNRQVRRMFDAIGFPVMKLKRERYGILDLKGLNAGDWRELKPHEVKTLRE 235


>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 =  140 bits (352), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 80/227 (35%), Positives = 127/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 20  RINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAVYNEEPV- 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 79  YYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             PS    +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 139 THPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 198

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 199 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 245


>gi|220912302|ref|YP_002487611.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859180|gb|ACL39522.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
          Length = 403

 Score =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 89/230 (38%), Positives = 131/230 (56%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E MIA+ RV+V+G ++    V +  +T  I VDG+ ++  E  
Sbjct: 164 RLQKVMASAGVASRRVCEEMIAEGRVEVDGQVVTELGVRIDPATAVIHVDGLRIQLDENL 223

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +++KP G+V+T  DPDGR  + D   N  +   R+  VGRLD+ TEGLLLLTNDG L
Sbjct: 224 VYMVFNKPKGVVSTMEDPDGRPCISDFLKNNKNTGERLFHVGRLDVATEGLLLLTNDGEL 283

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y V+  G   Q     LK G+ ++ G    D    +D+  G +  +
Sbjct: 284 ANRLTHPSYEVPKTYLVQVRGPFPQGIGAQLKAGVELEDGPAAVDSFRLVDSTPG-HVLI 342

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+
Sbjct: 343 EVVLHSGKNRIVRRMFDAVGFPVQRLVRVKVGPIGLGDQRQGSIRNLGKQ 392


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 132/234 (56%), Gaps = 3/234 (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 E    +L++KP G++++  D  GR TV D    +  R+  VGRLD +T GLLL+T
Sbjct: 61  PIEK-ETLHTYLFYKPRGVISSVKDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQK 183
           NDG LA  L  P  +  +VY  +  G +  + +  L  G+ I G       +++    +K
Sbjct: 120 NDGELANKLMHPRNEVPKVYVAKIKGLLSPEDIRSLTHGVRIDGRKSAPAKLKILKTDEK 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +   V + + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 180 KNTQIVQLTIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELT 233


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 128/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 227


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 94/242 (38%), Positives = 132/242 (54%), Gaps = 18/242 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AGIASRR  E+MIA  RV V+G ++    V V  +T  I VDG  L   E  
Sbjct: 12  RLQKVLAQAGIASRRASEQMIADGRVSVDGTVVRTQGVRVDPATQVIHVDGERLILDEAK 71

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L  +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI---VIQGICYGDMQVTLDTQK-----G 184
            L  PS +  + Y  R HG+V        K G+   ++ GI   D  + +D+ +     G
Sbjct: 132 RLTHPSYEIRKTYVARLHGEV--------KPGVRRRLLAGIELEDGPIAVDSFRLVDTYG 183

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V + + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR +    L   
Sbjct: 184 DITTVEIVVHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRIKGNALTAL 243

Query: 245 LG 246
            G
Sbjct: 244 YG 245


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 75/223 (33%), Positives = 130/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRKVVTDYFEDIETRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQPAQVKIKRQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEYFGHEVNKLTRIQFGPLDLKGLNAGEGR 227


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 77/215 (35%), Positives = 125/215 (58%), Gaps = 1/215 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+IA  G+ASRR+ E +I   RV +NG +++     V  + DH++VDG  LR A+  
Sbjct: 4   RLQKLIAGTGLASRRKAEELITSGRVTINGSVVKELGTKVDPARDHVKVDGKHLRAAQPY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP  +++T  DP+GR TV D L  +  RV  VGRLD ++EGL+LLTN G LA+ 
Sbjct: 64  VYLILNKPKNVMSTLDDPEGRPTVKDLLHGVTVRVFPVGRLDFDSEGLMLLTNHGDLAQA 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y ++  G +D  K+  L++G+ ++       +V   ++  SN+W+ V +
Sbjct: 124 LLHPRYHVPKTYLIKVKGVLDDAKIEALERGVKLEDGFTAPAKVKKVSRAESNSWLEVTI 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            EG+  ++K++ E     V +L+R+  GP  LG L
Sbjct: 184 HEGRKHQVKRMVEAVGHSVIKLVRVRMGPLLLGDL 218


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 123/228 (53%), Gaps = 3/228 (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 KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 62  YYLLY-KPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G   +  L  L KGI I+G        Q+     K +++ V +
Sbjct: 121 LTHPKHEVDKVYVAKVKGIATKSMLAPLTKGIKIEGRKTSPAKFQILSVDPKTNHSIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKK 228


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 90/217 (41%), Positives = 123/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAER 72
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG V   KA+ 
Sbjct: 3   EKLQKVLARAGHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAKAQE 62

Query: 73  ---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYL 219


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 87/220 (39%), Positives = 130/220 (59%), Gaps = 12/220 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLRK 69
             R+ K+IA AG  SRR VER+I Q R++VN    I+ ++  +    T  +++DG  +  
Sbjct: 2   ANRLQKLIANAGYGSRRWVERLIEQGRIEVNNKIAIIGDKTEI----TSLVKIDGRKINL 57

Query: 70  A----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +    + T++ + +K  G++ ++ D  GR +V+  LP   SR I VGRLD+NT GLLL+T
Sbjct: 58  SRYVEQETKVIILNKQAGVICSNRDDKGRKSVYSLLPK-ESRWIMVGRLDLNTSGLLLVT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  PS++  R Y VR  GQV    L  L +G+V         Q+T    KG+
Sbjct: 117 NNGDLANKLMHPSSEIDREYAVRVLGQVKNKDLKKLTQGVVFDDGFSKFNQITFSGGKGA 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V LREGK RE+++++E   +KV+RLIRI +G  +L
Sbjct: 177 NRWYKVVLREGKKREVRRLWEVLGFKVSRLIRIRFGEIRL 216


>gi|300070794|gb|ADJ60194.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 239

 Score =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 80/227 (35%), Positives = 127/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 2   RINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAVYNEEPV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 61  YYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             PS    +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 121 THPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 181 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 227


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 85/216 (39%), Positives = 126/216 (58%), Gaps = 12/216 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+AR G+ SRR +E +IA  RV +NG + +     +   D + +DG   RK +  
Sbjct: 3   EKLQKVLARVGLGSRRYMEEVIAAGRVSINGRIAQ-VGERIEPGDELRIDG---RKVQFQ 58

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
                R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL T
Sbjct: 59  VEDEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  R Y VR  G+V     N + KG+ ++         +     G 
Sbjct: 119 NDGELANRLMHPSNEVEREYAVRVMGEVTPQIRNNMLKGVELEDGPAKFESFSEIGGDGI 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           N W  V ++EG+NRE++++FE  N KV+RL+R  YG
Sbjct: 179 NRWYQVVVKEGRNREVRRIFESQNLKVSRLLRTRYG 214


>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 =  140 bits (352), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLHPGESRRLNKK 227


>gi|163857448|ref|YP_001631746.1| pseudouridine synthase [Bordetella petrii DSM 12804]
 gi|163261176|emb|CAP43478.1| pseudouridine synthase [Bordetella petrii]
          Length = 588

 Score =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 86/218 (39%), Positives = 123/218 (56%), Gaps = 19/218 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V  +D + V+G P+ +   
Sbjct: 124 KLHKVLADAGIGSRREMEELITAGRVSVNG---EPAHIGQRVAPSDQVRVNGKPVARPNT 180

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP GR++VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 181 KKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 240

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QK 183
            +A  +  P     R Y VR  G++D      L +GI ++     D Q            
Sbjct: 241 DMANRIMHPRYGTEREYAVRVLGEMDDATRKSLVEGIELE-----DGQAAFGALDYLGGD 295

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           GSN W  V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 296 GSNRWYRVTLQEGRNREVRRMFESVGVTVSRLIRTRFG 333


>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 =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 96/255 (37%), Positives = 139/255 (54%), Gaps = 16/255 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR- 68
           TP ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   V   D I+V+G P+R 
Sbjct: 122 TP-KLHKVLAQAGMGSRLEMEQLILEGRISVNN---EPAHIGQRVQFGDQIKVNGKPIRF 177

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
                  R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL T
Sbjct: 178 RIAPPPVRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTEGLLLFT 237

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           + G LA  L  P     R Y VR  G +  ++   L +G+ ++        V     +G+
Sbjct: 238 SSGELANKLMHPRFGLEREYAVRVLGALSTEEKQRLLEGVPLEDGMASFGSVEDGGGEGA 297

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ ++ +R  
Sbjct: 298 NCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLELDERDIRA- 356

Query: 245 LGPHLLEEAQVNLDA 259
               L++ A   LD 
Sbjct: 357 ----LMQAAGATLDG 367


>gi|124515286|gb|EAY56796.1| Pseudouridine synthase, Rsu [Leptospirillum rubarum]
          Length = 616

 Score =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 84/225 (37%), Positives = 132/225 (58%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K++A  G+ASRR  E MI    VKVNGI++      V   TD + VDG  +      
Sbjct: 19  RLQKLLAHRGLASRRNAEEMIRGGLVKVNGIVVTVPGTKVHPETDRVTVDGKTVPVEPEP 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L+L++KP G+V+T  DPD ++T+ D  P I + +I VGRLDI +EG+LLLTN+G LA+ 
Sbjct: 79  FLFLFYKPKGIVSTLHDPDEKTTLKDFFPQI-NPLIHVGRLDIQSEGVLLLTNNGDLAQR 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTVG 192
           +  P  +  R Y V+  G V  + L+ L+ G V + G     +++  +    +N+W  + 
Sbjct: 138 ILHPRYEIPRTYLVKVQGVVKPEHLDRLRSGKVRLDGRPVQPLELEQERLTETNSWYRIT 197

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+NRE++++F+  ++ V +L RI++G   L  L  G  R V+
Sbjct: 198 LTEGRNREVRRLFDALHYFVLKLTRIAFGNLDLAGLEPGEYRLVT 242


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 82/213 (38%), Positives = 124/213 (58%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV +NG + +     +  TD + +DG      +  
Sbjct: 3   EKLQKVLARVGLGSRRYMEEVIAAGRVSINGKIAQ-VGERIEPTDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLL+ TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLIFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V     N + KG+ ++         +     G N W
Sbjct: 122 ELANRLMHPSNEVEREYAVRVMGEVTPQIRNNMLKGVELEDGPAKFESFSEIGGDGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 129/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQVITDLATIVKSGDVVEVEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGEARRLNKK 227


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKDNLRPLTRGLDIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 91/256 (35%), Positives = 144/256 (56%), Gaps = 11/256 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           +++  E+  P ++ KV+A AG+ SRR++E +I   RV VNG   E A +   ++ TD + 
Sbjct: 188 RDLTAEDDAP-KLHKVLADAGLGSRRDMEELIVAGRVSVNG---EPAHIGQRILPTDAVR 243

Query: 62  VDGVPL-RKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G  + RK  +   R+ +YHKP G + +H+DP+GR++VFD LP++   + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V + EG+NRE++++FE     V+RLIR  YG   L  TL  G   E+
Sbjct: 364 ADGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRWEEL 423

Query: 237 SKKILREQLGPHLLEE 252
            +  +R  +    LE+
Sbjct: 424 EENAVRNLMAACGLEK 439


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 85/216 (39%), Positives = 126/216 (58%), Gaps = 12/216 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+AR G+ SRR +E +IA  RV +NG + +     +   D + +DG   RK +  
Sbjct: 3   EKLQKVLARVGLGSRRYMEEVIAAGRVSINGRIAQ-VGERIEPGDELRIDG---RKVQFQ 58

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
                R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL T
Sbjct: 59  VEDEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  R Y VR  G+V     N + KG+ ++         +     G 
Sbjct: 119 NDGELANRLMHPSNEVEREYAVRVMGEVTPQIRNNMLKGVELEDGPAKFESFSEIGGDGI 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           N W  V ++EG+NRE++++FE  N KV+RL+R  YG
Sbjct: 179 NRWYQVVVKEGRNREVRRIFESQNLKVSRLLRTRYG 214


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 81/223 (36%), Positives = 116/223 (52%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A AG+ASRR+ E MI Q RV VN +++E     V   D + VDG P+   E   
Sbjct: 5   RLQKYLAHAGVASRRKAEEMIKQGRVAVNNVIIENMGATVTCNDVVTVDGKPVTTEEAKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP+G V+T  D  GR  V D +     R+  VGRLD +T GL+LLTNDG     L
Sbjct: 65  YIMLNKPVGYVSTSKDQFGRPAVIDLVKDAGKRLYPVGRLDYDTSGLILLTNDGDFTYRL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VY     G  D++++   + G+ I        +  +  +KG N  V + + 
Sbjct: 125 THPKHEVNKVYEAVISGFPDKNEITRFETGLKIDDYQTSPAEFEVLNKKGINTLVRITIH 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           EGKNR+++K+ E    KV  L RI  GP  L  L  G  R +S
Sbjct: 185 EGKNRQVRKMCEAIGHKVLTLKRIQIGPIALENLPEGKWRHLS 227


>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 =  139 bits (351), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 94/235 (40%), Positives = 127/235 (54%), Gaps = 4/235 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    V V  T   I VDG  L   E  
Sbjct: 12  RLQKVLAQAGVASRRASEQMIADGRVSVDGTVVRNQGVRVDPTKQVIHVDGERLILDETK 71

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L  +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + Y  R HG+V       L  GI ++ G    D    +DT  G    V +
Sbjct: 132 RLTHPKYEIRKTYVARLHGEVKPGVKRTLMNGIELEDGPIKVDSFRIVDTY-GDITTVEI 190

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR V    L    G
Sbjct: 191 VVHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRVKGNALSALYG 245


>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 =  139 bits (351), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 127/226 (56%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E+MI   +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 8   ERLQKVIAQAGIASRRKAEKMITAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEK-EAL 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 67  HTYLFYKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G       +++    +K     V +
Sbjct: 127 LMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 187 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELT 232


>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 =  139 bits (351), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 86/232 (37%), Positives = 124/232 (53%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+ K E  
Sbjct: 6   ERLQKVIANAGIASRRHAETLIASGHVKVNGHVTTEMGIKIGPHDTVEVDGVPIGK-EAK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+++   D  GR  V D    +  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 65  RYFLFYKPRGVISAVEDNKGRKVVTDYFEDVQERLYPVGRLDYDTSGLLVMTNDGELANH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-SNAWVTV 191
           L  P     + Y  +  G  ++  L  LK G+ I G      +V  L T K    A V +
Sbjct: 125 LMHPRYALEKKYVAKVEGIPNRPALAPLKTGVSIDGKMTAPAKVEILSTDKAKKTAIVAL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L +
Sbjct: 185 TIHQGMNHQVKKMFKAVGFPVIKLSREAYGNLTLAGLQPGEHRPIKPQELHD 236


>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 =  139 bits (351), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 84/213 (39%), Positives = 122/213 (57%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARVGLGSRRYMEEVIAAGRVSVNGQIAQ-VGERIEPGDELRIDGRKVAFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + SDP+ R TVF+ LP+I   R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVIIYYKPEGEICSRSDPENRPTVFEQLPAIPGDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V     N + KG+V+          +     G N W
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPQIRNNMLKGVVLDDGPAKFESFSELGGDGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 FQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  139 bits (351), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 75/223 (33%), Positives = 130/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +V VNG ++      V ++D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVSVNGQVVTELGTKVSNSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR+ V D    I +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRTVVTDYFDDIETRIYPVGRLDYDTSGILLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEVKELEKGIQLEDGFTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +VN+L RI +GP  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVNKLTRIQFGPLDLKGLNAGEGR 227


>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 =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 90/228 (39%), Positives = 131/228 (57%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K+I+RAG+ASRR+ E +IA  RV V+G ++         ST  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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICY-GDMQVTLDTQKGSNAWVT 190
            L  P     + YR +  G++  + L  L+ GI +  G+    +++V   T+KG +  V 
Sbjct: 123 ALLHPRFLVHKTYRAKVAGELTPEALKKLRSGIELADGMTAPAEVRVYGVTEKGLSD-VE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V L EG+NR+++++FE     V  L R  +    L  +  G++R ++K
Sbjct: 182 VTLHEGRNRQVRRMFEAVGCDVRALKRTRFAQLTLDGVKRGASRPLTK 229


>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 =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V VNG ++   A  + S D +EV G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVSGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRPTVVDLLPNVTERIYPVGRLDWDTSGALILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  D++ L  L KG+ + G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVADKEVLRPLTKGVEVDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTQFGHLNLTGLRPGEARRLNKK 227


>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 =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 93/250 (37%), Positives = 138/250 (55%), Gaps = 12/250 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG+ SRR  + +IA  RV VNG ++  A + +  + D + VDG P+  A   
Sbjct: 10  RINKALASAGVCSRRHADDLIAAGRVTVNGAVVTEAGLRIDPARDALAVDGAPVNLAPEI 69

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
            + L  HK  G+VTT SDP+GR TVFD LP ++   R+  VGRLD  +EGLLLLT DG L
Sbjct: 70  PITLALHKKPGVVTTASDPEGRPTVFDGLPEVWRGKRLFPVGRLDFFSEGLLLLTTDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQV-TLDTQKGSNAW 188
           A  L  P     + YRV   GQV  D L  + +G+ + +G     +    ++      + 
Sbjct: 130 ALRLTHPRWHVPKRYRVTVRGQVTPDMLGTMARGMRLAEGERLAPVAARVVEGPAQDRSI 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQL 245
           + + L +G NR+I+++       V RL R+S GP  LG L  G+ RE++      LR+ +
Sbjct: 190 LEMELHQGVNRQIRRMCRDLGLTVLRLARVSQGPVALGDLPLGACRELTPAELATLRQSV 249

Query: 246 GPHLLEEAQV 255
           G   L++A V
Sbjct: 250 G---LDDADV 256


>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 =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 75/223 (33%), Positives = 130/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDLGRKVVTDYFEDIETRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQPAQVKIKRQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEYFGHEVNKLTRIQFGPLDLKGLNAGEGR 227


>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 =  139 bits (350), Expect = 6e-31,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 128/226 (56%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEK-EAL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFYKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G       +++    +K     V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELT 227


>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 =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGKVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRPTVIDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V  D +K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGLANKENLRPLTRGVTIDGKKTKPATYEILKV--DPEK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKK 227


>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 =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 132/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYIARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGEARRLNKK 227


>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 =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 87/218 (39%), Positives = 129/218 (59%), Gaps = 8/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E  IA  RV ++G  + +    + +   + +DG  V ++  +
Sbjct: 8   EKLQKVLARAGHGSRREMEAWIAAGRVSIDG-EIAKLGDRIEADAKVRIDGRTVSIKSED 66

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + +  DP+GR TVFD LP    SR ++VGRLDINT GLLL T+DG
Sbjct: 67  DLVCRVIAYHKPEGEICSRKDPEGRPTVFDRLPKTRDSRWVAVGRLDINTSGLLLFTSDG 126

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS +  R Y VR  G+V    +  L+ G+ ++ G  + D ++     +G N 
Sbjct: 127 ELANRLMHPSHEVEREYAVRTFGEVTDACIQRLRSGVTLEDGPAHFD-KIKPAGGEGMNK 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L EG+NRE+++++E    +V+RLIRI YG   L
Sbjct: 186 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIDL 223


>gi|325679067|ref|ZP_08158661.1| pseudouridylate synthase [Ruminococcus albus 8]
 gi|324109191|gb|EGC03413.1| pseudouridylate synthase [Ruminococcus albus 8]
          Length = 244

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 126/230 (54%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+IA +G  SRR+ E  IA  +V VNG  +      +   D I VDG+ + + ++  
Sbjct: 5   RIQKIIAESGFCSRRKAEEFIAAGKVTVNGRKVTLGDKALPGKDLIVVDGIKIDQPKKRN 64

Query: 75  LW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L+  + HKP G VTT +D   R  V D L  +  RV  VGRLD ++EGLLLLTNDGG A 
Sbjct: 65  LYYIMLHKPRGYVTTMNDELNRKCVTDLLDGVPERVYPVGRLDKDSEGLLLLTNDGGFAN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + YRV     ++ ++L  L  G+ I G    +  V +  ++ +   + + 
Sbjct: 125 DIMHPSRHVAKTYRVTVRPDINDEQLVKLASGVEIDGRMTAECSVVVLDKQPNRVVLQMT 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+I+K+ E    +V RL R + GP +LG L AG  RE+    LR
Sbjct: 185 IHEGRNRQIRKMCEAVGLEVARLKRTAVGPLRLGMLKAGEWRELKPDELR 234


>gi|310642601|ref|YP_003947359.1| pseudouridine synthase [Paenibacillus polymyxa SC2]
 gi|309247551|gb|ADO57118.1| Pseudouridine synthase [Paenibacillus polymyxa SC2]
          Length = 252

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 127/228 (55%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG+ +           D I V G P+ K E+
Sbjct: 2   ERLQKILAQAGVASRRKCEELIQAGSVEVNGVTVTELGTKADPDQDMITVKGRPI-KTEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP+GR  V D L  +  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 61  KIYLMMNKPKGVITSASDPEGRKIVSDYLKGVKERVYPVGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  P     + Y     G     +L+ LKKGIV++       +V        G  + + 
Sbjct: 121 LLTHPKHHVPKTYVATVKGVPHGTELDKLKKGIVLEDGITAPAEVEYKDVDPDGKESVIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + + EG+NR+++++FE  +  V RL RI++G   L  L  G TR ++K
Sbjct: 181 ITIYEGRNRQVRRMFEAISHPVIRLKRIAFGDLLLQNLKRGLTRPLTK 228


>gi|225620831|ref|YP_002722089.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
 gi|225215651|gb|ACN84385.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
          Length = 359

 Score =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 93/307 (30%), Positives = 151/307 (49%), Gaps = 22/307 (7%)

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 KPIG+V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 64  KRQTKRYMALY-KPIGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A ++  PS + L+VY V  +G++D + L    KGI I+ + Y   +  + ++    +
Sbjct: 123 GEFANIITHPSYEILKVYDVTVNGKIDSEALLNASKGITIKNVSYSPFKFKILSKGRIQS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ-----LGTLLAGSTREVSKKILR 242
            + + + EGKNREI+K+F+   +KV  L RIS G         GTL AG  R+++KK   
Sbjct: 183 KIRLTINEGKNREIRKIFDHLGYKVIDLERISVGCVSKYDEVSGTLEAGHIRDLTKK--- 239

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                         +D      +  ++D  +I   +PDD        S  N  +  K+  
Sbjct: 240 -------------EIDFFFKQKDKKLKDIESIFENIPDDIEDENYEDSILNSSNNDKEEN 286

Query: 303 TPVHRRN 309
             VH R+
Sbjct: 287 KKVHDRS 293


>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 =  139 bits (350), Expect = 7e-31,   Method: Compositional matrix adjust.
 Identities = 89/238 (37%), Positives = 135/238 (56%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG  +    V    +TD I V+G P+R  ++
Sbjct: 5   ERLQKILAQAGVASRRKCEELILAGAVEVNGEKVTTLGVKADPATDEITVNGKPIRSEKK 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L +KP G++T+  DP GR  V D LP I  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 65  IYLML-NKPKGVITSAKDPQGRKVVADFLPGIRERVYPVGRLDYDTEGLLLLTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWV 189
           +L  PS    + Y     G      L+ LKKG++++       +V    +D +K + + +
Sbjct: 124 LLTHPSHHVPKTYYATVKGVPHGSLLDQLKKGVMLEDGLTAPAEVEYQDIDEEK-NMSTI 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE---VSKKILREQ 244
            + + EG+NR+++++F+     V +L R+ +G   L TL  G  R    V  K LR+Q
Sbjct: 183 RITIYEGRNRQVRRMFDAIKHPVLKLRRVKFGELGLRTLARGQFRHLTPVEVKELRDQ 240


>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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 86/229 (37%), Positives = 123/229 (53%), Gaps = 1/229 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AGI SRR  E ++ + RV VN +          S D IEVDG PL  A
Sbjct: 1   MTRQRLQKLIAAAGICSRRHAEELMREGRVTVNQVTAGLGDQADPSIDRIEVDGRPLSHA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGG 129
            R RL L +KP G++++ SDP GR TV D +P    R +  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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V LREG+NR+I++V +     V  L R +     LG+L  G  RE+++
Sbjct: 181 KVILREGRNRQIRRVADALGHPVLDLQRTAISSIDLGSLPEGHWRELTR 229


>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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I +  V +NG ++   A  V S D +EV+G+P+   E+  
Sbjct: 2   RINKYIAHAGLASRRKAEELIKRGLVTLNGQVITDLATTVKSGDLVEVEGIPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRQTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G V ++ L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGVVTKESLRPLTRGVVIDGKKTKPARYRIIRVEPDKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG++ ++KK+FE     V++L R  +G   +  L  G  R +SKK
Sbjct: 178 ELTIHEGRHHQVKKMFEVVGHLVDKLSRTQFGSLDVRGLKPGEARRLSKK 227


>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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 89/230 (38%), Positives = 131/230 (56%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E MIA+ RV+V+G ++    V V   T  I VDG+ ++  E  
Sbjct: 161 RLQKVMASAGVASRRVCEEMIAEGRVEVDGQVVTELGVRVDPKTAVIHVDGIRIQLDENM 220

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +++KP G+V+T  DP+GR  + D   N  +   R+  VGRLD+ TEGLLLLTNDG L
Sbjct: 221 VYMVFNKPKGVVSTMEDPEGRPCISDFLKNAKNKGERLFHVGRLDVATEGLLLLTNDGEL 280

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y V+  G   Q     LK+G+ ++ G    D    +D+  G +  +
Sbjct: 281 ANRLTHPSYEVPKTYLVQVRGPFPQGIGAQLKEGVELEDGFASVDSFRLVDSTPG-HVLI 339

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+
Sbjct: 340 EVVLHSGKNRIVRRLFDAVGFPVLRLVRVKVGPIGLGDQRQGSIRNLGKQ 389


>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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMIVAGRVKVDGHVVTKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTAEDDRGRKTVVDYFEDLPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  L +G+ +         ++V     K     V +
Sbjct: 122 LMHPKNEVAKVYVAKIKGILTPDEIKTLTQGVKLDHFKAAPAKVKVLKTDHKKDTQIVQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG   ++K++F+     V++L R  Y    L +L +G  RE+SK
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLAREKYAFLTLDSLTSGQYRELSK 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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 93/234 (39%), Positives = 131/234 (55%), Gaps = 20/234 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKA 70
           +RV KV+A  G+ SRRE+E  I +  VKVN    +R A     V   D I V G  +  A
Sbjct: 3   ERVQKVLAARGLGSRREIEGWIERGEVKVN----QRTAKLGDQVGPNDVIRVRGRVIHMA 58

Query: 71  ERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           E    WL YHKP+G + + SDP+GR  VF +LP +   R ++VGRLD+NT GLLL T DG
Sbjct: 59  EHAHRWLVYHKPVGEICSRSDPEGRKPVFASLPRLKGQRWVAVGRLDLNTSGLLLFTTDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----- 183
            LA  L  PS    R Y VR  G+V  D   +L +G+ ++     D     D  +     
Sbjct: 119 ELANRLMHPSHSLEREYAVRVLGEVPDDTRRMLLEGVELE-----DGPARFDVLEERGGD 173

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           G+N W  V + EG+NR ++++++     V+RLIR+ YGP  LG  L  G++R++
Sbjct: 174 GANHWFHVVVSEGRNRLVRRLWDAVGVTVSRLIRVRYGPVVLGRGLKTGASRDL 227


>gi|396661|emb|CAA79503.1| unknown open reading frame [Buchnera aphidicola]
          Length = 258

 Score =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 85/218 (38%), Positives = 131/218 (60%), Gaps = 14/218 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV----NVMSTDHIEVDGVPL--- 67
           ++ K+++  G  SRR +E MI   ++ +NG   E+A +    N  +   I +D   +   
Sbjct: 4   KIQKILSDLGYGSRRFIECMIKCGKISING---EKAIIGQYLNKKNPGEILIDKKKIIVK 60

Query: 68  RKAERTRLWLYH-KPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           R     ++ +Y+ KPIG V T  D   R TVFD LP +  +R +SVGRLDINT+GLLL T
Sbjct: 61  RNKNLPKVLIYNNKPIGEVCTRDDFQKRLTVFDKLPKLNLNRWVSVGRLDINTKGLLLFT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQG-ICYGDMQVTLDTQK 183
           NDG LA  L  P +Q  R Y +R  G+++++K+N+L+KG+ +I G + + ++    D ++
Sbjct: 121 NDGTLANKLMHPRSQIEREYNIRIFGEMNKNKINILRKGVKIIHGYVSFKEIVPLYDKKE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           G N W    L EGKNREI+ +F+    +VN+LIR+ YG
Sbjct: 181 GKNKWFKGILCEGKNREIRLMFKSIQCQVNQLIRVRYG 218


>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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 79/237 (33%), Positives = 131/237 (55%), Gaps = 3/237 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           KN  +++    R+ K +A AG+ASRR  E++I + RVKVNG++++     V   D IEV+
Sbjct: 7   KNNKEDHMAEVRLQKAMADAGVASRRASEKLILEGRVKVNGVVVKELGTKVKGDDAIEVN 66

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G  + +      +L++KP G+++   D  GR  V D      +R+  +GRLD +T G+LL
Sbjct: 67  GTLIERERNKVYYLFYKPRGVISAVKDDKGRRVVTDYFEGEKNRIYPIGRLDYDTSGILL 126

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTLD 180
           LTNDG LA +L  P  +  + Y  +  G V  D L  L+KG+ ++   Y      +V   
Sbjct: 127 LTNDGELANLLMHPRYKVDKTYVAKVEGLVQSDDLKRLRKGVKMKDGHYSARAKAKVISS 186

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +  +++ V++ + EG+N ++K +FE     V +L R +Y    L  L++G  RE+S
Sbjct: 187 DRAKNHSIVSLTIHEGRNHQVKNMFEAIGHPVMKLKRETYDFLTLKGLVSGQYRELS 243


>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 =  139 bits (349), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLIIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKAGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  ++D L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 88/218 (40%), Positives = 126/218 (57%), Gaps = 9/218 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRK 69
           +R+ K +A AG+ SRRE+E  IA+ RV+VNG   E A V   V   D ++V G  V LR 
Sbjct: 34  ERLHKALASAGLGSRREMEEWIAEGRVQVNG---ETATVGSKVGPRDVVKVSGRRVYLRF 90

Query: 70  AE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
            E RTR+ +YHK  G + +  DP GR+TVFD LP +  S+ I+VGRLD NT+GL++ T  
Sbjct: 91  DEKRTRILIYHKSEGEIVSRDDPGGRATVFDALPRLRGSKWIAVGRLDYNTDGLMIFTTS 150

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G++ +D +  L  G+ +               +G+N 
Sbjct: 151 GDLANRLMHPRFEVEREYAVRVLGELTEDMIAELLAGVELDDGPAQLQSCFAAGGEGANR 210

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+ RE++++FE     V+RL RI +GP  L
Sbjct: 211 WYRVVIKEGRKREVRRLFEHLGLTVSRLTRIRFGPIVL 248


>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 =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 135/226 (59%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+++++A AG  SRR+ E +I + RV V+G  +      V      + VDG  LR  ++ 
Sbjct: 26  RINQLLASAGFGSRRQCEELIREGRVDVDGETITELGTTVDPDLQKVRVDGNYLR-PQKL 84

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+G+VTT+ DP GR  V D +P    RV  VGRLDI++EGL+LLTNDG LA+ 
Sbjct: 85  VYYVVNKPVGIVTTNRDPRGRPRVIDLVPPT-ERVFPVGRLDISSEGLILLTNDGDLAQK 143

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VYRV   G+V  + +  +++GI I +G+   D    +  +  +   + + 
Sbjct: 144 LAHPKFGIQKVYRVVVAGEVRGETMKKMREGIYIAEGLVQVDGAKIIKARTKAT-EMEIR 202

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L+EGKNREI+++   F  KV +L R++ GP +LG +  G+ R++++
Sbjct: 203 LKEGKNREIRRILARFGHKVQQLRRVAIGPLKLGDVPRGAYRKLTR 248


>gi|327538428|gb|EGF25099.1| ribosomal large subunit pseudouridine synthase B [Rhodopirellula
           baltica WH47]
          Length = 395

 Score =  139 bits (349), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 135/226 (59%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+++++A AG  SRR+ E +I + RV V+G  +      V      + VDG  LR  ++ 
Sbjct: 26  RINQLLASAGFGSRRQCEELIREGRVDVDGETITELGTTVDPDLQKVRVDGNYLR-PQKL 84

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+G+VTT+ DP GR  V D +P    RV  VGRLDI++EGL+LLTNDG LA+ 
Sbjct: 85  VYYVVNKPVGIVTTNRDPRGRPRVIDLVPPT-ERVFPVGRLDISSEGLILLTNDGDLAQK 143

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VYRV   G+V  + +  +++GI I +G+   D    +  +  +   + + 
Sbjct: 144 LAHPKFGIQKVYRVVVAGEVRGETMKKMREGIYIAEGLVQVDGAKIIKARTKAT-EMEIR 202

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L+EGKNREI+++   F  KV +L R++ GP +LG +  G+ R++++
Sbjct: 203 LKEGKNREIRRILARFGHKVQQLRRVAIGPLKLGDVPRGAYRKLTR 248


>gi|332974446|gb|EGK11370.1| ribosomal large subunit pseudouridine synthase B [Kingella kingae
           ATCC 23330]
          Length = 390

 Score =  139 bits (349), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 83/232 (35%), Positives = 134/232 (57%), Gaps = 11/232 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMST 57
           +++K        P+R+ KV+A +G+ SRRE+E  I    V+VNG    R A     V   
Sbjct: 127 LREKRTDLSRIEPERLQKVLAASGVGSRREMEEWINNGWVQVNG----RVATLGEKVSPD 182

Query: 58  DHIEVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGR 113
           D + V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GR
Sbjct: 183 DQVTVKGSAIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGR 242

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDINT GLL+LT  G L +    PS +  R Y VR  G++  +++N L +G++++     
Sbjct: 243 LDINTSGLLILTTSGELVQRFAHPSFEVEREYAVRVLGELSPEQMNDLCEGVMLEDGLAK 302

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             ++     +G N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 303 VERIYEQGGEGVNKWYNVIIKEGRNREVRRLFESQGVTVSRLVRVGFGPIGL 354


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 87/214 (40%), Positives = 126/214 (58%), Gaps = 8/214 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +++ K++AR G+ SRR +E +I   R+ +N  +       V+ TD I +DG  +R KAER
Sbjct: 24  EKLQKLLARLGLGSRRGLEEIIKSGRISINDKVAT-LGDRVILTDEIRIDGRQVRLKAER 82

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + + SDP GR TVFD LP + + R + VGRLDIN+ GLLL TNDG
Sbjct: 83  EKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLFTNDG 142

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  PS+  +R Y VR  G+V     + L  G+ ++ G+   D  +      G N 
Sbjct: 143 ELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFD-DIKEGGGIGVNK 201

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           W  V ++EG+ RE++++FE    KV+RLIR  YG
Sbjct: 202 WYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYG 235


>gi|159026975|emb|CAO86693.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 248

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 88/219 (40%), Positives = 122/219 (55%), Gaps = 5/219 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++A+ GIASRR  E MI  +RV+ NG +++         DH+E+DG  +  A R 
Sbjct: 3   ERVQKILAQWGIASRRRAEEMIVARRVRRNGKIVQLGEKADPEKDHLEIDGKKIEPANRP 62

Query: 74  -RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
            RL+ 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 227
           + V L EG+NR+I+ V E   + V +L R + GP QL +
Sbjct: 183 LEVILVEGRNRQIRCVAEELGYHVLKLHRSAIGPIQLNS 221


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 86/218 (39%), Positives = 129/218 (59%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ KV+ARAG  SRRE+E MIA  RV ++G + +    V+  +   + +DG  V L+  
Sbjct: 3   EKLQKVLARAGHGSRREIEAMIAAGRVSIDGQVAKLGDRVDGRAELKVRIDGHAVSLKAE 62

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + + SDP GR TVF+ LP +  SR ++VGRLDINT GLLL T D
Sbjct: 63  EEVICRVLAYYKPEGELCSRSDPQGRPTVFERLPRVRDSRWVAVGRLDINTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y +R  G+V ++ L  L+ G+ ++       ++     +G N 
Sbjct: 123 GELANRLMHPSQEVEREYAIRVFGEVTEEMLKNLRTGVELEDGTAQFKRLVPAGGEGLNT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W    L EG+NRE+++++E    +V+RL+RI YG   L
Sbjct: 183 WYHGVLSEGRNREVRRLWESQEVQVSRLMRIRYGDITL 220


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 125/231 (54%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K+I+ AG ASRR  E +I   RV V+G+ +        +  H 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EG+ R+++++F     +V RL R+ +    L  +  GS R ++   + E
Sbjct: 183 IHEGRKRQVRRMFAAIGCRVQRLCRVRFAMLTLDGVSCGSFRHLTSDEIHE 233


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 128/223 (57%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-AWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++ G+            K  N   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGLTQPADVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGR 227


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 89/224 (39%), Positives = 126/224 (56%), Gaps = 5/224 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KVIA+AG+ASRR+ E  I + RVKVNG  +      V  S D +EVDGVPL K E 
Sbjct: 2   ERLQKVIAKAGVASRRKAEEYIVEGRVKVNGETVTELGTKVNPSKDAVEVDGVPLDKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY KP G+V+T +D  GR  V D + S   R+  +GRLD +T GLLLLTNDG  A 
Sbjct: 62  VYHLLY-KPTGVVSTSNDEKGRKVVTDFIES-EQRIYPIGRLDYDTSGLLLLTNDGEFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
           +L  P  +  + Y  +  G  ++ ++  L+ GIV++         +V    +K   A V 
Sbjct: 120 LLMHPRYKIEKEYIAKVKGIPERKRIKELETGIVLEDGKTAPAKAKVLSIDKKKQTAIVR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EGKNR+++++FE     V +L R  YG   LG L  G +R
Sbjct: 180 LIIHEGKNRQVRRMFEAIGHPVVKLKRERYGFLTLGHLHPGESR 223


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/217 (39%), Positives = 127/217 (58%), Gaps = 19/217 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRK--- 69
           ++ KV+A++G+ SRRE+E +I   RV VNG   E A +   ++ TD I V+G  +++   
Sbjct: 173 KLHKVLAQSGVGSRREMEDLILAGRVSVNG---EPAHLGQRILPTDQIRVNGKIIKRRLR 229

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
             + R+  YHKP G V +  DP+GR TVF +LP +  ++  +VGRLDINTEGLLL T  G
Sbjct: 230 PAQARVLAYHKPTGEVVSFKDPEGRPTVFQHLPKLQGAKWTAVGRLDINTEGLLLFTTSG 289

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQK 183
            LA  L  PS    R Y VR  G++D    + L     ++G+  GD     + +     +
Sbjct: 290 DLANRLMHPSYGAEREYAVRVLGELDAAARDEL-----LEGVQLGDGPARFLSLEEAGGE 344

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           G+N W  V + EG+NRE++++FE     V+RLIR+ Y
Sbjct: 345 GANRWWRVVISEGRNREVRRMFEAVGLTVSRLIRVRY 381


>gi|294340472|emb|CAZ88853.1| putative Pseudouridine synthase [Thiomonas sp. 3As]
          Length = 562

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/217 (39%), Positives = 127/217 (58%), Gaps = 19/217 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRK--- 69
           ++ KV+A++G+ SRRE+E +I   RV VNG   E A +   ++ TD I V+G  +++   
Sbjct: 176 KLHKVLAQSGVGSRREMEDLILAGRVSVNG---EPAHLGQRILPTDQIRVNGKIIKRRLR 232

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
             + R+  YHKP G V +  DP+GR TVF +LP +  ++  +VGRLDINTEGLLL T  G
Sbjct: 233 PAQARVLAYHKPTGEVVSFKDPEGRPTVFQHLPKLQGAKWTAVGRLDINTEGLLLFTTSG 292

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQK 183
            LA  L  PS    R Y VR  G++D    + L     ++G+  GD     + +     +
Sbjct: 293 DLANRLMHPSYGAEREYAVRVLGELDAAARDEL-----LEGVQLGDGPARFLSLEEAGGE 347

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           G+N W  V + EG+NRE++++FE     V+RLIR+ Y
Sbjct: 348 GANRWWRVVISEGRNREVRRMFEAVGLTVSRLIRVRY 384


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 87/217 (40%), Positives = 121/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+ARAG  SRRE+E  I   RV VNGI+ +           + +DG      +++
Sbjct: 3   EKLQKVLARAGHGSRREIESFIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAKIQE 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYL 219


>gi|12724251|gb|AAK05373.1|AE006360_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 257

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 20  RINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVNGVAVYNEEPV- 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 79  YYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             P     +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 139 THPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 198

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 199 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRLSKK 245


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 127/230 (55%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V   D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKLGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +GIVI G       Y  ++V  D  +   + V
Sbjct: 121 THPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 227


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 84/217 (38%), Positives = 121/217 (55%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A V   +   D I+V+G P+R    
Sbjct: 114 KLHKVLAQAGLGSRLEMEQLILEGRISVNN---EPAHVGQRIQFGDQIKVNGQPIRFRID 170

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL T+ G
Sbjct: 171 PPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQHGKWQSVGRLDLNTEGLLLFTSSG 230

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y  R  G + +++   L  G+ ++        +     +G+N W
Sbjct: 231 ELANSLMHPRFGLEREYAARVLGALSKEEKQRLTDGVQLEDGVAAFGSIEDGGGEGANCW 290

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE++++FE     V+RLIRI YG   L
Sbjct: 291 YRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVL 327


>gi|222110298|ref|YP_002552562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729742|gb|ACM32562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 435

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 95/255 (37%), Positives = 138/255 (54%), Gaps = 16/255 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR- 68
           TP ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   V   D I+V+G P+R 
Sbjct: 110 TP-KLHKVLAQAGMGSRLEMEQLILEGRISVNN---EPAHIGQRVQFGDQIKVNGKPIRF 165

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
                  R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL T
Sbjct: 166 RIAPPPVRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTEGLLLFT 225

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           + G LA  L  P     R Y  R  G +  ++   L +G+ ++        V     +G+
Sbjct: 226 SSGELANKLMHPRFGLEREYAARVLGALSTEEKQRLLEGVPLEDGMASFGSVEDGGGEGA 285

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ ++ +R  
Sbjct: 286 NCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLELDERDIRA- 344

Query: 245 LGPHLLEEAQVNLDA 259
               L++ A   LD 
Sbjct: 345 ----LMQAAGATLDG 355


>gi|326406814|gb|ADZ63885.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis CV56]
          Length = 257

 Score =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 20  RINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVNGVAVYNEEPV- 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 79  YYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             P     +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 139 THPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 198

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 199 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 245


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 129/223 (57%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I   +VKVNG ++      V ++D +EV+G+ L + ++ 
Sbjct: 6   ERLQKRIASSGYTSRRKAETLITDGKVKVNGHVVTELGTKVSNSDTVEVEGIKLEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFNKPAQVITSVSDDRGRKVVTDYFKDIETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN-AWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q K  N   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQPAQVKVKNQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V++L RI +GP  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVSKLTRIQFGPLDLKGLNAGEGR 227


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V S+D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTLNGQVITDLATLVKSSDVVEVEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNR---SIV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG++ ++KK+FE     V++L R  +G   L  L  G  R ++KK
Sbjct: 178 ELTIHEGRHHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGEARRLNKK 227


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 20  RINKYLAHAGVASRRKAEELILAGKVTVNNVSMTNLGYQVSTGDIVEVNGVAVYNEEPV- 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 79  YYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             P     +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 139 THPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 198

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 199 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 245


>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 =  138 bits (348), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+
Sbjct: 95  MEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 153

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 154 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 213

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 214 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 273

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+RI +GP  L
Sbjct: 274 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGL 313


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+RI +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGL 312


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     +   D + V G  + L+
Sbjct: 92  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKITPDDQVLVKGNIIKLK 150

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 151 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 210

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    P  +  R Y VR  G +  +++ +L ++GI+++       ++     +G 
Sbjct: 211 SGELVQRFAHPRFEVEREYAVRTLGGLTTEQMRMLTEEGIMLEDGLAKVERIREQGGEGV 270

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE+F+  V+RL+RI +GP  L
Sbjct: 271 NKWYNVVIKEGRNREVRRIFEYFDLTVSRLVRIGFGPIGL 310


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 78/223 (34%), Positives = 131/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++ G+    +++V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYIMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGR 227


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 128/227 (56%), Gaps = 3/227 (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 KP G ++  +D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  YFLLY-KPRGTISAVTDDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +V++ +  +    A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGIPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDENAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLYGLAPGEFRELSK 227


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 127/226 (56%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKITELGTKVEPSDKIEVNGVPIEK-ETL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFYKPRGVISSVKDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  + +  L  G+ I G       +++    +K +   V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGLLSPEDIRSLTHGVRIDGRKSAPAKLKILKTDEKKNTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELT 227


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/216 (39%), Positives = 120/216 (55%), Gaps = 5/216 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++A+ GIASRRE E MI + RV++NG+L           D I VDG P+   +R  
Sbjct: 4   RLQKILAQWGIASRRESEEMIRRSRVRINGVLAHLGQKVDPERDKISVDGKPVYAQQRPP 63

Query: 75  L--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 129
           L   L HKP G+V+T  DP GR TV D LP      S +  VGRLD  + G L+LTNDG 
Sbjct: 64  LIYLLLHKPAGVVSTCYDPQGRKTVLDLLPPELRKGSGLHPVGRLDAESTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y+V   G   +  L + +KG+V++G      +V L      N+ +
Sbjct: 124 LTFGLTHPSHSIPKTYQVLVKGHPSEAVLEMWRKGVVLEGRKTRPAKVHLIESLAKNSHL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L+EG+NR+I++V +   + V +L R S GP QL
Sbjct: 184 EIVLKEGRNRQIRRVAQQLGYPVIQLHRTSIGPIQL 219


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GIASRR+ E +I Q  V VNG ++   A  + S D +EV G P+   E+  
Sbjct: 2   RINKYIAHSGIASRRKAEELIKQGLVTVNGQVVRELATTIKSGDRVEVSGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRPTVVDLLPNVTERIYPVGRLDWDTSGALILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  D++ L  L KG+ + G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVADKEVLRPLTKGVEVDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTQFGHLNLTGLRPGEARRLNKK 227


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKENLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  138 bits (347), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 127/226 (56%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V   D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPRDKIEVNGVPIEK-EAL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFYKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G       +++    +K     V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGILSTEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELT 227


>gi|126650120|ref|ZP_01722353.1| RluB [Bacillus sp. B14905]
 gi|126593292|gb|EAZ87254.1| RluB [Bacillus sp. B14905]
          Length = 243

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 128/227 (56%), Gaps = 3/227 (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 KP G ++  +D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  YFLLY-KPRGTISAVTDDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +V++ +  +K   A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGIPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLFGLAPGEFRELSK 227


>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 =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 129/228 (56%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V + D +EV G P+   E+  
Sbjct: 2   RINKYIAHAGLASRRKAEELIKQGLVTINGQVVTELATTVKNGDRVEVSGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVLDLLPDVKERIYPVGRLDWDTTGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G   G  +   + ++  K + + V +
Sbjct: 121 IHPRNEIDKVYLARLKGLATKENLRPLTRGVVIDGKKTGPARYKIIKVEPDK-NRSLVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K +F+     V++L R  +G   L  L  G +R +SKK
Sbjct: 180 TIHEGRNHQVKNMFQAVGLLVDKLSRTQFGTLNLRGLQPGESRRLSKK 227


>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 =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>gi|268596680|ref|ZP_06130847.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|268550468|gb|EEZ45487.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
          Length = 416

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 161 MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 219

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 220 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 279

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 280 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIREQGGEGA 339

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 340 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 379


>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 =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 125/229 (54%), Gaps = 1/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E +I Q RV VNG ++E A   V+ TD + VD V ++     
Sbjct: 15  ERLQKVMAAAGVASRRVCEDLIYQGRVAVNGEVVEAAGRRVLPTDRVTVDDVAIQLDTTK 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  + +KP+G+V++ +D  GR  + +       R+ +VGRLD NT GLL+LTNDG LA +
Sbjct: 75  QYVMLNKPVGVVSSMADESGRPDLREFTRDYDERLFNVGRLDANTSGLLILTNDGELAHI 134

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    + Y  +  G V    +  L KGI +  G    D    L    G+   V + 
Sbjct: 135 LAHPSFGVSKTYIAKVEGIVSAQTIAKLTKGIELDDGPIVADKARALGRASGNETMVEIT 194

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L  G+N  ++++ +     V  L+R  +GP  LG+L  G TR+++K  L
Sbjct: 195 LHSGRNHIVRRMLDAVGHPVIDLVRRQFGPLTLGSLPVGRTRDLTKAEL 243


>gi|30024033|ref|NP_267431.2| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 239

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 2   RINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVNGVAVYNEEPV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 61  YYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             P     +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 121 THPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 181 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRLSKK 227


>gi|254672143|emb|CBA04924.1| conserved hypothetical protein [Neisseria meningitidis alpha275]
          Length = 349

 Score =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+RI +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGL 312


>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 =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 95  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 153

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 154 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 213

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 214 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 273

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 274 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 313


>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 =  138 bits (347), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 77/223 (34%), Positives = 124/223 (55%), Gaps = 1/223 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           + K+++ AG+ASRR  E +I   RV V+G+ +         + H I VDG P++ +E   
Sbjct: 1   MQKILSHAGVASRRAAEALIRDGRVTVDGVPVTMLGSKYDPSFHEIAVDGTPVQGSEEKL 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L HKP G ++T  D  GR TV D LP    R+  VGRLD +TEGLL++TNDG + + L
Sbjct: 61  YILLHKPRGCLSTAHDDRGRRTVLDLLPHFPVRLYPVGRLDADTEGLLIITNDGAMTQGL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VY     G V +DKL+ L++GI++        Q+++  ++G    V   + 
Sbjct: 121 LHPRFEIDKVYHAEVTGTVTEDKLSKLRRGILLDDGKTAPAQLSILRREGGRTLVETIIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           EG+NR+++++F     +V RL R+ +    L  L  G+ R ++
Sbjct: 181 EGRNRQVRRMFAAVGCRVQRLRRVRFAMLTLDGLPCGAFRHLT 223


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 94/248 (37%), Positives = 140/248 (56%), Gaps = 13/248 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MI + RV+V+G++     + V  T   I VDG+ ++  E  
Sbjct: 165 RLQKVMAQAGVASRRVCEEMILEGRVEVDGVVTTELGMRVDPTSAVIHVDGIRIQLDETL 224

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +++KP G+V+T  DP+GR  + D   N  +   R+  VGRLD+ TEGLLLLTNDG L
Sbjct: 225 VYMVFNKPKGVVSTMEDPEGRPCISDFLKNNKNKGERLFHVGRLDVATEGLLLLTNDGEL 284

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y V+  G   Q     LK G+ ++ G+   D    +D+  G +  +
Sbjct: 285 ANRLTHPSYEVPKTYLVQVRGPFPQGVGAKLKNGVELEDGVAAVDSFRLVDSTPG-HVLI 343

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R +     R+++G HL
Sbjct: 344 EVVLHSGKNRIVRRMFDAVGFPVERLVRVKVGPIGLGDQRQGSIRNLG----RQEVG-HL 398

Query: 250 LEEAQVNL 257
           L  A V L
Sbjct: 399 L--ASVGL 404


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 161 MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 219

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 220 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 279

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 280 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 339

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 340 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 379


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 108/303 (35%), Positives = 154/303 (50%), Gaps = 13/303 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG + +           I +DG  +  + +E
Sbjct: 3   EKLQKVLARAGHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTITGKASE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V + K+  + +G+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNVTRGVQLEDGMARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK---ILREQ 244
             V + EG+NRE+++++E     V+RL R+ YG   L   L  G  +E+  +    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWKELDLQEVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  ++LD P  +S    R R   I        R ++ ++   G S Q K   P
Sbjct: 243 VELQPEKETLLDLD-PANTSRKRERSRSQKIRRA---VKRHEERANAPKGRSNQTKRKKP 298

Query: 305 VHR 307
             R
Sbjct: 299 ATR 301


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/233 (37%), Positives = 130/233 (55%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AGIASRR  E +I + RV+VNG I++E         D I VDG  +    R 
Sbjct: 40  RLQKVLAQAGIASRRASEGLITEGRVEVNGHIVVELGTRVDPEHDSIRVDGARIPPPRRH 99

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G+V+T  DP+GR T+ + +P    R+  VGRLD  TEGL++LTNDG     
Sbjct: 100 MYLLLNKPRGVVSTMDDPEGRPTLAEYVPR-HQRLFHVGRLDTETEGLIILTNDGEFGHR 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  + Y V   G +D   +  L+KG+ ++       +V L ++   +  + + L
Sbjct: 159 LSHPSYEVRKTYLVDAEGLMDNRTIRRLEKGLTLEDGPIKPDRVKLVSRGPVHTMLQITL 218

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             G+NR ++++ +     V +L RI  GP +LG L  G TRE+S    RE+LG
Sbjct: 219 HSGRNRIVRRMMDSVGHPVRQLARIGIGPVRLGNLAVGETRELS----REELG 267


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 93  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 151

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 152 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 211

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 212 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 271

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 272 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 311


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 273 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 312


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 273 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 312


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGIANKENLRPLTRGLEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E   
Sbjct: 2   RINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAVYNEEPV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++  D  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    ++
Sbjct: 61  YYLLNKPRGYISSVRDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNMM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
             PS    +VY  +  GQ +++ L  L  G+ I+G  +     ++    +  +++ V++ 
Sbjct: 121 THPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK
Sbjct: 181 IHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKK 227


>gi|325205871|gb|ADZ01324.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M04-240196]
          Length = 349

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 93/235 (39%), Positives = 126/235 (53%), Gaps = 4/235 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    V V      I VDG  L   E  
Sbjct: 12  RLQKVLAQAGVASRRASEQMIADGRVSVDGTVVRNQGVRVDPAKQVIHVDGERLILDETK 71

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L  +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + Y  R HG+V       L  GI ++ G    D    +DT  G    V +
Sbjct: 132 RLTHPKYEIRKTYVARLHGEVKPGVKRTLMNGIELEDGPIKVDSFRIVDTY-GDITTVEI 190

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR V    L    G
Sbjct: 191 VVHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRVKGNALSALYG 245


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++      + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGKPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+VI G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK
Sbjct: 178 ELTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKK 227


>gi|325132446|gb|EGC55139.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M6190]
          Length = 349

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>gi|291043642|ref|ZP_06569358.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|291012105|gb|EFE04094.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 399

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 144 MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 202

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 203 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 262

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 263 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIREQGGEGA 322

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 323 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 362


>gi|329667453|gb|AEB93401.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 239

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 127/226 (56%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEK-EAL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L+ KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFCKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G       +++    +K     V +
Sbjct: 122 LMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++
Sbjct: 182 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELT 227


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++      + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+VI G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK
Sbjct: 178 ELTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKK 227


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/223 (34%), Positives = 131/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++ G+    +++V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGR 227


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


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

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/224 (35%), Positives = 121/224 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA  G+ASRR+ E +I Q  VKVNGI++    + V S+D +EV+G  ++   +  
Sbjct: 5   RLQKYIADCGVASRRKAEELIQQGSVKVNGIVVSEMGIKVSSSDRVEVNGSVIKPESKKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KP G VTT  D   R TV D L  +  RV  VGRLD  T GLL+LTNDG     +
Sbjct: 65  YILLNKPSGYVTTVKDQFRRPTVIDLLKGVDERVFPVGRLDYETTGLLVLTNDGDFTHKM 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y+    G   +D+++  + G+ I+       ++ + + K     + V + 
Sbjct: 125 THPRHEIEKTYQATIAGTPTKDEIHSFESGLEIEDYVTSPAKLKIISTKERTCVIEVTIH 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           EG+NR+++K+ E     V  L RIS G   LG L  GS RE+++
Sbjct: 185 EGRNRQVRKMCEAIGHPVLALKRISLGKVTLGNLPEGSWRELTR 228


>gi|257869547|ref|ZP_05649200.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257803711|gb|EEV32533.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 238

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 81/232 (34%), Positives = 126/232 (54%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I   RV VNG +++   V V + D +EVDGVP+ + E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEELIVAGRVSVNGQIVKELGVQVSAKDRVEVDGVPIEQ-ESP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+++  +D   R  V D    +  R+  +GRLD +T GLLLLTNDG L++ 
Sbjct: 61  VYYMLYKPRGVISAVTDDKKRKVVLDFFTEVPERLYPIGRLDYDTSGLLLLTNDGDLSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 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|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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/231 (36%), Positives = 125/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+ K E  
Sbjct: 6   ERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPIGK-EAK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 65  RYFLFYKPRGVISAVQDNKGRDVVTDYFKDIAERLYPVGRLDYDTSGLLVMTNDGDLANH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-SNAWVTV 191
           L  P     + Y  +  G  ++  L  LK G+ + G      +V  + T K    A V++
Sbjct: 125 LMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTAIVSL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+
Sbjct: 185 TIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQ 235


>gi|292558985|gb|ADE31986.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 245

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 133/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++      + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELGTVIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRKTVVDLLPTVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+VI G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK
Sbjct: 178 ELTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKK 227


>gi|161870231|ref|YP_001599401.1| pseudouridine synthase [Neisseria meningitidis 053442]
 gi|161595784|gb|ABX73444.1| pseudouridine synthase [Neisseria meningitidis 053442]
          Length = 416

 Score =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 161 MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 219

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 220 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 279

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 280 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 339

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 340 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 379


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 79/220 (35%), Positives = 131/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 144 MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 202

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 203 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 262

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 263 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 322

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  + ++EG+NRE++++FE     V+RL+R+++GP  L
Sbjct: 323 NKWYNIVIKEGRNREVRRIFESQGLTVSRLVRVAFGPIGL 362


>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 =  137 bits (346), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIYEQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 87/217 (40%), Positives = 122/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG      +++
Sbjct: 3   EKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKIQE 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 KG+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVRNLVKGVELEDGLARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFL 219


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 123/228 (53%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGI SRR+ E  I   RVKVNG+++      V S D IEVD VP+ + E + 
Sbjct: 3   RLQKVIAQAGITSRRKAEVYILDGRVKVNGVVVNELGTKVSSKDTIEVDNVPISQ-EGSV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L++KP G+++  SD   R  V D    +  R+  +GRLD NT GLLLLTNDG  +++L
Sbjct: 62  YYLFYKPRGVISAVSDDKKRKVVTDFFTEVSERIYPIGRLDYNTSGLLLLTNDGEFSQLL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  + Y  +  G      L  L +G+  +G  Y   +   ++ DT +   + V +
Sbjct: 122 THPKNEIEKKYVAKVKGVALPHALKPLTRGLKYKGEKYAPAKYDILSTDT-RAETSIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EGKN ++K + E     V +L R  YG   LG L  G  R + KK
Sbjct: 181 TIHEGKNHQVKNMLEAVGLPVQKLKREQYGNLTLGNLKPGEYRPLLKK 228


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTTEQMRSLTEEGVMLEDGLAKVERIYEQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 95  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 153

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 154 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 213

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 214 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 273

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 274 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 313


>gi|330685968|gb|EGG97591.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU121]
          Length = 246

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/223 (34%), Positives = 129/223 (57%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I   +VKVNG ++      V ++D +EV+G+ L + ++ 
Sbjct: 6   ERLQKRIASSGYTSRRKAETLITDGKVKVNGQVVTELGTKVSNSDTVEVEGIKLEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFNKPAQVITSVSDDRGRKVVTDYFKDIETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN-AWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q K  N   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQPAQVKVKNQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V++L RI +GP  +  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVSKLTRIQFGPLDIKGLNAGEGR 227


>gi|302333165|gb|ADL23358.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 245

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 78/223 (34%), Positives = 131/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++ G+    +++V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGR 227


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 83/239 (34%), Positives = 127/239 (53%), Gaps = 6/239 (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  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +  DG P+    R    L +KP G V T SD  GR T  D L   +S 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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              ++     + + L EGKNREI++V + FN  + RL+R+  G  +LGTL AG  R+++
Sbjct: 181 AVNRR----KLRIVLVEGKNREIRRVLDSFNCTIKRLVRVRIGNLELGTLKAGEFRDLT 235


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 125/231 (54%), Gaps = 9/231 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN    E A V   +   D
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNN---EPAHVGQRIQFGD 206

Query: 59  HIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
            ++V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRL
Sbjct: 207 IVKVNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPKLQHGKWQSVGRL 266

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NTEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++      
Sbjct: 267 DLNTEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASF 326

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L
Sbjct: 327 GAVEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMML 377


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 122/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKVQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 KG+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVRNLVKGVELEDGLARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFL 219


>gi|254670545|emb|CBA06380.1| conserved hypothetical protein [Neisseria meningitidis alpha153]
          Length = 349

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 86/229 (37%), Positives = 135/229 (58%), Gaps = 11/229 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + ER+IA+ RV V G      ++ + +  D I VDG P+    R  
Sbjct: 28  LARALSKLGYCSRTQAERLIAEGRVSVGGRKTTDLSLWIDIDRDRITVDGTPVAAEARIY 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GLVTT  DP+GR TVFD L  + +R +S VGRLD  +EGLLL TND  LA+ 
Sbjct: 88  LML-NKPRGLVTTRDDPEGRPTVFDCLGKVDARFMSPVGRLDKASEGLLLFTNDTVLAQR 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----GSNAWV 189
           L  P+T   + Y V+  G  D+     +  G V +G   G+M   +D ++      N+W+
Sbjct: 147 LLDPATHLGKTYHVQVRGLFDEAAARAMMDG-VSEG---GEMLKAIDVRRLRSGDKNSWI 202

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L+EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +S+
Sbjct: 203 EVELQEGRNRQIRRMLDALGFECLRLVRVSIGEIRLGDLPKGASRPLSE 251


>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 =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 88/228 (38%), Positives = 131/228 (57%), Gaps = 4/228 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E MI++ RV+V+G ++    V V   T  I VDG+ ++  E  
Sbjct: 169 RLQKVMASAGVASRRVCEEMISEGRVEVDGKVVTELGVRVDPKTAVIHVDGLRIQLDENM 228

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              +++KP G+V+T  DPDGR  + D + +    R+  VGRLD+ TEGLLLLTNDG LA 
Sbjct: 229 VYMVFNKPKGVVSTMEDPDGRPCISDFVRNTHGERLFHVGRLDVATEGLLLLTNDGELAN 288

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+  G   Q     LK G+ ++ G+   D    +D+  G +  + V
Sbjct: 289 RLTHPSYEVPKTYLVQVRGPFPQGIGAQLKAGVELEDGMASVDSFKLVDSTPG-HVLIEV 347

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+
Sbjct: 348 VLHSGKNRIVRRLFDAVGFPVLRLVRVKVGPIGLGDQRQGSIRNLGKQ 395


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 87/217 (40%), Positives = 122/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG      +++
Sbjct: 3   EKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKIQE 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 KG+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEVTEQKVRNLVKGVELEDGLARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFL 219


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 82/220 (37%), Positives = 126/220 (57%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P R+ K +A +G+ SRRE+E  I    V VNG + +     V   D + V G  + L+
Sbjct: 71  IEPVRLQKALAASGVGSRREMEEWIQNGWVTVNGKVAQ-LGDKVQPEDQVLVKGSVIKLK 129

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
             +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 130 WPDRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 189

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G LA     PS +  R Y VR  G++  D++ LL  +G++++       ++     +G 
Sbjct: 190 SGELANRFAHPSFEVEREYAVRVLGELGMDEMRLLTSEGVMLEDGLARVERIHSQGGEGV 249

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V L+EG+NRE++++FE F   V+RL+R  +GP  L
Sbjct: 250 NKWYNVVLKEGRNREVRRIFEHFGLTVSRLVRTGFGPIGL 289


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 83/229 (36%), Positives = 134/229 (58%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AGIASRR+ E++I + RV VNG ++      V S+  IEVDG+P++K E  
Sbjct: 3   ERLQKLIAQAGIASRRKAEKLITEGRVAVNGKIVTELGTKVESSASIEVDGLPIQK-ESK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLLYKPRGVISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVT 190
           L  P     +VY  +  G +  ++++ LK G+ I G      +V +   + +KG+ + V 
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIHSLKHGVRIDGKKSAPAKVKIISTNREKGT-SIVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EG   ++K++F+     V++L R  Y    L +L AG  RE++++
Sbjct: 181 LTIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTRE 229


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 125/231 (54%), Gaps = 9/231 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN    E A V   +   D
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNN---EPAHVGQRIQFGD 206

Query: 59  HIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
            ++V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRL
Sbjct: 207 IVKVNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPKLQHGKWQSVGRL 266

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NTEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++      
Sbjct: 267 DLNTEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASF 326

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L
Sbjct: 327 GAVEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMML 377


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 88/225 (39%), Positives = 131/225 (58%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AGIASRR+ E +I   +VKVNG+++      V   D I V+GV L+K E+ 
Sbjct: 2   ERLQKTIAKAGIASRRKAEELIVSGKVKVNGVVVTELGTQVSPDDDISVNGVVLKKEEKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  ++++ SD  GR TV   L  +  R+  VGRLD +T G+LLLTNDG  A  
Sbjct: 62  -YYLLNKPRRVISSVSDEKGRETVLAYLSDVRERIYPVGRLDYDTSGILLLTNDGDFANA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT-V 191
           +  PS+   + Y V   G +  D LN L +GI++  G       V L+     N  V  +
Sbjct: 121 MMHPSSHLPKTYEVAVTGVLTDDMLNRLARGIMLSDGKTLPAEVVLLERSTKKNKTVLHI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            ++EG+NRE++++ E+F+ +V RL RI YG   LG L  G  R++
Sbjct: 181 TIQEGRNREVRRMMEYFHCEVTRLNRIGYGFLDLGNLRQGQYRKL 225


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/231 (36%), Positives = 125/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+ K E  
Sbjct: 6   ERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPIGK-EAK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 65  RYFLFYKPRGVISAVQDNKGRDVVTDYFKDITERLYPVGRLDYDTSGLLVMTNDGDLANH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-SNAWVTV 191
           L  P     + Y  +  G  ++  L  LK G+ + G      +V  + T K    A V++
Sbjct: 125 LMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTAIVSL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+
Sbjct: 185 TIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQ 235


>gi|308389478|gb|ADO31798.1| putative pseudouridine synthase [Neisseria meningitidis alpha710]
          Length = 349

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 130/220 (59%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 94  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 152

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT 
Sbjct: 153 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 212

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 213 SGELVQRFTHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 272

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 273 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 312


>gi|298694777|gb|ADI97999.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus ED133]
          Length = 245

 Score =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 78/223 (34%), Positives = 131/223 (58%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++ G+    +++V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIDYGPLNVVGLNAGEGR 227


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 128/226 (56%), Gaps = 5/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E  I + RVKVNG ++      V + D IEVDG+P+ K E  
Sbjct: 2   ERLQKVMAHAGVASRRKCEAFIQEGRVKVNGEVVRELGFKVGANDKIEVDGIPIYKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G++++ SD  GR+ V D    +  RV  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  -YFMFYKPKGVLSSASDDKGRTVVTDYFKDVEQRVYPVGRLDYDTTGLLLLTNDGEFSNL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD---MQVTLDTQKGSNAWVT 190
           +  P     + Y  +  G     ++  L++GIV+ G    +     +++DT KG+   V 
Sbjct: 121 MTHPKHHVEKKYIAKVKGIPTPRQMRQLERGIVLDGKKTSNAIAQILSVDTDKGT-GIVA 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EG N ++K++FE     V +L R  +G   L  L  G  RE+
Sbjct: 180 LTIHEGWNHQVKRMFEAVELPVMKLKREEFGFLTLENLRPGDYREL 225


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 127/227 (55%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMITAGRVKVDGQVVTKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G+V+T  D  GR TV D    I  RV  +GRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYIFYKPRGVVSTADDDKGRKTVVDYFEDIPYRVYPIGRLDYDTSGLLLMTNDGELANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAW-VTV 191
           L  P  +  +VY  +  G +  +++  L KG+ +        +V  L T K  N   V +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPEEIKSLTKGVKLGRFKSAPAKVKVLKTDKRKNTQIVQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSK 228


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 97/277 (35%), Positives = 143/277 (51%), Gaps = 15/277 (5%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           K ++Q      ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   +   D I+
Sbjct: 73  KRVLQPQAETPKLHKVLAQAGMGSRLEMEQLIMEGRISVNN---EPAHIGQRIQFGDQIK 129

Query: 62  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+
Sbjct: 250 EEGGGEGSNLWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLRRGAWMEL 309

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
             + +R      L++ A  ++++      T  R RP 
Sbjct: 310 DDRDIRA-----LMQAAGGSVESSEPGGGTSSRGRPG 341


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 125/231 (54%), Gaps = 9/231 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN    E A V   +   D
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNN---EPAHVGQRIQFGD 206

Query: 59  HIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
            ++V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRL
Sbjct: 207 IVKVNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPKLQHGKWQSVGRL 266

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NTEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++      
Sbjct: 267 DLNTEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLLDGVQLEDGEASF 326

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L
Sbjct: 327 GAVEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMML 377


>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 =  137 bits (345), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/231 (36%), Positives = 125/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+ K E  
Sbjct: 6   ERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPIGK-EAK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 65  RYFLFYKPRGVISAVQDNKGRDVVTDYFKDITERLYPVGRLDYDTSGLLVMTNDGDLANH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-SNAWVTV 191
           L  P     + Y  +  G  ++  L  LK G+ + G      +V  + T K    A V++
Sbjct: 125 LMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTAIVSL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+
Sbjct: 185 TIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQ 235


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 102/257 (39%), Positives = 139/257 (54%), Gaps = 14/257 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK---ILRE- 243
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYLDKKLPRGGWMELDLKEVNYLREL 242

Query: 244 -QLGPH---LLEEAQVN 256
            +L P    LL+E++ N
Sbjct: 243 VELRPERQTLLDESKAN 259


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 127/230 (55%), Gaps = 1/230 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AGI SRR  E ++ Q RVKVNG L        +  D +EVDG PL++A
Sbjct: 1   MTRQRLQKLIAAAGICSRRRAEDLLRQHRVKVNGQLAAIGDQADLDQDDVEVDGRPLQRA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP G++ +  DP  R TV D +P+ +   +  VGRLD  + G LLL+N G 
Sbjct: 61  LVPRVLLLNKPPGVICSCRDPQQRKTVLDLVPAHLRDGLHPVGRLDAESRGALLLSNQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   + +L   ++G+V+ G      +VTL      ++ +
Sbjct: 121 LTLQLTHPRYNHCKTYRVTVAGLPPEKQLRQWRRGVVLDGTVTRPAEVTLLEGTTRSSVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V LREG+NR+I+++      +V  L RI+ G   LG++  G  RE+S++
Sbjct: 181 EVVLREGRNRQIRRIALSLGHRVLDLQRIAIGDLMLGSVAEGCWRELSRQ 230


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 110/303 (36%), Positives = 154/303 (50%), Gaps = 13/303 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG + +           I +DG  V  + +E
Sbjct: 3   EKLQKVLARAGHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTVSGKASE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 ELANRLMHPSRQVEREYLVRVFGEVTEQKVKNLVRGVELEDGMARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK---ILREQ 244
             V + EG+NRE+++++E     V+RL R+ YG   L   L  G  +E+  +    LRE 
Sbjct: 183 FYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWKELDLQEVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  ++LD P  +S    R R   I        R ++ ++   G S Q K   P
Sbjct: 243 VELKPEKETLLDLD-PSNTSRKRERSRSQKIRRA---VRRHEERANAPKGRSNQAKRKKP 298

Query: 305 VHR 307
             R
Sbjct: 299 ATR 301


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/218 (38%), Positives = 124/218 (56%), Gaps = 19/218 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA-- 70
           ++ KV+A AGI SRRE+E +I   RV VNG   E A +   V + D + V+G  + +   
Sbjct: 3   KLHKVLADAGIGSRREMEELIVAGRVSVNG---EPAHIGQRVAANDQVRVNGKLISRPNA 59

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+ LYHKP G + +H DP+GR+ VF  LP +   + +SVGRLD+NTEGLL+ T  G
Sbjct: 60  KKPPRVILYHKPAGEIVSHDDPNGRANVFTRLPKLRTGKWLSVGRLDLNTEGLLIFTTSG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QK 183
            +A  +  P     R Y VR  G++D+ +   L     ++GI   D +    +       
Sbjct: 120 DMANRIMHPRYGTEREYAVRVLGEMDEAQRTSL-----VEGIDLDDGKAAFGSFDYLGGD 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           GSN W  V L+EG+NRE++++FE     V+RLIR  +G
Sbjct: 175 GSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFG 212


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 83/225 (36%), Positives = 124/225 (55%), Gaps = 7/225 (3%)

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
             +L++KP   V T SD   R+ V D       RV  VGRLD +T G L +TNDG  A +
Sbjct: 63  -YYLFYKPEKCVCTMSDEHDRTCVADYFADSNERVYPVGRLDYDTTGALFMTNDGEFANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWV 189
           +  PS+   +VY V   G + + + N L+KGI ++G+    C  ++ +T + ++     +
Sbjct: 122 IMHPSSHLEKVYEVSVKGLLTKAEKNQLEKGIYLEGVKTLPC--EIAITGNDEEHGTTML 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNR+IKK+FE     V RL RI  GP  L  L  G+ R
Sbjct: 180 LIRLVEGKNRQIKKMFEEVGHPVKRLRRIMIGPIDLKGLTPGTYR 224


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 135/236 (57%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 8   ERLQKRIANSGYTSRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKMEQEDKI 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    + +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 68  YI-LFHKPAQVITSVSDDHGRTVVTDYFKDLDTRIYPVGRLDYDTSGVLLLTNDGEFTNL 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+ GI ++ G+     +++    +  +   V +
Sbjct: 127 MTHPRYHIPKTYVAKLKGYLMREEVKTLEAGIELEDGLTQPATVKIKRQDKDKNTTLVEI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQ 244
            + EG+NR+++++FE F   VN+L RI +G   L  L AG  R ++    K+LR Q
Sbjct: 187 TISEGRNRQVRRMFEHFGHSVNKLTRIQFGSLNLKGLNAGEGRVLTPHEVKVLRHQ 242


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 122/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  V ++  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVSVKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIYL 219


>gi|317051704|ref|YP_004112820.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946788|gb|ADU66264.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 251

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 90/243 (37%), Positives = 133/243 (54%), Gaps = 12/243 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG+ASRR+ E  I Q RV VNG ++ E         D + VDG  ++     
Sbjct: 4   RLQKILAQAGVASRRKAEEYIRQGRVMVNGKVVTELGTQADPDEDFVAVDGKRIQIFHNH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + HKP G +T+ SD   R  V D LP+I   +I VGRLD +T GLLLLTNDG LA V
Sbjct: 64  AYIILHKPTGYITSRSDDKERPVVMDLLPNIREPLIPVGRLDWDTSGLLLLTNDGDLAYV 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGS---NAWV 189
           L  P+    + Y VR    +  + + + +KGI+++       +V  ++T K +   N W 
Sbjct: 124 LTHPAFHVAKTYLVRLDKPMTAEHMQVFEKGILLEDGKTKPARVRRVNTGKQTATPNLWY 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-------EVSKKILR 242
            V + EG+NR+I+K+FE   + V +L R+S G   LG +  G  R       E  +K+ R
Sbjct: 184 EVTITEGRNRQIRKMFEALKYDVRKLKRVSLGEILLGGVGVGKYRRAEAWEIEYFEKLKR 243

Query: 243 EQL 245
           E+L
Sbjct: 244 EKL 246


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 94/234 (40%), Positives = 132/234 (56%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR---EVSKKILRE 243
           L EG+NR+++++ +     V  L RI YG   +  L  G  R   E  ++ILR+
Sbjct: 183 LHEGRNRQVRRMCKAVGHPVLELTRIQYGNLTIDGLAPGEIRPLTEEEERILRQ 236


>gi|226941109|ref|YP_002796183.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226716036|gb|ACO75174.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 703

 Score =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 79/213 (37%), Positives = 126/213 (59%), Gaps = 7/213 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAER 72
           R+ K +A AG+ SRR+++ ++A  RV +NG + E  A  V   D + VD  P  +R  +R
Sbjct: 454 RLQKALALAGLGSRRDMDELVAAGRVSINGAVAELGA-RVRPGDKVRVDSKPVLIRWPDR 512

Query: 73  -TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
             R+ +YHK  G + T  DP+GR+TVFD LP    S+ +++GRLD+NT GLL+ T  G L
Sbjct: 513 LPRVIVYHKQEGEIVTRDDPEGRTTVFDRLPQTRSSKWVAIGRLDVNTSGLLIFTTSGDL 572

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAW 188
           A  +  PS +  R Y VR  G++  +++     G+ +      +  ++   D +   N W
Sbjct: 573 ANRMTHPSFEVEREYAVRVLGKLTPEQMKETTAGVQLDDGPASFQFIREDDDKEDSVNHW 632

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             VG+REG+NRE++++FE F   V+RL+R+ +G
Sbjct: 633 YRVGIREGRNREVRRMFEHFGLTVSRLMRVRFG 665


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 88/222 (39%), Positives = 131/222 (59%), Gaps = 8/222 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL---ERAA-VNVMSTD-HIEVDGVPLR 68
           +++ KV+ARAG+ SRR++E +I + RV V+G ++   ER   V V+  D HI  +  P  
Sbjct: 3   EKLQKVLARAGLGSRRKMEVVIQEGRVSVDGKVVGLGERVTDVQVIRVDGHIVKNLTP-- 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           +    R+  Y+KP G + T SD +GR+TVF+ LPS+  +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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           W  V L EG+ RE+++++E    +V+RL+R+ YG   L   L
Sbjct: 181 WFHVVLTEGRTREVRRLWESQGLQVSRLMRVRYGNITLSKQL 222


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 88/217 (40%), Positives = 121/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYL 219


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 129/228 (56%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ + E  
Sbjct: 4   ERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIER-ESH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  HTYLFYKPRGVISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQ-KGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  LKKG+ I        QV  L T  +     V +
Sbjct: 123 LMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPAQVKVLKTNPRAQTQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG   ++K++F+  N  V++L R  Y    L  L +G  RE+++K
Sbjct: 183 TIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNRK 230


>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 =  137 bits (344), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 86/217 (39%), Positives = 123/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+ARAG+ SRRE+E MI   RV VNG++ +           I VDG    V    
Sbjct: 3   EKLQKVLARAGLGSRREIESMIQAGRVSVNGVVAKLGDRLEDLNAAIRVDGHHVSVSASS 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
            +  R+  Y+KP G + T SDP+GR TVFD LP +  +R ++VGRLD NT GLLL T DG
Sbjct: 63  EQVCRVLAYNKPEGELCTRSDPEGRRTVFDRLPRLNGARWVAVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G+V++  +  L +G+ ++        V     +G+N  
Sbjct: 123 ELANRLMHPSRQVQREYMVRVFGEVNEQMVKNLVRGVELEDGEARFEDVVYAGGEGANHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVVITEGRNREVRRLWETQGVTVSRLKRVRYGDIYL 219


>gi|297570484|ref|YP_003691828.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
 gi|296926399|gb|ADH87209.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
          Length = 240

 Score =  137 bits (344), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 83/229 (36%), Positives = 130/229 (56%), Gaps = 1/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+ R+++K+F   N  V +L R++YG  +LG+L  G  R +S + L
Sbjct: 183 IHEGRKRQVRKMFAAINHPVLQLKRVAYGGLRLGSLPTGRYRRLSPEDL 231


>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 =  137 bits (344), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 87/217 (40%), Positives = 128/217 (58%), Gaps = 14/217 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG   RK +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDG---RKVQFQ 58

Query: 72  -----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
                R R+ +Y+KP G + + +DP+ R TVFD+LP+I + R + VGRLDIN+ GLLL T
Sbjct: 59  IEDEIRRRVLIYYKPEGEICSRNDPESRPTVFDHLPTIANDRWVMVGRLDINSTGLLLFT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           NDG LA  L  PS +  R Y VR  G+V  Q + N+L  G+V+          +     G
Sbjct: 119 NDGELANRLMHPSNEIEREYAVRVMGEVTPQIRQNML-NGVVLDDGPAKFESFSEIGGDG 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            N W  V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 178 INRWYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  137 bits (344), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 122/217 (56%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  V ++  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVSVKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIYL 219


>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 =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 134/234 (57%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV++  G+ASRR  E+MI   RV+VNG+++      V    D I VDG  L + + 
Sbjct: 2   ERLQKVMSNCGVASRRASEQMILDGRVRVNGVIVRELGTKVKPEQDIILVDGRRL-EIQP 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L++KP G++TT SD  GR TV D    I  R+ ++GRLD NTEGLLL+TNDG LA 
Sbjct: 61  KHYYLFNKPKGVITTCSDEQGRPTVLDYFKRIKDRIYAIGRLDQNTEGLLLMTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICY-GDM-QVTLDTQKGSNAWV 189
           +L  P     + Y V+  G +    L  L  G+++  G+    D+  V  DT  G  + +
Sbjct: 121 ILMHPGHMVDKTYEVKIKGHIADAVLQQLADGVLLSDGMTAPADVYYVGYDTHTGITS-L 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + EGKNR+++++ E F ++V+ L R+ Y    L  +  G+ R ++++ + E
Sbjct: 180 EITIHEGKNRQVRRMMEHFGYQVHNLRRVQYAFLTLSGVKRGAYRALTREEVME 233


>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 =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 128/227 (56%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +A AG+ASRR+ E++I Q RVKVNG ++      +    D +EVDG  + K E+
Sbjct: 2   ERLQKYMAHAGVASRRKSEKIITQGRVKVNGKIVTELGTKIDPDKDIVEVDGRVISK-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G +T+ SDP GR TV   +  +  R+  VGRLD +T GLL+LTNDG L  
Sbjct: 61  YVYILLNKPVGYITSVSDPHGRKTVTGLIKGVSQRIYPVGRLDYDTSGLLILTNDGELTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  PS    + YRV   G    + L  L+ G+ ++       +V+   +K  N    + 
Sbjct: 121 VLTHPSHMVEKTYRVEVKGFPSDEVLKKLETGVKLKDGLTAPARVSAVKRKEKNTIFNLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+NR+++++ +   + V  L RI++GP  L  L  G  R +++K
Sbjct: 181 IHEGRNRQVRRMCDKIGFPVVNLKRIAFGPLNLKGLKTGQYRFLTEK 227


>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 =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 126/230 (54%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR  E +I   RVKVNG ++      V    D +  D   L+     
Sbjct: 2   RLQKYLAHAGVASRRTSEELILNGRVKVNGEVVTELGYKVDPLKDKVYFDDKKLKLVREY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KPIG+V+T  D   R TV D +P+   R+  +GRLDI+T GLL+LTNDG LA  
Sbjct: 62  TYVMINKPIGIVSTAKDEKNRKTVVDLVPN-DERIYPIGRLDIDTTGLLILTNDGELANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY     G   +  L+ L+ GI I G      ++ +     S++ V V +
Sbjct: 121 LMHPRKEIDKVYIATVEGTPSKSGLDKLRNGITIDGYKLSKSEIKILKSYESDSIVRVTI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EG+NR++KK+FE     V +L RIS+GP +L  L  G+ R ++ + ++E
Sbjct: 181 HEGRNRQVKKMFERIGNPVKKLKRISFGPIELANLEIGAYRYLTNEEIKE 230


>gi|315646387|ref|ZP_07899505.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315278030|gb|EFU41350.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 251

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 130/227 (57%), Gaps = 4/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I + +V+VNG  + E       + D I V G P++  ++
Sbjct: 2   ERLQKIMAQAGVASRRKCEELILEGKVQVNGETVTELGTKADPAQDMITVSGKPIKHEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L +KP G++T+ SDP+GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  A 
Sbjct: 62  VYVML-NKPKGVITSASDPEGRKIVSDYLKGIKERVYPIGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y     G     +L+ L++GI+++       +V        N  + ++
Sbjct: 121 LLSHPKYHVPKTYLATVKGVPHGTELDKLRQGIMLEDGMTSPAEVEYKDVDPDNKQSVIS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE  +  V RL RISYG   L  L  G  R ++
Sbjct: 181 ITIHEGRNRQVRRMFEAISHPVLRLKRISYGDLLLQNLKRGLYRHLT 227


>gi|88859932|ref|ZP_01134571.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88817926|gb|EAR27742.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 293

 Score =  136 bits (343), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 89/221 (40%), Positives = 128/221 (57%), Gaps = 6/221 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E+ I   RV V+G +  R    V     I +DG  V + + E
Sbjct: 3   EKLQKVLARAGKGSRREIEKFIEAHRVSVDGNVA-RLGDRVEPHQLIRLDGHIVKIEEPE 61

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+ +YHKP G + T  DP+GR TVFD L  +   R I+VGRLD+NT GLLL TNDG
Sbjct: 62  ERVCRVLMYHKPEGELCTRKDPEGRPTVFDRLMRLDDDRWIAVGRLDVNTSGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  R Y VR  G+V  + L  L KG+ ++      +++     +G N W
Sbjct: 122 ELANRLMHPRYEVEREYAVRVFGEVTTETLKTLTKGVELEDGPAKFLKIMPHGGEGINKW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V L EG+NRE++++++    +V+RLIR+ YG  +L   L
Sbjct: 182 YNVLLTEGRNREVRRLWQSQGVEVSRLIRVRYGDLELNKRL 222


>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 =  136 bits (343), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 80/224 (35%), Positives = 129/224 (57%), Gaps = 10/224 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           +++  ++  P ++ KV+A AG+ SRR++E +I   RV VNG   E A +   +++ D + 
Sbjct: 198 RDLTADDDAP-KLHKVLAEAGLGSRRDMEELIISGRVSVNG---EPAHIGQRILAQDQVR 253

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G  +++    +  R+ +YHKP G + +H DPDGR +VF+ LP++   + ++VGRLD N
Sbjct: 254 INGKLIQRRVSKKPPRVLVYHKPAGEIVSHDDPDGRPSVFERLPNMKAGKWLAVGRLDFN 313

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T  G LA  L  P     R Y VR  G++++     L  G+ +        +V
Sbjct: 314 TEGLLLFTTSGDLANRLMHPRYNIDREYAVRTLGELEEGMRQKLLAGVELDDGVAQFSRV 373

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                +G N W  V + EG+NRE++++FE     V+RLIR  YG
Sbjct: 374 ADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYG 417


>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 =  136 bits (343), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 125/225 (55%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN-AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V  + T K  N   V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG   ++K +F+  N  V++L R  Y    L +L++G  RE++
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVDKLSRERYAFLTLKSLISGEYRELT 227


>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 =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 135/236 (57%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKMEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    + +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YI-LFHKPAQVITSVSDDRGRTVVTDYFKDLDTRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+ GI ++ G+     +++    +  +   V +
Sbjct: 125 MTHPRYHIPKTYVAKLKGYLMREEVKALEAGIELEDGLTQPATVKIKRQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQ 244
            + EG+NR+++++FE F   VN+L RI +G   L  L AG  R ++    K+LR Q
Sbjct: 185 TISEGRNRQVRRMFEHFGHSVNKLTRIQFGSLNLKGLNAGEGRVLTPHEVKVLRHQ 240


>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 =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 89/235 (37%), Positives = 126/235 (53%), Gaps = 1/235 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR 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|324018876|gb|EGB88095.1| hypothetical protein HMPREF9542_02380 [Escherichia coli MS 117-3]
          Length = 277

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 84/206 (40%), Positives = 119/206 (57%), Gaps = 6/206 (2%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKAER--TRLWLYHK 80
           A RRE+E +I   RV V+G + +    V V     I +DG  + +R++     R+  Y+K
Sbjct: 2   APRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYK 61

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           P G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T DG LA  L  PS 
Sbjct: 62  PEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSR 121

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +  R Y VR  GQVD  KL  L +G+ ++        +     +G N W  V L EG+NR
Sbjct: 122 EVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNR 181

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL 225
           E+++++E    +V+RLIR+ YG   L
Sbjct: 182 EVRRLWEAVGVQVSRLIRVRYGDIPL 207


>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 =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 134/229 (58%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AG+ASRR+ E+MI + RV VNG ++      V  + +IEVDG+P++K E  
Sbjct: 3   ERLQKLIAQAGVASRRKAEKMITEGRVAVNGRIVTELGTKVEPSANIEVDGLPIQK-ESK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLLYKPRGVISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVT 190
           L  P     +VY  +  G +  ++++ LK G+ I G      +V +   + +KG+ + V 
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIHSLKHGVRIDGKKSAPAKVKIISTNREKGT-SIVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EG   ++K++F+     V++L R  Y    L +L AG  RE++++
Sbjct: 181 LTIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTRE 229


>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 =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 84/217 (38%), Positives = 120/217 (55%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   V   D ++V+G P+R    
Sbjct: 150 KLHKVLAQAGLGSRLEMEQLILEGRISVNN---EPAHIGQRVQYGDQVKVNGRPIRYRID 206

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL T+ G
Sbjct: 207 PPAPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLAHGKWQSVGRLDLNTEGLLLFTSAG 266

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +  ++   L  G+ ++        +     +GSN W
Sbjct: 267 ELANKLMHPRFGLEREYAVRVLGALSNEEKQRLLDGVQLEDGMAAFGSIEDGGGEGSNCW 326

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE++++ E     V+RLIRI YG   L
Sbjct: 327 YRVTISEGRNREVRRMLESVGHAVSRLIRIRYGSMML 363


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 88/217 (40%), Positives = 120/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYL 219


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 84/228 (36%), Positives = 128/228 (56%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ + E  
Sbjct: 4   ERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIER-ESH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  HTYLFYKPRGVISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQ-KGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  LKKG+ I        QV  L T  +     V +
Sbjct: 123 LMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPAQVKVLKTNPRAQTQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG   ++K++F+  N  V++L R  Y    L  L +G  RE++ K
Sbjct: 183 TIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNHK 230


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 121/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHIVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 ELANRLMHPSRQVEREYLVRVFGEVNEKKVRNLVSGVELEDGMARFEDVVHAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQECTVSRLKRVRYGDIFL 219


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 87/226 (38%), Positives = 126/226 (55%), Gaps = 6/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K ++RAGIASRR+ E +I Q RV VNG ++ R    +   TD ++VDG P+ + E  
Sbjct: 2   RLQKFMSRAGIASRRKSEELIQQGRVTVNGQVITRLGTKINPDTDTVKVDGEPITQEESN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP   +T+  DP GR TV D L  +  RV  VGRLD ++ GL+LLTNDG LA  
Sbjct: 62  VYIMLNKPKDYITSKDDPQGRKTVMD-LIQVKERVYPVGRLDYDSRGLVLLTNDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y V+      QDKL+ L  GI + +G+C  D    LDT+   N  + + 
Sbjct: 121 LMHPKYNIPKTYMVKVDKLPLQDKLDNLVNGIYLEEGLCKADHVEILDTK---NNILKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EG+ R+I+++      +V  L R S G   L  L  G+ R+++K
Sbjct: 178 LSEGRKRQIRRMLASLGIEVKDLKRDSLGTLTLKDLSEGNYRKLTK 223


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I +  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 28  RINKYIAHAGVASRRKAEELIKRGLVTLNGQVVTDLATTVKSGDLVEIEGSPIYNEEKV- 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 87  YYLLNKPRGVISSVSDDKGRQTVIDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDKM 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G V ++ L  L +G+VI G       Y  ++V  D  +   + V
Sbjct: 147 IHPRNEIDKVYLARVKGVVTKESLRPLTRGVVIDGKKTKPARYRIIRVEPDKNR---SIV 203

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG++ ++KK+FE     V++L R  +G   +  L  G  R +SKK
Sbjct: 204 ELTIHEGRHHQVKKMFEAVGHLVDKLSRTQFGSLDVRGLKPGEARRLSKK 253


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 119/217 (54%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVAINEGRNREVRRLWESQETTVSRLKRVRYGDIYL 219


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 84/217 (38%), Positives = 120/217 (55%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   V   D ++V+G P+R    
Sbjct: 152 KLHKVLAQAGLGSRLEMEQLILEGRISVNN---EPAHIGQRVQYGDQVKVNGRPIRYRID 208

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL T+ G
Sbjct: 209 PPAPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLAHGKWQSVGRLDLNTEGLLLFTSAG 268

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +  ++   L  G+ ++        +     +GSN W
Sbjct: 269 ELANKLMHPRFGLEREYAVRVLGALSNEEKQRLLDGVQLEDGMAAFGSIEDGGGEGSNCW 328

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE++++ E     V+RLIRI YG   L
Sbjct: 329 YRVTISEGRNREVRRMLESVGHAVSRLIRIRYGSMML 365


>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 =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 80/223 (35%), Positives = 132/223 (59%), Gaps = 4/223 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLY 78
           ++  G+ASRR  E MIA  RV+VNG++++   V V +  D I VDG  L K  + + +L+
Sbjct: 1   MSNCGVASRRASEEMIAAGRVRVNGVIVKTPGVKVDLQKDIIVVDGKRLEKPAK-QYYLF 59

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G++TT  D   R+TV D   ++  R+  VGRLD NTEGLL++TNDG LA +L  PS
Sbjct: 60  NKPKGVLTTVKDDRERNTVMDYFKNVKDRIYPVGRLDQNTEGLLIMTNDGALANILMHPS 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-AWVTVGLREG 196
               + Y VR  G++    L  L +G+ ++ G+    + V +     +N   V + + EG
Sbjct: 120 KLVDKTYNVRIKGRITDAVLEKLAQGVPLKDGMTAPAVVVYVGYDGATNITEVEITIHEG 179

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +NR+++++FE+F ++V+ L R  Y    L  +  G+ R ++++
Sbjct: 180 RNRQVRRMFEYFGFQVHNLRRTQYAFLTLSGVKRGAYRRLTRE 222


>gi|317057433|ref|YP_004105900.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315449702|gb|ADU23266.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 244

 Score =  136 bits (342), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 88/231 (38%), Positives = 123/231 (53%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+I+ +G  SRR+ E  IA  +V VNG         +   D I VDG+ + +  +  
Sbjct: 5   RIQKIISESGFCSRRKAEEFIAAGKVTVNGRPCTLGDKALPGKDLIVVDGIKIDQPRKRT 64

Query: 75  LW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L+  + HKP G VTT +D   R  V D L  +  RV  VGRLD N+EGLLLLTNDG  A 
Sbjct: 65  LYYIMLHKPRGYVTTMNDELDRKCVTDLLTGLPERVYPVGRLDKNSEGLLLLTNDGAFAN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTV 191
            +  PS    + YRV     ++ ++L  L  G+ I G    +  VT LD Q G    + +
Sbjct: 125 DIMHPSKHVNKTYRVTVRPDINDEQLVKLASGVEIDGRMTSECSVTVLDKQPG-RVVLQM 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+I+K+ E    +V RL R + GP +LG L  G  RE+    LR
Sbjct: 184 TIHEGRNRQIRKMCEAVGLEVARLKRTAIGPLRLGMLKPGEYRELKPDELR 234


>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 =  135 bits (341), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 80/218 (36%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+ A
Sbjct: 3   PERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQLGD-KVTPDDHVTVKGSIIKLKWA 61

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 62  DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N 
Sbjct: 122 ELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+NRE++++FE     V+RL+RI +GP  L
Sbjct: 182 WYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGL 219


>gi|312277674|gb|ADQ62331.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 255

 Score =  135 bits (341), Expect = 6e-30,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV+G P+   E+  
Sbjct: 16  RINKYIAHAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIVEVNGSPIYNEEKV- 74

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 75  YYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 134

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+VI G       Y  ++V  D +K + + V
Sbjct: 135 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTQPAHYNIIKV--DHEK-NRSVV 191

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G +R +SKK
Sbjct: 192 ELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLSKK 241


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 88/217 (40%), Positives = 120/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++             + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVARLGERLEDENAVVRIDGHIVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVAINEGRNREVRRLWESQDTTVSRLKRVRYGDIYL 219


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 84/224 (37%), Positives = 131/224 (58%), Gaps = 5/224 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KVIA+AGIASRR+ E++I + +VKVNG +++   + V  + D IEV+GVP+ K E 
Sbjct: 2   ERLQKVIAQAGIASRRKAEQLILEGKVKVNGQVVKELGIKVNPNQDDIEVEGVPVEKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY KP G++++  D  GR  V D L  I  RV  VGRLD +T GLLLLTNDG  A 
Sbjct: 62  VYFLLY-KPTGVISSVKDDKGRKVVTDFL-EIEQRVYPVGRLDYDTSGLLLLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           +L  P  +  +VY  +  G   +D+L LL +G+ ++       +V + +  ++   A V 
Sbjct: 120 LLMHPRHKIEKVYVAKVKGIPTRDQLKLLARGVKLEDGPTAPAKVKMLSVDRRKQTAIVK 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG+NR+++++FE    +V +L R  +    L  +  G  R
Sbjct: 180 LTIHEGRNRQVRRMFETIGCEVMKLKREQFAFLDLSGMNPGDVR 223


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 83/229 (36%), Positives = 133/229 (58%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AGIASRR+ E+MI + RV VNG ++      V  + +IEVDG+P++K E  
Sbjct: 3   ERLQKLIAQAGIASRRKAEKMITEGRVAVNGRIVTELGTKVEPSANIEVDGLPIQK-ESK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLLYKPRGVISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVT 190
           L  P     +VY  +  G +  +++  LK G+ I G      +V +   + +KG+ + V 
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIYSLKHGVRIDGKKSAPAKVKIISTNREKGT-SIVQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EG   ++K++F+     V++L R  Y    L +L AG  RE++++
Sbjct: 181 LTIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTRE 229


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN-AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V  + T K  N   V + 
Sbjct: 123 MHPKNEIEKVYVAKIRGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELT 227


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGDLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN-AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V  + T K  N   V + 
Sbjct: 123 MHPKNEIEKVYVAKIRGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELT 227


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN-AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V  + T K  N   V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELT 227


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 134/237 (56%), Gaps = 7/237 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T  R++K IA AGIASRR  + ++ + +VKVNG L +   + V    D +EV+G  ++  
Sbjct: 5   TTIRLNKYIASAGIASRRGADELVQKGKVKVNGELADSPGIQVDPDNDRVEVNGKLVQHD 64

Query: 71  ERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTN 126
           E+++    L HK I  VTT  DP GR TV D LP   I  RV  VGRLD  +EG+LLLT 
Sbjct: 65  EKSKDLYILLHKTIETVTTAKDPQGRKTVLDLLPPDVINRRVFPVGRLDFYSEGMLLLTT 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKG 184
           DG L   +  P     ++Y V   G++ + +L++++ G+ ++  G     +++   ++ G
Sbjct: 125 DGELCNRMTHPKWHLPKIYHVTIRGKLSEKELSVMQNGMYLEDKGELLAPVKIKAISEVG 184

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 + LR+G NR+I+++F  F+  + RL R+  G  +LG L  G  RE+S K L
Sbjct: 185 ETTKYEMELRQGINRQIRRMFGEFDKTILRLKRVRQGRIELGALKPGKWRELSAKEL 241


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 130/228 (57%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKEGRVTLNGKTVTELATIVKNGDTVEVNGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDEKDRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   V +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIVKVDHEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKK 227


>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 =  135 bits (341), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 118/228 (51%), Gaps = 1/228 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            TP+R+ KV+ARAG+ SRR  E  IA  RV V+G  +    + V      I  DG PLR 
Sbjct: 1   MTPERLQKVLARAGVGSRRRAEEFIAAGRVTVDGRRVTEMGLRVDPEKQAITFDGRPLRL 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L +KP G VTT +DP GR  V   L     R+  VGRLD +TEG LLLTNDG 
Sbjct: 61  PENKVTVLLNKPAGYVTTMADPQGRPMVGSLLKEPGLRLFPVGRLDFDTEGALLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  R Y+    G      L  L++GI ++G       V    ++G    +
Sbjct: 121 LAHRLLHPSFEIKRTYQATVEGTPGAQALRALRQGIELEGRRTHPAMVKTLRRRGEQTVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+ R+++K+       V  L R++YG  +LG L  GS R ++
Sbjct: 181 EIIIHEGRKRQVRKMLAAVGHPVLHLKRVAYGDLRLGRLPLGSYRRLN 228


>gi|121535833|ref|ZP_01667633.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121305605|gb|EAX46547.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 241

 Score =  135 bits (341), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 89/229 (38%), Positives = 125/229 (54%), Gaps = 6/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P+R+ K++++AGIASRR  E++I   RV VNG I+ E  A      D + VDG P+  AE
Sbjct: 2   PERLQKILSQAGIASRRAAEKLILDGRVAVNGKIITELGAKVDWPRDRVTVDGKPI-AAE 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L +KP G++T+  DP GR TV D L  +  RV  VGRLD NTEGLLLLTNDG L 
Sbjct: 61  APVYILLNKPKGVITSLKDPRGRKTVIDLLKDVPERVYPVGRLDYNTEGLLLLTNDGDLT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAW 188
             L  PS +  + Y  +  G  ++++L+ L+ GI +         V L   D  K   A 
Sbjct: 121 HALTHPSHEIKKTYVSKIAGLPNEEQLDRLRAGIKLSDGMTSPAAVRLLDFDPVK-QVAV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V + + EG+NR+++++FE     V  L R  Y    L  L  G  R ++
Sbjct: 180 VEITIHEGRNRQVRRMFEAIGHPVKSLKRTKYAFLTLTGLKRGEYRRLT 228


>gi|283769102|ref|ZP_06342007.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283104288|gb|EFC05666.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 242

 Score =  135 bits (341), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 86/227 (37%), Positives = 135/227 (59%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KVIA+AGIASRR+ E +IAQ +VKVNG +++   V V   D I V+G  ++K E+ 
Sbjct: 2   QRLQKVIAQAGIASRRKAEELIAQGKVKVNGKVVKEMGVQVSFDDEIMVNGQSIQKEEKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  +++T  D   R+T+ D    +  R+  VGRLD  T GLLL+TNDG  A  
Sbjct: 62  -YFLLNKPKKMISTVHDDLKRATIMDCFRDVKQRIFPVGRLDYETTGLLLVTNDGEFANA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  PS    ++Y V  +G ++   L  LKKGI ++ G+     ++V   ++K +   + +
Sbjct: 121 MMHPSHHMDKIYEVYVNGYLEDHMLTKLKKGIPLEDGMTLPASVEVLERSRKTNKTRIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            ++EGKNRE++++  +F ++V+ L RI Y    LG L  G  R + K
Sbjct: 181 TIQEGKNREVRRMMAYFGFEVHTLQRIGYSFLNLGNLRQGEYRRLKK 227


>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 =  135 bits (341), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 86/228 (37%), Positives = 118/228 (51%), Gaps = 1/228 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            TP+R+ KV+ARAG+ SRR  E  IA  RV V+G  +    + V      I  DG PLR 
Sbjct: 1   MTPERLQKVLARAGVGSRRRAEEFIAAGRVTVDGRRVTEMGLRVDPEKQAITFDGRPLRF 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L +KP G VTT +DP GR  V   L     R+  VGRLD +TEG LLLTNDG 
Sbjct: 61  PENKVTVLLNKPAGYVTTMADPQGRPMVGSLLKEPGLRLFPVGRLDFDTEGALLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  R Y+    G      L  L++GI ++G       V    ++G    +
Sbjct: 121 LAHRLLHPSFEIKRTYQATVEGTPGAQALRALRQGIELEGRRTHPAMVKTLRRRGEQTVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+ R+++K+       V  L R++YG  +LG L  GS R ++
Sbjct: 181 EIIIHEGRKRQVRKMLAAVGHPVLHLKRVAYGDLRLGRLPLGSYRRLN 228


>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 =  135 bits (340), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 123/226 (54%), Gaps = 3/226 (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 KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAVKDDKGRKVVTDFFTEVEERIYPIGRLDYDTSGLLLLTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++G+ ++       +V L +  +K   + V +
Sbjct: 121 LMHPKYEINKTYVAKLKGIPLKENLKKLERGVRLEDGKTAPAKVKLLSLDKKKQTSIVQI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLNLAGLKTGEKRELT 226


>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 =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 79/224 (35%), Positives = 130/224 (58%), Gaps = 5/224 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I +  V+VNG ++++    V + D IEVDGVPL++ E+ 
Sbjct: 4   ERLQKVMAEAGVASRRKSEKLITEGHVRVNGKVIKQLGTKVTAHDKIEVDGVPLQR-EKM 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++T+ SD   R TV D  P +  R+  VGRLD +T G +L+TNDG LA  
Sbjct: 63  VYFLLNKPRGVITSVSDDKKRKTVMDFFPDVVERIYPVGRLDYDTSGAVLMTNDGTLANG 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  ++ + Y  +  G V+   L  L+ G+VI        +   ++ D +K + + V+
Sbjct: 123 LTHPKFKFEKTYTAKVKGIVNSLDLKKLENGLVIDHKKTAKAKAHLISTDDEKKT-SIVS 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG+N ++K +F      V +L R SY    +  + +G  R
Sbjct: 182 LTIHEGRNHQVKNMFMAVGHPVQKLRRDSYSFLNIDGVQSGKWR 225


>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 =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 96/248 (38%), Positives = 134/248 (54%), Gaps = 8/248 (3%)

Query: 3   DKNIVQENFTPQ-----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           D++ V E  T +     R+ KV+A+AG+ASRR  E MI   RV V+G ++ R    V   
Sbjct: 368 DRDYVDERDTTEVPDGVRLQKVLAQAGVASRRACEDMIGDGRVTVDGQVVRRFGARVDPA 427

Query: 58  DH-IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
              I VDG  L           +KPIG+V+T SDPDGR ++ D +     R+  VGRLD 
Sbjct: 428 KQVIHVDGKRLPTMPDLVYLAINKPIGVVSTMSDPDGRPSLADFVADRTERLFHVGRLDT 487

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM 175
            TEGL+LLTNDG LA  L  PS    + Y  +  G++++D    LKKGI ++ GI   D 
Sbjct: 488 ETEGLILLTNDGELANRLTHPSYGVQKKYWAKVPGRIERDLGRRLKKGIELEDGIAKAD- 546

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             TL  + G  A V V L EG+   ++++ E     V  L RI +GP +LG L  G+ R 
Sbjct: 547 SFTLVQEHGQQALVEVVLHEGRKHIVRRMLEEVGHPVIDLARIEFGPVKLGRLKPGTVRA 606

Query: 236 VSKKILRE 243
           ++ K + E
Sbjct: 607 LTVKEVGE 614


>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 =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 89/217 (41%), Positives = 120/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E  +  V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIFL 219


>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 =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 87/225 (38%), Positives = 123/225 (54%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR  E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRNAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN-AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V  + T K  N   V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELT 227


>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 =  135 bits (340), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 90/235 (38%), Positives = 130/235 (55%), Gaps = 27/235 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RAAVNVMSTDHIEVDG 64
           +R+ K +A+ G+ SRR++E  I   ++ VNG + +         R  ++  + D  +VD 
Sbjct: 3   ERIQKRLAQLGMGSRRQIEHWIRDGKITVNGKVAQLGDTLEWSDRVTLDGKAIDLEQVDT 62

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
           +P        + LYHKP G V T SDP GR+TVF+ LP + + R ISVGRLD+NT GLLL
Sbjct: 63  IP------KEVLLYHKPEGEVCTRSDPQGRTTVFERLPRLRAGRWISVGRLDVNTAGLLL 116

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQ 176
            T DG LA  L  PS +  R Y VR  G V  + LN L +G+ ++        I  GD +
Sbjct: 117 FTTDGELANRLMHPSREIDREYAVRVLGDVSDEMLNQLVEGVQLEDGAAKFSEIVIGDHE 176

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW-KVNRLIRISYGPFQLGTLLA 230
              D    +N W  V L+EG+NRE+++++E F+   V+RL R+ Y    L   LA
Sbjct: 177 YDSDR---ANRWYYVCLQEGRNREVRRLWESFSGVTVSRLKRVRYANIFLPKTLA 228


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 91/236 (38%), Positives = 125/236 (52%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+A AG+ASRR  E++IA  RV V+G+ +  A V V   T  I VDG  +     
Sbjct: 78  QRLQKVLAHAGVASRRACEQLIADGRVSVDGVTVTEAGVRVDPLTQEIRVDGSRILTNPE 137

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSRVISVGRLDINTEGLL 122
               + HKP G+VTT  DP+GR TV             LP    R++ VGRLD  TEGLL
Sbjct: 138 LITLMLHKPAGVVTTMEDPEGRPTVAQYGRDYLTEHPELPDSL-RLVHVGRLDTETEGLL 196

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT 181
           LL+NDG L+  L  PS +  + Y     GQV+      L++GI ++ G    D +VT+  
Sbjct: 197 LLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEPWVPRKLRRGIELEDGEAKAD-RVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                + V + L  GKNR ++++ +     V RL R   GP +LG L  G TR +S
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLRPGQTRPLS 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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 92/220 (41%), Positives = 125/220 (56%), Gaps = 11/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV VNG   IL ER       T  + +DG  V  +
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAILGERLE---DETAVVRIDGHAVSAK 59

Query: 69  KAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
             E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL T
Sbjct: 60  APEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS Q  R Y VR  G+++++K+  L +G+ ++        V     +G 
Sbjct: 120 TDGELANRLMHPSRQVEREYLVRVFGEINEEKIRNLVRGVQLEDGMARFEDVMYAGGEGM 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N    V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 180 NHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL 219


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATIIKTGDQVEVEGTPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR+TV D L  +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRTTVVDLLSQVPERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V ++  +   + V
Sbjct: 121 IHPRNEIDKVYVARVKGIANKENLRPLTRGVTIDGKKTKPATYEILKVDVEKNR---SVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKK 227


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/204 (41%), Positives = 115/204 (56%), Gaps = 6/204 (2%)

Query: 28  RREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLRKAERTRLWLYHKPI 82
           RRE+E  I   RV V+G I      V ++    I +DG    V     +  R+  Y+KP 
Sbjct: 9   RREIEAKIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKESAEQICRVLAYYKPE 68

Query: 83  GLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T DG LA  L  PS + 
Sbjct: 69  GELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            R Y VR  GQVD DKL  L +G+ ++        +     +G N W  V L EG+NRE+
Sbjct: 129 EREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGINQWYNVTLTEGRNREV 188

Query: 202 KKVFEFFNWKVNRLIRISYGPFQL 225
           ++++E    +V+RLIR+ YG   L
Sbjct: 189 RRLWEAVGVQVSRLIRVRYGDILL 212


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMIVAGRVKVDGKVVTKLGTKVETFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTADDDKGRKTVVDYFEDVPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVT-V 191
           L  P  +  +VY  +  G +  D++  L  G+ +        +V  L T K  +  +  +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPDEIKTLTTGVKLDRFKAAPAKVKILKTDKRKDTQIIQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSK 228


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 130/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATIIKTGDQVEVEGTPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GR+TV D L  +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDDKGRTTVVDLLSQVPERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V ++  +   + V
Sbjct: 121 IHPRNEIDKVYVARVKGIANKENLRPLTRGVTIDGKKTKPATYEILKVDVEKNR---SVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKK 227


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/218 (36%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+ A
Sbjct: 3   PERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQLGD-KVTPDDHVTVKGSIIKLKWA 61

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 62  DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N 
Sbjct: 122 ELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 182 WYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 219


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 83/213 (38%), Positives = 121/213 (56%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGQIAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEQRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V       L  G+V+          +     G N W
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPQIRQTLLNGVVLDDGPAKFESFSELGGDGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRLFESQGLKVSRLLRTRYG 214


>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 =  135 bits (340), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/227 (37%), Positives = 127/227 (55%), Gaps = 4/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E++I   +V VN  ++      V   + IEV+GVPL++ E+ 
Sbjct: 2   ERLQKVIAQAGIASRRKAEQLILDGKVTVNDKVVRELGTKVTGKEKIEVEGVPLQR-EKK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP G V+T SD  GR TV D     +  RV  VGRLD +T G+LL+TNDG  A 
Sbjct: 61  VYYVLHKPRGYVSTVSDELGRRTVLDFFADRVSERVYPVGRLDYDTSGVLLMTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            +  PS +  +VY  R  G V  + L    KGI I G        TL +  +K  ++ V 
Sbjct: 121 KMMHPSGEIDKVYLARVKGIVLPENLKPFGKGIEIDGYKTKPASATLVSVDKKNQSSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+  ++KK+F+   + V +L R  +G   +  L AG  R ++
Sbjct: 181 LTIHEGRYHQVKKMFDAIGFPVKKLRREQFGTIDVQGLAAGEFRPLT 227


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/231 (36%), Positives = 124/231 (53%), Gaps = 11/231 (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  VYFLLDKPRGVVTTNSDDKGRQTVMDIVDEP-ERVYPVGRLDYDTTGALLLTNDGDLANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----------DMQVTLDTQK 183
           L  P  +  +VY  +  G    ++L  L+ G+ ++ +  G            ++    +K
Sbjct: 122 LMHPKYRIDKVYVAKVKGIPTNEELEKLRHGVTVKTVQNGRHYTFNAAPAHAEILSTDKK 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              A V + + EGK  ++K++ +    +V +L R  YG   L  L  G  R
Sbjct: 182 KHTAIVKLTIHEGKYHQVKEMLKSVGHEVIKLTRERYGMLDLTGLTPGEYR 232


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/218 (36%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+ A
Sbjct: 3   PERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQLGD-KVTPDDHVTVKGSIIKLKWA 61

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 62  DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N 
Sbjct: 122 ELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 182 WYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 219


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 79/218 (36%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+ A
Sbjct: 3   PERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQLGD-KVTPDDHVTVKGSIIKLKWA 61

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 62  DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N 
Sbjct: 122 ELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 182 WYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 219


>gi|325201930|gb|ADY97384.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240149]
          Length = 256

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/218 (36%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+ A
Sbjct: 3   PERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQLGD-KVTPDDHVTVKGSIIKLKWA 61

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 62  DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N 
Sbjct: 122 ELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 182 WYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 219


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 86/219 (39%), Positives = 125/219 (57%), Gaps = 2/219 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            +P+R+ KV+A AGIASRR+ E +IA  RV VNG ++      V +  D + VDG PL+ 
Sbjct: 1   MSPERLQKVLASAGIASRRDCEALIAAGRVMVNGRVVVVPGTRVDLDHDEVLVDGQPLQM 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +    + HKP G+V+T  D  GR TV D L ++ +RV  VGRLD+++EGL+LLT+DG 
Sbjct: 61  PTKRTYIMLHKPAGVVSTAEDTHGRPTVLD-LVNVPARVFPVGRLDMDSEGLILLTDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  + YRV     +  + L   + G+++ G       V L        WV
Sbjct: 120 LAYALTHPSFEVEKEYRVLLDRALTPEALRSWRNGVLLDGEMTAPAWVELIGTAPEGVWV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            + LREG+ R+I+ V +   ++V RLIR+  G   LG L
Sbjct: 180 RIVLREGRKRQIRAVAKLLGYEVRRLIRVREGDLVLGDL 218


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 80/220 (36%), Positives = 129/220 (58%), Gaps = 6/220 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 95  MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 153

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR  ++GRLDINT GLL+LT 
Sbjct: 154 WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWGAIGRLDINTSGLLILTT 213

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 214 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 273

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 274 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 313


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 91/236 (38%), Positives = 125/236 (52%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+A AG+ASRR  E++IA  RV V+GI +  A V V   T  I +DG  +     
Sbjct: 78  QRLQKVLAHAGVASRRACEQLIADGRVSVDGITVTEAGVRVDPLTQEIRLDGSRILTNPE 137

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSRVISVGRLDINTEGLL 122
               + HKP G+VTT  DP+GR TV             LP    R++ VGRLD  TEGLL
Sbjct: 138 LITLMLHKPAGVVTTMDDPEGRPTVAQYGRDYLAEHPELPDSL-RLVHVGRLDTETEGLL 196

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT 181
           LL+NDG L+  L  PS +  + Y     GQV+      L++GI ++ G    D +VT+  
Sbjct: 197 LLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEPWVPRKLRRGIELEDGEAKAD-RVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                + V + L  GKNR ++++ +     V RL R   GP +LG L  G TR +S
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLRPGETRPLS 311


>gi|31789454|gb|AAP58568.1| pseudouridylate synthase [uncultured Acidobacteria bacterium]
          Length = 317

 Score =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 128/234 (54%), Gaps = 7/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----V 65
           F  +R+ K+IA AGIASRR  E++I    V VNG ++ E         DHI+V G     
Sbjct: 54  FMEERLQKIIATAGIASRRHAEQLITAGEVTVNGKVVTELGTKADAQNDHIKVRGKLINP 113

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            L++ E+  + L +KP G +++ SDP+GR TV + LP+   RV  VGRLD NTEGLLLLT
Sbjct: 114 TLKRVEKNYI-LLNKPRGYLSSVSDPEGRPTVLELLPASLGRVYPVGRLDFNTEGLLLLT 172

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG 184
           NDG     +     +  +VY  +  G   +  +  L++G+ +  G+     ++ L  +  
Sbjct: 173 NDGDFTNFITSARNKVDKVYEAKVKGVPTEASVERLRRGVTLDDGVRTAPAKIRLLGETE 232

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           SNAW  V L EGKN++I+++F+     V +L R   G  +   L  G  R +S+
Sbjct: 233 SNAWFEVLLHEGKNQQIRRMFDLIGHSVVKLRRSRIGGLRDDELKPGKWRRLSE 286


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 94/222 (42%), Positives = 126/222 (56%), Gaps = 15/222 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   IL ER     +  D+  + +DG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAILGER-----LEEDNAVVRIDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V +DK+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVTEDKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N    V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL 219


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 91/236 (38%), Positives = 124/236 (52%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+A AG+ASRR  E++IA  RV V+GI +    V V   T  I VDG  +     
Sbjct: 78  QRLQKVLAHAGVASRRACEQLIADGRVSVDGITVTEPGVRVDPLTQEIRVDGSRILTNPE 137

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSRVISVGRLDINTEGLL 122
               + HKP G+VTT  DP+GR TV             LP    R++ VGRLD  TEGLL
Sbjct: 138 LITLMLHKPAGVVTTMEDPEGRPTVAQYGLDYLAEHPELPDSL-RLVHVGRLDTETEGLL 196

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT 181
           LL+NDG L+  L  PS +  + Y     GQV+      L++GI ++ G    D +VT+  
Sbjct: 197 LLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEPWVPRKLRRGIALEDGETRAD-RVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                + V + L  GKNR ++++ +     V RL R   GP +LG L  G TR +S
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLRPGETRPLS 311


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 130/228 (57%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKEGRVTLNGKTVTELATIVKNGDIVEVNGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTV 191
             P  +  +VY  R  G   ++ L  L +G+VI G      +   + +D +K + + V +
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEK-NRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKK 227


>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 =  135 bits (339), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 132/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTINGQVVRELATLVKTGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGIANKENLRPLTRGVEINGKKTKPAVYEIIKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLEVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>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 =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 130/227 (57%), Gaps = 4/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I + +V+VNG  + E       + D I V G P++  ++
Sbjct: 2   ERLQKIMAQAGVASRRKCEELILEGKVQVNGETVTELGTKADPAQDIITVSGKPIKNEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L +KP G++T+ SDP+GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  A 
Sbjct: 62  VYVML-NKPKGVITSASDPEGRKIVSDYLKGIKERVYPIGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y     G     +L+ L++GI+++       +V        N  + ++
Sbjct: 121 LLSHPKYHVPKTYLATVKGVPHGTELDKLRQGIMLEDGMTSPAEVEYKDVDPDNKQSVIS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE  +  V RL RISYG   L  L  G  R ++
Sbjct: 181 ITIHEGRNRQVRRMFEAISHPVLRLKRISYGDLLLQNLKRGLYRHLT 227


>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 =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 84/227 (37%), Positives = 127/227 (55%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMITAGRVKVDGKVITKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T SD  GR TV D    I  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTASDDKGRRTVVDYFEDIPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAW-VTV 191
           L  P  +  +VY  +  G +  +++  L  G+ +        +V  L T K  +   V +
Sbjct: 122 LMHPRNEVQKVYVAKIKGILTPEEIEGLTHGVKLDRFKAAPAKVKILKTDKRKDTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSK 228


>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 =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 81/221 (36%), Positives = 123/221 (55%), Gaps = 2/221 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A AG ASRR+ E +I + RVKVN  ++    + V  + D + +DG  L      
Sbjct: 2   RLQKFMAHAGAASRRKSEELIKEGRVKVNNNIVTEMGLEVDPNKDRVYLDGKRLNLENEN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KPIG+VTT SD  GR  V D L     RV  VGRLDI+T GL+LLTNDG LA +
Sbjct: 62  IYIILNKPIGVVTTSSDEKGRINVVD-LVDETKRVYPVGRLDIDTTGLVLLTNDGTLANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y     G+ +  +LNLL+ G+ ++ +     +V +      ++ + + +
Sbjct: 121 LMHPKNNIYKTYIATVEGKPNARELNLLRNGLSLRDLKTSKAKVKILKNFDKDSIIEISI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            EGKN ++K++F +   +V +L RIS G  +LG L  G+ R
Sbjct: 181 HEGKNHQVKRMFSYIGHEVKKLKRISIGKIELGNLEIGNYR 221


>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 =  134 bits (338), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +EV+G P+   E+  
Sbjct: 16  RINKYIAHAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIVEVNGSPIYNEEKV- 74

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 75  YYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 134

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+VI G       Y  ++V  D +K + + V
Sbjct: 135 IHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTQPAHYNIIKV--DHEK-NRSVV 191

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK
Sbjct: 192 ELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLNKK 241


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 92/235 (39%), Positives = 130/235 (55%), Gaps = 4/235 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    + V  T   I VDG  L   E  
Sbjct: 12  RLQKVLAQAGVASRRAAEQMIADGRVSVDGQVVRGQGMRVDPTAQVIHVDGERLILDETK 71

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L  +KP+G+V+T SDP+GR TV D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HVVLAINKPVGVVSTMSDPEGRPTVADIVAGYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y  R HG+V       L  GI ++ G    D    +DT  G    V +
Sbjct: 132 RLTHPSYEISKTYVARLHGEVRPGVKRRLMAGIELEDGPIAVDGFRVVDTY-GDITTVEI 190

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EG+NR ++++ +   + V  L+R  +GP +L  L  G++R V    L    G
Sbjct: 191 VVHEGRNRLVRRMMDAVGFPVRELVRTGFGPIRLDHLQPGTSRRVKGNALTALYG 245


>gi|325128449|gb|EGC51330.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis N1568]
          Length = 256

 Score =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 80/218 (36%), Positives = 130/218 (59%), Gaps = 6/218 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
           P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+ A
Sbjct: 3   PERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQLGD-KVTPDDHVTVKGSIIKLKWA 61

Query: 71  ER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           +R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+LT  G
Sbjct: 62  DRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N 
Sbjct: 122 ELVQRFAHPSFEVEREYAVRVLGGLTGEQIRVLTEEGVMLEDGLAKVERIREQGGEGANK 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 182 WYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 219


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/206 (40%), Positives = 118/206 (57%), Gaps = 6/206 (2%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKAER--TRLWLYHK 80
             RRE+E +I   RV V+G + +    V V     I +DG  + +R++     R+  Y+K
Sbjct: 1   GPRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYK 60

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           P G + T +DP+GR TVFD LP +  +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 225
           E+++++E    +V+RLIR+ YG   L
Sbjct: 181 EVRRLWEAVGVQVSRLIRVRYGDIPL 206


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 87/237 (36%), Positives = 127/237 (53%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           + EG+NR+I+++ +     V RL R   G   +G L  G  R +++   K L+E  G
Sbjct: 194 ISEGRNRQIRRMCDSIGHPVVRLKRTKLGSLSIGNLRPGQYRHLTREEIKKLKEDAG 250


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 128/227 (56%), Gaps = 5/227 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KV+A AG+ASRR+ E++IA+  VKVNG +++     V   D IEVD VP+++ 
Sbjct: 1   MAEERLQKVMAEAGVASRRKSEKLIAEGHVKVNGRVVKELGTKVEQHDRIEVDEVPIQR- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   +L +KP G++T+ SD   R TV D  P +  R+  VGRLD +T G +L+TNDG L
Sbjct: 60  EQNVYFLLNKPRGVITSVSDDKNRKTVMDFFPDVTERIYPVGRLDYDTSGAVLMTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNA 187
           A  L  P  ++ + Y  +  G V+   L  L++G+VI        +  L   D +K + +
Sbjct: 120 ANRLMHPKFKFEKTYTAKVKGLVNGSALKRLEEGVVIDHRKTAKAKAKLISTDLEKKT-S 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V + + EG+N ++KK+F      V +L R SY    +  + +G  R
Sbjct: 179 IVQLTIHEGRNHQVKKMFMAVGHPVQKLHRNSYSFLSIDDVQSGKWR 225


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 82/231 (35%), Positives = 130/231 (56%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K++A AGIASRR  E MI   RV V+G+ +        +  H 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|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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 87/228 (38%), Positives = 129/228 (56%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A AGIASRR+ E++I + RVKVNG ++      V   D IEVD VP+ + E   
Sbjct: 3   RLQKVLAHAGIASRRKAEQIILEGRVKVNGEIINELGRQVSKQDKIEVDNVPIYQ-EAPV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L++KP G++T+ SD   R TV D       RV  VGRLD +T GLL++TNDG L + L
Sbjct: 62  YYLFYKPRGIITSVSDDKKRKTVADYFLHSNERVYPVGRLDYDTTGLLIVTNDGSLTQQL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV-TLDTQKGSNAWVTV 191
             PS +  +VY  +  G   +  L  L KGI I+G      + Q+ ++DT+K   + V +
Sbjct: 122 THPSHEIDKVYVAKVKGIALRKTLLPLTKGIKIKGRKTAPANFQILSVDTKK-QTSLVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+N ++K + +   + V +L R   G   L  L  G  R ++KK
Sbjct: 181 TIHEGRNHQVKDMLDTVGYPVQKLKRERIGDLTLEGLHPGEYRRLTKK 228


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 126/225 (56%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA +G  SRR+ E +I + +VKVNGI +    + V + D + V+G+ +   E+  
Sbjct: 8   RLQKFIAMSGYCSRRKAEVLINEGKVKVNGIKVTEQGLKVSTEDRVMVNGILINVEEKKV 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G+V++ +D   R +V D +P+   RV  VGRLD  T G L+LTNDG  A  +
Sbjct: 68  YYILNKPRGIVSSANDDKDRESVVDLVPNDI-RVFPVGRLDRETTGALILTNDGDFAYYM 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTV 191
             P     ++YRV   G++  +  N LK+GI I+G+ Y  ++++    D  K    + ++
Sbjct: 127 THPKFDLSKIYRVSVRGRLSYEVTNSLKEGITIEGVEYKGVEISRVKYDAAKDKTQF-SI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            L EGKNR+I+K+F  F   V +L R   G   +  L  G  RE+
Sbjct: 186 TLHEGKNRQIRKIFAHFGLPVLKLHRYQIGYLDIDELKIGQYREL 230


>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 =  134 bits (338), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 79/224 (35%), Positives = 131/224 (58%), Gaps = 10/224 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           +++  ++  P ++ KV+A AG+ SRR++E +I   RV VNG   E A +   ++ TD + 
Sbjct: 175 RDLTADDDAP-KLHKVLAEAGLGSRRDMEELIIAGRVSVNG---EPAHIGQRILPTDQVR 230

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G  +++    +  R+ +YHKP G + + +DP+GR +VFD LP++  ++ ++VGRLD N
Sbjct: 231 INGKLIQRKVSKKPPRVLVYHKPAGEIVSTNDPEGRPSVFDRLPTMKAAKWLAVGRLDFN 290

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T  G LA  L  P     R Y VR  G++++     L  G+ ++       ++
Sbjct: 291 TEGLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMRQKLLAGVELEDGLAQFSKI 350

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                +G N W  V + EG+NRE++++FE     V+RLIR  YG
Sbjct: 351 ADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYG 394


>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 =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 83/204 (40%), Positives = 118/204 (57%), Gaps = 6/204 (2%)

Query: 28  RREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKAER--TRLWLYHKPI 82
           RRE+E +I   RV V+G + +    V V     I +DG  + +R++     R+  Y+KP 
Sbjct: 1   RREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE 60

Query: 83  GLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G + T +DP+GR TVFD LP +  +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 225
           ++++E    +V+RLIR+ YG   L
Sbjct: 181 RRLWEAVGVQVSRLIRVRYGDIPL 204


>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 =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 81/213 (38%), Positives = 123/213 (57%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N W
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPKLRQNMVNGVELEDGPAKFESFSEIGGEGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE  + KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRIFESQDLKVSRLLRTRYG 214


>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 =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 127/228 (55%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ + E  
Sbjct: 4   ERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIER-ESH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 63  HTYLFYKPRGVISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGELANL 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  LKKG+ I         ++V     +     V +
Sbjct: 123 LMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPARVKVLKTNPRAQTQIVQL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG   ++K++F+  N  V++L R  Y    L  L +G  RE++ K
Sbjct: 183 TIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNHK 230


>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 =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 114/293 (38%), Positives = 156/293 (53%), Gaps = 38/293 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + VDG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNALVRVDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N    V + EG+NRE+++++E     V+RL R+ YG   L            KK+ R 
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL-----------DKKLPRG 226

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRP---NIISEVPDDFTRMKKNS-SQK 292
             G   L+  QVN     Y  E LV  RP    +++  PD  TR ++ + SQK
Sbjct: 227 --GWMELDLKQVN-----YLRE-LVELRPEKETVLNTAPDAATRKRERTRSQK 271


>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 =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 84/219 (38%), Positives = 126/219 (57%), Gaps = 18/219 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRIAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
            LA  L  PS +  R Y VR  G+V  Q + N+      + G+   D     ++      
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPQLRQNM------VNGVELEDGPAKFESFSEIGG 175

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +G N W  V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 176 EGINRWYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  134 bits (336), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 78/217 (35%), Positives = 125/217 (57%), Gaps = 6/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +++ K++A  G+ SRRE+ER I   RV +NG    +  + +     + +D   +R    K
Sbjct: 3   EKIQKILAHFGLGSRREIERWIHDGRVHING-QPAKLGMRIHLKAKVTIDNQRIRLTTNK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+ +YHKP+G + + SDP    TVF++LP +   R + +GRLD+NT GLL+ TN+G
Sbjct: 62  PFERRVLIYHKPLGEICSRSDPRHHVTVFEHLPRLRDQRWVMIGRLDMNTSGLLIFTNEG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  L  PS Q  R Y VR  G+V++  L+ LKKG++++        +      G+N W
Sbjct: 122 EFAYRLSHPSYQIEREYVVRVLGKVNKSMLDRLKKGVMLKEKRAAFTSIQASGGSGANRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L+EG+NRE+++++E     V+RL+RI +G   L
Sbjct: 182 YHVVLKEGRNREVRRLWETQGVTVSRLMRIRFGNVSL 218


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I + RV +NG  +   A  V S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKEGRVTLNGKTVTELATIVKSGDIVEVNGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTGLLILTNDGDFTDKM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G   ++ L  L +G+V+ G       Y  ++V  D +K + + V
Sbjct: 121 IHPRNEIDKVYLARVKGIATKENLRPLIRGVVLDGKKTQPARYNIIKV--DHEK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK
Sbjct: 178 ELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKK 227


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 114/293 (38%), Positives = 156/293 (53%), Gaps = 38/293 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + VDG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNALVRVDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N    V + EG+NRE+++++E     V+RL R+ YG   L            KK+ R 
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL-----------DKKLPRG 226

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRP---NIISEVPDDFTRMKKNS-SQK 292
             G   L+  QVN     Y  E LV  RP    +++  PD  TR ++ + SQK
Sbjct: 227 --GWMELDLKQVN-----YLRE-LVELRPEKETVLNTAPDAATRKRERTRSQK 271


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 122/218 (55%), Gaps = 7/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER   +  +   I+   V  +  
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLE-DENAVVRIDGHAVSAKAQ 61

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIFL 219


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 81/213 (38%), Positives = 122/213 (57%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N W
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPKIRQKMVTGVELEDGPAKFESFSEIGGEGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRIFESQELKVSRLLRTRYG 214


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 114/293 (38%), Positives = 156/293 (53%), Gaps = 38/293 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + VDG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNALVRVDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N    V + EG+NRE+++++E     V+RL R+ YG   L            KK+ R 
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL-----------DKKLPRG 226

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRP---NIISEVPDDFTRMKKNS-SQK 292
             G   L+  QVN     Y  E LV  RP    +++  PD  TR ++ + SQK
Sbjct: 227 --GWMELDLKQVN-----YLRE-LVELRPEKETVLNTAPDAATRKRERTRSQK 271


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 87/219 (39%), Positives = 121/219 (55%), Gaps = 5/219 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++A+ GIASRR  E MI   RV+ NG +++         DH+E+DG  +  A R 
Sbjct: 3   ERVQKILAQWGIASRRRAEEMIVAGRVRRNGKIVQLGEKADPEKDHLEIDGKKIEPANRP 62

Query: 74  -RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
            RL+ 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 227
           + V L EG+NR+I+ V E   + V +L R + G  QL +
Sbjct: 183 LEVILVEGRNRQIRSVAEELGYHVLKLHRSAIGRIQLNS 221


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 81/213 (38%), Positives = 122/213 (57%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N W
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPQLRQNMVNGVELEDGPAKFESFSEIGGEGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>gi|315180431|gb|ADT87345.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 315

 Score =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 91/218 (41%), Positives = 122/218 (55%), Gaps = 7/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER   +  +   I+   V  +  
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLE-DENAVVRIDGHAVSAKAQ 61

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E    R+  Y+KP G + T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIFL 219


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 84/219 (38%), Positives = 126/219 (57%), Gaps = 18/219 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
            LA  L  PS +  R Y VR  G+V  Q + N+      + G+   D     ++      
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPQLRQNM------VNGVELEDGPAKFESFSEIGG 175

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +G N W  V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 176 EGINRWYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 99/267 (37%), Positives = 135/267 (50%), Gaps = 15/267 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           PQR+ K++A AGIASRR  E +I Q RV VNG  + E  A        I +DG P+ K E
Sbjct: 125 PQRLQKILAHAGIASRRACEELILQGRVTVNGETVRELGARYNPYESKIAIDGEPI-KLE 183

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +  +KP G + ++ DPD R  V D LP I  RV ++GRLD  + GL+LLTNDG LA
Sbjct: 184 KLVYFAVNKPKGYICSNEDPDNRPRVVDLLPEIPQRVYTIGRLDEASTGLILLTNDGELA 243

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V   G  D+D L  L  G+ +        +V    ++G ++ + +
Sbjct: 244 NKLTHPKFGVEKRYEVVVAGHPDRDVLRKLIDGVWLSDGKVRAKKVRELGRRGDSSILEL 303

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-----EVS--KKILREQ 244
            L EGKNREI+++      KV  L R++ GP  L  L  G  R     EV   K+I R  
Sbjct: 304 VLAEGKNREIRRMLARLGHKVMSLTRVAVGPITLKGLRTGEVRVLGTAEVDRLKQIARNP 363

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDR 271
             P        +LD+   SS    RDR
Sbjct: 364 FPP------TESLDSDAGSSAPAQRDR 384


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 84/219 (38%), Positives = 126/219 (57%), Gaps = 18/219 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
            LA  L  PS +  R Y VR  G+V  Q + N+      + G+   D     ++      
Sbjct: 122 ELANRLMHPSNEIEREYAVRVMGEVTPQLRQNM------VNGVELEDGPAKFESFSEIGG 175

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +G N W  V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 176 EGINRWYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 214


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 77/218 (35%), Positives = 127/218 (58%), Gaps = 11/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLR--- 68
           ++ K++A+ G+ SRRE+E +IA  +VK+N    ++ +RA       D + +    +R   
Sbjct: 38  KLQKLLAQKGLGSRREMEALIASGQVKLNDHIAVIGDRAG----PGDIVRIGRRVIRIHE 93

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           + E  ++ LYHKP G + + +DP  R +VFD LP +  S+ I++GRLD NT GLL+ TND
Sbjct: 94  EEELPKVLLYHKPEGEIVSRNDPQDRPSVFDKLPYLRSSKWIAIGRLDFNTSGLLIFTND 153

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  +  P  +  R Y VR  G++ ++++  L  GI ++        +     +G+N 
Sbjct: 154 GALANRMMHPRFEMEREYAVRILGELTEEQMQQLTTGITLEDGEAAFTYLADQGGEGANH 213

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           W  V L+EGKNRE++++F      V+RL+R+ +GP  L
Sbjct: 214 WYRVILKEGKNREVRRMFGAIGLTVSRLMRVRFGPINL 251


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 121/226 (53%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ASRR+ E +I+Q RVKVNG  + +    V   D +EVDG  L K E+ +
Sbjct: 5   RLQKYLAECGVASRRKAEELISQGRVKVNGETVTQMGKKVSQNDVVEVDG-KLVKMEKRK 63

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++  +KP+G +++  D  GR TV D +  I  R+  VGRLD +T GLLLLTNDG  A  
Sbjct: 64  VYIALNKPVGYISSVKDQFGRKTVMDLVKDIKERIFPVGRLDYDTSGLLLLTNDGDFAYR 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY     G   +D +   K G+ I           +    G    V + +
Sbjct: 124 LTHPKHEIKKVYEADLLGVPSKDDIMRFKNGLWIDDYFTSPADFEILKSDGKTTKVRITI 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EGKNR+++K+       V RL RIS G   LG L  GS R ++++
Sbjct: 184 HEGKNRQVRKMCNKIGCPVIRLKRISIGEVSLGDLKEGSWRNLTER 229


>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 =  134 bits (336), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 93/222 (41%), Positives = 127/222 (57%), Gaps = 15/222 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + VDG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNALVRVDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V+++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVNEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N    V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL 219


>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 =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 132/230 (57%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V +NG ++   A  V + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTINGQVVRELATLVKTGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP +  R+  VGRLD +T GLL+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPQVKERIYPVGRLDWDTSGLLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGIANKENLLPLTRGVEIDGKKTKPAVYEIIKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+F+    +V++L R  +G   L  L  G +R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFQAVGLEVDKLSRTRFGHLDLTGLRPGESRRLNKK 227


>gi|323439505|gb|EGA97226.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus O11]
          Length = 245

 Score =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 76/223 (34%), Positives = 129/223 (57%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ + KVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKAKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++ G+    +++V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++ E F  +V +L RI YGP  +  L AG  R
Sbjct: 185 TITEGRNRQVRRMLEHFGHQVTKLSRIEYGPLNVVGLNAGEGR 227


>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 =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 131/231 (56%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K++A AGIASRR  E MI   RV V+G+ +        +  H 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|319794363|ref|YP_004156003.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315596826|gb|ADU37892.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 601

 Score =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 82/213 (38%), Positives = 119/213 (55%), Gaps = 9/213 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E +I Q R+ VN    E A +   +   D ++++G P+R    
Sbjct: 186 KLHKVLAQAGLGSRLEMEALILQGRISVNN---EPAHIGQRIQYGDQVKINGKPIRYRIA 242

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL ++ G
Sbjct: 243 PPPPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTEGLLLFSSSG 302

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +  ++   L  G+ ++        +     +GSN W
Sbjct: 303 DLANQLMHPRFGLEREYAVRVLGALSSEEKQKLLDGVRLEDGMAQFGTIEEGGGEGSNCW 362

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V + EG+NRE++++FE     V+RLIRI YG
Sbjct: 363 YRVTISEGRNREVRRLFESVGHAVSRLIRIRYG 395


>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 =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 81/213 (38%), Positives = 122/213 (57%), Gaps = 6/213 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRK 69
           +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      +  
Sbjct: 3   EKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIED 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
             R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VGRLDIN+ GLLL TNDG
Sbjct: 62  EIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVGRLDINSTGLLLFTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y VR  G+V       +  G+ ++         +    +G N W
Sbjct: 122 ELANRLMHPSNEVEREYAVRVMGEVTPKIRQNMVNGVELEDGPAKFESFSEIGGEGINRW 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 182 YQVVVKEGRNREVRRIFESQELKVSRLLRTRYG 214


>gi|291544370|emb|CBL17479.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus sp.
           18P13]
          Length = 242

 Score =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 89/233 (38%), Positives = 128/233 (54%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDG--VPLRK 69
           R+ K+IA +G  SRR+ E  IA  +VK NG    L ++A     S D I V+G  + + K
Sbjct: 5   RIQKIIADSGYCSRRKAESFIAAGQVKCNGRPVKLGDKAG----SRDLITVNGERIAIPK 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +REG+NR+I+++ E    +V RL RIS GP +LG L  G+ RE++ + LR
Sbjct: 181 LITIREGRNRQIRRMCEAVGLEVARLRRISIGPLKLGMLKPGTYRELTAEELR 233


>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 =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 81/227 (35%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKIIAEAGIASRRKAEKMITAGRVKVDGKVITKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T SD   R TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTASDDKDRKTVVDYFEDVPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAW-VTV 191
           L  P  +  +VY  +  G +  +++  L  G+ +        +V  L T K  +   V +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPEEIKTLTHGVKLDDFKAAPAKVKVLKTDKRKDTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSK 228


>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 =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 126/223 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++A  G+ASRR+ E +I Q +VKVNG + +        TDH+ V G  +  + +  
Sbjct: 7   RLQKMLADCGVASRRKAEELIQQGKVKVNGHVAQIGDKVNPKTDHVTVAGRRIVASRQYY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP G V+T SD  GR  V + +  I +RV  VGRLD ++EGLLL+TNDG  A ++
Sbjct: 67  YIMLHKPRGYVSTMSDEMGRKCVAELVKDIPARVYPVGRLDRDSEGLLLMTNDGEFANLI 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             PS    + YRV     + +++L L+  G+ I G+        + +++     + + LR
Sbjct: 127 MHPSKHVPKTYRVTVRPDISEEQLALMNVGMEIDGVRTAPADAWVISREPGRVVLEIILR 186

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           EG+NR+I+K+ E    +V RL R++ G  +LG L  G  R ++
Sbjct: 187 EGRNRQIRKMCEQLGVEVARLKRVAVGQVKLGMLQPGKWRNLT 229


>gi|239815173|ref|YP_002944083.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239801750|gb|ACS18817.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 604

 Score =  133 bits (335), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 86/218 (39%), Positives = 121/218 (55%), Gaps = 19/218 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E +I Q R+ VN    E A +   +   D ++++G P+R    
Sbjct: 199 KLHKVLAQAGLGSRLEMEALILQGRISVNN---EPAHIGQRIQYGDQVKINGKPIRYRIA 255

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+NTEGLLL ++ G
Sbjct: 256 PPPPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTEGLLLFSSSG 315

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QK 183
            LA  L  P     R Y VR  G      LN  +K  +++G+   D      T      +
Sbjct: 316 DLANQLMHPRFGLEREYAVRVLG-----ALNAEEKKKLLEGVRLDDGMAQFGTIEEGGGE 370

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           GSN W  V + EG+NRE++++FE     V+RLIRI YG
Sbjct: 371 GSNHWYRVTISEGRNREVRRLFESVGHAVSRLIRIRYG 408


>gi|40062484|gb|AAR37436.1| RNA pseudouridylate synthase, putative [uncultured marine bacterium
           105]
          Length = 255

 Score =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 122/226 (53%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AGI+SRR  ER+I   RV VNG  + +         D I VDG  + K  R 
Sbjct: 7   RLQKVLASAGISSRRAAERLIEVGRVTVNGRSVTKLGAKADPDLDDIRVDGRKV-KTGRP 65

Query: 74  RLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R++L   KP G VTT  DP+GR T+ + + ++   V  VGRLD ++EGL++LTNDG LA 
Sbjct: 66  RIYLLVCKPRGYVTTRFDPEGRRTILNLISNVREYVYPVGRLDYDSEGLVILTNDGTLAA 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAW 188
            L  P     RVY VR  G   Q  ++ L+ G++I G       V     L  +   NA 
Sbjct: 126 RLTHPRYGVERVYEVRVRGVPSQAAIDSLRHGVLINGRRTASSSVKFLRRLKAKSSENAL 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + V +REG+NR+++K+ E     V RL R   GP +  +L  G  R
Sbjct: 186 LRVAIREGRNRQVRKMCEAIGHPVIRLRRTQIGPLRDSSLKVGKHR 231


>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 =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 81/214 (37%), Positives = 127/214 (59%), Gaps = 4/214 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ SRR  E +IA  RV+VNG ++    + V   T  I VDG+ +  AE  
Sbjct: 97  RLQKVLAQAGVGSRRVSEDLIAAGRVEVNGEIVRHQGMRVDPETAVIRVDGMRISTAEGI 156

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + ++KP+G+V+   DPD R  + D +     R+  +GRLD++TEGL+LLTNDG LA  
Sbjct: 157 VHFAFNKPMGVVSAMDDPD-RPNLGDYVRGRNERLFHIGRLDVDTEGLILLTNDGELAHR 215

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS +  +VYR + +G V +D    L++G+ ++ G+   D    LD+  G NA V + 
Sbjct: 216 LAHPSYEIRKVYRAQVYGTVPKDLGRRLREGVDLEDGLARVDHFRLLDSV-GRNALVEIT 274

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + EG+NR ++++ +     V  L+R  +GP  LG
Sbjct: 275 IHEGRNRIVRRIMDAVGLPVRGLVRTKFGPISLG 308


>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 =  133 bits (334), Expect = 4e-29,   Method: Compositional matrix adjust.
 Identities = 87/232 (37%), Positives = 129/232 (55%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I+  RV+V+G +++   V +  +   + VDG  L+  E 
Sbjct: 67  ERLQKVLARAGFGSRRACETLISTGRVRVDGAVVQEQGVRIDPAAQVVHVDGRRLQLDET 126

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G+V+  SDP+GR  + +   +   R+  VGRLD  TEGLLLLTNDG LA 
Sbjct: 127 KLTLVLNKPRGVVSAMSDPEGRRDLSEFTAAHSQRLYHVGRLDYETEGLLLLTNDGELAH 186

Query: 133 VLELPSTQWLRVYRVRFH--GQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
            L  PS +  + Y  RF   G   +  +  L+ G+ ++ G    D    L  Q G  A V
Sbjct: 187 RLTHPSFEVAKTYVCRFDAPGGPPRGLVRTLRDGVELEDGPARADRARVL-AQDGREAVV 245

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+NR ++++F    +++  LIR   GP  LG L  G+TRE+S + L
Sbjct: 246 EVTLHEGRNRIVRRMFASRGFELTALIRTRIGPVLLGDLAPGTTRELSGREL 297


>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 =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 86/236 (36%), Positives = 126/236 (53%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR  E +I Q RV V+G ++ R    V     I  VDG  +  +  
Sbjct: 189 ERLQKVLARAGVASRRACEELIGQGRVTVDGQVVRRYGARVDPERQIIRVDGKRIPTSTG 248

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + ++KP G+V+T  DP+GR  + D +  +  R+  VGRLD  TEGLLL TNDG LA 
Sbjct: 249 LAYYAFNKPAGVVSTMDDPEGRPCLADYVQDLAPRLFHVGRLDTATEGLLLFTNDGELAH 308

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNA 187
            L  PS    + Y  +  G V +     L+ G+ ++     D +VT+D      Q G  A
Sbjct: 309 RLTHPSYGVRKKYIAKVAGPVPRKLARTLRAGVELE-----DGKVTVDGFTVIQQHGRQA 363

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V + L EG+   ++++ E     V  L RI +GP +LG L  G+ R ++   LRE
Sbjct: 364 LVEIVLHEGRKHIVRRLMEAVGHPVLELARIEFGPVKLGRLKPGTVRALT---LRE 416


>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 =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 127/230 (55%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVI  +G ASRR  E+ I   RV+VN  ++   A  V  +D + +D   + +  +  
Sbjct: 11  RLVKVILESGFASRRNCEKAIMSGRVRVNNQVILDPAYRVKESDSVSIDRNIIERQTKRY 70

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + LY KP+G+V+T     GR  + +    I  R+   GRLD  + G++++TNDG  A ++
Sbjct: 71  MALY-KPLGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITNDGEFANII 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             PS + L+VY V  +G++D + L     GI I+ + Y   +  + ++    + + + + 
Sbjct: 130 THPSYEILKVYDVTVNGKIDSEALLKASAGITIKNVTYSPFKFKILSKGRVQSKIRLTIN 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQ-----LGTLLAGSTREVSKK 239
           EGKNREI+K+F++  +KV  L RIS G         GTL AG  R+++KK
Sbjct: 190 EGKNREIRKIFDYLGYKVIDLERISVGCVSKYDDISGTLEAGHIRDLTKK 239


>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 =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 135/230 (58%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR  E +IA+ RV+V+G+++    V V  +T  I VDG+ ++    
Sbjct: 81  ERLQKVLAAAGVASRRVSEDLIAEGRVEVDGVVVTEPGVRVDPATAVIRVDGISVQTDVT 140

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + ++++KP G+++T  DP+GR ++   L      +  VGRLD  TEGLL+LTNDG LA 
Sbjct: 141 KQYFVFNKPRGVISTMVDPEGRPSIATYLKPGQEHLFHVGRLDNETEGLLILTNDGELAN 200

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y V+  G + +   N L++G+ ++ G+   D    +D+  G +  V V
Sbjct: 201 RLTHPSYEVPKTYVVQTRGPLAKGVSNRLREGVELEDGVAQVDSFKLVDSTPG-HVLVEV 259

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L  GKNR ++++F+     V RL+R+  GP  LG    G+ R ++ + L
Sbjct: 260 VLHSGKNRIVRRMFQEIGHPVERLVRVKVGPILLGDQKQGTVRALNAQEL 309


>gi|241764490|ref|ZP_04762511.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241366074|gb|EER60671.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 504

 Score =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 85/220 (38%), Positives = 121/220 (55%), Gaps = 10/220 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR- 68
           TP ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   V   D ++V+G P+R 
Sbjct: 156 TP-KLHKVLAQAGLGSRLEMEQLILEGRISVNN---EPAHIGQRVQFGDQVKVNGKPIRY 211

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
                  R+  YHKP+G V +H DP  R TVF  LP +   +  SVGRLD+NTEGLLL T
Sbjct: 212 RIDPPPARVIAYHKPVGEVVSHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLNTEGLLLFT 271

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           + G LA  L  P     R Y VR  G +  ++   L  G+ +         +     +GS
Sbjct: 272 SSGELANKLMHPRFGLEREYAVRVLGALSNEEKQQLLDGVRLDDGMAAFGSIEDGGGEGS 331

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N W  V + EG+NRE++++ E     V+RLIRI YG   L
Sbjct: 332 NCWYRVTISEGRNREVRRMLEAVGHAVSRLIRIRYGAMVL 371


>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 =  133 bits (334), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 81/232 (34%), Positives = 128/232 (55%), Gaps = 5/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KVI++AG+ASRR  E++I   RVKV+G ++    + V  S   I VDG  +    ++
Sbjct: 12  RLQKVISQAGVASRRHAEKLIISGRVKVDGNIVRTLGIRVDPSVQTIHVDGNQIMLDTKS 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+V+T  DPDGR  + + +     R+  VGRLD +T GL+LLTNDG L+  
Sbjct: 72  LTIALNKPAGVVSTMDDPDGRPCLAEFVEQYNQRLYHVGRLDTDTAGLILLTNDGELSHR 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  PS +  + Y    HG+V +     L +GI ++   +   D Q+T     G    V +
Sbjct: 132 LMHPSWEVPKTYVATVHGEVPRGLGRKLARGITLEDGPVKVEDFQIT--DHYGEMTLVQL 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L EG+NR ++++ +   + V  L+R  +GP  +G L +G TR +   +L+E
Sbjct: 190 TLHEGRNRIVRRIMDHVGFPVIELVRTQFGPVHIGRLHSGVTRRIEGPVLQE 241


>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 =  132 bits (333), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 86/230 (37%), Positives = 125/230 (54%), Gaps = 11/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ KV+A AG+ SRRE E +I Q RV+V+G ++    V V  T H+  VDG+ +      
Sbjct: 29  RLQKVMADAGVGSRRECENLIRQGRVEVDGQIVMELGVRVDPTAHVVTVDGLRIMADASK 88

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +V T  DP+GR+TV D +     R+  VGRLD  +EGLLLLTNDG LA  
Sbjct: 89  ITIAVNKPQKMVATMHDPEGRATVADLVSKRTERLFHVGRLDYESEGLLLLTNDGELANR 148

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAW 188
           L  P     + Y V   G+V     + L +GI ++     D +V LD+     Q  +   
Sbjct: 149 LSHPRYNVRKTYVVTVKGRVANGVGSQLLRGITLE-----DGEVALDSYRVIDQTDTETM 203

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + V L  G+NR ++++F+     V RL+R S GP +LG L  G TR +++
Sbjct: 204 IEVQLHSGRNRIVRRIFDSLGHPVTRLVRTSIGPIKLGDLKQGRTRVLNR 253


>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 =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 80/230 (34%), Positives = 131/230 (56%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + + D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKAGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D L ++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLSNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L    +G+ I+G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGVANKENLRPFTRGVEIEGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK
Sbjct: 178 QLTIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGEARRLNKK 227


>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 =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 86/225 (38%), Positives = 129/225 (57%), Gaps = 12/225 (5%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           + +  E+  P ++ KV+A AG+ SRR++E +I   RV VNG   E A +   ++ TD + 
Sbjct: 165 RELTAEDDAP-KLHKVLADAGLGSRRDMEELIVAGRVSVNG---EPAHIGQRILPTDQVR 220

Query: 62  VDGVPL-RKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G  + RK  ++  R+  YHKP G + +  DP+ R +VFD LP +  S+ ++VGRLD N
Sbjct: 221 LNGKLIQRKIAKSLPRVLTYHKPAGEIVSRDDPEKRPSVFDRLPLLKNSKWLAVGRLDFN 280

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL TN G LA  L  P     R Y VR  G++++     L  G+ + G   G    
Sbjct: 281 TEGLLLFTNSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVDL-GDGIGQFSK 339

Query: 178 TLD-TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            +D   +G N W  V + EG+NRE++++FE     V+RLIR  YG
Sbjct: 340 IVDGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYG 384


>gi|332977338|gb|EGK14123.1| ribosomal large subunit pseudouridine synthase B [Desmospora sp.
           8437]
          Length = 236

 Score =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 127/230 (55%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR+ E  I   +V+VNG  + +    V    D IEV+G  +R  E+
Sbjct: 2   ERLQKVMARAGVASRRKSEEWILSGKVRVNGKTVTQLGTRVDPERDRIEVEGRLIR-PEQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP G++T+ SDPDGR  V D    +  RV  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  KRYFLFYKPKGVITSLSDPDGRPVVTDWFREVEERVYPVGRLDYDTEGLLLLTNDGELTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY+    G   +  L  L+ G+ +        +V +       A + + 
Sbjct: 121 GLAHPRHEVDKVYQATVKGIPAKKSLRRLETGVKLTDGWTAPAKVRMLRSGKEQACLELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+++++ E     V  L+R+      L  L  G  RE+SK+ +R
Sbjct: 181 IHEGRNRQVRRMCEAVGHPVVHLVRVQLAFLTLSGLQPGEYRELSKEEIR 230


>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 =  132 bits (333), Expect = 6e-29,   Method: Compositional matrix adjust.
 Identities = 91/237 (38%), Positives = 130/237 (54%), Gaps = 15/237 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR 68
           N    R+ KV+A AG+ SRR  E +IA  RV+V+G ++E   + V   T  IEVDG    
Sbjct: 7   NAEGVRLQKVLAAAGVGSRRHSEELIAAGRVRVDGRVVETQGMRVDPQTAIIEVDG---- 62

Query: 69  KAER--TRLWLYH----KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             ER  TR  L H    KP+G+++  SD  GR TV D +      +  VGRLD+++EGLL
Sbjct: 63  --ERVVTRAGLVHLALNKPVGVLSAMSDDRGRPTVADLVTDAGPGLFHVGRLDVDSEGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDT 181
           L+TNDG LA  L  PS +  + Y V   G V +D    L++G+ +  G    D  V +  
Sbjct: 121 LVTNDGELAHRLSHPSFEVAKTYLVEVAGPVGRDVPRRLREGVELADGPVRAD-AVRIVG 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             GS   + + L EG+NR ++++ E  +  V RL+R   GP  LG+L  G TR +S+
Sbjct: 180 SAGSRVMLEITLHEGRNRVVRRLMEAVDHPVRRLVRTRIGPVHLGSLRVGRTRHLSR 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 =  132 bits (333), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 80/230 (34%), Positives = 126/230 (54%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +IA+ RVKVNG ++      V    D IEVDG  + K ++
Sbjct: 2   ERLQKVMAHAGVASRRKSEEIIAEGRVKVNGEIVTEMGFKVDPKKDEIEVDGEVIAKEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L HKP G +TT SDP  R TV D +P +  RV   GRLD ++ GLL+LTNDG L  
Sbjct: 62  VYLLL-HKPEGYITTVSDPKERQTVMDLIPDLKQRVYPAGRLDYDSSGLLILTNDGDLCY 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|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 =  132 bits (333), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 125/226 (55%), Gaps = 5/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E  I + RVKVNG ++      V  +D IEVDG+P+ K E  
Sbjct: 2   ERLQKVMAHAGIASRRKCEAFIEEGRVKVNGTVVRELGYKVSQSDKIEVDGIPIYKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP  ++++ +D  GR+ + D    I  RV  VGRLD +T GL+LLTNDG  A +
Sbjct: 62  -YFMFYKPKSVLSSVTDDRGRTVISDYFKDIPQRVYPVGRLDYDTTGLILLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           +  P     + Y  +  G      +  L++GI I G          +++DT+K +   V+
Sbjct: 121 MTHPKHHVEKKYIAKVKGVPTPRHMRQLERGIWIDGKKTSKAVARILSVDTEKNTGI-VS 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EG N ++KK+FE     V +L R  +G   L  L  G  RE+
Sbjct: 180 LTIHEGWNHQVKKMFEAVELPVQKLKREEFGFLTLENLRPGDYREL 225


>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 =  132 bits (333), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 82/217 (37%), Positives = 120/217 (55%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR---K 69
           ++ KV+A+AG+ SR E+E++I + R+ VN    E A +   +   D ++V+G P+R    
Sbjct: 172 KLHKVLAQAGLGSRLEMEQLILEGRISVNN---EPAHIGQRIQFGDQVKVNGKPIRYRID 228

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP+G V +H DP  R TVF  LP +   +  SVGRLD+NTEGLLLLT+ G
Sbjct: 229 PPPARVIAYHKPVGEVVSHDDPHNRPTVFRRLPRLVQGKWQSVGRLDLNTEGLLLLTSSG 288

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y VR  G +  ++   L  G+ +         +     +G+N W
Sbjct: 289 ELANQLMHPRFGLEREYAVRVLGALSNEEKQKLLDGVRLDDGIASFGTIEDGGGEGANCW 348

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE++++ E     V+RLIRI YG   L
Sbjct: 349 YRVTIAEGRNREVRRMLEAVGHAVSRLIRIRYGAMVL 385


>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 =  132 bits (332), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 86/260 (33%), Positives = 145/260 (55%), Gaps = 11/260 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           +++  ++  P ++ KV+A AG+ SRR++E +I   RV VNG   E A +   ++  D + 
Sbjct: 168 RDLTADDDAP-KLHKVLAEAGLGSRRDMEELIIAGRVSVNG---EPAHIGQRILPADQVR 223

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           ++G  +++    +  R+ +YHKP G + + +DP+GR +VF+ LP++  ++ ++VGRLD N
Sbjct: 224 INGKLIQRKVSNKPPRVLVYHKPAGEIVSTNDPEGRPSVFERLPTMKAAKWLAVGRLDFN 283

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T  G LA  L  P     R Y VR  G++++     L  G+ ++       ++
Sbjct: 284 TEGLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMRQKLLAGVELEDGLAQFSKI 343

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+
Sbjct: 344 ADGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGTLTLPKNLKRGRWEEM 403

Query: 237 SKKILREQLGPHLLEEAQVN 256
            +  +R+ L    LE+  V+
Sbjct: 404 EEHAVRDLLAMSGLEKKSVD 423


>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 =  132 bits (332), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR  E +IA  RV VNG ++      V    DH+ VDG  ++    
Sbjct: 8   ERLQKVMAAAGVASRRVSEELIAAGRVSVNGTVVTELGRRVDPVVDHVAVDGAAVQLDTT 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + +KP+G+V++  D  GR  +   +     R+ +VGRLD  T GLL+LTNDG LA 
Sbjct: 68  LRYVMLNKPVGVVSSLRDEQGRPDLSRFVADYEERLFNVGRLDAETSGLLILTNDGELAH 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
           VL  P     + Y  R  G V    +  L +G+ ++ G    D    L +  G  + V V
Sbjct: 128 VLAHPRFGVTKTYIARVRGAVTPQTIGRLTRGVELEDGPIAADRAKLLQSDPGGGSLVEV 187

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L  G+NR ++++       V  L+R  +GP  LGTL AG+ R+++K  L
Sbjct: 188 TLHSGRNRIVRRMLAEVGHPVVELVRRQFGPLHLGTLKAGALRDLTKAEL 237


>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 =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 92/222 (41%), Positives = 126/222 (56%), Gaps = 15/222 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + +DG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNAVVRIDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V ++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVTEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N    V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL 219


>gi|288556014|ref|YP_003427949.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
 gi|288547174|gb|ADC51057.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
          Length = 242

 Score =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 84/224 (37%), Positives = 127/224 (56%), Gaps = 5/224 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KVIA+AGI SRR+ E MI + +VKVNG ++    V V  + D IEV+GVP+ K E 
Sbjct: 2   ERLQKVIAQAGITSRRKAETMITEGKVKVNGQVVRELGVKVNPNKDEIEVEGVPIDKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++++  D  GR  V D L  I  RV  +GRLD +T GL+LLTNDG  A 
Sbjct: 62  V-YYLMYKPQGVISSVKDEKGRKVVTDFL-EIEQRVFPIGRLDYDTSGLILLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            L  P  +  +VY  +  G   ++ L  L+ G+V++       +V L +  +K   A V 
Sbjct: 120 QLMHPKFKIDKVYVAKVKGIPARESLKKLQHGVVLEDGKTAPAKVKLVSMDKKKQTAIVQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG+NR+++++FE     V +L R  Y    L ++  G  R
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHPVMKLKREQYSFLNLRSMNPGDVR 223


>gi|301165765|emb|CBW25337.1| putative RNA pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 343

 Score =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 86/234 (36%), Positives = 124/234 (52%), Gaps = 2/234 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K IA  GI SRR+ E +I Q RVKVNG  +      V    D + VDG         
Sbjct: 5   RLQKFIADCGITSRRKAEELIVQGRVKVNGETIRVLGTKVNPDIDAVIVDGQIADLGSVD 64

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++L  +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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L EG+NREI+K+ E     V++L R++     +  +  G  R ++KK L   +G
Sbjct: 185 LGEGRNREIRKICEACGLTVDKLKRVAIEGLTVEGIAPGKFRYINKKQLLSLIG 238


>gi|308176960|ref|YP_003916366.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307744423|emb|CBT75395.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 373

 Score =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 81/230 (35%), Positives = 131/230 (56%), Gaps = 7/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR  E MI + RV+VNG L+      V  + D I VDG+ ++  +  
Sbjct: 135 RLQKAMANAGVASRRVCEEMILEGRVEVNGNLVVELGSRVDPAKDRIHVDGMRIQMNQAN 194

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
           R ++++KP  ++ T  DP+GR T+ D   +     R+  VGRLD  TEG+L+LTNDG LA
Sbjct: 195 RYFVFNKPKHVMCTMDDPEGRRTIADYFKNEHHSLRLFHVGRLDYKTEGVLILTNDGELA 254

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
             L+ P  +  + Y V+  G + +   N L++G+ ++   I   D+++   T K  +  V
Sbjct: 255 NRLQHPKYEVPKTYLVQIPGPLPRAVSNQLREGVKLEDGWIKVDDLKIIATTPK--HVMV 312

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V L  G+NR ++++F+     V RL+R++ GP QLG    G+ R +  +
Sbjct: 313 EVTLHSGRNRIVRRMFDEVGHPVQRLVRVAVGPVQLGDQKQGTIRSLGNQ 362


>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 =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 83/246 (33%), Positives = 132/246 (53%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
             D   ++  +  R  L +KP+G V + SD  GR+T  D 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|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 =  132 bits (332), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 137/250 (54%), Gaps = 10/250 (4%)

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 +  +   V S+GRLD++TEGLL+LT+DG L R
Sbjct: 102 HTYILYNKPKGQLCSRLDKKKRPLIYDFI-DVAPNVQSIGRLDMDTEGLLMLTDDGALTR 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQVTLDTQKGSNAWVT 190
            L  P+ +  R YR R  G V+ + L  L++G   + +G      +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 IIILRGRWREVRRTLEECGHPVRRLMRTRFGPIKLDEDMPKGTWRALNRGEIRK------ 274

Query: 250 LEEAQVNLDA 259
           L +  +N DA
Sbjct: 275 LRDRVINPDA 284


>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 =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 82/224 (36%), Positives = 121/224 (54%), Gaps = 2/224 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAER 72
           R+ KV++  G+ SRR+ E  IAQ RV VNG   +       + D I +DGV   LRK ++
Sbjct: 14  RIQKVLSENGVMSRRKAEEAIAQGRVTVNGHPAQPGNPVDPARDVIAIDGVRVQLRKKKQ 73

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + HKP G VTT SD  GR  V D +    + V  VGRLD N+EGLLLLTNDG  A 
Sbjct: 74  NVYIMLHKPRGFVTTTSDELGRRCVTDLVKDAPAHVYPVGRLDRNSEGLLLLTNDGAFAN 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           ++  PS    + YRV     V  ++   +  G+++ G       V +  ++     + + 
Sbjct: 134 LVMHPSNHISKTYRVTVRPDVSDEQAAKMSAGVMLDGRMTLPATVLVLEKQDGRVVLQIT 193

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           ++EG+NR+++++ E    +V RL R S GP +LG L  G  RE+
Sbjct: 194 IQEGRNRQVRRMCEAVGLEVARLKRTSVGPLKLGMLQPGQWREL 237


>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 =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 92/222 (41%), Positives = 126/222 (56%), Gaps = 15/222 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + +DG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNAVVRIDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V ++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVTEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N    V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL 219


>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 =  132 bits (332), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 92/222 (41%), Positives = 126/222 (56%), Gaps = 15/222 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDH--IEVDG--VP 66
           +++ KV+ARAG  SRRE+E +I   RV VNG   +L ER     +  D+  + +DG  V 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGER-----LEDDNAVVRIDGHVVS 57

Query: 67  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
           ++  E    R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL
Sbjct: 58  VKAQEEVICRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLL 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS Q  R Y VR  G V ++K+  L +G+ ++        V     +
Sbjct: 118 FTTDGELANRLMHPSRQVEREYLVRVFGDVTEEKVRNLVRGVQLEDGMARFEDVMYAGGE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N    V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 178 GINHTFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFL 219


>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 =  132 bits (331), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 88/217 (40%), Positives = 125/217 (57%), Gaps = 11/217 (5%)

Query: 52  VNVMSTDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-S 106
           +NV S+  + +DG  + L +A++   R+ +Y+KP G + T  DP+GR+TVFD LP +  +
Sbjct: 12  INVHSSVKVRIDGNLINLTQAQKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGA 71

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           R I+VGRLDINT GLLL T DG LA  L  P+ +  R Y VR  G VD   LN LKKG+ 
Sbjct: 72  RWIAVGRLDINTSGLLLFTTDGELANRLMHPNREVEREYSVRVFGHVDDAMLNRLKKGVQ 131

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           ++        +      G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L 
Sbjct: 132 LEDGPANFKDIKFGGGVGMNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLM 191

Query: 226 GTLLAGSTREV---SKKILREQLGPHLLEEAQVNLDA 259
            TL  G  +E+       LR+ +G  L  E +  LD 
Sbjct: 192 KTLPRGGWQEMPLDEVNYLRDLVG--LAPETETKLDV 226


>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 =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 79/224 (35%), Positives = 130/224 (58%), Gaps = 5/224 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IAR+G  SRR+ + +I    VKVN  +++   ++V   D +EVDG  L   ++  
Sbjct: 3   RINKFIARSGYTSRRKADELIKNGLVKVNYKIIKEPGIDVKENDLVEVDGQILEIEDKFY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L LY KP+G +T++ DP     + +NL  +  R  + GRLD ++EGLL++TNDG     +
Sbjct: 63  LKLY-KPVGFITSNFDPYNDKDL-NNLLDLDKRFFAAGRLDKDSEGLLIITNDGDFTNEI 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGL 193
             PS +  + Y V+    ++  +++L +KGI I  G    D ++ L  +K +   VT+  
Sbjct: 121 IHPSKKLDKTYIVKVSKLLNNKEISLFEKGIDIGNGEVTSDSKIVLIDKKTNKYKVTI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +G NR+I+++FE+F+ KV  L RIS GP QL  +    TR+ +
Sbjct: 179 HQGYNRQIRRMFEYFSSKVINLKRISIGPIQLSNMKPYETRQFT 222


>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 =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 132/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D  H++ + + +RK +
Sbjct: 4   ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIRKDQ 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QMYYLALYKPRGYVTTASDELGRKTVMELVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+ ++  L  G+V+  G       + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADESQILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K
Sbjct: 184 MTLKEGKNREIRRMCETVGLEVVRLKRNAEGVVKLGMLKPGTYRELTK 231


>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 =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 98/247 (39%), Positives = 151/247 (61%), Gaps = 18/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      +DK     +  L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEDKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK-- 239
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV+++  
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKV 264

Query: 240 -ILREQL 245
             LR +L
Sbjct: 265 DALRAEL 271


>gi|311068833|ref|YP_003973756.1| RluB protein [Bacillus atrophaeus 1942]
 gi|310869350|gb|ADP32825.1| RluB [Bacillus atrophaeus 1942]
          Length = 244

 Score =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 126/227 (55%), Gaps = 5/227 (2%)

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 KP G+++   D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAADDDKGRKVVTDFFKEIPQRIYPIGRLDYDTSGLLLLTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  Q  + Y  +  G   ++ +  L++G+ ++       +   ++LD +K   + + 
Sbjct: 121 LMHPKYQIDKTYVAKVKGIPSKELVRKLERGVQLEEGKTAPAKAKLLSLDKRK-QTSIIQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLDLRGLHTGDARELT 226


>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 =  132 bits (331), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 127/233 (54%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +IA  RV+V+G+ + R  V V   T  I VDG  +  A   
Sbjct: 33  RLQKVLAAAGVGSRRACEELIAAGRVEVDGVPVTRLGVRVDPQTAVIRVDGKRIPPATPF 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP G+VTT SDP GR  V D +  +  RV  VGRLD ++EGLLLLTNDG L   
Sbjct: 93  AYFALNKPRGVVTTMSDPRGRPCVGDLVADLPVRVFHVGRLDTDSEGLLLLTNDGRLTHR 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    + Y     G++ +  ++LL+ G+ +  G    D    L+ + G+   V V 
Sbjct: 153 LTHPSHAVPKTYVADVEGRLGRTGVHLLRSGVDLADGPAQADAVRILE-RYGARTLVEVV 211

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + EG+   ++++       V RL+R + GP  LG L  G+ R+++ + L E L
Sbjct: 212 VHEGRTHLVRRMLAAVGHPVRRLVRTAIGPVALGQLRPGARRQLTPRELGELL 264


>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 =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 125/230 (54%), Gaps = 1/230 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR+ E ++  +RV+VNG L        +  D IEVD  PL+ A
Sbjct: 1   MTRQRLQKLIASAGVCSRRKAEDLLRDRRVRVNGQLATLGDQADLDVDTIEVDDRPLQTA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGG 129
            + R+ L +KP G++ +  DP  R TV + +P      +  VGRLD  + G LLL+N G 
Sbjct: 61  PQARVLLLNKPPGVICSCRDPQRRRTVLELVPPDLREGLHPVGRLDAESRGALLLSNQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   + +LN  ++G+V+ G      +V L  +    + +
Sbjct: 121 LTLQLTHPRYNHRKTYRVTVAGLPSEKQLNQWRRGVVLDGTVTRPAEVNLVKKSPQASVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V LREG+NR+I++V      +V  L RI+ G   LG++  G  RE+S++
Sbjct: 181 EVILREGRNRQIRRVALSLGHRVLDLQRIAIGRLTLGSMREGCWRELSRQ 230


>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 =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 86/234 (36%), Positives = 132/234 (56%), Gaps = 23/234 (9%)

Query: 7   VQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           ++  + P+   ++ KV+A+AG  SRR +E  IA  RV VNG   E A +   V+  D ++
Sbjct: 6   IEAEYQPEAGEKLQKVLAQAGFGSRRNMEEWIAAGRVSVNG---EPATLGMRVVPGDLVK 62

Query: 62  VDGVPLRKAER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            +   +R  ER    R+ LYHKP G + +  DP+ R++VFD LP +   + I+VGRLD N
Sbjct: 63  TERRTIRVGERDHTARVLLYHKPEGEIVSRDDPEKRASVFDKLPKLRGQKWIAVGRLDFN 122

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQ 176
           T GLL+ T  G LA  L  P  +  R Y VR  G + +D++  +LK+G++++     D  
Sbjct: 123 TSGLLIFTTSGELANRLMHPRFEVEREYAVRVQGSMTEDQITQVLKEGVMLE-----DGP 177

Query: 177 VTLDT-----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           VT D       +G N W  V L+EG+NR +++ F+     V+RLIR+ +G   L
Sbjct: 178 VTFDKLEDNGGEGFNHWYKVMLKEGRNRIVRRTFDALALPVSRLIRVRFGIINL 231


>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 =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 87/237 (36%), Positives = 123/237 (51%), Gaps = 7/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PL 67
            T +R+ KV+A  G+ASRR  E +I   +V VNG   +       + D IE  G    P 
Sbjct: 1   MTTERLQKVLAHWGVASRRHAETLIRSGQVFVNGQRAKLGDKVDPARDRIEYKGERLNPP 60

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLL 124
           R  +R  L L HKP G++ T  DP GR+TV D LP ++ RV     VGRLD ++ G LLL
Sbjct: 61  RPPQRLYL-LLHKPKGVLCTCHDPQGRTTVLDLLPPMYQRVGGLHPVGRLDADSSGALLL 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG     L  P     + YRV   GQ  ++ L   ++GI + G+      V     +G
Sbjct: 120 TNDGAFTYYLSHPRHHIPKTYRVWVQGQPPENVLQRWRQGIPLDGVMTLPATVKRLRSEG 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             A + + L EG+NR+I++V +   + V  L RI+ GP  LG L   + R +S+  L
Sbjct: 180 DRALLEIILHEGRNRQIRRVADQLGYPVLALQRIAIGPVHLGHLRPRAVRPLSRHEL 236


>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 =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 87/217 (40%), Positives = 119/217 (54%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +++ KV+ARAG  SRRE+E +I   RV VNG +             I +DG  V  +  E
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGQVARLGERLEDENAVIRIDGHTVSAKAQE 62

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL T DG
Sbjct: 63  EVVCRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  R Y VR  G++++ K+  +  G+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRQVEREYLVRVFGEINEKKVRNVVNGVELEDGMARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE+++++E     V+RL R+ YG   L
Sbjct: 183 FYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIYL 219


>gi|322434202|ref|YP_004216414.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
 gi|321161929|gb|ADW67634.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
          Length = 312

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 86/243 (35%), Positives = 129/243 (53%), Gaps = 22/243 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I   RV+VNG ++        +T DHI VDG  ++  E+
Sbjct: 24  ERLQKILAQAGLASRRKAEEIILDGRVQVNGTVVTELGTRADATKDHIRVDGKLIKGPEQ 83

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTN 126
            + ++ +KP G VTT  DP  R TV   +           R+  VGRLD  +EGLLL+TN
Sbjct: 84  QKYYMVNKPRGYVTTLDDPQHRPTVMQLMTPKSGPHETQVRLYPVGRLDYLSEGLLLMTN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-------------QGICYG 173
           DG LA  L   ST   + Y V+  G      L+ +++GI+I               I   
Sbjct: 144 DGDLANALSKASTGVEKTYLVKTSGVPPDSALDQIRRGIMIDRGRLDEVRAGRRDRILTA 203

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V L  ++G N W  V L EG+NR+++K+FE     V ++ RI YG  +L  +  G  
Sbjct: 204 PAKVEL-VRRGDNPWYEVTLTEGRNRQLRKMFEEVGHHVEKIRRIGYGALRL-DVAPGEF 261

Query: 234 REV 236
           RE+
Sbjct: 262 REL 264


>gi|197122579|ref|YP_002134530.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172428|gb|ACG73401.1| pseudouridine synthase [Anaeromyxobacter sp. K]
          Length = 329

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 82/237 (34%), Positives = 123/237 (51%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           + EG+   +K++ E    +V RL R  +G   +G L  G  R +     + LR+++G
Sbjct: 184 VGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGKFRRLEPEEVRALRQRVG 240


>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 =  131 bits (330), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 84/233 (36%), Positives = 123/233 (52%), Gaps = 1/233 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRK 69
            T +R+ K +ARAG+ASRR+ E +I   RV V+G ++      + S    + VDG  +  
Sbjct: 1   MTKERLQKYLARAGVASRRQGEELIRAGRVSVDGRIVTTLGQLIDSEKAEVMVDGRKVLP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R  + +KP G VTT +DP GR  V D LP    R+  VGRLD +  GLLLLTNDG 
Sbjct: 61  PPHCRTIVLNKPYGCVTTMADPQGRRKVIDLLPDQEERLYPVGRLDYDATGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  + YR    GQ        L++GI + G      QV L       + +
Sbjct: 121 LAHRLMHPRYKVAKTYRATVAGQFSPAARRRLREGITLDGRLTIPEQVRLVKTSSERSVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +REG+   +K++       V +L RI+YGP +LG L  G+ RE++++ +R
Sbjct: 181 ELTIREGRYHLVKRLCAAVGCPVLKLKRIAYGPLRLGRLALGTWRELTQEEVR 233


>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 =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 82/237 (34%), Positives = 123/237 (51%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           + EG+   +K++ E    +V RL R  +G   +G L  G  R +     + LR+++G
Sbjct: 184 VGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGRFRRLEPEEVRALRQRVG 240


>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 =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 86/243 (35%), Positives = 126/243 (51%), Gaps = 6/243 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R+ K+IA AG+ SRR+ E ++ QQRV+VNG ++          D I VDG PLR  
Sbjct: 1   MTGERLQKLIAAAGLCSRRKAEELLRQQRVRVNGQIVALGDRADPEQDRICVDGRPLRAP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGG 129
           E TRL L +KP+G++++  DP GR TV D +P+   R +  +GRLD ++ G LLLTN G 
Sbjct: 61  EATRLLLLNKPVGVISSCYDPRGRRTVLDLIPNHLRRGLHPIGRLDADSRGALLLTNRGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G      L   + G+ + G       V    ++G    +
Sbjct: 121 LTLRLSHPRYAHSKTYRVWLEGDPSPQHLQSWRDGVWLDGQRTQPATVQRLRREGGRTLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L+EG+NR+I++  +     V  L RI+     LG+L  G  R + +   R     HL
Sbjct: 181 EVTLQEGRNRQIRRTADQLGHPVLDLQRIAIAGIPLGSLAEGEWRALHRGEWR-----HL 235

Query: 250 LEE 252
           + E
Sbjct: 236 MPE 238


>gi|302533645|ref|ZP_07285987.1| pseudouridine synthase [Streptomyces sp. C]
 gi|302442540|gb|EFL14356.1| pseudouridine synthase [Streptomyces sp. C]
          Length = 239

 Score =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 125/225 (55%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V   D I+VDG+ +   +  
Sbjct: 4   ERLQKVLARAGMGSRRACEELIEQARVEVNGEIVTEQGKRVQPKDEIKVDGLTV-ATQSF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA  
Sbjct: 63  LFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELAHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G + +D    LK+GI ++ G    D    +D Q G N  V V 
Sbjct: 123 LTHPKYGVQKTYVAAITGSLPRDIGKRLKEGIELEDGYARADNFRVVD-QVGKNYLVEVT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+   ++++     + V++L+R S+GP +LG   +G  R ++
Sbjct: 182 LHEGRKHIVRRMLAEAGFPVDKLVRTSFGPIELGDQKSGWLRRLT 226


>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 =  131 bits (329), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 87/227 (38%), Positives = 125/227 (55%), Gaps = 3/227 (1%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L + +  RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYLAMNKPRGVVSTMADEKGRTAIADFLGNRVQERVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y     G + +     L  GI +  G    D    +DT  G  A V 
Sbjct: 138 HRLTHPSYGVPKTYLCEVSGPIPRTLGRRLAAGIELTDGPATVDAFRVVDTL-GRTAQVE 196

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+   ++++F+     V+RL+R S GP +LG L AG TR ++
Sbjct: 197 VTLHEGRKHIVRRLFDAVGHPVSRLVRTSIGPIRLGDLRAGRTRRLT 243


>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 =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 126/228 (55%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +ARAGI SRR  + ++   RVKVN  ++    + V    D I VDG P++     
Sbjct: 6   RLNKALARAGICSRRRADGLVFSGRVKVNDEVVREPGIRVDPEKDSIIVDGRPVKIETEQ 65

Query: 74  RLWLYH----KPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTND 127
              L H    KP+ +VTT SDP GR+ V D LP    R  +  VGRLD  + GLL+LTND
Sbjct: 66  ERELVHVMLNKPVQVVTTTSDPGGRAKVTDLLPDRLRRMRLFPVGRLDYFSRGLLILTND 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G LA  L  PS +  +VYRV+  G + + KL ++++G+V+ +G     ++V +  Q   +
Sbjct: 126 GDLAHSLTHPSRKIPKVYRVKMRGDLSKKKLQIMRRGMVLSEGEKLAPVEVKILQQTRDS 185

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L +G NR+I+++    +  V  L+RI  GP  LG L  G  R
Sbjct: 186 VLAEMTLVQGINRQIRRMCRDLDMVVLSLVRIRQGPLALGELKPGEWR 233


>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 =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 78/208 (37%), Positives = 115/208 (55%), Gaps = 2/208 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K+IARAG+ASRR  E +I   RV+VNG ++ E         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 LREGKNREIKKVFEFFNWKVNRLIRISY 220
           LREG+N++I+++ E   W V RL R ++
Sbjct: 182 LREGRNQQIRRMGEATGWPVMRLARTTF 209


>gi|154686561|ref|YP_001421722.1| RluB [Bacillus amyloliquefaciens FZB42]
 gi|154352412|gb|ABS74491.1| RluB [Bacillus amyloliquefaciens FZB42]
          Length = 244

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 125/227 (55%), Gaps = 5/227 (2%)

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 KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAADDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L++GI ++       +   ++LD +K   + + 
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPSKELLRKLERGIQLEEGKTAPARAKLLSLDKRK-QTSIIQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE     V +L R  Y    L  L  G  RE+S
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHDVLKLKREEYAFLDLRGLRTGDARELS 226


>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 =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 85/233 (36%), Positives = 130/233 (55%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG+ +RR+VE +I Q RV VNG ++E  AV V    D + VDG  +R  +R 
Sbjct: 2   RLNKFLAYAGLGARRKVEELIKQGRVTVNGEVVENPAVEVDPKKDEVRVDGERVRLPKRF 61

Query: 74  RLWLYHKPIGLVTT-HSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++KP G++T    +P D R  V D       R+  VGRLD NTEGLLL+TNDG LA
Sbjct: 62  IYLAFNKPQGVLTAMEREPGDKRPIVADYFRKYPVRLFPVGRLDYNTEGLLLMTNDGELA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYG----DMQVTLDTQKG 184
             L  P     + Y  +  G+V   ++  +KKG  +   +G  +     D+++   ++ G
Sbjct: 122 ERLAHPRYHIPKTYIAKVKGRVTPAEIERMKKGAKLVDDKGKPFFAKPIDIKLLKPSRTG 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            N +V +    GKNR +++ F+ F+  V +L RI+ GP +LG L  G  RE++
Sbjct: 182 RNTYVQISFDIGKNRVVRRFFDRFDHGVLKLKRIAIGPLKLGNLPKGMYRELT 234


>gi|315103786|gb|EFT75762.1| conserved hypothetical protein [Propionibacterium acnes HL050PA2]
          Length = 245

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 87/235 (37%), Positives = 129/235 (54%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+VNG +++E+        D I VDG  +  A R 
Sbjct: 8   RLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIPTARRH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTNDG  A
Sbjct: 68  VYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTNDGEFA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      ++ V V
Sbjct: 127 NRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQASEEHSLVEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+NR ++++ +     V RL R + GP +L  L  G  RE++     E+LG
Sbjct: 187 SLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTH----EELG 237


>gi|289665762|ref|ZP_06487343.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 527

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 97/247 (39%), Positives = 152/247 (61%), Gaps = 18/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK-- 239
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV+++  
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQEKV 264

Query: 240 -ILREQL 245
             LR +L
Sbjct: 265 DALRAEL 271


>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 =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 127/227 (55%), Gaps = 5/227 (2%)

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 KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L++GI ++       +   ++LD +K   + + 
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKK-QTSIIQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELT 226


>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 =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 121/226 (53%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G+ SRR+ + +I   +V++NG L E  A  V+  D I V+   L  A+   
Sbjct: 2   RLNKAIAATGLCSRRKADELILAGQVRINGTLEENPARRVLPGDCIAVNDRELAAAQEYY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             L HKP+  V T +DP+GR TV   LP      R+  VGRLD  +EGLLLLTNDG LA+
Sbjct: 62  YLLLHKPVQTVCTVNDPEGRPTVMAYLPPEVRHLRLYPVGRLDYFSEGLLLLTNDGELAQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V   G V +  L  +++G+ + +G     + V   T +  N  + +
Sbjct: 122 RLTHPRHHQPKTYEVLIRGSVPETALAAMRRGMRLDEGQALLPVDVEAKTAENGNTLLRM 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L +G NR+I+++       + RL R++ GP  LG L  G+ R ++
Sbjct: 182 VLHQGVNRQIRRMCRDLGLTILRLRRVAQGPLALGNLKPGAARALT 227


>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 =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 83/241 (34%), Positives = 136/241 (56%), Gaps = 8/241 (3%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M +     +N  P   +R+ KV+A AGI SRR+ E +I + RV+V+G  +    + V   
Sbjct: 1   MPENPAESDNPAPLRLERLHKVLAFAGIDSRRKCEALIQEGRVEVDGKFVTELGMKV-DP 59

Query: 58  DHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
           +H E  VDG  L+  +R   ++ +KP G+++T+ DP GR+ V D +P    R+ ++GRLD
Sbjct: 60  EHQEILVDGQRLKFGKRV-YYMLNKPPGVLSTNFDPAGRTRVIDMVPQDV-RLFTIGRLD 117

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             +EGL+++TNDG LA  L  P  +  + YRV   G  + D +  +++G+ +       +
Sbjct: 118 RASEGLIVVTNDGELANRLAHPRYEIEKTYRVEVAGHPEPDAITFVRRGVHLAEGFVQPV 177

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            V +  +   +  + V L EGKNREI+++      KV RL RI+ GP +LG +  G+ RE
Sbjct: 178 SVVMKRKNKQSTTLEVILDEGKNREIRRLMAKIGHKVLRLKRIAMGPLRLGEMPEGAFRE 237

Query: 236 V 236
           +
Sbjct: 238 L 238


>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 =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 84/251 (33%), Positives = 132/251 (52%), Gaps = 27/251 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE +++I   RVKVNG +++     V   D + V+G P++K+ +  
Sbjct: 2   RLNKFISHHTTYSRREADKLIFDGRVKVNGRVIKEPGFEVEEGDKVAVNGKPVKKSTKYT 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             +Y+KP G + T  D  GR T++D+LP  +   I VGRLD N+EGLL+LT+   +A  L
Sbjct: 62  CIVYNKPRGELVTKKDDRGRKTIYDSLPKKYRHFIPVGRLDFNSEGLLILTDSPKVAHAL 121

Query: 135 ---ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQV 177
              +LP     RVY+++  G++    +  ++ G+ +                  +   Q+
Sbjct: 122 MNSDLP-----RVYKLKIKGEITDKMIEAMQNGVEVGDAGAHEENEIKKMVLKPFLSAQI 176

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +T K S   V +G  EGKNRE+++ F  F  +V  L R+SYG   L  L  G TR   
Sbjct: 177 IKNTPKYSTLKVAIG--EGKNRELRRFFANFGSEVVDLKRLSYGWVSLNALPTGKTRYFD 234

Query: 238 K---KILREQL 245
           K   K+L+E L
Sbjct: 235 KKEYKLLKEFL 245


>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 =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 80/219 (36%), Positives = 120/219 (54%), Gaps = 5/219 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A+ GIASRRE E MI   RV++NG L           D I +DG  L + +R 
Sbjct: 3   ERLQKILAQWGIASRREAEEMIRHSRVQINGKLAHLGQKVDPQKDAIAIDGKTLSEKQRP 62

Query: 74  RL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDG 128
            L   L HKP G+V+T  DP  R TV D LP      S +  VGRLD ++ G L+LTNDG
Sbjct: 63  ALIYLLLHKPAGVVSTCYDPHRRKTVLDLLPKELREGSGIHPVGRLDADSTGALILTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + YRV   G   +  L + ++G+V++G      +V L   +   ++
Sbjct: 123 NLTFGLTHPRHSISKTYRVLVKGHPPEVVLQMWREGVVLEGRKTRAAEVHLIEHRAEQSF 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           + + L+EG+NR+I+++ +   + V +L R + GP QL T
Sbjct: 183 LEIVLQEGRNRQIRRIAQQLGYPVIKLHRTAIGPIQLQT 221


>gi|295105527|emb|CBL03071.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii SL3/3]
          Length = 275

 Score =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 131/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D  H++ + + ++K +
Sbjct: 4   ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G VTT SD  GR TV D +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QLYYLALYKPRGYVTTASDELGRKTVMDLVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+  +  L  G+V+  G       + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADEATILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K
Sbjct: 184 MTLKEGKNREIRRMCESVGLEVVRLKRNAEGVVKLGMLKPGTYRELTK 231


>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 =  130 bits (328), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 131/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D  H++ + + ++K +
Sbjct: 4   ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G VTT SD  GR TV D +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 64  QLYYLALYKPRGYVTTASDELGRKTVMDLVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+  +  L  G+V+  G       + + T +     + 
Sbjct: 124 QAVTHPSGGISKLYRVTVQPRADEATILKLSSGVVLDDGTKTMPCAINVVTDEPGRTVME 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K
Sbjct: 184 MTLKEGKNREIRRMCESVGLEVVRLKRNAEGVVKLGMLKPGTYRELTK 231


>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 =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 86/237 (36%), Positives = 128/237 (54%), Gaps = 7/237 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G+ SRR+ + +I   RV VNGI     A  V   D + VDG PL  A+   
Sbjct: 2   RLNKAIAASGLCSRRKADELILSGRVTVNGIAEPNPARQVSPEDALGVDGRPLTGAQDFY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP+ +V T +DP+GR TV + LP      R+  VGRLD  +EGLLLLTNDG LA+
Sbjct: 62  YLMLNKPVQVVCTVNDPEGRPTVMEYLPKNMRALRLYPVGRLDYFSEGLLLLTNDGQLAQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  PS    + Y V   G V    L  ++ G+ + +G     ++V     KG      V
Sbjct: 122 RLTHPSHHQPKTYEVLVRGAVSDASLAAMRHGMRLAEGEDLMPVEVEASFTKGRTLLRMV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQL 245
            L +G NR+I+++       +  L R+S GP +LG L +G  R+++    K+L+E +
Sbjct: 182 -LHQGLNRQIRRMCRDLGLTILYLKRVSQGPIELGGLASGRARQLTAAEIKVLKESV 237


>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 =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 147/237 (62%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 48  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQ-TGMSVRSGDKIELDGRSFVASALT 106

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 107 EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 166

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 167 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 226

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 227 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQ 281


>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 =  130 bits (327), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 126/227 (55%), Gaps = 5/227 (2%)

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 KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAAQDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L++GI ++       +   ++LD +K   + + 
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKK-QTSIIQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELT 226


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 87/235 (37%), Positives = 129/235 (54%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+VNG +++E+        D I VDG  +  A R 
Sbjct: 8   RLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIPTARRH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTNDG  A
Sbjct: 68  VYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTNDGEFA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      ++ V V
Sbjct: 127 NRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQAGEEHSLVEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+NR ++++ +     V RL R + GP +L  L  G  RE++     E+LG
Sbjct: 187 SLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTH----EELG 237


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 147/237 (62%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQ 261


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 86/249 (34%), Positives = 137/249 (55%), Gaps = 10/249 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +I   RV+VN  ++    V V    D I+VDG  ++  E+
Sbjct: 3   ERLQKVLAAAGVASRRKCEEIILAGRVEVNDKVVSTLGVKVNPHQDVIKVDGRAIQNQEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP G++T+ SDP+GR  V D L  I  RV  VGRLD +TEGLL+LTNDG  A 
Sbjct: 63  IYI-LFNKPKGVITSVSDPEGRRVVGDFLKGIKERVYPVGRLDYDTEGLLILTNDGEFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWV 189
           ++  P     + Y     G      L  L++G+ ++       +V    +D  K   + +
Sbjct: 122 MVTHPRHHVSKTYHATVKGVPHGSVLEKLREGVKLEDGMTAPAEVEYHDIDPDK-KQSVI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK----ILREQL 245
           ++ + EGKNR+++++FE   + V RL R+ +G   L  L  G  R + K+    +L E  
Sbjct: 181 SITIYEGKNRQVRRMFEAVGYPVTRLKRVKFGSIPLVGLPRGKFRRMRKEEVQALLNEAS 240

Query: 246 GPHLLEEAQ 254
             H +++ Q
Sbjct: 241 QSHKVQKGQ 249


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 80/229 (34%), Positives = 132/229 (57%), Gaps = 11/229 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           +K+  +      P R+ K ++ +G+ SRRE+E  I    V VNG   ++A++   V   D
Sbjct: 199 LKEVRVDHAEIEPVRLQKALSSSGVGSRREMEEWIEAGLVTVNG---KKASLGDKVGPQD 255

Query: 59  HIEVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
            + V G  + L+  +R  R+ +YHK  G + T  DP+GR TVFD LP    SR +++GRL
Sbjct: 256 KVLVKGDQIKLKWPDRLPRVIMYHKEEGEIVTRDDPEGRVTVFDRLPQAKSSRWVAIGRL 315

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY 172
           D+NT GLLL+T  G LA  +  PS +  R Y VR  G++  + +  + KG+ ++     +
Sbjct: 316 DVNTSGLLLITTSGELANRMMHPSFEVEREYSVRVLGELTPEIMKEMTKGVELEDGEARF 375

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             +  T   ++ +N W  V ++EG+NRE++++FE F   V+RL+R+ +G
Sbjct: 376 DRIFQTGGQEESANQWYNVVIKEGRNREVRRMFEHFGLTVSRLMRVRFG 424


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 79/228 (34%), Positives = 125/228 (54%), Gaps = 7/228 (3%)

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 KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAADDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWV 189
           L  P  +  + Y  +  G   ++ L  L++GI ++          M ++LD +K   + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPSKELLRKLERGIQLEEGKTAPARAKM-LSLDKRK-QTSII 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+NR+++++FE     V +L R  Y    L  L  G  RE++
Sbjct: 179 QLTIHEGRNRQVRRMFEAIGHDVLKLKREEYAFLDLRGLHTGDARELT 226


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 79/233 (33%), Positives = 122/233 (52%), Gaps = 2/233 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVP 66
           +E   P RV K +ARAG+ASRR  E ++   RV VNG ++ E  A      D + VDG  
Sbjct: 5   EERIVPMRVQKFLARAGVASRRRSEDLMTAGRVCVNGEVVTELGAKVDPRVDTVTVDGRE 64

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           +R  +     + +KP G +TT SDP GR+ V + +PS  +  +  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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +T+ + EG+ R+++++ +     V  L R  +GP  LG L  GS RE++K
Sbjct: 185 KSRITLVIHEGRTRQVRRMCQKVGHPVLELHRAQFGPLTLGDLPEGSWRELTK 237


>gi|166712399|ref|ZP_02243606.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 553

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 147/237 (62%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQ 261


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 77/219 (35%), Positives = 125/219 (57%), Gaps = 7/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ K+++  G  SRR +E MI    + +NG   ++ +R     +    I+ + V ++K 
Sbjct: 3   EKIQKILSHLGYGSRRNIENMIKFGDISINGKKIVIGQRLNNKNIEVITIKGETVSIKKT 62

Query: 71  E-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           + +T++ +Y+KP G + T +D   R  VFD LP +   R IS+GRLDINT GLLL TN+G
Sbjct: 63  DFKTKIIIYNKPEGEICTRNDYKKRPIVFDKLPLLNIHRWISIGRLDINTRGLLLFTNNG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSN 186
            LA  L  PS +  R Y +R  G+++++ +N+LK G+ I+     +  +Q         N
Sbjct: 123 NLANELMHPSNKIEREYYIRVFGKINKNTMNILKNGVKIKDGNAAFKSIQTIDHACSKKN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W    L EG+NREI+ +++    +V+RLIRI YG   L
Sbjct: 183 KWFKGVLCEGRNREIRSMWQAVQCQVSRLIRIRYGNIFL 221


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 151/247 (61%), Gaps = 18/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K     +  L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK-- 239
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E++++  
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKV 264

Query: 240 -ILREQL 245
             LR +L
Sbjct: 265 DALRAEL 271


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 90/242 (37%), Positives = 122/242 (50%), Gaps = 15/242 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T +R+ KV+A AG+ASRR  E +IA  RV V+G+++    V V  S   I VDG  +   
Sbjct: 74  TGERLQKVLAHAGVASRRACEEIIAAGRVSVDGVVVTEPGVRVDPSRQEIRVDGSRVLTD 133

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------------RVISVGRLDINT 118
                 L HKP G+VTT  DP GR TV D      S            R++ VGRLD  T
Sbjct: 134 PDVITVLLHKPAGVVTTMEDPQGRPTVADLAEQFISEHRTELEHPESVRLVHVGRLDTET 193

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQV 177
           EGLLLL+NDG LA  L  PS +  + Y     GQV+      L++GI +  G+   D  V
Sbjct: 194 EGLLLLSNDGDLAHRLMHPSFEISKTYVAIVEGQVEGWVPRKLRRGIELDDGLAQADRVV 253

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             D    S + V + L  GKNR ++++ +     V RL R   GP  +G L  G  R ++
Sbjct: 254 VKDAGP-SGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTKLGPLGIGGLRPGQMRRLT 312

Query: 238 KK 239
            +
Sbjct: 313 GE 314


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 147/237 (62%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQ 261


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 128/226 (56%), Gaps = 5/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KVIA+AG+ SRR+ E++I + +V VNG  +      V +  D + V+GVPL K E 
Sbjct: 5   ERLQKVIAQAGVTSRRKAEQLILEGKVIVNGNKVTELGTKVDLQHDEVIVEGVPLEKEEP 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY KP G++++  D  GR  V D +P+   R+  +GRLD +T GL+LLTNDG  A 
Sbjct: 65  IYFLLY-KPTGVISSVDDEKGRKVVTDFIPT-DKRIFPIGRLDYDTSGLILLTNDGDFAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
           +L  P  +  + Y  +  G   ++ +  L+KGI ++        ++V+   +K   + + 
Sbjct: 123 LLMHPKHEIYKTYIAKVEGVPLREDIKKLEKGIHLEDGRTAPAKVKVSRSDKKKGTSIIE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EG+NR+++++FE     V +L R +YG   L  L AG  RE+
Sbjct: 183 ISIHEGRNRQVRRMFEAIGHPVMKLKRENYGFLNLKGLNAGDFREL 228


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 147/237 (62%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSIEVAQ 261


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 124/229 (54%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V+VNG  +    + V   D + VDGVPL + E  
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIASGHVQVNGKTVTEMGIKVSEHDEVVVDGVPLHR-EAH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP  ++T+  D  GR TV D L    +  RV  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRSVITSAHDDKGRRTVVDILKEEGVAERVYPVGRLDYDTTGILLLTNDGELA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             L  P  +  + Y  +  G V+ + L  L+ G+ + G      +  L     K   + V
Sbjct: 121 NRLMHPKFEVEKTYIAKVRGIVNNNDLKQLRIGVEVNGRLTKKAKSRLIETDHKKQTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + + EG+  ++K +F+  +  V +L R +YGP  L  L +G  RE+ +
Sbjct: 181 KLTIHEGRYHQVKLMFDAIHHPVIKLHRETYGPLDLNGLQSGEFRELKQ 229


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 87/227 (38%), Positives = 125/227 (55%), Gaps = 4/227 (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 KP G++T+ +DP GR  V D L  I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  VYLLLY-KPTGVITSVTDPQGRRVVIDLLKGIQERVYPVGRLDYDTSGLLLLTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-AWVT 190
            L  PS +  +VYR    G    +K+  L  GI ++ G+        L  +  S  A V 
Sbjct: 121 RLAHPSYEIDKVYRAWVKGIPSPEKVRKLATGIRLEDGMTSPGQSKLLKAESSSQRALVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++ E     V  L RI  G   L  L  G  R+++
Sbjct: 181 LTIHEGRNRQVRRMCEAIGHPVLTLERIRLGFLTLDGLKPGEFRKLT 227


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 78/219 (35%), Positives = 125/219 (57%), Gaps = 7/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +++ K+++  G  SRR +E MI    V +NG   ++ +R     +    I+ + V ++K 
Sbjct: 3   EKIQKILSHLGYGSRRNIENMIKFGDVSINGKKIVIGQRLNNKNIEVITIKGETVSIKKT 62

Query: 71  E-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
           + +T++ +Y+KP G + T +D   R  VFD LP +   R IS+GRLDINT GLLL TN+G
Sbjct: 63  DFKTKIIIYNKPEGEICTRNDYKKRPIVFDKLPLLNIHRWISIGRLDINTRGLLLFTNNG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSN 186
            LA  L  PS +  R Y +R  G+++++ +N+LK G+ I+     +  +Q         N
Sbjct: 123 NLANELMHPSNKIEREYYIRVFGKINKNTMNILKNGVKIKDGYAAFKSIQTIDHACSKKN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W    L EG+NREI+ +++    +V+RLIRI YG   L
Sbjct: 183 KWFKGVLCEGRNREIRSMWQAVQCQVSRLIRIRYGNIFL 221


>gi|222084363|ref|YP_002542892.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221721811|gb|ACM24967.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 278

 Score =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 131/233 (56%), Gaps = 19/233 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNG---------ILLERAAVNVMSTDHIEVDGVP 66
           + + +++ G  SR + E +IA  RV V+G         I L+RA         I VDG  
Sbjct: 27  LPRALSKLGYCSRTQAEALIAAGRVTVDGREITDPTAWIDLDRA--------RIAVDGEA 78

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLT 125
           +  AE+   ++ +KP GLVTT  DP+GR TV+D L  I +R ++ VGRLD  +EGLLL T
Sbjct: 79  I-AAEKKLYFMLNKPRGLVTTRDDPEGRPTVYDCLRDIDARHLAPVGRLDKASEGLLLFT 137

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ND  LA+ L  P +   ++Y V+ +  ++Q+ L+ +++G++  G         L      
Sbjct: 138 NDTVLAQALLDPISHVGKIYHVQVNTIMEQELLDRMERGVIDDGELLTATAARLLRSGDR 197

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           N W+ V L+EG+NR+I+++ E    +  RL+R+++G   LG L  G+ R +++
Sbjct: 198 NGWIEVELKEGRNRQIRRMLEVLGVECLRLVRVAFGDIALGDLAKGAVRALTE 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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 127/229 (55%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KV+A  GI SRRE ER+IA  +VKVNG  +          D + +DG  +R   R 
Sbjct: 4   QRIQKVLADQGICSRREAERLIAAGKVKVNGRPVGLGDKMDPDYDKVSIDGKNVRIV-RK 62

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R + Y   HKP G +TT SD  GR TV D +  + + +  VGRLD ++EGLLL+T+DG  
Sbjct: 63  RQYTYIMLHKPRGYLTTRSDDRGRKTVMDLVADVPAMLRPVGRLDKDSEGLLLMTDDGAF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
             +L  PS    ++YRV  + +  ++++  +  G+V+  G+      + + T +     +
Sbjct: 123 INLLTHPSGGVGKLYRVTVNPRATEEQVVQMASGVVLDDGVRTQPCVIHVVTDEPGRTVL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + L EG+NR+I+++      +V RL R + GP +LG L  G  RE+ K
Sbjct: 183 EITLHEGRNRQIRRMCSAVGLQVVRLKRSAEGPVKLGMLQPGEYRELKK 231


>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 =  130 bits (326), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 87/235 (37%), Positives = 128/235 (54%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+VNG +++E+        D I VDG  +  A R 
Sbjct: 8   RLQKVLAQAGLASRRAAEEMIAAGRVEVNGELIVEQGRRVDPEHDEIRVDGSRIPTARRH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+T  DP+ R  + D   +P    R+  VGRLD  T GL+LLTNDG  A
Sbjct: 68  VYYVLNKPRGVVSTMDDPESRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTNDGEFA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + L+ Y     G+VD   +  L KG+ ++        V L      ++ V V
Sbjct: 127 NRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGDEHSLVEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+NR ++++ +     V RL R + GP +L  L  G  RE++    RE+LG
Sbjct: 187 SLHEGRNRIVRRMMDSVAHPVRRLSRTAIGPVRLKRLSRGDMRELT----REELG 237


>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 =  130 bits (326), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 151/247 (61%), Gaps = 18/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K     +  L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK-- 239
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E++++  
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKV 264

Query: 240 -ILREQL 245
             LR +L
Sbjct: 265 DALRAEL 271


>gi|221310234|ref|ZP_03592081.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
          Length = 245

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 129/234 (55%), Gaps = 5/234 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           I+ E    +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+
Sbjct: 10  IILEVKDMERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGL 69

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            + + E     LY KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLT
Sbjct: 70  KVEREEPVYFLLY-KPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLT 128

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQ 182
           NDG  A  L  P  +  + Y  +  G   ++ L  L++GI ++       +   ++LD +
Sbjct: 129 NDGEFANKLMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKK 188

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           K   + + + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 189 K-QTSIIQLTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 241


>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 =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 120/225 (53%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +G  SRR+ E +I Q +V+VNG ++      V   D + V+G P+   E  
Sbjct: 2   ERLQKVIAASGYTSRRKAEDLIVQGKVEVNGQVVRELGTKVKKGDIVTVEGKPIV-GENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G V T  D   R  V D    +  R+  VGRLD +T GL++++NDG  A +
Sbjct: 61  VYYVFYKPKGCVCTLDDEFDRPIVTDYFTDVKERIYPVGRLDFDTTGLIIMSNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWV 189
           +  P +   ++Y V   G ++   LN L+KGI ++G+    C   ++V     +     +
Sbjct: 121 IMHPRSHLEKIYEVSVKGLINGQTLNKLEKGIYLEGVKTLPC--KIKVVNKDIEHKTTML 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNR++KK+FE     V RL R+S G   L  L  G  R
Sbjct: 179 KIKLVEGKNRQVKKMFESVGHPVKRLHRVSIGCVNLKGLTPGKYR 223


>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 =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 125/230 (54%), Gaps = 5/230 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AG+ASRR  E +I   +VKVNG ++      V   D + V+G P+ + 
Sbjct: 1   MAKERLQKVIAHAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDG 128
           E+   +L  KP G++++  D  GR TV D L +  + +RV  VGRLD +T GLL++TNDG
Sbjct: 60  EQHEYYLLDKPRGVISSAHDDKGRKTVVDILKNEGVQTRVYPVGRLDYDTTGLLVMTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSN 186
            LA  L  P  +  +VY  +  G V  D++ LL++G+ I G      +  L    Q+   
Sbjct: 120 ELANRLMHPRFEVDKVYIAKVKGLVSNDEMRLLREGVKIDGKKSQPARTKLLEANQRQKT 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + V + + EG   ++KK+ E     V +L R SYGP  L  L  G  R++
Sbjct: 180 SVVKLTIHEGHYHQVKKMMEAVGHPVLKLHRESYGPLTLAGLNPGQFRKL 229


>gi|221314557|ref|ZP_03596362.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. NCIB
           3610]
          Length = 229

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 126/226 (55%), Gaps = 5/226 (2%)

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 KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L++GI ++       +   ++LD +K   + + 
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKK-QTSIIQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 225


>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 =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 124/225 (55%), Gaps = 9/225 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V VNG ++      V  +D + VDGVP+++ E  
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIAAGHVAVNGQVVTELGTKVTKSDQVTVDGVPIKR-EPL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + +L +KP G+V+T  D  GR TV D L    +  RV  VGRLD +T G+LLLTNDG LA
Sbjct: 61  KYYLLNKPRGVVSTAHDDKGRRTVVDILKDDDVEERVYPVGRLDYDTTGILLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----DTQKGSNA 187
             L  P  +  + Y  +  G +    L  L++G+++ G    + +  L    D ++ S  
Sbjct: 121 NKLMHPKFEVEKTYIAKVKGVLSNHDLQKLRQGVIVDGRKTREAKSKLLEVADNRQSSRV 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            +T+   EG   ++K++ +     V +L R SYGP  L  L +G 
Sbjct: 181 RLTI--HEGHYHQVKRMLKAVGHPVIKLHRESYGPLNLYGLASGG 223


>gi|327330001|gb|EGE71755.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL097PA1]
          Length = 245

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 88/235 (37%), Positives = 127/235 (54%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  +  A R 
Sbjct: 8   RLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVDQGRRVDPERDEIRVDGSRIPTARRH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTNDG  A
Sbjct: 68  VYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTNDGEFA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      ++ V V
Sbjct: 127 NRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQAGEEHSLVEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+NR ++++ +     V RL R + GP +L  L  G  RE++     E+LG
Sbjct: 187 SLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTH----EELG 237


>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 =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 124/226 (54%), Gaps = 6/226 (2%)

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  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +  +   R+  +GRLD NT GLLL+TNDG L +
Sbjct: 62  -YFLLNKPNGFLSTAKDKKNRPTVLDLIEEASIQRLYPIGRLDFNTTGLLLITNDGDLTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAW 188
            L  PS    + Y V+ +  + +  L+   KGI+I      +C     + +      + W
Sbjct: 121 KLTHPSFCIPKEYHVKINACLQKKDLSTFCKGIIIDKKYLAVCKEIDILKISYMPKPSTW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + + EGKNR+++K+ +   ++V +L R  Y    +  L  G+ R
Sbjct: 181 LKLVITEGKNRQVRKMMQALGYQVLKLKRYRYSFLTIENLTIGAYR 226


>gi|289671226|ref|ZP_06492301.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 291

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 94/238 (39%), Positives = 147/238 (61%), Gaps = 15/238 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K     +  L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV+++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGQSVEVAQE 262


>gi|288918462|ref|ZP_06412813.1| pseudouridine synthase [Frankia sp. EUN1f]
 gi|288350102|gb|EFC84328.1| pseudouridine synthase [Frankia sp. EUN1f]
          Length = 308

 Score =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 88/232 (37%), Positives = 127/232 (54%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A AGI SRR  E +I   RV+V+G ++      V      IEVDG   R   RT
Sbjct: 72  RLQKVLAAAGIGSRRASEELIDAGRVRVDGEVVREQGRRVDPERAVIEVDGE--RVVTRT 129

Query: 74  RL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L     HKP G+++T +D  GR T+ D L    +R+  VGRLD ++EGLLL+TNDG LA
Sbjct: 130 GLVHLALHKPRGVLSTMADDRGRPTIADLLTEFGTRLFHVGRLDADSEGLLLVTNDGDLA 189

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSN 186
             L  PS    + Y V   G V +D    L+ G+ ++     D  V +D+ +      S 
Sbjct: 190 HRLMHPSYGVQKTYLVEITGPVRKDLPRRLRSGVELE-----DGPVKVDSARIIDMAASR 244

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             + + L EG+N  +++V E     V+RL+R+S+GP  LGTL AG  R +++
Sbjct: 245 VMMEIVLHEGRNHVVRRVMESVGHPVHRLVRVSFGPVALGTLRAGRARHLTR 296


>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 =  129 bits (325), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 125/230 (54%), Gaps = 5/230 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AG+ASRR  E +I   +VKVNG ++      V   D + V+G P+ + 
Sbjct: 1   MVKERLQKVIAHAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDG 128
           E+   +L  KP G++++  D  GR TV D L +  + +RV  VGRLD +T GLL++TNDG
Sbjct: 60  EQHEYYLLDKPRGVISSAHDDKGRKTVVDILKNEGVQTRVYPVGRLDYDTTGLLVMTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSN 186
            LA  L  P  +  +VY  +  G V  D++ LL++G+ I G      +  L    Q+   
Sbjct: 120 ELANRLMHPRFEVDKVYIAKVKGLVSNDEMRLLREGVKIDGKKSQPARTKLLEANQRQKT 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + V + + EG   ++KK+ E     V +L R SYGP  L  L  G  R++
Sbjct: 180 SVVKLTIHEGHYHQVKKMMEAVGHPVLKLHRESYGPLTLAGLNPGQFRKL 229


>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 =  129 bits (325), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 82/219 (37%), Positives = 126/219 (57%), Gaps = 8/219 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +R+ KV+A+AGI SRRE+E  I+  RV VNG +     + V   D ++VDG  +R   + 
Sbjct: 12  ERLQKVLAQAGIGSRREMEEWISAGRVTVNGTVAT-LGMRVAEGDKVQVDGRNVRLQLQT 70

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E+T  R+ LYHK  G + +  DP  R++VFD LP +   + I++GRLD NT GLL+ T  
Sbjct: 71  EQTMPRILLYHKQEGEIVSRDDPGERASVFDALPKLRGQKWIAIGRLDFNTSGLLIFTTS 130

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           G LA  L  P  +  R Y VR  GQ+  + +  + K+GI +        Q++ +  +G N
Sbjct: 131 GELANRLMHPRFEVEREYAVRVQGQMTPEHMRQVTKEGIELDDGVVRFEQLSDEGGEGFN 190

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            W  + L+EG+NR +++ FE     V+RL+R+ +G   L
Sbjct: 191 HWYRLVLKEGRNRVVRRTFEALGLPVSRLMRVRFGIIGL 229


>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 =  129 bits (325), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 81/231 (35%), Positives = 124/231 (53%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+++AG+ASRR+ E +I   RV+VNG ++      V    D I+VDG  +++ E+
Sbjct: 2   ERLQKVMSQAGVASRRKSEDIITAGRVEVNGEVVTELGTKVDPEQDTIKVDGQQIKR-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +TT  DP  R TV D +  +   V  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  LVYLLLNKPQGYITTVDDPHNRRTVIDLIQDVSQAVHPVGRLDKDTEGLLLLTNDGDLTY 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|223940522|ref|ZP_03632370.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890803|gb|EEF57316.1| pseudouridine synthase [bacterium Ellin514]
          Length = 235

 Score =  129 bits (325), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 88/226 (38%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR  ER+I   RV VNG  +      V    D I +DG PLR   + 
Sbjct: 3   RLQKFLAEAGVASRRASERIILGGRVSVNGDTVRELGTKVDPIHDSIALDGAPLRLKRKL 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP G V +  D   R  + D LP+ +  + SVGRLD ++EGL+ LTNDG  +  
Sbjct: 63  YVAL-NKPRGYVCSRKDDRKRKVIGDLLPAEWDNLYSVGRLDSDSEGLIFLTNDGEFSLH 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVG 192
           L  P  + L+ Y     G+V+Q+ L   K GIV +G     D   TL  Q  S + V + 
Sbjct: 122 LTHPRYRVLKKYLATVEGRVEQEMLQRFKHGIVHEGEKLKVDRARTLSVQN-STSLVELE 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EGKNREI+++FE     V+RL+R+  G  +LG L +G  R +++
Sbjct: 181 LTEGKNREIRRLFESQGLTVSRLVRMQIGKIKLGELRSGKWRMLTE 226


>gi|13472018|ref|NP_103585.1| hypothetical protein mlr2177 [Mesorhizobium loti MAFF303099]
 gi|14022763|dbj|BAB49371.1| mlr2177 [Mesorhizobium loti MAFF303099]
          Length = 250

 Score =  129 bits (325), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 126/228 (55%), Gaps = 3/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +IA+ RV+V G ++  AA+ V ++ D I VDG P+  AER  
Sbjct: 19  LNRALSKLGLCSRTQAELLIAEGRVRVGGKVVRDAALRVDLNRDRIVVDGEPV-IAERKV 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP  R TV+  L  +    V  VGRLD  +EGLLL+TND   A  
Sbjct: 78  YVMLNKPRGLVTTRDDPQQRDTVYACLEGLDLPFVSPVGRLDKASEGLLLMTNDTHFANR 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y V+     D+  L  L+ G+ + G       + L    G  AW+ + L
Sbjct: 138 LMDPASHLPKTYHVQVGTVPDEAMLETLRAGVSVDGETLTANSIVLLRSGGRTAWLEIVL 197

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR I+++      +V RLIRI+ G   LG L  G+ R ++ + L
Sbjct: 198 DEGRNRHIRRLLAAHGIEVKRLIRIAIGRLPLGDLAKGTARHLTPEEL 245


>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 =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 122/226 (53%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 D L SI  RV  +GRLD +T GLLLLTNDG LA 
Sbjct: 62  NIYIMLNKPVGYITTVKDQFDRPSVID-LVSIDDRVYPIGRLDYDTSGLLLLTNDGDLAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +  G  D+ KL++ + G+ I        ++ +      N+ V + 
Sbjct: 121 KLMHPRHNINKVYIAQIKGVPDKMKLDMFRNGLRIDNYKTAKAEIDILKVTNGNSTVKIA 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + EG+NR+I+K+ E     V +L R+  G   +G L  G  R +SK
Sbjct: 181 IHEGRNRQIRKMCELIGHPVLKLKRVKIGNLDIGNLKTGQWRYLSK 226


>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 =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 87/235 (37%), Positives = 128/235 (54%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+VNG +++E+        D I VDG  +  A R 
Sbjct: 8   RLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIPTARRH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTNDG  A
Sbjct: 68  VYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTNDGEFA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + L+ Y     G+VD   +  L KG+ ++        V L      ++ V V
Sbjct: 127 NRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGEEHSLVEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+NR ++++ +     V RL R + GP +L  L  G  RE++     E+LG
Sbjct: 187 SLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTH----EELG 237


>gi|121308590|dbj|BAF43685.1| hypothetical protein [Vibrio fischeri]
          Length = 354

 Score =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 88/224 (39%), Positives = 125/224 (55%), Gaps = 11/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD-HIEVDGVPLRKA 70
           +++ KV+ARAG+ SRRE+E MI   RV V+G   +RA +   + + D  I +DG  +   
Sbjct: 3   EKLQKVLARAGLGSRRELETMIQAGRVSVDG---QRAKLGDRLENVDAKIRIDGHVVSVK 59

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           E T    R+  YHKP G + T  DP+GR TVFD LP I  SR +SVGRLD NT GLLL T
Sbjct: 60  ESTDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIRDSRWVSVGRLDANTAGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y  R  G++++  +  L  G+ ++        V     +G 
Sbjct: 120 TDGELANRLMHPSRKVEREYMCRVFGEINEKMIRNLVSGVKLEDGEARFEDVMYAGGEGM 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           N    V + EG+NRE++++++     V+RL R+ YG   L   L
Sbjct: 180 NHTFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKAL 223


>gi|325068740|ref|ZP_08127413.1| pseudouridine synthase family protein [Actinomyces oris K20]
          Length = 303

 Score =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 87/227 (38%), Positives = 120/227 (52%), Gaps = 14/227 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+A AG+ASRR  E++IA  RV V+G+ +  A V V   T  I VDG  +     
Sbjct: 78  QRLQKVLAHAGVASRRACEQLIADGRVSVDGVTVTEAGVRVDPLTQEIRVDGSRILTNPE 137

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSRVISVGRLDINTEGLL 122
               + HKP G+VTT  DP+GR TV             LP    R++ VGRLD  TEGLL
Sbjct: 138 LITLMLHKPAGVVTTMEDPEGRPTVAQYGRDYLAEHPELPDSL-RLVHVGRLDTETEGLL 196

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT 181
           LL+NDG L+  L  PS +  + Y     GQV+      L++GI ++ G    D +VT+  
Sbjct: 197 LLSNDGELSHRLMHPSFEIAKTYVAIVEGQVEAWVPRKLRRGIELEDGEAKAD-RVTVKD 255

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                + V + L  GKNR ++++ +     V RL R   GP +LG L
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNL 302


>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 =  129 bits (324), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 96/247 (38%), Positives = 151/247 (61%), Gaps = 18/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K     +  L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK-- 239
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E++++  
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKV 264

Query: 240 -ILREQL 245
             LR +L
Sbjct: 265 DALRAEL 271


>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 =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 123/226 (54%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHH-EQH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D +    I  R+  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDDKGRRTVVDIIHDADIDERIYPVGRLDYDTTGILLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P  +  + Y  +  G V  D+L  L+ G+VI G      +   + +D  K   + 
Sbjct: 121 NKLMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVVIDGRKTKPAKSKLLNVDRAK-KTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V + + EG+N ++K +F+     V +L R +YGP  L  L  G  R
Sbjct: 180 VQLTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFR 225


>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 =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 88/224 (39%), Positives = 125/224 (55%), Gaps = 11/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD-HIEVDGVPLRKA 70
           +++ KV+ARAG+ SRRE+E MI   RV V+G   +RA +   + + D  I +DG  +   
Sbjct: 3   EKLQKVLARAGLGSRRELETMIQAGRVSVDG---QRAKLGDRLENVDAKIRIDGHVVSVK 59

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           E T    R+  YHKP G + T  DP+GR TVFD LP I  SR +SVGRLD NT GLLL T
Sbjct: 60  ESTDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIRDSRWVSVGRLDANTAGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y  R  G++++  +  L  G+ ++        V     +G 
Sbjct: 120 TDGELANRLMHPSRKVEREYMCRVFGEINEKMIRNLVTGVKLEDGEARFEDVMYAGGEGM 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           N    V + EG+NRE++++++     V+RL R+ YG   L   L
Sbjct: 180 NHTFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKAL 223


>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 =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 88/224 (39%), Positives = 125/224 (55%), Gaps = 11/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD-HIEVDGVPLRKA 70
           +++ KV+ARAG+ SRRE+E MI   RV V+G   +RA +   + + D  I +DG  +   
Sbjct: 3   EKLQKVLARAGLGSRRELETMIQAGRVSVDG---QRAKLGDRLENVDAKIRIDGHVVSVK 59

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           E T    R+  YHKP G + T  DP+GR TVFD LP I  SR +SVGRLD NT GLLL T
Sbjct: 60  ESTDVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIRDSRWVSVGRLDANTAGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y  R  G++++  +  L  G+ ++        V     +G 
Sbjct: 120 TDGELANRLMHPSRKVEREYMCRVFGEINEKMIRNLVTGVKLEDGEARFEDVMYAGGEGM 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           N    V + EG+NRE++++++     V+RL R+ YG   L   L
Sbjct: 180 NHTFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKAL 223


>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 =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 82/216 (37%), Positives = 120/216 (55%), Gaps = 5/216 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV K+I++ GIASRRE E MI Q RV++NGIL           D I +DG P+ +  R  
Sbjct: 4   RVQKIISQWGIASRREAEEMIGQSRVRINGILARLGQKVDPRVDIISIDGKPVIQGNRPA 63

Query: 75  L--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
           L   L +KP G+V+T +DP GR+TV D LP+   +   +  VGRLD ++ G L+LTNDG 
Sbjct: 64  LVYLLLNKPTGVVSTCNDPQGRTTVLDLLPAKLRQGTGIHPVGRLDADSTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y V   G    + L +  +G+++ G      QV L  Q  + + +
Sbjct: 124 LTFALTHPSHDISKTYHVVVEGHPPTNVLRMWSQGVMLDGRKTRTAQVKLIEQGVTQSKL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L+EG+NR+I++V +   + V  L R + G  QL
Sbjct: 184 EIILQEGRNRQIRRVAQQLGYPVVHLDRRAVGTIQL 219


>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 =  129 bits (324), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 79/219 (36%), Positives = 122/219 (55%), Gaps = 5/219 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QRV K++++ G+ASRR  E MI   RV++NG ++        + D +EVDG  ++  +R 
Sbjct: 3   QRVQKILSQWGVASRRHAEDMIVAGRVRLNGEIVTLGDKADPNCDRLEVDGKLIQPNQRP 62

Query: 74  RLW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +L   L +KPIG+V T +DP  RS V D LP  FS+   +  VGRLD N+ G LLLTNDG
Sbjct: 63  QLLYILMNKPIGVVCTCNDPQNRSIVLDFLPKAFSQGTGIHPVGRLDFNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G   +++L   ++G+++ G      QV +  +   +  
Sbjct: 123 ELTLRLTHPRYHLPKTYEVWVQGYPTEERLQQWREGVMLMGKKTLPAQVEVIRRSRQHTC 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           + V L EG+NR+I+++ +   + V RL R + GP  L +
Sbjct: 183 LKVVLTEGRNRQIRRIVQHLGFHVLRLHRTAIGPLVLSS 221


>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 =  129 bits (324), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 79/228 (34%), Positives = 132/228 (57%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
           +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D  H++ + + ++K +
Sbjct: 21  ERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQKNQ 80

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG  A
Sbjct: 81  QLYYLALYKPRGYVTTASDELGRKTVMELVSDIPARLYPVGRLDKDSEGLLLMTNDGAFA 140

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
           + +  PS    ++YRV    + D+ ++  +  G+V+  G       + + T +     + 
Sbjct: 141 QAVTHPSGGISKLYRVTVQPRADESQILKMSSGVVLDDGTKTMPCAINVVTDEPGRTVME 200

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K
Sbjct: 201 MTLKEGKNREIRRMCEAVGLEVVRLKRNAEGVVKLGMLKPGTYRELTK 248


>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 =  129 bits (323), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 125/223 (56%), Gaps = 3/223 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG  +      V S+D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQTVTELGTKVKSSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFYKPTQVITSVSDDRGRTVVTDYFKDLETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-AWVTV 191
           +  P     + Y  +  G + ++++  L+ GI ++ G             K  N   V +
Sbjct: 125 MTHPRYHIQKKYVAKLKGYLMREEVKALENGIELEDGFTQPAQVKVKKQDKDKNITLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + EG+NR+++++FE F  +V++L RI +G   L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVDKLTRIEFGNLNLKGLNAGEGR 227


>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 =  129 bits (323), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 133/245 (54%), Gaps = 8/245 (3%)

Query: 9   ENFTPQRVS--KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           +N   +RV+  + +++ G  SR + ER+IA+ RV V+G  +  A+  V ++T  I +DG+
Sbjct: 18  DNAAAKRVTLPRALSKLGYCSRTQAERLIAENRVAVDGRTVSDASAWVDLATASISIDGL 77

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
            +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL 
Sbjct: 78  VI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLF 136

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TND   A++L  P T   + Y V+    +D + +  +  GI   G            Q  
Sbjct: 137 TNDTEFAQILLDPVTHVTKTYHVQIDRIMDDEDIAAMTAGIRHDGELLTATAARRLRQGD 196

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KIL 241
            N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++   + L
Sbjct: 197 RNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTEPELQAL 256

Query: 242 REQLG 246
           R + G
Sbjct: 257 RRKTG 261


>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 =  129 bits (323), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 123/226 (54%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHH-EQH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D +    I  R+  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDDKGRRTVVDIIHDAEIDERIYPVGRLDYDTTGILLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P  +  + Y  +  G V  D+L  L+ G+VI G      +   + +D  K   + 
Sbjct: 121 NKMMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVVIDGRKTKPAKSKLLNVDRAK-KTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V + + EG+N ++K +F+     V +L R +YGP  L  L  G  R
Sbjct: 180 VQLTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFR 225


>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 =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 129/224 (57%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG  +      V  +D++EV+GV L + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLIVEGKVKVNGETVTELGTKVKPSDNVEVEGVKLEQEDKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L++KP  ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFYKPAQVITSVSDDRGRTVVTDYFDDLETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  + Y  +  G + +D++  L+KGI ++       +V +  Q  + +   V +
Sbjct: 125 MTHPRYKIKKKYVAKLKGYLMRDEVKALEKGIQLEDGKTHPAEVKIKNQNKEKNTTVVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPF-QLGTLLAGSTR 234
            + EG+NR+++++FE F  +V++L R+    F  L  L AG  R
Sbjct: 185 TISEGRNRQVRRMFEHFGHEVSKLSRVELADFLTLKGLNAGEGR 228


>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 =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 123/227 (54%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + RV VNG  +    V V S+D IEV+G+ L + E  
Sbjct: 39  ERLQKVIAHAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGSSDKIEVNGLKLEREEPV 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G+++   D  GR  V D    +  R+  +GRLD +T GL+L+TNDG  A  
Sbjct: 99  YFMLY-KPRGVISAAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLILITNDGEFAHK 157

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L+KGI++        +   +++D +K     V 
Sbjct: 158 LMHPKYEIDKTYAAKLKGIPSKELLRKLEKGIMLDHKKTAPARAKMLSIDKRK-QTCIVQ 216

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE     V +L R  Y    +  +  G  RE+S
Sbjct: 217 LTIHEGRNRQVRRMFEAIGHDVLKLKREHYAFLHIEGMRPGDRRELS 263


>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 =  129 bits (323), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 78/233 (33%), Positives = 127/233 (54%), Gaps = 7/233 (3%)

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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV--- 189
            L  P  +  + Y     G++ ++KL +L+ G++++       +V+L  ++     V   
Sbjct: 125 GLLHPRFEVEKTYHAGVTGKLTEEKLQMLRDGLLLEDGMTAPAKVSLLPEREPGERVRGL 184

Query: 190 ---TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               + + EG+NR+++++F      V  L R+ +    L  +  G  R ++++
Sbjct: 185 TRAAITIHEGRNRQVRRMFAAVGCDVKSLKRVRFAGLTLKGVARGQHRALTEE 237


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 84/217 (38%), Positives = 119/217 (54%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +++ KV+ARAG  SRRE+E MI   RV V+G++ +        T ++ VDG  +      
Sbjct: 3   EKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDMTANVRVDGHRIELISSD 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E  R+  Y+KP G + T  DP+GR TVFD LP + + R +SVGRLD NT GLLL T DG
Sbjct: 63  EEICRILAYNKPEGELCTRHDPEGRRTVFDRLPRLNTGRWVSVGRLDANTSGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS    R Y VR  G V +  +  L KG+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRTVEREYMVRVFGDVTEQMVKNLVKGVELEDGLARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + EG+NRE++++++     V+RL R+ YG   L
Sbjct: 183 FYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYL 219


>gi|254385863|ref|ZP_05001182.1| pseudouridine synthase [Streptomyces sp. Mg1]
 gi|194344727|gb|EDX25693.1| pseudouridine synthase [Streptomyces sp. Mg1]
          Length = 260

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 126/226 (55%), Gaps = 5/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V   D I+VDG+ +  A ++
Sbjct: 25  ERLQKVLARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVQPKDEIKVDGLTV--ATQS 82

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 83  YLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELAH 142

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + ++    LK GI ++ G    D    +D Q G N  V V
Sbjct: 143 RLTHPKYGVKKTYVAAITGPLPREIGKRLKDGIELEDGYARADHFRVVD-QVGKNYLVEV 201

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V +L+R S+GP +LG   +G  R ++
Sbjct: 202 TLHEGRKHIVRRMMAEAGFPVEKLVRTSFGPIELGDQKSGWLRRLT 247


>gi|258591956|emb|CBE68261.1| Uncharacterized RNA pseudouridine synthase aq_1464 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [NC10
           bacterium 'Dutch sediment']
          Length = 282

 Score =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 119/226 (52%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ + +ARAG+ SRR  E++I   RV+VNG +  +    V    D +  D  P+  ++ 
Sbjct: 25  ERLQRYLARAGLGSRRSCEQLILDGRVRVNGRIASQLGTKVSPGLDTVTCDHKPVTSSQS 84

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + HKP G++T+ SDP GR  + D LP     R+  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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +G+  EI+++ +     V RL RI  GP  LG L  G  R+++
Sbjct: 205 IVHQGRYHEIRRMCDAIGHPVLRLQRIRVGPIVLGKLPKGCWRQLT 250


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 145/237 (61%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP +  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K     +  L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQ 261


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 85/231 (36%), Positives = 125/231 (54%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AER 72
           QR+ K+IA AG+ SRRE ER+I   +V+VNG + +      +S D I V+  PL K  ER
Sbjct: 7   QRIQKLIANAGLCSRREAERLIEDGKVRVNGKIAQLGDKARISDD-IFVNNKPLNKHVER 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           +   L +KP G++ T+SDP    TVFD LP    R  +   GRLD ++EGLL+LTNDG L
Sbjct: 66  SVTVLMNKPKGVLCTNSDPHADRTVFDLLPLDLQRQRMFCAGRLDKDSEGLLVLTNDGDL 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-- 188
           A  +  P++  ++ YRV  H   D+  +  L  G+  +G      +V      G      
Sbjct: 126 AHRITHPTSNVVKRYRVVLHRDFDKADIPKLLNGVDYEGDFLKAEKVIPAPAVGEGHLRR 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + V L  GK REI+++FE   + V +L+R+  G   L  +  G  + + KK
Sbjct: 186 LEVHLHHGKKREIRRLFEANRYYVKKLVRVQIGGMVLKNMPKGGIKVLGKK 236


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 146/237 (61%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP +  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQ 261


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 118/225 (52%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I Q +V+VNG ++      V   D I V+G PL   E  
Sbjct: 2   ERLQKAIAASGYTSRRKAEDLIVQGKVEVNGKVVTELGTKVKQGDLITVEGKPLV-GENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G V T  D   R  + D    +  R+  VGRLD +T GL++++NDG  A +
Sbjct: 61  VYYVFYKPKGCVCTLDDEFDRPIITDYFTEVKERIYPVGRLDFDTTGLIIMSNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWV 189
           +  P +   ++Y V   G +    LN L+KG+ ++G+    C   ++V     +     +
Sbjct: 121 IMHPRSHLEKIYEVSIKGLITGPTLNKLEKGVYLEGVKTLPC--KIKVVDKDTEHKTTML 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNR++KK+FE     V RL R+S G   L  L  G  R
Sbjct: 179 KIKLVEGKNRQVKKMFESVGHPVKRLHRVSIGGINLKGLTPGRYR 223


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 130/227 (57%), Gaps = 3/227 (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
            ++  + L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKLYI-LFYKPAQVITSVSDDRGRKVVTDYFKQIKTRIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-A 187
              ++  P  +  + Y V+  G + ++++  L++G+ ++ G+    +    +  K  N  
Sbjct: 121 FTNLMTHPRYKIKKKYVVKLKGYLMREEVKSLEQGVQLEDGVTQPAIIKVKNQDKDKNTT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V + + EG+NR+++++FE F  +V +L RI +GP  L  L AG  R
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLQRIEFGPLNLKGLNAGEGR 227


>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 =  128 bits (322), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 126/225 (56%), Gaps = 2/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G+ASRRE++R++ +  +KVNG +     + V  +D IE++G   RK     
Sbjct: 6   RINKYLSSIGVASRREIDRLVEKGSIKVNGAIAT-PGMQVSESDTIEINGKKFRKNRGKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G+++   D  GR TV D L     R+  VGRLD +TEGL+LLTNDG     +
Sbjct: 65  YFMLYKPTGVISAAKDDRGRKTVVD-LVKYQERIYPVGRLDFDTEGLILLTNDGDFFNKI 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P ++  + Y V   G+V++ +++ LK+G+ ++       +V L       + + + +R
Sbjct: 124 MHPKSEVYKEYHVDVMGKVNKLEIDKLKRGVRLEDGITLPAKVELLDSSHETSKLRISIR 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           EG+NR+I+++ +     V  L R   G   LG L  G  RE+SKK
Sbjct: 184 EGRNRQIRRMCKAVGHPVTHLKREKIGELSLGRLKKGGFRELSKK 228


>gi|317970403|ref|ZP_07971793.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CB0205]
          Length = 235

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 81/233 (34%), Positives = 123/233 (52%), Gaps = 5/233 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ K+IA+AG+ SRR  E ++   RV VNG   +       ++D I +DG PL  +
Sbjct: 1   MAAERLQKLIAQAGVCSRRRAEELLRDGRVTVNGQRAQLGDKADPNSDAISLDGQPLGAS 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
               + L +KP G++++  DP+GR  V D LP   +R   +  VGRLD  + G LLL+ND
Sbjct: 61  AEPMVLLLNKPAGVLSSCFDPEGRPIVLDLLPPELARGQGLHPVGRLDFESRGALLLSND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN 186
           G L   L  P     + YRV   GQ  Q  L+   +G+ + G+    +QV +L +++G  
Sbjct: 121 GALTLQLTHPRYAHSKTYRVWVQGQPSQRVLDQWARGVSLDGLPSQPVQVRSLSSEQGRT 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               V + EGKNR+I++  E     V  L RI+ GP  LG L  G  R ++ +
Sbjct: 181 LLELV-MGEGKNRQIRRTAELLGHHVLDLQRIAIGPIHLGALPEGRWRRINDQ 232


>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 =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 87/235 (37%), Positives = 127/235 (54%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+VNG +++E+        D I VDG  +  A R 
Sbjct: 8   RLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIPTARRH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTNDG  A
Sbjct: 68  VYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTNDGEFA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS + L+ Y     G+VD   +  L KG+ ++        V L      ++ V V
Sbjct: 127 NRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGEEHSLVEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L EG+NR ++++ +     V RL R   GP +L  L  G  RE++     E+LG
Sbjct: 187 SLHEGRNRIVRRIMDSVAHPVRRLSRTVIGPVRLKRLGRGDMRELTH----EELG 237


>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 =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 87/238 (36%), Positives = 124/238 (52%), Gaps = 16/238 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRK 69
           P R+   +ARAG+ SRR+ E +I Q RV+VNG    + AV    V   D +EVDG P+  
Sbjct: 4   PLRLQAFLARAGVGSRRKAEELIRQGRVRVNG----KVAVLGQKVNPGDVVEVDGKPVEP 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                +   HKP G  TT  DP  + TVFD LP I   +  +GRLD ++EGLLLLTNDG 
Sbjct: 60  PRERIVLALHKPRGYTTTRHDPHAQKTVFDLLPDIPG-LHPIGRLDRDSEGLLLLTNDGH 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     +VYRV      ++  L L     +++G+   D        + +    
Sbjct: 119 LTLRLTHPRYGVRKVYRV----YTERGTLPLAICQRLLEGVDLEDGPARALACRPAPGGA 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK----ILRE 243
            + L EG+ RE++++ +   + V RLIR+  GP  LG L  G  R++S +    +LRE
Sbjct: 175 LLTLAEGRKREVRRMLKAVGYPVKRLIRLQVGPIHLGHLPPGKWRQLSPREVEALLRE 232


>gi|268610237|ref|ZP_06143964.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 247

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 84/232 (36%), Positives = 128/232 (55%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----VPLRKA 70
           R+ K+IA +G+ SRR+ E +I++ RVK+NG  + +        D I +DG    +P +K+
Sbjct: 9   RIQKMIADSGVCSRRKAEELISRGRVKLNGHPV-KLGDKCGYKDIITIDGERLYIPKKKS 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R  + +KP G VTT SD   R  V D L  +  RV  VGRLD N+EGLLL TNDG  
Sbjct: 68  --FRYIIMNKPRGYVTTVSDELDRRCVMDLLDDVEDRVYPVGRLDRNSEGLLLFTNDGEF 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  PS    + YRV     +  ++L  L +G+ I G       V +  ++     + 
Sbjct: 126 ANSIMHPSRHISKTYRVTVRPDISDEQLIQLSEGVEIDGKRTLPATVIVKDKQPGRVVLL 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + ++EG+NR+I+K+ E    +V RL R S GP +LG L  G+ R+++ + LR
Sbjct: 186 MTIKEGRNRQIRKMCEAVGLEVARLRRTSIGPIKLGMLKPGTYRDLTAEELR 237


>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 =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV V+G  +  A+  V +ST  I VDG+ +  AE   
Sbjct: 72  LPRALSKLGYCSRTQAERLIAESRVAVDGRTVSDASAWVDLSTARISVDGLVI-AAEAKI 130

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L +     +  VGRLD  +EGLLL TND   A+ 
Sbjct: 131 YLMLNKPRGLVTTRQDPEGRPTVYDCLKNFDIPHLSPVGRLDKASEGLLLFTNDTEFAQT 190

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D +++  +  GI   G            Q   N+W+ V L
Sbjct: 191 LLDPLTHVTKTYHVQIDRLMDDEEIAAMTSGIRHDGELLTAAATRRLRQGDRNSWIEVEL 250

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++
Sbjct: 251 DEGRNRQIRRMLEALGAECLRLVRVAIGGLELGELPKGAVRALTE 295


>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 =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 94/237 (39%), Positives = 146/237 (61%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP +  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQ 261


>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 =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 121/229 (52%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG--VPLRKAE 71
           R++K I+ +G ASRR  + ++A  RV+VNG  +      V  T D + VDG  + L   +
Sbjct: 2   RINKYISLSGFASRRAADELVADGRVQVNGETISDLGHQVDETKDQVTVDGKLLKLPTNK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ ++HKP G V T  DP GR TV+D LP  +     VGRLD+ + GLLL T+DG L 
Sbjct: 62  KTKVIMFHKPAGCVCTKDDPQGRRTVYDYLPPGYHNFKYVGRLDLQSRGLLLFTDDGELL 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---SNAW 188
             L  PS +  R Y V     + +     L  G+ I+     D Q  +         N +
Sbjct: 122 YRLTHPSFEVPRSYYVWTTRPLSESAAQRLVDGVDIRDPEDPDAQEEIAFATDVYLENGF 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + L EGKNREI+++     +++  L R+SY   QLG L AG  RE++
Sbjct: 182 AELVLIEGKNREIRRMMRAIGYEIRDLKRVSYCQIQLGDLPAGEFRELT 230


>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 =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 80/237 (33%), Positives = 133/237 (56%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K ++  GIASRR +++ I + R+KVNG++     ++V   D I +D   +  +K E 
Sbjct: 2   RINKFLSSLGIASRRAIDKYIEEGRIKVNGVIAS-TGIDVTEDDEICIDDKKIETKKIEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+ +++  SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L  
Sbjct: 61  KVYFMLNKPLEVLSASSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELFN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------GICYGDMQVTLDTQ 182
            L  P ++  + Y ++  G+V +++++ LKKG++++          GI Y       D  
Sbjct: 120 RLVHPKSEIYKKYYIKVFGEVKKEEIDELKKGVLLEDGKTLPAKVAGIKY-------DKN 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 173 KTS---MYISIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLKEGKYRELTKE 226


>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 =  128 bits (321), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 123/226 (54%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHH-EQH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D +    I  R+  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDDKGRRTVVDIIHDADIDERIYPVGRLDYDTTGILLLTNDGTLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P  +  + Y  +  G V  D+L  L+ G++I G      +   + +D  K   + 
Sbjct: 121 NKLMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVIIDGRKTKPAKSKLLNVDRAK-KTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V + + EG+N ++K +F+     V +L R +YGP  L  L  G  R
Sbjct: 180 VQLTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFR 225


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

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 85/243 (34%), Positives = 131/243 (53%), Gaps = 9/243 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A+AGIASRR+ E +I   +V+VNG+ +           D I V G P+    +
Sbjct: 5   ERLQKILAQAGIASRRKCEELIISGQVEVNGVPVTTLGAKADPEEDVITVGGKPIVSENK 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L +KP G++T+ SDP GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  A 
Sbjct: 65  LYIML-NKPKGVITSASDPQGRKVVSDFLTGIKQRVYPIGRLDYDTEGLLLLTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y     G    DKL+ L+KGI ++       +V     + S+  + + 
Sbjct: 124 LLTHPKHHVPKTYWATVKGVPHGDKLDKLRKGIELEDGMTSPAEVEYQDIEPSDKESTIR 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++F+     V RL R+ +G   L  L  G  R +    ++E     LL
Sbjct: 184 ITIYEGRNRQVRRMFDAIGHPVIRLKRVKFGELGLQNLKRGGWRPLKPHEVQE-----LL 238

Query: 251 EEA 253
           +EA
Sbjct: 239 QEA 241


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 93/244 (38%), Positives = 127/244 (52%), Gaps = 16/244 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VP 66
            + +R+ K +ARAGIASRR  E +I   RV VNG   + A +   V  TD + VDG  V 
Sbjct: 1   MSAERLHKRLARAGIASRRAAEELIRAGRVTVNG---QTAGLGQGVNDTDDVRVDGRLVE 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L + E     LY KP+G VTT  D  GR  V D +P +   +  VGRLD ++EGLLLLTN
Sbjct: 58  LTRPETVTYALY-KPVGFVTTAHDEYGRRNVLDAMPDVPG-LHPVGRLDKDSEGLLLLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQ--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           DG L   L  P     + YR    G+    Q +L++L +GI +     G  Q        
Sbjct: 116 DGDLTLTLTHPRYGHEKAYRAWTEGREPPTQAELDVLVRGIAMDD---GPAQALSAAPAE 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             A+V +G  EG+NR+++++ E     V RL+R   G   LG L  G  RE+  + L + 
Sbjct: 173 DGAYVVLG--EGRNRQVRRMLEALGHPVGRLVRYRVGGLWLGDLNPGEYRELGPRDLEQL 230

Query: 245 LGPH 248
           L PH
Sbjct: 231 LHPH 234


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 80/237 (33%), Positives = 122/237 (51%), Gaps = 4/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           + EG+   +K++ E    +V RL R  +G   +G L  G  R +     + LR+++G
Sbjct: 184 VGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGKFRRLQPEEVRALRQRVG 240


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 124/227 (54%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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  KVYAILNKPKGYLTAASDYRGRKTVID-LLNFKERVFPVGRLDFNTTGLLIVTNDGEIFN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G+     L+ L+KGI I G    + +V++ +  G N+ + + 
Sbjct: 122 RIMHPRQNVNKCYLATVKGKPQFKHLDALRKGIDIGGYITKEAEVSVVSFDGKNSILKIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGK R+++++     + V  L RIS G  +LG L  G+ R ++K+
Sbjct: 182 IHEGKKRQVRRMCAAVGFPVEELKRISIGNIKLGDLKEGNVRMLNKE 228


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 129/230 (56%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AG+ASRR  E++IA+ R+ V G ++   A +V ++  +  DG P+R  E   
Sbjct: 2   RLAKFLAHAGVASRRASEQLIAEGRIAVGGEIVLDPARDVDASSGVTYDGEPVRGEEPRV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++  HKP G+V+T +D  GR TV + +P    R+  VGRLD ++ GL+LLTNDG LA  L
Sbjct: 62  VYALHKPAGVVSTAADTHGRRTVTELVPQ-GRRLYPVGRLDADSTGLILLTNDGELANRL 120

Query: 135 ELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             P  +  + YR    G Q+    L  L++G+ ++      M      ++ S   + + +
Sbjct: 121 THPRFEVPKTYRATVGGPQIGDRTLRQLREGVRLE----DGMTAPARVRRLSAHVLELTI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EG+ R+++++ E     V  L+R  +GP  LG L  G +R ++ + +RE
Sbjct: 177 HEGRKRQVRRMCEEVGHPVKSLVRTQFGPLSLGDLGTGRSRRLTAREVRE 226


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 88/233 (37%), Positives = 130/233 (55%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTM 120

Query: 135 ELPSTQWLRV-YRVRFHGQVDQDKLNL--LKKGIVIQG-----ICYGDMQVTLDTQKGSN 186
             P  +  +V +RV    +V Q K NL  L +GIVI G       Y  ++V  D  +   
Sbjct: 121 IHPRNEIDKVIWRV---SKVLQRKKNLRPLTRGIVIDGKKTKPARYNIVRVEADKNR--- 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + V + + EG+N ++KK+FE     V++L R   G   L  L  G  R ++KK
Sbjct: 175 SIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRLGTVDLKGLRPGEARRLNKK 227


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 77/224 (34%), Positives = 125/224 (55%), Gaps = 4/224 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ KVIA AG+ASRR+ E +IA   V +NG +++   + V ST  HIEVDGVPL + ++
Sbjct: 2   ERLQKVIANAGVASRRKAETLIATGHVTLNGKVVKEMGIKVDSTSAHIEVDGVPLTREKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               LY KP  +++  +D   R  V + L  I  RV  +GRLD +T GLLLLTNDG  A 
Sbjct: 62  VYYALY-KPRQVISAVTDDKKRRVVTEYLEDIQERVYPIGRLDYDTSGLLLLTNDGDFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVT 190
           ++  P  +  + Y  +  G    + L  L+KGI+++        +++    ++ + A ++
Sbjct: 121 MMMHPKYKVDKTYVAKVSGLPTAEMLRQLRKGIMLEKRKTAPAKVKIISTDRRKNTAILS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG N ++K +       V++L R +YG   L  L++G  R
Sbjct: 181 ITIHEGMNHQVKNMLAAVGLPVSKLKRETYGFLTLDGLVSGEYR 224


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 93/237 (39%), Positives = 146/237 (61%), Gaps = 15/237 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQ-TGMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G V T  DP+GR TVF++LP++  SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVITREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQ--GICYGDMQVTLDTQ 182
           LA  +  PS +  R Y VR      ++K++      L +G++++  G  + +++    T 
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + EV++
Sbjct: 207 --SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLRGHSVEVAQ 261


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 127/227 (55%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG I++E+     +  D I+VDG+ +  A+ 
Sbjct: 198 ERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTV-AAQS 256

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP G+V++  DPDGR  + D + +  +R+  VGRLD  TEG+++LTN G LA 
Sbjct: 257 YLFFALNKPAGVVSSMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIIMLTNHGELAH 316

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVT 190
            L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V 
Sbjct: 317 RLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENT--GKNYLVE 374

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++
Sbjct: 375 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLT 421


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 127/227 (55%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG I++E+     +  D I+VDG+ +  A+ 
Sbjct: 191 ERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTV-AAQS 249

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP G+V++  DPDGR  + D + +  +R+  VGRLD  TEG+++LTN G LA 
Sbjct: 250 YLFFALNKPAGVVSSMEDPDGRQCLGDYVNNRETRLFHVGRLDTETEGIIMLTNHGELAH 309

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVT 190
            L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V 
Sbjct: 310 RLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENT--GKNYLVE 367

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++
Sbjct: 368 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLT 414


>gi|298490451|ref|YP_003720628.1| pseudouridine synthase ['Nostoc azollae' 0708]
 gi|298232369|gb|ADI63505.1| pseudouridine synthase ['Nostoc azollae' 0708]
          Length = 254

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 85/244 (34%), Positives = 130/244 (53%), Gaps = 13/244 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+I++ GIASRRE E MI + RVK+NGIL           D I +DG P+ +++   
Sbjct: 4   RIQKIISQWGIASRREAEEMIKRSRVKINGILAHLGQKVDPQIDTISIDGQPISQSQHPS 63

Query: 75  L--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
           L   L +KP G+V+T  DP GR TV D LP        +  VGRLD ++ G L+LTNDG 
Sbjct: 64  LIYLLLNKPPGVVSTCDDPQGRPTVLDLLPQKLRHGLGIHPVGRLDADSTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y +   G   +  L   ++G+ ++G      +V L       + +
Sbjct: 124 LTFSLTHPSHNIAKTYHIVVKGHPPEVVLGRWREGVFLEGRKTRPAKVQLIESLAHQSKL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKK---IL 241
            + L+EG+NR+I++V E   + V +L R + G  QL T     LL G  R ++ +   +L
Sbjct: 184 EIILQEGRNRQIRRVAEQLGYPVIQLHRTAIGSIQLQTPKARFLLWGDYRHITPEEIIVL 243

Query: 242 REQL 245
           ++Q+
Sbjct: 244 KKQI 247


>gi|307578345|gb|ADN62314.1| RNA-binding S4 domain-containing protein [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 519

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 98/250 (39%), Positives = 144/250 (57%), Gaps = 24/250 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR TVF+ LP +  +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHG-----QVDQDKLNLLKKGIVIQGICYGDMQVTLDT--- 181
           LA  +  PS++  R Y VR         V  + L  L +G++++     D     DT   
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLE-----DGTAKFDTIER 200

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
                S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K
Sbjct: 201 IGNTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPK 260

Query: 239 ---KILREQL 245
              + LR QL
Sbjct: 261 TQVEALRTQL 270


>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 =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 124/224 (55%), Gaps = 3/224 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA +G  SRR+ E++I   +V VNG ++ +  V    +D I V+GV L K E 
Sbjct: 2   AERLQKLIAASGYTSRRKAEQLILDGKVTVNGTVVNQLGVKAEPSDIIIVEGVRLLK-EN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP  ++T+ SD   R+ V D   S+  RV+ VGRLD +T G L+++NDG    
Sbjct: 61  KRYYLFYKPEKVITSMSDEKDRTCVKDFFESVNERVVPVGRLDYDTSGALIMSNDGEFIN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
           ++  P  +  + Y  +  G++D   L +L+ G+ I        +V +  +  K SN  V 
Sbjct: 121 LITHPRHKIKKTYVAKISGKLDDRHLKILRSGVRIDNYKTAPAEVNIVKNKNKSSNTLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EGKNR+I+++FE   ++V +L R +     L  L  G  R
Sbjct: 181 LTIHEGKNRQIRRMFETLGYEVLKLKREAIEDLTLEGLKKGEYR 224


>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 =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 123/229 (53%), Gaps = 2/229 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GIASRR+ E  I Q RVKVNG +++     +    D IE D   +R+ E+ 
Sbjct: 3   RLQKYLAECGIASRRKCEEYILQGRVKVNGKVVKELGTKIDPDVDIIEFDDKIVRREEKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T+  DP GR TV D L  +  R+  VGRLD +T GLLLLTNDG LA +
Sbjct: 63  VYIMLYKPAGYITSVKDPFGRPTVLD-LVKVKERIYPVGRLDFDTSGLLLLTNDGELANI 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  + ++ Y  +  G   ++++   + G++I G      ++ +   K   + V + +
Sbjct: 122 LMHPKHEIVKTYVAKIKGIPTKEEMERFENGLIIDGRKTAKAKIRILNVKNGTSVVEIQI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR++KK+ +     V  L R   G  +L  L  G  R +++  +R
Sbjct: 182 HEGRNRQVKKMCKAIGHPVIALKRTKIGELELKGLKPGEWRYLTEDEIR 230


>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 =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 127/227 (55%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG I++E+     +  D I+VDG+ +  A+ 
Sbjct: 197 ERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTV-AAQS 255

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP G+V++  DPDGR  + D + +  +R+  VGRLD  TEG+++LTN G LA 
Sbjct: 256 YLFFALNKPAGVVSSMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIIMLTNHGELAH 315

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVT 190
            L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V 
Sbjct: 316 RLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENT--GKNYLVE 373

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++
Sbjct: 374 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLT 420


>gi|320011602|gb|ADW06452.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 389

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 128/228 (56%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++ARAG+ SRR  E +I Q RV+VNG I+LE+        D I+VDG+ +  A +
Sbjct: 153 ERLQKILARAGMGSRRACEELIEQARVEVNGEIVLEQGMRVDPQKDEIKVDGLTV--ATQ 210

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA
Sbjct: 211 SYLFFALNKPAGVVSTMGDPDGRQNLGDYVNNRETRLFHVGRLDTETEGIILLTNHGELA 270

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V
Sbjct: 271 HRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENT--GKNYLV 328

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++
Sbjct: 329 EVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLT 376


>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 =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 129/250 (51%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA+ GI SRR+ + +I + RV V GI L    VNV     I +DG P+   ++T 
Sbjct: 2   RINKYIAKCGICSRRKADELIKEGRVTVGGIPLLECGVNVDEDAVIAIDGRPIEIQKKTV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G V T SD  GR TV+D L  I  R+ ++GRLD ++EGL+LLTNDG LA+ L
Sbjct: 62  YIAMNKPCGYVCTVSDELGRRTVYDLLTDIDERLFTIGRLDKDSEGLILLTNDGDLAQKL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V   G    + +  L  GI I      D++++                
Sbjct: 122 LSPKRKIEKNYEVVVRGVPGANDIKKLSGGITI------DVEISQTKQNKPVKSIVKYHT 175

Query: 182 ---------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                    QK  +  +++ ++EGK R+I+K+F+    +V +L R+ +   +LG L  G 
Sbjct: 176 KPAKIFEIGQKQGDMKLSMIIKEGKKRQIRKMFDVIGHEVIKLKRVKFAGIELGDLRPGE 235

Query: 233 TREVSKKILR 242
            R +S+  +R
Sbjct: 236 FRHLSEDEVR 245


>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 =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 93/225 (41%), Positives = 131/225 (58%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +++ KV+AR G+ SRRE+E  I + RVKVN  +    A  V   D I V+   +R+++  
Sbjct: 3   EKLQKVLARVGLGSRREIETWIEEGRVKVNQYIATLGA-RVSPHDEIRVNERRIRQSDLQ 61

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
              R ++  YHKPIG V T  D +GR+T+F+ LPS    R IS+GRLD+NT GLLLLT D
Sbjct: 62  TPSRQQILCYHKPIGEVCTRHDEEGRTTIFERLPSPKHGRWISIGRLDLNTAGLLLLTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R Y VR  G+VD D L  L++GI ++       +V      G+N 
Sbjct: 122 GDLAHRLMHPSYDIEREYAVRILGEVDLDMLKRLREGIELEDGMAQFKRVFDAGGSGANH 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           W  V L EG+  E+++++E     V+RL+RI +GP  L   LA +
Sbjct: 182 WYHVTLMEGRKHEVRRLWESQGVTVSRLMRIRFGPVSLPKRLASA 226


>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 =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 85/222 (38%), Positives = 125/222 (56%), Gaps = 10/222 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKA 70
            +++ KV+AR+G+ SRR++E +I + RV V+G ++      V     + VDG  V     
Sbjct: 2   SEKLQKVLARSGLGSRRKMETVIQEGRVSVDGQVVG-LGTRVTVEQILRVDGHTVKYITE 60

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E T  R+  Y+KP G V T SD  GR TVF+ LP +  +R IS+GRLDINT GLLL T D
Sbjct: 61  ENTICRILAYNKPEGEVCTRSDEAGRKTVFERLPRLNGARWISIGRLDINTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----K 183
           G  A  +  PS +  R Y VR  G VD   LN L+ G+ ++      + +    +    +
Sbjct: 121 GEFANRMMHPSREVEREYAVRIFGNVDDAMLNRLRMGVKLEDGEAKFLSIKESGKEAGGE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G N W  V L EG+ RE+++++E    +V+RL+R+ YG   L
Sbjct: 181 GINRWYHVVLTEGRTREVRRLWESQGVQVSRLMRVRYGHLHL 222


>gi|410137|gb|AAA67493.1| ORFX13 [Bacillus subtilis subsp. subtilis str. 168]
          Length = 229

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 125/226 (55%), Gaps = 5/226 (2%)

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 KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 62  YFLLY-KPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L++GI ++       +   ++LD +K   + + 
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKK-QTSIIQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 225


>gi|295100683|emb|CBK98228.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii L2-6]
          Length = 278

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 79/231 (34%), Positives = 131/231 (56%), Gaps = 3/231 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLR 68
              +R+ K+++  G+ SRR  E++IA+ RVKVNG  ++       + D  H++ + + ++
Sbjct: 1   MAEERIQKIMSEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQ 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K ++      +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG
Sbjct: 61  KNQQMYYLALYKPRGYVTTASDELGRKTVMELVADIPARLYPVGRLDKDSEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
             A+ +  PS    ++YRV    + D+ ++  L  G+V+  G       + + T +    
Sbjct: 121 AFAQAVTHPSGGISKLYRVTVQPRADEAQILKLSSGVVLDDGTKTMPCAINVVTDEPGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + + L+EGKNREI+++ E    +V RL R + G  +LG L  G  RE++K
Sbjct: 181 VMEMTLKEGKNREIRRMCEAVGLEVIRLKRNAEGVVKLGMLQPGRYRELTK 231


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VDG+ +   +  
Sbjct: 181 ERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTV-ATQSY 239

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA  
Sbjct: 240 QFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDTETEGVILLTNHGELAHR 299

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V 
Sbjct: 300 LTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVE-QTGKNYLVEVT 358

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 359 LHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 403


>gi|282864458|ref|ZP_06273514.1| pseudouridine synthase [Streptomyces sp. ACTE]
 gi|282560945|gb|EFB66491.1| pseudouridine synthase [Streptomyces sp. ACTE]
          Length = 382

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 128/230 (55%), Gaps = 12/230 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++ARAG+ SRR  E +I Q RV+VNG I+LE+        D I+VDG+ +     
Sbjct: 146 ERLQKILARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVDPQKDEIKVDGLTVA---- 201

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           T+ +L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 202 TQSYLFFALNKPAGVVSTMGDPDGRQNLGDYVTNRETRLFHVGRLDTETEGIILLTNHGE 261

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNA 187
           LA  L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N 
Sbjct: 262 LAHRLTHPRYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENT--GKNY 319

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++
Sbjct: 320 LVEVTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLT 369


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 83/245 (33%), Positives = 133/245 (54%), Gaps = 8/245 (3%)

Query: 9   ENFTPQRVS--KVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGV 65
           +N   +RV+  + +++ G  SR + ER+IA+ RV V+G I+ + +A   ++T  I +DG+
Sbjct: 18  DNAAAKRVTLPRALSKLGYCSRTQAERLIAENRVAVDGRIVNDTSAWVDLATARISIDGL 77

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
            +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL 
Sbjct: 78  VI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLF 136

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TND   A++L  P T   + Y V+    +D + +  +  GI   G               
Sbjct: 137 TNDTEFAQILLDPVTHVTKTYHVQIDRIMDDEDIAAMTSGIRHDGELLTATAARRLRHGD 196

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KIL 241
            N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +S+   + L
Sbjct: 197 RNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALSEPELQAL 256

Query: 242 REQLG 246
           R + G
Sbjct: 257 RRKTG 261


>gi|283850767|ref|ZP_06368054.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283574010|gb|EFC21983.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 285

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 91/272 (33%), Positives = 145/272 (53%), Gaps = 19/272 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M DK ++       R++K +A AG+ SRR+ + +I   RV V+G ++      +  + + 
Sbjct: 1   MDDKALL-------RLNKALADAGVCSRRQADALITAGRVTVDGAVVTELGNKIDPARNR 53

Query: 60  IEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRL 114
           + VDG P+R    A+     L +K  G VTT +DP+GR TVFD LP+ +   R+  VGRL
Sbjct: 54  LAVDGRPVRLSGAADAPLTLLLNKRPGCVTTANDPEGRPTVFDELPAAYRARRLFPVGRL 113

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYG 173
           D  +EGLLLLT DG LA  L  P     + Y V   G V+   L+ + KG+ + +G    
Sbjct: 114 DYFSEGLLLLTTDGELANRLAHPRWHVDKRYLVTVRGTVNGQTLDTMAKGMTLAEGEQLA 173

Query: 174 DMQVTLDTQKGSNAWV-TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            ++  +  +  ++ +V  + L +G NR+I+++    +  V +L RI+ GP  LG L AG 
Sbjct: 174 PVRARITARLAADRFVLEMELSQGVNRQIRRMCRDLDLTVLKLCRIAQGPVSLGGLPAGK 233

Query: 233 TREVSKK---ILREQLG-PHLLEEAQVNLDAP 260
            RE++      LR  +G P     A+ ++ AP
Sbjct: 234 CRELAASELAALRRSVGLPSSAAPAKPSVKAP 265


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VDG+ +   +  
Sbjct: 220 ERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTV-ATQSY 278

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA  
Sbjct: 279 QFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDTETEGVILLTNHGELAHR 338

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V 
Sbjct: 339 LTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVE-QTGKNYLVEVT 397

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 398 LHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 442


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/217 (36%), Positives = 127/217 (58%), Gaps = 10/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKA-- 70
           R+ K+IA AG  SRR  E +I Q R++V+    + A++  N   TD +++DG  +  +  
Sbjct: 4   RLQKLIANAGYGSRRWAEHLIEQGRIEVDN---KTASIGDNAEITDCVKIDGQKIDLSRY 60

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +  ++ + +K  G++ ++ D  GR +V+  LP   SR + VGRLD+NT GLLL TN+G
Sbjct: 61  LEQEIKVIILNKQAGVICSNLDDKGRKSVYSLLPK-ESRWVMVGRLDLNTSGLLLFTNNG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS+Q  R Y VR  GQV+ + L  L +G+ +        Q+     +G+N W
Sbjct: 120 DLANKLMHPSSQIDREYAVRVLGQVEDEDLKKLTQGVKLDDGFAKFSQIIFGGGQGANRW 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V L+EG+  E+++++E   +KV+RLIRI +G  +L
Sbjct: 180 YKVVLKEGRKHEVRRLWEELGFKVSRLIRIRFGEIRL 216


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 80/224 (35%), Positives = 123/224 (54%), Gaps = 5/224 (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
             +L +KP   + T +D   R+TV D +P    R+ +VGRLD +T G+LLLTNDG  A  
Sbjct: 62  -YFLMNKPKKTMCTSNDEFDRTTVIDLIPC-KERIFTVGRLDYDTSGVLLLTNDGEFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           +  P     +VY +  +G +  +++  +KKGIV+   +      +++T      +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTPEEMIQIKKGIVLDDGKKTLPAKLKLTEKDVTKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG+NR+IK++ E   ++V RL R      +   L  G  R
Sbjct: 180 LTIYEGRNRQIKRMMEALGYEVRRLHRKELAFLKCSDLRQGEYR 223


>gi|302518236|ref|ZP_07270578.1| pseudouridine synthase [Streptomyces sp. SPB78]
 gi|302427131|gb|EFK98946.1| pseudouridine synthase [Streptomyces sp. SPB78]
          Length = 447

 Score =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VDG+ +   +  
Sbjct: 212 ERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVDGLTV-ATQSY 270

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA  
Sbjct: 271 QFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDTETEGVILLTNHGELAHR 330

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V 
Sbjct: 331 LTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVE-QTGKNYLVEVT 389

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 390 LHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 434


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/236 (33%), Positives = 122/236 (51%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K++A AG+ SRR  E +I Q RV +NG +        +S+D +E+DG P+  A
Sbjct: 1   MTAQRLQKLLASAGLCSRRRAEELILQGRVTLNGAVARLGDQADLSSDRLELDGTPVAAA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTND 127
             T   L +KP G++ +  DP+GR+TV D LP   S       VGRLD  + G LLL+ND
Sbjct: 61  APTITVLLNKPRGVICSCHDPEGRTTVLDLLPPELSEATGLHPVGRLDGASRGALLLSND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + YRV   G+   + L   ++G+ + G     + V    +     
Sbjct: 121 GALTLRLTHPRFGHRKHYRVWVTGEPAAEALEQWRRGVPLDGQPSQPVGVRELARGQRGT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + + EG+NR+I++  E     V  L R++ GP +LG L  G  R ++ +  R+
Sbjct: 181 LLELEMVEGRNRQIRRTAELLGHPVRDLQRVAIGPLRLGELPEGRWRHLAPQEWRD 236


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 91/256 (35%), Positives = 143/256 (55%), Gaps = 12/256 (4%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IE 61
           +K I  +    +R+ KV+A AGI SRR+ E +I + RV V+G ++      V      I 
Sbjct: 23  EKQIGPDGVVAERLQKVLAAAGIGSRRDCEELITEGRVDVDGKVVTELGTRVDPVKQTIR 82

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG  LRK +R   ++ +KP G+VTT+ D  GR+ V D +P+   RV +VGRLD  +EGL
Sbjct: 83  VDGEALRKPQRL-YFVVNKPEGVVTTNYDQAGRTRVIDLVPTD-ERVFAVGRLDRASEGL 140

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGD-MQVTL 179
           +++TNDG  A  +  P     + Y VR  G+    +L  L++GI +  G C  D +QV  
Sbjct: 141 IIVTNDGEFANRVTHPRYGVTKTYLVRVAGEASTAELAKLRRGIHLSDGFCKVDAIQVKR 200

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++ ++  + + L EGKNREI+++      KV +L R++ G  +LG L  G+ R + K+
Sbjct: 201 RHKQSTD--MVIQLSEGKNREIRRILARIGHKVLKLKRLAVGSLKLGELPLGAWRWLDKQ 258

Query: 240 ILREQLGPHLLEEAQV 255
            +       LL EA++
Sbjct: 259 EIE-----RLLSEARL 269


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 98/250 (39%), Positives = 144/250 (57%), Gaps = 24/250 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR TVF+ LP +  +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHG-----QVDQDKLNLLKKGIVIQGICYGDMQVTLDT--- 181
           LA  +  PS++  R Y VR         V  + L  L +G++++     D     DT   
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLE-----DGTAKFDTIER 200

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
                S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K
Sbjct: 201 IGNTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPK 260

Query: 239 ---KILREQL 245
              + LR QL
Sbjct: 261 TQVEALRTQL 270


>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 =  127 bits (319), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 75/201 (37%), Positives = 118/201 (58%), Gaps = 5/201 (2%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           VKVNG +++   + V S+D +EVDG+P+ + E   + LY KP G++++ +D  GR  V D
Sbjct: 6   VKVNGKVVKELGLKVSSSDRVEVDGIPVEREEPVYILLY-KPRGVISSVTDEKGRKVVTD 64

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            LP I  RV  VGRLD +T GLLL+TNDG  A +L  P  +  +VY  +  G   ++KL 
Sbjct: 65  LLPQIKERVYPVGRLDFDTSGLLLMTNDGEFANLLMHPKNEVEKVYVAKIKGIPAREKLK 124

Query: 160 LLKKGIVIQGICYGDMQV---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            L++G+ ++       +V   ++D QK + A V + + EG+NR+++++ E     V +L 
Sbjct: 125 SLERGVRLEDGKTAPARVKVLSIDKQKNT-AIVELVIHEGRNRQVRRMLEAIGHPVMKLK 183

Query: 217 RISYGPFQLGTLLAGSTREVS 237
           R  YG   L  L AG  RE++
Sbjct: 184 RERYGFLTLQGLSAGDARELT 204


>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 =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I + RV++NG I+LE+        D I+VDG+ +   + 
Sbjct: 136 ERLQKVLARAGFGSRRACEELIEEARVEINGEIVLEQGRRVDPEKDEIKVDGLTV-ATQS 194

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 195 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 254

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    +  Q G N  V V
Sbjct: 255 RLTHPKYGVKKTYLAHIVGPIPRDLGKQLKDGIQLEDGYARAD-HFRVVQQTGKNYLVEV 313

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R+++GP  LG   +G  R +S
Sbjct: 314 TLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLS 359


>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 =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I   RV+VNG I+LE+        D I+VDG+ +   + 
Sbjct: 115 ERLQKVLARAGYGSRRACEELIEDARVEVNGEIVLEQGLRVDPENDEIKVDGLTV-ATQS 173

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 174 YQFFSLNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 233

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 234 RLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 292

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R+++GP  LG   +G  R +S
Sbjct: 293 TLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLS 338


>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 =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 130/226 (57%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ SRR  E+MIA  RV+V+G+ +    V +  S   + VDG+P++  + 
Sbjct: 47  ERLQKVLAAAGLGSRRACEQMIADGRVEVDGVPVTELGVRIDPSRQKVAVDGLPVQLDDS 106

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +++KP+G+++T  D +GR +V D   +   R+  VGRLD +T GLLLLTNDG LA 
Sbjct: 107 KVYLVFNKPVGVISTMEDEEGRLSVGDYTYTRKERLFHVGRLDQDTSGLLLLTNDGELAH 166

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L+ PS    + Y  +  G V +   NLL++G+ ++ G+   D    + +Q G  A V +
Sbjct: 167 RLQHPSYSVPKTYVAKVPGPVKKGLGNLLREGVELEDGVVKVDDFSVVASQPGW-AMVQL 225

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+   ++++ E   + V  L+R   G  ++G L  G+ R V+
Sbjct: 226 VIHEGRKHVVRRLLEEVGYPVEELVRTQVGEIRMGDLRPGNLRAVT 271


>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 =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 124/227 (54%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + RV VNG  +    V V S+D IEV+G+ L + E  
Sbjct: 48  ERLQKVIAHAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGSSDKIEVNGLKLEREEPV 107

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G+++   D  GR  V D    +  R+  +GRLD +T GL+L+TNDG  A  
Sbjct: 108 YFMLY-KPRGVISAAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLILITNDGEFAHK 166

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  +  G   ++ L  L+KGI++        +   +++D +K   + V 
Sbjct: 167 LMHPKYEIDKTYAAKLKGIPSKELLRKLEKGIMLDHKKTARARAKMLSIDKRK-QTSIVQ 225

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EG+NR+++++FE     V +L R  Y    +  +  G  RE++
Sbjct: 226 LTIHEGRNRQVRRMFEAIGHDVLKLKREQYAFLHIEGMRPGDRRELT 272


>gi|299139090|ref|ZP_07032266.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
 gi|298598770|gb|EFI54932.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
          Length = 307

 Score =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 87/247 (35%), Positives = 128/247 (51%), Gaps = 25/247 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A+AGIASRR  E +I + RV+VNG ++        +T DHI VDG  L   E  
Sbjct: 14  RLQKILAQAGIASRRAAETIILEGRVQVNGQVVTELGTRADATRDHIRVDGKLLHGPEPQ 73

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-----------SIFSRVISVGRLDINTEGLL 122
           R ++ +KP G VTT  DP+ R TV   L            +   R+  VGRLD  +EGLL
Sbjct: 74  RYFMVNKPRGYVTTLDDPEHRPTVMQLLGQDAQKKSVGEHNKLPRLYPVGRLDYLSEGLL 133

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQV 177
           L+TNDG LA  L   +    + Y V+  G    + ++ L++GI+I       +  G    
Sbjct: 134 LMTNDGELANKLSKAAAGVEKTYLVKVSGSPTDEAIDQLRRGIMIDRGRLNEVRSGRRDR 193

Query: 178 TLDT-------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            L +       ++G N W  V L EG+NR+++K+FE     V ++ RI YG   L  +  
Sbjct: 194 VLTSPAKIEQVRRGENPWFEVTLTEGRNRQLRKMFEEIGHHVEKIRRIGYGALVL-DIPP 252

Query: 231 GSTREVS 237
           G  RE++
Sbjct: 253 GGFRELT 259


>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 =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 98/250 (39%), Positives = 144/250 (57%), Gaps = 24/250 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR TVF+ LP +  +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHG-----QVDQDKLNLLKKGIVIQGICYGDMQVTLDT--- 181
           LA  +  PS++  R Y VR         V  + L  L +G++++     D     DT   
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLE-----DGTAKFDTIER 200

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
                S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K
Sbjct: 201 IGNTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPK 260

Query: 239 ---KILREQL 245
              + LR QL
Sbjct: 261 TQVEALRTQL 270


>gi|297170719|gb|ADI21742.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [uncultured actinobacterium
           HF0130_15N16]
          Length = 239

 Score =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 128/232 (55%), Gaps = 12/232 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLRKA 70
           +R+ K ++RAG+ASRR  E MI   RV +N     + +R +V    TD IE+DG+P+ + 
Sbjct: 8   ERLQKALSRAGVASRRVSEGMIEAGRVTINRRVATVGDRVSV----TDRIELDGIPVIRD 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +L +KP+G+V+T  DP  R TV D L S   R+  VGRLD ++EGL++LTNDG L
Sbjct: 64  PDLVHYLLNKPVGVVSTSKDPQKRRTVVD-LVSSNERIFPVGRLDADSEGLIILTNDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  PS    + Y V   G   +  L LL++G+ ++  C     V +      +  + 
Sbjct: 123 THRLTHPSFGVSKEYLVHVEGVPSRSSLRLLREGVELEDGCTAPANVAMP----QDGVMR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++++       V RL+R+  G  +  +L  G+ R +S + +R
Sbjct: 179 ITIHEGRNRQVRRMCAAIGHPVQRLVRVRIGSIKDPSLRVGTARRLSVEEVR 230


>gi|289677286|ref|ZP_06498176.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. syringae FF5]
          Length = 208

 Score =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 87/209 (41%), Positives = 119/209 (56%), Gaps = 16/209 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58  DHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     R I++G
Sbjct: 60  DAISVDGRVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--I 170
           RLDINT GLL+ T DG LA  L  PS +  R Y VR  G+VD D L  LK G++++    
Sbjct: 120 RLDINTTGLLMFTTDGELANRLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPA 179

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
            + D+Q     + G N W    + EG+NR
Sbjct: 180 RFTDIQQAPGGE-GFNHWYHCVVMEGRNR 207


>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 =  127 bits (318), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 131/225 (58%), Gaps = 4/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA A   SRRE +  + + RVKVNG  +  + V V  +D +EVDG  L   ++  
Sbjct: 2   RINKYIATALKISRREADNYVKEGRVKVNGKSIT-SFVEVDGSDKVEVDGELLSLNKKKS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            + ++KP  ++++  D +GR+TV D   +I  ++I VGRLD  +EGLL++T+DG  A +L
Sbjct: 61  YFAFYKPPFVISSTKDNEGRTTVCDFFKNIEEKLICVGRLDYLSEGLLIITSDGEFANLL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y V+  G +  + L  + KG+ ++   +  +++    +  S  WV + + 
Sbjct: 121 MHPRFKIRKTYLVKTKGPIKTETLKAMSKGVNLEDGFFRPIRI---KKTNSPNWVLISID 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            G+NR I++  + F+ K+++L RI+ G  +LG L  G  RE++K+
Sbjct: 178 TGRNRIIRRFLKKFDIKIDKLKRIAIGNIELGNLRNGEFRELTKQ 222


>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 =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 126/234 (53%), Gaps = 12/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+++ +A AG+ASRR  E +IAQ RV+VNG ++      ++   D I VDG  ++    
Sbjct: 37  ERLARFLAHAGVASRRHAEELIAQGRVRVNGTIITAQGTRILPGQDRIVVDGKEIQAKAP 96

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               L HKP G V+T SDP+GR+TV D LP      R+  VGRLD +T GLLLLTNDG  
Sbjct: 97  HAYLLLHKPAGYVSTVSDPEGRATVLDLLPPELRSLRLYPVGRLDRDTSGLLLLTNDGAF 156

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGS-- 185
           A+ L  P  +  + Y V+  G   +  L  L+ G+      G  Y        T+K S  
Sbjct: 157 AQHLTHPRYEKEKHYEVQVKGIPTERTLQALRDGVTFTEDDGKHYTSSPAR--TRKLSST 214

Query: 186 --NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             ++W+T+ + EG+ R+++++ +  +  V +L R+  G   L  +  G  R ++
Sbjct: 215 EQSSWLTLTIHEGRKRQVRRMLQAVDHPVLQLRRVGLGSLTLRGVTPGKWRHLT 268


>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 =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 85/227 (37%), Positives = 125/227 (55%), Gaps = 3/227 (1%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L + +  RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 84  LVYLAMNKPRGVVSTMADEKGRTAIGDFLGNRVEQRVYHVGRLDADSEGLLLLTNDGTLA 143

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y     G + +     L  G+ +  G    D    +DT  G  A V 
Sbjct: 144 HRLMHPSYGVPKTYLCEVSGPIPRSLGRRLAAGVELTDGPATVDAFRVVDTL-GKTAQVE 202

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+   ++++F+     V+RL+R S GP +LG L AG TR ++
Sbjct: 203 VTLHEGRKHIVRRLFDAVGHPVSRLVRTSIGPIRLGDLRAGRTRRLT 249


>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 =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 84/219 (38%), Positives = 124/219 (56%), Gaps = 9/219 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGVPL 67
           +++ KV+ARAG  SRRE+E MI   RV ++G++      L+  +V V    H ++D V  
Sbjct: 6   EKLQKVLARAGQGSRREIELMIQSGRVSIDGVVAKLGDRLDDFSVLVRIDGH-KIDLVSP 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
              E  R+  Y+KP G + T  DP+GR TVFD LP + S R +SVGRLD NT GLLL T 
Sbjct: 65  -SEEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLSSGRWVSVGRLDANTSGLLLFTT 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS    R Y VR  G+++++ +  L +G+ ++        V     +G N
Sbjct: 124 DGELANRLMHPSRSVEREYMVRVFGEINENMVKNLVQGVELEDGMARFEDVVYSGGEGMN 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               V + EG+NRE++++++     V+RL R+ YG   L
Sbjct: 184 HTFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDIYL 222


>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 =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 97/250 (38%), Positives = 144/250 (57%), Gaps = 24/250 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR TVF+ LP +  +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHG-----QVDQDKLNLLKKGIVIQGICYGDMQVTLDT--- 181
           LA  +  PS++  R Y VR         V  + L  L +G++++     D     DT   
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLE-----DGTAKFDTIER 200

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
                S+ W  + ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K
Sbjct: 201 IGNTDSHDWFRIVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPK 260

Query: 239 ---KILREQL 245
              + LR QL
Sbjct: 261 TQVEALRTQL 270


>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 =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I Q RV+VNG I+LE+        D ++VDG+ +   + 
Sbjct: 122 ERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTV-ATQS 180

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 181 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 240

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 241 RLTHPKYGVRKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 299

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 300 TLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 345


>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 =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 79/219 (36%), Positives = 119/219 (54%), Gaps = 5/219 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QRV K++++ G+ASRR  E MI   RVK+NG ++        S D +EVDG  ++ ++R 
Sbjct: 3   QRVQKILSQWGVASRRHAEDMIIAGRVKLNGEIVTLGDKADPSCDRLEVDGRMIQPSQRP 62

Query: 74  RLW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +L   L +KP+G+V T  DP  RS V D LP   S+   +  VGRLD N+ G LLLTNDG
Sbjct: 63  QLLYILINKPVGVVCTCDDPQNRSIVLDLLPKQLSKGTGIHPVGRLDFNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G   +++L   ++G+++ G      QV +  +   N  
Sbjct: 123 ELTLRLTHPRYHLPKTYEVLIQGHPTEERLQQWREGVMLMGKKTLPAQVEVICRYRQNTR 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           + V L EG+NR+I+ + +   + V RL R + G   L +
Sbjct: 183 LKVILTEGRNRQIRHIVQHLGFHVLRLHRTAIGSLVLSS 221


>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 =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 85/247 (34%), Positives = 132/247 (53%), Gaps = 15/247 (6%)

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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +      R+  +GRLD NT GLLL+TNDG L +
Sbjct: 62  -YFLLNKPNGFLSTAKDNKKRPTVLDLIEEANIQRLYPIGRLDFNTTGLLLITNDGDLTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-----NA 187
            L  PS    + Y V+ +  + +  L   +KGI+I    Y      +D  K S     + 
Sbjct: 121 KLTHPSFCIPKEYHVKINACLQKKDLATFRKGIIIDK-NYLAFCKEIDILKSSYKPKPST 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-----EVSK-KIL 241
           W+ + + EGKNR+++K+ +   ++V +L R  Y    +  L  G+ R     E+ K K L
Sbjct: 180 WLKLVITEGKNRQVRKMMQSLGYQVLKLKRYRYSFLTIENLTIGAYRPLKIHEIKKLKTL 239

Query: 242 REQLGPH 248
             Q+ PH
Sbjct: 240 TTQI-PH 245


>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 =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 126/234 (53%), Gaps = 5/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R+ KV+A+ GIASRRE E MI + RV++NG L E         D I VDG  V  ++  R
Sbjct: 4   RLQKVLAQWGIASRREAEEMIRRSRVQINGTLAELGQKVNPEKDIITVDGKSVSAQRHPR 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
               L +KP G+V+T  DP GR TV D LP    +   +  VGRLD ++ G L+LTNDG 
Sbjct: 64  LTYLLLNKPTGVVSTCYDPQGRKTVLDLLPEELRKGPGLHPVGRLDADSTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y+V   G   +  L + ++G+++ G      +V+L       + +
Sbjct: 124 LTFRLTHPSHSIPKTYQVLVKGHPPKAVLEMWREGVLLDGRKTRKAKVSLLESLAEKSRL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L+EG+NR+I++V E   + V +L R + G  QL T      R  + +ILR+
Sbjct: 184 EIVLQEGRNRQIRRVAEQLGYPVIKLHRTAIGSIQLQTSKQPLLRAGNYRILRD 237


>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 =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 97/250 (38%), Positives = 144/250 (57%), Gaps = 24/250 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D IE+DG   V     
Sbjct: 27  ERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKIELDGRSFVASALT 85

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR TVF+ LP +  +R I++GRLDINT GLLLLT DG 
Sbjct: 86  EPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDINTTGLLLLTTDGE 145

Query: 130 LARVLELPSTQWLRVYRVRFHG-----QVDQDKLNLLKKGIVIQGICYGDMQVTLDT--- 181
           LA  +  PS++  R Y VR         V  + L  L +G++++     D     DT   
Sbjct: 146 LANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLE-----DGTAKFDTIER 200

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
                S+ W  + ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E+ K
Sbjct: 201 IGNTDSHDWFRIVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLRGQSTELPK 260

Query: 239 ---KILREQL 245
              + LR QL
Sbjct: 261 TQVEALRTQL 270


>gi|310658781|ref|YP_003936502.1| rlub [Clostridium sticklandii DSM 519]
 gi|308825559|emb|CBH21597.1| RluB [Clostridium sticklandii]
          Length = 235

 Score =  126 bits (317), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 77/222 (34%), Positives = 116/222 (52%), Gaps = 5/222 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  GIASRR+ E MI + RV++N  ++   +  V   D +++DG  + K E   
Sbjct: 2   RINKFIASCGIASRRKAEEMIQEGRVRINDSVVSDLSTKVSEIDIVKIDGKIISKVEEKY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KPIG V+T  D  GR +V D       R+  VGRLD ++ GLLL+TNDG L   L
Sbjct: 62  YYMLNKPIGYVSTAKDQFGRPSVVDFFDKK-QRIYPVGRLDYDSRGLLLMTNDGDLTYAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y V     +   ++   K GI I G      ++T       N    V ++
Sbjct: 121 THPKYHIEKIYEVIVSSTLSNSEIEKFKSGIDIGGYVTAKSRITFI----GNTSYEVIIK 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           EGKNR+I+K+F      V  L R+S G  +L  L  G+ R++
Sbjct: 177 EGKNRQIRKMFSALGKDVLDLKRVSIGKLKLMDLKEGTYRKL 218


>gi|213619052|ref|ZP_03372878.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 270

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 80/198 (40%), Positives = 110/198 (55%), Gaps = 6/198 (3%)

Query: 34  MIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLRKAERTRLWLYHKPIGLVTTH 88
           +I   RV V+G I      V V     I +DG    V     +  R+  Y+KP G + T 
Sbjct: 2   IIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCTR 61

Query: 89  SDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
           +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T DG LA  L  PS +  R Y V
Sbjct: 62  NDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAV 121

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           R  GQVD+ KL  L +G+ ++        +     +G N W  V L EG+NRE+++++E 
Sbjct: 122 RVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEA 181

Query: 208 FNWKVNRLIRISYGPFQL 225
              +V+RLIR+ YG   L
Sbjct: 182 VGVQVSRLIRVRYGDIPL 199


>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 =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 86/220 (39%), Positives = 122/220 (55%), Gaps = 11/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDH-IEVDGVP 66
           +++ KV+ARAG  SRRE+E MI   RV V+G++      LE  +V+V    H IE+    
Sbjct: 3   EKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDLSVSVRIDGHNIELISS- 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
               E  R+  Y+KP G + T  DP+GR TVFD LP + + R +SVGRLD NT GLLL T
Sbjct: 62  --DEEICRILAYNKPEGELCTRHDPEGRRTVFDRLPRLNTGRWVSVGRLDANTSGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS    R Y VR  G+V +  +  + KG+ ++        V     +G 
Sbjct: 120 TDGELANRLMHPSRTVEREYMVRVFGEVTEQMVKNVVKGVELEDGLARFEDVVYAGGEGM 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N    V + EG+NRE++++++     V+RL R+ YG   L
Sbjct: 180 NHTFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYL 219


>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 =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 86/220 (39%), Positives = 122/220 (55%), Gaps = 11/220 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDH-IEVDGVP 66
           +++ KV+ARAG  SRRE+E MI   RV V+G++      LE  +V+V    H IE+    
Sbjct: 3   EKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDLSVSVRIDGHNIELISS- 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
               E  R+  Y+KP G + T  DP+GR TVFD LP + + R +SVGRLD NT GLLL T
Sbjct: 62  --DEEICRILAYNKPEGELCTRHDPEGRRTVFDRLPRLNTGRWVSVGRLDANTSGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS    R Y VR  G+V +  +  + KG+ ++        V     +G 
Sbjct: 120 TDGELANRLMHPSRTVEREYMVRVFGEVTEQMVKNVVKGVELEDGLARFEDVVYAGGEGM 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           N    V + EG+NRE++++++     V+RL R+ YG   L
Sbjct: 180 NHTFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYL 219


>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 =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 128/238 (53%), Gaps = 5/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +     
Sbjct: 41  PERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHTDTV 100

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+G LA 
Sbjct: 101 LQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNNGELAN 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            +  PS +  + Y     GQV      +L++G+ ++ G    D    ++ ++GS + V +
Sbjct: 161 RIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGS-SIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLG 246
            L  GKNR ++++       V+ L R       L  L  G  R +  K    L+E +G
Sbjct: 220 TLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAALQEMVG 277


>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 =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 84/219 (38%), Positives = 124/219 (56%), Gaps = 9/219 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGVPL 67
           +++ KV+ARAG  SRRE+E MI   RV ++G++      L+  +V V    H ++D V  
Sbjct: 3   EKLQKVLARAGQGSRREIELMIQSGRVSIDGVVAKLGDRLDDLSVLVRLDGH-KIDLVSP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
              E  R+  Y+KP G + T  DP+GR TVFD LP + S R +SVGRLD NT GLLL T 
Sbjct: 62  -SDEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLSSGRWVSVGRLDANTSGLLLFTT 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS    R Y VR  G+++++ +  L +G+ ++        V     +G N
Sbjct: 121 DGELANRLMHPSRSVEREYMVRVFGEINENMVKNLVQGVELEDGMARFEDVVYSGGEGMN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               V + EG+NRE++++++     V+RL R+ YG   L
Sbjct: 181 HTFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDIYL 219


>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 =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 133/233 (57%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG  +RR+VE +I Q RV+VNG +++  AV V    D ++VDG  +R   + 
Sbjct: 2   RLNKFLAYAGFGARRKVEELIKQGRVEVNGQVVDSPAVEVDPKKDVVKVDGERVRLPNKF 61

Query: 74  RLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++KP G++T    +  D R  V D   +   R+  VGRLD NTEGLL++TNDG LA
Sbjct: 62  VYIAFNKPQGVLTAMERAPGDKRPIVADYFRNYPVRLFPVGRLDYNTEGLLIMTNDGELA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYG----DMQVTLDTQKG 184
             L  P     + Y  +  G+V   ++  +KKG ++   +G  +     D+++   ++ G
Sbjct: 122 DRLAHPRYHVPKTYIAKVKGRVKPAEIERMKKGALLVDDKGKKFFIKPLDVKLLHPSKTG 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            N +V + + +GKNR +++ F+ F+  V +L R++ GP +LG L  G  RE++
Sbjct: 182 RNTYVQITIDQGKNRVVRRFFDRFDHGVLKLKRVAIGPVKLGDLPKGYYRELT 234


>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 =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 128/238 (53%), Gaps = 5/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +     
Sbjct: 41  PERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHTDTV 100

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+G LA 
Sbjct: 101 LQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNNGELAN 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            +  PS +  + Y     GQV      +L++G+ ++ G    D    ++ ++GS + V +
Sbjct: 161 RIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGS-SIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLG 246
            L  GKNR ++++       V+ L R       L  L  G  R +  K    L+E +G
Sbjct: 220 TLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAALQEMVG 277


>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 =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 128/238 (53%), Gaps = 5/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +     
Sbjct: 41  PERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHTDTV 100

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+G LA 
Sbjct: 101 LQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNNGELAN 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            +  PS +  + Y     GQV      +L++G+ ++ G    D    ++ ++GS + V +
Sbjct: 161 RIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGS-SIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLG 246
            L  GKNR ++++       V+ L R       L  L  G  R +  K    L+E +G
Sbjct: 220 TLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAALQEMVG 277


>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 =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 128/234 (54%), Gaps = 5/234 (2%)

Query: 8   QENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG 64
           Q+   PQ  R+ KV+A AG+ASRR  E MI Q RV V G ++ +  + V   +  I VDG
Sbjct: 6   QDLHNPQGERLQKVLAHAGVASRRAAEDMIQQGRVSVEGTIVRQLGIRVDPQSAVIHVDG 65

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++  +       +KP G+V+T SD  GR T+ D +     R++ VGRLD++TEGL+LL
Sbjct: 66  NRVQLDQELITVALYKPPGVVSTMSDDQGRKTLADFVEDYPQRLVHVGRLDVDTEGLILL 125

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQK 183
           +NDG L   L  PS +  + Y  R  G V +    +++KGI ++ G  + D  +  +  K
Sbjct: 126 SNDGELVHRLTHPSYEVPKTYIARVEGTVTRGLQRVMEKGITLEDGPVHADRFIIREVAK 185

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             N+ V + L  G+NR ++++ E     V  L+R+ +G    G L  G  R+++
Sbjct: 186 -KNSIVEITLHSGRNRIVRRMMEEVGHPVMELVRMQFGNIVAGHLKPGQVRQIA 238


>gi|309389185|gb|ADO77065.1| ribosomal large subunit pseudouridine synthase B [Halanaerobium
           praevalens DSM 2228]
          Length = 236

 Score =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 126/226 (55%), Gaps = 2/226 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +IA+ RVKVNG ++      +  +   + VDG  + + ++
Sbjct: 2   ERLQKVMAHAGVASRRKSEEIIAEGRVKVNGQVITEMGYKIDPAQAEVMVDGQVISEEKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L +KP G +TT SDP+ R TV D +P +  R+   GRLD ++ GLL++TNDG L  
Sbjct: 62  VYILL-NKPEGYITTVSDPENRPTVMDLIPDLNQRLYPAGRLDFDSSGLLIMTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + YRV   G+++++     + G+VI G      +++    KG      + 
Sbjct: 121 KLTHPKKEVDKKYRVLIQGKLEEEDFEKFEAGMVIDGQETAPAEISNVDYKGEQTEFDIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + EG+NR+++++ +   + V  L RI +    L  +  G  R +++
Sbjct: 181 IHEGRNRQVRRMAKIAGFSVISLKRIGFAFLTLTGVEEGKFRYLTE 226


>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 =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 82/221 (37%), Positives = 119/221 (53%), Gaps = 5/221 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +++ KV+ARAG  SRRE+E MI   RV V+G + +        T  + +DG  +      
Sbjct: 3   EKLQKVLARAGQGSRREIELMIQNGRVSVDGDVAKLGDRLEDMTASVRIDGRRIELVAST 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E  R+  Y+KP G + T  DP+GR TVFD LP + + R +SVGRLD NT G+LL T DG
Sbjct: 63  DEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLNNGRWVSVGRLDANTSGMLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS    R Y VR  G++ +D +  L +G+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSHSVQREYMVRVFGEISEDMVRNLVRGVELEDGMARFEDVVYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V + EG+NRE+++++      V+RL R+ YG   L   L
Sbjct: 183 FYVVITEGRNREVRRLWASQGVTVSRLKRVRYGDIYLSKEL 223


>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 =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 81/243 (33%), Positives = 120/243 (49%), Gaps = 13/243 (5%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVP 66
            E   P R+ + +ARAG+ASRR  E +++  RV VNG +       V  + D + VDGVP
Sbjct: 22  DERVVPMRLQRFLARAGVASRRGSEALMSAGRVSVNGEVKTELGTKVDPAIDQVAVDGVP 81

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
           +         + +KP G++TT SDP GR  V D +P   +  +  VGRLD++T GLLL T
Sbjct: 82  VVLGVGAAYLMLNKPAGVLTTMSDPHGRPCVADIMPVRSYPGLFPVGRLDMDTTGLLLFT 141

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ-- 182
            DG L   L  PS    + Y     G   +  L  L++GIV+  G C        D +  
Sbjct: 142 TDGDLGHALLHPSRHVWKTYVAVVDGVCREGDLEPLRRGIVLDDGPCQPARCALRDERDV 201

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                   +     V + +REG+  ++K++       V RL R+ +GP +L  L  GS R
Sbjct: 202 RDIAPRGLRAGTTAVRIEIREGRKNQVKRMLSKIGHPVLRLHRLRFGPLELNDLPCGSWR 261

Query: 235 EVS 237
           E++
Sbjct: 262 ELT 264


>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 =  126 bits (316), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA +G  SRR+ E++I   +V VNG +++   V    +D I V+GV L K E 
Sbjct: 2   AERLQKLIAASGYTSRRKAEQLILDGKVSVNGEVVKELGVKAEPSDIIIVEGVRLLK-EN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP  ++T+ SD   R+ V D    +  RV+ VGRLD +T G L+++NDG    
Sbjct: 61  KRYYLFYKPEKVITSMSDEKDRTCVKDFFEDVNERVVPVGRLDYDTSGALIMSNDGEFIN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
           ++  P  +  + Y  + +G+++ + L +L+ G+ I        +V +  +  K  N  V 
Sbjct: 121 LITHPKHKIRKTYVAKINGKLEDNHLRILRNGVRIDNYKTAKAEVNIVKNKNKSGNTLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGKNR+++++FE   ++V +L R S     L  L  G  R ++
Sbjct: 181 LTIHEGKNRQVRRMFEALGYEVMKLKRESIEDLTLEGLKKGEYRTLT 227


>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 =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 125/228 (54%), Gaps = 3/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +IA+ RV+V G ++  AA+ V +  D I VD  P+  AER  
Sbjct: 19  LNRALSKLGLCSRTQAEVLIAEGRVRVGGKVVRDAALRVDLDRDRIVVDDRPV-VAERKV 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP  R TV+  L  +    +S VGRLD  +EGLLL+TND   A  
Sbjct: 78  YLMLNKPRGLVTTRDDPQQRDTVYACLEGLDLPFVSPVGRLDKASEGLLLMTNDTRFANR 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y V+     D   L  L+ G+++ G       + L    G  AW+ + L
Sbjct: 138 LMDPASHLPKTYHVQIGTVPDAPMLETLRAGVIVDGEVLTANAIELLRSGGRTAWLEIVL 197

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR I+++      +V RLIRI+ G   LG L  G+ R ++ + L
Sbjct: 198 DEGRNRHIRRLLAAHGVEVLRLIRIAIGRLPLGDLAKGTARHLTAEEL 245


>gi|309810348|ref|ZP_07704183.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
 gi|308435661|gb|EFP59458.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
          Length = 303

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 126/227 (55%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ SRR  E +IA+ RV+V+G ++      +   +  I VDG  ++  +  
Sbjct: 67  RLQKVLAQAGVGSRRHCENLIAEGRVEVDGQVVTELGTRIDPESAVIHVDGDRIQLDDTL 126

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP G+V+T  D +GR  V + L     R+  VGRLD +TEGLLLLTNDG LA  
Sbjct: 127 VYLAFNKPTGVVSTMQDEEGRPCVGEYLEGRTERLFHVGRLDYDTEGLLLLTNDGNLANR 186

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L+ P     +VY     G V +D    +++GI ++ G    D    +D+Q G  A V + 
Sbjct: 187 LQHPRYGVEKVYLATIPGPVPRDLGKRMREGIELEDGPAAVDSFKVVDSQPGM-ALVEIV 245

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L EG+NR ++++FE     V  L R   GP ++G L  G  R ++K+
Sbjct: 246 LHEGRNRIVRRMFEEVGHPVIALARPQVGPVKVGDLRPGKMRPLNKR 292


>gi|328881450|emb|CCA54689.1| Ribosomal large subunit pseudouridine synthase B [Streptomyces
           venezuelae ATCC 10712]
          Length = 453

 Score =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 126/229 (55%), Gaps = 10/229 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG I+LE+        D I+VDG+ +     
Sbjct: 217 ERLQKVLARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEIKVDGLTVA---- 272

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           T+ +L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G 
Sbjct: 273 TQSYLFFALNKPSGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGE 332

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P     + Y     G + ++    LK GI ++ G    D    +  Q G N  
Sbjct: 333 LAHRLTHPKYGVKKTYLAAITGPLPREVGKRLKDGIQLEDGYARAD-HFRVVEQTGKNYL 391

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V V L EG+   ++++     + V +L+R ++GP  LG   +G  R ++
Sbjct: 392 VEVTLHEGRKHIVRRMLAEAGFPVEKLVRTAFGPIALGDQKSGWLRRLT 440


>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 =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 125/224 (55%), Gaps = 3/224 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA +G  SRR+ E++I   +V VNG +++   V    +D I V+GV L K E 
Sbjct: 2   AERLQKLIAASGYTSRRKAEQLILDGKVSVNGEVVKELGVKAEPSDIIIVEGVRLLK-EN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP  ++T+ SD   R+ V D   ++  RV+ VGRLD +T G L+++NDG    
Sbjct: 61  KRYYLFYKPEKVITSMSDEKDRTCVKDFFENVNERVVPVGRLDYDTSGALIMSNDGEFIN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
           ++  P  +  + Y  + +G+++ + L +L+ G+ I        ++ V  +  K  N  V 
Sbjct: 121 LITHPKHKIKKTYVAKINGKLEDNHLRILRNGVRIDNYKTAKAEVNVVKNKNKSGNTLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EGKNR+++++FE   ++V +L R S     L  L  G  R
Sbjct: 181 LTIHEGKNRQVRRMFEALGYEVIKLKRESIEDLTLEGLKKGEYR 224


>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 =  125 bits (315), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 127/229 (55%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V  S D I VDGV +   E 
Sbjct: 63  ERLQKVLAKAGVASRRHAEILIDAGRVEVNGKIISKQGVKVNPSVDVIRVDGVRVNVNEE 122

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
              ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLL+LTNDG 
Sbjct: 123 HEYFVLNKPRGMQSTMSDDLGRPCVGDVVSEKVAAGQRLFHVGRLDADTEGLLILTNDGE 182

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P  +  + Y     G+ D+  +  LK+GI ++ G+   D    +DT +G  + 
Sbjct: 183 LANRLMHPKYEVTKTYLATVLGEADRKLVRQLKEGIELEDGLAKADFAQVVDTNQGY-SL 241

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V + L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 242 VRLELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTVQLGDMKPGGLRALN 290


>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 =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I Q RV+VNG I+LE+        D ++VDG+ +   + 
Sbjct: 123 ERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTV-ATQS 181

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 182 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 241

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 242 RLTHPKYGVKKTYLAAIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 300

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 301 TLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 346


>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 =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 132/236 (55%), Gaps = 4/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R++K IA++GI SRR+ + +I + +VKVNG  ++   + +    D +EV+G  ++  E+
Sbjct: 2   ERLNKYIAKSGICSRRKADELILEGKVKVNGKTVKNLGLKIDPKKDVVEVEGKIVKPTEK 61

Query: 73  TRLWLYHKPIG-LVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP+G L     D  GR T+ D  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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V +  GK R I++  + F  +V RLIR+  G   +G L     R +S+K +R  L
Sbjct: 182 LVEIHSGKKRIIRRFMDSFGHRVKRLIRVKIGSIDIGNLKPFDYRYLSEKEIRSIL 237


>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 =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 127/229 (55%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V  S D I VDGV +   E 
Sbjct: 63  ERLQKVLAKAGVASRRHAEILIDAGRVEVNGKIIAKQGVKVNPSVDVIRVDGVRVNVNEE 122

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
              ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLL+LTNDG 
Sbjct: 123 HEYFVLNKPRGMQSTMSDDLGRPCVGDVVSEKVAAGQRLFHVGRLDADTEGLLILTNDGE 182

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P  +  + Y     G+ D+  +  LK+GI ++ G+   D    +DT +G  + 
Sbjct: 183 LANRLMHPKYEVTKTYLATVLGEADRKLVRQLKEGIELEDGLAKADFAQVVDTNQGY-SL 241

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V + L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 242 VRLELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTVQLGDMKPGGLRALN 290


>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 =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 131/225 (58%), Gaps = 5/225 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K IA+AG+ SRR+ E++I + RVKVNG ++    V +    D +E+D   ++  ++
Sbjct: 3   ERLQKFIAKAGVTSRRKAEKLILEGRVKVNGEVIRTLGVKIDPEKDIVEIDNKIVKPDKK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + LY KP+G +++  DP GR T+ D L   +  RV  VGRLD ++EGLLL TNDG +A
Sbjct: 63  IYIALY-KPVGYISSLYDPFGRRTIKDLLRDKVPFRVYPVGRLDFDSEGLLLCTNDGEIA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
            VL  P  +  +VY V   G   +++L  L++G++++         ++  + ++ + + +
Sbjct: 122 NVLIHPRYKIPKVYEVLIDGIPKEEELKKLREGVILEEGRTLPAGFEIIWENRRKNISLL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L +G  R+I+++   FN+KV  L R+  G  +LG L  G  R
Sbjct: 182 KITLYQGWKRQIRRMLALFNYKVLNLKRVQIGKIKLGDLKPGEIR 226


>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 =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 84/221 (38%), Positives = 117/221 (52%), Gaps = 5/221 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG+ SRRE+E MI   RV ++G   +           I +DG  +   E T
Sbjct: 3   EKLQKVLARAGLGSRRELETMIQAGRVSIDGQKAKLGDRLENVDARIRIDGHVVSVKEST 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  YHKP G + T  DP+GR TVFD LP I  SR +SVGRLD NT GLLL T DG
Sbjct: 63  DVICRVLAYHKPEGELCTRHDPEGRRTVFDRLPKIKDSRWVSVGRLDANTAGLLLFTTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  R Y  R  G ++   +  L  G+ ++        V     +G N  
Sbjct: 123 ELANRLMHPSRKVEREYMCRIFGDINDKMVKNLVTGVKLEDGEARFEDVMYAGGEGMNHT 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V + EG+NRE++++++     V+RL R+ YG   L   L
Sbjct: 183 FYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKAL 223


>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 =  125 bits (315), Expect = 8e-27,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 128/228 (56%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +  A +
Sbjct: 130 ERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTV--ATQ 187

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA
Sbjct: 188 SYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELA 247

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V
Sbjct: 248 HRLTHPRYGVKKTYLAAIQGPLPRDLGKRLKSGIELEDGYARADHFRVVQNT--GKNYLV 305

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++
Sbjct: 306 EVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPIALGDQKSGWLRRMT 353


>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 =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 124/232 (53%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K+++ AG+ASRR  E +I   RV V+G+ +          +H 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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  +VY     G V +  L  L++GI+++ G+        L   KG     T+
Sbjct: 123 GLLHPRFEIDKVYHAEVAGPVTEGGLTRLRRGILLEDGMTASAKLRILRADKGYTVVETI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EG+NR+++++F     +V  L R+ +    L  L  GS R +++  + E
Sbjct: 183 -IHEGRNRQVRRMFAAIGCRVCALRRVRFAMLTLRGLSCGSFRHLTRDEIHE 233


>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 =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 87/230 (37%), Positives = 127/230 (55%), Gaps = 11/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +IA  RV V G ++    V V   T  I +DG+ ++     
Sbjct: 70  RLQKVLASAGLGSRRACEELIAAGRVTVAGQVVTELGVRVDPRTAVIHLDGMRVQLDSSV 129

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V+T  DP+GR ++   + +   R+  VGRLD ++EGLLLLTNDG LA  
Sbjct: 130 VTLALNKPVGVVSTMHDPEGRPSLAQYVANREERLFHVGRLDADSEGLLLLTNDGELANR 189

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSNA-W 188
           L  PS    + Y V   G+V       LK+G+ ++     D  V +D     Q  S+A  
Sbjct: 190 LAHPSHGVPKTYLVEVQGRVRDALGKQLKEGVELE-----DGTVRVDEFKVVQVASHASL 244

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V V L EG+NR ++++F+     V+RL+R   GP +LG L  G TR +SK
Sbjct: 245 VEVVLHEGRNRVVRRLFDEVGHPVDRLVRTRIGPIRLGDLRPGRTRVLSK 294


>gi|327188988|gb|EGE56177.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli CNPAF512]
          Length = 267

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 77/224 (34%), Positives = 122/224 (54%), Gaps = 3/224 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV ++G  +   +  V + T  I VDG+ +  AE   
Sbjct: 27  LPRALSKLGYCSRTQAERLIAESRVSIDGRTVNDPSAWVDLVTAKIRVDGLVI-AAEAKI 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL TND   A++
Sbjct: 86  YLILNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQI 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D +++  +  GI   G       V    Q   N+W+ V L
Sbjct: 146 LLDPVTHVTKTYHVQIDRLLDDEEIAAMTSGIRHDGELLTATAVRRLRQGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 206 DEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAARALT 249


>gi|213023264|ref|ZP_03337711.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 244

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 68/154 (44%), Positives = 94/154 (61%), Gaps = 1/154 (0%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
            R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T DG LA
Sbjct: 20  CRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELA 79

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS +  R Y VR  GQVD+ KL  L +G+ ++        +     +G N W  V
Sbjct: 80  NRLMHPSREVEREYAVRVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNV 139

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 140 TLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 173


>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 =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 84/224 (37%), Positives = 116/224 (51%), Gaps = 1/224 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR  E +I   RV+VNG +++   V V    D + VDG P+   ER 
Sbjct: 2   RLQKYLALAGVASRRRAEDLIRAGRVRVNGRVIKVMGVQVEPGQDKVTVDGQPVTGPERK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L  KP G VTT SDP GR  V D +  I +R+  VGRLD  TEGLLLLTNDG L   
Sbjct: 62  YYLLLFKPAGYVTTVSDPRGRPKVTDLVHGIPARLYPVGRLDYATEGLLLLTNDGELTLR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y     G  D + +  L+ G+ ++       +V L      +A + + L
Sbjct: 122 LTHPRYGVTKTYLALVRGIPDANTIQHLRCGVKLEDGPTAPARVNLCRAGKDSALLELTL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           REG+NRE++++       V RL RI      L  L  G+ R ++
Sbjct: 182 REGRNREVRRMLAAVGHPVLRLRRIRLAFLTLRGLKPGTYRHLT 225


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 76/230 (33%), Positives = 124/230 (53%), Gaps = 4/230 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA  G+ SRR+ E ++ +  + +N   +   +  V +  D +     PL   E+ 
Sbjct: 2   RIAKFIAACGVCSRRKAEELVNEGHITINNHRVTELSTQVDVDNDEVRYRRKPL-VLEKK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP+G V T+ DP       D LP    R+ +VGRLD  +EGL++LTNDG LA++
Sbjct: 61  LYYLLNKPVGYVCTNDDPFAEKKAIDLLPDK-GRLYTVGRLDKPSEGLIVLTNDGDLAKI 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  + YRV   G+V Q KL+ L++ G+  +G+ Y  +   +  Q      +   
Sbjct: 120 MTHPSFELEKKYRVTVKGRVSQKKLDYLVRDGLTFEGVNYRVLDARIKKQVPGGYMINFT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L EGKNREI+K+ +  + +V RL R       LG L  G+ R +++  +R
Sbjct: 180 LNEGKNREIRKICQSLDLQVKRLRRYEIAGIALGKLPPGAWRPMTQSEVR 229


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I Q RV+VNG I+LE+        D ++VDG+ +   + 
Sbjct: 111 ERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGRRVDPEKDEVKVDGLTV-ATQS 169

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 170 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 229

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 230 RLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 288

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 289 TLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 334


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 77/224 (34%), Positives = 122/224 (54%), Gaps = 3/224 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV ++G  +   +  V + T  I VDG+ +  AE   
Sbjct: 27  LPRALSKLGYCSRTQAERLIAESRVSIDGRTVNDPSAWVDLVTAKIRVDGLVI-AAEAKI 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL TND   A++
Sbjct: 86  YLILNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQI 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D +++  +  GI   G       V    Q   N+W+ V L
Sbjct: 146 LLDPVTHVTKTYHVQIDRVLDDEEIAAMTSGIRHDGELLTATAVRRLRQGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 206 DEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAARALT 249


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 87/262 (33%), Positives = 136/262 (51%), Gaps = 16/262 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ + +ARAG+ASRR  E ++   RV VNG++       V +  DHIEVDGVP++  +  
Sbjct: 31  RLQRFLARAGVASRRGSEDLMTAGRVTVNGLVATELGTKVDVDRDHIEVDGVPVKLNQGA 90

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G +TT SDP  R  V D +P + F  +  VGRLD +T GLLL T DG L++
Sbjct: 91  VYLMLYKPTGYLTTMSDPQERPCVADLVPRNRFPGLFPVGRLDRDTTGLLLFTTDGDLSQ 150

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--------- 182
            L  PS    + Y+    GQ+    L+ L++GI +  G+C   +   ++ +         
Sbjct: 151 DLLHPSKHVHKTYQALVDGQLTDRDLDQLRRGIELDDGLCQPAICRVINAREAVAVAPQG 210

Query: 183 -KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK-- 239
            K     V V +REG+  ++K++    +  V RL R ++   +L  +  GS RE++ +  
Sbjct: 211 VKPGTTAVEVIIREGRKNQVKRMLGKIHHPVIRLHRCNFAGLELEGVAKGSWRELTDREV 270

Query: 240 -ILREQLGPHLLEEAQVNLDAP 260
            IL+    P     A+ N D P
Sbjct: 271 QILKSGGIPPKQASAKRNGDKP 292


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 123/228 (53%), Gaps = 3/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV V+G  +   +  V ++T  I VDG+ +  AE   
Sbjct: 27  LPRALSKLGYCSRTQAERLIAESRVAVDGRTISDISAWVDLATARISVDGLVI-AAEAKI 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL TND   A++
Sbjct: 86  YLMLNKPRGLVTTRDDPEGRPTVYDCLREFDIPHLSPVGRLDKASEGLLLFTNDTEFAQI 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D + +  +  GI   G            Q   N+W+ V L
Sbjct: 146 LLDPVTHVTKTYHVQIDRIMDDEGIAAMTSGIRHDGELLTATAARRLRQGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++  L
Sbjct: 206 DEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTEAEL 253


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 126/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I Q RV+VNG I+LE+        D I+VDG+ +   + 
Sbjct: 120 ERLQKVLARAGYGSRRSCEELIEQARVEVNGEIVLEQGLRVDPEKDEIKVDGLTV-ATQS 178

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  D +GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 179 YQFFSLNKPAGVVSTMEDTEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 238

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 239 RLTHPKYGVKKVYLAHIVGPIPRDLGKRLKDGIQLEDGYAKADHFRVVE-QTGKNYLVEV 297

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R+++GP  LG   +G  R +S
Sbjct: 298 TLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLS 343


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 81/226 (35%), Positives = 124/226 (54%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A AG+ SRR  E +I Q RV+V+G ++    V +     +  VDGV +   E  
Sbjct: 98  RLQKLMAAAGVGSRRVCENLIEQGRVEVDGQVITELGVRINPQSQVVHVDGVRVNLDEER 157

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP G+VTT  D  GR ++ D + +   R+  VGRLD +TEGLLLLTNDG LA  
Sbjct: 158 VYLAFNKPKGVVTTMHDELGRISLADYVGNREQRLFHVGRLDADTEGLLLLTNDGDLAHR 217

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L+ P+   L+ Y     G V +D    L++G+ ++ G    D    +D+Q G  A + V 
Sbjct: 218 LQHPAYGVLKTYLATVRGPVGRDVGKQLREGVELEDGPVTVDSFKVVDSQPG-KALIEVV 276

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EG+   ++++ E     V  L+R   GP +LG L +G  R ++K
Sbjct: 277 LHEGRKHVVRRMLELVGHPVLELVRTEVGPIRLGDLRSGRMRRLNK 322


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 83/228 (36%), Positives = 128/228 (56%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I   RV+VNG I++E+        D I+VDG+ +  A +
Sbjct: 140 ERLQKVLARAGVGSRRACEELIEAGRVEVNGSIVIEQGVRVDPENDEIKVDGLTV--ATQ 197

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA
Sbjct: 198 SYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELA 257

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     + Y     G + ++    LK GI ++ G    D  +V  +T  G N  V
Sbjct: 258 HRLTHPRYGVKKTYLAAIQGPLPRELGKRLKDGIALEDGYARADHFRVVENT--GKNYLV 315

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+   ++++     + V+RL+R ++GP  LG   +G  R +S
Sbjct: 316 EVTLHEGRKHIVRRMLAEAGFPVDRLVRTAFGPIGLGDQKSGWLRRLS 363


>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 =  125 bits (314), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 123/227 (54%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD +T GL+LLTNDG    
Sbjct: 62  KKYIALNKPTGYISSVKDDKGRKTILD-LIDVKERIYPIGRLDYDTSGLILLTNDGDFYN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G  +  +L   KKG+VI        ++ + + K +NA V + 
Sbjct: 121 KVIHPREEKEKVYVATIKGIPNSSELQDFKKGLVIDDYLTSPSKIKIISVKNNNAEVIIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+NR+++K+ E  N  V +L RIS G   LG L  GS R +++K
Sbjct: 181 IMEGRNRQVRKMCEKINHPVIKLKRISVGHVGLGDLPIGSWRYLTQK 227


>gi|218663826|ref|ZP_03519756.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli IE4771]
          Length = 267

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 121/224 (54%), Gaps = 3/224 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV V+G  +   +  V + T  I VDG+ +  AE   
Sbjct: 27  LPRALSKLGYCSRTQAERLIAEGRVSVDGRTVNDPSAWVDLVTAEIRVDGLVI-AAEAKI 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL TND   A++
Sbjct: 86  YLMLNKPRGLVTTRHDPEGRPTVYDCLKDFEIPHLSPVGRLDKASEGLLLFTNDTEFAQI 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D + +  +  GI   G       V    Q   N+W+ V L
Sbjct: 146 LLDPITHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAVRRLRQGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 206 DEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALT 249


>gi|302871660|ref|YP_003840296.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
 gi|302574519|gb|ADL42310.1| pseudouridine synthase [Caldicellulosiruptor obsidiansis OB47]
          Length = 236

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 76/220 (34%), Positives = 117/220 (53%), Gaps = 2/220 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E +I Q RVKVNG  + +    +    D +EVDG  +      
Sbjct: 2   RLQKFMAQCGVASRRKCEEIIQQGRVKVNGKTVNQLGFKIDPEKDIVEVDGERISLQSHK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +   +  RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 62  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   +KG++I G      +  +  Q   NA V + 
Sbjct: 122 KVTHPKHDIEKTYIALIKGIPSKEEIERFEKGLLIDGKMTAPAKFKVLKQINGNAMVEIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G 
Sbjct: 182 IHEGRNRQIRKMCDMIGHKVLKLKRIAIGKLQLGKLKEGE 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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 88/242 (36%), Positives = 131/242 (54%), Gaps = 9/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR VE M+ Q R+ VNG  +    + V    D I VDGV +   + 
Sbjct: 43  ERLQKVLARAGVGSRRVVENMVDQGRISVNGKTVAVQGMRVDPERDKIAVDGVRIELRDD 102

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP G++T  SD   R TV D +  +   ++ VGRLD +TEGLLL+TNDG LA 
Sbjct: 103 RVTYALNKPPGVITAMSDDRNRPTVGDMVGDLAPGLVHVGRLDQDTEGLLLVTNDGELAH 162

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  + Y  +  G V +D    L+ G+ ++ G    D    +DT  G +  V V
Sbjct: 163 RLAHPSYEVKKTYLAQVSGSVPRDMARRLRSGVELEDGPVKVDSFRVVDTHAGQSV-VEV 221

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EG+   ++++       V+RL R + GP +L  + +GS R +S    R ++G   LE
Sbjct: 222 VLHEGRKHIVRRLLASVGLPVSRLTRTAVGPVKLERMRSGSIRRLS----RAEVG--ALE 275

Query: 252 EA 253
           EA
Sbjct: 276 EA 277


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 120/227 (52%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +IA  RV V+G  +    V V   T  I VDG+ ++     
Sbjct: 12  RLQKVLASAGLGSRRACEELIATGRVTVDGSTVRELGVRVDPLTAVIHVDGMRVQLDSSV 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+V+T  DP+GR +V   +     R+  VGRLD  TEGLLLLTNDG LA  
Sbjct: 72  VTLALNKPKGVVSTMHDPEGRPSVAQFVADRSERLFHVGRLDSETEGLLLLTNDGELANR 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVTV 191
           L  PS    + Y     G+V       L +G+ ++ G+   D  QV   T + S   V V
Sbjct: 132 LSHPSHGVAKTYLAHVEGRVAGSLAGRLARGVELEDGVVTVDRFQVVQTTPQAS--LVEV 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L EG+NR ++++ E     V RL+R   GP +LG L  G TR +SK
Sbjct: 190 VLHEGRNRVVRRLLEEVGHPVTRLVRTQIGPIRLGDLKPGRTRVLSK 236


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 126/227 (55%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR+ ER+I + RVKV+G ++      V      I VDG+ +      
Sbjct: 15  RLQKVLAEAGLGSRRQCERLIVEGRVKVDGEVVSWLGARVDPAKAVIHVDGLRVETRPEM 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +  +KP G+V+T +D  GR ++ D +  +  R+  VGRLD +TEGL+LLTNDG LA  
Sbjct: 75  RYYALNKPRGVVSTMADERGRKSLADYV-DVPERLFHVGRLDTDTEGLILLTNDGDLAHR 133

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    +VY     G + +D    L+ GI ++ G+   D +  L  Q G  A V + 
Sbjct: 134 LTHPSFGVEKVYLAEIVGPIRRDLGRRLRAGIELEDGLAKAD-RFRLVEQVGKRALVEIT 192

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L EG+   ++++ +     V +L RI +GP +LG L  GS R ++ K
Sbjct: 193 LHEGRKHIVRRMLKEAGHPVQKLARIRFGPIKLGRLKPGSLRALTIK 239


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 89/246 (36%), Positives = 132/246 (53%), Gaps = 17/246 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDG----VPLRK 69
           R++K +A+AG+ SRR+ +  IA  RV+VNG L+ +  V V    D + VDG    +P  +
Sbjct: 31  RLNKFLAQAGVCSRRKADTYIAAGRVQVNGSLVTQLGVQVHPGQDEVRVDGRVVELPEAQ 90

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSR-VISVGRLDINTEGLLLLTND 127
           +      L HKP+ +VTT  DP GR TV D LPS  F+R +  VGRLD  +EGLLLLT+D
Sbjct: 91  SAGHDYILLHKPVQVVTTAKDPQGRRTVLDLLPSQTFTRRIFPVGRLDFMSEGLLLLTSD 150

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     +VY V     V ++ +  +  G+ +     G+    +D Q+   A
Sbjct: 151 GELANRLTHPRWHVEKVYEVTLREAVTEEHMRQMSSGMRLS---EGEQLAPVDVQRRKTA 207

Query: 188 WVT----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KI 240
             T    + L +G NR+I+++       + RL RI  GP +LG L  G  R ++      
Sbjct: 208 ADTSSLELTLHQGVNRQIRRMCRDLGLTILRLKRIRQGPVRLGKLPQGHWRHLTATEITT 267

Query: 241 LREQLG 246
           L+++LG
Sbjct: 268 LKKRLG 273


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 128/234 (54%), Gaps = 15/234 (6%)

Query: 2   KDKNIVQENFTPQ--------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           K + +  + FTP         R+ K +A AG+ASRR+ E +I    V+VNG ++      
Sbjct: 11  KGRGMGVQPFTPNLREQRDGVRLQKFMASAGVASRRKAEELITAGVVRVNGQVVRELGTR 70

Query: 54  VMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVI 109
           V    D + V G P+ +AE    ++ +KP G+V++ +   D  GR TV   L  +  R+ 
Sbjct: 71  VFPERDRVTVRGEPI-QAESKVYYVLNKPDGVVSSAAGSVDERGRPTVISLLHGVSERLY 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ- 168
            VGRLD ++ G+LLLTNDGGLA  L  P    ++ Y V+F G++ +++  LL+ G+ +  
Sbjct: 130 PVGRLDFHSRGVLLLTNDGGLAEALTHPRHGVVKTYHVKFQGKLTEEQEQLLRDGVELDD 189

Query: 169 -GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             I     ++    +  +N W  +G+REG NR+I+++ E     V +LIR++ G
Sbjct: 190 GAITRPVAELFAFRETATNVWYQIGIREGLNRQIRRMGEAIGHPVLKLIRVAIG 243


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/257 (36%), Positives = 148/257 (57%), Gaps = 14/257 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D +  ++    +R+ KV+A+AG+ SRR +E+ IA   VKVNG + +   +++ S D IE
Sbjct: 17  RDASAAEQPKLEERLHKVLAQAGLGSRRALEQRIADGLVKVNGEVAQ-TGMSIKSGDRIE 75

Query: 62  VDG---VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
           +DG   V     E  R+ +Y+KP G VTT  DP+GR T+F+ LP++  +R I++GRLDIN
Sbjct: 76  LDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTIFEALPALKGARWIAIGRLDIN 135

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-----QVDQDKLNLLKKGIVIQGICY 172
           T GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G+V++    
Sbjct: 136 TTGLLLLTTDGELANAMMHPSYEIEREYVVRVRAPEGEESVPDSMIERLARGVVLEDGSA 195

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
              ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   +L G
Sbjct: 196 KFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVALPREVLRG 255

Query: 232 STREVSK---KILREQL 245
            + E+++   + LR +L
Sbjct: 256 QSMELAQDKVEALRAEL 272


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 83/234 (35%), Positives = 124/234 (52%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+ARAG+ASRR  E +I   RV VNGI      V V   D + VDG P+      
Sbjct: 6   ERLQKVLARAGVASRRAAEELITAGRVAVNGIP-AGLGVRVQPGDRVTVDGEPVAAPTPH 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ HKP G VTT  D  GR TV D +P +   +  VGRLD ++EGLL+LT DG L   
Sbjct: 65  VTYMLHKPAGFVTTAQDELGRRTVLDAMPPVPG-LHPVGRLDKDSEGLLILTTDGDLTLR 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VYRV    +  + +L  L++G+ ++    G  +  ++   G    +   L
Sbjct: 124 LTHPRFEHEKVYRVWCFPEPGEQELAALRRGVELE---EGFARAEVEPAPGGALAL---L 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           REG+ R+++++F      V+RL+R   G   LG L  G   ++ ++ L   L P
Sbjct: 178 REGRKRQVRRMFAEVGCPVDRLLRYRVGGLWLGDLGPGEFVQLGEQELDWLLQP 231


>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 =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 80/201 (39%), Positives = 118/201 (58%), Gaps = 18/201 (8%)

Query: 31  VERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDG--VPLRKAERTRLWLYHKPIGLV 85
           +ER I Q R++++G    R A     +     ++VDG  + L + E  R  LYHKP+G V
Sbjct: 1   MERWIEQGRIEIDG----RVATLGDRIYPDQRLKVDGRRLDLERKEEVRCLLYHKPVGEV 56

Query: 86  TTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            +  DP+GR TVFD+LP++ + R I +GRLD  T GLLL T DG LA  L  PS++  R 
Sbjct: 57  CSRKDPEGRRTVFDSLPALNNGRWIVIGRLDYTTSGLLLFTTDGELANGLMHPSSEIDRE 116

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----NAWVTVGLREGKNRE 200
           Y VR  G+VD   L+ L++G+++     G  + T D Q+G     N W  V L EG+NRE
Sbjct: 117 YLVRVMGEVDDAMLDRLRQGVLLDD---GPARFT-DIQEGGGDGINRWFYVVLMEGRNRE 172

Query: 201 IKKVFEFFNWKVNRLIRISYG 221
           +++++E     V+RL R+ +G
Sbjct: 173 VRRLWESQGLTVSRLKRVRFG 193


>gi|297161649|gb|ADI11361.1| putative pseudouridine synthase [Streptomyces bingchenggensis
           BCW-1]
          Length = 333

 Score =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 128/228 (56%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +  A +
Sbjct: 97  ERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTV--ATQ 154

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G L+
Sbjct: 155 SYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELS 214

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V
Sbjct: 215 HRLTHPRYGVTKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVQNT--GKNYLV 272

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++
Sbjct: 273 EVSLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPIALGDQKSGWLRRLT 320


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/234 (34%), Positives = 128/234 (54%), Gaps = 2/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++ AG+ASRR  E  +   RV VNG             D I +DG P+R A   
Sbjct: 3   ERIQKILSAAGLASRRRAEEYLTAGRVTVNGRTAALGEKADPQRDDIRLDGKPVRPAGAH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G VTT SD  GR TV   +    +RV  VGRLD+++EGLLL+T+DG   + 
Sbjct: 63  TYLMLYKPRGYVTTLSDERGRRTVAQLVSGCGARVWPVGRLDLDSEGLLLMTDDGNFTQR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVG 192
           L  PS Q  + Y V   G VD+  + +L   + + GI     ++ + +++G++ A ++V 
Sbjct: 123 LIHPSHQVEKEYLVTVEGDVDR-AIPVLSGPMELDGIPLAPARIGVLSREGADRARLSVV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+NR+++++      +V RL R+  G   LG L  G  R ++ + LR  LG
Sbjct: 182 IHEGRNRQVRRMCALAGLEVKRLKRVREGGLALGRLRPGEWRRLTPQELRLALG 235


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 73/201 (36%), Positives = 114/201 (56%), Gaps = 3/201 (1%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           +V VNG ++    V V  ++ IEV+G+ L K E  R +L++KP G V+  +D  GR+TV 
Sbjct: 1   KVTVNGKVVTELGVKVSGSERIEVEGIQLTKEEH-RYFLFYKPRGTVSAVTDDKGRTTVA 59

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
           D    I  R+  VGRLD +T GLLL+TNDG  A +L  P  +  + Y  R  G  +++ +
Sbjct: 60  DYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANLLMHPKNEVAKTYIARIKGIPEREVI 119

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             L++G+VI G      +V + +   +   A V + + EG+NR+++K+FE   ++V +L 
Sbjct: 120 RELERGVVIDGRKTAPAKVKIRSSDKAKDKAIVEITIHEGRNRQVRKMFEAVGFEVQKLS 179

Query: 217 RISYGPFQLGTLLAGSTREVS 237
           R  Y    L  L AG  RE+S
Sbjct: 180 REEYSFLNLRGLNAGERRELS 200


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 121/227 (53%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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 D L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVMD-LVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGELSLEGLKPGEWRYLTQK 227


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/231 (34%), Positives = 118/231 (51%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA AG+ SRR  E ++ Q R++VNG             D I VDG PL +  R 
Sbjct: 4   QRLQKLIAAAGVCSRRHAEELLRQGRIQVNGAAARLGDSADPDRDSIAVDGRPLDRPARP 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
            L L +KP+G++ + SDP GR TV D LP    +   +  +GRLD ++ G LLLTN G L
Sbjct: 64  VLLLLNKPLGVLCSCSDPQGRPTVLDLLPPELRQGQGLHPIGRLDADSRGALLLTNQGDL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQKGSNAW 188
              L  P     ++YRV   G      L     G+ + G+     D++V    ++G+   
Sbjct: 124 TLRLTHPRYGHRKLYRVWVSGTPSATTLERWAAGVPLDGVASQPVDVRVLQRGKRGTRLE 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +G  EG+NR+I++        V  L R+  GP +LG+L  G  R +  +
Sbjct: 184 LAMG--EGRNRQIRRTAALLGHPVLDLQRVGIGPLRLGSLAEGCWRALDHQ 232


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 85/234 (36%), Positives = 125/234 (53%), Gaps = 5/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R+ KV+A+ GIASRRE E MI + RV++NG L E         D I VDG  V  ++  R
Sbjct: 30  RLQKVLAQWGIASRREAEEMIRRSRVQINGTLAELGQKVNPERDIITVDGKSVSAQRHHR 89

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 129
               L +KP G+V+T  DP GR TV D LP      S +  VGRLD  + G L+LTNDG 
Sbjct: 90  LTYLLLNKPTGVVSTCYDPQGRKTVLDLLPEELRKGSGLHPVGRLDAYSTGALILTNDGD 149

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y++   G   +  L + ++G+++ G      +V+L       + +
Sbjct: 150 LTFKLTHPSHNIPKTYQILVKGHPPEAVLKMWREGVLLDGRKTRKAKVSLLESLAEKSRL 209

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L+EG+NR+I++V E   + V +L R + G  QL T      R  + +ILR+
Sbjct: 210 EIVLQEGRNRQIRRVAEQLGYPVIKLHRTAIGSIQLQTSKQPLLRAGNYRILRD 263


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 129/227 (56%), Gaps = 3/227 (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 KP G ++  +D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 62  YFLLY-KPRGTISAVTDDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +V++ +  +K   A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGVPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLFGLAPGEYRELSK 227


>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 =  124 bits (312), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 118/230 (51%), Gaps = 2/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A AGIASRR  E +I   RV+VNG ++      V S+ D +EVDG  +R   + 
Sbjct: 2   RLQKYLAEAGIASRRASEELILAGRVRVNGEVVRELGTTVDSSRDRVEVDGQKIRPEPKI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY KP G VTT  DP GR  V D +     RV  VGRLD ++EGLLLLTNDG LA  
Sbjct: 62  YVLLY-KPRGYVTTARDPQGRRKVTDLVAGAGGRVFPVGRLDYDSEGLLLLTNDGELAYR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V          L  + +G+ +         V L  + G  A V + +
Sbjct: 121 LTHPRFHVPKTYHVVLDRSPGPAALRAIARGVELDDGLTAPAGVRLVRRDGREALVEMTI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EG+ R++++++    ++V RL R+     +LG L  G  R +    +RE
Sbjct: 181 HEGRKRQVRRMWAALGFEVQRLKRVRMAGLELGGLEPGRWRHLRTTEVRE 230


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 121/225 (53%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 +  I  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  NIYIMLNKPTGFITTVKDQFGRPSVLD-IIKIKDRIYPVGRLDCDTSGLLLLTNDGDIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY  +  G  D   L+  + G+++        ++ +  +  ++A V + 
Sbjct: 121 KLMHPKHEIDKVYIAKIRGIPDDKDLDRFRNGLLLDNRLTAKAKIEILKKINNDALVKIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+NR+I+++ E     V  L RI  G  +LG L  G  R +S
Sbjct: 181 IHEGRNRQIRRMCELIGHPVMTLKRIKIGDLELGNLKVGQWRYLS 225


>gi|332637861|ref|ZP_08416724.1| ribosomal large subunit pseudouridine synthase B [Weissella cibaria
           KACC 11862]
          Length = 255

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/231 (35%), Positives = 121/231 (52%), Gaps = 11/231 (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  VYFLLNKPRGVVTTTNDDKGRQTVMDIVDEP-ERVYPVGRLDYDTTGVLLLTNDGELANR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM----------QVTLDTQK 183
           L  PS +  +VY  +  G    ++L  L+ G+ ++    G            ++T    K
Sbjct: 122 LMHPSYRIDKVYVAKVKGIPTNEQLEQLRHGVTVRTKQNGRYTTFKAAPARAEITSTNTK 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              A V + + EGK  ++K++ +    +V +L R  YG   L  L  G  R
Sbjct: 182 NHTAIVKLTIHEGKYHQVKEMMKAVGHEVLKLTRERYGMLDLAGLTPGEYR 232


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 121/228 (53%), Gaps = 7/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V+VNG  +      V + D IEVDG+PL + E+ 
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIATGHVQVNGQTVTTLGTKVTAKDKIEVDGIPLHR-EKQ 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D L    I  R+  VGRLD +T GLLLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDEKGRRTVVDILREDEIEERIYPVGRLDYDTTGLLLLTNDGTLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAW 188
             +  P     + Y  +  G +  D L  L+ G+ + G      +  L   D +K   + 
Sbjct: 121 NKMMHPKFAVDKTYVAKVKGLISNDDLKQLRTGVKVDGRRTKPAKTRLKGTDREK-KTSI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V + + EG   ++K++       V +L R SYG   L  +  G  RE+
Sbjct: 180 VQLTIHEGHYHQVKRMLAAVGHPVIKLHRESYGFLNLQGVQPGDYREL 227


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 120/226 (53%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  GIASRR+ E  I Q RVKVNG  ++   V +    D IE D   +R+ ++ 
Sbjct: 3   RLQKYLAECGIASRRKCEEYILQGRVKVNGKEVKELGVKINPDVDIIEFDDKIVRREKKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T+  D  GR TV D L  +  R+  VGRLD +T GLLLLTNDG +A +
Sbjct: 63  VYIMLNKPTGYITSVKDQFGRPTVMD-LVKVKERIYPVGRLDYDTSGLLLLTNDGEIANI 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G   +++L   + G++I+       ++ + T K   + V + +
Sbjct: 122 LMHPRHEIAKTYIAKIKGIPTEEELERFRNGLLIEDYVTSKAEIKVLTVKKGTSVVEIKI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EGKNR+++K+ E     V  L+R   G   L  L  G  R ++ K
Sbjct: 182 HEGKNRQVRKMCEAIGHPVISLMRTKIGELSLEGLKPGEWRYLTNK 227


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++ARAG  SRR  E +I Q RV+VNG I+LE+        D ++VDG+ +   + 
Sbjct: 77  ERLQKILARAGYGSRRSCEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTV-ATQS 135

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  D +GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 136 YQFFSLNKPAGVVSTMEDNEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 195

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G + +D    LK GI ++ G    D    +  Q G N  V V
Sbjct: 196 RLTHPKYGVKKVYLAHIVGPIPRDLGKQLKDGIQLEDGYARAD-HFRVVQQTGKNYLVEV 254

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R+++GP  LG   +G  R +S
Sbjct: 255 TLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLS 300


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 76/230 (33%), Positives = 128/230 (55%), Gaps = 4/230 (1%)

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  KVYIMLNKPEGYISSVKDEKGRDTILD-IVKVNERIYPIGRLDYDSSGLLLLTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P  + ++ Y     G++ D+DK+   + GI I G      ++ + +     + + +
Sbjct: 122 KIIHPRVEIIKRYVAVVKGEITDKDKMK-FEIGIDIGGYITAPAELKVISYDKGVSTIEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G+ EGKNR+I+K+    +  V  L RIS G  +LG L  G  R+++K+ L
Sbjct: 181 GIHEGKNRQIRKMCAAIHHDVLSLKRISIGEIKLGYLKRGEYRKLNKEEL 230


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 124/226 (54%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I Q RV++NG I+LE+        D ++VDG+ +   + 
Sbjct: 135 ERLQKVLARAGYGSRRACEELIEQARVEINGEIVLEQGRRVDPEKDEVKVDGLTV-ATQS 193

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 194 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 253

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 254 RLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 312

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V+ L+R ++GP  LG   +G  R +S
Sbjct: 313 TLHEGRKHIVRRMLAEAGFPVDNLVRTAFGPITLGDQKSGWLRRLS 358


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 82/227 (36%), Positives = 119/227 (52%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++IA   V+VNG  +      V + D IEVDGVPL + E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLIATGHVQVNGQTVTTLGTKVAARDRIEVDGVPLHR-EKH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D L    I  R+  VGRLD +T GLLLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDEKGRRTVVDILREDEIEERIYPVGRLDYDTTGLLLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWV 189
             L  P     + Y  +  G V  D L  L+ G+ + G      +  L    ++   + V
Sbjct: 121 NKLMHPKFAVDKTYVAKVKGLVSNDDLKRLRTGVKVDGRRTQPAKARLKATDREKRTSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EG   ++K++       V +L R SYG   L  +  G  RE+
Sbjct: 181 QLTIHEGHYHQVKRMLAAVGHPVIKLHRESYGFLTLQGVQPGDYREL 227


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 124/226 (54%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I Q RV++NG I+LE+        D ++VDG+ +   + 
Sbjct: 135 ERLQKVLARAGYGSRRACEELIEQARVEINGEIVLEQGRRVDPEKDEVKVDGLTV-ATQS 193

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 194 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 253

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 254 RLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 312

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V+ L+R ++GP  LG   +G  R +S
Sbjct: 313 TLHEGRKHIVRRMLAEAGFPVDNLVRTAFGPITLGDQKSGWLRRLS 358


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 118/227 (51%), Gaps = 3/227 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
           +R+ K++++ G+ASRR+ E+ I Q RV +NG + E      +  D I +DG  LR   R 
Sbjct: 3   ERLQKILSQLGVASRRQAEQWIQQGRVTINGRVAEIGQQADLKRDRIHLDGKRLRPKHRP 62

Query: 73  -TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R  L HKP+G+V+T  DP  R TV D + 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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+NR+I++V E     V RL R++ GP +LG+L  G  R ++
Sbjct: 183 VILHEGRNRQIRRVAEQLGHPVLRLTRVAIGPLRLGSLQPGEYRSLT 229


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 121/227 (53%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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 D L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVMD-LVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQK 227


>gi|329939210|ref|ZP_08288584.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
 gi|329302095|gb|EGG45988.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
          Length = 364

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 124/226 (54%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG  SRR  E +I   RV+VNG I+LE+        D I+VDG+ +   + 
Sbjct: 128 ERLQKVLARAGYGSRRACEELIEDARVEVNGEIVLEQGKRVDPEHDEIKVDGLTV-ATQS 186

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 187 YQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 246

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 247 RLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVE-QTGKNYLVEV 305

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R ++GP  LG   +G  R +S
Sbjct: 306 TLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLS 351


>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 =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 126/224 (56%), Gaps = 3/224 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA +G  SRR+ E++I + +V VNG ++++  V    +D I V+G+ L K E 
Sbjct: 2   AERLQKLIAASGYTSRRKAEQLILEGKVSVNGEVIKQLGVKAEPSDVIIVEGLRLLK-EN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +L++KP  ++T+ SD   R  V D   ++  RV+ VGRLD +T G L+++NDG    
Sbjct: 61  KKYYLFYKPEKVITSMSDEKDRVCVKDFFEAVNERVVPVGRLDYDTSGALIMSNDGEFIN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
           ++  P  +  + Y  + +G++++  L +L+ G+ I        +V +  +  K  N  V 
Sbjct: 121 LITHPKHKIKKTYVAKINGKLEEHHLKILRSGVRIDNYKTSPAEVNIVKNKNKSGNTLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EGKNR+++++FE   ++V +L R S     L  L  G  R
Sbjct: 181 LTIHEGKNRQVRRMFEALGYEVMKLKRESIEDLTLDGLRKGEYR 224


>gi|229916174|ref|YP_002884820.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
 gi|229467603|gb|ACQ69375.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
          Length = 252

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/240 (35%), Positives = 127/240 (52%), Gaps = 8/240 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E MI   RV+VNG ++      V     IEVDGV + + E  
Sbjct: 2   ERLQKVIAQAGVASRRKAEEMILDGRVRVNGKVVRELGTKVGPKSEIEVDGVKIEQEEHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G V+T  D  GR  + D +P   +RV  VGRLD NT GL++LTNDG  + +
Sbjct: 62  YYLLY-KPSGYVSTVDDDKGRKVITDLVPP-GARVFPVGRLDYNTTGLIILTNDGEFSNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNAWVT 190
           +  P  +  + Y  +         +  L+ G+ +  G   G  +V + +  QK + A + 
Sbjct: 120 MTHPKYKIQKRYVAKVKNIPSYLAIKQLESGVELDDGFKTGSAKVKMKSVDQKKNTAILE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLGP 247
           + + EG NR+I+++ E    +V +L R  +G   L  L  G  RE+S K    LRE   P
Sbjct: 180 IVISEGHNRQIRRMVEAIGSEVIKLKREQFGFLTLDGLNTGDWRELSHKEISKLRELANP 239


>gi|150390402|ref|YP_001320451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149950264|gb|ABR48792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 234

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 119/226 (52%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K IA  G+ASRR+ E +I Q  V VN  ++      + +  DH++V G  ++  E  
Sbjct: 2   RLQKYIANCGVASRRKSETLIQQGLVTVNDKVVTEMGFKLDVVEDHVKVRGKLIKPTEEM 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G VTT SD   R TV D L  +  R+  VGRLD +T G LLLTNDG L   
Sbjct: 62  IYILLNKPTGFVTTVSDQFDRKTVTD-LVGVSERIFPVGRLDYHTSGFLLLTNDGNLTFK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY  +  G+    KL+L +KG+ I+       ++++         V + L
Sbjct: 121 LTHPKFKVSKVYIAKVKGKPSSSKLSLFEKGLEIEDYVTAPAKISIIKILPHEVIVKITL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           REGKNR+++K+ +     V  L R S G  QLG L  G  R +++K
Sbjct: 181 REGKNRQVRKMCDAIGHPVVELNRESMGDLQLGDLEIGKWRHLTQK 226


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 132/251 (52%), Gaps = 27/251 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE +++I   +VKVNG ++   A  V+  D + V+G P++K+ +  
Sbjct: 2   RLNKFISHHTSFSRREADKLIFDGKVKVNGKVVTNPAYEVLDGDKVAVNGKPVKKSTKYT 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             +Y+KP G + T  D  GR T++D+LP  +   I +GRLD  +EGLL+LT+   +A  L
Sbjct: 62  CIIYNKPRGELVTKKDDRGRKTIYDSLPKKYKHFIPIGRLDFASEGLLILTDSPKVADAL 121

Query: 135 ---ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGI------------CYGDMQV 177
              +LP     RVY++R  G +  +    +++G+ I  +G              +   Q+
Sbjct: 122 MKSDLP-----RVYKLRIKGNITPEIEKAMQEGVEIGVEGAHEKTKQEKIKLKPFYSYQI 176

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +  K S   + V + EGKNRE+++ F  F   V  L R+SYG   L  L  G TR   
Sbjct: 177 IKNDPKYST--LKVAITEGKNRELRRFFAHFGRDVLDLKRLSYGWVALNALPTGKTRYFD 234

Query: 238 K---KILREQL 245
           K   K+L+E L
Sbjct: 235 KREYKLLKEFL 245


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 85/244 (34%), Positives = 129/244 (52%), Gaps = 9/244 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPL--R 68
           +P R++K +A AGIASRR  + +I   RV VNG++       V+   D +  +G P+  +
Sbjct: 5   SPVRLNKYLADAGIASRRGADALIQGGRVCVNGLIQREPGTRVIPGQDTVLCNGAPVSAK 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
           +   +   + HKP+  VTT +DP GR TV D LP      R+  VGRLD  +EGLLLLTN
Sbjct: 65  QNAPSSYIMLHKPVHTVTTVNDPQGRKTVVDLLPEELRTLRLFPVGRLDYMSEGLLLLTN 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGS 185
           DG +   L  PS +  + Y V     V +  L ++++G+ +Q G     ++V   +  G 
Sbjct: 125 DGEVTLRLTHPSYEHPKKYEVLVREAVTEKSLGIMRQGMRLQEGERLAPVEVESASDAGG 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
              + + LR+G NR+I+++       + RL RI  GP  LG L  G  R ++    K L+
Sbjct: 185 ATLLRMTLRQGVNRQIRRMCRDLGLTILRLRRIELGPLFLGNLEPGKWRALTDAEIKTLK 244

Query: 243 EQLG 246
             LG
Sbjct: 245 SSLG 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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 123/227 (54%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYLCTAKDEKGRKTILD-LVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTMKKDHIELFKKGIDIGDYITAPAALEIFKTNKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGKNR+++++ +     V  L RIS G    G L  G  R ++KK
Sbjct: 182 IHEGKNRQVRRMCKSIGHPVIDLDRISIGNISKGDLKLGEWRYLTKK 228


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 78/216 (36%), Positives = 118/216 (54%), Gaps = 5/216 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV K+I++ GIASRR+ E MI Q RV+VNG L           D I +DG P+ +     
Sbjct: 4   RVQKIISQWGIASRRQAEEMIGQSRVRVNGNLARLGQKVDPKVDMISIDGKPVTQGSPPA 63

Query: 75  L--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 129
           L   L +KP G+V+T +DP GR+TV D LP+     + +  VGRLD ++ G L+LTNDG 
Sbjct: 64  LVYLLLNKPAGVVSTCNDPQGRTTVLDLLPTKLRQGTGICPVGRLDADSTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   L  PS    + Y V   G    + L +  +G+++ G      QV L  Q  + + +
Sbjct: 124 VTFALTHPSHDVPKTYHVVVEGHPPTNVLRMWSQGVMLDGRKTRTAQVKLIEQGFTQSKL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L+EG+NR+I++V +   + V  L R + G  +L
Sbjct: 184 EIILQEGRNRQIRRVAQQLGYPVVHLDRRAIGTIEL 219


>gi|256752042|ref|ZP_05492910.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256749052|gb|EEU62088.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 236

 Score =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 121/227 (53%), Gaps = 2/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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 D L  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIILNKPTGYITSVKDQFGRPTVMD-LVKVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQK 227


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 129/228 (56%), Gaps = 11/228 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL---ERAAVNVMSTDHIEVDGVP--LR 68
           +++ K++AR G  SRR +E +I    VK+N  ++   +R ++NV+    I  +     L 
Sbjct: 3   EKIQKILARHGYGSRRYIESLIKSHSVKINDEVVKVGQRISINVIQKVIINNNNYKPKLN 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             +  ++ LY+KP G + T  D   R T+F+ LP +  +R I++GRLD+N+ GLLL T D
Sbjct: 63  INKSLKVLLYNKPEGEICTRKDQRNRRTIFEKLPKLSNARWINIGRLDLNSSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQ-VTLDTQKGS 185
           G LA  L  PS    R+Y+VR  GQ  ++ L  L   + ++ G  Y + + +     +G 
Sbjct: 123 GELAYRLTHPSFNIERIYKVRVFGQFTENILKQLNVRVKLLDG--YANFKSIQFKYGEGK 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
           N W  V L EG++R +++++E   ++VN+L+RISY    L  TL  G+
Sbjct: 181 NKWFNVSLCEGRHRIVRRIWEKLGFQVNKLVRISYAHLTLPKTLFPGT 228


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 91/245 (37%), Positives = 145/245 (59%), Gaps = 14/245 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   VKVNG + +    ++ S D +E+DG   V     
Sbjct: 29  ERLHKVLAQAGLGSRRALEQRIADGLVKVNGEVAQ-VGQSIRSGDRVELDGKAFVASALT 87

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR T+F++LP +  +R I++GRLDINT GLLLLT DG 
Sbjct: 88  EPARVLVYNKPEGEVTTREDPEGRPTIFESLPRLKGARWIAIGRLDINTTGLLLLTTDGE 147

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDMQVTLDTQKG 184
           +A  +  PS +  R Y VR      Q+      ++ L +G+ ++       Q+       
Sbjct: 148 IANAMMHPSYEVEREYVVRVRAPEGQESVPDNIVDRLARGVALEDGPAKFDQIERIGGTD 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK---KI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R+ YG   L   LL G ++E+ +   + 
Sbjct: 208 SHDWFKVVVKEGRNREVRRLWESQGCQVSRLKRVRYGKVSLPRELLRGQSQELPQEQVEA 267

Query: 241 LREQL 245
           LR++L
Sbjct: 268 LRKEL 272


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 79/226 (34%), Positives = 126/226 (55%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K++ARAG  SRR  E +I Q RV+VNG I+LE+        D ++VDG+ +   + 
Sbjct: 78  ERLQKILARAGYGSRRSCEELIEQARVEVNGEIVLEQGKRVDPERDEVKVDGLTV-ATQS 136

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +  +KP G+V+T  D +GR  + D + +  +R+  VGRLD  TEG++LLTN G LA 
Sbjct: 137 YQFFSLNKPAGVVSTMEDNEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGELAH 196

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY     G + +D    LK GI ++ G    D    ++ Q G N  V V
Sbjct: 197 RLTHPRYGVKKVYLAHIVGPIPRDLGKQLKDGIQLEDGYAKADHFRVVE-QTGKNYLVEV 255

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++     + V++L+R+++GP  LG   +G  R +S
Sbjct: 256 TLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLS 301


>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 =  124 bits (310), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 82/218 (37%), Positives = 119/218 (54%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A  GIASRR+ E+MI  +RV+VNG +         S+D IEVDG P++ + R 
Sbjct: 3   ERLQKIMATWGIASRRQAEQMILAKRVRVNGNIAHLGQKANPSSDDIEVDGKPIKPSHRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KPIG+V+T +DP GR  V D LP    +   V  VGRLD+++ G LLLTNDG
Sbjct: 63  VPIYLLLNKPIGVVSTCADPGGRRNVLDLLPRRLQKGQGVHPVGRLDVDSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNA 187
            L   L  P     + Y+V   G   +  L   ++G+++        +V  L     S  
Sbjct: 123 ELTFRLTHPRHHVPKTYQVWVQGHPPESVLQAWRQGVILSSRKTLSAEVRRLQQSIDSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + V L EG+NR+I+KV E   + V +L R + G  QL
Sbjct: 183 LLEVILFEGRNRQIRKVAEQLGYPVVKLHRSAIGSIQL 220


>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 =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 79/217 (36%), Positives = 120/217 (55%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ GIASRR  E+MIA  +V++NG  +         TD IEVDG P+   +R 
Sbjct: 3   ERVQKILSQWGIASRRRAEKMIAAGQVRLNGTTVHLGQKADPETDVIEVDGKPINPYQRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +    L +KP G+V+T  D   R TV D LP   ++   +  VGRLD ++ G LLLTNDG
Sbjct: 63  QSIYLLLNKPAGVVSTCRDSRNRPTVIDLLPDKLTKGQGIHPVGRLDADSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y+V   G   +  L   ++G+ + G      QV +  +KG +  
Sbjct: 123 ELTFRLTHPSHHIPKTYQVWVRGNPPESVLQTWREGVNLLGKKTLPAQVRVLKRKGQSTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V L EG+NR+I++V +  ++ V  L R + GP +L
Sbjct: 183 LEVVLTEGRNRQIRRVAQLLSYPVIHLHRTAIGPIKL 219


>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 =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 123/229 (53%), Gaps = 8/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+   +A++G  SRR  E++I   RVKVN  ++      V   D + VDGV     ER
Sbjct: 6   PIRLQSFLAKSGWGSRRSCEQLIIDGRVKVNSQVVRELGTKVDKDDAVYVDGVLAEPNER 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           T  +  HKP G V +++DP+  S    +L  +  R  + ++GRLD  + GL+L TNDG +
Sbjct: 66  TYYYALHKPAGYVCSNADPN-ESYFARDLIDVPERNLLFNIGRLDKESTGLVLFTNDGEI 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           ++++  PS +  + Y V     +  + L   + GI I  G  Y   +  L+T++    WV
Sbjct: 125 SQLITHPSYEIEKEYLVNTDRTIMIEDLQEARHGIRIDDGRPYRISRYKLETKR----WV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + L EG+NREI+K+F +  + V +LIRI  G  +LG L     R V+K
Sbjct: 181 RIILTEGRNREIRKIFTYLGYDVKKLIRIRIGTLELGDLAPAQFRRVTK 229


>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 =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 79/224 (35%), Positives = 118/224 (52%), Gaps = 6/224 (2%)

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
             ++ +KP G + T SD  GR TV D +P    R+ SVGRLD +T G+LLLTNDG     
Sbjct: 62  -YYIMNKPKGCLCTSSDDKGRKTVLDYMPK-NERIFSVGRLDYDTSGVLLLTNDGEFCNH 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---SNAWVT 190
           +  P     + Y V   G + +D +  L+KG+  +   Y   +V +  QK    +     
Sbjct: 120 MIHPRYHLEKTYVVNLQGILSEDDIKQLRKGLKTKTEKYQPAKVFV-LQKDLTRNRTQFE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EGKN ++K +      +V RL R+ +    +  L AG  R
Sbjct: 179 LTISEGKNHQVKNMMLALGHEVRRLHRVKFAFLDVKDLRAGEYR 222


>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 =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 81/229 (35%), Positives = 127/229 (55%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A+AG+ASRR  E +I + RV+VNG ++ +    V  + D I VDG  +   E 
Sbjct: 65  ERLQKVLAKAGVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDVIRVDGTRINVNEE 124

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
           T+ ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGLLLLTNDG 
Sbjct: 125 TQYFVLNKPRGMQSTMSDDMGRPCVGDVVADRVVAGQRLFHVGRLDADTEGLLLLTNDGE 184

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P  +  + Y     G+ D+  +  L++GI ++ G+   D    +D  +G  + 
Sbjct: 185 LANRLMHPKYEVTKTYLATVLGEADKKLIRQLREGIELEDGLAQADYVQIVDKNQGY-SL 243

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V V L EG+   ++++ +   + V RL+R      QLG +  GS R ++
Sbjct: 244 VRVELHEGRKHIVRRMLKEAGYPVQRLVRTKLHTVQLGDMKPGSLRALN 292


>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 =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 118/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 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 D L  +  R+  +GRLD ++ G++LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTVLD-LVKVNERIYPIGRLDYDSSGIILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  ++   KGI I G       + + + +   + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGEVSKKDIDTFNKGIDIGGYVTAPASLEVLSYENGKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELT 226


>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 =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 81/246 (32%), Positives = 133/246 (54%), Gaps = 25/246 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R++K +A AG+ SRR  + +IA  RV VNG  +    + V   TD +EVDG P++   + 
Sbjct: 6   RINKALADAGVCSRRRADELIAAGRVSVNGEPVASPGLQVTPGTDKLEVDGKPVQPIAQA 65

Query: 74  RLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             +L  +KP+ +V+T  DP+GR+TV D +P+ +   R+   GRLD  +EGL+LLT+DG L
Sbjct: 66  PCYLLLNKPVRVVSTAYDPEGRTTVLDLVPAKWKARRLYPAGRLDFFSEGLVLLTDDGEL 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------------VIQGICYGDMQ 176
              +  P     RVY V   G V    L +++KG+              V+ G  +    
Sbjct: 126 TNRVVHPRHHMPRVYHVLIRGGVSDRALEVMRKGMTLAEGEKLAPVEIRVLPGQVHDLSG 185

Query: 177 VTLDT-----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           V+ +      Q+G+   +T  L +G NR+I+++    +  + RL+R++ GP +LG +  G
Sbjct: 186 VSRNAGPPAGQRGTLLEMT--LHQGLNRQIRRMCRDLHLTILRLVRVAQGPLRLGVMKPG 243

Query: 232 STREVS 237
             RE++
Sbjct: 244 EARELT 249


>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 =  123 bits (309), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 119/227 (52%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  GIASRR+ E +I   +V VNG +++R    V    D IEV G PL      
Sbjct: 6   RLQKLLAEHGIASRRKAEALIVSGQVCVNGTVVDRLGTRVDPQIDLIEVFGQPLHCMPPL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
              L HKP+G ++T  DP GR TV D LP+ +     +  VGRLD ++ G L+++NDG  
Sbjct: 66  LYVLLHKPVGWLSTCFDPRGRRTVLDLLPAEWRTGQGLHPVGRLDCDSSGALIVSNDGEF 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  Q  + YRV   G+     L   + G+V++G       VT+ ++      + 
Sbjct: 126 TFRLTHPRHQLPKTYRVWVRGRPTAAVLGRWRAGVVLEGQKTLPAAVTVVSRAAEATELE 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+NR+I+KV E     V RL R + GP  L  L  G+ R +S
Sbjct: 186 VVLVEGRNRQIRKVAELLGHPVERLHRTAIGPVALAGLPPGAHRLLS 232


>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 =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 83/244 (34%), Positives = 130/244 (53%), Gaps = 18/244 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ KV+ARAG+ASRR  E++IA+ RV V+G L+    + V  +T  +EVDG  +   +R
Sbjct: 19  QRLHKVLARAGVASRRGAEQLIAEGRVVVDGRLVVEQGMQVDPATAVVEVDGKRVAVDDR 78

Query: 73  TRLWLYHKPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+VT  SD   R    +    P + + +  VGRLD +T GLLL++NDG L
Sbjct: 79  HATYLLNKPKGVVTAMSDQRERCVGDLLREQPDLPAGLFHVGRLDADTTGLLLVSNDGEL 138

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQV------------ 177
           A  L  PS +  + Y     G V +  L+ L++G+ ++ G    D               
Sbjct: 139 AHRLAHPSYEIPKTYLATVRGAVGKGALDALRRGVSLEDGPARADAVAVKGEARPAPLRK 198

Query: 178 --TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             T     G+ + V + L EG+NR ++++F+     V  L R+  GP +LG L AG+ R 
Sbjct: 199 AQTGHASGGARSVVEITLHEGRNRIVRRMFDAVGHPVVELARLRIGPIRLGGLQAGALRA 258

Query: 236 VSKK 239
           ++ +
Sbjct: 259 LAPE 262


>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 =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 82/232 (35%), Positives = 124/232 (53%), Gaps = 2/232 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++ AG+ SRR  E++I   RV VNG  +    V V    D +EVDG  ++  +  
Sbjct: 4   RLQKFLSMAGVCSRRAGEKLIESGRVTVNGSRVTAMGVTVDPENDVVEVDGRRVKVQQNN 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP+G VTT  D  GR TV + +  I +RV  VGRLD++T GLLLLTNDG LA  
Sbjct: 64  EYILLYKPVGYVTTLKDEFGRPTVKELVADIKTRVYPVGRLDLDTSGLLLLTNDGELANQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS    + Y  + H    ++ L +L KG+ +        +V L       + V++ +
Sbjct: 124 LTHPSFGVEKEYLAKVHDTPKKEALEILAKGVRLDDGMTAPAKVQLVKSGRLTSVVSLII 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +EG+NR+++++ E     V  L R+ +GP  L  L  G  R +  + + EQL
Sbjct: 184 KEGRNRQVRRMLEAVGHPVVSLKRVRFGPLTLSGLQEGRWRRLEPREI-EQL 234


>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 =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 129/228 (56%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +I   RV+VNG I++E+        D I+VDG+ +  A +
Sbjct: 132 ERLQKVLARAGMGSRRACEELIDAGRVEVNGKIVIEQGVRVDPEQDEIKVDGLTV--ATQ 189

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L+   +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA
Sbjct: 190 SHLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELA 249

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     + Y     G + ++    LK+GI ++ G    D  +V  +T  G N  V
Sbjct: 250 HRLTHPKYGVKKTYLAAIQGPLPRELGKRLKEGIQLEDGYARADHFRVVENT--GKNYLV 307

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++
Sbjct: 308 EVTLHEGRKHIVRRMLSEAGFPVDKLVRTAFGPIALGDQKSGWLRRLT 355


>gi|330953605|gb|EGH53865.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 343

 Score =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 77/190 (40%), Positives = 111/190 (58%), Gaps = 8/190 (4%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLL+ T DG LA 
Sbjct: 14  RVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLMFTTDGELAN 73

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
            L  PS +  R Y VR  G+VD D L  LK G++++     + D+Q     + G N W  
Sbjct: 74  RLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFTDIQQAPGGE-GFNHWYH 132

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK---KILREQLG 246
             + EG+NRE+++++E     V+RL R+ YGP  L + L  G  RE+S+    IL  ++G
Sbjct: 133 CVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRWREMSQYEVDILAAEVG 192

Query: 247 PHLLEEAQVN 256
              + + Q+N
Sbjct: 193 LQPVAQPQMN 202


>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 =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 79/217 (36%), Positives = 117/217 (53%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A+ GIASRR+ E MI   RV+VNG  ++       ++D IEVDGV ++   R 
Sbjct: 3   ERLQKILAQWGIASRRQAEEMILAGRVRVNGNTVQLGQKANPASDRIEVDGVRVKSERRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDG 128
           +    L +KP G+V+T SDP  R+TV D LP        +  VGRLD+ + G LLLTNDG
Sbjct: 63  QPVYLLLNKPAGVVSTCSDPAQRTTVLDLLPPKLRAGCGIHPVGRLDVESTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y+V   G   +  L    +G+++        QV +  + GS   
Sbjct: 123 NLTFALTHPRHCVPKTYQVWVEGDPPKSVLQTWSQGVLLSRRMTLPAQVRVQERNGSQTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V L EG+NR++++V E   + V  L R + GP  L
Sbjct: 183 LEVILYEGRNRQVRRVAEQLGYPVIHLHRTAIGPILL 219


>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 =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 122/221 (55%), Gaps = 1/221 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+++ +A  G+ SRR+VE  I   R+ VNG L++  +  ++   D + +DG P++ A+  
Sbjct: 41  RLNRYLADCGLGSRRKVEEFITTGRIAVNGNLVQDLSRQIIPGKDKVTLDGKPIQPAKEK 100

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G V + +D  GR TV+  LP    ++   GRLD  +EGLL  TND  L  +
Sbjct: 101 FYLILNKPRGYVVSQNDELGRKTVYSLLPPKGKQLAYAGRLDKESEGLLFFTNDTALINL 160

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VYRV  +  ++  +LN+L+KG+ I+G       + + ++  +   + + +
Sbjct: 161 LTHPKNKVEKVYRVDINRPLNNMELNMLRKGVEIEGGKTLPAGIFVKSKNANGMTLKIVI 220

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            EG+ R+I+++ E    KV  L R+ +GP +L  L  G  R
Sbjct: 221 TEGRKRQIRQMIEAVGAKVTYLKRLQFGPLKLKDLPVGRWR 261


>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 =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 85/232 (36%), Positives = 128/232 (55%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E++I + RV+V+G ++ R  V V  +T  I VDG  +   E  
Sbjct: 85  RLQKVLAQAGVASRRMAEKLIDEGRVEVDGKIVTRQGVRVDPNTSVIRVDGSRVIVNEDM 144

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           + ++ +KP G+ +T  D  GR  V D +    S   R+  VGRLD  TEGLLLLTNDG L
Sbjct: 145 QYFVLNKPRGVQSTMHDDMGRPCVGDIIGEKISAGQRLFHVGRLDAATEGLLLLTNDGEL 204

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G+VD   +  L+KGI +  GI   DM   +D  +G  + V
Sbjct: 205 ANRLMHPSYEVTKTYMATVVGEVDSKVMRELEKGIELDDGIAKADMAQIIDVWQG-RSIV 263

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EG+   ++++ +   + V RL+R      QLG    G+ R +++  L
Sbjct: 264 RIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTVQLGEQTPGALRALNRAEL 315


>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 =  123 bits (308), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 82/229 (35%), Positives = 122/229 (53%), Gaps = 3/229 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR 68
             T QR+ +V+A  G+ASRR+ E +I   RV V+G+++      V      I VDG PL 
Sbjct: 4   TMTEQRLQRVLAAHGVASRRKAEELILAGRVTVDGVVVRELGRKVDPERQEICVDGKPL- 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +E  R  + HKP+G +TT +D  GR TV D L  +  RV+ VGRLD ++ GLLLLTNDG
Sbjct: 63  HSEPRRYIVLHKPVGYITTTADEYGRKTVLD-LVQVPERVVPVGRLDRDSSGLLLLTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +  P  +  + Y V   G    +    L++G+ + G      ++     +     
Sbjct: 122 DLIYRITHPRYELEKEYEVLVDGFPPPEVEEALRRGVPVDGRPVRIRRLEAIRVEPQGTV 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             V + EG+NR I++VFE   + V RL R+  GP +LG L  G  R+++
Sbjct: 182 YRVVIHEGRNRIIRRVFERVGYPVLRLQRVRVGPLRLGDLPPGRWRDLT 230


>gi|312622236|ref|YP_004023849.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202703|gb|ADQ46030.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 122/233 (52%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E +I Q RVKVNG L+ +    V    D +EVDG  +    + 
Sbjct: 6   RLQKFMAQCGVASRRKCEEIILQGRVKVNGELVNQLGFKVDPEKDVVEVDGKRISPQMQK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +   +  RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 66  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   + ++   +KG++I G      +  +      NA V + 
Sbjct: 126 KVTHPKHDIEKTYIALIKGIPSKKEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIK 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS----TREVSKKIL 241
           + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G      RE + K+ 
Sbjct: 186 IHEGRNRQIRKMCDQIGHKVLKLKRIAIGKLQLGKLKEGEFVFLDRETANKVF 238


>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 =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 120/227 (52%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ + +ARAG+ASRR  E +++  RV+VNG++       V +  D +EVDG+ +      
Sbjct: 2   RLQRFLARAGVASRRGSEHLMSAGRVRVNGLVASELGTKVDVGADRVEVDGIEVVFGAPP 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G +TT SDP GR  V + +P   F  +  VGRLD +T G+LL T DG LA+
Sbjct: 62  VYIVLNKPAGYLTTMSDPAGRPCVAELVPIRRFPGLFPVGRLDKDTTGVLLFTTDGDLAQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICY-GDMQVTLDTQKGSNAWVT 190
            L  PS    + Y  R  G  D   L++L+ GI +  G C     ++      G ++ V 
Sbjct: 122 NLLHPSKHVAKTYLARVEGTPDSADLDVLRAGIELDDGPCLPARCRLVERRASGGSSLVE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + +REG+  ++K++       V RL+R S+G      L  G  RE++
Sbjct: 182 LIIREGRKNQVKRMLAAVGHPVQRLVRTSFGGVAASDLAEGEWRELT 228


>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 =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 89/235 (37%), Positives = 125/235 (53%), Gaps = 11/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +RV K++ARAG  SRR  E +I   RVK+NG      +    S D I VDG  +PL+   
Sbjct: 4   ERVQKILARAGYGSRRACEELILAGRVKINGQTAVLGSKADPSRDQILVDGQKIPLQPP- 62

Query: 72  RTRLWLYHKPIGL---VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                + HKP G+   V  H DP  R TV D +P +   + SVGRLD  +EGL+LLTNDG
Sbjct: 63  -PVYIMLHKPQGVLSDVEVHKDP--RPTVRDLVP-VEGHLFSVGRLDYESEGLILLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            LA  L  P     + YRV    + D+ +L   + G+V++ G      QV ++   G  A
Sbjct: 119 ELANRLTHPRYGHEKEYRVLVGTRPDERQLEAWRHGVVLEDGYRTAPAQVRVEGVAGKGA 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ V LREG+ R+I+++       V R+IRI  G   LG L  G  R ++ + +R
Sbjct: 179 WLRVILREGRKRQIREMGRLTGLPVLRIIRIRIGSLLLGDLKPGEWRYLTPQEVR 233


>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 =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 118/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 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 D L  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTVLD-LVKVNERIYPIGRLDYDSSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  ++   KGI I G       + + + +   + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGEVSKKDIDAFNKGIDIGGYVTAPASLEVLSYENGKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELT 226


>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 =  122 bits (307), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 83/237 (35%), Positives = 130/237 (54%), Gaps = 6/237 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG 64
           +V +N   +R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V  + D I VDG
Sbjct: 39  LVGDNPKGERLQKVLAKAGVASRRHAEIMIDAGRVEVNGKIVMQQGVRVDPNVDVIRVDG 98

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGL 121
           V +   E TR ++ +KP GL +T SD  GR  + D +    +   R+  VGRLD +TEGL
Sbjct: 99  VRINVNEETRYFILNKPRGLQSTMSDELGRPCIGDLIGDRVAAGQRLFHVGRLDADTEGL 158

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLD 180
           +L+TNDG LA  L  P  +  + Y     G+     +  LK+G+ ++ G+   D    +D
Sbjct: 159 ILITNDGELANRLMHPKYEVRKTYLATVLGEAGNGLVRTLKEGVELEDGLAKADYVQIVD 218

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +G  + V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 219 KNQGY-SLVRVELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTLQLGEMKPGILRALN 274


>gi|262182363|ref|ZP_06041784.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 286

 Score =  122 bits (307), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 81/229 (35%), Positives = 127/229 (55%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A+AG+ASRR  E +I + RV+VNG ++ +    V  + D I VDG  +   E 
Sbjct: 46  ERLQKVLAKAGVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDVIRVDGTRINVNEE 105

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
           T+ ++ +KP G+ +T SD  GR  V D +        R+  VGRLD +TEGLLLLTNDG 
Sbjct: 106 TQYFVLNKPRGMQSTMSDDMGRPCVGDVVADRVVAGQRLFHVGRLDADTEGLLLLTNDGE 165

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P  +  + Y     G+ D+  +  L++GI ++ G+   D    +D  +G  + 
Sbjct: 166 LANRLMHPKYEVTKTYLATVLGEADKKLIRQLREGIELEDGLAQADYVQIVDKNQGY-SL 224

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V V L EG+   ++++ +   + V RL+R      QLG +  GS R ++
Sbjct: 225 VRVELHEGRKHIVRRMLKEAGYPVQRLVRTKLHTVQLGDMKPGSLRALN 273


>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 =  122 bits (307), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 123/225 (54%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +ARAGIASRR+ E +I   RV +N  +    AV V   D + +DG  +R  ++  
Sbjct: 5   RLQQFLARAGIASRRKAEDLIRAGRVTINEQVASIGAV-VQPGDIVRLDGERVRMPQKKV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   HKP G  TTH D      V++ +P     + +VGRLD +TEGLLLLTNDG L + L
Sbjct: 64  VIALHKPKGYTTTHEDEHAEKIVYELVPK-HPGLHAVGRLDKDTEGLLLLTNDGHLTQHL 122

Query: 135 ELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNAWVTVG 192
             P  Q  ++YR    +G+V +     L     +QG+  GD +   L+     N  V + 
Sbjct: 123 THPRNQVPKLYRAWCKNGRVSEKACQQL-----VQGVVLGDGLAQALEAHPTRNG-VKLV 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L EG+ RE++++     + V RL+R++ GP +LG L AG  R ++
Sbjct: 177 LTEGRKREVRRMLNKVGYPVERLVRLAVGPIELGELEAGEWRYLT 221


>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 =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 128/225 (56%), Gaps = 5/225 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K I+R+G+ SRR+ E +I + RVKVNG ++    V +    D +EVD   ++  ++
Sbjct: 3   ERLQKFISRSGVTSRRKAEELILEGRVKVNGKVIRTLGVKIDPEKDVVEVDNKIIKPEKK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + LY KP+G +++  DP GR T+ D L   + SRV  VGRLD ++EGLLL TNDG +A
Sbjct: 63  LYIALY-KPVGYLSSLYDPFGRRTIKDLLKDKLSSRVYPVGRLDFDSEGLLLCTNDGEIA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWV 189
             +  P  +  ++Y V  +G   +++L   ++G++++       + +V     K   + +
Sbjct: 122 NFVIHPRYKIPKIYEVLVNGIPKEEELKKFREGVILEEGKTLPAEFEVVWKNSKTKRSLL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L +G  R+I+++   F ++V +L RI  G  +LG L  G  R
Sbjct: 182 KVVLYQGWKRQIRRMLALFGYEVLKLKRIQIGEIRLGNLKPGEFR 226


>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 =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 87/237 (36%), Positives = 124/237 (52%), Gaps = 9/237 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+   +AR G  SRR  E +I + RV+VNG ++   A  V    D + +DG  +    + 
Sbjct: 17  RLHVFLARCGEGSRRACEELIKKGRVRVNGRVITNPAHRVDPQEDRVTLDGRDVHLVGKF 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +HKP G + T SDP GR  V+D + 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           L EGKNREI+KVF   +  + R+ RI  GP +LG L  G  R ++K   ++LRE  G
Sbjct: 193 LEEGKNREIRKVFYSSHIPIVRIHRIRIGPVRLGRLRPGHFRNLTKEEIRLLREGRG 249


>gi|301062561|ref|ZP_07203199.1| pseudouridylate synthase [delta proteobacterium NaphS2]
 gi|300443326|gb|EFK07453.1| pseudouridylate synthase [delta proteobacterium NaphS2]
          Length = 295

 Score =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 117/230 (50%), Gaps = 1/230 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
           P R++++++ AG+ SRR+ ++ I   R+ VNG  +           D I VDG  +    
Sbjct: 56  PWRLNRILSSAGLTSRRKADQWILSGRITVNGKPVNAPGTTAFWGRDDIRVDGQKIPLPP 115

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    + +KP G + +  DP+GR  V D    I  RV  VGRLD +T GLLLLTNDG  A
Sbjct: 116 KKVYLMLNKPFGTICSLDDPEGRPLVTDLTKDIPIRVYPVGRLDFDTLGLLLLTNDGEFA 175

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y+V   G +  + L  L+ GI +     G  +  L  +    + + +
Sbjct: 176 HRLTHPRFHVPKTYKVTVQGAISDEALKRLQTGITLNDGPAGRARTELINRNNEKSILRM 235

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + +GK+R+++++ E   + V  LIRIS+G  QLG L  G  R +  + L
Sbjct: 236 TITQGKSRQVRRMLEKVGFTVIHLIRISFGTLQLGDLKIGHHRHLDSEEL 285


>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 =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 82/233 (35%), Positives = 119/233 (51%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+AG+ASRR  E +I Q RV+V+G ++      V  +   I VDG  +      
Sbjct: 8   RLQKALAQAGVASRRNAELLIEQGRVEVDGAVVTEFGTRVDPAVSVIRVDGERIPPVTAH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+VTT SDP GR  + D +     R+  +GRLD +TEGLLLLTN G  A  
Sbjct: 68  VYLVLNKPRGVVTTMSDPQGRPCIADYVQERPERLFHIGRLDTDTEGLLLLTNHGEFAHR 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS +  + Y     G V    L  L  G+ ++ G    D    +   KG    + + 
Sbjct: 128 LAHPSYEVSKTYVAEVDGNVKPIVLRRLLDGVELEDGFAQADTVKVMSEIKG-RTLIQIT 186

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L EG+NR ++++F+     V RL R + GP + G L  G  RE+  K L + L
Sbjct: 187 LHEGRNRIVRRMFDAVGHPVKRLTRTAIGPVRRGNLHTGELRELDPKELGQLL 239


>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 =  122 bits (306), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 124/229 (54%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  I  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKTILD-LVKIKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            +  P  + ++ Y+ +  G + +D + L KKGI I    Y     TL+  K     + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGD--YITAPATLEILKINKDTSEII 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGKNR+++++ +     V  L RIS G      L  G  R ++KK
Sbjct: 180 IKIHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTKK 228


>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 =  122 bits (306), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 78/226 (34%), Positives = 123/226 (54%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +I   RV V+ + +    V +    ++  VDG+ ++     
Sbjct: 27  RLQKVLATAGLGSRRACENLITAGRVTVDDVPVHELGVRIDPDKNVVHVDGLRIQLDMSL 86

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V+T  DP+GR T+   +     R+  VGRLD ++EGLLLLTNDG LA  
Sbjct: 87  LTLALNKPLGVVSTMHDPEGRPTLAQFVADRPERLFHVGRLDADSEGLLLLTNDGELANR 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + Y V+  G+V  +    L KGI ++ G+   D    +D    + + + V 
Sbjct: 147 LTHPKYKITKTYTVQVEGRVPANLGTTLLKGIELEDGVATVDKYRLVDATPQA-SLIEVE 205

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EG+NR I+++FE   + V +L+R   GP +LG L  G  R + +
Sbjct: 206 LHEGRNRIIRRMFETAGYPVTQLVRTKIGPIRLGDLRQGRVRVIGQ 251


>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 =  122 bits (306), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 75/226 (33%), Positives = 124/226 (54%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMSTDHIEVDGVPLRK-AE 71
           R++K +A  GIASRREV++MI +  +KVNG   E+AA  + V   D I + G  + K  E
Sbjct: 5   RINKYLASLGIASRREVDKMIEEGAIKVNG---EKAAPGIKVSDEDEIYIKGKKIEKNTE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   ++ +KP+ ++++  D  GR TV D L     R+  +GRLD NT GL++LTNDG L 
Sbjct: 62  KKVYYILNKPLEVLSSSKDDRGRKTVVD-LIKCKERIFPIGRLDYNTSGLIILTNDGELF 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y  +  G++ ++   LL+KG+ +         V +  ++     + V
Sbjct: 121 NRIIHPKAEIFKEYYAKVFGEIKEENAELLRKGVELDDGMTLPANVKILRRERGKTELLV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +REG+NR+++++ +  N  V  L R   G   LG L  G  RE++
Sbjct: 181 AIREGRNRQVRRMLDKINHPVITLRREKIGDLSLGNLKLGEYRELT 226


>gi|312127407|ref|YP_003992281.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777426|gb|ADQ06912.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score =  122 bits (306), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 76/219 (34%), Positives = 118/219 (53%), Gaps = 2/219 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E +I Q RVKVNG L+ +    V    D +EVDG  +    + 
Sbjct: 6   RLQKFMAQCGVASRRKCEEIILQGRVKVNGKLVNQLGFKVDPEKDVVEVDGKRISLQRQK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +   +  RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 66  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   +KG++I G      +  +      NA V + 
Sbjct: 126 KVTHPKHDIEKTYIALIKGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIK 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           + EG+NR+I+K+ +    KV +L R++ G  QLG L  G
Sbjct: 186 IHEGRNRQIRKMCDQIGHKVLKLKRVAIGKLQLGKLKEG 224


>gi|291542267|emb|CBL15377.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus
           bromii L2-63]
          Length = 249

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 132/248 (53%), Gaps = 9/248 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDG--VPL 67
           P R+ K IA+ GIASRR+ E +I    VKVNG    + A+    V+ TD + V G  + +
Sbjct: 6   PIRLQKFIAQCGIASRRKAEELILGGHVKVNG----KTAILGDKVLPTDKVFVRGKRIVV 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K    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 HLLEEAQV 255
             L   Q+
Sbjct: 242 PFLNGKQL 249


>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 =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 124/236 (52%), Gaps = 18/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ I+     SRRE + +I   RV +    +E  A  V   + + +DG  L++   E 
Sbjct: 12  RLNQYISHHSKYSRREADELIKAGRVNIEKRKIENLATQVKEDERVFIDGKFLKEKSEEN 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + T SD  GR T++D+LPS F   I VGRLD  +EGLLLLT+   +A+
Sbjct: 72  YTVIVYHKPKGELVTKSDDRGRKTIYDSLPSGFKHFIPVGRLDFASEGLLLLTDSPKVAK 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------LD 180
              L  ++  RVY ++   +V  + +  +++G+V++    G  + +             +
Sbjct: 132 A--LMESELERVYHLKIDKRVSPEMIKAMEEGLVLEDASAGGHEKSEIKSMSFSPFAGFE 189

Query: 181 TQKGS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             K S  ++ + V ++EGKNRE+++ F  F  KV  L R+SYG   L  L  G  R
Sbjct: 190 VAKDSPTHSKIKVAIKEGKNRELRRFFAHFGAKVLDLKRVSYGWVSLNALPDGKNR 245


>gi|312135342|ref|YP_004002680.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775393|gb|ADQ04880.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 236

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 117/220 (53%), Gaps = 2/220 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +E+DG  +    + 
Sbjct: 2   RLQKFMAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEIDGKRISLQRQK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +   +  RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 62  VYIMLNKPFGVISSAKDEKGRKTVVDLVREKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   + ++ + ++G++I G      +  +      NA V + 
Sbjct: 122 KVTHPKHDIEKTYIALVKGIPSKKEIEMFERGLLIDGKMTAPAKFKILKLINGNALVEIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G 
Sbjct: 182 IHEGRNRQIRKMCDMIGHKVLKLKRIAIGKLQLGKLKEGE 221


>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 =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 84/233 (36%), Positives = 126/233 (54%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +IAQ RV+VNG ++ R  V V   T  I VDGV ++  E  
Sbjct: 110 RLQKVLAQAGVASRRMSEELIAQGRVEVNGEIVMRQGVRVDPDTAVIRVDGVRVKVNEDL 169

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
                +KP+G+ +T  D  GR  V D +         +  VGRLD  TEGLLLLTNDG L
Sbjct: 170 VYIALNKPLGVQSTMKDDMGRPCVGDIVGEKVDAGLHLFHVGRLDAKTEGLLLLTNDGEL 229

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y     G+ D++ +  L++G+ ++ GI   D    +DT +G  + +
Sbjct: 230 ANRLMHPKYHVSKTYLATVLGEADRELVKKLREGVDLEDGIAKADYVQIVDTYEG-RSLI 288

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+   ++++ +   + V +L+R      QLG L  G+ R ++   LR
Sbjct: 289 RVELHEGRKHIVRRMLKELGFPVQQLVRTKIHTVQLGELTPGAIRHLNDSELR 341


>gi|260463018|ref|ZP_05811221.1| pseudouridine synthase [Mesorhizobium opportunistum WSM2075]
 gi|259031139|gb|EEW32412.1| pseudouridine synthase [Mesorhizobium opportunistum WSM2075]
          Length = 259

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 125/228 (54%), Gaps = 3/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +I + RV+V G ++   A+ V ++ D I VDG  +  AER  
Sbjct: 28  LNRALSKLGLCSRTQAELLITEGRVRVGGKVVRDPALRVDLNRDSIVVDGEKV-IAERKV 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP  R TV+  L ++    IS VGRLD  +EGLLL+TND   A  
Sbjct: 87  YVMLNKPRGLVTTRDDPQQRDTVYACLEALDLPFISPVGRLDKASEGLLLMTNDTRFANR 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y V+     D   L  L+ G  + G       + L    G  AW+ V L
Sbjct: 147 LMDPASHLPKTYHVQVATVPDAAMLETLRAGATVDGEILTANSIDLLRSGGRTAWLEVVL 206

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR I+++    + +V RLIRI+ G  +LG L  G+ R ++ + L
Sbjct: 207 DEGRNRHIRRLLAAHDIEVLRLIRIAIGGLRLGDLAKGTARHLTAEEL 254


>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 =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 114/224 (50%), Gaps = 2/224 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
           P R+ K +ARAG+ASRR  ER+I+  RV VNGI++      V    D + VDG  +    
Sbjct: 49  PLRLQKFLARAGVASRRGSERLISAGRVAVNGIVITELGTKVDPLVDEVCVDGAIVTWGA 108

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
                  +KP G++TT  D  GR  V D +P+  +  +  +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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + L EG+  ++K++ +     V +L R S+GP  L  L  G+ R
Sbjct: 229 LELHEGRKHQVKRMCQAVGHPVVKLHRASFGPIDLAGLATGAYR 272


>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 =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 127/227 (55%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRK-AE 71
           R++K +A  GIASRREV++MI +  +K+NG   E+A   + V   D I + G  + K  E
Sbjct: 5   RINKYLASLGIASRREVDKMIEEGSIKING---EKATPGIKVSDKDEIYIRGKKIEKHTE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   ++ +KP+ ++++  D  GR TV D L +   R+  +GRLD NT GL++LTNDG L 
Sbjct: 62  KKVYYILNKPLEVLSSSKDDRGRKTVVD-LINCKERIFPIGRLDYNTSGLIILTNDGELF 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P  +  + Y V+  G++ ++ + LLK G+ +  GI        L  +KG    + 
Sbjct: 121 NRIIHPKAEIFKEYYVKVLGEIKENNVELLKNGVELDDGITLPANVRILRREKGKTELL- 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V +REG+NR+++++ +  N  V  L R   G   LG L  G  RE++
Sbjct: 180 VAIREGRNRQVRRMMDKINHPVITLRREKIGNLSLGNLKLGEYRELT 226


>gi|289578329|ref|YP_003476956.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528042|gb|ADD02394.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
          Length = 236

 Score =  122 bits (305), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 119/226 (52%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  GIASRR+ E  I Q RVKVNG  ++   V +    D IE D   +R+ ++ 
Sbjct: 3   RLQKYLAECGIASRRKCEEYILQGRVKVNGKEVKELGVKINPDVDIIEFDDKIVRREKKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T+  D  GR TV D L  +  R+  VGRLD +T GLLLLTNDG +A +
Sbjct: 63  VYIMLNKPTGYITSVKDQFGRPTVMD-LVKVKERIYPVGRLDYDTSGLLLLTNDGEIANI 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + +
Sbjct: 122 LMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIKI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EGKNR+++++ E     V  L R   G   L  L  G  R +++K
Sbjct: 182 HEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQK 227


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 77/210 (36%), Positives = 109/210 (51%), Gaps = 4/210 (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  RSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           R TV D L S F R   +  VGRLD ++ G L+LTNDG    +L  P  Q  +VY+V+  
Sbjct: 61  RKTVLDLLDSAFQRREGIHPVGRLDADSTGALILTNDGDFTYLLTHPRHQMSKVYQVKVR 120

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           G   QD L   ++G++I G      +V+ L +       + + L+EG+NR+I++V E   
Sbjct: 121 GIPSQDTLRQWREGVIIDGRKTLPARVSLLKSHSADGTLLQIDLKEGRNRQIRRVAEMLG 180

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             V  L R   G   LG L  G  R +++K
Sbjct: 181 HPVTALHRTKIGSLSLGNLACGRYRSLTEK 210


>gi|311899116|dbj|BAJ31524.1| putative ribosomal large subunit pseudouridine synthase B
           [Kitasatospora setae KM-6054]
          Length = 428

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 80/227 (35%), Positives = 126/227 (55%), Gaps = 6/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ SRR  E +IAQ RV VNG  +LE+        D I+VDG+ +  A +
Sbjct: 192 ERLQKVLARAGMGSRRACEELIAQGRVDVNGETVLEQGRRVDPVKDEIKVDGLTV--ATQ 249

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L+   +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G LA
Sbjct: 250 SYLFFALNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELA 309

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G + +D    L KG+ ++ G    D    + +  G N  V 
Sbjct: 310 HRLTHPKYGVTKTYLAAIQGPLPRDLGKTLAKGVELEDGWARAD-SFKVISNLGKNYLVE 368

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++
Sbjct: 369 VTLHEGRKHIVRRLLAEVGFPVDKLVRTAFGPITLGDQKSGWLRRLT 415


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 83/248 (33%), Positives = 132/248 (53%), Gaps = 14/248 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M D N V       R++K +A AG+ SRR+ + +IA  RV V+G ++      +  +   
Sbjct: 1   MTDDNGV-------RLNKALAEAGVCSRRQADALIAAGRVAVDGSVVTELGRKIDPARSR 53

Query: 60  IEVDGVPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLD 115
           + VDG  + K +   T   + HK  G VTT  DP+GR TVFD LP  +   R+ SVGRLD
Sbjct: 54  LSVDGKDVVKPDTAGTLTLMLHKKPGCVTTARDPEGRPTVFDALPDPYRKRRLFSVGRLD 113

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGD 174
             +EGLLLLT DG LA  L  P     + Y V   G V  + +  + +G+ + +G     
Sbjct: 114 FFSEGLLLLTTDGELAYRLAHPRWHAPKRYLVTVRGHVGPEAIEAMGRGMRLAEGEPLAP 173

Query: 175 MQVTLDTQKGSNAWV-TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +   +  +  ++ +V  + LR+G NR+++++       V +L+R++ GP +LG L  G  
Sbjct: 174 VAARIVKRLAADRFVLEMELRQGINRQVRRMCRDLGLTVLKLVRVAQGPLELGGLAPGKC 233

Query: 234 REVSKKIL 241
           RE++ + L
Sbjct: 234 RELAGEEL 241


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 75/208 (36%), Positives = 109/208 (52%), Gaps = 1/208 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +ARAG+ASRR  E +I   RV VN   +      V   TD + 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 LREGKNREIKKVFEFFNWKVNRLIRISY 220
           + EG+   IK++       V RL R SY
Sbjct: 184 VAEGRPHLIKRLCAAVGHPVVRLFRPSY 211


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 124/229 (54%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKTILD-LVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            +  P  + ++ Y+ +  G + +D + L KKGI I    Y     TL+  K     + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGD--YITAPATLEILKINKDTSEII 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGKNR+++++ +     V  L RIS G      L  G  R ++KK
Sbjct: 180 IKIHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTKK 228


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 81/240 (33%), Positives = 128/240 (53%), Gaps = 6/240 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIE 61
           +K+    N   +R+ KV+A+AG+ASRR  E +I   RV+VNG +++R  V V  + D I 
Sbjct: 57  EKSTQNPNTEGERLQKVLAKAGVASRRHAEVLIDAGRVEVNGKIIKRQGVRVNPNADVIR 116

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINT 118
           VDGV +   E    ++ +KP G+ +T  D  GR  V D +    +   R+  VGRLD +T
Sbjct: 117 VDGVRVNVNEDHEYFILNKPRGVQSTMQDDMGRPCVGDMVAEKTASGQRLFHVGRLDADT 176

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQV 177
           EGLL+LTNDG LA  L  P  +  + Y     G+ D+  +  LK GI +  G+   D   
Sbjct: 177 EGLLILTNDGELANRLMHPKYEVSKTYLATVLGEADKSLVRTLKDGIELDDGMANADFVQ 236

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +D  +G  + + + L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 237 IVDKNQGM-SLIRLELHEGRKHIVRRMLKAAGYPVQRLVRTKIHTVQLGDMKPGGIRALN 295


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 129/246 (52%), Gaps = 20/246 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           F   R++K ++     SRRE +++I + +++VN  ++   A  V STD +E+ G  L K 
Sbjct: 17  FELIRLNKFLSHNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEI-GKKLIKE 75

Query: 71  ERTRLW---LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           E+ +L+   +Y+KP G + +  DP GR T++D L   +   +SVGRLD ++EGLLLL++ 
Sbjct: 76  EKNKLYTVIVYNKPKGEIVSKKDPQGRKTIYDGLEHKYKHFLSVGRLDYSSEGLLLLSDS 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------- 178
             +     L  +   RVY+++ +G +       ++ GI I+    G  + T         
Sbjct: 136 VDIVNA--LMHSDLERVYKIKLNGVITPAVEQAMQSGITIEDATSGAYKGTKIKSMSFAP 193

Query: 179 -----LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                + T    ++ + V + EGKNRE+++ F  FN  V  L R+ YG   L  L  G +
Sbjct: 194 FLAYDIQTNGTKHSKIKVVINEGKNRELRRFFAHFNLDVLDLKRLEYGGISLNNLPTGKS 253

Query: 234 REVSKK 239
           R ++K+
Sbjct: 254 RYLTKE 259


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/205 (33%), Positives = 115/205 (56%), Gaps = 1/205 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A +GI+SRR+ ER+I Q +VKVN   +   A  +   D +E  G  + + ++  
Sbjct: 2   RLAKYLAESGISSRRQAERLITQGKVKVNDKTITELAFTLKPGDRVEFAGKIIEQTDKIY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L HKP G +++ +DP GR  V D L ++ +RV  VGRLD +TEGLLLL+NDG  + ++
Sbjct: 62  LLL-HKPAGYISSLADPQGRPRVIDLLSAVNTRVFPVGRLDYDTEGLLLLSNDGEFSNLM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y     G V  D +  L++G+ ++       +V L + K   + + + + 
Sbjct: 121 THPRYLIPKKYEAWVQGLVKPDTIRQLEQGVALEDGITAPARVRLLSSKKGQSLLELEIH 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRIS 219
           EGK R+IK++      +V +L R +
Sbjct: 181 EGKKRQIKRMCLAVGHRVTKLKRTA 205


>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 =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 129/246 (52%), Gaps = 20/246 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           F   R++K ++     SRRE +++I + +++VN  ++   A  V STD +E+ G  L K 
Sbjct: 17  FELIRLNKFLSHNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEI-GKKLIKE 75

Query: 71  ERTRLW---LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           E+ +L+   +Y+KP G + +  DP GR T++D L   +   +SVGRLD ++EGLLLL++ 
Sbjct: 76  EKNKLYTVIVYNKPKGEIVSKKDPQGRKTIYDGLEHKYKHFLSVGRLDYSSEGLLLLSDS 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------- 178
             +     L  +   RVY+++ +G +       ++ GI I+    G  + T         
Sbjct: 136 VDIVNA--LMHSDLERVYKIKLNGLITPAVEQAMQSGITIEDATSGAYKGTKIKSMSFAP 193

Query: 179 -----LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                + T    ++ + V + EGKNRE+++ F  FN  V  L R+ YG   L  L  G +
Sbjct: 194 FLAYDIQTNGTKHSKIKVVINEGKNRELRRFFAHFNLDVLDLKRLEYGGISLNNLPTGKS 253

Query: 234 REVSKK 239
           R ++K+
Sbjct: 254 RYLTKE 259


>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 =  121 bits (304), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 126/234 (53%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+AG+ASRR  E +IA  RV V+G ++ R    V      I VDG+ +  ++  
Sbjct: 136 RLQKALAQAGVASRRACEELIAAGRVSVDGQIVRRFGARVDPEKSEIRVDGMRVVTSQNL 195

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R +  +KP G+V+T  DP+GR T+ D    +  I  R+  VGRLD +TEGL+LLTNDG L
Sbjct: 196 RYYALNKPRGVVSTMFDPEGRPTIGDYAAQIGPIEERLFHVGRLDTDTEGLILLTNDGEL 255

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y  +  G V +D +  ++KG+ +  G    D    +D  +   A V
Sbjct: 256 ANRLTHPRYKVTKTYLAKVPGPVPRDVIRQIRKGVELDDGFVKVDSFRVIDNIE-PKALV 314

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L EG+   ++++ +     V+ L R   GP  L  L +G+ R ++ + + E
Sbjct: 315 EIRLHEGRKHIVRRLMKAVGHPVSDLARTQIGPVGLNNLKSGTIRALTSQEVSE 368


>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 =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 141/275 (51%), Gaps = 6/275 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD  P+ 
Sbjct: 199 EAGEPIRLNKFLSNSGLCSRRMADQYIAAGRVKVNGAVISELGSQVLPTDQVMVDDKPVS 258

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              +  + L +KP   VTT +DP+GR TV D + +  + R+  +GRLD NT G+LLLTND
Sbjct: 259 LEAKVYVLL-NKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTND 317

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G LA  L  P+ +  ++Y V    +V  + + ++  G  ++ G  + D    +  Q  ++
Sbjct: 318 GDLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ--TH 375

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE-QL 245
             V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R  ++
Sbjct: 376 DKVGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRM 435

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           G    E+  V     +Y       D P    E+ D
Sbjct: 436 GVKEQEDNGVAPTTKVYHKHQETPDHPFASEEIED 470


>gi|307301432|ref|ZP_07581192.1| pseudouridine synthase [Sinorhizobium meliloti BL225C]
 gi|306903489|gb|EFN34077.1| pseudouridine synthase [Sinorhizobium meliloti BL225C]
          Length = 262

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 126/225 (56%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V +  D I VDG  +    R  
Sbjct: 27  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEADRIAVDGTVIAAQARVY 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GLVTT  DP+GR TVF  L ++    +S VGRLD  +EGLLL TND  LA+ 
Sbjct: 87  LML-NKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQR 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   +VY V+  G   +     + +G+   G     ++V        N+W+ V L
Sbjct: 146 LLDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKSGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++
Sbjct: 206 DEGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTE 250


>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 =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 71/199 (35%), Positives = 115/199 (57%), Gaps = 5/199 (2%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER-TRLWLYHKPIGLVTT 87
           +E  I    V+VNG   +     V   D + V G  + L+ A+R  R+ LY+K  G + +
Sbjct: 1   MEEWIGNGWVQVNGKTAQLGD-KVSPDDQVTVKGSAIKLKWADRLPRILLYYKQEGEIVS 59

Query: 88  HSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             DP GR +VFD LP +  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 FFNWKVNRLIRISYGPFQL 225
                V+RL+R+ +GP  L
Sbjct: 180 HIGLTVSRLVRVGFGPIGL 198


>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 =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 73/208 (35%), Positives = 114/208 (54%), Gaps = 6/208 (2%)

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 DQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            ++KL  LK+G+V++G      +V+++    T++ S   +T+   EG+N ++K +     
Sbjct: 121 TEEKLAPLKRGVVLKGRKTAPARVSIERIEPTKRTSMVRLTI--HEGRNHQVKNMLAKVG 178

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVS 237
             V +L R  Y  F +  L  G  R+++
Sbjct: 179 LPVQKLKREQYAFFDVTGLQPGEYRKLT 206


>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 =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 81/229 (35%), Positives = 125/229 (54%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V  + D I VDGV +   E 
Sbjct: 63  ERLQKVLAKAGVASRRHAEILIDAGRVEVNGNVILKQGVKVNPAVDVIRVDGVRVNVNED 122

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
              ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLL+LTNDG 
Sbjct: 123 QEYFILNKPRGMQSTMSDDLGRPCVGDVVSEKVASGQRLFHVGRLDADTEGLLILTNDGE 182

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P  +  + Y     G+ D   +  LK+GI ++ G+   D    +D  +G  + 
Sbjct: 183 LANRLMHPKYEVKKTYLATVLGEADNKLVRQLKEGIELEDGLAKADFVQVVDKNQGF-SL 241

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 242 VRVELHEGRKHIVRRLLKEAGYPVQRLVRTKLHTVQLGDMKPGGLRALN 290


>gi|307316843|ref|ZP_07596285.1| pseudouridine synthase [Sinorhizobium meliloti AK83]
 gi|306897465|gb|EFN28209.1| pseudouridine synthase [Sinorhizobium meliloti AK83]
          Length = 262

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 79/225 (35%), Positives = 126/225 (56%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V +  D I VDG  +    R  
Sbjct: 27  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEVDRIAVDGTVIAAQARVY 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GLVTT  DP+GR TVF  L ++    +S VGRLD  +EGLLL TND  LA+ 
Sbjct: 87  LML-NKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQR 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   +VY V+  G   +     + +G+   G     ++V        N+W+ V L
Sbjct: 146 LLDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKSGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++
Sbjct: 206 DEGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTE 250


>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 =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 125/242 (51%), Gaps = 22/242 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE +R+I +  VKVN  +++    +V   D + V G  ++      
Sbjct: 2   RLNKYISHNTTYSRREADRLIQEGFVKVNRQIVKEPFYDVQEGDKVFVKGKLIKPKVDYT 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+KP G + T  D  GR T++D+LP  F+  I VGRLD  +EGLLLLT+   +A+ L
Sbjct: 62  VIVYNKPKGELVTKKDDRGRKTIYDSLPKKFAHYIPVGRLDFASEGLLLLTDSPKIAQAL 121

Query: 135 ---ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
              ++P     RVY V+  G+V       +++G+ ++    G  + +             
Sbjct: 122 MESDIP-----RVYNVKIKGEVTPKMEEAMREGLELEDATAGGHEKSRVTSMKFAPFFAY 176

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +D    + + + V L EGKNREI++ F  F   V  L R+ YG  +L  L  G TR +S
Sbjct: 177 RIDKNAPTFSKLKVALTEGKNREIRRFFAHFGKDVVDLKRVEYGWIKLNALPTGKTRYLS 236

Query: 238 KK 239
           KK
Sbjct: 237 KK 238


>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 =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 78/225 (34%), Positives = 126/225 (56%), Gaps = 3/225 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V +  D I VDG  +    R  
Sbjct: 85  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEADRIAVDGTVIAAQARVY 144

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GLVTT  DP+GR TVF  L ++    +S VGRLD  +EGLLL TND  LA+ 
Sbjct: 145 LML-NKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQR 203

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   +VY V+  G   +     + +G+   G     ++V        N+W+ + L
Sbjct: 204 LLDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKGGDRNSWIEIEL 263

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++
Sbjct: 264 DEGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTE 308


>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 =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 117/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 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 D L  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTVLD-LVKVNERIYPIGRLDYDSSGLILLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  +++  KGI I G       + + +     + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGKVSKKDIDIFNKGIDIGGYITAPASLEVLSYANEKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELT 226


>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 =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/227 (38%), Positives = 124/227 (54%), Gaps = 1/227 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            T  R+ KV+A+AGIASRR  E +I Q RV VNGI++    V V    D I VD V +  
Sbjct: 1   MTKVRLQKVLAQAGIASRRGAEEVIRQGRVVVNGIVVTELGVKVDPHADRITVDRVTIAM 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L  KP   VTT  DP GR TVFD +P   +R+  VGRLD + EGLLLLTNDG 
Sbjct: 61  VESRVYLLLFKPRCCVTTARDPQGRKTVFDFVPDAGARLFPVGRLDFDAEGLLLLTNDGL 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L+ P     + Y V   G      L+ L+ G++++       +VT+      +  +
Sbjct: 121 LANRLQHPRYGVTKTYEVAAMGHPTPAALDRLRTGVMLEEGMTAPAEVTVIGSSPRSTRL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + L +G NR+IK++ E     V  + R+++GP +LG+L  G +R +
Sbjct: 181 RIVLHQGWNRQIKRMGEAVGHPVLSIKRVAFGPLKLGSLKPGGSRHL 227


>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 =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 78/220 (35%), Positives = 118/220 (53%), Gaps = 6/220 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+I+  G+ASRR  E MI   RVKVNG             D IE+DG  L  + + 
Sbjct: 3   ERLQKIISHWGVASRRHAEEMILSGRVKVNGDQAYLGQKADPKCDRIEIDGRALHPSSQP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
           +    L +KP+G+V+T ++P GR TV D LP    +   +  VGRLD ++ G LL+TNDG
Sbjct: 63  QPLYLLLNKPLGVVSTCAEPQGRKTVLDLLPRQLQVGQGLHPVGRLDTDSTGALLITNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNA 187
            L  +L  P     + Y+V   G   +  L   ++GI++ G      +V  +   +GS  
Sbjct: 123 ELTFLLTHPRYHVAKTYQVLVQGCPPESVLEQWRQGILLSGKNTLPAKVRRIGKPRGSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            + V LREG+NR+I++V E   + V +L R + GP  L +
Sbjct: 183 LLEVVLREGRNRQIRRVAEALGYPVVQLHRTAIGPIYLNS 222


>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 =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 79/217 (36%), Positives = 119/217 (54%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ GIASRR+ E++I   RV++NG +        +S D +EVDG  ++   R 
Sbjct: 3   ERVQKILSQWGIASRRQAEKLILAGRVRLNGNIACLGDKADLSQDRLEVDGKIIQPVHRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           R    L +KPIG+V+T  DP  R TV D LP   S    +  VGRLDIN+ G LLLTNDG
Sbjct: 63  RSIYILLNKPIGVVSTCDDPQKRRTVLDLLPKKLSHETGIHPVGRLDINSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y+V   G   ++ L   ++G+++ G      QV +  +      
Sbjct: 123 ELTLRLTHPRYHLPKTYQVWIDGDPGEEILQQWREGVMLMGKKTLPAQVNVIKRYQHQTQ 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V L EGKNR+I+++ +   + V +L R + G  QL
Sbjct: 183 LQVILTEGKNRQIRRIVQQMGFNVLKLHRTAIGLIQL 219


>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 =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 126/226 (55%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G ASRR+ E  I +  VKVN  ++      +  + D + +DG  L    + 
Sbjct: 2   RLQKYMAHCGAASRRKCEEFIQEGLVKVNDKVVTELGTKIDPNVDRVYLDGKRLTLEGKK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KPIG+VT+ SD   R TV D +P  + RV  VGRLDI+T GL+ LTNDG LA +
Sbjct: 62  VYMILNKPIGVVTSASDEKDRPTVTDLVPDDY-RVYPVGRLDIDTTGLVFLTNDGQLANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V   G  +  +L++L++G+ I+ +      V +      ++ + + +
Sbjct: 121 MMHPRYKIGKKYIVTVDGTPNARELSILREGLDIRDLKTSPANVRILKSFKQDSILEIEI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EG+N ++K++F++   KV +L RIS G  QL  L  G+ R +S+K
Sbjct: 181 FEGQNHQVKRMFDYIGHKVKKLKRISIGEIQLLDLEPGNYRYLSEK 226


>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 =  120 bits (302), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 125/226 (55%), Gaps = 4/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++A AG+ SRR  E MI + RV+V+G ++    V + S   + VDGV +   E TR
Sbjct: 71  RLQKLLASAGVGSRRVCENMITEGRVEVDGQIVTELGVRINSEQVVHVDGVRVTLDE-TR 129

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++L ++KP+ +VT+ +D  GR  + D       R+  VGRLD +TEGLLLLTNDG LA  
Sbjct: 130 VYLAFNKPLNVVTSMNDDLGRIDIGDYFGDRKERLFHVGRLDSDTEGLLLLTNDGDLAHR 189

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L+ P    L+ Y  +  G V +D    L++GI ++ G    D    +D+Q G  A V V 
Sbjct: 190 LQHPKYGVLKTYLAQIRGPVPRDLGKKLREGIELEDGPVKVDSFRVVDSQPG-KAIVEVI 248

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EG+   ++++       V  L+R   GP +LG    G  R ++K
Sbjct: 249 LHEGRKHIVRRMLAEAGHPVLSLVRTQIGPIRLGDTKPGKFRRLTK 294


>gi|255525211|ref|ZP_05392153.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255511074|gb|EET87372.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 234

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 123/228 (53%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E +I Q RVKVNG ++    V +    D + +DG  L K E+
Sbjct: 3   ERLQKYMAACGIASRRKCEEIILQARVKVNGKIVNELGVKIDEEKDLVTLDG-KLIKKEK 61

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++++  +KP G V+T  D  GR T+ D L  +  R+  +GRLD +T GL+LLTNDG + 
Sbjct: 62  NKVYIALNKPKGYVSTVKDERGRKTILD-LVDVTERIYPIGRLDYDTSGLILLTNDGDIY 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  ++Y     G   ++ +   + GI I G      +  +  +      V +
Sbjct: 121 NKIIHPKQEKNKIYIALIKGIPTENDIKKFEIGINIDGYVTAPAKFKIIKKFKDYCEVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+NR+I+K+ +F N +V  L RI  G  +LG L  G  R +S K
Sbjct: 181 IIHEGRNRQIRKMCDFINHQVLELKRIQIGDIKLGNLPLGKWRYLSNK 228


>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 =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 81/218 (37%), Positives = 113/218 (51%), Gaps = 1/218 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERT 73
           R+ K+IA +G  SRR+ E  I Q  VKVNG  +          D + V+G  +  +  + 
Sbjct: 5   RLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPVSLGDKADPKNDIVTVNGEKIASSGTQL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R    +KP G VTT +D  GR  V D L  I  RV  VGRLD ++EGLL+LTNDG LA  
Sbjct: 65  RYIKLYKPRGYVTTMADTHGRKIVTDLLDDIDERVYPVGRLDKDSEGLLILTNDGALANA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS    + YRV   G+V  DKL  L  G+ I         V +  ++ +   +   +
Sbjct: 125 VMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVIEFTI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            EGKNR+I+K+ E    ++ RL R + G  +LG L  G
Sbjct: 185 AEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPG 222


>gi|295099584|emb|CBK88673.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           cylindroides T2-87]
          Length = 241

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 79/227 (34%), Positives = 117/227 (51%), Gaps = 12/227 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIAR+GI SRR+ E +I + +V VNG L       V   D IEVDG  L + E  
Sbjct: 2   ERLQKVIARSGICSRRKAEELILEGKVYVNGELCTTLGTKVSGNDEIEVDG-KLLELEDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +K  G + + +D   R TV D L  I  RV +VGRLD +T G+LLLTNDG     
Sbjct: 61  VYYVINKTKGCICSSNDDRDRRTVLDYL-DIPQRVYTVGRLDYDTSGVLLLTNDGDFCNQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------VTLDTQKGSNA 187
           +  P     + Y V   G + QD + LL+KG+       GD Q      ++ D  +    
Sbjct: 120 MIHPRYHLPKTYVVNLQGTLTQDDIRLLRKGLKTN---IGDFQPAKVKIISNDVTRDRTI 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +  + + EGKN ++K + E    +V +L R+ +G  ++  L  G  R
Sbjct: 177 F-ELTIMEGKNHQVKNMMEALGHQVRKLHRVRFGSIEVNDLKPGEYR 222


>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 =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 77/208 (37%), Positives = 108/208 (51%), Gaps = 1/208 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +ARAG+ASRR  E +I   RV VN   +      V   TD + 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 LREGKNREIKKVFEFFNWKVNRLIRISY 220
           + EG+   IK++       V RL R +Y
Sbjct: 183 VAEGRPHLIKRLCAAVGHPVVRLFRPAY 210


>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 =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 141/275 (51%), Gaps = 6/275 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD  P+ 
Sbjct: 201 EAGEPIRLNKFLSNSGLCSRRTADQYIAAGRVKVNGAVVSELGSQVLPTDQVMVDDKPVT 260

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              +  + L +KP   VTT +DP+GR TV D + +  + R+  +GRLD NT G+LLLTND
Sbjct: 261 LEAKVYVLL-NKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTND 319

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G LA  L  P+ +  ++Y V    +V  + + ++  G  ++ G  + D    +  Q  ++
Sbjct: 320 GDLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ--TH 377

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE-QL 245
             V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R  ++
Sbjct: 378 DKVGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRM 437

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           G    E+  V     +Y       D P    E+ D
Sbjct: 438 GIKEQEDNGVAPTTKVYHKHQETPDHPFSSEEIED 472


>gi|318040247|ref|ZP_07972203.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CB0101]
          Length = 241

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 116/229 (50%), Gaps = 3/229 (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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EG+NR+I++  E     V  L R++ G  +LG L  G  R +  +
Sbjct: 184 LVMHEGRNRQIRRTAELLGHPVLDLQRVAIGSIELGELPEGRWRRLDPQ 232


>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 =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 130/237 (54%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ER 72
           R++K ++  GIASRR V++ I + R+ VNG  +    +N+   D+I +DG  ++    E 
Sbjct: 2   RINKFLSTLGIASRRAVDKYIEEGRINVNG-NIATTGMNISENDNIFIDGKKIKTDVNEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+ ++++ SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L  
Sbjct: 61  KVYFMLNKPLEVLSSSSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELFN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQ 182
            +  P ++  + Y V+  G++ ++++  LKKG++          I GI Y   + ++   
Sbjct: 120 RIVHPKSEIYKKYYVKIFGEIKKEEIAELKKGVLLNDGKTLPAKISGIKYNKNKTSM--- 176

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                   + +REG+NR+I+++ E F +KV  L R   G   LG L  G  R+++K+
Sbjct: 177 -------YISIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLEEGKYRKLTKQ 226


>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 =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 75/217 (34%), Positives = 118/217 (54%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ G+ASRR  E MI  +RVK+NG ++        S D +EVDG  ++  +R 
Sbjct: 3   ERVQKILSQWGVASRRRAEDMILARRVKLNGKIVTLGDKADPSCDRLEVDGKLIQPNKRP 62

Query: 74  RLW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +L   L +KP+G+V+T  DP  RS V D LP   ++   +  VGRLD N+ G LLLTNDG
Sbjct: 63  KLIYILLNKPVGVVSTCDDPQNRSIVLDLLPKKLTQGTGIHPVGRLDFNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G   ++ L   ++G+++ G      +V +  +      
Sbjct: 123 DLTLKLTHPRYHLPKTYEVLVKGHPPEETLQQWREGVILMGKKTLPAEVEVIRRSAQQTQ 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V L EG+NR+I+++ E   ++V RL R +     L
Sbjct: 183 LKVVLTEGRNRQIRRIVEQLGFRVLRLHRTAIDSLCL 219


>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 =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 116/229 (50%), Gaps = 11/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST------DHIEVDGVPLR 68
           R+ K +A AG+ASRR+ E +I   RVKVN       AV V+ +      D + VDG  + 
Sbjct: 13  RLQKYLAEAGVASRRKAEELILAGRVKVNA-----RAVTVLGSKVDPARDLVTVDGRLVS 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           ++E    +L +KP G VTT SDP+GR T  + L  +  RV SVGRLD + EG +L T+DG
Sbjct: 68  RSETRSYYLLYKPPGCVTTASDPEGRPTALEYLRGVKERVFSVGRLDFDAEGAVLFTDDG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     R Y V+  G+     L  L  G+ ++      ++     +   N W
Sbjct: 128 ELANRLAHPRYGHRRTYLVKVRGEPPPAALERLVAGVRLEDGPARALEAVPHERAERNVW 187

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + V + EG+   +K++ E    +V RL R  +G   +  L  G  R ++
Sbjct: 188 IRVVVGEGRFHLVKRLCEAVGLQVQRLYRPEFGGITVEGLRPGQFRPLA 236


>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 =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 81/229 (35%), Positives = 125/229 (54%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V  + D I VDGV +   E 
Sbjct: 63  ERLQKVLAKAGVASRRHAEILIDGGRVEVNGNVVLKQGVKVNPAVDVIRVDGVRVNVNED 122

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
              ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLL+LTNDG 
Sbjct: 123 QEYFILNKPRGMQSTMSDDLGRPCVGDVVSEKVASGQRLFHVGRLDADTEGLLILTNDGE 182

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           LA  L  P  +  + Y     G+ D   +  LK+GI ++ G+   D    +D  +G  + 
Sbjct: 183 LANRLMHPKYEVKKTYLATVLGEADNKLVRQLKEGIELEDGLAKADFVQVVDKNQGF-SL 241

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 242 VRVELHEGRKHIVRRLLKEAGYPVQRLVRTKLHTVQLGDMKPGGLRALN 290


>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 =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 118/229 (51%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVP--LRKAE 71
           R++K IA+ G+ SRR  + ++   RV VNG   +   + V  + DH+ VDG P  L  + 
Sbjct: 9   RLNKFIAQCGVTSRRGADDLVFGGRVAVNGEKADSPGIKVDPARDHVTVDGRPVVLPGSG 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGG 129
                + HKP+ +VTT  DP GR+TV D LP   +  R   VGRLD  +EGLLLLT DG 
Sbjct: 69  GDITIMLHKPVEIVTTARDPQGRTTVLDLLPPEIVELRPFPVGRLDYYSEGLLLLTTDGE 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAW 188
           L   L  P     +VY V   G V +  +  ++ G+ ++ G         L      +  
Sbjct: 129 LCHRLTHPKWHLPKVYEVTIRGSVPEKAIRTMQSGMTLKAGDRLAPADAILHPPVAGSQV 188

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + L +G NR+I+++ E     + RL R+  GP +LG L  G  RE++
Sbjct: 189 LEITLIQGLNRQIRRMCEELGLTILRLHRVKQGPMELGNLKRGQWRELT 237


>gi|194477231|ref|YP_002049410.1| Pseudouridine synthase, Rsu [Paulinella chromatophora]
 gi|171192238|gb|ACB43200.1| Pseudouridine synthase, Rsu [Paulinella chromatophora]
          Length = 242

 Score =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 128/239 (53%), Gaps = 3/239 (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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              L +KP G++++  DP GR T+ D +P SI    ++  +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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           + ++EG+ R+I++   F    V  L RI     +LG+L  G  R+++   L   L  +L
Sbjct: 184 IVMKEGRKRQIRRTATFLGHPVIDLQRIGIASIRLGSLPEGRWRKLNSYELSASLFSYL 242


>gi|146282670|ref|YP_001172823.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|145570875|gb|ABP79981.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
          Length = 297

 Score =  120 bits (300), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 73/179 (40%), Positives = 106/179 (59%), Gaps = 8/179 (4%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +Y+KP G + T +DP+GR TVFD LP     R I++GRLDINT GLLL T DG LA  
Sbjct: 1   MLIYNKPDGEICTRNDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDGELANR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  PS +  R Y VR  G+VD + +  LK G++++     + D+Q     + G N W   
Sbjct: 61  LMHPSYEMDREYAVRVRGEVDDEMIERLKTGVMLEDGPARFTDIQEAPGGE-GFNHWYHC 119

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSK---KILREQLG 246
            + EG+NRE+++++E     V+RL R+ +GP F    L  G  RE+S+    IL E++G
Sbjct: 120 VVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLPMGRWREMSQAEVDILSEEVG 178


>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 =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 124/229 (54%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKTILD-LVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P  + ++ Y+ +  G + +D + L KKGI I    Y     TL+  K S   + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGD--YITAPATLEILKISKDTSEII 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGKNR+++++ +     V  L RIS G      L  G  R ++KK
Sbjct: 180 IKIHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKNDLKLGEWRYLTKK 228


>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 =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 77/216 (35%), Positives = 115/216 (53%), Gaps = 6/216 (2%)

Query: 14  QRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ K+++ AG+ SRR+ E +I A +      ++ E      + TD IE  G  + K E 
Sbjct: 3   ERLQKILSHAGVCSRRKAEELILAGRVRVNGRVVRELGTEADVCTDKIEALG-EIVKPEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L+HKP  ++T+ SDP GR TV D    +  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 62  LRYYLFHKPDCVITSVSDPAGRRTVMDYFRRVRERVFPVGRLDYHSEGLLLVTNDGQLDF 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWV 189
           +L  P  +  + Y V   G+  +     ++KG+ I        ++ +   D +K      
Sbjct: 122 ILTHPCHEVQKEYEVVVRGKFSEKLAKKMEKGVKIDSGVTAPCEIEVLGYDAEKNKTRLR 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V L EGKNREI+K+ E F++ V  L RI Y    L
Sbjct: 182 MV-LHEGKNREIRKMMEIFHYPVFELKRIRYSFLTL 216


>gi|291558038|emb|CBL35155.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           siraeum V10Sc8a]
          Length = 251

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 81/218 (37%), Positives = 113/218 (51%), Gaps = 1/218 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERT 73
           R+ K+IA +G  SRR+ E  I Q  VKVNG  +          D + V+G  +  +  + 
Sbjct: 5   RLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPVSLGDKADPKNDIVTVNGEKIASSGTQL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R    +KP G VTT +D  GR  V D L  I  RV  VGRLD ++EGLL+LTNDG LA  
Sbjct: 65  RYIKLYKPRGYVTTMADTHGRKIVTDLLDDIDERVYPVGRLDKDSEGLLILTNDGALANA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS    + YRV   G+V  DKL  L  G+ I         V +  ++ +   +   +
Sbjct: 125 VMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVLEFTI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            EGKNR+I+K+ E    ++ RL R + G  +LG L  G
Sbjct: 185 AEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPG 222


>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 =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 91/250 (36%), Positives = 132/250 (52%), Gaps = 20/250 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKA 70
           +R+ K++A+ GIASRR+ E+MI   RV +NG   E A +   +  H   I+VDG  L+  
Sbjct: 5   ERLQKILAQWGIASRRQAEQMILDGRVWLNG---EPATLGQKADPHCDRIQVDGRTLQSD 61

Query: 71  ERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
               L+L  +KP G+++T SDP GR T+ D LP  +  +    VGRLD  T G LL+TND
Sbjct: 62  RPDLLYLLLYKPTGVISTCSDPQGRPTILDLLPPHYRNLGLHPVGRLDSETTGALLITND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P  Q  +VY+V   G   +  L   + G+++ G      QV L  +    +
Sbjct: 122 GWLTHALTHPCHQVSKVYQVWVSGHPPESVLQQWRDGVMLAGRLTLPAQVRLLERTEIPS 181

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSK- 238
            +T   V L EG+NR+I++V +   + V  L R   GP QL      TL  G  R ++  
Sbjct: 182 ALTCLEVILWEGRNRQIRRVAKKLGYPVVHLHRTGIGPVQLQATDQPTLAKGHYRHLTPG 241

Query: 239 --KILREQLG 246
             + LREQ+G
Sbjct: 242 ELEALREQVG 251


>gi|150376249|ref|YP_001312845.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150030796|gb|ABR62912.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 260

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 129/229 (56%), Gaps = 3/229 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++ +++ G  +R + E++IA+ RV V G  +   A  V +  D I VDG  +    +  
Sbjct: 25  LARALSKLGYCTRTQAEKLIAEGRVSVGGRRVTDLAHWVDIEADRIAVDGTVIAAQPKVY 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GLVTT  DP+GR TVF  L ++ +  +S VGRLD  +EGLLL TND  LA+ 
Sbjct: 85  LML-NKPRGLVTTRDDPEGRPTVFTCLETVDAPSLSPVGRLDKASEGLLLFTNDTVLAQR 143

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+  G + +     + +G+   G      +V L      N+W+ V L
Sbjct: 144 LLDPQTHLGKRYHVQVRGFLGEAMAARMVEGVTEGGELLRAARVALLRGGDRNSWIEVEL 203

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+++ +   ++  RL+R++ G  +LG L  G++R +++  +R
Sbjct: 204 TEGRNRQIRRMLDALGFECLRLLRVAIGEVRLGDLPKGASRPLAEAEIR 252


>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 =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 80/234 (34%), Positives = 122/234 (52%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR----- 68
           R++K +A AG+ SRR+ + ++    V VNGI      + V    D + V G P+      
Sbjct: 2   RLNKALAMAGVCSRRKADELVFAGNVAVNGITASSPGIQVDPQNDIVTVFGKPVAFLPQE 61

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT 125
            +A     ++ +KP+ +VTT SDP GR TV + LP      RV  VGRLD  +EGLLLLT
Sbjct: 62  GQATEHAYYMLNKPVEVVTTASDPQGRRTVLEILPEEVRKRRVFPVGRLDFFSEGLLLLT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQV-TLDTQK 183
           +DG L   +  P     +VY V   G+V +DKL  +++G+ + +G     ++V  LD Q 
Sbjct: 122 SDGDLTYRMTHPRYHLPKVYEVLVRGEVTRDKLEAMRRGMTLAEGEKLAPVEVKVLDKQM 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                + + L +G NR+I+++       V +L R   GP  LG L  G  R ++
Sbjct: 182 LGKTLLELTLIQGINRQIRRMCRDLGLTVLKLRRTCEGPLSLGALPTGKLRTLT 235


>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 =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 77/224 (34%), Positives = 123/224 (54%), Gaps = 8/224 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +ARAG+ASRR+ E +I + RV +N  +      +V  +D + +DG  +R  E+  
Sbjct: 2   RLQQFLARAGVASRRKAEDLIREGRVTINDQIAG-IGSSVSESDVVCLDGERVRLPEKKV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   HKP+G+ TT SDP    TV+  +P +   +  VGRLD ++EGLLLLTNDG L   L
Sbjct: 61  VIALHKPVGVTTTKSDPHAERTVYQLVPDVPG-LHPVGRLDKDSEGLLLLTNDGDLTLKL 119

Query: 135 ELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     +VYR    HG+V +     L +G+ +       ++    TQ+G+     + +
Sbjct: 120 THPRYGVRKVYRAWCKHGRVSEADCRRLVEGVALDDGLAQALEAE-PTQEGAR----IVM 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EGK RE++++     + V RL+R+  GP +LG L  G  R ++
Sbjct: 175 AEGKKREVRRMLGRLGYPVTRLVRLQVGPIKLGKLNPGEWRYLT 218


>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 =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 84/231 (36%), Positives = 121/231 (52%), Gaps = 18/231 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+   +ARAG+ASRR+ E +I + RV+VNG    + AV    V   D +EVDG  +   +
Sbjct: 5   RLQAFLARAGVASRRKAEDLIREGRVRVNG----KVAVLGQKVGPEDLVEVDGKRVELPQ 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  +   HKP G  TT  DP  R TVFD LP I   +  VGRLD ++EGLLLLTNDG L 
Sbjct: 61  KRLVLALHKPKGYTTTRHDPHARRTVFDLLPKIPG-LHPVGRLDRDSEGLLLLTNDGDLT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI---VIQGICYGDMQVTLDTQKGSNAW 188
             L  P     +VYRV   G         L K +   ++ G+   D        + +   
Sbjct: 120 HRLTHPRFGVRKVYRVWTEG-------GTLPKEVCRRLLLGVDLEDGPARALACRPAPGG 172

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             + L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S++
Sbjct: 173 AVLVLAEGRKREVRRMLQRVGYPVRRLLRLQVGPIRLGDLPPGKWRRLSER 223


>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 =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 124/229 (54%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKTILD-LVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            +  P  + ++ Y+ +  G + +D + L KKGI I    Y     TL+  K S   + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGD--YITAPATLEILKISKDTSEII 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGKNR+++++ +     V  L RIS G      L  G  R ++KK
Sbjct: 180 IKIHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKNDLKLGEWRYLTKK 228


>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 =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 84/230 (36%), Positives = 124/230 (53%), Gaps = 11/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +       + D I VDG  L+   R 
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGKVAQLGDKADPTRDVILVDGERLQADTRL 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+V+T +D  GR+ + D + + +  RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 79  VYLALNKPRGVVSTMADEKGRAALSDFIGNRVEQRVYHVGRLDADSEGLLLLTNDGDLAH 138

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNA 187
            L  PS    + Y     G + ++    L  GI ++     D  VT+D+ K     G  A
Sbjct: 139 RLTHPSYGVPKTYLCEVAGPIPRNLGKRLAAGIELE-----DGPVTVDSFKVVDTLGKTA 193

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V + L EG+   ++++       V RL+R S GP +LG L AG TR ++
Sbjct: 194 QVELTLHEGRKHIVRRLLGEVGHPVFRLVRTSIGPIRLGDLRAGRTRRLT 243


>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 =  119 bits (299), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 82/247 (33%), Positives = 134/247 (54%), Gaps = 16/247 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K++A++G+ASRR+ E ++ +  V V+G ++ R    V   T  I VDG  L      
Sbjct: 15  RLQKLLAQSGVASRRKCEELMLEGHVVVDGEVVTRLGTKVDPRTAVIRVDGKRLPPVSEK 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+V+T SDP+GR T+ D +     R+  VGRLD +T GLLLLTNDG  A  
Sbjct: 75  VYLVLNKPRGVVSTMSDPEGRRTLSDLVADRPERLFHVGRLDTDTSGLLLLTNDGDFAHR 134

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNAW 188
           +  PS +  + Y     G+V +  +  L     ++G+   D  VT+   +      + + 
Sbjct: 135 MAHPSYEVDKTYVAEVEGEVYRRTIKQL-----LEGVTLDDGPVTVSKARIVEATAAKSI 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           V + + EG+NR ++++ +     V RL R + GP  LG L +G  R+++    R++LG  
Sbjct: 190 VELVIHEGRNRIVRRLLDQVGHPVRRLTRTAIGPVSLGRLPSGELRDLT----RQELG-E 244

Query: 249 LLEEAQV 255
           LL+ AQ+
Sbjct: 245 LLDTAQL 251


>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 =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 76/229 (33%), Positives = 123/229 (53%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKTILD-LVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            +  P  + ++ Y+ +  G + +D + L KKGI I    Y     TL+  K     + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGD--YLTAPATLEILKINKDTSEII 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGKNR+++++ +     V  L RIS G      L  G  R ++ K
Sbjct: 180 IKIHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTNK 228


>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 =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 131/237 (55%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ER 72
           R++K ++  GIASRR V++ I + R+ VNG  +    +++   D+I +DG  ++    E 
Sbjct: 2   RINKFLSTLGIASRRAVDKYIEEGRITVNG-NIATTGMDISENDNIFIDGKKIKTDVNEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+ ++++ SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L  
Sbjct: 61  KVYFMLNKPLEVLSSSSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELFN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQ 182
            +  P ++  + Y V+  G++ ++++  LKKG++          I GI Y       D  
Sbjct: 120 RIVHPKSEIYKKYYVKIFGEIKKEEIAELKKGVLLNDGKTLPAKISGIKY-------DKN 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           K S   + + ++EG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 173 KTS---MYISIKEGRNRQIRRMIERFGYKVLMLRREKIGELSLGDLEEGKYRELTKQ 226


>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 =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 82/228 (35%), Positives = 122/228 (53%), Gaps = 5/228 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      + S    IEVDG P+   +R  
Sbjct: 33  LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIASPAPPIEVDGQPMAAPQRLY 92

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  
Sbjct: 93  LML-NKPRGVVTTAQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAH 151

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+     D+D L  L+ G+  +G     + V +       AW+ V L
Sbjct: 152 LTDPETGPQKTYHVQVDRLPDEDTLAALRAGVEDEGEFLVALAVRVLRSGDKTAWLEVVL 211

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVSKK 239
            EG+NR I+++   F+ +V RL+R++ G   LG L  G  R  EVS +
Sbjct: 212 DEGRNRHIRRLLAAFDLQVLRLVRVAIGELTLGDLGKGQWRVLEVSDQ 259


>gi|291531258|emb|CBK96843.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           siraeum 70/3]
          Length = 251

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 81/218 (37%), Positives = 112/218 (51%), Gaps = 1/218 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AERT 73
           R+ K+IA +G  SRR+ E  I Q  VKVNG  +          D + V+G  +     + 
Sbjct: 5   RLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPVSLGDKADPKNDIVTVNGEKIASLGTQL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R    +KP G VTT +D  GR  V D L  I  RV  VGRLD ++EGLL+LTNDG LA  
Sbjct: 65  RYIKLYKPRGYVTTMADTHGRKIVTDLLDDIDERVYPVGRLDKDSEGLLILTNDGALANA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS    + YRV   G+V  DKL  L  G+ I         V +  ++ +   +   +
Sbjct: 125 VMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVLEFTI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            EGKNR+I+K+ E    ++ RL R + G  +LG L  G
Sbjct: 185 AEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPG 222


>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 =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 118/226 (52%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R++K IA  G+ASRR+ E +I   RV +NG L+   +  V  T D +EVDGVP+ + E+ 
Sbjct: 2   RINKYIASCGVASRRKAEELIISGRVTINGELITELSTTVDETKDIVEVDGVPINQEEKK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G +TT  D   R +V D L  +  RV  VGRLD  T GLL+LTNDG L   
Sbjct: 62  VYILLNKPEGYITTVKDQFDRPSVLDILKDVDERVYPVGRLDYETSGLLILTNDGDLTYK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y    +G +  ++    + G+ I+        +++    ++ + +   +
Sbjct: 122 LTHPKHEVEKTYLAMVNGIITPEEKRRFENGLQIEDYTTAKAKLKIVKVNEEKNYSVCKI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+++K+ +  N  V  L RI  G   +  L  G  R ++
Sbjct: 182 TIHEGRNRQVRKMCKAINHPVRNLRRIQMGRINIRGLEVGEYRNLT 227


>gi|158316819|ref|YP_001509327.1| pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112224|gb|ABW14421.1| pseudouridine synthase [Frankia sp. EAN1pec]
          Length = 259

 Score =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 88/237 (37%), Positives = 126/237 (53%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER- 72
           R+ KV+A AGI SRR  E +I   RV+V+G ++      V   T  IEVDG      ER 
Sbjct: 22  RLQKVLASAGIGSRRHNEELIDSGRVRVDGEVVREQGRRVDPETAVIEVDG------ERV 75

Query: 73  -TRLWLYH----KPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            TR  L H    KP G+++  SD  GR T+ D L    S  +  VGRLD ++EGLLL+TN
Sbjct: 76  VTRTGLVHLALNKPRGVLSAMSDDRGRPTIADFLTEFGSVGLFHVGRLDGDSEGLLLVTN 135

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--- 183
           DG LA  L  PS    + Y V   G V +D    L+ G+ ++     D  V++D  +   
Sbjct: 136 DGDLAHRLTHPSFGVPKTYLVEISGPVRRDVPRRLRSGVTLE-----DGPVSVDAARIVD 190

Query: 184 --GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              S   + + L EG+   ++++ E     V+RL+R+S+GP  LGTL AG  R +++
Sbjct: 191 VAASRVMMELTLHEGRKHVVRRMMEAVGHPVHRLVRVSFGPVTLGTLRAGRARHLTR 247


>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 =  119 bits (298), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 131/237 (55%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ER 72
           R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E 
Sbjct: 2   RINKFLSTLGIASRRAIDKYIEEGRITVNG-NTATTGMDINENDNIFIDGKKIKTKIDEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+ ++++ SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L  
Sbjct: 61  KVYFMLNKPLEVLSSSSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELFN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQ 182
            +  P ++  + Y ++  G++ +++++ LKKG++          I GI Y       D  
Sbjct: 120 RVVHPKSEIYKKYYIKVFGEIKKEEIDELKKGVLLDDGKTLPAKISGIKY-------DKN 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 173 KTS---MYISIREGRNRQIRRMIEKFEYKVLMLRREKIGELSLGDLPEGKYRELTKQ 226


>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 =  119 bits (298), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 120/225 (53%), Gaps = 1/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K +A  G+ASRR+ E +I++ +V VNG ++ E   +  +  D ++V G  +    + 
Sbjct: 6   RINKYLASCGVASRRKCEEIISRGKVTVNGEVVRELGTIINVEKDLVKVYGKEVSLDTKK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+++      G  TV D L     R+  VGRLD +T GL++LTNDG  A  
Sbjct: 66  VYYMLNKPQGVISASKSKYGEETVVDLLGKKEHRLFPVGRLDKDTTGLIILTNDGDFAYK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y     G+VD   L+ LK+G+VI G      +V L    G N+ V + L
Sbjct: 126 LTHPKYEKEKTYEALVKGKVDSKSLDKLKQGVVIDGKKTSRAKVRLVKMIGVNSLVEITL 185

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+ R++KK+ E    KV +L R       LG L  G  R+++K
Sbjct: 186 IEGRKRQVKKMCEKVGHKVIKLNRTMENGLSLGDLEIGEYRKLTK 230


>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 =  119 bits (298), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 80/228 (35%), Positives = 123/228 (53%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   + + E  
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKINE-ESF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+++     + +V + L    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 64  EYYLLNKPAGYVSSNRSYPNQPSVIE-LIKTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           L  P  +  R Y     G V++D+L  L K I   G  Y     ++    QK   + + +
Sbjct: 123 LTHPKHRIKRTYAAWVKGIVNEDELEQLTKPIRFDGEIYFPQAARILKVDQKRQESLIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EGKN EIKK+ +F    V +L R  +    +G L  G  R +S++
Sbjct: 183 TIAEGKNHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQYRALSEQ 230


>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 =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 78/225 (34%), Positives = 125/225 (55%), Gaps = 4/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G  SRR  + ++ Q +V VNG L  +  +++   D + V+G  ++  E  +
Sbjct: 2   RINKFIANSGYCSRRNADLLLEQGKVFVNGKLATKG-IDISENDEVLVEGKKIKLEEAKK 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KPIG  +T         V D + S   R+  VGRLD ++ GLLLLTNDG LA  L
Sbjct: 61  YYLLNKPIGYSSTAKAQFQEKIVLDLIDSK-ERIYPVGRLDKDSFGLLLLTNDGDLAFRL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             PS    + Y V+    + +  L  L  GI+++G      +  +   K +   V V L+
Sbjct: 120 THPSHNVEKEYIVKVDKTLKESDLKKLSSGIMLEGKITRKARFEMLDFKSN--IVKVFLK 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           EG+NR+I+K+F+  ++ V  L RI++G  +LG L  G+ RE+SK+
Sbjct: 178 EGRNRQIRKMFKTLDYNVISLERIAFGKIKLGKLKVGNYRELSKE 222


>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 =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 120/230 (52%), Gaps = 1/230 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K++A AG+ SRR  E  +   RV V+G +         ++  IEVDGVPL   
Sbjct: 1   MTRQRLQKLMAAAGLCSRRRGEDWLQAGRVTVDGRVASLGDQADPNSQLIEVDGVPLISV 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGG 129
           +  R++L +KP+G++ +  DP GR+TV D LP    S +  VGRLD ++ G LLLT+ G 
Sbjct: 61  QEPRVFLLNKPVGVICSCRDPQGRATVLDCLPHQERSGLHPVGRLDADSRGALLLTDQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G      L   + G+++ G      +V     +G+++ +
Sbjct: 121 LTLRLTHPRYNHAKTYRVLVRGIPSSQALRRWRDGLLLDGRLTRPARVHCLRSRGASSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V L+EG+NR+I++V E     V  L R++    +L  L  G  R +  +
Sbjct: 181 EVELKEGRNRQIRRVAELLGHPVIDLQRVAIDGIRLDDLAEGCWRRLDAR 230


>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 =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 84/237 (35%), Positives = 123/237 (51%), Gaps = 30/237 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+   +ARAG+ASRR+ E +I + RV+VNG    + AV    V   D +EVDG  +   +
Sbjct: 5   RLQAFLARAGVASRRKAEDLIREGRVRVNG----KVAVLGQKVGPEDLVEVDGKRVELPQ 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  +   HKP G  TT  DP  R TVFD LP I   +  VGRLD ++EGLLLLTNDG L 
Sbjct: 61  KRLVLALHKPKGYTTTRHDPHARRTVFDLLPKIPG-LHPVGRLDRDSEGLLLLTNDGDLT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             L  P     +VYRV   G            G + + +C   + + +D + G       
Sbjct: 120 HRLTHPRFGVRKVYRVWTEG------------GTLPKEVCR-RLLLGVDLEDGPARALAC 166

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +     + L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S++
Sbjct: 167 CPAPGGAVLVLAEGRKREVRRMLQRVGYPVRRLLRLQVGPIRLGDLPPGKWRRLSER 223


>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 =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 123/226 (54%), Gaps = 4/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-RT 73
           R++K IA     SRR+ + +I  ++VK+NG +LE  A  V   D +E+DG  +   + + 
Sbjct: 2   RINKFIATKTAYSRRKADELIKDKKVKINGEVLENLAYTVNDDDEVELDGRIISDIKVKK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP  +V+T SD  GR  + D  P   S V  VGRLD ++ GL+++TNDG LA  
Sbjct: 62  YYYLFNKPKNVVSTVSDEFGRYCITDFFPPDIS-VFPVGRLDYDSTGLIIVTNDGDLANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS    + Y     G++ + ++ +  +G+VI       +   ++    S     + +
Sbjct: 121 IAHPSHHVKKTYIATLDGRLSEAQMKIFSEGVVID--SKKTLPAEIELYDFSETQYKISI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EG+NR+I+K+ +     V  L RIS G  +LG ++ G  R+++++
Sbjct: 179 YEGRNRQIRKMIDVLGRNVRELKRISIGKIKLGRIVEGKYRKLTEE 224


>gi|158320609|ref|YP_001513116.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140808|gb|ABW19120.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 234

 Score =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 118/226 (52%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ASRR+ E +I+  RVKVNG ++      V +  D I VD   +   ER 
Sbjct: 2   RLQKFLAANGVASRRKSEELISSGRVKVNGNIITEMGYKVDLDIDKISVDNKDIILQERK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G VTT S+   R  V D L  +  R+  VGRLD NT GLL+LTNDG L   
Sbjct: 62  VYILLNKPTGYVTTVSEQFNRKKVTD-LVDVPYRIFPVGRLDYNTSGLLILTNDGELTYK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY  +  G   ++ L   + G+ I+       ++ +  +   +  V V +
Sbjct: 121 LTHPKFKVEKVYIAKVKGIPTKEALEAFENGLKIEDYITAPAKIKILKEINQHTLVEVRI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           REGKNR+++K+ E     V  L RI+ G   LG L  G+ R  +++
Sbjct: 181 REGKNRQVRKMCEAIGHPVVELKRIAMGRIHLGNLDVGNWRYFTER 226


>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 =  119 bits (297), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 118/227 (51%), Gaps = 1/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA +G+ SRR  E+++ Q+RV +NG L +         D I VDG  L     T
Sbjct: 4   QRLQKLIAASGLCSRRHAEQLLLQERVTLNGHLAKLGDKADPELDKISVDGRVLNSNTET 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLAR 132
           R+ L++KP G++T+  DP GR TVF  LP    + +  VGRLD ++ G LL+TN G L  
Sbjct: 64  RVLLFNKPAGVITSCHDPHGRVTVFSMLPDKLCKGLHPVGRLDADSRGALLITNQGELTL 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y+V   G+     L+  + G+++ G      ++ L     S + + V 
Sbjct: 124 RLTHPRYAHDKTYQVLVEGKPSALVLSSWRHGVMLDGKTTLPAELELLQSHPSQSLLKVV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           LREG+NR+I++V E     V  L R +     L  L  G  R + ++
Sbjct: 184 LREGRNRQIRRVAEQLGHPVLDLQRTAIANVALNALPEGCWRALDER 230


>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 =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 82/243 (33%), Positives = 120/243 (49%), Gaps = 15/243 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
             P R+ + +ARAG+ASRR  E ++   RV+VNG +       V    D + VDG P+  
Sbjct: 18  LVPMRLQRFLARAGVASRRGSEGLMTAGRVRVNGEVKTELGTKVDPRCDEVTVDGAPVVL 77

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDG 128
                  + +KP G +TT SDP GR TV + +PS  F  +  VGRLD++T GLLL T DG
Sbjct: 78  GSGPAYIMLNKPAGFLTTMSDPHGRPTVAELVPSKKFPGLFPVGRLDMDTTGLLLFTTDG 137

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK---- 183
            L + L  PS    + YR    G+     L  L++G+ +  G C       L+       
Sbjct: 138 DLGQRLLHPSHHVWKTYRAIVDGRCLDGDLEPLRRGLTLDDGPCQPARCRVLEPADAHIP 197

Query: 184 -------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  G+ A V V +REG+  ++K++       V  L R  +G  +LG L  GS RE+
Sbjct: 198 GFPRLVTGATA-VEVIIREGRKNQVKRMLSKIGHPVIALHRCRFGELRLGDLAEGSWREL 256

Query: 237 SKK 239
           + +
Sbjct: 257 TDE 259


>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 =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 131/237 (55%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ER 72
           R++K ++  GIASRR V++ I + R+ VNG  +    +++   D+I +DG  ++    E 
Sbjct: 2   RINKFLSTLGIASRRAVDKYIEEGRITVNG-NIATTGMDISENDNIFIDGKKIKTDVNEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+ ++++ SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L  
Sbjct: 61  KVYFMLNKPLEVLSSSSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELFN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQ 182
            +  P ++  + Y V+  G++ ++++  LKKG++          I GI Y       D  
Sbjct: 120 RIVHPKSEIYKKYYVKIFGEIKKEEIAELKKGVLLNDGKTLPAKISGIKY-------DKN 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  R+++K+
Sbjct: 173 KTS---MYISIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLEEGKYRKLTKQ 226


>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 =  119 bits (297), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 114/226 (50%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KV+++AG+ SRR  E ++ Q RV +NG             D I VDG  +      
Sbjct: 6   QRLQKVLSQAGVCSRRRAEELMRQGRVLLNGRPASPGDQGDPLRDRILVDGELVSPPAEE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
              L HKP G+ +T  DP GR TV D LP+  +    +  VGRLD ++ G LLL+N+G L
Sbjct: 66  LTVLLHKPRGVHSTCFDPRGRRTVLDLLPAELAEGQGLHPVGRLDCDSRGALLLSNNGAL 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YR+   G      L   + G+++ G       V    Q   ++ + 
Sbjct: 126 TLALTHPRFSHRKSYRIWVSGHPSSAVLQQWRHGVLLDGRPTRSADVRELQQDAEHSQLE 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + +REG+NR+I++V E     V  L+R+S GP QLG L +G  R +
Sbjct: 186 LVMREGRNRQIRRVAEQLGHPVRDLLRVSIGPVQLGDLPSGQWRRL 231


>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 =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 118/225 (52%), Gaps = 2/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+++ +A AGI SRR+ E +I   RVKVNG ++ E   V     D +E+DG  L + E  
Sbjct: 11  RLARYLAAAGITSRRKAETLIQAGRVKVNGRVVRELGFVINEEKDQVELDGWLLHREEPV 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP G + T +D  GR TV D L  +  RV  VGRLD +TEGLLLL+NDG    +
Sbjct: 71  YILL-NKPSGYLCTLADTHGRPTVVDLLRGVTQRVYPVGRLDYDTEGLLLLSNDGDFTHL 129

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY     G V +  +  L+ G++I  +     +V +  ++     + + +
Sbjct: 130 MTHPRFEIEKVYEAWVQGMVSRKAIERLRAGVIIDAVKTAPAKVRVLAKRKDRTLMEIRI 189

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+ R++KK+       V  L R  +G   L  L  G  R ++K
Sbjct: 190 HEGRKRQVKKMCASVGHPVVALKRTRFGDLTLDGLRPGEFRYLTK 234


>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 =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 71/199 (35%), Positives = 114/199 (57%), Gaps = 9/199 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2   RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ +D  GR TV D LP++  R+  VGRLD +T G+L+LTNDG     +
Sbjct: 61  YYLLNKPRGVISSVTDDKGRKTVVDLLPNVKERIYPVGRLDWDTSGVLILTNDGDFTDEM 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWV 189
             P  +  +VY  R  G  +++ L  L +G+ I G       Y  ++V  D  K + + V
Sbjct: 121 IHPRNEIDKVYVARVKGIANKENLRPLTRGVEIDGKKTKPAVYEILKV--DPVK-NRSVV 177

Query: 190 TVGLREGKNREIKKVFEFF 208
            + + EG+N ++KK  +  
Sbjct: 178 QLTIHEGRNHQVKKCLKLL 196


>gi|312793758|ref|YP_004026681.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180898|gb|ADQ41068.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 117/220 (53%), Gaps = 2/220 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    + 
Sbjct: 6   RLQKYMAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRITLQMQK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +   +  RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 66  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   +KG++I G      +  +      NA V + 
Sbjct: 126 KVTHPKHDIEKTYIALIRGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIK 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + EG+NR+I+K+ +    +V +L R++ G  QLG L  G 
Sbjct: 186 IHEGRNRQIRKMCDQIGHEVLKLKRVAIGKLQLGKLKEGE 225


>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 =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 139/275 (50%), Gaps = 6/275 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD   L 
Sbjct: 199 EAGEPIRLNKFLSNSGLCSRRMADQYIAAGRVKVNGAVISELGSQVLPTDQVMVDD-KLV 257

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             E     L +KP   VTT +DP+GR TV D + +  + R+  +GRLD NT G+LLLTND
Sbjct: 258 SLEAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTND 317

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G LA  L  P+ +  ++Y V    +V  + + ++  G  ++ G  + D    +  Q  ++
Sbjct: 318 GDLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ--TH 375

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE-QL 245
             V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R  ++
Sbjct: 376 DKVGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRM 435

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
           G    E+  V     +Y       D P    E+ D
Sbjct: 436 GVKEQEDNGVAPTTKVYHKHQETPDHPFASEEIED 470


>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 =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 74/211 (35%), Positives = 113/211 (53%), Gaps = 9/211 (4%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI Q  V +NG ++   A  V S D +E++G P+   E+   +L +KP G +++ SD  G
Sbjct: 1   MIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPIYNEEKV-YYLLNKPRGAISSVSDDKG 59

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TV D LP +  R+  VGRLD +T G+L+LTNDG     +  P  +  +VY  R  G  
Sbjct: 60  RKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIA 119

Query: 154 DQDKLNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            ++ L  L +GIVI G       Y  ++V  D  +   + V + + EG+N ++KK+FE  
Sbjct: 120 TKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNR---SIVELTIHEGRNHQVKKMFESV 176

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              V++L R  +G   L  L  G  R ++KK
Sbjct: 177 GLLVDKLSRTRFGTVDLKGLRPGEARRLNKK 207


>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 =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 124/228 (54%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MI + RV+VNG ++ +  V V  + D I VDGV +   E  
Sbjct: 79  RLQKVLAQAGVASRRHSEVMIDEGRVEVNGKIVRQQGVRVDPNVDIIRVDGVRVNVNEDQ 138

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +  +KP G+ TT  D  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 139 QYFALNKPRGVHTTMEDELGRPCVGDFVADRVAAGQRLFHVGRLDADTEGLLLLTNDGEL 198

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G+     +  LKKGI ++ G+   D    +DT +G  + +
Sbjct: 199 SNRLMHPKYGVEKTYLATVLGEAKPALVRELKKGIELEDGVAKADYAQIVDTHQG-QSLI 257

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+   ++++ +   + V RL+R      QLG L  G+ R ++
Sbjct: 258 RLVIHEGRKHVVRRMLKEAGYPVQRLVRTKIHTVQLGELKPGAMRALN 305


>gi|218682180|ref|ZP_03529781.1| RNA-binding S4 domain protein [Rhizobium etli CIAT 894]
          Length = 130

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 55/83 (66%), Positives = 68/83 (81%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI + RV +NG  L+   VNV   D IEVDGVP+R  ERT
Sbjct: 48  ERISKVMARAGVASRRDIERMIMEGRVTLNGRALDTPVVNVTLADRIEVDGVPIRGIERT 107

Query: 74  RLWLYHKPIGLVTTHSDPDGRST 96
           RLWLYHKP GLVTT++DP+GRST
Sbjct: 108 RLWLYHKPAGLVTTNADPEGRST 130


>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 =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 79/221 (35%), Positives = 109/221 (49%), Gaps = 5/221 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +F P R+ K +A AG+ SRR  E +IA   V VNG   +         D +   G P+R 
Sbjct: 3   SFEPIRLQKYLADAGVCSRRAAEALIASGEVWVNGAPAQVGQKVTPGVDRVTTGGKPVRT 62

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
             + R+ L  HKP GLV T+ DP    T+F  LP  F+  R    GRLD ++EGL++LT 
Sbjct: 63  TAQPRVTLAMHKPRGLVCTNEDPHNPETIFSVLPREFAKLRFFCAGRLDKDSEGLVILTT 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS   ++ Y V         +L LL KG++ QG      +  L     S+
Sbjct: 123 DGDLAHRLMHPSNLVVKRYHVTLEKPFPAKRLPLLVKGVIAQGERLKVERAALINPSVSH 182

Query: 187 AW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               + V +  GK REI+ +F    + V RL R   G F+L
Sbjct: 183 EATNLDVHMHHGKKREIRLLFTELGYPVKRLRRYQIGGFRL 223


>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 =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 132/237 (55%), Gaps = 24/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ER 72
           R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++ +  E 
Sbjct: 2   RINKFLSTLGIASRRAIDKYIEEGRITVNGNT-ATTGMDINENDNIFIDGKKIKTSINEE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP+ ++++ SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L  
Sbjct: 61  KVYFMLNKPLEVLSSSSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELFN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQ 182
            +  P ++  + Y ++  G++ +++++ LKKG++          I GI Y       D  
Sbjct: 120 RVVHPKSEIYKKYYIKILGELKKEEIDELKKGVLLDDGKTLPAKISGIKY-------DKN 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 173 KTS---MFISIREGRNRQIRRMIEKFEYKVLMLRREKIGELALGDLPEGKYRELTKQ 226


>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 =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 76/228 (33%), Positives = 118/228 (51%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV + +AR G  SRRE ++ +A+ RV+VNG       +   + D I +DG P+       
Sbjct: 2   RVQRALARVGAVSRREADKAVAEGRVQVNGTTAIVGQLVDPARDRITLDGTPVATQVTAH 61

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            W+  HKP  ++TT  DP+GR+TVFD   + P +    + VGRLD  TEG+LLLT DG  
Sbjct: 62  RWIVLHKPAAVMTTRKDPEGRATVFDLVDDAPGL----VYVGRLDFMTEGVLLLTTDGTA 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV- 189
           A VL  PS +  R Y     G          ++G+ +        +VT     G   W  
Sbjct: 118 AHVLTHPSHEVERTYVATVRGDA-VTAAREARRGVKLDDGLVVPSEVTA-YPLGERRWAF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+  E++++ +    +V RL+R  +GP +LG L +G+ R ++
Sbjct: 176 ELTITEGRTHEVRRICDALGLEVERLVRTRFGPVRLGELPSGAARALT 223


>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 =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 124/232 (53%), Gaps = 9/232 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           EN   +R+ K+++ AGIASRR    +I   RV VNG  +      V   D +E DGVP+ 
Sbjct: 2   ENDNRERLVKILSAAGIASRRGAGDLIKAGRVTVNGETVFEPGFRVAPGDRVEYDGVPVL 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLT 125
             ER    + +KP G V T++DP       D +   P +  R+ S GRLD ++EGL+L +
Sbjct: 62  AEERKVYIMLNKPRGYVCTNADPHADLKAVDLIRLTPPL--RLFSAGRLDKDSEGLILFS 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG     L  P  + L+VY+VR   +    +L  +++G++ +G     ++V   ++ G 
Sbjct: 120 NDGDYVARLTHPRHEILKVYQVRVRREFKPAELEQMRRGVLERGEL---LKVHAVSRCGD 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             ++ + L EGKNREI+++         RL R+  G  +LG L  G+ RE++
Sbjct: 177 CTYL-ITLNEGKNREIRRLTAALGSPTRRLKRLQIGALRLGGLPVGNWRELT 227


>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 =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 122/227 (53%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AGI SRRE ++ IA  +VKVN  ++      V   D +  +G P+++ E+  
Sbjct: 55  RLNKFISNAGICSRREADKHIADGKVKVNNKVVTELGFKVKPMDDVAFEGKPIKR-EKLV 113

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G +TT  DP GR TV D + +    R+  VGRLD NT GLLL TNDG LA+ 
Sbjct: 114 YVLLNKPKGFITTMDDPKGRKTVMDLIATAGDERIYPVGRLDRNTTGLLLFTNDGELAKK 173

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVG 192
           L  P  +  ++Y+V     + ++    +++GI ++    G+++V  L         + + 
Sbjct: 174 LTHPKHKIKKIYQVELDKPITEEDFLKIQEGITLED---GEVKVDNLAILTPDAKSIGME 230

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +R G+NR +++ FE   + V +L R ++       L  G  R + +K
Sbjct: 231 IRMGRNRIVRRTFEHLGYDVVKLDRTTFAGLTKKDLARGKWRFLKEK 277


>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 =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 79/228 (34%), Positives = 123/228 (53%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   + + E  
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKINE-ESF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+++     + +V + L    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 64  EYYLLNKPAGYVSSNRSYPNQPSVIE-LIKTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           L  P  +  R Y     G V++D++  L K I   G  Y     ++    QK   + + +
Sbjct: 123 LTHPKHRIKRTYAAWVKGIVNEDEIEQLTKPIRFDGEIYFPQAARILKVDQKRQESLIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EGKN EIKK+ +F    V +L R  +    +G L  G  R +S++
Sbjct: 183 TIAEGKNHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQHRALSEQ 230


>gi|315506751|ref|YP_004085638.1| pseudouridine synthase [Micromonospora sp. L5]
 gi|315413370|gb|ADU11487.1| pseudouridine synthase [Micromonospora sp. L5]
          Length = 256

 Score =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 123/226 (54%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +       + D I VDG  L+   R 
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQLGDKADPARDVIVVDGERLQADVRL 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+VTT +D  GR+ + D + + +  RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 79  VYVAMNKPRGVVTTMADEKGRTELADFIGARLEQRVYHVGRLDADSEGLLLLTNDGTLAH 138

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS + L+ Y     G + ++    L  G+ ++ G    D    +DT  G  A V +
Sbjct: 139 KLMHPSYEVLKTYLAEVAGPIPRNLSKRLTAGVELEDGPVKVDGFKVVDTL-GKTAQVEL 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++       V+RLIR S GP +LG L  G  R ++
Sbjct: 198 TLHEGRKHIVRRLMAEVGHPVSRLIRTSIGPIKLGDLRTGRMRRLT 243


>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 =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/217 (35%), Positives = 114/217 (52%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ GIASRR+ E +I   RVKVNG L++         D +EVDG  +   +R 
Sbjct: 3   ERVQKILSQWGIASRRKAESLILAGRVKVNGNLVKLGDKVDPYCDRLEVDGKRIEPTQRP 62

Query: 74  RLW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KP+G+V+T  DP  R TV + LP    +   +  VGRLD N+ G LLLTNDG
Sbjct: 63  EFLYILVNKPLGVVSTCDDPQNRPTVLELLPQELRKGTGIHPVGRLDFNSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G + +  L   ++G+++ G      QV +  +      
Sbjct: 123 ELTLRLTHPRYHLPKTYEVSISGDISETSLQQWREGVMLMGKKTLPAQVEVIHRCRQQTC 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V L EG+NR+I+++ E   + V RL R + G   L
Sbjct: 183 LKVILIEGRNRQIRRIVEHLGFSVLRLHRTAVGSIAL 219


>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 =  118 bits (295), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/235 (36%), Positives = 125/235 (53%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+++ +AR G+ASRR+ E +I   RV++NG ++   AV V   D +EVDG P+    R 
Sbjct: 6   QRLNQYLARCGVASRRKAEALILGGRVRLNGCVVLDLAVRVQGEDRVEVDGEPV--LPRV 63

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
            L+L  HKP G+++   D     TV D LPS F   R   VGRLD ++EGLLLLTNDG  
Sbjct: 64  ALYLVLHKPRGVLSAVEDRR-EQTVVDLLPSRFRPERPFPVGRLDKDSEGLLLLTNDGDF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A+ L  PS   ++ Y V+    +  +    + +G+  +G     + +          W  
Sbjct: 123 AQRLLHPSAGIVKSYEVQLDRPLAPEHRERMLEGLWSEGEFLRPLSIR-SLGVPDRRWTV 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             L EGK REI+++   F + V RLIR   G  +L  L  G  +E+S + L  Q+
Sbjct: 182 FDLVEGKKREIRRLAALFEYGVLRLIRRRVGKLELRRLETGVAQELSGEALWRQI 236


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 72/225 (32%), Positives = 127/225 (56%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AERT 73
           R++K +A  G+ SRRE++++I + +++VNG ++  A V V   D IEV G  + K  E+ 
Sbjct: 5   RINKYLASLGVGSRREIDKLIEEGKIRVNGEVIS-AGVKVTDKDIIEVKGKKISKDIEKK 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+ ++++  D  GR TV D +     R+  +GRLD NT GL+LLTNDG L   
Sbjct: 64  VYYMLNKPLEVLSSAKDDRGRKTVVD-IVKCKERIFPIGRLDYNTTGLILLTNDGELFNR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P ++  + Y V+  G++    +  L+ G+ ++        V L +++   + + V +
Sbjct: 123 VIHPRSEVYKEYYVKVLGEIKDSSIKKLEDGVELEDGITLPAYVKLISRERGKSELMVSI 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           REG+NR+++++ E  N  V  L R   G   LG L  G  RE+++
Sbjct: 183 REGRNRQVRRMLEAVNTPVLVLRRERIGKLSLGKLKVGEYRELTE 227


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 79/188 (42%), Positives = 102/188 (54%), Gaps = 13/188 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRK 69
           P+R+ K++A+ GI SRR++E  I Q RVKVNG    L ++A+      D I  D   L  
Sbjct: 12  PERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVATLGDKAS----EADKISFDSKALHS 67

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
                 R R+ +YHK  G V T  D   R TVFD+LP +  SR I VGRLDINT GLLL 
Sbjct: 68  YGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLDINTTGLLLF 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++        +     +
Sbjct: 128 TTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGIAKFNSIKFSGGE 187

Query: 184 GSNAWVTV 191
           G+N W  V
Sbjct: 188 GANLWYYV 195


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 120/225 (53%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E MI A +      ++ E  +     TD ++VDG  ++     
Sbjct: 2   RLQKVLANAGVASRRVSEEMIVAGRVRVNGVVVTELGSRIHPETDLVDVDGTAIQLDTSK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP G+V++ SD  GR  +         R+ +VGRLD +T GLL+LTNDG LA V
Sbjct: 62  RYVILNKPTGVVSSMSDDRGRPDLRQYTKDWDERLFNVGRLDADTSGLLVLTNDGDLAHV 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    +VY  +  GQV    +  L KG+ ++ G    D    LD+ +G  + V + 
Sbjct: 122 LAHPSFGVTKVYIAKVEGQVLPQTIQHLLKGVDLEDGRIAADKARLLDSSRG-ESLVELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L  GKNR ++++       V  L+R  +GP  LGTL  G  RE++
Sbjct: 181 LHSGKNRIVRRLMAEVGHPVIELVRRQFGPLHLGTLPVGKARELT 225


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 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|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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/247 (34%), Positives = 125/247 (50%), Gaps = 13/247 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AER 72
           +R+ K +ARAG+ASRR  E +I   RV VNG +       VM  D + VDG  +   A+ 
Sbjct: 6   ERLQKRLARAGVASRRAAEDLITAGRVTVNGQIAT-LGRTVMPDDEVRVDGRLIEAPAQE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +  +L +KP G VTT  D  GR  V   +P I   +  VGRLD ++EGLLLLT DG L  
Sbjct: 65  SVTFLLYKPAGYVTTARDEYGRRNVLSAMPPIPG-LHPVGRLDKDSEGLLLLTTDGQLTL 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + YR    GQ    +L +L+ GI +      D      + + +     V 
Sbjct: 124 TLTHPRYGHEKAYRAWTAGQPVAAELRVLETGIEL-----ADGPARALSARPARGGALVT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP----- 247
           L EG+NR+++++ +   + V+RL+R   G   LG L  G  R +S + L + L P     
Sbjct: 179 LTEGRNRQVRRMLDAIGYPVHRLLRYRVGGLWLGDLEPGEYRLLSPRDLHDLLHPAQVPR 238

Query: 248 HLLEEAQ 254
           H+ E A+
Sbjct: 239 HVWERAE 245


>gi|254495132|ref|ZP_05108056.1| pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85819482|gb|EAQ40639.1| pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 282

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 116/225 (51%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G+ SRRE +  I    VKVNG L+      V   D ++ DG  +   E+ R
Sbjct: 50  RLNKYIANSGVCSRREADTYIEHGSVKVNGKLVTEMGYKVQPDDVVQFDGTSI-TPEQKR 108

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  D  GR TV D + +    R+  VGRLD NT GLLL TNDG LA+ 
Sbjct: 109 YILLNKPKNYITTMDDDRGRKTVMDLVSNASKERIYPVGRLDRNTTGLLLFTNDGDLAKK 168

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     ++Y      ++D   L  L+  ++I+G   + D    +D Q  +   + + 
Sbjct: 169 LTHPKHNVRKLYHASLDRKLDLKDLEKLRGEVIIEGRKVFIDAVSYVDGQPKTE--IGIE 226

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  G+NR ++K+FE   +KVN+L R+ +       L  G  R ++
Sbjct: 227 IHSGRNRIVRKIFEHVGYKVNKLDRVIFAELTKKNLPRGRWRALT 271


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 118/227 (51%), Gaps = 1/227 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA +G+ SRR  E+++ Q+RV +NG L +         D I VDG  L     T
Sbjct: 4   QRLQKLIAASGLCSRRHAEQLLLQERVTLNGHLAKLGDKADPELDKISVDGRVLNSNTET 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLAR 132
           R+ L++KP G++T+  DP GR TVF  LP    + +  VGRLD ++ G LL+TN G L  
Sbjct: 64  RVLLFNKPAGVITSCHDPHGRVTVFSLLPDKLCKGLHPVGRLDADSRGALLITNRGELTL 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y+V   G+     L+  + G+++ G      ++ L     S + + V 
Sbjct: 124 RLTHPRYAHDKTYQVLVEGKPSPLVLSSWRHGVMLDGKTTLPAELELLQSHPSQSLLKVV 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           LREG+NR+I++V E     V  L R +     L  L  G  R + ++
Sbjct: 184 LREGRNRQIRRVAEQLGHPVLDLQRTAIANVALDALPEGCWRALDER 230


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 122/239 (51%), Gaps = 16/239 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA     SRRE +R+I +  V +N  +L   A +V   DHI V   P++ +    
Sbjct: 2   RLNKYIAHHTKYSRREADRLIEEGEVTLNKKVLRDFAYDVQEGDHIYVKSRPIKPSNEIT 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+KP G++ T  D  GR+T++  LP  F   + VGRLD  +EGLL+LT+   +  V 
Sbjct: 62  VIVYNKPKGVLVTKKDDRGRATIYHKLPGKFRHFVPVGRLDYASEGLLILTD--SVEVVT 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-------------IQGICYGDM-QVTLD 180
            L  +   R Y ++    V Q+ +  + +G+V             I G+ +       + 
Sbjct: 120 ALMGSDLERTYNLKIDKPVTQEMVAAMNEGLVLDDARAGGHEKSKIYGMEFAPFAHFEIR 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           ++  S   + V + EGKNRE+++ F  F+ KV  L R++YG  +L  L    TR  S+K
Sbjct: 180 SEGKSYTKLRVTITEGKNRELRRFFGHFDAKVLDLKRVAYGGIELNNLPTNKTRFFSRK 238


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/237 (35%), Positives = 122/237 (51%), Gaps = 10/237 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAER 72
           +R+ K +ARAGIASRR  E MI   RV VNG++       V   D + VDG  +   A  
Sbjct: 4   ERLQKRLARAGIASRRAAEEMITAGRVTVNGVVAHLGQ-TVTDADDVRVDGSLVDSTAVP 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP G VTT  D  GR  V D +P I   +  VGRLD ++EGLLLLT DG L  
Sbjct: 63  AVTYALYKPRGYVTTARDEYGRRNVLDAMPEIPG-LHPVGRLDRDSEGLLLLTTDGQLTL 121

Query: 133 VLELPSTQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            +  P     + YR    G  D  Q +L+ L  G+ ++    G  +    +     A+V 
Sbjct: 122 TMTHPRYGHEKAYRAWTEGPHDPTQGELDTLVSGVELED---GPARAVSASPAYGGAFVV 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           +G  EG+NR+++++ E     V+RL+R   G   LG +  G  RE+++K L E + P
Sbjct: 179 LG--EGRNRQVRRMLEAVGHPVSRLLRYRVGGLWLGDMEVGEYRELTRKDLDELVNP 233


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 123/230 (53%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E+MI   RV+V+G L+      V     HI VDG  +      
Sbjct: 21  RLQKILAQAGFGSRRKCEQMITDGRVEVDGELVTELGTRVDPKKQHIRVDGSRVHLNPNH 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++   DP GR T+ D +   + RV  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 81  VTLALNKPKKVLSAMDDPKGRYTLADIIGDKYERVFHMGRLDYDSEGLILMTNDGELSQH 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-----W 188
           +  P  +  + Y     G++     N+ ++ +V QG+   D  V LD     +A      
Sbjct: 141 VMHPKYEVEKTYIATIDGKIGG---NVCRR-LVTQGVQLDDGLVKLDHCAIIDANRDQTI 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+
Sbjct: 197 VKVVLHSGKNRIVRRIFGAIGYPVRRLVRTQIGPIKLGDLKSGTYRVLSQ 246


>gi|325479564|gb|EGC82660.1| pseudouridylate synthase [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 233

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 126/226 (55%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA++G  SRR+ + +I   +VKVNGIL+      V   D +E+DG  L   +   
Sbjct: 2   RINKYIAKSGYTSRRKADDLIKASKVKVNGILINEPGYEVTDDDILEIDGKRLYIEKNFY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             LY KP+G VT++ DP     + ++L  +  R  + GRLD ++EGLL++TNDG     +
Sbjct: 62  KKLY-KPVGYVTSNYDPHNEKDL-NSLIDMKERFFAAGRLDKDSEGLLIITNDGHFTNGI 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGL 193
             PS +  + Y V    ++ + +    +KGI I +G    + ++ L   K +N +  V +
Sbjct: 120 IHPSNELEKTYIVTVSRKLSKSQEKKFEKGIDIGRGEITSNSKIKLLDSK-TNKY-EVKI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +G NR+I+++F +F+ KV  L RIS GP +L  +     R+ S+K
Sbjct: 178 HQGYNRQIRRMFAYFSSKVINLKRISIGPIKLDDMKEYEIRDFSEK 223


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 74/211 (35%), Positives = 112/211 (53%), Gaps = 1/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA++G  SRR+ + +I   +V VNG +L   +  V  +D +EV+G  + K E   
Sbjct: 2   RINKFIAQSGYCSRRKADELIKNSKVCVNGTILLDLSYQVNDSDIVEVEGKKISKKEEKI 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KPIG  +T  D      V D L    +RV  VGRLD ++ GLL+LTNDG L   L
Sbjct: 62  YIAINKPIGYTSTVKDKFADKKVVD-LIKFKTRVYPVGRLDKDSHGLLILTNDGELTYEL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VY V   G+  +DK+  LK GIV+ G       +        N    V + 
Sbjct: 121 THPKFEHKKVYEVLVKGRPTKDKIQELKNGIVLDGYKLKKSSIEFIANVKDNTKYMVTIY 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+NR+I+K+F++ N  V  L R+  G +++
Sbjct: 181 EGRNRQIRKMFDYINHPVLDLKRVQIGYYKM 211


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 123/226 (54%), Gaps = 3/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +       + D I VDG  L+   R 
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQLGDKADPARDVIVVDGERLQADVRL 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+VTT +D  GR+ + D + + +  RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 79  VYVAMNKPRGVVTTMADEKGRTELADFIGARLEQRVYHVGRLDADSEGLLLLTNDGTLAH 138

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS + L+ Y     G + ++    L  G+ ++ G    D    +DT  G  A V +
Sbjct: 139 KLMHPSYEVLKTYLAEVAGPIPRNLGKRLTAGVELEDGPVKVDGFKVVDTL-GKTAQVEL 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+   ++++       V+RLIR S GP +LG L  G  R ++
Sbjct: 198 TLHEGRKHIVRRLMAEVGHPVSRLIRTSIGPIKLGDLRTGRMRRLT 243


>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 =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 77/231 (33%), Positives = 113/231 (48%), Gaps = 1/231 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E    +R+ K+IA AG+ SRR  E ++   RVKVN  + +         D I +DG PL 
Sbjct: 8   ETVKAERLQKLIAAAGVCSRRHAEELLRAGRVKVNDRMAQLGDRAEPGLDRITIDGTPLP 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTND 127
             +  RL L +KP G++++  DP GR  V D +P    R +  VGRLD  + G LLLTN 
Sbjct: 68  ANDPPRLLLLNKPRGVISSCQDPQGRPIVLDLVPKHLRRGLHPVGRLDAESRGALLLTNQ 127

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + YRV   G+     L   ++G+ +        +V       +  
Sbjct: 128 GELTLQLTHPRYSHAKTYRVWVQGRPSHGALEHWRRGLRLDQRLTQPAEVRELHHNANRT 187

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + V LREG+NR+I++V E     V  L R +     LG+L  G  RE+++
Sbjct: 188 LLEVVLREGRNRQIRRVAELLGHPVLDLQRTAIATVVLGSLQEGRWRELTE 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 =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 76/228 (33%), Positives = 120/228 (52%), Gaps = 6/228 (2%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLY 78
           +A+ G+ASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    +    + 
Sbjct: 1   MAQCGVASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRISLQMQKVYIML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G++++  D  GR TV D +   +  RV  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 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS----TREVSKKIL 241
           NR+I+K+ +    KV +L R++ G  QLG L  G      RE + K+ 
Sbjct: 181 NRQIRKMCDQIGHKVLKLKRVAIGKLQLGKLKEGEFVFLDRETANKVF 228


>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 =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/227 (34%), Positives = 126/227 (55%), Gaps = 8/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA A + SRR+VE +I Q+RVKVN  ++ +    V ++D + +D V ++K    
Sbjct: 2   ERLQKFIASANLVSRRKVEILILQKRVKVNNQVVSQLGTKVKASDVVTLDDVLIKKTT-L 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +  S   R+ SVGRLD NT GL+L+TNDG + +
Sbjct: 61  FYYLLNKPQGYLSTTKDDKKRPTVLDLIKESQNQRLYSVGRLDFNTTGLILITNDGEMTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNA 187
            L  P     + Y V+ +  + +  L+LL KG++I    Y  +   ++  K       + 
Sbjct: 121 KLTHPCFGIPKEYHVKINVFLTKKDLSLLLKGVIIDH-NYLSIPKEINILKQRYLPKPST 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           W+ + + EGKNR+I+K+ E   ++V +L R SY    +  L  G+ R
Sbjct: 180 WLKIVITEGKNRQIRKMMEALGYQVLKLRRYSYAFLTIEGLKTGAYR 226


>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 =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 118/229 (51%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   V      
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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             +  P  ++L+ Y+    GQV++ ++N L KG+ I        Y    V  D  K + +
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKNT-S 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+
Sbjct: 183 IVELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIADLKPGQYREL 231


>gi|218682423|ref|ZP_03530024.1| pseudouridine synthase [Rhizobium etli CIAT 894]
          Length = 538

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 73/209 (34%), Positives = 115/209 (55%), Gaps = 5/209 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV V+G  +   +  V ++T  I VDG+ +  A  T+
Sbjct: 22  LPRALSKLGYCSRTQAERLIAESRVAVDGRTISDTSAWVDLATAKISVDGLVI--AAETK 79

Query: 75  LWLY-HKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++L  +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL TND   A+
Sbjct: 80  IYLMLNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKASEGLLLFTNDTEFAQ 139

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P T   + Y V+    +D + +  +  GI   G            Q   N+W+ V 
Sbjct: 140 ILLDPVTHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAARRLRQGDRNSWIEVE 199

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYG 221
           L EG+NR+I+++ E    +  RL+R++ G
Sbjct: 200 LDEGRNRQIRRMLEALGTECLRLVRVAIG 228


>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 =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 118/229 (51%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   V      
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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             +  P  ++L+ Y+    GQV++ ++N L KG+ I        Y    V  D  K + +
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKNT-S 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+
Sbjct: 183 IVELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIADLKPGQYREL 231


>gi|152967064|ref|YP_001362848.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361581|gb|ABS04584.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
          Length = 322

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 119/230 (51%), Gaps = 11/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ KV+A+AG  SRR  E MIA  RV V+G ++    V +  T  +  VDG+     +  
Sbjct: 86  RLQKVLAQAGAGSRRACEEMIAAGRVTVDGEVVTELGVRIDPTRQVVHVDGMRFSIDDEL 145

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+V+T  D +GR  + D +     R+  VGRLD+ TEGL+LLTNDG L   
Sbjct: 146 VYIMVNKPKGVVSTMYDEEGRLNLADMVGPREERLFHVGRLDLETEGLILLTNDGALTHR 205

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAW 188
           L+ PS    + Y     G V +D    L+ GI +      D  V++D+      K   A 
Sbjct: 206 LQHPSFGVQKTYLAEVRGPVKRDLGRNLRAGIELD-----DGPVSVDSFKLVDSKPGYAL 260

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V V L EG+   ++++ E   + V +L+R+  GP  LG L  G  R +++
Sbjct: 261 VEVVLHEGRKHIVRRMLEAEGYPVLKLVRVQMGPIVLGDLKPGKNRRLTR 310


>gi|222624207|gb|EEE58339.1| hypothetical protein OsJ_09447 [Oryza sativa Japonica Group]
          Length = 1194

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 123/226 (54%), Gaps = 13/226 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           PQR++KV+A AG+ASRR  E +I Q +V VNG +       V +S D I V+G  + K  
Sbjct: 77  PQRLAKVLAAAGVASRRTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRISKKL 136

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNL--------PSIF-SRVISVGRLDINTEGL 121
             +L+   +KP G + +  +P    ++FD+         P +   R+ +VGRLD+ T GL
Sbjct: 137 PPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVPKPRLFTVGRLDVATSGL 196

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD 180
           +++TNDG  A+ L  PS+  ++ Y V   G V ++ L  + +G  I G+ C  D+   LD
Sbjct: 197 IIITNDGEFAQKLSHPSSNIMKEYVVTIDGPVHRNHLIAISEGTKIDGVKCIPDLVEPLD 256

Query: 181 TQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            Q  +    + + + EG+N E++++ +    +V  L R+  G F+L
Sbjct: 257 VQSNTKRTRIRIAVHEGRNHEVRELVQNAGLEVYALKRVRIGRFRL 302


>gi|260905260|ref|ZP_05913582.1| pseudouridine synthase, Rsu [Brevibacterium linens BL2]
          Length = 238

 Score =  117 bits (293), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 72/213 (33%), Positives = 116/213 (54%), Gaps = 3/213 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A AG+ SRR  E++I   RV+V+G ++      +   T  + VD V +    + 
Sbjct: 2   RLQKILAEAGLGSRRACEQLILDGRVEVDGSIVTELGTRIDTETQAVYVDAVRISTQTQK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+V+T SDPDGR  + D + +   R+  VGRLD  TEGL+LLTNDG L+  
Sbjct: 62  VYLVLNKPAGVVSTMSDPDGRPCLADYVKNRVDRLFHVGRLDTETEGLILLTNDGELSNR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + Y  +  GQ+ +D  + LK G+ +  G    D    +D+  G +  V + 
Sbjct: 122 LAHPRYEIPKTYLAQVRGQLAKDVGSRLKAGMDLDDGFVKVDSFKLVDSTPGKSV-VELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           L  G+NR ++++ +     V RL+R  +GP  L
Sbjct: 181 LHSGRNRIVRRLLKEVGHPVERLVRTKFGPITL 213


>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 =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 117/224 (52%), Gaps = 5/224 (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
             +L +KP   + T  D  GR TV D L     R+ +VGRLD +T GL++LTNDG  A  
Sbjct: 62  -YFLMNKPKRTMCTSEDEFGRQTVVD-LIDCEQRIFTVGRLDYDTSGLIILTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGI--CYGDMQVTLDTQKGSNAWVT 190
           +  P     +VY +  +G +  + +  +K GIV+  GI       ++T    + +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTSEDMKKIKSGIVLDDGIKTLPAKYRITEKDPQKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG+NR+IK++ E   ++V RL R          L  G  R
Sbjct: 180 LTIVEGRNRQIKRMMEALGYEVRRLHRSKLAFLHCSDLRQGEYR 223


>gi|312196764|ref|YP_004016825.1| pseudouridine synthase [Frankia sp. EuI1c]
 gi|311228100|gb|ADP80955.1| pseudouridine synthase [Frankia sp. EuI1c]
          Length = 285

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 86/233 (36%), Positives = 128/233 (54%), Gaps = 17/233 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER- 72
           R+ KV+A AG+ SRR  E +I   RV+V+G ++      V   T  IEVDG      ER 
Sbjct: 47  RLQKVLASAGVGSRRHNEELIDAGRVRVDGKVVREQGRRVDPETAVIEVDG------ERV 100

Query: 73  -TRLWLYH----KPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLT 125
            TR  L H    KP G+V+T SDP+ R T+ D L    +   +  VGRLD+++EGLLL+T
Sbjct: 101 VTRTGLVHLALNKPRGVVSTMSDPEDRPTISDLLTEFGASAGLFHVGRLDVDSEGLLLVT 160

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG 184
           N+G LA  L  PS Q  + Y+V+ +G + ++ +  L   + +  G    D    +D Q G
Sbjct: 161 NNGDLAHRLTHPSYQVPKTYQVQINGPLRKETMRRLHTRVELSDGPVRVDSARIID-QVG 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           S   + + L EG+NR ++++ E     V RL+R  +G   LGTL +G  R ++
Sbjct: 220 SQILLEIVLHEGRNRIVRRMMEEVGHPVVRLLRTEFGAVHLGTLRSGRARHLT 272


>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 =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 120/224 (53%), Gaps = 3/224 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E+MI   RV+V+G I++E       +   + VD +P+  +   
Sbjct: 35  RLQKVMADAGLGSRRACEQMILDGRVEVDGHIVIELGTRIDPTKQRLVVDSMPIETSTEK 94

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP  +V++  DP+GR  + + +     R+  VGRLD  TEGLLLLTNDG +A  
Sbjct: 95  VYFALNKPAKVVSSMGDPEGRRNLDEFVRDRTERLFHVGRLDYETEGLLLLTNDGDMANR 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + Y  +  G V +D    L++GI +  GI   D    +D+Q G  A V V 
Sbjct: 155 LTHPRYEIPKKYLAQVKGPVAKDVGARLREGIELDDGISRVDSFKLIDSQPGV-ALVEVI 213

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           L  GKNR ++++       V RL+R  +GP +L     G  R++
Sbjct: 214 LHSGKNRIVRRLLSAVGNPVLRLVRTEFGPIELAEQRQGKMRQL 257


>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 =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 118/227 (51%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+   +AR+G+ SRR  E++I++  V+VNG +     + V+   D +   G P+    + 
Sbjct: 15  RLQLYLARSGVGSRRACEKLISEGCVRVNGQVANSQGIKVVPGRDSVTYRGKPVFPTGKH 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP+  + TH D +GR    D +   F  R+ +VGRLD  + GL+  TNDG  A+
Sbjct: 75  YYIALNKPVRYLCTHYDLEGRPLAEDLIKGKFPVRLFNVGRLDFLSSGLIFFTNDGEFAK 134

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           ++  PS +  + Y V    ++  + L   +KG+V++G  Y      +     S   V + 
Sbjct: 135 IITHPSHEIEKEYVVETAKRLSSELLEEFRKGVVVEGELYRIHAYNII----SPVKVKIV 190

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           LREGKNREI+K+F   N KV RL R+  GP Q+  +  G  R +  K
Sbjct: 191 LREGKNREIRKLFTSKNIKVKRLHRVRIGPVQIAGMHPGEFRNLKPK 237


>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 =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 122/227 (53%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AGI SRR  +  I + R+ +NG   E     + + D + VDG P+RK E T 
Sbjct: 6   RINKYLSEAGICSRRAADEYILKGRITINGKPAEMGQ-KIEANDRVMVDGKPVRKREETV 64

Query: 75  LWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +  Y+KP+GL  T  H DPD    +FD++     R+  VGRLD +++GLLLLTNDG L+ 
Sbjct: 65  ILAYNKPLGLTCTASHDDPD---NIFDHIKYPI-RLQYVGRLDKDSQGLLLLTNDGDLSN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            ++       + YRVR +  +  + L  +  G+ I        ++     K  N    + 
Sbjct: 121 SIQKSVNNHEKEYRVRVNKPITDEFLTQMAAGVPILDTVTKKCRLY----KIDNYSFKII 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +G NR+I+++ E+F +KV  L R+     +LG L  G  R ++K+
Sbjct: 177 ITQGLNRQIRRMCEYFGYKVVNLKRLRVINIRLGNLRPGEYRHLTKE 223


>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 =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 125/229 (54%), Gaps = 18/229 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA     SRRE +R+IAQ +V +N  +++  +  V     + V+G  LRK+E   
Sbjct: 2   RLNQYIAHHSKYSRREADRLIAQGKVSINKEIIKDFSYQVDDKVKVYVNGKCLRKSEEYT 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+KP G + +  D  GR T++++LP  F+  I VGRLD  +EGLLLL++D   ARV+
Sbjct: 62  VIVYNKPKGELVSKKDDRGRRTIYESLPKRFAHFIPVGRLDFASEGLLLLSDD---ARVV 118

Query: 135 -ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAWV 189
            +L  ++  R+Y ++  G++ ++    ++ G+ +Q    G  +     +++       WV
Sbjct: 119 TKLMESKMERIYLLKLSGKIQEEVFEAMENGLSLQDARAGGHKESKIQSMEFAPFLGYWV 178

Query: 190 ----------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      V + EGKNRE+++ F  F  ++  L RISYG   L  L
Sbjct: 179 LKNSTRYSKIKVAINEGKNRELRRFFAHFGLEILDLKRISYGFVSLNNL 227


>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 =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 127/224 (56%), Gaps = 15/224 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +RV K++++ GIASRR  E +I ++R+K+NG   +L ++A  N    D +E+DG  ++  
Sbjct: 3   KRVQKILSQLGIASRRHAEILILEKRLKLNGQIVLLGDKADPN---HDLLELDGKIIKSH 59

Query: 71  ERTRLW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLT 125
           ++T+L+  L +KP+G++ +  D   RS V D LPS   +   +  VGRLD+N+ G LLLT
Sbjct: 60  KKTQLFYILVNKPVGIICSCKDSQNRSIVMDLLPSNLRKGMGIHPVGRLDMNSSGALLLT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQK 183
           NDG L   L  P     ++Y V   G   Q  L   ++G+V+ G       ++V  + ++
Sbjct: 120 NDGNLTLRLTHPRYHLPKIYEVLVRGNFTQAILKDWRQGVVLDGKKTLPAYLEVINNNRQ 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            +N  +   L EGKNR I+++ + F   V +L R + GP  L T
Sbjct: 180 YTNLKII--LTEGKNRHIRRIAQKFELDVIKLHRTAIGPISLST 221


>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 =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 116/234 (49%), Gaps = 26/234 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLRKAE 71
           ++ K I++ G  SRR+ E +I Q+R+K+N     L +R    V++ D I +DG  L    
Sbjct: 13  KIQKAISQVGYCSRRQAEELIKQKRIKINHQVATLGQR----VLADDQIFIDGKKLNIKP 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +++KP   + T  DP+ R T+++ +  +     SVGRLD N+ G++L+TNDG  A
Sbjct: 69  PKFYLVFNKPKNTICTLKDPEKRKTIYEYM-GLKEYAYSVGRLDFNSTGIILVTNDGDFA 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--- 188
            ++  PS    RVY V    ++ +   N L    VI           L+ +K S +    
Sbjct: 128 NLIAHPSANIKRVYEVVLEKELSEGDFNYLNSNKVI-----------LNGKKSSQSLSKL 176

Query: 189 ----VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                +V L EG+N  +K +F   N  V  L R+SYGP     L  G TR +S+
Sbjct: 177 APFKYSVSLYEGRNHHVKNLFLLVNNYVKELHRVSYGPITDANLKIGKTRHLSE 230


>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 =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 122/229 (53%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKTILD-LVKVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVT 190
            +  P  + ++ Y+ +  G + +D + L KKGI I    Y     TL+  K     + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGD--YLTAPATLEILKINKDTSEII 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGKNR+++++ +     V  L RIS G      L  G  R ++ K
Sbjct: 180 IKIHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTNK 228


>gi|196233446|ref|ZP_03132289.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222442|gb|EDY16969.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 237

 Score =  117 bits (292), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 80/234 (34%), Positives = 126/234 (53%), Gaps = 7/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A AG+ SRR VE +I   +V++NG ++   +  V  TD ++V G  L + E+  
Sbjct: 2   RLNRFLASAGLGSRRGVEELITSGQVRINGQVVTDLSTQVGPTDAVKV-GSRLLRTEQKI 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KP G V T SD   R T+FD LP+ + RV  VGRLD ++EGLLL+TNDG L+  L
Sbjct: 61  TVLLNKPAGYVCTASDERDRKTIFDLLPANWPRVYHVGRLDKDSEGLLLVTNDGDLSLAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             P  +  + Y V      + QD+  LLK   +I G    +    L+        +++ L
Sbjct: 121 THPRYKIEKEYEVLLDKPFNPQDREKLLKGFHIIGGRAKAERVEILNPTH-----LSLTL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            +G  R+I+ +     ++V RL RI  GP ++G +  G  R ++ K +    GP
Sbjct: 176 TQGIKRQIRLMLYDLGYEVERLARIRLGPLKIGEMRPGEWRLLTSKEIAALKGP 229


>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 =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 124/225 (55%), Gaps = 2/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A +G ASRR+ E  I   RVKVNG I+ E   V   + D + +D   L+  +  
Sbjct: 2   RLQKYMAHSGAASRRKSEEYILDGRVKVNGKIVTELGYVVDENKDKVYLDDKRLKIIKEN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V+T  D   R TV D L    +R+  +GRLDI+T GL++LT+DG +   
Sbjct: 62  TYIALNKPMGIVSTVKDEKDRKTVVD-LIDGSTRLYPIGRLDIDTTGLIILTDDGAITNK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y     G+  + +L++++KGI +    +   +V +     +++ + V +
Sbjct: 121 LTHPKNEINKTYIATVEGKPTKTELDMIRKGIKVGAEKFSPAKVKILKSFEADSIIEVII 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EGKN E+K +F+  N  V +L RIS G  +LG L  G+ R +++
Sbjct: 181 HEGKNHEVKLMFDKINHPVKKLKRISIGDIELGDLEIGNFRYLTE 225


>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 =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 77/208 (37%), Positives = 113/208 (54%), Gaps = 7/208 (3%)

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
             +L +KP   + T +D  GR TV + L     R+ +VGRLD +T G+LLLTNDG  A  
Sbjct: 62  -YYLMNKPKKSMCTSNDEFGRKTVIE-LVEGTERIFTVGRLDYDTSGVLLLTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM----QVTLDTQKGSNAWV 189
           +  P     +VY +  +G +  + +  LK GIV+    Y  M    ++T    K +    
Sbjct: 120 IIHPRYHLPKVYNLTINGILKPEDMRKLKNGIVLDD-GYKTMPAKFKITEKDLKKNQCSF 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIR 217
            + + EG+NR+IK++ E   ++V RL R
Sbjct: 179 DLTIYEGRNRQIKRMMEALGYEVRRLHR 206


>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 =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 130/242 (53%), Gaps = 20/242 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +IA+ RVKVN   +   +  V+ +D + +D  P+ K E+ +
Sbjct: 13  RLNKFISHNSKYSRREADAIIAEGRVKVNKKTITDLSTKVLDSDIVAIDNKPI-KFEKNK 71

Query: 75  LW---LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++   +Y+KP G + T +DP GR  +FD L + +   + +GRLD  +EG+LLLT+   +A
Sbjct: 72  MYTVLVYNKPKGELVTKNDPQGRRIIFDTLGAKYKHFLPIGRLDYASEGVLLLTDSVDVA 131

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG---DMQV----------- 177
             L     Q  RVY+++  G +++   + +  G+ ++    G   D +V           
Sbjct: 132 NGLMHSDLQ--RVYKIKVSGPINKQVEDAMLHGLELEDATKGAWKDSKVKSMSFAPFLGY 189

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +D+ K + + + V + EGKNRE+++ F  F   V  L R+ YG   L  L  G +R ++
Sbjct: 190 KIDSVKDTFSKLKVAITEGKNRELRRFFAHFGLDVMDLKRVEYGGISLNNLPTGKSRYLT 249

Query: 238 KK 239
           ++
Sbjct: 250 RE 251


>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 =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 76/218 (34%), Positives = 120/218 (55%), Gaps = 6/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++++ GIASRR+ E+MI   RVKVNG +++         D+IEVDG+P+R   R 
Sbjct: 3   ERLQKILSQWGIASRRQAEQMIIAGRVKVNGKIVQLGEKAQPDLDNIEVDGLPIRPEARP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KP+G+++T S+P  RS V D L +       +  VGRLD ++ G LLLTNDG
Sbjct: 63  SPIYLLLNKPMGVISTCSEPRKRSKVLDILNAELRNGKGIHPVGRLDADSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNA 187
            +   L  P     + Y+V   G   +  L L ++GI++ G      +V  L     S  
Sbjct: 123 RVTYCLTHPKYCLSKTYQVLVEGHPQESILKLWRQGIILSGKKTLPAEVKVLKECNSSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + V + EG+NR+I++V +    +V +L R + G  +L
Sbjct: 183 LLEVVISEGRNRQIRRVADKLGHRVLKLHRTAIGQIKL 220


>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 =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 73/217 (33%), Positives = 118/217 (54%), Gaps = 5/217 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ GIASRR+ E++I   RV++NG +           D +EVDG  ++   R 
Sbjct: 3   ERVQKILSQWGIASRRQAEKLILAGRVRLNGNIASLGDKADPHQDLLEVDGTIIQPVNRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           R    L +KP+G+V+T  DP  R TV + LP+  ++   +  VGRLDIN+ G L+LTNDG
Sbjct: 63  RPIYILLNKPLGVVSTCHDPQNRPTVLELLPATLNQGTGIHPVGRLDINSTGALVLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y+V   G   +  L   ++G+++ G      QV +  +      
Sbjct: 123 ELTLSLTHPRYHLPKTYQVWIDGNPGEQILQQWREGVMLMGKKTQPAQVKVVKRHHQQTQ 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGKNR+I+++ +   + V +L R + G  QL
Sbjct: 183 LQVVITEGKNRQIRRIVQLLGFNVLKLHRTAIGLIQL 219


>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 =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 79/228 (34%), Positives = 122/228 (53%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   + + E  
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKINE-ESF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+++     + +V + L    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 64  EYYLLNKPAGYVSSNRSYPNQPSVIE-LIKTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           L  P  +  R Y     G V++D+L  L K I   G  Y     ++    QK   + + +
Sbjct: 123 LTHPKHRIKRTYAAWVKGIVNEDELEQLTKPIRFDGEIYFPQAARILKVDQKRQESLIEI 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EGK  EIKK+ +F    V +L R  +    +G L  G  R +S++
Sbjct: 183 TIAEGKTHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQYRALSEQ 230


>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 =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 82/239 (34%), Positives = 127/239 (53%), Gaps = 14/239 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           + QR+ KV+ARAG+ASRR  E++IA+ RV+V+G L+    V V   T  +EVDG  +   
Sbjct: 17  SAQRLHKVLARAGVASRRGSEQLIAEGRVRVDGRLVTEQGVLVDPHTAVVEVDGKRIAVD 76

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRST-----------VFDNLPSIFSRVISVGRLDINTE 119
           +R   +  +KP G++T  SD   R               D    + + +  VGRLD +T 
Sbjct: 77  DRHATYALNKPKGVLTAMSDTRERCVGDLLREAGPDFAADGRAGLPAGLFHVGRLDADTT 136

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVT 178
           GLLL++NDG LA  L  PS +  + Y     G V +  +  L+ G+V++ G    D +V 
Sbjct: 137 GLLLVSNDGELAHRLAHPSYEIPKTYIATVRGVVAKRAVEQLRAGVVLEDGPAKAD-EVC 195

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L   +     V + L EG+NR ++++F+     V  L R+  GP +LG L +G+ R +S
Sbjct: 196 LRGSQRDRTVVEITLHEGRNRIVRRMFDEVGHPVIELARLRIGPIRLGDLRSGALRALS 254


>gi|188996649|ref|YP_001930900.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931716|gb|ACD66346.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 244

 Score =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 124/232 (53%), Gaps = 4/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R++K IA++GI SRR+ + +I + +VKVNG +++     +    D +EV+G  ++  E+ 
Sbjct: 4   RLNKYIAQSGICSRRKADELIKEGKVKVNGEIIKDLGAKINPEKDIVEVEGNIIKPVEKK 63

Query: 74  RLWLYHKPIG-LVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP+G L     D  GR T+ D L   +I   +  VGRLD N+EGLL+LTNDG  
Sbjct: 64  IYIKIYKPVGYLSAVGKDKFGRKTLTDLLKELNIKENLFPVGRLDYNSEGLLILTNDGEF 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  +VY V    +VD++ LN +KKG +++   +   +V +      + W+ 
Sbjct: 124 ANKIAHPKHKIKKVYHVEVVPKVDEETLNQMKKGAILEDGFFKPDKVEILKHTKDSTWLL 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             +  GK R +++    FN KV RL+R+      +  L     + ++ K +R
Sbjct: 184 FEIHSGKKRILRRYVSKFNHKVKRLVRVKIDSISIENLKPHQFKHLTDKEVR 235


>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 =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 74/218 (33%), Positives = 113/218 (51%), Gaps = 4/218 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLY 78
           +A  GIASRR+ E +I Q RVKVNG  ++     +    D I VD V + K  +    L 
Sbjct: 1   MAYCGIASRRKCESIILQGRVKVNGETIKSLGTKIDDKVDKITVDDVKIEKENKKVYILL 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G V+T  D  GR+T+ D +  +  R+  +GRLD NT G+++LTNDG +   +  P 
Sbjct: 61  NKPTGYVSTVKDDRGRNTILD-IVKVKERIYPIGRLDYNTSGIIILTNDGEVYNKVAHPK 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +  +VY     G   ++ ++  K G+ I G      D  +    +  +N+ V + + EG
Sbjct: 120 MEKNKVYVAVIKGIPSKEDIDKFKNGVNIDGYITAKADFNILNINKSKNNSKVRIKIHEG 179

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           KNR+I+K+ +     V  L RIS G   +G L  G  R
Sbjct: 180 KNRQIRKMCDAIGHPVISLTRISIGNINVGNLEEGKWR 217


>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 =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 84/246 (34%), Positives = 129/246 (52%), Gaps = 11/246 (4%)

Query: 2   KDKNIVQENF-TPQ----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM- 55
           K +N+ Q +F +P     R+ KV+A+AG+ASRR  E +I   R++VNG ++    V V  
Sbjct: 29  KRQNVEQRDFGSPTGEGIRLQKVLAQAGVASRRHAEILIDAGRIEVNGKIVLTQGVRVNP 88

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVG 112
             D I VDGV +   E  + ++ +KP GL +T SD  GR  V D +    +   R+  VG
Sbjct: 89  HADIIRVDGVRINVNEDMQYFVLNKPRGLQSTMSDDMGRPCVGDIVGERIAAGQRLFHVG 148

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGIC 171
           RLD  TEGLLLLTNDG LA  L  P  +  + Y     G+ D+  +  L+ GI +  G  
Sbjct: 149 RLDAATEGLLLLTNDGELANRLMHPKYEVTKTYLATVLGEADKRLIKQLRDGIELDDGPA 208

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             D    +D  +G  + + + L EG+   ++++ +   + V RL+R      QLG    G
Sbjct: 209 KADFVQIVDAHQG-KSLIRIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTIQLGEQTPG 267

Query: 232 STREVS 237
           + R ++
Sbjct: 268 AVRALN 273


>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 =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 125/231 (54%), Gaps = 11/231 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV+A AG+ SRR  E +I +++V VNG + +       +T  I V+G  L+   R
Sbjct: 18  PERLQKVLAAAGVGSRRACEDLIFRRKVTVNGRVAQLGDKVDPATAVIHVNGERLQADTR 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L + +  RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYLAMNKPRGVVSTMADERGRTALADFLNNRVEQRVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSN 186
             L  PS    + Y     G + ++    L  GI ++     D  V++D  +     G  
Sbjct: 138 HRLMHPSYGVQKTYLCEVAGPIPRNLGKRLAAGIELE-----DGPVSVDAFRVVDSLGRT 192

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           A V + L EG+   ++++       V+RL+R + GP +LG L +G TR ++
Sbjct: 193 AQVELSLHEGRKHIVRRLLAEVGHPVSRLVRTAIGPIRLGDLRSGRTRRLT 243


>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 =  116 bits (291), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 78/252 (30%), Positives = 126/252 (50%), Gaps = 24/252 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R++K IA     SRRE ++ +    V+VN  +    A  V    D + + G  +   E+ 
Sbjct: 3   RLNKYIAHYSTYSRREADKAVQDGYVRVNSEIETNPATQVQEGVDIVYISGKQVSPQEKY 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + T +DP GR T++D+L   F   I VGRLD  +EGLLLLT+   +A  
Sbjct: 63  TVIVYNKPKGELVTKNDPKGRKTIYDSLSKEFRHFIPVGRLDFASEGLLLLTDASHVA-- 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----------DMQ--VTLDT 181
             L  +   R+Y+++  G+V  D  + +  GI +     G          D++  +    
Sbjct: 121 TSLMESDLERIYKLKIKGEVTPDMEDAMLNGIYLDDASAGAHSHSKITSMDIKPFIGYKI 180

Query: 182 QKGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK- 238
           QK    +  + V L+EGKNRE+++ F  F  +V  L R+S+   +L  L  G TR +S+ 
Sbjct: 181 QKNQPNYSILKVALKEGKNRELRRFFAHFGAEVADLKRVSFAEIELNNLPTGKTRYLSRS 240

Query: 239 ------KILREQ 244
                 K L+E+
Sbjct: 241 EYSALYKFLKEE 252


>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 =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 87/240 (36%), Positives = 121/240 (50%), Gaps = 9/240 (3%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
            R+  Y+KP G + T  DP+GR TVFD LP I  SR ISVGRLD NT GLLL T DG LA
Sbjct: 29  CRVLAYYKPEGELCTRHDPEGRRTVFDRLPKIRGSRWISVGRLDANTSGLLLFTTDGELA 88

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS Q  R Y VR  G+V + K+  + +G+ ++        V     +G N    V
Sbjct: 89  NRLMHPSRQVEREYLVRVFGEVTEQKVKNVTRGVQLEDGMARFEDVVYAGGEGMNHTFYV 148

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK---ILREQLGP 247
            + EG+NRE+++++E     V+RL R+ YG   L   L  G  +E+  +    LRE +  
Sbjct: 149 AINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWKELDLQEVNYLRELVEL 208

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              +E  ++LD P  +S    R R   I        R ++ ++   G S Q K   P  R
Sbjct: 209 QPEKETLLDLD-PANTSRKRERSRSQKIRRA---VKRHEERANAPKGRSNQTKRKKPATR 264


>gi|156340515|ref|XP_001620471.1| hypothetical protein NEMVEDRAFT_v1g223077 [Nematostella vectensis]
 gi|156205434|gb|EDO28371.1| predicted protein [Nematostella vectensis]
          Length = 275

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 117/226 (51%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G+ SRRE +  IA   V VNG ++      V  TD I  DG  +   E+ +
Sbjct: 44  RLNKYIANSGVCSRREADTYIASGNVVVNGKVITEMGFKVKPTDDIRFDGTAISPEEK-K 102

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  D  GR TV D + +    R+  VGRLD NT GLLL TNDG LA+ 
Sbjct: 103 YVLLNKPKNYITTMDDDRGRKTVMDLVQNAARERIYPVGRLDRNTTGLLLFTNDGDLAKK 162

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P     ++Y      +++   L+ ++  ++I+G  +   ++      +K     V +
Sbjct: 163 LTHPKHNVQKLYHASLDRKLEVKDLHKMRDEVIIEGKRVFIDEVDYVAGEKK---TEVGI 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +  G+NR ++K+FE F +KV +L R+ +       L  G  RE++
Sbjct: 220 KIHSGRNRIVRKIFEHFGYKVVKLDRVIFAGLTKKNLPRGRYRELT 265


>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 =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 122/230 (53%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLRK 69
           RV K+IA++G+ SRR+ E+MI++  V VNGI   + ++A++N    D I+V+G  + L K
Sbjct: 6   RVQKLIAQSGLMSRRDAEKMISKGLVFVNGIKSSIGDKASIN----DEIKVNGKIINLTK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               + +L +KP   +TT  DP GR TV D L +   R++ VGRLD NT G+LLLT D  
Sbjct: 62  NTVFKYYLLNKPKNTITTSKDPKGRHTVID-LINTSERIVPVGRLDRNTTGVLLLTTDYE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  RVYR R    +   +   L  GI I     G M   +  Q  + +++
Sbjct: 121 LVNKLTHPKYEIERVYRARIDSPLTLKEFKELNAGIEID----GKMSYQIVDQVDTKSYL 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + L  G    +KK+FE     V  L R+SY    +  L  G  RE++ K
Sbjct: 177 -ISLHVGSYHHVKKLFEKIGHSVLTLKRVSYANLTVDKLPEGMYRELTIK 225


>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 =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 79/223 (35%), Positives = 119/223 (53%), Gaps = 12/223 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS---TDHIEVDGVPLRKA 70
           +R+ K+I+  G+ASRR  E MI   RVKVNG   +RA +   +    D IE+DG  L  +
Sbjct: 3   ERLQKIISHWGVASRRHAEEMILSGRVKVNG---DRAYLGQKADPKCDRIEIDGRALHPS 59

Query: 71  ERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLT 125
            + +    L +KP+G+V T ++P GR  V D LP    +   +  VGRLD ++ G LL+T
Sbjct: 60  SQPQPLYLLLNKPLGVVCTCAEPQGRKAVLDLLPRQMRVGQGLHPVGRLDSDSTGALLIT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG 184
           NDG L  +L  P     + Y+V   G   +  L   ++GI++ G      QV  +     
Sbjct: 120 NDGELTFLLTHPRYHVAKTYQVLVQGCPPESVLEQWRQGILLSGKNTLPAQVRPIGKPSR 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           S   + V LREG+NR+I++V E   + V +L R + GP  L +
Sbjct: 180 SQTLLEVVLREGRNRQIRRVAEALGYPVVQLHRTAIGPIYLNS 222


>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 =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 76/212 (35%), Positives = 111/212 (52%), Gaps = 1/212 (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 +L   + + G      +V    + G    +++ +
Sbjct: 123 LLHPSHQVEKEYLVWVTGDVET-ALPILSGPMELDGEPLAPAKVARGRESGGVTQLSITI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +GKNR+++++      +V RL RI  G   L
Sbjct: 182 CQGKNRQVRRMCAQAGLEVTRLKRIREGQVSL 213


>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 =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 123/232 (53%), Gaps = 2/232 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVP 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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGS 185
           DG LA+ +  P  +  + Y     G +     + L++ G+ +        Q ++ TQ   
Sbjct: 133 DGELAQHVMHPKYEIEKTYIATVEGHIGGGVCHRLVRTGVQLDDGWIKLDQCSIITQNRE 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + V L  G+NR ++++F    + V RLIR   GP  LG L +GS R +S
Sbjct: 193 RSVLKVVLHSGRNRIVRRIFGSIGFPVTRLIRTQIGPISLGELKSGSYRILS 244


>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 =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 76/238 (31%), Positives = 128/238 (53%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ + +++ G+A+RR+ E +I    V VNG  +      V+   D + V G  +   E  
Sbjct: 6   RLQRYLSQCGVAARRKAEELITSGVVSVNGQRVTELGTKVVPGRDRVSVRGEAVYPEEPF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP G +T  +DP+ R TV + L  + +RV+ VGRLD  +EG+LLLTNDG L+  
Sbjct: 66  YVLL-NKPKGCLTAVTDPENRPTVMEYLHGLPARVVPVGRLDFYSEGVLLLTNDGDLSAR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQV-TLDTQKGSNAWVTV 191
           L+ P     + Y V+   QV +  L +L++G+ ++ G      Q+  L   K  + W+ +
Sbjct: 125 LQSPRHHVEKTYHVKVRDQVTERHLEVLRQGVRLEDGTVTRPAQIDMLGGTKSRHDWLVI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLG 246
            L EGK+R+I ++     + V +L R+++G      L  G  RE+++     LRE +G
Sbjct: 185 TLTEGKSRQIHRMLGVLGYTVMKLQRVAFGGLTFHGLRVGDARELTQAEVNDLRELVG 242


>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 =  116 bits (290), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 85/250 (34%), Positives = 130/250 (52%), Gaps = 11/250 (4%)

Query: 2   KDKNIVQENF-TPQ----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM- 55
           K +N+ Q +F +P     R+ KV+A+AG+ASRR  E +I   R++VNG ++    V V  
Sbjct: 116 KRQNVEQRDFGSPTGEGIRLQKVLAQAGVASRRHAEILIDAGRIEVNGKIVLTQGVRVNP 175

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVG 112
             D I VDGV +   E  + ++ +KP GL +T SD  GR  V D +    +   R+  VG
Sbjct: 176 HADIIRVDGVRINVNEDMQYFVLNKPRGLQSTMSDDMGRPCVGDIVGERIAAGQRLFHVG 235

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGIC 171
           RLD  TEGLLLLTNDG LA  L  P  +  + Y     G+ D+  +  L+ GI +  G  
Sbjct: 236 RLDAATEGLLLLTNDGELANRLMHPKYEVTKTYLATVLGEADKRLIKQLRDGIELDDGPA 295

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             D    +D  +G  + + + L EG+   ++++ +   + V RL+R      QLG    G
Sbjct: 296 KADFVQIVDAHQGK-SLIRIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTIQLGEQTPG 354

Query: 232 STREVSKKIL 241
           + R ++   L
Sbjct: 355 AVRALNSSEL 364


>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 =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 76/227 (33%), Positives = 117/227 (51%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE + +I    V VNG ++      +   D I+ DG  +  AE  R
Sbjct: 106 RLNKYLSNAGVCSRREADVLIQTGVVSVNGEVITEMGYKIKPGDKIQYDGETIN-AETKR 164

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G +TT  DP GR TV    + +   R+  VGRLD +T GLLL TNDG +A+ 
Sbjct: 165 YVLLNKPKGFITTMDDPLGRKTVMGLVIKACKERIYPVGRLDRDTTGLLLFTNDGDMAKK 224

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  ++Y V     V  + L  L  GI ++ G    D    +   K S+  V V 
Sbjct: 225 LTHPRYEATKIYHVEVDKPVQSEHLEQLMSGIELEDGTIKADKAEYVKDGK-SSREVGVE 283

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K
Sbjct: 284 IHSGKNRIVRRMFEKLGYEVVKLDRVQFASLTKKDLPRGYYRHLTEK 330


>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 =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 121/226 (53%), Gaps = 6/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++ + +ASRR+ E++I ++RVKVNG L+ +  V V   D I VD   ++ +E  
Sbjct: 2   ERLQKILSYSNVASRRKSEKLILEKRVKVNGKLVTKLGVKVSKKDIILVDDQIIKNSENC 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +      R+  VGRLD NT GLLL+TNDG L +
Sbjct: 62  -YYLINKPSGCISTVKDEKNRPTVIDLIKDTEKKRIYPVGRLDFNTTGLLLITNDGQLTK 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAW 188
            L  PS+   + Y V+ +  +   +L  L++G++I      +      +        + W
Sbjct: 121 KLTHPSSLIEKEYHVKINYCLSSLELKKLQQGVIIDENYLSVPKKIKILKKRLLPKPSTW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + + EGKN +I+K+ E   + + +LIR  Y    +  +  G  R
Sbjct: 181 LQIIITEGKNHQIRKMMEKLGFHILKLIRYRYAFLTIKGIKKGQYR 226


>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 =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 134/247 (54%), Gaps = 2/247 (0%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDH 59
           M+ K   QE  T + + +V ++AG  SR +  + I+  +V+VNG ++L          D 
Sbjct: 1   MEKKRNRQEKITLKTLERVFSKAGAGSRTDARKWISGGKVRVNGKVVLNPDHWVDPDHDK 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + ++G PL+ A ++ + LY KP G +TT+ DP+GR TV+  L  +   +  VGRLD++T 
Sbjct: 61  VTLEGKPLKAATKSYILLY-KPKGYLTTYRDPEGRPTVYALLGDVGKWLSPVGRLDLDTS 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 ILREQLG 246
            + E  G
Sbjct: 240 EVHELRG 246


>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 =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 127/238 (53%), Gaps = 17/238 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K+I++ GIASRR+ E+MI   RV++NG +++        TD IEV+G  L+ + R 
Sbjct: 3   ERVQKIISQWGIASRRQAEKMIVAGRVRLNGTVVQLGQKANPETDLIEVNGQRLKPSNRP 62

Query: 74  R--LWLYHKPIGLVTT-------HSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGL 121
           +    L +KP+G+V+T       ++  + R TV D LPS   +   +  VGRLD+ + G 
Sbjct: 63  QAIYLLLNKPVGVVSTCRNYRVCNTILEKRRTVLDLLPSTIRQGQGIHPVGRLDMESTGA 122

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG L   L  P     + YRV   G   +  L+  ++G+ + G      QV +  
Sbjct: 123 LILTNDGTLTYKLTHPRHHVPKTYRVWVKGHPPESILSAWRQGVDLSGRTTLPAQVRVLK 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTR 234
           Q+     + + L EG+NR+I++V +   + V  L R + GP QL       LL+G  R
Sbjct: 183 QQPDKTLLEIVLTEGRNRQIRRVADLLGYPVIHLHRTAIGPIQLQRPGEPILLSGHYR 240


>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 =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 90/231 (38%), Positives = 131/231 (56%), Gaps = 8/231 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---ER-AAVNVMSTDHIEVDGVPLR 68
            +++ K+++  G+ SRR +E+ I  + +K+NG ++   ER    N+ S            
Sbjct: 2   AEKIQKILSNCGVDSRRNIEKHILNKSLKINGKIVHIGERFLKKNIKSIF--LKKKKIFI 59

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           K E+T++ +YHKP+G + T  D   R TVF  LP +F S+ IS+GRLDINT GLLL TN 
Sbjct: 60  KNEKTKILIYHKPVGEICTKKDQYNRITVFKKLPKLFFSKWISIGRLDINTSGLLLFTNF 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y V   G++ + K+ LLKKGI+I        ++    +K  N 
Sbjct: 120 GELAHRLMHPSYRIKREYLVCVLGKILKKKILLLKKGILINNSISKFHEIIFLKKKKKNQ 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVS 237
           W  V L +GKNRE++ ++   N KVNRLIRI +G   L   L +G   E+S
Sbjct: 180 WFKVSLFQGKNREVRLLWNAINIKVNRLIRIKFGIITLPKFLKSGCFFELS 230


>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 =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 119/226 (52%), Gaps = 4/226 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKAERT 73
           +++V+++ G  SR     +I    V+VNG  +ER        + D +EV  + +R A R 
Sbjct: 15  LARVLSKLGYCSRARAFELIRADEVRVNG-KVERNPERPTDPARDRVEVAHIAIRAA-RF 72

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP GL+TT SD  GR T++  LP     V  VGRLD  +EGLLLLTND   A  
Sbjct: 73  LYYVVNKPRGLITTASDEKGRETIYSLLPPDSPWVAPVGRLDKASEGLLLLTNDSEWAAK 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P++   + Y V+      +  +  L +GI   G      +V++    G N W+ + L
Sbjct: 133 ITDPNSHLDKTYHVQVSTLPSEQMVEALSRGIRSDGELLLAKRVSILRAGGKNGWLEIVL 192

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EGKNR+I+++      +V RLIR++ GP  LG L  G  R ++ +
Sbjct: 193 EEGKNRQIRRMVAALQIEVLRLIRVAIGPLTLGELPKGGCRALTAE 238


>gi|327440834|dbj|BAK17199.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 247

 Score =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 81/235 (34%), Positives = 132/235 (56%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNG++++     V ++D IEV+GV L K ++ 
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLIVEGKVKVNGVVVKELGTKVSNSDTIEVEGVKLEKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              LY KP   ++  +D  GR TV D     +  R+  VGRLD +T GLLLLTNDG  + 
Sbjct: 62  YFLLY-KPRAYISAVTDDKGRKTVTDIFKKHVHQRIFPVGRLDYDTTGLLLLTNDGEFSN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           ++  P  +  + Y  R  G   +  L  L+ GI ++       +V++ +  +K   A   
Sbjct: 121 LMTHPKFKIDKTYIARVKGIPTKQGLMKLQSGIKLEDGKTAPAKVSMTSFDEKAGKAICE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
           + + EG+NR+++++FE     V +L R  +    L  L  G  R+++K   K+LR
Sbjct: 181 ITIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLTGLSPGEYRQLTKHEVKLLR 235


>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 =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 126/233 (54%), Gaps = 5/233 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           TP R++K +A +G+ SRR  +++I    V VNG ++ +   +V   D I VDG P+   E
Sbjct: 222 TPLRLNKFLASSGVCSRRVADQLIVDGHVSVNGEIVTQLGKHVTREDFISVDGKPV-SIE 280

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           +    L +KP   VTT SDP+ R T  D + +  + R+  VGRLD NT GLLLLTNDG L
Sbjct: 281 KKIYVLLNKPRNCVTTSSDPEKRLTAIDLVRNACNERIYPVGRLDRNTTGLLLLTNDGDL 340

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  ++Y+V     V  + +  +  GI ++ G  + D    +D  + + A V
Sbjct: 341 AAKLMHPKYEKKKIYQVTLDKPVSVEHMQQIASGIELEDGEIHADAISYVD--ENNLAIV 398

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +  G+NR ++++F+   ++V +L R+ +       L  G  R +++  +R
Sbjct: 399 GIEIHSGRNRIVRRIFKHLGYRVYKLDRVYFAGLTKKDLPRGRWRYLTEDEVR 451


>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 =  115 bits (289), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 121/233 (51%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ SRR+ + ++ Q RV ++G  +++    V     + VDG  +   E   
Sbjct: 24  RINKYIAHAGVCSRRDADDLVEQGRVHIDGERVDQHGTRVREGQTVTVDGEEVYPLEFEY 83

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L L +KP   ++T  DP  R TV D +       S +  VGRLD NT G+LL++NDG LA
Sbjct: 84  LLL-NKPKDTISTTDDPKDRRTVLDAIGVPEDNPSGLFPVGRLDRNTTGVLLVSNDGDLA 142

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P  +  ++Y VR    V   +L+ LK+G+ +  G    D    LD Q+ ++  + 
Sbjct: 143 HRLMHPRYEIPKIYYVRLQDDVKPHQLDQLKRGVELSDGAAAADQVAYLDPQRKTD--IA 200

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L EG+NR+I+++ E     + +L R  Y     G L  G  R +  + +RE
Sbjct: 201 LELHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRLEPEEVRE 253


>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 =  115 bits (289), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++ +  V +     I +D   V      
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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             +  P  ++L+ Y+    GQV++ ++N L KG+ I        Y    +  D  K   +
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQVNQLIKGVYIDNNYLTKAYSSKLIKYDKLKNV-S 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+
Sbjct: 183 IVELTINEGKKHHVKKMFESIQAQLLKLKRTRIEFLEIDNLKPGQYREL 231


>gi|254525127|ref|ZP_05137182.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722718|gb|EED41243.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 240

 Score =  115 bits (289), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 82/226 (36%), Positives = 118/226 (52%), Gaps = 5/226 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG PL   +R  
Sbjct: 5   LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIGQPAPPIEVDGQPLAAPQRLY 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  
Sbjct: 65  LML-NKPRGVVTTVQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAR 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+  G  D   L  L+ G+  +G       V +       AW+ V L
Sbjct: 124 LTDPQTGPDKTYHVQVDGMPDHATLAALQAGVEDEGEFLAAHAVRVLRSGDKTAWLEVVL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVS 237
            EG+NR I+++   F+ +V RL+R++ G   LG L  G  R  EVS
Sbjct: 184 DEGRNRHIRRLLAAFDLQVLRLVRVAIGGLVLGDLGKGQWRVLEVS 229


>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 =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 77/228 (33%), Positives = 121/228 (53%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+++ +A  GIASRR  ++M+ + RV +NG+L     V V+   D + VDG    + E  
Sbjct: 14  RINRYLAMCGIASRRAADQMVLEGRVTINGVLASEPGVKVVPGKDEVIVDGSKFAQPEGR 73

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++TT SD   R  V D +  +  RV  VGRLD  T G+LLLTNDG LA 
Sbjct: 74  KIYILFNKPRNVITTSSDERNREMVLDFI-DVNERVYPVGRLDRKTTGVLLLTNDGMLAN 132

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVT 190
            L  PS+   + Y         Q  L LL  G+ +   G      Q  +    GS  W++
Sbjct: 133 KLMHPSSNVKKEYIAVLDAPFPQASLPLLTGGMRLSDTGEKVSPCQAKI-MGDGSQVWIS 191

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   EGKN +++++F+   ++V RL R +Y    +G L  G  R +++
Sbjct: 192 I--HEGKNHQVRRMFKTLGFEVTRLDRPTYAGLTVGDLRRGQWRHLTR 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 =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 125/234 (53%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E+MI   RV+V+G L+      V  T   I VDG  +R + + 
Sbjct: 20  RLQKLLAQAGFGSRRKCEQMITDGRVEVDGELVTELGTRVDPTHQQIRVDGSRVRISNKH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  ITLALNKPRKVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-----W 188
           +  P  +  + Y     G++       + + +V  G+   D  + LD     +A      
Sbjct: 140 VMHPKYEVEKTYIATLEGRIS----GTVCRRLVTTGVQLDDGWIKLDRCAIIDATHDTTI 195

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R
Sbjct: 196 VKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKSGSYRVLSQTEVR 249


>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 =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 72/205 (35%), Positives = 111/205 (54%), Gaps = 7/205 (3%)

Query: 34  MIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLW-LYHKPIGLVTTHSDP 91
           MI +  V VNG  +    + V   +D I VDG PLRK    +++ + +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 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----AWVTVGLREGKNREIKKVFE 206
           + +  +L  LKKG+ I G       +    + G N      W  + + EGKNR+I+++F 
Sbjct: 121 KPEPFQLEKLKKGVSIVGGKVSARHIEKIKKTGDNKSEKYEWYKIVITEGKNRQIRQMFA 180

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAG 231
              + V RL R++ G  ++G +  G
Sbjct: 181 KIGFDVMRLQRVAIGRLRMGAVKTG 205


>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 =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/237 (34%), Positives = 126/237 (53%), Gaps = 7/237 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ SRR  E+++A+  V+VNG +  +  + V  +TD I VDG  L      
Sbjct: 11  RLQKVLAQAGLGSRRRCEQLMAEGHVEVNGEITTQMGIRVDPATDVIHVDGRRLPPPSDH 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G+VT+ +D  GR  +   L     R+  VGRLD +T GLL++TNDG LA  
Sbjct: 71  VYVLLNKPRGVVTSMADERGRPDLRSLLADRTERLFHVGRLDTDTSGLLMMTNDGDLAHR 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS ++ + Y     G VD      LK G+ +  G    D     DT +G  + V + 
Sbjct: 131 LAHPSFEFTKTYVALVEGVVDPAVGTRLKSGVELDDGPATVDRFRIKDTSQG-RSLVELD 189

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           L  G+NR ++++       V  L R ++GP +L  L +G  R+++    R++LG  L
Sbjct: 190 LHMGRNRIVRRLLAEVGHPVVELTRTAFGPLRLAGLGSGRARDLT----RDELGALL 242


>gi|330723277|gb|AEC45647.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyorhinis MCLD]
          Length = 242

 Score =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 120/229 (52%), Gaps = 12/229 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL---ERAAVNVMSTDHIEVDGVPLRKA 70
           +++ K+I++ G  SRR  E++I Q RV VN  L    ++A+ +    D I++D   L+KA
Sbjct: 3   EKIQKLISQTGYCSRRNAEKLILQNRVFVNNQLATIGQKASFD----DEIKIDNQILKKA 58

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    + ++KP  +V T  D   R  + D  P     +  VGRLD NT G++LLTNDG L
Sbjct: 59  EHI-YYAFYKPKRVVCTREDNFNRKKIIDFFPKK-EYLFPVGRLDFNTTGIILLTNDGEL 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  Q  R Y V  +G +  +++N   K ++         Q+    +K +N ++ 
Sbjct: 117 ANKLIHPKFQIERTYLVHTNGDLSDEQINFANKNVIKLNNEINSRQII--KKKATNKYI- 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V L++G N  +K++F+ F  +V  L R+ +    L  L  G  R+++ K
Sbjct: 174 VKLKQGSNHHVKRLFDHFQIEVLDLKRVQFASINLANLSLGQYRKLTPK 222


>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 =  115 bits (288), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 120/229 (52%), Gaps = 12/229 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL---ERAAVNVMSTDHIEVDGVPLRKA 70
           +++ K+I++ G  SRR  E++I Q RV VN  L    ++A+ +    D I++D   L+KA
Sbjct: 3   EKIQKLISQTGYCSRRNAEKLILQNRVFVNNQLATIGQKASFD----DEIKIDNQILKKA 58

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    + ++KP  +V T  D   R  + D  P     +  VGRLD NT G++LLTNDG L
Sbjct: 59  EHI-YYAFYKPKRVVCTREDNFNRKKIIDFFPKK-EYLFPVGRLDFNTTGIILLTNDGEL 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  Q  R Y V  +G +  +++N   K ++         Q+    +K +N ++ 
Sbjct: 117 ANKLIHPKFQIERTYLVHTNGDLSDEQINFANKNVIKLNNEINSRQII--KKKATNKYI- 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V L++G N  +K++F+ F  +V  L R+ +    L  L  G  R+++ K
Sbjct: 174 VKLKQGSNHHVKRLFDHFQIEVLDLKRVQFASINLANLSLGQYRKLTPK 222


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 75/223 (33%), Positives = 121/223 (54%), Gaps = 4/223 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+IA +G+ SRR+ E  I Q RVKV+G ++    V       IEVDG  + + ++  
Sbjct: 3   RLQKIIAASGLTSRRKAEEWILQGRVKVDGQVVTELGVKPRKGALIEVDGKAIAREDKV- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP  ++ T +D   R TV D +  +  RV  VGRLD +T G+L++TNDG  A  +
Sbjct: 62  YYVMNKPKKVLCTLNDEHDRRTVVDLMMDVPQRVFPVGRLDYDTTGVLIMTNDGEFANEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGI--CYGDMQVTLDTQKGSNAWVTV 191
             P     +VY V  +G +  +++  L++G+V+  GI      + VT            +
Sbjct: 122 IHPRYHIAKVYEVTINGILKTEEIKQLEQGVVLDDGIKTLPAKLWVTNKDFAHEQTMFEL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            ++EG+NR+IK++ E F ++V RL R S GP  +  L  G  R
Sbjct: 182 TIQEGRNRQIKRMLEVFGYEVRRLHRRSLGPITVRGLNPGEYR 224


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 115/225 (51%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K ++  G+ SRR+ +++I + RVKVNG+++      +    D +EVDG  L K  R 
Sbjct: 9   RLNKYLSMCGVTSRRKADQLIKEGRVKVNGLVVRELGYKIDPHRDTVEVDGKVL-KPPRK 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R    +KP   +T      G     D 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              G+   +K+    F  KV RLIRI+ GP +LG L  G  R+++
Sbjct: 188 FTIGRKHIVKRYCAHFGHKVLRLIRIAIGPIRLGKLSPGKWRDLT 232


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 123/228 (53%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +I   RV+VNG ++    + V  + D I VDGV +   E  
Sbjct: 82  RLQKVLAQAGVASRRHAEILIDAGRVEVNGKIVMTQGMRVNPNVDVIRVDGVRVNVNENL 141

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           + ++ +KP GL +T SD  GR  V D +    S   R+  VGRLD  TEGLLLLTNDG L
Sbjct: 142 QYFVLNKPRGLQSTMSDDMGRPCVGDIVGERISAGQRLFHVGRLDAATEGLLLLTNDGEL 201

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+ D+  +  L+ GI +  G    D+   +DT +G  + +
Sbjct: 202 ANRLMHPRYEVSKTYLATVLGEADKRLVKQLRDGIELDDGPAKADLVQIIDTFQG-KSLI 260

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L EG+   ++++ +   + V RL+R      QLG    G+ R ++
Sbjct: 261 RIELHEGRKHIVRRMLKTAGFPVQRLVRTKIHTIQLGEQTPGAIRALN 308


>gi|312876843|ref|ZP_07736820.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796358|gb|EFR12710.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
          Length = 230

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/215 (33%), Positives = 114/215 (53%), Gaps = 2/215 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLY 78
           +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    +    + 
Sbjct: 1   MAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRISLQMQKVYIML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G++++  D  GR TV D +   +  RV  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 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           NR+I+K+      +V +L R++ G  QLG L  G 
Sbjct: 181 NRQIRKMCAQIGHEVLKLKRVAIGKLQLGKLKEGE 215


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/228 (37%), Positives = 127/228 (55%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           R+ KV+++AG+ASRR  E+MI + RV+VNG I+LE        T  I VDG  +   A+ 
Sbjct: 17  RLQKVLSQAGVASRRAAEQMIVEGRVEVNGEIVLELGTRVDPDTAVIHVDGNRIMVNADL 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T L L +KP G++ T SD  GR  + D L     R+  VGRLD+++EGLLL+TNDG LA 
Sbjct: 77  THLLL-NKPKGILCTMSDDQGRPCIGDYLRERQGRLYHVGRLDVDSEGLLLITNDGELAH 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  PS + L+ Y     G + ++    L+ GI ++ G    D    +D  +G  A V V
Sbjct: 136 RLMHPSYRILKTYLAEVPGPIPKNLGRELRNGIELEDGPVKVDSFKLVDVNEG-RALVEV 194

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L EG+   ++++ +     V RL+R + G  +L T   G+ R + +K
Sbjct: 195 VLHEGRKHVVRRLLKQVGHPVLRLVRTAVGDVRLTTERQGAIRPLDRK 242


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 83/230 (36%), Positives = 122/230 (53%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLRK 69
           RV K+IA++G+ SRR+ E+MI++  V VNGI   + ++A++N    D I+V+G  + L K
Sbjct: 6   RVQKLIAQSGLMSRRDAEKMISKGLVFVNGIKSSIGDKASMN----DEIKVNGKIINLTK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               + +L +KP   +TT  DP GR TV D L +   R++ VGRLD NT G+LLLT D  
Sbjct: 62  NTVFKYYLLNKPKNTITTSKDPKGRHTVID-LINTSERIVPVGRLDRNTTGVLLLTTDYE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  RVYR R    +   +   L  GI I     G M   +  Q  + +++
Sbjct: 121 LVNKLTHPKYEIERVYRARIDSPLTLKEFRELNAGIEID----GKMSYQIVDQVDTKSYL 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + L  G    +KK+FE     V  L R+SY    +  L  G  RE++ K
Sbjct: 177 -ISLHVGSYHHVKKLFEKIGHSVLTLKRVSYANLTVDKLPEGMYRELTIK 225


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 119/227 (52%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA  GIASRR+ E +I + R+KVNG +++    NV    D +E D   ++ +E  
Sbjct: 2   RINKYIASCGIASRRKAEEIILEGRIKVNGSIVKELFFNVDEEKDIVEFDNKKVKPSENY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +TT  D   R +V D L  +  RV  +GRLD  T GLL+LTNDG L   
Sbjct: 62  IYIVLNKPEGYITTVKDQFNRPSVIDILKDVKERVYPIGRLDYETSGLLILTNDGDLTYK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y     G +  D++   + G+ I+        ++VT + ++ + +   +
Sbjct: 122 LTHPKHEIDKTYVASVKGIISGDEIRKFETGLKIEDYTTAPAKIKVTKENKEKNYSVCEI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++
Sbjct: 182 TIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTE 228


>gi|313665476|ref|YP_004047347.1| pseudouridylate synthase [Mycoplasma leachii PG50]
 gi|312949302|gb|ADR23898.1| pseudouridylate synthase [Mycoplasma leachii PG50]
          Length = 252

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 116/229 (50%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KVI+  G  SRR  E++I + R+KVN  ++ +  V +     I +D   V      
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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             +  P  ++L+ Y+    GQV + ++N L KG+ I        Y    V  D  K   +
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVSKQQVNQLIKGVYIDNNYLTKAYSAKLVKYDKLKNV-S 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+
Sbjct: 183 IVELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIDNLKPGQYREL 231


>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 =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 72/223 (32%), Positives = 121/223 (54%), Gaps = 2/223 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K++++AG+ASRR  E +I + RV+V+G  +    + V+ +  I V+G  +     
Sbjct: 41  PVRLQKLLSQAGVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQRIHTDAA 100

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++W ++KP+G V+T    D R  + D    +  RV  VGRLD+ T GL+LLTN+G LA 
Sbjct: 101 LQVWAFNKPVGTVSTMQPEDDRPCLGDWATKLPQRVFHVGRLDVATSGLILLTNNGDLAN 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + Y     GQV      +L++G+ ++ G+   D    ++ ++GS + V +
Sbjct: 161 RLVHPRYEVPKTYVAMVQGQVKPGLGKVLRRGVELEDGVTKVDTFKLVEVRRGS-SIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            L  GKNR ++++       V+ L R + G  +LG L  G  R
Sbjct: 220 TLHSGKNRVVRRLLSEVGHPVSALTRTAIGTLRLGDLKEGHFR 262


>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 =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 126/241 (52%), Gaps = 10/241 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVP 66
           QE+    R+ K++A AG  SRR+ E +I   RV+V+  L+      V  S   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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----T 181
           DG L++ +  P  +  + Y     G+++     ++ + +V QG+   D  + LD      
Sbjct: 133 DGELSQHVMHPKYEVEKTYIATVEGKIN----GMVCRRLVSQGVNLEDGWIKLDRCAIID 188

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q      V V L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +
Sbjct: 189 QNHDATIVKVVLHSGKNRIVRRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEV 248

Query: 242 R 242
           R
Sbjct: 249 R 249


>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 =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 121/224 (54%), Gaps = 6/224 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G  SRR+ + +I+Q RV +N     +  + V   D + +DG  ++      
Sbjct: 2   RLNKYIAESGFCSRRKADELISQNRVTINKDT-AKLGMEVRDGDIVRIDGEKIKVDTDYE 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  ++ T+SD   R    D + S   R+ + GRLD  TEG++L++NDG     +
Sbjct: 61  YYLLYKPKKVICTNSDNFARRLAVDFIRSK-KRLFTYGRLDYMTEGIILVSNDGDTYNKV 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y  +    ++   L  L+KGI+I G      ++    +K  +A V V + 
Sbjct: 120 MHPRKKLFKTYIAKLDKPIEDKDLARLEKGILIDGQKTAPAKI----KKTDDAEVKVSIF 175

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           EG+NR+I+K+FE  ++ V  L R++ G F++G L  G  R++++
Sbjct: 176 EGRNRQIRKMFENLHYNVKELKRVTIGEFKIGNLKPGEYRKLTE 219


>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 =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 121/233 (51%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ SRR+ + ++ Q RV ++G  +++    V     + VDG  +   E   
Sbjct: 12  RINKYIAHAGVCSRRDADDLVEQGRVHIDGERVDQHGTCVREGQTVTVDGEEVYPLEFEY 71

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L L +KP   ++T  DP  R TV D +       S +  VGRLD NT G+LL++NDG LA
Sbjct: 72  LLL-NKPKDTISTTDDPKDRRTVLDAIGVPEDNPSGLFPVGRLDRNTTGVLLVSNDGDLA 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P  +  ++Y VR    V   +L+ LK+G+ +  G    D    LD Q+ ++  + 
Sbjct: 131 HRLMHPRYEIPKIYYVRVQDDVKPHQLDQLKRGVELSDGAAAADQVAYLDPQRKTD--IA 188

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L EG+NR+I+++ E     + +L R  Y     G L  G  R +  + +RE
Sbjct: 189 LELHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRLEPEEVRE 241


>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 =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 72/223 (32%), Positives = 121/223 (54%), Gaps = 2/223 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K++++AG+ASRR  E +I + RV+V+G  +    + V+ +  I V+G  +     
Sbjct: 41  PVRLQKLLSQAGVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQRIHTDAA 100

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++W ++KP+G V+T    D R  + D    +  RV  VGRLD+ T GL+LLTN+G LA 
Sbjct: 101 LQVWAFNKPVGTVSTMQPEDDRPCLGDWATKLPQRVFHVGRLDVATAGLILLTNNGDLAN 160

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P  +  + Y     GQV      +L++G+ ++ G+   D    ++ ++GS + V +
Sbjct: 161 RLVHPRYEVPKTYVAMVQGQVKPGLGKVLRRGVELEDGVTKVDTFKLVEVRRGS-SIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            L  GKNR ++++       V+ L R + G  +LG L  G  R
Sbjct: 220 TLHSGKNRVVRRLLSEVGHPVSALTRTAIGTLRLGDLKEGHFR 262


>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 =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 68/171 (39%), Positives = 101/171 (59%), Gaps = 2/171 (1%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
           TR+ LYHKP+G + +  DP+GR  +F  LP +   R ++VGRLD+NT+GL+LLTN+G LA
Sbjct: 17  TRVLLYHKPVGELVSRRDPEGRPLIFSRLPRLELGRWVAVGRLDVNTQGLILLTNNGELA 76

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    R Y VR  G V +  +  L  G+ ++        V     +G+N W  V
Sbjct: 77  HRLMHPSHAVEREYAVRILGTVSEAVIERLLDGVQLEDGPARFESVAEAGGEGANRWFHV 136

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            +REG+NR +++++E  N  V+RLIR+ YG   L   L AG++ E+  + L
Sbjct: 137 VVREGRNRLVRRLWESQNLVVSRLIRVRYGDIVLPPRLRAGASIELEGEAL 187


>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 =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 76/229 (33%), Positives = 118/229 (51%), Gaps = 5/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G+ SRRE +  I    V+VNG L+      V   D +  DG  +   E+ +
Sbjct: 73  RLNKYIANSGVCSRREADTYIEHGSVEVNGNLVTEMGYKVQPDDVVRFDGTGI-TPEQKK 131

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  D  GR TV D +  +   R+  VGRLD NT GLLL TNDG LA+ 
Sbjct: 132 YILLNKPKNYITTMDDDRGRKTVMDLISNATKERIYPVGRLDRNTTGLLLFTNDGELAKK 191

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     ++Y      +++   L  L+  ++I+G   + D    +D Q  S   V + 
Sbjct: 192 LTHPKHDVRKLYHASLDKKLELKDLEKLRGEVLIEGKKVFIDAVSYVDGQPKSE--VGIE 249

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  G+NR ++K+FE   +KV++L R+ +       L  G  RE++ + L
Sbjct: 250 IHSGRNRIVRKIFEHLGYKVSKLDRVIFAELTKRNLPRGRWRELTNQEL 298


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 120/233 (51%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E MIA  RV VNG ++      +    D + VD   ++     
Sbjct: 21  RLQKVMAAAGVASRRVCEDMIAAGRVTVNGEVVTEPGRRIDPDVDEVAVDDQAVQLDTSK 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+G+ ++  D  GR  + +       R+ +VGRLD  T GLL+LTNDG LA V
Sbjct: 81  RYLMLNKPVGIYSSLRDERGRPDLREFTEEFEERLFNVGRLDAETSGLLILTNDGDLAHV 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS   L+ Y  +  G+V    +  L +G+ ++ G    D    L +  G    V + 
Sbjct: 141 LAHPSFGVLKTYIAKVTGRVTPQTIQRLTQGVDLEDGPIQADRARIL-SGGGDQTLVEIT 199

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L  G+NR ++++ +     V  L+R  +GP  LG+L  G  R+++   L + L
Sbjct: 200 LHSGRNRIVRRMLDEVGHPVEELVRRQFGPLHLGSLGVGRVRDLTSDELGQLL 252


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 123/232 (53%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +I Q RV+VN  ++    V V  + D I VDGV +   E  
Sbjct: 81  RLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVDPNNDVIRVDGVRIHINEDL 140

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 141 EYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLTNDGEL 200

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+     ++ L+ G+ ++ G    D    +D  +G  + +
Sbjct: 201 ANRLMHPKYEVSKTYLATVRGEATNKLVSALRDGVELEDGPAKADFAQIIDVFQGK-SLL 259

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EG+   ++++F+   + V RL+R      QLG    GS R ++   L
Sbjct: 260 RIEIHEGRKHIVRRLFDELGFPVERLVRTKLHTVQLGDQKPGSLRALNSSEL 311


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 117/225 (52%), Gaps = 1/225 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A AGIASRR  E++I + RV+VNG  +    V V  + D + VDG   R   + 
Sbjct: 4   RLQKFLAMAGIASRRACEKLILEGRVQVNGKTVRELGVKVDPALDEVRVDGNVCRLNNKP 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G++TT  DP GR TV D L  +  RV  VGRLD +TEGLL+LTNDG L+  
Sbjct: 64  IYILMNKPKGILTTVKDPFGRPTVIDLLKGVRERVFPVGRLDKDTEGLLILTNDGELSYR 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G  D+     L++GIV++       +V +         + + +
Sbjct: 124 LTHPKHEIEKTYVAKVVGTPDESDFIRLRRGIVLEDGRTAPAKVRILKAGRDFTVLEIII 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EG+ R+++++ +     V  L R   G   L  L  G  R +++
Sbjct: 184 HEGRKRQVRRMCKAIGHPVISLKRTRIGKLNLRGLAPGCWRYMTE 228


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 119/232 (51%), Gaps = 11/232 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD ++    P+   E+
Sbjct: 17  PLRLNKFLANAGVCSRREADEFIQAGLVTVNGEVVTELGTKILRTDEVKFHDAPV-TLEK 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 76  KVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTGVLLLTNDGDLA 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----A 187
             L  P     +VY V     +    ++ +++GI ++     D ++  D  + ++    A
Sbjct: 136 SKLTHPKFLKKKVYHVHLDKNLTAHDMDQIREGITLE-----DGEIKADAVEYADDRDKA 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K
Sbjct: 191 QVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFLTEK 242


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 123/232 (53%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +I Q RV+VN  ++    V V  + D I VDGV +   E  
Sbjct: 81  RLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVNPNNDVIRVDGVRIHINEDL 140

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 141 EYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLTNDGEL 200

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+     ++ L+ G+ ++ G    D    +D  +G  + +
Sbjct: 201 ANRLMHPKYEVSKTYLATVRGEATNKLVSALRDGVELEDGPAKADFAQIIDVFQG-KSLL 259

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EG+   ++++F+   + V RL+R      QLG    GS R ++   L
Sbjct: 260 RIEIHEGRKHIVRRLFDELGFPVERLVRTKLHTVQLGDQKPGSLRALNSSEL 311


>gi|301320594|gb|ADK69237.1| pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides SC
           str. Gladysdale]
          Length = 252

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 117/229 (51%), Gaps = 7/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   V      
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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             +  P  ++L+ Y+    GQV++ ++N L KG+ I        Y    V  D  K + +
Sbjct: 124 NFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKNT-S 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            V + + EGK   +KK+F+    ++ +L R      ++  L  G  RE+
Sbjct: 183 IVELTINEGKKHHVKKMFDSIQAQLLKLKRTKIEFLEIADLKPGQYREL 231


>gi|289664226|ref|ZP_06485807.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 285

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 78/238 (32%), Positives = 125/238 (52%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +  H  I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQHSSITVDGSPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      +G+     +V++  +   NA
Sbjct: 158 TVTDPTTGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPEGEGMLLRAKRVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RLIR++ GP  +G L  G+ R +S + +R  L
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLIRVAIGPLAMGELCKGAWRMLSAEEVRALL 275


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 113/224 (50%), Gaps = 5/224 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +A  G+ASRR  E  IA  RV VNG ++      V+  D + VDG  +   E  R
Sbjct: 25  RLQVYLAHCGVASRRSCETYIADGRVSVNGTVVTVPGTKVLPDDTVCVDGKRVTLEETKR 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G V + SD  GR T    L P    R+ +VGRLD+ + GL+L TNDG  A  
Sbjct: 85  YVLLNKPAGFVCSLSDEKGRQTAASLLEPHYSERLYNVGRLDMFSAGLVLFTNDGEFAAR 144

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS++  + Y V     V         KGI +  + Y         ++ ++  + + L
Sbjct: 145 VSHPSSEMEKEYVVDTSLPVPPALAEKFVKGIRVDNVFYR----CKSAERLNSRRMRIVL 200

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EGKNREI++VFE FN  V +L+RI  G   +  L  G  R+++
Sbjct: 201 IEGKNREIRRVFEAFNIGVKQLVRIRIGNLNIQGLGPGEFRDLT 244


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 116/227 (51%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR-KAER 72
           R++K IA AGIASRR+ E ++++ R+KVNG ++      V    D +E DG  +   +E+
Sbjct: 2   RINKYIASAGIASRRKAENLVSEGRIKVNGQIIYDLGYQVNEDKDIVEYDGKKIDINSEK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +T+  D  GR  V D +  I  R+  VGRLD  T GLLL+TNDG L  
Sbjct: 62  LVYILLNKPEGYITSSKDQFGRKDVMDLVTDIKERIYPVGRLDYETSGLLLMTNDGDLTY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVT- 190
            +  P  +  + Y     G    ++L   + G+ I+       ++  L T    N  V  
Sbjct: 122 KITHPKHEITKTYIASVKGIPTSEELERFENGLEIEDYVTSKAKIRVLKTDVKKNYSVCR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V + EG+NR+++K+F   N  V  L R++ G   +  +  G  R ++
Sbjct: 182 VSIHEGRNRQVRKMFNAINHPVMNLKRVALGKISVNNVEVGKYRHLT 228


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 119/227 (52%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA  GIASRR+ E +I   R+KVNG +++  + N+    D +E D   ++ +E  
Sbjct: 2   RINKYIASCGIASRRKAEEIILGGRIKVNGSVVKELSFNIDEEKDIVEFDNKKVKPSENY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +TT  D   R +V D L  +  RV  +GRLD  T GLL+LTNDG L   
Sbjct: 62  IYIVLNKPEGYITTVKDQFNRPSVIDILKDVRERVYPIGRLDYETSGLLILTNDGDLTYK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y     G +  D++   + G+ I+        ++VT + ++ + +   +
Sbjct: 122 LTHPKHEIDKTYVASVKGIISDDEIRQFETGLKIEDYTTAPAKIRVTKENKEKNYSVCEI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++
Sbjct: 182 TIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTE 228


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/226 (36%), Positives = 120/226 (53%), Gaps = 12/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R+  ++ARAG+ASRR+ E +I Q  V+VNG +       V   D +EV G   R+ E  R
Sbjct: 5   RLQALLARAGVASRRQAEVLIRQGLVRVNGEVAH-LGQKVGPDDLVEVAG---RRVEWPR 60

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            RL L  HKP G  TT SDP  R TVF+ LP +   + +VGRLD  +EGLLL TNDG L 
Sbjct: 61  ERLVLALHKPRGYTTTRSDPHARRTVFELLPEVPG-LQAVGRLDRESEGLLLFTNDGELL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VYRV      ++  L       +++G+   D      + + +     +
Sbjct: 120 FRLTHPRYGVKKVYRV----WTERGTLPEAVCRKLVEGVALEDGPARALSCRPAQGGAIL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S
Sbjct: 176 TLGEGRKREVRRMLQAVGYPVKRLLRLQVGPIRLGNLPPGRWRRLS 221


>gi|289668818|ref|ZP_06489893.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 285

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 128/245 (52%), Gaps = 10/245 (4%)

Query: 10  NFTPQR-VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVP 66
           N  P+  +++V+++ G+ SR E  R IA  RV V+  ++      + +  H  I VDG P
Sbjct: 32  NAAPRHGLARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQHSSITVDGSP 91

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           L    R  L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +
Sbjct: 92  LAGPARCYLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFS 150

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLD 180
           ND   A  +  P+T   + Y V+   +    +L  L+ G+V      +G+     +V++ 
Sbjct: 151 NDPQWAATVTDPTTGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPEGEGMLLRAKRVSVL 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +   NAW+ + L EG+NR+I+++    +  V RLIR++ GP  +G L  G+ R +S + 
Sbjct: 211 REGERNAWLEIVLDEGRNRQIRRLLAAVDIGVLRLIRVAIGPLAMGELCKGAWRMLSAEE 270

Query: 241 LREQL 245
           +R  L
Sbjct: 271 VRALL 275


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 121/233 (51%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +      
Sbjct: 46  RLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPKVDVIRVDGVRVNVNNNH 105

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
           + ++ +KP G+ +T SD  GR  + D +    S    +  VGRLD +TEGL+LLTNDG L
Sbjct: 106 QYFVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQGLFHVGRLDADTEGLILLTNDGEL 165

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+ D+  +  LK G+ +  G    D    +D  +G  + V
Sbjct: 166 ANRLSHPKYEVSKTYIAEVLGEADRSLVTTLKNGVELDDGPAAADYVQIVDVHQG-RSLV 224

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+   ++++ +   + V  L+R      QLG    G+ R ++   LR
Sbjct: 225 RVQLHEGRKHIVRRMLKAAGYPVQYLVRTKLHTVQLGEQKPGTIRALNDNELR 277


>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 =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 126/272 (46%), Gaps = 33/272 (12%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M + +  +    P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D 
Sbjct: 1   MGEVSDCESRIVPMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDE 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           + VDG  +R A+     + HKP G VTT SDP GR TV + +P+  +  +  +GRLD +T
Sbjct: 61  VAVDGAVVRLADGPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI------------- 165
            GLLL + DG L   L  P     + Y     G+  +  L LL++GI             
Sbjct: 121 TGLLLFSTDGELGNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVR 180

Query: 166 VIQGICYGDMQVTLD-----TQKGSNAWVTV-------------GLREGKNREIKKVFEF 207
           V++G      +  L+       + S  +  V             G+REG+ R++K++   
Sbjct: 181 VVEGGAARHAERLLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAA 240

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               V  L R S+GP +LG L  G+ R +  +
Sbjct: 241 VGHPVLALHRDSFGPLELGDLPRGAWRALDAE 272


>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 =  114 bits (285), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/224 (34%), Positives = 117/224 (52%), Gaps = 3/224 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           +++ +++ G+ SR E  R IA  RV V+G ++      ++   H + +DG PL  +ER  
Sbjct: 34  LARTLSKLGLCSRTEAVRWIAAGRVAVDGRIVTDPEFPILRGRHRLALDGAPLSASERLY 93

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GLVTT  D  GR TV+          +  VGRLD  +EGLLL TND   A  
Sbjct: 94  LML-NKPRGLVTTAQDERGRETVYRCFDGAGLPWLAPVGRLDKASEGLLLFTNDPQWAAR 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T   + Y V+     D   L  ++ G++  G      QV L  Q   +AW+ + L
Sbjct: 153 VTDPGTGPDKTYHVQVDVLPDAALLQRMRAGVMADGEALCAKQVRLLRQGERHAWLEIVL 212

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EG+NR+I+++   F   V RL+R++ G   LG L  G+ R +S
Sbjct: 213 DEGRNRQIRRLLAAFGVDVVRLVRVAIGTLVLGELGKGAWRTLS 256


>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 =  114 bits (285), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 79/228 (34%), Positives = 123/228 (53%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +I   RV+VNG ++      V  ++D I VDGV +   E  
Sbjct: 90  RLQKVLAQAGVASRRHAEILIDNGRVEVNGRIVTTQGTRVNPNSDVIRVDGVRININEDL 149

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 150 EYFVLNKPRGMHSTMSDDLGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLTNDGEL 209

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+   + +  L+KGI ++ G    D    +DT +G  + +
Sbjct: 210 ANRLMHPKYEVRKTYLATVRGEAGPNLVTTLRKGIELEDGPAKADYVQIIDTFQGK-SLI 268

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+   ++++ +   + V RL+R      QLG    GS R ++
Sbjct: 269 RLEIHEGRKHIVRRMLDEAGFPVERLVRTKLHTVQLGEQKPGSLRALN 316


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 118/226 (52%), Gaps = 3/226 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-MQVTL--DTQKGSNAWVT 190
           +  P  ++ + Y+    G+V + ++N L KG+ I+   +   +Q  L    Q+   + + 
Sbjct: 122 VMHPRYEFFKTYQGLCKGKVSKQQVNQLLKGVKIEDDYFTKAIQAELLNYDQEKDQSIIE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EGK   +K++F      + +L R      ++  L  G  RE+
Sbjct: 182 MTIAEGKKHHVKQMFSAIEANLMKLKRTKIEFLEVDDLEVGRYREL 227


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 119/233 (51%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E MIA  RV VNG  +      +    D + VD   ++     
Sbjct: 26  RLQKVMAAAGVASRRVCEDMIAAGRVTVNGETVTEPGRRIDPDVDEVAVDDQAVQLDTSK 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP+G+ ++  D  GR  + +       R+ +VGRLD  T GLL+LTNDG LA V
Sbjct: 86  RYLMLNKPVGIYSSLRDERGRPDLREFTEEFEERLFNVGRLDAETSGLLILTNDGDLAHV 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS   L+ Y  +  G+V    +  L +G+ ++ G    D    L +  G    V + 
Sbjct: 146 LAHPSFGVLKTYIAKVTGRVTPQTIQRLTQGVDLEDGPIQADRARIL-SGGGDQTLVEIT 204

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L  G+NR ++++ +     V  L+R  +GP  LG+L  G  R+++   L + L
Sbjct: 205 LHSGRNRIVRRMLDEVGHPVEELVRRQFGPLHLGSLGVGRVRDLTSDELGQLL 257


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 80/238 (33%), Positives = 131/238 (55%), Gaps = 24/238 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
            R++K ++  GIASRR +++ I + R+KVNG++     ++V   D I +D   +  ++ E
Sbjct: 1   MRINKFLSSLGIASRRAIDKYIEEGRIKVNGVITS-TGIDVTEDDEIYIDNKKIETKRIE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ +++  SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSASSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDT 181
             L  P ++  + Y ++  G+V ++++  LKKG++          I GI Y       D 
Sbjct: 119 NRLVHPKSEIYKKYYIKVFGEVKKEEIEELKKGVLLEDGKTLPAKISGIKY-------DK 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 172 NKTS---MYISIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLKEGKYRELTKE 226


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R++K IA     SRRE ++ I    V+VNG + +  A ++    D + V G P+   ++ 
Sbjct: 2   RLNKYIAHHSSYSRREADKAIQDGYVRVNGEIQDNPATDIYEGVDVVYVSGKPVTPRDKY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + T SDP  R T++D LP  +   + VGRLD  +EGLLLLT+   +A  
Sbjct: 62  TVIVYNKPKGELVTKSDPKERKTIYDTLPKEYKHYVPVGRLDYASEGLLLLTDASKVASA 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------VTLDT 181
           L    +   R+Y+++  G+V  +    +  G+++     G               +    
Sbjct: 122 LM--ESNLERIYKIKIKGEVTSEMEAAMLNGMMLDDATAGGHSHSKVTSMEFKPFIGYKI 179

Query: 182 QKGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           QK    +  + V L EGKNRE+++ F  F   +  L R+S+   +L  L  G  R +S+
Sbjct: 180 QKNEPNYSILKVALSEGKNRELRRFFAHFGTDIVDLKRVSFAEIELNNLPTGKVRFLSR 238


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/232 (36%), Positives = 120/232 (51%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER- 72
           R+ KV+A AG+ SRR  E +IA  RV+V+G ++      V   T  IEVDG      ER 
Sbjct: 16  RLQKVLAAAGVGSRRHGEELIAAGRVRVDGTVVREQGRRVDPETALIEVDG------ERI 69

Query: 73  -TRLWLYH----KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            TR  L H    KP G+++  SD  GR T+ D L      +  VGRLD ++EGLLL+TND
Sbjct: 70  VTRTGLVHLALNKPRGVLSAMSDDRGRPTIADLLTEFGGGLFHVGRLDADSEGLLLVTND 129

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G LA  L  PS    + Y V   G + +D L  L+  + +  G    D    +D   G  
Sbjct: 130 GELAHRLTHPSFAVPKTYLVEVSGPLRRDVLRQLRAEVELDDGPVRADSARIVDNANG-R 188

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             V V + EG+   ++++ +     V+RL+R  +G   LGTL AG  R +++
Sbjct: 189 VMVEVVVHEGRKHVVRRMMDAVGHPVHRLVRTRFGAVSLGTLRAGRARHLTR 240


>gi|298707966|emb|CBJ30337.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 468

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 129/236 (54%), Gaps = 13/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG--VPLRKA 70
           +R+ K ++ AG+ SRR+ E+MI   RV+VNG +++   V V    D + VDG  V +R  
Sbjct: 35  ERLQKFLSHAGLDSRRQCEQMILDGRVRVNGKMVKELGVKVNPRRDQVHVDGNRVSMRPD 94

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGG 129
              +    +KP G++ T SD  GR T   ++P  +  R++ VGRLD ++ GLLLLTN+  
Sbjct: 95  SEIKWVALNKPKGVICTVSDELGRPTAVASIPRGLEMRLVPVGRLDRDSCGLLLLTNENS 154

Query: 130 LARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQ 182
               L  PS    + YRV    G    ++ ++L +G+++ G       C   ++V    +
Sbjct: 155 WINPLTHPSYGHEKTYRVALTSGYPTTEEWDVLTQGMLLDGDPNPTRPCI--VEVVNYDR 212

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +     V + +REGKNR+I+++FE    +V  + R+S+GP +L  L  G  RE+ +
Sbjct: 213 RTRVTTVDIIIREGKNRQIRRMFEGIGHEVKSITRVSHGPIRLKNLRPGEWRELEQ 268


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 122/234 (52%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A AG  SRR+ E +I   RV+V+  L+      V      + VDG  ++   + 
Sbjct: 20  RLQKLLAEAGFGSRRKCEEIILDGRVEVDDELVTTLGTRVDPKRQKVRVDGSRVKFNTKL 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                HKP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  VTLALHKPKRVLSAMDDPKGRFTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQKGSNAW 188
           +  P  +  + Y     G+++     ++ + +V QG+   D  + LD      Q      
Sbjct: 140 VMHPKYEVEKTYIATVEGKIN----GMVCRRLVSQGVNLEDGWIKLDRCAIIDQNHDTTM 195

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V V L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R
Sbjct: 196 VKVVLHSGKNRIVRRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVR 249


>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 =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 77/228 (33%), Positives = 121/228 (53%), Gaps = 1/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++  G  SRR+ E  I   RV+VNG           S D + VDG  +  + +  
Sbjct: 7   RLQKYLSECGETSRRKAEIWITAGRVQVNGRPARLGQSVHPSKDLVTVDGRAVAPSPKVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP G VTT  D   R  V D L  + +RV  +GRLD ++EGLLLLT+DG  A  L
Sbjct: 67  IAL-NKPRGYVTTLHDELDRRCVTDLLKGVETRVYPIGRLDRDSEGLLLLTDDGAFANAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y V    +V ++++  L+ GI + G      +VT+       + + + L 
Sbjct: 126 THPRHHVPKIYHVSVRPRVTEEQVARLQNGIELDGRMTAPAKVTVLRSGSDRSVLELVLY 185

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EG+NR+I+++ E    +V RL R++ G  +LG L +G  RE++ K +R
Sbjct: 186 EGRNRQIRRMCEALGLEVARLSRVAVGTVKLGGLRSGQWRELTDKEVR 233


>gi|262091774|gb|ACY25362.1| pseudouridine synthase family [uncultured actinobacterium]
          Length = 237

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 117/225 (52%), Gaps = 5/225 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL-ERAAVNVMSTDHIEVDGVPLRKAER 72
            R++K+IA AGI SRR  + +I   RV VNGI++ E  +      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+ ++      M   L  ++ S  W+ V 
Sbjct: 124 RATHPSFGLEKTYIIEFDGILPTGVDKVLLKGVELE----DGMGRVLTFKQLSPKWIEVS 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+   I+++ E     V RLIR  +GP  LG    G  R+++
Sbjct: 180 IHEGRYHIIRRLMEAVGVNVLRLIRTKFGPISLGDTPEGRWRDLN 224


>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 =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 125/232 (53%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A     SRR+ ++ I + RV+VNG L E   V +   D + +DG  +  AE   
Sbjct: 3   RINKYLAARSQLSRRDADKAIEEGRVRVNGKLPEGPWVQLSEKDKVTLDGNDISGAEDYF 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            W ++KP  ++T + D  G+ T+ +  P +  +  +  GRLD ++EGL++ +NDG   R 
Sbjct: 63  YWAFYKPKSVLTAYGDGHGKDTL-EIYPFLREKKPAYSGRLDYDSEGLIIFSNDGDFIRR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L+    +  + Y V  +  + + +++ L+KGIV +GI Y +  V    ++ S+    V L
Sbjct: 122 LQRAEEKVEKEYIVTVNRVLKKGEMDDLRKGIVYEGIRYRECIV----EQHSHDRYQVVL 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EGK R+I+ +F  F  +V +L R+  G   L  L  G  RE S K +RE L
Sbjct: 178 HEGKKRQIRHMFRNFGIRVKKLKRVRIGSVNLNELQPGEFREFSPKEMREML 229


>gi|111221683|ref|YP_712477.1| pseudouridylate synthase [Frankia alni ACN14a]
 gi|111149215|emb|CAJ60900.1| Pseudouridylate synthase [Frankia alni ACN14a]
          Length = 254

 Score =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 83/232 (35%), Positives = 124/232 (53%), Gaps = 13/232 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AGI SRR  E +IA+ RV V+G+++      V   T  IEVDG  +     T
Sbjct: 16  RLQKVLASAGIGSRRRGEELIAEGRVSVDGVVVREQGRRVNPETAIIEVDGDRIV----T 71

Query: 74  RLWLYH----KPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTND 127
           R  L H    KP G+++  SD  GR T+ D L        +  VGRLD ++EGLLL+TND
Sbjct: 72  RTGLVHLALNKPRGVLSAMSDDRGRPTIADLLTEFDGGGGLFHVGRLDGDSEGLLLVTND 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G LA  L  PS +  + Y V   G + ++    L+ G+ ++ G    D  V L  Q    
Sbjct: 132 GELAHRLTHPSFEVPKTYLVEVSGPLRREVPRTLRTGVELEDGPARAD-SVQLVDQANGR 190

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             + + + EG+NR ++++ E   + V+RL+R   G   LGTL +G  R +++
Sbjct: 191 VMLEIVIHEGRNRIVRRMMETVGYPVHRLVRTRLGAVHLGTLRSGRARHLTR 242


>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 =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 123/234 (52%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + VDG  +R   R 
Sbjct: 21  RLQKILAQAGFGSRRKCEEMILDGRVEVDGELVTELGSRVDPKRQEVRVDGSRIRLNNRH 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 81  VTLALNKPKRVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-----W 188
           +  P  +  + Y V   G +     N+ ++ +V  G+   D  + LD     +A      
Sbjct: 141 VMHPRYEVAKTYVVTLDGHLSG---NVCRR-LVRTGVQLDDGWIKLDQCSIIDANRETTI 196

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S   +R
Sbjct: 197 VKVVLHSGKNRIVRRIFGAIGFPVRRLVRTQIGPIKLGDLKPGSYRVLSDAEVR 250


>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 =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 80/228 (35%), Positives = 119/228 (52%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MI Q RV+VNG  +    + V  S D I VDG  +   E  
Sbjct: 56  RLQKVLAQAGVASRRHAEIMITQGRVEVNGTRVTTQGMRVDPSRDVIRVDGTRINVNEEL 115

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
             ++++KP G+ +T  D   R++V   L    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 116 EYFVFNKPRGVQSTMKDEMDRTSVGSYLSERTASGQRLFHVGRLDADTEGLLLLTNDGEL 175

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+     +  L++GI +  G    D    +DT  G  + +
Sbjct: 176 ANRLMHPRYEIAKTYMATVLGEAKPALVKKLREGIELDDGPAKADYVQIVDTHNG-QSII 234

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+   ++++ +     V RL+R      QLG +  GS R ++
Sbjct: 235 RVELHEGRKHIVRRMLKAAGHPVQRLVRTKVHTVQLGDMKPGSLRALN 282


>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 =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 119/227 (52%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA  GIASRR+ E +I   R+KVNG +++  + N+    D +E D   ++ +E  
Sbjct: 2   RINKYIASCGIASRRKSEEIILGGRIKVNGSVVKELSFNIDEEKDIVEFDNKKVKPSENY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +TT  D   R +V D L  +  RV  +GRLD  T GLL+LTNDG L   
Sbjct: 62  IYIVLNKPEGYITTVKDQFNRPSVIDILKDVRERVYPIGRLDYETSGLLILTNDGDLTYK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y     G +  D++   + G+ I+        ++VT + ++ + +   +
Sbjct: 122 LTHPKHEIDKTYVASVKGIISDDEIRQFETGLKIEDYTTAPAKIRVTKENKEKNYSVCEI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++
Sbjct: 182 TIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTE 228


>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 =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 81/232 (34%), Positives = 129/232 (55%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  +R +V+R+I +  V VNG  ++  + NV    D + VDG  L + E+ 
Sbjct: 2   RLDKLLADSGFGTRSQVKRLIKKGFVTVNGETIKDPSFNVDPQKDEVLVDG-ELVEYEKD 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
              + HKP G +T  S  D + TV + +  I  F R+  VGRLD + EGLLL+TNDG LA
Sbjct: 61  YYLILHKPQGYIT--STKDRQMTVMELIADIPRFERLFPVGRLDKDAEGLLLITNDGELA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  +VY V   G+++++ L  LKKGI ++       +V +   + S +   +
Sbjct: 119 HRLTHPKWKVPKVYFVVVEGKLNEENLEPLKKGIELKDFRAKPAKVRILKAEESESEAEI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGK  ++K++FE     V  L RI +G  +LG L  G  R ++K+ L+E
Sbjct: 179 EITEGKYHQVKRMFEKIGHPVKYLRRIQFGNLKLGNLPVGEYRFLTKEELKE 230


>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 =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 78/230 (33%), Positives = 119/230 (51%), Gaps = 7/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R++K IA AG+ SRR+ + +I Q  V+VNG +++     V+   D IEV G  L      
Sbjct: 7   RLNKAIAGAGVCSRRQADDLIQQGVVRVNGEVVDTPGARVVPGRDRIEVRGQLLELDAAP 66

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
             + Y   HKP+ +V+T  DP GR TV   LP      R+  VGRLD  +EGLL+LT+DG
Sbjct: 67  AAFTYVMLHKPVQVVSTVRDPQGRPTVLGILPPDLRGGRLYPVGRLDYFSEGLLILTDDG 126

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            L   L  P     +VY V+  G V +  L  +++G+ + +G     + V L       +
Sbjct: 127 DLTNRLTHPRYHLPKVYMVKVRGHVTESTLAPMRQGMTLAEGEKLAPVDVRLLQSDRQAS 186

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++       V  L R+  GP +LG L  G+ R ++
Sbjct: 187 LFEMTLHQGVNRQIRRMCRDLGLTVLLLRRVRQGPLELGELPKGAARRLT 236


>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 =  113 bits (283), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 79/235 (33%), Positives = 120/235 (51%), Gaps = 11/235 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR  E MIA  RV V+G ++ R    V   +  I VDG+ +  A   
Sbjct: 458 RLQKALAAAGVASRRASEEMIAAGRVSVDGQVVRRFGARVDPESSEIRVDGMRVVTAPDK 517

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP G+V+T  DP+GR T+ D       R+  VGRLD  TEGL+LLTNDG LA  
Sbjct: 518 LYFALNKPRGVVSTMWDPEGRPTLADYTGQTEERIFHVGRLDTETEGLILLTNDGELANR 577

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAW 188
           L  P  + ++ Y  +  G V    +  ++KG+ ++     D  V +D+      +   A 
Sbjct: 578 LTHPRYKVVKTYIAKVPGPVPHRVVREVQKGVELE-----DGPVEVDSFRVVDNEPPKAL 632

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V + L EG+   ++++ E     V  L R   GP  L  L  G+ R ++ + + E
Sbjct: 633 VEIRLHEGRKHIVRRLMEAVGHPVADLARTQVGPIDLNALKLGTMRALTSREVSE 687


>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 =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 81/231 (35%), Positives = 128/231 (55%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL---RKA 70
           R++K +A AG+ SRR  + ++AQ  V VNG++++   V V+   D + V G  +     +
Sbjct: 49  RINKALADAGVCSRRAADELVAQGVVTVNGVVVDTPGVKVVPDRDELCVRGKKIFLKSSS 108

Query: 71  ERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            R+  +L  HKP+ +VTT SDP+GR TV D LP +    R+  VGRLD  +EGLLLLT+D
Sbjct: 109 SRSHTYLMMHKPVEVVTTVSDPEGRRTVIDILPPLHRKKRLFPVGRLDFFSEGLLLLTDD 168

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   L  PS    + Y V+  G V  + L  ++KG+ + +G     ++V + ++    
Sbjct: 169 GVLTHRLTHPSWHLPKTYLVKVRGVVQDNDLQAMRKGMTLAEGEKLAPVEVEVLSRHHDW 228

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + + L +G NR+I+++       V  L R+  GP  LG L  G  RE++
Sbjct: 229 LLLEMTLFQGINRQIRRMCRDAGLTVLSLHRVRQGPLSLGELRTGEVRELT 279


>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 =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 125/272 (45%), Gaps = 33/272 (12%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           + D     +   P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D 
Sbjct: 17  VSDMGECGDRVVPMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDE 76

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           + VDG  +R A+     + HKP G VTT SDP GR TV + +P+  +  +  +GRLD +T
Sbjct: 77  VAVDGAVVRLADGPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDT 136

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI------------- 165
            GLLL + DG L   L  P     + Y     G+  +  L LL++GI             
Sbjct: 137 TGLLLFSTDGELGNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVR 196

Query: 166 VIQGICYGDMQVTLD-----TQKGSNAWVTV-------------GLREGKNREIKKVFEF 207
           +++G      +  L+       + S  +  V             G+REG+ R++K++   
Sbjct: 197 MVEGGAARHAERLLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAA 256

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               V  L R S+GP +LG L  GS R +  +
Sbjct: 257 VGHPVLALHRDSFGPLELGDLPRGSWRALDAE 288


>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 =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 114/229 (49%), Gaps = 1/229 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR  E  I   RVKV+G +          +  I VDG PL   
Sbjct: 1   MTRQRLQKLIAAAGLCSRRTAEDWIDAGRVKVDGRISSLGDQADPESQLIHVDGRPLSFR 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGG 129
               + L +KP G+++T  DP GRSTV D LP    + +  VGRLD ++ G LLLT+ G 
Sbjct: 61  GEPTVLLINKPAGVISTCRDPRGRSTVLDLLPQQLRQGLHPVGRLDADSRGALLLTDYGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G      L   ++G+ + G      +V +  ++     +
Sbjct: 121 LTLRLTHPRYDHAKTYRVWVEGTPLDTSLQRWRQGVTLDGTRTRSAEVRVLQRRSDRTLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR+I++V E     V  L R++    +LG L  G  R +S+
Sbjct: 181 EVVLLEGRNRQIRRVAELLGHPVVDLQRVAIAGLRLGALPEGRWRRLSR 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 =  113 bits (282), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 85/248 (34%), Positives = 125/248 (50%), Gaps = 24/248 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI SRRE +  IA   V VNG  +      V  TD +  DG  L++ ER  
Sbjct: 71  RLNKYIANAGICSRREADTYIAAGNVTVNGKTITEMGYKVQPTDEVRFDGRLLQR-ERKE 129

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  D  GR TV + +  +  +R++ VGRLD NT GLLL TNDG LA+ 
Sbjct: 130 YVLLNKPRNFITTTRDEKGRRTVMELISRASNARLVPVGRLDRNTTGLLLFTNDGELAKK 189

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----GSNAWV 189
           L  P     ++Y V          L  L++G+ ++     D ++ +D        S   V
Sbjct: 190 LTHPKHGVRKIYHVELDKTFKSADLGKLREGLELE-----DGRIEVDEASYIDGASKKEV 244

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L  G+NR ++++FE   ++V +L R+         +LAG    ++KK L      HL
Sbjct: 245 GVELHSGRNRIVRRIFEHLGYQVVKLDRV---------VLAG----LTKKDLPRGHWRHL 291

Query: 250 LEEAQVNL 257
            E+  +NL
Sbjct: 292 TEQEVINL 299


>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 =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 89/241 (36%), Positives = 128/241 (53%), Gaps = 18/241 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVD 63
           +QE F   RV K+IA++G+ SRRE E+MI+   V VNGI   L ++A+ +    D I+V+
Sbjct: 1   MQELF---RVQKLIAQSGLMSRREAEKMISSGLVFVNGIKASLGDKASAD----DEIKVN 53

Query: 64  G--VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           G  + L K+   + +L +KP   +TT +DP GR TV D L +   R++ VGRLD NT G+
Sbjct: 54  GKILNLTKSPVFKYFLLNKPKNSITTSNDPKGRRTVID-LINTNERIVPVGRLDRNTTGV 112

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLT D  L   L  P  +  RVYR R    +   +   L   I I     G M   +  
Sbjct: 113 LLLTTDYELVNKLTHPKYEIERVYRARIDSPLTLKEFKELNARIEID----GKMSRQIVD 168

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q  + +++ V L  G    +KK+FE    KV  L R+SY    +  L  G  RE++ K +
Sbjct: 169 QVDTKSYL-VSLHVGSYHHVKKLFEKIGHKVLTLKRVSYANLTVDKLPEGMYRELTLKEV 227

Query: 242 R 242
           R
Sbjct: 228 R 228


>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 =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 69/215 (32%), Positives = 113/215 (52%), Gaps = 1/215 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA++G  SRR  + +I   +V VNG +L   +  V  TD +EV+G  +   E   
Sbjct: 2   RINKFIAQSGYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLKEDKI 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KPIG  +T  D      V D + S  +RV  VGRLD ++ GLL+LTNDG     L
Sbjct: 62  YIAINKPIGYASTVKDKFADKKVVDLIKSD-TRVYPVGRLDKDSHGLLILTNDGEFTYEL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V + 
Sbjct: 121 THPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTIF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           EG+NR+I+++F+F N  V  L R+  G +++   L
Sbjct: 181 EGRNRQIRRMFDFINHPVLDLKRVQIGNYKMDNSL 215


>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 =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 120/228 (52%), Gaps = 2/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA++G  SRR  + +I   +V VNG +L   +  V  TD +EV+G  +   E   
Sbjct: 2   RINKFIAQSGYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLKEDKI 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KPIG  +T  D      V D + S  +RV  VGRLD ++ GLL+LTNDG     L
Sbjct: 62  YIAINKPIGYASTVKDKFADKKVVDLIKSD-TRVYPVGRLDKDSHGLLILTNDGEFTYEL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V + 
Sbjct: 121 THPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTIF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EG+NR+I+++F+F N  V  L R+  G +++  +L +G  + +  K L
Sbjct: 181 EGRNRQIRRMFDFINHPVLDLKRVQIGNYKMENSLKSGEYKLLKSKDL 228


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 121/227 (53%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ I+ +G+ SRRE +++I    + VNG ++      V  TD ++  G  L K E+  
Sbjct: 160 RLNRFISNSGVCSRREADKLIEMGMISVNGKVITEMGFQVSPTDTVKY-GKRLLKREKFV 218

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT +DP  R TV D +  S   R+  VGRLD NT GLLL TNDG +A+ 
Sbjct: 219 YVLLNKPKDFITTTNDPQDRKTVMDLIKNSCDERIYPVGRLDRNTTGLLLFTNDGEVAKK 278

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    +VY+V     +  + L+ + +G++++ G    D    L+ ++     V V 
Sbjct: 279 LSHPSHDVKKVYQVELDKPLKDEDLDSIAEGVILEDGYAAVDEIAILNPER---TLVGVE 335

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  G+NR ++++F   +++V +L R  Y       +  G  R +S+K
Sbjct: 336 IHIGRNRIVRRIFNHLDYEVVKLDRTMYAGLNKKNIDRGDWRYLSEK 382


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 82/222 (36%), Positives = 120/222 (54%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A+AG+AS RR+ E +I   RV +NG +    A  V   D + VDG P+    R 
Sbjct: 5   RLQKYLAQAGVASSRRKAEALIRAGRVTINGQVAALGA-KVTPGDEVCVDGRPVAPTARR 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   HKP G+ TT  D     TVF+ +P+I   + +VGRLD ++EGLLLLTNDG L + 
Sbjct: 64  VVLALHKPPGVTTTRRDRFAERTVFELVPAIPG-LHTVGRLDRDSEGLLLLTNDGRLTQR 122

Query: 134 LELPSTQWLRVYRV-RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VYRV    G+V    L  L+KG+ ++    G  +      K     +T  
Sbjct: 123 LTHPRYGVPKVYRVWTAKGEVPPFILKRLEKGVRLED---GPARALKARPKVGGCVLT-- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           L EG+ RE++++     + V RL+R+  GP +LG L  G+ R
Sbjct: 178 LAEGRKREVRRMLRAVGYPVVRLLRVKIGPIRLGGLKPGAWR 219


>gi|291166791|gb|EFE28837.1| ribosomal large subunit pseudouridine synthase B [Filifactor alocis
           ATCC 35896]
          Length = 242

 Score =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 118/226 (52%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+++ IA  GI+SRR+ +++I + RV VNG  +    + V    D ++VDG  +      
Sbjct: 2   RINQYIAHCGISSRRKADQLIEEGRVFVNGKKVTSPGMQVEEGNDMVKVDGKIISSEVNK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+  ++  SD  GR+TV + L     R+  VGRLD  + GLLLLTNDG LA  
Sbjct: 62  VYYMLNKPLRYISAVSDDRGRNTVLE-LFRTKERIYPVGRLDYLSTGLLLLTNDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V+  G   ++     +KG+ + G      ++    ++       V L
Sbjct: 121 LIHPRYHLEKTYFVQVKGDAPENLKERFQKGMFLDGYKTKPAELEFLGKRDGIIKYKVTL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           REG+NR+I+K+FE    KV  L RIS G   +G L  G  R ++ K
Sbjct: 181 REGRNRQIRKMFEAARLKVVSLKRISMGDLYIGNLKEGEYRALTSK 226


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 74/256 (28%), Positives = 124/256 (48%), Gaps = 35/256 (13%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           V +VI++ G  SR + E ++ + RV + G ++          D I VDG P++ +E    
Sbjct: 30  VVRVISKRGFCSRSQAENLVREGRVSLRGKIVRDPDTPARENDEICVDGKPVKASEFV-Y 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLLTN 126
           ++ +KP G VTT SD  GR+TV D     ++++           VGRLD  +EGLLL TN
Sbjct: 89  FMMNKPRGYVTTASDEKGRATVMDLFREQYAKMFPGKPVPHISPVGRLDAASEGLLLFTN 148

Query: 127 DGGLARVL------------------ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           D   A  L                  E       ++YRV+ +G    ++L+ ++ G  + 
Sbjct: 149 DTQWADALLKTKDERRKTRDDKCVERESRGPIHTKIYRVQVNGHPTAEELSQMEAGFNVP 208

Query: 169 GICYGD-------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
              +G+       +   L +    N W+ + L EGKNREI+++     ++V RL+RI + 
Sbjct: 209 PRVFGEPEEFMHAVSAKLYSAGEKNCWLEITLDEGKNREIRRMLAKLGYEVLRLVRIKFC 268

Query: 222 PFQLGTLLAGSTREVS 237
            ++LG L  G  R+++
Sbjct: 269 NYELGDLKQGEIRKIN 284


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 78/225 (34%), Positives = 119/225 (52%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I++ RV VNG  +      V   D IEVDG  + K ++ 
Sbjct: 2   ERLQKVIAAAGITSRRKAEVLISEGRVAVNGETITELGYKVKRGDLIEVDGKAIEKEDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP   + T  D  GR TV D L     R+ +VGRLD +T G+++LTNDG  A  
Sbjct: 62  -YFLMNKPKRTMCTSDDEFGRQTVVD-LVDCRQRIFTVGRLDYDTSGVIILTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL---DTQKGSNAWV 189
           +  P     +VY +  +G +  + +  +K GIV+  GI     +  +   DT+K   ++ 
Sbjct: 120 IIHPRYHIPKVYNLTINGILTPEDMKKIKAGIVLDDGIKTLPAKYRMTEKDTEKNQCSF- 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + + EG+NR+IK++ E   ++V RL R          L  G  R
Sbjct: 179 DLTIVEGRNRQIKRMMEALGYEVRRLHRSRLAFLHCSDLRQGEYR 223


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 71/208 (34%), Positives = 108/208 (51%), Gaps = 3/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +GI SRRE +  I+   V VNG ++      V  TD +  DG  +   E+  
Sbjct: 61  RLNKYISNSGICSRREADMHISVGSVTVNGKVVTEMGYKVQLTDEVRFDGRII-NPEKAT 119

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G + T  D  GR TV D + +   +R++ VGRL+  T GLLL TNDG LAR 
Sbjct: 120 YILLNKPKGFLVTTKDEKGRKTVMDLVATATTARIVPVGRLERQTTGLLLFTNDGELARK 179

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     +++ V     + Q   N +K G+ I+G  YG  +++   Q  S   V + +
Sbjct: 180 LTDPHQNVRKIFHVELDRNLSQTDFNKIKDGVNIRGDIYGVDEISW-IQGASKREVGIKV 238

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
             G N  +K +FE  ++ V RL R+ + 
Sbjct: 239 STGSNGLVKAIFEHLSYTVARLDRVVFA 266


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 120/228 (52%), Gaps = 2/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA++G  SRR  + +I   +V VNG +L   +  V  TD +EV+G  +   E   
Sbjct: 2   RINKFIAQSGYCSRRNADELIKNSKVYVNGTILLDLSYQVNDTDIVEVEGKKINLKEDKI 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KPIG  +T  D      V D + S  +RV  VGRLD ++ GLL+LTNDG     L
Sbjct: 62  YIAINKPIGYASTVKDKFADKKVVDLIKSD-TRVYPVGRLDKDSHGLLILTNDGEFTYEL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V + 
Sbjct: 121 THPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENIKNDTKYRVTIF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           EG+NR+I+++F+F N  V  L R+  G +++  +L +G  + +  K L
Sbjct: 181 EGRNRQIRRMFDFINHPVLDLKRVQIGNYKMENSLKSGEYKLLKSKDL 228


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 82/264 (31%), Positives = 123/264 (46%), Gaps = 33/264 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           +   P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D + VDG  +
Sbjct: 6   DRVVPMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDEVAVDGAVV 65

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
           R A+     + HKP G VTT SDP GR TV + +P+  +  +  +GRLD +T GLLL + 
Sbjct: 66  RLADGPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDTTGLLLFST 125

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYG 173
           DG L   L  P     + Y     G+  +  L LL++GI             V++G    
Sbjct: 126 DGELGNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVRVVEGGAAR 185

Query: 174 DMQVTLD-----TQKGSNAWVTV-------------GLREGKNREIKKVFEFFNWKVNRL 215
             +  L+       + S  +  V             G+REG+ R++K++       V  L
Sbjct: 186 HAERLLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAAVGHPVLAL 245

Query: 216 IRISYGPFQLGTLLAGSTREVSKK 239
            R S+GP +LG L  G+ R +  +
Sbjct: 246 HRDSFGPLELGDLPRGAWRALDAE 269


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 73/226 (32%), Positives = 118/226 (52%), Gaps = 6/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI+SRRE + +I    V VNG ++      V  TD +  DG  +  AE+  
Sbjct: 65  RLNKYIANAGISSRREADELILTGVVTVNGKVITEMGYKVQPTDEVRFDGKKI-SAEKNV 123

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G +TT  D   R TV D +  +  +R+  VGRLD  T G+LL TNDG L + 
Sbjct: 124 YFILNKPKGYITTTKDEKNRQTVLDLMEGATTARIFPVGRLDRQTTGVLLFTNDGFLTKK 183

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  PS    +VY V    ++    +  ++KGI  + +G+   D    +D +   +  + +
Sbjct: 184 LTHPSHDVKKVYHVTLDRKLSSHDMAEIRKGIRLIPEGVATVDEVSFIDGR--PHNEIGL 241

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L  G NR ++++FE   ++V +L R+S+       L  G  R ++
Sbjct: 242 ELHIGWNRVVRRIFESLGYQVEKLDRVSFAGLTKSKLRQGQYRALT 287


>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 =  112 bits (281), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 121/233 (51%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +      
Sbjct: 2   RLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPEVDVIRVDGVRVNVNNNH 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
           + ++ +KP G+ +T SD  GR  + D +    S    +  VGRLD +TEGL+LLTNDG L
Sbjct: 62  QYFVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQGLFHVGRLDADTEGLILLTNDGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+ D+  +  LK G+ +  G    D    +D  +G  + V
Sbjct: 122 ANRLSHPKYEVSKTYIAEVLGEADRSLVTTLKNGVELDDGPAAADYVQIVDVHQG-RSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+   ++++ +   + V  L+R      QLG    G+ R ++   LR
Sbjct: 181 RVQLHEGRKHIVRRMLKAAGYPVQYLVRTKLHTVQLGEQKPGTIRALNDNELR 233


>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 =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 75/224 (33%), Positives = 116/224 (51%), Gaps = 4/224 (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  KVYIMLNKPEDVITSVKDEKDRKTVID-IVKVNERIFPIGRLDYDSSGLILLTNDGELYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +  P  +  + Y     G+V  D     + GI I G      ++ +   + +   + + 
Sbjct: 122 KIIHPRVELDKKYVAVVKGEVSLDDKEKFESGIDIGGYITAPAKLKMLEYSHRKDLSTIE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V + EGKNR+I+K+    N +V  L R+S G  +LG L  G  R
Sbjct: 182 VCIHEGKNRQIRKMCSAINHEVISLKRVSIGNIRLGQLKKGEYR 225


>gi|21324194|dbj|BAB98819.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Corynebacterium glutamicum
           ATCC 13032]
          Length = 252

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 122/228 (53%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +I Q RV+VN  ++    V V  + D I VDGV +   E  
Sbjct: 13  RLQKVLAQAGVASRRHAEILIDQGRVEVNDRIVTTQGVRVDPNNDVIRVDGVRIHINEDL 72

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+ +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 73  EYFVLNKPRGMHSTMSDELGRPCVGDLVSEKTASGQRLFHVGRLDADTEGLLLLTNDGEL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+     ++ L+ G+ ++ G    D    +D  +G  + +
Sbjct: 133 ANRLMHPKYEVSKTYLATVRGEATNKLVSALRDGVELEDGPAKADFAQIIDVFQGK-SLL 191

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + EG+   ++++F+   + V RL+R      QLG    GS R ++
Sbjct: 192 RIEIHEGRKHIVRRLFDELGFPVERLVRTKLHTVQLGDQKPGSLRALN 239


>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 =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 71/216 (32%), Positives = 122/216 (56%), Gaps = 13/216 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G  SRR+ + ++ + +VKVNG       +++  +D +E+DG  L   E+  
Sbjct: 2   RINKYIASSGYTSRRKADDLVKKGKVKVNGETTHELGLDIKDSDVVEIDGKVLEIEEKIY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + LY KP G +T++ DP     + D L  +  R  + GRLD ++EGLL++TNDG     +
Sbjct: 62  IKLY-KPRGYITSNFDPYNDRDLND-LVKLDQRFFAAGRLDKDSEGLLIITNDGIFTNQI 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----KGSNAWV 189
             PS +  + Y VR    +++++    + GI I     GD ++T D++     K S  + 
Sbjct: 120 IHPSKKLDKTYIVRVSRLLNKEECQQFESGIDI-----GDSEMTSDSRIELIDKTSKTY- 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + +G NR+I+++F +F+ +V  L RIS GP +L
Sbjct: 174 KVTIHQGYNRQIRRMFAYFSSEVKMLKRISIGPIKL 209


>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 =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVP 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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----T 181
           DG L++ +  P  +  + Y     G++       + + +V  G+   D  + LD      
Sbjct: 132 DGELSQHVMHPKYEVEKTYVATLEGKIS----GTVCRRLVTTGVQLDDGWIKLDHCAIID 187

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               +  V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S+  +
Sbjct: 188 SSRDHTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKPGSYRVLSQTEV 247

Query: 242 R 242
           R
Sbjct: 248 R 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 =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 75/241 (31%), Positives = 124/241 (51%), Gaps = 10/241 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVP 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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L++ +  P  +  + Y     G++       + + +V  G+   D  + LD     +
Sbjct: 132 DGELSQHVMHPKYEVEKTYVATLEGKIS----GTVCRRLVTTGVQLDDGWIKLDHCAIID 187

Query: 187 A-----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A      V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S+  +
Sbjct: 188 ASRDYTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKPGSYRVLSQTEV 247

Query: 242 R 242
           R
Sbjct: 248 R 248


>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 =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 75/227 (33%), Positives = 123/227 (54%), Gaps = 7/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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   P GR  V D L  +  R+  +GRLD N+ GLLLLT+DG +  
Sbjct: 64  RTYIMLNKPAGYLTTCKQP-GRKIVLD-LIDLPQRLFPIGRLDNNSTGLLLLTDDGRIHH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V          L+ +++G++++G      +V    + G  ++ T+ 
Sbjct: 122 RLSHPSFDHEKEYEVETVKDAPDQALDAMRRGMILEGKKTRPAKV---KRTGPRSF-TIV 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L+EG+NR+I+K+ E    KV RL R+     +LG L +G  R +++K
Sbjct: 178 LKEGRNRQIRKMVELTKNKVKRLHRVRMSTIRLGGLPSGKWRRLNEK 224


>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 =  112 bits (280), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 120/228 (52%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA  G+ASRR+ E +I   RV VN  ++   +  V    D ++VD   +++  + 
Sbjct: 2   RINKYIALCGVASRRKAEELILAGRVTVNDEVMTELSYKVDEENDIVKVDDKLIKEENKL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G +TT  D   R +V D +  I  RV  +GRLD  T GLLLLTNDG L   
Sbjct: 62  VYILLNKPEGYITTVKDQFDRPSVLDLVSDIKERVYPIGRLDYETSGLLLLTNDGDLTYK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           L  P  +  + Y  R  G++ ++++   K G+ I+       +   +  D Q+ S + + 
Sbjct: 122 LTHPKHEVDKTYVARVKGKLTKEEIERFKTGLKIEDYTTAPAKLKVIKYDEQRDS-SLLE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + + EGKNR+++K+ +  N  V RL R + G  ++G    G  R +++
Sbjct: 181 IKIHEGKNRQVRKMCKAINHPVLRLRRSAMGKIKIGDCEIGKYRYLTE 228


>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 =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 126/236 (53%), Gaps = 9/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A AGIASRR  E ++    V+VNG ++ R    V    D + V G  L      
Sbjct: 19  RLQKLLALAGIASRRGSEILMLNGEVEVNGEVVTRLGTKVDPGKDVVRVGGKRLPPISGK 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+V+T SDP+GR  + D +     R+  VGRLD +TEGL++LTNDG  A  
Sbjct: 79  VYLVLNKPRGVVSTMSDPEGRRNLSDLVADRPERLFHVGRLDTDTEGLIILTNDGDFAHR 138

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAWV 189
           L  PS +  + Y     G++  +    L  G+ ++    G + VT    ++T+K   + +
Sbjct: 139 LAHPSYEVDKTYVAEVKGEIFPNVRKRLLAGVTLED---GPVTVTKARIMETRK-DKSII 194

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + + EG+NR ++++ +     V RL R   GP +LG +  G  R++S++ L E L
Sbjct: 195 ELVIHEGRNRIVRRLLDHLGHPVTRLTRTRIGPVRLGAMKPGDMRDLSREELGELL 250


>gi|329571723|gb|EGG53404.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TX1467]
          Length = 205

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 68/202 (33%), Positives = 107/202 (52%), Gaps = 3/202 (1%)

Query: 46  LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           +++     V   D +EVDGVP+ + E    +L++KP G+++  SD  GR  V D    + 
Sbjct: 1   MVKELGTQVSKQDTVEVDGVPIYQEEYG-YYLFYKPRGVISAVSDDKGRKVVTDYFTDVT 59

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            R+  VGRLD +T GLLLLTNDG  ++ L  P  +  +VY  +  G   +  L  L KGI
Sbjct: 60  ERIYPVGRLDYDTSGLLLLTNDGSFSQKLTHPKHEVDKVYVAKIKGVPTKRDLLPLAKGI 119

Query: 166 VIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            I G      + Q+     K  ++ V + + EG+N ++KK+F+   + V +L R  YG  
Sbjct: 120 RIDGKRTAPANFQILSADIKTGSSVVELTIHEGRNHQVKKMFQAVGFPVQKLKRERYGEL 179

Query: 224 QLGTLLAGSTREVSKKILREQL 245
            L  L  G  R+++KK + + L
Sbjct: 180 TLQGLRPGQYRDLTKKEISQLL 201


>gi|269215383|ref|ZP_06159237.1| ribosomal large subunit pseudouridine synthase B [Slackia exigua
           ATCC 700122]
 gi|269130870|gb|EEZ61945.1| ribosomal large subunit pseudouridine synthase B [Slackia exigua
           ATCC 700122]
          Length = 256

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 116/229 (50%), Gaps = 2/229 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRK 69
             P RV K +ARAG+ASRR  E ++   RV VNG ++ E  +      D + VDG  +  
Sbjct: 15  IVPMRVQKFLARAGVASRRGSENLMTTGRVSVNGRVVTELGSRVDPRCDVVRVDGHVVHL 74

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
           ++ +   + +KP G +TT SDP GR+ V + +P   +  +  +GRLD +T G+LL + DG
Sbjct: 75  SDGSTTLMLNKPAGYITTMSDPFGRACVAELVPIDAYPGLFPIGRLDADTTGILLFSTDG 134

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y+    G V +++L  L+ G+ ++       +  L       + 
Sbjct: 135 ELGNGLLHPRKHVDKTYQALVEGSVSEEELERLRSGVELEDGMTAPAEARLTCVSEDESR 194

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + + EG+ R+++++       V  L R  +GP  LG L  GS R +S
Sbjct: 195 LDITIHEGRKRQVRRMCATVGHPVVTLHRSRFGPLVLGDLPEGSWRMLS 243


>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 =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/238 (34%), Positives = 120/238 (50%), Gaps = 14/238 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      VM TD ++  G  L   E+
Sbjct: 243 PVRLNKFLANAGVCSRREADEYIQAGSVTVNGQVVTELGTKVMRTDEVKF-GDNLVSLEK 301

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LLLTNDG LA
Sbjct: 302 KVYILINKPKDCVTTSDDPQQRKTVLDLVKNACPERIYPVGRLDRNTTGVLLLTNDGDLA 361

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---- 187
             L  P     +VY V     V Q+ L  + +GI ++     D ++  D    +N     
Sbjct: 362 SKLTHPKFLKKKVYHVFLDKPVAQEDLQKIAEGIELE-----DGEIHADEIAYANEEDKK 416

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILR 242
            V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K   ILR
Sbjct: 417 QVGIEIHSGKNRIVRRIFEHLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEKEVDILR 474


>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 =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 119/230 (51%), Gaps = 1/230 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+++ ++  G+ SRR+ +++I + RVKVNG ++    V +    D +EVDG  ++   + 
Sbjct: 4   RLNRYLSMCGVTSRRKADKLIEEGRVKVNGEVVRDLGVKIDPEVDRVEVDGKEVKPPRKI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L      L        G+ T+ + +  +  RV  VGRLD NTEGLLLLTNDG LA  
Sbjct: 64  YIILNKPCCYLTQLGKSQSGKKTIEELIKDVPERVFPVGRLDYNTEGLLLLTNDGELANR 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY     G+V ++ L  +K G  ++        V +   +G N  + +  
Sbjct: 124 VLHPRYKLPKVYLALVKGKVSKNTLRKMKHGAELEDGFAKPDDVRIVRYEGDNTLLEIVF 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EG+   +K+    F   V +L RI+ G  +LG L  G  RE+S++ LR+
Sbjct: 184 HEGRKHIVKRFLASFGHPVIKLKRIALGTLKLGKLPPGKWRELSQRELRQ 233


>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 =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 73/209 (34%), Positives = 115/209 (55%), Gaps = 6/209 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AGI SRRE + +I   R+ VNG  +      V +TD ++     L+  +   
Sbjct: 20  RLNKWISNAGICSRREADELIQAGRITVNGEKITTLGYQVKNTDIVKFRDKVLKPNKHVY 79

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP   +TT  DP+ R TV D +  +   RV  VGRLD NT GLL+LTNDG LA+ 
Sbjct: 80  ILL-NKPRNCITTAFDPERRRTVLDFVKGACQERVYPVGRLDRNTTGLLVLTNDGDLAQK 138

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVG 192
           L  PS Q  ++Y+V     +    L  +K GI ++    G +QV ++   +G  + + + 
Sbjct: 139 LAHPSYQIKKIYQVELASPIQPKDLAAIKAGICLKD---GIVQVDSISIVQGDESKLGIE 195

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +  GKNR I+++FE   +++  L R+ Y 
Sbjct: 196 IHSGKNRIIRRLFEHLGYQIINLDRVMYA 224


>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 =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 74/224 (33%), Positives = 115/224 (51%), Gaps = 1/224 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+IA +GI SRR+ E +I Q +V VNG   +         D I V+G  + K    
Sbjct: 4   QRLQKIIAESGICSRRKAEELIIQHKVLVNGFAAKIGDKANPENDQIIVNGYRIPKVIFN 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R+ L +KP G++++ +D  GR TV   +PS 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           ++EG+NR+I+++ E F   V  L R++    +LG L  G  REV
Sbjct: 184 MKEGRNRQIRRISEKFGHPVIDLKRVAISKIKLGNLQEGCWREV 227


>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 =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 126/237 (53%), Gaps = 23/237 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA+AG+ASRR+ E  I +  V VNG  L+  +  V   D ++V G  L   E+  
Sbjct: 11  RINKYIAKAGLASRRKSEEYIKKGLVFVNGKKLDDLSYQVKENDEVKVMGKLLEIKEKFY 70

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KPIG ++++ DP  +  + ++L  I  R    GRLD ++ GL+L+TNDG +   L
Sbjct: 71  YKL-NKPIGFISSNYDPHNKKDL-NSLVKIDQRFFCAGRLDKDSHGLMLITNDGKITNKL 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---- 190
             PS +  + Y V+    +++D   L +KGI +            D +K S+A +     
Sbjct: 129 IHPSKKIEKTYIVKVDKLLNKDDEALFRKGIKLS-----------DNEKTSDAKINLIDE 177

Query: 191 ------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 V + +G NR+++++F +F  KV  L RI  G  +LG L  G  ++++KK L
Sbjct: 178 NRKIYEVIIHQGFNRQVRRMFLYFGSKVIDLKRIKIGQIELGKLEDGKYKKLNKKEL 234


>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 =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 71/220 (32%), Positives = 113/220 (51%), Gaps = 2/220 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ASRR+ E +I Q RVKVNG  +      V    D + VDG  L   ++ 
Sbjct: 3   RLQKFMADCGVASRRKCEEIILQGRVKVNGRTITELGFKVDPQKDKVLVDGKKLVPVQKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +   +  RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 63  IYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVDVRVFPVGRLDFDTTGLILLTNDGEFAY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   KKG+ I G      +  +       + V + 
Sbjct: 123 KVTHPKHDIEKTYIALIEGVPTKEEIEQFKKGLFIDGKLTSPAKFRILKVFKGMSLVEIK 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + EG+NR+++K+ +    +V +L R++ G  +LG L  G 
Sbjct: 183 IHEGRNRQVRKMCDAIGHRVLKLKRVAIGKLKLGKLKEGE 222


>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 =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 117/232 (50%), Gaps = 11/232 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE ++ I    VKVNG ++      V+ +D I     P+   E+
Sbjct: 273 PLRLNKFLANAGVCSRREADQFIQSGMVKVNGNVVTELGTKVLRSDEIIFHDQPV-TLEK 331

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 332 KVYVLINKPKDYVTTSDDPQQRKTVMDLVKGVCPERIYPVGRLDRNTTGVLLLTNDGDLA 391

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----A 187
             L  P     +VY V    +V +  L  +  G+ +      D +V  D  + +N     
Sbjct: 392 SKLAHPKFLKKKVYHVFLDKEVTEHDLQQIATGVTLD-----DGEVHADAIEYANDKDKT 446

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V + +  GKNR ++++FE   ++V RL R+ +       L  G  R +++K
Sbjct: 447 QVGIEIHSGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLKRGDWRFLTEK 498


>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 =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 74/222 (33%), Positives = 118/222 (53%), Gaps = 2/222 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A+AG  SRR+ E MI   RV+V+G L+    V V      I VDG  +  + R 
Sbjct: 20  RLQKVLAQAGFGSRRKCETMITDGRVEVDGDLVTELGVRVDPLHQEIRVDGSRIHISNRH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++T  DP GR T+ D +   + R+  +GRLD +TEGL+L+T+DG LA+ 
Sbjct: 80  VTLALNKPRKVLSTMDDPKGRWTLRDIVGDRYERIFHMGRLDYDTEGLILMTDDGELAQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +  P  +  + Y     G +     + L++ G+ +        Q ++  Q    + V V 
Sbjct: 140 VMHPKYEVDKTYIATVEGHIGGSVCHRLVRTGVQLDDGWIKLDQCSIIDQNRDRSVVKVV 199

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +  G+NR +++VF    + V +LIR   GP +LG L +GS R
Sbjct: 200 IHSGRNRIVRRVFGAIGFPVVKLIRTQIGPIKLGELKSGSYR 241


>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 =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 122/234 (52%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A AG  SRR+ E +I   RV+V+  L+      V      + VDG  ++   + 
Sbjct: 47  RLQKLLAEAGFGSRRKCEEIILDGRVEVDDELVTTLGTRVDPKRQKVRVDGSRVKFNTKL 106

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                HKP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 107 VTLALHKPKRVLSAMDDPKGRFTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 166

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQKGSNAW 188
           +  P  +  + Y     G+++     ++ + +V QG+   D  + LD      Q      
Sbjct: 167 VMHPKYEVEKTYIATVEGKIN----GMVCRRLVSQGVNLEDGWIKLDRCAIIDQNHDTTM 222

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R
Sbjct: 223 VKIVLHSGKNRIVRRIFGAVGFPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVR 276


>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 =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/221 (34%), Positives = 114/221 (51%), Gaps = 3/221 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG P+   +R  
Sbjct: 42  LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIGQPAPPIEVDGQPMGAPQRLY 101

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  
Sbjct: 102 LML-NKPRGVVTTAQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAR 160

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+     D   L  L+ G+  +G       V +       AW+ V L
Sbjct: 161 LTDPETGPQKTYHVQVDRLPDDATLAALQAGVDDEGEFLVAQAVRVLRSGDKTAWLEVVL 220

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            EG+NR I+++   F+ +V RL+R++ G  QL  L  G  R
Sbjct: 221 DEGRNRHIRRLLAAFDLQVLRLVRVAIGGLQLADLGKGQWR 261


>gi|322490748|emb|CBZ26012.1| putative tRNA pseudouridine synthase A [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 694

 Score =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 115/225 (51%), Gaps = 8/225 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLW 76
           + + RAG  SRRE   +IA  +V+VN +        V + D + V G   R +    RLW
Sbjct: 336 RTLPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHRSRLRFAPPRLW 395

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +YHKP  ++ + +D  GR+ +  +   +    ++ VG L +   G+LLLTNDG L+R LE
Sbjct: 396 MYHKPAHVIVSRNDAAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLE 455

Query: 136 LPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            P +   R Y +R     D     KLN   +GI I G  Y + +  ++    S   V V 
Sbjct: 456 NPKSMVQRTYLLRVRPAFDPVLVHKLN--TEGIQINGRLYRNAEFFVNPATKSRYSVKVK 513

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G++  I ++ +    KV R  RIS+GPF L  L  GS REV+
Sbjct: 514 VR-GESMPIAQLMQHLGRKVERGGRISFGPFALSNLAVGSVREVT 557


>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 =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/227 (36%), Positives = 117/227 (51%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A+ G+ASRR  E MIA  RV VNG +++   V V   D + VDG  L   ER  
Sbjct: 2   RLQKYMAQCGVASRRGSEAMIADGRVMVNGSVVDTPGVQVTPGDVVFVDG-KLIAPERKV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KP G+VTT  D      + D L +   R+ ++GRLD +TEGLL+LTNDG L   L
Sbjct: 61  YLLLNKPRGVVTTSEDVHAERRILD-LVAAEVRLYAIGRLDKDTEGLLILTNDGDLTFRL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-------MQVTLDTQKGSNA 187
             PS    +VY     GQ+    L  L++G+VI     G         +VT+  +K  + 
Sbjct: 120 THPSYHLDKVYEAVVKGQLTAPALAALREGVVIPLDDAGTKTYRTQPAEVTVLRRKRGST 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +++ L EGK R+I+K+     + V  L R + G     TL  G  R
Sbjct: 180 RLSITLCEGKKRQIRKMCAAVGYPVVALRRTAIGDIADDTLKPGEWR 226


>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 =  111 bits (278), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 4/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR-KAER 72
           R++K IA +G+ASRR+ E +I + R++VN  +++  +  V    D +  D  P+  K E+
Sbjct: 2   RINKFIAASGVASRRKAETLILEGRIRVNNKVIKELSYQVDEDLDQVTFDNKPISVKDEK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D   R +V D    I  R+  VGRLD  T GLLL+TNDG L  
Sbjct: 62  LVYIMLNKPEGYITSVKDQFDRPSVSDLTSDIKERIYPVGRLDYETSGLLLMTNDGDLTY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVT- 190
            +  P  +  + Y     G V Q++    + G+ I+        +  L T    N  V  
Sbjct: 122 KITHPKHEMNKTYIASVRGIVTQEEKYAFENGLKIEDYTTAKANLKILKTDTNKNYSVCK 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + EGKNR+++K+F+  N     L R+  G   +G L  G  R+++K+
Sbjct: 182 VTIHEGKNRQVRKMFQAINHPTMNLKRVQVGKINIGDLELGKYRKLTKE 230


>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 =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 121/233 (51%), Gaps = 5/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +AR G+ASRR  E +I   RV V+G ++    + V   + I +DG  +      R
Sbjct: 6   RLQVYLARCGVASRRASENLILNGRVSVDGKIITELGIKVSGKEKICLDGKQIFPEAEKR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G V + +D   R      L   ++ R+ ++GRLD+ + G +L TNDG  +  
Sbjct: 66  YILLNKPEGYVCSLADEKDRPIAASLLKDTYTERLYNIGRLDMLSGGAILFTNDGDFSAK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +E PS++  + Y V    +   + L    +G+ I+G+ Y      L  ++ S   + + L
Sbjct: 126 VEHPSSEIEKEYEVITVFEYPDEILQKFLRGVRIEGVFYK----ALSAERISKNKMRIVL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNREI++V +FFN K+ +L R+  G   L  L +G  R ++ + ++  LG
Sbjct: 182 IEGKNREIRRVLKFFNIKIKKLTRVRIGCVYLADLPSGKHRPLTSEEIKGLLG 234


>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 =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 67/212 (31%), Positives = 110/212 (51%), Gaps = 12/212 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K IA +G+ SRR+    + + +V VNG L+   A  V + D + ++   +   +    
Sbjct: 282 LNKYIAHSGLCSRRKAVDFVKEGKVTVNGELITEPAFKVTAKDEVAINNRKINIQKNLVY 341

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L +KP G +TT  DP+GR TV +   +  +   RV  VGRLD NT GLLLLTNDG LA+
Sbjct: 342 ILLNKPKGYITTTDDPEGRKTVMELIQDATTEEQRVYPVGRLDRNTSGLLLLTNDGELAQ 401

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT----QKGSNAW 188
            L  P     ++Y V  +  + +          ++QG+   D    +D     + G    
Sbjct: 402 KLAHPKHNIKKIYHVGLNKPLTKAHFE-----NILQGVTLEDGVANVDALGYVEAGDKTQ 456

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           V + +  GKNR ++++FE   ++V +L R++Y
Sbjct: 457 VGIEIHSGKNRIVRRIFEHLEYEVEKLDRVTY 488


>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 =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 118/218 (54%), Gaps = 4/218 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R++K IA++GI SRR+ + +I +  VKVNG +++     +    D +EV+G  ++  E+ 
Sbjct: 4   RLNKYIAQSGICSRRKADELIKEGIVKVNGEIIKDLGAKINPEKDVVEVEGNIIKPVEKK 63

Query: 74  RLWLYHKPIG-LVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP+G L     D  GR T+ D L   +I   +  VGRLD N+EGLL+LTNDG  
Sbjct: 64  IYIKIYKPVGYLSAVGKDKFGRKTLTDLLKELNIKENLFPVGRLDYNSEGLLILTNDGEF 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  ++Y V    +V++++LN +KKG +++   +   +V +      + W+ 
Sbjct: 124 ANKIAHPRHEIRKIYHVEVVPKVNEERLNQMKKGAILEDGFFKPDKVEILKHTKDSTWLL 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
             +  GK R +++    FN KV RL+R+      +  L
Sbjct: 184 FEIHSGKKRILRRYVSKFNHKVRRLVRVKIDSISIENL 221


>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 =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 134/243 (55%), Gaps = 19/243 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  S   I V G  ++++   
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVETSLQKITVSGKQVKQSSE- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + +L +KP G+V+  SD + ++ +      D +P ++     VGRLD +TEGLLL+TN+G
Sbjct: 61  KYFLLNKPAGVVSAVSDKEHQTVIDLIKESDRVPQLYP----VGRLDRSTEGLLLITNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGS 185
            L   +  P     + Y V  +  +  D     + G+      IC    +++   + + S
Sbjct: 117 PLGYRMLHPKYHVAKTYYVEVNAFLADDAPAFFENGVSFDDGTICKPAKLEIITASTEES 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILR 242
           +A+VT+   EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   K+IL+
Sbjct: 177 SAYVTIS--EGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTEKEILK 234

Query: 243 EQL 245
             L
Sbjct: 235 NYL 237


>gi|296131694|ref|YP_003638941.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296030272|gb|ADG81040.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 126/230 (54%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ KV+A  G+ +R+E +++I +++V+VNG L +   ++V    D I V+G P+   + 
Sbjct: 7   QRLDKVLAHMGLGTRKEAKKLIKERKVEVNGELAQDPGLHVRPGQDRIVVNGEPVEYRQF 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP G+++   D  G+  V    P+  S     VGRLD +TEGLLLLTNDG LA
Sbjct: 67  VYLML-NKPQGVLSATGDESGQVVVDLLSPNYQSFHPFPVGRLDKDTEGLLLLTNDGHLA 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVT 190
             L  P     + Y     G V Q+ + + ++G+++    Y  +   L   + G  + V 
Sbjct: 126 HRLLSPKKHVPKTYYATVSGTVTQEDVEMFRQGVILDD-GYRTLPGCLKILRSGPESEVE 184

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           + + EGK  ++K++F+    KV  L RI+ GP  L  TL  G  RE++++
Sbjct: 185 LTIYEGKYHQVKRMFQAVGKKVTYLKRIAMGPLTLDNTLKPGEYRELTEE 234


>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 =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 122/231 (52%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E +I + RV+++G L+      V      + VDG  +R     
Sbjct: 20  RLQKLLAQAGFGSRRKCEEIITEGRVEIDGELVTELGTRVDPKHQEVRVDGSRVRVNPNH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  VTLALNKPKRVLSAMEDPKGRYTLSDIVGDKYDRIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y     G++  Q    L+  G+ +  G    D    LD  +  N  V V
Sbjct: 140 VMHPKYEVEKTYIATLEGRISGQVCRRLVTTGVQLDDGWIKLDRCAILDASR-DNTLVKV 198

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R
Sbjct: 199 VLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGSYRVLSQTEVR 249


>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 =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 117/237 (49%), Gaps = 8/237 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +EN  P    R++K +A AG+ SRRE +  I    V VNG ++      V+ TD ++   
Sbjct: 248 EENIDPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVTELGTKVLRTDEVKFHD 307

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LL
Sbjct: 308 NPV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTGVLL 366

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG +A  L  P     +VY V     V    L  + +G+ ++ G  + D     D  
Sbjct: 367 LTNDGDMASKLTHPKFLKKKVYHVHLDKNVTAHDLEQIAQGVTLEDGEIHADAVEYADEH 426

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             S   V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K
Sbjct: 427 DKS--QVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFLTEK 481


>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 =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 92/245 (37%), Positives = 130/245 (53%), Gaps = 14/245 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
           +R+ K +ARAG+ASRR  E +I   RV VNG+  +     V   D + VDG P+  R  +
Sbjct: 3   ERLQKRLARAGVASRRAAEALITSGRVTVNGVTAQ-LGQTVTEADEVLVDGQPIAQRPTQ 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                LY KP G VTT  D  GR TV D +P++   +  VGRLD ++EGLLLLT DG L 
Sbjct: 62  HVTFALY-KPRGFVTTARDELGRRTVLDAMPNVPG-LHPVGRLDRDSEGLLLLTTDGDLT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VYR    GQ D+  L  L +G+ ++    G  +V         AWVT+
Sbjct: 120 LTLTHPRYGHEKVYRAWTDGQPDEAALGRLARGMNLEDGPTGPAEV---RAAPDGAWVTI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG----P 247
             REG+NR+++++ +   + V RL+R   G   L  L  G  RE+ ++ L+E L     P
Sbjct: 177 --REGRNRQVRRMLDAVGYPVTRLVRTRVGGLWLEDLGPGEYRELDERALQELLNVSLVP 234

Query: 248 HLLEE 252
           H + E
Sbjct: 235 HRVRE 239


>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 =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 117/226 (51%), Gaps = 1/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +++AG+ SRR  E +I Q +V VNG  +++    V   TD I+V+G         
Sbjct: 4   RLQKYLSQAGVDSRRACEDIILQGKVSVNGKTIKKLGTKVNPETDIIKVNGKVCSLKYDF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G++TT  DP GR TV D LP    RV  VGRLD  TEGLL+LTNDG +   
Sbjct: 64  IYILINKPKGILTTVKDPLGRPTVLDLLPEFCERVFPVGRLDKETEGLLILTNDGEVTYK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  + ++ Y     G V  +K+  L+KGI+++       +  +     ++  + + +
Sbjct: 124 LTHPKYKVIKTYVAHVRGIVGNNKIKSLEKGIILEDGVTAPAKANILKVLRNSTIIKLEI 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EG+ R+++++ +     +  L R   G   +  L  G  R +S++
Sbjct: 184 HEGRKRQVRRMCDSIGHPIIELKRTQIGDISIKGLKPGEWRLLSQR 229


>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 =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 124/233 (53%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+++ +A  GIASRR  ++++A  RV VNG + +   + ++   D + VDG      E  
Sbjct: 11  RINRYLAMCGIASRRAADKLVADGRVTVNGKIADEPGLRILPFKDEVIVDGRKFVVPEAK 70

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L +KP  ++TT  D   R T+ D L S+  RV  VGRLD  T G++LLTNDG LA 
Sbjct: 71  KVYILLNKPRNVITTSHDEKDRETILD-LVSVEERVYPVGRLDRKTTGVILLTNDGILAH 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVT 190
            L  PS+   + Y      +  Q  L+ L  G+ ++  G      Q  L    G   W++
Sbjct: 130 RLMHPSSNVKKEYVAELDKRFPQGLLSQLVGGMKLKDTGEKVSPCQAKL-LDDGMRIWIS 188

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +   EGKN +++++ E   + V +L R++Y   + G L  G+ R +SK  +RE
Sbjct: 189 I--HEGKNHQVRRMLETLGFDVTKLERVAYAGLKAGDLRRGAWRHLSKNEVRE 239


>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 =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 117/237 (49%), Gaps = 8/237 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +EN  P    R++K +A AG+ SRRE +  I    V VNG ++      V+ TD ++   
Sbjct: 248 EENIDPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVTELGTKVLRTDEVKFHD 307

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LL
Sbjct: 308 NPV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTGVLL 366

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG +A  L  P     +VY V     V    L  + +G+ ++ G  + D     D  
Sbjct: 367 LTNDGDMASKLTHPKFLKKKVYHVHLDKNVTAHDLEQIAQGVTLEDGEIHADAVEYADEH 426

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             S   V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K
Sbjct: 427 DKS--QVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFLTEK 481


>gi|291513764|emb|CBK62974.1| pseudouridine synthase family [Alistipes shahii WAL 8301]
          Length = 455

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 123/240 (51%), Gaps = 12/240 (5%)

Query: 3   DKNIVQENFTPQ------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           DK      F P+      R+++ IA++GI SRRE +  I    V VNG ++      V+ 
Sbjct: 204 DKPASYPKFNPEKQTGEMRLNRFIAQSGICSRREADDFITAGVVSVNGKIVTELGTKVLP 263

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLD 115
           TD +  +  P++  ++  L L +KP G VT+  DP    TV + +  +   R+  VGRLD
Sbjct: 264 TDEVRFNDEPVQGEKKVYLVL-NKPKGYVTSLDDPHAGKTVMELVSGACTERIYPVGRLD 322

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD 174
            N+ GLLL TNDG L + L  PS +  ++Y+V     + +  ++ + +G+ ++ G  + D
Sbjct: 323 KNSLGLLLFTNDGDLTKQLTHPSYKKKKIYQVTLDKPLTRADMDRIAEGVTLEDGEIFAD 382

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +   K +   V + +  G+NR ++++FEF  + V +L R+ Y       L  G+ R
Sbjct: 383 ---EISYVKENKQEVGIEIHSGRNRIVRRIFEFLGYTVTKLDRVYYAGLTKKNLKRGAWR 439


>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 =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 122/229 (53%), Gaps = 11/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA+ G ASRR+ E  I   +V VNG  LE  +  V   D +++DG  L K ++  
Sbjct: 2   RINKYIAKTGFASRRKSEEYIKNGKVFVNGNKLEDLSYQVKEEDEVKIDGKIL-KIQKNF 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +  +KPIG ++++ DP     + + L +I  R    GRLD ++ GL+++TNDG +   +
Sbjct: 61  YYKLNKPIGYISSNYDPHNEKDL-NKLLNIDERFFCAGRLDKDSHGLMIITNDGKITNKI 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAWVT 190
             PS +  ++Y V+    VD+ KL   ++   + G+     ++T D +            
Sbjct: 120 IHPSKKIDKIYIVK----VDK-KLTAYQEKNFMDGLKLSQKEITSDAKISLIDKEKITYK 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + +G NR+I+++FE+F  KV  L RI  G   L  L  G  +++SKK
Sbjct: 175 VTIHQGYNRQIRRMFEYFKIKVIDLKRIKIGQICLDDLKDGDYKKLSKK 223


>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 =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 121/238 (50%), Gaps = 7/238 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+I+ +   P R++K +A AG+ SRRE +  I    V VNG ++      V  TD ++  
Sbjct: 8   KDILTDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKVKRTDEVKFH 67

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 68  DQPV-NIERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 126

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ + +GI +  G  + D +    D
Sbjct: 127 LLTNDGDLASKLTHPKFLKKKIYHVYCDKNVTKADLDQIVQGITLDDGEIHADAVSYASD 186

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           T K   + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++
Sbjct: 187 TDK---SQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTE 241


>gi|300934025|ref|ZP_07149281.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 335

 Score =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 127/233 (54%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV++ AG+ASRR  E++IA  RV+VNG ++++  + +  S D + VDG  ++  E  
Sbjct: 96  RLQKVLSSAGVASRRMSEKLIAAGRVEVNGEVVQQMGLRIDPSVDVVRVDGTRVQVNEEM 155

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             +  +KP G+ +T  D  GR  V + + + F++   +  VGRLD  TEGLLLLTNDG L
Sbjct: 156 VYFALNKPRGVHSTMHDDLGRPHVGELIEAKFNQGQGLFHVGRLDAATEGLLLLTNDGEL 215

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+ D+  +  LK G+ ++ G+   D    +D  +G  + +
Sbjct: 216 ANRLMHPKYEVSKTYMATVLGEADRGLIRTLKDGVDLEDGMARADYVQIVDVWQGK-SLI 274

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  L+
Sbjct: 275 KVELHEGRKHIVRRMLKAAGFPVQALVRTKIHTVQLGEQKPGTVRALNRSELQ 327


>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 =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 11/239 (4%)

Query: 4   KNIVQENFTPQ-----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-ST 57
           KN  Q++ TP+     R+++ IA +GI SRR+ + +I    + VN +++      V  +T
Sbjct: 146 KNTSQQSSTPKEPDQIRLNRYIANSGICSRRKADELITSGAITVNDVVVSELGAKVNPTT 205

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
           D ++ +G  L K E+    L +KP   +TT  DP  R TV + + +  S R+  VGRLD 
Sbjct: 206 DKVKYNG-QLLKREKMVYVLLNKPKDFITTTEDPQERKTVMELVKNATSERIYPVGRLDR 264

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM 175
           NT GLLLLTNDG LA  L  P     ++Y V     + Q   N +  G+ ++ G    D 
Sbjct: 265 NTTGLLLLTNDGDLAEKLSHPRNNITKIYNVELSKNLTQGDFNKIAFGVELEDGFIKPDA 324

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +    G+   + + +  GKNR ++++FE   ++V +L R+ Y       L  G  R
Sbjct: 325 VSYVSG--GTKKEIGIQIHSGKNRIVRRIFESLGYEVEKLDRVIYANLTKKDLTRGKWR 381


>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 =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 121/239 (50%), Gaps = 7/239 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++  
Sbjct: 240 KDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFH 299

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 300 DEPV-SIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 358

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +  G  + D +    +
Sbjct: 359 LLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASE 418

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           T K   + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 419 TDK---SQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 474


>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 =  110 bits (276), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/235 (33%), Positives = 130/235 (55%), Gaps = 12/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ KV+A   I +R+EV+ ++ Q+ + V+G++     ++V++ +  I VDG PL     
Sbjct: 4   ERLDKVLANMAIGTRKEVKALVKQRLIVVDGVVATDPGMHVIAEEQEILVDGEPLN---- 59

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            + W+Y   +KP G+V+   D +   TV D LP  ++ +V  VGRLDI+TEGLLLLTNDG
Sbjct: 60  FKRWVYVLLNKPPGVVSATED-NVHETVVDLLPYEWAIKVHPVGRLDIDTEGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L+  L  P  +  + Y  R  G+V +  +    KG+ ++       ++ +    G  + 
Sbjct: 119 HLSHSLLSPKKKVDKEYFARIEGRVTERHVQEFAKGVELEDFTTLPAKLEI-ISSGETSE 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + V + EGK  ++K++F  F+  V  L RI  GP  L   LA G  RE++++ L 
Sbjct: 178 IRVTIMEGKFHQVKRMFAAFDLHVVYLQRIRMGPLHLDPSLAPGEYRELTEEELH 232


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 116/225 (51%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A+ G+ASRR  E +I   RV VNG ++      V   D + VD   +   E+  
Sbjct: 15  RLQQYMAKCGVASRRASEAIICAGRVTVNGTVVTELGTKVDVQDKVCVDEKEIHLEEKKC 74

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G V + SD  GR    D L   +S R+ +VGRLD+ + GL++ TNDG  A  
Sbjct: 75  YVLLNKPSGYVCSASDEKGRPVAADLLKEAYSERLYNVGRLDMFSSGLIIFTNDGDFAAK 134

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  + Y V     + +   +    GI I G+ Y       D ++ ++  + + L
Sbjct: 135 LSHPSAELEKEYIVDTSLPMPRFLADDFMDGIRIDGVFYR----CKDARELNSHRMRIVL 190

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EGKNREI++VFE +   +  L+RI  G   +G L  G  R++++
Sbjct: 191 VEGKNREIRRVFEKYEVGIKSLMRIRIGCVGVGELQFGQFRDLTQ 235


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 121/239 (50%), Gaps = 7/239 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++  
Sbjct: 240 KDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFH 299

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 300 DEPV-SIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 358

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +  G  + D +    +
Sbjct: 359 LLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASE 418

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           T K   + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 419 TDK---SQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 474


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 126/228 (55%), Gaps = 5/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA+AG+ASRR+ E  I +  V VNG  L+  +  V   D ++V G  L   E+  
Sbjct: 2   RINKYIAKAGLASRRKSEEYIKKGLVFVNGKKLDDLSYQVKENDQVKVMGKLLEIKEKFY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KPIG ++++ DP  +  + ++L  I  R    GRLD ++ GL+L+TNDG +   L
Sbjct: 62  YKL-NKPIGFISSNYDPHNKKDL-NSLVKIDHRFFCAGRLDKDSHGLMLITNDGKITNKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGL 193
             PS +  + Y V+    +++D   L +KGI +       D ++ L   + S  +  + +
Sbjct: 120 IHPSKKIEKTYIVKVDKLLNKDDEALFRKGIKLSVNEKTSDAKINL-IDENSKIYEVI-I 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G NR+++++F +F  KV  L RI  G  +LG L  G  ++++KK L
Sbjct: 178 HQGFNRQVRRMFLYFGSKVIDLKRIKIGQIELGKLEDGKYKKLNKKEL 225


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 110/222 (49%), Gaps = 2/222 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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  KVYIALNKPEGYVSTVKDERGRKTILD-IVKVNERIFPIGRLDYNTSGLIILTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    D++     G+ I G         +  +      V + 
Sbjct: 122 KIIHPREEIDKVYIAVIKGVPSNDEIKNFCNGVDIGGYVTSKANFEIIEKLDDKCKVKIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + EGKNR+++++ E     V  L R+S G   L T+  G  R
Sbjct: 182 IHEGKNRQVRRMCEKIGHPVIALKRVSVGKISLSTIKRGEWR 223


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 129/238 (54%), Gaps = 8/238 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+++ I+  G+ASRR+ +++I + +VKVNGI ++     V    D +EV+G  + KA R 
Sbjct: 9   RLNRFISMCGVASRRKADKLIKEGKVKVNGITIKEMGYRVDPQKDVVEVEGRVI-KAPRY 67

Query: 74  RLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   +++ ++  DG+ ++ + + +I  RV   GRLD N EGLL+LTNDG LA 
Sbjct: 68  RYVILNKPCCYLSSLAEGKDGKKSIKELIKNIPERVYPAGRLDYNAEGLLVLTNDGELAN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y V   G+V+   L  + KG  ++ G    D    +  QK S   + V
Sbjct: 128 RIMHPRYKLKKTYLVWVEGRVNPKTLKEMAKGAHLEDGFARPDKVRIVKMQKDST-LLEV 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLG 246
              EG+   +K+    F  KV  L R + GP +LG L  G  R+++ +   +LR  LG
Sbjct: 187 VFHEGRKHIVKRFMAKFGHKVKALKRTAIGPIKLGKLPPGKWRDLTAEELSLLRRALG 244


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 114/207 (55%), Gaps = 13/207 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           PQR++KV+A AG+ASRR  E +I Q +V VNG +       V +S D I V+G  + K  
Sbjct: 172 PQRLAKVLAAAGVASRRTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRISKKL 231

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNL--------PSIF-SRVISVGRLDINTEGL 121
             +L+   +KP G + +  +P    ++FD+         P +   R+ +VGRLD+ T GL
Sbjct: 232 PPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVPKPRLFTVGRLDVATSGL 291

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD 180
           +++TNDG  A+ L  PS+  ++ Y V   G V ++ L  + +G  I G+ C  D+   LD
Sbjct: 292 IIITNDGEFAQKLSHPSSNIMKEYVVTIDGPVHRNHLIAISEGTKIDGVKCIPDLVEPLD 351

Query: 181 TQKGSN-AWVTVGLREGKNREIKKVFE 206
            Q  +    + + + EG+N E++++ +
Sbjct: 352 VQSNTKRTRIRIAVHEGRNHEVRELVQ 378


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 114/220 (51%), Gaps = 7/220 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++  
Sbjct: 242 KDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFH 301

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 302 DEPV-SIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 360

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +  G  + D +    +
Sbjct: 361 LLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASE 420

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           T K   + V + +  GKNR ++++FE   +KV +L R+ +
Sbjct: 421 TDK---SQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYF 457


>gi|126640866|ref|YP_001083850.1| putative ribosomal large subunit pseudouridine synthase B
           [Acinetobacter baumannii ATCC 17978]
          Length = 279

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 65/169 (38%), Positives = 96/169 (56%), Gaps = 5/169 (2%)

Query: 58  DHIEVDG----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVG 112
           D + +DG      +    R R+ +Y+KP G + + +DP+ R TVFD+LP I + R + VG
Sbjct: 18  DELRIDGRKVQFQIEDEIRRRVLIYYKPEGEICSRNDPEKRPTVFDHLPQIANDRWVMVG 77

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDIN+ GLLL TNDG LA  L  PS +  R Y VR  G+V       +  G+ ++    
Sbjct: 78  RLDINSTGLLLFTNDGELANRLMHPSNEIEREYAVRVMGEVTPQLRQNMVNGVELEDGPA 137

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                +    +G N W  V ++EG+NRE++++FE    KV+RL+R  YG
Sbjct: 138 KFESFSEIGGEGINRWYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYG 186


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 134/243 (55%), Gaps = 19/243 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  S   I V G  ++++   
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQKITVSGKQVKQSSE- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + +L +KP G+V+  SD + ++ +      D +P ++     VGRLD +TEGLLL+TN+G
Sbjct: 61  KYFLLNKPAGVVSAVSDKEHQTVIDLIKEADRVPKLYP----VGRLDRSTEGLLLVTNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGS 185
            L   +  P     + Y V  +  +  D     + G+      IC    +++   + + S
Sbjct: 117 PLGYRMLHPKYHVAKTYYVEVNAFLADDAPAFFENGVSFDDGTICKPAKLEIITASPETS 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILR 242
           +A+VT+   EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   K+IL+
Sbjct: 177 SAYVTIS--EGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTEKEILK 234

Query: 243 EQL 245
             L
Sbjct: 235 NYL 237


>gi|225448976|ref|XP_002270186.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 393

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 129/239 (53%), Gaps = 17/239 (7%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ENF   PQR+SKV+A AG+ASRR  E +I + RV VNG +       V  + D I V+G 
Sbjct: 136 ENFRDPPQRLSKVLAAAGVASRRNSEELIFEGRVTVNGSVCNTPQTRVDPARDMIYVNGN 195

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRS--TVFDNL--------PSIF-SRVISVGR 113
            L K    +++L  +KP G + +  + + +S   +FD+         P +   R+ +VGR
Sbjct: 196 RLPKKLPPKVYLALNKPKGYICSSGEKESKSVLCLFDDYLKSWNKQNPGVPKPRIFTVGR 255

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY 172
           LD+ T GL++LTNDG  A+ L  PS++  + Y     G V++  L  + +G VI+G+ C 
Sbjct: 256 LDVATTGLIILTNDGDFAQKLSHPSSKLSKEYIATIDGVVNKRHLIAISEGTVIEGVHCT 315

Query: 173 GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            D    L  Q   S   + V + EG+N E++++ +    +++ L RI  G F+L + L 
Sbjct: 316 PDSVELLPPQPNISKPRLRVVVHEGRNHEVRELVKSAGLQIHSLKRIRIGGFRLPSDLG 374


>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 =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 81/218 (37%), Positives = 110/218 (50%), Gaps = 9/218 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A AGI SRR  E +IA   V VNG             D I V G  +R   + +
Sbjct: 8   RLQKFLADAGICSRRAAETLIADGEVWVNGQPATLGQKITPDVDKITVRGKNVRTVAQPK 67

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           L L  HKP GLV ++ DP    TVFD LP   +R      GRLD ++EGLL+LT DG LA
Sbjct: 68  LTLAMHKPRGLVCSNDDPHNPETVFDLLPREMARHRFFCAGRLDKDSEGLLILTTDGDLA 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             L  PST  ++ Y V         +L  L +G+ I+G    + Y  + V  +  + S +
Sbjct: 128 NRLMHPSTVVVKRYHVVLAEPFPAKRLGALLRGVTIEGERLKVEYAAL-VNPNAAELSTS 186

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + V L  GK REI+++F    ++V RL R   G F L
Sbjct: 187 -LDVHLHHGKKREIRQLFMALGFEVRRLRRYQIGAFPL 223


>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 =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 128/240 (53%), Gaps = 15/240 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           V+ N    R+ K ++  G+ +R EV+++I   ++ +NG +  +    V    D + V+G 
Sbjct: 5   VERNINMIRLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNG- 63

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLL 124
            + K +R   +L++KP G V+   D +   TV D +  ++   +  VGRLDI+TEGLLL+
Sbjct: 64  RIVKYQRYEYYLFNKPSGCVSATCD-NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLI 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----L 179
           TNDG L+  L  PS    + Y  R  G+V  D +   K+GI I     G+ + T     +
Sbjct: 123 TNDGALSHELLSPSKHVAKTYYARIDGEVTLDDIIRFKEGIDI-----GEEKPTKPAELV 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
             + GS + + + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++
Sbjct: 178 IKKSGSVSEIELTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQ 237


>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 =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 122/231 (52%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + VDG  +R   R 
Sbjct: 20  RLQKLLAQAGFGSRRKCEEMITDGRVEVDGELVTELGTRVDPKRQQVRVDGSRIRLNPRH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  ITLALNKPRKVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y     G +       L++ G+ +  G    D    +D+ +     V V
Sbjct: 140 VMHPKYEVEKTYIATLEGHMSGTVCRRLVRTGVQLDDGWIKLDHCSIIDSNR-DQTIVKV 198

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L  G+NR ++++F    + V RL+R   GP +LG + +GS R +S+  +R
Sbjct: 199 VLHSGRNRIVRRIFGAIGFPVKRLVRTQIGPIKLGDIKSGSYRVLSQDEVR 249


>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 =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 114/220 (51%), Gaps = 7/220 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++  
Sbjct: 243 KDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFH 302

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 303 DEPV-SIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 361

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +  G  + D +    +
Sbjct: 362 LLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASE 421

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           T K   + V + +  GKNR ++++FE   +KV +L R+ +
Sbjct: 422 TDK---SQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYF 458


>gi|294775216|ref|ZP_06740740.1| pseudouridylate synthase [Bacteroides vulgatus PC510]
 gi|294450921|gb|EFG19397.1| pseudouridylate synthase [Bacteroides vulgatus PC510]
          Length = 488

 Score =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 114/220 (51%), Gaps = 7/220 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++  
Sbjct: 243 KDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFH 302

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 303 DEPV-SIERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 361

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +  G  + D +    +
Sbjct: 362 LLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASE 421

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           T K   + V + +  GKNR ++++FE   +KV +L R+ +
Sbjct: 422 TDK---SQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYF 458


>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 =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 129/228 (56%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
            R++K ++  GIASRR +++ I + R+KVNG  +    ++V   D I +D   +  ++ E
Sbjct: 1   MRINKFLSSLGIASRRAIDKYIEEGRIKVNG-AIPSIGIDVNEDDEIYIDNKKIETKRIE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ +++  SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFILNKPLEVLSASSDDRGRRTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P ++  + Y ++  G+V ++++  LKKG++++       +V+      +   + +
Sbjct: 119 NRLVHPKSEIYKKYYIKVFGEVKKEEIEELKKGVLLEDGKTLPAKVSGIKYDKNKTSMYI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 179 SIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLKEGKYRELTKE 226


>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 =  110 bits (275), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 116/246 (47%), Gaps = 22/246 (8%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVD 63
           N+    FT  R+ + +AR G+ASRR  E++I+  RV VNG++ +     V  + D + VD
Sbjct: 71  NLPSSTFT-MRLQRYLARCGVASRRGAEKLISAGRVTVNGVVQDVLGSKVDCAHDVVCVD 129

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
           G P    +     + +KP G++TT SDP G   V   +P   +  + +VGRLD +T GLL
Sbjct: 130 GTPCVLGDEHTYLILNKPQGVLTTMSDPFGHPCVAALVPKDTYPGLFAVGRLDGDTTGLL 189

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICY--------- 172
           L + DG +   L  PS    + Y     G + +     L+ GI++  G C          
Sbjct: 190 LFSTDGNMGNRLLHPSHHVWKTYVCLLQGSLTRAAQKQLEAGIMLDDGPCAPSHITRLAP 249

Query: 173 GDMQVTLDTQKG---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            D   TL  Q                ++ +REG+  ++K++F+     V RL R  +GP 
Sbjct: 250 TDALCTLAPQCHILDGIPSARGYTICSISIREGRYHQVKRMFDAVGCPVVRLHRAQFGPL 309

Query: 224 QLGTLL 229
            LG  L
Sbjct: 310 SLGDAL 315


>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 =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 129/235 (54%), Gaps = 9/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++  ++ AGI+SRR+ ++ I    ++VNG  + R    + + D +   G  ++   +  
Sbjct: 7   RLNHYLSNAGISSRRKADQFIQSGAIEVNGKPVRRLGTVIHTNDLVTFYGEKIKIQNKIY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G +TT  DP  R TV + +P++   R+  VGRLD +T G+LLLTNDG +A  
Sbjct: 67  LLL-NKPKGFITTTKDPFNRKTVMNLIPNLSKYRIFPVGRLDRSTTGVLLLTNDGSIAEK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P +   ++Y V    ++  + L+ ++KG +   +  G ++V    +  S   + +GL
Sbjct: 126 LTHPKSHVQKIYHVLLDKEIKNEDLDQIRKGKIY--LKEGKVKVIFVNKGHSKYQIKIGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPF-----QLGTLLAGSTREVSKKILRE 243
             G NR IK++F+  N++V +L R+++G       Q+G     + +EV   ++++
Sbjct: 184 YIGWNRIIKRIFKKLNYQVIQLDRVNFGGLSKKNIQIGNWCFLNQKEVENILIKK 238


>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 =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/233 (35%), Positives = 119/233 (51%), Gaps = 5/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +I+  RV V+G ++      V  T   I VDG+ L+     
Sbjct: 9   RLQKVLAGAGLGSRRACEDLISAGRVSVDGEVVRELGTRVDPTAAVIHVDGLRLQLDPGV 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+ +T  D  GR  + + +     R+  VGRLD +TEGLLLLTNDG LA  
Sbjct: 69  VTLALNKPRGVHSTMHDDRGRPALAELVADRPERLFHVGRLDADTEGLLLLTNDGELAHR 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  + Y  R  G+V +     LK GI +        + T+  Q   +A V + L
Sbjct: 129 LAHPSYEVPKTYVARVTGRVARGLGRRLKDGIELDDGPARVDRFTILEQGPDSAVVELVL 188

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EG+NR ++++ +     V RL R   GP  LG L  G+TR +      E+LG
Sbjct: 189 HEGRNRIVRRLLDAAGHPVQRLTRTRVGPVLLGQLRPGATRVIDG----EELG 237


>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 =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 119/226 (52%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G+ SRREV++++   +++VN I+++    N+  S D IE DG  L   E  
Sbjct: 6   RLDKFLTECGLGSRREVKKLLDNGKIRVNDIIVKNPQANIKESIDKIEYDGNKLEYKE-F 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   DP    TV + LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 65  RYYIMNKKGGYITATEDPK-EKTVMELLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLG 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +   ++ + ++  L++G+ I G      +  +  +K     + +
Sbjct: 124 HSLLSPKKHVDKTYYAKLEKEIGEVEIKKLEEGVDIGGYITQPAKAKIVGEK----EIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +REGK  ++KK+ E  N KV  L R+++G  +L  +  G  RE++
Sbjct: 180 TIREGKFHQVKKMLEAVNNKVVYLKRVTFGKLELKDMELGEVREIN 225


>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 =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 115/227 (50%), Gaps = 12/227 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+   +A++G  SRR  E +I   RV +N   +      V   D + VD   +  A+R
Sbjct: 6   PIRLQAYMAKSGCGSRRFCETLITAGRVTINTKRVTELGTKVNEEDVVMVDDQLIEPADR 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           T  +  +KP G V T+ DP+ +    D L  I  +  +  +GRLD  + GL+L TNDG +
Sbjct: 66  TYYYALYKPRGYVCTNYDPNEKLYARD-LIDIADKNLLFHIGRLDKESSGLILYTNDGDV 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---SNA 187
           A+ +  PS +  + Y V    +V ++ L    KGI I      D+      ++    S  
Sbjct: 125 AQKIMHPSREIEKEYLVSCSTEVRREDLEEALKGIYI------DIPQPYRIKRFEILSKK 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           WV + L EGKNREI+K+F ++ + V +L+R+  G  +LG +  G  R
Sbjct: 179 WVRIILTEGKNREIRKIFSYYGYDVKQLVRMRIGCIELGEMQPGQYR 225


>gi|289178586|gb|ADC85832.1| Ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           animalis subsp. lactis BB-12]
          Length = 266

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 122/231 (52%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + VDG  +R   R 
Sbjct: 29  RLQKLLAQAGFGSRRKCEEMITDGRVEVDGELVTELGTRVDPKRQQVRVDGSRIRLNPRH 88

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 89  ITLALNKPRKVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 148

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y     G +       L++ G+ +  G    D    +D+ +     V V
Sbjct: 149 VMHPKYEVEKTYIATLEGHMSGTVCRRLVRTGVQLDDGWIKLDHCSIIDSNR-DQTIVKV 207

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L  G+NR ++++F    + V RL+R   GP +LG + +GS R +S+  +R
Sbjct: 208 VLHSGRNRIVRRIFGAIGFPVKRLVRTQIGPIKLGDIKSGSYRVLSQDEVR 258


>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 =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 122/231 (52%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E +I + RV+++G L+      V      + VDG  +R     
Sbjct: 20  RLQKLLAQAGFGSRRKCEEIITEGRVEIDGELVTELGTRVDPKHQEVRVDGSRVRVNPNH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  VTLALNKPKRVLSAMEDPKGRYTLSDIVGDKYDRIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y     G++  Q    L+  G+ +  G    D    LD  + S   V V
Sbjct: 140 VMHPKYEVEKTYIATLEGRISGQVCRRLVTTGVQLDDGWIKLDRCAILDASRDST-LVKV 198

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R
Sbjct: 199 VLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKSGSYRVLSQTEVR 249


>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 =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 121/228 (53%), Gaps = 16/228 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA     SRRE +++I + +V +N  +++  +  V +   + V+G  L++ E   
Sbjct: 2   RLNQYIAHHSKFSRREADQLIKEGKVSINKEIIKDFSYQVKNHTKVYVNGKCLKEKEEYT 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+KP G + +  D  GR  ++++LP  F   I +GRLD  +EGLLLLT+   +A   
Sbjct: 62  VIVYNKPKGELVSKRDDRGRRVIYESLPKRFKDFIPIGRLDFASEGLLLLTDSVKVA--T 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAWVT 190
           +L  ++  RVY ++  G++ ++    ++ G+ +Q    G  Q +    ++       WV+
Sbjct: 120 KLMESKLERVYLLKLSGEIKEEVFEAMENGLSLQDARLGGHQKSKIKAMEFSPFMGYWVS 179

Query: 191 ----------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                     V + EGKNRE+++ F  FN KV  L R++YG   L  L
Sbjct: 180 KNTAKLSKIKVAINEGKNRELRRFFAHFNLKVLDLKRVAYGFVSLNNL 227


>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 =  110 bits (274), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 79/231 (34%), Positives = 128/231 (55%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ +V+A  G  +R+ ++++I ++RV+VNG   E   ++V+   D+IEV+G PL   E 
Sbjct: 7   QRLDRVLAHMGFGTRKMIKKLIKEKRVQVNGRPAEDPGLHVIPGRDYIEVNGEPLVYEEY 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G+++   D   +  V D LP  +       VGRLD + EGLLLLTNDG L
Sbjct: 67  IYLML-NKPQGVLSATEDRYAK-VVVDLLPPRYRAFHPFPVGRLDKDAEGLLLLTNDGEL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWV 189
           A  L  P     ++Y     G V +  +   ++GI++    Y  M   L   + G+ + V
Sbjct: 125 AHRLLSPKKHVSKMYYAVVDGIVTETDVEAFRQGIILND-GYRTMPGELTILRSGTESEV 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
            + + EGK  ++K++FE  + +V  L RI+ GP +L  LL  G  RE++++
Sbjct: 184 ELTIYEGKYHQVKRMFEAVSKRVLYLKRIAMGPLRLDELLRPGEYRELTEE 234


>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 =  110 bits (274), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 119/237 (50%), Gaps = 16/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+I+     SRRE + +I    VKV+G +++  +  V   + IE++G  L +     
Sbjct: 5   RLNKMISHNTHYSRREADELIKAGHVKVDGNVVQDLSTQVSFKNKIELNGKALFEKHGYS 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LPS F+  +SVGRLD  +EGLLLL +   +   L
Sbjct: 65  VIVYHKQKGELVSKKDDRGRKTIYDTLPSKFAHYLSVGRLDFASEGLLLLCDSPSVVSAL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------VTLDTQ 182
                +  RVY V+ +G V       +++G+ ++    G               V     
Sbjct: 125 MHGDLE--RVYYVKINGLVSPAMEKAMQEGLSLEDARRGGHAKSEIHAMDFAPFVNYRII 182

Query: 183 KGSNAWVT--VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           K S  + T  V + EGKNRE+++ F +F+  V  L R+SYG   LG L  G  R  S
Sbjct: 183 KNSPTFSTIKVTINEGKNRELRRFFGYFDVDVVDLKRVSYGKIDLGMLKPGKHRFFS 239


>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 =  110 bits (274), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 128/233 (54%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+++ +A  G+ASRR  ++++   RV +NG I+LE       S D + VDG  L   E  
Sbjct: 15  RINRYLAMCGVASRRASDQLVEAGRVMINGSIILEPGLKVDPSVDEVIVDGSMLALPEGK 74

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++TT+SD   R TV  N  S+  R+  VGRLD  T G+LLLTNDG LA 
Sbjct: 75  KVYILFNKPKNVITTNSDEKNRETVL-NYISVKERIYPVGRLDRKTTGVLLLTNDGNLAH 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVT 190
            L  PS+   + Y      +     L  L  G+ ++  G      Q  +   +G   W++
Sbjct: 134 KLMHPSSNVKKEYIAVLDKKFPHTLLLQLTGGMRLKDTGEKVSPCQAKI-LDEGFQVWLS 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           +   EGKN +++++FE   ++V++L R++Y   ++G L  G  R + +K +++
Sbjct: 193 I--HEGKNHQVRRMFETLGFEVDKLERVAYAGLKVGDLRRGEWRALDRKEIQQ 243


>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 =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 134/243 (55%), Gaps = 19/243 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  S   I V G  ++++   
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQKITVSGKQVKQSSE- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + +L +KP G+V+  SD + ++ +      D +P ++     VGRLD +TEGLLL+TN+G
Sbjct: 61  KYFLLNKPAGVVSAVSDKEHQTVIDLIKEADCVPKLYP----VGRLDRSTEGLLLITNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGS 185
            L   +  P     + Y V  +  +  D     + G+      IC    +++   + + S
Sbjct: 117 PLGYRMLHPKYHVAKTYYVEVNAFLADDVPAFFENGVSFDDGTICKPAKLEIITASPEKS 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILR 242
           +A+VT+   EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   K+IL+
Sbjct: 177 SAYVTIS--EGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTEKEILK 234

Query: 243 EQL 245
             L
Sbjct: 235 NYL 237


>gi|296085982|emb|CBI31423.3| unnamed protein product [Vitis vinifera]
          Length = 296

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 129/239 (53%), Gaps = 17/239 (7%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ENF   PQR+SKV+A AG+ASRR  E +I + RV VNG +       V  + D I V+G 
Sbjct: 39  ENFRDPPQRLSKVLAAAGVASRRNSEELIFEGRVTVNGSVCNTPQTRVDPARDMIYVNGN 98

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRS--TVFDNL--------PSIF-SRVISVGR 113
            L K    +++L  +KP G + +  + + +S   +FD+         P +   R+ +VGR
Sbjct: 99  RLPKKLPPKVYLALNKPKGYICSSGEKESKSVLCLFDDYLKSWNKQNPGVPKPRIFTVGR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY 172
           LD+ T GL++LTNDG  A+ L  PS++  + Y     G V++  L  + +G VI+G+ C 
Sbjct: 159 LDVATTGLIILTNDGDFAQKLSHPSSKLSKEYIATIDGVVNKRHLIAISEGTVIEGVHCT 218

Query: 173 GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            D    L  Q   S   + V + EG+N E++++ +    +++ L RI  G F+L + L 
Sbjct: 219 PDSVELLPPQPNISKPRLRVVVHEGRNHEVRELVKSAGLQIHSLKRIRIGGFRLPSDLG 277


>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 =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 121/236 (51%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+     SRRE + +I Q  VK+N    + A +N  V + D + ++G  L K  +
Sbjct: 2   RINKFISHNSKYSRREADELIKQGLVKINK---KTALLNDSVNAEDKVFINGKKLHKKTQ 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHK  G + +  D  GR T++  LP  FS  +SVGRLD  +EGLLLLT+   +A 
Sbjct: 59  FSVIIYHKQKGEIVSKKDDRGRKTIYHTLPKQFSTWLSVGRLDFASEGLLLLTDSPVIAD 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------- 183
            L     +  R Y ++  G +D++ +  ++ G+ IQ    G    T  T           
Sbjct: 119 ALMHSDLE--REYYLKVKGNIDKNVIEAMQNGLEIQNEKKGAHAKTKITSMSFAPFLGFE 176

Query: 184 --GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 177 IFGSSGGYTKLKVIINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYR 232


>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 =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 83/240 (34%), Positives = 119/240 (49%), Gaps = 12/240 (5%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +  AG A SRR+ E +I   RV VNG ++   A  V   D + V G      ER 
Sbjct: 8   RLQKYLVLAGAAPSRRKAEDLIRAGRVSVNGAVVGLGA-RVYPGDEVRVGGRRAELPERR 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   HKP G  TT     G  TV++ LP +   +  VGRLD ++EGLLL TNDG L + 
Sbjct: 67  VVLALHKPKGYETTRQSRSGAPTVYELLPDLPG-LHPVGRLDRDSEGLLLFTNDGALTQR 125

Query: 134 LELPSTQWLRVYRV-RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VYRV    G    D L  L++G+V++      ++V     +  +    + 
Sbjct: 126 LTHPRYGVKKVYRVWSRKGTPPPDLLRKLERGLVLKS----GVRVQALKARPKDGGAVIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS----KKILREQLGPH 248
           L EGK RE++ +     + V RL+R+  GP +LG    G+ RE+S    K + R   GP 
Sbjct: 182 LTEGKKREVRYMMAAIGYPVERLVRVKMGPIRLGGQKPGTWRELSASELKALDRAAFGPE 241


>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 =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 119/225 (52%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ +V+A  G+ASRR+ E +I   RV V+G ++    V V      I VDG  LR  ER
Sbjct: 2   ERLQRVLAAHGVASRRKAEELITAGRVTVDGQVVRELGVRVDPERQEIRVDGKRLR-PER 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + +KP G +TT SD  GR TV D L  +  RV+  GRLD  T GLLLLTNDG L  
Sbjct: 61  RRYIMLNKPPGYITTVSDERGRRTVMD-LVQVPERVVPAGRLDRPTAGLLLLTNDGDLLF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V   G    + L+ L++G+ + G      QV     + +   + + 
Sbjct: 120 RITHPRYELEKEYEVLVDGHPPPEVLDQLRRGVTVDGERVVPDQVRPLRIEEAGTVLRIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+NR ++++ +   + V +L R   GP  +  +  G+ R+++
Sbjct: 180 IHEGRNRIVRRMMDRVGYPVLKLTRTRIGPIHVRGVPLGAWRDLT 224


>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 =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 81/254 (31%), Positives = 130/254 (51%), Gaps = 20/254 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           + +E   P R+ + +ARAG+ASRR  ER++   RV VNG ++      V    D + VDG
Sbjct: 1   MTEERIVPMRLQRFLARAGVASRRGSERLMTSGRVTVNGQVVTELGSKVDPLVDVVAVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
           V    AE+    + +KP G +TT  DP GR T+ D +P+  +  +  VGRLD++T GLL 
Sbjct: 61  VVCSIAEKPVYLMLNKPAGYLTTMKDPQGRPTIVDMVPTDTYPGLFPVGRLDMDTTGLLF 120

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
            T DG +A+ L  PS    + Y     G   +++LN L++GI ++       +V +    
Sbjct: 121 FTTDGQMAQELLHPSKHVWKHYVAHVVGTPTEEQLNRLREGIELEDGPAAPAEVEIISDD 180

Query: 180 -------------DTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                         T  G  NA V+V +REG+  ++KK+    + +V  L R ++GP  L
Sbjct: 181 VKMKNLLAPQGLGKTGGGEPNALVSVTIREGRKHQVKKMLLAIHHRVLALHRDTFGPLHL 240

Query: 226 GTLLAGSTREVSKK 239
             +  G  R ++++
Sbjct: 241 TRVKEGEWRLLTEE 254


>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 =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 118/226 (52%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI SRR  +  I+   V VNG ++      V  TD +  DG  L  +E+  
Sbjct: 178 RLNKYIADAGICSRRNADMYISSGNVTVNGEVMTTLGYRVKPTDEVRFDG-KLLSSEKKE 236

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G +TT +D  GR TV D + +  S R++ VGRLD  T GLLLLTNDG L + 
Sbjct: 237 YILLNKPKGFITTTNDEKGRKTVMDLVANATSARILPVGRLDRATTGLLLLTNDGELTKK 296

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    ++Y V    ++D      ++ G+ ++       +++    K  N  + + +
Sbjct: 297 LTHPTHGVRKIYHVILDRKLDYKDFMKIQDGLELEDGFIEVDEISYVNDKPKNE-IGIKI 355

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             G+NR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 356 HSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQQ 401


>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 =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 16/234 (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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----------DMQVTLDTQ-K 183
                +  R Y ++  G++  + +  + +G        G          + +  LD +  
Sbjct: 125 MNSDVE--REYYLKVKGEITPEVITAMNEGFFAADATKGAHAKTAIKSMEFKPFLDYKIF 182

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R
Sbjct: 183 GSSGGFTKLKVVINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWR 236


>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 =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 151/285 (52%), Gaps = 20/285 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAE 71
           R++K ++ AG+ SRRE +R+I ++RV V+G    + AV  M  +    I+VDG  +++ E
Sbjct: 2   RLNKYLSDAGVCSRREADRLIEEKRVLVDG----KPAVQGMQVEDFQEIKVDGKAIKREE 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +  L ++HKP G+  T ++P+ +  V  + N P    RV   GRLD ++EGLLLLTN G 
Sbjct: 58  KKVLLVFHKPKGIECT-ANPNVKKNVISYINYPI---RVYYAGRLDKDSEGLLLLTNQGE 113

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +    +   + Y V     V ++ L  +++G+ + G      +V  +++K     +
Sbjct: 114 LVNQIMKAGSYHEKEYLVTVDKPVTEEFLQSMREGVPVLGTITRKCKVEKESEKVFRITL 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T GL    NR+I+++  +  ++V +L RI     +LG L  GS RE +K+ L ++L   +
Sbjct: 174 TQGL----NRQIRRMCNYLGYEVVKLKRIRIMNIELGNLPIGSYREATKEEL-DELKRQI 228

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
            E+A+   +   +  +  V++     +  P    + K+  + +NG
Sbjct: 229 SEKAEKRQETDFHKGKKPVKNAGKYRN--PSKVRKQKRQEASRNG 271


>gi|322503526|emb|CBZ38612.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 877

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 113/225 (50%), Gaps = 8/225 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLW 76
           + + RAG  SRRE   +IA  +V+VN +        V + D + V G   R +    RLW
Sbjct: 519 RTLPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHQSRLRFAPPRLW 578

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +YHKP  ++ + +D  GR+ +  +   +    ++ VG L +   G+LLLTNDG L+R LE
Sbjct: 579 IYHKPAHVIVSRNDAAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLE 638

Query: 136 LPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            P +   R Y +R     D     KLN   +GI I G  Y + +  ++    S   V V 
Sbjct: 639 NPKSMVQRTYLLRVRPAFDPVLVHKLN--TEGIQINGRLYRNAEFFVNPATKSRYSVKVK 696

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 697 VR-GESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 740


>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 =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 120/232 (51%), Gaps = 9/232 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      QG+     QV++  +   NA
Sbjct: 158 AVTDPATGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPQGQGVLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S +
Sbjct: 218 WLEIVLDEGRNRQIRRLVAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAE 269


>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 =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 123/229 (53%), Gaps = 5/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+IA +G  SRRE +R+I    V VNG+++   A      DH+ V+G  L   ++  
Sbjct: 10  RLNKLIASSGKYSRREADRLIQNGFVLVNGVVITNPAEKFSINDHVVVNGEKLDFNKKVY 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +  Y KPI ++T++     + ++ D      +R+   GRLD  +EGL++ TNDG L   +
Sbjct: 70  IKFY-KPIKVLTSYDKYRDKKSLLDIEFFKKNRLGYSGRLDYESEGLIIFTNDGDLIYKI 128

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           + PS++  + Y V     +++ +L L++ G+  + I Y   ++        N    + L 
Sbjct: 129 QHPSSRIEKEYIVAVDKILEEKELELIRAGLKTKEIKYLPCKINY----LGNYTYNIVLY 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           EGK REI+ +F+FF   V +L R+  GP ++  L  G  + +SKK + E
Sbjct: 185 EGKKREIRNIFKFFKINVKKLKRVRIGPIRIVDLKPGEYKHLSKKEIEE 233


>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 =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 113/225 (50%), Gaps = 8/225 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLW 76
           + + RAG  SRRE   +IA  +V+VN +        V + D + V G   R +    RLW
Sbjct: 519 RTLPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHQSRLRFAPPRLW 578

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +YHKP  ++ + +D  GR+ +  +   +    ++ VG L +   G+LLLTNDG L+R LE
Sbjct: 579 IYHKPAHVIVSRNDAAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLE 638

Query: 136 LPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            P +   R Y +R     D     KLN   +GI I G  Y + +  ++    S   V V 
Sbjct: 639 NPKSMVQRTYLLRVRPAFDPVLVHKLN--TEGIHINGRLYRNAEFFVNPATKSRYSVKVK 696

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 697 VR-GESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 740


>gi|323466661|gb|ADX70348.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 216

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 69/207 (33%), Positives = 109/207 (52%), Gaps = 3/207 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI   RVKV+G ++ +    V +  +I VD  P+ + E    +L++KP G+V+T  D  G
Sbjct: 1   MIVAGRVKVDGKVVTKLGTKVETFSNITVDDEPIER-ESLHTYLFYKPRGVVSTADDDKG 59

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TV D    +  R+  VGRLD +T GLLL+TNDG LA +L  P  +  +VY  +  G +
Sbjct: 60  RKTVVDYFEDVPCRLYPVGRLDYDTSGLLLMTNDGKLANLLMHPRNEVSKVYVAKIKGIL 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVT-VGLREGKNREIKKVFEFFNWK 211
             D++  L  G+ +        +V  L T K  +  +  + + EG   ++K++F+     
Sbjct: 120 TPDEIKTLTTGVKLDRFKAAPAKVKILKTDKRKDTQIIQLTIHEGHYHQVKRMFKAVGHL 179

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSK 238
           V +L R  Y    L +L +G  RE+SK
Sbjct: 180 VEKLSREKYAFLTLDSLTSGQYRELSK 206


>gi|310828101|ref|YP_003960458.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308739835|gb|ADO37495.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 241

 Score =  109 bits (273), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 84/240 (35%), Positives = 125/240 (52%), Gaps = 20/240 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E MIA  RV VNG  +    + V    D + VDG  +  AE  
Sbjct: 2   RLQKYMAQCGVASRRKSEEMIAAGRVCVNGEAVLTPGLQVDPEADTVTVDGKTI--AEDK 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L +KP G+V+T +D     TV D LP I  R+ +VGRLD +TEGLL+LTNDG L  
Sbjct: 60  KIYVLLNKPKGVVSTSADRHADQTVMDRLP-IKERLFTVGRLDKDTEGLLILTNDGDLTF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  PS ++ ++Y     G     +L L  +G+ I+     D   TL T           
Sbjct: 119 RLTHPSHEFNKIYEGLVKGIPSAGELRLFAEGVQIE-----DDDHTLHTTAPASVQVLKT 173

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             S A + + + EG+ R+I+K+       V  L R + G   L  L AG  R ++++ +R
Sbjct: 174 YRSTALLEMTIHEGRKRQIRKMCAAIGHPVIHLKRTAIGSITLKGLKAGEWRYLTEEEIR 233


>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 =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 119/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +AR G+ASRR+ E +I   +VKVN I+++     V  +  +      + + E  
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDIVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ + +KP G VTT+ D   R T+ D +  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILD-IVKVNERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S
Sbjct: 182 IHEGKNRQIRRMCAVFNHEVVSLKREAIGSLNLKNLKKGEWRYLS 226


>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 =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 80/230 (34%), Positives = 124/230 (53%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++   GI SR +V+ +I  Q+VKVN  ++     NV  S   I   G P++ AE  
Sbjct: 2   RIDKLLEEEGIGSRNQVKTLIKSQQVKVNEKVITDGKTNVDPSLQVITASGTPIQ-AEGH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+  SD     TV D L     ++++  +GRLD +TEGL+LLT++G L 
Sbjct: 61  HYFILNKPNGVVSARSD-GLHQTVIDCLSVEDRYAKLYPIGRLDRDTEGLVLLTDNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             +  PS    + Y VR +GQ+  D L   ++GIV      C    +Q+    +K S A 
Sbjct: 120 FRMLHPSHHVSKTYLVRVNGQLKDDALVFFEEGIVFHDGTKCKPAHLQILKKDEKCSEAV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           VT+   EGK  ++KK+F  +  KV  L RIS+    LG L  G  R++++
Sbjct: 180 VTIS--EGKFHQVKKMFLAYGLKVIYLKRISFAGLTLGELPVGQYRKLTE 227


>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 =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 125/231 (54%), Gaps = 6/231 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R +V+R+I +  V+VNG +++  +  V    D + VDG P+   E  
Sbjct: 2   RLDKLLAEGGFGTRSQVKRLIKKGHVEVNGEVVKDPSFQVDPLKDEVTVDGEPVYYEEEY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G VT  S  D + TV + +  I  F ++  VGRLD + EGLLL+T DG LA
Sbjct: 62  YLVL-NKPAGYVT--STKDRQMTVMELVADIPRFDKLFPVGRLDKDAEGLLLMTTDGELA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y V+  G++ ++ +  L++GI ++       +V +       +   +
Sbjct: 119 HRLTHPKWKVPKTYVVKVEGRLTEEAVEPLRRGIELKDFKAKPAEVRILRSSEEESEAEI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EGK  ++K++F      V  L R+++GP +LG L  G  R ++++ LR
Sbjct: 179 TITEGKFHQVKRMFAAIGHPVKELKRVAFGPLKLGELPTGEYRHLTEEELR 229


>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 =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 76/230 (33%), Positives = 116/230 (50%), Gaps = 7/230 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++    P+   ER
Sbjct: 7   PIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFHDEPV-SIER 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 66  KTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVLLLTNDGDLA 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     V +  L+ +  G+ +  G  + D +    +T K   + V
Sbjct: 126 SKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASETDK---SQV 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 183 GIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 232


>gi|291528900|emb|CBK94486.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale M104/1]
          Length = 240

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 126/232 (54%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++  G+ +R EV+++I   ++ +NG +  +    V    D + V+G  + K +R 
Sbjct: 3   RLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNG-RIVKYQRY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L++KP G V+  SD +   TV D +  ++   +  VGRLDI+TEGLLL+TNDG L+ 
Sbjct: 62  EYYLFNKPSGCVSATSD-NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----LDTQKGSNA 187
            L  PS    + Y  R  G+V  D +   K+GI I     G+ + T     +  + GS +
Sbjct: 121 ELLSPSKHVAKTYYARIDGEVTLDDIIRFKEGIDI-----GEERPTKPAELVIKKSGSVS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
            + + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++
Sbjct: 176 EIELTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQ 227


>gi|325473332|gb|EGC76527.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 234

 Score =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 120/233 (51%), Gaps = 5/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +AR G+ASRR  E +I   RV V+G ++      V   + I +DG  +      R
Sbjct: 6   RLQVYLARCGVASRRASENLILNGRVSVDGKIITELGTKVSGKEKICLDGKQIFPEAEKR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G V + +D   R      L   ++ R+ ++GRLD+ + G +L TNDG  +  
Sbjct: 66  YILLNKPEGYVCSLADEKDRPIAASLLKDTYTERLYNIGRLDMLSGGAILFTNDGDFSAK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +E PS++  + Y V    +   + L    +G+ I+G+ Y      L  ++ +   + + L
Sbjct: 126 VEHPSSEIEKEYEVITVFEYPDEVLQKFLRGVRIEGVFYK----ALSAERIAKNKMRIVL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNREI++V +FFN K+ +L R+  G   L  L +G  R ++ + ++  LG
Sbjct: 182 IEGKNREIRRVLKFFNIKIKKLTRVRIGCVYLADLPSGKHRPLTSEEIKGLLG 234


>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 =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 119/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +AR G+ASRR+ E +I   +VKVN I+++     V  +  +      + + E  
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDIVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ + +KP G VTT+ D   R T+ D +  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILD-IVKVNERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLNLKNLKKGEWRYLS 226


>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 =  109 bits (272), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 109/223 (48%), Gaps = 1/223 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR  E  +   RV V+G +             I VDG PL   
Sbjct: 1   MTRQRLQKLIAAAGLCSRRRAEEWLQAGRVTVDGQVARVGDQADPQQQTIHVDGQPLPSP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP+G++ +  DP GR TV D LP    + +  VGRLD ++ G LLLT+ G 
Sbjct: 61  GMARVLLMNKPVGVICSCDDPQGRRTVLDLLPPEHRAGLHPVGRLDADSHGALLLTDLGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   +  L+  ++G+ + G      +V      G  + +
Sbjct: 121 LTLKLTHPRYSHAKTYRVWVQGVPSEPVLDRWRRGVPLDGRLTRPARVRQLRTWGDRSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            + LREG+NR+I+++ E   + V  L R +     LG L  G 
Sbjct: 181 EIELREGRNRQIRRMAEALGYPVVDLQRTAIAGLPLGDLAEGC 223


>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 =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 121/239 (50%), Gaps = 7/239 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++ +   P R++K +A AGI SRRE +  I    V VNG ++      V  +D ++  
Sbjct: 8   KELLTDPDEPIRLNKFLANAGICSRREADEFITAGVVSVNGEIVTELGTKVKRSDEVKFH 67

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 68  DQPV-NIERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 126

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLD 180
           LLTNDG LA  L  P     ++Y V     V +  L+ + +GI +  G  + D +    D
Sbjct: 127 LLTNDGDLASKLTHPKFLKKKIYHVYCDKNVTKADLDQIVQGITLDDGEIHADAISYASD 186

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           T K   + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 187 TDK---SQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 242


>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 =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 76/217 (35%), Positives = 117/217 (53%), Gaps = 8/217 (3%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWL-YHKPI 82
           + SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +  A ++ L+   +KP 
Sbjct: 1   MGSRRACEDLIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTV--ATQSYLFFALNKPA 58

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA  L  P     
Sbjct: 59  GVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHPRYGVK 118

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVTVGLREGKNRE 200
           + Y     G + +D    LK GI ++ G    D  +V  +T  G N  V V L EG+   
Sbjct: 119 KTYLAAIQGPLPRDLGKQLKNGIELEDGYARADHFKVVQNT--GKNYLVEVSLHEGRKHI 176

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++++     + V +L+R S+GP  LG   +G  R ++
Sbjct: 177 VRRMLSEAGFPVEKLVRTSFGPIPLGDQKSGWLRRLT 213


>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 =  109 bits (272), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    + VNG ++      VM TD ++   
Sbjct: 187 EENFDPNEPIRLNKYLANAGVCSRREADEFIQAGVITVNGEVVTELGTKVMRTDEVKFHD 246

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLL 123
             +   E+    L +KP   VTT  DP  R TV D +  +   R+  VGRLD N  G+LL
Sbjct: 247 QNV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNPTGVLL 305

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG LA  L  P     +VY V     V    L  +  GI ++ G  + D     D  
Sbjct: 306 LTNDGDLASKLTHPKFLKKKVYHVYLDKPVAAHDLQQIADGITLEDGEIHADAIEYADEH 365

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +S+K
Sbjct: 366 --DKKQVGIEIHSGKNRIVRRIFEALGYRVTKLDRVQFAGLTKKNLRRGDWRFLSEK 420


>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 =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 120/229 (52%), Gaps = 4/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ASRRE   ++ Q  + VN ++       + + D ++  G  +R   R  
Sbjct: 39  RLNKYVAHCGVASRREAAEIVKQGHITVNSVVETEPFYQIKTGDIVKYKGQVIRPEVRRV 98

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP  ++TT SD  GR TV D +   +  RV  VGRLD +T GLLLLTNDG LA  
Sbjct: 99  YYLMNKPKNVITTTSDEKGRKTVLDLVADRVEERVFPVGRLDRDTTGLLLLTNDGELALK 158

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  ++Y    +  V ++ L  ++ G+ ++ G    D    +  +  S   +TV 
Sbjct: 159 MTHPSYKIKKIYHATLNKTVSKEDLEKIRAGLELEDGPAPVDAADYIIERPHSEVGLTVH 218

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  G+NR ++++FE   ++V +L R+  G      L  G  R ++ + L
Sbjct: 219 I--GRNRIVRRIFEHLGYEVLKLDRVYLGGLTKKDLPRGFVRRLTSQEL 265


>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 =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 119/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +AR G+ASRR+ E +I   +VKVN I+++     V  +  +      + + E  
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDIVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ + +KP G VTT+ D   R T+ D +  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILD-IVKVNERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLTLKNLKKGEWRYLS 226


>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 =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 77/231 (33%), Positives = 114/231 (49%), Gaps = 10/231 (4%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           K +  AG  SRRE+   +   RV VNG   E  +  +   D I +D  P+  AE  R++L
Sbjct: 10  KALRDAGCGSRRELAEAVKAGRVAVNGTTAESFSAAITPADVITLDSRPVVTAESARVYL 69

Query: 78  Y-HKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL 134
             +KP+G++TT  DP GR TV D LP  +   R+  VGRLD NT GL++LTNDG L   L
Sbjct: 70  LLNKPLGVITTTEDPQGRPTVIDLLPPDWQQKRLFPVGRLDENTTGLIILTNDGELTNRL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW---VTV 191
             P     + Y V     ++ +    +K G    G+   D   +       NA      +
Sbjct: 130 THPRYGVEKEYLVGIDRSLNSEDFEKIKSG----GLELDDGPASPARISPVNAAPFNYRI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+ R ++++F     +V  L RI  G  +LG L  G+ R+++   LR
Sbjct: 186 SIHEGRKRIVRRLFAALGHQVRVLRRIRVGSLELGNLKEGNWRQLTPLELR 236


>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 =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 118/234 (50%), Gaps = 16/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I   ++ VN  L+   A +V   D +++ G  ++  +   
Sbjct: 5   RLNKFISHNTSYSRREADELIKSGKISVNNKLVSELATSVSDEDKVKIGGRLVKPKKDFT 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + T  D  GR T++D LP  F++ +S+GRLD  +EGLLLLT+   +A   
Sbjct: 65  MIVYHKQKGELVTKKDDRGRKTIYDALPEGFAKFVSIGRLDYASEGLLLLTDAPAIATA- 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------DMQ----VTLDTQ 182
            L S+   R Y ++  G++  +    +++G        G         M+    V  D  
Sbjct: 124 -LMSSDIEREYYLKVKGEITDEVKTAMREGFFAADASKGAHAKSKIKSMEFKPFVAFDIF 182

Query: 183 KGSNAWVT--VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             S  +    V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R
Sbjct: 183 GSSGGYTKFRVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWR 236


>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 =  108 bits (271), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R++K IA     SRRE ++ I    V++NG + +  A  V   D I  V G  +   ++ 
Sbjct: 4   RLNKYIAHHSSYSRREADKAILDGYVRINGEIQDNPATQVDEKDDIVYVSGKQITPKDKY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + T SDP GR T++D L   +   I VGRLD  TEG+LLLT+   +A  
Sbjct: 64  TVIVYNKPKGELVTKSDPKGRRTIYDGLEKKYKHYIPVGRLDYATEGVLLLTDASKIASA 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG---DMQVTLDT--------- 181
             L ++   R+Y+V+  G+V  +    +  G+ +     G     +VT  T         
Sbjct: 124 --LMNSNLERIYKVKIKGEVTPEIEAAMMNGLELLDATAGGHSHSKVTSMTFAPFLGYKI 181

Query: 182 QKGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           QK  + +  + + + EG+NREI++ F  F  +V  L RIS+   +L  L  G  R +S+
Sbjct: 182 QKNEHNYSVLKIAISEGQNREIRRFFAHFGTEVADLKRISFAEVELNNLPTGKVRFLSR 240


>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 =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 74/211 (35%), Positives = 111/211 (52%), Gaps = 7/211 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    VKVNG ++      VM TD +     P+   E+
Sbjct: 252 PVRLNKFLANAGVCSRREADEFIQAGVVKVNGEVVTELGTKVMRTDEVVFHDQPV-SLEK 310

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + ++   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 311 KVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNVCPERIYPVGRLDRNTTGVLLLTNDGDLA 370

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     +VY V     V    +  + +GI ++ G  + D ++   +T K     V
Sbjct: 371 SKLTHPKYLKKKVYHVFLDKNVTAHDMQKIAEGIELEDGEVHADAIEYAHETDKNQ---V 427

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 428 GIEIHSGKNRIVRRIFESLGYRVIKLDRVQF 458


>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 =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 83/241 (34%), Positives = 124/241 (51%), Gaps = 16/241 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K IA  G ASRR+ + MI Q  V VNG +++E         D + V+G  L +  + 
Sbjct: 44  RLNKFIALCGEASRRKADEMIEQGEVMVNGKVVMELGYKVDRRADEVVVNGKKLHENTQK 103

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP  +VTT SD   R TV + L  +  RV  VGRLD +T G+LLLTNDG L   
Sbjct: 104 IYILLNKPKDVVTTSSDEKSRKTVVE-LVGLKDRVFPVGRLDRDTTGVLLLTNDGDLTYR 162

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWV 189
           L  P+    + Y      ++    L  +KKG  +    + +   + ++  D   G   WV
Sbjct: 163 LTHPTFGVQKQYVATLDKKITSVDLQNIKKGFRLKDTGEKVSPCNARILDD---GYTIWV 219

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-----EVSKKILREQ 244
            +   EGKN +I ++F  F + V +L+R++YG  ++GT+  G  R     EVSK   + Q
Sbjct: 220 AI--HEGKNHQIHRMFWSFGYNVKKLVRVAYGGLEVGTMRRGEWRFLTQLEVSKLYKQVQ 277

Query: 245 L 245
           L
Sbjct: 278 L 278


>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 =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/231 (33%), Positives = 119/231 (51%), Gaps = 11/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +IA  RV V+G+++      V   T  I VDG+ ++  +  
Sbjct: 11  RLQKVLAKAGVASRRASEELIAAGRVSVDGVVVRELGRRVDPDTAVIHVDGIRVQVRDDL 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+ +T SD  GR  V D +     R+  VGRLD +TEGLLLLTNDG LA  
Sbjct: 71  VYLALNKPRGVHSTMSDAQGRPCVGDYVADRPERLFHVGRLDADTEGLLLLTNDGDLAHK 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAW 188
           L  PS    + Y     G V +     L+ G+ +      D  VT D       + + + 
Sbjct: 131 LMHPSFHVTKTYLAEVEGAVARGLGKRLRAGVQLS-----DGPVTADAFRIKDVRPNRSL 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + L EG+   ++++       V +L+R + G  +LGT   G+ R ++++
Sbjct: 186 VEIVLHEGRKHIVRRLLAEVGHPVRKLVRTAIGEVRLGTTKPGTLRTLTQQ 236


>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 =  108 bits (271), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 113/225 (50%), Gaps = 8/225 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLW 76
           + + RAG  SRRE   +IA  +V+VN +        V + D + V G   R +    RLW
Sbjct: 336 RTLPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAEDDVHVAGHQSRLRFAPPRLW 395

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +YHKP  ++ + SD  GR+ +  +   +    ++ VG L +   G+LLLTNDG L+R LE
Sbjct: 396 MYHKPAHVIVSRSDTAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLE 455

Query: 136 LPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            P +   R Y +R     D     KLN   +G+ I G  Y + +  ++    S   V V 
Sbjct: 456 NPKSMVQRTYLLRVRPAFDPVLVHKLN--TEGVHINGRPYRNAEFFVNPATKSRYSVKVK 513

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 514 VR-GESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 557


>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 =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 118/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V + D + V G  LRK  +  
Sbjct: 2   RINKFISHNSPYSRREADELIKQGLVKINN-KIALLSDEVKTNDKVFVKGKALRKKTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDFASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYR 232


>gi|291524779|emb|CBK90366.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale DSM 17629]
          Length = 240

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 126/232 (54%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++  G+ +R EV+++I   ++ +NG +  +    V    D + V+G  + K +R 
Sbjct: 3   RLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNG-RIVKYQRY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L++KP G V+  SD +   TV D +  ++   +  VGRLDI+TEGLLL+TNDG L+ 
Sbjct: 62  EYYLFNKPSGCVSATSD-NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALSH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----LDTQKGSNA 187
            L  PS    + Y  R  G+V  D +   K+GI I     G+ + T     +  + GS +
Sbjct: 121 ELLSPSKHVAKTYYARIDGEVTWDDIIRFKEGIDI-----GEERPTKPAELVIKKSGSVS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
            + + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++
Sbjct: 176 EIELTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQ 227


>gi|282876081|ref|ZP_06284948.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|281295106|gb|EFA87633.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
          Length = 194

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 65/194 (33%), Positives = 111/194 (57%), Gaps = 11/194 (5%)

Query: 67  LRKAERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           L+  ++T+++ L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLT
Sbjct: 6   LKSNKKTKIYILFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLT 65

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--K 183
           NDG    ++  P  +  + Y  +  G + ++++  L+KGI ++       QV +  Q  +
Sbjct: 66  NDGEFTNLMTHPRYRIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKE 125

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KI 240
            +   V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++    KI
Sbjct: 126 KNTTLVEITISEGRNRQVRRMFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVKI 185

Query: 241 LREQLGPHLLEEAQ 254
           LR     HL E  +
Sbjct: 186 LR-----HLAENGK 194


>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 =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/225 (34%), Positives = 117/225 (52%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+++G ++    + +   T  I VDG  +   E  
Sbjct: 90  RLQKVLAQAGVASRRGAEEMIAAGRVEIDGEIVTEQGLRIDPDTAIIRVDGARVIIDETR 149

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +KP G  +T +D  GR  V D +        R+  VGRLD +TEGLLLLTNDG L
Sbjct: 150 QYLALNKPRGWQSTMADDQGRPCVGDIVAERVMAGQRLFHVGRLDADTEGLLLLTNDGEL 209

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G+V +    +L+ G+ +  G    D    +D  +G  + +
Sbjct: 210 AHRLMHPSYEVPKTYLATVRGEVPRSLSRMLRDGVELDDGPVAVDKLTIVDVHEG-QSLL 268

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EG+NR ++++ +   + V  L+R   G   LG    GS R
Sbjct: 269 RITLHEGRNRIVRRMMDEVGFPVVELVRTHVGSVALGEQRPGSLR 313


>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 =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/180 (34%), Positives = 106/180 (58%), Gaps = 3/180 (1%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +D IEV+G+ +   ++  + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD 
Sbjct: 4   SDTIEVEGIKIELEDKIYI-LFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDY 62

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GD 174
           +T GLLLLTNDG    ++  P  Q  + Y  +  G + ++++  L+KGI ++ G+    +
Sbjct: 63  DTSGLLLLTNDGEFTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAE 122

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           ++V    +  +   V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R
Sbjct: 123 VKVKKQDKDKNTTLVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGR 182


>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 =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 68/208 (32%), Positives = 112/208 (53%), Gaps = 6/208 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA +G+ SRRE + +IA   + VNG ++      V   D ++  G  +   ER  
Sbjct: 406 RLNRFIANSGVCSRREADELIAHGDISVNGKIVTEMGYKVKEGDTVKY-GTKVLNPERFV 464

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  DP+ R TV + +      R+  VGRLD NT GLLL+TNDG LA  
Sbjct: 465 YVLLNKPKDYITTTEDPEERKTVMELVADAGKFRMYPVGRLDRNTTGLLLITNDGELADK 524

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VG 192
           L  PS    ++Y+V     +  +    +KKGI ++        +++ T    +A+V  + 
Sbjct: 525 LTHPSNNIRKIYQVELDKPITDEHFEAIKKGIELEDGPIKPDAISIVT---PDAYVVGIE 581

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+NR ++++FE F ++V +L R +Y
Sbjct: 582 IHSGRNRIVRRIFESFGYEVTKLDRTTY 609


>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 =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/253 (33%), Positives = 123/253 (48%), Gaps = 16/253 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++++ GIASRR  E MI   RV VNG +           D + VDG  ++   R 
Sbjct: 3   ERIQKLLSQWGIASRRHAEEMILAGRVSVNGKVANLGDKADPQQDFLSVDGKQIKADNRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           R    L +KP  +++T  DP GR TV D LP    R   +  VGRLD N+ G LLLTNDG
Sbjct: 63  RDIYLLVNKPRDVLSTCDDPRGRKTVLDLLPQDLQRGKGLHPVGRLDRNSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G    + L   + G+++ G       + + ++      
Sbjct: 123 ELTLRLTHPRYHLPKTYDVWLEGNPSDEDLEKWRSGMMLDGKKTLPATLEVISENKDQIH 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT----LLAGSTREVSKKILREQ 244
           + V L EG+NR+I+++ E     V +L R + GP QL T    L +G  R +S   +R  
Sbjct: 183 LLVTLTEGRNRQIRRLAEELGLTVLKLHRRTIGPLQLHTRGKVLGSGQFRFLSPAEIR-- 240

Query: 245 LGPHLLEEAQVNL 257
                L + QVNL
Sbjct: 241 -----LLKKQVNL 248


>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 =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 118/226 (52%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI SRR  +  I+   V VNG ++      V  TD +  DG  L  +E+  
Sbjct: 155 RLNKYIADAGICSRRNADMYISAGNVTVNGEVMTTLGYRVKPTDEVRFDG-KLLSSEKKE 213

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G +TT +D  GR TV D + +  + R++ VGRLD  T GLLLLTNDG L + 
Sbjct: 214 YILLNKPKGFITTTNDEKGRKTVMDLVANATNVRILPVGRLDRATTGLLLLTNDGELTKK 273

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    ++Y V    ++D      ++ G+ ++       +++    K  N  + + +
Sbjct: 274 LTHPTHGVRKIYHVILDRKLDYKDFMKVQDGLELEDGLIEVDEISYVNDKPKNE-IGIKI 332

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             G+NR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 333 HSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQQ 378


>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 =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 118/226 (52%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI SRR  +  I+   V VNG ++      V  TD +  DG  L  +E+  
Sbjct: 155 RLNKFIADAGICSRRNADMYISAGNVMVNGEVMTTLGYRVKPTDEVRFDG-KLLSSEKKE 213

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G +TT +D  GR TV D + +  + R++ VGRLD  T GLLLLTNDG L + 
Sbjct: 214 YILLNKPKGFITTTNDEKGRKTVMDLVANATNVRILPVGRLDRATTGLLLLTNDGELTKK 273

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+    ++Y V    ++D      ++ G+ ++       +++    K  N  + + +
Sbjct: 274 LTHPTHGVRKIYHVILDRKLDYKDFMKVQDGLELEDGLIEVDEISYVNNKPKNE-IGIKI 332

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             G+NR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 333 HSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQQ 378


>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 =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA AGI SRRE + +I+  ++ VNG ++      V  TD ++  G      E+  
Sbjct: 324 RLNRYIANAGICSRREADDLISSGQISVNGKIVTEMGYKVRPTDVVKY-GKKALNPEKMV 382

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  DP+ R TV D +    S RV  VGRLD NT GLLLLTNDG LA  
Sbjct: 383 YILINKPKDYITTTDDPEERKTVLDIIAGACSERVYPVGRLDRNTTGLLLLTNDGELAEK 442

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM--QVTLDTQKGSNAWVT 190
           L  PS+   ++Y+      +  +    LK G+ ++ G    D    VT D Q      V 
Sbjct: 443 LTHPSSGIKKIYQAELDKPITTEDFEQLKAGVELEDGFIRPDEVGLVTPDAQ-----VVG 497

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  G+NR ++++FE   ++V +L R  +       L  G  R +++K
Sbjct: 498 LEIHSGRNRIVRRMFEHLGYEVQKLDRTVFAGLNKKDLPRGKWRFLTEK 546


>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 =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 118/230 (51%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  ERMI   RV+V+G ++      V  +   I VDG  +   +  
Sbjct: 8   RLQKVLSQAGIASRRVAERMIIDGRVEVDGQIVTELGTRVDPAVADIRVDGSRIILDDTM 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGLLLLTNDG L
Sbjct: 68  VYLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     LK G+ +  G  + D    +DT  G    V
Sbjct: 128 AHRLMHPSFEVPKTYVATVMGTVPRGLGKKLKAGVELDDGPAHVDDFAVVDTVPGKT-MV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V L EG+NR ++++    ++ V  L+R   G   LG    GS R +++K
Sbjct: 187 KVTLHEGRNRIVRRLLAAVDFPVQELVRTEIGSVSLGDQRPGSIRALTRK 236


>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 =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 109/223 (48%), Gaps = 1/223 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR  E  +   RV V+G++             I VDG PL   
Sbjct: 1   MTRQRLQKLIAAAGLCSRRRAEEWLQAGRVTVDGLVASVGDQADPQQQTIHVDGQPLPSR 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP+G++ +  DP GR TV D LP    + +  VGRLD ++ G LLLT+ G 
Sbjct: 61  GVARVLLMNKPVGVICSCDDPQGRRTVLDLLPPEHRAGLHPVGRLDADSHGALLLTDLGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   +  L+  ++G+ + G      +V      G  + +
Sbjct: 121 LTLKLTHPRYSHAKTYRVWVKGVPPEPVLDRWRRGLPLDGCLTRPARVRRLRTWGDRSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            + LREG+NR+I+++ E     V  L R +     LG L  G 
Sbjct: 181 EIELREGRNRQIRRMAEALGHPVLDLQRTAIAGLPLGDLAEGC 223


>gi|291538915|emb|CBL12026.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis XB6B4]
          Length = 235

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 118/232 (50%), Gaps = 5/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E  
Sbjct: 2   RLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQKVDEKNDTVCFRGNPLTYTEY- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             +L+HKP G VT   D   R TV D L       +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 61  EYYLFHKPAGCVTATEDNLHR-TVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    +VY  +  G+V ++ +NL + G+ I         +      G N+ + + 
Sbjct: 120 DLLSPAKHVSKVYYAKIDGRVTEEDVNLFENGVDIGEEKPAKPALLEVLHSGDNSEIRLT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           + EG+  ++K++FE    KV  L R+  G   L   LA G  R +++K L+E
Sbjct: 180 ITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEKELQE 231


>gi|291536218|emb|CBL09330.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis M50/1]
          Length = 235

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 79/232 (34%), Positives = 118/232 (50%), Gaps = 5/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E  
Sbjct: 2   RLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQKVDEKNDTVCFRGNPLTYTEY- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             +L+HKP G VT   D   R TV D L       +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 61  EYYLFHKPAGCVTATEDNLHR-TVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    +VY  +  G+V ++ +NL K G+ I         +      G N+ + + 
Sbjct: 120 DLLSPAKHVSKVYYAKIDGRVTEEDVNLFKNGVDIGEEKPAKPALLEVLHSGDNSEIRLT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           + EG+  ++K++FE    KV  L R+  G   L   LA G  R ++++ L+E
Sbjct: 180 ITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEEELQE 231


>gi|51922071|gb|AAU14148.1| rluB [Mycoplasma mobile 163K]
          Length = 235

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 119/227 (52%), Gaps = 12/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL---ERAAVNVMSTDHIEVDGVPLRKAE 71
           R+ K+I++AGI+SRR  E +I ++RVK+NG++    ++A++     D I VD   + K E
Sbjct: 5   RIQKLISQAGISSRRAAEDLILKKRVKINGVIAKIGDKASL----EDVILVDEKVISKEE 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +L +KP  +VTT  D   RS + D +     ++  VGRLD +T G+++LTNDG  A
Sbjct: 61  KV-YYLLNKPKNVVTTLKDNFNRSIITDFIDEKKYKIFPVGRLDYDTTGIIILTNDGETA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  R+Y V    ++  +++  L      Q +     +   +  K SN    +
Sbjct: 120 NKLLHPKYEIPRIYEVIIDKELSLEEIKYLNS----QEVFLNSKKSFQEVSKISNYKYKI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G    IKK+FE    KV  L R  Y  F L  L  G+ R+++K
Sbjct: 176 KLHQGSYHHIKKLFEIVGKKVKDLNRTEYAFFNLENLSIGNYRKLNK 222


>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 =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/227 (35%), Positives = 120/227 (52%), Gaps = 7/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ KV+A AG+ASRR+ E +I   RVKV+GI++      +   + +  VDG   R   RT
Sbjct: 13  RLQKVLASAGVASRRKAEELIRDGRVKVDGIVVREMGTRIDPENAVVHVDGN--RITTRT 70

Query: 74  RL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L     +K  G+++T SD  GR  +   L     R+  VGRLD+ +EGLLLLTNDG LA
Sbjct: 71  DLVYLALNKERGVLSTMSDELGRPHIGQMLEDRSERLFHVGRLDMESEGLLLLTNDGDLA 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y     G + +D    LK G+ ++ G    D    +D    + A V 
Sbjct: 131 HRLTHPSYGVAKTYVAEVPGPIPKDLGRRLKAGVELEDGPAKVDSFDVMDLHH-NRAVVE 189

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V + EG+   ++++ E  +  V+RL+R   GP QLG    G+ R+++
Sbjct: 190 VVIHEGRKHIVRRLLEAVDRPVSRLVRTQIGPVQLGHQRPGTLRKLN 236


>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 =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 118/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V + D + V G  LRK  +  
Sbjct: 2   RINKFISHNSPYSRREADELIKQGLVKINN-KIALLSDEVKTNDKVFVKGKALRKKTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDFASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVGKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYR 232


>gi|58220684|gb|AAW67949.1| putative rRNA pseudouridine synthase B [Desulfovibrio gigas]
          Length = 253

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/241 (35%), Positives = 122/241 (50%), Gaps = 18/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-----LRK 69
           R++KV+A+AG+ASRR  + ++   RV+VNG + E   + V   D IEVDG P     L  
Sbjct: 5   RLNKVLAQAGVASRRGADELVFAGRVRVNGAVAESPGMRVTPDDRIEVDGAPMPRKDLAA 64

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTN 126
                  L HKP+ +V+T  DP GR TV D LP      +R+  VGRLD  +EGLLLLT+
Sbjct: 65  GHALNYILLHKPVEVVSTVRDPQGRRTVLDLLPQALRANTRLYPVGRLDYFSEGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---- 182
           DG LA  L  P     + Y V   G V    L  ++ G+ +     GD       Q    
Sbjct: 125 DGDLANRLMHPRHHVPKRYEVLVRGDVPTTALQTMRSGMTLPPQA-GDPPAGTRLQTVPA 183

Query: 183 -----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                K     + + L +G NR+++++ E     + RL R+  G  +LGTL  GS R ++
Sbjct: 184 RILGIKDGKTLLELVLHQGVNRQVRRMCEALGLTILRLTRVGLGSLELGTLEKGSWRRLT 243

Query: 238 K 238
           K
Sbjct: 244 K 244


>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 =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 109/222 (49%), Gaps = 2/222 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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  KVYIALNKPEGYVSTVKDERGRKTILD-IVKVNERIFPIGRLDYNTSGLILLTNDGDVYN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    D++     GI I G         +  +      V + 
Sbjct: 123 KIIHPREEIDKVYIAVIKGIPSHDEIKNFCNGIDIGGYVTSKASFEILEKLNDKCKVKII 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + EGKNR+++++ E     V  L R+S G   L T+  G  R
Sbjct: 183 IHEGKNRQVRRMCEKIGHPVIALKRVSVGKISLNTIKRGEWR 224


>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 =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 123/235 (52%), Gaps = 9/235 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQQFSITVDGQPLTGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NA
Sbjct: 158 TVTDPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGMLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVR 272


>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 =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 118/229 (51%), Gaps = 7/229 (3%)

Query: 12  TPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +PQ  R  K++A AGI SRR  E  I    V +NG   E  +    + D + ++G  ++ 
Sbjct: 3   SPQLIRTQKLLADAGICSRRVAEEYIKNGEVTINGKTAELGSKVDPAIDDVRLNGRRIKV 62

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
            +  +L +  +KP G + ++ DP    TVFD LP+ ++R  +   GRLD ++EGLL+LTN
Sbjct: 63  VKHKQLVIALNKPKGFICSNDDPHNDRTVFDLLPTDYNRERLFCAGRLDKDSEGLLILTN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKG 184
           DG LA  L  PS    + Y V       + K+  L +G+ ++G      +     D  K 
Sbjct: 123 DGDLANRLMHPSNLVTKRYHVSLKQPFPKAKIFRLMRGVTVEGEKLKVEKAVFAGDKNKA 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +  + + +  GK REI+++F+  ++ V +L R   G + +  +  G++
Sbjct: 183 ESTELDLAMHHGKKREIRRLFQALHYDVKKLKRYQIGRYSIKGMPKGAS 231


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 124/228 (54%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR-KAE 71
           +R+ K +A+ G+ASRR+ E +I Q +V VN  ++      V    D I+V+ V +  +A+
Sbjct: 2   ERLQKYMAKCGVASRRKCEELILQGKVSVNNTIITELGYKVEEENDIIKVNNVIIYPEAQ 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + L +KP+  +++  D  GR  V D L  +  R+  +GRLD ++ GLLLLTNDG + 
Sbjct: 62  KVYIAL-NKPVKYISSVKDEKGRKNVID-LIDVKERIYPIGRLDYDSSGLLLLTNDGDIY 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS +  + Y V  +G    +++  L+ GI I G      +V ++    + A + +
Sbjct: 120 NNLMHPSKEVYKTYLVTVNGIPTIEEIKKLETGIDIGGYITAPAKVKIEKLDYNKASLKI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EGKNR+I+K+ +     V  L RI+ G  +L  +  G  R ++K+
Sbjct: 180 QIYEGKNRQIRKMCDSIGHSVIALKRIAIGDIKLKDIPQGKYRFLTKE 227


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 122/242 (50%), Gaps = 7/242 (2%)

Query: 2   KDKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           K K  V E   P    R+++ IA +GI SRRE + +I   ++ VNG  +      V  TD
Sbjct: 253 KQKKKVAEKVVPSDLIRLNRYIANSGICSRREADDLIESGQITVNGKTITEMGYQVKKTD 312

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
            ++  G  +   E+    L +KP   +TT  DP+GR TV + +      R+  VGRLD  
Sbjct: 313 VVKY-GRKILNPEKLVYVLLNKPKDFITTTEDPEGRRTVMELVAKAGPERIYPVGRLDRA 371

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL TNDG LA  L  PS +  ++Y+V     + ++    L +G+ ++       QV
Sbjct: 372 TTGLLLFTNDGELAEKLSHPSNEIRKIYQVEIDKPLAKEDFEKLIEGVELEDGFIKPDQV 431

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++ T       + + +  GKNR ++++FE   ++V +L R +Y       L  G+ R ++
Sbjct: 432 SIVTP--DQQVIGIEIHSGKNRVVRRIFEHLGYEVTQLDRTTYAGLTKKDLPRGNWRFLT 489

Query: 238 KK 239
           +K
Sbjct: 490 EK 491


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 123/235 (52%), Gaps = 9/235 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQQFAITVDGQPLTGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NA
Sbjct: 158 TVTDPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGMLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVR 272


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 122/234 (52%), Gaps = 16/234 (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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------LDTQ-K 183
                +  R Y ++  G++  + +  + +G        G    T          LD +  
Sbjct: 125 MNSDVE--REYYLKVKGEITPEVITAMNEGFFAADATKGAHAKTAIKSMEFRPFLDYKIF 182

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R
Sbjct: 183 GSSGGFTKLKVVINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWR 236


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 108/210 (51%), Gaps = 5/210 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I+   V VNG ++      V+ +D ++     L   E+
Sbjct: 254 PIRLNKYLANAGVCSRREADEFISAGVVSVNGTVVTELGTKVLRSDEVKFHDQ-LVSLEK 312

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 313 KVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTGVLLLTNDGDLA 372

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY V     V ++ L  +  GI ++ G  + D     D +      V 
Sbjct: 373 SKLTHPKFLKKKVYHVHLDKNVAEEDLQKIASGIELEDGEIHADAIEYADDR--DKKQVG 430

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + +  GKNR ++++FE   ++V RL R+ +
Sbjct: 431 IEIHSGKNRIVRRIFESLGYRVVRLDRVQF 460


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 116/228 (50%), Gaps = 7/228 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    VKVNG ++      V+ +D +     P+   E+
Sbjct: 17  PVRLNKYLANAGVCSRREADEFIQAGVVKVNGEVVTELGTKVLRSDEVVFHDQPV-SLEK 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LL TNDG LA
Sbjct: 76  KVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNACPERIYPVGRLDRNTTGVLLFTNDGDLA 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     +VY V     V    +  + +GI ++ G  + D ++ T +T+K     V
Sbjct: 136 SKLTHPKFLKKKVYHVFLDKNVTAHDMQQIAEGIELEDGEIHADAIEYTNETEKNQ---V 192

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++
Sbjct: 193 GIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRYLT 240


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 122/237 (51%), Gaps = 16/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+++ +A  GIASRR  ++++ + RV VNG ++ +    V    D + VDG    + E  
Sbjct: 11  RINRFLALCGIASRRAADQLVLEGRVMVNGTVITQPGTKVNPDKDEVIVDGQKYAQPESR 70

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  +++T SD   R  V D +  +  RV  VGRLD  T GL+LLTNDG LA 
Sbjct: 71  KVYILFNKPRNVISTSSDEKNREMVLDYI-DVKERVFPVGRLDRKTTGLILLTNDGTLAN 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGSN 186
            L  PS+   + Y      +     L  L  G+ ++        C   +   LD      
Sbjct: 130 KLMHPSSNVKKEYIAVLGEKFPASMLPQLTGGMRLKDTGEKVRPCRAKL---LD----EG 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             V + + EGKN +++++FE   ++V RL R++Y    +G L  G  R +S+  +RE
Sbjct: 183 MQVLLSIHEGKNHQVRRMFETLGYEVKRLERVAYAGLTIGELRRGEWRYLSRNEVRE 239


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 121/230 (52%), Gaps = 12/230 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++ +A  GIASRR  ++++   RV VNG ++    + V  T D + VDG    + E  
Sbjct: 11  RINRYLASCGIASRRAADQLVLDGRVMVNGTVITTPGIKVSPTRDEVIVDGEKFAQPEHR 70

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++TT+SD   R  V D +  +  RV  VGRLD  T G++LLTNDG LA 
Sbjct: 71  KVYILFNKPRNVITTNSDEKNREMVLDFI-DVEERVFPVGRLDRKTTGVILLTNDGTLAH 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAW 188
            L  PS+   + Y      +   + L  L  G+ +    + +     ++  D  +     
Sbjct: 130 KLMHPSSNVKKEYIAELSEKFTPNLLPQLTGGMRLKDTGEKVSPCRAKILEDGMQ----- 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V V + EGKN +++++FE   ++V RL R++Y     G L  G  R +S+
Sbjct: 185 VLVSIHEGKNHQVRRMFETLGFEVKRLERVAYAGLLAGELRRGEWRYLSR 234


>gi|218459923|ref|ZP_03500014.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli Kim 5]
          Length = 199

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 66/182 (36%), Positives = 98/182 (53%), Gaps = 2/182 (1%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLD 115
           T +I VDG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD
Sbjct: 1   TVNIRVDGLVI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLKDFEIPHLSPVGRLD 59

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             +EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G      
Sbjct: 60  KASEGLLLFTNDTEFAQILLDPITHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTAT 119

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            V    Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R 
Sbjct: 120 AVRRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRA 179

Query: 236 VS 237
           ++
Sbjct: 180 LT 181


>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 =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 122/234 (52%), Gaps = 13/234 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 17  LARVLSKLGVCSRTEAARWIAAGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L L +KP G+VTT  D  GR TV   FD+  +    +  VGRLD  +EGLLL +ND   
Sbjct: 77  YLML-NKPRGVVTTVRDEQGRDTVYRCFDD--AGLPWIAPVGRLDKASEGLLLFSNDPQW 133

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGS 185
           A  +  P+T   + Y V+   +    +L  L  G+V      QG+     QV++  +   
Sbjct: 134 AATVTDPATGPDKTYHVQIDCRPSAAQLVQLHAGVVDPDPQGQGLLLRAKQVSVLREGER 193

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           NAW+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S +
Sbjct: 194 NAWLEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAE 247


>gi|313159346|gb|EFR58710.1| pseudouridylate synthase [Alistipes sp. HGB5]
          Length = 423

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 129/245 (52%), Gaps = 12/245 (4%)

Query: 3   DKNIVQENFTPQ------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           DK      FTP+      R+++ +A++G+ SRRE +  I    V VNG ++ +    V+ 
Sbjct: 172 DKPASYPKFTPEKQIGEMRLNRFLAQSGLCSRREADDFITAGLVTVNGQIVTQLGTKVLP 231

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
           TD ++ +   ++  ++  L L +KP G VT+  DP    TV + +    + R+  VGRLD
Sbjct: 232 TDEVKFNDSRVQGEKKVYLVL-NKPKGYVTSLDDPHAGKTVMELVQGACTERIYPVGRLD 290

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD 174
            N+ GLLL TNDG L + L  P+ +  ++Y+V     + +  ++ + +GI ++ G  + D
Sbjct: 291 KNSLGLLLFTNDGDLTKQLTHPAFRKKKIYQVSLDKPLTRADMDRIAEGITLEDGEIFAD 350

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +   K +   V + +  G+NR ++++FEF  + V +L R+ Y       L  G+ R
Sbjct: 351 ---EISYVKDNKQEVGIEIHSGRNRIVRRIFEFLGYTVTKLDRVYYAGLTKKNLKRGAWR 407

Query: 235 EVSKK 239
            +S++
Sbjct: 408 FLSRE 412


>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 =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/255 (32%), Positives = 132/255 (51%), Gaps = 17/255 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AGI SRRE +RMI + R+ VNG   E +   V   D I  D +P+ K E+  
Sbjct: 15  RINKYLSEAGICSRREADRMIEEGRITVNGKKAE-SGQKVSLEDEICADNIPVHKNEKKV 73

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+V +       +TV D L     RV  VGRLD  ++GLLLLTN+G L   +
Sbjct: 74  LLLFNKPRGIVCSTKQQFDETTVTDYLDYPL-RVYPVGRLDKESQGLLLLTNEGDLVNKI 132

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V  +  VD++ +  + KG+ +        +V    Q G  ++  + L 
Sbjct: 133 MRAGNYHEKEYFVTVNKPVDREFVRRMSKGVPVLDTVTRPCRV---VQTGECSFRII-LT 188

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++  +  ++V +L RI      L  +  G  RE++ +   E+L  HLLE + 
Sbjct: 189 QGLNRQIRRMCRYLGYEVQKLKRIRIMNLTLDGIREGEYREITAQEW-EELN-HLLESS- 245

Query: 255 VNLDAPIYSSETLVR 269
                   +SET++R
Sbjct: 246 --------TSETVIR 252


>gi|325002515|ref|ZP_08123627.1| ribosomal large subunit pseudouridine synthase B [Pseudonocardia
           sp. P1]
          Length = 253

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 80/232 (34%), Positives = 118/232 (50%), Gaps = 9/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+ARAG+ASRR  E +IAQ RV+V+G  +      +   T  + VDG  +   +  
Sbjct: 11  RLQKVLARAGVASRRAAEELIAQGRVQVDGETVREMGRRIDPETAVLHVDGARVTLRDDQ 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINTEGLLLLTND 127
                +KP+GL +T SD  GR  V D       L +   R+  VGRLD +TEGLLLLTND
Sbjct: 71  VYLALNKPVGLHSTMSDDLGRPCVGDLLADRVELMNSAQRLFHVGRLDADTEGLLLLTND 130

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  PS +  + Y     G++ +D    L+ GI ++ GI   D    +D   G  
Sbjct: 131 GELGHRLMHPSYEVPKTYLAEVEGKIARDLGRRLRDGIELEDGIARVDAFKLVDAVPG-R 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + V + L EG+   ++++       V RL+R + G  +LG    G  R + +
Sbjct: 190 STVQLILHEGRKHIVRRMLSEVGHPVQRLVRTAVGEVRLGNQKPGKLRPLDR 241


>gi|312863475|ref|ZP_07723713.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101011|gb|EFQ59216.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 239

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 81/240 (33%), Positives = 124/240 (51%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+GIL +R  +NV  S   I V G  L      
Sbjct: 2   RLDKLLGQAGYGSRNQVKKLIRSRQVYVDGILADRDNLNVDASLQTITVSGKELEHTPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+  SD +   TV D +     R  +  VGRLD NTEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPAGVVSARSDKE-HQTVIDLIKPEDQRDGLYPVGRLDRNTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +  +  D     + G+V + G      Q+ + +     +   
Sbjct: 120 FAMLHPGYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTICKSAQLEILSSASDKSCAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQLG 246
           + + EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  LG
Sbjct: 180 ITISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRVLTEAEKVILRTYLG 239


>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 =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/230 (35%), Positives = 121/230 (52%), Gaps = 17/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++   G  SRR V+R++  ++V+VNG  +   ++NV      + V GVP+      
Sbjct: 2   RLDKLLFETGFGSRRTVKRLLKSKQVQVNGQTIMVDSLNVDPQLQEVTVAGVPIDYQPHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINTEGLLLLTND 127
             ++ HKP G+V+  SD   + TV D       +P +F     VGRLD +TEGLLLLTN+
Sbjct: 62  Y-YMLHKPAGVVSAVSDAVNQ-TVIDLIEPSQRVPGLFP----VGRLDKDTEGLLLLTNN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGS 185
           G L   L +P  +  + Y V  + +V  D       GIV  G  IC    Q+T+ +Q  +
Sbjct: 116 GQLGYQLLIPKKEVTKCYEVVVNERVTDDDQLAFTAGIVFDGGVIC-KPAQLTILSQSDT 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + V + + EGK  ++KK+F     KV  L R+S GP QL  TL  GS R
Sbjct: 175 ESRVLLEISEGKFHQVKKMFLSVGKKVIYLKRLSMGPLQLDKTLSLGSYR 224


>gi|323209958|gb|EFZ94867.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 150

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 68/148 (45%), Positives = 88/148 (59%), Gaps = 6/148 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G I      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           G LA  L  PS +  R Y VR  GQVD+
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQVDE 150


>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 =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 120/227 (52%), Gaps = 12/227 (5%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAERTR 74
           + + RAG  SRRE   +IA  +V+V+ ++ ER    ++  +   H+E     LR A   R
Sbjct: 347 RCLPRAGFCSRREALSIIASGQVRVDNVV-ERNPFRLVRAENSIHVESHSGRLRFAP-PR 404

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           LW+YHKP  ++ + +D  GR+ +  +   +    ++ VG L +   GLLLLTNDG L+R+
Sbjct: 405 LWMYHKPAYVIVSRNDVAGRTLITKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRL 464

Query: 134 LELPSTQWLRVYRVRFHGQVD---QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           LE P T   + Y +R    +D     KLN   +GI++ G  Y +++  ++    S   + 
Sbjct: 465 LENPKTMIQQTYLLRVRPAIDPVLAHKLN--TEGILVNGKRYNNVEFFVNPAMKSRHSLK 522

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V +R G+   +  + +     V R  RIS+GPF +  L  GS REV+
Sbjct: 523 VKVR-GETMPVAHLMQHLGRTVERGGRISFGPFSMSGLPVGSIREVT 568


>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 =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 122/234 (52%), Gaps = 16/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + ++   +V +N  +++  A +V   D I+++G  +R  +   
Sbjct: 2   RINKFISHNTNYSRREADELVKNGKVSINNKVIDNLATDVKEDDKIKINGRFIRLKKEFS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+K  G + T  D  GR T++DNLP   S+ IS+GRLD  +EGLLLLT+   +A  L
Sbjct: 62  IIVYNKQKGELVTKKDDRGRKTIYDNLPRGISKFISIGRLDFASEGLLLLTDAPAIAEAL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----DMQVTLDTQ-------- 182
                +  R Y ++  G++  + +  +++G   +    G      Q++++ +        
Sbjct: 122 MGSDIE--REYYLKIKGEITPNVIAAMQEGFFAKDATKGAHARTKQISMEFKPFLAYKII 179

Query: 183 --KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              G    + V + EG+NRE+++ F +F+ +V  L R+S+G   L  L  G  R
Sbjct: 180 SFSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWR 233


>gi|218533320|ref|YP_002424135.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218525623|gb|ACK86207.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 320

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 81/228 (35%), Positives = 124/228 (54%), Gaps = 3/228 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           +P  + +V+++ G  SRR  E +I   RV+V+G ++  A V V      I VDG  L  A
Sbjct: 23  SPVSLPRVLSKFGFCSRRSAEVLIESGRVRVDGRVVRNAGVRVDPQRAAICVDGRRLVSA 82

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
            +  L L +KP GL+TT+ DP GR TV+D L       +  VGRLD  +EGLLL+TND  
Sbjct: 83  AKVYL-LLNKPRGLLTTYGDPQGRKTVYDCLAGHDLPFLAPVGRLDCASEGLLLMTNDTR 141

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  L  P++   +VY V+   + D+  L  L++G+   G       V        NAW+
Sbjct: 142 WAHRLLDPASNVDKVYHVQIDRRPDEALLTGLREGVAHDGERLAAKSVAPLRVGERNAWL 201

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V L EG+NR+I+++      +V RL+R++ G  +LG +  G+ R ++
Sbjct: 202 EVVLSEGRNRQIRRMMALNGAEVLRLVRVAVGGVRLGDVRKGAFRHLT 249


>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 =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 119/232 (51%), Gaps = 9/232 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      QG+     QV++  +   NA
Sbjct: 158 AVTDPATGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPQGQGVLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L   + R +S +
Sbjct: 218 WLEIVLDEGRNRQIRRLVAAVDIGVLRLVRVAIGPLAMGELGKSAWRMLSAE 269


>gi|309792033|ref|ZP_07686509.1| pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308225926|gb|EFO79678.1| pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 637

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 66/165 (40%), Positives = 94/165 (56%), Gaps = 3/165 (1%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           +  D IEVDG P+RK   TR +L  +KP+G V+T  DP GR TV D L  + +RV  VGR
Sbjct: 3   LDADVIEVDGQPVRKPT-TRTYLVLNKPVGFVSTVDDPQGRPTVVD-LVDVPARVYPVGR 60

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD+++EGLLLLT+DG L   L  P  +  + YR      +D + L   ++G+++ G    
Sbjct: 61  LDVDSEGLLLLTDDGELTHQLTHPRFEIEKEYRALLDRPLDTEALRQWREGVLLNGEPTA 120

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
              V L        W  V LREG+ R+I++V     ++V RLIR+
Sbjct: 121 PAWVDLLETTAEGPWFRVVLREGRKRQIREVARLLGYEVLRLIRV 165


>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 =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 80/226 (35%), Positives = 120/226 (53%), Gaps = 4/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ASRR+VE  +   RV +NG ++   +  V  TD + +DG  +    R  
Sbjct: 4   RLNKYLASCGLASRRKVEEFVLSGRVALNGRVVRDLSTTVEETDTVTLDGKEVSPESRVY 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
           + + +KP G+V    D     TV D LP  +S  R+  VGRLD  +EGLL+LTNDG  A 
Sbjct: 64  I-VMNKPQGVVCAVED-RFDMTVIDVLPPAYSKFRLFPVGRLDKESEGLLVLTNDGDFAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS+   R Y V  + ++  +K+ L  KG  I+G     + V    +     WVTV 
Sbjct: 122 FLMHPSSNIKRDYEVLLNEELTVEKMKLWLKGFEIEGGFVRPLSVQPLCRPPYGRWVTVS 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + EG+ RE++ + E   +KV  LIR   G  +L  L  G T ++S+
Sbjct: 182 ITEGQKREVRLMAEHLGYKVMVLIRRRIGRMELRNLNKGQTVKLSQ 227


>gi|325136481|gb|EGC59087.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
          Length = 200

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 59/162 (36%), Positives = 100/162 (61%), Gaps = 3/162 (1%)

Query: 67  LRKAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLL 124
           L+ A+R  R+ LY+K  G + +  DP GR ++FD LP +  SR +++GRLDINT GLL+L
Sbjct: 2   LKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLIL 61

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQK 183
           T  G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +
Sbjct: 62  TTSGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGE 121

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G+N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L
Sbjct: 122 GANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGL 163


>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 =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 84/256 (32%), Positives = 134/256 (52%), Gaps = 20/256 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E   P R+ + +ARAG+ASRR  ER++ + RV+VNG+++      V  T D +EVDG  +
Sbjct: 4   ERIVPMRLQRFLARAGVASRRGSERLMTEGRVRVNGVVVSELGSKVDPTRDTVEVDGHIV 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTN 126
             A+     + +KP G +TT SDP GR T+   +P+  +  +  VGRLD++T GLLL T 
Sbjct: 64  GIADAPVYLMLNKPEGYLTTMSDPQGRPTIKTMVPTKRYPGLFPVGRLDMDTSGLLLFTT 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGIC-------------- 171
           DG +A+ L  PS    + Y     G   + +L  L++GI++  G+               
Sbjct: 124 DGTMAQELLHPSRHVWKHYLALVLGVPTEAELERLRRGIMLDDGMAQPAKVELRDDLLEL 183

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +G  +   +  K  NA V + + EG+  ++KK+      +V  L R ++GP +L  +  G
Sbjct: 184 HGTSRYPQNPNKPQNAIVGIWIHEGRKHQVKKMMSAIGHRVLVLHRDAFGPLRLTNVEEG 243

Query: 232 STREVSKK---ILREQ 244
             RE+  +    LREQ
Sbjct: 244 CWRELRDEEIAALREQ 259


>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 =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 82/240 (34%), Positives = 128/240 (53%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KVI      SR+E++R+ A+  V+++G ++   + NV S  H + VDG  +   ER 
Sbjct: 2   RIDKVIETQLHTSRKEMKRLFAKGLVQIDGEIMRNQSFNVDSHLHCLTVDGQVVEWYER- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
             WL +KP G VT + D     T+FD   +  + + + +VGRLD +TEGL+L+T +G L 
Sbjct: 61  -YWLMNKPAGYVTANHDKV-VPTIFDLFATDDLVAGLYAVGRLDRDTEGLVLVTTNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWV 189
             L  P+ +  + Y VR + ++ +  +    +GIV  G   C    Q+ L +     +  
Sbjct: 119 YQLLHPTKKVDKKYSVRVNARLTEKDVQAFSEGIVFHGGTRCL-PAQLLLKSCHDQESEA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EGK  ++KK+F     KV  L RIS+GP +L TL  G  R ++K  L E L P +
Sbjct: 178 EVVLSEGKFHQVKKMFLACGKKVTFLKRISFGPLELKTLPVGEYRSLTKHEL-EALRPFM 236


>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 =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 77/227 (33%), Positives = 116/227 (51%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +V  ++ARAG  SRR +E  I   RV++NG +    A      D +E DG+ +   E+  
Sbjct: 7   KVHVLLARAGCGSRRVLEDAIRDGRVRINGEVATIGARVRPGVDRVEFDGLEIATEEQRE 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            WL +KP G+V++  DP+GR TV  +L +  SRV  VGRLD+++EGLL+LTNDG L   L
Sbjct: 67  YWLLNKPRGVVSSVVDPEGRPTV-RSLVATTSRVYPVGRLDVDSEGLLILTNDGPLTYQL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V +     L++G+ + G       V     +     V + L 
Sbjct: 126 THPRFHVPKEYLVWVDRPVPRRLGRELREGVEVDGELLRASSVGTVGPR----LVRIVLT 181

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           EG+NR+I+++       V RL+R+  GP     L  G  R +  + L
Sbjct: 182 EGRNRQIRRMVGAVGLSVERLVRVRIGPLVDPHLPPGVARRLEPREL 228


>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 =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 123/236 (52%), Gaps = 10/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G  +R +V+ M+ + R+ VNG  + +A + +    D I +DG  +  A RT
Sbjct: 10  RLDKFLTEMGRGTRSQVKEMVRKGRITVNGQAVRQADLKINPEADQICLDGAAVAYA-RT 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D  GR      L   ++   +  VGRLDI+TEGLLLLTNDG LA
Sbjct: 69  EYYMLNKPQGVVSATED--GRYQTVTELITGALRGDIFPVGRLDIDTEGLLLLTNDGSLA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY  R  GQ+ +D +     G+V++    G   +    +      V +
Sbjct: 127 HNLLSPRKHVDKVYFARIEGQLPEDAVGRAAAGLVLED---GTKTLPARLEILEPGQVRL 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
            +REGK  ++K++FE    +V  L R+S GP  L   LA G  R ++++ +++  G
Sbjct: 184 TIREGKFHQVKRMFEAMGCRVTYLKRLSMGPLVLDPALAPGEYRPLTEQEIQDLQG 239


>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 =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 74/220 (33%), Positives = 111/220 (50%), Gaps = 7/220 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K I  +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD ++  
Sbjct: 204 KEINYDPNEPLRLNKFLANAGVCSRREADEFIQAGVVSVNGEIVTELGTKILRTDVVKFH 263

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLL 122
             P+   E+    L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+L
Sbjct: 264 DQPV-NIEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNACPERIYPVGRLDRNTTGVL 322

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLD 180
           LLTNDG LA  L  P     ++Y V     V    L  + +GI ++   I   D+Q    
Sbjct: 323 LLTNDGDLASKLTHPKYLKKKIYHVYLDKNVTAHDLAQIAEGIQLEDGEIKADDVQYAHP 382

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           T K     V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 383 TDK---KQVGIEIHSGKNRIVRRIFESLGYRVQKLDRVQF 419


>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 =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 118/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +AR G+ASRR+ E +I   +VKVN  +++     V  +  +      + + E  
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDTVVDSLGTKVDPSVDVVSVNNKVIRPEEN 62

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ + +KP G VTT+ D   R T+ D +  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILD-IVKVNERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLTLKNLKKGEWRYLS 226


>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 =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 80/230 (34%), Positives = 116/230 (50%), Gaps = 5/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRR+VE++I   RV VNG L+      V   D + VD V +    +T 
Sbjct: 4   RLNKYLASCGVGSRRKVEQLITAGRVTVNGYLVSDLGHQVEDGDAVAVDDVEVHVEAKTY 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLAR 132
           + +  KP G +   ++PD    V D LP  + R+    VGRLD+ +EG+L+LTNDG  A 
Sbjct: 64  I-VIRKPRGYICAVTNPD-YPVVLDLLPRSYDRLRLFPVGRLDLQSEGILILTNDGDFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTV 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|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 =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 78/237 (32%), Positives = 123/237 (51%), Gaps = 16/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+++ +A  GIASRR  ++M+ + RV VNG +++E      M  D + VDG      E  
Sbjct: 11  RINRYLAMCGIASRRAADQMVIEGRVMVNGQVVIEPGLQIKMGKDEVIVDGQKYALPEER 70

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++TT SD   R  V D +  +  RV  VGRLD  T G LL TNDG LA 
Sbjct: 71  KVYILFNKPRNVITTSSDERDREMVLDYI-KVKERVFPVGRLDRKTTGALLFTNDGILAN 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGSN 186
            L  PS+   + Y         Q  L LL  G+ ++        C   +   LD   G  
Sbjct: 130 KLMHPSSNVKKEYLAVLDTAFPQSSLPLLTGGMRLKDTGEKVRPCQAKI---LDG--GMQ 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            W++  L EGKN +++++F    ++V RL R++Y   + G L  G  R ++++ +R+
Sbjct: 185 VWMS--LHEGKNHQVRRMFWTLGFEVTRLERVTYAGLKTGDLRRGEWRYLNREEVRQ 239


>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 =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 77/238 (32%), Positives = 118/238 (49%), Gaps = 10/238 (4%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    V VNG +++     V+ TD +    
Sbjct: 9   EENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRTDVVLFQD 68

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LL
Sbjct: 69  KPV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLL 127

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  P     +VY V     V  + L  +  GI ++    G+++       
Sbjct: 128 LTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELED---GEIKADAIEYA 184

Query: 184 GSNAWVTVGLR--EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +    VG+    GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 185 SPDDLTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEK 242


>gi|332830420|gb|EGK03048.1| hypothetical protein HMPREF9455_01298 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 444

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 74/233 (31%), Positives = 120/233 (51%), Gaps = 11/233 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           TP R++K +A AG+ SRRE +  I    VKVNG ++++    V   D +     P+R   
Sbjct: 207 TPLRLNKYLANAGVCSRREADAYITSGVVKVNGEVVDQLGAKVTRGDLVTFQDKPVRLES 266

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LLLTNDG L
Sbjct: 267 KVYVLL-NKPKNCVTTSDDPQNRLTVMDLVKNACPERIYPVGRLDRNTTGVLLLTNDGDL 325

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P  +  ++Y+V     V  + +  +  G+ +      D ++  D+   +  +  
Sbjct: 326 ASKLMHPKFKKKKIYQVTLDRDVAIEDMQAIADGVELD-----DGEIHADSIAYQAEDVL 380

Query: 189 VTVGLR--EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             VG+    G+NR ++++FE   ++V +L R+ +       +L G  R +S+K
Sbjct: 381 NVVGIEIHSGRNRIVRRIFEKLGYQVMKLDRVYFAGLTKKNVLRGKWRYLSEK 433


>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 =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/232 (34%), Positives = 119/232 (51%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E++I + RV+VNG ++ R  V V    D I VDG  +   E  
Sbjct: 39  RLQKVLAAAGVASRRMSEKLIDEGRVEVNGDIVTRQGVRVDPDYDVIRVDGSRVVVDESM 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           + +  +KP G+ +T  D  GR  V D +        R+  VGRLD  T+GLLLLTNDG L
Sbjct: 99  QYFALNKPRGVQSTMHDDMGRPCVGDIVGEKVDAGQRLFHVGRLDAATQGLLLLTNDGEL 158

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y     G+VD+  L  L +GI +  G    D    +D  +G  + V
Sbjct: 159 ANRLIHPKYGIKKTYLATVLGEVDKKDLRRLTQGIELDDGTARADDADIIDVWQG-RSLV 217

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  L
Sbjct: 218 KVVLHEGRKHIVRRMLKAAGFPVQELVRTKIHTVQLGEQTPGTLRALNRSEL 269


>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 =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 119/227 (52%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E +I   RV+++G L+      V      + VDG  +R     
Sbjct: 20  RLQKLLAQAGFGSRRKCEEIITDGRVEIDGELITELGTRVDPKHQEVRVDGSRVRVNPNH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  VTLALNKPKRVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y     G++       L+  G+ +  G    D    LD+ + S   V V
Sbjct: 140 IMHPKYEVEKTYIATLDGRISGTVCRRLVTTGVQLDDGWIKLDRCAILDSSRDS-TLVKV 198

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+
Sbjct: 199 VLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGTYRVLSQ 245


>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 =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 120/227 (52%), Gaps = 12/227 (5%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAERTR 74
           + + RAG  SRRE   +IA  +V+V+ ++ ER    ++  +   H+E     LR A   R
Sbjct: 347 RCLPRAGFCSRREALSIIASGQVRVDNVV-ERNPFRLVRAENSIHVESHSGRLRFAP-PR 404

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           LW+YHKP  ++ + +D  GR+ +  +   +    ++ VG L +   GLLLLTNDG L+R+
Sbjct: 405 LWMYHKPAYVIVSRNDVAGRTLMTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRL 464

Query: 134 LELPSTQWLRVYRVRFHGQVD---QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           LE P T   + Y +R    +D     KLN   +GI++ G  Y +++  ++    S   + 
Sbjct: 465 LENPKTMIQQTYLLRVRPAIDPVLAHKLN--TEGILVNGNRYNNVEFFVNPAMKSRYSLK 522

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           V +R G+   +  + +     V R  RIS+GPF +  L  GS REV+
Sbjct: 523 VKVR-GETMPVAHLMQHLGRTVERGGRISFGPFSMSGLPVGSIREVT 568


>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 =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 78/231 (33%), Positives = 121/231 (52%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V++ I  Q+V+V+G L      NV  S   I V G  L  +   
Sbjct: 2   RLDKLLGQAGFGSRGQVKKFIRSQQVRVDGELARTGNQNVDPSLQTITVSGKQLSYSPHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP GLV+   D     TV D +  +  R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYILNKPAGLVSVVRDQH-YQTVIDLIAVVDRREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGIC-YGDMQVTLDTQKGSNAW 188
             L  P     + Y V  +G +  D +     GI      +C    +Q+   + + S A+
Sbjct: 120 FRLLHPKYHVDKTYYVEVNGDLGIDAIAFFDNGIAFLDGTVCKSAKLQIISSSSEVSRAY 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +T+   EGK  ++KK+F  +  KV  L RIS+GPF+LG L  G  RE++ +
Sbjct: 180 ITI--TEGKFHQVKKMFLAYGVKVTYLKRISFGPFELGDLSVGEYRELTAE 228


>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 =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 78/232 (33%), Positives = 118/232 (50%), Gaps = 5/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E  
Sbjct: 6   RLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQRVDEKNDTVCFRGNPLTYTEY- 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             +L+HKP G VT   D   R TV D L       +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 65  EYYLFHKPAGCVTATEDNLHR-TVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    +VY  +  G+V ++ +NL + G+ I         +      G N+ + + 
Sbjct: 124 DLLSPAKHVSKVYYAKIDGRVTEEDVNLFENGVDIGEEKPAKPALLEVLHSGDNSEIRLT 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           + EG+  ++K++FE    KV  L R+  G   L   LA G  R ++++ L+E
Sbjct: 184 ITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEEELQE 235


>gi|189499452|ref|YP_001958922.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
 gi|189494893|gb|ACE03441.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
          Length = 254

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/239 (33%), Positives = 118/239 (49%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K +A  GIASRR  +R++    V VNG I++++ A      D + V    L   E  
Sbjct: 18  RINKYLALCGIASRRAADRLVESGEVMVNGRIMMKKGATVRPGVDEVVVSNRLLALPEEK 77

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L +KP   +TT SD   R TV D L  +  RV  VGRLD  T G+LLLTNDG LA 
Sbjct: 78  KVYILLNKPRNYITTSSDEKERETVLD-LVDVRERVFPVGRLDRKTTGMLLLTNDGALAH 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGSN 186
            L  PS++  + Y         +  L  L  G+ ++        C G +      Q G  
Sbjct: 137 RLMHPSSEVEKEYLAELETPFSEKDLPSLTGGMRLKDTGEKTSPCKGKIM-----QGGLR 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             VT+   EGKN +++++F    + V RL R +Y   + G L  G  R  + K + EQL
Sbjct: 192 VLVTI--HEGKNHQVRRMFRSLGYDVKRLDRTAYAGLRAGKLRRGEWRYATSKEV-EQL 247


>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 =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 119/228 (52%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           ++ K IA  G  SRR+ E +I Q +VKVN        + V   D IE++G + + K    
Sbjct: 2   KIQKRIAHLGYCSRRQAEALILQNKVKVNSSFATIGQI-VSDQDIIEINGKILVEKENEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L HKP   +++  D   R  V D + S  SRV  VGRLD NT G+L+LTNDG L + 
Sbjct: 61  EYYLLHKPPKTISSTKDEKNRQVVTDLVKS-KSRVYPVGRLDYNTTGVLILTNDGDLTQK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  Q  R+Y  +    +++ +L  L +  +     Y D ++++    Q    +++ V
Sbjct: 120 LLHPKYQIKRLYHCKLDIPLEEKELIYLNEEKI-----YIDKKLSIHKVLQVEKKSYL-V 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G    +KK+FE  N KV +L R+++GP  +  L  G  R+++ K
Sbjct: 174 ELHQGSYHHVKKIFEKVNRKVVKLKRLAFGPITIDNLPEGYFRKLTFK 221


>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 =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 68/224 (30%), Positives = 117/224 (52%), Gaps = 11/224 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAERT 73
           + K++++AG+ SRRE E++I +++VKVNG   + A +   ++  D I V+  P+ + E  
Sbjct: 1   MQKILSQAGVCSRREAEKLILEKKVKVNG---QIATLGTKASFEDEILVNNKPITQREEL 57

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP   V T  D   R  V D L     ++  VGRLD +T G+LLLTNDG L+ +
Sbjct: 58  VYFVLNKPKNTVCTLKDNFNRVKVTD-LIDTDKKIFPVGRLDYDTTGVLLLTNDGKLSNL 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS++  R+YR R    +   ++ +L K ++I      + + T +          V L
Sbjct: 117 LTHPSSEIKRIYRARISAPLTDKEMEILSKPVII-----NNQRSTQEIYPADTKSYYVVL 171

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +G    +KK+FE  + KV  L R+ +    +  +  G  R ++
Sbjct: 172 HQGSYHHVKKLFELVDKKVLDLNRVEFANITVKNMQKGQYRRLT 215


>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 =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 118/235 (50%), Gaps = 9/235 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R +A  RV V G ++      + +  H  I +DG PL    R 
Sbjct: 37  LARVLSKLGVCSRTEAARWVADGRVSVAGRVVRDPEFPLRADQHDGIAIDGQPLAGPARL 96

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 97  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWLAPVGRLDKASEGLLLFSNDPQWAA 155

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-----IQGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   + D  +L  +  G+        G      QV +  +   NA
Sbjct: 156 AVTDPATGPDKTYHVQVDCRPDALQLARMHDGVADTDPESDGSLLRAKQVRVLREGERNA 215

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+I+++       V RL+R++ GP  +G L  GS R +S   +R
Sbjct: 216 WLEIVLDEGRNRQIRRLLAALEIGVLRLVRVAIGPLAMGELGKGSWRLLSAAEVR 270


>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 =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 79/238 (33%), Positives = 131/238 (55%), Gaps = 24/238 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRTIDKYIEEGRITVNG-NTAITGMDISENDNIFIDGEKIKTNIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   ++ +KP+ ++++ SD  GR TV D L     R+  VGRLD  T GL+LLTNDG L 
Sbjct: 60  KKVYFMLNKPLEVLSSSSDNRGRKTVVD-LIKTDKRIFPVGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDT 181
             +  P ++  + Y V+  G++ ++++  LKKG++          I GI Y       D 
Sbjct: 119 NRIVHPKSEIYKKYYVKILGEIKKEEIEELKKGVLLDDSKTLPAKISGIKY-------DK 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++K+
Sbjct: 172 NKTS---MYISIREGRNRQIRRMIEKFGYKVLMLRREKIGELSLGDLPEGKYRELTKQ 226


>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 =  106 bits (264), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 115/225 (51%), Gaps = 8/225 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLW 76
           + + RAG  SRRE   +IA  +V+VN ++       V + D + V G   R +    RLW
Sbjct: 334 RTLPRAGFCSRREAAAIIASGQVRVNNVVERNPFRLVEAQDDVHVAGHQSRLRFAPPRLW 393

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +Y+KP  ++ + +D  GR+ +  +   +    ++ VG L +   G+LLLTNDG L+R LE
Sbjct: 394 MYNKPANVIVSRNDVAGRTLITKHARILGMDHLVPVGSLPMRAHGILLLTNDGELSRFLE 453

Query: 136 LPSTQWLRVYRVRFH---GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            P +   R Y +R     G V   KLN   +GI I G  Y + +  ++    S   V V 
Sbjct: 454 SPKSMVQRTYMLRVRPAFGPVLVHKLN--TEGIQINGRRYRNTEFFVNPATKSRYSVKVK 511

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +R G++  I  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 512 VR-GESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 555


>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 =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 122/238 (51%), Gaps = 16/238 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ IAR    SRR+ + +IA+ +VK+N   +          D I ++G  L+  KA R
Sbjct: 2   RLNQFIARYAHCSRRQADTLIAEGKVKINH-QVASFTTPFNKEDKIFIEGRLLKIPKAPR 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G +    D   R T+F++L   F+  I VGRLD  + GLLLL++  G+A 
Sbjct: 61  YSVVIYHKPKGELVARRDDRARPTIFESLDRKFAHFIPVGRLDFASSGLLLLSDHSGVAS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT- 190
            L   + +  RVY ++  G +  + L  ++ GI   +G    + + +L+    ++  +  
Sbjct: 121 ALMHSALE--RVYLLKIQGPITPEILEGMQNGICSHKGAHPNNPKQSLELPPFAHCHIIK 178

Query: 191 ---------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    + L EGKNRE+++ F  F+  V  L R+SYG   L  L  G TR ++ K
Sbjct: 179 NHPHFSKLKITLTEGKNRELRRFFAHFDRAVLDLQRVSYGFTHLNALPEGKTRYLNPK 236


>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 =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 119/227 (52%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+AG  SRR+ E +I   RV+++G L+      V      + VDG  +R     
Sbjct: 20  RLQKLLAQAGFGSRRKCEEIITDGRVEIDGELITELGTRVDPKHQEVRVDGSRVRVNPNH 79

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ 
Sbjct: 80  VTLALNKPKRVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQH 139

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y     G++       L+  G+ +  G    D    LD+ + S   V V
Sbjct: 140 VMHPKYEVEKTYIATLDGRISGTVCRRLVTTGVQLDDGWIKLDRCAILDSSRDS-TLVKV 198

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+
Sbjct: 199 VLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGTYRVLSQ 245


>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 =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 123/230 (53%), Gaps = 20/230 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           PQR++KV+A AG+ASRR  E +I Q +V VNG +       V +S D I V+G  + K  
Sbjct: 157 PQRLAKVLAAAGVASRRTSEELIFQGKVTVNGSVCTSPQTKVDISKDSIYVNGNRISKKL 216

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTV--FDN-----------LPSIFSRVISVGRLDIN 117
             +L+   +KP G + +  + D +S V  F++           LP    R+ +VGRLD+ 
Sbjct: 217 PPKLYFAVNKPKGYICSCGE-DSKSVVSLFNDYLKGWNKIQPGLPK--PRLFTVGRLDVA 273

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQ 176
           T GL+++TNDG  A+ L  PS+   + Y V   G V +  L  + +G  I GI C  D+ 
Sbjct: 274 TSGLIIVTNDGEFAQKLAHPSSNVTKEYVVTIDGAVHKKHLIAISEGTKIDGIMCIPDLV 333

Query: 177 VTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +LD Q  +    + + + EG+N E++++ +    +V  L R+  G F+L
Sbjct: 334 ESLDAQSDTRKTRLKIVVHEGRNHEVRELVQNAGLQVYALKRVRIGRFRL 383


>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 =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 120/235 (51%), Gaps = 9/235 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSITVDGQPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+    + Y V+   +    +L  L+ G+       +G+     QV++  +   NA
Sbjct: 158 TVTDPARGPDKTYHVQIDCRPSAAQLTQLQAGVADTDPEGEGVLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVR 272


>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 =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 76/241 (31%), Positives = 129/241 (53%), Gaps = 9/241 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I +E F   R++  ++ AGI SRRE +++I    ++VNG ++ +    V   D I
Sbjct: 5   MNQKKIEEEKFI--RLNHYLSNAGITSRREADKLIQSGLIEVNGKIVTKFGTVVHKNDVI 62

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           +  G  ++  ++  + L +KP G +T+  DP  R TV + +P+  + R+  VGRLD  T 
Sbjct: 63  KFHGSRIKNKKKIYILL-NKPKGYITSTRDPFNRKTVMNLIPNFQNYRIYPVGRLDRLTT 121

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG +   L  P  +  ++Y V  +  +    L+ +++G     I   + +V +
Sbjct: 122 GVLLLTNDGFITEKLTHPKYKIQKIYLVVLNKTIHYQDLDKIRQG----KIYLNEGRVKI 177

Query: 180 D-TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           D   K +   V +GL  G NR I+++F+   ++V +L RI +G F    L  GS   +SK
Sbjct: 178 DFLHKYAKNIVKIGLHIGWNRVIRRIFKKLTYQVIKLERIHFGGFTNKNLKIGSWCFLSK 237

Query: 239 K 239
           +
Sbjct: 238 Q 238


>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 =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 124/236 (52%), Gaps = 6/236 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +++++++AG+ SR      I   RV+V+G  +L+  A   +S   I +DG+ +  + R  
Sbjct: 22  LARILSKAGLCSRTVAVEWIRAGRVEVDGRRILDPEARFPLSGPGIRIDGLDITASTRQV 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L HKP G++TT  D  GR+TV+D LP     +  VGRLD  + GLLL +ND   A+ L
Sbjct: 82  L-LLHKPRGVLTTRQDERGRATVYDLLPG-SPWLAPVGRLDQASSGLLLFSNDPHWAQRL 139

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+    +  D +  L    V+ G     MQ+      G   W+   L+
Sbjct: 140 LDPDQHVAKTYHVQIRPPLSTDTVVQLAADSVLDGEPCLPMQIRELRCGGKTQWLEFILQ 199

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV---SKKILREQLGP 247
           EG+NR+I+++    + +V RLIR++ G   LG L AG  R +    +++LR+   P
Sbjct: 200 EGRNRQIRRLLAACDREVLRLIRVAVGNLPLGELRAGEWRWLHSGEEELLRQTPTP 255


>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 =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 79/222 (35%), Positives = 117/222 (52%), Gaps = 5/222 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R I   RV+V+G ++      +      + VDG      ER  
Sbjct: 26  LARVLSKAGLCSRTEAARWIEAGRVQVDGRIVRDPEYPMRHGLRGVLVDGRAPAGPERIY 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGG-LAR 132
           L L +KP GLVTT  D  GR TV+  L  S    +  VGRLD  +EGLLL +ND    AR
Sbjct: 86  LAL-NKPRGLVTTARDEQGRDTVYRCLDGSGLPWLAPVGRLDRASEGLLLFSNDPAWAAR 144

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL+ P +   + Y V+     DQ  L  L+ G+   G     +  ++      NAW+ + 
Sbjct: 145 VLD-PDSGPDKTYHVQVDAIPDQTLLQALRTGVDADGEHLRAVSASVLRTGTRNAWLEIV 203

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           L EG+NR+I+++   F+  V RL+R++ G  QLG L  G  R
Sbjct: 204 LDEGRNRQIRRLLAAFDLSVLRLVRVAIGALQLGDLGKGQWR 245


>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 =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 74/221 (33%), Positives = 112/221 (50%), Gaps = 14/221 (6%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    V VNG ++      ++ +D I   G
Sbjct: 261 EENFDPNEPLRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVNELGTKILRSDVITFKG 320

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +  I   R+  VGRLD NT G+LL
Sbjct: 321 QPV-TLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGICPERIYPVGRLDRNTTGVLL 379

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  P     +VY V          L  +  GI ++     D ++  D  +
Sbjct: 380 LTNDGDLASKLTHPKFLKKKVYHVYLDKPATPQTLQQISDGIELE-----DGEIKADAIE 434

Query: 184 GSN----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            ++    + V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 435 YADSLDQSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQF 475


>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 =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 117/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +AR G+ASRR+ E +I   +VKVN  +++     V  +  +      +   E  
Sbjct: 3   ERLQKYMARCGVASRRKCEEIICSGKVKVNDTVVDSLGTKVDPSVDVVSVNNKVISPEEN 62

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ + +KP G VTT+ D   R T+ D +  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 63  KVYIMLNKPEGYVTTNKDEKNRKTILD-IVKVNERIYPIGRLDYDSSGLLLLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++N  +KG+ I      + ++ L  +  ++  V + 
Sbjct: 122 KIIHPRVNLNKEYIALVKGIFTEEEMNKFRKGVDIGDYKTAECEIELLEKYTNSCKVKII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+I+++   FN +V  L R + G   L  L  G  R +S
Sbjct: 182 IHEGKNRQIRRMCAAFNHEVVSLKREAIGSLTLKNLKKGEWRYLS 226


>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 =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 117/232 (50%), Gaps = 11/232 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AGI SRRE +  I    + VNG ++    V V+ TD +      +R +ER
Sbjct: 278 PIRLNKFLANAGICSRREADEYIQAGVISVNGEIVTEMGVKVLLTDKVMFHEQTVR-SER 336

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  D   R TV D + +  S R+  VGRLD NT G+LLLTNDG LA
Sbjct: 337 KVYLLLNKPKDCVTTSEDTHDRLTVLDLVKNACSERIYPVGRLDRNTTGVLLLTNDGDLA 396

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT----QKGSNA 187
             L  P     ++Y    H  +D+  L       ++ G+   D+ +  D     ++G   
Sbjct: 397 SKLTHPKYDKKKIY----HATLDK-PLEKADFETILAGVPLDDVNIAADALEFVKEGDLK 451

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V + +  G+NR ++++FE   +K+ RL R+ +       L  G  R +S++
Sbjct: 452 QVGIEIHSGQNRVVRRIFEKLGYKIIRLDRVYFAGLTKKQLPRGKYRFLSER 503


>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 =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 113/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +   G+ SR+EV+ ++  ++++VNG+ +     N+         G      +  R
Sbjct: 2   RIDKFLVECGVGSRKEVKELLKSRKIRVNGLFITSPKENIEEEKDEVYYGEKKLSYQEFR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ HK  G VT   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 62  YYILHKKAGYVTALEDSR-EATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTV 191
            L  P +   + Y       + ++ L  L++G++I     G+ + +    +K  +  + +
Sbjct: 121 RLLSPKSHVDKTYHASLECDITEEALEKLREGVMI-----GEYKTLPAKAEKLEDRKIAL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +REGK  ++KK+ E    KV  L RIS+G   LG L  G  +EVS
Sbjct: 176 TIREGKFHQVKKMLEAVGNKVIYLKRISFGKLVLGDLELGEVKEVS 221


>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 =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 119/226 (52%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   GI SR+EV+++I+   + VNGI    A  N+  ++D IE +   L + ++ 
Sbjct: 2   RLDKFLVECGIGSRKEVKKLISNNEITVNGISNISAKDNIDENSDIIEYNEEKL-EYKKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 61  RYYIMNKKSGYITATEDF-KENTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + +
Sbjct: 120 HKLLSPKNHVDKVYYVEIKNNISDEDIFKLEQGVDIGNYITQPAKV----EKISDNEIYL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++EGK  +IKK+ E  N KV  L R+S+G  +L  L  G  REV+
Sbjct: 176 TIKEGKFHQIKKMLEAINNKVCYLKRVSFGRLKLNDLALGEVREVN 221


>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 =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 116/227 (51%), Gaps = 9/227 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLW 76
           ++++ G+ SR E  R IA+ RV V+  ++      + +  H  I VDG PL    R  L 
Sbjct: 1   MLSKLGVCSRTEAARWIAEGRVSVDARVIHDPEFPIRADQHEAITVDGQPLAGPARVYLM 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  + 
Sbjct: 61  L-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAAVT 119

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVT 190
            P+    + Y V+   +   ++L  L+ G++       G      QV L  +   NAW+ 
Sbjct: 120 DPAIGPDKTYHVQVDCRPGAEQLAQLQAGVIDPAPDGDGALLRAKQVRLLREGERNAWLE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S
Sbjct: 180 IVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLS 226


>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 =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 124/236 (52%), Gaps = 6/236 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +++++++AG+ SR      I   RV+V+G  +L+  A   +S   I +DG+ +  + R  
Sbjct: 26  LARILSKAGLCSRTVAVEWIRAGRVEVDGRRILDPEARFPLSGPGIRIDGLDITASTRQV 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L HKP G++TT  D  GR+TV+D LP     +  VGRLD  + GLLL +ND   A+ L
Sbjct: 86  L-LLHKPRGVLTTRQDERGRATVYDLLPG-SPWLAPVGRLDQASSGLLLFSNDPHWAQRL 143

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+    +  D +  L    V+ G     MQ+      G   W+   L+
Sbjct: 144 LDPDQHVAKTYHVQIRPPLSTDTVVQLAADSVLDGEPCLPMQIRELRCGGKTQWLEFILQ 203

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV---SKKILREQLGP 247
           EG+NR+I+++    + +V RLIR++ G   LG L AG  R +    +++LR+   P
Sbjct: 204 EGRNRQIRRLLAACDREVLRLIRVAVGNLPLGELRAGEWRWLHSGEEELLRQTPTP 259


>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 =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 108/218 (49%), Gaps = 8/218 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +EN+ P    R++K +A AG+ SRRE +  I    V VNG +++     VM TD +    
Sbjct: 270 EENYDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVMRTDEVYFQD 329

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
             L   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LL
Sbjct: 330 K-LVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLL 388

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG LA  L  P     +VY V     +  + L  +  GI ++ G    D     D Q
Sbjct: 389 LTNDGDLASKLTHPKFLKKKVYHVFLDKAITANDLQKISDGIELEDGEIKADAIEYADPQ 448

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                 V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 449 --DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQF 484


>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 =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 120/244 (49%), Gaps = 26/244 (10%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           + F PQR+SK++A  G+ SRRE + +I    V+VNG +++     V+ T  I++D     
Sbjct: 99  DPFEPQRLSKIMAAKGLCSRREADYLIENGWVRVNGKVVDELGAKVLPTVTIDLDARAKN 158

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGR------------------STVFDNLPSIFSRVIS 110
              +    LYHKPIG+V+    P+GR                  ST F   P++   +  
Sbjct: 159 VLGKQVTILYHKPIGVVSGQ--PEGRYKAAMECLSLENQADRKTSTPFQ--PAMLKGLAP 214

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++    L +L+ G+ + G 
Sbjct: 215 AGRLDIDSTGLLVLTQDGRIAKQLIDANSTVEKEYLVRVEGELTDRGLEMLRYGLSLDGE 274

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V+   +      +   L EGK R+I+++ E    KV  L R+  G   LG L  
Sbjct: 275 ALKPARVSWQNED----QLRFILNEGKKRQIRRMCEIVGLKVVGLKRVRIGRVMLGDLPV 330

Query: 231 GSTR 234
           G  R
Sbjct: 331 GQWR 334


>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 =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 120/235 (51%), Gaps = 9/235 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 17  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSITVDGQPLAGPARC 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 77  YLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+    + Y V+   +    +L  L+ G+       +G+     QV++  +   NA
Sbjct: 136 TVTDPARGPDKTYHVQIDCRPSAAQLTQLQAGVADTDPEGEGVLLRAKQVSVLREGERNA 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R
Sbjct: 196 WLEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVR 250


>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 =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 127/236 (53%), Gaps = 24/236 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
            R++K ++  GIASRR ++R I + R+ VNG       +++   D+I +DG  +     E
Sbjct: 1   MRINKFLSTLGIASRRTIDRYIEEGRITVNG-NTATTGMDISGNDNIFIDGKKIETNIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ ++++ SD  GR TV D L     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKIYFMLNKPLEVLSSSSDDRGRKTVVD-LIKTDKRIFPIGRLDYMTSGLILLTNDGDLF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDT 181
             +  P ++  + Y V+  G++ ++++  LKKG++          I GI Y       D 
Sbjct: 119 NRIVHPKSEIYKKYYVKIFGEIKKEEIEELKKGVLLDDGKTLPAKISGIKY-------DK 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            K S   + + +REG+NR+I+++ E F +KV  L R   G   LG L  G  RE++
Sbjct: 172 NKTS---MYISIREGRNRQIRRMIEKFGYKVLMLKREKIGELSLGDLPEGKYRELT 224


>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 =  105 bits (263), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 122/233 (52%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E++IA  RV+VNG ++ +    +  S D + VDG  ++  E  
Sbjct: 51  RLQKVLASAGVASRRMSEKLIAAGRVEVNGEVVVKMGTRIDPSVDIVRVDGERVQVNEEM 110

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+ +T SD  GR  V D + +       +  VGRLD  TEGLLLLTNDG L
Sbjct: 111 VYFVLNKPRGVHSTMSDDLGRPCVGDLVGTRLKEGQGLFHVGRLDAQTEGLLLLTNDGEL 170

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + Y     G+  +  +  LK G+ +  GI   D    +D  +G  + +
Sbjct: 171 ANRLMHPKYEVKKTYMATVLGEASRKLIRELKDGVELDDGIARADSVQIVDVWQG-KSLI 229

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  L+
Sbjct: 230 KVELHEGRKHIVRRMLKEAGFPVQALVRTKIHTVQLGEQKPGTIRALNQAELQ 282


>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 =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 73/226 (32%), Positives = 113/226 (50%), Gaps = 5/226 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +A AG+ SRRE +  I+   V VNG ++      V+ +D ++     L   E+   
Sbjct: 1   MNKYLANAGVCSRREADEFISAGVVSVNGTVVTELGTKVLRSDEVKFHD-QLVSLEKKVY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA  L
Sbjct: 60  VLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTGVLLLTNDGDLASKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGL 193
             P     +VY V     V ++ L  +  GI ++ G  + D     D +      V + +
Sbjct: 120 THPKFLKKKVYHVHLDKNVAEEDLQKIASGIELEDGEIHADAIEYADDR--DKKQVGIEI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             GKNR ++++FE   ++V RL R+ +       L  G  R ++++
Sbjct: 178 HSGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLRRGDWRFLTEQ 223


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 65/209 (31%), Positives = 113/209 (54%), Gaps = 5/209 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE + +I Q  V+VNG ++      V  TD +  DG  +   E+  
Sbjct: 140 RLNKYIANSGICSRREADELITQGLVQVNGAVVTEMGYQVQKTDKVIFDGQGI-TPEKPV 198

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G ++T  D   R TV D + +    RV  VGRLD +T G++LLTNDG + + 
Sbjct: 199 YVLLNKPKGYISTTKDEKARKTVMDLVANASPYRVFPVGRLDRSTTGVILLTNDGHMTKK 258

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    ++Y V    ++D+  LN + +G+ + +G+   D    ++ +  +   + + 
Sbjct: 259 LTHPSFNMKKIYHVTLDRKLDRADLNAIAEGVRLEEGVAEVDSISYIEGKPKNEVGIEIH 318

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +  G NR ++++F+   ++V  L R+ + 
Sbjct: 319 I--GWNRVVRRIFQRLGYEVEALDRVMFA 345


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/240 (31%), Positives = 133/240 (55%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  S   I V G  L ++   
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQEIMVSGKRLEQSTE- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
           + ++ +KP G+V+  SD +   TV D +       R+  VGRLD +TEGLLL+TN+G L 
Sbjct: 61  KYFILNKPAGVVSAVSDKE-HQTVIDLIAEADRVPRLYPVGRLDRDTEGLLLITNNGLLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             +  P     + Y V  +G + +D     + G+      +C   ++++   + + S+A+
Sbjct: 120 FRMLHPKYHVTKTYYVEVNGLLAEDAPAFFENGVTFDDGTVCKPANLEIIEASSEKSSAY 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQL 245
           +++   EGK  ++KK+F  +  KV  L R+++G F+LG L  G  RE++   K+IL+  L
Sbjct: 180 ISIA--EGKFHQVKKMFLAYGVKVIYLKRMTFGDFELGDLPRGQYRELNTKEKEILKNYL 237


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 117/232 (50%), Gaps = 11/232 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AGI SRRE +  I    V VNG ++      V+ +D ++    P+   E+
Sbjct: 17  PLRLNKFLANAGICSRREADEFIQAGVVTVNGEVVTELGTKVLRSDEVKFRDQPV-TLEK 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG +A
Sbjct: 76  KVYVLLNKPKNYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTGVLLLTNDGDMA 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----A 187
             L  P     +VY V     +  + L  + +GI ++     D ++  D  + +N    +
Sbjct: 136 SKLTHPKFLKKKVYHVFLDKNIGVEDLQKIAEGIELE-----DGEIHADAVEYANENDKS 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V + +  G+NR ++++FE   ++V RL R+ +       L  G  R ++++
Sbjct: 191 QVGIEIHSGRNRIVRRIFEALGYRVVRLDRVLFAGLTKKNLRRGDWRFLTEQ 242


>gi|319949182|ref|ZP_08023271.1| pseudouridylate synthase [Dietzia cinnamea P4]
 gi|319437168|gb|EFV92199.1| pseudouridylate synthase [Dietzia cinnamea P4]
          Length = 252

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/235 (34%), Positives = 122/235 (51%), Gaps = 6/235 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR 68
           +  P R+ K++A+AG+ASRR  E +IA+ RV+V+G ++    V V  +T  I VDG  + 
Sbjct: 8   DGAPVRLQKILAQAGVASRRASEDLIARGRVEVDGKIVREMGVKVDPATAVIRVDGTRIV 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLT 125
             +       +KP G  TT SD  GR  V D +        R+  VGRLD +TEGLLL+T
Sbjct: 68  LDDTLVHLALNKPRGYHTTMSDEMGRPCVGDLVADRIDAGQRLFHVGRLDADTEGLLLVT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG 184
           NDG LA  L  PS +  + Y     G V +     L++G+ ++ G    D    LD   G
Sbjct: 128 NDGELAHRLMHPSYEVSKTYMATVTGVVGKGIGKQLREGVELEDGPAKVDQFSLLDVHDG 187

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             + V V L EG+   ++++       V  L+R  +G   LG   AG+ R+++++
Sbjct: 188 -RSLVKVVLHEGRKHIVRRLLAEVGHPVESLVRTRFGSVALGDQRAGTFRKLNRR 241


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 80/240 (33%), Positives = 124/240 (51%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G+L +R  +NV  S   I V G  L  A   
Sbjct: 2   RLDKLLGQAGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQSITVSGKELEHAPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+  SD     TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPAGVVSARSDKK-HQTVIDLIKPEDQREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +  +  D     + G+V + G      Q+ + +     +   
Sbjct: 120 FAMLHPRYHVAKTYYVEVNDILGPDTPAFFESGVVFEDGTICKSAQLEILSSASDKSCAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQLG 246
           + + EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  LG
Sbjct: 180 ITISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRALTEAEKVILRTYLG 239


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 119/224 (53%), Gaps = 3/224 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           +++V+++ G+ SR    + I   RV V+G ++          D  I +DG+P ++A R  
Sbjct: 6   LARVLSKWGLCSRTVAAQWIRAGRVAVDGRIVRDPEAPQRGLDLWISIDGIPQQRARRQV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + HK  G+V + SD  GR TVF ++P     +  +GRLD  + GLLL +ND   ++ L
Sbjct: 66  L-MLHKKRGVVVSRSDERGRPTVFADIPQ-EPWLAPIGRLDRASSGLLLFSNDPIWSQRL 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P+    + YRV+    +  + L+ +    V+ G     M+V      G   W+   L+
Sbjct: 124 LDPAGHLPKTYRVQIRPPLAAEALHHIATASVLDGRPCLPMEVRAVACGGKTQWLEFVLQ 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           EG+NR+I+++ E    +V RLIRI++G   LG L  GS R +S+
Sbjct: 184 EGRNRQIRRLLEAQGVEVLRLIRIAFGSVILGDLAPGSWRWLSE 227


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 117/233 (50%), Gaps = 7/233 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T QR+SKV+A AG+ASRR  E +I    V VNG +       V   D I   G  + K +
Sbjct: 31  TKQRLSKVMAAAGVASRRACEMLIFDGCVTVNGEVTLVPQTLVDENDVITCKGQSVGKKQ 90

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KPIG + ++        V D   ++  R+ +VGRLD +T GL+++TNDG  A
Sbjct: 91  NKVYYILNKPIGYICSNKRNKDSKIVLDLFDTVEERLFTVGRLDKDTSGLIIVTNDGHFA 150

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS    + Y V+ + +V+ + L+ L  G +++      ++V+    K     + +
Sbjct: 151 NRVIHPSANIHKEYLVKTNEEVEAEHLSALSSGTLVEKTFVRPIRVS----KVRRGTLKI 206

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGK REI+ + E     V  L RI  G   LG L  G  RE++    REQ
Sbjct: 207 TIAEGKKREIRLLMESAKLPVLELTRIRIGGLHLGPLQPGEWREMTA---REQ 256


>gi|329737424|gb|EGG73678.1| S4 domain protein [Staphylococcus epidermidis VCU028]
          Length = 180

 Score =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 57/155 (36%), Positives = 91/155 (58%), Gaps = 1/155 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  YILLY-KPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +  P     + Y  +  G + ++++  L+KGI ++
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELE 159


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 120/234 (51%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++     SRRE + +I Q  VK+N  + + +   V   D I +    + K  +  
Sbjct: 2   RINKFLSHNTSYSRREADELIKQGLVKINQKIAQLSD-EVKEEDKIFLKNKRIHKKTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T+++NLP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGELVSRKDDRGRKTIYENLPKNFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------LDTQ-- 182
                +  R Y ++  GQ+ +  +  ++ G+ IQ    G    T          LD +  
Sbjct: 121 MHSDLE--REYYLKIKGQISKKVIEAMQNGLEIQNSTKGAHAKTKINSMKFAPFLDFEIF 178

Query: 183 --KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              G    + V + EG+NRE+++ F +F+ +V  L R+++G  +LG L AG  R
Sbjct: 179 GWSGGYTKLRVVINEGQNRELRRFFGYFDLEVMDLKRVAFGIVELGMLKAGKYR 232


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 116/229 (50%), Gaps = 5/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG +++     V  +D ++ +G  L   E+
Sbjct: 201 PIRLNKYLANAGVCSRREADEFIETGAVTVNGEIVKELGTKVKRSDEVKFNG-ELVSIEK 259

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + +    R+  VGRLD  T G+LLLTNDG LA
Sbjct: 260 KVYVLLNKPKDCVTTMDDPQERQTVMDFVKNACDERIYPVGRLDRKTTGVLLLTNDGDLA 319

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y V     + +  L  + +GI ++ G+   D     D  K +   V 
Sbjct: 320 SKLTHPKYDKKKIYHVTLDRNIVKADLEKIAEGIELEDGLIKADEVGYTDEFKRNQ--VG 377

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++FE   ++V +L R+ +       L  G  R +S++
Sbjct: 378 IEIHSGKNRIVRRIFESLGYRVTKLDRVYFAGLTKKGLRRGQWRYLSEQ 426


>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 =  105 bits (262), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 75/226 (33%), Positives = 118/226 (52%), Gaps = 8/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+AR G+ SR+EV R++ Q +V+V G +++     V     +EV+G PL +  R 
Sbjct: 4   ERLDKVLARLGLGSRKEVARLVRQGKVRVLGQVVKDPGFRVPEGAALEVEGRPL-EVRRH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLAR 132
              L HKP G VT+ ++     +V+  L    +R +S VGRLD + EGLLL T DG L  
Sbjct: 63  LHVLLHKPPGFVTSRTE---GPSVYALLQGFPTRDLSPVGRLDKDAEGLLLFTTDGLLLH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y V     V        ++GI++ G      ++   T      W  V 
Sbjct: 120 RLTHPRHKVAKRYLVHLERPVGPKDQEAFREGILLDGKKTLPAEL---TPLEDPTWAEVV 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L+EG+  +IK++F     +V RL R++ GP +LG L  G  R +++
Sbjct: 177 LKEGRFHQIKRMFRARGNRVLRLKRLALGPLELGDLPPGKARPLTE 222


>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 =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 117/234 (50%), Gaps = 16/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA     SRRE +R+I + +V +N  ++   +  V     + ++G  LR+ ++  
Sbjct: 2   RLNQYIAHHSKFSRREADRLIKEGKVTINKEVVSDFSYQVDKNTKVYLNGKCLREQDQYS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+KP G + +  D  GR  ++D+LP  FS    VGRLD  +EGLLLL++   + R  
Sbjct: 62  VIVYNKPKGELVSKRDDRGRRVIYDSLPKRFSHFKPVGRLDFASEGLLLLSDSVKVVR-- 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--------------MQVTLD 180
            L  ++  RVY ++  G +     + ++ GI ++    G               +  T  
Sbjct: 120 SLMESELERVYLLKLSGLIKDSVFDAMESGITLEDASAGGHSKSKIKAMEFAPFVGYTCI 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 + + V L+EGKNRE+++ F  F  +V  L RI+YG   L  L +G  R
Sbjct: 180 KNTPKYSKIKVILKEGKNRELRRFFAHFGLEVLDLKRIAYGFVHLNNLPSGKVR 233


>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 =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/238 (32%), Positives = 131/238 (55%), Gaps = 24/238 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R++K ++  GIASRR +++ I + R+ VNG       +++   D+I +DG  ++    E
Sbjct: 1   MRINKFLSTLGIASRRTIDKYIEEGRITVNG-NTAITGMDISENDNIFIDGEKIKTNIDE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   ++ +KP+ ++++ SD  GR TV D L     R+  VGRLD  T GL+LLTNDG L 
Sbjct: 60  KKVYFMLNKPLEVLSSSSDNRGRKTVVD-LIKTDKRIFPVGRLDYMTSGLILLTNDGELF 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDT 181
             +  P ++  + Y V+  G++ ++++  LKKG++          I GI Y       D 
Sbjct: 119 NRIVHPKSEIYKKYYVKILGEIKKEEIEELKKGVLLDDSKTLPAKISGIKY-------DK 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            K S   + + +REG+NR+I+++ E F ++V  L R   G   LG L  G  RE++K+
Sbjct: 172 NKTS---MYISIREGRNRQIRRMIEKFEYRVLMLRREKIGELSLGDLPEGKYRELTKQ 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 =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           R+++ IA     SRR+ +++I + +VK+N   L   A      D I V+G  L   E+  
Sbjct: 7   RLNQFIAHNLPCSRRQADKLIKEGKVKINH-QLASFATPFSPYDKIFVEGRMLNSYEKRS 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + +  D  GR T+F++L S F     +GRLD  + GLLLL++   +  
Sbjct: 66  YTVLVYHKPKGELVSRIDHRGRKTIFESLESKFRHFTPIGRLDFASMGLLLLSDSKQVVN 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-------CYGDMQVT-LDTQKG 184
            L   S +  RVY V+  G + Q  L  ++ G+ +QG+        Y  M +  +  Q  
Sbjct: 126 ALMHSSLE--RVYLVKIQGNITQTMLEAMQTGLELQGLEGAHPKSKYTRMHIAPMACQIL 183

Query: 185 SN----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            N    + + + L+EG NREI++ F  F  +V  L R+S+G   L  L  G TR ++ K
Sbjct: 184 KNHRNYSKIKITLQEGHNREIRRFFAHFKKEVLDLRRVSFGFVSLNALPVGKTRYLNPK 242


>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 =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 73/220 (33%), Positives = 114/220 (51%), Gaps = 18/220 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R EV++++  +++ VNG ++ +    V    D I   G P+   E  
Sbjct: 26  RLDKFLTEMGLGTRSEVKKILKTKQITVNGEIVTKPETKVAPENDQISYKGEPVTYCEY- 84

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L++KP G VT   D     TV D L  ++ S +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 85  EYYLFYKPAGCVTATED-QLHKTVMDYLTDTVRSDLFPVGRLDIDTEGLLLITNDGALAH 143

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------LDTQKGS 185
            L  P+    + Y     G V +  +N  + G+ I     G+ ++T       L ++  S
Sbjct: 144 DLLSPAKHVEKTYYAVIDGVVTEKDVNSFENGVDI-----GEEKLTKPGKLRILKSEPES 198

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              +T+   EG+  ++K++FE    KV  L RIS GP QL
Sbjct: 199 EIELTI--TEGRFHQVKRMFEAVGKKVLYLKRISMGPLQL 236


>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 =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/218 (34%), Positives = 108/218 (49%), Gaps = 8/218 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    V VNG +++     V+ TD +    
Sbjct: 270 EENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRTDEVYFQ- 328

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
             L   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LL
Sbjct: 329 DKLVSLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLL 388

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG LA  L  P     +VY V     V  + L  +  GI ++ G    D     D Q
Sbjct: 389 LTNDGDLASKLTHPKFLKKKVYHVFLDKAVTANDLQKISDGIELEDGEIKADAIEYADPQ 448

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                 V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 449 --DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQF 484


>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 =  105 bits (261), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 124/232 (53%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R++K +A  GIASRRE +R++    V +NG +     V V    D + V G  L   E  
Sbjct: 12  RINKYLALCGIASRRESDRLVEAGEVMINGRIARTQGVKVHPGKDEVVVKGRILALPEEK 71

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L +KP  ++TT+ D   R TV D + S+  R+  VGRLD  + GLLLLTNDG LA 
Sbjct: 72  KVYILLNKPRNIITTNRDEKDRETVLD-IVSVPQRIFPVGRLDRKSTGLLLLTNDGDLAH 130

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-VTV 191
            L  PS+   + Y  +      + +L  L  G+ ++    G+   +   +  S+   V V
Sbjct: 131 RLMHPSSLVEKEYLAQLEKPFLEKELKNLTGGMRLKDT--GEKVSSCKAKLLSDGMQVLV 188

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGKN +++++F    + V +L R+SY   ++G L  G  R ++KK ++E
Sbjct: 189 TIHEGKNHQVRRMFWSLGYDVKKLDRVSYAGLKVGRLRRGEWRFLNKKEVKE 240


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 122/232 (52%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERT 73
           R+ KV+A AG+ASRR  E++IA  RV+VNG +++R  V +     +        +  +  
Sbjct: 52  RLQKVLAAAGVASRRMSEKLIAAGRVEVNGKVVDRMGVRIDPNKDVVRVDGVRVQVNDEM 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             ++++KP G+ +T SD  GR +V + +     +   +  VGRLD  TEGLLLLTNDG L
Sbjct: 112 HYYIFNKPRGVQSTMSDDMGRPSVGNFIDERLKQGQGLFHVGRLDAQTEGLLLLTNDGEL 171

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G+  +  ++ LKKGI +  GI   D    +D  +G  + +
Sbjct: 172 ANRLMHPSYEVSKTYMATVLGEAKKGLVHELKKGIELDDGIAKADDVQIVDVWQG-KSLI 230

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EG+   ++++ +   + V  L+R      QLG    GS R +++  L
Sbjct: 231 KLELHEGRKHIVRRLLKAAGFPVQALVRTKIHTVQLGDQKPGSVRALNRSEL 282


>gi|291522211|emb|CBK80504.1| ribosomal small subunit pseudouridine synthase A [Coprococcus catus
           GD/7]
          Length = 250

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 82/235 (34%), Positives = 128/235 (54%), Gaps = 12/235 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T  R+ K +A   + +R EV+ +I +  V VNG ++ +    V +  D +   G P+  A
Sbjct: 3   TSFRLDKYLADMSVGTRSEVKNLIKKGLVTVNGEVIRKPEYKVDIEKDDLVCRGEPV--A 60

Query: 71  ERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTND 127
            +T ++ + +KP G+++  +DP  + TV D L +  SR  +  VGRLD +TEGLLL+TND
Sbjct: 61  YQTLVYYMLNKPAGVISATNDPK-QKTVLD-LITDKSRKDLFPVGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDT-QKG 184
           G LA  L  P     +VYR R  GQV  +   L  KG+ I  +   +  M   L+    G
Sbjct: 119 GDLAHQLLSPKKHVDKVYRARIEGQVTAEDAALFAKGLGIDDEDGAWRAMPAKLNILSSG 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
             + + + +REGK  +IK++FE  + KV  L R+S G  +L   LA G  RE+++
Sbjct: 179 PESEIEITIREGKFHQIKRMFEAVDKKVVYLKRLSMGSLRLDETLALGEYRELTE 233


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 114/227 (50%), Gaps = 1/227 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKA 70
           T +R+ KV+AR G+ SRR  E +IAQ RV V+G ++      V      I VDG+ ++  
Sbjct: 8   TGERLQKVLARNGVGSRRACEGLIAQGRVSVDGHVVRELGTRVDPVASVIHVDGIRVQTD 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                   +KP G+V+T  D  GR  +   +     R+  VGRLD +TEGL+LL+NDG L
Sbjct: 68  SSLLTLALYKPPGVVSTMYDDMGRPGLAQYVEDRPERLYHVGRLDQDTEGLILLSNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  + Y  R  G V +    +L++GI ++       +  L      N+ V 
Sbjct: 128 THRLTHPKYEVPKTYIARVEGSVTRGLGRVLERGITLEDGPARVDRFILRESAPRNSIVE 187

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L  G+NR ++++       V  L+R+ +G   +G L  G TR V+
Sbjct: 188 ITLHSGRNRIVRRMMAEVGHPVMELVRMKFGTVVVGHLKPGKTRVVA 234


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 81/225 (36%), Positives = 115/225 (51%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +I Q RV+V+G I+LE+          + VDG+ +   +  
Sbjct: 82  RLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVLEQGLRVDPENAIVRVDGIRVVVKKDL 141

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G  +T SD  GR  + D +    S   R+  VGRLD +TEGL+LLTNDG L
Sbjct: 142 VHIALNKPRGWQSTMSDDLGRPCIGDIVSERVSAGQRLFHVGRLDADTEGLILLTNDGDL 201

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G VD++    LK G+ +  G    D    LD   G  + V
Sbjct: 202 AHRLMHPSYEVPKTYLATVQGVVDRNVGKTLKAGVELDDGPAKVDAFTLLDVN-GGKSLV 260

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+   ++++ E     V RL+R   G   LG    G+ R
Sbjct: 261 RVVLHEGRKHIVRRLLEAVGHPVVRLVRTDIGNVALGDGRPGTLR 305


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 116/231 (50%), Gaps = 20/231 (8%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGVPLRKAE 71
           + + RAG  SRRE   +IA  +V+V+ ++      L RA  N+    H+      LR A 
Sbjct: 348 RCLPRAGFCSRREALAVIASGQVRVDNVVERNPFRLVRAENNI----HVASHSGRLRFAP 403

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGG 129
             RLW+YHKP  ++ + +D  GR+ +F     I     ++ VG L +   GLLLLTNDG 
Sbjct: 404 -PRLWMYHKPAHVIVSRNDVAGRA-LFTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGE 461

Query: 130 LARVLELPSTQWLRVYRVRFHGQVD---QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           L+R LE P     + Y +R    VD     KLN   +GI I G  Y +M+  ++    S 
Sbjct: 462 LSRFLENPKCMIQQTYLLRVRPAVDPVLAHKLNF--QGITINGKQYKNMEFFVNPAMKSR 519

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + V +R G+   +  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 520 FSLKVKVR-GEVMPVAHLMQHLGRTVERGGRISFGPFSLSGLPVGSLREVT 569


>gi|261332662|emb|CBH15657.1| tRNA pseudouridine synthase A, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 688

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/231 (34%), Positives = 116/231 (50%), Gaps = 20/231 (8%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGVPLRKAE 71
           + + RAG  SRRE   +IA  +V+V+ ++      L RA  N+    H+      LR A 
Sbjct: 348 RCLPRAGFCSRREALAVIASGQVRVDNVVERNPFRLVRAENNI----HVASHSGRLRFAP 403

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGG 129
             RLW+YHKP  ++ + +D  GR+ +F     I     ++ VG L +   GLLLLTNDG 
Sbjct: 404 -PRLWMYHKPAHVIVSRNDVAGRA-LFTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGE 461

Query: 130 LARVLELPSTQWLRVYRVRFHGQVD---QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           L+R LE P     + Y +R    VD     KLN   +GI I G  Y +M+  ++    S 
Sbjct: 462 LSRFLENPKCMIQQTYLLRVRPAVDPVLAHKLNF--QGITINGKQYKNMEFFVNPAMKSR 519

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + V +R G+   +  + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 520 FSLKVKVR-GEVMPVAHLMQHLGRTVERGGRISFGPFSLSGLPVGSLREVT 569


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 125/249 (50%), Gaps = 18/249 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-- 64
           +++N    R++K I+     SRR+ +++I +  V VN + ++     V   D + V G  
Sbjct: 1   MKQNEEGMRLNKYISHNTPYSRRDADKLIEEGLVTVNRLPVKDFGYKVRPEDKVAVRGKL 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +  RK     + +Y+KP G++ T  D  GR+T++  LP  F   I VGRLD  +EGLLLL
Sbjct: 61  IHPRKRGEVTMVVYNKPRGVLVTKRDDRGRTTIYHKLPGKFRHFIPVGRLDYASEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD---------- 174
           T++  +A VL    ++  R Y ++    +  +    +K+G++++    G           
Sbjct: 121 TDNPEVADVLM--GSKLPRTYNLKIDKPLTPEMEKAMKEGLILEDAREGGHKESEITRME 178

Query: 175 ----MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               ++V    Q G N  + V + EGKNRE+++ F  F  KV  L R+ +G  +L  L  
Sbjct: 179 FAPFLEVQYRGQSGKNTKLRVTIAEGKNRELRRFFGHFGAKVLDLKRVGFGWVELNNLPE 238

Query: 231 GSTREVSKK 239
             TR  +++
Sbjct: 239 NKTRYFTRQ 247


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/234 (32%), Positives = 118/234 (50%), Gaps = 16/234 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P R++K IA + I SRRE +  I    V VNG ++ E     V +TD +      L   E
Sbjct: 160 PMRLNKFIANSNICSRREADEFIQAGVVSVNGQVVTELGTKIVPATDKVHFHD-QLVSME 218

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           +    L +KP  ++TT  DP  R TV D + +  S RV  VGRLD NT G+LL+TNDG L
Sbjct: 219 KKIYILMNKPKNIITTLDDPKERRTVLDLIKNACSERVYPVGRLDRNTTGVLLITNDGDL 278

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------VTLDTQKG 184
              L  P  +  ++Y VR   + +   +  ++ GIV++    GD++      V  D +K 
Sbjct: 279 TSKLIHPKYEKKKIYHVRLDREFESQDMEAMRSGIVLED---GDIKADDISYVKEDNKK- 334

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               V + +  GKNR ++++FE   +K+  L R+ +       L  G  R +S+
Sbjct: 335 ---EVGIEIHSGKNRIVRRMFEHLGYKIVALDRVYFAGLTKKNLPRGKWRYLSE 385


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 119/226 (52%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   GI SR+EV+++I+   + VNG+    A  N+  ++D IE +   L + ++ 
Sbjct: 2   RLDKFLVECGIGSRKEVKKLISNNEITVNGMSNISAKDNIDENSDIIEYNEEKL-EYKKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 61  RYYIMNKKSGYITATEDF-KENTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + +
Sbjct: 120 HKLLSPKNHVDKVYYVEIKNNISDEDIFKLEQGVDIGNYISQPAKV----EKISDNKIYL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++EGK  +IKK+ E  N KV  L R+S+G  +L  L  G  REV+
Sbjct: 176 TIKEGKFHQIKKMLEAINNKVCYLKRVSFGRLKLNDLALGEVREVN 221


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 119/232 (51%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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+ D L  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KLYIMLNKPEGYITSVKDEKGRKTILD-LVKVNERIYPIGRLDYDSSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGS-----N 186
            +  P  +  + Y     G    +++   + GI I G    + ++ L D +K       N
Sbjct: 122 KIIHPRVEVEKKYIALCKGVFSDEEIKKFENGIDIGGYITANAKIKLIDKEKDKKTNTVN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + V + + EGKNR+I+K+      +V  L R++ G  +LG L  G  R +++
Sbjct: 182 SLVEIIIHEGKNRQIRKMCSALGHEVITLKRVAVGDIKLGYLKRGEWRNLTE 233


>gi|238809688|dbj|BAH69478.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 269

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 129/251 (51%), Gaps = 19/251 (7%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLE---RAAVNV 54
           M + N + E F  +   RV K+IA+ G  SRR+ E  I ++ VKVNG +++   +A+ N 
Sbjct: 12  MNEINFLVERFAMKELIRVQKLIAQTGYCSRRKAEEYIEKKLVKVNGKIVQLGDKASEN- 70

Query: 55  MSTDHIEVDG--VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              D I+++   + L+K      +L +KP   ++T  DP GR TV D L +   R+  VG
Sbjct: 71  ---DEIKINNQLISLQKPNFV-YFLLNKPKKTISTVKDPKGRKTVVD-LINYSERIAPVG 125

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD +T G LLLTND  +   L  P  + LR YRVR    +   +  L+  G+++ G   
Sbjct: 126 RLDYDTTGALLLTNDWEMINKLTHPKYEILRTYRVRIDSPLSLKEFKLINAGLIVNGKFS 185

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             +   +DT+        V L  G    IK++F+  N +V  L R+S+    +  +  GS
Sbjct: 186 KQIVDQVDTKS-----YLVTLHVGSYHHIKELFKALNHEVINLKRVSFANLTVEKMPEGS 240

Query: 233 TREVSKKILRE 243
            R ++ K +++
Sbjct: 241 YRTLTLKEIKD 251


>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 =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 122/237 (51%), Gaps = 16/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+++ +A  GIASRR  ++++ + RV +NG ++    V V  S D + +DG    + E  
Sbjct: 14  RINRFLAMCGIASRRAADQLVQEGRVCINGKIVTTPGVKVNPSRDEVIIDGKRFAQPENR 73

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L +KP  ++TT SD   R  V D +  +  R+  VGRLD  T G++LLTNDG LA 
Sbjct: 74  KVYILLNKPRNVITTSSDERQREMVLDFI-DVPERIFPVGRLDRKTTGVILLTNDGELAH 132

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGSN 186
            L  PS+   + Y      +     L  L  G+ ++        C   +   LD      
Sbjct: 133 KLMHPSSGVKKEYIAELSERFPAAMLGKLTNGMRLKDTGEKVSPCRAKL---LD----DG 185

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             V + + EGKN +++++F+   ++V RL R++Y   Q G L  G  R +S+  +RE
Sbjct: 186 MRVLLSIHEGKNHQVRRMFDTLGFEVKRLDRVAYAGLQAGELRRGEWRYLSRNEVRE 242


>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 =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 113/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +   G+ SR+EV+ ++  ++++VNG+ +      +         G      +  R
Sbjct: 2   RIDKFLVECGVGSRKEVKELLKSRKIRVNGLFITSPKETIEEEKDEVYYGEKKLSYQEFR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ HK  G VT   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L  
Sbjct: 62  YYILHKKAGYVTALEDSR-EATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLNH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTV 191
            L  P +   + Y       + ++ L  L++G++I     G+ + +    +K  +  + +
Sbjct: 121 RLLSPKSHVDKTYHASLECDITEEALEKLREGVMI-----GEYKTLPAKAEKLEDRKIAL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +REGK  ++KK+ E    KV  L RIS+G   LG L  G+ +EVS
Sbjct: 176 TIREGKFHQVKKMLEAVGNKVIYLKRISFGKLVLGDLELGAVKEVS 221


>gi|322378546|ref|ZP_08052993.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|321149023|gb|EFX43476.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 257

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           R+++ IA     SRR+ +++I + +VK+N   L   A      D I V+G  L   E+  
Sbjct: 7   RLNQFIAHNLPCSRRQADKLIKEGKVKINR-QLASFATPFSPYDKIFVEGRMLNSYEKRS 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + +  D  GR T+F++L S F     +GRLD  + GLLLL++   +  
Sbjct: 66  YTVLVYHKPKGELVSRIDHRGRKTIFESLESKFRHFTPIGRLDFASMGLLLLSDSKQVVN 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-------CYGDMQVT-LDTQKG 184
            L   S +  RVY V+  G + Q  L  ++ G+ +QG+        Y  M +  +  Q  
Sbjct: 126 ALMHSSLE--RVYLVKIQGNITQTMLEAMQTGLELQGLEGAHPKSKYTRMHIAPMACQIL 183

Query: 185 SN----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            N    + + + L+EG NREI++ F  F  +V  L R+S+G   L  L  G TR ++ K
Sbjct: 184 KNHRNYSKIKITLQEGHNREIRRFFAHFKKEVLDLRRVSFGFVSLNALPVGKTRYLNPK 242


>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 =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 129/251 (51%), Gaps = 19/251 (7%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLE---RAAVNV 54
           M + N + E F  +   RV K+IA+ G  SRR+ E  I ++ VKVNG +++   +A+ N 
Sbjct: 1   MNEINFLVERFAMKELIRVQKLIAQTGYCSRRKAEEYIEKKLVKVNGKIVQLGDKASEN- 59

Query: 55  MSTDHIEVDG--VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
              D I+++   + L+K      +L +KP   ++T  DP GR TV D L +   R+  VG
Sbjct: 60  ---DEIKINNQLISLQKPNFV-YFLLNKPKKTISTVKDPKGRKTVVD-LINYSERIAPVG 114

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD +T G LLLTND  +   L  P  + LR YRVR    +   +  L+  G+++ G   
Sbjct: 115 RLDYDTTGALLLTNDWEMINKLTHPKYEILRTYRVRIDSPLSLKEFKLINAGLIVNGKFS 174

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             +   +DT+        V L  G    IK++F+  N +V  L R+S+    +  +  GS
Sbjct: 175 KQIVDQVDTKS-----YLVTLHVGSYHHIKELFKALNHEVINLKRVSFANLTVEKMPEGS 229

Query: 233 TREVSKKILRE 243
            R ++ K +++
Sbjct: 230 YRTLTLKEIKD 240


>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 =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 117/233 (50%), Gaps = 12/233 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+++ +A +G+ SRR+ ++ I    VK NGI +      V  TD+I      +R   +
Sbjct: 54  PIRLNRYLANSGLCSRRKADKYIQTGLVKKNGIPVTEFGTRVNRTDNITFCNSLVRSEHK 113

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP   VTT +DP GR TV D + +    ++  VGRLD NT G+LLLTNDG L+
Sbjct: 114 VYL-LLNKPKNCVTTTNDPQGRLTVMDLIKTACKEQIFPVGRLDRNTTGVLLLTNDGKLS 172

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWV 189
             L  P     ++Y V  +  +D   +  L KGI ++  GI   D+    D  K     +
Sbjct: 173 AKLTHPRHMKKKIYHVWLNRGIDAADIKKLSKGIQLEDGGIWADDISYVNDKDKTQ---I 229

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG-----STREVS 237
            + +  G+N  I+++FE   + V +L R+ +       L  G     + REVS
Sbjct: 230 NIEIHSGRNHIIRRMFESLGYHVVKLDRVYFAGLTKKKLKKGQWCFLNDREVS 282


>gi|166710887|ref|ZP_02242094.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 245

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/232 (32%), Positives = 120/232 (51%), Gaps = 9/232 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLW 76
           ++++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R  L 
Sbjct: 1   MLSKLGVCSRTEAARWIADGRVSVSTRVVRDPEFPIRADQQSSITVDGQPLTGPARCYLM 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  + 
Sbjct: 61  L-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAATVT 119

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVT 190
            P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NAW+ 
Sbjct: 120 DPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGVLLRAKQVSVLREGERNAWLE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R
Sbjct: 180 IVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVR 231


>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 =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 121/231 (52%), Gaps = 13/231 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           PQR++KV+A AG+ASRR  E +I Q +V VNG +       V +S D I V+G  + K  
Sbjct: 155 PQRLAKVLAAAGVASRRTSEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRISKKL 214

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNL--------PSIF-SRVISVGRLDINTEGL 121
             +L+   +KP G + +  +     ++ D+         P +   R+ +VGRLD+ T GL
Sbjct: 215 PPKLYFAVNKPKGYICSSGEEKSVISLLDDYLKGWNKLQPGVPKPRLFTVGRLDVATTGL 274

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLD 180
           +++TNDG  A+ +  PS+   + Y V   G V +  L  +  G VI G+    D+   LD
Sbjct: 275 IIVTNDGEFAQKVSHPSSNITKEYVVTIDGAVHKKHLVAISGGTVIDGVKVVPDLVEPLD 334

Query: 181 TQKGSNAW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           TQ  +    + + + EG+N E++++ +    KV  L R+  G F+L + L 
Sbjct: 335 TQADTKRMRLKIVVHEGRNHEVRELVQNAGLKVYALKRVRIGRFRLPSDLG 385


>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 =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 117/228 (51%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I  ++V VNG L+++A   V  TD ++V    +   E+  
Sbjct: 2   RIDKYLANMKVGSRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKVADETIA-YEQFH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +KP G++T   DP  + TV D +     +  +  VGRLD +T GLLLLTNDG L  
Sbjct: 61  YFMLNKPAGVITATEDPQ-QKTVLDLIEHKDRYQGLSPVGRLDKDTTGLLLLTNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    +V  + +    KG+ +  G      Q+ +D       ++T+
Sbjct: 120 NLLSPKKHVAKTYFVELDYEVSDELIVNFAKGVTLADGTKVSPSQLKIDKSNKKQGFITI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              EGK  +IK++F  F+  V RL RIS G   L   LL G  R+++K
Sbjct: 180 --HEGKFHQIKRMFGLFDLGVVRLKRISMGNLSLDENLLLGKYRKLTK 225


>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 =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 119/232 (51%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---VMSTDHIEVDGVPLRKAE 71
           R++K ++ AG+ SRRE + +I Q RV V+G    R AV    V     I VD   +R+ +
Sbjct: 7   RLNKYLSDAGVCSRREADSLILQGRVTVDG----RKAVTGEKVSVDQQIRVDNREIRQGQ 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L L +KP G++ T  +       F N P    RV  VGRLD++++GL+LLTN G L 
Sbjct: 63  PKVLLLLNKPRGIICTAKNQKDNIVDFVNYPI---RVYPVGRLDVDSQGLILLTNQGELV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y+V     V ++ L+ + KG+ I G      Q+    +K     +T 
Sbjct: 120 NKIMRAGNYHEKEYQVTVDHPVTKEFLSKMAKGVPILGTVTRPCQIKRTGEKSFQIILTQ 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           GL    NR+I+++ E+F ++V RL R      +LG L  G+ REV+ +  RE
Sbjct: 180 GL----NRQIRRMCEYFGYRVVRLNRTRIMNLKLGKLPVGAYREVTSEEWRE 227


>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 =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/237 (32%), Positives = 126/237 (53%), Gaps = 14/237 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R+ K+++  G  SR+E++  I +  V +N ++++     V      + D +  R  
Sbjct: 1   MSKMRIDKLLSNMGYGSRKEIKNFIKECLVAINDVIIDDPGFTVQP----DKDVITFRNE 56

Query: 71  ERT-RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPS-IFSR-VISVGRLDINTEGLLLL 124
           + + + ++Y   +KP G++    DP  R TV D LP  I SR V   GRLD +TEGLLL+
Sbjct: 57  KVSYKEYIYIMMNKPKGVICATYDPSER-TVVDLLPHHIKSRKVFPAGRLDKDTEGLLLI 115

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQK 183
           TNDG L+  L  P     + Y     G +D+D  +L  +GI++    Y  M  TL+    
Sbjct: 116 TNDGELSHKLLSPKKHVFKKYYAEVLGFIDEDDASLFSEGILLDD-GYKTMPATLEIISS 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           G+ + V + +REGK  +IK++FE  + KV  L R+S G  +L   L  G  RE++++
Sbjct: 175 GNISKVYISIREGKYHQIKRMFEAIDSKVIYLKRLSIGKLKLDENLKEGEWRELNEE 231


>gi|240047413|ref|YP_002960801.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239984985|emb|CAT04978.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 233

 Score =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAE 71
           QR+ K+IA+ G+ SRR+ E+MI   +V +NG   E+A +   ++  D IE+DG  + K  
Sbjct: 5   QRLQKLIAQVGLCSRRQAEQMIKDGKVYLNG---EKANLGDRASWEDKIEIDGEQIAKKV 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +   +L +KP G +TT  D   R TV   FDN   +F     VGRLD NT GLLL+TNDG
Sbjct: 62  KIVWYLLNKPAGYITTVRDQFNRPTVMDFFDNKTHLFP----VGRLDYNTTGLLLITNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNA 187
            LA  L  P  +  R+Y  +    +   +L+ L    + + G+           +K S+ 
Sbjct: 118 ELANKLLHPRNKIERIYLAKLDYSLADWELDFLNTTSLNLDGVISKQ-----KIEKVSSR 172

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + + +G N  +KK+F     +V  L RI +   +L  L  G  R++S
Sbjct: 173 KYKITIWQGSNHHVKKIFAIAKKQVIELKRIGFANLELANLPEGQFRKLS 222


>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 =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/222 (33%), Positives = 114/222 (51%), Gaps = 14/222 (6%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R+ K + +A   +R E ++ I +  V V+G ++++A + V S D I +DG  + 
Sbjct: 3   ETLKKMRLDKFLTQAAELTRSEAKQKIKKGSVTVDGEVVKKAEMKVSSEDAICLDG-EVV 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E+ R  + HKP G+V+   D   + TV D +      +  VGRLD +TEGLLLLTNDG
Sbjct: 62  TYEKYRYIMLHKPAGVVSATEDAQCQ-TVLDLITEGRKGLFPVGRLDKDTEGLLLLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQK 183
            LA  L  P     + Y     G+V + +  L      +QG+  GD + TL      T K
Sbjct: 121 ALAHNLLSPRKHVDKTYFAILDGEVGEKEQELF-----LQGLDIGDEKKTLPAKLEITDK 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +  ++TV  +EG+  ++K++ E    KV  L RIS GP  L
Sbjct: 176 ANEVFITV--QEGRFHQVKRMAEAVGRKVEYLKRISMGPLVL 215


>gi|282860273|ref|ZP_06269343.1| pseudouridylate synthase [Prevotella bivia JCVIHMP010]
 gi|282586947|gb|EFB92182.1| pseudouridylate synthase [Prevotella bivia JCVIHMP010]
          Length = 555

 Score =  104 bits (259), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 70/213 (32%), Positives = 109/213 (51%), Gaps = 11/213 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I   +V VNG ++      ++ TD ++     L   E+
Sbjct: 319 PLRLNKFLANAGVCSRREADDFILAGQVTVNGEVINELGTKILRTDEVKFQD-KLVSLEK 377

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LL TNDG LA
Sbjct: 378 KVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTGVLLFTNDGDLA 437

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----A 187
             L  P     +VY V     +  ++L  +  GI ++     D ++  D  + +N    A
Sbjct: 438 SKLTHPKFLKKKVYHVFLDKPITANELQKISDGIELE-----DGEIKADAIEYANPEDQA 492

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 493 QVGIEIHSGKNRIVRRIFESLGYRVVKLDRVMF 525


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 76/230 (33%), Positives = 120/230 (52%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG  SRR+ E++I   RV V+G ++    V V  + + I VDG+ L+     
Sbjct: 6   RLQKVLADAGYGSRRKAEQLIEDGRVSVDGQIIIELGVRVDPAKNVIHVDGLRLQLDTNK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+++  SD  GR T+ D + +   R+  VGRLD+++EGL+LLTNDG L   
Sbjct: 66  VTLAVNKPAGVISAMSDEKGRPTLADLVRNREERLFHVGRLDLDSEGLILLTNDGELGNR 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-----W 188
           L  P  +  + Y V   G    D    + + + + G+   D    +D  K   A      
Sbjct: 126 LAHPKYEVPKTYLVTVSG---GDVFPRIVRAL-LDGVDLEDGPARMDRVKIVQALEGMTM 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           V V L +G+NR ++++F+  +  V RL+R   GP  LG    G+ R +S+
Sbjct: 182 VEVVLHDGRNRVVRRMFDAVDRPVERLVRTKIGPIALGDQRPGTHRVLSR 231


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 72/221 (32%), Positives = 108/221 (48%), Gaps = 1/221 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A AG+ SRR  E  +   RV V+G +             I VDG+PL      R++L +
Sbjct: 1   MAAAGLCSRRRGEDWLQAGRVTVDGRVASLGDQADPDCQLIAVDGIPLISVREPRVFLLN 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLARVLELPS 138
           KP+G++ +  DP GRSTV D LP      +  VGRLD ++ G LLLT+ G L   L  P 
Sbjct: 61  KPVGVICSCRDPQGRSTVLDCLPHQERPGLHPVGRLDADSRGALLLTDQGELTLRLTHPR 120

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               + YRV   G  +   L   ++G+ + G       V     +G+++ + V LREG+N
Sbjct: 121 YSHAKTYRVLVKGIPNALVLRRWREGLQLDGRLTRPALVRCLRSRGTSSLLEVELREGRN 180

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           R+I++V E     V  L R++     L  L  G  R +  +
Sbjct: 181 RQIRRVAELLGHPVIDLQRVAIDGIHLDDLAEGCWRRLDAR 221


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 75/226 (33%), Positives = 117/226 (51%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ + +   GI SR+EV+++I+ + +KVNG     A  N+   +D IE +G  L   E  
Sbjct: 2   RLDRFLVECGIGSRKEVKKIISAKEIKVNGSYDISAKDNIDEYSDVIEYNGERLEYKE-F 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLLLTNDG L 
Sbjct: 61  RYYIMNKKAGYITATEDI-REATVMDLLPEWVIRKDLAPVGRLDKDTEGLLLLTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + Q+ +  L++G+ I       + +    +K S+  + +
Sbjct: 120 HKLLSPKNHVDKTYYVEIENNISQEDILKLEEGVDIGNY----ITLPAKVEKISDTKIYL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++EGK  ++KK+ E  N KVN L R ++    L  L  G  +EV+
Sbjct: 176 TIKEGKFHQVKKMLEAVNNKVNYLQRTTFAKLSLDGLALGEVKEVN 221


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 119/240 (49%), Gaps = 7/240 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG 64
           +  +N    R+ KV+A+AG+ASRR  E +IA  RV V+G ++      V   T  + VDG
Sbjct: 1   MTTQNSDGVRLQKVLAQAGVASRRAAEELIAAGRVSVDGEIVREMGRRVDPDTAVVHVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINT 118
             +   +       +KP G+++T SD  GR  V D       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


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 69/212 (32%), Positives = 109/212 (51%), Gaps = 7/212 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      V  TD ++    P+   ER
Sbjct: 17  PIRLNKFLANAGVCSRREADEFITAGVVSVNGTVVTELGTKVKRTDEVKFHEQPV-SIER 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + ++   R+  VGRLD NT G+LL TNDG LA
Sbjct: 76  KVYVLLNKPKDYVTTSDDPQNRKTVMDLVKNVCRERIYPVGRLDRNTTGVLLFTNDGELA 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSN-AWV 189
             L  P     ++Y V     V    +  + +GI ++    G+++   +D    ++   V
Sbjct: 136 SKLTHPKFLKKKIYHVTTDKNVTAADMRQIAEGITLED---GEIRADAIDYASPTDKKQV 192

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            + +  GKNR ++++FE   ++V +L R+ + 
Sbjct: 193 GIEIHSGKNRIVRRIFEALGYRVVKLDRVLFA 224


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 74/221 (33%), Positives = 114/221 (51%), Gaps = 8/221 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +AR G+ SRR+VE +I   RVK+NG+++      V   DH+EVDG  +   ++ 
Sbjct: 1   MRLNQYLARCGLGSRRKVEALIVTGRVKLNGLVVSDLGCRVEEGDHVEVDGCSVHPLDKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+V    D   R TV D LP      R   VGRLD  ++GLL+LTNDG   
Sbjct: 61  YI-VMNKPRGVVCAVEDRRYR-TVLDLLPPQIRALRPFPVGRLDKESQGLLILTNDGDFC 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P    ++ Y V     V  + L+ LK G+   G     + V+L   +     V V
Sbjct: 119 DAILHPRRGIIKTYEVTVDRDVPSESLDRLKGGVWSDGEILEPLMVSLMGPR----TVRV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            ++EGK RE++++     +KV  L+R   G  +L  L AG 
Sbjct: 175 DIQEGKKREVRRMMAALGFKVLSLLRRRIGKMELRRLRAGG 215


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 121/233 (51%), Gaps = 19/233 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A++G+ SRRE + +I +  V + G  +  A   ++    + +D    R    
Sbjct: 12  PVRLNKWLAQSGVCSRREADTLIEEGCVAIAGETVRDAGRKILPGQTVTLD----RGETL 67

Query: 73  TRLWLYHKPIGLVTTHSDPDG--------RSTVF---DNLPSIFSRVISVGRLDINTEGL 121
               +Y+KPIG+V+   +P          R+ VF   D  P   S++  +GRLD ++ GL
Sbjct: 68  PMTVIYNKPIGIVSGQPEPGETPAVRMIRRANVFGPADVYPDQTSKLAPIGRLDKDSHGL 127

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+L+ DG LA+ +  P ++  + Y V+  GQ+ + KL  L+ G+ + G      ++   T
Sbjct: 128 LVLSEDGVLAKAVIGPDSELDKAYHVQVRGQIIEAKLAWLRHGLELDGRKLKPAEI---T 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           Q G  + +T  L+EG+ R+I+++ +    +V  L R   GP QLG L  G  R
Sbjct: 185 QTGPQS-LTFVLKEGRKRQIRRMCDMVELRVTDLYRDRIGPLQLGDLPEGQWR 236


>gi|262091731|gb|ACY25320.1| ribosomal large subunit pseudouridine synthase B [uncultured
           actinobacterium]
          Length = 240

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/231 (33%), Positives = 121/231 (52%), Gaps = 14/231 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +R+ KV+A+ G  SRR  E +IA  RV VNG   +L  R  V+V   D +E+DG P+   
Sbjct: 6   ERLQKVLAQRGWGSRRACEEIIADGRVTVNGEVAVLGRRVNVDV---DRVEIDGAPVGVR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +L +KP+ +++T  D   R TV D +P+   RV  VGRLD ++EGLLL+TNDG L
Sbjct: 63  PDLVYYLLNKPVDVISTAIDTHDRETVVDFVPA-DPRVYPVGRLDGDSEGLLLITNDGEL 121

Query: 131 ARVLELPSTQWLRVYRVRFH---GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
              +  P     + Y V+       V    ++ L+ GI ++       +V+   Q+G   
Sbjct: 122 TNRITHPKYGLEKEYLVQVDVSSADVSDVAIHRLRNGIELEDGVTAPAEVS-RLQEGVLR 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V   + EGKNR+I+++ +   + V RL+R   GP     L  G  R +++
Sbjct: 181 MV---IHEGKNRQIRRMCDAVGYPVIRLVRTRIGPIMDKKLAPGQWRNLTQ 228


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 118/228 (51%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   GI SR+EV+++I+   + VNG     A  N+  ++D IE +G  L   E  
Sbjct: 2   RLDKFLVECGIGSRKEVKKLISNDEITVNGFNDISAKDNIDENSDIIEYNGEKLEYKE-F 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 61  RYYIMNKKAGYITATEDF-KENTVMDLLPEWVIRKDLAPVGRLDKDTEGLLLFTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNAWV 189
             L  P     +VY +     + D+D L L       QG+  G+ +      +K S+  +
Sbjct: 120 HRLLSPKNHIDKVYYIEIENNILDKDILKLE------QGVDIGNYITQPAKVEKISDNKI 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + ++EGK  ++KK+ E  N KV  L R+S+G  +L  L  G  +EV+
Sbjct: 174 YLTIKEGKFHQVKKMLEAVNNKVCYLKRVSFGKLKLDDLALGEVKEVN 221


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 119/230 (51%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ +R EV+R I++ RV V+G  +++    + + +   V    + +  +  
Sbjct: 4   RLDKYLADMGVGTRTEVKRAISKGRVSVDGACVKKPETKIDTEETTVVFDGQIVEYTKKE 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGGL 130
            ++ HKP G+++   D   + TV D    I SR    +  VGRLD +TEGLLL+TNDG L
Sbjct: 64  YYMLHKPAGVISATEDAREK-TVID---LIVSRKRKDLFPVGRLDKDTEGLLLITNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y  +  G V Q+ +    +G+ I         V    + G  + + 
Sbjct: 120 AHRLLSPKKHVDKTYYAKVQGIVTQEDVRKFAEGVDIHEKKLTAPAVLEVVKSGEVSEIL 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + + EGK  ++K++FE    KV  L R+S GP QL  TL+ G  RE+++K
Sbjct: 180 LTICEGKFHQVKRMFEAVGKKVIYLKRLSMGPLQLDETLMPGEYRELTEK 229


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 68/211 (32%), Positives = 111/211 (52%), Gaps = 11/211 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I+  ++ VNG ++      ++ TD I+  G  +   ++
Sbjct: 292 PLRLNKYLANAGVCSRREADNYISSGQITVNGEVVTELGTKILRTDEIKFKGQTVSLEKK 351

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP   VTT  DP  R  V D +      R+  VGRLD NT G+LL TNDG LA
Sbjct: 352 VYLLL-NKPKDYVTTSDDPQQRKKVVDLVKDACPERIYPVGRLDRNTTGVLLFTNDGDLA 410

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----A 187
             L  P     +VY V     V  + L  + +GI+++     D ++  D  + ++    +
Sbjct: 411 SKLTHPKFLKKKVYHVFLDKPVAANDLQKIAEGIMLE-----DGEIKADAIEYASPDDLS 465

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            V + +  GKNR ++++FE   ++V +L R+
Sbjct: 466 QVGIEIHSGKNRIVRRIFESLGYRVVKLDRV 496


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/218 (36%), Positives = 114/218 (52%), Gaps = 13/218 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K++A  G  SR+EV+ +IA+ RV V+G    R        +  I+VDG  +  A  
Sbjct: 4   ERLDKLLASTGRWSRKEVKELIARGRVLVDGRPAGRPEDKCEPQSACIQVDGEIVDCAPC 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             + L HKP GL++   D   +STV D LP    R  +  VGRLD +TEGLLLLT+DG L
Sbjct: 64  VYIML-HKPAGLLSATQDKK-QSTVLDLLPEHLRRRGLFPVGRLDKDTEGLLLLTDDGPL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---QKGSNA 187
              L  P     +VY  R  GQ+D++ + +L +G+ +     GD  V L       G  +
Sbjct: 122 GHDLLSPRKHVDKVYYARVDGQIDKEDVQVLAQGMTL-----GDGLVCLPAGLEPLGDGS 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              V LREGK  ++K++       V  L R+S GP +L
Sbjct: 177 ECLVTLREGKYHQVKRMLAARGKPVLYLKRLSMGPLKL 214


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 117/228 (51%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I  ++V VNG L+++A   V  TD ++V    +   E+  
Sbjct: 2   RIDKYLANMKVGSRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKVADETI-AYEQFY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +KP G++T   DP  + TV D +     +  +  VGRLD +T GLLLLTNDG L  
Sbjct: 61  YFMLNKPAGVITATEDPQ-QKTVLDLIEHKDRYQGLSPVGRLDKDTTGLLLLTNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    +V  + +    KG+ +  G      Q+ +D       ++T+
Sbjct: 120 NLLSPKKHVAKTYFVELDYEVSDELIVNFAKGVTLADGTKVSPSQLKIDKSNKKQGFITI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              EGK  +IK++F  F+  V RL RIS G   L   LL G  R+++K
Sbjct: 180 --HEGKFHQIKRMFGLFDLGVVRLKRISMGNLSLDENLLLGKYRKLTK 225


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 115/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 83  PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 141

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 142 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 201

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI ++ G  + D +  T D +K     V
Sbjct: 202 SKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISYTDDFKKDQ---V 258

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 259 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 307


>gi|195952397|ref|YP_002120687.1| pseudouridine synthase [Hydrogenobaculum sp. Y04AAS1]
 gi|195932009|gb|ACG56709.1| pseudouridine synthase [Hydrogenobaculum sp. Y04AAS1]
          Length = 239

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 124/238 (52%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+++ ++ AG+ SRR+ +  I +  VKVN  +++     +    D +E  G  + KA++
Sbjct: 1   MRLNRFLSLAGVCSRRKADEYIEKGYVKVNNNIVKELGTTINPDEDIVEFRG-RIVKAQK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   +T+  + + + T+ + +  +  RV   GRLD N EGLL+LTNDG LA 
Sbjct: 60  PVYIILNKPCCYLTSLGEKEEKPTIRELIKDVGVRVYPAGRLDYNVEGLLILTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVT 190
            +  P  +  +VY     G++D + L  +K+G+ ++ G    D +++    + G+N  +T
Sbjct: 120 RIIHPRYKLPKVYIATIKGEIDDETLEKMKRGVRLEDGFVKPDSLKLLKRFKNGANIEIT 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQL 245
               EGKN  +K+ F  F   V  LIR + GP  LG L  G  R +     K+L E L
Sbjct: 180 --FHEGKNHLVKRFFLAFKKPVKHLIRTAIGPISLGNLPKGKWRHLKPAEIKLLFEAL 235


>gi|240173130|ref|ZP_04751788.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           kansasii ATCC 12478]
          Length = 250

 Score =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 113/229 (49%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G L+      V      I VDG  +   E  
Sbjct: 11  RLQKVLSQAGIASRRAAEKMIIDGRVEVDGKLVTELGTRVDPDVSVIRVDGARVVLDESL 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T +D  GR  + D +         +  VGRLD +TEGL+LLTNDG L
Sbjct: 71  VYLALNKPRGMHSTMADDRGRPCIGDLIERKVRGNKNLFHVGRLDADTEGLILLTNDGEL 130

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L+ GI +  G+   D    +D   G    V
Sbjct: 131 AHRLMHPSHEVPKTYLATVAGTVPRGLGKKLRTGIELDDGLARVDGFAVVDAIPGKT-LV 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR ++++     + V  L+R   GP  LG    GS R + +
Sbjct: 190 RVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGPVTLGKQRPGSVRALGR 238


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 114/230 (49%), Gaps = 16/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDH--IEVDGVPLRKAE 71
           R+ KV+A AGI SRR  E +IA  RV VNG   ++A + N +   H  I VDG  +    
Sbjct: 9   RLQKVMAAAGIGSRRACENLIAAGRVTVNG---KKAQLGNRVDPQHAVIHVDGERVITDT 65

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +  +KP G V+T  D   R  + +    I  RV  VGRLD  +EGLLLLTNDG L 
Sbjct: 66  KLVHFALNKPRGYVSTMDDELKRPDLNEFTAGISERVFHVGRLDTESEGLLLLTNDGELG 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSN 186
             L  PS +  + YR +  G         L  G+V++     D  VT+D  K        
Sbjct: 126 NRLTHPSYEIAKTYRCQVTGYAGPAIARRLAAGVVLE-----DGPVTVDDFKVIDEHADQ 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           A V + + EG+   ++++       VNRL+R + G  +L  L  G+ R++
Sbjct: 181 ALVEIVVHEGRKHVVRRLLAEVGLPVNRLVRTAIGDIRLANLKPGTLRKL 230


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 117/226 (51%), Gaps = 6/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++AR G+ SR+EV R++   +V+V G ++   A +V     +EVDG PL      
Sbjct: 4   ERLDKLLARLGLGSRKEVARLVRSGQVQVEGQVVRDPAFHVPPGARLEVDGEPLVLRCHH 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L HKP G VT+  +      + +  P+    +  VGRLD +TEGLLL T DG L   
Sbjct: 64  HILL-HKPAGYVTSRREGPSVYALLEGFPT--RDLSPVGRLDKDTEGLLLFTTDGELLHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y V       ++     ++G+V++G      +++ D        V + L
Sbjct: 121 LTHPRHKVEKRYLVHLERPATREDQEAFREGLVLEGTRLLPAELSWDQ---DPTRVELVL 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           REG+  ++K++F+    +V  L R+S GP  LG L  G  R +S++
Sbjct: 178 REGRFHQVKRMFQARGNRVLYLKRLSLGPLTLGDLPVGQARYLSQE 223


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 72/221 (32%), Positives = 116/221 (52%), Gaps = 6/221 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEV 62
           KN+  ++    R+++ IA +GI SRR+ + +IA   V VNG ++      +  + D +  
Sbjct: 218 KNVAVKDDGLIRLNRYIANSGICSRRKADELIAAGVVSVNGEVVSELGHKIDPAKDQVRY 277

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGL 121
           +G  L++ ++  + L +KP   +TT  DP  R TV   +      R+  VGRLD NT GL
Sbjct: 278 NGELLKREKKVYVLL-NKPKDYITTTDDPQERRTVMQLVEKASRERIYPVGRLDRNTTGL 336

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLD 180
           LL+TNDG LA  L  P     ++Y V     + Q  LN ++ G+ ++ GI   D    + 
Sbjct: 337 LLMTNDGELADKLSHPKNGITKIYHVELSRSLSQGDLNKIQFGLELEDGIIKPDSVSYV- 395

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
              GS   V + +  GKNR ++++FE   + V +L R+ YG
Sbjct: 396 -AGGSKREVGIQIHSGKNRIVRRIFEHLGYDVVKLDRVVYG 435


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 80/232 (34%), Positives = 120/232 (51%), Gaps = 20/232 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKAE 71
           R++K +A  G+ SRR+ E +I   RVKV+G +     + V ++ ++EVDG    PL+   
Sbjct: 17  RLNKYLAMCGLGSRRKTEALIVSGRVKVDGEIAAGPWIMVNTSYNVEVDGKIVAPLKN-- 74

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDG 128
              L+L  +KP   V    D    +TV D LP   I  R+  VGRLD N+ GLL+LTNDG
Sbjct: 75  ---LYLVMNKPRNCVCAVVDSR-YTTVIDLLPKDLIGHRLFPVGRLDKNSSGLLILTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSN 186
             A+ +  P     + YRV  +  +    L   +KG+      Y D ++    D +  S+
Sbjct: 131 DFAQDIIHPRNGITKTYRVMLNKPMTSGDLEKWRKGV------YLDDRLIKPKDVKILSD 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            W  + + EGK REI+++ E   +KV  L+RI  G  +L TL  G   + SK
Sbjct: 185 KWCVIEIYEGKKREIRRMAECLGYKVVELVRIKIGRLELKTLDEGCFLKFSK 236


>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 =  103 bits (257), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 86  IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 145

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
             +  P++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 146 TFNEKPVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 204

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 205 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELE-----DGEIHA 259

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 260 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRY 319

Query: 236 VSKK 239
           ++++
Sbjct: 320 LNER 323


>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 =  103 bits (257), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 115/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 84  PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 142

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 143 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 202

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI ++ G  + D +  T D +K     V
Sbjct: 203 SKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISYTDDFKKDQ---V 259

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 260 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 308


>gi|315185613|gb|EFU19381.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 214

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 76/212 (35%), Positives = 110/212 (51%), Gaps = 9/212 (4%)

Query: 40  VKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           ++VNG ++   A  V    D + +DG  +    +     +HKP G + T SDP GR  V+
Sbjct: 1   MRVNGRVITNPAHRVDPQEDRVTLDGRDVHLVGKFLYLAFHKPPGYLCTRSDPQGRPLVY 60

Query: 99  DNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
           D + P +  +V S+GRLD  + GLLLLTNDG  A ++  P  +  + Y V     + +  
Sbjct: 61  DLIDPVLPYKVFSIGRLDFLSSGLLLLTNDGEFADIVMHPKHRVEKEYLVETKRPIPRAL 120

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           L    KGI I+G  Y    V    +  S   V + L EGKNREI+KVF   +  + R+ R
Sbjct: 121 LESYLKGIRIEGERY----VLKAYKSKSPHKVHLILEEGKNREIRKVFYSSHLPIVRIHR 176

Query: 218 ISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           I  GP +LG L  G  R ++K   ++LRE  G
Sbjct: 177 IRIGPVRLGRLRPGHFRNLTKEEIRLLREGRG 208


>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 =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 109/218 (50%), Gaps = 8/218 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +    
Sbjct: 265 EENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVVLFQE 324

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LL
Sbjct: 325 KPV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLL 383

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG LA  L  P     +VY V     V  + L  +  GI ++ G    D     D Q
Sbjct: 384 LTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEYADPQ 443

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                 V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 444 --DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQF 479


>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 =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 116/228 (50%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I  ++V +N  L+++A   V   D ++VD   +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQTIT-YQQFH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +KP G++T   DP  + TV D + S   +S +  VGRLD +T GLLL+TNDG L  
Sbjct: 61  YFMLNKPTGVITATEDPQ-QKTVLDLIASKDRYSDLAPVGRLDKDTTGLLLITNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    ++  +  +   KG+ +  G   G  Q+ +D        +T+
Sbjct: 120 NLLSPKKHVAKTYFVELDQEIANEVDSAFAKGVALADGTQVGSAQLIIDKSNKKQGLITI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              EGK  +IK++F  F+  V +L RI  G   L   L  G  RE+++
Sbjct: 180 --HEGKFHQIKRMFGLFDLGVVKLKRIKMGNLSLDENLPQGKYRELTE 225


>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 =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 116/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 17  PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHEEPV-SIER 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 76  KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  ++ +  GI ++ G  + D +  T D +K     V
Sbjct: 136 SKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISYTDDFKKDQ---V 192

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +++
Sbjct: 193 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLTE 241


>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 =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 65/141 (46%), Positives = 86/141 (60%), Gaps = 6/141 (4%)

Query: 34  MIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKAER--TRLWLYHKPIGLVTTH 88
           MIA  RV V G +      ++V S   + +DG  + L  A++   R+ +Y+KP G + T 
Sbjct: 1   MIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTR 60

Query: 89  SDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
           SDP+GR+TVFD LP +  SR I+VGRLDINT GLLL T DG LA  L  PS +  R Y V
Sbjct: 61  SDPEGRATVFDRLPRLTGSRWIAVGRLDINTSGLLLFTTDGELANRLMHPSREVEREYSV 120

Query: 148 RFHGQVDQDKLNLLKKGIVIQ 168
           R  GQVD   L  L+KG+ ++
Sbjct: 121 RVFGQVDDAMLARLRKGVQLE 141


>gi|332883058|gb|EGK03342.1| hypothetical protein HMPREF9456_01979 [Dysgonomonas mossii DSM
           22836]
          Length = 482

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 68/212 (32%), Positives = 110/212 (51%), Gaps = 7/212 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           TP R++K +A AG+ SRRE +  I    VKVNG ++++    V   D +     P+R   
Sbjct: 245 TPLRLNKYLANAGVCSRREADAFITSGVVKVNGEVVDQLGAKVTRGDLVTFHDQPVRLES 304

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LLLTNDG L
Sbjct: 305 KVYVLL-NKPKNCVTTSDDPQNRLTVMDLVKNACPERIYPVGRLDRNTTGVLLLTNDGDL 363

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  ++Y+V     V  + +  +  G+ +     G++       +  +    
Sbjct: 364 ASKLMHPKFKKKKIYQVTLDRDVAIEDMQAIADGVELDD---GEIHADSIAYQAEDVLNV 420

Query: 191 VGLR--EGKNREIKKVFEFFNWKVNRLIRISY 220
           VG+    G+NR ++++FE   ++V +L R+ +
Sbjct: 421 VGIEIHSGRNRIVRRIFEKLGYQVVKLDRVYF 452


>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 =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 116/236 (49%), Gaps = 11/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +ARAG+ASRR+ E +I    V VNG+  E     V + D + V G  +      
Sbjct: 3   ERLQKFLARAGVASRRKAEALILSGAVTVNGVRAE-LGQRVAAGDEVRVRGERVAPPAAH 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTNDGGL 130
             +  +KP G+++  +D  GR TV   +P   +RV     VGRLD ++EGLLLLT DG L
Sbjct: 62  VTYALYKPKGVISAVTDDRGRVTVLQLVPP-SARVPGLHPVGRLDADSEGLLLLTTDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + YRV        + L  L++G+ ++     D        + +    T
Sbjct: 121 TLTLTHPRYGHEKTYRVWCEPVPGPEALRRLERGVALE-----DGPARARRARAAPGGCT 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L EG+NR+++++      +V RL+R   G   LG +  G  R +S   L  QLG
Sbjct: 176 LVLSEGRNRQVRRMLAALGCEVTRLLRTRIGGLSLGAMRPGELRRLSDAEL-AQLG 230


>gi|323697859|ref|ZP_08109771.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457791|gb|EGB13656.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 251

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 86/231 (37%), Positives = 121/231 (52%), Gaps = 6/231 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG-VPLRKAER 72
           R++K IA+ G+ASRR  + M+   RV VNG   +   + V  + D + VDG V  +KA  
Sbjct: 10  RLNKFIAQCGVASRRGADEMVFAGRVTVNGATADSPGLQVDPARDEVAVDGKVIGQKASA 69

Query: 73  TRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
             L  L HKP+  VTT SDP GR TV D LP      R   VGRLD  +EGLLLLT DG 
Sbjct: 70  GDLTLLLHKPVETVTTASDPQGRKTVLDLLPPEIRKKRPFPVGRLDFFSEGLLLLTTDGD 129

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
           L   L  P     +VY V   G V Q  +  +++G+ + +G      +V L         
Sbjct: 130 LCYRLTHPKYHLPKVYVVTIRGSVPQKAVQTMRQGMTLREGDRLAPAKVRLLKPIAGTQQ 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + L +G NR+I+++ E     + RL R+  GP  LG L  G+ RE++ +
Sbjct: 190 LEITLIQGVNRQIRRMCEELGLTILRLRRVRQGPVALGDLKPGAWRELTSE 240


>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 =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 120/233 (51%), Gaps = 16/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A  GIASRR  ++++ + RV VNG + ++  + +    D + VDG  + + E  
Sbjct: 11  RINKYLAMCGIASRRAADQLVLEGRVMVNGHVADQPGLQIDPKHDEVIVDGRHMAQPEHK 70

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++TT  D   R  + D +  +  RV  VGRLD  + GLL+LTNDG LA 
Sbjct: 71  KVYILFNKPRNVITTSHDERDRQQILDFV-DVPERVFPVGRLDRKSTGLLILTNDGTLAH 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGSN 186
            L  PS+   + Y      +     L+ L  G+ ++        C   +   LD      
Sbjct: 130 RLMHPSSLVQKEYLAELDAKFPGSMLSKLTSGMRLKDTGEKVSPCRAKI---LD----DG 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             V V + EGKN +++++F    ++V RL R++Y     G L  G  R +S+K
Sbjct: 183 MSVLVSIHEGKNHQVRRMFSTLGFEVKRLDRVAYAGLTPGELRRGEWRYLSRK 235


>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 =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 80/248 (32%), Positives = 128/248 (51%), Gaps = 26/248 (10%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVD 63
           + +   P R++K +A+AGI SRRE +R+IA+ +V V+G     AAV    V+ +  I V+
Sbjct: 22  ITDTAEPVRINKYLAQAGICSRREADRLIAEGKVLVDGA----AAVAGQKVLPSQDIRVE 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G    +++   L + +KP G+V T +D     T  + L    SRV   GRLD ++EGL+L
Sbjct: 78  GEQAVRSQERILLVVNKPRGVVCT-TDKTWGDTTLEELVDYPSRVFYAGRLDKDSEGLIL 136

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-- 181
           +TNDG L   +   + +  + Y V+    VD   L  + KG+ ++          LDT  
Sbjct: 137 MTNDGELQDKIMRAANRHEKEYLVKVDRTVDDTFLKKMAKGVYLR---------ELDTVT 187

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 + G  A+  V L +G NR+I+++     ++V  L R+     +LG L AG  RE
Sbjct: 188 RPCRVEKTGRRAFRIV-LTQGLNRQIRRMCAALGYQVQELRRVRIMNIRLGGLPAGQYRE 246

Query: 236 VSKKILRE 243
            + + LRE
Sbjct: 247 ATDEELRE 254


>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 =  103 bits (256), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 118/228 (51%), Gaps = 17/228 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I   +V VNG ++    + +  +D I ++   ++  +   
Sbjct: 2   RLNKFISHNTGYSRREADELIKNGKVSVNGRIIS-DFIEINESDKIRINKHLIKLKKDFT 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+KP G + +  D  GR T++D+LP  FS+ +S+GRLD  +EGLLLLT+   +A  L
Sbjct: 61  MIIYNKPKGELVSKKDDRGRKTIYDSLPKGFSKFVSIGRLDYASEGLLLLTDAPAIATAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------VTLDTQ 182
              + +  R Y ++  G++  +    +K G   +    G               V  D  
Sbjct: 121 MQSNIE--REYYLKVKGEITDEIKTAMKDGFFAKDATKGAHPKTEIKSMNFAPFVAFDIF 178

Query: 183 KGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
             S  +  + V ++EG+NRE+++ F +F+ +V  L R+S+G   LG L
Sbjct: 179 GSSGGYTKLRVLIKEGQNRELRRFFGYFDLEVMDLKRVSFGIIDLGML 226


>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 =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 81/241 (33%), Positives = 126/241 (52%), Gaps = 14/241 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+R+I  ++V V+GIL +R  +NV  S   I V G  L      
Sbjct: 2   RLDKLLGQAGYGSRNQVKRLIRSRQVYVDGILADRDNLNVDASLQTITVSGKELEHTPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPAGVVSARKDKE-HQTVIDLITPEDQRDGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--IC-YGDMQVTLDTQKGSNAW 188
             +  P     + Y V  +  +  D     + G+V +   +C    +++    +  S+A 
Sbjct: 120 FAMLHPRYHVAKTYYVEVNDVLGPDAPAFFESGVVFEDGTVCKSAQLEILSSARDKSSAH 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQ 244
           +T+   EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  
Sbjct: 180 ITIS--EGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRTLTETEKTILRTY 237

Query: 245 L 245
           L
Sbjct: 238 L 238


>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 =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 69/208 (33%), Positives = 113/208 (54%), Gaps = 5/208 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE + +I Q  V+VNG ++      V  TD +  DG  +   E+  
Sbjct: 162 RLNKYIANSGICSRREADELITQGLVEVNGKVVTEMGYQVQKTDRVVFDGQSI-TPEKPV 220

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G ++T  D   R TV D + +    R+  VGRLD +T G++LLTNDG + + 
Sbjct: 221 YVLLNKPKGYISTTKDDKARKTVMDLVANASPYRLFPVGRLDRSTTGVILLTNDGHMTKK 280

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS    ++Y V    ++  + L L+ +GI + +G+   D Q++    K  N  V + 
Sbjct: 281 LTHPSFDAKKIYHVTLDKKLTGEDLRLIAEGIRLDEGVAVVD-QISYIEGKPKNE-VGIE 338

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G NR I+++F+   ++V  L R+ +
Sbjct: 339 IHIGWNRVIRRIFQRLGYEVEALDRVMF 366


>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 =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 72/224 (32%), Positives = 113/224 (50%), Gaps = 9/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +GI SRRE +++I +  VKVNGI++      V   D ++ +   L   E++ 
Sbjct: 330 RLNKYISNSGICSRREADQLIIEGTVKVNGIVVTELGYKVKPGDSVKYNNKVL-NPEKSV 388

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  D + R TV   +  +   R+  VGRLD NT GLLL TNDG LA+ 
Sbjct: 389 YVLLNKPKDFITTMEDENDRKTVMQLVANATKERIYPVGRLDRNTTGLLLFTNDGELAQK 448

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---KGSNAWVT 190
           L  PS +  ++Y V     +  +  +     IV   I   D  V +D       S   + 
Sbjct: 449 LTHPSNKVKKIYEVELDKPITAEDFDK----IVDGKIHLFDGPVKVDEAAIISPSKKIIG 504

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + + EG+NR ++++FE   + V +L R+ Y       +  GS R
Sbjct: 505 IEIHEGRNRIVRRIFESLGYDVLKLDRVMYAGLTKKNIPRGSWR 548


>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 =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 119/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++     SRRE + +I Q  VK+N  + + +   V   D I +    + K  +  
Sbjct: 2   RINKFLSHNTSYSRREADELIKQGLVKINQKIAQLSD-EVKDEDKIFLKNKRIYKKTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T+++NLP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGELVSRKDDRGRKTIYENLPKNFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------LDTQ-- 182
                +  R Y ++  GQ+ +  +  ++ G+ IQ    G    T          LD +  
Sbjct: 121 MHSDLE--REYYLKIKGQISKKVIEAMQNGLEIQNSTKGAHAKTKINSMKFAPFLDFEIF 178

Query: 183 --KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              G    + V + EG+NRE+++ F +F+ +V  L R+++G  +LG L  G  R
Sbjct: 179 GWSGGYTKLRVVINEGQNRELRRFFGYFDLEVMDLKRVAFGIVELGMLKVGKYR 232


>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 =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 78/228 (34%), Positives = 117/228 (51%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ + +   GI SR+EV+++I+ + VKVNG     A  N+   +D IE +G  L   E  
Sbjct: 2   RLDRFLVECGIGSRKEVKKIISTKEVKVNGSYDISAKDNIDEYSDIIEYNGKKLEYKE-F 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 61  RYYIMNKKAGYITATEDT-REATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             L  P     + Y V     + Q+ +  L++G+ I         VTL    +K S+  +
Sbjct: 120 HRLLSPKNHVDKTYYVEIENNISQEDILKLEEGVDIGS------YVTLPAKVKKISDTKI 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + ++EGK  ++KK+ E  N KV  L R S+   +L  L  G  +EV+
Sbjct: 174 FLTIKEGKFHQVKKMLEAVNNKVIYLQRTSFAKLKLADLALGEVKEVN 221


>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 =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 108/214 (50%), Gaps = 11/214 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      V  +D ++    P+   ER
Sbjct: 17  PIRLNKFLANAGVCSRREADEFITAGVVSVNGTVVTELGTKVKRSDEVKFHEQPV-SIER 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + ++   R+  VGRLD NT G+LL TNDG LA
Sbjct: 76  KVYVLLNKPKDYVTTSDDPQNRKTVMDLVKNVCRERIYPVGRLDRNTTGVLLFTNDGELA 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----A 187
             L  P     ++Y V     V    +  + +GI ++     D ++  D  + ++     
Sbjct: 136 SKLTHPKFLKKKIYHVTTDKNVTAADMRQIAEGITLE-----DGEIKADAIEYASPTDKK 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            + + +  GKNR ++++FE   ++V +L R+ + 
Sbjct: 191 QIGIEIHSGKNRIVRRIFEALGYRVVKLDRVLFA 224


>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 =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 124/242 (51%), Gaps = 7/242 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K ++ +   P R++K +A AG+ SRRE +  I    V VNG+++      V  +D +
Sbjct: 183 MEYKEVLADPNEPIRLNKFLANAGLCSRREADEFITAGVVSVNGVVVTELGTKVKRSDEV 242

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTE 119
           +    P+ K ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT 
Sbjct: 243 KFHDQPV-KIERKVYVLLNKPKDCVTTSDDPQERKTVLDLVKDACTERIYPVGRLDRNTT 301

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQV 177
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  GI +  G  + D +  
Sbjct: 302 GVLLLTNDGDLASKLTHPKYLKKKIYHVFLDKNVTKADLDQIASGITLDDGEIHADAISY 361

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             DT K   + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++
Sbjct: 362 ASDTDK---SQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLT 418

Query: 238 KK 239
           ++
Sbjct: 419 ER 420


>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 =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 118/232 (50%), Gaps = 16/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R++K +A  G+ASRR  ++++ + +V VNG + +     V    D + VDG  +   E  
Sbjct: 11  RINKYLAMCGVASRRAADQLVLEGKVSVNGHIADEPGFKVDPRNDEVIVDGRLMATPEAR 70

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++TT+ D   R  + D +  +  RV  VGRLD  + GLLLLTNDG LA 
Sbjct: 71  KVYILFNKPRNVITTNHDERDRQQILDFI-DVPERVFPVGRLDRKSTGLLLLTNDGTLAH 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGSN 186
            L  PS+Q  + Y      +     L  L  G+ ++        C   +   LD      
Sbjct: 130 RLMHPSSQVQKEYLAALDAKFPPAMLQKLTGGMRLKDTGEKVSPCRAKI---LD----DG 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             V V + EGKN +++++F    ++V RL R++Y    LG L  G  R +S+
Sbjct: 183 MSVLVSIHEGKNHQVRRMFSTLGFEVKRLDRVAYAGLTLGELRRGEWRFLSR 234


>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 =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 122/229 (53%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---MSTDHIEVDGVPLRKAE 71
           R+ K + +A + SR++V+++   Q++K+NG   +  +  V   + T  +    V L   E
Sbjct: 2   RLDKCLEKAKVGSRKQVKKLFKAQQIKINGHAAQSLSQIVDPELQTIQVSGKKVAL---E 58

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
            +  +L HKP G+V+  +D +   TV D +    SR  +  VGRLD +TEGL+L+TN+G 
Sbjct: 59  GSAYYLLHKPAGVVSAVTDQE-HQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGP 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAW 188
           L   +  PS    +VY V  +G + +D       G+  + G       +T+      ++ 
Sbjct: 118 LGYRMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSR 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            T+ L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++
Sbjct: 178 ATIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGAYRQLT 226


>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 =  102 bits (255), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 122/227 (53%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +   E +
Sbjct: 2   RLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKV-ALEGS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L HKP G+V+  +D +   TV D +    SR  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 61  AYYLLHKPAGVVSAVTDQE-HQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             +  PS    +VY V  +G + +D       G+  + G       +T+      ++  T
Sbjct: 120 YRMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSRAT 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++
Sbjct: 180 IKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGTYRQLT 226


>gi|303242956|ref|ZP_07329414.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302589505|gb|EFL59295.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 250

 Score =  102 bits (255), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 127/236 (53%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QRV ++++  G  +RRE+++++    VKV+G +++ + ++V   T  IE+ G  L     
Sbjct: 5   QRVDRILSNFGFGTRREIKQLVKNGEVKVDGEVIKDSGMHVDPKTSKIEISGQVLN---- 60

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
            R ++Y   +KP G+++   D +   TV D LP  +       VGRLDI+TEGLLL+TND
Sbjct: 61  YRQFIYVMMNKPAGVISATFD-NRHETVVDILPEEYKCFDPFPVGRLDIDTEGLLLMTND 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  P     + Y     G+V    + + ++GI++    Y  +   L   ++G +
Sbjct: 120 GQLAHELLSPRKHVPKKYFAYIEGEVSAGDVKMFEEGILLDD-GYKTLPAELHILEQGES 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           + V V + EGK  ++K++FE    KV  L RI+ G   L   LA G  RE+++  L
Sbjct: 179 SSVEVIIFEGKFHQVKRMFEAVGKKVKYLKRITMGNLVLDEALATGECRELTENEL 234


>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 =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 116/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 246 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 304

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 305 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 364

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  ++ +  GI ++ G  + D +  T D +K     V
Sbjct: 365 SKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISYTDDFKK---DQV 421

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 422 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 470


>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 =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 120/229 (52%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +   GI SR+EV+++I+   + VNG+  +L +  ++  ++D IE +G  L   E 
Sbjct: 2   RLDKFLVECGIGSRKEVKKLISNDEITVNGMSDILPKDNID-ENSDIIEYNGERLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDF-KENTVMDLLPEWVIRKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNAW 188
              L  P     +VY V     + D+D L L       QG+  G+ +      +K S+  
Sbjct: 119 NHRLLSPKNHIDKVYYVEIENNILDEDILKLE------QGVNIGNYITQPAKVEKISDNK 172

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + ++EGK  ++KK+ E  N KV  L R+S+G   L  L  G  +EV+
Sbjct: 173 IYLTIKEGKFHQVKKMLEAVNNKVCYLKRVSFGKLTLNDLTLGEVKEVN 221


>gi|312277957|gb|ADQ62614.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 239

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 124/240 (51%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ ++G  SR +V+++I  ++V V+G+L +R  +NV  S   I V G  L  A   
Sbjct: 2   RLDKLLGQSGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPSGVVSARKDKE-HQTVIDLIRPEDQREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +  +  D     + G+V + G      Q+ + +     +   
Sbjct: 120 FAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEVLSSASDKSCAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQLG 246
           V + EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  LG
Sbjct: 180 VTISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>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 =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 71/216 (32%), Positives = 116/216 (53%), Gaps = 9/216 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG  SRR+ + +I + +VK+N  ++    ++V   D +EV+G  L   ++  
Sbjct: 2   RINKFIAHAGYTSRRKADELILKGKVKINDEVILEPGIDVCDDDRVEVEGKVLSIEKKFY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + LY KP+G +T++ DP     + + L  I  R  + GRLD ++EGLL++TNDG     L
Sbjct: 62  IKLY-KPVGFITSNFDPYNEKDL-NELVDIDKRFFAAGRLDKDSEGLLIITNDGEFTNNL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVG 192
             P  +  + Y V+    VD+ KL   ++    QG+  G+ + T D   +   N    V 
Sbjct: 120 IHPKYKLDKEYIVK----VDK-KLKDYQEKQFAQGLDIGNGEKTSDAKIEYLENNTYRVI 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           + +G NR+I+++F+ F  KV  L RI  G   L  L
Sbjct: 175 IHQGYNRQIRRMFKVFGIKVVSLKRIRIGKISLSNL 210


>gi|256752686|ref|ZP_05493537.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256748448|gb|EEU61501.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 240

 Score =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 78/231 (33%), Positives = 123/231 (53%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + +   TD I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIINTETDEILFDGKKIYYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   DP  + TV D LP          VGRLD +TEGLLL+TNDG L
Sbjct: 64  IYIMM-NKPKGVISATYDPIEK-TVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           A  L  P    ++ Y  +  G V++  +    +GIV++   Y  +   L+    S+ + V
Sbjct: 122 AHKLLSPKKNVIKKYYAKILGFVNESDIKAFNEGIVLED-GYKTLPANLEILSSSDVSKV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            V +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++
Sbjct: 181 YVYIREGKYHQIKRMFESVGKKVIYLKRLAMGNLTLDENLKPGEWRELSEE 231


>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 =  102 bits (254), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 80/227 (35%), Positives = 117/227 (51%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   GI SR+EV+++I+   + VNG+    A  N+  ++D IE +G  L   E  
Sbjct: 2   RLDKFLVECGIGSRKEVKKLISNGEITVNGMSYILAKDNIDENSDTIEYNGERLEYKE-F 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D     TV D LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 61  RYYIMNKKAGYITATEDF-KEDTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY V     + D+D L  L++G+ I        +V    +K S+  + 
Sbjct: 120 HKLLSPKNHIDKVYYVEIEKNILDEDILK-LEQGVDIGNYITQPAKV----EKISDNKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + ++EGK  ++KK+ E  N KV  L R S+G   L  L  G  +EVS
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVCYLRRESFGKLTLNDLTLGEVKEVS 221


>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 =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/233 (33%), Positives = 124/233 (53%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + +   TD I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIINTETDEILFDGKKIYYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   DP  + TV D LP          VGRLD +TEGLLL+TNDG L
Sbjct: 64  IYIMM-NKPEGVISATYDPIEK-TVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           A  L  P    ++ Y  +  G V++  +    +GIV++   Y  +   L+    S+ + V
Sbjct: 122 AHKLLSPKKNVIKKYYAKILGFVNESDIKAFNEGIVLED-GYKTLPANLEILSSSDVSKV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 181 YVYIREGKYHQIKRMFESVGKKVIYLKRLAMGNLTLDENLKPGEWRELSEEEL 233


>gi|289810570|ref|ZP_06541199.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 147

 Score =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 65/145 (44%), Positives = 85/145 (58%), Gaps = 6/145 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG----VPLR 68
           +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG    V   
Sbjct: 3   EKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKES 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T +DP+GR TVFD LP +  +R I+VGRLD+NT GLLL T D
Sbjct: 63  AEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQ 152
           G LA  L  PS +  R Y VR  GQ
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQ 147


>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 =  102 bits (254), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 116/231 (50%), Gaps = 5/231 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++  + S  +  R++AQQR+ V+G L       V    H+ +DG  L  +    
Sbjct: 7   RLDRFISQNSVYSLSDTRRLLAQQRIFVDGHLAYSIQQQVTQFTHVVLDGNCLNDSTAVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + L +KP G V+  +DP    TV D +       +  VGRLD NT GL+LLTNDG  +R 
Sbjct: 67  MML-NKPKGFVSATTDPK-HPTVLDLIQHPQKNELHIVGRLDFNTTGLVLLTNDGAWSRK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           + LP T+  ++Y V     ++ + + + +KGI             L+      A ++  L
Sbjct: 125 ISLPETKLAKIYEVTLSKPLNDEYIEVFRKGIYFSYENITTQPAYLEILSEYQARLS--L 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EGK  ++K++F FF  +V  L R + GP  L  L  G ++ ++K+ +  Q
Sbjct: 183 IEGKYHQVKRMFGFFQNEVLALHRTAVGPISLDGLTVGHSKLLTKQTIEGQ 233


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 122/240 (50%), Gaps = 19/240 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K ++ AG+ SRRE +R +    V ++G++    A  V+    +   G P++K E 
Sbjct: 4   PVRINKYLSEAGVCSRREADRQVEAGNVTIDGVVASMGA-KVLPDQTVLFCGKPVKKEEE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L  +HKP G+V T    +  + V + N P    R+  +GRLD ++EGLLL+TN+G + 
Sbjct: 63  MILLAFHKPTGIVCTAEKREKNNVVDYINYPK---RIYPIGRLDKDSEGLLLMTNNGDIV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--- 188
             +        + Y V  +  V    L  L  G+ +       +++   T+K    W   
Sbjct: 120 NRIMRAGNMHEKEYIVTVNKPVTDSFLRGLAGGVPL-------VELNATTRK-CKVWRIG 171

Query: 189 ---VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+F ++V +L+R      +LG L AG+ REV+ +  +E +
Sbjct: 172 KRQFGIILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLKAGTYREVTPQEYKELM 231


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 119/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K+++  G  +R+EV+  I +  V VNG  +    + ++ TD  ++     +   R 
Sbjct: 4   MRIDKLLSNTGFGTRKEVKGFIKEGLVTVNGRTVNDPGL-IIETDKDDIIFNDEKIFYRK 62

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
            ++ + +KP G+++   DP    TV D LP      +V   GRLD +TEGLLLLTNDG L
Sbjct: 63  YIYIMMNKPRGVISATYDP-SEKTVLDLLPDDIKARKVFPAGRLDKDTEGLLLLTNDGIL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAWV 189
           A  L  P     + Y     G +D+D ++L   GIV+    Y  M   L+    GS + V
Sbjct: 122 AHKLLSPKKHVYKKYYAEISGFIDEDDISLFSNGIVLDD-GYKTMPAYLEIISSGSISKV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V ++EGK  +IK++FE    KV  L R+S G   L   L  G  RE++   L+
Sbjct: 181 YVSIKEGKYHQIKRMFESLGSKVIYLKRLSMGYLNLDENLKEGEWRELTDNELK 234


>gi|327312548|ref|YP_004327985.1| pseudouridylate synthase [Prevotella denticola F0289]
 gi|326945115|gb|AEA21000.1| pseudouridylate synthase [Prevotella denticola F0289]
          Length = 507

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 109/218 (50%), Gaps = 8/218 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +    
Sbjct: 263 EENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVVLFQE 322

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LL
Sbjct: 323 KPV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLL 381

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG LA  L  P     +VY V     V  + L  +  GI ++ G    D     D Q
Sbjct: 382 LTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEYADPQ 441

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                 V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 442 --DQTQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQF 477


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +R+ K+++  GI SRR+ E +I   ++ +N  + +     V   D I+++   ++    
Sbjct: 5   AKRIQKILSEQGICSRRKAEELILSGKILINNKIAKLGEC-VTINDEIKINNRIIKLNNN 63

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A   +  + +KP+  + T SDP  R T+++ L +   R+ S+GRLD NT G++L+TNDG
Sbjct: 64  IANNFKYIVLNKPMNTICTASDPQNRKTIYEYLKA-KERLFSIGRLDFNTTGIILITNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A +L  PS++  R+Y      ++   +LNLL    V+        +VT    K S   
Sbjct: 123 EFANLLSHPSSEIPRIYIATLEREMLDGELNLLNSNHVLLNGKISKQKVT----KLSAFK 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             V L EG+N  +K +F   N  V +L R S+G      L  G  R ++
Sbjct: 179 YEVLLYEGRNHHVKNLFLLVNNYVKKLHRKSFGCIDDSNLKIGQYRNLT 227


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 117/230 (50%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+++ I+ AGI SRR+ + +I    + VNG ++ E  +    + D I+ +G  L++ E+ 
Sbjct: 208 RLNRYISNAGICSRRKADELITAGVISVNGEVVTELGSKVDPAKDEIKYNGERLKR-EKM 266

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  DP  R TV   +  +   R+  VGRLD NT GLLLLTNDG LA 
Sbjct: 267 VYVLLNKPKDYITTTDDPQERRTVMQLVANATKERIYPVGRLDRNTTGLLLLTNDGNLAE 326

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y V     ++Q   N +  G+ ++ G    D    +  Q GS   V +
Sbjct: 327 KLSHPRNNISKIYNVELDKSLNQGDFNKIVFGLELEDGFVKPDDLSYV--QGGSKREVGI 384

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  GKNR ++++FE   + V +L R+ Y       L  G  R + +K L
Sbjct: 385 QIHSGKNRIVRRIFESLGYDVVKLDRVVYANLTKKDLPRGRWRYLEEKEL 434


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/240 (32%), Positives = 124/240 (51%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ ++G  SR +V+++I  ++V V+G+L +R  +NV  S   I V G  L  A   
Sbjct: 2   RLDKLLGQSGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPSGVVSARKDKE-HQTVIDLIRPEDRREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +  +  D     + G+V + G      Q+ + +     +   
Sbjct: 120 FAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCKSAQLEVLSSASDKSCAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQLG 246
           V + EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  LG
Sbjct: 180 VTISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 127/237 (53%), Gaps = 15/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           RV K++A  G  SR++V   + +    +NG+     A ++  T D + V+G+ ++   RT
Sbjct: 2   RVDKILASNGYGSRKDVRVFLKKNNCCINGVRCINPAQHIDPTKDTVTVNGISVQL--RT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            ++ + HKP G V++  DP  + TV D LP+ F+   +  +GRLDI+TEGLL++TNDG L
Sbjct: 60  SVYIMLHKPAGCVSSTKDPIHK-TVMDFLPAPFNAMDLFPIGRLDIDTEGLLIITNDGNL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQG--ICY-GDMQVTLDTQK 183
              +  P +  ++ Y +     + + +++     L +GI++     C    +++T +   
Sbjct: 119 THSITAPKSNCVKTYYLELERPLTETEIHNFTEKLAQGILLHTGYTCLPAALELTENIHT 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            +     + + EGK  +IKK+   F  K+  L R+S    +L  +L AG+ RE++ +
Sbjct: 179 KNAQAFLIHITEGKYHQIKKMCTAFGVKLTYLKRVSMAGLELDPSLAAGNCRELTSE 235


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/218 (34%), Positives = 109/218 (50%), Gaps = 8/218 (3%)

Query: 8   QENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +ENF P    R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +    
Sbjct: 263 EENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVVLFQE 322

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LL
Sbjct: 323 KPV-SLEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTTGVLL 381

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ 182
           LTNDG LA  L  P     +VY V     V  + L  +  GI ++ G    D     D Q
Sbjct: 382 LTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEYADPQ 441

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                 V + +  GKNR ++++FE   ++V +L R+ +
Sbjct: 442 --DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQF 477


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 122/240 (50%), Gaps = 19/240 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K ++ AG+ SRRE +R +    V ++G++    A  V+    +   G P++K E 
Sbjct: 4   PVRINKYLSEAGVCSRREADRQVEAGNVTIDGVVASMGA-KVLPDQTVLFCGKPVKKEEE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L  +HKP G+V T    +  + V + N P    R+  +GRLD ++EGLLL+TN+G + 
Sbjct: 63  MILLAFHKPTGIVCTAEKREKNNVVDYINYPK---RIYPIGRLDKDSEGLLLMTNNGDIV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--- 188
             +        + Y V  +  V    L  L  G+ +       +++   T+K    W   
Sbjct: 120 NRIMRAGNMHEKEYIVTVNKPVTDSFLRGLAGGVPL-------VELNATTRK-CKVWGIG 171

Query: 189 ---VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+F ++V +L+R      +LG L AG+ REV+ +  +E +
Sbjct: 172 KRQFGIILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLKAGTYREVTPQEYKELM 231


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 112/226 (49%), Gaps = 15/226 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ + +ARAG+ASRR  E +++  RV+VNG ++      V    D + VDGV  R ++  
Sbjct: 13  RLQRFLARAGVASRRGSENLMSAGRVRVNGRVVSELGSKVTPGIDVVTVDGVECRLSDEH 72

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G +TT SDP GR  V + +P+  +  +  VGRLD +T GLLL + DG +A 
Sbjct: 73  AYLMLNKPAGYLTTMSDPQGRPCVAELVPTARYPGLFPVGRLDADTTGLLLFSTDGEVAN 132

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------ICYGDMQVTLDTQK 183
            L  PS    + Y     G     +L +L+ G+ +           +   D  ++     
Sbjct: 133 ALLHPSRHVWKRYVALVRGTPTTRQLAMLRAGVPLDDGVARPADAHLLGADDPLSASVVT 192

Query: 184 G----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G      A V++ + EGK  ++K++ +    +V  L R  +GP  L
Sbjct: 193 GGADPGCAVVSIRIHEGKKHQVKRMLKAVGHEVVHLHRSEFGPLVL 238


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 115/225 (51%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRR  +R+I + RV VNG      +V V ++D + VDG  +    +  
Sbjct: 5   RINKYLSEAGVCSRRGADRLIEEGRVSVNGNHAFLGSV-VKNSDEVRVDGNLVTPVIKKI 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+V T +DP  +        +   R+  VGRLD  +EGL+LL+NDG L+  +
Sbjct: 64  LIAFNKPRGIVCTTADPKSKDVNIIEYINYPERIFPVGRLDKESEGLILLSNDGDLSNKI 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V      D + L  + +G+ I         +    +   N  +T GL 
Sbjct: 124 MKARNFHEKEYEVEVDKPFDDEFLKKMSEGVPILDTITRKCTLKRTGKTSFNIILTQGL- 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              NR+I+++ E+F +KV +L RI     +LG L +G+ R ++ K
Sbjct: 183 ---NRQIRRMCEYFGYKVLKLKRIRIMNIKLGNLKSGTYRNITDK 224


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 116/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 257 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 315

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 316 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 375

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  ++ +  GI ++ G  + D +  T D +K     V
Sbjct: 376 SKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISYTDDFKK---DQV 432

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 433 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 481


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  +K+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTCYSRREADELIKQGLIKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHR 232


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 73/210 (34%), Positives = 107/210 (50%), Gaps = 5/210 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      V+  D ++    P+   E+
Sbjct: 254 PIRLNKYLANAGVCSRREADEFILAGVVTVNGNVVTELGTKVLRADEVKFHDQPV-SLEK 312

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 313 KVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTGVLLLTNDGDLA 372

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY V     V +D L  +  GI ++ G  + D     D +      V 
Sbjct: 373 SKLTHPKFLKKKVYHVHLDKNVTEDDLQKIASGIELEDGEIHADAIEYADER--DKKQVG 430

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + +  GKNR ++++FE   ++V RL R+ +
Sbjct: 431 IEIHSGKNRIVRRIFESLGYRVLRLDRVQF 460


>gi|254775517|ref|ZP_05217033.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium subsp. avium ATCC 25291]
          Length = 247

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 112/229 (48%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  +   E  
Sbjct: 8   RLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGARVVLDESQ 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD  TEGL+LLTNDG L
Sbjct: 68  VYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLILLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G + +     L+ GI +  G+   D    +D   G    V
Sbjct: 128 AHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDATPGKT-LV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR ++++     + V  L+R   GP  LG    GS R + +
Sbjct: 187 RVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGR 235


>gi|291336628|gb|ADD96174.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 109

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 47/93 (50%), Positives = 68/93 (73%)

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             RV+SVGRLD+++EGL+LLTN+G LA +LE PST WLR Y+VR +G+      + L+ G
Sbjct: 1   MPRVVSVGRLDLDSEGLILLTNNGELANLLEAPSTNWLRQYKVRVYGRPQISGFDKLRLG 60

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
           + ++GI Y  +++ L+ Q GSNAW+ + LREGK
Sbjct: 61  VTLEGIKYKPIRIELERQTGSNAWLNIALREGK 93


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 122/244 (50%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K ++ +   P R++K ++ AG+ SRRE +  I +  V+VNG ++      +   D +
Sbjct: 1   MKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQEGVVQVNGQIVTELGTKITRQDTV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
                P++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 61  LFKDQPVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 120 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVSIEDMEKIANGLELE-----DGEIHA 174

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 175 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWRY 234

Query: 236 VSKK 239
           ++++
Sbjct: 235 LNER 238


>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 =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 124/240 (51%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ ++G  SR +V+++I  ++V V+G+L +R  +NV  S   I V G  L  A   
Sbjct: 2   RLDKLLGQSGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPSGVVSARKDKE-HQTVIDLIRPEDRREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +  +  D     + G+V + G      Q+ + +     +   
Sbjct: 120 FAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEILSSASDKSCAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQLG 246
           + + EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  LG
Sbjct: 180 ITISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 117/230 (50%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+++ I+ AGI SRR+ + +I    + VNG ++ E  +    + D I+ +G  L++ E+ 
Sbjct: 208 RLNRYISNAGICSRRKADELITAGVISVNGEVVTELGSKVDPAKDEIKYNGERLKR-EKM 266

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  DP  R TV   + +    R+  VGRLD NT GLLLLTNDG LA 
Sbjct: 267 VYVLLNKPKDYITTTDDPQERRTVMQLVANATKERIYPVGRLDRNTTGLLLLTNDGNLAE 326

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y V     ++Q   N +  G+ ++ G    D    +  Q GS   V +
Sbjct: 327 KLSHPRNNISKIYNVELDKSLNQGDFNKIVFGLELEDGFVKPDDLSYV--QGGSKREVGI 384

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  GKNR ++++FE   + V +L R+ Y       L  G  R + +K L
Sbjct: 385 QIHSGKNRIVRRIFESLGYDVVKLDRVVYANLTKKDLPRGRWRYLEEKEL 434


>gi|255012441|ref|ZP_05284567.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_7]
          Length = 495

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
             +  P++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELE-----DGEIHA 420

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 421 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRY 480

Query: 236 VSKK 239
           ++++
Sbjct: 481 LNER 484


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 115/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 249 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 307

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 308 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 367

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI ++ G  + D +  T D +K     V
Sbjct: 368 SKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISYTDDFKK---DQV 424

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 425 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 473


>gi|170288482|ref|YP_001738720.1| pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170175985|gb|ACB09037.1| pseudouridine synthase [Thermotoga sp. RQ2]
          Length = 239

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 124/246 (50%), Gaps = 10/246 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++ +G+ +R+EV+++I Q RV VNG ++      V+  D + +DG  +R  ++  
Sbjct: 2   RLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALDGEVVRFHKKVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G VT+  DP    T+ + LP +   +  VGRLD + EGLL++TNDG  A  +
Sbjct: 62  I-LFYKPSGYVTSTKDPHS-ETIMEFLPPL-KGIFPVGRLDKDAEGLLIITNDGDFAHRV 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + + 
Sbjct: 119 ISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKC---VEKLSNDTLKIVIT 175

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGK  +IK++      K   L R   G    G +L    +    + L E+    + E   
Sbjct: 176 EGKYHQIKRMTAAVGLKTVHLKRTRIG----GLVLPDDMKPGEYRFLSEEEVKKVFERED 231

Query: 255 VNLDAP 260
              D P
Sbjct: 232 QKEDTP 237


>gi|121533339|ref|ZP_01665167.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121307898|gb|EAX48812.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 245

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/234 (35%), Positives = 118/234 (50%), Gaps = 18/234 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+A  G  SRRE+++M+  +RV VNG ++    ++V    D IEVDG P+   E 
Sbjct: 7   QRLDKVLAHLGYGSRREIKKMVKAERVIVNGAVVRDPELHVFPWQDRIEVDGEPIHYREY 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G+++   D  G+  V    P    F+    VGRLD +TEGLLLLTNDG L
Sbjct: 67  IYLMM-NKPQGVLSATEDAAGKVVVDLLRPEHKAFAP-FPVGRLDKDTEGLLLLTNDGQL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----KG 184
           A  L  P     + Y  R  G V D+D      KG    GI   D   TL  +      G
Sbjct: 125 AHRLLAPKKHVPKRYYARVKGVVTDED------KGAFQAGITLDDGYRTLPAELTILHAG 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
             + V + + EGK  ++K++F      V  L R++ G   L   LA G  RE++
Sbjct: 179 PVSEVELVIYEGKFHQVKRMFAARGKTVTYLKRLAMGALVLDEKLAPGEYRELT 232


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 123/248 (49%), Gaps = 21/248 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 258 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 316

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 317 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 376

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  ++ +  GI ++ G  + D +  T D +K     V
Sbjct: 377 SKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISYTDDFKK---DQV 433

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + +  GKNR ++++FE   +KV +L R+           AG    ++KK LR       
Sbjct: 434 GIEIHSGKNRIVRRIFESLGYKVVKLDRV---------FFAG----LTKKGLRRGDW-RY 479

Query: 250 LEEAQVNL 257
           L EA+VN 
Sbjct: 480 LSEAEVNY 487


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 116/229 (50%), Gaps = 7/229 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 260 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 318

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 319 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 378

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  ++ +  G+ ++ G  + D +  T D +K     V
Sbjct: 379 SKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGVQLEDGEIHADAISYTDDFKK---DQV 435

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 436 GIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 484


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 130/234 (55%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+++ IAR+G  SRR+ +++I   +VKVNG +++     V    D +E+DG  L K E  
Sbjct: 4   RLNRFIARSGYCSRRKADQLIEMGKVKVNGKVVKDFGYRVDTEKDRVEIDG-KLIKLELK 62

Query: 74  RLWL-YHKPIGLVTT-HSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGG 129
           ++++  +KP G +T    D  GR T+ D      I   V   GRLD  +EGLLLLTNDG 
Sbjct: 63  KVYIKLYKPRGYLTQLGKDKFGRKTLTDLFKEVGIKDNVFPAGRLDYESEGLLLLTNDGD 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-A 187
            A ++  P ++  + Y V+  G+V+ +  N ++KG +++ G    D    L  +KG N  
Sbjct: 123 FANMIMHPKSKIKKTYVVKVKGRVNLESFNRMRKGALLEDGFIKPDEIKIL--KKGKNYT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           W+ + +  GK R I++  ++F + V RLIR   G  +LG+L     + + +KI+
Sbjct: 181 WLEITIHSGKKRIIRRFTKYFGYPVERLIRTRIGSIELGSLKEKEWKYIDEKII 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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 77/241 (31%), Positives = 120/241 (49%), Gaps = 11/241 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K+++ +   P R++K +A AGI SRRE +  I    V VNG+++      V  TD I+  
Sbjct: 8   KDVLTDPDEPIRLNKFLANAGICSRREADEFITAGVVSVNGVVVTELGTKVKRTDEIKFH 67

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
             P+   ER    L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+L
Sbjct: 68  DQPV-NIERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVL 126

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-- 180
           LLTNDG LA  L  P     ++Y V     V +  L+      ++ GI   D ++  D  
Sbjct: 127 LLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQ-----IVSGITLDDGEIHADAV 181

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               +   + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++
Sbjct: 182 SYASETDKSQVGIEIHSGKNRIVRRIFEALGYRVIKLDRVYFAGLTKKGLRRGDWRYLTE 241

Query: 239 K 239
           +
Sbjct: 242 Q 242


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 119/227 (52%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ I+  G+ SRR+ + +I   RVKVNG +++   + V   D +EVD V +   ++  
Sbjct: 177 RLNRYISMGGVCSRRDADELIVAGRVKVNGEVVQTVGLKVRKKDKVEVDDVQIFPEKKVY 236

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP   VTT  DP  R TV   +  +   R+  VGRLD  T G+LL TNDG LA+ 
Sbjct: 237 LVL-NKPKDYVTTVEDPLERKTVMALVEGACKERIYPVGRLDRQTTGVLLFTNDGDLAKK 295

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     ++Y V     + ++    +  G+ ++ G    D +++  +   +   V + 
Sbjct: 296 LTHPKYDHKKIYHVFLDRVLTEEDFQAIANGVQLEDGFIKAD-EISYTSPDCTE--VGIE 352

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  GKNR ++++FE F +++ +L R+ +       L  G+ R ++ K
Sbjct: 353 IHSGKNRIVRRIFEHFGYQIIKLDRVYFAGITKKNLPRGTWRFLTPK 399


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
             +  P++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELE-----DGEIHA 420

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 421 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRY 480

Query: 236 VSKK 239
           ++++
Sbjct: 481 LNER 484


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 121/233 (51%), Gaps = 14/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +R+I QQRV +NG + E     V   D++ VDG P+ K +   
Sbjct: 8   RINKYLSEQGFCSRRAADRLIEQQRVTINGTVPE-MGTKVQPNDNVAVDGEPISKKKEKP 66

Query: 75  LWL-YHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP G+V T     +PD     + N P   +R+  +GRLD  +EGL+ LTNDG +
Sbjct: 67  VYIAFHKPTGIVCTTDTRVEPDN-IIEYINYP---TRIFPIGRLDKMSEGLIFLTNDGDI 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +D   ++ +  GI I        +V    Q G   +  
Sbjct: 123 VNKILRSRNNHGKEYIVTVDHSIDDRFISRMASGIPILDTVTKKCEV---EQIGRKTFRI 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V L +G NR+I+++ E+ N++V +L RI     +L  +  G+ R+++K+ L E
Sbjct: 180 V-LTQGLNRQIRRMCEYLNYRVTKLKRIRIMNVELD-IPKGTYRDLTKEELDE 230


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVQFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHR 232


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 125/239 (52%), Gaps = 17/239 (7%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  S D I V+G 
Sbjct: 155 ENFKEPPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDIIYVNGN 214

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV--FDNLPSIF---------SRVISVGR 113
            + K    +++   +KP G + +  + + +S +  FD   S +          R+ +VGR
Sbjct: 215 RIPKKLPPKVYFALNKPKGYICSSGEKEIKSVISLFDEYLSSWDKRNPGTPKPRLFTVGR 274

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY 172
           LD+ T GL+++TNDG  A+ L  PS+   + Y     G + +  L  + +G +++G+ C 
Sbjct: 275 LDVATTGLIVVTNDGDFAQKLSHPSSSLPKEYITTVVGDIHKRHLMAISEGTIVEGVHCV 334

Query: 173 GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            D    +  Q     A + + + EG+N E++++ +    +V+ L R+  G F+L + L 
Sbjct: 335 PDSVELMPKQHDIPRARLRIVVHEGRNHEVRELVKNAGLEVHSLKRVRIGGFRLPSDLG 393


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/225 (31%), Positives = 112/225 (49%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+SKV+A AGIASRR  E +I Q  VKVNG +++     V    D I V    + + E  
Sbjct: 5   RLSKVLAAAGIASRRACEELIFQGLVKVNGEVIKVPQTKVNPEIDTITVRDEVINRKEDK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G + +         + D       R+ +VGRLD +T+GLL++TNDG  A  
Sbjct: 65  VYYLLNKPPGYICSARKSGQTKIILDLFQDEDHRLFTVGRLDKDTQGLLIVTNDGHFANQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS    + Y  +   ++  + L  +  G +++G+    ++V    QK     + + +
Sbjct: 125 IIHPSANIQKEYLAKTDQEISHEHLIAIANGTLVEGVFVKPIRV----QKVRKGTIKIII 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EGK RE++ +      KV  L RI  G   LG L  G+ R +++
Sbjct: 181 GEGKKREVRMLLSAAGLKVQELTRIRLGGLHLGRLPIGNWRPLTE 225


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
             +  P++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELE-----DGEIHA 420

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 421 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRY 480

Query: 236 VSKK 239
           ++++
Sbjct: 481 LNER 484


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
             +  P++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELE-----DGEIHA 420

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 421 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRY 480

Query: 236 VSKK 239
           ++++
Sbjct: 481 LNER 484


>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 =  101 bits (252), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIANAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHR 232


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 115/219 (52%), Gaps = 8/219 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++++ G+ASRR+ E++I   +V++NG   E         D I ++G  L   +R +
Sbjct: 4   RLQKLLSQWGVASRRQAEQLILAGQVQLNGHTAELGQKADPDQDQITLNGQILNPTDRPQ 63

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
               L +KP G+V+T  DP  R TV + LP  + +   +  VGRLD+ + G LLLTNDG 
Sbjct: 64  PLYLLVNKPKGVVSTCQDPQHRRTVLELLPKTYQQGQGLHPVGRLDVASTGALLLTNDGQ 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
           L   L  P     + Y+V   G    + L+  ++GI + G      QV +    Q  +N+
Sbjct: 124 LTFALTHPRFHIAKTYQVWIEGCPPPEILDRWRQGIHLDGRTTLPAQVEILKPYQSHTNS 183

Query: 188 -WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             + V L+EG+NR+I+++ E   + V +L R   G   L
Sbjct: 184 ICLEVILQEGRNRQIRRIAEQLGYPVRKLHRTQIGSISL 222


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 119/235 (50%), Gaps = 11/235 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDG----VP 66
           T  R++K +A AG+ SRR V++ I    V +NG  + +  + +    D I + G    + 
Sbjct: 22  TSIRINKALANAGVCSRRNVDKYILNGEVTINGKSVTQPGIYIHPDKDIIALHGRRVDIQ 81

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLL 124
           L+  +   L +Y KPI ++++  DP  R TV D +P  +   R+  VGRLD  +EGLLL+
Sbjct: 82  LKNKKYYYLSMY-KPIKVISSVKDPQNRLTVLDFIPFPWKNYRLYPVGRLDFFSEGLLLI 140

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDT 181
           TNDG L + L  P     +VY V    ++    L  + KGI +     +    ++V    
Sbjct: 141 TNDGELTQRLTHPRYHISKVYHVLIRERILNTTLKNISKGITLSDGTKLPPAKVRVLSSI 200

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + +  W+ + L++G NR+I+++ +     + +LIR+  G   L  L  G  R +
Sbjct: 201 TETNTTWLEITLQQGINRQIRRMCKELGLTILKLIRVKQGNINLSNLQPGEVRPL 255


>gi|329667573|gb|AEB93521.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 233

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 121/233 (51%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKV-AYQQYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   ++ +    P   +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQKTVLSLLKPKDRYKGIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +     +   ++++ +  ++   + + 
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVEIFASGMTLGDGTKLKPAELKILIQDKEADRSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + ++EGK  +IK++F     KV  L RIS G   L T L  G  +E+S K ++
Sbjct: 181 IEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPTSLKRGEYKEISLKEIK 233


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 115/228 (50%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I  ++V +N  L+++A   V   D ++VD   +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQTIT-YQQFH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +KP G++T   DP  + TV D + S   +  +  VGRLD +T GLLL+TNDG L  
Sbjct: 61  YFMLNKPTGVITATEDPQ-QKTVLDLIASKDRYPDLAPVGRLDKDTTGLLLITNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V    ++  +  +   KG+ +  G   G  Q+ +D        +T+
Sbjct: 120 NLLSPKKHVAKTYFVELDQEIANEVDSAFAKGVALADGTQVGSAQLIIDKSNKKQGLITI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              EGK  +IK++F  F+  V +L RI  G   L   L  G  RE+++
Sbjct: 180 --HEGKFHQIKRMFGLFDLGVVKLKRIKMGNLSLDENLPQGKYRELTE 225


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 119/238 (50%), Gaps = 9/238 (3%)

Query: 9   ENFTPQR---VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG 64
           E+F  +R   + KV+++AGIASRR  E++I   RV+V+G ++      V   T  I VDG
Sbjct: 5   EDFEQERGIRLQKVLSQAGIASRRAAEKLIIDGRVEVDGQVVTELGTRVDPDTSLIRVDG 64

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 121
           V +   +       +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL
Sbjct: 65  VRVILDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGNKNLFHVGRLDADTEGL 124

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLD 180
           +LLTNDG LA  L  PS +  + Y     G V +     L+ GI ++ G    D    +D
Sbjct: 125 ILLTNDGELAHRLMHPSHEVPKTYLATVAGTVPRGLGKKLRAGIELEDGPVRVDGFAVVD 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              G    V V L EG+NR ++++     + V  L+RI  G   LG    GS R + +
Sbjct: 185 AIPGKT-LVRVTLHEGRNRIVRRMLAAVGFPVQALVRIDIGGVSLGEQRPGSVRALRR 241


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 123/240 (51%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ ++G  SR +V+ +I  ++V V+G+L +R  +NV  S   I V G  L  A   
Sbjct: 2   RLDKLLGQSGYGSRNQVKNLIRSRQVYVDGVLADRDNLNVDASLQTIMVSGKELEHAPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPSGVVSARKDKE-HQTVIDLIRPEDQREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +  +  D     + G+V + G      Q+ + +     +   
Sbjct: 120 FAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEILSSASDKSCAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQLG 246
           + + EGK  ++KK+F  +  KV  L RIS+G F+L   +A GS R   E  K ILR  LG
Sbjct: 180 ITISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYLG 239


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/228 (35%), Positives = 116/228 (50%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   GI SR+EV+++I+   + VNG+    A  N+  ++D IE +G  L   E  
Sbjct: 2   RLDKFLVECGIGSRKEVKKLISNGEIAVNGMSDILAKDNIDENSDTIEYNGERLEYKE-F 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D     TV D LP   I   +  VGRLD +TEGLLL TNDG L 
Sbjct: 61  RYYIMNKKAGYITATEDF-KEDTVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNAWV 189
             L  P     +VY V     + D+D L L       QG+  G+ +      +K S+  +
Sbjct: 120 HKLLSPKNHIDKVYYVEIEKNILDEDILKLE------QGVDIGNYITQPAKVEKISDNKI 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + ++EGK  ++KK+ E  N KV  L R S+G   L  L  G  +EVS
Sbjct: 174 YLTIKEGKFHQVKKMLEAVNNKVCYLRRESFGKLTLNDLTLGEVKEVS 221


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 112/229 (48%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  +   E  
Sbjct: 9   RLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGARVVLDESQ 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD  TEGL+LLTNDG L
Sbjct: 69  VYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLILLTNDGEL 128

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G + +     L+ GI +  G+   D    +D   G    V
Sbjct: 129 AHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDAIPGKT-LV 187

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR ++++     + V  L+R   GP  LG    GS R + +
Sbjct: 188 RVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGR 236


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 116/235 (49%), Gaps = 17/235 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R++K IA     SRRE ++ I    V+++G +    A  V     ++ + G  +   ++ 
Sbjct: 3   RLNKFIAHYSTYSRREADQAILDGYVRIDGEIETNPATQVDERHANVMISGNKITPTDQF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + +Y+KP G + T  DP GR T++D+L   +   I +GRLD  +EGLLLLT+   +A  
Sbjct: 63  TVIVYNKPRGELVTKKDPQGRKTIYDSLAKQYRHYIPIGRLDFASEGLLLLTDASRVATA 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VTL 179
           L   +++  RVY+++  G V +     + +G+ ++    G  +                +
Sbjct: 123 LM--TSKMERVYKIKIKGPVTEAMKVAMGEGLELEDASAGAHEHAEAGPMSFAPFYAYQV 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +G  + + V + EG+NRE+++ F  F  +V  L R+S+G   L  L  G  R
Sbjct: 181 QKDQGDYSVLKVAIGEGQNRELRRFFAHFGAEVVDLKRLSFGGIDLNNLPTGKVR 235


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/226 (32%), Positives = 117/226 (51%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ + +   GI SR+EV+++I+   +KVNG     A  N+   +D IE +G  L + ++ 
Sbjct: 2   RLDRFLVECGIGSRKEVKKIISANEIKVNGSYDISAKDNINEYSDVIEYNGERL-EYKKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D    +TV D LP   I   +  VGRLD +TEGLLLLTNDG L 
Sbjct: 61  RYYIMNKKAGYITATEDI-REATVMDLLPEWVIRKDLAPVGRLDKDTEGLLLLTNDGKLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + Q+ +  L++G+ I       + +    +K S+  + +
Sbjct: 120 HRLLSPKNHVDKTYYVEIENNISQEDVLKLEEGVDIGNY----ITLPAKVEKISDTKIYL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++EGK  ++KK+ E  N KV  L R ++    L  L  G  +EV+
Sbjct: 176 TIKEGKFHQVKKMLEAVNNKVTYLQRTTFAKLSLADLALGEVKEVN 221


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/138 (38%), Positives = 81/138 (58%), Gaps = 1/138 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  YI-LFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHG 151
           +  P  Q  + Y  +  G
Sbjct: 125 MTHPRYQIKKKYVAKLKG 142


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 114/230 (49%), Gaps = 7/230 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD ++    P+   E+
Sbjct: 245 PIRLNKYLANAGVCSRREADEFIQAGVVTVNGQVITELGTKIVRTDEVKFHDQPV-TLEK 303

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV + +  +   R+  VGRLD NT G+LL TNDG LA
Sbjct: 304 KVYVLLNKPRDYVTTSDDPQQRKTVMELVKGACPERIYPVGRLDRNTTGVLLFTNDGDLA 363

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDTQKGSNAWV 189
             L  P     +VY V    +V    +  +  GI +  G  + D ++   D  K     V
Sbjct: 364 SKLTHPKFLKKKVYHVFLDKEVTMHDMQQIATGITLDDGEIHADAIEYAKDNDK---KQV 420

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +  G+NR ++++FE   ++V RL R+ +       L  G  R +++K
Sbjct: 421 GIEIHSGRNRIVRRIFESLGYRVVRLDRVQFAGLTKKYLRRGDWRFLTEK 470


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHR 232


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 118/228 (51%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++  G  +R +V+++I    V +N   +++A  NV   D + VD  P+   E   
Sbjct: 2   RLDKYLSHMGFGTRNDVKKLIKNGWVTINDETIKKADYNVKEDDKVFVDDEPVSYVE-FE 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V+   D     TV + + S    +  VGRLD++TEGLLL++NDG L   +
Sbjct: 61  YYILNKPQGYVSATEDM-LYPTVMELIQSQRHDLYPVGRLDVDTEGLLLISNDGKLTHEV 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVGL 193
             P     + Y V F G + ++ ++   + +  +       ++  LDT K   A++T+  
Sbjct: 120 LSPKKHVDKKYYVEFDGTLPENAVDFFNQPMEFEEFTSAPSKLEILDTNK---AYLTI-- 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EGK  ++K++FE  N  V  L RI +GP +L  L  G  R ++++ L
Sbjct: 175 HEGKFHQVKRMFEKANCTVTYLQRIEFGPLKLNDLPLGEFRALTQEEL 222


>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 =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 62/191 (32%), Positives = 98/191 (51%), Gaps = 21/191 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           TR  ++HKP  ++   +DPDGR T+ D  ++P +++     GRLD ++EGLLLLT+DG L
Sbjct: 7   TRTLVFHKPYDVLPCFTDPDGRPTLGDYIDVPGVYA----AGRLDRDSEGLLLLTSDGAL 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----- 185
           A  +  P     ++Y V+     D   +  L++G+V+ G      Q  L  +  S     
Sbjct: 63  AHRITDPEHHLPKIYFVQVERIPDAAAVERLQQGVVVGGRRTKPAQARLLLEAPSIPERP 122

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      AW+ + LREG NR+++++         RL+R++ GP  LG LL G  RE
Sbjct: 123 VPIRFRKHVPTAWLELTLREGMNRQVRRMTAAVGHPTLRLVRVAIGPITLGALLPGQWRE 182

Query: 236 VSKKILREQLG 246
           ++K    E  G
Sbjct: 183 LTKAETAEIYG 193


>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 =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHR 232


>gi|218289710|ref|ZP_03493918.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240167|gb|EED07351.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 242

 Score =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 77/222 (34%), Positives = 113/222 (50%), Gaps = 13/222 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG--VPLRKAE 71
           RV K +  AG  +R E +++    RV++NG  ++ AA +   + D +EVDG  VP    E
Sbjct: 5   RVDKWLTTAGYGTRSEAKKLCRAGRVRLNGETVKDAAKHADPAVDVLEVDGEIVPY---E 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDG 128
               ++ +KP G V++  DP  R  V   L     I+  V  VGRLD + EGLLLLTNDG
Sbjct: 62  PLVYFMMYKPPGYVSSTEDP--RDPVVIELLDEEDIWRDVFPVGRLDKDAEGLLLLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNA 187
            LA  L  P     + Y VR  G + +D    L +G+V+    Y  M   L+  + G+ +
Sbjct: 120 PLAHRLLAPKRHVPKRYFVRVRGALGEDDARALAEGVVLDD-GYKAMPAELEILRSGAES 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
              + + EGK  ++K++F     +V  L RIS GP  L   L
Sbjct: 179 EAIIQVYEGKYHQVKRMFASLGKRVTFLKRISMGPLSLDPAL 220


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 117/227 (51%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA  GI SRRE ++++A  RVKVNGI  + A + V  +D + VD   +   +   
Sbjct: 2   RLNQYIAACGICSRREADKLVAAGRVKVNGISAQ-AGIQVEDSDEVFVDNKKISLVKENV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +  Y+KP+G+V T  D     TV   +    +RV   GRLD ++EGLL+L+NDG L   +
Sbjct: 61  VLAYYKPVGVVCTEKDTHAERTVTSEVK-YPTRVTYAGRLDKDSEGLLILSNDGNLINAM 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
              S +  + Y V    ++  D LN +  G+ ++ +        + T+ G  ++  + L 
Sbjct: 120 MKSSNKHEKEYEVSVDREISGDFLNRMSNGVYLEELDRTTRGCKV-TRTGKKSFRII-LT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKK 239
           +G NR+I+++     + V  L RI     +L    ++ G   E+ KK
Sbjct: 178 QGLNRQIRRMCNALGYNVESLKRIRVMTVKLSDYDIMPGQYVELDKK 224


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 111/229 (48%), Gaps = 5/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 6   PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTV-SIER 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 65  KIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLA 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y V     + +  +  +  GI +  G  + D     D  K  +  V 
Sbjct: 125 SKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIHADAISYTDDFKKDD--VG 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 183 IEIHSGKNRIVRRIFESLGYKVMKLDRVYFAGLTKKGLRRGEWRYLTEQ 231


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 113/227 (49%), Gaps = 7/227 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +A AG+ SRRE +  I    V VNG ++      +   D ++    P+   ER   
Sbjct: 1   MNKFLANAGVCSRREADEFITAGVVSVNGAVVTELGTKIKRGDEVKFHDQPV-SIERKIY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA  L
Sbjct: 60  ILLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDTQKGSNAWVTVG 192
             P     ++Y V     V +  ++ +  GI +  G  + D +  T D ++     V + 
Sbjct: 120 THPKFLKKKIYHVHTDKNVTKADMDQIAAGIQLDDGEIHADAISYTDDVRRDE---VGIE 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  GKNR ++++FE   +KV +L R+ +       L  G  R +S++
Sbjct: 177 IHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLSEQ 223


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 74/216 (34%), Positives = 112/216 (51%), Gaps = 6/216 (2%)

Query: 32  ERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
           E +IAQ RV+VNG ++ R  V V   T  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 RFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G+ D++ +  L++G+ ++ GI   D    +DT +G  + + V L EG+   ++++ +
Sbjct: 123 TVLGEADRELVKKLREGVDLEDGIAKADYVQIVDTYEG-RSLIRVELHEGRKHIVRRMLK 181

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + V +L+R      QLG L  G+ R ++   LR
Sbjct: 182 ELGFPVQQLVRTKIHTVQLGELTPGAIRHLNDSELR 217


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 125/239 (52%), Gaps = 17/239 (7%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  S D I V+G 
Sbjct: 153 ENFKEQPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDIIYVNGN 212

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV--FDNLPSIF---------SRVISVGR 113
            + K    +++   +KP G + +  + + +S +  FD   S +          R+ +VGR
Sbjct: 213 RIPKKLPPKVYFALNKPKGYICSSGEKEIKSAISLFDEYLSSWDKRNPGTPKPRLFTVGR 272

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY 172
           LD+ T GL+++TNDG  A+ L  PS+   + Y     G + +  L  + +G +++G+ C 
Sbjct: 273 LDVATTGLIVVTNDGDFAQKLSHPSSSLPKEYITTVVGDIHKRHLMAISEGTMVEGVHCV 332

Query: 173 GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            D    +  Q     A + + + EG+N E++++ +    +V+ L R+  G F+L + L 
Sbjct: 333 PDSVELMPKQHDIPRARLRIVVHEGRNHEVRELVKNAGLEVHSLKRVRIGGFRLPSDLG 391


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 112/229 (48%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  +   E  
Sbjct: 8   RLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGARVVLDESQ 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD  TEGL+LLTNDG L
Sbjct: 68  VYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLILLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G + +     L+ GI +  G+   D    +D   G    V
Sbjct: 128 AHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDPIPGKT-LV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR ++++     + V  L+R   GP  LG    GS R + +
Sbjct: 187 RVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGR 235


>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 =  100 bits (250), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 112/232 (48%), Gaps = 11/232 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 95  PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAV-SIER 153

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    S R+  VGRLD NT G+LLLTNDG LA
Sbjct: 154 KIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLA 213

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--- 188
             L  P     ++Y V     + +  +  +  GI +      D ++  D    ++ +   
Sbjct: 214 SKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLD-----DGEIQADAISYTDDFKKD 268

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 269 EVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 320


>gi|295110375|emb|CBL24328.1| ribosomal large subunit pseudouridine synthase F [Ruminococcus
           obeum A2-162]
          Length = 310

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 123/239 (51%), Gaps = 12/239 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---ERAAVNVMSTDH 59
           DK +  E+    R++K ++ AG+ SRR+ +R+    RV VNG  +   ER  V+ +    
Sbjct: 2   DKKMKSEDQNTIRINKYLSSAGVCSRRDADRLTEAGRVTVNGKKIGTGERIPVDAV---- 57

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I +DG P+ K ER  L L++KP G+V + +    R T         +R+  VGRLD ++E
Sbjct: 58  ICLDGKPVEKEEREVLLLFYKPRGIVCS-TKKQRRETTVTEYIDYPTRIYPVGRLDKDSE 116

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL+TN G L   +        + Y+V    +V  + +  ++ G+ I G      +  +
Sbjct: 117 GLLLMTNQGELVNRIMRAGNYHEKEYQVTVDHEVTDEFVRHMQTGVPILGTV---TRPCI 173

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             + G N++ T+ L +G NR+I+++ E+  + V  L R+      L  L  G+ RE+ +
Sbjct: 174 VRKTGRNSF-TIVLTQGLNRQIRRMCEYHGYHVRTLKRVRIMNLTLDGLKCGAYREIRR 231


>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 =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 21/248 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 259 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 317

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 318 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 377

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI ++ G  + D +  T D +K     V
Sbjct: 378 SKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISYTDDFKK---DQV 434

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + +  GKNR ++++FE   +KV +L R+           AG    ++KK LR       
Sbjct: 435 GIEIHSGKNRIVRRIFESLGYKVVKLDRV---------FFAG----LTKKGLRRGDW-RY 480

Query: 250 LEEAQVNL 257
           L EA+VN 
Sbjct: 481 LSEAEVNY 488


>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 =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 117/227 (51%), Gaps = 12/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R++K IA  G  SRR+ + +I + RV VN    I+     ++V   D + +DG  ++   
Sbjct: 2   RLNKFIAETGFCSRRKADELINEGRVTVNKHEAII----GMDVKPEDVVRIDGERVKLNT 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R   ++ +KP  ++ ++ D  GR    D + S  +R+ + GRLD  TEGL++++NDG + 
Sbjct: 58  RYEYYILNKPKRVICSNEDKFGRRLAVDFIKS-RARLFTYGRLDFMTEGLIIISNDGEVY 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y  +   +++   +  L+ G+VI G      +V    +K     + +
Sbjct: 117 NHVMHPRKKLYKSYIAKVSREIEDKDIEALQHGVVIDGKRTAPAKV----KKIDKKELRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+I+K+ E   + VN L RI  G   LG L  G  R +++
Sbjct: 173 AIFEGRNRQIRKMLETLGYNVNSLKRIKVGELTLGNLQVGEYRALNE 219


>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 =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 82/248 (33%), Positives = 122/248 (49%), Gaps = 21/248 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER
Sbjct: 259 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIER 317

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA
Sbjct: 318 KVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLA 377

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI ++ G  + D +  T D +K     V
Sbjct: 378 SKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISYTDDFKK---DQV 434

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + +  GKNR ++++FE   +KV +L R+           AG    ++KK LR       
Sbjct: 435 GIEIHSGKNRIVRRIFESLGYKVVKLDRV---------FFAG----LTKKGLRRGDW-RY 480

Query: 250 LEEAQVNL 257
           L EA+VN 
Sbjct: 481 LSEAEVNY 488


>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 =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 81/248 (32%), Positives = 119/248 (47%), Gaps = 21/248 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 265 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAV-SIER 323

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 324 KIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACEERIYPVGRLDRNTTGVLLLTNDGDLA 383

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI +  G  + D +  T D +K     V
Sbjct: 384 SKLTHPKFLKKKIYHVHLDKNLTKSDMEQIAAGIQLDDGEIHADAISYTDDFKKDD---V 440

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + +  GKNR ++++FE   +KV +L R+           AG    ++KK LR       
Sbjct: 441 GIEIHSGKNRIVRRIFESLGYKVVKLDRV---------YFAG----LTKKGLRRGEW-RY 486

Query: 250 LEEAQVNL 257
           L EA+VN 
Sbjct: 487 LSEAEVNF 494


>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 =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 122/234 (52%), Gaps = 20/234 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---MSTDHIEVDGVPLRKAE 71
           R+ K + +A + SR++V+++   Q++K+NG   +  +  V   + T  +    V L   E
Sbjct: 2   RLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVAL---E 58

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
            +  +L HKP G+V+  +D +   TV D +    SR  +  VGRLD +TEGL+L+TN+G 
Sbjct: 59  GSAYYLLHKPAGVVSAVTDQE-HQTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGP 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQK 183
           L   +  PS    + Y V  +G + +D       G+        Q      ++ +LD   
Sbjct: 118 LGYRMLHPSHHVDKFYYVEVNGCLAEDASKFFASGVTFLDGTRCQPAVLTVLEASLD--- 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             ++  T+ L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++
Sbjct: 175 --HSRATIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGAYRQLT 226


>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 =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRRESDELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A VL
Sbjct: 61  VLIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADVL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L  G  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKVGKHR 232


>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 =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 111/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG  +   +  
Sbjct: 14  RLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAVVRVDGARVVLDDSL 73

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 74  VYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLMLLTNDGEL 133

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L+ GI +  G  + D    +D   G    V
Sbjct: 134 AHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAIPGKT-LV 192

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+NR ++++     + V  L+R   G   LG    GS R
Sbjct: 193 RVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVR 237


>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 =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 111/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG  +   +  
Sbjct: 15  RLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPPVAVVRVDGARVVLDDSL 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 75  VYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLMLLTNDGEL 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L+ GI +  G  + D    +D   G    V
Sbjct: 135 AHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAIPGKT-LV 193

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+NR ++++     + V  L+R   G   LG    GS R
Sbjct: 194 RVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVR 238


>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 =  100 bits (249), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 124/246 (50%), Gaps = 10/246 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++ +G+ +R+EV+++I Q RV VNG ++      V+  D + +DG  +R  ++  
Sbjct: 2   RLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALDGEVVRFHKKVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G VT+  DP    T+ + LP +   +  VGRLD + EGLL++TNDG  A  +
Sbjct: 62  I-LFYKPSGYVTSTKDPHS-ETIMEFLPPL-KGIFPVGRLDKDAEGLLIITNDGDFAHRV 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + + 
Sbjct: 119 ISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAK---RVEKLSNDTLKIVIT 175

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGK  +IK++      K   L R   G    G +L    +    + L E+    + E   
Sbjct: 176 EGKYHQIKRMTAAVGLKTVHLKRTRIG----GLVLPDDMKPGEYRFLSEEEVKKVFERED 231

Query: 255 VNLDAP 260
              D P
Sbjct: 232 QKEDTP 237


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/225 (33%), Positives = 111/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG  +   +  
Sbjct: 15  RLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAVVRVDGARVVLDDSL 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 75  VYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGLMLLTNDGEL 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L+ GI +  G  + D    +D   G    V
Sbjct: 135 AHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVDAIPGKT-LV 193

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+NR ++++     + V  L+R   G   LG    GS R
Sbjct: 194 RVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVR 238


>gi|315059155|gb|ADT73484.1| Putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni S3]
          Length = 253

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 117/234 (50%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ ++    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEVKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHR 232


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 116/219 (52%), Gaps = 7/219 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +VQ+     R++K IA +GI SRRE + +I Q  V++NG ++      V  TD +  DG 
Sbjct: 71  LVQQPKDTIRLNKYIANSGICSRREADELIQQGLVEINGKVVTELGYQVQKTDKVVFDGQ 130

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLL 123
            +   E+    L +KP G ++T  D   R TV D L +  S  R+  VGRLD  T G++L
Sbjct: 131 SI-TPEKPVYVLLNKPKGYISTTKDEKARKTVMD-LTANASPYRIFPVGRLDRQTTGVIL 188

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ 182
           LTNDG L + L  PS    ++Y V    ++  + + ++ KGI + +G+   D    +D +
Sbjct: 189 LTNDGHLTKKLTHPSFNIKKIYHVTLDRKLTGEDMAIIAKGIRLEEGVAEVDSISYIDGK 248

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             +   + + +  G NR I+++F+   ++V  L R+ + 
Sbjct: 249 PKNEIGIEIHI--GWNRVIRRIFQRLGYEVEALDRVMFA 285


>gi|315022583|gb|EFT35609.1| Ribosomal large subunit pseudouridine synthase B [Riemerella
           anatipestifer RA-YM]
          Length = 311

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 69/219 (31%), Positives = 116/219 (52%), Gaps = 7/219 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +VQ+     R++K IA +GI SRRE + +I Q  V++NG ++      V  TD +  DG 
Sbjct: 71  LVQQPKDTIRLNKYIANSGICSRREADELIQQGLVEINGKVVTELGYQVQKTDKVVFDGQ 130

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLL 123
            +   E+    L +KP G ++T  D   R TV D L +  S  R+  VGRLD  T G++L
Sbjct: 131 SI-TPEKPVYVLLNKPKGYISTTKDEKARKTVMD-LTANASPYRIFPVGRLDRQTTGVIL 188

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ 182
           LTNDG L + L  PS    ++Y V    ++  + + ++ KGI + +G+   D    +D +
Sbjct: 189 LTNDGHLTKKLTHPSFNIKKIYHVTLDRKLTGEDMAIIAKGIRLEEGVAEVDSISYIDGK 248

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             +   + + +  G NR I+++F+   ++V  L R+ + 
Sbjct: 249 PKNEIGIEIHI--GWNRVIRRIFQRLGYEVEALDRVMFA 285


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 117/230 (50%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  GI SRRE +++I  +RV +NG L E  +  V S D + +DG PL   ++  
Sbjct: 2   RINKFISETGICSRREADKLIESKRVTINGQLAELGST-VASGDDVRIDGQPLGVKKKDV 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT     G    F N P    R+  +GRLD +++GL+LLTNDG +   
Sbjct: 61  YIALNKPVGITCTTELHVKGNIIDFVNHPE---RIFPIGRLDKDSQGLILLTNDGDIVNK 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|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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 118/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE + +IA+  V VNG ++    + V   D +   G  +   E+  
Sbjct: 203 RLNKYIANSGICSRREADDLIAKGLVSVNGKVVTELGLKVSKFDRVVYQGKKIN-PEKPV 261

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  DP  R TV   + +    R+  VGRLD NT GLLL TNDG LA  
Sbjct: 262 YVLLNKPKDFITTTDDPLERKTVMALVGNACEERIFPVGRLDRNTTGLLLFTNDGELAAK 321

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV-TLDTQKGSNAWVT 190
           L  PS Q  ++Y+V     +  +    + +G+ ++   +   DMQV ++D +      + 
Sbjct: 322 LSHPSNQIKKIYQVTLDKPLTHNDEKDILEGLTLEDGEVEVDDMQVLSVDRK-----ILG 376

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++F    ++V  L R+ Y       L  G+ R +S++
Sbjct: 377 LEIHVGKNRIVRRIFAHLGYEVTALDRVMYAGLDKKDLKRGNYRFLSEQ 425


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 121/234 (51%), Gaps = 13/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + +R EV++MI +  V V+G+++++    V     + V    +    +  
Sbjct: 7   RLDKYLADMQVGTRSEVKQMIRKGLVTVDGLIVKKPEEKVDCEKQVVVCSGAIVSYHQYE 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   DP  + TV D +     + +   GRLD +TEGLLL+TNDG LA  
Sbjct: 67  YYMLNKPAGVVSATEDPRDK-TVIDLIEDRRRKDLFPAGRLDKDTEGLLLITNDGALAHD 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAW 188
           L  P     + Y  +  G V ++ + L  KGI I     G+ +VTL         G  + 
Sbjct: 126 LLSPKKHVDKKYYAKIEGTVTEEDVELFGKGIDI-----GEKRVTLPAVLTILSSGEESE 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           +T+ +REGK  ++K++FE    KV  L R+S G   L   LL G  R+++++ L
Sbjct: 181 ITLTIREGKFHQVKRMFEAVGKKVTYLKRLSMGSLVLDEKLLPGEYRKLTEQEL 234


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 114/232 (49%), Gaps = 18/232 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+  +++R G  SR EV  ++ + RV+V G LL +A+  V + + + VD  P+      
Sbjct: 6   ERMDHLLSRLGYCSRSEVRDLLREGRVRVAGELLRKASAKVNAAE-VWVDEEPIDHPHAF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
            L LYHKP+G V  H DP     ++ + P  +      + SVGRLD  T G+LLLT+DG 
Sbjct: 65  YL-LYHKPLGKVCAHDDP---RAIYQDFPLRWRYRRPALSSVGRLDRETSGVLLLTDDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
                  P     RVYRV     +  D  ++L  G ++       C       L  ++  
Sbjct: 121 WLHHWTSPRRAIPRVYRVTLQEPLRSDAADILAAGTLMLDGEDTPCRPAALHCLTERE-- 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              V + L EG+  E++++F   +  V  L R +YGPF L  L AG  RE++
Sbjct: 179 ---VRLTLTEGRYHEVRRMFAALDNLVLTLHREAYGPFLLDDLPAGQWRELT 227


>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 =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 74/232 (31%), Positives = 114/232 (49%), Gaps = 18/232 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+  +++R G  SR EV  ++ + RV+V G LL +A+  V + + + VD  P+      
Sbjct: 20  ERMDHLLSRLGYCSRSEVRDLLREGRVRVAGELLRKASAKVNAAE-VWVDEEPIDHPHAF 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
            L LYHKP+G V  H DP     ++ + P  +      + SVGRLD  T G+LLLT+DG 
Sbjct: 79  YL-LYHKPLGKVCAHDDP---RAIYQDFPLRWRYRRPALSSVGRLDRETSGVLLLTDDGD 134

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
                  P     RVYRV     +  D  ++L  G ++       C       L  ++  
Sbjct: 135 WLHHWTSPRRAIPRVYRVTLQEPLRSDAADILAAGTLMLDGEDTPCRPAALHCLTERE-- 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              V + L EG+  E++++F   +  V  L R +YGPF L  L AG  RE++
Sbjct: 193 ---VRLTLTEGRYHEVRRMFAALDNLVLTLHREAYGPFLLDDLPAGQWRELT 241


>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 =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 78/225 (34%), Positives = 110/225 (48%), Gaps = 27/225 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ K++A  G  SRREV+ ++   RV  NG      AV     +  + +G+ LR     
Sbjct: 2   ERLDKILASTGRWSRREVKELVRAGRVTANG------AVVRSPEEKYQREGLDLRVDGQS 55

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLT 125
              ER    + HKP GLV+   DP  ++TV + LP    ++     GRLD +TEGLLLLT
Sbjct: 56  VLCERYTYLMLHKPAGLVSATEDPR-QATVLELLPEHLRKIGLFPAGRLDRDTEGLLLLT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---- 181
           NDG LA  L  P     + Y V+  GQ+DQ  +   + G+ +     GD  V L      
Sbjct: 115 NDGALAHDLLSPRKHVDKTYFVQVEGQLDQSDVEAFQGGMTL-----GDGLVCLPAGLKL 169

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +    A VT  LREGK  +IK++       V  L R++ GP  L
Sbjct: 170 LEAPDEALVT--LREGKYHQIKRMLAARGKPVRYLKRLTMGPLVL 212


>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 =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 124/246 (50%), Gaps = 13/246 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++  +A+ G+ SRR+VE ++   RVK+NG  +   +  V   D I  DG P+ K E   
Sbjct: 2   RINAFLAKLGLGSRRKVEELVLAGRVKINGSTITDLSFQVNEEDSILFDGKPVTKEEGSD 61

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++  ++KP G +T+H D    +T+F  LP  F +    GRLD+++ GL+LL+ DG  
Sbjct: 62  SRPKIIAFNKPPGFLTSHEDKHHENTIFTLLPESFQKYNYAGRLDLDSRGLILLSIDGNF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGDMQVTLD-TQK 183
            + +  P  +  + Y +     V   K      L + + G  ++ +      V  + T  
Sbjct: 122 IQKVTHPKNKIDKEYIISLKQPVSWKKIAEEFMLGVREGGETLRALAVKPANVFPEKTPP 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKIL 241
           G  +++++ L+EGK R+I+++ +  +  V  L RI  G   L    LL G  + V+++ +
Sbjct: 182 GFTSYLSIVLKEGKKRQIRRMCKTKDLVVLDLYRIRIGKLDLRNFDLLEGKYKVVTEEQV 241

Query: 242 REQLGP 247
              L P
Sbjct: 242 LGNLNP 247


>gi|295093016|emb|CBK82107.1| ribosomal small subunit pseudouridine synthase A [Coprococcus sp.
           ART55/1]
          Length = 241

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 122/231 (52%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   GI SR +V++ + +  V VNG  ++ + V +  + D I+ +G  L  + R 
Sbjct: 2   RLDKFLVEMGIGSRSQVKQYVKKGTVTVNGAPVKSSDVKIDENNDTIKYNGRILNYS-RY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLAR 132
           R +L +KP G V+   D +   TV D L    ++ +S VGRLDI+TEGLLLLTNDG L  
Sbjct: 61  RYFLLNKPAGCVSATKD-NVHQTVIDLLKGENTKDLSPVGRLDIDTEGLLLLTNDGALTH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P+    + Y     G V  D +NL   G+ I   +     D+++       + + +
Sbjct: 120 HLLSPAHHIPKTYYAEIDGYVTDDTINLFATGVDIGDEKPTLPADLRILSSDSTAARSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + + EG+  ++K++FE    KV  L RI+ G  ++  +L  G+ R +S++
Sbjct: 180 ELIITEGRFHQVKRMFEAVGMKVTFLRRIAMGELKIDESLPTGAYRSLSEE 230


>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 =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 119/227 (52%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ +R+IA  R++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQRLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP+   TV + LP      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPE-HPTVLELLPPDHRDDLHIGGRLDYNTTGLMLLTNDGRWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L LP ++  +VY V     +DQ  ++    GI  +      +   L+     +A +T  L
Sbjct: 121 LTLPGSRRDKVYYVETEEPIDQRYVDAFAAGIHFRFEDLVTLPAQLEPLGPRSARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F  F+ +V RL R   G  QL  TL  G+ R ++ +
Sbjct: 179 HEGRYHQVKRMFGHFDNRVLRLHRERMGDIQLDPTLPPGAWRPLNAE 225


>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 =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 122/230 (53%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R+I   RV V+G   E   + V     + V    ++K +R  
Sbjct: 17  RLNKFLSEAGVCSRREADRLIESGRVTVDGRRAE-MGMRVTKDQEVCVGKKVIQKKDRMV 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L   +KP G+V T    + ++ + F N P+   R+  +GRLD ++EGLLL+TN+G +   
Sbjct: 76  LLAVNKPTGIVCTEEKREKKNIIRFLNYPT---RITYIGRLDKDSEGLLLMTNNGDIINK 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y+V  + +V ++ +  + +G+ I        +V    +K       + L
Sbjct: 133 MMRAGNCHEKEYKVTVNKEVTKEFVRKMSEGVPILDTVTRPCKV----EKTGKYKFRIIL 188

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+F ++V RL R+     +LG L +G  REV+ + L E
Sbjct: 189 TQGLNRQIRRMCEYFGYQVTRLERVRVMNIELGNLKSGEYREVTGRELDE 238


>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 =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 121/234 (51%), Gaps = 13/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + +R EV++MI +  V V+G+++++    V     + V    +    +  
Sbjct: 3   RLDKYLADMQVGTRSEVKQMIRKGLVTVDGLIVKKPEEKVDCEKQVVVCSGAIVSYHQYE 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   DP  + TV D +     + +   GRLD +TEGLLL+TNDG LA  
Sbjct: 63  YYMLNKPAGVVSATEDPRDK-TVIDLIEDRRRKDLFPAGRLDKDTEGLLLITNDGALAHD 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAW 188
           L  P     + Y  +  G V ++ + L  KG+ I     G+ +VTL         G  + 
Sbjct: 122 LLSPKKHVDKKYYAKIEGTVTEEDVELFGKGVDI-----GEKRVTLPAVLTILSSGEESE 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           +T+ +REGK  ++K++FE    KV  L R+S G   L   LL G  R+++++ L
Sbjct: 177 ITLTIREGKFHQVKRMFEAVGKKVTYLKRLSMGSLVLDEKLLPGEYRKLTEQEL 230


>gi|167464456|ref|ZP_02329545.1| pseudouridine synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 250

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 130/242 (53%), Gaps = 13/242 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E++++     V VNG +++ +   V    D+IEV+G  +   E  
Sbjct: 6   RLDKMLSHLGYGTRSELKKLAKNGGVTVNGKVVKDSGWKVYPDEDYIEVNGEQVIFREHV 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G+++   D   R+ V   D+   +F  V  VGRLD +TEGLLLLTNDG LA
Sbjct: 66  YVLL-NKPAGVISATEDMRDRTVVDLLDDHIRVFG-VFPVGRLDKDTEGLLLLTNDGKLA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDT---QKGS 185
             L  P     + Y  R +G V ++ + +  +G+V+    Y  M    V LD+   ++  
Sbjct: 124 HNLLSPRKHVPKTYYARVNGDVTEEDVRIFSEGVVLDD-GYMTMPAQLVVLDSGNPEEEK 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|319442276|ref|ZP_07991432.1| putative pseudouridylate synthase [Corynebacterium variabile DSM
           44702]
          Length = 282

 Score =  100 bits (248), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 116/232 (50%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E++I   RV+VNG ++    + V    D I VDGV +   E  
Sbjct: 43  RLQKVLAAAGVASRRMSEKLIEAGRVEVNGSIVTEQGMRVDPENDVIRVDGVRVIADEEI 102

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
             +  +KP G+ +T  D  GR  + D +        R+  VGRLD  TEGLLLLTNDG L
Sbjct: 103 VTFALNKPRGIHSTMHDEFGRPCLSDLVGERVEAGQRLFHVGRLDAQTEGLLLLTNDGEL 162

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y     G+ D+  +  L  GI +  GI   D    +D  +G  + +
Sbjct: 163 ANRLMHPRYGIKKTYLATVLGEADRRLVRQLLDGIELDDGIVIADEVQIIDAWQG-KSLI 221

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + EG+   ++++ +   + V  L+R      QLG    G+ R +++  L
Sbjct: 222 KVVIHEGRKHVVRRMLKEAGFPVQALVRTKVHTVQLGEQKPGTLRALNRSEL 273


>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 = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 128/234 (54%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +++AG+ SRR+ +  + Q +V V+G   E     V     +  +G P+R   +T 
Sbjct: 10  RINKFLSQAGLCSRRQADFYVEQGKVTVDGKTAE-PGTKVCEGQEVCFNGKPVRMDTQTV 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y+KP G+V T S  +  + +  +     SR+  VGRLD +++GL+LLTNDG  A  +
Sbjct: 69  YLAYNKPKGIVCTSSKEEANNII--DAVGYPSRIYPVGRLDKDSQGLILLTNDGEAANEI 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V  + ++  D +  ++ G+ +  +     + T+  ++G +++  + L 
Sbjct: 127 MKARNYHEKEYEVTVNKRITNDFIQGMRNGVPLSELDTVTRKCTVK-KEGPDSFRII-LT 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQL 245
           +G NR+I+++ E+F ++V +L R+     +LG L  GS R+++    K+L+E+L
Sbjct: 185 QGLNRQIRRMCEYFGYRVTKLRRVRVMNIRLGNLKEGSYRKLTPEEIKMLKEEL 238


>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 = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 117/227 (51%), Gaps = 12/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R++K IA  G  SRR+ + +I + RV VN    I+     ++V   D + +DG  ++   
Sbjct: 2   RLNKFIAETGFCSRRKADELINEGRVTVNKHEAII----GMDVKPEDVVRIDGERVKLNT 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R   ++ +KP  ++ ++ D  GR    D + S  +R+ + GRLD  TEGL++++NDG + 
Sbjct: 58  RYEYYILNKPKRVLCSNEDKFGRRLAVDFIKS-RARLFTYGRLDFMTEGLIIISNDGEVY 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y  +   +++   +  L+ G+VI G      +V    +K     + +
Sbjct: 117 NHVMHPRKKLYKSYIAKVSREIEDKDIEALQHGVVIDGKRTAPAKV----KKIDKKELRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + EG+NR+I+K+ E   + VN L RI  G   LG L  G  R +++
Sbjct: 173 AIFEGRNRQIRKMLETLGYNVNSLKRIKVGELTLGNLQVGEYRALNE 219


>gi|226360073|ref|YP_002777851.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226238558|dbj|BAH48906.1| pseudouridine synthase [Rhodococcus opacus B4]
          Length = 350

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 116/225 (51%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AG+ASRR  E +I+Q RV+V+G ++    + +   + +          ++  
Sbjct: 111 RLQKVLAQAGVASRRAAEELISQGRVEVDGRIVIEQGLRIDPENAVVRVDGVRVVVQKDL 170

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L  +KP G  +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 171 VHLALNKPRGWQSTMSDDLGRPCVGDIVSERVAAGQRLFHVGRLDADTEGLLLLTNDGDL 230

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G +++     LK+G+ +  G    D    LD  +G  + V
Sbjct: 231 AHRLMHPSFEVSKTYLATVSGALERGVGKKLKEGVELDDGPAKVDTFTLLDINEG-KSLV 289

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+   ++++F+     V RL+R   G   LG    G+ R
Sbjct: 290 RVTLHEGRKHIVRRLFDAVGHPVIRLVRTDIGAVALGDQRPGTLR 334


>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 = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 132/243 (54%), Gaps = 19/243 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  S   I V G  +  +   
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVEPSLQEITVSGKQVTLSTE- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + ++ +KP G+V+  SD + ++ +      D +P ++     VGRLD +TEG LL+TN+G
Sbjct: 61  KYFILNKPAGVVSAVSDKEHQTVIDLIVESDRVPKLYP----VGRLDRDTEGFLLITNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGS 185
            L   +  P     + Y V  +G++  D     + G+      +C    +++   + + S
Sbjct: 117 PLGYRMLHPKYHVTKTYYVEVNGRLADDTPAFFENGVTFDDGTVCKPAKLEIIESSSEKS 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILR 242
           +A++T+   EGK  ++KK+F  +  KV  L R+++G F+LG L  G  RE++   K+IL+
Sbjct: 177 SAYITIA--EGKFHQVKKMFLAYGVKVTYLKRMTFGEFELGDLPTGHYRELTINEKEILK 234

Query: 243 EQL 245
             L
Sbjct: 235 NYL 237


>gi|312601099|gb|ADQ90354.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 168]
          Length = 236

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 118/237 (49%), Gaps = 30/237 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++  G+ SRR+ E++I Q R+K+N    E A +   V   D IE+D   + K   
Sbjct: 5   RINKFLSEMGVCSRRQSEKLILQGRIKINN---ETAKIGQIVSQNDVIELDQQKITKKPP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
              +  +KP   +T+  DP+ R T+ +     FS+   +  VGRLD  T GL+L+TNDG 
Sbjct: 62  IFWYALNKPKNYITSRFDPENRPTIME----FFSKNEYLFPVGRLDFQTSGLILITNDGK 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------Q 182
               L  PS++  R Y V+    +   ++  L            D ++ LD+       +
Sbjct: 118 TTNKLLHPSSKIERTYLVKTDFSLSDKEIRFL-----------NDNKIQLDSVKSIQKIK 166

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           K S+    V + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++K+
Sbjct: 167 KCSSRTYLVTVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTKQ 223


>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 = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 118/228 (51%), Gaps = 12/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R++K +A AG+ SRR+ + MI + RV VN    ++ AV    + S D + VDG  ++   
Sbjct: 2   RLNKYMADAGVCSRRKADEMIKEGRVTVN----KKEAVLGMEISSGDIVRVDGEKIKLNT 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP  ++ ++ D  GR    D + S   R+ + GRLD  TEGL++++NDG + 
Sbjct: 58  VYEYYMLNKPKRVICSNEDRFGRRLAIDYIKS-KKRLFTYGRLDYMTEGLIIISNDGEVY 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y  +   +V++  +   K G+VI G      +V    +K     + +
Sbjct: 117 NHVMHPRKKLYKSYIAKLSREVEEKDMEAWKHGVVIDGKRTAPAKV----KKIDKKEIRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + EG+NR+I+K+ E   + V  L R+  G   LG L  G  R ++++
Sbjct: 173 AIFEGRNRQIRKMVEILGYTVESLKRVKVGELTLGYLQPGDYRALTEE 220


>gi|254818897|ref|ZP_05223898.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           intracellulare ATCC 13950]
          Length = 247

 Score = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 113/229 (49%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E++I + RV+V+G ++      V      I VDG  +   +  
Sbjct: 8   RLQKVLSQAGIASRRAAEKLIIEGRVEVDGQVVTELGTRVDPDVSVIRVDGARIVLDDSQ 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLTNDG L
Sbjct: 68  VYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDADTEGLILLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L+ GI +  G    D    +D   G    V
Sbjct: 128 AHRLMHPSHEVPKTYLATVTGSVPRGVGKALRAGIELDDGPARVDEFAVVDAIPGKT-LV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR ++++     + V  L+R   GP  LG    GS R + +
Sbjct: 187 RVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGPVSLGKQRPGSFRALGR 235


>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 = 99.8 bits (247), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 110/226 (48%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R    ++I Q  V V+GI++++ A ++     +E DGV L   +R R
Sbjct: 2   RLDKFLCDCSDLTRSLAGKLIRQGEVTVDGIVVKQPAFHINEQSQVEFDGVMLTLDQRNR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V ++ DPD  +  F        ++  VGRLD++T GL+L+T+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSNEDPDHPTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGKWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y V     V QD ++L   G+ ++          L+      A +T+   
Sbjct: 122 TSPRHECAKTYHVWLADPVHQDAISLFADGVFLRNETEKTRPAQLEILAECEARLTI--H 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EGK  ++K++F     KV  L R   G   L   LA G  RE++ +
Sbjct: 180 EGKYHQVKRMFASIGNKVVGLHREQIGTLALDEALAPGEYRELTAE 225


>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 = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 130/242 (53%), Gaps = 13/242 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E++++     V VNG +++ +   V    D+IEV+G  +   E  
Sbjct: 12  RLDKMLSHLGYGTRSELKKLAKNGGVTVNGKVVKDSGWKVYPDEDYIEVNGEQVIFREHV 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G+++   D   R+ V   D+   +F  V  VGRLD +TEGLLLLTNDG LA
Sbjct: 72  YVLL-NKPAGVISATEDMRDRTVVDLLDDHIRVFG-VFPVGRLDKDTEGLLLLTNDGKLA 129

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDT---QKGS 185
             L  P     + Y  R +G V ++ + +  +G+V+    Y  M    V LD+   ++  
Sbjct: 130 HNLLSPRKHVPKTYYARVNGDVTEEDVRIFSEGVVLDD-GYMTMPAQLVVLDSGNPEEEK 188

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            A + + + EGK  ++K++FE  + KV  L RIS G  +L  +L  G++RE++ K L   
Sbjct: 189 PAEIELTIHEGKFHQVKRMFEAVHKKVVYLKRISMGSLKLDPSLSPGASRELTAKELEAL 248

Query: 245 LG 246
            G
Sbjct: 249 QG 250


>gi|295100099|emb|CBK89188.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           cylindroides T2-87]
          Length = 230

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 67/224 (29%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++  G  +R +V+ +I    V + G  +++A   V     + VD  P+   +   
Sbjct: 2   RLDKFLSHMGYGTRNKVKNIIKNGWVTIEGKTIKKADHQVKEDQIVYVDDTPVSYIQY-E 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V+   D +   T+ + +PSI   +  VGRLDI+TEGLLL+ NDG L   L
Sbjct: 61  YYILNKPSGYVSATED-NVHPTIMELIPSIRKDLYPVGRLDIDTEGLLLVCNDGQLTHDL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGL 193
             P     + Y V F G + ++ + +  + + +   I        LDT K   A++T+  
Sbjct: 120 LSPKKHVQKKYYVEFEGTLPENAVEIFNQPMDLDDFIAKPSTLEILDTNK---AYLTIS- 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EGK  ++K++F+    +V  L R+S+GP +L  L  G  R +S
Sbjct: 176 -EGKFHQVKRMFQKIGCEVTYLQRVSFGPLELKNLEIGQARALS 218


>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 = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 75/233 (32%), Positives = 120/233 (51%), Gaps = 14/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +RM+ Q R+ VNG + E     V   D I VDGV +RK E   
Sbjct: 4   RINKYLSEVGFCSRREADRMLEQGRITVNGNIPE-MGTKVSGEDEILVDGVSIRKVEEEH 62

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +++  +KP+G+V T      R  +  F N P    R+  +GRLD  +EGL+LLT+DG + 
Sbjct: 63  VYIALNKPVGIVCTTDTKRERDNIVEFVNHPK---RIFPIGRLDKPSEGLILLTSDGDIV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVT 190
             +        + Y VR    +    L+ ++ G+ I GI     +V  +DT         
Sbjct: 120 NKILRARNNHEKEYIVRVDKPISPQFLHKMRNGVPILGIITNKCEVEQIDT-----LSFR 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E+  ++V +L RI     +L  L  G  R++S + L E
Sbjct: 175 IILTQGLNRQIRRMCEYLGYEVKKLKRIRIMNIKL-DLPIGKWRDLSAQELAE 226


>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 = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 113/229 (49%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  +   E  
Sbjct: 8   RLQKVLSQAGIASRRAAEKLIIDGRVEVDGRVVTELGTRVDPDASVIRVDGARVVLDESL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLTNDG L
Sbjct: 68  VYLALNKPRGMHSTMSDDRGRPCIGDLVERKVRGNKNLFHVGRLDADTEGLILLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     LK GI +  G    D    +D   G    V
Sbjct: 128 AHRLMHPSHEVPKTYLATVTGSVPRGIGKKLKAGIELDDGPARVDDFAVVDAIPGKT-LV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+NR ++++     + V  L+R   GP  LG    GS R +++
Sbjct: 187 RVVLHEGRNRIVRRLLGAAGFPVEALVRTDIGPVSLGKQRPGSIRALNQ 235


>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 = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 125/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRMIYESLERKYAHFVPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLIKIQGFVTKEMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN +V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKIRVVINEGKNRELRRFFAFFNARVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 74/223 (33%), Positives = 116/223 (52%), Gaps = 16/223 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           P R+ + +A  G  +R +V+ M+ + RV++NG  ++ A   V   +D +EVD   +  A 
Sbjct: 16  PMRLDRFLAEMGYGTRTQVKDMVKKGRVRMNGEAVKDADRKVNPESDIVEVDRSRVAYA- 74

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R   ++ +KP G+V+   D    + V     ++   +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 75  RMEYYMLNKPQGVVSATEDRKYPTVVGLIREALRKDLFPVGRLDIDTEGLLLITNDGELA 134

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNA 187
             L  P     +VY     G + +D +   ++GI ++     D  +TL  +    KG+  
Sbjct: 135 HNLLSPKKHVDKVYLAHVSGGLPEDAVKRFEEGIKLE-----DGTMTLPAELKILKGAGP 189

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 V V +REGK  +IK++FE    +V  L RIS GP  L
Sbjct: 190 EEDAQEVLVTIREGKFHQIKRMFEALGCRVEYLKRISMGPLIL 232


>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 = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 120/229 (52%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G+ +RR+V+ +I++  + +N   +      + +  D I++ G  + K ++
Sbjct: 1   MRLDKFLTECGVGTRRDVKNIISKNEITINDKKVNSPKEKIDLENDVIKI-GERVLKYKK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D   + TV + LP   I   +  VGRLD +TEGLLL TN+G +
Sbjct: 60  DRFYIMNKTSGFITATEDTREK-TVMELLPEWVIKKDLFPVGRLDKDTEGLLLFTNNGKI 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y V+   ++D+  +NLL++G+ I G      +V    Q  +N  + 
Sbjct: 119 AHELLSPKKHVDKTYLVKLLKEIDKKSVNLLEEGVDIGGYITKPSKV----QIINNTEIL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + EGK  ++KK+ E    KV  L R+S+G  +LG L  G  +EV  K
Sbjct: 175 LTICEGKFHQVKKMLEAVGNKVIYLKRLSFGNLELGDLPLGEVKEVDLK 223


>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 = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 116/229 (50%), Gaps = 14/229 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN---GILLERAAVNVMSTDHIEVDGVPLRKA 70
           +R+ K++++AGIASRR  E +I +  VK+N    ++ ++A+ N    D I V+G  + + 
Sbjct: 2   ERIQKLLSQAGIASRRSSEELIKKGLVKINDKVALVGQKASFN----DKITVNGKEILQ- 56

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   ++ +KP   V T+ D   R  V D LP+   R+  VGRLD +T G+LLLTNDG L
Sbjct: 57  EKKVYYILNKPAKYVCTNKDNFDRKKVIDLLPNDV-RIFPVGRLDYDTTGVLLLTNDGEL 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  PS + LR YR R    + +  LN L K  +I G         LD     N    
Sbjct: 116 SNKLIHPSFKILRKYRARLDEPLSRQDLNELNKDQIINGKLSSQSVEQLD-----NKTYL 170

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V L +G    +K++F      V  L R+ +    +  +  G  R ++ K
Sbjct: 171 VSLHQGTYHHVKELFSKVGRLVINLKRVEFAGLGVEKIPVGEFRSLTMK 219


>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 = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 16/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I   +V + G ++   A +V   D + ++G  ++  +   
Sbjct: 5   RLNKFISHNTNYSRREADELIKAGKVSIAGRVVSDLATSVDEDDKVRINGRLIKLKKEFT 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D L   F++ +SVGRLD  +EGLLLLT+   +A   
Sbjct: 65  VIVYHKQKGELVSKKDDRGRKTIYDTLDKKFAKFVSVGRLDYASEGLLLLTDAPAIATA- 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQK---------- 183
            L ++   R Y ++  G++ ++ +  +  G   +    G   + T+ + +          
Sbjct: 124 -LMNSDLEREYYLKVKGEISKEVIEAMTNGFFAKDATKGAHAKTTIKSMEFKPFLAYKVF 182

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EG+NRE+++ F +F+ +V  L R+S+G   L  L  G  R
Sbjct: 183 GSSGGYTKLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDMLKPGKWR 236


>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 = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 73/226 (32%), Positives = 113/226 (50%), Gaps = 7/226 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER   
Sbjct: 1   MNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPV-SIERKVY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL 134
            L +KP   VTT  DP  R TV D +    + R+  VGRLD NT G+LLLTNDG LA  L
Sbjct: 60  VLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVTVG 192
             P     ++Y V     + +  +  +  GI ++ G  + D +  T D +K     V + 
Sbjct: 120 THPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISYTDDFKKDQ---VGIE 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 177 IHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSE 222


>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 = 99.4 bits (246), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 117/228 (51%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVA-YQQYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   ++ +    P   +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDKSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +     +   ++++ +  ++   + + 
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVKVFASGMTLGDGTKLKPAELKILMQDKESDQSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E++
Sbjct: 181 IEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPANLKRGQYQEIT 228


>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 = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 113/230 (49%), Gaps = 7/230 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 258 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTV-SIER 316

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 317 KIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLA 376

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGD-MQVTLDTQKGSNAWV 189
             L  P     ++Y V     + +  +  +  GI +  G  + D +  T D +K     V
Sbjct: 377 SKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIHADAISYTDDFKKDD---V 433

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 434 GIEIHSGKNRIVRRIFESLGYKVMKLDRVYFAGLTKKGLRRGEWRYLTEQ 483


>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 = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 67/179 (37%), Positives = 97/179 (54%), Gaps = 2/179 (1%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           I VDG  L  A +  L L +KP GL+TT+ DP GR TV+D L       +  VGRLD  +
Sbjct: 8   ICVDGRRLVSAAKVYL-LLNKPRGLLTTYGDPQGRKTVYDCLAGHDLPFLAPVGRLDCAS 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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                  NAW+ V L EG+NR+I+++      +V RL+R++ G  +LG +  G+ R ++
Sbjct: 127 PLRVGERNAWLEVVLSEGRNRQIRRMMALNGAEVLRLVRVAVGGLRLGDVRKGAFRHLT 185


>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 = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 119/231 (51%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V++ I  Q+V+V+  L      NV  +   I V G  L  +   
Sbjct: 2   RLGKLLGQAGFGSRGQVKKFIRSQQVRVDDELARTGNQNVDPNLQTITVSGKQLSYSPHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP GLV+   D     TV D +  +  R  +  VG LD +TEGL+L+TN+G L 
Sbjct: 62  -YYILNKPAGLVSVVRDQH-YQTVIDLIAVVDRREGLYPVGCLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY-GDMQVTLDTQKGSNAW 188
             L  P     + Y V  +G +  D +     GI      +C    +Q+   + + S A+
Sbjct: 120 FRLLHPKYHVDKTYYVEVNGDLGIDAIAFFDNGIAFLDGTVCKPAKLQIISSSSEVSRAY 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +T+   EGK  ++KK+F  +  KV  L RIS+GPF+LG L  G  RE++ +
Sbjct: 180 ITI--TEGKFHQVKKMFLAYGVKVTYLKRISFGPFELGDLPVGEYRELTAE 228


>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 = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 74/226 (32%), Positives = 117/226 (51%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G+ SRREV+ ++    + VNGI+     +N+  ++D I      L + ++ 
Sbjct: 2   RLDKFLTECGLGSRREVKEILNTGEITVNGIIANNPQMNIKENSDEIFYQERKL-EYKKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D   + TV + LP   I   +  VGRLD +TEGLLLLTNDG L 
Sbjct: 61  RYYILNKKAGYITAVEDSRDQ-TVMELLPDWVIKKDLAPVGRLDKDTEGLLLLTNDGALN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y       + +D+L  L+ G+ I G  Y  M    D  +  +A + +
Sbjct: 120 HKLLSPKNHVEKTYYAELEKDISEDELVKLRNGVDIGG--YITMPAKAD--RIDSAKIHL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++EGK  ++KK+ E    KV  L RIS+G  +L  L  G+ +EV+
Sbjct: 176 TIKEGKFHQVKKMLEAVGNKVIFLKRISFGKLKLDNLELGAVKEVN 221


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 119/230 (51%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R+I   +V V+G   E   + V     I+V    + K     
Sbjct: 7   RLNKFLSEAGVCSRREADRLIEAGKVFVDGRRAE-TGMRVSPAQEIKVGKKVIHKGNEMV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L   +KP G+V T    +  + + F N P+   R+  +GRLD ++EGLLL+TN+G +   
Sbjct: 66  LLAVNKPAGIVCTEEKKEKHNIIRFLNYPT---RITYIGRLDKDSEGLLLMTNNGDIINK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y+V  +  V ++ +  + +G+ I        +V    +   N  +T GL
Sbjct: 123 MMRAGNRHEKEYKVTVNKPVTREFIEKMGQGVPILDTVTRPCKVKAIGKYKFNIVLTQGL 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               NR+I+++ E+F +KV RL R+     QLG+L  G  REV+   +RE
Sbjct: 183 ----NRQIRRMCEYFGYKVTRLERVRVMNIQLGSLKPGEYREVTDDEIRE 228


>gi|317181142|dbj|BAJ58928.1| hypothetical protein HPF32_1346 [Helicobacter pylori F32]
          Length = 257

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 120/236 (50%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRCVIYESLEKKYTHFVPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLKRVRYGFVNLNALPVGKMR 234


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 109/222 (49%), Gaps = 7/222 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A AGI SRR+ ++ I    + VNG ++      V+ +D I     P+R  E+    L +
Sbjct: 1   MANAGICSRRDADKYIQAGVITVNGKVVTELGTKVLRSDDILFHESPVR-LEKKVYVLLN 59

Query: 80  KPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           KP G +TT  DP  R TV + +  +   R+  VGRLD NT G+LLLTNDG LA  L  P 
Sbjct: 60  KPKGCITTSEDPQERKTVMNLVKGACQERIYPVGRLDRNTTGVLLLTNDGELAAKLTHPQ 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREG 196
               ++Y V     V    L  +  GI +    I   D+Q   +T K     + + +  G
Sbjct: 120 FMKKKIYHVYLDKNVSGVDLQKIADGITLDDGEIKADDIQYASETDK---KQIGIEIHSG 176

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           KNR ++++FE   + V +L R+ +       L  G  R +++
Sbjct: 177 KNRIVRRIFESLGYHVVKLDRVYFAGLTKKHLRRGDWRYLTQ 218


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 105/216 (48%), Gaps = 2/216 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I   RVKVNG ++      V  S D + VD   +   E+
Sbjct: 3   ERLQKYMASCGVASRRKCEEIIISNRVKVNGTIVNELGFKVDPSKDKVYVDSKLIFLEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D   R T+ D L  +  R+  +GRLD NT GLLL+TNDG +  
Sbjct: 63  KVYIALNKPEGYVSTVKDERNRKTIMD-LVEVEERIFPIGRLDYNTSGLLLMTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    ++++    G+ I           +  +    + V + 
Sbjct: 122 KIIHPRKEIDKVYIAIIKGVPSDEEIHKFCNGLDIGDYITSKANFEVIDKLEDKSKVRIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           + EGKNR+++++ +     V  L RIS G   L  L
Sbjct: 182 IHEGKNRQVRRMCDKIGHPVIALKRISVGKISLNNL 217


>gi|315648476|ref|ZP_07901575.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315276170|gb|EFU39516.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 253

 Score = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/241 (32%), Positives = 121/241 (50%), Gaps = 14/241 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T QR+ KV++  G  SR E+++M  Q  + VNG +++    +V   TD IE +G  ++  
Sbjct: 7   TTQRLDKVLSNLGFGSRAELKKMAKQGSIVVNGTVMKDPGKHVDPYTDIIEFEGETIQYR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDG 128
           E   + L HKP G+V+   D   R TV D L    +      VGRLD +TEGLLLLTNDG
Sbjct: 67  EYVYIML-HKPPGVVSATEDLRDR-TVLDLLDKDYLVFEPFPVGRLDKDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-- 186
            LA  L  P     + Y     G+V ++   L   G+ +    Y  M   L         
Sbjct: 125 KLAHELLSPRKHIPKTYEAIVEGRVGEEDARLFAAGVTLDD-GYATMPAELVIHSHEERD 183

Query: 187 -----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
                + +++ + EGK  ++K++FE    KV  L R+S G  +L  +L  G+ RE++++ 
Sbjct: 184 DGVILSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRVSMGELRLDKSLEIGTYRELTEEE 243

Query: 241 L 241
           L
Sbjct: 244 L 244


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 111/233 (47%), Gaps = 4/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRR+VE  I   RV   G  +     +V   + + VD V +R  ER  
Sbjct: 2   RLNKYLALCGVGSRRKVEEFIFAGRVVCGGYQVTEPGYDVPDGEIVTVDDVEVR-PERKI 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G +   SD +    + D LP  +   R+  VGRLD+ +EGLL+LTNDG  ++
Sbjct: 61  YMVLHKPRGYICAVSDRN-YPVILDLLPREYDYYRLFPVGRLDLQSEGLLMLTNDGDFSQ 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V      ++ ++  L+ G V +G     + V    ++    W+   
Sbjct: 120 EMIHPRAGITKEYEVLLDRMPNEREMRQLRDGTVFEGKRLHPVGVDFLQREPEGRWLRFV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L EG  REI+ + E    KV  L R   G  +L  L +G  RE S   LR  +
Sbjct: 180 LNEGVKREIRLIAEGAGLKVQVLFRRRIGRMELRHLKSGCAREYSADQLRRMI 232


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 115/226 (50%), Gaps = 4/226 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +A  GIASRR+ E +I   +V VNG ++ +  + V  ++ I V G  + + E+ 
Sbjct: 4   KRIAKHLASCGIASRRKCEDLIFAGKVSVNGEVVRQPQLLVDGSEKITVSGKKVNRQEKK 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+  + + +   G   V D    +  R+ +VGRLD  T GLL++TNDG     
Sbjct: 64  VYFMLNKPLNTLCSPNGKKGSKLVTDLFEGVKERLFTVGRLDKETTGLLIVTNDGEFTNQ 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  PS+   + Y  +   ++  D L  +  G  ++G+    + V    +K   A + V +
Sbjct: 124 VIHPSSNIQKEYIAKTDCEISNDHLKAIAAGTSVEGVFVQPLSV----KKVRKATLKVVV 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EGK RE++ +      +V  L R   G   LG+L  G  R ++++
Sbjct: 180 GEGKKREVRLLIAAAGLEVRALKRTRIGSLTLGSLPIGHWRSLTER 225


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 80/233 (34%), Positives = 123/233 (52%), Gaps = 13/233 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV+A  G  +R+EV+ ++ +  V++NG+  + + V V  + D I+V+G  +   + 
Sbjct: 2   ERLDKVLANLGYGTRKEVKVLVKKGAVEINGVQAKNSDVKVDTNEDIIKVNGETINYRKF 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD +T GLLLLTNDG 
Sbjct: 62  IYLMM-NKPAGVVSATFD-NYDETVIDLLDPEEQIFEP-FPVGRLDKDTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSN 186
           L   L  P     +VY       VD   +   +KGIV+        G +++   T+ GS 
Sbjct: 119 LNHKLISPKYHVDKVYYAEIDKPVDDKDVKCFEKGIVLDDGYKTMPGKLEILKATEHGSE 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            +VT+  +EGK  ++K++FE    KV  L RIS+G   L   L  G  RE+S+
Sbjct: 179 VYVTI--QEGKFHQVKRMFESLGKKVVFLKRISFGGIILDEDLEEGQYREISE 229


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 81/237 (34%), Positives = 121/237 (51%), Gaps = 11/237 (4%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+   +AR+G A SRR+ E MI   RV+VNG +         S+D + +DG   R+ E  
Sbjct: 5   RLQAFLARSGAAPSRRKAEEMIRAGRVRVNGRVASLGERVDPSSDRVSLDG---RRVEPP 61

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             + Y   HKP G +TT  D  GR TV   +P I   ++ VGRLD +T GLLLLTNDG L
Sbjct: 62  SGYAYYALHKPRGYLTTMRDDFGRRTVASLMPRIPG-LVPVGRLDRDTSGLLLLTNDGRL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV- 189
           A  +  PS++  + Y +   G   Q+ L  L  G  ++       +++   ++G  A   
Sbjct: 121 AHRIAHPSSRVEKEYELVVRGDPPQEALRRLAAGPTLEDGPMLPPRLS-HLRRGPRATTF 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + + EG+ R I++       ++  L R+  GP  LG L  G  R +S++ L E LG
Sbjct: 180 HLTIHEGRKRIIRRACAATGLELLSLRRVRVGPVLLGDLAPGRYRPLSEEEL-EGLG 235


>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 = 99.0 bits (245), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 72/210 (34%), Positives = 109/210 (51%), Gaps = 6/210 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++ I+ +GI SRR+ + +I    V VNG ++      +    D +  +G  L K E+ 
Sbjct: 238 RLNRYISNSGICSRRKADELIEAGVVSVNGEVVSELGHKIDPVKDQVRYNGE-LLKREKK 296

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  DP  R TV   +      R+  VGRLD NT GLLL+TNDG LA 
Sbjct: 297 IYVLLNKPKDYITTTDDPQERRTVMQLVEKASRERIYPVGRLDRNTTGLLLMTNDGDLAD 356

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     ++Y V     + Q  LN ++ G+ ++ GI   D  V+  T  GS   V +
Sbjct: 357 KLSHPKNGITKIYHVELSRSLSQGDLNKIQFGLELEDGIIKPD-SVSYVTG-GSKREVGI 414

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            +  GKNR ++++FE   + V +L R+ YG
Sbjct: 415 QIHSGKNRIVRRIFEHLGYDVVKLDRVVYG 444


>gi|291563383|emb|CBL42199.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SS3/4]
          Length = 265

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 121/237 (51%), Gaps = 14/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G  +R E++ MI + R+ VNG+++++    +    D I +D  P+   E  
Sbjct: 23  RLDKYLADMGKGTRTELKEMIRRGRITVNGVIVKKPETKIKKGEDTICLDNAPVEYVE-L 81

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G+++   D   R TV D +     + +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 82  EYYLLNKPQGVISATEDRR-RETVVDLIDEKSRKDLFPVGRLDIDTEGLLLITNDGALAH 140

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--------DTQK 183
            L  P     +VY  R  G V  + +   ++G+ +  G+     ++ +        +T  
Sbjct: 141 RLLAPGHHVDKVYEARCKGFVPDEAVQRFREGMTLADGLSCMPSELEILERKPEDPETGT 200

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
            + + V + L EGK  ++K++ E     V  L R+S GP +L   L  G  R+++ K
Sbjct: 201 AAESLVRLTLHEGKFHQVKRMMEETGCPVLHLKRLSMGPLKLDDALKTGEYRKLTDK 257


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 123/245 (50%), Gaps = 21/245 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKAER 72
           R+++ IA     SRRE +++I+Q RV +      +A ++ +  +   + +DG  +   E 
Sbjct: 2   RLNQYIAHHTKYSRREADKLISQGRVNIEKT---KATLHSLLGANQRVFIDGKKIIPKEH 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +YHKP G + +  D  GR  ++++L + F   + VGRLD  +EGLL+LT+   +AR
Sbjct: 59  FTCIVYHKPKGEIVSKRDERGRRVIYESLEAKFKHFVYVGRLDFASEGLLILTDSTPVAR 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI---CYGDMQVTLDTQKGSNAW- 188
              L  +  LR Y ++ +G + Q+ ++ ++ G++ +      +    +T       N++ 
Sbjct: 119 A--LMESDLLRTYILKINGFITQEIISAMENGLISEDTRVGAHSKSHITSMEFAPFNSYK 176

Query: 189 ----------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                     + V + +GKNRE+++ F  F  +V  L RISYG   L  L  G  R  + 
Sbjct: 177 ILKNDRRYSKIKVSIAQGKNRELRRFFGAFGREVLDLRRISYGFVHLNALPCGKKRFFTH 236

Query: 239 KILRE 243
           +  R+
Sbjct: 237 EEYRD 241


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 114/234 (48%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q +V +NG ++    + V   + I +    ++      
Sbjct: 5   RLNKFISHNTAYSRREADELIKQGKVSINGRVVS-DFIEVSGEEKIRIGSRLIKPKTEFT 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +Y+K  G + T  D  GR T++D+LP  FSR +SVGRLD  +EGLLLLT+   +A   
Sbjct: 64  MIVYNKRKGELVTKKDDRGRRTIYDSLPEGFSRFVSVGRLDFASEGLLLLTDAPAIATA- 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--------------MQVTLD 180
            L ++   R Y ++  G+V ++ +  +++G        G               +   + 
Sbjct: 123 -LMNSDIEREYYLKVKGEVKEEVVTAIREGFFAADASKGAHAKSKIKSMEFKPFLGYRIM 181

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              G    +   + EG+NRE+++ F +F+  V  L R ++G   LG L  G  R
Sbjct: 182 PSSGGYTKIKAIINEGQNRELRRFFGYFDLDVVELKRTAFGRMTLGMLKPGKWR 235


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 124/245 (50%), Gaps = 24/245 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K++   G  +R E+++ + Q RV +NG++++ + +      D +E+DG  +   E 
Sbjct: 8   QRLDKILGHLGYGTRSEIKKYVKQGRVTINGVVVKDSGIQCNPDVDVVELDGEQIFYREF 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTNDGG 129
             L L HKP G+++   D     TV D LP  F +V S   VGRLD +TEGLLLLTNDG 
Sbjct: 68  VYLML-HKPPGVISATEDMR-EKTVIDLLPVDF-QVFSPFPVGRLDKDTEGLLLLTNDGQ 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------- 179
           LA  L  P     + Y     G V  ++    ++G+ +      D  VTL          
Sbjct: 125 LAHDLLSPRKHVPKTYEAVVLGHVGDEEAARFREGVELD-----DGYVTLPAELKVLEHG 179

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            D      + V + + EGK  ++K++FE    +V  L R+S GP  L  +L  G+ RE++
Sbjct: 180 IDADGTRISRVQLTISEGKFHQVKRMFEAVGSRVIYLKRLSMGPLVLDESLPLGAFRELT 239

Query: 238 KKILR 242
           +  L+
Sbjct: 240 ESELQ 244


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 120/245 (48%), Gaps = 24/245 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+   G  SR +++R + Q  + VNG + + + + V    D IEV+G  +   E 
Sbjct: 9   QRLDKVLTHMGYGSRSDIKRQMKQGMITVNGKITKDSGLQVHPYQDQIEVNGERVVFREY 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             + L HKP G+++   D   R TV D L +         VGRLD +TEGLLLLTNDG L
Sbjct: 69  IYIML-HKPPGVISATEDSRER-TVLDLLSAEERHFEPFPVGRLDKDTEGLLLLTNDGKL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------- 182
           A  L  P     + Y     G V ++ ++    G+ +      D  VTL  Q        
Sbjct: 127 AHELLSPRRHVPKTYEATVSGHVTEEDIHQFTAGVELD-----DGYVTLPAQLTILRHEH 181

Query: 183 -----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREV 236
                 G  +++++ + EGK  ++K++FE    KV  L R + GP +L   L  GS RE+
Sbjct: 182 PYQADGGVISYISLVIHEGKFHQVKRMFEAVGKKVTYLKRTAMGPLKLDEQLPMGSYREL 241

Query: 237 SKKIL 241
           + + L
Sbjct: 242 TNEEL 246


>gi|332884211|gb|EGK04479.1| hypothetical protein HMPREF9456_00806 [Dysgonomonas mossii DSM
           22836]
          Length = 289

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 134/244 (54%), Gaps = 14/244 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +G  SRRE +++I Q  V +NG   +RA++   V++   ++V G  +    +
Sbjct: 2   RINKYISDSGYCSRREADKLIEQGSVTING---KRASIGSQVLAGQEVKVYGETVTCNTQ 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                Y+KP+G+V+T +D D  + + D +     R+  +GRLD +++GL++LTN+G +  
Sbjct: 59  PVFIAYNKPVGIVST-TDLDEPNNIIDAVGH-DERIFPIGRLDKDSQGLIILTNEGDMVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +++D +  ++ G+ I G+     +V    + G++++  V 
Sbjct: 117 KMLRADNNHEKEYHVTVDKLINEDFVKKMQGGVPILGVVTRKCEV---VKTGTHSFNIV- 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLGPHL 249
           LR+G NR+I+++ E+  + V RL RI     +LG +  G  R ++K   +ILR++    +
Sbjct: 173 LRQGLNRQIRRMCEYLGYNVVRLERIRIMHIKLGNIKVGQWRNITKEELEILRKKTASSV 232

Query: 250 LEEA 253
             E+
Sbjct: 233 KTES 236


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 58/126 (46%), Positives = 77/126 (61%), Gaps = 7/126 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNG----ILLERAAVNVMSTDHIEVDGVP 66
            +P R+ K +A +GI SRR+ E++I   RV +NG    IL  +   ++   D I VDG  
Sbjct: 97  MSPVRLQKFLAASGICSRRKAEQLILDGRVTLNGETVLILGTKITPDI---DKITVDGKL 153

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +++ E+   +L +KP G VTT SDP GR  V D L  I  RV  VGRLD +TEG LLLTN
Sbjct: 154 VKEEEQKVYYLLNKPKGYVTTLSDPQGRPVVTDLLHGINERVFPVGRLDFDTEGALLLTN 213

Query: 127 DGGLAR 132
           DG LA+
Sbjct: 214 DGDLAQ 219


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 119/221 (53%), Gaps = 3/221 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R++K +A  G+ASRR+++  I + ++ VNGIL   +   V + D I V+G  +  K E+ 
Sbjct: 7   RINKFLASKGVASRRQIDLWIEEGKILVNGILAT-SGQKVSAEDKILVNGKMISEKEEKK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +K   +++   D  GR TV D +P+  +R+  VGRLD  T GL+LLTNDG L   
Sbjct: 66  VYYILYKEEEVLSAVKDERGRKTVVDCIPTK-ARIFPVGRLDYRTSGLILLTNDGELFNR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V   G + +++L  L++G+ ++     +  V     +  N +  + +
Sbjct: 125 VMHPRAEIFKTYEVLAKGHLTREQLKTLEEGVELEEGKTLEALVAKVKYEKGNTFFEISI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           REG+NR+I+++ E    +V RL R   G   L  L  G  R
Sbjct: 185 REGRNRQIRRMVEAVGSRVYRLRRTKIGRLSLEGLKLGQYR 225


>gi|317013226|gb|ADU83834.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori Lithuania75]
          Length = 257

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAV-- 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
           V  L      + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 119 VSALMHADLEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/208 (33%), Positives = 104/208 (50%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+++ I+ AGI SRR+ + +I    V VNG ++      V    D I  +G  L++ E+ 
Sbjct: 283 RLNRYISNAGICSRRKADELIVAGVVSVNGQVISELGFKVDPYKDEIRYNGETLKR-EKM 341

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  DP  R TV   +      R+  +GRLD NT GLLL+TNDG LA 
Sbjct: 342 VYVLLNKPKDYITTTEDPQERRTVMHLVDKASKERIYPIGRLDRNTTGLLLMTNDGDLAD 401

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P +   ++Y V     + Q  LN +  GI ++        V+   Q  S   V + 
Sbjct: 402 KLSHPKSNISKLYHVELDKSLSQGDLNKIAYGIELEDGLIKPDSVSY-VQGASKREVGIQ 460

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  GKNR ++++FE   + V +L R  Y
Sbjct: 461 IHSGKNRVVRRIFESLGYDVVKLDRAIY 488


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 118/234 (50%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G ++      V  +   I VDG  +   +  
Sbjct: 8   RLQKVLSQAGIASRRVAEKMIRDGRVEVDGRIVTELGTRVDPAASVIRVDGARITVDDTL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGLLLLTNDG L
Sbjct: 68  VYLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L++G+ ++ G    D    +DT  G    V
Sbjct: 128 AHRLMHPSFEVPKSYVATVLGSVPKGLGRKLREGVELEDGPVQVDDFAVVDTTPG-RTLV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V L EG+   ++++     + V  L+R   G   LG    GS R +++K + E
Sbjct: 187 RVTLHEGRKHIVRRLLAEVGFPVQELVRTDIGTVSLGDQRPGSIRVLTQKEIGE 240


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 80/225 (35%), Positives = 117/225 (52%), Gaps = 2/225 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +ARAG+ SRR  E ++   RV VNG +       +    D I VDG  +     
Sbjct: 2   ERLHKFLARAGVDSRRACEELMLAGRVSVNGRVQRELGTQIDPDKDDIRVDGEQITPPTE 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L HKP  ++TT  DP+GR TV D L    +R+  VGRLD ++EGLLLLT+DG L  
Sbjct: 62  LHYVLLHKPSSVMTTLHDPEGRQTVAD-LVKSHNRLFPVGRLDYDSEGLLLLTDDGDLTF 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y+   +     ++L   + G+ +         + L  +     WV V 
Sbjct: 121 RLTHPSFEVEKEYQALLNQTPSVEQLREWRNGVELDDGKTAPAWIELLNETADGTWVRVV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EG+NR+I++V E    +V RLIR+  GP  LG L AG  R ++
Sbjct: 181 IHEGRNRQIRRVAEALGLEVRRLIRLREGPLTLGELQAGQWRALT 225


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/229 (33%), Positives = 116/229 (50%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+++AG+ASRR  E +IA  RV+V+G ++      V   +  I VDG  +   +  
Sbjct: 11  RLQKVLSQAGVASRRAAEDLIAAGRVEVDGEVVTELGRRVHPDEAVIHVDGTRVNLRDDL 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
               ++KP G+ +T SD  GR  V D L   +     V+ VGRLD NTEGLLLLTNDG L
Sbjct: 71  VYLAFNKPKGVHSTMSDDRGRPCVGDYLRGRWEETPGVVHVGRLDENTEGLLLLTNDGDL 130

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  PS + L+ Y     G V +     L+ G  +  GI   D     D   G  + +
Sbjct: 131 GHRLMHPSYRVLKTYFAEVEGLVPRGLGKELRAGWELPDGIVKVDQFRVKDMHSG-RSMI 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + + EG+   ++++       V +L+R + G  QLG    G+ R +++
Sbjct: 190 ELVIHEGRKHIVRRLMAATGHPVRKLVRTAVGDVQLGNQRQGTIRRLNR 238


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/220 (34%), Positives = 111/220 (50%), Gaps = 9/220 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           RV K +  AG  +R E +++    RV++NG  ++ AA +   + D +EVDG  L   E  
Sbjct: 5   RVDKWLTTAGYGTRSEAKKLCRAGRVRLNGETVKDAAKHADPAVDVLEVDG-ELVPYEPL 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G V++  DP  R  V   L     I+  V  VGRLD + EGLLLLTNDG L
Sbjct: 64  VYFMMYKPPGYVSSTEDP--RDPVVIELLDEEDIWRDVFPVGRLDKDAEGLLLLTNDGPL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWV 189
           A  L  P     + Y VR  G + +     L +G+V+    Y  M   L+  + G+ +  
Sbjct: 122 AHRLLAPKRHVPKRYFVRVRGALGEGDARALAEGVVLDD-GYKAMPAELEILRSGAESEA 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            + + EGK  ++K++F     +V  L RIS GP  L   L
Sbjct: 181 IIQVYEGKYHQVKRMFASLGKRVTFLKRISMGPLSLDPAL 220


>gi|257870927|ref|ZP_05650580.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257805091|gb|EEV33913.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 237

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/229 (33%), Positives = 126/229 (55%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      SR+E++R+  Q +V V+  +    + NV S  H I+V GV L+   R 
Sbjct: 2   RIDKLIEERLATSRKEMKRLFQQGKVLVDQQIERNPSRNVDSRLHEIKVAGVLLQT--RD 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+VT + D    +TV D L      + + +VGRLD +TEGL+LLT +G L 
Sbjct: 60  VYYLLNKPAGVVTANIDHQ-HATVIDLLQPEDRQATLYAVGRLDRDTEGLVLLTTNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
             L  P+ +  + Y V  +G V  + +    +GIV  G  +C    ++T++   G  ++V
Sbjct: 119 YELLHPNKKVPKRYDVIVNGPVTAEDVAAFAQGIVFHGGVVCQ-PAKLTIEMTSGRRSFV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + + EGK  ++KK+F     KV  L R++ GP +LG LL+G  R +++
Sbjct: 178 HLEIAEGKFHQVKKMFLARGKKVIALKRVAIGPLELGDLLSGEYRNLTQ 226


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 115/222 (51%), Gaps = 17/222 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA---VNVMSTDHIEVDGVPLR 68
           T  R++K IA AG+ SR++  R+I +  V VN     R A    +V   D I V+G  ++
Sbjct: 3   TKIRLAKYIAHAGVCSRKQASRLIDEGAVIVNN----RPANHIDHVDEQDQITVNGQIIK 58

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                  + YHKP+G +    D +  ++++ +LP+I +RV  +GRLD ++ GLL+LTNDG
Sbjct: 59  GTAELIYFAYHKPVG-IDCKLDQNDPASLYHHLPTI-TRVYPIGRLDKDSRGLLILTNDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSN 186
            L   L  P     + Y V  +  +D +    +  G+ +      D Q+TL    +K ++
Sbjct: 117 ELCNQLIHPDFHQPKRYLVSVNKSIDAEFCTKMAAGVPV------DKQITLPCSVEKIAD 170

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              ++ L++G NR+I+K+  +  +KV  L R       L TL
Sbjct: 171 KQFSIILKQGLNRQIRKMAHYCGYKVIDLYREQISELTLQTL 212


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 114/226 (50%), Gaps = 12/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R++K IA +G  SRR+ + +I   RV +N    +  AV    V   D + +DG  +   +
Sbjct: 2   RINKYIAESGFCSRRKADELIIDGRVTIN----KNIAVIGSEVEDGDIVRIDGEKVTVKK 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP  ++ ++ D  GR+     + S   R+ + GRLD  TEGL++++NDG + 
Sbjct: 58  EYEYYILNKPKRVLCSNEDRQGRTLAVSLIKS-KKRLFTYGRLDYMTEGLIIISNDGDIY 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y  +    +  D +  LK G+VI G+     +V   T++     V V
Sbjct: 117 NNVMHPKKKLYKSYIAKIDSDITDDHIEALKYGVVIDGVRTLPAKVKTITKR----EVRV 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG+NR+I+K+FE   + V  L R+  G   L  L  G  R+++
Sbjct: 173 AIHEGRNRQIRKMFEVLGYTVKTLRRVKVGELSLKGLEVGKYRKMT 218


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 114/221 (51%), Gaps = 19/221 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--------P 66
           R+++ +A  G+ SRR+ E +I +  +++NG    +   N+ +    E+D V        P
Sbjct: 16  RLNRFLADCGLGSRRKTEELIQKGHIEING----KRVTNLGTRIDPEIDVVSYLGDVVKP 71

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E  ++ +++KPIG + +H+D     T+F  LPS +      GRLD+N+ GLL+LTN
Sbjct: 72  I--VESKKILIFNKPIGYLCSHADRFHEKTIFSLLPSDYKNFKIAGRLDLNSRGLLILTN 129

Query: 127 DGGLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKG 184
           DG LA+ +  PS    + Y V   H   ++      +KGI+  G I +  M   +    G
Sbjct: 130 DGALAQKITHPSNGSEKEYLVTLKHDPGEKLIQAAFQKGILDAGEILHAKM---VKLVPG 186

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 V L EGK R+I+++F +F   V  L RI  GP +L
Sbjct: 187 KKCVYRVILEEGKKRQIRRMFRWFGVSVVDLQRIRIGPLKL 227


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 114/221 (51%), Gaps = 19/221 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--------P 66
           R+++ +A  G+ SRR+ E +I +  +++NG    +   N+ +    E+D V        P
Sbjct: 16  RLNRFLADCGLGSRRKTEELIQKGHIEING----KRVTNLGTRIDPEIDVVSYLGDVVKP 71

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E  ++ +++KPIG + +H+D     T+F  LPS +      GRLD+N+ GLL+LTN
Sbjct: 72  I--VESKKILIFNKPIGYLCSHADRFHEKTIFSLLPSDYKNFKIAGRLDLNSRGLLILTN 129

Query: 127 DGGLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKG 184
           DG LA+ +  PS    + Y V   H   ++      +KGI+  G I +  M   +    G
Sbjct: 130 DGALAQKITHPSNGSEKEYLVTLKHDPGEKLIQAAFQKGILDAGEILHAKM---VKLVPG 186

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 V L EGK R+I+++F +F   V  L RI  GP +L
Sbjct: 187 KKCVYRVILEEGKKRQIRRMFRWFGVSVVDLQRIRIGPLKL 227


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 118/228 (51%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDH----IEVDGVPLRK 69
           R++K +A+ GI+SRRE  R+I   R+ +NG + +   AV+V +  H    + +D  P+  
Sbjct: 2   RLAKYLAQCGISSRREACRLIEAGRISLNGKIAKHTDAVHVDADGHCLDSLCLDEKPISG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE    W+++K +G      D D +S++   LP+   R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  AEALSYWIFNKAVGTDCRLLDAD-KSSLLHLLPTT-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y V+     +   +  +  G+  + +     QVT    + S+   
Sbjct: 120 LTHKLMHPSFAHSKTYHVQLDRPFNDAFIEQMASGVQYKEVRTLPCQVT----RLSDVSF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L +G NR+I+++     +KV  L R++     LG+L  G  R +S
Sbjct: 176 EIVLTQGLNRQIRRMSNALGYKVVDLQRVALMTLTLGSLAEGEMRPLS 223


>gi|261840134|gb|ACX99899.1| pseudouridylate synthase [Helicobacter pylori 52]
          Length = 257

 Score = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 124/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRHVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 120/237 (50%), Gaps = 19/237 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRKAERT 73
           R+ K +A AG  +R EV++ I++ +V+VNG  +   A  +   + +EV  +  +   +R 
Sbjct: 5   RLDKYLADAGAGTRSEVKKYISKAQVQVNGKTVLNPAEKI-EPEEVEVCCLGQVVHVDRY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L HKP G V+   D   R TV + +PS    +  VGRLD +TEGLLL+TNDG LA  
Sbjct: 64  EYYLLHKPAGCVSATEDVRER-TVMEFVPSRRKDLFPVGRLDKDTEGLLLITNDGELAHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------LDTQKGSN 186
           L  P     + Y  +  G++ Q+     ++G+ I     G+   T       L  + G  
Sbjct: 123 LLAPRRHVPKQYFAQIKGKMTQEDAQKFRQGVEI-----GEKNPTLPAKLEILSVENGEE 177

Query: 187 AWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            W++   + + EGK  +IK++ +    +V  L RIS GP  L   L  G  R +++K
Sbjct: 178 GWISCINLTIEEGKFHQIKRMVQAVGKEVIYLKRISMGPLYLDENLERGQCRPLTEK 234


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 124/245 (50%), Gaps = 29/245 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRKA 70
           R+++ IA     SRRE +++I   RV +     E++  ++ S       + +DG  +   
Sbjct: 2   RLNQYIAHHTKYSRREADKLIESGRVNI-----EKSKASLQSVLREGMSVFIDGKRIVPK 56

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+    +YHK  G + + SD  GR  ++D+L S F   + VGRLD  +EGLL+LT+   +
Sbjct: 57  EQFTCIVYHKQKGELVSKSDERGRKVIYDSLESRFKHFMYVGRLDFASEGLLILTDSTPV 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------------IQGICYGD 174
           A+   L  +   RVY V+ +G++ ++ +  ++KG+V                ++   +  
Sbjct: 117 AKA--LMESHLERVYLVKINGEITKEIIEAMEKGLVSEDARAGGHIKSNIVAMEFAPFAH 174

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            ++  + ++ S   + V + EGKNRE+++ F  F  +V  L RI+YG   L  L  G  R
Sbjct: 175 YEILKNDKRHSK--LKVSITEGKNRELRRFFGVFGREVLDLRRIAYGFVNLNALPCGKKR 232

Query: 235 EVSKK 239
             +K+
Sbjct: 233 YFTKE 237


>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 = 98.2 bits (243), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 124/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAQLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 120/230 (52%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ASRR  E +IA  RV+V+G ++    + +   T  I+VDG  +   E  
Sbjct: 123 RLQKVLAAAGVASRRGAEELIAAGRVEVDGEVVVEQGLRIDPDTAIIKVDGARVVIDESK 182

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +KP G  +T SD  GR  + D +        R+  VGRLD +TEGLLLLTNDG L
Sbjct: 183 QYLALNKPKGWHSTMSDDQGRPCIGDIIAERVMAGQRLFHVGRLDADTEGLLLLTNDGEL 242

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G+V++     L++G+ ++ G    D    L+  +G  + V
Sbjct: 243 AHRLMHPSYEVPKTYLATVRGEVNRGLGRELRQGVELEDGPVAVDSFALLEVNQG-KSLV 301

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + L EG+ R ++++     + V  L+R   GP  LG    GS R +  K
Sbjct: 302 RLTLHEGRKRVVRRLLAEVGFPVVGLVRTDIGPVTLGKQRPGSLRVLDNK 351


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/218 (33%), Positives = 114/218 (52%), Gaps = 11/218 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V    D I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTEFDEILFDGEKINYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   DP  + TV D LP          VGRLD +TEGLLL+TNDG L
Sbjct: 64  IYIMM-NKPKGVISATYDPIEK-TVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGNL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           A  L  P    ++ Y     G V++  +   K+GIV++        D+++ L ++     
Sbjct: 122 AHKLLSPKKNVIKKYYAEILGFVNERDIKAFKEGIVLEDGYKTLPADLEILLSSEVSK-- 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V V +REGK  +IK++FE    KV  L R++ G   L
Sbjct: 180 -VYVYIREGKYHQIKRMFESVGKKVVYLKRLAMGSLTL 216


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 114/229 (49%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+++AG+ASRR  E +I   RV+V+G ++      V      I VDG  +   +  
Sbjct: 11  RLQKVLSQAGVASRRAAEDLIVAGRVEVDGEVVTELGRRVDPDAAIIHVDGTRVNLRDDL 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D L   +     V+ VGRLD NTEGLLLLTNDG L
Sbjct: 71  IYLALNKPKGVHSTMSDDRGRPCVGDYLRGRYEETPGVVHVGRLDENTEGLLLLTNDGDL 130

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  PS + L+ Y     G V +     L+ G  +  GI   D     D   G  + V
Sbjct: 131 GHRLMHPSYRVLKTYLAEVDGLVPRGLGKELRNGWELPDGIVKVDQFRVKDMHSG-KSLV 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + + EGK   ++++ +     V +L+R + G  QLG    GS R ++K
Sbjct: 190 ELVIHEGKKHIVRRLLKDTGHPVLKLVRTAVGDVQLGNQRVGSIRRLTK 238


>gi|160901833|ref|YP_001567414.1| pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359477|gb|ABX31091.1| pseudouridine synthase [Petrotoga mobilis SJ95]
          Length = 220

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/219 (32%), Positives = 114/219 (52%), Gaps = 15/219 (6%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPL------RKAERTRLWLYHKPIGLVTTHSDPDG 93
           +KVNG L++     +   + IE +          +KAE    +L +KP G++ T  D  G
Sbjct: 1   MKVNGKLVKEPWYELKENNFIEFNNKKYGLSDLQKKAENKVYYLLNKPKGILCTFKDDFG 60

Query: 94  RSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           R T+ D +   I  RV  VGRLD ++ GLLLLTNDG LA  L  P  +  +VY V   G 
Sbjct: 61  RKTINDLIKGKIEERVFYVGRLDYDSSGLLLLTNDGDLANYLLRPENKVTKVYEVLVKGS 120

Query: 153 VDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             + +L +L++GI ++ G      +V +  ++   + + + L EGK R+IK + +   +K
Sbjct: 121 PSKKELQMLEEGITLETGYKTMKSKVKILKKQKDLSLLQISLNEGKKRQIKLMIKALGYK 180

Query: 212 VNRLIRISYGPFQL------GTLLA-GSTREVSKKILRE 243
           V  L RI +GP+ +      G + + GS  EV  ++L +
Sbjct: 181 VIELKRIKFGPWSIKEVPKPGNIKSLGSMEEVKNRLLSD 219


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 120/230 (52%), Gaps = 20/230 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           PQR++KV+A AG+ASRR  E +I Q +  VNG +       V +S D I V+G  + K  
Sbjct: 156 PQRLAKVLAAAGVASRRTSEELIFQGKXTVNGSVCTSPQTKVDISKDSIYVNGNRISKKL 215

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTV--FDN-----------LPSIFSRVISVGRLDIN 117
             +L+   +KP G + +  + + +S V  F++           LP    R+ +VGRLD+ 
Sbjct: 216 PPKLYFAVNKPKGYICSCGE-ESKSVVSLFNDYLKGWNKIQPGLPK--PRLFTVGRLDVA 272

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQ 176
           T GL+++TNDG  A+ L  PS+   + Y V   G V +  L  + +G  I G+ C  D+ 
Sbjct: 273 TAGLIIVTNDGEFAQKLAHPSSNVTKEYVVTIDGAVHKKHLIAISEGTKIDGVMCIPDLV 332

Query: 177 VTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             L  Q  +    + + + EG+N E++++ +    +V  L R+  G F+L
Sbjct: 333 EPLAAQSDTRKTRLRIVVHEGRNHEVRELVQNAGLQVYALKRVRIGRFRL 382


>gi|207091745|ref|ZP_03239532.1| hypothetical protein HpylHP_01046 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 257

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 119/236 (50%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKCSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R
Sbjct: 179 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMR 234


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 116/235 (49%), Gaps = 30/235 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++  G+ SRR+ E++I Q R+K+N    E A +   V   D IE+D   + K   
Sbjct: 5   RINKFLSEMGVCSRRQSEKLILQGRIKINN---ETAKIGQIVSQNDVIELDQQKITKKPP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
              +  +KP   +T+  DP+ R T+ +     FS+   +  VGRLD  T GL+L+TNDG 
Sbjct: 62  IFWYALNKPKNYITSRFDPENRPTIME----FFSKNEYLFPVGRLDFQTTGLILITNDGK 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------Q 182
               L  PS++  R Y V+    +   ++  L            D ++ LD+       +
Sbjct: 118 TTNKLLHPSSKIERTYLVKTDFSLSDKEIRFL-----------NDNKIQLDSVKSIQKIK 166

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           K S+    V + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++
Sbjct: 167 KCSSRTYLVTVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLT 221


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 112/229 (48%), Gaps = 5/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 230 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVVKFHDETV-SIER 288

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 289 KVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTTGVLLLTNDGDLA 348

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y V     + +  ++ +  GI ++ G  + D     D  K     V 
Sbjct: 349 SKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIHADAISYSDEVK--RDQVG 406

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 407 IEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 455


>gi|72080505|ref|YP_287563.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 7448]
          Length = 237

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 116/235 (49%), Gaps = 30/235 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++  G+ SRR+ E++I Q R+K+N    E A +   V   D IE+D   + K   
Sbjct: 2   RINKFLSEMGVCSRRQSEKLILQGRIKINN---ETAKIGQIVSQNDVIELDQQKITKKPP 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
              +  +KP   +T+  DP+ R T+ +     FS+   +  VGRLD  T GL+L+TNDG 
Sbjct: 59  IFWYALNKPKNYITSRFDPENRPTIME----FFSKNEYLFPVGRLDFQTTGLILITNDGK 114

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------Q 182
               L  PS++  R Y V+    +   ++  L            D ++ LD+       +
Sbjct: 115 TTNKLLHPSSKIERTYLVKTDFSLSDKEIRFL-----------NDNKIQLDSVKSIQKIK 163

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           K S+    V + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++
Sbjct: 164 KCSSRTYLVTVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLT 218


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/222 (33%), Positives = 115/222 (51%), Gaps = 8/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I   RV VNG ++L++     +  D I VDGV +   ++ 
Sbjct: 2   RLDKLLANKAFGSRKEVHQIIRDGRVTVNGAVILKKDQSIHIDDDIIAVDGVQISTKQQY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            +  +HKP G +T   DP     V D LP  F +  V  VGRLD +TEGLLLLTNDG  A
Sbjct: 62  YIK-FHKPAGYITAVEDPT-HPVVMDLLPPEFKKMGVFPVGRLDKDTEGLLLLTNDGIWA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        +VY V F+G++ +D L  ++ GIV+ G         +D     +  +T+
Sbjct: 120 HSIINGHKHVPKVYYVEFNGKLTKDGLERIETGIVL-GDGTQCKPANIDVLSEQSLHITI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              EGK  ++K++      +V  L R+S G   L  + A +T
Sbjct: 179 --EEGKYHQVKRMIGAAGGEVTYLKRLSIGHITLNGIEAINT 218


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 116/248 (46%), Gaps = 25/248 (10%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRK 69
            T  R+S  +A  G+ASRR+  R+I   RV +N  L +    VN    + I VD  P+  
Sbjct: 1   MTSMRLSHYLAVCGVASRRQAARLIDTGRVSINHQLAKHTDRVNFCEIETILVDDKPILA 60

Query: 70  AERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +  + WLYHKP+G+       DP     V   LP    R+   GRLD ++ GLLLLTND
Sbjct: 61  VQDKQYWLYHKPVGIDCRLLVDDPHSLLHVLPELP----RLYPAGRLDKDSRGLLLLTND 116

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGS- 185
           G L + L  P     + Y V+    +    L+++       G+ YGD+Q  + D +  S 
Sbjct: 117 GQLTQALMHPDYYHPKTYVVQVDKPISTSFLSMMAN-----GVSYGDVQTRSCDIRPLSL 171

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                   + L +G NR+I+++ +   +KV  L+R          LL     E+++K +R
Sbjct: 172 TAEEDRFEIVLTQGLNRQIRRMCQTLGYKVIDLMRTQ--------LLDIRIDELAEKTMR 223

Query: 243 EQLGPHLL 250
                 LL
Sbjct: 224 PLTAAELL 231


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 112/229 (48%), Gaps = 5/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 230 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVVKFHDETV-SIER 288

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 289 KVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTTGVLLLTNDGDLA 348

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y V     + +  ++ +  GI ++ G  + D     D  K     V 
Sbjct: 349 SKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIHADAISYSDEVK--RDQVG 406

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 407 IEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 455


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 66/211 (31%), Positives = 111/211 (52%), Gaps = 6/211 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++  GI +R+EV  +I   RV VN   +   A  +   D ++VDG  +   E+  
Sbjct: 2   RLDRYLSNRGIGTRKEVRALIKHGRVTVNDRTVLDPAYKLSDKDVVKVDGKVIDLPEKVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G VT+  DP    T+ + LP I   +  VGRLD + EGLLL+TNDG  A  +
Sbjct: 62  I-LFYKPAGYVTSTRDPHS-ETIMEFLPDI-KGIFPVGRLDKDAEGLLLVTNDGEFAHRV 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y V+  G++ +DKL  L++G+ ++   +   +     +K SN  V + + 
Sbjct: 119 ISPRWKVEKEYVVKVEGEITEDKLEKLRRGVSLRDGFFAKAK---HVEKISNDTVKIVIT 175

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EGK  ++K++      K   L R+  G  +L
Sbjct: 176 EGKYHQVKRMMAAVGLKTIHLKRVRIGGLRL 206


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 117/230 (50%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ SR E++R I  +RV VNG+ +    + +   D I  D   +   +   
Sbjct: 9   RIDKYLANMGVGSRSEIKRYIKNKRVMVNGVYITDNGLIINLDDDIIFDEEKISYRKFVY 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + + +KP G+++   D   ++TV D L PS     +   GRLD +TEG LLLTNDG LA 
Sbjct: 69  IMM-NKPQGVISATEDK-YQNTVLDLLDPSYLHFDLFPAGRLDKDTEGFLLLTNDGKLAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
            +  P     + Y V   G +  + ++     I+I     C       LD+   S A+VT
Sbjct: 127 NMLSPKKHVEKKYYVEVIGHLVNEDIDAFSGNIIIDDGYECMPAKLEILDSNDISKAYVT 186

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           +  +EGK  +IK++FE    +V  L R++ GP +L   L  G  RE++++
Sbjct: 187 I--KEGKFHQIKRMFEAIGKEVTYLKRLTMGPLKLDENLELGEYRELTEQ 234


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 112/229 (48%), Gaps = 5/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER
Sbjct: 230 PIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVVKFHDETV-SIER 288

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 289 KVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTTGVLLLTNDGDLA 348

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y V     + +  ++ +  GI ++ G  + D     D  K     V 
Sbjct: 349 SKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIHADAISYSDEVK--RDQVG 406

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 407 IEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 455


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAV-- 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
           V  L      + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 119 VSALMHADLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 77/232 (33%), Positives = 122/232 (52%), Gaps = 21/232 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKA 70
           R+ K++   G  SRR V+R+I  ++V+VNG++   A V+ ++ D     + V G  +R  
Sbjct: 2   RLDKLLFETGFGSRRTVKRLIKSKQVQVNGLI---ALVDNLNVDPQLQEVIVSGELIRFQ 58

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINTEGLLLL 124
                ++ HKP G+V+  SD   + TV D       +P +F     VGRLD +TEGLLLL
Sbjct: 59  PHVY-YMLHKPAGVVSAVSDVLNQ-TVIDLIEPSQRVPGLFP----VGRLDKDTEGLLLL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQK 183
           TN+G L   L +P  + ++ Y    + +V  +       GIV   G+     ++T+ ++ 
Sbjct: 113 TNNGQLGYQLLIPKKEVIKCYEAVVNERVTSEDQFAFASGIVFNGGVKCKPAKLTILSES 172

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + V + + EGK  ++KK+F     KV  L R+S GP QL  TL  GS R
Sbjct: 173 DAESKVLLEISEGKFHQVKKMFLSVGKKVIYLKRLSMGPLQLDKTLPLGSYR 224


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 109/226 (48%), Gaps = 5/226 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER   
Sbjct: 1   MNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAV-SIERKIY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL 134
            L +KP   VTT  DP  R TV D +    S R+  VGRLD NT G+LLLTNDG LA  L
Sbjct: 60  VLLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLASKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     ++Y V     + +  +  +  GI +  G  + D     D  K  +  V + +
Sbjct: 120 THPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIHADAISYTDDFKKDD--VGIEI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 178 HSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 223


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A AG+ASRR   R+I   RV ++G     +   V  ++ + VDG PL  A+   
Sbjct: 11  RLCKYLAEAGVASRRGASRLIETGRVCIDGQQASHSD-RVFDSNRVTVDGAPLCPAQAKA 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +LYHKP+G+       D  S +   LP    R+   GRLD ++ GLLLLTNDG L + L
Sbjct: 70  YFLYHKPVGIDCRLRAEDPHSLIH-CLPGDL-RLFPAGRLDKDSRGLLLLTNDGELTQRL 127

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-------MQVTLD----TQK 183
             P     + Y +  +     D +       +  G  YG+       ++  +D    T+ 
Sbjct: 128 MHPDFHHQKGYLITLNKAPQPDDI-----AAIAAGFDYGEGPTRPCVVEAAIDCGYATED 182

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G+   + + L EGK R+I++++    ++V  L+R S     +G L  G  R ++   LR+
Sbjct: 183 GNPRKLRMRLTEGKKRQIRRLWRARGYRVLDLLRESIQQLNIGKLEQGEIRSLTASELRQ 242


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G L     + V     + +DG PL+      
Sbjct: 61  RLNKYISETGFCSRREADKLIEQGRVKIDG-LKATTGMKVSKGQSVSIDGKPLKVENELV 119

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 120 YIALNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 176

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V    +K S     + L
Sbjct: 177 ILRAGNNHEKEYIVTVNKSITDEFIKGMSNGVPILGTVTKKCLV----KKESKNSFRIIL 232

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 233 TQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLTKKELAE 282


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 112/227 (49%), Gaps = 2/227 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E +I    V VNG +++   + +    D + V G  +R     
Sbjct: 9   RLHKYMAQCGVASRRKSEELIKSGAVSVNGHVVKDMGILIDPQKDEVRVYGRIIRLKSDM 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G V+T  D  GR TV D +P +   R+  VGRLD +T GL+LLTNDG L  
Sbjct: 69  IYIAVNKPRGYVSTVKDQFGRPTVLDLVPVADEYRLYPVGRLDYDTTGLILLTNDGDLTY 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  ++Y     G  D   +   + G+V++G         L       + V + 
Sbjct: 129 RLTHPKHEIEKIYVAGLRGIPDNQDIFRFEHGLVLEGRLTAPAGFELIKADQRLSVVKIT 188

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           LREG+NR+I+K+ +     V  L R + G  +L  L  G  R ++ K
Sbjct: 189 LREGRNRQIRKMCDMIGHPVIWLRREAIGEVELCGLQPGQWRYLTPK 235


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 113/222 (50%), Gaps = 6/222 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA++GI SRRE +  I    V VNG+++      V  TD ++ +   +   ++  
Sbjct: 218 RLNRFIAQSGICSRREADDFIQAGLVTVNGVVVTTLGTKVQPTDEVKFNDSRVEGEKKVY 277

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G VT+  DP    TV + +    + R+  VGRLD N+ GLLL TNDG L R 
Sbjct: 278 LVL-NKPKGYVTSLDDPHADKTVMELVKDACTERIYPVGRLDKNSVGLLLFTNDGDLTRQ 336

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS Q  ++Y+V     + +  +  + +GI ++ G  Y D    +   K     V + 
Sbjct: 337 LTHPSFQKKKIYQVSLDKPLTKADMEQIAQGITLEDGEIYADEIAYVKEDK---TEVGIE 393

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +  G+NR ++++FE   + V +L R+ Y       L  G  R
Sbjct: 394 IHSGRNRIVRRIFEHLGYAVKKLDRVYYAGLSKKNLKRGQWR 435


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 115/230 (50%), Gaps = 17/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L A
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKA 228


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G L     + V     + +DG PL+      
Sbjct: 61  RLNKYISETGFCSRREADKLIEQGRVKIDG-LKATTGMKVSKGQSVSIDGKPLKVENELV 119

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 120 YIALNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 176

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V  +++      +T GL
Sbjct: 177 ILRAGNNHEKEYIVTVNKPITHEFIKGMSNGVPILGTVTKKCLVKKESKNSFRIILTQGL 236

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 237 ----NRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLTKKELAE 282


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G L     + V     + +DG PL+      
Sbjct: 61  RLNKYISETGFCSRREADKLIEQGRVKIDG-LKATTGMKVSKGQSVSIDGKPLKVENELV 119

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 120 YIALNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 176

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V  +++      +T GL
Sbjct: 177 ILRAGNNHEKEYIVTVNKPITHEFIKGMSNGVPILGTVTKKCLVKKESKNSFRIILTQGL 236

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 237 ----NRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKELAE 282


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/225 (32%), Positives = 112/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V   + +          ++  
Sbjct: 115 RLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVVEQGLRVDPENAVVRVDGVRVVVQKDL 174

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           ++L  +KP G   T SD  GR  V D +        R+  VGRLD +TEGLLL TNDG L
Sbjct: 175 VYLAMNKPRGWQCTMSDDLGRPCVGDIVSERVQSGQRLFHVGRLDADTEGLLLFTNDGDL 234

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y    HG V++     L+ G+ +  G    D    L+  +G    V
Sbjct: 235 AHRLMHPSFEVPKTYLATVHGVVERSTGKQLRDGVTLDDGPAKVDAFTVLEINEGKT-LV 293

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EG+   ++++ +     V RL+R + G   LG    G+ R
Sbjct: 294 KLVLHEGRKHIVRRLLDAVGHPVVRLVRTNVGVVALGDQRPGTQR 338


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRHVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKARFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>gi|308272550|emb|CBX29154.1| Ribosomal large subunit pseudouridine synthase F [uncultured
           Desulfobacterium sp.]
          Length = 235

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 116/226 (51%), Gaps = 7/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++ AG  SRR+ E+ I    VKVNG+++      V  + D +EVDG  +   +  
Sbjct: 6   RLQKYLSAAGFCSRRKGEKFILSGLVKVNGVVISELGTKVDPAKDVVEVDGNKIEAKDDL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G +TT S    R  +  +L +I  R+  VGRLD ++ GLLLLTNDG L  V
Sbjct: 66  IYIALNKPKGYITTCSRQ--RDRIVLDLVNIPQRIYPVGRLDKDSTGLLLLTNDGRLHNV 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS    + Y V     +  + L+ +K+G  + G      +++    + S     + L
Sbjct: 124 LSHPSFDHEKEYEVSLKWPIADEALDKMKEGFFLMGSKTRPAEIS----RISPEKFHITL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +EG+NR+I+++ +    +V  L RI     +LG L  G+ R ++ K
Sbjct: 180 KEGRNRQIRRMVDKVGNRVLELKRIRISDVKLGNLKEGAWRYLTDK 225


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 112/227 (49%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++ IA  RV +NG + E     V  +D +E+DG PL+   +  
Sbjct: 6   RLNKYISDTGFCSRREADKYIADGRVTLNGKIPE-VGTKVTDSDVVEIDGKPLKAKPKAV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              Y+KP+G VT  ++ + RS +    N P    R+  +GRLD  +EGL+ LTN+G +  
Sbjct: 65  FIAYNKPVG-VTCTTELNIRSNIISAINHPE---RIFPIGRLDRPSEGLIFLTNEGDIVN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +    +  +  G+ I G      +VT  +  G N  +T G
Sbjct: 121 KILRAGNNHEKEYLVTVDKAISPQFIKKMGAGVPILGTVTKQCKVTQVSSHGFNIVLTQG 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L    NR+I+++ EF  ++V  L R+      L  L +G  R ++ K
Sbjct: 181 L----NRQIRRMCEFLGYEVVTLKRVRIMNIDLTGLRSGQWRNLTDK 223


>gi|257462423|ref|ZP_05626837.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D12]
          Length = 231

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 120/233 (51%), Gaps = 23/233 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---EVDGVPLRKAE 71
           R+ K +   G+ SR+EV+ ++ +++++VN       A  V S   I   E D V   K +
Sbjct: 2   RMDKFLVECGLGSRKEVKELLKKRKIQVN-------ASIVTSGQQIIDEEKDEVFYEKEK 54

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
               + R ++ +K  G VT   D   R TV + LP   I   ++ VGRLD +TEGLLL T
Sbjct: 55  LVYKKFRYYILYKKAGYVTALEDSKER-TVMELLPEWVIRKDLVPVGRLDKDTEGLLLFT 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKG 184
           NDG L   L  P +   + Y V     + ++ +  L++G+ I        QV  L+ QK 
Sbjct: 114 NDGKLNHQLLSPKSHVDKTYHVCLEKIITEEAIEQLRQGVRIGDYTTLPAQVEQLEEQK- 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +++ ++EGK  ++KK+ E  + KV+ L R+S+G   LG L  G  REVS
Sbjct: 173 ----ISLTIQEGKFHQVKKMLEAVDNKVSYLKRVSFGRLVLGDLKPGEVREVS 221


>gi|126173147|ref|YP_001049296.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996352|gb|ABN60427.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 236

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 117/232 (50%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLRK 69
           R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D IE+DG P+ K
Sbjct: 2   RLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDESLNCLDSIELDGAPITK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  TETLAYWILNKAVGTDCRLLEQD-ETSLIRLLPKA-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
           L   L  PS    + Y VR +     + +  +  G+      Y D+Q TL  Q  + S+ 
Sbjct: 120 LTHKLMHPSFAHSKTYHVRLNRPFTDEFVEQMASGVR-----YKDLQ-TLPCQVRRLSSD 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              + L +G NR+I+++     +KV  L R++     L +L  G+ R ++ K
Sbjct: 174 SFEIVLTQGLNRQIRRMSSALGYKVIDLQRVALMTLTLKSLAEGAMRPLTPK 225


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 109/218 (50%), Gaps = 5/218 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  GI SRR  +R+I + RV+VNG +++   + V   D ++VDG  +   E   
Sbjct: 15  RINKFLASCGIDSRRVADRLIGEGRVEVNGKVIDTPGMRVTEKDFVKVDGRHMTPMEEV- 73

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP G V +        TV+D LP     +  VGRLD ++EGLL++TN G L +VL
Sbjct: 74  VVLLNKPRGYVCSREAQGAIGTVYDLLPPRLRHLNYVGRLDADSEGLLIMTNKGELTQVL 133

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P+    + Y V      D   L    +G+ I     G+ +      + S     + L 
Sbjct: 134 SHPTGGIEKEYWVTVDQNFDNSVLMQFLRGVRIP---EGNAKAKY-VCRASARRACIVLE 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           +G  R+++++F+    +V +L+R+  G    G L  G 
Sbjct: 190 QGLKRQVRQMFQCLGLRVRKLVRVRIGSLWGGDLEPGG 227


>gi|317014873|gb|ADU82309.1| hypothetical protein HPGAM_07680 [Helicobacter pylori Gambia94/24]
          Length = 257

 Score = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLIYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKARFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 97.1 bits (240), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 110/211 (52%), Gaps = 6/211 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++ +G+ +R+EV+++I Q RV VNG ++     +V   D + +DG  +    R  
Sbjct: 2   RLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVN-FHRKV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L+HKP G VT+  DP    T+ + LP +   +  VGRLD + EGLL++TNDG  A  +
Sbjct: 61  YILFHKPSGYVTSTKDPHS-ETIMEFLPPL-KGIFPVGRLDKDAEGLLIITNDGDFAHRV 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+  G++ +DK+  LK G+ ++   +   +     +K SN  + + + 
Sbjct: 119 TSPKWSVEKEYIVKVEGEITEDKIEKLKNGVTLRDGFFAKAKC---VEKLSNDTLKIVIT 175

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++      +   L R   G   L
Sbjct: 176 EGRYHQVKRMTAAVGLRTVHLKRTRIGELVL 206


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 116/234 (49%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G ++      V  T   I VDG  +   +  
Sbjct: 8   RLQKVLSQAGIASRRVAEKMILDGRVEVDGHIVTELGTRVDPTAADIRVDGTRVLLDDTL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLTNDG L
Sbjct: 68  VHLAINKPRGMHSTMSDDRGRPCIGDLVEHRVRGNKGLFHVGRLDADTEGLMLLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L+ G+ +  G    D    +D   G  + V
Sbjct: 128 AHRLMHPSYEVPKTYVATVLGTVPRGLGKKLRAGVELDDGPARVDDFAVVDAMPG-RSMV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V L EG+ R ++++     + V  L+R   G   LG    GS R +++K + E
Sbjct: 187 RVTLHEGRKRIVRRLLAAVGFPVQELVRTDIGAVSLGEQRPGSIRVLTRKEIGE 240


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 114/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G+      + V +   + +DG PL+      
Sbjct: 64  RLNKYISETGFCSRREADKLIEQGRVKIDGVKAT-TGMKVSNGQSVSIDGKPLKVENELV 122

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 123 YIALNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 179

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V  +++      +T GL
Sbjct: 180 ILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLVKKESKNSFRIILTQGL 239

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 240 ----NRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKELAE 285


>gi|308062723|gb|ADO04611.1| hypothetical protein HPCU_07355 [Helicobacter pylori Cuz20]
          Length = 257

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRCVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 122/228 (53%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL--LERAAVNVMSTDHIEVDGVPLRKAE 71
           +R+ K+I+ +GI SR++ E +I Q+RV +N  +  L   A  ++    I+   +P +  +
Sbjct: 3   ERLQKIISNSGICSRKKAEALIDQKRVFINNEIASLGEKADILIDIIRIDDYIIP-KNIK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGL 130
            +++ L +KP G+++T  D  GR TV D LP    + +  VGRLD ++ G L+++N+G L
Sbjct: 62  SSKVILLNKPTGVISTCRDTHGRKTVLDLLPDNLQKGMHPVGRLDKDSRGALIISNNGLL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V   G   ++ L   + GI I         V +  ++G+N  + 
Sbjct: 122 TLHLTHPRFNHKKRYSVLITGVPSKNTLKKWRNGIEIDKKTTRKALVNIVKRQGNNTLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L EG+NR+I+KV +     V  LIRI  G  +L  L  G+ RE+++
Sbjct: 182 IVLFEGRNRQIRKVADKLGHPVIDLIRIEIGNIKLNGLKEGAWREINE 229


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/235 (33%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K+++  G+ SR+E   +I +  V VNGIL  R         D I ++G PLR  +R
Sbjct: 6   ERLDKILSSQGVGSRKEAGILIRRGLVHVNGILATRPETKTDPERDQITIEGKPLR-FQR 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D +P + SR  +   GRLD +T GLL+LT+DG L
Sbjct: 65  HVYLMMNKPAGVVSASRDSR-EKTVVDLVPPVLSRRDLFPAGRLDRDTTGLLILTDDGEL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAW 188
           A  +  P     ++Y     G V  +++     G+ ++   +C   +   L   K   AW
Sbjct: 124 AHRMLSPKKHVYKLYEASVDGPVGAEEIEKFAAGVALEDGTVC---LPAGLTVVKQGTAW 180

Query: 189 VT-VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            T V +REGK  ++KK+F     +V RL R+  G  +L  TL  G  RE++K+ L
Sbjct: 181 ETLVEIREGKFHQVKKMFLAVGRRVLRLKRVRIGGLELDKTLKEGECRELTKEEL 235


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G L     + V     + +DG PL+      
Sbjct: 61  RLNKYISETGFCSRREADKLIEQGRVKIDG-LKATTGMKVSKGQSVSIDGKPLKVENELV 119

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 120 YIALNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 176

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V    +K S     + L
Sbjct: 177 ILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLV----KKESKNSFRIIL 232

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 233 TQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKELAE 282


>gi|332674227|gb|AEE71044.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 262

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKSLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/230 (32%), Positives = 115/230 (50%), Gaps = 17/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE- 71
           R+ K +   G+ SRREV+ ++    + VNG + +   +N+   D    D V    RK E 
Sbjct: 2   RLDKFLTECGLGSRREVKELLNTGEITVNGAVADNPQMNIKEND----DEVFYQERKLEY 57

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDG 128
            + R ++ +K  G +T   D   + TV D LP   I   +  VGRLD +TEGLLLLT+DG
Sbjct: 58  KKFRYYILNKKAGYITAVGDARDQ-TVMDLLPDWVIKKDLAPVGRLDKDTEGLLLLTSDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNA 187
            L   L  P     + Y      ++ +  L  L+ G+ I G I      V +D+ K    
Sbjct: 117 ALNHKLLSPKNHVEKTYYAELEKEISEADLERLRNGVDIGGYITMPGKAVKIDSCK---- 172

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + ++EGK  ++KK+ E    KV  L R+S+G  +L  L  G+ +EVS
Sbjct: 173 -IHLTIKEGKFHQVKKMLEAVGNKVTFLRRVSFGKLKLEDLELGAVKEVS 221


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 119/221 (53%), Gaps = 3/221 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R++K +A  G+ASRR+++  I + ++ VNGIL   +   V + D I V+G  +  K E+ 
Sbjct: 7   RINKFLASKGVASRRQIDLWIEEGKILVNGILAT-SGQKVSAEDKILVNGKMISEKEEKK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +K   +++   D  GR TV D +P+  +R+  VGRLD  T GL+LLTNDG L   
Sbjct: 66  VYYILYKEEEVLSAVKDERGRKTVVDCIPTK-ARIFPVGRLDYRTSGLILLTNDGELFNR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V   G + +++L  L++G+ ++     +  V     +  N +  + +
Sbjct: 125 VMHPRAEIFKTYEVLAKGHLTREQLKTLEEGVELEEGKTLEALVAKVKYEKGNTFFEISI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           REG+NR+I+++ E    +V +L R   G   L  L  G  R
Sbjct: 185 REGRNRQIRRMVEAVGSRVYQLRRTKIGRLSLEGLKLGQYR 225


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 65/206 (31%), Positives = 105/206 (50%), Gaps = 9/206 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I QQRV +NG + E     V+S D++E+DG P+R  E+ 
Sbjct: 8   KRLNKYISETGFCSRREADKLIEQQRVTINGKIPE-MGTKVLSGDNVEIDGKPVRSKEKP 66

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 67  VYIALNKPTGITCTTERDVPGNIVDF---VGHHKRIFPIGRLDKPSDGLIFLTNDGDIVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    V +D L  +  G+ I        +V  +T+      +T G
Sbjct: 124 KILRAGNNHEKEYVVRVDKPVTRDFLKKMGSGVAILDTVTLPCRVEQETKFSFRITLTQG 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L    NR+I+++ E   ++V +L R+
Sbjct: 184 L----NRQIRRMCEALGFEVLKLRRV 205


>gi|91200876|emb|CAJ73931.1| conserved hypothetical protein [Candidatus Kuenenia
           stuttgartiensis]
          Length = 260

 Score = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 117/233 (50%), Gaps = 14/233 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----IEVDGVPLRK 69
           +R+ KV+A AGI SRRE E +I   RV V+G   ER      + D     I  DG+P+R 
Sbjct: 3   ERLQKVLASAGIGSRRECENVILAGRVTVDG---ERVTALGATVDAGKSVIYCDGMPIR- 58

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    +L +KP   + T+ D   R    D + ++  R+ ++GRLD  +EGL+++TNDG 
Sbjct: 59  PEAKIYYLLNKPKDCLCTNYDELNRLRAIDIIKNVKQRLYTIGRLDKQSEGLIIITNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQKGS--N 186
           L+  L  P  +  + Y +   G +  + +  L+ G+    + +G  Q V +     S   
Sbjct: 119 LSNKLSHPKYEVNKTYFIEIDGYLSNETITALQSGV---WLAFGKTQPVRIKKMHRSFKK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +   + L EGKNREI+++      KV  L RI  G      L  G  R+++++
Sbjct: 176 SRFEMILCEGKNREIRRMLADHGHKVRTLRRIKIGSLCDPDLKVGKYRKLTEQ 228


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 120/244 (49%), Gaps = 25/244 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+++ IA     SRRE + +IAQ RV V     ++ AV    +     + VDG  LR+ +
Sbjct: 2   RLNQYIAHHSKYSRREADGLIAQGRVNVE----KKKAVLGQELKEGQRVFVDGKQLREKK 57

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              + + +YHKP G + T SD  GR ++FD+L   ++    VGRLD  +EGLLLL++D  
Sbjct: 58  DGPSTVIVYHKPKGELVTRSDDRGRRSIFDSLGRRYAHFTPVGRLDFASEGLLLLSDDKK 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------- 178
           +A    L  +   R Y ++  G V +     ++ G+ ++    G  + +           
Sbjct: 118 IAHF--LMQSDLEREYILKISGAVTEKMKEAMENGLELEDARAGGHEKSKIQKMSFKPFA 175

Query: 179 -LDTQKGSNAWVTVGLR--EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               QK    +  + +R  EGKNRE+++ F  F  +V  L R+ YG   L  L  G  R 
Sbjct: 176 FYQIQKNDRNFSKLKVRITEGKNRELRRFFAHFKAEVLDLRRVGYGFVTLSALPVGKVRF 235

Query: 236 VSKK 239
           +SK+
Sbjct: 236 LSKE 239


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 125/236 (52%), Gaps = 13/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+ V+ ++  + V VNG++ +    +V   TD IEV G  ++  E  
Sbjct: 2   RLDKLLANMGFGTRKTVKNVLKAKEVTVNGLVEKDGKTHVNPETDKIEVSGEVIQYQEFM 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTNDGGL 130
              L HKP G+V+  +D   ++ +  +L     +V+    VGRLD +TEGLL+LTNDG L
Sbjct: 62  YFML-HKPQGVVSATTDHVHKTVI--DLLQPQDQVMDPFPVGRLDKDTEGLLILTNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ---VTLDTQKGSN 186
           A  L  P     + Y     G VD+  +   + GI +  G      +   +++D +K S+
Sbjct: 119 AHNLLSPKKHVDKCYEAIIEGVVDEQDVQAFENGITLDDGFNCQSAKLEILSVDFEKESS 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + V + EGK  ++K++FE  +  V  L R+S G  QL  TL  G  R+++K+ L
Sbjct: 179 V-IQVTIHEGKFHQVKRMFEAVDKSVIYLKRLSMGSLQLDETLELGEYRQLTKEEL 233


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/229 (32%), Positives = 118/229 (51%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AG+ASRR  E +I+Q RV+V+G ++    + +   + +          ++  
Sbjct: 2   RLQKVLAQAGVASRRAAEELISQGRVEVDGRIVIEQGLRIDPENAVVRVDGVRVVVQKDL 61

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L  +KP G  +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG L
Sbjct: 62  VHLALNKPRGWQSTMSDDLGRPCVGDIVSERVAAGQRLFHVGRLDADTEGLLLLTNDGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G +++     LK+G+ +  G    D    LD  +G  + V
Sbjct: 122 AHRLMHPSFEVSKTYLATVSGALERGVGKKLKEGVELDDGPAKVDTFTLLDINEG-KSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            V L EG+   ++++F+     V RL+R   G   LG    G+ R + +
Sbjct: 181 RVTLHEGRKHIVRRLFDAVGHPVIRLVRTDIGAVALGDQRPGTLRVLGR 229


>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 = 96.7 bits (239), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 116/234 (49%), Gaps = 17/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++     SRRE + +I Q  VK+N   +   +  V   D I + G  ++K  +  
Sbjct: 2   RINKFVSHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKIFIKGKRVQKKTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPKQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGIVTKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIGFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           GS+   T   V + EGKNRE+++ F  F+ +V  L R+++G   LG L  G  R
Sbjct: 179 GSSGGYTKLRVIINEGKNRELRRFFGHFDVEVMDLKRVAFGVLDLGMLKPGKHR 232


>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 = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 130/240 (54%), Gaps = 21/240 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQRV+K +A++G+ SRRE E++I+   V ++G ++E     +     + +      K + 
Sbjct: 12  PQRVNKWLAQSGVCSRREAEQLISDGLVSIDGEVVEDVGRKIQPGQTLVLADRATAKLDG 71

Query: 73  TRLWLYHKPIGLVTTHSDPD--------GRSTVFDN-----LPSIFSRVISVGRLDINTE 119
           T  +L HKP G+V++  DP          R+ ++ +     +P     +  VGRLD ++ 
Sbjct: 72  TPTYLIHKPRGVVSSQPDPGQVPAARLLTRANLWGDARGVAIPQSGDLIPPVGRLDKDSR 131

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           GLLLL+ DG +A+ +  P +   + YRV   G++ ++KL LL+ G+ + G  +   +++V
Sbjct: 132 GLLLLSQDGVVAKAVIGPQSDLEKEYRVAVMGELTEEKLELLRFGLELDGRELRPAEVEV 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             D +      ++  LREG+NR+I+++ +  + KV  L R+  GP  LG +  G  R ++
Sbjct: 192 ISDQR------LSFVLREGRNRQIRRMCDLVDLKVVDLFRVRIGPLDLGDMPEGRWRPLT 245


>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 = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 120/226 (53%), Gaps = 13/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I QQR+ +NG + E     V   D + VDG PL KA++ R
Sbjct: 10  RLNKYISDTGYCSRREADKLIDQQRITINGNVPE-MGTKVAEGDDVLVDGKPL-KAKQER 67

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++ ++KP+G+  T S+      + D + +   R+  +GRLD  ++GL+ LT+DG +   
Sbjct: 68  IYIAFNKPVGITCT-SERHVEGNIIDYI-NHEQRIFPIGRLDKPSDGLIFLTSDGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +        + Y VR    +  D L  +  G+ I         VTL  Q  + S     +
Sbjct: 126 ILRAGNAHEKEYVVRVDKPITDDFLAQMAAGVPILDT------VTLPCQVKQESRFVFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L +G NR+I+++ E+ +++V +L R+      LGTL +G  R ++
Sbjct: 180 TLTQGLNRQIRRMCEYLDYEVFKLKRVRIMNIDLGTLASGEWRYLT 225


>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 = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 113/240 (47%), Gaps = 16/240 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG--------ILLERAAVNVMSTD 58
           ++ N T  R++K +A+ G+ SRR   R I    + + G        + L      + S++
Sbjct: 1   MEHNPTQMRLAKYLAQTGLCSRRAATRYIRDGLITIEGRIANHIDTVTLIETPQGIESSE 60

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +  DG P+   E    W +HK +G   +    D  S++   LP+   R+  VGRLD ++
Sbjct: 61  QLTFDGAPISAVEEKEYWAFHKAVG-TDSRLLIDDSSSLLHLLPAT-PRLYPVGRLDKDS 118

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG L + L  P     ++Y VR     D + L  +      QG+ Y D+   
Sbjct: 119 RGLLLLTNDGELTQTLMHPDFGHSKIYHVRVDRDFDDNFLQAMA-----QGVSYRDVTTL 173

Query: 179 LDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             T  + +     + L +G NR+I+++ +   +KV  L R+      LG L  G  R+++
Sbjct: 174 PCTLTRLAKDQFEITLTQGLNRQIRRMSQALGFKVIDLKRVKIQSLALGDLKEGEMRQLT 233


>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 = 96.7 bits (239), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 120/230 (52%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNV----MSTDHIEVDGVPLRK 69
           R++K +A+ GI+SRRE  R+I   R+ +NG + +   AV+V    +  D + +D  P+  
Sbjct: 2   RLAKYLAQCGISSRREACRLIEAGRISLNGKIAKHTDAVHVDADGLCLDSLCLDEKPISG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    WL++K +G      D D +S++   LP+   R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  VEALSYWLFNKAVGTDCRLLDAD-KSSLLHLLPAT-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
           L   L  PS    + Y V+     +   +  +  G+  + +   +++ TL  Q  + S+ 
Sbjct: 120 LTHKLMHPSFAHSKTYHVQLDSPFNDAFIEQMACGVQYKEVRNKEVR-TLPCQVTRLSDV 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++     +KV  L R++     LG+L  G  R +S
Sbjct: 179 SFEIVLTQGLNRQIRRMSNALGYKVIDLQRVALMTLTLGSLAEGEMRPLS 228


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 126/249 (50%), Gaps = 21/249 (8%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K + ++ +   P R++K ++ AG+ SRRE + +I +  + VNG ++      +   D +
Sbjct: 191 VKYREVLADPNEPIRLNKFLSNAGVCSRREADLLIEKGEITVNGEVVTELGRRITRQDEV 250

Query: 61  EVDGVPLRKAERTRLW-----LYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRL 114
                 + K +R  +      L +KP   VTT  DP+ R+TV D +  +   R+  VGRL
Sbjct: 251 ------IYKDKRVEIESKVYVLLNKPKNCVTTSDDPECRTTVMDIVRYACPERIYPVGRL 304

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D NT G+LL+TNDG LA  L  PS +  ++Y V  +  V  + +  +  G+ +      D
Sbjct: 305 DRNTTGVLLITNDGDLASKLTHPSFKKKKIYHVWLNKDVSIEDMQKIADGVELD-----D 359

Query: 175 MQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            ++  D     ++   + V + +  G+NR ++++FE   ++V +L R+ +       L  
Sbjct: 360 GEIHADAISYVKEDDLSQVGIEIHSGRNRIVRRLFEHLGYRVVKLDRVYFAGLTKKNLPR 419

Query: 231 GSTREVSKK 239
           G  R ++++
Sbjct: 420 GKWRYLNEQ 428


>gi|261408369|ref|YP_003244610.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261284832|gb|ACX66803.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 253

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 82/246 (33%), Positives = 124/246 (50%), Gaps = 24/246 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T QR+ KV++  G  SR E+++   Q  + VNG + +    +V    D IE +G  ++  
Sbjct: 7   TTQRLDKVLSNLGFGSRAELKKKAKQGSIVVNGTVTKDPGKHVDPYADIIEFEGETIQYR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTND 127
           E   L L HKP G+V+   D   R TV D L + + RV     VGRLD +TEGLLLLTND
Sbjct: 67  EYVYLML-HKPPGVVSATEDLRDR-TVLDLLDAEY-RVFEPFPVGRLDKDTEGLLLLTND 123

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     + Y     G+VD++ +     G+ +      D  VTL  +   ++
Sbjct: 124 GKLAHELLSPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLD-----DGYVTLPGELAIHS 178

Query: 188 W-----------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
                       +++ + EGK  ++K++FE    KV  L RIS G  +L   L  G+ RE
Sbjct: 179 HEEREDGVQLSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYRE 238

Query: 236 VSKKIL 241
           ++++ L
Sbjct: 239 LTEQEL 244


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 103/216 (47%), Gaps = 2/216 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +A  G+ASRR+ E +I   RV+VNG ++      V  S D + VD   +   E+
Sbjct: 3   ERLQKYMASCGVASRRKCEEIITSNRVQVNGTVVNELGFKVDPSKDKVYVDSKLIFLEEK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G V+T  D   R T+ D L  +  R+  +GRLD NT GLLL+TNDG +  
Sbjct: 63  NVYIALNKPEGYVSTVKDERDRKTIMD-LVEVEERIFPIGRLDYNTSGLLLMTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G    + +     G+ I           +     + + V + 
Sbjct: 122 KIIHPRKEIDKVYIAIIKGIPSNEAIRKFCNGLDIGDYITSKANFEVIDTSENKSKVKIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           + EGKNR+++++ +     V  L RIS G   L  L
Sbjct: 182 IHEGKNRQVRRMCDKIGHPVIALKRISVGKISLNYL 217


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 126/250 (50%), Gaps = 30/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAER 72
           R++K ++ AG+ SRRE +R+I   RV V+G+   RA   + V     I V    ++ AE+
Sbjct: 3   RLNKYLSEAGVCSRREADRLIEAGRVTVDGV---RAVPGMKVSEEQKICVGKKVIQGAEQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
             +   +KP G+V T     G   V +N+        RV   GRLD ++EGLL++TNDG 
Sbjct: 60  KVVLAVNKPAGIVCT-----GDMKVKNNIIRFLHYPVRVTYAGRLDKDSEGLLIMTNDGE 114

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------- 181
           L   +        + Y VR   ++  + +  + +G+ IQ     D++  LD         
Sbjct: 115 LINSMMRARYHHEKEYHVRVDKEITSEFVRQMSEGVHIQ-----DVEKNLDAVTRPCEVK 169

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK--- 238
           Q G   +  + L +G NR+I+++ E   +KV +L+RI     +LG+L +G+ R++     
Sbjct: 170 QIGKYTFSII-LTQGLNRQIRRMCEALGYKVTKLVRIRIMNVELGSLKSGAVRKIEGQEL 228

Query: 239 KILREQLGPH 248
           K L EQ G H
Sbjct: 229 KKLYEQAGTH 238


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 21/237 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQRV+K +A++G+ SRRE E++I+   V ++G ++E     +     + +      K + 
Sbjct: 12  PQRVNKWLAQSGVCSRREAEQLISDGLVSIDGEVVEDVGRKIQPGQTLTLADRATAKLDA 71

Query: 73  TRLWLYHKPIGLVTTHSDPD--------GRSTVFDN-----LPSIFSRVISVGRLDINTE 119
              +L HKP G+V++  DP          R+ ++ +     +P     +  +GRLD ++ 
Sbjct: 72  VPTYLVHKPRGVVSSQPDPGQVPAARLLTRANLWGDARGVAIPQSGDLIPPIGRLDKDSR 131

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQV 177
           GLLLL+ DG +A+ +  P ++  + YRV   G++ ++KL LL+ G+ + G  +   +++V
Sbjct: 132 GLLLLSQDGVVAKAVIGPQSELEKEYRVAVMGELTEEKLELLRFGLELDGRELRPAEVEV 191

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             D +      ++  LREG+NR+I+++ E  + KV  L R+  GP  LG +  G  R
Sbjct: 192 ISDQR------LSFVLREGRNRQIRRMCELVDLKVVDLFRVRVGPLDLGDMPEGHWR 242


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 115/229 (50%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  +   ++  
Sbjct: 9   RIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKIA-YQQYH 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV   L +   +  +  VGRLD +T GLLLLTNDG LA 
Sbjct: 68  YFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTNDGALAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P+    +VYR +  G  D +      +G+++     +    +++    Q  + + +
Sbjct: 127 ELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQDNNLSQI 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+ 
Sbjct: 187 EIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEID 235


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 TLMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 111/218 (50%), Gaps = 2/218 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A  G+ASRR  E +I   RVKV  +     A+++   D + VDG  +   +++ 
Sbjct: 2   RLNRYLALCGVASRRRSEDIIRTGRVKVENVTATDPAMDISEEDQVSVDGKSV-CFQKSV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V    D    + V    P + + 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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +EG  REI+ +   F+  VN L R   G  +L  L +G
Sbjct: 181 QEGLKREIRIMASHFSLSVNVLFRRKVGRMELRKLKSG 218


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 119/236 (50%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMR 234


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 122/233 (52%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V   +D I  DG  +   E  
Sbjct: 5   RIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTESDEILFDGEKINYKEFI 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+++   D +   TV D LP          VGRLD +TEGLLL+TNDG LA
Sbjct: 65  YIMI-NKPKGVISATYD-EVEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
             L  P    ++ Y     G V++  +    +GI+++   Y  +   L+    S+  + V
Sbjct: 123 HQLLSPKKNVIKKYYAEILGFVNESDIKAFNEGIILED-GYKTLPANLEILFSSSDVSKV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 182 YVYIREGKYHQIKRMFESVGKKVIYLKRLAMGSLTLDENLKPGEWRELSEEEL 234


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R +    + ++G + E  A  V+    +   G  + K E   
Sbjct: 7   RINKFLSEAGVCSRREADRQVELGNITIDGKVAETGA-RVLPGQTVLFQGKKVSKEEEMI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L  +HKP+G+V T    +  + + + N P    R+  +GRLD ++EGLLLLTN+G +   
Sbjct: 66  LIAFHKPVGIVCTAEKREKNNVIDYINYPK---RIYPIGRLDKDSEGLLLLTNNGDIVNK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  V +  ++ L  G+ +  +    M      ++       + L
Sbjct: 123 MMRSGNMHEKEYIVTVNRPVTESFIHGLANGVPLAEL--NTMTRKCHVKQIGKKQFKIIL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ E+F ++V +L+R      +LG L  G+ R+V+ +  R+ L
Sbjct: 181 TQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLPVGTYRDVTTEEYRQLL 232


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 76/229 (33%), Positives = 119/229 (51%), Gaps = 7/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++ +G  SR+EV++M+    V+VN  L++ A  +V   +D I V G P+   E  
Sbjct: 2   RLDKLLSNSGYGSRKEVKKMLKNGAVRVNDQLVKDAKKHVDPESDDITVYGAPVMYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L     R     VGRLD +TEGLLLLTNDG LA
Sbjct: 62  YLMM-NKPQGVLSATED-SRQETVVDLLDPELLRFEPFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +  +DQ  L+ L+KG+ I +G      + +L   +     + 
Sbjct: 120 HQLLSPKKHVPKTYEVHVNKPIDQAALDQLEKGVDIGEGYVTKPAEASLLASENGVERLL 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + + EGK  ++K++ +     V  L R+  G   L   LL G  RE+S+
Sbjct: 180 LTITEGKFHQVKRMLKAVGHDVIYLKRLKMGDVDLDEELLPGEYRELSE 228


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 115/229 (50%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKI-AYQQYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV   L +   +  +  VGRLD +T GLLLLTNDG LA 
Sbjct: 61  YFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P+    +VYR +  G  D +      +G+++     +    +++    Q  + + +
Sbjct: 120 ELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQDNNLSQI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+ 
Sbjct: 180 EIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEID 228


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/227 (31%), Positives = 116/227 (51%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AG+ SRR+  R+I Q  V VNG + +     V + D I V+   L       
Sbjct: 6   RLAKYIANAGLCSRRQASRLIDQGLVTVNGGIADHICF-VGTDDVITVNDELLVYQTEQV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L++KP+G + +   P+  +++   LPS   R+  +GRLD ++ GL++LTNDG L   +
Sbjct: 65  YYLFNKPVG-IDSRLLPNDSASLIHLLPSEI-RIYPIGRLDKDSYGLMILTNDGELYHQM 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---QKGSNAWVTV 191
             P     + YRV     +D +  N + +GI + G      Q+T      Q   N +  V
Sbjct: 123 NHPDHHQEKEYRVSVERPIDANFCNKMAQGIPVDG------QLTQPCSVWQTAENEFHIV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+K+ +   +KV  L RI      +G L AG  + ++K
Sbjct: 177 -LTQGLNRQIRKMAKHCGYKVVDLERIRIANLAIGDLSAGEFKTLTK 222


>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 = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 114/220 (51%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR EV++++ +++++VNG +     +++    D +   G  L   E  
Sbjct: 7   RLDKYLVDCGVGSRTEVKQVLKKKKIQVNGKVETSPKIHIDPDKDQVTYLGESLFHEEFV 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 67  -YYLLNKPKGVISATED-DHHQTVLDLLDDTARHKEVFPVGRLDIDTHGLLLLTNNGKLA 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWV 189
             +  P     +VYR +  G + Q+ ++  K+GI ++       ++++    Q+ ++  V
Sbjct: 125 HAMLSPKKHVDKVYRAQVAGIMTQEDIDRFKEGIELKDFTTLPAELEMLEVDQEANSCLV 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            + + EGK  ++K++      +V  L RIS GP  L   L
Sbjct: 185 QIRIAEGKFHQVKRMVAACGKEVTDLERISMGPLSLDPAL 224


>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 = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 118/234 (50%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVN-YQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +     +   ++++ +  ++  ++ + 
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILVQDEEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL------GTLLAGSTREVSK 238
           + +REGK  +IK++F     KV  L RIS G  +L      G  +  S  +VSK
Sbjct: 181 IKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELSLDDVSK 234


>gi|317010168|gb|ADU80748.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori India7]
          Length = 257

 Score = 96.3 bits (238), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 124/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDRVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+L+L++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLILSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREIENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 115/227 (50%), Gaps = 10/227 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKA 70
           +R++K ++ AG  SRRE +R++   RV ++G+    AAV    V     + VDG  +   
Sbjct: 4   ERINKYLSEAGYCSRREADRLVEAGRVTIDGV----AAVCGSKVADGQKVCVDGKEVSGR 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L  ++KP G+V T +D  G + + D       R+  VGRLD ++EGL+L+TNDG +
Sbjct: 60  SRHILLAFNKPAGIVCTTTDKQGSNNIVD-FIGYPERIYPVGRLDKDSEGLILMTNDGAM 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +    + Y VR +  V  + +  +  G+ ++ +           +K +     
Sbjct: 119 MDRILRSTNGHEKEYIVRVNKPVTDEFVKGMSDGVYLKEL--DRTTKVCVVEKVTKFCFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F +KV +L RI      LG L  G  R+V+
Sbjct: 177 IVLTQGLNRQIRRMCENFGYKVMKLKRIRIMNIMLGDLKQGCYRDVT 223


>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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 114/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++     R+ V  M+AQ RV ++G+L   AA  +     I VDGV L       
Sbjct: 91  RLDKHLSKQTGVPRKAVRLMLAQARVTIDGVLARDAAEVINPFSRIAVDGVGL-PTNTPH 149

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V    D   R TV D L   F   +  VGRLDI + GL+LLTNDG  +R 
Sbjct: 150 YIMLNKPSGVVCATRDARHR-TVIDILDLPFQHTLHIVGRLDIQSTGLVLLTNDGQWSRR 208

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L LP +++ + YRV     +  +++   + GI    +G+     ++ L     +N    V
Sbjct: 209 LSLPQSKFAKHYRVTTEQAITSEQIAGFEAGIFFAYEGLTTRPARLHLINSHEAN----V 264

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L EG+  +I+++F  +  +V  + R + GP+ L  L  G  RE+S
Sbjct: 265 TLTEGRYHQIRRMFGRYGNRVLSIHRYATGPYVLSNLRPGQYREIS 310


>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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 115/226 (50%), Gaps = 7/226 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL- 77
           ++A+AG+ASRR  E MI Q RV+V+G+++    + +     +             ++++ 
Sbjct: 1   MLAKAGVASRRAAEEMIDQGRVEVDGVIVREQGLRIDPQTAVVRVDGVRVVVRDEQVYVA 60

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLARVL 134
            +KP G  +T SD  GR  V D +    +   R+  VGRLD +TEGLLLLTNDG LA  L
Sbjct: 61  LNKPKGWQSTMSDDLGRPCVGDIVAERIAAGQRLFHVGRLDADTEGLLLLTNDGDLAHRL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
             PS +  + Y    HG+V    +   L+ GI ++ G    D    L+  +G  + V + 
Sbjct: 121 MHPSFEVSKTYLATVHGEVHHKVIGKRLRDGIELEDGPAKVDRFQVLELGEG-RSLVKIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L EG+   ++++ +     V RL+R   GP  LG    G+ R + +
Sbjct: 180 LHEGRKHIVRRLLDAVGHPVTRLVRTHIGPVALGDQRPGTLRVLGR 225


>gi|315585848|gb|ADU40229.1| RNA pseudouridine synthase [Helicobacter pylori 35A]
          Length = 262

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 120/233 (51%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVNGEKVA-YQQYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   ++ +    P   +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    + YR +  G  D++ + +   G+ +     +   ++++ +  ++   + + 
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|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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 115/229 (50%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  +   ++  
Sbjct: 14  RIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKI-AYQQYH 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV   L +   +  +  VGRLD +T GLLLLTNDG LA 
Sbjct: 73  YFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTNDGALAH 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P+    +VYR +  G  D +      +G+++     +    +++    Q  + + +
Sbjct: 132 ELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQDNNLSQI 191

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+ 
Sbjct: 192 EIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEID 240


>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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 85/243 (34%), Positives = 122/243 (50%), Gaps = 11/243 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G  SR+EV++ + +  V VNG  ++     ++ T D + V    +   E  
Sbjct: 2   RLDKFLAHHGYGSRKEVKQFLKKTEVTVNGKRVQDGKQAIVPTSDIVRVQDEVILYQEYV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
             W+ HKP G ++  +  D   TV D L P    R V  VGRLD +TEGLLLLT+DG LA
Sbjct: 62  -YWMLHKPSGYIS--ATEDQAKTVLDLLKPKDAGRAVFPVGRLDKDTEGLLLLTDDGQLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWV 189
             L  P     +VY     G V  D ++  KKGIV++   Y      L+  +  G    +
Sbjct: 119 HELLSPKKHVNKVYEATIEGVVTGDDVHAFKKGIVLED-DYQCKPAKLEILQVNGVKTDI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  +IK++F   + KV  L RI  G  QL   LA G  R ++ + L EQL   
Sbjct: 178 RITIQEGKYHQIKRMFLAVDKKVIYLKRIQMGSLQLDENLARGEYRPLTVEEL-EQLSKK 236

Query: 249 LLE 251
            LE
Sbjct: 237 RLE 239


>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 = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 115/230 (50%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG L+      V   D + VDG  +   ++  
Sbjct: 17  RIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTAPKQQVKEDDLVVVDGNEI-AYQQYH 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV   L +   +  +  VGRLD NT GLLLLTNDG LA 
Sbjct: 76  YFLLNKPKGVISATEDR-SQQTVISLLKTKDRYQGIAPVGRLDKNTTGLLLLTNDGALAH 134

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P+    +VYR +  G   ++ +     GI +     +    +++    +    + +
Sbjct: 135 ELLAPNKHVTKVYRAKISGVASEETIKTFASGITLGDGTKLKPAKLEILAQDKVHDLSQI 194

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
            + ++EGK  +IK++F     KV  L RIS G   L T L  G  +E+++
Sbjct: 195 EIQIQEGKYHQIKRMFGAVGMKVLELDRISMGKLSLPTDLKRGQYQEITR 244


>gi|308064218|gb|ADO06105.1| hypothetical protein HPSAT_07015 [Helicobacter pylori Sat464]
          Length = 257

 Score = 95.9 bits (237), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAQLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G + ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLIKIQGFITREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 69/216 (31%), Positives = 115/216 (53%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +  +G+ SR +V++++ + +V VNG  +  A   +   +D I VDG  L   E+ 
Sbjct: 2   RLDKFLVESGLGSRSQVKQLLKKGQVWVNGAAVTSAKTQINERSDQIVVDGQTL-VYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L     +  V  VGRLD++T GLLLLTN+G L+
Sbjct: 61  VYYLLNKPKGVISATED-DRHKTVLDLLDDTARQKEVFPVGRLDVDTHGLLLLTNNGQLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGS-NAWV 189
             +  P     +VY+ +  G +DQ  +    +GI ++       Q+  L+  +G+  + V
Sbjct: 120 HAMLSPKRHVAKVYQAQVAGLMDQADVERFAQGIELKDFTCQPAQLEILERDEGAKTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L EGK  ++K++      +V  L R+S GP QL
Sbjct: 180 RITLSEGKFHQVKRMVLACGKEVTDLQRLSMGPLQL 215


>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 = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 57/180 (31%), Positives = 92/180 (51%), Gaps = 14/180 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  L++KP G++T  +DP+GR T+ D +P     V   GRLD+++EGLL L+NDG L   
Sbjct: 12  RYILFYKPYGVLTAFTDPEGRPTLKDWIP--VPDVYPAGRLDMDSEGLLFLSNDGDLMHR 69

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------T 181
           +  P  Q  + Y V+  G V  + L  L++G+ ++G      QV +             T
Sbjct: 70  ITDPRYQHPKTYLVQVEGVVSGEALAKLRRGVEVKGRQTQRCQVMVIPEPDLPPRAKPVT 129

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             G   W+ + L EGK R+++ +         RL+R++ GP  L  L  G  R+++ + L
Sbjct: 130 PHGPTTWLRMVLTEGKKRQVRHMTAAVGHPTLRLVRVAIGPLSLEGLTPGEWRDLTPQEL 189


>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 = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 112/231 (48%), Gaps = 15/231 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER   
Sbjct: 1   MNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAV-SIERKIY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL 134
            L +KP   VTT  DP  R TV D +    S R+  VGRLD NT G+LLLTNDG LA  L
Sbjct: 60  VLLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLASKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAW---- 188
             P     ++Y V        DK NL K  +  +  GI   D ++  D    ++ +    
Sbjct: 120 THPKYLKKKIYHVHL------DK-NLTKADMEQIAAGIQLDDGEIQADAISYTDDFKKDE 172

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 173 VGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 223


>gi|317011592|gb|ADU85339.1| hypothetical protein HPSA_06915 [Helicobacter pylori SouthAfrica7]
          Length = 254

 Score = 95.9 bits (237), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 122/241 (50%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   +     VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYVHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  R Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--REYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFVGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 ILKNHAKYSKLKVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 116/229 (50%), Gaps = 5/229 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AGI SRRE +  I    V VNG ++      V+ +D ++    P+   E+
Sbjct: 243 PIRLNKYLANAGICSRREADEFIQAGVVTVNGNVVTELGTKVLRSDEVKFHEQPV-SLEK 301

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV + +  +   R+  VGRLD NT G+LLLTNDG LA
Sbjct: 302 KVYVLLNKPKDYVTTSDDPQQRKTVMELVKGACEERIYPVGRLDRNTTGVLLLTNDGDLA 361

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY V     V ++ +  + +GI ++ G  + D     D +      V 
Sbjct: 362 SKLTHPKFLKKKVYHVFLDKAVTEEDMQKIAEGIELEDGEIHADAIEYADER--DKKQVG 419

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 420 IEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNVRRGDWRYLTEK 468


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+L+L++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLILSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 109/224 (48%), Gaps = 3/224 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R    ++I Q  V V+GI++++ A ++     +E DGV L   +R R
Sbjct: 2   RLDKFLCDCSDLTRSLAGKLIRQGEVMVDGIVVKQPAFHINEQSQVEFDGVTLTLDQRNR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V ++ DPD  +  F        ++  VGRLD++T GL+L+T+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSNEDPDHPTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y V     V  D + L  +G++++          L+      A +T+   
Sbjct: 122 TSPRHECAKTYHVWLADPVSPDAIALFAEGVLLRSETEKTRPAQLEILGECEARLTI--H 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           EGK  ++K++F     KV  L R   G   L   LA G  RE++
Sbjct: 180 EGKYHQVKRMFAAIGNKVVGLHRERVGGLTLDEELAPGEYRELT 223


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 122/241 (50%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDRVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAV-- 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
           V  L      + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 124 VSALMHADLEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>gi|317179635|dbj|BAJ57423.1| hypothetical protein HPF30_1326 [Helicobacter pylori F30]
          Length = 262

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLVKIQGFVTREMENAIQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/225 (32%), Positives = 112/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V   + +          ++  
Sbjct: 28  RLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVVEQGLRVDPENAVVRVDGVRVVVQKDL 87

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           ++L  +KP G   T SD  GR  V D +        R+  VGRLD +TEGLLL TNDG L
Sbjct: 88  VYLAMNKPRGWQCTMSDDLGRPCVGDIVSERVQSGQRLFHVGRLDADTEGLLLFTNDGDL 147

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y    HG V++     L+ G+ +  G    D    L+  +G    V
Sbjct: 148 AHRLMHPSFEVPKTYLATVHGVVERSTGKQLRDGVTLDDGPAKVDAFTVLEINEGKT-LV 206

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EG+   ++++ +     V RL+R + G   LG    G+ R
Sbjct: 207 KLVLHEGRKHIVRRLLDAVGHPVVRLVRTNVGVVALGDQRPGTQR 251


>gi|144575100|gb|AAZ43829.2| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Mycoplasma synoviae 53]
          Length = 234

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 63/214 (29%), Positives = 113/214 (52%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA + + +R E++++I++  VKVN ++++++       D I ++G+ L   E   
Sbjct: 4   RIEKFIADSTLYTRNEIKKLISKGLVKVNDLIIKKSQSIDPKLDKIYLEGILLEAREEFS 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLA 131
             + +KP G +  + D + +  VF+ L  +        ++GRLDI+TEGLL++TNDG L+
Sbjct: 64  YIMMNKPAGYICANFDWN-KQVVFELLLDLEMNLKDFFTIGRLDIDTEGLLIITNDGKLS 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     ++++   LL+K ++I  I Y   + ++     +N W  +
Sbjct: 123 HNLLSPKKHIPKTYYVELDKPLEKNIKELLEKELLIDEIKY---KKSILNNISNNKW-EI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + EGK  +IK +F  F +KV  L RI      L
Sbjct: 179 TIFEGKFHQIKIIFAHFGYKVTYLKRIKMNNLSL 212


>gi|71894432|ref|YP_278540.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Mycoplasma synoviae 53]
          Length = 232

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 113/215 (52%), Gaps = 8/215 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA + + +R E++++I++  VKVN ++++++       D I ++G+ L   E  
Sbjct: 1   MRIEKFIADSTLYTRNEIKKLISKGLVKVNDLIIKKSQSIDPKLDKIYLEGILLEAREEF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
              + +KP G +  + D + +  VF+ L  +        ++GRLDI+TEGLL++TNDG L
Sbjct: 61  SYIMMNKPAGYICANFDWN-KQVVFELLLDLEMNLKDFFTIGRLDIDTEGLLIITNDGKL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P     + Y V     ++++   LL+K ++I  I Y   + ++     +N W  
Sbjct: 120 SHNLLSPKKHIPKTYYVELDKPLEKNIKELLEKELLIDEIKY---KKSILNNISNNKW-E 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK +F  F +KV  L RI      L
Sbjct: 176 ITIFEGKFHQIKIIFAHFGYKVTYLKRIKMNNLSL 210


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 127/242 (52%), Gaps = 17/242 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  SR+EV+++I    V+VNG  ++  ++N+    D I V      K   
Sbjct: 2   ERIDKILANMGYGSRKEVKKLIKNNLVEVNGEKVKDPSINIDPEKDKILVGD----KVVN 57

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
            R ++Y   +KP G+V+   D +   TV D L   +       VGRLD +T GLLL+TND
Sbjct: 58  YRKFIYIMMNKPEGVVSATFD-NYDETVIDLLEEEYQVFNPFPVGRLDKDTVGLLLITND 116

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKG 184
           G L   L  P  +  +VY    + +V++  +   + GIVI     C  G +++    + G
Sbjct: 117 GELNHKLISPKWKVDKVYYAEINKEVNEKDIEAFQNGIVISDGYKCMPGKLEIIKSDENG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           +  +VT+  +EGK  ++K++FE  + KV  L R+ +G   L  TL  G  RE++++ L  
Sbjct: 177 AEVYVTI--QEGKFHQVKRMFEALDKKVVYLKRVKFGNINLDETLEEGEYRELTEEELEN 234

Query: 244 QL 245
            L
Sbjct: 235 IL 236


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 118/227 (51%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I  QRV +NG +  +  ++V + +D I VDG  +   +  
Sbjct: 2   RLDKLLANKAYGSRKEVHQLIKDQRVTINGEVARKKDIHVDIESDVIAVDGQIVNTKQHY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            +  +HKP G VT   D      V D LP  + +  V+ VGRLD +TEGLLLLTNDG  +
Sbjct: 62  YIK-FHKPKGYVTAVEDA-SHPVVMDLLPPEYIKMGVVPVGRLDKDTEGLLLLTNDGVWS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   +    +VY V F G++ +D +  +K+GIV+ G         +D     +  +T+
Sbjct: 120 HSIINGNKHVEKVYYVEFEGELTEDGIQRIKEGIVL-GDGTHCKPALIDILSSKSVHITI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              EGK  ++K++       V  L R++ G   L G    GS +++S
Sbjct: 179 --EEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLTGIEEVGSAQDLS 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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 126/245 (51%), Gaps = 20/245 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG- 64
           + +EN T  R++K ++ AG  SRR  +++I Q RV +NG++ E     +   D ++VDG 
Sbjct: 1   MAEENLT--RINKFLSEAGYCSRRAADKLIDQGRVTINGVVPE-MGTKIAPGDEVKVDGE 57

Query: 65  -VPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEG 120
            +   + E+  +++ ++KPIG+V T      ++ + D  N P    R+  +GRLD  +EG
Sbjct: 58  LIATEEKEKPNVYIAFNKPIGIVCTTDTKREKNNIIDYINYPE---RIFPIGRLDKPSEG 114

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LT+DG +   +        + Y V+ +  +  D +  + KGI I      +  V   
Sbjct: 115 LIFLTSDGDIVNKILRARNNHEKEYIVKVNKPLQPDFVKKMSKGIPILDTVTRECFV--- 171

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL--IRISYGPFQLGTLLAGSTREVSK 238
            Q G N +  + L +G NR+I+++ E+  + V +L  IRI   P  +     G  R ++K
Sbjct: 172 EQTGENEFRII-LTQGLNRQIRRMCEYLGYAVTKLKRIRIMNVPLDIP---VGKWRHLTK 227

Query: 239 KILRE 243
             L+E
Sbjct: 228 AELKE 232


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 114/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G+      + V     + +DG PL+      
Sbjct: 61  RLNKYISETGFCSRREADKLIEQGRVKIDGVKAT-TGMKVSKGQSVFIDGKPLKVENELV 119

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 120 YIVLNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 176

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V    +K S     + L
Sbjct: 177 ILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLV----KKESKNSFRIIL 232

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 233 TQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLTKKELAE 282


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 122/230 (53%), Gaps = 7/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV+ ++  +++ VNG ++    V V   TD I  DG  ++  E  
Sbjct: 2   RIDKCLADCGLGTRSEVKSLLKSKKITVNGKVVTNGKVQVNPETDEILFDGEKIQYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+V+   D +   TV D + P  F + V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  YIMM-NKPKGVVSATED-NLHKTVLDLINPLYFKKGVFPVGRLDIDTHGLLLLTNDGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y+ R  G +  +     ++GIV+  G      ++ + +     + V 
Sbjct: 120 HRLLSPKKHVTKIYQARVEGVMTPEDAAAFERGIVLSDGTECMPARLDILSTTQDESIVQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + L+EGK  ++K++ +     V  L R++ G  +L   LA G +R ++++
Sbjct: 180 IHLKEGKFHQVKRMVKACGKNVVDLQRLTMGTLKLDERLALGESRPLTEE 229


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLIKIQGFVTREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 111/215 (51%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEIN-YQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    ++YR +  G  D + + +   G+ +     +   ++++    ++  ++ + 
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKIFASGMTLGDSTKLKPAELKILSQDEEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + +REGK  +IK++F     KV  L RIS G  +L
Sbjct: 181 IRIREGKYHQIKRMFGAVGMKVVELERISMGKLKL 215


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 116/225 (51%), Gaps = 9/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRR  +++I   RV +NG + E  +  V  TD +E+DG PL+      
Sbjct: 2   RINKFISETGYCSRRAADKLIDAGRVTINGNVAELGS-QVEKTDAVEIDGQPLQPKPDLE 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+  TT  D +G    F N P+   R+  +GRLD +++GL++LTNDG +   
Sbjct: 61  YLILNKPVGITCTTERDIEGNIIDFVNHPN---RIFPIGRLDKDSDGLIILTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     + +  +  +  G+ I G    +  V    Q  S  +  V L
Sbjct: 118 ILRAENNHDKEYIVTVDAPITETFIEGMAGGVDILGTTTKECVV---EQLESRTFRIV-L 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +G NR+I+++ + F ++V RL R+     +LG L  G  R++++
Sbjct: 174 TQGLNRQIRRMCKEFGYRVKRLQRVRIMNIELGDLPIGEWRDLTE 218


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/217 (31%), Positives = 112/217 (51%), Gaps = 7/217 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K     G+ SRRE +R+IA+ RV +NG  + +    V   D +  DGV L++  R  
Sbjct: 2   RINKFFTEQGLCSRREADRLIAEGRVTING-RVAKLGDQVSPQDAVARDGVVLQRGNRAV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              YHKP+G VTT ++P  R  +   +    +R+  +GRLD ++ GL+LLTNDG +   +
Sbjct: 61  YLKYHKPVG-VTTTTEPHVRRNIIAEIGHT-ARIFPIGRLDKDSSGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   R YRV    + D+  L  + +G+ I G+       TL  + G   +  + L 
Sbjct: 119 LRVEHGHEREYRVEVDREFDETFLARMARGVTILGV--PTRPCTL-ARLGPRRFRII-LT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           EG+NR+I+++ +   ++V  L R+      +  L AG
Sbjct: 175 EGRNRQIRRMCQALGYRVVSLHRVRIMHITIDGLHAG 211


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 117/234 (50%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVN-YQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +     +   ++++    ++  ++ + 
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILAQDEEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL------GTLLAGSTREVSK 238
           + +REGK  +IK++F     KV  L RIS G  +L      G  +  S  +VSK
Sbjct: 181 IKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELSLDDVSK 234


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLIKIQGFVTREIENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 123/228 (53%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R++K I+ +G  SRRE +++IA  RVK+NG+L E  AV V S D + VD  PLR   A++
Sbjct: 8   RLNKFISDSGHCSRREADKLIASDRVKINGLLPELGAV-VESGDVVTVDDQPLRASAADK 66

Query: 73  T-RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T R+++ Y+KP G+  T +D   +  + D +     R+  +GRLD  +EGL+LLT+DG +
Sbjct: 67  TDRIYIAYNKPFGITCT-TDQTVKGNIVDAIDH-DERIFPIGRLDKPSEGLILLTSDGDI 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  +    + +G+ I G      +V +    G   +  
Sbjct: 125 VNKILRAENAHDKEYIVTVNKNLAPNFAEKMSRGLPILGTITKPCKVRV---IGKTTFKI 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L +G NR+I+++ ++  + V +L+R      +LG L  G  R ++K
Sbjct: 182 I-LTQGLNRQIRRMCDYLGYDVKQLVRTRIMNIELGKLKPGQWRRLTK 228


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 127/238 (53%), Gaps = 2/238 (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  KVYILLNKPRGYISSVKDDRGRKTLLD-IVKVNERVYPIGRLDYNTSGAIILTNDGEVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   ++Y     G    +++   + GI I G      +    +    ++ V + 
Sbjct: 122 NIAHPGSNKSKIYIAAIKGIPSSEEIKRFENGIDIGGYITAKAKFDFISSNKESSKVKIE 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + EGKNR+++K+ +     V  L+RI+ G  +LG L  G+ R +++K ++   G  LL
Sbjct: 182 IHEGKNRQVRKMCDAIGHPVITLMRIAIGDIKLGNLKEGAWRYLTEKEIQYIKGGKLL 239


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 127/238 (53%), Gaps = 2/238 (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  KVYILLNKPRGYISSVKDDRGRKTLLD-IVKVNERVYPIGRLDYNTSGAIILTNDGEVYN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   ++Y     G    +++   + GI I G      +    +    ++ V + 
Sbjct: 128 NIAHPGSNKSKIYIAAIKGIPSSEEIKRFENGIDIGGYITAKAKFDFISSNKESSKVKIE 187

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + EGKNR+++K+ +     V  L+RI+ G  +LG L  G+ R +++K ++   G  LL
Sbjct: 188 IHEGKNRQVRKMCDAIGHPVITLMRIAIGDIKLGNLKEGAWRYLTEKEIQYIKGGKLL 245


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/190 (31%), Positives = 105/190 (55%), Gaps = 6/190 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++ +G+ +R+EV+++I Q RV VNG ++     +V   D + +DG  +    R  
Sbjct: 2   RLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETV-NFHRKV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L+HKP G VT+  DP    T+ + LP +   +  VGRLD + EGLL++T+DG  A  +
Sbjct: 61  YILFHKPSGYVTSTKDPHS-ETIMEFLPPL-KGIFPVGRLDKDAEGLLIITSDGDFAHRV 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + + 
Sbjct: 119 ISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKC---VEKLSNDTLKIVIT 175

Query: 195 EGKNREIKKV 204
           EGK  +IK++
Sbjct: 176 EGKYHQIKRM 185


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 122/236 (51%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKA 70
            R+ + +A A I +R EV ++I +  + VNG +++  + ++  TD +E  G   VP RK 
Sbjct: 1   MRLDRFLANAKIGTRSEVRKIIKKGEISVNGEIVKNISFHINETDIVEYMGKTVVPYRKI 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGG 129
                 +++KP G V+  ++   + +VFD +   F   + V GRLD + EGLL+LTNDG 
Sbjct: 61  ----YLIFNKPAGFVSDKTN--AQPSVFDLIDHPFIDQMHVAGRLDRDVEGLLILTNDGL 114

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               L  P     + Y + F G +  +K+ +++ GIV+    +   ++ L     S+  +
Sbjct: 115 FTHRLISPKFHVEKEYMIWFEGNLTAEKIQIVENGIVLAQNRFKPAKIKL----LSSNIM 170

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           T+ + EGK  ++KK+ +       ++ RI  G   LG +  G+ RE+ +  L E +
Sbjct: 171 TLTITEGKYHQVKKMIKIMGLTYRKIKRIRIGNINLGNMSTGNYRELDENELNELM 226


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 118/221 (53%), Gaps = 15/221 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++ AG+ SRR  +  I   +V +NG   E A +   VM  D +   G  +++ +R
Sbjct: 6   RLNKYLSEAGVCSRRAADTHIENGKVTING---ETAVMGQKVMPGDVVTFMGRKVQQKDR 62

Query: 73  TRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T +  Y+KPIGL  T S  DPD    +FD++     R+  VGRLD +++GLLLLTNDG L
Sbjct: 63  TVILAYNKPIGLTCTASKADPD---NIFDHIDYPI-RLQYVGRLDKDSQGLLLLTNDGDL 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|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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 124/230 (53%), Gaps = 7/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +++AGI SRR+ +  + + RV+V+G  +  +   V+    +  DG P++  E   
Sbjct: 13  RINKYLSQAGICSRRQADTYVEEGRVEVDG-EVAVSGTKVLPGQSVTFDGKPVKIQEDLI 71

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +HKP G+V T S  +  + + + N P+   R+  VGRLD +++GL+LLTNDG  A  
Sbjct: 72  FLAFHKPRGIVCTASKEEKDNIIDYINYPT---RIYPVGRLDKDSQGLILLTNDGEAANQ 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  + ++  + ++ ++  + +  I     +  +  ++G N +  + L
Sbjct: 129 IMKARNYHEKEYEVTVNKRITNEFIHDMRNPVPLDEINAVTRRCKV-IKEGPNEFRII-L 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E F ++V +L R+     +LG L  G  R+++   LRE
Sbjct: 187 TQGLNRQIRRMCEHFGYRVTKLKRVRVMNIKLGDLKEGRYRKLTPDELRE 236


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 116/233 (49%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R EV+  I + RV VNG + + A   V    D I +DG P+    R 
Sbjct: 5   RLDKLLAATGAGTRSEVKNAIRKGRVTVNGAVCKSADSKVDADKDVICLDGAPVVYT-RY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G VT   D     TV D + S   + +  VGRLD++TEGLLL+TNDG LA 
Sbjct: 64  EYHMLYKPAGCVTAVRDAR-YPTVMDYISSARKKDLFPVGRLDLDTEGLLLITNDGELAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----KGSNA 187
            L  P     + Y  R  G+V  + +   ++GI I     G+ + T+  +      G  +
Sbjct: 123 RLLAPGWHVDKTYYARVQGEVTAEDIRRFQEGIDI-----GEKRPTMPAELEILAAGQES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            V V + EGK  ++K++F      V  L R+  G   L   L AG +R ++++
Sbjct: 178 EVRVTIHEGKYHQVKRMFAAIGKPVLYLKRLRMGSLTLDENLQAGGSRLLTQE 230


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/218 (32%), Positives = 112/218 (51%), Gaps = 11/218 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V    D I  DG  +   E 
Sbjct: 4   MRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTEFDEILFDGEKINYKEF 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   DP  + TV D LP           GRLD +TEGLL +TNDG L
Sbjct: 64  IYIMM-NKPKGVISATYDPIEK-TVIDLLPQELKARNPFPAGRLDKDTEGLLFITNDGNL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           A  L  P    ++ Y     G V++  +   K+GIV++        D+++ L ++     
Sbjct: 122 AHKLLSPKKNVIKKYYAEILGFVNERDIKAFKEGIVLEDGYKTLPADLEILLSSEVSK-- 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V V +REGK  +IK++FE    KV  L R++ G   L
Sbjct: 180 -VYVYIREGKYHQIKRMFESVGKKVVYLKRLAMGSLTL 216


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 119/232 (51%), Gaps = 23/232 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---EVDGVPLRKAE- 71
           + K +   G+ SR+EV+ ++ +++++VN       A  V S   I   E D V   K + 
Sbjct: 1   MDKFLVECGLGSRKEVKELLKKRKIQVN-------ASIVTSGQQIIDEEKDEVFYEKEKL 53

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTN 126
              + R ++ +K  G VT   D   R TV + LP   I   ++ VGRLD +TEGLLL TN
Sbjct: 54  VYKKFRYYILYKKAGYVTALEDSKER-TVMELLPEWVIRKDLVPVGRLDKDTEGLLLFTN 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGS 185
           DG L   L  P +   + Y V     + ++ +  L++G+ I        QV  L+ QK  
Sbjct: 113 DGKLNHQLLSPKSHVDKTYHVCLEKIITEEAIEQLRQGVRIGDYTTLPAQVEQLEEQK-- 170

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +++ ++EGK  ++KK+ E  + KV+ L R+S+G   LG L  G  REVS
Sbjct: 171 ---ISLTIQEGKFHQVKKMLEAVDNKVSYLKRVSFGRLVLGDLKPGEVREVS 219


>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 = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 122/227 (53%), Gaps = 10/227 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +++    SR  +  ++A  RV+VNG+ +      +   D +E+DG PL ++E  
Sbjct: 6   HRLDRFLSQVLQVSRSGLRPVLAAGRVRVNGVPVRDRQQRIGPFDRVELDGQPL-QSEAP 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G+V+  SD D  +TV D LP+   + + + GRLD N+ GL+LLTNDG  +R
Sbjct: 65  RYLMVNKPAGVVSATSD-DQHTTVMDLLPASQRQGLHLAGRLDFNSTGLVLLTNDGAWSR 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVT 190
            L  P +Q  + YRV     + +  +    +G+    +GI     ++ + +   ++ W+ 
Sbjct: 124 QLSQPQSQVRKHYRVTVEQPLTEAYVAAFSEGMWFAFEGIKTRPAEIKIRSAYEADVWLC 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREV 236
               EG+  +IK++F  F+ KV  L R++ G   L   LA G +R++
Sbjct: 184 ----EGRYHQIKRMFGRFDNKVLTLHRLAIGHLVLDESLAPGESRDL 226


>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 = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 114/228 (50%), Gaps = 7/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI SRR+ +  IA   V VNG ++      V  TD ++ DG  +   ++  
Sbjct: 53  RLNKYIANAGICSRRDADIYIASGNVSVNGEVVTEMGYKVQLTDEVKFDGRSI-TPDKPE 111

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +K  G+  T S   G  TV D +     S++  +G+LD  T GLL+ TNDG LA+ 
Sbjct: 112 YFVLNKSKGVFVTGSVHKGGLTVMDIMAKASKSKLDPIGKLDTQTTGLLVFTNDGALAKK 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  P     ++Y ++    + QD L  +++G+ I+   I   D+    D  K     V +
Sbjct: 172 LANPKNGIRQIYHIKLDHALSQDDLEKIREGVYIESKKINVTDVSYVKDRPK---TEVGM 228

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L   K   ++K+F+  ++++  L R+ YG      L  G  R ++K+
Sbjct: 229 ELTSTKPHIVQKIFKSLSYEILNLDRVVYGGLTKKDLPRGRFRTLTKQ 276


>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 = 95.1 bits (235), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 124/230 (53%), Gaps = 7/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +++AGI SRR+ +  + + RV+V+G  +  +   V+    +  DG P++  E   
Sbjct: 18  RINKYLSQAGICSRRQADTYVEEGRVEVDG-EVAVSGTKVLPGQSVTFDGKPVKIQEDLI 76

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +HKP G+V T S  +  + + + N P+   R+  VGRLD +++GL+LLTNDG  A  
Sbjct: 77  FLAFHKPRGIVCTASKEEKDNIIDYINYPT---RIYPVGRLDKDSQGLILLTNDGEAANQ 133

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  + ++  + ++ ++  + +  I     +  +  ++G N +  + L
Sbjct: 134 IMKARNYHEKEYEVTVNKRITNEFIHDMRNPVPLDEINAVTRRCKV-IKEGPNEFRII-L 191

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E F ++V +L R+     +LG L  G  R+++   LRE
Sbjct: 192 TQGLNRQIRRMCEHFGYRVTKLKRVRVMNIKLGDLKEGRYRKLTPDELRE 241


>gi|324328601|gb|ADY23861.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 242

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 118/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L RI  GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRIEMGPLVLDEELELGQYRELT 226


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 127/254 (50%), Gaps = 24/254 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           QR+ +++A  G+ SRR++++M     ++V+G ++  A+++V     +  V G P+   + 
Sbjct: 4   QRLDRILAEMGVGSRRDIKKMARSGLIEVDGRVVRDASLHVDPGQQVLCVAGHPVHY-QP 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              W+ +KP G+V+   DP  R+ +      D  P +F      GRLDI+TEG +L+T+D
Sbjct: 63  FHYWMMNKPPGVVSAVIDPRHRTVIDLLDESDRTPRLFP----AGRLDIDTEGFVLITDD 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN 186
           G LA  +  P     + YR    G+V    +    +G+V+ G  Y  +   L  +  G  
Sbjct: 119 GQLAHAILSPKRHVSKTYRATVQGRVSDADVAAFARGLVL-GDGYRALPAHLQIRDAGER 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL------GTLLAGSTREVSKKI 240
           + V + LREGK  +IK++F      V  L R++ G   L      G   A +  EV++  
Sbjct: 178 SEVEIVLREGKFHQIKRMFAALGKPVLYLKRVAIGGVPLDPALPPGGYRALADDEVAR-- 235

Query: 241 LRE---QLGPHLLE 251
           LRE   +L PH  E
Sbjct: 236 LRETDPRLPPHPAE 249


>gi|330830315|ref|YP_004393267.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805451|gb|AEB50650.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 230

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 109/226 (48%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R    ++I Q  V V+GI++++ A ++     IE DGV L   +R R
Sbjct: 2   RLDKFLCDCSDLTRSLAGKLIRQGEVMVDGIVVKQPAFHINEQSQIEFDGVLLTLEQRNR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V ++ DPD  +  F        ++  VGRLD++T GL+L+T+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSNEDPDHPTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y V     V  D + L  +G+ ++          L+      A +T+   
Sbjct: 122 TSPRHECAKTYHVWLADPVSPDAIALFAEGVYLRNETDKTRPAQLEILGECEARLTI--H 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EGK  ++K++F     KV  L R   G   L   LA G  RE++ +
Sbjct: 180 EGKYHQVKRMFASIGNKVVGLHRERVGGLTLDDELAPGEYRELTAE 225


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/239 (33%), Positives = 129/239 (53%), Gaps = 19/239 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV++ AG  SR++V+++I +  V+VNG ++  A   V  + D I V G  L   E 
Sbjct: 6   ERLDKVLSMAGYGSRKDVKKIIKRGEVEVNGRVVTDAGTPVAPAVDSISVSGELLIFKEH 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   D    +TV D L   FS   +  VGRLD + EGLLLLT+DG L
Sbjct: 66  IYIMM-NKPQGVISATHDRR-ETTVIDLLEDEFSHRNLFPVGRLDKDAEGLLLLTDDGQL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------TLDTQKG 184
           A  L  P  +  +VY V   G++ ++ +   K+G+ +     GD +        L+  + 
Sbjct: 124 AHRLLSPRKKVEKVYYVEVKGRLVEEDVKAFKEGVFL-----GDYRALPAKLEILEAGEV 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           S+A VT+   EGK  +IK++ +    +V  L R+S GP +L   L  G  RE++ + +R
Sbjct: 179 SSALVTI--YEGKFHQIKRMMKARGKEVTYLKRLSMGPLKLDENLEPGEWRELTDEEIR 235


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/232 (31%), Positives = 119/232 (51%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +  AG+ SR +V+ ++ +++V VNG+     +  VN + TD++   G  L   E 
Sbjct: 2   RLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEL-TDNVTYQGQRLN-YET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  + TV D L     +  V  VGRLD +T GLLLLTNDG L
Sbjct: 60  FVYYMLNKPKGVISATEDPSHK-TVLDLLDDTARQKAVFPVGRLDKDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSN 186
           A  L  P     + Y  +  G + Q+ +    +GI ++   +  M   LD     +    
Sbjct: 119 AHALLSPKKHVAKQYLAKVDGTMTQEDVKHFAQGITLKD--HQCMPAYLDILEINESLKT 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           + V + + EGK  ++K++       V+ L RIS GP QL + LA G+ R ++
Sbjct: 177 SLVKITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLT 228


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 120/234 (51%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G+ SRRE ++ IA  RV +NG+  E  +  V   D I VDG PL + ++  
Sbjct: 2   RINKFISETGVCSRREADKWIAANRVTINGVPAELGS-TVEEGDEIRVDGKPLGEKKKGV 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT     G    F N P    R+  +GRLD +++GL+LLTNDG +   
Sbjct: 61  YIALNKPVGITCTTEKHVKGNIIDFVNHPE---RIFPIGRLDKDSQGLILLTNDGDIVNQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR +  V  + +  +  G+ I G      +VT    + ++    + L
Sbjct: 118 ILRAENNHEKEYVVRVNKPVTDEFVKGMAGGVRILGTKTKPCKVT----RINDHVFRIIL 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|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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 119/231 (51%), Gaps = 11/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+E++ ++    VK+NG +++ +++ +      IEV G  +   +  
Sbjct: 9   RIDKILANLGFGTRKEIKAVVKNGEVKINGTVIKDSSMKIDPDKSTIEVGGNVVEYKKNI 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G+V+   D +   TV D L   +   +   VGRLD +TEGLLL+TNDG L 
Sbjct: 69  YL-LMNKPQGVVSATFD-NYDETVIDILEPEYQAFKPFPVGRLDKDTEGLLLITNDGELN 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             +  P     +VY       +D+  +N  KKGI ++    C  G + +    + G+   
Sbjct: 127 HRMISPKNHVDKVYYAEIDKYLDERDVNRFKKGIQLKDGYKCLPGKLHIIESDEDGAKVE 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           VT+  +EGK  ++K++F      V  L RI +GP  L   L  G  RE+SK
Sbjct: 187 VTI--QEGKFHQVKRMFNALGKNVVYLKRIKFGPIDLDKDLNLGQYRELSK 235


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/221 (31%), Positives = 110/221 (49%), Gaps = 7/221 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+ 
Sbjct: 2   RLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTL-SYEKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D +   TV D L  I        VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYMLNKPKGVISATED-NHHKTVLDLLDKIAWDKEAFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS-NAWV 189
             +  P     + YR +  G +    +     GI ++   C     V L+T +    + V
Sbjct: 120 HAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSVV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + ++EGK  ++K++ +    KV  L R+S GP QL   LA
Sbjct: 180 EITIKEGKFHQVKRMVQACGKKVTDLQRLSMGPLQLDKQLA 220


>gi|291532977|emb|CBL06090.1| ribosomal large subunit pseudouridine synthase B [Megamonas
           hypermegale ART12/1]
          Length = 173

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 56/166 (33%), Positives = 89/166 (53%), Gaps = 6/166 (3%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +KP G +++  D  GR TV D L  +  R+  +GRLD NTEGLLLLTNDG     L  
Sbjct: 1   MLNKPKGYISSVKDEKGRKTVVDILSDVEERIFPIGRLDYNTEGLLLLTNDGEFMNKLLH 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSNAWVTVG 192
           P  +  + Y  R  G ++ + L+ L  G+ ++        V LD    T K S   +T+ 
Sbjct: 61  PKYEIGKTYVARIDGIINMEDLDKLANGVKLEDGKTAPADVYLDSINKTLKESRVEITI- 119

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             EGKNR+++++F+   ++V  L RI++    L  L  G  R++++
Sbjct: 120 -YEGKNRQVRRMFKALGYEVKALKRIAFAGLTLSKLKRGEYRKLTE 164


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 117/226 (51%), Gaps = 11/226 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I QQR+ +NG + E     V   D + VDG PL K ++ R
Sbjct: 10  RLNKFISDTGYCSRREADKLIDQQRITINGKIPE-MGTKVADGDEVLVDGKPL-KEKQDR 67

Query: 75  LWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ ++KP+G+  TT    +G    + N      R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 68  IYIAFNKPVGITCTTERHVEGNIVDYINHE---QRIFPIGRLDKPSDGLIFLTNDGDIVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I       + +    ++ S     + 
Sbjct: 125 KILRAGNAHEKEYVVRVDKPITDEFLQKMAAGVPI----LDTVTLPCKIKQESRFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L +G NR+I+++ E+ +++V +L R+      LG L +G  R +S+
Sbjct: 181 LTQGLNRQIRRMCEYLDYEVFKLKRVRIMNIDLGKLASGEWRYLSQ 226


>gi|323466841|gb|ADX70528.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 246

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 117/234 (50%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++  
Sbjct: 12  RIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVN-YQKYH 70

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 71  YFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNHE 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +     +   ++++    ++  ++ + 
Sbjct: 131 LLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILAQDEEHDSSEIE 190

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL------GTLLAGSTREVSK 238
           + +REGK  +IK++F     KV  L RIS G  +L      G  +  S  +VSK
Sbjct: 191 IKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELSLDDVSK 244


>gi|295093348|emb|CBK82439.1| ribosomal large subunit pseudouridine synthase F [Coprococcus sp.
           ART55/1]
          Length = 234

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 117/221 (52%), Gaps = 15/221 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++ AG+ SRR  +  I   +V +NG   E A +   VM  D +   G  +++ +R
Sbjct: 6   RLNKYLSEAGVCSRRAADTHIENGKVTING---ETAVMGQKVMPGDVVTFMGRKVQQKDR 62

Query: 73  TRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T +  Y+KPIGL  T S  DPD    +FD++     R+  VGRLD +++GLLLLTNDG L
Sbjct: 63  TVILAYNKPIGLTCTASKADPD---NIFDHIDYPI-RLQYVGRLDKDSQGLLLLTNDGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  ++       + YRVR + ++ +D +  +  G+ I        +V    +K  +    
Sbjct: 119 SNAIQKSVNNHEKEYRVRVNREITEDFIRKMSDGVPILDTVTKKCKV----RKIDDRSFM 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           + L +G NR+I+++ +   ++V  L R+     +LG +  G
Sbjct: 175 IVLTQGLNRQIRRMCDALGYRVVNLKRVRVCNVKLGNMRPG 215


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 9/232 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q   T  R++K ++ AG+ SRRE +R+I   +V V+G   E   + V  +  + V    +
Sbjct: 5   QTTETTVRLNKFLSEAGVCSRREADRLIENGKVTVDGKRAE-MGMRVSPSQRVCVGKKEV 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           R+     L   +KP+G+V T    +  + + F N P+   RV  +GRLD ++EGLLL+TN
Sbjct: 64  RQKNEMVLLAVNKPVGIVCTEEKKEKNNIIRFLNYPT---RVTYIGRLDKDSEGLLLMTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     Q  + Y+V  +  V ++ +  + +G+ I        +V +  +    
Sbjct: 121 NGDIINKMMRAGNQHEKEYKVTVNKPVTKEFIEKMAEGVPILDTVTRKCKVEMLGKYKFR 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             +T GL    NR+I+++ E+  +KV RL RI      LG L  G  R+V++
Sbjct: 181 IILTQGL----NRQIRRMCEYLGYKVTRLERIRVMNITLGELKPGEYRKVTE 228


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/235 (32%), Positives = 119/235 (50%), Gaps = 20/235 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    I SR +V++ I +  V VNG     + + +   TD I+ +G  L  + + 
Sbjct: 2   RLDKFLVEMNIGSRSQVKQYIKKGMVSVNGTNAASSDMKINEDTDTIKYNGKQLCYS-KY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R +L +KP G V+   D +   TV D L    ++ +  VGRLD++TEGLL++TNDG LA 
Sbjct: 61  RYFLLNKPAGCVSATKD-NVHQTVIDLLNGENTKDLFPVGRLDLDTEGLLIITNDGRLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------DTQK 183
            L  P+    + Y     G VD   ++L K+GI I     GD   TL         D   
Sbjct: 120 HLLSPAHHIAKTYYADIDGYVDDQTISLFKQGIDI-----GDDTPTLPASLKIIEADRST 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           GS + + + + EG+  ++K++F+  N  V  L RIS G   +   L  GS RE++
Sbjct: 175 GS-SRIELTITEGRFHQVKRMFQAVNMSVTFLKRISMGNLHIADDLPTGSYRELT 228


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 107/210 (50%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D  P      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L LP ++  +VY V     +DQ  ++    G+  +   + D+ VTL  Q          +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFR---FEDL-VTLPAQLEPIGPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EG+  ++K++F  F+ KV RL R   G
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMG 206


>gi|144227495|gb|AAZ44253.2| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae J]
          Length = 240

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 116/235 (49%), Gaps = 30/235 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++  G+ SRR+ E++I Q R+K+N    E A +   +   D IE+D   + K   
Sbjct: 5   RINKFLSEMGVCSRRQSEKLILQGRIKINN---ETAKIGQIISQNDVIELDQQKITKKPP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
              +  +KP   +T+  DP+ R T+ +     FS+   +  VGRLD  T GL+L+TNDG 
Sbjct: 62  IFWYALNKPKNYITSRFDPENRPTIME----FFSKNEYLFPVGRLDFQTTGLILITNDGK 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------Q 182
               L  PS++  R Y V+    +   ++  L            D ++ LD+       +
Sbjct: 118 TTNKLLHPSSKIERTYLVKTDFSLSDKEIRFL-----------NDNKIQLDSVKSIQKIK 166

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           K S+    V + +G N  IKK+F   + KV +L R+S+   +L  +  G  R+++
Sbjct: 167 KCSSRTYLVTVWQGSNHHIKKLFLSISKKVLKLKRVSFANIKLDNISEGKYRKLT 221


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR EV++++  ++V VNG +       +   +D I V G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQIDEKSDQIAVAGQVLSH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D D   TV D L +      V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYVLNKPKGVISATED-DRHRTVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
            V+  P     ++YR +  G + Q+ +     GI ++ +     Q+T+    +    + V
Sbjct: 120 HVMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDLTCQPAQLTILSTDEAKQTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
            + +REGK  ++K++ +     V  L R++ GP +L   LA G  R ++   L++
Sbjct: 180 DITIREGKFHQVKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQ 234


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 126/229 (55%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           QR+ K+++ +G  +R+E++++I    VKV+G++++ +A+ V   +  IEV G  L+  E 
Sbjct: 5   QRIDKILSNSGFGTRKEIKKLIKNGEVKVDGVVVKDSAMQVNPKESVIEVAGEILKYREY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   D   R TV D LP    F  +  VGRLDI+TEGLLLLTNDG L
Sbjct: 65  IYIMM-NKPQGVISATYDNRHR-TVIDILPDEYKFFNLFPVGRLDIDTEGLLLLTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWV 189
           A  L  P     + Y     G V    +++ ++G+V+    Y  +   L   K G  + V
Sbjct: 123 AHELLSPRKHVPKKYYALIDGIVTTKDVDVFREGVVLDD-GYKTLPSELFILKSGPYSEV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            + + EGK  ++K++FE    KV  L RI  G  +L  TL  G  RE++
Sbjct: 182 EIVIYEGKFHQVKRMFEAVGKKVKYLRRIGMGKLKLDETLEPGDVRELT 230


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/233 (33%), Positives = 121/233 (51%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V   +D I  DG  +   E  
Sbjct: 5   RIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTESDEILFDGEKINYKEFI 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+++   D +   TV D LP          VGRLD +TEGLLL+TNDG LA
Sbjct: 65  YIMI-NKPKGVISATYD-EVEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITNDGDLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
             L  P    ++ Y     G V++  +    +GI+++   Y  +   L+    S+  + V
Sbjct: 123 HQLLSPKKNVIKKYYAEILGFVNESDIKAFNEGIILED-GYKTLPANLEILFSSSDVSKV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V +REGK  +IK++FE    KV  L R++     L   L  G  RE+S+K L
Sbjct: 182 YVYIREGKYHQIKRMFESVGKKVIYLKRLAMDNLTLDENLKPGEWRELSEKEL 234


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 115/235 (48%), Gaps = 16/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+++  G  SRREV  +I +  +     L  ++   V S D I  +G PL   +   
Sbjct: 6   RLDKLLSSLGYCSRREVALLIREGIITHAHNLPLKSDTKV-SHDEILCEGEPLDPPQGI- 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           + L HKP GLV +H D +G+  V+D LP  +     ++ +VGRLD +T GLLLLT+DG L
Sbjct: 64  VILMHKPAGLVCSHDDGEGK-LVYDLLPERWRLRDPKISTVGRLDKDTSGLLLLTDDGAL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSN 186
              L  P  +  +VY  R    +  D+  +   G ++    +  C       +D     +
Sbjct: 123 LHRLTSPKHKVPKVYEARLDRALKGDEAEIFASGTLMLNGEKTPCLPAKLTVID-----D 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             VT+ + EG+  +++++F      V  L R S+G   LG L AG  R +  + L
Sbjct: 178 THVTLEIVEGRYHQVRRMFAAVGNHVTALHRCSFGTLTLGDLKAGEYRLIDAQSL 232


>gi|71893518|ref|YP_278964.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae J]
          Length = 237

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 116/235 (49%), Gaps = 30/235 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K ++  G+ SRR+ E++I Q R+K+N    E A +   +   D IE+D   + K   
Sbjct: 2   RINKFLSEMGVCSRRQSEKLILQGRIKINN---ETAKIGQIISQNDVIELDQQKITKKPP 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
              +  +KP   +T+  DP+ R T+ +     FS+   +  VGRLD  T GL+L+TNDG 
Sbjct: 59  IFWYALNKPKNYITSRFDPENRPTIME----FFSKNEYLFPVGRLDFQTTGLILITNDGK 114

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------Q 182
               L  PS++  R Y V+    +   ++  L            D ++ LD+       +
Sbjct: 115 TTNKLLHPSSKIERTYLVKTDFSLSDKEIRFL-----------NDNKIQLDSVKSIQKIK 163

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           K S+    V + +G N  IKK+F   + KV +L R+S+   +L  +  G  R+++
Sbjct: 164 KCSSRTYLVTVWQGSNHHIKKLFLSISKKVLKLKRVSFANIKLDNISEGKYRKLT 218


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 126/261 (48%), Gaps = 31/261 (11%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPL 67
           ++FT  R+ + +ARAG+ASRR  E++I+  RV VNG  +      VM   DH+ VDG   
Sbjct: 21  DHFT-MRLQRFLARAGVASRRGSEKLISAGRVCVNGKQVRVLGTKVMPQYDHVTVDGKEY 79

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLL 122
                    L +KP  ++TT SDP G   V      D+ P +F     VGRLD +T G+L
Sbjct: 80  VLGNDHVYLLLNKPSQVLTTMSDPFGFPCVASLVPCDDYPGLFP----VGRLDSDTTGVL 135

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GI---CY-----G 173
           L T +G +   L  PS    + Y     G++   ++  L +GI+++ G+   C+      
Sbjct: 136 LFTTNGNMGNRLLHPSHHVWKTYVALIEGKLTSSQMQKLSQGIMLEDGMTSPCFIRTITQ 195

Query: 174 DMQVT-LDTQ---------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           D   T LD             +++   + + EG+N ++K++ +     V +L R  +GP 
Sbjct: 196 DEPCTHLDKNHSLFDDMRLNAASSLCELKIHEGRNHQVKRMLQEIGHPVIKLHRFQFGPL 255

Query: 224 QLGTLLA-GSTREVSKKILRE 243
            L   +  GS R  +++ + +
Sbjct: 256 CLNAQIPLGSWRMCTQQEIHD 276


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/234 (33%), Positives = 116/234 (49%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+  ++      V   +  I VDG  +   +  
Sbjct: 8   RLQKVLSQAGIASRRVAEKMIRDGRVEVDDRIVTELGTRVDPAESVIRVDGARITVDDTL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGLLLLTNDG L
Sbjct: 68  VHLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L++G+ +  G    D    +DT  G    V
Sbjct: 128 AHRLMHPSYEVPKSYVATVLGSVPRGLGRKLREGVELDDGPVQVDDFALVDTTPG-RTLV 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V L EG+   ++++     + V  L+R   G   LG    GS R +++K + E
Sbjct: 187 RVTLHEGRKHIVRRLLAEVGFPVQNLVRTDIGGVSLGDQRPGSIRALTQKEIGE 240


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 124/233 (53%), Gaps = 14/233 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ KVI+  G  SR +++  + +  V V+G +++ + ++V      IE++G  L     
Sbjct: 5   QRLDKVISNFGFGSRNDIKSAVKKGLVTVDGAIVKDSGIHVDPEASIIEINGERLN---- 60

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
            R ++Y   +KP G+++  SD   R TVFD LP  +    +   GRLDI+TEGL+L+TND
Sbjct: 61  YRKFIYIMMNKPQGVISATSDRKQR-TVFDILPEEYKCFELFPAGRLDIDTEGLVLMTND 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G L+  +  P     + Y  +  G+V+Q+  +  ++G+ +    Y  +   L+  K    
Sbjct: 120 GQLSHEILSPKKHVPKQYYAKVLGRVNQEDADAFRQGVTLDD-GYSTLPAVLEVLKSDEL 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + + + + EGK  ++K++FE    KV  L R+S G  +L   L  G  +E+ +
Sbjct: 179 SEIKLTIVEGKFHQVKRMFEAVGKKVIYLKRLSMGNLRLDENLKLGECKELGE 231


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/244 (27%), Positives = 119/244 (48%), Gaps = 11/244 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K ++ +   P R++K ++ AG+ SRRE +  I    V+VN  ++      +   D +
Sbjct: 1   MKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQAGVVQVNDQVVTELGTKITRQDKV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
                 ++   +  + L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 61  LFKDQQVQIESKVYIVL-NKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++     D ++  
Sbjct: 120 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVSIEDMEKIANGLELE-----DGEIHA 174

Query: 180 D----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           D      +   + V + +  G+NR ++++FE   + V +L R+ +       L  G  R 
Sbjct: 175 DAISYASEDDKSQVGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWRY 234

Query: 236 VSKK 239
           ++++
Sbjct: 235 LNER 238


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/241 (32%), Positives = 123/241 (51%), Gaps = 14/241 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +AG  SR +V+++I  ++V V+G+L +R  +NV  S   I V G  L  A   
Sbjct: 2   RLDKLLGQAGYGSRNQVKKLIRSRQVYVDGVLADRDNLNVDASLQTITVSGKELEHAPEV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L 
Sbjct: 62  -YYLMNKPSGVVSARRDKE-HQTVIDLIKPEDQREGLYPVGRLDRDTEGLVLITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             L  P     + Y V  +  +  +     + G+V +   +C    +++       S A 
Sbjct: 120 FALLHPRYHVAKRYYVEVNDVLGPEAPAFFESGVVFEDGTVCKPAHLKILSSASDKSCAH 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR---EVSKKILREQ 244
           +T+   EGK  ++KK+F  +  KV  L RIS+G F L   L  GS R   E  K IL+  
Sbjct: 180 ITIS--EGKFHQVKKMFLAYGVKVTYLKRISFGDFVLDEKLPRGSYRPLTEEEKSILKRY 237

Query: 245 L 245
           L
Sbjct: 238 L 238


>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 = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 107/210 (50%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D  P      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L LP ++  +VY V     +DQ  ++    G+  +   + D+ VTL  Q          +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFR---FEDL-VTLPAQLEPIGPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EG+  ++K++F  F+ KV RL R   G
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMG 206


>gi|317182664|dbj|BAJ60448.1| hypothetical protein HPF57_1374 [Helicobacter pylori F57]
          Length = 257

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 119/236 (50%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  + +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTKEMESAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMR 234


>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 = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 118/236 (50%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 TLMHANLE--KEYLVKIQGFVTKEMENAMQEGLKLENATKGAHQKTSIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMR 234


>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 = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 124/243 (51%), Gaps = 27/243 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQRV+K +A++G+ SRRE E +IA   V ++G  +  A   ++        G  L  A+R
Sbjct: 17  PQRVNKWLAQSGVCSRREAEALIADGLVSIDGETIADAGRKILP-------GQTLTLADR 69

Query: 73  TRLWL------YHKPIGLVTTHSDPDG----RSTVFDNL------PSIFSRVISVGRLDI 116
               L       +KP+G V+   +P      R     NL      P   + +  +GRLD 
Sbjct: 70  AAASLGGFTAVLNKPVGYVSGQPEPGHVPAVRLLTAANLSGEGAAPDARASLPPLGRLDE 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+L++DG LA+ +  P +   + Y VR  GQVD+ KL  L+ G+ + G       
Sbjct: 130 DSRGLLILSDDGVLAKAVIGPQSDLDKEYVVRVAGQVDERKLARLRHGLELDGRKLKPAT 189

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V++  Q  +  +V   L+EG+ R+I+++ +    +V  L+R+  GP +LG L  G  R +
Sbjct: 190 VSV-IQGNTLRFV---LKEGRKRQIRRMCDLVGLRVVDLLRVRIGPLKLGDLPEGRWRVL 245

Query: 237 SKK 239
           + +
Sbjct: 246 TPQ 248


>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 = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/234 (32%), Positives = 119/234 (50%), Gaps = 15/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A A + +R+EV+++I  +RV+VN  +  +    +   D + VD   L   E   
Sbjct: 2   RLDKYLAHAQLGTRKEVKKLIRSKRVRVNDEICTKEDRQLQKEDCVYVDDELLVYDELVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           L LY KP G+++   D    +TV D   +   +    VGRLDI++EGLLL+TNDG LA  
Sbjct: 62  LMLY-KPQGVISATEDR-VHTTVMDIFDAPLPKNCFPVGRLDIDSEGLLLITNDGQLAHQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
           L  P     + Y V     +  + L LL+ G +       D +  L  Q      ++ ++
Sbjct: 120 LLSPKKHVDKTYYVECEKTLSSEDLQLLESGTI-----QLDKEHVLPAQAKRISANSLYL 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           T+  +EGK  ++K++ +    KV  L RIS G  QL   LA G  R +S++ +R
Sbjct: 175 TI--QEGKFHQVKRMLQACGNKVCYLKRISMGSLQLDKSLAPGEWRYLSEEEIR 226


>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 = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 121/231 (52%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A + SR EV++++ ++RV+VNG + + + + V  +T  I VD +P+   E+ 
Sbjct: 3   RLDRILANARVGSRSEVKKLVKEKRVRVNGEIAKSSDMRVDENTAEIFVDDIPV-TYEKY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G ++  ++     TV D +   +  +   GRLD +TEGLL++TNDG LA  
Sbjct: 62  VYYMLNKPAGYISA-TEGKNCPTVLDLITEDYKGMFPCGRLDKDTEGLLMITNDGPLAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V     + ++ +  ++ G+   G+ Y         +K S+   T+ +
Sbjct: 121 LLSPKKHVEKEYYVEHTLPLTEEDIAKIESGVTYNGVSYKPAVY----KKISDTSCTLTI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           +EGK  EIK +F     KV  L R+      L  TL  G  R ++K+ L +
Sbjct: 177 QEGKYHEIKFIFNSVGDKVVYLKRLRMKNLVLDETLKPGEYRPLTKEELED 227


>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 = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/211 (32%), Positives = 114/211 (54%), Gaps = 7/211 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+++ +ARAG+  SRR+ + +IA  +V+VNG + +   + V   D +EV+GV +    + 
Sbjct: 11  RLNRYLARAGVCPSRRKADELIASGQVRVNGQVAQ-LGMRVGPDDIVEVNGVRVVPQTQA 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSR-VISVGRLDINTEGLLLLTNDGGL 130
              L +KP   +TT  D  GR TV D  NLP      +  VGRLD NT G+LLLTNDG L
Sbjct: 70  LYILMNKPHDTITTCDDERGRRTVLDLINLPPEQKNGLFPVGRLDRNTTGVLLLTNDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  ++Y  R    V  ++   L++G+ ++      +QV ++        + 
Sbjct: 130 ANRLMHPRYRVEKIYVARTARPVKPEEAEQLRRGVQLEDGPARAVQVAVNPADPHE--IA 187

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + + EG+NR+++++ E    +V +L R  Y 
Sbjct: 188 LMIYEGRNRQVRRMLEAIGHEVVQLKRTHYA 218


>gi|307638112|gb|ADN80562.1| Ribosomal large subunit pseudo uridine synthase B [Helicobacter
           pylori 908]
          Length = 257

 Score = 94.4 bits (233), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  + +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMESAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 179 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 238

Query: 239 K 239
           +
Sbjct: 239 Q 239


>gi|327390694|gb|EGE89034.1| hypothetical protein SPAR5_0271 [Streptococcus pneumoniae GA04375]
          Length = 240

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDQIHFDGQKLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y+ +  G + ++ +    +GI ++       +   V++DT+K + + 
Sbjct: 120 HTLLSPKRHVDKTYQAQVKGMMTREDVETFAEGIPLKDFTCQPAKLELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L
Sbjct: 179 IRVTIAEGKFHQIKRMVAYCGKEVMDLQRLTMGTLVLDENLGRGEWRRLTKEEL 232


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 111/222 (50%), Gaps = 10/222 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +A     SRR+ + +IA+Q+V +N    +  A  +  +D I ++   +      
Sbjct: 15  ERLNKFLAFQLGVSRRQADNLIAKQKVYINNQPAQLGA-RIGESDTITINNHIVGGRSSY 73

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KPI  V +        T++  LP  F  +  VGRLD N+ GLLLLTNDG  A  
Sbjct: 74  TYLMLNKPINYVCSRKQQGKTPTIYSLLPDKFHNLKPVGRLDANSSGLLLLTNDGDFAFR 133

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----WV 189
           +  P  +  + Y V     +D++   L ++ I   GI   D    L   + SN     W+
Sbjct: 134 MTHPKFKKNKQYNV----TLDKELAPLHQQMIADFGIQLNDGLSKLGLSRQSNQDRHNWI 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            V + EG+NR+I++ F    + V +L R  +G ++LGTL AG
Sbjct: 190 -VTMSEGRNRQIRRTFAALGYTVIKLHRTHFGTYKLGTLGAG 230


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/231 (31%), Positives = 112/231 (48%), Gaps = 15/231 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER   
Sbjct: 1   MNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTV-SIERKIY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            L +KP   VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA  L
Sbjct: 60  VLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKL 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAW---- 188
             P     ++Y V        DK NL K  +  +  GI   D ++  D    ++ +    
Sbjct: 120 THPKYLKKKIYHVHL------DK-NLTKADMEQIAAGIQLDDGEIQADAISYTDDFKKDE 172

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 173 VGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 223


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/216 (31%), Positives = 112/216 (51%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR EV+R++ +++V VNG +   A + +  + D I V+   L   ER 
Sbjct: 6   RLDKFLVEMGLGSRTEVKRLLKKKQVLVNGKIETSAKIQIDENQDEISVNNQVLI-YERF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D  N  +    V  VGRLDI+T GLLLLTN+G LA
Sbjct: 65  VYYLLNKPKGVISATED-DKHRTVLDLLNENARQKEVFPVGRLDIDTHGLLLLTNNGALA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             +  P     +VYR +  G + +  +   + GI ++       ++T+    ++   + V
Sbjct: 124 HAMLSPKKHVAKVYRAKVDGIITEKDVEHFEAGIELKDFTCQPAKLTILEVNEEQQTSLV 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EGK  ++K++ +     V  L R+S GP  L
Sbjct: 184 EIIISEGKFHQVKRMVQACGKTVTDLERLSMGPLML 219


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  + +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLVKIQGFVTREMESAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>gi|291059845|gb|ADD72580.1| RNA pseudouridine synthase superfamily [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 284

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 21/243 (8%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           + F   R+   +AR+G ASRR  E +IA  RV V+G  +      V + + + VDG  ++
Sbjct: 28  QPFFRLRLQVYLARSGCASRRACEALIASGRVTVDGQTVTTQGRTVCAQNVVCVDGTVVQ 87

Query: 69  KAERTRLWLYHKPIGLVTTHSD--PDGRS--------------TVFDNL-PSIFSRVISV 111
                R  L +KP+G + + +   P G +                 D + P+   R+  +
Sbjct: 88  LERVQRYVLLYKPVGYICSLAPQFPAGYAHTQVRAGPSKQEYARAIDLVQPAYQERLYHI 147

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+ +EG LL TNDG  A+ L  P +   + Y V     V    L+   +G+ ++G  
Sbjct: 148 GRLDVRSEGALLFTNDGSFAQALGHPRSGIEKEYIVETREPVPAALLSSFVRGVWVEGCR 207

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           Y      +  +  +   V + L EGK REI+ VFE +   V RL+R+  G  +LG L  G
Sbjct: 208 YR----CVRARHLAAQCVQLVLVEGKKREIRVVFEAWGQDVVRLVRVRIGRVRLGPLRPG 263

Query: 232 STR 234
           + R
Sbjct: 264 AFR 266


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 123/227 (54%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ASRR+V+  I + R+ VNG L   +   V   D I V+G  + + ++ +
Sbjct: 7   RINKFLASKGLASRRQVDLWIEEGRISVNGSL-ATSGQKVSEEDDIVVNGKSISQKKQKK 65

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L +K   +++   D  GR TV D + S + R+  VGRLD  T GL+LLTNDG L   
Sbjct: 66  VYYLLYKEEEVLSAVKDDRGRRTVVDCVLSPY-RIFPVGRLDYRTSGLILLTNDGDLFNR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           +  P  +  + Y V   G + +++L  L++G+ ++       +   +  +KG N +  + 
Sbjct: 125 MMHPRAEIFKSYEVLAKGHLTKEQLKTLEEGVELEEGKTLAALIAKVKYEKG-NTFFEIS 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +REGKNR+I+++ E    +V RL R   G   L  L  G  R + +K
Sbjct: 184 IREGKNRQIRRMVEAVGSRVYRLRRTKIGKLSLDGLSLGEYRALEEK 230


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 112/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AG+ASRR  E MIA  RV+V+G ++    + V  +  +              
Sbjct: 80  RLQKVLAQAGVASRRVAEEMIADGRVEVDGEIVTEQGLRVDPSVAVVRVDGVRVVVNENL 139

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L  +KP G  +T SD  GR  V D +    +   R+  VGRLD +TEGLLL+TNDG L
Sbjct: 140 VHLALNKPRGWHSTMSDDMGRPCVGDIVAERVAAGQRLFHVGRLDADTEGLLLVTNDGEL 199

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G+V ++    L+ G+ ++ G    D    L+  +G +  V
Sbjct: 200 AHRLMHPSYEVPKTYLAWVAGEVPRNLGKKLRDGVELEDGPVTVDRFSVLEAAEGKST-V 258

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V L EG+   ++++       V RL+R   G   LG    GS R
Sbjct: 259 RVVLHEGRKHIVRRLLAEVGHPVQRLVRTHVGTVALGDQRPGSLR 303


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/210 (31%), Positives = 108/210 (51%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D LP      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLLPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L LP ++  +VY V     +DQ  ++    G+  +   + D+ +TL  Q          +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFR---FEDL-ITLPAQLEPIGPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EG+  ++K++F  F+ KV RL R   G
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMG 206


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 115/231 (49%), Gaps = 11/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+AGIASRR  E +I   RV+V+G ++      +     +          +   
Sbjct: 10  RLQKVLAKAGIASRRVAEELIELGRVQVDGEVVREQGRRIDPDKAVVHVDGVRVVLQEDV 69

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L  +KP G+++T  D   R  V D L +   R+  VGRLD +TEGLLL+TNDG LA  
Sbjct: 70  VTLVLNKPRGMLSTMHDDAHRPCVGDLLVNRKERLFHVGRLDADTEGLLLVTNDGDLAHR 129

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----GSNAW 188
           L  PS +  + Y     G + +D    L+ GI ++     D  V +D+ K        A 
Sbjct: 130 LMHPSYEVPKTYLAEVPGPIPRDLGKRLRSGIELE-----DGPVKVDSFKLISSLPGRAL 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V V L EG+   ++++ E     V  L+R + G  +LG    GS R ++++
Sbjct: 185 VEVVLHEGRKHIVRRLLEAVGHPVQTLVRTAVGEVRLGNQRPGSLRVLNRQ 235


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTISKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 113/227 (49%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+++ IA +G+ SRR+ + +I    V VNG+++      V  + D I  +G  L K E+ 
Sbjct: 187 RLNRYIANSGVCSRRKADELIQAGVVTVNGVVVTELGTKVDAAKDEIRYNGEKL-KREKM 245

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  DP  R TV   +      R+  VGRLD NT GLLLLTNDG LA 
Sbjct: 246 VYVLLNKPKDYITTTDDPQERKTVMHLVEKASRERIYPVGRLDRNTTGLLLLTNDGNLAE 305

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P    +++Y V  +  + Q   N +  G+ ++       +V+   Q  S   + + 
Sbjct: 306 KLSHPRNNIMKIYHVELNKSLTQGDFNKIGYGVELEDGFIKPDEVSY-IQGASKREIGIQ 364

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  G+NR ++++FE   + V +L R+ Y       L  G  R + +K
Sbjct: 365 IHSGRNRIVRRIFESLGYDVIKLDRVIYANLTKKDLPRGRWRYLEEK 411


>gi|297380685|gb|ADI35572.1| conserved hypothetical protein [Helicobacter pylori v225d]
          Length = 262

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 122/241 (50%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>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 = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/225 (31%), Positives = 111/225 (49%), Gaps = 11/225 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+  GI SRRE ++ I   RV +NG++  +    V S D + +DG PLR   +   
Sbjct: 6   LNKYISETGICSRREADKFIEAGRVSLNGVVATKGN-RVASGDTVLLDGKPLRSNPKRIY 64

Query: 76  WLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +HKP GL  T +D   R+ V  + N P    R+  +GRLD ++EGL+ LTNDG +   
Sbjct: 65  LAFHKPKGLTCT-TDLRDRTNVIAYINHPQ---RIFPIGRLDKDSEGLIFLTNDGDIVNK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +  GI I G       V    QKG + +  + L
Sbjct: 121 ILRSRNGHEKEYIVVVDKPFAPDFIRRMSNGIPILGTTTKKCVV---EQKGQSTFRII-L 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +G NR+I+++ E+  ++V +L RI     +L  L  G  R  S+
Sbjct: 177 TQGLNRQIRRMCEYMGYEVKKLKRIRIMSIKLDDLAPGKWRYFSE 221


>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 = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 119/242 (49%), Gaps = 25/242 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A AG  +R EV++ I + +V+VNG+  +++ + V   D + +DG  + +A    
Sbjct: 6   RLDKFLADAGAGTRSEVKKFIQKGKVQVNGVPAKKSEIKVSEEDEVVLDGNRISQAPEFV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L HKP G V+   D   + TV + + S    +  VGRLD +TEGLLL+T+DG LA  L
Sbjct: 66  YYLLHKPAGYVSATEDKRDK-TVMELVASDRKDLFPVGRLDKDTEGLLLITDDGALAHEL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------LDTQK---- 183
             P     + Y     G + ++ +     G+ I     G+   T       L T+K    
Sbjct: 125 LSPKKHVDKTYYAVTDGCMTKEDVQRFADGLEI-----GEKNPTMPAKLKILSTRKVEET 179

Query: 184 -------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
                  G ++ + + ++EGK  ++K++ E    KV  L RIS G   L   L  G  R+
Sbjct: 180 ELEQYPSGWSSEIQLTIKEGKFHQVKRMTEAVGKKVVYLKRISMGVLTLPDDLKKGECRQ 239

Query: 236 VS 237
           ++
Sbjct: 240 LT 241


>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 = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 113/222 (50%), Gaps = 17/222 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLR 68
           T  R++K IA AG+ SR++  R+I +  V VN     R A ++   D    I V+G  ++
Sbjct: 3   TKIRLAKYIAHAGVCSRKQASRLIDEGVVTVNN----RPANHIDHVDEQDDIIVNGQVVK 58

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A     + YHKP+G+    ++ D  S +  +LP++ +RV  +GRLD ++ GLL+LTNDG
Sbjct: 59  GAADLVYFAYHKPVGIDCKLNENDPASLIH-HLPTL-TRVYPIGRLDKDSRGLLILTNDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSN 186
                L  P     + Y V     ++      +  GI +      D Q+TL  +  K ++
Sbjct: 117 DFCNQLIHPDFHQPKRYLVTVDKPINNAFCEKMAAGIPV------DKQITLPCEVTKIAD 170

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              ++ L++G NR+I+K+  +  +KV  L R+ +    L  L
Sbjct: 171 NQFSIILKQGLNRQIRKMAHYCGFKVIDLFRVQFSELALSNL 212


>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 = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 78/252 (30%), Positives = 134/252 (53%), Gaps = 9/252 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            ++ + +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDAS-KKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITILAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAP 260
            +E+ Q +   P
Sbjct: 239 FIEKQQTSKALP 250


>gi|317178163|dbj|BAJ55952.1| hypothetical protein HPF16_1355 [Helicobacter pylori F16]
          Length = 262

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 118/236 (50%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMR 239


>gi|42523444|ref|NP_968824.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
 gi|39575650|emb|CAE79817.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
          Length = 245

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 114/238 (47%), Gaps = 27/238 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++A  GI SRRE +  I++  V VNG ++ +    V     I ++   L++ +R  
Sbjct: 8   RLSKLMAEKGICSRREADDYISRGLVMVNGEVVSQLGTKVSPDVKITLEAQALKQQKRLA 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--------FDNLPS-----IFSRVISVGRLDINTEGL 121
             L +KP+G V+   +P  +  +        F N  +      F  +   GRLDI+++GL
Sbjct: 68  TILLNKPVGYVSAQPEPPYQPAIKLITPQNQFGNSKTRLKEEHFKGLAVAGRLDIDSQGL 127

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG +A+ +    ++  + Y VR  G +  DKL LL  G+ + G      +V    
Sbjct: 128 LLFTQDGRIAKKIIGEESKVEKEYIVRVQGTLPPDKLKLLNFGLSLDGKKLKPAKVE--- 184

Query: 182 QKGSNAWVTVG-----LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 W+        L+EGK R+I+++ E    KV  L R+  G  +LG L  G  R
Sbjct: 185 ------WLNEDQLRFILQEGKKRQIRRMCELVGLKVTGLKRVRIGKIRLGQLPEGQWR 236


>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 = 93.6 bits (231), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 112/225 (49%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     +R++V  M+AQ+RV+V+G +      +V     +E+D   L+     R
Sbjct: 2   RLDRFLANLPSYNRQQVRLMLAQRRVRVDGKVASDPLTDVREFSRVELDEQLLQAGRPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + +KP G V+   DP  R TV D LP+     + + GRLD NT GL++LTNDG  +R 
Sbjct: 62  YLMLYKPTGCVSATHDPQHR-TVLDLLPTALRDDLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+T+  + Y V    ++ +  +   ++G              LD      A + +  
Sbjct: 121 LTQPATKLPKHYLVDTEDEIGEHYVAKFREGFYFAFEDLTTQPAQLDILGPHRARLAI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            EG+  ++K++F  FN KV  L R S G  +L   LA G  RE++
Sbjct: 179 VEGRYHQVKRMFGHFNNKVVGLHRESMGAIRLDPGLAPGEYRELT 223


>gi|313500364|gb|ADR61730.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 230

 Score = 93.6 bits (231), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 112/225 (49%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     +R+ V  M+AQ+RV+V+G ++     +V     +E+D   L+     R
Sbjct: 2   RLDRFLANLPSYNRQHVRLMLAQRRVRVDGQVVSDPLTDVREFSRVELDEQLLQAGRPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + +KP G V+   DP  R TV D LP+     + + GRLD NT GL++LTNDG  +R 
Sbjct: 62  YLMLYKPTGCVSATHDPQHR-TVLDLLPAALRDDLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+T+  + Y V    ++ +  +   ++G              LD      A + +  
Sbjct: 121 LTQPATKLPKHYLVDTEDEIGEHYVAKFREGFYFAFEDLTTQPAQLDILGPHRARLAI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            EG+  ++K++F  FN KV  L R S G  +L   LA G  RE++
Sbjct: 179 VEGRYHQVKRMFGHFNNKVIGLHRESMGAIRLDPGLAPGEYRELT 223


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 120/249 (48%), Gaps = 26/249 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV----------NVMSTDHIEVDG 64
           R++  IA     SRRE +R+I +  VK+N  L     +            M    I + G
Sbjct: 2   RLNHFIALHSKYSRREADRLIIEGAVKINHALATTKTLVPQIALQNPHAAMKEFKIFIHG 61

Query: 65  VPLRKAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             L  A++      +YHKP G + +  D  GR  ++D+L + ++  + VGRLD  +EGLL
Sbjct: 62  KMLHYAKKQNYTAIVYHKPKGELVSKKDSYGRKLIYDSLNARYAHFMPVGRLDFASEGLL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV----T 178
           +L++   +  V +L  +   R Y ++    + +  +  +++G+ +Q    G  ++    T
Sbjct: 122 ILSDSKEV--VSKLMHSNLPRTYILKIDSHITKQMIKAMEEGLTLQNAKAGGHRLSKIKT 179

Query: 179 LD--------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           ++         +  S + + V + EGKNRE+++ F  FN  V  L R+SYG   L  L  
Sbjct: 180 MEFMPMEYEIIKSASISKLKVRISEGKNRELRRFFAHFNANVLDLRRVSYGFINLNALPV 239

Query: 231 GSTREVSKK 239
           G TR  +K+
Sbjct: 240 GKTRFFTKQ 248


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 119/245 (48%), Gaps = 24/245 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ K++   G  SR ++++ + Q  + VNG  ++ + + V    D IEV+G  +   E 
Sbjct: 9   QRLDKILTHMGYGSRSDIKKQVKQGMITVNGRTIKDSGLQVHPYQDQIEVNGELVVFREF 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             + L HKP G+++   D   R TV D L +         VGRLD +TEGLLLLTNDG L
Sbjct: 69  IYIML-HKPPGVISATEDTRER-TVLDLLSAEERHFEPFPVGRLDKDTEGLLLLTNDGKL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------- 182
           A  L  P     + Y     G V ++ +     G+ +      D  VTL  Q        
Sbjct: 127 AHELLSPRRHVPKTYEATVSGHVTEEDILQFTAGVELD-----DGYVTLPAQLTILRHEQ 181

Query: 183 ----KGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREV 236
                G   +++++ + EGK  ++K++FE    KV  L R + GP +L   L  GS RE+
Sbjct: 182 PHQADGEVTSYISLVIHEGKFHQVKRMFEAIGKKVTYLKRTAMGPLKLDDQLPLGSYREL 241

Query: 237 SKKIL 241
           + + L
Sbjct: 242 TSEEL 246


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 21/243 (8%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           + F   R+   +AR+G ASRR  E +IA  RV V+G  +      V + + + VDG  ++
Sbjct: 5   QPFFRLRLQVYLARSGCASRRACEALIASGRVTVDGQTVTTQGRTVCAQNVVCVDGTVVQ 64

Query: 69  KAERTRLWLYHKPIGLVTTHSD--PDGRS--------------TVFDNL-PSIFSRVISV 111
                R  L +KP+G + + +   P G +                 D + P+   R+  +
Sbjct: 65  LERVQRYVLLYKPVGYICSLAPQFPAGYAHTQVRAGPSKQEYARAIDLVQPAYQERLYHI 124

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+ +EG LL TNDG  A+ L  P +   + Y V     V    L+   +G+ ++G  
Sbjct: 125 GRLDVRSEGALLFTNDGSFAQALGHPRSGIEKEYIVETREPVPAALLSSFVRGVWVEGCR 184

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           Y      +  +  +   V + L EGK REI+ VFE +   V RL+R+  G  +LG L  G
Sbjct: 185 YR----CVRARHLAAQCVQLVLVEGKKREIRVVFEAWGQDVVRLVRVRIGRVRLGPLRPG 240

Query: 232 STR 234
           + R
Sbjct: 241 AFR 243


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 81/244 (33%), Positives = 126/244 (51%), Gaps = 12/244 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE-- 71
           R++K ++ AG+ SRR+ +  IA  +V+VNG ++      V  +TD IEV+G  L   E  
Sbjct: 47  RLNKALSGAGVCSRRQADTFIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGEAL 106

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
              R    + +KP+ +V+T  DP GR+T+ D LP      R+  VGRLD  +EGLLLLT+
Sbjct: 107 NRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLLTD 166

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  +   
Sbjct: 167 DGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRSEY 226

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
              + + L +G NR+I+++       V RL+RI  GP +LG L  GS R +     K LR
Sbjct: 227 GVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGSCRRLEDHEVKALR 286

Query: 243 EQLG 246
           +  G
Sbjct: 287 KAAG 290


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 116/235 (49%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR EV++++  ++V VNG +       +    D I V G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQINEKKDQIAVAGQVLSH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L +      V  VGRLDI+T GLLLLTN G LA
Sbjct: 61  VYYLLNKPKGVISATED-DHHRTVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNKGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             +  P     ++YR +  G + Q+ +     GI ++       Q+T+    +    + V
Sbjct: 120 HAMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPAQLTILSTDEAKQTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
            + +REGK  +IK++ +     V  L R++ GP +L   LA G  R ++   L++
Sbjct: 180 DITIREGKFHQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQ 234


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/252 (30%), Positives = 134/252 (53%), Gaps = 9/252 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            ++ + +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDAS-KKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAP 260
            +E+ Q +   P
Sbjct: 239 FIEKQQTSKALP 250


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 72/217 (33%), Positives = 111/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDINT GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDINTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ +    +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVGKTYLAQVKGIMTQEDVETFAEGIPLKDFTCKPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RVK++G+      + V +   + +DG  L+      
Sbjct: 64  RLNKYISETGFCSRREADKLIEQGRVKIDGVKAT-TGMKVSNGQSVSIDGKSLKVENELV 122

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F N      R+  +GRLD +++GL+ +TNDG +   
Sbjct: 123 YIALNKPVGITCTTESKIKGNIVDFINHEK---RIFPIGRLDKDSQGLIFMTNDGDIVNK 179

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G       V    +K S     + L
Sbjct: 180 ILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLV----KKESKNSFRIIL 235

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK L E
Sbjct: 236 TQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKELAE 285


>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 = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 127/244 (52%), Gaps = 12/244 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE-- 71
           R++K ++ AG+ SRR+ + +IA  +V+VNG ++      V  +TD IEV+G  L   E  
Sbjct: 47  RLNKALSGAGVCSRRQADTLIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGEAL 106

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
              R    + +KP+ +V+T  DP GR+T+ D LP      R+  VGRLD  +EGLLLLT+
Sbjct: 107 NRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLLTD 166

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  +   
Sbjct: 167 DGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRSEY 226

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
              + + L +G NR+I+++       V RL+RI  GP +LG L  G+ R +     K LR
Sbjct: 227 GVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGACRRLEDHEVKALR 286

Query: 243 EQLG 246
           +  G
Sbjct: 287 KAAG 290


>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 = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 79/250 (31%), Positives = 124/250 (49%), Gaps = 16/250 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ +  V VNG   +    ++  T D I V G  L   E+ 
Sbjct: 2   RLDKFLVENGLGSRSQVKEVLKKGLVLVNGRAEKSPKTHINETADEIVVSGQKL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G ++   D +   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPKGYISATED-ERHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +    +GI ++       Q   V LD +K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQSDVEQFARGIELKDFTCQPAQLKIVELDEEK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGP 247
           V + L EGK  ++K++      +V  L R++ GP QL + LA G  R ++K+ ++     
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDSGLALGEWRRLTKEEMKS---- 234

Query: 248 HLLEEAQVNL 257
             LE  QV L
Sbjct: 235 --LERFQVEL 242


>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 = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 124/238 (52%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKAE 71
           R++K +A  G+ SRRE ++ I   RV +NG + E  A+ V   D + +DG  +   +  E
Sbjct: 2   RLNKFLASIGVCSRREADKAIEAGRVMINGEVAELGAM-VGEEDLVSLDGRYIATGKDVE 60

Query: 72  RTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           + +  +  ++KP G+V T SD DG + V D +  +  R+  VGRLD ++ GLLLLTN G 
Sbjct: 61  KVKPIIIAFNKPEGIVCTTSDNDGATNVVDYI-GMKERIYPVGRLDKDSSGLLLLTNQGS 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L   +    + Y V+ +  +D D +N +  GI +  +     +  +  +K +    
Sbjct: 120 LTNSLLRAANYHEKEYIVKVNKDIDDDFINKMSNGIYLYELKTKTRKCKV--KKLNKNTF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS----KKILRE 243
           ++ L +G NR+I+++      KV +L R+     +L  L  G+ R +S    KK+ +E
Sbjct: 178 SIVLTQGLNRQIRRMCLACGMKVQKLNRVRIVNIKLDGLALGAYRNLSDEEIKKLYKE 235


>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 = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 117/239 (48%), Gaps = 15/239 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K +A++G+ SRRE +  IA   V V G ++  A   V +   +  +   
Sbjct: 8   IYDGAEPIRLNKWLAQSGVCSRREADAFIADGLVSVEGEVVRDAGRKVEAGQSVSFNPQA 67

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFSRVISVGRLD 115
               +     +YHKP+G+V+   +      V               P+  S++  VGRLD
Sbjct: 68  QASLDAKLTVVYHKPVGIVSGQPEAGETPAVRMIRRPNHWGQLTQWPNQDSKLAPVGRLD 127

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLL+L+ DG LA+ +  P ++  + Y VR  G + + KL  L++G+ + G     +
Sbjct: 128 KDSRGLLILSEDGVLAKAIIGPDSELEKDYTVRVRGPIFEAKLKWLRQGLELDG---RKL 184

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +  +  Q G      V L+EG+NR+I+++ +    +V  L R   GP ++G L  G  R
Sbjct: 185 KPAVVQQVGEQTLRFV-LKEGRNRQIRRMCDMCELRVLDLYRSRIGPVEIGDLPEGQWR 242


>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 = 93.2 bits (230), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 123/230 (53%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K+++  GI +R+EV++ I    V+VNG I+L+ +       D +  DG  +   E  
Sbjct: 5   RLDKLLSNMGIGTRKEVKKYIKDGLVEVNGEIVLDPSKTVDTEKDEVLFDGEKVEYKEFI 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+++   D     TV D LP   +  +V  VGRLD +TEGLL++TNDG LA
Sbjct: 65  YVMM-NKPQGVISATHDK-SEETVIDLLPEEIALRKVFPVGRLDKDTEGLLIITNDGELA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVT 190
             L  P  + ++ Y     G++ +      K+G++++   Y  M   L+  + S+ + V 
Sbjct: 123 HKLLSPKKKVVKKYYAEVLGKITEKDAEKFKEGVILED-GYRTMPSQLEIIESSDISKVY 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           V L EGK  ++K++FE    KV  L R+  G  QL   L  G  RE++++
Sbjct: 182 VYLTEGKYHQVKRMFEAIGKKVLYLKRLCMGKLQLDENLEPGEWRELTEE 231


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 112/236 (47%), Gaps = 22/236 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++      VKVNG ++    V V +  D I  DG  +   E 
Sbjct: 22  QRIDKILSNLGYGSRSELKKFCKNGLVKVNGKVINNPGVQVDVENDEIIFDGEKVTYKEF 81

Query: 73  TRLWLYHKPIGLVTTHSDP---------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             L L +KP G ++   D          D    VF+  P        VGRLD +TEGLL+
Sbjct: 82  IYLML-NKPDGYISATFDKRDPIVLDLIDKEDLVFEPFP--------VGRLDKDTEGLLV 132

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  +  P     + Y  +  G V ++ +    KG+ +    Y  M   L   K
Sbjct: 133 LTNDGQLAHRVLSPKKHVPKTYYAKIEGIVTEEDIKAFAKGVTLDD-GYETMPAELIILK 191

Query: 184 GSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
               + + + + EGK  ++K++FE  + KV  L R+S G  +L   LA G  RE++
Sbjct: 192 SDEISEIELTIHEGKFHQVKRMFESVDKKVIYLKRLSMGKLKLDENLALGEYRELT 247


>gi|332365597|gb|EGJ43357.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 242

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 109/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIAVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++       Q   + LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKAFTCQPAQLKILELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTNLQRLTMGPLQLDPALA 220


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 118/226 (52%), Gaps = 11/226 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA   IASRRE + +I   +VKVNG ++   A  V  TD +E D     K E+ +
Sbjct: 2   RLNKYIASLNIASRREADNLIKDGKVKVNGEIILNPATQVSETDKVECD-----KDEKNK 56

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++  +KP G V + +  +G+ T+++ L +    V  VGRLD ++ GL+LLTNDG  A+ 
Sbjct: 57  IYIKLNKPRGYVVSTNKDEGK-TIYELLNNKLKGVYPVGRLDKDSNGLILLTNDGVFAKK 115

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   ++   + Y V+ +  +    L  L+ GI + G      +    T+   N  +T   
Sbjct: 116 IIGENSNCEKEYYVKVNDNIPDGALKKLEYGISLDGKKLKPAKTKRITKNSFNIILT--- 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EG+NR+I+++ E   ++V  L R+      L  L  G    ++K+
Sbjct: 173 -EGRNRQIRRMCEKVGFEVIILKRLRINNIFLNELKEGKFEYLTKE 217


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGIPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>gi|315151609|gb|EFT95625.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 320

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 77/260 (29%), Positives = 137/260 (52%), Gaps = 15/260 (5%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG 64
           ++QE     R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G
Sbjct: 53  LIQEWSGTMRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKG 112

Query: 65  VPLRKAERTRLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINT 118
             +  + +T ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +T
Sbjct: 113 QLI--SHKTHVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDT 166

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQV 177
           EGLLLLT++G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++
Sbjct: 167 EGLLLLTDNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKI 226

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREV 236
           T+     + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R +
Sbjct: 227 TVLAATETESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSL 286

Query: 237 SKKILREQLGPHLLEEAQVN 256
           +++ L+  L    +E+ Q +
Sbjct: 287 TREELQLLLPYFFIEKQQTS 306


>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 = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 76/239 (31%), Positives = 120/239 (50%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGKVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y V+  G + Q  +++  +GI ++       +   V++DT+K + + 
Sbjct: 120 HALLSPKRHVNKTYLVQVKGIMTQGDVDIFAEGIPLKDFTCQPARLELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELENLLA 237


>gi|295105192|emb|CBL02736.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii SL3/3]
          Length = 233

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 111/229 (48%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R E + M+A+ RV+VNG + ++    +   D + VDG PLR  +   
Sbjct: 2   RLDKYLAETAQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDNDTVTVDGAPLRYQKFVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DGG A 
Sbjct: 62  LML-NKPEGVVSASTDKR-DTTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V     + Q+       G+ +  G      +VT  +  G    V V
Sbjct: 120 DILSPRHHVSKTYTVTIDTPLTQEMRTGFAAGVTLADGTALSPAEVTALSPDGCT--VRV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            LR+G   +IK++F  +   VN L R + G   L   LA G  RE+S +
Sbjct: 178 VLRQGVYHQIKRMFGVYGAGVNALHREAIGGLALDAQLAPGQWRELSDE 226


>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 = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 112/229 (48%), Gaps = 7/229 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
            T  R++K ++ AGIASRR+ + +I    V +NG + +   V V    D + V G P+  
Sbjct: 1   MTKVRLNKFLSAAGIASRRKCDEIIFAGEVTINGRVAQGPFVQVDDQHDRVLVRGKPIAS 60

Query: 70  AERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            ++   ++ HKP+G V T      G   V D    +  RV +VGRLD  T GL+L+TNDG
Sbjct: 61  TKKV-YFMVHKPLGFVCTSERKFPGTKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++ +  V +  LN L +G +I G     + V+    K     
Sbjct: 120 DFANKIIHPSYGITKEYLLKVNRDVIEKDLNSLMQGTMIDGKRVRPVAVS----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++
Sbjct: 176 IKIVVNEGKKHEIRLFAEAAGLQILELKRIRIGSLVLGGLRYGEYRELT 224


>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 = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 5   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFV 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 65  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 122 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 181 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 229


>gi|296390923|ref|ZP_06880398.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PAb1]
          Length = 230

 Score = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 105/208 (50%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D  P      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLFPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L LP ++  +VY V     +DQ  ++    G+  +      +   L+      A +T  L
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLTTLPAQLEPIGPRCARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F  F+ KV RL R   G
Sbjct: 179 HEGRYHQVKRMFGHFDNKVLRLHRERMG 206


>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 = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 117/230 (50%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VK++G++++     V  ++ +  V G  +   E  
Sbjct: 4   RIDKMLANMGFGTRKEVKKLLKSGVVKIDGMIVKDPKTQVNPSEQVVTVRGEEVEYKEFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+++   D     TV D L     +F+    VGRLD +TEGLLLLTNDG L
Sbjct: 64  YLMM-NKPPGVISATEDM-AEETVIDLLEEEDRVFAP-FPVGRLDKDTEGLLLLTNDGQL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G+V ++ +   + GIV+           +  + G  + V 
Sbjct: 121 AHQLLSPKKHVPKTYFAVIDGEVTEEDIESFRHGIVLDDGYKTKPAELIILKSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           V + EGK  +IK++F     +V  L RI  GP  L  +L  G  RE+++K
Sbjct: 181 VTITEGKFHQIKRMFRALGKRVVYLKRIQMGPLALDPSLEVGEYRELTEK 230


>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 = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 92.8 bits (229), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESRNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>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 = 92.8 bits (229), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 116/234 (49%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ M+   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNMLKSGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+      KGI ++       +   V++DT+K + + 
Sbjct: 120 HALLSPKRHVDKTYLAQVKGIMTQEDAETFAKGIPLKDFTCQPARLELVSVDTKK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEEL 232


>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 = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 109/219 (49%), Gaps = 13/219 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +   G+ SR +V+  + +++V VNG +       +        D +     E T 
Sbjct: 2   RLDKFLVDCGVGSRSQVKNFLKKKQVIVNGQVETSPKTQIDENK----DRITYLDQELTH 57

Query: 75  ----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG 128
                +L +KP G+++   DP  + TV D L       RV  VGRLDI+T GLLLLTN+G
Sbjct: 58  ETFVYYLLNKPQGVISATEDPRHK-TVLDLLDDTARHKRVFPVGRLDIDTHGLLLLTNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSN 186
            LA  +  P     ++Y+ +  G +D++ +   +KGI ++   C    +++    +  S 
Sbjct: 117 DLAHAMLSPKKHVDKIYQAKVAGVMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNEST 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +WV + + EGK  ++K++      +V  L R+S GP  L
Sbjct: 177 SWVQITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSL 215


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 112/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     +  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEIFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ + +  +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVEIFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 66/210 (31%), Positives = 107/210 (50%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D  P      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLFPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L LP ++  +VY V     +DQ  ++    G+  +   + D+ +TL  Q          +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFR---FEDL-ITLPAQLEPIGPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EG+  ++K++F  F+ KV RL R   G
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMG 206


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 123/240 (51%), Gaps = 12/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKAE 71
           R++K +A  G+ SRRE +R I   RV +NG   E  A+ V   D + +DG  +   +  E
Sbjct: 2   RLNKFLASIGVCSRREADRAIEANRVMINGETAELGAI-VGEEDLVSLDGRYIATGKDVE 60

Query: 72  RTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           + +  +  ++KP G+V T SD DG + V D +  +  R+  VGRLD ++ GLLLLTN G 
Sbjct: 61  KVKPIIIAFNKPEGVVCTTSDNDGATNVVDYI-GMKERIYPVGRLDKDSSGLLLLTNQGS 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L   +    + Y V+ +  +D + +N +  GI +  +     +  +  +K +    
Sbjct: 120 LTNSLLRAANYHEKEYIVKVNKDIDDEFINKISNGIYLYELKTKTRKCKV--RKLNKNTF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLG 246
           ++ L +G NR+I+++      KV +L R+     +L  L  G  R +S    K L ++LG
Sbjct: 178 SIVLTQGLNRQIRRMCAACGRKVQKLNRVRIVNIKLDGLAVGDYRNLSDEEIKKLYKELG 237


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 112/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     +  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEIFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ + +  +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVEIFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 119/227 (52%), Gaps = 5/227 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKVIA+AG ASRR+ E +I + +VKVN  ++      V   D I V+G PL K E  
Sbjct: 2   ERLSKVIAQAGCASRRKAENLITEGKVKVNDEVINVLGYKVSPKDIITVEGKPLVK-EPL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G ++T +D   R  + D +       R+  + +L+ +T GLLL+TNDG L 
Sbjct: 61  VYYLLNKPTGYLSTTADIHKRRNILDLILKEDQNVRLFPIHKLEYDTSGLLLVTNDGELT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
           + L   S    + Y +R  G + ++++  +K+GI ++   I   D+ +    +   +  V
Sbjct: 121 KKLTSQSESIQKEYVIRTKGIMIKERIREIKRGIKVENKIIKPVDIAIVELDKAHQSTLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + +     +E+K +F+    +V  + RI +    L  +  GS R++
Sbjct: 181 KMIITNESAKELKTMFKQLGHEVKNMTRIRFDSLTLEGVNRGSYRKL 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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 108/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPGKDRVTFMGEDLVH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPAGVISATED-DHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWV 189
             +  P     ++YR +  G +D+  +   + GI ++        +Q+    +  ++++V
Sbjct: 120 HAMLSPKKHVSKIYRAQVAGIMDEADVARFEAGIALKDFTTLPARLQILEVNEANASSYV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EGK  ++K++      +V  L RIS GP  L
Sbjct: 180 EIEIAEGKFHQVKRMVAACGKEVADLERISMGPLTL 215


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 123/234 (52%), Gaps = 15/234 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
           +R++K ++  GI SRRE +RMI + R+ ++G +   AA+  M  D+  I VDG   RK +
Sbjct: 11  ERINKYLSAHGICSRREADRMIQEGRITIDGRI---AAMGEMVDDNTIICVDG---RKVD 64

Query: 72  RTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +     +  ++KP+G+V T +D  G++ + D       R+  VGRLD  ++GL+LLTND
Sbjct: 65  NSTPPQVVIAFNKPVGIVCTTTDKQGKNNIVD-FIGYKERIYPVGRLDKESDGLILLTND 123

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   L        + Y V  +  +++D +  +  GI ++ +     +  +  +K S+ 
Sbjct: 124 GDMMDRLLRSVNGHEKEYIVSVNKPINKDFIKRMSGGIYLKELDRTTRKCVV--EKISDR 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +G NR+I+++     + V +L RI     +LG L  G  RE+  K L
Sbjct: 182 TFRIILTQGLNRQIRRMCAECGYSVTKLTRIRIMNVELGDLKTGEYRELDGKEL 235


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 109/227 (48%), Gaps = 6/227 (2%)

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  RTRLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   ++ HK IG L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  
Sbjct: 62  KV-YFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGEF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  PS+   + Y ++    V    L  L +G  I G     + VT    K     V 
Sbjct: 121 ANKIIHPSSGITKEYLLKVSRDVSAKDLGKLMEGTFIDGKHVRPVSVT----KIRRGTVK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGK  EI+   +   + +  L RI  G   LG L  G  RE++
Sbjct: 177 IVVSEGKKHEIRLFADAAGFPILELKRIRIGSLVLGGLRYGEYRELT 223


>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 = 92.4 bits (228), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 110/227 (48%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +      +R++V  ++A +RV+V+G++       V     +EVD   ++     R
Sbjct: 2   RLDRFLGNLPCYNRQQVRLLLASKRVRVDGVVASDPLHEVREFSRVEVDDQVVQAGYPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + HKP G V+  SDP    TV D LP+     + + GRLD NT GL++LTNDG  +R 
Sbjct: 62  YLMLHKPTGCVSATSDP-LHPTVLDLLPAELRDGLHIAGRLDYNTTGLMILTNDGQWSRH 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T+  +VY V    ++    ++  ++G              LD      A +T+  
Sbjct: 121 LTQPRTKLPKVYLVHTEDEIGAHYVDKFREGFYFAFEDLTTQPAQLDILGPREARLTI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            EG+  ++K++F +F  KV  L R   G   L   LA G  RE+S +
Sbjct: 179 VEGRYHQVKRMFGYFQNKVVGLHRERMGAIALDPGLAPGEYRELSAE 225


>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 = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 116/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y     TL   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGTLTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>gi|315170843|gb|EFU14860.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 320

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 62  RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 119

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 175

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 176 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 235

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 236 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 295

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 296 PYFFIEKQQTSKALP 310


>gi|315159966|gb|EFU03983.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
          Length = 260

 Score = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESHNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>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 = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 120/233 (51%), Gaps = 10/233 (4%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A +    SR +V+++  ++++ VNG L+ R+   V + D I V+G  L   +  
Sbjct: 6   RLDKLVASQFSDVSRADVKKLCLKKKISVNGKLMARSDAKVDTDDEIFVNGERLVYKKHV 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G+V +  + D   TV D +P    R  +   GRLD +TEG +LLT+DG L+
Sbjct: 66  YIML-NKPAGVVCSTKEGDSM-TVLDLVPPELMRNGLFPAGRLDKDTEGFVLLTDDGELS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGS---NA 187
             +  P T   + Y VR       +  +++  G+ I+G+  G+ +  L  Q  GS   + 
Sbjct: 124 HRMLSPKTHVPKTYFVRLEKPYQPEYADIMAAGMTIKGLDGGEDEKCLPAQFSGSDENDC 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             T+ L EGK  ++K++F     KV  L R + G   L G L +G   E+  K
Sbjct: 184 ECTLILHEGKFHQVKRMFAELGNKVVYLKRTAIGEMPLNGELASGKCLEILHK 236


>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 = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/210 (31%), Positives = 106/210 (50%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA   ++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGHLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D  P      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L LP ++  +VY V     +DQ  ++    G+  +   + D+ VTL  Q          +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFR---FEDL-VTLPAQLEPIGPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EG+  ++K++F  F+ KV RL R   G
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMG 206


>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 = 92.4 bits (228), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 121/235 (51%), Gaps = 13/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAE 71
           R++K ++ AG+ SRRE +R+I + RV V+G    + AV  M  D    + V    +R  +
Sbjct: 2   RLNKFLSEAGVCSRREADRLIEEGRVTVDG----KKAVPGMQVDPSSEVRVGKKRIRSKD 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  +   HKP G+V T       + + F   P    R+   GRLD  +EGLL++T+DG L
Sbjct: 58  KKTVLAVHKPAGIVCTEDKRVKNNIIRFLKYPE---RITYAGRLDKESEGLLIMTDDGEL 114

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAW 188
              +        + Y+V  +  V ++ +N +  G+ +     G  +VT   + ++     
Sbjct: 115 INGMMRSRYGHEKEYKVWVNKPVTEEFVNRMSSGVRLVDKEKGLDEVTRPCEVRQCGTYI 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            T+ L +G NR+I+++ E   +KV RL+RI     +LG L  G+ R+++++ L E
Sbjct: 175 FTIILTQGLNRQIRRMCEALGYKVKRLVRIRIMNIELGNLKPGAYRKLTEQELNE 229


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 57/158 (36%), Positives = 89/158 (56%), Gaps = 4/158 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K +A  GIASRR+ E +I Q RVKVNG ++    V +    D + +DG  L K E+
Sbjct: 3   ERLQKYMAACGIASRRKCEEIILQARVKVNGKIVNELGVKIDEEKDLVTLDG-KLIKKEK 61

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++++  +KP G V+T  D  GR T+ D L  +  R+  +GRLD +T GL+LLTNDG + 
Sbjct: 62  NKVYIALNKPKGYVSTVKDERGRKTILD-LVDVTERIYPIGRLDYDTSGLILLTNDGDIY 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             +  P  +  ++Y     G   ++ +   + GI I G
Sbjct: 121 NKIIHPKQEKNKIYIALIKGIPTENDIKKFEIGINIDG 158


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 112/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER 
Sbjct: 7   KRLNKFISETGFCSRREADKLIEQGRVTLNGAQPE-VGSKVTEQDEVCIDGKPLRSKERP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D + S   R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-SHHKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA 232


>gi|261838734|gb|ACX98500.1| pseudouridine synthase B [Helicobacter pylori 51]
          Length = 262

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 123/241 (51%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A   + SRRE E+++ + RVK+N    + ++V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTMHSRREAEKLVLEGRVKINHEHAKLSSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+    V ++  + +++G+ ++    G  Q T              
Sbjct: 126 ALMHANLE--KEYLVKIQSFVTKEMESAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 K 239
           +
Sbjct: 244 Q 244


>gi|49081896|gb|AAT50348.1| PA0733 [synthetic construct]
          Length = 231

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 107/214 (50%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     SRR+ + +IA   ++V+G ++      V     +E+D   L+  +  R
Sbjct: 2   RLDRFLANLPELSRRDAQMLIAGGHLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP    TV D  P      + +G RLD NT GL+LLTNDG  +R 
Sbjct: 62  YYMLHKPMGCVSATRDPQ-HPTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           L LP ++  +VY V     +DQ  ++    G+  +   + D+ VTL  Q          +
Sbjct: 121 LTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFR---FEDL-VTLPAQLEPIGPRCARL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            L EG+  ++K++F  F+ KV RL R   G   L
Sbjct: 177 TLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICL 210


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 108/220 (49%), Gaps = 6/220 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++ +G+ SR+EV++++ Q+ +KVNG L +     +   D            ++  
Sbjct: 2   RLDKFLSDSGLGSRKEVKQLLKQKCIKVNGTLAKDGKQQISQIDDYVTHAGEKIVYQKYF 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +KP  ++++  DP  R TV D L     R  +  VGRLD +TEGLLLLTNDG LA 
Sbjct: 62  YYVLNKPKNVISSTKDPIER-TVVDLLAKKHYRKDIFPVGRLDKDTEGLLLLTNDGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y     G V +  + L  KG  ++ G      ++ +D     +    V
Sbjct: 121 QLLSPKKHVDKEYLAEIDGIVTEQDIKLFAKGFTLKNGEAVKPARLIIDQMDEGHQMTIV 180

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            L  +EGK  ++K+VFE    +V  L R+  G   L + L
Sbjct: 181 HLTIQEGKFHQVKRVFETIGKRVTYLKRLKMGSLSLDSDL 220


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 122/229 (53%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R++K ++ +G+ SRR+ E +I   +V+VN  ++   +  V  + D ++V+G  ++  ++
Sbjct: 1   MRINKFLSFSGLTSRRKAEDLILSGKVEVNDKVISDLSYKVDPNKDVVKVNGRLVKIRKK 60

Query: 73  TRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L++KP  ++T    DP G  T+ + +  +  R+   GRLD ++EGLLLLT+DG  A
Sbjct: 61  RHYLLFYKPRWVLTALGKDPGGLKTLDEYIKDLKIRLFPAGRLDFDSEGLLLLTDDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +  PS + ++ Y+V  +   D  DK  +L  G V+ G         +       +W+ 
Sbjct: 121 HKIHHPSFEVVKKYQVLVNPIFDIVDKEKVL-SGCVLMGKYVKPDSFKILKDLSDASWLE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +   EG    +K+  +   + V RLIR++ G F+L T + GS R +S++
Sbjct: 180 IAFHEGMKHLVKEYLKKMGYSVKRLIRVAIGDFRL-TGVPGSYRWLSEE 227


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/225 (32%), Positives = 116/225 (51%), Gaps = 10/225 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + K++ +A I SR EV++MI  Q+V ++G + +  + NV      + VDG  + +     
Sbjct: 1   MDKLLEKARIGSRTEVKKMIKNQKVVLDGKIAQSISQNVDTGFQELIVDGKKI-EGYSHH 59

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L HKP G VT   D +   T+FD L        +  VGRLD +TEGL+L+T++G L  
Sbjct: 60  YFLIHKPAGYVTARLDQN-HPTLFDLLKPEDRVEGLYPVGRLDRDTEGLVLVTDNGPLGF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKG-SNAWV 189
            +  PS    + Y V  +G + +D     + GIV     +C   +   ++ Q+  S A++
Sbjct: 119 RMLHPSHHVEKTYYVEVNGFLGEDAPLFFRSGIVFLDGTVCKPAVLEVINCQQNLSKAYL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           T+   EGK  ++KK+F  +  KV  L R+S+    LG L  G  R
Sbjct: 179 TIS--EGKFHQVKKMFLSYGLKVTYLRRVSFAGLSLGNLPLGKYR 221


>gi|46449495|gb|AAS96146.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio
           vulgaris str. Hildenborough]
          Length = 267

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/244 (32%), Positives = 127/244 (52%), Gaps = 12/244 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE-- 71
           R++K ++ AG+ SRR+ + +IA  +V+VNG ++      V  +TD IEV+G  L   E  
Sbjct: 22  RLNKALSGAGVCSRRQADTLIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGEAL 81

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
              R    + +KP+ +V+T  DP GR+T+ D LP      R+  VGRLD  +EGLLLLT+
Sbjct: 82  NRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLLTD 141

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  +   
Sbjct: 142 DGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRSEY 201

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILR 242
              + + L +G NR+I+++       V RL+RI  GP +LG L  G+ R +     K LR
Sbjct: 202 GVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGACRRLEDHEVKALR 261

Query: 243 EQLG 246
           +  G
Sbjct: 262 KAAG 265


>gi|224100741|ref|XP_002311995.1| predicted protein [Populus trichocarpa]
 gi|222851815|gb|EEE89362.1| predicted protein [Populus trichocarpa]
          Length = 397

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 123/241 (51%), Gaps = 21/241 (8%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ENF    QR+SKV+A AG+ASRR  E +I + +V VNG +       V    D I V+G 
Sbjct: 140 ENFRDQAQRLSKVLAAAGVASRRSSEALIFEGKVTVNGSVCNTPQTRVDPGRDSIYVNGN 199

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRS--TVFDN-----------LPSIFSRVISV 111
            L K    ++++  +KP G + +  + + +S   + D+           LP    R+ +V
Sbjct: 200 RLPKKLPPKIYIALNKPKGYICSLGEKESKSVMCLLDDYFQSWDKRNPGLPK--PRLFTV 257

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI- 170
           GRLD+ T GL+++TNDG  A+ +  PS+   + Y     G V +  L  + +G VI+G+ 
Sbjct: 258 GRLDVATTGLIIVTNDGDFAQQIAHPSSNLSKEYIATVDGVVSKRHLFAVSEGTVIEGVR 317

Query: 171 CYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           C  D    L  Q       + + + EG+N E++++ +    +++ L R+  G F+L + L
Sbjct: 318 CVPDSVELLPQQPDRPRPRLRIVVHEGRNHEVRELVKNAGLEIHSLKRVRIGGFRLPSDL 377

Query: 230 A 230
            
Sbjct: 378 G 378


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 124/236 (52%), Gaps = 12/236 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +N T  R++K ++ AG  SRRE +R+I   RV +N ++ E     V S D ++VDG  
Sbjct: 1   MSDNLT--RLNKYLSEAGYCSRREADRLIDAGRVTINDVVPE-MGTKVASGDIVKVDGEI 57

Query: 67  LRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLL 123
           + + ++  ++L ++KP+G+V T      +  + D  N P    R+  +GRLD  +EGL+L
Sbjct: 58  IGERKQGFVYLAFNKPVGIVCTTDTRVEKDNIIDYINYPK---RIFPIGRLDKPSEGLIL 114

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LT+DG +   +   S    + Y V     + Q  +  +  GI I+ +  G      + +K
Sbjct: 115 LTDDGDIVNKILRASNNHEKEYIVTVDKPISQTFVARMAGGIYIEEL--GKRTKKCEVKK 172

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 ++ L +G NR+I+++ E+ N++V  L R+     +L   L G  RE++K+
Sbjct: 173 IDKFTFSIILTQGLNRQIRRMCEYLNYEVQTLKRVRIMNIKLDMPL-GKYRELTKE 227


>gi|283769551|ref|ZP_06342447.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283103819|gb|EFC05205.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 231

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/231 (34%), Positives = 119/231 (51%), Gaps = 17/231 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ +V+A A + SR +V+ M+   RV VNG I L  + +   + D I +D   L+ A+  
Sbjct: 2   RLDRVLANASVGSRTQVKNMVKNGRVSVNGKIALASSMMVDPNQDVIRIDDEILQYAKYQ 61

Query: 74  RLWLYHKPIGLVTTHSDPDGR--STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L LY KP G +   S  +GR   TV + +P+ +  +   GRLD +TEGLLL+TNDG LA
Sbjct: 62  YLMLY-KPAGYI---SATEGRYDPTVLELVPN-YKGLFPCGRLDKDTEGLLLMTNDGRLA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWV 189
             L  P     + Y V     + Q+ +  +++GI  + I Y    +++  D Q       
Sbjct: 117 HNLLSPKKHVEKEYYVEHQLPLSQEDVLCIERGIRYKNITYKGAKLKILDDLQ------C 170

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           T+ L+EGK  EIK +F   + KV  L RI      L  TL  G  R +S++
Sbjct: 171 TIILQEGKYHEIKNIFLAIDNKVTYLKRIRMKNLILDETLKKGEYRPLSEE 221


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 109/225 (48%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     +R++   M+AQ+RV+V+G ++      V     +E+D   L+     R
Sbjct: 2   RLDRFLANLPSHNRQQARLMLAQRRVRVDGQVVSDPLAEVREFSRVELDEQLLQAGRPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + HKP G V+   DP    TV D LP+     + + GRLD NT GL++LTNDG  +R 
Sbjct: 62  YLMLHKPTGCVSATQDPQ-HPTVLDLLPAALRDDLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+T+  + Y V    ++ +  +   ++G              LD      A + +  
Sbjct: 121 LTQPATKLPKHYLVDTEDEIGEHYVARFREGFYFAFENLTTQPALLDILGPRQARLAI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            EG+  ++K++F  FN KV  L R S G   L   LA G  RE++
Sbjct: 179 VEGRYHQVKRMFGHFNNKVVGLHRESMGAICLDPGLAPGEFRELT 223


>gi|312868136|ref|ZP_07728340.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
 gi|311096540|gb|EFQ54780.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
          Length = 242

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/224 (29%), Positives = 109/224 (48%), Gaps = 23/224 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---------ILLERAAVNVMSTDHIEVDGV 65
           R+ K +   G+ SR EV++++ Q+++ VNG         I  ++  V  M  D +     
Sbjct: 2   RLDKFLVDCGVGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPDKDQVTFMGEDLVH---- 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLL 123
                E    +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLL
Sbjct: 58  -----ETFVYYLLNKPAGVISATED-DHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLL 111

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDT 181
           LTN+G LA  +  P     + YR +  G +D+  +   ++GI ++        +Q+    
Sbjct: 112 LTNNGKLAHAMLSPKKHVSKNYRAQVAGIMDEADVARFEEGIALKDFTTLPARLQILEVN 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +  ++++V + + EGK  ++K++      +V  L RIS GP  L
Sbjct: 172 EASASSYVEIEIAEGKFHQVKRMVAACGKEVVDLERISMGPLTL 215


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 111/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ +    +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+++   DP  R TV D L   ++R   V  VGRLDI+T GLLLLTNDG L
Sbjct: 62  -YYMMNKPQGVISATEDPKHR-TVLDLLDD-YARAKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNA 187
           A  L  P     + Y  +  G + Q+ +    KGI ++       +   V++D +K + +
Sbjct: 119 AHALLSPKRHVDKTYLAQVEGIMSQEDVETFAKGIPLKDFTCQPAKLEFVSVDPEK-NQS 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V V + EGK  ++K++  F   +V  L R++ G   L   L  G  R ++K+ L
Sbjct: 178 LVRVTIAEGKFHQVKRMVAFCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEEL 232


>gi|229032362|ref|ZP_04188334.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228728970|gb|EEL79974.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 242

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 114/229 (49%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHIAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDEISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE+S
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDAELELGEYRELS 226


>gi|332359298|gb|EGJ37119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 242

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 111/222 (50%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDERADEIVVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++       Q   + LD +K S + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMEQADVERFAAGIELKDFTCQPAQLKILELDEEKES-SL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACRKEVTDLQRLTMGPLQLDPTLA 220


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 114/236 (48%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+ V+ ++  + V VNG + +     V    D I V G  +   E  
Sbjct: 2   RLDKLLANMGFGTRKTVKNVLKAKEVTVNGTMEKDGKTQVDPDKDVIVVSGEAVHYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             ++ HKP G+V+   D +   TV D L     +F     VGRLD +TEGLLLLTNDG L
Sbjct: 62  Y-FMMHKPQGVVSATID-NLHETVIDLLQPQDQVFDP-FPVGRLDKDTEGLLLLTNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQ-KGSNA 187
           A  L  P     + Y     G V++  +   K GI +    IC       L T  +    
Sbjct: 119 AHNLLSPKKHVDKCYEAIIEGLVNEQDIQAFKDGITLNDGFICQSAKLEILSTDLEKEQT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + V + EGK  ++K++FE  +  VN L R+S G  QL  T+  G+ R ++ + L 
Sbjct: 179 LIHVTIHEGKFHQVKRMFEAVDKSVNYLKRLSMGKLQLDETVEIGNYRPLTNEELE 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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/217 (34%), Positives = 106/217 (48%), Gaps = 17/217 (7%)

Query: 24  GIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           GI S  E  R+I + R+ +NG  +++   V+V   D I V+G PL    R  L L HKP 
Sbjct: 2   GIPSGTEAGRLIERGRISINGRPIVQNRWVDV-RKDSILVNGTPLEATCRLTL-LMHKPA 59

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           G V +  DP  R TVF  LP     + + GRLD +T GLLLLTND  L   L  P  +  
Sbjct: 60  GYVVSRDDPLNRDTVFQLLPDPSVYIGASGRLDKDTTGLLLLTNDTYLQSSLVDPVYKVP 119

Query: 143 RVYRVRFHG-QVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------------QKGSNAW 188
           +VYRV   G  ++  +L  L+ G+ ++ G     +   LD              +     
Sbjct: 120 KVYRVVVKGAALNGAQLMALRSGVSLEDGPTLPALVEPLDVNGDPLPLEMSEYDRYKCKQ 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + L EG+NR+++++ E     V  L RI  GPF L
Sbjct: 180 LNITLWEGRNRQVRRMVEAVGSTVRDLCRIQLGPFSL 216


>gi|295113966|emb|CBL32603.1| pseudouridine synthase family [Enterococcus sp. 7L76]
          Length = 260

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I++ G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKLKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>gi|327484742|gb|AEA79149.1| Ribosomal large subunit pseudouridine synthase F LSU Psi2604
           [Vibrio cholerae LMA3894-4]
          Length = 328

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 112/235 (47%), Gaps = 7/235 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTINGLQPE-VGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T 
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLTQ 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           GL    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L 
Sbjct: 182 GL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILA 232


>gi|158520075|ref|YP_001527945.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158508901|gb|ABW65868.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
          Length = 241

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/234 (33%), Positives = 115/234 (49%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++ AG+ SRR  E  IA+ RV VNG ++      V   +D +  DG  +  AE  
Sbjct: 11  RLQKFLSGAGVCSRRRAEVYIAEGRVAVNGQVVTELGTKVDPESDDVMFDGHRVTLAESH 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G VT  S    + T    L ++  RV  VGRLD  + GLLL+T+DGGL + 
Sbjct: 71  VYIALNKPPGYVT--SCLQKQETTVMELVAVDQRVFPVGRLDKPSCGLLLMTSDGGLHQR 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS    + Y V     V    L+ +++G+VI G      +V    ++ S+    + L
Sbjct: 129 LSHPSFDHEKEYDVACDRPVSDADLDAMRRGMVITGRKTRPAKV----KRLSDRRFLIIL 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR---EVSKKILREQ 244
           +EG+NR+I+++ E    +V  L RI      LG L  G  R   E  KK L  Q
Sbjct: 185 QEGRNRQIRRMAEMLGNRVVLLRRIRIAHIHLGDLAEGRWRYLTEEEKKALLHQ 238


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 111/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ +    +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>gi|325697447|gb|EGD39333.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 242

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/222 (32%), Positives = 109/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIVVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++       Q   V LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAQLKIVELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLTMGPLQLDPALA 220


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTDQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 64  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 121 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 181 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 232


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 62  RLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 119

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 175

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 176 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 235

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 236 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 295

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 296 PYFFIEKQQTSKALP 310


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 117/236 (49%), Gaps = 10/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKSGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+      KGI ++       +   V++DT+K + + 
Sbjct: 120 HALLSPKRHVDKTYLAQVKGIMTQEDAETFAKGIPLKDFTCQPARLELVSVDTKK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L +
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELED 234


>gi|301793545|emb|CBW35921.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae INV104]
          Length = 240

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/217 (32%), Positives = 111/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVMDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ +    +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 64  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 121 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 181 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 232


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 244


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 74/233 (31%), Positives = 122/233 (52%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A  G  SR+EV++++    V VN   ++ A  +V    D I ++G  +   E  
Sbjct: 2   RIDKVLANLGYGSRKEVKKLLKDGSVTVNDEKIKDAKQHVDPEKDLIRINGETVEYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D +   TV D L +  +      VGRLD +TEGLLL+TNDG LA
Sbjct: 62  YLMM-NKPPGVISATED-NRDETVIDLLEAEDLIFEPFPVGRLDKDTEGLLLITNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVT 190
             L  P     + Y      +V ++ +   +KG+++    Y      L+  K G  + + 
Sbjct: 120 HRLLSPKKHVPKTYFAVIDQEVTEEDVTAFRKGVILDD-GYATKPGELNILKSGERSDIE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++FE    KV  L R+S GP +L  TL  G  RE++++ L+
Sbjct: 179 LTITEGKFHQVKRMFEAVGKKVVYLQRLSMGPLRLDETLELGEYRELTEEELQ 231


>gi|239997156|ref|ZP_04717680.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           ATCC 27126]
          Length = 252

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 121/234 (51%), Gaps = 13/234 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPL 67
           P+R++K I+  G+ SRRE +++I Q RV VN    E     V   D ++VDG     V  
Sbjct: 6   PKRLNKYISDTGLCSRREADKLIEQNRVTVNNQPPE-LGTKVGPGDTVKVDGKVVGAVAS 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K++R  + +Y+KPIG+  T ++   +  + D +     R+  VGRLD  +EGL++LT+D
Sbjct: 65  DKSDRVYI-VYNKPIGITCT-TERHVKGNIIDAIGH-KERIFPVGRLDKPSEGLIILTSD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  + +  +N + +G+ I G       V      G N 
Sbjct: 122 GDIVNKILRAENAHDKEYEVTVNQPISERFVNRMSRGVPILGTVTKPCVV---KPTGKNT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + T+ L +G NR+I+++ EF  ++V +L R      +LG+L  G  R ++ + L
Sbjct: 179 F-TIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELGSLKPGQWRNLTSREL 231


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 114/228 (50%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNV----MSTDHIEVDGVPLRK 69
           R++K +A+ GI+SRRE  R+I   R+ +NG + +   AV+        D + +D  P+  
Sbjct: 2   RLAKYLAQCGISSRREACRLIEAGRISLNGKIAKHTDAVHFDADGQCLDSLCLDEKPISG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE    W+++K +G      D D +S++   LP+   R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  AEALSYWIFNKAVGTDCRLLDAD-KSSLLHLLPTT-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y V+     +   +  +  G+  + +     QVT    + S    
Sbjct: 120 LTHKLMHPSFAHSKTYHVQLDRPFNDAFIAQMASGVQYKEVRTLPCQVT----RLSADRF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L +G NR+I+++     +KV  L R++     L +L  G  R +S
Sbjct: 176 EIVLTQGLNRQIRRMSNALGYKVIDLQRVALMTLTLASLAEGEMRPLS 223


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 131/254 (51%), Gaps = 13/254 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  L   +  
Sbjct: 62  RLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKG-QLISHKTH 120

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++ +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++G
Sbjct: 121 VYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDNG 176

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + +
Sbjct: 177 QLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETES 236

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
            V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L 
Sbjct: 237 HVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLP 296

Query: 247 PHLLEEAQVNLDAP 260
              +E+ Q +   P
Sbjct: 297 YFFIEKQQTSKALP 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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 125/239 (52%), Gaps = 21/239 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAER 72
           R++K ++ AG+ SRRE +R+I   +V V+G   +RA   + V     ++V    +R    
Sbjct: 3   RLNKYLSDAGVCSRREADRLIESGQVSVDG---QRAVPGMKVADGQEVKVGKKVIRSNTE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +   +KP G+V T    + ++ + +   P    RV   GRLD ++EGLL++TNDG L 
Sbjct: 60  KIVLAVNKPAGIVCTEDVREKKNIIRYLKYPI---RVTYAGRLDKDSEGLLIMTNDGDLI 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------TQKG 184
             +        + Y+V  +  V QD ++ +K+GI I      D +  LD        +K 
Sbjct: 117 NGMMRARHGHEKEYKVTVNKPVTQDFISKMKEGIRIV-----DKEKRLDVATRPCKAEKL 171

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                ++ L +G NR+I+++ E   +KV RL+R+     +LG+L  G+ R+++++ L+E
Sbjct: 172 GKYTFSITLTQGLNRQIRRMCEALGYKVERLVRVRIMNIELGSLKPGAYRKLTEQELKE 230


>gi|325688986|gb|EGD30994.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 242

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/232 (32%), Positives = 116/232 (50%), Gaps = 10/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
            V+  P     ++YR +  G ++Q        GI ++       Q   + LD  K   + 
Sbjct: 120 HVMLSPKKHVEKIYRAQVAGLMNQADEERFAAGIELKDFTCQPAQLKILELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           V + L EGK  ++K++      +V  L R++ GP QL   LA G  R +++K
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLTMGPLQLDPALALGEWRRLTEK 230


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 121/254 (47%), Gaps = 32/254 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A AG  +R EV++ I + +V+VNG   ++  + V    D + + G  +  A   
Sbjct: 6   RLDKFLADAGKGTRSEVKKFIQKGQVQVNGAPAKKPELKVDPEKDTVILSGETVGVAPEF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+   D + R TV + +PS    +  VGRLD +TEGLLL+T+DG LA  
Sbjct: 66  VYYLLNKPAGCVSATEDRNDR-TVMEYVPSDRKGIFPVGRLDKDTEGLLLITDDGMLAHE 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           L  P     + Y VR  G++  +K+  L+ G+ I     G+ ++T+  +      +W   
Sbjct: 125 LLAPGKHVDKTYFVRVEGKLTVEKIEKLENGVDI-----GEKKLTMPAKVEIVGGSWEGA 179

Query: 192 G----------------------LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTL 228
           G                      + EGK  ++K++ E     V  L RIS GP  L   L
Sbjct: 180 GEPEPGRVRRENLPEVYTELHLTIHEGKFHQVKRMMEAVGTPVIYLKRISMGPLILPDDL 239

Query: 229 LAGSTREVSKKILR 242
             G  R ++ + LR
Sbjct: 240 KKGECRSLTDEELR 253


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 112/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  ER 
Sbjct: 7   KRLNKFISETGFCSRREADKLIEQGRVTLNGVQPE-VGSKVTEQDEVCIDGKPLRSKERP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA 232


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTDQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 244


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 117/239 (48%), Gaps = 25/239 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPL---- 67
           R++K ++ AGI SRRE +R+I + +V V G    R AV    +   + +  +G  +    
Sbjct: 7   RLNKFLSGAGICSRREADRLIEEGKVTVGG----RTAVPGQKIKKGETVVCNGRTIAAGS 62

Query: 68  ----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
               +K ER  L   HKP G+V T SD D    + D +     R+   GRLD  +EGL+L
Sbjct: 63  RGAEKKPERV-LLAVHKPCGIVCTTSDKDRAPNIVDMVDCPV-RIYPAGRLDKESEGLIL 120

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--- 180
           +TN G L   +   S+   + Y V     V  + +  ++KG+ +      ++ VT     
Sbjct: 121 MTNQGDLVNRMMRGSSGHEKEYLVWIDRPVKPEFIQKMRKGVFLP-----ELDVTTKPCF 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +K       + L +G NR+I+++ E    KV +L R+     +LG L AG +R VSKK
Sbjct: 176 AEKTGEKSFRIVLTQGLNRQIRRMCEQLGCKVRKLKRVRIMNIELGDLKAGESRPVSKK 234


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 114/228 (50%), Gaps = 15/228 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLRK 69
           R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D IE+DG P+ K
Sbjct: 2   RLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDESLNCLDRIELDGAPITK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  TETLAYWILNKAVGTDCRLLEQD-ETSLIHLLPKA-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
           L   L  PS    + Y VR +     D +  +  G+      Y ++Q TL  Q  + S+ 
Sbjct: 120 LTHKLMHPSFVHSKTYHVRLNRPFTDDFVEQMASGVR-----YKNLQ-TLPCQVRRLSSD 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              + L +G NR+I+++ +   ++V  L R++     L  L  G  +E
Sbjct: 174 SFEIVLTQGLNRQIRRMSKALGYRVIDLERVAIMTLNLRELALGELQE 221


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 62  RLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 119

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 120 HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYR----VGRLDGDTEGLLLLTDN 175

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 176 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 235

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 236 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 295

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 296 PYFFIEKQQTSKALP 310


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 115/215 (53%), Gaps = 6/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S       G      + + 
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLICSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKESS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLA 131
            +L +KP G+V+   D + ++ +  +L S   +V     +GRLD +TEGLL++TN+G L 
Sbjct: 62  YYLLYKPSGVVSAVRDSEHKTVI--DLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +   
Sbjct: 120 YRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++KK+F  +  KV  L RIS+G  +L
Sbjct: 180 ITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRL 214


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 244


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/221 (33%), Positives = 111/221 (50%), Gaps = 13/221 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+ +V+A  G+ +R+EV ++I    V+V+G ++ +R          IEV G P+R A R
Sbjct: 3   ERLDRVLAHLGLGTRKEVGKLIRAGAVRVDGAVVRDRGYKLDPEAARIEVRGEPVRYA-R 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G++T  +  +  +TV D LP    R  +  VGRLD +TEGLLLLTN G L
Sbjct: 62  HFYVLLHKPAGVLTA-TRSERETTVLDLLPDALWRDDLRPVGRLDRDTEGLLLLTNHGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  +VY      ++ +D      +G++       D         G  A   
Sbjct: 121 LHRLTHPRWKVAKVYFAELASELPEDAARRFAEGVL-------DFAPAELEALGPRA-AR 172

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           V L EGK+R+++++F      V  L R  +GP +LG L  G
Sbjct: 173 VTLYEGKHRQVRRMFAALGAPVAYLRRERFGPLELGGLEPG 213


>gi|227517791|ref|ZP_03947840.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227074752|gb|EEI12715.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
          Length = 260

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 134/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPVRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>gi|325695507|gb|EGD37407.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 242

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 110/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ ++ V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKELVLVNGRAEKSPKTQIDETADEIIVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q        GI ++       Q   + LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADEERFAAGIELKDFTCQPAQLKILELDAAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALA 220


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 113/235 (48%), Gaps = 19/235 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  IA+  VKV+G ++      V+ T  I ++     K +   
Sbjct: 5   RLSKLMSEQGLCSRREADDFIAKGWVKVDGEIVSELGTKVLPTQKITLEKAAQAKQQGRV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLDINTE 119
             L +KP+G V+  ++   +  +           D  P  F R     +   GRLDI++ 
Sbjct: 65  TILLNKPVGYVSGQAEEGHKPAILLLDAATRWEQDTAPHRFHRSQLLGLAPAGRLDIDST 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +A+ L    +   + Y VR  G++  + LNLL  G+ + G      +V+ 
Sbjct: 125 GLLVLTQDGRIAKQLIGEDSPIEKEYLVRVQGKLVGNGLNLLNHGLSLDGKKLKPAKVSW 184

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +      +   L EGK R+I+++ E    KV  L R+  G  +LG L  G  R
Sbjct: 185 QNED----QLRFILNEGKKRQIRRMCEMVGLKVTALKRVRIGKVRLGDLPQGQWR 235


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 113/235 (48%), Gaps = 7/235 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTDQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T 
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLTQ 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 182 GL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 232


>gi|167645656|ref|YP_001683319.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167348086|gb|ABZ70821.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 255

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 119/236 (50%), Gaps = 15/236 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQRV++ +A+ G+ SRRE E +I Q  V ++G+ ++     +     + +      + E 
Sbjct: 12  PQRVNRWLAQNGVCSRREAEALILQGLVSIDGLRVDDVGRKIEPGQTLVLSDRAQAQLEG 71

Query: 73  TRLWLYHKPIGLVTTHSDPD--------GRSTVFDN---LPSIFSRVISVGRLDINTEGL 121
               + HKPIG+V+   D           R  ++     +P   +++  VGRLD+++ GL
Sbjct: 72  ALTVMIHKPIGIVSAQPDTGQVPAVRLLTREALYGQSPVIPGFENKLAPVGRLDMDSRGL 131

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+L+ DG +A+ +  P+++  + Y V   G +  +KL LL+ G+ +        QV +  
Sbjct: 132 LILSEDGVVAKAVIGPASEMEKEYLVWVDGWITDEKLVLLRHGLELDERALRPAQVEVVG 191

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++     +   L+EG+NR+I+++ E     V  L+RI  G   LG L  G  R +S
Sbjct: 192 RQQ----LKFILQEGRNRQIRRMCELVELTVVDLLRIRIGNVMLGDLPEGRWRPLS 243


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 120/232 (51%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G+ SR+EV++++  +R+ VN ++++ + ++V    D I VD   +   +  
Sbjct: 3   RLDKLLSNMGVGSRKEVKQLLKSKRITVNEVIVKDSGMHVDPEYDQIFVDDQLISYQKHI 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + HKP G+V+   D   R TV D L +   +     VGRLD +TEGLLL+TNDG LA
Sbjct: 63  YLMM-HKPPGVVSATVDNRDR-TVIDLLSADEKKFEPFPVGRLDKDTEGLLLITNDGELA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY     G+  ++ +   ++G+ ++   Y      L+     +  V V
Sbjct: 121 HRLTSPKKHVEKVYIAHISGEFPENIVEQFQEGLTLED-GYQTKPAKLEILNKQSKEVKV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            + EGK  +IK++F     KV  L R+     QL  +L  G  R +++  L+
Sbjct: 180 TITEGKYHQIKRMFIAVGCKVTYLKRVQMANLQLDDSLPIGDFRPLTEDELQ 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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/229 (32%), Positives = 114/229 (49%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L L HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLML-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDEISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE+S
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELS 226


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 108/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L   E  
Sbjct: 2   RLDKFLVDCGMGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPGKDRVTFMGEDLVH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPAGVISATED-DHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWV 189
             +  P     ++YR +  G +D+  +   + GI ++        +Q+    +  ++++V
Sbjct: 120 HAMLSPKKHVSKIYRAQVAGIMDEADVARFEAGIALKDFTTLPARLQILEVNEANASSYV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EGK  ++K++      +V  L RIS GP  L
Sbjct: 180 EIEIAEGKFHQVKRMVAACGKEVVDLERISMGPLML 215


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 115/215 (53%), Gaps = 6/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S       G      + + 
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKESS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLA 131
            +L +KP G+V+   D + ++ +  +L S   RV     +GRLD +TEGLL++TN+G L 
Sbjct: 62  YYLLYKPSGVVSAVRDSEHKTVI--DLISEKDRVEGLYPIGRLDRDTEGLLIITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +   
Sbjct: 120 YRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++KK+F  +  KV  L RIS+G  +L
Sbjct: 180 ITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRL 214


>gi|329929427|ref|ZP_08283175.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
 gi|328936514|gb|EGG32959.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
          Length = 243

 Score = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/242 (32%), Positives = 121/242 (50%), Gaps = 24/242 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + KV++  G  SR E+++   Q  + VNG + +    +V    D IE +G  ++  E   
Sbjct: 1   MDKVLSNLGFGSRAELKKKAKQGSIVVNGTITKDPGKHVDPYADIIEFEGETIQYREYVY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTNDGGLA 131
           L L HKP G+V+   D   R TV D L + + RV     VGRLD +TEGLLLLTNDG LA
Sbjct: 61  LML-HKPPGVVSATEDLRDR-TVLDLLDAEY-RVFEPFPVGRLDKDTEGLLLLTNDGKLA 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--- 188
             L  P     + Y     G+VD++ +     G+ +      D  VTL  +   ++    
Sbjct: 118 HELLSPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLD-----DGYVTLPGELAIHSHEER 172

Query: 189 --------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
                   +++ + EGK  ++K++FE    KV  L RIS G  +L   L  G+ RE++++
Sbjct: 173 EDGDQLSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYRELTEQ 232

Query: 240 IL 241
            L
Sbjct: 233 EL 234


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 108/221 (48%), Gaps = 7/221 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+ 
Sbjct: 2   RLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADQIRCQGQTL-SYEKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D +   TV D L           VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKETFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS-NAWV 189
             +  P     + YR +  G +    +     GI ++   C     V L+  +    + V
Sbjct: 120 HAMLSPKKHVDKTYRAKVAGLMTTTDVAAFANGIDLKDFTCQPAQLVILEINEAERTSVV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + ++EGK  +IK++ +    KV  L R+S GP QL   LA
Sbjct: 180 EITIKEGKFHQIKRMVQACGKKVTDLQRLSMGPLQLDKQLA 220


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 58/181 (32%), Positives = 95/181 (52%), Gaps = 16/181 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP  ++T  +D DGR+T+ D +P     V   GRLD ++EGLLLLTNDG L   
Sbjct: 31  RLLLLNKPFDVLTQFADADGRATLKDFVP--VPGVYPAGRLDRDSEGLLLLTNDGRLQAR 88

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----------- 181
           +  P  +  + Y V+  G+VD+ +L  L++G+ +  G+        LD            
Sbjct: 89  IADPKHKLPKTYWVQVEGEVDETQLERLRQGVELNDGMTLPAEARQLDEPELWPRNPPVR 148

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +    +W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  REV  +
Sbjct: 149 FRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWALDGLQPGEWREVPAQ 208

Query: 240 I 240
           +
Sbjct: 209 L 209


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 113/227 (49%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     +R++   M+AQ+RV+++G ++      V     +++D   L+     R
Sbjct: 2   RLDRFLANLPHCNRQQARLMLAQRRVRLDGQVISDPLAEVREFSRVQLDEQLLQAGRPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + HKP G V+   DP    TV + LP+     + + GRLD NT GL++LTNDG  +R 
Sbjct: 62  YLMLHKPAGCVSATHDPQ-HPTVLELLPAALRADLHIAGRLDFNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+T+  + Y V    ++ +  +   ++G              LD      A + +  
Sbjct: 121 LTQPATKLPKQYLVETEDEIAEHYVAKFREGFYFAFENLTTQPAQLDILGPRQARLAI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            EG+  ++K++F FF+ KV  L R S G  +L   LA G+ R+++ +
Sbjct: 179 VEGRYHQVKRMFGFFDNKVVGLHRESMGAIRLDPGLAPGAFRQLTPE 225


>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 = 91.7 bits (226), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 112/216 (51%), Gaps = 11/216 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ K +   G A RR+ ++ I   RV VNG ++++   +V   D + +D   L+  ++  
Sbjct: 9   KLQKYLQMCGFA-RRKADQYIIAGRVTVNGKVVDKPWFDVKDDDIVMLDNKKLKINQKFE 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G  TT  DP  + T+ + +  I + V   GRLD +  G+L+LTNDG L  +L
Sbjct: 68  YYVLHKPKGYATTLYDPKQKKTIKELIKHIKTPVKPAGRLDKDATGVLILTNDGKLIDIL 127

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSN-AWV 189
                   + Y V+  G V  + L  LKKGI  +     + Y D+      +KG + + +
Sbjct: 128 TNAKYGVKKEYIVKVSGSVSFNDLLKLKKGIYDERDFLKLEYFDI-----LEKGFDYSII 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V L +GK  EIK++F+    KV  L RI++GP  +
Sbjct: 183 KVVLIKGKKHEIKRLFKSIGHKVLELKRIAHGPISI 218


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L L HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLML-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDVSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGEYRELT 226


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 110/236 (46%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 64  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 121 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L 
Sbjct: 181 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILA 232


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 123/232 (53%), Gaps = 10/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G  SR+++++++AQ+ V +N  +  +    V   +D + V G  L   +R 
Sbjct: 2   RIEKYLADTGWGSRKDIKQLLAQKIVTINDQVCSKGGTQVTPGSDCVAVGG-QLVPYQRY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D     TV D L   +  +    VGRLDI+T GLLLLTN+G LA
Sbjct: 61  HYYLLNKPEGILSATEDRH-HQTVIDWLGEGYQHLDLFPVGRLDIDTTGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAW 188
             L  P  +  + Y     G VDQ  +   + G+ +        ++T+   D  +G++  
Sbjct: 120 HQLLSPKKKVDKTYTATIRGLVDQADIAAFEAGLDLGDFTSLPAELTVLSQDVDQGTSQ- 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + V ++EGK  ++K++F+    +V  L R++ GP +L + LA G  R ++++
Sbjct: 179 IQVIIQEGKFHQVKRMFQAVGKEVLSLHRLAMGPLRLESDLAHGQWRSLTEQ 230


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 244


>gi|328944867|gb|EGG39027.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 242

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 111/222 (50%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIAVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPRGVISATED-DRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++           + LD +K  ++ 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEK-EDSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALA 220


>gi|327462777|gb|EGF09099.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 112/222 (50%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++           + LD +K ++  
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEAS-L 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL + LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDSALA 220


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 115/234 (49%), Gaps = 19/234 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-------AVNVMSTDHIEVDGVPL 67
           R++K +A+ GI SRRE  R+I   R+ +NG +            +N +  D IE+DG P+
Sbjct: 2   RLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDELLNCL--DRIELDGAPI 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + E    W+++K +G      + D  S V  +L     R+  VGRLD ++ GLLLLTND
Sbjct: 60  TQTETLAYWVFNKAVGTDCRLLEQDETSLV--HLLPKAPRLYPVGRLDKDSRGLLLLTND 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGS 185
           G L   L  P     + Y VR       + +  +  G+      Y D+Q TL  Q  + S
Sbjct: 118 GELTHKLMHPCFAHSKTYHVRLDRPFTDEFVEQMASGVR-----YKDVQ-TLPCQVRRLS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +    + L +G NR+I+++     +KV  L R++     L +L  G+ R ++ +
Sbjct: 172 SDSFEIVLTQGLNRQIRRMAIALGYKVIDLQRVALMTLTLESLAEGAMRPLTPQ 225


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 116/235 (49%), Gaps = 15/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +RR+V  ++ ++RV V+G+ +     +V     + VD   ++  +  R
Sbjct: 2   RIDRFLSNLPRLNRRQVRLLLVERRVSVDGVAVSDPHHDVRDFSCVCVDDEVIQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SDP    TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATSDPQ-HPTVLDLLDEPDKDELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--- 190
           L  P+T+  +VYRV     +  +       G+      + D    L TQ    A +    
Sbjct: 121 LTQPTTKLPKVYRVHTEDTIGPEYAPTFAAGLY---FAFED----LTTQPAELALLGPTT 173

Query: 191 --VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
             + + EG+  ++K++F  FN KV  L R   GP +L + LA G  R +S + +R
Sbjct: 174 ARLSIIEGRYHQVKRMFGHFNNKVIGLHRERMGPLELDSALAPGEYRALSLEEIR 228


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/227 (33%), Positives = 114/227 (50%), Gaps = 15/227 (6%)

Query: 4   KNIVQENFTPQ----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +N  + N T Q    R++K IA AGI +RRE +R IA   V+VNG  +      V  TD 
Sbjct: 81  RNTPKPNATDQSKGIRLNKYIANAGICARREADRYIAAGNVEVNGKPMTELGYRVQPTDV 140

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINT 118
           ++ DG  +  AE+    L +KP G +TT  D  GR TV D +  +    +  VGRLD  T
Sbjct: 141 VKFDGKNI-SAEKKEYILLNKPKGFITTTQDEKGRKTVMDLVAGAAEGNIKPVGRLDRLT 199

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG L + L  PS    ++Y V     +   KL L     + +G+   D  + 
Sbjct: 200 TGLLLLTNDGDLMKKLTHPSHGVRKIYHV-----ILDKKLALADFHKIQEGLTLEDGFIQ 254

Query: 179 LD----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +D         +  + V +  G+NR ++++FE   + V +L R+ + 
Sbjct: 255 VDDINFVDGAPHNEIGVKIHSGRNRIVRRIFESLGYVVEKLDRVVFA 301


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 244


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 112/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER 
Sbjct: 7   KRLNKFISETGFCSRREADKLIEQGRVTLNGAQPE-VGSKVTEQDEVCIDGKPLRSKERP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D +  + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVQGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA 232


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 111/236 (47%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILA 244


>gi|171910347|ref|ZP_02925817.1| Pseudouridine synthase, Rsu [Verrucomicrobium spinosum DSM 4136]
          Length = 229

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 118/225 (52%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++A  G  +RREV  M+ +  VKV G++ E     V  T  + V G PL  A    
Sbjct: 6   RLDQLLASLGYGTRREVRNMVDRGLVKVGGVVAEDFDARVDPTT-VTVKGEPL-DAPFGL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTNDGGL 130
           + ++HKP+G V +H+  +G  T++D LP  +      V SVGRLD +T G+LLLT+ G L
Sbjct: 64  VAVFHKPVGYVCSHASDEG-PTIYDLLPKRWPFRNPTVTSVGRLDKDTSGILLLTDQGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
            +    P ++  +VY V     +++  + +  +G ++++      +   L+     +A +
Sbjct: 123 VQKWTSPKSEMDKVYEVTVDRPLEERLIGVFAEGTLLLESENKPCLPAKLEIVDALHARL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           T  L+EG+  +++++F    W V  L R  +G ++L  L  G  R
Sbjct: 183 T--LQEGRYHQVRRMFASQGWHVEALHRSRFGEYELEGLEVGQWR 225


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 110/236 (46%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 64  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 121 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L 
Sbjct: 181 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILA 232


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L L HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLML-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGEYRELT 226


>gi|325686573|gb|EGD28599.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 242

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 111/222 (50%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++           + LD +K  ++ 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEK-EDSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALA 220


>gi|302386350|ref|YP_003822172.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302196978|gb|ADL04549.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 241

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 16/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  +R +++ M  + R+ V+G   ++    +    + + VDG P+    R 
Sbjct: 5   RLDKYLTEMGEGTRSQIKEMARKGRIFVDGQPEKKTERKIHPEQNQVSVDGRPVSYV-RY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDG 128
             ++ +KP G+V+   D     + +D + S+        +  VGRLDI+TEGLLL+TNDG
Sbjct: 64  EYYMLNKPQGVVSATED-----SRYDTVISLIKSRKRDDLFPVGRLDIDTEGLLLITNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGS 185
            LA  L  P     +VY  R  G++  D    +++G+V+          ++V    ++ S
Sbjct: 119 DLAHQLLSPKKHVDKVYFARIQGELPPDAKEQMEEGLVLSDGTPTMPAHLEVLKQGREES 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           +  + + +REGK  ++K++FE    +V  L R++ G   L   LA G  R +S++
Sbjct: 179 SLEILLTIREGKFHQVKRMFETLGCRVIYLKRMTMGSLTLDEALAPGEYRPLSEE 233


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 115/215 (53%), Gaps = 6/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S       G      + + 
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLICSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKESS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLA 131
            +L +KP G+V+   D + ++ +  +L S   +V     +GRLD +TEGLL++TN+G L 
Sbjct: 62  YYLLYKPSGVVSAVRDSEHKTVI--DLISEKDKVEGLYPIGRLDRDTEGLLIVTNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +   
Sbjct: 120 YRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++KK+F  +  KV  L RIS+G  +L
Sbjct: 180 ITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRL 214


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 117/236 (49%), Gaps = 16/236 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K + ++G+ SRRE E +IA   V ++G ++  A   +     + ++         
Sbjct: 12  PVRINKWLGQSGVCSRREAEGLIADGLVSIDGEVVRDAGRKIEPGQTLTLNDTGEAALAA 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSRVISVGRLDINTEGLL 122
               L HKP+G V+   +P     V              P+  + +  VGRLD ++ GLL
Sbjct: 72  GVAILLHKPVGYVSGQPEPGKIPAVRLLTTANRVGDGETPARDASLPPVGRLDEDSRGLL 131

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDT 181
           +L++DG +A+ +  P +   + Y VR  G V + KL  L+ G+ + G      +VT ++ 
Sbjct: 132 MLSSDGVVAKAVIGPQSDLDKEYLVRVAGTVTEAKLTKLRHGLELDGRQLKPARVTQMEP 191

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           Q+     +   LREG+NR+I+++ E    +V  L RI  GP +LG L  G  R ++
Sbjct: 192 QR-----LRFILREGRNRQIRRMCELVGLEVVDLYRIRIGPVKLGDLPEGRWRMLT 242


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 119/226 (52%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           RV K+++  G  SR+E+++ +   ++K+N   +++    + S  D I  DG  + + E  
Sbjct: 4   RVDKILSELGFGSRQEIKKYVKAGKIKINDRTVKKPEEKINSKNDIIYFDGKEI-EVEEF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G V    D   R TV + + S    ++ VGRLD++TEG+L+LTNDG L   
Sbjct: 63  ETYILYKPAGYVCATKDNVHR-TVMELIDSKRKNIVPVGRLDLDTEGILILTNDGDLNHR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y   F G++D + + + + G+    I  G+     + +  S   + + +
Sbjct: 122 LVSPASHVDKSYYAVFDGKLDSNAIEMTQAGL---DIGEGEFSKPAELKILSENEILLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVS 237
            EGK  ++K++ +    +V  L R+++G  +L  L    G +R+++
Sbjct: 179 HEGKFHQVKRMVKALGGEVTYLKRVAFGGLKLDDLKLEKGESRKIT 224


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/173 (31%), Positives = 95/173 (54%), Gaps = 3/173 (1%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
           +E   ++L +KPIG ++  SD  GR T+ D +   I  RV  VGRLD ++ GL+L+TNDG
Sbjct: 31  SEEKVVYLVNKPIGYLSAMSDDRGRKTLSDLVSDRIKERVFHVGRLDQDSCGLILMTNDG 90

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            L+ ++  P+++  + Y V   G++    L  +K G+ +  G      ++ L    G  +
Sbjct: 91  DLSNLVSHPASEIEKTYVVGIKGKLTDRDLEAVKGGLTLGDGFKTSPAKIRLVRSDGDFS 150

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
              + + EG  REI+++F   N  V+ L+R+S GP  +  + + G  + +S+K
Sbjct: 151 KYAITIHEGHKREIREIFRVLNKSVSSLVRVSIGPLSISLVPSPGDIKRLSRK 203


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ KV+A  G  +R+EV+ ++    VK++G++++  ++ +   +  IEV+   +   +  
Sbjct: 3   RLDKVLANLGYGTRKEVKAIVKSGAVKIDGLVVKDNSMKIDPDECKIEVEETVVEYKKNI 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G+V    D + + TV D L   +   +   VGRLD +T+GLLL+TNDG L 
Sbjct: 63  YI-LMNKPEGVVCATFD-NYQETVIDILEPKYQAFKPFPVGRLDKDTKGLLLITNDGELN 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             L  P     +VY      +VD D +   K GIV++    C   ++++    + G+   
Sbjct: 121 HRLISPKNHVDKVYYAEIDKKVDMDDIRKFKMGIVLKDEYTCMPAELKIIESDENGARVE 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
           VTV  +EGK  +IK++F      V  L RI +GP  L   L  G  RE+
Sbjct: 181 VTV--QEGKFHQIKRMFNSLGKNVIYLERIKFGPLSLDDNLQEGEYREL 227


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 119/238 (50%), Gaps = 15/238 (6%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIE 61
           + I+  +F+  R++K+I++AG+ S+++ +  I Q RV VNG   + A+V   V   D + 
Sbjct: 22  QKIIATDFSSMRLNKLISQAGLGSKKQADAWIMQNRVTVNG---QVASVGQKVNQHDQVL 78

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +DG P+  +    L  YHKP+G+V TH      + V      +     ++GRLD  +EGL
Sbjct: 79  LDGRPVAWSSEVLLMAYHKPVGVVCTHDLSVANNLVVST--GLMQHFSAMGRLDKASEGL 136

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--L 179
           ++LTN G L   +  P     + Y V     + +  L  +++G+ I G      QVT   
Sbjct: 137 MILTNQGDLTNHILQPGFAHEKEYWVEVDQPLTEYFLTNMQQGVEIMG------QVTRPC 190

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + +        + L +G N++I+++ +   ++V RL R+      L  L   + RE++
Sbjct: 191 EIEATGEHCFRIVLTQGLNKQIRRMCKSLGYRVLRLQRVRIAQVWLDDLPVNTLRELN 248


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/222 (29%), Positives = 112/222 (50%), Gaps = 17/222 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLR 68
           T  R++K IA AGI SR++  R+I +  V VN     R A ++   D    I V+   ++
Sbjct: 3   TKIRLAKYIAHAGICSRKQASRLIDEGVVTVNN----RPANHIDHVDEQDTIIVNEKEIK 58

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A     + YHKP+G +    + D  +++  +LP++ +RV  +GRLD ++ GLL+LTNDG
Sbjct: 59  GAADLVYFAYHKPVG-IDCKLNIDDPASLIHHLPTL-TRVYPIGRLDKDSRGLLILTNDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSN 186
                L  P     + Y V  +  +D      +  G+ +      D  +TL  +  K ++
Sbjct: 117 DFCNQLIHPDFHQPKHYLVTVNKPLDDAFCKKMAAGVPV------DKHITLPCEVNKIAS 170

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              ++ L++G NR+I+K+  +  +KV  L R+ +    L  L
Sbjct: 171 NQFSIVLKQGLNRQIRKMAHYCGYKVIDLFRVQFSDLTLSKL 212


>gi|312863597|ref|ZP_07723835.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101133|gb|EFQ59338.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 243

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 109/219 (49%), Gaps = 13/219 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +   G+ SR +V+  + +++V VNG L       +        D +     E T 
Sbjct: 2   RLDKFLVDCGVGSRSQVKNFLKKKQVTVNGQLETSPKTQIDENK----DRIAYLDQELTH 57

Query: 75  ----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG 128
                +L +KP G+++   +P  + TV D L       +V  VGRLDI+T GLLLLTN+G
Sbjct: 58  ETFVYYLLNKPQGVISATENPRHK-TVLDLLDDTARHKQVFPVGRLDIDTHGLLLLTNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSN 186
            LA  +  P     ++Y+ +  G +D++ +   +KGI ++   C    +++    +  S 
Sbjct: 117 DLAHAMLSPKKHVDKIYQAKVAGVMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNEST 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +WV + + EGK  ++K++      +V  L R+S GP  L
Sbjct: 177 SWVQITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSL 215


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 122/225 (54%), Gaps = 9/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA   IASRRE +++I    VK+NGI+    A  V + D +E D   + + ++ +
Sbjct: 2   RLNKYIASLNIASRREADKLIQNGNVKINGIVNTNPAYQVSNDDKVECD---INEYKKDK 58

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++  +KP G V + +  +G+  ++  + + F+ +  VGRLD ++ GL++LTNDG  +R 
Sbjct: 59  IYIKLNKPRGYVVSSNKKEGKP-IYSLIKNDFNNIYPVGRLDKDSSGLIILTNDGVFSRK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   +T   + Y V+ +  +    L  L+ GI + G      +V    +   N++  + L
Sbjct: 118 IIGENTNCKKEYFVKVNDNIPDGALKKLEYGISLDGQKLKPAEV---KRINKNSFHII-L 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EGKNR+I+++ +   ++V  L R+      L  L  G+ + ++K
Sbjct: 174 TEGKNRQIRRMCQKIGFEVIILKRLRIADILLDDLKEGTFKHLTK 218


>gi|319744819|gb|EFV97158.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 239

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 115/215 (53%), Gaps = 6/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++ +AG  SR  V+++I  ++V V+G ++ +  V V S+      G      + + 
Sbjct: 2   RLDKLLGQAGFGSRNHVKKLIRSRQVSVDGQIVTKDNVIVDSSLQSIFVGKERVCLKESS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLA 131
            +L +KP G+V+   D + ++ +  +L S   +V     +GRLD +TEGLL++TN+G L 
Sbjct: 62  YYLLYKPSGVVSAVRDSEHKTVI--DLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +   
Sbjct: 120 YRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++KK+F  +  KV  L RIS+G  +L
Sbjct: 180 ITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRL 214


>gi|150020316|ref|YP_001305670.1| pseudouridine synthase [Thermosipho melanesiensis BI429]
 gi|149792837|gb|ABR30285.1| pseudouridine synthase [Thermosipho melanesiensis BI429]
          Length = 243

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 110/220 (50%), Gaps = 13/220 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +N   QR+ ++   A    RR+ + +I  ++VKVNG ++ +   +V   D I V+G    
Sbjct: 5   DNIKLQRILQICGFA----RRKADELIFSKKVKVNGKIVTKPWFDVKVDDEITVEGKKFT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLT 125
              +   ++ HKP G VT+  DP  ++T+   F + P     +   GRLD +  G+L+LT
Sbjct: 61  -LPKFEYYVLHKPKGYVTSLYDPKEKNTIKEFFKDKP-----LKPAGRLDKDVSGVLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L  VL        +VY  +  G+V  + L  LKKGI  +G         +  Q  +
Sbjct: 115 NDGDLIDVLTNAKYGVKKVYIAKITGRVKFEDLLSLKKGIYDKGDFLKLEHFDILEQGFN 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + V V + +GK  E+K++FE    KV  L RI +GP  +
Sbjct: 175 YSTVKVEMIKGKKHEVKRLFEKIGHKVLELRRIKHGPVSI 214


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 117/222 (52%), Gaps = 14/222 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R ++++ I++ +V VNG + + A   +    D +   G  +  AE  
Sbjct: 4   RLDKYLADMGLGTRSQIKKDISKGQVLVNGTVSKDAGTRIDTEKDQVSYLGQTVTYAEY- 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D   R TV D + +   + +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYYMLNKPAGVVSATEDRHDR-TVLDLIDTKQRKDLFPVGRLDKDTEGLLLITNDGALAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----KGSNA 187
            L  P +   +VY  R  G+V  + + L +KG+ I     G+  +TL  +       + +
Sbjct: 122 RLLSPKSHVDKVYFARIEGKVTAEDVFLFQKGVDI-----GEQALTLPARLEILSSDTVS 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            + + + EGK  ++K++FE    KV  L R+S G   L  LL
Sbjct: 177 EIRLTICEGKFHQVKRMFESVGKKVLYLKRLSMGTLILDDLL 218


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 60/182 (32%), Positives = 96/182 (52%), Gaps = 3/182 (1%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +D I+VDG+ +   +  + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD 
Sbjct: 4   SDEIKVDGLTV-ATQSYQFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDT 62

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM 175
            TEG++LLTN G LA  L  P     + Y     G + +D    LK GI ++ G    D 
Sbjct: 63  ETEGVILLTNHGELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARAD- 121

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +  Q G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R 
Sbjct: 122 HFRVVEQTGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRR 181

Query: 236 VS 237
           +S
Sbjct: 182 LS 183


>gi|269302650|gb|ACZ32750.1| RNA pseudouridine synthase [Chlamydophila pneumoniae LPCoLN]
          Length = 235

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 108/227 (47%), Gaps = 6/227 (2%)

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  RTRLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   ++ HK IG L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  
Sbjct: 62  KV-YFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGEF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  PS+   + Y ++    V    L  L +G  I G     + VT    K     V 
Sbjct: 121 ANKIIHPSSGITKEYLLKVSRDVSAKDLEKLMEGTFIDGKHVRPVSVT----KIRRGTVK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGK  EI+   +     +  L RI  G   LG L  G  RE++
Sbjct: 177 IVVSEGKKHEIRLFADAAGLPILELKRIRIGSLVLGGLRYGEYRELT 223


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 109/226 (48%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G+ SRR+ +  IA   V VNG  +      V   D +  DG  L   E+  
Sbjct: 64  RLNKYIANSGVCSRRDADMYIAAGNVTVNGKSITEMGYRVKLEDDVRFDGRRL-NPEKPE 122

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
             L +KP G   T +   G  TV + +    S  +S VG+LD   +GLLL TNDG LA+ 
Sbjct: 123 YILLNKPAGFFVTGNPEKGGKTVMELVARTTSAKVSPVGKLDNQAKGLLLFTNDGTLAKK 182

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     ++Y+V  +  + ++ L  ++KG+ I+G       ++    K  N  V + L
Sbjct: 183 LAKPKNGIRQIYQVTLNKNLTKEDLEGIEKGVYIEGSKVLITSISFIEDKPHNE-VGIEL 241

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              K   + ++F+   ++V  L R+ +G      L  G  R ++K+
Sbjct: 242 YSIKEHIVTRIFKSLGYEVESLDRVVFGGLTKKDLPRGRHRNLTKQ 287


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/227 (32%), Positives = 108/227 (47%), Gaps = 6/227 (2%)

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  RTRLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   ++ HK IG L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  
Sbjct: 62  KV-YFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGEF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  PS+   + Y ++    V    L  L +G  I G     + VT    K     V 
Sbjct: 121 ANKIIHPSSGITKEYLLKVSRDVSAKDLGKLMEGTFIDGKHVRPVSVT----KIRRGTVK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGK  EI+   +     +  L RI  G   LG L  G  RE++
Sbjct: 177 IVVSEGKKHEIRLFADAAGLPILELKRIRIGSLVLGGLRYGEYRELT 223


>gi|295692663|ref|YP_003601273.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030769|emb|CBL50248.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 234

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 60/215 (27%), Positives = 108/215 (50%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I +  V VNG+ ++     V  +D + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHLLIKKGIVAVNGVTVKTPKQQVKESDQVTVNGDAV-AYQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D    + +    P   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPKGVLSATEDRSQPTVISLLAPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    ++YR +  G  D + +     G+ +     +   ++++    ++ + +   
Sbjct: 121 LLAPNKHVDKIYRAKIAGVADDETVKTFAAGMTLGDGTKLQPAELKILSQDEEHNRSTTE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + +REGK  +IK++F     KV  L RIS G   L
Sbjct: 181 IKIREGKYHQIKRMFGAVGMKVVELERISMGDLTL 215


>gi|206603683|gb|EDZ40163.1| Protein of unknown function [Leptospirillum sp. Group II '5-way
           CG']
          Length = 298

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 123/241 (51%), Gaps = 17/241 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIE----VDGVPLRKA 70
           V + I++ G+ +R      +   R+ + +G L++     V  T   E    +D   L  A
Sbjct: 22  VDRWISKLGLGTRGMAREWVRDGRLSLGDGTLVQHVDQFVQGTPGSEPVFRLDQKIL-SA 80

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--------FSRVISVGRLDINTEGLL 122
           +   ++ ++KP G++ T +DP GR T+ +++            SR++ VGRLD  + GL+
Sbjct: 81  DPPAVFAFNKPRGVLVTRTDPGGRETICESIGRSSGQRTGMDMSRLMPVGRLDQASSGLI 140

Query: 123 LLTNDGG-LARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDMQVTLD 180
           LLTN    L R+L  P+ ++ R YRV+    + +    + L  G   + +    + V  +
Sbjct: 141 LLTNRSSELTRLLN-PALEFPREYRVQVRPSLKKRDWEMGLFGGKWARELGLKPVDVRYE 199

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +     W+ VGL+EGKNREI+++FE   ++V  LIR+ +GPF L  L  G   EVS   
Sbjct: 200 KENLRTTWLRVGLKEGKNREIRRLFESGGYEVLHLIRVGFGPFCLKNLPPGGIVEVSSFF 259

Query: 241 L 241
           L
Sbjct: 260 L 260


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 118/232 (50%), Gaps = 12/232 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +++I Q RV +NG + E     ++ TD + VDG  + +++   
Sbjct: 8   RINKYLSEVGYCSRRAADKLIDQGRVTINGKIPE-MGTKIIPTDEVRVDGELISESKEDF 66

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++L ++KP+G+V T      +  + D  N P    R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 67  VYLAFNKPVGIVCTTDTRVEKDNIIDYINYPK---RIFPIGRLDKPSEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+    +  D ++ +  GI I        +V    +K S     +
Sbjct: 124 NKILRARNHHEKEYIVKVDNIITDDFVHQMSNGIPILDTITRKCKV----EKLSKYEFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ E+  + V +L R+      L  +  G+ RE +K+ L+E
Sbjct: 180 ILTQGLNRQIRRMTEYLGYNVVKLKRVRIMNISLD-MPVGTYREFTKEELKE 230


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 125/239 (52%), Gaps = 23/239 (9%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRK 69
           P R++K I+  G  SRRE ++++ Q RV +NG   +L ++A     ++D + VDG PL K
Sbjct: 3   PVRINKFISETGFCSRREADKLVEQGRVMLNGRKAVLGDKAT----TSDDVRVDGKPL-K 57

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           A++  +++ ++KP+G+  T ++   +  + D +     R+  +GRLD  +EGL+ LT+DG
Sbjct: 58  AKKAGVYIAFNKPVGITCT-TERHIKGNIIDYIRHK-ERIFPIGRLDKPSEGLIFLTSDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKG 184
            +   +        + Y V  +  +  + +  +  G+ I G+    C+         +K 
Sbjct: 116 DIVNKILRAGNNHEKEYVVTVNKPITPEFIQKMSSGVPILGVVTKKCF--------VRKD 167

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           S+   T+ L +G NR+I+++ EF  + V +L R+      L  L  G  R+++   ++E
Sbjct: 168 SSYVFTIILTQGLNRQIRRMCEFLGYNVTKLKRVRIMNVTLKDLPVGKWRDLTAAEMQE 226


>gi|220929584|ref|YP_002506493.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219999912|gb|ACL76513.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 245

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 122/230 (53%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ KV++  G  SR  ++  + +  V V+G +++ + ++V      IE+DG  L   + 
Sbjct: 5   QRLDKVLSNFGFGSRNYIKGAVKKGLVTVDGRIIKDSGIHVDPEVSIIEIDGERLNYRKY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + L +KP G+++  SD   + TVFD LP  +    +   GRLDI+TEGL+L+TNDG L
Sbjct: 65  IYIML-NKPQGVISATSDRK-QKTVFDILPEEYKCFDLFPAGRLDIDTEGLVLMTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  +  P     + Y  +  G+V+Q+      +G+ +    Y  +   L+  K  + + +
Sbjct: 123 SHEILSPKKHVPKQYYAKVMGRVNQEDAEAFSRGVTLDD-GYQTLPAVLEILKSDDLSEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  +E+ +
Sbjct: 182 KLTIVEGKFHQVKRMFEAVGKKVIYLKRLSMGNLRLDESLQLGECKELGE 231


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 110/236 (46%), Gaps = 9/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG+  E     V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNGLQPE-VGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R      +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +
Sbjct: 76  RPIYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDI 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T
Sbjct: 133 VNKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            GL    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L 
Sbjct: 193 QGL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDTEVSEILA 244


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             REV+
Sbjct: 235 EWREVT 240


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 88/348 (25%), Positives = 156/348 (44%), Gaps = 41/348 (11%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N      +  R++K I+ +G  SRRE +++I  QRV +NG++ E     V+S D +
Sbjct: 1   MNTSNTSNTTVSSIRLNKFISDSGFCSRREADKLIDSQRVTINGVIPE-LGTKVLSGDEV 59

Query: 61  EVDGVPLRKAERT---RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            VDG  ++ +      R++L YHKP+G+  T ++   +  + D +     R+  +GRLD 
Sbjct: 60  RVDGNLIKASAENKSDRVYLAYHKPVGITCT-TERHVKGNIIDAIGHP-ERIFPIGRLDK 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      KN+ +     
Sbjct: 234 TPDEMREI------------SDAVEGSTKTALKTDQKIAANVTD------KNAPKTEPTR 275

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             K+     H R + S V  AK  H S      +R+  +  +P+ PS+
Sbjct: 276 SSKR----SHHRGIKSQVGEAK--HGS------RRQATNNTAPATPSR 311


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             REV+
Sbjct: 235 EWREVT 240


>gi|332830030|gb|EGK02658.1| hypothetical protein HMPREF9455_00908 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 342

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 120/226 (53%), Gaps = 13/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +G  SRRE +R I + RV +NG   +RA V   V+    ++V+G  +     
Sbjct: 4   RLNKYISNSGFCSRREADRFIEEGRVTING---KRAQVGMRVLPGQKVKVNGELIVNKIE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V+T +DP  R  +  N      R+  +GRLD +++GL+LLTNDG +  
Sbjct: 61  PVYIAFNKPVGIVST-TDPQERDNII-NFIRHEQRIFPIGRLDKDSQGLILLTNDGDIVN 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV-TV 191
            +        + Y V+ +  + +D L  + +G+ I        ++        N ++  +
Sbjct: 119 KILRAGNNHKKDYLVKVNRPITKDFLTRMAQGVPILDRVTRRCEIV-----EINPYMFRI 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L +G NR+I+++ E+F+++V +L RI     +LG L  G+ R ++
Sbjct: 174 SLIQGLNRQIRRMCEYFDYEVLKLERIQIMNIKLGDLGQGNWRNLT 219


>gi|295692648|ref|YP_003601258.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030754|emb|CBL50233.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 236

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 109/215 (50%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVNGEEI-AYQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D + ++ +   +L   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLVNKPKGVLSATEDRNQKTVISLLDLQDQYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW--VT 190
           L  P+    +VYR +  G  D++       G+++  G      ++ +  Q   NA   + 
Sbjct: 121 LLAPNKHVAKVYRAQIAGVADEETAKAFASGMMLGDGTKLKPAKLKILKQDRENATSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK++F     KV  L R+S G   L
Sbjct: 181 IEISEGKYYQIKRMFGAVGMKVTALDRLSMGNLHL 215


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 97/185 (52%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +K + TR+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  KKTQPTRVILFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
           G L   L  P  +  ++Y V+  G+ D+D L  L+ G+ +         V L ++     
Sbjct: 92  GALQATLTQPGKRTGKIYFVQVEGEPDEDALAKLRTGVTLNDGPTLSAGVELVSEPEWLW 151

Query: 185 ------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                         +W+ + L EG+NR+++++     +   RLIR + G + L +L  G+
Sbjct: 152 PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGRYTLDSLANGA 211

Query: 233 TREVS 237
            R+++
Sbjct: 212 WRDIA 216


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 113/227 (49%), Gaps = 14/227 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ ++ +R G  SR E+   +   RV V    +   ++ V     +++DG PL   E  
Sbjct: 6   ERLDRLFSRLGYGSRSELREWLRAGRVSVGSRPVGSPSLRV-DPKLVQIDGQPLDHPEGL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTNDGG 129
            L LYHKP G V  H +P    +V+ + P+ +S     + +VGRLD +T G+LL+T+DGG
Sbjct: 65  YL-LYHKPRGKVCAHGEP---RSVYGDFPAAWSVRRPAINTVGRLDADTSGVLLVTDDGG 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNA 187
                  P     R YRV     +    L  L+ G ++     G+    L  D +  +  
Sbjct: 121 WLHRWTHPRRAVPRTYRVGLAEPITDGALAQLRSGKLLLA---GETSPCLPADVEVLAPR 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + + LREG+  E++++      +V+ L R ++GPF++  L +GS R
Sbjct: 178 HLRLTLREGRYHEVRRMLAALGNRVDTLHREAFGPFRVDDLPSGSWR 224


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 61  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 118 NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 177

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 178 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 237

Query: 232 STREVS 237
             REV+
Sbjct: 238 EWREVT 243


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/224 (31%), Positives = 112/224 (50%), Gaps = 5/224 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLW 76
           KV+  A + SRR++   I Q  V +NG   E  +  V    D +  +G P+  +   R++
Sbjct: 13  KVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQQDKVTFEGKPVELSRIRRIY 72

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARV 133
           L  +KP  +V+T SD  GR TV D L   +  + +  VGRLD  T GLLLLTNDG L   
Sbjct: 73  LMLNKPPEIVSTTSDELGRKTVMDLLHRRYEGAGLFPVGRLDEATTGLLLLTNDGELTNR 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS Q  + Y +     + Q     L+KG+++        +++  T +    +  + +
Sbjct: 133 LTHPSYQIEKEYLISIDAALTQADKESLEKGMLLDDGLTSPARLSRVTDEPPYNYKLI-I 191

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EGK R ++++F    +++  L R      +LG L  G TRE++
Sbjct: 192 HEGKKRIVRRMFAHLGYQIKALKRSRIATLRLGKLEEGKTRELT 235


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             REV+
Sbjct: 235 EWREVT 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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             REV+
Sbjct: 235 EWREVT 240


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/221 (29%), Positives = 108/221 (48%), Gaps = 3/221 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRR+ +  I    VKVNGI +      V   D +  DG  L   E+  
Sbjct: 71  RLNKYISNSGACSRRDADIYIQSGNVKVNGIPVIEMGYMVKPGDVVNFDGSVLT-PEKKE 129

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP    T   +      V + +  S  S++ +VGR+D NT GLLL TND  + R 
Sbjct: 130 YILLNKPKNFTTAFDEGQENRNVLELVRGSTNSKIAAVGRMDKNTTGLLLFTNDTDMIRR 189

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             LPS +  ++Y+V     +  + L  + KG+VI G      +++   +K + + V + L
Sbjct: 190 FSLPSQKSSKIYQVSLDKNLKFEDLEKISKGLVIDGHRVFVEEISY-IEKEAKSEVGLKL 248

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +    + ++ +FE F + V R+ R+S+       L  G+ R
Sbjct: 249 KTANVKVVRAIFESFKYDVLRIDRVSFAGLTKKNLPRGNWR 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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 117/229 (51%), Gaps = 11/229 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRK 69
           P+R++K I+ +G  SRR  ++MI   RV +N  + E     V++ D ++VDG    P+  
Sbjct: 12  PKRLNKYISDSGFCSRRSADKMIEANRVTINDKVPE-LGTKVLAGDVVKVDGYDIAPISD 70

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +  R+++ Y+KPIG+  T ++   R  + D +     R+  +GRLD  +EGL+ LT+DG
Sbjct: 71  DKSDRIYIAYNKPIGITCT-TEKHVRGNIIDAIGH-KKRIFPIGRLDKPSEGLIFLTSDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V     + +  +  + +G+ I G       V    Q  S   
Sbjct: 129 DIVNKILRAENAHDKEYIVTVDKPISERFIERMSRGVPILGTITKPCIV----QVKSRFE 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            T+ L +G NR+I+++ E+ +++V +L R      +LG L  G  RE++
Sbjct: 185 FTIILTQGLNRQIRRMCEYLDYEVLKLKRSRIMKVELGDLTPGQWRELT 233


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTRPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             REV+
Sbjct: 235 EWREVT 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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 61  PLSPAER-KVVLFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 118 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 177

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 178 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 237

Query: 232 STREVS 237
             REV+
Sbjct: 238 EWREVT 243


>gi|170719828|ref|YP_001747516.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169757831|gb|ACA71147.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 209

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 59/184 (32%), Positives = 97/184 (52%), Gaps = 20/184 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            RL L++KP  ++T  SD DGR+T+ D  ++PSI+      GRLD ++EGLLLLTNDGGL
Sbjct: 30  PRLILFNKPFDVLTQFSDSDGRATLKDYIDIPSIYP----AGRLDRDSEGLLLLTNDGGL 85

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT-------- 181
              +  P  +  + Y V+  G+ + ++L  L++G+ +  G         LD         
Sbjct: 86  QARIADPRHKLAKTYWVQVEGEPNDEQLKRLREGVELNDGPTLPAEARRLDEPELWPRNP 145

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV
Sbjct: 146 PVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWREV 205

Query: 237 SKKI 240
             K+
Sbjct: 206 PAKL 209


>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 = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 109/221 (49%), Gaps = 3/221 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G+ SRR+ +  I    VKVNG+ +      V   D +  DGV L   E+  
Sbjct: 71  RLNKYISNSGVCSRRDADLYIQSGNVKVNGVPVTEMGYLVKLNDVVNFDGVTL-TPEKKE 129

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP    T   +      V + +  +  +++  +GR+D NT GLLL TND  + R 
Sbjct: 130 YILLNKPKNFTTALDEGQEYRNVLELVRAATNAKIAPIGRMDKNTTGLLLFTNDTDMIRK 189

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             LP+ +  ++Y+V     +  + L  + KG+V+ G      +++   +K   + V + L
Sbjct: 190 FSLPNQKSPKIYQVSLDKNLKFEDLEKISKGLVLDGHRVSVEEISY-IEKEPKSEVGLKL 248

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           R    + ++ +FE F++ V R+ R+S+       L  G+ R
Sbjct: 249 RSSNVKVVRAIFENFDYNVLRIDRVSFAGLTKKNLPRGNWR 289


>gi|153001970|ref|YP_001367651.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366588|gb|ABS09588.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 242

 Score = 90.9 bits (224), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 117/236 (49%), Gaps = 15/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLRK 69
           R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D+IE+DG P+ K
Sbjct: 2   RLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPVRLGESLNCLDNIELDGAPITK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  TETLAYWVLNKAVGTDCRLLEQD-ETSLIHLLPKA-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
           L   L  PS    + Y V  +     + +  +  G+      Y D+Q TL  Q  + S+ 
Sbjct: 120 LTHKLMHPSFAHSKTYHVHLNRPFTDEFVEQMASGVR-----YKDVQ-TLPCQVRRLSSD 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              + L +G NR+I+++ +   ++V  L R++     L  L  G  +E   + L E
Sbjct: 174 SFEIVLTQGLNRQIRRMSKALGYRVIDLERVAIMTLNLRELALGELQEGQMRRLTE 229


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 116/235 (49%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNFLKSGRVTVNGKKEKSAKLQIDEETDEICFDGQKLDYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+++   DP  + TV D L   ++R   V  VGRLDI+T GLLLLTNDG L
Sbjct: 62  -YYMMNKPQGVISATEDPKHK-TVLDLLDD-YARAKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNA 187
           A  L  P     + Y  +  G +    +    KGI ++       +   V++DT+K   +
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTDTDVETFAKGIPLKDFTCQPAKLELVSIDTEK-DQS 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R +SK+ L
Sbjct: 178 LVRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLTLDEDLKRGEWRRLSKEEL 232


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 112/215 (52%), Gaps = 12/215 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++ AG+ +R+EV+++I ++ V+VNG L+ +  ++V   D +++DG  +       
Sbjct: 2   RLDKYLSHAGVGTRKEVKQLIRKKHVRVNGELVVKDDMHVEEDDLVQLDGEHIYYEPFVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G++    D +   TV D    +  +    VGRLD++TEGL+L++NDG LA  
Sbjct: 62  LML-NKPSGVICATQDSE-HETVLDCFDVMLPKGCFPVGRLDMDTEGLVLISNDGKLAHH 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P     + Y V     +D+  +  L  G +I   + +    ++V  +T         
Sbjct: 120 LLSPKHHVRKTYYVEHQLCLDETAIKTLCNGSIILDEKTVLCAALEVINETS------CF 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             + EG+  +IK++F     +V  L R++ GP +L
Sbjct: 174 FHIEEGRYHQIKRMFSAVGNEVLYLKRVAMGPLRL 208


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D  D     + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIDDNIIEYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 118/238 (49%), Gaps = 16/238 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P RV+K + + G+ SRRE E +IA+  V ++G  +  A   +     + ++    +    
Sbjct: 12  PVRVNKWLGQTGVCSRREAESLIAEGLVSIDGETISDAGRKIEPGQTLTLNDTAQQALAS 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSRVISVGRLDINTEGLL 122
               + HKP+G V+   DP     V              P+  + +  +GRLD ++ GLL
Sbjct: 72  GMTLVLHKPVGYVSGQPDPGKIPAVRLLKIPNRIGEGETPARDASLPPIGRLDEDSRGLL 131

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDT 181
           LL++DG +A+ +  P+++  + Y V   G + + KL+ L+ G+V+        +VT ++ 
Sbjct: 132 LLSSDGVVAKAVIGPASELDKEYLVVVDGVITEAKLSRLRHGLVLNDKPLKPARVTQIEP 191

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           Q+     +   L EGK R+I+++ E    +V  L RI  GP ++G L  G  R ++ +
Sbjct: 192 QR-----LRFVLTEGKYRQIRRMCELVGLEVVDLYRIRIGPLEIGDLPEGRWRHLTDQ 244


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 117/232 (50%), Gaps = 15/232 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+ +GI SRRE E+ I + RV +NG   +     V   D +++DG  ++  + T  
Sbjct: 17  LNKYISSSGICSRREAEKFIKEGRVTLNGKATQLGN-RVTKKDVVKLDGRVVKPKDVTIY 75

Query: 76  WLYHKPIGLVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +KP+G+V+T    DGR         N P    R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 76  IALNKPVGIVST---TDGREPNNIVKHINYPE---RLFPIGRLDKPSEGLIFLTNDGDIV 129

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  + +D +  +  GI I G       V    +K ++    +
Sbjct: 130 NKILRAGNNHEKEYFVTVNKSITEDFIEKMGNGIPILGTVTQKCLV----EKVNDKIFKI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ E+ +++V +L R      +LG L  G  RE++++ + E
Sbjct: 186 ILTQGLNRQIRRMCEYLDYEVTKLKRTRIMNVELGYLQTGDWRELTEEEMNE 237


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 73/216 (33%), Positives = 105/216 (48%), Gaps = 17/216 (7%)

Query: 25  IASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIG 83
           I +  E  R+I + R+ +NG  +++   VNV   D I V+G PL    R  L L HKP G
Sbjct: 3   IPTGTEAGRLIERGRISINGRPIVQNRWVNV-HKDSILVNGTPLEATCRLTL-LMHKPAG 60

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
            V +  DP  R TVF  LP     + + GRLD +T GLLLLTND  L   L  P  +  +
Sbjct: 61  YVVSRDDPLNRDTVFQLLPDPSVYIGASGRLDKDTTGLLLLTNDTYLQSSLVDPVYKVPK 120

Query: 144 VYRVRFHG-QVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------------QKGSNAWV 189
           VYRV   G  ++  +L  L+ G+ ++ G     +   LD              +     +
Sbjct: 121 VYRVVVKGAALNGAQLMALRSGVSLEDGPTLPALVEPLDVNGDPLPLEMSEYDRYKCKQL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L EG+NR+++++ E     V  L RI  GPF L
Sbjct: 181 NITLWEGRNRQVRRMVEAVGSTVRDLCRIQLGPFSL 216


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>gi|229163701|ref|ZP_04291648.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228619763|gb|EEK76642.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGVLTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 115/215 (53%), Gaps = 6/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++ +AG  SR +V+++I  ++V V+G ++ +  V V S       G      + + 
Sbjct: 2   RLDKLLGQAGFGSRNQVKKLIRSRQVSVDGQIVTKDNVIVDSGLQSIFVGKERVCLKESS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLA 131
            +L +KP G+V+   D + ++ +  +L S   +V     +GRLD +TEGLL++TN+G L 
Sbjct: 62  YYLLYKPSGVVSAVRDSEHKTVI--DLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +   
Sbjct: 120 YRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTAR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++KK+F  +  KV  L RIS+G  +L
Sbjct: 180 ITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRL 214


>gi|327483844|gb|AEA78251.1| Ribosomal large subunit pseudouridine synthase E LSU Psi2457
           [Vibrio cholerae LMA3894-4]
          Length = 241

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 95/186 (51%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G++++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVILKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             +EV+
Sbjct: 235 EWQEVT 240


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 111/222 (50%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG + +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRVEKSPKTQIDETADEIIVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G + Q  ++    GI ++       Q   + LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMKQADVDRFAAGIELKDFTCQPAQLKVLELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   +A
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPAVA 220


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 109/221 (49%), Gaps = 7/221 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+ 
Sbjct: 13  RLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTL-SYEKY 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D +   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 72  VYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKLA 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS-NAWV 189
             +  P     + YR +  G +    +     GI ++   C     V L+T +    + V
Sbjct: 131 HAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSVV 190

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + ++EGK  ++K++ +    KV  L R+S  P QL   LA
Sbjct: 191 EITIKEGKFHQVKRMVQACGKKVTDLQRLSMVPLQLDKQLA 231


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 109/221 (49%), Gaps = 7/221 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+ 
Sbjct: 2   RLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTL-SYEKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D +   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGS-NAWV 189
             +  P     + YR +  G +    +     GI ++   C     V L+T +    + V
Sbjct: 120 HAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSVV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + ++EGK  ++K++ +    KV  L R+S  P QL   LA
Sbjct: 180 EITIKEGKFHQVKRMVQACGKKVTDLQRLSMVPLQLDKQLA 220


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R++  +++ ++RV V+G +++  A+ +     +E DG+ LR A   R
Sbjct: 3   RLDKFLCETVGVTRKQAAKILKEERVTVDGNIIKNGAIKIAEEADVEFDGMSLRLA-GPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H DP    TVF  L  I +  + + GRLD +T GLLLLT+DG  +  
Sbjct: 62  YYMMNKPAGYVCSHDDP-YNPTVFVLLDEIGAEKLHIAGRLDCDTTGLLLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTV 191
           +  P  +  +VYRV     V  +      +GI ++    G+   TL    Q+     V +
Sbjct: 121 VTSPKHKCDKVYRVWLDDPVSPETEQCFAEGIKLR----GERTETLPAQMQRVGEKEVLL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
            + EGK  ++K++F     KV  L R S G   L   L  G  RE++ +
Sbjct: 177 TIHEGKYHQVKRMFAAVGNKVVGLHRESVGGLVLDEALEPGEYRELTDE 225


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 116/230 (50%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           RV K +    + +R ++ ++I ++ V VN ++ +   V V    D + + G  +   ++ 
Sbjct: 2   RVDKFLHDMNVGTRSQIRKLIKEKAVFVNDVVAKSGRVKVDPVVDQVRL-GEQVITYQQY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP+G+VT   D   + TV D    +  R  +  VGRLD +TEGLLL+TN+G LA
Sbjct: 61  FYFMMNKPLGVVTATEDRK-QKTVMDLFNKVDFRKDLFPVGRLDKDTEGLLLITNNGPLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAW 188
             L  P     + Y     GQ+    +     GIV++    +   D+ +   +       
Sbjct: 120 HQLLAPERHVQKTYEAVVTGQITDPAVKQFADGIVLKDGTQLKPADLTILNYSALDEQTL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           V V L+EGK  +++++F     +V  L RIS+GP QL   LL G+ RE+S
Sbjct: 180 VHVTLKEGKYHQVRRMFGSLGERVVSLKRISFGPLQLEEGLLPGTYRELS 229


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 111/238 (46%), Gaps = 22/238 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +R I    V V+G  +      +  T  I+++     +     
Sbjct: 5   RLSKLMSEQGLCSRREADRYIELGWVFVDGEQISELGTKIYPTQKIKLNKAAQAQQISLV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF----DNL--------------PSIFSRVISVGRLDI 116
             L +KP+G V+   +P  R  +     +N               PS    +   GRLDI
Sbjct: 65  TILLNKPVGYVSGQPEPGYRPAIVLIKPENQFIPKQPAQPNKRFQPSHLKNLAPAGRLDI 124

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++GLL+LT DG +A+ +    +   + Y VR  G + ++KL LL  G+ + G       
Sbjct: 125 DSQGLLVLTQDGRIAKQMIGEDSNIEKEYLVRVEGVLPREKLALLNHGLSLDGQPLKPAN 184

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           VT   Q      +   L+EGK R+I+++ E  N KV  L R+  G  +LG L  G  R
Sbjct: 185 VTWQNQD----QLRFILQEGKKRQIRRMCELVNLKVTGLKRVRIGKVKLGNLPEGQWR 238


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/234 (31%), Positives = 117/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D   R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATEDSKHR-TVLDLLDDVARSKGVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+ +    KGI ++       +   +++DT+K + + 
Sbjct: 120 HALLSPKRHVDKTYLAQVKGIMSQEDVETFAKGIPLKDFTCQPARLEIISIDTEK-NQSK 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + EGK  ++K++  +   +V  L R++ G   LG  L  G  R ++K+ L
Sbjct: 179 IRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLALGENLERGEWRRLTKEEL 232


>gi|251773013|gb|EES53569.1| pseudouridine synthase [Leptospirillum ferrodiazotrophum]
          Length = 237

 Score = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 56/167 (33%), Positives = 87/167 (52%), Gaps = 6/167 (3%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +KP G++ T SDP+GR  V D L         F R+  +GRLD  + GLLLLTN      
Sbjct: 54  NKPRGVLVTLSDPEGRPVVGDFLRRTPWSDGSFGRIRPLGRLDAASAGLLLLTNYQEPWS 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P     R YRV+    +  +   L   G   +G  Y  ++V ++ +   ++W+ + 
Sbjct: 114 HFLSPEGGVRRRYRVKIRPGLRAEDRKLFLSGKAGEGAGYRRVEVEIEREGPKSSWLLIS 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L EG+NREI+ V  +  ++V  LIR+++GPF LG L  G    V+++
Sbjct: 174 LVEGRNREIRNVLTYHGYEVLHLIRLAFGPFLLGDLKPGEVSSVTEE 220


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 116/237 (48%), Gaps = 14/237 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K + ++G+ SRRE + +IA   V ++G ++  A   +     + +          
Sbjct: 12  PSRINKWLGQSGVCSRREADALIADGLVSIDGEVVTDAGRKIEPGQTLTLSDRAETALAA 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSRVISVGRLDINTEGLL 122
               + HKP+G V+   +PD    V              P+  + +  +GRLD ++ GLL
Sbjct: 72  GITIVMHKPLGYVSGQPEPDKVPAVRLLTEANRIGPGTAPAADASLPPIGRLDEDSRGLL 131

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LL+ DG +A+ +  P +   + Y VR  G V + KL +L+ GI++ G       V+    
Sbjct: 132 LLSADGVVAKAVIGPDSDLDKEYLVRVVGDVTEKKLKILRHGIMLDGRQLRPAYVS---- 187

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  +  +   LREG+NR+I+++    + +V  LIR+  GP +L  L  G  R ++ +
Sbjct: 188 RMESFRLKFILREGRNRQIRRMCAMVDLEVVDLIRVRIGPLKLDNLPEGHWRMLTAE 244


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 111/233 (47%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER 
Sbjct: 7   KRLNKFISETGFCSRREADKLIEQGRVTLNGAQPE-VGSKVTEQDEVCIDGKPLRSKERP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA 232


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 120/241 (49%), Gaps = 8/241 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR +V+ ++ ++ V+VNG +       +    D + + G  L K E  
Sbjct: 2   RLDKFLVDCTVGSRSQVKAILKKKEVQVNGQIESSPKRQIDEKKDRVTLAG-QLLKHETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D     TV D L  P+   +V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVVSATEDSQ-HQTVLDLLDEPAHQKQVFPVGRLDIDTTGLLLLTNNGPLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             +  P     +VY+ +  G +  + +    +GI ++  +C    +Q+    Q   +  V
Sbjct: 120 HAMLSPKKHVAKVYQAKVEGLMTDEDVVAFGQGIRLKDFVCRPAQLQILESDQAQGSCLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + + EGK  ++K++      KV  L RIS GP  L   L+ G  R +S + L +  G H
Sbjct: 180 QIEIAEGKFHQVKRMVASRGKKVLELKRISMGPLHLPHDLSEGHYRRLSAQELADLSGFH 239

Query: 249 L 249
           +
Sbjct: 240 V 240


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 76/235 (32%), Positives = 120/235 (51%), Gaps = 10/235 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V     I  V G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKQLLKQKAVTVDGAYVKDAALHVDPEQQIVSVFGERVVYTEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D     TV D L  +        VGRLD +TEGLLLLTNDG LA
Sbjct: 62  -YFIMNKPPGVISATEDLRDE-TVIDLLEPLHQHFQPFPVGRLDKDTEGLLLLTNDGHLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
             L  P     +VY  +  G V ++       GI +    +      V L + + S   +
Sbjct: 120 HNLLSPKKHVPKVYYAQIEGVVTEEDAEKFANGIELDDGYVTKPGKLVILKSAQQSEIEL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           T+  +EGK  ++K++FE    +V  L RIS G  +L   LA G  RE++ + L +
Sbjct: 180 TI--QEGKFHQVKRMFEAVGKRVTYLKRISMGSLKLDENLALGEYRELTAEELND 232


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 118/233 (50%), Gaps = 11/233 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            EN    R++K I+  GI SRRE + +I ++RV +NGI  E  +  V STD +++DG  L
Sbjct: 9   NENSDSMRINKFISEKGICSRREADTLIQEKRVTINGITAELGS-RVKSTDEVKLDGKLL 67

Query: 68  RKAER-TRLWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLL 124
            + E+  ++++  +KP+G++ T       + V F N P    R+  +GRLD ++EGL+ L
Sbjct: 68  TEKEKDDKVYIALNKPVGIICTTEKKIKNNIVDFVNYP---KRIFHIGRLDKDSEGLIFL 124

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y V     +    L  +  G+ I        +V    ++G
Sbjct: 125 TNDGDIVNKILRAGNNHEKEYIVTVDKCITNSFLKEMASGVSILNTVTKPCKV---YKEG 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           S+ +  + L +G NR+I+++ E   + V +L RI      L  +  G  R +S
Sbjct: 182 SHIFRII-LTQGLNRQIRRMCEALGYNVLKLKRIRIMNVTLKDIPVGKWRYLS 233


>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 = 90.5 bits (223), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 95/186 (51%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 61  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G++++       +V +  +   
Sbjct: 118 NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVILKDGPTLPAKVDIMPEPTL 177

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 178 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 237

Query: 232 STREVS 237
             +EV+
Sbjct: 238 EWQEVT 243


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 78/238 (32%), Positives = 117/238 (49%), Gaps = 8/238 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +  AGI SR +V+ ++ ++ V VNG    +A + +  + D +   G  L   E  
Sbjct: 2   RLDKFLVEAGIGSRTQVKSILKKKEVFVNGKPESQAKLQIKPNQDQVSFGGQVLV-YEEF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+V+   D     TV D L     R  V  VGRLD +T GLLLLTNDG LA
Sbjct: 61  LYYLLNKPQGVVSATEDK-VHQTVLDLLDDTARRKSVFPVGRLDKDTHGLLLLTNDGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     +VY  R  G + +  +    KGI +    C    +Q+     + +   V
Sbjct: 120 HRLLSPKKHVDKVYMARVDGIMTEQDVEAFAKGITLSDHQCLPAQLQIEEVDVERTCCKV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
            + +REGK  +IK++      +V  L RIS GP QL   LA G+ R +++  ++  L 
Sbjct: 180 RITIREGKFHQIKRMVLACGKEVTDLQRISMGPIQLDDSLALGAFRRLNETEMKALLA 237


>gi|332993044|gb|AEF03099.1| RNA pseudouridine synthase family protein [Alteromonas sp. SN2]
          Length = 246

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 122/235 (51%), Gaps = 13/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPLR 68
           +R++K I+  G+ SRRE +++I Q RV +N  L E     V   D ++VDG     V   
Sbjct: 7   KRLNKYISDTGLCSRREADKLIEQNRVTINDKLPE-LGTKVAQGDKVKVDGKLVKAVAED 65

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K++R  L +Y+KPIG+  T ++   +  + D +     R+  VGRLD  +EGL++LT+DG
Sbjct: 66  KSDRIYL-VYNKPIGITCT-TERHVKGNIIDAIKH-KQRIFPVGRLDKPSEGLIILTSDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  + +  +  + KG+ I G      +V     +G   +
Sbjct: 123 DIVNKILRAENSHDKEYEVTVNQPISERFVQKMAKGVPILGTVTKPCKV---NARGKFQF 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++ L +G NR+I+++ EF  ++V +L R      +LG L  G  R +++K L +
Sbjct: 180 -SIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELGNLKPGQWRNLTEKELNQ 233


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 75/228 (32%), Positives = 111/228 (48%), Gaps = 10/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLR--KA 70
           R    +A  G+ SRR  E +I +  VK+NG L  +    V   D +E       LR  K 
Sbjct: 10  RAHVFLAEKGMGSRRFCEELIRKNLVKINGTL-AKLGDKVFLGDRVEYRRQVFVLRDLKI 68

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
           E       HKP   + ++ DP+GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 69  ESKIYIALHKPKNYLCSNFDPEGRKLAISLVQPLFKERLFSIGRLDFKSSGLLLFTNDGQ 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P ++  + Y V     V++D L   K GI I+   +   ++      G+N+ V
Sbjct: 129 FANSIVHPRSEVEKEYIVESKKDVNEDLLINFKHGIKIEREIF---KLKSYEMLGNNS-V 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L EGKNREI+KVF   N  + ++ RI  G  +L  L  G  + +S
Sbjct: 185 KLVLTEGKNREIRKVFLSKNIFLKKVHRIRIGNIKLDNLKEGQIKVLS 232


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 111/233 (47%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER 
Sbjct: 7   KRLNKFISETGFCSRREADKLIEQGRVTLNGAQPE-VGSKVTEQDEVCIDGKPLRSKERP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L 
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA 232


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 121/234 (51%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A + SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKLCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 107 PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 163

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 164 NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 223

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 224 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 283

Query: 232 STREVS 237
             REV+
Sbjct: 284 EWREVT 289


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 120/240 (50%), Gaps = 18/240 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA---VNVMSTDHIEVDGVPLRK 69
           P R++K ++ AG+ SRRE +R+I   +VKV+G    +AA   + V     + +    + +
Sbjct: 15  PVRLNKYLSEAGVCSRREADRLIESGKVKVDG----KAAGMGMKVSPGQEVRIGRKIVSR 70

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +E   +   +KP G+V T    + +S V F N P    RV  VGRLD ++ GLLL+TN+G
Sbjct: 71  SEEMIVLAVNKPAGIVCTEETRERKSIVRFLNYPV---RVTYVGRLDKDSRGLLLMTNNG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +     +  + Y+V     +  + L  +  G+ I G      +V    QK     
Sbjct: 128 DIINKMMRAGNRHEKEYKVTVDKALTPEFLEKMSSGVAILGTVTRPCRV----QKIGKYT 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQL 245
            T+ L +G NR+I+++ E   ++V  L+R      +LG L  G  R+++ K    L EQ+
Sbjct: 184 FTIILTQGLNRQIRRMCEVLGYEVKDLVRTRIMNIELGKLKEGEYRKLTDKELDCLYEQI 243


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/205 (32%), Positives = 100/205 (48%), Gaps = 11/205 (5%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           VKVNG ++      V+ TD +     P+   E+    L +KP   VTT  DP  R TV D
Sbjct: 2   VKVNGNVVTELGTKVLRTDEVIFHEQPV-TLEKKVYVLINKPKDYVTTSDDPQQRKTVMD 60

Query: 100 NLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +  +   R+  VGRLD NT G+LLLTNDG LA  L  P     +VY V    +V +  L
Sbjct: 61  LVKGVCPERIYPVGRLDRNTTGVLLLTNDGDLASKLAHPKFLKKKVYHVFLDKEVTEHDL 120

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREGKNREIKKVFEFFNWKVNR 214
             +  G+ +      D +V  D  + +N      V + +  GKNR ++++FE   ++V R
Sbjct: 121 QQIATGVTLD-----DGEVHADAIEYANDKDKTQVGIEIHSGKNRIVRRIFESLGYRVVR 175

Query: 215 LIRISYGPFQLGTLLAGSTREVSKK 239
           L R+ +       L  G  R +++K
Sbjct: 176 LDRVQFAGLTKKNLKRGDWRFLTEK 200


>gi|217974541|ref|YP_002359292.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499676|gb|ACK47869.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 242

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 116/236 (49%), Gaps = 15/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLRK 69
           R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D+IE+D  P+ K
Sbjct: 2   RLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLGESLNCLDNIELDSAPITK 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG 
Sbjct: 62  TETLSYWILNKAVGTDCRLLEQD-ETSLIHLLPKA-PRLYPVGRLDKDSRGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
           L   L  PS    + Y VR +     D +  +  G+      Y ++Q TL  Q  + S+ 
Sbjct: 120 LTHKLMHPSFAHSKTYHVRLNRPFTDDFVEQMASGVR-----YKNLQ-TLPCQVRRLSSD 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              + L +G NR+I+++ +   + V  L R++     L  L  G  +E   + L E
Sbjct: 174 SFEIVLIQGLNRQIRRMSKALGYHVIDLERVAIMTLNLRELALGELQEGQMRRLTE 229


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 119/227 (52%), Gaps = 16/227 (7%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTRLWLYHKPIG 83
           + SRRE++++I  + V ++GI     + NV +T   I V+G  +   +  + ++ +KP G
Sbjct: 5   VLSRREMKKLIKNEAVLIDGIPATHVSNNVDATLQVITVNGTRIHD-DSQKYYMLNKPQG 63

Query: 84  LVTTHSDPDGRSTVFD-----NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           L++  +D +  +TV D     N+  ++     +GRLD +TEGLLL+TN+G L   +  P 
Sbjct: 64  LISATTDKE-HTTVIDLFANENVEGLYP----LGRLDGDTEGLLLVTNNGPLGYRMLNPD 118

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREG 196
               + Y V  +G +D D +   K+G+   G   C   M +T+     +    TV + EG
Sbjct: 119 QHIEKEYYVEVNGPLDNDAVETFKRGVTFHGGYQCKPSM-LTIIESSDNLGRATVTISEG 177

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           K  ++KK+F     KV  L RI +G F L   LA G  RE+++  L+
Sbjct: 178 KFHQVKKMFLCVGVKVTYLKRIRFGEFVLDESLAPGEYRELNEAELQ 224


>gi|229169439|ref|ZP_04297147.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228614044|gb|EEK71161.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 248

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 115/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G+ ++ A  +V +    + + G  +   E  
Sbjct: 8   RLDKLLANMGHGSRKEVKKLLKDGVVKIDGVPVKDAKFHVNVEEQEVMIHGEVVEYKEFV 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 68  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
              L  P     + Y     G V ++ +    KG++++   Y      L   K  + + +
Sbjct: 125 THQLLSPKKHVPKKYYAHISGVVTEEDVIEFAKGVILED-GYETKPGELTILKSDDISEI 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 184 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDEELELGQYRELT 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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 116/234 (49%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNFLKAGRVTVNGKKEKSAKLQIDEETDEICFDGKKLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   +P  + TV D +   +    V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATENPKHK-TVLDLMDDYACAKEVFPVGRLDIDTHGLLLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y  +  G +  + +    KGI ++       +   V++DT++ + + 
Sbjct: 120 HALLSPKRHVDKTYMAQVKGIMTDEDIETFAKGIPLKDFTCQPAKLELVSIDTEE-NKSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R +SK+ L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRVTMGTLTLDEELKRGEWRRLSKEEL 232


>gi|302387646|ref|YP_003823468.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302198274|gb|ADL05845.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 262

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 117/239 (48%), Gaps = 25/239 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---VMSTDHIEVDGVPLRKA- 70
           R++K ++ AGI SRRE +R I   +V +NG    +AA     V+    + ++G  ++   
Sbjct: 7   RLNKFLSEAGICSRREADRFIEAGKVSING----KAAATGQKVLPGQSVTINGRTVQAGK 62

Query: 71  ------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                 E       HKP G+V T S  D    + D +     R+  VGRLD ++EGL+L+
Sbjct: 63  GDQSHKEEPVFLAVHKPRGIVCTTSHKDRAPNIVD-MVDYPVRIYPVGRLDKDSEGLILM 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TN G L   +        + Y V+ +  V  D +  +KKG+ +      ++ VT      
Sbjct: 122 TNQGSLVNKMMRSGNAHEKEYLVKVNRPVTDDFIRTMKKGVFLP-----ELNVTTKPCFV 176

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           T+ G  A+  V L +G NR+I+++     ++V  L R+     +LG L  G+ RE+SK+
Sbjct: 177 TKAGEKAFRIV-LTQGLNRQIRRMCSQLGFEVRMLKRMRIMNIELGDLKPGAYRELSKR 234


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 113/229 (49%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A  +V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKFHVNVEEQEVTIHGEIVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LLLTNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVVDLLELEDAIFDP-FPVGRLDIDTEGFLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
              L  P     + Y     G V +  +    KG+++    Y      L   K  + + +
Sbjct: 119 THQLLSPKKHVPKKYYAHVAGVVTEKDVEEFAKGVILDD-GYETKPGELTILKSDDVSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+ +    KGI ++   C   +   V++D +K + + 
Sbjct: 120 HALLSPKRHVDKTYLAQVKGIMTQEDVETFAKGISLKDFTCQPAILELVSIDPEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + EGK  ++K++  +   +V  L R++ G   L  +L  G  R ++K+ L
Sbjct: 179 IRVTIAEGKFHQVKRMVTYCGKEVVDLQRLTMGTLVLDESLQRGEWRRLTKEEL 232


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I  +RV +NG +  +   ++ +  D + VDG   +    T
Sbjct: 2   RLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDG---KVVSTT 58

Query: 74  RLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           +L+   +HKP G VT   D +    V D LP  F +  V+ VGRLD +TEGLLLLTNDG 
Sbjct: 59  QLYYVKFHKPKGYVTAVEDSN-HPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGV 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +   +    +VY V F G +  + +  +K+GI++     G      + +  S   V
Sbjct: 118 WGHSIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGD---GTQCKPAEIESVSLHSV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            V + EGK  ++K++       V  L R++ G   L G    GS  E++
Sbjct: 175 HVTIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELT 223


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 114/234 (48%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+++RAGIASRR  E++I + RV+V+G L+      V     +          + + 
Sbjct: 18  RLQKILSRAGIASRRAAEKLIIEGRVEVDGQLVRELGTRVDPDVSVVRVDGVKVVVDDSL 77

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
           ++L  +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 78  VYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGEL 137

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L  G+ +  G  + D    +D   G    V
Sbjct: 138 AHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKT-LV 196

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+
Sbjct: 197 RLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQ 250


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 117/232 (50%), Gaps = 15/232 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+ +G+ SRRE E+ I + R+ +NG   +     V   D ++ DG   R  E   +
Sbjct: 11  LNKYISSSGVCSRREAEKFIKEGRITINGKATQLGN-RVGKKDVVKFDG---RLVEPKNV 66

Query: 76  WLY---HKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            LY   +KP+G+V+T  + +  + V   N P    R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 67  TLYIALNKPVGIVSTTDEREPHNIVKHVNYPE---RLFPIGRLDKPSEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +  D +  +  GI I     G M      +K S+    +
Sbjct: 124 NKILRAGNNHEKEYFVSVDKSITNDFITSMGNGIPI----LGTMTKRCKVEKVSDKIFKI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ E+ +++V +L R       LG L +G  RE++++ +++
Sbjct: 180 VLTQGLNRQIRRMCEYLDYEVTKLKRTRIMNVDLGYLQSGDWRELTEEEMKD 231


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 108/233 (46%), Gaps = 21/233 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +A  G+ SRRE +  IA   VKVNG +++     V     IEV     +    T 
Sbjct: 142 RLSKRMAELGLCSRREADEFIANGWVKVNGEVVDVLGTRVAPDAKIEVSKEAHQHQAETV 201

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFSR-----VISVGRLDINT 118
             L HKP+G V+  ++ DG                D   ++F R     +   GRLDI++
Sbjct: 202 TILLHKPVGYVSGQAE-DGYEPAVVLVHPDNQWKEDPSQTVFKRGHLRGLAPAGRLDIDS 260

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LT DG +AR L    +   + Y VR  G + ++ L  L  G+ + G+     +V+
Sbjct: 261 TGLLVLTQDGRVARRLIGEDSTVEKEYLVRVTGTLSEEGLRKLNHGLSLDGVKLKPAKVS 320

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              +      +   LREG+ R+I+++ E     V  L R+  G   LG L  G
Sbjct: 321 WQNED----QLRFVLREGRKRQIRRMCELVGLTVVGLKRVRIGSVTLGKLPVG 369


>gi|327438231|dbj|BAK14596.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 234

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 112/226 (49%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  GI SRR  ++ +   RVK+NG++    +  V + D + VDG P+++ E   
Sbjct: 2   RINKFLAETGIVSRRGADKWVEDGRVKINGVVATNGS-QVETGDEVLVDGKPVKRQEELV 60

Query: 75  LWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+  TT    +G    F N      R+  +GRLD ++EGLLLLTNDG +   
Sbjct: 61  YIVLNKPVGITSTTEKQIEGNVVDFVNHRL---RIFHIGRLDKDSEGLLLLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    +    ++ +  G+ I        +V    +K S+    + L
Sbjct: 118 ILRAENHHEKEYVVQVDKPITDQFIHDMSSGVEILDTTTLPCRV----EKVSSKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +G NR+I+++     + V RL RI      +G L  G  R+++ K
Sbjct: 174 EQGLNRQIRRMCSALGYSVQRLQRIRIMNIHIGNLKVGQWRDLTDK 219


>gi|291550320|emb|CBL26582.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           torques L2-14]
          Length = 241

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/231 (31%), Positives = 120/231 (51%), Gaps = 15/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI +R EV++ I + +V+VN   ++R  + +    DH+   G  +  AE  
Sbjct: 4   RLDKYLADMGIGTRTEVKKAITKGQVRVNEETVKRPEIKIDTEKDHVFYQGQMVAYAE-Y 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D +  STV D +     + +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYYMLNKPAGVVSATEDKND-STVLDLIDEKQRKDLFPVGRLDKDTEGLLLITNDGELAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNA 187
            L  P     +VY  R  G+V ++ +    +G+ I     G+ + TL       ++   +
Sbjct: 122 QLLSPKKHVDKVYFARIDGKVTEEDVRRFAEGLEI-----GEEKPTLPAHLEILKREEIS 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + +REGK  ++K++F     +V  L R+  G   L   LA G  RE++
Sbjct: 177 EIRLTIREGKFHQVKRMFHAVGKEVIYLKRLQMGSLVLDPRLALGEYRELT 227


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 116/230 (50%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           RV K +    + +R ++ ++I ++ V VN ++ +   V V    D + + G  +   ++ 
Sbjct: 2   RVDKFLHDMNVGTRSQIRKLIKEKVVFVNDVVAKSGRVKVDPVVDQVRL-GEQVITYQQY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP+G+VT   D   + TV D    +  R  +  VGRLD +TEGLLL+TN+G LA
Sbjct: 61  FYFMMNKPLGVVTATEDRK-QKTVMDLFNKVDFRKDLFPVGRLDKDTEGLLLITNNGPLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAW 188
             L  P     + Y     GQ+    +     GIV++    +   D+ +   +       
Sbjct: 120 HQLLAPERHVQKTYEAVVTGQITDPAVKQFADGIVLKDGTQLKPADLTILNYSALDEQTL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           V V L+EGK  +++++F     +V  L RIS+GP QL   LL G+ RE+S
Sbjct: 180 VHVTLKEGKYHQVRRMFGSLGERVVSLKRISFGPLQLEEGLLPGTYRELS 229


>gi|229062392|ref|ZP_04199708.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228716863|gb|EEL68550.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 114/229 (49%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A  +V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNIEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
              L  P     + Y     G V ++ +    KG++++   Y      L   K  + + +
Sbjct: 119 THQLLSPKKHVPKKYYAHISGVVTEEDVKEFSKGVILED-GYETKPGELTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDQELELGQYRELT 226


>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 = 90.1 bits (222), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/216 (32%), Positives = 104/216 (48%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A   +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKFQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDINT GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDINTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-AWV 189
            VL  P     + Y  +  G + Q+ +    +GI ++   C       L T    N + +
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPARLEILSTDAEKNQSQI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 180 RVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 114/228 (50%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKAER 72
           R++K I+ AG ASRR  +R+I + RV +NG   ++A +   V   D I V G  +R A  
Sbjct: 5   RINKFISEAGKASRRGADRLIEEGRVTING---KKAKIGDQVEPGDDIRVSGQQIRVARN 61

Query: 73  TRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G+  TT  +  G      N P    RV ++GRLD +++GL+LLTNDG + 
Sbjct: 62  NVYLALNKPVGITSTTEKNVKGNIVDLVNHPL---RVFNIGRLDKDSDGLILLTNDGDIV 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     Q  + Y V     +  + L  + +G+ I     G   +    ++ S     +
Sbjct: 119 NEILRAENQHEKEYIVSVDKPITPEFLTQMSEGVKI----LGTKTLPCKVEQLSKFDFKI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++ E   ++V RL R+      LG L  G  R+++KK
Sbjct: 175 ILTQGLNRQIRRMCEALGYEVFRLQRVRIMNIHLGNLPVGQWRDLTKK 222


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 114/234 (48%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+++RAGIASRR  E++I + RV+V+G L+      V     +          + + 
Sbjct: 17  RLQKILSRAGIASRRAAEKLIIEGRVEVDGQLVRELGTRVDPDVSVVRVDGVKVVVDDSL 76

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
           ++L  +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 77  VYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGEL 136

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L  G+ +  G  + D    +D   G    V
Sbjct: 137 AHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKT-LV 195

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+
Sbjct: 196 RLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQ 249


>gi|292559208|gb|ADE32209.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 235

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/227 (30%), Positives = 112/227 (49%), Gaps = 8/227 (3%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKP 81
            G+ SR EV++++  ++V VNG +       +    D I V G  L   E    +L +KP
Sbjct: 3   CGVGSRTEVKKLLKNKQVTVNGQVETSPKQQINEKKDQIAVAGQVLSH-ETFVYYLLNKP 61

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G+++   D D   TV D L +      V  VGRLDI+T GLLLLTN G LA  +  P  
Sbjct: 62  KGVISATED-DHHRTVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNKGQLAHAMLSPKK 120

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVGLREGK 197
              ++YR +  G + Q+ +     GI ++       Q+T+    +    + V + +REGK
Sbjct: 121 HVDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPAQLTILSTDEAKQTSLVDITIREGK 180

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
             +IK++ +     V  L R++ GP +L   LA G  R ++   L++
Sbjct: 181 FHQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQ 227


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 76/229 (33%), Positives = 109/229 (47%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-----DHIEVDGVPLRK 69
           R++K +A AG+ASRR+ + +I    V VNG    RAA     T     D +EV G  +  
Sbjct: 5   RLNKFLASAGVASRRKCDEIIFAGSVTVNG----RAATGPFVTVDEEFDSVEVGGQRI-G 59

Query: 70  AERTRLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           AE+   ++ HKP+G L ++     G   V D L     R+ +VGRLD  T GL+L+TNDG
Sbjct: 60  AEKKVYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++    V    L  L  G VI G     + V    +K     
Sbjct: 120 EFANRVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSV----KKVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++
Sbjct: 176 IKIIVNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELT 224


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 108/206 (52%), Gaps = 3/206 (1%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
           I+   V VNG ++      V  TD +  DG  L  +E+    L +KP G +TT +D  GR
Sbjct: 3   ISAGNVTVNGEVMTTLGYRVKPTDEVRFDG-KLLSSEKKEYILLNKPKGFITTTNDEKGR 61

Query: 95  STVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            TV D +  +  +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 EYKDFIAIEQGLELEDGFIQVDEISYVDQKPKNE-IGIKIHSGRNRIVRRIFEHLGYQVD 180

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKK 239
           +L R+ +       L  G  R ++++
Sbjct: 181 KLDRVVFAGLTKKDLPRGHWRRLTQQ 206


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 110/217 (50%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLL NDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLANDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ +    +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>gi|327439180|dbj|BAK15545.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 240

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/222 (29%), Positives = 118/222 (53%), Gaps = 11/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV+ ++ Q+ V V+G+ ++ +A++V     ++ V G  +   E  
Sbjct: 6   RLDKLLANMGYGSRKEVKLLLKQKAVTVDGVTVKDSAMHVNPEKQNVSVFGERVEYVEFI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L   +       VGRLD +TEGLLL+TNDG LA
Sbjct: 66  YLMM-NKPPGVISATEDRYDQ-TVIDLLDPEYQHFEPFPVGRLDKDTEGLLLITNDGNLA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTLDTQKGSNAW 188
             L  P     + Y  +  G V +  +    +G+ ++   +   G++++ +    G  + 
Sbjct: 124 HNLLSPKKHVPKWYYAKIDGVVTEADIEAFAQGVTLEDGYHTKPGELKILV---SGEQSE 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + ++EGK  ++K++FE    KV  L R+S G  +L   LA
Sbjct: 181 IELMIQEGKFHQVKRMFEAVGKKVTYLKRLSMGTLKLDEELA 222


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I  +RV +NG +  +   ++ +  D + VDG   +    T
Sbjct: 2   RLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDG---KVVSTT 58

Query: 74  RLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           +L+   +HKP G VT   D +    V D LP  F +  V+ VGRLD +TEGLLLLTNDG 
Sbjct: 59  QLYYVKFHKPKGYVTAVEDSN-HPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGV 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +   +    ++Y V F G +  + +  +KKGI++     G      + +  S   V
Sbjct: 118 WGHSIINGNKHVPKIYYVEFEGTLSDEGIQRIKKGILLGD---GTQCKPAEIEFVSLHSV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            V + EGK  ++K++       V  L R++ G   L G    GS  E++
Sbjct: 175 HVTIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELT 223


>gi|261403960|ref|YP_003240201.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261280423|gb|ACX62394.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 233

 Score = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 121/232 (52%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++++   +V +NG++    +      D + + G PL+  ++  
Sbjct: 2   RINKFISETGYCSRREADKLVESGKVTINGVVAVLGS-QAEEGDDVRIQGKPLQDKKKHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITST-TESHIKGNIVDFVGH-NERIFPIGRLDKDSEGLILLTNDGDIVNKI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     V +  L  +  G+ I     G+M +  +  + S     + L 
Sbjct: 119 LRSEGKHEKEYIVTVDRPVTESFLRGMAGGVKI----LGEMTLPCEVTRMSERVFRIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNR+I+++   F ++V +L RI     +LG+   GS R+++ K  +E+LG
Sbjct: 175 EGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRIGSWRDLNDK-EKEELG 225


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 62/209 (29%), Positives = 99/209 (47%), Gaps = 13/209 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K I+  G  SRRE +++I Q RV +NG   E     VM  D + VD  PLR  ER
Sbjct: 18  PVRLNKFISDTGYCSRREADKLIDQGRVTINGTQPE-MGTKVMPDDEVLVDDKPLRAKER 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
                 +KP G+  T         V DN+        R+  +GRLD  ++GL+ LTNDG 
Sbjct: 77  PIYIALNKPTGVTCTTE-----RHVKDNIVDFIGHRKRIFPIGRLDKPSDGLIFLTNDGD 131

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR   Q+  + L  +  G+ I       + +    +K ++   
Sbjct: 132 IVNKILRAGNSHEKEYVVRVDHQITPEFLEKMASGVEI----LDTVTLPCTVKKETDYSF 187

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            + L +G NR+I+++ E   + V +L R+
Sbjct: 188 RITLTQGLNRQIRRMCEALGYDVYKLRRV 216


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 113/229 (49%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A  +V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNVEEQEVMIHGEIVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LLLTNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVVDLLELEDAIFDP-FPVGRLDIDTEGFLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           A  L  P     + Y     G V +  +    KG+++    Y      L   K  + + +
Sbjct: 119 AHQLLSPKKHVPKKYYAHVAGIVTEKDVEEFAKGVILDD-GYETKPGALTILKSDDVSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVEKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 108/222 (48%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DQHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     + YR +  G + Q  +     GI ++       Q   + LD  K   + 
Sbjct: 120 HAMLSPKKHVEKTYRAQVAGLMKQADVERFAAGIELKDFTCQPAQLKILELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLAMGPLQLDPALA 220


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 116/232 (50%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +  AG+ SR +V+ ++ +++V VNG+     +  VN M TD +   G  L   E 
Sbjct: 2   RLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEM-TDEVSYQGQRLN-YEA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   + TV D L     +  V  VGRLD +T GLLL+TNDG L
Sbjct: 60  FVYYMLNKPKGVISATEDSSHK-TVLDLLDDTARQKAVFPVGRLDKDTHGLLLVTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSN 186
           A  L  P     + Y     G + Q+ +    +GI ++   +  M   LD     +    
Sbjct: 119 AHALLSPKKHVAKQYLAVVDGMMTQEDVKHFAQGITLKD--HQCMPAHLDILEINESLKT 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           + V + + EGK  ++K++       V+ L RIS GP QL + LA G+ R ++
Sbjct: 177 SLVKITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLT 228


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRVFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKSFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTCRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 123/248 (49%), Gaps = 28/248 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEV--DGVPLRKA 70
           +RVSK++AR G  SRRE E++IA  RV+VNG ++ E+     +++D +E+  DG     +
Sbjct: 84  ERVSKILARRGACSRREAEQLIADGRVRVNGTVITEQGHKCDVNSDRVEITSDGSAWLSS 143

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNL---PSIFSRVIS 110
           + T     +KP GLV+     D  +                    D+L    S  SR   
Sbjct: 144 KLT--LAVNKPPGLVSNLPSADEVAACSIVEPSNAWMRSMKWVAMDDLRRATSDPSRFNV 201

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLD ++ GLL+LT DG LAR + +     ++ Y V     V +  +  L   +++ G+
Sbjct: 202 CGRLDKDSRGLLILTEDGALARSV-IGGNGVVKRYVVTTDADVRESHMQSLNGTVMLDGV 260

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               M V     +GS   +   LREGKNR+I++V E F  +V  L R+  G   +G L  
Sbjct: 261 ELLPMNVK-RLGRGSRT-LEFNLREGKNRQIRRVCEKFGLRVVDLHRVQIGEIDIGDLPE 318

Query: 231 GSTREVSK 238
           G+ R +S+
Sbjct: 319 GAWRILSE 326


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 67/211 (31%), Positives = 104/211 (49%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ K +   G A RR+ +  I  +RV VNG  ++     V   D++ VDG  L K  +  
Sbjct: 27  KLQKYLQLCGFA-RRKADEYITSKRVIVNGKTVDEPWFEVNEDDNVLVDGKIL-KPNQFE 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP   VTT  DP  + T+ + +  I + +   GRLD +  G+L+LTNDG L  +L
Sbjct: 85  YYVLHKPKDYVTTLFDPKQKKTIGELIKHIKTPLKPAGRLDKDATGVLILTNDGELIDIL 144

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V+    V  ++L  LKKGI  +G         +  +    + V V L 
Sbjct: 145 TNAKYRVKKEYIVKVKSVVSAEELVKLKKGIYDKGEFLKLEHFKIIEKSSEYSIVRVELI 204

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +GK  EIK++F      V  L RIS+GP  +
Sbjct: 205 KGKKHEIKRLFSSIGHNVLELKRISHGPISI 235


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 125/234 (53%), Gaps = 15/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TEGLLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTRE 229


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 63/189 (33%), Positives = 95/189 (50%), Gaps = 7/189 (3%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           I VDG PL    R  L L +KP G+VTT  D  GR TV+          +  VGRLD  +
Sbjct: 17  ITVDGQPLAGPARCYLML-NKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKAS 75

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYG 173
           EGLLL +ND   A  +  P+T   + Y V+   +   ++L  L+ G+V       G    
Sbjct: 76  EGLLLFSNDPQWAAAVTDPATGPDKTYHVQIDCRPSAEQLAQLRAGVVDPDPEGDGALLR 135

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              V +  +   NAW+ + L EG+NR+I+++       V RL+R++ G   +G L  G+ 
Sbjct: 136 AKHVGVLREGERNAWLEIVLDEGRNRQIRRLLAALEIGVLRLVRVAIGALAMGELGKGAW 195

Query: 234 REVSKKILR 242
           R +S + +R
Sbjct: 196 RMLSAEEVR 204


>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 = 89.7 bits (221), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 109/234 (46%), Gaps = 18/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE + +I +  V V+G  +    + +     I +     R+     
Sbjct: 77  RLSKIMSERGLCSRREADEIIERGWVFVDGQRVSELGIRIDPNAEITLAAQAKRRQMEQV 136

Query: 75  LWLYHKPIGLVTTHSDPD--------GRSTVFDNL------PSIFSRVISVGRLDINTEG 120
             L HKP+G V+   +P         G    FD        PS    +   GRLDI++ G
Sbjct: 137 TILLHKPVGYVSGQPEPGFEPAVSLIGPDNQFDRADAQRFHPSHLKGIAPAGRLDIDSTG 196

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+LT DG +AR L    ++  + Y VR  G++D+  L LL  G+ + G      +V   
Sbjct: 197 LLVLTQDGRIARQLIGDDSKVEKEYLVRVEGRLDERGLALLNHGLELDGRTLRPAKVEWL 256

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +      +   LREG+ R+I+++ E    KV  L R+  G  +LG L  G  R
Sbjct: 257 NED----QLRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGRVKLGDLPLGQWR 306


>gi|145355350|ref|XP_001421926.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582165|gb|ABP00220.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 287

 Score = 89.7 bits (221), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 69/223 (30%), Positives = 112/223 (50%), Gaps = 17/223 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMST--DHIEVDGVPLRKA 70
           +R+  +++R G+ SR +  R IA++ V  +G    ERA    +      + VDG  L   
Sbjct: 48  ERLDALLSRLGLTSRADAARFIAERVVTTDGARATERATSGKLKARAADVRVDGETLEDV 107

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
           +   L + HK  G+V +H   +G ++V+D LP  + R    + SVGRLD +T GLLLLT+
Sbjct: 108 DGL-LIVMHKARGVVCSHDVREG-TSVYDALPERWRRRKPSIESVGRLDKDTSGLLLLTD 165

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQG---ICYGDMQVTLDTQ 182
           DG L   L  P  +  + YRV+    + +D + +   G + + G    C   +   +D +
Sbjct: 166 DGALVHALTTPKKEIGKWYRVKTDRPIPRDAVEVFASGELTLDGETRACKPAVCELMDDE 225

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +   +T    EGK  ++K++F FF   V  L R S+G   L
Sbjct: 226 TEARLRLT----EGKFHQVKRMFAFFGCTVIGLHRESFGSLTL 264


>gi|315644423|ref|ZP_07897556.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315280173|gb|EFU43466.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 233

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 121/232 (52%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++++   +V +NG++    +      D + + G PL+  ++  
Sbjct: 2   RINKFISETGYCSRREADKLVESGKVTINGVVAVLGS-QAEEGDDVRIQGRPLQDKKKHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   +
Sbjct: 61  YIALYKPVGITST-TELHIKGNIVDFVGH-KERIFPIGRLDKDSEGLILLTNDGDIVNKI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +    L  +  G+ I     G+M +  +  + S     + L 
Sbjct: 119 LRSEGKHEKEYIVTVDRPLTDTFLRGMSSGVKI----LGEMTLPCEVTRMSERVFRIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNR+I+++   F ++V +L RI     +LG+   GS R++++K  RE+LG
Sbjct: 175 EGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRVGSWRDLNEK-EREELG 225


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/234 (30%), Positives = 123/234 (52%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A +GI +R+EV+ +I  +++ VN  ++  + + +  T  I      +    + R
Sbjct: 2   RLDKFLANSGIGTRKEVKEIIKNRKIFVNDKIVMSSDLKIDETKDIIKYENNVINYTKFR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G ++  +D + + TV D +    + ++  VGRLDI+TEGLLLLTNDG LA  
Sbjct: 62  YIMLNKPKGYISATND-NKQKTVLDLITDFKTYKLFPVGRLDIDTEGLLLLTNDGDLAHN 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y V     +  D ++ ++KGI I +GI     ++     K  +  + + 
Sbjct: 121 LLSPKKHVEKKYYVELSQDISSDDISNIEKGIDIGEGIITRLSKII----KVDDNKLYII 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKKILREQL 245
           + EGK  ++K++F+  N +V  L RIS G   L   L  G  RE++ + LR  L
Sbjct: 177 ITEGKFHQVKRMFKAVNNEVKYLKRISMGSLILDEKLNLGEYRELTYEELRSLL 230


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 80/234 (34%), Positives = 117/234 (50%), Gaps = 16/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERA-----AVNVMSTDHIEVDGVPLR 68
           R+ KV+++AGIASRR  ERMI   RV+V+G I+ E+      AVNV+  D   V    + 
Sbjct: 24  RLQKVLSQAGIASRRVAERMIYDGRVEVDGEIVTEQGRRIDPAVNVVRVDGARV----IM 79

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLT 125
             +   L L +KP G+++T SD  GR  V   +         V +VGRLD +T GL+LLT
Sbjct: 80  NTDLVYLAL-NKPFGMLSTMSDDRGRPCVGKLIEERVRGNQGVRNVGRLDADTVGLILLT 138

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKG 184
           NDG L   L  PS +  + Y     G + +     L+ G+ +  G    D    L T  G
Sbjct: 139 NDGELTHRLMHPSYEVPKTYIATVAGTIPRGLGRQLRDGVELADGPAKVDEFKFLGTTDG 198

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             + V + L EG+NR ++++ +     V  L+R   G   LG    GS R + +
Sbjct: 199 -QSMVQLTLHEGRNRIVRRMMDAAGHPVVELVRTKIGDVTLGNQRPGSLRALGR 251


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 70/217 (32%), Positives = 111/217 (51%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTN+G LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
            VL  P     + Y  +  G + Q+ +    +GI ++   C   +   V++DT+K + + 
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 128/238 (53%), Gaps = 17/238 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTN 126
            ++ + +KP G+V+  SD   + TV D +      P ++     VGRLD +TEGLLLLT+
Sbjct: 60  HVYYMLNKPKGVVSAVSDAS-KKTVIDLIAPQDRRPGLYP----VGRLDGDTEGLLLLTD 114

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGS 185
           +G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     +
Sbjct: 115 NGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATET 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+
Sbjct: 175 ESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQ 232


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 109/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  L   E+ 
Sbjct: 2   RLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGT-LVSYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLLTNNGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY-GDMQVTLDTQKGSNAWV 189
             +  P     + Y V+  G + +D +    KGI+++   C    +++    Q    + V
Sbjct: 120 HKMLSPKKHVDKCYEVKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + ++EGK  ++K++      +V  L R+  G  QL
Sbjct: 180 KITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQL 215


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTCRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 69/217 (31%), Positives = 108/217 (49%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+ +    KGI ++       +   V++D +K + + 
Sbjct: 120 HDLLSPKRHVDKTYLAQVKGIMTQEDVETFAKGIPLKDFTCKPARLELVSIDAEK-NQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + V + EGK  ++K++  +   +V  L R++ G   L
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 115/233 (49%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVV-YQQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y     G  D++    +  G+ ++    +  G +++    +    + +
Sbjct: 121 QLLAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            + + EGK  ++K++F     KV +L R+S GP  L   LA GS R ++++ L
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEEL 233


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 110/217 (50%), Gaps = 7/217 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           + T +R+ KV+A  G+ SR+E+ ++    R+ V+G ++  A   +   +  I VDG  + 
Sbjct: 5   HLTKERLDKVLAHLGLGSRKEIHKLARAGRITVDGEVITDAGFKLDPRSARIAVDGEEVF 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E   + L +KP G VT+  D DG S V   L  +    + VGRLD +TEGLLL+T DG
Sbjct: 65  YREFFHVLL-NKPAGYVTSTQDRDGPS-VTHLLEMVRDDWMPVGRLDKDTEGLLLITTDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  +  + Y         Q  +     G  ++G      ++TL    G +  
Sbjct: 123 ELAHRLTHPRWKVPKRYYAELAEPATQADVEAFAAGFELEGEPLQPAELTL----GKDRR 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V + +REG+  ++K++F     +V  L R+++GP +L
Sbjct: 179 VELVIREGRYHQVKRMFAARGNRVVYLKRVAFGPLEL 215


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 113/246 (45%), Gaps = 30/246 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK+++  G+ SRRE +  I +  V V+G  +      V     I +D    R+ ++
Sbjct: 4   PVRLSKLMSERGLCSRREADAFIERGLVFVDGKRVSELGTKVDPACAIRLDNAASRQQQQ 63

Query: 73  TRLWLYHKPIGLVTTHSDP----------------DGRSTVFDNLPSIFSRVISVGRLDI 116
               L HKP+G V+   +P                D R      LP+    +   GRLDI
Sbjct: 64  RVTILLHKPVGYVSGQPEPGYQPAVALIRGETQWRDERRPGPAFLPAHLKGLAPAGRLDI 123

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +AR L    +   + Y VR  G++D   L LL  G+ + G+     +
Sbjct: 124 DSTGLLVLTQDGRVARQLIGDHSDVEKEYLVRVEGRLDARGLALLNHGLSLDGVRLRPAK 183

Query: 177 VTLDTQKGSNAW-----VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           V         AW     +   L+EG+ R+I+++ E    +V  L R+  G  +LG L  G
Sbjct: 184 V---------AWQNADQLRFSLKEGRKRQIRRMCELVGLRVVGLKRVRIGAVRLGDLPLG 234

Query: 232 STREVS 237
             R ++
Sbjct: 235 RWRYLA 240


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 100/211 (47%), Gaps = 17/211 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K I+  G  SRRE +++I Q RV +NG   E     VM  D + VD  PLR  ER
Sbjct: 18  PVRLNKFISDTGYCSRREADKLIDQGRVTINGTQPE-MGTKVMPDDEVLVDDKPLRAKER 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
                 +KP G+  T         V DN+        R+  +GRLD  ++GL+ LTNDG 
Sbjct: 77  PIYIALNKPTGVTCTTE-----RHVKDNIVDFIGHRKRIFPIGRLDKPSDGLIFLTNDGD 131

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNA 187
           +   +        + Y VR   Q+  + L  +  G+ I         VTL    +K ++ 
Sbjct: 132 IVNKILRAGNSHEKEYVVRVSHQITPEFLEKMASGVEILDT------VTLPCIVKKETDY 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
              + L +G NR+I+++ E   + V +L R+
Sbjct: 186 SFRITLTQGLNRQIRRMCEALGYDVYKLRRV 216


>gi|295090937|emb|CBK77044.1| ribosomal large subunit pseudouridine synthase F [Clostridium cf.
           saccharolyticum K10]
          Length = 271

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 110/224 (49%), Gaps = 6/224 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ +G  SRRE +R+I   +V V+G +     + +     IE DG  +   +R  
Sbjct: 14  RLNKFLSESGFCSRREADRLIEAGKVLVDGAVAS-MGMKIREGQQIEADGTLISGKDRPV 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP G+V T SD D    + D +     RV  VGRLD ++EGL+L+TN G L   +
Sbjct: 73  VLLVNKPRGIVCTTSDRDRAENIVDFIGYPL-RVYPVGRLDKDSEGLILMTNQGELVNRI 131

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V    ++ +  LN ++KG+ I         V    +K     +T GL 
Sbjct: 132 LKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDTVTRPCTVEKTGEKSFRIILTQGL- 190

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              NR+I+++ E   ++V  L R+     +L  L  G  RE+++
Sbjct: 191 ---NRQIRRMCEALGYRVRTLKRVRIMNLRLDGLKTGEYREITR 231


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 118/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   R  +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRACINGEVCTHGAL-VNEGDIVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++++  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKSFTDWFIDMMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKEL 222


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 111/218 (50%), Gaps = 10/218 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A AG  +R+ V+ ++ + RV+VNG  +++    +    D I+VDG  +      
Sbjct: 3   RLDKFLAHAGFGTRKAVKELVRKGRVEVNGQRVKKDDQKIDERQDQIQVDGRIVTYETEV 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP G+V+   D     TV D L +  S +  VGRLDI+TEGLLL+TNDG LA  
Sbjct: 63  YIML-NKPQGVVSATED-SRYETVLDCLETNRSDLFPVGRLDIDTEGLLLITNDGALAHD 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P     + Y V      D      ++ GI I      D +V L    ++ +   + +
Sbjct: 121 LLSPKKHVDKTYEVHLERPWDPQYEAAIQMGIRI-----SDEEVCLPATLRQTAEHIILL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            ++EGK  ++K++    + +V  L R++ GP +L   L
Sbjct: 176 TIQEGKFHQVKRMMHACDNEVVYLKRLTMGPLKLDAAL 213


>gi|224369318|ref|YP_002603482.1| RluB [Desulfobacterium autotrophicum HRM2]
 gi|223692035|gb|ACN15318.1| RluB [Desulfobacterium autotrophicum HRM2]
          Length = 230

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 73/226 (32%), Positives = 117/226 (51%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA-ER 72
           R+ K +A AG+ SRR  E  I + RV VN  ++      +    D +EVD  P+  A E+
Sbjct: 2   RLQKFLAHAGVCSRRRGEVYILEGRVSVNHKVVISLGTKIDPEIDLVEVDKKPIVLASEK 61

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++++  +KP G+V++ S P G   V D L  I  RV  +GRLD ++ GLLLLT+DG L 
Sbjct: 62  AKIYIALNKPAGVVSSCSHP-GEKVVVD-LIDIKDRVYPIGRLDKDSVGLLLLTDDGNLH 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y V     ++ + L  +  GIV+ G      +V    ++ S+    +
Sbjct: 120 NRLSHPSFDHEKEYVVETTAPINDEALAQMAAGIVLDGKITRKARV----RRLSDNRFNI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L++G NR+I+++      +V  L R+  G  +LG L  G  R ++
Sbjct: 176 VLKQGINRQIRRMVTAVGNRVKLLKRVRMGSVRLGNLGTGKWRYLT 221


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 56/171 (32%), Positives = 97/171 (56%), Gaps = 3/171 (1%)

Query: 58  DHIEVDGVPLRKAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLD 115
           D I +DG  +R  ++ R+ +  +KP G +++ SD  GR T+ D +   I  +V  VGRLD
Sbjct: 13  DSITLDGKKVRPRKQQRVVYALNKPRGYLSSMSDDRGRKTIADLIKGKIPEKVFHVGRLD 72

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD 174
           ++TEGL++LTNDG LAR L  PS++  + Y  R  G++   ++  L+ G+V++ G     
Sbjct: 73  MDTEGLIILTNDGELARKLSHPSSKIRKTYVARVTGKLSHHEIKRLENGVVLRDGFKTSG 132

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             + +      +  V + + EG  REI+++F+ F+  V  L R + G  ++
Sbjct: 133 ASIRVIRASLRDTLVEIIIHEGHKREIREMFKVFDKHVLYLKRTAIGSLKV 183


>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 = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 123/233 (52%), Gaps = 10/233 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
           P R+ K++A  G  SR++V+++I   +V +NG+++  A   V  S D I V G  +   +
Sbjct: 6   PARIDKILASCGYGSRKDVKKLIKSGQVSINGVIINDAGTLVNPSLDEIIVAGECIFYED 65

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
              + + +KP  +V++  D D  +TV D L   +   ++  VGRLD + EGL+ LT+DG 
Sbjct: 66  NVYIMM-NKPQDVVSSTYD-DFETTVIDLLEGEYFHRKLFPVGRLDKDAEGLIFLTDDGK 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNA 187
           +A  L  P  +  + Y V  +G++++  +     G+ ++       ++ +       S+A
Sbjct: 124 MAHRLLSPKNRVPKTYYVEVYGRLNESDVKAFAAGMELEDFTALPAELDILEKNNNISSA 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           +VT+   EGK  +IK++ +    +V  L R+  GP +L   L  G  R+++K+
Sbjct: 184 YVTI--YEGKFHQIKRMMKARGKEVTYLKRLFLGPLRLDEELEPGMWRKLTKE 234


>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 = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 106/226 (46%), Gaps = 9/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V   D + +DG PLR  ER 
Sbjct: 7   KRLNKFISETGFCSRREADKLIEQGRVTLNGAQPE-VGSKVTEQDEVCIDGKPLRSKERP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  IYIALNKPTGITCTTERDVPGNIVDFIGH---HKRIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + +  +  G+ I        +VT +TQ      +T G
Sbjct: 123 KILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L    NR+I+++ E   ++V +L R+      L  +  G  R +S+
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSE 224


>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 = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 106/225 (47%), Gaps = 9/225 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE ++ I Q RV VNG   E   V V +TD + VDG PL+   + 
Sbjct: 22  KRLNKFISETGFCSRREADKYIEQGRVSVNGYSPE-MGVKVAATDVVLVDGKPLKATPKR 80

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               Y+KP+G+  TT S          N P+   R+  +GRLD  +EGL+ LTN+G +  
Sbjct: 81  VYIAYNKPVGITCTTESKIQSNIIRAVNYPT---RIFPIGRLDRPSEGLIFLTNEGDIVN 137

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +++  +  +  G+ I        +VT    K     +T G
Sbjct: 138 KILRAGNNHEKEYVVTVDKPLNRQFVTKMANGVPILDTVTKKCKVTQTAPKEFKIVLTQG 197

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L    NR+I+++ E+  ++V  L R       L  L  G  R +S
Sbjct: 198 L----NRQIRRMCEYLGYEVVTLKRTRIMNVTLKGLKVGQWRHLS 238


>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 = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 109/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  L   E+ 
Sbjct: 2   RLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGT-LVSYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLL+TN+G LA
Sbjct: 61  VYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY-GDMQVTLDTQKGSNAWV 189
             +  P     + Y  +  G + +D +    KGI+++   C    +++    Q    + V
Sbjct: 120 HKMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + ++EGK  ++K++      +V  L R+S G  QL
Sbjct: 180 KITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQL 215


>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 = 89.4 bits (220), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/226 (31%), Positives = 115/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++IA+ RVKVNG  + +    V   D + V+G  +R A    
Sbjct: 2   RLNKFISDSGKASRRGADKLIAEGRVKVNG-RIAKIGDQVKPGDEVMVNGNIIRLARNHV 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT     G      N P    RV ++GRLD +++GL+LLTNDG +   
Sbjct: 61  YLALNKPVGITCTTEKGVKGNIVDLVNHPL---RVFNIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +  + +  + KG+ I G      +VT  ++   N  +T GL
Sbjct: 118 ILRAENNHEKEYIVSVDKPITPEFIEKMSKGVRILGQKTLPCKVTQISKYEFNIILTQGL 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               NR+I+++ E   ++V RL R+      LG L  G  R+++KK
Sbjct: 178 ----NRQIRRMCEVLGYEVYRLQRVRIMNITLGNLPVGQWRDLTKK 219


>gi|332365802|gb|EGJ43559.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 242

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 110/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRL-IYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISVTED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++       Q   V LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFICQPAQLKIVELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R+  GP QL + L+
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLRMGPLQLDSALS 220


>gi|327468371|gb|EGF13856.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK330]
          Length = 242

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 111/222 (50%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +  + D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDEAADDIVVSGQRL-IYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++           + LD +K ++  
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEAS-L 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPALA 220


>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 = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 114/229 (49%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  AG+ SR EV++++ +++V VNG L       +    D I   G  L   E+ 
Sbjct: 2   RLDKFLVEAGVGSRTEVKQLLKKKQVLVNGKLETSPKTQIDEKLDKIVCQGQNLS-YEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYMLNKPKGVISATED-DHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             +  P     ++Y  +  G +  + +     GI ++       Q+ +    +K + + V
Sbjct: 120 HAMLSPKKHVDKLYCAKVAGIMTDEDVKAFADGIELKDFTCQPAQLNIINADEKSNTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + ++EGK  ++K++      +V  L R+S GP +L   LA G  R +S
Sbjct: 180 EIVIKEGKFHQVKRMVLACGKEVTDLQRLSMGPLRLDDELALGEWRRLS 228


>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 = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 102/207 (49%), Gaps = 7/207 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L E     V   D + +D  PLR  E
Sbjct: 5   TEKRLNKYISETGFCSRREADKLIEQGRVTINGQLPE-MGTKVSDDDEVCIDDKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  KPVYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  D +  +  G+ I        +VT +T+      +T 
Sbjct: 122 NKILRAGNNHEKEYVVRVDKAITADFIKQMSSGVRILDTVTLPCKVTQETKFSFRIVLTQ 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
           GL    NR+I+++ E   ++V +L R+
Sbjct: 182 GL----NRQIRRMCEALGYEVFKLRRV 204


>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 = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/216 (32%), Positives = 105/216 (48%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-AWV 189
            VL  P     + Y  +  G + Q+ +    KGI ++   C       L T    N + +
Sbjct: 120 HVLLSPKRHVDKTYLAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 180 RVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


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

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 102/207 (49%), Gaps = 7/207 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L E     V   D + +D  PLR  E
Sbjct: 5   TEKRLNKYISETGFCSRREADKLIEQGRVTINGQLPE-MGTKVSDDDEVCIDDKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  KPVYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  D +  +  G+ I        +VT +T+      +T 
Sbjct: 122 NKILRAGNNHEKEYVVRVDKAITADFIKQMSSGVRILDTVTLPCKVTQETKFSFRIVLTQ 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
           GL    NR+I+++ E   ++V +L R+
Sbjct: 182 GL----NRQIRRMCEALGYEVFKLRRV 204


>gi|239828089|ref|YP_002950713.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239808382|gb|ACS25447.1| pseudouridine synthase [Geobacillus sp. WCH70]
          Length = 240

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 116/228 (50%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VK++G++++     V  T+ +  V G  +   E  
Sbjct: 4   RIDKMLANMGYGTRKEVKKLLKSGVVKIDGVVVKDPKTQVNPTEQVVTVRGKEVEYKEFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+V+   D     TV D L     +FS    VGRLD +TEGLLLLTNDG L
Sbjct: 64  YLMM-NKPPGVVSATEDV-VEETVVDLLEEEDRVFSP-FPVGRLDKDTEGLLLLTNDGQL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G+V ++ +   ++GIV+           +  + G  + V 
Sbjct: 121 AHQLLSPKKHVPKTYFAVIDGEVTEEDIASFRRGIVLDDGYETKPAELVVLKSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           V + EGK  ++K++F     +V  L RI  GP  L  +L  G  RE++
Sbjct: 181 VTITEGKFHQVKRMFRAIGKRVIYLKRIQMGPLVLDPSLDLGEYRELT 228


>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 = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 63/206 (30%), Positives = 105/206 (50%), Gaps = 4/206 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++A +G  +R+EV+  I +  V VNG + E+  + V   TD + V+G  +   E  
Sbjct: 2   RLDKLLAHSGFGTRKEVKDFIKKGIVTVNGEIAEKDKMQVDPQTDEVCVNG-EVITYEEF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G V+   D +   TV D +   +   +  VGRLD++TEGLLL++NDG LA 
Sbjct: 61  VYYMLNKPAGYVSATED-NLYPTVVDLIDDYYRDDLFPVGRLDVDTEGLLLISNDGVLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  + +G V    +     GI I        ++ + +   + + + V 
Sbjct: 120 QLLSPKKHCPKVYYAKINGIVTNQDVEAFFNGITIDDYQCQSAELKILSTSATTSEIEVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           + EGK  ++KK+F     +V  L RI
Sbjct: 180 IYEGKFHQVKKMFIAVGKEVTYLKRI 205


>gi|319745443|gb|EFV97749.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 240

 Score = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 64/216 (29%), Positives = 109/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  L   E+ 
Sbjct: 2   RLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGT-LVSYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   DP  + TV D L        V  VGRLDI+T G LLLTN+G LA
Sbjct: 61  VYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGFLLLTNNGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY-GDMQVTLDTQKGSNAWV 189
             +  P     + Y  +  G + +D +    KGI+++   C    +++    Q  + + V
Sbjct: 120 HKILSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKNQSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + ++EGK  ++K++      +V  L R+S G  QL
Sbjct: 180 KITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQL 215


>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 = 89.4 bits (220), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 58/186 (31%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 6   PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 62

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 63  NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 122

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 123 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 182

Query: 232 STREVS 237
             REV+
Sbjct: 183 EWREVT 188


>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 = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 60/188 (31%), Positives = 93/188 (49%), Gaps = 20/188 (10%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L +KP  ++    D  GRST+ D +P     V   GRLD ++EGL+LLTNDG L   L  
Sbjct: 7   LLYKPYRVLCQFQDQKGRSTLKDYVP--IPDVYPAGRLDYDSEGLVLLTNDGWLQHRLTD 64

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P     R Y V+  G+ D   L+ L  G+VIQG      +V +  Q              
Sbjct: 65  PRYGHPRTYWVQVEGKPDTAALSQLAAGVVIQGYRTRPARVEVLDQDPPLPPRYPPIRYR 124

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV---SK 238
               + W+++ LREG+NR+++++     +   RL+R++    QLG L  G  RE+    +
Sbjct: 125 RHIPSQWLSLTLREGRNRQVRRMTAAVGFPTLRLVRVAIANLQLGNLAPGQWREILPLER 184

Query: 239 KILREQLG 246
           ++L +  G
Sbjct: 185 QVLWQSCG 192


>gi|295108497|emb|CBL22450.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           obeum A2-162]
          Length = 257

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 113/231 (48%), Gaps = 21/231 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A AG  +R EV+++I + +V+VNG+  ++  + V+   D + + G  +  A   
Sbjct: 6   RLDKFLADAGKGTRSEVKKIIQKGQVQVNGVPAKKPEMKVVPENDVVVLSGETVGAAPEF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+   D + R TV + +PS    +  VGRLD +TEGLLL+T+DG LA  
Sbjct: 66  VYYLLNKPAGCVSATEDRNDR-TVMEYVPSDRKGLFPVGRLDKDTEGLLLITDDGMLAHE 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------GICYGDMQVTLDTQK 183
           L  P     + Y VR  G++  + +  L+ G+ I            I  G  +   D+Q 
Sbjct: 125 LLAPGKHVDKTYFVRVEGKLTVENIRNLENGVDIGEEKMTMPAKVEIVGGSWEGAGDSQS 184

Query: 184 GS---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G             + + + EGK  ++K++       V  L RIS GP  L
Sbjct: 185 GRVRIENLPEVYTELHLTIHEGKFHQVKRMMAAVGNPVIYLKRISMGPLTL 235


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 63/211 (29%), Positives = 105/211 (49%), Gaps = 20/211 (9%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           +N   ++   VN  ST  +   G P   A   R+ L++KP  ++   +D  GR+T+   +
Sbjct: 1   MNKFSVKNHKVNRFSTKALASQGKP---ASPRRVLLFNKPFDVLPQFTDESGRTTLKGFI 57

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P  F+ V + GRLD ++EGLL+LTNDG L   L  P+ +  +VY V+  G    D L+ L
Sbjct: 58  P--FTDVYAAGRLDRDSEGLLVLTNDGKLQAKLTQPAQKTGKVYFVQVEGTPGDDALSQL 115

Query: 162 KKGIVIQ-GICYGDMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFE 206
           ++G+V++ G         +D  +                  W+ + L EG+NR+++++  
Sbjct: 116 RQGMVLKDGPTLPAGAELVDEPEWLWPRNPPIRERKTIPTCWMKITLFEGRNRQVRRMTA 175

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +   RLIR S G   LG L  G  +E++
Sbjct: 176 HIGFPTLRLIRFSMGNLSLGDLKPGEWKEIN 206


>gi|332359960|gb|EGJ37774.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 242

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/222 (32%), Positives = 109/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIVVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++       Q   V LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAQLKIVELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ G  QL + LA
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLTMGSLQLDSALA 220


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 118/238 (49%), Gaps = 25/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A   I SR +V++ I +  + VNGI+ +     +  + D I  +G  +   ++ 
Sbjct: 2   RIDKFLANQDIGSRSQVKQYIKKGMISVNGIVCKSPEQKIDENADQISYNG-KVIGYQKH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G V+  +D +   TV D L +      +  VGRLDI+TEGLLL+T+DG L+
Sbjct: 61  HYYMLNKPSGCVSATND-NLHITVLDLLKASVPVKNLFPVGRLDIDTEGLLLITDDGELS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LD 180
             L  PS    + Y  R  G   ++ +   K+G+ I     GD + T           L+
Sbjct: 120 HNLLSPSKHVAKTYFARIDGLATEEHIKAFKEGLDI-----GDDKPTKPGTLVIKNTDLN 174

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           TQ    + + + + EG+  ++K+ FE    KV  L R+S G   L   LA G  RE++
Sbjct: 175 TQ---TSEILLTITEGRYHQVKRSFEALGMKVTYLKRLSMGSLTLDEALAPGEFRELT 229


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 121/237 (51%), Gaps = 19/237 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-----RK 69
           R++K IA  G  SRRE +R+IA++RV VNG      AV V   D + VDG PL     R 
Sbjct: 7   RLNKHIAGTGFCSRREADRLIAERRVTVNGQPAGVGAV-VGEGDEVRVDGQPLKLRAARP 65

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLT 125
            +R  +++  +KP+G+  T       S+V  N+        R+  +GRLD ++EGL+LLT
Sbjct: 66  GKRRHVYIALNKPVGITCTTE-----SSVKGNIVDFVGHEQRIFPIGRLDKDSEGLILLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +        + Y V  +  V  + L  + +G+ I    +  M +     + +
Sbjct: 121 SNGDIVNEILRAENGHQKEYLVAVNKPVTDEFLRGMSRGVRI----HNQMTLPCRASRIA 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                + L++G NR+I+ +   F+++V +L R+     +LGTL  G  R ++ + LR
Sbjct: 177 KFGFRIVLQQGLNRQIRLMAAAFDYRVTQLRRVRIDNIRLGTLKPGQWRNLTPEELR 233


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           RV K+++  G  SR E++R +   +V++N   +++    +    D +  DG  +   E  
Sbjct: 7   RVDKILSELGFGSRTEIKRYVKAGKVRINENPVKKPEEKINTEIDRLYFDGKDVV-IEEF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G V    D +   TV + + S    ++ VGRLD++TEGLL+LTNDG L   
Sbjct: 66  ETYVLYKPAGYVCATFD-NVHKTVMELIDSNRKNIVPVGRLDLDTEGLLILTNDGNLNHR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           L  PS+   +VY  +F G +  D + +  KG+ I     GD +V+     +  S   V +
Sbjct: 125 LVSPSSHVDKVYYAKFDGVLADDAIEMTAKGLDI-----GDGEVSKPAKLEIVSKNEVLL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILRE 243
            + EGK  ++K++ +    +V  L R ++G   L    L  G +R++S + +R+
Sbjct: 180 TIHEGKFHQVKRMIKALGGEVTYLKRTAFGGLGLDDLNLKRGESRKISMEEMRK 233


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 116/229 (50%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    V+++G  ++ A  +V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVRIDGKPVKDAKFHVNIEKQEVTIYGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEGLLLLTNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DHHETVVDLLEFEDAIFNP-FPVGRLDIDTEGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V +  +    KG+V+  G      ++T+       + +
Sbjct: 119 THQLLSPKKHVPKKYYAHIEGVVTEKDVEDFAKGVVLDDGYETKPGELTI-LNSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R+  GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRVEMGPLTLDEELELGQYRELT 226


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 108/213 (50%), Gaps = 6/213 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR++V++++    V  NG  +  +  +V    D I V    +  ++  
Sbjct: 2   RIDKLLAHCGYGSRKDVKQLLKDGLVTSNGKKIRSSGAHVDPEKDEIYVGDEKINYSKYV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G V+   D +   TV D +      +  VGRLD++TEGLLL+TNDG LA  
Sbjct: 62  -YYMLNKPDGYVSATED-NVYPTVIDLIKEYHPGLFPVGRLDVDTEGLLLITNDGQLAHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVG 192
           L  P T   + Y V+  G++    +N   KGI ++   C       + + + S   VT+ 
Sbjct: 120 LLSPRTHVPKTYYVKVKGRLGIGDINAFTKGIPLEDFTCMPSYLKIIKSDEISECEVTI- 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             EGK  ++K++F+    +V  L RIS G  +L
Sbjct: 179 -YEGKFHQVKRMFQACGKEVVYLKRISMGELKL 210


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 116/245 (47%), Gaps = 31/245 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA   V+VNG +     + V  TD IEVD     + ER  
Sbjct: 18  RLNKRMAELGLCSRREADDWIASGWVRVNGQVAA-MGLQVAPTDRIEVDPAARGQQERQA 76

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL----------------PSIFSRVISVGRLDINT 118
             L HKP+G V+  ++ DG +     +                P     +   GRLDI++
Sbjct: 77  TILLHKPMGYVSGQAE-DGHTPAVALINPRTHWREDPSRQRFSPPQLRGLAPCGRLDIDS 135

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQV 177
            GLL+LT DG +AR L    ++  + Y VR H G +  D  +    G + + +C+G   +
Sbjct: 136 VGLLVLTQDGRVARHLIGEDSEVEKEYLVRVHYGDIATDVQSAFPAGQLAR-LCHG---L 191

Query: 178 TLDTQKGSNA---W-----VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +LD Q    A   W     +   L+EGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 192 SLDGQALKPAKVEWQNPEQLRFVLKEGKKRQIRRMCELVGLKVVGLKRIRIGRVVLGNLP 251

Query: 230 AGSTR 234
            G  R
Sbjct: 252 VGQWR 256


>gi|318606116|emb|CBY27614.1| ribosomal large subunit pseudouridine synthase E; LSU Psi2457
           [Yersinia enterocolitica subsp. palearctica Y11]
          Length = 208

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 94/179 (52%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ + +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDEAGRSTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P+ +  +VY V+  G  D+D L+ L+ GI ++          L ++           
Sbjct: 88  LTQPAQKTGKVYFVQVEGLPDEDALSQLRTGITLKDGPTLPAGAELVSEPAWLWPRHPPI 147

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKAIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSIGNLSLGDLQPGEWKEIN 206


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 115/229 (50%), Gaps = 13/229 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I  +RV +NG +  +   ++ +  D + VDG   +    T
Sbjct: 2   RLDKLLANKAYGSRKEVHQLIKDRRVTINGSITTKKDTHIDIDVDIVAVDG---KVVSTT 58

Query: 74  RLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           +L+   +HKP G VT   D +    V D LP  F +  V+ VGRLD +TEGLLLLTNDG 
Sbjct: 59  QLYYVKFHKPKGYVTAVEDSN-HPVVMDLLPLEFIKMGVVPVGRLDKDTEGLLLLTNDGV 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +   +    +VY V F G +  + +  +K+GI++     G      + +  S   V
Sbjct: 118 WGHSIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGD---GTQCKPAEIEFVSLHSV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            V + EGK  ++K++       V  L R++ G   L G    GS  E++
Sbjct: 175 HVTIEEGKYHQVKRMISAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELT 223


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 114/233 (48%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVV-YQQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y     G  D++    +  G+ ++    +  G + +    +    + +
Sbjct: 121 QLLAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLNILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            + + EGK  ++K++F     KV +L R+S GP  L   LA GS R ++++ L
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEEL 233


>gi|225621236|ref|YP_002722494.1| pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225216056|gb|ACN84790.1| pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 229

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 120/244 (49%), Gaps = 29/244 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA   +ASRRE +R+I    VKVNGI+    A  V   D IE     + + +  +
Sbjct: 2   RLNKYIASLNLASRREADRLIQNGNVKVNGIINTNPATQVDENDKIEC---SIEQYKENK 58

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++  +KP G V + +  +G+  +++ +   F  +  VGRLD ++ GL+L TNDG  A+ 
Sbjct: 59  IYIKLNKPRGYVVSSNKNEGKP-IYNLIKKDFDNIYPVGRLDKDSSGLILFTNDGVFAKQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--- 190
           +   +T   + Y VR    +    L  L+ GI            +LD QK   A V    
Sbjct: 118 IIGENTNCEKEYYVRVDDNIPDGALQKLEYGI------------SLDGQKLKPAKVKRVN 165

Query: 191 -----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS----TREVSKKIL 241
                + L EGKNR+I+++ +   ++V  L R+      L  L  G+    T+E  + IL
Sbjct: 166 KNSFHIILTEGKNRQIRRMCQKVGFEVIILKRLRISGILLEDLKEGTFKSLTKEEIESIL 225

Query: 242 REQL 245
           + +L
Sbjct: 226 KNEL 229


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 115/233 (49%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVI-YQQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATED-SRQKTVLDLLKDQDSYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y     G  D++    +  G+ ++    +  G +++    +    + +
Sbjct: 121 QLLAPEYHVPKPYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            + + EGK  ++K++F     KV +L R+S GP  L   LA GS R ++++ L
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEEL 233


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/215 (33%), Positives = 105/215 (48%), Gaps = 8/215 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A  G  SR E++  I +  V +NG  ++ A     +  D +      ++  E  
Sbjct: 7   RIDKYLADMGAGSRTEIKDDIRKGLVYINGNKVKSAGEKADTLNDEVAYKENIIKYIEFE 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP G+V+   D   + TV D + S    +  VGRLD +TEGLLLLTNDG LA  
Sbjct: 67  YILL-NKPAGVVSATEDRKEK-TVLDIIDSKRKDLFPVGRLDKDTEGLLLLTNDGMLAHE 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVT 190
           L  P     + Y V   G +  +   L K GI +         ++Q+     KGS A++T
Sbjct: 125 LLSPKKHVDKKYYVETDGLLTDEHRKLFKNGIKVDDEFTAKEAELQILSSGDKGSKAYLT 184

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +  REGK  ++K++ E     V  L RIS GP  L
Sbjct: 185 I--REGKYHQVKRMMEAVGNTVTYLKRISMGPLTL 217


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 133/255 (52%), Gaps = 15/255 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV      I+V G  +  + +T
Sbjct: 2   RLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLI--SHKT 59

Query: 74  RLW-LYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            ++ + +KP G+V+  SD   ++ +      D  P ++     VGRLD +TE LLLLT++
Sbjct: 60  HVYYMLNKPKGVVSAVSDASKKTVIDLIAPQDRRPGLYP----VGRLDGDTERLLLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + 
Sbjct: 116 GQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
           + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 176 SHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235

Query: 246 GPHLLEEAQVNLDAP 260
               +E+ Q +   P
Sbjct: 236 PYFFIEKQQTSKALP 250


>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 = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 94/179 (52%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ + +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDEAGRSTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P+ +  +VY V+  G  D+D L+ L+ GI ++          L ++           
Sbjct: 88  LTQPAQKTGKVYFVQVEGLPDEDALSQLRTGITLKDGPTLPAGAELVSEPAWLWPRQSPI 147

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKAIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSIGNLSLGDLQPGEWKEIN 206


>gi|311031252|ref|ZP_07709342.1| ribosomal small subunit pseudouridine synthase A [Bacillus sp.
           m3-13]
          Length = 236

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 113/219 (51%), Gaps = 15/219 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AERT 73
           R+ K++A +G  +R+EV++++    VKV+G +++ A V+V      EV  V +       
Sbjct: 2   RLDKMLANSGFGTRKEVKKLLKTGVVKVDGNVVKDAKVHVDP----EVQEVTVHDDIVEY 57

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTND 127
           R ++Y   HKP GL++   D   + TV D L     +F     VGRLD +TEGLLLLTND
Sbjct: 58  REFIYLMMHKPPGLLSATED-HRQETVVDILQEEDKMFEP-FPVGRLDKDTEGLLLLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  P     + Y  +  G+V  + +   KKG+ +    Y  +   L   + G  
Sbjct: 116 GQLAHQLLSPKKHVPKTYYAKIDGEVTTEDMEAFKKGVTLDD-GYETLPAELVILEAGPE 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + + + EGK  ++K++F+     V  L R+S G  +L
Sbjct: 175 SQIEITIVEGKFHQVKRMFQAVGKTVTYLKRLSMGELKL 213


>gi|170720236|ref|YP_001747924.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758239|gb|ACA71555.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 233

 Score = 89.0 bits (219), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 104/217 (47%), Gaps = 4/217 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A     +R++V  ++ Q+RV+V+G  +      V     IEVD   L+     R
Sbjct: 2   RLDRFLANLPSYNRQQVRLLLVQRRVRVDGETVADPRAEVREFSRIEVDDQLLQAGRPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + HKP+G V+   D   R TV D LP      + + GRLD NT GL++LTNDG  +R 
Sbjct: 62  YLMLHKPVGCVSATHDSQHR-TVLDLLPEPLRADLHIAGRLDYNTTGLMILTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+T+  + Y V    ++    +   + G          +   LD      A + +  
Sbjct: 121 LTQPATKLPKHYLVETEDEIGAHYIEKFRAGFYFAFEDLTTLPAQLDILGPRTARLAI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EG+  ++K++F +F+ KV  L R + G  QL   LA
Sbjct: 179 IEGRYHQVKRMFGYFDNKVVGLHRETMGAIQLDPGLA 215


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 108/207 (52%), Gaps = 11/207 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  ++++ + R+K+NG + E     V   D +EVDG P+R+ +   
Sbjct: 5   RINKYLSEVGYCSRRAADKLLEEGRIKINGKIPE-LGTKVSDEDLVEVDGKPIREPQEKP 63

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +++ ++KP+G+V T      ++ + D  N P    R+  +GRLD  +EGL+LLT+DG + 
Sbjct: 64  VYIVFNKPVGIVCTTDTKREKNNIVDYINHPK---RIFPIGRLDKPSEGLILLTSDGDIV 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +    L  ++ G+ I        +V    +K       +
Sbjct: 121 NKILRARNNHEKEYLVRVDKPITPKFLEKMRNGVPILDTITRKCKV----EKIDEMNFRI 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
            L +G NR+I+++ E+  ++V +L RI
Sbjct: 177 ILTQGLNRQIRRMCEYLGYEVKKLKRI 203


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 112/228 (49%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++  +G  +R+E++ +     V VNG ++  ++V V     + V G  + + E   
Sbjct: 3   RLDKLLGHSGYGTRKEIKSLCKSGDVTVNGEIVRDSSVKVDEGATVIVAGEKV-EYEAVS 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G+V+   D   R TV D LPS +  SRV  VGRLDI+T GLLLL+NDG  A 
Sbjct: 62  YLMLHKPAGVVSATQDSRVR-TVLDILPSRYAASRVAPVGRLDIDTTGLLLLSNDGTWAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     +VY  +  G +  D       GIV++    G   +    +K +   + + 
Sbjct: 121 KVISPKKHVPKVYEAQVEGVIPADVGERFAAGIVLED---GVECLPARAEKTAEGRLQIT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + EGK  ++K++       V  L R   G   L   L AG  R+++K+
Sbjct: 178 VCEGKFHQVKRMCSVVGLTVTSLHRSRIGGLALDKNLQAGEYRKLTKE 225


>gi|262365460|gb|ACY62017.1| RNA pseudouridylate synthase-family protein [Yersinia pestis
           D182038]
          Length = 152

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 51/117 (43%), Positives = 77/117 (65%), Gaps = 6/117 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG--VPLRKA 70
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  + ++++
Sbjct: 29  EKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIKES 88

Query: 71  ER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
           E    R+  Y+KP G + T +DP+GR TVFD LP +  SR ++VGRLD+NT GLLL 
Sbjct: 89  EENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLF 145


>gi|257870825|ref|ZP_05650478.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804989|gb|EEV33811.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 241

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 117/233 (50%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A  G  SR+EV++ I +  V VNG  ++     V    D +   G  L + ++ 
Sbjct: 2   RLDKFLADMGYGSRKEVKQAIKKGVVAVNGQQVKSDKFQVAEQEDQVSFAG-ELVRYQKD 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++  +DP+   TV D   +   R  +  VGRLD +TEGLLL+TNDG LA
Sbjct: 61  FYYLLNKPAGVISATTDPE--KTVLDLFAAEDYRRDLFPVGRLDKDTEGLLLITNDGQLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             L  P     + Y     G + ++  +   +GI + G      Q+T+    ++   + +
Sbjct: 119 HRLLSPKKHVEKEYYAEVRGIMTEEDRHQFLQGIELDGETLMPAQLTILKVDEQAETSTI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           T+ L EGK  ++K++ +    +V  L R   G  QL   LA G  R V++K L
Sbjct: 179 TLILHEGKFHQVKRMVQAVGKEVTYLKRTRMGGLQLPKDLALGEYRSVTEKEL 231


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 92  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 148

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 149 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 208

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 209 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 268

Query: 232 STREVS 237
             +EV+
Sbjct: 269 EWQEVT 274


>gi|325684334|gb|EGD26503.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 241

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 114/231 (49%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVI-YQQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y     G  D++    +  G+ ++    +  G +++    +    + +
Sbjct: 121 QLLAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            + + EGK  ++K++F     KV +L R+S GP  L   LA GS R ++++
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLALGSYRPLTEE 231


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/216 (32%), Positives = 106/216 (49%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTN+G LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLAQSKEVFPVGRLDIDTHGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-AWV 189
            VL  P     + Y+ +  G + Q+ +    KGI ++   C       L T    N + +
Sbjct: 120 HVLLSPKRHVDKTYQAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 180 RVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/216 (32%), Positives = 106/216 (49%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   DP  R TV D L  +     V  VGRLDI+T GLLLLTN+G LA
Sbjct: 62  -YYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-AWV 189
            VL  P     + Y+ +  G + Q+ +    KGI ++   C       L T    N + +
Sbjct: 120 HVLLSPKRHVDKTYQAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  +IK++  +   +V  L R++ G   L
Sbjct: 180 RVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVL 215


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 94/179 (52%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ + +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDEAGRSTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P+ +  +VY V+  G  D+D L+ L+ GI ++          L ++           
Sbjct: 88  LTQPAQKTGKVYFVQVEGLPDEDALSQLRIGITLKDGPTLPAGAELVSEPAWLWPRHPPI 147

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKAIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEWKEIN 206


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 118/227 (51%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A A I SR+E+++ +  +++ ++G      + NV S    I + G  L      
Sbjct: 18  RLDKFLALAKI-SRKEMKQKLRLRQIVIDGQAARSLSQNVDSGLQSISLAGKTLNHLAH- 75

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R +L +KP G VT +SD D  + +    P  F+ ++ ++GRLD +T GLLL+T++G L  
Sbjct: 76  RYFLMNKPAGAVTANSDADKLTVLELIAPEDFNDQLYAIGRLDRDTRGLLLITDNGPLGF 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V  +G +DQ+     ++GIV + G      Q+ + T    ++  +V
Sbjct: 136 QLLHPQYHIAKTYYVEVNGPLDQEATIAFQQGIVFLDGTRCKPAQLQIHTTSPEHSTASV 195

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            + EGK  ++KK+F     KV  L R  +G FQL   L  GS R ++
Sbjct: 196 TISEGKFHQVKKMFLAVGVKVTYLKRTHFGDFQLDPNLTEGSYRPLN 242


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/225 (33%), Positives = 112/225 (49%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     SR+ V  ++A+  VKV+G +       V    HI ++G  L+      
Sbjct: 7   RLDRFISATKRVSRKHVRVLLAKGLVKVDGEIARDIDQIVDEFSHITLEGEVLQANTPIY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L HKP+G+V+   D D   TV D L     + +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  LML-HKPVGVVSATVD-DKHKTVIDLLSHPDKQQLHIVGRLDLNTSGLLLLTNDGRWSKR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++YRV     +D   +    +G+  +      +   L+      A VT  L
Sbjct: 125 LMSPEHKVAKLYRVSLENPIDASYIQAFHEGMYFEFEDITTLPAKLEIVDPHTALVT--L 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
            EG+  +IK++F  F   V  L RIS G   L + LLAG +R +S
Sbjct: 183 MEGRYHQIKRMFGRFRNPVIGLHRISVGEIVLDSQLLAGQSRVLS 227


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 113/236 (47%), Gaps = 22/236 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QRV KV++  G  SR E+++   Q  V VNG  +    + V    D I  +G  +   E 
Sbjct: 5   QRVDKVLSNLGYGSRAELKKFCKQGLVFVNGKAVSNPGLQVDTDIDEIVFNGEKINYREF 64

Query: 73  TRLWLYHKPIGLVTT---HSDP------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             L + +KP G ++      DP      D    VF+  P        VGRLD +TEGLL+
Sbjct: 65  IYLMM-NKPDGYISATFDKHDPIVLDLIDDEYLVFEPFP--------VGRLDKDTEGLLV 115

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  +  P     + Y  +  G+V ++ +   K+G+V+    Y  M   L   K
Sbjct: 116 LTNDGQLAHRVLSPKKHVPKTYYAKIDGKVTEEDIEAFKQGVVLDD-GYETMPSELVILK 174

Query: 184 GSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
             + + + + + EGK  ++K++FE     V  L R+S G  +L  TL  G  RE++
Sbjct: 175 SDDISEIELTIHEGKFHQVKRMFESVGKTVVYLKRLSMGALKLDETLELGEYRELT 230


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 115/233 (49%), Gaps = 18/233 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------EVDGVPLR 68
           R+ K++A  G  +R+EV++++    VKV+G +++ A  +V     +      EV+  P  
Sbjct: 3   RIDKLLANMGYGTRKEVKKLLKAGVVKVDGTIIKDAKTHVDPKAQVVTVWGEEVEYKPFI 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLT 125
                   + +KP G+++   D     TV D L     IF     VGRLD +TEGLLLLT
Sbjct: 63  ------YLMMNKPKGVISATEDA-VEETVVDLLEEEDRIFDP-FPVGRLDKDTEGLLLLT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P     ++Y     G+V +D +   ++G+V+           +  + G 
Sbjct: 115 NDGQLAHQLLSPKKHVPKIYEAIIDGEVTEDDVVAFQRGVVLDDGYETKPAELVVIRTGL 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            + V + + EGK  +IK++F+    +V  L RI  GP  L  TL  G  RE++
Sbjct: 175 RSDVRITITEGKFHQIKRMFQAVGKRVIYLKRIQMGPIPLDETLELGEYRELT 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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 129/236 (54%), Gaps = 17/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAER 72
           R+ +++A +G+ SR +V++MI ++   V+G+ +   +  ++ TD   I +DG PL    R
Sbjct: 4   RLDRILALSGLGSRSDVKKMIRKKNCCVDGVRIVSPSF-ILDTDLNKITIDGEPL--VLR 60

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           T ++L ++KP G VT+ SDP  + TV D + + F R  +  +GRLDI+TEGLL++T+DG 
Sbjct: 61  TNVYLMFNKPQGCVTSTSDPVHK-TVMDYIKAPFDRMTLFPIGRLDIDTEGLLIITDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-VDQDKLNL---LKKGIVIQG--ICYGDMQVTLDTQK 183
           +   +  P +  ++ Y +    +  D++  N     +KGIV++    C        + + 
Sbjct: 120 ITHKITSPKSGTVKTYYLELSREPSDEEFKNYCEEFEKGIVLKNGYKCLPAKFEKCENKT 179

Query: 184 GS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           GS  +   + + EGK  ++KK+      ++  L RI+ G   L  TL  G  RE+S
Sbjct: 180 GSFRSGFLMHITEGKFHQVKKMCLSAGNELCYLRRIAVGSIVLDETLKTGEYRELS 235


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 111/223 (49%), Gaps = 6/223 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AGI SRRE +R+I   +V V+G       + V ++  I V+G  +   ER  
Sbjct: 12  RLNKYLSEAGICSRREADRLIEDGKVTVDG-RTASMGMKVFTSQEITVNGKRVEGKERPV 70

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G+V T SD D    + + L     R+  VGRLD ++EGLLL+TN G L   +
Sbjct: 71  LLAVNKPRGIVCTTSDKDRAENIVEFLKYPV-RIYPVGRLDKDSEGLLLMTNQGDLVNRI 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     V +  +  ++ G+ I G      +  +  ++  +  +T GL 
Sbjct: 130 LRGRYGHEKEYLVTVDRPVTEAFIRQMRNGVEILGTRTKPCEAEITGKRSFSIILTQGL- 188

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              NR+I+++ E   ++V  L R+     +LG L  G  RE++
Sbjct: 189 ---NRQIRRMCEALGYQVKTLKRVRIMNVKLGNLKTGQYRELT 228


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 59/178 (33%), Positives = 95/178 (53%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ +++KP  ++   +D  GR+T+ D +P  F  V + GRLD ++EGLL+LTNDG L   
Sbjct: 49  RVLIFNKPYDVLPQFTDEMGRTTLKDFIP--FPDVYAAGRLDRDSEGLLILTNDGKLQAK 106

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV---------TLDT 181
           L  P  +  +VY V+  G  D+  LN L+ G+ ++    +  G   V         T   
Sbjct: 107 LTQPHKKTAKVYYVQVEGIPDESTLNKLRNGVTLKDGPTLSAGAELVEEPEWLWERTPPI 166

Query: 182 QKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           ++  N   +W+ + L EG+NR+++++     +   RLIR S G  QLG L  G  RE+
Sbjct: 167 RERKNIPVSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRFSIGSLQLGQLSPGEWREI 224


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 94/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 92  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 148

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 149 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 208

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 209 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 268

Query: 232 STREVS 237
             +EV+
Sbjct: 269 EWQEVT 274


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 114/226 (50%), Gaps = 12/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AGI SRRE +R+I   +V V+G       + V ++  I V+G  +   ER  
Sbjct: 15  RLNKYLSEAGICSRREADRLIEDGKVTVDG-RTASMGMKVFTSQEITVNGKRVEGKERPV 73

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G+V T SD D R+   +N+   F    R+  VGRLD ++EGLLL+TN G L 
Sbjct: 74  LLAVNKPRGIVCTTSDKD-RA---ENIVEFFKYPVRIYPVGRLDKDSEGLLLMTNQGDLV 129

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V +  +  ++ G+ I G      +  +  ++  +  +T 
Sbjct: 130 NRILRGRYGHEKEYLVTVDRPVTEAFIRQMRNGVEILGTRTKPCEAEITGERSFSIILTQ 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           GL    NR+I+++ E   ++V  L R+     +LG L  G  RE++
Sbjct: 190 GL----NRQIRRMCEALGYQVKTLKRVRIMNVKLGNLKTGQYRELT 231


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 93/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
              EV+
Sbjct: 235 EWSEVT 240


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 108/225 (48%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG+ASRR+ + +I    V VNG +     V V    D +EV G  +  AE+ 
Sbjct: 5   RLNKFLASAGVASRRKCDEIIFAGSVTVNGRVAAGPFVTVDEEFDSVEVGGQRI-GAEKK 63

Query: 74  RLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP+G 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    +K     + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSV----KKVRRGTIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELT 224


>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 = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 120/236 (50%), Gaps = 14/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVTINGEICTHGAI-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP+G+  T ++      + DN+        R+  VGRLD  +EGL+LLTNDG +
Sbjct: 61  VYIAFHKPVGITCTAAEH-----IEDNIIDYIDYPERIFPVGRLDKASEGLILLTNDGAI 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +     +  + Y V          ++ +  G+ I+       +VT    + + +   
Sbjct: 116 ANQILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVNQSTFR 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L   +G
Sbjct: 172 IVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELEILIG 227


>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 = 88.6 bits (218), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 109/224 (48%), Gaps = 6/224 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ +G  SRRE +R+I    V V+G +     + +     IE DG  +   +R  
Sbjct: 26  RLNKFLSESGFCSRREADRLIEAGEVLVDGAVAS-MGMKIREGQQIEADGTLISGKDRPV 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP G+V T SD D    + D +     RV  VGRLD ++EGL+L+TN G L   +
Sbjct: 85  VLLVNKPRGIVCTTSDRDRAENIVDFIGYPL-RVYPVGRLDKDSEGLILMTNQGELVNRI 143

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V    ++ +  LN ++KG+ I         V    +K     +T GL 
Sbjct: 144 LKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDTVTRPCTVEKTGEKSFRIILTQGL- 202

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              NR+I+++ E   ++V  L R+     +L  L  G  RE+++
Sbjct: 203 ---NRQIRRMCEALGYRVRTLKRVRIMNLRLDGLKTGEYREITR 243


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 115/232 (49%), Gaps = 13/232 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R++K ++ AG  SRRE +R++ Q  VKVNG   ++ ++  +N    D I V G  + + E
Sbjct: 18  RLNKFLSDAGYCSRREADRLVEQGVVKVNGKTAVMGQKVTIN----DSIMVKGKNISREE 73

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L   +KP+G+  T +D +    + D   +   RV  +GRLD N++GL+LLTNDG + 
Sbjct: 74  EQILIALNKPVGIECT-TDLNNPDNIVD-FINFDKRVYPIGRLDKNSQGLILLTNDGSIV 131

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   S    + Y V     V  D +  +  G+ I        +VT   +   N  +T 
Sbjct: 132 NNILKGSNYHEKEYVVTVDKPVTDDFIKKMSTGVRILDQVTRPCKVTKVKKHVFNIVLTQ 191

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           GL    NR+I+++     + V +L RI     +LG L  G  R+V+   L+E
Sbjct: 192 GL----NRQIRRMCGELGYNVQKLKRIRIMNIELGNLPVGQYRKVTDSELKE 239


>gi|10304093|gb|AAG16128.1|AF261151_1 pseudouridylate synthase-like protein [Vibrio cholerae]
          Length = 241

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 93/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +P       + GRLD ++EGLL+LT
Sbjct: 58  PLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDGYAAGRLDRDSEGLLILT 114

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 115 NDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 174

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 175 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 234

Query: 232 STREVS 237
             REV+
Sbjct: 235 EWREVT 240


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 96/180 (53%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L
Sbjct: 54  EERKVILFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGIL 111

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKG----- 184
              L  P ++  + Y V+  G   +D L+ L++G+V++       +V+L DT        
Sbjct: 112 QARLTQPKSKSEKTYWVQVDGAPSEDDLDKLRRGVVLKDGPTLPAKVSLMDTPDVWERHP 171

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+++ + EG+NR+++++     +   RLIR S   F++G LL G   E+
Sbjct: 172 PVRFRANIPTTWLSITIIEGRNRQVRRMTANIGFPTLRLIRASMAGFEIGGLLPGDWLEI 231


>gi|324328441|gb|ADY23701.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 229

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE + +I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDSLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEGNIIDYINYPG---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRVDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRVFGFTVKKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/225 (32%), Positives = 108/225 (48%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG+ASRR+ + +I    V VNG +     V V    D +EV G  +  AE+ 
Sbjct: 5   RLNKFLASAGVASRRKCDEIIFAGSVTVNGRVATGPFVTVDEEFDSVEVGGQRI-GAEKK 63

Query: 74  RLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP+G 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    +K     + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSV----KKVRRGTIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELT 224


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 112/240 (46%), Gaps = 11/240 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P  +S+ +ARAG    +E E  I + RV VNG ++ +    V     + VDG  +R+   
Sbjct: 29  PDWLSRALARAGALPLQEAEDAIQEGRVTVNGRVVRQPLAPVPEGAVLRVDGTEVRREVE 88

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVI--SVGRLDINTEGLLLLTN 126
           TR+  +HKP  L+T+        TV++     LPS  +R    +VGRLD  T GLLL TN
Sbjct: 89  TRVLAFHKPADLLTSTVSQHRTGTVYEVLLPQLPSELARYTWHAVGRLDRGTTGLLLFTN 148

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           D  L      P T   + Y     G  D+ ++  L++G+ ++       QV +       
Sbjct: 149 DEKLVAHATSPETHLAKRYVATVQGTADEARVAPLRQGVQLEDGPTRPAQVRIRDAHTVE 208

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             VT    EG+N ++K++       V  L R + G   L  +  G+ R ++ + + E LG
Sbjct: 209 VIVT----EGRNHQVKRMLGAVGLPVRALHREAIGGVAL-DVPVGTFRLLTPEEVTEGLG 263


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 114/229 (49%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++ A  +V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
              L  P     + Y     G V ++ +    KG++++   Y      L   K  + + +
Sbjct: 119 THQLLSPKKHVPKKYYAHISGVVTEEDVIEFAKGVILED-GYETKPGELTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDEELELGQYRELT 226


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 11/225 (4%)

Query: 10  NFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +F P  +R+ ++++  G  SR+E   ++   RV V G   +  A  V +   + VDG PL
Sbjct: 34  SFMPVLKRLDQLLSNLGYCSRKEARYLLKDNRVTVAGEYAKSPAQKVDAAT-VRVDGEPL 92

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLL 123
              E   L + +KP+G V +H   +G   ++D LP  +     +++SVGRLD +T GL+L
Sbjct: 93  DFPEGI-LVMLNKPLGYVCSHDSGEGMR-IYDLLPERWEFRNPKIVSVGRLDKDTTGLIL 150

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +T+D  L   L  P     ++Y+V  +  +  D +    KG+V+       +   ++   
Sbjct: 151 VTDDTKLVHQLTSPKHHVDKLYKVTVNSPLQPDIIEAFAKGVVLGDGAEQCLPAKVEIIS 210

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            + A VT  L EGK  +++++F    + V  L R  +GP+ L  L
Sbjct: 211 ENMANVT--LNEGKYHQVRRMFAACGYHVEALHRSQFGPYSLHDL 253


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 112/232 (48%), Gaps = 21/232 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKAER 72
           R++K ++  GI SRR  ++ IA+ +V +NG   E A V   V   D + +DG  ++K ++
Sbjct: 2   RINKYLSETGIISRRGADKWIAEGKVTING---EPATVGSQVQDGDIVCIDGKEVKKEQQ 58

Query: 73  TRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G+  TT     G    F N P    R+  +GRLD  +EGLLLLTNDG + 
Sbjct: 59  LVYIALNKPVGITSTTERHIKGNVVDFVNHPL---RIFHIGRLDKESEGLLLLTNDGDIV 115

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSNA 187
             +        + Y V+    + +  +N +  G+ I       CY         +K S+ 
Sbjct: 116 NKILRAENHHEKEYIVQVDKPITEQFINKMSAGVDILDTTTLPCY--------VEKISDK 167

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              + L +G NR+I+++     + V RL RI     +LG L  G  R+++ K
Sbjct: 168 VFKIILEQGLNRQIRRMCSALGYSVKRLQRIRIMNIKLGNLKVGQWRDLTDK 219


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 104/207 (50%), Gaps = 11/207 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +++I   R+ VNG + E     V S D I VDG  + + +   
Sbjct: 8   RINKFLSEVGYCSRREADKLIDAGRITVNGNIPE-MGTKVSSEDEIRVDGKIVGEQKDPP 66

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++L +HKP+G+V T      +  + D  N P+   R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 67  VYLIFHKPVGIVCTTDTRVEKDNIIDYINYPT---RIFPIGRLDKASEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +D   +  +  GI I        +V    Q G   +  +
Sbjct: 124 NKILRARNNHDKEYIVDVDKPIDASFVKRMSDGIPILDTITRKCEV---EQLGKKRFKII 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
            L +G NR+I+++ E+ ++ V RL R+
Sbjct: 181 -LTQGLNRQIRRMCEYLDYNVTRLKRV 206


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 109/229 (47%), Gaps = 11/229 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KVIA     SRR+V+R++ + ++ VNG  +++A + +   TD + V G  L   +R
Sbjct: 8   ERLDKVIAAQTKLSRRDVQRLVGRGQISVNGTPVKKADLKIDPDTDVVMVSGKTL-ALKR 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V   SD     TV D +P    R  +   GRLD +TEG +L+T+DG  
Sbjct: 67  HVYIMLNKPRGVVCATSDA-ALPTVLDLVPDSLMRRGLFPAGRLDKDTEGFVLITDDGAF 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
           A  +  P +   + Y  R    V Q  +     G+ + G +C       LDT   +    
Sbjct: 126 AHRILAPKSHVPKTYTARLDAPVTQQMIEAFAAGVQLDGAVCMPAELCVLDTPDTAR--- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            V +R+G   +IK++F      V  L R   G   L   L  G  RE+S
Sbjct: 183 -VVIRQGMYHQIKRMFAACGAHVLALRRDRIGGLSLDIALGPGECRELS 230


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/226 (31%), Positives = 119/226 (52%), Gaps = 13/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+++  GI SR +  ++I   RVKVNG L       V  TD I +D  P+++ ER  
Sbjct: 2   RINKLLSNKGICSRSQAHQLIVAGRVKVNGQLCIPGQW-VEETDEILLDDRPVKEKERLY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP+G+V T ++    + + + N P+       VGRLD +++GL+LLTNDG LA  
Sbjct: 61  IIL-NKPVGIVCTAAEGVKDNIIRYMNYPAYL---FPVGRLDKDSQGLILLTNDGDLASD 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--V 191
           +        + Y V+     ++D L+ +      QG+  GD  +T   Q  +    T  +
Sbjct: 117 ILEAEKGHEKEYMVQVDRPYEEDFLHKMS-----QGVNLGDGVITRICQVSAINEDTFRI 171

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L +G NR+I+++ + F + V RL RI      LG L  G  R+++
Sbjct: 172 ILTQGMNRQIRRMTKAFGYNVVRLERIRLLNIALGPLAYGEWRKLT 217


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V V+G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETKES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             + LP  +  + Y+   + +V    +   +KGIV     Y      L   K      TV
Sbjct: 119 YEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFAD-GYQCQPANLKILKADKHQSTV 177

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            L  +EGK  ++KK+F     KV  L R+S GP +L   LA G  R ++
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLT 226


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 121/220 (55%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+A I SR+++++ + ++++ V+     + + NV      I ++  P+   +  
Sbjct: 11  RLDILLAQAHI-SRKKMKQALLKKKILVDDCPARKLSQNVDTGLQTITLEEQPVL-GKPH 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
           + ++ +KP+G+VT +SD   + TV D + P  FS  + SVGRLD +T GLLL+T++G L 
Sbjct: 69  QYFMMNKPLGVVTANSDAKFQ-TVLDLIRPEDFSEDLYSVGRLDRDTSGLLLITDNGPLG 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
            +L  P     + Y V  +G +D   +   +KGIV + G       +T+ +   + +  T
Sbjct: 128 FLLLHPQYHVTKTYEVEVNGLLDDQAVQSFQKGIVFLDGTICKPATLTIRSSSSNKSRAT 187

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + EGK  +IKK+F     KV  L RI +G F+L   LA
Sbjct: 188 VTISEGKFHQIKKMFLTVGVKVTSLKRIHFGDFELEPNLA 227


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 122/237 (51%), Gaps = 14/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++ G  +R E +++I  +RV++NG +++   + +   +D I +DG  L    + 
Sbjct: 2   RLDKFLSQTGKFTRAEAKKVIKAKRVRLNGEVVKDGKIKINEDSDKIFLDGELLALNNKE 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D D   TV D  N P     +  VGRLD +T GLL++TNDG  A
Sbjct: 62  VYYMLNKPAGVVSATRD-DKDKTVIDLINFPGRKEDLFPVGRLDKDTTGLLIITNDGKFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD------MQVTLDTQKGS 185
             +  P     + Y     G++ + ++ +  +G+    +  GD      + +   ++K  
Sbjct: 121 HNIISPKKHVSKTYEAVVTGKISEKEVKIFSQGM---ELANGDKLQPAQLDIISYSEKDD 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + V V + EGK  +++++F   + +V  L R+  G  +L  TL  G  RE+++K L
Sbjct: 178 TSKVRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRELTEKEL 234


>gi|300214283|gb|ADJ78699.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 240

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/237 (27%), Positives = 122/237 (51%), Gaps = 14/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++ G  +R E +++I  +RV++NG +++   + +   +D I +DG  L    + 
Sbjct: 4   RLDKFLSQTGKFTRAEAKKVIKAKRVRLNGEVVKDGKIKINEDSDKIFLDGELLALNNKE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KPIG+V+   D D   TV D  N P     +  VGRLD  T GLL++TNDG  A
Sbjct: 64  VYYMLNKPIGVVSATRD-DKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD------MQVTLDTQKGS 185
             +  P     + Y     G++ + ++ +  +G+    +  GD      + +   ++K  
Sbjct: 123 HDIISPKKHVSKTYEAVVTGKISEKEVKIFSQGM---ELANGDKLQPAQLDIISYSEKDD 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + V V + EGK  +++++F   + +V  L R+  G  +L  TL  G  RE++++ L
Sbjct: 180 TSKVRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRELTEEEL 236


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 114/229 (49%), Gaps = 13/229 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I  +RV +NG +  +   ++ +  D + VDG   +    T
Sbjct: 2   RLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDG---KIVSTT 58

Query: 74  RLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           +L+   +HKP G VT   D      V D LP  F +  V+ VGRLD +TEGLLLLTNDG 
Sbjct: 59  QLYYVKFHKPKGYVTAVEDSS-HPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGV 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +   +    +VY V F G +  + +  +K+GI++     G      + +  S   V
Sbjct: 118 WGHSIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGD---GTQCKPAEIEFVSLHSV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            V + EGK  ++K++       V  L R++ G   L G    GS  E++
Sbjct: 175 HVTIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELT 223


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 116/238 (48%), Gaps = 8/238 (3%)

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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
            P+   +    +L +KP G+++   D     TV D       R  +  VGRLD +TEG L
Sbjct: 71  EPI-AYQSQFYYLLNKPAGVISATVDS-YEETVLDLFSEEAFREDLFPVGRLDKDTEGFL 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLD 180
           L+TNDGGLA  L  P     + Y  +  G +  +   +  KGI + G      ++Q+   
Sbjct: 129 LITNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKIFAKGIKLDGEWTLPAELQILNV 188

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            ++   + + + L EGK  ++K++      +V  L RI  G   L   LA G  RE++
Sbjct: 189 DEEEMRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELT 246


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/222 (31%), Positives = 109/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG + +     +  T D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQLLKKGLVLVNGRVEKSPKTQIDETADEIVVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q        GI ++       Q   + LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQTDEERFAAGIELKDFTCQPAQLKILELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP Q    LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQSDPALA 220


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 120/233 (51%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I++A   SRRE +R+I   RV +NG +    A+ V + D + +DG  + K  + +
Sbjct: 2   KINQFISKALSCSRRETDRLIKANRVAINGEICTHGAL-VAADDIVSIDGKTIEKEAKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  IYIAFHKPVGITCTAAEHIEGNIIEYINHPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT       ++   + 
Sbjct: 118 QILHGDHEHEKEYIVTVDKPFTDWFIDSMSRGVKIKDGMTKPCKVT----GVDHSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L +G NR+I+++   F + V +L R+      L  L  G  R VS++ L E +
Sbjct: 174 LTQGMNRQIRRMSRAFGYTVTKLKRVRIMNITLDGLEVGEWRNVSEQELIELM 226


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 115/230 (50%), Gaps = 5/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V  ++ Q+R++++G  +      V     +E+D   L+  +  R
Sbjct: 2   RIDRFLSNLPRFNRQQVRVLLVQRRIRIDGQPVSDPKAEVREFSRVELDDEVLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP+G V+   DP+ + TV + +     + + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPMGCVSATRDPEHK-TVLELIHEPDPQDLHIAGRLDYNTTGLMLITNDGNWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T+  ++Y V    ++  + +     G+         +   L      +A +++  
Sbjct: 121 LTQPQTKLPKLYYVETEQEIGPEYVETFAHGLYFAFEDLTTLPAQLQILGPRSARLSIV- 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            EG+  ++K++F  FN KV RL R   GP  L   LA G  R +S   +R
Sbjct: 180 -EGRYHQVKRMFGHFNNKVLRLHRERMGPLLLDERLAPGEYRALSDAEIR 228


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/225 (30%), Positives = 108/225 (48%), Gaps = 17/225 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A   + +R +V+  I ++ V VNG+ + +  V V +  D I V G  +    + 
Sbjct: 5   RLDKYLADMQVGTRSQVKEQIRKKLVSVNGVTVTKPDVKVDTDRDKIMV-GSDIIGYTQF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+++  +DP  ++ V     +I   +  VGRLD +TEGL+L+TNDG LA  
Sbjct: 64  EYFMLNKPKGVLSAANDPKAQTVVDLITDNICRDLFPVGRLDKDTEGLMLITNDGELAHK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------LD 180
           L  P     + Y VRF G +  + +    KGI I      D +V              L 
Sbjct: 124 LLSPRKHVDKSYYVRFEGIIADNTVESFAKGIDINIAKCADDEVDNNPKEIYHTKPAKLR 183

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 A +T+   EGK  +IK++F     +V  L RIS G  QL
Sbjct: 184 LMSADEAVITIS--EGKFHQIKRMFMAAGCRVTYLKRISMGTLQL 226


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 116/232 (50%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +  AG+ SR +V+ ++ +++V VNG+     +  VN M+ D +   G  L   E 
Sbjct: 2   RLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEMA-DEVSYQGQRLN-YEA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   + TV D L     +  V  VGRLD +T GLLL+TNDG L
Sbjct: 60  FVYYMLNKPKGVISATEDSSHK-TVLDLLDDTARQKAVFPVGRLDKDTHGLLLVTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSN 186
           A  L  P     + Y     G + Q+ +    +GI ++   +  M   LD     +    
Sbjct: 119 AHALLSPKKHVAKQYLAVVDGMMTQEDVKHFAQGITLKD--HQCMPAYLDILEINESLKT 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           + V + + EGK  ++K++       V+ L RIS GP QL + LA G+ R ++
Sbjct: 177 SLVKITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLT 228


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 7/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++  I+  GI SRRE + +I Q++VKVNG +     + V S D IEV+G  L+K +   
Sbjct: 2   RLNNFISSTGICSRREADELIKQKKVKVNGEIAPLGYI-VNSKDKIEVNGKLLQKKKNDI 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT     G    F N      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 61  YIALNKPVGITCTTERHIKGNIIDFINHTE---RIFPIGRLDKDSEGLILLTNDGSIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +        + Y V  +  +    +N + KG+ I         +T   +  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|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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 116/238 (48%), Gaps = 17/238 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI------LLERAAVNVMSTDHIEVDGVPLR 68
           R++K +A+ GI SRRE  R+I   R+ +NG       L++R A   +  D I +D  P+ 
Sbjct: 2   RLAKYLAQCGIGSRREACRLINAGRITLNGKIAKHTNLVQRDAQG-LCLDSICLDAEPIV 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    W+++K +G      + D ++++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  ETEALAYWIFNKAVGTDCRLLEQD-KTSLLHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSN 186
            L   L  PS    + Y VR       D +  +  G+      Y D+Q TL  Q  + S 
Sbjct: 119 ELTHKLMHPSFAHSKTYHVRLDKPFTDDFVEQMASGVR-----YKDLQ-TLPCQVRRLSL 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               + L +G NR+I+ + +   ++V  L R++     L  L +G   E   + L  Q
Sbjct: 173 DSFEIVLTQGLNRQIRHMSKALGYRVIDLERVAIMALNLRELASGELPEGQMRPLTPQ 230


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 116/238 (48%), Gaps = 8/238 (3%)

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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
            P+   +    +L +KP G+++   D     TV D       R  +  VGRLD +TEG L
Sbjct: 64  EPIV-YQSQFYYLLNKPAGVISATVDS-YEETVLDLFSEEAFREDLFPVGRLDKDTEGFL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLD 180
           L+TNDGGLA  L  P     + Y  +  G +  +      KGI + G      ++Q+   
Sbjct: 122 LITNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKTFAKGIKLDGEWTLPAELQILNV 181

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            +  + + + + L EGK  ++K++      +V  L RI  G   L   LA G  RE++
Sbjct: 182 DEDETRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELT 239


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>gi|163857342|ref|YP_001631640.1| pseudouridylate synthase [Bordetella petrii DSM 12804]
 gi|163261070|emb|CAP43372.1| pseudouridylate synthase [Bordetella petrii]
          Length = 243

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 116/237 (48%), Gaps = 23/237 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAERT 73
           R+SK++A  G+ SRRE +  I +  VKV+G+++            I ++     R+  R 
Sbjct: 5   RISKLMAERGLCSRREADSYIERGWVKVDGVVVAELGARAFPDQVITLERAAQARQTARV 64

Query: 74  RLWLYHKPIGLVTTHSDP---------DGRSTVF-DNLPSIFSR-----VISVGRLDINT 118
            + L +KP+G V+  ++          D RS    D  P  F+R     +   GRLDI++
Sbjct: 65  TI-LINKPVGYVSGQAEKGYTPASALVDARSRYARDRSPLRFTRAHLQGLAVAGRLDIDS 123

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GLL+LT DG +AR L    +   + Y VR  G++D   L LL  G+ + G      QV 
Sbjct: 124 QGLLVLTQDGRIARQLIGEDSSVDKEYLVRVQGRLDAGGLALLNHGLSLDGKPLRPAQV- 182

Query: 179 LDTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +  NA  +   LREGK R+I+++ E    KV  L R+  G  +LG L  G  R
Sbjct: 183 ----RWQNADQLCFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVKLGDLPPGQWR 235


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 124/251 (49%), Gaps = 22/251 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K IA   + SR+EV+++I  +R+ VN  +  R  + +   TD I +DG  +   E  
Sbjct: 2   RLDKFIANFTLYSRKEVKKLIKAKRITVNDSIASRPEMQIDEETDTISLDGQWI-GYEPY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS----IFSRVISVGRLDINTEGLLLLTNDGG 129
             +L +KP   ++T + P   S V D LP+    I+ +   VGRLD +TEGLLLLTNDG 
Sbjct: 61  IYYLLNKPQNCLST-TRPGPTSIVTDFLPANEVEIY-QPFPVGRLDKDTEGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGI-CYGDMQVTLDTQKGSN- 186
            A  L  P     + Y     G V ++ +    KG+ I QG  C       L T    N 
Sbjct: 119 FAHDLLSPKKLVSKEYYAEIEGIVTEEDVKAFAKGLTIDQGDHCAPSQLDILATDPAKNR 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + +TV L EGK  ++K++F+    +V  L R     F++G+L      E+       +L 
Sbjct: 179 SEITVTLTEGKYHQVKRMFQAVGKEVIYLQR-----FRIGSLYLPEELELGTAF---KLL 230

Query: 247 PHLLEEAQVNL 257
           P   EEAQ+ L
Sbjct: 231 P---EEAQLAL 238


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 32/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V+V+G +++     V +  HI+V  +P  +A + R
Sbjct: 275 RLSKRMSELGLCSRREADEWIEKGWVRVDGQIVDTLGAKVTAAQHIDV--LPNARAAQAR 332

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFS-----RVISVGRLDIN 117
               + +KP+G V+   + D    V           D  P+ FS      +   GRLDI+
Sbjct: 333 QVTIVLNKPVGYVSGQPEGDYPPAVALITPANRWSDDPAPTRFSATHLRSLAPAGRLDID 392

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQ-------DKLNLLKKGIVIQ 168
           + GLL+LT DG +A+ L    ++  + Y  RVR+     Q       DKL  L++G+ + 
Sbjct: 393 STGLLVLTQDGRIAKQLIGEQSEVEKEYLVRVRYGTHTQQVERYFPIDKLAQLREGLSLD 452

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+     QV  D Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L
Sbjct: 453 GVRLKPAQV--DWQNGEQ--LRFVLREGRKRQIRRMCELVGLEVVGLKRVRIGQLVLGAL 508

Query: 229 LAGSTR 234
            +G  R
Sbjct: 509 PSGKWR 514


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 121/232 (52%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++++   +V +NG++    +      D + + G PL+  ++  
Sbjct: 2   RINKFISETGYCSRREADKLVESGKVTINGVVAVLGS-QAEEGDDVRIQGKPLQDKKKHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITST-TESHIKGNIVDFVGH-NERIFPIGRLDKDSEGLILLTNDGDIVNKI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     V +  L  +  G+ I     G++ +  +  + S     + L 
Sbjct: 119 LRSEGKHEKEYIVTVDRPVTESFLRGMAGGVKI----LGEITLPCEVTRMSERVFRIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNR+I+++   F ++V +L RI     +LG+   GS R+++ K  +E+LG
Sbjct: 175 EGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRIGSWRDLNDK-EKEELG 225


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V V+G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             + LP  +  + Y+   + +V    +   +KGIV     Y      L   K      TV
Sbjct: 119 YEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFAD-GYQCQPANLKILKADKHQSTV 177

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            L  +EGK  ++KK+F     KV  L R+S GP +L   LA G  R ++
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLT 226


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/217 (33%), Positives = 115/217 (52%), Gaps = 11/217 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V ++G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMIDGTVELRQNRNVDSLLHQIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPEKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             + LP  +  + Y+V  + +V    +   + GIV      C   D+++    +  S   
Sbjct: 119 YEMLLPEKKVSKTYQVVVNERVTSADVTAFENGIVFADGYQCKPADLKILKADKHQSTVL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +T+  +EGK  ++KK+F     KV  L R+S GP +L
Sbjct: 179 LTI--QEGKFHQVKKMFLAQGKKVTALKRLSMGPLEL 213


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 110/229 (48%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R E + M+A+ RV+VNG + ++    +  TD + VDG  L   +   
Sbjct: 2   RLDKYLAETAQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDTDTVAVDGALLTYQKFVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DGG A 
Sbjct: 62  LML-NKPEGVVSASTDKR-DTTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V     + Q+       G+ +  G      +VT  +  G    V V
Sbjct: 120 DILSPRHHVSKTYTVTIDTPLTQEMCTGFAAGVTLADGTALSPAEVTALSPDGLT--VRV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            LR+G   +IK++F  +   VN L R + G   L   LA G  RE+S +
Sbjct: 178 VLRQGVYHQIKRMFGVYGAGVNALHREAIGGLALDAQLAPGQWRELSDE 226


>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 = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 56/208 (26%), Positives = 106/208 (50%), Gaps = 3/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ I+ +G+ SRR+ +  I    VKVNG ++      V  TD ++ DGV +   E+  
Sbjct: 65  RLNRYISNSGMCSRRDADIYIQSGNVKVNGEVITEMGYRVKLTDSVQFDGVNIT-PEKKE 123

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP    T   D  G + V D +  +  + ++ VGR+D  T GLLL TND  + + 
Sbjct: 124 YILLNKPKNFSTAGDDSAGSANVLDLVRNATKANLMPVGRMDKTTTGLLLFTNDTEIVQK 183

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             +P+ +  +VY+V     +  + L  ++KG+ I        +VT   Q    + + + +
Sbjct: 184 FTVPNQRSSKVYQVTLDKNLKFEDLEKIQKGLTIDDHKVFVEEVTY-IQDQPKSEIGIKM 242

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
           +    + ++K+FE F + V ++ R+++ 
Sbjct: 243 KTSNVKVVRKIFEHFKYDVLKVDRVTFA 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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 120/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A+  I SR+ +++ + ++ + V+G+     A N       +   G+ ++  E T
Sbjct: 2   RLDKLLAQEKI-SRKAMKQALLKKEILVDGLPASSLAQNTDTGLQELMFQGIRIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D     TV D LP      ++ ++GRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGVVTASKDKK-LPTVMDLLPQHLQSDQLYAIGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K GI+ + G      Q+ + +   S +  T
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGPLTPDHIQEFKDGIIFLDGTICKPAQLEILSSSPSLSKAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++KK+F     KV  L R+ +G F L   LA G  R ++K+ L+
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTALKRVQFGNFILNPDLAEGDFRLLNKEELQ 231


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 117/234 (50%), Gaps = 14/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKAER 72
           R++K I+ +G ASRR+ +R++ + RV +NG   ++A +   V   D + V+G   R A  
Sbjct: 2   RINKFISESGKASRRQADRLVEEGRVTING---KKAKIGDQVKPGDEVLVNGSVARVARN 58

Query: 73  TRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 HKP+G+  TT     G      N P    R+ ++GRLD ++EGL+L+TNDG + 
Sbjct: 59  NVYIAVHKPVGITSTTEKKVKGNLVDMVNHPL---RIFNIGRLDKDSEGLILMTNDGDIV 115

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     +  + +  ++ G+ I     G   +    +  S     +
Sbjct: 116 NEILRAEGEHEKEYIVSVDKPITPEFVEQMEAGVKI----LGQKTLPCKVRPLSKFDFNI 171

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G NR+I+++ E   ++V RL R+      LG L  G  R++SKK  REQL
Sbjct: 172 TLTQGLNRQIRRMCEALGYEVFRLQRVRVMNITLGKLPPGQWRDLSKK-EREQL 224


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 106/215 (49%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVNGEEI-AYQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   ++ +    P   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPKGVLSATEDRSQKTVISLLDPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW--VT 190
           L  P+    +VYR    G  D++       G+++  G      ++ +  Q   NA   + 
Sbjct: 121 LVAPNKHVAKVYRAEIAGVADEETAKAFASGMMLGDGTKLKPAKLKILKQDRENATSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK++F     KV  L R+S G   L
Sbjct: 181 IEISEGKYHQIKRMFGAVGMKVTALDRLSMGNLHL 215


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 111/229 (48%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV + ++     +R++V  ++ ++RV+++G  +      V     +EVD   L+     R
Sbjct: 2   RVDRFLSNLPRFNRQQVRLLLVERRVRIDGQTVSDPHAQVREFSRVEVDDDVLQAGRPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   DP    TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPPGCVSATRDPQ-HPTVLDWLDEPDKNDLHIAGRLDFNTTGLMLITNDGSWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +  +  +   +G+    + +     ++TL   + +     +
Sbjct: 121 LTQPQTKLPKVYYVETEQIITAEYADTFARGLYFAFEDLTTQPAELTLLGPRSAR----L 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
            + EG+  ++K++F  FN KV RL R   GP  L   L  G  R +S +
Sbjct: 177 SIVEGRYHQVKRMFGHFNNKVLRLHRERMGPLTLDAHLEPGQYRALSPE 225


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 116/235 (49%), Gaps = 12/235 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           TP R++K ++  G  SRR  +++I Q RV +NG + E     + + D I VDG  + K +
Sbjct: 5   TPTRINKYLSEVGYCSRRAADKLIDQGRVTINGKVPE-MGTKITAADEIRVDGELIGKPK 63

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               +L ++KP+G+V T      +  + D  N P    R+  +GRLD  +EGL+ LT+DG
Sbjct: 64  GKHTYLAFNKPVGIVCTTDTGVEKDNIIDFINYPK---RIFPIGRLDKPSEGLIFLTDDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  ++ D L  +  G+ I        +V    ++     
Sbjct: 121 DIVNKILRARNNHEKEYIVSVNKPINSDFLRQMSSGVPILDTVTRPCKV----ERIDKYT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++ L +G NR+I+++ +   ++V RL R+     +L  L  G  R++++  L E
Sbjct: 177 FSIILTQGLNRQIRRMCDHLEYRVKRLQRVRIMNVELD-LEVGKYRDLTEAELSE 230


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 116/236 (49%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR+ E  R
Sbjct: 4   RLNKYIAETGSCSRREADRLIGERRVTVNGMPAGTGAV-VGEEDTVLVDGQPLRRREAKR 62

Query: 75  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKDSEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRRMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 105/216 (48%), Gaps = 9/216 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++   + +R+ ++ ++   RV+V   +++ A   V     + VD  P+R  +   
Sbjct: 2   RIDRFLSHMNVGTRKTLKPLLKAGRVRVADKVIKEAKYQVTPETVVYVDDEPIR-YQTNF 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
            WL +KP G+++  +DP  + TV D       R  +  VGRLD +T GLLL+TNDG LA 
Sbjct: 61  YWLLNKPAGVISATTDP--QKTVMDLFAPADYREDLFPVGRLDKDTTGLLLITNDGDLAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWV 189
            L  P     + YR +  G V          G+ ++       Q+T+   DT +   + +
Sbjct: 119 DLLSPKKHVAKTYRAKIAGVVTAADQAQFAAGLKLRDFDAQPAQLTILRTDTAR-QESLI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  ++K++F     +V  L RI  GP  L
Sbjct: 178 EVEIHEGKFHQVKRMFHAVGKEVLTLERIKMGPLSL 213


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/229 (31%), Positives = 113/229 (49%), Gaps = 17/229 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI------LLERAAVNVMSTDHIEVDGVPLR 68
           R++K +A+ GI SRRE  R+I   R+ +NG       L++R A   +  D I +D  P+ 
Sbjct: 2   RLAKYLAQCGIGSRREACRLINAGRITLNGKIAKHTNLVQRDAQG-LCLDSICLDAEPIV 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    W+++K +G      + D ++++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  ETEALAYWIFNKAVGTDCRLLEQD-KTSLLHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSN 186
            L   L  PS    + Y VR       D +  +  G+      Y D+Q TL  Q  + S 
Sbjct: 119 ELTHKLMHPSFAHSKTYHVRLDKPFTDDFVEQMASGVR-----YKDLQ-TLPCQVRRLSL 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + L +G NR+I+ + +   ++V  L R++     L  L +G   E
Sbjct: 173 DSFEIVLTQGLNRQIRHMSKALGYRVIDLERVTIMALNLRELASGELPE 221


>gi|257899452|ref|ZP_05679105.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257837364|gb|EEV62438.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 238

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V ++G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMIDGTVEFRQNRNVDSLLHRIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             + LP  +  + Y+   + +V    +   +KGIV     Y      L   K      TV
Sbjct: 119 YEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFAD-GYQCQSANLKILKADKHQSTV 177

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            L  +EGK  ++KK+F     KV  L R+S GP +L   LA G  R ++
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLT 226


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 63/215 (29%), Positives = 109/215 (50%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV ++I +  V VNG  ++     V  TD + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHQLIKKGIVSVNGQTVKTPKEKVAETDEVTVNGEKIV-YQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   R+ +   +L   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLMNKPKGVLSATEDRSQRTVISLLDLKDQYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P+    +VYR +  G  D++ +     G+ +     +    + V     +  ++ + 
Sbjct: 121 LLAPNKHVAKVYRAKIAGVADENTVKTFASGMTLGDETKLKPAKLTVLKQDLEHDSSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK++F     KV  L RIS G  +L
Sbjct: 181 IEISEGKYHQIKRMFGAVGMKVVELERISMGKLKL 215


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 121/234 (51%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G  +R E++++I   RV V+G  +++  + +  +T  + ++G  +  A++ 
Sbjct: 3   RIDKYLAEMGQGTRSEIKKLIRSGRVMVDGETVKKPELKIDETTQKVSLEGKQIGYAKKE 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              LY KP G+++   D D   TV D +     + +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  YYMLY-KPAGVISATKD-DRDKTVLDLITDKKRNDLFPVGRLDKDTEGLLLITNDGELAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC---YGDMQVTLDTQKGSNAWV 189
            L  P     +VY  +  G+VD+  +     G+ I         D+++    + G  + +
Sbjct: 121 RLLSPKKHVDKVYYAKVQGKVDESDVKAFADGVDIGDDTPAKSADLRI---LKSGEESEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EG+  ++K++F     +V  L R+S G   L  TL  G  R ++++ ++
Sbjct: 178 ELTITEGRFHQVKRMFHAVGKEVIYLKRLSMGSLALDKTLTKGEYRSLTEEEIK 231


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 107/219 (48%), Gaps = 9/219 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDG---VPLRKA 70
           R+++ +A  G+ SRR+ E +I + ++ +NG  +      +   +D +   G    P RK 
Sbjct: 14  RLNRFLADCGLGSRRKTEELILRGQITINGKRVTDLGTKIKPGSDVVSYLGNVVEPTRKP 73

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +R  + + +KP+G + +H D     TVF  LP  +      GRLD+N+ GLL+LTNDG L
Sbjct: 74  KR--ILILNKPVGYLCSHGDRFHEKTVFSLLPLTYKNFKIAGRLDLNSRGLLILTNDGEL 131

Query: 131 ARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           A+ +  PS    + Y V   H   ++      +KGI+  G       V L    G N   
Sbjct: 132 AQKISHPSNGSEKEYLVTLNHDPGEKWIQAAFQKGILDAGEILRAKMVKL--VPGKNCVY 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            V L EGK R+I+++F      V  L RI  G  QL  L
Sbjct: 190 RVILAEGKKRQIRRMFHASGASVIDLQRIRIGSIQLEKL 228


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/229 (34%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V V+G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             + LP  +  + Y+   + +V    +   +KGIV     Y      L   K      TV
Sbjct: 119 YEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFAD-GYQCQPANLKILKADKHQSTV 177

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            L  +EGK  ++KK+F     KV  L R+S GP +L   LA G  R ++
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDERLAVGEYRSLT 226


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

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 117/242 (48%), Gaps = 8/242 (3%)

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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
            P+   +    +L +KP G+++   D     TV D       R  +  VGRLD +TEG L
Sbjct: 71  EPI-AYQSQFYYLLNKPAGVISATVDS-YEETVLDLFSEEAFREDLFPVGRLDKDTEGFL 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLD 180
           L+TNDGGLA  L  P     + Y  +  G +  +   +  KGI + G      ++Q+   
Sbjct: 129 LITNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKIFAKGIKLDGEWTLPAELQILNV 188

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            +    + + + L EGK  ++K++      +V  L RI  G   L   LA G  RE++ +
Sbjct: 189 DEDEMRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTSE 248

Query: 240 IL 241
            L
Sbjct: 249 EL 250


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ ++ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYLSEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/245 (32%), Positives = 116/245 (47%), Gaps = 31/245 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA   V+VNG +     + V  TD IEVD     + ER  
Sbjct: 101 RLNKRMAELGLCSRREADDWIASGWVRVNGQVAA-MGLQVAPTDRIEVDPAARGQQERQV 159

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL----------------PSIFSRVISVGRLDINT 118
             L HKP+G V+  ++ DG +     +                P     +   GRLDI++
Sbjct: 160 TILLHKPMGYVSGQAE-DGHTPAVALINPRTHWREDPSRQRFSPPQLRGLAPCGRLDIDS 218

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQV 177
            GLL+LT DG +AR L    ++  + Y VR H G V  D  ++     + + +C+G   +
Sbjct: 219 VGLLVLTQDGRVARHLIGEDSEVEKEYLVRVHYGDVATDVQSVFPAAQLAR-LCHG---L 274

Query: 178 TLDTQKGSNA---W-----VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +LD Q    A   W     +   L+EGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 275 SLDGQALKPAKVDWQNPEQLRFVLQEGKKRQIRRMCELVGLKVVGLKRIRIGRVVLGNLP 334

Query: 230 AGSTR 234
            G  R
Sbjct: 335 VGQWR 339


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/218 (31%), Positives = 110/218 (50%), Gaps = 11/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDQIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+++   D   R TV D L   ++R   V  VGRLDI+T GLLLLTNDG L
Sbjct: 62  -YYMMNKPQGVISATEDNKHR-TVLDLLDD-YARAKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNA 187
           A  L  P     + Y  +  G + Q+ ++   KGI ++       +   V++D +K + +
Sbjct: 119 AHALLSPKRHVDKTYLAQVEGIMSQEDVDTFAKGIPLKDFTCQPAKLELVSVDPEK-NQS 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V V + EGK  ++K++  +   +V  L R++ G   L
Sbjct: 178 LVRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLAL 215


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRVDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 121/241 (50%), Gaps = 9/241 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++++ VN        V V    D I+ +G  L   E+ 
Sbjct: 2   RLDKFLVECGLGSRTQVKLILKKKQISVNSNSETSPKVQVDEYRDEIKYNGT-LVSYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLL+TN+G LA
Sbjct: 61  VYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY-GDMQVTLDTQKGSNAWV 189
             +  P     + Y  +  G + +D +    KGI+++   C    +++    Q    + V
Sbjct: 120 HKMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKKILREQLGPH 248
            + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + E+L  H
Sbjct: 180 KITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEI-EKLEKH 238

Query: 249 L 249
           +
Sbjct: 239 M 239


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 91/179 (50%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P+ +  +VY V+  G  D D L  LK+G+ ++          L              
Sbjct: 88  LTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWPRHPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKTIPTSWLKITLYEGRNRQVRRITAHVGFPTLRLIRFSIGNLSLGNLQPGEWKEIT 206


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 118/238 (49%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAER 72
           R++K I+  G  SRRE ++++   RV +NG   E A +   +   D + V+G PLR    
Sbjct: 2   RINKFISETGFCSRREADKLVESGRVTING---EVAVLGSQAEEGDDVRVNGKPLRDKSD 58

Query: 73  TRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G+  TT S   G    F   P    R+  +GRLD ++EGL+LLTNDG + 
Sbjct: 59  HVYIALNKPVGITSTTESHIRGNIVDFVGHPQ---RIFPIGRLDKDSEGLILLTNDGDIV 115

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     V    +  +  G+ I     G   +  +  + S     +
Sbjct: 116 NKILRAEGKHEKEYIVTVDRPVTPSFVQGMSSGVKI----LGHRTLPCEVTRVSEYVFRI 171

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            L EGKNR+I+++   F ++V +L R+     +LG+L  G+ R++++   +++LG  L
Sbjct: 172 ILTEGKNRQIRRMCAAFGYEVKKLQRLRIMNIRLGSLQKGAWRDLTEA-EKQELGQML 228


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 119/233 (51%), Gaps = 18/233 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RKAE 71
           +R+SKV+A AG+ASRR  E +I   +V VNG +      +V    D I +DG P+ R+  
Sbjct: 20  ERLSKVMAAAGVASRRACEEIIFAGKVVVNGKVCRTPETHVDPLKDLIYIDGKPIPRRLP 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-RVISVGRLDINTE 119
              ++  +KP G + + +  D + TV+            N P +   R  +VGRLD+ T 
Sbjct: 80  PKMVFALYKPKGYICSDAK-DDKKTVYLLLEKYLKTWEKNNPGLTKPRFFTVGRLDVATT 138

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVT 178
           GL+ +TNDG  A+ +  PS+   + Y V    + V + +L  +  G  I G+    + V 
Sbjct: 139 GLIFVTNDGEFAQKVSHPSSGITKEYLVTVDSESVTKRQLKRIASGTEIDGVMCVPISVE 198

Query: 179 L-DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           L  ++ G S   + V + EG+N E++++ E    KV+ L R+  G  +L + L
Sbjct: 199 LVKSEPGDSRHRIRVVVTEGRNHEVRQLVESAFLKVHALKRVRVGGLRLPSKL 251


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 120/239 (50%), Gaps = 17/239 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +R+SKV+A AG+ASRR  E +I   RVKVNG    + +  VN +  D I +DG  L K  
Sbjct: 242 ERLSKVLAAAGVASRRGSEDIIFAGRVKVNGKVCTVPQTPVNPLK-DTIFLDGRSLPKKP 300

Query: 72  RTRLWL-YHKPIGLVTTHSD--PDGRSTVFDNLPSIF---------SRVISVGRLDINTE 119
             + +   +KP G + + +   P    ++ ++   I+          R+ +VGRLD+ T 
Sbjct: 301 PPKFYFALNKPKGYICSSAKDAPKPALSLLEDYWKIWDKKNPGVSRPRLFTVGRLDVATS 360

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL+TNDG  A+ +  PS+   + Y      +V + +L L+  G  +Q +     +V L
Sbjct: 361 GLLLITNDGDFAQRVSHPSSGLTKEYIATVTERVTKRQLQLIAGGTKVQDVHCVPTEVEL 420

Query: 180 DTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              +  +A   + + + EG+NRE++++      +V  L R+  G   L   L+    EV
Sbjct: 421 LPPEPGDARNRIRIVVCEGRNREVRELVANAGLEVLALKRVRIGGLSLSRKLSPGKFEV 479


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 59/175 (33%), Positives = 92/175 (52%), Gaps = 20/175 (11%)

Query: 84  LVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           ++T  S  +GR T+ D  ++P ++     VGRLD ++EGLLLLT+DG LA  L  P    
Sbjct: 1   MLTQFSGGEGRHTLKDYIDIPGVYP----VGRLDRDSEGLLLLTDDGALAHRLTDPRFAH 56

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDM---QVTLDTQKG-SNA 187
            R Y V+  G  D + L  L  G+ IQG          I   D+    V +  +K    +
Sbjct: 57  PRTYWVQVEGTPDGEALGRLAAGVEIQGIRTRPATAVAIAEPDLPERPVPIRVRKSIPTS 116

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+++++     +   RL+R++ G   LG L  G  RE+S++ LR
Sbjct: 117 WIALTLTEGRNRQVRRMTAAVGYATLRLVRVAIGALSLGDLAPGRWRELSERELR 171


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/227 (31%), Positives = 116/227 (51%), Gaps = 13/227 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE ++ I Q RV VNG L E   V V  +D + VDG  L KA   
Sbjct: 5   KRLNKFISETGFCSRREADKYIEQGRVTVNGELPE-MGVKVAQSDVVLVDGKQL-KAPPK 62

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R+++ Y+KP+G+  T ++   +S +    N P    R+  +GRLD  +EGL+ LTN+G +
Sbjct: 63  RVYIAYNKPVGITCT-TERKIQSNIVKAVNYP---ERIFPIGRLDRPSEGLIFLTNEGDI 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +++  +N +  GI I        +V   TQ G+  +  
Sbjct: 119 VNKILRAGNNHEKEYVVTVDKPLNRQFVNKMANGIPILDTVTKKCKV---TQTGAQQFSI 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E+  ++V  L R+      L  L  G  R +S
Sbjct: 176 I-LTQGLNRQIRRMCEYLGYEVVTLKRVRIMNVTLKGLKVGQWRHLS 221


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/224 (29%), Positives = 110/224 (49%), Gaps = 21/224 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---VMSTDHIEVDGVPLR 68
           T  R++K IA AGI SR++  R+I +  V VN     R A +   V   D + V+G  ++
Sbjct: 3   TKIRLAKYIAHAGICSRKQASRLIDEGVVIVNN----RPANHIDHVDENDRVIVNGHAIK 58

Query: 69  KAERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                  + YHKP+G+     H DP   S++  +LP + +RV  +GRLD ++ GL++LTN
Sbjct: 59  GPADLVYFAYHKPVGIDCKLNHHDP---SSLIHHLPQL-TRVYPIGRLDKDSRGLIILTN 114

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKG 184
           DG     L  P     + Y V  +  +D      +  G+ +      D Q+T   +  K 
Sbjct: 115 DGDFCNQLIHPDFHQPKRYLVTVNKPLDAHFCEKMAAGVPV------DKQITRPCEVVKI 168

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           ++   ++ L++G NR+I+K+  +  + V  L R+      L  L
Sbjct: 169 ASNQFSIVLKQGLNRQIRKMAHYCGYTVIDLYRVQISELLLDNL 212


>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 = 87.8 bits (216), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 123/243 (50%), Gaps = 10/243 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ E     ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG 
Sbjct: 4   LIYEKEQNMKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDDDVVTIDGQ 62

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLL 123
            + K E+ ++++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+L
Sbjct: 63  VIAKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLIL 119

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG +A  +     +  + Y V          ++ +  G+ I+    G  +    T+ 
Sbjct: 120 LTNDGAIANQILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKD---GMTKPCKVTRV 176

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G + +  V L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L  
Sbjct: 177 GQSTFRIV-LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELHELEVGKWRSVTAEELEI 235

Query: 244 QLG 246
            +G
Sbjct: 236 LIG 238


>gi|218192109|gb|EEC74536.1| hypothetical protein OsI_10056 [Oryza sativa Indica Group]
          Length = 279

 Score = 87.8 bits (216), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/210 (29%), Positives = 107/210 (50%), Gaps = 13/210 (6%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWL-YHKPIGLVT 86
           R  E +I Q +V VNG +       V +S D I V+G  + K    +L+   +KP G + 
Sbjct: 46  RTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRISKKLPPKLYFAVNKPKGYIC 105

Query: 87  THSDPDGRSTVFDNL--------PSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +  +     ++FD+         P +   R+ +VGRLD+ T GL+++TNDG  A+ L  P
Sbjct: 106 SCGERKSIISLFDDYLKGWNKIQPGVPKPRLFTVGRLDVATSGLIIITNDGEFAQKLSHP 165

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-AWVTVGLRE 195
           S+  ++ Y V   G V ++ L  + +G  I G+ C  D+   LD Q  +    + + + E
Sbjct: 166 SSNIMKEYVVTIDGPVHRNHLIAISEGTKIDGVKCIPDLVEPLDVQSNTKRTRIRIAVHE 225

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G+N E++++ +    +V  L R+  G F+L
Sbjct: 226 GRNHEVRELVQNAGLEVYALKRVRIGRFRL 255


>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 = 87.8 bits (216), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/238 (31%), Positives = 126/238 (52%), Gaps = 17/238 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ KVI+  G  SR++V+  + +  ++V+G++++   ++V      I+++G  +   + 
Sbjct: 2   ERLDKVISNLGYGSRKDVKAFVKKGLIEVDGVIVKDNGLSVDPEKSVIKINGEEVFYRKY 61

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDG 128
             L + +KP G+++ TH + D   TV D L     +F     VGRLD +T GLLLLTNDG
Sbjct: 62  IYLMM-NKPAGVISATHDNRD--ETVIDLLYVDHQVFEP-FPVGRLDKDTVGLLLLTNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKG 184
            L   L  P     +VY  +   +VD+  +   K GI +    Y  M+  L+    +++G
Sbjct: 118 ELNHRLISPKWHVDKVYYAKIDKKVDEKDIQAFKSGITLDD-GYKCMEAKLEIISASEEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           S   VT+  +EGK  ++K++FE    KV  L R  +G   L T L  G  RE+S + L
Sbjct: 177 SEIRVTI--QEGKFHQVKRMFEAVGKKVEYLKREEFGGLSLDTDLEEGEYRELSDEEL 232


>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 = 87.8 bits (216), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 111/230 (48%), Gaps = 11/230 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T  R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG   R+ 
Sbjct: 9   TKVRLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDG---RRV 65

Query: 71  ERTR--LWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             T+   ++ HKP+G L ++     G   V D    +  RV +VGRLD  T GL+L+TND
Sbjct: 66  GMTKKVYFMVHKPLGYLCSSERKFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTND 125

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  +  +  PS    + Y ++    V    L  L  G +I G     + V    +K    
Sbjct: 126 GEFSNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMGGTIIDGKRVRPVSV----EKIRRG 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + + EGK  EI+   E     +  L RI  G F LG L  G  RE++
Sbjct: 182 TIKIIVNEGKKHEIRLFAEAAGLPILELSRIRIGSFVLGGLRYGEYRELT 231


>gi|150391402|ref|YP_001321451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149951264|gb|ABR49792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 243

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 78/239 (32%), Positives = 119/239 (49%), Gaps = 18/239 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K++A  G  SR ++ R+  Q  V VNG      AV   S+ H+E +   +   E  
Sbjct: 5   QRLDKILANLGHGSRSDIRRLCRQGVVTVNG------AVVKSSSQHVEPENDKITVGEEE 58

Query: 74  ---RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLT 125
              R ++Y   +KP  +++   D   + TV D L S +    V  VGRLD +TEGLL+LT
Sbjct: 59  IYYREFVYIMMNKPQDVISATEDFKEK-TVVDLLESKYQAFDVFPVGRLDKDTEGLLMLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P     + Y  +  G V    +   +KGI I+      M   L   K  
Sbjct: 118 NDGKLAHQLLSPKKHVPKTYYAKIEGVVTDADVEAFEKGIFIEE-NLQTMPSQLKILKAD 176

Query: 186 N-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
             + V V + EGK  ++K++F+  + +V  L R+S G   L  +L  G+ RE+S++ L+
Sbjct: 177 EISEVEVTIYEGKYHQVKRMFQATDKEVVYLKRLSMGSLMLDNSLDLGTYRELSEEELQ 235


>gi|291522303|emb|CBK80596.1| ribosomal large subunit pseudouridine synthase F [Coprococcus catus
           GD/7]
          Length = 261

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 131/262 (50%), Gaps = 23/262 (8%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+I+ EN   +  R+++ ++ AG  SRRE +R+I   RV V+G   E     V     ++
Sbjct: 6   KDILHENEDKSDVRLNRFLSDAGFCSRREADRLIEAGRVTVDGTKAE-LGTRVRPGQVVK 64

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V    +R+ +R  L  ++KP G+V T      ++ + D +     R+  +GRLD ++EGL
Sbjct: 65  VGSKVVRQNDRMVLIAFNKPRGIVCTTDRVREKNNIIDYI-HYPERIYPIGRLDKDSEGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +LLTNDG +   +   S    + Y VR + ++  + +  + KG+ I           LDT
Sbjct: 124 ILLTNDGTIVNHILKASQYHEKEYIVRVNKKITDEFIQGMSKGVPI-----------LDT 172

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  ++  +   ++ L +G NR+I+ +   F++ V +L R+     +LG+L  G  R
Sbjct: 173 VTRPCTLRRIDDYTFSIILTQGLNRQIRYMCRHFDYHVTKLKRVRIMNIRLGSLPVGKWR 232

Query: 235 EVSKKILREQLGPHLLEEAQVN 256
           +V+ + L EQL    +   + N
Sbjct: 233 DVTAEEL-EQLKRQFIANDRRN 253


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/268 (27%), Positives = 133/268 (49%), Gaps = 29/268 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---E 71
           R++K I+ +G  SRRE +++IA  RVK+NG   E     V S D + VDG  +  +   +
Sbjct: 8   RLNKFISESGHCSRREADKLIASNRVKINGTRPE-LGTKVESGDVVTVDGQEIMGSAPGK 66

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R+++ Y+KP+G+  T ++   +  + D +     R+  +GRLD  +EGL+LLT+DG +
Sbjct: 67  SDRVYIAYNKPVGITCT-TERSVQGNIVDAIDH-HQRIFPIGRLDKPSEGLILLTSDGDI 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  + +     +  GI I        +V++  +   N +  
Sbjct: 125 VNKILRAENAHEKEYLVTVNKSIGKGFSEKMAGGIPILNTVTKPCKVSVVRR---NVFKI 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L EG NR+I+++ EF +++V +L+R+      LG L  G  R ++++           
Sbjct: 182 I-LTEGLNRQIRRMCEFLDYEVTQLVRLRIMNVHLGKLKVGQWRNLTEQ----------- 229

Query: 251 EEAQVNL-------DAPIYSSETLVRDR 271
           E AQ+N+         P  SS++  + R
Sbjct: 230 EMAQLNIAISGSTGSPPKKSSQSAAKKR 257


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/217 (33%), Positives = 115/217 (52%), Gaps = 11/217 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V ++G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMIDGTVEFRQNRNVDSLLHQIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPEKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLDTQKGSNAW 188
             + LP  +  + Y+V  + +V    +   + GIV      C   D+++    +  S   
Sbjct: 119 YEMLLPEKKVSKTYQVVVNERVTPADVTAFENGIVFADGYQCKPADLKILKADKHQSTVL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +T+  +EGK  ++KK+F     KV  L R+S GP +L
Sbjct: 179 LTI--QEGKFHQVKKMFLAQGKKVTALKRLSMGPLEL 213


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 119/236 (50%), Gaps = 14/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +     + V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVCINGEMCTHGVL-VSDGDVVMIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP+G+  T +D      + DN+        R+  VGRLD  +EGL+LLTNDGG+
Sbjct: 61  VYIAFHKPVGITCTAADH-----IEDNIIDYIHYPERIFPVGRLDKASEGLILLTNDGGI 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +     +  + Y V          +N +  G+ I+       +VT    +   +   
Sbjct: 116 AHQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFR 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L +G NR+I+++   F + V +L R+     +L  L +G  R+++ + L   +G
Sbjct: 172 IVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNGLESGKWRDITAEELEILIG 227


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 119/233 (51%), Gaps = 18/233 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RKAE 71
           +R+SKV+A AG+ASRR  E +I   +V VNG +      +V    D I +DG P+ R+  
Sbjct: 20  ERLSKVMAAAGVASRRACEEIIFAGKVVVNGKVCRTPETHVDPLKDLIYIDGKPIPRRLP 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-RVISVGRLDINTE 119
              ++  +KP G + + +  D + TV+            N P +   R  +VGRLD+ T 
Sbjct: 80  PKMVFALYKPKGYICSDAK-DDKKTVYLLLEKYLKTWEKNNPGLTKPRFFTVGRLDVATT 138

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVT 178
           GL+ +TNDG  A+ +  PS+   + Y V    + V + +L  +  G  I G+    + V 
Sbjct: 139 GLIFVTNDGEFAQKVSHPSSGITKEYLVTVDNESVTKRQLKRIASGTEIDGVMCVPISVE 198

Query: 179 L-DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           L  ++ G S   + V + EG+N E++++ E    KV+ L R+  G  +L + L
Sbjct: 199 LVKSEPGDSRHRIRVVVTEGRNHEVRQLVESAFLKVHALKRVRVGGLRLPSKL 251


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 111/249 (44%), Gaps = 30/249 (12%)

Query: 11  FTPQ---------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           FTP+         R+SK +A  G+ SRRE +  I    V+VNG +++     V    +IE
Sbjct: 204 FTPKPVASQPDLPRLSKRMAELGLCSRREADEWIVNGWVRVNGQVVDELGSRVEPDANIE 263

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFSR--- 107
           V     +        L HKP+G V+  ++ DG                D +   F R   
Sbjct: 264 VSKEAEKHQSEIVTILLHKPVGYVSGQAE-DGYEPAVVLVHPDNHWAEDPVQKEFRRGFL 322

Query: 108 --VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 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 SLDGVQLKPAKVSWQNED----QLRFVLREGRKRQIRRMCELVGLHVVGLKRVRIGSVAL 438

Query: 226 GTLLAGSTR 234
           G L  G  R
Sbjct: 439 GKLPPGQWR 447


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 78/255 (30%), Positives = 129/255 (50%), Gaps = 28/255 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K+++  GI +RR+V+R+I   ++ VN I++     +V  S+D I VDG PL   E+
Sbjct: 8   ERLDKILSNNGIGTRRDVKRLIRSGKISVNRIIVREPEFHVDGSSDEILVDGKPL-TVEQ 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTN 126
              ++ +K  G V + +  D R TVF+ + S  +R      + +VGRLD +TEGLL++T+
Sbjct: 67  NAYFMMNKASGAVCS-TKSDRRKTVFEYIFSEDNRKYPGGNLSTVGRLDADTEGLLIITS 125

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKK---GIVI-------QGICYGDM 175
           DG L   +  P  +  + Y V     VD  +KL+  KK   G+ I       +  C   +
Sbjct: 126 DGNLIHRVTFPKYEVPKTYLVYLRDSVDDSEKLSYEKKLAAGVHIEAEGKDGEADCRPAV 185

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-T 227
                  Q    T +  +    + + EGK  E+K++F+    +V  L RI      L  T
Sbjct: 186 IEWKEKNQYHTKTSECPSEVCCLTVTEGKFHEVKRIFKALGNEVVYLKRIRINNLFLDET 245

Query: 228 LLAGSTREVSKKILR 242
           L  GS R ++K+ +R
Sbjct: 246 LKEGSYRPLTKEEIR 260


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 111/227 (48%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG   R+   T
Sbjct: 5   RLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDG---RRVGMT 61

Query: 74  R--LWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   ++ HKP+G L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  
Sbjct: 62  KKVYFMVHKPLGYLCSSERKFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDGEF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  PS    + Y ++    V    L  L +G VI G     + V    +K     + 
Sbjct: 122 SNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMEGTVIDGKRVRPVSV----EKIRRGTLK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGK  EI+   E     +  L RI  G F LG L  G  RE++
Sbjct: 178 IIVNEGKKHEIRLFAEAAGLSILELSRIRIGSFVLGGLRYGEYRELT 224


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 58/191 (30%), Positives = 93/191 (48%), Gaps = 20/191 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  L+HKP G+++  S  +G  T+ D +    + V  VGRLD ++EGL+LLTN G L   
Sbjct: 4   RYLLFHKPYGVLSQFSGGEGPPTLKDYI--TVADVYPVGRLDRDSEGLMLLTNHGELQHR 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P     R Y V+  G    + L  L  G+++QG C    QV +   +          
Sbjct: 62  LSDPRFAHPRTYWVQVEGCPTPEALEQLATGVMVQGKCTRPAQVEVLAAEPDLPPRDPPI 121

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE--- 235
                    W+++ LREG+NR+++++     +   RL+R++     LG+L  G  R+   
Sbjct: 122 RFRLSIPTTWLSLTLREGRNRQVRRMTAAVGFPTLRLVRVAIAHLNLGSLAPGQWRDLTP 181

Query: 236 VSKKILREQLG 246
           V ++ L  Q G
Sbjct: 182 VEQQTLLRQTG 192


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 116/236 (49%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR+ E  R
Sbjct: 4   RLNKYIAETGSCSRREADRLIGERRVTVNGMPAGTGAV-VGEEDTVLVDGQPLRRREAKR 62

Query: 75  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKDSEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 111/249 (44%), Gaps = 30/249 (12%)

Query: 11  FTPQ---------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           FTP+         R+SK +A  G+ SRRE +  I    V+VNG +++     V    +IE
Sbjct: 174 FTPKPVASQPDLPRLSKRMAELGLCSRREADEWIVNGWVRVNGQVVDELGSRVEPDANIE 233

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFSR--- 107
           V     +        L HKP+G V+  ++ DG                D +   F R   
Sbjct: 234 VSKEAEKHQSEIVTILLHKPVGYVSGQAE-DGYEPAVVLVHPDNHWAEDPVQKEFRRGFL 292

Query: 108 --VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 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 SLDGVQLKPAKVSWQNED----QLRFVLREGRKRQIRRMCELVGLHVVGLKRVRIGSVAL 408

Query: 226 GTLLAGSTR 234
           G L  G  R
Sbjct: 409 GKLPPGQWR 417


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/222 (33%), Positives = 111/222 (50%), Gaps = 8/222 (3%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+++  M+AQ RV+V+GI+ +     V    H+ VD   L K  R    + +KP+G+V+ 
Sbjct: 20  RKDIRLMLAQNRVRVDGIVAKDIQQLVDEFSHVSVDDAVL-KNNRPSYVMLNKPVGVVSA 78

Query: 88  HSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
             D D   TV D L  P+  S +  VGRLD+NT GL+LLTNDG  +R L  P ++  + Y
Sbjct: 79  TKD-DKHKTVIDLLDHPAK-SELHIVGRLDLNTSGLMLLTNDGRWSRKLMSPESKVEKRY 136

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           RV     +  + ++   KG   +          L+      A VT  L EGK  +IK++F
Sbjct: 137 RVTLQNPLSTEYIDAFAKGFYFEFEDITTQAAKLEIISEHIAEVT--LTEGKYHQIKRMF 194

Query: 206 EFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
             F   V  L R S G   L   L  G +RE+S + + +  G
Sbjct: 195 GRFRNPVIGLHRYSVGELLLDPDLDEGGSRELSVEEVNDIFG 236


>gi|227872023|ref|ZP_03990406.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227842134|gb|EEJ52381.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 239

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 125/242 (51%), Gaps = 30/242 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K ++  G+ SR  ++R I +  VK+NG +++  ++ V      I     P+   E +
Sbjct: 2   RLDKYLSDMGVESRSVLKREIRKGLVKINGEIVKDPSMEVQPGNSEIVYKDEPIHYEEFS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDG 128
             ++ +KP+G++++  D   + TV D    +FS      +  VGRLD ++EGLLL+ NDG
Sbjct: 62  -YYMMNKPVGVLSSTED-RKQKTVLD----LFSDKHRKDLFPVGRLDKDSEGLLLIMNDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------D 180
            LA  L  P     + Y V   G++ +++L+ L+     QGI Y    + +         
Sbjct: 116 ALAHKLLSPKMHIEKKYLVEIPGKISEEELDRLR-----QGIQYDTDLIAMPAKARCLSS 170

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFF--NWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           T++GS   V +   EGK  +IKK+F     ++ V +L R+S GP  L   LA G  R++S
Sbjct: 171 TEEGSRVEVII--MEGKFHQIKKMFLALSTDYVVTKLQRLSMGPLHLDPALAPGEYRKLS 228

Query: 238 KK 239
           ++
Sbjct: 229 EE 230


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 114/230 (49%), Gaps = 12/230 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ +++   G+ +R+E++++I  ++V VNG L     +++    DHIEV G  +   E  
Sbjct: 8   RLDRLLNHMGLGTRKEIKKLIKAKQVMVNGELAMDPGLHIFPQRDHIEVQGEVIEYREYI 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP  +++   D   +  V D L   +       VGRLD +TEGLLLLTN+G LA
Sbjct: 68  YLML-NKPQDVLSATEDASDK-VVIDLLDPTYHSFNPFPVGRLDKDTEGLLLLTNNGKLA 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAW 188
             L  P     + Y     G V ++ +    +G+ +        G +++    +    + 
Sbjct: 126 HQLLSPKKHVPKTYYALVQGLVTEEDVAAFARGVELDDGYRTLPGQLKI---IRSAPQSE 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           + + + EGK  ++K++FE    +V  L R+S GP  L   L  G  RE++
Sbjct: 183 IELTIYEGKYHQVKRMFEAVGKRVIYLKRLSMGPLVLDNNLKPGEYRELT 232


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/264 (28%), Positives = 129/264 (48%), Gaps = 15/264 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--V 65
           N +  R++K I+ +GI SRR+ +R I Q  V +NG   +RA+V   V++ D + V+G  +
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVFING---KRASVGDQVVAGDTVRVNGQII 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             + A+     + +KP+G+V+T    +  + V  +  S   R+  +GRLD +++GL+ LT
Sbjct: 60  EPQDADDFVFIVLNKPVGIVSTTESSEKNNIV--DFVSHGVRIFPIGRLDKDSQGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G L   +        + Y V  +  +  D +  L  G+ I G       VT    K S
Sbjct: 118 NNGDLVNKVLRAGNNHEKEYLVTVNKPITDDFIAGLAGGVPILGTMTKKCPVT----KVS 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++ K L   L
Sbjct: 174 PTVFNITLVQGLNRQIRRMCEYFGYEVVKLERTRIMNVSLKGIPVGEWRDLTPKELSVLL 233

Query: 246 GPHLLEEAQVNLDAPIYSSETLVR 269
               +E++     AP   S    R
Sbjct: 234 --KSIEDSSSEASAPAKKSRNAPR 255


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 78/229 (34%), Positives = 117/229 (51%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V ++G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMIDGTVEFRQNRNVDSLLHRIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             + LP  +  + Y+   + +V    +   +KGIV     Y      L   K      TV
Sbjct: 119 YEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFAD-GYQCQPANLKILKADKHQSTV 177

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            L  +EGK  ++KK+F     KV  L R+S GP +L   LA G  R ++
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEHLAVGEYRSLT 226


>gi|324989740|gb|EGC21683.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 242

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 110/222 (49%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V++++ +  V VNG   +     +  + D I V G  L   E+ 
Sbjct: 2   RLDKFLTENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDEAADDIVVSGQRL-IYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++           + LD +K ++  
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEAS-L 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPALA 220


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 115/232 (49%), Gaps = 16/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++G  ++    +V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDPKFHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY----GDMQVTLDTQKGSN 186
              L  P     + Y     G V ++ +    KG++++   Y    GD+ +    +    
Sbjct: 119 THQLLSPKKHVPKKYYAHVSGVVTEEDVKEFAKGVILED-GYETKPGDLTI---LKSDDI 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           + + + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 175 SEIELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 226


>gi|31747805|gb|AAO38400.1| Lfe193p2 [Leptospirillum ferrooxidans]
          Length = 164

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 52/132 (39%), Positives = 78/132 (59%), Gaps = 2/132 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  GI SRR  E +IA   V VNG +       V    D + V+G  L + + T
Sbjct: 29  RLQKLLAHRGITSRRNAEELIAGGLVTVNGKVETTPGTKVDPQRDVVVVEGRMLPREKET 88

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L+L++KP G+++   DPDG+ T+ D  P+I S ++ +GRLD  TEG+LLLTN+G L++ 
Sbjct: 89  FLFLFYKPKGVISAVFDPDGKPTLKDFFPNI-SPLLHIGRLDFQTEGVLLLTNNGDLSQR 147

Query: 134 LELPSTQWLRVY 145
           +  P     R Y
Sbjct: 148 ILHPRFAIPRTY 159


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 108/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  AGI SR +V++++ +++V VNG +       +    D I   G  L   E+ 
Sbjct: 2   RLDKFLVGAGIGSRNDVKQLLKKKQVTVNGEIETSPKTQIDEKIDKIVCQGENLS-YEKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D +   TV D L        V  VGRLDI+T GLL LTN+G LA
Sbjct: 61  VYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLFLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY-GDMQVTLDTQKGSNAWV 189
             +  P     ++YR +  G +  + +    KGI ++   C    +++    +    + V
Sbjct: 120 HAMLSPKKHVDKLYRAKVAGIMTAEDVEHFAKGIELKDFTCQPAQLEILEIDEAAKTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + ++EGK  ++K++      +V  L R+S GP QL
Sbjct: 180 AITIKEGKFHQVKRMVLACGKEVTDLERLSMGPLQL 215


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 111/227 (48%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG   R+   T
Sbjct: 5   RLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDG---RRVGMT 61

Query: 74  R--LWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   ++ HKP+G L ++     G   V D    +  RV +VGRLD  T GL+L+TNDG  
Sbjct: 62  KKVYFMVHKPLGYLCSSERTFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDGEF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  PS    + Y ++    V    L  L +G VI G     + V    +K     + 
Sbjct: 122 SNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMEGTVIDGKRVRPVSV----EKIRRGTLK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + EGK  EI+   E     +  L RI  G F LG L  G  RE++
Sbjct: 178 IIVNEGKKHEIRLFAEAAGLPILELSRIRIGSFVLGGLRYGEYRELT 224


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/216 (31%), Positives = 108/216 (50%), Gaps = 12/216 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A     SR+EV ++I  +RV +NG I  ++     +  D + VDG   +    T
Sbjct: 2   RLDKLLANKAFGSRKEVHQIIKDRRVTINGEITTKKDIHIDIDIDTVAVDG---QTVNTT 58

Query: 74  RLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           +L+   +HKP G VT   D      V D LP  + +  V+ VGRLD +TEGLLLLTNDG 
Sbjct: 59  QLYYVKFHKPKGYVTAVEDST-HPVVMDLLPPEYLKMGVVPVGRLDKDTEGLLLLTNDGV 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +        +VY V F G++ ++ +  +K+GIV+     G        +  SN   
Sbjct: 118 WGHSIINGHKHVPKVYYVEFEGELSEEGIQRIKEGIVLGD---GTQCKPALIELLSNQSA 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           T+ + EGK  ++K++       V  L R++ G   L
Sbjct: 175 TITIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHVDL 210


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 91/179 (50%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P+ +  +VY V+  G  D D L  LK+G+ ++          L              
Sbjct: 88  LTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWPRHPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEWKEIT 206


>gi|170023963|ref|YP_001720468.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|169750497|gb|ACA68015.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
          Length = 208

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 91/179 (50%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P+ +  +VY V+  G  D D L  LK+G+ ++          L              
Sbjct: 88  LTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWPRHPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEWKEIT 206


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVTRVDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITTEELELLIG 227


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 59/208 (28%), Positives = 103/208 (49%), Gaps = 3/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A +G+ SRR+ +  I+   V VNG  +      V  TD ++ DG  L   E+  
Sbjct: 46  RLNKYVANSGVCSRRDADIYISAGNVTVNGKPITEMGYKVRKTDEVKFDGR-LLNPEKKE 104

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP    TT  D  G+  V   + S   S+++ V ++D N  GLLL TNDG L R 
Sbjct: 105 YVLLNKPKDFSTTIRDERGKRNVNGLISSASNSKLLPVDKMDKNATGLLLFTNDGDLTRR 164

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L+ P     ++Y V  +  +    L  +++G+V+        +V+          V + +
Sbjct: 165 LKSPKNGLRKIYHVVLNRDLRSADLKKIQEGVVLDEKPVRVQEVSF-IDNAPKREVGIEI 223

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
              KN+ ++++FE   ++V ++ R+SY 
Sbjct: 224 YSSKNKVVERIFEELEYEVAKIDRVSYA 251


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 89/177 (50%), Gaps = 16/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 68  LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILTNDGILQARLTQ 125

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L  L+ G+ ++       +V + ++              
Sbjct: 126 PQSKAPKTYWVQVEGVPQESDLEALRHGVTLKDGPTLPAKVEIMSEPELWPRNPPVRFRA 185

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                W+ + L EG+NR+++++     +   RLIR S G + LG L  G  REV+ K
Sbjct: 186 AIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPGEWREVTLK 242


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 122/233 (52%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + + ++ V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 60/224 (26%), Positives = 114/224 (50%), Gaps = 8/224 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE ++++ Q R+ +NG + E     V + D I+VDG  + + +   
Sbjct: 6   RINKYLSEVGFCSRREADKILEQGRITINGKIPE-LGTKVSAEDEIKVDGKLITEPKEEN 64

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++ ++KP+G+V T      ++ + D +     R+  +GRLD  +EGL+LLT+DG +   
Sbjct: 65  VYIAFNKPVGIVCTTDTKREKNNIIDYI-KYPKRIFPIGRLDKPSEGLILLTSDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +    L  ++ G+ I G      +V    ++       + L
Sbjct: 124 ILRARNNHEKEYIVRVDKPITNKFLEQMRAGVPILGTVTRKCEV----EQLDKMQFRIVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +G NR+I+++ E+  ++V +L RI      L  L  G  RE++
Sbjct: 180 TQGLNRQIRRMCEYLGYEVKKLKRIRIMNIHLD-LPIGKWRELT 222


>gi|300072082|gb|ADJ61482.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 242

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 114/238 (47%), Gaps = 21/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +G+ SR EV+ ++ + RV V G +       V  ++  +  DG  L   E  
Sbjct: 2   RLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQEYY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
             +L +KP G+V+   D      VF  +  + S       +  VGRLD NTEGLL+LTND
Sbjct: 62  -YYLLNKPQGVVSATKD-----NVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLD 180
           G L   L  P     + Y  R  G+V  + +N   +G+ ++       G  + +     D
Sbjct: 116 GALGHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGD 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +Q G  + + V + EGK  ++K++FE     V  L RI  G   L + LA G+ R ++
Sbjct: 176 SQSGWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLT 233


>gi|327482354|gb|AEA85664.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 177

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 95/180 (52%), Gaps = 20/180 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +KP  ++T  +D DGR+T+  F ++P ++      GRLD ++EGLLLLTNDG L   +
Sbjct: 2   LLNKPFDVLTQFADADGRATLKDFVSVPGVYP----AGRLDRDSEGLLLLTNDGRLQARI 57

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT------------ 181
             P  +  + Y V+  G+VD+ +L  L++G+ +  G+        LD             
Sbjct: 58  ADPKHKLPKTYWVQVEGEVDETQLERLRQGVELNDGMTLPAEARQLDEPELWPRNPPVRF 117

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +    +W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  REV  ++
Sbjct: 118 RKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWALDGLQPGEWREVPAQL 177


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 107/226 (47%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R I  +++ +NG ++   A  V+  D +  DG PL +    R
Sbjct: 2   RLDKFISQQLEISRAISAREIRAKKITINGEVVRDTAYKVLPDDDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + +F     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILFFIEEPMVGKLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VYRV     +D   +     GI +          TL+      A +T+   
Sbjct: 122 TSPRHHCEKVYRVGVESPIDPSLVEKFAAGIQLHNEKDLTKPATLEIVGPQEALLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  RE++++
Sbjct: 180 EGRYHQVKRMFAASGNHVVTLHRERIGDIVLDADLAEGEYRELTEE 225


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +     + V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGTL-VSDGDRVTIDGKVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G++ T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGIICTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 15/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +V+ +AG+ SR +V+R++   +V+V+G +  R   NV      I+V G  L +   T
Sbjct: 2   RLDQVMNQAGLGSRNQVKRLLKSCQVQVDGQVERRPNRNVDPGLQEIKVQGRILTQPAET 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
             WL HKP G++T  +D D  +TV D L      P ++     VGRLD +T GL+ LT +
Sbjct: 62  -YWLLHKPQGVLTAVTD-DRFTTVIDCLAPQDQAPGLYP----VGRLDRSTTGLVFLTTN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  P     + Y+V  +G + QD +    +GI+I Q        + ++      
Sbjct: 116 GPLGYRMLHPQYHVEKEYQVVVNGPLTQDHVASFAQGILIDQNRPCAPAHLVIEASGPQE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           +   + +REGK  ++KK+F     KV +L R+  G   L   LA G+ R +  + L
Sbjct: 176 SRARLTIREGKFHQVKKMFLSVGVKVTQLHRLRMGHLVLDQDLAPGAYRPLKPEEL 231


>gi|325473314|gb|EGC76509.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 245

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 129/239 (53%), Gaps = 23/239 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAER 72
           R+ +++A +G+ SR +V++MI ++   V+G+ +   +  ++ TD   I +DG PL    R
Sbjct: 4   RLDRILALSGLGSRSDVKKMIRKKNCCVDGVRIVSPSF-ILDTDLNKITIDGEPL--VLR 60

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           T ++L ++KP G VT+ SDP  + TV D + + F R  +  +GRLDI+TEGLL++T+DG 
Sbjct: 61  TNVYLMFNKPQGCVTSTSDPVHK-TVMDYIKAPFDRMTLFPIGRLDIDTEGLLIITDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-VDQDKLNL---LKKGIVIQGICYGDMQVTLDTQKGS 185
           +   +  P +  ++ Y +    +  D++  N     +KGI+++    G   +    +K  
Sbjct: 120 ITHKITSPKSGTVKTYYLELSREPSDEEFTNYCEEFEKGIMLKN---GYKCLPAKFEKCG 176

Query: 186 N------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           N      +   + + EGK  ++KK+      ++  L RI+ G   L  TL  G  RE+S
Sbjct: 177 NKTGSFRSGFLMHITEGKFHQVKKMCLSAGNELCYLRRIAVGSIVLDETLKTGEYRELS 235


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 108/216 (50%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  L   E+ 
Sbjct: 2   RLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGT-LVSYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLL+TN+G LA
Sbjct: 61  VYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CY-GDMQVTLDTQKGSNAWV 189
             +  P     + Y  +  G + +D +    KGI+++   C    +++    Q    + V
Sbjct: 120 HKMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + ++EGK  ++K++      +V  L R+  G  QL
Sbjct: 180 KITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQL 215


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 114/239 (47%), Gaps = 20/239 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A   + SRRE +  I Q  VKVNG++       V+ TD I++D +  ++ 
Sbjct: 4   IQPIRLSKRMAELKMCSRREADHYIEQGWVKVNGVVAVLGQ-KVVPTDRIDLDKIAHQQQ 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV----FDNL-----------PSIFSRVISVGRLD 115
            +    L +KP+G V+   + D R+ +     DN            P     +   GRLD
Sbjct: 63  AQRVTILLNKPVGFVSGQPEKDYRAAIELIAADNHWNGDTSKIPFHPKQLKGLAPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L    +   + Y VR  G + ++ L LL  G+ + G      
Sbjct: 123 IDSVGLLVLTQDGRIAKQLIGEHSDSEKEYLVRVKGNLIENGLALLNHGLSLDGEKLRPA 182

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 183 KVEWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRIGKVKLGALPVGQWR 237


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 57/186 (30%), Positives = 93/186 (50%), Gaps = 17/186 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL  AER ++ L++KP   ++  +D DGR T+ D +      V + GRLD ++EGLL+LT
Sbjct: 61  PLSPAER-KVVLFNKPYDTLSQFTDGDGRKTLADYI--QIKDVYAAGRLDRDSEGLLILT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +   
Sbjct: 118 NDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTL 177

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + L EG+NR+++++     +   RLIR S G + LG L  G
Sbjct: 178 WPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPG 237

Query: 232 STREVS 237
             REV+
Sbjct: 238 EWREVT 243


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 61/210 (29%), Positives = 107/210 (50%), Gaps = 13/210 (6%)

Query: 13  PQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           PQ  R++K ++ AG  SRR  +++I Q+RV +NG++       +   D + VDG  +   
Sbjct: 4   PQLTRINKFLSEAGYCSRRAADKLIEQRRVTINGVV-PAMGTKIAPGDEVRVDGELISDP 62

Query: 71  ERTRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   ++L ++KPIG+V T      +  + D  N PS   R+  +GRLD  +EGL+ LT+D
Sbjct: 63  KEKPVYLAFNKPIGIVCTTDTKVEKDNIIDYINYPS---RIFPIGRLDKPSEGLIFLTSD 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  +  D +  +  GI I G      +V   T+     
Sbjct: 120 GDIVNKILRARNNHEKEYEVTVNRPITSDFIQKMGNGIPILGTLTRKCKVEQLTKYTFKI 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
            +T GL    NR+I+++ E+ +++V +L R
Sbjct: 180 ILTQGL----NRQIRRMCEYLDYRVVKLKR 205


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 114/238 (47%), Gaps = 21/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +G+ SR EV+ ++ + RV V G +       V  ++  +  DG  L   E  
Sbjct: 88  RLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQEYY 147

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
             +L +KP G+V+   D      VF  +  + S       +  VGRLD NTEGLL+LTND
Sbjct: 148 -YYLLNKPQGVVSATKD-----NVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILTND 201

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLD 180
           G L   L  P     + Y  R  G+V  + +N   +G+ ++       G  + +     D
Sbjct: 202 GALGHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGD 261

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +Q G  + + V + EGK  ++K++FE     V  L RI  G   L + LA G+ R ++
Sbjct: 262 SQSGWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLT 319


>gi|324996011|gb|EGC27922.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK678]
          Length = 242

 Score = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 108/222 (48%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   E+ 
Sbjct: 2   RLDKFLAENGLGSRAQVKQILKKGLVLVNGRAEKSPKTQIDERADEIVVSGQRL-TYEKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATED-DRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++YR +  G ++Q  +     GI ++       Q   + LD  K   + 
Sbjct: 120 HAMLSPKKHVEKIYRAQVAGLMEQADVERFAAGIELKDFTCQPAQLKILELDEAK-ETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V + L EGK  ++K++      +V  L R++ GP Q    LA
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQSDPALA 220


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 116/243 (47%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q RV VNG    + AV    V+  D IE+D     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGRVTVNG----KTAVLGQKVLPADRIELDKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     + S GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFD--PKHKIGLASAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +AR L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIARQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             ++ +KP G+++   D   R TV D L   ++R   V  VGRLDI+T GLLLLTNDG L
Sbjct: 62  -YYMMNKPQGVISATEDTKHR-TVLDLLDD-YARAKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNA 187
           A  L  P     + Y  +  G + Q+ ++   KGI ++       +   V++D +K + +
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTQEDVDAFAKGIPLKDFTCQPARLELVSVDPEK-NQS 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L
Sbjct: 178 LVRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEEL 232


>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 = 87.0 bits (214), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 126/236 (53%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +   G  +R  V+++I  ++VKV+G  I+    AVN + T  +EV+G  +   E 
Sbjct: 7   RLDKYLVHVGYGTRSTVQKIIRGKKVKVDGQVIIKPETAVNSL-TSVVEVNGERMDYQEF 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS-TVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGG 129
               L +KP G +T  +  DGR  TV D L        V  VGRLD +TEGLL+LTNDG 
Sbjct: 66  YHFIL-NKPRGYIT--ATEDGRDQTVLDLLEERDQNKEVFPVGRLDKDTEGLLILTNDGK 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICY--GDMQVTLDTQKGSN 186
           +A  L  P     +VY  R  G++ ++ + +  +GI +  G  Y  G +++ + + + S 
Sbjct: 123 MAHGLLSPKRHVDKVYYARVAGKMTEEDIKMFAEGIALTDGTKYAPGKLEI-IRSDEESE 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            +VT+   EGK  ++K++ +    +V  L RI  G  +L   L+ G+ R ++K+ L
Sbjct: 182 IYVTI--HEGKFHQVKRMVQAVGKEVVYLKRIKMGGLELPEDLSLGTYRTLTKEEL 235


>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 = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 118/239 (49%), Gaps = 16/239 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G  SRRE +R+I ++RV VNG+     AV V + D + VDG PLR  E  +
Sbjct: 17  RLNKYIAESGFCSRREADRLIGERRVTVNGVPAGTGAV-VGAEDTVLVDGQPLRIREAKK 75

Query: 75  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+T+
Sbjct: 76  LGGRKHVYIALNKPVGITCTTESSVKGNIVKFVGHE---QRIFPIGRLDKDSEGLILMTS 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 133 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 188

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 189 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 247


>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 = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 112/225 (49%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ IA     SRRE + +I    V VNG  +      V   D + V G  + ++    
Sbjct: 2   RLNRFIAFNSNYSRREADELIFNGHVTVNGKPVLVPGYEVKDDDKVSVLGKVISRSNFLY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +  Y KP G +T++ DP GR  + D      +++   GRLD ++EGL+  +NDG +   +
Sbjct: 62  VKFY-KPRGFLTSYGDPYGRKNLDDFEFFKKTKLAYSGRLDNDSEGLIFFSNDGSIIHRM 120

Query: 135 ELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           + P     + Y V     + D++KL  ++ G+ I G  +    V    + G N +  + +
Sbjct: 121 QTPKYDVEKEYIVYTKRPLGDEEKL-AMENGLEIDGYKFKKCSVE---KIGRNKYRVI-I 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            EGK R+I+ +F+ FN +V RL+RI      LG L  G  + ++K
Sbjct: 176 TEGKKRQIRNMFKHFNIEVERLVRIRIANITLGELKPGDFKFLTK 220


>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 = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 106/216 (49%), Gaps = 4/216 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV + ++     +R++V  ++ ++RV+++G ++      V+    +EVD   L+  +  R
Sbjct: 2   RVDRFLSNLPRYNRKQVRLLLVEKRVRIDGKVVSDPHSEVLEFSRVEVDDEVLQPGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V+   DP+   TV D +       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLNKPQGCVSATRDPE-HPTVLDLIHEPDKDDLHIAGRLDFNTTGLMLITNDGSWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T+  +VY V    ++  +      +GI             L       A +++  
Sbjct: 121 LTQPQTKLPKVYYVETEQEIGPEYAIKFAEGIYFAFEDLTTQPAQLQVLGPRTARLSIV- 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            EG+  ++K++F  FN KV RL R S GP  L   L
Sbjct: 180 -EGRYHQVKRMFGHFNNKVLRLHRESMGPLALDHAL 214


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 103/216 (47%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D   R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYIMNKPKGVISATEDSKHR-TVLDLLDDLARTKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSN-AWV 189
             L  P     + Y  +  G + Q+ +    KGI ++   C       L    G + + V
Sbjct: 120 HALLSPKRHVDKTYLAQVKGIMSQEDVETFAKGISLKDFTCQPAKLEILSVDSGKDESQV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  ++K++  +   +V  L R++ G   L
Sbjct: 180 RVTIAEGKFHQVKRMVSYCGKEVVDLQRLTMGTLAL 215


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+ LTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLIFLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVTRVDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 109/226 (48%), Gaps = 11/226 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE ++ I Q RV VNG   E   V V +TD + VDG PL+   + 
Sbjct: 22  KRLNKFISETGFCSRREADKYIEQGRVSVNGNAPE-MGVKVAATDVVLVDGKPLKTPPKR 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               Y+KP+G+  T ++   +S +    N P    R+  +GRLD  +EGL+ LTN+G + 
Sbjct: 81  VYIAYNKPVGITCT-TERKIQSNIVKAVNYPD---RIFPIGRLDRPSEGLIFLTNEGDIV 136

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +++  ++ +  GI I        +VT    K     +T 
Sbjct: 137 NKILRAGNNHEKEYVVTVDKPLNRQFVSKMANGIPILDTVTKKCKVTQTAPKEFKIILTQ 196

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           GL    NR+I+++ E+  ++V  L R       L  L  G  R +S
Sbjct: 197 GL----NRQIRRMCEYLGYEVVTLKRTRIMNVTLKGLKVGQWRHLS 238


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLQVGKWRDITGEELELLIG 227


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 114/236 (48%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V+V+G+++       +    I ++     +     
Sbjct: 5   RISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARALPDQVITLERAAAARQTARV 64

Query: 75  LWLYHKPIGLVTTHSDP---------DGRS-TVFDNLPSIFSR-----VISVGRLDINTE 119
             L HKP+G V+  ++          D RS    D  P  F R     +   GRLDI+++
Sbjct: 65  TILLHKPVGYVSGQAEKGYTPAVALIDARSRYAGDRAPQRFERGQLQGLAVAGRLDIDSQ 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      QV  
Sbjct: 125 GLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPAQV-- 182

Query: 180 DTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +  NA  +   LREGK R+I+++ E    +V  L R+  G   LG L AG  R
Sbjct: 183 ---RWQNADQLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPAGQWR 235


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K I++ G  SRRE  R+IA  R+ +NG + E+ A  V   D + +DG  +P   +E 
Sbjct: 2   RINKYISQTGFCSRRETNRLIASGRITINGKVCEKGA-EVEPEDIVLIDGQEIPHNDSEP 60

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP+G+V T ++  +G    + N PS   R+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 61  VYLAL-NKPMGIVCTAAEEVEGNIIRYVNYPS---RIFAIGRLDKASEGLILLTNDGDIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  + +  + +G+ I  +     +V     + S A   +
Sbjct: 117 NKMMRSEHDHEKEYVVTVDRPVTDEFMRRMSQGVEILDVVTKPCEVF----RQSEAVFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G N +I+++ +   ++V +L RI      L  L  G  R + ++ L + L
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERIRIMNITLDQLERGKWRHLEERELHKLL 226


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGIKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|304403869|ref|ZP_07385531.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304346847|gb|EFM12679.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 260

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 118/243 (48%), Gaps = 29/243 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++A  G  +R E+++ + Q +V V+G +++ + + +   +        L       
Sbjct: 16  RLDKLLANMGYGTRSEIKKAVKQGKVTVDGRVVKDSGLQIKPNEQQVAFSGELVVYRDVV 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTNDGGLA 131
             + HKP G+V+   D   R     +L     R++    VGRLD +TEGLLLLTNDG LA
Sbjct: 76  YLMLHKPPGVVSATED--SRDETVIDLLDADDRILQPFPVGRLDKDTEGLLLLTNDGQLA 133

Query: 132 RVL-----ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
             L      +P T + RV      GQ D+++           G+   D  VT+       
Sbjct: 134 HDLLSPRKHVPKTYFARVLGEEPVGQADRERFA--------AGVELDDGYVTMPAELEVE 185

Query: 180 DTQKGSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
             ++  + WV+   + ++EGK  +IK++F+    +V  L R+S GP  L  TL  G+ RE
Sbjct: 186 QAEQSDDGWVSLIRITIQEGKFHQIKRMFQAVGKQVIYLKRLSMGPLHLDETLPIGAYRE 245

Query: 236 VSK 238
           +++
Sbjct: 246 LTE 248


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 119/231 (51%), Gaps = 13/231 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPL 67
           P+R++K I+  G+ SRRE +++I Q+RV VN    E     +   D ++VDG     V  
Sbjct: 6   PKRLNKYISDTGLCSRREADKLIEQKRVSVNNHPPE-LGTKIGPNDIVKVDGKIVGAVAK 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K++R  + +Y+KPIG+  T ++   +  + D +    +R+  VGRLD  +EGL++LT+D
Sbjct: 65  DKSDRVYI-VYNKPIGITCT-TERHVKGNIIDAIGH-KARIFPVGRLDKPSEGLIILTSD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  + +  +  + +G+ I G       V      G N 
Sbjct: 122 GDIVNKILRAENAHDKEYEVTVNQPISERFVKRMARGVPILGTVTKPCVV---KPTGKNT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + T+ L +G NR+I+++ EF  ++V +L R      +L  L  G  R +++
Sbjct: 179 F-TIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELKALKPGQWRNLTQ 228


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 124/242 (51%), Gaps = 17/242 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV----NV-MSTDHIEVDGVPLRK 69
           R+ K++    I SR +V+++I+ +++ V+    +R A+    NV      I VDG  LR 
Sbjct: 2   RLDKLLETCQIGSRGQVKKLISAKKIIVD----DRVAIGGQQNVDPGLQTIIVDGKVLR- 56

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTND 127
           A+    +  +KP G+V+   D +   TV D L     F  +  VGRLD +TEGL+LLT++
Sbjct: 57  AKGHHYFFLNKPRGVVSALKDRE-HPTVIDCLTEADRFPSLYPVGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSN 186
           G L   +  P     + Y V  +G +  D L+  + G+V + G       V + + +   
Sbjct: 116 GPLGFRMLHPKHHVDKSYYVVVNGFLGDDLLSFFRSGVVFLDGTVCKAAAVEILSAREKQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILRE 243
           +   V L EGK  +IKK+F  +  KV  L R+++  F +G L AG  R ++   K I+++
Sbjct: 176 SVAKVTLSEGKFHQIKKMFLAYGVKVIYLKRLTFAEFSVGNLAAGEYRTLTAHEKTIVKQ 235

Query: 244 QL 245
            L
Sbjct: 236 YL 237


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD NT GLLLLTNDG 
Sbjct: 62  IYLMM-NKPQGVVSATFD-NYDETVIDLLEDEDRIFEP-FPVGRLDKNTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGI++    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGEYRELT 228


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 115/232 (49%), Gaps = 16/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKV-AYQQYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   ++ +    P   +  +  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  YFLLNKPKGVISATEDRSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--------MQVTLDTQKGS 185
           L  P+    + YR +  G  D++ +      I   G+  GD        +++ +  ++  
Sbjct: 121 LLAPNKHVTKKYRAKIAGVADEETVK-----IFASGMTLGDGTKLKPARLKILMQDKESD 175

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREV 236
            + + + ++EGK  +IK++F     KV  L RIS     L T L  G  +E+
Sbjct: 176 ESEIEIEIQEGKYHQIKRMFGAVGMKVIELDRISMEKLVLPTSLKRGEYKEI 227


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQL 245
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ +   IL +QL
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELDILIDQL 229


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 121/229 (52%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ + +V+VNG   +++  ++   TD I VDG  +   ++ 
Sbjct: 2   RLDKYLANMGVGTRSEVKQLLKKNKVQVNGKNEKQSKAHINPDTDEITVDGNLIEYVDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D + +ST+   +      ++  VGR+  +TEGL+LLTNDG    
Sbjct: 62  YIML-NKPAGYISATEDEE-QSTIVSLIKDFQHMKIFPVGRVGKDTEGLILLTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-V 191
            +  P+    ++YRV     +  D +    +G+ +        Q+    ++  N  V  V
Sbjct: 120 DIMSPNKHVSKIYRVEAKNPITDDDIKQFAEGVELSDGKTKPAQL----ERTENEKVAFV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            +REG+  ++K++F   + +V  L R+  G  +L + L  GS RE++++
Sbjct: 176 SIREGRYHQVKRMFHAIDNEVLNLKRVQIGKLKLDSNLPKGSYRELTQE 224


>gi|255099545|ref|ZP_05328522.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-63q42]
          Length = 240

 Score = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 113/229 (49%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G ++  +D     TV D  +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 65  IYLMM-NKPAGYISATTDK-YDPTVLDLIDLSYLVFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  K  + + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDD-GYKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELT 230


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 111/220 (50%), Gaps = 10/220 (4%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E   L + HKP 
Sbjct: 2   GYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMM-HKPQ 60

Query: 83  GLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 61  GVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKN 198
              + Y     G V ++ +    KG+++    Y      L   K  + + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 217


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 120/236 (50%), Gaps = 19/236 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRK 69
           +R+ K+I+  G  SR++V+++I   RVKV+G   E    N    D     I V+G  +  
Sbjct: 2   ERLDKIISNMGYGSRKDVKKIIKDGRVKVDG---EVVKDNNKQLDPQKSKIIVNGEEISY 58

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTN 126
            +   L + +KP G+++  SD D   TV D L  +  +V     +GRLD +T GLL LTN
Sbjct: 59  KKYIYLMM-NKPDGVISATSD-DYDKTVID-LLEVEDQVFEPFPIGRLDKDTVGLLFLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQK 183
           DG     L  P     +VY  +    V  + +   K+GIV+          ++V  ++++
Sbjct: 116 DGDFNHRLISPKWHVDKVYYAKIDKDVTSEDVVAFKEGIVLDDGYKCMSAKLEVLNNSKE 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           GS   VTV  REGK  ++K++FE    KV  L RIS+   +L   L  G  RE+++
Sbjct: 176 GSEVKVTV--REGKYHQVKRMFEAQGKKVVYLKRISFAGIKLDENLEEGEYRELTE 229


>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 = 86.7 bits (213), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 121/234 (51%), Gaps = 13/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G  SRRE +R+IA +RV VN  L       V   D ++VDG PLR   + +
Sbjct: 17  RLNKHIAESGFCSRREADRLIAARRVTVND-LPGGVGSVVGEGDEVKVDGQPLRARAKHK 75

Query: 75  LWLYH------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +H      KP+G VT  ++ + +  + D +     R+  +GRLD ++EGL+L+T++G
Sbjct: 76  GGRHHVYIALNKPVG-VTCTTEREVKGNIVDFVGH-EQRIFPIGRLDKDSEGLILMTSNG 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +     +  + Y V  +  V  + L  + +G+ +    +  M +   T + +   
Sbjct: 134 DIVNEILRAENRHQKEYLVAVNKPVTDEFLRGIARGVRV----HDQMTLPCRTARIAKFG 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + L +G NR+I+ +   F+++V +L R+     +LG L  G  R ++++ LR
Sbjct: 190 FRIVLEQGLNRQIRLMAAAFDYRVTQLRRVRIDNIKLGALKPGQWRNLTEQELR 243


>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 = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 112/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAER 72
           R++K I+  G  SRRE ++++   RV +NG   E A +   +   D + V+G PLR+   
Sbjct: 2   RINKFISETGFCSRREADKLVESGRVTING---EVAVLGSQAEEGDDVRVNGKPLREKSD 58

Query: 73  TRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G+  TT S   G    F   P    R+  +GRLD ++EGL+LLTNDG + 
Sbjct: 59  HVYIALNKPVGITSTTESHIRGNVVDFVGHPQ---RIFPIGRLDKDSEGLILLTNDGDIV 115

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     V    +  +  G+ I     G   +  +  + S     +
Sbjct: 116 NKILRAEGKHEKEYIVTVDRPVIPSFVQGMSSGVKI----LGQRTLPCEVTRVSEYVFRI 171

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L EGKNR+I+++   F ++V +L R+     +LG+L  G+ R +++
Sbjct: 172 ILTEGKNRQIRRMCAAFGYEVKKLQRLRIMNIRLGSLQKGAWRNLTE 218


>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 = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 116/247 (46%), Gaps = 28/247 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMST-------DHIEVDGVP 66
           R++K +A  G  SRR   R+I   +V  N  L     +V ++ T       +H+ V+G  
Sbjct: 2   RLAKYLAITGCCSRRAATRLIRDGQVIFNDRLANHVDSVTLIDTPEGQRCQEHVIVNGEL 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR------STVFDNLPSIFSRVISVGRLDINTEG 120
           ++  E    WL++K +G        D R      +++   LP +  R+  VGRLD ++ G
Sbjct: 62  IQAVEAKAYWLFNKAVG-------TDSRLLAELPNSLIHLLP-VSPRLYPVGRLDKDSHG 113

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-L 179
           LLLLTNDG L   L  P     + Y V+     D+  L  +  G+  +G+      +T L
Sbjct: 114 LLLLTNDGELTHQLMHPDFGHSKTYHVQVDRPFDEVFLANMAAGVSYKGVTTLPCTITRL 173

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D  +       + L +G NR+I+++     +KV  L RIS    QLG LL GS R +S  
Sbjct: 174 DVDR-----YEIILTQGLNRQIRRMSHALGFKVIDLKRISIQSLQLGNLLEGSMRPLSST 228

Query: 240 ILREQLG 246
            L + L 
Sbjct: 229 ELADLLA 235


>gi|327479891|gb|AEA83201.1| pseudouridylate synthase [Pseudomonas stutzeri DSM 4166]
          Length = 230

 Score = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 108/225 (48%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +      SR++V R+++  R +VNG +       V   D +E+DG  L+  +  R
Sbjct: 2   RLDRYLGSRAQLSRQDVRRLVSDGRARVNGEVTRTLDREVRIFDCVELDGQVLQPGKVAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + HKP G V+   D   R TV D +       + + GRLD NT GL+LLTNDG  +R 
Sbjct: 62  YLMLHKPPGCVSATRDAAHR-TVIDLIDEPDKDDLHIAGRLDFNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   +VY V    ++D   +    +G+  +      +   L       A +T  L
Sbjct: 121 LTQPTSLQGKVYLVETEDEIDPGCVEAFARGLYFRFEDLTTLPAELVLLGPRRARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            EG+  ++K++F  F  KV  L R S GP  L  +L  G  R ++
Sbjct: 179 HEGRYHQVKRMFGHFGNKVTALHRESMGPLLLDASLSPGCYRPLT 223


>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 = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 115/241 (47%), Gaps = 25/241 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +A  G+ SRRE +  IA+  V V+G ++      V     I +D    R+A+ TR
Sbjct: 9   RLSKRMAELGLCSRREADDYIARGWVSVDGQIISELGSKVSPDQRITLDARA-REAQNTR 67

Query: 75  L-WLYHKPIGLVTT-----------------HSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +  L HKPIG V+                  H   D   TV+   P+    +   GRLDI
Sbjct: 68  VTILLHKPIGYVSGQAEKGYQPAATLIVPERHWQQDPSRTVWK--PAQLQGLAPAGRLDI 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++ ++ L LL  G+ + G+     +
Sbjct: 126 DSTGLLVLTQDGRIAKQLIGENSPVDKEYLVRVEGRLSEEGLRLLNHGLALDGVPLKPAR 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L EGK R+I+++ E    +V  L RI  G   LG L  G  R +
Sbjct: 186 VWWQNRDQ----LRFVLVEGKKRQIRRMCELVGLRVVGLKRIRIGRIMLGDLPQGQWRYL 241

Query: 237 S 237
           +
Sbjct: 242 A 242


>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 = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 111/220 (50%), Gaps = 10/220 (4%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E   L + HKP 
Sbjct: 2   GYGSRKEVKKLLKDGVVKIDGIPVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMM-HKPQ 60

Query: 83  GLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 61  GVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKN 198
              + Y     G V ++ +    KG+++    Y      L   K  + + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 217


>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 = 86.7 bits (213), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 119/236 (50%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  +R +++ M+ + RV+VNG +++     +   TD + VD   +  A R 
Sbjct: 2   RLDKFLGEMGYGTRTQIKEMVRKGRVQVNGQVIKAPESKLAPETDQVMVDQSVVGYA-RM 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  +V+  +D    + V     ++   +  VGRLD++TEGLL++TNDG +A  
Sbjct: 61  EYYMLNKPKDVVSATTDSRYPTVVGLIGDALRKDLFPVGRLDVDTEGLLIITNDGEMAHN 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW---- 188
           L  P     +VY  R  G++  +      +GIV+  G+    +   L+ +   N      
Sbjct: 121 LLSPKKHVDKVYMARLSGRLPVNAKERFSEGIVLDDGV--KTLPALLEYEGCGNGTEGLT 178

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V + +REGK  ++K++FE     V  L R+S GP  L   L  G  R ++++ +R
Sbjct: 179 EVLLTIREGKFHQVKRMFEALGCHVEYLKRMSMGPLGLDPELEPGQYRPLTEEEIR 234


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD NT GLLLLTNDG 
Sbjct: 62  IYLMM-NKPQGVVSATFD-NYDETVIDLLEDEDRIFEP-FPVGRLDKNTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGI++    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELT 228


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|332202557|gb|EGJ16626.1| hypothetical protein SPAR69_0668 [Streptococcus pneumoniae GA41317]
          Length = 241

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|222640395|gb|EEE68527.1| hypothetical protein OsJ_26969 [Oryza sativa Japonica Group]
          Length = 1502

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 120/242 (49%), Gaps = 14/242 (5%)

Query: 15   RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
            R++K IA  G  SRRE +R+IA +RV VNG      AV V   D + VDG PLR      
Sbjct: 1266 RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQVLVDGQPLRARVARK 1324

Query: 70   --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              A R      +KP+G VT  ++   +  + D +     R+  +GRLD ++EGL+L+T++
Sbjct: 1325 PGARRHVYIALNKPVG-VTCTTETSVKGNIVDFVGH-EQRIFPIGRLDKDSEGLILMTSN 1382

Query: 128  GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
            G +   +        + Y V  +  V  + L  + +G+ I    +  M +   T + +  
Sbjct: 1383 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRI----HDQMTLPCKTSRIAKF 1438

Query: 188  WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
               + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L  
Sbjct: 1439 GFRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLLPK 1498

Query: 248  HL 249
             L
Sbjct: 1499 QL 1500


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 114/225 (50%), Gaps = 9/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R I   +V ++G+   +    V+    +  +G  + K E   
Sbjct: 7   RINKFLSEAGVCSRREADRQIEAGKVGIDGVT-AKTGDRVLKGQTVTYNGQVVSKEEEMI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L   +KP G+V T ++   ++ V D  N P    R+  +GRLD ++EGLLLLTN+G +  
Sbjct: 66  LIALNKPAGIVCT-AEKREKNNVIDYLNYPK---RIYPIGRLDKDSEGLLLLTNNGEIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V  +  +    +  L  G+ +  +  G        +K S+    + 
Sbjct: 122 KMMRSGNRHEKEYIVTVNKTISDSFIRGLAGGVPL--VELGVTTRKCHVKKLSSKQFKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L +G NR+I+++ E+F ++V +L R+     +LG L  G  R V+
Sbjct: 180 LTQGYNRQIRRMCEYFGYRVVKLERVRIMNIELGDLPRGKYRAVT 224


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 111/220 (50%), Gaps = 10/220 (4%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E   L + HKP 
Sbjct: 2   GYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMM-HKPQ 60

Query: 83  GLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 61  GVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKN 198
              + Y     G V ++ +    KG+++    Y      L   K  + + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 217


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 62/232 (26%), Positives = 123/232 (53%), Gaps = 12/232 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRRE ++ I  ++V VNG  + +   +V   D + V+ + ++  ++  
Sbjct: 8   RLNKFISDSGYCSRREADQYIENRQVYVNG-RIAKVGQHVQLHDQVVVNNIEIKPRDK-E 65

Query: 75  LWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + +Y   +KP+G+  T +DP+  + + D L S   R+  +GRLD +++GL+LLT+DG + 
Sbjct: 66  MAIYIALNKPVGITCT-TDPNDPTNIIDFL-SFGERIFPIGRLDKDSQGLILLTSDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     +  D    ++ G+ I G+      V    +K +     +
Sbjct: 124 NKILRAGNKHEKEYIVTVDKPITDDFCTKMENGVPILGVNTKKCTV----EKLNTNTFKI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ E+F+++V +L R       L   + G  R+++K+ L E
Sbjct: 180 ILIQGLNRQIRRMCEYFDYRVTKLERTRIMNIDLNVPI-GQYRDLTKEELME 230


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 120/230 (52%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVQVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQK 228


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/211 (30%), Positives = 106/211 (50%), Gaps = 20/211 (9%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           +N   ++   VN  ST+     G PL      R+ L++KP  ++   +D  GR+T+ + +
Sbjct: 1   MNKFSVKNHKVNRFSTNAPAKLGKPLSP---RRVLLFNKPFDVLPQFTDESGRATLKEFI 57

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P  F+ V + GRLD ++EGLL+LTNDG L   L  P+ +  +VY V+  G    D L  L
Sbjct: 58  P--FNDVYAAGRLDRDSEGLLVLTNDGKLQAKLTQPAQKTGKVYFVQVEGVPGDDALMQL 115

Query: 162 KKGIVIQ-------GICYGDMQVTL--------DTQKGSNAWVTVGLREGKNREIKKVFE 206
           ++GI ++       G    D    L        + +    +WV + L EG+NR+++++  
Sbjct: 116 RRGISLKDGPTLPAGAELVDEPEWLWPRNPPIRERKNIPTSWVKITLFEGRNRQVRRMTA 175

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +   RLIR S G   LG L  G  +E++
Sbjct: 176 HVGFPTLRLIRFSMGNLSLGNLQPGEWKEIN 206


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 112/236 (47%), Gaps = 15/236 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           PQR++K + ++G+ SRRE E ++ Q  + ++G+ +      +   + + +      K   
Sbjct: 12  PQRINKWLGQSGVCSRREAEGLVEQGLISIDGVKVTEPGRKIEKGETLTLADAATDKLAS 71

Query: 73  TRLWLYHKPIGLVTTHSD----PDGR-------STVFDNLPSIFSRVISVGRLDINTEGL 121
               + +KPI  V+ H +    P  R       S   + +P   +R+  VGRLD ++ GL
Sbjct: 72  AMSVILNKPIDYVSAHPNEGEVPAVRLLTKANLSGQSETIPDRDTRLAPVGRLDKDSRGL 131

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LT DG L + +  P     + Y V  +G +  +K+  L  G+ + G     ++  + T
Sbjct: 132 LILTEDGVLTKAVIGPDADSEKEYLVTVNGTITHEKIRRLCHGLRMDGRA---LKPAIVT 188

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +G      + L EG+NR+I+++ E     V  L RI  G   +G L  G  R ++
Sbjct: 189 HEGGQVLRFI-LTEGRNRQIRRMAELVQLHVVDLFRIRIGHVHIGELPEGKWRTMT 243


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/225 (30%), Positives = 108/225 (48%), Gaps = 5/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +      SR++V R+++  R +VNG +       V   D +E+DG  L+  +  R
Sbjct: 2   RLDRYLGSRAQLSRQDVRRLVSDGRARVNGEVTRTLDREVRIFDCVELDGQVLQPGKVAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + HKP G V+   D   R TV D +       + + GRLD NT GL+LLTNDG  +R 
Sbjct: 62  YVMLHKPPGCVSATRDAAHR-TVIDLIDEPDKDDLHIAGRLDFNTTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   +VY V    ++D   +    +G+  +      +   L       A +T  L
Sbjct: 121 LTQPTSLQGKVYLVETEDEIDPGCVGAFARGLYFRFEDLTTLPAELVLLGPRRARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            EG+  ++K++F  F  KV  L R S GP  L  +L  G  R ++
Sbjct: 179 HEGRYHQVKRMFGHFGNKVTALHRESMGPLLLDASLTPGCYRPLT 223


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/216 (31%), Positives = 106/216 (49%), Gaps = 12/216 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + + + V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKMQVNPDKDEITVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G+V  + +    +GIV+    IC       ++  +     +
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGEVLLEDVKAFAEGIVLDDGYICKPARLEIINPNE-----I 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V ++EGK  ++K++F      V+ L RIS G  QL
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKTVSYLKRISMGQLQL 210


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 74/234 (31%), Positives = 114/234 (48%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D   R TV D L  I     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATEDSKHR-TVLDLLDDIARTKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y     G + Q+ +    KGI ++       +   V++D+ K + + 
Sbjct: 120 HALLSPKRHVDKTYLAHVEGIMTQEDVETFVKGIPLKDFTCQPAKLEIVSVDSVK-NQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEEL 232


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 68/262 (25%), Positives = 121/262 (46%), Gaps = 37/262 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG--VPLRKAE 71
           R++K+I+     SRR+ +  I    VK+N  +++    ++ +S D I++ G  V + + +
Sbjct: 57  RLNKIISMEKKISRRKSDEFIKDGNVKLNNKVVKNPGTHIDVSKDKIKISGKLVNIVRTQ 116

Query: 72  RT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTE 119
           +          + ++ HKP G + T +D   R++++   P       R++SVGRLD NT 
Sbjct: 117 KMINRNDNNFYKWFVLHKPKGFLCTSNDEKDRASIYSLFPQDIMDNYRLVSVGRLDRNTS 176

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG------ 173
           G+LLLTN+      L  P  Q +R YRV   G      L  L  GI +Q    G      
Sbjct: 177 GVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGPAQMKVLKQLATGIYLQDDNRGKENKKI 236

Query: 174 ---------------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                          +  + +  Q    + + + +REG+NR+I+K+FE  N  V ++ R 
Sbjct: 237 VKKKRTQPAFIEILREETIKVKDQVKKVSVLNISVREGRNRQIRKMFEQINQPVIKIKRT 296

Query: 219 SYGPFQL-GTLLAGSTREVSKK 239
           ++    L         RE++++
Sbjct: 297 AFENITLKDVFFPKQYRELTQR 318


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 118/231 (51%), Gaps = 6/231 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V     ++ V G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKQLLKQKAVTVDGASVKDAAMHVDPEQQNVSVYGERVVYTEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D     TV D L  +        VGRLD +TEGLL+LTNDG LA
Sbjct: 62  -YFMMNKPPGVISATEDLRDE-TVIDLLEPLDQHFQPFPVGRLDKDTEGLLVLTNDGILA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY     G V ++ +    +G+ +           +  +    + + +
Sbjct: 120 HKLLSPKKHVPKVYYAHIEGVVTEEDVEKFAEGVELDDGYMTKPGKLVILKSAPQSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            ++EGK  ++K++FE    +V  L RIS G  +L   LA G  RE++ + L
Sbjct: 180 TIQEGKFHQVKRMFESVGKRVTYLKRISMGNLKLDDHLALGEYRELTAEEL 230


>gi|332075974|gb|EGI86440.1| hypothetical protein SPAR68_0695 [Streptococcus pneumoniae GA41301]
          Length = 241

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 122/233 (52%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 116/236 (49%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V + D + VDG PLR  E  +
Sbjct: 17  RLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGAEDTVLVDGQPLRIREAKK 75

Query: 75  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+T+
Sbjct: 76  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKDSEGLILMTS 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 133 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 188

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 189 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 244


>gi|289668229|ref|ZP_06489304.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 240

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 115/236 (48%), Gaps = 16/236 (6%)

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  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKDSEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G V+  +D     TV D  +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 65  IYLMM-NKPDGYVSATTDK-YDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  K  + + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDD-GYKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEIK 235


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRAAVGDQVFAGDIVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G++TT  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIITTMEDSE-RDNISD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ + G      +V    QK ++    
Sbjct: 123 VNKILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPMLGTVTKKCKV----QKEASFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V RL R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTRLERTRIMNVNLKGLPQGEWRDLTDDELIE 231


>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 = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 88/177 (49%), Gaps = 16/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 102 LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILTNDGILQARLTQ 159

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +              
Sbjct: 160 PQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVEIIPEPELWPRNPPVRFRA 219

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                W+ + L EG+NR+++++     +   RLIR S G + LG L  G  REV+ K
Sbjct: 220 AIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPGEWREVTLK 276


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   T+ D L     IF     VGRLD NT GLLLLTNDG 
Sbjct: 62  IYLMM-NKPQGVVSATFD-NYDETIVDLLEDEDRIFEP-FPVGRLDKNTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGIV+    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIEKFKKGIVLDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELT 228


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 114/217 (52%), Gaps = 12/217 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+R++    V+V+G ++    + +  +   +EV G  +     
Sbjct: 6   ERIDKILAHLGFGTRKEVKRLLRAGGVRVDGRVVRDPGMKLDPARARLEVAGEVVVWQRH 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             + LY KP G+VT   D    +TV D LP+  +R  ++ VGRLD +TEGLLLLT DG L
Sbjct: 66  HHVMLY-KPAGVVTATRDAR-HATVLDCLPASLARKDLLPVGRLDRDTEGLLLLTTDGAL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICY-GDMQVTLDTQKGSNAW 188
              L  P  +  +VY          +      +G+V+ +G C   ++++  D ++     
Sbjct: 124 LHRLTHPRWKVPKVYYAELEQPARPEDAQAFAEGLVLSEGRCLPAELELLEDPRR----- 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V + L EG+  ++K++F     +V  L R++ GP +L
Sbjct: 179 VRLVLWEGRYHQVKRMFAARGNRVTYLKRLAVGPLEL 215


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 113/239 (47%), Gaps = 11/239 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +K I  +  T  R++K ++ AG+ SRRE +++    RV V G  +      + +   +
Sbjct: 1   MDEKRITTDQTTI-RINKYLSAAGVCSRREADQLTDAGRVTVAGKEIG-TGERIPADAEV 58

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINT 118
            +DG P++   R  L L++KP G+V +       +TV  F + P    RV  VGRLD ++
Sbjct: 59  FLDGRPVKAETRQVLLLFYKPRGIVCSTKKQRQETTVTEFLDYPV---RVYPVGRLDKDS 115

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLLLTN G L   +        + Y V    ++ +  +  +  G+ I     G +   
Sbjct: 116 EGLLLLTNQGDLVNRIMRAGNYHEKEYEVTVDKKITETFIRKMSSGVPI----LGTVTRP 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               K  +   ++ L +G NR+I+++ E+  + V  L RI      L  L  G  RE+ 
Sbjct: 172 CTVYKTGDKSFSIILTQGLNRQIRRMCEYLGYHVCTLKRIRIMNLTLDGLKCGEYREIC 230


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +N  +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINSEICTHGAL-VSDGDRVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIINYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>gi|301336267|ref|ZP_07224469.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           muridarum MopnTet14]
          Length = 241

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 70/225 (31%), Positives = 109/225 (48%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG+ASRR+ + ++    V VNG +     V V    D +EV+G  +   E+ 
Sbjct: 5   RLNKFLASAGVASRRKCDEIVFAGAVTVNGKVAAGPFVIVDEELDSVEVEGQRI-GTEKK 63

Query: 74  RLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP+G 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 +   +  +K     + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVSARDLETLMAGVVID----GRIVRPVSVKKVRRGTIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGQYRELT 224


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 117/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE + +I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDCLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELDNLEVGKWRSVTSEELEILIG 227


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 115/228 (50%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ ++++  G  SR+E   ++  +RV V G   +  A+ V     + VDG  L  A   
Sbjct: 14  KRLDQLLSNLGYCSRKEARYLLKGKRVTVKGEFAKSPALKVDPAT-VRVDGEAL-DAPDG 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTNDGG 129
            L + +KP+G V +H + +G   ++D LP  +     +++SVGRLD +T GL+L+T+D  
Sbjct: 72  ILVMLNKPLGYVCSHDNNEGMR-IYDLLPERWEFRNPKIVSVGRLDKDTSGLILVTDDTK 130

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     +VY+V     +  D ++   KG+V+       +   ++    + A V
Sbjct: 131 LVHQLTSPKHHVDKVYQVSVDCPLQSDIIDSFAKGVVLGEGAEQCLPAKIEIVSENVANV 190

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T  L EGK  +++++F    + V  L R  +G ++L  L  G  + V+
Sbjct: 191 T--LNEGKYHQVRRMFAACGYHVEALHRSQFGQYRLQDLAQGEWQTVA 236


>gi|322833615|ref|YP_004213642.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321168816|gb|ADW74515.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 208

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 89/175 (50%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR+T+ D +P   + + + GRLD ++EGLL+LTNDG L   L  
Sbjct: 33  LFNKPFDVLPQFTDEAGRATLKDYIP--LTDIYAAGRLDRDSEGLLVLTNDGKLQAALTQ 90

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------------ICYGDMQVTLDT 181
           P  +  ++Y V+  G+ D   +  L++GI ++                  +       + 
Sbjct: 91  PGKRTGKIYYVQVEGEPDDAAVKSLREGITLKDGPTLPAGAAIVPEPEWLWARNPPIRER 150

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    AW+ + L EG+NR+++++     +   RLIR S G F LG L  G  +E+
Sbjct: 151 KSIPTAWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYSMGEFTLGDLQPGQWKEI 205


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 110/233 (47%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I   RV +NG + E     VM  D +E+D  P+R  E+ 
Sbjct: 8   KRLNKYISETGFCSRREADKLIDAGRVTINGKIPE-MGTKVMPGDDVEIDNKPVRSKEKP 66

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 67  IYIALNKPTGITCTTERDIPGNIVDF---IGHHKRIFPIGRLDKPSDGLIFLTNDGDIVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I       + +    +K +     + 
Sbjct: 124 KILRAGNNHEKEYVVRVDKPITGEFLQKMAAGVPI----LDTVTLPCKVEKETKFSFRIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L +G NR+I+++ E   ++V +L R+      L  +  G  R +S++ + E L
Sbjct: 180 LTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSEEEIAEIL 232


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 118/215 (54%), Gaps = 7/215 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+A I SR+++++ + ++++ V+     + + NV      I ++  P+   +  
Sbjct: 2   RLDVLLAQAHI-SRKKMKQALLKKKILVDDCPARKLSQNVDTGLQTITLEEQPVL-GKPH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
           + ++ +KP+G+VT +SD   + TV D + P  F+ ++ SVGRLD +T GLLL+T++G L 
Sbjct: 60  QYFMMNKPLGVVTANSDAKSQ-TVLDLIKPEDFNDKLYSVGRLDRDTSGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +G +D   +   +KGIV + G       +T+ +   + +  T
Sbjct: 119 FQLLHPQYHVTKTYEVEVNGLLDDRAVQSFQKGIVFLDGTSCKPAILTIHSSSSNKSCAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V + EGK  +IKK+F     KV  L R  +G F+L
Sbjct: 179 VTISEGKFHQIKKMFLTVGVKVTSLKRTHFGDFEL 213


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 122/241 (50%), Gaps = 20/241 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR    K 
Sbjct: 24  RLNKHIAETGFCSRREADRLIGERRVTVNGVIAGTGAV-VGEDDTVLVDGQPLRVREAKK 82

Query: 71  ERTRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLL 124
             TR  +Y   +KP+G+ +T       S+V  N+        R+  +GRLD ++EGL+L+
Sbjct: 83  PGTRRHVYIALNKPVGITSTTE-----SSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILM 137

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T++G +   +     +  + Y V  +  V  + L  + +G+ +    + +  +   T + 
Sbjct: 138 TSNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRL----HDETTLPCRTARI 193

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +     + L +G NR+I+ +   F ++V +L R+     +L  L  G  R ++ + L+  
Sbjct: 194 AKFGFRIVLEQGLNRQIRLMAAAFGFRVTQLRRVRIDNIKLAALKPGQWRNLTDQELQGL 253

Query: 245 L 245
           L
Sbjct: 254 L 254


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 121/233 (51%), Gaps = 12/233 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
            R+ K++A  GI +R+EV+ +I +  VKVNG+++++    V   DH E+D +    +   
Sbjct: 3   MRLDKLLANYGIGTRKEVKSLIRKGFVKVNGMIIKKDDFKV---DH-EIDEIVFDDELIE 58

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
            R ++Y   +KP G ++   D +   TV + +    +  +  VGRLD++TEGLLL+TNDG
Sbjct: 59  YRPYVYIMLNKPAGYISATKD-NLHPTVLELIEGYENYDLFPVGRLDLDTEGLLLITNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
             +  L  PS    ++Y     G +D+  +   K GI++  G       + +  +   + 
Sbjct: 118 DFSHKLLAPSRNHSKIYFANIAGVMDEQDIQAFKDGIILNTGYHCKPANLEIINKNNDSC 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            V + + EGK  ++KK+ E    +V  L R+S    +L  +L  G  RE+S +
Sbjct: 178 DVRIEIFEGKFHQVKKMVEVCGKEVIYLKRLSIRNLELDRSLSLGDFRELSNE 230


>gi|322807584|emb|CBZ05159.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           botulinum H04402 065]
          Length = 238

 Score = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD NT GLLLLTNDG 
Sbjct: 62  IYLMM-NKPQGVVSATFD-NYDETVVDLLEDEDRIFEP-FPVGRLDKNTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGI++    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELT 228


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGKICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYIVTVDKPFTDWFIDEMSGGVKIKDGMTKPCKVTRVDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVKKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 108/225 (48%), Gaps = 9/225 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +N  + E     VM  D + +DG PL + E+T
Sbjct: 7   KRLNKYISETGFCSRREADKLIEQGRVSINDSVPE-MGTKVMPDDKVCIDGKPLSQKEKT 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+LLTNDG +  
Sbjct: 66  IYIALNKPTGITCTTERDVPGNIVDFIGHKK---RIFPIGRLDKPSDGLILLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    + +  ++ +  G+ I        +V  +T+      +T G
Sbjct: 123 KILRAGNNHEKEYVVRVDKPITKKFVDQMSSGVEILDTKTLPCKVIQETKFSFRITLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L    NR+I+++ E   ++V +L R+      L  +  G  R +S
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLS 223


>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 = 86.3 bits (212), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 95/185 (51%), 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 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  +VY V+  G  D+  L+ L+ GI+++        V L        
Sbjct: 84  GKLQAQLTQPHKKTAKVYYVQVEGVPDEISLDKLRNGIILKDGPTLPAGVELVHEPTWLW 143

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   LG +  G 
Sbjct: 144 SRHPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGNLPLGKMKPGE 203

Query: 233 TREVS 237
            +E++
Sbjct: 204 WKEIN 208


>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 = 86.3 bits (212), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 115/233 (49%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR+EV+ ++    V V+G   +    +V   T  + V G P+   +  
Sbjct: 2   RLDKLLANSGYGSRKEVKAVVKAGAVMVDGKPAKDVKAHVDPDTQEVTVYGEPVDYRKFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG LA
Sbjct: 62  YLMM-NKPQGVLSATED-SRQQTVIDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    Q+  + ++ L+ G+ I+ G      +  +      N  V 
Sbjct: 120 HRLLSPKKHVPKTYEVHLKSQISPEDISDLETGVYIEGGYKTKPAKAEIKANDNGNTVVY 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++K++ +    +V  L R+S GP  L   LA G  RE++++ L+
Sbjct: 180 LTITEGKFHQVKQMAKAVGNEVIYLKRLSMGPVSLDPALAPGEYRELTEEELK 232


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 123/243 (50%), Gaps = 8/243 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG  SRRE +R+I   RV +NG + E     V   D +EVDG  + + +   
Sbjct: 7   RLNKYLSEAGYCSRREADRLIDAGRVTINGTVPE-LGTKVGENDVVEVDGKSITERKTDF 65

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++L ++KP+G+V T      +  + D +     R+  +GRLD  +EGL+ LT+DG +   
Sbjct: 66  VYLAFNKPVGIVCTTDTRVEKDNIIDFI-KYPKRIFPIGRLDKPSEGLIFLTDDGDIVNK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   S    + Y V     + Q  +  +  GI ++ +     + T+  +K  +   ++ L
Sbjct: 125 ILRASNNHEKEYIVTVDKPISQTFIKRMAGGIYLEDLDKTTKKCTV--RKIDSQTFSIIL 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E+  ++V  L R+     +L   + G  RE + + L+      LLE++
Sbjct: 183 TQGLNRQIRRMCEYLTYEVTSLKRVRIMNIKLDVPI-GEYREFTAEELKTL--NMLLEDS 239

Query: 254 QVN 256
             N
Sbjct: 240 DKN 242


>gi|237653664|ref|YP_002889978.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237624911|gb|ACR01601.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 229

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 94/188 (50%), Gaps = 21/188 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           TRL L +KP G++   +D  GR T+ D   +P +++     GRLD ++EGL+LLT DG L
Sbjct: 29  TRLLLLNKPFGVLCQFTDEAGRRTLKDYVEVPGVYA----AGRLDADSEGLVLLTGDGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLD------ 180
              +  P  +  + Y V+  G++D+  L +L+ G+ +       C        D      
Sbjct: 85  QHRIADPRHKLAKTYLVQVEGEIDEAALAILRAGVDLGDFRSLPCAARRMPAPDWLWPRD 144

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +    +W+ + L EGKNR+++++    +    RL+R++ GP+ L  L  G  RE
Sbjct: 145 PPVRFRKSVPTSWIEIVLCEGKNRQVRRMTAKVDHPTLRLVRVAIGPWTLAGLGVGEWRE 204

Query: 236 VSKKILRE 243
           ++   + E
Sbjct: 205 LAGAEIAE 212


>gi|110004423|emb|CAK98761.1| probable ribosomal large subunit pseudouridine synthase b protein
           [Spiroplasma citri]
          Length = 267

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 112/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA  G  SRR+ E +I Q RVKVN +++      V   D I    +    + + 
Sbjct: 2   ERLQKVIAAKGYCSRRKAEELIIQGRVKVNNVVVTTLGTKVGKNDQINNQILMNENSNKI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L L +K    V+T  DP  R TV   +  I  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 62  YLML-NKRRNCVSTMYDPQHRKTVLTYVKGISERIYPVGRLDYDTSGLLLLTNDGEFTNI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL-DTQKGSNAWV-T 190
           +  PS    + Y V   G + + +L  L  GI I+ GI     Q  L   ++  N  +  
Sbjct: 121 ITHPSHIINKTYHVLLSGYLSKQQLQQLATGIEIEPGIIRSQAQAKLVKYEEVKNVSILL 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + + E    ++KK+ +    +V +L RI+ G  QL  TL  G  R +  K
Sbjct: 181 LTIHEVTKHQVKKMIQSLGHEVIKLKRIAIGFLQLDETLKPGEWRYLKPK 230


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 114/222 (51%), Gaps = 7/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + + ++ V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + + EGK  +IKK+F     KV  L RI +G F L   LA S
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAES 220


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD NT GLLLLTNDG 
Sbjct: 62  IYLIM-NKPQGVVSATFD-NYDETVVDLLEDEDRIFEP-FPVGRLDKNTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGI++    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQCRELT 228


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 96/185 (51%), Gaps = 16/185 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           RK   T+L L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 16  RKPAVTQLVLFNKPFDVLCQFTDEAGRQTLKDFIP--LPGVYAAGRLDRDSEGLLLLTND 73

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------- 177
           G L   L  P  Q  + Y V+  G  D+  L+ L++G+ ++       +V          
Sbjct: 74  GQLQSRLTEPKKQTYKTYWVQVEGIPDESALDKLREGVELKDGPTLPARVRRIDAPQIWP 133

Query: 178 ----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +   + W+ + + EG+NR+++++     +   RL+R + G  +LG L +G  
Sbjct: 134 RNPPVRERKSIPDCWLEIQICEGRNRQVRRMTAHIGYPTLRLVRAAIGEIRLGHLGSGEY 193

Query: 234 REVSK 238
           R++++
Sbjct: 194 RKLNR 198


>gi|301156469|emb|CBW15940.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus parainfluenzae
           T3T1]
          Length = 232

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 110/227 (48%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  A  V   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKNGATKVSLEDEIYFEDELLPWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V +H D D   T++    P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGYVCSHDDGD-YPTIYQFFEPPLSGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     V+    +  ++GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLADPVENHYASACEEGILLRGEKEPTKPAKLEVLDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G  +L  +L  G  R ++++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGNVELDESLEEGEFRPLTQE 225


>gi|288553832|ref|YP_003425767.1| pseudouridine synthase [Bacillus pseudofirmus OF4]
 gi|288544992|gb|ADC48875.1| pseudouridine synthase [Bacillus pseudofirmus OF4]
          Length = 233

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 115/226 (50%), Gaps = 8/226 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWL 77
           +++  G  SR+EV++++    V++N  +++  +  V      + V G  +       L L
Sbjct: 1   MLSNMGYGSRKEVKKVLKSGSVRINEKVIKDGSYKVDPDQSDVTVHGELVEYKPYVYLML 60

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +KP G+++   D +   TV D L    +      VGRLD +TEG+LLLTNDG  +  L 
Sbjct: 61  -NKPQGVISATED-NHHKTVIDLLDESYLLYDPFPVGRLDKDTEGMLLLTNDGKFSHSLM 118

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLR 194
            P     + Y  +  G V ++ + L KKG+ +  G       +T+ T  G  + V + + 
Sbjct: 119 SPKKHVKKTYYAKVKGTVTEEDIGLFKKGVTLDDGYVTKPADLTIITA-GEQSEVELTIT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           EGK  ++K++FE  + KV  L RIS G  +L  +L  G  RE++++
Sbjct: 178 EGKFHQVKRMFEAVDKKVTFLKRISIGGLKLDPSLEKGMVRELTEE 223


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 62/209 (29%), Positives = 107/209 (51%), Gaps = 7/209 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ I+ +G+ SRRE +  IA   +KVNG  +      V  +D +  DGV L   +R  
Sbjct: 102 RLNRYISNSGVCSRREADIFIAAGSIKVNGKAVVEMGYKVALSDVVSFDGVVLNPEKRAY 161

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP    ++ +D     +    + +   S++  VGRLD +  GLLL TNDG L   
Sbjct: 162 ILL-NKPKDFDSSATDASQPKSALGLVANATKSKIKPVGRLDKSASGLLLFTNDGELQTK 220

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAW-VTV 191
           L  P   + ++Y       +  D L  ++KGIV++    G ++V  +   +GS A  V +
Sbjct: 221 LTKPKNGFRKIYHATLSKSLKADDLEKVRKGIVLED---GPVRVHEISNIEGSPATEVGI 277

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISY 220
            +   KN  IK++F+   +++ +L R+ Y
Sbjct: 278 EILSAKNNIIKRLFDHLGYELIKLDRVVY 306


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 110/218 (50%), Gaps = 13/218 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR 68
           N   +R+ KV+   G+ SR+E+ R+     + +NG ++  A      S  HIEV G PL 
Sbjct: 15  NMAYERLDKVLGHLGVGSRKEIHRLARAGLITINGKIVADAGFKFDPSQAHIEVAGEPLV 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
             +   L L +KP G +T+  DP G + +   LP  F R   + VGRLD +TEGLLLLT 
Sbjct: 75  YQKFFYL-LLNKPAGYITSTKDPSG-TPITALLPEEFWRNDWMPVGRLDKDTEGLLLLTT 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQG--ICYGDMQVTLDTQK 183
           DG L   L  P  +  + Y V        + + +   G + ++G  +   ++ +  D +K
Sbjct: 133 DGELLHRLTHPRWKVTKRYYVELASPATPEDVAVFAAGTLELEGEPLQPAELYLGPDPRK 192

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                V + LREG+  ++K++F     +V  L R+++G
Sbjct: 193 -----VELVLREGRFHQVKRMFAARGNQVTYLKRLAFG 225


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 112/239 (46%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+   G  +R +V++ I Q  VKVNG++++     +  TD +      L + E  
Sbjct: 4   ERLDKVLGNYGFGTRSDVKKEIYQGNVKVNGLVVKDPGYKITLTDIVVYYDETLNRKEFY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              +   P   +T   DP  + TV D L        +  +GRLD  TEGLLL T DG LA
Sbjct: 64  YFMMNKAP-DCITATEDPREK-TVMDYLSERHRNMNLFPIGRLDKETEGLLLFTTDGTLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV-T 190
                P     + Y       V    ++  + GI +    Y  +   L     SN  + T
Sbjct: 122 HYYTSPKHFVEKEYYAEISAPVTAFDISQFESGITLDD-GYKTLPARLAIPDPSNPHIAT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS---KKILREQL 245
           V LREGK R+I+++F+    +V  L R+  G  +L   L  GS RE++   +KIL+ ++
Sbjct: 181 VWLREGKYRQIRRMFQSLGKEVQYLKRVKMGNLELDRDLEVGSYRELTEAEEKILKTKI 239


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 110/217 (50%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+  + +++V VNG +       +  + D I   G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRSQVKTFLKKKQVAVNGQVETSPKTQIDENQDQIAFQGQVLTH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV D L       +V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATEDARHK-TVLDLLDDTARHKQVFPVGRLDIDTHGLLLLTNNGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             +  P     ++Y+ +  G ++Q+ +   +KGI ++       +   +++D   G+ + 
Sbjct: 120 HAMLSPKKHVDKIYQAKVDGIMNQEDILAFEKGIELKDYTCQPAKLEIISVDRATGT-SL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V + + EGK  ++K++      +V  L R+S GP  L
Sbjct: 179 VQITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSL 215


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 114/238 (47%), Gaps = 21/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +G+ SR EV+ ++ + RV V G +       V  ++  +  DG  L   E  
Sbjct: 2   RLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQEYY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
             +L +KP G+V+   D      VF  +  + S       +  VGRLD NTEGLL+L+ND
Sbjct: 62  -YYLLNKPQGVVSATKD-----NVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILSND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLD 180
           G L   L  P     + Y  R  G+V  + +N   +G+ ++       G  + +     D
Sbjct: 116 GALGHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGD 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +Q G  + + V + EGK  ++K++FE     V  L RI  G   L + LA G+ R ++
Sbjct: 176 SQSGWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLT 233


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 118/237 (49%), Gaps = 12/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E  
Sbjct: 2   RLDKYLVACAVGSRTEVKNFLKAGRVMVNGKKEKSAKLQINEETDEICFDGQKLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D   + TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATEDSKHK-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDM--QVTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+ +    +GI ++   C   +   V++D +K + + 
Sbjct: 120 HALLSPKRHVDKTYLAQVGGIMTQEDVETFAQGIPLKDFTCQPAILELVSIDREK-NQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V V + EGK  ++K++  +   +V  L R++ G     TL  G  R   +++ +E+L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTL---TLDEGLKRGEWRRLTKEEL 232


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 120/234 (51%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV ++G +    A+ V   D I +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAIDGEICTHGAL-VSDGDVITIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+    G  +    T+ G + +  V 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKD---GMTKPCKVTRVGQSTFRIV- 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELHELEVGKWRSVTAEELEILIG 227


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 107/217 (49%), Gaps = 9/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E  
Sbjct: 2   RLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D   R TV D L  +     V  VGRLDI+T GLLLLTNDG LA
Sbjct: 62  -YYMMNKPQGVISATEDSKHR-TVLDLLDDVARSKEVFPVGRLDIDTHGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
             L  P     + Y  +  G + Q+ +    +GI ++       +   V++D +K + + 
Sbjct: 120 HALLSPKRHVDKTYLAQVEGIMTQEDVETFAEGIPLKDFTCQPARLELVSVDPEK-NQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V V + EGK  ++K++  +   +V  L R++ G   L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGALIL 215


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 71/225 (31%), Positives = 109/225 (48%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K +A AG+ASRR+ + +I    V +NG +     V V    D+IEV G  +  AE+ 
Sbjct: 5   RLNKFLASAGVASRRKCDEIIFAGSVTINGKVAAGPFVTVDEEFDYIEVGGQRI-GAEKK 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP+G + +      +S  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 +   +  +K     + + 
Sbjct: 124 RVIHPSFGITKEYLLKVSRDVTAKDLESLMSGTMID----GRIVRPVSVKKVRRGTIKII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGK  EI+   E    ++  L RI  G   LG L  G  RE++
Sbjct: 180 VNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELT 224


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 75/251 (29%), Positives = 119/251 (47%), Gaps = 29/251 (11%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPL 67
           E   P R+SK ++  G+ASRRE +  I Q  V+V+G ++++    V     I +D    L
Sbjct: 166 EELNP-RLSKRMSELGLASRREADEWIEQGYVRVDGEVVDQLGARVRPEQQITIDPQARL 224

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------------PSIFSRVISV 111
            +A+R  + L HKP+G V+  ++ DG +  F  +                 S    ++  
Sbjct: 225 EQAQRVTI-LLHKPLGYVSGQAE-DGHAPAFTLVTAANRWATDGSKQRFNASQLKHLVPA 282

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD+++ GLL+LT DG +A++L    +   + Y VR      + +L  LK+    + + 
Sbjct: 283 GRLDLDSTGLLVLTQDGRVAKLLIGEDSPVEKEYVVRVQWTA-RPELTDLKQHFPPEALA 341

Query: 172 YGDMQVTLDTQKGSNAWVT--------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                + LD +K   A V+          LREGK R+I+++ E    KV  L RI  G  
Sbjct: 342 RLRHGLALDGEKLKPAKVSWQNEQHLRFVLREGKKRQIRRMCELVGLKVESLKRIRIGRV 401

Query: 224 QLGTLLAGSTR 234
            LG L  G  R
Sbjct: 402 GLGELPPGQWR 412


>gi|205374821|ref|ZP_03227614.1| tRNA pseudouridine synthase A [Bacillus coahuilensis m4-4]
          Length = 235

 Score = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 116/227 (51%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ AG ASRR  +++I + RV +NG    RA +   V   D + V+G  +R A  
Sbjct: 2   RINKYISDAGKASRRGADKLIEEGRVYING---RRAKIGDQVNPGDDVLVNGNHVRLARN 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+ +T ++   +  + D L +   R+ ++GRLD  ++GL+LLTNDG +  
Sbjct: 59  NVYIALNKPVGITST-TEKGVKGNIID-LVNHPLRIFNIGRLDKESDGLILLTNDGDIVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V     + Q+ L+ +  G+ I     G   +    ++ S     + 
Sbjct: 117 EILRAENKHEKEYFVSVDKPITQEFLDNMASGVKI----LGTKTLPCKIEQISKYDFQIT 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L +G NR+I+++ E   ++V RL R       LG L  G  R++SKK
Sbjct: 173 LTQGLNRQIRRMCEALGYEVYRLQRTRIMNIHLGNLPVGQWRDLSKK 219


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 123/244 (50%), Gaps = 18/244 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     RV    VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRVDLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQKG 184
             L  P     + Y     G V  +   L  +G  ++    G+M         T++ ++G
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVKPSRLVIETINEEEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           ++  V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +
Sbjct: 177 TSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-Q 234

Query: 244 QLGP 247
           QL P
Sbjct: 235 QLQP 238


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIENNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRIDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQL 245
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ +   IL +QL
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELDILIDQL 229


>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 = 85.9 bits (211), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + ++G  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAI-VSDDDVVTINGRVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 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 = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 129/247 (52%), Gaps = 13/247 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE---RAAVNVMSTDHIEVDGVPLRKAE 71
           R++K ++ +G  SRRE +R++    V +NG + E   +A  N + T    V G  +   E
Sbjct: 2   RINKYLSASGHCSRREADRLVEAGHVSINGKIAEPGSQADENSIVT----VKGKRVTLEE 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +      +KP+G+V T    +  + + + N P    RV   GRLD N+EGLL+LTNDG L
Sbjct: 58  KKIYLKMYKPVGIVCTAEKRERDNLIEYLNYPV---RVTYAGRLDRNSEGLLILTNDGDL 114

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            + +        + Y V  +  + ++ L+ +++G+ ++ +       T+  Q G   +  
Sbjct: 115 IQSMMAARNAHEKEYEVTVNKDLRKEDLDSMREGVYLRELEVRTRPCTI-VQTGERTFRI 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ + F++ V +L RI      L  L  G TRE+S++ +R+      +
Sbjct: 174 I-LTQGLNRQIRRMCKEFSYGVKKLKRIRVVNITLDGLKYGQTRELSEQEVRDLKKNLGI 232

Query: 251 EEAQVNL 257
           EE++ +L
Sbjct: 233 EESKNDL 239


>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 = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 124/236 (52%), Gaps = 15/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRKAERT 73
           R+ K +A  G+ +R EV+++I Q +V V+G + E++    +   H +V  +      E  
Sbjct: 9   RLDKYLADMGVGTRTEVKKLIRQGKVTVDGSI-EKSPERKIDISHQKVCCMGEAVSYETH 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+  +D   + TV + + S   R +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 68  EYYMLNKPAGVVSATTDRQDK-TVVELISSKKRRDLFPVGRLDKDTEGLLLITNDGELAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----KGSNA 187
            L  P     +VY  +  G VD+     + + I   G+  G+ +  L ++      G  +
Sbjct: 127 RLLSPKKHVDKVYYAKVQGIVDE-----VDQEIFAVGMSIGNGETALPSKLEILYSGEIS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + V ++EGK  ++K++F     +V  L R+S G   L  TL +G  R ++K+ L+
Sbjct: 182 EIRVTIQEGKFHQVKRMFHAVGKEVIYLKRLSMGTLLLDETLKSGEYRALTKEELK 237


>gi|227325901|ref|ZP_03829925.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 231

 Score = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    R
Sbjct: 2   RLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGEPLKQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  DPD  + + F ++P  + ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFMDVPVAY-KLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     + +D       G+ +          TL  +K ++  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPATL--EKITDYVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGIYLDSELEPGEYRELSAE 225


>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 = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 120/236 (50%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR++V++++    V VN   ++     V    D + ++G  +   E  
Sbjct: 2   RIDKMLANLGYGSRKDVKKLLKDGAVTVNDEKVKDPKHQVDPEQDAVIINGEKVEYKEFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+++   D     TV D L     +FS    VGRLD +TEGLLLLTNDG L
Sbjct: 62  YLMM-NKPPGVISATEDSQ-FETVVDLLEMRDLVFSP-FPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY----GDMQVTLDTQKGSN 186
           A  L  P     + Y      +V  D +   KKG+++    Y    G++++    + G  
Sbjct: 119 AHRLLSPKKHVPKTYFAVIDREVTADDVAAFKKGVILDD-GYETKPGELEI---LKSGIT 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + + + EGK  ++K++FE    +V  L RIS GP +L  TL  G  RE++ + L
Sbjct: 175 SDIELTITEGKFHQVKRMFEAVGKRVIYLKRISMGPLELDKTLELGEYRELTDEEL 230


>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 = 85.9 bits (211), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 112/232 (48%), Gaps = 11/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERT 73
           R++K I+ +G  SRRE +R+I + RV +NG    +    V   D +EVDG  ++ K ++ 
Sbjct: 2   RLNKFISDSGFCSRREADRLIEEGRVLINGRRC-KTGQQVEDKDFVEVDGQRIKAKRQKE 60

Query: 74  RLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R++L ++KP G+  TT     G    F N P    ++  +GRLD  + GL+ +TNDG + 
Sbjct: 61  RVYLAFNKPEGITCTTEGSVKGNIVDFINYP---EKIFPIGRLDKFSNGLIFMTNDGDIV 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  + L  +  GI I        +VT    K S     +
Sbjct: 118 NKILRAGNAHEKEYVVTIDRPVTDEFLRKMSNGIPILDTVTKKCKVT----KVSKNTFRI 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ E+   +V  L R       LG L  G+ R ++ K + E
Sbjct: 174 ILTQGLNRQIRRMCEYLACRVLSLQRTRIMKVDLGKLKPGTWRHLNPKEMAE 225


>gi|293363190|ref|ZP_06610074.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
 gi|292553049|gb|EFF41798.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
          Length = 237

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 113/229 (49%), Gaps = 14/229 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +R+ K++A+AGIASRR+ E +I +  VK+NG    + ++A  N    D I V+G  + + 
Sbjct: 2   ERIQKLLAQAGIASRRKAEELITKGLVKINGDVATIGQKATFN----DKISVNGKEIVQ- 56

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   ++ +KP   V T  D   R  V D + +   R+  VGRLD +T G+L+LTNDG L
Sbjct: 57  EKKVYFVLNKPSKTVCTLKDNFNRRKVVDLIETNL-RIFPVGRLDYDTTGVLILTNDGEL 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P    +R YR R    + +D +  L    +I G     +   +DT+        
Sbjct: 116 SNKLIHPKYNIIRKYRARLDEPLSKDDIKELNNEQLINGKPSKQVVEQIDTK-----SYL 170

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V L +G    +K++F      V  L R+ +    +  +  G  R ++ K
Sbjct: 171 VTLTQGTYHHVKELFSKVGRLVINLKRVEFAGIGVDKIPMGEYRSLNMK 219


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 124/248 (50%), Gaps = 28/248 (11%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +QE     R++K ++  G  SRR  +R+I + RV++NG+ +      V   D IEVDGV 
Sbjct: 1   MQEQTEGIRLNKYLSEIGHCSRRAADRLIEEGRVQINGVQVIMGQ-KVTPLDRIEVDGVL 59

Query: 67  LRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLL 123
           +   +   +++ ++KPIG+V T      +  + D  N P+   R+  +GRLD  +EGL+L
Sbjct: 60  VEDLQERNVYIAFNKPIGIVCTTDTRVEKDNIIDYINYPT---RIFPIGRLDKPSEGLIL 116

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-- 181
           LTNDG +   +        + Y V  +  V  + +  +  GI I           LDT  
Sbjct: 117 LTNDGDIVNKILRARNNHEKEYIVTVNKPVTTEFVEKMANGIPI-----------LDTIT 165

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 Q   N +  + L +G NR+I+++ E+ +++V +L RI     +L  +  G  R+
Sbjct: 166 RKCVVEQIHKNQFRII-LTQGLNRQIRRMCEYLDYRVVKLKRIRIMNIELN-VGVGKYRD 223

Query: 236 VSKKILRE 243
           ++KK + E
Sbjct: 224 LTKKEMVE 231


>gi|311032169|ref|ZP_07710259.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus sp.
           m3-13]
          Length = 235

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 113/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G+ASRR  +++I + +VK+NG + +     V   D + V+G  +R A    
Sbjct: 2   RINKFISDSGVASRRGADKLIEEGKVKINGKVAQIGG-QVNPGDEVLVNGQIIRIARDNV 60

Query: 75  LWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KPIG+  TT     G      N P    R+  +GRLD  +EGL+LLTNDG +   
Sbjct: 61  YIALNKPIGITSTTEKKVKGNIIDLVNHPL---RLSHIGRLDKESEGLILLTNDGDIINE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     +  D +  + +G+ I     G   +  + ++ S     + L
Sbjct: 118 ILRPENKHEKEYIVSVDKPITPDFVKQMSEGVKI----LGTKTLPCEVEQLSKFDFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +G NR+I+++     ++V RL R      +LG L  G  R++SKK
Sbjct: 174 TQGLNRQIRRMCAELGYEVLRLQRTRIMNIELGNLPMGQWRDLSKK 219


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 117/231 (50%), Gaps = 17/231 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +++  ++++GI+SRR  + +I    +KVNG ++++    + + D ++     L   ++  
Sbjct: 8   KLNSYLSKSGISSRRNADNLIKSGNIKVNGKIIKKLGYIISNNDIVKYKDKRLYPEKKIY 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G V++    D  + V D L  I  ++ S+GRLDI T G+LL TNDG L+  L
Sbjct: 68  LIL-NKPKGYVSSMKKQDNNNIVLD-LIKINYKIFSIGRLDIETSGVLLFTNDGYLSNKL 125

Query: 135 ELPSTQWLRVYRVRFHGQV-DQDKLNL-----LKKG-IVIQGICYGDMQVTLDTQKGSNA 187
             P     ++Y V  + ++ ++D L +      K+G + I  I Y         +K    
Sbjct: 126 THPKFNIKKIYHVVLNKKINNKDLLKIKNSFSFKEGKLKIYNISY--------IKKLPKN 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + + L  G N+ +K++F    +KV  L RI++G   +  L  G  R + K
Sbjct: 178 NIKLELHIGWNKIVKRIFNKIKYKVLYLKRINFGGITIKGLKIGEYRYLKK 228


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 82/251 (32%), Positives = 123/251 (49%), Gaps = 41/251 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +AR G+ SRRE +  I+Q  V++NG  +E     VM  D +EV     R+A R 
Sbjct: 28  ERLNKHLARTGVCSRREADDWISQGWVRINGRPVEMGQ-KVMPGDVVEV-----RQAARA 81

Query: 74  R-----LWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGR 113
           R       L +KP+G V+  ++   R  V           D  P  F R     +   GR
Sbjct: 82  RQQDKVTILLNKPVGYVSGQAEDGYRPAVTLIDAQSRWAGDTNPRRFERNQLRGLAVAGR 141

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ--------DKLNLLKK 163
           LDI++ GLL+LT DG +AR L  E  ST    + RVR+ G+V++        D+L LL+ 
Sbjct: 142 LDIDSVGLLVLTQDGRVARQLIGEDSSTTKEYLVRVRY-GEVERNVQAAFPPDRLKLLRH 200

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ + G      QV  +  +     +   L+EG++R+I+++ E     V  L RI  G  
Sbjct: 201 GLSLDGHKLKPAQVDWENPEQ----LRFVLQEGRHRQIRRMCELVGLAVTGLKRIRVGNV 256

Query: 224 QLGTLLAGSTR 234
            LG L  G  R
Sbjct: 257 LLGRLPPGQWR 267


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 105/225 (46%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV VNG +++  A  ++    IE DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVNGDIVKDTAFKLLPDHEIEYDGNPLTQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D   L  KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAALFAKGVQLNN--EKDLTKPAQLEVITPTEVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           EG+  ++K++F      V  L R   G  +L   LA G  R +++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPELAPGEYRPLTE 224


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 123/236 (52%), Gaps = 13/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++VN+     I +++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKEAKLLAKKGLIEVDGKIIKDSSVNIDPEKSIVKINGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
             L + +KP G+++ TH   D   TV D L     IF     VGRLD +T GLLLLTNDG
Sbjct: 62  IYLMM-NKPTGVISATHDSKD--ETVIDLLELDHQIFDP-FPVGRLDKDTVGLLLLTNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--N 186
                +  P     +VY  +   +V++      KKG+V+    Y  ++  LD    S   
Sbjct: 118 DFNHRMISPKWHVDKVYYAKIDKEVNEKDQEAFKKGVVLDD-GYKCLEAKLDIISASPEG 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + ++EGK  ++K++FE  + KV  L R  +G   L  TL  G  RE+S + L
Sbjct: 177 SEVRITIQEGKYHQVKRMFEARDKKVVYLKREEFGGLILDETLEEGEYRELSDEEL 232


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +     + V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGEL-VSDGDVVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKVSEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 RILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>gi|227112086|ref|ZP_03825742.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 231

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    R
Sbjct: 2   RLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  DPD  + + F ++P  + ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFMDVPVAY-KLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     + +D       G+ +          TL  +K ++  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPATL--EKITDYVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGIYLDSELEPGEYRELSAE 225


>gi|255305403|ref|ZP_05349575.1| putative RNA pseudouridine synthase [Clostridium difficile ATCC
           43255]
          Length = 240

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 113/229 (49%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G ++  +D     TV D  +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 65  IYLMM-NKPDGYISATTDK-YDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  K  + + +
Sbjct: 123 SHRVLSPKKHVSKTYYAKIDGVVTEEDVEAFLEGVVLDD-GYKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELT 230


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 120/229 (52%), Gaps = 13/229 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G  +R+EV +++  ++V+VNG++++    N+ + TD + V G  + K + 
Sbjct: 1   MRIDKFLAHMGFGTRKEVRKLLKARKVEVNGVVVKDPGYNLNVDTDKVIVKGEEV-KYKP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G V+   D     TV D +P +  ++  VGRLDI+TEGLL+LT+DG LA 
Sbjct: 60  FVYFMLNKPKGYVSATVD-RRYPTVVDLVP-VHRKIFPVGRLDIDTEGLLILTDDGQLAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---KGSNAWV 189
            L  P  +  + Y       ++++  + +K GI ++     D  +T   +   K  +   
Sbjct: 118 HLTSPKKEVEKEYYFELDKPLEEEDFSKIKTGIRLE-----DNYLTKPARLLGKVGDKHG 172

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           T+ + EGK  ++K++F      V  L RI  G   L   L+ G  RE++
Sbjct: 173 TIVITEGKYHQVKRMFLALGKTVVYLKRIRIGGLILDNKLSPGEYRELT 221


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 119/233 (51%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q +V +NG   +RA +   V + D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGQVFING---KRAGIGDQVFAGDLVKVNGQVIEAREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +     + +KP+G+V+T    +  + V  +  +  +RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DSLVFIVLNKPVGIVSTTEAGEKDNIV--DFVNHSTRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  D +  +  G+ I G      +V    +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDDFIKGMGAGVPILGAVTKKCKV----KKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIE 231


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/216 (29%), Positives = 107/216 (49%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV D L       +V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATEDSRHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             +  P     ++Y+ +  G +D++ +   +KGI ++   C    +++    +  S + V
Sbjct: 120 HAMLSPKKHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EGK  ++K++      KV  L R+  GP  L
Sbjct: 180 QITVAEGKFHQVKRMVAACGKKVADLQRLKMGPLSL 215


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 117/240 (48%), Gaps = 17/240 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++ +  V VN  L++     +  S DHIEV G  +      
Sbjct: 2   RIDKLLSNTGFGSRKEVKGLLKKGGVTVNSELIKDGKRQIDPSEDHIEVFGEVIEYKPFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L +         VGRLD +T G +LLTNDG LA
Sbjct: 62  YLMM-NKPKGVISATEDVTDK-TVVDLLATEHALYDPFPVGRLDKDTTGFMLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---TQKGSNAW 188
             L  P  +  + YRV          L    +  +I G+   D  +T     T    N  
Sbjct: 120 HQLTSPKKKVDKTYRVHIDAP-----LTSADEASLIAGVELDDGYITKPAKLTYGNDNTV 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQ 244
           + + + EGK  ++K++F+    KV  L R + GP +L  +LL G  RE++ +    LREQ
Sbjct: 175 IFLTITEGKFHQVKRMFQALGRKVINLKRETIGPLKLDPSLLLGEYRELTDEEVAGLREQ 234


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/232 (30%), Positives = 113/232 (48%), Gaps = 9/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR+EV+++I    V VN   +E  + ++    D +E++G  +   E  
Sbjct: 2   RLDKFLVNQGFGSRKEVQKLIKAGIVYVNNFPVEDPSFHINPEKDVVEIEGQEIEYKENY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L +KP G +T   D +   TV D   S  I S++  VGRLD++TEGLL++T+DG LA
Sbjct: 62  YFML-NKPKGYITATYD-ENYPTVMDLFASEPIVSKLFPVGRLDVDTEGLLIITSDGVLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
             L  P     + Y V   G + D D     K+G+ ++   Y      +   K S   + 
Sbjct: 120 HRLSHPKWNVEKEYFVIVEGDISDIDFSKYEKEGMYLKKEKYKTKPFKVKVLKTSFEESE 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
           + + + EGK   +KK+      +V  L R+  GP  L   L  G  RE++K+
Sbjct: 180 LLITITEGKYHIVKKIMYAVGHEVKYLKRVRIGPLILDEDLEVGEYRELTKE 231


>gi|158320760|ref|YP_001513267.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140959|gb|ABW19271.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 228

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 118/227 (51%), Gaps = 7/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  GI SRRE ++ I  +RV +NGI+ E  + +V   D + VD  P+ +  +  
Sbjct: 2   RINKYISETGICSRREADQWIIDKRVTINGIVAELGS-DVSPGDAVFVDHKPIGQKRKPV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T ++   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-TEKHVKGNIVDFVHH-KERIFPIGRLDKDSQGLILLTNDGDIVNKI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V  +  +  + +  +  G+ I G      +VT    K ++    + L 
Sbjct: 119 LRAENNHEKEYIVTVNKPITPEFIKGMSSGVKILGTKTKPCKVT----KINDTVFRIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +G NR+I+++ + F +KV +L RI     +L  L  G  R+++K+ L
Sbjct: 175 QGLNRQIRRMCQVFGYKVVKLQRIRIMNVKLKGLEIGQWRDLTKEEL 221


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 74/231 (32%), Positives = 119/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD NT GLLL TNDG 
Sbjct: 62  IYLMM-NKPQGVVSATFD-NYDETVIDLLEDEDRIFEP-FPVGRLDKNTVGLLLFTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGI++    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELT 228


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 111/234 (47%), Gaps = 20/234 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +      V   +  + V G  +   +  
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGLVKVDGAAVYDPKTKVRPDEQTVTVWGETVEYKQFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---------FDNLPSIFSRVISVGRLDINTEGLLLL 124
            L + +KP G+++   D    + V         FD  P        VGRLD +TEGLLLL
Sbjct: 64  YLMM-NKPPGVISATEDAVEETVVDLLEEEDRLFDPFP--------VGRLDKDTEGLLLL 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  P     + Y     G+V +D +   ++G+V+           +  + G
Sbjct: 115 TNDGQLAHQLLAPKKHVPKTYFAVIDGEVTEDDVEAFRRGVVLDDGYETKPAELVVLKSG 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
             + V V + EGK  ++K++F+    +V  L R+  GP  L   LA G  RE++
Sbjct: 175 LRSDVEVTITEGKFHQVKRMFQAVGKRVVYLKRVQMGPLSLDPNLAVGEYRELT 228


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 114/230 (49%), Gaps = 11/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI +RRE +R I    V+VNG  +      V   D ++ DG  +  AE+  
Sbjct: 61  RLNKYIANAGICARREADRYITAGNVEVNGKPMTELGYRVQPNDIVKFDGKNI-SAEKKE 119

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G +TT  D  GR TV +  + +    +  VGRLD  T GLLLLTNDG L + 
Sbjct: 120 YILLNKPKGFITTTQDEKGRKTVMELVVGAAQGNIKPVGRLDRLTTGLLLLTNDGDLIKK 179

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSNAWV 189
           L  PS    ++Y V     +   KL L     + +G+   D  + +D     +   +  +
Sbjct: 180 LTHPSHGVRKIYHV-----ILDKKLALPDFHKIQEGLTLEDGFIQVDDISFVEGAPHNEI 234

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            V +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 235 GVKIHSGRNRIVRRIFESLGYTVEKLDRVVFAGLTKKDLPRGHWRPLTQQ 284


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 125/238 (52%), Gaps = 17/238 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++VN+     I +++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKEAKLLAKKGLIEVDGKIIKDSSVNIDPEKSIVKINGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
             L + +KP G+++ TH   D   TV D L     IF     VGRLD +T GLLLLTNDG
Sbjct: 62  IYLMM-NKPTGVISATHDSKD--ETVIDLLELDHQIFDP-FPVGRLDKDTVGLLLLTNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKG 184
                +  P     +VY  +   +V++      KKG+V+    Y  ++  LD    + +G
Sbjct: 118 DFNHRMISPKWHVDKVYYAKIDKEVNEKDQEAFKKGVVLDD-GYKCLEAKLDIISASTEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           S   +T+  +EGK  ++K++FE  + KV  L R  +G   L  TL  G  RE+S + L
Sbjct: 177 SEVRITI--QEGKYHQVKRMFEARDKKVVYLKREEFGGLILDETLEEGEYRELSDEEL 232


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 119/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + ++ + V+G +    A N+      +   G  ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKKEILVDGQVAISLAQNIDTGLQELIFQGRKIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D     TV D LP      +V ++GRLD +T GLLLLTN+G L 
Sbjct: 61  YLML-HKPNGVVTASKDKK-LPTVMDLLPQHLQSDQVYAIGRLDRDTTGLLLLTNNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K GIV + G      Q+ + +   S +  T
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQQFKNGIVFLDGTICKPAQLEILSSSPSISRAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++KK+F     KV  L R+ +G F L   LA G  R ++++ L+
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTALKRVQFGDFLLDPDLAEGQYRLLNQEELK 231


>gi|329297161|ref|ZP_08254497.1| 23S rRNA pseudouridine synthase E [Plautia stali symbiont]
          Length = 222

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   SD  GR T+ D +P   S V + GRLD ++EGL++LTNDG L   
Sbjct: 43  RVILFNKPFDVLPQFSDEAGRRTLKDFVP--VSEVYAAGRLDRDSEGLMILTNDGALQAQ 100

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---------------GICYGDMQVT 178
           L  P  +  ++Y V+  G   +  L+ L++GI +                   +      
Sbjct: 101 LTQPGKRTGKIYYVQVEGVPQESDLSRLRRGIPLNDGPTLPAGAEVVPEPAWLWPRTPPI 160

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +     W+ + L EG+NR+++++     +   RLIR + G +QL  L  G  R++S 
Sbjct: 161 RERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFAMGDYQLQDLAPGEWRDISD 220

Query: 239 K 239
           +
Sbjct: 221 Q 221


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    R
Sbjct: 2   RLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  DPD  + + F ++P  + ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFMDVPVAY-KLHAAGRLDIDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     + +D       G+ +          TL  +K ++  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPATL--EKITDHVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGDIWLDSELEPGEFRELSDE 225


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 58/190 (30%), Positives = 94/190 (49%), Gaps = 16/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +P       RL L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLL
Sbjct: 1   MPKAPPSEPRLLLFNKPFDVLTQFNDERGRSTLKDFIP--VPGVYPAGRLDRDSEGLLLL 58

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT-- 181
           TNDG L   +  P  +  + Y V+  G  ++D+L  L++G+ +  G         LD   
Sbjct: 59  TNDGRLQARIADPRHKLPKTYWVQVEGTPEEDQLRRLREGVTLNDGPSLPAEARLLDEPA 118

Query: 182 -----------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  
Sbjct: 119 LWERVPPVRFRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGL 178

Query: 231 GSTREVSKKI 240
           G  REV  ++
Sbjct: 179 GEWREVPARL 188


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 11/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   + 
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+V+   D +   TV D L     IF     VGRLD NT GLLLLTNDG 
Sbjct: 62  IYLIM-NKPQGVVSATFD-NYDETVVDLLEDEDRIFEP-FPVGRLDKNTVGLLLLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--A 187
           L   L  P     ++Y  + + +V  + +   KKGI++    Y      L+  K  N  +
Sbjct: 119 LNHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDD-GYECFPAKLEIIKSFNEES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            V V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++
Sbjct: 178 EVRVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELT 228


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 119/238 (50%), Gaps = 17/238 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP+G+  T +D      + DN+        R+  VGRLD  +EGL+LLTNDG +
Sbjct: 61  VYIAFHKPVGITCTAADH-----IEDNIIDYIHYPERIFPVGRLDKASEGLILLTNDGTI 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +     +  + Y V          +N +  G+ I+       +VT    +   +   
Sbjct: 116 ANQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFR 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQL 245
           + L +G NR+I+++   F + V +L R+     +L  L  G  R V+ +   IL +QL
Sbjct: 172 IILTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELDILIDQL 229


>gi|315166874|gb|EFU10891.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
          Length = 257

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 78/258 (30%), Positives = 127/258 (49%), Gaps = 18/258 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRN-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++    G+M  
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVK 175

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                  T++ ++G++  V + ++EGK  ++K++       V  L R+  G   L  TL 
Sbjct: 176 PSRLVIETINEEEGTSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLE 234

Query: 230 AGSTREVSKKILREQLGP 247
            G  R +++  L +QL P
Sbjct: 235 LGEYRPLTEAEL-QQLQP 251


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 98/204 (48%), Gaps = 15/204 (7%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGL 84
           + SRRE +  I    V VNG ++      +   D ++     +   ER    L +KP   
Sbjct: 1   MCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTV-SIERKIYVLLNKPKDT 59

Query: 85  VTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           VTT  DP  R TV D +  +   R+  VGRLD NT G+LLLTNDG LA  L  P     +
Sbjct: 60  VTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKYLKKK 119

Query: 144 VYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAW----VTVGLREGK 197
           +Y V        DK NL K  +  +  GI   D ++  D    ++ +    V + +  GK
Sbjct: 120 IYHVHL------DK-NLTKADMEQIAAGIQLDDGEIQADAISYTDEFKKDEVGIEIHSGK 172

Query: 198 NREIKKVFEFFNWKVNRLIRISYG 221
           NR ++++FE   +KV +L R+ + 
Sbjct: 173 NRIVRRIFESLGYKVVKLDRVFFA 196


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVQVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSFSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST-REVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA S  R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>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 = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 115/238 (48%), Gaps = 15/238 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A+ G+ SRRE + +I +  ++++G  +  A   V     + +     R+ + 
Sbjct: 12  PLRINKWLAQEGVCSRREADALIEKGLIQLDGKPVTVAGERVTKGQTLSLTDAASRRLDN 71

Query: 73  TRLWLYHKPIGLVTTHSDP-----------DGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
               + +KP+G V+   +P           +  S     +P   +++  +GRLD ++ GL
Sbjct: 72  QLSVILNKPVGYVSGTPEPGEIPAIRLISEENLSGSAHAIPQRSNKMAPLGRLDKDSHGL 131

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+L+ DG LA+ +  P +   + Y V+  G +   K+ LL+ G+ + G      +VT + 
Sbjct: 132 LILSEDGVLAKAIIGPLSDMDKEYLVKVRGDITTAKVALLRHGLELDGRQLRPAEVTQE- 190

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  +   L+EG+NR+I+++ E    +V  L RI  GP  L  L  G  R +  K
Sbjct: 191 ---RGQVLRFVLKEGRNRQIRRMCELVELRVLDLQRIRVGPILLAGLPQGKWRPLGAK 245


>gi|317055194|ref|YP_004103661.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315447463|gb|ADU21027.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 246

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 120/243 (49%), Gaps = 16/243 (6%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A +    SR +V+++  ++++ VNG L+ R+   V + D I +DG  L   +  
Sbjct: 6   RLDKLVASQFADISRADVKKLCLKKKIMVNGKLMARSDAKVDTDDEIIIDGRKLTYKKHI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G+V + +     +TV D +P    R  +   GRLD +TEG +L+T+DG L+
Sbjct: 66  YIML-NKPAGVVCS-TKEGASTTVLDLVPDELRRDGLFPAGRLDKDTEGFVLITDDGELS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----VTLDTQKGSN 186
             +  P T   + Y VR     +    +++  G+ I G+  GD +             + 
Sbjct: 124 HRVLSPKTHVPKTYFVRLEKPWEDSYKDIMAAGMTIDGLHEGDSEEKCQPAQFLASDENV 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP------FQLGTLLAGSTREVSKKI 240
              T+ + EGK  ++K++FE    KV  L R++ G        +LG  L    ++V K +
Sbjct: 184 CECTLIIHEGKFHQVKRMFEKLGNKVVYLKRVAIGEMPLDRGLELGECLEIMHKDVEKLL 243

Query: 241 LRE 243
            R+
Sbjct: 244 ARK 246


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 126/236 (53%), Gaps = 17/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ ++++   IA+R+E+++M+ +  + VN + +++      S++HI+ +   ++  +   
Sbjct: 2   RLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKK------SSEHIDENNDVVKIYDEVI 55

Query: 74  --RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTND 127
             R +LY   +K  G VT+HS      TV D++  +    ++ VGRLD++T GLL++TND
Sbjct: 56  EYRKYLYFVMNKRKG-VTSHSKDPMYKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITND 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  L  P     + Y+V    +VD+   +  +KGI +          T++     N 
Sbjct: 115 GKFAHNLISPKKDVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIVTKPATMEIIDDYNC 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++T+  +EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 175 YLTI--KEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 113/222 (50%), Gaps = 7/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT+ G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDSGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + + EGK  +IKK+F     KV  L RI +G F L   LA S
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAES 220


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/217 (30%), Positives = 110/217 (50%), Gaps = 8/217 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G  SR+EV+++I    V VN + ++  + ++  +TD +E++G  +   E  
Sbjct: 2   RLDKFLVNQGFGSRKEVQKLIKAGIVYVNDVPVKDPSFHIDPNTDVVEIEGQEVEYKENY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L +KP G +T   D +   TV D   +  I +++  +GRLDI+TEGLL++T+DG LA
Sbjct: 62  YFML-NKPKGYITATYD-ENYPTVMDLFSAEPIVNKLFPIGRLDIDTEGLLIITSDGVLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
             L  P     + Y V   G V D D     K+GI ++   Y      ++  K S   + 
Sbjct: 120 HRLSHPKWNVEKEYFVIVEGDVSDIDFSKYEKEGIYLKKDKYKTKPFKVNVLKTSFEESE 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + + EGK   IKK+    + +V  L R+  GP  L
Sbjct: 180 LLITITEGKYHIIKKIMYALDHEVKYLKRVRIGPLTL 216


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/209 (30%), Positives = 102/209 (48%), Gaps = 10/209 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           + +R++K I+  G  SRRE +R+I Q RV +NG + E     V+  D + VD  P+  A 
Sbjct: 5   SAKRLNKFISETGFCSRREADRLIEQGRVTINGRVPE-MGTKVLPGDDVRVDDKPISAAT 63

Query: 72  RTRLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +++  +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG 
Sbjct: 64  DKPVYIALNKPTGITCTTERDIPGNIVDFVGHKK---RIFPIGRLDKPSDGLIFLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    V  D +N +  G+ I         VT +T+      +
Sbjct: 121 IVNKILRAGNNHEKEYVVRVDKPVSDDFINKMSSGVNILDTVTLPCTVTRETKFSFRIVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           T GL    NR+I+++ E   ++V +L R+
Sbjct: 181 TQGL----NRQIRRMCEALGYEVFKLRRV 205


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 121/234 (51%), Gaps = 19/234 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR-KAE 71
           R++K I+ +GI SRRE +R I Q  V++NG   +RA+V   V+ TD + V+G  +  +AE
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVRING---KRASVGDQVLPTDTVMVNGQIIEPRAE 64

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTND 127
             ++++  +KP+G+V+T       S   DN+        R+  +GRLD +++GL+ +T++
Sbjct: 65  EDQVFIALNKPVGIVSTTD-----SAERDNIQRFVGHTVRIFPIGRLDKDSQGLIFMTSN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     + +  ++ +  G+ I G      +V+ +    S  
Sbjct: 120 GDLVNKILRAGNNHEKEYLVTVDKPITKTFIDGMAGGVPILGTVTKKCRVSQE----SRF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +G NR+I+++ E F + V RL R       LG L  G  R+++ K L
Sbjct: 176 VFRIVLVQGLNRQIRRMAEHFGFDVTRLERQRIMNISLGNLPVGQWRDLTSKEL 229


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 109/206 (52%), Gaps = 11/206 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +++AG  SRRE ++++ Q RV +NG  +E     V S D + VDG  + K    +
Sbjct: 7   RINKYLSQAGFCSRREADKLMEQGRVTINGEYIE-MGTKVNSGDKVYVDGKLVEKETEEK 65

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++L  +KP G+V T +    ++ + D  + P   +R+  +GRLD  +EGL+L+TNDG + 
Sbjct: 66  VYLAVYKPKGVVCTTNSKVEKNNIVDFVDYP---TRIFPIGRLDKMSEGLILMTNDGEIV 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  +  D +  ++KG+ I       M    + +K  +    +
Sbjct: 123 NHILRARHFHDKEYLVTVNKTITDDFIEKMRKGVPI----LDTMSRRCEVEKLGDRSFKI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIR 217
            L +G NR+I+++ E  +++V  L R
Sbjct: 179 VLTQGLNRQIRRMCEALDYRVRTLKR 204


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 116/231 (50%), Gaps = 16/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR  E   
Sbjct: 4   RLNKHIADTGFCSRREADRLIGERRVTVNGVVAGTGAV-VGEEDTVLVDGQPLRAREAKK 62

Query: 72  ---RTRLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
              R  +++  +KP+G+  TT S   G    F        R+  +GRLD  +EGL+L+T+
Sbjct: 63  PGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKESEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKAVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               + L +G NR+I+ +   F+++V +L R+     +L  L  G  R +S
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFDYRVTQLRRVRIDNIKLAALKPGQWRNLS 226


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/217 (31%), Positives = 109/217 (50%), Gaps = 10/217 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R+EV++ I Q +V VNG +++ A   +  T D + + G  +      
Sbjct: 3   RLDKYLAEMGVGTRQEVKKQIRQGKVTVNGTVVKAADTKIDETCDEVTIGGRNISYVS-Y 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D   R T   +L     R  +  VGRLD +TEGLLL+TNDG LA
Sbjct: 62  EYYMLNKPGGVVSATEDR--RDTTVIDLIKDKKRKDLFPVGRLDKDTEGLLLITNDGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGS-NAW 188
             L  P     +VY  +  G V ++ +    +GI I G    +M     LD  K +  + 
Sbjct: 120 HRLLAPKKHVDKVYYAKIDGMVTEEDVKRFAEGIDI-GAEEEEMTRPAKLDIMKSAEESE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + + EGK  ++K++F     +V  L R   GP  L
Sbjct: 179 IRLTIHEGKFHQVKRMFLAVGKEVTYLKRERMGPLCL 215


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 78/258 (30%), Positives = 127/258 (49%), Gaps = 18/258 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++    G+M  
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVK 175

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                  T++ ++G++  V + ++EGK  ++K++       V  L R+  G   L  TL 
Sbjct: 176 PSRLVIETINEEEGTSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLE 234

Query: 230 AGSTREVSKKILREQLGP 247
            G  R +++  L +QL P
Sbjct: 235 LGEYRPLTEAEL-QQLQP 251


>gi|158319769|ref|YP_001512276.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158139968|gb|ABW18280.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 242

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 109/219 (49%), Gaps = 5/219 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K+++  G  SR+++ ++     VKV+G +++ ++ +V   +   + G  +      
Sbjct: 5   QRIDKILSNLGYGSRKDIRQICKNGLVKVDGKVVKDSSAHVDPENSQIIIGNEVVNYREF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + HKP G+++   D +   TV D L   +    V  VGRLD +TEGLLLLTNDG LA
Sbjct: 65  VYLMMHKPQGVISATED-NRDQTVVDLLDEEYLPFSVFPVGRLDKDTEGLLLLTNDGKLA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVT 190
             L  P     + Y  +  G V +  +   K+G+ I+   Y  +   L+  K    + + 
Sbjct: 124 HNLLSPKKNVPKTYYAKVLGTVTRSDIESFKEGVFIEE-DYKTLPAELNILKSDEISEIE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           + + EGK  ++K++FE  +  V  L R+S G   L   L
Sbjct: 183 LTIYEGKFHQVKRMFEAVDKTVVYLKRLSMGTLNLDPTL 221


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 111/232 (47%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRREADRLIEQGRVTINGNKPE-MGTKVLPGDDVCVDGKPVAAKEKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-GHQKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +VT +T+      +T GL
Sbjct: 124 ILRAGNSHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVTKETKFSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
               NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEVAEIL 231


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQL 245
           L +G NR+I+++   F + V +L R+     +L  L  G  R ++    +IL+ QL
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELGVGKWRNIATEELEILKGQL 229


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 122/237 (51%), Gaps = 23/237 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +G+ SRRE +R I Q  V +NG   +RA     V   D ++V+G  +  ++A
Sbjct: 8   RINKYISESGLCSRREADRFIDQGSVFING---KRAGTGDQVSPGDLVKVNGQIIEPQEA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTND 127
           E       +KP+G+V+T       S+   N+ S     +R+  +GRLD +++GL+ LTN+
Sbjct: 65  EDLIFIALNKPVGIVSTTE-----SSEPANIVSFVKHGARIFPIGRLDKDSQGLIFLTNN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGS 185
           G L   +   +    + Y V  +  + Q  ++ +  G+ I G      QVT   +  K S
Sbjct: 120 GDLVNKILRAANNHEKEYLVTVNKPITQAFIDGMSGGVPILG------QVTKKCKVVKES 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                + L +G NR+I+++ E F ++V RL RI      L  L  G  R++++K L+
Sbjct: 174 TYVFNITLVQGLNRQIRRMAEHFGYEVTRLERIRIMNVSLKGLALGDWRDLTQKELQ 230


>gi|315149408|gb|EFT93424.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 257

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 78/258 (30%), Positives = 127/258 (49%), Gaps = 18/258 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++    G+M  
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVK 175

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                  T++ ++G++  V + ++EGK  ++K++       V  L R+  G   L  TL 
Sbjct: 176 PSRLVIETINEEEGTSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLE 234

Query: 230 AGSTREVSKKILREQLGP 247
            G  R +++  L +QL P
Sbjct: 235 LGEYRPLTEDEL-QQLQP 251


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 104/240 (43%), Gaps = 24/240 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SKV+A  GI SRRE +  I    V V+G++++     +     I +          T 
Sbjct: 169 RLSKVMAERGICSRREADEWIMNSWVMVDGVIIDTLGTRINPDAEIVISSYAHEVQAETV 228

Query: 75  LWLYHKPIGLVTTHSD-----------PDGRSTVFDNLPSIFSR---------VISVGRL 114
             + HKP+G V+  ++           PD        L  +  R         +   GRL
Sbjct: 229 TIILHKPVGYVSGQAEDGYQPAIVLVHPDNEWLDDPELNQLHEREFQRRYLNGLAPAGRL 288

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ G+L+LT DG +AR L    +   + Y VR  G +D D L  L  G+ + G     
Sbjct: 289 DIDSTGMLVLTQDGRVARHLIGEDSTVEKEYLVRVEGSLDDDGLKRLNHGLSLDGEKLKP 348

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V+   +      +   LREGK R+I+++ E     V  L R+  G   LG L  G  R
Sbjct: 349 AKVSWQNED----QLRFVLREGKKRQIRRMCEMVGLHVVGLKRVRIGSVNLGKLPVGQWR 404


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 93/183 (50%), Gaps = 25/183 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L +KP  ++   +D  GR+T+   +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RIVLLNKPFDVLPQFTDEAGRATLKGLVP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA------ 187
           L  P  +  +VY V+  G+ D++ L  L++G++++        +  D +K          
Sbjct: 88  LTQPGQKTAKVYYVQVEGEPDEEALRHLRQGVILKD----GPTLPADAEKVEQPEWLWPR 143

Query: 188 -------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                        W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +
Sbjct: 144 NPPIRERKSIPTHWLKMTLYEGRNRQVRRMTAHIGFPTLRLIRFSMGNLTLGNLQPGEWK 203

Query: 235 EVS 237
           E+S
Sbjct: 204 EIS 206


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 113/229 (49%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G ++  +D     TV D  +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 65  IYLMM-NKPDGYISATTDK-YDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  K  + + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDD-RYKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELT 230


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 104/220 (47%), Gaps = 10/220 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G V  + +     GI +  G      ++ + T       + 
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTAEDVEAFAAGIELDDGYTCKPARLEIITPN----EIK 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V ++EGK  ++K++F      V+ L RIS G  QL   LA
Sbjct: 176 VTIQEGKFHQVKRMFAARGKSVSYLKRISMGNLQLDESLA 215


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/176 (36%), Positives = 96/176 (54%), Gaps = 6/176 (3%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
           E T L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G
Sbjct: 58  EHTYLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNA 187
            L   L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +
Sbjct: 116 PLGFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTICKPARLEILSASPSLS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
             ++ + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 176 QASITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 112/237 (47%), Gaps = 17/237 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPL 67
           E  T  R+ ++IA  G  S+R+V+ MI   RV + +G +L+       + D I VDG PL
Sbjct: 10  EGHTDMRLIRLIANLGYGSQRDVKAMIKAGRVTLADGTVLDDG--TKAAHDDIRVDGEPL 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLL 123
                  L L HKP G   + SDP GR  V++ LP  F      V  VGRLD ++ GLLL
Sbjct: 68  DPPPGLVLML-HKPEGYTCSTSDP-GR-IVYELLPERFMHRNPIVAPVGRLDRDSTGLLL 124

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLD 180
           LT+DG LA  +  P     + Y V     +  ++  +   G ++   +       ++ + 
Sbjct: 125 LTDDGPLAHRITSPKRHVPKTYEVTLARPLSGEEGAVFASGTLMLRSESTPLAPAELVVS 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +   +T    EG+  ++K++F      V RL R + G   LG L  G  R +S
Sbjct: 185 GPQTARITIT----EGRYHQVKRMFAAVGNHVERLHRAAIGGLDLGDLAEGQWRPLS 237


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/222 (31%), Positives = 114/222 (51%), Gaps = 7/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + + ++ V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + + EGK  +IKK+F     KV  L RI +G F L   LA S
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAES 220


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/214 (32%), Positives = 101/214 (47%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SRREV+ ++    V VNG + + + + V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGYGSRREVKPLLKSGSVTVNGTIQKDSKLQVNPEKDQITVHGNPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V    +   + GI +    Y      L+    S   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIEGNVTVADIEAFQTGITLDD-GYTCKPAHLEIITPSEINVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V  L RIS G  +L
Sbjct: 179 --QEGKFHQVKRMFAATGKTVTYLKRISMGKLKL 210


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 109/227 (48%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+N  +++  A  V   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINDEIVKNGATKVSQEDEIYFEDELLSWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V +H D D   T++    P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGYVCSHDD-DDYPTIYQFFEPPLSGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     V+    +  ++GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLADPVENHYASACEEGILLRGEKEPTKPAKLEVLDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G  +L  +L  G  R ++++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGNVELDESLEEGEFRPLTQE 225


>gi|289663281|ref|ZP_06484862.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 240

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 115/236 (48%), Gaps = 16/236 (6%)

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  LW----LY---HKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L     +Y   +KP+G+  TT S   G    F        R+  +GRLD  +EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKESEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V    L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDQFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 115/236 (48%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR      
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDGQPLRTRAASK 62

Query: 70  -AERTRLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
              R  +++  +KP+G+  TT S   G    F        R+  VGRLD  +EGL+L+T+
Sbjct: 63  PGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPVGRLDKESEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMASEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>gi|303233542|ref|ZP_07320201.1| pseudouridylate synthase [Finegoldia magna BVS033A4]
 gi|302495346|gb|EFL55093.1| pseudouridylate synthase [Finegoldia magna BVS033A4]
          Length = 235

 Score = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 126/236 (53%), Gaps = 17/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ K+++   IA+R+E+++M+ +  + VN + +++      S++HI+ +   ++  +   
Sbjct: 2   RLDKMLSEMKIATRKEIKQMVKKGIITVNDVTVKK------SSEHIDENNDVVKIYDEVI 55

Query: 74  --RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTND 127
             R +LY   +K  G VT+HS      TV D++  +    ++ VGRLD++T GLL++TND
Sbjct: 56  EYRKFLYFVMNKRKG-VTSHSKDPMHKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITND 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  L  P  +  + Y+V    +VD+   +  +KGI +           ++     N 
Sbjct: 115 GKFAHNLISPKKEVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIITKPAKMEIIDDYNC 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++T+  +EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 175 YLTI--KEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 106/215 (49%), Gaps = 7/215 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    VKV+G  ++ A V+V   +  I V G  +   E  
Sbjct: 2   RLDKLLSTIGYGSRKEVKGLLKTGAVKVDGTAVKDAKVHVNPDEQEITVHGEAVSYREFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP G+++   D     TV D   L         VGRLD +TEGLLLLTNDG LA
Sbjct: 62  YFML-HKPQGVISATEDS-LHETVLDLLELDDAVYDPFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  + +  V ++     ++G+ +  G      ++ + T  G  + + 
Sbjct: 120 HQLLSPKKHVPKTYFAKINAPVTEEDAEAFRQGVTLDDGYVTKSAELKILTS-GVESEIE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++K++FE    KV  L R+S G   L
Sbjct: 179 LTIVEGKFHQVKRMFEARGKKVTYLKRLSMGALLL 213


>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 = 85.1 bits (209), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 121/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 120/256 (46%), Gaps = 43/256 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDGVPLR--- 68
           R++K IA  GIASRR  + ++A  R+ +NG   E A +  M    +D IE+DG PL+   
Sbjct: 32  RINKYIAGLGIASRRAADELLADGRITING---ETAGLGEMVDPQSDRIELDGRPLKVEC 88

Query: 69  ---------KAERTRLW--------------LY---HKPIGLV-TTHSDPDGRSTVFDNL 101
                    KA   RL               +Y   +KP G+V TT S      T + N 
Sbjct: 89  APLPYAPYGKASPPRLTSKDDNQATSNYPQRVYIALNKPKGIVCTTDSREPENITEYMNF 148

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P    R+  +GRLD  + GLLLLTNDG +   +        + YRV     + +  L  +
Sbjct: 149 PI---RIFPIGRLDKASSGLLLLTNDGSIVNRILRAHNHHEKEYRVEVDKPLTEAALQTM 205

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + G+ I G+     ++ L     +   +T+ L +G NR+I+++ E+  +KV +L R    
Sbjct: 206 RTGVPILGVVTLPCRIKLL----NPTTMTIILTQGLNRQIRRMCEYCGYKVVKLERRRIM 261

Query: 222 PFQLGTLLAGSTREVS 237
              LG +  G+ R ++
Sbjct: 262 NITLGKMPVGAWRYLT 277


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 56/191 (29%), Positives = 94/191 (49%), Gaps = 16/191 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P       RL L++KP  ++T     DGR+T+ D +P     V   GRLD ++EGLLL
Sbjct: 22  GPPEAPQAAPRLILFNKPFDVLTQFRGGDGRATLKDFIP--VPGVYPAGRLDRDSEGLLL 79

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDT- 181
           LT+DG L   +  P  +  + Y V+  G+ D+ +L  L++G+ +        +V  LD  
Sbjct: 80  LTDDGRLQARIADPRHKLAKTYWVQVEGEPDEAQLQRLREGVTLNDGPTRPAEVRRLDAP 139

Query: 182 ------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                       +    AW+ + +REG+NR+++++         RL+R+  GP+ +  L 
Sbjct: 140 ELWPRDPPVRFRKSVPTAWLELTIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSVDGLA 199

Query: 230 AGSTREVSKKI 240
            G  RE   ++
Sbjct: 200 PGEWREAPARL 210


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 111/233 (47%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRREADRLIEQGRVTINGNKPE-MGTKVLPGDDVCVDGKPVAAKEKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-GHQKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +VT +T+      +T GL
Sbjct: 124 ILRAGNSHEKEYVVRVDKPITVEFLKQMSSGVKILDTVTLPCKVTKETKFSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L 
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEVAEILA 232


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 117/236 (49%), Gaps = 24/236 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER------AAVNVMSTDHIEVDGVPLR 68
           R+ K +A AG+ +R+EV+  I + RV VNG +  +        V+V+  D  E+      
Sbjct: 2   RLDKYLAHAGLGTRKEVKLAIRKGRVSVNGEVCRKDDRKIQEGVDVVCLDKEEI------ 55

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
             E     + +KP  +V+  SDP    TV D + +   +    VGRLD++TEGLLL+TND
Sbjct: 56  YYEAVVYIMLNKPQDVVSATSDP-TYETVLDCIDAFLPKDCFPVGRLDMDTEGLLLITND 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKG 184
           G LA  L  P     + Y V     + +     L+ G ++   + +    +++  DTQ  
Sbjct: 115 GKLAHRLLSPKHHVEKTYLVDLAQPLQEGDQKKLENGSIVLDEEPVLPARVEILEDTQ-- 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
               + + ++EG+  ++K++      +V  L RI+ GP +L   LA G  R +S++
Sbjct: 173 ----ILLHIQEGRFHQVKRMLHAIGNEVVHLKRIAMGPLRLDEALASGEWRYLSEE 224


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 101/205 (49%), Gaps = 7/205 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRREADRLIEQGRVTINGNKPE-MGTKVLPGDDVCVDGKPVAAKEKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDVPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +VT +T+      +T GL
Sbjct: 124 ILRAGNSHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVTKETKFSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRI 218
               NR+I+++ E   ++V +L R+
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRV 204


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/230 (31%), Positives = 116/230 (50%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+  I +  V+VNG ++++    V    D I  DG  +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSYIRKGFVEVNGEIIKKDDYKVDYQKDEIIFDGELIEYRPY 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP G V+   D +   TV D +    +  +  VGRLDI+TEGLLL++NDG  A
Sbjct: 63  VYLML-NKPKGYVSATKD-NVHPTVIDLIVGYENYDLFPVGRLDIDTEGLLLISNDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P+    +VY  R  G +++  +   K G+++  G       + +      +  V 
Sbjct: 121 HRLMSPNRNHAKVYVARIAGIMNEFDILAFKDGVILDNGYKCKPANLKILEVFDDSCEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + + EGK  ++KK+ E  N KV  L RIS     +  +L  G  RE++K+
Sbjct: 181 IEIFEGKFHQVKKMVEACNKKVTYLKRISIKGLTIDRSLQLGDFRELTKE 230


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 118/236 (50%), Gaps = 14/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   R  +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRACINGEVCTHGAL-VNEGDIVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP+G+  T ++      + DN+        R+  VGRLD  +EGL+LLTNDG +
Sbjct: 61  VYIAFHKPVGITCTAAEH-----IEDNIIDYIDYPERIFPVGRLDKASEGLILLTNDGAI 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +     +  + Y V          ++ +  G+ I+       +VT   Q    +   
Sbjct: 116 ANQILHGDHEHEKEYVVAVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVNQ----STFR 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L   +G
Sbjct: 172 IVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELEILIG 227


>gi|323488402|ref|ZP_08093649.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323397909|gb|EGA90708.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 237

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/222 (30%), Positives = 108/222 (48%), Gaps = 21/222 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K ++  G  SR+EV+ ++  + V+VNG ++    V+V   TD + V G  +   E  
Sbjct: 2   RLDKYLSNMGHGSRKEVKVLLKSKAVEVNGEIVRDPKVHVNEHTDLVSVGGEAVTYTEFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---------FDNLPSIFSRVISVGRLDINTEGLLLL 124
            L L +KP G+++   D   ++ +         F+  P        VGRLD +TEG LLL
Sbjct: 62  YL-LMNKPQGVISATEDKYDKTVIDLLGKDEQHFEPFP--------VGRLDKDTEGFLLL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  P     + Y     G V ++     KKG+V+    Y     +L+    
Sbjct: 113 TNDGKLAHELLSPKKHVDKTYFAHVEGVVTEEDTEAFKKGVVLDD-GYETKPASLNILDS 171

Query: 185 S-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +  + + + + EGK  ++K++FE    +V  L R+S GP  L
Sbjct: 172 AVVSKIELTITEGKFHQVKRMFESVGKRVVYLKRLSMGPLSL 213


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 121/238 (50%), Gaps = 20/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR    K 
Sbjct: 4   RLNKHIAETGFCSRREADRLIGERRVTVNGVIAGTGAV-VGEDDTVLVDGQPLRVREAKK 62

Query: 71  ERTRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLL 124
             TR  +Y   +KP+G+ +T       S+V  N+        R+  +GRLD ++EGL+L+
Sbjct: 63  PGTRRHVYIALNKPVGITSTTE-----SSVKGNIVEFVGHEQRIFPIGRLDKDSEGLILM 117

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T++G +   +     +  + Y V  +  V  + L  + +G+ +    + +  +   T + 
Sbjct: 118 TSNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRL----HDETTLPCRTARI 173

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +     + L +G NR+I+ +   F ++V +L R+     +L  L  G  R ++ + L+
Sbjct: 174 AKFGFRIVLEQGLNRQIRLMAAAFGFRVTQLRRVRIDNIKLAALKPGQWRNLTDQELQ 231


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 78/258 (30%), Positives = 127/258 (49%), Gaps = 18/258 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++    G+M  
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVK 175

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                  T++ ++G++  V + ++EGK  ++K++       V  L R+  G   L  TL 
Sbjct: 176 PSRLVIETINEEEGTSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLE 234

Query: 230 AGSTREVSKKILREQLGP 247
            G  R +++  L +QL P
Sbjct: 235 LGGYRPLTEAEL-QQLQP 251


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQL 245
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ +   IL +QL
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEELDILIDQL 229


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 57/179 (31%), Positives = 96/179 (53%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ +++KP  ++   +D  GR+T+ D +P   + V + GRLD ++EGLL+LTNDG L   
Sbjct: 31  RVLVFNKPYDVLPQFTDEMGRTTLKDFIP--LTDVYTAGRLDRDSEGLLVLTNDGKLQAR 88

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV---------TLDT 181
           L  P  +  ++Y V+  G  D+  LN L+ GI ++    +  G   V         T   
Sbjct: 89  LTQPHKKTAKIYYVQVEGIPDESALNKLRNGITLKDGPTLPAGAELVKEPEWLWERTPPI 148

Query: 182 QKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++  N   +W+ + L EG+NR+++++     +   RLIR S G  QL TL  G  +E++
Sbjct: 149 RERKNIPVSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSLGSIQLETLSPGEWKEIN 207


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 114/227 (50%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    R
Sbjct: 2   RLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQSGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  DPD  + + F ++P  + ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFMDVPVAY-KLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     + +D       G+ +      ++      +K ++  V + +
Sbjct: 121 ITSPKHECEKTYLVTLEQPLAEDTAAQFTAGVQLHS--EKNLTKPASLEKVTDYVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGISLDSELEPGEYRELSAE 225


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 123/244 (50%), Gaps = 18/244 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQKG 184
             L  P     + Y     G V  +   L  +G  ++    G+M         T++ ++G
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVKPSRLVIETINEEEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           ++  V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +
Sbjct: 177 TSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-Q 234

Query: 244 QLGP 247
           QL P
Sbjct: 235 QLQP 238


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 122/242 (50%), Gaps = 14/242 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           R++K IA  G  SRRE +R+IA +RV VNG      AV V   D + VDG PLR    + 
Sbjct: 4   RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQVLVDGQPLRARVARK 62

Query: 71  ERTRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             TR  +Y   +KP+G VT  ++   +  + D +     R+  +GRLD  +EGL+L+T++
Sbjct: 63  PGTRRHVYIALNKPVG-VTCTTETSVKGNIVDFVGH-EQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  V  + L  + +G+ I    +  M +   T + +  
Sbjct: 121 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRI----HDQMTLPCKTSRIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L  
Sbjct: 177 GFRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLLPK 236

Query: 248 HL 249
            L
Sbjct: 237 QL 238


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 90/338 (26%), Positives = 149/338 (44%), Gaps = 46/338 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE ++ I   RV VNGI  E   V V STD + VDG  L+   + 
Sbjct: 5   KRLNKFISDTGFCSRREADKYIEDGRVTVNGIRPE-MGVKVSSTDVVLVDGKTLKAIPKR 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               Y+KP+G+  T ++   +S +    N P    R+  +GRLD  +EGL+ LTN+G + 
Sbjct: 64  VYIAYNKPVGITCT-TERKIQSNIVKAVNYP---DRIFPIGRLDRPSEGLIFLTNEGDIV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +++  +  +  G+ I        +V   TQ G+  + T+
Sbjct: 120 NKILRAGNNHEKEYVVTVDKPLNRQFVAKMGNGVPILDTITKKCKV---TQTGAQQF-TI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+  ++V  L R+      L  L  G  R             HL E
Sbjct: 176 ILTQGLNRQIRRMCEYLGYEVVTLKRVRIMNVTLKGLKVGQWR-------------HLTE 222

Query: 252 EAQVNLDAPIYSS----ETLVRDRPNII-SEVPDDFTRMKKNSSQKNGLS---------- 296
           +    ++  I  S    E  V D  N +  + P    + +K S +K              
Sbjct: 223 QEMAIINNSISDSGKTQEHSVYDEANALQQQSPQAVAKPQKTSDKKRDFQGENPKRFNQG 282

Query: 297 ------KQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
                 K+++  TP  +R+  + V   K I ++  SDS
Sbjct: 283 ERTEERKKERSKTPYQKRS-TTYVGKPKSIKANKSSDS 319


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 111/228 (48%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V   + I  V G  +      
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEYKPFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+V+   D     TV D L      FS    VGRLD +TEGLLLLTNDG L
Sbjct: 64  YLMM-NKPSGVVSATEDA-VEETVVDFLEEEDRAFSP-FPVGRLDKDTEGLLLLTNDGQL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G+V +  +   ++G+V+           +  + G  + V 
Sbjct: 121 AHQLLSPKKHVPKTYFAVVDGEVTEADVAAFQRGVVLDDGYETKPAKLVVLKSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           V + EGK  ++K++F+    +V  L RI  GP  L   LA G  RE++
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLALDPDLAVGEYRELT 228


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 113/235 (48%), Gaps = 19/235 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++++ G+ SRRE +  I +  V V+G  + +  + V  T  I++  +   +     
Sbjct: 5   RLSKLMSQKGLCSRREADDYIERGWVFVDGERISQLGIKVFPTQEIKLARMAQAQQCDQI 64

Query: 75  LWLYHKPIGLVTTHSDPD--------GRSTVFDN--LPSIFS-----RVISVGRLDINTE 119
             L HKP+G V+   +           R + F +    S FS      +   GRLDI++ 
Sbjct: 65  TVLLHKPVGYVSGQPERGYKPAISLINRESEFQDSKASSSFSPLNLKGMAPAGRLDIDSS 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T DG +AR L    ++  + Y VR  G+V Q  LNLL  G+ + G       V +
Sbjct: 125 GLLVFTQDGRIARKLIGAESEIEKEYLVRAEGEVSQRTLNLLSHGLSLDGQAL-KRAVVV 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              K    ++   L+EG+ R+I+++ E    KV  L R+  G  +LG L  G  R
Sbjct: 184 QQNKDQLRFI---LKEGRKRQIRRMCELVGLKVTGLKRVRIGKVRLGELPLGKWR 235


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/209 (29%), Positives = 101/209 (48%), Gaps = 10/209 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +R+I Q RV +NG + E     V S D + VD  P+  A 
Sbjct: 5   TGKRLNKFISETGFCSRREADRLIEQGRVTINGKIPE-MGTKVQSGDDVRVDDKPIAAAS 63

Query: 72  RTRLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +++  +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG 
Sbjct: 64  DKPIYIALNKPTGITCTTERDIPGNIVDFVGHKK---RIFPIGRLDKPSDGLIFLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    +  D +  +  G+ I        +V  +T+      +
Sbjct: 121 IVNKILRAGNNHEKEYVVRVDKPISDDFIKKMSSGVNILDTVTLPCKVEKETKYSFRIVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           T GL    NR+I+++ E   ++V +L R+
Sbjct: 181 TQGL----NRQIRRMCEALGYEVFKLRRV 205


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 117/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQIIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +   + I+       QVT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSGVVKIKDGMTKQCQVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELDNLEVGKWRNVTSEELEILIG 227


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 117/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE + +I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEANSCSRRETDHLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+ LTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLIFLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRVDQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 112/226 (49%), Gaps = 6/226 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++AR G+ SR+EV R+I   +V+V G ++     +V     +EV+G PL    R 
Sbjct: 13  ERLDKLLARLGLGSRKEVGRLIRSGKVRVGGGVVLDPGFHVPEGAALEVEGRPL-AVRRH 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L HKP G VT+  +      + +  P+    +  VGRLD +TEGLLL T DG L   
Sbjct: 72  LHLLLHKPAGYVTSRKEGPSVYALLEGFPT--RDLSPVGRLDKDTEGLLLFTTDGELLHR 129

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y V          +   ++GI++ G      ++ L        WV + L
Sbjct: 130 LTHPRHKVEKRYLVHLLHPATAADVRAFQEGILLSGEKTLPARLHLGE---DPTWVELTL 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            EG+  ++K++F+    +V  L R++ GP  L  L  G+ R ++ +
Sbjct: 187 LEGRFHQVKRMFQARGNQVLYLKRLALGPLTLEDLPLGAARPLTPE 232


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 114/236 (48%), Gaps = 16/236 (6%)

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  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD  +EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKESEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHKKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCHTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>gi|313622662|gb|EFR93029.1| RNA pseudouridine synthase family protein [Listeria innocua FSL
           J1-023]
          Length = 233

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/215 (30%), Positives = 101/215 (46%), Gaps = 10/215 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPEKDQVTVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G V  + +     G+ +  G       + + T       + 
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EIK 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V ++EGK  +IK++F      V+ L RIS G  QL
Sbjct: 176 VTIQEGKFHQIKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 124/239 (51%), Gaps = 20/239 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-------MSTDHIEVDGVPL 67
           R+  ++A+  + SR+ +++ + +  + V+G      A N+       +  D I      +
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDQI------I 54

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLT 125
           +  E T L L HKP G+VT + D +   TV D LP      ++ ++GRLD +T GLLLLT
Sbjct: 55  QGYEHTYLML-HKPAGVVTANKDKE-LPTVMDLLPPDIQSDKLYALGRLDRDTTGLLLLT 112

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKG 184
           ++G L   L  P     + Y+V+ +G +  D + + +KGIV + G      ++ +     
Sbjct: 113 DNGPLGFQLLHPQYHVDKTYQVQVNGLLTPDHIQVFQKGIVFLDGTVCKPARLKILAASP 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           S++  ++ + EGK  ++KK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 173 SHSQASITISEGKFHQVKKMFLSVGVKVTSLKRIQFGDFTLKPDLAEGNYRPLNQKELQ 231


>gi|295111666|emb|CBL28416.1| pseudouridine synthase family [Synergistetes bacterium SGP1]
          Length = 244

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 108/226 (47%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++  +A  G+ASRR  E +I   RV+V   ++      V    D +  DG  L+  E  
Sbjct: 7   RLNAFLAACGVASRRRAEEVIRAGRVRVGDRIVLAPFFQVDPEVDEVTCDGRTLKATEPV 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+V   SD      V D LP      RV   GRLD  +EGLL+LTNDG L 
Sbjct: 67  YV-VMNKPGGVVCAVSDKYD-PVVVDLLPEAVKSRRVYPAGRLDRESEGLLILTNDGALT 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  PS    + Y    +  +++ +L   + G  I+G     + VTL  ++    WV+V
Sbjct: 125 QEVMHPSKGLHKEYEALLNVPINERQLARWRGGFEIEGRRAVPISVTLMDREPEGRWVSV 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + EG  RE++ +     + V RL+R   G   L  L  G   ++S
Sbjct: 185 VIGEGLKREVRVMANLAGFSVERLVRRRLGKMVLEKLRPGEFVDLS 230


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/227 (30%), Positives = 111/227 (48%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++     R++V  ++A+ RV V+G ++  A   +     + +DG  LR+ +   
Sbjct: 7   RLDRFISQHCQIPRKQVRLILAKGRVSVDGQVVRDADCQIDQFSQVMLDGQALRQEQPIY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           L L HKP+G+V+   D D   TV D LP    + +  VGRLD+NT GLLLLTND   ++ 
Sbjct: 67  LML-HKPVGVVSATKD-DEHKTVMDLLPDYQDKGLHIVGRLDLNTSGLLLLTNDSRWSKR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     + Q  +    +G              L+  +   A VT  L
Sbjct: 125 IMSPEHKVAKQYLVTLKAPLTQAYVKAFAEGFYFAFENITTQPAQLEILEPHLARVT--L 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  +IK++F  F  +V  L R+S G   L  TL  G  R ++ +
Sbjct: 183 HEGRYHQIKRMFGRFRNQVMALHRLSVGNLILDETLAVGQYRPLTPQ 229


>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 = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 118/234 (50%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +     + V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGEL-VSDGDVVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 RILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/214 (29%), Positives = 106/214 (49%), Gaps = 7/214 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R+ + I++    S  +   +IAQ+R+ V+G +       V    ++E+DG  L+   
Sbjct: 31  TTNRLDRFISQNSTFSISDTRLLIAQKRILVDGHVAHSNQQKVTKFTYVELDGNCLQDNN 90

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + L +KP G+V+   D    STV D +  S  + +  VGRLD NT GL+LLTNDG  
Sbjct: 91  PVYIVL-NKPKGVVSATKDIK-HSTVLDLIQHSQKNELHIVGRLDFNTTGLVLLTNDGAW 148

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +R + LP T+  +VY V     +  + + + ++GI      Y D+       +  + +  
Sbjct: 149 SRKISLPETKLAKVYEVTLSKPLSDEYITVFREGIYFG---YEDITTKPACLEILSEYTA 205

Query: 191 -VGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            + L EGK  ++K++F FF  K    I   +G F
Sbjct: 206 RLSLVEGKYHQVKRMFGFFKTKCWNFIEFLWGIF 239


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 105/215 (48%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHQLIKKGLVDVNGKTVKTPKEKINEDDVVTVNGEKV-AYQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D   ++ +    P   +  +  VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPTGVLSATEDRSQKTVISLLKPEDRYQGIAPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW--VT 190
           L  P+    +VYR +  G  D + +     G+ +  G      ++ +  Q   NA   + 
Sbjct: 121 LLAPNKHVAKVYRAQIAGVADDETVKTFASGMTLGDGTKLKPAKLRILKQDRENATSEIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK++F     KV  L R++ G   L
Sbjct: 181 IEISEGKYHQIKRMFGAVGMKVMALDRLAMGKLCL 215


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/176 (36%), Positives = 96/176 (54%), Gaps = 6/176 (3%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
           E T L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G
Sbjct: 58  EHTYLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNA 187
            L   L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +
Sbjct: 116 PLGFQLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST-REVSKKILR 242
             ++ + EGK  +IKK+F     KV  L RI +G F L   LA S  R +++K L+
Sbjct: 176 QASITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKELQ 231


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 107/216 (49%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV D L       +V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATEDSRHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             +  P     ++Y+ +  G +D++ +   +KGI ++   C    +++    +  S + V
Sbjct: 120 HAMLSPKKHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EGK  ++K++      +V  L R+  GP  L
Sbjct: 180 QITIAEGKFHQVKRMVAACGKEVADLQRLKMGPLSL 215


>gi|257086025|ref|ZP_05580386.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994055|gb|EEU81357.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 244

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 123/244 (50%), Gaps = 18/244 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQKG 184
             L  P     + Y     G V  +   L  +G  ++    G+M         T++ ++G
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVKPSRLVIETINEEEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           ++  V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +
Sbjct: 177 TSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAEL-Q 234

Query: 244 QLGP 247
           QL P
Sbjct: 235 QLQP 238


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/235 (31%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGAVTANKDKE-LPTVMDLLPSNIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY-GDMQVTLDTQKGSNAW 188
             L  P     + Y+V  +G +  D +   +KGIV     +C    +++   +   S A 
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDDTVCKPAKLEILSASPSLSQAS 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           +T+   EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITIS--EGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 231


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 124/240 (51%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    I SR +V+++I  +R+ ++  +      NV      I VDG  L +A+  
Sbjct: 2   RLDKLLETCQIGSRGQVKKLINAKRITIDDKVAIDGRQNVDPGLQRIGVDGNIL-QAKGH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D +   TV D L     F  +  VGRLD +TEGL+LLT++G L 
Sbjct: 61  HYFILNKPRGVVSALKDKE-HPTVIDCLIEADRFPNLYPVGRLDRDTEGLVLLTDNGPLG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGIC-YGDMQVTLDTQKGSNAW 188
             +  P+    + Y V  +G +D D  +  + G+V     +C    +++    +K S A 
Sbjct: 120 FRMLHPNHHVDKSYYVVVNGFLDDDLPSFFRAGVVFFDGTVCKAAAVEILSAGEKQSVAK 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQL 245
           VT  L EGK  +IKK+F  +  KV  L R+++  F LG L  G  R ++   K I+++ L
Sbjct: 180 VT--LSEGKFHQIKKMFLAYGVKVIYLKRMTFAEFTLGNLAEGEYRTLTDQEKTIVKQYL 237


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/259 (25%), Positives = 117/259 (45%), Gaps = 34/259 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLR----- 68
           R++K I+     SRR+ ++ I    +K+N   +     +V ++ D I+V+   +      
Sbjct: 47  RLNKFISINNNISRRKSDKFIQNGNIKINNKTIINPGTHVDITKDQIKVNDKKINIQNIK 106

Query: 69  -------KAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDIN 117
                      +  W+  HKP GL+ T+ D   R +VF   P       R++SVGRLD N
Sbjct: 107 NILNNYNINNNSYKWIVLHKPKGLICTNQDEKDRKSVFSIFPEDLLQKYRIVSVGRLDRN 166

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------- 170
           T G+LL TN+      L  P  + +R Y +   G V  D L +L  G+ ++         
Sbjct: 167 TSGILLFTNEYAWVNKLTHPKYERVRKYMIHIEGPVRMDALKMLANGVYLKDEDNDKKKN 226

Query: 171 ---------CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                       +  V +  Q    + + + ++EG+NR+I+K+F+  N  + ++ R ++ 
Sbjct: 227 KKTQPALIEVLREENVKIQNQIKKISVLNISIKEGRNRQIRKMFQQINQPIIKIKRTAFE 286

Query: 222 PFQLGTL-LAGSTREVSKK 239
              L  + L    RE++KK
Sbjct: 287 NITLKNIHLPKQYRELTKK 305


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 18/240 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ + +      SR EV++MI   RV V+G +   A   +  S   + +DG  +  A   
Sbjct: 11  RLDRYLVEMKKGSRSEVKKMIKSGRVSVDGEICREAERKIQPSASEVSLDGTQVGYAA-Y 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D  GR     +L     R  +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 70  EYFMLNKPAGVVSATED--GRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGKLA 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------ICYGDMQVTLDTQ 182
             L  P     + Y  R  G++ ++ +   K+G+ ++          +     +   D  
Sbjct: 128 HRLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDGTRTLPARLVIQKASETAEDDG 187

Query: 183 KGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           K  ++   + + + EGK  ++K++FE    +V  L R+S G  +L   LA G+ R ++++
Sbjct: 188 KADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLDESLAPGAYRRLTEE 247


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 69/222 (31%), Positives = 114/222 (51%), Gaps = 7/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + + ++ V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + + EGK  +IKK+F     KV  L RI +G F L   LA S
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAES 220


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 102/214 (47%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      + +  VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTDLFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V    +     GI +    Y     +L+    +   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDD-GYTCKPASLEIITPNEINVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V+ L RIS G  QL
Sbjct: 179 --QEGKFHQVKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 122/243 (50%), Gaps = 19/243 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----IEVDGVPLRKA 70
           R+ K++   G  SR +V+++I  + V ++G   + A     S D     I V+G  + KA
Sbjct: 2   RLDKLLEVTGFGSRNQVKQLIKGRSVLIDG---QPARAGCQSVDSGLQVIMVNGRQI-KA 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
              R +L HKP G+V+  SD     TV D +      + +  +GRLD +T GL+LLT++G
Sbjct: 58  FAHRYYLLHKPAGVVSACSDRK-HQTVIDLIRKEDRVANLYPIGRLDRDTTGLVLLTDNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGI-C-YGDMQVTLDTQKGS 185
            L   +  P     + Y V  +G +  D +   + G+  + G  C    +++    Q  S
Sbjct: 117 PLGFRMLHPKHHVNKTYLVTVNGSLAADAVPFFENGVTFLDGTRCKSAALRIIKADQMES 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILR 242
            A VT  L EGK  +IKK+F  +  KV +L RI +    LG L  G+ R+++   KK+++
Sbjct: 177 QAEVT--LSEGKYHQIKKMFLSYGLKVTQLKRIGFAEIALGDLAEGAYRQLTVKEKKLIK 234

Query: 243 EQL 245
             L
Sbjct: 235 TYL 237


>gi|313636574|gb|EFS02285.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL S4-171]
          Length = 233

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 101/214 (47%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SRREV+ ++    V VNG++ + + + V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKLQVNPEKDQITVHGNPVIYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V    +   + GI +    Y      L+    +   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDD-GYTCKPAHLEIMAPNEIRVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V  L R+S G   L
Sbjct: 179 --QEGKFHQVKRMFAATGKTVTYLKRLSMGKLML 210


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 95/179 (53%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ + +P  FS V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRSTLKEFIP--FSDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT------------ 178
           L  P+ +  +VY V+  G    D L+ L+ G+ ++    +  G   V+            
Sbjct: 88  LTQPAQKTGKVYFVQVEGVPGDDTLSQLRTGMTLKDGPTLPAGAELVSEPEWLWPRNPPI 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKTIPTSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGDLQPGEWKEIN 206


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 94/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  ++T  SD +GR+T+  F ++P ++      GRLD ++EGLLLLTNDGGL 
Sbjct: 32  RLILFNKPFDVLTQFSDGEGRATLKDFIDIPGVYP----AGRLDRDSEGLLLLTNDGGLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         L+          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVALNDGPTLPAEARRLEEPELWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV 
Sbjct: 148 VRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLGQGCWREVP 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 105/215 (48%), Gaps = 5/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR+EV ++I +  V VN ++++     V  +D + V+G  +   ++  
Sbjct: 2   RIDKYLANMNVGSRKEVHQLIKKGIVAVNDVIVKTPKQQVKESDQVTVNGDAV-AYQKYH 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP G+++   D +  + +    P   +  ++ VGRLD +T GLLLLTNDG L   
Sbjct: 61  YFLLNKPKGVLSATEDRNQPTVISLLAPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLNHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVT 190
           L  P     +VYR    G  +   +     G+ +     +   ++++    ++   +   
Sbjct: 121 LLAPGKHVDKVYRAEIAGVANDATVKTFASGMTLGDGTKLQPAELKILSQDEEHDRSTTE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK++F     KV  L RIS G   L
Sbjct: 181 IKICEGKYHQIKRMFGAVGMKVVELERISMGKLSL 215


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 68  LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILTNDGILQARLTQ 125

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L  L+ G+ ++       +V + ++              
Sbjct: 126 PQSKAPKTYWVQVEGVPQESDLEALRHGVTLKDGPTLPAKVKIMSEPELWPRNPPVRFRA 185

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + L EG+NR+++++     +   RLIR S G + LG L  G  RE++
Sbjct: 186 AIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRHSMGDWNLGDLQPGEWREMT 240


>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 = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 116/239 (48%), Gaps = 22/239 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           RVSK+++  G+ SRRE +  I Q  V V+G ++    V       IE+  G   ++A R 
Sbjct: 6   RVSKLLSELGLCSRREADSYIEQGLVTVDGEVVNELGVRAYRHQKIELQSGAKAQQASRI 65

Query: 74  RLWLYHKPIGLVTTHSD-----PDGRSTVFDNL----------PSIFSRVIS-VGRLDIN 117
            + L +KP+G ++   D     P       DN           P   ++ ++  GRLDI+
Sbjct: 66  TVIL-NKPVGYISHFDDEQEYQPAASLITPDNYFASPLDKGRNPRFNTKGLAPAGRLDID 124

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+LT DG +A++L   ++   + Y VR  G++  + L+ L+ G+ +  +     QV
Sbjct: 125 STGLLVLTQDGRIAKLLIGENSPIEKEYLVRVEGKLSFEDLDKLRHGLTLDDVVLKPAQV 184

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +   +      +   LREG+ R+I+++ E    KV  L R+  G   LG L  G  R V
Sbjct: 185 SWQNED----QLRFVLREGRKRQIRRMCEMVGLKVIGLKRVRIGRISLGPLPPGQWRFV 239


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 109/220 (49%), Gaps = 10/220 (4%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           G  SR+EV++++    VK++G  ++ A V+V +    + + G  +   E   L + HKP 
Sbjct: 2   GYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKEFVYLMM-HKPQ 60

Query: 83  GLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 61  GVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKN 198
              + Y     G V ++ +    KG+++    Y      L   K  + + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 217


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 119/242 (49%), Gaps = 14/242 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R++K IA  G  SRRE +R+IA +RV VNG      AV V   D + VDG PLR      
Sbjct: 4   RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQVLVDGQPLRARVARK 62

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A R      +KP+G VT  ++   +  + D +     R+  +GRLD  +EGL+L+T++
Sbjct: 63  PGARRHVYIALNKPVG-VTCTTETSVKGNIVDFVGH-EQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  V  + L  + +G+ I    +  M +   T + +  
Sbjct: 121 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRI----HDQMTLPCKTSRIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L  
Sbjct: 177 GFRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLLPK 236

Query: 248 HL 249
            L
Sbjct: 237 QL 238


>gi|227874423|ref|ZP_03992604.1| RluF protein [Oribacterium sinus F0268]
 gi|227839739|gb|EEJ50188.1| RluF protein [Oribacterium sinus F0268]
          Length = 240

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 123/243 (50%), Gaps = 23/243 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL----R 68
           R++K ++  GI SRRE +R I++ ++ VNG   E+A++   ++  + I +DG  +     
Sbjct: 2   RINKWLSAMGICSRREADRYISEGKLLVNG---EKASLGMEILGKEEILLDGKLISGKGH 58

Query: 69  KAERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           K E+ +  L  Y+KP G++ T  + D    V + +     R+  +GRLD ++EGLLLLTN
Sbjct: 59  KKEKPKPVLLKYYKPRGIICTTGEKDRGKNVIEAI-GYKERIYPIGRLDKDSEGLLLLTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVT 178
            G L   +   S    + Y V     V ++ L  +  G+ +        + + + D ++ 
Sbjct: 118 QGDLVNQINKASGYKEKEYIVSVDKPVTKEFLQEMSSGVYLPELERTTRRAVLWQDPKLP 177

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + Q+     V   L EG NR+I+++ E   ++V RL RI     +LG +  G   E+ +
Sbjct: 178 KEIQRRQFHIV---LTEGLNRQIRRMCEALGYEVTRLKRIRVMNIELGKMKPGEYFEIKR 234

Query: 239 KIL 241
           + L
Sbjct: 235 EEL 237


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 106/215 (49%), Gaps = 7/215 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    VKV+G  ++ A V+V   +  I V G  +   E  
Sbjct: 2   RLDKLLSTIGYGSRKEVKGLLKTGAVKVDGSAVKDAKVHVNPDEQEITVHGEAVSYREFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP G+++   D     TV D   L         VGRLD +TEGLLLLTNDG LA
Sbjct: 62  YFML-HKPQGVISATEDS-LHETVLDLLELDDAVYDPFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  + +  V ++     ++G+ +  G      ++ + T  G  + + 
Sbjct: 120 HQLLSPKKHVPKTYFAKINAPVTEEDAEAFRQGVTLDDGYVTKSAELKILTS-GVESEIE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++K++FE    KV  L R+S G   L
Sbjct: 179 LTIVEGKFHQVKRMFEARGKKVTYLKRLSMGALLL 213


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 116/234 (49%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  L K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAI-VNDGDVVTIDGQVLAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R ++   L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELDDLEVGKWRNITDGELEILIG 227


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 77/244 (31%), Positives = 116/244 (47%), Gaps = 30/244 (12%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR 68
             P R+SK +A  G+ SRRE +  I Q  VKV+G   E A +   V+  + IE+D    +
Sbjct: 1   MEPVRLSKRMAELGLCSRREADSYIEQGWVKVDG---EVAVLGQKVLPHNQIEIDK-KAQ 56

Query: 69  KAERTRL-WLYHKPIGLVTTHSD-----------------PDGRSTVFDNLPSIFSRVIS 110
            A+  R+  L +KP+G V+  ++                  DG    F   PS    +  
Sbjct: 57  DAQSARVTILLNKPVGYVSGQAEDGYLPAAALIKPENRWAEDGSRKRFQ--PSHLRGLAP 114

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLDI++ GLL+LT DG +A+ L    ++  + Y VR  G++    L LL  G+ + G 
Sbjct: 115 AGRLDIDSVGLLVLTQDGRIAKQLIGEHSEVEKEYLVRVEGELTPSGLALLNHGLELDGK 174

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V    +      +   LREGK R+I+++ E    +V  L RIS G  +LG L  
Sbjct: 175 KLLPAKVGWQNED----QLRFVLREGKKRQIRRMCELVGLRVVGLKRISIGKVKLGNLPT 230

Query: 231 GSTR 234
           G  R
Sbjct: 231 GQWR 234


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 111/240 (46%), Gaps = 26/240 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRK 69
           P R+SK +A  GI SRRE +  I +  V+VNGI     AV    V   D I+++     +
Sbjct: 4   PVRLSKRMAELGICSRREADSYIEKGWVRVNGI----PAVLGQKVSPADRIDLNKQAHEQ 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRL 114
                  L +KP+G V+   + D R+ V                   PS    +   GRL
Sbjct: 60  QANRVTILLNKPVGFVSGQPEKDYRAAVELITAENQWEGDTSRIAFHPSHTRNLAPAGRL 119

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   +    + Y VR  G + ++ L LL  G+ + G     
Sbjct: 120 DIDSVGLLVLTQDGRIAKQLIGDNGNSEKEYLVRVKGSLKENGLALLNHGLSLDGEKLRP 179

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV+   Q      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 180 AQVSWQNQD----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRVGRIKLGALPQGKWR 235


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 118/232 (50%), Gaps = 24/232 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  GI SRR  ++ I   RV +NG L E  +  + S+D ++VDG  + +  +  
Sbjct: 2   RINKFLSETGITSRRGADKFIEAGRVTINGNLAELGS-KIESSDEVKVDGKVIEQPNQQY 60

Query: 75  LWL-YHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++L  +KP+G+  TT    +G    F N      R+  +GRLD ++EGL+LLTNDG +  
Sbjct: 61  VYLALNKPVGITSTTERHIEGNIVDFVNHAE---RIFHIGRLDKDSEGLILLTNDGDIVN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------QKGS 185
            +     +  + Y V+    + +  L+ +++G+ I           LDT       +K S
Sbjct: 118 EILRVENEHEKEYVVKVDMPITESFLSKMEEGVEI-----------LDTKTLPAKAEKLS 166

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    + LR+G NR+I+++     ++V  L R+      LG L  G  R+++
Sbjct: 167 SYTFKLTLRQGLNRQIRRMCTALGYEVRSLKRVRIINIFLGDLPVGEWRDLT 218


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 92/181 (50%), Gaps = 16/181 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLTNDG L   
Sbjct: 10  KLLLFNKPFDVLTQFNDEQGRSTLKDFIP--VPGVYPAGRLDRDSEGLLLLTNDGRLQAR 67

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----------- 181
           +  P  +  + Y V+  G  D+++L  L++G+ +  G         LD            
Sbjct: 68  IADPRHKLPKTYWVQVEGTPDEEQLRRLREGVTLNDGPTLPAEARLLDEPTLWERVPPVR 127

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  REV  +
Sbjct: 128 FRKSVPTQWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLGEWREVPAR 187

Query: 240 I 240
           +
Sbjct: 188 L 188


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 114/221 (51%), Gaps = 13/221 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A AG  SR+EV++ I +  V++N +   +    +    D + V+G  +   E  
Sbjct: 2   RLDKYLAHAGYGSRKEVKQAIRKGLVRINEVECRKDDTRIQEGIDVVCVNGEEV-VYEAV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP  +V+  SDP    TV D + +I  R    VGRLDI+TEGLLL+TNDG LA 
Sbjct: 61  VYIMLNKPQDVVSATSDP-THETVLDCIDAILPRDCFPVGRLDIDTEGLLLITNDGKLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWV 189
            L  P    ++ Y V+    + + DK  L    IV+  + +    +++  +TQ      +
Sbjct: 120 RLLSPKNHVVKTYFVQLAKPLQEADKKRLEDGSIVLDEEPVQCARVELLEETQ------I 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + ++EG+  ++K++      +V  L RI+ GP QL   LA
Sbjct: 174 LLHIQEGRFHQVKRMLHAVGNEVVYLRRIAMGPLQLDEQLA 214


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 95/191 (49%), Gaps = 20/191 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T + L++KP  +++  SD  GR+T+ D +P     V  VGRLD ++EGLLLLTN+G +  
Sbjct: 37  TIVLLFNKPYNVLSQFSDQQGRATLKDFIP--IENVYPVGRLDRDSEGLLLLTNNGEIQH 94

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------ 186
            L  P  + ++ Y  +  GQ     L  L  G+ ++       +V++      N      
Sbjct: 95  RLAHPKFEKVKTYLAQLEGQPQAVDLAKLTCGVELKDGLTRPAKVSVIAPPNYNWHTAPN 154

Query: 187 ---------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--- 234
                    +W+ + + EGKNR+++++     +   RLIR++   F+LG L  G  R   
Sbjct: 155 IRERKTIPTSWLELKIYEGKNRQVRRMTAHIGFPTLRLIRVALSGFELGNLATGEYRLLT 214

Query: 235 EVSKKILREQL 245
           E+ K+ L  QL
Sbjct: 215 EIEKRQLFAQL 225


>gi|315146884|gb|EFT90900.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
          Length = 257

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 125/254 (49%), Gaps = 10/254 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++ G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGP 247
           R +++  L +QL P
Sbjct: 239 RPLTEAEL-QQLQP 251


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/185 (28%), Positives = 97/185 (52%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++++  R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  QESQPKRVILFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CY 172
           G L   L  P  +  ++Y V+  G+ D++ L  L+ G+ +        GI         +
Sbjct: 92  GALQAKLTQPGKRTGKIYFVQVEGEPDEEALAALRNGVTLNDGPTLPAGIERVNEPEWLW 151

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L  G 
Sbjct: 152 PRNPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRYAMGSYTLDSLANGE 211

Query: 233 TREVS 237
            R+V+
Sbjct: 212 WRDVA 216


>gi|257083600|ref|ZP_05577961.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256991630|gb|EEU78932.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 244

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 121/240 (50%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT--QKGSNAW 188
             L  P     + Y     G V  +   L  +G  ++ G      ++ ++T  ++   + 
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEVVKPSRLVIETINEEEGTSV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL P
Sbjct: 180 VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-QQLQP 238


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 52/178 (29%), Positives = 92/178 (51%), Gaps = 18/178 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP   +   +D +GR+T+ + LP   +      GRLD+++EGLL+LTN+G L   
Sbjct: 4   LLLINKPYNTLCQFTDGEGRNTLANLLPDGKYKDYYPAGRLDLDSEGLLILTNNGSLQHR 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----------------QGICYGDMQV 177
           +  PS +  + Y V+  G + Q+ +  L+ G+ +                Q +   +  V
Sbjct: 64  ISHPSQKLEKTYWVQVEGDITQEAIAQLEAGVELKDGKTKPAKAKKIAPPQNLWERNPPV 123

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             + +    +W+ + + EGKNR+++++    N+   RLIR + GP+QL  L  GS +E
Sbjct: 124 R-ERKNIPTSWLRLTISEGKNRQVRRMTAAVNYPTLRLIRAAIGPWQLDNLAPGSYKE 180


>gi|295098123|emb|CBK87213.1| ribosomal small subunit pseudouridine synthase A [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 235

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 106/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ +A  +     +E DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVKDSAFKLQPEHQVEYDGNPLTQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPEGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     V  D      KG+ +           L+    ++  +T+   
Sbjct: 122 TSPRHHCDKTYRVMLESPVSDDTAEQFAKGVQLHNEKDLTKPAVLEILTPTDVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G  +L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPDLAPGEYRPLTEE 225


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 96/179 (53%), Gaps = 21/179 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++T  +D +GR T+ D   +P++++     GRLD ++EGLLLLT+DG L  +L
Sbjct: 11  LFNKPYDVLTKFTDGEGRKTLKDYIKIPNVYA----AGRLDKDSEGLLLLTDDGKLNHLL 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 67  TDPKSKSYKTYLVQVEGEFSSEAAQKLQKGLLLKDGKTLPAKVKLIDEPDWLWERTPPIR 126

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  + + K
Sbjct: 127 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYSLGNLKSGEYKIIQK 185


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L +KP  ++T  +D  GR+T+  F ++P ++      GRLD ++EGLLLLTNDG L 
Sbjct: 10  RLLLLNKPFDVLTQFNDEQGRATLKDFVDVPGVYP----AGRLDRDSEGLLLLTNDGRLQ 65

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+  +++L  L+ G+++  G         LD          
Sbjct: 66  ARIADPKHKLAKTYWVQVEGEPSEEQLQQLRTGVMLNDGPTLPAEARRLDEPELWERNPP 125

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + +REG+NR+++++         RL+R++ GP++L  L  G  RE++
Sbjct: 126 VRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVAIGPWRLDGLQPGQWRELA 185

Query: 238 KKI 240
            ++
Sbjct: 186 ARL 188


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 96/186 (51%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P    E  ++ +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LT
Sbjct: 46  PKVAPEDRKVIVFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLT 103

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   ++ L+ L+KG+ ++       +V +  +   
Sbjct: 104 NDGVLQAKLTQPQSKSPKTYWVQVDGAPSEEDLDKLRKGVELKDGMTLPAKVEVMDEPSV 163

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+++ + EG+NR+++++     +   RLIR S G  +LG L  G
Sbjct: 164 WERNPPVRFRANIPTTWLSITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIKLGDLQPG 223

Query: 232 STREVS 237
           + +EVS
Sbjct: 224 AWKEVS 229


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 116/227 (51%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   VM  D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVMPGDVVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EELVFIALNKPVGIVSTTEDSE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E+F ++V +L R       L  L  G  R+++
Sbjct: 179 ITLIQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLAGLPPGEWRDLT 225


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 78/258 (30%), Positives = 127/258 (49%), Gaps = 18/258 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++    G+M  
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTVEDCQLFAQGFALKD---GEMVK 175

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                  T++ ++G++  V + ++EGK  ++K++       V  L R+  G   L  TL 
Sbjct: 176 PSRLVIETINEEEGTSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLE 234

Query: 230 AGSTREVSKKILREQLGP 247
            G  R +++  L +QL P
Sbjct: 235 LGEYRPLTEAEL-QQLQP 251


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 118/239 (49%), Gaps = 19/239 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--V 65
           N T  R++K I+ +G+ SRR+ +R I Q  V +NG    RA V   V+  D ++V+G  V
Sbjct: 3   NRTSTRLNKYISESGMCSRRDADRFIEQGNVHING---RRAQVGDQVLPGDVVKVNGQVV 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLL 122
             R  E       +KP+G+V+T       S   DN+        R+  +GRLD +++GL+
Sbjct: 60  EPRDEEDLVFIALNKPVGIVSTTD-----SAEKDNIQRFVGHSERIFPIGRLDKDSQGLI 114

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            LT++G L   +        + Y V     V ++ +  +  G+ I     G M      +
Sbjct: 115 FLTSNGDLVNKILRAGNNHEKEYLVTVDKPVTREFVEGMSNGVPI----LGTMTKRCKVE 170

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           K S     + L +G NR+I+++ E+F ++V RL R+      L  L  G+ R++++K L
Sbjct: 171 KVSRFVFRITLVQGLNRQIRRMAEYFGYEVARLERVRIMNVSLQGLPVGAWRDLTEKEL 229


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 57/179 (31%), Positives = 90/179 (50%), Gaps = 17/179 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   SD  GR T+ D +P   S + + GRLD ++EGL++LTNDG L   L  
Sbjct: 62  LFNKPFDVLPQFSDEAGRRTLKDFIPQ--SGIYAAGRLDRDSEGLMILTNDGTLQARLTQ 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQVTLDTQ 182
           P  +  +VY V+  G   ++ L  L+ G              IV       D    +  +
Sbjct: 120 PGKRTGKVYFVQVEGCPHENDLVPLRAGVDLKDGPTLPAEVEIVAAPDWLWDRHPPVRER 179

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K    +W+ + L EG+NR+++++     +   RLIR S G  QL TL  G  R++S +I
Sbjct: 180 KAIPTSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGTLQLQTLAPGEWRDISSEI 238


>gi|166711386|ref|ZP_02242593.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 240

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 114/236 (48%), Gaps = 16/236 (6%)

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  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD  +EGL+L+T+
Sbjct: 63  LGGRRHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKESEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>gi|163942282|ref|YP_001647166.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|163864479|gb|ABY45538.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
          Length = 229

 Score = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 118/236 (50%), Gaps = 14/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   R  +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRACINGEVCTHGAL-VNEGDIVTIDGQVIVKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP+G+  T ++      + DN+        R+  VGRLD  +EGL+LLTNDG +
Sbjct: 61  VYIAFHKPVGITCTAAEH-----IEDNIIDYIDYPERIFPVGRLDKASEGLILLTNDGAI 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +     +  + Y V          ++ +  G+ I+       +VT   Q    +   
Sbjct: 116 ANQILHGDHEHEKEYVVAVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVNQ----STFR 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L   +G
Sbjct: 172 IVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELEILIG 227


>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 = 84.3 bits (207), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 5/231 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV + ++     +R++V  ++ ++RV ++G+ +      V +   + VD   L+  +  R
Sbjct: 2   RVDRFLSNLPRFNRKQVRLLLVERRVSIDGVAVSDPHHEVRTFSRVCVDDEVLQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  +DP    TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATADPQ-HPTVLDLLDEPDKDELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T+  +VY V     +  +       G+             L+    + A +++  
Sbjct: 121 LTQPQTKLPKVYHVETEQDIGPEYATTFAGGLYFAFEDLTTQPAELELLGPTTARLSI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            EG+  ++K++F  F+ KV  L R   GP  L  TL  G  R ++   +R+
Sbjct: 179 IEGRYHQVKRMFGHFDNKVIGLHRERMGPLVLDATLAPGQYRALTDDEIRQ 229


>gi|119897392|ref|YP_932605.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669805|emb|CAL93718.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 201

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 58/183 (31%), Positives = 94/183 (51%), Gaps = 17/183 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +RL L +KP G++   S   GR+T+ D++P     V   GRLD ++EGLLLLT+DG L  
Sbjct: 2   SRLILLNKPYGVLCQFSGEPGRATLKDHVP--IPEVYPAGRLDTDSEGLLLLTDDGALQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLD-------- 180
            +  P  +  + Y V+  G+ D   L  L+ G+ +       C     V  D        
Sbjct: 60  RIADPRHKLPKTYLVQVEGEPDDAALAALRAGVDLGDFRTRPCSARRVVEPDWLWPRDPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +WV + LREGKNR+++++     +   RL+R++ GP++L  L  G+ REV 
Sbjct: 120 VRYRKSVPTSWVEIVLREGKNRQVRRMTAKVGFPTLRLLRVAIGPWRLDGLAPGAWREVE 179

Query: 238 KKI 240
            ++
Sbjct: 180 PRL 182


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 122/233 (52%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +   G  ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQGRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVI-SVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LP  I S ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPTGVVTANKDRE-LPTVMDLLPPDIQSDMLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++KK+F     KV  L RI +G F L   LA G  R ++++ L+
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTSLKRIQFGEFTLDPELAEGQYRPLNQEELK 231


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 122/244 (50%), Gaps = 18/244 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I   G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIAFMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQKG 184
             L  P     + Y     G V  +   L  +G  ++    G+M         T++ ++G
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVKPSRLVIETINEEEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           ++  V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +
Sbjct: 177 TSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAEL-Q 234

Query: 244 QLGP 247
           QL P
Sbjct: 235 QLQP 238


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 111/225 (49%), Gaps = 7/225 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R+ + I++    S  +   +IAQ+R+ ++G +       V    ++E+DG  L+   
Sbjct: 4   TTNRLDRFISQNSPFSISDTRLLIAQKRILLDGHVAHSNQQKVTKFTYVELDGNCLQDNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGL 130
              + L +KP G+V+   D    STV D +       +  VGRLD NT GL+LLTNDG  
Sbjct: 64  PLYIML-NKPKGVVSATKDIK-HSTVLDLIQHPQKNELHIVGRLDFNTTGLVLLTNDGAW 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +R + LP T+  +VY V     + ++ + + ++GI      Y D+       +  + +  
Sbjct: 122 SRKISLPETKLAKVYEVTLSKPLTEEYVAVFREGIYFG---YEDITTKPACLEILSEYTA 178

Query: 191 -VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGK  ++K++F FF  +V  L R S G   L  L  G +R
Sbjct: 179 RLSLVEGKYHQVKRMFGFFQNEVLELHRASVGNISLEGLEEGHSR 223


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 11/237 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A  G+ SR+EV+ +I +  ++VNG ++  ++A VN    D +   G  +   ++
Sbjct: 2   RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFE-DTVTYLG-EIIAYQK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 60  DFYYILHKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           A  L  P     + Y    +G + ++ + L  +G++I G        +Q+    Q+   +
Sbjct: 119 AHQLLSPKKHVEKEYLAEVNGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFCLPKDLNRGQYRPMTKEELEQ 235


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 89/176 (50%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 2   LFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDGKLQARLTQ 59

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DT 181
           P+ +  +VY V+  G  D D L  LK+G+ ++          L               + 
Sbjct: 60  PAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWPRHPPIRER 119

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 120 KTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEWKEIT 175


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 107/214 (50%), Gaps = 12/214 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN T  R++K ++  G  SRRE ++++ + R+ +NGI+ E     V   D + VDG  
Sbjct: 1   MEENLT--RINKFLSETGHCSRREADKLLDEGRITINGIVPE-MGTKVSHHDEVRVDGKL 57

Query: 67  LR-KAERTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +R K E+     ++KP+G+  TT+ D       F N P    R+  +GRLD  +EGL+ +
Sbjct: 58  VREKTEKPVYLAFNKPVGIECTTNLDVRYNIVDFINYPK---RIFPIGRLDKASEGLIFM 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y V  +  +    +  +  GI I        +V    ++ 
Sbjct: 115 TNDGDIVNKILRARNNHEKEYTVTVNKLITDRFIQKMSNGIPILDTVTKKCKV----EQI 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           S     + L +G NR+I+++ E+  ++V  L RI
Sbjct: 171 SKTTFKIVLTQGLNRQIRRMCEYLGYEVTSLKRI 204


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 111/228 (48%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V   + I  V G  +      
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEYKPFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+V+   D     TV D L      FS    VGRLD +TEGLLLLTNDG L
Sbjct: 64  YLMM-NKPSGVVSATEDA-VEETVVDLLEEEDRAFSP-FPVGRLDKDTEGLLLLTNDGQL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G+V +  +   ++G+V+           +  + G  + V 
Sbjct: 121 AHQLLSPKKHVPKTYFAVVDGEVTEADVAAFQRGVVLDDGYETKPAKLVVLKSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           V + EGK  ++K++F+    +V  L RI  GP  L   LA G  RE++
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLPLDPDLAVGEYRELT 228


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 113/241 (46%), Gaps = 27/241 (11%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R+SK+++  G+ SRRE +  I    V V+GI +            IE+ G   R  
Sbjct: 1   MTLVRISKLLSNQGVCSRREADHFIELGFVYVDGIKVTELGAKANPEQKIELRGEGHRLQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGR-----STVF-------DNLPSIFSRVISVGRLDINT 118
           +  +  L +KPIG V+ H+D +G+     S +        + L  +  ++   GRLDI++
Sbjct: 61  KSKKTILLNKPIGFVS-HADDEGKYKSSLSLILKENFFGDEKLDKLSFKLAPAGRLDIDS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LT DG +A+ +    ++  + Y VR  G +  + L LLK G+ +           
Sbjct: 120 TGLLVLTEDGVIAKKIIQEDSEIEKEYLVRVSGNLIPNGLKLLKHGLFLD---------N 170

Query: 179 LDTQKGSNAWVT-----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              +K   +W+        L+EGK R+I+++ E    KV  L R+  G  +L  L  G  
Sbjct: 171 KPLKKAIVSWINEDQLKFILKEGKKRQIRRMCELVGLKVVGLKRVRIGKIRLSNLPIGKW 230

Query: 234 R 234
           R
Sbjct: 231 R 231


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 114/236 (48%), Gaps = 16/236 (6%)

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  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD  +EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKESEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHKKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 109/229 (47%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R E + ++ + RV VNG + ++    +   D + VDG PL   +   
Sbjct: 2   RLDKYLAETAQCTRSEAKTLLNRGRVTVNGAVCKKGDTQLREGDSVAVDGAPLAYRQFVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP G+V+  +D    +TV D +   + R  +  VGRLD  + G +LLT+DGG A 
Sbjct: 62  LML-NKPEGVVSASTDKR-DTTVVDLIGDAYPRRELFPVGRLDKTSTGFVLLTDDGGFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V     + ++      +G+ +  G      +V   T  G    V V
Sbjct: 120 EILAPKRHVSKTYTVVIDTPLTEEMRRGFAEGVTLADGTALSPAEVEALTPDGLT--VKV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            LR+G   +IK++F  +   VN L R + G   L   LA G  RE+S +
Sbjct: 178 RLRQGVYHQIKRMFGVYGAGVNALHRDAIGGLALDPALAPGQWRELSAE 226


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 125/254 (49%), Gaps = 10/254 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++ G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGY 238

Query: 234 REVSKKILREQLGP 247
           R +++  L +QL P
Sbjct: 239 RPLTEAEL-QQLQP 251


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 108/220 (49%), Gaps = 12/220 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRK 69
            T  R++  +A+ G+ASRR+  R+I   RV +NG        ++  +   + VDG  +  
Sbjct: 1   MTSIRLAHYLAQCGVASRRQASRLIEAGRVLLNGNQASHTDYIDEHNASSLRVDGKAI-A 59

Query: 70  AERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E    WLY+KPIG+       DP   +++   LPS   R+   GRLD ++ GLLLLTND
Sbjct: 60  PEAKAYWLYNKPIGIDCRLLAQDP---ASLIHQLPSA-PRLYPAGRLDKDSRGLLLLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V+ +  +  + +  L  G+   G+    +    + ++ ++ 
Sbjct: 116 GDLTHKLMHPDFYHPKTYHVQVNQPLKDEDIMALSTGVAYPGV----LTRRCEVRRLADD 171

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
              + L +G NR+I+++ +   +KV  L R +    +L +
Sbjct: 172 KFEMILTQGLNRQIRRMCKALGYKVIDLQRTAIMKLELNS 211


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 74/230 (32%), Positives = 125/230 (54%), Gaps = 17/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     SR EV+  + ++ +KVNGI+L +       +D++EVD V + K E+ +
Sbjct: 5   RIEKFIADLTGLSRNEVKAKLKKKAIKVNGIVLSKLIKIDPESDYVEVDNV-VVKYEKFQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++++KP   V  +SDP+  +T+FD   LP+   +  S GRLD +TEGLL+L+NDG +  
Sbjct: 64  YYMFNKPANFVCANSDPN-EATIFDIVGLPN--KKFFSFGRLDKDTEGLLILSNDGEMCH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWV 189
            L  P     + Y V+   +++ D L L  + I I      D  V+   L+     + ++
Sbjct: 121 KLLSPKNHIPKKYYVKVDKKINSDVL-LNNRPIKIS----DDFIVSKYELEPIDEKSCFL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           T+   EGK  ++K++F  F   V  L R+ +G  +L  +L  G  R++S+
Sbjct: 176 TI--YEGKFHQVKRMFGAFGISVLYLKRVQFGNLKLDNSLKLGEIRKLSE 223


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 112/236 (47%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     +     
Sbjct: 5   RISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARAFPDQAITLERAAAARQTARV 64

Query: 75  LWLYHKPIGLVTTHSDP---------DGRST-VFDNLPSIFSR-----VISVGRLDINTE 119
             L HKP+G V+  ++          D RS    D  P  F R     +   GRLDI+++
Sbjct: 65  TILLHKPVGYVSGQAEKGYTPAVALIDARSRHAGDRAPLRFERGQLQGLAVAGRLDIDSQ 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      QV  
Sbjct: 125 GLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPAQV-- 182

Query: 180 DTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +  NA  +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R
Sbjct: 183 ---RWQNADQLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPVGQWR 235


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 121/237 (51%), Gaps = 14/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++ G  +R E +++I  +RV++NG +++   + +   +D I +DG  L    + 
Sbjct: 2   RLDKFLSQTGKFTRAEAKKVIKAKRVRLNGEVVKDGKIKINEDSDKIFLDGELLALNNKE 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KPIG+++   D D   TV D  N P     +  VGRLD  T GLL++TNDG  A
Sbjct: 62  VYYMLNKPIGVLSATRD-DKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD------MQVTLDTQKGS 185
             +  P     + Y     G++ + ++    +G+    +  GD      + +   ++K  
Sbjct: 121 HDIISPKKHVSKTYEAVVTGKISEKEVKTFSQGM---ELANGDKLQPAQLDIISYSEKDD 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + V V + EGK  +++++F   + +V  L R+  G  +L  TL  G  R+++++ L
Sbjct: 178 TSKVRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRKLTEEEL 234


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 107/216 (49%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E  
Sbjct: 2   RLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV D L       +V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPQGVISATEDSRHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             +  P     ++Y+ +  G +D++ +   +KGI ++   C    +++    +  S + V
Sbjct: 120 HAMLSPKRHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EGK  ++K++      +V  L R+  GP  L
Sbjct: 180 QITIAEGKFHQVKRMVAACGKEVADLQRLKMGPLSL 215


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 112/236 (47%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     +     
Sbjct: 5   RISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARAFPDQAITLERAAAARQTARV 64

Query: 75  LWLYHKPIGLVTTHSDP---------DGRS-TVFDNLPSIFSR-----VISVGRLDINTE 119
             L HKP+G V+  ++          D RS    D  P  F R     +   GRLDI+++
Sbjct: 65  TILLHKPVGYVSGQAEKGYTPAVALIDARSRYAGDRAPLRFERGQLQGLAVAGRLDIDSQ 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      QV  
Sbjct: 125 GLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPAQV-- 182

Query: 180 DTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +  NA  +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R
Sbjct: 183 ---RWQNADQLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPVGQWR 235


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 57/211 (27%), Positives = 106/211 (50%), Gaps = 20/211 (9%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           +N   ++   VN  ST       +P+      R+ L++KP  ++   +D  GR T+ + +
Sbjct: 1   MNKFSVKNHKVNRFSTQSPAKTAIPVPPQ---RVLLFNKPFDVLPQFTDESGRRTLKEFI 57

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P  F+ V + GRLD ++EGLL+LTN+G L   L  P+ +  +VY V+  G   ++ L  L
Sbjct: 58  P--FNDVYAAGRLDRDSEGLLVLTNNGKLQAKLTQPAQKTGKVYFVQVEGVPTEEALTQL 115

Query: 162 KKGIVIQG----------ICYGDM-----QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           ++G++++           +C  +          + +    +W+ + L EG+NR+++++  
Sbjct: 116 QRGVILKDGPTLPAGAELVCEPEWLWPRNPPIRERKSIPTSWLKITLFEGRNRQVRRMTA 175

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +   RLIR S G   LG L  G  +E++
Sbjct: 176 HIGFPTLRLIRFSMGNLSLGDLQPGEWKEIN 206


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 107/203 (52%), Gaps = 7/203 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++ A + SR++V+++I ++RVKVNG ++ +   NV   D + VD + +       + +++
Sbjct: 1   MSNAKVGSRKQVKKLIKEKRVKVNGSIVTKPEFNVDENDEVFVDDIEIIPHHNVYI-VFN 59

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           KP G  ++ S+ +     F + P +   +  VGRLD + EGL+L+TNDG     +  P +
Sbjct: 60  KPSGFTSSKSEYERNIFEFIDHPYL-DELHIVGRLDKDVEGLILITNDGNFTHKVISPKS 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y V+  G + ++ + +   GI +  GI +   ++T    K  +  +++ + EGK 
Sbjct: 119 NIEKEYIVKIEGILTKEMIEIASNGITLNNGIKFKPAKIT----KIDDETISLVITEGKF 174

Query: 199 REIKKVFEFFNWKVNRLIRISYG 221
            E+K +  F   K  ++ R+  G
Sbjct: 175 HEVKLIVGFLGLKYKKIKRVRIG 197


>gi|313617518|gb|EFR89863.1| RNA pseudouridine synthase family protein [Listeria innocua FSL
           S4-378]
          Length = 233

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 102/215 (47%), Gaps = 10/215 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVIYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NLSETVIDLLEQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G+V  + +     G+ +  G       + + T       + 
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGEVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EIK 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V ++EGK  ++K++F      V+ L RIS G  QL
Sbjct: 176 VTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 87/175 (49%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILTNDGILQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +              
Sbjct: 61  PQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTLWPRNPPVRFRA 120

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + L EG+NR+++++     +   RLIR S G + LG L  G  REV+
Sbjct: 121 AIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPGEWREVT 175


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 117/233 (50%), Gaps = 14/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAER 72
           R++K I+  G  SRRE ++++   +V +NG+   +A +   +   D + V+G P+     
Sbjct: 2   RINKFISETGFCSRREADKLVESGQVTINGV---KAVLGSQAEPGDDVRVNGRPIAAKRS 58

Query: 73  TRLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             +++  +KP+G+  TT +   G    F   P    R+  +GRLD ++EGL+LLT+DG +
Sbjct: 59  KHVYIALNKPVGITCTTETHVKGNIVDFVGHPE---RIFPIGRLDKDSEGLILLTSDGDI 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +     +  + Y V     +    +  + +G+ I     G+M +     + S+    
Sbjct: 116 VNKILRAEGKHEKEYIVTVDRPITPSFVKAMSEGVKI----LGEMTLPCKVTRVSDRVFR 171

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L EGKNR+I+++     ++V RL RI      LG    G+ R+++++  RE
Sbjct: 172 IILTEGKNRQIRRMCSALGYEVRRLQRIRIMNIHLGQQKVGTWRDLTEQEKRE 224


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 108/228 (47%), Gaps = 10/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           RV   +A  GI SRR  E +I +  +KVNGI   +    V   D +E    V + +  + 
Sbjct: 10  RVHVFLAEKGIGSRRFCEELIRKNLIKVNGIF-AKLGDKVFLGDRVEYGKQVFVFQDSKV 68

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
              +Y   +KPI  + ++ DP GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 69  VNKIYIALNKPINYLCSNFDPMGRKLAISLVQPLFRERLFSIGRLDFKSSGLLLFTNDGR 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  + Y +     V +D L   K GI +    +   ++      G+N   
Sbjct: 129 FANSIVHPKNEIEKEYIIESKRVVSEDLLVNFKNGIKVDNELF---KLKSYVMLGNNTAR 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L EGKNREI+KVF   N  + ++ R+  G   L  L  G  + +S
Sbjct: 186 LI-LTEGKNREIRKVFLSRNIFLKKVHRVRIGNITLSNLKEGQIKVLS 232


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 118/227 (51%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +G+ SRR  +R I Q  V +NG   ++A V   V   D + V+G  +  ++ 
Sbjct: 7   RLNKYISESGLCSRRAADRYIEQGNVYING---KKAKVGDKVFFGDLVMVNGQTIEPKEV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E + L  Y+KP+G+ +T ++   +  + D++ +   RV  +GRLD +++GL+ LTN+G L
Sbjct: 64  EHSVLIAYNKPVGITST-TEAGVKGNIVDHV-NHSERVFPIGRLDKDSQGLIFLTNNGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  + +  +  + KG+ I GI     +VT    K S     
Sbjct: 122 VNKILRAGNNHEKEYLVTVNKPLTEQFITNMSKGVPILGIMTKKCKVT----KESPFVFK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  RE++
Sbjct: 178 ITLIQGLNRQIRRMCEHFGFEVTKLERTRIMNIGLKGIPLGEWRELT 224


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 96/179 (53%), Gaps = 21/179 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++T  +D +GR T+ D   +P++++     GRLD ++EGLLLLT+DG L  +L
Sbjct: 11  LFNKPYDVLTKFTDGEGRKTLKDYIKIPNVYA----AGRLDKDSEGLLLLTDDGKLNHLL 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 67  TDPKSKSYKTYLVQVEGEFSPEAAQKLQKGLLLKDGKTLPAKVKLIDEPDWLWERTPPIR 126

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  + + K
Sbjct: 127 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYSLGNLKSGEYKIIQK 185


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 92/181 (50%), Gaps = 16/181 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLTNDG L   
Sbjct: 10  KLLLFNKPFDVLTQFNDEQGRSTLKDFIP--VPGVYPAGRLDRDSEGLLLLTNDGRLQAR 67

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----------- 181
           +  P  +  + Y V+  G  D+++L  L++G+ +  G         LD            
Sbjct: 68  IADPRHKLPKTYWVQVEGTPDEEQLRRLREGVTLNDGPTLPAEARLLDEPTLWERVPPVR 127

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  REV  +
Sbjct: 128 FRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLGEWREVPAR 187

Query: 240 I 240
           +
Sbjct: 188 L 188


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 123/244 (50%), Gaps = 18/244 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQKG 184
             L  P     + Y     G V  +   L  +G  ++    G+M         T++ ++G
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTVEDCQLFAQGFALKD---GEMVKPSRLVIETINEEEG 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           ++  V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +
Sbjct: 177 TSV-VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-Q 234

Query: 244 QLGP 247
           QL P
Sbjct: 235 QLQP 238


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 113/236 (47%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV V+G +++  AV +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTVDGEVVKSGAVKLTPEQEVAFDGNPLQQLSGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRV 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + +D      +G+ +      D+      +K  +  V + + 
Sbjct: 122 TSPKHHCEKTYLVTLEHPLAEDTAQQFAEGVQLHN--EKDLTRPAQLEKIEDTLVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G   +   LA G  R ++++ +     PHL
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAIVMDEDLAPGEYRPLTEEEIASVGAPHL 235


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 117/232 (50%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ K+++  G  +R+E++ ++ Q  V+++  +++ + + +   D  I V G  +   + 
Sbjct: 2   ERLDKILSNLGYGTRKEIKALVKQGLVEIDNEVVKDSGMKIDPDDKEIRVSGEMVNYRQN 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G+V+   D +   TV D L       +   VGRLD +T GLLLLTNDG L
Sbjct: 62  IYLIM-NKPNGVVSATFD-NYDETVVDLLDPEHQAFKPFPVGRLDKDTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
              L  P     ++Y       VDQ+ +   K GI +        G +++    + GS  
Sbjct: 120 NHRLISPKWHVDKIYYAEIDKPVDQNDVEKFKIGITLDDGYKCLPGKLKILESDENGSKV 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            VT+  +EGK  ++K++F   +  V  L RI +GP +L   L  G  RE+S+
Sbjct: 180 EVTI--QEGKFHQVKRMFNALDKNVVYLKRIKFGPMELDLDLEEGEYRELSE 229


>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 = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 99/205 (48%), Gaps = 9/205 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E   V VM  D + +D  PLR  ER  
Sbjct: 15  RLNKFISDTGYCSRREADKLIDQGRVTINGQKPE-MGVRVMDNDDVLIDDKPLRSKERPI 73

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP G+  TT    +G    F        R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 74  YIALNKPTGITCTTERHIEGNIVDF---IGHRKRIFPIGRLDKPSDGLIFLTNDGDIVNK 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +VT +T    N    + L
Sbjct: 131 ILRAGNSHEKEYVVRVDKVITPEFLEKMASGVEILDTVTLPCKVTKET----NFSFRIVL 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRI 218
            +G NR+I+++ E   ++V +L R+
Sbjct: 187 TQGLNRQIRRMCEALGYEVYKLRRV 211


>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 = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 54/189 (28%), Positives = 94/189 (49%), Gaps = 20/189 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L+L HKP  +++  +D  GR+T+ +  ++P I+      GRLD ++EGLLLLT DG LA 
Sbjct: 62  LYLLHKPYQMLSQFTDTRGRATLAEAIDVPDIYP----AGRLDYDSEGLLLLTGDGALAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDT---------- 181
            +  P  +  + Y V+  G+ +   L  L++G+ ++       +V  L++          
Sbjct: 118 RISHPRHKQPKTYWVQVEGEPEPAALQALRQGVTLRDGPTRPAKVRRLESPDVAPRHPPV 177

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    AW+ + L EG+NR+++++         RLIR++ G + L  L  G  R  + 
Sbjct: 178 RHREAVPTAWLELTLSEGRNRQVRRMTAHVGHPTLRLIRVAIGSWHLAGLAPGEWRRETL 237

Query: 239 KILREQLGP 247
              R Q  P
Sbjct: 238 HAPRAQAAP 246


>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 = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 116/240 (48%), Gaps = 19/240 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E+++++ Q +V V G +++ +   V    D +  DG  +   E  
Sbjct: 6   RIDKLLSHTGYGTRSEIKKLVKQGKVTVAGKVVKDSGQLVDPELDEVAFDGELVLYREVI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            L + +KP G+++   D   R+ +      D L   F     VGRLD +T GLLLLTNDG
Sbjct: 66  YLMM-NKPPGVISATEDRRERTVIDLLEQEDQLMDPFP----VGRLDKDTVGLLLLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----- 183
            LA  L  P     + Y     G V ++     K G+ +    Y  M   L   K     
Sbjct: 121 QLAHELLSPRKHVPKTYEAVVQGDVGEEDQEQFKAGVTLDD-GYVTMPSDLKILKKDSGE 179

Query: 184 -GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            G  + +++ + EGK  ++K++FE    KV  L RIS GP +L   L  G+ RE++ + L
Sbjct: 180 GGVTSVISLTIMEGKFHQVKRMFEAVGKKVVFLKRISMGPLELDADLEEGTYRELTDEEL 239


>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 = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/228 (31%), Positives = 108/228 (47%), Gaps = 10/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL----RKA 70
           RV   +A  G+ SRR  E +I +  V++N  L  +    V   D +E           K 
Sbjct: 10  RVHVFLAEKGVGSRRFCEDLIRKNSVRINNTL-AKLGDKVFLGDRVECRKQVFVFRDCKV 68

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
           E       HKP   + ++ DP+GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 69  ESKIYIALHKPKNYLCSNFDPEGRQLAISLVQPLFKERLFSIGRLDFKSSGLLLFTNDGQ 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P ++  + Y V     V+++ L   K GI I    +   ++      G+N+ V
Sbjct: 129 FANNIVHPRSKVEKEYIVESKRAVNENLLINFKHGIKIGREIF---KLKSYVMLGNNS-V 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L EGKNREI+KVF   N  + ++ RI  G  +L  L  G  + +S
Sbjct: 185 KLVLTEGKNREIRKVFLSKNIFLKKIHRIRIGNIKLDDLKEGQIKVLS 232


>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 = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 59/209 (28%), Positives = 104/209 (49%), Gaps = 13/209 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +++ G  SRR  +++I Q R+ +N  + E     V   D ++VDG P+ K E   
Sbjct: 6   RINKYLSQLGYCSRRAADKLIDQGRITINDKVPE-MGTKVTPGDLVKVDGKPVSKEELKE 64

Query: 75  LWLY---HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +Y   +KP+G+V T      +  + D  N P    R+  +GRLD  +EGL+ LTNDG 
Sbjct: 65  PNVYIAFNKPVGIVCTTDTRVEKDNIIDYINYPK---RIFPIGRLDKPSEGLIFLTNDGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  V  + L  +  G+ I      + ++    +K  +   
Sbjct: 122 IVNKILRARNNHEKEYVVSVNKPVSSEFLKKMSAGVPILDTVTRECEI----EKLGHHTF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            + L +G NR+I+++ EF +++V  L RI
Sbjct: 178 RIVLTQGLNRQIRRMCEFLDYQVTSLKRI 206


>gi|315170764|gb|EFU14781.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 257

 Score = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 76/254 (29%), Positives = 125/254 (49%), Gaps = 10/254 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGNVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++ G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGY 238

Query: 234 REVSKKILREQLGP 247
           R +++  L +QL P
Sbjct: 239 RPLTEAEL-QQLQP 251


>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 = 84.0 bits (206), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 119/239 (49%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ + +      SR EV++MI   RV V+G +   A   +  S   + +DG  +  A   
Sbjct: 6   RLDRYLVEMKKGSRSEVKKMIKSGRVSVDGEICREAERKIQPSASEVSLDGTQVGYAA-Y 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D  GR     +L     R  +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 65  EYFMLNKPAGVVSATED--GRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGKLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG------ 184
             L  P     + Y  R  G++ ++ +   K+G+ ++ G      ++ +  + G      
Sbjct: 123 HRLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDGTRTLPARLLIQKEAGTAEEGK 182

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
              S + + + + EGK  ++K++FE    +V  L R+S G  +L   LA G+ R ++++
Sbjct: 183 ADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLYESLAPGAYRRLTEE 241


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 115/230 (50%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A AG  SR +V+ ++  ++V VNG    +A   +  + D +EV+G  +   E  
Sbjct: 2   RLDKFLAEAGFGSRSQVKNLLKTKKVCVNGKNESQAKKQINPNLDRVEVEGQEVLYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D     TV D L +   +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  -YYMLNKPKGVVSATQDK-VHQTVLDLLDATAKQKAVFPVGRLDKDTHGLLLLTNNGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     +VY     G +    +   +KGI +    C    +++    +    + V
Sbjct: 120 HRLLSPKKHVNKVYVAEVDGLMTSQDIEAFEKGIQLSDHQCQPAVLEILASDRDKFQSRV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
            + ++EGK  ++K++      +V  L R+  GP QL  TL  G+ R++ K
Sbjct: 180 KIVIKEGKFHQVKRMVLACGKEVRDLQRLEMGPLQLDSTLDLGAFRKLEK 229


>gi|145342798|ref|XP_001416276.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576501|gb|ABO94569.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 249

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 79/251 (31%), Positives = 116/251 (46%), Gaps = 24/251 (9%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E+   +RVSK++AR G  SRRE ER+I   RV V+G  +E       +   IE+ G   R
Sbjct: 2   EDDELERVSKILARRGTCSRREAERLIEDGRVLVDGETIE-LGFKARANARIEITGEGTR 60

Query: 69  KAERTRLWLYHKPIGLVT-----------THSDPDG------RSTVFDNLPSIFSRVIS- 110
                   + +KP G V+              +P          T  D+L  +   V S 
Sbjct: 61  WLREKLTVIVNKPPGYVSNLPAEGEIAAAACVEPRNAWMRAMEGTPMDDLKRVTRDVSSF 120

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++ GLL+LT DG LAR + +     L+ Y V     V +  +  L   + + 
Sbjct: 121 NVCGRLDKDSRGLLILTEDGALARSV-IGGNGVLKKYVVTTDADVRESHMRSLNGRVQLD 179

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+    M V      GS   +   LREGKNR+I++V E F  +V  L R+  G  Q+G L
Sbjct: 180 GVELLPMNVQ-RLGHGSRT-LEFNLREGKNRQIRRVCEKFGLRVVDLHRVQIGDVQIGDL 237

Query: 229 LAGSTREVSKK 239
             G+ R +S++
Sbjct: 238 PEGAWRLMSER 248


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/236 (28%), Positives = 116/236 (49%), Gaps = 13/236 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--V 65
           N +  R++K I+ +GI SRRE +R I Q  V +NG   +RA V   V   D ++V+G  +
Sbjct: 3   NDSTTRLNKYISESGICSRREADRYIEQGNVYING---KRAEVGDRVAPGDTVKVNGQII 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             ++ E       +KP+G+V+T    +  + V        +R+  +GRLD +++GL+ LT
Sbjct: 60  EPQEPEDFVFIALNKPVGIVSTTESSERNNIV--RFVGHSTRIFPIGRLDKDSQGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G L   +        + Y V  +  +  + +  +  G+ I     G M      +K S
Sbjct: 118 NNGDLVNKILRAGNDHEKEYLVEVNKPIRDNFIEGMANGVPI----LGTMTKKCKVKKES 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + L EG NR+I+++ E+F + V  L R+      L  L  G  R++++K L
Sbjct: 174 PTVFRITLVEGLNRQIRRMCEYFGYDVVALERVRIMNVDLKGLATGDWRDLTQKEL 229


>gi|160880922|ref|YP_001559890.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429588|gb|ABX43151.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 240

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/228 (32%), Positives = 114/228 (50%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV++MI + RV VNG         V S  D I VD   L      
Sbjct: 9   RLDKYLADLSVGTRTEVKQMIRKGRVMVNGNTETSPETKVDSNHDKIFVDSRELSYV-TL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+  +D   ++TV D +     + +  VGRLD +TEGLL++TNDG LA 
Sbjct: 68  EYFMLNKPAGVVSASNDK-KQTTVVDLIDEAKRKDLFPVGRLDKDTEGLLIITNDGDLAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +    + ++       G+ I    +  +   L+      A+VT+ 
Sbjct: 127 QLLSPKKHVDKVYFAKLRDPLKKEDEEAFAAGLKIDE-EFTALPAKLERISEQEAYVTI- 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            REGK  +IK++FE    +V  L RIS G   L   L+ G  RE++++
Sbjct: 185 -REGKFHQIKRMFEATRNEVIYLKRISMGSLVLDESLSLGEYRELTEE 231


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/255 (27%), Positives = 125/255 (49%), Gaps = 15/255 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VP 66
           T +R++K I+ +G  SRRE +++I + RVK+NG + E     V+  D + VDG     V 
Sbjct: 5   TGKRLNKYISDSGFCSRREADKLIEKSRVKINGTIPE-LGTKVLPGDIVLVDGRAINAVA 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             K++R  +  Y+KPIG+  T ++ D R  + D +     R+  +GRLD  +EGL+ LT+
Sbjct: 64  ENKSDRIYIA-YNKPIGITCT-TERDVRGNIIDAIRH-KKRIFPIGRLDKPSEGLIFLTS 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V     + +  +  +++G+ I         V +     S 
Sbjct: 121 DGDIVNKILRAENAHDKEYLVTVDKPLSERFVERMQRGVPILDTITKPCIVKVQ----SR 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE--Q 244
              ++ L +G NR+I+++ E+  ++V  L R       L  L  G  R +S + ++E  Q
Sbjct: 177 FVFSIILTQGLNRQIRRMCEYLGYEVQALQRTRIMQVTLKNLKPGQWRNLSVQEMQEINQ 236

Query: 245 LGPHLLEEAQVNLDA 259
              H  + AQ+   A
Sbjct: 237 AVSHSSKTAQITTPA 251


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 109/234 (46%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I   RV +NG + E     V+  D +E+D  P+R  E+ 
Sbjct: 8   KRLNKYISETGFCSRREADKLIDAGRVTINGKIPE-MGTKVLPGDDVEIDNKPVRSREKP 66

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 67  IYIALNKPTGITCTTERDIPGNIVDF---IGHHKRIFPIGRLDKPSDGLIFLTNDGDIVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I       + +    +K +     + 
Sbjct: 124 KILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHI----LDTVTLPCKVEKETKFSFRIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L 
Sbjct: 180 LTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILA 233


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 108/225 (48%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ +A  +++ + +E DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVDGEIVKDSAFKLLADNDVEYDGNPLIQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D   L  KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAALFAKGVQLNN--EKDLTKPAQLEVITPTEVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           EG+  ++K++F      V  L R   G  +L   LA G  R +++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPELAPGEYRPLTE 224


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/229 (31%), Positives = 117/229 (51%), Gaps = 18/229 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV+R I + R+ VNG +++     + + TD +  DG  +   E  
Sbjct: 5   RLDKYLADMGLGTRTEVKRDIKKGRISVNGEIVKSPEYKIDIQTDVVLADGKEIAYEELV 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D   + TV D +     + +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 65  -YYMLNKPQGVVSATEDRRDK-TVLDLISEKKRKDLFPVGRLDKDTEGLLLITNDGELAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------QKGSN 186
            L  P     + Y VR    + ++    L++G+ I     G+ ++TL +      +K   
Sbjct: 123 NLLSPKKHVDKKYFVRLRDALSEEDKKHLEEGVDI-----GEDKLTLPSHVFVLNEKRDE 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           A + +  REGK  +IK++F     +V  L R+S G   L   LL G  R
Sbjct: 178 AEIVI--REGKFHQIKRMFHAVGNEVVFLKRLSMGSLTLDEALLTGEYR 224


>gi|313500758|gb|ADR62124.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 210

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 94/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  ++T  SD +GR+T+  F ++P ++      GRLD ++EGLLLLTNDGGL 
Sbjct: 32  RLILFNKPFDVLTQFSDGEGRATLKDFIDIPGVYP----AGRLDRDSEGLLLLTNDGGLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         L+          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLEEPELWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV 
Sbjct: 148 VRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWREVP 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 93/188 (49%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    +V  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQVYPVGRLDRDSEGLLLLTNNGEI 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGS---- 185
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 156 PKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 215

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 216 LDEKEKRQ 223


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 53/160 (33%), Positives = 86/160 (53%), Gaps = 17/160 (10%)

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           GR+T+ D +P  FS V + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G 
Sbjct: 2   GRTTLKDFIP--FSDVYAAGRLDRDSEGLLILTNDGKLQAQLTQPGKKTAKVYYVQVEGV 59

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQKGSNAWVTVGLREGK 197
            D++ L+ L+KGI+++        V L               + +    +W+ + L EG+
Sbjct: 60  PDEESLDKLRKGIILKDGLTLPAGVELVNEPTWLWVRHPPIRERKSIPVSWLKITLYEGR 119

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           NR+++++     +   RLIR S G  QLG +  G  +E++
Sbjct: 120 NRQVRRMTAHIGFPTLRLIRFSMGTLQLGEIKPGEWKEIN 159


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 74/228 (32%), Positives = 111/228 (48%), Gaps = 13/228 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +S+ +AR G  SR++V+ +I Q RV   +G+ L          D + VDG PL   E   
Sbjct: 3   LSRYLARLGYGSRKQVDILIRQHRVTTRDGVALRDG--ECPPHDTLAVDGEPLDPPEGA- 59

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SR---VISVGRLDINTEGLLLLTNDGGL 130
           + L HKP+G V + +D      V++ LPS F SR   + +VGRLD +T GLLLLT+DG L
Sbjct: 60  VVLLHKPLGYVCSTNDRP--PIVYELLPSRFLSRSPVMATVGRLDADTSGLLLLTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              +  P T   + YRV     +  D+      G ++++G        TL         V
Sbjct: 118 NHRITSPRTHVPKTYRVTLAESLHGDEAAQFASGTLMLKGEDAPLRPATLFVHDART--V 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L EG+  +++++F      V  L RI+ G   L  L  G  R +S
Sbjct: 176 DLSLVEGRYHQVRRMFAATGNHVVTLQRIALGSLTLEGLAEGEWRVLS 223


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 120/229 (52%), Gaps = 17/229 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRRE +R I Q  V +NG   +RA++   V + D ++V+G  +   + 
Sbjct: 18  RLNKYISESGICSRREADRYIEQGLVLING---KRASIGDQVFAGDEVKVNGRLIEAQDN 74

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L   +KP+G+V+T  D +  + V  +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 75  SELVLIALNKPVGIVSTTDDGEKDNIV--DYVNHSTRIFPIGRLDKDSQGLIFLTNHGDL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  + ++ +  G+ I G      Q T   +    A + 
Sbjct: 133 VNKILRAGNDHEKEYLVTVNKPITDEFIHGMGAGVPIMG------QKTKKCKVKKEAPMV 186

Query: 191 --VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + L +G NR+I+++ E+F ++V +L R+      L  L  G  R+++
Sbjct: 187 FRITLVQGLNRQIRRMCEYFGYEVTKLERVRIMNVSLSGLPVGEWRDLT 235


>gi|323455461|gb|EGB11329.1| hypothetical protein AURANDRAFT_61729 [Aureococcus anophagefferens]
          Length = 294

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 109/231 (47%), Gaps = 21/231 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRLWL 77
           SRR  +  +A  RV+VNG    + ++ + S D + +DG           L        + 
Sbjct: 36  SRRAADAAVAAGRVRVNGET-AKPSLRLRSGDTLALDGKKRDWEALAAKLEGGGGLEYYA 94

Query: 78  YHKPIGLVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           YHKP G+  T    D RS         L +   R+   GRLD+++ GL++LTNDG  A  
Sbjct: 95  YHKPEGVACTTDANDRRSLRRAPALKKLFAGGKRIFPAGRLDVDSCGLVVLTNDGAAADA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTL--DTQKGSN 186
              PS++  +VY V    +   D +  L  G+ I     +G        TL  D  +G  
Sbjct: 155 ALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIATPLQRGSKAEKTGKTLPCDVARGDG 214

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + + L EG+NR+++++ E   ++V  L R+++GP  LG L  G+ R ++
Sbjct: 215 RGLVITLAEGRNRQLRRMAEALGYEVTGLRRVAFGPVSLGDLRPGTLRPLA 265


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 58/177 (32%), Positives = 92/177 (51%), Gaps = 32/177 (18%)

Query: 77  LYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA- 131
           L++KP G++   +D D     R T+ D +P     + SVGRLD ++EGLLLLTN+G L  
Sbjct: 6   LFNKPYGVLCQFTDTDNPNAPRPTLKDYIP--LPDIYSVGRLDFDSEGLLLLTNNGRLKH 63

Query: 132 ----RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-- 185
               R    P T W++V R+      D+  L+ L++G++I+  C    QV L   + +  
Sbjct: 64  RLSHREFSHPRTYWVQVERI-----PDEIALDRLRQGVLIKDYCTRPAQVKLLATEPNLS 118

Query: 186 -------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                         AW+ + L EG+NR+++++     +   RLIRIS G F++G  L
Sbjct: 119 PRNPPIRYRKTVPTAWLEITLTEGRNRQVRRMTAAIGYPTLRLIRISMG-FKIGKTL 174


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 122/233 (52%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  + SR+ +++ + ++ + V+       A N+      +   G  +R  E T
Sbjct: 2   RLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNIDTGLQELLFQGRIIRGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LP       + +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPPDIQSDSLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K+GIV +  I     ++ + +   + +  +
Sbjct: 119 FQLLHPQYHVDKSYQVVVNGPLTSDHIQQFKEGIVFLDEITCKPAKLDILSASPTESRAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++KK+F   + KV  L R+ +G F L + LA G  R +++K L+
Sbjct: 179 ITISEGKFHQVKKMFLSVSVKVTALKRVQFGDFTLDSELAEGQYRPLNQKELQ 231


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/220 (31%), Positives = 103/220 (46%), Gaps = 10/220 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G V    +     GI +  G      ++ + T       + 
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPARLEIITPN----EIK 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V ++EGK  ++K++F      V+ L RIS G  QL   LA
Sbjct: 176 VTIQEGKFHQVKRMFAARGKSVSYLKRISMGNLQLDESLA 215


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 120/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+   +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTNLKRIQFGDFTLNPDLAEGNYHPLNQKELQ 231


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 114/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q RV VNG    + AV    V   D IE+D     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGRVTVNG----KTAVLGQKVSPADRIELDKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +AR L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIARQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|205374450|ref|ZP_03227246.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus coahuilensis m4-4]
          Length = 236

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 114/241 (47%), Gaps = 30/241 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV+ ++    V VNG   +    +V  S D + V G  +   E  
Sbjct: 2   RIDKLLANMGYGSRKEVKSLLKSGNVVVNGTGCKDGKQHVNPSQDEVFVHGEKVVYREFI 61

Query: 74  RLWLYHKPIGLVTTHSD-----------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
            L L +KP G+++   D           PD R  VF+  P        VGRLD +TEGLL
Sbjct: 62  YL-LMNKPQGVISATEDLRDETVIDLLEPDHR--VFNPFP--------VGRLDKDTEGLL 110

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTL 179
           ++TNDG L+  L  P     + Y     G V ++ +    +G+ +    +   GD+ +  
Sbjct: 111 IITNDGQLSHQLLSPKKHVPKTYYAEVKGVVTEEDVAAFSEGVTLDDGYHTKPGDLVI-- 168

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
               G  + + + + EGK  ++K++FE    KV  L RI  GP  L   L  G  RE+S+
Sbjct: 169 -LSSGEMSEIELTITEGKFHQVKRMFESVGKKVVYLQRIKMGPILLDENLELGEYRELSQ 227

Query: 239 K 239
           +
Sbjct: 228 E 228


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 105/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +    Y     TL+        +T+   
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKYLTKPATLEVITPVQVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 114/229 (49%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K I+ +G+ SRRE +R I    V +NG   +     V+  D + V+G  +  R  E 
Sbjct: 8   RLNKYISESGMCSRREADRYIENGNVAINGKAAQ-VGDQVLPGDKVTVNGQLIEPRDEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T +DP  R  + +++     R+  +GRLD +++GL+ LT++G L  
Sbjct: 67  LIFIALNKPVGVVST-TDPAERRNIVNHV-GHGERIFPIGRLDKDSQGLIFLTSNGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V    +K S     + 
Sbjct: 125 KILRAGNNHEKEYLVTVNKPVTTEFVQGMSAGVPILGTVTKRCKV----EKVSRFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L +G NR+I+++ EFF ++V +L R+      L  L  G  R++  K L
Sbjct: 181 LVQGLNRQIRRMCEFFGYEVTKLERVRIMNISLKGLSVGEWRDLGPKEL 229


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 109/233 (46%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I   RV +NG + E     V+  D +E+D  P+R  E+ 
Sbjct: 8   KRLNKYISETGFCSRREADKLIDAGRVTINGKIPE-MGTKVLPGDDVEIDNKPVRSKEKP 66

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 67  IYIALNKPTGITCTTERDIPGNIVDF---IGHHKRIFPIGRLDKPSDGLIFLTNDGDIVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I       + +    +K +     + 
Sbjct: 124 KILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHI----LDTVTLPCKVEKETKFSFRIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L
Sbjct: 180 LTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEIL 232


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/300 (26%), Positives = 144/300 (48%), Gaps = 23/300 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +G+ SRR  +R I Q  V +NG   ++A V   V   D + V+G  +  ++ 
Sbjct: 7   RLNKYISESGLCSRRAADRYIEQGNVYING---KKAKVGDKVFFGDIVTVNGQTIDPKEV 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E + L  Y+KP+G+ +T ++   +  + D++ +   RV  +GRLD +++GL+ LTN+G L
Sbjct: 64  ENSVLIAYNKPVGITST-TEAGVKGNIVDHV-NHSERVFPIGRLDKDSQGLIFLTNNGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +    +  + KG+ + G+     +V     K S     
Sbjct: 122 VNKILRAGNNHEKEYVVTVNKPLTDQFITGMAKGVPVLGVMTKKCKVV----KESPLIFK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+F ++V +L R+      L  +  G  RE++ + L      +++
Sbjct: 178 ITLIQGLNRQIRRMCEYFGYEVTKLERVRIMNIPLKGIPLGEWRELTPEELTGIF--NMV 235

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR--MKKNSSQKNGLSKQKKLATPVHRR 308
            ++    DA    +   V  +P    E  +DF        SS +N   K K  A P   R
Sbjct: 236 AKSSAEADA----TPKRVSKKPKTPKE--EDFLENVTPGRSSGRNAKPKSKGKAAPASVR 289


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 56/181 (30%), Positives = 91/181 (50%), Gaps = 16/181 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLTNDG L   
Sbjct: 10  KLLLFNKPFDVLTQFNDEQGRSTLKDFIP--LPGVYPAGRLDRDSEGLLLLTNDGRLQAR 67

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----------- 181
           +  P  +  + Y V+  G  D+ +L  L++G+ +  G         LD            
Sbjct: 68  IADPRHKLPKTYWVQVEGTPDEKQLRRLREGVTLNDGPTLPAEARLLDEPTLWERVPPVR 127

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +     W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  REV  +
Sbjct: 128 FRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWSLDGLGLGEWREVPAR 187

Query: 240 I 240
           +
Sbjct: 188 L 188


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/262 (25%), Positives = 120/262 (45%), Gaps = 37/262 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEV-----DGVPLR 68
           R++K+I+     SRR+ ++ I    +K+N  ++     +V ++ D I+V     D   ++
Sbjct: 47  RLNKLISINNNISRRKSDKFIQNANIKINNKVVLNPGTHVDITKDQIKVHDKKIDIENIK 106

Query: 69  KA----------ERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRL 114
           K             +  W+  HKP GL+ T+ D   R ++F   P       R++SVGRL
Sbjct: 107 KILNNYNISNTNHNSYKWIVMHKPKGLICTNQDEKDRKSIFSIFPDDLLQKYRIVSVGRL 166

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----- 169
           D NT G+LL TN+      L  P  + +R Y +   G V  D L +L  G+ ++      
Sbjct: 167 DRNTSGVLLFTNEYTWVNKLTHPKYERVRKYMIHIEGPVRMDALKMLANGVYLKDEDNNK 226

Query: 170 -----------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                          +  V +  Q      + + ++EG+NR+I+K+F+  N  + ++ R 
Sbjct: 227 KKKKKTQPAFIEVLREENVKIQNQIKKITVLNISIKEGRNRQIRKMFQQINQPIVKIKRT 286

Query: 219 SYGPFQLGTL-LAGSTREVSKK 239
           ++    L  + L    RE++KK
Sbjct: 287 AFENITLKNIHLPKQYRELTKK 308


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 109/234 (46%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I   RV +NG + E     V+  D +E+D  P+R  E+ 
Sbjct: 8   KRLNKYISETGFCSRREADKLIDAGRVTINGKIPE-MGTKVLPGDDVEIDNKPVRSREKP 66

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 67  IYIALNKPTGITCTTERDIPGNIVDF---IGHHKRIFPIGRLDKPSDGLIFLTNDGDIVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I       + +    +K +     + 
Sbjct: 124 KILRAGNNHEKEYVVRVDKPITTEFLKQMGAGVHI----LDTVTLPCKVEKETKFSFRIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L 
Sbjct: 180 LTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEITEILA 233


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 120/237 (50%), Gaps = 11/237 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A  G+ SR+EV+ +I +  ++VNG ++  ++A VN    D +   G  +   ++
Sbjct: 2   RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFE-DAVTYLG-EIITYQK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 60  DFYYILHKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G        +Q+    Q+   +
Sbjct: 119 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQETETS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQ 235


>gi|295095390|emb|CBK84480.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 290

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V+  D ++V+G  +  R A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVVPGDVVKVNGQVIEPRDA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D   +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDGE-RDNIVD-FVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G      +V    +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTVTKKCKV----RKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIE 231


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 88/177 (49%), Gaps = 16/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 55  LFNKPFDVLCQFTDEQGRQTLKDFIP--IPGVYAAGRLDRDSEGLLLLTNDGKLQSKLTE 112

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  + Y  +  G  D+ +L+LL+KG+ ++       ++++ +Q              
Sbjct: 113 PKKKTFKTYWAQVEGAPDEAQLDLLRKGVELKDGMTLPAKISIMSQPTVWERVPPIRERK 172

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                W+ + + EG+NR+++++     +   RLIR   G + L  L  G  + +  K
Sbjct: 173 AIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLSPGQYQSIDMK 229


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 113/232 (48%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++++   RV +NG   E  +   +  D + +DG  + + +   
Sbjct: 2   RINKFISETGYCSRREADKLVDSGRVTINGAKAELGSQAELGDD-VRIDGKRIGEQKHHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T ++   R  + D +     R+  +GRLD ++EGL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITST-TELHIRGNIVDFVGH-KERIFPIGRLDKDSEGLILLTNDGDVVNPI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     V  + +  +  G+ I     G M +     + +     + L 
Sbjct: 119 LRSEGKHEKEYIVTVDRPVTAEFVKGMSSGVRI----LGSMTLPCQVTRVAERVFRIVLT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNR+I+++ E F + V +L RI      LG L  G  R++++    E  G
Sbjct: 175 EGKNRQIRRMCEAFGYHVRKLQRIRIMNIHLGQLPTGKWRDLTETEKAELFG 226


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 121/240 (50%), Gaps = 10/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++ 
Sbjct: 2   RLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEIL-TYQKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG LA
Sbjct: 61  FYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT--QKGSNAW 188
             L  P     + Y     G V  +   L  +G  ++ G      ++ ++T  ++   + 
Sbjct: 120 HQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSRLVIETINEEEGTSV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL P
Sbjct: 180 VRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAEL-QQLQP 238


>gi|229030086|ref|ZP_04186150.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228731256|gb|EEL82174.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 248

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 120/239 (50%), Gaps = 7/239 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K  ++++    R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D +
Sbjct: 1   MSLKFCLEKDVPNLRINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDV 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V+G  LR A        +KP+G+  T S+   +  + D L +   R+  +GRLD +++G
Sbjct: 60  RVNGEQLRIARDHVYIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLTNDG +   +     +  + Y V     +  D L  +  G+ I G      ++T  
Sbjct: 118 LILLTNDGDIVNEILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQL 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           ++   N  +T GL    NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 178 SKYEFNIILTQGL----NRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 232


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 114/227 (50%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V     ++ V G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKQLLKQKAVTVDGASVKDAAMHVDPEQQNVSVYGERVIYTEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+++   D     TV D L  +        VGRLD +TEGLL+LTNDG LA
Sbjct: 62  -YFMMNKPPGVISATEDLRDE-TVIDLLEPVDQHFQPFPVGRLDKDTEGLLVLTNDGILA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY     G V ++ +     G+ +           +  +    + + +
Sbjct: 120 HNLLSPKKHVPKVYYAHIEGVVTEEDVEKFANGVELDDGYMTKPGKLVILKSAPQSEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++
Sbjct: 180 TIQEGKFHQVKRMFEAVGKRVTYLKRISMGNLKLDDQLELGEYRELT 226


>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 = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 118/239 (49%), Gaps = 23/239 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R+ K++A  G+ S++++ R++ ++  ++NG  +  A   ++  +H  +     R  E   
Sbjct: 4   RIDKILAANGLGSQKDIRRLLRKEDFRINGTRVTDAG-TLLDPEHDALS----RNGETLH 58

Query: 72  -RTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
            RT  +L  +KP G+VT+ +DP   STV + LP  F    +  +GRLD++TEGLL++TND
Sbjct: 59  LRTCCYLMLNKPAGVVTSTADPL-HSTVMELLPPPFPAMELFPIGRLDLDTEGLLIITND 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------D 180
           G L   L  P +  ++ Y +       +      +     +G+  G     L        
Sbjct: 118 GALTHRLTAPKSACIKSYYLETAEPFTESTFTAARIACA-EGLPLGKNFTCLPATFERTT 176

Query: 181 TQKGSNAWV-TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           +Q+    W   + + EGK  ++KK+ +    +V  L RI+ G   L   L AGS RE++
Sbjct: 177 SQRVKTEWAFLMHICEGKYHQVKKMVKALGNEVVYLKRIAMGGVTLDPKLPAGSCRELT 235


>gi|229161332|ref|ZP_04289317.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622146|gb|EEK78987.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 238

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 114/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T  ++   N  +T GL 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEITQLSKYEFNIILTQGL- 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 181 ---NRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 222


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 64/206 (31%), Positives = 107/206 (51%), Gaps = 9/206 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++++    VK++GI ++ A V+V +    + + G  +   E  
Sbjct: 2   RLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + HKP G+++   D D   TV D L    +IF+    VGRLDI+TEG LL+TNDG L
Sbjct: 62  YLMM-HKPQGVISATED-DNHETVIDLLELEDAIFNP-FPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           +  L  P     + Y     G V ++ +    KG+++    Y      L   K  + + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGALTILKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRL 215
            + + EGK  ++K++FE    K + L
Sbjct: 178 ELVITEGKFHQVKRMFEAVGEKSSLL 203


>gi|329576942|gb|EGG58425.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 257

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 77/258 (29%), Positives = 127/258 (49%), Gaps = 18/258 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEIL-TYQKFFYYMLHKPQGVISATEDQRD-ETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  ++    G+M  
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKD---GEMVK 175

Query: 177 ------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                  T++ ++G++  V + ++EG+  ++K++       V  L R+  G   L  TL 
Sbjct: 176 PSRLVIETINEEEGTSV-VRLVIQEGEFHQVKRMLATVGKPVTYLKRLRMGELWLDETLE 234

Query: 230 AGSTREVSKKILREQLGP 247
            G  R +++  L +QL P
Sbjct: 235 LGEYRPLTEAEL-QQLQP 251


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 113/235 (48%), Gaps = 22/235 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RVSK+++  GI SRRE +  I +  VK +G ++      V+    + +D   L    +  
Sbjct: 5   RVSKLLSEQGICSRREADVFIERGWVKADGNVVS-LGTKVLPNAKLTLDKKALESKSKQV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--------FDNLPSIFSR-----VISVGRLDINTEGL 121
             + +KP+G V++  + + +S +        +D + + FS      + + GRLDI ++GL
Sbjct: 64  TIILNKPVGYVSSQPEKNYKSALSLITKANQYDRVHNEFSESHLKGLATAGRLDIESQGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-- 179
           L++T DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G    D +V    
Sbjct: 124 LVMTQDGSIAKQLIGEDSEVEKEYIVRVEGKLSERGLQLLNHGLSLDGQPLRDAEVEWIN 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           D Q     W      EGK R+I+++ E    KV  L R+  G   L  L  G  R
Sbjct: 184 DDQLRFILW------EGKKRQIRRMCELVGLKVIGLKRVRMGNVTLADLPTGKWR 232


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 118/226 (52%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+++G+ SRR  +++I +  V +NG++ E  +  V   D + +D   +   +  +
Sbjct: 5   RINKYISKSGVCSRRAADKLINEGHVTINGVVAETGS-KVTEKDIVRIDDDIINLIKDIK 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++ ++KP+G +++ SD  G + +   LP     +  VGRLD ++EGL+L+TNDG L   +
Sbjct: 64  VYAFYKPVGYISSLSDEQG-TGIASFLPQGMG-LFPVGRLDKDSEGLMLITNDGNLMNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTVG 192
              S    + Y V    + + D L  + KG+ I     G   +T    T+   +    + 
Sbjct: 122 LNASNGHEKEYIVTTRQKFNNDFLVKMAKGVPITNRATGKKIITAPCKTEALEDNSFKIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + +G NR+I+++  +F+  V  L R+      LG +  G  +E+S+
Sbjct: 182 IIQGLNRQIRRMCGYFDIDVVSLKRVRIMNIMLGNMRPGELKELSQ 227


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 37  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEI 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 95  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 155 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 214

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 215 LDEKEKRQ 222


>gi|257900337|ref|ZP_05679990.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838249|gb|EEV63323.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 255

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 120/237 (50%), Gaps = 11/237 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A  G+ SR+EV+ +I +  ++VNG ++  ++A VN    D +   G  +   ++
Sbjct: 18  RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFE-DTVTYLG-EIIAYQK 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 76  DFYYILHKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G        +Q+    Q+   +
Sbjct: 135 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETS 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 195 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFCLPKDLNRGQYRPMTKEELEQ 251


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 71/233 (30%), Positives = 120/233 (51%), Gaps = 6/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++    +R+ V  M+A+ +V+V+G L     + V    HI V+   ++  + + 
Sbjct: 7   RLDRFISQHLKINRKNVRLMLAKGQVRVDGELARDIDLIVDEFSHICVNDEVIQAKQASY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + L HKP+G+V+   D D   TV + L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  IML-HKPVGVVSATVD-DKHKTVIELLKCDDRNSLHIVGRLDLNTSGLLLLTNDGRWSKQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++YRV     +  + ++   KG+  +      +   L+      A VT  L
Sbjct: 125 LMDPEYKVGKLYRVELQNPLTVEYISAFAKGMYFEFEDITTLPAELEIVDSHTALVT--L 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            EG+  +IK++F  F   V  L RIS G   L  TL +G +R ++ + ++ +L
Sbjct: 183 YEGRYHQIKRMFGRFRNPVVGLHRISVGQIVLDKTLASGQSRPLTPEEIKHKL 235


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 119/238 (50%), Gaps = 17/238 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRK 69
           T  R++K I+ +G+ SRRE +R I Q  V +N    +RA V   V   D + V+G  +  
Sbjct: 5   TSTRLNKYISESGMCSRREADRFIEQGNVFIN---KKRAEVGDQVNPGDVVRVNGAKIEP 61

Query: 70  AERTRLWL--YHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            E   L     +KP+G+V+T    +PD   +  ++     SR+  +GRLD +++GL+ LT
Sbjct: 62  PEAEDLVFIALNKPVGIVSTTEMEEPDNMVSFVNH----SSRIFPIGRLDKDSQGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G L   +        + Y V     + +D +N +  G+ + G      +V    Q+  
Sbjct: 118 SNGDLVNKILRAGNNHEKEYVVTVDKPLTEDAINTMASGVPMLGTKTKKCKV---VQEAP 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           N +  + L +G NR+I+++ EF  ++V  L R+      L  L  G  R++++K + E
Sbjct: 175 NVF-RIFLVQGLNRQIRRMCEFCGYQVTELERVRIMNISLKGLPVGDWRDLTEKEMTE 231


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 94/175 (53%), Gaps = 21/175 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++T  +D +GR T+ D   +P++++     GRLD ++EGLLLLT+DG L  +L
Sbjct: 4   LFNKPFDVLTKFTDSEGRKTLKDYIEIPNVYA----AGRLDKDSEGLLLLTDDGKLNHLL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 60  TDPKSKSFKTYLVQVEGEFSIEAAQKLEKGVLLKDGKTLPAKVKLIDEPEWLWERTPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 120 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYTLGNLKSGDYK 174


>gi|313632172|gb|EFR99245.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL N1-067]
          Length = 233

 Score = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SRREV+ ++    V VNG++ + +   V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKSQVNPEKDQITVHGNPVIYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V    +   + GI +    Y      L+    +   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDD-GYTCKPAHLEIMAPNEIRVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V  L R+S G   L
Sbjct: 179 --QEGKFHQVKRMFAATGKTVTYLKRLSMGKLML 210


>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 = 83.6 bits (205), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 43/96 (44%), Positives = 60/96 (62%), Gaps = 1/96 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEEPV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              LY KP G++++ SD  GRS V D  P I  R+ 
Sbjct: 62  YFLLY-KPTGVISSVSDDKGRSVVTDFFPEITQRLF 96


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/196 (31%), Positives = 99/196 (50%), Gaps = 24/196 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E T + L++KP  ++T  +D  GR T+  F ++P I+     VGRLD ++EGLLLLTN+G
Sbjct: 29  EETIIVLFNKPYDVLTQFTDEQGRKTLKDFIDIPKIYP----VGRLDRDSEGLLLLTNNG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------LDTQ 182
            +   L  P  +  + Y V+  G   Q  L  L+KG+ ++       +         D Q
Sbjct: 85  EIQHRLAHPKFEKEKTYWVQVEGIPSQADLAKLEKGVELKDGLTQPAKAKQIEAPDFDWQ 144

Query: 183 KG---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                        +W+ + + EGKNR+++++     +   RLIR+  G +QLG L +G  
Sbjct: 145 TAPKIRERKTVPTSWIELKITEGKNRQVRRMTAHIGFPTLRLIRVGLGHYQLGELGSGEY 204

Query: 234 REVS---KKILREQLG 246
           R +S   K  L +QLG
Sbjct: 205 RILSLSEKSRLFKQLG 220


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/183 (30%), Positives = 93/183 (50%), Gaps = 16/183 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  ++T  SD +GR+T+ D +    + V   GRLD ++EGLLLLTNDGGL   
Sbjct: 32  RLILFNKPFDVLTQFSDCEGRATLKDFI--DIAGVYPAGRLDRDSEGLLLLTNDGGLQAR 89

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----------- 181
           +  P  +  + Y V+  G+   ++L  L+ G+ +  G         L+            
Sbjct: 90  IADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLEEPELWPRNPPVR 149

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV  K
Sbjct: 150 FRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWREVPAK 209

Query: 240 ILR 242
           + R
Sbjct: 210 LKR 212


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 107/217 (49%), Gaps = 4/217 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     SR++   +I+  R++V+G ++     ++     +E+D   L+     R
Sbjct: 2   RLDRFLSNFSRFSRQDSRLLISAGRLRVDGEIIIDPRFDIRDFQRVELDDELLQAGRSAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            W+ HKP+G+V+  ++ D   TV D L       + + GRLD+NT GLLL+TNDG  +R 
Sbjct: 62  YWMLHKPVGVVSA-TEHDEHRTVLDLLDEPDKHELHLAGRLDLNTSGLLLITNDGLWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY V     + ++   +  +G+         +   LD     +A +T  L
Sbjct: 121 ITQPQQRKPKVYHVTTEQPITEEYAEVFARGLYFAFEDLTTLPAQLDVLDSHHARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EG+  ++K++F  F  +V  L R S G   L   LA
Sbjct: 179 FEGRYHQVKRMFGHFRNRVVALHRESMGEIVLDPQLA 215


>gi|268608512|ref|ZP_06142239.1| 16s pseudouridylate synthase [Ruminococcus flavefaciens FD-1]
          Length = 255

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 102/211 (48%), Gaps = 8/211 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K I+     +R +++ + A+  V VNG  ++R+   +    D + V G  +  +ER 
Sbjct: 5   RLDKFISERTEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAI-SSERF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP G V++  D DG + +    P + S+ +   GRLD ++ G LL+T+DG LA 
Sbjct: 64  RYILLNKPKGYVSSTDDKDGETVIKLVPPEMRSKGLFPAGRLDKDSTGALLITDDGALAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVT 190
            +  P+    ++Y        +Q+ +    KGIV+     G+       QK  NA     
Sbjct: 124 RICSPNNHISKIYAAELSRPFEQEYVEKFAKGIVLAN---GEACSPCKVQKAENADNLAF 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           V L EG   ++K++F      V  L RIS G
Sbjct: 181 VELHEGMYHQVKRMFAAVGNHVENLKRISIG 211


>gi|295115835|emb|CBL36682.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SM4/1]
          Length = 346

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 117/241 (48%), Gaps = 20/241 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ + +      SR EV++MI   RV V+G     A   +  S   + +DG  +  A   
Sbjct: 6   RLDRYLVEMKKGSRSEVKKMIKSGRVSVDGETCREAERKIQPSASEVSLDGTQVGYAA-Y 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+  +  DGR     +L     R  +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 65  EYFMLNKPAGVVS--ATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGKLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----- 186
             L  P     + Y  R  G++ ++ +   K+G+ ++      +   L  QK S      
Sbjct: 123 HRLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDGTR-TLPARLVIQKASGTAEDD 181

Query: 187 -------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
                  + + + + EGK  ++K++FE    +V  L R+S G  +L   LA G+ R +++
Sbjct: 182 GKADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLDESLAPGAYRRLTE 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 105/207 (50%), Gaps = 11/207 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +++I Q RV +NG + E     ++S D + VDG  + + +   
Sbjct: 7   RINKYLSEVGYCSRRAADKLIDQGRVTINGKVPE-MGTKIISGDEVRVDGELISEPKEKP 65

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++L ++KPIG+V T      +  + D  N P    R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 66  VYLAFNKPIGIVCTTDTRVEKDNIIDFINYPK---RIFPIGRLDKPSQGLIFLTNDGDIV 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +++  L+ +  G+ I        ++T    + +     +
Sbjct: 123 NKILRARNHHEKEYLVTVDKPINKKFLDQMASGVPILDTVTRKCEIT----EVNKYQFKI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
            L +G NR+I+++ E+  + V +L RI
Sbjct: 179 ILTQGLNRQIRRMCEYLGYNVKKLKRI 205


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 110/228 (48%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDGVPLRKAER 72
           R++K ++  GI SRR  ++ IA+ +V +NG   E A V   V + D + VDG  ++K ++
Sbjct: 2   RINKYLSETGIISRRGADKWIAEGKVTING---EVATVGSQVEAGDIVCVDGKEVKKEQQ 58

Query: 73  TRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G+  TT     G    F N P    R+  +GRLD  +EGLLLLTNDG + 
Sbjct: 59  LVYIALNKPVGITSTTERHIKGNVVDFVNHPL---RIFHIGRLDKESEGLLLLTNDGDIV 115

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V+    +    +  +  G+ I         +    +K S     +
Sbjct: 116 NKILRAENHHEKEYIVQVDKPITAQFIQKMGAGVDI----LDTTTLPCHVEKISEKVFKI 171

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++     + V RL RI     +LG L  G  R++++K
Sbjct: 172 ILEQGLNRQIRRMCSALGYSVKRLQRIRIMNIKLGNLKVGQWRDLTEK 219


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 113/240 (47%), Gaps = 24/240 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R+SK +A  G+ SRRE +  I +  V VNG   E+A +   V   D IE+      +   
Sbjct: 9   RLSKRMAELGLCSRREADAYIERGWVSVNG---EKAVLGQKVGEGDRIELHRAAHEEQAG 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLDIN 117
               L HKP+G V+  ++   RS             D  P  F       +   GRLDI+
Sbjct: 66  RVTILLHKPVGFVSGQAEKGYRSAAELITEANHWPEDRSPQKFKAAHRHGLAPAGRLDID 125

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+LT DG +A+ L   ++   + Y VR  G++ ++ L LL  G+ + G      +V
Sbjct: 126 SVGLLVLTQDGRVAKSLIGENSGVEKEYLVRVKGKLSEEGLRLLNHGLKLDGEALRPAKV 185

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   Q      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R ++
Sbjct: 186 SWQNQD----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRIGKVKLGALPPGQWRYLA 241


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 101/214 (47%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V  + +     GI +    Y      L+    +   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVVAEDVTAFADGITLDD-GYTCKPARLEIINPNEIKVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V+ L RIS G  QL
Sbjct: 179 --QEGKFHQVKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 68/214 (31%), Positives = 101/214 (47%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V    +     GI +    Y     +L+    +   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDD-GYTCKPASLEIITPNEINVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V+ L RIS G  QL
Sbjct: 179 --QEGKFHQVKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 68/215 (31%), Positives = 102/215 (47%), Gaps = 10/215 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G V    +     GI +  G      ++ + T    N    
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTLADVEAFAAGIELDDGYTCKPARLEIITPNEIN---- 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V ++EGK  ++K++F     KV+ L RIS G  QL
Sbjct: 176 VTIQEGKFHQVKRMFAARGKKVSYLKRISMGNLQL 210


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 120/237 (50%), Gaps = 11/237 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A  G+ SR+EV+ +I +  ++VNG ++  ++A VN    D +   G  +   ++
Sbjct: 8   RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFE-DAVTYLG-EIITYQK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 66  DFYYILHKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G        +Q+    Q+   +
Sbjct: 125 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQETETS 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 185 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQ 241


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 108/239 (45%), Gaps = 19/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  GI SRRE +  I Q  V V+G  +      +     I +D     +  +  
Sbjct: 5   RLSKLMSARGICSRREADVYIEQGSVYVDGQPVRELGTKIYPWQEIVLDRAAQIRQNQQV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
             L +KP+G V+   +P  +S +                  +P     +   GRLDI+++
Sbjct: 65  TILLNKPVGYVSGQPEPGYKSAISLVNNDSHFHQDRSSLRFVPQHLKNIAPAGRLDIDSQ 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T DG +A+ L    +Q  + Y VR  G + ++ L LL  G+ + G      +V+ 
Sbjct: 125 GLLVFTQDGRIAKQLIGEYSQIEKEYLVRVSGNLTREGLALLNHGLQLDGQALKPARVSR 184

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             Q      +   L+EGK R+I+++ E     V  L R+  G  +L  L  G  R + K
Sbjct: 185 LNQD----QLRFILQEGKKRQIRRMCELVGLNVTGLKRVRIGQIRLADLPEGKWRYLGK 239


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 114/238 (47%), Gaps = 21/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +G+ SR EV+ ++ + RV V G +       V  ++  +  DG  L   E  
Sbjct: 33  RLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQEYY 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
             +L +KP GLV+   D      +F  +  + S       +  VGRLD NTEGLL+LTND
Sbjct: 93  -YYLLNKPQGLVSATKD-----NLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTND 146

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLD 180
           G L   L  P     + Y  R  G+V  + +N   +G+ ++       G  + +     +
Sbjct: 147 GALGHDLTQPKKHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYKGE 206

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +Q G  + + V + EGK  ++K++FE     V  L RI  G   L + LA G+ R ++
Sbjct: 207 SQSGWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLT 264


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 69/228 (30%), Positives = 111/228 (48%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV  ++   RV+V+G  +  A   V      + +DG  L    R 
Sbjct: 5   RLDKLLAGQGQGSRKEVHTLLRGGRVQVDGQTVTDAGQKVDPDRQRVTLDGHAL--LWRA 62

Query: 74  RLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            L+L  +KP G+++   DP  R TV D LP+   R  +   GRLD +TEG LL+T+DG  
Sbjct: 63  HLYLMMNKPAGVISASRDPKAR-TVLDLLPADLCRPGLFPAGRLDKDTEGFLLITDDGAF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P     ++Y        D    +    G+ ++   +  +   L   +G++A+  
Sbjct: 122 AHDILAPRRHVEKIYLATLDRPADTADTDAFATGLTLEDGLHC-LPARLWLGEGTDAYAA 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           V  REGK  +++++F     +V  L RI  G   L   LA G  RE++
Sbjct: 181 V--REGKFHQVRRMFAARGKQVVHLRRIQIGGLALDESLAPGEARELT 226


>gi|16801498|ref|NP_471766.1| hypothetical protein lin2436 [Listeria innocua Clip11262]
 gi|16414958|emb|CAC97663.1| lin2436 [Listeria innocua Clip11262]
          Length = 233

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 101/215 (46%), Gaps = 10/215 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVIYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NLSETVIDLLEQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G V  + +     G+ +  G       + + T       + 
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EIK 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V ++EGK  ++K++F      V+ L RIS G  QL
Sbjct: 176 VTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 57/177 (32%), Positives = 92/177 (51%), Gaps = 32/177 (18%)

Query: 77  LYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA- 131
           L++KP G++   +D D     R T+ D +P     + SVGRLD ++EGLLLLTN+G L  
Sbjct: 6   LFNKPYGVLCQFTDTDNPNSPRPTLKDYIP--LPDIYSVGRLDFDSEGLLLLTNNGRLKH 63

Query: 132 ----RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-- 185
               R    P T W++V R+      D+  L+ L++G++I+  C    Q+ L   + +  
Sbjct: 64  RLSHREFSHPRTYWVQVERI-----PDEIALDRLRQGVLIKDYCTRPAQIKLLATEPNLS 118

Query: 186 -------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                         AW+ + L EG+NR+++++     +   RLIRIS G F++G  L
Sbjct: 119 PRNPPIRYRKTVPTAWLEITLTEGRNRQVRRMTAAIGYPTLRLIRISMG-FKIGKTL 174


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 63/205 (30%), Positives = 99/205 (48%), Gaps = 9/205 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG   E   V VM  D + +D  PLR  ER  
Sbjct: 15  RLNKFISDTGYCSRREADKLIDQGRVTINGQKPE-MGVRVMDNDDVLIDDKPLRSKERPI 73

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP G+  TT    +G    F        R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 74  YIALNKPTGITCTTERHIEGNIVDF---IGHRKRIFPIGRLDKPSDGLIFLTNDGDIVNK 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +VT +T    N    + L
Sbjct: 131 ILRAGNSHEKEYVVRVDKVITPEFLEKMASGVEILDTVTLPCKVTKET----NFSFRIVL 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRI 218
            +G NR+I+++ E   ++V +L R+
Sbjct: 187 TQGLNRQIRRMCEALGYEVYKLRRV 211


>gi|271500470|ref|YP_003333495.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344025|gb|ACZ76790.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 218

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 89/179 (49%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L +KP  +++  +D  GR T+ D +P  F  + + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RIVLLNKPFDVLSQFTDEGGRPTLKDYVP--FRDIYAAGRLDRDSEGLLILTNDGKLQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLDTQKG-- 184
           L  P  Q  ++Y  +  G  D+D L   + G+V+        G    D  V L  ++   
Sbjct: 98  LTQPGKQTPKIYYAQVEGIPDEDALRAFRTGLVLNDGPTLPAGAECVDEPVWLWPRQPPI 157

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   +W+ + L EG+NR+++++     +   RLIR S     L  LL G  +E+ 
Sbjct: 158 RQRKNIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMANLTLDGLLPGDWKEID 216


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEV 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 156 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 215

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 216 LDEKEKRQ 223


>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 = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 114/233 (48%), Gaps = 16/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R+ K + +    SR +  +++   R+ VN ++++  A +V   D + +D  PL    E+ 
Sbjct: 2   RLDKHLHQCLGISRSQASQLLKAGRISVNSLIIKSGAQHVTEQDSVLLDDKPLDTPGEKL 61

Query: 74  RLWLYHKPIGLVTTHSDPD--GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKP G V  + D    G + +FD LP   S + + GRLD +T GL+L+TNDG  +
Sbjct: 62  YYFMLHKPQGYVCANGDASHPGITRLFD-LPCA-SELHAAGRLDADTTGLVLVTNDGQWS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNA 187
             +  P  Q  + YRV     +  +   +  KGI+++     + QVT    L+T      
Sbjct: 120 HRVTSPRKQCDKTYRVWLAEPISPETEEIFAKGILLR----SETQVTRPAQLETITPQEV 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            +T+   EGK  ++K++F      V RL R   G   L   L  GS RE++ +
Sbjct: 176 LLTI--HEGKYHQVKRMFAAVGNHVERLHRERIGELVLDADLPEGSYRELTPE 226


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 58/180 (32%), Positives = 93/180 (51%), Gaps = 19/180 (10%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLEL 136
           ++KP G++T  +D  GR T+   +P    +V  VGRLD ++EGLLLLT+DG L AR+++ 
Sbjct: 6   FYKPYGVLTQFTDRQGRPTLKSFIP--VPKVYPVGRLDRDSEGLLLLTDDGRLNARLID- 62

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P     R Y V+  G      L  L++G+VIQG      +V +  ++             
Sbjct: 63  PKFGHERTYWVQVEGIPTPQALQQLQEGVVIQGRKTRPAEVRVLAEEPELPPRDPPIRFR 122

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 W+ + LREG+NR+++++         RL+R+  GP  L  L  G  +E+S+  L
Sbjct: 123 RSIPTTWLELMLREGRNRQVRRMTAAVGIPTLRLVRVGLGPLSLQGLAPGQWQELSEAEL 182


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 65/217 (29%), Positives = 107/217 (49%), Gaps = 8/217 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +GIA+R +V+ ++ Q+RV+ N   +    V +    D I +D   +   E+ 
Sbjct: 2   RLDKFLADSGIATRSQVKLILKQKRVRKNQETVTNGKVQIDEKLDEIYLDDERVY-YEKY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D    +TV D +  +  +  V  VGRLDI+T G LLLTN+G L+
Sbjct: 61  LYYVMNKPKGVVSATEDTK-HATVLDLIGELAQKRGVFPVGRLDIDTHGFLLLTNNGALS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNA-W 188
             +  P     + Y  +  G + Q+     +KGI +     C       L   K   A  
Sbjct: 120 HAMLSPKKHVEKTYVAKIEGIMTQEDQVSFEKGITLDDGYECMPAHLEILSVDKNHQASL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V + ++EGK  ++K++ +     V  L RIS GP  L
Sbjct: 180 VQIKIKEGKFHQVKRMVKACGKTVIDLQRISMGPLHL 216


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEI 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 156 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 215

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 216 LDEKEKRQ 223


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++ +  + SR+ +++ + ++ + V+ +     A NV      +   G  ++  E T
Sbjct: 2   RLDKLLTQEKV-SRKAIKQALLKKEILVDELPATSLAQNVDTGLQELIFQGRKIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D     TV D LP       + ++GRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGVVTASKDKK-LPTVMDLLPQSLQSEELYAIGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + YRV  +G +  DK+   K GIV + G      Q+ + +   S++   
Sbjct: 119 FQLLHPQYHVDKTYRVEVNGPLTPDKVQEFKDGIVFLDGTVCKPAQLDILSSSSSHSKAI 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++KK+F     KV  L RI +G F L + LA G  R ++++ L 
Sbjct: 179 ITIAEGKFHQVKKMFLSIGVKVTSLKRIQFGDFTLDSELAEGQYRSLNQEELE 231


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 119/241 (49%), Gaps = 19/241 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLR----- 68
           ++K +++ G+ SRRE +R+I   +V V+G     AA+   V     +  DGVP+      
Sbjct: 36  LNKWLSQMGVCSRREADRLIEAGKVWVDG---SPAAMGQKVKPGQKVVCDGVPVNGGSGA 92

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             +  +  L + +KP G+V T SD D    + + L     R+  VGRLD ++EGLLL+TN
Sbjct: 93  DSRKPKPVLLVVNKPRGIVCTTSDKDRAMNIVEYL-DYPERIYPVGRLDKDSEGLLLMTN 151

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKG 184
            G L   +        + Y V     +  D ++ + KGI ++ +      VT     ++ 
Sbjct: 152 QGDLVNKIMRSGNAHEKEYIVTVDRPLTDDAMDRMAKGIYLREL----ETVTRPCKVKRV 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                ++ L +G NR+I+++ E     V RL+R+     +L  L  G++REV ++  RE 
Sbjct: 208 DGKTFSIILTQGLNRQIRRMCEACGCHVERLVRVRIMNIRLDGLETGASREVGQEEYREL 267

Query: 245 L 245
           +
Sbjct: 268 M 268


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 92/179 (51%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ + +P  FS V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRRTLKEFIP--FSDVYAAGRLDRDSEGLLVLTNDGKLQAK 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P+ +  +VY V+  G   ++ L  L++G+ ++          L              
Sbjct: 88  LTQPAQKTGKVYFVQVEGVPGEEALTQLQRGVTLKDGPTLPAGAELVAEPEWLWPRHPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEWKEIN 206


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 122/250 (48%), Gaps = 20/250 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R++K ++  G+ SRRE +R IA+ RV++NG   E     V   D +E+DG  ++K     
Sbjct: 2   RINKCLSELGLCSRREADRWIAEGRVRLNGETAE-MGQQVEEKDRLELDGKLVKKAGKAV 60

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
              A R  L   +KP G+V + SD D R+     L +   RV  +GRLD ++EGL+LLTN
Sbjct: 61  RAQAPRRVLLACYKPRGVVCSCSDKD-RAKNIVELVNYPERVYPIGRLDKDSEGLILLTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLD 180
            G L   +        + Y V     + ++ L+ L  G+ +  +      C     + L 
Sbjct: 120 QGELVNRINRGGRNE-KEYVVTVDRPLTREALDRLADGVELSELNQKTRPCEVWQDLRLP 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV--SK 238
             +    +  V L +G NR+I+++ E   ++V RL R+     +L  L  G  RE+  S+
Sbjct: 179 PGRRQRQFHIV-LSQGLNRQIRRMCEALGYEVKRLKRVRILSLRLEGLRPGEFREIGLSE 237

Query: 239 KILREQLGPH 248
             L E+L P 
Sbjct: 238 LGLSEELWPE 247


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V    DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCATDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +    Y     TL+        +T+   
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKYLTKPATLEVITPVQVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 119/234 (50%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++ G  +R E +++I  +RV++N  +++   + +   +D I +DG  L    + 
Sbjct: 4   RLDKFLSQTGKFTRAEAKKVIKAKRVRLNDEVVKDGKIKINEESDKIFLDGELLALNNKE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D D   TV D  N P     +  VGRLD  T GLL++TNDG  A
Sbjct: 64  VYYMLNKPAGVVSATRD-DKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAW 188
             +  P     + Y     G++ + ++ +  +G+ +     +    + +   ++K   + 
Sbjct: 123 HDIISPKKHVSKTYEAVVTGKISEKEVKIFSQGMELSNGDKLQPAQLDIISYSEKDDTSK 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           V V + EGK  +++++F   + +V  L R+  G  +L  TL  G  RE++++ L
Sbjct: 183 VRVIIHEGKYHQVRRMFGAVSQRVLELDRVKIGLLELDDTLERGEYRELTEEEL 236


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 37  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEV 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 95  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 155 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 214

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 215 LDEKEKRQ 222


>gi|323447017|gb|EGB02989.1| hypothetical protein AURANDRAFT_34656 [Aureococcus anophagefferens]
          Length = 273

 Score = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 109/231 (47%), Gaps = 21/231 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRLWL 77
           SRR  +  +A  RV+VNG    + ++ + S D + +DG           L        + 
Sbjct: 36  SRRAADAAVAAGRVRVNGET-AKPSLRLRSGDTLALDGKKRDWEALAAKLEGGGGLEYYA 94

Query: 78  YHKPIGLVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           YHKP G+  T    D RS         L +   R+   GRLD+++ GL++LTNDG  A  
Sbjct: 95  YHKPEGVACTTDANDRRSLRRAPALKKLFAGGKRIFPAGRLDVDSCGLVVLTNDGAAADA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTL--DTQKGSN 186
              PS++  +VY V    +   D +  L  G+ I     +G        TL  D  +G  
Sbjct: 155 ALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIATPLQRGSKAEKTGKTLPCDVARGDG 214

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + + L EG+NR+++++ E   ++V  L R+++GP  LG L  G+ R ++
Sbjct: 215 RGLVITLAEGRNRQLRRMAEALGYEVTGLRRVAFGPVSLGDLRPGTLRPLA 265


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 114/238 (47%), Gaps = 21/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +G+ SR EV+ ++ + RV V G +       V  ++  +  DG  L   E  
Sbjct: 33  RLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQEYY 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
             +L +KP GLV+   D      +F  +  + S       +  VGRLD NTEGLL+LTND
Sbjct: 93  -YYLLNKPQGLVSATKD-----NLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTND 146

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLD 180
           G L   L  P     + Y  R  G+V  + +N   +G+ ++       G  + +     +
Sbjct: 147 GALGHDLTQPKKHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYEGE 206

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +Q G  + + V + EGK  ++K++FE     V  L RI  G   L + LA G+ R ++
Sbjct: 207 SQSGWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLT 264


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 93/188 (49%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 37  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEI 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGS---- 185
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 95  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 154

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 155 PKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 214

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 215 LDEKEKRQ 222


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 61/207 (29%), Positives = 100/207 (48%), Gaps = 10/207 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG + E     VM  D + VD  P+      
Sbjct: 7   KRLNKFISETGFCSRREADRLIEQGRVTINGQVPE-MGTKVMPGDDVRVDDKPINAVTDK 65

Query: 74  RLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +++  +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 66  PVYIALNKPTGITCTTERDIPGNIVDFVGHKK---RIFPIGRLDKPSDGLIFLTNDGDIV 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  D +  +  G+ I        +VT +T+      +T 
Sbjct: 123 NKILRAGNNHEKEYVVRVDKPISDDFIKKMSSGVNILDTITLPCKVTKETKFSFRIVLTQ 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
           GL    NR+I+++ E   ++V +L R+
Sbjct: 183 GL----NRQIRRMCEALGYEVFKLRRV 205


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 107/212 (50%), Gaps = 5/212 (2%)

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
            + +++KP G  ++ S+ +     F + P + +  I+ GRLD + EGLLL+TNDG     
Sbjct: 61  YI-IFNKPTGYTSSKSEFERNIFEFIDHPYVENLHIA-GRLDKDVEGLLLITNDGIFTHK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P ++  + Y V+   ++  + +   K GIV++    G        ++  + ++++ +
Sbjct: 119 ITSPKSKIEKEYIVKVDKEISDEMIQKAKDGIVLKN---GTRFKPAIIKRLKDNFISITI 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  EIK + +F      ++ RI  G  +L
Sbjct: 176 TEGKYHEIKLIVKFLGLSYKKIERIRIGKLKL 207


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 121/243 (49%), Gaps = 31/243 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           +R+ KV++  G  SR+E++ ++ +  ++++G +++   + V     I +V+G  +     
Sbjct: 2   ERLDKVLSNLGYGSRKEIKALVKKGEIEIDGKVIKDNGLKVDPNKSIIKVNGEKIN---- 57

Query: 73  TRLWLY---HKPIGLVTTHSDP---------DGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            R ++Y   +KP G+V+   D          D   TVFD  P        VGRLD +TEG
Sbjct: 58  YRKYIYIMMNKPAGVVSATFDNYDETVIDLLDYEYTVFDPFP--------VGRLDKDTEG 109

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQV 177
           LL++TNDG L   L  P     ++Y      +VD+  +   +KGI +     C    +++
Sbjct: 110 LLIITNDGELNHRLTSPKWHVDKIYYAEIDKRVDEKDVEKFEKGITLDDGYKCLPAKLEI 169

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV 236
               + GS   V V ++EGK  ++K++FE  + KV  L R+  G   L   L  G  RE+
Sbjct: 170 LSADENGSE--VNVIIQEGKFHQVKRMFEARDKKVVYLKRLKMGNISLDNELEEGEYREL 227

Query: 237 SKK 239
           ++K
Sbjct: 228 TEK 230


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 114/236 (48%), Gaps = 16/236 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VD  PLR  E  +
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDDQPLRIREAKK 62

Query: 75  LW-------LYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L          +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+T+
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIVEFVGHE---QRIFPIGRLDKDSEGLILMTS 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +     +  + Y V  +  V  + L  + +G+ I    + +  +   T + + 
Sbjct: 120 NGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRI----HNETTLPCRTARIAK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR
Sbjct: 176 FGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELR 231


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 119/233 (51%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           RV K +    + +R ++ +MI  + + VN  +++   V V       VD V L+    + 
Sbjct: 2   RVDKFLHDMNMGTRTQIRKMIKDKLIFVNDTVVKTGRVKVDPV----VDEVRLKDQVIEY 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           ++   ++ +KP+G++T   D   + TV D  N   + + +  VGRLD +T+GLLL+TN+G
Sbjct: 58  QQYFYFMMNKPLGVLTATEDR-KQKTVMDLFNKVDLRNDLFPVGRLDKDTQGLLLITNNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLD--TQKGS 185
            LA  L  P     + Y     G++    +   +KGI ++ G      Q+ ++  ++   
Sbjct: 117 QLAHDLLAPERHVDKTYEAVVTGKITDQAVEEFQKGITLRDGTTLKPAQLIIEHYSELDD 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              V V L+EGK  +++++F     KV  L R S+GP +L   LL G+ RE++
Sbjct: 177 QTVVKVVLKEGKYHQVRRMFGSLGEKVVTLRRTSFGPLELDVGLLPGTYRELT 229


>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 = 83.2 bits (204), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 118/239 (49%), Gaps = 25/239 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+++  G  SR+E++ ++ +  ++++G +++   + V  +   I+V G  +   + 
Sbjct: 2   ERLDKILSNLGYGSRKEIKALVKKGEIEIDGKIIKDNGIKVDPNKSTIKVSGEEINYRKY 61

Query: 73  TRLWLYHKPIGLVTTHSDP---------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             L + +KP G+V+   D          D   TVFD  P        VGRLD +TEG LL
Sbjct: 62  IYLMM-NKPAGVVSATFDNYDETVIDLLDYEYTVFDPFP--------VGRLDKDTEGFLL 112

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQVTLD 180
           +TNDG L   L  P     ++Y       VD+  +   +KGIV+     C    +++   
Sbjct: 113 ITNDGDLNHRLTSPKWHVDKIYYAEIDKIVDEKDIRAFEKGIVLDDGYKCLPAKLEILSA 172

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + GS   +T+  +EGK  ++K++FE    KV  L R+  G   L  +L  G  RE+++
Sbjct: 173 DENGSEVNITI--QEGKFHQVKRMFEAREKKVIYLKRLQMGNLVLDESLNEGEYRELTE 229


>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 = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 106/207 (51%), Gaps = 12/207 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K I+  G  SRRE  R+IA  R+ +NG + E A   V   D + +DG  +P+  +E 
Sbjct: 2   RINKYISETGFCSRRETNRLIAAGRITINGSVCE-AGAEVEPLDIVLIDGKPIPINHSEP 60

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KPIG+V T ++  +G    + N PS   R+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 61  VYLAL-NKPIGIVCTAAEQVEGNIIRYVNYPS---RIFAIGRLDKASEGLILLTNDGSIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  +    + +G+ I  +     +V     + S     +
Sbjct: 117 NQMMRSEHGHEKEYVVTVDKPVTDEFTQTMSRGVEILNVITKPCKV----DRISEYEFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
            L +G N +I+++ +   ++V +L R+
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERV 199


>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 = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 125/236 (52%), Gaps = 17/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ ++++   IA+R+E+++M+ +  + VN + +++      S++HI+ +   ++  +   
Sbjct: 2   RLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKK------SSEHIDENNDVVKIYDEVI 55

Query: 74  --RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTND 127
             R +LY   +K  G VT+HS      TV D++  +    ++ VGRLD++T GLL++TND
Sbjct: 56  EYRKFLYFVMNKRKG-VTSHSKDPMHKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITND 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  L  P     + Y+V    +VD+   +  +KGI +           ++     N 
Sbjct: 115 GKFAHNLISPKKDVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIVTKPAKMEIIDDYNC 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++T+  +EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 175 YLTI--KEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 116/235 (49%), Gaps = 16/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     SR+E +++++  RVKV+G    +A   V +   + +DG P+       
Sbjct: 2   RLDQYLSNGTELSRKEAKKVVSAGRVKVDGETCRQANRQVEAEQSVHLDGKPVNPPGDIY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L + HKP G+++  +D   + T  D LP  + SRV   GRLD +T GLLLLT+DG  +  
Sbjct: 62  L-MMHKPAGVLSATTD-SSQPTALDLLPRGLASRVHIAGRLDKDTTGLLLLTSDGQWSHA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-----SNAW 188
           +  P  +  + YRV     + +     L+KG+++ G        T +T+       +N  
Sbjct: 120 VTSPRRECRKSYRVWLAEAIPEQACRALEKGVMLNG-------ETTETRPAEVRVHNNQL 172

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + + EG+  ++K++      +V  L R   G  +L   LA G  R ++ + +R
Sbjct: 173 IDLTIGEGRYHQVKRMLAAVGNRVEALHRFRIGSIELDDKLAPGEFRALTYQEIR 227


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 59/205 (28%), Positives = 100/205 (48%), Gaps = 7/205 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKYISETGFCSRREADRLIEQGRVTINGQQPE-MGTKVLPGDDVCVDGSPVAAKEKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +V  +T+      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVEKETKFSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRI 218
               NR+I+++ E   ++V +L R+
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRV 204


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 117/236 (49%), Gaps = 22/236 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+SK+++  G+ SRRE ++ I    V ++G  +         T  +E+ D   + ++ + 
Sbjct: 5   RISKILSEQGLCSRREADKFIELGLVLLDGKTVSELGTKACRTQKVELKDRAQIAQSAKA 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSR-------------VISVGRLDINT 118
            + L +KP+G ++ H D D   T   +L  P  F +             +   GRLDI++
Sbjct: 65  TIIL-NKPVGFIS-HLDDDKEFTPAASLVTPDKFYQTNDTRRPTFNTDGLAPAGRLDIDS 122

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LT DG +A+ +   +    + Y VR  G +  + L+LL  G+ + G      +V 
Sbjct: 123 SGLLVLTQDGRIAKQIIGENVIVEKEYLVRIEGTLTDEALSLLNHGLTLDGYELKPAKVL 182

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 ++A ++  L EG+NR+I+K+ +    KV  L R+  G  +LG + +GS R
Sbjct: 183 WQ----NDAQLSFTLIEGRNRQIRKMCQLVGVKVTALKRVRIGNVRLGNIPSGSWR 234


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/207 (30%), Positives = 104/207 (50%), Gaps = 12/207 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K I+  G  SRRE  R+IA  R+ +NG + E A   V   D + +DG  +PL  +E 
Sbjct: 2   RINKYISETGFCSRRETNRLIAAGRITINGNVCE-AGAEVEPQDIVLIDGEAIPLNSSEP 60

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KPIG+V T ++   G    + N PS   R+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 61  VYLAL-NKPIGIVCTAAEQVAGNIISYVNYPS---RIFAIGRLDKASEGLILLTNDGSIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  +    +  G+ I  +     +V     + S     +
Sbjct: 117 NQMMRSEHGHEKEYVVTVDKPVTNEFTQAMSCGVEILNVITKPCKV----DRTSEYEFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
            L +G N +I+++ +   ++V +L R+
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERV 199


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 112/236 (47%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAERT 73
           R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     R+  R 
Sbjct: 5   RISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGAKAFPDQVITLERAAQARQTSRV 64

Query: 74  RLWLYHKPIGLVTTHSDP---------DGRSTVF-DNLPSIFSR-----VISVGRLDINT 118
            + L +KP+G V+  ++          D RS    D  P  F R     +   GRLDI++
Sbjct: 65  TI-LINKPVGYVSGQAEKGYTPAVALIDARSRFANDRHPQRFERAHLEGLAVAGRLDIDS 123

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GLL+LT DG +A+ L    +   + Y VR  G++    L LL  G+ + G      QV 
Sbjct: 124 QGLLVLTQDGRIAKHLIGEDSSVDKEYLVRVQGELSDRGLQLLNHGLSLDGKALKPAQVR 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 ++  +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R
Sbjct: 184 WQ----NHDQLRFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVSLGDLPLGQWR 235


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 114/240 (47%), Gaps = 11/240 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAE 71
           P  +S+ +ARAG+  ++E E  I   RV +NG + + A   V     ++VDG+ +  +A 
Sbjct: 23  PDWLSRALARAGVFPQKEAEDAIRAGRVSINGRVAKMALTPVPPGATVKVDGLVVSLEAP 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVI-----SVGRLDINTEGLLLLT 125
            TR+  +HKP GL+++        TVF+  LP +   +      +VGRLD+++ GLLL T
Sbjct: 83  PTRVLAFHKPAGLLSSTERQHRTGTVFEALLPQLPPELAGYTWHAVGRLDVDSTGLLLFT 142

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ND  L      P     + Y          +++  L++G+ +        +V +  +   
Sbjct: 143 NDDKLVAHATSPDAHLPKRYVATVFSTASDERVEPLRRGMTLDDGPARPAKVNVRDEHT- 201

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              V V L EG++ ++K++       V  L R + G   L  +  G+ R ++   +RE L
Sbjct: 202 ---VEVTLTEGRHHQVKRMLGAVGLPVRALHREAVGSVDLEGIPEGTFRLLTDDEVREGL 258


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 53/196 (27%), Positives = 98/196 (50%), Gaps = 19/196 (9%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           M+ D  +    P+R   R+++ L++KP  ++T  +D  GR T+ D +P     + + GRL
Sbjct: 1   MNIDQYKKRKAPIR---RSKIVLFNKPFNVLTQFTDATGRQTLKDFIP--IPDIYAAGRL 55

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D ++EGLL+LTNDG L   L  P  +  + Y V+  G+  + +L  L+ G+ ++      
Sbjct: 56  DKDSEGLLVLTNDGKLQHKLTDPKKKTSKTYWVQVEGEPQEYQLQALRDGVALKDGMTRP 115

Query: 175 MQVTLDT--------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            +V                  Q    +W+ + + EGKNR+++++     +   RL+R   
Sbjct: 116 AKVERMQEPSLWARNPPVRFRQSIPTSWLAITISEGKNRQVRRMTAHIGFPTLRLVRYRV 175

Query: 221 GPFQLGTLLAGSTREV 236
           G + L  + +G+ RE+
Sbjct: 176 GNWTLDGIASGTYREL 191


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 67/215 (31%), Positives = 101/215 (46%), Gaps = 10/215 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SRREV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRREVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y  +  G V    +     GI +  G      ++ + T       + 
Sbjct: 120 HNLLSPKKHIDKTYYAKIDGDVTATDVEAFAAGIELDDGYTCKPARLEIITPN----EIK 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V ++EGK  ++K++F      V+ L RIS G  QL
Sbjct: 176 VTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQL 210


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 110/229 (48%), Gaps = 7/229 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q++    R++K I+  G  SRRE +R+I Q RV +NG + E     V   D + V+G 
Sbjct: 1   MTQQDIKLTRLNKYISDTGYCSRREADRLIEQGRVTINGKIPE-MGTKVSDGDMVSVNGR 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+++ ++      +KP G+  T ++      V D L    +R+  +GRLD  +EGL+ LT
Sbjct: 60  PVKEKQKRIYIALNKPAGITCT-TERHIHGNVID-LIDYSTRIFPIGRLDKPSEGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V+    V    L  + +G+ I        +V   T++G 
Sbjct: 118 NDGDIVNKILRAGNAHEKEYIVKVDSTVTDKFLTGMARGVPILDTVTKPCKV---TREGR 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +  + L +G N++I+++ E F ++V  L R       +  L  G  R
Sbjct: 175 FEFKII-LTQGLNQQIRRMCEHFGFQVKSLTRTRIMNIDIKGLATGQWR 222


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 115/250 (46%), Gaps = 36/250 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVK--------VNGILLERAAVNVMSTDHIEVDGVP 66
           R++K +A  G  SRR   R+I    V+        V+ + L    +   S + I V+  P
Sbjct: 2   RLAKYLALTGCCSRRAATRLIRDGLVRIDERLANHVDSVTLIDTPIGQRSIEQIYVNDEP 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTE 119
           +R  E    WL++K +G           S +  +LP+          R+  VGRLD ++ 
Sbjct: 62  IRVVEAKAYWLFNKAVG---------TDSRLLAHLPNSLLHLLPESPRLYPVGRLDKDSR 112

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGDMQV 177
           GLL+LTNDG L   L  P     + Y    H QVD+  D   L+       G+ Y D+ V
Sbjct: 113 GLLILTNDGELTHKLMHPDFGHAKTY----HVQVDRPFDDAFLVNMA---AGVSYKDV-V 164

Query: 178 TLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           TL    Q+ +     + L +G NR+I+++ +   +KV  L R+S    QLG L  GS R 
Sbjct: 165 TLPCIMQRLAADKYEITLTQGLNRQIRRMSQALGFKVIDLKRVSIQSLQLGDLPEGSMRP 224

Query: 236 VSKKILREQL 245
           +S   L + L
Sbjct: 225 LSSAELADLL 234


>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 = 82.8 bits (203), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 139/304 (45%), Gaps = 32/304 (10%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           NIV  N +  R++K I+ +G  SRRE +++I Q RVK+NG + E     V   D + VDG
Sbjct: 15  NIVDNN-SEIRLNKFISDSGFCSRREADKLIEQNRVKINGDIPE-LGTKVQLGDLVLVDG 72

Query: 65  VPLRKAERTRL----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDIN 117
             +  + + +L     +Y+KPIG+  T         +  N+ +      R+  +GRLD  
Sbjct: 73  KRINASAQDKLDRIYIVYNKPIGITCTTE-----RHIHGNIINAIGHKKRIFPIGRLDKP 127

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGL+ LT+DG +   +        + Y V     + +  +  +++G+ I        +V
Sbjct: 128 SEGLIFLTSDGDIVNKILRAENAHDKEYLVTVDKPLSERFVERMQRGVPILDTITKPCKV 187

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T+D    S     + L +G NR+I+++ E   ++V +L R       LG L  G  R ++
Sbjct: 188 TVD----SRFIFRIVLTQGLNRQIRRMCEHLGYEVLKLKRTRIMKVGLGNLKPGQWRNLT 243

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                       +E A++N    + SS     D    +S+ P     +KK++   N    
Sbjct: 244 N-----------IELAEIN--QAVSSSSKTATDPAKPVSKAPQS-EAIKKSTGANNSHQP 289

Query: 298 QKKL 301
            KK+
Sbjct: 290 AKKI 293


>gi|91070007|gb|ABE10933.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [uncultured Prochlorococcus marinus clone
           ASNC3046]
          Length = 240

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 121/234 (51%), Gaps = 9/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-T 73
           R++K ++  G  SRRE +++I + +V +NG + E  A  V   D +EV G  + K++R  
Sbjct: 4   RINKYLSEVGYCSRREADKLILEGKVTINGKIPEIGA-KVEEIDQVEVKGQRIEKSDRQE 62

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++L ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  KIYLAFNKPLGIVCTTDRKVEPNNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ +  ++ + +  +  G+ I      +  V    Q G   +  + 
Sbjct: 122 KILRARNNHEKEYIVKVNRPINSEFIQKMSNGVEILDTITKNCSV---KQLGPRKFKII- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++ E   ++V  L R+     +L  + +G  RE S++ L+E  G
Sbjct: 178 LTQGLNRQIRRMCETLGYRVRSLKRVRIMNIKL-DMPSGKYREFSREELQELNG 230


>gi|326407871|gb|ADZ64942.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis CV56]
          Length = 273

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 114/238 (47%), Gaps = 21/238 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +G+ SR EV+ ++ + RV V G +       V  ++  +  DG  L   E  
Sbjct: 33  RLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQEYY 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
             +L +KP GLV+   D      +F  +  + S       +  VGRLD NTEGLL+LTND
Sbjct: 93  -YYLLNKPQGLVSATKD-----NLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTND 146

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLD 180
           G L   L  P     + Y  R  G+V  + +N   +G+ ++       G  + +     +
Sbjct: 147 GALGHDLTQPKRHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYKGE 206

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +Q G  + + V + EGK  ++K++FE     V  L RI  G   L + LA G+ R ++
Sbjct: 207 SQSGWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLT 264


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 94/185 (50%), Gaps = 20/185 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  ++T  SD +GR+T+  F ++P ++      GRLD ++EGLLLLTNDGGL 
Sbjct: 1   RLILFNKPFDVLTQFSDGEGRATLKDFIDIPGVYP----AGRLDRDSEGLLLLTNDGGLQ 56

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------------VIQGICYGDMQV 177
             +  P  +  + Y V+  G+   ++L  L+ G+              + +   +     
Sbjct: 57  ARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLAEPALWPRNPP 116

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV 
Sbjct: 117 VRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWREVP 176

Query: 238 KKILR 242
            K+ R
Sbjct: 177 AKLQR 181


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 58/193 (30%), Positives = 97/193 (50%), Gaps = 20/193 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    +V  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQVYPVGRLDRDSEGLLLLTNNGEI 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR- 234
               + +    +W+ + + EGKNR+++++     +   RLIR+  G FQLG L +G  R 
Sbjct: 156 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRVGLGQFQLGDLDSGEYRI 215

Query: 235 --EVSKKILREQL 245
             E  K+ L +Q+
Sbjct: 216 LNETGKRQLFQQI 228


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEI 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 156 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPPLRLIRIGLGQFQLGELNSGEYRV 215

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 216 LDEKEKRQ 223


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 94/175 (53%), Gaps = 21/175 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++T  +D +GR T+ D   +P++++     GRLD ++EGLLLLT+DG L  +L
Sbjct: 4   LFNKPFDVLTKFTDGEGRKTLKDYIEIPNVYA----AGRLDKDSEGLLLLTDDGKLNHLL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 60  TDPKSKSFKTYLVQVEGEFSIEAAQKLEKGVLLKDGKTLPAKVKLIDEPEWLWERTPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 120 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYTLGNLKSGDYK 174


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 99/206 (48%), Gaps = 9/206 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKYISETGFCSRREADKLIEQGRVTINGKQPE-MGTKVLPGDDVCVDGKPVAAKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  VYIALNKPTGITCTTERDIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + +  +  G+ I        +VT +T+      +T G
Sbjct: 123 KILRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVTQETKFSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L    NR+I+++ E   ++V +L R+
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRV 204


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 58/209 (27%), Positives = 103/209 (49%), Gaps = 7/209 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + T +R++K I+  G  SRRE +++I Q RV +NG L    +  V   D + +DG P+  
Sbjct: 3   SLTEKRLNKYISETGFCSRREADKLIEQGRVTINGQLPPMGS-KVTEHDQVCIDGKPVGY 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG 
Sbjct: 62  KEKPIYIALNKPTGITCT-TERDVPGNIVDFIGH-NKRIFPIGRLDKPSDGLIFLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR +  +  + +  +  G+ I        +V  +TQ      +
Sbjct: 120 IVNKILRAGNNHEKEYVVRVNKPISAEFIRQMSAGVNILDTVTLPCKVVQETQYSFRIIL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           T GL    NR+I+++ E   ++V +L R+
Sbjct: 180 TQGL----NRQIRRMCEALGYEVFKLRRV 204


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 108/231 (46%), Gaps = 7/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAER 72
            + +++ + G   R+E  ++I    V+VNG +++  RA   +     + VDG P      
Sbjct: 2   ELYRLLQQQGFGGRKECRQLIEYGLVEVNGEVVDDYRAQFELADIASLAVDGEPWPLVTG 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP    T+H  P    +V+  LP  F+R  V +VGRLD++T GL+LL+NDG  
Sbjct: 62  PLYLLLHKPANYETSHK-PQCHPSVYRLLPDQFARLDVSAVGRLDVDTTGLILLSNDGQF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VYRV    +   + +  L+ G+ +          +++        +T
Sbjct: 121 IHALSSPKKLVPKVYRVTLKHEATPELIAKLQSGVYLNDEAREFAADSVEQIDPHTILLT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +   EGK  ++K++    + +V  L R S G   LG L  G  R ++ + L
Sbjct: 181 I--TEGKYHQVKRMVAAASNRVEALHRESLGAIVLGDLPVGEWRHLTAEEL 229


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 120/225 (53%), Gaps = 11/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +G  SRRE +++I   +VKVNG   ++A++   V     + V+G  +     
Sbjct: 4   RLNKYISNSGYCSRREADKLIEAGQVKVNG---KKASIGDRVYPKQKVTVNGELIVNDIE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V+T +DP+ ++ +   + S   R+  +GRLD +++GL+LLTNDG +  
Sbjct: 61  PVYIAFNKPVGIVST-TDPNEKANIVKYI-SHEQRIFPIGRLDKDSQGLILLTNDGDIVN 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        +VY V+    +  + +  +K G+ I       +    + +K +     + 
Sbjct: 119 KILRAGNNHKKVYIVQVDKPITDEFIEKMKTGVPI----LDRVTRKCEVEKINPYTFKIE 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L +G NR+I+++  +F+++V +L R      +L  L  GS R+++
Sbjct: 175 LIQGLNRQIRRMCAYFDYEVLKLERTQIMNIELEGLGLGSWRDLN 219


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 126/236 (53%), Gaps = 17/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ ++++   IA+R+E+++M+ +  + VN + +++      S++HI+ +   ++  +   
Sbjct: 2   RLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKK------SSEHIDENKDVVKIYDEVI 55

Query: 74  --RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTND 127
             R +LY   +K  G VT+HS      TV D++  +    ++ VGRLD++T GLL++TND
Sbjct: 56  EYRKYLYFVMNKRKG-VTSHSKDPMHRTVIDDMGELCVFDLNPVGRLDLDTTGLLIITND 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  L  P     + Y+V    +VD+   +  +KGI +          T++     N 
Sbjct: 115 GKFAHNLISPKKDVSKKYKVTLRYKVDEKYNDTFEKGIKLMPEDIITKPATMEIIDDYNC 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++T+  +EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + L+
Sbjct: 175 YLTI--KEGKYHQVKRMFEKVGNEVVELQRVQIGSFKLPEDLEEGDFRELTDEELK 228


>gi|110835398|ref|YP_694257.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110648509|emb|CAL17985.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 229

 Score = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 117/228 (51%), Gaps = 10/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +A +   +R+E +++I++  V V G    +A + +     + V G  ++     R
Sbjct: 2   RLDYFLAHSAGLTRKEAKQLISRGAVTVEGEAKPKANLQLRPDQAVTVHGERVQPPGH-R 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+ +V +  DP G  TV D LP  + ++V   GRLD +T GL+LLT+DG  +  
Sbjct: 61  YLMLHKPVDVVCSTEDP-GHRTVLDLLPPELRAQVHPAGRLDRDTTGLVLLTSDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           L  P+    + YRV+    V  + +  L++G++++    G+ + TL  Q  +   A + +
Sbjct: 120 LTSPNHACGKRYRVQCADPVSDEDMQALREGVLLR----GEDKPTLPAQVERLDEACLLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
            +REG+  ++K++      KV  L R   G  QL   LA G  R +++
Sbjct: 176 TIREGRYHQVKRMLAACGNKVLGLHREQIGEIQLDAALAPGEYRALTE 223


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 118/231 (51%), Gaps = 13/231 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R + Q  V +NG    RA V  + +  D ++V+G  +  R A
Sbjct: 7   RLNKYISESGICSRRDADRYVEQGNVFING---RRAQVGDLVSIGDKVKVNGQDIEPRDA 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T ++   R  + D   +  SR+  +GRLD +++GL+ LTN+G L
Sbjct: 64  ENLVFIALNKPVGIVST-TEGSERDNIVD-FVNHSSRIFPIGRLDKDSQGLIFLTNNGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  D +  +  G+ I G+      V    ++ S     
Sbjct: 122 VNKILRAGNNHDKEYVVTVNKPITDDFIKGMGAGVPILGVVTKKCVV----EQVSPFAFK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L +G NR+I+++ E+F ++V +L R       L  L  G  R++ K+ L
Sbjct: 178 IVLVQGLNRQIRRMCEYFGFEVTKLERQQIMNVSLKGLPIGEWRDLDKQEL 228


>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 = 82.8 bits (203), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 222


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 122/235 (51%), Gaps = 15/235 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
           +R+ KV++  G  +R+E+++++ +  ++VNG   E    N M  D  EVD + +   E  
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVRKGLIEVNG---EIVKDNGMQIDP-EVDKILVNGEEIF 57

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTN 126
            R ++Y   +KP G+V+  +  D R     +L  I  +V     VGRLD +T GLLLLTN
Sbjct: 58  YRKYIYLMMNKPDGVVS--ATFDNRDETVIDLLEIEHQVFEPFPVGRLDKDTVGLLLLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P  +  +VY  +   +V +  +   K GI +  G    + ++ +     S
Sbjct: 116 DGELNHRLISPKWKVDKVYYAKIDKKVTEADIKKFKNGITLDDGYTCKEAKLEILESSDS 175

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + V + ++EGK  ++K++FE  +  V  L R+ +G  QL   L  G  RE++++
Sbjct: 176 GSEVMITIQEGKFHQVKRMFEAVDKSVVYLKRVEFGTLQLDEDLEEGEYRELTEE 230


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 114/227 (50%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV V+G +++  A  +    ++E DG PL++    R
Sbjct: 2   RLDKFLSQQLEISRSLVARELHAQRVTVDGEVVKSGAFKLSPEHNVEFDGNPLKQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  DPD  + + F ++P  + ++ + GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFMDVPVAY-KLHAAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     + +D       G+ +          TL  +K ++  V + +
Sbjct: 121 ITSPKHECEKTYLVTLELPLAEDTAEQFTVGVQLHNEKNLTKPATL--EKITDHVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGICLDSELEPGEFRELSAE 225


>gi|317403818|gb|EFV84295.1| pseudouridylate synthase [Achromobacter xylosoxidans C54]
          Length = 243

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 113/236 (47%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAERT 73
           R+SK+++  G+ SRRE +  I +  V+V+G ++            I ++     R+  R 
Sbjct: 5   RISKLMSERGLCSRREADSYIERGWVRVDGEVVSELGARAFPNQVITLERAAQARQTSRV 64

Query: 74  RLWLYHKPIGLVTTHSDP---------DGRSTVF-DNLPSIFSR-----VISVGRLDINT 118
            + L +KP+G V+  ++          D RS    D  P  F R     +   GRLDI++
Sbjct: 65  TI-LINKPVGYVSGQAEKGYTPAVALIDARSRFAGDRSPQRFERGHLDGLAVAGRLDIDS 123

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GLL+LT DG +A++L    +   + Y VR  G + ++ L LL  G+ + G      QV 
Sbjct: 124 QGLLVLTQDGRVAKLLIGEDSSIDKEYLVRVQGDLSENGLALLNHGLSLDGKALKPAQVR 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 ++  +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R
Sbjct: 184 WQ----NHDQLRFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVALGELPLGQWR 235


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 112/233 (48%), Gaps = 14/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKAE 71
           R++K I+ +GI SRRE +R+I + RV +NG    +    V + D + VD   L   +  E
Sbjct: 12  RLNKAISDSGICSRREADRLIEEGRVTING-KTAKVGDRVSAFDEVIVDDRRLKLNKTGE 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R     ++KP G+V T ++PD +  + D  N P    R+  +GRLD  +EGL+ LT+DG 
Sbjct: 71  RPVYIAFNKPRGIVCT-TEPDVKDNIIDYINFP---KRIFPIGRLDKPSEGLIFLTSDGN 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V     +  + +  + KG+ I        QV     K      
Sbjct: 127 IVNKILRAGNNHEKEYIVTVDKPITDEFIKGMMKGVPILDTVTKKCQVF----KEGELVF 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + L +G  R+++K+ E+F + V +L R       L  L  G+ R ++ + L+
Sbjct: 183 RIILTQGLYRQVRKMCEYFGYHVTKLKRTRIMNISLAKLPLGTWRYLTPEELQ 235


>gi|315929678|gb|EFV08855.1| conserved hypothetical protein [Campylobacter jejuni subsp. jejuni
           305]
          Length = 204

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 101/205 (49%), Gaps = 17/205 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+     SRRE + +I Q  VK+N   +   +  V   D + V G  ++K  +  
Sbjct: 2   RINKFISHNTRYSRREADELIKQGLVKINN-KIALLSDEVKFDDKVFVKGKRVQKRTQFS 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +YHK  G + +  D  GR T++D LP  FS  +SVGRLD  +EGLLLLT+   +A  L
Sbjct: 61  VIIYHKQKGEIVSKKDDRGRKTIYDTLPRQFSTWLSVGRLDYASEGLLLLTDSPVIADAL 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
                +  R Y ++  G V +  +  ++ G+ I+    G    T  T             
Sbjct: 121 MHSDLE--REYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEIF 178

Query: 184 GSNAWVT---VGLREGKNREIKKVF 205
           GS+   T   V + EGKNRE+++ F
Sbjct: 179 GSSGGYTKLRVVINEGKNRELRRFF 203


>gi|331270360|ref|YP_004396852.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329126910|gb|AEB76855.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 240

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 118/242 (48%), Gaps = 25/242 (10%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRK 69
            T +R+ K+++  G  SR+E++ ++ +  ++++G  ++   V V     I +V G  +  
Sbjct: 1   MTMERLDKILSNLGYGSRKEIKVLVKKGEIEIDGEKIKDNGVKVDPNKSIIKVSGEEINY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDP---------DGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +   L + +KP G+V+   D          D   TVFD  P        VGRLD +TEG
Sbjct: 61  RKYIYLMM-NKPAGVVSATFDNYDETVIDLLDYEYTVFDPFP--------VGRLDKDTEG 111

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV 177
            LL+TNDG L   L  P     ++Y       VD+  +   +KGI+++         ++V
Sbjct: 112 FLLITNDGDLNHRLTSPKWHVDKIYYAEIDKIVDEKDIKAFEKGIMLEDGYRCLPAKLRV 171

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
               + GS   +T+  +EGK  ++K++FE  + KV  L R+  G   L  +L  G  RE+
Sbjct: 172 LSADENGSEVNITI--QEGKFHQVKRMFEARDKKVIYLKRLQMGNLVLDESLSEGEYREL 229

Query: 237 SK 238
           ++
Sbjct: 230 TE 231


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   L + E+ 
Sbjct: 6   RLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDH-KLIQFEQF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+V+   D   + TV D +   +  R+  VGRLD +TEGLLLLT+DG LA 
Sbjct: 65  HYLMLHKPQGVVSATKDHHDQ-TVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGMLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  P     +VY  +  GQ  ++++   K+G+ I G      Q  L   K     + V 
Sbjct: 124 ELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDI-GNGEKSKQARLQILKADVQESEVL 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           + + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E
Sbjct: 183 ITIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQE 236


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 120/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDQIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HK  G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKSAGVVTANKDRE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+ R +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKELQ 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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 115/240 (47%), Gaps = 25/240 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---AE 71
           R+SK+++  GI SRRE +RMI +  V+ NG ++      V     IE+  +P  K   AE
Sbjct: 5   RLSKLMSLRGICSRREADRMIEKGLVRANGKVISELGTKVPENAEIEL--LPHAKKWQAE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGR-------------STVFDNLPSIFSRVISVGRLDINT 118
           +  + L +KPIG V+T  +   +             S  FD  P    ++   GRLDI++
Sbjct: 63  KVTIIL-NKPIGYVSTQPEKGYKQALDLITPERQWNSKSFD--PKHLRKLSVAGRLDIDS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +G+L+LT DG +A+ +    ++  + Y VR  G V    +  L  G+V+         + 
Sbjct: 120 KGILILTQDGVIAKKIIGNESEIEKEYLVRVDGAVTPGIIKRLSFGLVLDNTPLKKANI- 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q+     +   L EGK R+I+++ E    KV  L R+  G  +LG L  G  R + K
Sbjct: 179 ---QQLDEHLMKFTLIEGKKRQIRRMCELVGLKVVDLKRVRIGKIRLGDLPTGYWRYLKK 235


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  RLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>gi|297583540|ref|YP_003699320.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297141997|gb|ADH98754.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 236

 Score = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 117/230 (50%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           RV K++A  G  SR++V++++ +    VNG +++ A  +V   TD +   G P+   E  
Sbjct: 2   RVDKLLAHVGYGSRKDVKQLLKKGLFTVNGEVVKSAKAHVDPETDDLAFGGEPILYREHL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + + HKP G+++   D   R+ V   +    +F +   VGRLD +T GLLLLTNDG  A
Sbjct: 62  YVMM-HKPAGVLSATEDVSERTVVDLLEEEDRLF-QPFPVGRLDKDTTGLLLLTNDGKWA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P+ +  + Y V     V  +  + L++G+ +  G       V    +  S  ++T
Sbjct: 120 HGITSPARKIPKTYEVLTAEPVTDEMADQLQQGVTLDDGYETRPAGVAFPDESRSRLYLT 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           +   EGK  ++K++       V+ L RI  G   L  +L AG+ RE+++K
Sbjct: 180 I--DEGKYHQVKRMLAAVGNHVDGLKRIRIGGLPLDESLEAGTYRELTEK 227


>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 = 82.4 bits (202), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 56/194 (28%), Positives = 97/194 (50%), Gaps = 21/194 (10%)

Query: 66  PLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           P+R+  R     R+ L++KP  ++   SD  GR T+ D +P   + V + GRLD ++EGL
Sbjct: 28  PVRRDARPKGPLRVILFNKPFDVLPQFSDEAGRRTLKDFVP--VTDVYAAGRLDRDSEGL 85

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI---- 170
           ++LTNDG L   L  P  +  ++Y V+  G+     L+ L+ G+ +        G+    
Sbjct: 86  MVLTNDGALQARLTQPGKRTGKIYFVQVEGEPQDSDLSRLRSGVTLNDGPTLPAGVERVA 145

Query: 171 ---CYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                   Q  +  +K     W+ + L EG+NR+++++     +   RLIR + G +QL 
Sbjct: 146 APEWLWPRQPPIRERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYAMGEYQLD 205

Query: 227 TLLAGSTREVSKKI 240
            L  G  R++S + 
Sbjct: 206 HLAPGEWRDISAEF 219


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/209 (29%), Positives = 108/209 (51%), Gaps = 14/209 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +R+I   +V +NG + E     V  +D +EV G  + K++R +
Sbjct: 4   RINKYLSEVGYCSRREADRLILDGKVTINGKIPE-IGTKVEDSDQVEVKGQRIEKSKRQK 62

Query: 75  -LWL-YHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++L ++KP+G+V T     +PD     F   P    R+  +GRLD  +EGL+ LTNDG 
Sbjct: 63  NIYLAFNKPVGIVCTTDRKVEPDN-VIDFIKYPK---RIFPIGRLDKLSEGLIFLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V+ +  ++ D +  +  G+ I G    +  V    Q G   + 
Sbjct: 119 IVNKILRARNNHEKEYIVKVNRPINNDFIQSMSNGVEILGTITKNCFV---KQLGPRNFK 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            + L +G NR+I+++ E   ++V  L RI
Sbjct: 176 II-LTQGLNRQIRRMCEALGYRVQSLKRI 203


>gi|330987630|gb|EGH85733.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 210

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 94/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L+L++KP  ++T  SD  GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L +L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDSLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 118/250 (47%), Gaps = 16/250 (6%)

Query: 1   MKDKN------IVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           MK KN      I+  +  P+ R++K I+  G  SRRE +++I   RV V+GI        
Sbjct: 1   MKQKNNEDKFVIIHNDRGPEIRLNKFISETGFCSRREADKLIENGRVTVDGIK-AVMGTK 59

Query: 54  VMSTDHIEVDGVPLRKAERTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           V  +  ++VDG  ++K +       +KP+G+  TT     G    F N      R+  +G
Sbjct: 60  VKESADVKVDGKSIKKVDELVYIALNKPVGITCTTEKKVKGNIVDFVNHKK---RIFPIG 116

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD +++GL+LLTNDG +   +        + Y V     +D+  +  +  G+ I G   
Sbjct: 117 RLDKDSQGLILLTNDGDVVNKILRAGNNHEKEYIVTVDKPIDEKFIKSMSSGVKILGTIT 176

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
               V   T++  N +  + L +G NR+I+++ E   + V +L RI      +  L  G 
Sbjct: 177 KKCIV---TKENKNTFRII-LTQGMNRQIRRMCEALGYNVVKLNRIRIMNINIERLKIGE 232

Query: 233 TREVSKKILR 242
            R ++ K L+
Sbjct: 233 WRNLTSKELK 242


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 120/233 (51%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA V   V + D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRAGVGDQVFAGDLVKVNGQVIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +     + +KP+G+V+T ++   +  + D + +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DSLVFIVLNKPVGIVST-TEAGEKDNIVDFV-NHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I G      +V    +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGAVTKKCKV----KKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIE 231


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 86/175 (49%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP   ++  +D DGR T+ D +      V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 69  LFNKPYDTLSQFTDGDGRKTLADYI--SIKDVYAAGRLDRDSEGLLILTNDGILQARLTQ 126

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +              
Sbjct: 127 PQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTLWPRNPPVRFRA 186

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + L EG+NR+++++     +   RLIR S G + LG L  G  REV+
Sbjct: 187 AIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRHSMGDWNLGDLQPGEWREVT 241


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 109/220 (49%), Gaps = 10/220 (4%)

Query: 34  MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           M+   RV VNG   + A + +    D I  DG  L   E    ++ +KP G+++   DP 
Sbjct: 1   MLKAGRVTVNGKKEKSAKLQIDEERDEIIFDGQVLEYEEFV-YYMMNKPKGVISATEDPK 59

Query: 93  GRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            R TV D L  +     V  VGRLDI+T GLLLLTNDG LA  L  P     + Y+ +  
Sbjct: 60  HR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAHALLSPKRHVDKTYQAQVK 118

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G + Q+ + +  KGI ++       +   V++DT+K   + + V + EGK  ++K++  +
Sbjct: 119 GIMTQEDVEIFAKGIPLKDFTCQPAKLEIVSIDTEK-IQSQIRVTIAEGKFHQVKRMVAY 177

Query: 208 FNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 178 CGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELEALLA 217


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V+S D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVSGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNYSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|237745528|ref|ZP_04576008.1| pseudouridylate synthase [Oxalobacter formigenes HOxBLS]
 gi|229376879|gb|EEO26970.1| pseudouridylate synthase [Oxalobacter formigenes HOxBLS]
          Length = 249

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 117/242 (48%), Gaps = 25/242 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK ++  GI SRRE +  I +  VKV+G  + +    V+    I ++    ++  R
Sbjct: 5   PVRLSKRMSELGICSRREADEWIERGWVKVDGKTVSQLGSKVLPHQKISIEKQASQEQAR 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------------PSIFSRVISVGRLDI 116
               L +KP+G V+  ++ DG       +                PS    ++  GRLDI
Sbjct: 65  RVTILINKPVGYVSGQAE-DGYKPAVSLISEATRWKGDPSKEKFKPSQLRSLVPAGRLDI 123

Query: 117 NTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRF--HGQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L  E  +T    + RV++   G++ ++ L LL+ G+ + G   
Sbjct: 124 DSVGLLVLTQDGRIAKRLIGENSATDKEYLVRVKYLKPGKLPENDLQLLRHGLKLDGKPL 183

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V       ++  +   LREGK R+I+++ E    KV  L RI  G  +LG L  G 
Sbjct: 184 LPAKVNWQ----NDDQLRFVLREGKKRQIRRMCEAVGLKVIGLKRIRIGQIKLGDLPPGQ 239

Query: 233 TR 234
            R
Sbjct: 240 WR 241


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 120/248 (48%), Gaps = 31/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IAQ RV+VNG +     + V ++D I VD    R A+R R
Sbjct: 59  RLNKRMAELGLCSRREADDWIAQGRVRVNGQVAP-IGLRVTASDRIAVDK-QARGAQRQR 116

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTV--FDN-------------LPSIFSRVISVGRLDINT 118
           +  L HKP+G V+  ++   R  V   D               P+    +   GRLDI++
Sbjct: 117 VTILLHKPMGYVSGQAEDGHRPAVALIDQRTHWRDDTSRNRFAPAQLRGLAPAGRLDIDS 176

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQV 177
            GLL+LT DG +AR L    +   + Y VR  +G V  D  ++   G  +  +C+G   +
Sbjct: 177 VGLLVLTQDGRVARQLIGADSTVDKEYLVRVQYGAVALDVRSVFPAG-QLASLCHG---L 232

Query: 178 TLDTQKGSNAWVT--------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +LD Q    A V           L EG+ R+I+++       V  L R+  G  +LG L 
Sbjct: 233 SLDGQPLKPAVVDWQNPEQLRFVLTEGRKRQIRRMCALVGLTVVGLKRVRIGRVRLGLLP 292

Query: 230 AGSTREVS 237
           AG  R ++
Sbjct: 293 AGQWRYLA 300


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 91/178 (51%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ + +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRRTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAK 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------------ICYGDMQVT 178
           L  P+ +  ++Y V+  G  + D L+ L+ G+V++                  +  +   
Sbjct: 88  LTQPTAKTGKIYFVQVEGVPEDDALDKLRHGVVLKDGPTLPAGAELVSEPEWLWPRVPPI 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + +     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  +E+
Sbjct: 148 RERKNIPTRWLQITLYEGRNRQVRRMTAHIGFPTLRLIRFSVGNLSLADLQPGEWKEI 205


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 59/205 (28%), Positives = 100/205 (48%), Gaps = 7/205 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKYISETGFCSRREADRLIEQGRVTINGQQPE-MGTKVLPGDDVCVDGNPVAAKEKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  IYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +  + L  +  G+ I        +V  +T+      +T GL
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVEKETKFSFRIVLTQGL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRI 218
               NR+I+++ E   ++V +L R+
Sbjct: 184 ----NRQIRRMCEALGYEVFKLRRV 204


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 91/175 (52%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 60  IFNKPYDTLSQFTDGDGRKTLADYIP--IKNVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 117

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ------------ 182
           P ++  + Y V+  G   +  L  L+KG+ ++ G+    +++V  + Q            
Sbjct: 118 PKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAEVEVIPEPQVWDRTPPVRFRA 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + + EG+NR+++++     +   RLIR S G   L  L+ G  RE+S
Sbjct: 178 NIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLIRHSMGDIVLNDLMPGEWREIS 232


>gi|323254500|gb|EGA38311.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 289

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V+S D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVSGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNYSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 114/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I++ RV VNG  + +    V   D I V G  LR A    
Sbjct: 5   RLNKFISESGKASRRGADKLISEGRVTVNG-KVAKVGDQVKPGDDIRVSGQQLRIARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T S+   +  + D L +   R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITST-SEKKVKGNIID-LVNHPLRIHHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + +  + +G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVAVDKPITPEFIKNMSEGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V RL R       L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEVLGYEVYRLQRTRIMNIHLNNLPVGQWRDLTKK 222


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 110/228 (48%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V   + I  V G  +      
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEYKPFI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+V+   D     TV D L      F     VGRLD +TEGLLLLTNDG L
Sbjct: 64  YLMM-NKPSGVVSATEDA-VEETVVDLLEEEDRAFCP-FPVGRLDKDTEGLLLLTNDGQL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G+V +  +   ++G+V+           +  + G  + V 
Sbjct: 121 AHQLLSPKKHVPKTYFAVVGGEVTEADVAAFQRGVVLDDGYETKPAKLVVLKSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           V + EGK  ++K++F+    +V  L RI  GP  L   LA G  RE++
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLALDPDLAVGEYRELT 228


>gi|332971035|gb|EGK10006.1| ribosomal large subunit pseudouridine synthase F [Kingella kingae
           ATCC 23330]
          Length = 243

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 108/237 (45%), Gaps = 20/237 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A   I SRRE +  I Q  VKVNG +       V+  D I++D    ++  +
Sbjct: 4   PIRLSKRMAELKICSRREADSYIEQGWVKVNGAV-AVLGQKVLPNDRIDLDKRAHQQQTQ 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDIN 117
               L +KP+G V+   + D R+ +                   PS    +   GRLDI+
Sbjct: 63  RVTILLNKPVGFVSGQPEKDYRAAIELITESNHWQGDTSRIAFHPSQLRGLAPAGRLDID 122

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+LT DG +A+ L    +   + Y VR  G +    L LL  G+ + G      +V
Sbjct: 123 SVGLLVLTQDGRIAKQLIGEQSDSEKEYLVRVKGTLSPQGLALLNHGLSLDGEKLRPAKV 182

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 183 EWQNEDQ----LRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGALPTGQWR 235


>gi|310659128|ref|YP_003936849.1| pseudouridylate synthase [Clostridium sticklandii DSM 519]
 gi|308825906|emb|CBH21944.1| pseudouridylate synthase [Clostridium sticklandii]
          Length = 236

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 107/227 (47%), Gaps = 15/227 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++  I+ +G+ SRR+ + +I   +VKVN  + +     V   D +EVDG  ++  E   
Sbjct: 2   RLNNYISSSGLCSRRKADELIKNNKVKVNSKIAD-LGYQVSEGDIVEVDGTIIKPKEDKV 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT    +G    + N      R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 61  YIALYKPVGITCTTEEHIEGNIVDYVNYKE---RIFPIGRLDKDSEGLILLTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------QKGSNA 187
           +        + Y V     +D   L  + +G+ I    Y  ++ T  T       K S  
Sbjct: 118 ILREENHHEKEYIVTVDKPLDSKTLKQMSQGVRI----YNPVKNTYTTTKPCKIHKISEK 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              + L +G NR+I+++ + F +KV +L R+      L  L  G  R
Sbjct: 174 SFKIVLSQGLNRQIRRMCQHFGYKVRKLKRVRILNITLDGLSYGKWR 220


>gi|104783740|ref|YP_610238.1| pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95112727|emb|CAK17455.1| pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 209

 Score = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 94/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  ++T  SD +GR+T+  F ++P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 31  RLILFNKPFDVLTQFSDGEGRATLKDFIDIPGIYP----AGRLDRDSEGLLLLTNDGRLQ 86

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  +  + Y V+  G+  +++L  L++G+ +        +  L  +         
Sbjct: 87  ARIADPKHKLAKTYWVQVEGEPSEEQLKRLREGVELNDGPTLPAEARLLEEPELWPRNPP 146

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    AW+ + +REG+NR+++++         RL+R+  G + +  L  G  REV 
Sbjct: 147 VRFRKSVPTAWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLEQGCWREVV 206

Query: 238 KKI 240
            K+
Sbjct: 207 AKL 209


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 127/247 (51%), Gaps = 15/247 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V S D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFING---KRAGIGDQVFSGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T ++   +  + D + +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVST-TESGEKDNIVDYV-NHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I     G M      +K +     
Sbjct: 123 VNKILRAGNSHEKEYLVTVNKPVTDEFIRGMGAGVPI----LGTMTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E     ++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERVRIMNVRLTGIPVGEWRDLTDDELIELF--DMM 236

Query: 251 EEAQVNL 257
           E+++ ++
Sbjct: 237 EKSESDI 243


>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 = 82.4 bits (202), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQRRDLTKK 222


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 91/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>gi|284920961|emb|CBG34024.1| ribosomal large subunit pseudouridine synthase E (rRNA
           pseudouridylate synthase E) [Escherichia coli 042]
          Length = 217

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 91/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/256 (27%), Positives = 120/256 (46%), Gaps = 41/256 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           RVSK+++  G+ SRRE +  I Q  V ++G ++    V       IE+  G   ++A R 
Sbjct: 6   RVSKLLSELGLCSRREADSYIEQGLVTIDGEVVNELGVRAYRHQKIELQSGAKAQQASRI 65

Query: 74  RLWLYHKPIGLVTTHSDPD---------------------GRSTVFDNLPSIFSRVISVG 112
            + L +KP+G ++ + D                       G+S  F+        +   G
Sbjct: 66  TVIL-NKPVGYISHYDDEQEYQPAASLITPANYFASPLDKGKSPRFNT-----KGLAPAG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDI++ G+L+LT DG +A++L   ++   + Y VR  G++  + L+ L+ G+ +  +  
Sbjct: 120 RLDIDSTGMLVLTQDGRIAKLLIGENSPIEKEYLVRVAGRLSFEGLDRLRHGLSLDEVEL 179

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              QV+   ++     +   LREG+ R+I+++ E    KV  L R+  G   LG+L  G 
Sbjct: 180 KPAQVSWQNEE----QLRFVLREGRKRQIRRMCEIVGLKVLGLKRVRMGRISLGSLPPGQ 235

Query: 233 TREVSKKILREQLGPH 248
            R V         GPH
Sbjct: 236 WRYV---------GPH 242


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 112/238 (47%), Gaps = 34/238 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR +K  AR    S ++     A++R   N I   + A++                +ER 
Sbjct: 57  QRTTKNTARPHTTSGKK--SFSAKKRATSNDITSPKRAIS---------------PSER- 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP   ++  +D DGR T+ + +      V + GRLD ++EGLL+LTNDG L   
Sbjct: 99  KVVLFNKPYDTLSQFTDGDGRKTLANYI--QIKDVYAAGRLDRDSEGLLILTNDGILQAR 156

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P ++  + Y V+  G   +  L  L++G+ ++       +V +  +           
Sbjct: 157 LTQPQSKAPKTYWVQVEGVPQESDLEALRQGVTLKDGPTLPAKVEIMPEPELWPRNPPVR 216

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   W+T+ L EG+NR+++++     +   RLIR S G + LG L  G  REV+
Sbjct: 217 FRAAIPTTWLTITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPGEWREVT 274


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   VM  D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFING---KRATIGDQVMPGDVVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDSE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  D +  +  G+ I G      +V  +    +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDDFIRGMGAGVPILGTVTKKCKVKKE----APFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++
Sbjct: 179 ITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGLPPGEWRDLT 225


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 95/179 (53%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR+T+ + +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVLLFNKPFDVLPQFTDESGRTTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT------------ 178
           L  P+ +  +VY V+  G    D L  L++G+ ++    +  G   V+            
Sbjct: 88  LTQPAKKTGKVYFVQVEGVPSDDALLQLQRGMTLKDGPTLPAGAELVSEPEWLWPRNPPI 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++
Sbjct: 148 RERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEWKEIN 206


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/232 (30%), Positives = 108/232 (46%), Gaps = 17/232 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   ++  G  SRRE ER++A  R+ VNG    +    V + D I +DG P+   ER  
Sbjct: 2   RIQLYMSNTGYCSRRETERLLAAGRITVNGKTATKDTF-VDTDDCILLDGSPVPMKERNI 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLA 131
             L HKP G+V T      +  V +NL    +   R+ +VGRLD ++EGLLLLTNDG + 
Sbjct: 61  YLLLHKPTGIVCT-----AQRQVKNNLIDYMNYRERIFAVGRLDKDSEGLLLLTNDGDIV 115

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWV 189
             +        + Y V          L  +  G+ I        QVT      +      
Sbjct: 116 NKIMRVENGHEKEYIVTVDRPYPDTFLKSMASGVEILD------QVTEPCTVTRIDEMTF 169

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L++G NR+I+++ + F + V RL R+      +  L  G  RE++ + L
Sbjct: 170 RIILKQGLNRQIRRMTKEFGYYVTRLRRVRIMNLSIDRLPYGQWRELTDEEL 221


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/209 (28%), Positives = 103/209 (49%), Gaps = 10/209 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K     G  SRR+ +++I    V VNG   E       + D + V+G  + + E 
Sbjct: 3   PIRINKYFTTIGFCSRRKADKLIEAGYVTVNGKRPEMGQKIDPAKDKVRVNGKLVGQEEE 62

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             ++L ++KP+G+V T      +  + D  N PS   R+  +GRLD  +EGL+ LTNDG 
Sbjct: 63  KPVYLVFNKPVGIVCTTDTHVEKDNIIDYINYPS---RIFPIGRLDKPSEGLIFLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V     +  D +N +K GI I      + +V    +K ++   
Sbjct: 120 IVNKILRARNHHEKEYIVTVDRVISDDFVNRMKSGIPILDTVTRECEV----EKITDYMF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            + L +G NR+I+++ E+  ++V  L RI
Sbjct: 176 KIVLTQGLNRQIRRMCEYLGYEVLTLKRI 204


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 90/179 (50%), Gaps = 17/179 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   SD  GR T+ D +P +   + + GRLD ++EGL++LTNDG L   L  
Sbjct: 42  LFNKPFDVLPQFSDGSGRRTLKDYVPQL--GIYAAGRLDRDSEGLMVLTNDGELQAQLTQ 99

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYGDM----QVTLDTQ 182
           P  +  +VY V+  G   +  L  L+ G+          V++ +   D     Q  +  +
Sbjct: 100 PGKRTGKVYYVQVEGCPQEGDLQPLRDGVNLKDGPTLPAVVEKVAAPDWLWDRQPPIRER 159

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +I
Sbjct: 160 KAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGSLGLRALAPGEWRDISDEI 218


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/202 (31%), Positives = 100/202 (49%), Gaps = 7/202 (3%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V VNG ++      +  +D ++    P+   ER    L +KP   VTT  DP  R TV D
Sbjct: 2   VSVNGEVVTELGTKIKRSDVVKFHDEPV-SIERKVYVLLNKPKDTVTTSDDPQERRTVMD 60

Query: 100 NLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +    + R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     + +  +
Sbjct: 61  LVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADM 120

Query: 159 NLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           + +  GI ++ G  + D +  T D +K     V + +  GKNR ++++FE   +KV +L 
Sbjct: 121 DQIAAGIQLEDGEIHADAISYTDDFKKDQ---VGIEIHSGKNRIVRRIFESLGYKVVKLD 177

Query: 217 RISYGPFQLGTLLAGSTREVSK 238
           R+ +       L  G  R +S+
Sbjct: 178 RVFFAGLTKKGLRRGDWRYLSE 199


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 112/236 (47%), Gaps = 21/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAERT 73
           R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     R+  R 
Sbjct: 5   RISKLMSERGLCSRREADTYIERGWVRVDGVVVSELGARAYPDQVITLERAAQARQTSRV 64

Query: 74  RLWLYHKPIGLVTTHSDP---------DGRS-TVFDNLPSIFSR-----VISVGRLDINT 118
            + L +KP+G V+  ++          D RS    D  P  F R     +   GRLDI++
Sbjct: 65  TI-LINKPVGYVSGQAEKGYTPAVALIDSRSRYAGDRAPQRFERAHLDGLAVAGRLDIDS 123

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GLL+LT DG +A+ L    +   + Y VR  G +  + L LL  G+ + G      QV 
Sbjct: 124 QGLLVLTQDGRIAKHLIGEDSSVDKEYLVRVQGNLSDNGLALLNHGLSLDGKALKPAQVR 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 ++  +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R
Sbjct: 184 WQ----NSDQLRFVLREGKKRQIRRMCELVGLKVIGLKRVRIGRVSLGDLPLGQWR 235


>gi|323127651|gb|ADX24948.1| Putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. equisimilis ATCC 12394]
          Length = 238

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 115/231 (49%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SRR+V+++I  Q V+++  +      NV      IE+ G  +   + +
Sbjct: 2   RLDKLLEVVTDGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEISGKRISHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
             ++ +KP G+V+  SD +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  -YFILNKPAGVVSARSDIN-HVTVLDQLSEKDRHPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G +D+D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVAKTYMVTVNGFLDEDAPDFFAAGIKFPTGEQCRPAQLTILQASQEK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   + + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R V+
Sbjct: 176 SQARLVISEGKFHQVKKMFLTYGLKVISLKRTSFAGLELGELASGAYRSVT 226


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 55/181 (30%), Positives = 91/181 (50%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RLILFNKPYDVLPQFTDEAGRQTLKDFIP--VADVYAAGRLDRDSEGLLVLTNDGALQAK 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT------------ 178
           L  P  +  +VY V+  G+   + L  L+ G+ +     +  G  +V             
Sbjct: 98  LTQPGKRTGKVYFVQVEGEPTDEALAQLRTGVTLNDGPTLPAGVERVAEPAWLWPRNPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV  
Sbjct: 158 RERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYATGDYTLDALACGQWREVPL 217

Query: 239 K 239
           K
Sbjct: 218 K 218


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 114/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I++ RV VNG  + +    V   D I V G  LR A    
Sbjct: 5   RLNKFISESGKASRRGADKLISEGRVTVNG-KVAKVGDQVKPGDDIRVSGQQLRIARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T S+   +  + D L +   R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITST-SEKKVKGNIID-LVNHPLRIHHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + +  + +G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVAVDKPITPEFIKNMSEGVKILGTKTLPCKVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V RL R       L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEVLGYEVYRLQRTRIMNIHLNNLPVGQWRDLTKK 222


>gi|254743404|ref|ZP_05201089.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. Kruger B]
          Length = 235

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 113/227 (49%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP+G+  T S+   +  + D  N P    R+  +GRLD +++GL+LLTNDG +  
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL---RISHIGRLDKDSDGLILLTNDGDIVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + 
Sbjct: 117 EILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKII 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 173 LTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQRRDLTKK 219


>gi|119897119|ref|YP_932332.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669532|emb|CAL93445.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 500

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 110/240 (45%), Gaps = 30/240 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SKV+A  GI SRRE + +I +  V V+G  +      +   D   V     +KA+  R
Sbjct: 263 RLSKVMADRGICSRREADELIERGWVFVDGRRVSELGTRI-DPDARVVLAPEAKKAQAQR 321

Query: 75  LW-LYHKPIGLVTTHSDPD--------GRSTVFDN------LPSIFSRVISVGRLDINTE 119
           +  L HKP+G V+   +P         G    FD        PS    +   GRLDI++ 
Sbjct: 322 VTILLHKPVGYVSGQPEPGYEPAVTLIGGDNQFDRDVAQRFHPSQLKGLAPAGRLDIDST 381

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +AR L    ++  + Y VR  G++  D L LL  G+ +        +V  
Sbjct: 382 GLLVLTQDGRIARQLIGDDSKVEKEYLVRVEGELVDDGLALLNHGLSLDDKPLRPAKVE- 440

Query: 180 DTQKGSNAWVTVG-----LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                   W+        L+EG+ R+I+++ E    +V  L R+  G  +LG L  G  R
Sbjct: 441 --------WINEDQLRFVLKEGRKRQIRRMCELVGLRVVGLKRVRIGRVKLGDLPLGEWR 492


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/210 (30%), Positives = 102/210 (48%), Gaps = 11/210 (5%)

Query: 12  TPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +PQ  R++K I+  G  SRRE +++I Q RV +NG   E   V V  +D + +D  PLR 
Sbjct: 10  SPQGVRLNKFISDTGYCSRREADKLIDQGRVTINGKKPE-MGVRVTDSDDVLIDDKPLRS 68

Query: 70  AERTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            ER      +KP G+  TT    +G    F        R+  +GRLD  ++GL+ LTNDG
Sbjct: 69  KERPIYIALNKPTGITCTTERHIEGNIVDF---IGHRKRIFPIGRLDKPSDGLIFLTNDG 125

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y VR    +  + L  +  G+ I        +VT +T    N  
Sbjct: 126 DIVNKILRAGNSHEKEYVVRVDKVITPEFLEKMASGVEILDTVTLPCKVTKET----NFS 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
             + L +G NR+I+++ E   ++V +L R+
Sbjct: 182 FRIVLTQGLNRQIRRMCEALGYEVYKLRRV 211


>gi|310767366|gb|ADP12316.1| Ribosomal large subunit pseudouridine synthase E [Erwinia sp.
           Ejp617]
          Length = 218

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 90/179 (50%), Gaps = 17/179 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   SD  GR T+ D +P +   + + GRLD ++EGL++LTNDG L   L  
Sbjct: 42  LFNKPFDVLPQFSDGSGRRTLKDYVPQL--GIYAAGRLDRDSEGLMVLTNDGELQAQLTQ 99

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYGDM----QVTLDTQ 182
           P  +  +VY V+  G   +  L  L+ G+          V++ +   D     Q  +  +
Sbjct: 100 PGKRTGKVYYVQVEGCPQEGDLQPLRDGVNLKDGPTLPAVVEKVAAPDWLWDRQPPIRER 159

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +I
Sbjct: 160 KAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGSLGLRALAPGEWRDISNEI 218


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 118/229 (51%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +R+I + +V +NG + E     V   D +EV+G+ + K  + +
Sbjct: 4   RINKYLSEVGYCSRRVADRLIEEGKVTINGKISE-IGTKVKEDDQVEVEGIIIDKPTKQK 62

Query: 75  -LWL-YHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++L ++KP+G+V T     +PD    + D   +  +R+  +GRLD N+EGL+ LTNDG 
Sbjct: 63  YIYLAFNKPVGIVCTTDRRVEPDN---IID-FINYSTRIFPIGRLDKNSEGLIFLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  +++D ++ +  G+ I      +  V    Q G   + 
Sbjct: 119 IVNKILRARNNHEKEYIVSVNRPINRDFIHNMSNGVKILDTITKNCFV---KQLGVKKFK 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + L +G NR+I+++ E   ++V  L RI     +L  +  G  RE +K
Sbjct: 176 II-LTQGLNRQIRRMCESLGYRVQSLKRIRIMNIKLD-IPTGKYREFTK 222


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 7/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V   +        +   ++  
Sbjct: 18  RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKTQVNEFEDTVTYLGEIIAYQKDF 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
            ++ HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  A 
Sbjct: 78  YYILHKPAGVISATQD-NHDQTVIDLLKDQDYREDLFPVGRLDKDTEGLLILTNDGIFAH 136

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y     G + ++ + L  +G++I G        +Q+    Q+   + +
Sbjct: 137 QLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETSII 196

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 197 RLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFWLPKDLNKGQYRPMTKEELEQ 251


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 91/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGRTLPAGVELVDEPTWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/205 (29%), Positives = 101/205 (49%), Gaps = 4/205 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K ++     SR +  + + Q  VKVN  L++  A+ V   D +E DG  L      
Sbjct: 3   QRLDKFLSEYTGLSRSQATKALRQNLVKVNQQLVKDGALKVSPEDVVEFDGETLEWVSGN 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + +L +KP G V +H D +  +   F + P + SR+ + GRLD++T GL+LLT+DG  + 
Sbjct: 63  QYFLLYKPEGYVCSHDDGEYPTVYQFFDYP-LSSRLHTAGRLDVDTTGLVLLTDDGQWSH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P   + + Y V     V+   L    +GI+++G         ++     N  +T+ 
Sbjct: 122 RITSPKYHYKKTYLVTLAAPVEDFYLEQCAQGILLRGEKQPTKPAQIEIIDDYNLNLTI- 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIR 217
             EGK  ++K++F     KV  L R
Sbjct: 181 -VEGKYHQVKRMFAALGNKVIALHR 204


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 106/240 (44%), Gaps = 24/240 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SKV+A  G+ SRRE +  I+   VKV+G ++E     +     I +            
Sbjct: 184 RLSKVMAERGLCSRREADEWISNGWVKVDGEIIETLGTRIKPDAEIIISSYAQEYQAENV 243

Query: 75  LWLYHKPIGLVTTHSD-----------PDGR----STVFDNLPSIFSR-----VISVGRL 114
             + HKP+G V+  ++           PD +      +  + P  F R     +   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 AKVSWQNED----QLRFVLREGKKRQIRRMCEMVGLHVVGLKRIRMGSITLGKLPVGQWR 419


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 219


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 120/243 (49%), Gaps = 23/243 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAE 71
           R++K ++ AG+ SRRE +R+I    V V+G    + AV  M  +    + V    ++   
Sbjct: 3   RLNKYLSEAGVCSRREADRLIESGVVTVDG----KNAVPGMKVEDGQEVCVGKKRIKSKT 58

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  +   +KP G+V T    + ++ + F N P    RV   GRLD ++EGLL++TNDG L
Sbjct: 59  KKTVLAVYKPAGIVCTEDKREKKNIIRFLNYPL---RVTYAGRLDKDSEGLLIMTNDGDL 115

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------QK 183
              +        + Y+V  + ++  + +  + +G+ I+     D +  LD        +K
Sbjct: 116 INGMMRARFSHEKEYKVTVNKEITPEFIEKMSRGVHIR-----DREKNLDAVTRPCKVRK 170

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                 ++ L +G NR+I+++ E   +KV  L RI     +LG L  G  R ++++ L+E
Sbjct: 171 NGKYTFSIILTQGLNRQIRRMCEALGYKVTTLKRIRIMNVELGNLKPGEVRGLTEQELKE 230

Query: 244 QLG 246
             G
Sbjct: 231 LYG 233


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/214 (31%), Positives = 100/214 (46%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+++  G  SRREV+ ++    V VNG++ + +   V    D I V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKSQVNPEKDQITVHGNPVIYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG LA
Sbjct: 62  YFML-HKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  +  G V    +   + GI +    Y      L+    +   VT+
Sbjct: 120 HNLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDD-GYTCKPAHLEIMAPNEIRVTI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +EGK  ++K++F      V  L R+S G   L
Sbjct: 179 --QEGKFHQVKRMFAATGKTVIYLKRLSMGKLML 210


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/220 (31%), Positives = 108/220 (49%), Gaps = 10/220 (4%)

Query: 34  MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           M+   RV VNG   + A + +    D I +DG  L   E    ++ +KP G+++   DP 
Sbjct: 1   MLKAGRVTVNGKKEKSAKLQIDEERDEIRLDGQVLEYEEFV-YYMMNKPQGVISATEDPK 59

Query: 93  GRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            R TV D L  +     V  VGRLDI+T GLLLLTNDG LA  L  P     + Y  +  
Sbjct: 60  HR-TVLDLLDDLARTKEVFPVGRLDIDTHGLLLLTNDGQLAHALLSPKRHVDKTYLAQVK 118

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G + Q+ +    KGI ++       +   V++DT K + + + V + EGK  ++K++  +
Sbjct: 119 GIMTQEDVETFAKGIPLKDFTCQPARLELVSIDTAK-NQSQIRVTIAEGKFHQVKRMVAY 177

Query: 208 FNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 178 CGKEVVDLQRLTMGTLMLDENLQRGEWRRLTKEELENLLA 217


>gi|302187757|ref|ZP_07264430.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 230

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 109/227 (48%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +DG  L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDGEILQAGKAPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    +G+     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGLTTQPAQLTLLGPRSARLSIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVLRLHRENIGALALDPGLRPGSYRALN 223


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 74/227 (32%), Positives = 112/227 (49%), Gaps = 6/227 (2%)

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  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + L HKP+G+V+   D D   TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 81  VML-HKPVGVVSATID-DKHRTVIDLLEQDDKESLHIVGRLDLNTSGLLLLTNDGRWSKR 138

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++YRV     +  D ++   +G+  +      +   L+      A VT  L
Sbjct: 139 LMDPEHKVGKLYRVHLQNPLTPDYISGFAQGMYFEFEDITTLPAELEIIDSYTALVT--L 196

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            EG+  +IK++F  F   V  L RIS G   L   L  G +R ++ K
Sbjct: 197 YEGRYHQIKRMFGRFRNPVIGLHRISVGNIVLDNNLKPGESRVLTPK 243


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 103/216 (47%), Gaps = 10/216 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +++ + RAG+  ++E E+ I   RVKV G L       V    ++ VDG   R      +
Sbjct: 29  LARALGRAGVMPQQEAEQAIRDGRVKVEGRLELEPFAPVRLGSNVFVDGWAHRLEAPLHV 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L EG++ ++K++       V  L R + G   L
Sbjct: 205 ELVLTEGRHHQVKRMLAAVGHPVRTLHRQAVGTVSL 240


>gi|260890235|ref|ZP_05901498.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           hofstadii F0254]
 gi|260859855|gb|EEX74355.1| ribosomal small subunit pseudouridine synthase A [Leptotrichia
           hofstadii F0254]
          Length = 238

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 122/242 (50%), Gaps = 25/242 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A +GI +R+EV+ ++  +++ VN   ++   + +     I        K E   
Sbjct: 2   RLDKFLANSGIGTRKEVKEILKNKKISVNDAFVKDGKIQIDEEKDI-------VKYEDNI 54

Query: 75  LW-------LYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLT 125
           ++       + +KP G+++   D   R TV D L   +    +  VGRLDI+TEGLLLLT
Sbjct: 55  IYYKPFVYIMMNKPAGVISATEDNHHR-TVIDLLNDEYRTYDIFPVGRLDIDTEGLLLLT 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL---DT 181
           NDG L+  L  P     + Y V+    + ++ +  L+ GI + +       +V +   ++
Sbjct: 114 NDGILSHNLLSPKKHVDKKYYVKISNPLTEEDIKTLENGIKLEENFVTKKAKVKIICNNS 173

Query: 182 QKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           +K  N A++T+   EGK  ++K++F+  N +V  L R+  G   L   L  G  RE++++
Sbjct: 174 EKNENLAYITIS--EGKFHQVKRMFKAVNNEVLYLKRVKMGSLSLDEKLKLGEYRELTEE 231

Query: 240 IL 241
            L
Sbjct: 232 EL 233


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/230 (30%), Positives = 111/230 (48%), Gaps = 11/230 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLR 68
           TP RV   +A  G+ SRR  E +I ++ V+VNG +  +    V   D I       V   
Sbjct: 6   TP-RVQVFLAEKGVGSRRFCEELIKKKLVRVNGSI-AKLGDKVALGDRITYKKQIYVFTD 63

Query: 69  KAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
              +++++L  +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TN
Sbjct: 64  FQSKSKIYLALNKPKNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  P  +  R Y +     +D++ L   K GI I+   +  ++      K S 
Sbjct: 124 DGKFANYIIHPKGKVEREYIIESKKDIDENLLISFKSGIKIKKEFF-KLKSYEILNKNSA 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 183 RLI---LDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLREGQVKIV 229


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 7/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V   +        +   ++  
Sbjct: 2   RLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKTQVNEFEDTVTYLGEIIAYQKDF 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
            ++ HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  A 
Sbjct: 62  YYILHKPAGVISATQD-NHDQTVIDLLKDQDYREDLFPVGRLDKDTEGLLILTNDGIFAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y     G + ++ + L  +G++I G        +Q+    Q+   + +
Sbjct: 121 QLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETSII 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 181 RLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFWLPKDLNKGQYRPMTKEELEQ 235


>gi|240950257|ref|ZP_04754536.1| pseudouridylate synthase [Actinobacillus minor NM305]
 gi|240295234|gb|EER46035.1| pseudouridylate synthase [Actinobacillus minor NM305]
          Length = 224

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/196 (31%), Positives = 99/196 (50%), Gaps = 24/196 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E T + L++KP  ++T  +D  GR T+  F ++P I+     VGRLD ++EGLLLLTN+G
Sbjct: 29  EETIIVLFNKPYDVLTQFTDEQGRKTLKDFIDIPKIYP----VGRLDRDSEGLLLLTNNG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------LDTQ 182
            +   L  P  +  + Y V+  G   Q  L  L+KG+ ++       +         D Q
Sbjct: 85  EIQHRLAHPKFEKEKTYWVQVEGIPSQADLAKLEKGVELKDGLTQPAKAKQIEAPDFDWQ 144

Query: 183 KG---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                        +W+ + + EGKNR+++++     +   RLIR+  G +QLG L +G  
Sbjct: 145 TAPKIRERKTIPTSWIELKITEGKNRQVRRMTAHIGFPTLRLIRVGLGHYQLGELGSGEY 204

Query: 234 REVS---KKILREQLG 246
           + +S   K  L +QLG
Sbjct: 205 QVLSLSEKSRLFKQLG 220


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 106/214 (49%), Gaps = 10/214 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V+VN   ++    ++  + DH+ V+G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGAVEVNDKKIKTPKTHINPNEDHVTVNGSTISYIENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G+++   D D   TV D +P  +S   +  VGRLD +TEGLLLLTNDG   
Sbjct: 62  YIML-NKPKGVISATED-DSHKTVIDLIPE-YSHLGIFPVGRLDKDTEGLLLLTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + Q  +   + G+ +        ++     KG++    V
Sbjct: 119 HELMNPNKHVSKTYEVVSKYPIKQADIEAFESGVELSDGKVKPAKLI----KGNDHLSYV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + EGK  ++K++F     +V  L RI     +L
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIANLEL 208


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 117/231 (50%), Gaps = 23/231 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R+I   +V V+G+  +   + V +   ++V    + K +   
Sbjct: 17  RLNKYLSEAGVCSRREADRLIESGKVTVDGVTAQ-MGMRVTAGQIVKVGKKTVSKQDEMI 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +   +KP G+V T    +  S V F N P    RV   GRLD ++ GLLL+TN+G +   
Sbjct: 76  VLAVNKPKGIVCTEDQRERDSIVRFLNYPV---RVTYAGRLDKDSRGLLLMTNNGDIINQ 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------QKGSN 186
           +   + +  + Y+V    ++ +  +  + +G+ I           LDT       +K   
Sbjct: 133 MMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPI-----------LDTVTRPCTVKKIGK 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              ++ L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++
Sbjct: 182 YTFSIILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLT 232


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 120/233 (51%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV + LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMNLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  +IKK+F     KV  L RI +G F L   LA G+   +++K L+
Sbjct: 179 ITISEGKFHQIKKMFLSIGVKVTNLKRIQFGDFTLNPDLAEGNYHPLNQKELQ 231


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 111/227 (48%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A +   +R +  +++ Q  V +NG + +  +V V S D I  DG  L   E  +
Sbjct: 2   RLDKFLAESTGLTRSQANKVLKQSAVTMNGKVEKNGSVKVNSEDEICFDGELLTWIEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D D  +   F + P + +++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YIMLYKPQGYVCSHDDGDYPTIYQFFDYP-LSTKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     ++ +     + GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPIESNYQQACEAGILLRGEKELTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G  +L  TL  G  R +S++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIGCIELDETLEEGGYRSLSEQ 225


>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 = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 117/227 (51%), Gaps = 7/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++ A I +R EV+++I + RV VN  ++     +V   D IE+DG  +   +   
Sbjct: 16  RLDKFLSNAHIGTRNEVKKIIKEGRVSVNFEIIRNPDFHVKLDDIIELDGNRIEPHKNVY 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + ++HKP G V+T SD +       + P +    I+ GRLD + EGLL+LTNDG     L
Sbjct: 76  I-IFHKPSGFVSTTSDREPSVLNLIDHPYLNELHIA-GRLDKDVEGLLILTNDGEFTHNL 133

Query: 135 ELPSTQWLRVYRV--RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
             P     + Y +  + + +V Q+ + ++ +GI ++    G   +    +K S   +++ 
Sbjct: 134 ISPKKHIEKEYWIYTKENVEVTQNMVKMVSEGIELEK---GTKTLPGKIRKVSEKIISLT 190

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EGK  ++KK+      +  +++R+  G   L  L  G  +E+SK+
Sbjct: 191 IVEGKYHQVKKMCISLGIEWEKIVRVRIGNLTLEGLEKGKWKELSKE 237


>gi|330952996|gb|EGH53256.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 210

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  RLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARRLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>gi|312172141|emb|CBX80398.1| ribosomal large subunit pseudouridine synthase [Erwinia amylovora
           ATCC BAA-2158]
          Length = 218

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 89/179 (49%), Gaps = 17/179 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   SD  GR T+ D +P     + + GRLD ++EGL++LTNDG L   L  
Sbjct: 42  LFNKPFDVLPQFSDEAGRRTLKDYIPH--PGIYAAGRLDRDSEGLMVLTNDGALQAQLTQ 99

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGIC----YGDMQVTLDTQ 182
           P  +  +VY V+  G   +  L  L+ G+          V++ +       D Q  +  +
Sbjct: 100 PGKRTGKVYFVQVEGCPQESDLQPLRDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIRER 159

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +I
Sbjct: 160 KAIPTCWLKITLYEGRNRQVRRMTAHIGYPTLRLIRFSMGNLGLRALAPGEWRDISHEI 218


>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 = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 112/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I++ G+ASRR  + +I   R+KVNG+      + +   D + +D   +   E  
Sbjct: 1   MRLNLYISKTGVASRRGADSLIEHGRIKVNGVT-AVLGMQITKNDVVTLDNNIIEPLEEK 59

Query: 74  RLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP+G+V TT++   G    F N      ++  VGRLD ++ GL+LLTNDG +  
Sbjct: 60  FYILLNKPVGIVSTTNTAISGNMITFMNFKE---KIFPVGRLDKDSHGLILLTNDGSIVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            +        + Y V  +   D   +  +  G+ I      + Q+T+ +  +       +
Sbjct: 117 KILRVENGHDKEYHVTLNKPYDDYFIETMTSGVEIYNPVAHEKQMTMPSILKPLDERTFS 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + +R+G NR+I+++ +   ++V  L R+      LG L  G  R ++   L+E
Sbjct: 177 LTIRQGLNRQIRRMADSLGYRVESLERVRIMHLTLGDLPVGYWRYLTSDELKE 229


>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 = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +F   R+SK +A+ G+ SRRE +  I Q  VKVNG         V+     E+D + L K
Sbjct: 5   DFETMRLSKRMAQLGLCSRREADSYIEQGWVKVNG------QTAVLGQKVTELDRIDLNK 58

Query: 70  ------AERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV---------- 108
                 A R  + L +KP+G V+  ++   +S     T  ++     SR+          
Sbjct: 59  QAHEKQAARVTIIL-NKPVGYVSAQAEKGYKSAAELITANNHWEDDDSRIPFSEKHKFGL 117

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + 
Sbjct: 118 APAGRLDIDSVGLLVLTQDGRIAKQLIGENSNSEKEYLVRVRGKLDDKGLALLNHGLSLD 177

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G      +V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L
Sbjct: 178 GEKLRPAKVEWQNEDQ----LRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRL 233

Query: 229 LAGSTR 234
             G  R
Sbjct: 234 PPGKWR 239


>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 = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 95/186 (51%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P   A+  ++ +++KP   ++  +D +GR T+ D +P     + + GRLD ++EGL++LT
Sbjct: 46  PRISAQDRKVVVFNKPFDTLSQFTDGEGRKTLADYIP--IKDIYAAGRLDRDSEGLMVLT 103

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  PS++  + Y V+  G  ++  L+ L+KG+ ++       +V +  +   
Sbjct: 104 NDGILQARLTQPSSKSPKTYWVQVDGAPNEADLDKLRKGVELKDGMTLPAKVEVMAEPSV 163

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RLIR S G   LG L  G
Sbjct: 164 WERNPPVRFRANIPTTWIAITIVEGRNRQVRRMTANIGFPTLRLIRYSMGDVTLGDLQPG 223

Query: 232 STREVS 237
             +E++
Sbjct: 224 EWKEIT 229


>gi|311693777|gb|ADP96650.1| pseudouridine synthase family 1 protein [marine bacterium HP15]
          Length = 312

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 115/231 (49%), Gaps = 13/231 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +G+ SRRE +R I Q  V +NG   +RA V   V+  D ++V+G  +  R  
Sbjct: 8   RLNKYISESGMCSRREADRYIEQGNVYING---KRATVGDQVLPGDTVKVNGQVIEPRAE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T    +  +           R+  +GRLD +++GL+ +T++G L
Sbjct: 65  EDLVFIALNKPVGIVSTTDSAEKHN--IQRFVGHSERIFPIGRLDKDSQGLIFMTSNGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V ++ +  +  G+ I G      +V+ +    S     
Sbjct: 123 VNKILRAGNNHEKEYLVTVDKPVTREFVEGMANGVPILGTMTKKCKVSRE----SRFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L +G NR+I+++ E+F ++V +L RI      L  L  G  R++S+K L
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVTKLERIRIMNVSLKGLAVGQWRDLSEKEL 229


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/256 (26%), Positives = 126/256 (49%), Gaps = 19/256 (7%)

Query: 5   NIVQENFT----PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD 58
           N ++E F     P R++K ++ AG+ SRRE +R+I   +V V+G   +RA +   +    
Sbjct: 3   NRIREEFIQKKEPVRLNKYLSEAGVCSRREADRLIETGKVSVDG---KRAGMGMKIYPGQ 59

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDIN 117
            ++V    + + +   +   +KP G+V T    +  S V F N P    RV  +GRLD +
Sbjct: 60  TVKVGNKTVSRQDEMIVLAVNKPKGIVCTEERRERDSIVRFLNYPV---RVTYIGRLDKD 116

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLLL+TN+G +   +   +    + Y+V    ++ +D L  + +G+ I        +V
Sbjct: 117 SRGLLLMTNNGDIINKIMRAANYHEKEYKVTVDHEITEDFLKKMSRGVAILDTVTRPCKV 176

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +K       + L +G NR+I+++ E   ++V  L+R+      L  L  G  R+++
Sbjct: 177 ----EKLGKYTFKIILTQGLNRQIRRMCEALGYEVKDLLRVRVMNITLDGLKEGKYRKLT 232

Query: 238 KKILREQLGPHLLEEA 253
            + L E     LLE++
Sbjct: 233 DRELNEL--DQLLEQS 246


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 73/235 (31%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A  GI +R+EV+R I Q RV ++GI  +     +      I  DG  +  A+  
Sbjct: 8   RLDKYLADMGIGTRQEVKRYIRQGRVSIDGIPAKSPETKIEEKARKITFDGREVDYAD-Y 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+  +  D R T   +L     R  +  VGRLD +TEGLLL+TNDG L+
Sbjct: 67  EYYMLNKPSGVVS--ATEDARCTTVVDLIRDKKRKDLFPVGRLDKDTEGLLLITNDGQLS 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---TLDTQKGSN-A 187
             L  P     + Y  +  G+V ++     ++G+ I G    +       LD  K    +
Sbjct: 125 HRLLSPKKHVDKTYYAKVAGKVTKEDAKAFREGVNI-GTEEKEEWTRPGVLDILKSEEVS 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + ++EGK  ++K++F+    +V  L R S G  +L  TL  G  R ++KK L
Sbjct: 184 EIRLTIQEGKYHQVKRMFQAVGKEVLYLKRESMGCLKLDETLKPGEYRPLTKKEL 238


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 106/233 (45%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG   E     V   D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRREADRLIEQGRVTINGQQPE-MGTKVQPGDDVCVDGNPVAAKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  IYIALNKPTGITCTTERDIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I        +V  +T+      +T G
Sbjct: 123 KILRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVEKETKFSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDNEVSEIL 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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/222 (30%), Positives = 113/222 (50%), Gaps = 7/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V+ +  +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVQVNELLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           + + EGK  +IKK+F     KV  L RI +G F L   LA S
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAES 220


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 117/236 (49%), Gaps = 9/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K ++  G  SR +V+++I +  VKVN  +++  + ++    D +E++   +   E  
Sbjct: 2   RLDKFLSNQGFGSRSQVQKLIKKGFVKVNDEIVKDPSYHIDPMKDKVELEDEEILYKE-N 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G +T   D +  + +  F +LP I S++  VGRLDI+TEGLL+LT DG   
Sbjct: 61  HYFMLNKPAGYITATEDEEYPTVLDLFSDLP-IASKLFPVGRLDIDTEGLLILTTDGQFG 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICYGD--MQVTLDTQKGSNAW 188
             L  P     + Y     G +   D      KGI ++   Y     +V +       + 
Sbjct: 120 HRLSHPKWNIEKEYYAIVEGDISNIDFSESENKGIYLKKEKYQTKPFKVKVLNTSKDKSE 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + + L EGK   +K++ +   + V  L RI  G  +L   LL G  RE+++K +++
Sbjct: 180 ILITLTEGKYHIVKRIMQELGYPVLYLKRIRIGNLKLDEDLLPGEFRELTEKEIKD 235


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 117/231 (50%), Gaps = 23/231 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R+I   +V V+G+  +   + V +   ++V    + K +   
Sbjct: 22  RLNKYLSEAGVCSRREADRLIESGKVTVDGVTAQ-MGMRVTAGQIVKVGKKTVSKQDEMI 80

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +   +KP G+V T    +  S V F N P    RV   GRLD ++ GLLL+TN+G +   
Sbjct: 81  VLAVNKPKGIVCTEDQRERDSIVRFLNYPV---RVTYAGRLDKDSRGLLLMTNNGDIINQ 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------QKGSN 186
           +   + +  + Y+V    ++ +  +  + +G+ I           LDT       +K   
Sbjct: 138 MMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPI-----------LDTVTRPCTVKKIGK 186

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              ++ L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++
Sbjct: 187 YTFSIILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLT 237


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 111/232 (47%), Gaps = 16/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--------ILLERAAVNVMSTDHIEVDGVP 66
           R++K +A  G+ SRR   R I   ++ ++G        I L  +    +S + ++ DGV 
Sbjct: 9   RLAKYLAMTGLCSRRAATRYIRDGQITLDGRLANHIDTISLTDSDSGFISQEILKFDGVL 68

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++  E  + W+ +K +G       P   S++   LP+   R+  VGRLD ++ G LLLTN
Sbjct: 69  IQGIESKQYWMLNKSVG-TDCRLLPHDPSSLLHLLPA-SPRLYPVGRLDKDSRGQLLLTN 126

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGS 185
           DG L + L  P     + Y V      D   L  + +G+  + +     Q+T LD  K  
Sbjct: 127 DGELTQKLMHPDFGHSKTYHVLVDRNFDDSFLISMAQGVSYRDVTTLPCQMTRLDDDK-- 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                + L +G NR+I+++ +   +KV  L R+     +LG L  G  RE++
Sbjct: 185 ---FEIILTQGLNRQIRRMSQALGYKVIDLKRVQIQTLKLGELEEGEMRELT 233


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 116/231 (50%), Gaps = 11/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLR--KA 70
           R+ K +    + SR EV++ I Q R+ V+G    + AV       +H +   V  R    
Sbjct: 3   RLDKYLCEMNVGSRSEVKKYIRQGRITVDG----KTAVKPEEKIDEHSQKVCVDSRVIGY 58

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
           E    ++ +KP G+V+  +D   + TV D +     + +  VGRLD +TEGLLL+TNDG 
Sbjct: 59  EAFEYYMLYKPSGVVSATTDRKEK-TVLDLIEEKKRKDLFPVGRLDKDTEGLLLITNDGE 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +A  L  P     +VY  +  G+V + ++ +  +G+ I    Y         ++G+ + +
Sbjct: 118 MAHRLLSPKKHVDKVYYAKIDGKVTEREVQIFSEGLSIGNDEYAKPSALKILKEGNISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + ++EGK  ++K++F     +V  L RIS G   L  +L  G  R +++K
Sbjct: 178 ELTIQEGKFHQVKRMFHAVGMEVIYLKRISMGNLVLDESLKKGEYRRLTEK 228


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 114/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q RV VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGRVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +AR L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIARQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVIGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|291561019|emb|CBL39819.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SSC/2]
          Length = 242

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   L + E+ 
Sbjct: 6   RLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDH-KLIQFEQF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+V+   D   + TV D +   +  R+  VGRLD +TEGLLLLT+DG LA 
Sbjct: 65  HYLMLHKPQGVVSATKDHHDQ-TVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGMLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  P     +VY  +  GQ  ++++   K+G+ I G      Q  L   K     + V 
Sbjct: 124 ELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDI-GNGERSKQARLQILKADVQESEVL 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           + + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E
Sbjct: 183 ITIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQE 236


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 92/178 (51%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ D +P     + + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVVLFNKPYDVLPQFTDEAGRSTLKDFIP--VPGIYAAGRLDRDSEGLLVLTNDGALQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------- 179
           L  P  +  ++Y V+  G+   + L+ L+ G+ +        GI   +  V L       
Sbjct: 88  LTQPGKRTGKIYYVQVEGEPTAEALDALRNGVTLNDGPTLPAGIEVVEEPVWLWPRNPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE+
Sbjct: 148 RERKNIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLENLANGEWREL 205


>gi|170693595|ref|ZP_02884753.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170141377|gb|EDT09547.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 239

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 97/220 (44%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + GI+      +  + D      VDGVP    E 
Sbjct: 3   LESILFSQGFGSRRQCRALIADARVAIGGIVCTDPDADFATDDASFSFSVDGVPWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L+ G+++ G         +D        + 
Sbjct: 121 VHMFTSPKRKVPKVYVATTRHPIDDRQLSALRDGVMLHG--ESKAVAAIDAHARGEHSLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++      +   L R   G   L   LA
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERVGGLALPATLA 218


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   L + E+ 
Sbjct: 9   RLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDH-KLIQFEQF 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+V+   D   + TV D +   +  R+  VGRLD +TEGLLLLT+DG LA 
Sbjct: 68  HYLMLHKPQGVVSATKDHHDQ-TVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGMLAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  P     +VY  +  GQ  ++++   K+G+ I G      Q  L   K     + V 
Sbjct: 127 ELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDI-GNGERSKQARLQILKADVQESEVL 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILRE 243
           + + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E
Sbjct: 186 ITIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQE 239


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 106/214 (49%), Gaps = 12/214 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-V 65
           ++EN   +R++K I   G  SRRE +++I + RV +NG   E     V S D I +DG +
Sbjct: 1   MEENL--KRLNKFIGETGYCSRREADKLIEEGRVTINGAAAE-MGTKVSSDDEIRIDGKL 57

Query: 66  PLRKAERTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            + K E+     ++KP+G+  TT+ +       + N P    R+  +GRLD  +EGL+ +
Sbjct: 58  IVEKHEKLVYLAFNKPVGIECTTNLEVKNNIVDYINYP---KRIFPIGRLDKASEGLIFM 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y V  +  + +  +  +  G+ I        +V    ++ 
Sbjct: 115 TNDGDIVNKILRARNNHEKEYTVTVNKPITERFIQRMGNGVPILDTVTKKCKV----EQI 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           S     + L +G NR+I+++ E+  ++V  L RI
Sbjct: 171 SKYTFKIILTQGLNRQIRRMSEYLGYEVTALKRI 204


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 118/239 (49%), Gaps = 28/239 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVD-GVPLRKA 70
           R+SK +A+ G+ SRRE +  I Q  VKVNG    + AV    V   D I+++     R+A
Sbjct: 10  RLSKRMAQLGLCSRREADSYIEQGWVKVNG----QTAVLGQKVTERDRIDLNRQAHERQA 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSR-----VISVGRLD 115
           ER  + L +KP+G V+  ++   +S             D+    FS      +   GRLD
Sbjct: 66  ERVTI-LLNKPVGYVSAQAEKGYKSAAELITADNRWESDDSHIPFSEKHKFGLAPAGRLD 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G      
Sbjct: 125 IDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPA 184

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 185 KVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGKLPPGKWR 239


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/229 (30%), Positives = 112/229 (48%), Gaps = 9/229 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           TP R+   +A  G+ SRR  E +I ++ V+VNG + +      +    I    + + K  
Sbjct: 6   TP-RIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAKLGDKVALGDRIIYKKQIYVFKDL 64

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             ++R++L  +KP   + ++ D +GR      +  +F  RV S+GRLD  + GLLL TND
Sbjct: 65  QSKSRVYLALNKPRNYLCSNFDANGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  +  P  +  R Y +     +D++ L   K GI I+   +  ++      K S  
Sbjct: 125 GKFANDIIHPRQKVEREYIIESKKDIDENLLISFKLGIKIKKEFF-KLKSYEILNKNSAR 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +   L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 184 LI---LDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 117/238 (49%), Gaps = 26/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  VKVNG   + AA+    T+   +D       ++AE
Sbjct: 10  RLSKRMAQLGLCSRREADSYIEQGWVKVNG---QTAALGQKVTERDRIDLNRQAHEKQAE 66

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFSR-----VISVGRLDI 116
           R  + L +KP+G V+  ++   +S             D+    FS      +   GRLDI
Sbjct: 67  RVTI-LLNKPVGYVSAQAEKGYKSAAELITADNRWEGDDSRIPFSEKHKFGLAPAGRLDI 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G      +
Sbjct: 126 DSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAK 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 186 VKWQNED----QLRFVLKQGKKRQIRRMCELVGLRVIGLKRIRMGKVKLGKLPPGKWR 239


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLDTQKGS 185
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L  +  S
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPS 156

Query: 186 --------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>gi|302185134|ref|ZP_07261807.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 210

 Score = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 112/220 (50%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  + SR+ +++ + ++ + V+       A NV      +   G  ++  E T
Sbjct: 2   RLDRLLAQE-MVSRKAMKQALLKKEILVDDCPARSLAQNVDTGLQKLVFQGRQIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G VT   D  G  TV D LP      ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGSVTASKD-KGLPTVMDLLPPDIQSDQLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K+GIV + G      ++ + +   + +  +
Sbjct: 119 FQLLHPQYHVDKSYQVVVNGLLTPDHIQYFKEGIVFLDGTTCKPAKLDILSASPTESRAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++KK+F     KV  L R+ +G F L + LA
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTTLKRVQFGDFTLDSELA 218


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/202 (31%), Positives = 99/202 (49%), Gaps = 7/202 (3%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V VNG ++      +  +D ++    P+   ER    L +KP   VTT  DP  R TV D
Sbjct: 2   VSVNGEVVTELGTKIKRSDVVKFHDEPV-SIERKVYVLLNKPKDTVTTSDDPQERRTVMD 60

Query: 100 NLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +    + R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     + +  +
Sbjct: 61  LVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADM 120

Query: 159 NLLKKGIVIQ-GICYGD-MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             +  GI ++ G  + D +  T D +K     V + +  GKNR ++++FE   +KV +L 
Sbjct: 121 EQIAAGIQLEDGEIHADAISYTDDFKKDQ---VGIEIHSGKNRIVRRIFESLGYKVVKLD 177

Query: 217 RISYGPFQLGTLLAGSTREVSK 238
           R+ +       L  G  R +S+
Sbjct: 178 RVFFAGLTKKGLRRGDWRYLSE 199


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 117/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   VM  D ++V+G  +  R A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVMPGDVVKVNGQLIEPRDA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D   +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDGE-RDNIVD-FVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIE 231


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.6 bits (200), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLDTQKG- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L  +   
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLSPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREVT 216


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 56/189 (29%), Positives = 93/189 (49%), Gaps = 17/189 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 56  PRKENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLT 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI-------- 170
           NDG L   L  P  +  ++Y V+  G  D + L  L+ G+ +        GI        
Sbjct: 114 NDGALQARLTQPDKRTGKIYYVQVEGIPDHEALQALRAGVTLNDGPTLPAGIEIVAEPDW 173

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            +       + +     W+ V L EG+NR+I+++         RLIR S G + L  L  
Sbjct: 174 LWPRTPPIRERKNIPTTWLKVTLYEGRNRQIRRMTAHVGHPTLRLIRYSMGDYMLNGLNN 233

Query: 231 GSTREVSKK 239
           G  RE++++
Sbjct: 234 GQWREIAQE 242


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 112/233 (48%), Gaps = 11/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R++K I+ +G  SRRE +++I   RV +NG++ E     V+  D + VDG  ++ +    
Sbjct: 12  RLNKFISDSGFCSRREADKLIDSNRVTINGVIPE-LGTKVLPGDEVRVDGNLVKASAENK 70

Query: 74  --RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R++L YHKP+G+  T ++   +  + D +     R+  +GRLD  +EGL+ LT+DG +
Sbjct: 71  SDRVYLAYHKPVGITCT-TERHVKGNIIDAIGH-RERIFPIGRLDKPSEGLIFLTSDGDI 128

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + +  +  +  G+ I         VT+     S     
Sbjct: 129 VNKILRAENAHDKEYIVTVDRPLTERFIQAMAAGVPILDTVTKPCTVTMQ----SKFVFR 184

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E+  + V +L R      +L  L  G  R ++   + E
Sbjct: 185 IILTQGLNRQIRRMCEYLGYGVTKLKRSRIMSIRLAGLKVGQWRNLTPDEMHE 237


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 89/180 (49%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  ++  ++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LTNDG L
Sbjct: 51  EARKVIAFNKPFDTLSQFTDGDGRKTLADFIP--VKDVYAAGRLDRDSEGLLILTNDGVL 108

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P ++  + Y V+  G   +  L+ L+KG+ ++       QV +           
Sbjct: 109 QAKLTQPKSKSPKTYWVQVDGAPSEADLDKLRKGVELKDGMTLPAQVEVMEAPEIWERNP 168

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+ + + EG+NR+++++     +   RLIR S G  +LG L  G  +EV
Sbjct: 169 PVRFRANIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIKLGDLQPGEWKEV 228


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 121/229 (52%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGI SRR+ +  I    V VNG  +      V  +D ++ DG  +   ++  
Sbjct: 28  RLNKYIANAGICSRRDADIYITAGNVTVNGKTITEMGYKVKLSDEVKFDGRSI-TPDKKE 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +L +KP  +  + S  +   TV D +  +  +R+  +G+L+ +  GL++LTNDG L++ 
Sbjct: 87  YYLLNKPKDVFVSGSLNESGMTVLDIVGRATKARLSPIGKLERSAMGLVVLTNDGTLSKS 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---TQKGSNAWVT 190
           L  P     ++Y V+ + ++ Q  L  +++GI ++    G+++V +D    +  S   V 
Sbjct: 147 LANPRHGIRQIYHVQLNKELSQVDLEKIRQGITLED---GEIKV-VDISYVENKSKREVG 202

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + ++  K+  ++++F+  N+++  L R+ +G      L  G  R ++K+
Sbjct: 203 IEIKSTKSHIVQRLFKSLNYEIKYLDRVVFGTLTKKDLPRGMFRHLTKQ 251


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/226 (30%), Positives = 113/226 (50%), Gaps = 6/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +++ V  ++A+ +V V+G +     + +    H+ +DG  L+    + 
Sbjct: 7   RLDRFISVKTGINKKYVRLLLAKGQVLVDGEIARDIDLIIDQFSHVSLDGQVLQANAPSY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + LY KP+G+V+   D D   TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  VMLY-KPVGVVSATID-DKHKTVIDLLDREDKHSLHIVGRLDLNTSGLLLLTNDGRWSKK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VYRV     +D+  +     G+             L+      A VT  L
Sbjct: 125 LMSPQHKVDKVYRVTLKNPIDESYIVAFAAGMYFAFEDITTQPAKLEIVDDHTALVT--L 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
            EG+  +IK++F  F   V  L R+S G  +LG  LA G +R++S+
Sbjct: 183 VEGRYHQIKRMFGRFRNPVIGLHRLSVGTIELGLQLAVGESRDLSE 228


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 112/229 (48%), Gaps = 9/229 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           TP R+   +A  G+ SRR  E +I ++ V+VNG + +      +    I    + + K  
Sbjct: 6   TP-RIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAKLGDKVALGDRIIYKKQIYVFKDL 64

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             ++R++L  +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TND
Sbjct: 65  QSKSRVYLALNKPRNYLCSNFDANGRKLAISLVQPLFKERLFSIGRLDFKSSGLLLFTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  +  P  +  R Y +     +D++ L   K GI I+   +  ++      K S  
Sbjct: 125 GKFANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKIKKEFF-KLKSYEILNKNSAR 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +   L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 184 LI---LDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 123/232 (53%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--NVMSTDHIEVDG---VPLRK 69
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +  +V   D ++V+G    P  +
Sbjct: 7   RLNKYISESGICSRREADRYIEQGNVFING---KRAKIGDSVEFGDKVKVNGHDIAPRDE 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A+   + L +KP+G+V+T  + + R  + D   +   RV  +GRLD +++GL+ LT++G 
Sbjct: 64  ADLVFIAL-NKPVGIVSTTENTE-RDNIVD-FVNHSERVFPIGRLDKDSQGLIFLTSNGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  + +  L  ++ G+ + G+     +V    ++ S    
Sbjct: 121 LVNKILRAGNNHDKEYVVTVNKPITEAFLQGMRAGVPMLGVITKKCKV----EQVSTFVF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L +G NR+I+++ E FN++V +L R S     L  L  G  R++ ++ L
Sbjct: 177 KIILVQGLNRQIRRMCEHFNFEVTKLERQSIMNVSLKGLPVGEWRDLDEQEL 228


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 92/181 (50%), Gaps = 20/181 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T++++++KP  ++T  +D D R T+ D   +P I++     GRLD ++EGLLLLTN+G L
Sbjct: 58  TQVYVFNKPYMVLTQFTDADNRETLKDYIKVPDIYA----AGRLDRDSEGLLLLTNNGRL 113

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P  +  + Y V+  G+   +KL+ L+ GI+++       +V + T+        
Sbjct: 114 QAKLTQPGEKTEKTYWVQVEGEPSPEKLSDLRYGIILKDGPTLPAKVEIMTEPSVWPRVP 173

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+ + + EG+NR+I+++         RLIR   GP+ L  +  G   E 
Sbjct: 174 PIRERQNIPTTWLAITIIEGRNRQIRRMTAHIGHPTLRLIRYRIGPWTLDNIQPGELVES 233

Query: 237 S 237
           S
Sbjct: 234 S 234


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 108/234 (46%), Gaps = 10/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG + E     V   D + VD  P+  A   
Sbjct: 7   KRLNKFISETGFCSRREADRLIEQGRVTINGQVPE-MGTKVQLGDDVRVDDKPIAAATDK 65

Query: 74  RLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +++  +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 66  PVYIALNKPTGITCTTERDIPGNIVDFVGHKK---RIFPIGRLDKPSDGLIFLTNDGDIV 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  D +  +  G+ I         VT +T+      +T 
Sbjct: 123 NKILRAGNSHEKEYVVRVDKPISDDFIKKMSSGVNILDTITLPCTVTKETKYSFRIVLTQ 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           GL    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L
Sbjct: 183 GL----NRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLSDSEVTEIL 232


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/225 (31%), Positives = 109/225 (48%), Gaps = 7/225 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG--VPLRKAERTR 74
           KV+  A + SRR++   I Q  V +NG   E  +  V    D +  +G  V L +  R  
Sbjct: 13  KVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQKDKVTFEGKLVVLSRVRRIY 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP  +V+T SD  GR TV D L   +  + +  VGRLD  T GL+LLTNDG +  
Sbjct: 73  LML-NKPPEIVSTTSDELGRKTVMDLLHRRYEGAGLFPVGRLDEATTGLILLTNDGEMTN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y +     + Q     L+KGI++        +++  T +    +  + 
Sbjct: 132 RLTHPSYEIEKEYLISIDAALTQADKESLEKGILLDDGLTSPARLSRVTDEPPYNYKLI- 190

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGK R ++++F      +  L R      +LG L  G TRE++
Sbjct: 191 IHEGKKRIVRRMFARLGHPIKALKRSRIATLRLGKLEEGKTRELT 235


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 55/202 (27%), Positives = 99/202 (49%), Gaps = 22/202 (10%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           ++KP  ++T  SD  GR T+ D +P   S V + GRLD ++EGLLLLT+DG L   +  P
Sbjct: 6   FNKPFEVLTQFSDGAGRQTLADFIP--VSGVYAAGRLDRDSEGLLLLTDDGPLQNRISHP 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------------ 185
             +  +VY V+  G +  + +  L+ G+ ++       +V++     +            
Sbjct: 64  LHKLKKVYWVQVDGAISDEAVERLRHGVELKDGMTSPARVSVMEAPATLWPRNPPIRTRA 123

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               +W+++ + EG+NR+++++     +   RLIR + GP  L  L  G+  EV  + L 
Sbjct: 124 QIPTSWISLEISEGRNRQVRRMTAAVGFPTLRLIRYAIGPITLDGLQPGTYDEVDAQQLW 183

Query: 243 EQLGPHLLEEAQVNLDAPIYSS 264
                +L       +D P+ S+
Sbjct: 184 -----NLFPTQGSGVDRPVVSA 200


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 116/229 (50%), Gaps = 10/229 (4%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT 86
           SR  +  ++A  RV+VNG +       +   D +  DG  L +A R R  + +KP G+V+
Sbjct: 26  SRSNLRLLLAAGRVRVNGQVERDRQRRIGLFDAVVCDGEIL-QANRPRYLMINKPAGVVS 84

Query: 87  THSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
              D +   TV + LP      + + GRLD N+ GL+LLTNDG  +R L LP T   + Y
Sbjct: 85  ATRD-EHHPTVLELLPRGQREGLHLAGRLDFNSTGLVLLTNDGAWSRRLSLPETGLWKHY 143

Query: 146 RVRFHGQV-DQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           RV     + D+D ++  ++     + I     ++T+ +   ++ W    L EGK  +IK+
Sbjct: 144 RVSVDKPLSDEDVVSFSQRMWFDFEQIYTQPARLTIRSSFEADVW----LHEGKYHQIKR 199

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHLLE 251
           +F     KV  L R++ G  QL   LA G +RE+++   +  L P  +E
Sbjct: 200 MFGRTGKKVTALHRLAVGRIQLDAYLAPGESRELTQAEQQTALDPEPVE 248


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMATGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVAVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDIVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDIVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|237747726|ref|ZP_04578206.1| pseudouridylate synthase [Oxalobacter formigenes OXCC13]
 gi|229379088|gb|EEO29179.1| pseudouridylate synthase [Oxalobacter formigenes OXCC13]
          Length = 248

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 117/243 (48%), Gaps = 27/243 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK ++  GI+SRRE +  I +  VKV+G ++ +    V+    I ++    ++  R
Sbjct: 4   PVRLSKRMSELGISSRREADEWIEKGWVKVDGKVVSQLGSKVLPHQKITIEKQASQEQSR 63

Query: 73  TRLWLYHKPIGLVT-----------------THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
               L +KP+G V+                 TH   D     F   PS    ++  GRLD
Sbjct: 64  RVTILINKPMGYVSGQAEDGYKPAVALISEDTHWKDDPSKEKFR--PSQLRSLVPAGRLD 121

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH--GQVDQDKLNLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L  E   T    + RV++   G++   +LN+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 LLPAKVEWQ----NDDQLRFVLREGKKRQIRRMCEAVGLRVIGLKRIRIGNVRLGDLPTG 237

Query: 232 STR 234
             R
Sbjct: 238 QWR 240


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/229 (28%), Positives = 117/229 (51%), Gaps = 17/229 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V + D ++V+G  +   + 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGLVLING---KRAGIGDRVTAGDEVKVNGRLIEAQDN 64

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L   +KP+G+V+T +D   +  + D +    +RV  +GRLD +++GL+ LTN G L
Sbjct: 65  SELVLIALNKPVGIVST-TDEGEKDNIVDYVNH-STRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G      Q T   +    A + 
Sbjct: 123 VNKILRAGNSHEKEYLVTVDKPITDEFIRGMGAGVPILG------QKTKKCKVKKEAAMV 176

Query: 191 --VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + L +G NR+I+++ E+F ++V +L RI      L  L  G  R+++
Sbjct: 177 FRITLVQGLNRQIRRMCEYFGYEVTKLERIRIMNVSLAGLPVGEWRDLT 225


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|330938238|gb|EGH41915.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 210

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 8/219 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  R
Sbjct: 2   RLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   D     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATVDTQ-HPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+        G+    + I     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSARLTIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EG+  ++K++F  FN KV RL R + G   L   LA
Sbjct: 180 ---EGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALA 215


>gi|330889469|gb|EGH22130.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 230

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 8/219 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  R
Sbjct: 2   RLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVRDFSRVALDGEILQAGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   D     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATVDTQ-HPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+        G+    + I     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLRPRSARLTIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EG+  ++K++F  FN KV RL R + G   L   LA
Sbjct: 180 ---EGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALA 215


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       QV L ++      
Sbjct: 92  ELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKQAQVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSIDGLANGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 101/219 (46%), Gaps = 8/219 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  R
Sbjct: 2   RLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   D     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATVDTQ-HPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+        G+    + I     Q+TL   + +   +  
Sbjct: 121 LTQPKTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSARLTIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EG+  ++K++F  FN KV RL R + G   L   LA
Sbjct: 180 ---EGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALA 215


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKSITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDILPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>gi|171911201|ref|ZP_02926671.1| ribosomal large subunit pseudouridine synthase B [Verrucomicrobium
           spinosum DSM 4136]
          Length = 345

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 53/169 (31%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + HKP GLV +  D   R T++  LP  F  +  VGRLD  +EGLLL+TN G +++ L  
Sbjct: 43  VLHKPRGLVCSRRDERDRDTIYSLLPEKFHTLHHVGRLDKESEGLLLMTNRGEVSQRLLH 102

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW------VT 190
           PS    + Y V    + D + L  L KG                  K   AW      + 
Sbjct: 103 PSQGVEKEYEVILETRFDPENLTRLTKGF----------HTEDGYAKAERAWMIGDYKIG 152

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + L++G  R+I+ +  F  ++V RL+R+  G   +  +L G+ +E+S K
Sbjct: 153 MVLKQGLKRQIRMMLYFLGYEVKRLVRVRIGNLAIKGILEGNWKELSDK 201


>gi|330976863|gb|EGH76892.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 210

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLEGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>gi|19879252|gb|AAK38326.1| hypothetical pseudouridine synthase [Flavobacterium johnsoniae
           UW101]
          Length = 304

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/214 (27%), Positives = 106/214 (49%), Gaps = 12/214 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-V 65
           ++EN   +R++K I   G  SRRE +++I + RV +NG   E     V S D I +DG +
Sbjct: 1   MEENL--KRLNKFIGETGYCSRREADKLIEEGRVTINGAAAE-MGTKVSSDDEIRIDGKL 57

Query: 66  PLRKAERTRLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            + K E+     ++KP+G+  TT+ +       + N P    R+  +GRLD  +EGL+ +
Sbjct: 58  IVEKHEKLVYLAFNKPVGIECTTNLEVKNNIVDYINYP---KRIFPIGRLDKASEGLIFM 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y V  +  + +  +  +  G+ I        +V    ++ 
Sbjct: 115 TNDGDIVNKILRARNNHEKEYTVTVNKPITERFIQRMGNGVPILDTVTKKCKV----EQI 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           S     + L +G NR+I+++ E+  ++V  L RI
Sbjct: 171 SKYTFKIILTQGLNRQIRRMSEYLGYEVTALKRI 204


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L+L++KP  ++T  SD  GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 99/201 (49%), Gaps = 25/201 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLL 123
           PL  AE T L L +KP  ++T  +D  GR T+  F  +P+I+     VGRLD ++EGLLL
Sbjct: 28  PLTFAETT-LVLLNKPYDVLTQFTDEQGRKTLKDFITMPNIYP----VGRLDRDSEGLLL 82

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYG 173
           LTN+G +   L  P     + Y V+  G    + L  L KG+           ++ I   
Sbjct: 83  LTNNGEIQHRLAHPKFDKQKTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATP 142

Query: 174 DMQVTLDTQ-----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           D    +  Q         +W+ + + EGKNR+++++     +   RLIR+  G F+LG L
Sbjct: 143 DFAWNIAPQIRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTLRLIRVGIGQFRLGNL 202

Query: 229 LAGSTREVS---KKILREQLG 246
             G  + +S   K+ L  QLG
Sbjct: 203 GCGEFQVLSENEKRKLFTQLG 223


>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 = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 110/226 (48%), Gaps = 11/226 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +   G+ SR+++++++ + RVK+NG++     + +    D I +D   L + +  
Sbjct: 2   RLEKYLVNCGVGSRKDIKKIVEEGRVKINGLVTLNFGLWIEEDRDDITLDNRHL-EFKTL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D D   T+ + LP       +  VGRLD +TEGLLL TNDG   
Sbjct: 61  RYYILYKTKGYITAVKD-DRHPTIMELLPGWLETKDLFPVGRLDKDTEGLLLFTNDGDTN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P  +  + Y V     + +  +  L+KG+ I   IC     +    Q      + 
Sbjct: 120 YKMTHPDKKISKKYYVELDKPISEGDIKDLEKGVDIGTHIC-----LPAKVQYIEQNKIF 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + ++EGK  ++KK+      KV+ L R+ +G   L  +  G  RE+
Sbjct: 175 LTIQEGKYHQVKKMVGSIKNKVSYLKRVKFGNLTLEDMKPGELREI 220


>gi|330963493|gb|EGH63753.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 210

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK------- 183
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD  +       
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTPEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>gi|309379383|emb|CBX21950.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 252

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 116/241 (48%), Gaps = 26/241 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q RV VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGRVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLDI 116
                L +KP+G V+  ++   +S     T  +   S  SR+             GRLDI
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWESDTSRIRFDPKHKIGLAPAGRLDI 130

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G      +
Sbjct: 131 DSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAK 190

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R +
Sbjct: 191 VEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYL 246

Query: 237 S 237
           +
Sbjct: 247 A 247


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 113/224 (50%), Gaps = 8/224 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+++  GI SR+E  R+I Q R+ VNG L       V  +D I +D   ++  ++  
Sbjct: 2   RINKLLSNYGICSRKEANRIIEQNRIIVNGKLCIPGQW-VEESDEILLDNKRIKPKKKVY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP+G+  T S  D ++ + D   +    +  VGRLD  +EGL++LTNDG L+  +
Sbjct: 61  ILL-NKPVGITCTSS-KDIKANIID-FVNYRDYIFPVGRLDKKSEGLIILTNDGELSNKI 117

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V+     D + +  + KG+ ++G+       T   ++       + L 
Sbjct: 118 LESENMHEKEYVVKVDKPFDDEFIENMSKGVQLKGV----KTRTCIVRRIDECTFKIILT 173

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +G NR+I+K+   F + V +L RI     ++  +  GS R  ++
Sbjct: 174 QGLNRQIRKMTRAFGYTVVKLKRIRIMNLKIDGIDIGSFRHFTE 217


>gi|322412114|gb|EFY03022.1| Putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 238

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 115/237 (48%), Gaps = 26/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K++      SRR+V+++I  Q V+++  +      NV         G+ L +  R R
Sbjct: 2   RLDKLLELVANGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDP-------GLQLIEVSRKR 54

Query: 75  L-------WLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGL 121
           +       ++ +KP G+V+  SD +   TV D L      P ++     VGRLD +TEGL
Sbjct: 55  ISHPKHSYFILNKPAGVVSARSDIN-HVTVLDQLAEKDRHPDLYP----VGRLDRDTEGL 109

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD 180
           +LLT++G L   +  PS    + Y V  +G +D+D  +    GI    G      Q+T+ 
Sbjct: 110 VLLTDNGPLGFRMLHPSHHVAKTYMVTVNGFLDEDAPDFFASGIKFPTGEQCRPAQLTIL 169

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                 +   + + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R ++
Sbjct: 170 QASQEKSQARLVISEGKFHQVKKMFLTYGLKVISLKRTSFAGLELGELASGAYRSLT 226


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 63/231 (27%), Positives = 115/231 (49%), Gaps = 9/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRRE +R+I + +V +NG  + +    V  +D +EV G  ++K   ++
Sbjct: 4   RINKYLSEVGYCSRREADRLIHEGKVTING-KIPKIGSKVEESDQVEVKGQRIKKITGQK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDRKVEPNNVIDFIKYP-KRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ + Q++ D +  +  G+ I      +  V    Q G   +  + 
Sbjct: 122 KILRARNNHEKEYIVKVNRQINSDFIQSMSSGVEILDTITKNCFV---KQLGPKKFKII- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K+ L E
Sbjct: 178 LTQGLNRQIRRMCESLGYRVRSLKRVRIMNIEL-DVSTGKYREFTKEELFE 227


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L+L++KP  ++T  SD  GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>gi|213163156|ref|ZP_03348866.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 289

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/210 (29%), Positives = 111/210 (52%), Gaps = 13/210 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
              + L +G NR+I+++ E+F ++V +L R
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLER 205


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/217 (28%), Positives = 111/217 (51%), Gaps = 7/217 (3%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLYHKPIGLV 85
           +R+++++++A++++ V+ +  ++ + N+      I++ G  + +  R   ++ HKPIG V
Sbjct: 23  TRKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI-GERIIQEPRHHYYMLHKPIGAV 81

Query: 86  TTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           T   D     TV D  +    +  +  +GRLD +T GLLLLT++G L   L  P     +
Sbjct: 82  TAKRDAH-HPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLLLTDNGPLGFQLLHPQYHVEK 140

Query: 144 VYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           VY V  +G +    +   + GI    G       +T+     S +   V + EGK  ++K
Sbjct: 141 VYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTPSYSKAQVRISEGKYHQVK 200

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           K+F     KV  L R+S+GPF L   LA G +R +++
Sbjct: 201 KMFLAIGVKVMTLKRLSFGPFTLDPQLAPGESRPLNE 237


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 117/233 (50%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K++A +GI SR+EV++++    V ++G   +    +V  ++H + V G P+   E  
Sbjct: 2   RLDKLLANSGIGSRKEVKKIVKAGAVSIDGKQAKDVKTHVDPSEHEVTVYGEPIEYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L     R      GRLD +T GLLLLTNDG LA
Sbjct: 62  YLMM-NKPQGVLSATED-SRQKTVIDLLAPDDMRFEPFPAGRLDKDTVGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + ++ +  L+ G+ I+G  Y      ++T   S     +
Sbjct: 120 HRLLSPKKHVPKTYEVHLRSGLSEEDIANLESGVFIEG-GYKTKPAKVETIANSEEHTEI 178

Query: 192 GL--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L   EGK  ++K++ +    +V  L R+S G   L  +L  G  RE++++ L
Sbjct: 179 RLTITEGKYHQVKQMAKAVENEVIFLKRLSMGSLLLDPSLEPGEYRELTEEEL 231


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 128/247 (51%), Gaps = 15/247 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRREADRYIEQGHVFING---KRAGIGDQVSAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T ++   +  + D + +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVST-TESGEKDNIVDYV-NHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I     G M      +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPI----LGTMTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E    +L+
Sbjct: 179 ITLVQGLNRQIRRMTEHFGYEVTKLERVRIMNVRLTGIPVGEWRDLTDDELIELF--NLI 236

Query: 251 EEAQVNL 257
           E+++ ++
Sbjct: 237 EKSESDV 243


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 118/227 (51%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAA+   V S D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRAAIGDQVFSGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T ++   R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVST-TESGERDNIVDYV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +     +  + Y V  +  +  D +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNEHEKEYLVTVNKPITDDFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E+F ++V +L R+      L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEYFGFEVTKLERVRIMNVNLSGIPLGEWRDLT 225


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 216


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTPEQLQQLRNGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 61/191 (31%), Positives = 95/191 (49%), Gaps = 7/191 (3%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLD 115
           D I V G  L   E    +L +KP G+++   D D   TV D L +   +  V  VGRLD
Sbjct: 37  DQIAVAGQVLSH-ETFVYYLLNKPKGVISATED-DHHRTVLDLLDNTARQKEVFPVGRLD 94

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+T GLLLLTN G LA  +  P     ++YR +  G + Q+ +     GI ++       
Sbjct: 95  IDTHGLLLLTNKGQLAHAMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPA 154

Query: 176 QVTL--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GS 232
           Q+T+    +    + V + +REGK  +IK++ +     V  L R++ GP +L   LA G 
Sbjct: 155 QLTILSTDEAKQTSLVDITIREGKFHQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGE 214

Query: 233 TREVSKKILRE 243
            R ++   L++
Sbjct: 215 YRRLTAAELKQ 225


>gi|324326400|gb|ADY21660.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 235

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 96/208 (46%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R +  +++ Q  V +NG + +  A  V   D I  DG  L   E  +
Sbjct: 2   RLDKFLAETTGLTRSQAAKVLRQSAVTINGKIEKSGAAKVSPDDEIYYDGERLTWVENGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G + +H D D   T++       S  + S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YIMLHKPQGYICSHEDGD-HPTIYQFFDYPLSTCLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P   + + Y V     V+ +      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHYPKTYLVTLADPVEANYAQACAEGILLRGEKEPTKPAELEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 122/236 (51%), Gaps = 13/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++V +     I +++G  +   + 
Sbjct: 2   ERLDKIISNLGYGSRKEAKVLARKGLIEVDGKIIKDSSVTIDPEKSIVKINGEEIFYRKY 61

Query: 73  TRLWLYHKPIGLVT-THSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
             L + +KP G+++ TH   D   TV D L     IF+    VGRLD +T GLLLLTNDG
Sbjct: 62  IYLMM-NKPTGVISATHDSKD--ETVIDLLELDHQIFNP-FPVGRLDKDTVGLLLLTNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--N 186
                +  P     +VY  +   +V++      KKG+V+    Y  ++  LD    S   
Sbjct: 118 EFNHRMISPKWHVDKVYYAKIDKEVNEKDQQAFKKGVVLDD-GYKCLEAKLDIISASPEG 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + ++EGK  ++K++FE  + KV  L R  +G   L   L  G  RE+S + L
Sbjct: 177 SEVRITIQEGKYHQVKRMFEACDKKVVYLKREEFGGLILDENLEEGEYRELSDEEL 232


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 92/181 (50%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RLILFNKPYDVLPQFTDEAGRQTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAK 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------- 179
           L  P  +  ++Y V+  G+  +  L  L+ G+ +        G+   +    L       
Sbjct: 98  LTQPGKRTGKIYFVQVEGEPTEAALAQLRSGVTLNDGPTLPAGVERVEEPAWLWPRNPPI 157

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L  G  R+V  
Sbjct: 158 RERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDSLACGQWRDVPL 217

Query: 239 K 239
           K
Sbjct: 218 K 218


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/227 (29%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   VM  D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFLNG---KRATIGDQVMPGDVVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDSE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  D +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDDFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++
Sbjct: 179 ITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVGLSGLPLGEWRDLT 225


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 106/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D +    KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTVAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 111/238 (46%), Gaps = 26/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A  G+ SRRE +  I++  V VNG+     AV    V   D IE++ V  R   
Sbjct: 2   RLSKRMAELGLCSRREADEYISRGLVSVNGV----PAVLGQKVTERDRIEMNRVAERDQS 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFS-----RVISVGRLDI 116
           R    L HKP+G V+  ++   R              D  P  F       ++  GRLD+
Sbjct: 58  RRVTILLHKPLGYVSGQAEDGYRPARVLIRPENCWSGDKSPLRFDLRQLQNLVPAGRLDV 117

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           N+ GLL+LT DG +AR L    +   + Y VR  G + +  L LL  G+ +     G+  
Sbjct: 118 NSTGLLVLTQDGRVARRLVGEDSAVEKEYLVRVAGSLSERGLALLNHGLSLD----GEEL 173

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +    +  ++  +   L++GK R+I+++      +V  L R+  G  +LG L  G  R
Sbjct: 174 LPARVRWQNDDQLRFVLQQGKKRQIRRMCALVGLEVLALKRVRVGSVRLGALPPGQWR 231


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 62/201 (30%), Positives = 98/201 (48%), Gaps = 7/201 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           VNG+++      +   D ++     +   ER    L +KP   VTT  DP  R TV D +
Sbjct: 1   VNGVVVTELGTKIKRADEVKFHD-QMVSIERKIYILLNKPKDTVTTSDDPQARRTVMDLV 59

Query: 102 P-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
             +   R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     V +  ++ 
Sbjct: 60  KGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHTDKNVTKADMDQ 119

Query: 161 LKKGIVI-QGICYGD-MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           +  GI +  G  + D +  T D ++     V + +  GKNR ++++FE   +KV +L R+
Sbjct: 120 IAAGIQLDDGEIHADAISYTDDVRRDE---VGIEIHSGKNRIVRRIFESLGYKVVKLDRV 176

Query: 219 SYGPFQLGTLLAGSTREVSKK 239
            +       L  G  R +S++
Sbjct: 177 FFAGLTKKGLRRGEWRYLSEQ 197


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK------- 183
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD  +       
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTPEQLQQLRNGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 80/267 (29%), Positives = 116/267 (43%), Gaps = 50/267 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ASRRE +  IA+  VKVNG++     + V+    IE+D     +  +  
Sbjct: 39  RLNKRMAELGLASRREADDWIAKGWVKVNGVV-ATMGMQVLPDVRIEIDKQAQGQQAKQV 97

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNL-----PSIFSRVISVGRLDINT 118
             L HKPIGLV+  ++ DG                DN      PS    ++  GRLDI++
Sbjct: 98  TVLVHKPIGLVSGQAE-DGHLPAITLVQPQNRWAQDNARFFFHPSQLKSLVPAGRLDIDS 156

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ----------------------- 155
            GLL+LT DG +AR L        + Y VR     DQ                       
Sbjct: 157 TGLLVLTQDGRVARQLIGEDAVMEKEYLVRVVYNADQGAATSTGQLSRIDDDDPVSTDVQ 216

Query: 156 -----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                +KL LL+ G+ + G      +V  D Q      +   L EGK R+I+++ E    
Sbjct: 217 SVFPREKLALLRHGLSLDGQALQPAKV--DWQNPEQ--LRFILTEGKKRQIRRMCELVGL 272

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVS 237
           KV  L R+  G   LG L  G  R ++
Sbjct: 273 KVVGLKRVRIGKVMLGNLPLGQWRYLA 299


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 206


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 99/206 (48%), Gaps = 9/206 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKYISETGFCSRREADKLIEQGRVTINGKQPE-MGTKVLPGDDVCVDGKPVAAKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  +  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  VYIALNKPTGITCTTERNIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + +  +  G+ I        +VT +T+      +T G
Sbjct: 123 KILRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVTQETKFSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L    NR+I+++ E   ++V +L R+
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRV 204


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 93/187 (49%), Gaps = 19/187 (10%)

Query: 68  RKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           RK E   TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LT
Sbjct: 27  RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLT 84

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVT 178
           N+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    
Sbjct: 85  NNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAW 144

Query: 179 L--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           L        + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  
Sbjct: 145 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLAN 204

Query: 231 GSTREVS 237
           G  RE +
Sbjct: 205 GEWREAT 211


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 216


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMATGVKILGTKTLPCEIT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 120/228 (52%), Gaps = 14/228 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+ +  GI SR+E  ++I + RV VNG   +E   V +  +D I +DG PL   E+ 
Sbjct: 2   RINKLFSNFGICSRKETNKIIREGRVIVNGKPCIEGQWVEL--SDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIAL-NKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V        D +  +++G+ I G      QVT     ++ +    ++
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILG------QVTKPCKLKRINENTYSI 170

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++ + F + V +L RI      +  +  G  R +++K
Sbjct: 171 ILTQGLNRQIRRMSKVFGFNVVKLERIRILNITIDNIEYGKWRYINRK 218


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 76/226 (33%), Positives = 111/226 (49%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++   G  SR+E+  ++   RV V+G  +      V   T  + VDG P+R  +R 
Sbjct: 2   RLDRLLGHMGFGSRKELRALLKAGRVTVDGRPVTDPGTLVDPGTSSVAVDGEPVR-FQRH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              L HKP G++T  +DP  R TV D LP    R  ++ VGRLD +TEGLLLLT DG LA
Sbjct: 61  FHVLLHKPAGVITATADPRQR-TVMDVLPEDLRRRDLVPVGRLDKDTEGLLLLTTDGTLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y  R    +D         G+ +    Y  +   L+        VTV
Sbjct: 120 HRLMAPRWHQPKRYLARVDRPLDPADQEAFAAGVPLAD-GYVTLPARLEILSPQEGIVTV 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             REGK  +++++F     +V  L R+S GP  LG L  G+ R ++
Sbjct: 179 --REGKYHQVRRMFAARGKRVVYLKRLSMGPLSLGDLPPGAARPLT 222


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 34  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 91

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G+   D    L      
Sbjct: 92  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGSTLPAGVELVDEPAWLWPRNPP 151

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 152 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 211


>gi|330873550|gb|EGH07699.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 210

 Score = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK------- 183
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD  +       
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTPEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 99/206 (48%), Gaps = 9/206 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +++I Q RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKYISETGFCSRREADKLIEQGRVTINGKQPE-MGTKVLPGDDVCVDGKPVAAKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  +  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  VYIALNKPTGITCTTERNIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + +  +  G+ I        +VT +T+      +T G
Sbjct: 123 KILRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVTQETKFSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L    NR+I+++ E   ++V +L R+
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRV 204


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 117/232 (50%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR++V++++  + V VNG L ++   +V  S D + V G  +   E  
Sbjct: 2   RLDKLLASSGFGSRKDVKKLVKARAVTVNGELAKQVKDHVDPSNDEVLVHGERVEYKEFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D     TV D L P   +R    VGRLD +T GLLLLTNDG LA
Sbjct: 62  YLMM-NKPDGVISATEDVRD-ETVVDLLEPEDIAREPFPVGRLDKDTVGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V     +    +N L++G++I         +V +D  +  +  + 
Sbjct: 120 HQLLSPKKHVPKTYEVHLKYPLGDQDINRLEEGVIILDDYRTKPAKVEVDANESEDTRIR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           + + EGK  ++K + +    +V  L R S G   L   LA G  RE++ + L
Sbjct: 180 LTITEGKYHQVKLMAQAVGNEVIFLKRRSMGSLSLDEDLAPGEYRELTDEEL 231


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 93/180 (51%), Gaps = 17/180 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVILFNKPYDVLPQFTDEAGRSTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAS 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT------------ 178
           L  P  +  ++Y V+  G+   + L  L+ G+ +     +  G  +V+            
Sbjct: 98  LTQPGKRTGKIYYVQVEGEPTDETLAALRHGVELNDGPTLPAGVERVSEPEWLWPRNPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    AW+ + L EG+NR+++++     +   RLIR + G + L +L  G  R+ ++
Sbjct: 158 RERKSIPTAWLKITLYEGRNRQVRRMTAHVGYPTLRLIRYAMGHYTLDSLANGEWRDATE 217


>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 = 80.9 bits (198), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/218 (30%), Positives = 108/218 (49%), Gaps = 16/218 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  + K  R 
Sbjct: 2   RLDKFLTHCGFGSRSQVKKLIREGIVTVNGKRIVEVDFKINPEEDVVEVDG-RVAKFSRQ 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              + +KP G V ++ DP    TVF    D+L   +  + +VGRLD + EGLL++T+DG 
Sbjct: 61  IYIMMNKPKGYVCSNDDP-ASLTVFSLISDDLK--YRDLHTVGRLDKDAEGLLIITDDGE 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
               +  P  +  + Y VR   +VD++KL   + GI++      D   TL  +     + 
Sbjct: 118 YTHRVISPKKRIEKEYLVRLEKEVDEEKLKEFENGIILD-----DGYKTLPAKYTIIDST 172

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + + EGK  ++K++FE    KV  L R+  G   L
Sbjct: 173 TVKLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNL 210


>gi|319426627|gb|ADV54701.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 270

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 50/169 (29%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 93  LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 150

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  GI        +D+             +
Sbjct: 151 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGITLPAKVKIMDSPDVWPRNPPVRERK 210

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L +G
Sbjct: 211 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSG 259


>gi|311279960|ref|YP_003942191.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749155|gb|ADO48907.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 215

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 52/178 (29%), Positives = 91/178 (51%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVILFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVLTNDGPLQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDT--------- 181
           L  P  +  ++Y V+  G+  ++ L  L+ G+ +     +  G  +V   T         
Sbjct: 98  LTQPGKRTGKIYFVQVEGEPGEEALAALRSGVTLNDGPTLPAGAERVAEPTWLWPRNPPI 157

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              +    +W+ + L EG+NR+++++     +   RLIR + G + L  L +G  R+ 
Sbjct: 158 RERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLASGEWRDA 215


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 124/248 (50%), Gaps = 17/248 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFING---KRAGIGDQVSAGDIVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L   +KP+G+V TT S   G    + N      R+  +GRLD +++GL+ LTN G 
Sbjct: 65  DDLVLIALNKPVGIVSTTESGEKGNIVDYVNHSK---RIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  +  G+ I     G M      +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFIQGMASGVPI----LGTMTKKCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E    +L
Sbjct: 178 RITLVQGLNRQIRRMTEHFGYEVTKLERVRIMNVKLTGIPVGEWRDLTDDELIELF--NL 235

Query: 250 LEEAQVNL 257
           +E+++ ++
Sbjct: 236 IEKSESDV 243


>gi|289810128|ref|ZP_06540757.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 256

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 115/241 (47%), Gaps = 24/241 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-LRK 69
             P R+SK +A  GI SRRE +  I Q  VKV+G  +      V+   HIE+D  P  +K
Sbjct: 1   MEPVRLSKRLAELGICSRREADSYIEQGWVKVDG-QVAVLGFKVLPHQHIELD--PRAKK 57

Query: 70  AERTRL-WLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGR 113
           A+  R+  L +KP+G V+  ++                +G  +     P+    +   GR
Sbjct: 58  AQLERVTILLNKPVGYVSGQAEKGYKPAAMLAVPANHWEGDKSGIRFSPNHLKGLAPAGR 117

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI++ GLL+LT DG +A+ L   ++   + Y VR  G++  + L LL  G+ + G    
Sbjct: 118 LDIDSVGLLVLTQDGVVAKRLIGENSTVEKEYLVRVTGELSPEGLKLLNHGLSLDGQPLR 177

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V+   +      +   LREGK R+I+++ E     V  L R+  G   LG L  G  
Sbjct: 178 PAKVSWQNED----QLRFILREGKKRQIRRMCEQVGLYVVGLKRVRIGNVMLGDLPTGQW 233

Query: 234 R 234
           R
Sbjct: 234 R 234


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSIRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVSI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 206


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 117/232 (50%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQEQIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D +   TV D LP      ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKE-LPTVMDLLPPDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + YRV  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYRVEVNGLLTLDHIQAFQKGIVFLDGTICKPARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDENLQAGDYRPLNSEEL 230


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD +TEGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDTEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 113/246 (45%), Gaps = 30/246 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           RVSK+I   G+ASRRE +  I    VKV+G   +L +RAA +      IE+D     +  
Sbjct: 13  RVSKLITERGLASRREADAWIEAGWVKVDGKMAVLGQRAAADC----RIEIDPRARNEQA 68

Query: 72  RTRLWLYHKPIGLVTTHSD-----------PDGR----STVFDNLPSIFSRVISVGRLDI 116
           R    L HKP+G V+  ++           P  R     T     P     +   GRLDI
Sbjct: 69  RRVTVLLHKPMGFVSGQAEDGYKPAATLVIPANRWKDDPTRLAFHPGQLRGLAPAGRLDI 128

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L    T+  + Y VR      G++    L  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 TREVSK 238
            R + +
Sbjct: 245 WRYLGE 250


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 113/229 (49%), Gaps = 11/229 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+I  +G+ +R+ +++   +  + VNG +++  A  V    D +   G  +   E 
Sbjct: 1   MRLDKMIGNSGLDTRKNIKKNAKKGAILVNGEVVKDTATQVDPEVDEVYYMGHFVDYFEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---GRLDINTEGLLLLTNDGG 129
             + + +KP G ++   D D   TV D L   F +VI +   GRLD +T GLLLL+ DG 
Sbjct: 61  IYVMM-NKPAGFLSATEDKD--PTVIDLLDD-FYKVIDLSIAGRLDKDTTGLLLLSTDGK 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P++   + Y V    ++D+  ++L K+G+ I+   Y      L+  +   A V
Sbjct: 117 FIHKVTSPNSNIEKTYLVECRDKIDESLIDLFKEGVYIKEDDYTARSAKLEILEEKKAIV 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            V   EGK   +K++F     KV +L RI+ G   L   LA G  RE+S
Sbjct: 177 KV--TEGKFHLVKRLFSNCCNKVEKLKRIAIGDLSLDEHLAEGEYRELS 223


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 70/227 (30%), Positives = 109/227 (48%), Gaps = 9/227 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           TP R+   +A  G+ SRR  E +I ++ V+VNG + +      +    I    V L K  
Sbjct: 6   TP-RIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAKLGDKVTLGDRIIYKKQVYLFKDF 64

Query: 70  AERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
             + R++L  +KP   + ++ D +GR      +  +F  RV S+GRLD  + GLLL TND
Sbjct: 65  QSKDRVYLALNKPKNYLCSNFDANGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A  +  P  +  R Y +     +D++ L   K GI I+   +      +   K S  
Sbjct: 125 GKFANDIIHPRLKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEI-LNKNSAR 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   L EGKNREI+KVF   +  + ++ RI  G   L +L  G  +
Sbjct: 184 LI---LDEGKNREIRKVFLSKSVFLKKIHRIRIGNINLDSLKEGQVK 227


>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 = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 50/169 (29%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 93  LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 150

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  GI        +D+             +
Sbjct: 151 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGITLPAKVKIMDSPDIWPRNPPVRERK 210

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L +G
Sbjct: 211 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSG 259


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/201 (32%), Positives = 99/201 (49%), Gaps = 25/201 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLL 123
           PL  AE T L L +KP  ++T  +D  GR T+  F  +P+I+     VGRLD ++EGLLL
Sbjct: 28  PLTFAETT-LVLLNKPYDVLTQFTDEQGRKTLKDFITMPNIYP----VGRLDRDSEGLLL 82

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYG 173
           LTN+G +   L  P     + Y V+  G    + L  L KG+           ++ I   
Sbjct: 83  LTNNGEIQHRLAHPKFDKQKTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATP 142

Query: 174 DMQVTLDTQ-----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           D    +  Q         +W+ + + EGKNR+++++     +   RLIR+  G F+LG L
Sbjct: 143 DFAWHIAPQIRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTLRLIRVGIGQFRLGNL 202

Query: 229 LAGSTREVS---KKILREQLG 246
             G  + +S   K+ L  QLG
Sbjct: 203 GCGEFQVLSENEKRKLFTQLG 223


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 100/219 (45%), Gaps = 8/219 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  R
Sbjct: 2   RLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   D     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATVDTQ-HPTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+        G+    + I     Q+TL     +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPHSARLTIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EG+  ++K++F  FN KV RL R + G   L   LA
Sbjct: 180 ---EGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALA 215


>gi|213424484|ref|ZP_03357281.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 267

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|302135159|ref|ZP_07261149.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato NCPPB 1108]
          Length = 222

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 44  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 99

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 100 ARIADPKHKLAKTYWVQVEGEPTPEQLQQLRNGVQLNDGPTLPAEARQLDEPQLWPRNPP 159

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 160 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 219

Query: 238 KKI 240
            K+
Sbjct: 220 AKL 222


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 60/214 (28%), Positives = 110/214 (51%), Gaps = 14/214 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN T  R++K ++  G  SRRE +R+I Q RV +NG + E     V  +D + V+G  
Sbjct: 1   MEENAT--RINKFLSETGFCSRREADRLIEQGRVTINGKVPE-MGTKVTPSDEVRVNGKL 57

Query: 67  LRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLL 123
           +++     ++L ++KP G+  T ++ D R  + D  N P    R+  +GRLD  +EGL+ 
Sbjct: 58  IQERTEKPIYLAFNKPAGIECT-TNLDVRDNIIDFINYP---ERIFPIGRLDKASEGLIF 113

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TNDG +   +        + Y V  +  +    ++ +  GI I        +V    ++
Sbjct: 114 MTNDGDIVNKILRARNNHEKEYIVTVNHPITDRFIDRMANGIPILETITKKCKV----EQ 169

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
            S     + L +G NR+I+++ E+ +++V  L R
Sbjct: 170 ISKFVFRIILTQGLNRQIRRMCEYLDYEVTALKR 203


>gi|311281430|ref|YP_003943661.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308750625|gb|ADO50377.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 292

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVAPGDVVKVNGQLIEPRDA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R+ + D   +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDGE-RNNIVD-FVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFIRAMGAGVPI----LGTVTKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L E
Sbjct: 179 ITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLAGIPPGEWRDLTDDELIE 231


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 113/227 (49%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 21  RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 79

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP+G+  T S+   +  + D  N P    R+  +GRLD +++GL+LLTNDG +  
Sbjct: 80  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL---RISHIGRLDKDSDGLILLTNDGDIVN 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + 
Sbjct: 136 EILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQII 191

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 192 LTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 238


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 119/245 (48%), Gaps = 28/245 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDG--VPLRKAE 71
           R+ K +      +R E  +MI Q RV     ++++    V    D I  DG  +  RK E
Sbjct: 5   RLDKFLCDVLGCTRSEARKMIRQGRVLAGDEIIKKPEYKVNPEEDEITADGQRLNFRKYE 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
                + +KP G+VT  +  DGR  TV D L     + +   GRLD +TEGLLL+TNDG 
Sbjct: 65  ---YLMMNKPKGVVT--ATKDGRDKTVMDLLTGRHRKGLFPAGRLDKDTEGLLLITNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQ 182
           LA  L  P     + Y V   G++ +++  + + G+ I     GD +       V L + 
Sbjct: 120 LAHRLLSPKHHVTKCYSVTVTGEIGREQQEIFESGMDI-----GDDKPLKPAKLVILTSG 174

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK--- 238
           + S A V +   EG+  +IK++FE    KV  L R+S G   L   LL G  RE+++   
Sbjct: 175 EVSQAEVFI--TEGRFHQIKRMFEAVGSKVLELKRLSMGSLVLDPELLPGQVRELTEEEI 232

Query: 239 KILRE 243
           K L+E
Sbjct: 233 KCLKE 237


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSIRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 67/221 (30%), Positives = 109/221 (49%), Gaps = 8/221 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K++A +G  SR+EV+ ++    V ++G   +  +A VN   T  + V G P+   E 
Sbjct: 2   RLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKAHVNP-DTQEVTVYGEPVDYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 61  IYLMM-NKPQGVLSATED-SRQQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V    Q+ ++ ++ L+ G+ I+ G      +  + T    N  +
Sbjct: 119 AHRLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPARAEIKTNDSGNTVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + + EGK  ++K++ +    +V  L R+S G   L   LA
Sbjct: 179 YLTITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALA 219


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 114/245 (46%), Gaps = 16/245 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++      S+ + + +  ++ V V+  ++   ++NV     I   G  L    +  
Sbjct: 2   RIDRLLQVNDFGSKSDRKHLFQRKIVTVDQRVITDGSINVDPGLQIIKVGNHLITGPQEY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDG 128
            W+ +KP G VT + D   +  VFD L      P ++S    +GRLD  TEGLL+LT +G
Sbjct: 62  YWMMNKPAGYVTANKDIT-KPVVFDLLQAQDRHPDLYS----LGRLDRFTEGLLILTTNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            L+R L  P     + Y V  +G +  D++    +GIVI Q       Q+ +     S +
Sbjct: 117 PLSRRLLQPHQHVAKTYAVEVNGFLGYDQVQAFAQGIVIDQSYQCQPAQLQIIQAGSSAS 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK----KILRE 243
              V L EGK  ++KK+F     KV +L R+S+    L   LA     V K     +++ 
Sbjct: 177 RAQVTLHEGKFHQVKKMFLSLGVKVTQLKRLSFAGIDLDPDLAPGQYRVLKADELALIKA 236

Query: 244 QLGPH 248
            LGP 
Sbjct: 237 FLGPQ 241


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSIRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRR+ +R IA+  V ++G+        V+    + V+G  +   +   
Sbjct: 27  RLNKYISDSGYCSRRQADRFIAEGVVAIDGVTAT-VGQQVLPGQRVTVEGNHVTIDDEKV 85

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP G+  TT    +G  + F N P +   +  +GRLD ++ GL+LLTNDG +   
Sbjct: 86  YIALNKPRGITCTTDGAIEGNISDFMNYPKM---IFPIGRLDKDSSGLILLTNDGDIVNK 142

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V  +  +D+D +  + KG+ I       MQVT   D ++ +     +
Sbjct: 143 ILREEYGHDKEYIVSVNKTIDEDFITKMSKGVEIYNQQTHRMQVTNPSDVEQVAPKTFRI 202

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ +   +KV  L R+      LG L  G  R +S   L E
Sbjct: 203 VLNQGLNRQIRRMTKALGFKVTTLNRVRIMNINLGDLKVGEWRYLSVHELEE 254


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSIRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIES 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSIRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I     G +      +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 110/237 (46%), Gaps = 14/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKV--------NGILLERAAVNVMSTDHIEVDGVP 66
           R+++ +A  G  SRR   R+I   RV +        + I L        ++  + VDG P
Sbjct: 2   RLAQYLALTGRCSRRAASRLIRNGRVSLGDRLAKHTDSIELIETPTGTQASLSVCVDGEP 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L        W+++K +G        D  S +  +L     R+  VGRLD ++ GLLLLTN
Sbjct: 62  LPPIADKAYWIFNKAVGTDCRLLAEDTTSLI--HLLPRQPRLYPVGRLDKDSRGLLLLTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L + L  PS    + Y VR     D D +  +  G+  + +     QV   T+ G +
Sbjct: 120 DGELTQRLMHPSFAHHKRYHVRLDRPFDDDFVVKMAAGVSYKDVTTQPCQV---TRLGQD 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           ++  V L +G NR+I+++ +    KV  L R++     LG L  G  R +++  L E
Sbjct: 177 SFEIV-LTQGLNRQIRRMSKTLGHKVIDLKRVAIESLTLGDLPEGEMRPLTQAELDE 232


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 112/236 (47%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV V+G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTVDGEVVKSGALKLTPEQEVTFDGNPLQRQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D      +G+ +      D+      ++  +  V + + 
Sbjct: 122 TSPKHHCEKTYLVTLEHPLAADTAQQFAEGVQLHN--EKDLTRPAQLEQIEDKLVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G   +   LA G  R ++++ +     PHL
Sbjct: 180 EGRYHQVKRMFAAVGNRVLELHRERIGAIVMDEDLAEGEYRPLTEEEIASVGAPHL 235


>gi|328473478|gb|EGF44326.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 371

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 98/206 (47%), Gaps = 9/206 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRR  +++I + RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRRAADKLIEEGRVTINGKQPE-MGTKVLPGDDVCVDGKPVASKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  IYIALNKPTGITCTTERDIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I        +VT +T+      +T G
Sbjct: 123 KILRAGNNHEKEYVVRVDKPITDEFLKQMSSGVRILDTVTLPCKVTKETKFSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L    NR+I+++ E   ++V +L R+
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRV 204


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 89/179 (49%), Gaps = 17/179 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   SD  GR T+ D +P     + + GRLD ++EGL++LTNDG L   L  
Sbjct: 32  LFNKPFDVLPQFSDEAGRRTLKDYIPH--PGIYAAGRLDRDSEGLMVLTNDGALQAQLTQ 89

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGIC----YGDMQVTLDTQ 182
           P  +  +VY V+  G   +  L  L+ G+          V++ +       D Q  +  +
Sbjct: 90  PGKRTGKVYFVQVEGCPQESDLLPLRDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIRER 149

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +I
Sbjct: 150 KAIPTCWLKITLYEGRNRQVRRMTAHIGYPTLRLIRFSMGNLGLRALAPGEWRDISHEI 208


>gi|327393520|dbj|BAK10942.1| ribosomal large subunit pseudouridine synthase E RluE [Pantoea
           ananatis AJ13355]
          Length = 219

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 90/179 (50%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +    S V + GRLD ++EGL++LTNDG L   
Sbjct: 40  RVLLFNKPFDVLPQFTDEAGRRTLKDFID--VSEVYAAGRLDRDSEGLMVLTNDGALQAA 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  ++  L  L+ G+ ++       GI         +      
Sbjct: 98  LTQPGKRTGKIYYVQVEGAPEERDLQPLRDGVNLKDGLTLPAGIEKVAEPEWLWARQPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +     W+ + L EG+NR+++++     +   RL+R + G F+L  L  G  R++S
Sbjct: 158 RERKAIPTQWLKITLYEGRNRQVRRMTAHIGFPTLRLVRYAMGDFELDNLAPGEWRDIS 216


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 89/179 (49%), Gaps = 17/179 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   SD  GR T+ D +P     + + GRLD ++EGL++LTNDG L   L  
Sbjct: 42  LFNKPFDVLPQFSDEAGRRTLKDYIPH--PGIYAAGRLDRDSEGLMVLTNDGALQAQLTQ 99

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGIC----YGDMQVTLDTQ 182
           P  +  +VY V+  G   +  L  L+ G+          V++ +       D Q  +  +
Sbjct: 100 PGKRTGKVYFVQVEGCPQESDLLPLRDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIRER 159

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +I
Sbjct: 160 KAIPTCWLKITLYEGRNRQVRRMTAHIGYPTLRLIRFSMGNLGLRALAPGEWRDISHEI 218


>gi|291485437|dbj|BAI86512.1| hypothetical protein BSNT_04375 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 239

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 107/220 (48%), Gaps = 6/220 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR+EV+ ++    V ++G   +    +V   T  + V G P+   E  
Sbjct: 2   RLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKAHVDPDTQEVTVYGEPVDYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG LA
Sbjct: 62  YLMM-NKPQGVLSATED-SRQQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    Q+ ++ ++ L+ G+ I+ G      +  + T    N  + 
Sbjct: 120 HRLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPARAEIKTNDSGNTVIY 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++ +    +V  L R+S G   L   LA
Sbjct: 180 LTITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALA 219


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 107/226 (47%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +GI SRR+ +  I    V VNG  +      V  TD ++ DG  ++  ++  
Sbjct: 95  RLNKYISNSGICSRRDADIYIKAGSVTVNGKPVSEMGYRVKLTDEVKFDGQNIQPYQKQY 154

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G +          TV D + S   + +  VGRL   + GL+L TND  +A  
Sbjct: 155 LLL-NKPKGFIAPRKGERASKTVLDLMQSAGVANLHYVGRLGRQSVGLMLFTNDLEMANK 213

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+ +  ++Y+V        + L  L+ GI I G    D++     + G N  + + +
Sbjct: 214 LNNPNLEMRKIYQVALDRSFKHEDLMQLRNGIAINGEVI-DVKEINYVEDGRNNEIGIEI 272

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             GK+  ++ +FE   +++  L R+  G      L  G  R ++++
Sbjct: 273 HSGKDNIVQALFEAVKYEIKVLDRVVLGGLTKKDLPRGHYRALTEQ 318


>gi|330960137|gb|EGH60397.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 210

 Score = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 93/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD  GR+T+  F ++P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEGGRATLKDFIDIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+  +++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPSEEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV 
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVV 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 110/237 (46%), Gaps = 14/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     SR +V  ++  +R++VNG      +  + S D + +D  PL+      
Sbjct: 2   RLDKFVADNTSYSRSQVRGLLKAKRIRVNGQTALAPSAALKSDDEVTLDDAPLQARSDVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--------FSRVISVGRLDINTEGLLLLTN 126
           L L HKP G V  ++D +   TVFD LP           +R+   GRLD++T GL+L+T+
Sbjct: 62  LML-HKPAGYVCANTDAE-HPTVFD-LPGFSARYSNADIARLQIAGRLDLDTTGLVLITS 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG     +  P  +  + Y V     +  +  +   +G+++ G     +   L+    + 
Sbjct: 119 DGQWNHRITSPRQKCRKAYYVECAAPIAAETKSAFAEGVLLHGEKRPTLPAELELLSANT 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           A + +   +G   ++K++F     KV RL R   G   L T LL G  R ++   +R
Sbjct: 179 ANLYI--EQGIYHQVKRMFASTGNKVLRLHRFQIGALALETDLLPGDMRALTSDEIR 233


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 219


>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 = 80.5 bits (197), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 80/245 (32%), Positives = 119/245 (48%), Gaps = 28/245 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDG--VPLRKAE 71
           R+ K +      +R E  +MI Q RV     ++++    V    D I  DG  +  RK E
Sbjct: 10  RLDKFLCDVLGCTRSEARKMIRQGRVLAGDEIIKKPEYKVNPEEDEITADGQRLNFRKYE 69

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
                + +KP G+VT  +  DGR  TV D L     + +   GRLD +TEGLLL+TNDG 
Sbjct: 70  ---YLMMNKPKGVVT--ATKDGRDKTVMDLLTGRHRKGLFPAGRLDKDTEGLLLITNDGE 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQ 182
           LA  L  P     + Y V   G++ +++  + + G+ I     GD +       V L + 
Sbjct: 125 LAHRLLSPKHHVTKCYSVTVTGEIGREQQEIFESGMDI-----GDDKPLKPAKLVILTSG 179

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK--- 238
           + S A V +   EG+  +IK++FE    KV  L R+S G   L   LL G  RE+++   
Sbjct: 180 EVSQAEVFI--TEGRFHQIKRMFEAVGSKVLELKRLSMGSLVLDPELLPGQVRELTEEEI 237

Query: 239 KILRE 243
           K L+E
Sbjct: 238 KCLKE 242


>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 = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 59/206 (28%), Positives = 98/206 (47%), Gaps = 9/206 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRR  +++I + RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRRAADKLIEEGRVTINGKQPE-MGTKVLPGDDVCVDGKPVASKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  IYIALNKPTGITCTTERDIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIVN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y VR    +  + L  +  G+ I        +VT +T+      +T G
Sbjct: 123 KILRAGNNHEKEYVVRVDKPITDEFLKQMSSGVRILDTVTLPCKVTKETKFSFRIVLTQG 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L    NR+I+++ E   ++V +L R+
Sbjct: 183 L----NRQIRRMCEALGYEVFKLRRV 204


>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 = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 53/183 (28%), Positives = 95/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F ++P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 33  KLILFNKPFDVLTQFSDGEGRATLKDFIDVPGIYP----AGRLDRDSEGLLLLTNDGQLQ 88

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G+       +LD          
Sbjct: 89  ARIADPKHKLAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARSLDEPQLWPRNPP 148

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +WV + +REG+NR+++++         RL+R+  G + +  L  G  +EV 
Sbjct: 149 VRFRKSVPTSWVELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWKEVP 208

Query: 238 KKI 240
            ++
Sbjct: 209 ARL 211


>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 = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 66/182 (36%), Positives = 94/182 (51%), Gaps = 7/182 (3%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDIN 117
           IEV G  L+  E   + + +KP G+++   D   R TV D LP    F  +  VGRLDI+
Sbjct: 10  IEVAGEILKYREYIYIMM-NKPQGVISATYDNRHR-TVIDILPDEYKFFNLFPVGRLDID 67

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLLLTNDG LA  L  P     + Y     G V    +++ ++G+V+    Y  +  
Sbjct: 68  TEGLLLLTNDGQLAHELLSPRKHVPKKYYALIDGIVTTKDVDVFREGVVLDD-GYKTLPS 126

Query: 178 TLDTQK-GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
            L   K G  + V + + EGK  ++K++FE    KV  L RI  G  +L  TL  G  RE
Sbjct: 127 ELFILKSGPYSEVEIVIYEGKFHQVKRMFEAVGKKVKYLRRIGMGKLKLDETLEPGDVRE 186

Query: 236 VS 237
           ++
Sbjct: 187 LT 188


>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 = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ +A  +     +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVKDSAFKLQPEHQVEYDGNTLTQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +           L+    +   +T+   
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEHFAKGVQLHNEKDLTRPAVLEVITPTEVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G  +L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVGLHRERIGAIELDPELAPGEYRPLTEE 225


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 55/188 (29%), Positives = 94/188 (50%), Gaps = 17/188 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D   R T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 37  EDTVVVLFNKPFDVLTQFTDEQRRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEI 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL---------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++ G+        +          
Sbjct: 95  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 155 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 214

Query: 236 VSKKILRE 243
           + +K  R+
Sbjct: 215 LDEKEKRQ 222


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 106/208 (50%), Gaps = 11/208 (5%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           M+AQ+R+ V+G +    +  +     +++DG   +      L L +KP G+V    DP  
Sbjct: 1   MLAQRRIMVDGKVASDMSQTIDKFSRVQLDGEWTQNHTAHYLML-NKPQGVVCATKDPLH 59

Query: 94  RSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           R T+ D   LP    ++  VGRLD N+ GL+LLTNDG  +R L  P ++ ++ YRV    
Sbjct: 60  R-TILDLLELPDK-EQLHIVGRLDYNSTGLVLLTNDGQWSRKLSHPDSKLIKRYRVTTEQ 117

Query: 152 QVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + ++ +   + G+    +GI      +T+   K +     V L EG+  +IK++F  F 
Sbjct: 118 TITEEYVQAFQSGMYFDFEGITTRPAPLTILDSKTAQ----VDLTEGRYHQIKRMFGRFQ 173

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVS 237
            KV  + R + G ++LG L  G  + ++
Sbjct: 174 NKVLSIHRFAVGSYELGELSPGEYKSIA 201


>gi|291617070|ref|YP_003519812.1| RluE [Pantoea ananatis LMG 20103]
 gi|291152100|gb|ADD76684.1| RluE [Pantoea ananatis LMG 20103]
          Length = 219

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 90/179 (50%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +    S V + GRLD ++EGL++LTNDG L   
Sbjct: 40  RVLLFNKPFDVLPQFTDEAGRRTLKDFID--VSEVYAAGRLDRDSEGLMVLTNDGALQAA 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  ++  L  L+ G+ ++       GI         +      
Sbjct: 98  LTQPGKRTGKIYYVQVEGAPEERDLQPLRDGVNLKDGLTLPAGIEKVAEPEWLWARQPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +     W+ + L EG+NR+++++     +   RL+R + G F+L  L  G  R++S
Sbjct: 158 RERKAIPTQWLKITLYEGRNRQVRRMTAHIGFPTLRLVRYAMGDFELDNLAPGEWRDIS 216


>gi|312127717|ref|YP_003992591.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777736|gb|ADQ07222.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 233

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/218 (30%), Positives = 109/218 (50%), Gaps = 16/218 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR +V+++I    V VNG  +      +    D +EVDG  ++ + R 
Sbjct: 2   RLDKFLTHCGFGSRSQVKKLIRGGIVTVNGKRIVEVDFKINPEEDVVEVDGRIVKFSRRI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + + +KP G V ++ DP    TVF    DNL   +  + +VGRLD + EGLL++T+DG 
Sbjct: 62  YIMM-NKPKGYVCSNDDP-ASLTVFSLISDNLK--YRDLHTVGRLDKDAEGLLIITDDGE 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
               +  P  +  + Y VR   +VD+++L   + GI++      D   TL  +     + 
Sbjct: 118 YTHRVISPRKRIEKEYLVRLEKEVDEERLKEFENGIILD-----DGYKTLPAKYTIIDST 172

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + + EGK  ++K++FE    KV  L R+  G   L
Sbjct: 173 TVKLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNL 210


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ VKVN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAKLGDKVALGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D DGR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 52/155 (33%), Positives = 85/155 (54%), Gaps = 3/155 (1%)

Query: 90  DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
           DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ +  P  +  + Y    
Sbjct: 3   DPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQHVMHPKYEVEKTYIATL 62

Query: 150 HGQVD-QDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            G++  Q    L+  G+ +  G    D    LD+ + S   V V L  GKNR ++++F  
Sbjct: 63  EGRISGQVCRRLVTTGVKLDDGWIKLDRCAILDSSREST-LVKVVLHSGKNRIVRRIFGS 121

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             + V RL+R   GP +LG L +G+ R +S+  +R
Sbjct: 122 IGFPVKRLVRTQIGPIKLGDLKSGTYRVLSQAEVR 156


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 105/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ VKVN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAKLGDKVALGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D DGR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRKKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 112/225 (49%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  ++ I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKXINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIID-LVNHPLRISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKK 222


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 53/185 (28%), Positives = 95/185 (51%), Gaps = 16/185 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 60  PKVAPEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLLVLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ- 182
           NDG     L  P+++  + Y V+  G   +  L+ L+KG+ ++ G+    +++V  + Q 
Sbjct: 118 NDGIFQAKLTQPNSKSTKTYWVQVEGAPSEKDLDKLRKGVELKDGMTLPAEVEVMQEPQV 177

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RLIR S G   +G L  G
Sbjct: 178 WERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMNVGQLQPG 237

Query: 232 STREV 236
             +EV
Sbjct: 238 EWKEV 242


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 120/238 (50%), Gaps = 31/238 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR+ +R+I + +V +NG + E  A  V   D +EV+G  ++K+ + +
Sbjct: 4   RINKYLSEVGYCSRRKADRLIEEGKVTINGKIPEIGA-KVEDGDQVEVEGQRIKKSTKQK 62

Query: 75  -LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
            ++L ++KPIG+V T      R    DN+        R+  +GRLD ++EGL+ LTNDG 
Sbjct: 63  NIYLAFNKPIGVVCTTD----RGVEPDNIIDFIKYPKRIFPIGRLDKSSEGLIFLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  ++++ +  +  G+ I           L+T K  N +V
Sbjct: 119 IVNKILRARNNHEKEYIVSVNRPINREFIQTMSNGVEI-----------LET-KTKNCFV 166

Query: 190 --------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    + L +G NR+I+++ E   ++V  L R+     +L  L  G  RE +K+
Sbjct: 167 KKLGPKKFKIILTQGLNRQIRRMCESLGYRVQSLKRVRIMNIKL-DLPIGKYREFTKE 223


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 113/229 (49%), Gaps = 28/229 (12%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPLRKAERTRL------W 76
           RRE +  ++  RV VNG L+ R +  V+  D + +DG      P  ++  + L      +
Sbjct: 106 RREADDAVSAGRVLVNGELV-RPSRRVVHGDVVTLDGKAMDWEPYAQSVESELGDARFVY 164

Query: 77  L-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
           L Y+KP G+V T SD + R+++F  L           R+  VGRLD ++ GL+LLTNDG 
Sbjct: 165 LKYNKPRGVVCTMSDTE-RTSMFHALHHERKALGKDVRLFPVGRLDKDSSGLVLLTNDGR 223

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------TQ 182
           ++  L  P  +  + Y V     V +     L +G+VI      D++ T+        T+
Sbjct: 224 VSDALLDPERKAEKTYDVDVDRIVSEADARTLARGVVISTTQQRDLKETVAATLPCEVTK 283

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            G  +   V L+EG+NR+I+K+ E  ++ V RL R       LG L  G
Sbjct: 284 TGEKSLRFV-LKEGRNRQIRKMCEVLSYDVERLHRTRIDDVALGDLEVG 331


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 108/230 (46%), Gaps = 23/230 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++++K +A  G  SR+E+E  I + RV   G             + +E DG PL      
Sbjct: 5   RKLAKYLASLGYGSRKEMEVAIRRGRVTGWG-------------EDVEFDGEPLDPGPGM 51

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
            + L HKP G   +H D  G+  V+D LP  F     ++ SVGRLD +T GLLL T+DG 
Sbjct: 52  VI-LMHKPAGYTCSHQD-QGK-LVYDLLPPRFLKRDPKISSVGRLDADTTGLLLFTDDGA 108

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   L  P +   + Y       ++  +      G ++++G     +   L+      A 
Sbjct: 109 LLHRLISPKSDIPKTYEATLARPLEGFEKEFFASGSLILRGEDKPCLPAELEVTGERTAR 168

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +T  L EG+  +++++F      V  L R  +GP +LG L  G+ R +++
Sbjct: 169 LT--LSEGRYHQVRRMFAAAGNHVEALHRSRFGPLELGDLSEGAWRLLTE 216


>gi|311695566|gb|ADP98439.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 232

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 105/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++S++++     SRR+   +IA  RV VN +    AA  V     + +DG  +++AE   
Sbjct: 2   KLSRILSNRNDISRRQANFLIASGRVAVNDVTCRDAAAEVDRFSCVRMDGDIIQEAEACH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP G ++   D   R+ +    P +   +   GRLD  + GLL+LTNDG  +R L
Sbjct: 62  HLMLHKPAGFLSATLDDTHRTVMELISPELREDLHIAGRLDRASTGLLILTNDGRWSRQL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  +VYRV     +  +  +   +GI  +          LD      A VT+   
Sbjct: 122 TEPRIKIPKVYRVSTAYPISPETPHRFAEGIWFEFEQLTTSPADLDLLSPCEARVTI--Y 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F     +V  L R   G  +L   L AG  R ++ +
Sbjct: 180 EGRYHQVKRMFHAVGNRVTALHREQMGNIRLDDDLAAGEYRSLTAE 225


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 121/228 (53%), Gaps = 14/228 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+ +  GI SR+E  ++I + RV VNG   +E   V +  +D I +DG PL   E+ 
Sbjct: 2   RINKLFSNFGICSRKETNKIIREGRVIVNGNPCIEGQWVEL--SDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP+G+V T ++ + ++ + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIAL-NKPVGVVCTAAE-EVKNNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V        D +  +++G+ I G      QVT     ++ +    ++
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMERGVEILG------QVTKPCKLKRINENTYSI 170

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++ + F + V +L RI      L  +  G  R ++++
Sbjct: 171 ILTQGLNRQIRRMSKVFGFNVIKLERIRILNITLEDIEYGKWRYINRE 218


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 105/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKIYLVTLESPVADDTAAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNCVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 113/248 (45%), Gaps = 28/248 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++++ G+ SRRE +  I +  V V+G  ++     V     I++D           
Sbjct: 78  RLSKLMSKLGLCSRREADEWIEKGWVMVDGERVDTLGTKVFPDQRIDIDPAAEAFQSSQV 137

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP---------------SIFSRVISVGRLDINTE 119
             + HKP+GLV+  ++   +  +    P               S   ++   GRLDI++ 
Sbjct: 138 TVIVHKPVGLVSGQAEDGYQPAITLVTPENRWEGDRSGVRFSVSHLRQLAPAGRLDIDST 197

Query: 120 GLLLLTNDGGLARVL-----ELPSTQWLRV----YRVRFHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L     ++     +RV    Y V        +KL LL+ G+ +  +
Sbjct: 198 GLLVLTQDGRIAKQLIGGHSDVDKEYLVRVAYGEYTVDVESHFPAEKLALLRHGLSLDDV 257

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 258 ALKPAQVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVVGLKRVRMGQVMLGALPP 313

Query: 231 GSTREVSK 238
           G  R +S+
Sbjct: 314 GQWRYLSE 321


>gi|295100310|emb|CBK97855.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii L2-6]
          Length = 234

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 107/227 (47%), Gaps = 8/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R E + ++A+ RV VNG +  +    +   D + VDG  L   +   
Sbjct: 2   RLDKYLAETAQCTRSEAKALLAKGRVTVNGAVCRKGDTQLKEADAVAVDGKALAYRQFVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DGG A 
Sbjct: 62  LML-NKPEGVVSASADKR-DTTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V     + ++       G+ +  G      +V+  T  G    V V
Sbjct: 120 DILAPKRHVSKTYTVVIDTPLTEEMKAGFAAGVTLADGTALSPAEVSALTPDGLT--VRV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
            LR+G   +IK++F  +   VN L R + G   L  +L AG  RE++
Sbjct: 178 LLRQGVYHQIKRMFGVYGAGVNALHRDAIGGLALDESLAAGQWRELT 224


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ VKVN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAKLGDKVALGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D DGR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  +A  +     +E DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVRDSAFKLQPDHQVEYDGNPLTQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPEGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTEVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G  +L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPDLAPGEYRPLTEE 225


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 109/236 (46%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRV 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D       G+ +           LD  +     +T+  R
Sbjct: 122 TSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLHNEKSLTKPAQLDVIEPQRVRLTI--R 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G   L   LA G  R ++ + +     PHL
Sbjct: 180 EGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 119/242 (49%), Gaps = 18/242 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLR-- 68
           +R++K +++ G+ SRRE +R+I   +V V+     R A     V     +  +G  +R  
Sbjct: 3   ERLNKWLSQMGVCSRREADRLIEAGKVLVDN----RPASMGQKVTPGQKVVCNGKMVRVD 58

Query: 69  KAERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +++R R  L   +KP G+V T +D D    + D L     R+  VGRLD ++EGLLL+TN
Sbjct: 59  RSQRPRPVLLAVNKPKGIVCTTTDKDRAENIVDFL-GYPERIYPVGRLDKDSEGLLLMTN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKG 184
            G L   +        + Y V     V +  L  +  GI +  +     QVT     +K 
Sbjct: 118 QGDLVNKIMRSGNAHEKEYIVTIDKPVTERFLEQMAGGIRLPEL----DQVTRPCKVKKV 173

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                ++ L +G NR+I+++ E    +V RL+R+     +LG L  G+ R+++K+   E 
Sbjct: 174 ERNTFSIILTQGLNRQIRRMCEACGCQVKRLVRVRIMNIRLGNLRTGAYRQITKEEYEEL 233

Query: 245 LG 246
            G
Sbjct: 234 TG 235


>gi|153000988|ref|YP_001366669.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151365606|gb|ABS08606.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 282

 Score = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 105 LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 162

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  G+        +D+             +
Sbjct: 163 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIWPRNPPVRERK 222

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L +G
Sbjct: 223 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSG 271


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 119/234 (50%), Gaps = 16/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV++ +      VNG +++     V   +D + V G  +   E  
Sbjct: 2   RIDKLLSNMGYGSRKEVKKHLKGGGTVVNGEVVKDPKFQVDPESDTVTVHGEEVVYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+++   D +G  TV D L     IF+    VGRLD +TEGLLL+TNDG L
Sbjct: 62  YLMM-NKPPGVLSATEDAEGE-TVIDLLEMEDQIFNP-FPVGRLDKDTEGLLLITNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY----GDMQVTLDTQKGSN 186
           +  L  P     + Y     G+V ++ ++   +G+ +    Y    G++++      G  
Sbjct: 119 SHQLLSPKKHVPKTYFAVIEGEVTEEDVSAFAEGVTLDD-GYETKPGELEI---ISSGIR 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + + + + EGK  ++K++FE    +V  L RI+ G   L  TL  G  RE++ +
Sbjct: 175 SEINLTITEGKFHQVKRMFESVGKRVIYLKRITMGLLPLDETLELGEYRELTDE 228


>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 = 80.1 bits (196), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 111/236 (47%), Gaps = 30/236 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
           +R+ KV++  G  SR+E++  + +  ++V+G +++   + V     I +V+G  +     
Sbjct: 2   ERLDKVLSNLGYGSRKEIKAFVKKGEIEVDGKVVKDNGIKVDPNKSIIKVNGEEIN---- 57

Query: 73  TRLWLY---HKPIGLVTTHSDP---------DGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            R ++Y   +KP G+V+   D          D   TVFD  P        VGRLD +TEG
Sbjct: 58  YRKYIYIMMNKPAGVVSATFDNYDETVIDLLDYEYTVFDPFP--------VGRLDKDTEG 109

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICY-GDMQV 177
           LLL+TNDG L   L  P     + Y       VD+  +   KKGI +     C    +++
Sbjct: 110 LLLITNDGELNHRLTSPKWHVDKTYYAEIDKMVDEKDVEKFKKGITLDDGYKCLPAKLEI 169

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
               + GS   +T+  +EGK  ++K++FE     V  L R++ G   L   L   T
Sbjct: 170 LSSDENGSEVNITI--QEGKFHQVKRMFEARGKNVVYLKRLTMGNISLDEELDEGT 223


>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 = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 71/256 (27%), Positives = 122/256 (47%), Gaps = 26/256 (10%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEV---DGV 65
           N +  R++KV+A  G+ASRR  E +I++ RV+VNG ++ E+      +TD +E+     V
Sbjct: 72  NESRPRLAKVLAACGVASRRACEELISEGRVRVNGRVVSEQGTTIDPTTDRVELLVKYSV 131

Query: 66  PLRKAERTRL--WLYHKP-IGLVTTHSDPDGRSTVFDNL---------------PSIFSR 107
            L +  R R    +Y +P  G + + SD  GR  +   L                 +  R
Sbjct: 132 NLHRGHRVRRHNLIYPEPDKGYICSSSDVSGRGKLAVQLLNPWLEQWRRNSKDTKRLPPR 191

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
             +VGRLD+ + GL+ +TNDG  A  +  PS+   + Y V       + +L  L  G  +
Sbjct: 192 FFTVGRLDVASSGLIFITNDGHWANRVIHPSSGLTKEYVVGLGRDASRPQLQALAAGTEV 251

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G     ++V +    G +  + + ++EGK  E++++ +    ++  L R+  G F+L  
Sbjct: 252 AGTFVSPVEVEV---LGDSRRLRIVVQEGKKHEVRELVKAAGLELTSLKRVRIGGFRLPR 308

Query: 228 LLA-GSTREVSKKILR 242
            L  G  RE+    LR
Sbjct: 309 DLGIGGFRELKPSDLR 324


>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 = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 105 LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 162

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  G+        +D+             +
Sbjct: 163 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIWPRNPPVRERK 222

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L +G
Sbjct: 223 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSG 271


>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 = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISESGKASRRGADKLINERRVIING-KVAKIGDQVQPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   RV  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRVNHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLKQMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      QL  L  G  R+++KK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIQLNNLPVGQWRDLTKK 222


>gi|213859463|ref|ZP_03385167.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 231

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +          TL+        +T+   
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNRKSLTKPATLEVITPVQVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 65/212 (30%), Positives = 106/212 (50%), Gaps = 7/212 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  G+ SR+EV+++I   +++VN + + +    V   DH +V  +      +  
Sbjct: 3   RLDKFLATLGLGSRKEVKKLITSGQIQVNDVTVTKVNHGV-DEDHDQVAYLGQELVYQAY 61

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP GLV+   D     TV D +   F  V    VGRLDI+T GLLLLTN+G LA
Sbjct: 62  YYVMLNKPDGLVSATEDK-MHETVIDWVALDFDHVDLFPVGRLDIDTTGLLLLTNNGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVT 190
             L  P     + Y+    GQV +  +     GI ++       ++  LD     +  +T
Sbjct: 121 HQLLSPKKHVAKTYQALVTGQVSEVDIAAFAAGIRLKDFTAQAAELEILDYDPDKDQSLT 180

Query: 191 -VGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            V + EGK  ++K++F   + +V  L R+S G
Sbjct: 181 KVTIHEGKFHQVKRMFLARDHEVLHLHRVSMG 212


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 96/183 (52%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T + L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETTVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       QV L ++      
Sbjct: 92  ELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKQAQVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 216

Query: 238 K 238
           +
Sbjct: 217 E 217


>gi|217973052|ref|YP_002357803.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217498187|gb|ACK46380.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 282

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 105 LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 162

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  G+        +D+             +
Sbjct: 163 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIGPRNPPVRERK 222

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L +G
Sbjct: 223 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSG 271


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/174 (30%), Positives = 88/174 (50%), Gaps = 17/174 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR+T+ + +P  F+ V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVILFNKPFDVLPQFTDEAGRATLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQAQ 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------- 179
           L  P  +  +VY V+  G    D +  L+ G+ ++       G+   D    L       
Sbjct: 88  LTQPGKRTGKVYYVQVEGAPQDDDVAPLRAGVTLKDGPTLPAGVELVDEPTWLWPRHPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            + +     W+ + L EG+NR+++++     +   RLIR S G   LG L  G 
Sbjct: 148 RERKAIPTRWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYSMGELALGELQPGE 201


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 69/221 (31%), Positives = 103/221 (46%), Gaps = 12/221 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K ++ +G  SR+EV  +  Q RV VNG I  + A +     D ++VD  P+   E  
Sbjct: 6   RLDKWLSHSGQGSRKEVRDLCRQGRVLVNGEICRDGAQLVETGVDRVQVDRQPVCYEEFY 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            + L HKP G+++  +D   R TV D LP       V  VGRLD +T GLLLLTNDG  A
Sbjct: 66  YIML-HKPRGVISATTDAACR-TVLDFLPPPCRTGGVFPVGRLDKDTTGLLLLTNDGVWA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV 189
             +  P     +VY     G + +D        IV+    +C     + +D Q      V
Sbjct: 124 HRILSPKKHCYKVYEATVSGSIPEDLTVRFASRIVLADGTVCLPARALRIDGQT-----V 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + + EG+  ++K++      +V  L R   G   L   L+
Sbjct: 179 EITVYEGRYHQVKRMCAAVGLQVLSLHRHKIGALGLDPALS 219


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +         V L T+          
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVTEPEWLWPRNPP 146

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYTLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +          TL+        +T+   
Sbjct: 122 TSPRHHCEKTYLVTLESPVTDDTAAQFAKGVQLHNEKELTKPATLEVVTPVQVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGAITLDEDLAPGEYRPLTEE 225


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 113/238 (47%), Gaps = 26/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  VKVNG    + AV    V   D I+++     K  
Sbjct: 10  RLSKRMAQLGLCSRREADSYIEQGWVKVNG----QTAVLGQKVTERDRIDLNKQAHEKQA 65

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLDI 116
                L +KP+G V+  ++   +S     T  ++     SR+             GRLDI
Sbjct: 66  ARVTILLNKPVGYVSAQAEKGYKSAAELITADNHWEGDDSRIPFSEKHKFGLAPAGRLDI 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G      +
Sbjct: 126 DSVGLLVLTQDGRIAKQLIGENSSSEKEYLVRVRGKLDNKGLALLNHGLSLDGEKLRPAK 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 186 VEWQNED----QLRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 239


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 90/175 (51%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 33  IFNKPFDVLPQFTDEAGRSTLKDFIP--LTDVYAAGRLDRDSEGLLVLTNDGKLQAQLTQ 90

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ------------ 182
           P  +  +VY V+  G  D   L   ++G+ ++ G+     +++  + +            
Sbjct: 91  PGQKTGKVYYVQVEGVPDDAALAQFRQGLELKDGMTLPAGIEIVAEPEWLWPRNPPIRER 150

Query: 183 -KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                AW+ V L EG+NR+++++     +   RLIR S G + L  L  G  RE+
Sbjct: 151 KSIPTAWIKVILFEGRNRQVRRMTAHIGFPTLRLIRYSMGDYTLDNLANGEWREM 205


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 63/179 (35%), Positives = 96/179 (53%), Gaps = 6/179 (3%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFS-RVISVGRLDINTEGLLLL 124
           +R  E T L L HKP G+VT + D +   TV D L P I S ++ +VGRLD +T GLLL+
Sbjct: 54  IRGYEHTYLML-HKPAGVVTANKDRE-LPTVMDLLSPDIQSDKLYAVGRLDRDTTGLLLV 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQK 183
           T++G L   L  P     + YRV  +G +  D +   +KGIV + G      ++ + +  
Sbjct: 112 TDNGPLGFQLLHPQYHVDKTYRVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSAS 171

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            S +  ++ + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 172 PSLSQASITISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDENLQAGDYRPLNSEEL 230


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 117/229 (51%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A    A R+++++++A++++ V+ +  ++ + N+      I++ G  + +  R 
Sbjct: 2   RLDQLMADHQYA-RKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI-GERIIQEPRH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ HKPIG VT   D     TV D  +    +  +  +GRLD +T GLLL+T++G L 
Sbjct: 60  HYYMLHKPIGAVTAKRDAH-HPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY V  +G +    +   + GI    G       +T+     S +   
Sbjct: 119 FQLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTPSYSKAQ 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           V + EGK  ++KK+F     KV  L R+S+GPF L   LA G +R +++
Sbjct: 179 VRISEGKYHQVKKMFLAIGVKVMTLKRLSFGPFTLDPQLAPGESRPLNE 227


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 107/217 (49%), Gaps = 11/217 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K ++ AG  SRR  +++I +  V +NG + E     V   D + V G  + +    
Sbjct: 6   KRINKFLSEAGYCSRRNADKLIEEGAVTINGKIPE-MGTKVGPDDEVRVKGELITEPNSN 64

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            ++L ++KP G+V T      +  + D  N P    R+  +GRLD  +EGL+LLTNDG +
Sbjct: 65  FVYLAFNKPRGIVCTTDTRREKDNIIDYINYPE---RIFPIGRLDKYSEGLILLTNDGDI 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  D +  +  G+ I         V    Q G +++  
Sbjct: 122 VNKILRARNNHEKEYIVHLNKPIKGDFIQKMGDGVPILDTVTKKCFV---EQIGKSSFKI 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           + L +G NR+I+++ E+F++KV  L RI     +L T
Sbjct: 179 I-LTQGLNRQIRRMCEYFDYKVAGLKRIRIMNVKLDT 214


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 113/238 (47%), Gaps = 26/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  VKVNG    + AV    V   D I+++     K  
Sbjct: 10  RLSKRMAQLGLCSRREADSYIEQGWVKVNG----QTAVLGQKVTERDRIDLNKQAHEKQA 65

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLDI 116
                L +KP+G V+  ++   +S     T  ++     SR+             GRLDI
Sbjct: 66  ARVTILLNKPVGYVSAQAEKGYKSAAELITAENHWEGDDSRIPFSEKHKFGLAPAGRLDI 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G      +
Sbjct: 126 DSVGLLVLTQDGRIAKQLIGENSSSEKEYLVRVRGKLDDKGLALLNHGLSLDGEKLRPAK 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 186 VEWQNED----QLRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 239


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D + L  L+ G+ +        GI         +      
Sbjct: 98  LTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 158 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLSGLDNGQWREIAQ 217

Query: 239 K 239
           +
Sbjct: 218 E 218


>gi|145580106|pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
          Length = 189

 Score = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 57/187 (30%), Positives = 93/187 (49%), Gaps = 19/187 (10%)

Query: 68  RKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           RK E   TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LT
Sbjct: 4   RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLT 61

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVT 178
           N+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    
Sbjct: 62  NNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAW 121

Query: 179 L--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           L        + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  
Sbjct: 122 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLAN 181

Query: 231 GSTREVS 237
           G  REV+
Sbjct: 182 GEWREVT 188


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 49/169 (28%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 105 LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 162

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  G+        +D+             +
Sbjct: 163 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIGPRNPPVRERK 222

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L +G
Sbjct: 223 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSG 271


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 114/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK IA+ G+ SRRE +  I Q  V VNG    + AV    V  TD IE++     +  
Sbjct: 15  RLSKRIAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPTDRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTSRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 113/238 (47%), Gaps = 26/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  VKVNG    + AV    V   D I+++     K  
Sbjct: 10  RLSKRMAQLGLCSRREADSYIEQGWVKVNG----QTAVLGQKVTERDRIDLNKQAHEKQA 65

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLDI 116
                L +KP+G V+  ++   +S     T  ++     SR+             GRLDI
Sbjct: 66  ARVTILLNKPVGYVSAQAEKGYKSAAELITADNHWEDDDSRIPFSEKHKFGLAPAGRLDI 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D   L LL  G+ + G      +
Sbjct: 126 DSVGLLVLTQDGRIAKQLIGENSSSEKEYLVRVRGKLDDKGLALLNHGLSLDGEKLRPAK 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V    +      +   LR+GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 186 VEWQNEDQ----LRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 239


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 115/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I  +GI SRR+ +R I Q  V +NG   +RAAV   V S D ++V+G  +  R  
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGHVFING---KRAAVGDQVYSGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               L   +KP+G+++T  +  G S    +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  NDLVLIALNKPVGIISTTEE--GESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G      +V+    K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFILGLGAGVPMMGTVTKKCKVS----KVATFVFN 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPMGEWRDLTDDELIE 231


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 90/189 (47%), Gaps = 20/189 (10%)

Query: 67  LRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           L K +R+R    + L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL
Sbjct: 23  LNKPKRSRGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLL 80

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQG 169
           +LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+             VI+ 
Sbjct: 81  VLTNDGVLQARLTQPKSKQAKVYWVQVEGAPTETNLQALRDGVELKDGMTLPAGVEVIES 140

Query: 170 ICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
               D    +  +K     W+ + L+EG+NR+++++         RLIR     + +  L
Sbjct: 141 PIVWDRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYQMAQWTVSDL 200

Query: 229 LAGSTREVS 237
             G  REV+
Sbjct: 201 APGEWREVT 209


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 108/226 (47%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIHQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEDQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            EG+  ++K++F     KV  L R   G   L  +L  G  R +++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQ 224


>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 = 79.7 bits (195), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 54/183 (29%), Positives = 92/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L+L++KP  ++T  SD  GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + ++EG NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGCNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
            K+
Sbjct: 208 AKL 210


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 116/233 (49%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++K +  AG+ SRRE +  I   +V ++G   E     V+    + V+G  +   E  
Sbjct: 24  QRLNKFLTNAGVCSRREADHRIRAGQVTIDGQTAE-LGQRVLPGQRVAVNGRIIEGKEEE 82

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L+HKP G+V T    +  + V F   PS   RV  VGRLD  + GL+L+TN G +  
Sbjct: 83  IILLFHKPRGIVCTAEKREKNNIVDFIGYPS---RVYPVGRLDKESRGLILMTNQGDIVN 139

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +   + +  + Y+V  +  + +  +  ++ GI ++ +  G+        +  +   T+ 
Sbjct: 140 RMMRAANRHEKEYQVTVNRGISETFVRRMRAGIYLKEL--GETTRPCQIHQTGDRTFTII 197

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L +G NR+I+++     ++V  L+R+     +L  +  G  R++ ++  RE+L
Sbjct: 198 LTQGLNRQIRRMCHTLGYEVTDLLRVRIMNLRLDGIPEGEYRKIGRR-EREEL 249


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 107/220 (48%), Gaps = 6/220 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR+EV+ ++    V ++G   +    +V   T  + V G P+   E  
Sbjct: 2   RLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKEHVDPDTQEVTVYGEPVDYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG LA
Sbjct: 62  YLMM-NKPQGVLSATED-SRQQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    Q+ ++ ++ L+ G+ I+ G      +  + T    N  + 
Sbjct: 120 HRLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPAKAEIKTNDSGNTVIY 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++ +    +V  L R+S G   L   LA
Sbjct: 180 LTITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALA 219


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 109/237 (45%), Gaps = 36/237 (15%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           + R G + R   ER  A+ R + +            ST   +  G P+       + L++
Sbjct: 48  LQRGGTSERNSSERGGAKSRPQRHS-----------STTRTKPQGDPM-------IVLFN 89

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   L  P  
Sbjct: 90  KPFDVLCQFTDEQGRKTLKDYIP--IPGVYAAGRLDRDSEGLLLLTNDGQLQAKLTEPKK 147

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------DTQKGS 185
           +  + Y V+  G+  +  L  L++G+ ++       +V+L              + +   
Sbjct: 148 KTFKTYWVQVEGEPTEADLAKLRQGVELKDGMTLPAKVSLMATPNVWPRNPPIRERKNIP 207

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVSKKI 240
             W+ + + EG+NR+++++     +   RLIR   G + L  L  G  +  +V++K+
Sbjct: 208 TTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATGEHKCIQVTQKM 264


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 52/175 (29%), Positives = 91/175 (52%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 60  IFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 117

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ------------ 182
           P ++  + Y V+  G   +  L  L+KG+ ++ G+    +++V  + Q            
Sbjct: 118 PKSKSPKTYWVQVDGAPLEQDLEKLRKGVELKDGMTLPAEVEVIPEPQVWDRTPPVRFRA 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + + EG+NR+++++     +   RLIR S G   L  L+ G  RE+S
Sbjct: 178 NIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLIRHSMGDIVLKDLMPGEWREIS 232


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 114/231 (49%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++      SRR+V+++I  Q V+++  +      NV      IE+ G  +   + +
Sbjct: 2   RLDKLLEVVTDGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEISGKRISHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
             ++ +KP G+V+  SD +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  -YFILNKPAGVVSARSDIN-HVTVLDQLSEKDRHPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G +D D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVAKTYMVTVNGFLDADAPDFFAAGIKFPTGEQCRPAQLTILQASQEK 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   + + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R ++
Sbjct: 176 SQARLVISEGKFHQVKKMFLTYGLKVISLKRASFAGLELGELASGAYRSLT 226


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 119/233 (51%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA V V   + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRATVGVQVSAGDVVKVNGQIIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+LLTN G L
Sbjct: 65  EDLILIALNKPVGVISTTEDGEQNNIV--DFVNHSKRVFPIGRLDKDSQGLILLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G      +V    ++ +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKV----KREATFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R+      L  L  G  R++++  L E
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERVRIMNISLKGLPQGEWRDLTEDELIE 231


>gi|152978114|ref|YP_001343743.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150839837|gb|ABR73808.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 243

 Score = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 95/181 (52%), Gaps = 16/181 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+LTN+G L 
Sbjct: 52  QTQVVLFNKPFDVLTQFTDESGRKTLKDFIP--VPGIYAAGRLDRDSEGLLILTNNGELQ 109

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYGDM-QVTLD 180
             L  P  +  + Y V+  GQ  +  L  L++G+           ++ I   D+ Q    
Sbjct: 110 HRLANPKFKLPKTYWVQVEGQPTEADLERLRRGVELKDGMTKPAKVRSIAEPDLWQRVPP 169

Query: 181 TQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++  N   AW+ + L EGKNR+++++     +   RL+R +     L  L +G  RE++
Sbjct: 170 IRERKNIPTAWLEIQLGEGKNRQVRRMTAHIGFPTLRLVRAATAGLTLHGLPSGQYRELT 229

Query: 238 K 238
           +
Sbjct: 230 E 230


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 90/175 (51%), Gaps = 20/175 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP+ ++T  +D  GR+T+ D +  P +++     GRLD ++EGLLLLT+DG +   +
Sbjct: 6   VFNKPMNVLTQFNDSQGRATLSDFIDKPGVYA----AGRLDYDSEGLLLLTDDGAIQARI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P  +  + Y V+  G + +  L  L+KG+++          +L +             
Sbjct: 62  SQPKFKLPKTYWVQVEGVIGEAALRRLEKGVMLNDGPTRPAHASLISPPEVWERDPPIRQ 121

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            +    +W+ + L EG+NR+++++     +   RLIR S GP+ +  L  G  RE
Sbjct: 122 RKNIPTSWIALTLFEGRNRQVRRMTAAVGFPTLRLIRYSIGPWSINGLQPGEWRE 176


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 65/216 (30%), Positives = 104/216 (48%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +  AGI SR +V+ ++ ++ V VNG +   A   + S  D I   G  L   E  
Sbjct: 2   RLDKFLVDAGIGSRSQVKSLLKKKEVLVNGQVESSAKRQIDSDKDQIVFQGQKLV-YEEF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D +   TV D L   +    V  VGRLD +T GLLLLTN+G LA
Sbjct: 61  LYYMLNKPAGVVSATED-NLHQTVVDLLDDRARQKEVFPVGRLDKDTHGLLLLTNNGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     ++Y     G + +      + GI +    C    ++V    +      V
Sbjct: 120 HQLLTPKKHVDKIYLAHIEGMMTKKDQEAFENGIQLSDHHCLPATLEVLETDEHKQTCKV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + L+EGK  ++K++ +    +V  L R++ GP +L
Sbjct: 180 KITLKEGKFHQVKRMVKACGKEVTDLQRLTMGPLKL 215


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 115/230 (50%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+++  GI SR+E  R+I + R+ VNG +       V   D I +D  P++K E+  
Sbjct: 2   RINKLLSNYGICSRKEANRIIEENRIIVNGEVCIPGQW-VEEYDEILMDNEPIKKKEKIY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP+G+  T +     + + F N P     +  VGRLD ++EGL+L+TNDG L+  
Sbjct: 61  IAL-NKPVGITCTAAREVKDNIIDFLNYPEY---IFPVGRLDKDSEGLILMTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V      D   +  + +G+ + G+      VT    + +N    + L
Sbjct: 117 ILESENHHEKEYIVTVDKPFDDSFIKGMSEGVQLNGVKTRPCIVT----RINNDTFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++   F + V +L RI     ++  +  G  R ++ K + E
Sbjct: 173 TQGLNRQIRRMTRAFRYTVIKLERIRILNIKINEIDVGKWRYLTHKEIDE 222


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  + SR+ +++ + ++ + V+       A NV      +   G  ++  E  
Sbjct: 2   RLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNVDTGLQKLVFQGRQIQGYEHN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D     TV D LP      ++ ++GRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGVVTASKD-KKLPTVMDLLPPDIQSDQLYAIGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K GIV + GI     Q+ + +   + +  +
Sbjct: 119 FQLLHPQYHVDKSYQVVVNGLLTSDHIQKFKDGIVFLDGITCKPAQLEILSSSPTESRAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           + + EGK  ++KK+F     KV  L R+ +G F L   LA G  R ++ + L+
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTALKRVQFGDFTLDPELAKGQYRPLNPEELK 231


>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 = 79.7 bits (195), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 118/239 (49%), Gaps = 28/239 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVD-GVPLRKA 70
           R+SK +A+ G+ SRRE +  I Q  VKVNG    + AV    V   D I+++     ++A
Sbjct: 10  RLSKRMAQLGLCSRREADSYIEQGWVKVNG----QTAVLGQKVTERDRIDLNRQAHEKQA 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLD 115
           ER  + L +KP+G V+  ++   +S     T  +      SR+             GRLD
Sbjct: 66  ERVTI-LLNKPVGYVSAQAEKGYKSAAELITADNRWEGDDSRIPFNEKHKFGLAPAGRLD 124

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G      
Sbjct: 125 IDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPA 184

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 185 KVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGKLPPGKWR 239


>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 = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 216

Query: 238 K 238
           +
Sbjct: 217 E 217


>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 = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 120/250 (48%), Gaps = 16/250 (6%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VM 55
           +KD+    E   P    R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V 
Sbjct: 18  LKDEVYTGEIMLPDSSIRLNKYISESGICSRREADRFIEQGNVFLNG---KRATIGDQVK 74

Query: 56  STDHIEVDG--VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
             D ++V+G  +  R+AE       +KP+G+V+T  D + R  + D   +   RV  +GR
Sbjct: 75  PGDVVKVNGRLIEPREAEDLVFIALNKPVGIVSTTEDSE-RDNIVD-FVNHSKRVFPIGR 132

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD +++GL+ LTN G L   +        + Y V     +  D +  +  G+ I     G
Sbjct: 133 LDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITDDFIRGMGAGVPI----LG 188

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +      +K +     + L +G NR+I+++ E F ++V RL R       L  L  G  
Sbjct: 189 TVTKKCKVKKEAPFVFRITLIQGLNRQIRRMCEHFGYEVTRLERTRIMNVGLSGLPLGEW 248

Query: 234 REVSKKILRE 243
           R+++   L E
Sbjct: 249 RDLTDDELIE 258


>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 = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 120/228 (52%), Gaps = 14/228 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+ +  GI SR+E  ++I + RV VNG   +E   V +  +D I +DG PL   E+ 
Sbjct: 2   RINKLFSNFGICSRKETNKIIREGRVIVNGKPCIEGQWVEL--SDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIAL-NKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V        D +  +++G+ I G      QVT     ++ +    ++
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMERGVEILG------QVTKPCKLKRINENTYSI 170

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++ + F + V +L RI      L  +  G  R ++++
Sbjct: 171 ILTQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINRE 218


>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 = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 120/240 (50%), Gaps = 21/240 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---MSTDHIEVDGVPLRKA 70
           +R+ K+I+  G  SR++V+    +  ++V+G++++ +A+ V    S   I  + V  RK 
Sbjct: 2   ERLDKIISNLGYGSRKDVKSFAKKGIIEVDGLIVKDSAMLVDPEKSVIKINGEEVLYRK- 60

Query: 71  ERTRLWLY---HKPIGLVT-THSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLL 124
                ++Y   +KP G+++ TH + D   TV D  NL         +GRLD +T GLLLL
Sbjct: 61  -----YIYIMMNKPDGVISATHDNRD--ETVIDLLNLEHQVFDPFPIGRLDKDTVGLLLL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L   L  P     +VY       VD+  +   K GI +    Y  ++  L+    
Sbjct: 114 TNDGELNHRLISPKWHVDKVYYAEIDKSVDEKDIKAFKDGITLDD-GYKCLEANLEILSS 172

Query: 185 SN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           SN  + + + ++EGK  ++K++FE    KV  L R  +G   L   L  G  RE++ + L
Sbjct: 173 SNDGSEIRLTIQEGKFHQVKRMFEAVGKKVTYLKREEFGGLLLDPDLEEGEYRELTDEEL 232


>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 = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 113/231 (48%), Gaps = 13/231 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL 67
           N  P R++K ++ AG+ SRR+ +R + Q R+ V+G   E A +   V +   I VDG  +
Sbjct: 32  NGEPMRLNKFLSDAGVCSRRQADRYVEQGRILVDG---EPAQMGQKVHAGQDIRVDGKRV 88

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             + +  +   +KP G+V T    +  + V F   P    R+  VGRLD ++EGL+L+TN
Sbjct: 89  SVSRKQIVLAVNKPKGIVCTTEKREKDNIVDFIGYPE---RIYPVGRLDKDSEGLILMTN 145

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   +        + Y V  +  V    L  + +G+ I        +V    + G  
Sbjct: 146 DGELMNEILKARNYHEKEYEVTINRPVTNVFLKQMSEGVEILDTVTRPCKV---KRTGVY 202

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +  + L +G NR+I+++ E   ++V  L R+      LG+L  G  RE++
Sbjct: 203 TFRII-LTQGLNRQIRRMCEACGYRVRELKRLRIMNIHLGSLPTGKYREIT 252


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 116/226 (51%), Gaps = 13/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA V   V + D ++V+G  +   ++
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRATVGEQVYAGDVVKVNGQLIEPRDQ 64

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L L   +KP+G++ T  D +G + V  +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  NDLVLIALNKPVGIICTTEDGEGDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  + +  L  G+ + G      +V    +K +    +
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPLTDEFILGLGAGVPMLGTVTKKCKV----RKEAPFVFS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + L +G NR+I+++ ++F ++V +L R       L  L  G  R++
Sbjct: 179 ITLVQGLNRQIRRMCKYFGYEVTKLERTRIMNINLKGLPIGEWRDL 224


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D + L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLSGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 115/241 (47%), Gaps = 26/241 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLDI 116
                L +KP+G V+  ++   +S     T  +   S  SR+             GRLDI
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWESDTSRIRFDPKHKIGLAPAGRLDI 130

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G      Q
Sbjct: 131 DSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQ 190

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R +
Sbjct: 191 VEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWRYL 246

Query: 237 S 237
           +
Sbjct: 247 A 247


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 47  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 102

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 103 ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKSAKVRLISEPNLWER 162

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 163 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFR 222

Query: 235 EVS 237
            +S
Sbjct: 223 LLS 225


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 30  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 86  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 145

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 146 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 205

Query: 235 EVS 237
            +S
Sbjct: 206 LLS 208


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 88/180 (48%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L             
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPEWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 65/224 (29%), Positives = 105/224 (46%), Gaps = 5/224 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G+        V     +  D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRKSVRLALASGRVQVDGLTTSDPHHEVREFSCVMFDTEILQPGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  +D     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPPGCVSATTDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T+  +VY V     +D   +    +G+             L+     +A +++  
Sbjct: 121 LTQPQTKMPKVYYVETEQLIDDRYVLKFAEGLYFSFENITTQPAQLNVLGPRSAHLSI-- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            EG+  ++K++F  F+ KV RL R S G   L  TL AGS R +
Sbjct: 179 VEGRYHQVKRMFGHFDNKVLRLHRESIGALTLDPTLAAGSYRAL 222


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +L      NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMLARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLT 226


>gi|160881056|ref|YP_001560024.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429722|gb|ABX43285.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 477

 Score = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 115/241 (47%), Gaps = 24/241 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ +GI SRRE +  IA+  V ++G       V VM +  +    V L K E +R
Sbjct: 20  RINKYLSESGICSRREADTRIAKGEVTIDG------EVAVMGSKVLPGQKVVLGKKEVSR 73

Query: 75  -----LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                L  +HKP G+V T    +PD    + D +     R+  +GRLD ++EGL+ LTN+
Sbjct: 74  EEKMVLIAFHKPKGIVCTTEKREPD---NIIDYIK-YSQRIYPIGRLDKDSEGLIFLTNN 129

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  +    L  +  G+ I          TL+       
Sbjct: 130 GDIVNKILRAGNHHEKEYIVTVNKPITAAFLKGMAGGVPILDTVT--KPCTLEAI--DKV 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL---REQ 244
              + L +G NR+I+++ E F++KV +L+RI      LG L  G  R ++ K L   +EQ
Sbjct: 186 TFRIILTQGLNRQIRRMCEHFDYKVTKLVRIRIMNVNLGRLKVGGYRNLTDKELEGIKEQ 245

Query: 245 L 245
           +
Sbjct: 246 I 246


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 55/183 (30%), Positives = 94/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L+L++KP  ++T  SD  GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK--GSN-- 186
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD  +   SN  
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPSNPP 147

Query: 187 ---------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVA 207

Query: 238 KKI 240
             +
Sbjct: 208 ANL 210


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 118/245 (48%), Gaps = 23/245 (9%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK ++  G+ SRRE +  IA+  V+V+G ++      ++ T  + V+     +  +
Sbjct: 4   PLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGTKILPTQRVTVERQAAAEQSK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFS-----RVISVGRLDIN 117
               L +KP+G V+  ++   +  V           D  P+ F       ++  GRLDI+
Sbjct: 64  RVTILINKPMGYVSGQAEDGYKPAVALVKAESRWKEDTSPTQFHPTQLRSLVPAGRLDID 123

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICYG 173
           + GLL+LT DG +A+ L   ++   + Y VR      G++ +  L  L  G+++ G    
Sbjct: 124 SVGLLVLTQDGRIAKHLIGENSSVEKEYLVRVQYIKPGKLPEADLQRLNHGLMLDGKKLL 183

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             QV    +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G  
Sbjct: 184 PAQVKWQNEDQ----LSFILREGKKRQIRRMCDIVGLKVVGLKRVRIGRVKLGDLPVGEW 239

Query: 234 REVSK 238
           R +++
Sbjct: 240 RYLAE 244


>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 = 79.3 bits (194), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 49  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 104

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 105 ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKSAKVRLISEPNLWER 164

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 165 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFR 224

Query: 235 EVS 237
            +S
Sbjct: 225 LLS 227


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D + L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 105/222 (47%), Gaps = 4/222 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  ++S++++     SR++   +IA  +V VN +    A  +V     + V+G  L++
Sbjct: 12  TMSAMKLSRIVSNQPDISRKQANWLIATGQVYVNDLSCRTADADVDEFAAVSVNGKTLQQ 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDG 128
                  + HKP G ++   D D   TV   LP   S+ + + GRLD  T GL++LTN+G
Sbjct: 72  GHCAHYIMLHKPAGYLSATED-DTHPTVLQLLPPGLSQCLHIAGRLDRATTGLMILTNNG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +R L LP     +VYRV     +  D      +GI  +         TL+  + + A 
Sbjct: 131 TWSRQLTLPGMGIAKVYRVTTAYPIGPDTPQRFAEGIWFEYEQLTTAPATLELLEPTLAR 190

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +T+   EG+  ++K++F     +V  L R   G  QL + LA
Sbjct: 191 LTI--YEGRYHQVKRMFHAVGNRVIALHREQIGHLQLNSDLA 230


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+R     ++ +++KP  ++   +D +GR T+ D +P     + + GRLD ++EGLL+LT
Sbjct: 23  PVRPRGERKVVIFNKPFDVLVQFTDENGRKTLKDFIP--IRDIYAAGRLDRDSEGLLVLT 80

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------ 179
           NDG L   L  PS    ++Y  +  G      L   + G+ ++       QV +      
Sbjct: 81  NDGKLQAKLTQPSKNTGKIYYAQVEGVPCTAALQQFRDGLALKDGKTLPAQVEIVEQPEW 140

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + Q     W+ + L EGKNR+++++     +   RLIR S G   L  LL 
Sbjct: 141 LWERNPPIRERQTIPTTWLRITLFEGKNRQVRRMTAHIGYPTLRLIRFSMGNITLDNLLP 200

Query: 231 GSTREVS 237
           G  +E++
Sbjct: 201 GEWKEIN 207


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 90/189 (47%), Gaps = 20/189 (10%)

Query: 67  LRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           L K +R R    + L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL
Sbjct: 23  LNKPKRARGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLL 80

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQG 169
           +LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+             VI+ 
Sbjct: 81  VLTNDGVLQARLTQPKSKQAKVYWVQVEGAPTEADLQALRDGVELKDGMTLPAGVEVIES 140

Query: 170 ICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
               D    +  +K     W+ + L+EG+NR+++++     +   RLIR     + +  L
Sbjct: 141 PQIWDRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGFPTLRLIRYKMAQWTVDDL 200

Query: 229 LAGSTREVS 237
             G  REV+
Sbjct: 201 APGEWREVT 209


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>gi|148827048|ref|YP_001291801.1| malic enzyme [Haemophilus influenzae PittGG]
 gi|148718290|gb|ABQ99417.1| malic enzyme [Haemophilus influenzae PittGG]
          Length = 232

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQKDEIYFEDELLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEKNYAEACAEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 112/231 (48%), Gaps = 9/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV+ ++ + +V VN  + +    ++  T D + V+G  +      
Sbjct: 2   RLDKFLANMGVGTRTEVKHLLKKGKVTVNTSVEKSPKSHINPTEDIVHVNGKQVEFVNNV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   R TV D +P      +  VGRLD +TEGLLL+TNDG  + 
Sbjct: 62  YIML-NKPKGYISATHDESNR-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGQFSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V     V +  ++  KKGI++        Q+T   +  S+    V 
Sbjct: 120 DLMSPSKHVSKTYEVTSKKPVTKVDIDAFKKGIILSDGPVKPAQLTRINETISH----VT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F     +V  L R+      L   L +G  + +S K L+
Sbjct: 176 IYEGKYHQVKRMFHAIENEVLELKRLKIANLALDENLKSGEYKLLSDKELK 226


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 107/227 (47%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R +  +++ Q  V VNG + +  A  V  TD I ++G  L      +
Sbjct: 2   RLDKFLAENTGLTRSQANKVLKQSAVTVNGHVEKNGAQKVSQTDEICLEGEHLPWVSAGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YLMLYKPQGYVCSHEDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+        +G++++G        TL+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVESHYQQACAEGMLLRGEKTPTKPATLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            EG+  ++K++F     KV  L R   G  +L   LA G  R +S +
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIGQIELDDRLAEGEYRSLSAE 225


>gi|330720777|gb|EGG98994.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC2047]
          Length = 239

 Score = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 77/230 (33%), Positives = 116/230 (50%), Gaps = 16/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     S++ V  ++AQ RV V+G +       + +   I +DG  L+    T 
Sbjct: 7   RLDRFISSKMAISQKAVRPILAQGRVAVDGCVCRDRQQIINTFSRITLDGQILQA--NTP 64

Query: 75  LWLY-HKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L+L  +KP G+V+   D +   TV D L  P   S++  VGRLD N+ GLLLLTND G +
Sbjct: 65  LYLMMNKPKGVVSATRD-NQYQTVIDLLDHPE-RSKLHLVGRLDFNSTGLLLLTNDSGWS 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAW 188
           + L  P  +  + YRV  +  +DQ  ++    G+      Y D       L+      A 
Sbjct: 123 QQLMKPDQKVSKRYRVTVNNPLDQQTVDAFAAGMY---FAYEDATTRPAGLNIINDYEAE 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           VT  L EG+  +IK++F   N KV  L RI+ G   L  +L AG +RE+S
Sbjct: 180 VT--LTEGRYHQIKRMFARCNNKVLALHRIAIGNLLLDPSLSAGQSRELS 227


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 116/230 (50%), Gaps = 13/230 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 23  TSIRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 79

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  VGRLD +++GL+ LTN 
Sbjct: 80  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPVGRLDKDSQGLIFLTNH 137

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V  + +  +  G+ I     G +      +K +  
Sbjct: 138 GDLVNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPF 193

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              + L +G NR+I+++ E F + V +L R       L  +  G  R+++
Sbjct: 194 VFRITLVQGLNRQIRRMCEHFGYDVTKLERTRIMNVSLSGIPLGEWRDLT 243


>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 = 79.3 bits (194), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 66/221 (29%), Positives = 106/221 (47%), Gaps = 18/221 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   SR E  ++I  +RV VNG+ +   A  V   +HI +DG  L      R
Sbjct: 2   RLDKFVCKSTPLSRTEAVQVIHHERVLVNGVAIVDEAAQVHENNHIILDGKHLVP-RPFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP   ++ +     +ST +   PS+F        S +  VGRLD +T GLLL T+
Sbjct: 61  YLLLHKPANCLSANISEPSKSTKY---PSVFDVLNIDNSSELHLVGRLDADTTGLLLATD 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           DG  +  +  P++   +VYRV     +  +  +    GI++Q    G+ ++TL  +    
Sbjct: 118 DGRWSFTITSPNSDCSKVYRVGLAKPLGPEVADKFLAGILLQ----GEHELTLPAKLEVI 173

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           S   V + L +GK  ++K++F     KV  L R   G   L
Sbjct: 174 SPNQVLLTLTQGKFHQVKRMFAAVGNKVVSLHREKIGAISL 214


>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 = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 65/208 (31%), Positives = 104/208 (50%), Gaps = 15/208 (7%)

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGR 113
           + D + V G  L   E+   +L +KP G ++   D +   TV D L   ++   V  VGR
Sbjct: 39  TEDEVVVSGQKL-TYEKFVYYLLNKPKGYISATED-ERHKTVLDLLDETALQKEVFPVGR 96

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI+T GLLLLTN+G LA  +  P     ++YR +  G ++Q  +    +GI ++     
Sbjct: 97  LDIDTHGLLLLTNNGKLAHAMLSPKKHVEKIYRAQVAGLMNQSDVEQFARGIELKDFTCQ 156

Query: 174 DMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             Q+ +   D +K   + V + L EGK  ++K++      +V  L R++ GP QL   LA
Sbjct: 157 PAQLKILEVDEEK-ETSLVEISLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPELA 215

Query: 231 -GSTREVSKKILREQLGPHLLEEAQVNL 257
            G  R ++++ L+       LE  QV L
Sbjct: 216 LGEWRRLTEEELKS------LERFQVEL 237


>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 = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 117/234 (50%), Gaps = 13/234 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R + +  V +NG   +RA V   V + D ++V+G  +  
Sbjct: 5   TTTRLNKYISESGICSRREADRFVEKGSVFING---KRAKVGDQVSAGDTVKVNGQIIDP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  ER  L   +KP+G+V T    + ++ + D + +   R+  +GRLD +++GL+ LTN+
Sbjct: 62  RDEERLVLIALNKPVGVVCTTEGSE-KNNIVDYV-NHGERIFPIGRLDKDSQGLIFLTNN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +     +  + Y V     +    +  + KG+ I G      ++  +T      
Sbjct: 120 GDLVNKILRAGNRHEKEYLVTVDKPITDTFIRDMAKGVPILGEVTRKCKIVKETP----T 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +G NR+I+++ + F + + RL R+      +  L  G  R+ S+  L
Sbjct: 176 LFRITLVQGLNRQIRRMCDHFGYDIVRLERVRIMNVSMKGLGVGEWRDFSQNEL 229


>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 = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 92/181 (50%), Gaps = 21/181 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           + HKP G+++   +P  R  T+  +L       +++GRLD+ +EGLLLLT DG ++   E
Sbjct: 1   MVHKPWGMISQFVNPAKRKKTLLGDLYGFPEGTMAIGRLDVPSEGLLLLTTDGKVSA--E 58

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------QGICYGDMQVTLDTQK 183
           + S  + + Y V+  G +    L  LK G+ I            + +   D +  L +QK
Sbjct: 59  IRSNAYEKEYYVQVDGIMTAAALENLKTGVEIGFKGTKYVTKPGKAMLLKDPRFPLRSQK 118

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                 G  +W+++ ++EGK R+++K+     +   RL+R+  G  +LG L  G+  EV 
Sbjct: 119 IRDERHGPTSWISIIIKEGKFRQVRKMTAAVGFPTLRLVRVRIGTMKLGELAIGAVVEVE 178

Query: 238 K 238
           K
Sbjct: 179 K 179


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 54/210 (25%), Positives = 107/210 (50%), Gaps = 19/210 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 2   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+L+L++   +  
Sbjct: 61  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLILSDSKAVVS 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   + +  + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 121 ALMHANLE--KEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +       + + V + EGKNRE+++ F  F
Sbjct: 179 IIKNHAKYSKLRVVINEGKNRELRRFFVVF 208


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 91/180 (50%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG  
Sbjct: 65  EDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLTNDGIF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P+++  + Y V+  G   ++ L+ L+KG+ ++       +V L  +        
Sbjct: 123 QAKLTQPNSKSPKTYWVQVEGAPSEEDLDKLRKGVELKDGMTLPAKVELMAEPEVWDRNP 182

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+ + + EG+NR+++++     +   RLIR S G   +G L  G  +E+
Sbjct: 183 PVRFRAAIPTTWLVITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDMNVGQLQPGEWKEI 242


>gi|254804685|ref|YP_003082906.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
 gi|254668227|emb|CBA05021.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
          Length = 252

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 115/241 (47%), Gaps = 26/241 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRV----------ISVGRLDI 116
                L +KP+G V+  ++   +S     T  +   S  SR+             GRLDI
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWESDTSRIRFDPKHKIGLAPAGRLDI 130

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G      Q
Sbjct: 131 DSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRPAQ 190

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R +
Sbjct: 191 VEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPLGKWRYL 246

Query: 237 S 237
           +
Sbjct: 247 A 247


>gi|254670635|emb|CBA06652.1| pseudouridylate synthase [Neisseria meningitidis alpha153]
          Length = 252

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIGQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTSRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/176 (28%), Positives = 88/176 (50%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  ++   +D  GR T+ + +P   S V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 48  IFNKPFDVLPQFTDEQGRETLKNYIP--ISDVYAAGRLDRDSEGLLVLTNDGKLQARLTQ 105

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DT 181
           P  +  ++Y  +  G  D+  L   ++G+V+        ++ L               + 
Sbjct: 106 PQKKTGKIYYAQVEGIPDEIALANFRRGLVLNDGPTLPAEIELVEEPDWLWERIPPIRER 165

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR S G F L  L  G  +EV+
Sbjct: 166 KNIPTSWLKITLFEGRNRQVRRMTANIGFPTLRLIRYSTGEFSLDNLSPGEWKEVT 221


>gi|297585561|ref|YP_003701341.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297144018|gb|ADI00776.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 237

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 107/226 (47%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +++I + +V +NG   +     V   D + V+G P+   +   
Sbjct: 4   RINKYVSETGKTSRRGADKLIQEGKVTINGKPAQLGD-QVEPGDDVIVNGEPVHIVKENV 62

Query: 75  LWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT     G      N P    R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 63  YIALNKPVGITSTTERKVKGNIIDLVNHPL---RIFHIGRLDKDSEGLILLTNDGDIVNE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V  +  +  + L  + +G+ I         +    +K S     + L
Sbjct: 120 ILRAENKHEKEYIVTVNKPITPEFLKQMSEGVDI----LDTTTLPCKVKKLSKYEFNITL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +G NR+I+++ +   + V RL+R       LG L  G  R++SKK
Sbjct: 176 TQGLNRQIRRMCDALGYDVQRLLRTRIMNIHLGKLPPGQWRDLSKK 221


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 120/228 (52%), Gaps = 14/228 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+ +  GI SR+E  ++I + R+ VNG   +E   V +  +D I +DG PL   E+ 
Sbjct: 2   RINKLFSNFGICSRKETNKIIREGRIIVNGKPCIEGQWVEL--SDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIAL-NKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V        D +  +++G+ I G      QVT     ++ +    ++
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILG------QVTKPCKLKRINENTYSI 170

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++ + F + V +L RI      L  +  G  R ++++
Sbjct: 171 ILTQGLNRQIRRMSKVFGFNVVKLERIRILNITLKDIEYGKWRYINRE 218


>gi|320184392|gb|EFW59203.1| 23S rRNA pseudouridine synthase E [Shigella flexneri CDC 796-83]
          Length = 207

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 207


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 120/228 (52%), Gaps = 14/228 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+ +  GI SR+E  ++I + R+ VNG   +E   V +  +D I +DG PL   E+ 
Sbjct: 2   RINKLFSNFGICSRKETNKIIREGRIIVNGKPCIEGQWVEL--SDEILLDGKPLVPKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + L +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  YIAL-NKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V        D +  +++G+ I G      QVT     ++ +    ++
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILG------QVTKPCKLKRINENTYSI 170

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            L +G NR+I+++ + F + V +L RI      L  +  G  R ++++
Sbjct: 171 ILTQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINRE 218


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/225 (28%), Positives = 113/225 (50%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISESGKASRRGADKLINERRVIING-KVAKIGDQVQPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRINHVGRLDKDSDGLILLTNDGDIINEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I G      ++T    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPEFLKEMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      QL  L  G  R+++KK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIQLNNLPVGQWRDLTKK 219


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 88/180 (48%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +         V L             
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVDLVEEPEWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 206


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L +KP  ++   +D DGR+T+ D +P     V + GRLD ++EGL++LT+DG L  
Sbjct: 7   TRVILLNKPYDVLCQFTDADGRATLKDFVP--VPGVYAAGRLDRDSEGLVVLTDDGALTA 64

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG------- 184
            +  P  +  + Y  +  G  +   L  L++G+V+        +V  +    G       
Sbjct: 65  RIADPRHKMAKTYWAQVEGIPEDAALEALRRGVVLNDGPTLPAEVRAIPEPPGLWPRTPP 124

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    AW+ + LREG+NR+++++         RL+R + GP+ L  L  G  RE +
Sbjct: 125 VRFRKSIPTAWLELTLREGRNRQVRRMTAAVGLPTLRLVRRAVGPWTLEGLAPGEWREAA 184


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 97/183 (53%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 80/250 (32%), Positives = 112/250 (44%), Gaps = 35/250 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IAQ  V+VNG +     + V   D I+VD        +  
Sbjct: 114 RLNKRMADLGLCSRREADDWIAQGWVRVNGQVAA-MGLQVGPHDRIDVDRAAQGHQRQQV 172

Query: 75  LWLYHKPIGLVT-----------------THSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             L HKP+G V+                 TH   D   T F   P+    +   GRLDI+
Sbjct: 173 TILLHKPMGYVSGQAEDGHTPAVALINPRTHWKDDESRTRFS--PAQLKGLAPCGRLDID 230

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQD--------KLNLLKKGIVIQ 168
           + GLL+LT DG +AR L    +   + Y VR  +G   QD        KL LL  G+ + 
Sbjct: 231 SVGLLVLTQDGRVARQLIGEDSTVDKEYLVRVQYGDRAQDVRAVFPADKLALLNHGLALD 290

Query: 169 GICYGDMQVTLDTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           G      Q+     +  N   +   LREGK R+I+++ E    KV  L RI  G   LG 
Sbjct: 291 G-----QQLKPAVVEWQNPEQLRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGQVLLGK 345

Query: 228 LLAGSTREVS 237
           L  G  R ++
Sbjct: 346 LPPGQWRYLA 355


>gi|312148012|gb|ADQ30671.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi JD1]
          Length = 249

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ V+VN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVRVNNTIAKLGDKVALGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D DGR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/196 (29%), Positives = 89/196 (45%), Gaps = 17/196 (8%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           M T H         +    +L L +KP G+++  S      T+ D +P   S V   GRL
Sbjct: 1   MPTQHRRKRSPKRPRPVNPKLVLLNKPYGVLSQFSGEPDDVTLKDFVPH--SNVYPAGRL 58

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYG 173
           D ++EGL+LLTNDG     L  P  +  + Y V+  G  D+ +L  L+ G  +  G+   
Sbjct: 59  DKDSEGLMLLTNDGVYQARLANPKYKVAKTYWVQVEGIPDEAQLTALRNGCELNDGLTKP 118

Query: 174 DMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
                +D   G               ++W+++ + EGKNR+++++         RLIR  
Sbjct: 119 AQAFAIDAPIGLWPRNPPVRERKTVPDSWLSLSITEGKNRQVRRMTAHVGLPTLRLIRAQ 178

Query: 220 YGPFQLGTLLAGSTRE 235
            GPF+L  L  G  RE
Sbjct: 179 IGPFKLAGLQPGEWRE 194


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 92/180 (51%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG  
Sbjct: 65  EDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLTNDGIF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P+++  + Y V+  G   ++ L+ L+KG+ ++       Q+ + ++        
Sbjct: 123 QAKLTQPNSKSPKTYWVQVEGAPSEEDLDKLRKGVELKDGMTLPAQIEVMSEPVVWERTP 182

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+ + + EG+NR+++++     +   RLIR S G   +G L  G  +E+
Sbjct: 183 PVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMNVGQLQPGEWKEI 242


>gi|332093194|gb|EGI98254.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           5216-82]
          Length = 231

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+TNDG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTNDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 65/220 (29%), Positives = 110/220 (50%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  + SR+ +++ + +  + V+G      A N+      +      ++  E T
Sbjct: 2   RLDNLLAQEKV-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D     TV D LP      ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKK-LPTVMDLLPLDIQSDKLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSRAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++KK+F     KV  L R+ +G F L T L 
Sbjct: 179 ITISEGKFHQVKKMFLSIGVKVTSLKRVQFGDFTLDTELT 218


>gi|3402689|gb|AAC28992.1| unknown protein [Arabidopsis thaliana]
          Length = 303

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 55/146 (37%), Positives = 81/146 (55%), Gaps = 15/146 (10%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  S D I V+G 
Sbjct: 153 ENFKEQPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDIIYVNGN 212

Query: 66  PLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV--FDNLPSIF---------SRVISVGR 113
            + K    +++   +KP G + +  + + +S +  FD   S +          R+ +VGR
Sbjct: 213 RIPKKLPPKVYFALNKPKGYICSSGEKEIKSAISLFDEYLSSWDKRNPGTPKPRLFTVGR 272

Query: 114 LDINTEGLLLLTNDGGLARVLELPST 139
           LD+ T GL+++TNDG  A+ L  PS+
Sbjct: 273 LDVATTGLIVVTNDGDFAQKLSHPSS 298


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 110/243 (45%), Gaps = 35/243 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+SKV++  G+ SRRE +  I +  V VNG  +      +  S   I V     +   + 
Sbjct: 141 RLSKVMSERGMCSRREADLWIERGWVFVNGEQVSELGSRIDPSVSEITVSQEAKKDQAKA 200

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF--------------DNLPSIFSRVISVGRLDINTE 119
              L HKP+G V+   +P     V               +  P +   +   GRLDI++ 
Sbjct: 201 VTILLHKPVGYVSGQPEPGCIPAVTLITAETQVEQSGGPEFKPWMLRGLAPAGRLDIDST 260

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT+DG +A+ L    ++  + Y VR  G++ +  L+LL+ G+             L
Sbjct: 261 GLLVLTSDGRVAKRLIGEDSEAEKEYLVRVSGEMIKGGLDLLRHGL------------EL 308

Query: 180 DTQKGSNAWVT--------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           D +    AWV         + L+EGK R+I+++ E    +V  L R+  G  +LG L  G
Sbjct: 309 DGKPLKPAWVKQLNEDQLHIILKEGKKRQIRRMCELVGLQVIGLKRVRIGRIRLGDLPMG 368

Query: 232 STR 234
             R
Sbjct: 369 QWR 371


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 121/236 (51%), Gaps = 14/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ KVI +    SR+E++R+  Q +V V+  +  R   NV S  H I V G  L   ER 
Sbjct: 2   RLDKVIEQQLNTSRKEMKRLFQQGKVLVDQRIEGRPERNVDSAIHQIIVAGRQLETQER- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++ +KP G+VT + D   ++ +      D  P +++    VGRLD +TEGL+L+T +G
Sbjct: 61  -YYIVNKPNGVVTANVDQQHQTVIDLIAPKDQHPDLYA----VGRLDRDTEGLVLVTTNG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            L   L  P+ +  + Y V  +  V  + +     GI    G+      +T+   + + +
Sbjct: 116 QLGYDLLHPTKKVTKRYEVVVNDLVTPEDVAAFATGITFHGGVTCKPAALTIIDARAARS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           +V++ + EGK  ++KK+F     KV +L R + G   L   LA GS R ++++ L+
Sbjct: 176 FVSLEIAEGKFHQVKKMFLARGKKVIQLKRTAMGSLVLPDDLAVGSYRSLTQEELK 231


>gi|152978349|ref|YP_001343978.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150840072|gb|ABR74043.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 231

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/208 (28%), Positives = 102/208 (49%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    +R +  + I Q  V+VNG + +  A+ V   D I  DG PL   E  +
Sbjct: 2   RLDKFIAQQTGLTRSQATKSIRQGVVEVNGNMEKSGALKVSPQDEIVFDGEPLPWLEGLQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D  +   F + P +  ++ + GRLD +T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGYVCSHEDGDYPTVYQFFDYP-LAGKLHTAGRLDADTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+ +  +  ++GI+++G         L+     N  V + +
Sbjct: 121 VTSPKHYCEKTYLVTLADPVESNYQSACEQGILLRGEKEATKPAKLEIIDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 TEGRYHQVKRMFAALGNKVVALHRWRVG 206


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 89/189 (47%), Gaps = 20/189 (10%)

Query: 67  LRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           L K +R R    + L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL
Sbjct: 23  LNKPKRARGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLL 80

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQG 169
           +LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+             VI+ 
Sbjct: 81  VLTNDGVLQARLTQPKSKQAKVYWVQVEGTPTEANLQALRDGVELKDGMTLPAGVEVIES 140

Query: 170 ICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
               D    +  +K     W+ + L+EG+NR+++++         RLIR     + +  L
Sbjct: 141 PIVWDRNPPIRERKSIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYQMAQWTVNDL 200

Query: 229 LAGSTREVS 237
             G  REV+
Sbjct: 201 APGEWREVT 209


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 88/179 (49%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVVLFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------- 179
           L  P  +  ++Y V+  G+   + L  L+ G+ +        GI   D    L       
Sbjct: 98  LTQPGKRTGKIYYVQVEGEPTAEALEALRNGVTLNDGPTLPAGIEVVDEPEWLWPRTPPI 157

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +     W+ V L EG+NR+++++         RLIR + G + L  L  G  R+ +
Sbjct: 158 RERKSIPTRWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYAMGNYTLDNLANGEWRDAT 216


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEGDTSRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|322715286|gb|EFZ06857.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 231

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNCVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ V+VN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVRVNNTIAKLGDKVTLGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D DGR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 114/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V+  D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVLPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEDDTSRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|260685750|ref|YP_003216883.1| pseudouridine synthase [Clostridium difficile R20291]
 gi|260211766|emb|CBE02116.1| pseudouridine synthase [Clostridium difficile R20291]
          Length = 258

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 113/246 (45%), Gaps = 24/246 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWL-----------------YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGR 113
             L +                  +KP G ++  +D     TV D  +L  +      VGR
Sbjct: 65  IYLIMQNSVKQEPCDFSHGRFRMNKPDGYISATTDK-YDPTVLDLIDLSYLAFEPFPVGR 123

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD +TEGLL+LTNDG L+  +  P     + Y  +  G V ++ +    +G+V+    Y 
Sbjct: 124 LDKDTEGLLVLTNDGKLSHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDD-GYK 182

Query: 174 DMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
            M   L+  K  + + + + + EGK  ++K++FE    KV  L R+S G  +L  +L  G
Sbjct: 183 TMPSQLNILKSDDESEIELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELG 242

Query: 232 STREVS 237
             RE++
Sbjct: 243 EYRELT 248


>gi|315617385|gb|EFU97991.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           3431]
          Length = 290

 Score = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D  GR  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTED-GGRDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 79.0 bits (193), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/188 (26%), Positives = 97/188 (51%), Gaps = 19/188 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L + +KP  +++  +  DG+ T+ + +      V + GRLD ++EGLLLLTN+G L  +
Sbjct: 4   KLIILNKPFHVLSQFTADDGKDTLANYIDD--ENVYAAGRLDYDSEGLLLLTNNGSLQHL 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  +  + Y V+  G++  D +  L +G+ ++       +     Q           
Sbjct: 62  IASPKFKMPKTYWVQVEGEITDDAIGSLCRGVELKDGMTKPAECRKIDQPNIWDRTPAVR 121

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EVS 237
                  +WV + + EGKNR+++++     +   RLIR S GP+ + +L +G ++  E++
Sbjct: 122 YRANIPTSWVALTITEGKNRQVRRMTAAVGFPTLRLIRYSIGPYTVDSLRSGESKIAELT 181

Query: 238 KKILREQL 245
            + LREQ+
Sbjct: 182 SQ-LREQV 188


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 100/219 (45%), Gaps = 8/219 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  R
Sbjct: 2   RLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   D     T+ D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATVDTQ-HPTILDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY V     +D+        G+    + I     Q+TL   + +   +  
Sbjct: 121 LTQPQNKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSARLTIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EG+  ++K++F  FN KV RL R + G   L   LA
Sbjct: 180 ---EGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALA 215


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 84/169 (49%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 93  LFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQARLTE 150

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P  +  + Y V+  G   +D L  L++G+ +  G+        +D+             +
Sbjct: 151 PKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIWPRNPPVRERK 210

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + +  L +G
Sbjct: 211 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSIDNLPSG 259


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T + L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  THVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 216


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 95/182 (52%), Gaps = 17/182 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AER ++ +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG 
Sbjct: 53  AER-KIIIFNKPYDTLSQFTDGEGRKTLADFIP--VKEVYAAGRLDRDSEGLMVLTNDGI 109

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ----- 182
           L   L  P ++  + Y V+  G   + +L  L++G+ ++ G+     +++  D Q     
Sbjct: 110 LQAKLTQPKSKSPKTYWVQVEGAPTEAQLEPLRRGVELKDGLTLPAQVEIIQDPQLWERN 169

Query: 183 -------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                       W+ + + EG+NR+++++     +   RL+R S G   L  L  G  +E
Sbjct: 170 PPVRFRAAIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGMTLQDLQPGEWKE 229

Query: 236 VS 237
           +S
Sbjct: 230 IS 231


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD +  L+ G+ +        G    D    L      
Sbjct: 97  RLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 156

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 216

Query: 238 K 238
           +
Sbjct: 217 E 217


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/241 (29%), Positives = 116/241 (48%), Gaps = 31/241 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+SK ++  G+ SRRE +  I +  V V+G       V+++ T       + LR A    
Sbjct: 5   RLSKRMSELGLCSRREADSYIEKGWVDVDG-----ETVSLLGTKVYPNQQITLRTAAQVV 59

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGR--STVFDNL--------PSIFSR-----VISVGR 113
             ER  + L +KP+G V+  ++   +  S + D          P  F R     +   GR
Sbjct: 60  QHERVTI-LINKPVGYVSGQAEHGYKPASALLDEATHWKDDPSPIKFHRSQFIGLAPAGR 118

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI+++GLL+LT DG +A+ L    ++  + Y VR  G+++   L LL +G+ + G    
Sbjct: 119 LDIDSQGLLILTQDGRVAKQLIGEDSKVDKEYLVRVQGKLESSGLALLCQGLKLDGEYLK 178

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V+   +      +   LREGK R+I+++ E     V  L RI  G  +LG L AG  
Sbjct: 179 PAKVSWQNEDQ----LRFVLREGKKRQIRRMCELVGLTVTGLKRIRIGKIKLGLLPAGQW 234

Query: 234 R 234
           R
Sbjct: 235 R 235


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 104/220 (47%), Gaps = 14/220 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++     +R +V+  I + RV  NG++++     V    D I +DG P+   E  
Sbjct: 6   RLDKYLSDMTSETRSKVKEYIRKGRVTANGVVIKSPETKVDTDNDEICIDGKPVGYVEY- 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRS-TVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             ++ +KP G++T  S   GR+ TV D           F+ +  VGRLD +TEGLLL+TN
Sbjct: 65  YYYMMNKPQGVIT--STEKGRTKTVMDVFKETGTGCPRFNELSPVGRLDKDTEGLLLITN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGS 185
           DG L   L  P     +VY       V    + +   G+ +   IC        D  K  
Sbjct: 123 DGELNHKLLSPKNHVDKVYYAELKSPVKVSDIEIFAGGLDLGDFICKPARLEICDDVKKF 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            A +T+   EGK  ++K++FE    +V  L R+S G  +L
Sbjct: 183 AAKITIS--EGKFHQVKRMFEAVENEVIYLKRLSMGSLKL 220


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 115/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V   D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFING---KRAAIGDQVAPGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D   +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDGE-RDNIVD-FVNHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  D +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPITDDFIRGMGAGVPI----LGTVTKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERTRIMNVSLSGIPLGEWRDLNGDELIE 231


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|310765941|gb|ADP10891.1| 23S rRNA pseudouridine synthase F [Erwinia sp. Ejp617]
          Length = 292

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 117/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I  +GI SRR+ +R I Q  V +NG   +RA+V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGNVFING---KRASVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   +   +KP+G+++T  + + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVVIALNKPVGIISTTEEGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G      +V     K S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTKKCKV----NKESTFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V++L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYEVSKLERTRIMNISLKGLPPGEWRDLTDDELIE 231


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 116/229 (50%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +R+I + +V +NG + E+    V   D ++VDG  + K+ + +
Sbjct: 4   RINKYLSEVGYCSRRVADRLIEEGKVVINGKIPEKGT-KVEEGDQVKVDGQRIEKSTKQK 62

Query: 75  -LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 129
            ++L ++KP+G+V T      R    DN+       +R+  +GRLD  +EGL+ LTNDG 
Sbjct: 63  NIYLAFNKPVGIVCTTD----RRVEHDNIIDFIKYPTRIFPIGRLDKPSEGLIFLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  +++D +  +  G+ I      +  V    Q G+  + 
Sbjct: 119 IVNKILRARNNHEKEYIVSVNRPINRDFIQSMSNGVEILETITKNCFV---KQLGAKKFK 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + L +G NR+I+++ E   ++V  L R+     +L   + G  RE +K
Sbjct: 176 II-LTQGLNRQIRRMCESLGYRVESLKRVRIMNIKLDVPI-GKYREFTK 222


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|329577701|gb|EGG59128.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 197

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 61/188 (32%), Positives = 100/188 (53%), Gaps = 5/188 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134
           + +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L   L
Sbjct: 1   MLNKPKGVVSAVSDAS-KKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGYQL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGL 193
             P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + + V + +
Sbjct: 60  IRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFLTI 119

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHLLEE 252
           +EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +E+
Sbjct: 120 QEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFIEK 179

Query: 253 AQVNLDAP 260
            Q +   P
Sbjct: 180 QQTSKALP 187


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 94/182 (51%), Gaps = 20/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L+L++KP  ++T  SD  GR+T+  F ++P I+      GRLD ++EGLLLLTNDG L  
Sbjct: 35  LFLFNKPFDVLTQFSDEGGRATLKDFIDIPGIYP----AGRLDRDSEGLLLLTNDGQLQA 90

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT---------- 181
            +  P  +  + Y V+  G+ ++ +L  L+ G+ +  G         L+           
Sbjct: 91  RIADPKHKLAKTYWVQVEGEPNEAQLQQLRDGVQLNDGPTLPAEARQLEEPQLWPRNPPV 150

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    +W+ + ++EG+NR+++++         RL+R+  G + L  L  G  REV+ 
Sbjct: 151 RFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRVKIGNWTLDGLDQGQYREVAA 210

Query: 239 KI 240
           ++
Sbjct: 211 QL 212


>gi|52426397|ref|YP_089534.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52308449|gb|AAU38949.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 247

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 92/179 (51%), Gaps = 21/179 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T++ L++KP  ++T  +D +GR+T+  F ++P +++     GRLD ++EGLL+LTN+G +
Sbjct: 54  TQVILFNKPFDVLTQFTDENGRATLKDFIHIPDVYA----AGRLDRDSEGLLILTNNGEI 109

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P  +  + Y V+  G+  +  L  L++G+ ++       +V L  Q        
Sbjct: 110 QHRLADPKFKMEKTYFVQVEGEPTETDLAKLRQGVELKDGMTRPAKVRLIAQPDFIWQRT 169

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                      +W+ + + EGKNR+++++     +   RLIR +   F L  L  GS R
Sbjct: 170 PPIRERKSIPTSWLEIKISEGKNRQVRRMTANIGFPTLRLIRYAVSSFTLDNLANGSYR 228


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 105/226 (46%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + +   +V VNG++ + +A  +   D I  DG PL   +  +
Sbjct: 2   RLDKFIAENTGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICFDGEPLAWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP   V +H D D   TVF      + +++   GRLD +T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQNCVCSHDDGD-YPTVFQFFDYPLTTKLHCAGRLDADTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+        +GI+++G        TL+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYATQFAEGILLRGEKTLTKPATLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            EG+  ++K++F     KV  L R   G   L  TL  G  R +++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGNVVLDETLAEGEFRALTE 224


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENRWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|323967074|gb|EGB62500.1| RNA pseudouridylate synthase [Escherichia coli M863]
          Length = 217

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   QD L  L+ G+ +     +  G   V            
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 156

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 216


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 114/246 (46%), Gaps = 31/246 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++A+ G+ SRRE E  I    V V+G  ++   + V     + +D    R   +  
Sbjct: 45  RLAKLMAQKGLCSRREAEAYIQAGDVLVDGERVQADWLKVPVDSDVSLDFRAQRHQNKKV 104

Query: 75  LWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRV--------------ISVGRLDI 116
             + +KP+G V++  +    P  R   F+N     SRV                 GRLD+
Sbjct: 105 TLVLNKPLGYVSSQPELNKTPAVRLLTFENECQELSRVKPRQNVEPVALWKMAVCGRLDV 164

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVI-QG 169
           N+ GLLL T DG +A+ L  P     + Y VR    +D      + K+ +L+ G+   +G
Sbjct: 165 NSTGLLLFTQDGTVAKKLLDPKGGIEKEYLVRVDLNLDPLTDKIRRKIEVLQAGVTSDEG 224

Query: 170 ICYGDMQVTLDTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           I Y    V +      NA  + V L EGKNR I+++ E    +V  L R+  G  +LG+L
Sbjct: 225 ITYRAKSVEI-----LNANQLRVVLTEGKNRHIRRMCEHVGLRVMALKRVRIGGVKLGSL 279

Query: 229 LAGSTR 234
             G  R
Sbjct: 280 PVGQWR 285


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 70/248 (28%), Positives = 116/248 (46%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMST-------DHIEVDGVP 66
           R++K +A  G  SRR   R+I   +V++N  L     +V+++ T       + I V+   
Sbjct: 2   RLAKYLALTGCCSRRAATRLIRDGQVRINDRLANHVDSVSLIDTPEGQRSAEQIYVNDEL 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTE 119
           +   E    WL++K +G        D R  +  +LP+          R+  +GRLD ++ 
Sbjct: 62  VCPIEAKAYWLFNKSVG-------TDSR--LLAHLPNSLIHLLPETPRLYPIGRLDKDSR 112

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-QVT 178
           GLL+LTNDG L   L  P     + Y    H Q+D+D  +     +   G+ Y D+  + 
Sbjct: 113 GLLILTNDGELTHKLMHPDFGHAKTY----HVQLDRDFDDAFLASMA-AGVSYKDVTTLP 167

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q+ +     + L +G NR+I+++ +   +KV  L R+S    QLG L  GS R +S 
Sbjct: 168 CIMQRLAADKYQITLTQGLNRQIRRMSQALGFKVIDLKRVSIQSLQLGDLAEGSMRPLSS 227

Query: 239 KILREQLG 246
             L + L 
Sbjct: 228 AELADLLA 235


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENHWEGDTGRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            QV    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWLEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 98  LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 158 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 217

Query: 239 K 239
           +
Sbjct: 218 E 218


>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 = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++   ++  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRANRVTVDGEIVRNAAFKLLPEHNVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGIMLDADLAPGEYRPLTEE 225


>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 = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 116/232 (50%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+  ++A+  I SR+ +++ + +  + V+       A N+      +   G  ++  E T
Sbjct: 2   RLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQGRIIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT + D     TV D LP      ++ +VGRLD +T GLLL+T++G L 
Sbjct: 61  YLML-HKPAGVVTANKDKK-LPTVMDFLPPDIQSDKLYAVGRLDRDTTGLLLVTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  +
Sbjct: 119 FQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTVCKAARLEILSASPSLSQAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDDNLQAGDYRPLNSEEL 230


>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 = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--MSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV V     D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRAAVGVQVFPGDVVKVNGQTIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+LLTN G L
Sbjct: 65  EDLVLIALNKPVGVISTTEDGEQNNIV--DFVNHSKRVFPIGRLDKDSQGLILLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G      +V  +    S     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKVKKE----STFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R+      L  L  G  R++++  L E
Sbjct: 179 ITLVQGLNRQIRRMTKHFGYEVTKLERVRIMNISLKGLPQGEWRDLTEDELIE 231


>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 = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 112/238 (47%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPESDVRFDGNPLQQTLGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     V +D       G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEHPVAEDTAQRFADGVQL----HNETSLTKPAQLEIIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           L EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 178 LSEGRYHQVKRMFGAVGNRVLALHRERIGAMKLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 = 78.6 bits (192), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVNPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFVTGMAAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIE 231


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 86/174 (49%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 59  IFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 116

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P ++  + Y V+  G   +  L  L+KG+ ++ G+        +D               
Sbjct: 117 PKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAPTIWERNPPVRFRA 176

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RL+R S G   LG L  G  +E+
Sbjct: 177 NIPTTWLAITIVEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGGLQPGQWKEI 230


>gi|332342737|gb|AEE56071.1| ribosomal pseudouridine synthase, large subunit [Escherichia coli
           UMNK88]
          Length = 207

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------ 179
            L  P  +  ++Y V+  G   QD +  L+ G+ +        G    D    L      
Sbjct: 87  RLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 146

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREAT 206

Query: 238 K 238
           +
Sbjct: 207 E 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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP G++   +D  GR T+ + +P     V + GRLD ++EGLL L++DG L   
Sbjct: 25  RLILLNKPYGVLPQFTDDQGRPTLAELVP--VKGVYAAGRLDRDSEGLLALSDDGPLIAR 82

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P+++  + Y V+  G    + L  L++G+ ++       +V    +           
Sbjct: 83  IAAPASKMPKTYWVQVEGVPTDEALEALRRGVTLKDGPTLPAEVRRMEEPDPLWPRDPPV 142

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                   +W+ + LREG+NR+++++     +   RLIR S G + L  L  G  REV +
Sbjct: 143 RYRAAIPTSWIALTLREGRNRQVRRMTAAVGFPTLRLIRWSIGDWTLDGLAPGQWREVPQ 202


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 89/185 (48%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  RENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
           G L   L  P  +  ++Y V+  G    + LN L+ G+ +         V L  +     
Sbjct: 92  GALQARLTQPGKRTGKIYFVQVEGDPTAEALNALRNGVTLNDGPTLPAGVELVAEPDWLW 151

Query: 185 ------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                          W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKTIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGE 211

Query: 233 TREVS 237
            R+++
Sbjct: 212 WRDIT 216


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 118/248 (47%), Gaps = 38/248 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+SK ++  G+ SRRE +  I++  VKV+G ++      V     I +D    RKA    
Sbjct: 10  RLSKRMSELGLCSRREADEWISKGWVKVDGQVVSELGSKVRPDQKITID----RKAKDQQ 65

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNL------PSIFSRVISVGR 113
            ER  + + +KP+G V+  ++ DG          R+   D+       PS    ++  GR
Sbjct: 66  NERVTI-ILNKPLGYVSGQAE-DGHEPARILITPRNRWIDDPSPRRFNPSQLKSLVPAGR 123

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV-----RFHGQVDQDKLNLLKKGIV 166
           LDIN+ GLL+LT DG +A+ +  E  S +   + RV     R + +    KL LL  G+ 
Sbjct: 124 LDINSTGLLVLTQDGRIAKTIIGENSSVEKEYIVRVAMTDGRSNSEFPPAKLALLNHGLE 183

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   +      +   LREG+NR+I+++ +    KV  L R+  G   LG
Sbjct: 184 LDGKPLEKAEVSWLNEDQ----LKFVLREGRNRQIRRMCDLVGLKVLALKRVRVGNIPLG 239

Query: 227 TLLAGSTR 234
            L  G  R
Sbjct: 240 NLPVGKWR 247


>gi|242239490|ref|YP_002987671.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242131547|gb|ACS85849.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 208

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 53/190 (27%), Positives = 94/190 (49%), Gaps = 19/190 (10%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V  +P+ +A R  + L++KP  +++  +D  GR T+ + +P  F  + S GRLD ++EGL
Sbjct: 20  VKSIPIGQARR--IVLFNKPFDVLSQFTDESGRETLKNYIP--FGDIYSAGRLDRDSEGL 75

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGD 174
           +LLTNDG L   L  P  +  ++Y  +  G  D+  L   + G+ +        G    D
Sbjct: 76  MLLTNDGKLQARLTQPGKKTPKIYYAQIEGIPDEAALQAFRTGLQLNDGLTQPAGAERVD 135

Query: 175 MQVTL--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
             + L        + ++   +W+ + L EG+NR+++++     +   RLIR S     L 
Sbjct: 136 APLWLWPRNPPIRERKQIPTSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYSMANHTLD 195

Query: 227 TLLAGSTREV 236
            L  G  +E+
Sbjct: 196 GLQPGEWKEI 205


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 111/225 (49%), Gaps = 9/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRRE +R+I + +V +NG  + +    V  +D +EV G  ++K   ++
Sbjct: 4   RINKYLSEVGYCSRREADRLIHEGKVTING-KIPKIGSKVEESDQVEVKGQRIKKITGQK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDRKVEPNNVIDFIKYP-KRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ + Q++ D +  +  G+ I      +  V    Q G   +  + 
Sbjct: 122 KILRARNNHEKEYIVKVNRQINSDFIQSMSSGVEILDTITKNCFV---KQLGPKKFKII- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +
Sbjct: 178 LTQGLNRQIRRMCESLGYRVRSLKRVRIMNIEL-DVSTGKYREFT 221


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 111/233 (47%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ + +   GI SR E+++ +   RVK+NG   + +   V +  D I  D   +   E T
Sbjct: 4   RIDRFLCHMGIGSRSEIKKYLKTCRVKLNGKFEKNSNTQVDIEKDEILFDDEIVIYKEFT 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP   ++   D     TV D L   +S   +  VGRLDI+T G L+LTNDG  +
Sbjct: 64  YLML-NKPKDFISATFDT-KLPTVLDLLEFPYSNMELFPVGRLDIDTTGFLILTNDGKFS 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + Y V    ++  +++  L+ GI  +   +      +  +K S   + +
Sbjct: 122 YNVTNPKKKVNKKYFVTLRDEIISEQIEKLENGIYFEKEDFTTENAKV--EKISEKEINL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + EGK  ++K++ E+   +V  L ++  G   L  +L  G  RE++   L E
Sbjct: 180 TISEGKFHQVKRMLEYVENEVVELKKVCIGNLNLDDSLKLGEYREITNSELEE 232


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/226 (29%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ ++VN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNNTIAKLGDKVTLGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D DGR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDVDGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 90/181 (49%), Gaps = 26/181 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +R+ L++KP G++    DPDG  T+ D  ++P +++     GRLD ++EGLL+LT+DG L
Sbjct: 2   SRVILFNKPCGVLCQFRDPDGVPTLGDYIDVPDVYA----AGRLDKDSEGLLVLTDDGRL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--------------------GI 170
              +  P  +  + Y V+  G+   + L  L++G+ ++                    G 
Sbjct: 58  QNRITSPENKLPKTYWVQVEGEPSDEALKQLRRGVHLKDGKTRRADVKRMAGEPLSEHGG 117

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            +         +     W+++ L+EGKNR+++++         RL+R   GP+QL  L +
Sbjct: 118 LWPRNPPVRYRKSVPTCWLSITLKEGKNRQVRRMTAAVGHPTLRLVRWRIGPWQLADLAS 177

Query: 231 G 231
           G
Sbjct: 178 G 178


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 91/187 (48%), Gaps = 19/187 (10%)

Query: 68  RKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           RK E   TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LT
Sbjct: 31  RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLT 88

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------ 179
           N+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +         V L      
Sbjct: 89  NNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVDLVEEPEW 148

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  
Sbjct: 149 LWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTANVGFPTLRLIRYAMGDYSLDNLAN 208

Query: 231 GSTREVS 237
           G  RE +
Sbjct: 209 GEWREAT 215


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 95/185 (51%), Gaps = 16/185 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGLL+LT
Sbjct: 60  PKVAPEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLLVLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ- 182
           NDG     L  P+++  + Y V+  G   +  L+ L+KG+ ++ G+    +++V  + Q 
Sbjct: 118 NDGIFQAKLTQPNSKSTKTYWVQVEGAPSEKDLDKLRKGVELKDGMTLPAEVEVMQEPQV 177

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RLIR S G   +G L  G
Sbjct: 178 WERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMDVGQLQPG 237

Query: 232 STREV 236
             +++
Sbjct: 238 EWKDI 242


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 89/181 (49%), Gaps = 16/181 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG 
Sbjct: 54  PEDRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGI 111

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
           L   L  P ++  + Y V+  G   ++ L  L+KG+ ++       +V +  +       
Sbjct: 112 LQAKLTQPQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGMTLPAKVEVMPEPEIWDRT 171

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                       W+ + + EG+NR+++++     +   RL+R S G   L  L  G  RE
Sbjct: 172 PPVRFRANIPTTWLAITITEGRNRQVRRMTAHIGFPTLRLVRYSMGGIVLDDLKPGEWRE 231

Query: 236 V 236
           +
Sbjct: 232 I 232


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/232 (31%), Positives = 116/232 (50%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR++V++++  + V VNG L ++   +V  S D + V G  +   E  
Sbjct: 2   RLDKLLASSGFGSRKDVKKLVKARAVTVNGELAKQVKDHVDPSNDEVLVHGERVEYKEFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+++   D     TV D L P   +R    VGRLD +T GLLLLTNDG LA
Sbjct: 62  YLMM-NKPDGVISATEDLRD-ETVVDLLEPEDIAREPFPVGRLDKDTVGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V     +    +  L++G+VI         +V +D  +  +  + 
Sbjct: 120 HQLLSPKKHVPKTYEVHLKYPLGDQDIKRLEEGVVILDDYRTKPAKVEVDANESEDTRIR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           + + EGK  ++K + +    +V  L R S G   L   LA G  RE++ + L
Sbjct: 180 LTITEGKYHQVKLMAQAVGNEVIFLKRRSMGAVSLDEDLAPGEYRELTDEEL 231


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 110/215 (51%), Gaps = 10/215 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A +G  +R EV+R+I +  VKVNG   +   + +     +   G  + + ++  
Sbjct: 2   RLDRFLAHSGFGTRSEVKRLIKKGLVKVNGKQAKSPDLKIDEDKDVVQVGEEIVELQKRV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G V ++ DP    T+F  +P    +  + +VGRLD + EGLL++TN+G    
Sbjct: 62  YIMMNKPQGYVCSNDDPLS-PTIFSLIPENLKYRNLHTVGRLDKDAEGLLIITNNGEYTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P     + Y V+   +++++K+ + + G+V+      D   TL  +     +  V+
Sbjct: 121 KVISPKKHIEKEYIVKLEKELNREKIKVFEDGVVLD-----DGYKTLPAKYTILDDFTVS 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IK++FE    KV  L R+  G  +L
Sbjct: 176 LTIYEGKYHQIKRMFESIGNKVVYLKRVRIGRLKL 210


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 119/248 (47%), Gaps = 38/248 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+SK ++  G+ SRRE +  I++  VKV+G ++      V     I +D    RKA    
Sbjct: 10  RLSKRMSELGLCSRREADEWISKGWVKVDGQVVSELGSKVRPDQKITID----RKAQDQQ 65

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNL------PSIFSRVISVGR 113
            ER  + + +KP+G V+  ++ DG          R+   D+       PS    ++  GR
Sbjct: 66  NERVTI-ILNKPLGYVSGQAE-DGHEPARILITPRNRWIDDPSPRRFNPSQLKSLVPAGR 123

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV-----RFHGQVDQDKLNLLKKGIV 166
           LDIN+ GLL+LT DG +A+ +  E  S +   + RV     R + +    KL LL  G+ 
Sbjct: 124 LDINSTGLLVLTQDGRIAKTIIGENSSVEKEYIVRVAMTDGRSNSEFPPAKLALLNHGLE 183

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   +      +   LREG+NR+I+++ +    KV  L R+  G  +LG
Sbjct: 184 LDGKPLEKAEVSWLNEDQ----LKFVLREGRNRQIRRMCDLVGLKVLALKRVRVGNVRLG 239

Query: 227 TLLAGSTR 234
            L  G  R
Sbjct: 240 KLPVGKWR 247


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 86/174 (49%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 65  IFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 122

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P ++  + Y V+  G   +  L  L+KG+ ++ G+        +D               
Sbjct: 123 PKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAPTIWERNPPVRFRA 182

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RL+R S G   LG L  G  +E+
Sbjct: 183 NIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGDLQPGQWKEI 236


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 47/186 (25%), Positives = 92/186 (49%), Gaps = 21/186 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +R  L++KP  ++T  +DPD R T+ D  ++P ++S     GRLD ++EGLLLLT+DG L
Sbjct: 2   SRYLLFNKPFQVLTQFTDPDNRQTLADFIDVPEVYS----AGRLDYDSEGLLLLTDDGAL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---------------GICYGDM 175
              +  P  +  + Y  +  G +  + +  L+ G+ ++                  +   
Sbjct: 58  IHSMMNPRFKTPKTYLAQVEGDITDEAIRRLESGLQLKDGPTLPAKARRVSEPAWLWPRQ 117

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               +      +WV + L EG+NR+++++     +   RLIR++     + +L  G  +E
Sbjct: 118 PPIRERATIPASWVELTLVEGRNRQVRRMTAAVGFPTLRLIRVALAELTVESLSVGQYKE 177

Query: 236 VSKKIL 241
           V ++++
Sbjct: 178 VDRELI 183


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 106/217 (48%), Gaps = 4/217 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     SR++   +I+  R++V+G  +     +V     +E+D   L+     R
Sbjct: 2   RLDRFLSNFPRFSRQDSRLLISAGRLRVDGETVRDPRFDVRDFQRVELDDELLQAGRSAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            W+ HKP+G+V+  +  + R TV D L       + + GRLD+NT GLLL+TNDG  +R 
Sbjct: 62  YWMLHKPVGVVSATAHDEHR-TVLDLLDEPDRHDLHLAGRLDLNTSGLLLITNDGRWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY V     +  +   + ++G+         +   L+     +A +T  L
Sbjct: 121 ITQPQQRKPKVYHVSTEQPITAEYAEVFERGLYFAFEDLTTLPARLELLGSHSARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EG+  ++K++F  F  +V  L R S G   L   LA
Sbjct: 179 FEGRYHQVKRMFGHFRNRVVALHRESMGEIVLDPQLA 215


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRRE +R+I Q RV +NG + E     V+  D + VD  P+      
Sbjct: 6   KRLNKFISETGFCSRREADRLIEQGRVTINGKVPE-MGTKVLPGDDVCVDDKPISAVTDK 64

Query: 74  RLWL-YHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +++  +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 65  PVYIALNKPTGITCTTERDIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    + +  +  +  G+ I        +V+ +T+      +T 
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITEQFIKKMSSGVDILDTTTLPCKVSKETKFSFRIVLTQ 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GL    NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   + E
Sbjct: 182 GL----NRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGQWRYLSDDEIGEILA--MCE 235

Query: 252 EAQVNLDA 259
            +    DA
Sbjct: 236 SSSGTEDA 243


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 56/187 (29%), Positives = 92/187 (49%), Gaps = 20/187 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R  L++KP  ++T  +D +    RST+ D +P  F  +  VGRLD ++EGLLLLT+DG +
Sbjct: 4   RYILFYKPYDVLTQFTDAESENKRSTLKDYIPISF--IYPVGRLDRDSEGLLLLTDDGQM 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P     R Y V+      +D +  L+ GI IQ       +V L + +       
Sbjct: 62  QHRLSDPKFAHPRTYWVQVEKIPSEDAIAHLRSGITIQNYRTRPTKVQLLSTEPLLPPRN 121

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      AW+ + L EGKNR+++++     +   RL+R++    +L  L  G  RE
Sbjct: 122 PPIRFRKNIPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVAIAHLRLDGLEPGQWRE 181

Query: 236 VSKKILR 242
           ++ + L+
Sbjct: 182 LNPEELK 188


>gi|327253839|gb|EGE65468.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           STEC_7v]
          Length = 207

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/180 (28%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   QD L  L+ G+ +     +  G   V            
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 146

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 206


>gi|152981336|ref|YP_001353751.1| pseudouridylate synthase [Janthinobacterium sp. Marseille]
 gi|151281413|gb|ABR89823.1| pseudouridylate synthase [Janthinobacterium sp. Marseille]
          Length = 248

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 114/243 (46%), Gaps = 27/243 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK ++  G+ SRRE +  IA+  V+V+G ++      V+ T  + V+     +  +
Sbjct: 4   PLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGSKVLPTQRVTVERQAAAEQSK 63

Query: 73  TRLWLYHKPIGLVTTHSD-----------------PDGRSTVFDNLPSIFSRVISVGRLD 115
               L +KP+G V+  ++                  D  +T F   P+    ++  GRLD
Sbjct: 64  RVTVLINKPMGYVSGQAEDGYKPAVALVNASTRWSEDQAATQFH--PTQLRSLVPAGRLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGIC 171
           I++ GLL+LT DG +A+ L    T   + Y VR      G++ +  L  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 STR 234
             R
Sbjct: 238 QWR 240


>gi|328473240|gb|EGF44088.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 232

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 86/174 (49%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 59  VFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 116

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------------Q 182
           P ++  + Y V+  G   +  L  L+KG+ ++ G+        +D               
Sbjct: 117 PKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAPTIWERNPPVRFRA 176

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RL+R S G   LG L  G  +E+
Sbjct: 177 NIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGDLQPGQWKEI 230


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 105/234 (44%), Gaps = 18/234 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++A  G+ SRR+ +  IA+  V V+G  +            I +D     +  +  
Sbjct: 68  RISKLMAERGLCSRRDADDYIARGWVFVDGRRVSELGTRADPGAAITLDTAAQTQQRKQM 127

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--------FDNL------PSIFSRVISVGRLDINTEG 120
             L HKP+G V+   +P     V        F         PS    +   GRLDI++ G
Sbjct: 128 TILLHKPVGYVSGQPEPGCTPAVTLIQPERQFRTPDTPVFHPSCLRGLAPAGRLDIDSTG 187

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+LT DG +AR L    +   + Y VR  G++    L LL  G+ + G      +V   
Sbjct: 188 LLVLTQDGRVARQLIGEESTVEKEYLVRVDGRLADKDLALLNHGLSLDGRQLKPARV--- 244

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +  ++  +   LREG+ R+I+++ E    +V  L R+  G  +L  L  G  R
Sbjct: 245 -EWLNDDQLRFVLREGRKRQIRRMCELVGLRVTGLKRVRIGAVRLADLPLGQWR 297


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 71/284 (25%), Positives = 125/284 (44%), Gaps = 61/284 (21%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEV--------DGV 65
           R++K+I+     SRR+ +  I   +VK+N  ++     +V +  D + +        + +
Sbjct: 47  RLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGKDSLRIYDKKIKLTNII 106

Query: 66  PLRKAERTRL--WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTE 119
            + K    +L  W+  HKP GL+ T +D   R +++   P       R+++VGRLD NT 
Sbjct: 107 NMIKQNENKLHKWIVLHKPKGLLCTSNDEKNRKSIYTLFPEEMLQKYRLVTVGRLDRNTS 166

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------- 165
           G+LLLTND      L  P  Q +R YRV   G V  + L  L +GI              
Sbjct: 167 GVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALKELARGIYLEEDEKTQPKKIY 226

Query: 166 -----------------------------VIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
                                         I+ +    +++  DT+K +   + + ++EG
Sbjct: 227 NYKESREKSNIDDKKKKKMSKMKKKTNPAFIEILREEKIKIKEDTKKIT--VLNISIKEG 284

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKK 239
           +NR+I+K+F+  N  V ++ R S+    L  +      RE+++K
Sbjct: 285 RNRQIRKMFQQINQPVIKIKRTSFENITLKNIYFPKQYRELNQK 328


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/216 (28%), Positives = 104/216 (48%), Gaps = 7/216 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+  + +++V VNG +       +    D I      L   E  
Sbjct: 2   RLDKFLVDCGLGSRSQVKIYLKKKQVTVNGQVETSPKTQIDEKKDQIAYQSQELTH-ETF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV D L       +V  VGRLDI+T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPKGVISATEDARHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             +  P     ++Y+ +  G +D+  +   +KGI ++   C    +++    Q    + V
Sbjct: 120 HAMLSPRKHVDKIYQAKVAGVMDEADMQAFEKGIELKDHTCQPAKLEILSVDQAVKTSTV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + EGK  ++K++      +V  L R+S G   L
Sbjct: 180 QVTIAEGKFHQVKRMVAACGKEVTDLQRLSMGSLVL 215


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 102/226 (45%), Gaps = 34/226 (15%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           + R G + R   ER  A+ R + +            ST   +  G P+       + L++
Sbjct: 48  LQRGGTSERNSSERGGAKSRPQRHS-----------STTRTKPQGDPM-------IVLFN 89

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   L  P  
Sbjct: 90  KPFDVLCQFTDEQGRKTLKDYIP--IPGVYAAGRLDRDSEGLLLLTNDGQLQAKLTEPKK 147

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------DTQKGS 185
           +  + Y V+  G+  +  L  L++G+ ++       +V++              + +   
Sbjct: 148 KTFKTYWVQVEGKPTEADLAKLRQGVELKDGMTLPAKVSIMATPNVWPRNPPIRERKNIP 207

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             W+ + + EG+NR+++++     +   RLIR   G + L  L  G
Sbjct: 208 TTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATG 253


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 94/182 (51%), Gaps = 17/182 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AER ++ +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG 
Sbjct: 53  AER-KIIIFNKPYDTLSQFTDGEGRKTLADFIP--VKEVYAAGRLDRDSEGLMVLTNDGI 109

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ----- 182
           L   L  P ++  + Y V+  G   + +L  L+ G+ ++ G+     +++  D Q     
Sbjct: 110 LQAKLTQPKSKSPKTYWVQVEGAPTEAQLEPLRSGVELKDGLTLPAQVEIIQDPQLWERN 169

Query: 183 -------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                       W+ + + EG+NR+++++     +   RL+R S G   L  L  G  +E
Sbjct: 170 PPVRFRAAIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGMTLQDLQPGEWKE 229

Query: 236 VS 237
           +S
Sbjct: 230 IS 231


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/219 (29%), Positives = 105/219 (47%), Gaps = 12/219 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V+VN   ++     +   TD + VDG  +   +  
Sbjct: 2   RIDKFLANMGLGTRTEVKQLLKKGLVEVNEKKIKTPKSQIDPETDKVVVDGEEISYVDNV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G ++   D +   TV D +P  FS   +  VGRLD +TEGLLLLTNDG   
Sbjct: 62  YMML-NKPKGYISATED-NAHQTVLDLIPE-FSHLGIFPVGRLDKDTEGLLLLTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVT 190
             L  P     + Y V     + Q  +   K G+ +      D +V   +  KG++    
Sbjct: 119 HELMSPKKHVSKTYEVISKYPIKQSDIEAFKLGVEL-----SDGKVKPAELIKGNDRLSY 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           V + EGK  ++K++F     +V  L R+     +L   L
Sbjct: 174 VTIYEGKYHQVKRMFHSIENEVLELKRVKIANLELDKTL 212


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 86/186 (46%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P R     ++ L++KP  ++T  S   G  T+ D +      +   GRLD ++EGLL+LT
Sbjct: 26  PKRPRGPQKIILFNKPFNVLTQFSGEPGDKTLADYI--SIKDIYPAGRLDKDSEGLLVLT 83

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------------QGIC 171
           NDG L   L  P ++  + Y V+  G    D L  L+KG+ +              Q + 
Sbjct: 84  NDGILQARLTQPQSKQPKTYWVQVEGAPSDDDLEQLRKGVTLKDGLTLPADIERMEQPVI 143

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +       + +     W+ + LREG+NR+++++     +   RLIR     + +  L  G
Sbjct: 144 WDRTPPIRERKNIPTTWLALTLREGRNRQVRRMTAHIGFPTLRLIRYKMADWTVDDLAPG 203

Query: 232 STREVS 237
             REV+
Sbjct: 204 EWREVT 209


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/237 (24%), Positives = 111/237 (46%), Gaps = 3/237 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D       G+ +           L+  +     V + L 
Sbjct: 122 TSPRHHCEKTYLVTLEHPLADDTAQQFTDGVQLHNEESLTKPARLEVIEPQ--LVRLTLS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHLL 250
           EG+  ++K++F     +V  L R   G  +L   LA G  R ++++ +     PHLL
Sbjct: 180 EGRYHQVKRMFAAVGNRVLELHRERIGEIKLDDDLAPGEYRPLTEEEIASVGAPHLL 236


>gi|323527102|ref|YP_004229255.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323384104|gb|ADX56195.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 239

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 97/220 (44%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +  + D      VDGV     ER
Sbjct: 3   LESILFSQGFGSRRQCRALIVDARVSIDGTVCADADADFPAGDAAFCFSVDGVVWPYRER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  +VY       +D  +L LL+ G+++ G         +D +      + 
Sbjct: 121 VHTFTSPKRKVPKVYVATTRHPLDDAQLGLLRHGVLLHG--ESKPVAAVDAEARGEHSLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++      +   L R   G   L   LA
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPATLA 218


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 96/183 (52%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T + L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETTVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 70/219 (31%), Positives = 109/219 (49%), Gaps = 7/219 (3%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHK 80
           A+ GI +++ V  ++A+ +V V+G +       +    H+ +DG  L+    + + LY K
Sbjct: 14  AKTGI-NKKHVRLLLAKGQVLVDGEVARDIDQIIDEFSHVCLDGKVLQANAPSYVMLY-K 71

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARVLELPST 139
           P+G+V+   D D   TV D L       +  VGRLD+NT GLLLLTNDG  ++ L  P  
Sbjct: 72  PVGVVSATVD-DKHRTVIDLLERDDKHSLHIVGRLDLNTSGLLLLTNDGRWSKKLMSPDH 130

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +  +VYRV     +D+  +     G+             L+      A VT  L EG+  
Sbjct: 131 KVGKVYRVTLKNPIDESYIAAFAGGMYFAFEDITTQPAKLEIVDEHTALVT--LVEGRYH 188

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +IK++F  F   V  L R+S G  +L   LA G +R++S
Sbjct: 189 QIKRMFGRFRNPVIGLHRLSVGAIELDPQLAVGQSRDLS 227


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  + R +  QRV V+G +++  A  +     +  DG PL +    R
Sbjct: 2   RLDKFLSQQLGISRSLIARELRAQRVTVDGDVIKNGAFKLAPEHQVAFDGNPLVQQTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPQGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     ++         GI + G         L+      A +T+   
Sbjct: 122 TSPKHHCEKTYLVALDRPIEPGTAEHFAAGIQLNGEKELTKPAVLEVLDEQLARLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L  +L  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVTALHRERIGAIVLDSSLEPGEYRALTQE 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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 105/232 (45%), Gaps = 11/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE +  I+  +V VNG ++      V   D +  DG  +    +  
Sbjct: 54  RLNKYIANSGICSRREADLYISTGQVTVNGEIINEMGFKVNLDDDVRFDGRRINPEAKAY 113

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP G   T S+  G + +     S  SR+  VGRL  N  GLLL TND  + + L
Sbjct: 114 VLL-NKPKGFSVTTSNAKGMTVMDLVASSTKSRIQPVGRLGRNATGLLLFTNDDKVMKKL 172

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVG 192
               T   R++ +     +  + L+ +KKG+ + G  +   D+       K     V + 
Sbjct: 173 TNSKTGLPRLFHIELDKNLKAEDLDKIKKGLTVDGKRLEIEDLSYVDGAPK---KEVGLK 229

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +R   N  I+ +FE   ++V R+  +  G      L  G  R      L+EQ
Sbjct: 230 MRNVGNSIIRSIFEHLGYQVVRVDCVILGTLTKKDLPRGKYRH-----LKEQ 276


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEMVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/175 (28%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 61  IFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 118

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQK------------ 183
           P ++  + Y V+  G   ++ L  L+KG+ ++ GI    +   +   +            
Sbjct: 119 PQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGITLPAIVEVMPEPEIWERNPPVRFRA 178

Query: 184 -GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + + EG+NR+++++     +   RL+R S G   L  L  G  RE++
Sbjct: 179 NIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGSIVLDNLKPGEWREIN 233


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 104/230 (45%), Gaps = 3/230 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL + 
Sbjct: 30  ITHMRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQ 89

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  
Sbjct: 90  HGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQW 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P     + Y V     V  D      KG+ +      D+      +  +   V 
Sbjct: 150 SHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVR 207

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + + EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 208 LTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 257


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 107/235 (45%), Gaps = 19/235 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++A  G+ SRRE +  I +  V+V+G+++            I +D    R+     
Sbjct: 5   RISKLMAERGLCSRREADAYIERGWVRVDGVVVSELGSKAWPDQKITLDKQAQRRQTSRV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV----------FDNLPSIFS-----RVISVGRLDINTE 119
             L +KP+G V+  ++   R  V           D  P  F       +   GRLDI+++
Sbjct: 65  TILLNKPVGYVSGQAEQGYRPAVSLISASTRYRVDKSPLKFEPGHLRGLAPAGRLDIDSQ 124

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +AR L    ++  + Y VR  G++  + L  L  G+ + G       V  
Sbjct: 125 GLLVLTQDGRIARQLINEDSEIDKEYLVRVQGKIAGNGLAQLNFGLSLDGKPLRRAHVEW 184

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +      +   L+EGK R+I+++ E    KV  L R+  G   LG L  G  R
Sbjct: 185 QNED----QLRFVLQEGKKRQIRRMCEQVGLKVIGLKRVRMGRIVLGDLPPGQWR 235


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/183 (26%), Positives = 96/183 (52%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 30  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 86  ELQHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWER 145

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+  G   +  L  GS R
Sbjct: 146 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVGMGSLSINGLANGSFR 205

Query: 235 EVS 237
            +S
Sbjct: 206 LLS 208


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 108/236 (45%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRV 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D       G+ +           LD  +     +T+   
Sbjct: 122 TSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLHNEKSLTKPAQLDVIEPQRVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G   L   LA G  R ++ + +     PHL
Sbjct: 180 EGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 105/229 (45%), Gaps = 31/229 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
           E  +L L +KP  ++   +D  GR T+ D +  P I++     GRLD ++EGLLLLTNDG
Sbjct: 41  EDRKLLLLNKPYMVLCQFTDEAGRETLKDYIKEPGIYA----AGRLDRDSEGLLLLTNDG 96

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------ 181
            L   L  P  +  + Y V+  G   ++KL  L+ G+ +  G+        +D       
Sbjct: 97  KLQARLTQPGEKTPKTYWVQVEGIPSEEKLAALRAGVELNDGMTLPAGARIMDEPAVWPR 156

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  ++   +W+ + + EG+NR+++++         RLIR + G + L  L  G +R
Sbjct: 157 NPPIRERKEIPTSWLEIKIIEGRNRQVRRMTAHIGHPTLRLIRYAIGDWTLDGLAPGESR 216

Query: 235 EVSKKIL-----------REQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
            +    L             + G H  + A+   DAP  +S+    +RP
Sbjct: 217 SLPAPELTPSSSRSPRPASSRSGAHTAKPAKPAGDAPRRASQPRQDERP 265


>gi|320667979|gb|EFX34882.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 231

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D  +   KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTADQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 89/176 (50%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  ++   +D  GR T+ + +P   S V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   IFNKPFDVLPQFTDEQGRETLKNYIP--VSDVYAAGRLDRDSEGLLVLTNDGKLQAELTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  +VY  +  G  D+  L   ++G+ +        GI   D    L        + 
Sbjct: 61  PQKKTGKVYYAQVEGVPDETALAKFRQGLTLNDGPTLPAGIERVDEPEWLWVRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR S G F L  L +G  +EV+
Sbjct: 121 KNIPTSWLKITLYEGRNRQVRRMTANIGFPTLRLIRYSMGSFTLNNLSSGEWKEVT 176


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/191 (26%), Positives = 93/191 (48%), Gaps = 20/191 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++L L++KP   +   +  +G ST+ D  ++P ++      GRLD ++EGLLLLT+DG L
Sbjct: 2   SKLVLFNKPFNTLCQFTGENGDSTLADYIDIPEVYP----AGRLDKDSEGLLLLTDDGQL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              +  P  +  + Y V+  G  + ++L  L+ G++IQ       +V L           
Sbjct: 58  QNQIASPKHKMEKTYWVQVEGVPEDNELEPLRLGVIIQNYKTKPAKVRLLETPEVWPRNP 117

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EGKNR+++++     +   RLIR   G +QL  L  G  + +
Sbjct: 118 PIRERKNIPTSWLEITISEGKNRQVRRMTAAVGFPTLRLIRAQIGQWQLDDLKVGEYKVI 177

Query: 237 SKKILREQLGP 247
                +   GP
Sbjct: 178 EVSTPKAMAGP 188


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/212 (28%), Positives = 110/212 (51%), Gaps = 13/212 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--V 65
           N +  R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V++ D ++V+G  +
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVYLNG---KRAAVGDQVVAGDTVKVNGQLI 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             ++A+     + +KP+G+V+T    +  + V     S+  R+  +GRLD +++GL+ LT
Sbjct: 60  EPKEADDFVFIVLNKPVGIVSTTESSEKNNIVDFVRHSV--RIFPIGRLDKDSQGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G L   +        + Y V  +  +    +  L  G+ +     G M       K +
Sbjct: 118 NNGDLVNKVLRAGNNHEKDYVVTVNKPITDSFIEGLAGGVPM----LGKMTKKCPVTKVA 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
                + L +G NR+I+++ E F ++V +L R
Sbjct: 174 PNVFNITLVQGLNRQIRRMCEHFGYEVVKLER 205


>gi|301169983|emb|CBW29587.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus influenzae
           10810]
          Length = 232

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 108/226 (47%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENVGLTRSQATKAIHQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            EG+  ++K++F     KV  L R   G   L  +L  G  R +++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRSLTQ 224


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 109/229 (47%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R E + ++++ RV+VNG + ++    +  +D + VDG  L   +   
Sbjct: 2   RLDKYLAETAQCTRSEAKALLSKGRVQVNGAVCKKGDTQLKESDTVAVDGRALSYQQFVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DG  A 
Sbjct: 62  IML-NKPEGVVSASTDKR-DTTVVDLVGDAYPRRQLFPAGRLDKTSTGFVLLTDDGTFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V     + ++       G+ +  G      +VT  +  G    V V
Sbjct: 120 DILAPKRHVSKTYTVVLDTPLTEEMRTGFAAGVTLADGTALSPAEVTALSADGCT--VRV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            L++G   +IK++F  +   VN L R + G   L   LA G  RE+S +
Sbjct: 178 VLKQGVYHQIKRMFGVYGAGVNGLHRDAIGGLALDPALAPGQWRELSAE 226


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 146

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWREAT 206


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +  
Sbjct: 36  THMRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQH 95

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +
Sbjct: 96  GPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWS 155

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     V  D      KG+ +      D+      +  +   V +
Sbjct: 156 HRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRL 213

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            + EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 214 TISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 262


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDCDSEGLLVLTNDGVLQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 115/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R++
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPRES 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRPGNDHEKEYLVTVDKPITDEFIRGMGPGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|325181472|emb|CCA15906.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 246

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 109/235 (46%), Gaps = 27/235 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V++  +P  +  +               +   P   S++   GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGDMQV- 177
           T DG LA+ +  P+    + Y VR    +++D       ++ L++G +   ICY    V 
Sbjct: 121 TQDGVLAKQILDPNGGVEKEYLVRVDMDLERDTKQAEEVVDKLREGFIWNDICYRARSVR 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            L+  +     +   L EGK R I+ + E    KV  L R+  G  +LG L  G+
Sbjct: 181 VLNANQ-----LQFILTEGKKRHIRYMCEAVGIKVIALKRVRIGNIRLGALPVGN 230


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 112/240 (46%), Gaps = 11/240 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRV 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAWVT 190
             P     + Y V     +  D       G+ +    Y +  +T    LD  +     +T
Sbjct: 122 TSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQL----YNEKSLTKPAQLDVIEPQRVRLT 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           +   EG+  ++K++F     +V  L R   G   L   LA G  R ++ + +     PHL
Sbjct: 178 IS--EGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTTEEIASVGAPHL 235


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 52/177 (29%), Positives = 87/177 (49%), Gaps = 17/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +    + V + GRLD ++EGL++LTNDG L   L  
Sbjct: 46  LFNKPFDVLPQFTDEAGRRTLKDFV--SVADVYAAGRLDRDSEGLMVLTNDGALQAALTQ 103

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------------VIQGICYGDMQVTLDTQ 182
           P  +  +VY V+  G   +  L  L+ G+              V +       Q  +  +
Sbjct: 104 PGKRTGKVYYVQVEGDPQEADLQPLRDGVNLKDGMTLPAGVEKVAEPAWLWPRQPPIRER 163

Query: 183 KG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           K     W+ V L EG+NR+++++     +   RLIR + G + L  L +G  RE+S+
Sbjct: 164 KNIPTQWLKVTLYEGRNRQVRRMTAHIGFPTLRLIRYAMGSYSLDDLASGMWREISE 220


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWREAT 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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL      R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLALQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTEDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 225


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 92/180 (51%), Gaps = 21/180 (11%)

Query: 77  LYHKPIGLVTTHSDPD-----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L +KP  +++  +D +      R T+ D L +   RV   GRLD ++EGLLLLTNDG L 
Sbjct: 6   LINKPFRVLSQFTDREQTSRGPRKTLADYLSAPGFRV--AGRLDYDSEGLLLLTNDGVLQ 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
           + +  P  +  + Y V+  G V+ + L  L KG+ ++       + T  ++         
Sbjct: 64  QRIANPRHKQWKTYWVQIEGAVNNEILGQLMKGVELKDGPTQPCKATAISEPALWSRDPP 123

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   ++W+ + LREG+NR+I+++     +   RL+R + GP+QL TL  G  R ++
Sbjct: 124 VRYRRNVPDSWIEMSLREGRNRQIRRMTAAVGFPTLRLVRRAIGPWQLDTLRPGEHRRLT 183


>gi|301169411|emb|CBW29011.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 240

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 96/183 (52%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN G
Sbjct: 49  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNHG 104

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 105 ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 164

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 165 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFR 224

Query: 235 EVS 237
            +S
Sbjct: 225 LLS 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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 109/226 (48%), Gaps = 10/226 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + ++++  G   R+EV  ++AQ R+ ++G   +     V     + +D   L +A + R 
Sbjct: 1   MDRLVSERGGVHRKEVRLLLAQGRIHIDGRPADSINQAVGPFTRVTLDARVL-QANKARY 59

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARVL 134
            + HKP G+V+   D   + TV D L   +S  +  VGRLD N+ GL+LLTNDG  +R L
Sbjct: 60  VMLHKPSGVVSATRDKQHK-TVIDLLSVPYSSELHIVGRLDFNSTGLMLLTNDGRWSRSL 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P     + YRV     +D   +     G+    +G+     ++ +  Q  +     V 
Sbjct: 119 SDPQNNIAKTYRVLLEKALDDSYVKAFADGMYFDFEGVTTRPAELRILGQYEAE----VD 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           L EG+  +IK++F  F+ +V  L R S G   +    A G  RE++
Sbjct: 175 LIEGRYHQIKRMFGRFDNRVKALHRTSVGSLSMAAGPALGQWRELT 220


>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 = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 112/238 (47%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     +  D      +G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEHPLADDTAQQFTEGVQL----HNEKSLTKPAQLEVIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           L EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 178 LSEGRYHQVKRMFAAVGNRVVELHRERIGDIKLDDDLAPGEYRPLTAEEIASVGAPHL 235


>gi|309751708|gb|ADO81692.1| 23S rRNA U2457 pseudouridine synthase [Haemophilus influenzae
           R2866]
          Length = 227

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 96/183 (52%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNHG 91

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 92  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 151

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 152 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFR 211

Query: 235 EVS 237
            +S
Sbjct: 212 LLS 214


>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 = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/218 (27%), Positives = 98/218 (44%), Gaps = 2/218 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           EG+  ++K++F      V  L R   G   L   LA S
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPS 217


>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 = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 114/227 (50%), Gaps = 8/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+ +  GI SR++  ++I + R+ VNG+   +    V   D I +D  PL   E+  
Sbjct: 2   RINKLFSNLGICSRKDTSKLIEENRIIVNGLPCIQGQW-VELEDEILLDNKPLPIKEKIY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP+G+  T +D    + +  N  +    +  VGRLD  ++GL+LLTNDG LA  +
Sbjct: 61  IAL-NKPVGVTCTAADEVEHNII--NFMNYNEYIFPVGRLDKASQGLILLTNDGDLANKI 117

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V      + + +  +  G+ I  +     +V   ++   N  +T GL 
Sbjct: 118 LESENEHEKEYIVTLDRPFNDEFILGMTSGVEICNVKTRQCKVRRISEDTFNIILTQGL- 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              N++I+++ + F + V +L RI     +LG L  G  R +S++ L
Sbjct: 177 ---NKQIRRMSKAFGYNVKKLERIRIVNIELGNLEYGKWRYLSEEEL 220


>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 = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/190 (27%), Positives = 93/190 (48%), Gaps = 25/190 (13%)

Query: 66  PLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTE 119
           PLR+ +R R    + L++KP  +++  +D   R+T+ D +  P +++     GRLD ++E
Sbjct: 22  PLRRPDRPREARRIVLFNKPFDVLSQFTDGGNRATLADYIQEPGVYA----AGRLDRDSE 77

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-- 177
           GLLLLTNDG L   L  P  +  + Y V+  G+ D+  L  L+ G+ +        +V  
Sbjct: 78  GLLLLTNDGALQAKLTQPGKKTSKTYYVQVEGEPDEAALQALRDGVTLNDGPTLPAKVER 137

Query: 178 -------------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                          + +    +W+++ + EG+NR+++++     +   RLIR   G + 
Sbjct: 138 IDEPHWLWPRNPPIRERKAIPTSWLSISIIEGRNRQVRRMTAHIGYPTLRLIRYRIGSWT 197

Query: 225 LGTLLAGSTR 234
           L  L  G  R
Sbjct: 198 LDGLANGEYR 207


>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 = 77.8 bits (190), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 68/226 (30%), Positives = 107/226 (47%), Gaps = 8/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           RV   +A  G+ SRR  E +I ++ VKVN  + +      +    I    + + K  +  
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAKLGDKVALGDRIIYKKQIFVFKDFQIN 67

Query: 73  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
            R++L  +KP   + ++ D +GR      +  +F  RV S+GRLD  + GLLL TNDG  
Sbjct: 68  NRIYLALNKPRNYLCSNFDINGRRLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGKF 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   + 
Sbjct: 128 ANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI- 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L EGKNREI+KVF   N  + ++ RI  G   L +L  G  + V
Sbjct: 186 --LDEGKNREIRKVFLTKNIFLKKIHRIRIGNINLDSLKEGQVKIV 229


>gi|86130476|ref|ZP_01049076.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85819151|gb|EAQ40310.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 260

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 118/249 (47%), Gaps = 13/249 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG  SRR  +++I Q RV +NG + E     +   D + V+G  +  +    
Sbjct: 8   RINKYLSEAGYCSRRAADKLIDQGRVTINGKVPE-MGTKITEGDEVRVNGELITSSTEKP 66

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +++  +KP+G+V T      +  + D  N PS   R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 67  VYIALNKPVGIVCTTDTRVEKDNIIDFINYPS---RIFPIGRLDKPSEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +    +  +  G+ I         V    ++ S     +
Sbjct: 124 NKILRARNNHEKEYEVWVDKPITPSFIQQMSNGVPILDTVTRKCHV----EQLSRFSFKI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E  +++V RL R      +L  +  G  R +S   + E++   + +
Sbjct: 180 ILTQGLNRQIRRMCEALDYEVTRLKRNRIMNIELD-VPVGKWRYISDTEM-EEINRLVED 237

Query: 252 EAQVNLDAP 260
            A+ + DAP
Sbjct: 238 SAKTHTDAP 246


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 54/192 (28%), Positives = 94/192 (48%), Gaps = 17/192 (8%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           H   D    ++ + +RL L++KP G+++  + P+GR     +  +I   V   GRLD ++
Sbjct: 19  HQPTDSPLTQRHDASRLILFNKPYGVLSQFT-PEGRWRGLKDFIAIPG-VYVAGRLDADS 76

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQV 177
           EGLLLL NDG L   +  P  +  ++Y V+  G   +  L  L++G+ +  G        
Sbjct: 77  EGLLLLANDGKLQAHIADPRFKMEKIYWVQVEGTPGEAALQALREGVALNDGPTRPARAR 136

Query: 178 TLDT--------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            +D               Q    AW+ +G+REG+NR+++++     +   RL+R + G +
Sbjct: 137 LMDAPAALWQREPPVRVRQSIPTAWIELGIREGRNRQVRRMTAAVGFPTLRLVRAAIGNW 196

Query: 224 QLGTLLAGSTRE 235
            L  L  GS R+
Sbjct: 197 SLDGLAPGSWRD 208


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 112/238 (47%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++   +R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGSR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     +  D       G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEHPLADDTAQQFADGVQL----HNEKSLTKPAQLEVIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           L EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 178 LSEGRYHQVKRMFAAVGNRVLELHRERIGAIKLDDDLAPGEYRRLTAEEIASVGAPHL 235


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 115/230 (50%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE ++++   R+ +NG + E     VM  D + VDG P+ K  +  
Sbjct: 8   RINKYLSEVGFCSRREGDKLLEAGRITLNGKIPE-IGTKVMPKDVVCVDGKPVGKPIQDH 66

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +++ ++KP+G+V+T      ++ + D +     R+  +GRLD ++EGL+ LT++G +   
Sbjct: 67  VYIAFNKPVGIVSTTDTKAEKNNMIDYIGH-QQRIFPIGRLDKDSEGLIFLTSEGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +    +  +  GI I        +V    +K S     + L
Sbjct: 126 ILRSKNNHEKEYIVTVDKPITDRFIQKMGAGIPILDTVTDPCKV----EKISKVKFRIIL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+  ++V +L RI      L  +  G  R+++   L+E
Sbjct: 182 TQGLNRQIRRMCEYLGYEVRQLKRIRIMNVHL-DIPVGKWRDLTASELKE 230


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 114/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++A   SR+E ++++    V VN  +++   V+V +  D ++  G PL  A   
Sbjct: 2   RLDKFLSKATELSRKESKKILHAGEVTVNEQVIKDPGVHVDIVNDDVQWAGEPLSVATGN 61

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G   T  +      T    +P + S  I+ GRLD++T G LL+++DGG   
Sbjct: 62  RYILLHKPEGFECTLKAKEYPIVTDLIAVPELGSLRIA-GRLDVDTTGALLISDDGGWLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD-KLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  +  +VY +     +D D + N +K   +GI+++G        TL+    ++A 
Sbjct: 121 RVTSPKHEHAKVYELTLADAMDSDAQANAIKEVAEGILLEGDHEETKPATLEFIDETHAR 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +T  L +GK  ++K++  +F  +V  L R S G   L  L  G +R
Sbjct: 181 LT--LEQGKYHQVKRMMGYFGNRVVELHRASVGHITLDGLEKGDSR 224


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/215 (26%), Positives = 100/215 (46%), Gaps = 2/215 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV VNG +++  A  ++    +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRALVARELRAQRVTVNGEVIKSGAFKLLPEHEVAFDGNVLEQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D  +  + G+ + G        TL  ++ S   V + + 
Sbjct: 122 TSPKHHCEKTYLVTLEQPLAPDTADNFQAGVQLHGEKNLTRPATL--EQISEHQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           EG+  ++K++F      V  L R   G   L   L
Sbjct: 180 EGRYHQVKRMFAAVGNHVVALHRERIGAITLDDAL 214


>gi|304397253|ref|ZP_07379132.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304355402|gb|EFM19770.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 184

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 52/179 (29%), Positives = 90/179 (50%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +    + V + GRLD ++EGL++LTNDG L   
Sbjct: 4   RVILFNKPFDVLPQFTDEAGRRTLKDFV--SVAEVYAAGRLDRDSEGLMVLTNDGALQAA 61

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  +VY V+  G+  +  L  L+ G+ ++       GI         +      
Sbjct: 62  LTQPGKRTGKVYYVQVEGEPQEADLQPLRDGVNLKDGMTLPAGIEKVPEPQWLWPRQPPI 121

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +     W+ V L EG+NR+++++     +   RLIR + G + L  L  G+ RE+S
Sbjct: 122 RERKNIPTQWLKVTLYEGRNRQVRRMTAHIGFPTLRLIRYAMGQYSLDDLAPGAWRELS 180


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 92/184 (50%), Gaps = 17/184 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T++ L++KP  ++T  SD +GR+T+ D +P   S+V   GRLD ++EGL+LLTN+G +  
Sbjct: 49  TKVILFNKPYDVLTQFSDENGRATLKDFIP--VSQVYPAGRLDRDSEGLVLLTNNGEIQH 106

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  + Y  +      +  L  L++G+V+        +V L ++          
Sbjct: 107 RLAEPKFKTEKTYFAQVEAIPQEVDLEQLRQGVVLNDGKTLPAKVRLVSEPNWLWERNPP 166

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + + EG+NR+++++     +   RLIR     F L  L  G  R++S
Sbjct: 167 IRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMALFTLDNLPQGQYRQLS 226

Query: 238 KKIL 241
           +  L
Sbjct: 227 EAEL 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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHEVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>gi|238916961|ref|YP_002930478.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           eligens ATCC 27750]
 gi|238872321|gb|ACR72031.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           eligens ATCC 27750]
          Length = 244

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 116/231 (50%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV+ +I ++RV VN  ++ +    + +  D + VDG  +   E  
Sbjct: 4   RLDKYLADMQVGTRSEVKELIRKKRVTVNDNIVTKPESKINTDGDSVNVDGNAVGYHEY- 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+  +D +  +TV D + +   + +  VGRLD +TEGLL++TNDG +A 
Sbjct: 63  EYFMLNKPAGVVSA-TDDNTCTTVIDLIKNKNRKDLFPVGRLDKDTEGLLIITNDGAMAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWV 189
            L  P     + Y  +  G++   ++     G+ +          ++V         + +
Sbjct: 122 DLLSPKKHVDKTYYAKVKGKISDMEVKQFADGLFVDEELTALPAILKVLSYNSDKDYSEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            V + EGK  ++K++F     +V  L RI++G   L  +L  G  R ++K+
Sbjct: 182 HVTIHEGKFHQVKRMFTAIGSEVLFLKRITFGALPLDESLKTGEYRALTKE 232


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 110/227 (48%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDGDRYIEQGNVFING---KRATVGDQVFAGDVVKVNGQIIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP G++TT  +  G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPAGIITTMEE--GERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G      +V    QK +     
Sbjct: 123 VNKILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPILGTVTKKCKV----QKEAPLVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNISLKGLPLGEWRDLT 225


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 103/218 (47%), Gaps = 7/218 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+   I+     +R +++R+I   RV ++   + + A  +  T+ + VDG  L +    
Sbjct: 3   QRLDAFISNNSDFTRSQIQRLIKAGRVHIDDKPVSQGAQKLNGTESVRVDG-ELIEPLSL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  + HKP G V  ++D +   TV D  +LP   +  I+ GRLD++T GL+LLT+DG   
Sbjct: 62  RYLMLHKPQGYVCANTDSE-HPTVLDLIDLPRKQTLQIA-GRLDLDTTGLVLLTDDGQWN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + YRV     +  D  +    GI + G  +      L+     NAW+ +
Sbjct: 120 HRITSPRRECSKRYRVTTAEPIAADTAHYFTDGIQLHGEKHKTRPAHLELIDDYNAWLDI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
              EGK  ++K++F     KV  L R   G   L   L
Sbjct: 180 --HEGKYHQVKRMFAATGNKVIALHRTRIGSITLDNQL 215


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 117/232 (50%), Gaps = 13/232 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAER 72
           R++K ++ AG+ SRRE +R+I   RV V+G   +RA   + ++    ++V    + K + 
Sbjct: 17  RLNKYLSEAGVCSRREADRLIESGRVSVDG---KRAQTGMKIVPGQVVKVGKKVVSKQDE 73

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +   +KP G+V T    +  S V F + P    R+  VGRLD +++GLLL+TN+G + 
Sbjct: 74  MVVLAVNKPAGIVCTEERRERNSIVRFLDYPI---RITYVGRLDKDSKGLLLMTNNGDII 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y+V    ++ Q+ L  +  G+ I        +V    +K      ++
Sbjct: 131 NKMMRAGNRHEKEYKVTVDKEITQEFLEKMASGVPILDTVTRPCKV----EKIGKYTFSI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++ E   ++V  LIR+      LG L  G  R+++   L E
Sbjct: 187 ILTQGLNRQIRRMCEALGYQVRELIRVRIMNIHLGRLKEGEYRKLTDAELNE 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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVDGEIVRNAAFKLLPEHAVEYDGNTLVQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+    + +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTRPAELEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVALHRERIGAIALDADLAPGEYRPLTEE 225


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 96/183 (52%), Gaps = 20/183 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN G
Sbjct: 30  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNHG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L ++      
Sbjct: 86  ELQHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWER 145

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R
Sbjct: 146 NPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFR 205

Query: 235 EVS 237
            +S
Sbjct: 206 LLS 208


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 113/229 (49%), Gaps = 9/229 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRK 69
           +T   +++ + +    S+ +   M+ + +V +NG+  L+R   +V+ +DHI V+G  L++
Sbjct: 56  YTFMNINEFLIKRFHISKDKASNMVLENQVFINGVKALQRN--DVLKSDHIVVNGEVLQE 113

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 + Y+KP G+  T  +    + +   LP     V  VGRLD  +EGLLLLTNDG 
Sbjct: 114 GRNFTYYAYYKPRGIECT-LNAAIENNLLHTLP-FGEHVYPVGRLDKESEGLLLLTNDGK 171

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L + +        + Y V     +  + +  L  GIVI G      +V++ T+      +
Sbjct: 172 LYKDIAFSDNFKEKEYLVEVDKPLTDEAVEQLSSGIVIMGQKTRPARVSMVTEHSFRIIL 231

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           T GL    NR+I+++     ++V  L RI     +LG L  G+ R +++
Sbjct: 232 TQGL----NRQIRRMCYKLRYEVTMLKRIRITSIELGDLKPGAYRVLTR 276


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 68/215 (31%), Positives = 102/215 (47%), Gaps = 11/215 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+GI  +   + V    HI  DG  L+  +   
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLTERVYVDGIPAKALDLLVDEFSHIVFDGQVLQANKPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
           L L HKP+G+V+   D + R TV D L       + + GRLD+N+ GLLLLTND   +  
Sbjct: 67  LML-HKPVGVVSATKDTEHR-TVIDLLDCDARHELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---NAWVT 190
           L  P  +  +VYRV     + ++ +         QG+ +G   +T    K +        
Sbjct: 125 LMSPDQKVDKVYRVTLANPLSEEYI-----AAFAQGMYFGFEDITTQPAKLTILDTHIAE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           V LREGK  +IK++F  F   V  L R S G   L
Sbjct: 180 VTLREGKYHQIKRMFGRFRNPVVGLHRHSIGEITL 214


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 90/180 (50%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--IQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   +D L  L+ G+ +     +  G   V            
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 156

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+V+
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDVT 216


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGYIGQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITSENRWEGDTSRIRFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGEKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/226 (29%), Positives = 114/226 (50%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++A   SR+E ++++    V VN  +++   V+V +  D ++  G PL  A   
Sbjct: 7   RLDKFLSKATELSRKESKKILHAGEVTVNEQVIKDPGVHVDIVNDDVQWAGEPLSVATGN 66

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G   T  +      T    +P + S  I+ GRLD++T G LL+++DGG   
Sbjct: 67  RYILLHKPEGFECTLKAKEYPIVTDLIAVPELGSLRIA-GRLDVDTTGALLISDDGGWLH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD-KLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  +  +VY +     +D D + N +K   +GI+++G        TL+    ++A 
Sbjct: 126 RVTSPKHEHAKVYELTLADAMDSDAQANAIKEVAEGILLEGDHEETKPATLEFIDETHAR 185

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +T  L +GK  ++K++  +F  +V  L R S G   L  L  G +R
Sbjct: 186 LT--LEQGKYHQVKRMMGYFGNRVVELHRASVGHITLDGLEKGDSR 229


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEYFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQQVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLT 226


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V S D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKSGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQQVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLT 226


>gi|291618129|ref|YP_003520871.1| RsuA [Pantoea ananatis LMG 20103]
 gi|291153159|gb|ADD77743.1| RsuA [Pantoea ananatis LMG 20103]
          Length = 239

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 62/226 (27%), Positives = 101/226 (44%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R I  QRV VNG ++   A  +     +E DG  L+     R
Sbjct: 2   RLDKFISQQLEISRAIAAREIRGQRVTVNGDVVRDTAFKLQPDHEVEYDGNVLQMQTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + V+     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTIVYFIEEPMAFKLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     V  D       G+ +           L+    +   +T  L 
Sbjct: 122 TSPRHHCEKTYRVTLEAPVSDDTAAQFSAGVQLHNEKSLTKPAQLEVITPTEVLLT--LS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   L  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVGLHRERIGEIVLDEALEPGEYRPLTEE 225


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 117/234 (50%), Gaps = 15/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERT 73
           R++K ++  G  SRR  + +I + +V +NG + E     V   D +EV+G  + K+ +  
Sbjct: 4   RINKYLSEVGYCSRRVADSLIEEGKVTINGEIPE-MGTKVEEGDQVEVEGQRIEKSMKHE 62

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 129
           +++L ++KP+G+V T      R    DN+       +R+  +GRLD  +EGL+ LTNDG 
Sbjct: 63  KIYLVFNKPVGIVCTTD----RRVESDNIIDFIKYPTRIFPIGRLDKPSEGLIFLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V  +  +++D +  +  G+ I G    +  V    Q G   + 
Sbjct: 119 IVNKILRARNNHEKEYIVSVNRPINRDFIQSMSNGVEILGTITKNCFV---KQLGPKKFR 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L +G NR+I+++ E   ++V  L R+     +L   + G  RE +K+ L E
Sbjct: 176 II-LTQGLNRQIRRMCESLGFRVKSLKRVRIMNIKLDVSI-GEYREFTKEELFE 227


>gi|307730739|ref|YP_003907963.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307585274|gb|ADN58672.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 239

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 97/220 (44%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV +   +   A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVTIGDTVCTDADADFPAEDTSFCFSVDGVTWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       VD  +L+LL+ G+++ G         +D Q      + 
Sbjct: 121 VHLFTSPKRKVPKVYVASTRHPVDDTQLSLLRNGVLLHG--ESKPVAAVDAQLRGERSLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++      +   L R   G   L   LA
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERVGGLALPATLA 218


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 90/189 (47%), Gaps = 23/189 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP  +++  S    R T+ D  ++P+++      GRLD ++EGLLLLT+DG L  
Sbjct: 3   LILLNKPFQVMSQFSAHPERQTLADYIDIPNVYP----AGRLDADSEGLLLLTDDGKLQH 58

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            +  P  +  + Y  +  GQ   + L+ L++ + +        Q  L  + G        
Sbjct: 59  AIAHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPP 118

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 235
                    +W+ + + EGKNR+++++         RL+RI+ GPF L T  ++ G  RE
Sbjct: 119 IRQRQNQPTSWIALTISEGKNRQVRRMTAAVGLPTLRLVRIAIGPFSLATHPVMPGEWRE 178

Query: 236 VSKKILREQ 244
           V    L  Q
Sbjct: 179 VDPLELERQ 187


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 48/174 (27%), Positives = 88/174 (50%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 1   MFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 58

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L+ L+KG+ ++       +V +  +              
Sbjct: 59  PKSKSPKTYWVQVDGAPSESDLDKLRKGVELKDGMTLPAKVEVMAEPNVWERTPPVRFRA 118

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RLIR S G  +LG L  G  +E+
Sbjct: 119 NIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIKLGELQPGEWKEI 172


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/217 (27%), Positives = 99/217 (45%), Gaps = 4/217 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + +   +V VNG++ + +A  +   D I  DG PL   +  +
Sbjct: 2   RLDKFIAENTGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICFDGEPLAWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP   V +H D D   TVF      + +++   GRLD +T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQNCVCSHDDGD-YPTVFQFFDYPLTTKLHCAGRLDADTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+        +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYATQFAEGILLRGEKTATKPAQLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EG+  ++K++F     KV  L R   G   L   LA
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGDVVLDENLA 215


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 110/227 (48%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDGDRYIEQGNVFING---KRATVGDQVFAGDVVKVNGQIIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP G++TT  +  G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPAGIITTMEE--GERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G      +V    QK +     
Sbjct: 123 VNKILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPILGTVTKKCKV----QKEAPLVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNISLKGLPLGEWRDLT 225


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 95/183 (51%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P ++      GRLD ++EGLLLLTNDG L 
Sbjct: 34  KLILFNKPFDVLTQFSDGEGRATLKDFIAVPGVYP----AGRLDRDSEGLLLLTNDGQLQ 89

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L++G+ +  G+        L+          
Sbjct: 90  ARIADPKHKLAKTYWVQVEGEPSAEQLQRLREGVQLNDGMTLPAEARQLEEPTLWPRNPP 149

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  +EV+
Sbjct: 150 VRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLEQGQWKEVA 209

Query: 238 KKI 240
            ++
Sbjct: 210 ARL 212


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/212 (30%), Positives = 106/212 (50%), Gaps = 11/212 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA--AVNVMSTDHIEVDGVPLRKAE 71
           QR+ K ++     SR +V+ +I +  + VNG + ++    VNV + D +EVDG  L    
Sbjct: 11  QRLDKFVSSMTPYSRSDVKTLIKKSAIYVNGSVAKKPNQPVNV-TEDKVEVDGQELVYEP 69

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDG 128
              + + HKP G+++   D +   TV D LP    +  +   VGRLD +T GLLL+TNDG
Sbjct: 70  YVYIMM-HKPDGVISATED-NRWETVIDLLPEDLILTYQPFPVGRLDKDTTGLLLITNDG 127

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGS 185
                L  P     + Y V   G +    ++  +KG+ I QG      Q+ +D   ++  
Sbjct: 128 QFNHALMAPKKHVEKEYAVLVDGLLSDKHIDQFEKGLDIGQGEKTKPAQLFIDQVDEEAG 187

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
            +   V + EGK  ++K++F   + +V +L R
Sbjct: 188 QSLARVVIAEGKYHQVKRMFHAVDCEVVQLHR 219


>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 = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/212 (27%), Positives = 99/212 (46%), Gaps = 4/212 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R +  +++ Q  V +NG + +  A  V   D I  DG  L      +
Sbjct: 2   RLDKFLAEMTDLTRSQATKVLRQSAVTINGKIEKSGAAKVGPNDEICYDGERLAWVAEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G + +H D D  +   F   P + +R+ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YIMLNKPQGYICSHEDGDHPTIYQFFGYP-LSARLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+ + +    +GI+++G        TL+     N  V + +
Sbjct: 121 ITSPKHHQPKTYLVTLADPVEANYVQACTEGILLRGEKDPTKPATLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EG+  +IK++F     KV  L R   G   L
Sbjct: 179 SEGRYHQIKRMFAALGNKVVGLHRWKIGALVL 210


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 105/215 (48%), Gaps = 7/215 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++   IA+R + + M+   RV VNG  ++ A + V    D I VDG      E  
Sbjct: 4   RIDKFLSTQAIATRSQAKEMLRAGRVLVNGTPVKAADLKVDPEGDEIRVDGRVYGYQEHL 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G+V+   D   R TV D +P    R  +   GRLD +T G +L+T+DG  A
Sbjct: 64  YLML-NKPQGVVSATDDKVHR-TVLDLVPPELRRRGLFPAGRLDRDTVGFVLITDDGEFA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y     G + +++L++L +G+V+  G      ++T+  Q G    + 
Sbjct: 122 HNILSPRHHVPKTYEAGLDGPIGENELSVLAQGVVLGDGTKCRPAELTV-LQSGERPLIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EG+  +IK++F     +V  L R   G   L
Sbjct: 181 IVIVEGRYHQIKRMFAAVGRRVLTLKRTKIGGLAL 215


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 89/176 (50%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L L+HKP  +++  +D +GR T+ D +    +   + GRLD ++EGLLLL NDG L +
Sbjct: 2   SELILFHKPYRVLSQFTDSEGRGTLGDFITK--AGFYAAGRLDYDSEGLLLLCNDGRLQQ 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            +  P  +  + Y V+  G + +  L  L+ G+ ++       + ++             
Sbjct: 60  RIADPRFKLWKSYAVQLEGDITEAALCSLRDGVELKDGATLPARASIIRTPAFWPRNPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +  + +WV + +REG+NR+++++     + V RLIR   G + L  L  G  R
Sbjct: 120 RERKTQTTSWVEISIREGRNRQVRRMCAKVGFPVLRLIRTRIGDWGLDDLAPGEYR 175


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P    E  ++ +++KP   ++  +D DGR T+ D +      V + GRLD ++EGL++LT
Sbjct: 46  PKVAPEDRKVVVFNKPFDTLSQFTDGDGRKTLADYI--TVKDVYAAGRLDRDSEGLMVLT 103

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG 184
           NDG L   L  P+++  + Y V+  G    + L+ L+KG+ ++ G+        +D    
Sbjct: 104 NDGILQARLTQPNSKSPKTYWVQVDGAPSDEDLDKLRKGVELKDGMTLPAKVEVMDAPNV 163

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + + EG+NR+++++     +   RLIR S G   LG L  G
Sbjct: 164 WERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDVTLGDLQPG 223

Query: 232 STREV 236
             +E+
Sbjct: 224 EWKEI 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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 100/225 (44%), Gaps = 2/225 (0%)

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 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+L+T+DG  +  +  P     + Y V     V  D      KG+ +      D+     
Sbjct: 121 LVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVAADTAEQFAKGVQLHN--EKDLTKPAV 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +  +   V + + EG+  ++K++F      V  L R   G   L
Sbjct: 179 LEVITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAIVL 223


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAMLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V+  D ++V+G  +  R A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVVPGDVVKVNGQLIEPRDA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E       +KP+G+V+T  D + R  + D + +  SR+  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVFIALNKPVGIVSTTEDGE-RDNIVDFV-NHSSRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFAFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F + V +L R       L  +  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYDVTKLERTRIMNVSLSGIPLGEWRDLTDDELIE 231


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   +D L  L+ G+ +     +  G   V            
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 156

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 216


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRYHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 86/186 (46%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P R     ++ L++KP  ++T  S   G  T+ D +      +   GRLD ++EGLL+LT
Sbjct: 26  PKRPRGPQKIILFNKPFNVLTQFSGEPGDKTLADYI--SIKDIYPAGRLDKDSEGLLVLT 83

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------------QGIC 171
           NDG L   L  P ++  + Y V+  G    D L  L+KG+ +              Q + 
Sbjct: 84  NDGILQARLTQPQSKQPKTYWVQVEGVPSDDDLEQLRKGVTLKDGLTLPADIERMEQPVI 143

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +       + +     W+ + LREG+NR+++++     +   RLIR     + +  L  G
Sbjct: 144 WDRTPPIRERKNIPTTWLALTLREGRNRQVRRMTAHIGFPTLRLIRYKMADWTVDDLAPG 203

Query: 232 STREVS 237
             REV+
Sbjct: 204 EWREVT 209


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 108/227 (47%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P ++  +VY V     +D+       +G+    +GI     Q+TL   + +   +  
Sbjct: 121 LTQPQSKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGITTQPAQLTLLGPRSARLSIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVLRLHRETIGALLLDPDLRPGSYRALN 223


>gi|304405744|ref|ZP_07387402.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304344987|gb|EFM10823.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 235

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 113/230 (49%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++++ + RV +NGI+ +  +      D + ++G  +  + R  
Sbjct: 2   RINKFISETGFCSRREADKLVDEGRVTINGIVAQLGS-QAEQGDDVRINGKRIGASRRHV 60

Query: 75  LWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT S   G    F        R+  +GRLD ++EGL+L+TNDG +   
Sbjct: 61  YIALNKPVGITSTTESQIKGNIVDFVGHSE---RIFPIGRLDKDSEGLILMTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  + +G+ I G      QVT   ++       + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVTPMFIKGMSEGVRILGTMTLPCQVTRIAER----IFKIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EGKNR+I+++ E F ++V RL R+      LG L  G  R++ +  L E
Sbjct: 174 TEGKNRQIRRMCEVFGYRVVRLRRVRIMNIHLGDLANGRWRDLHQDELDE 223


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 107/227 (47%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+      L +GI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G   L   L  G  R +S++
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQ 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 53/160 (33%), Positives = 88/160 (55%), Gaps = 14/160 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R++K+ +  GI SR+E  R+I ++R+ +NG   +E   VN   +D I  DG P+   E+ 
Sbjct: 2   RINKLFSNYGICSRKETNRLIEEKRIIINGRYCVEGQWVN--DSDEIIFDGKPISTVEKV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
            + L +KP+G+  T       + V DN+ S       +  VGRLD +++GL+L+TNDG +
Sbjct: 60  YIVL-NKPVGITCT-----AENKVSDNIISYMKYPHYIFPVGRLDKDSQGLILMTNDGEV 113

Query: 131 A-RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           A R+LE  +    + Y V+ +   D + L  +  G+ I G
Sbjct: 114 ANRILESDNMHE-KEYLVQVNKNFDDEFLKRMSNGVEITG 152


>gi|238910944|ref|ZP_04654781.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Tennessee str.
           CDC07-0191]
          Length = 211

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/181 (29%), Positives = 89/181 (49%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAEGRLDRDSEGLLVLTNDGALQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 88  LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 148 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 207

Query: 239 K 239
           +
Sbjct: 208 E 208


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 110/236 (46%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + +D       G+ +           L+  +     +T+   
Sbjct: 122 TSPRHHCEKTYLVTLEHPLAEDTAQQFADGVQLHNEQSLTKPAQLEVIEPQVVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 180 EGRYHQVKRMFAAVGNRVLELHRERIGEIKLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 91/180 (50%), Gaps = 17/180 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T + L++KP  +++  +D  GR+T+ D +P     + S GRLD ++EGL++LTNDG L 
Sbjct: 28  KTHIVLFNKPFDVLSQFTDEGGRATLKDYVP--LRDIYSAGRLDRDSEGLMILTNDGKLQ 85

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV----------- 177
             L  P  +  ++Y  +  G  D++ L+  + G+++     +  G  QV           
Sbjct: 86  ARLTQPGKKTPKIYYAQVEGVPDKEALHAFRTGLILSDGPTLPAGVEQVEEPAWLWPRQP 145

Query: 178 -TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + L EG+NR+++++     +   RLIR S     L  L  G  RE+
Sbjct: 146 PIRERKTIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMAGQTLDGLHPGEWREI 205


>gi|221134863|ref|ZP_03561166.1| pseudouridine synthase, Rsu [Glaciecola sp. HTCC2999]
          Length = 196

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 88/177 (49%), Gaps = 20/177 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E+  + L++KP  ++T  +D  GR T+ D  ++P+I++     GRLD ++EGLL+LTNDG
Sbjct: 19  EKKLVVLFNKPFNVLTQFTDQAGRQTLKDYIDIPNIYA----AGRLDRDSEGLLVLTNDG 74

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   L  P+ +  + Y V+  G +  + +  L  G+ ++       +V           
Sbjct: 75  KLQHALAHPTQKTTKTYWVQVEGDITDEAIEQLSNGVNLKDGMTAPAKVEKMAAPAIWPR 134

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                       +WV++ + EG+NR+++++    N+   RLIR   G + +  +  G
Sbjct: 135 TPPIRERASIPTSWVSITISEGRNRQVRRMTAHVNYPTLRLIRYRVGQWTIDNIANG 191


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 88/175 (50%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 43  LFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAKLTQ 100

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G+   + L  L+ G+ +        G+   +  V L        + 
Sbjct: 101 PGKRTGKIYYVQVEGEPTPEALTALRDGVTLNDGPTLPAGVELVEEPVWLWPRNPPIRER 160

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ 
Sbjct: 161 KSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGDWRKA 215


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 48/174 (27%), Positives = 87/174 (50%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 60  LFNKPFDVLCQFTDEQGRQTLKDYIP--IPDVYAAGRLDRDSEGLLLLTNDGKLQSKITE 117

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------------K 183
           P  +  + Y  +  G+ ++  ++ L+ G+ ++       +V + TQ             K
Sbjct: 118 PKKKTFKTYWAQVEGEPNEADVDKLRHGVELKDGMTLPAKVMIMTQPDVWPRTPPIRERK 177

Query: 184 G-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           G    W+ + + EG+NR+++++     +   RLIR   G + L  L +G  + +
Sbjct: 178 GIPTTWLEIQICEGRNRQVRRMTANIGFPTLRLIRYKIGQWSLNDLQSGEYQRI 231


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 110/227 (48%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R    + +    + VNG +++  A+ + S D +  +G  L   E  +
Sbjct: 2   RLDKFIAENIGLTRSLANKALKSSLITVNGQVVKSGAMKITSADGVCYEGNRLTWLESGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G + ++ D +   TVF      +  R+ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYICSNDDSE-YPTVFQFFDYRLMVRLHTAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+QD    L KGI+++G     +   ++     N  +T+  
Sbjct: 121 ITSPKYHCEKSYLVTLADPVEQDYALKLAKGILLRGERDPCLPAAMEIIDDYNVNLTIC- 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G   L  TL  G+ R ++K+
Sbjct: 180 -EGRYHQVKRMFAALGNKVQALHRWRIGEIILDETLQEGTFRHLTKQ 225


>gi|289664922|ref|ZP_06486503.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 190

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 88/176 (50%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G+   ++L  L+ G+V+        QV +LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTLPAQVRSLDPAPQLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDTLAPGQWR 176


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 113/235 (48%), Gaps = 14/235 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
           T  R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   
Sbjct: 15  TNMRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP 74

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLL 124
           + + + L +KP G+V+   D +   T+ D L      P ++     VGRLD +TEGL+LL
Sbjct: 75  KHSYIIL-NKPSGVVSAKKDTN-YLTIIDQLAEEDKSPDLYP----VGRLDRDTEGLVLL 128

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           T++G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+    
Sbjct: 129 TDNGPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKAD 188

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++
Sbjct: 189 TDQSQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTE 243


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 96/185 (51%), Gaps = 22/185 (11%)

Query: 74  RLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ HKP G ++    +    +  +   L       +++GRLD  +EGLLLLT DG ++
Sbjct: 5   RHFILHKPYGYLSQFITNQTKRKKKMLGELYDFPEGTMAIGRLDFASEGLLLLTTDGKVS 64

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY----------GDMQVTL 179
           +  E+ S+++ + Y V+  G + Q+ +N LKKG+ I  +G  Y           + +  L
Sbjct: 65  Q--EIRSSKYEKEYYVQVDGLITQEAINQLKKGVEIGFEGKKYITKPGKASIINNPEFPL 122

Query: 180 DTQK------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +QK      G  +W++V +REGK R+++K+     +   RL+RI  G   +  L  G  
Sbjct: 123 RSQKIRDDRHGPTSWISVIIREGKFRQVRKMTAAVGYPTLRLVRIRIGTITIDDLKNGEV 182

Query: 234 REVSK 238
           +EV++
Sbjct: 183 KEVNQ 187


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 92/180 (51%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E  ++ +++KP   ++  +D +GR T+ D +      V + GRLD ++EGLL+LTNDG L
Sbjct: 47  EERKVIIFNKPFDTLSQFTDGEGRKTLADYI--SIKGVYAAGRLDRDSEGLLVLTNDGIL 104

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG----- 184
              L  PS++  + Y V+  G   +  L+ L++G+ ++ G+        +D  K      
Sbjct: 105 QARLTQPSSKSPKTYWVQVDGSPGEVDLDKLRQGVELKDGLTLPARVEIIDEPKVWPRNP 164

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+++ + EG+NR+++++     +   RLIR S G   L +L  G  +E+
Sbjct: 165 PVRFRANIPTTWLSITIIEGRNRQVRRMTAHIGYPTLRLIRYSVGDIHLDSLKPGEWKEI 224


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 112/225 (49%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I ++RV +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERRVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRINHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 222


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 68/228 (29%), Positives = 109/228 (47%), Gaps = 15/228 (6%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW-LYHK 80
           R G+ +R E  + I + RV VNG++  +A   V     I VDG PL  + +  ++ + +K
Sbjct: 11  RTGL-TRSESRKAITKGRVAVNGMVCRKADTQVAEDAAIAVDGTPLAGSYQKYVYIMLNK 69

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           P G+V+   D    +TV D + + F R  +   GRLD  + G +LLT+DG LA  L  P+
Sbjct: 70  PEGVVSASRDKR-DTTVVDLVAADFPRRALFPAGRLDKTSTGFVLLTDDGALAHDLLSPA 128

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---KGSNAWVT-VGLR 194
               + Y V     +D    + ++ G    G+   D +     +    G +  V  V L 
Sbjct: 129 HHVDKQYLV----TLDTPLTDAMRAGFA-AGVTLADGETMAPAEAEPAGEDPCVVKVTLH 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           +G   +IK++F  +   VN L R + G   L   LA G  RE++ + L
Sbjct: 184 QGVYHQIKRMFGVYGAGVNALHRYAIGGVALDAALAPGQWRELTAEEL 231


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     +  D       G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQL----HNEKSLTKPAQLEVIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           + EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 178 ISEGRYHQVKRMFAAVGNRVLELHRERIGAIKLDDDLAPGEYRPLTPEEIASVGAPHL 235


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 91/183 (49%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD  GR+T+  F ++P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 33  KLILFNKPFDVLTQFSDEGGRATLKDFIDIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 88

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  +  + Y V+  G+  +++L  L+ G+ +        +  L  +         
Sbjct: 89  ARIADPKHKLAKTYWVQVEGEPTEEQLQRLRDGVALNDGKTLPAEARLLEEPALWPRNPP 148

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + +REG+NR+++++         RL+R+  G + +  L  G  +EV 
Sbjct: 149 VRFRKSVPTHWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIDGLDQGQWKEVP 208

Query: 238 KKI 240
            ++
Sbjct: 209 ARL 211


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACAEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 53/182 (29%), Positives = 90/182 (49%), Gaps = 20/182 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           + RL L +KP  ++T  +D  GR+T+  F  +P ++      GRLD ++EGLLLLTNDG 
Sbjct: 25  QPRLILLNKPFDVLTQFNDEQGRATLKDFVEVPGVYP----AGRLDRDSEGLLLLTNDGR 80

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK----- 183
           L   +  P  +  + Y V+  G+  + +L  L+ G+ +  G         LD  +     
Sbjct: 81  LQARIADPRHKLAKTYWVQVEGEPSEAQLQQLRDGVTLNDGPTLPAEARLLDEPQLWDRH 140

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      +W+ + +REG+NR+++++         RL+R++ GP+ L  L  G   E
Sbjct: 141 PPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVAIGPWALNGLQPGQWCE 200

Query: 236 VS 237
           V 
Sbjct: 201 VP 202


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 90/181 (49%), Gaps = 17/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T++ L++KP  ++T  SD +GR+T+   +P     V   GRLD ++EGL+LLTN+G +  
Sbjct: 49  TQVILFNKPYDVLTQFSDEEGRATLKAFIP--IPHVYPAGRLDRDSEGLVLLTNNGEIQH 106

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L +P     + Y  +  G   +  L  L++G+V+        +V L             
Sbjct: 107 RLAVPKFNTEKTYFAQVEGIPQETDLAQLRQGVVLNDGKTLPAKVRLVPEPNWLWQRNPP 166

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + ++   +W+ + + EG+NR+++++     +   RLIR     F L  L  G  R++S
Sbjct: 167 IRERKQIPTSWLEIKIHEGRNRQVRRMTAHIGFPTLRLIRYQMALFNLANLEQGQYRQLS 226

Query: 238 K 238
           +
Sbjct: 227 E 227


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 59/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   L+ G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLVPGEYRPLTEE 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 92  LFNKPFDVLCQFTDEQGRKTLKDYIP--IPGVYAAGRLDRDSEGLLLLTNDGQLQAKLTE 149

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------DTQ 182
           P  +  + Y V+  G+     L  L++G+ ++       +V++              + +
Sbjct: 150 PKKKTFKTYWVQVEGEPTDADLAKLRQGVELKDGITLPAKVSIMATPNVWPRNPPIRERK 209

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  L  G
Sbjct: 210 NIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATG 258


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 90/182 (49%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++    +L L +KP G+++  +  +G  T+   +P   + V   GRLD ++EGLLLLTND
Sbjct: 6   KRPANPKLVLLNKPYGVLSQFTGEEGDQTLKPFIPH--NDVYPAGRLDKDSEGLLLLTND 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL------- 179
           G     L  P  +  + Y V+  G   +++L  L+ G+ +  G+        +       
Sbjct: 64  GVYQARLANPKYKVWKTYWVQVEGDPSEEQLEQLRNGVELNDGMTRPAEAFVMPEPMNLW 123

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +   ++W+ + +REGKNR+++++         RLIR + GPFQL T+  G 
Sbjct: 124 PRNPPVRERKSVPDSWLCLKIREGKNRQVRRMTAHVGLPTLRLIRAAVGPFQLKTMQPGE 183

Query: 233 TR 234
            R
Sbjct: 184 WR 185


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 107/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKAHIEPKNDKISVRGELIEYVENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + ++ +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEEDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G+ R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVIHLKRIKIADLELDSNLESGNYR 218


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 50/187 (26%), Positives = 95/187 (50%), Gaps = 17/187 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   SD +GRST+ D +    + V  VGRLD ++EGLLLLTN+G + 
Sbjct: 40  QTQVILFNKPFDVLCQFSDENGRSTLKDFID--IAEVYPVGRLDRDSEGLLLLTNNGEIQ 97

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------ 185
             L  P  +  + Y ++  G  D+  L  L++G+ ++       +V L ++         
Sbjct: 98  HRLAEPKFKMEKTYWMQVEGVPDETALEQLRRGVQLKDGMTKPAKVRLISEPDCLWQRVP 157

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+ + + EG+NR+++++     +   RLIR     F L  L   + R +
Sbjct: 158 PIRERKNIPTSWLEIKIYEGRNRQVRRMTAHIGFPTLRLIRCQLAGFTLQNLAPKTYRTL 217

Query: 237 SKKILRE 243
           ++  L++
Sbjct: 218 TQDELKQ 224


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>gi|145636895|ref|ZP_01792560.1| malic enzyme [Haemophilus influenzae PittHH]
 gi|145269976|gb|EDK09914.1| malic enzyme [Haemophilus influenzae PittHH]
          Length = 232

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDMDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVKLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 115/244 (47%), Gaps = 26/244 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRK 69
           P R+SK +A   + SRRE +  I Q  VKVNG    + AV    V  +D IE+       
Sbjct: 6   PVRLSKRMAELKLCSRREADGYIEQGWVKVNG----QTAVLGQKVTPSDRIELAKQAHET 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTV--------FDN----LPSIFSR---VISVGRL 114
             +    L +KP+G V+   + D R+ V        +D     +P   S    +   GRL
Sbjct: 62  QAQRVTVLLNKPVGYVSGQPEKDYRAAVELITAENRWDGDTSRIPYRDSHKKGLAPAGRL 121

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L    +   + Y VR  G++ ++ L LL  G+ + G     
Sbjct: 122 DIDSVGLLVLTQDGRIAKQLIGGDSGIEKEYLVRVKGRLSEEGLRLLNYGLSLDGEKLRP 181

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 182 AKVEWQNED----QLRFILKQGKKRQIRRMCELVGLRVIGLKRIRMGQVKLGALPPGKWR 237

Query: 235 EVSK 238
            + K
Sbjct: 238 YLGK 241


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/225 (29%), Positives = 108/225 (48%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           RV   +A  G+ SRR  E +I ++ ++VNG  + +    V   D I     + + K  ++
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNG-SIAKLGDKVSPGDRIIYKKQIYVFKGFQS 66

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
           +  +Y   +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KNKIYLALNKPRNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y V     +D++ L   K GI ++   +  ++      K S   +
Sbjct: 127 FANDIIHPRRKVEREYIVESKKDIDENLLISFKSGIKVKKEFF-KLKSYEILNKNSARLI 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 186 ---LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 64/226 (28%), Positives = 114/226 (50%), Gaps = 13/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRR+ +R + Q  V +NG   +RAAV   V   D ++V+G  +   + 
Sbjct: 8   RLNKYISESGICSRRDADRYVEQGNVFING---KRAAVGDQVYVGDVVKVNGQLIEPRDE 64

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L   +KP+G+++T  D  G S    +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  SDLILIALNKPVGIISTTED--GESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G      +V    +K +    +
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKV----RKEAPFVFS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + L +G NR+I+++ + F ++V +L R       L  L  G  R++
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPIGEWRDL 224


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 60/234 (25%), Positives = 105/234 (44%), Gaps = 3/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +   +V V+  +++  AV V     +  +G  L      R
Sbjct: 2   RLDKFLSQQLGISRSLVARELRAGKVTVDDEIVKSGAVQVSPEQVVAYEGSVLVHVTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DP   + ++     +  ++ S GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPQGYVCSTDDPAHPTILYFIDEPLADKLHSAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     +  D      +G+++ G  Y      L+        +T+   
Sbjct: 122 TSPKHHCEKTYRVELENDIADDVAKRFAEGVMLNGEKYPTKPAQLEVISPKEVLLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGP 247
           EG+  ++K++F      V  L R   G   L   LA G  RE+++  +   + P
Sbjct: 180 EGRYHQVKRMFAAVGNHVCGLHRERIGDIWLDDDLAPGEYRELTEDEINSVIVP 233


>gi|331268777|ref|YP_004395269.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329125327|gb|AEB75272.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 226

 Score = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 105/205 (51%), Gaps = 10/205 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+++  GI SR+E  R+I + R+ VNG +       V   D I +D  P++K E+  
Sbjct: 2   RINKLLSNYGICSRKEANRIIEENRIIVNGEVCIPGQW-VEEYDEILMDNEPIKKKEKIY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP+G+  T +     + + F N P     +  VGRLD ++EGL+L+TNDG L+  
Sbjct: 61  IAL-NKPVGITCTAAREVKDNIIDFLNYPE---YIFPVGRLDKDSEGLILMTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     Q  + Y V      D   +  + +G+ + G       VT    + +N    + L
Sbjct: 117 ILESENQHEKEYIVTVDKPFDDLFIKAMSEGVQLNGPKTRPCIVT----RINNDTFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRI 218
            +G NR+I+++   F + V +L RI
Sbjct: 173 TQGLNRQIRRMTRAFGYTVIKLERI 197


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 108/226 (47%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  + R +  +RV V+G +++  A  +     +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRALIARELRAKRVTVDGEIVKSGAHKLTPEQEVAFDGQVLEQIHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSTDDPDHSTILYFIDEPLAEKLHAAGRLDLDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y V     +  D       G+ + G        TL+ Q  +N  V + + 
Sbjct: 122 TSPKHECDKTYLVTLEHPLADDTAEQFAHGVQLHGEKDLTKPATLE-QLDANV-VRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F     +V  L R   G  +L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVVELHRERIGAIELDEDLAPGEYRPLTEE 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 88/175 (50%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 33  LFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAKLTQ 90

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G+   + L  L+ G+ +        G+   +  V L        + 
Sbjct: 91  PGKRTGKIYYVQVEGEPTPEALTALRDGVTLNDGPTLPAGVELVEEPVWLWPRNPPIRER 150

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ 
Sbjct: 151 KSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGDWRKA 205


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     +  D       G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQL----HNEKSLTKPAQLEVIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           + EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 178 ISEGRYHQVKRMFAAVGNRVLELHRERIGDIKLDDDLAPGEYRPLTPEEIASVGAPHL 235


>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 = 77.0 bits (188), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 91/175 (52%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L +KP  +++  +D +GR+T+ D +     ++   GRLD ++EGLLLLT++G +   +  
Sbjct: 6   LLNKPFNVLSQFTDSEGRATLADFVTE--KKLYPAGRLDYDSEGLLLLTDNGTVQHRISH 63

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM------------QVTLDTQK 183
           P T+  + Y V+  G   +  +  L+ G +++ G C   M            +  +  +K
Sbjct: 64  PRTKMPKTYWVQVEGAPTEQDIEPLRVGAILKDGPCLPAMVELIPEPNIWKREPPIRARK 123

Query: 184 G-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ + + EG+NR+++++     +   RLIR+  G + + TL  G TR+++
Sbjct: 124 AIPTTWLQLVITEGRNRQVRRMTASLGFPTLRLIRVKIGEWSIDTLKPGETRQIT 178


>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 = 77.0 bits (188), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 110/220 (50%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  + SR+ +++ + ++ + V+       A NV      +   G  ++  E  
Sbjct: 2   RLDRLLAQEKV-SRKAMKQALLKKEILVDDCPTSSLAQNVDTGLQKLVFQGRQIQGYEHI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D     TV D +P      ++ ++GRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGVVTASKDKK-LPTVMDLVPKNIQSGQLYAIGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K+GIV + G      Q+ + +   + +  +
Sbjct: 119 FQLLHPQYHVDKSYQVVVNGPLTSDHIQKFKEGIVFLDGTTCKPAQLEILSSSPTESRAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++KK+F     KV  L R+ +G F L   LA
Sbjct: 179 ITISEGKFHQVKKMFLSVGVKVTSLKRVQFGDFTLDPELA 218


>gi|327473408|gb|EGF18828.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK408]
          Length = 241

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 119/239 (49%), Gaps = 22/239 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--------MSTDHIEVDGVP 66
           R+ +++A   I SR+++++ + Q+++ V+G    + + NV          + H+      
Sbjct: 2   RLGQLLAANHI-SRKKMKQSLLQKQIFVDGKPACKLSQNVDTGLQQITFQSKHVS----- 55

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLL 124
                  R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+
Sbjct: 56  ---GPAHRYYMLNKPAGSVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLI 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQK 183
           T++G L   L  P     + Y V  +G +     +  ++GI  + G      Q+++ +  
Sbjct: 112 TDNGPLGFQLLHPQYHVEKTYYVEVNGPLTPKDKSSFQEGIRFLDGTTCQPAQLSILSTN 171

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            S +  TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R +++K L
Sbjct: 172 SSLSCATVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLATGDYRPLNQKEL 230


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLTDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>gi|289669952|ref|ZP_06491027.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 190

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 89/176 (50%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDT----------- 181
           L  P  +  + Y V+  G+   ++L  L+ G+V+        QV +LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTLPAQVRSLDPVPQLWPRDPPV 120

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDTLAPGQWR 176


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 105/226 (46%), Gaps = 25/226 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A     +R +V+  + + RV V+G +   +          + +DG P+  A R 
Sbjct: 6   RLDKFLAEMKKGTRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVSYA-RM 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRV--------ISVGRLDINTEGLLLL 124
             ++ +KP G+V         S   DNL P++ S +          VGRLDI+TEGLLL+
Sbjct: 65  EYFMLNKPQGVV---------SATEDNLHPTVISLIGDAKRKDLFPVGRLDIDTEGLLLI 115

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDT 181
           TNDG LA  L  P     +VY  +  G + +D +     GI +     +   ++ +    
Sbjct: 116 TNDGKLAHELLSPKKHVDKVYFAKVKGTLREDIVQAFAGGITLADQTTVLPAELLIESSY 175

Query: 182 QKGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++         + + EGK  ++K++FE    +V  L R+S GP  L
Sbjct: 176 EEAGEPVCEARLTIHEGKFHQVKRMFEAAGGQVVFLKRLSMGPLTL 221


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 88/178 (49%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     + + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVVLFNKPYDVLPQFTDEAGRKTLKDFIP--VPGIYAAGRLDRDSEGLLVLTNDGALQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL------- 179
           L  P  +  ++Y V+  G+   + L  L+ G+ +        G+   +    L       
Sbjct: 88  LTQPGKRTGKIYYVQVEGEPTPEALEALRTGVALNDGPTLPAGVEVVEEPAWLWPRNPPI 147

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + +     W+ V L EG+NR+++++     +   RLIR + G + L  L  G  RE+
Sbjct: 148 RERKNIPTRWLKVTLYEGRNRQVRRMTAHVGYPTLRLIRYAMGNYTLDNLANGEWREL 205


>gi|223043526|ref|ZP_03613571.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Staphylococcus capitis
           SK14]
 gi|222443014|gb|EEE49114.1| ribosomal small subunit pseudouridine synthase A
           (16Spseudouridylate 516 synthase) (16S pseudouridine 516
           synthase) (rRNA-uridine isomerase A) (rRNA
           pseudouridylate synthase A) [Staphylococcus capitis
           SK14]
          Length = 230

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 108/225 (48%), Gaps = 13/225 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V+VN   ++     +   TD + VDG  +   +  
Sbjct: 2   RIDKFLANMGLGTRTEVKQLLKKGLVEVNEKKIKTPKSQIDPETDKVVVDGEEISYVDNV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP   ++   D +   TV D +P  FS   +  VGRLD +TEGLLLLTNDG   
Sbjct: 62  YMML-NKPKDYISATED-NAHQTVLDLIPE-FSHLGIFPVGRLDKDTEGLLLLTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVT 190
             L  P     + Y V     + Q  +   K G+ +      D +V   +  KG++    
Sbjct: 119 HELMSPKKHVSKTYEVISKYPIKQSDIEAFKLGVEL-----SDGKVKPAELIKGNDRLSY 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           V + EGK  ++K++F     +V  L R+     +L  TL +G  R
Sbjct: 174 VTIYEGKYHQVKRMFHSIENEVLELKRVKIANLELDETLNSGEYR 218


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLT 226


>gi|327394528|dbj|BAK11950.1| ribosomal small subunit pseudouridine synthase A RsuA [Pantoea
           ananatis AJ13355]
          Length = 239

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/215 (27%), Positives = 95/215 (44%), Gaps = 2/215 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R I  QRV VNG ++   A  +     +E DG  L+     R
Sbjct: 2   RLDKFISQQLEISRAIAAREIRGQRVTVNGDVVRDTAFKLQPDHEVEYDGNVLQMQTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + V+     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTIVYFIEEPMAFKLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     V  D       G+ +           L+    +   +T  L 
Sbjct: 122 TSPRHHCEKTYRVTLEAPVSDDTAAQFSAGVQLHNEKSLTKPAQLEVITPTEVLLT--LS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           EG+  ++K++F     +V  L R   G   L   L
Sbjct: 180 EGRYHQVKRMFAAVGNRVVGLHRERIGEIVLDEAL 214


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDEIYFEDQLLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYATACAEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>gi|254496292|ref|ZP_05109179.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354480|gb|EET13128.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 240

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 83/178 (46%), Gaps = 20/178 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L++KP  +V   +      T+  F + P  ++     GRLD N+EGLLLLTNDG L
Sbjct: 53  SELILFNKPFAVVCQFTGEKHEHTLAEFIDKPDFYA----AGRLDKNSEGLLLLTNDGAL 108

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P     + Y V+  G      L  LKKG+V++ I +   +V    +        
Sbjct: 109 QHQLTHPKFNKKKYYWVQVEGIPTAADLEPLKKGLVLKDITFLPAEVRCIEEPALWPRTP 168

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                     +W+ + LREGKN +++++     +   RL+R   G +QLG L  G  R
Sbjct: 169 PVRFRQSIPTSWLEIILREGKNHQVRRMTAAMGFPTLRLVRHRIGDWQLGDLQPGEFR 226


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 111/238 (46%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 13  RLDKFLSQQLGVSRALVARELRAKRVTIDGEIVKSGAIKLTPEQDVRFDGNPLQQTVGPR 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 73  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 132

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     V  D       G+ +    + +  +T   Q        V + 
Sbjct: 133 TSPRHHCEKTYLVTLEHPVADDTAQQFTDGVQL----HNEKSLTKPAQLEVIEPQLVRLT 188

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           + EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 189 ISEGRYHQVKRMFGAVGNRVLELHRERIGDIKLDDDLAPGEYRPLTAEEIASVGAPHL 246


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 108/215 (50%), Gaps = 7/215 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  + SR+ +++ + ++ + V+       + NV      +   G  ++  E T
Sbjct: 2   RLDRLLAQEKV-SRKAMKQALLKKEILVDNCPASSLSQNVDTGLQKLVFQGRQIQGYEHT 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D     TV D LP      ++ +VGRLD +T GLLLLT++G L 
Sbjct: 61  YLLL-HKPNGVVTASKD-KKLPTVMDLLPPDIKSYQLYAVGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y++  +G +  + +   K GIV + G      Q+ + +   + +  +
Sbjct: 119 FQLLHPQYHVDKSYQMVVNGPLTSEHIQKFKDGIVFLDGTTCKPAQLEILSSSPTESHAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  +IKK+F     KV  L R+ +G F L
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTSLKRVQFGDFTL 213


>gi|301155121|emb|CBW14585.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 228

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 99/189 (52%), Gaps = 21/189 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E+T + L++KP  ++T  +D +GR+T+  F  +P++++     GRLD ++EGLL+LTN+G
Sbjct: 32  EQTIVILFNKPFDVLTQFTDENGRATLKDFITIPNVYA----AGRLDRDSEGLLILTNNG 87

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            +   L  P  +  + Y V+  G  ++  L+ L+KG+ ++       +V L         
Sbjct: 88  EVQHRLADPKFKTEKTYFVQVEGIPEETDLDKLRKGVELKDGMTKPAKVRLISEPDFLWP 147

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + Q  + +W+ + + EG+NR+++++     +   RLIR       L  L  G  
Sbjct: 148 RNPPIRERQSITTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMSHLTLDGLGNGEY 207

Query: 234 REVSKKILR 242
           R ++K+ +R
Sbjct: 208 RCLNKEEMR 216


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 68/250 (27%), Positives = 112/250 (44%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A + +  R+ V   I    VKVNG ++   ++N+    D +E  G  +    + 
Sbjct: 2   RLDKFLAESAVGRRKIVRTYIKDGMVKVNGKIITEPSININEKLDDVEYLGKKVIHNGKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G +T   D +   TVFD      + V  VGRLD +TEGLLLLTNDG     
Sbjct: 62  -YYIFNKPAGCITATRD-NIHKTVFDYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEFEHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------QGICYGDMQVT 178
           +  P     + Y     G +D +    L+ GI I               +   Y + +  
Sbjct: 120 VMYPEKHVEKTYFFWALGSLDDEDKKQLEAGIFIGNNESLTKPAKIDLYKSGLYKEFKEE 179

Query: 179 L--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
           +        D Q   + ++T+   EG+  ++K++ +     V  L RIS G  +L  +L 
Sbjct: 180 IPIKNLENKDHQPVVSGYLTIS--EGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLK 237

Query: 230 AGSTREVSKK 239
            G  R ++KK
Sbjct: 238 MGDYRNLTKK 247


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 65/218 (29%), Positives = 110/218 (50%), Gaps = 16/218 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR +V+++I +  V VNG  +      +    D IEVDG   + +++ 
Sbjct: 2   RLDKFLTHCGFGSRSQVKKLIREGIVTVNGKQIVEVDFKINPEEDIIEVDGRVAKFSKQI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + + +KP G V ++ +     TVF    D+L   +  + +VGRLD + EGLL++T+DG 
Sbjct: 62  YIMM-NKPKGYVCSNEEL-ASLTVFSLISDDLK--YRDLHTVGRLDKDAEGLLIITDDGE 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
               +  P  +  + Y VR   +VD++KLN  + GI++      D   TL  +     + 
Sbjct: 118 YTHRVISPKKRIEKEYLVRLEKEVDEEKLNEFENGIILD-----DGYKTLPAKYTIIDST 172

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + + EGK  ++K++FE    KV  L R+  G   L
Sbjct: 173 TVKLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNL 210


>gi|330950091|gb|EGH50351.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 230

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 61/214 (28%), Positives = 102/214 (47%), Gaps = 8/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + I     Q+TL   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENITTQPAQLTLLGPRSAR----L 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + EG+  ++K++F  F+ KV RL R + G   L
Sbjct: 177 SIVEGRYHQVKRMFGHFDNKVLRLHRENIGALAL 210


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 105/226 (46%), Gaps = 21/226 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA +   SR+E +R IA   V+VNG + + +A  V +   + + G  L      R
Sbjct: 2   RLDQFIATSSELSRKEAKRAIAAGDVQVNGDVWKNSATAVPANAEVMLQG-ELVALPAER 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + +KP G ++   D D + T  D LP+  +R + + GRLD +T GLLLLT+DG  +  
Sbjct: 61  YLMLNKPAGFISATRDSD-QPTALDLLPAELTRNLHIAGRLDADTTGLLLLTSDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-- 191
           +  P  +  + Y+V     + Q  +  L+ G++++           DT+    A VTV  
Sbjct: 120 VTSPRVECPKTYQVALSVPISQAAIAALETGVMLRN----------DTKPTKPAQVTVLQ 169

Query: 192 ------GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  + EG+  ++K++       V  L R   G   L   LA 
Sbjct: 170 SQLVELTISEGRYHQVKRMLAAVGNHVTALHRSRIGGVTLDPALAA 215


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/251 (26%), Positives = 113/251 (45%), Gaps = 28/251 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A++ I +R+ V + +    VK+NGI +  AAV +   + I      + + +   
Sbjct: 2   RLDKFLAQSQIGTRKIVRQYVKDGLVKINGITIFEAAVEINEIEDIIEYNGQITEYKEKV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++++KP G +T   D D + TVFD    I    V  VGRLD +TEGLLL TNDG     
Sbjct: 62  YYMFNKPSGCITARKDADDK-TVFDYFKEINMDGVFHVGRLDKDTEGLLLFTNDGDFNNK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------QGICYGDMQVT 178
           L  P     + Y     G +D+     L+ G+ I               +   Y +++  
Sbjct: 121 LMSPKFHVDKKYFFIALGSIDEKNKKNLESGVSIGENEPITKPAKIENLKNGTYEELKDK 180

Query: 179 LDTQK----GSNAWVT------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           L+ +K     S  ++       + + EG+  ++K++ +     V  L R+S G   L   
Sbjct: 181 LNLKKYYHVNSEYYIQPVVCGHITISEGRRHQVKRMLKSIGCHVIYLKRMSIGNLALDEF 240

Query: 229 L-AGSTREVSK 238
           L  G  R ++K
Sbjct: 241 LKKGDYRSLTK 251


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 75/240 (31%), Positives = 127/240 (52%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A   SR+++++++ Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLA-ANHISRKKMKQILLQKQILVDGNPACKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKIT-FQEGIRFLDGTVCQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK---ILREQL 245
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R +++K   I++E L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQKELEIIKEYL 237


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 111/232 (47%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++  I+  G  SRRE + +I Q++V VNG  +      V   D + + G PL+      
Sbjct: 2   RLNNFISSTGKCSRREADELIKQKKVTVNG-KIATLGCKVDPGDQVMLKGKPLQAKNNDV 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP+G+  TT     G    F N P    R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 61  YIALNKPVGITCTTERHIRGNIIDFINHPE---RIFPIGRLDKDSEGLILLTNDGSIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +     +  + Y V  + ++    +  + KG+ I         +T   +  + ++    +
Sbjct: 118 ILAEENKHEKDYIVTVNKKITPSFIEGMSKGVKIYNPVKNKDTMTKRCKLVRINDRTFKI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            L +G NR+I+++   F ++V +L R+      L  L  G  R ++++ +++
Sbjct: 178 TLCQGLNRQIRRMCTHFGYRVVKLKRVRIMNLTLKDLTIGKWRNLTEEEVKD 229


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDAT 216


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 107/227 (47%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFGYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+      L +GI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G   L   L  G  R +S++
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQ 225


>gi|281178245|dbj|BAI54575.1| conserved hypothetical protein [Escherichia coli SE15]
          Length = 217

 Score = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDAT 216


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 85/175 (48%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L   L  
Sbjct: 60  LFNKPFDVLCQFTDEAGRQTLKDFIP--VADVYAAGRLDRDSEGLLLLTNDGQLQAKLTQ 117

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------IC-------YGDMQVTLDTQ 182
           PS +  + Y V+  G+   + +N L  G+ ++        +C       +       + +
Sbjct: 118 PSQKTFKTYWVQVEGEPSDEAINALCNGVGLKDGMTLPAKVCVMASPDIWPRTPPVRERK 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+ V + EG+NR+++++         RLIR   G + L  L  G  + +S
Sbjct: 178 AIPTTWLEVQICEGRNRQVRRMTAHVGHPTLRLIRYKIGQWCLDDLPNGEYKVIS 232


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 107/227 (47%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  R +    V +NG L +  +V +  TD I  +G  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAARALKSGLVTINGKLEKSGSVKIGDTDEICYEGERLEWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+      L +GI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G   L   L  G  R +S++
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQ 225


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 57/187 (30%), Positives = 93/187 (49%), Gaps = 22/187 (11%)

Query: 74  RLWLYHKPIGLVTTHS-DPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R  +++KP G+++  + D    ST+ D  ++P ++     VGRLD ++EGLLLLTNDG L
Sbjct: 6   RYIIFYKPYGVLSQFTKDAPTHSTLKDYIDVPDVYP----VGRLDWDSEGLLLLTNDGQL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----- 185
              L  P     R Y V+     D+D +  L+ G+ IQ       QV L +++       
Sbjct: 62  QHRLAHPRFGHKRTYWVQVERIPDEDAIKRLQTGVKIQDYRTQPAQVRLLSKEPELPERT 121

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      AW+ + L EGKNR+++++     +   RL+R+S    QL  L  G  R+
Sbjct: 122 PPIRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVSIAHLQLDDLQLGEWRD 181

Query: 236 VSKKILR 242
           ++   L+
Sbjct: 182 LTTSELQ 188


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDMISVRGELIEYVENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISGTEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--V 65
           N +  R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V++ D ++V+G  +
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVYLNG---KRAAVGDQVVAGDTVKVNGQLI 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             ++A+     + +KP+G+V+T    +  + V     S+  R+  +GRLD +++GL+ LT
Sbjct: 60  EPKEADDFVFIVLNKPVGIVSTTESSEKNNIVDFVRHSV--RIFPIGRLDKDSQGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G L   +        + Y V  +  +    +  L  G+ +     G M       K +
Sbjct: 118 SNGDLVNKVLRAGNNHEKEYLVTVNKPLTDSVIEGLAGGVPM----LGKMTKKCPVTKVA 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + L +G NR+I+++ E F ++V +L R       L     G  R+++ K L
Sbjct: 174 PNVFNITLVQGLNRQIRRMCEHFGYEVVKLERTRIMNVSLKGTPVGDWRDLTPKEL 229


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 88/176 (50%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 43  LFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAKLTQ 100

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G+   + L  L+ G+ +        G+   +  V L        + 
Sbjct: 101 PGKRTGKIYYVQVEGEPTPEALTALRDGVPLNDGPTLPAGVELVEEPVWLWPRNPPIRER 160

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+  
Sbjct: 161 KSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGDWRKAE 216


>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 = 76.6 bits (187), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVKPGDVVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGHIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENCWEGDTSRISFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGDKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 111/227 (48%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +++A   SR++ ++++    V VNG +++ A++++    D IE  G PL  A   
Sbjct: 2   RLDKFLSKATELSRKDCKKILHAGEVTVNGEVVKDASLHIDEVGDDIEWAGEPLSVAMGN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L +KP G   T   P     V D  ++P + S  I+ GRLD++T G LLL++DGG  
Sbjct: 62  RYLLLYKPEGFECTLK-PKEWPIVTDLIDVPQLGSLRIA-GRLDVDTTGALLLSDDGGFL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P     +VY +     + + +    +  L KGI+++          L     ++A
Sbjct: 120 HRVTSPKHHVAKVYELTLADPMTEAQQAFAIKELAKGIMLEDEYDKTKPAELSFSDATHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   L EGK  ++K++  +F  KV  L R S G   L  L  G +R
Sbjct: 180 KLV--LTEGKYHQVKRMMGYFGNKVIELHRASIGNITLAGLEKGESR 224


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 114/228 (50%), Gaps = 10/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+++  G  SR+EV R I  +R+ VNG L E+    V  +D I +DG  ++  E+  
Sbjct: 2   RINKLLSNYGYCSRKEVSRWIEDKRIIVNGKLCEQGQW-VEESDEILLDGEKIKPKEKVY 60

Query: 75  LWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP G+V T + + D     F N       V  VGRLD +++GL+L+TNDG LA  
Sbjct: 61  IAL-NKPPGIVCTSAREIDNNIIDFLNYKD---YVFPVGRLDKDSQGLILMTNDGELANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +    +   + Y V      D+  +  +  G+ I     G +      ++      ++ L
Sbjct: 117 ILSSDSYHEKEYIVTIDRDFDESFIEGMSNGVEI----LGTITRPCKLRRIDKNIFSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G NR+I+++ + F + V +L RI         +  G  + ++K+++
Sbjct: 173 TQGLNRQIRRMTKAFGYNVIKLERIRIMNIMSNDIELGQWKFINKEVI 220


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 72/275 (26%), Positives = 120/275 (43%), Gaps = 69/275 (25%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG--VPLRKAE 71
           R++K+I+     SRR+ ++ I    VK+N  +++    ++ +  D I++ G  V + K +
Sbjct: 23  RLNKIISLEKKMSRRKSDQFIKDGNVKLNNKIVKNPGTHIDVKKDKIKICGKTVNILKTQ 82

Query: 72  RT---------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTE 119
           +          + ++ HKP GL+ T  D   R++++   P       R++SVGRLD NT 
Sbjct: 83  KMISPNDSSMYKWFVLHKPKGLLCTSDDEKERASIYSLFPQDILDNYRLVSVGRLDRNTS 142

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV---------------DQDKLNLLKKG 164
           G+LLLTN+      L  P  Q +R YRV   G                 D D+   +KKG
Sbjct: 143 GVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGAAQMKVLRELAAGVYLPDDDRGGKVKKG 202

Query: 165 I-------------------VIQGICYG---DMQVTLDTQKG-----------------S 185
           +                   V +GI  G    MQ    TQ                    
Sbjct: 203 MQKGMQKGMQKGMQKGMQKGVPKGIQKGFPTGMQKGFPTQPAFIEILRQETIKVKDQVKR 262

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            + + + +REG+NR+I+K+FE  N  V ++ R ++
Sbjct: 263 VSVLNISVREGRNRQIRKMFEQINQPVIKIKRTAF 297


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + ++ +   K+GI +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEEDIQAFKEGITLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 64/220 (29%), Positives = 98/220 (44%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G +   A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVSIGGAVCTDADADFPTGDTTFSFTVDGVVWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPAGYECS-RDPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L  G+++ G       V ++ +      +T
Sbjct: 121 VHLFTSPKRKVPKVYVATTRHPIDDVQLSALHDGVLLHGESKPIAAVNVEARGDHTLALT 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V   EGK  ++K++      +   L R   G F L   LA
Sbjct: 181 V--MEGKYHQVKRMIAAAGNRCEALHRERIGGFALPGALA 218


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 109/230 (47%), Gaps = 12/230 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+G   +   + V    HI  DG  L+  +   
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLAERVYVDGAPAKSLDLLVDEFSHIVFDGQVLQANQPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
           L LY KP+G+V+   D + R TV D L     + + + GRLD+N+ GLLLLTND   +  
Sbjct: 67  LMLY-KPVGVVSATKDKEHR-TVIDLLDCDTRQELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVT 190
           L  P  +  +VYRV     +  + +         QG+ +G   +T    K    +     
Sbjct: 125 LMSPEQKVDKVYRVTLANPLSDEYI-----AAFAQGMYFGFEDITTQPAKLVILAPHVAE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
           V LREGK  +IK++F  F   V  L R+S G   L   L  G +R ++ +
Sbjct: 180 VTLREGKYHQIKRMFGRFRNPVLGLHRLSIGEITLDEALKPGESRMLTAQ 229


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 105/226 (46%), Gaps = 25/226 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A     +R +V+  + + RV V+G +   +          + +DG P+  A R 
Sbjct: 6   RLDKFLAEMKKGTRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVSYA-RM 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRV--------ISVGRLDINTEGLLLL 124
             ++ +KP G+V         S   DNL P++ S +          VGRLDI+TEGLLL+
Sbjct: 65  EYFMLNKPQGVV---------SATEDNLHPTVISLIGDAKRKDLFPVGRLDIDTEGLLLI 115

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDT 181
           TNDG LA  L  P     +VY  +  G + +D +     GI +     +   ++ +    
Sbjct: 116 TNDGKLAHELLSPKKHVDKVYFAKVKGTLREDIVQAFAGGITLADQTTVLPAELLIESSY 175

Query: 182 QKGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++         + + EGK  ++K++FE    +V  L R+S GP  L
Sbjct: 176 EEAGEPVCEARLTIHEGKFHQVKRMFEAAGGQVVFLKRLSMGPLTL 221


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGHVFING---KRAGIGDQVQVGDLVKVNGQVIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+V+T    +  + V  +  +  +RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DSLVLIALNKPVGIVSTTEAGEKDNIV--DFVNHSTRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFVRGMAAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLT 225


>gi|162138450|ref|YP_540277.2| 23S rRNA pseudouridine synthase E [Escherichia coli UTI89]
          Length = 207

 Score = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 146

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDAT 206


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLVQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 76.6 bits (187), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAER 72
           R++K I+ +G+ SRRE ++ I Q  V +NG    RA V    + H  + ++G  +   E 
Sbjct: 6   RLNKFISDSGVCSRREADKYIEQGHVFING---RRATVGAQVSKHDKVTLNGNLIEAKEG 62

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T      ++KP+G+++T ++   + ++ D +     R+  +GRLD  ++GL+ LTN+G +
Sbjct: 63  TDFAFIAFNKPVGIIST-TEIGVKDSIIDYI-GYHERIFPIGRLDKESQGLIFLTNNGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +     +  + Y V  +  +  + +  +  G+ I     G+M       K S     
Sbjct: 121 VNKILRAGNKHEKEYLVTVNKPITDEFILKMGNGVPI----LGEMTKKCSVIKESVFSFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E+F ++V +L RI      L  +  G  R++  + + E
Sbjct: 177 IVLIQGLNRQIRRMCEYFEYEVVKLERIRIMNIGLKGIPLGEWRQLEAEEMNE 229


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 87/176 (49%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L        + 
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 176


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKSYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 86/173 (49%), Gaps = 17/173 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 43  LFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAKLTQ 100

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G+   + L  L+ G+ +        G+   +    L        + 
Sbjct: 101 PGKRTGKIYYVQVEGEPTAEALAALRNGVTLNDGPTLPAGVEVVEEPAWLWPRNPPIRER 160

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 161 KSIPTCWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGEWR 213


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 112/236 (47%), Gaps = 20/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G  SR++V++++    V+V G  ++  + +V   ++ I V G  +      
Sbjct: 2   RIDKFLANMGFGSRKDVKKLLKTGAVRVQGQPIKDPSTHVEPESESITVYGEEVEYKPYV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--------PSIFSRVISVGRLDINTEGLLLLT 125
            L + +KP G++    D +   TV D L        PS       VGRLD +T GLLL+T
Sbjct: 62  YLMM-NKPKGVICATEDLE-HETVIDLLGEEERHYEPS------PVGRLDKDTVGLLLIT 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKG 184
           NDG     L  P     + YR    G V ++ +     G+V+    Y     TL   + G
Sbjct: 114 NDGKFNHWLMSPKHHVPKTYRALVEGHVTEEDVGAFSHGVVLDD-GYVTKPATLHILEAG 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + + + + L EGK  ++K++F+    +V  L RI  G   L   LA G  RE++K+
Sbjct: 173 ARSHIELILTEGKFHQVKRMFQAVGKRVLELERIKIGNLLLDPELARGEYRELTKE 228


>gi|318606383|emb|CBY27881.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
          Length = 235

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 111/238 (46%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQTVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     +  D       G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQL----HNEKSLTKPAQLEVIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           + EG+  ++K++F     +V  L R   G  +L   LA G  R ++ + +     PHL
Sbjct: 178 ISEGRYHQVKRMFAAAGNRVLELHRERIGDIKLDDDLAPGEYRPLTPEEIASVGAPHL 235


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 92/189 (48%), Gaps = 23/189 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLL 122
           P  + E TRL  +HKP G+++  + P+G+     +   +P ++      GRLD ++EGLL
Sbjct: 34  PAPRPEVTRLLCFHKPYGVLSQFT-PEGKWQGLKDWIDVPGVYV----AGRLDADSEGLL 88

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------------- 167
           LLTNDG L   +  P  +  + Y V+  G  D+  L  L++G+ +               
Sbjct: 89  LLTNDGQLQARIADPRHKMEKTYWVQVEGIPDEAALQRLREGVELSDGKTLPAKARLIEP 148

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           Q + +         Q   + W+ + +REGKNR+++++         RL+R++ GP+ +  
Sbjct: 149 QPLMWPRNPPIRVRQNIPDCWIELIIREGKNRQVRRMTAAVGHPTLRLVRMAVGPYSIEG 208

Query: 228 LLAGSTREV 236
           L  G   +V
Sbjct: 209 LEPGQWLDV 217


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 87/176 (49%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L        + 
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 176


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLDPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLT 226


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 116/228 (50%), Gaps = 6/228 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A    A R+++++++A++++ V+ +  ++ + N+      I++ G  + +  R 
Sbjct: 2   RLDQLMADHQYA-RKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI-GDRIIQEPRH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKPIG VT   D    + +    P   +  +  +GRLD +T GLLL+T++G L  
Sbjct: 60  HYYMLHKPIGAVTAKRDAHHPTVIELVDPQQEYPDLYPLGRLDRDTSGLLLITDNGPLGF 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY V  +G +    +   + GI    G       +T+     S +   +
Sbjct: 120 QLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTLSYSKAQI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
            + EGK  ++KK+F     KV  L R+S+GPF L   LA G +R +++
Sbjct: 180 RISEGKYHQVKKMFLAIGVKVMTLNRLSFGPFTLDPQLAPGESRPLNE 227


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R+SK +A+ G+ SRRE +  I Q  V VNG    + AV    V   D IE++     +  
Sbjct: 15  RLSKRMAQLGLCSRREADGHIEQGWVTVNG----KTAVLGQKVSPADRIELNKKAHEQQA 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGRL 114
                L +KP+G V+  ++   +S                   FD  P     +   GRL
Sbjct: 71  ARITILLNKPVGYVSAQAEKGYKSAAELITPENCWEGDTSRISFD--PKHKIGLAPAGRL 128

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G     
Sbjct: 129 DIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDGDKLRP 188

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    ++  L RI  G  +LG L  G  R
Sbjct: 189 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRIVGLKRIRMGKVKLGRLPPGKWR 244

Query: 235 EVS 237
            ++
Sbjct: 245 YLA 247


>gi|145355123|ref|XP_001421818.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582057|gb|ABP00112.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 238

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 72/233 (30%), Positives = 111/233 (47%), Gaps = 28/233 (12%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERTRL----------- 75
           RRE +  ++  RV VNG L+ R +  V + D + +DG V L +A   R+           
Sbjct: 1   RREADAAVSAGRVLVNGELV-RPSQRVKAGDVVTLDGKVMLWEAYARRVEEEIANDATSS 59

Query: 76  ---WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTND 127
               LY+KP G+V T  +P  R+++   L    +R     +  VGRLD ++ GL+LLTND
Sbjct: 60  FVYLLYNKPRGVVCTM-EPHQRTSLHFALERERARMKKIRIFPVGRLDKDSSGLVLLTND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------LDT 181
           G ++  L  PS +  + Y V     V    +  L  G+VI  +    M  T       + 
Sbjct: 119 GRVSDALLDPSRKAEKEYDVDVDRDVSAADVERLAAGVVITTLQQRTMTETTAPTQPCEV 178

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +K     +   L+EG+NR+I+K+ E  ++ V RL R      +LG L  G  R
Sbjct: 179 RKIGPRTLRFVLKEGRNRQIRKMCEALSYDVTRLHRTRIAELELGDLEIGGLR 231


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 109/230 (47%), Gaps = 12/230 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+G   +   + V    HI  DG  L+  +   
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLAERVYVDGAPAKALDLLVDEFSHIVFDGQVLQANQPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
           L LY KP+G+V+   D + R TV D L     + + + GRLD+N+ GLLLLTND   +  
Sbjct: 67  LMLY-KPVGVVSATKDKEHR-TVIDLLDCDTRQELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVT 190
           L  P  +  +VYRV     +  + +         QG+ +G   +T    K    +     
Sbjct: 125 LMSPEQKVDKVYRVTLANPLSDEYI-----AAFAQGMYFGFEDITTQPAKLVILAPHVAE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
           V LREGK  +IK++F  F   V  L R+S G   L   L  G +R ++ +
Sbjct: 180 VTLREGKYHQIKRMFGRFRNPVLGLHRLSIGEITLDEALKPGESRMLTAQ 229


>gi|325497996|gb|EGC95855.1| 16S rRNA pseudouridylate synthase A [Escherichia fergusonii ECD227]
          Length = 231

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 102/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G  +  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGETVRNAAFKLLPEHEVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRDAT 216


>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 = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 107/225 (47%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           RV   +A  G+ SRR  E +I ++ ++VNG  + +    V   D I     + + K  ++
Sbjct: 8   RVQVFLAEKGVGSRRFCEELIRKKLIRVNG-SIAKLGDKVSPGDRIIYKKQIYVFKDFQS 66

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
           +  +Y   +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KNKIYLALNKPKNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +   K S   +
Sbjct: 127 FANDIIHPRRKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEI-LNKNSARLI 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 186 ---LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 113/234 (48%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAER 72
           R+ K +A  G  +R EV++ + +  V VNG  +E++A   ++  H  +++ G  +   E 
Sbjct: 3   RLDKFLAHMGQGTRTEVKQSLKKGNVTVNG-KVEKSAKTQINPHHDVVQIHGHQIDYVET 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP G ++   DP  ++TV D +    +  +  VGRLD +TEGLLL+TNDG  +
Sbjct: 62  VYLML-NKPKGYISATEDP-KQATVIDLIKDYKYLDLFPVGRLDKDTEGLLLITNDGQFS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     V +D   + K+G+++        ++T+     S     V
Sbjct: 120 HNLMNPNKHVAKTYLVTSKYPVTKDNQYMFKQGVMLSDGLTKPAELTIIDDYHSK----V 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  +IK++F     +V  L RI     +L   L      V  +   EQL
Sbjct: 176 TIYEGRYHQIKRMFHSIENEVLELKRIQIANLRLDEELDEGQYRVLTQTDIEQL 229


>gi|330937693|gb|EGH41591.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 230

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 107/227 (47%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVGEFSCVALDEEILQAGKVPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSARLSIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVLRLHRETIGALALDPDLCPGSYRALN 223


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN---VMSTDHIEVDGVPLRKAE 71
           R++K+ +  GI SR+E  ++I + RV VNG    +  +    V  +D I +D  PL   E
Sbjct: 2   RINKLFSNFGICSRKETNKIIREGRVIVNG----KPCIEGQWVELSDEILLDEKPLVPKE 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + L +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA
Sbjct: 58  KIYIAL-NKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLA 114

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWV 189
             +        + Y V        D +  +++G+ I G      QVT     ++ +    
Sbjct: 115 NEVLAAENNHEKEYIVTLDQPFYDDFIKKMERGVEILG------QVTKPCKLKRINENTY 168

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           ++ L +G NR+I+++ + F + V +L RI      L  +  G  R ++++
Sbjct: 169 SIILTQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINRE 218


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 112/232 (48%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADIDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTE 227


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 112/225 (49%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I +++V +NG  + +    V   D + V+G  LR A    
Sbjct: 5   RINKFISEAGKASRRGADKLINERKVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRINHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 222


>gi|325697062|gb|EGD38949.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 241

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 75/238 (31%), Positives = 124/238 (52%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKQVSDPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDKL   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKLA-FQEGIRFLDGTICQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++    +E+LG
Sbjct: 178 TVKISEGKFHQIKKMFLALGVKVTYLKRIQFGNFTLDPDLATGDCRPLN----QEELG 231


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 117/237 (49%), Gaps = 26/237 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--------ILLERAAVNVMSTDHIEVDGVP 66
           R++K +A  G+ SR+   R I    + ++G        I L  +   + S + ++ DGV 
Sbjct: 9   RLAKYLAMTGLCSRKAATRYIRDGHITLDGRLANHIDTISLIESPSGLTSLEILKFDGVL 68

Query: 67  LRKAERTRLWLYHKPIGL---VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           ++  E  + W+ +K +G    +  H DP   S++   LP    R+  VGRLD ++ G L+
Sbjct: 69  IQGVESKQYWMLNKSVGTDCRLLAH-DP---SSLLHLLPD-NPRLYPVGRLDKDSRGQLI 123

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--- 180
           LTNDG L + L  P     + Y V+  G  +    + L K  + QG+ Y D+  TL    
Sbjct: 124 LTNDGELTQQLMHPDFGHSKTYHVQVDGNFED---SFLIK--MAQGVSYRDV-TTLPCKM 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T+   N +  + L +G NR+I+++ +   +KV  L R++     LG L  G  R+++
Sbjct: 178 TRLNDNKFEII-LTQGLNRQIRRMSQALGYKVVDLKRVNIQSLALGDLKEGEMRQLT 233


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 52/177 (29%), Positives = 90/177 (50%), Gaps = 21/177 (11%)

Query: 78  YHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP  ++   +D   P   +     LP    RV + GRLD ++EGLLLLT++G LA  L
Sbjct: 15  FNKPFNVLCQFTDRSVPPRPTLAGFGLPP---RVYAAGRLDHDSEGLLLLTDNGTLAHKL 71

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQKG--- 184
             P  +  + Y V+  G    ++L  L+ G+V+         I   D   +L T+     
Sbjct: 72  TDPKHKADKTYWVQVEGMPSDEQLQQLRTGVVLNDGPTLPAKIERLDPAPSLWTRDPPVR 131

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                 ++W+ + +REG+NR+++++    N    RL+R+S GP++L  L  G  R++
Sbjct: 132 FRKTVPDSWLAITIREGRNRQVRRMTAAVNLPTLRLVRVSMGPYRLDDLQPGQWRQI 188


>gi|188581487|ref|YP_001924932.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179344985|gb|ACB80397.1| pseudouridine synthase [Methylobacterium populi BJ001]
          Length = 242

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 111/230 (48%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL----ERAAVNVMSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+ +G  L    +R A+    +  + V G PL   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRRDGEALRDASQRIALEPDLSARMTVQGAPLDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP+G+  +H +      ++  LP  + R    + +VGRLD  T GLLL+T+
Sbjct: 65  PGVCLML-HKPLGVTCSHKEAG--PLIYSLLPERWRRRDPALSTVGRLDKETSGLLLMTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++ +  +
Sbjct: 122 DGALLHRIIAPKAKVAKRYRVTLARPLQGDEAAILASGELMLEGEDKPLLPVEMEGEDAT 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           +  VT  L EG+  +++++F      V+ L R   G   L   L AG  R
Sbjct: 182 HCTVT--LHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFR 229


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 108/227 (47%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+      L +GI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAQMEIIDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EG+  ++K++F     KV  L R   G   L  +L  G  R ++++
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDESLEEGEYRPLTEQ 225


>gi|291543398|emb|CBL16507.1| pseudouridine synthase family [Ruminococcus sp. 18P13]
          Length = 255

 Score = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 100/210 (47%), Gaps = 7/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K IA     SR+EV+ ++ +  V+VNG   +     V    D I + GV L  A   
Sbjct: 2   RLDKCIADHSAYSRKEVKELLRRGSVRVNGAPEQDPGRQVDPEGDEIMLAGVILPTALH- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G +++      ++ V    P +   +   GRLD++TEG+LLLTNDG LA  
Sbjct: 61  RTYMLNKPKGCISSTRTGKTKTVVEFLPPELRKGIFPAGRLDVDTEGMLLLTNDGDLAHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V+    V +  +   + G+V++    C   +   +    G      V
Sbjct: 121 ILSPRRHIPKYYLVQLAKPVVEKTVETFENGVVLEDGTRC---LPARVAALPGVENTALV 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            L EGK  ++K++F      V +L+R+  G
Sbjct: 178 ELHEGKFHQVKRMFAAVENHVEQLLRVQMG 207


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLIIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 76.3 bits (186), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 69/250 (27%), Positives = 113/250 (45%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A + I  R+ V   I    VKVNG ++   ++++    D +E  G  +    + 
Sbjct: 2   RLDKFLAESAIGRRKIVRTYIKDGMVKVNGKIITEPSLDINEKLDDVEYLGKKVIHNGKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G VT   D +   TVFD      + V  VGRLD +TEGLLLLTNDG     
Sbjct: 62  -YYMFNKPAGCVTATRD-NVHKTVFDYFHEDMNGVFHVGRLDKDTEGLLLLTNDGEFEHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------QGICYGDMQVT 178
           +  P     + Y     G  D +    L++GI I               +   Y + +  
Sbjct: 120 VMYPEKHVEKTYFFWALGSFDDEDKKQLEEGIFIGNNESLTKPAKIDVHKSGLYKEFKEE 179

Query: 179 L--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
           +        D Q   + ++T+   EG+  ++K++ +     V  L RIS G  +L  +L 
Sbjct: 180 IPIKNLENKDHQLVVSGYLTIS--EGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLK 237

Query: 230 AGSTREVSKK 239
            G  R+++KK
Sbjct: 238 MGDYRDLTKK 247


>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 = 76.3 bits (186), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 112/242 (46%), Gaps = 30/242 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G+++++    V     I++D       ++  
Sbjct: 377 RLSKLMSELGLCSRREADEWIEKGWVTVDGVVVDKLGTKVRPDADIQIDPAAQAAQQKQV 436

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFSRV-----ISVGRLDINT 118
             L HKP+G V+  ++ DG                D     FS V        GRLDI++
Sbjct: 437 TILVHKPVGYVSGQAE-DGYEPAVTLVKPENRWDGDRTDIRFSAVHLRQLAPAGRLDIDS 495

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQD--------KLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    ++  + Y VR  +G ++ D         L  L+ G+ + G
Sbjct: 496 TGLLVLTQDGRIAKQLIGGHSEIDKEYLVRVSYGDIETDVEHEFPAESLAKLRHGLELDG 555

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 556 VPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLHVVGLKRVRMGHVMLGALP 611

Query: 230 AG 231
            G
Sbjct: 612 PG 613


>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 = 76.3 bits (186), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 88/181 (48%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+     D   L  L+ G+ +        GI         +      
Sbjct: 98  LTQPGKRTGKIYYVQVESIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE+++
Sbjct: 158 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQ 217

Query: 239 K 239
           +
Sbjct: 218 E 218


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 66/227 (29%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|283471019|emb|CAQ50230.1| RNA pseudouridine synthase family protein [Staphylococcus aureus
           subsp. aureus ST398]
          Length = 231

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + ++ +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEEDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 51/175 (29%), Positives = 87/175 (49%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 43  LFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAKLTQ 100

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G+   + L  L+ G+ +        G+   +    L        + 
Sbjct: 101 PGKRTGKIYYVQVEGEPTAEALAALRDGVTLNDGPTLPAGVEVVEEPAWLWPRNPPIRER 160

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +     W+ V L EG+NR+++++     +   RLIR + G + L  L  G  R+ 
Sbjct: 161 KSIPTRWLKVTLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGEWRKA 215


>gi|324113926|gb|EGC07900.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 217

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   +D L  L+ G+ +     +  G   V            
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 156

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 157 IRERKSIPTSWLKITIYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 216


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 112/225 (49%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I +++V +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERKVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRINHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        +VT    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVT----QLSKYEFQIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 219


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 56/224 (25%), Positives = 110/224 (49%), Gaps = 14/224 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV   ++  G  +R E ++ +    + +N   +   ++     D I+++G  L   + T
Sbjct: 6   KRVDAHLSSLGYCTRSEAKKFLRMNEICINDNRVYNTSIKAYHDD-IKINGEVLD--DET 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L L +KP G + +H+D      ++  LP  +SR    + ++GRLDI+T G++LLT+DG 
Sbjct: 63  LLILLNKPQGYICSHND--SGKLIYSLLPQRYSRRNPKISTIGRLDIDTTGVILLTDDGV 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
           L+  L  P     ++Y       +  D++ +   G ++     G+ +  L  +    +  
Sbjct: 121 LSHRLTSPKKDISKIYEATLEKPLKGDEVEIFASGTLMLN---GEEKPLLPAKLEIITPT 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +V + + EGK  ++K++F   + KV +L R  +  F+L  L  G
Sbjct: 178 FVKIEIVEGKYHQVKRMFAAVSNKVIKLHRTKFADFELEDLKEG 221


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 112/225 (49%), Gaps = 7/225 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I +++V +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERKVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+  T S+   +  + D L +   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIID-LVNHPLRINHIGRLDKDSDGLILLTNDGDIVNEI 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        +VT    + S     + L 
Sbjct: 119 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVT----QLSKYEFEIILT 174

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 175 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 219


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 112/234 (47%), Gaps = 10/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAER 72
           R+ K +A  G  +R EV++ + +  V VNG  +E++A   +   H  +++ G  +   E 
Sbjct: 3   RLDKFLAHMGQGTRTEVKQSLKKGNVTVNG-KVEKSAKTQIDPHHDVVQIHGHQIDYVET 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
             L L +KP G ++   DP  ++TV D +    +  +  VGRLD +TEGLLL+TNDG  +
Sbjct: 62  VYLML-NKPKGYISATEDP-KQATVIDLIKDYKYLDLFPVGRLDKDTEGLLLITNDGQFS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     V +D   + K+G+++        ++T+     S     V
Sbjct: 120 HNLMNPNKHVAKTYLVTSKYPVTKDNQYMFKQGVMLSDGLTKPAELTIIDDYHSK----V 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  +IK++F     +V  L RI     +L   L      V  +   EQL
Sbjct: 176 TIYEGRYHQIKRMFHSIENEVLELKRIQIANLRLDEELDEGQYRVLTQTDIEQL 229


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLVSPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 225


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 121/251 (48%), Gaps = 29/251 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERT 73
           R+ K +A +GI +R+EV+ ++  ++V VN + ++   ++V      E D V    K    
Sbjct: 2   RLDKFLANSGIGTRKEVKEILKNKKVSVNNVFVKDGKIHVDE----EKDIVKYENKIINY 57

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
           + ++Y   +KP G+++   D   + TV D L   +    +  VGRLDI+TEGL+LLTNDG
Sbjct: 58  KPFVYIMMNKPAGVISATEDSHHK-TVIDLLNDEYRTYDIFPVGRLDIDTEGLILLTNDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-----------ICYGDMQV 177
            L+  L  P     + Y V+    + +D +  L+ GI ++            IC    + 
Sbjct: 117 ILSHNLLSPKKHVDKKYYVKITKSLSEDDIKTLENGIKLEENFITKNAKVEIICNNSEKE 176

Query: 178 TLDTQKGSNAW------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLA 230
           + D   G N        V + + EGK  ++K++F+    +V  L R+  G       L  
Sbjct: 177 SEDFDFGENENNKNENSVYITISEGKFHQVKRMFKAVGNEVLYLKRVKMGNLLLDENLEL 236

Query: 231 GSTREVSKKIL 241
           G  RE+++K L
Sbjct: 237 GGYRELTQKEL 247


>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 = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 46/174 (26%), Positives = 84/174 (48%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 66  LFNKPFDVLCQFTDEQGRQTLKDFIP--IPGVYAAGRLDRDSEGLLLLTNDGKLQSQITE 123

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  + Y  +  G  ++D L  L++G+ ++       ++++                 
Sbjct: 124 PKKKTYKTYWAQVEGAPNEDDLEKLRQGVELKDGMSLPAKISIMNNPDIWPRTPPIRERA 183

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RLIR   G + L  L  G  R++
Sbjct: 184 NIPTTWLEIKICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLKNGEYRQL 237


>gi|321223855|gb|EFX48918.1| Ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
          Length = 181

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 87/178 (48%), Gaps = 17/178 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVTLDT 181
           P  +  ++Y V+  G  D   L  L+ G+ +        GI         +       + 
Sbjct: 61  PGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE++++
Sbjct: 121 KNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQE 178


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 118/235 (50%), Gaps = 19/235 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLR-KAE 71
           R++K I+ +G  SRRE ++ I Q  V +NG+   RA +    T  D + V+G  L+ K++
Sbjct: 6   RLNKFISDSGYCSRREADKYIEQGSVFINGV---RAKIGTQVTRRDKVVVNGHTLQQKSQ 62

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTND 127
              +++  +KP G+ +T         V DN+        R+  +GRLD +++GL+ LT++
Sbjct: 63  EEEIYIALNKPPGVTSTTE-----KGVVDNIVDYVGHPQRIFPIGRLDKDSQGLIFLTSN 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V     +  D +  +  G+ I G+     +  +  Q  SN 
Sbjct: 118 GDIVNKILRAGNEHQKEYLVTVDKPITPDFIAKMATGVPILGVV---TKKCIVEQISSNV 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  V L +G NR+I+++ E+F + V +L R      +L  +  G  RE+++  +R
Sbjct: 175 FKIV-LIQGLNRQIRRMCEYFQYNVTKLERTRIMNIELKGIPLGEWRELTESEMR 228


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 119/276 (43%), Gaps = 50/276 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +A  G+ SRRE +  IA   VKVNG   E   V V  +D IEVD     +  
Sbjct: 6   APIRLNKRMAELGLCSRREADEWIANGWVKVNGKPAE-MGVKVTPSDRIEVDKAAKGQQA 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---TVF--------DNLPSIFSR-----VISVGRLD 115
                L +KPIG V+  ++ DG     T+F        DN    FS      +   GRLD
Sbjct: 65  NQVTILINKPIGYVSGQAE-DGHEPAVTLFTPQNRWAEDNARFFFSPQQLRGLAPCGRLD 123

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHG-----------QVDQDKLNLLK 162
           I++ GLL++T DG +AR L    +   + Y  RV +HG           ++D D      
Sbjct: 124 IDSIGLLVMTQDGRIARQLIGEDSVMEKEYLVRVAYHGLGQPAPTGQLVRMDDDDPVTTN 183

Query: 163 KGIVIQGICYGDMQ--VTLDTQKGSNA---W-----VTVGLREGKNREIKKVFEFFNWKV 212
              V        ++  ++LD Q    A   W     +   L EGK R+I+++ E    KV
Sbjct: 184 VQAVFPPAMLARLRHGLSLDGQPLKPARVEWQNPEQLRFVLTEGKKRQIRRMCELVGLKV 243

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             L R+  G   LG L  G  R          LGPH
Sbjct: 244 VGLKRVRIGKVMLGNLPVGQWR---------YLGPH 270


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 63/213 (29%), Positives = 109/213 (51%), Gaps = 15/213 (7%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
           + +++AQ R+ ++G+  E  +  V    H+ +D   L +AE+ R  + +KP G+V+   D
Sbjct: 1   MHQLLAQGRILLDGLAAESISQVVGPFTHVVLDQRVL-QAEQPRYIMLNKPPGMVSATCD 59

Query: 91  PDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
            +  STV D + +  ++ +  VGRLD N+ GLLLLTNDG  +R +  P    ++ YRV+ 
Sbjct: 60  -EQHSTVLDLVSAPNAKSLHIVGRLDFNSTGLLLLTNDGRWSRGVSSPQKGVVKTYRVQL 118

Query: 150 HGQVDQDKLNLLKKGI--VIQGICY--GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                 D       G+    + I     +++   D  +G +        EG+  +IK++F
Sbjct: 119 EQPFRSDYREAFAAGLYFAFENITTRPAEIRRLSDLSRGRSV-------EGRYHQIKRMF 171

Query: 206 EFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
            +FN +V  L R+S G   L   L  G+ RE++
Sbjct: 172 GYFNNRVLNLHRLSIGALSLDPKLHQGAWRELT 204


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 105/216 (48%), Gaps = 9/216 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++I+ +   +R++V  ++AQ+RV V+G+L    A  V    H+ +D   L +A +T 
Sbjct: 7   RLDRLISDSRQINRKKVRLILAQKRVYVDGVLATDIAQLVDQFSHVVMDNEVL-QANQTH 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----SVGRLDINTEGLLLLTNDGG 129
             + +KPIG+V    D   + TV D L   F + +      VGRLD+NT GL+LLTND  
Sbjct: 66  YIMLNKPIGVVCATKDKKHK-TVIDLLAEQFDQDVLDSLHIVGRLDLNTSGLVLLTNDSR 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +  L  P  +  + Y+V     +  D ++   KG+             L       A V
Sbjct: 125 WSERLTSPEHKVSKGYQVTLENALTTDYIDAFAKGMYFPYENITTKPAILHIVSLFEAQV 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +  L EG+  +IK++F  F   V  L R S G  +L
Sbjct: 185 S--LTEGRYHQIKRMFGRFRNPVIALHRYSIGSLRL 218


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 55/186 (29%), Positives = 88/186 (47%), Gaps = 20/186 (10%)

Query: 68  RKAERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           R  +  +L L++KP G++T  T   P+   + F  LP  ++     GRLD  +EGLL+LT
Sbjct: 19  RNHKMPQLILFNKPYGILTQFTGELPEQTLSAFIKLPGFYA----AGRLDKQSEGLLILT 74

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           +DG L   L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L ++   
Sbjct: 75  DDGKLQHRLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKI 134

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + LREGKN +I+K+     +   RLIR   G + L  L  G
Sbjct: 135 WPRIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPG 194

Query: 232 STREVS 237
             + ++
Sbjct: 195 EYKLIN 200


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLNGIPLGEWRDLT 225


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 60/213 (28%), Positives = 103/213 (48%), Gaps = 7/213 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A++   SR+EV R +    V VN + ++  A+++   D + + G P+ +A   +
Sbjct: 2   RLDKYLAQSTGFSRKEVRRFMKAGEVVVNDLEIKDPALHISDEDDVYLSGYPV-EAPGEK 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP+G V ++ D     TV    +LP      I  GRLD++T GL+L+T++G  A 
Sbjct: 61  YLMLHKPLGCVCSNDD-STHPTVLSLLDLPRAEELTI-CGRLDVDTTGLVLITSNGKWAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y+V     + QD +    KG+++           L       A V   
Sbjct: 119 KVTSPKHKTGKRYQVTTADPIPQDAITKFAKGLMLINEKERTKPAELTIIGEYEAEVV-- 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           L EG+  ++K++F     KV  L R+S G   L
Sbjct: 177 LTEGRYHQVKRMFAAIGNKVEELHRVSIGAISL 209


>gi|330877468|gb|EGH11617.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 230

 Score = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 105/218 (48%), Gaps = 8/218 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G +      +V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVALDAEILQPGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  +D    +TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATTDAQ-HATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + I     Q+T+   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSAR----L 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            + EG+  ++K++F  F+ KV +L R S G   L   L
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPAL 214


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 117/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I  +GI SRR+ +R I Q  V +NG   +RA+V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGNVFING---KRASVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   +   +KP+G+++T  + + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVVIALNKPVGIISTTEEGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G      +V  +    S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTKKCKVKKE----STFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V++L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYEVSKLERTRIMNVSLKGLPPGEWRDLTDDELIE 231


>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 = 75.9 bits (185), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 83/177 (46%), Gaps = 16/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 65  LFNKPFDVLCQFTDEQGRKTLKDYIP--VPGVYAAGRLDRDSEGLLLLTNDGKLQSQITE 122

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  + Y  +  G  D   L  L++G+ ++       ++++                 
Sbjct: 123 PKKKTYKTYWAQVEGAPDDSDLEKLRQGVELKDGMTLPAKISIMDNPAIWPRTPPIRERA 182

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                W+ + + EG+NR+++++     +   RLIR   G + L  L  G  R++  K
Sbjct: 183 NIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLQNGEYRQLDMK 239


>gi|157370266|ref|YP_001478255.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157322030|gb|ABV41127.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 178

 Score = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 52/170 (30%), Positives = 84/170 (49%), Gaps = 17/170 (10%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR+T+ + +P  F  V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   LFNKPFDVLPQFTDEAGRATLKEFIP--FPDVYAAGRLDRDSEGLLVLTNDGKLQAQLTE 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DT 181
           P  +  +VY V+  G    + L  L+ G+ ++        V L               + 
Sbjct: 61  PGKRTGKVYYVQVEGAPQDNDLVSLRNGVTLKDGPTLPAGVELVAEPQWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +    AW+ + L EG+NR+++++     +   RLIR S G   LG L  G
Sbjct: 121 KSIPTAWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYSMGNISLGELQPG 170


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 113/218 (51%), Gaps = 13/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K I+   + SR E +++I ++ V VN +L+++    V    D + +DG  L   +  
Sbjct: 2   RLDKYISSITVYSRAETKKII-KKGVLVNNVLVKQPDYQVDEENDQVVIDGKSLFYQKHV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP  +++   D    +TV D  N      +   VGRLD +TEGL+LLTNDG LA
Sbjct: 61  YIMM-NKPGNIISATEDKKD-TTVIDILNEKDRLFKPFPVGRLDKDTEGLMLLTNDGELA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
             L  P    ++ Y V   G++  + + +++ G+V++      C     +T +T+K S A
Sbjct: 119 HKLISPKKDVIKKYYVEVDGELKVEHVTIIRDGVVLEDGYKTKCAALEILTSNTEK-SRA 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++++   EGK  ++K++ +     V  L R+S G   L
Sbjct: 178 YISI--TEGKFHQVKRMMKSLGVNVTYLKRLSIGSLVL 213


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVKPGDLVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLT 225


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 109/235 (46%), Gaps = 18/235 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++A  G  SRRE  R I Q  VKVNG++   A   V  TD +E+    +    + +
Sbjct: 9   RLNKLLAHQGWCSRREANRFIEQGLVKVNGVVSRDA--RVAPTDTVELLPQAVTVQAQQK 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----SVGRLDINTEGLLLLTNDGG 129
             L HKP+G V++  + D       +   +F         + GRLDIN+ GLL+LT  G 
Sbjct: 67  TILVHKPVGYVSSQPETDSIPQEQASSRRLFHPRTQLGWATAGRLDINSTGLLVLTQSGR 126

Query: 130 LARVLELPSTQWLRVYRVRF-------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +A+ L  P  +  + Y VR          Q     L  L+ GI       G++   +  +
Sbjct: 127 VAKTLIGPDVRVDKEYLVRVRPSPFFDRNQSTAAVLERLRDGIR----DAGELLHAVSVE 182

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + +   +   L EGK+R I+++      +V+ L R+  G   LG L  G  R ++
Sbjct: 183 RVNTDQLRFVLHEGKHRHIRRMCRAVGLEVDGLKRVRIGEIVLGNLPVGQWRYLA 237


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 120/233 (51%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV++++    ++V+G ++     +V + +  + + G P+   +  
Sbjct: 2   RLDKLLSNMGAGSRKEVKQLLKSGAIQVDGEIVYDPKQHVDTENQQVLLYGEPVTYQKFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L + +KP G+++   D   ++ +   FD++   + +   VGRLD +TEGLLLLTNDG  
Sbjct: 62  YLMM-NKPPGVISATEDKRDQTVIDLLFDDV--TYFKPFPVGRLDKDTEGLLLLTNDGSF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY----GDMQVTLDTQKGSN 186
              L  P     +VY     G + ++ +  + +G+ ++   Y    G + +   T + S 
Sbjct: 119 NHALMSPKKHVEKVYYAEVIGTLTEEDVEEVAEGVTLED-GYKTKPGKLIILEATDETST 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             +T+   EGK  ++K++      +V  L R+S G   L  TL AG  RE+++
Sbjct: 178 LELTI--TEGKFHQVKRMMLALGKEVTYLKRLSIGQLPLDPTLEAGEYRELTR 228


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 112/223 (50%), Gaps = 10/223 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A   + SR+EV++ I + +V VNG +   ++A +N    D I  +G  + + ++
Sbjct: 25  RLDKFLATMQLGSRKEVKQFIKKGKVTVNGEITRSDKAQINEYE-DQISFEG-EVIQYQK 82

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG L
Sbjct: 83  DYYYLLNKPAGVISATVD-NYDETVMDLLVDEDFREDLFPVGRLDKDTEGLLVLTNDGQL 141

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QG-ICY-GDMQVTLDTQKGSNA 187
           A  L  P     + Y     G +  + + L  +G++I QG  C    + +    +    +
Sbjct: 142 AHRLLSPKKHVEKEYHATVAGVMTAEDVALFSEGLMIDQGEQCLPAKLTILSVDESAQTS 201

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            +++ L EGK  ++K++      +V  L RI  G   L   LA
Sbjct: 202 QISLILHEGKFHQVKRMVAAVGKEVVYLKRIRMGQLTLDESLA 244


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.9 bits (185), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVKPGDLVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 89/179 (49%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP G++   +   G  ++ D +P  F+     GRLD ++EGL+LLT++G L   
Sbjct: 3   RIILFNKPYGVICQFTPTCGHRSLQDFIP--FAGFYPAGRLDADSEGLVLLTDNGKLQDK 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  +  + Y V+  G+ D   LN +++GIV+        QV+L  +           
Sbjct: 61  ICSPKYKLSKTYWVQVEGKPDDVALNAMRRGIVLSDFKTKSAQVSLMNEPSFIWDRQPPI 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    W+++ L+EGKNR+I+++     +   RLIR + G   L  +  G  R ++
Sbjct: 121 RFRKSIPTTWLSLILKEGKNRQIRRMTAAVFFPTLRLIRYAIGLHTLKGIAPGEWRMLA 179


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/187 (26%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P R     ++ +++KP  ++   +D  GR T+ D +P     + + GRLD ++EGLL+LT
Sbjct: 23  PSRPRGERKVIIFNKPFDVLVQFTDDSGRKTLKDFIP--IPDIYAAGRLDRDSEGLLVLT 80

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------------I 170
           NDG L   L  P+ +  +VY  +  G   +  L   ++G+ ++                 
Sbjct: 81  NDGKLQAKLTQPNKKTGKVYYAQVEGIPTEIALQQFREGLNLKDGKTLPAKIERVEQPTW 140

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            +       + Q    +W+ + L EGKNR+++++     +   RLIR S G   L  LL 
Sbjct: 141 VWTRFPPIRERQSIPTSWLKITLFEGKNRQVRRMTAHIGYPTLRLIRFSMGNITLDNLLP 200

Query: 231 GSTREVS 237
           G  +E++
Sbjct: 201 GQWKEIN 207


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 52/183 (28%), Positives = 93/183 (50%), Gaps = 23/183 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDG---RSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +L L++KP  +++  +D      R+T+ D  + P ++      GRLD ++EGLLLLT+ G
Sbjct: 3   KLILFNKPFHVLSQFTDERASHPRATLADWIDQPGVYP----AGRLDYDSEGLLLLTDQG 58

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------ 181
            L   +  P+ +  + Y V+  G++  + L+ L+KG+V++ GI        L+T      
Sbjct: 59  ALQHRIASPTNKMPKTYWVQVEGELTDEALHKLRKGVVLKDGITRPARAERLETPDLWPR 118

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  Q     W+ + + EGKNR+++++     +   RLIR+  G + L  L  G  R
Sbjct: 119 NPPVRFRQNVPTTWLALTITEGKNRQVRRMTAAVGYPTLRLIRVRIGDWTLDNLKPGEYR 178

Query: 235 EVS 237
            V+
Sbjct: 179 SVT 181


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/206 (27%), Positives = 106/206 (51%), Gaps = 8/206 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +++I + +V +NG + E     V   D +EV G  + K++R +
Sbjct: 4   RINKYLSEVGYCSRREADKLILEGKVTINGEIPE-IGTKVEDNDQVEVKGQRIEKSKRQK 62

Query: 75  -LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++L ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDKKLEPNNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ +  ++ + +  +  G+ I      +  V    Q G   +  + 
Sbjct: 122 KILRARNNHEKEYIVKVNRPINSNFIKSMSNGVEILDTITKNCFV---EQLGPRNFKII- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRI 218
           L +G NR+I+++ E   ++V  L R+
Sbjct: 178 LTQGLNRQIRRMCEALGYRVRSLKRV 203


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 108/226 (47%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G+ SRR+ +  I    V VNG ++     +V   D ++ DG  +    +  
Sbjct: 41  RLNKYISNSGVCSRRDADIYIKSGNVTVNGEVIIEMGHHVKLEDEVKFDGRRINPEPKAY 100

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP     T S   G+ T  D + +   S++  VG+LD +  GL+L TNDG LA+ 
Sbjct: 101 VLL-NKPKSFYVTGSYEKGKLTALDLVQNASKSKLAPVGKLDTSAMGLILFTNDGTLAKK 159

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L        ++Y+V     + +  L ++K G  I+G      +      +  N  V + L
Sbjct: 160 LSGHKNGIRQIYQVELTKPLRESDLEVIKDGPFIEGSKVKIEEAAFVDNRPKN-IVGLEL 218

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           R  +   ++++F+   +++ ++ R+ Y       L  G  R ++++
Sbjct: 219 RSQRAHIVQRIFKKLGYEIEKMDRVIYANLDKKNLPRGHYRHLTRQ 264


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 116/227 (51%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA +   V + D ++V+G  +  R  
Sbjct: 7   RLNKYISESGICSRRDADRYIEQGNVFING---KRAVIGDQVYAGDVVKVNGQLIDARDE 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L + +KP+G+++T  D +  + V  +  +   R+  +GRLD +++GL+ LTN G L
Sbjct: 64  DDLVLIVLNKPVGIISTTEDSEHNNIV--DFVNHSKRIFPIGRLDKDSQGLIFLTNQGDL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ +     G +      +K S     
Sbjct: 122 VNKVLRAGNDHEKEYVVTVNKPVTEEFILGLGAGVPM----LGTVTKKCKVKKVSTFVFN 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ ++F ++V +L R       L  L  G  R+++
Sbjct: 178 ITLVQGLNRQIRRMCQYFGYEVTKLERTRIMNINLKGLPLGEWRDLN 224


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 92/181 (50%), Gaps = 18/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +R+ +++KP G++T  +D + GR+T+ D +P     V   GRLD ++EGL++LT+DG L 
Sbjct: 2   SRIIVFNKPYGVLTQFTDREHGRATLADFIP--IPGVRPAGRLDRDSEGLIVLTDDGRLQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  +  + YRV+  G  D+  LN L++G+ +        +  +  +         
Sbjct: 60  ARIADPRHKMAKTYRVQVEGLPDEAALNRLRRGVRLNDGLTLPAEANIIPEPAWLWPRDP 119

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+ + +REG+NR+++++     +   RLIR + G + L  L  G  RE+
Sbjct: 120 PVRFRATIPTTWLELVIREGRNRQVRRMTAAVGFPTLRLIRWAIGAWTLEGLAPGEWREL 179

Query: 237 S 237
            
Sbjct: 180 P 180


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 88/179 (49%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GRST+ D +P   S + + GRLD ++EGL++LTNDG L   
Sbjct: 40  RIVLFNKPFDVLPQFTDEAGRSTLKDYIP--ISGIYAAGRLDRDSEGLMILTNDGKLQAQ 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQVTL 179
           L  P+ +  ++Y V+  G  D   L   + G              IV +          +
Sbjct: 98  LTQPTKKTAKIYYVQVEGIPDDAILTRFRTGLELNDGKTQPAGAEIVPEPDWLWPRNPPI 157

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K   + W+ + L EG+NR+++++     +   RLIR S     +  LL G  +E++
Sbjct: 158 RERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYSMANQTVENLLPGEWKEIA 216


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 71/121 (58%), Gaps = 10/121 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ +
Sbjct: 2   KINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
           +++ +HKP+G+  T +D      + DN+        R+  VGRLD  +EGL+LLTNDG +
Sbjct: 61  VYIAFHKPVGITCTAADH-----IEDNIIDYIHYPERIFPVGRLDKASEGLILLTNDGTI 115

Query: 131 A 131
           A
Sbjct: 116 A 116


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVKPGDLVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 107/207 (51%), Gaps = 13/207 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     + ++ +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIR 217
           + L +G NR+I+++ E F ++V +L R
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLER 205


>gi|323975348|gb|EGB70451.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
          Length = 290

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|289677892|ref|ZP_06498782.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae FF5]
          Length = 230

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 107/227 (47%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSARLSIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVLRLHRETIGALALDPGLRPGSYRALN 223


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 117/233 (50%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I  +GI SRR+ +R I Q  V +NG   +RA+V   V++ D ++V+G  +  R  
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGNVFING---KRASVGDRVLAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   +   +KP+G+V+T  + + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVVIALNKPVGIVSTTEEGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G      +V  +    S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTKKCKVKKE----STFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYEVTKLERTRIMNVSLKGLPPGEWRDLTDDELIE 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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 114/227 (50%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVKPGDLVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 86/180 (47%), Gaps = 20/180 (11%)

Query: 74  RLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP G++T  T   P+   + F  LP  ++     GRLD  +EGLL+LT+DG L 
Sbjct: 3   QLILFNKPYGILTQFTGELPEQTLSAFIKLPGFYA----AGRLDKQSEGLLILTDDGKLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L ++         
Sbjct: 59  HRLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKIWPRIPP 118

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  + ++
Sbjct: 119 IRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEYKLIN 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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P   A RT++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+LT
Sbjct: 9   PKTPASRTKIVLFNKPFNVLTQFTDATGRQTLKDFIP--IPDIYASGRLDKDSEGLLVLT 66

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P  +  + Y V+  G   + +L  L+ G+ ++       +V    +   
Sbjct: 67  NDGKLQSKLTDPKKKTSKTYWVQVEGIPQERQLQALRDGVELKDGLTRPAKVESMPEPAL 126

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                          +W+++ + EGKNR+++++     +   RL+R   G + L  +  G
Sbjct: 127 WPRTPPVRFRQSIPTSWLSITISEGKNRQVRRMTAHIGFPTLRLVRYRIGNWTLDGIDTG 186

Query: 232 STREV 236
              E+
Sbjct: 187 QYVEL 191


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/217 (29%), Positives = 105/217 (48%), Gaps = 8/217 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++ + +  VKVN  +++     +  + D I V+   +   ++ 
Sbjct: 2   RLDKFLANMGVGTRNEVKQSLKKGYVKVNNEVIKSPKTQIDPNEDIITVNDEKIIYIDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G+V+   D D   TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPSGVVSATED-DKHQTVIDLIPEYQHLEIFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     V Q  +   K+G+ +        Q+ +   + S     V 
Sbjct: 120 DLMSPNKHVPKTYEVVSKNDVTQSDVERFKEGLELSDGLVKPAQLEIIENRRSR----VT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           + EGK  ++K++F     +V +L RI     +L T L
Sbjct: 176 IYEGKYHQVKRMFHEIENEVLQLKRIKIANLELDTSL 212


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 19/178 (10%)

Query: 77  LYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP  +++  +D +   R T+ D +P   S V  VGRLD ++EGLLLLTN G L   L
Sbjct: 1   MFYKPYDVLSQFTDREDSPRRTLKDYIP--VSEVYPVGRLDRDSEGLLLLTNHGRLQHRL 58

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  R Y V+     D+  LN L++G+VI+       QV   +Q+           
Sbjct: 59  SNPRFRHPRTYWVQVERIPDEAALNQLRQGVVIKDYQTRKAQVQRLSQEPDLPPRDPPIR 118

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   W+ + L EG+NR+++++     +   RLIR++    +L  L  G  R+++
Sbjct: 119 FRKTVPTCWLEITLTEGRNRQVRRMTAVVGFPTLRLIRVAIAHLRLDGLQPGQWRDLT 176


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 114/231 (49%), Gaps = 11/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           RV K +    I +R +V R+I    +  NG  ++  +  +N  S D + +D V +R  ++
Sbjct: 2   RVDKFLHAMRIGTRTQVRRLIKDGHITANGEPVISGKQQINPGS-DTVFLDDVQVRY-QQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP+G++T  +D   + TV D  N       +  VGRLD +TEG+L++TNDG L
Sbjct: 60  YFYYVMNKPVGVITATTDSAAK-TVMDLFNTTDFRDDLFPVGRLDKDTEGILVITNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNA 187
           +  L  P+    +VY     G++   +L     GI ++    +     ++    +  +  
Sbjct: 119 SHDLLSPNHHVTKVYEAEVTGEITAAQLANFNDGITLKDGTELQPAQAEIVQFHEIENFT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
            + + + EGK  ++K++      +V  L RI +G   L   LLAG+ R ++
Sbjct: 179 TIRIMIHEGKYHQVKRMVGTLGERVVGLRRIKFGSLTLPVGLLAGNYRALT 229


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 113/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA+V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRASVGAQVFAGDEVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G++TT    +G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIITTME--EGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ + G      +V  +    S     
Sbjct: 123 VNKILRAGNNHEKEYVVTVDKPITDEFITGMGAGVPMLGTVTKKCKVKKE----STFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMTKHFGYEVTKLERTRIMNVNLKGLPLGEWRDLTDDELIE 231


>gi|229060031|ref|ZP_04197402.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228719250|gb|EEL70858.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 227

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 112/227 (49%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ AG ASRR  +++I +++V +NG  + +    V   D + V+G  LR A    
Sbjct: 2   RINKFISEAGKASRRGADKLINERKVIING-KVAKIGDQVNPGDDVRVNGEQLRIARDHV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP+G+  T S+   +  + D  N P    R+  +GRLD +++GL+LLTNDG +  
Sbjct: 61  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL---RINHIGRLDKDSDGLILLTNDGDIVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V     +  + L  +  G+ I        ++T    + S     + 
Sbjct: 117 EILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEIT----QLSKYEFEII 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           L +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK
Sbjct: 173 LTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKK 219


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   +D L  L+ G+ +     +  G   V            
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 156

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRDAT 216


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 87/175 (49%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 43  LFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTNDGALQAKLTQ 100

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G+   + L  L+ G+ +        G+   +    L        + 
Sbjct: 101 PGKRTGKIYYVQVEGEPTPEALAALRDGVTLNDGPTLPAGVEVVEEPAWLWPRNPPIRER 160

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ 
Sbjct: 161 KSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGEWRKA 215


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 89/182 (48%), Gaps = 17/182 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ +++KP  ++   SD  GRST+ D +P   + V + GRLD ++EGL++LTNDG L   
Sbjct: 29  RVIIFNKPFDVLPQFSDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLMVLTNDGALQAT 86

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P  +  ++Y V+  G  D   +  L+ G+ ++          L              
Sbjct: 87  LTQPGKRTGKIYYVQVEGIPDISHIQALRDGVNLKDGPTLPAGAELVAEPEWLWPRNPPI 146

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ + L EG+NR+++++     +   RLIR + G   L  L  G  R+V+ 
Sbjct: 147 RERKAIPTSWLKITLYEGRNRQVRRMTAQIGFPTLRLIRFAMGTQMLQDLPPGEWRDVTA 206

Query: 239 KI 240
           + 
Sbjct: 207 EF 208


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/207 (28%), Positives = 106/207 (51%), Gaps = 14/207 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+++  G  SRRE  RMI + R+ VNG    +    V   D I +D  P+   E+  
Sbjct: 2   RINKLLSNYGYCSRRETNRMIEENRITVNGQNCIKGQW-VEEDDIILIDNEPISLKEKIY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLA 131
           +  ++KP+G+  T        TV +N+    +    +  VGRLD  ++GL++LTNDG LA
Sbjct: 61  I-AFNKPVGITCTLE-----KTVKNNIGDYINFSDYIFPVGRLDKESQGLIILTNDGDLA 114

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V  +   +   +N + +G+ I G+     QV+    K S+    +
Sbjct: 115 NKILESENKHEKEYIVTLNRPFNDSFINGMSEGVEICGVKTRKCQVS----KISDNVFRI 170

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRI 218
            L +G N++I+++ + F + V +L RI
Sbjct: 171 ILTQGLNKQIRRMSKTFGYTVIKLERI 197


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 87/177 (49%), Gaps = 17/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L        + 
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE ++
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREATE 177


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 116/240 (48%), Gaps = 22/240 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E+++M  Q  V VNG  +++   ++    D + ++G  +R  E  
Sbjct: 2   RLDKMLSNLGYGTRSEIKKMCRQGMVTVNGQEVKKPDHHIDPDQDQVCLNGQAVRYREYI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G V+   D   + TV D + P   +     VGRLD +TEGLL++TNDG L+
Sbjct: 62  YLMM-NKPAGCVSATYDKYDQ-TVIDLIDPEYLAFEPFPVGRLDKDTEGLLVITNDGQLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------LDT 181
             +  P     ++Y      +V    +    KG+ I     GD   T           + 
Sbjct: 120 HRVLSPKKHVPKIYYAEIDHEVLARDIEAFSKGVYI-----GDDYTTKPAKLEVIKSFEA 174

Query: 182 QKGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           + G+ ++ + V + EGK  ++K++FE     V  L RI  G  +L   L  G  RE++++
Sbjct: 175 EDGAIHSEIYVTISEGKFHQVKRMFEAVGKSVLYLKRIQMGGLKLDESLGLGEYRELTEE 234


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 102/217 (47%), Gaps = 4/217 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R +  + + Q  V +NG + +  A  V   D I  DG  L   +  +
Sbjct: 2   RLDKFLAEHTGLTRSQATKALRQSAVTINGKIEKSGATKVSPQDAIYFDGELLTWLDVGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +++KP G V +H + +  S   F + P + +R+ S GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YLMFNKPQGYVCSHDEDEHPSIYQFFDYP-LSARLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+ + +    +GI+++G         L+     N  V + +
Sbjct: 121 VTSPKHHQPKTYLVTLADPVEANYVQACAEGILLRGEKDPTKPAVLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EG+  ++K++F     KV  L R   G   L   LA
Sbjct: 179 SEGRYHQVKRMFAALGNKVLGLHRWKIGNLTLDDNLA 215


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++++ I+ A   SRRE +R+I   RV +N  +     + V   D + VDG  + K E+ +
Sbjct: 2   KINQFISEALSCSRRETDRLIKAGRVAMNDKVCTHGVL-VKPDDVVTVDGKVIEKEEKEK 60

Query: 75  LWL-YHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ +HKP+G+  T +   +G    + N P    R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 61  VYIAFHKPVGITCTAAKHIEGNIIAYINYPE---RIFPVGRLDKASEGLILLTNDGKIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V          ++ +  G+ I+      M       +  ++   + 
Sbjct: 118 QILHGDHGHEKEYVVTVDKSFTDGFIHGMSCGVKIK----DGMTKPCKVTRVDDSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           L +G NR+I+++   F + V +L R+     +LG L  G  R ++ + L+E  G 
Sbjct: 174 LTQGMNRQIRRMSRAFGYTVTKLKRVRIMNIKLGELEVGKWRYLTDEELQELRGA 228


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 110/238 (46%), Gaps = 7/238 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A  +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGATKLTPESDVRFDGNPLQQTLGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P     + Y V     V +D       G+ +    + +  +T   Q        V + 
Sbjct: 122 TSPRHHCEKTYLVTLEHPVAEDTAQRFADGVQL----HNETSLTKPAQLEIIEPQLVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           L EG+  ++K++F     +V  L R   G   L   LA G  R ++ + +     PHL
Sbjct: 178 LSEGRYHQVKRMFGAVGNRVLALHRERIGAMILDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 108/225 (48%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           RV   +A  G+ SRR  E +I ++ ++VNG  + +    V   D I     + + K  ++
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNG-SIAKLGDKVSPGDRIIYKKQIYVFKDFQS 66

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
           +  +Y   +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KNKIYLALNKPRNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +  ++      K S   +
Sbjct: 127 FANDIIHPRGKVEREYIIESKKDIDENLLISFKSGIKVKKEFF-KLKSYEILNKNSARLI 185

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 186 ---LDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>gi|213620819|ref|ZP_03373602.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 165

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 45/154 (29%), Positives = 75/154 (48%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             P     + Y V     V  D      KG+ + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLH 155


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 48/174 (27%), Positives = 83/174 (47%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 48  LFNKPFDVLCQFTDEQGRKTLKDFIP--IQEVYAAGRLDRDSEGLLLLTNDGKLQAQITE 105

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  + Y V+  G   +  L  L+ G+ ++       +V + +               
Sbjct: 106 PKKKTFKTYWVQVEGAPSETDLEKLRTGVELKDGLTLPAKVNIMSNPAVWPRNPPIRERA 165

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+T+ + EG+NR+++++     +   RLIR   G + L  L  G  R++
Sbjct: 166 NIPTTWLTIEICEGRNRQVRRMTANIGFPTLRLIRYKIGQWSLDDLPNGQYRKL 219


>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 = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 111/241 (46%), Gaps = 16/241 (6%)

Query: 12  TP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----VDGVP 66
           TP  R+ +++A  G ASRRE++ +    R++++G     A   +  T  +E    VDG  
Sbjct: 4   TPTSRLDRLLANMGYASRREIQMLARNGRIQLDGAAFHDADKRIALTPDLETRLVVDGEA 63

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLL 122
           L       L L HKP+G+  +H +      V+D LP  + R    + +VGRLD  T GLL
Sbjct: 64  LDPLPGFALML-HKPLGVTCSHKE--AGPLVYDLLPQRWRRRDPAISTVGRLDKETSGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+T+DG L   +  P     + YRV     +  D+  L   G ++++G         L+ 
Sbjct: 121 LMTDDGKLLHRIISPKRHVAKRYRVHLARSMTGDEAALFAAGTLMLEGEEKPLAPAELEV 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKI 240
                A + V   EG+  +++++F      V  L R S G   L   LA G+ R +    
Sbjct: 181 VGPQEALLEV--HEGRYHQVRRMFAATGNHVEALHRESVGGLSLPADLAPGAIRRLDDAD 238

Query: 241 L 241
           L
Sbjct: 239 L 239


>gi|332346017|gb|AEE59351.1| 23S rRNA pseudouridylate synthase F YjbC [Escherichia coli UMNK88]
          Length = 277

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 106/224 (47%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP   ++   D   + TV D +P      + +VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKDYISATEDHHSK-TVIDLIPEYQHLNIFTVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>gi|330981482|gb|EGH79585.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 230

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 107/227 (47%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  HFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSARLSIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
              EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVLRLHRETIGALALDPNLRPGSYRALN 223


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 93/181 (51%), Gaps = 25/181 (13%)

Query: 77  LYHKPIGLVTTHSD----PDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L++KP  +++  +D       R T+  F ++P +++     GRLD ++EGLL+LTNDG L
Sbjct: 6   LFNKPFNVLSQFTDKGTEASERKTLSEFIDMPGVYA----AGRLDKDSEGLLVLTNDGVL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG----- 184
            + +  P  +W + Y V+  G   QD + +L+ G+ ++ GI        +D  +G     
Sbjct: 62  QQEISNPKHKWPKTYVVQVEGTPTQDDIKVLESGVTLKDGITKPAEAEIIDKPEGLWDRL 121

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                     ++W+ + + EG+NR+++++     +   RLIR S G F +  +  G  ++
Sbjct: 122 PPIRYRKAIPDSWLMITITEGRNRQVRRMTAAIGFPTLRLIRYSIGNFTIDDIPNGQWKQ 181

Query: 236 V 236
           +
Sbjct: 182 L 182


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 87/177 (49%), Gaps = 17/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G   QD L  L+ G+ +        G    D    L        + 
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE ++
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREATE 177


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 86/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G    ++L  L+ G+V+        QV  LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGAPQAEQLQALRDGVVLNDGPTRPAQVRMLDPAPQLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLETLAPGQWR 176


>gi|312945697|gb|ADR26524.1| 23S rRNA pseudouridine synthase E [Escherichia coli O83:H1 str. NRG
           857C]
          Length = 207

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 89/180 (49%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------ 177
            L  P  +  ++Y V+  G   +D L  L+ G+ +     +  G   V            
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPP 146

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRDAT 206


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--IQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   Q+ L  L+ G+ +           L  +          
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQEALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDAT 216


>gi|332752067|gb|EGJ82460.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           4343-70]
          Length = 290

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 106/207 (51%), Gaps = 13/207 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIR 217
           + L +G NR+I+++ E F ++V +L R
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLER 205


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +R  +   V   D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRVTLGDRVFPGDVVKVNGQVIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +       +KP+G+V+T  D +  + V  +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DNLIFIALNKPVGIVSTTEDGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNQGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + YRV  +  +  D +  L  G+ + G      +V  +T         
Sbjct: 123 VNKILRAGNGHEKEYRVTVNKPLTDDVIRGLGDGVPMLGTVTKKCKVKKETP----LVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E+F ++V +L R       L  L  G  R+++
Sbjct: 179 IVLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLIGLPLGEWRDLT 225


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 117/234 (50%), Gaps = 15/234 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V   D ++V+G  +   + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRAAVGDQVYVGDVVKVNGQLIEPRDE 64

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L L   +KP+G+++T  D  G S    +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  NDLVLIALNKPVGIISTTED--GESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV- 189
              +        + Y V  +  V  + +  L  G+ + G      +V  +      A+V 
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKVKKEA-----AFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           ++ L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E
Sbjct: 178 SITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPQGEWRDLTDDELTE 231


>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 = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 87/179 (48%), Gaps = 16/179 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  ++HKP G+++  +    +     +   +   V  VGRLD ++EGLLLLTN+G L   
Sbjct: 6   RYIIFHKPYGVLSQFTQESPKHITLKDYIDV-PNVYPVGRLDWDSEGLLLLTNNGRLQHR 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------------CYGDMQVTL 179
           L  P     R Y V+     D++ +N L+ G+ IQ                  GD Q  +
Sbjct: 65  LSDPRFGHERTYWVQVERIPDEEAINRLQAGVEIQDYRTRPAKVRLLPEYPPVGDRQPPI 124

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K    AW+ + L EGKNR+++++     +   RL+R+S G  +L  L  G  R+++
Sbjct: 125 RFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLLRVSIGHLRLDGLALGEWRDLT 183


>gi|144900938|emb|CAM77802.1| Ribosomal small subunit pseudouridylate synthase [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 230

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 110/237 (46%), Gaps = 21/237 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ ++IA  G  S+R++  ++   RV+  +G   E    + ++ D I VDG PL      
Sbjct: 2   RLVRLIANLGYGSQRDIRFLLRDGRVRHADG--RELVESDKVAHDDIRVDGEPLDPPAGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            + L HKP G   + SDP GR  V++ LP  F      +  VGRLD +T GLLLLT+DG 
Sbjct: 60  VIML-HKPAGYTCSSSDP-GR-IVYELLPPRFMHRNPVLAPVGRLDRDTTGLLLLTDDGK 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKG 184
           L   L  P     + Y V     ++  +  +   G ++       +    +QV    Q  
Sbjct: 117 LLHRLTSPRHHVPKTYDVTLDRPLEGTEAEIFASGTLMLRSEKTPLAPAQLQVLGPNQ-- 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             A +T  L EG+  ++K++F      V  L R   GP  LG L  G  R ++ + L
Sbjct: 175 --ARLT--LHEGRYHQVKRMFAAVGNHVVSLHRAGLGPLTLGDLPEGQWRVMAAEEL 227


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/176 (30%), Positives = 86/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G    ++L  L+ G+V+        QV  LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGAPQAEQLQALRDGVVLNDGPTRPAQVRMLDPAPQLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLETLAPGQWR 176


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 88/181 (48%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 64  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 122 LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G   E+++
Sbjct: 182 RERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWCEIAQ 241

Query: 239 K 239
           +
Sbjct: 242 E 242


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 126/254 (49%), Gaps = 16/254 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R + Q  V +NG   +RAAV   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYVEQGNVFING---KRAAVGDQVYAGDVVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIISTTEDGEHDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G      +V  +    S     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKVKKE----STFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E     L+
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPQGEWRDLTDDELIELF--KLI 236

Query: 251 EEAQVNLDAPIYSS 264
           E +  + +AP+  S
Sbjct: 237 ENSSSD-EAPVKKS 249


>gi|217969527|ref|YP_002354761.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217506854|gb|ACK53865.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 234

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 105/231 (45%), Gaps = 22/231 (9%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A  G+ SRRE +  I +  V V+G  +    V V     + +     R  ++    L H
Sbjct: 1   MAERGLCSRREADEFIERGWVFVDGRRVSELGVRVGQDARVTLAPEATRTQQQRATILLH 60

Query: 80  KPIGLVTTHSDPDGRSTVF----DNL----------PSIFSRVISVGRLDINTEGLLLLT 125
           KP+G V+   +P     V     DN           PS    +   GRLDI++ GLL+LT
Sbjct: 61  KPVGYVSGQPEPGYSPAVSLIGPDNQADRDVAQRFHPSHLKNLAPAGRLDIDSTGLLVLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQK 183
            DG +AR L    ++  + Y VR  G + ++ L LL  G+ +    +   +++   D Q 
Sbjct: 121 QDGRIARQLIGEDSKVEKEYIVRVEGTLAENGLALLNHGLWLDDRPLRPAEVEWINDDQ- 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +   LREG+ R+I+++ E    KV  L R+  G  +LG L  G  R
Sbjct: 180 -----LRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGHVKLGDLPLGQWR 225


>gi|328554622|gb|AEB25114.1| 16S pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
          Length = 239

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 112/232 (48%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR++V++++    V ++G   +   ++V      I V G P    E  
Sbjct: 2   RLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKIHVDPDKQDITVYGEPAEYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG LA
Sbjct: 62  YVMM-NKPQGVLSATED-SRQQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y VR    +  + +  L++G+VI+ G       V   T+      + 
Sbjct: 120 HRLLSPKKHVPKTYEVRLTSPLSPEDIIDLERGVVIEGGYKTKPAAVKTITESPDETVIH 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EGK  ++K + +    +V  L R+S G   L   L  G  RE++++ L
Sbjct: 180 LTITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPELKPGEFRELTEEEL 231


>gi|330910949|gb|EGH39459.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           AA86]
          Length = 207

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 86/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--IQGVYAAGRLDRDSEGLLVLTNNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   Q+ L  L+ G+ +           L  +          
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQEALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 146

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDAT 206


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/235 (26%), Positives = 109/235 (46%), Gaps = 16/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + +    V VNG + +  +  +  TD I  +G  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAGKALKSGLVTVNGKIEKSGSAKISETDEICYEGECLEWVDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICY-GDMQVTLDTQKGSNAWV 189
           +  P     + Y V     V+   +  L +GI+++G    C    M++  D        V
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYVEKLAEGILLRGEREPCLPAQMEIIDDYN------V 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EG+  ++K++F     KV  L R   G      +L  S  E   ++L EQ
Sbjct: 175 NLTISEGRYHQVKRMFAALGNKVEALHRWRIGD----VVLDESLEEGEYRLLTEQ 225


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 90/182 (49%), Gaps = 20/182 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +T++ L++KP  ++   +D  GR+T+  F  +P I+     VGRLD ++EGLLLLTN+G 
Sbjct: 23  QTKVILFNKPFDVLCQFTDEQGRATLKDFIKIPHIYP----VGRLDRDSEGLLLLTNNGE 78

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
           L   L  P  +  + Y V+  G   +  L  L+KGI +        +V L ++       
Sbjct: 79  LQHRLTNPKFKMEKTYWVQIEGIPVETDLAQLRKGIELNDGLTKPAKVRLISEPNIWQRH 138

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      +W+ + + EG+NR+++++     +   RLIR       L  L+ G  RE
Sbjct: 139 PPIRERKTVPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYETAGLTLTNLVNGQFRE 198

Query: 236 VS 237
           ++
Sbjct: 199 LT 200


>gi|323167301|gb|EFZ53010.1| ribosomal large subunit pseudouridine synthase F [Shigella sonnei
           53G]
          Length = 291

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|297521296|ref|ZP_06939682.1| 16S rRNA pseudouridylate synthase A [Escherichia coli OP50]
          Length = 207

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 93/203 (45%), Gaps = 2/203 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIR 217
           EG+  ++K++F      V  L R
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHR 202


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 114/233 (48%), Gaps = 14/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+ +  GI SR++  ++I + R+ VNG    +    V   D I +D  PL   ++  
Sbjct: 2   RINKLFSNLGICSRKDTSKLIEENRIIVNGFPCIQGQW-VELEDEILLDNKPLPIKKKIY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KPIG+  T +D    + + F N P     +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 61  IVL-NKPIGITCTAADEVENNIINFMNYPE---YIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  +  G+ I  +     +V   ++   N  +T GL
Sbjct: 117 ILESENKHEKEYIVTLDKPFNDEFILGMTSGVEICNVKTRQCKVRRISEDTFNIVLTQGL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               N++I+++ + F + V +L RI     +LG L  G  R     +L E+L 
Sbjct: 177 ----NKQIRRMSKTFGYTVKKLERIRIVNIELGDLEYGKWR----YLLEEELA 221


>gi|332999092|gb|EGK18679.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-218]
          Length = 291

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/207 (29%), Positives = 106/207 (51%), Gaps = 13/207 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIR 217
           + L +G NR+I+++ E F ++V +L R
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLER 205


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 117/237 (49%), Gaps = 23/237 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R++K I+ +G  SRR+ +++I + +V +NG    L +RA    M  D I V+G  + +  
Sbjct: 9   RLNKAISDSGYCSRRQADKLIEEGKVTLNGNPVSLGDRA----MPDDVIHVEGNLITENN 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                + +KP+G+  T +D      V D +     R+  VGRLD  +EGLLL+TNDG + 
Sbjct: 65  NLVYIILNKPVGITCT-TDLRVEGNVVDYIDHK-ERIFHVGRLDKPSEGLLLMTNDGDIV 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKGS 185
             +        + Y V+    +  + +  +  GI ++ +      C+         ++ S
Sbjct: 123 NKILRAGNSHEKEYFVKVDRPITTEFIRRMGNGIPLEELETTTKKCF--------VEQVS 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                + L +G NR+I+++ E+ +++V  L R      +LG L  G  R+++K+ L+
Sbjct: 175 RFVFRIILVQGLNRQIRRMCEYLDYEVMELKRERIMNIELGDLPYGEWRDLTKEELQ 231


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 116/238 (48%), Gaps = 17/238 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   +R E ++++    V+VN  + + AA+ V   + I +DG  L  A  +R
Sbjct: 2   RLDKFICKSTELTRTEAKKVLKSGEVRVNNEVAKNAAMQVHENNLITIDGQQL-SARGSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HK +  + ++ D    S +    +   F   I+ GRLD +T GL+L+T+DG  +  
Sbjct: 61  YYILHKIVDTICSNVDEIYPSVLHSLEVDKAFDLHIA-GRLDADTTGLVLITDDGRWSHN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLL----KKGIVIQG---------ICYGDMQVTLD 180
           +  P  Q  + YRV    ++D DKL+ L      G+ +QG         +   ++   +D
Sbjct: 120 VISPKKQCQKTYRVWLRSEIDDDKLSALVARFDSGLQLQGEDSLTRPAILTRVEIDNLVD 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    + V + + EGK  ++K++F     +V  L R   G   LG L  G  RE+++
Sbjct: 180 -EASYRSEVLLTITEGKYHQVKRMFAAVGNRVVGLHREQIGKITLGDLAPGEWRELTE 236


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 101/217 (46%), Gaps = 4/217 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R +  + + Q  V +NG + +  A  V   D I  DG  L   +  +
Sbjct: 2   RLDKFLAEHTGLTRSQATKALRQSAVTINGKIEKSGATKVSPQDAIYFDGELLTWLDVGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +++KP G V +H + +  S   F + P + +R+ S GRLDI+T GL+LLT+DG  +  
Sbjct: 62  YLMFNKPQGYVCSHDEDEHPSIYQFFDYP-LSARLHSAGRLDIDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+ +      +GI+++G         L+     N  V + +
Sbjct: 121 VTSPKHHQPKTYLVTLADPVEANYAQACAEGILLRGEKDPTKPAVLEILDNYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EG+  ++K++F     KV  L R   G   L   LA
Sbjct: 179 SEGRYHQVKRMFAALGNKVLGLHRWKIGNLTLDDNLA 215


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 117/227 (51%), Gaps = 8/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A  G  +R++V+ ++ +  V VN  ++  A + + +  D + V G  +   ++ 
Sbjct: 2   RLDKFLAHNGFGTRKDVKILVKKGMVTVNHDVVRDAGMVLNLEKDEVFVKGESV-SYQKD 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G +  H+ P+   +V + + S    ++ VGRLD +TEGLLL+TNDG  +  
Sbjct: 61  IYFMMNKPAGYICEHN-PEMYPSVLELIESYHRDLVFVGRLDADTEGLLLITNDGQFSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +    +   + Y V      D      L+KG+++        QV +  ++  +  +T+G 
Sbjct: 120 VAHSKSNVHKQYYVELDKPFDLRFCEELEKGMMLGDELLKPAQVEVVGERAIH--LTIG- 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            EGK  ++K++    + +V  L RI  G  +L  +L  G+ R++S++
Sbjct: 177 -EGKYHQVKRMMHACDNEVTYLKRIKIGALELDSSLQPGAYRDLSEE 222


>gi|271500910|ref|YP_003333935.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344465|gb|ACZ77230.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 232

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  + R +  QRV VNG +++  A  ++    +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRSLIVRELRAQRVTVNGEVVKSGAFKLLPEHEVAFDGNVLEQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D     + G+ +          TL+    S   V + + 
Sbjct: 122 TSPKHHCEKTYLVTLEQPLAADTAEKFQAGVQLHNEKNLTRPATLEVL--SEHQVRLTIT 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L  TL  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAIGNHVVALHRERIGAITLDDTLEPGEYRPLTQE 225


>gi|254521474|ref|ZP_05133529.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219719065|gb|EED37590.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 179

 Score = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 90/178 (50%), Gaps = 21/178 (11%)

Query: 78  YHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP  ++   +D   P   +     LP    RV + GRLD ++EGLLLLT++G LA  L
Sbjct: 5   FNKPFNVLCQFTDRSVPPRPTLAGFGLPP---RVYAAGRLDHDSEGLLLLTDNGTLAHKL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQKG--- 184
             P  +  + Y V+  G    ++L  L+ G+++         I   D   +L T+     
Sbjct: 62  TDPKHKADKTYWVQVEGTPSDEQLQQLRDGVLLNDGPTLPAKIERLDPAPSLWTRDPPVR 121

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                 +AW+ + +REG+NR+++++    N    RL+R++ GP++L  L  G  R++ 
Sbjct: 122 FRKTVPDAWLAITIREGRNRQVRRMTAAVNLPTLRLVRVAMGPYRLDDLQPGQWRQIG 179


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 112/232 (48%), Gaps = 14/232 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV   ++  G  +R E ++ +    + +N   +   ++     D I+++G  L   + T
Sbjct: 6   KRVDAHLSSLGYCTRSEAKKFLRMNEICINDNRVYNTSIKAYHDD-IKINGEVLD--DET 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L L +KP G + +H+D      ++  LP  ++R    + ++GRLDI+T G++LLT+DG 
Sbjct: 63  LLILLNKPQGYICSHND--SGKLIYSLLPQRYNRRNPKISTIGRLDIDTTGVILLTDDGV 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
           L   L  P     ++Y       +  D++ +   G ++     G+ +  L  +    +  
Sbjct: 121 LNHKLTSPKKDISKIYEATLEKPLKGDEVEIFASGTLMLN---GEEKPLLPAKLEIITPT 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +V + + EGK  ++K++F   + KV +L R  +  F+L  L  G  + +  K
Sbjct: 178 FVKIEIVEGKYHQVKRMFAAVSNKVIKLHRTKFADFELEDLKEGEFKIIKSK 229


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 89/174 (51%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 3   IFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQ------------ 182
           P ++  + Y V+  G   ++ L  L+KG+ ++ G+     ++V  + +            
Sbjct: 61  PQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGMTLPAKIEVMPEPEIWERTPPVRFRA 120

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RL+R S G   L  L  G  RE+
Sbjct: 121 NIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGIALDDLKPGEWREI 174


>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 = 75.1 bits (183), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 98/211 (46%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ +A  ++    +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRANRVTVDGEIVKNSAFKLLPEHDVEYDGNSLIQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V +D      +G+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVAEDTAEQFARGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F      V  L R   G  +L
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGAIKL 210


>gi|255084639|ref|XP_002508894.1| predicted protein [Micromonas sp. RCC299]
 gi|226524171|gb|ACO70152.1| predicted protein [Micromonas sp. RCC299]
          Length = 248

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 103/220 (46%), Gaps = 30/220 (13%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPLRKAERTRLWL----- 77
           RRE +  ++  RV+VNG L+ + +  V S D + +DG      P   A    +       
Sbjct: 1   RREADEAVSAGRVRVNGALV-KPSFRVRSGDVVTLDGKALDWEPFAAATEGSIGAHAGSN 59

Query: 78  ------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 Y+KP G VT   +   R+     + S  +RV  VGRLD ++ GL+LLT+DG + 
Sbjct: 60  GFFYLKYNKPRG-VTCTMESSQRTKPAKGVGS--ARVFPVGRLDRDSSGLVLLTDDGRVP 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGIC----YGDMQVTLDT 181
             L  PS +  + Y V        D +  L+ G+VI       G+          V L  
Sbjct: 117 EALLDPSRKAPKTYEVDVRPAPTPDAIEALRDGVVITTTQQRDGVTTTSPTAPCPVDLIK 176

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +  ++A +   LREG+NR+I+K+ E    +V RL R+S G
Sbjct: 177 KSETSATLRFELREGRNRQIRKMCEAVGVEVVRLHRVSVG 216


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA +   V + D ++V+G  +  R A
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGHVFING---KRAGIGDQVFAGDVVKVNGQLIEPRDA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+V+T  + +  + V  +  +  +RV  +GRLD +++G++ LTN G L
Sbjct: 65  DDLVLIALNKPVGIVSTTENGEKDNIV--DYVNHSTRVFPIGRLDKDSQGIIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ I G      +V  +          
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTDEFIRGMGAGVPILGTVTKKCKVKKEAP----FVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGLPLGEWRDLTDDELIE 231


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/228 (31%), Positives = 118/228 (51%), Gaps = 8/228 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A AG  +R EV++ + Q  V+V+G +++   ++V      +   G P+R     
Sbjct: 2   RLDKMLANAGYGTRNEVKKALKQGVVEVDGAVVKDGKLHVQPERQSVCYAGTPVRYKAEL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G+VT   D   + TV D + + +  +    VGRLD +T GLLLLT DG  +
Sbjct: 62  YLML-NKPAGVVTATEDAR-QKTVLDLMKNEWGHMKPFPVGRLDKDTTGLLLLTTDGAFS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + YR    G+V Q  +   K G+V+  G C    Q+ ++ + G  + ++
Sbjct: 120 HELMAPKKHIAKEYRALVEGKVTQADVEAFKNGVVLDDGYCTKPAQLEIE-ESGPLSAIS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           + L EGK  ++K++F     KV +L RI  G   L  +L  G  RE++
Sbjct: 179 LELTEGKFHQVKRMFAAVGKKVIKLERIRIGSLLLDSSLPKGGYRELT 226


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 113/229 (49%), Gaps = 9/229 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           + ++I  AG  +R+  +R++    V V+G ++ + A V   S   I VD + + +     
Sbjct: 3   LGQLIMDAGQVTRKACKRLLKDGHVTVDGQVVTQFATVVDPSWQEIAVDQIVIDRHFGHT 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
            +L HKP G ++ + D     TV D + P+     +++ GRLD +  GL+ +TN+G L  
Sbjct: 63  YYLVHKPKGYLSANKD-QTHPTVIDLIQPADNPGDLAITGRLDRDAHGLVFVTNNGQLHY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGD-MQVTLDTQKGSNAWV 189
           + + P     + YR+  +G +D+  +   + G++ Q   IC    +++   + + S   V
Sbjct: 122 IFQQPKFDIPKTYRITVNGLIDKKMVAQFQAGVIFQDGTICKAARLEIISASPQSSTGLV 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           T+   EG+  ++KK+F     KV  L R   G  ++  L  G  R +++
Sbjct: 182 TIS--EGRRHQVKKMFLACGVKVTDLYRQKIGDLRIDDLAVGDYRRLNE 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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/232 (28%), Positives = 112/232 (48%), Gaps = 7/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR++V++++    V ++G   +   ++V      I V G P    E  
Sbjct: 3   RLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKIHVDPDKQDITVYGEPAEYREFI 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG LA
Sbjct: 63  YVMM-NKPQGVLSATED-SRQQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y VR    +  + +  L++G+VI+ G       V   T+      + 
Sbjct: 121 HRLLSPKKHVPKTYEVRLTSPLSPEDIIDLERGVVIEGGYKTKPAAVKTITESPDETVIH 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EGK  ++K + +    +V  L R+S G   L   L  G  RE++++ L
Sbjct: 181 LTITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPELKPGEFRELTEEEL 232


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 114/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +R A+   V   D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRVALGDRVFPGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +       +KP+G+V+T  + +  + V  +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DNLIFIALNKPVGIVSTTEEGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + YRV  +  V  D +  L  G+ + G      +V  +          
Sbjct: 123 VNKILRAGNDHEKEYRVTVNKPVTDDFIRGLGAGVPMLGTVTKKCKVKKEAP----FVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       +  L  G  R+++   L E
Sbjct: 179 IVLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSMAGLPPGEWRDLTDDELVE 231


>gi|255081278|ref|XP_002507861.1| predicted protein [Micromonas sp. RCC299]
 gi|226523137|gb|ACO69119.1| predicted protein [Micromonas sp. RCC299]
          Length = 257

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 120/243 (49%), Gaps = 33/243 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL--LERAAVNVMSTDHIEVDGVPLRKAE 71
           QR+SK +A  G+ASRR  E +I   RV+VNG+   + + AV+  S D I VDG  ++   
Sbjct: 4   QRLSKALAALGVASRRASEELIFAGRVQVNGVTVTMPQHAVST-SRDVIAVDGKVVQGGL 62

Query: 72  RTR------LWLYHKPIGLVTTHSDPDG---RSTVFDNL-----------------PSIF 105
            +        +L HKP G + + S P G   R++  D L                   + 
Sbjct: 63  ESLGDGGHLYFLLHKPKGYLCS-SKPAGAGARASGQDRLVLDLFEDWREGWRKRHPGQLA 121

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            R+ +VGRLD+NT G+LL+T DG   + +  PS+Q  + Y V    +  + ++  + +G 
Sbjct: 122 PRLFTVGRLDVNTTGMLLVTTDGQWCQRVAHPSSQIPKSYIVTAATRPTKAQIKKMAEGC 181

Query: 166 VIQGICYGDMQV-TLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
            + G+    ++V +++  +  G    + V + +G+NRE++ +       V +L R+  G 
Sbjct: 182 EVDGVHVTPLRVESMEGARDGGPAHRILVDVVDGRNREVRVLSASAGVDVKKLKRVRVGG 241

Query: 223 FQL 225
            ++
Sbjct: 242 LRM 244


>gi|328945586|gb|EGG39737.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 241

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 124/238 (52%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A   SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RIDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDTGLQQINFQGKHV-SGPAH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTPQDKIA-FQEGIRFLDGTICQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++    +E+LG
Sbjct: 178 TVKISEGKFHQIKKMFLAIGVKVTYLKRIQFGDFTLDPDLAKGDYRALN----QEELG 231


>gi|320179014|gb|EFW53973.1| 23S rRNA pseudouridine synthase F [Shigella boydii ATCC 9905]
          Length = 290

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDIVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/220 (28%), Positives = 98/220 (44%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G +   A  +  + D      VDGV     E 
Sbjct: 28  LESILFTQGFGSRRQCRALIADARVSIGGAVCTDADADFPTGDTTFSFTVDGVDWPYREH 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 88  AYL-LLNKPAGYECSR-DPQHHLSVFSLLPPQFAGRGVQCVGRLDQDTTGLLLLSDDGKF 145

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L+ G+++ G       V ++ +      +T
Sbjct: 146 VHLFTSPKRKVPKVYVATTRHPIDDAQLSALRDGVLLNGEARPIAAVDVEARGDHTLALT 205

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           V   EGK  ++K++      +   L R   G   L   LA
Sbjct: 206 V--MEGKYHQVKRMIAAAGNRCEALHRERIGGLALPEALA 243


>gi|319425419|gb|ADV53493.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 236

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV+V+G +++     V    HI++D   L +A      + HKP+G+V+ 
Sbjct: 20  RKLVRDLLLSGRVQVDGQIVKEMDRQVDEFSHIQLDDQVL-QANTPVYMMLHKPVGVVSA 78

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D +   TV D L + +   + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 79  TKD-NQHKTVIDLLDNEYRHELHIAGRLDLNSSGLLLLTNDSRWSEALMSPTEKVDKVYR 137

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     +  D +         +G+ +G   +T    K     +    V L+EGK  +IK+
Sbjct: 138 VTLANPLTHDYVTAFA-----EGMYFGFEDITTQPAKLVILDSHLAEVTLKEGKYHQIKR 192

Query: 204 VFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           +F  F   V  L R+S G   L   L  G +R ++
Sbjct: 193 MFGRFRNPVIGLHRLSIGAIVLDEQLQPGESRTLT 227


>gi|322835106|ref|YP_004215133.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321170307|gb|ADW76006.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 290

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 114/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG    RAAV   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---RRAAVGAQVFAGDVVKVNGQIIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G++TT  +  G      +  +   RV  +GRLD +++GL+LLTN G L
Sbjct: 65  EDLVLIALNKPVGIITTMEE--GERDNIRDFVNHSKRVFPIGRLDKDSQGLILLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  + +  +  G+ + G      +V  +    +     
Sbjct: 123 VNKILRAGNDHEKEYIVTVNKPITDEFIAGMGAGVPMLGTVTKKCKVKKE----APMVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F + V +L R+      L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMTKHFGFDVTKLERVRIMNINLKGLPLGEWRDLTDDELIE 231


>gi|330964551|gb|EGH64811.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 230

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 60/218 (27%), Positives = 104/218 (47%), Gaps = 8/218 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G +      +V     +  D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVAFDTEILQPGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  +D    +TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATTDAQ-HATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + I     Q+T+   + +     +
Sbjct: 121 LTQPQTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSAR----L 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            + EG+  ++K++F  F+ KV +L R S G   L   L
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPAL 214


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 109/220 (49%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  + SR+ +++ + ++ + V+       A NV      +   G  ++  E  
Sbjct: 2   RLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNVDTGLQKLVFQGRQIQGYEHN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G VT   D     TV D LP      ++ ++GRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGAVTASKD-KKLPTVMDLLPPDIQSDQLYAIGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K+GIV + G      Q+ + +   S +  +
Sbjct: 119 FQLLHPQYHVNKSYQVVVNGPLTSDHIQSFKEGIVFLDGTTCKPAQLEILSSSPSESHAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  +IKK+F     KV  L R+ +G F L   LA
Sbjct: 179 ITISEGKFHQIKKMFLSVGVKVTALKRVQFGDFTLDPELA 218


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 85/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L N+G L  
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLANNGALQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 97  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 156

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 157 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRDAT 216


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/232 (28%), Positives = 115/232 (49%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+++   D     TV D L     +F     VGRLD +T GLLLLTNDG 
Sbjct: 62  IYLMM-NKPAGVISATYDKRDE-TVIDLLYMEDQVFEP-FPVGRLDKDTVGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
           L   L  P     +VY    +  + +  +   + G+ +    Y  M   L   +    +A
Sbjct: 119 LNHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDD-GYKCMSAKLKVIENLEDSA 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            V V ++EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+
Sbjct: 178 RVEVTVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSE 229


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 107/219 (48%), Gaps = 18/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG   R  + +
Sbjct: 2   RLDKFLTHCGFGSRTQVKKLIREGIVTVNGKQIVEVDFKINPEEDVVEVDG---RIVKFS 58

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
           R W+Y   +KP G V ++ DP    TVF  +        + +VGRLD + EGLL++T+DG
Sbjct: 59  R-WIYIMMNKPKGYVCSNEDP-MSLTVFSLISDDLKHRDLHTVGRLDKDAEGLLIITDDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SN 186
                +  P  +  + Y VR   +VD+++L   + GI++      D   TL  +     +
Sbjct: 117 EYTHRVISPKKRIEKEYLVRLEKEVDEERLKEFENGIILD-----DGYKTLPAKYTIIDS 171

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + + EGK  ++K++FE    KV  L R   G   L
Sbjct: 172 TTVKLCIYEGKYHQVKRMFEAIGNKVVDLKRRRIGGLNL 210


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 88/173 (50%), Gaps = 16/173 (9%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           ++KP G++   SD  GR T+ D +P   + V   GRLD ++EGL+LLT+DG L   +  P
Sbjct: 17  FNKPYGVLCQFSDQQGRKTLKDFVP--VADVYPAGRLDYDSEGLVLLTDDGRLQARIAQP 74

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------- 184
            ++  + Y V+  G + ++ +  L  G+ ++       +  + T+               
Sbjct: 75  HSKLPKTYWVQVEGMITENAVRQLAAGVRLKDGMTQPARARILTKPTLWAREPPVRFRKT 134

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              +W+ + L EG+NR+++++     +   RL+R++ G ++L  L  G+  EV
Sbjct: 135 IPTSWLELTLYEGRNRQVRRMTAAVGFPTLRLVRVAIGMWRLNDLALGAYEEV 187


>gi|171914565|ref|ZP_02930035.1| putative pseudouridylate synthase [Verrucomicrobium spinosum DSM
           4136]
          Length = 235

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 106/233 (45%), Gaps = 9/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +S++IAR     R    + IA +RVKV   ++      V     + +D   +++ E    
Sbjct: 3   LSRLIARHKGMGRTAAMQAIAGKRVKVEDQVVTDGQHEVDRFSTVWLDDTLVQEGESALY 62

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVL 134
            + HKP+G ++   DP    TV D +       + + GRLD ++ GLLLLTNDG  +R L
Sbjct: 63  IMLHKPVGYLSATRDPQ-HPTVIDLIDHPARETLHIAGRLDRSSSGLLLLTNDGRWSRRL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVG 192
             P  +  +VY V     +  + + L  KG       + +   TL  + G        V 
Sbjct: 122 TEPGEKVDKVYLVETAEPIAPEAVELFAKGFYF----HTEDLTTLPAELGILGERLARVT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           L EG+  +IK++F     +V  L R S G   L   L  G  RE+ + +LR Q
Sbjct: 178 LHEGRYHQIKRMFHRVGNRVISLHRESIGSLVLPVELFPGQWREIRRDVLRSQ 230


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 111/249 (44%), Gaps = 33/249 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A   + SRRE +  IAQ  V+VNG +     + V   D I+VD        +  
Sbjct: 2   RLNKRMADLRLCSRREADDWIAQGWVRVNGQVAA-MGLQVGPHDRIDVDRAAQGHQRQQV 60

Query: 75  LWLYHKPIGLVT-----------------THSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             L HKP+G V+                 TH   D   T F   P+    +   GRLDI+
Sbjct: 61  TILLHKPMGYVSGQAEDGHTPAVALINPRTHWKDDESRTRF--APAQLKGLAPCGRLDID 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQD--------KLNLLKKGIVIQ 168
           + GLL+LT DG +AR L    +   + Y VR  +G   QD        KL LL  G+ + 
Sbjct: 119 SVGLLVLTQDGRVARQLIGEDSTVDKEYLVRVQYGDRAQDVRAVFPADKLALLNHGLALD 178

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G     ++  L   +       V LREGK R+I+++ E    KV  L RI  G   LG L
Sbjct: 179 G---QQLKPALVEWQNPEQLRFV-LREGKKRQIRRMCELVGLKVVGLKRIRIGQVLLGKL 234

Query: 229 LAGSTREVS 237
             G  R ++
Sbjct: 235 PPGQWRYLA 243


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+++   D     TV D L     +F    +VGRLD +T GLLLLTNDG 
Sbjct: 62  IYLMM-NKPAGVISATYDKRDE-TVIDLLYMEDQVFEP-FTVGRLDKDTVGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSN 186
           L   L  P     +VY    +  + +  +   + G+ +          ++V  + +  S 
Sbjct: 119 LNHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSR 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             VTV  +EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+
Sbjct: 179 VEVTV--QEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSE 229


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 112/235 (47%), Gaps = 15/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL----ERAAVNVMSTDHIEVDGVPLRKA 70
           R+ K++A  G  SRRE++ +     ++++G  L    +R A+     + + VDG  L   
Sbjct: 8   RLDKLLANLGYGSRREIQALARAGAIRLDGAELADAGDRVALAPDLPERLTVDGESLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP+G+  +H +      V+  LP  + R    + +VGRLD  T GLLLLT+
Sbjct: 68  PGLCLML-HKPLGVTCSHKE--AGPLVYGLLPERWRRRDPPLSTVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  Q  + YRV     +   +  +   G +V++G     + V LD +  +
Sbjct: 125 DGALLHRIISPKAQVAKRYRVTLDRPLTGREAEVFAAGTLVLEGEERPLLPVRLDVEDAT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
              VT  L EG+  +++++F      V  L R   G   L   L AG+ R ++ +
Sbjct: 185 RCAVT--LTEGRYHQVRRMFAAVGNHVAALHRDRVGGLALPADLPAGAHRVMTAE 237


>gi|313904278|ref|ZP_07837656.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
 gi|313470828|gb|EFR66152.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
          Length = 256

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 67/253 (26%), Positives = 113/253 (44%), Gaps = 27/253 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++   + +R+E++  I +    VNGI +     ++   + +  DG P+R  E   
Sbjct: 2   RLDKYLSDMNVGTRKELKTKIRKGAATVNGIRITDPGFSIKGDEDVTFDGKPIRYNE-YE 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G++T   D   + TV D L     + +  VGRLD NT GLLL+TNDG L   
Sbjct: 61  YYMLNKPAGVITATEDR-KQQTVLDLLGKDRRKDLFPVGRLDKNTVGLLLITNDGDLNHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----------------QGICYGDMQ 176
           L  P     + Y  +  G+V    +    KG+ I                 +     D +
Sbjct: 120 LLSPKKHTDKKYYAKIDGRVTDADVEAFAKGLRIDDELTALPAKLEILSFRETATDADRE 179

Query: 177 VTLDTQKGSNAW------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
             L  +   ++       + V + EGK  +IK++F     +V  L R+S G   L  +L 
Sbjct: 180 DLLTAEHPESSLSSGVSEICVTIHEGKFHQIKRMFHAVEKEVLYLKRLSMGSLVLDPSLP 239

Query: 230 AGSTREVSKKILR 242
            GS R +++  +R
Sbjct: 240 EGSWRPLTEDEIR 252


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 85/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P  +  + Y V+  G    ++L  L+ G+V+        QV +  Q           
Sbjct: 61  LTDPRHKQPKTYWVQVEGAPQPEQLQALRDGVVLNDGPTRPAQVRMLDQAPQLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/232 (28%), Positives = 111/232 (47%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  P     + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPIHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTE 227


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/183 (28%), Positives = 92/183 (50%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+ D  ++P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 33  KLILFNKPFDVLTQFSDGEGRATLKDYIDIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 88

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG------ 184
             +  P  +  + Y V+  G    ++L  L+ G+ +  G+        LD  +       
Sbjct: 89  ARIADPRHKLAKTYWVQVEGLPTAEQLQRLRDGVELNDGMTLPARARQLDEPELWPRNPP 148

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + +REG+NR+++++         RL+R+  G + +  L  G  +EV 
Sbjct: 149 VRFRATIPTTWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWKEVP 208

Query: 238 KKI 240
            ++
Sbjct: 209 ARL 211


>gi|312622542|ref|YP_004024155.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203009|gb|ADQ46336.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 233

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 110/218 (50%), Gaps = 16/218 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ +++ 
Sbjct: 2   RLDKFLTHCGFGSRSQVKKLIREGIVTVNGKQIVEVDFKINPEEDIVEVDGRVVKFSKQI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + + +KP G V ++ +     TVF    D+L   +  + +VGRLD + EGLL++T+DG 
Sbjct: 62  YIMM-NKPKGYVCSNEEL-ASLTVFSLISDDLK--YRDLHTVGRLDKDAEGLLIITDDGE 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
               +  P  +  + Y VR   +VD++KL   + GI++      D   TL  +     + 
Sbjct: 118 YTHRVISPKKRIEKEYLVRLEKEVDEEKLKEFENGIILD-----DGYKTLPAKYTIIDST 172

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + + EGK  ++K++FE    KV  L R+  G   L
Sbjct: 173 TVKLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNL 210


>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 = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 95/211 (45%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R I  QRV VNG ++   A  ++    +  DG  L+     R
Sbjct: 2   RLDKFISQQLEISRAIAHREIRGQRVTVNGEVVRDTAFKLLPDHEVAYDGNVLQMLTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFIEEPMSFKLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     +  D       G+ +      D+      +  +   V + L 
Sbjct: 122 TSPRHHCEKTYRVTLESPIGDDTAAQFTAGVQLHN--EKDLTKPAQLEVITPTDVRLTLS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F     +V  L R   G   L
Sbjct: 180 EGRYHQVKRMFAAVGNRVIELHRERIGDIAL 210


>gi|213618826|ref|ZP_03372652.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 276

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 112/221 (50%), Gaps = 13/221 (5%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKAERTRLW 76
           + +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  R+A+   L 
Sbjct: 1   SESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEPREADDLVLI 57

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
             +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN G L   +  
Sbjct: 58  ALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNHGDLVNKILR 115

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
                 + Y V     +  + +  +  G+ I     G +      +K +     + L +G
Sbjct: 116 AGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFRITLVQG 171

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            NR+I+++ E+F ++V +L R       L  +  G  R+++
Sbjct: 172 LNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLT 212


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 105/224 (46%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E  
Sbjct: 2   RIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP   ++   D   + TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKDYISATEDHHSK-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P+    + Y V     + +D +   K+G+ +  G     +   +D Q        V
Sbjct: 120 ELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH-----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L + L +G  R
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYR 218


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 116/258 (44%), Gaps = 39/258 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G  +R +V++ I +  V VNG + ++A   V    D I   G  +  A   
Sbjct: 4   RLDKYLTEMGCGTRSQVKKEILKGSVSVNGEIAKKAERKVDTEKDEIIFKGEKIFYA-GY 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+V+   D   R+ +     S    +   GRLD +TEGLLL+TNDG LA  
Sbjct: 63  EYFMLNKPAGVVSATEDKKERTVIDLIKESKRKDLFPAGRLDKDTEGLLLITNDGQLAHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P     ++Y  +  G V ++ + L +KG+ I     GD + T+              
Sbjct: 123 LLSPKKHVDKIYYAKIKGIVTEEDVRLFEKGVHI-----GDEKPTMPAALEILSVQKERR 177

Query: 180 -----------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                            D ++   + + + ++EG+  ++K++F     +V  L RI +G 
Sbjct: 178 KEKIKEQKILPETKNETDEKEDGYSEIYLTIKEGRFHQVKRMFRAVGKEVVYLKRIQFGT 237

Query: 223 FQLG-TLLAGSTREVSKK 239
             L  +L  G  R+++++
Sbjct: 238 LTLDPSLKPGQYRKLTEE 255


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 62/213 (29%), Positives = 102/213 (47%), Gaps = 12/213 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +++ + +AG+  R + E  I + RV ++G +       V     + VDG+ +R  E   L
Sbjct: 31  LARALGKAGVMPRAQAEAAIREGRVTLDGRVEHEPFAPVRPEMEVRVDGL-VRNLEAPVL 89

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDG 128
            L +HKP GLV   SD +G  TVF+ L    ++       ++VGRLD +T GLLL TND 
Sbjct: 90  TLMFHKPAGLVVHGSDAEGVGTVFECLRERLTQPLRDYEWLAVGRLDRDTTGLLLFTNDE 149

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L +    P     + Y     G   +D L  L++G+V++    G  +      +  +  
Sbjct: 150 RLVQHGTSPERHLPKRYVAGVVGPPPEDALRRLREGLVLED---GPTRPAGARLRAPDV- 205

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           V + L EG+N ++K++       V  L R + G
Sbjct: 206 VELTLTEGRNHQVKRMLAAVGHPVRTLHREAVG 238


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 85/180 (47%), Gaps = 17/180 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L N+G L  
Sbjct: 29  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLANNGALQA 86

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L  +          
Sbjct: 87  RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPP 146

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 147 IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRDAT 206


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 54/206 (26%), Positives = 99/206 (48%), Gaps = 11/206 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +++I Q RV +NG + E     +   D + V+G  +       
Sbjct: 8   RINKYLSEVGYCSRRAADKLIEQGRVTINGRIPE-MGTKISQGDEVHVNGELISAPTEKP 66

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +++ ++KP+G+V T      +  + D  N PS   R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 67  VYIAFNKPVGIVCTTDTRVEKDNIIDYINYPS---RIFPIGRLDKPSEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +    +  +  G+ I       +  T   ++ S     +
Sbjct: 124 NKILRARNNHEKEYEVWVDRPITPSFIQQMGNGVPI----LDTVTRTCHVEQLSRFSFKI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIR 217
            L +G NR+I+++ E  +++V RL R
Sbjct: 180 ILTQGLNRQIRRMCEALDYEVTRLKR 205


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 90/189 (47%), Gaps = 23/189 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLL 122
           P  + E TRL  +HKP G+++  + P+G+     +    P ++      GRLD ++EGLL
Sbjct: 34  PAPRPEVTRLLCFHKPYGVLSQFT-PEGKWQGLKDWIDAPGVYV----AGRLDADSEGLL 88

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT 181
           LLTNDG L   +  P  +  + Y V+  G  D+  L  L+ G+ +  G         ++ 
Sbjct: 89  LLTNDGQLQARIADPRHKMEKTYWVQVEGVPDEAALQRLRDGVELSDGKTLPARARLIEP 148

Query: 182 QKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           Q                 + W+ + +REGKNR+++++         RL+R++ GP+ +  
Sbjct: 149 QPSMWPRNPPIRVRQNIPDCWIELIIREGKNRQVRRMTAAVGHPTLRLVRMAVGPYSIEG 208

Query: 228 LLAGSTREV 236
           L  G   +V
Sbjct: 209 LEPGQWLDV 217


>gi|170718088|ref|YP_001785122.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168826217|gb|ACA31588.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 227

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 89/182 (48%), Gaps = 20/182 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +T++ L++KP  ++   +D  GR+T+  F  +P I+     VGRLD ++EGLLLLTN+G 
Sbjct: 35  QTKVILFNKPFDVLCQFTDEQGRATLKDFIKIPHIYP----VGRLDRDSEGLLLLTNNGE 90

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
           L   L  P  +  + Y V+  G   +  L  L+KGI +        +V L ++       
Sbjct: 91  LQHRLTNPKFKMEKTYWVQIEGIPVETDLAQLRKGIELNDGLTKPAKVRLISEPNIWQRH 150

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      +W+ + + EG+NR+++++     +   RLIR       L  L  G  RE
Sbjct: 151 PPIRERKTVPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYETAGLTLTNLANGQFRE 210

Query: 236 VS 237
           ++
Sbjct: 211 LT 212


>gi|159028310|emb|CAO87208.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 194

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 93/188 (49%), Gaps = 32/188 (17%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA----- 131
           L++KP  ++   +D +GRST+ D +P     + SVGRLD ++EGLLLLT++G L      
Sbjct: 6   LFYKPYDVLCQFTDENGRSTLKDYIP--IPNIYSVGRLDRDSEGLLLLTDNGQLQHRLGH 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQKG 184
           R    P T W++V R+      D + L  L++G+ IQ        +   D +  L  ++ 
Sbjct: 64  RQFAHPRTYWVQVERI-----PDLNALEKLRQGLAIQDYRTRPAIVNILDFEPDLPPREP 118

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY-----GPFQLGTLLAG 231
                     AW+ + L EG+NR+++++     +   RLIR +          L  L  G
Sbjct: 119 PIRYRKSIPTAWLEITLTEGRNRQVRRMTAAVGYPTLRLIRTAITIDKNNKLCLTGLQPG 178

Query: 232 STREVSKK 239
             REV++K
Sbjct: 179 QWREVTEK 186


>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 = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV+V+G +++     V    HI++D   L +A      + HKP+G+V+ 
Sbjct: 20  RKLVRDLLLSGRVQVDGQIVKEMDRQVDEFSHIQLDDQVL-QANTPVYMMLHKPVGVVSA 78

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D +   TV D L + +   + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 79  TKD-NQHKTVIDLLDNEYRHELHIAGRLDLNSSGLLLLTNDSRWSEALMSPTEKVDKVYR 137

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     +  D +         +G+ +G   +T    K     +    V L+EGK  +IK+
Sbjct: 138 VTLANPLTHDYVTAFA-----EGMYFGFEDITTQPAKLVILDSHLAEVTLKEGKYHQIKR 192

Query: 204 VFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           +F  F   V  L R+S G   L   L  G +R ++
Sbjct: 193 MFGRFRNPVIGLHRLSIGDIVLDEQLQPGESRTLT 227


>gi|330898470|gb|EGH29889.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 230

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 107/227 (47%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +   +  
Sbjct: 121 LTQPQTKMPKVYYVETEQPIDERYAIKFAEGLYFAFENLTTQPAQLTLLGPQSARLSIV- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVLRLHRETIGALALDPGLRPGSYRALN 223


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 85/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G    ++L  L+ G+V+        QV  LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGAPQPEQLQALRDGVVLNDGPTRSAQVRMLDPAPQLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 113/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R++
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPRES 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|325529283|gb|EGD06232.1| putative RNA pseudouridylate synthase [Burkholderia sp. TJI49]
          Length = 306

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 113/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +  HIE+D           
Sbjct: 59  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQHIEIDERAQAAQAAQV 118

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS      +   GRLDI++
Sbjct: 119 TILLHKPVGYVSGQAE-DGYEPAAVLITRDNHWSGDRSPLRFSPQHLRTLAPAGRLDIDS 177

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L  E        + RV+F  +   +DQ    + L  L+ G+ + G
Sbjct: 178 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVKFGERLTDIDQHFPAESLAKLRHGLELDG 237

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 238 VALKPAMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 293

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 294 QGQWRYLS 301


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 119/235 (50%), Gaps = 11/235 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A +GI +R+EV+ ++ ++R+ VN  ++  A  ++    D +  DG  +   E  
Sbjct: 2   RIDKFLANSGIGTRKEVKELLKKKRISVNDEVVTEAKTHIDEDNDFVAFDGKRIEFKEFL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP  +++   D   R TV D L    ++V    VGRLD +TEGLL+LTNDG +A
Sbjct: 62  YIML-NKPQDVISATDDERHR-TVLDLLEEPLTKVGLFPVGRLDKDTEGLLVLTNDGKMA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + +++  +L+ G+ ++       +V   T+      V +
Sbjct: 120 HELLSPKKHVPKRYYVELKKTLSKEEAAILENGVELETFTTKPAKVEFITED----KVYI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
            + EGK  ++K++F+    +V  L R   G   L   LA G  RE++   L EQL
Sbjct: 176 IISEGKYHQVKRMFKCVGNRVLFLKRTGMGNLGLDENLAPGEYRELTSDEL-EQL 229


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 110/248 (44%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 3   RLSKLMSELGMCSRREADEWIEKGWVMVDGERIDTLGTKVRPDQRIEIDPAAEAAQMSQV 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+GLV+  ++ DG                D+    FS     ++   GRLDI++
Sbjct: 63  TVLIHKPVGLVSGQAE-DGYQPAITLVTPENRWEGDHADIRFSVAHLRQLAPAGRLDIDS 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    ++  + Y VR                + L LL  G+ +  
Sbjct: 122 TGLLVLTQDGRIAKQLIGGHSEIDKEYLVRVAFGEHTTDVESHFPPESLELLCHGLSLDD 181

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +     QV  + Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 182 VPLKPAQV--NWQNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 237

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 238 PGQWRYLS 245


>gi|325688213|gb|EGD30232.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 241

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 127/240 (52%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A   SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHV-SGPAH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPSGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKIA-FQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK---KILREQL 245
           TV + EGK  +IKK+F     KV  L RI +G F+LG  L  G  R +++   +I++E L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIRFGNFKLGPELTTGEYRPLNQEELEIIKEYL 237


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/186 (29%), Positives = 88/186 (47%), Gaps = 20/186 (10%)

Query: 68  RKAERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           R  +  +L L++KP G++T  T   P+   + F   P  ++     GRLD  +EGLL+LT
Sbjct: 16  RNHKMPQLILFNKPYGVLTQFTGELPEQTLSAFIKFPGFYA----AGRLDKQSEGLLVLT 71

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           +DG L   L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L ++   
Sbjct: 72  DDGKLQHRLTHPKFEKKKHYWVQVEGAPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKI 131

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ + LREGKN +I+K+     +   RLIR   G ++L  L  G
Sbjct: 132 WPRIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRHQIGDWRLDQLQPG 191

Query: 232 STREVS 237
             + ++
Sbjct: 192 EYKLIN 197


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 69/224 (30%), Positives = 112/224 (50%), Gaps = 5/224 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLW 76
           KV+  A + SRR++   I Q  V +NG   E  +  V    D +  +G P+  +   R++
Sbjct: 13  KVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQQDKVTFEGKPVELSRIRRIY 72

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARV 133
           L  +KP  +V+T SD  GR TV D L   +  + +  VGRLD  T GLLLLTNDG L   
Sbjct: 73  LMLNKPPEIVSTTSDELGRKTVMDLLHRRYEGAGLFPVGRLDETTTGLLLLTNDGELTNR 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  + Y +     + Q     L+KG+++        +++  T +    +  + +
Sbjct: 133 LTHPSYEIEKEYLISIDAALTQADKESLEKGMLLDDGLTSPARLSRVTDEPPYNYKLI-I 191

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EGK R ++++F    +++  L R      +LG L  G TRE++
Sbjct: 192 HEGKKRIVRRMFAHLGYQIKALKRSRIATLRLGKLEEGKTRELT 235


>gi|46203293|ref|ZP_00208890.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 187

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 98/189 (51%), Gaps = 22/189 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG-RSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           TRL +++KP  ++T  +D +G R+T+  F N+P +++     GRLD ++EGLL+LT+ G 
Sbjct: 2   TRLIVFNKPYDVLTQFTDREGGRATLKDFINVPGVYA----AGRLDRDSEGLLVLTDSGP 57

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG---- 184
           LA  +  P  +  + Y  +  G   +D L+ L++G+V++ G        T+         
Sbjct: 58  LAARISDPKHKLAKTYWAQVEGIPSEDDLDKLRRGVVLKDGPTLPAGVRTMPEPDNLWPR 117

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + +REG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 118 DPPIRYRAAIPTSWIELTIREGRNRQVRRMTAAMGFPTLRLIRWAVGEWTLAGLAPGEWR 177

Query: 235 EVSKKILRE 243
           +   + L++
Sbjct: 178 DEPVRALKK 186


>gi|166714192|ref|ZP_02245399.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 200

 Score = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 87/176 (49%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 14  LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 70

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           +  P  +  + Y V+  G+   ++L  L+ G+V+        QV +LD            
Sbjct: 71  VTDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTRPAQVRSLDPAPPLWPRDPPV 130

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 131 RVRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 186


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 110/231 (47%), Gaps = 14/231 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  P     + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPIHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++
Sbjct: 176 SQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLT 226


>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 = 74.3 bits (181), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG--VPLRKAE 71
           R+ +++A+A I SR+ ++R + +  + ++       + NV      I  D   VP   A 
Sbjct: 2   RLDRLLAQASI-SRKSMKRALLRGAILIDQTPARSLSQNVDTGLQEILFDKQKVP---AP 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R ++ +KP G +T +SD   + TV D +        + S+GRLD +T GLLL+T++G 
Sbjct: 58  AHRYFMMNKPRGYITANSDA-SKETVIDLIQKEDYSGELYSIGRLDRDTTGLLLITDNGP 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAW 188
           L   L  P     + Y V+ +G ++   +   ++G+  + G      Q+T+ +     + 
Sbjct: 117 LGFQLLHPQYHVDKTYYVQVNGLLNNQAIEAFQQGVRFLDGKVCKPAQLTIHSTTPVLST 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
            +V + EGK  ++KK+F     KV  L R  +G FQL   LA G  R +++  L+
Sbjct: 177 ASVTISEGKFHQVKKMFLAIGVKVTYLKRTHFGDFQLDPSLAEGDYRSLNQDELK 231


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +    V V+  +++  A  V     +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRSLVARELRAGLVTVDDEIVKSGAFQVTIDHEVAYDGNVLVQVTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G + +  DP   + +F     +  ++ S GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPQGYICSTDDPTHPTILFFIDEPLAQKLHSAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV+    +  D      +G+++ G  Y      L+     +  +T+   
Sbjct: 122 TSPKHHCEKTYRVQLSDDIANDVAEQFAQGVMLNGEKYLTKPAKLEIISPRDVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L  TL  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVCGLHRERVGEIWLDETLEPGEYRPLTEE 225


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 58/226 (25%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  QRV V+G +++  A  ++    +  D   L +    R
Sbjct: 2   RLDKFLSQQLGISRSLVARELRAQRVTVDGEVIKNGAFKLLPEHEVAFDDNVLVQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP+G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPLGYVCSTDDPDHPTILYFIDEPVAHKLHAAGRLDIDTSGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D     + G+ + G        TL+    S   V + + 
Sbjct: 122 TSPKHHCEKTYLVTLDQPLAPDTAEKFQAGVQLHGEQSLTRPATLEII--SEHQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
           EG+  ++K++F      V  L R   G   L   L AG  R ++ +
Sbjct: 180 EGRYHQVKRMFAAVGNHVVALHRERIGAITLDDALEAGEYRPLTPE 225


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 100/226 (44%), Gaps = 3/226 (1%)

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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 125 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EG+  ++K+ F      V  L R   G   L   LA G  R ++++
Sbjct: 183 EGRYHQVKRXFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEE 228


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 89/175 (50%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  +++  +D   R T+ D +      V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 33  IFNKPFDVLSQFTDDQHRQTLADFI--SVKDVYAAGRLDRDSEGLLILTNDGVLQARLTQ 90

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +D L+ L++G+ ++       +V +  +              
Sbjct: 91  PESKSPKTYWVQVEGAPTEDDLDKLRQGVELKDGMTLPAKVEIIPEPNVWERNPPVRFRA 150

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+++ + EG+NR+++++     +   RLIR S G + +  +  G+ +EVS
Sbjct: 151 AIPTTWISITITEGRNRQVRRMTANIGFPTLRLIRYSMGDWTIKDVAHGTWKEVS 205


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 50/177 (28%), Positives = 87/177 (49%), Gaps = 17/177 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DT 181
           P  +  ++Y V+  G   QD +  L+ G+ +        G    D    L        + 
Sbjct: 61  PGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE ++
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREATE 177


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 60/184 (32%), Positives = 88/184 (47%), Gaps = 20/184 (10%)

Query: 70  AERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           A   R  +++KP G+++  T   P   ST+ D +P     V  VGRLD ++EGLLLLTND
Sbjct: 2   ANHYRYIIFYKPYGVLSQFTQETPK-HSTLKDYIP--VRDVYPVGRLDWDSEGLLLLTND 58

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQ-- 182
           G L   L  P     R Y V+     D D +N L+ G+ IQG      +V L    TQ  
Sbjct: 59  GQLQHRLAHPRFGHQRTYWVQVERIPDVDAINKLQTGVEIQGYRTQPAEVRLLLAATQLP 118

Query: 183 ----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                         AW+ + L EGKNR+++++     +   RL+R++     L  L  G 
Sbjct: 119 ERNPPIRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVNIAHLNLDGLDLGE 178

Query: 233 TREV 236
            R++
Sbjct: 179 WRDL 182


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 64/233 (27%), Positives = 114/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAA+   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRAAIGDQVYAADVVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIISTTEDGEQDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ +     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKDYVVTVNKPVTDEFILGLSAGVPM----LGTVTKKCKVKKEATFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++   F ++V +L R       L  L  G  R+ +   L E
Sbjct: 179 ITLVQGLNRQIRRMCSHFGYEVTKLERTRIMNINLKGLPQGEWRDFTDDELIE 231


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 87/175 (49%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  +DPDGR T+ D +     RV + GRLD+++EGLLLLT+ G L   L  
Sbjct: 4   LFNKPYNVLTKFTDPDGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHDLTD 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDMQVTLDT----- 181
           P  +  + Y V+  G   + +L  L++GI ++           I Y       +      
Sbjct: 62  PENKAYKTYVVQVEGIPTKAQLKALEQGIELKDGMTLPAKVKRIPYPKWLWEREKPIRVR 121

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           Q    +++ + ++EG+NR+++++         RLIR     + +G L  G  R +
Sbjct: 122 QNQPTSFLQIKIKEGRNRQVRRMTAAVGIPTLRLIRTHIDAYHIGDLKPGMYRVI 176


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/223 (28%), Positives = 111/223 (49%), Gaps = 9/223 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V  ++D I V+   +   ++ 
Sbjct: 2   RLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYIDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D +   T+ D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATED-EVHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    + Y V     + Q  ++  K GI +     G ++  +  +K  N    V 
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSD---GKLKPAI-LKKVDNYVSHVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           + EGK  ++K++F     +V  L RI     +L   L  GS R
Sbjct: 176 IYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYR 218


>gi|332993406|gb|AEF03461.1| ribosomal large subunit pseudouridine synthase E [Alteromonas sp.
           SN2]
          Length = 180

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/168 (27%), Positives = 89/168 (52%), Gaps = 20/168 (11%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTND 127
           A  +++ L++KP  +++  +D DGR T+ D  ++P +++     GRLD ++EGLL+LTND
Sbjct: 2   ANESKIVLFNKPFQVLSQFTDADGRETLKDYIDIPGVYA----AGRLDRDSEGLLVLTND 57

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT----- 181
           G L   L  P  +  + Y V+  G  ++  L+ L+ G+ ++ G+      V +D      
Sbjct: 58  GKLQHKLAHPEAKTSKTYWVQVEGIPNEAALDALRNGVELKDGMTKPAKVVAIDPPELWD 117

Query: 182 --------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                   Q    +W+++ + EG+NR+++++     +   RL+R   G
Sbjct: 118 RIPPVRFRQAIPTSWLSITISEGRNRQVRRMTAHIGFPTLRLVRYRVG 165


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 50/172 (29%), Positives = 82/172 (47%), Gaps = 16/172 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG     L  
Sbjct: 48  LFNKPFDVLCQFTDEAGRKTLKDFIP--VPGVYAAGRLDRDSEGLLLLTNDGKFQSKLTE 105

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------DTQ 182
           P  +  + Y V+  G+ +Q  ++ L  G+ ++       +V L              + Q
Sbjct: 106 PKQKTFKTYWVQVEGEPNQAAIDALCAGVELKDGMTLPAKVRLMATPDVWPRTPPVRERQ 165

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               AW+ V + EG+NR+++++         RLIR   G + L  L  G  +
Sbjct: 166 SIPTAWLEVQICEGRNRQVRRMTAHVGHPTLRLIRYKIGQWSLDDLNNGDYK 217


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 57/188 (30%), Positives = 93/188 (49%), Gaps = 32/188 (17%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA----- 131
           L++KP  ++   +D +GRST+ D +P     + SVGRLD ++EGLLLLT++G L      
Sbjct: 6   LFYKPYDVLCQFTDENGRSTLKDYIP--IPNIYSVGRLDRDSEGLLLLTDNGQLQHRLGH 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQKG 184
           R    P T W++V R+      D + L  L++G+ IQ        +   D +  L  ++ 
Sbjct: 64  RQFAHPRTYWVQVERI-----PDLNALEKLRQGLPIQDYRTRPAIVNLLDFEPDLPPREP 118

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY-----GPFQLGTLLAG 231
                     AW+ + L EG+NR+++++     +   RLIR +          L  L  G
Sbjct: 119 PIRYRKSVPTAWLEITLTEGRNRQVRRMTAAVGYPTLRLIRTAITIDKNNKLCLTGLQPG 178

Query: 232 STREVSKK 239
             REV++K
Sbjct: 179 QWREVTEK 186


>gi|304397506|ref|ZP_07379384.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304355124|gb|EFM19493.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 239

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 93/203 (45%), Gaps = 2/203 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R I  QRV VNG ++   A  ++    +  DG  L+     R
Sbjct: 2   RLDKFISQQLEISRAIAHREIRGQRVTVNGEVVRDTAFKLLPDHEVVYDGNVLQMQTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTIIYFIEEPMSFKLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     +  D       G+ +           L+    ++  +T  L 
Sbjct: 122 TSPRHHCEKTYRVTLESPISDDTAAQFTAGVQLHNEKSLTKPAQLEVITPTDVRLT--LS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIR 217
           EG+  ++K++F     +V  L R
Sbjct: 180 EGRYHQVKRMFAAVGNRVIELHR 202


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 89/175 (50%), Gaps = 20/175 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T + L+HKP G++   S    R T+  + +LP I++     GRLD ++EGLL+LTNDG L
Sbjct: 77  TTILLFHKPFGVICQFSRDGTRPTLANYISLPDIYA----AGRLDQDSEGLLVLTNDGKL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-------------IQGICYGDMQV 177
            + +  P  +  + Y  +  G + ++ L+ L+ GI              I+   + +   
Sbjct: 133 QQRITHPKHKLEKTYLAQVEGIISEEALHQLRTGIALKDGKTLPAKAQRIEPPNFAERIP 192

Query: 178 TLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            +  +K    +W+ + + EG+NR+++++     +   RLIR   G +QLG L  G
Sbjct: 193 PIRERKNIPTSWLELRICEGRNRQVRRMTAATGFPTLRLIRTRIGEWQLGELQPG 247


>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 = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 116/245 (47%), Gaps = 34/245 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKA 70
           +R+SK +A  G+ASRRE +  I    V+V+G   +L +R    V     I VD    ++ 
Sbjct: 173 ERLSKRMAALGLASRREADEWIEAGWVRVDGKMAVLGQR----VGPQAKIHVDPAAHKQQ 228

Query: 71  ERTRLWLYHKPIGLVTTHSD-----------PDGR----STVFDNLPSIFSRVISVGRLD 115
            +    L +KP+G V+  ++           P+ R    S+  +  P     +   GRLD
Sbjct: 229 AQRVTILVNKPVGYVSGQAEDGYEPAAALIRPENRWSEDSSGVNWHPGQLRGLAPAGRLD 288

Query: 116 INTEGLLLLTNDGGLARVL----ELPSTQWLRVYRVRFHGQ--VDQDKLNLLKKGIVIQG 169
           I++ GLL+LT DG +A++L     L   ++L   RV + GQ  +    L LL  G+ + G
Sbjct: 289 IDSVGLLVLTQDGRVAKLLIGDESLVEKEYL--VRVAYQGQGRLPDSALALLNHGLELDG 346

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 +V+   +      +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 347 QALRPAKVSWQNEDQ----LRFVLREGKKRQIRRMCEAVGLQVLGLKRVRIGSVSLGHLP 402

Query: 230 AGSTR 234
           AG  R
Sbjct: 403 AGQWR 407


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 109/227 (48%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      R
Sbjct: 18  RLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNEL-NVHGPR 76

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D   R T F+ L  I   ++   GRLD++T GL+L+T+DG  +  
Sbjct: 77  YIMLYKPEGFVCSHEDGSNR-TAFELLDEIKMDKLHFAGRLDVDTTGLVLMTDDGKWSHR 135

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  ++YRV     V+ D +   K+GI ++      +   L+ +      +T+  
Sbjct: 136 ITSPKHKCEKMYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEVRAEREVLLTI-- 193

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++
Sbjct: 194 HEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQE 240


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 109/236 (46%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV V+G ++   A+ +     +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRALVARELRAKRVTVDGEVVRSGALKLTPETEVAFDGNVLEQLNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLEEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D  +    G+ +      D+      ++     V + + 
Sbjct: 122 TSPKHHCEKTYLVTLEQPLAADTASHFAAGVQLHN--EKDLTRPAQLEQLDEHRVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G  +L   LA G  R ++++ +     PHL
Sbjct: 180 EGRYHQVKRMFAAVGNRVVDLHRERIGAIRLDDDLAPGEYRPLTEEEIASVGAPHL 235


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 109/227 (48%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      R
Sbjct: 2   RLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNEL-NVHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D   R T F+ L  I   ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGSNR-TAFELLDEIKMDKLHFAGRLDVDTTGLVLMTDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  ++YRV     V+ D +   K+GI ++      +   L+ +      +T+  
Sbjct: 120 ITSPKHKCEKMYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEVRAEREVLLTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++
Sbjct: 178 HEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQE 224


>gi|323187623|gb|EFZ72930.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           RN587/1]
          Length = 177

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 49/176 (27%), Positives = 83/176 (47%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  ++Y V+  G   QD L  L+ G+ +           L  +              
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPPIRER 120

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 176


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 51/201 (25%), Positives = 93/201 (46%), Gaps = 21/201 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP   +   S     +T+ D +P   + V   GRLD ++EG++LLT+ G L   
Sbjct: 3   RLILLNKPFDTICQFSASPPHATLADWVP--VAGVYPAGRLDTDSEGMVLLTDHGPLQHA 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P+ +  + Y V+  G  + ++L  L++G+ +         V +  +           
Sbjct: 61  IAHPAAKAPKTYWVQVEGTPEAEQLEQLRQGVDLGDFVTQPASVRILPEPELWPRQPPVR 120

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                   W+ + + EGKNR+++++         RL+R++ G  +LG L  G  RE++K 
Sbjct: 121 FRKTVPTHWLEIIISEGKNRQVRRMTAKVGLPTLRLVRVAVGSLKLGELQPGEWREIAKG 180

Query: 240 ILREQLGPHLLEEAQVNLDAP 260
            L     P + ++A     AP
Sbjct: 181 EL-----PAVWQQAWSQTAAP 196


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 85/180 (47%), Gaps = 20/180 (11%)

Query: 74  RLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP G++T  T   P+   + F   P  ++     GRLD  +EGLL+LT+DG L 
Sbjct: 3   QLILFNKPYGVLTQFTGELPEQTLSAFIKFPGFYA----AGRLDKQSEGLLILTDDGKLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L ++         
Sbjct: 59  HRLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWPRIPP 118

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  + ++
Sbjct: 119 IRERKHIPTTWLGIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEYKLIN 178


>gi|330895553|gb|EGH27863.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 190

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 47/162 (29%), Positives = 84/162 (51%), Gaps = 20/162 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+ + ++L  L+ G+ +  G         LD          
Sbjct: 88  ARIADPKHKLAKTYGVQVEGEPNDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
               +    +W+ + ++EG+NR+++++         RL+R+S
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRMTAAVGLPTLRLVRLS 189


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 105/230 (45%), Gaps = 12/230 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE +  I+  +V VNG ++      V   D +  DG  +    +  
Sbjct: 66  RLNKYIANSGICSRREADMYISIGQVTVNGKVVNEMGYQVKLEDDVRFDGRRINPEAKAY 125

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP G  TT S+  G +TV D +  S  SR+  +GRL  N  GLLL TND  L + 
Sbjct: 126 VLL-NKPKGFATTTSNDKG-NTVMDLVAGSTKSRIQPIGRLGRNAMGLLLFTNDDELVQK 183

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGSNAWV 189
                    ++Y V     +    +  + +G+ I G       +T+D            V
Sbjct: 184 FTNSKKGVDKLYHVELSNNLKGADIERINEGLKIDG-----KTITVDEISYVDGAPKKEV 238

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +R   N  I+ +FE  N++V R+  ++        L  G  R ++K+
Sbjct: 239 GLRIRNTGNSVIRTIFEHLNYEVVRVDCVTIAGLTKKDLPRGHWRYLTKQ 288


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 112/237 (47%), Gaps = 23/237 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V+V+G ++            I ++     +A +T 
Sbjct: 5   RISKLMSEQGLCSRREADSYIERGWVRVDGEVVSELGAKAYPHQKITLERAA--RAAQTS 62

Query: 75  LW--LYHKPIGLVTTHSDP---------DGRSTV-FDNLPSIFSR-----VISVGRLDIN 117
           L   L +KP+G V+  ++          D RS    D     F R     +   GRLDI+
Sbjct: 63  LATILINKPVGYVSGQAEDGYKPAVALVDARSQYEGDRSGRRFDRANLRGLAVAGRLDID 122

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GLL+LT DG +A+ L    +   + Y VR  G++ +  L LL  G+++ G       V
Sbjct: 123 SQGLLVLTQDGRVAKQLIGEDSLVDKEYLVRVEGRLSERGLALLNHGLMLDGKPLKPANV 182

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +      +   LREGK R+I+++ E    +V  L R+  G  +LG L  G  R
Sbjct: 183 CWQNED----QLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVRLGDLPVGQWR 235


>gi|298492438|ref|YP_003722615.1| pseudouridine synthase ['Nostoc azollae' 0708]
 gi|298234356|gb|ADI65492.1| pseudouridine synthase ['Nostoc azollae' 0708]
          Length = 195

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 85/179 (47%), Gaps = 22/179 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++HKP G+++  +    +      + ++P I+     VGRLD ++EGL+LLTNDG L   
Sbjct: 9   IFHKPYGVLSQFTQESPKHITLKDYIDVPEIYP----VGRLDWDSEGLMLLTNDGQLQHR 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-------- 185
           L  P     R Y V+     D + +N L  G+ IQ       QV L  ++ +        
Sbjct: 65  LANPRFGHKRTYWVQLEHIPDGEAINKLCTGVEIQNYQTRPAQVKLFLEEPTVSERNPPI 124

Query: 186 -------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   AW+ + L EGKNR+++++     +   RLIR+S    QL  L  G  R ++
Sbjct: 125 RFRKNIPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLIRVSITNLQLNGLQPGEWRYLT 183


>gi|329725501|gb|EGG61981.1| pseudouridylate synthase [Staphylococcus epidermidis VCU144]
          Length = 230

 Score = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/224 (28%), Positives = 112/224 (50%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V  ++D I V+   +   ++ 
Sbjct: 2   RLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYIDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D +   T+ D LP      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATED-ELHPTIIDLLPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-V 191
            +  P+    + Y V     + Q  ++  K GI +      D ++     K  + +V+ V
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIEL-----SDGKLKPAILKKVDDYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L   L  GS R
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYR 218


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K I+     SR E +++I ++ V +N IL++     V   +D + V+G  L   +  
Sbjct: 2   RLDKFISTTTTLSRAEAKKII-KKGVLINNILVKSPDYKVDELSDQVIVNGERLVYQKYI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP  +V+   D     TV D L       +V  VGRLD +TEGL+LLTNDG LA
Sbjct: 61  YIMM-NKPKNVVSATEDA-VEKTVVDILEEKDRIHKVFPVGRLDKDTEGLMLLTNDGELA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--IC-YGDMQVTLDTQKGSNAW 188
             L  P     + Y V   G++  + + L++ GI+I G   C    +++    ++ S A 
Sbjct: 119 HKLISPKKDVEKKYYVEVSGKLKDEYIELVENGIIIDGGYKCKSARLEILESNEEKSRA- 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++ + EGK  ++K++ +     V  L R+S G  +L   L  G  R +++K L+
Sbjct: 178 -SIFITEGKFHQVKRMMKALGTTVTYLKRLSIGSLKLDENLKLGEYRYLTEKELK 231


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 86/175 (49%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  ++   +D  GR+T+   +P   + + + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   IFNKPFDVLPQFTDEQGRTTLKQYIP--LTGIYAAGRLDRDSEGLLVLTNDGQLQAQLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------------TLDT 181
           P  +  +VY V+  G+  +  L   ++G+ ++       Q                  + 
Sbjct: 61  PGKRTGKVYYVQVEGEPTEHDLARFRQGLTLKDGPTLPAQAERVAEPEWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    +W+ + L EG+NR+++++     +   RLIR S G   L  L +G  RE+
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMGSITLEDLASGCWREI 175


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 109/245 (44%), Gaps = 30/245 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRK 69
           P R+SK +A  G+ SRRE +  I +  V+VNG    + AV    V   D I++       
Sbjct: 6   PLRLSKRMAELGLCSRREADAYIERGWVRVNG----QTAVLGQKVSPADRIDLAREAHET 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVG 112
             R    L +KP+G V+   +   R+ V                 FD  P     +   G
Sbjct: 62  QARRVTVLLNKPVGYVSGQPEKGYRAAVELFTPENRWEGDQSRIPFD--PRHLRGLAPAG 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDI++ GLL+LT DG  A+ L        + Y VR  G++ ++ L LL  G+ + G   
Sbjct: 120 RLDIDSVGLLVLTQDGRTAKQLVGADGGSEKEYLVRVRGRLKENGLALLNHGLSLDGEPL 179

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V    +      +   LR+GK R+I+++ E     V  L RI  G  +LG L  G 
Sbjct: 180 RPAKVEWQNRD----QLRFVLRQGKKRQIRRMCELVGLTVVGLKRIRIGRVKLGALPPGK 235

Query: 233 TREVS 237
            R ++
Sbjct: 236 WRYLA 240


>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 = 73.9 bits (180), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 13/233 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+++   D     TV D L     +F     VGRLD +T GLLLLTNDG 
Sbjct: 62  IYLMM-NKPAGVISATYDKRDE-TVIDLLYMEDQVFEP-FPVGRLDKDTVGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSN 186
           L   L  P     +VY    +  + +  +   + G+ +          ++V  + +  S 
Sbjct: 119 LNHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSR 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             VTV  +EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+
Sbjct: 179 VEVTV--QEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSE 229


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 67/256 (26%), Positives = 116/256 (45%), Gaps = 35/256 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM----STDHIEVDGVPLRKA 70
           R+ K +A + +  R+ V   I    VKVNG ++   ++++       +++E   V   K 
Sbjct: 2   RLDKFLAESAVGRRKIVRTYIKDGMVKVNGEIITEPSIDINEKLDDVEYLEKKVVHTGKV 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                ++++KP G +T   D   R TVFD      + V  VGRLD +TEGLLLLTNDG  
Sbjct: 62  ----YYMFNKPSGCITATKDNIHR-TVFDYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEF 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------QGICYGDM 175
              +  P     + Y     G +D +    L++G+ I               +   Y + 
Sbjct: 117 EHKVMHPEKHVEKTYFFWALGSLDDEDKKQLQEGVFIGSNEALTKPAKIDIHKSGSYIEF 176

Query: 176 QVTL--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG- 226
           +  +        D Q   + ++T+   EG+  ++K++ +     V  L RIS G  +L  
Sbjct: 177 KEEIPINSLKNKDHQPVVSGYLTIS--EGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDE 234

Query: 227 TLLAGSTREVSKKILR 242
           +L  G  R+++KK ++
Sbjct: 235 SLKMGDYRDLTKKEIK 250


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/210 (27%), Positives = 102/210 (48%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A  RV+V+G +      +V     +  D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVAFDMQILQPGKAAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+  +D    +TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATTDAQ-HATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + I     Q+T+   + +     +
Sbjct: 121 LTQPHTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSAR----L 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            + EG+  ++K++F  F+ KV +L R S G
Sbjct: 177 SIIEGRYHQVKRMFGHFDNKVLQLHRESIG 206


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 126/240 (52%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A   SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPSGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKIA-FQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK---KILREQL 245
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R +++   +I++E L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEELEIIKEYL 237


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 109/227 (48%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E   ++  + V VN ++ +  +V V     +E  G  L      R
Sbjct: 2   RLDKFLCDALGITRKEATHLLKTKTVTVNDVMQKSGSVKVTEQCVVEWQGNEL-NVHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D   R T F+ L  I   ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGSNR-TAFELLDEIKMDKLHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  ++YRV     V+ D +   K+GI ++      +   L+ +      +T+  
Sbjct: 120 ITAPKHKCEKMYRVWLVDPVEPDYVEKFKEGIQLKSEDGLTLPAHLEVRAEREVLLTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++
Sbjct: 178 HEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQE 224


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 49/179 (27%), Positives = 85/179 (47%), Gaps = 16/179 (8%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  S   G  T+ D +P     V   GRLD ++EGLL+LTNDG L   L  
Sbjct: 37  LFNKPFNVLTQFSGEPGDITLADFIP--VKDVYPAGRLDKDSEGLLVLTNDGILQARLTQ 94

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   ++ L  L+KG+ ++        V + ++              
Sbjct: 95  PKSKQPKTYWVQVEGAPSEESLQALRKGVELKDGMTLPAGVEVMSEPNIWPRNPPIRERK 154

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                W+ + L+EG+NR+++++         RLIR     + +  L  G  RE++ + L
Sbjct: 155 NIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYKMADWTVDDLEPGQWREITLETL 213


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 112/231 (48%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + I+R    + + V  ++ ++++ V+G +       V     + VDG  +++ +  
Sbjct: 6   HRLDRFISRRLSVTNKAVRELLVRKKIIVDGEVASLMNQTVGPFTFVVVDGEVIQQRQPV 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
            L + +KP G+V+   D D  + V D +       + + GRLD NT GLLLLTNDG  ++
Sbjct: 66  YLMM-NKPKGVVSATKD-DKHTIVLDLIDHPLKEELHIAGRLDFNTTGLLLLTNDGAWSK 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWV 189
            L LP    ++ YRV     +    + + +K    +G+      +T         S+  V
Sbjct: 124 QLSLPENNIMKKYRVTLKDHLFSSDVLIYQKKFS-EGVFLSSENITTRPATLLALSSNIV 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            + + EG+  ++K++F FF  +V  L R+S G  ++ G L  G  R ++ K
Sbjct: 183 ELSICEGRYHQVKRMFGFFQNEVLELHRLSVGSLEMEGGLALGRYRVLTPK 233


>gi|205373779|ref|ZP_03226581.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           coahuilensis m4-4]
          Length = 125

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 59/100 (59%), Gaps = 1/100 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +GIASRR+ E +I + +VKVNG++++     V   D +EV+GV + + E+ 
Sbjct: 2   ERLQKVIAHSGIASRRKSEELIVEGKVKVNGVIVKELGTKVGPNDTVEVEGVKVEREEKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
              LY KP G+++   D   R  V D  P I  R+   GR
Sbjct: 62  YFLLY-KPRGVISAVRDDKDRKVVTDFFPHIQERIYPXGR 100


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 114/227 (50%), Gaps = 8/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K+ +  GI SR++  ++I + R+ VNG+   +    V   D I +D   L   E+  
Sbjct: 2   RINKLFSNLGICSRKDTSKLIEENRIIVNGLPCIQGQW-VELEDEILLDNKLLPIKEKIY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP+G+  T +D    + +  N  +    +  VGRLD  ++GL+LLTNDG LA  +
Sbjct: 61  IAL-NKPVGVTCTAADEVEHNII--NFMNYNEYIFPVGRLDKASQGLILLTNDGDLANKI 117

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V      + + +  ++ G+ I  +     +V   ++   N  +T GL 
Sbjct: 118 LESENEHEKEYIVTLDRPFNDEFILGMENGVEICNVKTRQCKVRRISEDTFNIILTQGL- 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              N++I+++ + F + V +L RI     +LG L  G  R +S++ L
Sbjct: 177 ---NKQIRRMSKAFGYNVEKLERIRIVNIELGDLEYGKWRYLSEEEL 220


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 106/206 (51%), Gaps = 10/206 (4%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDP-DGRSTVFD 99
           +NG + +   + V   D + +DG  + K ++ ++++ +HKP+G+  T +D  DG    + 
Sbjct: 3   INGEVCKHGTI-VTENDIVMIDGKTIEKEDKEKIYIAFHKPVGITCTAADHIDGNIIEYI 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           N P    R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++
Sbjct: 62  NHPE---RIFPVGRLDKASEGLILLTNDGRIANQILHGDYEHEKEYIVTVDKPFTDWFID 118

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            + +G+ I+       +VT    + +++   + L +G NR+I+++   F + V +L R+ 
Sbjct: 119 GMSRGVKIKDGITKQCKVT----RVNSSTFRIILTQGMNRQIRRMSRAFGYTVTKLKRVR 174

Query: 220 YGPFQLGTLLAGSTREVSKKILREQL 245
               +L  L AG  R V+ + L+E L
Sbjct: 175 IMNIKLDGLEAGEWRNVTVQELQELL 200


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 115/233 (49%), Gaps = 13/233 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   + 
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEYKKY 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
             L + +KP G+++   D     TV D L     +F     VGRLD +T GLLLLTNDG 
Sbjct: 62  IYLMM-NKPAGVISATYDKRDE-TVIDLLYMEDQVFEP-FPVGRLDKDTVGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSN 186
           L   L  P     +VY    +  + +  +   + G+ +          ++V  + +  S 
Sbjct: 119 LNHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSR 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             VTV  +EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+
Sbjct: 179 VEVTV--QEGKYHQVKRMFEARGKKVIYLKRTSFGNLPLDESLEEGEYKELSE 229


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 94/185 (50%), Gaps = 17/185 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++ L++KP  ++T  +D +GR+T+ D +  I   V + GRLD ++EGLL+LTN+G +  
Sbjct: 36  SQVILFNKPFDVLTQFTDENGRATLKDFI--IIPNVYAAGRLDRDSEGLLILTNNGEVQH 93

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y  +  G  ++  L+ L++G+ ++       +V L             
Sbjct: 94  RLADPKFKTEKTYFAQVEGIPEESDLDKLRQGVELKDGMTKPAKVRLISEPDFLWPRNPP 153

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + Q    +W+ + + EG+NR+++++     +   RLIR       L  L  G  R ++
Sbjct: 154 IRERQSIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMSHLTLDGLSNGEYRRLN 213

Query: 238 KKILR 242
           ++ +R
Sbjct: 214 EEEMR 218


>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 = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 113/237 (47%), Gaps = 6/237 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A  GI +R+EV++ I Q +VKV+  +++     V   +   + G    + E   
Sbjct: 8   RLDKYLADMGIGTRQEVKKHIRQGKVKVDAAVVKSPEYKVNEKESTVLYGDSPVRYEAFV 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+++   D   + TV D + +   + +   GRLD +TEGLLL+TNDG LA  
Sbjct: 68  YYMLNKPAGVISATEDRREK-TVVDLIKTKERKDLFPAGRLDKDTEGLLLITNDGKLAHS 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSNAWVT 190
           L  P     + Y  R  G V ++      +GI I      +     V      G  + V 
Sbjct: 127 LLSPKKHVDKTYYARVKGIVTEEDARAFAEGIDIGTSALPEWTRPAVLEIISSGQESAVR 186

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           + ++EGK  ++K++F     +V  L R   G   L  +L  G  R+++ + LR   G
Sbjct: 187 LTIQEGKFHQVKRMFLARGKEVVYLKRERMGGLVLDSSLKPGEYRKLTDEELRNIYG 243


>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 = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 55/211 (26%), Positives = 97/211 (45%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G ++  +A  ++    +E DG  L +   +R
Sbjct: 2   RLDKFIAQQLSVSRAIAGREIRASRVTVDGDIVRDSAFKLLPEHDVEFDGNTLTQQIGSR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLEEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVMLESPVADDTAEQFTKGVQLHN--EKDLTKPAVLEVITPTEVRLTII 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F     +V  L R   G   L
Sbjct: 180 EGRYHQVKRMFAAVGNRVVGLHRERIGEIAL 210


>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 = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 91/182 (50%), Gaps = 23/182 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +RL  ++KP G+++  + P+GR      + ++P + +     GRLD ++EGLLLLTNDG 
Sbjct: 32  SRLLCFNKPYGVLSQFT-PEGRWRGLKEYIDVPGVHA----AGRLDADSEGLLLLTNDGP 86

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT------- 181
           L   +  P  +  + Y V+  G  D+  L  L++G+ +  G+        L+        
Sbjct: 87  LQARIADPRFKMEKTYWVQVEGLPDEAALQALRQGVQLNDGMTLPAQARRLEPPPVLWQR 146

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  +
Sbjct: 147 DPPIRVRQNIPDCWIELVIREGRNRQVRRMTAAIGHPTLRLVRAAIGPYTLDGLEPGQWK 206

Query: 235 EV 236
           +V
Sbjct: 207 DV 208


>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 = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 112/228 (49%), Gaps = 17/228 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     SR EV+R+I  + V V+  +    +  V + + + +DG  + +A +  
Sbjct: 2   RLDKFIANNSSYSRTEVKRLIKNKTVCVDKKITTDPSFTVTNLNTVRIDG-EIIEAIKPL 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSRVISV-GRLDINTEGL 121
             + +KP G V  + D +  S V D +            P   ++ + + GRLD++T GL
Sbjct: 61  YIMLNKPTGYVCANKD-NIHSPVVDLITEQHARQSDQTPPKYRAQSLQIAGRLDVDTTGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +LLT++G     +  P+    + YRV+    +D   + LL +G+++ G     +  T++ 
Sbjct: 120 VLLTDNGEWNHRVTSPNKACFKRYRVKLEKPLDDAAIKLLSEGVMLHGEKAATLPATVEL 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
              SN  V + ++EG+  ++K++F      V +L R + G  +L T L
Sbjct: 180 I--SNTEVLLSIQEGRFHQVKRMFVKVGTCVVKLHREAIGAIELDTNL 225


>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 = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 53/180 (29%), Positives = 86/180 (47%), Gaps = 20/180 (11%)

Query: 74  RLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP G++T  T   P+   + F   P  ++     GRLD  +EGLL+LT+DG L 
Sbjct: 3   QLILFNKPYGVLTQFTGELPEQTLSAFIKFPGFYA----AGRLDKQSEGLLVLTDDGKLQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L ++         
Sbjct: 59  HRLTHPKFEKKKHYWVQVEGAPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWPRIPP 118

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + LREGKN +I+K+     +   RLIR   G ++L  L  G  + ++
Sbjct: 119 IRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRHQIGDWRLDQLQPGEYKLIN 178


>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 = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 104/224 (46%), Gaps = 10/224 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAERT 73
           + K++ R G  SR+    ++ Q RV    ++          TD  H  VDG      E  
Sbjct: 8   LEKILQRQGFGSRKLCRTLVRQGRVHAGDVVCTDPDRR-FETDALHFSVDGEDWVYREHL 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G   +H  P   S+VF   P+ F +  +  VGRLD +T GLLLL++DG   
Sbjct: 67  YIVL-NKPSGFECSHQ-PQHHSSVFTLFPTQFIQRGLQCVGRLDQDTTGLLLLSDDGDFI 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  +VY +  + ++D+ +L  LK G+ ++      M   L  +      + +
Sbjct: 125 HRYTSPKKKVPKVYEISTNAEIDESQLEKLKNGVQLKD--ETGMTKALSCESFDEYRMRL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
            + EGK  ++K++      +V +L R + G F L  +L AG  R
Sbjct: 183 VIAEGKYHQVKRMVAAAGNRVEKLHRSAIGGFALEESLPAGEWR 226


>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 = 73.6 bits (179), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 60/226 (26%), Positives = 106/226 (46%), Gaps = 5/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V ++ D D  +   F + P +  ++ S GRLD++T G +LLT+DG  +  
Sbjct: 62  YFMLHKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGFVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++          L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRREKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            EG+  ++K++F     KV  L R   G   L  +L  G  R +++
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQ 224


>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 = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 104/239 (43%), Gaps = 24/239 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK++++  + SRRE +  I    V V+G+++ R    V     IE+     +    
Sbjct: 176 PPRLSKLVSQLALCSRREADEWIENGWVTVDGVVVTRLGARVSPKAKIEITNAASQHQTA 235

Query: 73  TRLWLYHKPIG-----------LVT-----THSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           +   +++KPIG           + T     TH   DG    F    S    +   G+LD 
Sbjct: 236 SVTIVFNKPIGDAAAPDAGLAAIATLIRPDTHWAEDGTCRRFQA--SHLRGLAVAGKLDT 293

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
              G+L+ T DG +AR L     +    Y +R  G++  D L LL+ G+ +  +     Q
Sbjct: 294 EEHGMLVFTQDGSVARRLTGGGARLENEYHLRVQGELSPDGLQLLRHGLSLDNVRLERAQ 353

Query: 177 VT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           V+ L  Q+     +   + E + R+I++  E    +V  + R+  G   LG L  G  R
Sbjct: 354 VSWLSEQQ-----LRFVVHENRKRQIQRQCELVGLQVTDIKRVRIGGVSLGKLPPGQWR 407


>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 = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 114/231 (49%), Gaps = 21/231 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAER 72
           ++K I+  G  SRRE + +I   RV    +L +R A         D +EVDG  +  A++
Sbjct: 7   LNKFISDTGYCSRREADNLITSGRV----LLNDRPAALGNRYKPGDTVEVDGSLITAAKK 62

Query: 73  -TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTND 127
             R++L  +KP G+ TT         + DN+ S  +   R+  +GRLD ++EGL+ LTND
Sbjct: 63  EKRVYLALNKPPGITTTTE-----LHIKDNIISFVNYPQRIFPIGRLDKDSEGLIFLTND 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +   +    + Y VR +  +D + L+ + +G+ I        +V +  ++    
Sbjct: 118 GDIINKILRAANNHEKEYVVRVNKPIDTNFLHQMSQGVPILDTRTLPCKVQMTGRQTFRI 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +T GL    NR+I+++ E+  + V  L R+     +L  L  G  R +S+
Sbjct: 178 TLTQGL----NRQIRRMCEYLGYTVVGLQRVRIMNVRLDKLPLGKWRYLSE 224


>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 = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 67/233 (28%), Positives = 114/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I  +GI SRR+ +R I Q  V +NG   +RAAV   V + D ++V+G  +  R  
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGNVFING---KRAAVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   +   +KP+G+V+T ++   R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVIIALNKPVGIVST-TEGGERDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G      +V  +    S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTAEFIRGLGAGVPMLGTVTKKCKVKKE----STFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F + V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYDVTKLERTRIMNVSLKGLPPGEWRDLTDDELIE 231


>gi|110834141|ref|YP_693000.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110647252|emb|CAL16728.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 206

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 51/180 (28%), Positives = 89/180 (49%), Gaps = 20/180 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +L L +KP  +++  SD  GR T+  F  +P ++      GRLD ++EGLLLLT+DG L
Sbjct: 2   AQLILLNKPFRVLSQFSDDQGRRTLREFVCVPGVYP----AGRLDWDSEGLLLLTDDGAL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYGDMQV 177
              +  P  +  + Y V+  GQ    +L  L++GI             +I   C      
Sbjct: 58  QARISDPRFKLPKTYLVQVEGQPGPQELQKLRQGIRLKDGPTRPAKVSLIDDPCLWPRTP 117

Query: 178 TLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + ++K   ++W+++ + EG+NR+++++         RLIR   G + L  L  G +R +
Sbjct: 118 PVRSRKTVPDSWLSLTIDEGRNRQVRRMTAAIGHPTLRLIRWQIGDWSLADLAPGESRSM 177


>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 = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 56/208 (26%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLNKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVVGLHRWKIG 206


>gi|325478230|gb|EGC81349.1| putative 16S pseudouridylate 516 synthase [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 232

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 114/228 (50%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+I  +G+ +R+ ++R   +  + VNG +++ ++  V    D +   G  +   E  
Sbjct: 2   RLDKMIGNSGLDTRKNIKRNAKKGAILVNGEVIKDSSYQVDPEVDEVYYMGQFVDYFENI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---GRLDINTEGLLLLTNDGGL 130
            + + +KP G ++   D D   TV D L   F RV+ +   GRLD +T GLLLL+ DG  
Sbjct: 62  YIMM-NKPQGYLSATEDKD--PTVIDLLDD-FYRVLDLSIAGRLDKDTTGLLLLSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y  +    +D+  ++L K+G+ I+   Y      L+    + A VT
Sbjct: 118 IHRVTSPNSNIEKTYIAKTRDPIDESLIDLFKEGVYIKEDDYTARSAKLEIIGKNEAKVT 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           V   EGK   +K++F     +V  L R++ G  +L + L  G  RE+S
Sbjct: 178 V--TEGKFHLVKRLFSNSGNEVVDLKRVAIGDLKLDSHLGLGEYRELS 223


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 125/240 (52%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSLLQKQILVDGKPACKLSQNVDTGLQQITFQGKQVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  HYYMLNKPAGAVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+T+ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTPQDKIA-FQEGIRFLDGTVCQPAQLTIFSSCFSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK---KILREQL 245
           +V + EGK  +IKK+F     K+  L RI +G F L   LA G  R +++   +I++E L
Sbjct: 178 SVRISEGKFHQIKKMFLVVGVKIIYLKRIQFGNFTLDPDLATGDCRPLNQEELEIIKEYL 237


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 40  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 98  LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 157

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+N +++++         RLIR S G + L  L  G   E+++
Sbjct: 158 RERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWCEIAQ 217

Query: 239 K 239
           +
Sbjct: 218 E 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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/206 (27%), Positives = 105/206 (50%), Gaps = 10/206 (4%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDP-DGRSTVFD 99
           +NG +     + V   D + +DG  + K ++ ++++ +HKP+G+  T +D  DG    + 
Sbjct: 3   INGEVCTHGTI-VTENDIVTIDGKTIEKEDKEKIYIAFHKPVGITCTAADHIDGNIIEYI 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           N P    R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++
Sbjct: 62  NHPE---RIFPVGRLDKASEGLILLTNDGRIANQILHGDHEHEKEYIVTVDKPFTDWFID 118

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            + +G+ I+       +VT    + +++   + L +G NR+I+++   F + V +L R+ 
Sbjct: 119 GMSRGVKIKDGITKQCKVT----RVNSSTFRIILTQGMNRQIRRMSRAFGYTVTKLKRVR 174

Query: 220 YGPFQLGTLLAGSTREVSKKILREQL 245
               +L  L AG  R V+ + L+E L
Sbjct: 175 IMNIKLDGLEAGEWRNVTVQELQELL 200


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 56/210 (26%), Positives = 102/210 (48%), Gaps = 8/210 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A +G+ SRRE +  IA   V VNG ++      V  TD +  DG  +    +  
Sbjct: 49  RLNKYVANSGMCSRREADENIAIGLVSVNGKVVTEMGYKVKRTDEVRFDGQRITPEAKVY 108

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP G  TT ++  GR TV D +  +  + V  +GRL  N+ GLLL TND  + + 
Sbjct: 109 VLL-NKPKGFATTTAEGKGR-TVMDLVANATNANVKPIGRLGRNSLGLLLFTNDDKIVQK 166

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
                    R+++V     +  + L  +K+G  ++G  I   D+       K     + +
Sbjct: 167 FTNSKNGVARLFQVELDKNLKYEDLKKIKEGFKVEGKLITVEDISYIEGESKNK---IGL 223

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            ++   N  ++ +F+ FN+ + ++  ++ G
Sbjct: 224 KIKNTGNTILRTIFDNFNYDIVKIDCVAIG 253


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 110/236 (46%), Gaps = 18/236 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++   G  +R E+++   Q  V+VNG   +++ V+V    D I  +G  +   E  
Sbjct: 2   RLDKLLGNLGYGTRSEIKKYCKQGFVRVNGAEAKKSDVHVDPENDEIVFNGELVNYREFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G V+   D     TV D +   +       VGRLD +TEGLL++TNDG L+
Sbjct: 62  YLLL-NKPAGYVSATFDK-YDPTVIDLIGEEYLPFEPFPVGRLDKDTEGLLVITNDGKLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------DTQ 182
             +  P     + Y      +VD   + + +KG+ I G  Y      L         D  
Sbjct: 120 HRVLSPKNHVPKKYYAIIDKEVDDMDVRIFEKGVYI-GEDYTTKPSKLEVLNPFEFEDGS 178

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVS 237
            GS   VT+   EGK  ++K++FE    +V  L RI  G  +L   L  G  RE++
Sbjct: 179 LGSEVHVTIS--EGKFHQVKRMFEAVGKEVVYLQRIQMGGLELDEELDLGEYRELT 232


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 98/216 (45%), Gaps = 2/216 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ A+  +     +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGSRVTVDGDIVKDASFKLQPEHEVEYDGNTLTQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + +    L  KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVELESPLAEGTAELFAKGVQLHN--EKDLTKPAVLEVITPTEVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           EG+  ++K++F      V  L R   G   L   LA
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGDILLDDALA 215


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 103/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ +A  ++    +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRANRVTVDGEIVKNSAFKLLPEHDVEYDGNSLVQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D       G+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVTLESPVADDTAEQFAHGVQLHN--EKDLTKPAVLEVITPTQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           EG+  ++K++F      V  L R   G  +L   L  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGDIRLDDDLEPGEYRPLTEE 225


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 84/174 (48%), Gaps = 17/174 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG-------- 184
           +  P  +  + Y V+  G  D   L+ L+ G++++ G+        +DT  G        
Sbjct: 61  ITDPKHKLPKTYWVQVEGVPDSAALDALRAGVLLKDGMTQPAGAALIDTPPGLWPRTPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                   +W+ + +REGKNR+++++     +   RLIR   G + L  L  G+
Sbjct: 121 RARKAIPTSWLELTIREGKNRQVRRMTAAVGFPTLRLIRYRIGAWTLDGLDQGT 174


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 92/185 (49%), Gaps = 22/185 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP G+++  +  DG+ T+  F + P +++     GRLD ++EGLL+LT+DG L   +
Sbjct: 6   LFNKPCGVLSQFTAQDGQRTLAEFIDQPGVYA----AGRLDKDSEGLLVLTDDGALQHRI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------------ 181
             P    ++ Y  +  G      L+ L++G+ ++ G         LD             
Sbjct: 62  ASPRHASVKRYWAQVEGTPTNAALDALREGVELKDGWTRPAGARRLDAPPLWPRDPPIRE 121

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK-- 238
            +    AW+ + L EG+NR+++++     +   RL+R S GP+ L  L  G  R ++   
Sbjct: 122 RKSIPTAWIELSLSEGRNRQVRRMTAAVGFPTLRLVRWSVGPWDLEGLAPGELRVITAPD 181

Query: 239 KILRE 243
            +LRE
Sbjct: 182 SMLRE 186


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 89/175 (50%), Gaps = 16/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  +++  +D   R T+ D +      V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 33  IFNKPFDVLSQFTDDQHRQTLADFIS--VKDVYAAGRLDRDSEGLLILTNDGVLQARLTQ 90

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +D L+ L++G+ ++       +V +  +              
Sbjct: 91  PESKSPKTYWVQVEGAPTEDDLDKLRQGVELKDGMTLPAKVEIIPEPNVWERNPPVRFRA 150

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                W+++ + EG+NR+++++     +   RLIR S G + +  +  G+ +EVS
Sbjct: 151 AIPTTWISITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDWTIKDVAHGTWKEVS 205


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 56/208 (26%), Positives = 100/208 (48%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 4   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V ++ D D  +   F + P +  ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 64  YFMLNKPQGCVCSNDDGDYPTIYQFFDYP-LAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 123 ITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYN--VNLTI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 181 SEGRYHQVKRMFAALGNKVVGLHRWKIG 208


>gi|327458771|gb|EGF05119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 241

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 127/240 (52%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++ + Q+++ V+G    + + NV +    I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSLLQKQILVDGKPACKLSQNVDIGLQQITFQGKHV-SGPAH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKIA-FQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK---KILREQL 245
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R +++   +I++E L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGDFTLDPDLAKGDYRALNQEELEIIKEYL 237


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 58/224 (25%), Positives = 101/224 (45%), Gaps = 3/224 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR  V R +   RV V+G++    ++ V     +  +G  L      R
Sbjct: 2   RLDKFISQQLGISRSLVIRELRAARVTVDGVVARSGSLQVTPDQEVAYEGNVLTFITGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSTDDPDHATILYFIDEPMAEKLHAAGRLDLDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +      L  +GI++ G    D+      +      V + + 
Sbjct: 122 TSPRHHCEKSYLVTLEQPLAPQTAALFAQGIMLNGET--DLTKPAQLEAFDEHHVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           EG+  ++K++F     +V  L R   G   L   LA G  R +S
Sbjct: 180 EGRYHQVKRMFAAVGNRVVGLHRERIGAIALDAALAPGEYRALS 223


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 89/178 (50%), Gaps = 21/178 (11%)

Query: 78  YHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP  ++   +D   P   +     LP    RV + GRLD ++EGLLLLT++G LA  L
Sbjct: 5   FNKPFNVLCQFTDRSVPARPTLAGFGLPP---RVYAAGRLDHDSEGLLLLTDNGTLAHKL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQKGS-- 185
             P  +  + Y V+  G    ++L  L+ G+ +         I   D   +L T+     
Sbjct: 62  TDPRHKADKTYWVQVEGTPSDEQLQQLRDGVELNDGPTLPAKIERLDPAPSLWTRDPPVR 121

Query: 186 ------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                 +AW+ + +REG+NR+++++    N    RL+R++ GP++L  L  G  R++ 
Sbjct: 122 FRKTVPDAWLAITIREGRNRQVRRMTAAVNLPTLRLVRVAMGPYRLDDLQPGQWRQIG 179


>gi|46202419|ref|ZP_00053237.2| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 236

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 112/233 (48%), Gaps = 21/233 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ ++IA  G  S+R+V+ MI    V + +G +L+    + ++ + I VDG PL      
Sbjct: 2   RLIRLIANLGYGSQRDVKAMIKDGLVTRADGSVLDD--TSKVAHEDIRVDGEPLDPPPGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L L +KP G   + SDP GR  V++ LP  F      V  VGRLD ++ GLLLLT+DG 
Sbjct: 60  VLML-NKPEGYTCSTSDP-GR-VVYELLPPRFMHRNPIVAPVGRLDRDSSGLLLLTDDGP 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKG 184
           LA  +  P     + Y V     +  ++  +   G ++       +   ++ VT      
Sbjct: 117 LAHRVTSPKRHVPKTYEVTLARPLTGEEGAVFASGTLMLRSENTPLAPAELMVT----GP 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             A +T+   EG+  ++K++F      V RL R + G   LG L  G  R ++
Sbjct: 173 QTARITI--TEGRYHQVKRMFAAVGNHVERLHRAAIGGLDLGDLPEGQWRMLT 223


>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 = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 100/225 (44%), Gaps = 20/225 (8%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERA-------AVNVMSTDHIEVDGVPLRKA 70
           K I   G+ SR++ + +I    + +NG +  RA        V+ +S D  E+  VP+   
Sbjct: 5   KYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVPMPHF 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 65  ----YILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSN 186
                +  P  +  ++YRV      D      LK G+++    + D +     +      
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLL----HDDNETVAAAEAVLADP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             + + + EGK  ++K++      +V +L R  +G + +  L AG
Sbjct: 176 TTLMMTITEGKYHQVKRMIAAAGNRVEQLHREKFGDWNVDDLAAG 220


>gi|324112367|gb|EGC06345.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 290

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 112/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFING---KRATIGDQVKPGDVVKVNGRLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +K +G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKSVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>gi|261821431|ref|YP_003259537.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
 gi|261605444|gb|ACX87930.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 209

 Score = 73.2 bits (178), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 49/179 (27%), Positives = 87/179 (48%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++LTNDG L   
Sbjct: 31  RIVLFNKPFDVLPQFTDEAGRRTLKDYIP--ISGIYAAGRLDRDSEGLMILTNDGKLQAR 88

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQVTL 179
           L  P+ +  ++Y V+  G  D+  L   + G              IV +          +
Sbjct: 89  LTQPTEKTAKIYYVQVEGIPDEAALTHFRTGLELNDGKTLPAGAEIVPEPDWLWPRNPPI 148

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K   + W+ + L EG+NR+++++     +   RLIR       +  LL G  +E++
Sbjct: 149 RERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLLPGEWKEIT 207


>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 = 73.2 bits (178), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 99/207 (47%), Gaps = 7/207 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I ++ V VNG ++      +   D +   G PL    +
Sbjct: 4   PCRLDKFISHLAEIPRTQARASIKRKEVSVNGEVITSHNFQLAQQDEVLHQGTPLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP+G V  +SD +   TVFD L  P++ S     GRLDI+T GL+++TNDG  
Sbjct: 64  -RYYMLNKPVGYVCANSD-ELHKTVFDLLDEPNM-SDFHVAGRLDIDTTGLVIITNDGDW 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P     + Y V     +  + L  L+ G+++      D+      ++ +N  + 
Sbjct: 121 SHKITSPKNNKFKTYLVETQEPITDEALEQLRTGVMLHN--EKDLTRPAIAERLANYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIR 217
           + + EGK  ++K++    + KV  L R
Sbjct: 179 LSISEGKYHQVKRMLYAVDNKVVELHR 205


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 64/227 (28%), Positives = 112/227 (49%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R++
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPRES 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD + +GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDFQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPI----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLT 225


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 86/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP+    V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPA---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G     +L  L+ G+V+        +V ++D            
Sbjct: 61  LTDPRHKQPKTYWVQVEGTPAPSQLQALRDGVVLNDGPTRPAKVRSIDPSPQVWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RLIR++ G + L TL  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTASVGLPTLRLIRVAIGDWTLDTLAPGQWR 176


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 96/204 (47%), Gaps = 4/204 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  +++    V VNG + +  A  +   D I  +   L   E  +
Sbjct: 2   RLDKFIAENTGLTRSQAAKVLKSGVVTVNGNIEKSGAAKISQEDEIYYEDQKLEWVEEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G + +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYICSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+      L +GI+++G     +   L+     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAQRLAEGILLRGEKEPTLPAQLEILDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIR 217
            EG+  ++K++F     KV  L R
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHR 202


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 86/181 (47%), Gaps = 23/181 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP  ++   S   GR T+ D+L  P I+      GRLD ++EGL+LLT+DG L  
Sbjct: 3   LILFNKPYLVLCQFSPQAGRRTLADHLAIPDIYP----AGRLDADSEGLMLLTDDGRLQH 58

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            +  P+ +  + Y V+  G  D   LN L+ G+ +        +V               
Sbjct: 59  DISDPTHKQPKAYLVQIEGIPDPVALNTLRTGVFLGDFTSKAAKVIEVATPAWLWPRNPP 118

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 235
                     W+ + + EGKNR+++++         RL+R++ GP+ L +  LL G +R 
Sbjct: 119 IRQRAVTPTRWLLLTITEGKNRQVRRMTAAVGLPTLRLVRVAIGPYSLESHPLLPGESRV 178

Query: 236 V 236
           V
Sbjct: 179 V 179


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 105/220 (47%), Gaps = 7/220 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I ++ V VNG ++      +   D +  +G PL    +
Sbjct: 4   PCRLDKFISHLAEVPRTQARASIKRKEVSVNGEVITAHNFQLAKDDVVLHNGEPLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP+G V  +SD D   TVFD L  P++ S     GRLDI+T GL+++TNDG  
Sbjct: 64  -RYFMLNKPVGYVCANSD-DLHKTVFDLLDEPNM-SDFHVAGRLDIDTTGLVIITNDGDW 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P +   + Y V     +  + L  L++G+++      D       ++ +N  + 
Sbjct: 121 SHKITSPRSNKFKTYLVETQEPITDEALEQLREGVMLHN--EKDATRPAIAERLANYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++    + KV  L R      +L   LA
Sbjct: 179 LSISEGKYHQVKRMLYAVDNKVVELHREQIAGIKLDEDLA 218


>gi|332363998|gb|EGJ41777.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 241

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 119/232 (51%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++ + Q+++ V+     + + NV  S   I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSLLQKQILVDDKPACKLSQNVDTSLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDEEVEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +G +     +  ++GI  + G      Q+++ +   S +  T
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTPKDKSSFQEGIRFLDGTTCQPAQLSILSTSSSLSCAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           V + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++++ L
Sbjct: 179 VKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPELATGDYRPLNQEEL 230


>gi|291518121|emb|CBK73342.1| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           fibrisolvens 16/4]
          Length = 234

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 105/218 (48%), Gaps = 14/218 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ K++    I +R EV+ ++ +  + V+G   E+A       D   V  +  +  E T 
Sbjct: 3   RLDKLLVELNIGTRSEVKALLKKGLIFVDG---EKATKPEQKVDENSVV-ITYQGKEYTY 58

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRST--VFDNL-PSIFSRVISVGRLDINTEGLLLLTND 127
                ++ +KP G++T   D   ++   VF +L P     +  VGRLD +T GLLL+TND
Sbjct: 59  QKFSYYVINKPKGVITATEDAHEKTVMDVFYSLCPDAPKGLAPVGRLDKDTTGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  +  P     + Y V   G++ ++ +  L+ G+ I G        T+  + G   
Sbjct: 119 GQLAHDMLSPKKHVDKTYFVTLDGELSEEDVAALEAGVHI-GEGEPTAPATVKYEGGKTC 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++T+   EGK  ++K++F      V  L R ++GP  L
Sbjct: 178 YITI--HEGKFHQVKRMFFAVGKTVLELKRTAFGPLVL 213


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 30  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 88  LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ V L EG+N +++++         RLIR S G + L  L  G   E+++
Sbjct: 148 RERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWCEIAQ 207

Query: 239 K 239
           +
Sbjct: 208 E 208


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 102/227 (44%), Gaps = 24/227 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-------MSTDHIEVDGVPLRKA 70
           K I   G+ SR++ + +I    + +NG +  RA  N+       +S D  E+  VP+   
Sbjct: 5   KYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDNIDPSQVHTLSVDGEEIAAVPMPHF 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 65  ----YILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKG 184
                +  P  +  ++YRV      D      LK G+++    + +   +  +T  T   
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVLTDPTT-- 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               + + + EGK  ++K++      +V +L R  +G + +  L AG
Sbjct: 178 ----LMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLAAG 220


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 47/177 (26%), Positives = 88/177 (49%), Gaps = 16/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L +KP G++   S+     T+   +P   + V   GRLD ++EGLLLLT DG L   
Sbjct: 26  QLILLNKPYGVICQFSEHPTHPTLKSCVPQ--AGVYPAGRLDTDSEGLLLLTGDGALQHR 83

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDT----------- 181
           +  P  +  + Y V+  G   +++L +L++G+ +        +V  ++T           
Sbjct: 84  IADPRWKLPKTYWVQVEGDPKEEQLEMLRRGVDLGDFVTRPAEVRRIETPELWPRNPPVR 143

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   + W+ + + EGKNR+++++         RL+R++ GP++L  L  G  R +
Sbjct: 144 FRKTVPDCWLEIIISEGKNRQVRRMTAKAGLPTLRLVRVAIGPWKLDGLQPGEMRAI 200


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 52/206 (25%), Positives = 102/206 (49%), Gaps = 31/206 (15%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLL 123
           P  + E+ ++ L++KP  ++T  +D  GR T+  F ++P I+      GRLD ++EGLLL
Sbjct: 19  PKLQLEQIKVVLFNKPYDVLTQFTDEQGRKTLKNFIHIPDIYP----CGRLDRDSEGLLL 74

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------- 167
           LTN G +   L  P+ +  + Y V+  G   +  L  L++G+++                
Sbjct: 75  LTNCGEIQHRLTTPAFKSKKTYWVQVEGVPSEQDLEALRQGVILKDGKTLPALVKFIPPP 134

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS-------- 219
           Q +   D  +  + +    +W+ + + EG+NR+++++     +   RLIRI+        
Sbjct: 135 QNLWQRDPPIR-ERKTIPTSWLEIAIHEGRNRQVRRMTAHIGYPTLRLIRIATAGLNLFD 193

Query: 220 YGPFQLGTLLAGSTREVSKKILREQL 245
           +   QLG   + ++ E+ + + R +L
Sbjct: 194 FPQLQLGCSYSLNSNEIEQLLTRLKL 219


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 122/239 (51%), Gaps = 12/239 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ K ++  G+ +R+EV++ I + +V+V+G + +R  + V  T  ++ +DG  +  A   
Sbjct: 8   RLDKFLSEMGVGTRQEVKQYIRKGKVEVDGEIAKRPELKVDETKANVTLDGERIGYASYV 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D     TV D +     + +  VGRLD +T GLLL+TNDG LA 
Sbjct: 68  -YYMLNKPSGVVSATEDKR-EKTVIDLIKGQKRKDLFPVGRLDKDTVGLLLITNDGNLAH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSN-A 187
            L  P     + Y  +  G V +D      +G+ I      + ++T    LD  K  + +
Sbjct: 126 RLLSPKHHVDKCYFAKVQGNVTKDDAEKFAEGVNIG--TEDEPEITMPGKLDIIKSDDLS 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQL 245
            + + ++EGK  ++K++F+    +V  L R   G   L   LA G  R ++++ L+  L
Sbjct: 184 EIRLTIQEGKFHQVKRMFQAVGKEVVYLKRERMGSLILDDNLAEGEYRMLTEEELKNLL 242


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 112/224 (50%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V  ++D I V+   +   ++ 
Sbjct: 2   RLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYIDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D +   T+ D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATED-ELHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-V 191
            +  P+    + Y V     + Q  ++  K GI +      D ++     K  + +V+ V
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIEL-----SDGKLKPAILKKVDDYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L   L  GS R
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYR 218


>gi|330685516|gb|EGG97168.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU121]
          Length = 230

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 64/217 (29%), Positives = 103/217 (47%), Gaps = 8/217 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  GI +R EV++ + +  VKVN  + +     +    D I V+G  +   ++ 
Sbjct: 2   RLDKFLANMGIGTRNEVKQSLKKGYVKVNDKVNKSPKTQINPDEDIITVNGEKIIYIDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP  +V+   D D   TV D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPSDVVSATED-DKHQTVIDLIPEYKHLGIFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + Y V     V Q  +   K+G+ +        Q+ +   + S     V 
Sbjct: 120 NLMSPNKHVPKTYEVVSKNDVTQSDVERFKEGLELSDGLLKPAQLEIIENRRSR----VT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           + EGK  ++K++F     +V +L RI     +L T L
Sbjct: 176 IYEGKYHQVKRMFHEIENEVLQLKRIKIANLELDTSL 212


>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 = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 90/183 (49%), Gaps = 20/183 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD  GR+T+  F ++P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 33  KLILFNKPFDVLTQFSDEGGRATLKDFIDIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 88

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG------ 184
             +  P  +  + Y V+  G+  ++ L  L+ G+ +  G         LD  +       
Sbjct: 89  ARIADPKHKLAKTYWVQVEGEPTEEHLQRLRDGVELNDGKTLPAEARRLDEPQLWPRNPP 148

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + +REG+NR+++++         RL+R+  G + +  L  G  + V 
Sbjct: 149 VRFRKNIPTYWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIDGLDQGQWKAVP 208

Query: 238 KKI 240
            ++
Sbjct: 209 ARL 211


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 111/227 (48%), Gaps = 11/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +++A   SR++ ++++    + VNG +++ ++ +V ++ D I   G  L  A+  
Sbjct: 2   RLDKFLSKATELSRKDAKKVLHAGEITVNGTIIKDSSHHVDLANDEILWAGEALSVADGN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L +KP G   T   P     V D   +P + +  I+ GRLD++T G LLL++DG   
Sbjct: 62  RYILLYKPDGFECTLK-PKEYPMVTDLIAVPEVANLRIA-GRLDVDTTGALLLSDDGAWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P     + Y++     +D+D     +  +  GI+++G         L     ++A
Sbjct: 120 HRVTSPKRHQPKQYQLTLADAMDKDAQAYAIKQIANGILLEGETEKTRPAVLSFIDETHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +T  L EGK  ++K++  +F  KV +L R S G   L  L  G  R
Sbjct: 180 VLT--LTEGKYHQVKRMMAYFGNKVIKLHRASIGHISLEGLQMGECR 224


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 65/223 (29%), Positives = 112/223 (50%), Gaps = 12/223 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           R+ + ++  GI+SR E+++ I + +V +NG   E A    +  D      V  R      
Sbjct: 2   RLDRFLSEMGISSRSELKKEIRRGQVLLNG---EEARDPSLFVDPENPPVVLYRGREFHY 58

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
           E    ++ +KP G+++   D   +STV D +     R +  VGRLD + EGLLL++NDG 
Sbjct: 59  EAFSYYMMNKPAGILSASRD-KKQSTVLDLIQEDRRRDLFPVGRLDKDCEGLLLISNDGP 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAW 188
           L+  L  P +   ++Y VR  G++ +    L ++G+   + +     ++T+ + +   + 
Sbjct: 118 LSHRLLRPKSHVPKLYFVRVSGRLTESDAELFRRGLRYDEDLTALPAELTILSAEDIISE 177

Query: 189 VTVGLREGKNREIKKVFEFFNWK--VNRLIRISYGPFQLGTLL 229
             V + EGK  +IKK+F     K  V  L RI+ GP +L   L
Sbjct: 178 ACVRITEGKFHQIKKMFLALPKKKEVLFLKRIALGPLRLDEAL 220


>gi|187925109|ref|YP_001896751.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716303|gb|ACD17527.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 236

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 50/159 (31%), Positives = 76/159 (47%), Gaps = 7/159 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G+    A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVSIGGVACTDADADFPTGDTAFFFSVDGVDWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             +   P  +  +VY       +D  +L+ L+ G+++ G
Sbjct: 121 VHLFTSPKRKVPKVYIATTRHPLDDAQLSALRDGVLLHG 159


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 68/233 (29%), Positives = 111/233 (47%), Gaps = 18/233 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG   R  + +
Sbjct: 2   RLDKFLTHCGFGSRTQVKKLIREGIVTVNGKQIVEVDFKINPEEDVVEVDG---RVVKFS 58

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
           R W+Y   +KP G V ++ DP    TVF  +        + +VGRLD + EGLL++T++G
Sbjct: 59  R-WIYIMMNKPKGYVCSNEDP-MSLTVFSLISDDLKHRDLHTVGRLDKDAEGLLIITDNG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SN 186
                +  P  +  + Y VR   +VD+++L   + GI++      D   TL  +     +
Sbjct: 117 EYTHRVISPKKRIEKEYLVRLEKEVDEERLKEFENGIILD-----DGYKTLPAKYTIIDS 171

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             V + + EGK  ++K++FE    KV  L R   G   L   L      V K+
Sbjct: 172 TTVKLCIYEGKYHQVKRMFEAIGNKVVDLKRRRIGGLNLDESLKPGEYRVMKE 224


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 84/176 (47%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+   +P   + V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   LFNKPFDVLPQFTDEQGRDTLKKYIP--ITDVYAAGRLDRDSEGLLILTNDGKLQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVTLDT 181
           P     +VY  +  G  D   L   ++G+ ++       GI         +       + 
Sbjct: 61  PQKNTNKVYYAQVEGIPDDAALVKFRQGLTLKDGPTRPAGIERVNEPDWLWPRTPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR   G + L  L  G  +E++
Sbjct: 121 KNIPTSWLKITLSEGRNRQVRRMTAHIGYPTLRLIRYQIGEYTLNNLAPGEWKEIT 176


>gi|332362872|gb|EGJ40665.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 241

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 125/238 (52%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+T+ + + S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTPQDKIAF-QEGIRFLDGTVCQPAQLTIFSSRSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           +V + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++    +E+LG
Sbjct: 178 SVRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALN----QEELG 231


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 51/185 (27%), Positives = 90/185 (48%), Gaps = 26/185 (14%)

Query: 75  LWLYHKPIGLVTTHSDPDG------RSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           L L++KP G++   +D  G      R+T+ D   +P+I+      GRLD ++EGLLLLT+
Sbjct: 4   LILFNKPFGVLCQFTDEKGGTNGNPRATLADWLTIPAIYP----AGRLDYDSEGLLLLTD 59

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT----- 181
           +G L   +  P  +  + Y V+  G++++  L  L++G+ ++        V   T     
Sbjct: 60  NGQLQHRIASPRLKMPKTYWVQVEGEINESALTKLREGVELKDGKTRPADVATMTPPEIW 119

Query: 182 ---------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                    +    +WV + + EGKNR+++++     +   RLIR   G + L  L  G 
Sbjct: 120 PRNPPVRYRESIPTSWVRITITEGKNRQVRRMTAAVGFPTLRLIRYGIGDWTLDGLTPGE 179

Query: 233 TREVS 237
            R +S
Sbjct: 180 YRAIS 184


>gi|154687141|ref|YP_001422302.1| YtzF [Bacillus amyloliquefaciens FZB42]
 gi|154352992|gb|ABS75071.1| YtzF [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 62/215 (28%), Positives = 103/215 (47%), Gaps = 6/215 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A +G  SR++V++++    V ++G   +    +V      I V G P    E  
Sbjct: 2   RLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKTHVDPEKQDITVYGEPADYREFI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG LA
Sbjct: 62  YVMM-NKPQGVLSATED-SRQQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y VR    +  + +  L++G+VI+ G       V + T+      + 
Sbjct: 120 HRLLSPKKHVPKTYEVRLTSPLSPEDIVHLERGVVIEGGYKTKPAAVEIITESPDETVIH 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + + EGK  ++K + +    +V  L R+S G   L
Sbjct: 180 LTITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSL 214


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 54/200 (27%), Positives = 100/200 (50%), Gaps = 7/200 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A AGI SRR+ +  IA   V VNG ++      V   D +  DG  +   E+  
Sbjct: 56  RLNKYVANAGICSRRDADVHIATGLVTVNGKVVTEMGYKVKLEDEVRYDGARIN-PEKKA 114

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G  TT S+  G+ TV D +  +  SR+  +GRL  N+ GLLL TND  +   
Sbjct: 115 YVLLNKPKGFATTTSEYKGK-TVMDLVANATSSRIKPIGRLGRNSTGLLLFTNDDKVVDR 173

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTVG 192
               +   +R++ +     +  + L  +++G+ I+G      ++  +D +K     + + 
Sbjct: 174 FTNSNKGVVRLFHLELDKNLKLEDLKKIREGLRIEGKQINVEEIDYVDNRKNE---IGIK 230

Query: 193 LREGKNREIKKVFEFFNWKV 212
           ++   N  +  +F++F +++
Sbjct: 231 IKNTGNTILHTIFDYFKYEL 250


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 9/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E  
Sbjct: 2   RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLV-YESF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G + +   +   +GI ++   C    ++V     +   + V
Sbjct: 120 HDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++K++      +V  L R+S GP +L   LA G  R ++ + L + L P+
Sbjct: 180 KITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEEL-QSLAPY 238


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 9/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E  
Sbjct: 3   RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLV-YESF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  VYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G + +   +   +GI ++   C    ++V     +   + V
Sbjct: 121 HDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++K++      +V  L R+S GP +L   LA G  R ++ + L + L P+
Sbjct: 181 KITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEEL-QSLAPY 239


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 86/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           +  P  +  + Y V+  G+    +L  L+ G+V+        QV +LD            
Sbjct: 61  VTDPRHKQPKTYWVQVEGEPQAGQLQALRDGVVLNDGPTRTAQVRSLDPAPPLWPREPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 121 RVRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 176


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 52/176 (29%), Positives = 86/176 (48%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 14  LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 70

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           +  P  +  + Y V+  G+    +L  L+ G+V+        QV +LD            
Sbjct: 71  VTDPRHKQPKTYWVQVEGEPQAGQLQALRDGVVLNDGPTRTAQVRSLDPAPPLWPREPPV 130

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 131 RVRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 186


>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 = 72.8 bits (177), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 49/176 (27%), Positives = 86/176 (48%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQV------------TLDT 181
           P  +  ++Y V+  G   +D L  L+ G+ +     +  G   V              + 
Sbjct: 61  PGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE +
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREAT 176


>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 = 72.8 bits (177), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 116/227 (51%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K+I  +G+ +R+ ++R   +  ++VNG +++  ++ V    D +      +   E  
Sbjct: 2   RLDKMIGNSGLDTRKNIKRNAKKGAIRVNGQVVKDTSIQVDPDLDEVYYMDQFVDYFENI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISV-GRLDINTEGLLLLTNDGGLA 131
            + + +KP G ++   D D   TV D L   +  + +S+ GRLD +T GL+LL+ DG   
Sbjct: 62  YIMM-NKPAGFLSATEDKD--PTVIDILDDFYKGLDLSIAGRLDKDTTGLILLSTDGKFI 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P++   + Y+V    ++  D + + ++G+ I+   Y      L+  +   A V V
Sbjct: 119 HKVTSPNSNIEKTYQVETRDEIKNDLIKIFEEGVYIKEDDYTARPAKLEILEEKKALVRV 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
              EGK   +K++F   + +V +L R++ G  +L + LA G  RE+S
Sbjct: 179 --TEGKFHLVKRLFANCDNEVLKLKRLAIGKLKLDSHLAEGEYRELS 223


>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 = 72.8 bits (177), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 48/172 (27%), Positives = 89/172 (51%), Gaps = 16/172 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  +++  SD +GR T+ D L +   R  + GRLD ++EGLLLLT++G L + +  
Sbjct: 15  LFNKPFRVLSQFSDTEGRRTLADFLSAPEFR--AAGRLDYDSEGLLLLTDNGQLQQQIAN 72

Query: 137 PSTQWLRVYRVRFHGQVD-------------QDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           P  +  + Y V+  G++D             +D L L  +   I+          +  +K
Sbjct: 73  PRHKQWKTYLVQVEGELDDLSIAALCAPLKLKDGLTLPARARRIEPPALWPRHPPVRERK 132

Query: 184 G-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              ++W+ + +REG+NR+++++     +   RL+R + G + LG +  G  R
Sbjct: 133 SVPDSWLELSIREGRNRQVRRMTAAVGFPTLRLVRQAVGDWSLGDIAPGEYR 184


>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 = 72.8 bits (177), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 47/172 (27%), Positives = 82/172 (47%), Gaps = 16/172 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +      V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 62  LFNKPFDVLCQFTDEQGRKTLKDFI--AVKDVYAAGRLDRDSEGLLLLTNDGKLQSKITE 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P+ +  + Y V+  G  DQ  L  L+ G+ ++       ++T  ++              
Sbjct: 120 PNKRTFKTYWVQVEGTPDQADLQALRDGVKLKDGMTLPAKITSISEPKVWDREPPIRERK 179

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                W+ + + EG+NR+++++     +   RLIR   G + L  +  G  R
Sbjct: 180 NIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDIDIGQYR 231


>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 = 72.8 bits (177), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 9/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E  
Sbjct: 2   RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLV-YESF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 61  VYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKTVFPVGRLDKDTRGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G + +   +   +GI ++   C    ++V     +   + V
Sbjct: 120 HDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++K++      +V  L R+S GP +L   LA G  R ++ + L + L P+
Sbjct: 180 KITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEEL-QSLAPY 238


>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 = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 86/157 (54%), Gaps = 10/157 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
            R+ K++A  GI +R+EV+ +I +  VKVNG+++++    V   DH E+D +    +   
Sbjct: 3   MRLDKLLANYGIGTRKEVKSLIRKGFVKVNGMIIKKDDFKV---DH-EIDEIVFDDELIE 58

Query: 73  TRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
            R ++Y   +KP G ++   D +   TV + +    +  +  VGRLD++TEGLLL+TNDG
Sbjct: 59  YRPYVYIMLNKPAGYISATKD-NLHPTVLELIEGYENYDLFPVGRLDLDTEGLLLITNDG 117

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +  L  PS    ++Y     G +D+  +   K G+
Sbjct: 118 DFSHKLLAPSRNHSKIYFANIAGVMDEQDIQAFKDGL 154


>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 = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 117/240 (48%), Gaps = 9/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E  
Sbjct: 3   RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLV-YESF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  VYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKTVFPVGRLDKDTRGLLLLTNNGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G + +   +   +GI ++   C    ++V     +   + V
Sbjct: 121 HDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++K++      +V  L R+S GP +L   LA G  R ++ + L + L P+
Sbjct: 181 KITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEEL-QSLAPY 239


>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 = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 60/219 (27%), Positives = 98/219 (44%), Gaps = 10/219 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+  +++R G  SRRE    I +  +   G     +  + +  + I +DG P+   +   
Sbjct: 2   RLDALLSRYGYCSRREAPGWIKRHSITFKGKPCS-SPTDKVQAEGILLDGEPVEFPDGLY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
             LY KP G   +H D +G + ++D LP  +      V SVGRLD  T GLLLLT+DG  
Sbjct: 61  AALY-KPEGYTCSHDDGEG-NLIYDLLPFQWRHRNPAVSSVGRLDKETSGLLLLTDDGKF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              +  P     +VY       +  + + L   G + + G         L+ ++   A +
Sbjct: 119 IHRMTSPRHHVAKVYEAVTEEDIPTEAVELFASGTLTLNGETRPCAPALLEIREPRRALL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           T  L EGK  +++++       V  L R+S G   L +L
Sbjct: 179 T--LTEGKYHQVRRMLAAVGAPVLSLCRVSIGSLHLDSL 215


>gi|325694128|gb|EGD36046.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 241

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 120/237 (50%), Gaps = 12/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++   Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSHLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANHDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +G +  QDK+   +    + G      Q+++ +   S +  T
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTPQDKIAFHEGIRFLDGTVCQPAQLSILSTSSSLSRAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           V + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++    +E+LG
Sbjct: 179 VKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALN----QEELG 231


>gi|227327062|ref|ZP_03831086.1| putative RNA pseudouridylate synthase [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 208

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 49/179 (27%), Positives = 86/179 (48%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++LTNDG L   
Sbjct: 30  RIVLFNKPFDVLPQFTDEAGRRTLKDYIP--VSGIYAAGRLDRDSEGLMILTNDGKLQAQ 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQVTL 179
           L  P+ +  ++Y V+  G  D   L   + G              IV +          +
Sbjct: 88  LTQPTKKTAKIYYVQVEGIPDDAALTRFRTGLDLNDGKTLPAGAEIVPEPDWLWPRNPPI 147

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K   + W+ + L EG+NR+++++     +   RLIR       +  LL G  +E++
Sbjct: 148 RERKSIPDCWLKITLNEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLLPGEWKEIT 206


>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 = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 116/248 (46%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 265 RLSKRMSELGLCSRREADEWIEKGWVIVDGERIDTLGTKVRADQRIEIDERAQAAQAAQV 324

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS    R ++  GRLDI++
Sbjct: 325 TILLHKPVGYVSGQAE-DGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 383

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    ++L  L+ G+ + G
Sbjct: 384 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 443

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 444 VALKPAMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 499

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 500 QGQWRYLS 507


>gi|167586851|ref|ZP_02379239.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 298

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 110/247 (44%), Gaps = 28/247 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 51  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERASAAQAAQV 110

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 111 TILLHKPVGYVSGQAEDGYEPATVLITRENHWSGDRSALRFSPQHLHSLAPAGRLDIDST 170

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G+
Sbjct: 171 GLLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDGV 230

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 231 ALKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 286

Query: 231 GSTREVS 237
           G  R +S
Sbjct: 287 GQWRYLS 293


>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 = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 50/184 (27%), Positives = 91/184 (49%), Gaps = 25/184 (13%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           R RL  ++KP G+++  + P+GR      F +LP ++      GRLD ++EGLLLLT+ G
Sbjct: 4   RARLIRFNKPYGVLSQFT-PEGRWRGLKDFIDLPGVYV----AGRLDADSEGLLLLTDSG 58

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------------GICY 172
            L   +  P  +  + Y V+  G  D   L  L++GI +                  +C 
Sbjct: 59  PLQARISDPRHKMEKTYWVQVEGIPDDAALAALQRGITLNDGPTRPARVHRLEPPPALCP 118

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            D  + +  +   ++W+ + +REG+NR+++++         RL+R + GP+ L  L  G+
Sbjct: 119 RDPPIRV-RRNIPDSWIELVIREGRNRQVRRMTAAVGHPTLRLVRTAIGPYTLDGLAPGA 177

Query: 233 TREV 236
             ++
Sbjct: 178 WDDI 181


>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 = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 70/230 (30%), Positives = 119/230 (51%), Gaps = 17/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     SR EV+  + ++ +KVNG++L +        D +E+D   L K E+ +
Sbjct: 5   RIEKYIADLTNLSRNEVKNKLKKKAIKVNGVILTKLIKIDPEKDVVELDNGIL-KYEKFQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++++KP   +  +SD +  +T+FD   LP+   +  S GRLD +TEGLL+L+NDG +  
Sbjct: 64  YYMFNKPANFICANSDSE-EATIFDIVGLPA--EKFFSFGRLDKDTEGLLILSNDGQMCH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWV 189
            L  P     + Y V+   ++D + L L    I I      D  V+   L+     + ++
Sbjct: 121 RLLSPKNHVPKKYYVKVDKKIDSEIL-LNNSPIKIN----DDFVVSKYILELIDDKSCFL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           T+   EGK  +IK++F    + V  L R+ +G  +L   L  G  R++S+
Sbjct: 176 TI--YEGKFHQIKRMFGSLGFSVLYLKRVEFGKLKLDNNLKLGQVRKLSE 223


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 52/174 (29%), Positives = 90/174 (51%), Gaps = 20/174 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L +++KP G++T  S+ +    V+ +L    S   V   GRLD ++EGL++LT++G L  
Sbjct: 2   LIIFNKPYGVITQFSEHE----VYPSLKEFISHKNVYPAGRLDADSEGLVILTDNGALQN 57

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-----------DT 181
            L  P++   +VY V+       + L  L+KG++I        +V L             
Sbjct: 58  KLSDPTSNIEKVYVVQVENIPSSEDLAKLEKGVMISKYITKPAKVRLIEDPMLWERVPPI 117

Query: 182 QKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           +K S+   AW+ + + EGKNR+++K+     +   RLIR S G +++G L  G+
Sbjct: 118 RKRSSIPTAWLEIRITEGKNRQVRKMTAAVGFPTLRLIRTSVGNYKIGDLEPGN 171


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 116/248 (46%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 363 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQV 422

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS    R ++  GRLDI++
Sbjct: 423 TILLHKPVGYVSGQAE-DGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 481

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    ++L  L+ G+ + G
Sbjct: 482 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 541

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 542 VALKPAMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 597

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 598 QGQWRYLS 605


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+V   S  +   T+ D +      V + GRLD ++EGLL+LT+DG L   +
Sbjct: 2   LILFNKPFGVVCQFSAHENHPTLKDYI--AMPDVYAAGRLDTDSEGLLILTDDGRLQHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
             P  + +++Y  +  G  D + L+ L++G+ +        QV +  +  +         
Sbjct: 60  AHPKHKEIKIYWAQVEGAPDDEALSPLRRGVDLGDFVTQPAQVKIIAEPANLWARVPPIR 119

Query: 186 ------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                   W+ + + EGKNR+++++     +   RLIR + G   L  L  G  +
Sbjct: 120 ERKAIPTTWLEIRISEGKNRQVRRMTAKIGFPTLRLIRYAIGAHTLAGLQPGEFK 174


>gi|320195863|gb|EFW70488.1| Ribosomal large subunit pseudouridine synthase E [Escherichia coli
           WV_060327]
          Length = 177

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 83/176 (47%), Gaps = 17/176 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  ++Y V+  G   QD L  L+ G+ +           L  +              
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPPIRER 120

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ +
Sbjct: 121 KSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDAT 176


>gi|319762719|ref|YP_004126656.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117280|gb|ADU99768.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 188

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/184 (27%), Positives = 91/184 (49%), Gaps = 25/184 (13%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           R RL  ++KP G+++  + P+GR      F +LP ++      GRLD ++EGLLLLT+ G
Sbjct: 4   RARLIRFNKPYGVLSQFT-PEGRWRGLKDFIDLPGVYV----AGRLDADSEGLLLLTDSG 58

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------------GICY 172
            L   +  P  +  + Y V+  G  D   L  L++GI +                  +C 
Sbjct: 59  PLQARISDPRHKMEKTYWVQVEGIPDDAALAALQRGITLNDGPTRPARVHRLEPPPALCP 118

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            D  + +  +   ++W+ + +REG+NR+++++         RL+R + GP+ L  L  G+
Sbjct: 119 RDPPIRV-RRNIPDSWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYTLDGLAPGA 177

Query: 233 TREV 236
             ++
Sbjct: 178 WDDI 181


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 62/227 (27%), Positives = 106/227 (46%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+RRE  R+I    V VN ++ +  +V V     +E  G  L+K     
Sbjct: 2   RLDKYLCDALGATRREATRIIKSGDVTVNDVVQKSGSVKVTDGCTVEWQGRELQKPGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+ KP G V +H D   + T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLF-KPDGFVCSHEDGFNQ-TAFMLLDEVKIEELHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADPIQADYVEKFAEGIQLRNEKGLTLPAQLEIVDEEENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGDIELCESLEPGEYRYLTEE 226


>gi|209517428|ref|ZP_03266269.1| pseudouridine synthase [Burkholderia sp. H160]
 gi|209502082|gb|EEA02097.1| pseudouridine synthase [Burkholderia sp. H160]
          Length = 236

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 94/220 (42%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +           VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIGDARVSIDGAICTDADADFAVESGALRFSVDGVEWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP+G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPVGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  ++Y       +D  +L  L+ G+++ G         LD Q      + 
Sbjct: 121 VHQFTSPKRKVPKLYVATTRHPLDDAQLTALRHGVLLHG--ETRPSAALDAQARDTHTLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++      +   L R   G   L   LA
Sbjct: 179 LTVLEGKYHQVKRMIAASGNRCEALHRERIGGLALPATLA 218


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 68/218 (31%), Positives = 104/218 (47%), Gaps = 25/218 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I ++    + +  ++I    V VNG+++   AV V   + I ++G  L  A   R
Sbjct: 2   RLDRFICKSTELVKYDAIQLIHNGEVFVNGVVVRNEAVQVHENNDISLNGQKL-AARAFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---------GRLDINTEGLLLLT 125
             L +KP    T  S+ DG        PS+FS +I V         GRLD NT GL+L+T
Sbjct: 61  YMLINKPAN--TLCSNVDGV------YPSLFS-LIDVERPSELHIAGRLDANTTGLVLIT 111

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           +DG     +  PS Q  +VYRV+    +  D      +GI +Q    G+ ++TL  Q   
Sbjct: 112 DDGRWTFAITSPSGQCHKVYRVKLAKPIAADAGESFLQGIALQ----GEQELTLPAQLQI 167

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            +   V + L EGK  ++K++F     KV  L R S G
Sbjct: 168 ITPQEVLLTLTEGKFHQVKRMFAAVGNKVVSLHRESIG 205


>gi|227111561|ref|ZP_03825217.1| putative RNA pseudouridylate synthase [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 208

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/178 (27%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++LTNDG L   
Sbjct: 30  RIVLFNKPFDVLPQFTDEAGRRTLKDYIP--ISGIYAAGRLDRDSEGLMILTNDGKLQAR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQVTL 179
           L  P+ +  ++Y V+  G  D   L   + G              IV +          +
Sbjct: 88  LTQPTQKTAKIYYVQVEGIPDAAALTRFRTGLDLNDGKTLPAGAEIVPEPSWLWPRNPPI 147

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +K   + W+ + L EG+NR+++++     +   RLIR       +  LL G  +E+
Sbjct: 148 RERKSIPDCWLKITLHEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLLPGEWKEI 205


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 89/182 (48%), Gaps = 23/182 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           TRL  +HKP G+++  + P+G+     +   +P ++      GRLD ++EGLLLLTNDG 
Sbjct: 41  TRLLCFHKPYGVLSQFT-PEGKWQGLKDWIDVPGVYV----AGRLDADSEGLLLLTNDGQ 95

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---------------QGICYGD 174
           L   +  P  +  + Y V+  G  D+  L  L++G+ +               Q + +  
Sbjct: 96  LQARIADPRHKMEKTYWVQVEGIPDEAALQRLREGVELSDGKTLPAKARLIEPQPLMWPR 155

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  Q   + W+ + +REG+NR+++++         RL+R++ GP+ +  L  G   
Sbjct: 156 NPPIRVRQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRMAVGPYSIEGLEPGQWL 215

Query: 235 EV 236
           +V
Sbjct: 216 DV 217


>gi|152999616|ref|YP_001365297.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151364234|gb|ABS07234.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 256

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 106/215 (49%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV+V+G++++     V    HI++D   L+      + L HKPIG+V+ 
Sbjct: 41  RKAVRELLLSGRVRVDGLIVKDMDRQVDEFSHIQLDEHILQANAPVYVML-HKPIGVVSA 99

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D   + TV D L       + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 100 TKDIQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDALMSPTHKVDKVYR 158

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     + ++ +    +G+      +G   +T    K    ++    V L EGK  +IK+
Sbjct: 159 VTLANPITEEYIAAFAEGMY-----FGFEDITTQPAKLVILADNVAEVTLHEGKYHQIKR 213

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +F  F   V  L R+S G   L   LA G +R ++
Sbjct: 214 MFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALT 248


>gi|224824759|ref|ZP_03697866.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224603252|gb|EEG09428.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 225

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/183 (27%), Positives = 91/183 (49%), Gaps = 23/183 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP G++   S  +   T+ D  ++P ++      GRLD ++EGLLLLT DG L 
Sbjct: 3   QLILFNKPYGVICQFSQHELHPTLKDHIDIPGVYP----AGRLDTDSEGLLLLTGDGELQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  +  + Y V+  G   +++L  L+ G+ +        +V L ++         
Sbjct: 59  HRISDPRWKQSKTYWVQVEGTPVEEQLEALRAGVNLGDFITQPAEVRLLSEPPQLWERKP 118

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-- 234
                    +AW+ + + EGKNR+++++         RL+R++ GP++L  L  G  R  
Sbjct: 119 PVRFRKTVPDAWLEIIISEGKNRQVRRMTAKVGLPTLRLVRVAVGPWRLDGLQPGEFRRL 178

Query: 235 EVS 237
           EVS
Sbjct: 179 EVS 181


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 55/182 (30%), Positives = 82/182 (45%), Gaps = 19/182 (10%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L HKP G ++  +          +L      V  VGRLD ++EGLLLL+ND  L   L  
Sbjct: 6   LLHKPFGYLSQFTPETPGQLTLADLGPFPPEVYPVGRLDQDSEGLLLLSNDSRLNVQLLD 65

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQV---TLDTQKG------- 184
           P     R Y V+  G  D+  L  L+ G+ I+     Y  +      LD Q         
Sbjct: 66  PRHAHWRTYWVQVEGIPDEAALAHLRSGVEIRFNKKTYHTLPARAQLLDPQPTVAERNPP 125

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + L+EGKNR+++++     + V RLIR++    QLG L  G+ R  +
Sbjct: 126 IRYRANIPETWLELSLQEGKNRQVRRMCAKVGYPVLRLIRVNIENLQLGDLAVGAWRACT 185

Query: 238 KK 239
           +K
Sbjct: 186 QK 187


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 115/233 (49%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +R A+   V   D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRVALGDRVFPGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +       +KP+G+V+T  D +  + V  +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DNLIFIALNKPVGVVSTTEDGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + ++ L  G+ +     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTDEFIHGLGAGVPM----LGTVTKKCKVKKVAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 IVLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVGLAGLPLGEWRDLTDDELVE 231


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 57/193 (29%), Positives = 95/193 (49%), Gaps = 24/193 (12%)

Query: 70  AERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           A R    L+HKP G+++  + +P  R     +  ++   V + GRLD ++EGLLLLT +G
Sbjct: 10  ASRPTTLLFHKPYGVLSQFTPEPGSRWRCLADFIAVPG-VYAAGRLDADSEGLLLLTANG 68

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQG--------ICYGDMQVT 178
            L + L  P+    R Y V+  G+  Q  + L  L++G+VIQG         C  D ++ 
Sbjct: 69  RLQQRLTDPAFGHWRTYWVQVEGEAGQRPEALQQLRQGVVIQGRLTRPALVRCLSDPKLP 128

Query: 179 LDT----QKGS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLG 226
                  Q+ +   +W+ + L+EG+NR+++++         RLIR++        P  L 
Sbjct: 129 ERDPPIRQRATIPVSWLELQLQEGRNRQVRRMTARVGLPTLRLIRVAIDLMDGEAPLSLS 188

Query: 227 TLLAGSTREVSKK 239
            L  G  R VS +
Sbjct: 189 GLKPGDWRRVSHR 201


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 105/231 (45%), Gaps = 22/231 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDG-----VPLR 68
           + K +   GI +R+  + ++    V++NG  +  E+A +   S   + +DG     +PL 
Sbjct: 3   IIKYLQAQGIDTRKGCQWLVKHGLVQINGATVPDEKADIAPDSVQTLTIDGEDAVVIPLP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTN 126
                   L +KP G  T+H  P    +VF  LP     + + +VGRLD +T G+LL+TN
Sbjct: 63  YF----YILLNKPAGYETSHK-PRDYPSVFSLLPDQVRAADIQAVGRLDADTTGVLLITN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           DG     +  P  +  ++YR       D      L+ G+++      D   T+  Q    
Sbjct: 118 DGQFNHRMTSPKHKVDKIYRATLKHAADPSLCAQLQAGVLLH-----DDNETVSAQAAEL 172

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + + +REGK  ++K++      +V  L R+ +GP+    L AG  R
Sbjct: 173 HDAHTLILTIREGKYHQVKRMVAAAGNRVEHLHRLQFGPWDTQDLQAGEWR 223


>gi|167563192|ref|ZP_02356108.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           EO147]
          Length = 321

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 115/246 (46%), Gaps = 32/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 74  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 132

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS      +   GRLDI+
Sbjct: 133 VTILLHKPVGYVSGQAE-DGYAPAVTLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 191

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRF---HGQVDQ----DKLNLLKKGIVIQ 168
           + GLL+LT +G +A+ L    +   + Y  RVRF      +DQ    + L  L+ G+ + 
Sbjct: 192 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERMADIDQHFPAESLAKLRHGLELD 251

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G       V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L
Sbjct: 252 GAPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGAL 307

Query: 229 LAGSTR 234
             G  R
Sbjct: 308 PQGEWR 313


>gi|239994883|ref|ZP_04715407.1| ribosomal large subunit pseudouridine synthase E [Alteromonas
           macleodii ATCC 27126]
          Length = 180

 Score = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 47/172 (27%), Positives = 88/172 (51%), Gaps = 20/172 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  +++  +D DGR T+ D  ++P +++     GRLD ++EGLL+LTNDG L   L
Sbjct: 9   LFNKPFQVLSQFTDADGRETLKDYIDVPGVYA----AGRLDRDSEGLLVLTNDGKLQHKL 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------------ 181
             P  +  + Y V+  G +D+  +  L+ G+ ++ G+        ++             
Sbjct: 65  ANPKAKTSKTYWVQVEGIMDEKAMQALRDGVELKDGMTRPAKVKAMEAPSVWPRNPPVRF 124

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            Q    +WV + + EG+NR+++++     +   RLIR   G + +  +  GS
Sbjct: 125 RQSIPTSWVEITITEGRNRQVRRMTANVGYPTLRLIRYRVGNWTIDGIDNGS 176


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 110/233 (47%), Gaps = 20/233 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV   ++  G  +R E +R +    V V    +      V  ++ I V+G  L  AER 
Sbjct: 6   KRVDAHLSSLGYCTRSEAKRFLTTNNVSVYNERIFDVTKKVHHSE-IRVNG-ELLDAERL 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            + L +KP G+V +HSD      ++  LP  + R    V ++GRLDI+T G +LL++DG 
Sbjct: 64  -VILMNKPHGVVCSHSDSG--VLIYSLLPPRWQRRNPKVSTIGRLDIDTTGAILLSDDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQG----ICYGDMQVTLDTQKG 184
           L   L  P ++  ++Y V     +  D+  +   G +++ G    +    M+V       
Sbjct: 121 LNHKLTSPKSEVTKIYEVTLAQALRGDEAEIFASGELLLNGEKKPLLPAKMEVI------ 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               V V + EG+  ++K++F     +V  L R S+G F +  L     RE+S
Sbjct: 175 GPIHVRVEICEGRYHQVKRMFASVGNRVTALHRASFGDFSVEDLKPSEFREIS 227


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/192 (26%), Positives = 92/192 (47%), Gaps = 4/192 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR    R +   +V V+G ++ + A  +   + +E DG PL      R
Sbjct: 2   RLDKFLSQQLEISRAIALRELRAHKVTVDGEVVRQGAFKLKPENQVEYDGNPLHLQFGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  DPD  + + F   P+ + ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLEEPTAY-KLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +    Y     TL+    S   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPLADDTAAQFTAGVQLHNEKYLTKPATLEVV--SECQVRLTI 178

Query: 194 REGKNREIKKVF 205
            EG+  ++K++F
Sbjct: 179 SEGRYHQVKRMF 190


>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 = 72.4 bits (176), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/216 (25%), Positives = 98/216 (45%), Gaps = 2/216 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ A+  +     +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGSRVTVDGDIVKDASFKLQPEHEVEYDGNTLTQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + +    L  KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVALESPLAEGTAELFAKGVQLHN--EKDLTKPALLEVITPTEVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           EG+  ++K++F      V  L R   G   L   LA
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGDILLDESLA 215


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 116/248 (46%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 365 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQV 424

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS    R ++  GRLDI++
Sbjct: 425 TILLHKPVGYVSGQAE-DGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 483

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    ++L  L+ G+ + G
Sbjct: 484 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 543

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 544 VALKPAMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 599

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 600 QGQWRYLS 607


>gi|167570375|ref|ZP_02363249.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           C6786]
          Length = 414

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 117/246 (47%), Gaps = 32/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 167 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 225

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 226 VTILLHKPVGYVSGQAE-DGYAPAVTLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 284

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFH---GQVDQ----DKLNLLKKGIVIQ 168
           + GLL+LT +G +A+ L    +   + Y  RVRF      +DQ    + L  L+ G+ + 
Sbjct: 285 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERMADIDQHFPAESLAKLRHGLELD 344

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G       V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L
Sbjct: 345 GAPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGAL 400

Query: 229 LAGSTR 234
             G  R
Sbjct: 401 PQGEWR 406


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 111/248 (44%), Gaps = 27/248 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++   + +R E++R I +  V+VNG  +      V   D I   G P+    R  
Sbjct: 19  RLDKFLSDMNMGTRTELKRDIRKGAVQVNGEKITDPGFMVNENDEIIFAGEPVPYF-RYE 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G++T   D   + TV D       + +S VGRLD +T GLLL+TNDGG    
Sbjct: 78  YYMLNKPAGVITATEDR-YQKTVLDFFGERRRKDLSPVGRLDKDTVGLLLVTNDGGFHHR 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----------YGDMQVTLDTQ 182
           L  P     + Y  R  G+VD+      +KGI +  I            Y +  +  D  
Sbjct: 137 LLSPKKHIDKEYYARIDGRVDEADREKFEKGIYVDEIFTALPAKLMIDGYRENALESDFM 196

Query: 183 KGSN------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
             +N            + + V ++EGK  +IK++F     +V  L RI  G   L  TL 
Sbjct: 197 DLANSRAPKSALENGVSEIRVVVQEGKFHQIKRMFHALGKEVIYLKRIRIGSVVLDPTLE 256

Query: 230 AGSTREVS 237
            G+ R ++
Sbjct: 257 EGTYRRLT 264


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/164 (31%), Positives = 79/164 (48%), Gaps = 21/164 (12%)

Query: 77  LYHKPIGLVTTHSD--PDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L HKP  ++   +D  P G  R T+ D +P     + SVGRLD+++EGLLLLTND  L  
Sbjct: 7   LLHKPYNVLCQFTDNSPQGSQRQTLKDFVP--VPDIYSVGRLDLDSEGLLLLTNDAPLKH 64

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------- 185
            L  P     R Y V+     D   L  L++G+++QG         L T + +       
Sbjct: 65  YLCEPKFAHSRTYWVQVENIPDGQALEQLRQGVMVQGKKTRPAIANLLTPEPTVPAREPP 124

Query: 186 --------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                    AW+ + L EG+NR+++++         RL+R++ G
Sbjct: 125 IRFRKNVPTAWLELTLTEGRNRQVRRMTAAVGHPTLRLMRVAIG 168


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 105/232 (45%), Gaps = 16/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--------ILLERAAVNVMSTDHIEVDGVP 66
           R++K +A  G+ SRR   R I    + + G        + L  +   ++  + +  DG+ 
Sbjct: 24  RLAKYLALTGLCSRRAATRYIRDGLIMIEGRQANHIDTVTLIESPDGLICKELLLFDGMA 83

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +   E  +  + +K +G       PD   ++   LP+   R+  VGRLD ++ GLLLLTN
Sbjct: 84  VEGIEPKQYRMLNKCVG-TDCRLLPDDSDSLLHLLPA-SPRLYPVGRLDKDSRGLLLLTN 141

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGS 185
           DG L + L  P     + YRVR       + L  +      QG+ Y D+     T  + S
Sbjct: 142 DGELTQHLMHPDFGHTKTYRVRVDRPYGDEFLQKMA-----QGVSYRDVTTLPCTMTRLS 196

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                + L +G NR+I+++ +   +KV  L R+      L  L  G  RE++
Sbjct: 197 EDQFEIVLTQGLNRQIRRMSQALGFKVIDLKRVKIQTLMLEDLNEGEMRELT 248


>gi|196233257|ref|ZP_03132103.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222728|gb|EDY17252.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 188

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/177 (30%), Positives = 85/177 (48%), Gaps = 22/177 (12%)

Query: 78  YHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +HKP G+++  + PDG   R     + P     V  +GRLD  +EGLLLL+++  L   L
Sbjct: 5   FHKPYGVLSQFT-PDGSRHRPLAEFDFPK---GVYPLGRLDAESEGLLLLSDEAALNARL 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG--------- 184
             P+    R Y  +      ++ L  L++G+VI G      +V  LD Q           
Sbjct: 61  LHPTRGHYRTYWAQVERVPTREALTQLERGVVIGGRQTLPCRVWLLDPQPAVSPRVPPIR 120

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                   W+ + L EGKN +++++         RL+R+  G F+LG+L AGS RE+
Sbjct: 121 FRKNVPETWIALELVEGKNHQVRRMTAAVGHPTLRLVRVKIGKFELGSLAAGSWREL 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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 93/183 (50%), Gaps = 23/183 (12%)

Query: 73  TRLWLYHKPIGLVTTHSD---PDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            R+ L++KP G+++  +D   P  R T+  + ++P+++      GRLD ++EGLL+LT+D
Sbjct: 2   ARVILFNKPFGVLSQFTDTRSPTERPTLSRYVDVPAVYP----AGRLDRDSEGLLVLTDD 57

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYGD 174
           G L   +  P  +  +VY  +  G  D D L  L++G+             +I+     +
Sbjct: 58  GRLQARIASPKARTEKVYLAQVEGDPDDDALAPLRRGLELKDGPTRPAVARLIEPPALWE 117

Query: 175 MQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
               +  +K   + WV V + EG+NR+++++     + V RL+R   G + L  L  G+ 
Sbjct: 118 RDPPVRFRKSVPDRWVEVTITEGRNRQVRRMCAAIGFPVLRLVRWRVGDWTLEGLAPGAW 177

Query: 234 REV 236
           R+ 
Sbjct: 178 RDA 180


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 84/174 (48%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 10  IFNKPFDTLSQFTDGDGRKTLADFIP--VKEVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 67

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L+ L+ G+ ++        V +  +              
Sbjct: 68  PQSKSPKTYWVQVEGAPQEADLDKLRNGVELKDGPTLPAIVEIMPEPEVWERHPPVRFRA 127

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RLIR S G   LG L  G  + +
Sbjct: 128 AIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIVLGDLQPGEWKHI 181


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 103/225 (45%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++ A+  +     +E DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRGSRVTVDGDIVKDASFKLQPEHEVEYDGNTLTQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + +    L  KG+ +      D+      +  +   V + + 
Sbjct: 122 TSPRHHCEKTYLVALENPLAEGTAELFAKGVQLHN--EKDLTKPALLEVITPTEVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
           EG+  ++K++F      V  L R   G   L   LA G  R +++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGDILLDESLAPGEYRPLTE 224


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/213 (27%), Positives = 96/213 (45%), Gaps = 5/213 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +     A+R E  R++    V VNG+  +  +V V     +E DG  L K    R
Sbjct: 2   RLDKFLCETTGATRSEATRIVKSGTVTVNGVKTKVTSVKVTDDSTVEWDGREL-KFHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  KP G V +H D    S  T+ D +     ++   GRLD++T GL+L+T+DG  + 
Sbjct: 61  YIMLFKPDGYVCSHEDSTHPSALTLLDEVN--LEKLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +       L +GI ++      M  T++        + + 
Sbjct: 119 KITSPKRKCPKTYRVWLDEPIGAYYAEQLTEGIQLKSETGLIMPATMEVVNEEEHELLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++EGK  ++K++F     KV  L R   G   L
Sbjct: 179 IQEGKYHQVKRMFAALGNKVEGLHRSQIGGLGL 211


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 63/233 (27%), Positives = 104/233 (44%), Gaps = 17/233 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A +G+ SRRE +  IA   V VNG ++      V   D ++ DG  L   +R  
Sbjct: 44  RLNKYVANSGVCSRREADVFIAAGSVTVNGKVVSEMGYKVKLDDVVKFDGRHLNPEKREY 103

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP    TT  +  G+  V   + S   + ++ V ++   + GLLL TND  L R 
Sbjct: 104 VLL-NKPKDFSTTVRNEHGKRNVAGLISSASKATLLPVDKMAKASTGLLLFTNDKELTRR 162

Query: 134 LELPSTQWLRVYRVRFHGQVD-------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           L  P     ++Y V     +        QD L + +K + +  I Y D            
Sbjct: 163 LLNPKNGLRKIYHVELSKALSPADLKKIQDGLAIDEKVVNVHDISYVD--------NAPK 214

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             V + L   ++  + K+FE   ++V +L R+ YG      L  G  R ++K+
Sbjct: 215 NQVGIELFSSRSNIVTKIFEHLGYEVAKLDRVVYGGLTKKDLPRGHWRYLTKQ 267


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 118/248 (47%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 2   RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQV 61

Query: 75  LWLYHKPIGLVTTHSDPDGR--STVF---------DNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG   ++V          D  P  FS    R ++  GRLDI++
Sbjct: 62  TILLHKPVGYVSGQAE-DGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L  E        + RVRF  +   +DQ    ++L  L+ G+ + G
Sbjct: 121 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 180

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 181 VALKPAMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 236

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 237 QGQWRYLS 244


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 49/179 (27%), Positives = 86/179 (48%), Gaps = 17/179 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++LTNDG L   
Sbjct: 40  RIVLFNKPFDVLPQFTDEAGRRTLKDYIP--VSGIYAAGRLDRDSEGLMILTNDGKLQAR 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQVTL 179
           L  P+ +  ++Y V+  G  D   L   + G              IV +          +
Sbjct: 98  LTQPTQKTAKIYYVQVEGIPDDAALTRFRTGLDLNDGKTLPAGAEIVPEPSWLWPRNPPI 157

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K   + W+ + L EG+NR+++++     +   RLIR       +  LL G  +E++
Sbjct: 158 RERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLLPGEWKEIA 216


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 52/161 (32%), Positives = 80/161 (49%), Gaps = 10/161 (6%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L + +KP G V T SD  GR TV+D LP  +     + +GRLD+ ++GLLL T DG + 
Sbjct: 6   KLLVLNKPKGYVVTRSDELGRKTVYDLLPDWAFHDGWMPIGRLDLESKGLLLFTTDGKIG 65

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P    ++VY +   G V  + +   K+G+  +      + V      G+   + +
Sbjct: 66  DALTRPGNC-IKVYEIWVRGHVTDEHIAEAKRGVESKHGLLKALVVEKLGTGGAKTKLKI 124

Query: 192 GLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQL 225
            + EGKNR I+++F            KV  L RIS G F+L
Sbjct: 125 VIDEGKNRHIRRLFGALKDPKFGTPLKVLELKRISIGSFEL 165


>gi|217974432|ref|YP_002359183.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499567|gb|ACK47760.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 235

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 105/215 (48%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV V+G++++     V    HI++D   L+      + L HKPIG+V+ 
Sbjct: 20  RKAVRELLLSGRVCVDGLIVKDMDRQVDEFSHIQLDEQILQANAPVYVML-HKPIGVVSA 78

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D   + TV D L       + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 79  TKDIQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDALMSPTHKVDKVYR 137

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     + ++ +    +G+      +G   +T    K    ++    V L EGK  +IK+
Sbjct: 138 VTLANPITEEYIAAFAEGMY-----FGFEDITTQPAKLVILADNVAEVTLHEGKYHQIKR 192

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +F  F   V  L R+S G   L   LA G +R ++
Sbjct: 193 MFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALT 227


>gi|56808584|ref|ZP_00366315.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 109

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 38/90 (42%), Positives = 56/90 (62%), Gaps = 1/90 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E+  
Sbjct: 2   RINKYIAHAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIEGSPIYNEEKV- 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            +L +KP G +++ SD  GR TV D LP +
Sbjct: 61  YYLLNKPRGAISSVSDDKGRKTVLDLLPQV 90


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 102/228 (44%), Gaps = 26/228 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++S+V+   G  +RRE E +I    V V G+++E  +  V        +G+      +T 
Sbjct: 2   KLSQVLFSQGFGARRECEGLICAGLVSVGGVVIEEPSHEVAP------EGLLFTVEGQT- 54

Query: 75  LWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLL 124
            W YH        KP G   +   P    ++++ LP+ F R  + +VGRLD +T GLLL 
Sbjct: 55  -WAYHAKALIVMNKPAGFECS-KKPRHHPSIYNLLPAQFKRRDMQTVGRLDEDTTGLLLF 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-------IQGICYGDMQV 177
           T+DG L      P     ++Y       VD+ ++  L  G+V       +Q +       
Sbjct: 113 TDDGNLIHRWTSPKHHVPKIYEAGCKHPVDEAQVARLLAGVVLHDDPLPVQALAAEITGA 172

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 G+   + + L EGK  ++K++    + +V  L R  +G ++L
Sbjct: 173 FEHPTHGTLHGLRLTLAEGKYHQVKRMLAAVSNRVETLHRSGFGAYRL 220


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 51/184 (27%), Positives = 86/184 (46%), Gaps = 20/184 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L +KP  ++   +D  GR T+ D +  P I++     GRLD ++EGLLLLTNDG L 
Sbjct: 58  KLLLLNKPYMVLCQFTDEAGRETLKDYITEPGIYA----AGRLDRDSEGLLLLTNDGKLQ 113

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--------------IVIQGICYGDMQV 177
             L  P  +  + Y V+  G   ++KL  L  G              I+ +   +     
Sbjct: 114 ARLTQPGEKTPKTYWVQVEGVPSEEKLAALCAGVELNDGMTLPAGARIMEEPAVWPRNPP 173

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + ++    W+ + + EG+NR+++++         RLIR + G + L  L  G +R + 
Sbjct: 174 IRERKEIPTCWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDWSLDGLAPGESRALP 233

Query: 238 KKIL 241
              L
Sbjct: 234 APEL 237


>gi|300714626|ref|YP_003739429.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299060462|emb|CAX57569.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 292

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 113/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I  +GI SRR+ +R I Q  V +NG   +RAAV   V + D ++V+G  +  R  
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGNVFING---KRAAVGDQVYAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G+++T  + +  + V  N  +   RV  +GRLD  ++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIISTTEEGERDNIV--NFVNHSKRVFPIGRLDKESQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G      +V  +    +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKLVTDEFIAGLGAGVPMLGTVTKKCKVKKE----APFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R       L  L  G  RE +   L E
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVSLKGLPIGEWREFTDDELIE 231


>gi|308805586|ref|XP_003080105.1| unnamed protein product [Ostreococcus tauri]
 gi|116058564|emb|CAL53753.1| unnamed protein product [Ostreococcus tauri]
          Length = 405

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 113/231 (48%), Gaps = 23/231 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA---- 70
           ++K +A  G+ASRR  + +I   RVKVNG  +      V ++TD + VDG  +       
Sbjct: 145 LNKALASLGVASRRGADDLIFGGRVKVNGTTITAPQTKVNLNTDVVMVDGKVVEGGVSFV 204

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRS--TVFD-----------NLPS-IFSRVISVGRLD 115
            E T  ++ +KP G V + + P   S  TV D             P  +  R+ +VGRLD
Sbjct: 205 KEHT-YFMLNKPKGFVCS-ARPGSESGKTVLDLFEQWREEFRSEYPGKLPPRLFTVGRLD 262

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           + T GLLL+T DG  ++ +  PS++ ++ Y V  + +  + ++  + KG  + G     +
Sbjct: 263 VATTGLLLVTTDGDWSQRVSHPSSEVVKQYVVTANAKPTRAQIVAMSKGTEVDGAHVVPV 322

Query: 176 QVTL-DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +V +     G    + V + +G+NRE++ + E    +V  L R   G  ++
Sbjct: 323 RVEVAGADGGPKNRIIVEVVDGRNREVRVLCESAGVEVKNLKRTRVGGLRM 373


>gi|332366092|gb|EGJ43848.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 241

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 120/237 (50%), Gaps = 12/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+ +++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLEQLLAANHI-SRKNMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +G +   K    ++GI  + G      Q+++ +   S +  T
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQKKISFQEGIRFLDGTVCQPAQLSILSTSSSLSRTT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           V + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++K    E+LG
Sbjct: 179 VRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNK----EELG 231


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 56/167 (33%), Positives = 82/167 (49%), Gaps = 8/167 (4%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + HKP G+++   D D   TV D L    +IF     VGRLDI+TEG LL+TNDG L+ 
Sbjct: 9   LMMHKPQGVISATED-DNHETVIDLLELEDAIFDP-FPVGRLDIDTEGFLLITNDGKLSH 66

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTV 191
            L  P     + Y     G V ++ +    KG+++    Y     TL   K  + + + +
Sbjct: 67  QLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDD-GYETKPGTLTILKSDDISEIEL 125

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++
Sbjct: 126 VITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELT 172


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/235 (25%), Positives = 106/235 (45%), Gaps = 6/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +     A+R+E  R+I    V V+G+  +  +V V     +E DG  L K    R
Sbjct: 2   RLDKFLCETLGATRKEATRIIKSGTVTVDGVKTKVTSVKVTDDSTVEWDGREL-KFHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +  KP G V +H D    S  ++ D +     ++   GRLD++T GL+L+T+DG  + 
Sbjct: 61  YIMLFKPDGYVCSHEDSTHPSALSLLDEVN--LEKLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D    L+ GI ++      M   ++        + + 
Sbjct: 119 KITSPKRKCAKTYRVWLADPIGADYAEKLEAGIQLKSEKDLTMPAVMEIVDEEEHELLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++ +    G
Sbjct: 179 IHEGKYHQVKRMFAALGNKVEGLHRAQIGGLGLDYSLEPGEYRYLTEEEVEAVFG 233


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 110/235 (46%), Gaps = 6/235 (2%)

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  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   D +  ST  D +    S  + + GRLDI+T GLLL+T+DG     
Sbjct: 62  YFMLNKPAGVVSATKDSN-NSTALDLIFEHRSDELQIAGRLDIDTTGLLLITDDGQWNHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P +   ++YRV     +  D    L  G+ ++G  +  +  T+  ++  +  V + +
Sbjct: 121 LTSPRSDCQKIYRVTLGIPITPDYAEKLANGVWLKGEKHPCLPATM--EQIDDETVLLSI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
            EGK  ++K++F      V  L R   G   L  +L  G  R ++   +   + P
Sbjct: 179 AEGKYHQVKRMFAALGNHVEALHRTQVGGIILDESLEPGDYRALTDAEVASIMAP 233


>gi|311278834|ref|YP_003941065.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308748029|gb|ADO47781.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 235

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 93/211 (44%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA+    SR    R I   RV V+G +++  A  +     +  DG  L +    R
Sbjct: 2   RLDKFIAQQLGVSRAIAGREIRASRVTVDGDIVKDTAFKLQPEHDVAYDGNSLVQQTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAHKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV     + +D       GI +           L+    +   +T+   
Sbjct: 122 TSPRHHCEKTYRVTLESPLAEDTAEQFAHGIQLHNEKALTKPAQLEVITATEVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F      V  L R   G   L
Sbjct: 180 EGRYHQVKRMFAAVGNHVVGLHRERIGAIAL 210


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 58/227 (25%), Positives = 106/227 (46%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  ++I    V VN ++ +  A  V     +E  G  ++K     
Sbjct: 2   RLDKYLCDALGATRKEATKIIKSGDVTVNDVMQKSGAFKVTDACVVEWQGREIQKPGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+ KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLF-KPDGFVCSHEDG-FNQTAFALLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D  + L +G+ ++      +  T++        + + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDPIGDDYADKLAQGVELRNEKEPTLPATMEVVNHDENELLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGAIELDYSLEPGEYRYLTEE 226


>gi|325690206|gb|EGD32210.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 241

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 123/239 (51%), Gaps = 11/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A   SR+++++   Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLA-ANHISRKKMKQSHLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +G +  +  +  ++GI  + G      Q+++ +   S +  +
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTPNDSSSFQEGIRFLDGTVCQPAQLSILSTSSSLSRAS 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK---ILREQL 245
           V + EGK  +IKK+F     KV  L RI +G F L   LA G  R +++K   I++E L
Sbjct: 179 VRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQKELEIIKEYL 237


>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 = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 110/245 (44%), Gaps = 25/245 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IAQ  V+VNG  +    + V   D IEVD     +  +  
Sbjct: 60  RLNKRMADLGLCSRREADDWIAQGWVRVNG-QVAVMGLQVGPQDRIEVDRAAQGRQSQQV 118

Query: 75  LWLYHKPIG---------------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G               LV   S   G ++     P+    +   GRLDI++ 
Sbjct: 119 TILLHKPMGYVSGQAEDGHTPAVALVNARSHWQGDASRMRFAPAQLKGLAPCGRLDIDSV 178

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLK--KGIVIQGICYGDMQ 176
           GLL+LT DG +AR L    +   + Y VR  +G+  QD   +    +  ++      D Q
Sbjct: 179 GLLVLTQDGRVARQLIGEDSAVDKEYLVRVQYGERTQDVRAVFPADRLALLCHGLLLDGQ 238

Query: 177 ----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                 +D Q      +   LREGK R+I+++ E    KV  L RI  G   LG L  G 
Sbjct: 239 PLKPAQVDWQNPEQ--LRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGRVLLGNLPVGQ 296

Query: 233 TREVS 237
            R ++
Sbjct: 297 WRYLA 301


>gi|241766432|ref|ZP_04764306.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241363374|gb|EER58885.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 237

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 76/249 (30%), Positives = 111/249 (44%), Gaps = 40/249 (16%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGL 84
           + SRRE +  IAQ  VKVNG +     + V +TD IEVD       E+    L HKP+G 
Sbjct: 1   MCSRREADDWIAQGWVKVNGQVAP-MGLQVHATDRIEVDKKAQGFQEQRVTILLHKPMGY 59

Query: 85  VTTHSDPDGRSTVFDNL----------------PSIFSRVISVGRLDINTEGLLLLTNDG 128
           V+  ++ DG +     +                P     +   GRLDI++ GLL+LT DG
Sbjct: 60  VSGQAE-DGHTPAVALINPRTHWREDPSRNRFSPPQLRGLAPAGRLDIDSVGLLVLTQDG 118

Query: 129 GLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
            +AR +    +   + Y VR  +G V  +   +     + + +C+G   ++LD Q    A
Sbjct: 119 RVARQIIGEDSSMDKEYLVRVQYGDVATNVQAVFPAQQLAR-LCHG---LSLDGQALKPA 174

Query: 188 ---W-----VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              W     +   L EGK R+I+++ E    +V  L RI  G   LG L  G  R     
Sbjct: 175 RVEWQNPEQLRFVLTEGKKRQIRRMCELVGLRVVGLKRIRIGRVTLGNLPVGQWR----- 229

Query: 240 ILREQLGPH 248
                LGPH
Sbjct: 230 ----YLGPH 234


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 105/228 (46%), Gaps = 21/228 (9%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-----AAVNVMSTDHIEVDGVPL 67
           P  + K++   G  +RR    ++  + VKVNG+L E      A  N+M    + V+G   
Sbjct: 4   PISLEKILFSQGFGTRRYCSDLVYAELVKVNGVLAEDPEERIATENLM----LNVEGKDW 59

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLT 125
              E+  L  ++KP     +H       +V+  LPS F    +  VGRLD +T GLLL++
Sbjct: 60  EYHEKAYL-AFNKPANYECSHKTIH-HPSVYSLLPSPFVERGLQCVGRLDYDTTGLLLIS 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQ 182
           +DG     +  P     +VYR+     + Q +++ L  G+V+      C+         +
Sbjct: 118 DDGQFIHKMTTPKKNIGKVYRITTSEPITQKQIDHLLNGVVLDDDPKPCFATA-----CK 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + S+  + + + +G+  ++K++       V +L R   G +Q+   LA
Sbjct: 173 QVSDHVLAMTIVDGRYHQVKRMMAAVGNHVTQLHRTEIGAYQMPVDLA 220


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/215 (26%), Positives = 101/215 (46%), Gaps = 17/215 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A +G+ SRRE +  IA   V VNG  +      V  +D +  DG  L   ++  
Sbjct: 48  RLNRYVANSGVCSRREADIYIAAGSVTVNGKPVIEMGYKVQLSDEVRFDGRLLNPIKKEY 107

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP    T+  D  G  T    + +   ++++ VG++D ++ GLLL TNDG L   
Sbjct: 108 VVL-NKPKDFATSTRDGAGNRTAMGLVSNASKAKLLPVGKMDKSSTGLLLFTNDGDLTAR 166

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-------IQGICYGDMQVTLDTQKGSN 186
           L  P     +++ V     +    L  +K+GI        IQ I Y  ++    TQ G  
Sbjct: 167 LNSPKNGLRKIFHVELTKPLKSTDLKRIKEGIEIEESVVRIQDISY--IENAPKTQVGVE 224

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            + T      +N  ++++FE  ++ V +L  + Y 
Sbjct: 225 IFST------RNNIVRRLFEKLDYDVVKLDLVVYA 253


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 51/182 (28%), Positives = 86/182 (47%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R A   ++ +++KP  ++   +D  GR+T+ D +      + + GRLD ++EGLL+LTND
Sbjct: 29  RPAAPRQVVIFNKPFDVLPQFTDEQGRATLKDYI--SLQGIYAAGRLDRDSEGLLVLTND 86

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLN------LLKKGIVIQGICYGDMQVTL-- 179
           G L   L  P  +  +VY V+  G+ D+  L        LK G  +  +     Q     
Sbjct: 87  GRLQAQLTQPGKRTGKVYYVQVEGEPDEADLRRFCQGLTLKDGPTLPALAERVAQPEWLW 146

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   L  L  G 
Sbjct: 147 PRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMGSLTLQDLAPGE 206

Query: 233 TR 234
            R
Sbjct: 207 WR 208


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 118/238 (49%), Gaps = 10/238 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R+   +A +   +R+E +++I+   V V      +A + +     + + G  + 
Sbjct: 10  ETVLPMRLDYFLAHSAGLTRKEAKKLISGGAVTVADEAKPKANLQLRPDQVVMLHG-EVV 68

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +    R  + HKP+ +V +  DP+ R TV D LP++  ++V   GRLD +T GL+LLT+D
Sbjct: 69  QLPGHRYLMLHKPVDVVCSTDDPEHR-TVLDLLPAVLRTQVHPAGRLDRDTTGLVLLTSD 127

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGS 185
           G  +  L  P+    + YRV     V  + L  L++GI+++    G+   TL    ++ +
Sbjct: 128 GQWSHRLTSPNHACGKCYRVICADPVSDEDLQALREGILLR----GEDSPTLPALAERVN 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
              + + + EG+  ++K++      KV  L R   G   L   LA G  R ++++ +R
Sbjct: 184 THTLRLTITEGRYHQVKRMLAARGNKVVGLHREQIGDIVLDADLAPGEFRALTEEEIR 241


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 86/180 (47%), Gaps = 16/180 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P   A+  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLLT
Sbjct: 39  PQIDAKDKKIVLFNKPFDVLCQFTDDADRKTLAEFIP--IKDVYAAGRLDRDSEGLLLLT 96

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------ 179
           N G L   L  P+ +  + Y V+  G+   + +  L KG+ ++        V +      
Sbjct: 97  NCGKLQNTLTAPNKKTNKTYWVQVEGEPSTESIQALCKGVELKDGLTLPANVKMIEEPNI 156

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   + +    +W+++ + EGKNR+++++         RLIR S G + L  +  G
Sbjct: 157 WQRTPPVRERKSIPTSWLSITINEGKNRQVRRMTAHIGHPTLRLIRYSIGNYTLDDINTG 216


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 85/182 (46%), Gaps = 23/182 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP   +   S    R ++ D  ++P+I+      GRLD ++EGLLLL +DG L  
Sbjct: 27  LILFNKPFQTMCQFSPHPTRKSLADHIDIPNIYP----AGRLDADSEGLLLLNDDGKLQH 82

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--------------- 177
            +  P  +  + Y V+  G  D D L  L+  + +      + +V               
Sbjct: 83  AISHPDRKHTKTYLVQVEGVPDADALARLRAPLDLGDFVTQECEVKRVAEPDWLWPRNPP 142

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 235
             +      +W+ + L EGKNR+++++     +   RL+RI+ GP  L +  L  G  RE
Sbjct: 143 IRERANAPTSWLAITLSEGKNRQVRRMTGAVGYPTLRLVRIAIGPVSLQSHPLWPGEWRE 202

Query: 236 VS 237
           +S
Sbjct: 203 IS 204


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/180 (30%), Positives = 86/180 (47%), Gaps = 23/180 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV----FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L++KP G+++  +D    S      F  +P I+     VGRLD ++EGLLLL+N GGL  
Sbjct: 7   LFYKPYGVLSQFTDRQETSHPTLKEFIPIPDIYP----VGRLDRDSEGLLLLSNHGGLQH 62

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P     R Y V+     DQ  L  LK+G+ I+       Q +L ++          
Sbjct: 63  QLCNPKFGHPRTYWVQVENIPDQIALQKLKQGVTIRNYRTRPTQASLLSEPPLLPPRTPP 122

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    AW+T+ L EG+NR+++++     +   RL+R++    QL  L  G  R +S
Sbjct: 123 VRFRKHIPTAWMTMTLYEGRNRQVRRMTAAVGFPTLRLVRVAIAHLQLQDLQPGQWRHLS 182


>gi|330957838|gb|EGH58098.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 230

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 65/226 (28%), Positives = 104/226 (46%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     +R+ V   +A   VKV+G+        V     +  D   L+  +  R
Sbjct: 2   RLDRFLSNLPRFNRKNVRLALAGGHVKVDGLTSTDPHHEVREFSCVVFDEEILQAGKPAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G V+   D     TV D L       + + GRLD NT GL+L+TNDG  +R 
Sbjct: 62  YFMLHKPQGCVSATVDAQ-HPTVIDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  +VY V     +D+       +G+    + I     Q+TL   + +   +T 
Sbjct: 121 LTQPQTRLAKVYYVETEQIIDERYAARFAEGLYFSFENITTQPAQLTLLGPRCARLSIT- 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
              EG+  ++K++F  F+ KV  L R S G   L  TL  G+ R +
Sbjct: 180 ---EGRYHQVKRMFGHFDNKVVTLHRESVGELLLDPTLEPGNYRAL 222


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 112/231 (48%), Gaps = 20/231 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V +    +R+ K +++    SR+E   +I + RV V+G     AA+ +     I +D  
Sbjct: 1   MVSDKVQKERLDKCVSKLTGLSRKEASALIKEGRVLVDGQAALEAALKIPVNSIITIDDD 60

Query: 66  PLRKAE---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRLDI 116
            +   E   + R+++ +KP  +V    D + R      + S+F   +        GRLDI
Sbjct: 61  EISLYEEGFKKRVYMLNKPSDMVCADRDRNHRI-----VTSLFVEELRPDTLHCAGRLDI 115

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGD 174
           +T GLL++T+DG L   +  P  +  ++YR      + +  ++   KGI    +   Y  
Sbjct: 116 DTTGLLIVTDDGELIHEITHPKKEITKLYRAVTDKPIPEKAVSAFLKGIKHPEEKFPYKS 175

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            ++T+++   +N  + V ++EG+  E+K++FE    +V  L R+  G  +L
Sbjct: 176 AKLTIES---ANVGL-VEVKEGRFHEVKRLFECVGCEVIELTRLKIGSLEL 222


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/190 (28%), Positives = 89/190 (46%), Gaps = 21/190 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLLLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG-------- 184
           L  P  +  + Y V+  G+  + +L  L+ G+V+  G         LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGEPQEAQLQALRDGVVLNDGPTRPASVRMLDPAPELWPRTPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R    
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTASVGLPTLRLVRVAIGDWRLDGLAPGQWRVDDA 180

Query: 239 KILREQLGPH 248
              R+  G H
Sbjct: 181 PSPRQGRGSH 190


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 116/248 (46%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 363 RLSKRMSELGLCSRREADEWIEKGWVIVDGERIDTLGTKVRADQRIEIDERAQAAQAAQV 422

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS    R ++  GRLDI++
Sbjct: 423 TILLHKPVGYVSGQAE-DGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 481

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    ++L  L+ G+ + G
Sbjct: 482 TGLLVLTQNGRIAKQLIGEQSDVDKEYLVRVRFGDRLTDIDQHFPAERLAQLRHGLELDG 541

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREG+ R+I+++ E    +V  L R+  G   LG L 
Sbjct: 542 VALKPAMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 597

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 598 QGQWRYLS 605


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 87/183 (47%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  +  ++  ++KP   ++  +D  GR T+ D +      + + GRLD ++EGL++LTND
Sbjct: 45  RSPDERKVIAFNKPYDTLSQFTDGQGRQTLADFI--TIKDIYAAGRLDRDSEGLMILTND 102

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQ--- 182
           G L   L  P  +  + Y V+  G+  +  L  L++G+ ++        +++    Q   
Sbjct: 103 GVLQARLTQPKAKAPKTYWVQVEGEPQEADLEQLRRGVTLKDGPTLPAKVEIIKPPQVWE 162

Query: 183 ---------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                         W+ + + EG+NR+++++     +   RLIR S G   L TL  G  
Sbjct: 163 RNPPVRFRAAIPTTWLAMTIIEGRNRQVRRMTACIGFPTLRLIRYSIGNTTLETLQPGEW 222

Query: 234 REV 236
           RE+
Sbjct: 223 REI 225


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 115/236 (48%), Gaps = 27/236 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V+V+G ++      V+ + H+ ++     +  +    L +
Sbjct: 1   MSELGLCSRREADVWIEKGWVRVDGKVVSELGSKVLPSQHVTIERQAAAEQSKLVTILIN 60

Query: 80  KPIGLVTTHSD-----------PDGR------STVFDNLPSIFSRVISVGRLDINTEGLL 122
           KP+G V+  ++           P+ R      +T F   P+    ++  GRLDI++ GLL
Sbjct: 61  KPMGYVSGQAEDGYQPAVTLIKPENRWAEDQATTQFH--PTQLRSLVPAGRLDIDSIGLL 118

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +LT DG +A+ L   +T+  + Y VR      G++ +++L  L+ G+ + G      +V 
Sbjct: 119 VLTQDGRVAKQLIGETTEVEKEYLVRVQYDRPGRLPENQLLKLQHGLTMDGKELLPAKVR 178

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G  R
Sbjct: 179 WQNEDQ----LSFILREGKKRQIRRMCDMVGLKVLGLKRVRIGNIKLGDLPVGEWR 230


>gi|327396520|dbj|BAK13941.1| ribosomal large subunit pseudouridine synthase F [Pantoea ananatis
           AJ13355]
          Length = 290

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 110/227 (48%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRFIEQGNVFING---KRAAVGAQVFAGDVVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP G++TT    +G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPTGIITTME--EGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ + G      +V  +    +     
Sbjct: 123 VNKILRAGNNHEKEYVVTVDKPVTDEFIAGMASGVPMLGTVTKKCKVKKE----APYVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ + F ++V +L R       L  +  G  R+++
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGIPLGEWRDLT 225


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 107/226 (47%), Gaps = 19/226 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-------TDHIEVDGVPL 67
           R+ +++A   I  R+E+++ +A++++ V+G+   + + NV +        D +  D    
Sbjct: 2   RLDQLLAHYQIP-RKEIKQSLAKRQILVDGLAATKLSQNVDTGLQEVRWKDQVLTDC--- 57

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLT 125
                   +L HKP GLVT   D    STV D L +     +   +GRLD +T GLLLLT
Sbjct: 58  ----SHHYFLLHKPQGLVTATKDAQ-HSTVLDLLRTEDRTPKTYPIGRLDRDTTGLLLLT 112

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKG 184
           ++G L   L  P     + Y    +G ++   +   ++GI  + G      ++ + +   
Sbjct: 113 DNGPLGFQLLHPQYHIEKEYAATVNGPLEPAHIEKFQEGITFLDGTTCKPAKLEILSSSL 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + +   V L EGK  ++KK+      KV  L RI +G F L   LA
Sbjct: 173 TESQALVTLSEGKFHQVKKMLLSVGVKVTSLKRIKFGDFSLDPNLA 218


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 98/208 (47%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + +    V VN  + +  +V + + D I  DG  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDGELLEWMDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+       ++GI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAQRFEEGILLRGEREPCLPAKMEVLDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHRWRIG 206


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 107/242 (44%), Gaps = 25/242 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I Q  V V+G         +     I +D     K  +  
Sbjct: 5   RLSKLMSAQGMCSRREADVYIEQGWVYVDGQPARELGTKIYPWQEITLDRTAQIKQNQQV 64

Query: 75  LWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSR--------------VISVGRLDI 116
             L +KP+G V+   +    P       D   S F R              +   GRLDI
Sbjct: 65  TILLNKPVGYVSGQPELGYKPAASLICHD---SRFHRDRSSLKFTSQHLKNLAPAGRLDI 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 VSLLNQD----QLRFILQEGKKRQIRRMCELVGLNVSGLKRVRIGQIRLADLPEGKWRYL 237

Query: 237 SK 238
            K
Sbjct: 238 GK 239


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 118/236 (50%), Gaps = 14/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I    + SR E +++I ++ V VNG +++     +   D +  + +   K    +
Sbjct: 2   RLDKYIGHTTLLSRAESKKII-KKGVLVNGNIVKAPDFKI---DELNDEVIVNEKKLIYQ 57

Query: 75  LWLY---HKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDG 128
            ++Y   +KP G+++   D   R TV D L     IF     VGRLD +TEGL+LLTNDG
Sbjct: 58  KYIYIMMNKPKGVISATEDSISR-TVIDLLEEKDCIFEP-FPVGRLDKDTEGLMLLTNDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
            L   L  P     + Y V  +G +  + +  LK+GI+++ G      ++ + T   S +
Sbjct: 116 NLGHQLTSPKKDVEKQYYVEVNGVLKVEHIPYLKEGIILEDGYKCKSAKLDILTSDVSKS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              + + EGK  ++K++ +    +V  L R+S G   L  TL  G  R ++++ L+
Sbjct: 176 TAYIYVTEGKFHQVKRMMKALGCEVTYLKRLSIGELVLDETLELGKYRYLTEQELK 231


>gi|242243012|ref|ZP_04797457.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233613|gb|EES35925.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 230

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 111/224 (49%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R EV++++ +  VKVN   ++   ++V  ++D I V+   +   ++ 
Sbjct: 2   RLDKFLANMGVGTRSEVKQLLKKGAVKVNQNKVKSPKLHVNPNSDEIMVNDEVVSYIDKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G ++   D +   T+ D +P      +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYISATED-ELHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-V 191
            +  P+    + Y V     + Q  ++  K GI +      D ++     K  + +V+ V
Sbjct: 120 EVMNPNKHVSKTYEVYSKHPITQFDIDEFKSGIEL-----SDGKLKPAILKKVDDYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + EGK  ++K++F     +V  L RI     +L   L  GS R
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAELELDHNLDLGSYR 218


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 111/229 (48%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +R+ V  ++A+  V+V+G +       +     + ++G  L+    + 
Sbjct: 7   RLDRFISVKTGINRKNVRLLLAKGLVEVDGDIARNIDQIIDEFSDVSLEGEVLQSNSPSY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + L HKP+G+V+   D D   TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  VML-HKPVGVVSATVD-DKHKTVIDLLTDKSKHDLHIVGRLDLNTSGLLLLTNDGRWSKK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  ++YRV     +D   +    +GI    + I     Q+ L       A VT 
Sbjct: 125 LMSPHHKVGKLYRVTLQNPIDDSYVKAFAEGIYFEFEDIITKPAQLAL--VDSHTALVT- 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            L EG+  +IK++F  F   V  L RIS G   L + L  G +R ++ +
Sbjct: 182 -LVEGRYHQIKRMFGRFRNPVIGLHRISVGKILLDSQLTPGMSRSLTAQ 229


>gi|315179854|gb|ADT86768.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 183

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 84/174 (48%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 10  IFNKPFDTLSQFTDGDGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 67

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P ++  + Y V+  G   +  L+ L+ G+ ++        V +  +              
Sbjct: 68  PQSKSPKTYWVQVEGAPQEADLDKLRNGVELKDGPTLPAIVEIMPEPEVWERHPPVRFRA 127

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RLIR S G   LG L  G  + +
Sbjct: 128 AIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIVLGDLQPGEWKHI 181


>gi|324990675|gb|EGC22611.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 241

 Score = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 124/238 (52%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A   I SR+++++ + Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLAANHI-SRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKYVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPAGAVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKIA-FQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R ++    +E+LG
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGDFTLDPDLAKGDYRALN----QEELG 231


>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 = 71.6 bits (174), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 44/169 (26%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 62  LFNKPFDVLCQFTDEQGRKTLKDFIP--VKDVYAAGRLDRDSEGLLLLTNDGKLQSKITE 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  + Y V+  G  ++  L  L+ G+ ++       ++++ ++              
Sbjct: 120 PKKKTFKTYWVQVEGAPNEAALQTLRNGVKLKDGMTLPAKISILSEPNIWDREPPIRERK 179

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                W+ + + EG+NR+++++     +   RLIR   G + L  +  G
Sbjct: 180 NIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDIDIG 228


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 98/208 (47%), Gaps = 4/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + +    V VN  + +  +V + + D I  DG  L   +  +
Sbjct: 2   RLDKFIAENTGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDGELLEWMDEGQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  +  
Sbjct: 62  YFMLYKPQGYVCSHDDGE-YPTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+       ++GI+++G     +   ++     N  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLADPVEDFYAQRFEEGILLRGEREPCLPAKMEVLDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EG+  ++K++F     KV  L R   G
Sbjct: 179 SEGRYHQVKRMFAALGNKVEALHRWRIG 206


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 116/240 (48%), Gaps = 9/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E  
Sbjct: 3   RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLV-YESF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  VYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G + +   +   +GI ++   C    ++V     +   + V
Sbjct: 121 HDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++K++       V  L R+S GP +L   LA G  R ++ + L + L P+
Sbjct: 181 KITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEEL-QSLAPY 239


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 67/220 (30%), Positives = 114/220 (51%), Gaps = 7/220 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A+  I SR+ +++ + ++ + V+       + NV      +   G  ++  E  
Sbjct: 2   RLDRLLAQEKI-SRKAMKQALLKKEILVDECPARFLSQNVDTGLQKLVFQGRQIQGYEHN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G+VT   D +   TV D L P I S ++ ++GRLD +T GLLLLT++G L 
Sbjct: 61  YLML-HKPNGVVTASRDKN-LPTVMDLLSPDIQSDQIYAIGRLDRDTTGLLLLTDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y+V  +G +  D +   K+GIV + G       + + +   S++  T
Sbjct: 119 FQLLHPQYHVDKSYQVVVNGPLTPDHIQRFKEGIVFLDGTTCKPATLEILSSSPSSSQAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++KK+F     KV  L R+ +G F L + LA
Sbjct: 179 ITISEGKFHQVKKMFFSVGVKVVSLKRVQFGDFTLDSELA 218


>gi|289209534|ref|YP_003461600.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288945165|gb|ADC72864.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
          Length = 180

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 85/176 (48%), Gaps = 20/176 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +R+ L+HKP G++   +DP+GR T+ D  ++P ++      GRLD ++EGL++LT+DG L
Sbjct: 2   SRIVLFHKPWGVLPQFTDPEGRPTLADYIDIPGVYP----AGRLDRDSEGLMVLTDDGRL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P  +  + Y V+  G+ D   L  L+ G+ ++       +V   T         
Sbjct: 58  NARLTQPRHKTSKTYWVQVEGEPDDAALEALRTGVDLKDGRTQPAKVERMTPPDLPERDP 117

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                      W+ + L EG+NR+++++         RL+R     + L  +  G+
Sbjct: 118 PVRFRKSVPTTWLALTLHEGRNRQVRRMTAAVGHPTLRLVRYRVASWTLDGVERGA 173


>gi|291619766|ref|YP_003522508.1| RluF [Pantoea ananatis LMG 20103]
 gi|291154796|gb|ADD79380.1| RluF [Pantoea ananatis LMG 20103]
          Length = 297

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 110/227 (48%), Gaps = 13/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V + D ++V+G  +  R  
Sbjct: 15  RLNKYISESGICSRRDADRFIEQGNVFING---KRAAVGAQVFAGDVVKVNGQLIEPRDE 71

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP G++TT    +G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 72  DDLVLIALNKPTGIITTME--EGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     V  + +  +  G+ + G      +V  +    +     
Sbjct: 130 VNKILRAGNNHEKEYVVTVDKPVTDEFIAGMASGVPMLGTVTKKCKVKKE----APYVFR 185

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++ + F ++V +L R       L  +  G  R+++
Sbjct: 186 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGIPLGEWRDLT 232


>gi|251789551|ref|YP_003004272.1| pseudouridine synthase [Dickeya zeae Ech1591]
 gi|247538172|gb|ACT06793.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 218

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 48/182 (26%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A + R+ L++KP  +++  +D   R+T+ D +P     + + GRLD ++EGL++LTNDG 
Sbjct: 36  AAQARIVLFNKPFDVLSQFTDEGSRATLKDYVP--LRDIYAAGRLDRDSEGLMILTNDGQ 93

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------------VIQGICYGDM 175
           L   L  P  +  ++Y  +  G  D + L+  + G+              V +       
Sbjct: 94  LQARLTQPGKKTPKIYYAQVEGIPDDEALHAFRTGLQLNDGTTLPAGAERVEEPAWLWPR 153

Query: 176 QVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           Q  +  +K    +W+ + L EG+NR+++++     +   RLIR S     L  L  G  +
Sbjct: 154 QPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMANQTLDGLSPGEWK 213

Query: 235 EV 236
           E+
Sbjct: 214 EI 215


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 78/161 (48%), Gaps = 10/161 (6%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L   HKP G V T SD  GR TV+D LP  +  +  + VGRLD++++GLLL T DG + 
Sbjct: 10  KLLALHKPKGYVVTRSDELGRKTVYDLLPDWAFENGWMPVGRLDMDSKGLLLFTTDGKIG 69

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY +   G V  + +   KKG+  +      + V      G+   + V
Sbjct: 70  DALTRPGNC-KKVYEIWVRGYVTDEHIAAAKKGVESKQGLLKALSVEKLGTGGAKTKLRV 128

Query: 192 GLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQL 225
            + EGKNR I+++F            KV  L R+  G F L
Sbjct: 129 VIDEGKNRHIRRLFGALKDPKFSTPLKVLDLKRVRIGTFDL 169


>gi|322412052|gb|EFY02960.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 243

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/221 (28%), Positives = 104/221 (47%), Gaps = 7/221 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++ + VN  +     V +    D +   G PL   E  
Sbjct: 2   RLDKFLVETGVGSRSQVKSLLKKKAILVNQEVETSPKVQINEHKDVVTYLGKPL-TYEAF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G ++   D   ++TV D L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 61  VYYVLNKPAGFLSATKDR-AQATVIDLLDETARQKDVFPVGRLDKDTRGLLLLTNNGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAW-V 189
             L  P     + Y  +  G + +   +   KGI ++   C       LD         V
Sbjct: 120 HDLLSPKKHVTKEYLAKVAGIMTEADKDDFAKGISLKDYQCLPAKLEVLDKDVSQETCVV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           ++ ++EGK  ++K++      +V  L R+S GP +L   LA
Sbjct: 180 SITIQEGKFHQVKRMVAACGKEVLELQRLSMGPLRLDPSLA 220


>gi|218530506|ref|YP_002421322.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218522809|gb|ACK83394.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 242

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTD---HIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  + +  D    + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP+G+  +H +      V+  LP  + R    + +VGRLD  T GLLL+T+
Sbjct: 65  PGVCLML-HKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T   +
Sbjct: 122 DGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMETDDPT 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           +  VT  L EG+  +++++F      V+ L R   G   L T L AG  R
Sbjct: 182 HCTVT--LHEGRYHQVRRMFAALGNHVDALHRDRVGGLVLPTDLPAGEFR 229


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 103/220 (46%), Gaps = 14/220 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKA 70
           R+ +++A  G  SRRE++ +    R++++G  L  A   + +T      + V G PL   
Sbjct: 8   RLDRLLANLGYGSRREIQALARAGRIRLDGEALREADGRIAATADLPARLTVSGEPLDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP G+  +H +      V+  LP  + R    + +VGRLD +T GLLL+T+
Sbjct: 68  APLALML-HKPTGVTCSHKEAG--PLVYGLLPERWRRREPALSTVGRLDKDTSGLLLVTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V    Q   
Sbjct: 125 DGALLHRIISPKAKIEKQYRVELDRPLRGDEGAILVSGTLMLEGEEAPLLPVGFTAQGPR 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            A V   L EG+  +++++F      V  L R   G   L
Sbjct: 185 QARVV--LTEGRYHQVRRMFAALGNHVTALHRDRVGGLTL 222


>gi|163851700|ref|YP_001639743.1| pseudouridine synthase [Methylobacterium extorquens PA1]
 gi|163663305|gb|ABY30672.1| pseudouridine synthase [Methylobacterium extorquens PA1]
          Length = 242

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 111/230 (48%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTD---HIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  V +  D    + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRVPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP+G+  +H +      V+  LP  + R    + +VGRLD  T GLLL+T+
Sbjct: 65  PGVCLML-HKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T   +
Sbjct: 122 DGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMETDDPT 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           +  VT  L EG+  +++++F      V+ L R   G   L   L AG  R
Sbjct: 182 HCTVT--LHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFR 229


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R+ L++KP G+++  +D     +    L            GRLD ++EGL++LT++G L 
Sbjct: 3   RVILFNKPFGVLSQFTDKGTEGSPRPTLSGFIDEKGFYPAGRLDRDSEGLIVLTDNGALQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKG------ 184
             +  P  +  + Y V+  G  D   +N L++G+ ++       +V+L DT  G      
Sbjct: 63  ARISHPKYKLAKTYWVQVEGTPDDAAINALRQGVTLKDGKTAPAKVSLIDTPAGLWDRDP 122

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                    +AW+++ + EG+NR+++++         RLIR   G +QL  +  G+ R  
Sbjct: 123 PVRFRKSVPDAWLSITITEGRNRQVRRMTAHVGLPTLRLIRAQIGDWQLNAMRPGTWRFS 182

Query: 237 SK 238
           S+
Sbjct: 183 SE 184


>gi|318042073|ref|ZP_07974029.1| pseudouridine synthase, Rsu [Synechococcus sp. CB0101]
          Length = 232

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/191 (29%), Positives = 92/191 (48%), Gaps = 36/191 (18%)

Query: 77  LYHKPIGLVTTHS-DPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP G+++  + +P  R   + D++P     V + GRLD ++EGLLLLT +G L + L
Sbjct: 12  LFYKPYGVLSQFTPEPGSRWGCLADHIP--VPDVYTAGRLDADSEGLLLLTANGRLQQRL 69

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P+    R Y V+  G  D  +L  L++G+VIQG      Q TL               
Sbjct: 70  TDPAWGHWRRYWVQVEGIPDAAQLQQLEQGLVIQG------QRTLPARANAIADPDLPPR 123

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLGTL 228
                  Q+   +W+ V LREG+NR+++++         RL+R++        P  L  L
Sbjct: 124 DPPIRSRQQIPTSWLAVELREGRNRQVRRMTAAVGLPTLRLLRVAIDLMDGGAPLSLDGL 183

Query: 229 LAGSTREVSKK 239
             G  R V+ +
Sbjct: 184 EPGQWRAVTPE 194


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 62/211 (29%), Positives = 99/211 (46%), Gaps = 7/211 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLW 76
           +++   G  +R E   +I Q R +VNG  +     ++ + D   EVDGV     E+  + 
Sbjct: 5   QILFSQGFGTRHECTGLIVQGRFRVNGTAVTDPDEDIPTEDLTFEVDGVQWPFFEKA-II 63

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +KP     +   P    +V   LP      +V  VGRLD +T GLLLLT+DG L   L
Sbjct: 64  LLNKPEHYECS-LKPIHHPSVLSLLPPPLRVRKVQPVGRLDEDTTGLLLLTDDGKLIHRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++YRV     V + ++  L KG  +Q     D+   +   K S   + +G+ 
Sbjct: 123 THPKKHVTKIYRVTLKHPVTEKQIAQLLKG--VQLADSPDIVKAVSCDKVSELVIDLGIT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +GK  ++K++    + +V  L RI +G   L
Sbjct: 181 QGKYHQVKRMMAAVSNRVVALERIRFGNLSL 211


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 46/172 (26%), Positives = 82/172 (47%), Gaps = 16/172 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLLTN G L   
Sbjct: 45  KVILFNKPYDVLCQFTDEQNRQTLANFIP--IKDVYAAGRLDRDSEGLLLLTNCGKLQNT 102

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L  P  +  + Y V+  G   +  ++ L +G+ ++       QV L  +           
Sbjct: 103 LTAPGKKTNKTYWVQVEGVPTEASIDALSQGVELKDGLTLPAQVKLIDEPALWPRTPPVR 162

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  +W+++ + EGKNR+++++         RLIR S G + L  +  G
Sbjct: 163 ERKSIPTSWLSITINEGKNRQVRRMTAHIGHPTLRLIRYSIGKYTLDGIETG 214


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 110/233 (47%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K +A  G  SR+EV  M  + RV   +G +L +   + +  D++ VDG PL   +  
Sbjct: 2   KLVKHLANLGYGSRKEVAWMFREGRVTDADGEVLYQD--DPLDHDNVRVDGEPLDPPQGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  V+D LP  F     V+S VGRLD  T GLLL+T+DG 
Sbjct: 60  LLML-HKPAGYTCSTKD-KGR-IVYDLLPPRFRLRDPVLSTVGRLDRETTGLLLMTDDGQ 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P ++  +VY       +  D+  L   G ++++      +   ++      A 
Sbjct: 117 LLHRIVSPKSKLAKVYEADLAEDLRGDEAQLFASGTLMLESETTPLLPAQMEVLGPRRAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V   L EG+  +++++F      V  L R   G   LG L  G  R++ +  L
Sbjct: 177 VV--LHEGRYHQVRRMFAAVGNNVVALHRPRIGGLALGDLAEGQWRQLGQDDL 227


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 113/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 378 RLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQV 437

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D+ P  FS      +   GRLDI++
Sbjct: 438 TILLHKPVGYVSGQAE-DGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 496

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 497 TGLLVLTQNGVIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 556

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 557 VALKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 612

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 613 QGQWRYLS 620


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 87/173 (50%), Gaps = 17/173 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  +D +GR+T+ D +     RV + GRLD+++EGLLLLT+ G L   L  
Sbjct: 4   LFNKPYNVLTKFTDTEGRATLADYID--IPRVYAAGRLDMDSEGLLLLTDQGHLNHALTD 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GIC--------------YGDMQVTLDT 181
           P  +  + Y V+  G   + +L  L++G+ ++ G+               +   +     
Sbjct: 62  PDNKAYKTYVVQVEGIPTKAQLKQLEQGVDLKDGLTLPAKVKRIPYPKWLWAREKPIRTR 121

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           Q    +++ + ++EG+NR+++++         RLIR   G + L  L  G  R
Sbjct: 122 QNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGDYHLADLQPGQYR 174


>gi|167561885|ref|ZP_02354801.1| RNA pseudouridine synthase family protein [Burkholderia
           oklahomensis EO147]
          Length = 240

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 94/210 (44%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++   RV V G     A  +  +     EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGRVAVGGATCTDAHASFDTARLAFEVDGVAWPYHARAYVVL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   S+VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHSSVFRLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G       V    +      +TV   EGK  +
Sbjct: 129 VPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPIAAVAAHARGERLLEMTVA--EGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V  L R S G F L   LA
Sbjct: 187 VKRMVAAASNRVEALHRASIGGFTLPADLA 216


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 89/187 (47%), Gaps = 23/187 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP  ++   S    R+++ D  ++P I+      GRLD ++EGLLLLT+DG L  
Sbjct: 3   LILFNKPFQVMCQFSPHPTRASLADYLDIPDIYP----AGRLDADSEGLLLLTDDGKLQH 58

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDMQ----------V 177
            +  P  +  + Y  +  G    + L  L+  +     + QG     +Q           
Sbjct: 59  AISHPDHKQTKTYLAQVEGIPHTEALARLRAPLNLGDFITQGCEVKRVQEPDWLWPRNPP 118

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 235
             +  +   +W+ + L EGKNR+++++         RLIRI+ GP  L +  LL G  RE
Sbjct: 119 IRERAQVPTSWLAITLAEGKNRQVRRMTGAVGLPTLRLIRIAIGPISLQSHPLLPGQWRE 178

Query: 236 VSKKILR 242
           VS   LR
Sbjct: 179 VSAAELR 185


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 110/227 (48%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +RRE  +++  + ++V+G ++  A+ +V   + +E +G PL K +  R
Sbjct: 2   RLDKFLGTTLGITRREAGKLLRDKMIEVDGEIVRSASFSVSDDNDVEFNGRPL-KLQGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D   TVF     +    + V GRLD +T GL+LLT+DG  +  
Sbjct: 61  YFMLNKPEGFVCSHVD-DFNPTVFVLFDEVSPEKMHVAGRLDGDTTGLVLLTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +D +   + G+ ++          L+      A +T+  
Sbjct: 120 ITSPRHLCSKTYFVEAADPITEDYIKQFEAGVQLRSEKELTRPAKLEILGEREALLTIS- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            EGK  ++K++F     KV  L R   G  +L   LA G  R ++++
Sbjct: 179 -EGKYHQVKRMFAAMGNKVVGLHRERIGTVELDEDLAPGEYRPLTEE 224


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 53/184 (28%), Positives = 89/184 (48%), Gaps = 21/184 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP    +V + GRLD ++EGLLLLT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSTPPKRTLAEFGLPP---QVYAAGRLDHDSEGLLLLTDDGPLAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLDTQKG-- 184
           L  P  +  + Y V+  G  D  +L  L  G+++         +   +   TL  +    
Sbjct: 61  LTDPRHKQPKTYWVQVEGDPDTSQLQALCDGVLLNDGPTRPANVRRLECAPTLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                  +AW+ V + EG+NR+++++         RL+R++ G + L +L  G  R    
Sbjct: 121 RVRKTVPDAWLEVQITEGRNRQVRRMTASVGLPTLRLVRVAIGAWSLASLQPGQWRVDDA 180

Query: 239 KILR 242
           + +R
Sbjct: 181 RAVR 184


>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 = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 110/236 (46%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           ++ K IA  G  SR+EV R+  + R+  NG         + + DH++      DG PL  
Sbjct: 2   KLLKYIANLGYGSRKEVARIFREGRI-TNG-----EGEVLYADDHVQHTAVRFDGEPLDP 55

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLT 125
                + L HKP G + +  D  GR  V+D LP+ F   S ++S VGRLD +T GLLLLT
Sbjct: 56  PPGLMVML-HKPSGYICSTKDA-GR-LVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLT 112

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG L   +  P T   +VY       +  D+  L   G ++       +Q  +    G 
Sbjct: 113 DDGALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP 172

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 173 -CQVRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 66/228 (28%), Positives = 112/228 (49%), Gaps = 10/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA      ++ V  ++   +V V+G   +   + V    HIE +GV LR+ ++ +
Sbjct: 7   RLDQFIAGTLQIPKKAVRLLLVTNKVLVDGQFAKSPDLQVDEFTHIECNGVVLRQYQK-Q 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   D D  +T    +  + + ++ + GRLD+++ GLLLLTND   +  
Sbjct: 66  YYMLNKPDGVVSATID-DKHATALGLITGVNTDMLHIAGRLDLHSTGLLLLTNDAKWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + Y V     ++Q+ +    KG+    + I     Q+TL     S+    V
Sbjct: 125 LMDPQHKVDKQYLVTLANPLEQEYVEAFSKGMYFGFEDITTLPAQLTL----LSSHRARV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK 238
            LREGK  +IK++F  F   V  L R S G   L   L  G  R ++K
Sbjct: 181 VLREGKYHQIKRMFGRFRNPVVALHRESIGKIVLDKQLELGEFRSLTK 228


>gi|326692342|ref|ZP_08229347.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           argentinum KCTC 3773]
          Length = 177

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 85/175 (48%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  +D DGR T+ D +     RV + GRLD+++EGLLLLT+ G L   L  
Sbjct: 4   LFNKPYNVLTKFTDADGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHALTD 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDMQVTLDT----- 181
           P  +  + Y V+  G   + +L  L+ G+ ++           I Y       +      
Sbjct: 62  PENKAYKTYVVQVEGVPTKAQLKQLENGVELKDGWTLPAKAKRIPYPKWLWPRENPIRVR 121

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    +++ + ++EG+NR+++++         RLIR   G + L  L  G  R +
Sbjct: 122 KNQPTSFIQLKIKEGRNRQVRRMTAAVGLPTLRLIRTHIGDYHLADLKPGEYRVI 176


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 101/226 (44%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV--MSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  +  A  ++   S   +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVSINGTCMNDADADIDSASVHTLDIDGKAVTIIPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPADYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLVTNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V      D      LK G+++    + +C  D  +       S
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPADGILCETLKNGVLLHDENETVCAADANLE------S 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 175 PTTLLLTITEGKYHQVKRMIAAAGNRVQHLHRRQFAHLETKNLKPG 220


>gi|322832033|ref|YP_004212060.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167234|gb|ADW72933.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 235

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 50/207 (24%), Positives = 97/207 (46%), Gaps = 2/207 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV V+G +++  ++ +     +E DG  L +    R
Sbjct: 2   RLDKFLSQQLGVSRALVLRELRNKRVTVDGEIVKTGSMKISPEQRVEFDGNVLDQITGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLEEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D     + G+ +       +      +K  +  V + L 
Sbjct: 122 TSPRHHCEKTYLVTLEHPLADDTAAQFEAGVQLHN--EDSLTKPAQLEKIEDCLVRLTLS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYG 221
           EG+  ++K++F     +V  L R   G
Sbjct: 180 EGRYHQVKRMFAAVGNRVVALHRERIG 206


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/208 (27%), Positives = 97/208 (46%), Gaps = 3/208 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  ++I    V VN I+ +  AV V     +E  G  ++K     
Sbjct: 2   RLDKYLCDALGATRKEATKIIKSGDVTVNDIVQKSGAVKVTDDCIVEWQGREIQKPGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+ KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLF-KPDGFVCSHEDG-FNQTAFMLLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     ++ D +   ++GI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDPIEADYVAQFEQGIELRNEKAATLPAKLEIVDEEEKEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYG 221
            EGK  ++K++F     KV  L R   G
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIG 207


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/182 (31%), Positives = 88/182 (48%), Gaps = 22/182 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L HKP G+++  S P+  S      P +    V + GRLD ++EGLLLLT+DG L + L 
Sbjct: 18  LLHKPYGVLSQFS-PEPLSPWSTLAPLVPVPGVYAAGRLDADSEGLLLLTSDGPLQQRLT 76

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------ICYGDM----QVTLDTQK 183
            P     R Y V+  G      L  L++G+++QG        I   D     +V    Q+
Sbjct: 77  DPRWGHWRRYWVQVEGTPSDAALQQLREGVMVQGRRTLSAQAIALADPGLAERVPPIRQR 136

Query: 184 GS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLGTLLAGSTRE 235
            S   +W+ +GLREG+NR+++++         RL+R++        P  L  L  G  R 
Sbjct: 137 RSIPTSWLELGLREGRNRQVRRMTAAVGLPTLRLLRVAIDLMDGEPPLSLEGLAPGQWRP 196

Query: 236 VS 237
           V+
Sbjct: 197 VT 198


>gi|332361775|gb|EGJ39579.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 241

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 74/240 (30%), Positives = 125/240 (52%), Gaps = 13/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ +++A A   SR+++++   Q+++ V+G    + + NV      I   G  +      
Sbjct: 2   RLDQLLA-ANHISRKKMKQSHLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPAH- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L 
Sbjct: 60  RYYMLNKPSGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
             L  P     + Y V  +G +  QDK+   ++GI  + G      Q+++ +   S +  
Sbjct: 119 FQLLHPQYHVEKTYYVEVNGPLTSQDKIA-FQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSK---KILREQL 245
           TV + EGK  +IKK+F     KV  L RI +G F L   LA G  R +++   +I++E L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGNFTLDPDLAKGDCRPLNQEELEIIKESL 237


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 89/182 (48%), Gaps = 21/182 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP G+++  +   G   +  F   P +++     GRLD ++EG LLLT++G L + L
Sbjct: 6   IFNKPFGVLSQFTPEAGHPALDSFGFPPGVYA----AGRLDHDSEGALLLTDNGKLIKKL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLDTQKGSN---- 186
             P  +  R Y  +  GQ+ ++ +  L KG+ I+G     C  ++    +     N    
Sbjct: 62  LDPKYEHPRTYLAQVDGQITEEAVCKLAKGVDIKGYHTKPCKAEIVEAPEWIWERNPPVR 121

Query: 187 -------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 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|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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/263 (26%), Positives = 120/263 (45%), Gaps = 36/263 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A A + SR+ V   I +  VKVN  L+   A+ +  + D IE     +  A + 
Sbjct: 2   RLDKFLAEAAVGSRKNVRIYIKEGMVKVNKELVTEPAIEIDENCDVIEYLNEIVSYAGKL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++++KP G +T  +D +   TVFD L    ++ +  VGRLD +TEGLLL TNDG    
Sbjct: 62  -YYMFNKPAGCITAKTD-EIHKTVFDFLGEAGTKGIFHVGRLDKDTEGLLLFTNDGEFEH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC----------------YGDMQ 176
            +  P     + Y     G + ++    L++G  I G C                Y +++
Sbjct: 120 KIMYPEKHVEKTYFFWALGSLSEEDKKQLEQGTYI-GQCKILTKPAKIEVDKFGIYEELK 178

Query: 177 VTLDTQKGSN------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
             + T   +N             ++T+   EG+  ++K++ +     V  L RIS G   
Sbjct: 179 HEMATDNVNNINSNHGTQPVVSGYLTI--SEGRKHQVKRMLKSVGCYVVYLKRISIGGLA 236

Query: 225 LG-TLLAGSTREVSKKILREQLG 246
           L  +L  G  R +++  +++ LG
Sbjct: 237 LDKSLKKGQYRPLTELEIQKVLG 259


>gi|319794805|ref|YP_004156445.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315597268|gb|ADU38334.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 182

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 52/181 (28%), Positives = 88/181 (48%), Gaps = 23/181 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +RL  ++KP G+++  + P+GR      F ++P ++      GRLD ++EGLLLLTNDG 
Sbjct: 7   SRLIRFNKPYGVLSQFT-PEGRWRGLKDFIDIPDVYV----AGRLDADSEGLLLLTNDGQ 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG---- 184
           L   +  P  +  + Y V+  G   ++ L  L++G+ +  G+        LD        
Sbjct: 62  LQARIADPRFKMEKTYWVQVEGVPTEEALAALRQGVQLNDGLTRPARASLLDPPPDVWPR 121

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       AW+ + + EG+NR+++++         RLIR + GP  L  L  G+ R
Sbjct: 122 QPPIRERKSIPTAWLELAISEGRNRQVRRMTAAVGLPTLRLIRAAIGPHTLDGLAPGTWR 181

Query: 235 E 235
           E
Sbjct: 182 E 182


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 56/223 (25%), Positives = 96/223 (43%), Gaps = 16/223 (7%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERA-------AVNVMSTDHIEVDGVPLRKA 70
           K I   G+ SR++ + +I    + +NG +  RA        V+ +S D  E+  VP+   
Sbjct: 5   KYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVPMPHF 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 65  ----YILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                +  P  +  ++YRV      D      LK G+++                 +   
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVLAAPTTLM 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +T+   EGK  ++K++      +V +L R  +G + +  L  G
Sbjct: 180 MTI--TEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLATG 220


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 49/150 (32%), Positives = 80/150 (53%), Gaps = 4/150 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLE 135
           + +KP G+++  SD + + TV D L     + +  VGRLD +TEGLLL+TNDG L+  L 
Sbjct: 1   MLNKPAGVLSAVSDNNCK-TVIDLLDVTPKKGLFPVGRLDKDTEGLLLITNDGELSHNLL 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P+    + Y V  +G +    + L +KG+ I         +    +K S A +T+   E
Sbjct: 60  SPAKHVDKTYYVELNGDLIDSDIELFEKGLDIGEKNLTKPAILKILEKRSTALITI--TE 117

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           GK  ++K++F+     V  L R++ GP +L
Sbjct: 118 GKYHQVKRMFQAIGLTVTFLKRLTMGPLKL 147


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/215 (30%), Positives = 104/215 (48%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV V+G++++     V    HI++D   L +A      + HKPIG+V+ 
Sbjct: 41  RKAVRELLLSGRVCVDGLIVKDMDRQVDEFSHIQLDEQIL-QANVPVYVMLHKPIGVVSA 99

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D   + TV D L       + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 100 TKDTQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDALMSPTHKVDKVYR 158

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     + ++ +     G+      +G   +T    K    ++    V L EGK  +IK+
Sbjct: 159 VTLANPITEEYIAAFAAGMY-----FGFEDITTQPAKLVILADNVAEVTLHEGKYHQIKR 213

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +F  F   V  L R+S G   L   LA G +R ++
Sbjct: 214 MFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALT 248


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 50/184 (27%), Positives = 95/184 (51%), Gaps = 24/184 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           +RL L++KP G+++  +D       R+T+ D  N+P ++      GRLD ++EGLLLLT+
Sbjct: 2   SRLLLFNKPFGVLSQFTDRGTADSPRATLSDHINIPGVYP----AGRLDRDSEGLLLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDM- 175
           DG L   +  P  +  + Y V+  G+ D   L  L++G+ ++           I   D+ 
Sbjct: 58  DGRLQARISHPKFKAPKTYLVQVEGEPDDAALAALRRGVTLKDGPTRPAQAERIAPPDLW 117

Query: 176 --QVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                +  +K   ++W+ + + EG+NR+++++     +   RL+R S G + L  +  G+
Sbjct: 118 PRDPPVRYRKSVPDSWLRLTITEGRNRQVRRMTAHVGYPTLRLVRWSVGDWTLDGIAPGT 177

Query: 233 TREV 236
            +E 
Sbjct: 178 WQEA 181


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 113/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 422 RLSKRMSELGMCSRREADEWIEKGWVLVDGARIDTLGTKVRADQKIEIDERASAAQAAQV 481

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D+ P  FS      +   GRLDI++
Sbjct: 482 TILLHKPVGYVSGQAE-DGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 540

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 541 TGLLVLTQNGVIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 600

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 601 VALKPALVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 656

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 657 QGQWRYLS 664


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 111/230 (48%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTD---HIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  + +  D    + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP+G+  +H +      V+  LP  + R    + +VGRLD  T GLLL+T+
Sbjct: 65  PGVCLML-HKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T   +
Sbjct: 122 DGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMETDDPT 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           +  VT  L EG+  +++++F      V+ L R   G   L   L AG  R
Sbjct: 182 HCTVT--LHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFR 229


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/269 (26%), Positives = 115/269 (42%), Gaps = 45/269 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K+ +  GI SR+E  ++I Q+R+K+NG   E   +   V   D I  DG  ++  E+
Sbjct: 2   RINKLFSNLGICSRKETNKLIEQKRIKING---EYCVLGQWVEDNDEILFDGERVKSMEK 58

Query: 73  TRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             L  Y KP G+  T   +  G    + N       V  VGRLD ++EGL++LTNDG  +
Sbjct: 59  VYLAFY-KPKGITCTLEKNAQGNIGEYINYNQY---VFPVGRLDKDSEGLIILTNDGVFS 114

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------------QGICYGDMQ- 176
             +     +  + Y V+     D + L  ++ G+ I              +GI   D + 
Sbjct: 115 NHILECDNKHEKEYIVKVDKPFDDNFLLSMRTGVEISAKSGSGVKRISDSEGIVIKDGKD 174

Query: 177 --VTLDTQKG------------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             + LD  K                   +     + L +G NR+I+K+     +KV  L 
Sbjct: 175 EIIMLDEAKNGKMKKDIVKTRPCKVERINEDTFKIILTQGLNRQIRKMSSVLGYKVISLK 234

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQL 245
           RI      L  L  G  R + K+ + E +
Sbjct: 235 RIRIMNIHLDYLECGEYRLIPKEHIDELM 263


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 83/176 (47%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLL+LT+DG LA  
Sbjct: 6   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLVLTDDGALAHR 62

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G    + L  L+ G+ +        QV  LD            
Sbjct: 63  LTDPRHKQPKTYWVQVEGAPQAEHLQALRDGVALNDGPTRPAQVRMLDPAPQLWPRDPPV 122

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 123 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 178


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 108/236 (45%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV V+G +++  A+ +     +  DG  L++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTVDGEIVKTGALKLTPEQEVMFDGNLLQQQVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D       G+ +           L+  +     +T+   
Sbjct: 122 TSPKHHCEKTYLVTLEHPVADDTAEQFAVGVQLHNEPTLTKPAQLEVIEPQQVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G   +   LA G  R ++++ +     PHL
Sbjct: 180 EGRYHQVKRMFGAVGNRVVALHRERIGAIVMDDDLAPGEYRPLTEEEIASVGAPHL 235


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 52/183 (28%), Positives = 90/183 (49%), Gaps = 18/183 (9%)

Query: 74  RLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           RL L +KP  +++  +D  +GR+T+   +P     V   GRLD ++EGLLLLT++G L  
Sbjct: 3   RLILLNKPYDVLSQFTDRAEGRATLASLVP--IPGVYVCGRLDRDSEGLLLLTDNGPLQH 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG------- 184
            +  P ++  + YR +  G  D+  L+ L++G+ ++ G         +D   G       
Sbjct: 61  HISHPRSKVPKTYRAQVEGVADKAALDRLRQGVTLRDGPARAVTVEAIDEPAGLWPRDPP 120

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + + EG+NR ++++         RLIR S G + L  L  GS RE +
Sbjct: 121 IRWRANIPTSWIELTIDEGRNRMVRRMTAAVGLPTLRLIRWSIGDWTLENLPPGSWREET 180

Query: 238 KKI 240
             +
Sbjct: 181 ASL 183


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 107/227 (47%), Gaps = 6/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      R
Sbjct: 2   RLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNEL-NVHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D   R   F+ L  I   ++   GRLDI+T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDGANR-IAFELLDEIKMDKLHFAGRLDIDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V+ D +   K+GI ++      +   L+ +      +T+  
Sbjct: 120 ITSPKHKCEKTYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEVRAEREVLLTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++
Sbjct: 178 HEGKYHQVKRMFAALGNKVEGLHRERIGEIEMDESLELGEYRYLTQE 224


>gi|332976275|gb|EGK13136.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter sp.
           1501(2011)]
          Length = 234

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 69/229 (30%), Positives = 116/229 (50%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K I++A   SR+E ++++    + VN  +++  +++V +  D +   G PL  A  +
Sbjct: 2   RLDKFISKATELSRKEAKKVLHASEITVNDEVVKDGSLHVDVLNDEVMWAGEPLSVATGS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L +KP G   T   P     V D   +P + +  I+ GRLD++T G LLL++DGG  
Sbjct: 62  RYLLLYKPEGFECT-LKPKEYPMVTDLIAVPELGNLRIA-GRLDVDTTGALLLSDDGGWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICY-GDMQ----VTLDTQKGS 185
             +  P     +VY +     +D+ ++ + +KK  V QGI   GD +     TL+    +
Sbjct: 120 HRVTSPRHLHEKVYELTLAEPMDEAEQAHAVKK--VAQGILLDGDYEPTKPATLEFIDET 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +A +   L EGK  ++K++  +F  KV  L R S G   L  L  G +R
Sbjct: 178 HARLI--LTEGKYHQVKRMMGYFGNKVIELHRASIGGVTLEGLEKGESR 224


>gi|213024491|ref|ZP_03338938.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           404ty]
          Length = 182

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 83/174 (47%), Gaps = 17/174 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 10  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQAR 67

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVT 178
           L  P  +  ++Y V+  G  D   L  L+ G+ +        GI         +      
Sbjct: 68  LTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPI 127

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            + +    +W+ V L EG+N +++++         RLIR S G + L  L+  S
Sbjct: 128 RERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGLIMDS 181


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 107/227 (47%), Gaps = 14/227 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV   ++  G  SR E ++ +   +V+VNG  +      V   D I +D + L     T
Sbjct: 6   KRVDAHLSSLGYCSRSEAKKFLKIFQVRVNGERVFDTNKKVYHND-IIIDEIVLDPETLT 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L   HKP G++ +H D      ++  LP  + +    + ++GRLD +T G +LLT+DG 
Sbjct: 65  VLM--HKPSGIICSHDDVG--VLIYSLLPERWQKRNPKLSTIGRLDGDTTGAILLTDDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
           L   L  P +   ++Y V     +  ++  +   G +   I  G+ +  L  +    S +
Sbjct: 121 LNHRLTSPKSDISKLYEVTLAQPLKGNEAEIFTSGTL---ILRGEKKPLLPAKMNVISES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            V + + EGK  ++K++F     KV  L R+S+G + +  L  G  +
Sbjct: 178 VVHLEISEGKYHQVKRMFAAVGNKVTALHRVSFGKYSIENLAIGEYK 224


>gi|229916458|ref|YP_002885104.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
 gi|229467887|gb|ACQ69659.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
          Length = 237

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 57/214 (26%), Positives = 109/214 (50%), Gaps = 12/214 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR++V+ ++ Q  V+V+  L++ A  +V  S++ + V G    +    
Sbjct: 2   RIDKLLANMGYGSRKDVKILLKQGAVRVDEALVKDAKRHVDPSSEKVTVFG----EVVEY 57

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
           R ++Y   +KP G+++   D    +TV + + S ++   +  VGRLD +T GLLL+TNDG
Sbjct: 58  RPYIYFMMNKPEGVISATED-QVETTVIELIDSEYAHYDLFPVGRLDKDTTGLLLITNDG 116

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA 187
                L  P     +VY     G++  + +     G+ ++ G      ++ + ++ G  +
Sbjct: 117 AFNHALMSPRKHVDKVYIAEVDGEMTVEDIKTFANGVELEDGYTTKPARLEILSRSGRRS 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            + + L EGK  ++K++       V RL R+  G
Sbjct: 177 VIRLTLSEGKYHQVKRMVAAVGKHVERLERVQIG 210


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 119/276 (43%), Gaps = 50/276 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +A   + SRRE +  IA   VKVNG   E   V V  +D IE+D     +  
Sbjct: 10  APVRLNKRMAELKMCSRREADEWIANGWVKVNGKPAE-MGVKVTPSDRIEIDKAAKGQQA 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---TVF--------DNLPSIFSR-----VISVGRLD 115
                L +KPIG V+  ++ DG     T+F        DN    FS      +   GRLD
Sbjct: 69  NQVTILINKPIGYVSGQAE-DGHEPAVTLFTPQNRWAEDNARFFFSPQQLRGLAPCGRLD 127

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHG-----------QVDQDKLNLLK 162
           I++ GLL++T DG +AR L    +   + Y  RV ++G           ++D D      
Sbjct: 128 IDSIGLLVMTQDGRVARQLIGEDSVMEKEYLVRVAYYGPGQSAPTGQLIRMDDDDPVTQN 187

Query: 163 KGIVIQGICYGDMQ--VTLDTQKGSNA---W-----VTVGLREGKNREIKKVFEFFNWKV 212
              V        ++  ++LD Q+   A   W     +   L EGK R+I+++ E    KV
Sbjct: 188 VQAVFPPAMLARLRHGLSLDGQQLKPARVEWQNPEQLRFVLTEGKKRQIRRMCELVGLKV 247

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             L R+  G   LG L  G  R          LGPH
Sbjct: 248 VGLKRVRIGKVMLGNLPVGQWR---------YLGPH 274


>gi|167581475|ref|ZP_02374349.1| pseudouridine synthase family protein [Burkholderia thailandensis
           TXDOH]
          Length = 324

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 112/245 (45%), Gaps = 30/245 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 77  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 136

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI++
Sbjct: 137 TILLHKPVGYVSGQAE-DGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 195

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQ-------DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +          + L  L+ G+ + G
Sbjct: 196 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDG 255

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 256 VPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 311

Query: 230 AGSTR 234
            G  R
Sbjct: 312 QGQWR 316


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 67/227 (29%), Positives = 104/227 (45%), Gaps = 19/227 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +   G+ SR +V+ ++ ++ + VN  +     V +    D +   G PL   E  
Sbjct: 4   RLDKFLVETGVGSRSQVKSLLKKKAILVNQEVETSPKVQINEHKDVVTYLGKPL-TYEAF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G ++   D   ++TV D L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 63  VYYILNKPAGFLSATKDR-AQATVIDLLDETARQKDVFPVGRLDKDTRGLLLLTNNGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQV------TLDTQKG 184
             L  P     + Y  +  G   D DK +  K      GI   D Q        LD    
Sbjct: 122 HDLLSPKKHVTKEYLAKVAGIMTDADKDDFAK------GISLKDHQCLPAKLEVLDKDLS 175

Query: 185 SNAW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V++ ++EGK  ++K++      +V  L R+S GP +L   LA
Sbjct: 176 QETCVVSITIQEGKFHQVKRMVAACGKEVLELQRLSMGPLRLDPGLA 222


>gi|213028620|ref|ZP_03343067.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 122

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 75/123 (60%), Gaps = 9/123 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPL 67
           T  R++K I+ +GI SRRE +R I Q  V +NG   +RAA+   V++ D ++V+G  +  
Sbjct: 5   TSTRLNKYISESGICSRREADRFIEQGNVFING---KRAAIGDQVVAGDVVKVNGRLIEP 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D   +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGL 130
           G L
Sbjct: 120 GDL 122


>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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 71/231 (30%), Positives = 109/231 (47%), Gaps = 9/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ K IA  G  SR+EV R+  + R+  +   +  A  +V  T  +  DG PL       
Sbjct: 2   KLLKYIANLGYGSRKEVARIFREGRITNDEGEVLYADDHVQHT-AVRFDGEPLDPPPGLM 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGGL 130
           + L HKP G + +  D  GR  V+D LP+ F   S ++S VGRLD +T GLLLLT+DG L
Sbjct: 61  VML-HKPSGYICSTKDA-GR-LVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDGAL 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|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 = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/176 (28%), Positives = 83/176 (47%), Gaps = 21/176 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP G+++  SD   P  R+     LP     V + GRLD ++EGLL+LT+DG LA  
Sbjct: 4   LLNKPYGVLSQFSDRSQPPKRTLAEFGLPP---DVYAAGRLDHDSEGLLVLTDDGALAHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG-------- 184
           L  P  +  + Y V+  G    + L  L+ G+ +        QV  LD            
Sbjct: 61  LTDPRHKQPKTYWVQVEGAPQAEHLQALRDGVALNDGPTRPAQVRMLDPAPQLWPRDPPV 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 121 RVRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>gi|167919518|ref|ZP_02506609.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           BCC215]
          Length = 361

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 114 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEID-SNARAAQAAQ 172

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 173 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 231

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 232 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 290

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 291 DGVPLKPAMVSW--QNGEQ--LCFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 346

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 347 LPQGEWR 353


>gi|86132523|ref|ZP_01051117.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85817084|gb|EAQ38268.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 296

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 103/226 (45%), Gaps = 4/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +G+ SRRE +  I+  +V VNG ++      V   D +  DG  +   E   
Sbjct: 66  RLNKYIANSGVCSRREADMYISIGQVTVNGKVINEMGYQVKIEDDVRFDGRRI-NPEAKA 124

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP G  TT S+  G +TV D +  S  SR+  +GRL  N  GLLL TND  L + 
Sbjct: 125 YVLLNKPKGFATTTSNDKG-NTVMDLVAGSTKSRIQPIGRLGRNAMGLLLFTNDDELVQR 183

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
                    ++Y +     +       +++G+ I G      +++          V + +
Sbjct: 184 FTNSKKGVDKLYHIELSNNLKAADAERIREGLKIGGKTIMVEEISF-VDGAPKKEVGLRI 242

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +   N  I+ +FE  N++V R+  ++        L  G  R ++K+
Sbjct: 243 KNTGNSIIRTIFEHLNYEVVRVDCVTIAGLTKKDLPRGHWRHLTKQ 288


>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 = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/173 (29%), Positives = 90/173 (52%), Gaps = 24/173 (13%)

Query: 80  KPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           KP G ++    P+ R   ++   L +    ++++GRLD ++EGLLLLT DG ++   ++ 
Sbjct: 26  KPYGFLSQFV-PEKRKKKSLLGELFNFPENIMAIGRLDHDSEGLLLLTTDGMMS--YKIR 82

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYG---------DMQVTL------- 179
           S    + Y V+  G++    ++LL+KG  I I G  Y          D++  L       
Sbjct: 83  SKGIEKEYYVQVDGEITAQAMSLLQKGVEIAINGATYLTLPCKAFKLDVEPKLPTRGRKI 142

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            D + G  +WV++ L EGKNR+I+K+     +   RL+R+  G   + +++AG
Sbjct: 143 RDPRHGPTSWVSITLCEGKNRQIRKMTAAVGFATLRLVRVRIGDIHIDSMIAG 195


>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 = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ ++++  GI  R  V R + ++RV ++G   ++A ++   S D + +DG  +      
Sbjct: 10  RIDRLLSNLGIVERSSVPRFLNEKRVTISG---KKATLSSKASPDEVRIDGKLIENPSAL 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISV-GRLDINTEGLLLLTNDGG 129
            L L HKP G + +  +      V+D LP  F     + S+ GRLD    GL++ + DG 
Sbjct: 67  HLAL-HKPSGYICSTVNDGDHKVVYDLLPKDFQSRKPIPSIAGRLDKWVTGLVIFSQDGK 125

Query: 130 LARVLELPSTQWL-RVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
           L   +  P      + Y V    ++  D++ + + G ++++G         L+    S  
Sbjct: 126 LVERIITPKDDGCGKDYEVVLKNKLGGDEIGVFESGGLMLRGEEAPCKPAKLEILDESKN 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V V L EG+  +++++F   + K   + R   GP +LG L  G  R +++K +++
Sbjct: 186 KVKVTLFEGRYHQVRRMFAANDNKALEIHRTRIGPVELGDLPVGKWRHLTEKEIQD 241


>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 = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 108/229 (47%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSRVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL +G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLESGEYRYLTEE 224


>gi|167619584|ref|ZP_02388215.1| pseudouridine synthase family protein [Burkholderia thailandensis
           Bt4]
          Length = 364

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 110/245 (44%), Gaps = 30/245 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 117 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 176

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG +              D  P  FS      +   GRLDI++
Sbjct: 177 TILLHKPVGYVSGQAE-DGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 235

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQ-------DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +          + L  L+ G+ + G
Sbjct: 236 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDG 295

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 296 VPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 351

Query: 230 AGSTR 234
            G  R
Sbjct: 352 QGQWR 356


>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 = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 87/179 (48%), Gaps = 16/179 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  ++HKP G+++  +    +     +   +   V  VGRLD ++EGLLLLTN+G L   
Sbjct: 6   RYIIFHKPYGVLSQFTQESPKHITLKDYIDV-PDVYPVGRLDWDSEGLLLLTNNGRLQHR 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------------CYGDMQVTL 179
           L  P     R Y V+     D++ ++ L+ G+ I+                  GD Q  +
Sbjct: 65  LSDPRFGHERTYWVQVERIPDEEAISKLQTGVEIRDYRTRPAKVGLLPEYPPVGDRQPPI 124

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K    AW+ + L EGKNR+++++     +   RL+R+S G  +L  L  G  R+++
Sbjct: 125 RFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVSIGHLRLDGLALGEWRDLT 183


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/236 (23%), Positives = 110/236 (46%), Gaps = 3/236 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +R+ V+G +++  AV +     ++ DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRALVARELRARRITVDGEVVKNGAVKLAVEQEVKFDGNLLAQQNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +   + + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYNLHAAGRLDIDTTGLVLMTDDGQWSHRV 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  +       G+ +       +   +  +K ++  V + + 
Sbjct: 122 TSPKHHCEKTYLVTLEHSLAANTAQRFAAGVQLHN--EKSLTRPVQLEKINDRQVRLAIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPHL 249
           EG+  ++K++F     +V  L R   G   +   LA G+ R ++ + +     PHL
Sbjct: 180 EGRYHQVKRMFAAIGNRVIALHRERIGTIVMDKDLASGAYRPLTAEEIASVGAPHL 235


>gi|304395011|ref|ZP_07376895.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304357264|gb|EFM21627.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 292

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 113/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA+V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRASVGAQVFAGDVVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G++TT    +G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIITTME--EGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ +     G +      +K +     
Sbjct: 123 VNKILRAGNNHEKEYVVTVDKPITDEFIAGMSAGVPM----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCKHFGFEVTKLERTRIMNVNLKGLPLGEWRDLTDDELVE 231


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 110/238 (46%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  V  V G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAVTDVQGEVLY--ADDQVEHDAIRIDGEPLDPPPGF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SR---VISVGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F SR   +  VGRLD +T G+LL+T+DG 
Sbjct: 60  SLLL-HKPSGYTCSTKD-TGR-LIYELLPPRFRSRAPVLAPVGRLDRDTSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY V     +  D+  L   G ++++G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYEVSLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGPRQAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L AG  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVAALHRSRIGGLSLDALPAGQWRALDASDLEVLFG 232


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 102/219 (46%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   ++ + +  I    VK+N  ++      V + + + +D   L      R
Sbjct: 2   RLDKFICKSTNLNKEQAQAQIQAGIVKINNDIVCDIKAQVHANNQVRLDN-RLLYLRPFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTN 126
             L+HKP   + ++ D        +N PS+F+         +  VGRLD++T G++L+T+
Sbjct: 61  YILFHKPANTICSNLD--------ENYPSLFNFLDIEYLDELHIVGRLDVDTTGMVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  Q ++ YRV     +D+  +   K G+ +QG     +   L      N
Sbjct: 113 DGHWSFNITRPEKQCVKEYRVSLSQTLDESAIEQFKYGLKLQGEAELTLPARLTFIDDKN 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V +G+ +GK  ++K++F     +V RL R + G   L
Sbjct: 173 --VVLGITQGKFHQVKRMFAALGNRVVRLHRQAIGSVTL 209


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT 73
           R+ ++++  G+  R  V + +  +RV V G  +  A   N+     I++DG P+   E  
Sbjct: 10  RIERILSNLGVCERSRVPQFLRDKRVTVLGKKVTPATKANIKD---IQIDGEPIENGETL 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISV-GRLDINTEGLLLLTNDGG 129
            + + HKP G + +  +      ++D LP  F +    +S+ GRLD    GL++L+ DG 
Sbjct: 67  HIAV-HKPSGYICSTVNDHDHKIIYDILPKEFFKRKPTLSIAGRLDKWVTGLVVLSQDGK 125

Query: 130 LA-RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQG---ICYGDMQVTLDTQKG 184
           L  R++        + Y V    ++  D+  + + G I+++G    C       LD +K 
Sbjct: 126 LVDRIISPKDDGCGKDYEVVLKDKLVGDEAEVFESGKIMLRGESTPCKPAKLQVLDKEKN 185

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               V V L EG+  +I+++F     K   + R   GP +LG L  G  R ++++ L+E
Sbjct: 186 K---VKVTLYEGRYHQIRRMFASTENKAVEIHRTRIGPVELGDLGLGKWRHLTEQELKE 241


>gi|167646666|ref|YP_001684329.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167349096|gb|ABZ71831.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 245

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 110/225 (48%), Gaps = 14/225 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----VDGVPLRKA 70
           R+ +++A  G  SRR+V+ +++  +V ++G+ ++ A   +  T  +     + GVP+   
Sbjct: 8   RLDRLLANLGYGSRRDVQALVSTGKVTLDGVAIKDAGQKIAVTADLPLRMRIRGVPVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTN 126
               L L HKP+G+V +H + DG   ++D LP  +      + SVGRLD +T GLLL+T+
Sbjct: 68  APLVL-LMHKPLGVVCSHRE-DGER-IYDLLPKRWQIRDPALSSVGRLDKDTSGLLLITD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     +VYR      ++  +      G ++++G     +  TLD     
Sbjct: 125 DGDFLHRVISPKRHVPKVYRATLDRPLNGTEGAAFASGALMLEGEEKPLLPATLDVLGDH 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            A +T+   EG+  +++++F      V  L R   G   L   LA
Sbjct: 185 EARLTI--TEGRYHQVRRMFAAVGNHVVGLHRERIGGIDLPEDLA 227


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 118/242 (48%), Gaps = 16/242 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLRKAE 71
           R+   ++R G  SRR+  ++I   RV+VNG  +      +     I +DG   VP  K  
Sbjct: 2   RLDTFLSRFGGISRRQSRKLIKTGRVEVNGAKIRNPEFKIPENSSIFLDGNRIVPYGK-- 59

Query: 72  RTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGG 129
              L++  +KP+G V + S  +G S V+D +  +FS  +S+ GRLD N+ GLLLL+NDG 
Sbjct: 60  ---LYIAMNKPVGYVCSKSRTEGLS-VYDLINEVFSSKLSIAGRLDKNSRGLLLLSNDGN 115

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P  +  + Y V+   ++  ++L +L + +    I  G+       Q       
Sbjct: 116 FVHEIISPRKKIEKEYIVKVEEKILPEQLQILLQHV---DIGKGEYARAESVQFIDIVTF 172

Query: 190 TVGLREGKNREIKKVFE-FFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           ++ L EGK  EI+++ +      V  L RI  G + L G L  G  R ++++ ++   G 
Sbjct: 173 SIVLTEGKYHEIRRMVKSALKNNVVDLKRIRIGGYHLPGDLHEGEWRILTEEEIKAATGK 232

Query: 248 HL 249
            L
Sbjct: 233 IL 234


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 54/180 (30%), Positives = 90/180 (50%), Gaps = 19/180 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR+T+   +P  F+ V + GRLD ++EGLL+L N+G L   
Sbjct: 25  RVVLFNKPFDVLPQFTDAAGRTTLKAFIP--FTDVYAAGRLDRDSEGLLVLNNEGKLQAQ 82

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK-LNLLKKGIVIQ-GICYGDMQVTLDTQKG------- 184
           L  P  +  +VY V+  G V QD+ L  L+ G+ ++ G     +   +D  +        
Sbjct: 83  LTQPGKRIGKVYFVQVEG-VPQDRDLTPLRHGVTLKDGPTLPAIVERVDEPQWLWPRNPP 141

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + L EG+NR+I+++     +   RLIR S G   LG L  G  + + 
Sbjct: 142 IRERKSIPTTWLKITLFEGRNRQIRRMTAHIGFPTLRLIRYSMGNLSLGELQPGEWKNLD 201


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 52/184 (28%), Positives = 87/184 (47%), Gaps = 27/184 (14%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA--- 131
           L++KP  ++   +D D  ++    L    S   V  VGRLD ++EGLLLLTN G +    
Sbjct: 7   LFYKPYDVLCQFTDNDPTTSPRKTLKDFISIPGVYPVGRLDRDSEGLLLLTNQGKIQHRL 66

Query: 132 --RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---- 185
             R    P T W++V  +      D+  LN L+ G+ I+       QV L   + +    
Sbjct: 67  SHRKFNHPRTYWVQVEHI-----PDETALNALRAGVQIKDYQTRSAQVQLLPTEPALPPR 121

Query: 186 -----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       AW+ + L EG+NR+I+++     +   RL+R++   F+L  L  G  R
Sbjct: 122 DPPIRFRKTVPTAWLEITLTEGRNRQIRRMTAAVGFPTLRLVRVAIADFRLDGLKPGQWR 181

Query: 235 EVSK 238
           ++++
Sbjct: 182 DLTQ 185


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 113/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +RA+V   V + D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRASVGAQVFAGDVVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L   +KP+G++TT    +G      +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVLIALNKPVGIITTME--EGERDNISDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ +     G +      +K +     
Sbjct: 123 VNKILRAGNNHEKEYVVTVDKPITDEFIAGMSAGVPM----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E
Sbjct: 179 ITLVQGLNRQIRRMCKHFGFEVTKLERTRIMNVNLKGLPLGEWRDLTDDELVE 231


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 88/182 (48%), Gaps = 21/182 (11%)

Query: 79  HKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G+++  SD   P  R+     LP    +V + GRLD ++EGLLLLT+DG LA  L 
Sbjct: 42  NKPYGVLSQFSDRSTPPKRTLAEFGLPP---QVYAAGRLDHDSEGLLLLTDDGPLAHRLT 98

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTLDTQKG---- 184
            P  +  + Y V+  G  D  +L  L  G+++         +   +   TL  +      
Sbjct: 99  DPRHKQPKTYWVQVEGDPDTSQLQALCDGVLLNDGPTRPANVRRLECAPTLWPRDPPVRV 158

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +AW+ V + EG+NR+++++         RL+R++ G + L +L  G  R    + 
Sbjct: 159 RKTVPDAWLEVQITEGRNRQVRRMTASVGLPTLRLVRVAIGAWSLASLQPGQWRVDDARA 218

Query: 241 LR 242
           +R
Sbjct: 219 VR 220


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 113/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 376 RLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQV 435

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D+ P  FS      +   GRLDI++
Sbjct: 436 TILLHKPVGYVSGQAE-DGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 494

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 495 TGLLVLTQNGVVAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 554

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 555 VALKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 610

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 611 QGQWRYLS 618


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 54/182 (29%), Positives = 85/182 (46%), Gaps = 21/182 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R  L++KP  +++  +D D     R T+ D +P     V SVGRLD+++EGLLLLT+D  
Sbjct: 4   RYILFYKPYNVLSQFTDRDSHTPSRQTLKDYIP--IPSVYSVGRLDLDSEGLLLLTDDRK 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------- 181
           L   L  P     R Y V+         L  L++GI IQ       +V L          
Sbjct: 62  LKYRLGQPEFAHPRTYWVQVERIPTTQALEQLRRGITIQNYRTRTARVQLLLTEPLLPPR 121

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  Q    AW+ + L EG+NR+++++     +   RL+R++     L +L  G  R
Sbjct: 122 IPPIRFRQNVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRVAIAHLTLNSLQPGDWR 181

Query: 235 EV 236
           ++
Sbjct: 182 DL 183


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 56/219 (25%), Positives = 101/219 (46%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   +R E  ++I    + VN  ++   A  V   + + +DG+ L  A  +R
Sbjct: 6   RLDKFICKSTDLTRTEATQLINAGNIIVNNEVVSNEATQVHENNDVLLDGIKL-IARASR 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             L HKP+  + ++ D        +  PS+F+ +           GRLD +T GL+L+T+
Sbjct: 65  YILMHKPLNTICSNID--------EVYPSLFNYIDVEKADDLHIAGRLDADTTGLVLITD 116

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P+ Q  + YRV     + +D      +G+ +QG     +   LD    + 
Sbjct: 117 DGRWSFNIITPNKQCEKTYRVGLRNPIAEDAAEKFAQGVKLQGEKQLTLPAKLDVVTSNE 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +T+   EGK  ++K++F     +V  L R   G  +L
Sbjct: 177 VLLTI--TEGKYHQVKRMFSAIGNRVVTLHREQIGNIKL 213


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 50/182 (27%), Positives = 89/182 (48%), Gaps = 25/182 (13%)

Query: 73  TRLWLYHKPIGLVTTHSDP----DGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           + L L++KP  ++   +D     D R T+ D  N P  ++     GRLD ++EGLLLLTN
Sbjct: 2   SELLLFNKPFNVLCQFTDEPEFKDQRQTLADFINQPGFYA----AGRLDRDSEGLLLLTN 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG- 184
           DG L + +  P  +  + Y V+  G ++++ +  L++G+ ++ G+        +   K  
Sbjct: 58  DGKLQQHIANPKHKQPKTYLVQVEGDINKEAIKQLQQGVTLKDGLTRPAKARKIPEPKWL 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                          +WV + + EGKNR+++++     +   RLIR   G +QL  L  G
Sbjct: 118 WPRNPPIRERKNIPTSWVELIITEGKNRQVRRMTAAVGFPTLRLIRTQIGDYQLKNLQPG 177

Query: 232 ST 233
            +
Sbjct: 178 ES 179


>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 = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLDI+T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDIDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRKRIGQITLDETLEPGEYRYLTEE 224


>gi|186475366|ref|YP_001856836.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184191825|gb|ACC69790.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 234

 Score = 70.5 bits (171), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 50/157 (31%), Positives = 79/157 (50%), Gaps = 5/157 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  V+   G  SRR+   MIA  RV + G  L+   ++V +   + EVDG      ER  
Sbjct: 3   LESVLFSQGFGSRRQCRAMIADGRVSIGGATLDDPDIDVDAKALVFEVDGTVWPYHERAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  DP    +VF+ LP+ F+   +  VGRLD +T GLLLL++DG    
Sbjct: 63  V-LLNKPAGYECS-RDPQHHLSVFNLLPAQFATRGIQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
               P  +  + Y       +D  +L  L++G+++ G
Sbjct: 121 AYTSPKRKVPKRYLATTRHPLDDAQLAALREGVLLHG 157


>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 = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 57/226 (25%), Positives = 102/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  ++ A  ++ S     +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCIDDADADIHSASVHTLDIDGKAVTVIPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPADYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLVTNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V      D      LK G+++    + +C  D  +       S
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPADGILCETLKNGVLLHDENETVCAADANLE------S 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 175 PTTLLLTITEGKYHQVKRMIAAAGNRVQHLHRRQFAHLETENLKPG 220


>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 = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 44/174 (25%), Positives = 83/174 (47%), Gaps = 16/174 (9%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P   A+  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLLT
Sbjct: 39  PAIAAQDIKIVLFNKPFDVLCQFTDDANRKTLAEFIP--IKEVYAAGRLDRDSEGLLLLT 96

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           N G L   L  P  +  + Y V+  G+   + +  L  G+ ++       +V++ ++   
Sbjct: 97  NCGKLQNTLTAPGKKTSKTYWVQVEGEPSSESIAALCTGVELKDGLTLPAKVSIISEPTV 156

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                           W+++ + EG+NR+++++         RLIR S G + L
Sbjct: 157 WTRNPPVRERKLIPTTWLSITISEGRNRQVRRMTAHIGHPTLRLIRYSIGKYTL 210


>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 = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 117/229 (51%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           RV K+I  A + +R+ +++   +  + +NG +++ ++V V  + D +   G  +   E  
Sbjct: 4   RVDKMIGNANLDTRKNIKKNAKKGGLVINGEIIKDSSVKVDPNIDEVIYMGELVDYFENI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +K  GL+   ++ DG  TV  +L   +  +     GRLD +T GLLL++ DG   
Sbjct: 64  YIMM-NKREGLICQSNELDG--TVMSDLDEFYLNLDLAIAGRLDKDTTGLLLMSTDGKFI 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P++   + Y V    ++D D + + K+G+ I+   Y      L+  +   A+V V
Sbjct: 121 HRVISPNSNIWKKYEVETSKKIDPDLVEIFKEGVYIKEDDYYARSAKLEIIEDKKAYVYV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
              EGK   +K++F   + +V +L R++ G  QL  TL  G  RE++++
Sbjct: 181 --TEGKFHLVKRLFSNNDNEVVKLKRLAIGKLQLDKTLNPGDYRELTQE 227


>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 = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 109/236 (46%), Gaps = 19/236 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           ++ K IA  G  SR+EV R+    R+  NG         + + DH++      DG PL  
Sbjct: 2   KLLKYIANLGYGSRKEVARIFRDGRI-TNG-----EGEVLYADDHVQHTAVRFDGEPLDP 55

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLT 125
                + L HKP G + +  D  GR  V+D LP+ F   S ++S VGRLD +T GLLLLT
Sbjct: 56  PPGLMVML-HKPSGYICSTKDA-GR-LVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLT 112

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG L   +  P T   +VY       +  D+  L   G ++       +Q  +    G 
Sbjct: 113 DDGALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP 172

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 173 -CQVRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 51/206 (24%), Positives = 106/206 (51%), Gaps = 6/206 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++     +R E++ ++   RV +NG L +   +     + + +DG+     +   
Sbjct: 2   RIEKWLSDVTDYTRSEIKNLLKNNRVYINGRLYDET-IKYNEFNSLRIDGIDYATDKYVY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L +KP G +T++ D +   +VF+ +      +I+ GRLD++TEGLL+L+++  L   L
Sbjct: 61  IML-NKPQGYITSNKD-ELYPSVFNLIDVPRKNLIAYGRLDVDTEGLLVLSDNHKLCHEL 118

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+   Q++ + +++ K+G  I G     +   L+       ++T+   
Sbjct: 119 LAPKKHVFKKYLVQVDKQLEPNLIDIFKQGFSI-GEDKNTLPSKLEIIDNFTCYLTIS-- 175

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISY 220
           EGK  ++K++F+   + V  L R+S+
Sbjct: 176 EGKFHQVKRMFKTNGYNVIFLKRVSF 201


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 110/248 (44%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 99  RLSKLMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAVQASQV 158

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HK +G V+  ++ DG                D+    FS     ++   GRLDI++
Sbjct: 159 TVLIHKTVGYVSGQAE-DGYQPAITLVTPENRWEGDHSDIRFSVAHLRQLAPAGRLDIDS 217

Query: 119 EGLLLLTNDGGLARVL-----ELPSTQWLRV----YRVRFHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L     E+     +RV    + V        + L LL+ G+ +  
Sbjct: 218 TGLLVLTQDGRIAKQLIGGHSEIDKEYLVRVAYGEHTVDVESHFPAESLELLRHGLSLDD 277

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +     QV+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 278 VPLKPAQVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVVLGALP 333

Query: 230 AGSTREVS 237
            G  R ++
Sbjct: 334 PGQWRYLA 341


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 63/227 (27%), Positives = 105/227 (46%), Gaps = 20/227 (8%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           ++ +  + +  E   +I    V+VN  ++      V   D I V G    KA  ++ ++Y
Sbjct: 16  ILMKNNLGNMNECRTLIKHGFVEVNNQVINDHRYVVHDDDKINVFG----KAIHSQPFVY 71

Query: 79  H---KPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           +   KP G +  + D +    V      +  R   I VGRLD +T G LLLTND  + + 
Sbjct: 72  YMMNKPKGYICANYDKNHLCVV-----DLIERNDCICVGRLDKDTTGFLLLTNDKSIVKA 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L LP     + Y V     +D++ +   + GIVI Q IC   +   L+       ++T  
Sbjct: 127 LLLPQNHQPKTYLVTTRFPIDENSIYRFEMGIVIDQDICC--LPAQLELINTHQCYLT-- 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           L EGK  ++KK+F     +V  L RI++    L  +L  G  R++++
Sbjct: 183 LHEGKYHQVKKMFLSCQNEVVDLKRIAFAGLVLDASLGYGEYRQLNQ 229


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLDVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 51/161 (31%), Positives = 83/161 (51%), Gaps = 10/161 (6%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L++ +KP G + T SD  GR TV+D LP  +     + +GRLD++++GLLL T +G ++
Sbjct: 13  KLFVLNKPKGYLVTRSDDLGRKTVYDLLPDWAFNEGWMPIGRLDLDSKGLLLFTTNGHIS 72

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  +VY +   G V  + +    KG+         ++V      G+   ++V
Sbjct: 73  NALTTPK-KCTKVYEIWVRGHVMDEHIAEALKGVQTSQGLLKALEVKKIGMGGAKTKLSV 131

Query: 192 GLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQL 225
            + EGKNR I+++F            KV  L RIS G F+L
Sbjct: 132 VIDEGKNRHIRRLFGALKDPKFGTPLKVLELNRISIGDFKL 172


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 115/248 (46%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 2   RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQV 61

Query: 75  LWLYHKPIGLVTTHSDPDGR--STVF---------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG   ++V          D  P  FS      +   GRLDI++
Sbjct: 62  TILLHKPVGYVSGQAE-DGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            G+L+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 121 TGMLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLLDIDQHFPAESLAKLRHGLELDG 180

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 181 VALKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 237 QGQWRYLS 244


>gi|257138757|ref|ZP_05587019.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
          Length = 547

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 113/246 (45%), Gaps = 32/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 300 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 359

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI++
Sbjct: 360 TILLHKPVGYVSGQAE-DGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 418

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVIQ 168
            GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ + 
Sbjct: 419 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTTDIERHFPAESLAKLRHGLELD 477

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L
Sbjct: 478 GVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGAL 533

Query: 229 LAGSTR 234
             G  R
Sbjct: 534 PQGQWR 539


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 100/224 (44%), Gaps = 3/224 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR  V R +   RV V+G++    ++ V     +  +G  L      R
Sbjct: 2   RLDKFISQQLGISRSLVIRELRASRVTVDGVVSRSGSLQVTPDQEVAYEGNVLAFITGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSTDDPDHATILYFIDEPMAEKLHAAGRLDLDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +         +GI++ G    D+      +      V + + 
Sbjct: 122 TSPRHHCEKSYLVTLEQPLAPQTAAQFAEGILLNGET--DLTKPAQLEAFDEHHVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           EG+  ++K++F     +V  L R   G   L   LA G  R +S
Sbjct: 180 EGRYHQVKRMFAAVGNRVVGLHRERIGAIALDAALAPGEYRALS 223


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 48/186 (25%), Positives = 90/186 (48%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P    E  ++ +++KP  +++  +D   R T+ D +      V + GRLD ++EGLL+LT
Sbjct: 22  PRPAPEDRKVLIFNKPFDVLSQFTDDQHRQTLADFI--SVKDVYAAGRLDRDSEGLLILT 79

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           NDG L   L  P ++  + Y V+  G   +D L  L++G+ ++       +V + T+   
Sbjct: 80  NDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLEKLRQGVELKDGMTLPAKVEVMTEPEL 139

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                           W+ V + EG+NR+++++     +   RLIR S G + +  +   
Sbjct: 140 WERNPPVRFRAAIPTTWIAVTIIEGRNRQVRRMTAHIGFPTLRLIRYSMGDWTIKDVPHR 199

Query: 232 STREVS 237
             +EV+
Sbjct: 200 EWKEVT 205


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 312 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 370

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 371 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 429

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 430 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 488

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 489 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 544

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 545 LPQGEWR 551


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 58/220 (26%), Positives = 96/220 (43%), Gaps = 21/220 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +  ++   G  SRR+   ++A  RV + G + +    +   TD +E D       + TR 
Sbjct: 3   LETILFSQGFGSRRQCRALVAAGRVAIGGAICDDPEQS-FPTDGLEFD------VDGTR- 54

Query: 76  WLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLT 125
           WLY        +KP G   +  +P    +VF  LP   +   V  VGRLD +T GLLLL+
Sbjct: 55  WLYRQHAYLVLNKPAGYECSR-EPQHHESVFALLPPQLATRGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L  L+ G+++ G         LD Q   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYLATLKHPLDAAQLTALRDGVLLHG--EPKPIAALDAQARG 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              + + ++EGK  ++K++      +  +L R   G F L
Sbjct: 172 THQLEMTVQEGKYHQVKRMIAAAGNRCEQLHRERIGGFAL 211


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 312 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 370

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 371 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 429

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 430 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 488

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 489 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 544

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 545 LPQGEWR 551


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/227 (26%), Positives = 102/227 (44%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  ++I    V VN ++ +  +V V     +E  G  + K     
Sbjct: 2   RLDKYLCDALGATRKEATKIIKSGDVTVNDVVQKSGSVKVTDDCTVEWQGREIHKPGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+ KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLF-KPDGFVCSHEDG-FNQTAFMLLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D       GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADPVQDDYAEKFANGIQLRNEKDLTLPAQMELVDAQENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  +L  TL  G  R ++++
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGDIELCDTLEPGEYRYLTQQ 226


>gi|325181473|emb|CCA15907.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 241

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 103/222 (46%), Gaps = 27/222 (12%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V++  +P  +  +               +   P   S++   GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGDMQV- 177
           T DG LA+ +  P+    + Y VR    +++D       ++ L++G +   ICY    V 
Sbjct: 121 TQDGVLAKQILDPNGGVEKEYLVRVDMDLERDTKQAEEVVDKLREGFIWNDICYRARSVR 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            L+  +     +   L EGK R I+ + E    KV  L R++
Sbjct: 181 VLNANQ-----LQFILTEGKKRHIRYMCEAVGIKVIALKRMN 217


>gi|299472407|emb|CBN77595.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 390

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 81/237 (34%), Positives = 114/237 (48%), Gaps = 21/237 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPLRK 69
           R+SK++A   I +R EV+ ++ + RVKV+G +++     +     IEV+G     VPL  
Sbjct: 137 RLSKLLADRAIGTRSEVDTLVRRGRVKVDGAVVKSPKTKLPVDCVIEVNGEVHGPVPL-- 194

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
                L  +HKP G++TT SD   R  + D LP S+  +   VGRLD ++ GLLLL++DG
Sbjct: 195 -----LVAFHKPKGVITTLSDDWDREDLSDVLPKSLLLKHHPVGRLDADSSGLLLLSSDG 249

Query: 129 GLARVLELPSTQWLRVY----RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
            L   L  P  +  R Y     V   G+   D L    K    +GI   D     D    
Sbjct: 250 ALTHRLLNPRFEVEREYVASVDVPPEGEEPGDSLVTALK----EGITTADGVYKADVPAI 305

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           S   V V +REGKNR ++++     + V  L R  YG   LG L  G    VS   L
Sbjct: 306 SGRDVGVVVREGKNRMVRRMLANAGYPVLELRRERYGKILLGDLPEGEHVPVSGDAL 362


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 107/214 (50%), Gaps = 10/214 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   ++R G  SR E  R+I    V +NG+L    +  V  TD + VDG PL       
Sbjct: 2   RLDAFVSRFGRFSRSESRRIIRSNGVSLNGVLTNNPSEVVDETDTVIVDGRPLEAFWNVY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
           + L +KP G V +    +GRS VF+ + + FS  +S  GRLD +  GLL+L+NDG     
Sbjct: 62  IAL-NKPEGYVCSRERSEGRS-VFELIDANFSADLSTGGRLDKDATGLLILSNDGKFIHE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           +  P     + Y V    ++ + +++++ +G+ I     G+ + +  T  ++  +  + +
Sbjct: 120 VISPRKLVEKEYLVETAKEITKKEISMISQGLFI-----GNNEFSKPTHVEQIDHFHMRI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            L EG+  E+K++      KV +L R   G + L
Sbjct: 175 VLTEGRYHEVKRLVSASGNKVIQLHRRRIGSYCL 208


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 111/230 (48%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTD---HIEVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  A+  + +  D    + V G  L   
Sbjct: 5   RLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEALDPL 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP+G+  +H +      V+  LP  + R    + +VGRLD  T GLLL+T+
Sbjct: 65  PGVCLML-HKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLLLMTD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T   +
Sbjct: 122 DGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMETDDPT 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           +  VT  L EG+  +++++F      V+ L R   G   L   L AG  R
Sbjct: 182 HCTVT--LHEGRYHQVRRMFAALGNHVDALHRDRVGGLVLPADLPAGEFR 229


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 113/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 403 RLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQV 462

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D+ P  FS      +   GRLDI++
Sbjct: 463 TILLHKPVGYVSGQAE-DGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 521

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 522 TGLLVLTQNGVIAKQLIGEQSDIDKEYLVRVRFGERLIDIDQHFPAESLAKLRHGLELDG 581

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E     V  L R+  G   LG L 
Sbjct: 582 VALKPALVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 637

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 638 QGQWRYLS 645


>gi|167903268|ref|ZP_02490473.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei NCTC 13177]
          Length = 444

 Score = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 197 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 255

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 256 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 314

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 315 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 373

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 374 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 429

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 430 LPQGEWR 436


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 102/220 (46%), Gaps = 12/220 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   +R E   +I   +V VNG  +   +  V   +HI ++G     A  +R
Sbjct: 2   RLDKFLCKSTQLTRHEACELILAGKVLVNGESVVSPSAQVHENNHIRLEGGQRLTARASR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP   ++++ D D  S   F NL    S +   GRLD +T GLLL+T+DG  +  
Sbjct: 62  YIMLHKPADTLSSNVDGDHPSVFNFINLEHT-SELHIAGRLDADTTGLLLITDDGRWSFN 120

Query: 134 LELPSTQWLRVYRVRFH--------GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +  P     +VYRV           G++D +     K+G+ +QG     +   L+     
Sbjct: 121 VFNPKYHCEKVYRVYLRDSIEGEIAGEIDAELKARFKQGLDLQGEQALTLPAKLEFVSPK 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              +T+   EG+  ++K++F     +VN L R   G  +L
Sbjct: 181 EVLLTI--TEGRYHQMKRMFARVGNRVNALHREQVGKIKL 218


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 338 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 396

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 397 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 455

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 456 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 514

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 515 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 570

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 571 LPQGEWR 577


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 113/246 (45%), Gaps = 32/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 310 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 369

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDINT 118
             L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI++
Sbjct: 370 TILLHKPVGYVSGQAE-DGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDS 428

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVIQ 168
            GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ + 
Sbjct: 429 TGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTTDIERHFPAESLAKLRHGLELD 487

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L
Sbjct: 488 GVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGAL 543

Query: 229 LAGSTR 234
             G  R
Sbjct: 544 PQGQWR 549


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 89/175 (50%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  +D +GR T+ D +     RV + GRLD+++EGLLLLT+ G L   L  
Sbjct: 4   LFNKPYNVLTKFTDAEGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHELTD 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYG----DMQVTLDTQ 182
           P  +  + Y V+  G   + +L  L++G+ ++           I Y     + +  +  +
Sbjct: 62  PDNKAYKTYVVQVEGVPTKSQLKQLEQGVALKDGLTLPAKVKRIPYPKWLWEREKPIRIR 121

Query: 183 KGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           K    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R V
Sbjct: 122 KNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGEYHIADLKPGQYRIV 176


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 109/247 (44%), Gaps = 28/247 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I Q  V V+G  ++     V     IE+D           
Sbjct: 2   RLSKRMSELGLCSRREADEWIEQGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQV 61

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 62  TILLHKPVGYVSGQAEDGYEPAAVLITRANQWSGDRSQIRFSPQHLHALAPAGRLDIDST 121

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQ----VDQ----DKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR  +G+    +DQ    + L  L+ G+ + G+
Sbjct: 122 GLLVLTQNGRIAKQLIGEQSDIDKEYLVRVRYGEHLIDIDQHFPAESLAKLRHGLELDGV 181

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 182 PLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCEMVGLEVIGLKRVRMGRVMLGALPQ 237

Query: 231 GSTREVS 237
           G  R +S
Sbjct: 238 GQWRYLS 244


>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 = 70.1 bits (170), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 54/185 (29%), Positives = 86/185 (46%), Gaps = 21/185 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R  L++KP  +++  +D D     R T+ D +P     V SVGRLD+++EGLLLLT+D  
Sbjct: 4   RYILFYKPYNVLSQFTDRDSHAQSRQTLKDYIP--IPSVYSVGRLDLDSEGLLLLTDDRK 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------- 181
           L   L  P     R Y V+         L  L++GI IQ       +V L          
Sbjct: 62  LKYRLGQPEFAHPRTYWVQVERIPTTQALEQLRQGITIQNYRTRTARVQLLLTEPLLPPR 121

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  Q    AW+ + L EG+NR+++++     +   RL+R++     L +L  G  R
Sbjct: 122 IPPIRFRQNVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRVAIAHLTLNSLEPGHWR 181

Query: 235 EVSKK 239
           ++  +
Sbjct: 182 DLHPQ 186


>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 = 70.1 bits (170), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 112/249 (44%), Gaps = 33/249 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D     + ++  
Sbjct: 46  RINKRIADMGMCSRREADEWVENGWVTVNGEVATMGQ-NVVPGDRIEIDQKAQERQDQQV 104

Query: 75  LWLYHKPIGLVTTHSDPDG-----------------RSTVFDNLPSIFSRVISVGRLDIN 117
             L +KP+G V+  ++ DG                 RS    N  S    +   GRLDI+
Sbjct: 105 TILLNKPMGYVSGQAE-DGHEPAVVLITNENRWNEDRSKTRFNF-SQLKGLAPCGRLDID 162

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQD--------KLNLLKKGIVIQ 168
           + GLL+LT DG +AR +    ++  + Y VR   G  D D        KL LL+ G+ + 
Sbjct: 163 SVGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRHGLSLD 222

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  QV  D Q      +   L EGK R+I+++ E    KV  L RI  G   LG L
Sbjct: 223 EQPLKPAQV--DWQNPEQ--LRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGVTLGNL 278

Query: 229 LAGSTREVS 237
             G  R ++
Sbjct: 279 PTGQWRYLA 287


>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 = 70.1 bits (170), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 324 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 382

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 383 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 441

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 442 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 500

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 501 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 556

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 557 LPQGEWR 563


>gi|167894879|ref|ZP_02482281.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
          Length = 307

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 60  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEID-SNARAAQAAQ 118

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 119 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 177

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 178 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 236

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 237 DGVPLKPAMVSW--QNGEQ--LCFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 292

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 293 LPQGEWR 299


>gi|330722223|gb|EGH00111.1| Ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium IMCC2047]
          Length = 220

 Score = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 45/174 (25%), Positives = 85/174 (48%), Gaps = 16/174 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP  +++  +D  GR T+ D +      V + GRLD N+EGLLLLT++G L   +
Sbjct: 4   LILFNKPYDVLSQFTDDKGRPTLADFITQ--KGVYAAGRLDYNSEGLLLLTDNGQLQHHI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  + Y V+  G + +  +  L+ GI ++       +V    +            
Sbjct: 62  AHPRHKQEKTYWVQVEGDISEQAVKQLRTGIQLKDGLTRPAKVQKLPEPELWPRNPPVRF 121

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 +WV + + EG+NR+++++     +   RL+R++ G ++L  L  G  +
Sbjct: 122 RAEIPTSWVEIKISEGRNRQVRRMTAAVGFPTLRLVRVAIGNWELENLQPGEYK 175


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 117/239 (48%), Gaps = 30/239 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++     SR+E++ M+    VKV  + ++ + V +  + D I V+G  +   E  
Sbjct: 2   RLDKFLSNLNYGSRKEIKLMVKNGLVKVGNLTVKSSDVKIDPNYDKIFVNGTEVIYKENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLL 124
            L  Y KP G +++H     ++ ++   PS+F  + +          GRLD ++EGL++L
Sbjct: 62  ILSFY-KPAGYLSSH-----KAEIY---PSLFELIGAPYNQYDLKIAGRLDYDSEGLVIL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQ---GICYGDMQVTLD 180
           T  G L   +  P  +  +VY  +     ++  KL LL +G+ I    G+ Y  + + LD
Sbjct: 113 TTSGDLVHQITHPKKKIRKVYEAKLDKHFNESSKLKLL-QGVEIMGEDGMPY--IGIALD 169

Query: 181 TQ-KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              K   A++T+   EGK  ++KK+F    + V  L RI  G   L  L  G+ +E+ +
Sbjct: 170 LHYKEDVAYITI--DEGKFHQVKKMFLEVGFLVTNLKRIQIGALTL-DLEPGTYKEIEE 225


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 91/185 (49%), Gaps = 21/185 (11%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLL 123
           P+  A R ++ L++KP  +++  +D D R T+ D  ++P +++     GRLD ++EGLLL
Sbjct: 39  PVSDATR-KILLFNKPFNVLSQFTDQDNRQTLKDYIDIPEVYA----AGRLDRDSEGLLL 93

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG L   +  P+ +  + Y V+  G+  +  L  L+ G+ ++        + L  Q 
Sbjct: 94  LTNDGKLQAKITEPNAKTSKTYWVQVEGRPTEADLQKLRDGVNLKDGLTLPAGIELMEQP 153

Query: 184 G--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                             W+++ + EG+NR+++++     +   RLIR   G + +  + 
Sbjct: 154 AIWARVPPIRERANIPTTWLSITISEGRNRQVRRMTAHIGFPTLRLIRYRIGDWTIDDID 213

Query: 230 AGSTR 234
            G  +
Sbjct: 214 NGQYK 218


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 116/240 (48%), Gaps = 9/240 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E  
Sbjct: 3   RLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLV-YESF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  VYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-GDMQVTLDTQKGSNAWV 189
             L  P     + Y  +  G + +   +   +GI ++   C    ++V     +   + V
Sbjct: 121 HDLLSPKKHVTKEYLAKVVGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQRTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGPH 248
            + ++EGK  ++K++       V  L R+S GP +L   LA G  R ++ + L + L P+
Sbjct: 181 KITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEEL-QSLAPY 239


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 228 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 286

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 287 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 345

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 346 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 404

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 405 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 460

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 461 LPQGEWR 467


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 332 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 390

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 391 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 449

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 450 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 508

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 509 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 564

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 565 LPQGEWR 571


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 324 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 382

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 383 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 441

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 442 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 500

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 501 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 556

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 557 LPQGEWR 563


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 58/208 (27%), Positives = 108/208 (51%), Gaps = 13/208 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           R++K ++ AGI SRR  ++ I   R+K+NG+  E  +  V   D +EVD  V     ++ 
Sbjct: 2   RINKFLSEAGICSRRGADKWIEAGRIKINGVKAELGS-KVTEGDSVEVDNKVVTLNTDKG 60

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +++  +KP G+ +T ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +  
Sbjct: 61  YVYIKLNKPRGITST-TERHIKGNIVDFVGH-SERIFHIGRLDKDSEGLILLTNDGDIVN 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
            +     +  + Y V     +  D +  + +G+ I         VTL  + +K +     
Sbjct: 119 EILRKEGRHEKEYIVTVDKPITDDFVKQMSEGVAILD------TVTLPAEVEKLNTKTFK 172

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRI 218
           + L +G NR+I+++ E   ++V +L RI
Sbjct: 173 IILTQGLNRQIRRMTEALGYEVKQLRRI 200


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 63/228 (27%), Positives = 102/228 (44%), Gaps = 8/228 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I  Q   VNG ++      V   D +     PL    +
Sbjct: 4   PCRLDKFISHLAELPRSKARAAIKSQAATVNGEVITAFDFQVSQQDDVLFYDEPLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP+G V  +SD +   TVFD L  P++ S     GRLDI+T GL+L+TNDG  
Sbjct: 64  -RYFMLNKPVGYVCANSD-ELHKTVFDLLDEPNL-SDFHVAGRLDIDTTGLVLITNDGDW 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P     + Y V     +    L  L+ G+ +      D+      ++  N  + 
Sbjct: 121 SHKITSPKKNKFKTYLVETQEPITDAALQQLRDGVQLHN--EKDLTRPAIAERLGNYGLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           + + EGK  ++K++    + KV  L R      +LG  L AG  R ++
Sbjct: 179 LSISEGKYHQVKRMLAAVDNKVVELHREQIAGIKLGEDLAAGEYRPLT 226


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 327 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 385

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 386 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 444

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 445 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 503

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 504 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 559

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 560 LPQGEWR 566


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 48/175 (27%), Positives = 89/175 (50%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  +D +GR T+ D +     RV + GRLD+++EGLLLLT+ G L   L  
Sbjct: 12  LFNKPYNVLTKFTDAEGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHGLTD 69

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYG----DMQVTLDTQ 182
           P  +  + Y V+  G   + +L  L++G+ ++           I Y     + +  +  +
Sbjct: 70  PDNKAYKTYVVQVEGVPTKSQLKQLEQGVALKDGLTLPAKVKRIPYPKWLWEREKPIRIR 129

Query: 183 KGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           K    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R V
Sbjct: 130 KNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGEYHIADLKPGQYRIV 184


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 327 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 385

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 386 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 444

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 445 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 503

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 504 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 559

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 560 LPQGEWR 566


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 327 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 385

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 386 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 444

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 445 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 503

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 504 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 559

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 560 LPQGEWR 566


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 316 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 374

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 375 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 433

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 434 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 492

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 493 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 548

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 549 LPQGEWR 555


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 45/169 (26%), Positives = 82/169 (48%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L   +  
Sbjct: 90  LFNKPFDVLCQFTDEQGRQTLKDFIP--IQDVYAAGRLDRDSEGLLLLTNDGQLQSRITE 147

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDM----QVTLDTQ 182
           P  +  + Y V+  G    + +  L+ G+           ++ I   D+        + +
Sbjct: 148 PKKKTDKTYWVQVEGIPSDEAIQALRDGVTLKDGPTLPAKVERIAEPDVWPRNPPVRERK 207

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +   +W+ + + EG+NR+++++     +   RLIR   G + L  +  G
Sbjct: 208 QIPTSWLAITICEGRNRQVRRMTAHVGYPTLRLIRYKIGQWSLNGVANG 256


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 66/216 (30%), Positives = 98/216 (45%), Gaps = 6/216 (2%)

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 +KP G+V+  SDP   +TV D L   +  +   GRLD  + GLLLLTNDG  +  L
Sbjct: 67  LML-NKPAGVVSATSDPQ-HTTVIDLLDDHYKDLHIAGRLDRFSTGLLLLTNDGEWSNSL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGL 193
             P  +  + Y V     +     +   KG+      Y D+       K     V  V L
Sbjct: 125 SHPDNRVAKRYIVELKEPITDAYGDAFAKGM---HFAYEDITTQPAQLKQLEPRVAEVTL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            EG+  +IK++F  F  +V  L R+S G   L   L
Sbjct: 182 HEGRYHQIKRMFGRFRNQVLSLHRVSIGNLPLDDAL 217


>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 = 69.7 bits (169), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 9/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++  G+ +R EV++++ +  VKVN  + +     V    D I VDG  +      
Sbjct: 2   RLDKFLSNMGVGTRTEVKQLLKKNSVKVNDKVEKSPKSQVDPEQDEITVDGKIIEYINHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G V+   D D   TV D +       +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYVSATYD-DINQTVIDLIADYCHLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y+V     +  + +   K GI +        Q+    +K  +    V 
Sbjct: 120 NLMSPSKHVSKTYKVTSKYPIKNEDIIAFKNGIELSDGKVKPAQL----EKLDHNVSLVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F   + +V  L R+      L   L +G  R ++ + L+
Sbjct: 176 IYEGKYHQVKRMFHSIDNEVLELKRLKIANLTLDENLKSGEYRLLTSEELK 226


>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 = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 95/212 (44%), Gaps = 3/212 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  ++I    V VN  + +  A  V     +E  G  ++K     
Sbjct: 2   RLDKYLCDALGATRKEATKIIKSGDVTVNDAVQKSGAFKVTDECVVEWQGREIQKPGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+ KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLF-KPDGFVCSHED-GFNQTAFALLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     + +D      +GI ++      +   LD        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDPIGEDYAEKFAQGIELRSEKEPTLPAQLDIVNQDENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     KV  L R   G  +L
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGAIEL 211


>gi|330752330|emb|CBL87284.1| RNA pseudouridine synthase family protein [uncultured Flavobacteria
           bacterium]
          Length = 195

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 52/188 (27%), Positives = 90/188 (47%), Gaps = 19/188 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + ++ +KP G ++  S   G+  + D  +LP+    V  VGRLD ++EGLLL++ND  + 
Sbjct: 6   KYYIIYKPKGCLSQFSKEHGKRALGDVFDLPT---DVYPVGRLDEDSEGLLLISNDKSIN 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQ------------V 177
             L  P     R Y V+  GQ+ +  +  L  G  IV++G  +  +             +
Sbjct: 63  SKLLNPLNGHWRTYWVQVSGQIHKSAIKALVNGVDIVVKGKIHSTLPARVKKGNPPKNIL 122

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L+  +   +WV + L EGK R+++K+     +   RL+R      +LG L     + + 
Sbjct: 123 PLNVSEKETSWVKISLCEGKYRQVRKMTAKVGFPTLRLVRTHIEELELGELKPSEFKSLD 182

Query: 238 KKILREQL 245
           KK L  +L
Sbjct: 183 KKALFHKL 190


>gi|89092944|ref|ZP_01165896.1| RsuA protein [Oceanospirillum sp. MED92]
 gi|89082969|gb|EAR62189.1| RsuA protein [Oceanospirillum sp. MED92]
          Length = 223

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 87/180 (48%), Gaps = 20/180 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++T  +  D + T+ D   LP  ++     GRLD ++EGLL+LTNDG     L
Sbjct: 6   LFNKPFQVLTQFTTDDDKQTLADYIELPDYYA----AGRLDYDSEGLLILTNDGPTQHYL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY----------GDMQVTLDTQK 183
             P  +  + Y  +  G+V ++ L  L  G+ ++ G+               Q T   ++
Sbjct: 62  ANPQFKMEKTYWAQVEGEVTEEALETLSSGVELKDGMTRPAKAKKINEPAIWQRTPPIRE 121

Query: 184 GSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             N   +W+ + + EGKNR+++++     +   RL+R + G + L  L  G +  +   I
Sbjct: 122 RKNIPTSWIELKITEGKNRQVRRMTAAVGFPTLRLVRYAIGEWTLDNLKPGQSSLIESDI 181


>gi|167816387|ref|ZP_02448067.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
          Length = 351

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 104 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEID-SNARAAQAAQ 162

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 163 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 221

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 222 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 280

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 281 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 336

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 337 LPQGEWR 343


>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 = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>gi|298710181|emb|CBJ26256.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 387

 Score = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 61/205 (29%), Positives = 98/205 (47%), Gaps = 39/205 (19%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRS--TVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGL 130
           R ++ HKP G VT+  D  GR   TV+D   +        VGRLD +T G+LL T+D  L
Sbjct: 2   RYFMLHKPRGCVTSTVDDTGRGRPTVYDVAKAAGVPNFGPVGRLDFDTSGVLLFTDDYKL 61

Query: 131 ARVLELPSTQ----------WLRVYRVRFHGQV-DQDK-LNLLKKGIVIQGICYGD---- 174
            + +  P+ +            +VY +   G +  +DK ++LL++ +       G     
Sbjct: 62  KKAISSPTYKGKAAVGTVPSMEKVYHLLVAGTITPEDKGMDLLQEPLHFSRKLDGPGGSW 121

Query: 175 ---------MQVTLDT--------QKGSNA---WVTVGLREGKNREIKKVFEFFNWKVNR 214
                    +  T  T        + G+ A   W+ V LREGKNR+I+++     +++ R
Sbjct: 122 TKPAEARVLLTKTFKTGQPVPWRFKPGTVATITWIEVVLREGKNRQIRRLCRRSEFELTR 181

Query: 215 LIRISYGPFQLGTLLAGSTREVSKK 239
           L RIS GP  LG +  GS RE++++
Sbjct: 182 LHRISVGPIVLGDVEEGSCRELTRQ 206


>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 = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 63/226 (27%), Positives = 112/226 (49%), Gaps = 13/226 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRR+ +R I Q  V +NG   +RAAV   V   + ++V+G  +   + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRAAVGDQVYVGNVVKVNGQLIEPRDE 64

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L L   +KP+G+++T  +  G S    +  +   RV  +GRLD +++GL+LLTN G L
Sbjct: 65  NDLVLIALNKPVGIISTTEE--GESDNIVDFVNHSKRVFPIGRLDKDSQGLILLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G     +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYVVTVNKPVTDEFIVGLAAGVPMMGT----VTKKCKVKKIAPFVFN 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + L +G NR+I+++ + F ++V +L R       L  L  G  R++
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPQGEWRDL 224


>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 = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 100/225 (44%), Gaps = 20/225 (8%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERA-------AVNVMSTDHIEVDGVPLRKA 70
           K I   G+ SR++ + +I    + +NG +  RA        V+ +S D  E+  VP+   
Sbjct: 5   KYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVPMPYF 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 65  ----YILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSN 186
                +  P  +  ++YRV      +      LK G+++    + D +     +      
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPANDTLCATLKNGVLL----HDDNETVAAAEAVLADP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             + + + EGK  ++K++      +V +L R  +G + +  L AG
Sbjct: 176 TTLMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLAAG 220


>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 = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 323 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSN-ARAAQAAQ 381

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 382 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 440

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 441 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 499

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 500 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 555

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 556 LPQGEWR 562


>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 = 69.7 bits (169), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 61/233 (26%), Positives = 113/233 (48%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRR+ +R I Q  V +NG   +R  +   V   D ++V+G  +  R  
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFING---KRVTLGDQVFPGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +       +KP+G+V+T  + +  + V  +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DNLIFIALNKPVGIVSTTEEGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  D +  L  G+ +     G +      +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTDDFIRGLGAGVPM----LGTVTKKCKVKKEAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ E F ++V +L R       +  L  G  R+++   L E
Sbjct: 179 IVLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVGMAGLPPGEWRDLTDDELVE 231


>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 = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 59/180 (32%), Positives = 84/180 (46%), Gaps = 17/180 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ HKP G V  + D      +   LP     +  VGRLD NT GL++LTND  L + 
Sbjct: 58  KYYIIHKPSGYVCANKD-SHDPCLISLLPD--DNLHYVGRLDRNTTGLVILTNDLKLRKR 114

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV-TVG 192
           L LP     R Y   F        +   K+GI I G    D++      + ++ +   + 
Sbjct: 115 LTLPEFHIPRTYA--FTCLNPLKDITPFKEGITIDG----DVKCLPAIVEMTSEYEGVIT 168

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS-------KKILREQL 245
           L EG+  EIKK+F   N K+  L RI YG   LG L +G+ R ++       K I R QL
Sbjct: 169 LEEGRYHEIKKMFLSLNNKITSLHRIMYGDISLGDLPSGTYRTLTQEEINHLKDITRRQL 228


>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 = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 93/182 (51%), Gaps = 22/182 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG-RSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           TRL +++KP  ++T  +D +G R+T+  F  +P +++     GRLD ++EGLL+LT+ G 
Sbjct: 16  TRLIVFNKPYDVLTQFTDREGGRATLKDFIKVPGVYA----AGRLDRDSEGLLVLTDSGP 71

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------GICYGDMQVTL 179
           LA  +  P  +  + Y  +  G   +  L+ L++GIV++           +   D     
Sbjct: 72  LAARISDPKHKLAKTYWAQVEGVPTEADLDRLRRGIVLKDGPTLPAGARAMAEPDNLWPR 131

Query: 180 DT-----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           D           +W+ + LREG+NR+++++     +   RLIR + G + L  L  G  R
Sbjct: 132 DPPIRYRAAIPTSWIELTLREGRNRQVRRMTAAMGFPTLRLIRWAVGEWNLEGLAPGEWR 191

Query: 235 EV 236
           +V
Sbjct: 192 DV 193


>gi|167846297|ref|ZP_02471805.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           B7210]
          Length = 334

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 87  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEID-SNARAAQAAQ 145

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 146 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 204

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 205 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 263

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 264 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 319

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 320 LPQGEWR 326


>gi|224008973|ref|XP_002293445.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220970845|gb|EED89181.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 253

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 112/245 (45%), Gaps = 39/245 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN-------GILLERAAVN 53
           + +KN+    F P R++KV  +    SRR+ ++++A  R+ +N       G  +     N
Sbjct: 3   VSNKNVT---FQPIRINKVFKKT--HSRRQADQLVADGRITINDEPVHSAGQRVSNGGAN 57

Query: 54  VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
             S+  +          E  + W   KP+G+  T    D R  ++DNL            
Sbjct: 58  SESSTQV---------FEYIKYW---KPLGVTCT---TDRR--IYDNLIDALQQDGCRPK 100

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
           SR+  VGRLD  T G++L+T+DG L         +  + Y V+ +  V  D +  L++G+
Sbjct: 101 SRIFPVGRLDKETSGIILMTSDGRLPNAALRGKYKHPKTYVVKANRPVANDDIKRLREGV 160

Query: 166 VIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            +    +      V L T   S+ ++ + L EG+NR+I+K+ E   ++V  L R S+   
Sbjct: 161 PLTAPTLPCKVKAVQLSTLDLSSRYLEITLVEGRNRQIRKMLEAIGYRVMELHRKSFMNL 220

Query: 224 QLGTL 228
            L  L
Sbjct: 221 TLENL 225


>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 = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 108/218 (49%), Gaps = 13/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----A 70
           R+ +++A+A I SR+ +++ + ++ + V+    +  A N+       +  +   K    A
Sbjct: 2   RLDRLLAQASI-SRKSMKQALLRRAILVD----QTPARNLSQNVDTGLQDILFYKQKISA 56

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
              R ++ +KP G +T +SD   ++TV D +        + S+GRLD +T GLLL+T++G
Sbjct: 57  PAHRYFMMNKPRGYITANSDA-SKATVIDLIQKEDFSEELYSIGRLDRDTTGLLLITDNG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNA 187
            L   L  P     + Y V+ +G +D   +   ++G+  + G      Q+ + +     +
Sbjct: 116 PLGFQLLHPQYHVDKTYFVQVNGLLDNQAIEAFQQGVRFLDGKVCKPAQLIIHSATPVLS 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +V + EGK  ++KK+F     KV  L R   G FQL
Sbjct: 176 TASVTISEGKFHQVKKMFLAIGVKVTYLKRTHLGDFQL 213


>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 = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 103/207 (49%), Gaps = 10/207 (4%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV-FD 99
           +NG +    A+ V   D + +DG  + K E+ ++++ +HKP+G+  T +D    + + + 
Sbjct: 3   INGEICTHGAL-VSDGDRVTIDGQVIVKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYI 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           N P    R+  VGRLD  +EGL+LLTNDGG+A  +     +  + Y V          ++
Sbjct: 62  NYPE---RIFPVGRLDKASEGLILLTNDGGIANQILHGDHEHEKEYVVTVDKPFTDWFID 118

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            + +G+ I+       +VT    +   +   + L +G NR+I+++   F + V +L R+ 
Sbjct: 119 EMSRGVKIKDGMTKPCKVT----RVDQSTFRIVLTQGMNRQIRRMSRAFGFTVIKLKRVR 174

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLG 246
               +L  L  G  R V+ + L   +G
Sbjct: 175 IMNIELNELEVGKWRSVTAEELEILIG 201


>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 = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/224 (27%), Positives = 107/224 (47%), Gaps = 15/224 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+  ++ +    SR++++++I+   V ++       + NV     I+V  V   + E   
Sbjct: 2   RLEHLLMKHFDISRKQMKKLISSGEVLIDSTPATHVSNNV--DPQIQVITVQGSRMEDNS 59

Query: 74  -RLWLYHKPIGLVTTHSDPDGRSTVFD-----NLPSIFSRVISVGRLDINTEGLLLLTND 127
            + +L +KP G++T  +D     TV D     N+  ++     +GRLD +TEGLL++TN+
Sbjct: 60  QKYYLLNKPKGVITATTDSQ-LPTVIDLFKNENIEGLYP----IGRLDRDTEGLLIITNN 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L   L  P     + Y V  +G +D   +     GI+   G      ++++     S 
Sbjct: 115 GPLGYRLLNPIQHIEKEYYVEVNGPLDNSCIQRFYDGIMFHDGTICKPAKLSILESSPSF 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +  TV + EGK  +IKK+F     KV  L RI +G F L   L+
Sbjct: 175 SKATVTISEGKFHQIKKMFLCVGVKVTFLKRIRFGEFLLDESLS 218


>gi|167569105|ref|ZP_02361979.1| RNA pseudouridine synthase family protein [Burkholderia
           oklahomensis C6786]
          Length = 240

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 63/210 (30%), Positives = 93/210 (44%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++   RV V G     A  +  +     EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGRVAVGGATCTDAHASFDTARLAFEVDGVAWPYHARAYVVL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   S+VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHSSVFRLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D   L+ L+ G+++ G       V    +      +TV   EGK  +
Sbjct: 129 VPKTYVATVRHPLDDALLDALRAGVLLHGEPKPIAAVAAHARGERLLEMTVA--EGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V  L R S G F L   LA
Sbjct: 187 VKRMVAAASNRVEALHRASIGGFTLPADLA 216


>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 = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>gi|255069983|ref|XP_002507073.1| pseudouridylate synthase [Micromonas sp. RCC299]
 gi|226522348|gb|ACO68331.1| pseudouridylate synthase [Micromonas sp. RCC299]
          Length = 334

 Score = 69.3 bits (168), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 111/246 (45%), Gaps = 39/246 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+SK+IA     SRRE ER+I++ +V VNG+L+ + +         E D          
Sbjct: 90  QRISKIIALREFCSRREAERLISRSQVVVNGVLIHQGS-------KAECDSEIQLAEIGD 142

Query: 74  RLWL-------YHKPIGLVT---THSDPDGRSTVFDNLPS-IFSRVIS------------ 110
           ++W         +KP G V+   +H + +  S +     S I S   S            
Sbjct: 143 QVWFQSKSTVALNKPRGYVSNLPSHGEVEACSLLITTTGSHIHSSKWSSRTENDNGQLNV 202

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLD N+ GLL+L+ DG LAR + +      + Y V     V Q+ L+ L       G 
Sbjct: 203 CGRLDKNSRGLLVLSQDGVLAREV-IAGVFVSKTYLVEVDKMVTQNDLDRL------NGP 255

Query: 171 C--YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           C    D+   +  +  +   +   LREGKNR+I+++ E     V  L R+  G  +LG+L
Sbjct: 256 CKFLTDVIRPIRVRLLAPTLLEFVLREGKNRQIRRMCEQMGLIVVDLFRVRLGKSELGSL 315

Query: 229 LAGSTR 234
             GS R
Sbjct: 316 PEGSWR 321


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 108/241 (44%), Gaps = 24/241 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R+  V  R GI++ R V R++ +  V VNG  +LE      ++TD + +DG+    A  
Sbjct: 7   ERLDTVFIRRGISTHRRVRRLLQKHNVCVNGTRVLESGFGLNLATDELSIDGIKKNLAPD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLL 123
             L + +K  G + +  D     TV+  +P  +          ++ +VGRLD +TEGLL+
Sbjct: 67  IYLMM-NKKSGTICSTKDDGLYKTVYSFIPQKYFYYAKENSLQKIHTVGRLDTDTEGLLI 125

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC---------YGD 174
            T +G  +  L  P     + Y V       +++   L+K    +G           +  
Sbjct: 126 FTTNGDFSHSLANPLFHVKKTYYVELEKSEPEEQRKFLEKKFS-EGFFIPPEKNEREFIS 184

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GST 233
               L+    ++  +T+   EGK  ++K++F     KV  L RIS G   L   LA G +
Sbjct: 185 RPAILEWNSANSCRLTI--TEGKFHQVKRMFSAQGNKVIFLKRISIGSLALDEKLAPGDS 242

Query: 234 R 234
           R
Sbjct: 243 R 243


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 69/230 (30%), Positives = 117/230 (50%), Gaps = 17/230 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     SR EV+  + ++ +KVN ++L +        D +E+D   L K E+ +
Sbjct: 5   RIEKYIADLTNLSRNEVKNKLKKKAIKVNRVILTKLIKIDSEKDVVELDNSIL-KYEKFQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++++KP   +  +SD +  +T+FD   LP+   +  S GRLD +TEGLL+L+NDG +  
Sbjct: 64  YYMFNKPANFICANSDSE-EATIFDIVGLPA--EKFFSFGRLDKDTEGLLILSNDGQMCH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWV 189
            L  P     + Y V+   ++D + L L    I I      D  V+   L+       ++
Sbjct: 121 RLLSPKNHVPKKYYVKVDKKIDSEIL-LNHSPIKIN----DDFIVSKYILELIDDKGCFL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           T+   EGK  +IK++F    + V  L R+ +G  +L   L  G  R++S+
Sbjct: 176 TI--YEGKFHQIKRMFGSLGFSVLYLKRVEFGKLKLDNNLKLGQVRKLSE 223


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 84/174 (48%), Gaps = 20/174 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP G+V   S  +   T+ D  N+P+I+      GRLD ++EGLL+LT++G +   +
Sbjct: 4   LFNKPFGVVCQFSKHEIHPTLKDYLNIPNIYP----AGRLDTDSEGLLVLTDNGKIQHEI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P++   + Y V+  G +  + +  L+ GI ++       +V    +            
Sbjct: 60  SSPNSHKYKGYWVQVEGDIKNEAIQKLQNGIKLKDFTSLPARVEKINEPEIWERSTPIRF 119

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 +WV + +REGKNR+++K+     +   RLIR     + L  LL G  +
Sbjct: 120 RKNLPTSWVKIQIREGKNRQVRKMTAAVGFPTLRLIRYHVDDYYLNKLLPGDYQ 173


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 58/223 (26%), Positives = 99/223 (44%), Gaps = 19/223 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R + +++I Q R+  +G ++      V+    I  DG  L     TR
Sbjct: 2   RLDKYICESTTMTRSQAKKVIIQGRITSDGTVMRNTGYKVLENTPICFDG-NLINVRGTR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTN 126
             + +KP   +         STV +  PSI +        ++   GRLD +T GL L+T+
Sbjct: 61  YIMLNKPKDFIC--------STVDEQFPSIINLIKVDKPDQLCIAGRLDADTTGLALITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P     + YR      V+Q+ + L K+GI ++      +  TL+    + 
Sbjct: 113 DGQWSHKITSPRRNCSKRYRATLAQPVEQNAVTLFKEGIQLKSENVPCLPATLEILTDNE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             +T+   EGK  ++K++F      V  L R   G  +L T L
Sbjct: 173 VLLTI--HEGKYHQVKRMFAAIGNLVVELHREQIGEIKLDTDL 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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 90/181 (49%), Gaps = 25/181 (13%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           TRL  ++KP  ++   +D   + +       + N P +++     GRLD ++EGL+LLT+
Sbjct: 2   TRLIRFNKPYDVLPQFTDSGSQGSARPTLSAYINCPGVYA----AGRLDRDSEGLMLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------ICYGDMQV 177
           +G L   +  P  +  + Y V+  G+ D   L  L++G+ ++          +     Q+
Sbjct: 58  NGRLQAWISDPQHKMAKTYWVQVEGEPDSRALAALQQGVALKDGMTRPAKAHLMEAPAQL 117

Query: 178 -----TLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + T+K    +W+++ L+EGKNR+++++     +   RLIR S G + L  L  G
Sbjct: 118 WQREPPIRTRKSIPTSWISLTLKEGKNRQVRRMTAAVGFPTLRLIRYSIGVWTLDGLPQG 177

Query: 232 S 232
           S
Sbjct: 178 S 178


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREIM-LHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>gi|167739176|ref|ZP_02411950.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
          Length = 313

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 66  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDS-NARAAQAAQ 124

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 125 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 183

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 184 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 242

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 243 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 298

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 299 LPQGEWR 305


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 48/169 (28%), Positives = 83/169 (49%), Gaps = 20/169 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L +KP  ++   +D  GR T+ D +  P I++     GRLD ++EGLLLLTNDG L 
Sbjct: 58  KLLLLNKPYMVLCQFTDEAGRETLKDYIKEPGIYA----AGRLDRDSEGLLLLTNDGKLQ 113

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             L  P  +  + Y V+  G   +++L  L+ G+ +  G+        +D          
Sbjct: 114 ARLTQPGEKTPKTYWVQVEGIPSEEELAALRAGVELNDGLTLPAEARLMDEPNVWPRNPP 173

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
               ++    W+ + + EG+NR+++++         RLIR + G + LG
Sbjct: 174 IRERKEVPTRWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDWTLG 222


>gi|167470950|ref|ZP_02335654.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           FV-1]
          Length = 165

 Score = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 75/151 (49%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHRV 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             P     + Y V     +  D       G+
Sbjct: 122 TSPRHHCEKTYLVTLEHPLSDDTAQQFADGV 152


>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 = 69.3 bits (168), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 49/211 (23%), Positives = 98/211 (46%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +    + V+  +++  ++ + + + +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRNLVARELRAGNITVDDKVVKSGSMQISADNEVSYDGNVLIQITGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ HKP G V +  DP   + ++     +  ++ + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLHKPEGYVCSTDDPTHPTILYFIDEPVTQKLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV+    +  D +   + G+++ G         L+        +T+   
Sbjct: 122 TSPKHHCEKTYRVQLSEDITDDVIQKFEIGVMLNGEKSPTKPAQLEIISPREVLLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F      V  L R   G  +L
Sbjct: 180 EGRYHQVKRMFAAVGNHVCGLHRERVGEIRL 210


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/234 (23%), Positives = 103/234 (44%), Gaps = 3/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR  V R +  + V V+G++    ++ + +   +   G  L      R
Sbjct: 2   RLDKFISQQLGISRALVARELRARYVTVDGVVARSGSLQITAEQEVAYQGNVLTFITGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLD++T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPEGYVCSTDDPDHATILYFIDEPMAEKLHAAGRLDLDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +D        +G+ + G    D+      +      V + + 
Sbjct: 122 TSPRHHCEKTYLVTLEQPLDPQTAEQFAQGVQLHG--EKDLTKPARLEALDEHQVRLTIS 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLGP 247
           EG+  ++K++F     +V  L R   G   L   LA G  R +S   +   L P
Sbjct: 180 EGRYHQVKRMFAAVGNRVVALHRERIGAIALDAALAPGEYRALSDDEVASVLAP 233


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 90/178 (50%), Gaps = 21/178 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T + L +KP G+++  ++     T+  F ++P+++     +GRLD ++EGLLLLTN+G
Sbjct: 23  DETIVVLVNKPYGVLSQFTNNQACKTLKEFISIPNVYP----IGRLDKDSEGLLLLTNNG 78

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            +   L  P  +  + Y V+  G    + LN L  G++++       +V +         
Sbjct: 79  QIQHRLANPKFEKEKTYWVQIEGIPQPEDLNRLASGVILKDGLTKPAKVKIIPDPHFKWQ 138

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + +    +W+ + + EGKNR+++++     +   RL+R+    F+LG+L  G
Sbjct: 139 SAPKIRERKNIPTSWIELKIVEGKNRQVRRMTAHIGFPTLRLVRVGVSYFKLGSLAPG 196


>gi|295677418|ref|YP_003605942.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295437261|gb|ADG16431.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 236

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/220 (26%), Positives = 94/220 (42%), Gaps = 9/220 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +           VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIGDGRVGIDGAICTDADADFAVDSGALRFSVDGVEWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP+G   +  DP    +VF  LP  F+   V  VGRLD +T GLLLL++DG  
Sbjct: 63  AYL-LLNKPVGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  ++Y       +D  +L  L+ G+++ G         LD +      + 
Sbjct: 121 VHQFTSPKRKVPKLYVATTRHPLDDAQLAALRDGVLLHG--ETKPSAALDAEARDTHTLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++      +   L R   G   L   LA
Sbjct: 179 LTVLEGKYHQVKRMIAASGNRCEALHRERIGGLVLPATLA 218


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 101/218 (46%), Gaps = 20/218 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLE-RAAVNVMST-DHIEVDGVPLRKAERTRLWL----YHK 80
           SRRE +++I   RV VN I ++ +    V+   D I +DG+P+       +      Y K
Sbjct: 1   SRREADKLIEAGRVSVNDIPVKSKGGFKVVPFHDKITLDGIPVTGTSDATINFDYVKYWK 60

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSI----FSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           P+G VT  +D      + D L         R+  VGRLD  T GL+LLT+DG +   +  
Sbjct: 61  PVG-VTCTTDRKIAGNIIDALEEAGFDSSKRIFPVGRLDKETSGLILLTSDGRVPNAVLR 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTVG-- 192
              +  ++Y+V     V    +  L+ G++I  +    G+    L  +  S A   +G  
Sbjct: 120 GRHKQPKIYQVWVDRPVLAKDVAQLRDGVIITTVAQRDGNRAEPLTARTKSCAVQVLGRE 179

Query: 193 -----LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                L EG+NR+I+K+    N+ V RL R+ +    L
Sbjct: 180 KLQLTLVEGRNRQIRKMLGALNYTVKRLHRVQFMELTL 217


>gi|167911508|ref|ZP_02498599.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 112]
          Length = 298

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 51  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDS-NARAAQAAQ 109

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 110 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 168

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 169 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 227

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 228 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 283

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 284 LPQGEWR 290


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 55/173 (31%), Positives = 81/173 (46%), Gaps = 20/173 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + HKP G+VT  +D  GR      + +  P +F+ + +VGRLD++  GLLL T DG L  
Sbjct: 62  MLHKPHGVVTARAD--GRHPTAYALLEGAP-LFAELRAVGRLDLDAVGLLLWTTDGQLVH 118

Query: 133 VLELPSTQWLRVYRVRFHGQV------DQDKLNL-LKKGIVIQGICYGDM-----QVTLD 180
            L  P     R Y V            D   + L L+ G+  + +  G +        L 
Sbjct: 119 ALTHPRRAVPRTYHVALAAPFEAPPRDDDGAVALELRDGLRPRVVALGALDEAAAHPALL 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGS 232
           T  G+ A  TV L +G   E+K++F      V  L R+ +GP +L  TL AG+
Sbjct: 179 TPPGTEALATVTLLDGAYHEVKRIFAALGSHVLCLARVRHGPVELPRTLEAGA 231


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 106/227 (46%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR    R +  ++V V+G ++   +  + +   IE DG  L++    R
Sbjct: 2   RLDKFLSQQLEVSRAIAARELRAKKVTVDGEVVRDGSYKLSADSAIEYDGNALQQQLGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP+G V +  DPD  + + F   PS + ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 62  YFMLNKPVGYVCSTDDPDHPTILYFLEEPSAY-KLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  + +   +T+  
Sbjct: 121 ITSPRHHCEKTYLVTLESPIGHDTAQQFADGVQLHNEKTLTKPAALEVIEPNLVRLTIS- 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L T +  G  R +S +
Sbjct: 180 -EGRYHQVKRMFAAVGNRVVALHRERIGAILLDTGMQPGEYRPLSDE 225


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 112/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 399 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQV 458

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS      +   GRLDI++
Sbjct: 459 TILLHKPVGYVSGQAE-DGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 517

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            G+L+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 518 TGMLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLLDIDQHFPAESLAKLRHGLELDG 577

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 578 VALKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 633

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 634 QGQWRYLS 641


>gi|167720171|ref|ZP_02403407.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
          Length = 305

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 58  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEID-SNARAAQAAQ 116

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 117 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 175

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 176 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 234

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 235 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 290

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 291 LPQGEWR 297


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 24/242 (9%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKA 70
           P R+SK +A+ G+ SRRE +  I Q  VKVNG   E A +   V+  D I++D    ++ 
Sbjct: 4   PIRLSKQMAQLGLCSRREADHYIEQGWVKVNG---EVAVLGQKVLPGDRIDLDKNAHQQQ 60

Query: 71  ERTRLWLYHKPIG---------------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                 L +KP+G               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+   +      +T    +GK R+I+++ E    +V  L R+  G  +LG L  G  R 
Sbjct: 181 KVSWQNEDQLRFILT----QGKKRQIRRMCELVGLRVVGLKRVRIGRIKLGALPPGKWRY 236

Query: 236 VS 237
           +S
Sbjct: 237 LS 238


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 104/215 (48%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV V+G++++     V     I++D   L+      + L HKPIG+V+ 
Sbjct: 20  RKAVRELLLSGRVCVDGLIVKDMDRQVDEFSRIQLDEHILQANAPVYVML-HKPIGVVSA 78

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D   + TV D L       + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 79  TKDTQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDALMSPTHKVDKVYR 137

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     + ++ +         +G+ +G   +T    K    ++    V L EGK  +IK+
Sbjct: 138 VTLANSITKEYIAAFA-----EGMYFGFEDITTQPAKLVILADNVAEVTLHEGKYHQIKR 192

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +F  F   V  L R+S G   L   LA G +R ++
Sbjct: 193 MFGRFRNPVVGLHRLSIGEIVLDEKLAPGESRALT 227


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/220 (30%), Positives = 96/220 (43%), Gaps = 9/220 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +RR+V   IAQ+R+ VNG         V    HI  D   L+      
Sbjct: 7   RLDRFISLNSNLNRRDVRLAIAQKRILVNGKHASTIHQVVSQFCHITFDNQTLQANAPVY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + L +KP G V+   D     TV   LP      I  VGRLD N+ GL+LLTN+G  +R 
Sbjct: 67  IML-NKPAGRVSATKD-STHPTVVGCLPQQLQANIHIVGRLDFNSTGLMLLTNNGAWSRH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L  P  +  ++Y V     ++ D+    ++    G+             L+    + A V
Sbjct: 125 LTSPENKVNKIYEVELERTINDDEWPQYISAFASGMYFAFEDLTTQPAKLERLTATRARV 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           T  L EG+  +IK++F  F  KV  L R   G   L   L
Sbjct: 185 T--LVEGRYHQIKRMFGRFRNKVIALHRTQLGALPLDPAL 222


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 106/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++ +
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTAE 224


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 9/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++  G+ +R EV++++ +  VKVN  + +     V    D I VDG  +      
Sbjct: 2   RLDKFLSNMGVGTRTEVKQLLKKNSVKVNDKVEKSPKSQVDPEQDEITVDGKIIEYINHV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + L +KP G V+   D D   TV D +       +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YIML-NKPKGYVSATYD-DINQTVIDLIADYRHLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y+V     +  + +   K GI +        Q+    +K  +    V 
Sbjct: 120 NLMSPSKHVSKTYKVTSKYPIKNEDIIAFKNGIELSDGKVKPAQL----EKLDHNVSLVT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EGK  ++K++F   + +V  L R+      L   L +G  R ++ + L+
Sbjct: 176 IYEGKYHQVKRMFHSIDNEVLELKRLKISNLTLDENLKSGEYRLLTSEELK 226


>gi|149198178|ref|ZP_01875225.1| RsuA protein [Lentisphaera araneosa HTCC2155]
 gi|149138780|gb|EDM27186.1| RsuA protein [Lentisphaera araneosa HTCC2155]
          Length = 239

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/216 (28%), Positives = 102/216 (47%), Gaps = 11/216 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+IA+    +R E  R +    VKVN I  +     + ++ D +  DG  L   E T
Sbjct: 9   RLDKMIAKCTDLTRSEATRALKNGFVKVNDIPQKVGKSTIDLANDVVTFDGEVLEYRE-T 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G V    D +   TV D LP   +     S GRLDI+T GL++LT+DG  A
Sbjct: 68  IYFMLNKPKGYVCAAKD-ERLKTVLDLLPPALASREPFSCGRLDIDTTGLVILTDDGTWA 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWV 189
             +  P  +  + Y V    ++  + +  L++G+ +     GD ++T     +K      
Sbjct: 127 HGITSPKRKCEKSYLVGSVSELSDEDMRNLEQGVYLD----GDDKITAPAKIEKIDEKTY 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + EG+  ++K++FE  +  V  L R   G   L
Sbjct: 183 RLKITEGRYHQVKRMFEAVDNMVKSLHREQIGGLSL 218


>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 = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 104/225 (46%), Gaps = 14/225 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL----ERAAVNVMSTDHIEVDGVPLRKA 70
           R+ +++A  G  SRRE++ +     + ++G  L    ER  V     + + V GV L   
Sbjct: 8   RLDRLLANLGYGSRREIQALARAGAIILDGARLRAADERIPVTRDLPERLTVGGVALDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               L L HKP G+  +H +      V+  LP  + R    + +VGRLD  T GLLLLT+
Sbjct: 68  PGLVLML-HKPTGVTCSHKE--AGPLVYGLLPERWRRRDPPLSTVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  L   G ++++G     + V L  +  +
Sbjct: 125 DGALLHRIISPKAKVAKRYRVELARPLAGDEGALFASGTLMLEGEDKPLLPVELVAEGPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            A VT  L EG+  +++++F      V  L R   G   L   LA
Sbjct: 185 RASVT--LTEGRYHQVRRMFAAVGNHVTALHRDRVGRLDLPADLA 227


>gi|167824765|ref|ZP_02456236.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
          Length = 300

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 117/247 (47%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 53  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDS-NARAAQAAQ 111

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 112 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 170

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 171 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 229

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 230 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 285

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 286 LPQGEWR 292


>gi|52424446|ref|YP_087583.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306498|gb|AAU36998.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 246

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 101/212 (47%), Gaps = 4/212 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R +  +++ Q  V+VNG +++  ++ +   D +  +G  L   E   
Sbjct: 18  RLDKFLAENTGLTRSQAAKILRQGNVQVNGQVVKSGSLKITPQDEVLFEGESLEWLEDGV 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D +  +   F + P +  ++ + GRLD +T GL+LLT+DG  +  
Sbjct: 78  YIMLNKPQGYVCSHDDGEYPTVYQFFDYP-LAGKLHTAGRLDADTSGLVLLTDDGKWSHR 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+ +     ++GI+++G         L+     N  V + +
Sbjct: 137 VTSPKYHCQKTYLVTLADPVESNYRQACEQGILLRGEKEPTKPAILEIIDDYN--VNLTI 194

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EG+  ++K++F     KV  L R   G  +L
Sbjct: 195 SEGRYHQVKRMFAALGNKVVGLHRWKIGNIEL 226


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 89/179 (49%), Gaps = 23/179 (12%)

Query: 78  YHKPIGLVTTHSDPD---GRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++KP G++   +D      R T+  F ++P ++      GRLD+++EGLLLLT+DG L  
Sbjct: 5   FNKPYGVLCQFTDESTGPARPTLATFIDVPGVYP----AGRLDLDSEGLLLLTDDGRLQA 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-------------TL 179
            +  P  +  + Y V+  G+ D+D L  L++G+ ++       QV              +
Sbjct: 61  RIADPRYKAPKTYLVQVEGEPDEDALAALRRGVRLKDGMTLPAQVERIEAPDLWPRNPPV 120

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K   + W+ + LREG+NR+++++         RL+R   G + L  +  G  REV 
Sbjct: 121 RFRKSVPDCWLKLILREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLEGIAPGEWREVP 179


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 87/182 (47%), Gaps = 24/182 (13%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------GRLDINTEGLLLLTN 126
            R+ L +KP  +++  +D + R+T    L  +F+   +V      GRLD ++EGLLLLT+
Sbjct: 2   ARIILVNKPYNMLSQFTDSENRAT----LRQLFTDAAAVEGFYPAGRLDYDSEGLLLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           +G L   +  P  +  + Y V+  G+ D + L  L+ G+ ++       QV L       
Sbjct: 58  EGSLQHRISEPKMKLAKTYWVQVEGEPDSEALAQLRGGVDLKDGRTHPAQVKLLETPTLW 117

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                     +   +W+ + + EG+NR+++++         RLIR + G +QL  L  G 
Sbjct: 118 ERTPPVRHRAQIPTSWLELKISEGRNRQVRRMTAAVGHPTLRLIRYAIGSWQLAGLQPGE 177

Query: 233 TR 234
            R
Sbjct: 178 HR 179


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 98/215 (45%), Gaps = 22/215 (10%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
             + +  + + +I   R++VN  +++     V   D I  DGV L+       ++ +KP 
Sbjct: 3   CNLGNVNKCKNLIKSSRIRVNNQIIKDIRYQVDIDDVIVFDGVELKWP--FVYYMLNKPK 60

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G +  + D   +  +      +  R     +GRLDI+T GLLL+TND  L++ L LP   
Sbjct: 61  GYICANHDKKYKCVI-----DLIGRDDCYCLGRLDIDTTGLLLITNDKTLSKRLLLPENH 115

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-----TLDTQKGSNAWVTVGLRE 195
             + Y V    ++  D + +   GI+I      D +V      L+     + ++T+   E
Sbjct: 116 IDKKYYVTVKNKLTDDLIEIFNNGIII------DQKVKCKPSYLEIIDDYHCYLTIN--E 167

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           G+  +IKK+F   N KV  L R+ +    L   L+
Sbjct: 168 GRYHQIKKMFLSCNNKVLELKRVMFASINLDNNLS 202


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 63/229 (27%), Positives = 107/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  IE  G  +  A   R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDLVQKSGAFKLKETSRIEWQGREI-TAHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFILLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D       GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQVDYAEQFTNGIELR----GERELTLPAQLEVVSETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEE 224


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 115/247 (46%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 2   RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDS-NARAAQAAQ 60

Query: 75  L-WLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS      +   GRLDI+
Sbjct: 61  VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 120 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 178

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G+      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 179 DGVPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 234

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 235 LPQGEWR 241


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 108/230 (46%), Gaps = 12/230 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G+V +H D   ++  T+ D +      +   GRLD++T GLLL+T+DG  + 
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQTALTLLDEVN--IQDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVT 190
            +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           + + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 175 LTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 105/229 (45%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I+R    SR    R +  ++V V+G ++   +  + +   +  DG  L +    R
Sbjct: 2   RLDKFISRQLEVSRAIAARELRARKVTVDGEVVREGSYQLSADSTVAYDGKVLEQQLGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP+G V +  DPD  + + F   P  F R+ + GRLDI+T GL+L+T+DG  +  
Sbjct: 62  YFMLNKPVGYVCSTDDPDHPTILYFLEEPGAF-RLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--WVTV 191
           +  P     + Y V     +  D       G+ +    + +  +T        A   V +
Sbjct: 121 ITSPRHHCEKTYLVTLESAISDDTAQQFADGVQL----HNEKTLTKPAMLAVIAPNLVRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            + EG+  ++K++F     +V  L R   G  +L + L  G  R +S +
Sbjct: 177 TISEGRYHQVKRMFAAVGNRVVALHRERIGAIRLDSDLQPGEYRPLSAE 225


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 53/185 (28%), Positives = 86/185 (46%), Gaps = 20/185 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + ++ +KP  ++T     +G++++ D    + S V  VGRLD ++EGLL+LTND  L   
Sbjct: 4   KYYIIYKPFQVLTRFGKEEGKASLADYF-DVPSDVYPVGRLDYDSEGLLILTNDKSLNHR 62

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGD--MQVTLDTQKG----- 184
           L  P     R Y V+  G V+ + +  LK+G  I I G  Y     Q  +  ++      
Sbjct: 63  LLDPKFSHEREYWVQVDGAVNAEAIQQLKQGVKIAIDGKPYQTRRCQAAIFEEEPPVPER 122

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                        W+ + L EGKNR+++K+     +   RLIR       +  L  G  R
Sbjct: 123 NPPIRFRKLIPAPWIRLTLGEGKNRQVRKMTAAVGFPTLRLIRYRIARITVEGLEPGQMR 182

Query: 235 EVSKK 239
           E+ +K
Sbjct: 183 EMDRK 187


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/227 (26%), Positives = 108/227 (47%), Gaps = 12/227 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I +Q   VNG ++      +   D +   G  L    +
Sbjct: 4   PCRLDKFISHLAELPRSKARASIKRQAALVNGEVVTAFDFQIKQQDEVVFQGEQLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP+G V+ +SD +   TVFD  + P++ S     GRLDI+T GL++LTNDG  
Sbjct: 64  -RYFMLNKPVGYVSANSD-ELHKTVFDLIDEPNM-SDFHVAGRLDIDTTGLVILTNDGDW 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAW 188
           +  +  P     + Y V     +  + L+ L++G+ +    + +  +T     ++ +N  
Sbjct: 121 SHKITSPKNNKFKTYLVETQEPITDESLDALREGVQL----HNEKALTRPAKAERLANYG 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           + + + EGK  ++K++    + KV  L R   G  +L   L AG  R
Sbjct: 177 LRLSICEGKYHQVKRMLAAVDNKVVELHREQIGNIKLDENLAAGEYR 223


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 103/217 (47%), Gaps = 5/217 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +RRE  +++  + ++V+G ++  A+  V   + +E +G PL K +  R
Sbjct: 2   RLDKFLGTTLGITRREASKLLRDKMIEVDGEIVRSASFAVSDDNDVEFNGRPL-KLQGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D   TVF     +    + V GRLD +T GL+L+T+DG  +  
Sbjct: 61  YFMLNKPEGFVCSHVD-DFNPTVFVLFDEVSPEKMHVAGRLDGDTTGLVLVTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +D +   + G+ ++          L+      A +T+  
Sbjct: 120 ITSPRHLCSKTYFVEAADPITEDYIKQFEAGVQLRSEKELTRPAKLEILSEREALLTIS- 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            EGK  ++K++F     +V  L R   G  +L   LA
Sbjct: 179 -EGKYHQVKRMFAAMGNRVVGLHRERIGTVELDEDLA 214


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 107/229 (46%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++ +    +RR V  ++ Q RV VN +++      V + D +  DG   +  +   
Sbjct: 2   RLDRLLCQHPKWNRRHVLGLLVQGRVTVNEVVVTNPTHEVSAFDTVHADGELCQAGKPAH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-RLDINTEGLLLLTNDGGLARV 133
             + +KP G+++  SDP    TV   LP   ++ + +G RLD  + GL+LLTNDG  +R 
Sbjct: 62  YLMLNKPAGILSATSDPV-HPTVMQLLPEALAKDLHIGGRLDRASTGLMLLTNDGQWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
              P  +  +VYRV     +  D   +  +GI    + I     Q+    ++       +
Sbjct: 121 ATDPDKRSPKVYRVTLANPIHPDTEQVFAEGIYFPFEAITTSPAQL----ERLGECECRL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EG+  +IK++F  F   V  L R S G   L  TL  G  R ++ +
Sbjct: 177 TIYEGRYHQIKRMFGRFRNPVVALHRESMGAITLDPTLAPGQYRALTAE 225


>gi|308389419|gb|ADO31739.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha710]
          Length = 256

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T 
Sbjct: 144 DGKLNHSLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT 203

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 204 ------LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 246


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/229 (29%), Positives = 115/229 (50%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K I++A   SR+E ++++    + VN  +++  +V+V +  D +   G PL  A  +
Sbjct: 2   RLDKFISKATELSRKEAKKVLHASEITVNDEVVKDGSVHVDVLNDEVMWAGEPLSVATGS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L HKP G   T   P     V +   +P + +  I+ GRLD++T G L+L++DG   
Sbjct: 62  RYILLHKPEGFECT-LKPKEYPIVTELIAVPELSNLRIA-GRLDVDTTGALILSDDGSWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICY-GDMQVT----LDTQKGS 185
             +  P     +VY +     +D++ + + +KK  V QGI   GD + T    L+    +
Sbjct: 120 HRVTSPRHLHEKVYELTLADAMDEEAQAHAIKK--VGQGILLDGDYEPTKPALLEFIDET 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +A +   L EGK  ++K++  +F  KV  L R S G   L  L  G +R
Sbjct: 178 HARLI--LTEGKYHQVKRMMAYFGNKVVELHRASIGGITLEGLEKGDSR 224


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 44/183 (24%), Positives = 86/183 (46%), Gaps = 25/183 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
            R+ L++KP G+++  +D      P    + F + P  +      GRLD ++EGL++LT+
Sbjct: 2   ARVILFNKPFGVLSQFTDKGSEGSPRPTLSAFIDAPGFYP----AGRLDRDSEGLMVLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS- 185
           DG L   +  P  +  + Y  +  G  +   +  L+ G+ ++       QV++ T   + 
Sbjct: 58  DGKLQARISNPKHKMTKTYLAQIEGTPEPQHIEALRAGVRLKDGMTRPAQVSVATPPDTL 117

Query: 186 --------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         +AW+ + + EG+NR+++++         RLIR+  G + L  L+ G
Sbjct: 118 WERSPPVRFRKTVPDAWLQISISEGRNRQVRRMCAHVGLPCLRLIRMRIGDWALNDLVPG 177

Query: 232 STR 234
           + R
Sbjct: 178 AWR 180


>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 = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 112/248 (45%), Gaps = 30/248 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 443 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQV 502

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D  P  FS      +   GRLDI++
Sbjct: 503 TILLHKPVGYVSGQAE-DGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 561

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            G+L+LT +G +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G
Sbjct: 562 TGMLVLTQNGRIAKQLIGEQSDIDKEYLVRVRFGERLLDIDQHFPAESLAKLRHGLELDG 621

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +      V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L 
Sbjct: 622 VALKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 677

Query: 230 AGSTREVS 237
            G  R +S
Sbjct: 678 QGQWRYLS 685


>gi|254673145|emb|CBA07952.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha275]
          Length = 256

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENPTT 203

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 204 ------LLLTITEGKYHQVKRMIAAVGNRVQHLHRRRFAHLETENLKPG 246


>gi|167837045|ref|ZP_02463928.1| pseudouridine synthase family protein [Burkholderia thailandensis
           MSMB43]
          Length = 325

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 116/247 (46%), Gaps = 34/247 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D    R A+  +
Sbjct: 78  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDS-NARAAQAAQ 136

Query: 75  LW-LYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS----RVIS-VGRLDIN 117
           +  L HKP+G V+  ++ DG +              D  P  FS    R ++  GRLDI+
Sbjct: 137 VTILLHKPVGYVSGQAE-DGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDID 195

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQVDQD--------KLNLLKKGIVI 167
           + GLL+LT +G +A+ L    +   + Y  RVRF G+   D         L  L+ G+ +
Sbjct: 196 STGLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRF-GERTADIERHFPAESLAKLRHGLEL 254

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G       V+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG 
Sbjct: 255 DGAPLKPAMVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGA 310

Query: 228 LLAGSTR 234
           L  G  R
Sbjct: 311 LPQGQWR 317


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/177 (32%), Positives = 95/177 (53%), Gaps = 19/177 (10%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLEL 136
           ++KP G++T  +D +GR T+   +P    RV  VGRLD ++EGLLLLT+DG L AR+++ 
Sbjct: 33  FYKPYGVLTQFTDREGRPTLQSFIP--VPRVYPVGRLDRDSEGLLLLTDDGRLNARLID- 89

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----------- 185
           P     R+Y V+  G      L  L++G++IQG      QV +  ++ +           
Sbjct: 90  PKFGHERIYWVQVEGIPTPQALQQLQQGLIIQGRKTRPAQVKVLAEEPTLPPRDPPIRFR 149

Query: 186 ----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                 W+ + LREG+NR+++++         RL+R+  GP  L  L  G  +++S+
Sbjct: 150 RSIPTTWLELTLREGRNRQVRRMTAAVGIPTLRLVRVGLGPLSLAGLAPGQWQDLSE 206


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 12/231 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  +++    V VN  + +  AV V     IE  G  L   +  R
Sbjct: 2   RLDKFLCDALGATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVIEWQGREL-AMQGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDG-FNHTAFVLLDEVKMDELHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
           +  P  +  + YRV     +  D    L +G+ ++     + ++TL  Q          V
Sbjct: 120 ITSPKHKCDKTYRVWLADPIGSDYAEKLAEGVQLR----NEKELTLPAQMSIVNADENEV 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + + EGK  ++K++F     KV +L R   G  +L  +L  G  R ++++
Sbjct: 176 LLTIHEGKYHQVKRMFAALGNKVEQLHRERIGAIELDESLEPGEYRYLTQE 226


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/221 (27%), Positives = 104/221 (47%), Gaps = 16/221 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A     +R EV+ ++  +RV VNG+     +  +N +S D + +D   L   + 
Sbjct: 2   RLDKFLAECNQGTRSEVKVLLKSKRVTVNGVTENSGKRQINEVS-DVVCLDEKKLT-YQS 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP  ++T   D   + TV D +        +  VGRLD +T GL+LLTNDG L
Sbjct: 60  FAYYMLNKPKDVITATEDS-VQKTVLDLIDKKDRIKGLFPVGRLDKDTTGLVLLTNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------VTLDTQKG 184
           A  L  P     +VY  +  G V + ++ L  K I ++    G++       V    +  
Sbjct: 119 AHNLLAPKKHVEKVYEAKIEGIVTEAEVELFSKPIELKN---GEVTKPSRLVVKKADEDA 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             + + + + EGK  +IK++F      V  L R+  G  +L
Sbjct: 176 GMSEIEITISEGKYHQIKRMFASTGMHVLELKRLKMGSLEL 216


>gi|325181474|emb|CCA15908.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 248

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 54/209 (25%), Positives = 97/209 (46%), Gaps = 27/209 (12%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V++  +P  +  +               +   P   S++   GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGDMQV- 177
           T DG LA+ +  P+    + Y VR    +++D       ++ L++G +   ICY    V 
Sbjct: 121 TQDGVLAKQILDPNGGVEKEYLVRVDMDLERDTKQAEEVVDKLREGFIWNDICYRARSVR 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            L+  +     +   L EGK R I+ + E
Sbjct: 181 VLNANQ-----LQFILTEGKKRHIRYMCE 204


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 83/177 (46%), Gaps = 21/177 (11%)

Query: 78  YHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP  ++   +D +    R+     LP     V   GRLD ++EGLLLLT+DG LA  L
Sbjct: 5   FNKPFNVLCQFTDRNASPRRTLAGFGLPG---GVYVAGRLDYDSEGLLLLTDDGALAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKG--------- 184
             P  +  + Y V+  G    ++L  L  G+ +        QV+ LD             
Sbjct: 62  TDPRHKQPKTYWVQVEGVPQPEQLQRLGDGVALNDGPTAPAQVSRLDAAPALWPRDPPVR 121

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                 +AW+ + LREG+NR+++++         RL+R++ G  +L  L  GS R +
Sbjct: 122 FRKTVPDAWLQIVLREGRNRQVRRMTAAVGLPTLRLVRVAMGTHRLDGLAPGSWRAL 178


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 102/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +    V ++G +++  A  +     +  DG  L +    R
Sbjct: 12  RLDKFLSQQLGISRNLVARELRAGLVTIDGEMVKTGATKITPEQEVAYDGNVLTQILGPR 71

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KPIG V +  DP   + ++     +  ++ + GRLDI+T GL+LLT++G  +  +
Sbjct: 72  YFMLNKPIGYVCSTDDPVNPTILYFIDEPLAHKLHAAGRLDIDTTGLVLLTDNGQWSHRI 131

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D     K G+ + G        TL+    +   +T+   
Sbjct: 132 TAPKHHCEKTYVVTLEQPIATDVAEKFKTGVQLNGEKELTKPATLEVITPTEVKLTIS-- 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EGK  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 190 EGKYHQVKRMFAAVGNHVVALHRERIGDITLDDALAPGEYRPLTEE 235


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 102/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +    V ++G +++  A  +     +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRNLVARELRAGLVTIDGEMVKTGATKITPEQEVAYDGNVLTQILGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KPIG V +  DP   + ++     +  ++ + GRLDI+T GL+LLT++G  +  +
Sbjct: 62  YFMLNKPIGYVCSTDDPVNPTILYFIDEPLAHKLHAAGRLDIDTTGLVLLTDNGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D     K G+ + G        TL+    +   +T+   
Sbjct: 122 TAPKHHCEKTYVVTLEQPIATDVAEKFKTGVQLNGEKELTKPATLEVITPTEVKLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           EGK  ++K++F      V  L R   G   L   LA G  R ++++
Sbjct: 180 EGKYHQVKRMFAAVGNHVVALHRERIGDITLDDALAPGEYRPLTEE 225


>gi|167835760|ref|ZP_02462643.1| RNA pseudouridine synthase family protein [Burkholderia
           thailandensis MSMB43]
          Length = 240

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/215 (28%), Positives = 97/215 (45%), Gaps = 8/215 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++   RV   G     A  +  +T  + EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGRVAAVGATCTDAHASFDTTQLVFEVDGVAWPYRARAYVVL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   ++VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G         L         + + + EGK  +
Sbjct: 129 TPKTYVATVRHPLDDAQLDALRAGVLLHG--EPKPVAALAAVARGERLLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           +K++    + +V+ L R   G F L G L  G+ R
Sbjct: 187 VKRMVAAASNRVDALHRSRIGGFALPGDLAEGAWR 221


>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 = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 122/235 (51%), Gaps = 15/235 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++++   SR+E + +I + RVKV+G ++++A   V   + +EV+G  ++  +   
Sbjct: 2   RLDKYLSKSLHISRKEAKELIREGRVKVSGKVVKQAEYRVKEGEEVEVEGKSVKPKKNVY 61

Query: 75  LWLYHKPIG-LVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L LY KP G L TT  D   P     + ++ PS   ++ S GRLD++ EGLLL+T+DG L
Sbjct: 62  LMLY-KPKGYLSTTEEDKKYPSFLELIREHFPS--RKLFSAGRLDVDAEGLLLITDDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAWV 189
           A  L  P  +  + Y VR    +  ++L  L +      +   +  V L   +K S   V
Sbjct: 119 AHRLTHPKWKVEKEYIVRLDRDIGDEELKKLYE------VKLEEKPVQLVKAEKLSGDTV 172

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
              L EG++  +K++F+     V  L R   G  +L   +  G  RE++++ ++E
Sbjct: 173 KAILTEGRHHVVKRLFKAVGHNVVYLKRTRVGNLRLDENMEPGEWRELTEEEVKE 227


>gi|310768104|gb|ADP13054.1| 16S rRNA pseudouridylate synthase A [Erwinia sp. Ejp617]
          Length = 234

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 105/227 (46%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R +  ++V V+G ++   +  + +   +E DG  L +    R
Sbjct: 2   RLDKFISQQLEVSRAIAARELRARKVTVDGEVVREGSYKLNADSTVEYDGNVLEQQLGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP+G V +  DPD  + + F   P  + R+ + GRLDI+T GL+L+T+DG  +  
Sbjct: 62  YFMLNKPVGYVCSTDDPDHPTILYFLEEPGAY-RLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  + +   +T+  
Sbjct: 121 ITSPRHHCEKTYLVTLESAISDDNAQQFADGVQLHNEKTLTKPAALEVIEPNVVRLTIS- 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G  +L + L  G  R +S +
Sbjct: 180 -EGRYHQVKRMFAAVGNRVVGLHRERIGAIRLDSDLHPGEYRPLSAE 225


>gi|126173257|ref|YP_001049406.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996462|gb|ABN60537.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 256

 Score = 68.6 bits (166), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 64/215 (29%), Positives = 104/215 (48%), Gaps = 12/215 (5%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           R+ V  ++   RV V+G++++     V     I++D   L+      + L HKPIG+V+ 
Sbjct: 41  RKAVRELLLSGRVCVDGLIVKDMDRQVDEFSRIQLDEQILQANAPVYVML-HKPIGVVSA 99

Query: 88  HSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             D   + TV D L       + + GRLD+N+ GLLLLTND   +  L  P+ +  +VYR
Sbjct: 100 TKDTQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDALMSPTHKVDKVYR 158

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVGLREGKNREIKK 203
           V     + ++ +    +G+      +G   +T    K    ++    V L EGK  +IK+
Sbjct: 159 VTLANPITEEYIAAFAEGMY-----FGFEDITTQPAKLVILADNVAEVTLHEGKYHQIKR 213

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           +F  F   V  L R+S G   L   LA G +R ++
Sbjct: 214 MFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALT 248


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 86/175 (49%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++T  +D  GR+T+ D +     RV + GRLD+++EGLLLLT++G L   L  
Sbjct: 4   LFNKPYNVLTKFTDDQGRATLADFID--IPRVYAAGRLDMDSEGLLLLTDNGQLNHALTD 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDMQVTLDT----- 181
           P  +  + Y V+  G   + ++  L+ G+ ++           I Y       +      
Sbjct: 62  PENKAYKTYIVQVEGVPTKAQIKTLETGVELKDGMTLPAKVKRIPYPKWLWEREKPIRVR 121

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           Q    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R V
Sbjct: 122 QNKPTSFLQIKIKEGRNRQVRRMTAAVGVPTLRLIRTHIGDYHIADLKPGQYRVV 176


>gi|330751986|emb|CBL80499.1| ribosomal large subunit pseudouridine synthase F [uncultured
           Polaribacter sp.]
          Length = 164

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 79/161 (49%), Gaps = 11/161 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+ +G+ SRRE E+ I + R+ +NG   +     V   D ++ DG   R  E   +
Sbjct: 11  LNKYISSSGVCSRREAEKFIKEGRITINGKKTQLGN-RVGKKDVVKFDG---RLVEPKNI 66

Query: 76  WLY---HKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            LY   +KP+G+V+T  D +  + V   N P    R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 67  TLYIALNKPVGIVSTTDDREPNNIVQHVNYPE---RLFPIGRLDKPSEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
             +        + Y V     +  D +  +  GI I   CY
Sbjct: 124 NKILRAGNNHEKEYFVSVDKSITDDFIASMGNGIPIFRNCY 164


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 101/230 (43%), Gaps = 22/230 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +  ++   G  SRR+   +I   RV V G     +A +  +T   + DG+     +    
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVTVAGA----SATDPDAT--FDTDGLVFSVDDTA-- 54

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHAHAYLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +LN L+ G+ + G       V  D +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLNTLRTGVQLHGEPKPIAAVAADARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
              +TV   EGK  ++K++    + +V  L R S G F L G L  G+ R
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVEALHRESIGGFTLPGDLAPGAWR 221


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/185 (29%), Positives = 90/185 (48%), Gaps = 13/185 (7%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGR 113
           IEV G  +   + + + L +KP G+V+   D +   TV D L      P ++     VGR
Sbjct: 31  IEVTGQRVTHPKHSYIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGR 84

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICY 172
           LD +TEGL+LLT++G L   +  PS    + Y V  +G + +D  +    GI    G   
Sbjct: 85  LDRDTEGLVLLTDNGPLGFRMLDPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQC 144

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              Q+T+       +  ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G 
Sbjct: 145 QPAQLTILKADTDQSQASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGE 204

Query: 233 TREVS 237
            R ++
Sbjct: 205 YRYLT 209


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/226 (26%), Positives = 112/226 (49%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           RV K+I  A + +R+ ++R   +  + +NG +++ ++V V  + D +   G  +   +  
Sbjct: 2   RVDKMIGNANLDTRKNIKRNAKKGELIINGQIVKDSSVKVDPNLDEVIYMGELVDYFDNI 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +K  GL+   ++ DG  TV  +L   +  +     GRLD +T GLLLL+ DG   
Sbjct: 62  YIMM-NKREGLICQSNELDG--TVMSDLDEFYLNLDLAIAGRLDKDTTGLLLLSTDGKFI 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P++   + Y V    ++D   + + K G+ I+   Y      LD   G  A+V V
Sbjct: 119 HKVISPNSHIWKKYEVETSKKIDPSLVEIFKDGVYIKEDDYYARSAKLDIIGGKKAYVYV 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
              EGK   +K++F   + +V +L R++ G  +L  +L  G  RE+
Sbjct: 179 --TEGKFHLVKRLFSNNDNEVIKLKRLAIGDLELDQSLNPGQYREL 222


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 102/212 (48%), Gaps = 5/212 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R+E  +++  + V+VNG +++  A+ V     +E  G  L   +  R
Sbjct: 2   RLDKFLCTTLGITRKEAGKILKDKLVEVNGEIVKNGALKVTDDCDVEFSGRTL-SLQGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D   TVF     +   R+   GRLD +T GL+L+T+DG  +  
Sbjct: 61  YYMLNKPSGYVCSHVD-DFNPTVFILFDEVAPERMHVAGRLDGDTTGLVLVTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +++  +   ++G+ ++G     +   L+  +   A +T+  
Sbjct: 120 ITSPRHVCEKTYYVETADPIEESYIQAFEEGVQLRGEKELTLPAKLEILEEKVALLTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     KV  L R   G  +L
Sbjct: 178 TEGKYHQVKRMFAAMGNKVELLHRERVGAIEL 209


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 103/219 (47%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV ++GI+L+ A  +  + D H +VDG   R   R +
Sbjct: 3   LETILYSQGFGSRRQCRALVEAGRVSIDGIVLDDADADFATDDLHFDVDGT--RWPYRAQ 60

Query: 75  LWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            +L  +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG   
Sbjct: 61  AYLVLNKPAGYECSR-DPQHHLSVFSLLPPQFGARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D  +L  L++G+++ G       V    ++  +  +TV
Sbjct: 120 HAYTSPKKKVPKTYLAEVKHALDDRQLAALREGVLLHGEPKPIAAVAARARELRSLELTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EGK  ++K++      +V  L R   G + L   LA
Sbjct: 180 --LEGKYHQVKRMVAASGNRVEALHRERVGGYTLPADLA 216


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 58/236 (24%), Positives = 109/236 (46%), Gaps = 4/236 (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+    + + V
Sbjct: 132 WSRRLTEPRIKLPKVYRVTTVEPVSTNAIERFAQGIWFEYERLTTSPARLEPLSANESRV 191

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV-SKKILRE 243
           T+   EG+  +IK++F     +V+ L R   G   L  TL  G +R + S++I+ E
Sbjct: 192 TI--YEGRYHQIKRMFHATGNRVSSLHREQMGAITLDPTLEPGESRPLTSREIILE 245


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 80/280 (28%), Positives = 119/280 (42%), Gaps = 76/280 (27%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNL---------------------PSIF-- 105
           ERT + LYHKPI +VTTH+  D  GR  V+D++                     P+ F  
Sbjct: 29  ERTVVLLYHKPINVVTTHAANDVKGRMNVYDDVLSMKGFSGWNHVGKSADRERTPASFAE 88

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--------ELPSTQWLRVYRVRFHGQ 152
                S++ ++GRLD  T GLLLLTNDGGL   +        +       + Y     G 
Sbjct: 89  ATQIRSKLHAIGRLDAETTGLLLLTNDGGLVHHVTNKDSVSHQHHGNPVFKTYEALVMGF 148

Query: 153 VDQDKLNLLKKGIVIQGICYGDM---------QVTLDTQKG-SNAWVTVGLREGKNREIK 202
            D     LL+K +  QG+  GD          ++ + T     +  V++ + EGKNR+I+
Sbjct: 149 YDNHS-PLLEK-MRTQGVNIGDKYGGTTRPVDELIVKTNPTLKSTLVSLTICEGKNRQIR 206

Query: 203 KVFEFFNWKVNRLIRISYG-PFQLGTL-LAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
           ++F      V RL R   G    L ++ +AG  R              +L E +V     
Sbjct: 207 RMFHALGSGVIRLCRTQIGRSLTLSSVPMAGQWR--------------ILTEKEV----- 247

Query: 261 IYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
               ET +  RP  I EV    +R  K +    G S+++K
Sbjct: 248 ----ETALDWRPRYIGEV-SALSRAGKTTKAVTGTSRRRK 282


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 101/223 (45%), Gaps = 14/223 (6%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K I   G+ SR++ + +I    + VNG +    ++++     + + +DG P+        
Sbjct: 5   KYIQAQGLGSRKQCQWLIDNGCIAVNGEIRSDAKSSIKPEEVETLAIDGEPIFAVPLPYF 64

Query: 76  W-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP    T+H  P    +VF   P+    +   +VGRLD +T G+LL+TNDG    
Sbjct: 65  YILLNKPANYETSHK-PQQYPSVFSLFPNHMRNIDMQAVGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  ++YRV      D      LK G+++      D   T+   +      TV 
Sbjct: 124 RVTSPKHKVPKLYRVTLKHAADNRLCETLKNGVLLH-----DDNETVAADEAVLEKPTVL 178

Query: 193 L---REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           L    EGK  ++K++      +V RL R  +G +    L +GS
Sbjct: 179 LMTITEGKYHQVKRMVAAAGNRVERLHREKFGDWSADDLPSGS 221


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENPTT 203

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 204 ------LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 246


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 16/229 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT 203

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 204 ------LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 246


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 101/225 (44%), Gaps = 3/225 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR +V R +   RV V+  +++  A  +     I  +G  L +   +R
Sbjct: 2   RLDKFLSQQLGISRNDVGRELRASRVTVDDEVIKSGAYKLKPDHQIAYEGSVLEQLGGSR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DP   + ++     +  ++ S GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPTNPTILYFIDEPVAHKLHSAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  D       G+ + G         L+  +     V + +R
Sbjct: 122 TSPKHHCEKTYLVTLEYPISDDTEMKFLAGVQLNGEKTLTKPAKLEIIEPHR--VRLSIR 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           EG+  ++K++F      V  L R   G   L  TL  G  R ++K
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERVGQIYLDSTLEPGEYRALTK 224


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 93/210 (44%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++    V V G     A  +  +T  + EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGVAWPYRARAYVAL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   S+VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G         L         + + + EGK  +
Sbjct: 129 VPKTYVATVRHPLDDAQLDALRAGVLLHG--EPKPVAALAAVARGERLLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V  L R   G F L   LA
Sbjct: 187 VKRMVAAASNRVEALHRSRIGGFALPEDLA 216


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 109/237 (45%), Gaps = 10/237 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +Q +    R+ K +  A   +R+E   ++    V V+ ++ +  A  +  T  +E  G  
Sbjct: 20  LQADEVSMRLDKFLCDALGTTRKEATMLLKSGEVTVDDLVQKSGAFKLKETSRVEWQGRE 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           +  A   R  + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T
Sbjct: 80  I-TAHGPRYIMMHKPDGVVCSHEDGFNQ-TAFILLDEVNIQDLHFAGRLDVDTTGLLLIT 137

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           +DG  +  +  P  +  + YRV     +  D       GI ++    G+ ++TL  Q   
Sbjct: 138 DDGQWSHRVTSPKHKCEKTYRVWLADPIQADYAEQFTNGIELR----GERELTLPAQLEV 193

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            S   V + + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++
Sbjct: 194 VSETEVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEE 250


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 102/219 (46%), Gaps = 15/219 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-T 73
           R+ K + ++   +R      I    V VNG++    A+ V   + + ++G PL  A R +
Sbjct: 2   RLDKFLCKSTDLNRDAASVAILSGSVTVNGVIATDCAMQVHENNAVSLNGKPL--APRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
           R ++ HKP    T  S+ DG      +L  I   F   I VGRLD +T GL+LLT+DG  
Sbjct: 60  RYFVLHKPAD--TLCSNVDGAYPSLFHLLDIERAFDLHI-VGRLDADTTGLVLLTDDGRW 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +  +  P  Q  +VYRV+    +D +           G+ +QG     +  TL  Q+  +
Sbjct: 117 SFNIISPQYQCKKVYRVQLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDD 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + L EGK  ++K++F     KV  L R   G   L
Sbjct: 175 KTVLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL 213


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 93/210 (44%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++    V V G     A  +  +T  + EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGVAWPYRARAYVAL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   S+VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G         L         + + + EGK  +
Sbjct: 129 VPKTYVATVRHPLDDAQLDALRAGVLLHG--EPKPVAALAAVARGERLLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V  L R   G F L   LA
Sbjct: 187 VKRMVAAASNRVEALHRSRIGGFALPENLA 216


>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 = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/268 (25%), Positives = 114/268 (42%), Gaps = 41/268 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHI-------- 60
           +R++K+++  G+ SRRE +R+I   +V V+G+  +     R    V+    +        
Sbjct: 4   ERLNKLLSAMGVCSRREADRLIESGKVLVDGVPAKMGQKVRMDQTVVCRGKVVGRGEAAA 63

Query: 61  --------------EVDGVPLRKAE-----------RTRLWLYHKPIGLVTTHSDPDGRS 95
                           DG   + A            R  L   +KP G+V T SD D   
Sbjct: 64  GAGNGKTARRVGSGRADGTAAQDARPASLPRSMKKPRPVLLAVNKPKGVVCTASDKDKAP 123

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
            + D +     RV  VGRLD ++EGL+L+TN G L   +        + Y+V     V  
Sbjct: 124 NIVDMIQYPV-RVYYVGRLDKDSEGLVLMTNQGDLVNKIMRSGNAHEKEYQVVVDRPVTA 182

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           + L  ++KG+ ++ +      +    +K  +   ++ L +G NR+I+++ E     V  L
Sbjct: 183 EFLARMEKGVRLKEL--DRTTLPCKVRKTGDKRFSIVLTQGLNRQIRRMCEACGCHVRSL 240

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILRE 243
            R+      LG L +G  R+V     RE
Sbjct: 241 KRVRVMNICLGDLKSGEYRQVEGAEYRE 268


>gi|144897678|emb|CAM74542.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 195

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 90/185 (48%), Gaps = 22/185 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD-GRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL L++KP  ++T  +D + GR+T+ D  ++P ++      GRLD ++EGLL+L++DG L
Sbjct: 3   RLILFNKPYDVLTQFTDREAGRATLADYVDVPGVYP----AGRLDRDSEGLLVLSDDGPL 58

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              +  P  +  + Y  +  G      L  L++G++++          L  +        
Sbjct: 59  IARIAQPRHKLAKTYFAQVEGIPTAAALAQLRQGVMLKDGPTLTAGAELVAEPDWLWPRH 118

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      AWV + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 119 PPIRWRAAIPTAWVKLTLHEGRNRQVRRMTAAVGFPTLRLIRWAVGDWNLAGLAPGQWRE 178

Query: 236 VSKKI 240
           V+  +
Sbjct: 179 VTAPV 183


>gi|327484245|gb|AEA78652.1| Ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           LMA3894-4]
          Length = 231

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 106/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIM-LHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGIVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 101/207 (48%), Gaps = 10/207 (4%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV-FD 99
           +NG +    A+ V   D + +DG  + K E+ ++++ +HKP+G+  T +D    + + + 
Sbjct: 3   INGEICTHGAL-VSDGDRVTIDGQVIVKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYI 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           N P    R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++
Sbjct: 62  NYPE---RIFPVGRLDKASEGLILLTNDGAIANQILHGDHEHEKEYVVTVDKPFTDWFID 118

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            +  G+ I+       +VT    +   +   + L +G NR+I+++   F + V +L R+ 
Sbjct: 119 EMSSGVKIKDGMTKPCKVT----RVDQSTFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVR 174

Query: 220 YGPFQLGTLLAGSTREVSKKILREQLG 246
               +L  L  G  R V+ + L   +G
Sbjct: 175 IMNIELNELEVGKWRSVTAEELEILIG 201


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 87/180 (48%), Gaps = 22/180 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR+T+ D +     RV   G LD ++EGL++LT+DG L   +  
Sbjct: 10  LFNKPFNVLCQFTDKSGRATLADFVD--VPRVYPAGLLDYDSEGLVVLTDDGRLQARIAD 67

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------------- 182
           P  + ++ Y V+  G  D+  L  L+ G+ ++     + Q TL                 
Sbjct: 68  PRFKLVKTYWVQVEGVPDEAALVQLRAGVWLKDKGKREAQRTLPAAVRVIAEPPLWPRVP 127

Query: 183 ------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     AW+ + +REG+NR+++++         RL+R+  G + L  L +G+ ++V
Sbjct: 128 PVRFRLSVPTAWLELSIREGRNRQVRRMTAAVGLPTLRLVRVQVGDWSLRGLQSGAWKKV 187


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 109/237 (45%), Gaps = 10/237 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +Q +    R+ K +  A   +R+E   ++    V V+ ++ +  A  +  T  +E  G  
Sbjct: 20  LQADEVSMRLDKFLCDALGTTRKEATMLLKSGEVTVDDLVQKSGAFKLKETSCVEWQGRE 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
           +  A   R  + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T
Sbjct: 80  I-TAHGPRYIMMHKPDGVVCSHEDGFNQ-TAFILLDEVNIQDLHFAGRLDVDTTGLLLIT 137

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           +DG  +  +  P  +  + YRV     +  D       GI ++    G+ ++TL  Q   
Sbjct: 138 DDGQWSHRVTSPKHKCEKTYRVWLADPIQADYAEQFTNGIELR----GERELTLPAQLEI 193

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            S   V + + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++
Sbjct: 194 VSETEVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGDYRYLTEE 250


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 106/237 (44%), Gaps = 29/237 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------ 68
           R++K I+ +G  SRRE +++I    V VNG             D + V+G  ++      
Sbjct: 6   RLNKFISDSGYCSRREADKLIEDDLVLVNG-QPPTLGTRCHPGDVVYVEGKRIKSRANAG 64

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLL 124
            +A+R  +  Y+KP     TH      + V  N+ S      R+  +GRLD  +EGL+LL
Sbjct: 65  SQADREYIA-YNKP-----THITCTTEADVVGNIISAVGYKKRIFPIGRLDKMSEGLILL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYGDMQVTLD 180
           T+DG +   +        + Y V     +    +  +  G+ I G     C  +MQ    
Sbjct: 119 TSDGDIVNKILRAENAHDKEYLVTVDKPITDKFIEKMGNGVPILGTKTLPCKINMQ---- 174

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     + L EG NR+I+++ E+F ++V +L R+      LG L  G  R+++
Sbjct: 175 ----GEFMFKIILTEGLNRQIRRMCEYFGYEVTKLKRVRIMNITLGNLKPGEWRKLT 227


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 46/171 (26%), Positives = 82/171 (47%), Gaps = 16/171 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP+ +++  S    +  +   L +   R+   GRLD ++EGLL+LT+ G L   L
Sbjct: 4   LILLNKPMNMLSQFSSEGEKQGISTLLSAPGYRI--AGRLDSDSEGLLVLTSYGRLQAYL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P     + Y V+  GQ+D+  +  L+ G+ ++       +V +               
Sbjct: 62  TAPKHNTWKYYYVQVEGQIDEQAVCRLQAGVQLKDGPTLPARVKVIEPPSLWQRTPPVRY 121

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 +W+ +GL+EG+NR+I+++     +   RL+R   GPF+L  L  G
Sbjct: 122 RAHIPTSWLEIGLQEGRNRQIRRMTAHVGYPTLRLVRFRSGPFKLADLGPG 172


>gi|222110563|ref|YP_002552827.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730007|gb|ACM32827.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 216

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 87/179 (48%), Gaps = 25/179 (13%)

Query: 78  YHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP G+++  + P+GR      F ++P ++      GRLD ++EGLLLLT+DG L   +
Sbjct: 33  FNKPYGVLSQFT-PEGRWRGLQDFIDVPGVYV----AGRLDADSEGLLLLTDDGALQARI 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----------------QGICYGDMQVT 178
             P  +  + Y V+  G  D+  L  L++G+ +                  +   D  + 
Sbjct: 88  SDPRHKMEKTYWVQVEGIPDEAALQALRQGVQLGDGPTLPARVRRLEPPPALWERDPPIR 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  +  S
Sbjct: 148 V-RQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYALDGLEPGCWQPAS 205


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 118/250 (47%), Gaps = 36/250 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+SK ++  G+ SRRE +  I +  V V+G  +      V +  +IE+       + ER 
Sbjct: 443 RLSKRMSELGLCSRREADEWIPRGWVIVDGKPVTELGSRVRADANIEIHQAARSEQGERV 502

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDIN 117
            + L HKP+G V+  ++ DG                D     F+      +   GRLDI+
Sbjct: 503 TV-LLHKPMGYVSGQAE-DGYEPAAVLFTAENQWSEDPTRKRFAPWQRKSLAPAGRLDID 560

Query: 118 TEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH---GQVDQ--------DKLNLLKKG 164
           + GLL+LT DG +AR L  E  + +   + RV++H   G V++        DKL LL+ G
Sbjct: 561 STGLLVLTQDGRVARALIGEDSNVEKEYLVRVQWHSPDGVVERNVSEVFPADKLELLRHG 620

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L R+  G   
Sbjct: 621 LSLDGVVLKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLEVVGLKRVRMGRIV 676

Query: 225 LGTLLAGSTR 234
           LG L  G  R
Sbjct: 677 LGDLPPGQWR 686


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 117/233 (50%), Gaps = 12/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ +R EV+ ++ +  V  NG  ++ +   +    D +EV G  +      
Sbjct: 2   RIDKFLAQMGVGTRTEVKALLKKGHVLHNGAKIKSSKTQIDPEHDVVEVKGRVIAYEPFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L + +KP  +++   D D   TV D +       +  VGRLD +TEGLLL+TNDG    
Sbjct: 62  YLMM-NKPQNVISATVD-DQHQTVIDIIEGYRHLDLFPVGRLDKDTEGLLLITNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
            L  P+    + Y V+    +  +     ++GI ++   +    +++  D+     A+VT
Sbjct: 120 ALMNPNKHVSKTYWVKAKYALKTNDPKRFEEGITLKEGRLQPAHLEILDDSM---TAFVT 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILR 242
           +  +EGK  ++K++F   + +V  L R+S G   L + L+ G+ R +++  L+
Sbjct: 177 I--QEGKYHQVKRMFHAIDNEVVGLKRVSIGDLTLDSSLSPGAYRSLTEDELK 227


>gi|289675786|ref|ZP_06496676.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae FF5]
          Length = 179

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/147 (29%), Positives = 77/147 (52%), Gaps = 20/147 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L L++KP  ++T  SD +GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLILFNKPFDVLTQFSDEEGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--------- 181
             +  P  +  + Y V+  G+   ++L  L+ G+ +  G         LD          
Sbjct: 88  SRIADPKHKLAKTYWVQVEGEPSDEQLQQLRDGVQLNDGPTLPAEARQLDEPQLWPRNPP 147

Query: 182 ----QKGSNAWVTVGLREGKNREIKKV 204
               +    +W+ + ++EG+NR+++++
Sbjct: 148 VRFRKSVPTSWLELVIKEGRNRQVRRM 174


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 106/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIM-LHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 107/231 (46%), Gaps = 12/231 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  +++    V VN  + +  AV V     +E  G  L   +  R
Sbjct: 2   RLDKFLCDALGATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVVEWQGREL-AMQGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPEGFVCSHEDG-FNHTAFVLLDEVKMDELHFAGRLDVDTTGLVLITDDGKWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
           +  P  +  + YRV     +  D    L +G+ ++     + ++TL  Q          V
Sbjct: 120 ITSPKHKCDKTYRVWLADPIGSDYAEKLAEGVQLR----NEKELTLPAQMTIVNADENEV 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + + EGK  ++K++F     KV +L R   G  +L  +L  G  R ++++
Sbjct: 176 LLTIHEGKYHQVKRMFAALGNKVEQLHRERIGAIELDESLEPGEYRYLTQE 226


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 110/246 (44%), Gaps = 33/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D     + ++  
Sbjct: 396 RINKRIADMGMCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQERQDQQV 454

Query: 75  LWLYHKPIGLVTTHSDPDG-----------------RSTVFDNLPSIFSRVISVGRLDIN 117
             L +KP+G V+  ++ DG                 RS    N  S    +   GRLDI+
Sbjct: 455 TILLNKPMGYVSGQAE-DGHEPAVVLITNENRWNEDRSKTRFNF-SQLKGLAPCGRLDID 512

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVD--------QDKLNLLKKGIVIQ 168
           + GLL+LT DG +AR +    ++  + Y VR   G  D        ++KL LL+ G+ + 
Sbjct: 513 SVGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRHGLSLD 572

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  QV     +     +   L EGK R+I+++ E    KV  L RI  G   LG L
Sbjct: 573 EQPLKPAQVDWQNPE----QLRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGVTLGNL 628

Query: 229 LAGSTR 234
             G  R
Sbjct: 629 PTGQWR 634


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/169 (32%), Positives = 88/169 (52%), Gaps = 11/169 (6%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSR-VISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP G +T   D +   TV D    + FS+ +  VGRLDI+TEGLL++T+DG LA  +
Sbjct: 1   MFNKPSGYITAVKD-ERYPTVMDFFADLPFSKKLFPVGRLDIDTEGLLIITDDGQLAHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICY----GDMQVTLDTQKGSNAWV 189
             P  +  + Y     G + D D     K+GIV++   Y      + +   +++ S  ++
Sbjct: 60  AHPKWEIEKEYYAVVKGDISDLDLSRFEKEGIVLKKEKYRTKPFKINIISTSEERSEIYI 119

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           TV  REGK   +K++ E     V  L R+  GP +L   L  G  RE++
Sbjct: 120 TV--REGKYHIVKRIMEELGHPVLYLKRVRIGPLRLDEDLEEGDFRELT 166


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 86/186 (46%), Gaps = 25/186 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL   +KP G +   S  + R+++ D    P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 45  RLIALNKPFGTICQFSAHETRASLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQ 100

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------ 185
             +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G+      
Sbjct: 101 AKIAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNP 160

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGST 233
                     AW+ + + EGKNR+++++     +   RL+R+  G    F LG L  G T
Sbjct: 161 PIRHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALG-LAPGET 219

Query: 234 REVSKK 239
           RE+  +
Sbjct: 220 RELPPR 225


>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 = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 63/232 (27%), Positives = 105/232 (45%), Gaps = 20/232 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G PL+  E  R
Sbjct: 2   RLDKYLCKSTDLTKPEAIERIHNGEVNVNSETVTDESAQVHESNTILLNGTPLKLRE-FR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP G + ++ D        +  PS+F        S +   GRLD +T GL+L+T+
Sbjct: 61  YLLMHKPAGTICSNID--------EVYPSLFNYIEIDKASELHIAGRLDADTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  + LP+    +VYRV     +  D  +  K GI +QG         L+      
Sbjct: 113 DGRWSFNITLPTKSCKKVYRVTLSRGIKDDVADKFKAGIQLQGEQKPTRPAELEVITSKQ 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             +T+   EGK  ++K++F     +V  L R   G  +L  + AG  R ++K
Sbjct: 173 VLLTI--TEGKFHQVKRMFAAVGNRVVGLHREQIGDVRLD-VEAGQWRYLTK 221


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 46/184 (25%), Positives = 92/184 (50%), Gaps = 25/184 (13%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L++KP  +++  +D    ++       F ++P++++     GRLD ++EGLL+LT+DG L
Sbjct: 6   LFNKPFNVLSQFTDAGNEASSRRTLSHFIDVPNVYA----AGRLDKDSEGLLVLTDDGKL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----- 185
              +  PS +  + Y V+  G  D+  L+LL+ G++++       +V L  Q        
Sbjct: 62  QHRISDPSNKMEKSYWVQVEGIPDETALDLLRAGVLLKDGMTKPAKVKLMDQPVDLWVRE 121

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                     ++W+ + + EG+NR+++++     +   RLIR   G + +  + +G    
Sbjct: 122 PPVRYRKSVPDSWIEITISEGRNRQVRRMTACVGFPTLRLIRYRVGNWTIDGIESGDWIM 181

Query: 236 VSKK 239
            SKK
Sbjct: 182 HSKK 185


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 103/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHSLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 110/246 (44%), Gaps = 33/246 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D     + ++  
Sbjct: 454 RINKRIADMGLCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQDRQDQQV 512

Query: 75  LWLYHKPIGLVTTHSDPDG-----------------RSTVFDNLPSIFSRVISVGRLDIN 117
             L +KP+G V+  ++ DG                 RS    N  S    +   GRLDI+
Sbjct: 513 TILLNKPMGYVSGQAE-DGHEPAVVLITNENRWNEDRSKTRFNF-SQLKGLAPCGRLDID 570

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVD--------QDKLNLLKKGIVIQ 168
           + GLL+LT DG +AR +    ++  + Y VR   G  D        ++KL LL+ G+ + 
Sbjct: 571 SVGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRHGLSLD 630

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  QV     +     +   L EGK R+I+++ E    KV  L RI  G   LG L
Sbjct: 631 EQPLKPAQVDWQNPE----QLRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGVTLGNL 686

Query: 229 LAGSTR 234
             G  R
Sbjct: 687 PTGQWR 692


>gi|157371821|ref|YP_001479810.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157323585|gb|ABV42682.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 266

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 109/229 (47%), Gaps = 15/229 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K I+ +GI SRR+ +R I   +V +N    E  A  V   D + V+G  +  R    
Sbjct: 8   RLNKYISDSGICSRRQADRYIKLGKVFINDNQAEVGAP-VFIGDVVSVNGQRIEPRNDAD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
             L   +KP+G++T+         V +N+    +   R   VGRLD +++GL+ LTN G 
Sbjct: 67  LVLIALNKPVGIITSMG-----KHVPNNIGDFVNHSQRTFPVGRLDKDSQGLIFLTNRGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G      QV    ++ +   +
Sbjct: 122 LVNKILRAGNNHQKEYLVTVDKPLTDEFIQGMGAGVPILGKVTHKCQV----EQEAPQVL 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + L +G NR+I+++ ++F ++V +L R+      L  L  G  R++S+
Sbjct: 178 RITLVQGLNRQIRRMCKYFGYQVTKLERVRIMNISLQGLALGEWRDLSE 226


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 106/229 (46%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIM-LHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      +GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELR----GERELTLPAQLEVISETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEE 224


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 103/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMIAAVGNRVQHLHRRRFAHLETENLKPG 220


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 80/174 (45%), Gaps = 17/174 (9%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP  ++   +D  GR+T+ D +P     V + GRLD ++EGLL+LTNDG L   L  P 
Sbjct: 2   NKPFDVLPQFTDEQGRATLKDYIP--LQGVYAAGRLDRDSEGLLVLTNDGRLQAQLTQPG 59

Query: 139 TQWLRVYRVRFHGQVDQDKLN------LLKKGIVIQGICYGDMQVTL---------DTQK 183
            +  +VY V+  G+  +  L        LK G  +  +     Q            + + 
Sbjct: 60  KRTGKVYYVQVEGEPSEADLQRFCQGLTLKDGPTLPALAERVAQPDWLWPRNPPIRERKN 119

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
              +W+ + L EG+NR+++++     +   RLIR S     L  L  G  R + 
Sbjct: 120 IPTSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMDSLTLQDLAPGEWRRID 173


>gi|253995971|ref|YP_003048035.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982650|gb|ACT47508.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 184

 Score = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 84/179 (46%), Gaps = 23/179 (12%)

Query: 77  LYHKPIGLVTTHS-----DPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L++KP  +V   S     +PD R +T+ D +P     V + GRLD ++EGLL+LT+DG L
Sbjct: 4   LFNKPFNVVCQFSPHDSPNPDNRHATLKDFIP--IPDVYAAGRLDTDSEGLLILTDDGAL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----- 185
              L  P  + ++ Y V+  G    + L  L+ G+ +        +V++  +        
Sbjct: 62  QHRLSHPKHKEIKTYWVQVEGAPSDEALQPLRVGVDLGDFITQPAEVSVMNEPAGIWLRN 121

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       W+ + + EGKNR+++++     +   RLIR + G + L  +  G  +
Sbjct: 122 PPIRERKAIPTTWLQIKISEGKNRQVRRMTAKVGFPTLRLIRYAIGRYTLDGIANGEYK 180


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 61/232 (26%), Positives = 109/232 (46%), Gaps = 20/232 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G PL+  E  R
Sbjct: 2   RLDKYLCKSTDLTKPEAIERIHNGEVNVNSETVTDESTQVHESNTILLNGTPLKLRE-FR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP G + ++ D        +  PS+F        S +   GRLD +T GL+L+T+
Sbjct: 61  YLLMHKPAGTICSNVD--------EVYPSLFKYIEIDKASELHIAGRLDADTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  + LP+    +VYRV     +  D  +  K G+ +QG    ++    + +  ++
Sbjct: 113 DGRWSFNITLPTKSCKKVYRVTLSRDIKDDVADKFKAGVKLQG--EQNLTRPAELEVITS 170

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             V + + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K
Sbjct: 171 KEVLLTITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRLD-VEAGQWRYLTK 221


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 49/202 (24%), Positives = 91/202 (45%), Gaps = 18/202 (8%)

Query: 44  GILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           G    R+A+N   +   E+   P   ++  ++ L++KP  ++   +D   R T+ + +P 
Sbjct: 20  GRTYSRSALNKTPSGKREIK--PQIASKDRKIVLFNKPFDVLCQFTDDADRKTLAEFIP- 76

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
               V + GRLD ++EGLLLLTN G L   L  P  +  + Y  +  G+   + +N L  
Sbjct: 77  -IKEVYAAGRLDRDSEGLLLLTNCGKLQNSLTAPDKKTNKTYWAQVEGEPTSESINDLCN 135

Query: 164 G--------------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           G              I+ +   +       + +     W+++ + EG+NR+++++     
Sbjct: 136 GVELKDGLTLPANVKIIDEPTIWARNPPVRERKAIPTTWLSITINEGRNRQVRRMTAHIG 195

Query: 210 WKVNRLIRISYGPFQLGTLLAG 231
               RLIR S G + L  +  G
Sbjct: 196 HPTLRLIRYSIGNYTLDDINCG 217


>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 = 67.8 bits (164), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 93/210 (44%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++    V V G     A  +  +T  + EVDG+      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGIAWPYRARAYVAL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   S+VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G         L         + + + EGK  +
Sbjct: 129 VPKTYVATVRHPLDDAQLDALRAGVLLHG--EPKPVAALAAVARGERLLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V  L R   G F L   LA
Sbjct: 187 VKRMVAAASNRVEALHRSRIGGFALPEDLA 216


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/202 (28%), Positives = 93/202 (46%), Gaps = 6/202 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +GI SRRE +  I    V VNG ++      V   D +  DG  +     T 
Sbjct: 61  RLNKYISNSGICSRREADTYIETGLVSVNGKIVNEMGYKVKLEDDVRFDGRRINPEPMTY 120

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP G  TT S+  G +TV D + +   SR+  +GRL  N  GLLL TND  L   
Sbjct: 121 VLL-NKPKGFATTTSESKG-NTVMDLVANASNSRITPIGRLGRNATGLLLFTNDDKLKE- 177

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            +L      R++ V     +    +  +++G  I G      ++     K +   + + +
Sbjct: 178 -KLSKKGMSRLFHVELDKNLKAADIQKIREGFTIAGKKIEIEEINYVEGK-TKKEIGLKI 235

Query: 194 REGKNREIKKVFEFFNWKVNRL 215
           +   N  I+ +F  F + + RL
Sbjct: 236 KNLGNSVIRDIFAHFEYDIVRL 257


>gi|330973498|gb|EGH73564.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 173

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 54/168 (32%), Positives = 84/168 (50%), Gaps = 9/168 (5%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       + + GRLD NT GL+L+TNDG  +R
Sbjct: 4   RYFMLHKPEGCVSATSDAQ-HPTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 62

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVT 190
            L  P ++  +VY V     +D+       +G+    +GI     Q+TL   + +     
Sbjct: 63  RLTQPQSKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGITTQPAQLTLLGPRRAR---- 118

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++
Sbjct: 119 LSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALLLDPDLRPGSYRALN 166


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 54/187 (28%), Positives = 86/187 (45%), Gaps = 25/187 (13%)

Query: 77  LYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L HKP G+++  + +P  R     +L  +  +V + GRLD ++EGLLLLT +G L + L 
Sbjct: 9   LLHKPYGVLSQFTPEPGSRWRCLADLVPV-PQVYAAGRLDADSEGLLLLTTEGRLQQRLT 67

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDMQVTLDT---- 181
            P     R Y V+  G     +L  L  G+++QG          + +  +Q   D     
Sbjct: 68  DPRFGHWRTYWVQVEGTATDKQLQQLCDGVLVQGRQTLPAQAQRLRHDQIQPWPDRVPPI 127

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
              +     W+ + LREG+NR+++++         RLIR +        P  L  L  GS
Sbjct: 128 RERRSIPTDWLELSLREGRNRQVRRMTAAVGLPTLRLIRSAIDLMDGGLPLNLNGLAPGS 187

Query: 233 TREVSKK 239
            R VS +
Sbjct: 188 WRPVSTE 194


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 52/186 (27%), Positives = 84/186 (45%), Gaps = 25/186 (13%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G +   S  + R ++ D    P ++      GRLD ++EGLLLLT+DG L   +  
Sbjct: 7   NKPFGTICQFSPHETRGSLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQAKIAE 62

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA----- 187
           P  + ++ Y  +  G  D   L  L++G+     +   C        DT    N      
Sbjct: 63  PRHKLVKRYWAQVEGAPDAGALATLERGVDLGDYVTRPCRARFVTPPDTLWPRNPPVRYR 122

Query: 188 ------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVSK 238
                 W+ + + EGKNR+++++     +   RLIR+  G    F LG L  G TRE+  
Sbjct: 123 AAIPTTWIELEIAEGKNRQVRRMTAAVGFPTLRLIRVGIGALDLFALG-LAPGETRELPP 181

Query: 239 KILREQ 244
           +   E+
Sbjct: 182 RAPWER 187


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 58/229 (25%), Positives = 104/229 (45%), Gaps = 22/229 (9%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDG-----VPLRKA 70
           K +   GI SR+  + +I    V++NG ++  E+A +   +   + +DG     +PL   
Sbjct: 5   KYLQAQGIGSRKMCQTLIRCGLVQINGEIINNEKAEITPENVQTMNIDGEDAVVIPLPY- 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
                 L +KP    T+H  P    +VF   P     + + ++GRLD +T G+LL+TNDG
Sbjct: 64  ---YYILLNKPENYETSHK-PRDYPSVFMLFPDHLRATDIQAIGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---S 185
                +  P  +  ++YRV      ++     LK G+++      D   T+  +     S
Sbjct: 120 QFNHKMTSPKHKVAKIYRVTLKHSANESICETLKNGVLLH-----DDNETVSAENAELTS 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              + + + EGK  ++K++      +V  L R+ +G +    L AG  R
Sbjct: 175 PTELILTISEGKYHQVKRMVAAAGNRVEALHRLQFGDWGTEDLAAGEWR 223


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 115/245 (46%), Gaps = 31/245 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  + +  V+VNG L      NV++ D I V+     + ++  
Sbjct: 345 RINKRLADMGLCSRREADEWVDKGWVRVNGELAV-MGQNVVAADRITVEREARERQDQQV 403

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFS-----RVISVGRLDINT 118
             L HKP+G V+  ++ DG                D   + F+      +   GRLDI++
Sbjct: 404 TILIHKPMGYVSGQAE-DGHEPAVVLVTPQNHWNQDTSRTRFNFAQLKGLAPCGRLDIDS 462

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQV 177
            GLL++T DG +AR +    ++  + Y VR  +G  D D  ++     + + +C+G   +
Sbjct: 463 VGLLVMTQDGRVARQIIGEDSEMDKEYLVRVTYGDRDIDVQSVFPAEQLAR-LCHG---L 518

Query: 178 TLDTQKGSNAWVT--------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +LD +    A V           L EGK R+I+++ E    +V  L RI  G   LG L 
Sbjct: 519 SLDGEALKPAKVDWQNPEQLRFVLTEGKKRQIRRMCELVGLRVVGLKRIRIGRVTLGNLP 578

Query: 230 AGSTR 234
            G  R
Sbjct: 579 VGQWR 583


>gi|167844683|ref|ZP_02470191.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
          Length = 240

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/210 (28%), Positives = 92/210 (43%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++    V V G     A     +T  + EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGHVAVGGATCADAHAPFDTTQLVFEVDGVAWPYRARAYVAL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   S+VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G         L         + + + EGK  +
Sbjct: 129 VPKTYVATVRHPLDDAQLDALRAGVLLHG--EPKPVAALAAVARGERLLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V  L R   G F L   LA
Sbjct: 187 VKRMVAAASNRVEALHRSRIGGFALPEDLA 216


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 70/144 (48%), Gaps = 14/144 (9%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V + GRLD ++EGLL+LTNDG L   L  P ++  + Y V+  G   +  L  L+ G+ +
Sbjct: 10  VYAAGRLDRDSEGLLILTNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTL 69

Query: 168 QGICYGDMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +       +V +  +                   W+ + L EG+NR+++++     +   
Sbjct: 70  KDGPTLPAKVEIMPEPTLWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRMTAHIGFPTL 129

Query: 214 RLIRISYGPFQLGTLLAGSTREVS 237
           RLIR S G + LG L  G  +EV+
Sbjct: 130 RLIRYSMGDWNLGDLQPGEWQEVT 153


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 100/231 (43%), Gaps = 27/231 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P  + K++   G  +RR    ++    VKVNG+L E         + I  +G+ L   +R
Sbjct: 4   PISLEKILFSQGFGTRRYCSDLVYADLVKVNGVLAEDPE------ERIATEGLVLTVEDR 57

Query: 73  TRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
              W YH        KP     +H       +V+  LPS F    +  VGRLD +T GLL
Sbjct: 58  D--WEYHEKAYIAFNKPENYECSHKTTH-HPSVYSLLPSPFVERGLQCVGRLDFDTTGLL 114

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTL 179
           L+++DG     +  P     +VY +     + Q +++ L  G+V+      C+      +
Sbjct: 115 LISDDGQFIHKMTTPKKNIGKVYEITTPEPITQSQIDHLLNGVVLDDDPKPCFA-----V 169

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              + +   + + + EG+  ++K++       V +L R   G + + T LA
Sbjct: 170 ACNQLTEYTLAMTIVEGRYHQVKRMMAAVGNHVAKLHRTEIGAYLMPTDLA 220


>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 = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 50/187 (26%), Positives = 89/187 (47%), Gaps = 24/187 (12%)

Query: 74  RLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R +  +KP G ++   T+  P  +  +   L +     ++VGRLD ++EGLLLLT +G  
Sbjct: 3   RYFKIYKPYGYLSQFITNEKPRKKKKLLGELGNFPEETMAVGRLDQDSEGLLLLTTNGKE 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQVTL--------- 179
           +  +   S +  + Y V+  G++ ++ + LLK G  I I G  Y  +             
Sbjct: 63  SARITGSSVE--KEYYVQVDGEITEEAIALLKNGVEISINGTKYRSLPCKAFKLYTRPVF 120

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 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|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 = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 87/177 (49%), Gaps = 26/177 (14%)

Query: 77  LYHKPIGLVTTHSD---PDG---RSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L++KP  +++  +D   P     R+T+ D  N P I+      GRLD ++EGLLLLT+DG
Sbjct: 6   LFNKPFQVLSQFTDERRPTDKPRRATLADWINQPGIYP----AGRLDYDSEGLLLLTSDG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------ 181
            L   +  P  +  + Y V+  G ++   L  L++G+ ++ G+    +   +D       
Sbjct: 62  QLQHCIASPRGKMEKTYWVQVEGTINPQTLRQLEQGVQLKDGLTRPALARAMDEPVIWLR 121

Query: 182 -------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  Q    +W+ + + EG+NR+++++     +   RLIR   G + LG L  G
Sbjct: 122 TPPVRFRQNIPTSWLELTICEGRNRQVRRMTAALGFPTLRLIRYRIGDWSLGLLEPG 178


>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 = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 85/179 (47%), Gaps = 22/179 (12%)

Query: 79  HKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G ++    +   R  +   L S  S+ +++GRLD ++EGLLLLT DG ++   ++ 
Sbjct: 24  YKPYGFLSQFLPEARKRKKLLGELFSFPSKTMAIGRLDHDSEGLLLLTTDGMMSH--QIR 81

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQVTL---------------- 179
           S    + Y V+  G +    +  L+ G  I I G  Y  +   +                
Sbjct: 82  SKGIEKEYYVQVDGDITASAITALQLGVEIGINGEKYQTLPCNVFRLTEEPQLPVRGRKI 141

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            D + G  +WV++ L EGKNR+I+K+     +   RL+R+  G   +G + AG    +S
Sbjct: 142 RDPRHGPTSWVSITLCEGKNRQIRKMTAAVGFATLRLVRVRIGNIFVGGMQAGDVTPLS 200


>gi|167582947|ref|ZP_02375821.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis TXDOH]
          Length = 240

 Score = 67.4 bits (163), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 96/210 (45%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAYVAL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   ++VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G     +       +G    + + + EGK  +
Sbjct: 129 VPKTYVAAVRHPLDDAQLDALRAGVLLHGE-PKPIAALAAAARGER-LLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V+ L R   G F L   LA
Sbjct: 187 VKRMVAAVSNRVDALHRSRIGGFALPEDLA 216


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 103/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 58/219 (26%), Positives = 102/219 (46%), Gaps = 9/219 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +A+     ++ V  ++  +RV V+G +    A+ +     I +    LR A+  R
Sbjct: 7   RLDSFLAKTLNIPKKAVRELLKAERVTVDGKVALEMALQIGPFSQIYLGDTALR-ADTPR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+V+   D + + TV D +P      +  VGRLD+NT GL+LL+ND   +  
Sbjct: 66  YLMLNKPVGVVSATKDKEHK-TVLDLIPEALRAGLHIVGRLDLNTSGLVLLSNDSRWSES 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D +   ++G     +GI     ++ +  ++ +     V
Sbjct: 125 MMQPGAHVPKEYWVTLEHPLTEDYIAAFERGFYFETEGITTLPARLAILGEREAR----V 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            L EGK  +IK++F  F   V  L R   G   L   LA
Sbjct: 181 ELCEGKYHQIKRMFGRFQNPVVALHRHRIGALMLDPGLA 219


>gi|309379227|emb|CBX22184.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 230

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 101/222 (45%), Gaps = 8/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NGI ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGICMDDTDADIDSSSVETLDIDGKAVTVIPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPTDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGH 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P+ +  ++Y V       +     LK G+++      +     D    S + +
Sbjct: 121 LNHKLTSPNHKIPKLYEVTLKHPAGETLCETLKNGVLLHD--ENETVYAADAVLESPSAL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 179 LLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 45/170 (26%), Positives = 81/170 (47%), Gaps = 23/170 (13%)

Query: 78  YHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G++   S  +   ++  F NLP  +      GRLD ++EGLLLLT+DG L   + 
Sbjct: 7   FNKPYGVICQFSPHEKHKSLKDFINLPGFYP----AGRLDTDSEGLLLLTDDGRLQAQIT 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------- 187
            P  +  + Y  +  G  D+ +L  L+KGI + G       + +     +++        
Sbjct: 63  DPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPPI 122

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                    W+ + + EGKNR+++++     +   RLIR++ G  +L  L
Sbjct: 123 RVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDL 172


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 53/179 (29%), Positives = 86/179 (48%), Gaps = 22/179 (12%)

Query: 77  LYHKPIGLVT--THSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++HKP G+++  T   P+  +   + ++P ++     VGRLD ++EGLLLLTNDG L   
Sbjct: 9   IFHKPYGVLSQFTRELPEHVTLKDYIDVPDVYP----VGRLDWDSEGLLLLTNDGKLQHH 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P     R Y V+     D   +  L +G+ IQ       QV L  ++          
Sbjct: 65  IANPRFGHQRTYWVQVERIPDPVAIAKLGQGVEIQNYRTLPAQVKLLLEEPIVGERYPPI 124

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   AW+ + L+EGKNR+++++     +   RLIR+     QL  L  G+ R +S
Sbjct: 125 RFRKNVPTAWLEMTLKEGKNRQVRRMTAAVGFPTLRLIRVRIAQLQLDDLPVGTWRYLS 183


>gi|467162|gb|AAA50926.1| u0247g [Mycobacterium leprae]
          Length = 186

 Score = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 53/169 (31%), Positives = 80/169 (47%), Gaps = 5/169 (2%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGL+LLTNDG LA  L 
Sbjct: 12  NKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGELAHRLM 71

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLR 194
            PS +  + Y     G V +     L  G+ +  G  + D    +D   G    V + L 
Sbjct: 72  HPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKT-LVRLTLH 130

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+
Sbjct: 131 EGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQ 179


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 86/179 (48%), Gaps = 16/179 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP  ++   +D  GR T+ D +      + + GRLD ++EGLL+LTNDG L   
Sbjct: 44  KIVLFNKPFDVLCQFTDEAGRQTLADFID--IKDIYAAGRLDRDSEGLLVLTNDGQLQNK 101

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           L  P  +  + Y V+  G    + +  L +G+ ++       QV L              
Sbjct: 102 LASPKHKTSKTYWVQVEGIPSAEAIKSLCQGVELKDGPTLPAQVELMHAPDIWPRNPPIR 161

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + +    +W+++ L EG+NR+++++         RLIR   G + +  +  G  + V+K
Sbjct: 162 ERKNIPTSWLSITLTEGRNRQVRRMTAHIGHPTLRLIRYRIGHWTIDGIENGQFKSVAK 220


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 103/222 (46%), Gaps = 8/222 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  + L +KP 
Sbjct: 23  GFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAYVAL-NKPA 81

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   ++VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 82  GYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 140

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G     +       +G    + + + EGK  +
Sbjct: 141 VPKTYVATVRHPLDDAQLDALRAGVLLHGE-PKPIAALAAAARGERL-LEMTIAEGKYHQ 198

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
           +K++    + +V+ L R   G F L   LA G+ R + ++ L
Sbjct: 199 VKRMVAAASNRVDALHRSRIGGFALPEDLAEGAWRWLDERDL 240


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 77/171 (45%), Gaps = 18/171 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +L +KP  +++  S      T+ D   +    +  VGRLD ++EGLLLLTND  L   
Sbjct: 3   QYFLIYKPFNMLSQFSREGDHQTLADLGFTFAKDIYPVGRLDADSEGLLLLTNDNFLKTK 62

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQVTLDT---------- 181
           L  P  +  R Y V+  G+V  +    L  G  I I G  Y  +   +            
Sbjct: 63  LLEPRNRHTRTYYVQVEGEVTDEACRQLSAGVSISINGKQYKTLPAEIAKIAEPELPERN 122

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                 +    +W++V LREGKNR+++++     +   RL+R S G   L 
Sbjct: 123 PPIRFRKNIPTSWLSVTLREGKNRQVRRMTAAVGFPTLRLVRWSIGKISLA 173


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 49/185 (26%), Positives = 88/185 (47%), Gaps = 25/185 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           TRL  ++KP  ++   +D      P    + + + P +++     GRLD ++EGLLLLT+
Sbjct: 2   TRLIRFNKPYDVLPQFTDSGSQDSPRATLSKYIDCPGVYA----AGRLDRDSEGLLLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           +G L   +  P  +  + Y V+  G  DQ+ L  L +G+ ++       +V L  +    
Sbjct: 58  NGRLQAWITDPKHKMDKTYWVQVEGIPDQEALKNLAEGVELKDGITRPAKVRLMPEPTGL 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + LREG+NR+++++         RLIR S G + L  L  G
Sbjct: 118 WARTPPVRVRKTVPDSWIALTLREGRNRQVRRMTAAVGHPTLRLIRYSIGAWTLDGLAQG 177

Query: 232 STREV 236
           +  +V
Sbjct: 178 AWEDV 182


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 78/244 (31%), Positives = 127/244 (52%), Gaps = 16/244 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +    I +R++++  +   R  VNG ++ R  ++V  + D I  DG  LR + + 
Sbjct: 2   RLDKFLGLFDIGTRKQIKEYLKNGRCSVNGEVVTRPDIHVDENNDEISFDGKTLRYS-KY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGR-STVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+  +D  GR +TV D L     + +S  GRLDI+TEGLLLLT+DGGL 
Sbjct: 61  HYYMLYKPQGVVSATTD--GRNTTVLDLLQEENVKGLSPAGRLDIDTEGLLLLTDDGGLI 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTL-------DTQK 183
             L  P     +VY V     +    +  L+KG+ I      G++  TL       D   
Sbjct: 119 HRLLSPKKHVDKVYEVHLRKDLSDKDIESLEKGVNIGDTKDNGEIDYTLPARVVRMDEDD 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            +   V + + EG+  ++K++ E    +V  L R+S GP  L  TL  G  R+++++ L+
Sbjct: 179 ENRPVVHLIIHEGRFHQVKRMMEAVGNEVLFLKRLSMGPLILDETLEPGEYRQLTQEELK 238

Query: 243 EQLG 246
            QLG
Sbjct: 239 -QLG 241


>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 = 67.0 bits (162), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 59/210 (28%), Positives = 96/210 (45%), Gaps = 7/210 (3%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPI 82
           G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  + L +KP 
Sbjct: 11  GFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAYVAL-NKPA 69

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
           G   +  +P   ++VF  LP  F+   V  VGRLD +T GLLLL++DG        P  +
Sbjct: 70  GYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKRK 128

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y       +D  +L+ L+ G+++ G     +       +G    + + + EGK  +
Sbjct: 129 VPKTYVATVRHPLDDAQLDALRAGVLLHGE-PKPIAALAAAARGER-LLEMTIAEGKYHQ 186

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +K++    + +V+ L R   G F L   LA
Sbjct: 187 VKRMVAAASNRVDALHRSRIGGFALPEDLA 216


>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 = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 106/232 (45%), Gaps = 20/232 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  M+   RV V+ ++++   + +     + VDG  L+  +   
Sbjct: 7   RLDQFLAGKLQVPRKSVRFMLLAGRVSVDNMIIKDMDLQLDEFSQVCVDGAALQNNQPCY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
           L L +KP+G+V+   D D   T  + L  I   ++ + GRLD+N+ GLLL+TND   +  
Sbjct: 67  LML-NKPVGVVSATKD-DIHKTALELLHGIKLEMLHIAGRLDLNSSGLLLITNDARWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKG-----SN 186
           L  P  +  + Y V     +D+  ++    G+    +GI          TQ       S 
Sbjct: 125 LMSPDNKVSKKYLVTLANPIDETYISAFAGGMYFAFEGIT---------TQAAGFEILSE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               V L+EGK  +IK++F  F   V  L R + G   L  TL  G  R ++
Sbjct: 176 YQARVSLKEGKYHQIKRMFGRFRNPVIGLHREAIGELVLDETLAPGEFRHLT 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 = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 97/211 (45%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +  +RV V+G ++++ A  +     +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGVSRALVARELRAKRVTVDGEIIKQGAFQLRPEHQVRFDGNLLHQILTAR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+LLT+DG  +  L
Sbjct: 62  YFMLNKPQGYVCSTDDPDHPTILYFIDEPVPDKLHAAGRLDIDTTGLVLLTDDGQWSYRL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     +  +       GI+++G         L T       +T+   
Sbjct: 122 TSPRHHCEKDYLVTLEQPLAAEITAQFAAGILLRGEKLPTRPARLATLSPLKVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F     +V  L R   G   L
Sbjct: 180 EGRYHQVKRMFAAVGNRVVALHRERIGAIVL 210


>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 = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 62/218 (28%), Positives = 102/218 (46%), Gaps = 7/218 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR E +R+I   RV+V G ++     NV +   I V+G  LR A   R
Sbjct: 2   RLDKYLSQVTDYSRSEGKRLIRSGRVRVAGHVVIDPRENVDNNAVIVVNGQQLRSAS-PR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ HKP G ++   D    + +  FD       ++   GRLDI+T GLLL+++DG    
Sbjct: 61  YFMLHKPDGYISATKDRQHLTALELFDE--DNVDQLHIAGRLDIDTTGLLLVSDDGQWCH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   + YRV     +  + +  +++GI +       +   LD      A +T+ 
Sbjct: 119 RVTSPKSDCKKTYRVEAVDPITPEAIKNIEQGIHLSQEKKPTLPADLDLLDEHTARLTI- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             EGK  ++K++F     KV  L R   G   L   LA
Sbjct: 178 -TEGKYHQVKRMFAAVGNKVECLHRERIGNIVLDDDLA 214


>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 = 67.0 bits (162), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 62/214 (28%), Positives = 100/214 (46%), Gaps = 7/214 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           ++ +++ + G  SRRE   +I + RV VNG + +   V + +   +  VDGV    AE  
Sbjct: 2   QLERILQKHGFGSRRECRGLIRRDRVAVNGQVCDDPFVELDTEGLVFTVDGVDWPYAEFA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP G   +   P   + V + LP       V  +GRLD +T GLLL+TNDG L 
Sbjct: 62  TLML-HKPAGYECSRK-PKHHAGVLELLPIPLRERDVQPIGRLDEDTTGLLLITNDGQLN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L     +  +VY       +DQ +++ L  G+++    Y  +        G    + +
Sbjct: 120 HQLSSAKRKVPKVYLATTKHPLDQAQIDQLVAGVLLADE-YEPISAAAAEIVGEK-LLRL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            L EGK  ++K++    + +V  L R + G   L
Sbjct: 178 TLTEGKYHQVKRMVAAVSNRVEALHREAVGELTL 211


>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 = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 54/217 (24%), Positives = 100/217 (46%), Gaps = 11/217 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++  G  +R++V   I    + V G   E  A  V ++D + ++G PL   +  
Sbjct: 7   ERLDKLLSNLGYGARKDVRHWIKAGWITVQGEAAESPAQKVFASD-VLLEGEPLDHPDGL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
            + +YHKP+  V +  +  G   ++D+LP+ +         VGRLD +T GLL++T+DG 
Sbjct: 66  TI-IYHKPLDTVCSRKE--GGRLIYDDLPARWLDRKPPFSPVGRLDKDTSGLLIVTDDGQ 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   L  P     + Y V     +   +  ++  G ++++      +   L     + A 
Sbjct: 123 LNHCLTSPKQHISKTYSVTLAEPLQGREAEIMAAGTLLLENDDRPCLPAELIVHSPTQAS 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +T  L EG+  + +++F      V  L R   G   L
Sbjct: 183 LT--LHEGRYHQARRMFVALGNHVTALQRTHIGALAL 217


>gi|331004981|ref|ZP_08328391.1| pseudouridine synthase [gamma proteobacterium IMCC1989]
 gi|330421223|gb|EGG95479.1| pseudouridine synthase [gamma proteobacterium IMCC1989]
          Length = 237

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 83/177 (46%), Gaps = 18/177 (10%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134
           L H P  + T  +       + D L S   +  V   GRLD ++EGLLLLT+DG L + +
Sbjct: 22  LQHAPTNITTPSNT--AEKPLKDTLASYIKQKHVYPAGRLDYDSEGLLLLTDDGALQQHI 79

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------------ 181
             P  +  + Y V+  G+ + + +  L+KG+ ++ G+    +   ++             
Sbjct: 80  SHPQYKLPKTYWVQVEGEQNLEAIIALRKGVELKDGLTKPALVEAIEEPDLWPRNPPVRF 139

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            Q     W+++ + EGKNR+++++         RL+R S G + L  L  G  R ++
Sbjct: 140 RQSIPTHWLSITISEGKNRQVRRMTAAVGLPTLRLVRASIGDWTLEGLQPGEHRSIA 196


>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 = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 109/238 (45%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  V  V G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAVTDVQGEVL--YADDQVEHDAIRIDGEPLDPPSGF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SR---VISVGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F SR   +  VGRLD  T G+LL+T+DG 
Sbjct: 60  SLLL-HKPSGYTCSTKD-TGR-LIYELLPLRFRSRAPVLAPVGRLDRETSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY V     +  D+  L   G ++++G     +   LD      A 
Sbjct: 117 LLHRIISPKSALDKVYDVTLAEDLRGDEAALFSSGTLLLEGETKPLLPAELDVLGPREAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLEGLPSGQWRTLEAPDLEVLFG 232


>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 = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 85/176 (48%), Gaps = 22/176 (12%)

Query: 77  LYHKPIGLVT--THSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++HKP G+++  T   P+  +   + ++P ++     VGRLD ++EGLLLLTNDG L   
Sbjct: 9   IFHKPYGVLSQFTRELPEHVTLKDYIDVPDVYP----VGRLDWDSEGLLLLTNDGKLQHH 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-------- 185
           +  P     R Y V+     D   +  L +G+ IQ       QV L  ++ +        
Sbjct: 65  IANPRFGHQRTYWVQVERIPDPVAIAKLGQGVEIQNYRTLPAQVKLLLEEPTVGERHPPI 124

Query: 186 -------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                   AW+ + L+EGKNR+++++     +   RLIRI     QL  L  G+ R
Sbjct: 125 RYRKNVPTAWLEMTLKEGKNRQVRRMTAAVGFPTLRLIRIRIAQLQLDDLPVGTWR 180


>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 = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 39/110 (35%), Positives = 58/110 (52%), Gaps = 2/110 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   V      
Sbjct: 4   ERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNRLVLSDSNN 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GL
Sbjct: 64  QKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGL 113


>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 = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 56/227 (24%), Positives = 104/227 (45%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I++    SR    R +  ++V V+G ++   A  + +   +E DG  L +    R
Sbjct: 2   RLDKFISQQLEVSRAIAARELRARKVTVDGEVVREGAYKLSADSTVEYDGNVLEQQLGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP+G V +  DPD  + + F   P  + R+ + GRLD +T GL+L+T+DG  +  
Sbjct: 62  YFMLNKPVGYVCSTDDPDHPTILYFLEEPGAY-RLHAAGRLDNDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  + +   +T+  
Sbjct: 121 ITSPRHHCEKTYLVTLESAISDDNAQQFADGVQLHNEKTLTKPAMLEVIEPNVVRLTIS- 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
            EG+  ++K++F     +V  L R   G  +L + L  G  R +S +
Sbjct: 180 -EGRYHQVKRMFAAVGNRVVGLHRERIGAIRLDSDLQPGEYRPLSAE 225


>gi|297517087|ref|ZP_06935473.1| 23S rRNA pseudouridine synthase F [Escherichia coli OP50]
          Length = 147

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 46/121 (38%), Positives = 71/121 (58%), Gaps = 9/121 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
           R++K I+ +GI SRRE +R I Q  V +NG   +RA +   V   D ++V+G  +  R+A
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNG---KRATIGDQVKPGDVVKVNGQLIEPREA 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 A 131
            
Sbjct: 123 V 123


>gi|323527142|ref|YP_004229295.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323384144|gb|ADX56235.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 189

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 49/173 (28%), Positives = 83/173 (47%), Gaps = 23/173 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL   +KP G +   S  + R+++ D   +P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLLALNKPFGTICQFSPHETRASLADWVKVPGVYP----AGRLDSDSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDT----- 181
           AR+ E P  + ++ Y  +  G VD   L  L +G+     +   C  D     DT     
Sbjct: 58  ARIAE-PRHKLVKRYWAQVEGTVDAAALKKLARGVDLGDYVTKPCRADYVEPGDTLWTRT 116

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      +W+ + + EGKNR+++++     +   RL+R+  G   + +L
Sbjct: 117 PPIRYRAAIPTSWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSL 169


>gi|6689331|emb|CAB65436.1| hypothetical protein [Synechococcus elongatus PCC 6301]
          Length = 199

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 56/188 (29%), Positives = 88/188 (46%), Gaps = 28/188 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPD--GRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R  L+HKP   V   S  D   + T+ D  ++P ++     VGRLD ++EGLLLLTN+G 
Sbjct: 4   RYLLFHKPYDAVCQFSPSDRPDQQTLKDYIDVPEVYP----VGRLDRDSEGLLLLTNNGA 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQK----- 183
           L   L  P     R Y V+   +  +  L  L++G+ IQ       +V  LD  +     
Sbjct: 60  LQHRLCHPRFGHDRTYWVQVEREPTEAALQALRQGVQIQDYRTRPAKVQRLDDPQIPERD 119

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLL 229
                      AW+ + L+EG+NR+++++         RLIR +        P QL  L 
Sbjct: 120 PPIRFRKTVPTAWLALTLQEGRNRQVRRMTAAVGHPTLRLIRAAIATHPDQPPLQLQGLA 179

Query: 230 AGSTREVS 237
            G+ R+++
Sbjct: 180 PGTWRDLT 187


>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 = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 107/267 (40%), Gaps = 50/267 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  +    VKVNG + E     V   D IEVD     +     
Sbjct: 37  RLNKRMAELGLCSRREADAWVENGWVKVNGRVAEMGQ-QVSPADRIEVDPQAQNQQATQV 95

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIFSR-----VISVGRLDINT 118
             L HKPIG V+  ++ DG                D  P  F+      +   GRLDI++
Sbjct: 96  TILLHKPIGYVSGQAE-DGHEPAVVLVQAQNRWREDRAPHRFNGGQLRGLAPAGRLDIDS 154

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVR----------------------------FH 150
            GLL+LT DG +AR L    ++  + Y VR                              
Sbjct: 155 TGLLVLTQDGRVARQLIGEDSEIEKEYLVRVVYLGTPAAASAPTELQPIHANDPVSANVQ 214

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                  L  L+ G+ + G      +V  +    +   +   L+EGK R+I+++ E    
Sbjct: 215 AVFPPAMLAKLRHGLSLDGQALKPARVDWE----NTEQLRFVLKEGKKRQIRRMCELVGL 270

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVS 237
           KV  L R+  G   LG L  G  R ++
Sbjct: 271 KVVGLKRVRIGRVMLGQLPQGQWRYLA 297


>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 = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/214 (27%), Positives = 99/214 (46%), Gaps = 9/214 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++ +  V V+ ++ +  A  +  T  +E     +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKRGEVTVDDVVQKSGAFKLKETSRVEWQDREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D      KGI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQGDYAEQFTKGIELR----GERELTLPAQLEVVSETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + EGK  ++K++F     KV  L R   G   L
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITL 209


>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 = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 108/237 (45%), Gaps = 21/237 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEV--DGVPLR 68
           ++ K IA  G  SR+EV R+  + R+  NG         V+  D    HI V  DG PL 
Sbjct: 2   KLLKYIANLGYGSRKEVARIFREGRI-TNG------EGEVLYADDQVQHIAVRFDGEPLD 54

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLL 124
                 + L HKP   + +  D  GR  V+D LP  F   S ++S VGRLD +T GLLLL
Sbjct: 55  PPPGLMVML-HKPSDYICSTKDA-GR-LVYDLLPPRFRLRSPLLSTVGRLDGDTSGLLLL 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG L   +  P T   +VY       +  D+  L   G ++       +Q  +    G
Sbjct: 112 TDDGALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLG 171

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 172 P-CQVRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>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 = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 50/172 (29%), Positives = 85/172 (49%), Gaps = 19/172 (11%)

Query: 77  LYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +KP  +++  SD D    R T+ + L +   RV   GRLD ++EGL LLT+DG L + 
Sbjct: 28  LLNKPFRVLSQFSDRDNDPPRLTLANLLSAPEFRV--AGRLDYDSEGLTLLTDDGKLQQQ 85

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG-------- 184
           +  P  +  + Y V+  G   Q  +  L  G+V+  G+        +D            
Sbjct: 86  IANPKFKVWKTYWVQVEGAPKQQAIEQLTSGVVLNDGLTKPAKVRAIDPPDLWERSPSVR 145

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 +AW+ + ++EG+NR+I+++    N    RL+RI+ G +++G L  G
Sbjct: 146 FRAHIPDAWLEISIQEGRNRQIRRMTAAVNLPTLRLVRIAIGDWEIGNLQPG 197


>gi|326623646|gb|EGE29991.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. 3246]
          Length = 172

 Score = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 49/171 (28%), Positives = 81/171 (47%), Gaps = 17/171 (9%)

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  P  +  +
Sbjct: 1   MLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGK 58

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVTLDTQKGSNAW 188
           +Y V+  G  D   L  L+ G+ +        GI         +       + +    +W
Sbjct: 59  IYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSW 118

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + V L EG+NR+++++         RLIR S G + L  L  G   E++++
Sbjct: 119 LKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWCEIAQE 169


>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 = 66.6 bits (161), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 97/220 (44%), Gaps = 15/220 (6%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++A   V VNGI  E     V +   + +VDG   R A   R +
Sbjct: 38  RILQSQGFGTRRYCKDLVAAGLVHVNGIEAEDPDAQVDTAGLVLDVDGE--RWAYHARAY 95

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG     
Sbjct: 96  LMLHKPAGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHT 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---TQKGSNAWVT 190
           L  P  Q  +VY +     V   ++  L +G+++      D   T+     ++     + 
Sbjct: 155 LTSPRHQVPKVYEITTADPVTDAQVAQLCRGVLLD-----DEDATVAAAWAERVDTCHLR 209

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + L +GK  ++K++       V  L R + G   L   LA
Sbjct: 210 MALTQGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLA 249


>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 = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 55/222 (24%), Positives = 101/222 (45%), Gaps = 8/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS +  ++Y V       +     LK G+++      +     D    S + +
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPAGETLCETLKNGVLLHD--ENETVYAADAVLESPSAL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 179 LLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPG 220


>gi|325524840|gb|EGD02796.1| ribosomal small subunit pseudouridine synthase A [Burkholderia sp.
           TJI49]
          Length = 238

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 95/219 (43%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           +  ++   G  SRR+   +I   RV + G            TD +   VDG P     R 
Sbjct: 3   LESILYTQGFGSRRQCRGLIDAGRVAIAGAPATDPDAR-FDTDGLVFTVDGTPWPFHARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL++DG   
Sbjct: 62  YLAL-NKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D  +L+ L+ G+ + G       V  D +      +TV
Sbjct: 120 HAYTSPKRKVPKTYVATVRHPLDDAQLDALRTGVQLHGEPRPIAAVAADARDTHALALTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EGK  ++K++    + +V  L R   G F L   LA
Sbjct: 180 --LEGKYHQVKRMVAAASNRVEALHRERIGGFTLPDDLA 216


>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 = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 84/178 (47%), Gaps = 21/178 (11%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L++KP G++T  +D   P  R T+   NLP     V + GRLD ++EGLL+LT+DG L  
Sbjct: 32  LFNKPFGVLTQFTDAKSPTERPTLSGFNLPK---GVYAAGRLDRDSEGLLVLTDDGKLQA 88

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P+ +  + Y V+  G      L  L+  + ++       QV L             
Sbjct: 89  QLSKPTFKTPKTYLVQIEGDPTDADLAPLRTRVTLKDGPTLPAQVRLIDPPDVWHRDPPV 148

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  +AW+ V + EG+NR+++++     +   RL+R S G + L  +  G  R +
Sbjct: 149 RVRKSIPDAWIEVTITEGRNRQVRRMCAHIGFPCLRLVRWSVGAWTLDGIDQGQWRTI 206


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 51/163 (31%), Positives = 84/163 (51%), Gaps = 6/163 (3%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G ++  +D     TV D  +L  +      VGRLD +TEGLL+LTNDG L+  +  
Sbjct: 2   NKPDGYISATTDK-YDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVLS 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLRE 195
           P     + Y  +  G V ++ +    +G+V+    Y  M   L+  K  + + + + + E
Sbjct: 61  PKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDD-GYKTMPSQLNILKSDDESEIELTIHE 119

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           GK  ++K++FE    KV  L R+S G  +L  +L  G  RE++
Sbjct: 120 GKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELT 162


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 45/179 (25%), Positives = 85/179 (47%), Gaps = 20/179 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP  +++  +D  GR T+  F   P  +      GRLD ++EGLLLL ++G L +
Sbjct: 4   LILLNKPYQVLSQFTDSAGRDTLAKFIRTPGFYP----AGRLDYDSEGLLLLCDEGRLQQ 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYGDMQVTL 179
            +  P  +  + Y V+  G++    L  LK G+              +Q   + +    +
Sbjct: 60  RIADPHFKLWKTYCVQLEGEITAQALQSLKNGLNLKDGPTRPARVKTLQEPLFWERNPPI 119

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             +K    +W+ + + EG+NR+++++     + V RL+R   G + +  L  G  R ++
Sbjct: 120 RQRKHQPTSWIEISINEGRNRQVRRMCAAVGFPVLRLVRTRIGDWAIDGLQPGQHRRMT 178


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 114/236 (48%), Gaps = 11/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  +R EV++++ +++      ++ +      +S   + V    +   E  
Sbjct: 2   RLDKLLAHTGYGTRTEVKKLLKSKEVKVDGVVVKDAKVKVDLSKQCVTVFDEVVEYREFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP   ++   D   R+ +   D+   +F  V   GRLD +TEGL+LLTNDG LA
Sbjct: 62  YLMM-NKPQDCLSATRDQRYRTVIDLLDDYYLMFD-VAPAGRLDRDTEGLVLLTNDGKLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAW 188
             +  P     + Y     G++  +KLN L+ G+ I    G  +      +   + ++ W
Sbjct: 120 HEIISPKKDVYKRYVAHVTGELTDEKLNQLETGVEILDGTGEVFSTKPAKVKILQKNDEW 179

Query: 189 --VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             V + + EGK  ++K++F     KV  L R++ G  +L  +L  G  RE++ + L
Sbjct: 180 TEVEICITEGKFHQVKRMFASVGGKVIYLKRLAIGGLELDESLELGEYRELTDEEL 235


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 106/221 (47%), Gaps = 23/221 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   ++ E    IA+ RVKVN  ++   +  V   +H+ ++G  L  A   R
Sbjct: 2   RLDKFVCKSTTLTKNEALECIAEGRVKVNAKIVTVESTQVHENNHVTLNG-DLLTARPFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L +KP   + ++ D        +  PS+F        S +   GRLD +T GL+L+T+
Sbjct: 61  YLLMNKPANTICSNID--------EAYPSLFNYIKEGNNSELHIAGRLDSDTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           DG  +  +  PS +  +VYRV     +  + +  ++ G+ +Q    G++++T   +    
Sbjct: 113 DGRWSYNIITPSKKCEKVYRVGLRNIITSEAIIKIELGVQLQ----GEVELTRPAKLKII 168

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +   V + + EGK  ++K++F     KV  L R  +G   L
Sbjct: 169 TEREVLLTIIEGKFHQVKRMFSAVGNKVILLHREQFGEISL 209


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 81/175 (46%), Gaps = 19/175 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +R+ L++KP G++   S      T+ D +      V   GRLD ++EGLLLLT+DG L  
Sbjct: 2   SRILLFNKPYGVICQFSRDGMHPTLADYI--AVPDVYPAGRLDTDSEGLLLLTDDGKLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----------------QGICYGDMQ 176
            +  P  +  + Y V+  G  D   L  L++GI +                QG+   D  
Sbjct: 60  RITDPKHKQPKTYWVQVEGIPDATALEQLRRGIQLKDGMTLPAEANLMAEPQGLWLRDPP 119

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           V    +     W+ + + EGKNR+++++     +   RLIR S G + +  L  G
Sbjct: 120 VRF-RKDIPTCWLWLTIHEGKNRQVRRMTAAVGFPTLRLIRYSIGKWTIDGLAPG 173


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 47/164 (28%), Positives = 83/164 (50%), Gaps = 24/164 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L +KP  +++  +D  GR T+ D   +P++++    VGRLD ++EGLLLLT+DG + 
Sbjct: 4   RYLLLYKPYDVLSQFTDESGRRTLKDLVAVPNVYA----VGRLDRDSEGLLLLTDDGPMQ 59

Query: 132 RVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------ 181
             L  P     R Y V+       Q  +  ++ L+ G+ I+G      QV++        
Sbjct: 60  HRLSHPRFGHRRQYWVQVECGPKSQPIEAAIDQLRAGVTIRGYRTRPAQVSVIPDPDLPP 119

Query: 182 --------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
                   ++ + AW+ + L EGKNR+++++     +   RL+R
Sbjct: 120 RNPPIRYRKQIATAWLEIALTEGKNRQVRRMTAAVGFPTLRLVR 163


>gi|330818088|ref|YP_004361793.1| Pseudouridine synthase [Burkholderia gladioli BSR3]
 gi|327370481|gb|AEA61837.1| Pseudouridine synthase [Burkholderia gladioli BSR3]
          Length = 192

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 87/191 (45%), Gaps = 27/191 (14%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R ++ D +  P ++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVRTPGVYP----AGRLDADSEGLLLLTDDGALQARIAE 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA---- 187
            P  + ++ Y  +  G  D   L  L +G+     +   C  D     +T    N     
Sbjct: 63  -PRHKLVKRYWAQVEGTPDDAALKALARGVDLGDYVTRPCRADYVEPPETLWPRNPPVRF 121

Query: 188 -------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVS 237
                  W+ + + EGKNR+++++     +   RL+R+  G    F LG L  G T  + 
Sbjct: 122 RAAIPTTWIELSITEGKNRQVRRMTAAVGYPTLRLVRVGIGALDLFALG-LAPGDTLALP 180

Query: 238 KKILREQLGPH 248
            +   +   PH
Sbjct: 181 PRAPWDGFAPH 191


>gi|262365461|gb|ACY62018.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis D182038]
          Length = 194

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 34/96 (35%), Positives = 54/96 (56%)

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 225
            V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 61  NVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINL 96


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 25/191 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL   +KP G +   S  + R+++ D    P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLIALNKPFGTICQFSAHETRASLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQ 57

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------ 185
             +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G+      
Sbjct: 58  AKIAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNP 117

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGST 233
                     AW+ + + EGKNR+++++     +   RL+R+  G    F LG L  G T
Sbjct: 118 PIRHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALG-LAPGET 176

Query: 234 REVSKKILREQ 244
           RE+  +   E+
Sbjct: 177 RELPPRAPWER 187


>gi|291336757|gb|ADD96295.1| hypothetical protein [uncultured organism MedDCM-OCT-S08-C1656]
          Length = 169

 Score = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 84/166 (50%), Gaps = 8/166 (4%)

Query: 10  NFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-- 64
           NFT     ++ K +A AG+ SRR+ E  I    V +NG   +     +  +D ++V+G  
Sbjct: 2   NFTNSQRPKLQKFLADAGLCSRRKGEEWIEDGLVTINGENAKLGERVIPDSDIVKVNGKR 61

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLL 122
           V +++     L L +KP G   ++ D      +F+ L S +   R+   GRLD+++EG++
Sbjct: 62  VQVKRIPNITL-LVNKPKGYTCSNDDEYADRLIFELLESKYRSVRLFCAGRLDVDSEGMV 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +LTN+G LA  L  PS    + Y++      D   L  L  G +++
Sbjct: 121 ILTNNGTLAHRLTHPSQMVRKKYKIEIDTPFDTKDLPSLINGELVE 166


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 83/173 (47%), Gaps = 16/173 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T+L L++KP  ++T  +D  GR T+ D++     +V   GRLD ++EGLLLLT+ G L  
Sbjct: 2   TQLILFNKPYDVLTQFTDSAGRRTLKDHID--LEQVYPAGRLDRDSEGLLLLTDSGPLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG------- 184
           ++  P  +  + Y V+     D+  L  L+ G+ ++ G+        +D           
Sbjct: 60  LIANPKFKLEKTYWVQVENIPDETALQQLRDGVELKDGLTLPAKARLIDPPPVWPRTPPI 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                    W+ + ++EG+NR+++++         RLIR S   + L  L  G
Sbjct: 120 RERKSIPTQWLELKIQEGRNRQVRRMTAAIGCPTLRLIRYSIDIWTLDNLSQG 172


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 108/228 (47%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K +A  G  SR++V  M  + R+   +G +L   A + +    I VDG  L      
Sbjct: 2   KLVKHLANLGYGSRKQVALMFREGRITDADGDVLY--ADDQVPHAAIRVDGEVLDPPPGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            L L HKP+G   +  DP GR  V+D LPS F   S ++S VGRLD +T GLLL+T+DG 
Sbjct: 60  ILAL-HKPVGYTCSTKDP-GR-IVYDLLPSRFRLRSPLMSTVGRLDRDTSGLLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P ++  ++Y       +  D+      G +++ G     + V L+        
Sbjct: 117 LLHRIVSPKSRLAKIYEATLAEDLRGDEAAQFASGTLLLDGETTPLLPVQLEVLGPRQ-- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V V L EG+  +++++F      V  L R   G   L  L AG  R +
Sbjct: 175 VRVVLHEGRYHQVRRMFAAVGNHVLALHRSRIGGLALDALPAGQWRAL 222


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 100/222 (45%), Gaps = 13/222 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++    +    N  + D   +V G   +  E   
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGAVSIDSQTCDNPKQNFSTEDLSFQVFGEQYQYREYVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + L HKP G   +H     RS VF  LP I     V  VGRLD +T GLLLLT+DG   +
Sbjct: 63  IVL-HKPQGYECSHQATHHRS-VFSLLPEILVHRGVQCVGRLDQDTTGLLLLTDDGQYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V     V  ++   L+ G+ +   +GI Y    + L +++     +
Sbjct: 121 ALTHPKKHVPKVYCVSTADPVTTEQKQQLELGVELRNEKGI-YAATDIKLISER----QL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + + +G   ++K++      KV RL R   G  +L  L  G
Sbjct: 176 AMTIHQGVYHQVKRMIAAVGNKVERLHRQQIGLLELPNLEEG 217


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 53/185 (28%), Positives = 84/185 (45%), Gaps = 25/185 (13%)

Query: 77  LYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP G+++  +   G R     +  S+   V + GRLD ++EGLLLLT++G L + L 
Sbjct: 12  LLNKPYGVLSQFTREQGSRWGCLADWVSV-PEVYAAGRLDADSEGLLLLTSNGRLQQRLT 70

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------- 187
            P     R Y  +  G+    +L  L++G+ IQG      +      + S+A        
Sbjct: 71  DPRFGHWRTYWAQVEGEATASQLTQLEQGVPIQGKLTLPARAQPLASQLSDALPPRDPPI 130

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLGTLLAGS 232
                    W+T+ LREG+NR+++++         RLIR +        P  L  L AG 
Sbjct: 131 RTRATIPTSWITLSLREGRNRQVRRMTAAVGLPTLRLIRTTIDLMDGEAPLSLEGLSAGE 190

Query: 233 TREVS 237
            R  S
Sbjct: 191 WRPAS 195


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 56/212 (26%), Positives = 102/212 (48%), Gaps = 5/212 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R+E  R+++ + ++VNG +++ A++ +     +E +G  L   +  +
Sbjct: 2   RLDKFLATTLGITRKEAGRLLSNKMIEVNGNVVKSASLKITDDCDVEFNGKKL-ALQGPQ 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D   TVF     +    + V GRLD +T GL LLT+DG  +  
Sbjct: 61  YFMLNKPEGFVCSHVD-DHNPTVFVLFDEVSPEKMHVAGRLDGDTTGLTLLTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     +VY V     V ++ +    +G+ ++G         L+      A +T+  
Sbjct: 120 VTSPRHVCEKVYHVELADPVPEETIQTFLEGVQLRGEKDITRPAKLEILSEREAILTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     +V  L R   G   L
Sbjct: 178 TEGKYHQVKRMFAAVGNRVVGLHREQVGAVVL 209


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 108/247 (43%), Gaps = 28/247 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V    +IE+D           
Sbjct: 489 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPEQNIEIDQRAQAAQAAQV 548

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 549 TILLHKPVGYVSGQAEDGYEPAVTLITRENHWSGDHSALRFSPQHLRTLAPAGRLDIDST 608

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L    +   + Y  RVRF  +   +DQ    + L  L+ G+ + G 
Sbjct: 609 GLLVLTQDGRIAKQLIGEQSDIDKEYLVRVRFGERLTDIDQHFPAESLAKLRHGLELDGA 668

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+   Q G        LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 669 PLKPAMVSW--QNGEQLRFV--LREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALPQ 724

Query: 231 GSTREVS 237
           G  R +S
Sbjct: 725 GEWRYLS 731


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 110/245 (44%), Gaps = 30/245 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D   +       
Sbjct: 296 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDDQAIAAQAAQV 355

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---------------NLPSIFSRVIS-VGRLDINT 118
             L HKP+G V+  ++ DG                      L  +  R ++  GRLDI++
Sbjct: 356 TILLHKPVGYVSGQAE-DGYEPAVTLITRENHWSGDRSALRLSPLHLRTLAPAGRLDIDS 414

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHGQ---VDQ----DKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    +   + Y  RVRF      VDQ    + 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 VPLKPAMVSWQ----NSEQLRFVLREGKKRQIRRMCELVGLEVVGLKRVRMGRVMLGALP 530

Query: 230 AGSTR 234
            G  R
Sbjct: 531 QGQWR 535


>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 = 66.2 bits (160), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 55/188 (29%), Positives = 89/188 (47%), Gaps = 28/188 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPD--GRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R  L+HKP  ++   S  D   + T+ D  ++P ++     VGRLD ++EGLLLLTN+G 
Sbjct: 4   RYLLFHKPYDVLCQFSPSDRPDQQTLKDYIDVPEVYP----VGRLDRDSEGLLLLTNNGA 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQK----- 183
           L   L  P     R Y V+   +  +  L  L++G+ IQ       +V  LD  +     
Sbjct: 60  LQHRLCHPRFGHDRTYWVQVEREPTEAALQALRQGVQIQDYRTRPAKVQRLDDPQIPERD 119

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLL 229
                      AW+ + L+EG+NR+++++         RLIR +        P QL  L 
Sbjct: 120 PPIRFRKTVPTAWLALTLQEGRNRQVRRMTAAVGHPTLRLIRAAIATHPDQPPLQLQGLA 179

Query: 230 AGSTREVS 237
            G+ R+++
Sbjct: 180 PGTWRDLT 187


>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 = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 90/178 (50%), Gaps = 23/178 (12%)

Query: 74  RLWLYHKPIGLVTTHSD---PDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           R+ L++KP G+++  +D   P  R T+  F ++P ++      GRLD ++EGLL+LT+DG
Sbjct: 3   RVILFNKPFGVLSQFTDAKSPTPRPTLSAFIDVPGVYP----AGRLDRDSEGLLVLTDDG 58

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYGDM 175
            L   +  P  +  + Y V+  G+  +  L+LL+ G+             +I      D 
Sbjct: 59  KLQARIAAPKNKMSKTYFVQVEGEPTEKDLSLLRDGVTLKDGPTRPAKLRLIDPPQLWDR 118

Query: 176 QVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +  +K   + W+ + + EG+NR+++++     +   RL+R   G + L  + +G+
Sbjct: 119 DPPVRFRKSVPDTWIEITISEGRNRQVRRMTAHIGFPTLRLVRWRIGNWTLDGIESGT 176


>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 = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 84/182 (46%), Gaps = 23/182 (12%)

Query: 73  TRLWLYHKPIGLVTTHSD---PDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +R+ L +KP G+++  +D   P  R T+  F  +P ++      GRLD ++EGLL+LT+D
Sbjct: 2   SRILLLNKPYGVLSQFTDARSPSPRPTLSGFVTVPGVYP----AGRLDRDSEGLLVLTDD 57

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
           G L   +  P  +  + Y V+  G      L LL+ G+ +        QV          
Sbjct: 58  GALQARIADPRHKLPKTYLVQVEGAPTDADLALLRHGVTLNDGPTRPAQVQRIAPPALWE 117

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       + W+ + + EG+NR+++++     +   RL+R   G + L  L  G+ 
Sbjct: 118 RDPPVRFRKSVPDQWIEITIHEGRNRQVRRMTAHIGFPTLRLVRWQIGDWTLDGLAPGAW 177

Query: 234 RE 235
           R+
Sbjct: 178 RD 179


>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 = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 100/222 (45%), Gaps = 13/222 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++    +    N  + D   +V G   +  E   
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGAVSIDSQTCDHPKQNFSTEDLSFQVFGEQYQYREHIY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + L HKP G   +H     RS VF  LP I     V  VGRLD +T GLLLLT+DG   +
Sbjct: 63  IVL-HKPQGYECSHQATHHRS-VFSLLPEILIHRGVQCVGRLDQDTTGLLLLTDDGQYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V     V  ++   L+ G+ +   +GI Y    + L +++     +
Sbjct: 121 ALTHPKKHVPKVYCVSTADPVTTEQKQQLELGVELRNEKGI-YAATDIKLISER----QL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + + +G   ++K++      KV RL R   G  +L  L  G
Sbjct: 176 EMTIHQGVYHQVKRMIAAVGNKVERLHRQQIGLLELPNLEEG 217


>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 = 66.2 bits (160), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 44/165 (26%), Positives = 83/165 (50%), Gaps = 25/165 (15%)

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R  +   L +  + ++++GRLD ++EGLLLLT DG  +  +   S +  + Y ++  G++
Sbjct: 19  RKPLLGELANFPTGIMAIGRLDHDSEGLLLLTTDGKTSHAVRSKSIE--KEYYLQLDGEI 76

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTL---------------------DTQKGSNAWVTVG 192
            +  ++ L +G+ I GI  G+   TL                     D + G  +W+ + 
Sbjct: 77  TEQAISSLCEGVEI-GI-KGEKYRTLPCRARRLDQAPDLPPRGRKIRDARHGPTSWLAIT 134

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + EGKNR+++K+     +   RL+R+  G  +LGTL  G  + ++
Sbjct: 135 ITEGKNRQLRKMTAAVGFATLRLVRVRIGDIRLGTLQPGEVKSLA 179


>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 = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 44/170 (25%), Positives = 80/170 (47%), Gaps = 23/170 (13%)

Query: 78  YHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G++   S  +   ++  F N P  +      GRLD ++EGLLLLT+DG L   + 
Sbjct: 7   FNKPYGVICQFSPHEKHKSLKDFINFPGFYP----AGRLDTDSEGLLLLTDDGRLQAQIT 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------- 187
            P  +  + Y  +  G  D+ +L  L+KGI + G       + +     +++        
Sbjct: 63  DPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPPI 122

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                    W+ + + EGKNR+++++     +   RLIR++ G  +L  L
Sbjct: 123 RVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDL 172


>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 = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 57/196 (29%), Positives = 95/196 (48%), Gaps = 43/196 (21%)

Query: 77  LYHKPIGLVTTHSDPDG----RSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L++KP  ++   +D  G    R T+  F ++P ++S    VGRLD+++EGLLLLT++G L
Sbjct: 6   LFYKPYNVLCQFTDNSGDKTNRQTLKDFIDIPHVYS----VGRLDLDSEGLLLLTDNGPL 61

Query: 131 A-----RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKG 184
                 R    P T W++V  +      D+  LN L++G+ I+        V  L T+  
Sbjct: 62  QHRLGHRQFAHPRTYWVQVENI-----PDEAALNRLREGVKIEDYWTRKASVIKLPTEPV 116

Query: 185 --------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQ 224
                            W+ + L EG+NR+++++     +   RL+R++ G       FQ
Sbjct: 117 LPPRNPPIRYRKSIPTCWLEITLTEGRNRQVRRMTAAVGYPTLRLVRVAMGIGKGKNEFQ 176

Query: 225 LGT--LLAGSTREVSK 238
           LG   L  G  REV++
Sbjct: 177 LGLEGLEPGQWREVTE 192


>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 = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 48/171 (28%), Positives = 81/171 (47%), Gaps = 20/171 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP G+V+  S  +   T+  F ++P+ ++     GRLD N+EGLLLLT+ G L   L
Sbjct: 6   LFNKPYGVVSQFSGEEHEHTLAAFIDIPNFYA----AGRLDKNSEGLLLLTDSGALQHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P     + Y V+  G      L++L+ G+V++ I +      L  +            
Sbjct: 62  TAPKFNKRKYYWVQVEGTPCNQDLDILRNGLVLKDISFLPAGARLIDEPHLWPRNPPIRF 121

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 +W+ + L EGKN +I+K+     +   RL+R     ++L  L  G
Sbjct: 122 RKNIPTSWLEIILSEGKNHQIRKMTAAIGFPTLRLVRHRISDWRLDNLQPG 172


>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 = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 86/179 (48%), Gaps = 25/179 (13%)

Query: 78  YHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP G+++  + P+GR      F ++P ++      GRLD ++EGLLLLT+DG L   +
Sbjct: 33  FNKPYGVLSQFT-PEGRWRGLQDFIDVPGVYV----AGRLDADSEGLLLLTDDGALQARI 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----------------QGICYGDMQVT 178
             P  +  + Y V+  G  D+  L  L+ G+ +                  +   D  + 
Sbjct: 88  SDPRHKMEKTYWVQVEGIPDEAALQALRHGVQLGDGPTLPARVRRLEPPPALWERDPPIR 147

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  +  +
Sbjct: 148 V-RQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYALDGLEPGCWQPAT 205


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 50/181 (27%), Positives = 87/181 (48%), Gaps = 19/181 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL L++KP  +++  +D      R T+ D +     RV   GRLD ++EGLLLLT+DG L
Sbjct: 3   RLILFNKPYDVLSQFTDSSIGADRRTLSDFI--DVPRVYPAGRLDRDSEGLLLLTDDGRL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------- 181
              +  P  +  + Y V+  G V  D L  L+ G+ ++ G         +D         
Sbjct: 61  QARISNPRFKTPKTYLVQVEGDVTSDALACLRAGVSLKDGPTLPAEAERIDPPALWPRDP 120

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   + W+++ +REG+NR+++++         RL+R   G + L  +  G+ R+ 
Sbjct: 121 PVRFRKTVPDCWISLTIREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLDGVAPGTWRDA 180

Query: 237 S 237
           S
Sbjct: 181 S 181


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 111/245 (45%), Gaps = 36/245 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D  P  +A +  
Sbjct: 402 RLSKLMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEID--PAAEAAQAS 459

Query: 75  --LWLYHKPIGLVTTHSDPDG-----------------RSTVFDNLPSIFSRVISVGRLD 115
               L HK +G V+  ++ DG                 RS +  ++ +   ++   GRLD
Sbjct: 460 QVTVLIHKTVGFVSGQAE-DGYQPAITLVTPENRWEGDRSNIRFSV-AHLRQLAPAGRLD 517

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIV 166
           I++ GLL+LT DG +A+ L    ++  + Y VR                + L LL+ G+ 
Sbjct: 518 IDSTGLLVLTQDGRIAKRLVGGHSEIDKEYLVRVAFGEHTTDVESHFPPESLALLRHGLS 577

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           +  +     QV+   Q G        LREGK R+I+++ E    +V  L R+  G   LG
Sbjct: 578 LDDVPLKPAQVSW--QNGEQLRFV--LREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLG 633

Query: 227 TLLAG 231
            L  G
Sbjct: 634 ALPPG 638


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 17/175 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            ++KP G+++  + P+G+    +   ++   V   GRLD ++EGLL+LT+DG L   +  
Sbjct: 6   FFNKPYGVLSQFT-PEGKWRALNEFITV-KDVYVAGRLDADSEGLLILTDDGKLQAKIAD 63

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKG----------- 184
           P  +  + Y  +  G  D+  L+ L+ GI +        +V L D   G           
Sbjct: 64  PRHKLEKTYWAQVEGVPDEAALDRLRAGIELSDFTAKPAKVRLIDEPAGLWQRDPPIRFR 123

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +W+ + + EGKNR+++++     +   RLIR + G   L  L  G  R++
Sbjct: 124 AAIPTSWLEIRISEGKNRQVRRMTAAIGYPTLRLIRAAIGAATLDGLALGQWRKI 178


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 85/180 (47%), Gaps = 25/180 (13%)

Query: 74  RLWLYHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTND 127
           RL  ++KP  ++   +D       R T+ D  + P ++      GRLD ++EGL+LLT+ 
Sbjct: 3   RLIRFNKPYDVLPQFTDRGSQESSRKTLSDFIDCPGVYP----AGRLDRDSEGLMLLTDF 58

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---------------GICY 172
           G L   +  PS +  + Y V+  GQ D+  L  L KG+ ++                + +
Sbjct: 59  GRLQAWISDPSHKMAKTYWVQVEGQPDRAGLEALSKGVELKDGLTLPASAHLMEEPAMLW 118

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+++ ++EGKNR+++++         RLIR S G + L  L  GS
Sbjct: 119 ARTPPIRERKNIPTSWISLTIKEGKNRQVRRMTAAIGHPTLRLIRYSIGTWTLEGLSQGS 178


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 118/258 (45%), Gaps = 52/258 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+SK ++  G+ SRRE +  I +  V V+G  +      +     IE+    L++A    
Sbjct: 356 RLSKRMSELGLCSRREADEWIPRGWVLVDGKPVTELGSRIRPDAEIEI----LQEARSEQ 411

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------------------RVI 109
            ER  + L +KP+G V+  ++ DG    ++   ++F+                     + 
Sbjct: 412 GERVTV-LLNKPVGYVSGQAE-DG----YEPAAALFAPENQWEGDPTRKRFAPWQRKNLA 465

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVDQ--------D 156
             GRLDI++ GLL+LT DG +AR L    +   + Y VR      HG V++        D
Sbjct: 466 PAGRLDIDSTGLLVLTQDGRVARALIGEDSTVEKEYLVRVVWHSPHGPVERNISAEFPAD 525

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            L LL+ G+ + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L 
Sbjct: 526 DLELLRHGLSLDGVPLKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLQVVGLK 581

Query: 217 RISYGPFQLGTLLAGSTR 234
           R+  G   LG L  G  R
Sbjct: 582 RVRMGRVVLGDLPPGKWR 599


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 62/233 (26%), Positives = 106/233 (45%), Gaps = 14/233 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERT 73
           + K++   G  SR+  +++I    V + G ++        S +++E    G   R  E+ 
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIEGEIVTDLKKQ-FSPENLEFSLFGETYRYREKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L  KP G   +H +P    +VF  LP I  +  V ++GRLD +T GLLLLT+DG   
Sbjct: 62  YLAL-KKPQGFECSH-NPQHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + L  P     +VY V     V  +++ +L +G+ +      D+    D     +  +T+
Sbjct: 120 QALTHPRKHVPKVYHVTTIDSVTPEQIEMLTQGVNLHQ--EKDVFAATDVALLGSHQLTM 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 178 TIHQGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGDWVYLSEQ 225


>gi|224826005|ref|ZP_03699108.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224601642|gb|EEG07822.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 236

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 112/234 (47%), Gaps = 9/234 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAER 72
            + +++ + G  SR+E  +++    V+++G +++  R  ++  + D + +DG P      
Sbjct: 2   ELYRLMQQQGFGSRKECRKLVEHGLVELDGAVVDDYRLEIDPAAIDELVIDGEPWEILML 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G  T+H  P    +VF  LP  FS+  + +VGRLD++T GLLLLT DG  
Sbjct: 62  PLYILLHKPAGYETSHK-PMHNPSVFTLLPWQFSQLGIAAVGRLDVDTTGLLLLTTDGQF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAWV 189
              L  P     + Y V     V +  +  LK G+ ++     + +V  D  +      +
Sbjct: 121 VHALTSPKKHVPKCYEVTLKHPVSEALVKHLKAGVFLKD---DNEKVVADQVEVVDEITI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + +GK  ++K++      +V  L R++ G  QLG L  G  R +    L E
Sbjct: 178 RMTITQGKYHQVKRMIAAAGNRVQELHRVALGTLQLGELDEGEWRHLDAAELAE 231


>gi|325204300|gb|ADY99753.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M01-240355]
          Length = 230

 Score = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 102/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 43/136 (31%), Positives = 67/136 (49%), Gaps = 9/136 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K I+  G  SRR  +++I + RV +NG   E     V+  D + VDG P+   E+ 
Sbjct: 7   KRLNKFISETGFCSRRAADKLIEEGRVTINGKQPE-MGTKVLPGDDVCVDGKPVASKEKP 65

Query: 74  RLWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+  TT  D  G    F        R+  +GRLD  ++GL+ LTNDG +  
Sbjct: 66  IYIALNKPTGITCTTERDIPGNIVDFIGHKK---RIFPIGRLDKPSDGLIFLTNDGDIV- 121

Query: 133 VLELPSTQWLRVYRVR 148
                S +W    ++R
Sbjct: 122 ---TDSARWYNHEKIR 134


>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 = 65.9 bits (159), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 111/236 (47%), Gaps = 26/236 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV     DG PL  
Sbjct: 2   RLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADG-PLEV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLL 123
                 +L +KP G++T   DP  +STV D +      P ++     VGRLD +T GLLL
Sbjct: 61  D-----YLMNKPAGVITATEDP-TQSTVLDLIRPHDYRPGLY----PVGRLDKDTTGLLL 110

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQ 182
           LT DG L   L  P+    + Y       +  D    L+ GI ++       Q V L   
Sbjct: 111 LTTDGNLGHALLSPNRHIAKTYAATLAKTLTADMKQQLETGIDLKDFTTAPAQVVVLPDT 170

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            G    +T+   EGK  ++K++    + +V  L RI+ GP  L   L AG  R ++
Sbjct: 171 DGKRIQITI--TEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYRALT 224


>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 = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/221 (27%), Positives = 100/221 (45%), Gaps = 23/221 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   +R +   MI    V VN  ++   A  V   +HI  +G  L  A  +R
Sbjct: 2   RLDKFVCKSTELTRVDATAMITGGCVSVNHDVILDVATQVHENNHISFNGEVL-TARPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP   + ++ D        +  PS+F        S +   GRLD +T GL+L+T+
Sbjct: 61  YILLHKPADTICSNID--------EAYPSLFNYIDVENASELHVAGRLDADTTGLVLVTD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKG 184
           DG  +  +  P+    +VYRV     +  D +     G+ +Q    G+ Q+T     +  
Sbjct: 113 DGRWSFNIITPTKHCQKVYRVGLSRPIGDDVVAKFAHGVQLQ----GEQQLTRPAILEVV 168

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           S+  V + + EGK  ++K++F     +V  L R   G  QL
Sbjct: 169 SSKEVLLTITEGKFHQVKRMFSAVGNRVVSLHREKIGAIQL 209


>gi|241889378|ref|ZP_04776679.1| ribosomal small subunit pseudouridine synthase A [Gemella
           haemolysans ATCC 10379]
 gi|241863921|gb|EER68302.1| ribosomal small subunit pseudouridine synthase A [Gemella
           haemolysans ATCC 10379]
          Length = 235

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/219 (27%), Positives = 108/219 (49%), Gaps = 15/219 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K I+     SR E +++I ++ + +N  L++     V    D + +DG  L   +  
Sbjct: 2   RLDKFISTTTTLSRAEAKKVI-KKGILINDKLIKSPDYKVDEINDQVILDGKRLVYQKYV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP   ++   D   + TV D L       +V  VGRLD +TEGL+LLTNDG LA
Sbjct: 61  YIMM-NKPQDTISATEDAIEK-TVVDILKEEDRIHKVFPVGRLDKDTEGLMLLTNDGELA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDT---QKGSN 186
             L  P    ++ Y V   G++ ++ L +++ G+ ++    C       L++   +  +N
Sbjct: 119 HRLISPKKDVVKKYYVEVSGELKEEHLPIIEAGVTLEDGYKCKAAKLEILESNEDESKAN 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            ++T    EGK  ++K++ +     V  L R+S G  +L
Sbjct: 179 IYIT----EGKFHQVKRMMKSLGTTVTYLKRLSIGSLKL 213


>gi|325205754|gb|ADZ01207.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M04-240196]
          Length = 186

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/170 (25%), Positives = 80/170 (47%), Gaps = 23/170 (13%)

Query: 78  YHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G++   S  +   ++  F N P  +      GRLD ++EGLLLLT+DG L   + 
Sbjct: 7   FNKPYGVICQFSPHEKHKSLKDFINFPGFYP----AGRLDTDSEGLLLLTDDGRLQAQIT 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------- 187
            P  +  + Y  +  G  D+ +L  L+KGI + G       + +     +++        
Sbjct: 63  DPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPPI 122

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                    W+ + + EGKNR+++++     +   RLIR++ G  +L  L
Sbjct: 123 RVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDL 172


>gi|325130337|gb|EGC53103.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis OX99.30304]
          Length = 230

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 51/200 (25%), Positives = 95/200 (47%), Gaps = 16/200 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +IA   V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVF 205
              + + + EGK  ++K++ 
Sbjct: 178 ---LLLTITEGKYHQVKRMI 194


>gi|296136628|ref|YP_003643870.1| pseudouridine synthase [Thiomonas intermedia K12]
 gi|295796750|gb|ADG31540.1| pseudouridine synthase [Thiomonas intermedia K12]
          Length = 300

 Score = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 116/254 (45%), Gaps = 40/254 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R+SK ++  G+ASRRE +  I +  V ++G   +L  + A N+ ++  +       R+A 
Sbjct: 45  RLSKRMSELGLASRREADDWIERGWVLLDGTPAVLGTKVAGNLPASRIVIRKAAQHRQAA 104

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFS----RVISV-GRLDI 116
           +  + L HKP+G V+  ++      V              P  FS    R ++V GRLDI
Sbjct: 105 QVTI-LLHKPVGYVSAQAEHGYTPAVALIKAENRWAECEAPQPFSPAHLRHLAVAGRLDI 163

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------HGQVDQDKLNLL 161
           ++ GLL+LT DG +AR L    +   + Y VR                     + +L LL
Sbjct: 164 DSTGLLVLTQDGRIARQLIGEDSAVEKEYLVRVSLTDAPARNGAEEDVQAAFPESRLALL 223

Query: 162 KKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + G+ +        QV  ++ Q+     +   LREGK R+I+++ E    +V  L R+  
Sbjct: 224 RHGLKLDDQPLRPAQVEWINPQQ-----LRFVLREGKKRQIRRMCELVGLRVTGLKRVRI 278

Query: 221 GPFQLGTLLAGSTR 234
           G  +LG L  G  R
Sbjct: 279 GGLRLGALPLGQWR 292


>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 = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/167 (31%), Positives = 77/167 (46%), Gaps = 30/167 (17%)

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 QGICYGDMQVT-LDTQKGSN----------------AWVTVGLREGKNREIKKVFEFFNW 210
           +G      Q T LD     +                +W+++ LREG+NR+I+++      
Sbjct: 61  KGQSTRPAQATFLDASHWRDLPERTPPIRVRRSIPTSWLSISLREGRNRQIRRMTAAVGL 120

Query: 211 KVNRLIRISYG------PFQLGTLLAGSTREVS-------KKILREQ 244
              RLIR S        P  L  L  G  R V        K +LR Q
Sbjct: 121 PTLRLIRRSIDLMDSEPPLSLEGLAPGQWRPVKPAEQERLKALLRNQ 167


>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 = 65.9 bits (159), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/188 (29%), Positives = 89/188 (47%), Gaps = 22/188 (11%)

Query: 78  YHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G+++  T   P  R+      P     V  VGRLD ++EGLLLL+++ GLA  L 
Sbjct: 5   FNKPYGILSQFTKEAPHHRTLAEFGFPP---GVYPVGRLDADSEGLLLLSDEKGLADRLL 61

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKG---------- 184
            PS +  R Y  +  G   +  L  L+  G+ I+G C    +  L  ++           
Sbjct: 62  NPSGRHPRTYWSQVEGTPSETDLRPLELGGLRIRGHCTLPCRARLMRREPDVPPRIPPVR 121

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  +W+ + L EGKNR+++++     +   RL+R   G F L  L  G+ +E+  +
Sbjct: 122 YRASIPTSWLELTLVEGKNRQVRRMTAAIGFPTLRLLRARIGNFSLAGLKPGAWKELDSR 181

Query: 240 ILREQLGP 247
             R QL P
Sbjct: 182 E-RRQLMP 188


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 96/211 (45%), Gaps = 3/211 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   +R E   +I    V VNG  +  A+  V   + I +DG  L     +R
Sbjct: 2   RLDKFLCKSTELTRIEATALIVAGEVLVNGQTVTSASTQVHENNRITLDGQVL-TPRASR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP+  ++++ D D  S +          +   GRLD +T GL+L+T+DG  +  +
Sbjct: 61  YIMMHKPLDTLSSNVDGDYPSVMNCLDVDKVCDLHIAGRLDADTTGLVLVTDDGRWSFNI 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     +VYRV     ++ D       G+ +QG     +   L+    +   +T+   
Sbjct: 121 INPKYHCEKVYRVSLRDPINDDVAGKFACGVQLQGEASLTLPAKLEVVSPTEVLLTI--T 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F     +VN L R   G  +L
Sbjct: 179 EGRYHQVKRMFAAVGNRVNGLHRQQVGDIKL 209


>gi|217974985|ref|YP_002359736.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217500120|gb|ACK48313.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 233

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/218 (29%), Positives = 98/218 (44%), Gaps = 13/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++    R      I    V VNG +    A+ V   + + ++  PL     +R
Sbjct: 2   RLDKFLCKSTDLDRDAASVAIINGSVTVNGAIATDCAMQVHENNAVCLNEKPLMP-RPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++ HKP    T  S+ DG      +L  I   F   I VGRLD++T GL+LLT+DG  +
Sbjct: 61  YFMLHKPAD--TLCSNVDGAYPSLFHLLDIERAFDLHI-VGRLDVDTTGLVLLTDDGRWS 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P  Q  +VYRV     +D +           G+ +QG     +  TL  Q+  + 
Sbjct: 118 FNIISPQYQCKKVYRVTLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDDK 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + L EGK  ++K++F     KV  L R   G F L
Sbjct: 176 TVLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAFIL 213


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/226 (23%), Positives = 104/226 (46%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  + R +    V ++G +++  +  +     +  DG  L +    R
Sbjct: 12  RLDKFLSQQLGISRSLILRELRAGLVTIDGEMVKSGSTKIAPEQEVAYDGKVLTQILGPR 71

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KPIG V +  DP   + ++     +  ++ + GRLDI+T GL+LLT++G  +  +
Sbjct: 72  YFMLNKPIGYVCSTDDPVNPTILYFIDEPLAHKLHAAGRLDIDTTGLVLLTDNGQWSHRI 131

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + +      +KG+ + G    D+      +  +   V + + 
Sbjct: 132 TAPKHHCEKTYLVTLEEPIGEGVAEQFQKGVQLNG--EKDLTKPAKLEILTPTEVKLTIS 189

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           EGK  ++K++F      V+ L R   G   L  TL  G  R ++++
Sbjct: 190 EGKYHQVKRMFAAVGNHVSALHRERIGDITLDETLAEGEYRPLTEE 235


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 57/224 (25%), Positives = 104/224 (46%), Gaps = 11/224 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERT 73
           R+   +A     SR+E +R IA+ +++VNG ++ +   +V     +E  G V L + E+ 
Sbjct: 2   RLDYFLAHTTSWSRKEAKRFIAKGKIRVNGDVVTKPNASVTEDCKVESHGEVILWRKEK- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +  +KP   V+   D +  S V  +L  P     +  VGRLD +T GL+ LT DG   
Sbjct: 61  -YFALYKPADYVSALEDSE--SPVLIDLIEPEERKNLKIVGRLDKDTTGLIFLTTDGQWL 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVT 190
             +  P     + YRV     + +     L+ G+++ G    D+  +    ++ S+  + 
Sbjct: 118 HRITSPKHDCYKTYRVYCADPISEANCKSLETGVMLNG---EDLPTSPAKVERVSDTEIL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + ++EGK  ++K++      +V +L R +     L  L  G  R
Sbjct: 175 LSIKEGKYHQVKRMLAAVGNRVEKLHREAISDVNLDGLQEGQYR 218


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/185 (28%), Positives = 88/185 (47%), Gaps = 28/185 (15%)

Query: 76  WLYHKPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L +KP G ++    P+ R +  +   L     + +++GRLD ++EGLLLLT DG  + +
Sbjct: 15  FLIYKPYGFLSQFV-PETRKSKPLLGQLYEFPEKTMAIGRLDHDSEGLLLLTTDGMQSHL 73

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           +   S    + Y V+  G+V Q +L  L++G+ I GI  G   +TL              
Sbjct: 74  IR--SKTIEKEYYVQVDGEVSQAQLAKLRQGVEI-GIS-GGKYLTLPCKVELLIHEPNLP 129

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G   W++V + EGKNR+++K+         RL+R+  G   L  +  G 
Sbjct: 130 ARGKKIRDPRHGPTNWLSVTIDEGKNRQVRKMTAAVGLPTLRLVRVRIGAIHLKQMQPGE 189

Query: 233 TREVS 237
              V+
Sbjct: 190 VIPVT 194


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 111/236 (47%), Gaps = 26/236 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV     DG PL  
Sbjct: 2   RLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADG-PLEV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLL 123
                 +L +KP G++T   DP  +STV D +      P ++     VGRLD +T GLLL
Sbjct: 61  D-----YLMNKPAGVITATEDP-TQSTVLDLIRPHDYRPGLY----PVGRLDKDTTGLLL 110

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQ 182
           LT DG L   L  P+    + Y       +  D    L+ GI ++       Q V L   
Sbjct: 111 LTTDGNLGHALLSPNRHIAKTYAATLAKTLTADMKQRLETGIDLKDFTTAPAQVVVLPDT 170

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            G    +T+   EGK  ++K++    + +V  L RI+ GP  L   L AG  R ++
Sbjct: 171 DGKRIQITI--TEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYRALT 224


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 43/183 (23%), Positives = 87/183 (47%), Gaps = 25/183 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
            R+ L++KP G+++  +D      P    + + + P  +      GRLD ++EGL++LT+
Sbjct: 2   ARVILFNKPYGVLSQFTDKGSEGSPRPTLSAYIDQPGFYP----AGRLDRDSEGLMVLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS- 185
           DG L   +  P  +  + Y V+  G  +  +L +L+ G+ ++       + TL     + 
Sbjct: 58  DGKLQARISNPKHKMAKTYLVQVEGTPEPQQLEVLRAGVRLKDGMTKPAKATLACPPENL 117

Query: 186 --------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + + EG+NR+++++         RLIR+  G + L  L+ G
Sbjct: 118 WERTPPVRYRKTVPDSWLQISISEGRNRQVRRMTAHVGLPCLRLIRMRVGDWALNDLVPG 177

Query: 232 STR 234
           + R
Sbjct: 178 AWR 180


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 102/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + + +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYIMLNKPEDYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 220


>gi|294340758|emb|CAZ89150.1| putative ribosomal large subunit pseudouridine synthase [Thiomonas
           sp. 3As]
          Length = 300

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 116/254 (45%), Gaps = 40/254 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMSTDHIEVDGVPLRKAE 71
           R+SK ++  G+ASRRE +  I +  V ++G   +L  + A N+ ++  +       R+A 
Sbjct: 45  RLSKRMSELGLASRREADDWIERGWVLLDGTPAVLGTKVAGNLPASRIVIRKAAQHRQAA 104

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFS----RVISV-GRLDI 116
           +  + L HKP+G V+  ++      V              P  FS    R ++V GRLDI
Sbjct: 105 QVTI-LLHKPVGYVSAQAEHGYTPAVALIKAENRWAECEAPQPFSPAHLRHLAVAGRLDI 163

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------HGQVDQDKLNLL 161
           ++ GLL+LT DG +AR L    +   + Y VR                     + +L LL
Sbjct: 164 DSTGLLVLTQDGRIARQLIGEDSAVEKEYLVRVSLTDAPARNGAEEDVQAAFTESRLALL 223

Query: 162 KKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + G+ +        QV  ++ Q+     +   LREGK R+I+++ E    +V  L R+  
Sbjct: 224 RHGLKLDDQPLRPAQVEWINPQQ-----LRFVLREGKKRQIRRMCELVGLRVTGLKRVRI 278

Query: 221 GPFQLGTLLAGSTR 234
           G  +LG L  G  R
Sbjct: 279 GGLRLGALPLGQWR 292


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/193 (28%), Positives = 97/193 (50%), Gaps = 12/193 (6%)

Query: 58  DHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLD 115
           D + ++G  + K E+ ++++ +HKP+G+  T +D    + + + N P    R+  VGRLD
Sbjct: 18  DIVTINGQVIEKEEKEKVYIAFHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLD 74

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             +EGL+LLTNDG +A  +     +  + Y V          ++ +  G+ I+       
Sbjct: 75  KASEGLILLTNDGTIANQILHGDHEHEKEYVVTVDKPFTDWFIDEMSGGVKIKDGMTKPC 134

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +VT   Q    +   V L +G NR+I+++   F + V +L R+     +L  L AG  R+
Sbjct: 135 KVTRIDQ----STFRVVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRD 190

Query: 236 VSKK---ILREQL 245
           ++ K   IL  QL
Sbjct: 191 ITPKELEILTGQL 203


>gi|325128404|gb|EGC51287.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis N1568]
          Length = 230

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 102/226 (45%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDLDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPEDYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLENPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 96/220 (43%), Gaps = 15/220 (6%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++    V VNGI  E     V +   + +VDG   R A   R +
Sbjct: 12  RILQSQGFGTRRYCKDLVLAGLVHVNGIEAENPDAQVDTAGLVLDVDGE--RWAYHARAY 69

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG     
Sbjct: 70  LMLHKPAGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHT 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---TQKGSNAWVT 190
           L  P  Q  +VY +     V   +L  L +G+++      D   T+     ++     + 
Sbjct: 129 LTSPRHQVPKVYEITTADPVTDAQLAQLCQGVLLD-----DEDATVAAAWAERVDTCHLR 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + L +GK  ++K++       V  L R + G   L   LA
Sbjct: 184 MALTQGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLA 223


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 57/228 (25%), Positives = 102/228 (44%), Gaps = 27/228 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R+ K I  +   +R + +++I+Q R+  +  ++   A        I  DG  + +R    
Sbjct: 2   RLDKTICESTTLTRSQAKKVISQGRITCDDKIIRSCAFKPRKDAVIVFDGKTIAIRGP-- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLL 124
            R  + +KP   + ++ D        + LPS+F+ V           GRLD +T GL L+
Sbjct: 60  -RYMMLNKPENFICSNVD--------EQLPSLFNLVDVDKKELLFIAGRLDADTTGLTLI 110

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG  +  +  P  + ++ YRV     + +D + L K GI ++     + Q  L  +  
Sbjct: 111 TDDGKWSHKITSPRNKCIKRYRVGLDAPICEDAVALFKAGIQLK----SENQPCLPAELN 166

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             S+  V + + EGK  ++K++F      V  L R   G  +L   LA
Sbjct: 167 ILSSTEVILSISEGKYHQVKRMFGAIGNVVIELHREKIGDIELDNTLA 214


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 83/173 (47%), Gaps = 23/173 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL   +KP G +   S  + R+++ D   +P+++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLLALNKPFGTICQFSPHETRASLADWVKVPNVYP----AGRLDSDSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDT----- 181
           AR+ E P  + ++ Y  +  G VD   L  L +G+     +   C  +     DT     
Sbjct: 58  ARIAE-PRHKLVKRYWAQVEGAVDAATLRKLARGVDLGDYVTRPCRAEYVEPTDTLWSRT 116

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R+  G   + +L
Sbjct: 117 PPIRYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFSL 169


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 52/191 (27%), Positives = 88/191 (46%), Gaps = 25/191 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL   +KP G +   S  + R+++ D    P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLIALNKPFGTICQFSVHETRASLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQ 57

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------ 185
             +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G+      
Sbjct: 58  AKIAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNP 117

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGST 233
                     AW+ + + EGKNR+++++     +   RL+R+  G    F LG L  G T
Sbjct: 118 PIRHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALG-LAPGET 176

Query: 234 REVSKKILREQ 244
           RE+  +   E+
Sbjct: 177 RELPPRAPWER 187


>gi|295677452|ref|YP_003605976.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295437295|gb|ADG16465.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 189

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 81/173 (46%), Gaps = 23/173 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL  ++KP G +   S  + R+++ D   +P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLLAFNKPFGTICQFSPHETRASLADWVKVPGVYP----AGRLDSDSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----- 185
           AR+ E P  + ++ Y  +  G +D   L  L +G+ +        Q        S     
Sbjct: 58  ARIAE-PRHKLVKRYWAQVEGALDDAALKKLARGVDLGDFVTRPCQANYVEPSSSLWTRT 116

Query: 186 ----------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R+  G   + +L
Sbjct: 117 PPIRYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSL 169


>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 = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 114/239 (47%), Gaps = 30/239 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGIL-----------LERAAVNVMSTDHIEVD 63
           R+ K ++  G+ +R EV++ + +++V ++  +           LE   VN    D +   
Sbjct: 2   RLDKFLSNMGVGTRTEVKQRLKKKQVTIDDKVETSPKKQINPELEIVKVNDQKIDFVN-- 59

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLL 122
                   +  L L +KP   ++  +D +   TV D +    +  +  VGRLD +TEGLL
Sbjct: 60  --------KVYLML-NKPKDYISATTD-EQHKTVLDLIEDYRYLDLFPVGRLDKDTEGLL 109

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT 181
           L+TNDG     L  P     + Y V     + ++ +N  K GI + +G+      V  D 
Sbjct: 110 LITNDGQFNHELMSPGKHVAKTYEVISQKNITKNDINAFKVGIELNEGLAKPAKLVQGD- 168

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            + + ++VT+   EG+  ++K++F   + +V  L RI  G  QL  TL +G  R ++++
Sbjct: 169 -ELNKSFVTI--YEGRYHQVKRMFHAIDNEVLALKRIRIGDLQLDSTLASGEYRHLTQQ 224


>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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 83/173 (47%), Gaps = 23/173 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL   +KP G +   S  + R+++ D   +P+++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLLALNKPFGTICQFSPHETRASLADWVKVPNVYP----AGRLDSDSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDT----- 181
           AR+ E P  + ++ Y  +  G VD   L  L +G+     +   C  +     DT     
Sbjct: 58  ARIAE-PRHKLVKRYWAQVEGAVDAATLKKLARGVDLGDYVTRPCRAEYVEPTDTLWVRT 116

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R+  G   + +L
Sbjct: 117 PPIRYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFSL 169


>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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 103/222 (46%), Gaps = 17/222 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E      ++ E T 
Sbjct: 2   RLDKFLCDALGTTRKESTQLLKSGEVTVDDVVQKSGAFKLKETSRVE-----WQEREITL 56

Query: 74  ---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
              R  + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG 
Sbjct: 57  HGPRYIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQ 115

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNA 187
            +  +  P  +  + YRV     +  D  +   +GI ++    G+ ++TL  Q    S  
Sbjct: 116 WSHRVTSPKHKCEKTYRVWLADPIQADYADQFTQGIELR----GERELTLPAQLEVVSET 171

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            V + + EGK  ++K++F     KV  L R   G   L   L
Sbjct: 172 EVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDEAL 213


>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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 84/180 (46%), Gaps = 23/180 (12%)

Query: 77  LYHKPIGLVTTHSDP---DGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L++KP G++   +D      R T+ D++  P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 5   LFNKPYGVLCQFTDERTGPPRPTLADHIHRPGVYP----AGRLDHDSEGLLLLTDDGRLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  +  + Y  +  G  D+  L  L+KG+ ++       +  L            
Sbjct: 61  ARIADPRHKMPKTYLAQVEGVPDEAALASLRKGVRLKDGMTLPAEAALIEDPALWPRDPP 120

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   ++W+ + +REG+NR+++++         RL+R   G + L  L  G  REV 
Sbjct: 121 IRVRKTVPDSWLRLTIREGRNRQVRRMTAAVGHPTLRLVRWQVGDWSLDGLRPGEWREVE 180


>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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 81/173 (46%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +++KP G++   S  +   ++  F NLP  +      GRLD ++EGLLLLT+DG L  
Sbjct: 4   LIIFNKPYGVICQFSPHEKHKSLKDFINLPGFYP----AGRLDTDSEGLLLLTDDGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  +  + Y  +  G  D+ +L  L+KGI +         V +     +N      
Sbjct: 60  QITDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRVLEHGETNPLWERI 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R++ G  +L  L
Sbjct: 120 PPIRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDL 172


>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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 44/174 (25%), Positives = 82/174 (47%), Gaps = 20/174 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++   +D + R T+  F  +P I++     GRLD ++EGLLLLTNDG L   +
Sbjct: 29  LFNKPFDVLCQFTDENNRRTLKDFITIPGIYA----AGRLDRDSEGLLLLTNDGKLQHQI 84

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  + Y V+  G   +  L  L++G+ ++       +V +  +            
Sbjct: 85  ANPVKKTEKTYWVQIEGAPSEQDLAKLRQGVELKDGMTKPAKVAIMLEPNVWPRNPPIRE 144

Query: 185 ----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  W+ + + EG+NR+++++     +   RLIR   G + L  +  G  +
Sbjct: 145 RASIPTTWLEITITEGRNRQVRRMTANIGFPTLRLIRYRIGNWTLDNINNGEYK 198


>gi|56808585|ref|ZP_00366316.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 141

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/131 (32%), Positives = 67/131 (51%), Gaps = 8/131 (6%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---- 169
           +D +T G+L+LTNDG     +  P  +  +VY  R  G   ++ L  L +GIVI G    
Sbjct: 1   MDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTK 60

Query: 170 -ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              Y  ++V  D  +   + V + + EG+N ++KK+FE     V++L R  +G   L  L
Sbjct: 61  PARYNIVRVEADKNR---SIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGL 117

Query: 229 LAGSTREVSKK 239
             G  R ++KK
Sbjct: 118 RPGEARRLNKK 128


>gi|307730777|ref|YP_003908001.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307585312|gb|ADN58710.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 189

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 50/176 (28%), Positives = 83/176 (47%), Gaps = 26/176 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL   +KP G +   S  + R+++ D  ++P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLLALNKPFGTICQFSAHETRASLADWVSVPGVYP----AGRLDSDSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLD------ 180
           AR+ E P  + ++ Y  +  G VD   L  L +G+     +   C  D     D      
Sbjct: 58  ARIAE-PRHKLVKRYWAQVEGAVDAAALKKLARGVDLGDYVTKPCRADYVDPADRLWPRT 116

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R+  G    F LG +
Sbjct: 117 PPIRYRAAIPTTWIELSIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGLM 172


>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 = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/224 (28%), Positives = 95/224 (42%), Gaps = 23/224 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++A   V VNGI  E     V +   + +VDG       R  L 
Sbjct: 38  RILQSQGFGTRRYCKDLVAAGLVHVNGIEAEDPDAQVDTAGLVLDVDGERWAYHARAYLM 97

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134
           LY KP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG     L
Sbjct: 98  LY-KPAGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTL 155

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---- 190
             P  Q  +VY +     V   ++  L +G+++      D   T+     + AW      
Sbjct: 156 TSPRHQVPKVYEITTADPVTDAQVAQLCRGVLLD-----DEDATV-----AAAWAERVDT 205

Query: 191 ----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               + L +GK  ++K++       V  L R + G   L   LA
Sbjct: 206 CDLRMALTQGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLA 249


>gi|303286517|ref|XP_003062548.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456065|gb|EEH53367.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 230

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/201 (29%), Positives = 96/201 (47%), Gaps = 15/201 (7%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT 86
           SRR  +R++A   V VNG ++   A+ V   D +E+ G  +R  E      Y KP G VT
Sbjct: 11  SRRNADRLVASGAVTVNGAVVAAGAM-VFPGDVVELRGERVR-WETLNYVKYWKPRG-VT 67

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             +D   R+ + D +    +R+  VGRLD ++ GL+LLT+DG L         +  + Y 
Sbjct: 68  CTTDARDRTNIVDAVNYPDARLFPVGRLDKDSTGLILLTSDGRLPNAALRSGRKRDKKYL 127

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGD----------MQVTLDTQKGSNAWVTVGLREG 196
           V     V  + + +L+ G+VI      D          +   +D        +T  LREG
Sbjct: 128 VVVDAVVRPEDVRMLRDGVVISTPVQRDRVDRVLTARTLPCEIDVVGARTLEIT--LREG 185

Query: 197 KNREIKKVFEFFNWKVNRLIR 217
           +NR+I+++ +   ++V  L R
Sbjct: 186 RNRQIRRMLDAVGYRVINLHR 206


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 86/191 (45%), Gaps = 25/191 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL   +KP G +   S  + R+++ D    P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLIALNKPFGTICQFSPHEARASLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQ 57

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDT------ 181
             +  P  + ++ Y  +  G  D   L  L++G+     +   C        DT      
Sbjct: 58  AKIAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFVTPPDTLWPRTP 117

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGST 233
                      W+ + + EGKNR+++++     +   RLIR+  G    F LG L  G T
Sbjct: 118 PIRYRAAIPTTWIELEIAEGKNRQVRRMTAAIGFPTLRLIRVGIGALDVFALG-LAPGET 176

Query: 234 REVSKKILREQ 244
           RE+  +   E+
Sbjct: 177 RELPPRAPWER 187


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +++KP G++   S  +   ++  F NLP  +      GRLD ++EGLLLLT+DG L  
Sbjct: 4   LIIFNKPYGVICQFSPHEKHKSLKDFINLPGFYP----AGRLDTDSEGLLLLTDDGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  +  + Y  +  G  D+ +L  L+KGI +         V L     +++     
Sbjct: 60  QITDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRLLEHGEADSLWERI 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R++ G  +L  L
Sbjct: 120 PPIRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDL 172


>gi|293363560|ref|ZP_06610316.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
 gi|292552909|gb|EFF41663.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
          Length = 230

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 55/234 (23%), Positives = 110/234 (47%), Gaps = 22/234 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ K I+     +R ++++++ +++V +N  L+   ++N    + + +D +     E   
Sbjct: 2   KLEKFISNVTDLTRSQIKKLLKEKKVFINDNLVTSDSIN-FKVEKLVIDQIAYNTDEYVY 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTN 126
           + L +KP   +T+H D        +  PS+F+ V        I+ GRLD++TEGLLL+++
Sbjct: 61  IML-NKPQNYITSHKD--------ELYPSLFNLVSDAKRKNLIAYGRLDVDTEGLLLISD 111

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           D   +  L  P     + Y V    ++    + +   G +I      D  +       S+
Sbjct: 112 DTESSHKLLSPKHHVEKKYYVEVDKKIPTSLVEIFLNGFIIDK---NDKVLPSKLLIISD 168

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
               + ++EGK  ++K++F+     V  L RI +   +L  TL  G  R ++KK
Sbjct: 169 NKCYLTIKEGKFHQVKRMFKTHYLNVTFLKRIEFNNLKLDETLKPGQWRYLTKK 222


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 72/137 (52%), Gaps = 9/137 (6%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +GRLD ++EGL+L+TNDG L++ +  P  +  + Y     G++       + + +V  G+
Sbjct: 1   MGRLDYDSEGLILMTNDGELSQHVMHPKYEVEKTYIATLEGRIS----GTVCRRLVTTGV 56

Query: 171 CYGDMQVTLDTQKGSNA-----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              D  + LD     ++      V V L  GKNR ++++F    + V RL+R   GP +L
Sbjct: 57  QLDDGWIKLDHCAIIDSSRDFTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKL 116

Query: 226 GTLLAGSTREVSKKILR 242
           G L  GS R +S+  +R
Sbjct: 117 GELKPGSYRVLSQAEVR 133


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/161 (33%), Positives = 81/161 (50%), Gaps = 13/161 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L + +KP G + T +D  GR TV+D LP  +     + +GRLD+ ++GLLL T +G +  
Sbjct: 11  LLVLNKPKGYLVTRTDDLGRKTVYDLLPDWAFHEGWMPIGRLDLESKGLLLFTTNGKIGD 70

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTV 191
           +L  P    ++VY V   G V  + +    KG+  I G+     +V      G+   + V
Sbjct: 71  ILTKPGNC-IKVYEVWVRGFVTDEHIIQASKGVESIYGLL--KAKVVKVGIGGAKTKLLV 127

Query: 192 GLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQL 225
            L EGKNR I+++F            KV  L RIS G F+L
Sbjct: 128 ELEEGKNRHIRRLFGALKDPKFGTPLKVLTLNRISIGNFKL 168


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 25/185 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           +RL  ++KP  ++   +D       R+T+ D  + P ++      GRLD ++EGL+LLT+
Sbjct: 2   SRLIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDCPGVYP----AGRLDRDSEGLMLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           +G L   +  P  +  + Y  +  G  D+D LNLL++G+ ++       +  L  +    
Sbjct: 58  NGRLQAWISDPKHKLEKTYWAQVEGIPDEDALNLLRQGVELKDGMTRPAKARLINEPAQL 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                          AW+ + + EGKNR+++++         RLIR + G + L  L  G
Sbjct: 118 WARTPPIRERKSVPTAWLELKITEGKNRQVRRMTAAVGHPTLRLIRYAIGAWTLDGLAQG 177

Query: 232 STREV 236
             +++
Sbjct: 178 KWQDL 182


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/219 (26%), Positives = 96/219 (43%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   +R E   +I    V VN  +    A  V   + + +D   L  A  +R
Sbjct: 2   RLDKFICKSTDLTRNEATLLINAGNVTVNNEVASNEATQVHENNDVLLDEKKL-IARASR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             L HKP+G + ++ D        +  PS+F+ +           GRLD +T GL+L+T+
Sbjct: 61  YILMHKPLGTICSNID--------EVYPSLFNYIDVEKADDLHIAGRLDADTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P+ Q  + YRV     + +D       G+ +QG         LD    + 
Sbjct: 113 DGRWSFNIITPNKQCEKTYRVGLRNPIAEDAAEKFALGVQLQGEKQLTFPAKLDVVTSNE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +T+   EGK  ++K++F     +V  L R   G  +L
Sbjct: 173 VLLTI--TEGKFHQVKRMFSAIGNRVVTLHREQIGNIKL 209


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 101/228 (44%), Gaps = 14/228 (6%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--STDHIEVDGVPLRKAERTRL 75
           K +   G+ SRR+ ER+     V+VNG  +  A   +   S   + + G  +        
Sbjct: 5   KYLQAQGVGSRRQCERLAECGGVEVNGETVSGAKTEIAPDSVRTLRIGGAAVCVVPLPYF 64

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLAR 132
           ++  +KP G  T+H  P     VF   P+    +   +VGRLD +T G+LL+TNDG    
Sbjct: 65  YIVLNKPAGYETSHK-PRDWPGVFTLFPANLRNLDMQAVGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---WV 189
            +  P     ++YR       D      L+ G+++      +  V  D  + ++     +
Sbjct: 124 RMTSPKHHVAKLYRATLKHAADAALCETLQNGVLLHD---DNETVAADAAELADPHTLLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           T+G  EGK  ++K++      +V +L R+ +G +    L  G  R VS
Sbjct: 181 TIG--EGKYHQVKRMVAAAGNRVEKLHRLRFGSWSAEDLAVGEWRFVS 226


>gi|309378696|emb|CBX22646.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 186

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 81/173 (46%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +++KP G++   S  +   ++  F NLP  +      GRLD ++EGLLLLT+DG L  
Sbjct: 4   LIVFNKPYGVICQFSPHEKHKSLKDFINLPGFYP----AGRLDTDSEGLLLLTDDGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  +  + Y  +  G  D+ +L  L+KGI +         V +     +N      
Sbjct: 60  QITDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRVLEHGETNPLWERI 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R++ G  +L  L
Sbjct: 120 PPIRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDL 172


>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 = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 113/229 (49%), Gaps = 9/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           RV K+I  A + +R+ ++R   +  + +NG +++ ++V V  + D +   G  +   +  
Sbjct: 4   RVDKMIGNANLDTRKNIKRNAKKGELIINGQIVKDSSVKVDPNLDEVIYMGELVDYFDNI 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
            + + +K  GL+   ++ DG  TV  +L   +  +     GRLD +T GLLLL+ DG   
Sbjct: 64  YIMM-NKREGLICQSNELDG--TVMSDLDEFYLNLDLAIAGRLDKDTTGLLLLSTDGKFI 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P++   + Y V    ++D   +   K G+ I+   Y      LD      A+V V
Sbjct: 121 HKVISPNSHIWKKYEVETSKKIDPSLVENFKDGVYIKEDDYYARSAKLDIIGEKKAYVYV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
              EGK   +K++F   + +V +L R++ G  +L  +L  G  RE+S++
Sbjct: 181 --TEGKFHLVKRLFSNNDNEVIKLKRLAIGDLELDQSLNPGQYRELSEE 227


>gi|217978386|ref|YP_002362533.1| pseudouridine synthase [Methylocella silvestris BL2]
 gi|217503762|gb|ACK51171.1| pseudouridine synthase [Methylocella silvestris BL2]
          Length = 255

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 104/225 (46%), Gaps = 14/225 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----IEVDGVPLRKA 70
           R+ +++A  G  +R +++ M    R+K++G  L   A+ V +T      + ++G  L   
Sbjct: 12  RLDRLLANLGYGTRTQMQAMAHAGRIKLDGAALRDPALRVAATPEFCARLSINGEALDPP 71

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
               + L +KP G+  T S  +    VFD LP  F      + +VGRLD +T GLLL+T+
Sbjct: 72  PGMVIAL-NKPRGV--TCSRKEAGPLVFDLLPPRFRLREPALSTVGRLDKDTSGLLLITD 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   L  P     + Y  +    +  D+  +   G +++       +   L     +
Sbjct: 129 DGALLHRLISPKHNIAKRYCAKLARPLRGDEAEIFASGEMMLDDEAKPLLPAVLRVLSPT 188

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            A V+V   EG+  +I+++F      V  L R+S G F L   LA
Sbjct: 189 EAEVSV--TEGRYHQIRRMFAATGNHVLELHRMSIGDFALPLTLA 231


>gi|170693552|ref|ZP_02884711.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170141707|gb|EDT09876.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 189

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL   +KP G +   S  + R+++ D   +P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLIALNKPFGTICQFSAHETRASLADWVKVPGVYP----AGRLDSDSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDT----- 181
           AR+ E P  + ++ Y  +  G VD   L  L +G+     +   C  +     DT     
Sbjct: 58  ARIAE-PRHKLVKRYWAQVEGAVDSAALKKLARGVDLGDYVTKPCRAEYVEPGDTLWTRT 116

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + + EGKNR+++++     +   RL+R+  G   + +L
Sbjct: 117 PPIRYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGMGALDIFSL 169


>gi|307545654|ref|YP_003898133.1| pseudouridine synthase [Halomonas elongata DSM 2581]
 gi|307217678|emb|CBV42948.1| pseudouridine synthase [Halomonas elongata DSM 2581]
          Length = 343

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 34/98 (34%), Positives = 60/98 (61%), Gaps = 6/98 (6%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +RL+L+HKP   ++  +D +GR+T+ +++  P I+      GRLD ++EGLLLL++DG L
Sbjct: 2   SRLYLFHKPYRTLSQFTDSEGRATLAEHIDVPGIYP----AGRLDHDSEGLLLLSDDGEL 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              +  P  +  + Y V+  GQ + D L  L+ G+ ++
Sbjct: 58  IHRISHPKHKQPKTYWVQVEGQPNDDALAALRDGVELK 95


>gi|187925144|ref|YP_001896786.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716338|gb|ACD17562.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 189

 Score = 65.1 bits (157), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 86/182 (47%), Gaps = 27/182 (14%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R+++ D   +P ++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 7   NKPFGTICQFSPHETRASLADWVKVPDVYP----AGRLDSDSEGLLLLTDDGALQARIAE 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDT---------- 181
            P  + ++ Y  +  G VD   L  L +G+     +   C  +     D           
Sbjct: 63  -PRHKLVKRYWAQVEGAVDAATLKKLARGVDLGDYVTRPCRAEYVEPTDALWTRTPPIRF 121

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVS 237
                  W+ + + EGKNR+++++     +   RL+R+  G    F LG L  G + E+S
Sbjct: 122 RAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLG-LQPGESVELS 180

Query: 238 KK 239
            K
Sbjct: 181 PK 182


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 54/222 (24%), Positives = 100/222 (45%), Gaps = 8/222 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NG  ++   A ++  S + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGH 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P+ +  ++Y V       +     LK G+++      +     D    S + +
Sbjct: 121 LNHKLTSPNHKIPKLYEVTLKHPAGETLCETLKNGVLLHD--ENETVYAADAVLESPSAL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 179 LLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 117/237 (49%), Gaps = 28/237 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV     DG PL  
Sbjct: 2   RLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADG-PLEV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLL 123
                 +L +KP G++T   DP  +STV D +      P ++     VGRLD +T GLLL
Sbjct: 61  D-----YLMNKPAGVITATEDP-TQSTVLDLIRPHDYRPGLY----PVGRLDKDTTGLLL 110

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDT 181
           LT DG L   L  P+    + Y  +    +  +  + L++G+ ++       D+QV   T
Sbjct: 111 LTTDGNLGHTLLAPNHHVPKTYAAKLAKALTTEMKHQLEQGVALKDFTTAPADVQVVPAT 170

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               N  + + + EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++
Sbjct: 171 ---DNKEIHITITEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALT 224


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 115/255 (45%), Gaps = 46/255 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+  +P  ++E+  
Sbjct: 380 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEI--LPAARSEQGE 437

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--------------------VISVG 112
               L HKP+G V+  ++ DG    ++   ++F+                     +   G
Sbjct: 438 RVTVLLHKPVGYVSGQAE-DG----YEPAAALFTAENQWEEDPTRKHFAAWQHKGLAPAG 492

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVD--------QDKLN 159
           RLDI++ GLL+LT DG +AR L    +   + Y VR       G V+        +D L 
Sbjct: 493 RLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWNAPQGPVEHDISKVFPEDLLE 552

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
           +L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI 
Sbjct: 553 MLRHGLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIR 608

Query: 220 YGPFQLGTLLAGSTR 234
            G   LG L  G  R
Sbjct: 609 MGSVVLGDLPVGKWR 623


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 105/221 (47%), Gaps = 12/221 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    + +N  I  +  A   +     EV G      E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKSGAISINHEICADTKAKFDLKNFTFEVHGEEFEYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVI-SVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +H       +VFD   P++ +R I  VGRLD +T GLLLLT+DG   +
Sbjct: 63  IAL-NKPQGYECSHQ-AQYHFSVFDLFDPALLNRGIQCVGRLDQDTTGLLLLTDDGQFLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVT 190
            L  P     +VY +     +  +++ LL++G+ ++  GI         + ++ S+  ++
Sbjct: 121 ALTHPRKHVAKVYDLITVDPITPEQIRLLEQGVELRNDGIFKAS-----NIKQTSSHQLS 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           + + +G   ++K++      KV +L R   G  +L  L  G
Sbjct: 176 LAIHQGVYHQVKRMLAAVGNKVEKLHRSKIGELELPMLAEG 216


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/181 (26%), Positives = 89/181 (49%), Gaps = 23/181 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----ISVGRLDINTEGLLLLTNDG 128
           R+ L +KP G+++  +D   + T   + P++ + +        GRLD ++EGLL+LT+ G
Sbjct: 4   RVILLNKPYGVLSQFTD---KGTEGSSRPTLSTYIDEKGFYPAGRLDRDSEGLLVLTDHG 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKG--- 184
            L   +  P  +  + Y V+  G  D   L  L+KG+ ++       +V  +D  +    
Sbjct: 61  PLQARIAHPKYKRPKTYLVQVEGTPDAAALEALRKGVDLKDGLTKPAEVDQIDAPETLWP 120

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       +AW+ + +REG+NR+++++    +    RLIR S G ++L  L  G+ 
Sbjct: 121 RDPPVRFRKTVPDAWLRITIREGRNRQVRRMTAHVDLPTLRLIRASVGDWELAGLQPGAW 180

Query: 234 R 234
           R
Sbjct: 181 R 181


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 107/244 (43%), Gaps = 25/244 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILL---ERAAVNVMSTDHIEVDG-VPLRK 69
           RV +++A  G   RRE + ++ + RV + +G  L   ++     +  D  ++D   PL  
Sbjct: 80  RVERLLANLGYGKRRECQVLVKKGRVTRRDGGKLKVGDKVCWGDVVLDEEDLDPPSPL-- 137

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSR----VISVGRLDINTEGLLL 123
                L   HKP G V T  D +  +   V+D LP  F+R    +  VGRLD +T GLLL
Sbjct: 138 -----LLALHKPGGYVVTSPDDENITDPVVYDLLPYRFARRRPFLAPVGRLDKDTSGLLL 192

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFH-----GQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           LT+DG L   +  P     +VY           Q            +V++G     +   
Sbjct: 193 LTDDGALLHRINSPRRGIWKVYEATLAEPMSTNQAAAAARRFASGSLVLEGDHTPLLPAK 252

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           LD      A V +   EGK  +++++F      V  L R+S G   LG+L  G  R +  
Sbjct: 253 LDLIGARTARVAIC--EGKYHQVRRMFAAVGSHVVALHRVSVGGLTLGSLPEGEWRYLQP 310

Query: 239 KILR 242
           + L+
Sbjct: 311 QELQ 314


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 87/174 (50%), Gaps = 26/174 (14%)

Query: 80  KPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           KP G ++    P+ R    +   L +   + +++GRLD ++EGLLLLT DG ++   ++ 
Sbjct: 26  KPYGFLSQFV-PESRKKKHLLGELFNFPDKTMAIGRLDHDSEGLLLLTTDGMMS--YKVR 82

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI---------CYG---DMQVTL------ 179
               ++ Y V+  G++  D ++ L+ G+ I GI         C     D +  L      
Sbjct: 83  DKSIVKEYYVQVDGEITTDAISQLQNGVEI-GINSTKYLTMPCKAFKLDCEPQLPARGRK 141

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             D + G  +W+++ L EGKNR+I+K+     +   RL+R+  G   +  L+AG
Sbjct: 142 IRDPKHGPTSWISITLCEGKNRQIRKMTAAVGFATLRLVRVRIGNIGIDNLIAG 195


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 117/231 (50%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     SR E  + + Q+RV VNG L++  +  V + D + +DG   R+ E   
Sbjct: 2   RLDKFLANYSSLSRTEATKALKQKRVLVNGDLVKTGSHKVANDDQVWLDG---RRIEMNT 58

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP   +  ++DP   + VFD +    + V+ +VGRLD++T GLLL+T+DG  +
Sbjct: 59  AVYFMMNKPANYLCANADPQ-HALVFDLIDEASTYVLHTVGRLDLDTTGLLLITDDGQWS 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + YRV     +  D     ++G++++      +   L+    +   +T+
Sbjct: 118 HRLTSPKHHIPKTYRVWLDEPLVADAEIQCEQGLLLRSESKPTLPAELNRITDTEVLITI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
              EG+  ++K++F     +V RL R   GP +L   LA G  R ++++ L
Sbjct: 178 S--EGRYHQVKRMFAAMGNRVVRLHRERIGPLELDPNLAPGEYRSLTQQEL 226


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/214 (26%), Positives = 98/214 (45%), Gaps = 9/214 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++ +  V V+ ++ +  A  +  T  +E     +      R
Sbjct: 2   RLDKFLCDALGTTRKEATQLLKRGEVTVDDVVQKSGAFKLKETSCVEWQDREI-TLHGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+V +H D   + T F  L  +    +   GRLD++T GLLL+T+DG  +  
Sbjct: 61  YIMMHKPDGVVCSHEDGFNQ-TAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  + YRV     +  D       GI ++    G+ ++TL  Q    S   V +
Sbjct: 120 VTSPKHKCEKTYRVWLAEPIQADYAEQFTNGIELR----GERELTLPAQLEIVSETEVLL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + EGK  ++K++F     KV  L R   G   L
Sbjct: 176 TIHEGKYHQVKRMFAALGNKVIGLHRERIGQITL 209


>gi|221133423|ref|ZP_03559728.1| pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 226

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/219 (23%), Positives = 102/219 (46%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K ++++ + +  +V  +IA+  + VN  + +  +  V   + +      L +    R
Sbjct: 2   RLDKYVSKSTVLTAAQVLEVIARGEISVNDSVTDDPSYQVHKNNTVHWLDTRL-ECRPFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTN 126
             + +KP  ++ ++ D        ++ PS+F+ V           GRLD +T GL+L+T+
Sbjct: 61  YIMLNKPPNMICSNID--------EHYPSVFNLVDIPHQHELHIAGRLDADTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  L  P     +VYRV     +  D +  L+KG+++QG     +   +D    + 
Sbjct: 113 DGSWSYRLTHPDNHCPKVYRVCLAKPISDDMIMRLEKGVLLQGESAPTLPAAIDVVGANE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +T+   +GK  ++K++F     +V  L R + G   L
Sbjct: 173 VLLTI--TQGKFHQVKRMFAAVGNRVKALHREAIGEINL 209


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/219 (30%), Positives = 99/219 (45%), Gaps = 15/219 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-T 73
           R+ K + ++    R      I    V VNG +    A+ V   + + ++G PL  A R +
Sbjct: 2   RLDKFLCKSTDLDRDAASVAIINGSVTVNGTIATDCAMQVHENNAVCLNGKPL--APRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
           R ++ HKP    T  S+ DG      +L  I   F   I VGRLD +T GL+LLT+DG  
Sbjct: 60  RYFMLHKPAD--TLCSNVDGAYPSLFHLLDIEHAFDLHI-VGRLDADTTGLVLLTDDGRW 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +  +  P  Q  +VYRV+    +D +           G+ +QG     +  TL  Q+   
Sbjct: 117 SFNIISPQYQCEKVYRVQLRDPLDSEATAAIATTFAAGLQLQGETALTLPATL--QQVDE 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             V + L EGK  ++K++F     KV  L R   G   L
Sbjct: 175 KTVLLTLTEGKFHQVKRMFAAVGNKVIALHRAQIGAVVL 213


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 48/182 (26%), Positives = 89/182 (48%), Gaps = 19/182 (10%)

Query: 73  TRLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            RL L++KP G+++  +D   P  RST+ D +      V   GRLD ++EGLLLL +DG 
Sbjct: 2   ARLLLFNKPFGVLSQFTDRGSPTVRSTLSDFI--AVKGVYPAGRLDRDSEGLLLLCDDGR 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT------- 181
           L   +  P  +  + Y V+  G   + +L  L++G+ ++ G+        +D        
Sbjct: 60  LQARIADPRFKMPKTYLVQVEGDPQEPELERLRQGVQLKDGMTLPADVARIDEPDLWLRD 119

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   + W+ + +REG+NR+++++         RL+R S G + +  +  G   +
Sbjct: 120 PPIRQRKAIPDNWLKLTIREGRNRQVRRMTAAVGLPTLRLVRWSIGDWSVAGIAPGRFEQ 179

Query: 236 VS 237
           +S
Sbjct: 180 LS 181


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 87/180 (48%), Gaps = 18/180 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           +RL L +KP G+++  +   G+  V D L  +     V   GRLD ++EGLLLLT+DG L
Sbjct: 2   SRLILLNKPFGVLSQFTG--GKEGVEDTLAHLVDVPDVYPAGRLDKDSEGLLLLTDDGKL 59

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-------- 181
              +  P  +  + Y V+  G+   D L  L +G+ ++ G+        +D         
Sbjct: 60  QSRIAEPRYKIAKAYLVQVEGEPGDDALEKLSRGVELKDGMTRPARAKRIDPPPVWERDP 119

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   ++W+ + + EG+NR+++++         RLIR   G + +  +  G+ R++
Sbjct: 120 PVRYRKSVPDSWIALEITEGRNRQVRRMTAAVGLPTLRLIRWRIGEWSVDGIAPGTYRKI 179


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 109/238 (45%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  V    G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAVTDAQGEVL--YADDQVEHDAIRIDGEPLDPPPGF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SR---VISVGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F SR   +  VGRLD  T G+LL+T+DG 
Sbjct: 60  SLLL-HKPGGYTCSTKD-TGR-LIYELLPPRFRSRAPVLAPVGRLDRETSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY +    ++  D+  L   G ++++G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYDITLAEELRGDEAALFASGSLLLEGETKPLLPAELEVLGPREAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLEVLFG 232


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 108/243 (44%), Gaps = 30/243 (12%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D             L H
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQVTILLH 60

Query: 80  KPIGLVTTHSDPDGR--STVF---------DNLPSIFS-----RVISVGRLDINTEGLLL 123
           KP+G V+  ++ DG   +TV          D  P  FS      +   GRLDI++ GLL+
Sbjct: 61  KPVGYVSGQAE-DGYEPATVLITRENHWSGDRSPLRFSPQHLRTLAPAGRLDIDSTGLLV 119

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRF-HGQVDQD--------KLNLLKKGIVIQGICYGD 174
           LT +G +A+ L    +   + Y VR  +G +  D         L  L+ G+ + G+    
Sbjct: 120 LTQNGRIAKQLIGEQSDVDKEYLVRVRYGDMLTDIDRHFPAESLAKLRHGLELDGVALKP 179

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             V+   Q G    +   LREG+ R+I+++ E     V  L R+  G   LG L  G  R
Sbjct: 180 AMVSW--QNGEQ--LRFVLREGRKRQIRRMCELVGLDVIGLKRVRMGRVMLGALPQGQWR 235

Query: 235 EVS 237
            +S
Sbjct: 236 YLS 238


>gi|330864071|emb|CBX74147.1| ribosomal large subunit pseudouridine synthase F [Yersinia
           enterocolitica W22703]
          Length = 162

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 43/121 (35%), Positives = 70/121 (57%), Gaps = 9/121 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPLRKAER 72
           R++K I+ +GI SRR+ +R + Q  V +NG   +RAAV   V   D ++V+G  +   + 
Sbjct: 8   RLNKYISESGICSRRDADRYVEQGNVFING---KRAAVGDQVYVGDVVKVNGQLIEPRDE 64

Query: 73  TRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L   +KP+G+++T  D  G S    +  +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  SDLILIALNKPVGIISTTED--GESDNIVDFVNHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 A 131
            
Sbjct: 123 V 123


>gi|297537798|ref|YP_003673567.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257145|gb|ADI28990.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 183

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 49/183 (26%), Positives = 84/183 (45%), Gaps = 27/183 (14%)

Query: 77  LYHKPIGLVTTHS--DP----DGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L++KP  +V   S  DP     G  T+  F  +P +++     GRLD ++EGLL+LT+DG
Sbjct: 4   LFNKPFNVVCQFSAHDPGNGKTGHPTLKDFIQIPDVYA----AGRLDTDSEGLLILTDDG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--- 185
            L   L  P  +  + Y V+  G    + L  L +GI +        QV L  +  S   
Sbjct: 60  MLQHRLSDPKRKEFKTYWVQVEGTPSTEDLEPLIRGIDLSDFVAKPAQVRLIPEPESLWL 119

Query: 186 ------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                        +W+ + + EGKNR+++++     +   RLIR + G + +  +  G  
Sbjct: 120 RNPPIRERKAIPTSWLEIKISEGKNRQVRRMTAKIGFPTLRLIRYAIGQYTIDGIQNGQH 179

Query: 234 REV 236
           + +
Sbjct: 180 KVI 182


>gi|152995917|ref|YP_001340752.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150836841|gb|ABR70817.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 238

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 107/236 (45%), Gaps = 24/236 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   +R+E  + I    V VNG ++   A  V   + + ++G  L K    R
Sbjct: 6   RLDKFVCKSTELTRKEAVQCIHSGEVCVNGEVVTSEATQVHENNTVLLNGDRL-KTRDFR 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L +KP G V ++ D        +  PS+F        S +   GRLD +T GL+L+T+
Sbjct: 65  YILMNKPAGTVCSNID--------EVYPSVFNYLDVDKASELHIAGRLDADTTGLVLITD 116

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQ 182
           DG  +  + LPS    +VYRV+    +  ++    +   K+G+ +QG         LD  
Sbjct: 117 DGRWSFNITLPSNDCCKVYRVQLSQAIPAERSGELVTQFKQGLQLQGEQGLTRPAKLDII 176

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                 +T+   EGK  ++K++F     +V  L R   G   L  L  G  R +SK
Sbjct: 177 TPKEVLLTI--TEGKFHQVKRMFSAVGNRVVGLHREQIGEVYLD-LDVGQWRYLSK 229


>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 = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 102/231 (44%), Gaps = 21/231 (9%)

Query: 10  NFTPQRVSKVIARAGIASRREVERM-------IAQQRVKVNGILLERAAVNVMSTDHIEV 62
            F    +  ++   G  SRRE   +       I +QR      + E A +         V
Sbjct: 22  EFQRMNLENILFSQGFGSRRECRALVIRGAVTIGEQRCDDPDAVFEPAGLV------FHV 75

Query: 63  DGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLP-SIFSR-VISVGRLDINTE 119
           DGV  R A R + +L  HKP G   +H+ P    +V+  LP ++ +R V  VGRLD +T 
Sbjct: 76  DGV--RWAYRHQAYLVLHKPPGYECSHA-PQHHPSVYSLLPPALITRGVQCVGRLDADTT 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLL++DG     L  P  +  + Y       V   +L+ L++G+ + G     + V  
Sbjct: 133 GLLLLSDDGAFIHRLSSPKHKIPKTYVATTRHPVRDAQLDALRQGVQLHG--EPAVSVAR 190

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             +      + + L EGK  ++K++      +V +L R + G   L   LA
Sbjct: 191 SARLRDEHTIELVLTEGKYHQVKRMIAAAGNRVEQLHREAIGALVLPAALA 241


>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 = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 72/229 (31%), Positives = 107/229 (46%), Gaps = 25/229 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV     DG PL  
Sbjct: 2   RLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADG-PLEV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLL 123
                 +L +KP G++T   DP  +STV D +      P ++     VGRLD +T GLLL
Sbjct: 61  D-----YLMNKPAGVITATEDP-TQSTVLDLIRPHDYRPGLY----PVGRLDKDTTGLLL 110

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQ 182
           LT DG L   L  P+    + Y       +  D    L+ GI ++       Q V L   
Sbjct: 111 LTTDGNLGHALLSPNRHIAKTYAATLAKTLTADMKQRLETGIDLKDFTTAPAQVVVLPDT 170

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            G    +T+   EGK  ++K++    + +V  L RI+ GP  L   LA 
Sbjct: 171 DGKRIQITI--TEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAA 217


>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 = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 10  TIMKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTV 69

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 70  VPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+ +    + +C  D  +   T 
Sbjct: 129 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENPTT 188

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 189 ------LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPG 231


>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 = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 87/187 (46%), Gaps = 29/187 (15%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTNDGGL 130
           L L++KP G+++     D  +  F  L   F+    RV   GRLD  +EGLLLLT DG +
Sbjct: 4   LILFNKPYGVLSQFRSDDNNN--FATLSDYFTDKSLRV--AGRLDATSEGLLLLTADGQV 59

Query: 131 ARVLELP-----STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-------GDMQV 177
            + L  P       Q  + Y ++  G     +L  L+ G+ ++ GI          + Q+
Sbjct: 60  NKALTHPPKANAGKQQGKTYWIQVEGDASDAQLQQLQTGVPLKDGITLPAEVVRLSEAQI 119

Query: 178 TLDTQKGSN--------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                + S+         W+ + + EGKNR+++++         RLIR++   F LG L 
Sbjct: 120 AEHIWQASDKIAKRKVTTWLAITIFEGKNRQVRRMAAHVGLPCLRLIRMASSGFSLGNLE 179

Query: 230 AGSTREV 236
            G++ ++
Sbjct: 180 VGASTQI 186


>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 = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 19/180 (10%)

Query: 74  RLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL L++KP  +++  +D   P  R+T+ D +     +V   GRLD ++EGLLLLT+DG L
Sbjct: 3   RLILFNKPFDVLSQFTDTKSPSPRATLSDYI--DVPKVYPAGRLDRDSEGLLLLTDDGRL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              +  P ++  + Y  +  G      L+ L+KG+ ++       +V L           
Sbjct: 61  QARISSPKSRTPKTYLAQVEGAPTDADLDPLRKGVTLKDGLTRPAEVHLIDPPDLWERDP 120

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                    + W+ + + EG+NR+++++     +   RL+R   G + +  +  G+ R+ 
Sbjct: 121 PVRYRKSVPDRWIELTITEGRNRQVRRMTAAVGFPTLRLVRWRVGDWSVEGIAPGTWRDA 180


>gi|56807363|ref|ZP_00365352.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 228

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 58/196 (29%), Positives = 95/196 (48%), Gaps = 8/196 (4%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLD 115
           D +   G PL   E    +L +KP G V+   D   ++TV + L     +  V  VGRLD
Sbjct: 31  DLVTYQGTPLV-YESFVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLD 88

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY-G 173
            +T GLLLLTN+G LA  L  P     + Y  +  G + +   +   +GI ++   C   
Sbjct: 89  KDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPA 148

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GS 232
            ++V     +   + V + ++EGK  ++K++      +V  L R+S GP +L   LA G 
Sbjct: 149 HLEVLASDLQQQTSLVKITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGE 208

Query: 233 TREVSKKILREQLGPH 248
            R ++ + L + L P+
Sbjct: 209 FRRLTPEEL-QSLAPY 223


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 81/171 (47%), Gaps = 23/171 (13%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP G++   S  +   ++  F  LP ++      GRLD ++EGLLLLT +G L   +
Sbjct: 6   VFNKPYGVICQFSPHEKHRSLKEFIGLPDVYP----AGRLDTDSEGLLLLTANGRLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------- 185
             P  + ++ Y  +  G  D+ KL+LL+ G+ +        Q+ L  +  +         
Sbjct: 62  ADPRHKTVKTYWAQLEGSPDEAKLDLLRHGVDLGDFVTRPAQIRLPEKSETDRLWSRVPP 121

Query: 186 --------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                   + W+ + + EGKNR+++++     +   RL+R+  G   L  L
Sbjct: 122 IRVRKSVPDFWLEIRISEGKNRQVRRMTAKAGYPCLRLVRVGIGRLDLWQL 172


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 109/238 (45%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  +    G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAITDAQGEVLY--ADDQVEHDAIRIDGEPLDPPAGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F   + V++ VGRLD  T GLLL+T+DG 
Sbjct: 60  SLLL-HKPSGYTCSTKD-TGR-LIYELLPPRFRLRAPVLAPVGRLDRETSGLLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY +     +  D+  L   G ++++G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYDITLAEDLRGDEAALFASGSLLLEGETKPLLPAELEVLGPRQAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGSHVVALHRSRIGGLSLDGLPSGQWRALEASDLEVLFG 232


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 85/180 (47%), Gaps = 26/180 (14%)

Query: 80  KPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           KP G ++    +   R  +   L       +++GRLD ++EGLLLLT DG ++   ++ S
Sbjct: 23  KPYGFLSQFVPETRKRKKLLAELADFPKGTMAIGRLDHDSEGLLLLTTDGMVSH--QVRS 80

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------------- 179
            +  + Y V+  G +  D +  L+ G+ I GI  GD  +TL                   
Sbjct: 81  KKVEKEYYVQLDGDITADAITQLQNGVEI-GI-KGDKYLTLPCRVFKLASEPNLPANGRK 138

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             D + G  +W+++ + EGKNR+I+K+     +   RL+R+  G   +  + AG    +S
Sbjct: 139 VRDLRHGPMSWISITISEGKNRQIRKMTAAAGFPTLRLVRVRIGNIDINEMQAGDVLPLS 198


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 50/165 (30%), Positives = 79/165 (47%), Gaps = 19/165 (11%)

Query: 74  RLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R  L++KP G++   +D   + R T+ D +P     V SVGRLD ++EGLL LTN+G L 
Sbjct: 7   RYLLFNKPYGVLCQFTDNTENPRPTLKDYIP--VPDVYSVGRLDRDSEGLLFLTNNGLLK 64

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L        R Y V+     D+  LN L++G+ I+       +V L            
Sbjct: 65  HRLSHRQFAHPRTYLVQVERIPDETTLNQLRQGVAIKDYKTRPAKVKLLKSPPAIPPRDP 124

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                +    AW+ + L EG+NR+++++     +   RLIR + G
Sbjct: 125 PIRYRKTVPTAWLAMTLTEGRNRQVRRMTAAVGYPTLRLIRTAIG 169


>gi|120436300|ref|YP_861986.1| pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117578450|emb|CAL66919.1| pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 194

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 47/187 (25%), Positives = 87/187 (46%), Gaps = 24/187 (12%)

Query: 74  RLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R +  +KP G ++   T+  P G+  +  +L       +S+GRLD ++EGLLLLT +G L
Sbjct: 7   RHFKIYKPYGYLSQFITNQKPGGKHKLLGDLYDFPEGTMSIGRLDKDSEGLLLLTTNGKL 66

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTL--------- 179
           +  +     +  + Y  +  G +  + +  L+ G+ I   G  Y  ++            
Sbjct: 67  STKINRGGIE--KEYYAQVDGDITDEAMIKLQNGVEISIFGKAYKSLKCKAEKLKNRPSF 124

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   D + G  +W+++ L EGK R++KK+     +   RL+R+  G   +  + AG
Sbjct: 125 PERAKKIRDERHGPTSWISISLTEGKFRQVKKMTSAVGFPTLRLVRVRIGNETIKNMDAG 184

Query: 232 STREVSK 238
              E++K
Sbjct: 185 EVIELNK 191


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 101/223 (45%), Gaps = 17/223 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA------VNVMSTDHIEVDGVPLR 68
           R+ K +  A  A+R++  ++I    + V+G + +  A      V VM  D   V G P  
Sbjct: 2   RLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPEGVEVMWEDR--VIGAP-- 57

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTN 126
                R  + +KP   V +H D   + T F  L  P I   +   GRLD++T GL+L+T+
Sbjct: 58  ---GPRYIMLYKPADFVCSHEDGYNQ-TAFALLDEPKI-ENLHFAGRLDVDTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + YRV     +  D    L++GI+++      +   L+    + 
Sbjct: 113 DGKWSHRITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
             V + + EGK  ++K++F     KV  L R   G  +L   L
Sbjct: 173 NEVLLTIVEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEAL 215


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 95/211 (45%), Gaps = 2/211 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +    V V+  +++  ++ V   + +  DG  L +    R
Sbjct: 2   RLDKFLSQQLGISRSLVARELRAGNVTVDDEVVKSGSMQVGLDNEVAYDGNVLVQVTGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DP   + ++     I   + + GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPEGYVCSTDDPTHPTILYFIDEPIAQNLHAAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + YRV+    +  D     ++G+++ G         L+        +T+   
Sbjct: 122 TSPKHHCEKTYRVQLSEDIADDVTIQFEQGVMLNGEKSPTKPAQLEIISPREVLLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EG+  ++K++F      V  L R   G   L
Sbjct: 180 EGRYHQVKRMFAAVGNHVCGLHRERVGEIHL 210


>gi|325122669|gb|ADY82192.1| 16S rRNA synthase [Acinetobacter calcoaceticus PHEA-2]
          Length = 234

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 104/223 (46%), Gaps = 15/223 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERT 73
           + K++   G  SR+  +++I    V ++G + +       S++++E    G   +  E+ 
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGYVSIDGEVADDLKKQ-FSSENLEFSLFGETYQYREKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L  KP G   +H  P    +VF  LP I  +  V ++GRLD +T GLLLLT+DG   
Sbjct: 62  YLAL-KKPKGFECSHQ-PHHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAW 188
           + L  P     +VY V     V  +++ +L +G+ +   +G+        L+T +     
Sbjct: 120 QALTHPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGLFAATDVAILETHQ----- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +T+ + +G   ++K++      KV  L R   G   L  L  G
Sbjct: 175 LTMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDG 217


>gi|313200941|ref|YP_004039599.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440257|gb|ADQ84363.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 237

 Score = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 100/220 (45%), Gaps = 9/220 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAER 72
            + +++   G  SR+    +I    V VNG   +    +   TD +   V+  P    E+
Sbjct: 2   HLERILHAQGFGSRKNCRILIRHHAVTVNGEPCDNPFAD-FDTDKLAFTVNDEPWEYREK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSR-VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP     +H  P    +VF  LP  +  R V  +GRLD +T GL+LL++DG  
Sbjct: 61  AYLML-NKPANYECSHK-PQHHPSVFALLPHPLLERGVQCIGRLDEDTTGLILLSDDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P  +  ++Y V     VD D++  L++G  +Q +        L  ++ S+  + 
Sbjct: 119 IHRMSSPKWKVPKIYEVGAKHAVDADQIRQLQEG--VQLVDEPAPIAALACEQISDQVLH 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + L EGK  ++K++      +V  L RI  G   L   LA
Sbjct: 177 LTLAEGKYHQVKRMLAAVGNRVESLKRIRIGELVLPDDLA 216


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/155 (29%), Positives = 76/155 (49%), Gaps = 7/155 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV  +++R G  +R       ++  + V+G  +        ++  + VDG  L   +  
Sbjct: 40  ERVDALLSRLGYCTRSTARAFASRHEIVVDGTRVRGVDAKARAST-LRVDGEALDHPDGV 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L   HKP G V +H + +G + V++ LP  + R    + ++GRLD +T GLLLLT+DG 
Sbjct: 99  -LVAMHKPRGTVCSHDEREG-ANVYELLPERWRRRKPSIETIGRLDKDTSGLLLLTDDGA 156

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           L   L  P     + YRVR  G + +  + +   G
Sbjct: 157 LNHALTSPKKDVGKWYRVRTDGPIPRACVEVFASG 191


>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 = 64.3 bits (155), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 42/166 (25%), Positives = 82/166 (49%), Gaps = 23/166 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +++KP G++   S  +   ++ D++  P  +      GRLD ++EGLLLLT+DG L  
Sbjct: 4   LIIFNKPCGVICQFSPHEKHPSLKDHIDAPGFYP----AGRLDTDSEGLLLLTDDGQLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  +  + Y  +  G  D DKL LL++ + +        ++ L +++ ++      
Sbjct: 60  RITQPRFKVEKTYWAQLEGIPDTDKLQLLQRPMDLGDFTTRPAKIRLLSEEETDGLWPRN 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                       W+ + + EGKNR+++++     +   RLIR++ G
Sbjct: 120 PPVRVRKTVPDFWLEIKISEGKNRQVRRMTAKAGYPCLRLIRVAIG 165


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 53/226 (23%), Positives = 101/226 (44%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR EV R +   R+ V+  +++  A  +     I  DG  L + +  R
Sbjct: 2   RLDKFLSQQLGISRNEVGRELRAGRITVDDEIIKTGAYKITPEQQIMFDGSLLEQQQGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DP   + ++        ++ + GRLD++T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPSGYVCSTDDPVNPTVLYFIDEPAAHKLHTAGRLDMDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  +  +    G+ + G         L+  +     +T+   
Sbjct: 122 TSPKHHCKKTYLVTLECPVAAETADKFLAGVQLHGEKTLTKPAQLEMLEPQVTRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   L  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVIELHRERIGEIILDPALEPGEYRPLTEQ 225


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 116/237 (48%), Gaps = 28/237 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV     DG PL  
Sbjct: 2   RLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADG-PLEV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLL 123
                 +L +KP G++T   DP  +STV D +      P ++     VGRLD +T GLLL
Sbjct: 61  D-----YLMNKPAGVITATEDP-TQSTVLDLIRPHDYRPGLY----PVGRLDKDTTGLLL 110

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDT 181
           LT DG L   L  P+    + Y  +    +  +  + L+ G+ ++       D+QV   T
Sbjct: 111 LTTDGNLGHTLLAPNHHVPKTYAAKLAKALTTEMKHQLEHGVALKDFTTAPADVQVVPAT 170

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               N  + + + EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++
Sbjct: 171 ---DNKEIYITITEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALT 224


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 116/237 (48%), Gaps = 28/237 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV     DG PL  
Sbjct: 2   RLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADG-PLEV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLL 123
                 +L +KP G++T   DP  +STV D +      P ++     VGRLD +T GLLL
Sbjct: 61  D-----YLMNKPAGVITATEDP-TQSTVLDLIRPHDYRPGLY----PVGRLDKDTTGLLL 110

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDT 181
           LT DG L   L  P+    + Y  +    +  +  + L+ G+ ++       D+QV   T
Sbjct: 111 LTTDGNLGHTLLAPNHHVPKTYAAKLAKALTTEMKHQLEHGVALKDFTTAPADVQVVPAT 170

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               N  + + + EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++
Sbjct: 171 ---DNKEIHITITEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALT 224


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 101/226 (44%), Gaps = 16/226 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+ +    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 178 ---LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPG 220


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/213 (30%), Positives = 90/213 (42%), Gaps = 10/213 (4%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWL-YHKP 81
           G  SR E   ++   RV V G +                VDG P   A R  ++L  +KP
Sbjct: 11  GFGSRAECRGLVCTGRVSVEGRVCNDPLAQFEPEGLSFAVDGQPW--AYRRFVYLALNKP 68

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G   +   P    +VF  LP    R  V +VGRLD +T GLLLLT+DG        P  
Sbjct: 69  AGHECSRR-PIHYPSVFSLLPIPLVRRGVQAVGRLDADTTGLLLLTDDGAFIHACTSPRR 127

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
              +VY V     VD  ++  L  G+V+       M    D Q   +  +TV L  GK  
Sbjct: 128 MVPKVYEVSTRHAVDDGQVAALLSGVVLHDESQAIMAAACDRQGERSLRLTVTL--GKYH 185

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG 231
            +K++      +V  L R++ G   L  TL AG
Sbjct: 186 LVKRMVAAAGNRVEALHRVAIGGLALPATLAAG 218


>gi|56475798|ref|YP_157387.1| pseudouridine synthase [Aromatoleum aromaticum EbN1]
 gi|56311841|emb|CAI06486.1| Pseudouridine synthase [Aromatoleum aromaticum EbN1]
          Length = 230

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 81/180 (45%), Gaps = 23/180 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRST---VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +RL L +KP G++   S  DG       F  +P ++      GRLD ++EGLLLLT+DG 
Sbjct: 29  SRLILLNKPYGVICQFSG-DGVHVTLKAFVPVPGVYP----AGRLDTDSEGLLLLTDDGA 83

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLD----- 180
           L   +  P  +  + Y  +  G+  +  L  L+ G+     +   C        D     
Sbjct: 84  LQHRIADPRHKLPKTYLAQVEGEPGETALTALRGGLDLGDFVTRPCSARRVAEPDWLWPR 143

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + L EGKNR+++++     +   RLIR++ G + L  L  G  R
Sbjct: 144 DPPVRFRKNVPTSWLEIVLHEGKNRQVRRMTAKAGFPTLRLIRVAIGDWSLAGLAPGQWR 203


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 102/227 (44%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R+E  ++I    V VN  + +  A  V     +E  G  ++K     
Sbjct: 2   RLDKYLCDALGATRKEATKIIKSGDVTVNEQVQKSGAFKVDDHSIVEWQGREVQKPGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + L+ KP G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLF-KPDGFVCSHED-GFNQTAFMLLDEVRIEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +     +   KGI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADPIQPHYADEFTKGIQLRNEKGLTLPAKLELVDAQENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++
Sbjct: 180 NEGKYHQVKRMFAALGNKVEHLHRERIGQIELCESLEPGDYRYLTQE 226


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 105/232 (45%), Gaps = 14/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           R+ K +  A  A+R++  ++I    + V+G + +  A  V     +     V G P    
Sbjct: 2   RLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEVMWEDRVIGAP---- 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
              R  + +KP   V +H D   + T F  L  P I   +   GRLD++T GL+L+T+DG
Sbjct: 58  -GPRYIMLYKPADFVCSHEDGYNQ-TAFALLDEPKI-ENLHFAGRLDVDTTGLVLITDDG 114

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +  +  P  +  + YRV     +  D    L++GI+++      +   L+    +   
Sbjct: 115 KWSHRITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENE 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           V + + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++
Sbjct: 175 VLLTIVEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRHLTQE 226


>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 = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 103/215 (47%), Gaps = 6/215 (2%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT 86
           SRR+ + ++A  RV V+G       +++     + VD   ++ A  +   + +KP G ++
Sbjct: 14  SRRQAKALLAAGRVHVDGERCHDPDLDIPRFREVCVDQRIIQSAAPSYYLMLNKPSGYLS 73

Query: 87  THSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
              D D   TV + + P +   V   GRLD  + GLL+LT+DG  +R L  P+ +  +VY
Sbjct: 74  ATRD-DQHPTVMELIDPLLRPHVHIAGRLDRASTGLLILTSDGVWSRRLTEPAVKIPKVY 132

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKV 204
           RV     +  +  +  ++GI  +   Y  ++ +    +      V + + EG+  ++K++
Sbjct: 133 RVTTAYAISPETEDRFREGIWFE---YEQLRTSPASLEPLGEREVRLTIYEGRYHQVKRM 189

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           F     +V  L R S G   +  L  GS R +S +
Sbjct: 190 FHAVGNRVTSLHRESMGGLTVDGLEPGSYRHLSAQ 224


>gi|209517462|ref|ZP_03266303.1| pseudouridine synthase [Burkholderia sp. H160]
 gi|209502116|gb|EEA02131.1| pseudouridine synthase [Burkholderia sp. H160]
          Length = 204

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 79/168 (47%), Gaps = 23/168 (13%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R+++ D   +P ++      GRLD ++EGL+LLT+DG L AR+ E
Sbjct: 22  NKPFGTICQFSPHETRASLADWVKVPGVYP----AGRLDSDSEGLVLLTDDGALQARIAE 77

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------- 185
            P  + ++ Y  +  G VD   L  L +G+ +        Q T      S          
Sbjct: 78  -PRHKLVKRYWAQVEGAVDDAALKKLARGVDLGDYVTRPCQATYVEPDSSLWARTPPIRY 136

Query: 186 -----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  W+ + + EGKNR+++++     +   RL+R+  G   + +L
Sbjct: 137 RAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFSL 184


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 100/220 (45%), Gaps = 15/220 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKA 70
           P  + +++   G  +RR    +IA   V+VNG L E  RA   V     + VDG      
Sbjct: 15  PMTLDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQFEVDGL-RLTVDGEEWLAC 73

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
            +  L L +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG
Sbjct: 74  TKAYLML-NKPAGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDG 131

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---S 185
                   P  +  +VY V     V Q++++ L+ G+ +      D  V +  +      
Sbjct: 132 QFIHAQTSPKRKVPKVYEVTTAEPVTQEQVDALRTGVKLD-----DEPVPIAAEGCEITG 186

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              + + L +GK  ++K++       VN L R + G  +L
Sbjct: 187 ECSLRLTLLQGKYHQVKRMVAAAGNHVNALHRSAVGGLRL 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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 63/219 (28%), Positives = 96/219 (43%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           +  ++   G  SRR+   +I   RV V G            TD +   +DG       R 
Sbjct: 3   LESILYTQGFGSRRQCRGLIESGRVTVAGASATDPDA-AFDTDGLVFTLDGTAWPYHARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G   +  DP   ++VF  LP+ + +R V  VGRLD +T GLLLL++DG   
Sbjct: 62  YLAL-NKPAGYECSR-DPQHHASVFSLLPAPLLARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D+ +LN L+ G+ + G       V    +      +TV
Sbjct: 120 HAYTSPKRKVPKTYVATVRHPLDETQLNALRSGVQLHGEPKPIAAVAAVARDTHTLALTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EGK  ++K++    + +V  L R   G F L   LA
Sbjct: 180 --LEGKYHQVKRMVAAASNRVEALHRERIGGFALPAGLA 216


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 43/162 (26%), Positives = 78/162 (48%), Gaps = 23/162 (14%)

Query: 79  HKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G++   S  +   T+  F N+P+++      GRLD ++EGLLLLT+DG     +  
Sbjct: 6   NKPYGVICQFSPHEKYRTLKDFVNVPNVYP----AGRLDTDSEGLLLLTDDGKQQARITD 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------------- 179
           P  + ++ Y  +  G  D DKL  L++ + +        Q+ L                 
Sbjct: 62  PRNKIVKTYWAQLEGSPDADKLARLQQPLDLGDFVAQPAQIRLLETNEIAQIWTRHPPIR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + +   + W+ + +REGKNR+++++     +   RLIR+  G
Sbjct: 122 ERKTVPDFWLQIQIREGKNRQVRRMTAKAGYPCLRLIRVGIG 163


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 84/185 (45%), Gaps = 23/185 (12%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G ++  S+   R T+    ++P ++      GRLD ++EGLLLLT+DG L   +  
Sbjct: 7   NKPFGTMSQFSEHPTRPTLAACVSVPGVYP----AGRLDADSEGLLLLTDDGALQARIAD 62

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG----------- 184
           P  +  + Y  +  G  D   L  L+ G+ +        +V  +D               
Sbjct: 63  PRHKLEKTYLAQVEGIPDAAALARLRAGVDLGDFVTQPARVRAIDAPDWLWPRQPPVRFR 122

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                AW+ + +REGKNR+++++     +   RL+R+  GP  L  L  G       ++L
Sbjct: 123 AAIPTAWLELKIREGKNRQVRRMTAAVGFPTLRLVRVGIGPLDLRAL--GLAPGACCEVL 180

Query: 242 REQLG 246
             QLG
Sbjct: 181 PAQLG 185


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 85/177 (48%), Gaps = 21/177 (11%)

Query: 84  LVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           ++   +D  GRST+  F N+  ++     +GRLD ++EGLLLLTN+G +   L  P  + 
Sbjct: 1   MLCQFTDEAGRSTLKDFINVAGVYP----IGRLDRDSEGLLLLTNNGDIQHRLAEPKFKM 56

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------------SN 186
            + Y V+  G  D+  L  L++G+ +        +V L ++                   
Sbjct: 57  EKTYWVQVEGVPDEIALERLRRGVELNDGMTLPAKVRLISEPNFLWPRVPPIRERKNIPT 116

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           AW+ + + EG+NR+++++     +   RLIR     F L  L   + R +++  L++
Sbjct: 117 AWLEIKIYEGRNRQVRRMTAHIGFPTLRLIRYQQAGFSLQHLAPKTYRTLTQDELKQ 173


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 25/185 (13%)

Query: 73  TRLWLYHKPIGLVTTH----SDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           TRL  ++KP  ++       SD   R+T+ D  +LP ++      GRLD ++EGL+LLT+
Sbjct: 2   TRLIRFNKPYDVLPQFTDRGSDSSPRATLSDWIDLPGVYP----AGRLDRDSEGLMLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG- 184
            G L   +  P  +  + Y V+  G  D   +  L  G+ ++ G+        ++  +G 
Sbjct: 58  HGRLQAWISDPQHKMPKTYWVQVEGTPDAAAIQALANGVELKDGMTRPAKAALIEEPEGI 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + +REG+NR+++++         RLIR + G + L  L  G
Sbjct: 118 WARNPPIRVRKSVPDSWIALTIREGRNRQVRRMTAAVGHPTLRLIRAAIGIWTLDGLSPG 177

Query: 232 STREV 236
           +  ++
Sbjct: 178 TWEDL 182


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 60/220 (27%), Positives = 100/220 (45%), Gaps = 9/220 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAER 72
            + +++   G  SR+    +I    V VNG   +    +   TD +   V+  P    E+
Sbjct: 2   HLERILHAQGFGSRKNCRILIRHHAVTVNGEPCDNPFAD-FDTDKLAFTVNEEPWEYREK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSR-VISVGRLDINTEGLLLLTNDGGL 130
             L L +KP     +H  P    +VF  LP  +  R V  +GRLD +T GL+LL++DG  
Sbjct: 61  AYLML-NKPANYECSHK-PQHHPSVFALLPHPLLERGVQCIGRLDEDTTGLILLSDDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P  +  ++Y V     VD D++  L++G  +Q +        L  ++ S+  + 
Sbjct: 119 IHRMSSPKWKVPKIYEVGAKHAVDADQIRQLQEG--VQLVDEPAPIAALACEQISDQVLH 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + L EGK  ++K++      +V  L RI  G   L   LA
Sbjct: 177 LTLAEGKYHQVKRMLAAVGNRVESLKRIRIGELVLPDDLA 216


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 108/238 (45%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  V    G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAVTDAQGEVLY--ADDQVEHDAIRIDGEPLDPPPGF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SR---VISVGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F SR   +  VGRLD  T G+LL+T+DG 
Sbjct: 60  SLLL-HKPGGYTCSTKD-TGR-LIYELLPPRFRSRAPVLAPVGRLDRETSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY +     +  D+  L   G ++++G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYDITLAEDLRGDEAALFASGSLLLEGETKPLLPAELEVLGPREAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLEVLFG 232


>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 = 63.9 bits (154), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 61/218 (27%), Positives = 98/218 (44%), Gaps = 11/218 (5%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++    V VNG+  E     V +   + +VDG   R A   R +
Sbjct: 12  RILQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDAQVDTAGLVLDVDGE--RWAYHARAY 69

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG     
Sbjct: 70  LMLHKPTGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHT 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVG 192
           L  P  Q  +VY +     V   ++  L +G++++     D+ V     ++     + + 
Sbjct: 129 LTSPRHQVPKVYEITTAEPVTDAQVTQLCQGVLLED---EDVPVAAAWAERADACHLRMA 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           L +GK  ++K++       V  L R + G   LG  LA
Sbjct: 186 LTQGKYHQVKRMVAAAGNHVAALHRSAIGGLTLGADLA 223


>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 = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 94/212 (44%), Gaps = 5/212 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A   +R+E  +++    V V+GI+ +  +  V     +E  G  L  +   R
Sbjct: 2   RLDKFLCDALGTTRKESTQLLKSGDVTVDGIVRKSGSCQVTELSQVEWQGRALTLS-GPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
             + HKP G V +H D   + T F  L     R +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLHKPQGYVCSHEDSFNQ-TAFVLLDEANQRDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     +  +      KGI ++G    D+      +      V + +
Sbjct: 120 VTSPKHHCEKTYRVWLADPIAAEYTEQFAKGIELRG--ERDLTRPAQLEIIDQQQVLLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     KV  L R   G   L
Sbjct: 178 HEGKYHQVKRMFAALGNKVVGLHRERVGDIVL 209


>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 = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 105/227 (46%), Gaps = 4/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  A+R++  ++I    V V+G + +  +  V     +E DG  +  A   R
Sbjct: 2   RLDKYLCDALGATRKQATKIIKSGEVLVDGEVQKSGSFKVPEGGVVEWDGREV-GAPGPR 60

Query: 75  LWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP   V +H D  +  + V  + P +   +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGYNPTAFVLLDEPKV-ENLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCKKTYRVWLADAIQPDYVEKFAQGIELRNEREATLPAHLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            EGK  ++K++F     KV  L R   G   L  TL  G  R ++++
Sbjct: 180 VEGKYHQVKRMFAALGNKVELLHRERIGDIVLDDTLEPGDYRYLTQE 226


>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 = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 95/192 (49%), Gaps = 28/192 (14%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +E  R +   KP G ++    P+ R +  +   L    + ++++GRLD ++EGLLLLT D
Sbjct: 19  SEPHRHFKIFKPHGFLSQFV-PETRKSKKLLGELALFPTGIMAIGRLDHDSEGLLLLTTD 77

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G ++  +   S +  + Y V+  G +D + +  L+ G+ I GI  G+  +TL        
Sbjct: 78  GMVSHRVR--SKKVEKEYYVQVDGDIDDEAIIRLRLGVEI-GI-KGEKYLTLPCKVFKLD 133

Query: 180 -------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        D + G  +W+++ + EGKNR+I+K+    ++   RL+R+  G   L 
Sbjct: 134 GEPELPSNGRKIRDPRHGPMSWISITISEGKNRQIRKMTAAADFPTMRLVRVRIGNIMLD 193

Query: 227 TLLAGSTREVSK 238
            +  G   E+++
Sbjct: 194 NMQPGKVIELTE 205


>gi|260222138|emb|CBA31404.1| hypothetical protein Csp_F37360 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 282

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 79/287 (27%), Positives = 117/287 (40%), Gaps = 81/287 (28%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ASRRE +  IA+  VKVNG + E   + V+    IE+D     +     
Sbjct: 2   RLNKRMADLGMASRREADEWIAKGWVKVNGKVAE-MGMQVLPDVRIEIDKQAQGQQANQV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF-----------DNLPSIF-----SRVISVGRLDINT 118
             L +KP+G+V+  ++ DG                DN    F       ++  GRLDI++
Sbjct: 61  TILLNKPLGIVSGQAE-DGHEPAIKLIQPQNRWRDDNARFFFHGSQLKSLVPAGRLDIDS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVY--RVRFHG------------------------- 151
            GLL+LT DG +AR L    +   + Y  RV + G                         
Sbjct: 120 TGLLVLTQDGRVARQLIGEDSVMEKEYLVRVAYTGVENPGAANSPAATYPALAGRGKPQQ 179

Query: 152 --QVDQD--------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---W---- 188
             ++D D              KL LL+ G++            LD Q+   A   W    
Sbjct: 180 LIRLDDDDPVTSDVQSVFPPEKLQLLRHGLI------------LDDQRLKPAKVEWQNPE 227

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   L EGK R+I+++ E    KV  L R+  G   LG L  G  R
Sbjct: 228 QLRFVLTEGKKRQIRRMCELVGLKVVGLKRVRVGKVMLGNLPVGQWR 274


>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 = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 50/135 (37%), Positives = 76/135 (56%), Gaps = 6/135 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
           R+ K+I      +R+E++R+ A ++V V+G +  R   NV S  H IEV G  L   E  
Sbjct: 2   RLDKLIEEKLETTRKEMKRLFALKQVMVDGTVEFRQNRNVDSLLHRIEVAGEHLETNES- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP   VT  SDP+ ++TV D + S   F  +  VGRLD +T GLLL+T++G L 
Sbjct: 61  -YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQLG 118

Query: 132 RVLELPSTQWLRVYR 146
             + LP  +  R+ +
Sbjct: 119 YEMLLPEKRSQRLIK 133


>gi|46205033|ref|ZP_00209673.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 228

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 97/204 (47%), Gaps = 24/204 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---------MSTDHIEVDGV 65
           R+ +++A  G  SRREVE +     V+++G  L  AA  +         M+     +D +
Sbjct: 6   RLDRLLANLGYGSRREVEGLAWAGLVRLDGETLTDAAQRIPLDPDLSARMTIQGQLLDPL 65

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGL 121
           P          + HKP+G+  +H +      V+  LP  + R    + +VGRLD  T GL
Sbjct: 66  P------GLCLMLHKPLGVTCSHKE--AGPLVYSLLPERWRRRDPALSTVGRLDKETSGL 117

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLD 180
           LLLT+DG L   +  P  +  + YRV     +  D+ ++L  G +++ G     + V ++
Sbjct: 118 LLLTDDGALLHRIISPKAKVAKRYRVTLARPLQGDETSILASGELMLDGEDKPLLPVEME 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKV 204
               ++   TV L EG+  +++ +
Sbjct: 178 ADDATH--CTVTLHEGRYHKVRAL 199


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 94/202 (46%), Gaps = 16/202 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 10  TIMKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTV 69

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 70  VPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+ +    + +C  D  +   T 
Sbjct: 129 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENPTT 188

Query: 183 KGSNAWVTVGLREGKNREIKKV 204
                 + + + EGK  ++K++
Sbjct: 189 ------LLLTITEGKYHQVKRM 204


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 44/170 (25%), Positives = 85/170 (50%), Gaps = 23/170 (13%)

Query: 78  YHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G++   S  +   ++  F +LPS +      GRLD ++EGLLLLT+DG L   + 
Sbjct: 7   FNKPYGVICQFSPHEKHKSLKDFIDLPSFYP----AGRLDTDSEGLLLLTDDGWLQAKIT 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYGDMQVTLD----- 180
            P  +  + Y  +  G  D+ +L  L+KGI          +++ +  G+ +   +     
Sbjct: 63  DPKFKHPKTYWAQLEGLPDESRLESLRKGIDLGDFVTRPALVRVLNPGEAERLWERVPPI 122

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              +   + W+ + + EGKNR+++++     +   RL+R++ G  +L  L
Sbjct: 123 RVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDL 172


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 83/181 (45%), Gaps = 25/181 (13%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L++KP  +++  +D     T       F +LP ++      GRLD ++EGL++LT+DG L
Sbjct: 6   LFNKPFDVLSQFTDAGTAGTPRRTLSDFIDLPGVYP----AGRLDRDSEGLMILTDDGRL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG----- 184
              +  P  +  + Y  +  G  D   L  L++G+ ++       +V  +D  +      
Sbjct: 62  QARIAHPRYKAAKTYLAQVEGLPDHAALEALRRGVTLKDGPTRPARVRRIDVPEDLWDRD 121

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                     + W+ + L EG+NR+++++         RLIRI  G +QL  L  G  R+
Sbjct: 122 PPVRYRKSVPDCWIELTLTEGRNRQVRRMTAHVGHPTLRLIRIRIGDWQLDHLPPGHWRD 181

Query: 236 V 236
            
Sbjct: 182 A 182


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 49/189 (25%), Positives = 92/189 (48%), Gaps = 24/189 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDP----DGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
            RL L++KP G+++  +D       R+T+ D  +LP ++      GRLD ++EGLLLLT+
Sbjct: 2   ARLILFNKPYGVLSQFTDKGMADSKRATLSDHIDLPGVYP----AGRLDRDSEGLLLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------ICYGDM- 175
           DG L   +  P  +  ++Y V+     D   +  L +G+ ++           I   D+ 
Sbjct: 58  DGKLQERIASPRFKTEKIYLVQVERIPDDAAIEALCRGVTLKDGPTRPARVSRIAPPDLW 117

Query: 176 --QVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                +  +K   + W+++ + EG+NR+++++         RL+R   G + L  L  G+
Sbjct: 118 ERDPPVRFRKSVPDCWLSITISEGRNRQVRRMTAHVGHPTLRLVRWRIGAWSLDGLAPGT 177

Query: 233 TREVSKKIL 241
            R+   + L
Sbjct: 178 WRDAPPETL 186


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 46/162 (28%), Positives = 75/162 (46%), Gaps = 21/162 (12%)

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R      L S     + +GRLD  +EGLLLLT DG L+  +   S+   + Y     G +
Sbjct: 14  RKRFLGELGSFPQGTMPIGRLDEKSEGLLLLTTDGKLSDYVN--SSGIEKEYYALVDGDI 71

Query: 154 DQDKLNLLKKGIVI--QGICYGDMQVTL-----------------DTQKGSNAWVTVGLR 194
            Q++++ LKKG+ I   G  Y      +                 D + G  +W+++ L 
Sbjct: 72  SQEEISSLKKGVEIGFDGKKYQTKPCKVFKLDNAPLLPERGKKIRDARHGPVSWISITLT 131

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           EGK R+++K+         RL+R+  G  QLG L +G+ + +
Sbjct: 132 EGKFRQVRKMTSAVGCPTLRLVRVRVGNIQLGNLESGAVKPI 173


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 93/225 (41%), Gaps = 21/225 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +  ++   G  SRR+   +I   RV V G      A         + DG+     +    
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVSVAG------ASATDPDASFDTDGLVFTVDDTA-- 54

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +LN L+ G+ + G       V    +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVEALHRESIGGFTLPVDLA 216


>gi|330873630|gb|EGH07779.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 129

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 57/96 (59%), Gaps = 6/96 (6%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +L+L++KP  ++T  SD  GR+T+  F  +P I+      GRLD ++EGLLLLTNDG L 
Sbjct: 32  KLFLFNKPFDVLTQFSDEGGRATLKDFIKIPGIYP----AGRLDRDSEGLLLLTNDGQLQ 87

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
             +  P  +  + Y V+  G+   ++L  L+ G+ +
Sbjct: 88  ARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQL 123


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 112/250 (44%), Gaps = 35/250 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV---NVMSTDHIEVDGVPLRKAE 71
           R++K +A  G+ SRRE +  IA+  V VNG      AV    V     IEVD    ++  
Sbjct: 20  RLNKRMAELGLCSRREADDWIARGWVLVNGA----PAVMGQPVAPDARIEVDRQAEQQQR 75

Query: 72  RTRLWLYHKPIGLVTTHSD-----------PDGRSTVFDNL----PSIFSRVISVGRLDI 116
           +    L +KP+G V+  ++           P  R    ++     P     +   GRLDI
Sbjct: 76  QQVTILINKPVGYVSGQAEDGHEPAVVLVQPQNRWRECNSRMRWGPEQLRGLAPAGRLDI 135

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVI 167
           ++ GLL+LT DG +AR L   +++  + Y VR               ++KL LL+ G+ +
Sbjct: 136 DSIGLLVLTQDGRVARQLIGENSEIEKEYLVRVSYGAETSNVQAVFPREKLALLRHGLSL 195

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G      QV  D Q      +   L+EGK R+I+++ E     V  L R+  G   LG 
Sbjct: 196 DGQALRPAQV--DWQNPEQ--LRFVLKEGKKRQIRRMCEQVGLFVTGLKRVRIGRVNLGH 251

Query: 228 LLAGSTREVS 237
           L  G  R ++
Sbjct: 252 LPVGQWRYLA 261


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 82/177 (46%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G++   S  +   T+ D +      V + GRLD ++EGLL+LT+DG L   +
Sbjct: 2   LILFNKPYGVICQFSPHEKHKTLKDYI--AVPGVYAAGRLDTDSEGLLILTDDGRLQHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG--------- 184
             P  +  + Y V+  G    + L  L+ G+ +        +V  ++   G         
Sbjct: 60  SHPRHKEFKTYWVQVEGDPSDEALEPLRHGMDLGDFVTQPAKVRRIEEPAGLWPRHPPIR 119

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  AW+ V + EGKNR+++++     +   RL+R + G   L  +  G  R++
Sbjct: 120 ERKAIPTAWLEVIIAEGKNRQVRRMTAKAGFPTLRLVRYAVGQHTLEGIAPGEWRQL 176


>gi|328870986|gb|EGG19358.1| hypothetical protein DFA_02145 [Dictyostelium fasciculatum]
          Length = 534

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 119/255 (46%), Gaps = 28/255 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K+++  G+ +R +V++ I   +V   G  +  +A V+V   + I V G   RK +  
Sbjct: 6   RLDKLLSNLGLCTRSKVQQFINANKVTYQGQKVSPKAKVDV---EDIRVMG---RKVDHP 59

Query: 74  RLWL--YHKPIGLVTTHSDPDG-RSTVFDNLPSIF---SRVISV-GRLDINTEGLLLLTN 126
            L     HKPIG V ++S  DG    ++D LP  F   S  +S+ GRLD    GL++++ 
Sbjct: 60  ELLTIAVHKPIGYVCSNSREDGDHKIIYDLLPKEFADRSPTLSIAGRLDKWVTGLVVMSQ 119

Query: 127 DGGLA-RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDT 181
           +G +  R++     +  +VY V    + +  + + +  G V      G C       +D 
Sbjct: 120 NGKIVERIITPKDDKMGKVYEVVCESKFNGTEADEMASGRVQLRSEDGPCKPAHFEVVDQ 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +   N    + L EGK  +++++      K   + R   GP QLG L  G  R +SK+ +
Sbjct: 180 E---NKMARLTLYEGKYHQVRRMMSAVGNKAIGIHRTQVGPIQLGDLEVGKWRILSKEEM 236

Query: 242 REQLGPHLLEEAQVN 256
                  LLE  QV+
Sbjct: 237 ------ELLEAIQVS 245


>gi|254670490|emb|CBA06210.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha153]
          Length = 256

 Score = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 102/229 (44%), Gaps = 16/229 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +I    V +NG  ++   A ++  S + +++D   +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDEEAVTV 84

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTN 126
                 + + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L   L  PS +  ++Y V       +     LK G+++    + +C  D  +   T 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAADAVLKNPTT 203

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                 + + + EGK  ++K++      +V  L R  +   +   L  G
Sbjct: 204 ------LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPG 246


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 111/240 (46%), Gaps = 14/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE----RAAVNVMSTDHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G +L+    R AV+    + + + G P+   
Sbjct: 3   RLDRLLANLGYGSRKEVQALVAGGKVVLDGAILKDAGARIAVDATLPERMTIRGAPVDPP 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
               L + HKP+G+V +H + DG   ++D LP  +      + +VGRLD +T GL+L+T+
Sbjct: 63  APLVL-IMHKPLGVVCSHKE-DGEK-IYDLLPRRWRLRDPGLSTVGRLDKDTSGLILITD 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     + Y       ++  +  +   G +++       +   LD     
Sbjct: 120 DGDFLHRVISPKRHVPKTYLATLDRPLNGSEGEVFAAGTLMLDSEEKPLLPARLDVVNAH 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            A +T+   EG+  +++++F      V  L R   G   L   LA     +      EQ+
Sbjct: 180 AARLTI--TEGRYHQVRRMFAAVGNHVVALHRERIGGIALPDDLAAGQHRILTAAAAEQV 237


>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 = 63.5 bits (153), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 59/225 (26%), Positives = 105/225 (46%), Gaps = 9/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER 72
           R++K I+ +GI SRR  +R I    V +N  L    A  V S D + V+   +  R A+ 
Sbjct: 8   RLNKYISDSGICSRRHADRHIKLGNVFINDRLAAVGA-QVFSGDRVRVNDRQIAPRDADD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G++T+    + R  + D   +   R   +GRLD  ++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGVLTSMGKHE-RDNIGD-FVNHSQRTFPIGRLDKASQGLIFLTNQGELVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +    +  +  G+ I G       V    +K ++    + 
Sbjct: 125 KILRAGNNHEKEYLVTVNKPLTDAFIQGMGAGVPILGKVTHPCLV----EKEASQVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L +G NR+I+++ ++F ++V +L R+      L  L  G  R+ +
Sbjct: 181 LVQGLNRQIRRMCKYFGYEVTKLERVRIMNVDLTGLALGEWRDFT 225


>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 = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 110/230 (47%), Gaps = 21/230 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K++A  G  SR+E++++I +  +    G  L+    + ++ D I + G PL  A+  
Sbjct: 2   KLIKLLANLGYGSRKEMQQLIRRGTITDAAGQPLDDD--SAIAHDDIRLRGKPLDPAQGM 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVIS-VGRLDINTEGLLLLTNDGG 129
            L L HKP G V +  D  GR  V++ LP  FS    VIS VGRLD +T GLLL+T+DG 
Sbjct: 60  ILLL-HKPTGFVCSTKD-RGR-LVYELLPERFSLRKPVISTVGRLDSDTSGLLLMTDDGD 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKG 184
               +  P     ++Y V     +    + +   G ++     + +    M++T +T   
Sbjct: 117 FLHKVISPRNHVAKIYEVTTARPISPTYVPVFASGELMLESEKEPLKPAQMEITGET--- 173

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             A +T  L EG+  +++++F      V  L R   G   L  L  G  R
Sbjct: 174 -TARLT--LYEGRYHQVRRMFAAVGNHVEALHRAQMGELTLDDLAPGKWR 220


>gi|167835720|ref|ZP_02462603.1| pseudouridine synthase family protein [Burkholderia thailandensis
           MSMB43]
          Length = 192

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 53/189 (28%), Positives = 87/189 (46%), Gaps = 21/189 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSPHETRASLGDWVKT--PDVYPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA-- 187
           +  P  + ++ Y  +  G  D   L  L++G+     +   C        +T    N   
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFVTPPETLWPRNPPV 119

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTRE 235
                    W+ + + EGKNR+++++     +   RLIR+  G    F LG L  G TRE
Sbjct: 120 RYRAAIPTTWIELEIAEGKNRQVRRMTAAVGFPTLRLIRVGIGALDVFALG-LSPGETRE 178

Query: 236 VSKKILREQ 244
           +  +   E+
Sbjct: 179 LPPRAPWER 187


>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 = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 52/189 (27%), Positives = 85/189 (44%), Gaps = 31/189 (16%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV----FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L HKP G+++  +  D         F ++P +++     GRLD ++EGLL+LT++G L +
Sbjct: 2   LLHKPYGVLSQFTPEDNSRWDCLRDFVDIPDVYA----AGRLDADSEGLLVLTSNGRLQQ 57

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----------------CYGDMQ 176
            L  P     R Y V+  G     +L  L+ GI IQG                   G+  
Sbjct: 58  QLTNPRFGHWRTYWVQVEGSPQPHQLQQLRDGITIQGYRTRPAKAAWLNAEAIPTIGERI 117

Query: 177 VTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLL 229
             +  +      W+ + L+EG+NR+++++         RLIR +        PF L  L 
Sbjct: 118 PPIRVRAAIPTHWLEISLQEGRNRQVRRMTAAVGLPTLRLIRHTIDLMDGDTPFTLKGLE 177

Query: 230 AGSTREVSK 238
            G+ R V+K
Sbjct: 178 PGAWRTVTK 186


>gi|332971549|gb|EGK10499.1| ribosomal large subunit pseudouridine synthase E [Kingella kingae
           ATCC 23330]
          Length = 203

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 43/162 (26%), Positives = 77/162 (47%), Gaps = 23/162 (14%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G++   S  +   T+ D  N+P+++      GRLD ++EGLLLLT+DG     +  
Sbjct: 25  NKPYGIICQFSPHEKHRTLKDLVNVPNVYP----AGRLDTDSEGLLLLTDDGKQQARIAD 80

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------------- 179
           P  +  + Y  +  G  D DKL  L++ + +        Q+ L                 
Sbjct: 81  PRNKITKTYWAQLEGSPDADKLARLQQPLDLGDFVAQPAQIRLLNENEIAQIWTRNPPIR 140

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + +   + W+ + +REGKNR+++++     +   RLIR+  G
Sbjct: 141 ERKTVPDFWLQIQIREGKNRQVRRMTAKAGYPCLRLIRVGIG 182


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 111/240 (46%), Gaps = 14/240 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE----RAAVNVMSTDHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G +L+    R AV+    + + + G P+   
Sbjct: 8   RLDRLLANLGYGSRKEVQALVAGGKVVLDGAILKDAGARIAVDATLPERMTIRGAPVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
               L + HKP+G+V +H + DG   ++D LP  +      + +VGRLD +T GL+L+T+
Sbjct: 68  APLVL-IMHKPLGVVCSHKE-DGEK-IYDLLPRRWRLRDPGLSTVGRLDKDTSGLILITD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     + Y       ++  +  +   G +++       +   LD     
Sbjct: 125 DGDFLHRVISPKRHVPKTYLATLDRPLNGSEGEVFAAGTLMLDSEEKPLLPARLDVVNAH 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            A +T+   EG+  +++++F      V  L R   G   L   LA     +      EQ+
Sbjct: 185 AARLTI--TEGRYHQVRRMFAAVGNHVVALHRERIGGIALPDDLAAGQHRILTAAAAEQV 242


>gi|238028429|ref|YP_002912660.1| Pseudouridine synthase [Burkholderia glumae BGR1]
 gi|237877623|gb|ACR29956.1| Pseudouridine synthase [Burkholderia glumae BGR1]
          Length = 192

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 86/190 (45%), Gaps = 27/190 (14%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R ++ D +  P ++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 7   NKPFGTICQFSPHETRPSLGDWVRAPGVYP----AGRLDADSEGLLLLTDDGALQARIAE 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------- 185
            P  + ++ Y  +  G  D   L  L +G+ +        + +L     +          
Sbjct: 63  -PRHKLVKRYWAQVEGAPDAAALKALARGVDLGDYVTRPCRASLVEPPATLWPRTPPVRF 121

Query: 186 -----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVS 237
                  W+ + + EGKNR+++++     +   RL+R+  G    F LG L  G T E+ 
Sbjct: 122 RAAIPTTWIELAISEGKNRQVRRMTAAVGFPTLRLVRVGIGALDLFALG-LAPGETIELP 180

Query: 238 KKILREQLGP 247
            +   +   P
Sbjct: 181 PRAPWDGFAP 190


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 93/225 (41%), Gaps = 21/225 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +  ++   G  SRR+   +I   RV V G      A         + DG+     +    
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVTVAG------ASATDPDASFDTDGLVFTVDDTA-- 54

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +LN L+ G+ + G       V    +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVEALHRESIGGFTLPEDLA 216


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 93/225 (41%), Gaps = 21/225 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +  ++   G  SRR+   +I   RV V G      A         + DG+     +    
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVSVAG------ASATDPDASFDTDGLVFTVDDTA-- 54

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECSR-DPQHHASVFSLLPTPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +LN L+ G+ + G       V    +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVEALHRESIGGFTLPDDLA 216


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 112/234 (47%), Gaps = 24/234 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   ++ E  + I    V VN +++   +  V  ++ I ++G  L   E  R
Sbjct: 11  RLDKYLCKSTELTKLEAVQRIQNGEVSVNSVVVLDESTQVHESNAILLNGDALTLRE-FR 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP G + ++ D        +  PS+F        S +   GRLD +T GL+L+T+
Sbjct: 70  YILMHKPAGTICSNID--------EVYPSLFNYLELEKASELHIAGRLDADTTGLVLITD 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKG 184
           DG  +  + LP+    +VYRV     +  D  +  K GI +Q    G+ ++T   + +  
Sbjct: 122 DGRWSFNITLPTKSCKKVYRVILSRDIKDDVADKFKAGIQLQ----GEQKLTRPAELEVI 177

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           ++  V + + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K
Sbjct: 178 TSKEVLLTITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRLD-VEAGQWRYLTK 230


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 108/250 (43%), Gaps = 36/250 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+SK ++  G+ SRRE +  I +  V V+G  +      +     IE+       + ER 
Sbjct: 359 RLSKRMSELGLCSRREADEWIPRGWVLVDGKPVTELGTRIRPEAEIEILQAARSEQGERV 418

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFS-----RVISVGRLDIN 117
            + L +KP+G V+  ++ DG                D     F+      +   GRLDI+
Sbjct: 419 TV-LLNKPVGYVSGQAE-DGYEPAAVLFAPENQWELDPTRKRFAPWQRKNLAPAGRLDID 476

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKG 164
           + GLL+LT DG +AR L    +   + Y VR   +  Q             D L  L+ G
Sbjct: 477 STGLLVLTQDGRVARALIGDDSNVEKEYLVRVEWESPQGLVERNISAVFPDDLLERLRHG 536

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + + G+     +V+   ++     +   LREG+ R+I+++ E    KV  L R+  G   
Sbjct: 537 LSLDGVALKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLKVVGLKRVRMGRVV 592

Query: 225 LGTLLAGSTR 234
           LG L  G  R
Sbjct: 593 LGDLPPGQWR 602


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 99/221 (44%), Gaps = 13/221 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           R+ K +  A  A+R++  ++I    + V+G + +  A  V     +     V G P    
Sbjct: 2   RLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEVMWEDRVIGAP---- 57

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
              R  + +KP   V +H D   + T F  L  P I   +   GRLD++T GL+L+T+DG
Sbjct: 58  -GPRYIMLYKPADFVCSHEDGYNQ-TAFALLDEPKI-ENLHFAGRLDVDTTGLVLITDDG 114

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +  +  P  +  + YRV     +  D    L++GI+++      +   L+    +   
Sbjct: 115 KWSHRITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENE 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           V + + EGK  ++K++F     KV  L R   G  +L   L
Sbjct: 175 VLLTIVEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEAL 215


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 88/181 (48%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFIDDPTLRI--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVTLDTQKG- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        + I   + +   D     
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTRE 235
                   +W+ + + EG+NR+++++     +   RLIR   G     QLG L  G T+E
Sbjct: 120 RYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLG-LQPGETKE 178

Query: 236 V 236
           +
Sbjct: 179 I 179


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 113/251 (45%), Gaps = 38/251 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+  +P  ++E+  
Sbjct: 2   RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEI--LPAARSEQGE 59

Query: 75  --LWLYHKPIGLVTTHSDPDGR---STVF--------DNLPSIFSR-----VISVGRLDI 116
               L HKP+G V+  ++ DG    +T+F        D     F+      +   GRLDI
Sbjct: 60  RVTVLLHKPMGYVSGQAE-DGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDI 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVDQD--------KLNLLKK 163
           ++ GLL+LT DG +AR L    +   + Y VR       G V+ D         L  L+ 
Sbjct: 119 DSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRH 178

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G  
Sbjct: 179 GLSLDGEALKPAKVSWQNEEQ----LRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSV 234

Query: 224 QLGTLLAGSTR 234
            LG L  G  R
Sbjct: 235 VLGDLPVGKWR 245


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 60/225 (26%), Positives = 103/225 (45%), Gaps = 27/225 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   ++ +  + I    V VNG ++   +  V   + + + GV L  A   R
Sbjct: 2   RLDKFVCKSTQLTKADAVQCIHLGEVGVNGEVITSESTQVHENNTVTLRGVKL-IARDFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP G + ++ D        +  PS+F        S +   GRLD++T GL+L+T+
Sbjct: 61  YILMHKPAGTICSNID--------EVYPSLFNSLDVENVSELHIAGRLDVDTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL----KKGIVIQGICYGDMQVTLDT- 181
           DG     + +PS Q  + YRV     +  D ++ L      G+ +Q    G+ Q+TL   
Sbjct: 113 DGRWTFDITVPSKQCAKTYRVTLSRGIAADGVDDLVSRFAAGVKLQ----GEQQLTLPAT 168

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            Q  +   V + + EGK  ++K++F     +V  L R   G   L
Sbjct: 169 LQVITPTEVLLTITEGKFHQVKRMFAAVGHRVVALHRERIGDICL 213


>gi|304311685|ref|YP_003811283.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HdN1]
 gi|301797418|emb|CBL45638.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium HdN1]
          Length = 248

 Score = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 62/229 (27%), Positives = 104/229 (45%), Gaps = 12/229 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
           QR+ + ++++G  SR    + I    V +NG L   A+  +   D  H   D V    A 
Sbjct: 15  QRLDRFLSQSGRLSRSMARKAILAGEVTINGTLCRDASTKIGPNDTVHHHHDIV---VAP 71

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGG 129
                + HKP G+V   +  DGR  TV D L   +   + + GRLDI+T GL+LLT+DG 
Sbjct: 72  SHHYLMLHKPEGVVC--ATEDGRHRTVIDLLGEPWRSDLHIAGRLDIDTTGLVLLTSDGD 129

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +  +  P     + Y V     +        ++G+++ G         L+     +A  
Sbjct: 130 WSHRVTSPRHNKAKRYHVTTADPIASSWCASFEQGVMLDGETKLTRPAQLEILDEFHA-- 187

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + L+EG+  ++K++F     +V +L R + G   L  TL  G  R ++
Sbjct: 188 NLCLQEGRYHQVKRMFAAMGTRVVKLHRYAIGELILDNTLPLGHYRALT 236


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 57/222 (25%), Positives = 101/222 (45%), Gaps = 13/222 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V V+G + +       S +++E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSVDGEIADDLKKQ-FSPENLEFSLFGQTYQYREQV 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP I     V ++GRLD +T GLLLLT+DG   +
Sbjct: 62  YIALKKPKGFECSHQ-PQHHQSVFSLLPEIMIHRGVQAIGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V     V  +++ +L +G+ +   +GI        L+T +     +
Sbjct: 121 ALTHPRKHVPKVYHVTTLDPVTPEQIAMLSEGVSLHQEKGIFAATDVAMLETHQ-----L 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           T+ + +G   ++K++      KV  L R   G   L  +  G
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPEIADG 217


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 82/173 (47%), Gaps = 26/173 (15%)

Query: 80  KPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           KP G++   S  +    + D  +LP  +      GRLD ++EGLLLLTNDG L   +  P
Sbjct: 11  KPYGVICQFSAHEKYGCLKDYVSLPDFYP----AGRLDTDSEGLLLLTNDGRLQARIADP 66

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGS----------- 185
             +  + Y  +  G  D+ KL++L++G+ +        +V  L+T +             
Sbjct: 67  KFKLEKTYWAQVEGSPDEAKLDMLRRGVDLGDFVTRPAKVRVLETGEADVLWQRVPPIRV 126

Query: 186 -----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG---PFQLGTLLA 230
                + WV + + EGKNR+++++     +   RL+R++ G    F LG  L 
Sbjct: 127 RKSVPDFWVEIRISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLGLALG 179


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 93/199 (46%), Gaps = 16/199 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAER 72
           ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +     
Sbjct: 2   KLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVPE 61

Query: 73  TRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGG 129
              + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG 
Sbjct: 62  PYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGK 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGS 185
           L   L  PS +  ++Y V       +     LK G+ +    + +C  D  +   T    
Sbjct: 121 LNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAADAVLENPTT--- 177

Query: 186 NAWVTVGLREGKNREIKKV 204
              + + + EGK  ++K++
Sbjct: 178 ---LLLTITEGKYHQVKRM 193


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 113/242 (46%), Gaps = 25/242 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAE 71
           P R+SK ++  G+ SRRE +  I +  V+V+G+++      V+    + V+      +A+
Sbjct: 4   PVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAEQAQ 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNL-----PSIFSRVISVGRLDI 116
           R  + L +KP+G V+  ++   +  V           D       P     ++  GRLDI
Sbjct: 64  RVTI-LLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDI 122

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L    +   + Y VR      G++ +  L  L  G+++ G   
Sbjct: 123 DSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKPL 182

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V    +      +   LREGK R+I+++ +    KV  L R+  G  +LG L  G 
Sbjct: 183 RPAKVVWQNEDQ----LRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQ 238

Query: 233 TR 234
            R
Sbjct: 239 WR 240


>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 = 63.2 bits (152), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 107/240 (44%), Gaps = 16/240 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           + K++   G  SR+  +++I    V +   + +    N   T+H+  EV G      E  
Sbjct: 3   LEKILQSQGFGSRKYCQQIIKNGSVTIENQICDNPKQN-FPTEHLCFEVFGEEYLFRENV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G   +H     +S VF   P I     +  VGRLD +T GLLLLT+DG   
Sbjct: 62  YIVL-NKPKGYECSHQATHHKS-VFSLFPEILLHRGIQCVGRLDQDTTGLLLLTDDGQYL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + L  P     +VY V     + Q++   L++G+ ++      +    D    S   +++
Sbjct: 120 QALTNPRKHVPKVYHVTTADPITQEQKQALEQGVELRN--EKGIYAATDVHLFSEHQLSM 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-------LAGSTREVSKKILREQ 244
            + +G   ++K++      KV  L R   G F+L  +       L+ + +++S  I  E+
Sbjct: 178 TIHQGIYHQVKRMLAAVGNKVEDLHRHQVGLFELPKIPEGEWLYLSATQKQLSHNIALEK 237


>gi|239501492|ref|ZP_04660802.1| hypothetical protein AbauAB_04211 [Acinetobacter baumannii AB900]
          Length = 234

 Score = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 106/235 (45%), Gaps = 18/235 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V ++G ++        S ++ E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVGDLKKQ-FSPENFEFSVFGQNYQYREKI 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L T +     +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALLGTHQ-----L 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           T+ + +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGGWVYLSEQ 225


>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 = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 98/212 (46%), Gaps = 5/212 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R+E  +++  + V+VNG ++   +V V     +E +G  L   +  R
Sbjct: 2   RLDKFLGTTLGITRKEAGKILKDRMVEVNGEVVRNGSVQVSDDCDVEFNGRSL-SLQGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D   T+F     I    + V GRLD +T GL+L+T+DG  +  
Sbjct: 61  YYMLNKPQGFVCSHVD-DFNPTIFVLFDEISPEKMHVAGRLDGDTTGLVLVTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +D +     G+ ++          L+    + A +T+  
Sbjct: 120 ITSPRHVCEKTYYVETADPITEDYIQQFADGVQLRSEKELTRPAKLEILGENEALLTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     KV  L R   G  +L
Sbjct: 178 TEGKYHQVKRMFAAMGNKVVGLHRERVGAVEL 209


>gi|223940798|ref|ZP_03632631.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890528|gb|EEF57056.1| pseudouridine synthase [bacterium Ellin514]
          Length = 192

 Score = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/174 (28%), Positives = 77/174 (44%), Gaps = 26/174 (14%)

Query: 78  YHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G+++  T      R       P     V  +GRLD ++EGLLLL+++  L   L 
Sbjct: 5   FNKPYGVLSQFTRDGSPNRPLAHFGFPK---NVYPIGRLDADSEGLLLLSDEAALNERLL 61

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKG------- 184
            P  Q  R+Y  +       + L  L+KG+++Q      C   +   +D Q         
Sbjct: 62  HPRQQHGRIYWAQVEHVPSPEVLTRLEKGVIVQARRTLPCKAWL---IDPQPAVPPRVPP 118

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                     WV + L EGKNR+++++         RL+R+  G FQL  L AG
Sbjct: 119 IRERKSIPAVWVGLELVEGKNRQVRRMTAAVGHPTLRLMRMQIGKFQLADLPAG 172


>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 = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 85/180 (47%), Gaps = 16/180 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
            R+ L++KP+G+++  +D     +    L        V   GRLD ++EGLL+LT+DG L
Sbjct: 2   ARVILFNKPMGVLSQFTDKGNADSPRSTLSEFVDVKGVYPAGRLDRDSEGLLVLTDDGRL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT-------- 181
              +  P  +  + Y V+  G   +D++  L+ G+ +  G       V +D         
Sbjct: 62  QARIASPKFKRPKTYLVQVEGTPSEDQIRALRAGVDLNDGPTRRAECVAIDPPDLWPRNP 121

Query: 182 -----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +AW+++ + EG+NR+++++         RL+R S G + +  L  G  R+ 
Sbjct: 122 PVRFRKSVPDAWLSLTISEGRNRQVRRMTAHVGLPCLRLVRWSVGDWSVEGLAPGEWRDA 181


>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 = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 46/179 (25%), Positives = 82/179 (45%), Gaps = 23/179 (12%)

Query: 77  LYHKPIGLVTTHSD-----PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L++KP G++   +D     P      F   P ++      GRLD+++EGLLLLT+DG L 
Sbjct: 5   LFNKPYGVLCQFTDESTGPPRPTLAAFIKRPGVYP----AGRLDLDSEGLLLLTDDGRLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDT--------- 181
             +  P  +  + Y  +  G  D+  L  L++G+ ++       QV  +D          
Sbjct: 61  AQIADPRFKTPKTYLAQVEGDPDEAALEALRRGVKLKDGPTLPAQVERIDDPALWPRDPP 120

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   + W+ + +REG+NR+++++         RL+R   G + L  +  G  RE 
Sbjct: 121 VRFRKSVPDCWLRLTIREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLDGIAQGQWREA 179


>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 = 63.2 bits (152), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 88/181 (48%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRI--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVTLDTQKG- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        + I   + +   D     
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTRE 235
                   +W+ + + EG+NR+++++     +   RLIR   G     QLG L  G T+E
Sbjct: 120 RYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGTIDLVQLG-LQPGETKE 178

Query: 236 V 236
           +
Sbjct: 179 I 179


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 88/181 (48%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRI--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVTLDTQKG- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        + I   + +   D     
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTRE 235
                   +W+ + + EG+NR+++++     +   RLIR   G     QLG L  G T+E
Sbjct: 120 RYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGTIDLVQLG-LQPGETKE 178

Query: 236 V 236
           +
Sbjct: 179 I 179


>gi|299067456|emb|CBJ38655.1| Pseudouridine synthase [Ralstonia solanacearum CMR15]
          Length = 687

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 69/255 (27%), Positives = 115/255 (45%), Gaps = 46/255 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     +E+  +P  ++E+  
Sbjct: 436 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEVEI--LPAARSEQGE 493

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--------------------VISVG 112
               L HKP+G V+  ++ DG    ++   ++F+                     +   G
Sbjct: 494 RVTVLLHKPVGYVSGQAE-DG----YEPAAALFTAENQWEEDPTRKHFAAWQHKGLAPAG 548

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVD--------QDKLN 159
           RLDI++ GLL+LT DG +AR L    +   + Y VR       G V+        +D L 
Sbjct: 549 RLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWNAPQGPVEHDISKVFPEDLLE 608

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
           +L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI 
Sbjct: 609 MLRHGLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIR 664

Query: 220 YGPFQLGTLLAGSTR 234
            G   LG L  G  R
Sbjct: 665 MGSIVLGDLPVGKWR 679


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 88/185 (47%), Gaps = 25/185 (13%)

Query: 73  TRLWLYHKPIGLVTTH----SDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           TRL  ++KP  ++       SD   R+T+ D  +LP ++      GRLD ++EGL+LLT+
Sbjct: 2   TRLIRFNKPYDVLPQFTDRGSDSSPRATLSDWIDLPGVYP----AGRLDRDSEGLMLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG- 184
            G L   +  P  +  + Y V+  G  D   +  L  G+ ++ G+        ++  +G 
Sbjct: 58  HGRLQAWISDPQHKMPKTYWVQVEGTPDAAAIQALANGVELKDGMTRPAKAALIEEPEGI 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + +REG+NR+++++         RLIR + G + L  L  G
Sbjct: 118 WARNPPIRVRKSVPDSWIALTIREGRNRQVRRMTAAVGHPTLRLIRAAIGIWTLDGLSPG 177

Query: 232 STREV 236
           +  ++
Sbjct: 178 TWEDL 182


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 47/173 (27%), Positives = 80/173 (46%), Gaps = 33/173 (19%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP   ++  S    R+T+ D  ++P ++      GRLD ++EGLLLLT+DG L   +  
Sbjct: 7   NKPYQTMSQFSAHPSRATLADCVDVPGVYP----AGRLDADSEGLLLLTDDGALQARIAD 62

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  + ++ Y  +  G  D+  L  L+ G+ +     GD + TL  +              
Sbjct: 63  PRHKLVKTYLAQVEGVPDEAALATLRTGVDL-----GDFK-TLPAKARVVDEPAWLWERH 116

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       W+ + +REGKNR+++++         RL+RIS G  +L  L
Sbjct: 117 PPIRYRAAIPTTWIELSIREGKNRQVRRMTAAVGLPTLRLVRISIGNLKLPEL 169


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 105/221 (47%), Gaps = 13/221 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDGVPL--RKA 70
           R+ K ++  G  SR + E +I ++++ VNG   ++A +   V   + I ++G  L  +K 
Sbjct: 2   RLQKFLSDIGYCSRGQAEDLIRKRKIMVNG---KQATLGDKVRGNEKIVIEGRLLERKKG 58

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ L+HKP  +  + +      T+ D       RV  VG LD  +EG+LLLTNDG +
Sbjct: 59  PAKKVLLFHKPEAVDCSLAPSKTTKTLLD-FDFGTDRVFPVGYLDQASEGILLLTNDGEI 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L LP  +    Y +    ++D + +  L      Q       +  +D ++     + 
Sbjct: 118 ANKLSLPEFRPEDEYLLTSPEEIDAEMIEKL-----TQARKAEKNKSVVDIEQIDAKHLR 172

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +  + G++++IKK+ E     + +L+R+  G   L  L  G
Sbjct: 173 ILQQGGRSKDIKKMCEAVELVIEQLVRVRVGNITLEGLEKG 213


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 54/218 (24%), Positives = 102/218 (46%), Gaps = 6/218 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K ++     SR EV+R++    + VN +  + AA+ +    D I +   PL  A   
Sbjct: 2   RLDKYVSSVTDYSRAEVKRLLKNGSITVNDVSTKNAALQLDTQKDIICLFDEPL-SAPAP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R ++ +KPI  +    D     TV D L    ++ + + GRLD +T GL+L+T+DG  + 
Sbjct: 61  RYFMLNKPIDTICATED-SMHPTVIDLLDEPNTQQLHIAGRLDKDTTGLVLITDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+   ++ YRV       +     L++G+++          T++    +   + + 
Sbjct: 120 QITSPNKHCIKTYRVELEEAFTETAKKALEEGVLLHNEKKPTRSSTVNI--INKYCIELA 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + EGK  ++K++       V +L R   G  QL + L+
Sbjct: 178 ISEGKYHQVKRMLAAVGNHVKQLHRQQIGHIQLDSSLS 215


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 44/152 (28%), Positives = 79/152 (51%), Gaps = 25/152 (16%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           ++++GRLD ++EGLLLLT DG ++  +   S +  + Y V+  G +D + +  L++G+ I
Sbjct: 58  IMAIGRLDHDSEGLLLLTTDGMVSHRVR--SKKVEKEYYVQVDGIIDDEAIIRLQQGVEI 115

Query: 168 QGICYGDMQVTL---------------------DTQKGSNAWVTVGLREGKNREIKKVFE 206
            GI  G+  +TL                     D + G  +WV++ + EGKNR+I+K+  
Sbjct: 116 -GI-KGEKYLTLPCKVVKLDGEPNLPDNGRRVRDPRHGPLSWVSITISEGKNRQIRKMTA 173

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +   RL+R+  G   L  +  G   E+++
Sbjct: 174 AAGFPTMRLVRVRIGNIHLSDMQPGEVFELTQ 205


>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 = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 98/225 (43%), Gaps = 25/225 (11%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++    V VNG+  E     V +   + +VDG   R A   R +
Sbjct: 12  RILQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDTQVDTAGLVLDVDGE--RWAYHARAY 69

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  HKP G   +   P    +V+  LP+      V  VGRLD +T GLLLLT+DG     
Sbjct: 70  LMLHKPAGFECSQK-PRHHPSVYTLLPAPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHT 128

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--- 190
           L  P  Q  +VY +     V   ++  L +G+++      D  V++     + AW     
Sbjct: 129 LTSPRHQVPKVYEITTAEPVTDAQVAQLCQGVLLD-----DEDVSV-----AAAWAERVD 178

Query: 191 -----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                + L +GK  ++K++       V  L R + G   L   LA
Sbjct: 179 ALHLRMALTQGKYHQVKRMVAAAGNHVAALHRSAIGALTLDAGLA 223


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 59/223 (26%), Positives = 103/223 (46%), Gaps = 15/223 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERT 73
           + K++   G  SR+  +++I    V ++G + +       S +++E    G   +  E+ 
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVADDLKKQ-FSPENLEFSLFGETYQYREKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L  KP G   +H  P    +VF  LP I  +  V ++GRLD +T GLLLLT+DG   
Sbjct: 62  YLAL-KKPKGFECSHQ-PHHHQSVFSLLPEILIQRGVQAIGRLDQDTTGLLLLTDDGKYL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAW 188
           + L  P     +VY V     V  +++ +L +G+ +   +G+        L+T +     
Sbjct: 120 QALTHPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGVFAATDVKILETHQ----- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +T+ + +G   ++K++      KV  L R   G   L  L  G
Sbjct: 175 LTMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDG 217


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/209 (25%), Positives = 96/209 (45%), Gaps = 7/209 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V ++G ++        S ++ E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVSDLKKQ-FSPENFEFSVFGQNYQYREKI 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  P     +VY V  +  V  +++ +L +G+ +      ++    D        +T+ 
Sbjct: 121 VLTHPRKHVPKVYHVTTYDPVTPEQIEMLIQGVNLHQ--EKEVFAATDVALLGTHQLTMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + +G   ++K++      KV +L R   G
Sbjct: 179 IHQGVYHQVKRMIAAVGNKVEKLHRHQIG 207


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 52/182 (28%), Positives = 86/182 (47%), Gaps = 19/182 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R  L++KP  +++  +D      RS+      S+ S V  VGRLD ++EGLLLLTN G L
Sbjct: 7   RYILFNKPYNVLSQFTDNRNVKHRSSTLKEYISVDS-VYPVGRLDQDSEGLLLLTNHGQL 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 VS 237
           ++
Sbjct: 186 LN 187


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 52/226 (23%), Positives = 102/226 (45%), Gaps = 3/226 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR +V R +   R+ V+  +++  A  +     +  DG  L + +  R
Sbjct: 2   RLDKFLSQQLGISRNDVGRELRAGRITVDDEIVKTGAYKLTPEQQVMFDGSLLEQQQGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DP   + ++        ++ + GRLD++T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPINPTVLYFIDEPAAHKLHTAGRLDMDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  +  +    G+ + G         L+  +   A +T+   
Sbjct: 122 TSPKHHCKKTYLVTLECPVAAETADKFLAGVQLNGEKTVTKPAQLEILEPQIARLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
           EG+  ++K++F     +V  L R   G   L   L  G  R ++++
Sbjct: 180 EGRYHQVKRMFAAVGNRVTALHRERIGEIILAPELEPGEYRSLTEQ 225


>gi|299067788|emb|CBJ38998.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           CMR15]
          Length = 239

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 96/212 (45%), Gaps = 11/212 (5%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLY-HKP 81
           G  +RR  + ++    V VNG+  E     V +   + +VDG   R A   R +L  HKP
Sbjct: 5   GFGTRRYCKDLVFAGLVHVNGVEAEDPDAQVDTAGLVLDVDGE--RWAYHARAYLMLHKP 62

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG     L  P  
Sbjct: 63  TGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTLTSPRH 121

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-VTVGLREGKN 198
           Q  +VY +     V   ++  L +G++++     D+ V     +  +A  + + L +GK 
Sbjct: 122 QVPKVYEITTAEPVTDAQVTQLCQGVLLED---EDVPVVAAWAERVDACHLRMALTQGKY 178

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            ++K++       V  L R + G   LG  LA
Sbjct: 179 HQVKRMVAAAGNHVVALHRSAIGGLTLGADLA 210


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 53/216 (24%), Positives = 97/216 (44%), Gaps = 3/216 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +     A+R++  ++I    V V+G + +  +  V     +E +G  L  A   R
Sbjct: 2   RLDKYLCDGLGATRKQATKIIKSGDVTVDGEVQKSGSFKVPEAGVVEWEG-RLVGAPGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP   V +H D    +  V  + P +  ++   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGHNPTAFVLLDEPKV-EKLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADAIQPDYIEKFAEGIELRNESGPTLPAHLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            EGK  ++K++F     KV  L R   G   L   L
Sbjct: 180 VEGKYHQVKRMFAALGNKVEYLHRERIGSIVLDEAL 215


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 70/143 (48%), Gaps = 17/143 (11%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-G 169
            GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ ++ G
Sbjct: 37  AGRLDMDSEGLVFLTDHGGLNQYITNPANKKFKTYMVQVEGDVTEEALEQLRKGVELKDG 96

Query: 170 ICYGDMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           I        +   +                 +WV + + EG+NR+++++     +   RL
Sbjct: 97  ITLPARAEKVSEPEWLWERNPPVRFRASVPTSWVEISICEGRNRQVRRMTSAVGFPTLRL 156

Query: 216 IRISYGPFQL--GTLLAGSTREV 236
           IR   G   L    L  G TRE+
Sbjct: 157 IRTKIGEIDLVRMGLQPGETREI 179


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 57/221 (25%), Positives = 92/221 (41%), Gaps = 21/221 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ + +   G+ SRR    ++    V  NG+          +    EVD V L       
Sbjct: 2   KLYRALQSQGLGSRRGCAALVRAGAVLANGL--------ACADPEAEVDPVGLELTVDGT 53

Query: 75  LWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLL 124
           +W Y        HKP G   +H  P    +VF  LP+   +  V  VGRLD +T GLLL 
Sbjct: 54  VWAYRDKAYLVMHKPEGYECSHH-PRHHPSVFSLLPAPLVQRGVQCVGRLDQDTTGLLLF 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           ++DG     +  P  +  +VYR R    V+   L  L+ G+ +           L  +  
Sbjct: 113 SDDGQFIHRMTSPKKRVGKVYRARCAEPVNAATLAALRAGVQLND--EPAPLAALACEAV 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +  + + L EGK  +++++       V RL R + G + L
Sbjct: 171 DDRTLRLVLAEGKYHQVRRMIAAAGNHVARLHREAVGEYPL 211


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 73/230 (31%), Positives = 117/230 (50%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G  SR +V+ ++  ++V VNG    +A   +  + D +EV+G  +   E  
Sbjct: 2   RLDKFLAETGFGSRTQVKSLLKTKKVCVNGKKESQAKKQINPNLDRVEVEGQEVLYEEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G+V+   D     TV D L +   +  V  VGRLD +T GLLLLTN+G LA
Sbjct: 62  -YYMLNKPKGVVSATQDK-VHQTVLDLLDATAKQKEVFPVGRLDKDTHGLLLLTNNGNLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQ--VTLDTQKGSNAW 188
             L  P     +VY     G +    +   KKGI +    C   +   + LD +K S + 
Sbjct: 120 HRLLSPKKHVNKVYVADVDGLMTNQDIEAFKKGIHLSDHQCQPALLEILALDYEK-SQSR 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           V + ++EGK  ++K++      +V  L R+  GP QL + LA G+ R++ 
Sbjct: 179 VKIVIKEGKFHQVKRMVLACGKEVRDLQRLEMGPLQLDSKLALGAFRKLE 228


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 102/242 (42%), Gaps = 28/242 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V V+G  ++     V     IE+D             L H
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQVTVLIH 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLP---------------SIFSRVISVGRLDINTEGLLLL 124
           K +G V+  ++   +  +    P               +   ++   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+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R 
Sbjct: 181 QVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALPPGQWRY 236

Query: 236 VS 237
           ++
Sbjct: 237 LA 238


>gi|323526492|ref|YP_004228645.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383494|gb|ADX55585.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 243

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 101/239 (42%), Gaps = 28/239 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V V+G  ++     V     IE+D             L H
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQVTVLIH 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLP---------------SIFSRVISVGRLDINTEGLLLL 124
           K +G V+  ++   +  +    P               +   ++   GRLDI++ GLL+L
Sbjct: 61  KTVGYVSGQAEDGYQPAITLVTPENRWEGDRSDIRFSVAHLRQLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVL-----ELPSTQWLRV----YRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           T DG +A+ L     E+     +RV    + V        + L LL+ G+ +  +     
Sbjct: 121 TQDGRIAKQLIGGHSEIDKEYLVRVAYGEHTVDVESHFPPESLALLRHGLSLDDVPLKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           QV+   Q G    +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R
Sbjct: 181 QVSW--QNGEQ--LRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPPGQWR 235


>gi|187927714|ref|YP_001898201.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187724604|gb|ACD25769.1| pseudouridine synthase [Ralstonia pickettii 12J]
          Length = 248

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 99/229 (43%), Gaps = 25/229 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++    V +NG+ +E     V +   + +VDG   R A   R +
Sbjct: 11  RILQSQGFGTRRYCKDLVLAGLVFINGVEMESPDALVDTAGLVLDVDGE--RWAYHARAY 68

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  +KP G V     P    +V+  LP       V  VGRLD +T GLLLLT+DG     
Sbjct: 69  LMLNKPAG-VECSQKPKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVHT 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--- 190
           +  P  Q  +VY +     V + ++  L  G+++            + +  + AW     
Sbjct: 128 ITSPRHQVPKVYEITTAEPVTEAQIAQLYAGVLLAD----------ENENVAAAWAERVD 177

Query: 191 -----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + L +GK  ++K++       V+ L R + G   LG L  G  R
Sbjct: 178 THHLRMALTQGKYHQVKRMVAAAGNHVDGLHRSAIGGLSLGDLAPGEWR 226


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 65/213 (30%), Positives = 107/213 (50%), Gaps = 7/213 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +   G  SR EV+R++ +++V VNG +   A + +  + D I V+   L   +R 
Sbjct: 6   RLDKFLVEMGFGSRTEVKRLLKKKQVLVNGKIETSAKIQIDENQDEISVNNQVLI-YKRF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D D   TV D L        V  VG LDI+T GLLLLTN+G LA
Sbjct: 65  VYYLLNKPKGVISATED-DKHRTVLDLLDENARQKEVFPVGWLDIDTHGLLLLTNNGTLA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWV 189
             +  P     +VYR +  G + +  +   + GI ++       ++T+    ++   + V
Sbjct: 124 HAMLSPKKHAAKVYRAKVDGIITEKDVEHFEAGIELKDFTCRPAKLTILEVNEEPQTSLV 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
            + + EGK  + K++ +    KV  L R S GP
Sbjct: 184 EITISEGKFHQEKRMVQACGKKVTDLERFSMGP 216


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 56/231 (24%), Positives = 105/231 (45%), Gaps = 22/231 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDG-----VPLR 68
           + K +   GI +R+  + ++  Q V++NG  I  ++A V   +   + ++G     +PL 
Sbjct: 3   IIKYLQAQGIDTRKGCQWLVKHQLVQINGDTIASDKAEVQPENVRSLSIEGEDALIIPLP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTN 126
                   L +KP     +H  P    +VF  LP     + + ++GRLD +T G+LL+TN
Sbjct: 63  HF----YILLNKPADYEVSHK-PRDYPSVFTLLPDQIRAADIQAIGRLDADTTGVLLITN 117

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           DG     +  P  +  ++YR+           + LK G+++      D   T+  Q+   
Sbjct: 118 DGQFNHRMTSPKHKVAKIYRITLKHPASDTLCSSLKNGVLLH-----DDNETVAAQEAIL 172

Query: 185 -SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +   + + + EGK  ++K++      +V +L R  +G +    L AG  R
Sbjct: 173 QTPTTLLMTISEGKYHQVKRMIAAAGNRVAQLHRQQFGDWDTQDLAAGEWR 223


>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 = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 52/230 (22%), Positives = 104/230 (45%), Gaps = 11/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     SR++V R + ++RV ++  ++   AV ++    +  D   L+     R
Sbjct: 2   RLDRFLSHQLGKSRKQVTRALKEKRVILDSKVITNGAVKLLPEQKVLFDQQLLKYPITGR 61

Query: 75  LWLYHKPIGLVTTHSDPDGR--STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ +KP G + +  DP     +  FD   ++   + + GRLDI+  GL+L+T+DG  + 
Sbjct: 62  YFMLNKPKGYLCSTRDPHHPVVNDFFDE--TVSGELHAAGRLDIDATGLVLMTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVT 190
            L  P     + Y V     +  D       G+ ++         Q+ + T +     +T
Sbjct: 120 RLTSPKYHCKKTYWVTLASPISHDPTQNFLDGLRLKNEKTLTRPAQLKIVTPQSMELTIT 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
               EG+  ++K++F      V  L R+  G  +L   L+ G  R ++K+
Sbjct: 180 ----EGRYHQVKRMFAAIGHHVTELHRMQIGSIKLDEALMPGQYRLLTKQ 225


>gi|193077698|gb|ABO12547.2| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 234

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 107/236 (45%), Gaps = 20/236 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V ++G ++        S ++ E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQ-FSPENFEFSVFGQNYQYREKI 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAW 188
            L  P     +VY V  +  V  +++ +L +G+ +     G    D+ + L T +     
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGGFAATDVAL-LGTHQ----- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +T+ + +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 175 LTMTIHQGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGGWVYLSEQ 225


>gi|153002415|ref|YP_001368096.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151367033|gb|ABS10033.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 233

 Score = 62.8 bits (151), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 97/218 (44%), Gaps = 13/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++    R      I    V VNG++    A+ V   + +  +G  L     +R
Sbjct: 2   RLDKFLCKSTDLDRDAASVAILSGSVTVNGVIATDCAMQVHENNAVCFNGKSLVP-RPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++ HKP    T  S+ DG      +L  I   F   I VGRLD +T GL+LLT+DG  +
Sbjct: 61  YFMLHKPAD--TLCSNVDGAYPSLFHLLDIERAFDLHI-VGRLDADTTGLVLLTDDGRWS 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P  Q  +VYRV+    +D +           G+ +QG     +  TL  Q+  + 
Sbjct: 118 FNIISPQYQCKKVYRVQLRDPLDSEATAAIAATFTAGLQLQGETALTLPATL--QQVDDK 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + L EGK  ++K++F     KV  L R   G   L
Sbjct: 176 TVLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL 213


>gi|260425703|ref|ZP_05779683.1| ribosomal large subunit pseudouridine synthase E [Citreicella sp.
           SE45]
 gi|260423643|gb|EEX16893.1| ribosomal large subunit pseudouridine synthase E [Citreicella sp.
           SE45]
          Length = 179

 Score = 62.8 bits (151), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 85/176 (48%), Gaps = 20/176 (11%)

Query: 77  LYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +KP G+++  +D       R+T+ D +     RV   GRLD ++EGLLLLT+DG L  
Sbjct: 4   LLNKPYGVLSQFTDKGNADSPRATLSDYV--EVPRVYPAGRLDRDSEGLLLLTDDGALQA 61

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYGDMQVTLDT- 181
            +  P  +  + Y V+  G    D+L  L++G+           ++ +   D+   +   
Sbjct: 62  RIAHPKFRKPKTYLVQVEGDPTDDQLAQLRRGVSLNDGPTRPATVRRLPPPDLWPRVPPV 121

Query: 182 ---QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +   +AW+ + + EG+NR+++++         RL+R S G + +  L  G  R
Sbjct: 122 RFRKSVPDAWLELTITEGRNRQVRRMTAHVGLPCLRLVRWSIGDWSVAGLAPGEWR 177


>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 = 62.8 bits (151), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 106/235 (45%), Gaps = 18/235 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V ++G ++        S ++ E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQ-FSPENFEFSVFGQNYQYREKI 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L T +     +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALLGTHQ-----L 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           T+ + +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGGWVYLSEQ 225


>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 = 62.8 bits (151), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 106/235 (45%), Gaps = 18/235 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V ++G ++        S ++ E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQ-FSPENFEFSVFGQNYQYREKI 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHQ-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L T +     +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALLGTHQ-----L 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           T+ + +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGGWVYLSEQ 225


>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 = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 105/236 (44%), Gaps = 25/236 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   +R +    I    + VNG  +   +  V  ++ +   G  L  A  +R
Sbjct: 2   RLDKFICKSTELNRAQASECIECAEISVNGETITEVSFQVHESNSVVFKGQRL-VARPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLLT 125
             + HKPI  ++++ D D         PS+F R I+         VGRLD +T GL+LLT
Sbjct: 61  YIMLHKPIHTLSSNVDGD--------YPSLF-RCINIERAEELHIVGRLDADTTGLVLLT 111

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK---GIVIQGICYGDMQVTLDTQ 182
           +DG  +  +  P  Q  + YRV     +  D  +++ +   G+ +Q      +   L+  
Sbjct: 112 DDGRWSFDIIRPDKQCEKTYRVTLRDAIRDDVADMVARFAHGLQLQNEPALTLPAKLEVV 171

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                 +T+   EGK  ++K++F     +VN L R   G   L  L  G  R +S+
Sbjct: 172 TEKEVLLTIT--EGKYHQVKRMFAAVGNRVNGLHRERIGGLSL-ELDVGCWRHLSE 224


>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 = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 57/232 (24%), Positives = 112/232 (48%), Gaps = 20/232 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRK 69
           +R+   ++  G  +R +     A++ +K+N +L+    V   ST    D I ++G  L  
Sbjct: 6   KRIDAHLSSLGYCTRGD-----AKKFLKINELLVNENRVFNPSTKAYHDDITINGEKLDP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLT 125
              T   L +KP G++ +H+D      ++  LP  ++    ++ +VGRLD++T G ++LT
Sbjct: 61  --ETLTILLNKPSGVICSHND--AGVLIYSLLPYRWTQRNPKISTVGRLDVDTTGAIILT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKG 184
           +DG L   L  P  +  ++Y       +  D+  +   G +++ G     +   L+    
Sbjct: 117 DDGTLNHKLANPKKEISKIYEAHLKVPLKGDEEKIFASGELLLNGEDKPLLPAKLEVL-- 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           S   V + + EGK  ++K++F   + +V +L RIS+  F +  L  G  + +
Sbjct: 175 SPTCVRLEIVEGKYHQVKRMFAAVDNRVVKLHRISFDNFTVEDLKEGEYKSI 226


>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 = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 52/187 (27%), Positives = 85/187 (45%), Gaps = 21/187 (11%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +L +KP  +++  S  +G  +   NL   F + V  VGRLD ++EGLLLLTND  L   L
Sbjct: 8   FLIYKPYLMLSQFSK-EGDKSTLANLDFDFPTDVYPVGRLDADSEGLLLLTNDKQLNHRL 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN------ 186
             P  +  R Y V+  G +  +    L  G+ I   G  Y  +       +  N      
Sbjct: 67  LNPKFRHNRTYYVQVDGALTDEACQQLSAGVTISVDGKAYDTLPAKAILIEAPNLPERNP 126

Query: 187 ----------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+++ L EGKNR+++K+     +   RL+R +        +  G  R +
Sbjct: 127 PIRFRASIPTSWLSITLHEGKNRQVRKMTAAVGFPTLRLVRWAIESLTAEEMAPGEVRLL 186

Query: 237 SK-KILR 242
           S+ ++LR
Sbjct: 187 SRAEVLR 193


>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 = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 53/181 (29%), Positives = 81/181 (44%), Gaps = 21/181 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   HKP G+++  +   G   R+     LP     V  +GRLD ++EGLLLL+++ GL 
Sbjct: 2   LCALHKPYGVLSQFTPEPGSRWRTLAEFGLPPA---VYPLGRLDADSEGLLLLSDEPGLN 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----CYG---DMQVTLDTQKG 184
             L  P     R Y V+         L  L++G+ I       C     D   TL  +  
Sbjct: 59  TRLLNPDQAHRREYWVQVERVPTDAALAQLQRGVKIGDYATRPCAARRLDPAPTLPPRDP 118

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                    + W+ + L EGKNR+++++         RL+R+  G F LG L  G  RE+
Sbjct: 119 PIRARKNVPDCWLALELIEGKNRQVRRMTAAIGHPTLRLVRVRIGDFALGKLAVGQWREL 178

Query: 237 S 237
           +
Sbjct: 179 T 179


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 102/223 (45%), Gaps = 15/223 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERT 73
           + K++   G  SR+  +++I    V V+G + +       S +++E    G   +  E+ 
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSVDGEVADDLKKQ-FSPENLEFSLFGETYQYREKV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L  KP G   +H  P    +VF  LP I  +  V ++GRLD +T GLLLLT+DG   
Sbjct: 62  YLAL-KKPKGFECSHQ-PHHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAW 188
           + L  P     +VY V     V  +++ +L +G+ +   +GI        L+  +     
Sbjct: 120 QALTHPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGIFAATDVAILEMHQ----- 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +T+ + +G   ++K++      KV  L R   G   L  L  G
Sbjct: 175 LTMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDG 217


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/186 (28%), Positives = 88/186 (47%), Gaps = 27/186 (14%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVL 134
           ++KP G++   S  +   ++ D++  P  +      GRLD ++EGLLLLTNDG L AR+ 
Sbjct: 10  FNKPCGVICQFSPHETHPSLKDHIDAPGFYP----AGRLDTDSEGLLLLTNDGRLQARIA 65

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK----GIVIQGICYGDMQVTLDTQK------- 183
           E P     + Y  +  G  D+ KL LL++    G  I       +    +T++       
Sbjct: 66  E-PRHGKEKTYWAQVEGAPDEHKLALLRRPMDLGDFITQPARTRLLAADETERLWPRQPP 124

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 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|302327988|gb|ADL27189.1| ribosomal small subunit pseudouridine synthase A [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 231

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 106/218 (48%), Gaps = 18/218 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           + +++A  G  SR++   ++    V+++G +L+   +   +  + I V+G      E+  
Sbjct: 3   LERLLASMGFGSRKDARGLVRMGLVELDGKVLDDPFMEFKTRPEFITVNGEEAPTVEKLY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + LY KP  +  +H+  D +  V+D LP  F+   + SVGRLD ++ GLLLL+N G    
Sbjct: 63  VMLY-KPTDVECSHNARDHKP-VYDLLPERFTAMGIQSVGRLDADSSGLLLLSNQGDFIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
            +E P     + YRV       D  K  LL  G++++     +   +++V+ D       
Sbjct: 121 KVESPKKGLWKKYRVTLARPFTDAQKAELL-AGVMLKDERRPVLAREIEVSGDA------ 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + + EG   +++++F      V  L RI+ GP  L
Sbjct: 174 -VDISIGEGLYHQVRRMFAAVGNHVETLERIAIGPVVL 210


>gi|149377680|ref|ZP_01895416.1| pseudouridylate synthase [Marinobacter algicola DG893]
 gi|149358033|gb|EDM46519.1| pseudouridylate synthase [Marinobacter algicola DG893]
          Length = 234

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 66/233 (28%), Positives = 112/233 (48%), Gaps = 10/233 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           +   R+   +A A   SRR+ ++ I+  RV+V+G    + A  V     + +D  PL   
Sbjct: 2   YLSMRLDYFVANATTLSRRDAKKAISAGRVRVDGETCRKPASPVAKDTRVSLDDQPLSLP 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGG 129
           E   L LY KP G+++  +D   + T  D LP+     + + GRLD +T GLLLLT DG 
Sbjct: 62  EERYLMLY-KPAGVISATTDSQ-QPTALDLLPADVRHGLHIAGRLDADTTGLLLLTTDGQ 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNA 187
            +  +  P  +  + YRV     +D   +  L++G+++    +G+ + T   D    +  
Sbjct: 120 WSHRITSPRLKCHKTYRVTLAEPIDDFAITQLQQGVLL----HGESRPTRPADVHLLNAG 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            + + L EG+  ++K++       V  L R   GP  L   LA G  RE++ +
Sbjct: 176 EIDLTLSEGRYHQVKRMLAAVGNHVTGLHRWRVGPLILDDSLAPGDYRELTAE 228


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/218 (26%), Positives = 106/218 (48%), Gaps = 18/218 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTR 74
           + +++A  G  SR++   ++    V+++G +L+   +   +  + I V+G      E+  
Sbjct: 6   LERLLASMGFGSRKDARGLVRMGLVELDGKVLDDPFMEFKTRPEFITVNGEEAPTVEKLY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + LY KP  +  +H+  D +  V+D LP  F+   + SVGRLD ++ GLLLL+N G    
Sbjct: 66  VMLY-KPTDVECSHNARDHKP-VYDLLPERFTAMGIQSVGRLDADSSGLLLLSNQGDFIH 123

Query: 133 VLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNA 187
            +E P     + YRV       D  K  LL  G++++     +   +++V+ D       
Sbjct: 124 KVESPKKGLWKKYRVTLARPFTDAQKAELL-AGVMLKDERRPVLAREIEVSGDA------ 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + + EG   +++++F      V  L RI+ GP  L
Sbjct: 177 -VDISIGEGLYHQVRRMFAAVGNHVETLERIAIGPVVL 213


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 100/212 (47%), Gaps = 5/212 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     +R+E  R++  + ++VNG +++  ++ +     +E +G  L   +  +
Sbjct: 2   RLDKFLATTLGITRKEAGRLLNNKMIEVNGDVVKSISLKITDDCDVEFNGKKL-TLQGPQ 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +H D D   TVF     +    + V GRLD +T GL LLT+DG  +  
Sbjct: 61  YFMLNKPEGFVCSHVD-DHNPTVFVLFDEVSPEKMHVAGRLDGDTTGLTLLTDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     +VY V     V ++ +    +G+ ++G         L+      A +T+  
Sbjct: 120 VTSPRHVCEKVYHVELADPVPEETIQTFLEGVQLRGEKDITRPAKLEILGEREAILTI-- 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     +V  L R   G   L
Sbjct: 178 TEGKYHQVKRMFAAVGNRVVGLHREQVGAVVL 209


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 87/182 (47%), Gaps = 22/182 (12%)

Query: 76  WLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++ HKP G ++    +   +  +   L      ++++GRLD ++EGLLLLT DG ++ ++
Sbjct: 14  FIIHKPYGYLSQFKYELKRKKKLLGELYDFPEGIMAIGRLDEDSEGLLLLTTDGKMSEIV 73

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY----------------GDMQ 176
              S +  + Y V+  G + Q+ +  +K G+ I  +G  Y                G+  
Sbjct: 74  R--SKKVEKEYYVQVDGLITQEAIEKMKNGVEIGFEGTKYMTKPCKAFIVNEIPNFGERG 131

Query: 177 VTL-DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             + D + G  +W ++ + EGK R+++K+     +   RL+R+  G   LG L A    E
Sbjct: 132 KKIRDERHGPTSWASIVVTEGKFRQVRKMTAAVGFPTLRLVRVRVGNIHLGNLQAREVLE 191

Query: 236 VS 237
            S
Sbjct: 192 TS 193


>gi|91229061|ref|ZP_01262887.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|91187454|gb|EAS73794.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
          Length = 177

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 56/95 (58%), Gaps = 2/95 (2%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   
Sbjct: 57  KVIIFNKPYDTLSQFTDGDGRKTLADYIP--IKNVYAAGRLDRDSEGLMVLTNDGILQAK 114

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           L  P ++  + Y V+  G   +  L  L+KG+ ++
Sbjct: 115 LTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELK 149


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 40/167 (23%), Positives = 80/167 (47%), Gaps = 17/167 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   +     TV   +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPYDVLSQFREDSAHLTVSSFIADPELRI--AGRLDLDSEGLMFLTDHGGLNQY 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKG-------- 184
           +  PS +  + Y V+  G + +D L  L+KG+ +  G+        ++  +         
Sbjct: 60  ITHPSNKKYKTYLVQVDGDITEDALEKLRKGVELADGLTLPAQATKVEEPEWLWERNPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                   +WV + + EG+NR+++++     +   RLIR   G   L
Sbjct: 120 RFRASIPTSWVEISICEGRNRQVRRMTATVGFPTLRLIRTQIGSINL 166


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 99/212 (46%), Gaps = 13/212 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V ++G ++        + ++ E          R ++
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVSDLKKQ-FAPENFEFSVFGQNYQYREKI 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++   KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L+T +     +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLIQGVNLHQEKGVFAATDVALLETHQ-----L 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           T+ + +G   ++K++      KV +L R   G
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIG 207


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 57/199 (28%), Positives = 95/199 (47%), Gaps = 14/199 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   + +
Sbjct: 2   RLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHPKHS 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + L +KP G+V+   D +   TV D L      P ++     VGRLD +TEGL+LLT++
Sbjct: 62  YIIL-NKPSGVVSAKKDTN-YLTVIDQLAEEDKSPDLYP----VGRLDRDTEGLVLLTDN 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       
Sbjct: 116 GPLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQ 175

Query: 187 AWVTVGLREGKNREIKKVF 205
           +  ++ + EGK  ++KK F
Sbjct: 176 SQASLTISEGKFHQVKKCF 194


>gi|148242785|ref|YP_001227942.1| pseudouridine synthase [Synechococcus sp. RCC307]
 gi|147851095|emb|CAK28589.1| Pseudouridine synthase [Synechococcus sp. RCC307]
          Length = 205

 Score = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 54/186 (29%), Positives = 82/186 (44%), Gaps = 27/186 (14%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L HKP G+++  +   G  + +D L S+     V + GRLD ++EGLLLLT+DG L   L
Sbjct: 10  LLHKPYGVLSQFTPEVG--SRWDCLASLVPIKGVYAAGRLDADSEGLLLLTSDGALQHQL 67

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNA------ 187
             P     R YR +  G   +  L  L++GI ++ G         LD    +        
Sbjct: 68  TNPRFGHWRQYRAQVEGAPTEADLEPLRRGIQLKDGPSRPARAQLLDPSVAAGIAERNPP 127

Query: 188 ----------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAG 231
                     W+ + L EG+NR+++++     +   RLIR S        P  L  +  G
Sbjct: 128 IRHRLSVPTRWLELELTEGRNRQVRRMTAAIGFPTLRLIRWSLDLMDGQPPLNLDGMEPG 187

Query: 232 STREVS 237
             R VS
Sbjct: 188 QWRWVS 193


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/278 (23%), Positives = 122/278 (43%), Gaps = 45/278 (16%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERT 73
           +++ I+ +G  SR + E  I    V V+G ++     NV  +DH +V     P+      
Sbjct: 24  LARRISLSGQMSRSQAEVAIRNGEVVVDGQVVRH---NVQVSDHCDVICRDQPVEPPGDP 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD------------------NLPSIFSRVISVGRLD 115
           ++WL +KP G+V + +   G +T+ D                  N+  I    I +  + 
Sbjct: 81  KVWLINKPRGVVCSATRIRGLTTLPDLFEIWHKRRANELSHNINNVDLIPPHFIVINPIP 140

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYG 173
           +   GL++LTNDG  A  +  P ++ L V+ VR  G++ +D+    ++  G+ +  + YG
Sbjct: 141 VMCSGLVILTNDGEFAHNMAHPRSKVLSVFLVRVKGRLPEDRFKSWRRREGVKVGNVDYG 200

Query: 174 DMQVTLDTQKGSNA-WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            + V +D +   +  W+ V L     + +          V ++   S+GP++  T     
Sbjct: 201 QVFVGIDKRPSEDVTWLRVRLVMTNEKNL----------VTKINSSSFGPYRSSTAYV-- 248

Query: 233 TREVSKKILREQLGPHL--LEEAQVNLDAPIYSSETLV 268
                  I  + + PH+  L   ++  DA + +  TLV
Sbjct: 249 -----DYICPQPVSPHVRHLAPRRIARDAIMAAKGTLV 281


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 31/101 (30%), Positives = 53/101 (52%)

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           PS +  + Y     G   + KL  L++GI+++G      +V + +QK  +  V + + EG
Sbjct: 18  PSYETFKTYEADLSGTPSRAKLQRLEQGILLEGKPTAPARVKILSQKKHSTKVAITIHEG 77

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +  ++KK+F      VN L RI+YG  +L TL  G  + +S
Sbjct: 78  RKHQVKKMFAAIGHPVNHLKRIAYGKLELQTLATGQFKRLS 118


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L + +KP G++   S  +    + D +  P  +      GRLD ++EGLLLLTN+G L  
Sbjct: 4   LIILNKPYGVICQFSAHEKHQCLKDFVEKPGFYP----AGRLDTDSEGLLLLTNNGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +  ++      
Sbjct: 60  QIADPKFKQIKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTHPAEVRVLEEGEADVLWPRV 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       WV + + EGKNR+++++     +   RL+R++ G   L  L
Sbjct: 120 PPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDL 172


>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 = 62.4 bits (150), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 96/219 (43%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           +  ++   G  SRR+   +I   RV + G        + + TD +   VDG P     R 
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDAD-LDTDGLVFTVDGTPWPFHARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G   +  DP    +VF  LP+  +   V  VGRLD +T GLLLL++DG   
Sbjct: 62  YVAL-NKPAGYECSR-DPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D  +L+ L+ G+ + G       V  D +      +TV
Sbjct: 120 HAYTSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGEPKPVAAVAADARDPHTLALTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EGK  ++K++    + +V  L R S G   L   LA
Sbjct: 180 --LEGKYHQVKRMVAAASNRVEALHRESVGGLALPADLA 216


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 82/186 (44%), Gaps = 27/186 (14%)

Query: 79  HKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G+++  +   G     + D +P    RV + GRLD ++EGLL+LT  G L   L  
Sbjct: 2   NKPYGVLSQFTPEPGSQWRCLADLIP--IPRVYAAGRLDADSEGLLVLTAHGRLQHRLTN 59

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----------- 185
           P     RVY V+  G   + +L  L  G++IQG       V+    K +           
Sbjct: 60  PHLSHWRVYWVQVEGSPSESQLQKLASGVIIQGKRTRPALVSWLKGKAAPIVRERDPPIR 119

Query: 186 ------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI------SYGPFQLGTLLAGST 233
                  +W+ + L+EG+NR+++++         RLIR          P  +  L  G  
Sbjct: 120 VRQSIPTSWLELKLKEGRNRQVRRMTAAVGLPTLRLIRHRIELMDGEPPLSIEGLDPGQW 179

Query: 234 REVSKK 239
           R+VS +
Sbjct: 180 RQVSSR 185


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 107/229 (46%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            RV K+I   G+ +R+ ++R   +  + +NG +++ ++V V    D +   G  +   E 
Sbjct: 1   MRVDKMIGNTGLDTRKNIKRNAKKGALVINGEIVKDSSVKVDPLVDEVFYMGHFVEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISV-GRLDINTEGLLLLTNDGGL 130
             L L +KP G+++  +  D   TV D L   +    +S+ GRLD +T GL++L+ DG  
Sbjct: 61  LYLIL-NKPSGVLS--ATQDAEETVIDLLDDFYKNYDLSIAGRLDKDTTGLIILSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y V+    + ++     KKG+ I+   Y      L       A V 
Sbjct: 118 IHKITSPNSHITKTYEVKTRDPIAENLKEEFKKGVYIKEDDYTARPAELTITGEKEAIVK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSK 238
           V   EGK   +K++F     +V  L R + G   L   L  G  RE+++
Sbjct: 178 V--TEGKYHLVKRLFSNLGNEVVGLKRTAIGKLVLDPYLKEGDYRELTE 224


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 40/176 (22%), Positives = 83/176 (47%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           ++L L++KP  +++  +D + R T+ + +      V   GRLD ++EGLLLLT+DG L  
Sbjct: 2   SKLLLFNKPFHVLSQFTDSEARKTLSEFIE--IKGVYPAGRLDYDSEGLLLLTDDGQLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            +  P  +  + Y  +  G   +     L  G+ ++      +   L             
Sbjct: 60  QISNPKFKLNKTYWAQVEGTATETHCLELIAGVSLKDGPAAAVACKLMDPPNLWPRIPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + Q  +++W+ + + EG+NR+++++         RL+R + G +++  +  G  R
Sbjct: 120 RERQNVADSWIELTINEGRNRQVRRMTAAVGLPTLRLVRAAIGDWKVTDIAPGEHR 175


>gi|152995450|ref|YP_001340285.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150836374|gb|ABR70350.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 229

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 66/217 (30%), Positives = 108/217 (49%), Gaps = 10/217 (4%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT 86
           +R+  +   ++ RV VNG ++++A   V   D I +D + L        +L HKP G V 
Sbjct: 14  ARKAAKIAASKGRVTVNGEVVKKANYTVQEGDQICLDDILLAWPSEG-YYLLHKPAGYVC 72

Query: 87  THSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
              DPD   TV D LPS   + +  VGRLD +T GLLLLT DG     +  P     + Y
Sbjct: 73  ATQDPD-HPTVLDLLPSHLGQELKIVGRLDKDTTGLLLLTTDGQWLHRITSPRNACNKRY 131

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKK 203
           R+     +  + L  L++G+++     G+ Q TL    ++ S+  + + ++EGK  ++K+
Sbjct: 132 RMMLADPISDEDLKQLEEGVMLN----GESQPTLPAIAERISDCDIYLTIQEGKYHQVKR 187

Query: 204 VFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           +      KV  L R   G   L   + AG  RE++++
Sbjct: 188 MLAAVGNKVEELHRDQIGLLSLDADIQAGEFRELTEE 224


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/229 (26%), Positives = 98/229 (42%), Gaps = 25/229 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++    V VNG+ +E     V +   + +VDG   R A   R +
Sbjct: 11  RILQSQGFGTRRYCKDLVLAGLVFVNGVEMESPDALVDTAGLVLDVDGE--RWAYHARAY 68

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  +KP G V     P    +V+  LP       V  VGRLD +T GLLLLT+DG     
Sbjct: 69  LMLNKPAG-VECSQKPKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVHT 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--- 190
           +  P  Q  +VY +     V + ++  L  G+++            + +  + AW     
Sbjct: 128 ITSPRHQVPKVYEITTAEPVTEAQIAQLCAGVLLAD----------ENENVAAAWAERVG 177

Query: 191 -----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + L +GK  ++K++       V  L R + G   LG L  G  R
Sbjct: 178 THHLRMALTQGKYHQVKRMVAAAGNHVAGLHRSAIGGLSLGDLAPGEWR 226


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/169 (22%), Positives = 85/169 (50%), Gaps = 16/169 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP  +++  +  + ++T+   +    +     GRLD ++EGLLLLT+ G L  ++  
Sbjct: 6   VFNKPFQVLSQFTTDEEKATLSSFIDK--ANFYPAGRLDYDSEGLLLLTDHGALQHLIAS 63

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDTQKG---------- 184
           P  +  + Y V+  G++ ++ +  L+ G+ ++ G+    + ++  D +            
Sbjct: 64  PQHKMPKTYLVQVEGELTKEAVEQLRVGVELKDGLTKPAEAKIASDFEPWPRHPPIRERK 123

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               +W+ + + EGKNR+++++     +   RLIR   GP+ L  +  G
Sbjct: 124 NIPTSWLELTITEGKNRQVRRMTAAVGFPTLRLIRTQIGPYSLTDIELG 172


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 21/240 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAERT 73
           R+SK +   G+ SRRE +  I    VKV+G+++      V     IE+    +  +AER 
Sbjct: 6   RLSKRMTELGLCSRREADEFIEMGLVKVDGVVVNVLGSRVRPEQTIELTRQAMALQAERV 65

Query: 74  RLWLYHKPIGLVTTHSD-----------PDGRS----TVFDNLPSIFSRVISVGRLDINT 118
             +L +KP+G  +  S+           P+ RS    + +  L    + +   G+LD+++
Sbjct: 66  -TFLLNKPVGYGSGPSEAGERPAWQLIKPETRSPRDRSGYTFLKKHLNYLAPAGKLDVDS 124

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+LT DG +AR L   +  + + + V   G+V    L  L+ G+ + G     ++V+
Sbjct: 125 SGLLVLTQDGRIARALMAKAADFEQEFLVWVEGEVSDAMLEQLRHGLSLDGEALKPVKVS 184

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               + S++ +   LR+   R+I+++ E    +V  + RI  G   LG L  G  R +++
Sbjct: 185 ----RQSDSQLRFVLRDPVRRQIRRMAELVGLRVTAVRRIRIGRIALGDLEQGQWRYLTE 240


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L + +KP G++   S  +    + D +  P  +      GRLD ++EGLLLLTN+G L  
Sbjct: 4   LIILNKPYGVICQFSAHEKHQCLKDFVEKPGFYP----AGRLDTDSEGLLLLTNNGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +  ++      
Sbjct: 60  QIADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTHPAEVRVLEEGEADVLWPRV 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       WV + + EGKNR+++++     +   RL+R++ G   L  L
Sbjct: 120 PPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDL 172


>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 = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 46/150 (30%), Positives = 75/150 (50%), Gaps = 6/150 (4%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +Y+K  G V+   D     T +D+LP  +     VGRLD + EGLLLLT++G L   LE 
Sbjct: 65  VYNKAAGQVSAKKDAH-WPTPYDHLPECYQGTSIVGRLDRDVEGLLLLTDNGQLHYFLEH 123

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                 + Y+V  +G +  D +   + G+    G      Q+ +   +   A++T+   +
Sbjct: 124 ARFHIPKTYQVTVNGDLGADLVEKFQAGVTFADGTTCRPAQLEIIGPR--QAYLTI--DQ 179

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G   ++KK+F     KV+ L R+S GP +L
Sbjct: 180 GMRHQVKKMFLANGLKVSYLKRLSLGPLRL 209


>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 = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 86/185 (46%), Gaps = 25/185 (13%)

Query: 78  YHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++KP  ++   +D       RST+ D  +LP ++      GRLD ++EGL++LT+ G L 
Sbjct: 7   FNKPYDVLPQFTDRANADSPRSTLSDFIDLPGVYP----AGRLDRDSEGLMVLTDHGRLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG------ 184
             +  P  +  + Y V+  G+ D   L  L+ G+ ++ G+      + ++  KG      
Sbjct: 63  AQISDPRHKMAKTYWVQVEGRPDAAALKALQDGVELKDGLTRPAKALMINEPKGLWPRNP 122

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                    ++W+ + LREG+NR+++++         RLIR   G + L  L  G    +
Sbjct: 123 PIRVRQTIPDSWIELTLREGRNRQVRRMTAAVGHPTLRLIRARIGDWSLDGLAPGQWESL 182

Query: 237 SKKIL 241
               L
Sbjct: 183 PMPAL 187


>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 = 62.0 bits (149), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 96/219 (43%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           +  ++   G  SRR+   +I   RV + G        + + TD +   VDG P     R 
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDAD-LDTDGLVFTVDGTPWPFHARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G   +  DP    +VF  LP+  +   V  VGRLD +T GLLLL++DG   
Sbjct: 62  YVVL-NKPAGYECSR-DPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D  +L+ L+ G+ + G       V  D +      +TV
Sbjct: 120 HAYTSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGEPKPVAAVAADARDPHTLALTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EGK  ++K++    + +V  L R S G   L   LA
Sbjct: 180 --LEGKYHQVKRMVAAASNRVEALHRESVGGLALPADLA 216


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L + +KP G++   S  +    + D +  P  +      GRLD ++EGLLLLTN+G L  
Sbjct: 4   LIILNKPYGVICQFSAHEKHQCLKDFVEKPGFYP----AGRLDTDSEGLLLLTNNGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +  ++      
Sbjct: 60  QIADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTRPAEVRVLEEGEADVLWPRV 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       WV + + EGKNR+++++     +   RL+R++ G   L  L
Sbjct: 120 PPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDL 172


>gi|121606483|ref|YP_983812.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120595452|gb|ABM38891.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
          Length = 278

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 105/244 (43%), Gaps = 29/244 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA+  V+VNG L       V +   IEV     ++  +  
Sbjct: 32  RLNKRMADLGLCSRREADDWIARGWVRVNG-LPAVMGQPVAANARIEVAREAEQQQRQQV 90

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------------VISVGRLDINTE 119
             L +KP+G V+  ++      V    P    R               +   GRLDI++ 
Sbjct: 91  TILINKPVGYVSGQAEDGHEPAVALVQPENRWRECNSRMRWGFEQLRGLAPAGRLDIDSI 150

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L    +   + Y VR               ++KL LL  G+ + G 
Sbjct: 151 GLLVLTQDGRVARQLIGEDSDMEKEYLVRVSYGAENVNVQAAFPREKLALLCHGLSLDGQ 210

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV+    +     +   L+EGK R+I+++ E     V  L R+  G   LG L  
Sbjct: 211 LLRPAQVSWQNPEQ----LRFVLKEGKKRQIRRMCEQVGLFVTGLKRVRIGRVNLGHLPI 266

Query: 231 GSTR 234
           G  R
Sbjct: 267 GQWR 270


>gi|319638581|ref|ZP_07993343.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400330|gb|EFV80989.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 186

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/173 (25%), Positives = 82/173 (47%), Gaps = 23/173 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L + +KP G++   S  +    + D +  P  +      GRLD ++EGLLLLTN+G L  
Sbjct: 4   LIILNKPYGVICQFSAHEKHPCLKDFVEKPGFYP----AGRLDTDSEGLLLLTNNGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +  +  ++      
Sbjct: 60  QIADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTRPAEVRVLEEGEADVLWPRV 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                       WV + + EGKNR+++++     +   RL+R++ G   L  L
Sbjct: 120 PPIRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDL 172


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 43/171 (25%), Positives = 84/171 (49%), Gaps = 23/171 (13%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP G++   S  +   ++  F +LP  +      GRLD ++EGLLLLT+DG L   +
Sbjct: 6   IFNKPYGVICQFSPHEKHKSLKDFIDLPGFYP----AGRLDTDSEGLLLLTDDGWLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----------VIQGICYGDMQVTLD---- 180
             P  +  + Y  +  G  D+ +L  L+KGI           ++ + +G+     +    
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLERLRKGIDLGDFVTRPATVRILKHGETDPLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L  L
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDL 172


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 61/225 (27%), Positives = 93/225 (41%), Gaps = 21/225 (9%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +  ++   G  SRR+   +I   RV V G      A         + DG+     +    
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVNVAG------ASATDPDASFDTDGLVFTVDDTA-- 54

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHAHAYLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +LN L+ G+ + G       V    +   
Sbjct: 114 DDGQFVHGYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVEALHRESIGGFTLPDDLA 216


>gi|300928307|ref|ZP_07143843.1| RNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|300463693|gb|EFK27186.1| RNA pseudouridine synthase [Escherichia coli MS 187-1]
          Length = 167

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/102 (35%), Positives = 58/102 (56%), Gaps = 4/102 (3%)

Query: 68  RKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           RK E   TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LT
Sbjct: 32  RKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLT 89

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           N+G L   L  P  +  ++Y V+  G   QD +  L+ G+ +
Sbjct: 90  NNGALQARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTL 131


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/185 (25%), Positives = 85/185 (45%), Gaps = 25/185 (13%)

Query: 78  YHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++KP  ++   +D       RST+ D  +LP ++      GRLD ++EGL+LLT++G L 
Sbjct: 11  FNKPFDVLPQFTDRQNTDSPRSTLSDFIDLPGVYP----AGRLDRDSEGLMLLTDNGRLQ 66

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG------ 184
             +  P  +  + Y V+  G  D   +  L+ G+ +  G+        +D  +G      
Sbjct: 67  SHISDPKHKMPKTYWVQVEGIPDAAAIRALRDGVELNDGMTRPAKARLIDEPEGLWPRTP 126

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                    + W+ + LREG+NR+++++         RLIR   G + L  L  GS   +
Sbjct: 127 PIRERKTVPDCWLELTLREGRNRQVRRMTAAVGHPTLRLIRARIGDWTLDDLAPGSWDSL 186

Query: 237 SKKIL 241
              +L
Sbjct: 187 PMPVL 191


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 104/243 (42%), Gaps = 23/243 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH------IEVDGVPLR 68
           ++ K IA  G  SR++V ++  Q  +         AA  V+  D       I +DG PL 
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAIT-------DAAGEVLYADDQVDHAAIRIDGEPLD 54

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLL 124
                 + L HKP G   +  D  GR  +++ LP  F      +  VGRLD  T G+LL+
Sbjct: 55  PPPGFSVLL-HKPSGYTCSTKD-TGR-LIYELLPPRFRLRAPVLAPVGRLDRETSGMLLM 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQK 183
           T+DG L   +  P +   +VY V     +  D+  L   G ++++G     +   L+   
Sbjct: 112 TDDGALLHRIISPKSALDKVYDVTLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLG 171

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              A +T  L EG+  +++++F      V  L R   G   L  L AG  R +    L  
Sbjct: 172 ARQARLT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLDAGHWRPLGPDDLEV 229

Query: 244 QLG 246
             G
Sbjct: 230 LFG 232


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 52/179 (29%), Positives = 79/179 (44%), Gaps = 27/179 (15%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           L + HKP G V +H + +G   V+D LP  +     +V S+GRLD +T GLL+LT+   L
Sbjct: 84  LLMLHKPTGFVCSHDEREG-PRVYDLLPPRWRARNPQVTSIGRLDKDTSGLLILTDRTEL 142

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  ++YR      V    ++L   G            + LD +K   A  T
Sbjct: 143 VHTYTSPRHKVPKLYRATLDRDVPASLVDLFAAGT-----------LQLDGEKAPCAPAT 191

Query: 191 VGLR----------EGKNREIKKVF-EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L           EGK  +++++F       V  L R  +G   LG L  G  RE+S+
Sbjct: 192 LRLPAPRVAELVLVEGKYHQVRRMFAAAAGATVLTLHRECFGRLTLGDLKPGEYREISE 250


>gi|213423650|ref|ZP_03356630.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 165

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/119 (28%), Positives = 58/119 (48%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           L+ AA  ++    +  DG PL +    R ++ +KP G V +  DPD  + ++     +  
Sbjct: 24  LKNAAFKLLPEHAVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAY 83

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
           ++ + GRLDI+T GL+L+T+DG  +  +  P     + Y V     V  D      KG+
Sbjct: 84  KLHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGV 142


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 71/143 (49%), Gaps = 21/143 (14%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--I 165
            +S+GRLD  +EGLLLLT DG ++  +   S+++ + Y V+  G + +  +N ++ G  I
Sbjct: 46  TMSIGRLDEMSEGLLLLTTDGKVSAAVT--SSKYEKEYIVQVSGDITEGAINEMRNGLTI 103

Query: 166 VIQGICYGDMQVTL-----------------DTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            I G  Y     T                   ++ G  +W+++ +REGK R+++K+    
Sbjct: 104 PINGKQYDTKPCTAFKLNKTPQFPERQKAIRSSRHGETSWLSISIREGKFRQVRKMTAKV 163

Query: 209 NWKVNRLIRISYGPFQLGTLLAG 231
            +   RL+RI  G + L  +  G
Sbjct: 164 GFPTLRLVRIRIGNYHLEDMQPG 186


>gi|221134604|ref|ZP_03560907.1| RNA pseudouridine synthase family protein [Glaciecola sp. HTCC2999]
          Length = 211

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/176 (26%), Positives = 86/176 (48%), Gaps = 7/176 (3%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           +  V   K++R  + LYHKP+G+  T ++   +  + D +    +R+  VGRLD  +EGL
Sbjct: 26  ISAVAADKSDRVYV-LYHKPVGITCT-TERHIKGNIIDAIGH-KTRIFPVGRLDKPSEGL 82

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++LT+DG +   +        ++YRV     +    + ++  G+ I        +V    
Sbjct: 83  IILTSDGDIVNKILRAENAHDKLYRVTVDKPITSKFIEIMSGGVPILDTVTKPCKV---K 139

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           Q G  ++  + L +G NR+I+++ E+  + V RL+R       L  L  G  R ++
Sbjct: 140 QIGKFSF-DITLTQGLNRQIRRMCEYCGYDVKRLVRTRIMHLTLAKLPVGQWRNLT 194


>gi|241662183|ref|YP_002980543.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864210|gb|ACS61871.1| pseudouridine synthase [Ralstonia pickettii 12D]
          Length = 248

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 98/229 (42%), Gaps = 25/229 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLW 76
           +++   G  +RR  + ++    V +NG+ +E     V +   + +VDG   R A   R +
Sbjct: 11  RILQSQGFGTRRYCKDLVLAGLVCINGVEMESPDALVDTAGLVLDVDGE--RWAYHARAY 68

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
           L  +KP G V     P    +V+  LP       V  VGRLD +T GLLLLT+DG     
Sbjct: 69  LMLNKPAG-VECSQKPKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVHT 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT--- 190
           +  P  Q  +VY +     V + ++  L  G+++            + +  + AW     
Sbjct: 128 ITSPRHQVPKVYEITTAEPVTEAQIAQLCAGVLLAD----------ENENVAAAWAERVG 177

Query: 191 -----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + L +GK  ++K++       V  L R + G   LG L  G  R
Sbjct: 178 THHLRMALTQGKYHQVKRMVAAAGNHVVGLHRSAIGGLSLGDLAPGEWR 226


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 109/249 (43%), Gaps = 34/249 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+SK ++  G+ SRRE +  I    V V+G  +      +     IE+       + ER 
Sbjct: 332 RLSKRMSELGLCSRREADEWIPHGWVLVDGKPVTELGSRIRPDAEIEIMQEARSEQGERV 391

Query: 74  RLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINT 118
            + L +KP+G V+  ++                +G  T     P     +   GRLDI++
Sbjct: 392 TV-LLNKPVGYVSGQAEDGYEPAAVLFTPENQWEGDPTRKRFAPWQRKSLAPAGRLDIDS 450

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH-----------GQVDQDKLNLLKKGI 165
            GLL+LT DG +AR L  E  + +   + RV +H            +   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 SLDGVPLKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLQVVGLKRVRMGRVVL 566

Query: 226 GTLLAGSTR 234
           G L  G  R
Sbjct: 567 GDLPPGKWR 575


>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 = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 98/224 (43%), Gaps = 3/224 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR +V R +    V V+  +++  A  +     +  DG   ++    R
Sbjct: 2   RLDKFLSQQLGISRNDVGRELRAGLVTVDNEVIKTGAYKLKLDQQVAYDGTIFQQLNGPR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G V +  DP   + ++     +  ++ S GRLDI+T GL+LLT+DG  +  +
Sbjct: 62  YFMLNKPQGYVCSTDDPSNPTVLYFIDEPVAHKLHSAGRLDIDTTGLVLLTDDGQWSHRI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     + ++       GI + G         L+  +     +T+   
Sbjct: 122 TSPKHHCEKTYLVTLEQPISEETEEKFLAGIQLNGEKTLTKPAKLEIIEPQIVRLTIS-- 179

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVS 237
           EG+  ++K++F      V  L R   G   L   L AG  R ++
Sbjct: 180 EGRYHQVKRMFAAVGNHVVELHRERIGEIYLDPALEAGEYRALT 223


>gi|311694975|gb|ADP97848.1| RNA pseudouridylate synthase [marine bacterium HP15]
          Length = 175

 Score = 61.6 bits (148), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 39/152 (25%), Positives = 71/152 (46%), Gaps = 18/152 (11%)

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           ++P I+      GRLD ++EGLLLLT +G L   +  PS +  + Y V+  G + ++ L 
Sbjct: 2   HIPGIYP----AGRLDYDSEGLLLLTAEGSLQHRIASPSLKMPKTYWVQVEGNISEEALR 57

Query: 160 LLKKGIVIQG--------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            L  G+ ++                 +  +           +W+ + + EGKNR+++++ 
Sbjct: 58  HLASGVQLKDGLTRPAKADRMPAPTVWPRVPPVRHRDNIPTSWIELTITEGKNRQVRRMT 117

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +   RLIR   G + L  L +G+ R V+
Sbjct: 118 AAVGFPTLRLIRYRIGDWTLDGLESGAHRTVT 149


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 109/238 (45%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  V    G ++   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAVTDAQGEVVY--ADDQVEHDAIRIDGEPLDPPPGF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SR---VISVGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F SR   +  VGRLD +T G+LL+T+DG 
Sbjct: 60  SLLL-HKPSGYTCSTKD-TGR-LIYELLPPRFRSRAPVLAPVGRLDRDTSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY +     +  D+  L   G ++++G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYDITLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGLREAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLLLDGLPSGQWRALEASDLEVLFG 232


>gi|167585734|ref|ZP_02378122.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 238

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 67/223 (30%), Positives = 99/223 (44%), Gaps = 10/223 (4%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLWLYHKP 81
           G  SRR+   ++   RV V G            TD   + VDGV      R  L L +KP
Sbjct: 11  GFGSRRQCRGLVDAARVAVAGAPCTDPDAE-FDTDGLVVSVDGVAWPFHARAYLAL-NKP 68

Query: 82  IGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL++DG        P  
Sbjct: 69  AGYECSR-DPQHHASVFSLLPTPLVARGVQCVGRLDQDTTGLLLLSDDGQFVHAYTSPKR 127

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +  + Y       +D  +L+ L+ G+ + G       V  D +      +TV   EGK  
Sbjct: 128 KVPKTYVATVRHPLDDAQLHALRTGVQLHGEPKPIAAVAADARDAHVLALTV--LEGKYH 185

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           ++K++    + +V  L R S G F L   L  G+ R +S+  L
Sbjct: 186 QVKRMVAAASNRVEALHRESIGGFALPADLEPGAWRWLSEADL 228


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 87/180 (48%), Gaps = 25/180 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD--PDG--RSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           +RL  ++KP  ++   +D   +G  R+T+ D  + P ++      GRLD ++EGL+LLT+
Sbjct: 2   SRLIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDCPGVYP----AGRLDRDSEGLMLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           +G L   +  P  +  + Y V+  G   +D L  L++G+ ++       +  L ++    
Sbjct: 58  NGRLQAWISDPKHKLEKTYWVQVEGIPTEDALKALRQGVDLKDGMTRPAKAELISEPAQL 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                          AW+ + + EGKNR+++++     +   RLIR + G + L  L  G
Sbjct: 118 WARTPPIRERKSVPTAWLELKISEGKNRQVRRMTAAMGYPTLRLIRYAIGAWTLDGLAQG 177


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 59/92 (64%), Gaps = 9/92 (9%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEVDG--VPLR 68
          +++ K++AR+G  SRRE+E  + + R+ ++G    L +R  ++V ST  I +DG  + +R
Sbjct: 9  EKLQKILARSGHGSRREIEGYLQEGRISIDGTKAKLGDR--IDVTSTAKIRLDGRILNIR 66

Query: 69 KAER--TRLWLYHKPIGLVTTHSDPDGRSTVF 98
          +A++   R+  Y+KP G + T SDP GR TVF
Sbjct: 67 EAQKDVCRVLAYYKPEGELCTRSDPQGRPTVF 98


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 72/144 (50%), Gaps = 19/144 (13%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--- 167
            GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ +   
Sbjct: 15  AGRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDG 74

Query: 168 -----QGICYGDMQVTLDTQKG-------SNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
                + I   + +   D             +W+ + + EG+NR+++++     +   RL
Sbjct: 75  MTLPAKAIKVSEPEWLWDRDPPVRYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRL 134

Query: 216 IRISYGPF---QLGTLLAGSTREV 236
           IR   G     QLG L  G T+E+
Sbjct: 135 IRTKIGTIDLVQLG-LQPGETKEI 157


>gi|303285788|ref|XP_003062184.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456595|gb|EEH53896.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 244

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 59/244 (24%), Positives = 110/244 (45%), Gaps = 33/244 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL--ERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +A+ G+ASRR  E +I   RV VNG+++   +  V +          V     E 
Sbjct: 1   RLGKALAQLGVASRRASEDLIFAGRVAVNGVVVTAPQHHVVLADDVVAVDGKVIQGGVEE 60

Query: 73  TRLWLY---HKPIGLVTTHSD----PDGRST------------VFDNLPSIF-------- 105
           TR  LY   +KP G +  ++     P G+              +FD   + +        
Sbjct: 61  TREHLYFLLNKPKGYICANAKSPNKPPGKGERGGGASGKLVMDLFDEWKAAWRKKHPKRL 120

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R+ +VGRLD+NT G+LL+T DG   + +  P ++ ++ Y +    +  + ++  +  G
Sbjct: 121 PPRLFTVGRLDVNTTGMLLVTTDGQWCQRVAHPKSEVVKSYVLTASARPTKAQIRAMAAG 180

Query: 165 IVIQGICYGDMQV-TLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             + G     + V ++D  +  G    V V + +G+NRE++++         +L R+  G
Sbjct: 181 AEVDGAFVKPVNVRSMDNDRDGGPPNRVLVEVVDGRNREVRQLASSAGVDCKKLKRVRVG 240

Query: 222 PFQL 225
             ++
Sbjct: 241 GLRM 244


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/186 (25%), Positives = 88/186 (47%), Gaps = 27/186 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           RL L++KP G+++  +D  G             + ++P ++      GRLD ++EGLL+L
Sbjct: 3   RLILFNKPYGVLSQFTDRGGADGTGGGRATLSDYIDVPGVYP----AGRLDKDSEGLLVL 58

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-------------IQGIC 171
           T+DG L   +  P  +  + Y  +  G+ D   L+ L +G+              I    
Sbjct: 59  TDDGALQARISSPKHKMPKTYLAQVEGEPDDAALDALARGVTLNDGPTRPATVRRIGAPK 118

Query: 172 YGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             D    +  +K   ++W+ + + EG+NR+++++         RL+R   G +++G L  
Sbjct: 119 LWDRDPPVRYRKSVPDSWLELTITEGRNRQVRRMTAAVGHPTLRLVRWRIGGWEIGDLAV 178

Query: 231 GSTREV 236
           G+ REV
Sbjct: 179 GAWREV 184


>gi|126172676|ref|YP_001048825.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125995881|gb|ABN59956.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 233

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/218 (28%), Positives = 95/218 (43%), Gaps = 13/218 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++    R      I    V VNG +    A+ V   + + ++  PL     +R
Sbjct: 2   RLDKFLCKSTDLDRDAASVAIINGSVTVNGAIATDCAMQVHENNAVCLNEKPLMP-RPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLA 131
            ++ HKP    T  S+ DG      +L  I   F   I VGRLD +T GL+LLT+DG  +
Sbjct: 61  YFMLHKPAD--TLCSNVDGAYPSLFHLLDIEHAFDLHI-VGRLDADTTGLVLLTDDGRWS 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P  Q  +VYRV     +D +           G+ +QG     +  TL  Q+    
Sbjct: 118 FNIISPQYQCEKVYRVTLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDEK 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            V + L EGK  ++K++F     KV  L R   G   L
Sbjct: 176 TVLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL 213


>gi|300691607|ref|YP_003752602.1| pseudouridine synthase [Ralstonia solanacearum PSI07]
 gi|299078667|emb|CBJ51325.1| Pseudouridine synthase [Ralstonia solanacearum PSI07]
          Length = 641

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 70/255 (27%), Positives = 113/255 (44%), Gaps = 46/255 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+  +P  ++E+  
Sbjct: 390 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEI--LPAARSEQGE 447

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--------------------VISVG 112
               L HKP+G V+  ++ DG    ++   ++F+                     +   G
Sbjct: 448 RVTVLLHKPVGYVSGQAE-DG----YEPAAALFTAENQWEEDPTHKRFAAWQHKGLAPAG 502

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVDQDK--------LN 159
           RLDI++ GLL+LT DG +AR L    +   + Y VR       G V+ D         L 
Sbjct: 503 RLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDVSKVFPEELLE 562

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI 
Sbjct: 563 KLRHGLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIR 618

Query: 220 YGPFQLGTLLAGSTR 234
            G   LG L  G  R
Sbjct: 619 MGRVVLGDLPVGKWR 633


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 75/167 (44%), Gaps = 21/167 (12%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G ++  S+   R T+    ++P ++      GRLD ++EGLLLLT+DG L   +  
Sbjct: 7   NKPFGTMSQFSEHPTRPTLASCVSVPGVYP----AGRLDADSEGLLLLTDDGVLQARIAD 62

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------ 184
           P  +  + Y  +  G  D D L  L+ G+ +        +V                   
Sbjct: 63  PRHKLEKTYLAQVEGIPDADALARLRAGVDLGDFVTRPAKVRAVEAPDWLWPRHPPVRFR 122

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                +W+ + +REGKNR+++++         RLIR+  G   L +L
Sbjct: 123 AAIPTSWLELKIREGKNRQVRRMTAAVGLPTLRLIRVGIGALDLRSL 169


>gi|255654429|ref|ZP_05399838.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-23m63]
          Length = 141

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 48/136 (35%), Positives = 69/136 (50%), Gaps = 10/136 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G V+  +D     TV D  +L  +      VGRLD +TEGLL+LTNDG L
Sbjct: 65  IYLMM-NKPDGYVSATTD-KYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 A-RVL----ELPSTQW 141
           + RVL     +P T +
Sbjct: 123 SHRVLSPKKHVPKTYY 138


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/219 (28%), Positives = 95/219 (43%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           +  ++   G  SRR+   +I   RV + G          + TD +   VDG P     R 
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDAE-LDTDGLVFTVDGTPWPFHARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP G   +  DP    +VF  LP+  +   V  VGRLD +T GLLLL++DG   
Sbjct: 62  YVVL-NKPAGYECSR-DPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D  +L+ L+ G+ + G       V  D +      +TV
Sbjct: 120 HAYTSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGEPKPVAAVAADARDPHTLALTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              EGK  ++K++    + +V  L R S G   L   LA
Sbjct: 180 --LEGKYHQVKRMVAAASNRVEALHRESVGGLALPADLA 216


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 108/238 (45%), Gaps = 13/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  +    G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAITDAQGEVLY--ADDQVEHDAIRIDGEPLDPPAGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F   + V++ VGRLD  T G+LL+T+DG 
Sbjct: 60  SLLL-HKPSGYTCSTKD-TGR-LIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY +     +  ++  L   G +++ G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYDITLAEDLHGEEAALFASGSLLLDGETKPLLPAELEVLGPRQAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEANDLEVLFG 232


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 108/241 (44%), Gaps = 30/241 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A +   +R   +R + +  V VNG L ++AA +V  TD I   G  L     TR
Sbjct: 2   RLDRFLAESTELTRGLAKRALIRGEVSVNGELEKKAARHVQETDRITWLGERLSLVG-TR 60

Query: 75  LWLYHKPIGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP G+  T       R+    ++P +  R+  VGRLD+ T GLLL+T+DG  +  
Sbjct: 61  YIMLHKPEGVECTARRGLYPRAVDLLDVPKV-ERLQPVGRLDVETTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQG----------ICYGDMQVTL 179
           +  P  +  + Y  R    ++ D+    +    +GIV++G           C  D +V L
Sbjct: 120 ITSPRRRCPKAYVARLARPLEGDEARRAMQAFAEGIVLEGEDAPTRPAELTCLDDHRVRL 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
                        + EG+  +++++       V  L R S G   L  TL  G  RE++ 
Sbjct: 180 ------------VIDEGRYHQVRRMLAAIGNHVETLHRESVGALVLDDTLEPGEWRELTP 227

Query: 239 K 239
           +
Sbjct: 228 E 228


>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 = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/162 (27%), Positives = 75/162 (46%), Gaps = 16/162 (9%)

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           G +T+ D +P     V   GRLD ++EGLL+LTNDG L   L  P ++  + Y V+  G 
Sbjct: 9   GDATLADFIP--VKDVYPAGRLDKDSEGLLVLTNDGILQARLTQPKSKSAKTYWVQVEGI 66

Query: 153 VDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQ-------------KGSNAWVTVGLREGKN 198
             ++ L  L+ G+ ++ G     +   +D                    W+++ L EG+N
Sbjct: 67  PSENALKSLRNGVELKDGWTLPAIVEIMDEPAIWDRNPPIRHRPSVPTTWLSITLTEGRN 126

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           R+++++         RL+R   G + +  L  G  REV   +
Sbjct: 127 RQVRRMTAAVGHPTLRLVRYQMGHWTVDGLQPGEWREVPPPV 168


>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 = 61.2 bits (147), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 52/195 (26%), Positives = 86/195 (44%), Gaps = 41/195 (21%)

Query: 77  LYHKPIGLVTTHSDPDGRSTV----FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L HKP G+++  +  +         F + P +++     GRLD ++EGLL+LT++G L +
Sbjct: 5   LLHKPYGVLSQFTREENSRWASLQDFVDTPDVYA----AGRLDADSEGLLVLTSNGRLQQ 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------------ICYGD-- 174
            L  P     R Y V+  G     +L  L+ GI +QG                   GD  
Sbjct: 61  QLTDPRFGHWRTYWVQVEGTPQPHQLQQLRDGITVQGHRTRPAKAAWLKAEAIPTIGDRV 120

Query: 175 ----MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQ 224
                + T+ T      W+ + L EG+NR+++++         RL+R +        P  
Sbjct: 121 PPIRYRATIPTH-----WLEISLTEGRNRQVRRMTAAVGLPTLRLVRHTIDLMDGGTPLT 175

Query: 225 LGTLLAGSTREVSKK 239
           L  L  G++R VSK+
Sbjct: 176 LTGLEPGASRAVSKE 190


>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 = 61.2 bits (147), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/169 (30%), Positives = 80/169 (47%), Gaps = 21/169 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   
Sbjct: 66  RVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDCDSEGLLVLTNDGVL--- 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVT 190
                 Q LR         V  +    L  GI I       +       + +    +W+ 
Sbjct: 121 ------QALRT-------GVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLK 167

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V L EG+NR+++++         RLIR S G + L  L  G  RE++++
Sbjct: 168 VTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQE 216


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/144 (27%), Positives = 71/144 (49%), Gaps = 19/144 (13%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V ++ L  L+KG+ ++  
Sbjct: 37  AGRLDMDSEGLVFLTDHGGLNQYITNPANKKFKTYLVQVDGDVTEEALEQLRKGVELKDG 96

Query: 171 CYGDMQVTLDTQKG---------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
                + +   Q                   +WV + + EG+NR+++++     +   RL
Sbjct: 97  MTLPAEASKVEQPEWLWERDPPVRFRASVPTSWVEISICEGRNRQVRRMTAAVGFPTLRL 156

Query: 216 IRISYGPF---QLGTLLAGSTREV 236
           IR   G     Q+G L  G T+E+
Sbjct: 157 IRTKIGAIDLVQMG-LQPGETKEI 179


>gi|261856640|ref|YP_003263923.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837109|gb|ACX96876.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 180

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 66/139 (47%), Gaps = 15/139 (10%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V + GRLD ++EGLLLLT+DG L   L  P  +  + Y  +  G V    L  L+ G+V+
Sbjct: 35  VYAAGRLDRDSEGLLLLTDDGRLQAQLTQPDAKQPKTYLAQVDGDVTAQALAQLRAGVVL 94

Query: 168 QGICYGDMQVTLDTQKG---------------SNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +       +  +  +                   +W+ + + EGKNR+++++     +  
Sbjct: 95  KDGKTRPAEAHVVPEPDWLWPRTPPIRVRKNIPTSWIELTITEGKNRQVRRMTAAVGFPT 154

Query: 213 NRLIRISYGPFQLGTLLAG 231
            RLIR++ G   LG+L  G
Sbjct: 155 LRLIRVAVGSHNLGSLQPG 173


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 36/129 (27%), Positives = 63/129 (48%), Gaps = 13/129 (10%)

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           +  +  VG LD +T GLLLLTNDG L   L  P     ++YR +  G ++++ +     G
Sbjct: 29  YQGISPVGCLDKDTTGLLLLTNDGQLNHELLAPGKHVDKIYRAKIAGPINEETVKTFASG 88

Query: 165 IVIQGICYGD--------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           + +     GD        +++    +K   + + + ++EGK  +IK++F     K   L 
Sbjct: 89  MTL-----GDDTKLKPATLKILSQDEKEDTSQIEIKIQEGKYHQIKRIFAAVGMKAIELD 143

Query: 217 RISYGPFQL 225
           RI+ G  +L
Sbjct: 144 RIAMGNLRL 152


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 50/213 (23%), Positives = 99/213 (46%), Gaps = 7/213 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    ++++G ++      + +   + +V G      E+  
Sbjct: 3   LEKMLQSQGFGSRKHCQQLIKNAAIEIDGQIITDPKYKLKLDALNYKVHGKSFEYREKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +H       +VFD    +     +  VGRLD +T GLLLLT+DG   +
Sbjct: 63  IAL-NKPQGYECSHQ-ATHHFSVFDLFDDVLLNRGIQCVGRLDQDTTGLLLLTDDGQFLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VYR++    V  +++  L++G+ ++    G    T D ++ +   + + 
Sbjct: 121 ALTHPKKHVAKVYRMKTADPVTDEQVQQLEQGVELRNE-KGSFAAT-DVKRLAECELQMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           + +G   ++K++      KV  L R   G   L
Sbjct: 179 VHQGVYHQVKRMLAAVGNKVESLHRQQIGALDL 211


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 88/187 (47%), Gaps = 33/187 (17%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            RL L++KP G+++  + P+GR     +   LP +++     GRLD ++EGLL+LT+DG 
Sbjct: 2   ARLILFNKPYGVLSQFT-PEGRWQGLRDHLALPGVYA----AGRLDADSEGLLILTDDGP 56

Query: 130 L-ARVLE----LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             AR+ +    LP T W +V      G      L  L++G+ +           +  +  
Sbjct: 57  TQARIADPRHKLPKTYWAQV-----EGAPADADLEPLRRGVDLGDFVTRPAGARIIAEPP 111

Query: 185 S---------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           S                AW+ + + EGKNR+++++     +   RLIR + G + L  L 
Sbjct: 112 SLWPRNPPIRFRANIPTAWIELVIAEGKNRQVRRMTAKVGFPTLRLIRAAVGEWNLNGLQ 171

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 172 PGQWKEL 178


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/89 (34%), Positives = 50/89 (56%)

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           PS +  R Y VR  G++D  K+  L +G+ ++        V+    +G N W  V L EG
Sbjct: 3   PSREVEREYAVRVFGEIDDAKIRQLTRGVQLEDGPASFRSVSYRGGEGINQWYNVSLTEG 62

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +NRE+++++E    +V+RLIR+ YG   L
Sbjct: 63  RNREVRRMWEAVGVQVSRLIRVRYGDIDL 91


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 46/173 (26%), Positives = 81/173 (46%), Gaps = 17/173 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L +KP  ++   +D +GR T+   +P     V + GRLD ++EGL++LT+DG L   
Sbjct: 3   RIILLNKPFDVLCQFTDREGRRTLAVYVPE--PGVYAAGRLDRDSEGLVVLTDDGRLQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG-------- 184
           +  P  +  + Y V+  G  D   L  L +G+ ++ G+        +D   G        
Sbjct: 61  ISDPKHKMSKTYWVQVEGVPDAQALKALAEGVELKDGLTLPARVKIIDEPPGLWPRDPPI 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   +W+ + + EG+NR+++++         RLIR   G + L  L  G
Sbjct: 121 RVRQSIPTSWLELTISEGRNRQVRRMTAAVGHPTLRLIRYRVGSWTLDGLGPG 173


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 86/180 (47%), Gaps = 27/180 (15%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP G+ +  SD    +  F  L   F+   +   GRLD  +EGLLLLT+DG + + +
Sbjct: 8   LFNKPYGVQSQFSD--DANNKFAPLSQFFTDKSLRVAGRLDATSEGLLLLTSDGQVNKAI 65

Query: 135 ELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTL 179
             P       +  + Y V+  G    ++L  L++G++          ++ I   D+ + L
Sbjct: 66  THPPKANAGRKQGKTYLVQVEGIPSNEQLEQLRQGVLLKDGQTLPAEVKHISEEDLPMPL 125

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   + +   ++W+ + + EGKNR+++++         RLIR S   F+LG L  G
Sbjct: 126 WQRDPPIRERKSVPDSWLMMTIYEGKNRQVRRMTAHVGLPCLRLIRWSAAGFELGNLAVG 185


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 45/160 (28%), Positives = 75/160 (46%), Gaps = 21/160 (13%)

Query: 77  LYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +KP G ++  +   G     + D +P    RV + GRLD ++EGLL+LT+ G L   L
Sbjct: 12  LLNKPYGFLSQFTPEPGSQWRCLADLIP--IPRVYAAGRLDADSEGLLVLTSHGRLQHRL 69

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------ICYGDMQVTLDT---- 181
             P     RVY V+  G   + +L  L  G++I+G            G++   +      
Sbjct: 70  TNPHLSHWRVYWVQVEGSPSESQLQKLASGVIIKGKRTRPALASWLKGNVAPIVREREPP 129

Query: 182 ----QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
               Q    +W+ + L+EG+NR+++++         RLIR
Sbjct: 130 IRVRQSIPTSWLELKLKEGRNRQVRRMTAAVGLPTLRLIR 169


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 55/188 (29%), Positives = 86/188 (45%), Gaps = 28/188 (14%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++HKP G VT   D D   TV D    + + R+  VGRLD  T GLLL+T+DG   + L
Sbjct: 26  YMFHKPFGCVTARRD-DRYPTVMDYFEELQNDRLSPVGRLDRETTGLLLITDDGIFNQKL 84

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------------ICYGDMQVTL 179
             PS    + Y     G +  + ++ L+ G++++G                   D+  TL
Sbjct: 85  THPSYHKEKTYEFTLLGDLTPELVHKLETGVILKGADTLTAPAKITVTGHAVMSDILSTL 144

Query: 180 ------DTQKG-SNAWVTVG---LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TL 228
                 D  K   +  +T G   + EGK R+I+++ +  +  V  L RIS G   L   L
Sbjct: 145 PEEIQKDIHKNRPDHPITYGIITISEGKKRQIRRMMKSVHCCVIELKRISIGDIVLDKAL 204

Query: 229 LAGSTREV 236
             G  +E+
Sbjct: 205 CPGEWKEI 212


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 87/181 (48%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRL--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG-------- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ +  G+      + +   +         
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPATAIKVSEPEWLWERNPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTRE 235
                   +WV + + EG+NR+++++     +   RLIR   G     QLG L  G  +E
Sbjct: 120 RYRANIPTSWVEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLG-LRPGDVKE 178

Query: 236 V 236
           +
Sbjct: 179 I 179


>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 = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 49/182 (26%), Positives = 83/182 (45%), Gaps = 22/182 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +L HKP G ++       R   +   L       +++GRLD ++EGLLLLT DG ++ ++
Sbjct: 5   FLIHKPYGYLSQFIYELKRPKKLLGELYDFPGNTMAIGRLDEDSEGLLLLTTDGMMSEIV 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVTL------- 179
              S +  + Y  +  G + ++ +  LK  + I           C   +  T+       
Sbjct: 65  R--SKKVEKEYYAQVDGLITEEAIEKLKNRVEIGFNGKKYLTKKCNAFILETIPNLGERG 122

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               D + G  +WV++ L EGK R+++K+     +   RL+R+  G   L  L AG   E
Sbjct: 123 KKIRDERHGPTSWVSITLTEGKFRQVRKMTSAVGFPTLRLVRVRVGNIHLNDLKAGEVLE 182

Query: 236 VS 237
           VS
Sbjct: 183 VS 184


>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 = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 54/213 (25%), Positives = 100/213 (46%), Gaps = 10/213 (4%)

Query: 54  VMSTDHIEVDGVPL--RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
           V   D + V+G P+  RKAE   L   +KP+G++T+      R+ + D + +   R   +
Sbjct: 8   VFVGDSVSVNGQPIAPRKAEDLVLIALNKPVGVITSMGK-QVRNNIGDWV-NHSQRTFPI 65

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           GRLD +++GL+ LTN G L   +        + Y V     +  + +  +  G+ I G  
Sbjct: 66  GRLDKDSQGLIFLTNHGELVNKILRAGNNHQKEYLVSVDRPITDEFIQAMGAGVPILGTV 125

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                V    +K ++  + + L +G NR+I+++ ++F ++V +L R+      L  L  G
Sbjct: 126 TKPCLV----EKIASQILRITLVQGLNRQIRRMCKYFGYQVTKLERVRIMNINLHGLALG 181

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
             R+ + +  RE     L+E +      P  +S
Sbjct: 182 EWRDFTDEERRELF--RLIEHSSSEASQPATTS 212


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 47/153 (30%), Positives = 72/153 (47%), Gaps = 23/153 (15%)

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 QGICYGDMQVT-LDT----------------QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +G      + T LD+                +    +W+++ LREG+NR+I+++      
Sbjct: 61  KGQRTRPARATSLDSSFWFDLPERTPPIRERRTIPTSWLSISLREGRNRQIRRMTAAVGL 120

Query: 211 KVNRLIRISYG------PFQLGTLLAGSTREVS 237
              RLIR S        P  L  L  G  R V+
Sbjct: 121 PTLRLIRRSIDLMDGGPPLSLEGLAPGQWRPVN 153


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 51/186 (27%), Positives = 82/186 (44%), Gaps = 21/186 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +  +KP  +V+    PD    + D          +VGRLD N+EGLLLLT +  + R+
Sbjct: 7   RYFAINKPYNMVSQFISPDKVRLLGDLDFDFPEGTHAVGRLDNNSEGLLLLTTNKRVTRL 66

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           L        R Y V     V Q+ +  L+ G+ I+ I  G   VT   +           
Sbjct: 67  LFESEQPHKRAYLVMVKNIVTQETIEKLRNGVTIR-IKGGVDWVTTPCEAEIVEKPAYIA 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|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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 59/221 (26%), Positives = 100/221 (45%), Gaps = 23/221 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K + ++   ++ E    I    V VN   +L E   V+  +T  +  D + LR    
Sbjct: 2   RLDKYLCKSTDLTKSEAIERIHNGEVSVNSEFVLDESTQVHESNTILLNGDALTLRAF-- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLL 124
            R  L HKP G + ++ D        +  PS+F        S +   GRLD +T GL+L+
Sbjct: 60  -RYILMHKPAGTICSNID--------EVYPSLFNYLELDKVSELHIAGRLDADTTGLVLI 110

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG  +  + LP+    +VYRV     +  D  +  K G+ +QG    ++    + +  
Sbjct: 111 TDDGRWSFNITLPTKSCKKVYRVTLSRDIKDDVADKFKAGVPLQG--EKNLTRPAELEVI 168

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           S   V + + EGK  ++K++F     +V  L R   G  +L
Sbjct: 169 SPKEVLLTITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL 209


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 97/213 (45%), Gaps = 19/213 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-------HIEVDGV 65
           P R+ K I+      R + +  I ++  KVNG ++      V  +D        +EV G 
Sbjct: 4   PCRLDKFISHLTELPRTKTKAGIKRKYAKVNGTVITSFDYQVTESDVVLWQDKQLEVLG- 62

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
                   R ++ +KP G V   SD +   TV + L   + S++   GRLD++T GL+L+
Sbjct: 63  -------DRYFMLNKPEGYVCATSD-ELHQTVLELLDEPVMSKLHIAGRLDLDTTGLVLI 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG  +  +  P  Q  + Y V     +  D L  L+ G+ + G   G  Q  +  +  
Sbjct: 115 TNDGEWSHKVTSPKYQKYKTYLVETLEPMTDDALQELRDGVQLHGE-KGLTQPAI-VELL 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +   V + + EGK  ++K++F     KV  L R
Sbjct: 173 AEYSVRISICEGKYHQVKRMFAAVGNKVEVLHR 205


>gi|253996871|ref|YP_003048935.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253983550|gb|ACT48408.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 245

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 51/213 (23%), Positives = 94/213 (44%), Gaps = 7/213 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + +++   G  SR+    ++  + V VNG L +       +   H  + G      E++ 
Sbjct: 10  IERILHNQGFGSRKLCRILVINEEVTVNGELCDDPDTTFELENLHYTIKGEAWVYHEKSY 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L + HKP     +H       T++  LP       V  +GRLD +T GL+L+++DG    
Sbjct: 70  L-MMHKPSNYECSHK-TQHHPTIYSLLPHPLVERGVQCIGRLDEDTTGLILISDDGQFIH 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY V     V  +++  + KG  +Q +        L   K ++  + + 
Sbjct: 128 RMSSPKHKVPKVYEVTCKHAVSDEQIAHILKG--VQLVDEDAPIAALACTKINDHVIHMT 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           L EGK  ++K++    + +V  L RI  G  +L
Sbjct: 186 LAEGKYHQVKRMVAAISNRVEALKRIKIGRLEL 218


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 45/185 (24%), Positives = 87/185 (47%), Gaps = 23/185 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----ISVGRLDINTEGLLLLTNDG 128
           R+ L++KP G+++  +D   + T     P++ + +        GRLD ++EGL++LT+ G
Sbjct: 3   RVILFNKPFGVLSQFTD---KGTEGSPRPTLSAYIDEKGFYPAGRLDRDSEGLMVLTDSG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG--- 184
            L   +  P  +  + Y V+  G  D+  L  L+ G+ ++ G         +D  +    
Sbjct: 60  PLQARISHPKYKLAKTYWVQVEGTPDEQALAALRSGVTLKDGKTAPAKARLMDPPEPLWD 119

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       +AW+ + + EG+NR+++++         RLIR   G ++L  L  G+ 
Sbjct: 120 RDPPVRFRKSVPDAWLEITITEGRNRQVRRMTAHVGLPTLRLIRARVGDWELHKLQPGAW 179

Query: 234 REVSK 238
           R  S+
Sbjct: 180 RFSSE 184


>gi|303275424|ref|XP_003057006.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461358|gb|EEH58651.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 305

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 116/242 (47%), Gaps = 13/242 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ ++++R G  +R E +R     RV ++G  + RA   V   D + +DG P  +A 
Sbjct: 53  APERLDRLLSRLGYCTRAEAKRWARDGRVLLHGEPVARAEAKVTPRD-VLIDGEPA-EAP 110

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
              L L HKP G V  H   +G S V+D LP  +      V ++GRLD +T GLLLLT+D
Sbjct: 111 DGLLALMHKPRGRVCGHDASEGPS-VYDLLPERWRARRPGVETIGRLDKDTTGLLLLTDD 169

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQG---ICYGDMQVTLDTQK 183
           G L   L  P  +  +VY +     + +D ++L   G + + G    C     +  +   
Sbjct: 170 GDLLHRLASPKKRVEKVYELVVDAPIPRDAVDLFASGSLTLTGEKKPCLPAKLIVSERAD 229

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            +    ++ + EGK  ++K++      +V  L R S+G   L    L  G  R +S++  
Sbjct: 230 HNRTRASLSVTEGKFHQVKRMMRAVGCEVTALHRESFGGMALSRMELREGEVRVLSRETA 289

Query: 242 RE 243
            E
Sbjct: 290 LE 291


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 57/205 (27%), Positives = 97/205 (47%), Gaps = 39/205 (19%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           R  +++KP  ++   +D +G ST        + N+P+++     VGRLD+++EGLLLLT+
Sbjct: 4   RYIVFYKPYNVLCQFTD-EGNSTTSRQTLKDYINIPNVYP----VGRLDLDSEGLLLLTD 58

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-- 184
           DG L   L        R Y V+     D+  LN L++G+ I+        V +   +   
Sbjct: 59  DGQLQHRLAHRKFAHPRTYWVQVENIPDEPALNRLREGVKIKDYQTRKAWVKVFPTEPPL 118

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQL 225
                           W+ + L EG+NR+++++     +   RL+R++ G       FQL
Sbjct: 119 PPRNPPIRYRKNIPTCWLEITLTEGRNRQVRRMTAAVGYPTLRLVRVAMGIGKGKNGFQL 178

Query: 226 GT--LLAGSTREVS---KKILREQL 245
               L  G  R+V+   +K+L EQL
Sbjct: 179 DLKGLEPGQWRDVTDIERKVL-EQL 202


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/180 (25%), Positives = 85/180 (47%), Gaps = 25/180 (13%)

Query: 73  TRLWLYHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTN 126
           TRL  ++KP  ++   +D       R+T+ D  +LP ++      GRLD ++EGL+LLT+
Sbjct: 2   TRLIRFNKPYDVLPQFTDRGSTDSPRATLSDWIDLPGVYP----AGRLDRDSEGLMLLTD 57

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG- 184
            G L   +  P  +  + Y V+  G  D   +  L +G+ ++ G+        +   +G 
Sbjct: 58  QGRLQAWISDPQHKMPKTYWVQVEGTPDAAAITALAEGVELKDGLTRPAKARLIAEPEGL 117

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + +REG+NR+++++         RLIR + G + L  L  G
Sbjct: 118 WARNPPIRVRKSVPDSWIELTIREGRNRQVRRMTAAVGHPTLRLIRAAIGAWTLNGLGQG 177


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 113/251 (45%), Gaps = 38/251 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+  +P  ++E+  
Sbjct: 426 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEI--LPAARSEQGE 483

Query: 75  --LWLYHKPIGLVTTHSDPDG---RSTVF--------DNLPSIFSR-----VISVGRLDI 116
               L HKP+G V+  ++ DG    +T+F        D     F+      +   GRLDI
Sbjct: 484 RVTVLLHKPMGYVSGQAE-DGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDI 542

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVDQD--------KLNLLKK 163
           ++ GLL+LT DG +AR L    +   + Y VR       G V+ D         L  L+ 
Sbjct: 543 DSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRH 602

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G  
Sbjct: 603 GLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSV 658

Query: 224 QLGTLLAGSTR 234
            LG L  G  R
Sbjct: 659 VLGDLPVGKWR 669


>gi|300704234|ref|YP_003745837.1| pseudouridine synthase [Ralstonia solanacearum CFBP2957]
 gi|299071898|emb|CBJ43227.1| Pseudouridine synthase [Ralstonia solanacearum CFBP2957]
          Length = 677

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 113/251 (45%), Gaps = 38/251 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+  +P  ++E+  
Sbjct: 426 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEI--LPAARSEQGE 483

Query: 75  --LWLYHKPIGLVTTHSDPDG---RSTVF--------DNLPSIFSR-----VISVGRLDI 116
               L HKP+G V+  ++ DG    +T+F        D     F+      +   GRLDI
Sbjct: 484 RVTVLLHKPMGYVSGQAE-DGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDI 542

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVDQD--------KLNLLKK 163
           ++ GLL+LT DG +AR L    +   + Y VR       G V+ D         L  L+ 
Sbjct: 543 DSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRH 602

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G  
Sbjct: 603 GLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSV 658

Query: 224 QLGTLLAGSTR 234
            LG L  G  R
Sbjct: 659 VLGDLPVGKWR 669


>gi|297538780|ref|YP_003674549.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297258127|gb|ADI29972.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 245

 Score = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 100/219 (45%), Gaps = 9/219 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERT 73
           + ++I   G  +R+    +I  Q V VNG + +     V  T++++  V G      E++
Sbjct: 11  LERIICNQGFGARKLCRILILNQEVTVNGEICDDPDA-VFDTENLQYTVKGEAWDYREKS 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP     +H       T++  LP   +   V  +GRLD +T GL+L+++DG   
Sbjct: 70  YLML-HKPSNYECSHKT-QHHPTIYSLLPHPLVVRDVQCIGRLDEDTTGLILISDDGQFI 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  +VY V     +  +++  + KG  +Q +        L   + +   + +
Sbjct: 128 HRMSSPKHKVPKVYEVTCKHPMSDEQIAHILKG--VQLVDEDAPIAALACTRITQNIIHM 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            L EGK  ++K++    + +V  L RI  G  +L   LA
Sbjct: 186 TLAEGKYHQVKRMVAAISNRVEGLKRIQIGEVKLPDDLA 224


>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 = 60.5 bits (145), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 60/224 (26%), Positives = 97/224 (43%), Gaps = 25/224 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   +R+     I +  V VNG ++      V  ++ +   G  L  A  +R
Sbjct: 2   RLDKFICKSTELNRKHASDCIERAEVSVNGEVITDVRFQVHESNEVRYKGQRL-VARPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLLT 125
             + HKPI  ++++ D D         PS+F R I          VGRLD +T GL+LLT
Sbjct: 61  YIMLHKPIHTLSSNVDGD--------YPSLF-RCIDIDRVEDLHIVGRLDADTTGLVLLT 111

Query: 126 NDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +DG  +  +  P  Q  + YRV       G V  D +   + G+ +Q      +   L+ 
Sbjct: 112 DDGRWSFDIIRPDKQCAKTYRVMLRDPIAGDVAADVIARFEAGLQLQNEQALTLPAKLEI 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                  +T+   EGK  ++K++F     +V  L R   G   L
Sbjct: 172 VAPREVLLTIT--EGKYHQVKRMFAAVGNRVIGLHREQIGDLSL 213


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 83/177 (46%), Gaps = 23/177 (12%)

Query: 77  LYHKPIGLVTTHSD---PDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L++KP G++T  +D   P  R T+  FD LP     V + GRLD ++EGLL+LT+DG L 
Sbjct: 5   LFNKPFGVLTQFTDAKCPTERPTLSGFD-LPK---GVYAAGRLDRDSEGLLVLTDDGKLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             L  P  +  + Y V+  G      L+ ++  + ++       +V L            
Sbjct: 61  AQLSSPKFKTPKTYLVQVEGDTTDADLDPMRASLSLKDGPTLPARVHLIDPPDLWLRDPP 120

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                   + W+ V + EG+NR+++++     +   RL+R S G + L  +  G  R
Sbjct: 121 VRVRKSIPDTWIKVTITEGRNRQVRRMCAALGFPCLRLVRWSVGSWTLDGISQGQWR 177


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 48/170 (28%), Positives = 81/170 (47%), Gaps = 39/170 (22%)

Query: 77  LYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L++KP G+++  + P+  S       F N+P +++     GRLD ++EGLLLL++ G L 
Sbjct: 13  LFNKPYGVLSQFT-PETASRWRCLAEFINVPGVYA----AGRLDADSEGLLLLSDQGRLQ 67

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----KGSN- 186
           + L  P     R Y V+  G  D  +L  L++GI IQ       Q TL  +    +G + 
Sbjct: 68  QRLTDPRCGHWRSYWVQVEGHPDDPQLQKLREGIEIQ------HQRTLPARARWLQGEDI 121

Query: 187 ------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                             +W+ + LREG+NR+++++         RL+R 
Sbjct: 122 PLLPERDPPIRVRATIPTSWLELSLREGRNRQVRRMTAAVGLPTLRLVRC 171


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 64/228 (28%), Positives = 106/228 (46%), Gaps = 13/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  +    G +L   A + +  D I +DG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAITDAQGEVLY--ADDQVEHDAIRIDGEPLDPPAGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F   + V++ VGRLD  T G+LL+T+DG 
Sbjct: 60  SLLL-HKPSGYTCSTKD-TGR-LIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY +     +  ++  L   G +++ G     +   L+      A 
Sbjct: 117 LLHRIISPKSALDKVYDITLAEDLRGEEAALFASGSLLLDGETKPLLPAELEVLGPRQAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLSSGQWRAL 222


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 61/223 (27%), Positives = 97/223 (43%), Gaps = 15/223 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDG--VPLRKAE 71
           ++ +++   G  +RR    ++    V+V G +++  + +  +   + EVDG   P R+  
Sbjct: 2   KLEQILFTQGFGTRRVCAGLVDCGAVRVGGQVVDDPSADFDTAGLVFEVDGREWPFRQPA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
              L + HKP G   +   P    +V   LP       V  VGRLD +T GLLL T+DG 
Sbjct: 62  ---LVMLHKPAGYECSQK-PRHHPSVMSLLPPPLRTRGVQPVGRLDEDTTGLLLFTDDGK 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--TLDTQKGSNA 187
           L   L  P     +VY       VD+  +  L  G+V+      D Q    L  Q     
Sbjct: 118 LIHRLTSPKHHVPKVYEATTKHPVDEAVVQRLLAGVVLD----DDPQPVRALQAQCTGPN 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + + L EGK  ++K++      +V  L R ++G   L   LA
Sbjct: 174 TLRLVLAEGKYHQVKRMVAAAGNRVEALHRSAFGALTLPADLA 216


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 45/179 (25%), Positives = 79/179 (44%), Gaps = 23/179 (12%)

Query: 77  LYHKPIGLVTTHSD-----PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L++KP G++   SD     P      + + P  +      GRLD+++EGLLLLT+DG L 
Sbjct: 5   LFNKPYGVLCQFSDERTGPPRPTLAAYIDRPGFYP----AGRLDLDSEGLLLLTDDGRLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             +  P  +  + Y V+  G  D+  L  L+ G+ ++       QV              
Sbjct: 61  ARIADPRFKMPKTYLVQVEGDPDEAALAALRHGVRLKDGPTLPAQVERIEAPALWPRDPP 120

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                   + W+ + +REG+NR+++++         RL+R   G + L  +  G  R+ 
Sbjct: 121 VRFRKSVPDRWLRLTIREGRNRQVRRMTAAIGHPTLRLVRWRIGDWTLDGIPQGQWRDA 179


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 52/216 (24%), Positives = 96/216 (44%), Gaps = 3/216 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +     A+R++  ++I    + V+G + +  A  V     +E +G  +  A   R
Sbjct: 2   RLDKYLCDGLGATRKQATKIIKSGEITVDGEVQKSGAFKVPEGGVVEWEGREV-GAPGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP   V +H D    +  V  + P +   +   GRLD++T GL+L+T+DG  +  
Sbjct: 61  YIMLYKPADFVCSHEDGHNPTAFVLLDEPKV-ENLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + +
Sbjct: 120 ITSPKHKCEKTYRVWLVDAIQPDYVEKFAEGIELRNEREPTLPAHLEIVNEAENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            EGK  ++K++F     KV  L R   G   L   L
Sbjct: 180 VEGKYHQVKRMFAALGNKVEHLHRERIGSIVLDEAL 215


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 42/164 (25%), Positives = 79/164 (48%), Gaps = 25/164 (15%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G++   S+ +    + D +  P  +      GRLD ++EGLLLLT++G L   + 
Sbjct: 7   FNKPCGVICQFSEHEKHPCLKDYVDRPGFYP----AGRLDTDSEGLLLLTDNGVLQAQIA 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------- 185
            P  +  + Y  +  G  D++KL+LL  G+ + G      +V L  + G           
Sbjct: 63  DPKFKREKTYWAQVEGSPDEEKLDLLCNGMDLGGFVTRPAKVRL-LEAGEADILWPRNPP 121

Query: 186 --------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                   + W+ + + EGKNR+++++     +   RL+R++ G
Sbjct: 122 VRMRKTVPDFWLEIRIAEGKNRQVRRMTAKAGYPCLRLVRVAVG 165


>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 = 60.1 bits (144), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 44/185 (23%), Positives = 85/185 (45%), Gaps = 23/185 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-----ISVGRLDINTEGLLLLTNDG 128
           R+ L++KP G+++  +D   + T     P++ + +        GRLD ++EGL++LT+ G
Sbjct: 3   RVILFNKPFGVLSQFTD---KGTEGSPRPTLSAYIDEKGFYPAGRLDRDSEGLMVLTDSG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P  +  + Y V+  G  D+  L  L+ G+ ++       +  L         
Sbjct: 60  PLQARISHPKYKLAKTYWVQVEGTPDEQALAALRSGVTLKDGKTAPARARLMDPPDPLWD 119

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       +AW+ + + EG+NR+++++         RLIR   G ++L  L  G+ 
Sbjct: 120 RDPPVRFRKSVPDAWLEITITEGRNRQVRRMTAHVGLPTLRLIRARVGDWELHKLQPGAW 179

Query: 234 REVSK 238
           R  S+
Sbjct: 180 RFSSE 184


>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 = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 63/238 (26%), Positives = 101/238 (42%), Gaps = 22/238 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ +++   G  SR+    MI    V VNG         V      E D   L    R  
Sbjct: 2   QLERILHSQGFGSRKICRSMIRHGEVAVNG--------EVCDFPFTEFDPEHLVFTVRGE 53

Query: 75  LWLY--------HKPIGLVTTHSDPDGRSTVFDNLPS-IFSR-VISVGRLDINTEGLLLL 124
            W Y        +KP     +H  P    ++F  LP+ +  R V S+GRLD +T GLLLL
Sbjct: 54  TWTYREKAYLMLNKPAHYECSHK-PQHHPSIFSLLPAPLLERGVQSIGRLDEDTTGLLLL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           ++DG     +  P  +  +VY V     +D+ ++  L  G  +Q +        L  +  
Sbjct: 113 SDDGQFIHRMSSPKWKVPKVYEVTTKHPLDETQVTSLLSG--VQLLDEPAPVAALSAKIV 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKIL 241
            +  + + L EGK  ++K++    + +V  L RI  G   L   LA G+ R +   +L
Sbjct: 171 GDHVLHLTLAEGKYHQVKRMLAAVSNRVEALKRIRIGSLDLPEDLAPGAWRWLDAAML 228


>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 = 60.1 bits (144), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 87/181 (48%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRL--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG-------- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ +  G+      + +   +         
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPATAIKVSEPEWLWERNPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTRE 235
                   +W+ + + EG+NR+++++     +   RLIR   G     QLG L  G  +E
Sbjct: 120 RFRANIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLG-LKPGDVKE 178

Query: 236 V 236
           +
Sbjct: 179 I 179


>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 = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 55/216 (25%), Positives = 103/216 (47%), Gaps = 14/216 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE----RAAVNVMSTDHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G  L+    R AV+    + + + GV +   
Sbjct: 8   RLDRLLANLGYGSRKEVQALVAAGKVVLDGKPLKDAGLRIAVDATLPERMTIRGVAVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
               L + HKP+G+V +H + DG   ++D LP  +      + +VGRLD  T GL+L+T+
Sbjct: 68  APLVLMM-HKPLGVVCSHKE-DGEK-IYDLLPRRWRLRDPALSTVGRLDKETSGLILITD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     + Y  R    +   +      G ++++G     +   L+     
Sbjct: 125 DGDFLHRVISPKRHVPKTYLARLDRPLSGSEGETFAAGTLMLEGEEKPLLPARLEIVDER 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            A +T+   EG+  +++++F      V  L R   G
Sbjct: 185 TARLTI--TEGRYHQVRRMFAAVGNHVTDLHRERIG 218


>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 = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 74/145 (51%), Gaps = 25/145 (17%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            +++GRLD ++EGLLLLT DG ++   ++ S +  + Y V+  G +D   +  L+ G+ I
Sbjct: 67  TMAIGRLDHDSEGLLLLTTDGMVSH--QVRSKKVEKEYYVQVDGDIDDAAILKLQTGVEI 124

Query: 168 QGICYGDMQVTL---------------------DTQKGSNAWVTVGLREGKNREIKKVFE 206
            GI  G+  +TL                     D + G  +WV++ + EGKNR+I+K+  
Sbjct: 125 -GI-KGEKYLTLPCKVFKLENEPELPSNGRKPRDPKHGPMSWVSITIGEGKNRQIRKMTA 182

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAG 231
              +   RL+R+  G   L  + +G
Sbjct: 183 AAGFPTLRLVRVRIGNIHLDRMQSG 207


>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 = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 33/121 (27%), Positives = 60/121 (49%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG  I
Sbjct: 226 LIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKIELLRKGCTI 285

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            GI    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++   
Sbjct: 286 GGITIRPLELKIIKPNFLYKWIKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKSSD 345

Query: 228 L 228
           L
Sbjct: 346 L 346



 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+SK+++ + + SR + + +I    VKV N I+ +   ++V S   IEV+G  +     T
Sbjct: 14 RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQNTVIDVNS--KIEVNGCEINVDITT 71

Query: 74 RLWLYHKP 81
          +LW  +KP
Sbjct: 72 KLWGIYKP 79


>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 = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 54/204 (26%), Positives = 89/204 (43%), Gaps = 22/204 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +R ++ +KP G+++  S   G      +L      V  VGRLD ++EGLLL+T+D  L  
Sbjct: 2   SRYFIIYKPFGVLSQFS---GEGQTLASLFDFPKEVYPVGRLDKDSEGLLLITDDKWLNH 58

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICY----------------GD 174
            L  PS    R Y  +  G    + L  L  G+ I+  G  Y                 D
Sbjct: 59  HLLNPSFGHQRTYWAQVEGIPTPESLKALGNGVKIKVDGKEYLTKPSIAKLLSESPELPD 118

Query: 175 MQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
               +  +K   ++W+ + L EGKNR+++K+     +   RL R S     +     G  
Sbjct: 119 RDPPIRYRKNVPDSWIELTLIEGKNRQVRKMTAAVGFPTLRLARKSMEKINIIGFKVGEV 178

Query: 234 REVSKKILREQLGPHLLEEAQVNL 257
           +E+ ++ +  QLG    +E+  N 
Sbjct: 179 QELDRETVYHQLGLTGFKESAKNF 202


>gi|325204476|gb|ADY99929.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M01-240355]
          Length = 185

 Score = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 43/170 (25%), Positives = 79/170 (46%), Gaps = 24/170 (14%)

Query: 78  YHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           ++KP G++   S  +   ++  F N P  +      GRLD ++EGLLL T+DG L   + 
Sbjct: 7   FNKPYGVICQFSPHEKHKSLKDFINFPGFYP----AGRLDTDSEGLLL-TDDGRLQAQIT 61

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------- 187
            P  +  + Y  +  G  D+ +L  L+KGI + G       + +     +++        
Sbjct: 62  DPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPPI 121

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                    W+ + + EGKNR+++++     +   RLIR++ G  +L  L
Sbjct: 122 RVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDL 171


>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 = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 44/181 (24%), Positives = 87/181 (48%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRL--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG-------- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ +  G+      + +   +         
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWERNPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF---QLGTLLAGSTRE 235
                   +W+ + + EG+NR+++++     +   RLIR   G     QLG L  G  +E
Sbjct: 120 RYRANIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLG-LRPGDVKE 178

Query: 236 V 236
           +
Sbjct: 179 I 179


>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 = 59.7 bits (143), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 45/180 (25%), Positives = 85/180 (47%), Gaps = 22/180 (12%)

Query: 75  LWLYHKPIGLVTTHSDP-DGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L L++KP G+++  +D   G+ T+  F  LP ++      GRLD ++EGLL+LT+DG   
Sbjct: 3   LILFNKPYGVLSQFTDEGSGKRTLKEFIALPGVYP----AGRLDFDSEGLLILTDDGREQ 58

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------ 185
             +  P  +  + Y  +  G   ++ L  L+KG+ ++          L  +  +      
Sbjct: 59  ARIADPKHKIPKTYLAQVEGIPSEEALQALRKGVDLKDGRTRPATARLAAEPENLWPRDP 118

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                    + W+ + + EG+NR+++++         RLIR+  G + L  L  G+ R+ 
Sbjct: 119 PIRYRKSVPDTWIELTITEGRNRQVRRMTAAAGHPTLRLIRLRIGDWDLENLPPGAWRKA 178


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 104/225 (46%), Gaps = 14/225 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----VDGV 65
           N  P R+ K+++  G  +R+E++ +   QR+ +     +  +  V   + ++    +D  
Sbjct: 4   NAKPVRLDKLLSNMGYGTRKEIDALARYQRILLGDKGFKSGSDKVTPNEDLQNRLTIDDK 63

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGL 121
           P+       + L +KP G+  T S  D  + + +  PS + +    +  +GRLD  T GL
Sbjct: 64  PVDPLPGFAVML-NKPAGV--TCSRKDSGTLITELFPSRWDKRDPLLSPIGRLDKETSGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLD 180
           LLLT+DG L   +  P TQ  + Y V     ++ D+ ++   G ++++      +   L 
Sbjct: 121 LLLTDDGQLNHRVSSPKTQTPKRYHVILDRDLNGDEDSIFAAGELMLESETKPLLPAELS 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 A +T  L EG+  +++++F      VN L R S G   L
Sbjct: 181 ALGKREAILT--LHEGRYHQVRRMFAAVGNHVNALHRESIGGLTL 223


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 41/143 (28%), Positives = 70/143 (48%), Gaps = 17/143 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GI--------CYGDMQVTLDT 181
           P  +  ++Y V+  G  D   L  L+ G+ +        GI         +       + 
Sbjct: 61  PGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRER 120

Query: 182 QKGSNAWVTVGLREGKNREIKKV 204
           +    +W+ V L EG+N +++++
Sbjct: 121 KNIPTSWLKVTLYEGRNHQVRRM 143


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 50/180 (27%), Positives = 84/180 (46%), Gaps = 21/180 (11%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLLTN 126
           ++ +KP+G +T   D        +N P++ S         ++  +GRLD++TEGLL+LT 
Sbjct: 20  FMLNKPLGYITATYD--------ENFPTVISLLDDETVKDKLFPIGRLDLDTEGLLILTT 71

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICYGD--MQVTLDTQK 183
           DG LA  L  P     + Y     G V + D     K+GI ++   Y     +V + +  
Sbjct: 72  DGQLAHRLAHPKWNIEKEYYAIVEGDVSKIDFSPFEKEGIYLKKDKYKTKPFKVKVLSAL 131

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              + V + + EGK   +KK+ E     V  L R+  G  +L   L  G  R ++++ +R
Sbjct: 132 EEESKVLITVSEGKYHIVKKIMESLGHPVKYLKRVRMGNLKLDENLQPGDYRPLTEEEIR 191


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 61/231 (26%), Positives = 102/231 (44%), Gaps = 8/231 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+    ++   RV++ G +       + + D    VDG      E+  
Sbjct: 5   LEKILQSQGFGSRKFCRNLVLGHRVEIAGKICTDPDRKLETDDLAFRVDGETWEYREKLY 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP G   +   P    +VF  LP  F +  +  VGRLD +T GLLLLT+DG    
Sbjct: 65  LVL-NKPAGYECSRQ-PQHHPSVFALLPEPFVQRGLQCVGRLDQDTTGLLLLTDDGHFIH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  ++Y V      +  +L  L  G+ ++      +   L  Q      + + 
Sbjct: 123 QYTSPRKKVPKIYTVTGVSPFEATQLEKLVTGVQLKD--EKTLTSALACQLIDEYRLRLS 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + EGK  ++K++      +V  L R + G F L  TLL G  R +++  L+
Sbjct: 181 ITEGKYHQVKRMIAAAGNRVETLHRSAIGGFTLEETLLPGHWRFLNENDLK 231


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 46/167 (27%), Positives = 83/167 (49%), Gaps = 22/167 (13%)

Query: 79  HKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G+V T    +  S V F N P    RV   GRLD ++ GLLL+TN+G +   +   
Sbjct: 30  NKPKGIVCTEDQRERDSIVRFLNYPV---RVTYAGRLDKDSRGLLLMTNNGDIINQMMRA 86

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-------QKGSNAWVT 190
           + +  + Y+V    ++ +  +  + +G+ I           LDT       +K      +
Sbjct: 87  ANRHEKEYKVTVDKEITEQFIKKMSEGVPI-----------LDTVTRPCTVKKIGKYTFS 135

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++
Sbjct: 136 IILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLT 182


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 86/178 (48%), Gaps = 20/178 (11%)

Query: 77  LYHKPIGLVTTHSDP----DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +KP G+++  +D       R+T+ D +     +V   GRLD ++EGLLLLT+DG L  
Sbjct: 4   LLNKPYGVLSQFTDKGTADSPRATLSDYV--DVPKVYPAGRLDRDSEGLLLLTDDGRLQA 61

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-------------TL 179
            +  P  +  + Y V+  G    +++  L++G+ ++       QV              +
Sbjct: 62  RIAHPKFKKPKTYLVQVEGDPSDEQIARLRRGVTLKDGPTRPAQVRRLPPPDLWPRVPPV 121

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +K   +AW+ + + EG+NR+++++         RL+R S G + +  L  G  R +
Sbjct: 122 RFRKSVPDAWLEMTITEGRNRQVRRMTAHVGLPCLRLVRWSIGDWSVEGLAPGEWRNI 179


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 47/170 (27%), Positives = 83/170 (48%), Gaps = 8/170 (4%)

Query: 78  YHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +HKP+G+  T +D    + + + N P    R+  VGRLD  +EGL+LLTNDGG+A  +  
Sbjct: 5   FHKPVGITCTAADHIEDNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIANQILH 61

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
              +  + Y V          ++ + +G+ I+       +VT    +   +   + L +G
Sbjct: 62  GDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIVLTQG 117

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 118 MNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 167


>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 = 59.3 bits (142), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 55/187 (29%), Positives = 90/187 (48%), Gaps = 26/187 (13%)

Query: 76  WLYHKPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L +KP G ++    P+ R +  +   L     + +++GRLD ++EGLLLLT DG  + +
Sbjct: 15  FLIYKPYGFLSQFV-PETRKSKPLLGQLYDFPDKTMAIGRLDHDSEGLLLLTTDGMQSHL 73

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTL--------- 179
           +   S +  + Y V+  G V Q +L  L++G+ I GI  G       QV L         
Sbjct: 74  IRSKSIE--KEYYVQVDGLVSQAQLLQLQQGVEI-GISGGKYLTLPCQVELLTTEPNLPA 130

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 D + G  +W++V + EGKNR+++K+         RL+R+  G   L  +  G  
Sbjct: 131 RGKKIRDPRHGPTSWLSVTIAEGKNRQVRKMTAAVGLPTLRLVRVRIGHICLKQMQPGEV 190

Query: 234 REVSKKI 240
             VS  I
Sbjct: 191 LPVSSFI 197


>gi|289807291|ref|ZP_06537920.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           AG3]
          Length = 153

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 42/147 (28%), Positives = 69/147 (46%), Gaps = 15/147 (10%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G  D   L  L+ G+ +
Sbjct: 4   VYAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTL 63

Query: 168 Q-------GI--------CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                   GI         +       + +    +W+ V L EG+N +++++        
Sbjct: 64  NDGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPT 123

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKK 239
            RLIR S G + L  L  G   E++++
Sbjct: 124 LRLIRYSMGDYTLNGLDNGQWCEIAQE 150


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 100/224 (44%), Gaps = 16/224 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V +   + +     +                 R ++
Sbjct: 7   LEKMLQSQGFGSRKYCQQLIKNGAVSIQDEIQKDLKYRIHDLTDFNFQVFDQNYVYREKV 66

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           ++  +KP G   +H  P    +VF  LP +  +  + +VGRLD +T GLLLLT+DG    
Sbjct: 67  YIILNKPKGFECSHQ-PHHHQSVFSLLPDLLIQRNIAAVGRLDQDTTGLLLLTDDGQYLH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTL--DTQKGSNA 187
            L  P     +VY V     +  D+++ L++G+ +    G+ +    VTL  +TQ     
Sbjct: 126 TLTHPKKHVPKVYHVATIDPITVDQMHQLEQGVELHNEKGV-FAATNVTLLNETQ----- 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            +++ + +G   ++K++      KV  L R   G  +L  L  G
Sbjct: 180 -LSMTIHQGVYHQVKRMIAAVGNKVTALHRHKIGQLELPNLAEG 222


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 53/193 (27%), Positives = 88/193 (45%), Gaps = 36/193 (18%)

Query: 73  TRLWLYHKPIGLVTTHS----DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           T+L L++KP G+   HS    D DG  T+ D +     RV   GRLD ++EGLLLLT++G
Sbjct: 2   TKLVLFNKPYGV---HSQFKKDHDGMITLADFIDDKTMRV--AGRLDKDSEGLLLLTDNG 56

Query: 129 GLARVLELPST---------QWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQG 169
            L   +  P T         +  + Y V+        ++  L++G++          +Q 
Sbjct: 57  RLNHAITTPPTAKNAKDKYTKCAKTYLVQVENIATNVQIQALEQGVMLKDGKTLPAKVQK 116

Query: 170 ICYGDMQVTLDTQKGS--------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +   ++ + L  +             W+ + + EGKNR+I+++         RLIR   G
Sbjct: 117 LDENELPIRLWQRNPPVRQRVNIPTTWLKITIVEGKNRQIRRMVAHVGLPCLRLIRSQIG 176

Query: 222 PFQLGTLLAGSTR 234
            +QL  L  G +R
Sbjct: 177 IWQLNGLAVGESR 189


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 104/233 (44%), Gaps = 13/233 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V ++  Q  +    G +L   A + +    I VDG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVTQLFRQGAITDAQGEVLY--ADDQVEHGAIRVDGEPLDPPAGF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
            L L HKP G   +  D  GR  +++ LP  F      +  VGRLD  T G+LL+T+DG 
Sbjct: 60  SLLL-HKPGGYTCSTKD-TGR-LIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDDGA 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
           L   +  P +   +VY V    ++  D+  L   G ++++G     +   L+        
Sbjct: 117 LLHRIISPKSALDKVYDVTLAEELRGDEAALFASGSLLLEGETKPLLPAELEVLGPRQTR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +T  L EG+  +++++F      V  L R   G   L  L +G  R +    L
Sbjct: 177 LT--LHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDL 227


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 84/180 (46%), Gaps = 16/180 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           +R+ L +KP G+++  +D     T    L +     +V   GRLD ++EGLL+LT+DG L
Sbjct: 2   SRVILLNKPFGVLSQFTDKGLEGTTRPTLSAYVDVPQVYPAGRLDRDSEGLLVLTDDGRL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------- 177
              +  P  +  + Y V       +D L  L+KGI ++       QV             
Sbjct: 62  QAQIADPKFKKPKTYLVLVERIPSEDALQSLRKGITLKDGMTRPAQVERVEPPELWERDP 121

Query: 178 TLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +  +K   + W+   +REG+NR+++++         RL+R S G + L  + +G  R+ 
Sbjct: 122 PVRFRKSVPDCWLKFTIREGRNRQVRRMTAAVGHPTLRLVRWSVGEWTLDGIASGVWRDA 181


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 43/166 (25%), Positives = 82/166 (49%), Gaps = 19/166 (11%)

Query: 77  LYHKPIGLVTTHSDP---DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L++KP  ++   +D      R T+ D +      V + GRLD ++EGLLLLTNDG L   
Sbjct: 40  LFNKPFDVLCQFTDDAEQGQRRTLADYIEE--KEVYAAGRLDRDSEGLLLLTNDGKLQAQ 97

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY-GDMQVTLDT---------- 181
           +  P+ +  + Y V+  G      L+ L++G++++ G+     ++   D           
Sbjct: 98  ITQPNKKTDKTYWVQVEGAPTDADLDKLRQGVILKDGLTLPAKIEFLKDAKIWPRVPPIR 157

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +     W+++ + EG+NR+++++     +   RLIR S G + +
Sbjct: 158 QRENIPTTWLSITICEGRNRQVRRMTANIGFPTLRLIRYSIGQWNI 203


>gi|326562796|gb|EGE13091.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 46P47B1]
          Length = 250

 Score = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 51/190 (26%), Positives = 87/190 (45%), Gaps = 30/190 (15%)

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           T+L L++KP G+ +    D DG  T+ D +     RV   GRLD ++EGLLLLT++G L 
Sbjct: 2   TKLVLFNKPYGVHSQFKKDHDGMITLADFIDDKTMRV--AGRLDKDSEGLLLLTDNGRLN 59

Query: 132 RVLELPST---------QWLRVYRVRFHGQVDQDKLNLLKKGIV----------IQGICY 172
             +  P T         +  + Y V+        ++  L++G++          +Q +  
Sbjct: 60  HAITTPPTAKNAKDKYTKCAKTYLVQVENIATNVQIQALEQGVMLKDGKTLPAKVQKLDE 119

Query: 173 GDMQVTLDTQKGS--------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
            ++ + L  +             W+ + + EGKNR+I+++         RLIR   G +Q
Sbjct: 120 NELPIRLWQRNPPVRQRVNIPTTWLKITIVEGKNRQIRRMVAHVGLPCLRLIRSQIGIWQ 179

Query: 225 LGTLLAGSTR 234
           L  L  G +R
Sbjct: 180 LNGLAVGESR 189


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 45/177 (25%), Positives = 79/177 (44%), Gaps = 15/177 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+ L +KP G+++  +D         +   I   V + GRLD ++EGLL+LT+DG L  
Sbjct: 2   ARVILLNKPFGVLSQFTDEGTNHPTLKDYVKIPG-VYAAGRLDRDSEGLLVLTDDGRLQN 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYGDMQVTL 179
            +  P  +  + Y  +  G  D   L  L+ G+             +I      +    +
Sbjct: 61  RIASPKFKQPKTYWAQVEGTPDDAALEALRAGVKLKDGMTKPARARIIDAPDVWERDPPI 120

Query: 180 DTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             +K   + W+ + L EG+NR+++++         RLIR S G + +  L  G  R+
Sbjct: 121 RVRKAIPDTWIELVLTEGRNRQVRRMTAAVGHPTLRLIRYSIGDWTIDNLALGQWRD 177


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 113/230 (49%), Gaps = 11/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEV-DGVPLRKAE 71
            R+ K +   G  +R+EV+ ++ +  VKVN ++++++ + ++   D + V D V +   E
Sbjct: 1   MRLDKFLGNHGFGTRKEVKLLVKRGAVKVNDVVVKKSDIKIVPENDTVTVYDEVVMY--E 58

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
                + +KP G +++  D    + +   L   F    +  VGRLD +TEGLL+LTNDG 
Sbjct: 59  PFVYIMLNKPAGYISSTKDYKDETVL--ELIEGFEHYDLHPVGRLDKDTEGLLILTNDGQ 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAW 188
            +  +  P     + Y  R  G V  D + L K GI +    Y  M   L     G  + 
Sbjct: 117 FSHDVLSPRKHVNKTYFARVDGYVTDDTVELFKAGITLDD-GYKAMPAELQIISAGEISE 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           + + ++EGK  ++K++F   +  V  L RI  G   L  +L  G+ R+++
Sbjct: 176 IELVIQEGKFHQVKRMFIAVDMIVIYLKRIKMGGLPLDESLTPGAYRKLT 225


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 77/166 (46%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     DT    N       
Sbjct: 64  RHKLVKRYWAQVEGAPGPTDLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFAL 169


>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 = 59.3 bits (142), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 40/145 (27%), Positives = 68/145 (46%), Gaps = 15/145 (10%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V + GRLD ++EGLLLLT+DG L   +  P  +  + Y     G+  QD +N L +G+ +
Sbjct: 33  VYAAGRLDRDSEGLLLLTDDGRLQARITDPRAKMPKTYYALVEGRPSQDAINRLCEGVSL 92

Query: 168 Q----------GICYGDMQVTLDT-----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +           +   D     D      +   +AW+ + + EG+NR+++++        
Sbjct: 93  KDGPTRPAKVAAVPAPDWLWPRDPPVRLRKTVPDAWLRLTITEGRNRQVRRMCAAVGLPC 152

Query: 213 NRLIRISYGPFQLGTLLAGSTREVS 237
            RLIR   G + L  L  G  R ++
Sbjct: 153 LRLIRTQIGDWTLDGLAPGQWRRIA 177


>gi|319792471|ref|YP_004154111.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315594934|gb|ADU36000.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 249

 Score = 59.3 bits (142), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 93/234 (39%), Gaps = 30/234 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
            +  ++   G  +RR    ++ Q  V ++G  +     +V     +  V G P    E+ 
Sbjct: 2   HLQDILYTQGFGTRRVCAGLVQQGHVTIDGKAVTDPFADVDPEGLLYTVQGTPWAYHEKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLLL 124
            L L HKP G   +   P    +++  LPS             V ++GRLD +T GLLL+
Sbjct: 62  YLML-HKPAGTECSQK-PSTYPSIYTLLPSPLRLRPNKGAVQGVQAIGRLDQDTTGLLLM 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--------GICYGDMQ 176
           T+DG     +  P     +VY V     VD+ ++  L  G+V+           C  D  
Sbjct: 120 TDDGQFIHKMGSPKHHVPKVYEVTAKHPVDEAQIAKLLAGVVLDDDPKPVRAAACESDSP 179

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + L           + L EGK  ++K++      +V  L R   G   L   LA
Sbjct: 180 LHL----------RLTLTEGKYHQVKRMLAAVGNRVEGLHRSRIGELSLPADLA 223


>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 = 59.3 bits (142), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 99/220 (45%), Gaps = 14/220 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLRKA 70
           R+ +++   G  SR ++ RM     + ++   +  A   +  T  +    V    PL   
Sbjct: 8   RIDQLLGSLGYGSRGDIARMAKSGWITLDDARIWDATTRIAVTPDLPARMVVSREPLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VIS-VGRLDINTEGLLLLTN 126
               + L HKP+G+  +H + DG   V+D LP  + R   VIS VGRLD  T GLLLLT+
Sbjct: 68  AGMVI-LLHKPLGMTCSHKE-DG-PLVYDILPDRWKRRQPVISTVGRLDKQTSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P     + YR      ++ ++  +   G +V+QG         L     +
Sbjct: 125 DGPLLHRIISPKQHIKKTYRATLARPLEGNEAAIFAAGDLVLQGEDKPLAPAELRVISPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            A +TV   EG+  +++++F      V  L R + G   L
Sbjct: 185 EAVLTV--TEGRYHQVRRMFAATGNHVTALHRDALGGLVL 222


>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 = 59.3 bits (142), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/130 (25%), Positives = 64/130 (49%), Gaps = 15/130 (11%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQG 169
            GRLD+++EGL+ LT+ GGL + +  P+ +  + Y  +  G V ++ L  L+KG+ +  G
Sbjct: 37  AGRLDLDSEGLMFLTDHGGLNQYITNPTNKKFKTYLAQVDGDVTEEALEQLRKGVELADG 96

Query: 170 ICYGDMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           +      + +D  +                 +W+ + + EG+NR+++++     +   RL
Sbjct: 97  MTLPAKAIKVDQPEWLWDRDPPVRFRANIPTSWIELQICEGRNRQVRRMTAAVGFPTLRL 156

Query: 216 IRISYGPFQL 225
           IR   G   L
Sbjct: 157 IRTKIGAIDL 166


>gi|239814633|ref|YP_002943543.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239801210|gb|ACS18277.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 249

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 94/239 (39%), Gaps = 31/239 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
            +  ++   G  +RR    ++ Q  V + G  +     ++   D +  V G      E+ 
Sbjct: 2   HLQDILYSQGFGTRRVCAGLVQQGHVSIAGAAVTDPFADLDPEDLLFTVQGTEWAYHEKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLLL 124
            L L HKP G   +   P    +++  LPS             V ++GRLD +T GLLLL
Sbjct: 62  YLML-HKPAGTECSQK-PSTYPSIYTLLPSPLRLRPNKGAVQGVQAIGRLDQDTTGLLLL 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--------GICYGDMQ 176
           T+DG     +  P     +VY V     VD  ++  L  G+V+           C  D  
Sbjct: 120 TDDGQFIHKMGSPKHHVPKVYEVTAKHPVDAAQIEKLLAGVVLDDDPKPVRAAACESDSP 179

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           + L           + L EGK  ++K++      +V  L R   G   L G L AG  R
Sbjct: 180 LHL----------RLTLTEGKYHQVKRMLAAVGNRVEGLHRSRIGDLALPGDLAAGQWR 228


>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 = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 74/165 (44%), Gaps = 13/165 (7%)

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECS-RDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G       V  D +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLA 216


>gi|315179963|gb|ADT86877.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio furnissii
           NCTC 11218]
          Length = 233

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 93/212 (43%), Gaps = 3/212 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  ++R+E  +++    V V+G + +  +V V     +      L       
Sbjct: 2   RLDKFLCDALGSTRKEATQILKSGDVTVDGKVQKSGSVQVTEASVVAWQERQLSLTGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + LY KP G V +H D   + T F  L  +  R +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLY-KPEGFVCSHEDGFNQ-TAFVLLDEVNMRGLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D    L  GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADAVQADYAEQLAHGIELRNERELTLPAHMELVNADENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     KV  L R   G   L
Sbjct: 180 HEGKYHQVKRMFAALGNKVEALHRERVGEIVL 211


>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 = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 46/177 (25%), Positives = 85/177 (48%), Gaps = 20/177 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP  ++   ++P  R T+ D  ++P +++     GRLD ++EGLL+LT+ G + + +
Sbjct: 17  LFNKPFNILCQFTEPGKRLTLADYISIPGVYA----AGRLDYDSEGLLVLTDTGRIQQRI 72

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDM-------QVTLDT----- 181
             P     + Y V+  G      +  L  G++++ G+    +        V L T     
Sbjct: 73  ADPRADMAKSYWVQVEGVPTLAAIQQLTCGVLLEDGLTLPAIVEQIKPPSVWLRTPQIRE 132

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            ++    W+ + L E +NR I+++         RLIR + GP+QL  L  G  +  S
Sbjct: 133 RRQIPTTWLAITLTEDRNRLIRRMTAAVGLPTLRLIRQAVGPWQLNKLQPGDWKVAS 189


>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 = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 74/165 (44%), Gaps = 13/165 (7%)

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECS-RDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G       V  D +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLA 216


>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 = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/178 (30%), Positives = 89/178 (50%), Gaps = 21/178 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+ KP G+++  +D +GR T+ D  ++P ++     VGRLD+++EGLLLLTNDG L   L
Sbjct: 9   LFWKPYGVLSQFTDREGRPTLKDYIDVPDVYP----VGRLDMDSEGLLLLTNDGLLKYRL 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTLD 180
             P     R Y  +     D + L  L +G+VI G                     V + 
Sbjct: 65  LHPRYGHWRTYWAQVERIPDDEALRRLAEGVVIAGGYRTRPARVRRIEPPELPPRPVPIR 124

Query: 181 TQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +K     W+ + +REGKNR+++++         RL+R++ GP +L  L  G  R ++
Sbjct: 125 YRKTVPTYWLEISIREGKNRQVRRMTAAVGHPTLRLVRVAIGPLRLDGLEPGHWRPLT 182


>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 = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 76/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     DT    N       
Sbjct: 64  RHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFAL 169


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/118 (27%), Positives = 58/118 (49%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
            +I +  L+  +EGLLLLTNDG  A+ L+      L  Y ++    +  DK+ LL+KG  
Sbjct: 225 HLIIINSLNSGSEGLLLLTNDGDFAKNLKDIQNNILTTYLIKVQEDLCIDKIKLLRKGCF 284

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           I       + + +   K ++ W+     E  +  +  +F  +N  + +  R S+GP++
Sbjct: 285 INNQHIYPVNIEIIKSKHTSKWIKFTYVEKSHNYLLYLFSKYNITIRKCKRFSFGPYK 342


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 93/212 (43%), Gaps = 3/212 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +  A  ++R+E  +++    V V+G + +  +V V     +      L       
Sbjct: 2   RLDKFLCDALGSTRKEATQILKSGDVTVDGKVQKSGSVQVTEASVVAWQERQLSLTGPRY 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
           + LY KP G V +H D   + T F  L  +  R +   GRLD++T GL+L+T+DG  +  
Sbjct: 62  IMLY-KPEGFVCSHEDGFNQ-TAFVLLDEVNMRGLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D    L  GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADAVQADYAEKLAHGIELRNERELTLPAHMELVNADENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F     KV  L R   G   L
Sbjct: 180 HEGKYHQVKRMFAALGNKVEALHRERVGDIVL 211


>gi|330955284|gb|EGH55544.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 132

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 57/114 (50%), Gaps = 2/114 (1%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
           +A  RV+V+G         V     + +D   L+  +  R ++ HKP G V+  SD    
Sbjct: 18  LASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKAARYFMLHKPEGCVSATSDAQ-H 76

Query: 95  STVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
            TV D L       + + GRLD NT GL+L+TNDG  +R L  P T+  +VY V
Sbjct: 77  PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRRLTQPQTKMPKVYYV 130


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 77/166 (46%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     DT    N       
Sbjct: 64  RHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFAL 169


>gi|332968985|gb|EGK08027.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter sp.
           1501(2011)]
          Length = 201

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 84/180 (46%), Gaps = 27/180 (15%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL 134
           L++KP G+ +  SD    +  F  L   F+   +   GRLD  +EGLLLLT+DG + + +
Sbjct: 6   LFNKPYGVQSQFSD--DANNKFAPLSQFFTDKSLRVAGRLDATSEGLLLLTSDGRVNKAI 63

Query: 135 ELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
             P       +  + Y V+  G+   ++L  L +G+V++       +V   T+K      
Sbjct: 64  THPPKANAGRKQGKTYLVQVEGEPTAEQLEQLCQGVVLKDGKTLPAEVKHLTEKELPMPL 123

Query: 185 -------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                         ++W+ + + EGKNR+++++         RLIR S   F+LG L  G
Sbjct: 124 WQRDPPIRERKNIPDSWLMMTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFELGDLGVG 183


>gi|126642165|ref|YP_001085149.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 201

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 51/171 (29%), Positives = 80/171 (46%), Gaps = 18/171 (10%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   + L  P
Sbjct: 34  KPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQALTHP 92

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGL 193
                +VY V  +  V  +++ +L +G+ +     G    D+ + L T +     +T+ +
Sbjct: 93  RKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGGFAATDVAL-LGTHQ-----LTMTI 146

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 147 HQGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGGWVYLSEQ 192


>gi|307102233|gb|EFN50580.1| hypothetical protein CHLNCDRAFT_14498 [Chlorella variabilis]
          Length = 183

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 50/175 (28%), Positives = 83/175 (47%), Gaps = 25/175 (14%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTRLWLY 78
           IA AG+ASRR  + +I   +VKVNG ++      V +  D + V G  +  A   R + +
Sbjct: 1   IAAAGVASRRGADDLIFGGQVKVNGKVVTEPGTQVDLRKDRVAVSGREISAAAVQRKYYF 60

Query: 79  --HKPIGLVTT----HSDP-DGRSTV--FDNLPSIFSR---------------VISVGRL 114
             +KP G + +    H D  +GR  +  FD+  + + +               + +VGRL
Sbjct: 61  ALNKPKGYICSNKSEHEDGGEGRLVISLFDDWLARWRQRQARPGGGGGGLPPRLFTVGRL 120

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           D+ + GL+ +TNDG  A  +  PST   + Y V    +  Q++L  +  G  + G
Sbjct: 121 DVASIGLIFVTNDGDWAHKVMHPSTGITKEYSVTLDCKPRQEELQAMAAGCDMGG 175


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 44/148 (29%), Positives = 69/148 (46%), Gaps = 18/148 (12%)

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ- 168
           +VGRLD  +EGLL+LT +  +  +L L      R Y V     V  + + LL+ GI I+ 
Sbjct: 47  AVGRLDSMSEGLLILTTNKKVTNLLFLGEVPHTRTYWVNVGHIVPPETVQLLRTGIPIRV 106

Query: 169 --GICYGDMQVTLDT--------------QKG-SNAWVTVGLREGKNREIKKVFEFFNWK 211
             G  Y      ++               Q G  N W+++ L EGK  +++K+    N +
Sbjct: 107 KGGGYYTTAPCEVEVIERPAILPWHQSEGQPGVPNTWLSITLTEGKYHQVRKMVREANHR 166

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKK 239
             RL+R S    +LG L  G  RE+ ++
Sbjct: 167 CKRLVRASIEDLELGDLPPGGVREIGEE 194


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 66/225 (29%), Positives = 106/225 (47%), Gaps = 6/225 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +A A   SR+E +  IA+ RV VNG    +A   V     + +D  PL   ++ R
Sbjct: 2   RLDYYLAHAANLSRKEAKIAIAKGRVLVNGESKLKANSPVTDLCDVILDKSPLS-FQQNR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V    D D    V D LP    + +  VGRLD +T GLLLLT DG     
Sbjct: 61  YYMMYKPAGVVCALQD-DEHDVVLDLLPHEIQKELKIVGRLDKDTTGLLLLTTDGQWLHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V    ++ +D +  L+KG++++G    D+         +   +++ +
Sbjct: 120 ITSPKHDCPKTYLVDLADEITKDAIEALEKGVLLKGEI--DLTKPAKVVSHTEKQISLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
            EGK  ++K++      KV  L R   G   L   +A G   E+S
Sbjct: 178 SEGKYHQVKRMLAAVGNKVEALHRTQIGEVCLSQDMALGEFTELS 222


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 38/167 (22%), Positives = 80/167 (47%), Gaps = 17/167 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   + +   TV   +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPYDVLSQFREDEAHLTVSSFIKDPELRI--AGRLDLDSEGLMFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKG-------- 184
           +  PS +  + Y  +  G V ++ L  L+ G+ +  G+      + +D  +         
Sbjct: 60  ITHPSNKKYKTYLAQVDGDVTEEALEQLRNGVELADGMTLPAKAMKVDEPEWLWDRDPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                   +W+ + + EG+NR+++++     +   RLIR   G   L
Sbjct: 120 RYRASIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLIRTQIGSINL 166


>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 = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 101/223 (45%), Gaps = 23/223 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   +R E   +I   +V+VNGI++      V   + I + G  L  A  +R
Sbjct: 2   RLDKFLCKSTDFTRVESIDLIEAGKVRVNGIVIITPQTQVHENNSIMLSGQRL-VARPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + HKPI  + ++ D D         PS+ + +           GRLD +T GLLLLT+
Sbjct: 61  YIMLHKPINTLCSNVDGD--------YPSVMNYIHMDRAEDLHITGRLDADTTGLLLLTD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL----KKGIVIQGICYGDMQVTLDTQ 182
           DG  +  +  P     + YRV     ++++ ++ L    ++G+ +QG     +   L+  
Sbjct: 113 DGRWSFNIINPKYHCEKTYRVTLRDPIEEEDIDELVSRFEQGLQLQGEKSLTLAAKLEVI 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 +T  L EG+  ++K++F     +V  L R   G   L
Sbjct: 173 APHQVLLT--LSEGRYHQVKRMFFTVGNRVVGLHRQQVGKLSL 213


>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 = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/168 (26%), Positives = 76/168 (45%), Gaps = 23/168 (13%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R ++ D    PS++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKTPSVYP----AGRLDADSEGLLLLTDDGALQARIAE 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA---- 187
            P  + ++ Y  +  G      L  L +G+     +   C  +     D     N     
Sbjct: 63  -PHHKLVKRYWAQVDGAPGPADLKALTRGVDLGDYVTRPCRAEFIEPPDALWPRNPPIRY 121

Query: 188 -------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 122 RAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFAL 169


>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 = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 74/165 (44%), Gaps = 13/165 (7%)

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECS-RDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G       V  D +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADARDTH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLA 216


>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 = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 76/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSN------- 186
             + ++ Y  +  G      L  L +G+     +   C  +     D     N       
Sbjct: 64  RHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDALWPRNPPIRYRA 123

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   + TL
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFTL 169


>gi|308050759|ref|YP_003914325.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
 gi|307632949|gb|ADN77251.1| ribosomal small subunit pseudouridine synthase A [Ferrimonas
           balearica DSM 9799]
          Length = 232

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 103/226 (45%), Gaps = 6/226 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +      +R   ++++ +  V+ +G +++     V     + ++GVPL     TR
Sbjct: 2   RLDKYLCSCTDLTRSMAKKLLHKGEVQCDGEVVKDPGFKVTDDTQVVLEGVPLGPV-ATR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP   + ++ D    S +    LP   +  I+ GRLD++T GL+LL+ DG     
Sbjct: 61  YIMLHKPAEFLCSNVDELYPSVLNLIELPKRETLRIA-GRLDVDTTGLVLLSEDGQWCHQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + YR      +  D    L +G+ +       +    +  + S+  V + +
Sbjct: 120 ITSPRRQCSKRYRAWLAEPLVADAEQQLAQGVQLHN--EEGLTRPAELVRISDTEVLLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            EGK  ++K++F     KV  L R + G  +L  TL  G  R +S+
Sbjct: 178 EEGKYHQVKRMFAALGNKVVALHREAIGAIELDETLEPGEWRLLSE 223


>gi|301510575|ref|ZP_07235812.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB058]
          Length = 210

 Score = 58.5 bits (140), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/170 (29%), Positives = 78/170 (45%), Gaps = 16/170 (9%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           KP G   +H  P    +VF  LP   I   V +VGRLD +T GLLLLT+DG   + L  P
Sbjct: 43  KPQGFECSHQ-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQALTHP 101

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLR 194
                +VY V  +  V  +++ +L +G+ +    G+        L T +     +T+ + 
Sbjct: 102 RKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALLGTHQ-----LTMTIH 156

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +G   ++K++      KV +L R      Q+G L+     E     L EQ
Sbjct: 157 QGVYHQVKRMIAAVGNKVEKLHR-----HQIGQLVLPEIEEGGWVYLSEQ 201


>gi|330752219|emb|CBL87177.1| ribosomal large subunit pseudouridine synthase B [uncultured
           Sphingobacteria bacterium]
          Length = 230

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/240 (23%), Positives = 106/240 (44%), Gaps = 15/240 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA     +RRE  R++A+  +KVN  +++  +  VM  D +     PL++    R
Sbjct: 2   RLNKYIAHTRYCTRREASRLLARGEIKVNNKVVKEESYRVMEGDEVTHLNKPLQEQLLYR 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L +KP    T   D D +  +        + +I+V  +   + GLLLLT+D  L   L
Sbjct: 62  YLLINKPKHFTTDIGDKDSKYIMGLIKKEDPTGLIAVDHMGPKSVGLLLLTSDKALVEKL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLL---KKGIVIQGICYGDMQVTLDTQKGSNA-WVT 190
              + +  RVY +  +  +++  +N L   +K I I+   + D         G  A ++ 
Sbjct: 122 NQKNRKVRRVYLIELNKDIEKKDINKLLKDRKTIKIESASHVD---------GYQANYIG 172

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + +  G    +K V     +++ R+ R  Y       L  G  R + +  + E++  H +
Sbjct: 173 LEMTIGSENILKGVINRMGFEIERIDRSYYAGLTKKDLKRGWIRPLQE--MEERMMKHFI 230


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/225 (27%), Positives = 96/225 (42%), Gaps = 11/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV++ I    V    G LL   A    + + I  +  PL  A   
Sbjct: 2   RLIKLLANLGYGSRKEVQKYIRMGIVTDAEGNLLNDDAKT--AHEDIRFNERPLDPAHGV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L L +KP G V +  D      V++ LP  FS     + +VGRLD +T GLLL T+DG 
Sbjct: 60  VLML-NKPTGYVCSLKDTG--KLVYELLPHRFSERKPVLSTVGRLDADTSGLLLFTDDGD 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     ++Y V     +   +  +   G ++       ++     Q G     
Sbjct: 117 YLHRIISPKNHVAKIYEVTLARPLQGHEAAIFASGELMLESEKTPLKPAAMEQTGEKT-A 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EG+  +++++F      V  L R   G   LG L  G  R
Sbjct: 176 RLTLYEGRYHQVRRMFAAVGNHVEALHRSQMGDLTLGELRPGKWR 220


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/161 (26%), Positives = 74/161 (45%), Gaps = 23/161 (14%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R ++ D    P ++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 43  NKPFGTICQFSAHETRPSLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQARIAE 98

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA---- 187
            P  + ++ Y  +  G      L  L +G+     +   C  +     +T    N     
Sbjct: 99  -PRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIRY 157

Query: 188 -------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                  W+ + + EGKNR+++++     +   RL+R+  G
Sbjct: 158 RAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIG 198


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 38/167 (22%), Positives = 80/167 (47%), Gaps = 17/167 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   + +   TV   +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPYDVLSQFREDEAHLTVSSFIKDPELRI--AGRLDLDSEGLMFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKG-------- 184
           +  PS +  + Y  +  G V ++ L  L+ G+ +  G+      + +D  +         
Sbjct: 60  ITHPSNKKYKTYLAQVDGDVTEEALEQLRNGVELADGMTLPAKAMKVDEPEWLWDRDPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                   +W+ + + EG+NR+++++     +   RLIR   G   L
Sbjct: 120 RYRASIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLIRTQIGSINL 166


>gi|291326167|ref|ZP_06573862.1| ribosomal large subunit pseudouridine synthase E [Providencia
           rettgeri DSM 1131]
 gi|291315271|gb|EFE55724.1| ribosomal large subunit pseudouridine synthase E [Providencia
           rettgeri DSM 1131]
          Length = 182

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 54/95 (56%), Gaps = 2/95 (2%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T++ L++KP  ++   +D  GR T+   +P   + V + GRLD ++EGLL+LTNDG L  
Sbjct: 39  TKIILFNKPFDVLPQFTDEQGRDTLKKYIP--ITDVYAAGRLDRDSEGLLILTNDGKLQA 96

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            L  P  +  ++Y  +  G   +D L   ++G+ +
Sbjct: 97  RLTQPQKKTGKIYYAQVEGIPSEDALLKFRRGLTL 131


>gi|171909920|ref|ZP_02925390.1| Pseudouridine synthase, Rsu [Verrucomicrobium spinosum DSM 4136]
          Length = 189

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 77/167 (46%), Gaps = 20/167 (11%)

Query: 79  HKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           HKP G+++  T   P  R+     LP+    V  +GRLD ++EGLLLL+++    + L  
Sbjct: 6   HKPYGVLSQFTKEHPSHRTLAEFGLPA---GVYPIGRLDSDSEGLLLLSDEARWNQQLLH 62

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DT 181
           P+    R Y V+  G    + +  L +G+ +        +V L               + 
Sbjct: 63  PTRGHERTYHVQVEGIPTAEAITRLTRGVQLPDFYTLACKVQLLEPAPLYPARVPPIRER 122

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           +    +W+ + L EGKNR+++++     +   RLIR + G  +L  L
Sbjct: 123 KSIPTSWLAMKLVEGKNRQVRRMTAAVGYPTLRLIRAAMGRLELARL 169


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 41/156 (26%), Positives = 71/156 (45%), Gaps = 6/156 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K +   GI SR++ + +I    V++N  +    +A ++      + +DG  +        
Sbjct: 5   KYLQSQGIGSRKQCQWLIQNDCVEINDTIRNDTKADIDPAEVQTLRIDGEDIVVVPMPYF 64

Query: 76  W-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG    
Sbjct: 65  YILLNKPADYETSHK-PQQYPSVFSLFPDHMRNIDMQAVGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            +  P  +  ++YRV      D      LK G+++ 
Sbjct: 124 RVTSPKHKVPKIYRVTLKHPADDSLCETLKNGVLLH 159


>gi|167585691|ref|ZP_02378079.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 192

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSN------- 186
             + ++ Y  +  G      L  L +G+     +   C  +     D     N       
Sbjct: 64  RHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRACRAEFIEPPDALWPRNPPIRYRA 123

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AKPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFAL 169


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/179 (26%), Positives = 82/179 (45%), Gaps = 23/179 (12%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G++   S  +   ++ D +P     V   GRLD ++EGLLLLT+DG     +  P 
Sbjct: 6   NKPYGVICQFSPHEKHRSLKDFVP--VPNVYPAGRLDTDSEGLLLLTDDGRQQARIANPR 63

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGS------------ 185
            +  + Y  +  G  D ++L LL++ + +        ++  LD  + +            
Sbjct: 64  FKLTKTYWAQLEGSPDDERLALLQRPLDLGDFVAQPARIRLLDEHETARIWQRDPPIRVR 123

Query: 186 ----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVS 237
               + W+ + + EGKNR+++++     +   RLIR+  G    F LG  L G  RE  
Sbjct: 124 KSVPDFWLQIQICEGKNRQVRRMTAKAGYPCLRLIRVGIGRVNLFDLGIEL-GQWRECP 181


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/166 (29%), Positives = 80/166 (48%), Gaps = 25/166 (15%)

Query: 77  LYHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L++KP  ++   +D     + R T+ D   +P ++S    VGRLD ++EGLL LTN+  L
Sbjct: 10  LFNKPYNVLCQFTDNSNLENPRPTLKDYIKVPDVYS----VGRLDKDSEGLLFLTNNAQL 65

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDT-------- 181
              L        R Y V+     DQ  LN L++G+ I+       +V  LD+        
Sbjct: 66  KHRLSHRQFAHPRTYLVQVERIPDQVALNQLRQGVRIKDYKTRPAKVKLLDSPPSVPPRD 125

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                 +    AW+ + L EG+NR+++++     +   RLIRI+ G
Sbjct: 126 PPIRYRKTVPTAWLEMTLTEGRNRQVRRMTAAVGYPTLRLIRIAIG 171


>gi|269468805|gb|EEZ80409.1| 16S rRNA uridine-516 pseudouridylate synthase [uncultured SUP05
           cluster bacterium]
          Length = 174

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 40/170 (23%), Positives = 78/170 (45%), Gaps = 19/170 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP G++   S      + + ++ +I+      GRLD ++EGL++LT+DG L   +  
Sbjct: 4   LFNKPFGVLCQFSGEGKTLSDYIDIKNIYP----AGRLDKDSEGLIVLTDDGKLQHQISH 59

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--------------- 181
           P     + Y V+  G +  + +  L +G+ ++       +  + T               
Sbjct: 60  PKFDKEKTYVVQVEGSITDNAITQLCRGVALKDGMTKPAKAKIITKPSWVWDRIPPIRKR 119

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           Q    +W+ + + EGKNR+++++     +   RLIR   G + L  L  G
Sbjct: 120 QNIPTSWIELSITEGKNRQVRRMSAHVGFPTLRLIRTEIGSWSLKRLPLG 169


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 52/222 (23%), Positives = 96/222 (43%), Gaps = 14/222 (6%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K +   GI SR++ + +I    V++N  +    +A ++      + +DG  +        
Sbjct: 5   KYLQSQGIGSRKQCQWLIQNDCVEINDTVRNDTKADIDPAEVQTLRIDGEDIVVVPMPYF 64

Query: 76  W-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG    
Sbjct: 65  YILLNKPADYETSHK-PQQYPSVFSLFPDHMRNIDMQAVGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---SNAWV 189
            +  P  +  ++YRV      D      LK G+++      D   T+   +    +   +
Sbjct: 124 RVTSPKHKVPKIYRVTLKHPADDSLCETLKNGVLLH-----DDNETVHAAEAVLENPTTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + + EGK  ++K++      +V  L R  +    +  L +G
Sbjct: 179 LMTITEGKYHQVKRMVAAAGNRVEHLHRDEFNGRTVENLASG 220


>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 = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 76/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     +T    N       
Sbjct: 64  RHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVSRPCRAEFIEPPETLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                WV + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWVELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFAL 169


>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 = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/167 (25%), Positives = 78/167 (46%), Gaps = 22/167 (13%)

Query: 79  HKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G ++    H +      +   L +    V++VGRLD  +EGLLLLT DG  +  + 
Sbjct: 9   YKPYGYLSQFINHQNKRRNKKLLSELYTFSDNVMAVGRLDEKSEGLLLLTTDGKFSNYI- 67

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQVTL-------------- 179
             S++  + Y V   G + ++ +  L+ G  I ++G  Y                     
Sbjct: 68  -TSSKIEKEYHVMVDGVITEEAVLKLQNGVEISVEGKPYKTKNCKAKILRDTSHIVERFV 126

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            D + G  +W+++ L EGK R+++K+     +   RL+R+  G ++L
Sbjct: 127 RDERHGITSWLSITLAEGKFRQVRKMTAKVGFPTLRLVRVRIGDYKL 173


>gi|254251646|ref|ZP_04944964.1| Pseudouridine synthase [Burkholderia dolosa AUO158]
 gi|124894255|gb|EAY68135.1| Pseudouridine synthase [Burkholderia dolosa AUO158]
          Length = 238

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/222 (28%), Positives = 95/222 (42%), Gaps = 9/222 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           +  ++   G  SRR+   +I   RV V G            TD +   VDG       R 
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVGGATATDPD-TAFDTDGLVFTVDGTAWPFHARA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL++DG   
Sbjct: 62  YLTL-NKPAGYECS-RDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +   +L+ L+ G+ + G       V  D +      +TV
Sbjct: 120 HAYTSPKRKVPKTYVATVRHPLSDTQLHTLRTGVQLHGEPKPIAAVAADARDAHTLVLTV 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              EGK  ++K++    + +V+ L R S G   L   LA  T
Sbjct: 180 --VEGKYHQVKRMVAAVSNRVDALHRESIGGLTLPDNLAPGT 219


>gi|134296698|ref|YP_001120433.1| pseudouridine synthase [Burkholderia vietnamiensis G4]
 gi|134139855|gb|ABO55598.1| pseudouridine synthase [Burkholderia vietnamiensis G4]
          Length = 192

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/180 (26%), Positives = 82/180 (45%), Gaps = 23/180 (12%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------------ 185
             + ++ Y  +  G  D   L  L +G+ +        +        +            
Sbjct: 64  RHKLVKRYWAQVDGAPDAADLKALARGVDLGDYVTRPCRAEFIEPPAALWPRTPPIRYRA 123

Query: 186 ---NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVSKK 239
                W+ + + EGKNR+++++     +   RL+R+  G    F LG +  G T E+  +
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGVLDIFALG-IAPGETIELPPR 182


>gi|26247383|ref|NP_753423.1| hypothetical protein c1514 [Escherichia coli CFT073]
 gi|26107784|gb|AAN79983.1|AE016759_257 Hypothetical protein c1514 [Escherichia coli CFT073]
          Length = 118

 Score = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 52/91 (57%), Gaps = 2/91 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L  
Sbjct: 3   LFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLTQ 60

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           P  +  ++Y V+  G   QD L  L+ G+ +
Sbjct: 61  PGKRTGKIYYVQVEGIPTQDALEALRNGVTL 91


>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 = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 56/224 (25%), Positives = 94/224 (41%), Gaps = 19/224 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   +R     ++A   V VNG ++  A   V   + +   G  L  A  +R
Sbjct: 2   RLDKFLCKSTKLTRSAATEVLALGEVSVNGSIVTEARFQVHENNSVLWRGERL-IARPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + HKP+  ++++ D D         PS+F  +          VGRLD +T GL+LLT+
Sbjct: 61  YIMLHKPLNTLSSNVDGD--------YPSLFHCIDIERAEDLHIVGRLDADTSGLVLLTD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P     + YRV     +  D       G+ +Q          L       
Sbjct: 113 DGRWSFEIIRPDKLCPKTYRVTLRDPIAADVAEKFNVGVQLQNESKLTAPAMLKVINERE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             +T+   EG+  ++K++F     +VN L R   G  QL  +L 
Sbjct: 173 VLLTI--TEGRYHQVKRMFAAVGNRVNGLHREQIGDLQLDVVLG 214


>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 = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/189 (30%), Positives = 93/189 (49%), Gaps = 23/189 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLL 122
           P+ +A  +RL  +HKP G+++  + P+GR      F +LP ++      GRLD ++EGLL
Sbjct: 20  PVERAGPSRLLRFHKPYGVLSQFT-PEGRWRGLKDFIDLPGVY----VAGRLDADSEGLL 74

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT 181
           LLT+DGGL   +  P  +  + Y V+  G  D   L  L++G+ +  G         LD 
Sbjct: 75  LLTDDGGLQARIADPRFKMEKTYWVQVEGVPDAAALQALERGVQLNDGPTLPARARRLDV 134

Query: 182 --------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                         Q   + W+ + +REG+NR+++++         RL+R + GPF L  
Sbjct: 135 PPPVGEREPPIRVRQHIPDTWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPFALDG 194

Query: 228 LLAGSTREV 236
           L  G+  E 
Sbjct: 195 LAPGTWAEA 203


>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 = 57.8 bits (138), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 92/230 (40%), Gaps = 33/230 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           ++  ++   G  +RR    +I Q  V V GI     A+  ++ D    V GV     E+ 
Sbjct: 2   QLQDILFSQGFGTRRVCAGLIQQGFVAVAGIPCTEPAMEFVAEDLRFTVQGVAWEYHEKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--------RLDINTEGLLLLT 125
            L L HKP G   +   P    +++  LPS   +             RLD +T GLLLL+
Sbjct: 62  YLML-HKPAGYECSQK-PSTYPSIYTLLPSPIRQRGGGAAAGVQAVGRLDQDTTGLLLLS 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--------GIC--YGDM 175
           +DG     +  P     +VY V     VD  ++  L  G+V+           C   G++
Sbjct: 120 DDGKFIHRMSSPRHHVPKVYEVTAKHAVDDRQVQKLLAGVVLDDDPKPVRAAACEKTGEL 179

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           Q++L             L EGK  ++K++      +V  L R   G   L
Sbjct: 180 QLSLT------------LTEGKYHQVKRMIAAVGNRVEDLHRSQLGGLML 217


>gi|323253055|gb|EGA36888.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 171

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 42/167 (25%), Positives = 77/167 (46%), Gaps = 3/167 (1%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 1   RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +      D+      +  +   V + +
Sbjct: 61  ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHN--EKDLTKPATLEVITPVQVRLTI 118

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
            EG+  ++K++F     +V  L R   G   L   LA G  R ++++
Sbjct: 119 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEE 165


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 100/234 (42%), Gaps = 29/234 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-----DHIEVDGVPLRK 69
           R+ K+IA  G  SR+E++  I       NG + +R    + +T     + I  D  PL  
Sbjct: 2   RLVKLIANLGYGSRKEIQTAIK------NGWVTDRDGNTLKATSQTPHEDILFDDEPLDP 55

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLT 125
           A    L + +KP+G   T S  D    V+D LP  +      + ++GRLD  T GLLL T
Sbjct: 56  APGMVLAM-NKPLGY--TCSTNDQGKLVYDLLPDRYRMRKPVLSTIGRLDKETSGLLLFT 112

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLD 180
           +DG     +  P     +VY V     +  ++  L   G ++     + +    ++V  D
Sbjct: 113 DDGTFLHKVISPKANVGKVYEVTLDRPMKGNETALFASGEMMLESEDKPLKPAMLEVLDD 172

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           T         V L EG+  +++++F      V  L R   G   LG L  G  R
Sbjct: 173 TH------ARVILHEGRYHQVRRMFAATGNHVTNLSRTQIGGLSLGCLEDGQWR 220


>gi|11967881|emb|CAC19451.1| hypothetical pseudouridine synthase [Streptococcus pneumoniae]
          Length = 75

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 47/73 (64%), Gaps = 1/73 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K IA AG+ASRR+ E +I Q  V VNG ++   A  + S D +EV+G P+   E+  
Sbjct: 2  RINKYIAHAGVASRRKAEELIKQGLVTVNGQVVRELATTIKSGDKVEVEGQPIYNEEKV- 60

Query: 75 LWLYHKPIGLVTT 87
           +L +KP G++++
Sbjct: 61 YYLLNKPRGVISS 73


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 55/219 (25%), Positives = 97/219 (44%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   ++ E    I    + VN  ++   A  V  ++ + +DG  L  A   R
Sbjct: 2   RLDKFICKSTQLTKAEAIERIHDGDISVNDAVIINEATQVHESNTVIMDGKRL-IAREFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP G + ++ D        +  PS+F        + +   GRLD +T G++L+T+
Sbjct: 61  YILMHKPAGTICSNID--------EVYPSLFNYLDIENTAELHIAGRLDADTTGMVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G  +  +  P+ +  +VYRV    ++  D     K GI +QG         L       
Sbjct: 113 NGRWSFNITSPNQKCSKVYRVGLSREIAADVAEKFKAGIKLQGEQKLTAPALLTVISAKE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             +T+   EGK  ++K++F     +V  L R + G  +L
Sbjct: 173 VLLTI--TEGKFHQVKRMFAAVGNRVVSLHREAIGEVRL 209


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 44/168 (26%), Positives = 75/168 (44%), Gaps = 23/168 (13%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R ++ D    P ++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQARIAE 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA---- 187
            P  + ++ Y  +  G      L  L +G+     +   C  +     D     N     
Sbjct: 63  -PRHKLVKRYWAQVDGAPGPADLKALARGVDLGDCVTRPCRAEFIEPPDALWPRNPPIRY 121

Query: 188 -------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 122 RAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFAL 169


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 110/249 (44%), Gaps = 34/249 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+       + ER 
Sbjct: 376 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQSARSEQGERV 435

Query: 74  RLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINT 118
            + L HKP+G V+  ++                +G  T     P     +   GRLDI++
Sbjct: 436 TV-LMHKPVGYVSGQAEDGYQPAVSLFVPENQWEGDPTRKRFAPWQRRALAPAGRLDIDS 494

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH---GQVDQD--------KLNLLKKGI 165
            GLL+LT DG +AR L  E  + +   + RV +H   G V+ D         +  L+ G+
Sbjct: 495 TGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVEHDISKVFPEELMEKLRFGL 554

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   L
Sbjct: 555 SLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGSIVL 610

Query: 226 GTLLAGSTR 234
           G L  G  R
Sbjct: 611 GDLPVGQWR 619


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 61/212 (28%), Positives = 101/212 (47%), Gaps = 4/212 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +      +RR    ++A  RV+V+G ++      +     IEVDG  L+      
Sbjct: 2   RLDRFLGNLPDFNRRNSRLLLASGRVRVDGQVVRDGCSEIREFSRIEVDGRILQPGRAAL 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
            ++ HKP G+V+       R TV D L     + + + GRLD+ T GLLLLTNDG  +R 
Sbjct: 62  YFMLHKPAGVVSATRHERHR-TVLDLLDEPDRQGLHLAGRLDLGTTGLLLLTNDGHWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY V     + ++ +    +G+             L+     +A +T  L
Sbjct: 121 ITHPRYKLAKVYYVETAEPIGEEYIETFARGLYFAFEDLVTQPAHLELLGSHSARLT--L 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EG+  ++K++F +F   V RL R S GP +L
Sbjct: 179 FEGRYHQVKRMFGYFRNPVLRLHRESMGPLRL 210


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 109/244 (44%), Gaps = 21/244 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS---TDHIEV--DGVPLR 68
            R+ +++A  G  +R+EV   I       NG + +RA   + +   T H ++  D  PL 
Sbjct: 1   MRLVRLLANLGYGTRKEVALAIR------NGWVTDRAGRPLTADARTPHEDILFDDEPLD 54

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLL 124
            A    L L +KP+G   +  D  GR  V+D LP  F      + +VGRLD +T G LL 
Sbjct: 55  PAPGMVL-LLNKPVGYTCSTKD-RGR-LVYDLLPDRFRLRKPVLSTVGRLDRDTSGALLF 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQK 183
           T+DG L   +  P ++  +VY       +  D+      G +++ G         L+   
Sbjct: 112 TDDGVLLHRIIAPKSEVPKVYEAELDRPLKGDEAAQFASGTLMLDGEDKPLKPAELEVLG 171

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              A +T  L EG+  +++++F      V  L RI  G   L  L  G+ R + ++ + +
Sbjct: 172 ERRARLT--LHEGRYHQVRRMFAATGNHVTALARIRIGALTLDGLAEGTWRLLDERDVAK 229

Query: 244 QLGP 247
              P
Sbjct: 230 IFAP 233


>gi|291545735|emb|CBL18843.1| pseudouridine synthase family [Ruminococcus sp. SR1/5]
          Length = 610

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 43/142 (30%), Positives = 73/142 (51%), Gaps = 7/142 (4%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           R+  +GRLD ++EGLLLLTN+G L   +        + Y+V  +  V ++ +  +  G+ 
Sbjct: 12  RIYPIGRLDKDSEGLLLLTNEGDLVNRIMKAGNYHEKEYQVTVNKPVTEEFIRGMGGGVP 71

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           I        +V   T+ G N++  + L +G NR+I+++ E+F +KV  L R+      + 
Sbjct: 72  ILDTVTRPCKV---TKTGKNSFRII-LTQGLNRQIRRMCEYFGYKVVTLKRVRIMNLYID 127

Query: 227 TLLAGSTREV---SKKILREQL 245
            L  G  RE+    +K L E L
Sbjct: 128 GLEEGKYREIRPEERKELEEML 149


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 100/227 (44%), Gaps = 20/227 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           ++  ++   G  +RR    +I Q RV ++        +   +T  I+V+G+ LR      
Sbjct: 2   QLQDILYSQGFGTRRICAGLIQQGRVAIHATGTLEPTICQDATQDIDVEGLVLRVQGVDW 61

Query: 70  AERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTE 119
             + R + + HKP G   +   P    +++  LP+   +         V +VGRLD +T 
Sbjct: 62  PYQPRAYVMLHKPAGTECSQK-PSAYPSIYTLLPAPLRQRPSKGSVDGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLL++DG     +  P     +VYRV     V +++++ L +G+V+         V  
Sbjct: 121 GLLLLSDDGQFIHRMSSPKKHVPKVYRVTAKHPVTKEQIDRLLEGVVLDD---DPRPVRA 177

Query: 180 DTQKGSNAWV-TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 +A V  + L EGK  ++K++      +V  L R   G   L
Sbjct: 178 AACALVDAHVLDLTLTEGKYHQVKRMIAAVGNRVEALHRSHIGRLAL 224


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 53/204 (25%), Positives = 93/204 (45%), Gaps = 34/204 (16%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDIN 117
             G    +A+ T L L +KP G+++  +  +G      + F ++P +++     GRLD +
Sbjct: 6   CGGCAKTQADLTTL-LLNKPYGVLSQFTSEEGSRWRCLSDFVDVPQVYA----AGRLDAD 60

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-------- 169
           +EGLL+LT++G L + L  P     R Y  +  G  + ++L  L  G+V+QG        
Sbjct: 61  SEGLLILTSNGRLQQRLTDPRFGHWRSYWAQVEGTPNTEQLQQLCDGVVVQGRRTLPAKA 120

Query: 170 --ICYGDM--------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
             +   D+        Q+       +N W+ + L EG+NR+++++         RL+R  
Sbjct: 121 RWLQGQDLPQLPERTPQIRFRAAIPTN-WLQLSLSEGRNRQVRRMTAAVGLPTLRLVRCC 179

Query: 220 YG------PFQLGTLLAGSTREVS 237
                   P  L  L  GS R V+
Sbjct: 180 IDLMDNGPPLDLTGLQPGSWRTVT 203


>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 = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 44/175 (25%), Positives = 82/175 (46%), Gaps = 25/175 (14%)

Query: 78  YHKPIGLVTTHSD----PDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           ++KP  +++  +D       R+T+ D  +LP ++      GRLD ++EGL+LLT+ G L 
Sbjct: 7   FNKPYDVLSQFTDRGSADSPRATLSDHIDLPGVYP----AGRLDRDSEGLMLLTDVGRLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG------ 184
             +  P  +  + Y V+  G  D   L  L +G+ ++ G+        +    G      
Sbjct: 63  ARIADPRHKLAKTYWVQVEGVPDAAALRALAEGVELKDGLTRPARARAMPEPPGLWPRNP 122

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                    ++W+ + +REG+NR+++++         RLIR   G + L  L+ G
Sbjct: 123 PIRERKSVPDSWIELTIREGRNRQVRRMTAAVGHPTLRLIRARIGDWTLDGLVPG 177


>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 = 57.4 bits (137), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 44/168 (26%), Positives = 76/168 (45%), Gaps = 23/168 (13%)

Query: 79  HKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLE 135
           +KP G +   S  + R ++ D    P ++      GRLD ++EGLLLLT+DG L AR+ E
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKTPGVYP----AGRLDADSEGLLLLTDDGALQARIAE 62

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA---- 187
            P  + ++ Y  +  G      L  L +G+     +   C  +     +T    N     
Sbjct: 63  -PRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIRY 121

Query: 188 -------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 122 RAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFAL 169


>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 = 57.4 bits (137), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKA--PGVYPAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     +T    N       
Sbjct: 64  RHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFAL 169


>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 = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 110/249 (44%), Gaps = 34/249 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERT 73
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+       + ER 
Sbjct: 362 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQSARSEQGERV 421

Query: 74  RLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINT 118
            + L HKP+G V+  ++                +G  T     P     +   GRLDI++
Sbjct: 422 TV-LMHKPVGYVSGQAEDGYQPAVSLFVPENQWEGDPTRKRFAPWQRRALAPAGRLDIDS 480

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH---GQVDQD--------KLNLLKKGI 165
            GLL+LT DG +AR L  E  + +   + RV +H   G V+ D         +  L+ G+
Sbjct: 481 TGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVEHDISKVFPEELMEKLRFGL 540

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   L
Sbjct: 541 SLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGSIVL 596

Query: 226 GTLLAGSTR 234
           G L  G  R
Sbjct: 597 GDLPVGQWR 605


>gi|303286639|ref|XP_003062609.1| pseudouridylate synthase [Micromonas pusilla CCMP1545]
 gi|226456126|gb|EEH53428.1| pseudouridylate synthase [Micromonas pusilla CCMP1545]
          Length = 386

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 117/262 (44%), Gaps = 43/262 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---------------------------IL 46
           QRVSK++++ G+ASRRE E +I +  V VNG                            L
Sbjct: 92  QRVSKLMSQRGMASRREAEALIDRGDVIVNGGEVATRGMKVAIDATIDIAGDSDGGANAL 151

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERT-------RLWLYHKPIGLVTTHSDPDGRSTVFD 99
           L +    V++     V  +P R  ER        R  +YH   G        D  +    
Sbjct: 152 LAKKVTVVLNKPPGYVSNLPSR-GEREASELITPRNAIYHHSTGGGVVGGGADADAATRR 210

Query: 100 NLPSIF--SRVISV-GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
            L  +   +R ++V GRLD ++ GLL+LT DG LAR + +   +  +VY V       ++
Sbjct: 211 KLEDVCRDARALNVCGRLDKDSRGLLVLTTDGVLARAI-VGGNEIPKVYEVVVDAIATRE 269

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           +L  L   + + G     M+V  +T +G+   +   LR+GK R+I+++ E    +V  L 
Sbjct: 270 QLAALNGPVALDGERLLPMRV--ETLEGTT--LRFELRQGKKRQIRRLCEGLALRVLDLR 325

Query: 217 RISYGPFQLGTLLAGSTREVSK 238
           R+  G   +G L  G  R +S+
Sbjct: 326 RVHVGTCDVGDLPEGRWRLMSE 347


>gi|260220876|emb|CBA28881.1| hypothetical protein Csp_A09350 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 201

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/170 (28%), Positives = 76/170 (44%), Gaps = 19/170 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKV-------NGILLERAAVNVMSTD-HIEVDGVP 66
           ++ +++   G  +RR    +I Q  V+V         + + +AA   ++      V GV 
Sbjct: 2   QLQEILYTQGFGTRRVCAGLIQQGLVQVYMPNEGPAPVTIAQAATEFVAEGLRFRVQGVD 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDIN 117
              AER  L L HKP G   +   P    +++  LPS             V +VGRLD +
Sbjct: 62  WPYAERAYLML-HKPAGTECSQK-PSTYPSIYTLLPSPLRLRPQKAAVQGVQAVGRLDQD 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           T G+LLLT+DG     +  P     +VY V     +D  ++N L  G+V+
Sbjct: 120 TTGMLLLTDDGKFIHRMSSPKHHVPKVYEVTVKHPLDDKQVNKLLSGVVL 169


>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 = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 100/229 (43%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +  I    V VNG ++      V  TD ++ DG  +++     
Sbjct: 24  RLNKFLSNAGLCSRREADSHIEMGLVHVNGKIITEMGYQVKPTDEVKFDGARVQQTPPVY 83

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP G V T        +V D + S + + V +VG +     GLL  TND  L + 
Sbjct: 84  LLL-NKPKGFVATSQGGKIVKSVQDLIRSAVKTPVPAVGDMGRPMTGLLFFTNDEVLRKK 142

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVT 190
           L   S     +Y+V     V  D +  LK+G ++    +  MQ   +       S   V 
Sbjct: 143 LN-NSKSIPMIYQVLLDKNVTTDMMRQLKEGQMV----FEKMQKINEVSHMDGKSKKEVG 197

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +       I K+F     KV  L RI+Y       L  G+ R ++ K
Sbjct: 198 IEVHSLSPAIIVKLFAAVGCKVVLLDRITYAGLTKKELPRGNWRRLNTK 246


>gi|146297843|ref|YP_001192434.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146152261|gb|ABQ03115.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
          Length = 190

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 42/148 (28%), Positives = 73/148 (49%), Gaps = 21/148 (14%)

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI- 167
           +++GRLD ++EGLLLLT DG ++   ++ S +  + Y V+  G +  + +  L+KG+ I 
Sbjct: 39  MAIGRLDEDSEGLLLLTTDGKVSE--QIRSKKVDKEYYVQVDGIITPEAIEKLQKGVEIG 96

Query: 168 -QGICYGDMQVTL-----------------DTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +G  Y     T                  D + G  +W ++ + EGK R+++K+     
Sbjct: 97  FEGGKYKTKPCTAFIVTEIPDFGPRAKKIRDERHGPTSWASITVNEGKFRQVRKMTAAVG 156

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   RL+R+  G   L  L AG   EV+
Sbjct: 157 FPTLRLVRVRIGNVYLQNLKAGEVLEVN 184


>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 = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 75/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     D     N       
Sbjct: 64  RHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDALWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFAL 169


>gi|145309058|gb|ABP57738.1| 16S rRNA pseudouridine synthase [Chromobacterium violaceum]
          Length = 150

 Score = 57.0 bits (136), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 57/103 (55%), Gaps = 8/103 (7%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +T  G LA  +  PS +  R Y VR  G++  + +  +  G+ ++    G+ +     QK
Sbjct: 1   ITTSGELANRMMHPSFEVEREYSVRVLGELTPEIMKQMVAGVELED---GEARFDRVFQK 57

Query: 184 G-----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           G     +N W  V ++EG+NRE++++FE F   V+RLIR+ +G
Sbjct: 58  GGPEEAANQWFNVVIKEGRNREVRRMFEHFGLTVSRLIRVRFG 100


>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 = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 55/204 (26%), Positives = 97/204 (47%), Gaps = 17/204 (8%)

Query: 43  NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +GI ++     +   D + +DG    +  + +  L HKP G  T+H  P    +VFD LP
Sbjct: 4   DGIQIDPEIDEISLGDTLLIDGKSF-EITQYKYVLMHKPAGYETSHL-PSHNPSVFDLLP 61

Query: 103 SIFSR--VISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWL-RVYRVRFHGQVDQD 156
             + +  + + GRLD++T GLLL ++DG     L   ++ + Q + ++Y V         
Sbjct: 62  KHYIKRGLQAAGRLDVDTTGLLLFSDDGQFIHRLISGKVGTKQEIEKIYEVTGARPFSDL 121

Query: 157 KLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +L  L +G+ +     I Y      L     ++  + +G+  GK  ++K++       V+
Sbjct: 122 QLQRLLEGVDLDDEPEIIYASRATLL-----ADGRLELGITTGKYHQVKRMVAAVGNHVD 176

Query: 214 RLIRISYGPFQL-GTLLAGSTREV 236
            L R S GP++L   L AGS  E+
Sbjct: 177 GLHRRSVGPYELPADLAAGSYIEI 200


>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 = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/118 (26%), Positives = 58/118 (49%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
            +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG  
Sbjct: 12  HLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKVELLRKGCT 71

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           I  I    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++
Sbjct: 72  IDDIHIRPLELKIIKPNLLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYK 129


>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 = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 54/230 (23%), Positives = 98/230 (42%), Gaps = 27/230 (11%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + K++   G  SR+  +++I    V +   +++    + +  +H+  +     +  R ++
Sbjct: 3   LEKMLQSQGFGSRKHCQQLIKNGAVSIQDEVIDNPK-HKLDLNHLNFEVYGKSQTYREKV 61

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           ++  +KP G   +H      S VFD    I     +  VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALNKPQGYECSHQATHHFS-VFDLFDDILLNRGIQCVGRLDHDTTGLLLLTDDGQFLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY+++    V  +++  L++G            V L  +KG  A   V 
Sbjct: 121 ALTHPKKHVAKVYQMQTADPVTDEQIQQLEQG------------VELRNEKGIFAATEVA 168

Query: 193 ----------LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                     + +G   ++K++      KV +L R   G   L  L  G 
Sbjct: 169 RLAENRLQMTIHQGVYHQVKRMLAAVGNKVEQLHRAQIGALALPELAEGE 218


>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 = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 101/232 (43%), Gaps = 20/232 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   ++ E    I    + VN  ++   A  V  ++ + +DG  L  A   R
Sbjct: 2   RLDKFICKSTQLTKAEAIERIHAGDINVNSAVIINEATQVHESNTVIMDGKRL-IAREFR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTN 126
             L HKP G + ++ D        +  PS+F        + +   GRLD +T G++L+T+
Sbjct: 61  YILIHKPAGTICSNID--------EVYPSLFNYLDVDNIAELHIAGRLDADTMGMVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G  +  +  P+ +  +VYRV     +  D     K GI +QG         L       
Sbjct: 113 NGRWSFNITSPNQKCSKVYRVGLSRDITADVAEKFKAGIKLQGAQKLTAPALLTIISAKE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
             +T+   EGK  ++K++F     +V  L R + G   L  L  G  R ++K
Sbjct: 173 VLLTI--TEGKFHQVKRMFASVGNRVVSLHREAIGEVTLD-LEVGQWRYLTK 221


>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 = 56.6 bits (135), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 113/250 (45%), Gaps = 36/250 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+     R  +  R
Sbjct: 423 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQA-ARSEQGER 481

Query: 75  LW-LYHKPIGLVTTHSDPDGRST-----VFDN-----------LPSIFSRVISVGRLDIN 117
           +  L HKP+G V+  ++ DG        V +N            P     +   GRLDI+
Sbjct: 482 VTVLMHKPVGYVSGQAE-DGYQPAVSLFVPENQWEADPTRKRFAPWQRRALAPAGRLDID 540

Query: 118 TEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH---GQVDQD--------KLNLLKKG 164
           + GLL+LT DG +AR L  E  + +   + RV +H   G V++D         +  L+ G
Sbjct: 541 STGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVERDISKVFPEELMEKLRFG 600

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   
Sbjct: 601 LSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGSIV 656

Query: 225 LGTLLAGSTR 234
           LG L  G  R
Sbjct: 657 LGDLPVGQWR 666


>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 = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 66/239 (27%), Positives = 111/239 (46%), Gaps = 26/239 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS---TDHIEV--DGVPLRK 69
           R+ K++A  G  SR+E+++ I       +G + +R    + +   TDH ++  D  PL  
Sbjct: 2   RLVKLLANLGYGSRKEMQQAIR------HGWVTDRKGNQLKADAKTDHKDILFDDEPLDP 55

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLT 125
           A+   + L +KP+G V +  D  GR  V+D LP  F      + ++GRLD  T G LL T
Sbjct: 56  AQGVVI-LMNKPLGYVCSTKD-QGR-LVYDLLPDRFRMRKPVLSTIGRLDKETSGALLFT 112

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKG 184
           +DG     +  P +   +VY V     ++  +  L   G ++++          LD    
Sbjct: 113 DDGTFLHQVISPKSNVPKVYEVTLDRPMNGSEAALFASGEMMLENEQKPLKPAELDVIDE 172

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           ++A +T  L EG+  +++++F      V  L R      ++GTL      E   KIL E
Sbjct: 173 THARLT--LHEGRYHQVRRMFAATGNHVTDLAR-----SRIGTLTLEGVDEGQWKILSE 224


>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 = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 87/188 (46%), Gaps = 31/188 (16%)

Query: 73  TRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L++KP G+ +   D   +  +T+ +       R+   GRLD  +EGLL+LT+DG +
Sbjct: 4   SSLILFNKPYGVQSQFRDESNNDHTTLSEYFTDKSLRI--AGRLDATSEGLLILTSDGRI 61

Query: 131 ARVLELPST---------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------IC 171
            + +  P +         +  + Y V+  G V   +L  L  G+V++           + 
Sbjct: 62  NKAITQPPSAKGFAQNKQKQGKTYLVQVEGMVTSVQLKALASGVVLKDGKTLPASAVLVD 121

Query: 172 YGDMQVTL--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
             D+ +TL        + +    +W+ + + EGKNR+++++         RLIR S   F
Sbjct: 122 EVDLPITLWEREPPIRERKNIPTSWLMLTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGF 181

Query: 224 QLGTLLAG 231
           +LG L  G
Sbjct: 182 ELGELGVG 189


>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 = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 83/184 (45%), Gaps = 30/184 (16%)

Query: 79  HKPIGLVTTHSDPDGRS------TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +KP G+++  +  D         + F N P     ++ +GRLD  +EGLLLLT DG L+ 
Sbjct: 12  YKPYGVLSQLASNDNNQVKKKFLSEFYNFPQ---GIMPIGRLDEKSEGLLLLTTDGKLSD 68

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVT---LDTQKG--- 184
            +     +  + Y  +  G +  + L+ ++KG+VI   G  Y         ++T K    
Sbjct: 69  TINRAGIE--KEYYAQLDGIITNEALHKIEKGVVIGLNGTTYTTKTCIVKHIETPKNIPE 126

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       N+W+++ + EGK R+++K+     +   RL+R+      L  L  G+ 
Sbjct: 127 PSTKIRLGRHRPNSWISICITEGKFRQVRKMTAAVGFPTLRLVRVRIHNITLDNLTLGAV 186

Query: 234 REVS 237
             ++
Sbjct: 187 TPIN 190


>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 = 56.2 bits (134), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 42/160 (26%), Positives = 74/160 (46%), Gaps = 22/160 (13%)

Query: 77  LYHKPIGLVTTHSDPDG--RSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +++KP G++   +D     R T+ D  NLP ++     VGRLD ++EGLLLLT++G L  
Sbjct: 43  VFYKPYGVLCQFTDNSAHPRPTLKDYINLPDLYP----VGRLDQDSEGLLLLTSNGKLQH 98

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L        R Y  +  G    + L  L++GI             + T+          
Sbjct: 99  RLAHREFAHQRTYFAQVEGSPTDEDLEPLRRGITFADYPTRPAIAKIITEPDFPPRNPPI 158

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                   +W+++ L EG+NR+++++     +   RL+R+
Sbjct: 159 RYRASIPTSWLSITLTEGRNRQVRRMTAAVGFPTLRLVRV 198


>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 = 56.2 bits (134), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 59/122 (48%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
            +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG  
Sbjct: 235 HLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKIELLRKGCT 294

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           I  I    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++  
Sbjct: 295 IGDIIIRPLELKIIKPNFLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKSS 354

Query: 227 TL 228
            L
Sbjct: 355 DL 356



 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRK 69
          F   R+SK+++ + + SR + + +I    VKV N I+ +   ++V S   IEV+G  +  
Sbjct: 25 FIFLRLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQNTVIDVNSK--IEVNGCEINV 82

Query: 70 AERTRLWLYHKP 81
             T+LW  +KP
Sbjct: 83 DITTKLWGIYKP 94


>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 = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 81/181 (44%), Gaps = 24/181 (13%)

Query: 74  RLWLYHKPIGLVTTHSD------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           RL L++KP  +++  +D      P    + F ++P    RV   GRLD ++EGLLLLT+D
Sbjct: 3   RLILFNKPYDVLSQFTDRGSEGSPRATLSDFIDIP----RVYPAGRLDRDSEGLLLLTDD 58

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------TLDT 181
           G L   +  P  +  + Y  +  G  D   L  L+ G+ +        +V      TL  
Sbjct: 59  GQLQARIANPRFKTEKTYYAQVEGLPDDTALAALRAGVTLSDGPTRPARVERTEPPTLWP 118

Query: 182 QKG--------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +           + W+ + + EG+NR+++++         RLIR   G + L  L  G  
Sbjct: 119 RTPPVRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTLRLIRWRIGDWTLDGLGPGEW 178

Query: 234 R 234
           R
Sbjct: 179 R 179


>gi|325526198|gb|EGD03833.1| pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 192

 Score = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 45/166 (27%), Positives = 75/166 (45%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     DT    N       
Sbjct: 64  RHKLVKRYWAQVDGAPGAADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+ +++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQGRRMTAAVGFPTLRLVRVGIGALDIFAL 169


>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 = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/134 (25%), Positives = 63/134 (47%), Gaps = 13/134 (9%)

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
           I   +I V  L  ++EGL+LLTNDG  AR L+      +  Y ++   ++  +K+ L+++
Sbjct: 219 IPEHLIVVNSLSASSEGLVLLTNDGDFARNLKDAHNNIITTYIIKVKEELTNEKIKLIER 278

Query: 164 GIVIQGICY-GDMQV------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
           G      C+ GD+ +       +     S  W+     E  +  +  +F  +N  + +  
Sbjct: 279 G------CHVGDLHIRPLTVHVIKPNCASPKWIKFTYVEKSHTHLDLLFSKYNLTIRKCK 332

Query: 217 RISYGPFQLGTLLA 230
           R S+GP++   L A
Sbjct: 333 RFSFGPYKASDLSA 346



 Score = 40.4 bits (93), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 42/68 (61%), Gaps = 3/68 (4%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNG-ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+SK+++ + + SR + + +I   +VKVN  ++ +  AV++ S   IE++G P+     T
Sbjct: 14 RLSKILSLSAVTSRGKAQELIKNGKVKVNNQVVRQNVAVDINSA--IELEGKPILVDVTT 71

Query: 74 RLWLYHKP 81
          +LW  +KP
Sbjct: 72 KLWGIYKP 79


>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 = 55.8 bits (133), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/233 (24%), Positives = 99/233 (42%), Gaps = 22/233 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++  ++   G  +RR    +I Q  V V+        V +    +++  G+ LR   +  
Sbjct: 2   QLQDILYSQGFGTRRICAGLIQQGWVAVHSAGSLEPVVCLEPAQNLKEQGLVLRVQGQD- 60

Query: 75  LWLYH--------KPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISVGRLDIN 117
            W YH        KP G   +   P    +V+  LP         S  S V +VGRLD +
Sbjct: 61  -WPYHAKAYVMLNKPAGTECSQK-PSAYPSVYTLLPAPLRQRPGKSAVSGVQAVGRLDQD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLLL++DG     +  P     +VY+V     VD  ++  L  G+V+       ++ 
Sbjct: 119 TTGLLLLSDDGQFIHRMSSPKKHVPKVYQVTVRHPVDAAQVECLLAGVVLDDD-PKPVRA 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               Q+ ++  + + L EGK  ++K++      +V  L R   G  +L   +A
Sbjct: 178 VACVQRDAHR-IDLTLTEGKYHQVKRMIAAVGNRVEALHRARIGGLELPADMA 229


>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 = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 59/121 (48%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG  I
Sbjct: 216 LIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKVELLRKGCTI 275

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
             I    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++   
Sbjct: 276 DDIHIRPLELKIIKPNLLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKSSD 335

Query: 228 L 228
           L
Sbjct: 336 L 336



 Score = 38.5 bits (88), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 22/68 (32%), Positives = 39/68 (57%), Gaps = 3/68 (4%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+SK+++ + + SR + + +I    VKV N I+ +   ++V S   IEV+G  +     T
Sbjct: 14 RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQNTVIDVNS--KIEVNGCEINVDITT 71

Query: 74 RLWLYHKP 81
          +LW  +KP
Sbjct: 72 KLWGIYKP 79


>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 = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 49/199 (24%), Positives = 94/199 (47%), Gaps = 19/199 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I ++   +R   +R IA+  VK+NG ++ +A   V +   +   G  L +    R
Sbjct: 2   RLDKFICQSTNLTRTLAKREIARSNVKINGEVVRKADHKVTADMDVWFSGKSLSQ-RAPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + HKP+ ++         STV +  PS+ + + +         GRLD++T GL+L+T+
Sbjct: 61  YIMMHKPLDVIC--------STVDEEHPSVMNLIEADKREELHIAGRLDVDTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P     + YRV+    +    +   + GI ++      +   L+    S 
Sbjct: 113 DGKWSHRVTSPKRACNKRYRVQLAEAIAPTAVADFEAGIHLRSEDKPCLPAKLEIL--SE 170

Query: 187 AWVTVGLREGKNREIKKVF 205
             V + ++EGK  ++K++F
Sbjct: 171 KEVLLTIQEGKYHQVKRMF 189


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/156 (26%), Positives = 76/156 (48%), Gaps = 24/156 (15%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--I 165
           ++++GRLD  +EGL+LLT +G  A    + ++   + Y  +  G + + ++ +L+KG  I
Sbjct: 23  IMAIGRLDETSEGLILLTTNG--AYSYHVNNSNIEKEYYAQVDGIITEKEIKILQKGLPI 80

Query: 166 VIQGICYGDM----------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            I G  Y                   Q   D + G  +WV++ + EGK R+++K+     
Sbjct: 81  SINGSIYHTKPCKAKRIDTPLLPPTRQRIRDDRHGPTSWVSITVTEGKFRQVRKMTAAVG 140

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +   RL R+  G +++  +  G     S+KI+ E L
Sbjct: 141 FPTLRLARVRIGEYKIEQMQPGD----SEKIVVEAL 172


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/188 (25%), Positives = 87/188 (46%), Gaps = 31/188 (16%)

Query: 73  TRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L L++KP G+ +   D   +  +T+ +       R+   GRLD  +EGLL+LT+DG +
Sbjct: 4   SSLILFNKPYGVQSQFRDDSNNDHTTLSEYFTDKSLRI--AGRLDATSEGLLILTSDGRI 61

Query: 131 ARVLELPST---------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------IC 171
            + +  P +         +  + Y V+  G V   +L  L  G++++           + 
Sbjct: 62  NKAITQPPSAKNFAQNKQKQGKTYLVQVEGVVTAVQLKELASGVILKDGKTLPASATLLD 121

Query: 172 YGDMQVTL--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
             D+ +TL        + +    +W+ + + EGKNR+++++         RLIR S   F
Sbjct: 122 EADLPITLWQRDPPIRERKNIPTSWLMLTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGF 181

Query: 224 QLGTLLAG 231
           +LG L  G
Sbjct: 182 ELGELGVG 189


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 47/160 (29%), Positives = 71/160 (44%), Gaps = 19/160 (11%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + +++   G  +RR    ++A   V+VNG L E            EVDG  LR       
Sbjct: 5   LDRILQSQGFGTRRYCGDLVAAGLVEVNGELCEDPGAR------FEVDG--LRLMVDGEE 56

Query: 76  WL--------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLT 125
           WL         +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT
Sbjct: 57  WLACTKAYVMLNKPTGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
           +DG        P  Q  ++Y V     V  +++  L+ G+
Sbjct: 116 DDGQFIHAQTSPKKQVPKIYEVTTFDPVTPEQVEALRTGV 155


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 56/182 (30%), Positives = 89/182 (48%), Gaps = 23/182 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL  +HKP G+++  + P+GR      F +LP ++      GRLD ++EGLLLLT+DGGL
Sbjct: 8   RLLRFHKPYGVLSQFT-PEGRWRGLKDFIDLPGVY----VAGRLDADSEGLLLLTDDGGL 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT-------- 181
              +  P  +  + Y V+  G  D   L  L++G+ +  G         LD         
Sbjct: 63  QARIANPRFKMEKTYWVQVEGVPDAAALQALERGVQLNDGPTLPARARRLDAPPPVGERE 122

Query: 182 ------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 Q   + W+ + +REG+NR+++++         RL+R + GPF L  L  G+  E
Sbjct: 123 PPIRVRQHIPDTWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPFPLDGLAPGTWAE 182

Query: 236 VS 237
           V 
Sbjct: 183 VE 184


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 118/249 (47%), Gaps = 29/249 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG--VPLRKA 70
           +R+ K+++  G  SR++V +++    V VNG +     V+V    D + VDG  VP+R  
Sbjct: 4   ERLDKILSHHGFGSRKDVRKLLHAGSVAVNGTVCVSPDVHVDPDADELTVDGSSVPMR-- 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
            R    + +K  G+V +  D   R TVFD L   + +      +  VGRLDI+TEGLLLL
Sbjct: 62  -RHIYIMMNKCAGVVCSARDGLHR-TVFDLLDDSYRQEFLGGSLHMVGRLDIDTEGLLLL 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK----GIVIQGICYGDMQVTLD 180
           T DG L   L  P T   + Y +R    V  +   L+ +    GI I     GD     D
Sbjct: 120 TTDGTLTHRLTSPKTHVTKTYTIRLKNCVPDEAQPLITRRFSDGIHIAP--DGD-DGEYD 176

Query: 181 TQKGSNAW-----VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTR 234
            +     W      ++ + EG+  ++K++      +V  L RI+ G   L   L  G+ R
Sbjct: 177 CKPADLHWFSGTECSLVITEGRFHQVKRMIAAAGNEVVYLKRIAIGALLLDPALENGAYR 236

Query: 235 EVSKKILRE 243
           E+S   LRE
Sbjct: 237 ELS---LRE 242


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/187 (26%), Positives = 85/187 (45%), Gaps = 20/187 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGL 130
           + R ++ +KP  +V+     D  + +  NL   F     +VGRLD  +EGLL+LT +  +
Sbjct: 27  KNRYFIINKPFNMVSQFISSDAVN-LLGNLDFTFPEGTHAVGRLDNESEGLLILTTNKKV 85

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI---------VIQGICYGDM------ 175
            R+L   + +  R Y V    +V ++ L  L+ GI          I   C   +      
Sbjct: 86  TRLLFQGTKKHTRTYLVLVKNKVSEETLKQLQTGISIRVKGGGNYISSPCEASIVTDAKA 145

Query: 176 --QVTLDTQKGS-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                 DT++   + W+ + L EGK  +++K+    N +  RLIR+S     L  L  G+
Sbjct: 146 IYSYAADTRENYPHTWLLLTLTEGKFHQVRKMVLAVNHRCLRLIRVSIENMLLHDLQPGA 205

Query: 233 TREVSKK 239
            +E  ++
Sbjct: 206 VKEFEEE 212


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 95/224 (42%), Gaps = 19/224 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     SR   ++ I    V  +G++++  A  V     +   G  L      R
Sbjct: 2   RLDKYLAETTALSRGLAKKAINSGDVSCDGVVMKDPAFKVPQGARVCFQGEVLALV-GVR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTN 126
             + HKP+  + +  D        +  PS+ S        ++   GRLD +T GL+L+T+
Sbjct: 61  YLMLHKPVDTICSTQD--------EYYPSVLSLLDIARPDKLHIAGRLDADTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P     + YRV+    +  D +    +G+ + G         L+    + 
Sbjct: 113 DGLWSHKVTSPKRDCAKRYRVQLAESLTDDLIAQFAEGVQLNGEDGLTKPAKLELLSDTE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           A +++   EGK  ++K++F     KV  L R + G  +L   LA
Sbjct: 173 ALLSI--TEGKYHQVKRMFAAVGNKVIGLHREAVGAIELDPQLA 214


>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 = 55.1 bits (131), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 91/208 (43%), Gaps = 5/208 (2%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           A +ASR+   R      V V+G + +  A  V     +E +G  +  A   R  + +KP 
Sbjct: 4   ARLASRQR--RSYKSGEVTVDGEVQKSGAFKVPEGGVVEWEGREV-GAPGPRYIMLYKPA 60

Query: 83  GLVTTHSDPDGRST-VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
             V +H D    +  V  + P +   +   GRLD++T GL+L+T+DG  +  +  P  + 
Sbjct: 61  DFVCSHEDGHNPTAFVLLDEPKV-ENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKC 119

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            + YRV     +  D +    +GI ++      +   L+    +   V + + EGK  ++
Sbjct: 120 EKTYRVWLVDAIQPDYVEKFAEGIELRNEREATLPAHLEIVNEAENEVLLTIVEGKYHQV 179

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           K++F     KV  L R   G   L   L
Sbjct: 180 KRMFAALGNKVEHLHRERIGSIVLDEAL 207


>gi|76665077|emb|CAJ17986.1| rRNA pseudouridylate synthase [Candidatus Phytoplasma solani]
          Length = 96

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 49/88 (55%), Gaps = 5/88 (5%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          +R+ KV+A A + SRR+ E +I Q+RVKVN  ++      V  +D I VD   + K   T
Sbjct: 2  ERLQKVLAAANLVSRRKAETLILQKRVKVNNQIVYELGTKVSPSDVITVDNTLITK---T 58

Query: 74 RLWLY--HKPIGLVTTHSDPDGRSTVFD 99
           L+ Y  +KP G ++T  D   R TV D
Sbjct: 59 PLFYYLLNKPQGYLSTAKDNKTRQTVLD 86


>gi|290977401|ref|XP_002671426.1| predicted protein [Naegleria gruberi]
 gi|284084995|gb|EFC38682.1| predicted protein [Naegleria gruberi]
          Length = 244

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 118/250 (47%), Gaps = 31/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV----KVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+ +V++  GI SR +V   I +  V    K   IL  +  ++    + + V+G P    
Sbjct: 3   RIDRVLSGMGICSRSDVIHYIRKNEVMDTIKKQRILSLKHKISEHQLESLMVNGKPFPFP 62

Query: 71  ERTRLWLYHKPIG-LVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLT 125
                   +KP   L +T  +      ++D LP  F      + +VGRLD+++ GLL++T
Sbjct: 63  TLNLTIALNKPESYLCSTQRESSNHKIIYDLLPPEFLNRNPTLGNVGRLDLDSCGLLIMT 122

Query: 126 NDGGL-ARVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQV-----T 178
            DG L  R+L   S    + Y V F   ++ D +LN +K+         GD+Q+     T
Sbjct: 123 QDGDLHHRIL---SADVEKTYLVEFVPPIESDVELNQMKELFF-----SGDLQLRSEDST 174

Query: 179 L----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL---LAG 231
           L    + +  + + +++ + EGK  +++++F   + +V  L RI  G   L  L    +G
Sbjct: 175 LKPITNFEYINPSTISISIVEGKYHQVRRMFAACSKRVVGLKRIKIGDLTLEGLNIETSG 234

Query: 232 STREVSKKIL 241
           +   +SK++L
Sbjct: 235 AWCVLSKEVL 244


>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 = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 51/229 (22%), Positives = 102/229 (44%), Gaps = 25/229 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I  +   +R   ++ + +  +  +G++++ +   V+    + +DG P+     
Sbjct: 6   PVRLDKFICESTSLTRSLAKKALHRGEITCDGVVVKDSGFKVLEGMQVCLDGEPISLVGE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLL 124
            R  + +KP+  +         ST+ +  PS+ S         +   GRLD +T GL+L+
Sbjct: 66  -RYLMLNKPVDTIC--------STIDEAYPSVLSLLDIEKPETLHIAGRLDADTTGLVLI 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDT 181
           T+DG  +  +  P     + Y V     VD+  + +   G+ ++   G+    +   ++ 
Sbjct: 117 TSDGQWSHRITSPKKDCGKRYLVALADPVDESLVGIFAAGVELRNEDGLTKPAVLEIIEP 176

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           Q      V + + EGK  ++K++F      V  L R S G  +L + LA
Sbjct: 177 Q-----LVRLTITEGKYHQVKRMFAAVGNHVVGLHRESIGRIELDSDLA 220


>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 = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/138 (23%), Positives = 69/138 (50%), Gaps = 4/138 (2%)

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           + ++ + +++P     +I V  L  ++EGL+LLTNDG  AR L+      +  Y V+   
Sbjct: 211 ETKNNIANDIPE---HLIVVNSLSASSEGLVLLTNDGDFARNLKGIENNIITSYIVKVKE 267

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-WVTVGLREGKNREIKKVFEFFNW 210
           ++  +K+ L++KG  +  +    + V +  Q  S+  W+ +   E  +  +  +F  +  
Sbjct: 268 ELTNEKIKLIEKGCNVGDVHIRPLDVHVIKQHSSSPKWIKLTYVEKSHTYLNLLFSKYGL 327

Query: 211 KVNRLIRISYGPFQLGTL 228
            + +  R S+GP++   L
Sbjct: 328 TIRKCKRFSFGPYKASDL 345


>gi|237735675|ref|ZP_04566156.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229381420|gb|EEO31511.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 235

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 101/224 (45%), Gaps = 16/224 (7%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           V+ +  + + +  + +I    ++VN  ++      V + D I    + L  A+    ++ 
Sbjct: 12  VLMKNKLGNHKICKTLIRHGEIRVNDQVITDVRYPVKADDIIMYHHIQLN-AQPFVYYMM 70

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP   +  + D   +  +      +  R     +GRLDI+T GLL++TND  L++ L L
Sbjct: 71  NKPADYLCANHDKYHQCVI-----DLIGREDCYCLGRLDIDTTGLLIITNDTSLSKKLLL 125

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLR 194
           P     + Y V     +  + +     G+VI     C   +   LD     +  VT+   
Sbjct: 126 PQNHVNKKYYVTTKFPLKDELIKKFSDGVVIDHKVQCLPSLLEILDE---YHCLVTIN-- 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           EG+  +IKK+F+    +V  L RI++   +L   LA G  R+++
Sbjct: 181 EGRYHQIKKMFKSCQNEVCTLKRIAFAGIELDQKLALGEYRDLT 224


>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 = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/174 (27%), Positives = 82/174 (47%), Gaps = 25/174 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL- 130
           RL   +KP G +   S  + R+++  + N+P ++      GRLD ++EGLLLLT+DG L 
Sbjct: 2   RLIALNKPYGTICQFSAHETRASLATWVNVPDVYP----AGRLDADSEGLLLLTDDGALQ 57

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----------------QGICYGD 174
           AR+ E P  + ++ Y  +  G      L  L++G+ +                 G+   D
Sbjct: 58  ARIAE-PRHKLVKRYWAQLDGAAPASALAALERGVDLGDYVSRPCRARFIEPPSGLWQRD 116

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
             V       +  W+ + L EG+NR+++++     +   RLIR+  G   L  L
Sbjct: 117 PPVRYRAAIPTT-WIELALGEGRNRQVRRMTAAVGFPTLRLIRVGIGALDLFAL 169


>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 = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 45/182 (24%), Positives = 87/182 (47%), Gaps = 27/182 (14%)

Query: 79  HKPIGLVT---THSDPDGRSTVF-DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +KP G+++   ++ + + R   F   L      ++ VGRLD  +EGLLLLT DG L+  +
Sbjct: 10  YKPFGMLSQFISNDEKEARKKHFLGELYDFPEGIMPVGRLDEKSEGLLLLTTDGKLSDTI 69

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY------------------GD 174
                +  + Y  +  G++  + +  L++G++I   G  Y                   D
Sbjct: 70  NQSGIE--KEYYAQLDGEIPHEDILQLERGVLIGLSGKKYITKPCRVKALLDPPLLTDPD 127

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            ++ + T +  N+W+++ + EGK R+++K+     +   RLIR+  G   L  L  G+  
Sbjct: 128 KKLRIGTHR-PNSWISITITEGKFRQVRKMTAAVGFPTLRLIRVRIGTQILEDLQPGTVA 186

Query: 235 EV 236
           ++
Sbjct: 187 QI 188


>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 = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/136 (29%), Positives = 67/136 (49%), Gaps = 9/136 (6%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAERTRL 75
           K +   GI SR++ + +I    V +NG  ++   A ++  S + +++DG  +        
Sbjct: 5   KYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGKAVTVIPEPYF 64

Query: 76  W-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG L  
Sbjct: 65  YILLNKPTDYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDGHLNH 123

Query: 133 VLELP---STQWLRVY 145
            L  P   + Q +R Y
Sbjct: 124 KLTSPNHKNPQTVRSY 139


>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 = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 61/246 (24%), Positives = 104/246 (42%), Gaps = 22/246 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++ +++   G  +RR    +I    V++     +     V +   +++D   L    + +
Sbjct: 2   QLQEILYSQGFGTRRVCAGLIQHGHVQLRK-KNDTGDAWVCTDASLDIDPEGLTFHVQGK 60

Query: 75  LWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
           +W +H        KP   V     P    +V+  LP    +         V ++GRLD +
Sbjct: 61  VWQWHERAYVMMNKPAA-VECSQKPSTYPSVYTLLPDPLRQRPGPGKILGVQTIGRLDQD 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLLL++DG     +  P  Q  + YRV     + Q + + L KG+V+       +  
Sbjct: 120 TTGLLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQLLKGVVLNDDPKPVIAA 179

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
               Q+GS   +TV   EGK  +IK++      +V +L RI  G   L   L AG  R +
Sbjct: 180 DCVLQEGSVFDLTV--TEGKYHQIKRMVAAVGNRVEQLHRIRIGGLHLPDDLQAGDWRWL 237

Query: 237 SKKILR 242
               +R
Sbjct: 238 GDDDVR 243


>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 = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/154 (28%), Positives = 72/154 (46%), Gaps = 20/154 (12%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            ++VGRLD ++EGLLL+T DG L+  +   S    + Y     G + +  +  L+ G+ I
Sbjct: 40  AMAVGRLDEHSEGLLLITTDGQLSHHIN-KSGIVDKEYAALVDGLITEQAIEQLQNGVTI 98

Query: 168 --QGICYG-------------DM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
              G  Y              D+    Q   D + G  +WV V L EGK R+++K+    
Sbjct: 99  SINGSTYDTKPCQVQKPNQIPDLPETKQKIRDERHGPTSWVNVTLSEGKFRQVRKMTGVV 158

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +   RL R+  GP+ + +L      E+S + +R
Sbjct: 159 GFPTLRLARVRIGPYNVLSLRNQQVIELSDQEIR 192


>gi|291550526|emb|CBL26788.1| pseudouridine synthase family [Ruminococcus torques L2-14]
          Length = 194

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 52/95 (54%), Gaps = 2/95 (2%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARVL 134
           ++++KP G VT   D     TV D    + +  ++ VGRLD  T GLLL+T+DG   + L
Sbjct: 5   YMFNKPFGCVTARRD-SLYPTVMDYFSELNNDNLNPVGRLDRETTGLLLITDDGVFNQKL 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             PS    + Y     G + +D+   L+KGI+++G
Sbjct: 64  THPSYHKEKTYHFTVLGDLTEDRCQQLEKGILLKG 98


>gi|311696250|gb|ADP99123.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 230

 Score = 54.3 bits (129), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 60/229 (26%), Positives = 110/229 (48%), Gaps = 10/229 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA +   SR+E +R I +  V +N  + + A   +   + + + G PL      R
Sbjct: 2   RLDQFIANSTELSRKEAKRAIGRGEVTINEQICKGANTRLAGDERVALSGTPL-SLPGER 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V+  +D D   T  D LP+  +R + + GRLD +T GLLLLT DG  +  
Sbjct: 61  YLMMNKPAGVVSATTDSD-HPTALDLLPAEITRHLHIAGRLDADTTGLLLLTTDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P T   + YRV  +  +       L++G+ +    + D + T   +     +  + +
Sbjct: 120 VTSPRTDCPKTYRVTLNEPLSDAAAQQLERGVDL----HNDPRPTRPARVHFLEDRIIEL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            + EG+  ++K++       V  L R+  G  +L   L+ G  RE++ +
Sbjct: 176 TISEGRYHQVKRMMAAVGNHVEALHRVRIGQVELDDALMPGEYRELTAE 224


>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 = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 98/223 (43%), Gaps = 17/223 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERT 73
           + +++   G  +RR    +IA   V+VNG L E  RA   V     + VDG       + 
Sbjct: 3   LDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQFEVDGL-RLTVDGEEWLACTKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG   
Sbjct: 62  YLML-NKPAGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFI 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNA 187
                P  +  ++Y V     V  ++   L+ G+ +      I     ++T +       
Sbjct: 120 HAQTSPKRKVPKIYEVTTAEPVTPEQAEALRSGVQLLDEPAPIAAEACEITGERS----- 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + + L +GK  ++K++       V+ L R + G   L   LA
Sbjct: 175 -LRLTLVQGKYHQVKRMVVAAGNHVDALHRSAIGSLPLDPALA 216


>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 = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 100/227 (44%), Gaps = 21/227 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   +R + +  V  +G++++ +   V+    + +DG  L      
Sbjct: 1   MRLDKFICESTELTRSLAKRALHRGDVTCDGVVVKNSGFKVLPQMAVHLDGT-LISVIGE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---------GRLDINTEGLLLL 124
           R  + +KP+  +         ST+ +  PS+ S +I +         GRLD++T GL+L+
Sbjct: 60  RYIMLNKPVDTIC--------STIDEEYPSVLS-LIDIEKMDTLHIAGRLDVDTTGLVLI 110

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG  +  +  P     + Y V     +D   + +   G+ ++          LD    
Sbjct: 111 TSDGQWSHKITSPKKDCGKRYWVELAEPIDDSLIQVFADGVELRNEDGLTKPALLDIIDS 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           ++  +T+   EGK  ++K++F     +V  L R + G  +L   LA 
Sbjct: 171 THVRLTIS--EGKYHQVKRMFAAVGNRVVNLHREAVGAIELNADLAA 215


>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 = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 69/151 (45%), Gaps = 25/151 (16%)

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-----LRVYRVRFHG-----QV 153
           + S++ ++GRLD +T GLLLLTNDGGL   +  P+++       + Y     G     Q 
Sbjct: 1   VHSKLHAIGRLDADTTGLLLLTNDGGLVHWITNPTSKQDSDPIPKTYEAVIMGHHYLPQC 60

Query: 154 DQDKLN----------LLKKGIVIQGICYG-----DMQVTLDTQKGSNAWVTVGLREGKN 198
           D    N          L++ G ++     G     D    L     S   V++ + EGKN
Sbjct: 61  DGPFTNNDNNTYPLMTLIQNGALLPQKYGGHTRPVDRLSVLSHPTRSTTRVSITISEGKN 120

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           R+I+++F      V +L R+S G   L  L+
Sbjct: 121 RQIRRMFHAIGSGVMKLHRVSVGDLNLSGLM 151


>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 = 53.9 bits (128), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 101/224 (45%), Gaps = 16/224 (7%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           V+ +  + + +  + +I    ++VN  ++      V + D I    + L  A+    ++ 
Sbjct: 12  VLMKNKLGNHKICKTLIRHGEIRVNDQVITDVRYPVKADDIIMYHHIQLN-AQPFVYYMM 70

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP   +  + D   +  +      +  R     +GRLDI+T GLL++TND  L++ L L
Sbjct: 71  NKPADYLCANHDKYHQCVI-----DLIGREDCYCLGRLDIDTTGLLIITNDTSLSKKLLL 125

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLR 194
           P     + Y V     +  + +     G+VI     C   +   LD     +  VT+   
Sbjct: 126 PQNHVNKKYYVTTKFPLKDELIKKFFDGVVIDHKVQCLPSLLEILDE---YHCLVTIN-- 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVS 237
           EG+  +IKK+F+    +V  L RI++   +L   LA G  R+++
Sbjct: 181 EGRYHQIKKMFKSCQNEVCTLKRIAFAGIELDQKLALGEYRDLT 224


>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 = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 110/241 (45%), Gaps = 28/241 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEV--DGVPLR 68
           R+ K++A  G  SR+E++  I       NG + ++   N +  D    H E+  D  PL 
Sbjct: 2   RLVKLLANLGYGSRKEMQAAIR------NGWITDKDG-NAIKADSKLPHEEILFDDEPLD 54

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLL 124
             E + + L +KP+G   +  D  GR  VFD LP  +      +  VGRLD +T GLLL 
Sbjct: 55  PPEGSVI-LLNKPLGYTCSMKD-RGR-LVFDLLPDRYRVRKPALSFVGRLDKDTTGLLLF 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQK 183
           T+DG L   +  P     ++Y V     +   + +L   G ++++          L+   
Sbjct: 112 TDDGKLLHRIISPKADVAKIYEVELDRPMTGGEGDLFASGEMMLENETNPLKPAELEVLS 171

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++A +T  L EG+  +++++F      V  L R      QLG L      E + K+L +
Sbjct: 172 ETSARLT--LHEGRYHQVRRMFAATGNHVTNLHRA-----QLGGLTLEGVEEGTWKLLAQ 224

Query: 244 Q 244
           +
Sbjct: 225 E 225


>gi|241765880|ref|ZP_04763813.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241364178|gb|EER59374.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 249

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 99/241 (41%), Gaps = 37/241 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++  ++   G  +RR    ++ Q  V+      + AA +  +    E D   LR   +  
Sbjct: 2   QLQDILYSQGFGTRRVCAGLVQQGWVETASGDPD-AAFSACTEASAEFDVDDLRLKVQGV 60

Query: 75  LWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
           LW YH        KP G   +   P    +++  LP+   +         V +VGRLD +
Sbjct: 61  LWPYHAKAYIMLHKPAGTECSQK-PSTYPSIYTLLPAPLRQRPCKGAIQGVQAVGRLDQD 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--------G 169
           T GLLLL++DG     +  P     +VY+V     VD+ ++  L  G+V+          
Sbjct: 120 TTGLLLLSDDGQFIHRMSSPKKHVPKVYQVTTKHPVDERQIAALLAGVVLDDDPKPVRAA 179

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
            C       +D+ +     +++ L EGK  ++K++      +V  L R   G   L   L
Sbjct: 180 AC-----SVVDSHR-----LSLTLTEGKYHQVKRMLAAVGNRVEALHRSRIGTLDLPADL 229

Query: 230 A 230
           A
Sbjct: 230 A 230


>gi|222110316|ref|YP_002552580.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729760|gb|ACM32580.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 245

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 96/227 (42%), Gaps = 20/227 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------ 68
           ++  ++   G  +RR    +I Q RV ++        +   +T  I+V+ + LR      
Sbjct: 2   QLQDILYSQGFGTRRICAGLIQQGRVAMHATGTLEPTICQDATQDIDVESLVLRVQGVDW 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTE 119
             +     + HKP G   +   P    +++  LP+   +         V +VGRLD +T 
Sbjct: 62  PYQPKAYVMLHKPAGTECSQK-PSAYPSIYTLLPAPLRQRPSKGAVDGVQAVGRLDQDTT 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLL++DG     +  P     +VYRV     V +++++ L  G+V+         V  
Sbjct: 121 GLLLLSDDGQFIHRMSSPKKHVPKVYRVTAKHPVTKEQVDRLLAGVVLDD---DPRPVRA 177

Query: 180 DTQKGSNAWV-TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 +A V  + L EGK  ++K++      +V  L R   G   L
Sbjct: 178 AACALVDAHVLDLTLTEGKYHQVKRMIAAVGNRVEALHRSHIGRLAL 224


>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 = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 98/223 (43%), Gaps = 17/223 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERT 73
           + +++   G  +RR    +IA   V+VNG L E  RA   V     + VDG       + 
Sbjct: 3   LDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQFEVDGL-RLTVDGEEWLACTKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            L L +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG   
Sbjct: 62  YLML-NKPTGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFI 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNA 187
                P  +  ++Y V     V  ++   L  G+ +      I     ++T +       
Sbjct: 120 HAQTSPKRKVPKIYEVTTAEPVTPEQAEALCSGVQLLDEPAPIAAEACEITGERS----- 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + + L +GK  ++K++       V+ L R + G  +L   LA
Sbjct: 175 -LRLTLVQGKYHQVKRMVAAAGNHVSALHRSAIGGLRLDPALA 216


>gi|329119600|ref|ZP_08248281.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327464197|gb|EGF10501.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 186

 Score = 53.5 bits (127), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 38/166 (22%), Positives = 74/166 (44%), Gaps = 23/166 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L +++KP G+V      +   ++  F + P  +      GRLD ++EGLLLLT +G +  
Sbjct: 4   LIVFNKPCGVVCQFGAHEKHRSLKDFIDAPGFYP----AGRLDTDSEGLLLLTCNGRMQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA----- 187
            +  P  +  + Y  +  G    DKL  L++ + +        ++ L     ++A     
Sbjct: 60  RIAHPKFKLEKTYWAQLEGSPQADKLAALQRPMDLGDFVARPAKIRLPDAGETDALWPRV 119

Query: 188 ------------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                       W+ + + EGKNR+++++     +   RL+R+  G
Sbjct: 120 PPVRLRKTVPDFWLEIKIAEGKNRQVRRMTAKAGYPCLRLVRVGIG 165


>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 = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 53/191 (27%), Positives = 86/191 (45%), Gaps = 36/191 (18%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDGGLA 131
           +++KP G VT       R T++  +   FS     R+  VGRLD  T GLLL+T+DG   
Sbjct: 1   MFNKPFGCVTAR-----RDTLYPTVMDYFSELHNDRLNPVGRLDRETTGLLLITDDGNWN 55

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTL---DTQKG-- 184
           + L  P+    + Y     G + +D+   L+ GI+++G  +     ++TL   DT     
Sbjct: 56  QQLTHPAYHKKKTYLFTVLGDLTEDRRQFLENGILLKGSPVPTSPAKITLFKKDTLANIL 115

Query: 185 ---------------SNAWVTVG---LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                           +  VT G   + EG+ R+I+++ +  +  V  L RIS     L 
Sbjct: 116 DTLHPEVRNAVRTNLPSHPVTYGEITISEGRKRQIRRMMKAVHCCVIELKRISIDDIHLD 175

Query: 227 TLLA-GSTREV 236
             LA G  +E+
Sbjct: 176 ESLAPGKWKEI 186


>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 = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 97/220 (44%), Gaps = 14/220 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIE---VDGVPLRKA 70
           R+ +++   G  SR E+ ++   +R+ ++G  +   A  + MS D  E   V G PL   
Sbjct: 8   RIDRLLGSLGYGSRGEIAQIARARRIVLDGARVANVAKRIPMSPDLTERMTVHGAPL-DP 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               + + +KP G + +  D      V+D LP  +      +  VGRLD  T GLLLLT+
Sbjct: 67  LLGMVVMMNKPAGYICSRKD--SGPLVYDLLPDRWRHRKPMLSPVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
            G L   +  P+    + YR      ++  ++N+   G +++ G         L     +
Sbjct: 125 HGDLLHRITSPNLAVEKTYRASLARPLEGHEVNVFASGELMLSGEKKPLHPAKLSVLSPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            A + +   EG+  +++++F      V  L R + G   L
Sbjct: 185 EARLNI--TEGRYHQVRRMFAAVGNHVEALHREALGDLTL 222


>gi|289807462|ref|ZP_06538091.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 74

 Score = 53.1 bits (126), Expect = 6e-05,   Method: Compositional matrix adjust.
 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|262038667|ref|ZP_06012031.1| ribosomal large subunit pseudouridine synthase B [Leptotrichia
           goodfellowii F0264]
 gi|261747309|gb|EEY34784.1| ribosomal large subunit pseudouridine synthase B [Leptotrichia
           goodfellowii F0264]
          Length = 112

 Score = 53.1 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 34/94 (36%), Positives = 53/94 (56%), Gaps = 3/94 (3%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +KP G++++  D + R TV D L + +    V  +GRLDI+TEGLL+LTNDG L   L
Sbjct: 17  MMNKPDGVISSTEDDEHR-TVIDLLENKYRTYSVFPIGRLDIDTEGLLILTNDGILTHKL 75

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             P+    + Y V     V +  +  L+ GI ++
Sbjct: 76  LAPNKHVDKKYYVELKNPVLKSDIEKLENGIELE 109


>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 = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 41/173 (23%), Positives = 74/173 (42%), Gaps = 25/173 (14%)

Query: 79  HKPIGLVTTHSDPDGRST----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +KP G+++  +  + R          L       + VGRLD  +EGLLL+T DG L+  +
Sbjct: 12  YKPFGMLSQLASNEERQIRSKRFLSELHEFPEGTMPVGRLDEKSEGLLLMTTDGKLSDTI 71

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLD------------ 180
                +  + Y  +  G +    + +L  G+ I  +GI Y     T+             
Sbjct: 72  NRKGIE--KEYYAQLDGDISPKAIEILATGVEIGFEGIRYTTKPCTVQKINFKPSLPAPD 129

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                 +   N+W+++ + EGK R+++K+     +   RL+R+  G   L  L
Sbjct: 130 KRIRLARHRPNSWISIVITEGKFRQVRKMTAAVGFPTLRLVRVRIGALILDDL 182


>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 = 52.8 bits (125), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 51/179 (28%), Positives = 90/179 (50%), Gaps = 16/179 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RL L++KP  +++  SD +G+ T+ D + +    V   GRLD ++EGLLLLT+DG L  
Sbjct: 2   ARLILFNKPYQVISQFSDSEGKKTLADFIDT--KNVYPAGRLDFDSEGLLLLTDDGLLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-----------DT 181
            +  P  +  + Y V+  G  D   +  L  G+ ++       +V +             
Sbjct: 60  RISDPKHKSYKTYWVQVEGIPDNLAIQHLVNGVDLKDGKTLPAKVNIIDEPNLWDRHPPI 119

Query: 182 QKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++ SN   +W+ + + EGKNR+++++         RL+R+S G + L  L  G  +E+S
Sbjct: 120 RQRSNDVTSWLEIQIMEGKNRQVRRMTAAVGHPTLRLVRVSIGQWHLEQLKPGEFKELS 178


>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 = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 68/165 (41%), Gaps = 25/165 (15%)

Query: 80  KPIGLVTTHSDPDGRST----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           KP G ++     D R          L       +++GRLD  +EGLLL+T DG L+  + 
Sbjct: 10  KPYGFISQLLSNDERQARKKKFLSELHDFPEGTMAIGRLDEKSEGLLLMTTDGKLSDTIN 69

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL-------------- 179
               +  + Y V+  G +  D ++ +  G+ I   G  Y      +              
Sbjct: 70  RSGIE--KEYYVQVDGMITDDAIDQMAAGVEIGFDGKKYQTKPCKVRRLIENPTLPERSK 127

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
              D + G   W+ V + EGK R+++K+     +   RL+RI  G
Sbjct: 128 KIRDARHGPTPWIAVTITEGKFRQVRKMTSAVGFPTLRLVRIRIG 172


>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 = 52.8 bits (125), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 31/130 (23%), Positives = 61/130 (46%), Gaps = 15/130 (11%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQG 169
            GRLD+++EGL+ LT+ GGL + +  P  +  + Y  +  G + ++ L  L++G+ +  G
Sbjct: 37  AGRLDLDSEGLMFLTDHGGLNQFITNPKNKKFKTYLAQVDGDITEEALEQLRRGVELADG 96

Query: 170 ICYGDMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           +        ++  +                  WV + + EG+NR+++++     +   RL
Sbjct: 97  MTLPAKARKVEQPEWLWDRDPPVRFRASIPTTWVELQICEGRNRQVRRMTAAVGFPTLRL 156

Query: 216 IRISYGPFQL 225
           IR   G   L
Sbjct: 157 IRTQIGTIDL 166


>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 = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 53/222 (23%), Positives = 92/222 (41%), Gaps = 17/222 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           ++ +++   G  +RR    ++ Q  V V G+     A+  ++      V GV     E+ 
Sbjct: 2   QLQEILFSQGFGTRRVCAGLVQQGFVTVAGVPCTEPAMEFIAVGLRFTVQGVAWEYHEKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--------RLDINTEGLLLLT 125
            L L HKP G   +   P    +++  LP+   +             RLD +T GLLLL+
Sbjct: 62  YLML-HKPAGHECSQK-PSTYPSIYTLLPAPIRQRGGGAAAGVQAVGRLDQDTTGLLLLS 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--TLDTQK 183
           +DG     +  P     +VY V     VD  ++  L  G+V+      D +       ++
Sbjct: 120 DDGKFIHRMSSPRHHVPKVYEVTAKHPVDAQQVQKLLAGVVLD----DDPKPVRAAACEQ 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            S   +++ L EGK  ++K++      +V  L R   G   L
Sbjct: 176 TSELQLSLTLTEGKYHQVKRMIAAVGNRVEGLHRSRIGSLAL 217


>gi|255018863|ref|ZP_05290989.1| hypothetical protein LmonF_16091 [Listeria monocytogenes FSL
           F2-515]
          Length = 128

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 56/110 (50%), Gaps = 2/110 (1%)

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNA 187
            A +L  P  +  + Y  R  G  +++ +  L++G+VI G       ++V    +    A
Sbjct: 1   FANLLMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKA 60

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V + + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S
Sbjct: 61  IVEITIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELS 110


>gi|120600175|ref|YP_964749.1| pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146291897|ref|YP_001182321.1| pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120560268|gb|ABM26195.1| ribosomal small subunit pseudouridine synthase A [Shewanella sp.
           W3-18-1]
 gi|145563587|gb|ABP74522.1| ribosomal small subunit pseudouridine synthase A [Shewanella
           putrefaciens CN-32]
 gi|319425188|gb|ADV53262.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 229

 Score = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 52/227 (22%), Positives = 101/227 (44%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +G++++ A   V     I ++G P+      R
Sbjct: 2   RLDKFICESTSLTRSLAKKALHRGDITCDGVVIKDAGFKVTEGMQICLEGEPIVLVGE-R 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S         +   GRLD +T GL+L+T+
Sbjct: 61  YVMLNKPVDTIC--------STIDEAYPSVLSLLDIPKPETLHIAGRLDADTTGLVLITS 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +  KG+ ++   G+    +   +D Q+
Sbjct: 113 DGQWSHKITSPKKECGKRYLVQLADPVDDGLIEVFAKGVALRNEDGLTKPAVLEIIDPQQ 172

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R   G  +L   LA
Sbjct: 173 -----VRLTITEGKYHQVKRMFAAVGNLVVGLHRERIGQIELDPDLA 214


>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 = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 45/142 (31%), Positives = 69/142 (48%), Gaps = 3/142 (2%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P     V ++GRLD +T GLLLL++DG     +  P  Q  + YRV     + Q + + L
Sbjct: 109 PGKILGVQTIGRLDQDTTGLLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQL 168

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
            KG+V+       + V    Q+G    +TV   EGK  +IK++      +V +L RI  G
Sbjct: 169 LKGVVLNDDPKPVIAVDCVLQEGPVFDLTV--TEGKYHQIKRMVAAVGNRVEQLHRIRIG 226

Query: 222 PFQL-GTLLAGSTREVSKKILR 242
              L   L AG  R + ++ +R
Sbjct: 227 GLHLPDDLQAGDWRWLREEDVR 248


>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 = 52.4 bits (124), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 49/165 (29%), Positives = 74/165 (44%), Gaps = 13/165 (7%)

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLT 125
           W +H        KP G   +  DP   ++VF  LP+  +   V  VGRLD +T GLLLL+
Sbjct: 55  WPFHARAYLALNKPAGYECS-RDPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLS 113

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG        P  +  + Y       +D  +L+ L+ G+ + G       V  D +   
Sbjct: 114 DDGQFVHAYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADARAPH 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
              +TV   EGK  ++K++    + +V  L R S G F L   LA
Sbjct: 174 ALALTV--LEGKYHQVKRMVAAASNRVELLHRESIGGFTLPADLA 216


>gi|255066492|ref|ZP_05318347.1| ribosomal large subunit pseudouridine synthase E [Neisseria sicca
           ATCC 29256]
 gi|255049372|gb|EET44836.1| ribosomal large subunit pseudouridine synthase E [Neisseria sicca
           ATCC 29256]
          Length = 149

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 51/93 (54%), Gaps = 6/93 (6%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L + +KP G++   S  +    + D  +LP  +      GRLD ++EGLLLLTNDG L  
Sbjct: 6   LIVLNKPYGVICQFSAHEKYGCLKDYVSLPDFYP----AGRLDTDSEGLLLLTNDGRLQA 61

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            +  P  +  + Y  +  G  D+ KL++L++G+
Sbjct: 62  RIADPKFKLEKTYWAQVEGSPDEAKLDMLRRGV 94


>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 = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/228 (25%), Positives = 96/228 (42%), Gaps = 11/228 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R+S+V+   G  +RR+   +I    V+V G +++     + + D +  V G      ++ 
Sbjct: 2   RISQVLFSQGFGTRRDCAGLIHAGAVEVAGRVVDDPDEELPTEDLVFSVQGRAWPFHDKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            L L HKP     +   P     V   LP+      +  VGRLD +T G LLLT+DG L 
Sbjct: 62  -LVLLHKPTHYECSQK-PRHHPGVLSLLPTPLRVRGLQPVGRLDEDTTGALLLTDDGTLI 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--TLDTQKGSNAWV 189
             L  P     +VY +     +  +++  L +G+V+      D Q       ++     +
Sbjct: 120 HRLTSPKHHVPKVYEITAKHALADEQIARLTEGVVLD----DDPQPVRAAAAERTGEFTL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + L EGK  ++K++      +   L R   G   L  L  G  R V 
Sbjct: 176 RLTLTEGKYHQVKRMLAAVGNRCEALHRSRIGALALDDLPVGQWRWVG 223


>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 = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/229 (22%), Positives = 101/229 (44%), Gaps = 25/229 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I  +   +R   ++ + +  +  +GI+++ +   V+    + ++G P+     
Sbjct: 6   PVRLDKFICESTSLTRSLAKKALHRGEITCDGIVVKDSGFKVLEGMQVCLEGEPISLVGE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLL 124
            R  + +KP+  +         ST+ +  PS+ S         +   GRLD +T GL+L+
Sbjct: 66  -RYLMLNKPVDTIC--------STIDEAYPSVLSLLDIEKPETLHIAGRLDADTTGLVLI 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDT 181
           T+DG  +  +  P     + Y V     VD   + +   G+ ++   G+    +   ++ 
Sbjct: 117 TSDGQWSHRITSPKKDCGKRYLVTLADPVDGSLVGIFAAGVELRNEDGLTKPAVLEIIEP 176

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           Q      V + + EGK  ++K++F      V  L R S G  +L + LA
Sbjct: 177 Q-----LVRLTITEGKYHQVKRMFAAVGNHVVGLHRESIGRIELDSDLA 220


>gi|241767931|ref|ZP_04765482.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241360905|gb|EER57713.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 142

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 41/144 (28%), Positives = 68/144 (47%), Gaps = 23/144 (15%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL  ++KP G+++  +  +GR      + +LP ++      GRLD ++EGLLLLT+DG L
Sbjct: 4   RLIRFNKPYGVLSQFTA-EGRWQGLKDYIDLPGVYV----AGRLDADSEGLLLLTSDGKL 58

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG----- 184
              +  P  +  + Y V+  G  D+  L  L+ G+V+  G         L+         
Sbjct: 59  QARIADPRFKMEKTYWVQVEGIPDEAALAALRHGVVLNDGPTLPARARLLEPAPAVWPRN 118

Query: 185 ---------SNAWVTVGLREGKNR 199
                      AW+ + +REG+NR
Sbjct: 119 PPIRERKAIPTAWIELAIREGRNR 142


>gi|188495145|ref|ZP_03002415.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           53638]
 gi|188490344|gb|EDU65447.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           53638]
          Length = 104

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/67 (41%), Positives = 45/67 (67%), Gaps = 3/67 (4%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-A 131
           TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L A
Sbjct: 39  TRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQA 96

Query: 132 RVLELPS 138
           R++ LP+
Sbjct: 97  RLVMLPT 103


>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 = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 103/228 (45%), Gaps = 10/228 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ +++A  G  SRRE    I   RV + G     +     + D + +DG PL   +  
Sbjct: 2   RRLDQLLANLGYCSRREARSWIEAGRVTIGGEAANDSGQKAAAAD-VRIDGEPLDHPDGL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            L L+   +GLV +H + +G   ++  LP  + R    V SVGRLD  T GLLLLT+   
Sbjct: 61  LLLLHKP-LGLVCSHDEREG-PNIYSLLPERWRRRNPAVTSVGRLDKETSGLLLLTDQSL 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAW 188
           L   L  P  +  +VYR      +  D + L   G + ++G  +      L       A 
Sbjct: 119 LVHRLTSPKHKVPKVYRASVDRDLSPDLVPLFASGTLQLEGEAHPCAPAELRLLGPREAE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +T  L EG+  +++++       V  L R  +G   L  L  G+ RE+
Sbjct: 179 LT--LTEGRYHQVRRMLAACGLTVLTLHRARFGHLALDDLAPGAWREL 224


>gi|328463102|gb|EGF34868.1| 16S pseudouridylate synthase [Lactobacillus helveticus MTCC 5463]
          Length = 170

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 42/151 (27%), Positives = 72/151 (47%), Gaps = 4/151 (2%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G+++T  +   R+ +    P   +  ++ VGRLD +T  LLLLTNDG L   L  P
Sbjct: 2   NKPKGVLSTTENRSQRTVISLLDPQDRYQGIVPVGRLDKDTTDLLLLTNDGQLNHELLAP 61

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA--WVTVGLR 194
           +    ++Y  +  G  D + +     G+ +  G     +   +  Q   N    + + + 
Sbjct: 62  NKHVAKIYHAKIAGVADSNTVKTFATGMTLGDGTKLKTVTFNVLKQDVENGSSEIEIEIS 121

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           EGK  +IK++F     +V  L R+S G  +L
Sbjct: 122 EGKYHQIKRMFSVVGMEVVELERVSMGKLRL 152


>gi|167944991|ref|ZP_02532065.1| ribosomal large subunit pseudouridine synthase B [Endoriftia
          persephone 'Hot96_1+Hot96_2']
          Length = 88

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 47/79 (59%), Gaps = 5/79 (6%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
          +R+ KV+A AG+ SRRE+E  I++ R++VNG    +    V+ +D I +DG P  +    
Sbjct: 10 ERLQKVLANAGVGSRREIEGWISEGRIEVNGETA-KLGQRVVGSDRIRIDGRPFSQKRME 68

Query: 70 AERTRLWLYHKPIGLVTTH 88
          A   R+ +Y+KP G + T 
Sbjct: 69 APERRVLVYNKPEGELVTR 87


>gi|284007248|emb|CBA72545.1| ribosomal small subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 231

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 103/227 (45%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++    SR  V R +   +V V+  +++  +  +     +  DGV L+     R
Sbjct: 3   RLDKFLSQQLTISRGLVIRELRAGKVMVDNEIIKTGSYQITPEMIVSYDGVVLQHIIGPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V +  D    + + F + P+I +++   GRLDI+T GL+++T+DG     
Sbjct: 63  YFMLNKPQGYVCSTVDSVNLTILSFIDEPAI-TKLHIAGRLDIDTTGLVIITDDGKWTHK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  +  +    GI ++G         L     S+  V + +
Sbjct: 122 MISPKHHCEKTYLVTLAQPVSTELADKFLAGIWLKGEKLPTKPAKLSIV--SSKQVRLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKK 239
            EG+  ++K++F      V  L R   G   L   L AG  R ++++
Sbjct: 180 SEGRYHQVKRMFAAVGNHVCALHRERIGGIYLDPALRAGEYRSLTQE 226


>gi|217974709|ref|YP_002359460.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499844|gb|ACK48037.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 250

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T 
Sbjct: 82  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITT 133

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 134 DGQWSHKITSPKKECGKRYLVQLADPVDASLIAIFAAGVELRGEDGLTKPALLEIIEPQ- 192

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 193 ----LVRLTITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALA 235


>gi|281202742|gb|EFA76944.1| hypothetical protein PPL_09696 [Polysphondylium pallidum PN500]
          Length = 614

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 40/170 (23%), Positives = 78/170 (45%), Gaps = 12/170 (7%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISV-GRLDINTEGLLLLTNDGGLA-RV 133
           HKP G + +++       ++D LP  F++    +SV GRLD    GL+L++ DG +  R+
Sbjct: 180 HKPNGYICSNAREGDHKIIYDLLPPEFAKRLPTLSVAGRLDKWVTGLVLMSQDGKIVERI 239

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWV 189
           +      + ++Y V        ++    + G ++    +  C       LD  +      
Sbjct: 240 ITPKDDSFGKIYDVVCKAPFKGNEAEAFESGTMMLRSEEEPCKAAKFEVLDNDRN---LA 296

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + L EG+  +++++    + K   + RI  GP  LG L AG  R ++++
Sbjct: 297 RLTLYEGRYHQVRRMMAALDNKAMEIHRIKVGPIDLGDLPAGKWRYLTEE 346


>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 = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 55/223 (24%), Positives = 99/223 (44%), Gaps = 23/223 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K + ++   SR E   +I   +V+VN +++  A   V   + I + G  L  A  +R
Sbjct: 2   RLDKFLCKSTDFSRAESIDLIEAGQVRVNELVIVTAQTQVHENNCIMLAGRRL-VARPSR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + HKPI  + ++ D D         PS+ + +           GRLD +T GL+L+T+
Sbjct: 61  YIMLHKPIDTLCSNVDGD--------YPSVMNYIQVDRAEDLHITGRLDADTTGLVLITD 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL----KKGIVIQGICYGDMQVTLDTQ 182
           DG  +  +  P     + YRV     ++   ++ L    ++G+ +QG     +   L+  
Sbjct: 113 DGRWSFNIINPKYHCEKTYRVTLRDPIEDGDIDELVSRFEQGLQLQGEKKLTLAAKLEVI 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 +T  L EG+  ++K++F     +V  L R   G   L
Sbjct: 173 TPHQVLLT--LSEGRYHQVKRMFFTVGNRVVGLHRQQVGKLSL 213


>gi|303289291|ref|XP_003063933.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454249|gb|EEH51555.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 126

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/126 (30%), Positives = 61/126 (48%), Gaps = 16/126 (12%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V  VGRLD +++GL+LLT+DG +   L  P+ +  + Y V       +++L  L+ G+VI
Sbjct: 1   VFPVGRLDRDSDGLVLLTDDGRVPDALLDPTRKATKTYHVDVRPAPSEEELRRLRGGVVI 60

Query: 168 Q------GICY---------GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWK 211
           +      G+           GD       Q+G  N    +   EG+NR+I+K+ E     
Sbjct: 61  ETTQQRGGVSTTAPTVRARRGDSLSNPTRQRGLPNHIARIRDAEGRNRQIRKMCEAIGVD 120

Query: 212 VNRLIR 217
           V RL R
Sbjct: 121 VLRLRR 126


>gi|307304763|ref|ZP_07584513.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|306912165|gb|EFN42589.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 250

 Score = 51.2 bits (121), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T 
Sbjct: 82  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPDTLHIAGRLDADTTGLVLITT 133

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 134 DGQWSHKITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEPQ- 192

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 193 ----LVRLTITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALA 235


>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 = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + + G P+      R
Sbjct: 19  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLQGEPIALV-GVR 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T+
Sbjct: 78  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLVTS 129

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 130 DGQWSHKITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEPQ- 188

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 189 ----LVRLTITEGKYHQVKRMFAAVGNHVQELHRESVGQIELDPALA 231


>gi|160876850|ref|YP_001556166.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862372|gb|ABX50906.1| pseudouridine synthase [Shewanella baltica OS195]
          Length = 256

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 29  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T 
Sbjct: 88  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITT 139

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 140 DGQWSHKITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEPQ- 198

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 199 ----LVRLTITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALA 241


>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 = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 61/136 (44%), Gaps = 26/136 (19%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           ++SVGRLD ++EGLL LT DG  +    + S+   + Y V+  G   ++ +  L KG+ I
Sbjct: 39  IMSVGRLDQDSEGLLFLTTDGKFSH--HITSSGMEKEYWVQVDGIAKKEHVEKLSKGLKI 96

Query: 168 QGICYGDMQVTLDTQ----------------------KGSNAWVTVGLREGKNREIKKVF 205
               YG    TL  Q                       G  +W+++ L EGK R+++K+ 
Sbjct: 97  S--IYGKPYQTLACQVKLMEPPQDLPKRAKDIRNENDHGVTSWLSITLTEGKFRQVRKMT 154

Query: 206 EFFNWKVNRLIRISYG 221
                   RL+R   G
Sbjct: 155 AKIGLPTLRLVRYRIG 170


>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 = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 46/189 (24%), Positives = 81/189 (42%), Gaps = 14/189 (7%)

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           A ++    + +++DG  +        + L +KP    T+H  P    +VF   P     +
Sbjct: 6   ADIDSSYVETLDIDGEAVTVVPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNI 64

Query: 109 I--SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
              +VGRLD +T G+LL+TNDG L   L  PS +  ++Y V       +     LK G+ 
Sbjct: 65  DMQAVGRLDADTTGVLLITNDGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVP 124

Query: 167 I----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           +    + +C  D  +   T       + + + EGK  ++K++      +V  L R  +  
Sbjct: 125 LHDENETVCAADAVLENPTT------LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAH 178

Query: 223 FQLGTLLAG 231
            +   L  G
Sbjct: 179 LETENLKPG 187


>gi|315269053|gb|ADT95906.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 250

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T 
Sbjct: 82  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITT 133

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 134 DGQWSHKITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEPQ- 192

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 193 ----LVRLTITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALA 235


>gi|328462442|gb|EGF34470.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 102

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/77 (38%), Positives = 40/77 (51%)

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           GR  V D    +  R+  VGRLD +T GLL++TNDG LA  L  P     + Y  +  G 
Sbjct: 3   GRKVVTDYFEDVQERLYPVGRLDYDTSGLLVMTNDGELANHLMHPRYALEKKYVAKVEGI 62

Query: 153 VDQDKLNLLKKGIVIQG 169
            ++  L  LK G+ I G
Sbjct: 63  PNRPALAPLKTGVSIDG 79


>gi|153002130|ref|YP_001367811.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366748|gb|ABS09748.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 246

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 19  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T 
Sbjct: 78  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITT 129

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 130 DGQWSHKITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEPQ- 188

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 189 ----LVRLTITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALA 231


>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 = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 46/181 (25%), Positives = 81/181 (44%), Gaps = 24/181 (13%)

Query: 74  RLWLYHKPIGLVT------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           RL L++KP  +++      +   P    + F ++P    RV   GRLD ++EGLL+LT+D
Sbjct: 3   RLILFNKPYDVLSQFTGRGSADSPRATLSDFIDVP----RVYPAGRLDRDSEGLLVLTDD 58

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------TLDT 181
           G L   +  P  +  + Y  +  G  D   L  L++G+ +        +V      TL  
Sbjct: 59  GQLQARIANPRFKTEKTYFAQVEGLPDDATLAALRQGVTLNDGPTRPARVDRMEPPTLWP 118

Query: 182 QKG--------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +           + W+ + + EG+NR+++++         RLIR   G + L  +  G  
Sbjct: 119 RTPPVRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTLRLIRWRIGDWTLDGIGPGQW 178

Query: 234 R 234
           R
Sbjct: 179 R 179


>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 = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 109/227 (48%), Gaps = 5/227 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++ +   +R   ++ + +  V+VNG +++ AA  +     +   G PL +    R
Sbjct: 2   RLDRFLSESTELTRSLAKKALHRGEVEVNGDVVKNAAFKLGDEHVVRWLGEPLARIG-VR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G   T + P    +V + L  +   R+   GRLD++T GL+L+T DG  +  
Sbjct: 61  YLMLNKPAGYECT-TRPGRYPSVIELLDVAKRGRLHIAGRLDVDTTGLVLITEDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-VTVG 192
           L  P  +  + Y V     + +     L +G++++G     +   L+    ++   V + 
Sbjct: 120 LTSPRRRCDKHYLVTLARPLAEGAETALAEGLMLEGEDKPTLPARLERLDDADGVRVRLV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           ++EG+  +IK++F   + +V  L R   G   L   L AG  RE+++
Sbjct: 180 IQEGRFHQIKRMFAALDNEVVALHRERIGEIALDPALAAGEWRELTQ 226


>gi|145348269|ref|XP_001418577.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578806|gb|ABO96870.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 230

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 114/234 (48%), Gaps = 27/234 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDGVPLRKA-- 70
           R+SK +A  G+ASRR  + +I   RVKVNG  +   +  VN ++ D + VDG  +     
Sbjct: 1   RLSKALASLGVASRRGADDLIFGGRVKVNGETVTAPQTKVN-LNADVVMVDGKIVEGGVN 59

Query: 71  --ERTRLWLYHKPIGLV-TTHSDPDGRSTVFD---------------NLPSIFSRVISVG 112
             +    ++ +KP G V +T S+     TV+D                LP    R+ +VG
Sbjct: 60  FVKEHAYFMLNKPKGFVCSTKSNSAQGKTVYDLFEQWRDEFKAAYPGKLP---PRLFTVG 116

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD+ T GLLLLT DG  ++ +  PS++ ++ Y V  + +  + ++  + KG  + G   
Sbjct: 117 RLDVATTGLLLLTTDGDWSQRVAHPSSEVVKQYVVTANNKPTRAQIAAMAKGTEVDGARV 176

Query: 173 GDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             ++V ++    G    + V + +G+NRE++ +       V  L R   G  ++
Sbjct: 177 VPVRVESMGADGGPANRILVEVVDGRNREVRVLCADAGVDVKNLKRTRVGGLRM 230


>gi|205373780|ref|ZP_03226582.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus coahuilensis
           m4-4]
          Length = 131

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 31/116 (26%), Positives = 58/116 (50%), Gaps = 2/116 (1%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +TNDG  + +L  P  +  + Y  +  G   + +L  L++GI ++       +V   +  
Sbjct: 1   MTNDGEFSNLLTHPKYEIDKTYIAKIKGIPTRQELTKLQRGIKLEDGMTAPAKVKFISAD 60

Query: 184 GS--NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            S     V + + EG+NR+++++FE   + V +L R  +G   L  L AG  RE++
Sbjct: 61  RSKNTCIVELTIHEGRNRQVRRMFEALGFPVMKLRRERFGTLTLKGLNAGEARELT 116


>gi|304410666|ref|ZP_07392284.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|304351150|gb|EFM15550.1| pseudouridine synthase [Shewanella baltica OS183]
          Length = 250

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 51/227 (22%), Positives = 99/227 (43%), Gaps = 25/227 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + + G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVYLQGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S V           GRLD +T GL+L+T+
Sbjct: 82  YLMLNKPVDTIC--------STIDETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLVTS 133

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG  +  +  P  +  + Y V+    VD   + +   G+ ++   G+    +   ++ Q 
Sbjct: 134 DGQWSHKITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEPQ- 192

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                V + + EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 193 ----LVRLTITEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALA 235


>gi|323435911|ref|ZP_01048953.2| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|321496226|gb|EAQ40187.2| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 190

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 35/133 (26%), Positives = 63/133 (47%), Gaps = 21/133 (15%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--I 165
            ++VGRLD ++EGLL +T DG L+  +     +  + Y  +  G +  + +  L +G  I
Sbjct: 41  TMAVGRLDEHSEGLLFMTTDGKLSHTINTSGVE--KEYYAQVDGAITDEAILALTQGVEI 98

Query: 166 VIQGICY-----------GD------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            ++G  Y           GD       +   D + G   W+++ + EGK R+++K+    
Sbjct: 99  SVEGKKYITKPCKARRIDGDPGFPERSKKIRDLRHGPAPWISITITEGKFRQVRKMTSAV 158

Query: 209 NWKVNRLIRISYG 221
            +   RL+RI  G
Sbjct: 159 GFATLRLVRIKIG 171


>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 = 50.1 bits (118), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 52/224 (23%), Positives = 98/224 (43%), Gaps = 19/224 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I+ +   +R   ++ + +  V V+G +++  +  +  +  + +DG P+      R
Sbjct: 2   RLDKFISESTQLTRSLAKKALHRGEVTVDGQVIKDGSFKLNESQQVCLDGEPISLI-GPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTN 126
             + HKP   +         STV +  PS+ +         +   GRLD +T GL+L+T+
Sbjct: 61  FIMLHKPADTLC--------STVDEVYPSVLNLLDLPHKEDLHIAGRLDADTTGLVLITS 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + Y V+    +  + +     G+ ++         TL+      
Sbjct: 113 DGQWSHRVTSPKRECGKTYLVQLADPLKAEWVEQFATGLALRSEEGLTKPATLELLGSHE 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           A +T+   EGK  ++K++F     KV  L R S G   L   LA
Sbjct: 173 ARLTI--TEGKYHQVKRMFAAVGNKVVGLHRESVGEIVLDESLA 214


>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 = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 42/159 (26%), Positives = 73/159 (45%), Gaps = 5/159 (3%)

Query: 83  GLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G V +H D     T F  L  +    +   GRLD++T GL+L+T+DG  +  +  P  + 
Sbjct: 1   GFVCSHEDG-FNHTAFVLLDEVKMENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKC 59

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            + YRV     V  + +   ++GI ++      +   L+        +T+   EGK  ++
Sbjct: 60  AKTYRVWLADPVQDNYIKAFEEGIELRNEKAPTLPAQLEIIDEKEVLLTI--HEGKYHQV 117

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKK 239
           K++F     KV  L R S G   L  +L  G  R ++++
Sbjct: 118 KRMFAALGNKVEGLHRESVGDIVLDEMLEPGEYRYLTQE 156


>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 = 49.7 bits (117), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 41/141 (29%), Positives = 66/141 (46%), Gaps = 23/141 (16%)

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------IC 171
           +LLLT++G L + L  P     R Y V+  G  ++ +LN L++G+ IQG         I 
Sbjct: 1   MLLLTDNGRLQQRLTDPRFGHWRQYWVQVEGCANEVQLNQLQRGVTIQGRLTRPAKARIL 60

Query: 172 YGDMQVTLDTQKG--------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-- 221
             D + T+  +K            W+ + LREG+NR+++++         RLIR S    
Sbjct: 61  SDDERQTISDRKPPIRERRSIPTCWLCLELREGRNRQVRRMTAAVGLPTLRLIRHSIDLM 120

Query: 222 ----PFQLGTLLAGSTREVSK 238
                  +  L AG  REV++
Sbjct: 121 DGEIVLSIKDLSAGMWREVTR 141


>gi|258544931|ref|ZP_05705165.1| RNA pseudouridine synthase family protein [Cardiobacterium hominis
           ATCC 15826]
 gi|258519851|gb|EEV88710.1| RNA pseudouridine synthase family protein [Cardiobacterium hominis
           ATCC 15826]
          Length = 141

 Score = 49.7 bits (117), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 53/93 (56%), Gaps = 6/93 (6%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L +KP  ++   +D  GR+T+ D  ++P+++      G LD ++EGL++LT+DG L  
Sbjct: 30  LILLNKPFNVLCQFTDKSGRATLADYVDVPNVYP----AGLLDFDSEGLVVLTDDGRLQA 85

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            +  P  +  + Y V+  G+ D+  L  L+ G+
Sbjct: 86  RIADPRFKLAKRYWVQVEGEADEAALVQLRAGV 118


>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 = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 98/235 (41%), Gaps = 25/235 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKV-------NGILLERAAVNVMSTD-HIEVDGVP 66
           ++  ++   G  +RR    MI Q  V V         ++  +AA   ++    + V GV 
Sbjct: 2   QLQDILYSQGFGTRRVCAGMIQQGLVGVYESNQALAPVIYTQAATEFIAEGLRLRVQGVD 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDIN 117
               E+  + L HKP     +   P    +V+  LPS             V +VGRLD +
Sbjct: 62  WPYHEKAYVML-HKPSATECSQK-PSTYPSVYTLLPSALRLRPQKGAVQGVQAVGRLDQD 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLLLT+DG     +  P     +VY V     +D  ++  L  G+V+      D + 
Sbjct: 120 TTGLLLLTDDGQFIHRMNSPRHHVPKVYEVTVKHPLDDTQVARLLAGVVLD----DDPKP 175

Query: 178 --TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 +  S+  + + L EGK  ++K++    + +V  L R   G  +L   LA
Sbjct: 176 VRAAAAEAVSSHHLRLTLTEGKYHQVKRMVAAVSNRVEALHRSQIGGLRLPDDLA 230


>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 = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 48/219 (21%), Positives = 91/219 (41%), Gaps = 13/219 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + +++   G  +R+   ++IA   +++ G  +      +  TD +E          R R+
Sbjct: 6   LDRILHTQGFGTRKYCRQLIAAGAIRIGGDTITDTNTPI-ETDGLEFSVDDEHCIYRERI 64

Query: 76  WL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
           ++  +KP  +  +   P     V   LP  F+R  V  VGRLD +T GLLL+++DG    
Sbjct: 65  YVALNKPANIECSRK-PSHHPGVLSILPDQFTRRDVQPVGRLDHDTTGLLLMSDDGAFIH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWV 189
               P     +VY    +  V  + +  L  G+ +    G    ++   +D        +
Sbjct: 124 TQSSPKHHVPKVYVATTYAPVTGELIERLLAGVKLHDEPGTLAAEICRMIDDHH-----L 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            + L +GK  ++K++    +     L R   G  +L  L
Sbjct: 179 EIVLEQGKYHQVKRMLAAADNHCTALNRSQIGNLKLAEL 217


>gi|291336629|gb|ADD96175.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 74

 Score = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 29/37 (78%)

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + +VNRLIR+++GPFQLG L AG+  EV +  L+EQL
Sbjct: 5   DLQVNRLIRVAFGPFQLGNLSAGAVEEVPENKLKEQL 41


>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 = 49.3 bits (116), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 45/189 (23%), Positives = 80/189 (42%), Gaps = 14/189 (7%)

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           A ++    + +++DG  +        + L +KP    T+H  P    +VF   P     +
Sbjct: 6   ADIDSSYVETLDIDGEAVTVVPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNI 64

Query: 109 I--SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
              +VGRLD +T G+LL+TNDG L   L  PS +  ++Y V       +     LK G+ 
Sbjct: 65  DMQAVGRLDADTTGVLLITNDGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVP 124

Query: 167 I----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           +    + +C  D  +   T       + + + EGK  ++K++      +   L R  +  
Sbjct: 125 LHDENETVCAADAVLENPTT------LLLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAH 178

Query: 223 FQLGTLLAG 231
            +   L  G
Sbjct: 179 LETENLKPG 187


>gi|325115730|emb|CBZ51285.1| pseudouridine synthase, related [Neospora caninum Liverpool]
          Length = 567

 Score = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 31/122 (25%), Positives = 59/122 (48%), Gaps = 1/122 (0%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIV 166
           +I V  L +  +G +LLTNDG  A  ++ P  +   V+ VR  G +   ++    + G+ 
Sbjct: 253 LIVVRPLPVEADGFVLLTNDGDFAHAVQKPENRVQSVFDVRVSGTLPSYRVWESWRCGVA 312

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
             G  +G + V L     + AW+ + L E    +++ +      K+ RL R + GP++  
Sbjct: 313 SGGFDFGPVWVELLRAWHNAAWLRLHLVERPGMDLRMLLSSIGLKLRRLRRYAIGPYRAS 372

Query: 227 TL 228
           ++
Sbjct: 373 SI 374


>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 = 49.3 bits (116), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/220 (24%), Positives = 95/220 (43%), Gaps = 11/220 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  SR+    +I   RV ++G + +    ++ + D +  VD    R  ++  
Sbjct: 3   IERILHSQGFGSRKVCRALIRAGRVTISGQIQDNPFADLPTADLVFTVDRETWRFRDKAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L HKP G   +   P   + VF  LP   +   V  +GRLD +T GLLLL++DG    
Sbjct: 63  LML-HKPSGYECSRQ-PQFHAPVFALLPEPLVNRGVQPIGRLDQDTTGLLLLSDDGQFIH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
           V      +  ++Y V     V++     L  G+ +    + D +       ++     + 
Sbjct: 121 VWSSGRKRVPKIYEVAVRHPVNETMTEALLAGVQL----HDDPEPVAAAACERTGERSLK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           + + EGK  ++K++      +V  L R   G   L   LA
Sbjct: 177 LTITEGKYHQVKRMVAAAGNRVESLHRSGIGGLMLPDDLA 216


>gi|169837001|ref|ZP_02870189.1| pseudouridylate synthase [candidate division TM7 single-cell
           isolate TM7a]
          Length = 92

 Score = 48.9 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/71 (38%), Positives = 37/71 (52%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +KPI  V +        T++  LP  F  +  VGRLD N+ GLLLLTNDG  A  +  
Sbjct: 1   MLNKPINYVCSRKQQGKTPTIYSLLPDKFHNLKPVGRLDANSSGLLLLTNDGDFAFRMTH 60

Query: 137 PSTQWLRVYRV 147
           P  +  + Y V
Sbjct: 61  PKFKKNKQYNV 71


>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 = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 93/237 (39%), Gaps = 40/237 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           ++  ++   G   RR    ++ Q  V++           + ST  I+ +G  LR   +  
Sbjct: 4   QLQDILYSQGFGIRRVCSGLVQQGWVELWDTEANDWVRCLDSTQDIDPEG--LRYRVQGV 61

Query: 75  LWLYHKPIGLVTTHSDPDGR--STVFDNLPSIFSR----------------VISVGRLDI 116
            W YH  +G V  H  P G   S      PSI+S                 V +VGRLD 
Sbjct: 62  EWAYHA-LGYVLLHK-PAGTECSQKPSTYPSIYSLLPLPLRLRPNKGAVQGVQAVGRLDQ 119

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------- 168
           +T GLLLL++DG     +  P     ++YRV     VD  ++  L  G+V+         
Sbjct: 120 DTTGLLLLSDDGQFIHRMSSPKKHVPKIYRVTTKHPVDASQVQRLLDGVVLDDDPKPVKA 179

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
             C    +  LD          + L EGK  ++K++      +V  L R   G  +L
Sbjct: 180 AACEQVSEHVLD----------LTLTEGKYHQVKRMIAAVGNRVEGLHRWKIGELEL 226


>gi|317969165|ref|ZP_07970555.1| pseudouridine synthase [Synechococcus sp. CB0205]
          Length = 178

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 60/136 (44%), Gaps = 20/136 (14%)

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTL 179
           +LLT++G L + L  PS    R Y  +  G   +D LN L+ G+VIQG        Q   
Sbjct: 1   MLLTSNGRLQQRLTDPSWGHWRRYWSQVEGVPSEDALNALRSGLVIQGQRTLPAQAQALQ 60

Query: 180 DT------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------ 221
           D             Q    +W+ + LREG+NR+++++         RL+R++        
Sbjct: 61  DPGWPERDPPIRVRQSIPTSWLQLELREGRNRQVRRMTAAVGLPTLRLLRVAMDLMDGGP 120

Query: 222 PFQLGTLLAGSTREVS 237
           P  L  L  G  R V+
Sbjct: 121 PLSLDGLAPGQWRSVN 136


>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 = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/219 (22%), Positives = 92/219 (42%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   SR   ++ + +  V  NG +++ +   V     I +DG  L      R
Sbjct: 2   RLDKFICESTSHSRVSAKKALHRGDVTCNGEVVKNSGFKVTDEHEIRLDGEVLTII-GPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--------GRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S +  +        GRLD +T GL+L+T 
Sbjct: 61  FIMLNKPVDTIC--------STIDEEYPSVISLLDVIRPEDLHIAGRLDADTTGLVLITT 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + Y +     +  D +     G+ +           L+    + 
Sbjct: 113 DGQWSHKITSPKKECGKRYLLETAESLSDDLVQQFVDGLQLNNEDGLTKPAELEILAPNQ 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           A +T+   EGK  ++K++      KV +L R S G  +L
Sbjct: 173 ARLTI--TEGKYHQVKRMLAAVGNKVTKLHRESVGAIEL 209


>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 = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 51/224 (22%), Positives = 96/224 (42%), Gaps = 19/224 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  V  +G +++ +   V     I ++G PL      R
Sbjct: 2   RLDKYICESTSLTRSLAKKALHRGDVTCDGKVIKDSGFKVTDKQVICLEGEPL-SVIGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--------GRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+   +  V        GRLD++T GL+L+TN
Sbjct: 61  FIMLNKPLDTIC--------STIDEEYPSVLGLLDVVKADELHIAGRLDVDTTGLVLITN 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + Y +     + Q+ +     G+ +          TL+      
Sbjct: 113 DGQWSHKITSPKKECGKRYLLETAEPLKQEWVEEFAAGLQLNNEDGLTKPATLEILGSHQ 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           A +T+   EGK  ++K++       V +L R S G  +L   LA
Sbjct: 173 ARLTI--TEGKYHQVKRMLAAVGNCVTQLHRESVGEIELDESLA 214


>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 = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 97/226 (42%), Gaps = 21/226 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  A   SR   ++ + +  V  +G++++ +   V     + ++G  L      
Sbjct: 1   MRLDKFITEASELSRSLAKKALHRGDVTCDGVIVKDSGFKVEPGTKVCLEGREL-SLFGV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---------GRLDINTEGLLLL 124
           R  + +KP+  +         ST+ +  PS+ S +I V         GRLD +T GL+L+
Sbjct: 60  RYLMLNKPVDTIC--------STIDEVYPSVLS-LIDVEKASNLHIAGRLDADTTGLVLI 110

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG  +     P     + Y V     +D+  +    +GI ++         TL+    
Sbjct: 111 TSDGQWSHRATSPKKDCGKRYLVEVAEPLDESLIETFAEGIALRNEDGLTKPATLEIIDS 170

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            +A +T+   EGK  ++K++F      V  L R   G  +L   LA
Sbjct: 171 HHARLTI--TEGKYHQVKRMFAATGNAVINLHRECVGSIELDPGLA 214


>gi|218184438|gb|EEC66865.1| hypothetical protein OsI_33363 [Oryza sativa Indica Group]
          Length = 513

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 35/104 (33%), Positives = 53/104 (50%), Gaps = 2/104 (1%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P     V ++GRLD +T GLLLL++DG     +  P  Q  + YRV     + Q + + L
Sbjct: 44  PGKILGVQTIGRLDQDTTGLLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQL 103

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
            KG+V+       +      Q+GS   +TV   EGK  +IK++F
Sbjct: 104 LKGVVLNDDPKPVIAADCVLQEGSIFDLTV--TEGKYHQIKRMF 145


>gi|270587172|ref|ZP_06221422.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae HK1212]
 gi|270318484|gb|EFA29582.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae HK1212]
          Length = 91

 Score = 48.5 bits (114), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 43/60 (71%), Gaps = 6/60 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+  F ++P++++     GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFISIPNVYA----AGRLDRDSEGLLILTNNG 91


>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 = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 116/243 (47%), Gaps = 21/243 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K+IA  G  SR++V+ M  + RV   +G +L   A + +  + I VDG PL      
Sbjct: 2   KLVKLIANLGYGSRKQVQWMFREGRVTDADGEVL--YADDQVPHEAIRVDGEPLDPPVGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            + L HKP G   +  D  GR  ++D LP  F     V+S VGRLD  T GLLLLT+DGG
Sbjct: 60  SIAL-HKPAGYTCSTKD-TGR-LIYDLLPPRFRDRDPVLSTVGRLDRETSGLLLLTDDGG 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKG 184
           L   +  P ++  +VY V     +  D++ L   G ++       +   +++V LD ++ 
Sbjct: 117 LLHRIISPKSKLPKVYEVELSDDLRGDEVALFASGTLMLESEKTPLLPAELEV-LDARRA 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG+  +++++F      V  L R   G   L  L  G  R+++   L   
Sbjct: 176 R-----LVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTSTDLDTL 230

Query: 245 LGP 247
             P
Sbjct: 231 FAP 233


>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 = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 90/221 (40%), Gaps = 17/221 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + +++   G  +R+    +I    V +NG++++     V +TD   ++     +  R R 
Sbjct: 6   LDRILQSQGFGTRKYCRGLIEDGEVSINGVVVDNFKTAVDTTD---LEFTIFDEVWRYRE 62

Query: 76  WLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
            +Y   +KP     +   P     V   LP  F+   +  VGRLD +T G+LL+++DG  
Sbjct: 63  HVYIVLNKPANFECSRK-PSHHPGVLTLLPEQFTWRDLQPVGRLDHDTTGMLLMSDDGPF 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---SNA 187
                 P     ++Y    H  V  + +  L  G+ +      D    L  Q     +  
Sbjct: 122 IHAQSSPKRHIPKIYVATTHDPVTPELIAQLLGGVQLH-----DEPAPLAAQTCRMLAEH 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            + + L +GK  ++K++        + L R   G   L +L
Sbjct: 177 QIEIVLEQGKYHQVKRMLAAAGNHCSALNRAEIGELTLESL 217


>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 = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 36/160 (22%), Positives = 72/160 (45%), Gaps = 19/160 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G +   S P  +      L ++  RV   GRLD ++EGLLLLT++G     +  P 
Sbjct: 6   NKPYGYICQFS-PHEKHPNLKELVNV-PRVYPAGRLDTDSEGLLLLTDNGQQQARIASPK 63

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------------- 185
            + ++ Y  +  G  + +++  L++ + +        +  L T   +             
Sbjct: 64  FKLIKTYWAQLEGTPNPEQIAQLEQPMDLGDFIARPAKTRLLTPAETARIWPRNPPVRYR 123

Query: 186 ----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
               + W+ + + EGKNR+++++    ++   RL+R   G
Sbjct: 124 KTVPDFWLEIQIAEGKNRQVRRMAAKAHYPCLRLVRTGIG 163


>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 = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 37/131 (28%), Positives = 68/131 (51%), Gaps = 2/131 (1%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICY 172
           +D +TEGL+L+T +G L   L  P+ +  + Y V  +  V  + +     GI    G+  
Sbjct: 1   MDRDTEGLVLVTTNGQLGYDLLHPTKKVTKRYEVVVNDLVTPEDVAAFAAGITFHGGVTC 60

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-G 231
               +T+   +  +++V++ + EGK  ++KK+F     KV +L R + G   L   LA G
Sbjct: 61  KPAALTIIDARADHSFVSLEIAEGKFHQVKKMFLARGKKVIQLKRTAMGSLVLPDDLAVG 120

Query: 232 STREVSKKILR 242
           S R ++++ L+
Sbjct: 121 SYRSLTQEELK 131


>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 = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 61/247 (24%), Positives = 99/247 (40%), Gaps = 30/247 (12%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRK 69
             P ++  ++   G  +RR    ++ Q RV V G   ++  A       H+ V+G+  R 
Sbjct: 1   MPPMQLQDILFGQGFGARRVCAGLVQQGRVSVAGAACIDPLAEFEPEGLHLRVEGLEGRT 60

Query: 70  AER----------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP------------SIFSR 107
             R          + L + +KP G   +   P    +V+  LP               + 
Sbjct: 61  GLREGGLDWVCHLSALIMLNKPAGYECSQK-PSAWPSVYTLLPLPLRQRPAQGKKGATAG 119

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV----DQDKLNLLKK 163
           V +VGRLD +T GLLLLT+DG L   L  P  +  +VY V     V    +   +  L  
Sbjct: 120 VQAVGRLDQDTTGLLLLTDDGQLIHKLASPRHKVSKVYEVGLKHPVPSPAEASFVQRLLD 179

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+V+    +       +     +  +T  L +GK  ++K++      +V  L R   G  
Sbjct: 180 GVVLDDDPHPVRAAACELLTPQHLRLT--LTDGKYHQVKRMVAAVGNRVETLHRSRIGAL 237

Query: 224 QLGTLLA 230
           QL   LA
Sbjct: 238 QLPDDLA 244


>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 = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 41/163 (25%), Positives = 75/163 (46%), Gaps = 6/163 (3%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP+G+V+T  D + R  + D   +   RV  +GRLD +++GL+ LTN G L   +
Sbjct: 16  LIALNKPVGIVSTTEDGE-RDNIVD-FVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVNKI 73

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     + ++ +     G+ I G      +V  +    +     + L 
Sbjct: 74  LRAGNDHEKEYLVTVDKPITEEFIRGXSAGVPILGTVTKKCKVKKE----APFVFRITLV 129

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +G NR+I++  E F ++V +L R       L  +  G  R+++
Sbjct: 130 QGLNRQIRRXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLT 172


>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 = 47.4 bits (111), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 117/243 (48%), Gaps = 21/243 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K+IA  G  SR++V+ M  + RV   +G +L   A + +  + + VDG PL      
Sbjct: 2   KLVKLIANLGYGSRKQVQWMFREGRVTDADGEVL--YADDQVPHEAVRVDGEPLDPPVGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            + L HKP G   +  D  GR  ++D LP  +     V+S VGRLD +T GLLLLT+DGG
Sbjct: 60  SIAL-HKPAGYTCSTKD-KGR-LIYDLLPPRYRDRDPVLSTVGRLDRDTSGLLLLTDDGG 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKG 184
           L   +  P ++  +VY V     +  D++ L   G ++       +   +++V LD ++ 
Sbjct: 117 LLHRIISPKSKLPKVYEVELSDDLRGDEVALFASGTLMLESEKTPLLPAELEV-LDARRA 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG+  +++++F      V  L R   G   L  L  G  R+++   L   
Sbjct: 176 R-----LVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTPTDLDTL 230

Query: 245 LGP 247
             P
Sbjct: 231 FAP 233


>gi|226939001|ref|YP_002794072.1| RsuA [Laribacter hongkongensis HLHK9]
 gi|226713925|gb|ACO73063.1| RsuA [Laribacter hongkongensis HLHK9]
          Length = 231

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 100/238 (42%), Gaps = 23/238 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           ++ +++ R G +SR+    +I Q RV V G + +   + V      E +G+      +A 
Sbjct: 2   QLERLLHREGWSSRKGCRILINQGRVCVAGEVADDPGLEV------EPEGLAYSVDDEAA 55

Query: 72  RTRLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
             R  LY   +KP+ L  +   P  R+ V    P  +S   V  VGRLD +T GLLLL++
Sbjct: 56  IAREHLYLILNKPLDLECSRK-PTVRTGVLTLFPPRYSERGVQPVGRLDADTSGLLLLSD 114

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQK 183
           DG     +  P     + Y       V+ + L  L  G+V+             TLD   
Sbjct: 115 DGQFIHRITSPKHLVPKTYVATCARPVEPEHLRQLLAGVVLNDDPAPVVARSARTLDEHT 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + + + EG+  +++++        + L R   G   L  L  G  RE++   L
Sbjct: 175 -----LELVVTEGRYHQVRRMIAAVGNHCDALHRSRIGELVLDGLAPGQWRELTAAEL 227


>gi|82523723|emb|CAI78504.1| S4 domain protein [uncultured beta proteobacterium]
          Length = 240

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 55/232 (23%), Positives = 94/232 (40%), Gaps = 17/232 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +A     SRRE E++I    V+V+G+++E     V S   IE+D           
Sbjct: 6   RLSKRVAELRACSRREAEQIITGGWVRVDGVVIEEPQFRVAS-QRIEIDPQADPSQIEPV 64

Query: 75  LWLYHKPIGLVTTHSDP------------DGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             L HKP G+  +  D             +   T    L + F+++ +   L+ +  GL+
Sbjct: 65  TLLLHKPAGVRISDDDKTALQLLRADSLWEHDGTGISPLKAHFTQLTACVPLEADASGLV 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R L   +        V   G++  + L  L KGI   G     ++V+   +
Sbjct: 125 VFTQDWRIVRKLTDDAATLEHEVIVEVSGELIPNGLKRLNKGIPYHGHTPAAIKVSWQNE 184

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 + V L+  +  +I  + E    +V  + RI  G   L  +  G  R
Sbjct: 185 TR----LRVALKGCQIGQIAHLCEAVGLQVVSMKRIRLGGIPLAKVPPGQWR 232


>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 = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 95/235 (40%), Gaps = 22/235 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAER 72
           R++K +A     SR E E+ I    + V+G+L E A   V     I +  D VP      
Sbjct: 6   RLAKRVAEELGCSRTEAEQFIEGGWITVDGVLTEEAGARVAPEQAIVLLPDAVPAPLDPV 65

Query: 73  TRLWLYHKPIGLVTTHS-------------DPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           T L   HKP G+ T  +              PD RS     L      +     L+ +  
Sbjct: 66  TIL--LHKPAGMRTIDAIDPEQSWITPATLGPDDRSG-LRFLRRHTKALTLTNPLEDSAS 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT D  + R L   +++  + + V   G +D   L LL+KG+   G     M+V+ 
Sbjct: 123 GLLVLTQDWRIERALVQEASRIEQEFVVEVTGTLDAAGLELLQKGLKWNGKPIASMKVSW 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            ++      +   ++  +  +I  + E    +V  + RI  G   +  L  G  R
Sbjct: 183 QSEHK----LRFAIKAAERGQIPYLCEKVGLQVVSIKRIRIGRMSMAALPVGQWR 233


>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 = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 91/224 (40%), Gaps = 23/224 (10%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNG--ILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           + +++   G  +R+    +I    V +NG  +   RAA +    +    D V      R 
Sbjct: 6   LDRILQSQGFGTRKYCRNLIEDGEVSINGESVTDYRAAFDTSDLEFTIFDEV-----WRY 60

Query: 74  RLWLY---HKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           R  +Y   +KP     +   P     V   LP  F+   +  VGRLD +T G+LL+++DG
Sbjct: 61  RQHVYIVLNKPANFECSRK-PSHHPGVLTLLPEQFTWRELQPVGRLDHDTTGMLLMSDDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----G 184
                   P     +VY    H  V  + +  L  G+ +      D    L  Q     G
Sbjct: 120 PFIHAQSSPKRHIPKVYVATTHDPVTPELIAQLLGGVQLH-----DEPAPLAAQTCRMLG 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           +N  + + L +GK  ++K++        + L R++ G   L +L
Sbjct: 175 ANE-LEIVLEQGKYHQVKRMLAAAGNHCSALRRVAIGALTLESL 217


>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 = 47.0 bits (110), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 20/67 (29%), Positives = 42/67 (62%)

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           +L ++G++++       ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+
Sbjct: 3   SLTEEGVMLEDGLAKVERIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRV 62

Query: 219 SYGPFQL 225
            +GP  L
Sbjct: 63  GFGPIGL 69


>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 = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 56/209 (26%), Positives = 96/209 (45%), Gaps = 13/209 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+E++  I    V  + G  L+  A    + + I  D  PL  A   
Sbjct: 2   RLVKLLANLGYGSRKEMQVAIRNGWVTDLKGNRLKADAKT--AHEDILFDDEPLDPAHGV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDGG 129
            + L +KP+G   +  D  GR  V+D LP  F      + ++GRLD  T G LL T+DG 
Sbjct: 60  VI-LMNKPLGYTCSIKD-QGR-LVYDLLPDRFRMRKPVLSTIGRLDKETSGALLFTDDGT 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
               +  P ++  ++Y V     +  D+  L   G ++++          L+    ++A 
Sbjct: 117 FLHRVISPKSEVPKIYEVALDRPMKGDEGALFASGDMMLESEDKPLKPAELEVIDETHAR 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +T  L EG+  +++++F      V  L R
Sbjct: 177 LT--LHEGRYHQVRRMFAATGNHVTDLTR 203


>gi|192361547|ref|YP_001983032.1| pseudouridylate synthase [Cellvibrio japonicus Ueda107]
 gi|190687712|gb|ACE85390.1| pseudouridylate synthase [Cellvibrio japonicus Ueda107]
          Length = 258

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 44/176 (25%), Positives = 86/176 (48%), Gaps = 20/176 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP G+++  +  + R T+  +  +P+++      GRLD ++EGLLLLT+DG L  
Sbjct: 9   LILFNKPYGVLSQFTAKEERPTLAQYIRIPNVY----PAGRLDHDSEGLLLLTDDGDLQH 64

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
           ++  P+ +  + Y V+  G  +   L  L++G+ +        +V L             
Sbjct: 65  LISHPAHKQPKTYWVQVEGAPNSYALTKLRQGVELNDGMTQPAEVRLIPAPKLWERKPPI 124

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +       W+ + + EG+NR+++++         RL+R+  GP+ L  +  G  R
Sbjct: 125 RERANIPTQWLEIVITEGRNRQVRRMTAAVGHPTLRLVRVKIGPWTLEGIEPGKYR 180


>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 = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 49/187 (26%), Positives = 82/187 (43%), Gaps = 22/187 (11%)

Query: 56  STDHIEVDGVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           ST  ++ +G  LR   +   W YH        KP G   +   P    +++  LP+   +
Sbjct: 43  STQQVDPEG--LRFRVQGVEWEYHELGYVLLNKPAGTECSQK-PSAYPSIYTLLPAPLRQ 99

Query: 108 ---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                    V +VGRLD +T G+LLL++DG     +  P     +VYRV     VD  ++
Sbjct: 100 RPNKGAVQGVQAVGRLDQDTTGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQI 159

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
             L  G+V+       ++     Q  S+  + + L EGK  ++K++    + +V  L R 
Sbjct: 160 QRLLDGVVLDDD-PKPVKAAACEQVDSHV-LDLTLTEGKYHQVKRMIAAVSNRVEGLHRR 217

Query: 219 SYGPFQL 225
             G  +L
Sbjct: 218 RIGGMEL 224


>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 = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 97/220 (44%), Gaps = 11/220 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  V  +G +++ +   V     I +DG  +      R
Sbjct: 14  RLDKFICESTELTRSFAKKALHRGDVTCDGEVVKNSGFKVKVGQTICLDG-KVISVVGPR 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARV 133
             + +KP   +    D     TV D L    +  + + GRLDI+T GL+L+T DG  +  
Sbjct: 73  FLMLNKPADTICATFDI-VHPTVIDLLDIEKADTLHIAGRLDIDTTGLVLITTDGQWSHK 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVT 190
           +  P     + Y V+   ++D   +    +G+ ++   G+    +   +DT     A +T
Sbjct: 132 ITSPKKDCSKCYLVKLTDELDASLVETFAQGVELRNEDGLTKPAVLEIIDTH---TARLT 188

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +   EGK  ++K++F     KV  L R S G   L   LA
Sbjct: 189 I--TEGKYHQVKRMFAAVGNKVVGLHRESVGKIVLDDDLA 226


>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 = 46.6 bits (109), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 21/243 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           ++ K IA  G  SR++V+ M  + RV   +G +L   A + +  + I VDG PL      
Sbjct: 2   KLVKHIANLGYGSRKQVQWMFREGRVTDADGEVL--YADDQVPHEAIRVDGEPLDPPVGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS-VGRLDINTEGLLLLTNDGG 129
            + L HKP G   +  D  GR  ++D LP  F     V+S VGRLD  T GLLLLT+DGG
Sbjct: 60  SIAL-HKPAGYTCSTKD-TGR-LIYDLLPPRFRDRDPVLSTVGRLDRETSGLLLLTDDGG 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKG 184
           L   +  P ++  +VY V     +  D++ L   G ++       +   +++V LD ++ 
Sbjct: 117 LLHRIISPKSKLPKVYEVELSEDLRGDEVALFASGTLMLESEKTPLLPAELEV-LDARRA 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG+  +++++F      V  L R   G   L  L  G  R+++   L   
Sbjct: 176 R-----LVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTSTDLDTL 230

Query: 245 LGP 247
             P
Sbjct: 231 FAP 233


>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 = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 31/122 (25%), Positives = 55/122 (45%), Gaps = 14/122 (11%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           +GRLD ++EGLLLLT++G L   L        R Y  +  G    + L  L++GI     
Sbjct: 1   MGRLDQDSEGLLLLTSNGKLQHRLAHREFAHQRTYFAQVEGSPTDEDLEPLRRGITFADY 60

Query: 171 CYGDMQVTLDTQKG--------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                   + T+                  +W+++ L EG+NR+++++     +   RL+
Sbjct: 61  PTRPAIAKIITEPDFPPRNPPIRYRASIPTSWLSITLTEGRNRQVRRMTAAVGFPTLRLV 120

Query: 217 RI 218
           R+
Sbjct: 121 RV 122


>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 = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 49/187 (26%), Positives = 82/187 (43%), Gaps = 22/187 (11%)

Query: 56  STDHIEVDGVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           ST  ++ +G  LR   +   W YH        KP G   +   P    +++  LP+   +
Sbjct: 43  STQQVDPEG--LRFRVQGVEWEYHELGYVLLNKPAGTECSQK-PSAYPSIYTLLPAPLRQ 99

Query: 108 ---------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                    V +VGRLD +T G+LLL++DG     +  P     +VYRV     VD  ++
Sbjct: 100 RPNKGAVQGVQAVGRLDQDTTGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQI 159

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
             L  G+V+       ++     Q  S+  + + L EGK  ++K++    + +V  L R 
Sbjct: 160 QRLLDGVVLDDD-PKPVRAAACEQVDSHV-LDLTLTEGKYHQVKRMIAAVSNRVEGLHRR 217

Query: 219 SYGPFQL 225
             G  +L
Sbjct: 218 RIGGMEL 224


>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 = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 73/167 (43%), Gaps = 20/167 (11%)

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINT 118
           W YH        KP G   +   P    +++  LP+   +         V +VGRLD +T
Sbjct: 63  WEYHELGYVLLNKPAGTECSQK-PSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQDT 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+       ++  
Sbjct: 122 TGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDDD-PKPVKAA 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
              Q  S+  + + L EGK  ++K++    + +V  L R   G  +L
Sbjct: 181 ACEQVDSHV-LDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMEL 226


>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 = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 40/127 (31%), Positives = 60/127 (47%), Gaps = 8/127 (6%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           VGRLD +T GLLL ++ G L + L  P  +  + Y     G V +D+L    +  +  G+
Sbjct: 4   VGRLDYDTSGLLLFSSSGALTQRLLHPKHEVEKEYVAVVTGIVVEDEL----RATLAAGV 59

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             G + V  D Q  S   +TV   EGK+R ++++       V  L R   G   L  L A
Sbjct: 60  -RGYLNV-FDAQALSTVRLTVS--EGKHRMVRRILANCGHPVVSLHRDRLGAVALNDLPA 115

Query: 231 GSTREVS 237
           G  R ++
Sbjct: 116 GEYRPLT 122


>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 = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 52/218 (23%), Positives = 95/218 (43%), Gaps = 5/218 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  V  +G +++ ++  V +   I +DG  +      
Sbjct: 1   MRLDKFICESTELTRSFAKKALHRGDVTCDGEVVKSSSFKVKAGQIICLDG-KVISVVGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   +    D     TV D L    +  + + GRLDI+T GL+L+T DG  + 
Sbjct: 60  RFLMLNKPADTICATFDI-VHPTVIDLLDIEKADTLHIAGRLDIDTTGLVLITTDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V    ++D   +    +G+ ++          L+     +A +T+ 
Sbjct: 119 KITSPKKDCGKCYLVTLTDELDASLVETFAQGVELRNEDGLTKPAVLEIIDSHHARLTI- 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             EGK  ++K++F     KV  L R S G   L   LA
Sbjct: 178 -TEGKYHQVKRMFAAVGNKVVGLHRESVGKIVLDDDLA 214


>gi|289806402|ref|ZP_06537031.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. AG3]
          Length = 100

 Score = 46.2 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 43/84 (51%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R+ K IA+    SR    R I   RV V+G +++ AA  ++    +  DG PL +    R
Sbjct: 2  RLDKFIAQQLGVSRAIAGREIRGNRVTVDGDIIKNAAFKLLPEHAVAYDGNPLAQQHGPR 61

Query: 75 LWLYHKPIGLVTTHSDPDGRSTVF 98
           ++ +KP G V +  DPD  + ++
Sbjct: 62 YFMLNKPQGYVCSTDDPDHPTVLY 85


>gi|217968594|ref|YP_002353828.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217505921|gb|ACK52932.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 245

 Score = 46.2 bits (108), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 60/228 (26%), Positives = 95/228 (41%), Gaps = 19/228 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMSTD-----HIEVDGVPL 67
           ++ +++   G  SR++   +I    V V G + +      +  S D        VD  P 
Sbjct: 2   QLERLLHAQGFGSRKDCRALIRAGYVSVAGEVCDDPTEEFDPGSRDGSPGLEFTVDDQPW 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSR-VISVGRLDINTEGLLLLT 125
           R   +  + L HKP G   +   P    +VF  LP  + +R V  VGRLD +T GLLLL+
Sbjct: 62  RFRAQAYVVL-HKPAGYECSQK-PTFHPSVFTLLPPQLLARGVQCVGRLDQDTTGLLLLS 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG- 184
           +DG           +  +VY V     V+QD  + L  G+ +      D  V +      
Sbjct: 120 DDGQFIHQWSSGKKRTPKVYEVTLKHAVEQDFADRLVAGVELN-----DEPVPIAAAACE 174

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             S   + + + EGK  ++K++      +V  L R   G   L   LA
Sbjct: 175 LLSPTTLRLTICEGKYHQVKRMVGAAGNRVEVLHRSRVGGLDLPAGLA 222


>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 = 45.8 bits (107), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 57/184 (30%), Positives = 91/184 (49%), Gaps = 26/184 (14%)

Query: 78  YHKPIGLV---TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++KP G++   T  S P   +     LP     V + GRLD ++EGLLLLT+DGGLA  L
Sbjct: 26  FNKPYGVLCQFTDRSQPPRPTLAGFGLPK---DVYAAGRLDHDSEGLLLLTDDGGLAHRL 82

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKG--------- 184
             P  +  + Y V+  G   +++L  L+ G+V+        +V  LD             
Sbjct: 83  TDPLHKQPKTYWVQVEGDPREEQLQALRDGVVLNDGPTRPAKVRRLDPVPALWPRDPPVR 142

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL----GTLLA-GSTR 234
                 ++W+ V + EG+NR+++++         RL+R++ GP +L    GT LA G  R
Sbjct: 143 FRKTVPDSWLEVVIIEGRNRQVRRMTAAAGLPTLRLVRVAMGPHRLHDRDGTPLAPGEWR 202

Query: 235 EVSK 238
           EV +
Sbjct: 203 EVGR 206


>gi|255523816|ref|ZP_05390781.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255512519|gb|EET88794.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 180

 Score = 45.8 bits (107), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 26/60 (43%), Positives = 33/60 (55%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V  VGRLD +TEGLLLLTNDG     L  P     + Y     G +D++    L++GI I
Sbjct: 12  VFHVGRLDKDTEGLLLLTNDGEFEHKLMHPQEHIEKTYFFWALGSLDEENRKQLEQGIYI 71


>gi|166712972|ref|ZP_02244179.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 236

 Score = 45.8 bits (107), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 70/164 (42%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K +A A   SR E +R I    V V+G+++E       +      D   L   E 
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQRYIEGGWVSVDGVVVEEPQAPATAAQITLADDAVLSPVEP 63

Query: 73  TRLWLYHKPIGL----VTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+        + P  RS +  +    L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGVSAEAALALATPTTRSALDQSDIRVLKRHFLRLTAPLPLEEAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           ++DG + R L   ++   + + V   G V    +  L  G+V Q
Sbjct: 123 SHDGRVLRRLSADASSIEQEFLVEVQGDVRPYGMARLAHGLVYQ 166


>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 = 45.8 bits (107), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 51/220 (23%), Positives = 86/220 (39%), Gaps = 15/220 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + +++   G  SR+    +I    V +NG +++       + D +      L   E    
Sbjct: 6   LDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLV------LTIFEEEWE 59

Query: 76  WLYHKPIGL-----VTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           +  H  I +     +     P     V   LP  F+   V  VGRLD +T GLLL+++DG
Sbjct: 60  YREHVYIAINKPPNIECSRKPSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                   P     +VY       V +  +  LK G+ +       +  T   Q G N  
Sbjct: 120 AFIHAQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDE-PAPLAATRCRQLGEN-L 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           + + L +GK  ++K++        + L R + G  QL  L
Sbjct: 178 LEIVLEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEAL 217


>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 = 45.8 bits (107), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 33/133 (24%), Positives = 62/133 (46%), Gaps = 8/133 (6%)

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           +VGRLD +T G+LL+TNDG     +  P  +  ++YR       D+     LK G+++  
Sbjct: 8   AVGRLDADTTGVLLITNDGQFNHRMTSPKYKAAKLYRAGLKHPADETFCQSLKNGVLLH- 66

Query: 170 ICYGDMQVTLDTQKG---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
               D   T+   +    +   + + + EGK  ++K++      +V  L R+ +G +   
Sbjct: 67  ----DDDETVQAAEAVLENPHTLLLTITEGKYHQVKRMVAAAGNRVETLHRLKFGEWSAE 122

Query: 227 TLLAGSTREVSKK 239
            L  G  + ++ K
Sbjct: 123 HLAPGEWQFITIK 135


>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 = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 49/219 (22%), Positives = 93/219 (42%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   SR   ++ + +  V  NG +++ +   V     I ++G  L      R
Sbjct: 2   RLDKFICESTSHSRVSAKKALHRGDVTCNGEVVKNSGFKVTDEHEIRLEGEVLTII-GPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-IS-------VGRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+ S + +S        GRLD +T GL+L+T 
Sbjct: 61  FIMLNKPVDTIC--------STIDEEYPSVISLLDVSRPEDLHIAGRLDADTTGLVLITT 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + Y +     + +  +     G+ +           L+    + 
Sbjct: 113 DGQWSHKITSPKKECGKRYLLETADPLSEALVQQFADGLQLNNEDGLTKPAELEMLGSNQ 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           A +T+   EGK  ++K++      KV +L R S G  +L
Sbjct: 173 ARLTI--TEGKYHQVKRMLAAVGNKVTKLHRESVGAIEL 209


>gi|224003727|ref|XP_002291535.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220973311|gb|EED91642.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 441

 Score = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 48/177 (27%), Positives = 78/177 (44%), Gaps = 28/177 (15%)

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV---- 153
           FD   +  S   + GRLDI++ G+++ T  G +AR L  P T+  + Y V+    V    
Sbjct: 254 FDE--ATLSGYATAGRLDIDSTGVIIFTRAGIMARRLIAPDTKIPKEYIVKVQPAVQPTT 311

Query: 154 ---DQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------GSNAWVTVG------LR 194
              +   L+L      +  +  G  ++  D +             N  ++ G      L+
Sbjct: 312 HEKEAGLLSLPSPTRNLTSLLRGGKRLWNDKKALKPVLEAEWLEENPVLSNGGTLRLVLQ 371

Query: 195 EGKNREIKKVF-EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--PH 248
           EGK R+I+++  E     V  L+R S GP QL TL  G  R + ++ +RE     PH
Sbjct: 372 EGKKRQIRRMCREILGMHVVSLVRKSIGPIQLDTLPEGKWRPLKEQEVREIFADTPH 428


>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 = 45.4 bits (106), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 43/145 (29%), Positives = 73/145 (50%), Gaps = 15/145 (10%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V + GRLD ++EGLLLLT+DGGL   +  P  +  +VY     G  D   L+ L++G+ +
Sbjct: 43  VYAAGRLDRDSEGLLLLTDDGGLQARISSPKYRSPKVYFALVEGVPDDAALDHLRRGVTL 102

Query: 168 Q----GICYGDMQVTLDT-----------QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +      C  +     D            +  ++ W+ + L EG+NR+++++     + V
Sbjct: 103 KDGQTAPCEAEAVAAPDWIWDRDPPVRIRKSITDTWLKLTLTEGRNRQVRRMCAGVGFPV 162

Query: 213 NRLIRISYGPFQLGTLLAGSTREVS 237
            RL+R S GP  +  L  G  RE++
Sbjct: 163 IRLVRFSIGPHDIRDLPPGMWRELA 187


>gi|229016829|ref|ZP_04173757.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|228744390|gb|EEL94464.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 96

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 49/80 (61%), Gaps = 2/80 (2%)

Query: 160 LLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +L++G++++       ++++T   ++   A V + + EG+NR+++++FE  + KV +L R
Sbjct: 1   MLERGVMLEDGKTAPANVKITSWDKRKETAIVQLTIHEGRNRQVRRMFEALDCKVVKLKR 60

Query: 218 ISYGPFQLGTLLAGSTREVS 237
             Y   ++G+L  G  RE++
Sbjct: 61  ERYAFLEVGSLRPGDARELT 80


>gi|126727906|ref|ZP_01743733.1| RNA pseudouridylate synthase [Rhodobacterales bacterium HTCC2150]
 gi|126702798|gb|EBA01904.1| RNA pseudouridylate synthase [Rhodobacterales bacterium HTCC2150]
          Length = 102

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 28/89 (31%), Positives = 55/89 (61%), Gaps = 15/89 (16%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDG----RSTV--FDNLPSIFSRVISVGRLDINTEG 120
            R    +++ L++KP G+++  +D       R+T+  F ++P++++     GRLD ++EG
Sbjct: 18  FRAVAMSQVILFNKPFGVLSQFTDKGTQGSERATLSKFIDVPNVYA----AGRLDRDSEG 73

Query: 121 LLLLTNDGGL-ARVL----ELPSTQWLRV 144
           LL+LT+DG L A++     ++P T W++V
Sbjct: 74  LLVLTDDGKLQAKIAHPKNKMPKTYWVQV 102


>gi|119896376|ref|YP_931589.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119668789|emb|CAL92702.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 248

 Score = 45.1 bits (105), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 38/127 (29%), Positives = 60/127 (47%), Gaps = 19/127 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVP-LRKAE 71
           ++ +++   G  SR++   ++    V V G+  +  RA  +  S D     G P L    
Sbjct: 5   QIERLLHSQGFGSRKDCRALLRAGYVSVAGVPCDDPRAEFDPGSKD-----GSPGLEFTV 59

Query: 72  RTRLW--------LYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSR-VISVGRLDINTEGL 121
              +W        + HKP G   +H  P    +VF  LP  + +R V  +GRLD +T GL
Sbjct: 60  DDEIWHFRAQAYLMLHKPAGYECSHK-PTFHPSVFTLLPPQLLNRGVQCIGRLDQDTTGL 118

Query: 122 LLLTNDG 128
           LLL++DG
Sbjct: 119 LLLSDDG 125


>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 = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 49/226 (21%), Positives = 96/226 (42%), Gaps = 19/226 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I  +   +R   ++ + +  +  +G +++ A   V+    + ++G  +     
Sbjct: 6   PVRLDKFICESTSLTRSLAKKALHRGDITCDGAVIKDAGFKVLEGMQVCLEGEFISLVGE 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLL 124
            R  + +KP+  +         ST+ +  PS+ S         +   GRLD +T GL+L+
Sbjct: 66  -RYLMLNKPVDTIC--------STIDEVYPSVLSLLDIEKPETLHIAGRLDADTTGLVLI 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG  +  +  P     + Y V     VD+  + +   G+ ++          L+  + 
Sbjct: 117 TSDGQWSHRITSPKKDCGKRYLVTLAEPVDESLIGVFAAGVELRNEDCLTKPALLEIIEP 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               +T+   EGK  ++K++F      V  L R S G  +L   LA
Sbjct: 177 QLVRLTI--TEGKYHQVKRMFAAVGNHVVGLHRESIGKIELDAELA 220


>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 = 45.1 bits (105), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 41/73 (56%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          QR++KV+A     SRRE E+ IAQ  V V+G  ++   V V ++  +++D     +A   
Sbjct: 13 QRLAKVVAALVPCSRREAEQYIAQGWVSVDGQCVDAPQVRVTTSQRVQIDPQARLQAVVP 72

Query: 74 RLWLYHKPIGLVT 86
            +L HKP G+ T
Sbjct: 73 ATFLVHKPAGMET 85


>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 = 44.7 bits (104), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 100/237 (42%), Gaps = 17/237 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++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 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG---KELPAVKASW 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  N  +   ++  +   I ++ E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 178 QNENR-LRFAMKNPQPGIIAQLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTK 233


>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 = 44.7 bits (104), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 107/231 (46%), Gaps = 24/231 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS---------TDHIEVDG 64
            RV +++   G  SR E+ R+      K  GI+L+ A +  +S            +E+DG
Sbjct: 8   SRVDQLLGSMGYGSRAEMARL-----GKAGGIVLDGADLTDVSKRIPVTPDLPGRMEIDG 62

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEG 120
            PL       + L +KP+G+  +H + DG + V+D LP  + R    + ++GRLD  T G
Sbjct: 63  EPLDPVAGL-VVLLNKPLGMTCSHKE-DG-ALVYDVLPDRWRRRDPAISTIGRLDKQTSG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTL 179
           LLLLT+DG L   +  P     +VYR      ++  +  L   G +V++G         L
Sbjct: 120 LLLLTDDGDLLHRVISPKRHVAKVYRATLARPLNGTEGALFASGELVLEGEDKPLAPAVL 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
           +    + A +TV   EG+  +++++F      V  L R   G   L   LA
Sbjct: 180 EVVSPTEALLTV--TEGRYHQVRRMFAAAGNHVEALHRERLGGLVLPDELA 228


>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 = 44.3 bits (103), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 45/164 (27%), Positives = 70/164 (42%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K +A A   SR E +  I    V V+G+++E       +      D   L  AE 
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATAAQITLADDAVLSPAEP 63

Query: 73  TRLWLYHKPIGL----VTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+        + P  RS +  +    L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGVSVEAALALATPTTRSALDQSDIRVLKRHFLRLTAPLPLENAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           ++DG + R L   ++   + + V   G V    +  L  G+V Q
Sbjct: 123 SHDGRVLRRLSADASSIEQEFLVEVQGDVRPYGMARLAHGLVYQ 166


>gi|218674542|ref|ZP_03524211.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli GR56]
          Length = 110

 Score = 44.3 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 38/61 (62%)

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++  L
Sbjct: 37  QGDRNSWIEVELDEGRNRQIRRMLEALGAECLRLVRVAIGGLELGELPKGAVRALTEAEL 96

Query: 242 R 242
           +
Sbjct: 97  Q 97


>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 = 44.3 bits (103), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 47/219 (21%), Positives = 89/219 (40%), Gaps = 19/219 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  V  +G +++ +   V     I +DG  L      R
Sbjct: 28  RLDKFICESTSLTRSLAKKAMHRGDVTCDGEIIKNSGFKVTDAHTICLDGEVLSII-GPR 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--------GRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+   +  +        GRLD +T GL+L+TN
Sbjct: 87  FIMINKPVDTIC--------STIDEEYPSVLGLIDVIKPEELHIAGRLDADTTGLVLITN 138

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + Y +     +    +     G+ +           LD      
Sbjct: 139 DGQWSHKITSPKKECGKRYLLETAEPLADSLVEQFATGLQLNNEDGLTKPAILDILGAHE 198

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           A +T+   EGK  ++K++      +V RL R   G  +L
Sbjct: 199 ARLTI--TEGKYHQVKRMLAAVGNRVTRLHRECVGTIEL 235


>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 = 44.3 bits (103), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 39/136 (28%), Positives = 59/136 (43%), Gaps = 9/136 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +   G+ SRRE +  I Q  VKV+G ++      V     I + G P   A    
Sbjct: 7   RLSKRMVELGLCSRREADACIEQGLVKVDGKVVNTLGARVRPEQQITLAGKPQAMATLPV 66

Query: 75  LWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTN 126
             L ++P G     +    PD R+   D    ++       + +VG +D    GLL+LT 
Sbjct: 67  TMLLNRPAGEEAPPAQLLGPDSRAPQ-DGAEQVWLARHRQHLTAVGAVDERCHGLLVLTQ 125

Query: 127 DGGLARVLELPSTQWL 142
           D  L R L     ++L
Sbjct: 126 DKKLPRHLAECEMEFL 141


>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 = 44.3 bits (103), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 94  RSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           R  V  NL P+  ++++  GRLD+++ GL + T DG LA  L  P  +  + Y V     
Sbjct: 52  RREVKSNLSPAKCNKLVCAGRLDVDSTGLTVFTQDGRLASQLVGPGKRVSKEYHVEVDLP 111

Query: 153 VDQDKLNLLKKGIVIQGI 170
           V    L LL+ G+ + G+
Sbjct: 112 VSAGALTLLRHGLSLDGL 129


>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 = 43.9 bits (102), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 56/231 (24%), Positives = 91/231 (39%), Gaps = 18/231 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A A   SRRE E+ I    V V+G+++E     V     I +       A    
Sbjct: 6   RLAKRVADAVPCSRREAEQYIEGGWVTVDGVVIEEPGHRVSPQQAIHLSPDATLVAINPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----------IFSRVISVGRLDINTEGLLL 123
             L HKP G+    +D   R    +NL +             S +  V  L+    GL++
Sbjct: 66  TILLHKPAGI---DADAALRLITPENLYAEDRSGIRFLKKHTSELKPVDVLETYASGLMV 122

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  +AR L   +    + Y     G +  + L LL  G+   G     ++V+   + 
Sbjct: 123 FTQDWHVARKLVDDAATVEQEYIAEVSGDLIPNGLALLNHGLNFNGKPLAPIKVSWQNET 182

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +   L+ G+  +I  + E    K+  L RI      + +L AG  R
Sbjct: 183 R----LRFALKAGRRGQIAHMCEMVGLKLLNLKRIRIARLPMASLPAGQWR 229


>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 = 43.9 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 45/84 (53%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    R
Sbjct: 2  RLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGPR 61

Query: 75 LWLYHKPIGLVTTHSDPDGRSTVF 98
           ++ +KP G V +  DPD  + ++
Sbjct: 62 YFMLNKPQGYVCSTEDPDHPTVLY 85


>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 = 43.9 bits (102), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 40/170 (23%), Positives = 77/170 (45%), Gaps = 13/170 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+++ +A     SR E E+ I    VKV+G ++E    ++++++ +E+D     +   
Sbjct: 34  PIRLARRVAELAQCSRSEAEQYIEGGWVKVDGQVVELPG-HMVTSERVEIDPKARLQPVE 92

Query: 73  TRLWLYHKPIG------------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
              +L HKP G            L+      +G ++    L   F R+ S+  L+    G
Sbjct: 93  PATFLLHKPAGVDLEAVADTLATLLPPQERWEGDTSNIRTLRKNFQRLASLVPLEPEASG 152

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           L++L+ DG + R L        + + V   G ++   L+ L  G+  +G+
Sbjct: 153 LVVLSQDGRVRRRLVEDFATIEQEFVVEVEGSLEPWGLSRLSHGLTFEGL 202


>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 = 43.5 bits (101), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 22/38 (57%), Positives = 28/38 (73%), Gaps = 2/38 (5%)

Query: 9   ENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNG 44
           ENF   PQR+SKV+A +G+ASRR  E +I Q +V VNG
Sbjct: 144 ENFREPPQRLSKVLAASGVASRRNSEELIFQGKVTVNG 181


>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 = 43.5 bits (101), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 94  RSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           R  V  NL P+  ++++  GRLD+++ GL + T DG LA  L  P  +  + Y V     
Sbjct: 52  RREVKSNLSPAKCNKLVCAGRLDVDSTGLTVFTQDGRLASQLVGPGKRVSKEYHVEVDLP 111

Query: 153 VDQDKLNLLKKGIVIQGI 170
           V    L LL+ G+ + G+
Sbjct: 112 VSAGALTLLRHGLSLDGL 129


>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 = 43.5 bits (101), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 48/223 (21%), Positives = 93/223 (41%), Gaps = 19/223 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   SR   ++ + +  V  NG +++ +   V     I ++G  L K    R
Sbjct: 2   RLDKFICESTSHSRVSAKKALHRGDVTCNGEVVKTSGFKVTDEHEIRLEGEVL-KVIGPR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--------GRLDINTEGLLLLTN 126
             + +KP+  +         ST+ +  PS+   +  +        GRLD +T GL+L+T 
Sbjct: 61  FIMLNKPVDTIC--------STIDEEYPSVIGLLDVIRPEDLHIAGRLDADTTGLVLITT 112

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P  +  + Y +     + ++ +     G+ +           L+      
Sbjct: 113 DGKWSHKITSPKKECGKRYLLETADPLTEELIGKFATGLQLNNEDGLTKPAKLELLGTHQ 172

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           A +T+   EGK  ++K++      KV +L R   G  +L + L
Sbjct: 173 ARLTI--TEGKYHQVKRMLAAVGNKVTKLHREVVGEIELDSSL 213


>gi|20451741|emb|CAD30266.1| ribosomal small chain pseudouridine synthase A [Listonella
           anguillarum]
          Length = 109

 Score = 43.5 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 12/98 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------GRLDINTEGLLLLTND 127
           R  + HKP G V +H D       F++   I    ++V      GRLD++T GL+L+T+D
Sbjct: 17  RYIMLHKPTGYVCSHEDG------FNHTAFILLDEVNVQDLHFAGRLDVDTTGLVLITDD 70

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
           G  +  +  P  +  + YRV     ++ + +     GI
Sbjct: 71  GQWSHRITSPKHKCDKTYRVWLADPIEANYVEQFLTGI 108


>gi|268611607|ref|ZP_06145334.1| RNA pseudouridine synthase family protein [Ruminococcus
           flavefaciens FD-1]
          Length = 201

 Score = 43.5 bits (101), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 56/178 (31%), Positives = 79/178 (44%), Gaps = 24/178 (13%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL 134
           ++++KP   VT   D   R TV D  P+  S R+  VGRLD +T GLLLLT+DG L   +
Sbjct: 7   YMFNKPQNCVTAKRDAVHR-TVMDFFPADLSERLHPVGRLDKDTCGLLLLTDDGDLDFRI 65

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----------YGDMQV------ 177
             P     + Y     G +D +K+  L+KGI + G             Y   Q+      
Sbjct: 66  MQPDRHVSKTYFFYAIGTMDDEKIRSLEKGISMVGFTSRPASFRLIRKYRISQLEEFFPS 125

Query: 178 -----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 L    G      + + EGK  E+K++ E  + K+  L RIS G   L   LA
Sbjct: 126 ERRERYLKNPDGPAFAAELTIHEGKKHEVKRMLEAVHCKIFYLKRISIGGLSLDDSLA 183


>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 = 43.5 bits (101), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 44/166 (26%), Positives = 79/166 (47%), Gaps = 26/166 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-----------STDHIEVD 63
           R+ + +A   + SR   ++++AQ  V+VNG ++E+A+ ++              DH  V 
Sbjct: 15  RLDQFLAATELFSRSMAQKLVAQGHVQVNGTVIEKASYSLQPGDLVCVQQPAPVDHATVV 74

Query: 64  G--VPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFS--RVIS 110
           G  +PL    E   L + +KP G+V   +  +  +T+         D LP+I    R   
Sbjct: 75  GQEIPLNIWYEDESLLVVNKPAGMVVHPAAGNYDATLVNALVHYLGDGLPAIGGVLRPGI 134

Query: 111 VGRLDINTEGLLLLT-NDGGLARVLELPSTQWL-RVYRVRFHGQVD 154
           V RLD +T GL+L+   +    R++ + + + + R Y    HG +D
Sbjct: 135 VHRLDKDTSGLMLVAKTEVAHQRLVSMFAAKEIDRCYLALCHGSLD 180


>gi|294893081|ref|XP_002774329.1| hypothetical protein Pmar_PMAR007910 [Perkinsus marinus ATCC 50983]
 gi|239879651|gb|EER06145.1| hypothetical protein Pmar_PMAR007910 [Perkinsus marinus ATCC 50983]
          Length = 100

 Score = 43.1 bits (100), Expect = 0.060,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 48/91 (52%), Gaps = 3/91 (3%)

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK--GIVIQGICYGDM 175
             GL++LTNDG  A  +  P ++ L V+ VR  G++ +D+    ++  G+ +  + YG +
Sbjct: 2   CSGLVILTNDGEFAHNMAHPRSKVLSVFLVRVKGRLPEDRFKSWRRREGVKVGNVAYGQV 61

Query: 176 QVTLDTQKGSNA-WVTVGLREGKNREIKKVF 205
            V +D +   +  W+ V L     + + K+F
Sbjct: 62  FVGIDKRPSEDVTWLRVRLVMTNEKNLVKLF 92


>gi|229023034|ref|ZP_04179549.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228738257|gb|EEL88738.1| Pseudouridine synthase [Bacillus cereus AH1272]
          Length = 90

 Score = 43.1 bits (100), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 40/65 (61%)

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            ++++T   ++   A V + + EG+NR+++++FE  + KV +L R  Y   ++G+L  G 
Sbjct: 10  ANVKITSWDKRKETAIVQLTIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGD 69

Query: 233 TREVS 237
            RE++
Sbjct: 70  ARELT 74


>gi|323210422|gb|EFZ95309.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 127

 Score = 43.1 bits (100), Expect = 0.071,   Method: Compositional matrix adjust.
 Identities = 19/49 (38%), Positives = 30/49 (61%)

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +     +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L
Sbjct: 8   IKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPL 56


>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 = 42.7 bits (99), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 47/166 (28%), Positives = 68/166 (40%), Gaps = 15/166 (9%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---MSTDHIEVDGVPLRK 69
           P R++K +      SRRE E  IA   V V+G ++E     V   +   H   D  P+  
Sbjct: 4   PVRLAKRLVELVACSRREAELYIAGGWVMVDGQIVEEPQFMVSEQLVELHPNADLTPIEP 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLL 123
           A      L+H      TT      RS   D+L  I      F ++     L+ N  GL +
Sbjct: 64  AT----LLFHHLNATNTTAICAGTRSA--DDLSGIHLLRQHFFKLTPCTPLERNASGLTV 117

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           LT D  + R L+  +    + Y V   G++  D L LL  G+   G
Sbjct: 118 LTQDFRIIRKLKDEAATIEQEYIVEIAGEIMADGLKLLNHGLKFNG 163


>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 = 42.7 bits (99), Expect = 0.082,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 48/102 (47%), Gaps = 1/102 (0%)

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLRE 195
           P     + Y V   G V    L  +++G+ + +G     ++V    Q   +  + + L +
Sbjct: 3   PRHHQPKTYDVLVRGIVPASALATMRRGMTLAEGEQLRPVEVESRLQANGHTRLRMVLHQ 62

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           G NR+I+++       + RL RIS GP  LG L  GS R +S
Sbjct: 63  GVNRQIRRMCRDLGLTILRLKRISLGPIGLGDLPVGSCRFLS 104


>gi|330959244|gb|EGH59504.1| S4 domain-containing protein [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 236

 Score = 42.7 bits (99), Expect = 0.086,   Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 95/235 (40%), Gaps = 13/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G+++E     V ST  +E+       +  
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKVELSPDAKADSPE 62

Query: 73  TRLWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + HKP        + ++T  +  +  S     L   F R+  +  L  N  GL++ 
Sbjct: 63  AVTIILHKPASASAESALQMITPGTLSEEHSYSKRPLKGHFMRLEPISSLQANASGLMVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           + D  + R L    ++  + Y V   G +    LN L  G+  +G    ++     + + 
Sbjct: 123 SQDWKILRKLTDDRSKIEQEYVVEITGDMVAHGLNRLNHGLTYKG---KELPAVKASWQN 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            N  +   ++  +   I ++ E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 180 ENR-LRFAMKNPQPGIIAQLCEAVGLKIVSIRRIRIGGVSMGKLPEGQWRYMTSK 233


>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 = 42.4 bits (98), Expect = 0.098,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 95/245 (38%), Gaps = 30/245 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
           P R++K +A     SRRE E+ I    V V+G+++E     V+  T  +  D   L  A 
Sbjct: 3   PVRLAKRLAEMLSCSRREAEQYIEGGWVTVDGVVVEEPQFRVLDQTIELSKDASLLALAP 62

Query: 72  RTRLWLYHKPIG-------------------LVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            T   L HKP G                   LV  +  PD RS +   L   FS    V 
Sbjct: 63  VT--LLLHKPAGHEAGLDAPAGRGVPSAAELLVAANQSPDDRSGI-RPLKKHFSAAELVT 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQG 169
            L     GL++ T D  +AR L   +        V   G++     ++LN +  G    G
Sbjct: 120 PLATAASGLVVFTQDWRVARKLREDAGVLEHEVIVEVTGEIKPGGLERLNRIDHGFTFNG 179

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           +     +V+      S A +   L+  +  +I  + E    +V  + R+  G   +  L 
Sbjct: 180 VLLPPAKVSWQ----SEARLRFALKGERPGQIAYMCESVGLRVEAMKRLRIGRVPMSNLQ 235

Query: 230 AGSTR 234
           +G  R
Sbjct: 236 SGRWR 240


>gi|291336627|gb|ADD96173.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 59

 Score = 42.4 bits (98), Expect = 0.099,   Method: Composition-based stats.
 Identities = 21/43 (48%), Positives = 30/43 (69%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV 54
          T +R+SK +ARAG+ SRRE ER I   RV ++  ++  AA+NV
Sbjct: 13 TEERISKRLARAGLCSRREAERWINAGRVSIDNEVINTAAINV 55


>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 = 42.4 bits (98), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 50/222 (22%), Positives = 90/222 (40%), Gaps = 33/222 (14%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           + +++   G  +R+   ++I    V V G ++         TD+    E DG+  R  + 
Sbjct: 6   LDRLLQSQGFGTRKWCRQLIDDGEVSVAGTVV---------TDYRTAFEPDGLTFRLFDE 56

Query: 73  TRLWLYHKPIGLVTTHSDPDGRST--------VFDNLPSIFS--RVISVGRLDINTEGLL 122
              W +H+ +  V  H  P+   +        V   LP  F+   V  VGRLD +T GLL
Sbjct: 57  D--WDFHEHV-FVALHKPPNFECSRKPSHHPGVLSILPENFTWRDVQPVGRLDHDTTGLL 113

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+++ G        P +   +VY       V  + + LL  G+ +      D    L   
Sbjct: 114 LMSDHGPFIHAQSSPKSHIPKVYIATTAEAVTPELVALLLAGVQLH-----DEPAPLAAV 168

Query: 183 KGS---NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + S   +  + + L +GK  ++K++          L R++ G
Sbjct: 169 RCSMVDSHRIEIVLEQGKYHQVKRMLAAAGNHCAALQRVAIG 210


>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 = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 36/112 (32%), Positives = 57/112 (50%), Gaps = 11/112 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL----ERAAVNVMSTDHIEVDGVPLRKA 70
           RV K++   G  SR E+ R+     + ++G+ L    +R AV       ++VDG PL   
Sbjct: 7   RVDKLLGSMGYGSRSEIARLGKVGGIVLDGVDLTDVSKRIAVTPDLPSRMQVDGRPLDPP 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
               L L +KP+G+  +H + DG   V+D LP  + R    + ++GRLD  T
Sbjct: 67  AGVVLIL-NKPLGMTCSHKE-DG-DLVYDVLPDRWRRRDPAISTIGRLDKQT 115


>gi|163858109|ref|YP_001632407.1| hypothetical protein Bpetpseudo_11 [Bordetella petrii DSM 12804]
 gi|163261837|emb|CAP44139.1| pseudogene [Bordetella petrii]
          Length = 217

 Score = 42.4 bits (98), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + +KP   +   SD  GR+T+ D +    S     GRLD ++EGLLLLTNDG   R L
Sbjct: 128 LLMLNKPFDALAQLSDDQGRATLKDFVD--VSDFYPAGRLDRDSEGLLLLTNDGRCNREL 185

Query: 135 ELPST 139
           ++  T
Sbjct: 186 QILGT 190


>gi|325116556|emb|CBZ52110.1| putative 16S pseudouridylate synthase [Neospora caninum Liverpool]
          Length = 255

 Score = 42.0 bits (97), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 40/186 (21%), Positives = 71/186 (38%), Gaps = 53/186 (28%)

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P+  ++++  GRLD+++ GL + T DG LA  +  P  +  + Y V     V    L LL
Sbjct: 61  PAKCNKLVCAGRLDVDSTGLTVFTQDGRLASQIVGPGKRVSKEYYVEVDLPVSVGALTLL 120

Query: 162 KKGIVIQGICYGDMQVTL------------------------------------------ 179
           + G+ + G+     +V L                                          
Sbjct: 121 RHGLSLDGLELLPAKVRLLPPLRDAFFASLPPSGVSTSAPSSPTSLASYAFAEEKRVGSA 180

Query: 180 -----DTQKGSNAWV------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                + +  S  WV      ++ L EG++R+I+++ E    +V ++ R+  G   LG L
Sbjct: 181 EDTGAEGKDESEIWVGRTTRLSIELLEGRHRQIRRMCELVGLRVLKIHRVRIGKISLGAL 240

Query: 229 LAGSTR 234
             G  R
Sbjct: 241 PQGRWR 246


>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 = 42.0 bits (97), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 28/110 (25%), Positives = 49/110 (44%), Gaps = 15/110 (13%)

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQVTL--------DTQKGSNA 187
           ++Y V+  G   QD L  L+ G+ +        G    D    L        + +    +
Sbjct: 17  KIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRERKSIPTS 76

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 77  WLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 126


>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 = 42.0 bits (97), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 34/112 (30%), Positives = 54/112 (48%), Gaps = 11/112 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           R+ K++A  G  SRREV+ +     + ++G  + +A   +  T  +    +VDG PL   
Sbjct: 6   RLDKLLANMGYGSRREVQALARAGAITLDGAPVPKADTRIALTPDLPARMQVDGRPLDPL 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINT 118
               L L HKP G+  +H +      V+  LPS +      + +VGRLD  T
Sbjct: 66  PGMALML-HKPTGVTCSHKETG--ELVYSLLPSRWRMREPPLSTVGRLDKET 114


>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 = 42.0 bits (97), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 64/230 (27%), Positives = 105/230 (45%), Gaps = 24/230 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS---------TDHIEVDGV 65
           RV +++   G  SR E+ RM      K  GI+L+ A +  +S            +E+DG 
Sbjct: 8   RVDRLLGSMGYGSRAEMARM-----AKAGGIVLDGADLTDVSRRIPVTRDLPTRMEIDGE 62

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGL 121
           PL   +   + L +KP+G+  +H +    + V+D LP  +      + ++GRLD  T GL
Sbjct: 63  PLDPVQGL-VILLNKPLGMTCSHKEEG--ALVYDILPGRWRSRDPAISTIGRLDKQTTGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLD 180
           LLLT+DG L   +  P     +VYR      +   + +L   G +V++G         L+
Sbjct: 120 LLLTDDGDLLHRVISPKRHVAKVYRAGLARPLMGTEGDLFASGELVLEGEDKPLAPAVLE 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               + A +TV   EG+  +++++F      V  L R   G   L   LA
Sbjct: 180 VVSPTEALLTV--TEGRYHQVRRMFAAAGNHVETLHRERLGGLVLPADLA 227


>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 = 41.6 bits (96), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 70/165 (42%), Gaps = 9/165 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G++++     V ST  IE+       +  
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIDEPHFKV-STQKIELSPEAKADSPE 62

Query: 73  TRLWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +   + HKP        + ++T  +     S     L   F R+ ++  L  N  GL++ 
Sbjct: 63  SVTIILHKPASASAESALQMITPGTLSAEHSYSKRPLKGHFMRLEAISSLQANASGLMVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           + D  + R L    ++  + Y V   G++    LN L  G+  +G
Sbjct: 123 SQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG 167


>gi|296390524|ref|ZP_06879999.1| hypothetical protein PaerPAb_20321 [Pseudomonas aeruginosa PAb1]
          Length = 236

 Score = 41.6 bits (96), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 71/169 (42%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTV---FDNLPSI-------FSRVISVGRLDINTEG 120
                 L HKP G    H D +G       + + PS        F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G++    L  L++G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVTGELAAGGLERLRQGLAYQG 167


>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 = 41.6 bits (96), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++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 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 181 NR----LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTK 233


>gi|330956144|gb|EGH56404.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
          syringae Cit 7]
          Length = 75

 Score = 41.6 bits (96), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 8/74 (10%)

Query: 2  KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---ILLERAAVNVMST 57
          KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG    L +R  ++    
Sbjct: 4  KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDATLGQRVDLH---- 59

Query: 58 DHIEVDGVPLRKAE 71
          D I VDG  +++ E
Sbjct: 60 DAISVDGRVIKREE 73


>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 = 41.2 bits (95), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 70/165 (42%), Gaps = 9/165 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G++++     V ST  IE+       +  
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIDEPHFKV-STQKIELSPDAKADSPE 62

Query: 73  TRLWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +   + HKP        + ++T  +     S     L   F R+ ++  L  N  GL++ 
Sbjct: 63  SVTIILHKPASASAESALQMITPGTLSAEHSYSKRPLKGHFMRLEAISSLQANASGLMVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           + D  + R L    ++  + Y V   G++    LN L  G+  +G
Sbjct: 123 SQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG 167


>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 = 41.2 bits (95), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 45/167 (26%), Positives = 72/167 (43%), Gaps = 13/167 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++T  +     S     L   F R+ ++  L  N  GL+
Sbjct: 61  PEPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLM 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           + + D  + R L    ++  + Y V   G++    LN L  G+  +G
Sbjct: 121 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG 167


>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 = 41.2 bits (95), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 42/165 (25%), Positives = 69/165 (41%), Gaps = 9/165 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+       +  
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELSPDAKANSPE 62

Query: 73  TRLWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + HKP        + ++T  +     S     L   F R+ ++  L  N  GL++ 
Sbjct: 63  PVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLMVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           + D  + R L    ++  + Y V   G++    LN L  G+  +G
Sbjct: 123 SQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG 167


>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 = 41.2 bits (95), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 68/165 (41%), Gaps = 9/165 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G +++     V +T  +E+D      A  
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKV-TTQKVELDPEAKATAPE 62

Query: 73  TRLWLYHKPIGL-VTTHSDPDGRSTVFDN-------LPSIFSRVISVGRLDINTEGLLLL 124
               L + P G  V T     G  T+ +        L   F R+ +   L  N  GLL+ 
Sbjct: 63  PVTLLLNVPAGTDVDTAMASLGPQTLSEEHRFGKRPLKGHFLRLTASADLQANASGLLVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           T D  + R L   + +  + Y V   G++    LN L  G+  +G
Sbjct: 123 TQDWKILRKLTADAAKIEQEYVVEVEGEMVAHGLNRLNHGLTYKG 167


>gi|255024632|ref|ZP_05296618.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 105

 Score = 41.2 bits (95), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 49/104 (47%), Gaps = 5/104 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E  
Sbjct: 2   RLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQEFV 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLD 115
              L HKP  +V+   D +   TV D L      +    VGRLD
Sbjct: 62  YFML-HKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLD 103


>gi|159486376|ref|XP_001701217.1| hypothetical protein CHLREDRAFT_179001 [Chlamydomonas
          reinhardtii]
 gi|158271917|gb|EDO97727.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 235

 Score = 40.8 bits (94), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 22/49 (44%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEV 62
          R++KV+A  G+ASRR  E +IA  RV+VNG L++     V  + D +EV
Sbjct: 48 RLAKVLAACGVASRRACEGLIADGRVRVNGNLVKEQGTTVDPARDKVEV 96


>gi|289667011|ref|ZP_06488086.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 236

 Score = 40.8 bits (94), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 42/164 (25%), Positives = 70/164 (42%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K +A A   SR E ++ I    V V+G+++E       +      +   L  AE 
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQALATAGQVTLAEDAVLAPAEP 63

Query: 73  TRLWLYHKPIGL----VTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+        + P  RS ++ +    L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGVSAEAALALATPTTRSALYPSDIRVLKRHFLRLTAPLPLEDAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + DG + R L   +    + + V    ++    +  L  G+V Q
Sbjct: 123 SQDGRVLRRLSAEARSIEQEFLVEVQCELRPYGMARLAHGLVYQ 166


>gi|218506712|ref|ZP_03504590.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli Brasil 5]
          Length = 102

 Score = 40.8 bits (94), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 43/77 (55%), Gaps = 2/77 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV ++G  +   +  V + T  I VDG  +  AE   
Sbjct: 27  LPRALSKLGYCSRTQAERLIAESRVSIDGRTVNDPSAWVDLVTAKIRVDGHVI-AAEAKI 85

Query: 75  LWLYHKPIGLVTTHSDP 91
             + +KP GLVTT  DP
Sbjct: 86  YLILNKPRGLVTTRHDP 102


>gi|302187180|ref|ZP_07263853.1| RNA-binding S4 [Pseudomonas syringae pv. syringae 642]
          Length = 236

 Score = 40.8 bits (94), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 98/237 (41%), Gaps = 17/237 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++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 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG---KELPAVKASW 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  N  +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 178 QNENR-LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAK 233


>gi|289661981|ref|ZP_06483562.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 236

 Score = 40.4 bits (93), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 43/164 (26%), Positives = 70/164 (42%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K +A A   SR E ++ I    V V+G+++E       +      +   L  AE 
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQALATAGQVTLAEDAVLAPAEP 63

Query: 73  TRLWLYHKPIGL----VTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+        + P  RS +  +    L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGVSAEAALALATPTTRSALDPSDIRVLKRHFLRLTAPLPLEDAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + DG + R L   +    + + V   G++    +  L  G+V Q
Sbjct: 123 SQDGRVLRRLSAEARSIEQEFLVEVQGELRPYGMARLAHGLVYQ 166


>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 = 40.4 bits (93), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 54/225 (24%), Positives = 87/225 (38%), Gaps = 25/225 (11%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERT 73
           + +++   G  +R+    +I    V V G  +     +   TD++E  V G   R  E  
Sbjct: 6   LDRILQSQGFGTRKWCRELIEDGEVLVAGDSITDYR-HAFETDNLEFSVYGESWRFREHV 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + L +KP     +   P     V   LP  F+   V  VGRLD +T GLLL+++DG   
Sbjct: 65  YIAL-NKPADYECSRK-PSHHPGVLSLLPEQFALRDVQPVGRLDHDTTGLLLMSDDGAFI 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------ICYGDMQVTLDTQK 183
                P     +VY    H  V    +  L  G+ +          +C       LDT +
Sbjct: 123 HAQSSPKRHIPKVYVATTHDPVTPQLVRQLMSGVKLHDEPAPLAAVVCN-----MLDTCQ 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                + + L +GK  ++K++          L R   G  +L  L
Sbjct: 178 -----LKIVLEQGKYHQVKRMLAAAGNHCTALRRTEIGKLRLEAL 217


>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 = 40.4 bits (93), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 54/233 (23%), Positives = 93/233 (39%), Gaps = 19/233 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+S+ +      SRRE E  I    V V+G ++E     V+      V+ +P  + E 
Sbjct: 4   PIRLSRRLVELIACSRREAELYIEGGWVSVDGTVVEEPQFKVLDQ---RVELLPGARPEP 60

Query: 73  TR--LWLYHKPIG---------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
                 L HKP G         LV  H   +  ++V   L   F+R  +   LD    GL
Sbjct: 61  LAPVTLLLHKPAGCREDEAARLLVAAHRW-EADASVLRPLKKHFARQRATLPLDTEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+ +   G+ R L     +  + Y V   G++    L  L+ G+  +G      +V+   
Sbjct: 120 LVFSQQHGVLRKLVEDGARIEQEYLVEVAGELPPGGLERLRHGLAYRGRALPPCKVSWQN 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +      +   L+  +  +++ + E    +V  + R+  G   L  L +G  R
Sbjct: 180 ENH----LRFALKGAQPGQLRFMCESEGLEVRGIRRLRIGALSLARLPSGEWR 228


>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 = 40.4 bits (93), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 36/137 (26%), Positives = 55/137 (40%), Gaps = 4/137 (2%)

Query: 91  PDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           P    +V + LP       V  VGRLD +T GLLL T++G L   L  P     +VYR  
Sbjct: 77  PSAHPSVMNLLPGPLRTRGVQPVGRLDWDTTGLLLFTDNGALLHRLTHPKKHVNKVYRAT 136

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       L  G+V+            +        +T+   +GK  ++K++    
Sbjct: 137 LSHPAANGTCEKLLSGVVLDDDPKPVFAKAAELMAPDVLMLTI--SQGKYHQVKRMVAAC 194

Query: 209 NWKVNRLIRISYGPFQL 225
             +V  L RI  G ++L
Sbjct: 195 GNRVVALHRIKVGAYEL 211


>gi|213858018|ref|ZP_03384989.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
          enterica serovar Typhi str. M223]
          Length = 82

 Score = 40.4 bits (93), Expect = 0.45,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 34/66 (51%)

Query: 33 RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
          R I   RV V+G ++  AA  ++    +  DG PL +    R ++ +KP G V +  DPD
Sbjct: 6  REIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPD 65

Query: 93 GRSTVF 98
            + ++
Sbjct: 66 HPTVLY 71


>gi|330950630|gb|EGH50890.1| RNA-binding S4 [Pseudomonas syringae Cit 7]
          Length = 236

 Score = 40.0 bits (92), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 94/235 (40%), Gaps = 13/235 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       A  
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADAPE 62

Query: 73  TRLWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + HKP        + ++T  +     S     L   F R+ ++  L  N  GL++ 
Sbjct: 63  PVTIILHKPASASAEEALQMITPGTLSVEHSYSKRPLKGHFMRLEAISSLQANASGLMVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           + D  + R L    ++  + Y V   G++    LN L  G+  +G    ++     + + 
Sbjct: 123 SQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG---KELPAVKASWQN 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            N  +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 180 ENR-LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAK 233


>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 = 40.0 bits (92), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 69/169 (40%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTV---FDNLPSI-------FSRVISVGRLDINTEG 120
                 L HKP G    H D +G       + + PS        F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQG 167


>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 = 40.0 bits (92), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 67/169 (39%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEG 120
                 L HKP G    H D +G            +    L   F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDLEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQG 167


>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 = 40.0 bits (92), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 69/169 (40%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTV---FDNLPSI-------FSRVISVGRLDINTEG 120
                 L HKP G    H D +G       + + PS        F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQG 167


>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 = 40.0 bits (92), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 47/169 (27%), Positives = 69/169 (40%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTV---FDNLPSI-------FSRVISVGRLDINTEG 120
                 L HKP G    H D +G       + + PS        F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVTGDLAAGGLERLRHGLAYQG 167


>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 = 40.0 bits (92), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 67/169 (39%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEG 120
                 L HKP G    H D +G            +    L   F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQG 167


>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 = 40.0 bits (92), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 72/165 (43%), Gaps = 11/165 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
           P R+ K +A     SR E ++ I    V V+G+++E     +      +  D V L +AE
Sbjct: 4   PIRLDKHVAAVFGCSRGEAQQYIEGGWVSVDGVVVEEPQAPITGQQVSLAADAV-LGQAE 62

Query: 72  RTRLWLYHKPIGL----VTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLL 123
              L L +KP G+        + P  RS++       L   F R+ +   LD    GLL+
Sbjct: 63  PATL-LLNKPAGMSCEAAVALATPQSRSSLDQTEIRVLKRHFLRLSAPMPLDDEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           L+ DG + R L   +    + Y V   G++    +  L  G+V Q
Sbjct: 122 LSQDGRILRRLTADAATIEQEYLVEVRGELRPYGMARLASGLVYQ 166


>gi|15618318|ref|NP_224603.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           CWL029]
 gi|15835936|ref|NP_300460.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           J138]
 gi|33241749|ref|NP_876690.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
 gi|4376683|gb|AAD18547.1| predicted pseudouridine synthetase family [Chlamydophila pneumoniae
           CWL029]
 gi|8978775|dbj|BAA98611.1| pseudouridine synthetase family [Chlamydophila pneumoniae J138]
 gi|33236258|gb|AAP98347.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
          Length = 232

 Score = 40.0 bits (92), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 19/104 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHK 80
           S++E+   I Q R +VNG +    +  V   D + +  +P  K + + LW      +Y K
Sbjct: 40  SKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQPSILWEDDYSIIYEK 99

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           P  L T                +  +R  +V RLD  T G LL+
Sbjct: 100 PPHLTTEQM-------------AHMTRFFTVHRLDKGTSGCLLM 130


>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 = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++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 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               + +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 181 ----SRLRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAK 233


>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 = 39.7 bits (91), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 45/165 (27%), Positives = 74/165 (44%), Gaps = 11/165 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAE 71
           P R+ K +A     SR E ++ I    V VNG+++E   A+   +   +  D V L  AE
Sbjct: 4   PIRLDKCVAAQFGCSRGEAQQYIEGGWVSVNGVVVEEPQALATAAQVELAADAV-LEPAE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---TVFDN-----LPSIFSRVISVGRLDINTEGLLL 123
              L L HKP G+    +    +    +  DN     L   F R+ +   L+ +  GLL+
Sbjct: 63  PATL-LLHKPAGMTAAAAVALAKPASRSELDNAELRVLKRHFLRLNAPLPLEDDASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q
Sbjct: 122 LSQDGRVLRRLTADASSIEQEFLVEVRGELRPYGMARLAHGLVYQ 166


>gi|49081944|gb|AAT50372.1| PA1110 [synthetic construct]
          Length = 237

 Score = 39.7 bits (91), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 67/169 (39%), Gaps = 17/169 (10%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +A     SRRE E  I    V V+G ++E     V+      V+ +P  +AE 
Sbjct: 4   PIRLSKRLAELTACSRREAELHIEGGWVSVDGEVIEEPQFKVLDQ---RVELLPGARAET 60

Query: 73  TR--LWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEG 120
                 L HKP G    H D +G            +    L   F+R      LD    G
Sbjct: 61  IEPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           L++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG
Sbjct: 119 LVVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQG 167


>gi|269303280|gb|ACZ33380.1| RNA pseudouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 283

 Score = 39.7 bits (91), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 19/104 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHK 80
           S++E+   I Q R +VNG +    +  V   D + +  +P  K + + LW      +Y K
Sbjct: 26  SKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQPSILWEDDYSIIYEK 85

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           P  L T                +  +R  +V RLD  T G LL+
Sbjct: 86  PPHLTTEQM-------------AHMTRFFTVHRLDKGTSGCLLM 116


>gi|289674640|ref|ZP_06495530.1| RNA-binding S4 [Pseudomonas syringae pv. syringae FF5]
          Length = 236

 Score = 39.7 bits (91), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++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 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG---KELPAVKASW 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  N  +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 178 QNENR-LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAK 233


>gi|281342232|gb|EFB17816.1| hypothetical protein PANDA_004950 [Ailuropoda melanoleuca]
          Length = 532

 Score = 39.7 bits (91), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 72/312 (23%), Positives = 120/312 (38%), Gaps = 64/312 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R  K+I R    +  +V  ++  Q   + G LL + +V  +  +++E D   L +     
Sbjct: 64  REIKIIRRLDHDNIVKVYEVLGPQGTDLQGELL-KFSVAYIVQEYMETDLARLLEQGTLT 122

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  +L++Y    GL   HS             ++  R +    + I+TE L+L   D G
Sbjct: 123 EEHAKLFMYQLLRGLKYIHS------------ANVLHRDLKPANIFISTEDLVLKIGDFG 170

Query: 130 LARVL-----------ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----- 173
           LAR++           E   T+W R  R+          +++   G ++  +  G     
Sbjct: 171 LARIVDQHYSHKGYLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCILAEMLTGRMLFA 230

Query: 174 ------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF---NWKVNRLIRISYGPFQ 224
                  MQ+ L+T       + V +RE    E+ +V   F   +W+V R +R      Q
Sbjct: 231 GAHELEQMQLILET-------IPV-IREEDKEELLRVMPSFVSGSWEVKRPLR------Q 276

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI-----ISEVP 279
           L   + G   +  +KIL     P     A++ L  P  S  +   D P       I +  
Sbjct: 277 LLPEVNGEAIDFLEKIL--TFNPMDRLTAEMGLQHPYMSPYSCPEDEPTSQHPFRIEDEI 334

Query: 280 DDFTRMKKNSSQ 291
           DD   M  N SQ
Sbjct: 335 DDILLMAANQSQ 346


>gi|223992791|ref|XP_002286079.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977394|gb|EED95720.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 370

 Score = 39.3 bits (90), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 63/274 (22%), Positives = 108/274 (39%), Gaps = 47/274 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRV----KVNGILLERAAVN-----VMSTDHIEVDG 64
           QR+ KV+A  G+ +R +   +   +R+      +    ER  +      V S   + +DG
Sbjct: 90  QRIDKVLADRGVGTRSQTFDLAKAKRITWSTSPDATHEERTRIKGPSEKVPSNASLFLDG 149

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDP-----DGRSTVFDNLPSIFSR--VISVGRLDIN 117
             L  A    L +YHKP  +++   D        R  +   L   ++R  +  VGRLD +
Sbjct: 150 N-LLPAPTPLLLVYHKPKFVLSVMEDDKKYQDQQRKHLGHILEPRYARSGMHPVGRLDYD 208

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICY---- 172
           T GL+L ++DG L + L  P     + Y     G+V+  +L  +L  G+      +    
Sbjct: 209 TTGLILFSSDGKLTQRLLHPRRGVEKEYVATVQGEVNASELREMLANGVETTDGTFAANL 268

Query: 173 -------------------------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                                    G  + T +   G  + V + + EGK R ++++   
Sbjct: 269 IAVTSSNGPSEVSEEDLNNVPEEDEGGDETTDEPYNGPYSDVRLVVSEGKYRMVRRILAN 328

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               V  L R  +G   L  L  G  R+V+ + L
Sbjct: 329 SGHPVVELRRERHGEILLDDLPVGKFRDVTPEEL 362


>gi|301762832|ref|XP_002916837.1| PREDICTED: mitogen-activated protein kinase 4-like [Ailuropoda
           melanoleuca]
          Length = 547

 Score = 39.3 bits (90), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 72/312 (23%), Positives = 120/312 (38%), Gaps = 64/312 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R  K+I R    +  +V  ++  Q   + G LL + +V  +  +++E D   L +     
Sbjct: 64  REIKIIRRLDHDNIVKVYEVLGPQGTDLQGELL-KFSVAYIVQEYMETDLARLLEQGTLT 122

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E  +L++Y    GL   HS             ++  R +    + I+TE L+L   D G
Sbjct: 123 EEHAKLFMYQLLRGLKYIHS------------ANVLHRDLKPANIFISTEDLVLKIGDFG 170

Query: 130 LARVL-----------ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----- 173
           LAR++           E   T+W R  R+          +++   G ++  +  G     
Sbjct: 171 LARIVDQHYSHKGYLSEGLVTKWYRSPRLLLSPNNYTKAIDMWAAGCILAEMLTGRMLFA 230

Query: 174 ------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF---NWKVNRLIRISYGPFQ 224
                  MQ+ L+T       + V +RE    E+ +V   F   +W+V R +R      Q
Sbjct: 231 GAHELEQMQLILET-------IPV-IREEDKEELLRVMPSFVSGSWEVKRPLR------Q 276

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI-----ISEVP 279
           L   + G   +  +KIL     P     A++ L  P  S  +   D P       I +  
Sbjct: 277 LLPEVNGEAIDFLEKIL--TFNPMDRLTAEMGLQHPYMSPYSCPEDEPTSQHPFRIEDEI 334

Query: 280 DDFTRMKKNSSQ 291
           DD   M  N SQ
Sbjct: 335 DDILLMAANQSQ 346


>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 = 39.3 bits (90), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 54/243 (22%), Positives = 95/243 (39%), Gaps = 26/243 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAER 72
           +R++K +A     SRRE E+ I    V VNG ++E     V S   +EVD    L +   
Sbjct: 16  ERLAKRVAEMVPCSRREAEQYIEGGWVSVNGQVVEEPMFRV-SDQRVEVDPDASLLELSA 74

Query: 73  TRLWLYHKPIGL---------------------VTTHSDPDGRSTVFDNLPSIFSRVISV 111
             L L HKP G                        TH+  D        L   F+++ + 
Sbjct: 75  VTL-LLHKPPGFDAMAAPGQANRHVKSAQQLLSAATHATDDASGVRL--LKRHFAKLTAC 131

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
             L+    GL++ T D  + R L   +    +   V   G+V    L  + +G+ + G  
Sbjct: 132 VPLETAASGLVVFTQDWRVLRKLTEDAQLMEQEVIVEVAGEVPAQSLQRINQGLAVDGQP 191

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              ++V+L++   +++ +   L+      I  + E    ++  + R+  G   +  L  G
Sbjct: 192 LPAVKVSLNSTGETSSKLRFALKGSHPGLIAYLCERLGLQIVSMKRLRIGRVSMTQLPLG 251

Query: 232 STR 234
             R
Sbjct: 252 QWR 254


>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 = 39.3 bits (90), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 91/235 (38%), Gaps = 18/235 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A     SRRE E  I    V V+G L+E   + V     IE+      K   
Sbjct: 4   PVRLAKRVAEQFGCSRREAELYIEGGWVTVDGELVEAPFLKVGPQQRIELQPGATAKEIA 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVF-------------DNLPSIFSRVISVGRLDINTE 119
               L HKP  L    SD DG                  + L     R   +  LD +  
Sbjct: 64  PVTLLLHKPAEL-PIDSDNDGPRRALQASEHWADDPSRTEPLQRHLLRHTLLLPLDADAS 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL +L+    + R+L     +  + Y V   G+ ++  L LL KGI  +G      +V+ 
Sbjct: 123 GLSVLSQQREVIRLLGDTRNKLEQEYVVEVSGEAEEGGLALLAKGIGHRGRILPKAKVSW 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            ++      + V ++E    E++ + E    +V    RI  G   +  L  G  R
Sbjct: 183 QSENR----LRVVVKEPAPGEVRMLCEAIGLRVVASKRIRIGRLSMAKLPVGHWR 233


>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 = 39.3 bits (90), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 44/172 (25%), Positives = 76/172 (44%), Gaps = 26/172 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V ENF  +R+ +V+A+     SR +V ++I  + +K+NG +L+  +  V S D IE + 
Sbjct: 7   VVDENFDQKRIDQVVAKQYPKISRSKVSKIIKTELLKLNGQILKDPSHKVKSGDQIEFEN 66

Query: 65  --------VPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                   +P +       E   + +  KPIG+V      +   T+ + L       +S 
Sbjct: 67  LIEETINLIPKKMDLNIIFEDQDIIIIDKPIGMVVHPGAGNYEDTMVNGLLYHCKNNLSG 126

Query: 111 ---------VGRLDINTEGLLLLT-NDGGLARVL-ELPSTQWLRVYRVRFHG 151
                    V R+D +T GLL++  ND   A +  +       R Y V  +G
Sbjct: 127 MNGEDRPGIVHRIDKDTSGLLVVAKNDQAHAFIAKQFEEHSIKRSYLVFVYG 178


>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 = 39.3 bits (90), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+   P  KA+ 
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELS--PDAKADS 60

Query: 73  TR--LWLYHKP--------IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 + HKP        + ++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 VFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKG---KELPAVKASW 177

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  N  +   ++  +   I  + E    K+  + RI  G   +G L  G  R ++ K
Sbjct: 178 QNENR-LRFAMKNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAK 233


>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 = 39.3 bits (90), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 7/69 (10%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
          R++K+++ AGI SRREVE+ I   RV +NG   ERA +   V+  D + +DG  +P+   
Sbjct: 4  RINKLLSDAGIGSRREVEKYIVAGRVMLNG---ERAELTDIVVEDDIVTLDGEELPVNDI 60

Query: 71 ERTRLWLYH 79
           R  L + H
Sbjct: 61 LREALSMKH 69


>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 = 38.9 bits (89), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 53/212 (25%), Positives = 97/212 (45%), Gaps = 5/212 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I      +RREV+ ++    + VN  +  +  +++   D + V G  + +  + R
Sbjct: 4   RLDRYIGNNTELTRREVKFLLKAGEITVNDEVPSKPGLHLKEGDVVAVQGR-VVEPRQPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP   ++  S  +      D +   F   +  VGRLD++T GLLL+T+DG  ++ 
Sbjct: 63  YFMLHKPPECISARSTEEHLGA-LDLIEEPFHDELHIVGRLDLDTTGLLLVTDDGQWSQR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY V     +        + GI ++   +      LD      A +T+  
Sbjct: 122 LRSPRHKVPKVYWVTTAKPIASTVAARFEAGIYLKTEDHTTAPAQLDVVAECRARLTIT- 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            EGK  ++K++F   + +V  L R S G   L
Sbjct: 181 -EGKFHQVKRMFAAVDNEVTALHRASVGEIVL 211


>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 = 38.9 bits (89), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 32/112 (28%), Positives = 53/112 (47%), Gaps = 2/112 (1%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           +DI+T GL+LLT+DG  +  +  P     + Y V     V+      ++KGI+++G    
Sbjct: 1   MDIDTTGLVLLTDDGQWSHRVTSPKHLCDKTYLVTLADPVEDFYQAEIEKGILLRGEKTP 60

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               TL+     N  V + + EG+  ++K++F     KV  L R   G   L
Sbjct: 61  TKPATLEILDDYN--VNLTISEGRYHQVKRMFAALGNKVVDLHRWKIGVIML 110


>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 = 38.9 bits (89), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 41/69 (59%), Gaps = 7/69 (10%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTDHIEVDG--VPLRKA 70
          R++K+++ AGI SRREVE+ I   RV +NG   ERA +   V+  D + +DG  +P+   
Sbjct: 4  RINKLLSDAGIGSRREVEKYIVAGRVMLNG---ERAELTDIVVEDDIVTLDGEELPVNDI 60

Query: 71 ERTRLWLYH 79
           R  L + H
Sbjct: 61 LREALSMKH 69


>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 = 38.9 bits (89), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 32/125 (25%), Positives = 54/125 (43%), Gaps = 5/125 (4%)

Query: 111 VGRLDINTEGLLLLTNDG-GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            GRLD N+ GLL+ T D    + +L     Q  + Y +    ++++  L +LK  + +  
Sbjct: 410 CGRLDANSSGLLIYTQDSIASSYLLNKYKYQVEKEYIITTFNEINECHLKMLKDNLFVD- 468

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
              G +      Q   +  +   L +G ++ I+K+    N K+  L RI  G   L  L 
Sbjct: 469 ---GKLIYKCHIQYVDSFTLIFKLYQGFHKIIRKICLLSNIKIRSLHRIRIGKIHLNNLP 525

Query: 230 AGSTR 234
            G  R
Sbjct: 526 LGKWR 530


>gi|327480070|gb|AEA83380.1| S4 domain-containing protein [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 90/235 (38%), Gaps = 18/235 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A     SRRE E  I    V V+G L+E   + V     IE+      K   
Sbjct: 4   PVRLAKRVAEQFGCSRREAELYIEGGWVTVDGELVEAPFLKVGPQQRIEMQPGATAKEIA 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVF-------------DNLPSIFSRVISVGRLDINTE 119
               L HKP  L    SD DG                  + L     R   +  LD    
Sbjct: 64  PVTLLLHKPAEL-PIDSDNDGPRRALQASEHWADDPSRTEPLQRHLLRHTLLLPLDAGAS 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL +L+    + R+L     +  + Y V   G+ ++  L LL KGI  +G      +V+ 
Sbjct: 123 GLSVLSQQREVIRLLGDTRNKLEQEYVVEVSGEAEEGGLALLAKGIGHRGRILPKAKVSW 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            ++      + V ++E    E++ + E    +V    RI  G   +  L  G  R
Sbjct: 183 QSENR----LRVVVKEPAPGEVRMLCEAIGLRVVASKRIRIGRLSMAKLPVGHWR 233


>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 = 38.5 bits (88), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 64/165 (38%), Gaps = 9/165 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G +++     V +T  +E+D         
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKV-TTQKVELDPEAKATVPE 62

Query: 73  TRLWLYHKPIGL------VTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLL 124
               L H P G+       +  ++       F   P    F R+ +   L     GLL+ 
Sbjct: 63  PVTILMHAPAGMDAETAMASISAETLSEEHRFSKRPLKGHFLRLTASADLQAKASGLLVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           T D  + R L   + +  + Y V   G +    LN L  G+  +G
Sbjct: 123 TQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKG 167


>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 = 38.5 bits (88), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 37/56 (66%), Gaps = 3/56 (5%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
          R++K+++  G+ SRREVE +I + RV +NG   E + V V   D +E+DG  +P+R
Sbjct: 4  RINKLLSDTGLGSRREVEALIEEGRVWINGDRAELSDV-VSEDDVVELDGEELPVR 58


>gi|323969847|gb|EGB65128.1| RNA pseudouridylate synthase [Escherichia coli TA007]
          Length = 191

 Score = 38.1 bits (87), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 30/130 (23%), Positives = 60/130 (46%), Gaps = 4/130 (3%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +  +GRLD +++GL+ LTN G L   +        + Y V     + ++ +  +  G+ I
Sbjct: 1   MFPIGRLDKDSQGLIFLTNHGDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPI 60

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G      +V  +    +     + L +G NR+I+++ E F ++V +L R       L  
Sbjct: 61  LGTVTKKCKVKKE----APFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSG 116

Query: 228 LLAGSTREVS 237
           +  G  R+++
Sbjct: 117 IPLGEWRDLT 126


>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 = 38.1 bits (87), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 42/164 (25%), Positives = 68/164 (41%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K IA A   SR E ++ I    V V+G+++E       +      +   L  AE 
Sbjct: 4   PIRLDKCIAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAAQVTLAENAVLAPAEP 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS---TVFDN-----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+    +         +  D      L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGICVDAALALATPATRSALDQADVRVLKRHFLRLHAPLPLEDAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + DG + R L   ++   + + V   G++    +  L  G+V Q
Sbjct: 123 SQDGRVLRRLSADASAIEQEFLVEVRGELRPYGMARLAHGLVYQ 166


>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 = 38.1 bits (87), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 41/165 (24%), Positives = 64/165 (38%), Gaps = 9/165 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+SK +      SRRE E  I    V V+G +++     V +T  +E+D         
Sbjct: 4   PIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKV-TTQKVELDPEAKATVPE 62

Query: 73  TRLWLYHKPIG------LVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLL 124
               L H P G      + +  ++       F   P    F R+ +   L     GLL+ 
Sbjct: 63  PVTILLHAPAGVDAETAMASISAETLSEEHRFSKRPLKGHFLRLTASADLQAKASGLLVF 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           T D  + R L   + +  + Y V   G +    LN L  G+  +G
Sbjct: 123 TQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKG 167


>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 = 38.1 bits (87), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 32/130 (24%), Positives = 60/130 (46%), Gaps = 5/130 (3%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLA-RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           +++   GRLD N+ GLL+ T +  L   +L     Q  + Y ++    +++  + LL+K 
Sbjct: 334 NKLYVCGRLDANSTGLLVFTQNTLLCSYLLNKHKHQVEKEYMIKTAEPIEEVHMELLRKN 393

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           I++     G +      Q   +  ++  L +G ++ I+K+    N K+  L R+  G   
Sbjct: 394 ILVD----GKLIYKCRIQYVDSFTLSFTLYQGFHKIIRKLCLLSNIKIKALHRVRIGGIH 449

Query: 225 LGTLLAGSTR 234
           L  L  G  R
Sbjct: 450 LKGLPLGKWR 459


>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 = 37.7 bits (86), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          +R+   +   G+A SRRE +R++   RV+VNG L+ +    V   D IEVDGV +R
Sbjct: 5  RRLDAFLRDVGLAESRREAKRLVESGRVRVNGKLVRKPWWLVSPGDEIEVDGVTVR 60


>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 = 37.7 bits (86), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 32/58 (55%)

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            AW+ V + EG+NR+++++     +   RLIR     F L  L+  + R +++  LRE
Sbjct: 25  TAWLEVKIDEGRNRQVRRMTAHIGFPTLRLIRYQLAGFNLQNLMPKTYRTLTQNELRE 82


>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 = 37.7 bits (86), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 16/30 (53%), Positives = 24/30 (80%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNG 44
          R++K+I+ AG+ SRRE E+ I + RVK+NG
Sbjct: 4  RINKLISDAGLGSRREAEKYITEGRVKING 33


>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 = 37.7 bits (86), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 49/206 (23%), Positives = 86/206 (41%), Gaps = 18/206 (8%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT--T 87
           ++ R++ Q RVKVN  L++     V ++D + VDG+ +    R +  +++KP+G+ T  T
Sbjct: 17  QIFRLLRQGRVKVNDRLIDSPRETVDTSDQVTVDGLAV-TGRRPQYLVFNKPVGVQTDLT 75

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
              P    ++ + L    S  I +  L     GL L+T+D     + E+    W    RV
Sbjct: 76  PVVPHSLGSMLNALDQQQSLQI-LADLPRTIAGLTLVTDDNTF--LTEVQGQTWPSTLRV 132

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +  G         L + I  + +     QV        + W  + L+      +    E 
Sbjct: 133 QLTGTTPLT----LPQNIAAEVVEQRPDQV--------HQWTMLTLQTTALDSVTAWLES 180

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGST 233
            +     + RI +GP +L   LA  T
Sbjct: 181 LSRVSGAINRIGWGPIKLSPDLAVGT 206


>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 = 37.7 bits (86), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           ++LD +K   + V + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 15  LSLDKKK-QTSIVQITIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLNLAGLKTGEKREL 73

Query: 237 S 237
           +
Sbjct: 74  T 74


>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 = 37.7 bits (86), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 49/214 (22%), Positives = 86/214 (40%), Gaps = 39/214 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--------------ER 72
           SR  +++++AQ  V +NG  + +AA  V + D + ++  P  ++              E 
Sbjct: 63  SRSYLQQLLAQGGVSLNGRPVRKAASRVNAGDRVVLEMRPTVQSQAFRPQPMDIDVVYED 122

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------IFSRVISVGRLDINTEGLLLLTN 126
             L + +KP GLV   +     +T+ + L +      +  R   V RLD +T GL+++  
Sbjct: 123 AHLLVLNKPAGLVVHPAPGHWSATLLNGLLARDANALLLPRAGIVHRLDKDTSGLMVVAR 182

Query: 127 DGGL--ARVLELPSTQWLRVYRVRFHGQ------------VDQDKLNLLKKGIV----IQ 168
           D     A V ++   Q  R Y    HG             + +D  N L+  +V      
Sbjct: 183 DRATMDALVAQIARRQVQRQYLALAHGAWSGPRSRSVQAPIGRDPRNRLRMAVVDLARHA 242

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           G C     + LD       W+   L  G+  +I+
Sbjct: 243 GKCARTDVLCLDATP-QGCWLQCRLHTGRTHQIR 275


>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 = 37.7 bits (86), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 16/30 (53%), Positives = 24/30 (80%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNG 44
          R++K+I+ AG+ SRRE E+ I + RVK+NG
Sbjct: 4  RINKLISDAGLGSRREAEKYITEGRVKING 33


>gi|237746066|ref|ZP_04576546.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s)
           [Oxalobacter formigenes HOxBLS]
 gi|229377417|gb|EEO27508.1| diguanylate cyclase/phosphodiesterase with PAS/PAC sensor(s)
           [Oxalobacter formigenes HOxBLS]
          Length = 1049

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 37/144 (25%), Positives = 62/144 (43%), Gaps = 14/144 (9%)

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST-----REVSKKILR 242
           W+   L E   +  +K  E F W+ + ++ +      +G +   S       E S+++L 
Sbjct: 415 WMQDFLHEPAMKHWQKHIEHFKWRSSAILPLHRNGNVIGVMFFYSNVLNAFTESSQRLLL 474

Query: 243 EQLG------PHLLEEAQVNLDAPIY--SSETLVRDRPNI-ISEVPDDFTRMKKNSSQKN 293
           E +        H  +E Q+ L A I+  SSE ++   PN  I  V   FT +   S ++ 
Sbjct: 475 ELVEDIDFALEHFEKEEQLQLSAQIFAQSSEGIMLLDPNCHIVMVNSAFTHITGYSEEET 534

Query: 294 GLSKQKKLATPVHRRNLASNVWMA 317
                K LA+  H RN  + +W A
Sbjct: 535 LGRNPKMLASGQHDRNFYATMWEA 558


>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 = 37.4 bits (85), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 43/164 (26%), Positives = 70/164 (42%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K +A A   SR E +  I    V V+G+++E       +      +   L  AE 
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATAAQVTLAENAVLAPAEP 63

Query: 73  TRLWLYHKPIGLVT----THSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+        + P  RS +  +    L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGICVDAALALATPATRSALDQSDLRVLKRHFLRLQAPLPLEDAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + DG + R L   ++   + + V   G++    +  L  G+V Q
Sbjct: 123 SQDGRVLRRLSADASAIEQEFLVEVQGELRPYGMARLAHGLVYQ 166


>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 = 37.4 bits (85), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 91/229 (39%), Gaps = 40/229 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------------HIEV 62
           R+ KV+      SR +++ +I Q  V VNG  +E+A   +   +             IE 
Sbjct: 22  RLDKVLVEESELSRTQIQSLIKQGLVTVNG-QVEKANYKLSGQELIEMQVPEEEVLEIEA 80

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--------- 112
             +PL    E   L + +K  G+V   S    R T+ + L   F   ++ G         
Sbjct: 81  QAIPLDIIYEDDDLLVINKEAGMVVHPSKGHPRDTLVNALVYHFGNHLAAGSDSYRPGLV 140

Query: 113 -RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----------QDKL 158
            R+D +T GLL++  +    R L  +L      R+Y     GQ++           +D  
Sbjct: 141 HRIDKDTSGLLVVAKNNESHRYLSQQLMDHTLGRIYYCLVEGQMEVKQGSIEIPLARDPK 200

Query: 159 NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           N LK     QG   + D +V       S + +   L+ G+  +I+  FE
Sbjct: 201 NRLKYHADAQGKPAWTDFEVL--ESYPSASLIQAELKTGRTHQIRAHFE 247


>gi|290891290|ref|ZP_06554352.1| hypothetical protein AWRIB429_1742 [Oenococcus oeni AWRIB429]
 gi|290479254|gb|EFD87916.1| hypothetical protein AWRIB429_1742 [Oenococcus oeni AWRIB429]
          Length = 336

 Score = 37.4 bits (85), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 50/113 (44%), Gaps = 7/113 (6%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT------THSDPD 92
           +VK N +L+E     +  TDH   +G+P   A    + L H+  G+V+      T     
Sbjct: 24  QVKANEVLIETKYAGICGTDHALYNGLPGSAAAVPPIVLGHENSGVVSEVGEKVTSVKVG 83

Query: 93  GRSTVFDNLPSIFSRVISVGRLDI-NTEGLLLLTNDGGLARVLELPSTQWLRV 144
            R TV  N+          GR ++ +    + +T +GGL +    PSTQ  +V
Sbjct: 84  DRVTVDPNIYCGHCFYCRTGRPELCDNLSAVGVTRNGGLEQYFTAPSTQVYKV 136


>gi|116491674|ref|YP_811218.1| threonine dehydrogenase or related Zn-dependent dehydrogenase
           [Oenococcus oeni PSU-1]
 gi|116092399|gb|ABJ57553.1| Threonine dehydrogenase-like Zn-dependent dehydrogenase [Oenococcus
           oeni PSU-1]
          Length = 336

 Score = 37.4 bits (85), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 50/113 (44%), Gaps = 7/113 (6%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT------THSDPD 92
           +VK N +L+E     +  TDH   +G+P   A    + L H+  G+V+      T     
Sbjct: 24  QVKANEVLIETKYAGICGTDHALYNGLPGSAAAVPPIVLGHENSGVVSEVGEKVTSVKVG 83

Query: 93  GRSTVFDNLPSIFSRVISVGRLDI-NTEGLLLLTNDGGLARVLELPSTQWLRV 144
            R TV  N+          GR ++ +    + +T +GGL +    PSTQ  +V
Sbjct: 84  DRVTVDPNIYCGHCFYCRTGRPELCDNLSAVGVTRNGGLEQYFTAPSTQVYKV 136


>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 = 37.4 bits (85), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 24/109 (22%), Positives = 50/109 (45%), Gaps = 14/109 (12%)

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------------SNAW 188
           + Y V+  G  ++  L  L+KG+ ++       +V L ++                  +W
Sbjct: 10  KTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWERNPPIRERKNIPTSW 69

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + + + EG+NR+++++     +   RL+R+S G   +  L  GS R +S
Sbjct: 70  LEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLLS 118


>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 = 37.0 bits (84), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 43/165 (26%), Positives = 72/165 (43%), Gaps = 11/165 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
           P R+ K +A     SR E ++ I    V V+G+++E     +      +  D V L +A+
Sbjct: 4   PIRLDKHVAAVFGCSRGEAQQYIEGGWVSVDGVVVEEPQAPITGQQVSLAADAV-LGQAK 62

Query: 72  RTRLWLYHKPIGL----VTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLL 123
              L L +KP G+        + P  RS++       L   F R+ +   LD    GLL+
Sbjct: 63  PATL-LLNKPAGMSCEAAVALATPQSRSSLDQTEIRVLKRHFLRLSAPMPLDDEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           L+ DG + R L   +    + Y V   G++    +  L  G++ Q
Sbjct: 122 LSQDGRILRRLTADAATIEQEYLVEVRGELRPYGMARLASGLLYQ 166


>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 = 37.0 bits (84), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 41/164 (25%), Positives = 68/164 (41%), Gaps = 9/164 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K +A A   SR E ++ I    V V+G+++E       +      +   L  AE 
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAAQVTLAENAVLAPAEP 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS---TVFDN-----LPSIFSRVISVGRLDINTEGLLLL 124
             L L HKP G+    +         +  D      L   F R+ +   L+    GLL+L
Sbjct: 64  ATL-LLHKPAGICVDAALALATPATRSALDQADVRVLKRHFLRLHAPLPLEDAASGLLIL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + DG + R L   ++   + + V   G++    +  L  G+V Q
Sbjct: 123 SQDGRVLRRLSADASAIEQEFLVEVRGELRPYGMARLAHGLVYQ 166


>gi|291545734|emb|CBL18842.1| 16S rRNA uridine-516 pseudouridylate synthase and related
          pseudouridylate synthases [Ruminococcus sp. SR1/5]
          Length = 68

 Score = 37.0 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R++K ++  G+ SRRE +R+    RV VNG L+    + ++    I +DG P++  ++
Sbjct: 6  RINKYLSDIGVCSRREADRLTEAGRVTVNGELVS-TGMKILPDAEICIDGKPVKNRKK 62


>gi|224418218|ref|ZP_03656224.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           canadensis MIT 98-5491]
          Length = 340

 Score = 37.0 bits (84), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 39/167 (23%), Positives = 78/167 (46%), Gaps = 32/167 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           VQ+  T  R+ K + +    SR ++ ++I ++++ +NG+ +++   ++   D I +  +P
Sbjct: 15  VQQEETKMRLDKFLTQKLGLSRNQISKIIQEKQITLNGVFIQKNGTSLNFNDQI-ILTLP 73

Query: 67  LRKAERTR--------------LWLYHKPIGLVT--THSDPDGRSTVFD----------N 100
             K E+++              L + +KPI L+   TH D D + T+ D          N
Sbjct: 74  -NKQEKSKPNHLNIPILYEDEDLLILNKPINLIVHQTHQD-DSQYTLQDWLQENNFSLSN 131

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVY 145
           L   + + I + RLD  T G +++  +     +L  +L S +  R Y
Sbjct: 132 LGDSYRQGI-IHRLDKTTSGAIVIAKNNYAHEILSQQLKSKEMGRYY 177


>gi|294905868|ref|XP_002777696.1| Ribosomal large subunit pseudouridine synthase E, putative
           [Perkinsus marinus ATCC 50983]
 gi|239885587|gb|EER09512.1| Ribosomal large subunit pseudouridine synthase E, putative
           [Perkinsus marinus ATCC 50983]
          Length = 85

 Score = 37.0 bits (84), Expect = 5.0,   Method: Composition-based stats.
 Identities = 18/58 (31%), Positives = 31/58 (53%)

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           GRLD +  GLL+ T DG +A+ +    +     Y V        D++++L +G++I G
Sbjct: 11  GRLDSDCSGLLVYTQDGRIAKAISDRYSSIPMEYEVALKAPCTDDQMSMLSQGMLIDG 68


>gi|46191229|ref|ZP_00206720.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and
          related pseudouridylate synthases [Bifidobacterium
          longum DJO10A]
          Length = 329

 Score = 36.6 bits (83), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 1/59 (1%)

Query: 7  VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDG 64
           Q++    R+ K++A+AG  SRR+ E MI + RV+V+G L+      V      + VDG
Sbjct: 11 AQDDSNSIRLQKLLAQAGFGSRRKCEDMITEGRVEVDGELVTELGTRVDPHKQQVRVDG 69


>gi|268610335|ref|ZP_06144062.1| pseudouridine synthase rRNA-specific [Ruminococcus flavefaciens
          FD-1]
          Length = 108

 Score = 36.6 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 24/84 (28%), Positives = 44/84 (52%), Gaps = 2/84 (2%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
          R+ K I+     +R +++ + A+  V VNG  ++R+   +    D + V G  +  +ER 
Sbjct: 5  RLDKFISERTEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAI-SSERF 63

Query: 74 RLWLYHKPIGLVTTHSDPDGRSTV 97
          R  L +KP G V++  D DG + +
Sbjct: 64 RYILLNKPKGYVSSTDDKDGETVI 87


>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 = 36.6 bits (83), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 44/163 (26%), Positives = 74/163 (45%), Gaps = 27/163 (16%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G ++  S+   R T+ + + +    V   GRLD ++EGLLLLT+DGGL   +  P 
Sbjct: 7   NKPFGTMSQFSEHPSRPTLAEWIAT--PGVYPAGRLDADSEGLLLLTDDGGLQARIADPR 64

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------------- 184
            +  + Y  +  G  D+  L  L+     QGI  GD        +               
Sbjct: 65  HKLAKTYFAQVEGIPDEAALARLR-----QGIDLGDFHTLPAKVRAVEEPSWLWPRNPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                   +W+ + +REGKNR+++++     +   RL+R + G
Sbjct: 120 RFRAAIPTSWLELQIREGKNRQVRRMTAAVGFPTLRLLRATIG 162


>gi|25453489|gb|AAL25966.2| probable pseudouridylate synthase [Azotobacter vinelandii]
          Length = 152

 Score = 36.2 bits (82), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 31/117 (26%), Positives = 55/117 (47%), Gaps = 3/117 (2%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG  +R +  P  +  +VY V     + ++ +    +G+             L+   
Sbjct: 33  LTNDGHWSRRITHPRYKLAKVYYVETAEPIGEEYIETFARGLYFAFEDLVTQPAHLELLG 92

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
             +A +T  L EG+  ++K++F +F   V RL R S GP +L + L  G  R ++ +
Sbjct: 93  SHSARLT--LFEGRYHQVKRMFGYFRNPVLRLHRESMGPLRLESELPPGHYRPLTSE 147


>gi|11967875|emb|CAC19446.1| putative pseudouridine synthase [Streptococcus mitis]
          Length = 46

 Score = 36.2 bits (82), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 19/44 (43%), Positives = 27/44 (61%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
          R++K IA AG+ASRR+ E +I Q  V VN  ++   A  + S D
Sbjct: 2  RINKYIAHAGVASRRKAEELIKQGLVTVNSQVVRELATTIKSGD 45


>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 = 36.2 bits (82), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 46/166 (27%), Positives = 78/166 (46%), Gaps = 19/166 (11%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DGGL AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGGLQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSN------- 186
             + ++ Y  +  G      L  L +G+     +   C  +     DT    N       
Sbjct: 64  RHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIRYRA 123

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFAL 169


>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 = 36.2 bits (82), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 77/177 (43%), Gaps = 27/177 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV-- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +    V V    H EV  
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVRE 66

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFS 106
                   + +PL    E   + + +KP G+V   S      T+        D+L  I  
Sbjct: 67  PEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGING 126

Query: 107 RVIS--VGRLDINTEGLLLLT-NDGG---LARVLELPSTQWLRVYRVRFHGQVDQDK 157
           ++    V R+D +T GLL++  ND     LA+ L+  ++   R Y    HG +   K
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSD--REYIALVHGDIVHQK 181


>gi|255522642|ref|ZP_05389879.1| hypothetical protein LmonocFSL_15771 [Listeria monocytogenes FSL
           J1-175]
          Length = 279

 Score = 36.2 bits (82), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 76/173 (43%), Gaps = 27/173 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV-- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +    V V    H EV  
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVRE 66

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFS 106
                   + +PL    E   + + +KP G+V   S      T+        D+L  I  
Sbjct: 67  PEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGING 126

Query: 107 RVIS--VGRLDINTEGLLLLT-NDGG---LARVLELPSTQWLRVYRVRFHGQV 153
           ++    V R+D +T GLL++  ND     LA+ L+  ++   R Y    HG +
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSD--REYIALVHGDI 177


>gi|255022986|ref|ZP_05294972.1| hypothetical protein LmonocyFSL_05005 [Listeria monocytogenes FSL
           J1-208]
          Length = 302

 Score = 36.2 bits (82), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 76/173 (43%), Gaps = 27/173 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV-- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +    V V    H EV  
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVRE 66

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFS 106
                   + +PL    E   + + +KP G+V   S      T+        D+L  I  
Sbjct: 67  PEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGING 126

Query: 107 RVIS--VGRLDINTEGLLLLT-NDGG---LARVLELPSTQWLRVYRVRFHGQV 153
           ++    V R+D +T GLL++  ND     LA+ L+  ++   R Y    HG +
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSD--REYIALVHGDI 177


>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 = 36.2 bits (82), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 43/165 (26%), Positives = 72/165 (43%), Gaps = 11/165 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAE 71
           P R+ K +A A   SR E +  I    V V+G+++E   A+  ++   +  + V L  AE
Sbjct: 4   PIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATVAQVTLAANAV-LAPAE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---TVFDN-----LPSIFSRVISVGRLDINTEGLLL 123
              L L HKP G+    +         +  D      L   F R+ +   L+    GLL+
Sbjct: 63  PATL-LLHKPAGICADAALALATPATRSALDQSDLRVLKRHFLRLQAPLPLEDAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           L+ DG + R L   ++   + + V   G++    +  L  G+V Q
Sbjct: 122 LSQDGRVLRRLSADASAIEQEFLVEVQGELRPYGMARLAHGLVYQ 166


>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 = 36.2 bits (82), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 77/177 (43%), Gaps = 27/177 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV-- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +    V V    H EV  
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVRE 66

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFS 106
                   + +PL    E   + + +KP G+V   S      T+        D+L  I  
Sbjct: 67  PEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGING 126

Query: 107 RVIS--VGRLDINTEGLLLLT-NDGG---LARVLELPSTQWLRVYRVRFHGQVDQDK 157
           ++    V R+D +T GLL++  ND     LA+ L+  ++   R Y    HG +   K
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSD--REYIALVHGDIVHQK 181


>gi|254994200|ref|ZP_05276390.1| hypothetical protein LmonocytoFSL_15395 [Listeria monocytogenes FSL
           J2-064]
          Length = 296

 Score = 36.2 bits (82), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 49/177 (27%), Positives = 77/177 (43%), Gaps = 27/177 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV-- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +    V V    H EV  
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAKPNYKVQVGDEIHYEVRE 66

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFS 106
                   + +PL    E   + + +KP G+V   S      T+        D+L  I  
Sbjct: 67  PEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGING 126

Query: 107 RVIS--VGRLDINTEGLLLLT-NDGG---LARVLELPSTQWLRVYRVRFHGQVDQDK 157
           ++    V R+D +T GLL++  ND     LA+ L+  ++   R Y    HG +   K
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSD--REYIALVHGDIVHQK 181


>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 = 36.2 bits (82), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 46/84 (54%), Gaps = 3/84 (3%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERT 73
          R+ KVI +    SR+E++R+  Q +V V+  +  R   NV S+ H I V G  L   E  
Sbjct: 2  RLDKVIEQQLNTSRKEMKRLFQQGKVFVDHRIERRPERNVDSSLHQIMVAGRQLETQE-- 59

Query: 74 RLWLYHKPIGLVTTHSDPDGRSTV 97
          R ++ +KP G+VT + D   ++ +
Sbjct: 60 RYYIVNKPKGVVTANLDQQHQTVI 83


>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 = 36.2 bits (82), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 76/173 (43%), Gaps = 27/173 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV-- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +    V V    H EV  
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKSGDITVNGELAKPNYKVQVGDEIHYEVRE 66

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFS 106
                   + +PL    E   + + +KP G+V   S      T+        D+L  I  
Sbjct: 67  PEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGING 126

Query: 107 RVIS--VGRLDINTEGLLLLT-NDGG---LARVLELPSTQWLRVYRVRFHGQV 153
           ++    V R+D +T GLL++  ND     LA+ L+  ++   R Y    HG +
Sbjct: 127 KIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSD--REYIALVHGDI 177


>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 = 36.2 bits (82), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 32/126 (25%), Positives = 55/126 (43%), Gaps = 7/126 (5%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            GRLD N+ GLL+ T    L+    L   ++   + Y ++ +  + Q+ + LLK+   + 
Sbjct: 435 CGRLDANSSGLLIFT-QNTLSNNYLLYRYKYNIEKEYVIKTYNSITQENMKLLKEHFYVD 493

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
               G +      Q   N  +   + +G ++ I+K+    N K+  L RI  G   L  L
Sbjct: 494 ----GKLIYKCHIQYVDNFTLIFKIYQGFHKIIRKMCMLSNIKIKSLHRIRIGNIHLNDL 549

Query: 229 LAGSTR 234
             G  R
Sbjct: 550 PIGKWR 555


>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 = 36.2 bits (82), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 95/226 (42%), Gaps = 39/226 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A+     R ++E++I Q  V++NG + ++A   + S D +EV  +P  K  + 
Sbjct: 12  ERLDKALAKKLQKPRNQIEQLIKQGYVRINGKIEKKAGSKLKSGDLVEVT-IPEPKVSQP 70

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVIS------- 110
           +              + + +KP GLV   +      T+ D L +  I    +S       
Sbjct: 71  KDVHFDVERIYEDEDILVLNKPAGLVVHPAPSVKEPTLVDWLKANDISLSTLSGEERHGI 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL---------- 158
           V RLD  T GL+++  +    + L  +L      R Y       + +D +          
Sbjct: 131 VHRLDKETSGLIVIAKNNETHQALSKQLQDKSMGRYYLAIVEPPLKEDLIIEKPIARNPK 190

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG--LREGKNREIK 202
           N LK G+V  G       V L T K +N +  +G  L  G+  +I+
Sbjct: 191 NRLKMGVVEGGRYAKSAFVKLTTSK-NNKYELIGAKLFTGRTHQIR 235


>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 = 35.8 bits (81), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 51/188 (27%), Positives = 86/188 (45%), Gaps = 23/188 (12%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL-ARVLELP 137
           +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DGGL AR+ E P
Sbjct: 7   NKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGGLQARIAE-P 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA------ 187
             + ++ Y  +  G      L  L +G+     +   C  +     DT    N       
Sbjct: 64  RHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIRYRA 123

Query: 188 -----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP---FQLGTLLAGSTREVSKK 239
                W+ + + EGKNR+++++     +   RL+R+  G    F LG +  G T  +  +
Sbjct: 124 AIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALG-IAPGETIALPPR 182

Query: 240 ILREQLGP 247
              +   P
Sbjct: 183 APWDGFAP 190


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


Results from round 2




>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 =  475 bits (1223), Expect = e-132,   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|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 =  374 bits (962), Expect = e-102,   Method: Composition-based stats.
 Identities = 246/362 (67%), Positives = 292/362 (80%), Gaps = 15/362 (4%)

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   +  +  DD ++ K   S+ +G +K+K 
Sbjct: 248 LREQLGANLLKEARVNLEGLVYSSETPIRDHSKMKVKS-DDISKTKNKKSKVHGFNKKKH 306

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDS--------------GQREENHRRSPSFPSKRS 346
           +  P+ RRN +SNVWMA+GIHSS   +                +R+ +H+R+     K  
Sbjct: 307 VDFPIQRRNRSSNVWMAQGIHSSLPYEKQGEKDYQSMHDTGFKKRKYSHKRNKKLHKKSP 366

Query: 347 LR 348
           L 
Sbjct: 367 LD 368


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

 Score =  340 bits (873), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 171/382 (44%), Positives = 221/382 (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 REQLGPHLLEEAQVNLDAPIYS--SETLVRDRPNIISEV--------------------- 278
           R+QLG  L+ +A  + DAPI    S + V ++ NI                         
Sbjct: 269 RDQLGERLIMQANADFDAPILKPFSNSAVSEKQNITKPPVIKDNWIVSSKENLSYGKKSR 328

Query: 279 ---PDDFTRMKKNSSQKNGL-SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
                     KK   +  G    +         R+  SNVWMA G     +      + +
Sbjct: 329 FLGHSQVRLSKKIDEKLRGKEQNKGGKEERAFLRSRCSNVWMAPGACPKIVRKKSYSDTD 388

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


>gi|319405144|emb|CBI78750.1| Pseudouridine synthase [Bartonella sp. AR 15-3]
          Length = 459

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 168/377 (44%), Positives = 215/377 (57%), 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 PHLLEEAQVNLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-------- 295
             L+ +A  N DAPI   +S+ T+V  + +  + V  D   +    S   G         
Sbjct: 241 ERLILQANANFDAPILKPFSNSTVVEKQNSTKAPVIKDSWIISSKESLLYGKKRKFSGHS 300

Query: 296 ----------------SKQKKLATPVHRRNLASNVWMAKGIHSSFLSD--SGQREENHRR 337
                             +         R+  SNVWMA G          S     +H R
Sbjct: 301 QAQLSKKIDEKLRGKDQNKGGKEERAFLRSRCSNVWMAPGACPQITRKKSSSNANNHHDR 360

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


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

 Score =  339 bits (871), Expect = 3e-91,   Method: Composition-based stats.
 Identities = 170/381 (44%), Positives = 221/381 (58%), 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 EQLGPHLLEEAQVNLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS--- 296
           +QLG  L+ +A  + DAPI   +S+  +V  +    S V +D   +    +   G     
Sbjct: 271 DQLGERLIVQANADFDAPILKPFSNSAVVAKQNITKSSVIEDSWIVSSKENLLYGRKSRF 330

Query: 297 ---------------------KQKKLATPVHRRNLASNVWMAKGIHSSFLSD--SGQREE 333
                                 +         R+  SNVWMA G          S   + 
Sbjct: 331 LGHSQVRLSKKIDTKLRAKDHNKGGKEERAFLRSRCSNVWMAPGACPQIARKKSSSDADN 390

Query: 334 NHRRSPSFPSKRSLRRTSAKK 354
           ++ R  ++  KRS  R   K+
Sbjct: 391 HYDRKSNWVGKRSTDRGKEKR 411


>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 =  339 bits (869), Expect = 5e-91,   Method: Composition-based stats.
 Identities = 174/377 (46%), Positives = 224/377 (59%), 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 PHLLEEAQVNLDAPIYSS--------------ETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             L+ +A  N DAPI  S              +  + +   I S + D   R +   S++
Sbjct: 241 ERLIMQANANFDAPILKSFSNSVVVAEKQNHKDLAITNDGWIFSSIGDVQRRRRGGFSER 300

Query: 293 NG-----------LSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSG--QREENHR 336
           +            + ++K       R   R+  SNVWMA G              +  H 
Sbjct: 301 SRARLSTKPGEKFMRQEKSEGGKAERFLPRSRRSNVWMAPGARPQSTRKKSFYSEDTPHD 360

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


>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 =  337 bits (864), Expect = 2e-90,   Method: Composition-based stats.
 Identities = 171/380 (45%), Positives = 222/380 (58%), Gaps = 35/380 (9%)

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 PHLLEEAQVNLDAPI---------------------------YSSETLVRDRPNIISEVP 279
             L+ +A  + DAPI                           +SSE ++R R N  S   
Sbjct: 241 ERLIMQANADFDAPILKPFSNSPVIAEKQSQKDVSVANDGWVFSSERVIRRRSNDGSVEH 300

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREE--N 334
           D   R +  +     ++K K       R   R+  +NVWMA G             E  +
Sbjct: 301 D---RARLRAKSHENMNKGKSEEGKAERFLPRSRRANVWMAPGARPQSARRKPSYNEEKS 357

Query: 335 HRRSPSFPSKRSLRRTSAKK 354
           H        K+S  R   K+
Sbjct: 358 HDHKGDTADKKSFYRGKEKR 377


>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 =  336 bits (863), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 182/372 (48%), Positives = 238/372 (63%), 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 EEAQVNLDAPIYSS-----------------------ETLVRDRPNIISEVPDDFTRMKK 287
            +++ N DAPIY+                        E     R   ++ +       + 
Sbjct: 284 ADSKANFDAPIYNDQPAAAEPEAEPADHGKAEWGSKREKAEDKRERALARLDTRRDDGRP 343

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN-----HRRSPSFP 342
           +   ++    +++ A P  RRN +SNVWMA G   +        E++      RR+P+  
Sbjct: 344 SERGRSRGKPEERPARPPVRRNRSSNVWMAPGARPTVEKKPKAAEDDLSPKGARRAPAEG 403

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


>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 =  336 bits (863), Expect = 3e-90,   Method: Composition-based stats.
 Identities = 182/372 (48%), Positives = 238/372 (63%), 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 EEAQVNLDAPIYSS-----------------------ETLVRDRPNIISEVPDDFTRMKK 287
            +++ N DAPIY+                        E     R   ++ +       + 
Sbjct: 284 ADSKANFDAPIYNDQPAAAEPEAEPADHDKAEWGSKREKAEDKRERALARLDTRRDDGRP 343

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN-----HRRSPSFP 342
           +   ++    +++ A P  RRN +SNVWMA G   +        E++      RR+P+  
Sbjct: 344 SERGRSRGKPEERPARPPVRRNRSSNVWMAPGARPTVEKKPKAAEDDLSPKGARRAPAEG 403

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


>gi|319898380|ref|YP_004158473.1| Pseudouridine synthase [Bartonella clarridgeiae 73]
 gi|319402344|emb|CBI75883.1| Pseudouridine synthase [Bartonella clarridgeiae 73]
          Length = 496

 Score =  336 bits (862), Expect = 4e-90,   Method: Composition-based stats.
 Identities = 163/377 (43%), Positives = 217/377 (57%), Gaps = 29/377 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R++K +ARAG+ASRR+ E MI   R+ VNG ++     NV  +D I VDG P
Sbjct: 34  MSEKSESERIAKRLARAGVASRRDAEMMIFAGRIVVNGAIIATPVFNVTRSDVITVDGKP 93

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   ERTRLWLYHKP+G VTT+ DP GR TVFDNLP    RV+SVGRLD+NTEGLLLLTN
Sbjct: 94  LPPIERTRLWLYHKPVGFVTTNRDPQGRPTVFDNLPKDMPRVLSVGRLDMNTEGLLLLTN 153

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLARVLELP T W+R YRVR HG+V Q  L  LK GI + GI YG ++ +++ ++GSN
Sbjct: 154 DGGLARVLELPLTGWVRKYRVRAHGKVKQSALQDLKNGIAVNGIFYGSIEASIEREQGSN 213

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W++V LREGKNREIK V       VNRLIR+SYGPFQL  L  G+ RE+  ++LR+QLG
Sbjct: 214 VWLSVALREGKNREIKNVLGALGLSVNRLIRVSYGPFQLSDLKEGAVRELKGRMLRDQLG 273

Query: 247 PHLLEEAQVNLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-------- 295
             L+ +A  + +API   +S+  ++  + +    V  +   + +  S   G         
Sbjct: 274 ERLILQANADFNAPIIKPFSNSAVIEKQNSTKPPVMKNSWIVSRKESILRGKKGRFPGHS 333

Query: 296 ----------------SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ--REENHRR 337
                             +      V  R+  SNVWMA G              + ++ R
Sbjct: 334 QVRLSKKFDEKLRVKDQNKSGKEERVFLRSRCSNVWMAPGACPQIARKKPSSVADNHYGR 393

Query: 338 SPSFPSKRSLRRTSAKK 354
             ++  KR   R   K+
Sbjct: 394 KINWVGKRFTDRGKEKR 410


>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 =  335 bits (859), Expect = 7e-90,   Method: Composition-based stats.
 Identities = 178/378 (47%), Positives = 226/378 (59%), 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 PHLLEEAQVNLDAPI---YSSETLVRDRPN----------IISEVPDDFTRMKKNSSQKN 293
             L+ +A  + DAPI   +S+  +V ++ +           IS    D  R ++ SS + 
Sbjct: 241 ERLIMQANADFDAPILKPFSNTAVVAEKRSHKDLTVANDGWISSHGGDLRRRQRKSSAER 300

Query: 294 GL------------SKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREE--NHR 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|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 =  334 bits (858), Expect = 9e-90,   Method: Composition-based stats.
 Identities = 170/379 (44%), Positives = 223/379 (58%), Gaps = 35/379 (9%)

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 PHLLEEAQVNLDAPI---------------------------YSSETLVRDRPNIISEVP 279
             L+ +A  + DAPI                           +SSE  +R RP   S   
Sbjct: 241 ERLIMQANADFDAPILKPFSNSAVVAEKQSQKDLSVANDGWVFSSERAIRRRPRDGSV-- 298

Query: 280 DDFTRMKKNSSQKNGLSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQR--EEN 334
            + +R + ++     + K+K       R   R+  +NVWMA G              E++
Sbjct: 299 -EHSRARLSTKSHENVKKEKSEEGKAERFLPRSRRANVWMAPGARPQSTRRKPSYSEEKS 357

Query: 335 HRRSPSFPSKRSLRRTSAK 353
           H        ++S  R   K
Sbjct: 358 HDHKSDLDGRKSFHRGKEK 376


>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 =  334 bits (857), Expect = 1e-89,   Method: Composition-based stats.
 Identities = 173/378 (45%), Positives = 229/378 (60%), 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 REQLGPHLLEEAQVNLDAPI----YSSETLVRDRP-NIISEVPDDFTRMKKNSSQKNGLS 296
           R+QLG  L+ +A  N DAPI     +S  +V+ +    +S+  D++     +  Q+N   
Sbjct: 273 RDQLGERLIMQANANFDAPILKPFSNSAVVVKQQSNKKLSQANDEWISSSGHHKQRNKKD 332

Query: 297 ----------KQKKLATPVHRRN--------LASNVWMAKGIHSSFLSDSGQR--EENHR 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|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 =  333 bits (855), Expect = 2e-89,   Method: Composition-based stats.
 Identities = 180/369 (48%), Positives = 233/369 (63%), 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 EEAQVNLDAPIYSSETLVRDRPNIISEVPD-----DFTRMKKNSSQKNGLSK-------- 297
            E++ N DAP+Y+ +    +R       P+        R K    ++  L++        
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


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

 Score =  332 bits (851), Expect = 6e-89,   Method: Composition-based stats.
 Identities = 170/375 (45%), Positives = 222/375 (59%), 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 REQLGPHLLEEAQVNLDAPI-----YSSETLVRDRPNIISEVPDDF-------TRMKKNS 289
           R+QLG  L+ +A  + D+PI      S  ++ +     +    DD        TR +K S
Sbjct: 269 RDQLGERLIAQANADFDSPILKPFSNSVVSVKKQNSKKLFVAGDDEVVSRVNGTRHEKQS 328

Query: 290 SQKNGLSKQKKLATPVHR---------RNLASNVWMAKGIHSSFLSDSGQREEN--HRRS 338
               G   +    +             R+  SNVWMA G             E   H RS
Sbjct: 329 GFCEGRRARLNTKSDEQSMGKTKNLSLRSRHSNVWMAPGARPQVERKKFCYNEGSYHNRS 388

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


>gi|150395641|ref|YP_001326108.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150027156|gb|ABR59273.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 576

 Score =  329 bits (844), Expect = 5e-88,   Method: Composition-based stats.
 Identities = 182/370 (49%), Positives = 236/370 (63%), Gaps = 29/370 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            PQR+SK+++RAG+ASRR+VERMI + RV +NG++L+   VN    D IEVDG P+R  E
Sbjct: 46  QPQRISKILSRAGVASRRDVERMIMEGRVSLNGLVLDTPVVNATLADRIEVDGHPIRGIE 105

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWLYHKP GLVTT++DP+GR TVF+NLP    RV+S+GRLDINTEGLLLLTNDGGLA
Sbjct: 106 RTRLWLYHKPGGLVTTNADPEGRPTVFENLPEDLPRVLSIGRLDINTEGLLLLTNDGGLA 165

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           RVLELPST WLR YRVR HG++DQ  L+ LK+GI ++G+ YG ++ TLD  +GSN W+T+
Sbjct: 166 RVLELPSTGWLRRYRVRAHGEIDQAALDRLKEGIAVEGVLYGAIEATLDRVQGSNVWITM 225

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNREIK V       VNRLIRISYGPFQLG L  G  +E+  + LREQLGP L+ 
Sbjct: 226 GLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGELPIGQVQEIRGRTLREQLGPRLIA 285

Query: 252 EAQVNLDAPIYSS------------------------ETLVRDRPNIISEVPDDFTRMKK 287
           +A+ N DAPIY+                         E     R   ++ +       + 
Sbjct: 286 DAKANFDAPIYNDQSTAAEPEAEPVADHGKAEWGSKREKAGDKRERALARLDTRRDDGRP 345

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE-----NHRRSPSFP 342
           N   ++    +++ A P  RRN +SNVWMA G   +        E+     + RR+P+  
Sbjct: 346 NDRGRSRGKAEERPARPPLRRNRSSNVWMAPGARPTVEKKPKAAEDELSPKSTRRAPADV 405

Query: 343 SKRSLRRTSA 352
            +R   +  A
Sbjct: 406 KRRDRAKDPA 415


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

 Score =  324 bits (831), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 223/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  324 bits (830), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 169/350 (48%), Positives = 221/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 221/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 435


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

 Score =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 167/350 (47%), Positives = 222/350 (63%), Gaps = 12/350 (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 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  323 bits (828), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 435


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

 Score =  322 bits (827), Expect = 3e-86,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRTPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAKFS 448


>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 =  322 bits (827), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGVRPKGEKETAKPARVEHQQPHRSAKFS 448


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

 Score =  322 bits (826), Expect = 5e-86,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 339 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 398

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 399 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 448


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

 Score =  322 bits (826), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 96/261 (36%), Positives = 138/261 (52%), Gaps = 1/261 (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 AQVNLDAPIYSSETLVRDRPN 273
            +  + AP+ SS T     P 
Sbjct: 243 REQRMAAPVKSSTTPQSQTPG 263


>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 =  322 bits (825), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRSNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  322 bits (825), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 435


>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 =  321 bits (823), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKAEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  320 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 223/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAKFS 418


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

 Score =  320 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 223/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  320 bits (822), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 165/343 (48%), Positives = 219/343 (63%), Gaps = 12/343 (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 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           +++K      RR   +NVWMA G       ++ +      + P
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQP 411


>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 =  320 bits (822), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 169/350 (48%), Positives = 220/350 (62%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 435


>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 =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 326 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 385

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 386 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 435


>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 =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>gi|254702620|ref|ZP_05164448.1| hypothetical protein Bsuib36_01462 [Brucella suis bv. 3 str. 686]
          Length = 581

 Score =  320 bits (820), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 353 REEKTEKVEPRRRSNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 402


>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 =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRTPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  319 bits (819), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  319 bits (819), Expect = 4e-85,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G+      ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGVRPKGEKETAKPARVEHQQPHRSAKFS 418


>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 =  319 bits (818), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  319 bits (817), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 309 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 368

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 369 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 418


>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 =  319 bits (817), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 402


>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 =  318 bits (816), Expect = 6e-85,   Method: Composition-based stats.
 Identities = 165/343 (48%), Positives = 219/343 (63%), Gaps = 12/343 (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 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           +++K      RR   +NVWMA G       ++ +      + P
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQP 395


>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 =  318 bits (816), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 402


>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 =  318 bits (815), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 171/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 402


>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 =  316 bits (811), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 170/350 (48%), Positives = 222/350 (63%), Gaps = 12/350 (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 LLEEAQVNLDAPIYS--SETLVRDR----------PNIISEVPDDFTRMKKNSSQKNGLS 296
           L+EE+  + DAP+ +  S   V+ R          P           R   +S+ +    
Sbjct: 293 LIEESGADFDAPVLNEFSNAAVQGRTRREMEEGELPQEGERRRAPREREWISSTGERRRG 352

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
           +++K      RR   +NVWMA G       ++ +      + P   +K S
Sbjct: 353 REEKTEKVEPRRRGNANVWMAPGARPKGEKEAAKPARVEHQQPHRSAKFS 402


>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 =  315 bits (807), Expect = 8e-84,   Method: Composition-based stats.
 Identities = 151/311 (48%), Positives = 191/311 (61%), Gaps = 8/311 (2%)

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 PHLLEE-------AQVNLDAPIYSSETLVRDRPNIISEVPDDFTR-MKKNSSQKNGLSKQ 298
               EE       A+    A   S  +    RP+    +P D  R   K + +  G    
Sbjct: 241 LDPREEDGRPPKAARPPRGAGAASGRSHPGARPSGSKPLPPDEARGGSKGAPRGRGAGAA 300

Query: 299 KKLATPVHRRN 309
            K A P  RR+
Sbjct: 301 PKSAGPARRRD 311


>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 =  315 bits (807), Expect = 9e-84,   Method: Composition-based stats.
 Identities = 167/355 (47%), Positives = 224/355 (63%), Gaps = 12/355 (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 QLGPHLLEEAQVNLDAPI----YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS--- 296
           QLG  L+EE+  + DAP+     ++    R R  +    P+     ++   ++  +S   
Sbjct: 292 QLGDKLIEESGADFDAPVLNEFSNAAVQGRTRREMEEGQPEQDGETRRAPREREWISSRP 351

Query: 297 -----KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                ++ K      RR   +NVWMA G        + +      + P   +K S
Sbjct: 352 ERRRGREDKTEKVEPRRRGNANVWMAPGARPKGEKAAAKPPRVEHQVPHRSAKFS 406


>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 =  314 bits (805), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 158/327 (48%), Positives = 200/327 (61%), Gaps = 10/327 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           F  +R++KV+ARAG+ SRRE E  IA  RV+VNG  L+  A+ V + D + VDG PL   
Sbjct: 13  FEGERIAKVMARAGLCSRREAETWIAAGRVEVNGKKLDTPAITVGAKDKVLVDGNPLPTR 72

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ERTRLWLYHKP GLVTT+ DP+GR TVFD LP    RV++VGRLDINTEGLLLLTNDGGL
Sbjct: 73  ERTRLWLYHKPRGLVTTNKDPEGRKTVFDRLPKDLPRVLTVGRLDINTEGLLLLTNDGGL 132

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           ARVLELP+T WLR YRVR  G+V Q  L+ L  G+ I G+ YG ++ +LD ++G N W+T
Sbjct: 133 ARVLELPATGWLRRYRVRAFGKVTQADLDTLADGVAIDGVLYGGIEASLDKEQGDNVWLT 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           VGLREGKNRE+K+V E     VNRLIR+S+GPFQL  +  G  RE+  ++LR+QLG  L 
Sbjct: 193 VGLREGKNREVKRVLEHLGLSVNRLIRLSFGPFQLQDIAEGEVREIRGRVLRDQLGDKLA 252

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           EEA  + DAPI + +    ++P     V       +                 P  R   
Sbjct: 253 EEAGADFDAPILN-QPKQDEQPKKKKSVGQKGGGSEARWMSSRDGEAAVNRKKPGTR--- 308

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRR 337
                  KG  S        R++   R
Sbjct: 309 ------DKGAKSYRDQQRPSRDQRPSR 329


>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 =  314 bits (804), Expect = 2e-83,   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|27262400|gb|AAN87481.1| Ribosomal large subunit pseudouridine synthase B [Heliobacillus
           mobilis]
          Length = 253

 Score =  312 bits (801), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 132/234 (56%), Gaps = 1/234 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           T +R+ KV+A  G+ASRRE E  I   RV+VNG ++    + V    D I+VDG PL   
Sbjct: 9   TAERLQKVLAAHGLASRREAEDWIRAGRVQVNGTVVTELGLRVEEGKDVIQVDGKPLTVR 68

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ER + +L +KP G VTT  DP+GR TV D L  + +R+  VGRLD +TEGLLLLTNDG L
Sbjct: 69  ERHQYFLLYKPRGFVTTRKDPEGRPTVIDLLKDVPARIYPVGRLDQDTEGLLLLTNDGEL 128

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y  R  G V    +    +G++++       +V +  ++G   W+ 
Sbjct: 129 AYRLTHPKYGVEKTYHARMRGNVPDPVIKAFAEGVMLEDGLTAPAKVKVLDREGGATWIE 188

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++ +   + V  L R+S+GP  +  L  G+ R +  + +R  
Sbjct: 189 LTIHEGRNRQVRRMGDAVGYPVVHLTRVSFGPLTISGLKPGAYRPLKPQEVRAL 242


>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 =  312 bits (800), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 153/306 (50%), Positives = 197/306 (64%), Gaps = 4/306 (1%)

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 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-KQKKLATPVH 306
               +A +   A   S+    +++              K+ +S K     + ++   P  
Sbjct: 286 ---GKAVLKPKAETKSAGEREKEQRVAAKARKQKLAEDKRAASAKKDKPYEARQAGKPDA 342

Query: 307 RRNLAS 312
            R  +S
Sbjct: 343 HRRRSS 348


>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 =  312 bits (800), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 153/350 (43%), Positives = 198/350 (56%), Gaps = 18/350 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             +    E   P+R++KV+ARAG+ASRR+ E MI + RV +NG  L   AV V   D I 
Sbjct: 28  PARPAPSETAEPERIAKVMARAGVASRRDAEAMILEGRVSLNGETLTTPAVTVGPGDRIV 87

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL   ERTRLW++HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGL
Sbjct: 88  VDGEPLPVRERTRLWIFHKPRGVVTTARDPEGRQTVFDILPEDLPRVVAIGRLDINTEGL 147

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGLA+V+  P T WLR YRVR +G VDQ  L+ L+ G+ I G+ YG ++ ++D 
Sbjct: 148 LLLTNDGGLAKVIAHPETGWLRRYRVRAYGDVDQAALDRLRGGVTIDGMEYGPVEASIDR 207

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G N W+T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  K+L
Sbjct: 208 QQGDNVWLTLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTKVL 267

Query: 242 REQLGPHLLEEAQVNLDAPIY---------------SSETLVRDRPNIISEVPDDFTRMK 286
           +EQLG  L E+A V+  +P+                +  T    R     E PD   R  
Sbjct: 268 KEQLGRSLAEQAGVDFTSPVREPIAPFGSPKPPAPAAGRTGAPGRDRPRGERPDRSARPD 327

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
           +      G    +    P   +        A G                R
Sbjct: 328 RGERLDRGERPARPGRDPARPQFARPP---APGARPERDRKPATGPALRR 374


>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 =  311 bits (798), Expect = 8e-83,   Method: Composition-based stats.
 Identities = 169/354 (47%), Positives = 228/354 (64%), Gaps = 11/354 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++   +  T +R++K +ARAGIASRRE E MIA  R+ VNG +LE  AVNV  TD I VD
Sbjct: 48  RDAEGQEDTGERIAKRLARAGIASRREAETMIAAGRIAVNGKVLESPAVNVKRTDIITVD 107

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G PL++ ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP+   RV+SVGRLDINTEGLLL
Sbjct: 108 GKPLKQTERTRLWLYHKPAGLVTTNRDPEGRPTVFEALPAEMPRVLSVGRLDINTEGLLL 167

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDGGL+RVLELPST WLR YRVR HG+V Q +L+ LK GI + G+ YG ++ TL+ ++
Sbjct: 168 LTNDGGLSRVLELPSTGWLRRYRVRAHGKVTQVQLDELKNGIAVDGVFYGSIEATLEREQ 227

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G+N W+++GLREGKNRE+K +       V RLIR+S+GPFQLG L  G+ RE+  +ILR+
Sbjct: 228 GANVWISIGLREGKNREVKNILGALGLTVGRLIRVSFGPFQLGDLEEGAVREIKGRILRD 287

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK-----------NSSQK 292
           QLG  L+E++  + DAP+ +  +    +     +V D+    ++           +S Q+
Sbjct: 288 QLGDKLIEDSGADFDAPVLNEFSNAAVQGRTRRDVEDEGEEGERRRGPREREWISSSPQR 347

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                 K       RR   +NVWMA G      + + +     R+ P   +K S
Sbjct: 348 RRGRDDKGAEKVEPRRRGNANVWMAPGARPKGENAAAKPARVERQVPHRSAKFS 401


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

 Score =  311 bits (797), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 82/232 (35%), Positives = 121/232 (52%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K IA AG+ASRR  E MI Q RV VN  +++     V + D + VDG P++  
Sbjct: 1   MLGIRLQKFIAHAGVASRRTAEEMIKQGRVAVNNTVVQDMGFTVSNDDFVTVDGKPVKIE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     + HKP+G V+T  D  GR TV D +     R+  VGRLD +T GL+LLTNDG  
Sbjct: 61  EEKVYIMLHKPVGYVSTSQDQFGRPTVVDLVKDAGKRLYPVGRLDYDTSGLILLTNDGDF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  +VY     G  +++++   + G+ I+       +  +  ++G N  V 
Sbjct: 121 TYRLTHPKHEINKVYEAVISGFPEKNEIKSFESGLKIENYQTSPAEFVVLEKQGINTLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EGKNR+++K+ E    KV  L RI  GP  L  L  G  R +S + L+
Sbjct: 181 ITIHEGKNRQVRKMCEAIGHKVLTLKRIQIGPIALDNLPVGKWRHLSLRELK 232


>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 =  310 bits (796), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 81/232 (34%), Positives = 119/232 (51%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            +  R+ K +A AG+ASRR+ E MI Q RV VN +++E     V   D + VDG P+   
Sbjct: 1   MSEIRLQKYLAHAGVASRRKAEEMIKQGRVAVNNVIIENMGATVTCNDVVTVDGKPVTTE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     + +KP+G V+T  D  GR  V D +     R+  VGRLD +T GL+LLTNDG  
Sbjct: 61  EAKVYIMLNKPVGYVSTSKDQFGRPAVIDLVKDAGKRLYPVGRLDYDTSGLILLTNDGDF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  +VY     G  D++++   + G+ I        +  +  +KG N  V 
Sbjct: 121 TYRLTHPKHEVNKVYEAVISGFPDKNEITRFETGLKIDDYQTSPAEFEVLNKKGINTLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EGKNR+++K+ E    KV  L RI  GP  L  L  G  R +S   ++
Sbjct: 181 ITIHEGKNRQVRKMCEAIGHKVLTLKRIQIGPIALENLPEGKWRHLSDNEVK 232


>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 =  310 bits (795), Expect = 2e-82,   Method: Composition-based stats.
 Identities = 148/347 (42%), Positives = 203/347 (58%), Gaps = 2/347 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D   + E    +R++K +ARAGIASRR+ E MI   RV VNG  L   A NV   D I +
Sbjct: 75  DTEGLIETPPGERIAKAMARAGIASRRDAETMIVAGRVSVNGETLTSPARNVTENDRILI 134

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG P+   ER+RLW++HKP G+VTT  DP+GR TVFD LP    RV++VGRLDINTEGLL
Sbjct: 135 DGEPMPSRERSRLWIFHKPRGVVTTARDPEGRQTVFDVLPEDLPRVVAVGRLDINTEGLL 194

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDGGLA+V+  P T WLR YRVR HG  DQ +L+ L KG+ I G+ YG ++ TLD  
Sbjct: 195 LLTNDGGLAKVIAHPDTGWLRRYRVRAHGDTDQAQLDRLAKGVTIDGMEYGPVEATLDRV 254

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +G N W+T+GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   EV  ++L+
Sbjct: 255 QGDNVWLTLGLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEVRTRVLK 314

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +QLG  L E+A V+ D+P+               +         + ++ +   + +    
Sbjct: 315 DQLGKSLAEQAGVDFDSPVREPIAPFGGTRPADRDAKSAQPAPARRNAARPAPAPRVSTG 374

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                    S+ W  +       +   +R  + R + +  ++R   R
Sbjct: 375 GAGP--GPRSSTWRDEDAAKPRGTRVPRRGADPRTAQAAAAERGRER 419


>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 =  310 bits (794), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 176/406 (43%), Positives = 224/406 (55%), Gaps = 57/406 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K   ++   P+R+SK++ARAGIASRR+VERMI + RV VNG +L+   +N    D IEVD
Sbjct: 73  KTGSEDTLKPERISKLLARAGIASRRDVERMIMEGRVAVNGKVLDSPVLNATLADRIEVD 132

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P+R  ERTRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLL
Sbjct: 133 GEPIRGIERTRLWLYHKPSGLVTTNSDPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLL 192

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDGGLARVLELP+T WLR YRVR +G++DQ KL+ LK GI + G+ YG +   LD  +
Sbjct: 193 LTNDGGLARVLELPTTGWLRRYRVRAYGEIDQAKLDTLKDGIAVDGVLYGAIDAVLDRSQ 252

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N W+T+GLREGKNREIK V      +VNRLIRISYGPFQLG L     +EV  ++LR+
Sbjct: 253 GHNVWITMGLREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPESQVQEVRGRMLRD 312

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT---RMKKNSSQKNGLSKQKK 300
           QLGP L+EE++ N DAP+YS+     +                +     ++  G   ++ 
Sbjct: 313 QLGPRLIEESKANFDAPLYSNAPAEEEDAPAPKAKAKAEEGNWKKDTRPAKPRGFDNRED 372

Query: 301 LATPVHRR--------------------------------------------------NL 310
                  R                                                  + 
Sbjct: 373 AREKALSRLDTRRDGAKPAFGSKPGFGGKPGFKGKPAAGRDGDDAARDGKPKRMPLGQSR 432

Query: 311 ASNVWMAKGIHS----SFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            +NVWMA G          SD  ++     R    P  +   RT  
Sbjct: 433 TANVWMAPGARPVSEKKTASDEARKSGPRARPDGAPQTKRYGRTKD 478


>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 =  309 bits (793), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 89/232 (38%), Positives = 128/232 (55%), Gaps = 1/232 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++ E     V RL RI  GP  L  L  G  R +++  L++ 
Sbjct: 183 IHEGRNRQVRRMCEHIGHPVLRLKRIRVGPLVLEGLKPGQFRPLTEVELKKL 234


>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 =  309 bits (792), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 183/386 (47%), Positives = 235/386 (60%), Gaps = 46/386 (11%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+SK++ARAG+ASRR+VERMI + RV +NG+LL+   VN   +D IEVDG+P+R AER
Sbjct: 56  PERISKIMARAGVASRRDVERMIMEGRVSLNGVLLDTPVVNATLSDKIEVDGMPIRGAER 115

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGL+R
Sbjct: 116 TRLWLYHKPAGLVTTNSDPEGRPTVFDNLPGELPRVLSIGRLDINTEGLLLLTNDGGLSR 175

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELP+T WLR YRVR HG+VDQ  L+ LK GI + G+ YG +  TLD  +G N W+T+G
Sbjct: 176 VLELPTTGWLRRYRVRAHGEVDQAALDKLKDGIAVDGVLYGAIDATLDRTQGHNVWITMG 235

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  ++LR+QLGP L+EE
Sbjct: 236 LREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGKVLEVRGRMLRDQLGPRLIEE 295

Query: 253 AQVNLDAPIYSS-----ETLVRDRPN---IISEVPDDFTRMKKNSSQKNGLSKQ------ 298
           A  N DAPIY++     E     R       S+ P+   R +K + +     ++      
Sbjct: 296 AGANFDAPIYNTSVDDEEEAPAKRAKSEWAKSDAPEGKPRFEKAAGKPEDRREKALGRLD 355

Query: 299 ------------------------------KKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
                                          +   P    +  +NVWMA G   +   D 
Sbjct: 356 TKRSDKPAGKFGAKPAGKFGGKGRNDDEGDDRRPRPPAGTSRTANVWMAPGAKPTR--DG 413

Query: 329 GQREENHRRSPSFPSKRSLRRTSAKK 354
            +R+ + R       K+   +  A++
Sbjct: 414 KERKSSARAEAESLFKKPSAQDEARR 439


>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 =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 179/389 (46%), Positives = 234/389 (60%), Gaps = 49/389 (12%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+SK++ARAG+ASRR++ERMI + RV +NG+ L+   +N   +D IEVDG+P+R AER
Sbjct: 52  PERISKIMARAGVASRRDIERMIMEGRVSLNGVKLDTPVMNATLSDKIEVDGMPIRGAER 111

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TRLWLYHKP GLVTT+SDP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGL+R
Sbjct: 112 TRLWLYHKPAGLVTTNSDPEGRPTVFDNLPGELPRVLSIGRLDINTEGLLLLTNDGGLSR 171

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VLELP+T WLR YRVR HG+VDQ  L+ LK+GI + G+ YG +  TLD  +G N W+T+G
Sbjct: 172 VLELPTTGWLRRYRVRAHGEVDQAALDKLKEGIAVDGVLYGAIDATLDRTQGHNVWITMG 231

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           LREGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  ++LR+QLGP L+E+
Sbjct: 232 LREGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGKVLEVRGRMLRDQLGPRLIEQ 291

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPD-------------------------------- 280
           +  N DAPIY +     +  N     P                                 
Sbjct: 292 SGANFDAPIYDAPVADDEEENTPKRAPRSEWAKSDAPEGKPRFDRAAGKPEDRREKALGR 351

Query: 281 -DFTRMKKNSSQKNGLS--------------KQKKLATPVHRRNLASNVWMAKGIHSSFL 325
            D  R  K + +  G                ++++ A P    +  +NVWMA G   +  
Sbjct: 352 LDTKRGDKPAGKFGGKPAGKFGAKTRGEEDGEERRPARPPAGTSRTANVWMAPGAKPTR- 410

Query: 326 SDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            D  +R+ + R       K+   +  A++
Sbjct: 411 -DGKERKFSARAEAESLFKKPSAQAEARR 438


>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 =  309 bits (791), Expect = 6e-82,   Method: Composition-based stats.
 Identities = 98/259 (37%), Positives = 142/259 (54%), Gaps = 2/259 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP-HLLE 251
           + EG+NR+++++ E  +  V RL R+ YG  ++  L  G  R +++   R  L P   L 
Sbjct: 183 IHEGRNRQVRRMCEAVSLSVVRLKRVRYGALEMRGLKPGQHRLLTEAEARALLTPGAGLR 242

Query: 252 EAQVNLDAPIYSSETLVRD 270
            A+   +    ++    R+
Sbjct: 243 SAEAPREKRARNAGQPPRE 261


>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 =  308 bits (789), Expect = 1e-81,   Method: Composition-based stats.
 Identities = 176/341 (51%), Positives = 219/341 (64%), Gaps = 30/341 (8%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP+R 
Sbjct: 48  EAKAERISKVMARAGVASRRDIERMIMEGRVTLNGKVLDTPVVNVTLADRIEVDGVPIRG 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L
Sbjct: 228 TMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVVEVRGRTLRDQLGPRL 287

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS------------- 296
           +EEA+ N DAPIY++  +  +     +         +    ++  LS             
Sbjct: 288 IEEAKANFDAPIYNAPAVAAEEETEAAAPEKRERPRRDEDKRERALSRLDTKRDDRRGAG 347

Query: 297 ---------------KQKKLATPVHRRNLASNVWMAKGIHS 322
                          K K+   P  RR+  +NVWMA G   
Sbjct: 348 RRDDDRRDGGRKDDDKPKRSQPPGQRRS--ANVWMAPGARP 386


>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 =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 91/232 (39%), Positives = 133/232 (57%), Gaps = 1/232 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++ E     V RL R  YG  ++G L  G  RE+S   +   
Sbjct: 183 IHEGRYRQVRRMCEAVGLTVVRLKRSRYGFLEIGELKPGQYRELSSTEVERL 234


>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 =  307 bits (787), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 138/326 (42%), Positives = 183/326 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMI   RV+VNG  ++  A+NV   D I VD  P+   E  R
Sbjct: 26  RIAKVLSRAGVASRREAERMIEAGRVRVNGEQIDSPALNVTPEDKITVDNTPVGAPEPPR 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLYHKP GLVTT  D  GR T+FD+LP    RV+++GRLD+N+EGLLLLTNDGG+ R L
Sbjct: 86  MWLYHKPAGLVTTARDEKGRETIFDDLPEDMPRVMTIGRLDLNSEGLLLLTNDGGVKRKL 145

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YR R +G+   + L  L++GI ++G  +  M VTLD Q+G+NAW+T+GLR
Sbjct: 146 ELPSTGWLRRYRARVNGRPTDEMLEPLRRGITVEGENFLPMDVTLDRQQGANAWLTIGLR 205

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EG+NREI++  E     VNRLIR SYGPFQLG L  G   E+ +KI+R+QLG  L +   
Sbjct: 206 EGRNREIRRAMEAVGLTVNRLIRTSYGPFQLGELKTGEVEELRRKIVRDQLGLELEDPTG 265

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
             +  P        R                +    +        K       +  A   
Sbjct: 266 TAVKKPTAVRRPPRRKPGGFGGAGQPGMPVQRGEDDEPPPRRGGGKAKNAPRGKAAAGRT 325

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPS 340
               G      +      +   R P 
Sbjct: 326 ADKPGARPGSRTGGKPAGKPGSRGPK 351


>gi|222085015|ref|YP_002543544.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221722463|gb|ACM25619.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 680

 Score =  307 bits (786), Expect = 2e-81,   Method: Composition-based stats.
 Identities = 177/370 (47%), Positives = 228/370 (61%), Gaps = 31/370 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKV+ARAG+ASRR++ERMI   RV++NG+LL+   VNV   D IEVDG+P+R  ERT
Sbjct: 52  ERISKVMARAGVASRRDIERMIMDGRVRLNGVLLDSPVVNVTLADKIEVDGMPIRGIERT 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTNDGGLARV
Sbjct: 112 RLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTNDGGLARV 171

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG++DQD L+ LK+GI + G+ YG ++ TLD  +GSN W+T+GL
Sbjct: 172 LELPTTGWLRRYRVRAHGEIDQDALDKLKEGIAVDGVLYGSIEATLDRTQGSNVWITMGL 231

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREIK V      +VNRLIRISYGPFQLG L  G   EV  + LR+QLGP L+E+A
Sbjct: 232 REGKNREIKNVLGALGLEVNRLIRISYGPFQLGDLPEGRVLEVRGRTLRDQLGPRLVEDA 291

Query: 254 QVNLDAPIYSSETLV--------------------------RDRPNIISEVPDDFTRMKK 287
           + N DAP+Y++                                R   +  +       + 
Sbjct: 292 KANFDAPLYNASAPAGEDEAEAKPERAAKEERPRRDRERPEDKRERALGRLDTKRDDRRD 351

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS-----PSFP 342
              ++ G  +  +   P       +NVWMA G        + +  +N R +     P  P
Sbjct: 352 EGRREGGHKEDDRPKRPPLGARRNANVWMAPGARPLGEKAAAKAAKNTRTAAKRGEPERP 411

Query: 343 SKRSLRRTSA 352
            +    R   
Sbjct: 412 QRSGFDRPDE 421


>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 =  306 bits (785), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 98/347 (28%), Positives = 165/347 (47%), Gaps = 11/347 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K+IA  G+ASRR+ E +I   RV +NG +++     V    DH++VDG  LR A+  
Sbjct: 4   RLQKLIAGTGLASRRKAEELITSGRVTINGSVVKELGTKVDPARDHVKVDGKHLRAAQPY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP  +++T  DP+GR TV D L  +  RV  VGRLD ++EGL+LLTN G LA+ 
Sbjct: 64  VYLILNKPKNVMSTLDDPEGRPTVKDLLHGVTVRVFPVGRLDFDSEGLMLLTNHGDLAQA 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y ++  G +D  K+  L++G+ ++       +V   ++  SN+W+ V +
Sbjct: 124 LLHPRYHVPKTYLIKVKGVLDDAKIEALERGVKLEDGFTAPAKVKKVSRAESNSWLEVTI 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLL 250
            EG+  ++K++ E     V +L+R+  GP  LG L     R ++ +    LRE +   + 
Sbjct: 184 HEGRKHQVKRMVEAVGHSVIKLVRVRMGPLLLGDLAPREYRFLTDREANRLRELVEDRVA 243

Query: 251 EEAQVNLDAPIYSSE-TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
              +  LDA    +      +        P+   R  K+   + G   Q+ LA     R+
Sbjct: 244 RAERPELDASGKPTRWMPPTEPAPPRPPKPERSGRGPKSQRSERGPRSQRSLAGSKPSRS 303

Query: 310 LASNVW--MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              N    M+ G           +    +R+ + P  +   R    +
Sbjct: 304 GRGNTRRPMSPGAK----FRRPAKGVGFQRTQAGPIPQGADRGPGSR 346


>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 =  306 bits (784), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 147/333 (44%), Positives = 190/333 (57%), Gaps = 16/333 (4%)

Query: 7   VQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           + +N TP   R++KV+ARAGIASRRE ER+IA+ RV VNG  ++  A+NV   D I  DG
Sbjct: 1   MADNTTPPGDRIAKVLARAGIASRREAERLIAEGRVAVNGKTVDSPALNVTEADKITFDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P+ + E  RLW YHKP+GLVTT  D  GR TVFD LP+   RV+SVGRLD+N+EGLLLL
Sbjct: 61  TPIAEPEPPRLWRYHKPVGLVTTAKDEKGRETVFDALPADLPRVMSVGRLDLNSEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG + R LELP+T WLR YRVR  G   +D L  L+ GI ++G  +  M+  LD  +G
Sbjct: 121 TNDGEIKRRLELPTTGWLRRYRVRVKGAPTEDDLAPLRAGIEVEGERFKPMEARLDRLQG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+T+GLREG+NREI++        VNRLIRISYGPF+LG L  G   E+  +ILREQ
Sbjct: 181 ANAWLTLGLREGRNREIRRAMGALGLVVNRLIRISYGPFRLGELKPGEVEEIKGRILREQ 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           LG    E        P+ +++   +  P              K S   N     K    P
Sbjct: 241 LGLESPEP-------PVGTAQARPKRGPGRKPGATPGGKPTGKPSRAPNARPGAKPGGKP 293

Query: 305 VHRRNLASNVWMAKGIH-SSFLSDSGQREENHR 336
             + +         G    S    +  R    R
Sbjct: 294 GAKPDPK------PGARAGSARRKAPARPRPER 320


>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 =  306 bits (784), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 169/359 (47%), Positives = 215/359 (59%), Gaps = 24/359 (6%)

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 GPHLLEEAQVNLDAPIYS--SETLVRDRPNIISEVPD-----------------DFTRMK 286
           G  L EEA  + DAPI+    +   + RP       D                   T  K
Sbjct: 291 GDALAEEAGADFDAPIFHMPKQEEEKKRPGPRGGSRDSSSEKGQGKWLTAREGKSATDRK 350

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           K +   +G  KQ K      RR   S             S+   R++ +   PS P +R
Sbjct: 351 KAARSDDGGPKQGKRRNEGPRREKVS-----PRSKFRMTSEPRFRKDYNEERPSPPQRR 404


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

 Score =  305 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 80/231 (34%), Positives = 122/231 (52%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K IA  G+ASRR+ E +I Q  VKVNGI++    + V S+D +EV+G  ++  
Sbjct: 1   MEMTRLQKYIADCGVASRRKAEELIQQGSVKVNGIVVSEMGIKVSSSDRVEVNGSVIKPE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +    L +KP G VTT  D   R TV D L  +  RV  VGRLD  T GLL+LTNDG  
Sbjct: 61  SKKVYILLNKPSGYVTTVKDQFRRPTVIDLLKGVDERVFPVGRLDYETTGLLVLTNDGDF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P  +  + Y+    G   +D+++  + G+ I+       ++ + + K     + 
Sbjct: 121 THKMTHPRHEIEKTYQATIAGTPTKDEIHSFESGLEIEDYVTSPAKLKIISTKERTCVIE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + EG+NR+++K+ E     V  L RIS G   LG L  GS RE+++  +
Sbjct: 181 VTIHEGRNRQVRKMCEAIGHPVLALKRISLGKVTLGNLPEGSWRELTRDEV 231


>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 =  305 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 153/339 (45%), Positives = 202/339 (59%), Gaps = 12/339 (3%)

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+          P    +           + Q  G  +  +   P         +
Sbjct: 276 VDFTSPV-----REPIAPFGSPKGARKTAAATAQAPQGRGEGRPARGERPAW---GERPM 327

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           W   G   +       R +   R+P   ++    RT   
Sbjct: 328 W---GERPARGGRDPARPQ-FGRAPGPGTRPERSRTPEA 362


>gi|296133130|ref|YP_003640377.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296031708|gb|ADG82476.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score =  305 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 131/235 (55%), Gaps = 1/235 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              QR+ K +A AG+ASRR+ E +IA  +VKVNG ++      V  + D +EV G+ +  
Sbjct: 1   MERQRLQKFMAHAGVASRRKCEELIAAGKVKVNGKVVTEMGYTVDPSVDRVEVAGLGIIV 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+    L +KP G++++ SD  GR TV D + +  +R+  VGRLD +TEGL+LLTNDG 
Sbjct: 61  HEKKEYILLYKPAGVLSSASDDRGRKTVVDLIKNAKTRLYPVGRLDYDTEGLILLTNDGR 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L  +L  P  +  + YR    G   +DKL  L+ GI+++       +V +  Q   N  V
Sbjct: 121 LTNLLIHPRYKVDKTYRAVVQGIPGEDKLAALRNGIMLEDGPTYPARVKMLKQINGNGLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EG+NR+++++F+     V +L R  +G  +LG L  G  R +S   + + 
Sbjct: 181 EITIHEGRNRQVRRMFDAIGHPVLKLKRTRFGFLELGNLQPGQYRALSAAEVAKL 235


>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 =  305 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 91/234 (38%), Positives = 132/234 (56%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR  E +I   RV VNG ++ +    V+   D IEVDG PL   E 
Sbjct: 3   ERLQKVMARAGVASRRHCEALIQAGRVTVNGQVVTQLGTKVVPGKDVIEVDGRPLGTPET 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G V+T  DP GR  V D L   +  RV  VGRLD +TEGLLLLTNDG LA
Sbjct: 63  KVYVMLNKPKGYVSTLYDPQGRPKVIDLLGDEVAQRVYPVGRLDFDTEGLLLLTNDGDLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVT 190
             L  PS    + Y V+  G     KL  L++GI ++       +V  LD +  ++A ++
Sbjct: 123 HGLMHPSRMVKKTYIVKVRGVPGPAKLRALQEGIELEDGPTAPAEVKMLDVRPPNSATLS 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + EG+NR+++++F     +V  L R + GP +LG L  G  R ++ + + + 
Sbjct: 183 VRIHEGRNRQVRRMFAALGHEVIHLRRTTLGPLKLGDLSVGEWRYLTDQEVADL 236


>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 =  305 bits (783), Expect = 5e-81,   Method: Composition-based stats.
 Identities = 146/348 (41%), Positives = 195/348 (56%), Gaps = 4/348 (1%)

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 PHLLEEAQVNLDAPIYSSETLVRDRP-NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                + +     P    +     RP                  ++  G ++ ++ A P 
Sbjct: 241 LDPHADGEAR---PARGRKPEGAARPARSEGAARPARAEGGARPARAEGAARSERTARPP 297

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                       +G  S   +   +    H  +    + +   R++ K
Sbjct: 298 RGAAAEGPARAGRGAGSEGAAGPAKGRSPHGAARRAGAPKDSARSAGK 345


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

 Score =  305 bits (782), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 81/238 (34%), Positives = 137/238 (57%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E++I Q +VKVNG ++    V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIAHAGIASRRKAEQLILQGKVKVNGKVVTELGVKVGPQDKVEVDGIPVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++  D  GR  V D    +  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 61  VYYLFYKPRGVISSVKDDKGRKVVTDFFKDVDKRIYPIGRLDYDTSGILLLTNDGDFANL 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++++FE    KV +L R  Y    L  L  G  R+++   +++     L
Sbjct: 181 RIHEGRNRQVRRMFEAIGCKVMKLKRERYAFLDLKGLNPGEYRKLTPHEVKQLRALAL 238


>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 =  305 bits (782), Expect = 7e-81,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 119/235 (50%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K +A  G+ASRR+ E +I+Q RVKVNG  + +    V   D +EVDG  ++  
Sbjct: 1   MKEMRLQKYLAECGVASRRKAEELISQGRVKVNGETVTQMGKKVSQNDVVEVDGKLVKME 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +R      +KP+G +++  D  GR TV D +  I  R+  VGRLD +T GLLLLTNDG  
Sbjct: 61  KRKVYIALNKPVGYISSVKDQFGRKTVMDLVKDIKERIFPVGRLDYDTSGLLLLTNDGDF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  +VY     G   +D +   K G+ I           +    G    V 
Sbjct: 121 AYRLTHPKHEIKKVYEADLLGVPSKDDIMRFKNGLWIDDYFTSPADFEILKSDGKTTKVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EGKNR+++K+       V RL RIS G   LG L  GS R ++++ +   L
Sbjct: 181 ITIHEGKNRQVRKMCNKIGCPVIRLKRISIGEVSLGDLKEGSWRNLTEREINSFL 235


>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 =  305 bits (781), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 162/350 (46%), Positives = 210/350 (60%), 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 EAQVNLDAPI---YSSETLVRDRPNIISEVP--DDFTRMKKNSSQKNGLSKQKKLATPVH 306
            A  + +AP+      +  ++ + NI       +  +  +  ++ + G  +      P  
Sbjct: 325 AAGADFEAPVLTQAEPDKPLKKKENIQKSRAGGEWMSAREGAAATRTGGRRSASDEAPER 384

Query: 307 RRNLASN---VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           RR  A N        G       D  Q+     R       R   R   +
Sbjct: 385 RRKGAGNPPETRRPSGKSQDRPQDRPQKVSPRSRFRLTSEPRPRSRAPER 434


>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 =  305 bits (781), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 82/232 (35%), Positives = 130/232 (56%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K +A AG+ASRR+ E++I Q RVKVNG ++      +    D +EVDG  + K E+
Sbjct: 2   ERLQKYMAHAGVASRRKSEKIITQGRVKVNGKIVTELGTKIDPDKDIVEVDGRVISK-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP+G +T+ SDP GR TV   +  +  R+  VGRLD +T GLL+LTNDG L  
Sbjct: 61  YVYILLNKPVGYITSVSDPHGRKTVTGLIKGVSQRIYPVGRLDYDTSGLLILTNDGELTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  PS    + YRV   G    + L  L+ G+ ++       +V+   +K  N    + 
Sbjct: 121 VLTHPSHMVEKTYRVEVKGFPSDEVLKKLETGVKLKDGLTAPARVSAVKRKEKNTIFNLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++ +   + V  L RI++GP  L  L  G  R +++K ++  
Sbjct: 181 IHEGRNRQVRRMCDKIGFPVVNLKRIAFGPLNLKGLKTGQYRFLTEKEVKAL 232


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

 Score =  305 bits (781), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 152/372 (40%), Positives = 198/372 (53%), Gaps = 28/372 (7%)

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 --PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL--- 301
             PH   EA+         +    R          +   R +K +    G + +      
Sbjct: 241 LDPHADGEARPAKGRKPEGAARPARSESAARRARAEGGARSEKPARSPRGAAAEGPTRPA 300

Query: 302 -----------------------ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                                  A         +    A+G   +  S  G  E + R  
Sbjct: 301 RGAGSEGSAGATRGRSPQGAAPKAGAPKDGARFAGKGPAEGARPARASRPGGAEASGRTR 360

Query: 339 PSFPSKRSLRRT 350
           P+     +  R+
Sbjct: 361 PADGKSAAAGRS 372


>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 =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 89/232 (38%), Positives = 127/232 (54%), Gaps = 1/232 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++ E     V RL R  YG  ++G L  G  R ++   +   
Sbjct: 183 IHEGRYRQVRRMCEAVGLTVVRLKRSRYGFLEIGELKPGEYRLLTPAEVERL 234


>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 =  304 bits (780), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 174/362 (48%), Positives = 223/362 (61%), Gaps = 27/362 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP
Sbjct: 41  TEGEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGAVLDTPVVNVTLADRIEVDGVP 100

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  ERTRLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLDINTEGLLLLTN
Sbjct: 101 IRGIERTRLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLDINTEGLLLLTN 160

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T WLR YRVR HG +DQD L+ LK GI + G+ YG ++ TLD  +GSN
Sbjct: 161 DGGLARALELPATGWLRRYRVRAHGDIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSN 220

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLG
Sbjct: 221 VWITMGLREGKNREIKNVMGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGRTLRDQLG 280

Query: 247 PHLLEEAQVNLDAPIYSSETL---------------------VRDRPNIISEVPDDFTRM 285
           P L+EEA+ N DAPIY++  +                        R   +S +       
Sbjct: 281 PRLIEEAKANFDAPIYNAPAVAAEEEAEAPVPERREQRPRRDEDKRERALSRLDTKRDDR 340

Query: 286 KKNSSQKNGLSKQKKLATPVHRR------NLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           +    + +      +      +R        ++NVWMA G        + +  +N + + 
Sbjct: 341 RGGGRRDDDRRDGGRFDDDKPKRPQPLGQRRSANVWMAPGARPLGEKAAAKAAKNEQTAR 400

Query: 340 SF 341
             
Sbjct: 401 RG 402


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 98/300 (32%), Positives = 155/300 (51%), Gaps = 5/300 (1%)

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 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              +    +  +  + + +P+    V     ++ +  S ++  SK  +       R   S
Sbjct: 243 NYND----MQLTTEVQKKKPSPCGRVGRIKGKVSEQKSNRSAKSKVNEFFEKGTLRGKNS 298


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 175/372 (47%), Positives = 230/372 (61%), Gaps = 33/372 (8%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDG+P
Sbjct: 45  TESEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGKVLETPVVNVTLADRIEVDGMP 104

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTEGLLLLTN
Sbjct: 105 VRGIERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTEGLLLLTN 164

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN
Sbjct: 165 DGGLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSN 224

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLG
Sbjct: 225 VWITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVIEVRGRTLRDQLG 284

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK--------- 297
           P L+EEA+ N DAPIY++  +  +    ++         +    ++  LS+         
Sbjct: 285 PRLIEEAKANFDAPIYNAPAVAAEEEAEVAAPEKRERPRRDEDKRERALSRLDTKRDDRR 344

Query: 298 -----------------------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
                                  + K + P+ +R  ++NVWMA G        + +  +N
Sbjct: 345 GDDRRGGARRDDDRRDGGRRDDEKPKRSEPLGQR-RSANVWMAPGARPLGEKAAAKAAKN 403

Query: 335 HRRSPSFPSKRS 346
            + +     +  
Sbjct: 404 AQTARRRGEQAP 415


>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 =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 153/362 (42%), Positives = 198/362 (54%), Gaps = 15/362 (4%)

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 --PHLLEEAQVNL---------DAPIYSSETLVRDRPNIISEVPDDFTRM---KKNSSQK 292
             PH   EA+                  SE   R      +E P    R    + ++   
Sbjct: 241 LDPHADGEARPARGRKPEGAARAEGAARSERTARPPRGAAAEGPTRPARAAGSEGSAGAT 300

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
            G S Q         ++ A           +  + S   +      P+        RT+ 
Sbjct: 301 RGRSPQGAAPKAGAPKDGARFAGKGP-AEGARPARSAATDPARASRPASTETTGRTRTAE 359

Query: 353 KK 354
            +
Sbjct: 360 GR 361


>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 =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 85/238 (35%), Positives = 136/238 (57%), Gaps = 3/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E++I Q +VKVNG ++    V V   D +EVDG+P+ K E  
Sbjct: 2   ERLQKVIARAGIASRRKAEQLILQGKVKVNGKIVTELGVKVGPRDKVEVDGIPVEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++  D  GR  V D    I  R+  VGRLD +T G+LLLTNDG  A +
Sbjct: 61  VYYLFYKPRGVISSVKDDKGRKVVTDFFKDIDKRIYPVGRLDYDTSGILLLTNDGDFANL 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + EG+NR+++++FE     V +L R  Y    L  L  G  RE++   +++     L
Sbjct: 181 RIHEGRNRQVRRMFEAIGCNVMKLKRERYAFLDLKGLNPGEYRELTPHEVKQLRALAL 238


>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 =  304 bits (778), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 143/283 (50%), Positives = 184/283 (65%), Gaps = 3/283 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   RV+VNG  ++  A+NV  +D I VDG P+ + E  R
Sbjct: 19  RIAKVLSRAGIASRREAERMIEAGRVRVNGAQIDSPALNVTPSDAITVDGKPVGEPEPPR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WL+HKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R L
Sbjct: 79  VWLFHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGEVKRRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  WLR YRVR +G+   D L  L+KGI + G  +  M VTLD Q+G+NAW+TVGLR
Sbjct: 139 ELPSNGWLRRYRVRVNGRPTDDMLEPLRKGITVDGEDFQPMTVTLDRQQGANAWLTVGLR 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG   LE A 
Sbjct: 199 EGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKTGEVEELKRKVVRDQLG---LEIAD 255

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
               A       +++ +     E       + K    K    K
Sbjct: 256 TTGTAIKKKPARIIKRKARKPGEPGPGRPGLPKEPGDKTATGK 298


>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 =  303 bits (776), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 143/283 (50%), Positives = 184/283 (65%), Gaps = 3/283 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   RV+VNG  ++  A+NV  +D I VDG P+ + E  R
Sbjct: 19  RIAKVLSRAGIASRREAERMIEAGRVRVNGAQIDSPALNVTPSDAITVDGKPVGEPEPPR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WL+HKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+N+EGLLLLTNDG + R L
Sbjct: 79  VWLFHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDLNSEGLLLLTNDGEVKRRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  WLR YRVR +G+   D L  L+KGI + G  +  M VTLD Q+G+NAW+TVGLR
Sbjct: 139 ELPSNGWLRRYRVRVNGRPTDDMLEPLRKGITVDGEDFQPMTVTLDRQQGANAWLTVGLR 198

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+ +K++R+QLG   LE A 
Sbjct: 199 EGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKTGEVEELKRKVVRDQLG---LEIAD 255

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
               A       +++ +     E       + K    K    K
Sbjct: 256 TTGTAVKKKPARIIKRKARKPGEPGPGRPGLPKEPGDKTATGK 298


>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 =  303 bits (776), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 177/368 (48%), Positives = 227/368 (61%), Gaps = 26/368 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP
Sbjct: 45  TEGEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVP 104

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  ERTRLWLYHKP GLVTT++DP+GRSTVFDNLP    RV+S+GRLDINTEGLLLLTN
Sbjct: 105 IRGIERTRLWLYHKPAGLVTTNADPEGRSTVFDNLPEELPRVMSIGRLDINTEGLLLLTN 164

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T WLR YRVR HG++DQD L+ LK GI + G+ YG ++ TLD  +GSN
Sbjct: 165 DGGLARALELPATGWLRRYRVRAHGEIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSN 224

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV  + LR+QLG
Sbjct: 225 VWITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVVEVRGRTLRDQLG 284

Query: 247 PHLLEEAQVNLDAPIYSSETL--------------------VRDRPNIISEVPDDFTRMK 286
           P L+EEA+ N DAPIY++  +                       R   +S +        
Sbjct: 285 PRLIEEAKANFDAPIYNAAAVAAEEEAEPAAAERRERPRRDEDKRERALSRLDTKRDDRH 344

Query: 287 KNSSQKNGLSKQKKLATPVHRR------NLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
             + +++      +      +R        ++NVWMA G        + +  +N + +  
Sbjct: 345 GGARKEDDRRDGGRRDDERPKRPQPLGQRRSANVWMAPGARPLGEKAAAKAAKNAQTARK 404

Query: 341 FPSKRSLR 348
              +   R
Sbjct: 405 RGEQSPAR 412


>gi|322420558|ref|YP_004199781.1| pseudouridine synthase [Geobacter sp. M18]
 gi|320126945|gb|ADW14505.1| pseudouridine synthase [Geobacter sp. M18]
          Length = 262

 Score =  302 bits (775), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 86/232 (37%), Positives = 132/232 (56%), Gaps = 1/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++++AGIASRRE E +IA+ RV VNG ++          TD 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++ E     V RL R  Y    +G +  G  R ++   + + 
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRSRYDFLVIGEMKPGDFRHLTADEVAKL 234


>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 =  302 bits (775), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 147/338 (43%), Positives = 190/338 (56%), Gaps = 12/338 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   +V VNG ++   A+NV + D I VDG P+   E  R
Sbjct: 19  RIAKVLSRAGIASRREAERMIELGQVAVNGKVITSPALNVTAKDRITVDGKPVAAPEPAR 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVT+ +D  GR T++D +P    RV++VGRLD+N+EGLLLLTNDG L R L
Sbjct: 79  LWLYYKPEGLVTSDNDEKGRETIYDQMPEDLPRVMAVGRLDLNSEGLLLLTNDGELKRRL 138

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR  G      L  L+ GI ++G  +  M V +D  +G+NAW+TVGLR
Sbjct: 139 ELPSTGWLRKYRVRIKGNPTDPDLEPLRAGITVEGERFQPMLVVIDRIQGANAWLTVGLR 198

Query: 195 EGKNREIKK-VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           EGKNREI++ +F   N  VNRLIRISYGPF+LG L  G   EV  K+LR+QLG     E 
Sbjct: 199 EGKNREIRRAMF-ALNLTVNRLIRISYGPFRLGDLQPGEVAEVRGKVLRDQLGFDPRAE- 256

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
               D  + +S      +P   +  P    +       K      K  A     R     
Sbjct: 257 ----DEELSTSGKPAPKKPATRTLAPRTPAKPGAKPGAKPSRGVAKPAAEAPVARAKPVK 312

Query: 314 -----VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
                     G  S     +  R E  + +P  P +R 
Sbjct: 313 PGPGWAKAQPGGKSGPGPKATSRNEGAKPAPRSPGRRP 350


>gi|196248745|ref|ZP_03147445.1| pseudouridine synthase [Geobacillus sp. G11MC16]
 gi|196211621|gb|EDY06380.1| pseudouridine synthase [Geobacillus sp. G11MC16]
          Length = 243

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 88/231 (38%), Positives = 134/231 (58%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E MI Q RVKVNG ++    V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEEMILQGRVKVNGRVVTELGVKVGPRDDVEVDGIPVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 61  VYYLLYKPRGVISSVKDEKGRKVVTDFFKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G   +++L  L+KG++++       +V L +  +K   A 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|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 =  302 bits (774), Expect = 5e-80,   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 KSRSG-DPAKQRSGAPPRTRSGDPVKARTDGPARARADGPGKPRGSGPR 348


>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 =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 132/232 (56%), Gaps = 1/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE E +IA  RV VNG ++          TD 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++ E     V RL R  Y   ++G +  G  R ++ + +   
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRARYDFLEIGDMKPGEYRHLAPEEVTRL 234


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

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 95/334 (28%), Positives = 146/334 (43%), Gaps = 8/334 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
           +R+ K++A+AGIASRR+ E +I   +V+VNG+ +           D I V G P+  +E 
Sbjct: 5   ERLQKILAQAGIASRRKCEELIISGQVEVNGVPVTTLGAKADPEEDVITVGGKPIV-SEN 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP GR  V D L  I  RV  +GRLD +TEGLLLLTNDG  A 
Sbjct: 64  KLYIMLNKPKGVITSASDPQGRKVVSDFLTGIKQRVYPIGRLDYDTEGLLLLTNDGEFAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
           +L  P     + Y     G    DKL+ L+KGI ++       +V     + S+  + + 
Sbjct: 124 LLTHPKHHVPKTYWATVKGVPHGDKLDKLRKGIELEDGMTSPAEVEYQDIEPSDKESTIR 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + + EG+NR+++++F+     V RL R+ +G   L  L  G  R +    ++E L     
Sbjct: 184 ITIYEGRNRQVRRMFDAIGHPVIRLKRVKFGELGLQNLKRGGWRPLKPHEVQELL----Q 239

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E A+    +    S              P   T     +          +      R   
Sbjct: 240 EAAKAEGKSSYVPSGKPATKPEWKPKPKPKHLTASGDKNHSNGQKEGGSETGRKPFRSKQ 299

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
           ASN     G      S     E     + +   K
Sbjct: 300 ASNAAATTGSRKGKRSRQSYAESVLGAAAATQGK 333


>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 =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 141/277 (50%), Positives = 182/277 (65%), Gaps = 8/277 (2%)

Query: 1   MKDKNIVQENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+    +     P  R++KV+ARAGIASRRE ERMI   RV VNG  ++  A+NV  +D 
Sbjct: 16  MRYAQGMSNTPPPGDRIAKVLARAGIASRREAERMIEAGRVTVNGKTIDSPALNVTPSDR 75

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG P+ + E  RLWLYHKP GLVTT+ D  GR T+FDNLP    RV+SVGRLD+N+E
Sbjct: 76  ITVDGKPVAEPEPARLWLYHKPTGLVTTNRDEKGRPTIFDNLPEDMPRVMSVGRLDLNSE 135

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG + R LELPST WLR YRVR +G+   +    L++G+VI+G  +  M VTL
Sbjct: 136 GLLLLTNDGTIKRKLELPSTGWLRKYRVRINGRPKDEDFAPLRQGLVIEGERFQPMTVTL 195

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D Q+G+NAW+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+ ++
Sbjct: 196 DRQQGANAWLTIGLREGKNREIRRAIEDIGFTVNRLLRVSYGPFQLGNLKPGEVEEIRRR 255

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           +LR+QLG           D P  +       R    +
Sbjct: 256 VLRDQLGLGP-------EDKPTPAKRPARPQRSRKPA 285


>gi|253699802|ref|YP_003020991.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251774652|gb|ACT17233.1| pseudouridine synthase [Geobacter sp. M21]
          Length = 266

 Score =  302 bits (774), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 132/232 (56%), Gaps = 1/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++++AG+ASRRE E +IA  RV VNG ++          TD 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++ E     V RL R  Y   ++G +  G  R ++ + +   
Sbjct: 183 IHEGRYRQVRRMCEAVGLNVVRLKRARYDFLEIGDMKPGEYRHLAPEEVTRL 234


>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 =  302 bits (774), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 144/335 (42%), Positives = 194/335 (57%)

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 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           +  ++         S     G +  +   +     
Sbjct: 357 SGKASAGKPGAGKPSGTKSFGSKPASGAGARKTGG 391


>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 =  302 bits (773), Expect = 6e-80,   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|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 =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 132/234 (56%), Gaps = 2/234 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  + Y  +  G +  D +  L+ G+VI G      +  + ++  K + + V++
Sbjct: 123 MMHPRYKVDKTYVAKVEGLITPDSIKKLRNGVVIDGKPTSRARAKILSRDAKKNTSIVSL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  ++KK+F+    KV +L R +YG   L  L +G  RE+S   +RE L
Sbjct: 183 TIHEGRYHQVKKMFDAVGHKVQKLSRTTYGTLTLDGLTSGEYRELSHNEVRELL 236


>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 =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 146/341 (42%), Positives = 204/341 (59%), Gaps = 11/341 (3%)

Query: 2   KDKNIVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +    + E   P+  R++KV++RAG+ASRRE ERMIA+ RV VNG  ++  A+NV + D 
Sbjct: 23  RKAPAIPEGAAPEGDRIAKVLSRAGVASRREAERMIAEGRVSVNGKKIDSPALNVTARDR 82

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I +DG PL +AE  R+WLY+KPIGLVT++SD  GR T+FD LP    RV++VGRLD+N+E
Sbjct: 83  ISIDGQPLPEAEGPRMWLYYKPIGLVTSNSDEKGRKTIFDELPEDMPRVMTVGRLDLNSE 142

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDGG+ R LELP+T WLR YRVR +G+   +    L+KG+VI+G  +  M V+L
Sbjct: 143 GLLLLTNDGGIKRKLELPATGWLRRYRVRINGRPKDEDFAPLRKGLVIEGERFQPMTVSL 202

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D Q+G+NAW+TVGLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +
Sbjct: 203 DRQQGANAWLTVGLREGKNREIRRAMEDIGFSVNRLLRVSYGPFQLGNLKPGEVEELRPR 262

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           ++R+QLG  L EE ++    P  +       +P +         +     + K       
Sbjct: 263 VVRDQLG--LAEEEEIPAARPTRARGGKPAGKP-MGKPAGKPMGKPAGKPAGKQAAQPSG 319

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           K   P            A     +     G  +    ++P 
Sbjct: 320 KQGNPG------RTAGKAPPARGTRPDQRGGGKRPAGKNPR 354


>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 =  302 bits (773), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 132/234 (56%), Gaps = 2/234 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  + Y  +  G +  D +  L+ G+VI G      +  + ++  K + + V++
Sbjct: 123 MMHPRYKVDKTYVAKVEGLITPDSIKKLRNGVVIDGKPTSRARAKIISRDAKKNTSIVSL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+  ++KK+F+    KV +L R +YG   L  L +G  RE+S   +RE L
Sbjct: 183 TIHEGRYHQVKKMFDAVGHKVQKLSRTTYGTLTLDGLTSGEYRELSHNEVRELL 236


>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 =  302 bits (773), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 148/338 (43%), Positives = 196/338 (57%), Gaps = 9/338 (2%)

Query: 1   MKDKNIVQENFT----PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M  +N  Q   T      R++KV++RAG+ASRRE ERMI   RV+VNG+ ++  A+NV +
Sbjct: 1   MSQENPTQPPKTDTPPGDRIAKVLSRAGLASRREAERMIEAGRVRVNGVQIDSPALNVTA 60

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            D+I VDG P+   E  R+WLYHKP GLVTT+ D  GR T+FD+LP    RV+S+GRLD+
Sbjct: 61  ADNITVDGKPVGDPEPPRMWLYHKPTGLVTTNRDEKGRGTIFDDLPEDMPRVMSIGRLDL 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           N+EGLLLLTNDG + R LELPS  WLR YRVR +G+   + L  L++GI + G  +  M 
Sbjct: 121 NSEGLLLLTNDGDVKRKLELPSNGWLRRYRVRVNGRPSDEVLEPLRRGITVDGEEFQPMT 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           VTLD Q+G+NAW+TVGLREGKNREI++  E  N  VNRLIR SYGPFQLG L  G   E+
Sbjct: 181 VTLDRQQGANAWLTVGLREGKNREIRRAMEAVNLSVNRLIRTSYGPFQLGELKPGEVEEL 240

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +K++R+QLG   +E       A       +V+ +P            + K   +K    
Sbjct: 241 KRKVVRDQLG---IEIEDNTGTAVKKKPSHIVKRKPRKPGAPGPGRPGLPKEPGEKTATG 297

Query: 297 K--QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE 332
           K    K      +         A G           R+
Sbjct: 298 KVIPGKPKPGYGKSKAPRPPSDAPGPRKFGTRVKSTRK 335


>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 =  301 bits (772), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 83/235 (35%), Positives = 131/235 (55%), Gaps = 4/235 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N   +R+ K++A AG+ASRR+ E +I   +V+VNG  +         + D I V+G P+ 
Sbjct: 6   NANMERLQKILAAAGVASRRKCEELILSGKVQVNGETVTTLGTKADPSVDVITVEGKPI- 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            AE+    +++KP G++T+ SDP GR  V D L  I  RV  VGRLD +TEGLLLLTNDG
Sbjct: 65  GAEKKLYLMFNKPKGVITSASDPQGRKIVTDYLKGIKERVYPVGRLDYDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSN 186
             A +L  P     + Y     G      L+ LK+G++++       +V       +   
Sbjct: 125 EFAHLLTHPKHHVPKTYLATVKGVPHGTALDKLKQGVMLEDGMTAPAEVEYYDIDPEEKY 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A +++ + EG+NR+++++F+  +  V RL RIS+G   LG L  G  R ++K+ +
Sbjct: 185 ATISITIHEGRNRQVRRMFDAISHPVTRLKRISFGDLVLGNLKRGLYRHLTKEEV 239


>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 =  301 bits (772), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 161/383 (42%), Positives = 213/383 (55%), Gaps = 33/383 (8%)

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 REQLGPHLLEEAQVNLDAPI-------------------------------YSSETLVRD 270
           R+QLG  L+ EA ++ DAPI                                 +  ++  
Sbjct: 265 RDQLGERLVSEADLDFDAPIINQMDARTSKKAEMKKKKKSSGGAGGGWISAKDAAAVLAK 324

Query: 271 RPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
                    +D        S++N    +K++       +  S      G       D G+
Sbjct: 325 HNKKPMRHGEDKRDGDGEGSERNPFGDRKRVGVKPTFGDRKS-FGDRDGGERKSFGDRGE 383

Query: 331 REENHRRSPSFPSKRSLRRTSAK 353
           R+    R      K    R   K
Sbjct: 384 RKSFGDRD-RGDRKPFGDRGERK 405


>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 =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 153/342 (44%), Positives = 192/342 (56%), Gaps = 5/342 (1%)

Query: 9   ENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +N TP   R++KVIARAG ASRRE ERMIA+ RV VNG +++  A+NV   D I VD  P
Sbjct: 2   DNKTPPGDRIAKVIARAGRASRREAERMIAEGRVAVNGTVIDSPALNVTDKDRITVDDTP 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E  RLWLYHK  GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLTN
Sbjct: 62  LDGPEEARLWLYHKSTGLVTTTKDEQGRPTIYDDLPDDLPRVMSVGRLDLNSEGLLLLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGL R LELPST WLR YRVR +G+     L  L+ G+ + G  +  M V+LD Q+G+N
Sbjct: 122 DGGLKRRLELPSTGWLRRYRVRINGRPTDPMLQPLRDGLTVDGQTFQPMIVSLDRQQGAN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVGLREGKNREI++        VNRLIRISYGPFQLG +  G  +EV +KILR+QLG
Sbjct: 182 AWLTVGLREGKNREIRRAMADLGLSVNRLIRISYGPFQLGQMKPGEVQEVRRKILRDQLG 241

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             L  E +     P    +   R      +       R      +       +K  +P  
Sbjct: 242 LGLDAEPEAE-AKPKPGLQPRTRKSRAAPTSAKPVPARSGAGGGKSVTGGPARKSTSPGA 300

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           +    S      G  +        R    R        +  R
Sbjct: 301 KPAGKS--GPKPGGRAGPAKGKPTRSAPSRPGAGHGPSKPRR 340


>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 =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 76/229 (33%), Positives = 122/229 (53%), Gaps = 2/229 (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 D +  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVMDLV-KVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K +
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGELSLEGLKPGEWRYLTQKEI 229


>gi|46201216|ref|ZP_00208014.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 294

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 156/300 (52%), Positives = 195/300 (65%), Gaps = 9/300 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R++K +ARAG+ SRRE ER I   RV VNG  L+  A  V   D I VDG PL +
Sbjct: 3   EEKGERIAKRLARAGLCSRREAERWIEMGRVSVNGKTLDSPACVVGPGDIILVDGTPLSE 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+TRLW YHKP GLVTTH DP+GR TVFD+LP    RVISVGRLD+N+EGLLLLTNDG 
Sbjct: 63  PEKTRLWRYHKPAGLVTTHKDPEGRPTVFDHLPEGMPRVISVGRLDLNSEGLLLLTNDGE 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LAR LELPS  WLR YRVR HG+V +D L  L+ GI I G+ YG +  TLD ++G+NAW+
Sbjct: 123 LARKLELPSNAWLRRYRVRVHGEVSEDALARLENGITIDGMAYGPISATLDRRQGANAWL 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           +V LREGKNREI++V EF  W V+RLIR+SYGPFQLGTL  G+  EV+ K+LREQ+G   
Sbjct: 183 SVSLREGKNREIRRVMEFLGWPVSRLIRVSYGPFQLGTLEEGAADEVAGKVLREQMG--- 239

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            E   V    P   S         + ++      R +K +  K+  S +K  +    RR+
Sbjct: 240 -EGKAVLKPRPENKSAGEREKEQRVAAKA-----RKQKLADDKHAASAKKAKSDAHRRRS 293


>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 =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 148/352 (42%), Positives = 202/352 (57%), Gaps = 12/352 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMIA+ RVKVNG  ++  A+NV   D I VDG PL +AE  R
Sbjct: 42  RIAKVLSRAGVASRREAERMIAEGRVKVNGTKIDSPALNVTERDRIIVDGKPLPQAEAPR 101

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVT++SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 102 LWLYNKPTGLVTSNSDEKGRRTIFDELPEDLPRVMTVGRLDLNSEGLLLLTNDGGIKRRL 161

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   +    L+KG+VI+G  +  M V LD Q+G+NAW+T+GLR
Sbjct: 162 ELPSTGWLRRYRVRINGRPKDEDFEPLRKGMVIEGERFQPMTVALDRQQGANAWLTIGLR 221

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP-----HL 249
           EGKNREI++  E   + VNRL+R+SYGPFQLG+L  G   E+  +++R+QLG        
Sbjct: 222 EGKNREIRRALEDIGFNVNRLLRLSYGPFQLGSLKLGEVEELRPRVVRDQLGLEAEDMEE 281

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
              A+     P          +P   +          K   +  G    +    P  + +
Sbjct: 282 TPAARPTRGRPGAKPGQKPSGKPGSKTAPKSGGMTFGKPKGKPTGRPADESTGRPTGKSS 341

Query: 310 LASNVWMA--KGIHSS-----FLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  +   G  S+         SG    N +  P   S ++       +
Sbjct: 342 GKPGGKPSGKPGTRSAGSFNDKPGGSGAASRNGKPGPRGASSKARPMGKNPR 393


>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 =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 133/233 (57%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I Q RVKVNG ++      V   D IEVD VP+  +E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIGQGRVKVNGKVVRELGTKVGPNDKIEVDEVPVE-SEAP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+++  +D  GR TV D  P +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFMLYKPRGVISAANDDKGRKTVVDFFPHVEERIYPIGRLDYDTSGLLLLTNDGEFANQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G   ++K+  L++G++++       +  + +   S   A V +
Sbjct: 121 LMHPKFEVDKVYVAKIKGIPSREKIRQLQRGVMLEDGKTAPARAKVLSIDKSKQTAIVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGKNR+++++F+     V +L R  YGP  L  L AG  RE++   +++ 
Sbjct: 181 TIHEGKNRQVRRMFDAIGHSVLKLKRERYGPLDLRGLNAGEARELTAHEVKQL 233


>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 =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 160/361 (44%), Positives = 215/361 (59%), Gaps = 10/361 (2%)

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 REQLGPHLLEEAQVNLDAPIY--------SSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R+QLG  L+E+A  + +API          +E    +     + + ++  R ++  + + 
Sbjct: 277 RDQLGERLIEQAGADFEAPIAIPFANKPVRAERRKPEEEKRKTGLEENAGRQERKPANRR 336

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKG--IHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
              ++K        +    + +  KG   H        +  +  R   S   + S    +
Sbjct: 337 KSREEKHEEARDRLQTKRPDDFKGKGSAAHKGKDQRPPRISKTARPEKSGQERMSGDSKA 396

Query: 352 A 352
            
Sbjct: 397 E 397


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

 Score =  300 bits (770), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 83/245 (33%), Positives = 135/245 (55%), Gaps = 3/245 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            E    +R+ KVIA AG+ASRR+ E++I + +VKVNG ++    V V   D IEVDG+PL
Sbjct: 6   SEVNEMERLQKVIAHAGVASRRKAEQLIVEGKVKVNGKVVTELGVKVSPQDRIEVDGIPL 65

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + E    +L +KP G++++  D  GR  V D    +  R+  +GRLD +T GLLLLTND
Sbjct: 66  EREE-PVYYLLYKPRGVISSVKDEKGRKVVTDFFKHVNKRIYPIGRLDYDTSGLLLLTND 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGS 185
           G  A +L  P  +  +VY  +  G   ++K+  L+KG++++       +  + +  ++  
Sbjct: 125 GEFANILMHPRYEIEKVYIAKVKGIPAREKVKQLEKGVMLEDGVTAPAKAKVLSIDKRKQ 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            A V + + EG+NR+++++FE     V +L R  Y    L  L  G  RE+S   +++  
Sbjct: 185 TAIVELRIHEGRNRQVRRMFEAIGHPVLKLKRERYAFLDLKGLNPGDYRELSPHEVKQLR 244

Query: 246 GPHLL 250
              L 
Sbjct: 245 ALALA 249


>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 =  300 bits (770), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 145/278 (52%), Positives = 186/278 (66%), Gaps = 5/278 (1%)

Query: 1   MKDKNIVQENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+    +     P  R++KV+ARAGIASRRE ERMI   RV VNG  +   A+NV   D 
Sbjct: 22  MRYGRGMSNTPPPGDRIAKVLARAGIASRREAERMIEAGRVAVNGKPINSPALNVTGKDK 81

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG P+ + E +RLWLYHKP GLVTT  D  GR+T+FD LP    RV+SVGRLD+N+E
Sbjct: 82  ITVDGKPVSEPEPSRLWLYHKPPGLVTTARDEKGRTTIFDKLPENMPRVMSVGRLDLNSE 141

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDGG+ R LELPST WLR YRVR +G+   +    L+KG+VI G  +  M VTL
Sbjct: 142 GLLLLTNDGGIKRKLELPSTGWLRKYRVRVNGRPRDEDFAPLRKGLVIDGERFQPMTVTL 201

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D Q+G+NAW+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+ ++
Sbjct: 202 DRQQGANAWLTIGLREGKNREIRRAIEDIGYVVNRLLRVSYGPFQLGDLKPGEVEEIRRR 261

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           ++R+QLG     +A+ +  AP        R RP I  +
Sbjct: 262 VMRDQLGL----DAEGDGKAPAKRPARPQRKRPAIGKK 295


>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 =  300 bits (770), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 76/229 (33%), Positives = 122/229 (53%), Gaps = 2/229 (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 D +  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIMLNKPTGYITSVKDQFGRPTVMDLV-KVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K +
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQKEI 229


>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 =  300 bits (770), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 139/304 (45%), Positives = 177/304 (58%), Gaps = 1/304 (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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK-QKKLATPV 305
                + +               +                     + G     +  A P 
Sbjct: 241 LDPHADGEARPARGRKPEGAARAEGAARSERAARPPRGAAAEGPARAGRGAGSEGAAGPA 300

Query: 306 HRRN 309
             R+
Sbjct: 301 KGRS 304


>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 =  300 bits (770), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 83/236 (35%), Positives = 138/236 (58%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K 
Sbjct: 1   MEMERLQKVIAQAGIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVNNIPLEKE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L +KP G++++ SD  GR  V D  P I  R+  +GRLD +T G+LL+TNDG  
Sbjct: 61  E-PIYFLLYKPTGVISSVSDDKGRKVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A +L  P  +  + Y  +  G +  +K+ +L+KG+V++       +V + +  ++   A 
Sbjct: 120 ANILMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVVLEDGKTAPARVKILSWDKRKEMAI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + + EG+NR+++++FE    KV +L R  Y   ++G+L  G  RE+S   +++ 
Sbjct: 180 VQLTIHEGRNRQVRRMFEALGCKVMKLKRERYAFLEVGSLRPGDARELSPHEVKQL 235


>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 =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 143/312 (45%), Positives = 191/312 (61%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +  +     T  R++KV++RAG+ASRRE ERMIA+ R+ VNG +++  A+NV   + I 
Sbjct: 57  SNDKVDHPPSTGDRIAKVLSRAGVASRREAERMIAEGRISVNGTVIDSPALNVTGQERIL 116

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL +AE  RLWLYHKP GLVTT+ D  GR T+FD+LP    RV++VGRLD+N+EGL
Sbjct: 117 VDGAPLPQAEAPRLWLYHKPSGLVTTNRDEKGRKTIFDDLPETLPRVMTVGRLDLNSEGL 176

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGG+ R LELPST WLR YRVR +G+  ++    L+KG+VI G  +  M V LD 
Sbjct: 177 LLLTNDGGIKRKLELPSTGWLRRYRVRINGRPKEEDFAPLRKGLVIDGERFQPMIVDLDR 236

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G+NAW+TVGLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  ++L
Sbjct: 237 QQGANAWLTVGLREGKNREIRRAMEDIGYNVNRLLRVSYGPFQLGDLKPGEVEELRPRVL 296

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+QLG     E          S         +          R K  +S+ +     K  
Sbjct: 297 RDQLGLEAETEESTPKPRAQRSRGPAPSKGKSDAVRAGAKPGRGKPLASRNSSEGAAKAG 356

Query: 302 ATPVHRRNLASN 313
             P   ++    
Sbjct: 357 GKPRQGQSRKKP 368


>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 =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 163/394 (41%), Positives = 222/394 (56%), Gaps = 59/394 (14%)

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 QVNLDAPIY------------------------SSETLVRDRPNIISEVPDDFTRMKKNS 289
             + DAP+                         +SET    +    ++  D   R+   +
Sbjct: 309 GADFDAPVAKPFSNRPVEAERTERPKKADEWISASETAPNKKRVREAKREDALGRLDTRA 368

Query: 290 SQKNGLSKQKK-------------LATPVHRRN--------------------LASNVWM 316
            +     +  +                P   R+                     ++NVWM
Sbjct: 369 GRPERNDRGDRKPYGERPAKRFEGPKKPYGDRDAAGGRDDAASPPKRPIDAPKRSANVWM 428

Query: 317 AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           A G        +   +    R    PS+      
Sbjct: 429 APGARPQGTKKALGSQAG--RPDRGPSRGERPSG 460


>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 =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 139/263 (52%), Positives = 177/263 (67%), Gaps = 3/263 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRRE E+MI   RV VNG ++ RAA+NV   D + VDG P+   E  R
Sbjct: 56  RIAKVLARAGVASRREAEKMIEMGRVAVNGEIITRAALNVTDKDKVTVDGKPVDAPEDPR 115

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLYHKP GLVTT  D  GR T++D+LP    RV+SVGRLD+N+EGLLLLTNDG + R L
Sbjct: 116 IWLYHKPAGLVTTTKDEQGRPTIYDDLPEELPRVMSVGRLDLNSEGLLLLTNDGSIKRRL 175

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+   D L  L+ GIV+ G  +  M+VTLD Q+G+NAW+T+GLR
Sbjct: 176 ELPSTGWLRKYRVRVNGKPSDDMLAPLRAGIVVDGQAFQPMEVTLDRQQGANAWLTIGLR 235

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++        VNRLIR+SYGPFQLG L  G  +EV  +++R+QLG   LE A+
Sbjct: 236 EGKNREIRRAMTDIGLTVNRLIRVSYGPFQLGQLKQGEVQEVRSRVVRDQLG---LEGAK 292

Query: 255 VNLDAPIYSSETLVRDRPNIISE 277
            N   P    +            
Sbjct: 293 SNRPQPTRRRKPAPDGAKQSPKR 315


>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 =  300 bits (768), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 194/323 (60%), Gaps = 5/323 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV + D I VDG PL +AE  R
Sbjct: 63  RIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVTNLDRIVVDGNPLPEAEAPR 122

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LWLY+KP GLVTT SD  GR T+FD LP    RV++VGRLD+N+EGLLLLTNDGG+ R L
Sbjct: 123 LWLYYKPNGLVTTTSDEKGRKTIFDALPEDLPRVMTVGRLDLNSEGLLLLTNDGGVKRQL 182

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G+    + ++L+KG+VI G  +  M ++LD Q+G+NAW+T+GLR
Sbjct: 183 ELPSTGWLRRYRVRINGRPQDHEFDVLRKGVVIDGERFQPMTISLDRQQGANAWLTIGLR 242

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI++  E   + VNRL+RISYGPFQLGTL  G   E+  +++R+QLG    E   
Sbjct: 243 EGKNREIRRAMEEVGYPVNRLLRISYGPFQLGTLKEGEVEELRPRVVRDQLGLAAPEGDG 302

Query: 255 VNLDAPIYSSETLVRDRPNIISE---VPDDFTRMKKNSSQKNGL--SKQKKLATPVHRRN 309
                P                +    P+     K       G   S +        +  
Sbjct: 303 EAKKKPTRPGRGPRNPGAKTAGKGIGAPNARPTGKGAVKAPEGRVFSGKTFSGKTTGKTA 362

Query: 310 LASNVWMAKGIHSSFLSDSGQRE 332
                   +G   S     G ++
Sbjct: 363 GKPAAHKGQGGKPSGPKSFGTKQ 385


>gi|256752042|ref|ZP_05492910.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256749052|gb|EEU62088.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 236

 Score =  300 bits (768), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 76/229 (33%), Positives = 122/229 (53%), Gaps = 2/229 (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 D +  +  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  KVYIILNKPTGYITSVKDQFGRPTVMDLV-KVKERIYPVGRLDYDTSGLLLLTNDGEIAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + 
Sbjct: 121 ILMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIK 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ E     V  L R   G   L  L  G  R +++K +
Sbjct: 181 IHEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQKEI 229


>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 =  299 bits (767), Expect = 3e-79,   Method: Composition-based stats.
 Identities = 151/352 (42%), Positives = 201/352 (57%), Gaps = 13/352 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K IARAGIASRR+ E MI   RV +NG +L   A+NV  +D I +DG PL   E
Sbjct: 24  EGERIAKAIARAGIASRRDAEAMIEAGRVSLNGKILTSPAINVTESDRIAIDGEPLPARE 83

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA
Sbjct: 84  RTRLWLLHKPRGVVTTARDPEGRQTVFDGLPDDLPRVVAIGRLDINTEGLLLLTNDGGLA 143

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +V+  P T WLR YRVR  G + Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+
Sbjct: 144 KVIAHPDTGWLRRYRVRAFGDITQADLDRLKKGVTVDGMEYGPVEATLDRVQGDNLWLTL 203

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L+EQLG  L E
Sbjct: 204 GLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKEQLGKSLAE 263

Query: 252 EAQVNLD-------APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +A V+ +       AP  S +   R   +  +E P      +    +     +       
Sbjct: 264 QAGVDFESPVREAIAPFGSPKKAARAAQSPRAEAPAGRGGRQGAHDEGRSEPRSGARGGA 323

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG------QREENHRRSPSFPSKRSLRRT 350
             R         A    +     +         +E   R+   P + +  +T
Sbjct: 324 AGRPPRDPARPAAPRAGARPAQRAPSPTVWRADDETRPRASKVPRRGTDPKT 375


>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 =  299 bits (767), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 140/304 (46%), Positives = 188/304 (61%), Gaps = 1/304 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRRE E++I   RV VNG  +   A+NV   D I VDG PL + E  R
Sbjct: 24  RIAKVLARAGVASRREAEKIIEAGRVTVNGKTILTPALNVTDKDRIVVDGKPLAEPEPPR 83

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLY+KPIGLVT+  D  GR TVFD LP    RV+SVGRLDIN+EGLLLLTNDG L R +
Sbjct: 84  IWLYYKPIGLVTSERDEKGRETVFDTLPDDMPRVVSVGRLDINSEGLLLLTNDGELKRKM 143

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G + + KL+ L+ GI I G+ Y  ++V  D Q+G+NAW+T+GLR
Sbjct: 144 ELPSTGWLRRYRVRINGSLSEAKLDELRAGIQIDGVHYAPVEVKFDRQQGANAWLTMGLR 203

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREI+K+ E     VNRL+RISYGPFQLGTL  G   EV ++I+R+Q+G     +  
Sbjct: 204 EGKNREIRKLMEAMGVVVNRLLRISYGPFQLGTLKPGKVEEVKQRIVRDQMGLRETPKPT 263

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
           +   A         +      ++   D  + + +   K      ++ + P    +   + 
Sbjct: 264 MVGKAAEKGKRPPPKRGTAASAKRFTDPEK-RNSDPTKRNTGAVERNSGPTSGHSAGRSA 322

Query: 315 WMAK 318
               
Sbjct: 323 GKPP 326


>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 =  299 bits (766), Expect = 4e-79,   Method: Composition-based stats.
 Identities = 148/325 (45%), Positives = 201/325 (61%), Gaps = 2/325 (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 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L+  +  + DAP+ +  T  ++ P           +   N+ +K    ++     P  +
Sbjct: 253 KLISASGADFDAPLAA--TAPKNNPVGEKIEKARPNKRGTNTPRKADPLERLTTQKPTQK 310

Query: 308 RNLASNVWMAKGIHSSFLSDSGQRE 332
                +    +G      +  G ++
Sbjct: 311 PGTKPSDGRGRGAKDKSSNKPGNKQ 335


>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 =  299 bits (766), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 89/248 (35%), Positives = 134/248 (54%), Gaps = 12/248 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           TPQR+ K++A+ G+ASRR+VE  I   R++VNG ++           D +EVDG  +   
Sbjct: 3   TPQRLQKLLAQQGLASRRQVEAWILAGRIRVNGKVVTELGFKADPERDRVEVDGRVIPFG 62

Query: 71  ERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTN 126
           +  R   L HKP+G+++T  DP GR TV D LP  ++R   +  VGRLD ++ G LLLTN
Sbjct: 63  DPARYVLLLHKPLGVLSTCKDPWGRKTVLDLLPPPWNRQIRLYPVGRLDADSSGALLLTN 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG L   L  P     ++YRV+  G+  +  L   + G+ ++G      +V         
Sbjct: 123 DGDLTLKLTHPRYHLPKIYRVQVQGRPSRATLQQWRDGVNLEGYTTLPAEVEFCPAPNFG 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             Q  +++W+ V L EG+NR+I++V E     V RL R + GP  LG L AG  R +  +
Sbjct: 183 YRQDANSSWLRVVLFEGRNRQIRRVAEQLGHPVLRLHREAIGPLHLGNLKAGQFRLLEPQ 242

Query: 240 ILREQLGP 247
            ++  L P
Sbjct: 243 EVQALLAP 250


>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 =  299 bits (766), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 92/256 (35%), Positives = 139/256 (54%), Gaps = 5/256 (1%)

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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ----LGPH 248
           + EG+ R+++++ E  +  V RL R+ YG   +G L  G+ R ++   +       +G  
Sbjct: 183 IHEGRYRQVRRMCEAVSLSVVRLRRVRYGALSMGDLKIGAYRHLTSGEVAALSDGKIGAR 242

Query: 249 LLEEAQVNLDAPIYSS 264
                +    AP    
Sbjct: 243 GGAPRRRGPSAPPRKG 258


>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 =  299 bits (766), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 160/346 (46%), Positives = 205/346 (59%), Gaps = 2/346 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + N   +R++KV+AR G+ SRRE E  I   RV++NG LL   AV V   D + VDG PL
Sbjct: 97  EANDRGERIAKVMARVGLCSRREAEVWIENGRVELNGKLLTTPAVTVTPDDKVVVDGQPL 156

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              ERTRLWLYHKP GLVTT+ DP+GR TVF+ LP    RV++VGRLDINTEGLLLLTND
Sbjct: 157 PMRERTRLWLYHKPRGLVTTNKDPEGRPTVFERLPDDLPRVLTVGRLDINTEGLLLLTND 216

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLARVLELP+T WLR YRVR  G+V Q  L+ LK GI I+G+ YG ++ TLD ++G+N 
Sbjct: 217 GGLARVLELPATGWLRRYRVRAFGKVTQPDLDTLKDGIAIEGVLYGAIEATLDKEQGNNV 276

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+TVGLREGKNRE+K+V E     VNRLIR+SYGPFQL  L  G  RE+  ++LR+QLG 
Sbjct: 277 WMTVGLREGKNREVKRVLEHLGLAVNRLIRLSYGPFQLMDLPEGDVREIRGRVLRDQLGD 336

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L EEA  + DAPI+ +     ++                   +      +        +
Sbjct: 337 ALAEEAGADFDAPIFHAPKPEAEK-KPAGAKRGGSRDGGNREGRDRDGGGRDGGGRDGGK 395

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R      WM         +D  +  +N R       K+   +   K
Sbjct: 396 REGGQGRWMTA-REGRSETDRKRAAKNERNEQREERKKGAGKGPRK 440


>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 =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 84/231 (36%), Positives = 133/231 (57%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E +I Q RVKVNG +++   V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEELILQGRVKVNGRVVKELGVKVGPRDDVEVDGIPIEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 61  VYYLLYKPRGVISSVKDDRGRKVVTDFFKDLDKRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 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|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 =  299 bits (765), Expect = 7e-79,   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|260893153|ref|YP_003239250.1| pseudouridine synthase [Ammonifex degensii KC4]
 gi|260865294|gb|ACX52400.1| pseudouridine synthase [Ammonifex degensii KC4]
          Length = 251

 Score =  298 bits (763), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 95/232 (40%), Positives = 138/232 (59%), Gaps = 1/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ KV+ARAGIASRR+ E +I   RVKVNG ++++  V V    D IEVDG P++ 
Sbjct: 1   MPEERLQKVLARAGIASRRKAEELIVAGRVKVNGQVVDKLGVKVDPERDSIEVDGKPVKL 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ER     +HKP G+VTT  DP GR  V D L  I  RV  VGRLD ++EGLLLLTNDG 
Sbjct: 61  PERLVYLAFHKPRGVVTTLHDPQGRPKVADFLKGIKERVFPVGRLDYDSEGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     + Y V   G+V ++KLNLL++GI ++       +V +  +      +
Sbjct: 121 LAHRLLHPRFHVPKTYLVWVKGEVGKEKLNLLRRGIKLEDGPTLPAEVRVLRRARGETVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + +REG+ R+I+++ +    +V RL R++ GP +LG L  G  R ++ + +
Sbjct: 181 QLTIREGRKRQIRRMLKALGCEVLRLKRVAVGPVRLGPLRPGEYRHLTPREV 232


>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 =  298 bits (763), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 176/372 (47%), Positives = 229/372 (61%), Gaps = 28/372 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              +   +R+SKV+ARAG+ASRR++ERMI + RV +NG +L+   VNV   D IEVDGVP
Sbjct: 45  TDSDAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLDTPVVNVTLADRIEVDGVP 104

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  ERTRLWLYHKP GLVTT++DP+GRSTVFDNLP    RV+S+GRLDINTEGLLLLTN
Sbjct: 105 IRGIERTRLWLYHKPTGLVTTNADPEGRSTVFDNLPEELPRVMSIGRLDINTEGLLLLTN 164

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T WLR YRVR HG++DQD L+ LK GI + G+ YG ++ TLD  +GSN
Sbjct: 165 DGGLARALELPATGWLRRYRVRAHGEIDQDALDKLKDGIAVDGVLYGSIEATLDRTQGSN 224

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L      EV  + LR+QLG
Sbjct: 225 VWITMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPESHVVEVRGRTLRDQLG 284

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK--------- 297
           P L+EEA+ N DAPIY++  +  +     +         +    ++  LS+         
Sbjct: 285 PRLIEEAKANFDAPIYNTTAVAAEEEAEPAAPEKRERPRRDEDKRERALSRLDTKRDDRH 344

Query: 298 ------------------QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
                             + K   P+ +R  ++NVWMA G        + +  +N + + 
Sbjct: 345 GGARKEDDRRDGGRRDDEKPKRPQPLGQR-RSANVWMAPGARPLGEKAAAKAAKNAQTAR 403

Query: 340 SFPSKRSLRRTS 351
               +   +   
Sbjct: 404 RRGEQAPAKNDR 415


>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 =  298 bits (763), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 97/288 (33%), Positives = 136/288 (47%), 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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  Q  +VY  +  G   +  L  L+ GIV+ G      +  L +Q   N  A 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|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 =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 77/229 (33%), Positives = 123/229 (53%), Gaps = 2/229 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  GIASRR+ E  I Q RVKVNG +++     +    D IE D   +R+ E+ 
Sbjct: 3   RLQKYLAECGIASRRKCEEYILQGRVKVNGKVVKELGTKIDPDVDIIEFDDKIVRREEKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T+  DP GR TV D +  +  R+  VGRLD +T GLLLLTNDG LA +
Sbjct: 63  VYIMLYKPAGYITSVKDPFGRPTVLDLV-KVKERIYPVGRLDFDTSGLLLLTNDGELANI 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  + ++ Y  +  G   ++++   + G++I G      ++ +   K   + V + +
Sbjct: 122 LMHPKHEIVKTYVAKIKGIPTKEEMERFENGLIIDGRKTAKAKIRILNVKNGTSVVEIQI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR++KK+ +     V  L R   G  +L  L  G  R +++  +R
Sbjct: 182 HEGRNRQVKKMCKAIGHPVIALKRTKIGELELKGLKPGEWRYLTEDEIR 230


>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 =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 169/403 (41%), Positives = 222/403 (55%), Gaps = 64/403 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++AR G+ASRR+VERM+A+ R++VNG LL+  AV V  +D IEVDG  +   ERTR
Sbjct: 42  RIAKILARVGVASRRDVERMVAEGRIRVNGKLLDSPAVVVSLSDRIEVDGEEVAGIERTR 101

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW+YHKP GLVTT+ DP+GR TVF+ LP    RV+S+GRLDINTEGLLLLTNDGGLAR L
Sbjct: 102 LWIYHKPAGLVTTNRDPEGRRTVFETLPKHLPRVLSIGRLDINTEGLLLLTNDGGLARTL 161

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP T WLR YRVR +G +DQ++L+ LK GI + G+ YG ++ TLD ++G N W+T+GLR
Sbjct: 162 ELPETGWLRRYRVRAYGDIDQNRLDTLKDGIAVDGVLYGAIEATLDRKQGHNVWITMGLR 221

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNREIK V       VNRLIRIS+GPFQLG +  G   E+  + LREQLG  L+EE+ 
Sbjct: 222 EGKNREIKNVLSALGLDVNRLIRISFGPFQLGDVREGDVVEIKSRTLREQLGVRLIEESG 281

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTR------------------------------ 284
            N DAP+  S    +                                             
Sbjct: 282 ANFDAPLNDSAPASKKEAKPSPAAKPAQREWISSSEKVERARARFDTKPGRPDRDGKPGE 341

Query: 285 ---------------------MKKNSSQKNGLSKQKKLATPVHR----RNLASNVWMAKG 319
                                 +  S    G   ++  A P  R    R+ ASNVWMA G
Sbjct: 342 RRSEWGPGKERGERKSSGDKASRPRSGGPEGKRNEEPGAKPAKRGFIQRSRASNVWMAPG 401

Query: 320 IHSSFLSDSGQ-----REENHRRSPSFP----SKRSLRRTSAK 353
                 +D  +      +  H+++ + P     + S  +  AK
Sbjct: 402 ARPVADADKPEGGRGGAKSGHKKADADPRAETRRGSFPKGRAK 444


>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 =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 127/263 (48%), Positives = 165/263 (62%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           N  +    P R++K +ARAG+ SRRE ER IA  RV VNG LL+  A  V   D + VDG
Sbjct: 29  NTAETRDGPMRIAKAMARAGLCSRREAERWIADGRVSVNGKLLKTPACEVGPKDKVIVDG 88

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  A   +LW YHKP G+VTTHSDP GR TVF+ LP    RVIS+GRLD NTEGLLLL
Sbjct: 89  KPLPAASTPQLWRYHKPKGVVTTHSDPQGRPTVFEKLPPEMPRVISIGRLDFNTEGLLLL 148

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LAR  ELP+  W+R YRVR  G+V    L  LK G+ I G+ YG ++ ++DT +G
Sbjct: 149 TTDGALARHFELPANGWVRRYRVRAKGRVTPADLAKLKDGVEIDGVSYGPIEASVDTVQG 208

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +N+W+++ +REGKNRE++ V  +    VNRLIR+S+GPFQL  L  G+   V +++L  Q
Sbjct: 209 ANSWLSISIREGKNREVRNVLAYLGLTVNRLIRVSFGPFQLLDLAPGAVEAVRRRVLVAQ 268

Query: 245 LGPHLLEEAQVNLDAPIYSSETL 267
           LGP       ++           
Sbjct: 269 LGPKAAASLGLSESQEERKERHA 291


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

 Score =  297 bits (762), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 126/234 (53%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+   E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 61  GYYLFYKPKGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  297 bits (761), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 81/232 (34%), Positives = 124/232 (53%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+++AG+ASRR+ E +I   RV+VNG ++      V    D I+VDG  +++ E+
Sbjct: 2   ERLQKVMSQAGVASRRKSEDIITAGRVEVNGEVVTELGTKVDPEQDTIKVDGQQIKR-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +TT  DP  R TV D +  +   V  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  LVYLLLNKPQGYITTVDDPHNRRTVIDLIQDVSQAVHPVGRLDKDTEGLLLLTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y     G  +Q K+  L+KGI ++       +  L  +    A V++ 
Sbjct: 121 ALTHPSHGIDKTYMATVKGVPNQSKIEALEKGIKLKDGWTAPAEAKLVAELAERAVVSLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+  ++K++ +     V  L RI +GP  L  L  G  R ++   ++E 
Sbjct: 181 IHEGRKHQVKRMLKSVGHPVEELKRIKFGPLDLTGLSPGEYRHLTNSEIKEL 232


>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 =  297 bits (761), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 78/246 (31%), Positives = 123/246 (50%), Gaps = 5/246 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M  +   +E   P RV K +ARAG+ASRR  E ++   RV VNG ++      V    D 
Sbjct: 1   MPQQ---EERIVPMRVQKFLARAGVASRRRSEDLMTAGRVCVNGEVVTELGAKVDPRVDT 57

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINT 118
           + VDG  +R  +     + +KP G +TT SDP GR+ V + +P   +  +  VGRLD +T
Sbjct: 58  VTVDGREVRLTDGPVTIMLNKPCGFITTMSDPYGRACVAELVPSDDYPGLFPVGRLDTDT 117

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL + DG L   L  P     + Y     G++  + L  L+ G+ +         VT
Sbjct: 118 SGLLLFSTDGELGNSLLHPRHHVDKTYEACVQGRISDEALQTLRDGVELDDGVTSPAAVT 177

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L ++    + +T+ + EG+ R+++++ +     V  L R  +GP  LG L  GS RE++K
Sbjct: 178 LVSRSKEKSRITLVIHEGRTRQVRRMCQKVGHPVLELHRAQFGPLTLGDLPEGSWRELTK 237

Query: 239 KILREQ 244
             +   
Sbjct: 238 AEVESL 243


>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 =  297 bits (761), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 137/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKVVTELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR  V D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 61  IYFLLYKPTGVISSVSDDKGRKVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG+V++       +V + +  ++   A V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVVLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE    KV +L R  Y   + G+L  G  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALGCKVMKLKRERYAFLEAGSLRPGDARELSPHEVKQL 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 =  297 bits (761), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 141/266 (53%), Positives = 177/266 (66%), Gaps = 2/266 (0%)

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 QLGPHLLEEAQVNLDAPIYSSETLVR 269
           QLG  + EE +     P        R
Sbjct: 245 QLG--MKEEPEAEQPKPARPKPQRRR 268


>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 =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 140/233 (60%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       QV + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQVKIISWDKRKETAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELSPHEVKQL 233


>gi|13476819|ref|NP_108388.1| hypothetical protein mlr8253 [Mesorhizobium loti MAFF303099]
 gi|14027580|dbj|BAB53849.1| mlr8253 [Mesorhizobium loti MAFF303099]
          Length = 546

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 148/307 (48%), Positives = 200/307 (65%), Gaps = 3/307 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +         +R++K +ARAG+ASRR+ E +IA  RVKVNG  L   A NVM  D I +D
Sbjct: 88  RPAEATEEAGERIAKRLARAGLASRRDAEELIAAGRVKVNGRALTSPAFNVMPGDIIHLD 147

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ +   ERTRL+L+HKP G+VTT+ DP+GR TVFD LP+   R++++GRLDINTEGLLL
Sbjct: 148 GMEIPPIERTRLFLFHKPAGVVTTNRDPEGRKTVFDVLPAELPRLMTIGRLDINTEGLLL 207

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDGGL+RVLELP+T WLR YRVR HG+V++  L  L++GI + G+ YG ++ +LD ++
Sbjct: 208 LTNDGGLSRVLELPATGWLRRYRVRVHGKVEESALAGLREGIAVDGVFYGAIEASLDREQ 267

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           GSNAW+T+GLREGKNRE+K +       V RLIRISYGPFQL  L  G   E+  ++LR+
Sbjct: 268 GSNAWLTIGLREGKNREVKNILGALGLDVTRLIRISYGPFQLEDLPEGHVLEIKGRVLRD 327

Query: 244 QLGPHLLEEAQVNLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           QLG  L+EE+  N DA I   +S++ + R            FTR  +      G   + +
Sbjct: 328 QLGERLVEESGANFDAEIAKPFSNKPVRRTEVREPEPERPKFTRDGERRPIGEGGLIKNR 387

Query: 301 LATPVHR 307
                 R
Sbjct: 388 KRREGSR 394


>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 =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 126/234 (53%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+   E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 61  GYYLFYKPRGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 146/340 (42%), Positives = 197/340 (57%), Gaps = 3/340 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R++KV++RAG+ASRRE ERMIA  RV+VNG +++  A+NV+   D I VDG  + + E  
Sbjct: 46  RIAKVLSRAGLASRREAERMIADGRVEVNGKVIDSPALNVVVGKDRIVVDGKQVEEPEPP 105

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLWLYHKP GLVTT SD   R T+FD+LP    RV++VGRLD+N+EGLLLLTNDGG+ R 
Sbjct: 106 RLWLYHKPAGLVTTTSDELDRKTIFDDLPEDLPRVMTVGRLDLNSEGLLLLTNDGGIKRQ 165

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPST WLR YRVR +G+        L+KG+VI+G  +  M VTLD Q+G+NAW+TVGL
Sbjct: 166 LELPSTGWLRRYRVRINGRPQDSDFEPLRKGLVIEGEKFQPMIVTLDRQQGANAWLTVGL 225

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           REGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++R+QLG    EE 
Sbjct: 226 REGKNREIRRAMEDIGFSVNRLLRLSYGPFQLGQLKPGEVEELRPRVVRDQLGLAAPEEE 285

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           Q +   P  + +  +R +P                +                  +     
Sbjct: 286 QDSPKRP-GTRQRPMRGKPGTRPGSGQSDRGTDSRAGAGRTGRPGSAPNAKGTGKGTGKP 344

Query: 314 VWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRRTSA 352
           +  A G      +   G R  +     S P   +     +
Sbjct: 345 LSKAGGKSMGKPTGRPGARSSDKAAGNSGPKGNARPSGKS 384


>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 =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 87/231 (37%), Positives = 133/231 (57%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIARAGIASRR+ E MI Q RVKVNG ++    V V   D +EVDG+P+ + E  
Sbjct: 2   ERLQKVIARAGIASRRKAEEMILQGRVKVNGRVVTELGVKVGPRDDVEVDGIPVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A +
Sbjct: 61  VYYLLYKPRGVISSVKDEKGRKVVTDFFKDIHQRIYPIGRLDYDTSGLLLLTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G   +++L   +KG++++       +V L +  +K   A 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|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 =  296 bits (759), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 143/296 (48%), Positives = 189/296 (63%), Gaps = 10/296 (3%)

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 SLREGKNREIRRVMEHLGLPVSRLIRVAYGPFQLGQLEEGTVDEIPGKIMREQLGK---- 239

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                 DAP        + + N  +  P   T     SS    +++  +     H+
Sbjct: 240 ------DAPPPPRRAEAKAKGNKGAAPPPKGTLSLPESSNTGRVARIARATRRAHK 289


>gi|229160522|ref|ZP_04288517.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622932|gb|EEK79763.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 140/233 (60%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLERGVALEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  296 bits (758), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 144/241 (59%), Positives = 174/241 (72%)

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 G 246
           G
Sbjct: 241 G 241


>gi|311030759|ref|ZP_07708849.1| pseudouridine synthase [Bacillus sp. m3-13]
          Length = 242

 Score =  296 bits (758), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 136/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E +I + +V+VN  +++   V V   D IEV+G+P+ + E+ 
Sbjct: 2   ERLQKVIAHAGIASRRKAEELIKEGKVRVNDKVVKELGVKVNPNDKIEVEGIPVER-EKP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR    D  P I  R+  VGRLD +T GLLL+TNDG  A V
Sbjct: 61  VYFLLYKPRGVISSVSDDKGRKVATDFFPYIEERIYPVGRLDYDTSGLLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P+++  +VY  +  G   ++ +  L++GI ++       ++ L +  +  + +   +
Sbjct: 121 LMHPASEVEKVYVAKLKGIPSREAIKSLERGIKLEDGKTAPARIKLLSMERTKNTSIFEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  YG   L  L AG  RE++   +++ 
Sbjct: 181 SIHEGRNRQVRRMFEAIGHPVMKLKRERYGFLNLHGLSAGEARELTPHEVKQL 233


>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 =  296 bits (758), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 135/237 (56%), Gaps = 3/237 (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+    L+HKP G++T+ SD  GR  V D  P +  R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  PEKI-YILFHKPTGVITSVSDEKGRKVVTDYFPGLNLRIFPVGRLDYDTSGLLLLTNDGD 120

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

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V + + EG+NR+++++F  F  +V +L RI YGP  L  L AG  RE++   ++  
Sbjct: 181 LVEITIYEGRNRQVRRMFAHFGHEVVKLSRIEYGPLTLKGLNAGDARELTPHEVKTL 237


>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 =  296 bits (758), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 161/291 (55%), Positives = 202/291 (69%), Gaps = 2/291 (0%)

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 QVNLDAPIYS--SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            V+ D PI    S   V  R +       D+        +K    K+++ A
Sbjct: 424 GVDFDGPINKPFSNAPVEGRQDARPSKKSDWVSAGGKVDRKTFGEKKREEA 474


>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 =  295 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 137/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG ++      V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVTELGTKVTPQDKVEVNHIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR  V D    I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRKVVTDFFQDIPQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L+KG++++       +V + +  ++   + V +
Sbjct: 121 LMHPKYKVEKTYVAKVKGPLTGEKIRMLEKGVILEDGKTSPARVKIISWDKRKEMSIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE    KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEAIGCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  295 bits (757), Expect = 5e-78,   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|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 =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 158/339 (46%), Positives = 199/339 (58%), Gaps = 9/339 (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 GLREGKNREIRRVMEALGFVVNRLIRISYGPFQLGALEAGEVQEVRRKVLRDQLG----- 252

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
              ++ DAP       +     I+ E P      K         S  +            
Sbjct: 253 ---LDQDAPDLQRSRRIIRNEKIVDETPKRGRPAKPGFKPGAKPSGDRPSYGDRPSFGDK 309

Query: 312 SNVWMAK-GIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                   G   SF       ++     PSF  K    R
Sbjct: 310 PRFGDKPRGDRPSFGDKPRFGDKPRGDRPSFGDKPRGDR 348


>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 =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 127/234 (54%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+   E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 61  GYYLFYKPRGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>gi|289578329|ref|YP_003476956.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
 gi|289528042|gb|ADD02394.1| pseudouridine synthase [Thermoanaerobacter italicus Ab9]
          Length = 236

 Score =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 76/228 (33%), Positives = 120/228 (52%), Gaps = 2/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  GIASRR+ E  I Q RVKVNG  ++   V +    D IE D   +R+ ++ 
Sbjct: 3   RLQKYLAECGIASRRKCEEYILQGRVKVNGKEVKELGVKINPDVDIIEFDDKIVRREKKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T+  D  GR TV D +  +  R+  VGRLD +T GLLLLTNDG +A +
Sbjct: 63  VYIMLNKPTGYITSVKDQFGRPTVMDLV-KVKERIYPVGRLDYDTSGLLLLTNDGEIANI 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  + ++ Y  +  G   Q++L   + G++I        ++ +   K   + V + +
Sbjct: 122 LMHPRHEIVKTYIAKIKGIPTQEELERFRNGLLIGDYLTSKAEIEILAVKNGTSVVEIKI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EGKNR+++++ E     V  L R   G   L  L  G  R +++K +
Sbjct: 182 HEGKNRQVRRMCEAIGHPVISLTRTKIGDLSLEGLKPGKWRYLTQKEI 229


>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 =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 156/343 (45%), Positives = 208/343 (60%), Gaps = 8/343 (2%)

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  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLL 124
                TRL+L+HKP GLVTT+ DP+GR TVFD L        RV+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 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK--KLA 302
           LGP L   A V+     +  +      P    + P       K+ ++ +G + +   +  
Sbjct: 324 LGPSLAAAAGVDWTR--HDEDAAEPAAPERARKTPSKTRTEGKSVTKSHGAAPRPSSRTF 381

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           T    R        AK    S    S  R E+  R  + P KR
Sbjct: 382 TKDKPREDEHPARTAKPAPRSRKHISLLRAEDENRKGA-PRKR 423


>gi|167629967|ref|YP_001680466.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
 gi|167592707|gb|ABZ84455.1| pseudouridine synthase [Heliobacterium modesticaldum Ice1]
          Length = 333

 Score =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 97/279 (34%), Positives = 140/279 (50%), Gaps = 3/279 (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 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
            ++EA  +        +T    R    ++V        K
Sbjct: 242 GMKEATAHGRDERR--QTARPSRTAATAKVASAHKDAGK 278


>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 =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 139/233 (59%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRNVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++        V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPANVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 139/233 (59%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A +
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++        V + +  ++   A V +
Sbjct: 121 LMHPKYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAHVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  295 bits (757), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 141/233 (60%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G++++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 140/233 (60%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>gi|229058206|ref|ZP_04196594.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228720070|gb|EEL71654.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 140/233 (60%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  DK+ +L++G+ ++       QV + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGDKIRMLERGVALEDGKTAPAQVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  295 bits (756), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 81/235 (34%), Positives = 130/235 (55%), Gaps = 4/235 (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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EG+NR+++++FE  +  V RL RISYG   L  L  G  R ++   + + L
Sbjct: 181 ITIHEGRNRQVRRMFEAISHPVLRLKRISYGDLLLQNLKRGLYRHLTADEINQLL 235


>gi|315172332|gb|EFU16349.1| conserved hypothetical protein [Enterococcus faecalis TX1346]
          Length = 238

 Score =  295 bits (756), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 126/234 (53%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA AG+ SRR+ E +I + RVKVNG +++     V   D +EVDGVP+   E  
Sbjct: 2   ERLQKAIAHAGVTSRRKAEELIVKGRVKVNGQVVKELGTQVSKQDTVEVDGVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  SD  GR  V D    +  R+  VGRLD +T GLLLLTNDG  ++ 
Sbjct: 61  GYYLFYKPRGVISAVSDDKGRKVVTDYFTDVTERIYPVGRLDYDTSGLLLLTNDGSFSQK 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F+   + V +L R  YG   L  L  G  R+++KK + + L
Sbjct: 181 TIHEGRNHQVKKMFQAVGFPVQKLKRERYGELTLQGLRPGQYRDLTKKEISQLL 234


>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 =  295 bits (756), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 142/308 (46%), Positives = 195/308 (63%), Gaps = 2/308 (0%)

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 GPHLLEEAQVNLDAPIYSSETLVRDRPNI--ISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           G    +++      P  +       RP    +   P D        S    + + +    
Sbjct: 241 GLAKGDDSGHAKAKPERTGTQPPGRRPGTLRLRSKPTDIEVESDRPSSGGRVQRTRADMV 300

Query: 304 PVHRRNLA 311
               R+  
Sbjct: 301 KSAPRSGT 308


>gi|126650120|ref|ZP_01722353.1| RluB [Bacillus sp. B14905]
 gi|126593292|gb|EAZ87254.1| RluB [Bacillus sp. B14905]
          Length = 243

 Score =  295 bits (755), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 131/233 (56%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E++I + +VKVNG ++      V ++D IEV+GV L K E  
Sbjct: 2   ERLQKVIAYAGIASRRKAEQLILEGKVKVNGKVIRELGTKVSNSDTIEVEGVKLEK-EDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G ++  +D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 61  VYFLLYKPRGTISAVTDDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +V++ +  +K   A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGIPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK  +++ 
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLFGLAPGEFRELSKHEVKQL 233


>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 =  295 bits (755), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 145/348 (41%), Positives = 203/348 (58%), Gaps = 7/348 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K++AR+G+ SRR+VER+IA+ RV +NG +L   AV V   D + VDG  + + E  
Sbjct: 151 ERIAKLLARSGVGSRRDVERLIAEGRVAINGQVLTTPAVKVEPGDILTVDGAVVGEPEPV 210

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R++ YHKP+GLVTTH DP GR TVF+ LP    R+ISVGRLD+N+EGLLLLTNDGGLAR 
Sbjct: 211 RVFRYHKPVGLVTTHKDPQGRPTVFEALPEGLPRLISVGRLDLNSEGLLLLTNDGGLARA 270

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----GSNAWV 189
           LELP+T  +R YR R HG++ Q++L+ LK GI ++G+ YG ++  LD  K    G+N W+
Sbjct: 271 LELPATGVVRRYRARAHGRITQERLDTLKDGITVEGVRYGAIEARLDKAKEGHQGANLWL 330

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           TV L+EGKNRE+++V E    KVNRLIR+SYGPF LGTL  G   EV  +++REQL  H+
Sbjct: 331 TVTLQEGKNREVRRVLEALGLKVNRLIRLSYGPFALGTLDVGEIEEVGPRVIREQLEGHI 390

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ---KNGLSKQKKLATPVH 306
             E     D P Y S      R    S   +      +  ++   K G +K K  A P  
Sbjct: 391 PPENMPKGDRPQYRSPARKSRRAQAESRQAELVPPRPEAPAKKAYKAGWAKPKAKAKPHA 450

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           +    +     +                 +R+ S        +   ++
Sbjct: 451 KTAGKAAKAKLQAKIEGKTIGPRHEPAAGKRTASQGKPPGRPKGGPQR 498


>gi|52143877|ref|YP_082953.1| pseudouridylate synthase [Bacillus cereus E33L]
 gi|51977346|gb|AAU18896.1| pseudouridylate synthase [Bacillus cereus E33L]
          Length = 242

 Score =  295 bits (755), Expect = 8e-78,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 141/233 (60%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVAPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G++++       +V + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVMLEDGKTAPARVKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  295 bits (755), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I   RVKVNG  +      V   D I VDGVP+  +E  
Sbjct: 2   ERLQKVLAHAGVASRRQSEKLIMSGRVKVNGAAVTELGTKVGVHDQILVDGVPIS-SEAP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G+V+T +D  GR TV D + ++  RV  VGRLD +T GLLLLTNDG LA  
Sbjct: 61  IYIMLYKPRGVVSTANDDKGRKTVVDLVENVSQRVYPVGRLDYDTSGLLLLTNDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  + Y  R  G    D +  L++GI + G  Y   +  +         A +++
Sbjct: 121 LTHPRYEVEKTYIARVTGVPTNDAMKQLRQGITVDGETYAPAKSKVLSAADDRKTAIISL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGKN ++KK+       V +L R  YG   L  L AG  R++  + ++E 
Sbjct: 181 TIHEGKNHQVKKMLAAVGCPVEKLKREQYGFLTLKGLNAGEARQLKPEEVKEL 233


>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 =  295 bits (755), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 153/361 (42%), Positives = 205/361 (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 LEEAQVNLD-------APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS------ 296
            E+A V+ +       AP  S +   R      +       R +  S  ++G        
Sbjct: 258 AEQAGVDFESPVRETIAPFGSPKKATRATQAAPAGRGRQGARDEGASEARSGSRGGAAGR 317

Query: 297 --------KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                      +       R  +  VW A        S   +R  + + + +  ++R   
Sbjct: 318 PPRDPARPAAPRAGARPAPRPPSPTVWRADEETRPRASKVPRRGMDPKTARAEAAERGRE 377

Query: 349 R 349
           R
Sbjct: 378 R 378


>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 =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 77/228 (33%), Positives = 121/228 (53%), Gaps = 2/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A  GIASRR+ E  I Q RVKVNG  ++   V +    D IE D   +R+ ++ 
Sbjct: 3   RLQKYLAECGIASRRKCEEYILQGRVKVNGKEVKELGVKINPDVDIIEFDDKIVRREKKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T+  D  GR TV D +  +  R+  VGRLD +T GLLLLTNDG +A +
Sbjct: 63  VYIMLNKPTGYITSVKDQFGRPTVMDLV-KVKERIYPVGRLDYDTSGLLLLTNDGEIANI 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y  +  G   +++L   + G++I+       ++ + T K   + V + +
Sbjct: 122 LMHPRHEIAKTYIAKIKGIPTEEELERFRNGLLIEDYVTSKAEIKVLTVKKGTSVVEIKI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EGKNR+++K+ E     V  L+R   G   L  L  G  R ++ K +
Sbjct: 182 HEGKNRQVRKMCEAIGHPVISLMRTKIGELSLEGLKPGEWRYLTNKEI 229


>gi|229166414|ref|ZP_04294170.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228616988|gb|EEK74057.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 242

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 139/233 (59%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>gi|121535833|ref|ZP_01667633.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121305605|gb|EAX46547.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 241

 Score =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 85/232 (36%), Positives = 123/232 (53%), Gaps = 4/232 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
           P+R+ K++++AGIASRR  E++I   RV VNG ++      V    D + VDG P+  AE
Sbjct: 2   PERLQKILSQAGIASRRAAEKLILDGRVAVNGKIITELGAKVDWPRDRVTVDGKPI-AAE 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                L +KP G++T+  DP GR TV D L  +  RV  VGRLD NTEGLLLLTNDG L 
Sbjct: 61  APVYILLNKPKGVITSLKDPRGRKTVIDLLKDVPERVYPVGRLDYNTEGLLLLTNDGDLT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
             L  PS +  + Y  +  G  ++++L+ L+ GI +         V L         A V
Sbjct: 121 HALTHPSHEIKKTYVSKIAGLPNEEQLDRLRAGIKLSDGMTSPAAVRLLDFDPVKQVAVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EG+NR+++++FE     V  L R  Y    L  L  G  R ++   +
Sbjct: 181 EITIHEGRNRQVRRMFEAIGHPVKSLKRTKYAFLTLTGLKRGEYRRLTPDEV 232


>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 =  294 bits (754), Expect = 1e-77,   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|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 =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 139/233 (59%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +  ++   A V +
Sbjct: 121 LMHPRYKIEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 139/233 (59%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++ SD  GR+ V D  P I  R+  +GRLD +T G+LL+TNDG  A V
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRNVVTDFFPEIRQRLFPIGRLDYDTSGVLLMTNDGEFANV 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G +  +K+ +L++G+ ++       Q  + +  ++   A V +
Sbjct: 121 LMHPRYKVEKTYVAKIKGPLTGEKIRMLERGVALEDGKTAPAQAKIISWDKRKEMAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 181 TIHEGRNRQVRRMFEALDCKVMKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  294 bits (754), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 146/344 (42%), Positives = 195/344 (56%), Gaps = 4/344 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             E    +R++KV+A AGIASRRE ER+I + RV VNG +L   A  VM+ D + VDG  
Sbjct: 10  TPEEEGGERIAKVLAHAGIASRREAERLIEKGRVSVNGEILRTPAFKVMAGDDVRVDGES 69

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + +   TR+W YHKP+GL+TTHSDP GR TVF  LP    RVISVGRLD+N+EGLLLLTN
Sbjct: 70  IGQRPPTRVWRYHKPVGLLTTHSDPQGRDTVFQTLPQDMGRVISVGRLDLNSEGLLLLTN 129

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LARVLELPST W R YRVR +G      L  L+ G V+ G+ YG ++VT+D + G+N
Sbjct: 130 DGELARVLELPSTGWTRRYRVRAYGNASDKALAELENGTVVDGVVYGPVEVTVDRRTGAN 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+TVG++EGKNRE++KV +     VNRL+R++YGPFQLG+L  G   E    +LR+QLG
Sbjct: 190 VWLTVGIKEGKNREVRKVLQSVGLTVNRLMRVAYGPFQLGSLKRGEISESKLSVLRDQLG 249

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                +       P+   ET   D     ++      R  + S  K           P  
Sbjct: 250 KLYPLDTD---GLPLKPGETAKPDTRTGTAKAKPKANRPHQKSGGKPRAGLDADSIMPAG 306

Query: 307 RRNLASNVW-MAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            ++  +  W  AK   +     S + +       +   K    R
Sbjct: 307 GKSKTAKGWAKAKPKANEKPKSSKRSDPKGSGGKASKGKSDADR 350


>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 =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 131/233 (56%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNGI++      V ++D IEV+GV L K E  
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLIVEGKVKVNGIVVRELGTKVSNSDTIEVEGVKLEK-EDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G ++  +D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 61  VYFLLYKPRGTISAVTDDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +V++ +  +    A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGIPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDENAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK  +++ 
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLYGLAPGEFRELSKHEVKQL 233


>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 =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 139/268 (51%), Positives = 178/268 (66%), Gaps = 2/268 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +      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  L EE       P   ++   + +  
Sbjct: 241 G--LTEEEAGRTPGPQAKAKPRGKPQRR 266


>gi|144897623|emb|CAM74487.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 287

 Score =  294 bits (753), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 142/287 (49%), Positives = 189/287 (65%), Gaps = 9/287 (3%)

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 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           LG                 ++T  R RP    + P       +N  +
Sbjct: 250 LG---------QGGGNWAKADTEDRPRPPSNHKKPHAGKASHENRRR 287


>gi|312143709|ref|YP_003995155.1| pseudouridine synthase [Halanaerobium sp. 'sapolanicus']
 gi|311904360|gb|ADQ14801.1| pseudouridine synthase [Halanaerobium sp. 'sapolanicus']
          Length = 236

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 80/232 (34%), Positives = 126/232 (54%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +IA+ RVKVNG ++      V    D IEVDG  + K E+
Sbjct: 2   ERLQKVMAHAGVASRRKSEEIIAEGRVKVNGEIVTEMGFKVDPKKDEIEVDGEVIAK-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L HKP G +TT SDP  R TV D +P +  RV   GRLD ++ GLL+LTNDG L  
Sbjct: 61  KVYLLLHKPEGYITTVSDPKERQTVMDLIPDLKQRVYPAGRLDYDSSGLLILTNDGDLCY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y VR  G +  +  N  ++G+VI G      ++       +     + 
Sbjct: 121 KLTHPKKEVDKRYWVRAKGTIFAEDFNKFEEGMVIDGRKTAPAKIANINYLDNYTEFEIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++     + V +L R ++    L  L  G  R ++++ +++ 
Sbjct: 181 IHEGRNRQVRRMCRIAGFSVVKLKRTAFAFLSLDGLAEGEYRYLNEEEIKKL 232


>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 =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 115/231 (49%), Gaps = 2/231 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
           P R+ K +ARAG+ASRR  ER+I+  RV VNGI++      V    D + VDG  +    
Sbjct: 49  PLRLQKFLARAGVASRRGSERLISAGRVAVNGIVITELGTKVDPLVDEVCVDGAIVTWGA 108

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                  +KP G++TT  D  GR  V D +P   +  +  +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|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 =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 140/248 (56%), Gaps = 4/248 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N        +R+ KV+A+AGIASRR  E +I Q RVKVNG ++      V+STD I
Sbjct: 1   MNRNNERGRPRQEERLQKVLAQAGIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRI 60

Query: 61  EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 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 DTQKGSNAW--VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            + KG  +     + + EG+NR+++++F+   + ++ L R+ +GP +L  +L  G+ R +
Sbjct: 181 VSPKGRGSLPTYEITIHEGRNRQVRRMFKAVGFPLSTLKRLRFGPLELDPSLAPGAFRTL 240

Query: 237 SKKILREQ 244
           SK  ++  
Sbjct: 241 SKTEIQHL 248


>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 =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 140/292 (47%), Positives = 189/292 (64%), Gaps = 1/292 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV  +D I VD  PL   E
Sbjct: 20  EGERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDSDRITVDDEPLPARE 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA
Sbjct: 80  RTRLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLA 139

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +V+  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+
Sbjct: 140 KVIAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLTL 199

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L E
Sbjct: 200 GLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLAE 259

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +A V+ ++P+  +       P   +         +     ++  + + +  +
Sbjct: 260 QAGVDFESPVRET-IAPFGSPKKATRATQAAPAGRGRQGARDEGASEPRSGS 310


>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 =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 139/269 (51%), Positives = 180/269 (66%), Gaps = 2/269 (0%)

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 LREQLGPHLLEEAQVNLDAPIYSSETLVR 269
           +R+QLG  + +E +     P        R
Sbjct: 241 MRDQLG--MPQEPEAEPAKPARPKPQRRR 267


>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 =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 141/294 (47%), Positives = 188/294 (63%)

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 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            E+A V+ ++P+  +                      +  ++  G S+ +  + 
Sbjct: 258 AEQAGVDFESPVRETIAPFGSPKKATRAAQAAPAGRGRQGARDEGASEARSGSR 311


>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 =  293 bits (751), Expect = 2e-77,   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|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 =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 85/233 (36%), Positives = 135/233 (57%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG ASRR+ E ++A+ RVKVNG  ++   V V  +D IEVDG+P+ + E  
Sbjct: 2   ERLQKVIAHAGFASRRKAEELMAEGRVKVNGKTVKELGVKVSPSDRIEVDGIPVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++  SD  GR  V D    I  R+  VGRLD +T G+L+LTNDG  A +
Sbjct: 61  VYFLLYKPRGVISAVSDDKGRKVVTDFFEGIKQRIYPVGRLDYDTSGILILTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  PS +  +VY  +  G   ++ +  L++G+V++       +  L +  +K   A V +
Sbjct: 121 LMHPSNEIEKVYVAKIKGIPSKEGMRSLQRGVVLEDGKTAPAKTKLLSMDKKKQTAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  YG   L  L AG  RE++   +++ 
Sbjct: 181 SIHEGRNRQVRRMFEAIGHPVLKLKRERYGYLTLQGLSAGDARELTAHEVKQL 233


>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 =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 140/292 (47%), Positives = 188/292 (64%), Gaps = 1/292 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K IARAGIASRR+ E +I   RV +NG +L   A+NV   D I VD  PL   E
Sbjct: 20  EGERIAKAIARAGIASRRDAEALIEAGRVTLNGKVLTSPAINVTDADRITVDDEPLPARE 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRLWL HKP G+VTT  DP+GR TVFD LP    RV+++GRLDINTEGLLLLTNDGGLA
Sbjct: 80  RTRLWLLHKPRGVVTTARDPEGRPTVFDGLPEELPRVVAIGRLDINTEGLLLLTNDGGLA 139

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +V+  P T WLR YRVR  G V Q  L+ LKKG+ + G+ YG ++ TLD  +G N W+T+
Sbjct: 140 KVIAHPDTGWLRRYRVRAFGDVTQPDLDKLKKGLTVDGMEYGPIEATLDRAQGDNVWLTL 199

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           GLREGKNRE+K++ E     VNRLIR+S+GPFQLG L  G   E+  K+L++QLG +L E
Sbjct: 200 GLREGKNREVKRILEHLGLSVNRLIRLSFGPFQLGDLEVGLVEEIRTKVLKDQLGKNLAE 259

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +A V+ ++P+  +       P   +         +     ++  + + +  +
Sbjct: 260 QAGVDFESPVRET-IAPFGSPKKATRATQAAPAGRGRQGARDEGASEARSGS 310


>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 =  293 bits (751), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 144/357 (40%), Positives = 196/357 (54%), Gaps = 9/357 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIE 61
           D     +     R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV +  D I 
Sbjct: 41  DTPATGDGPEGDRIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVVLGKDRIV 100

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG P++  E  RLW+YHKP GLVTT +D   R T+FD LP    RV++VGRLD+N+EGL
Sbjct: 101 VDGNPMQDPEPPRLWMYHKPSGLVTTTNDELDRRTIFDALPEDMPRVMTVGRLDLNSEGL 160

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGG+ R LELPST WLR YRVR +G+        L++G+VI+G  +  M V LD 
Sbjct: 161 LLLTNDGGIKRQLELPSTGWLRRYRVRINGRPKDTDFEPLRQGLVIEGERFQPMTVALDR 220

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G+NAW+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++
Sbjct: 221 QQGANAWLTIGLREGKNREIRRAIEDIGFTVNRLLRLSYGPFQLGNLKPGEVEELRPRVV 280

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD-----DFTRMKKNSSQKNGLS 296
           R+QLG    E  +                        PD                     
Sbjct: 281 RDQLGLAAPETEEDEKPKRPVRQRPGAGKPGTKPGAKPDFKSGGKPGGKPSGKPSGRSFG 340

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              + +     R+ A       G  +S    S +        P+    R+  RTS +
Sbjct: 341 SADRSSEKPGDRSGARPAGKPGGKFASKGKPSDRFAGKSEGKPTG---RTADRTSDR 394


>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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 125/232 (53%), Gaps = 1/232 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ KV+A AG+ASRR+ E++I +  VKVNG +++     V  +D +EVD VP+ K E 
Sbjct: 2   SERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVDEVPISK-EV 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L  
Sbjct: 61  PVYYLLYKPRGVITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDN 120

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

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+N ++KK+F      V +L R SYG   L  L  G  R +    + E 
Sbjct: 181 IHEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPHEVEEL 232


>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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 82/232 (35%), Positives = 139/232 (59%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E   
Sbjct: 3   RLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-PV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A VL
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVG 192
             P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V + 
Sbjct: 122 MHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 182 IHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 149/331 (45%), Positives = 206/331 (62%), Gaps = 5/331 (1%)

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 NLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           N DA +   +S++ + R            FTR  +      G   + +      R     
Sbjct: 464 NFDADVTKPFSNKPVRRTEVREPEPERPKFTRDGERRPIGEGGLIKNRKRREGSRDEALG 523

Query: 313 NVWMAK--GIHSSFLSDSGQREENHRRSPSF 341
            +  +       SF   + + E +    P  
Sbjct: 524 KLSTSPDRNAEKSFGERAPRPERSFGDKPRG 554


>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 =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 128/241 (53%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRK 69
              +R+ K+I++AGIASRR  E+MI + RV+V+G ++      V    H I VDG  +  
Sbjct: 2   MQEERLQKIISQAGIASRRAAEKMILEGRVRVDGQVVRELGTKVDPAAHTILVDGKKIAG 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+    L +KP G ++T  D  GR TV D LP +  RV  VGRLD NTEGLLL+TNDG 
Sbjct: 62  EEQHVYLLLNKPKGYLSTAKDDRGRRTVLDLLPEVRERVYPVGRLDNNTEGLLLITNDGA 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  + Y     G++ ++KL +L+ G++++       +V+L  ++     V
Sbjct: 122 LMNGLLHPRFEVEKTYHAGVTGKLTEEKLQMLRDGLLLEDGMTAPAKVSLLPEREPGERV 181

Query: 190 T------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                  + + EG+NR+++++F      V  L R+ +    L  +  G  R ++++ +  
Sbjct: 182 RGLTRAAITIHEGRNRQVRRMFAAVGCDVKSLKRVRFAGLTLKGVARGQHRALTEEEVSS 241

Query: 244 Q 244
            
Sbjct: 242 L 242


>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 =  293 bits (750), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 126/232 (54%), Gaps = 2/232 (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 D +P+   R+  +GRLDI+T GLL+LTNDG LA 
Sbjct: 61  YTYVMINKPIGIVSTAKDEKNRKTVVDLVPND-ERIYPIGRLDIDTTGLLILTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY     G   +  L+ L+ GI I G      ++ +     S++ V V 
Sbjct: 120 KLMHPRKEIDKVYIATVEGTPSKSGLDKLRNGITIDGYKLSKSEIKILKSYESDSIVRVT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR++KK+FE     V +L RIS+GP +L  L  G+ R ++ + ++E 
Sbjct: 180 IHEGRNRQVKKMFERIGNPVKKLKRISFGPIELANLEIGAYRYLTNEEIKEL 231


>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 =  292 bits (749), Expect = 4e-77,   Method: Composition-based stats.
 Identities = 81/238 (34%), Positives = 134/238 (56%), 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 E    +L++KP G++++  D  GR TV D    +  R+  VGRLD +T GLLL+T
Sbjct: 61  PIEK-ETLHTYLFYKPRGVISSVKDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QK 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|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 =  292 bits (749), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 143/282 (50%), Positives = 178/282 (63%), Gaps = 12/282 (4%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
               +     R++KV++RAGIASRRE ERMI + RV VNG  +   A+NV   D I VDG
Sbjct: 13  KTPTDTPPGDRIAKVLSRAGIASRREAERMIEEGRVTVNGETIASPALNVTDKDRITVDG 72

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL   E  R+W+YHKP GLVTT  D  GR T+FD LP    RV++VGRLD+N+EGLLLL
Sbjct: 73  KPLEAPEAPRMWMYHKPAGLVTTTKDEQGRETIFDKLPEDLPRVMTVGRLDLNSEGLLLL 132

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGG+ R LELPST WLR YRVR +G+  ++ L  L+ GI + G  +  MQV LD Q+G
Sbjct: 133 TNDGGIKRKLELPSTGWLRRYRVRVNGKPTEEMLKPLRDGITVDGQTFQPMQVELDRQQG 192

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           SNAW+TVGLREGKNREI++        VNRLIRISYGPFQLG +  G   E+  +I+R+Q
Sbjct: 193 SNAWLTVGLREGKNREIRRAMSDIGLTVNRLIRISYGPFQLGQMKVGEVVELRGRIVRDQ 252

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           LG   LE A+     P          R      +PD   R +
Sbjct: 253 LG---LEGAKTTRPEP---------SRRRKPRPIPDKSRRTR 282


>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 =  292 bits (748), Expect = 5e-77,   Method: Composition-based stats.
 Identities = 136/306 (44%), Positives = 185/306 (60%), Gaps = 2/306 (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 LLEEAQVNLDAPIYSSETLVRDR--PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              E     D    +    +R    P    +           +  +    +++    P  
Sbjct: 266 FAAEDAAAADGRPAAGPVRMRYDRLPRAARDAAPPSATKGGRAPAREAGGQEQARRGPRA 325

Query: 307 RRNLAS 312
           + +  S
Sbjct: 326 KPSARS 331


>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 =  292 bits (748), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 145/282 (51%), Positives = 180/282 (63%), Gaps = 3/282 (1%)

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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                + Q    A     +     RP   +       R    
Sbjct: 241 LDARPKPQRRRAAGRDDGDAA---RPRGPARPGPTGPRKPPR 279


>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 =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 89/235 (37%), Positives = 138/235 (58%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A+AGIASRR  E +I Q RVKVNG ++      V+STD I VDG  L   +  
Sbjct: 16  ERLQKVLAQAGIASRRHAEEIILQGRVKVNGEVIRTLGTKVVSTDRIVVDGRLLSIPQND 75

Query: 74  R-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L HKP G +T+ +DP GR TV + +P I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 76  YAYYLLHKPTGYITSVTDPQGRKTVMELMPKIPRRVYPVGRLDYDTSGLLLLTNDGDLAH 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW--VT 190
            L  PS    + YRV    ++ +  L  L+KG++++       ++   + KG  +     
Sbjct: 136 RLMHPSYGVEKTYRVEVGEKIPEQALKRLEKGVLLEDGKTAPARIREVSPKGRGSLPTYE 195

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EG+NR+++++F+   + ++ L R+ +GP +L  +L  G+ R +SK  ++  
Sbjct: 196 ITIHEGRNRQVRRMFKAVGFPLSTLKRLRFGPLELDPSLAPGAFRTLSKTEIQHL 250


>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 =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 125/232 (53%), Gaps = 1/232 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ KV+A AG+ASRR+ E++I +  VKVNG +++     V  +D +EVD VP+ K E 
Sbjct: 2   SERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVKELGTKVTESDEVEVDEVPISK-EV 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L  
Sbjct: 61  PVYYLLYKPRGVITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDN 120

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

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+N ++KK+F      V +L R SYG   L  L  G  R +    + E 
Sbjct: 181 IHEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPHEVEEL 232


>gi|315646387|ref|ZP_07899505.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315278030|gb|EFU41350.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 251

 Score =  292 bits (747), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 132/246 (53%), Gaps = 4/246 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I + +V+VNG  +           D I V G P++  E+
Sbjct: 2   ERLQKIMAQAGVASRRKCEELILEGKVQVNGETVTELGTKADPAQDMITVSGKPIKH-EK 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 EEAQVN 256
            +   N
Sbjct: 241 AKPGGN 246


>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 =  292 bits (747), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 128/235 (54%), Gaps = 6/235 (2%)

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
               L++KP G++TT SD  GR TV D    I  R+ ++GRLD NTEGLLL+TNDG LA 
Sbjct: 62  HYY-LFNKPKGVITTCSDEQGRPTVLDYFKRIKDRIYAIGRLDQNTEGLLLMTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWV 189
           +L  P     + Y V+  G +    L  L  G+++         V     DT  G  + +
Sbjct: 121 ILMHPGHMVDKTYEVKIKGHIADAVLQQLADGVLLSDGMTAPADVYYVGYDTHTGITS-L 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EGKNR+++++ E F ++V+ L R+ Y    L  +  G+ R ++++ + E 
Sbjct: 180 EITIHEGKNRQVRRMMEHFGYQVHNLRRVQYAFLTLSGVKRGAYRALTREEVMEL 234


>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 =  292 bits (747), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 124/232 (53%), Gaps = 1/232 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ KV+A AG+ASRR+ E++I +  VKVNG ++      V  +D +EVD VP+ K E 
Sbjct: 2   SERLQKVMAHAGVASRRKAEKLIVEGHVKVNGKVVRELGTKVTESDEVEVDEVPISK-EV 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L  
Sbjct: 61  PVYYLLYKPRGVITAVTDDKHRKTVIDLLSEVTERIYPVGRLDYDTSGLLLLTNDGDLDN 120

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

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+N ++KK+F      V +L R SYG   L  L  G  R +    + E 
Sbjct: 181 IHEGRNHQVKKMFLALGHPVEKLSRQSYGFLNLDGLQPGDYRRLKPHEVEEL 232


>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 =  292 bits (747), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 88/238 (36%), Positives = 130/238 (54%), Gaps = 2/238 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R+ KV+A AG+ASRRE E++I   RV+VNG  +      V   D I VDG  L +  
Sbjct: 4   TKERLQKVMAAAGVASRRECEKIILAGRVQVNGKPVTELGTRVGKADRITVDGKALHRKS 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +L +KP G+VTT  DP GR TV D +  +  R+  VGRLD  TEGLLL+TNDG LA
Sbjct: 64  ARHTYLLYKPGGVVTTMKDPQGRRTVADLMAGLHQRLYPVGRLDYLTEGLLLMTNDGELA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
           + L  PS    + Y V  HG+V ++KL++L+ G+ ++        V +            
Sbjct: 124 QHLTHPSHHVDKTYEVEVHGRVPEEKLDVLRLGVPLEDGLTAPAVVYVKKWDPEKNLTRF 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           TV + EG+NR+++++ +F  + V  L RI  G   L  +  G  RE++ + +     P
Sbjct: 184 TVTIHEGRNRQVRRMCDFIGFPVKSLKRIQVGTLTLEGMKKGEFRELTPEEVASLESP 241


>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 =  291 bits (746), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 144/290 (49%), Positives = 190/290 (65%), Gaps = 8/290 (2%)

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 WLTVGLREGKNREIRRAMESIGLSVNRLIRISYGPFQLGPLAPGAVEEVRRRVMRDQLG- 244

Query: 248 HLLEEAQVNLDAPIYS-----SETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             L++A+ +   P  S     +    + R  + +      +   +     
Sbjct: 245 --LDDAEADAPRPKRSRAGQRTGPETKTRDKVRARTGGKTSGGGRTPDAP 292


>gi|163791509|ref|ZP_02185915.1| RluB [Carnobacterium sp. AT7]
 gi|159873232|gb|EDP67330.1| RluB [Carnobacterium sp. AT7]
          Length = 244

 Score =  291 bits (746), Expect = 1e-76,   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|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 =  291 bits (746), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 143/287 (49%), Positives = 185/287 (64%), Gaps = 4/287 (1%)

Query: 7   VQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +    TPQ  R++KV++RAG+ASRRE ERMI   RVKVNG  +   A+NV ++D I VDG
Sbjct: 1   MTSELTPQGDRIAKVLSRAGVASRREAERMIEAGRVKVNGKPISSPALNVQASDKITVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   E  RLWLYHKP GLVTT +D  GR T++  LP+   RV+SVGRLDIN+EGLLLL
Sbjct: 61  KDVSPPEPARLWLYHKPTGLVTTDNDEKGRETIYSALPADLPRVMSVGRLDINSEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG + R LELP+T WLR YRVR +G+     L  L++GI  +G  +  MQVTLD Q+G
Sbjct: 121 TNDGSIKRRLELPTTGWLRRYRVRVNGRPTDATLEPLRRGISSEGENFQPMQVTLDRQQG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+T+GLREGKNREI++        VNRLIRISYGPFQLG L +G+  EV +K+LR+Q
Sbjct: 181 ANAWLTMGLREGKNREIRRALAELGLTVNRLIRISYGPFQLGELKSGAVEEVRRKVLRDQ 240

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           LG  L E+A  +    + +            +       R  K   +
Sbjct: 241 LG--LEEDAGTDPAKRLEAGRKRGPPIRRTRATAGAKPARYAKKPRK 285


>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 =  291 bits (746), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 86/240 (35%), Positives = 127/240 (52%), Gaps = 4/240 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AG+ASRR+ E +IA+  VKVNG +++     V   D ++VD VP+ K 
Sbjct: 1   MNEERLQKVIAHAGVASRRKAEELIAKGHVKVNGEVVKELGTKVTPNDEVKVDEVPISK- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L +KP G++T  +D   R TV D L  +  R+  VGRLD +T GLLLLTNDG L
Sbjct: 60  EAPVYYLLYKPRGVITAVTDDKHRKTVVDILEEVPERIYPVGRLDYDTSGLLLLTNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  + Y  +  G V  D L  L+ G+VI+       +  L      ++ V 
Sbjct: 120 DNKLTHPKYEVEKTYVAKVKGIVTNDDLKHLRTGVVIEHRKTAKAKTKLIRTNKDSSIVQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQLGP 247
           + + EG+N ++K +FE   + V +L R +YG   L  L  G  R +     + L+E  G 
Sbjct: 180 LTIHEGRNHQVKNMFEKIGYPVEKLSRETYGFLTLKGLQPGDYRPLKPHEVEELKELTGK 239


>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 =  291 bits (746), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 93/231 (40%), Positives = 129/231 (55%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+NR+++++ E     V+RL RI Y    LG L  G  R++S+  +   
Sbjct: 183 HEGRNRQVRRMCEAVGCPVSRLKRIRYAFLDLGDLRPGQHRQLSRNEVARL 233


>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 =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 81/230 (35%), Positives = 130/230 (56%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEK-EAL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFYKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 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|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 =  291 bits (745), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 139/272 (51%), Positives = 180/272 (66%), Gaps = 3/272 (1%)

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 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           G   L +  +  D+   +      +RP    +
Sbjct: 241 G---LSDKDLGKDSAKPTRVRKPVNRPVTGKK 269


>gi|325679067|ref|ZP_08158661.1| pseudouridylate synthase [Ruminococcus albus 8]
 gi|324109191|gb|EGC03413.1| pseudouridylate synthase [Ruminococcus albus 8]
          Length = 244

 Score =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 124/234 (52%), Gaps = 2/234 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K+IA +G  SRR+ E  IA  +V VNG  +      +   D I VDG+ + + 
Sbjct: 1   MEKIRIQKIIAESGFCSRRKAEEFIAAGKVTVNGRKVTLGDKALPGKDLIVVDGIKIDQP 60

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           ++      + HKP G VTT +D   R  V D L  +  RV  VGRLD ++EGLLLLTNDG
Sbjct: 61  KKRNLYYIMLHKPRGYVTTMNDELNRKCVTDLLDGVPERVYPVGRLDKDSEGLLLLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           G A  +  PS    + YRV     ++ ++L  L  G+ I G    +  V +  ++ +   
Sbjct: 121 GFANDIMHPSRHVAKTYRVTVRPDINDEQLVKLASGVEIDGRMTAECSVVVLDKQPNRVV 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + + EG+NR+I+K+ E    +V RL R + GP +LG L AG  RE+    LR
Sbjct: 181 LQMTIHEGRNRQIRKMCEAVGLEVARLKRTAVGPLRLGMLKAGEWRELKPDELR 234


>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 =  290 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 133/240 (55%), Gaps = 3/240 (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 E    +L++KP G++++  D  GR TV D    +  R+  VGRLD +T GLLL+TN
Sbjct: 61  IEK-ETLHTYLFYKPRGVISSVKDDKGRKTVVDYFEDVPYRLYPVGRLDYDTSGLLLMTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKG 184
           DG LA  L  P  +  +VY  +  G +  + ++ L  G+ I G      ++ +    +K 
Sbjct: 120 DGELANKLMHPRNEVPKVYVAKIKGLLSPEDIHSLTHGVRIDGRKSAPAKLKILKTDEKK 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +   V + + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +   
Sbjct: 180 NTQIVQLTIHEGHYHQVKRMFEAVHHFVEKLSREKYAFLTLKSLTSGEYRELTHEEVSRL 239


>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 =  290 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 157/346 (45%), Positives = 205/346 (59%), Gaps = 5/346 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           F   R++KV+ARAG  SRR+ E  IA+ RV VNG +L+  A NV   D IEVDG PL + 
Sbjct: 38  FEGDRIAKVMARAGACSRRDAEIWIAEGRVAVNGAVLDSPAFNVREGDRIEVDGAPLAER 97

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
           E TRL+L+HKP GLVT+  DP+GR TVF  L        R++SVGRLDINTEGLLLLTND
Sbjct: 98  EPTRLFLFHKPEGLVTSAKDPEGRDTVFGFLEERHPDLPRLVSVGRLDINTEGLLLLTND 157

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP+T W R YRVR HG++DQ +L+ L+KG+ +  + Y  ++  LD  +G+N 
Sbjct: 158 GGLARTLELPATGWTRRYRVRAHGEIDQARLDELRKGVTVDDVDYAPIEARLDRVQGANV 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+T+ LREGKNREIK+V E     VNRLIRIS+GPFQLG L  G+  EV  KILREQLG 
Sbjct: 218 WITMALREGKNREIKRVLEHLGLGVNRLIRISFGPFQLGELAEGAVEEVKLKILREQLGK 277

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L E A V+  +P    ET   +            TR +K+ S      ++ +       
Sbjct: 278 GLAELAGVDFSSPRR--ETAEPEHVIEEERRQHAKTRARKHVSTLRAEVEESRGKKAPRA 335

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           R   S     KG   +  +    R      +P   ++ + R  + +
Sbjct: 336 RIERSATADRKGRAVAVETIKPVRRRLEEEAPPLATRNARRFQAER 381


>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 =  290 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 89/237 (37%), Positives = 125/237 (52%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I    VKVNG  +    V V  +DH+EVDGVPL  AE+ 
Sbjct: 3   ERLQKVMAEAGIASRRKSEVLITSGHVKVNGKTVTTLGVKVEPSDHVEVDGVPLN-AEKL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+VTT  D  GR TV D    +  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 62  VYYLFYKPRGVVTTVHDEKGRKTVLDFFEDVPERIYPVGRLDYDTSGLLIMTNDGALANR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           L  P  +  + Y  +  G      L  L+ G+ I G      +  L     K +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|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 =  290 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 93/255 (36%), Positives = 142/255 (55%), Gaps = 5/255 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + +EN    R+ K IA +G+ASRR  E M+ + RVKVNG+++    + V  TD IEVDG
Sbjct: 16  QVNEENQIRMRLQKAIALSGLASRRRAEEMMTEGRVKVNGVVVTELGMKVCGTDTIEVDG 75

Query: 65  V-----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                  ++  E    ++ +KP+G++T+  DP GR TV D L  +  RV  VGRLD +T 
Sbjct: 76  KTVQSLEVKGKENKVYYMLNKPVGVITSLRDPQGRKTVRDLLGDVKERVYPVGRLDYDTS 135

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++YRV+   ++    +  L+KG++++       +V  
Sbjct: 136 GILLLTNDGDLAYRLTHPKFGVSKIYRVQTGSRIPPKSIEQLEKGLLLEDGWTAPAKVHR 195

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             Q  ++  V + + EG+NR+I+++FE   + V RL R S+GP   G L  G  R +S+K
Sbjct: 196 LPQGQNDHIVEITIHEGRNRQIRRMFERIGYPVQRLHRKSFGPLFTGELAPGGHRRLSQK 255

Query: 240 ILREQLGPHLLEEAQ 254
            +R       L  AQ
Sbjct: 256 EIRALKAAVGLSSAQ 270


>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 =  290 bits (744), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 85/235 (36%), Positives = 128/235 (54%), Gaps = 3/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRRE E++IA  RVKVNG ++      V + D IEVD VP+   E  
Sbjct: 2   ERLQKVMAHAGVASRRESEKLIAAGRVKVNGEVVRELGYKVSNNDRIEVDQVPI-YKEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KPIG+++   D   R  V D  P I  R+  VGRLD NT GLLLLTNDG  A  
Sbjct: 61  VYYVFYKPIGVISAVKDDKDRKVVTDFFPGIEQRIYPVGRLDYNTSGLLLLTNDGEFANT 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  ++   L++G+ I G+     Q  + +  +      + +
Sbjct: 121 LMHPRYEINKVYVAKVEGVITGEERKQLERGVEIDGVKTAPAQAKILSVDKDKKTTIIEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + EG+NR+++K+ E     V +L R  YG   L  L  G +R + K  + E L 
Sbjct: 181 VIHEGRNRQVRKMLEAVGHPVTKLKRERYGFLDLKGLKPGDSRTLLKHEIEELLA 235


>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 =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 83/229 (36%), Positives = 127/229 (55%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +ARAG+A+RR+ E++I   RVKVNG +++     V   D +EVDG  + K E+ 
Sbjct: 2   ERLQKYLARAGVAARRDAEQLILAGRVKVNGKVVKELGFKVSDRDVVEVDGR-IVKPEKL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP G +TT  DP GR TV   L      RV  VGRLD+NTEGLL+LTNDG LA 
Sbjct: 61  VYILMYKPAGYITTVDDPFGRPTVLSLLAGKVKERVFPVGRLDMNTEGLLILTNDGDLAM 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  Q  + Y     G  ++ KL  L++G++++       +V     +G N+W+ + 
Sbjct: 121 ALTHPKHQVPKTYLALVRGTPNRAKLKELERGVLLEDGYTAPAKVNFKKPEGKNSWIEIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+ R+++++F+     V +LIR          L  GS R ++   +
Sbjct: 181 IHEGRKRQVRRMFKKIGHPVLKLIRTRIAFLTGYGLKKGSFRYLTPAEV 229


>gi|65318840|ref|ZP_00391799.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Bacillus anthracis str.
           A2012]
          Length = 242

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 82/232 (35%), Positives = 139/232 (59%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E   
Sbjct: 3   RLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-PV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP G++++ SD  GRS V D  P I  R+  +GRLD +T G+LL+TNDG  A VL
Sbjct: 62  YFLLYKPTGVISSVSDDKGRSVVTDFSPEITQRLFPIGRLDYDTSGVLLMTNDGDFANVL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVG 192
             P  +  + Y  +  G +  +K+ +L++G+ ++       +V + +  ++   A V + 
Sbjct: 122 MHPRYKVEKTYVAKIKGPLTGEKIRMLERGVTLEDGKTAPARVKIISWDKRKEMAIVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++FE  + KV +L R  Y   ++G+L  G  RE++   +++ 
Sbjct: 182 IHEGRNRQVRRMFEALDCKVVKLKRERYAFLEVGSLRPGDARELTPHEVKQL 233


>gi|292558985|gb|ADE31986.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 245

 Score =  290 bits (743), Expect = 2e-76,   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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 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|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 =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 140/317 (44%), Positives = 187/317 (58%), Gaps = 14/317 (4%)

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 L--LEEAQVNLDAPIYS------------SETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                 A+V       +                    P          T+ K  + ++  
Sbjct: 250 AEQFAPAEVRPSKGAATGSTGKWTGGKPVGRKAGDKPPAKPERTKPGGTKPKLKTFREKK 309

Query: 295 LSKQKKLATPVHRRNLA 311
                K   P   R   
Sbjct: 310 ADTAGKRKAPNADRRRR 326


>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 =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 127/239 (53%), Positives = 173/239 (72%)

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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           W+TV L EGKNRE+++V +     V RLIRI+YGPF L  L  G+  E++ K+LREQLG
Sbjct: 185 WLTVSLSEGKNREVRRVLQHLGLTVTRLIRIAYGPFALADLPRGAVEEINAKVLREQLG 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 =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 120/234 (51%), Gaps = 2/234 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K+I+ +G  SRR+ E  IA  +V VNG         +   D I VDG+ + + 
Sbjct: 1   MEKVRIQKIISESGFCSRRKAEEFIAAGKVTVNGRPCTLGDKALPGKDLIVVDGIKIDQP 60

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +      + HKP G VTT +D   R  V D L  +  RV  VGRLD N+EGLLLLTNDG
Sbjct: 61  RKRTLYYIMLHKPRGYVTTMNDELDRKCVTDLLTGLPERVYPVGRLDKNSEGLLLLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + YRV     ++ ++L  L  G+ I G    +  VT+  ++     
Sbjct: 121 AFANDIMHPSKHVNKTYRVTVRPDINDEQLVKLASGVEIDGRMTSECSVTVLDKQPGRVV 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + + EG+NR+I+K+ E    +V RL R + GP +LG L  G  RE+    LR
Sbjct: 181 LQMTIHEGRNRQIRKMCEAVGLEVARLKRTAIGPLRLGMLKPGEYRELKPDELR 234


>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 =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 91/249 (36%), Positives = 130/249 (52%), Gaps = 13/249 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV--PLR 68
            PQR+ K++A+ G+ASRR+VE  I   RV+VNG ++           D IEV+G   PL 
Sbjct: 3   EPQRLQKLLAQQGLASRRQVEAWILAGRVRVNGKVVTELGSKADPERDCIEVNGQVIPLA 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLT 125
           K     + L HKP+G+++T +DP GR TV D LP  + R   +  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 KILREQLGP 247
             L+  L P
Sbjct: 243 HELQALLAP 251


>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 =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 79/230 (34%), Positives = 125/230 (54%), 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  KVYAILNKPKGYLTAASDYRGRKTVIDLL-NFKERVFPVGRLDFNTTGLLIVTNDGEIFN 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|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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 81/238 (34%), Positives = 130/238 (54%), Gaps = 3/238 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +  
Sbjct: 15  KVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAV-Y 73

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG 
Sbjct: 74  NEEPVYYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGE 133

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNA 187
              ++  PS    +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++
Sbjct: 134 FTNMMTHPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHS 193

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +
Sbjct: 194 IVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKKEVSQLI 251


>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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 126/234 (53%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR  E +IAQ +V+VNG ++    + V    D I V+G  ++  E+
Sbjct: 2   ERLQKVLAHAGVASRRHCEELIAQGKVQVNGQVVREQGIKVDPLKDKIVVNGQQVKL-EQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G++T+ +DP GR  V D L  I  RV  VGRLD +T GLLLLTNDG LA 
Sbjct: 61  HVYLLLYKPTGVITSVTDPQGRRVVIDLLKGIQERVYPVGRLDYDTSGLLLLTNDGELAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVT 190
            L  PS +  +VYR    G    +K+  L  GI ++       Q  L   + S   A V 
Sbjct: 121 RLAHPSYEIDKVYRAWVKGIPSPEKVRKLATGIRLEDGMTSPGQSKLLKAESSSQRALVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++ E     V  L RI  G   L  L  G  R+++ + +   
Sbjct: 181 LTIHEGRNRQVRRMCEAIGHPVLTLERIRLGFLTLDGLKPGEFRKLTHEEVESL 234


>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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 80/230 (34%), Positives = 129/230 (56%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKITELGTKVEPSDKIEVNGVPIEK-ETL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFYKPRGVISSVKDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 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|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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 137/267 (51%), Positives = 177/267 (66%), Gaps = 1/267 (0%)

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 EAQVNLDA-PIYSSETLVRDRPNIISE 277
           E      A P +  +           E
Sbjct: 243 EGHAEPKAKPAFKGKRRKAPDARKSGE 269


>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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 125/233 (53%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           L  P  Q  +VY  +    +D++ L  L++GI+I G      +  +         + V +
Sbjct: 121 LMHPRYQVDKVYVAKLDKILDKEALRKLERGIIIDGKKTSKARAKVLDTNLEKKMSVVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG N ++KK+FE     V +L R  +GP  LG +  G  RE+    + E 
Sbjct: 181 TIHEGWNHQVKKMFEAVGAHVVKLKREKFGPLNLGKMQPGEYRELLPNEVTEL 233


>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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 83/235 (35%), Positives = 122/235 (51%), Gaps = 1/235 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
            T +R+ K +ARAG+ASRR+ E +I   RV V+G ++      +      + VDG  +  
Sbjct: 1   MTKERLQKYLARAGVASRRQGEELIRAGRVSVDGRIVTTLGQLIDSEKAEVMVDGRKVLP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R  + +KP G VTT +DP GR  V D LP    R+  VGRLD +  GLLLLTNDG 
Sbjct: 61  PPHCRTIVLNKPYGCVTTMADPQGRRKVIDLLPDQEERLYPVGRLDYDATGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  + YR    GQ        L++GI + G      QV L       + +
Sbjct: 121 LAHRLMHPRYKVAKTYRATVAGQFSPAARRRLREGITLDGRLTIPEQVRLVKTSSERSVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + +REG+   +K++       V +L RI+YGP +LG L  G+ RE++++ +R  
Sbjct: 181 ELTIREGRYHLVKRLCAAVGCPVLKLKRIAYGPLRLGRLALGTWRELTQEEVRRL 235


>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 =  290 bits (742), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 82/230 (35%), Positives = 129/230 (56%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E+MI   +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 8   ERLQKVIAQAGIASRRKAEKMITAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEK-EAL 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 67  HTYLFYKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ I G      ++ +    +K     V +
Sbjct: 127 LMHPRNEVPKVYVAKIKGILSPEEIRSLTHGVRIDGRKSAPAKLKILKTDEKKKTQIVQL 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG   ++K++FE  +  V +L R  Y    L +L +G  RE++ + +
Sbjct: 187 TIHEGHYHQVKRMFEAVHHFVEKLAREKYAFLTLKSLNSGEYRELTNEEV 236


>gi|300070794|gb|ADJ60194.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 239

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 130/234 (55%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E  
Sbjct: 1   MRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAV-YNEEP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 60  VYYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  PS    +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++ V++
Sbjct: 120 MTHPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +
Sbjct: 180 TIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKKEVSQLI 233


>gi|329667453|gb|AEB93401.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 239

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 81/230 (35%), Positives = 129/230 (56%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V  +D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPSDKIEVNGVPIEK-EAL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L+ KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFCKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 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|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 =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 143/357 (40%), Positives = 198/357 (55%), Gaps = 9/357 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIE 61
           D     +     R++KV++RAG+ASRRE ERMIA+ RV VNG +++  A+NV +  D I 
Sbjct: 41  DTPATGDGPEGDRIAKVLSRAGVASRREAERMIAEGRVAVNGKVIDSPALNVVLGKDRIV 100

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG  ++  E  RLW+YHKP GLVTT +D   R T+FD LP    RV++VGRLD+N+EGL
Sbjct: 101 VDGNQMQDPEPPRLWMYHKPSGLVTTTNDELDRRTIFDELPEDMPRVMTVGRLDLNSEGL 160

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGG+ R LELPST WLR YRVR +G+        L++G+VI+G  +  M V LD 
Sbjct: 161 LLLTNDGGIKRQLELPSTGWLRRYRVRINGRPKDTDFEPLRQGLVIEGERFQPMTVALDR 220

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G+NAW+T+GLREGKNREI++  E   + VNRL+R+SYGPFQLG L  G   E+  +++
Sbjct: 221 QQGANAWLTIGLREGKNREIRRAIEDIGFTVNRLLRLSYGPFQLGNLKPGEVEELRSRVV 280

Query: 242 REQLGPHLLE-EAQVNLDAPIYSSETLVRDRPNIISE----VPDDFTRMKKNSSQKNGLS 296
           R+QLG    E E       P+       +  P   ++                       
Sbjct: 281 RDQLGLTAPETEEDEKPKRPVRQRPGAGKPGPKPGAKPDFKSGSKPGGKPGGKPSGRSFG 340

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
              + +     R+ A       G  +     S +        P+    R+  RTS +
Sbjct: 341 SSDRSSEKPGDRSGARPAGKPGGKFAGKGKPSDRFAGKAEGKPTG---RTADRTSDR 394


>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 =  289 bits (741), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 85/237 (35%), Positives = 133/237 (56%), Gaps = 7/237 (2%)

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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  PS    + Y     G      L+ LKKG++++       +V      ++ + + + 
Sbjct: 124 LLTHPSHHVPKTYYATVKGVPHGSLLDQLKKGVMLEDGLTAPAEVEYQDIDEEKNMSTIR 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILREQ 244
           + + EG+NR+++++F+     V +L R+ +G   L TL  G  R ++    K LR+Q
Sbjct: 184 ITIYEGRNRQVRRMFDAIKHPVLKLRRVKFGELGLRTLARGQFRHLTPVEVKELRDQ 240


>gi|149181685|ref|ZP_01860178.1| RluB [Bacillus sp. SG-1]
 gi|148850663|gb|EDL64820.1| RluB [Bacillus sp. SG-1]
          Length = 243

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 131/233 (56%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG   +     V  TD IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELILEGKVKVNGKTEKELGTKVSGTDKIEVNGIQIER-ENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++  +D   R  V D  P I  R+  VGRLD +T GL+LLTNDG  A +
Sbjct: 61  VYYLLYKPRGVISAVTDDKDRKVVTDFFPYIQERIYPVGRLDYDTSGLILLTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P     + Y  R  G   + KL  L+KGI+++       +V +    +K   + V +
Sbjct: 121 LTHPRYNIDKTYVARLKGIPPKFKLKELEKGIMLEDGKTAPAKVKVLKIEKKQDKSIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGKNR++K++FE   ++V +L R  +    L  L AG +RE+S   +++ 
Sbjct: 181 TIHEGKNRQVKRMFEAIGYQVQKLKRERFAFLDLHGLNAGESRELSPHEVKQL 233


>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 =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 146/295 (49%), Positives = 197/295 (66%), Gaps = 3/295 (1%)

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 NLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           N DA I   +S++ + R  P           R   +     G   + +      R
Sbjct: 403 NFDAEISKPFSNKPVRRTEPRQEEAERPKIMREGDHRPIGEGGLIKNRKRREGSR 457


>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 =  289 bits (740), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 128/243 (52%), Gaps = 3/243 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K + +     +R+ KVIA AG+ASRR+ E +I + RV VNG  +    V V S+D IEV+
Sbjct: 38  KIVHEVKDKMERLQKVIAHAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGSSDKIEVN 97

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ L + E    ++ +KP G+++   D  GR  V D    +  R+  +GRLD +T GL+L
Sbjct: 98  GLKLEREE-PVYFMLYKPRGVISAAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLIL 156

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-- 181
           +TNDG  A  L  P  +  + Y  +  G   ++ L  L+KGI++        +  + +  
Sbjct: 157 ITNDGEFAHKLMHPKYEIDKTYAAKLKGIPSKELLRKLEKGIMLDHKKTARARAKMLSID 216

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++   + V + + EG+NR+++++FE     V +L R  Y    +  +  G  RE++   +
Sbjct: 217 KRKQTSIVQLTIHEGRNRQVRRMFEAIGHDVLKLKREQYAFLHIEGMRPGDRRELTPHEV 276

Query: 242 REQ 244
           +  
Sbjct: 277 KRL 279


>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 =  289 bits (740), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 124/230 (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 +  I  R+  VGRLD +T GLLLLTNDG +A 
Sbjct: 62  NIYIMLNKPTGFITTVKDQFGRPSVLDII-KIKDRIYPVGRLDCDTSGLLLLTNDGDIAN 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|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 =  289 bits (740), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 123/234 (52%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+   E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKHDTVEVDEVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 61  GYYLLYKPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLL 234


>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 =  289 bits (740), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 148/285 (51%), Positives = 187/285 (65%), Gaps = 4/285 (1%)

Query: 7   VQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +    TPQ  R++KV++RAG+ASRRE ERMI   RVKVNG  +   A+NV  TD I VDG
Sbjct: 1   MTSEPTPQGDRIAKVLSRAGVASRREAERMIEAGRVKVNGQHISSPALNVQGTDKITVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   E  RLWLYHKP GLVTT +D  GR T++  LP    RV+SVGRLDIN+EGLLLL
Sbjct: 61  KEVSPPEPARLWLYHKPTGLVTTDNDEKGRETIYSALPEDMPRVMSVGRLDINSEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGG+ R LELP+T WLR YRVR +G+     L+ L++GI  +G  +  MQ+TLD Q+G
Sbjct: 121 TNDGGVKRRLELPTTGWLRRYRVRINGRPTDATLDPLRRGISSEGENFQPMQITLDRQQG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +NAW+TVGLREGKNREI++     +  VNRLIRISYGPFQLG L  G+  EV +KILR+Q
Sbjct: 181 ANAWLTVGLREGKNREIRRALAELDLSVNRLIRISYGPFQLGELKPGAVEEVRRKILRDQ 240

Query: 245 LGP--HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           LG    + E A  + DA       + R R     +      + +K
Sbjct: 241 LGLEGEVEESAPKHPDAGKKRGPNVNRTRTAAPGKSFKHTKKPRK 285


>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 =  289 bits (740), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 75/243 (30%), Positives = 127/243 (52%), Gaps = 3/243 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K + +     +R+ KVIA AG+ASRR+ E +I + RV VNG  +    V V S+D IEV+
Sbjct: 29  KIVHEVKDKMERLQKVIAHAGVASRRKAEELIKEGRVTVNGQTVTELGVKVGSSDKIEVN 88

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ L + E    ++ +KP G+++   D  GR  V D    +  R+  +GRLD +T GL+L
Sbjct: 89  GLKLEREE-PVYFMLYKPRGVISAAEDDKGRKVVTDFFDDVPQRLYPIGRLDYDTSGLIL 147

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-- 181
           +TNDG  A  L  P  +  + Y  +  G   ++ L  L+KGI++        +  + +  
Sbjct: 148 ITNDGEFAHKLMHPKYEIDKTYAAKLKGIPSKELLRKLEKGIMLDHKKTAPARAKMLSID 207

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++     V + + EG+NR+++++FE     V +L R  Y    +  +  G  RE+S   +
Sbjct: 208 KRKQTCIVQLTIHEGRNRQVRRMFEAIGHDVLKLKREHYAFLHIEGMRPGDRRELSPHEV 267

Query: 242 REQ 244
           +  
Sbjct: 268 KRL 270


>gi|12724251|gb|AAK05373.1|AE006360_2 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 257

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +  KN          R++K +A AG+ASRR+ E +I   +V VN + +      V + D 
Sbjct: 5   LSQKNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDI 64

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +EV+GV +   E    +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T 
Sbjct: 65  VEVNGVAV-YNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTS 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG    ++  P     +VY  +  GQ +++ L  L  G+ I+G      +  +
Sbjct: 124 GLLLLTNDGEFTNMMTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEI 183

Query: 180 DTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +S
Sbjct: 184 IKQEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRLS 243

Query: 238 KKILREQL 245
           KK + + +
Sbjct: 244 KKEVSQLI 251


>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 =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 123/234 (52%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+   E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKQDTVEVDEVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 61  GYYLLYKPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLL 234


>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 =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 82/237 (34%), Positives = 132/237 (55%), Gaps = 2/237 (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 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NA 187
           +A  L  P T+  + Y  +  G   ++KL  LK+G+V++G      +V+++  + +   +
Sbjct: 122 VANQLMHPKTKVDKTYVAKVEGIATEEKLAPLKRGVVLKGRKTAPARVSIERIEPTKRTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V + + EG+N ++K +       V +L R  Y  F +  L  G  R+++   ++  
Sbjct: 182 MVRLTIHEGRNHQVKNMLAKVGLPVQKLKREQYAFFDVTGLQPGEYRKLTSVEIKRL 238


>gi|30024033|ref|NP_267431.2| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 239

 Score =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 129/234 (55%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E  
Sbjct: 1   MRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDIVEVNGVAV-YNEEP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 60  VYYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P     +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++ V++
Sbjct: 120 MTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +
Sbjct: 180 TIHEGQNHQVKKMFAAAGLPVQKLSRIQYGSLTLDGLPTGQFRRLSKKEVSQLI 233


>gi|326406814|gb|ADZ63885.1| ribosomal large subunit pseudouridine synthase B [Lactococcus
           lactis subsp. lactis CV56]
          Length = 257

 Score =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +  KN          R++K +A AG+ASRR+ E +I   +V VN + +      V + D 
Sbjct: 5   LSQKNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDI 64

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +EV+GV +   E    +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T 
Sbjct: 65  VEVNGVAV-YNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTS 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG    ++  P     +VY  +  GQ +++ L  L  G+ I+G      +  +
Sbjct: 124 GLLLLTNDGEFTNMMTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEI 183

Query: 180 DTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +S
Sbjct: 184 IKQEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLS 243

Query: 238 KKILREQL 245
           KK + + +
Sbjct: 244 KKEVSQLI 251


>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 =  289 bits (739), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 135/256 (52%), Positives = 178/256 (69%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T QR++KV+ARAG+ASRRE ERMI   RV+VN  L+E  A+NV+ +D I VDG  +   E
Sbjct: 11  TGQRIAKVLARAGVASRREAERMIEAGRVRVNSKLIESPALNVVPSDRISVDGKLIGDPE 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            TR+WL+HKP GL+T+  D +GR TVFD LP    RV+SVGRLD+N+EGLL+LTNDG + 
Sbjct: 71  PTRMWLFHKPQGLITSERDEEGRETVFDVLPPEMPRVLSVGRLDLNSEGLLVLTNDGEVK 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELPST WLR YRVR  G + + KL+ L++GI ++G+ Y  M VT D Q+G+NAW+T+
Sbjct: 131 RKLELPSTGWLRRYRVRIKGSLSEAKLDELREGITVEGVHYQPMDVTFDRQQGANAWLTI 190

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
           G+REGKNREI++  E     VNRLIRISYGPFQLG + AG   E+  +++R+QLG     
Sbjct: 191 GIREGKNREIRRTMEALGVTVNRLIRISYGPFQLGNIKAGEVEELKSRVVRDQLGLDPRP 250

Query: 252 EAQVNLDAPIYSSETL 267
           + +           T 
Sbjct: 251 KPERTRKTGAKGKNTR 266


>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 =  289 bits (739), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 127/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E +I + RV VNG  +    V V S+D IEV+GV L  +E  
Sbjct: 2   ERLQKVIAHAGIASRRKAEELIKEGRVTVNGKTVRELGVKVSSSDRIEVNGVQLE-SEEP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAVKDDKGRKVVTDFFTEVEERIYPIGRLDYDTSGLLLLTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++G+ ++       +V L +  +K   + V +
Sbjct: 121 LMHPKYEINKTYVAKLKGIPLKENLKKLERGVRLEDGKTAPAKVKLLSLDKKKQTSIVQI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++  
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLNLAGLKTGEKRELTPHEVKRL 233


>gi|291542267|emb|CBL15377.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus
           bromii L2-63]
          Length = 249

 Score =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 128/248 (51%), Gaps = 3/248 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P R+ K IA+ GIASRR+ E +I    VKVNG         V+ TD + V G  +  
Sbjct: 3   KIEPIRLQKFIAQCGIASRRKAEELILGGHVKVNGKTAI-LGDKVLPTDKVFVRGKRIVV 61

Query: 70  AER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 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 HLLEEAQV 255
             L   Q+
Sbjct: 242 PFLNGKQL 249


>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 =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 133/233 (57%), Gaps = 3/233 (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 KP G++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLLY-KPRGVISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P     +VY  +  G +  ++++ LK G+ I G      +V + +  ++   + V +
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIHSLKHGVRIDGKKSAPAKVKIISTNREKGTSIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG   ++K++F+     V++L R  Y    L +L AG  RE++++ + + 
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTREEVAKL 234


>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 =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 153/352 (43%), Positives = 204/352 (57%), Gaps = 7/352 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +F  +R++K +ARAG+ SRRE E+ IA+ RV VNG++L  AA NV   D I +DG P+++
Sbjct: 83  SFEGERIAKAMARAGVCSRREAEQWIAEGRVAVNGVVLPNAAFNVKEGDRITIDGAPMQE 142

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTN 126
            ERTRL+L+HKP G VTT  DP+GR TVF  L        RV+SVGRLDINTEGLLLLTN
Sbjct: 143 RERTRLFLFHKPAGYVTTAHDPEGRPTVFAFLEERHGELPRVVSVGRLDINTEGLLLLTN 202

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T W R YRVR HG  DQ +L+ L+KG+ I G+ Y  ++  L+  +G+N
Sbjct: 203 DGGLARTLELPATGWTRRYRVRVHGDTDQAQLDELRKGVTIDGVVYAPIEARLERVQGAN 262

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+ + L EGKNREIK+V       V RLIR+SYGPFQLG L  G+  EV  KILREQLG
Sbjct: 263 AWIAMSLTEGKNREIKRVMAHLGLDVTRLIRVSYGPFQLGELAEGAVEEVKLKILREQLG 322

Query: 247 PHLLEEAQVNLDAPIY----SSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
             L E A V+  +P+     + E  +R+R            R +++     G   + +  
Sbjct: 323 KSLAELAGVDFSSPVRERTATEEQEMRERAEKRPRKHVSVLRKQRDEKSGKGPRARIERG 382

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R+  A  V           S++  R      +     +R        +
Sbjct: 383 ATADRKGRAVVVERVTPTARKAESETTTRNARRFEAMRGEGRRPGPEGGRAE 434


>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 =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 88/231 (38%), Positives = 133/231 (57%), Gaps = 5/231 (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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---AWV 189
            L  PS +  +VYRV   G VD++    L +G+ ++       +V +  Q       A V
Sbjct: 121 RLLHPSREIEKVYRVSVRGIVDRETRRALMEGVELEDGVTAPAKVEVLRQADREDGVAVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EG+NR+++++FE     V RL RI++GP  LG L  G  R ++++ 
Sbjct: 181 HLAIHEGRNRQVRRMFERLGLPVLRLKRIAFGPVSLGHLKTGEWRALTQEE 231


>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 =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 125/232 (53%), Gaps = 1/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+I+++ +     V RL R   G   +G L  G  R ++++ +++ 
Sbjct: 194 ISEGRNRQIRRMCDSIGHPVVRLKRTKLGSLSIGNLRPGQYRHLTREEIKKL 245


>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 =  288 bits (738), Expect = 8e-76,   Method: Composition-based stats.
 Identities = 80/230 (34%), Positives = 122/230 (53%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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 D + SI  RV  +GRLD +T GLLLLTNDG LA 
Sbjct: 62  NIYIMLNKPVGYITTVKDQFDRPSVIDLV-SIDDRVYPIGRLDYDTSGLLLLTNDGDLAN 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|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 =  288 bits (738), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 123/234 (52%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+   E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVIRELGIKVGKHDTVEVDEVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 61  GYYLLYKPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLL 234


>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 =  288 bits (738), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 90/237 (37%), Positives = 137/237 (57%), Gaps = 2/237 (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 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNA 187
           +A  L  P ++  +VY  +  G    +KL  LK G+VI+G      +VT++   +    +
Sbjct: 122 VANQLMHPKSRVDKVYVAKVEGIATDEKLAPLKHGVVIKGRKTAPARVTIERVDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V + EG+N +IK + +  +  V +L R  Y  F L  L +G  R+++   +R  
Sbjct: 182 MVRVIIHEGRNHQIKNMLQKVHLPVVKLTREQYAFFDLIGLQSGEYRKLTGAEVRRL 238


>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 =  288 bits (738), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 143/350 (40%), Positives = 198/350 (56%), Gaps = 5/350 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D      N    R++KV+ARAG+ASRRE ERMI + RV VNG  ++  A++V   D I 
Sbjct: 3   EDSPETAPNPQADRIAKVMARAGVASRREAERMILEGRVTVNGKKIDSPALDVTPADRIR 62

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL + + TRLWLY+KP+GLVT++SD  GR TVFD LP    RV++VGRLD+N+EGL
Sbjct: 63  VDGKPLEEPQETRLWLYYKPLGLVTSNSDEKGRQTVFDALPRDLPRVMTVGRLDLNSEGL 122

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG L R LELP+T WLR YRVR +GQ +      L++G+ I G  +  M++ LD+
Sbjct: 123 LLLTNDGELKRRLELPTTGWLRRYRVRVNGQPNDLTFAPLRRGVTIDGEEFAPMEINLDS 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+G+NAW+TVG+REG+NREI++        VNRLIRI YGPF+L  L     REV +K+L
Sbjct: 183 QQGANAWLTVGIREGRNREIRRAMAHVGLIVNRLIRIGYGPFKLTGLEENEVREVKRKVL 242

Query: 242 REQLGPHL---LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           R+QLG  L    EE   +      +       RP    +        ++    +   +++
Sbjct: 243 RDQLGGLLTGETEEKPRSFRERGAAKPAEGDARPRKPRDEGGRKPFARREDGDRKPFARR 302

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           ++       R          G           + E+  R P F  +    
Sbjct: 303 EEGDRKPFAR-REDGERKPFGKRPDGGRKPFAKREDGERKP-FARREDRD 350


>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 =  288 bits (738), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 79/243 (32%), Positives = 137/243 (56%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +V+VNG  +      V  +D + V+G+PL + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLIEEGKVQVNGKTVTELGTKVRPSDEVTVEGIPLEQEDKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFYKPAQVITSVSDDRGRKVVTDYFDDLVTRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  + Y  +  G + ++++  L+KGI ++       +V +  Q  + + + V +
Sbjct: 125 MTHPRYKIPKTYVAKIEGYILREQVKQLEKGIQLEDGLTQPAKVKVKKQNKEKNTSLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F + V +L R+S+GP  L  L AG  R +S   ++     HL E
Sbjct: 185 TITEGRNRQVRRMFEHFGFSVQKLSRVSFGPLTLKGLGAGEGRVLSPHEVKSL--RHLAE 242

Query: 252 EAQ 254
             Q
Sbjct: 243 NGQ 245


>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 =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 139/315 (44%), Positives = 192/315 (60%), Gaps = 17/315 (5%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  E     R++KV+ARAG+ASRRE ERMI   R+ V+G +++  A+NV+ T  I VDG 
Sbjct: 1   MNTETPKGDRIAKVLARAGVASRREAERMIDAGRISVDGKIIDSPALNVLPTARISVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E  R+W+YHKP GLVTT SD  GR T+FD+LP    RV+SVGRLD+N+EGLLLLT
Sbjct: 61  PMAAPEPPRVWMYHKPTGLVTTDSDEKGRKTIFDDLPEDMPRVMSVGRLDLNSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDGGL R LELPST WLR YRVR +G+  ++    L+KG+ +QG  +  M V++D Q+G+
Sbjct: 121 NDGGLKRKLELPSTGWLRKYRVRINGRPTEETFEPLRKGLNLQGEHFQPMLVSIDRQQGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           NAW+TVG+REGKNREI++  E     VNRLIR+SYGPFQLG L      E+ ++ L++QL
Sbjct: 181 NAWLTVGIREGKNREIRRAMEAIQLNVNRLIRVSYGPFQLGNLKTSGVEEIRRRALKDQL 240

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS------------SQKN 293
           G      +  +L+ P    +   R + ++         +                  + +
Sbjct: 241 GL-----SDEDLEVPGAKPKPTQRGKNSVTRGKRPPLPKGPLRGRDRFSDSDPMARPKSS 295

Query: 294 GLSKQKKLATPVHRR 308
           G  K K    P  +R
Sbjct: 296 GKPKSKPANKPRPKR 310


>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 =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 126/241 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
           +  P     + Y  +  G     ++  L++GIV+ G        Q+           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|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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 123/234 (52%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E  I   RVKVNG ++    + V   D +EVD VP+   E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEEFILAGRVKVNGQVVRELGIKVGKHDTVEVDEVPI-YQEEY 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++  +D  GR  V D LP +  R+  VGRLD +T G+LLLTNDG  A+ 
Sbjct: 61  GYYLLYKPKGVISAVADDKGRKVVTDLLPMVKERIYPVGRLDYDTSGILLLTNDGDFAQR 120

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

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK +   L
Sbjct: 181 TIHEGRNHQVKNMLQAVGLPVQKLKREKYGDLTLQGLRPGDYRELNKKEVSSLL 234


>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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 82/230 (35%), Positives = 123/230 (53%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA++G  SRR+ E +I Q +V VNG ++      V   D I V+G  + K E  
Sbjct: 3   ERLQKVIAQSGYTSRRKAEELIQQGKVTVNGEVVTVLGTKVTKKDTICVNGKLINK-EDK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP   V T SD   R+ V D       RV  VGRLD +T G L +TNDG  A +
Sbjct: 62  VYYLFYKPEKCVCTMSDEHDRTCVADYFADSNERVYPVGRLDYDTTGALFMTNDGEFANL 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|257869547|ref|ZP_05649200.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257803711|gb|EEV32533.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 238

 Score =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 128/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I   RV VNG +++   V V + D +EVDGVP+ + E  
Sbjct: 2   ERLQKVIAHAGITSRRKAEELIVAGRVSVNGQIVKELGVQVSAKDRVEVDGVPIEQ-ESP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+++  +D   R  V D    +  R+  +GRLD +T GLLLLTNDG L++ 
Sbjct: 61  VYYMLYKPRGVISAVTDDKKRKVVLDFFTEVPERLYPIGRLDYDTSGLLLLTNDGDLSQK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G  D+ +L  L +GI I+G      +  + +   +   + V +
Sbjct: 121 LMHPKHEVDKVYVAKVKGIADKKQLLPLSRGIRIEGKKTAPARFEILSTDAATQTSIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++K + +     V +L R  YG   L  L  G  RE++KK + E 
Sbjct: 181 TIHEGRNHQVKNMLKAVGLPVQKLKREMYGSLTLAGLRPGEYRELTKKEVNEL 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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 149/326 (45%), Positives = 201/326 (61%), Gaps = 11/326 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V  +D I VDG PL + ERTR
Sbjct: 477 RIAKVVARAGLCSRRDAEAWIVEGRVAVNGRVIDSPALDVTYSDVITVDGKPLPERERTR 536

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLAR L
Sbjct: 537 LFLYHKPRGLMTTHADPEGRPTVFDNLPEDLPRLISIGRLDFNTEGLLLLTNDGGLARAL 596

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP T WLR YRVR HG+V Q +L+ L  G+ + G+ YG ++  L+  +G+N W+   +R
Sbjct: 597 ELPETGWLRRYRVRAHGEVTQAQLDQLASGVEVDGVKYGPIEAKLERDQGANVWLVFAIR 656

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  +++ A+
Sbjct: 657 EGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLEIEEGQVEEVKTRVLREQLGEKIIKLAE 716

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
            +   P   SET  + RP       D     KK   ++  +  +K     V R       
Sbjct: 717 ADFGGP-SPSETRPKPRPGKPVAAEDGPAPKKKAVVKRGAVEDRKGRKVKVER------- 768

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPS 340
               G      S    R  + +R P+
Sbjct: 769 ---TGSGDRDPSRGPARRYHGKREPA 791


>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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 144/240 (60%), Positives = 175/240 (72%), Gaps = 3/240 (1%)

Query: 10  NFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             TP+   R++KV++RAGIASRRE ERMI   RV VNG ++   A+NV   D I+VDG  
Sbjct: 2   TDTPEKGDRIAKVLSRAGIASRREAERMIEAGRVSVNGKVIPSPALNVTPKDKIKVDGKE 61

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  AE  RLWLYHKP+GLVTT  D  GR TVFDNLP    RV+SVGRLDIN+EGLLLLTN
Sbjct: 62  VGDAEPARLWLYHKPVGLVTTERDEKGRDTVFDNLPDGLPRVMSVGRLDINSEGLLLLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGL R LELPST WLR YRVR +G V +D L  L+KG+VI G  +  M +++D Q+GSN
Sbjct: 122 DGGLKRKLELPSTGWLRKYRVRVNGIVIEDHLTPLRKGLVIDGEKFQPMNISVDRQQGSN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           AW+TVG+REGKNREI++ FE     VNRLIR+SYGPFQL  L A    E+  ++LR+QLG
Sbjct: 182 AWLTVGIREGKNREIRRAFETIFLPVNRLIRVSYGPFQLNDLRADEVEEIKGRVLRDQLG 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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 82/248 (33%), Positives = 132/248 (53%), Gaps = 4/248 (1%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +  KN          R++K +A AG+ASRR+ E +I   +V VN + +      V + D 
Sbjct: 5   LSQKNKPYLTKVKKMRINKYLAHAGVASRRKAEELILAGKVTVNNVSMTNLGYQVSTGDI 64

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +EV+GV +   E    +L +KP G +++ SD  GR TV D +P +  R+  VGRLD +T 
Sbjct: 65  VEVNGVAV-YNEEPVYYLLNKPRGYISSVSDDKGRQTVMDLMPQVKERIYPVGRLDWDTS 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG    ++  P     +VY  +  GQ +++ L  L  G+ I+G      +  +
Sbjct: 124 GLLLLTNDGEFTNMMTHPRHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEI 183

Query: 180 DTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             Q+   +++ V++ + EG+N ++KK+F      V +L RI YG   L  L  G  R +S
Sbjct: 184 IKQEKTKNHSIVSLTIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLS 243

Query: 238 KKILREQL 245
           KK + + +
Sbjct: 244 KKEVSQLI 251


>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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 79/232 (34%), Positives = 122/232 (52%), Gaps = 1/232 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           ++EG+NR+++++ E     V  L R+ +GP  L  L  G  R +  + + + 
Sbjct: 183 IKEGRNRQVRRMLEAVGHPVVSLKRVRFGPLTLSGLQEGRWRRLEPREIEQL 234


>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 =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 81/230 (35%), Positives = 129/230 (56%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E+MI+  +V VNG  +      V   D IEV+GVP+ K E  
Sbjct: 3   ERLQKVIAQAGVASRRKAEKMISAGQVTVNGKKVTELGTKVEPRDKIEVNGVPIEK-EAL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G++++ SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 62  HTYLFYKPRGVISSVSDDKGRKTVVDFFEDVPYRLYPVGRLDYDTSGLLLMTNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 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|218289586|ref|ZP_03493806.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240236|gb|EED07419.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 273

 Score =  288 bits (737), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 88/231 (38%), Positives = 133/231 (57%), Gaps = 5/231 (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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---AWV 189
            L  PS +  +VYRV   G VD++    L +G+ ++       +V +  Q       A V
Sbjct: 121 RLLHPSREIEKVYRVSVRGIVDRETRRALMEGVELEDGVTAPAKVEVLRQADREDGVAVV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EG+NR+++++FE     V RL RI++GP  LG L  G  R ++++ 
Sbjct: 181 HLAIHEGRNRQVRRMFERLGLPVLRLKRIAFGPVSLGHLKTGEWRALTQEE 231


>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 =  287 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 133/233 (57%), Gaps = 3/233 (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 KP G++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLLY-KPRGVISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P     +VY  +  G +  ++++ LK G+ I G      +V + +  ++   + V +
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIHSLKHGVRIDGKKSAPAKVKIISTNREKGTSIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG   ++K++F+     V++L R  Y    L +L AG  RE++++ + + 
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTREEVAKL 234


>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 =  287 bits (736), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 132/233 (56%), Gaps = 3/233 (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 KP G++++  D  GR TV D       R+  VGRLD +T GLLL+TNDG LA  
Sbjct: 63  TYLLY-KPRGVISSVKDDKGRKTVLDFFEESPYRLYPVGRLDYDTSGLLLITNDGELANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P     +VY  +  G +  +++  LK G+ I G      +V + +  ++   + V +
Sbjct: 122 LMHPRHMVDKVYVAKIKGFLTPEEIYSLKHGVRIDGKKSAPAKVKIISTNREKGTSIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG   ++K++F+     V++L R  Y    L +L AG  RE++++ + + 
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLSRERYAFLTLKSLTAGKYRELTREEVAKL 234


>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 =  287 bits (736), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 129/234 (55%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ASRR+ E +I   +V VN + +      V + D +EV+GV +   E  
Sbjct: 1   MRINKYLAHAGVASRRKAEELILAGKVTVNNVPMTNLGYQVSTGDVVEVNGVAV-YNEEP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++  D  GR TV D +P +  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 60  VYYLLNKPRGYISSVRDDKGRQTVMDLMPQVKERIYPVGRLDWDTSGLLLLTNDGEFTNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  PS    +VY  +  GQ +++ L  L  G+ I+G      +  +  Q+   +++ V++
Sbjct: 120 MTHPSHGVDKVYVAKVEGQANKENLRPLTLGMTIEGKKVSPARYEIIKQEKTKNHSIVSL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG+N ++KK+F      V +L RI YG   L  L  G  R +SKK + + +
Sbjct: 180 TIHEGQNHQVKKMFAAAGLPVQKLSRIQYGTLTLDGLPTGQFRRLSKKEVSQLI 233


>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 =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 134/354 (37%), Positives = 192/354 (54%), Gaps = 11/354 (3%)

Query: 11  FTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            T + R++K++ARAG+ASRREVERMIA+ R+ +NG  ++  A  + S D + VDG P+  
Sbjct: 1   MTSEHRIAKLLARAGVASRREVERMIAEGRIALNGTTIDTPATLLSSLDGVTVDGNPVDA 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E TRL+LY+KP GL+ T  DP GR T++D LP    R++ VGRLD+NTEGLLLLT DGG
Sbjct: 61  PEPTRLFLYNKPNGLLVTERDPKGRPTIYDRLPEGLPRLMPVGRLDLNTEGLLLLTTDGG 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             R LELP+T   R YR R +G + Q +L  L  GI I GI YG +   L+ + G+N W+
Sbjct: 121 FKRQLELPATGVERTYRARAYGDITQAQLEELIHGIEIDGIRYGQIDANLERRTGANVWI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQL 245
            + LREGKNRE+++V E+   +V+RLIR+ YGPF LG L  G   EV    +    +  L
Sbjct: 181 ELTLREGKNREVRRVLEYLGLQVSRLIRLRYGPFVLGDLPVGEIGEVKGAAIVEFRKTLL 240

Query: 246 GPHLLE----EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           G    +      +     P   ++T   DRP      P D     ++ +++         
Sbjct: 241 GGIPADAVRPSPRAGFRTPPTRAKTDRPDRPAAQDRRPSDGRDRPQSDAKRRAAGPGGDR 300

Query: 302 ATPVHRRN-LASNVWMAKGIHSSFLSDSGQREENH-RRSPSFPSKRSLRRTSAK 353
             P   R   +++        + F    G+R     +R+P    +     T AK
Sbjct: 301 QRPAAPRTARSTDRGERPSADAQFRPSGGERSRPTGKRAPRSGDRSERPATEAK 354


>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 =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 87/236 (36%), Positives = 135/236 (57%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + 
Sbjct: 1   MKMERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   +L++KP G+++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L
Sbjct: 60  EQHVYYLFYKPRGVISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           ++ L  P  +  +VY  +  G  D+ +L  L KGI I+G      +  + +  Q   ++ 
Sbjct: 120 SQTLMHPKHEVDKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTAQSSI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + + EG+N ++K + +     V +L R +YGP  L  L  G  RE++KK + + 
Sbjct: 180 VQLTIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELTKKEVSQL 235


>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 =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 118/245 (48%), Gaps = 2/245 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +D         P RV K +ARAG+ASRR  E ++   RV VNG ++      V    D +
Sbjct: 6   RDDASNAPRIVPMRVQKFLARAGVASRRGSENLMTTGRVSVNGRVVTELGSRVDPRCDVV 65

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTE 119
            VDG  +  ++ +   + +KP G +TT SDP GR+ V + +P   +  +  +GRLD +T 
Sbjct: 66  RVDGHVVHLSDGSTTLMLNKPAGYITTMSDPFGRACVAELVPIDAYPGLFPIGRLDADTT 125

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL + DG L   L  P     + Y+    G V +++L  L+ G+ ++       +  L
Sbjct: 126 GILLFSTDGELGNGLLHPRKHVDKTYQALVEGSVSEEELERLRSGVELEDGMTAPAEARL 185

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + + + EG+ R+++++       V  L R  +GP  LG L  GS R +S  
Sbjct: 186 TCVSEDESRLDITIHEGRKRQVRRMCATVGHPVVTLHRSRFGPLVLGDLPEGSWRMLSGS 245

Query: 240 ILREQ 244
            +   
Sbjct: 246 EVAAL 250


>gi|257876560|ref|ZP_05656213.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257810726|gb|EEV39546.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 240

 Score =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 86/236 (36%), Positives = 134/236 (56%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + 
Sbjct: 1   MKMERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVSSKDVVEVDGVPIEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   +L++KP G+++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L
Sbjct: 60  EQHVYYLFYKPRGVISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
           ++ L  P  +  +VY  +  G  D+ +L  L KGI I+G      +  + +   +   + 
Sbjct: 120 SQTLMHPKHEVDKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTTQSSI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + + EG+N ++K + +     V +L R +YGP  L  L  G  RE++KK + + 
Sbjct: 180 VQLTIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELTKKEVSQL 235


>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 =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 145/329 (44%), Positives = 199/329 (60%), Gaps = 4/329 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + + +R++KV+ARAG+ SRR+ E  I Q RV VNG ++   A++V + D I VDG PL +
Sbjct: 362 DKSGERIAKVVARAGLCSRRDAEDWIMQGRVAVNGRVIGSPALDVTARDVITVDGQPLPE 421

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRL+LYHKP GL+TTH DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGG
Sbjct: 422 RERTRLFLYHKPRGLMTTHDDPEGRPTVFDHLPDGLPRLISIGRLDFNTEGLLLLTNDGG 481

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L+R LE P T WLR YRVR HG V Q +L+ LK G+ + G+ YG +  TL+  +G+N W+
Sbjct: 482 LSRALEHPDTGWLRRYRVRAHGDVTQARLDELKNGVEVDGVKYGSIDATLERDQGANVWL 541

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T  +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++LREQLG  +
Sbjct: 542 TFAIREGKNREVRNVMAHLGLEVNRLIRVSYGPFQLGEIPEGQVEEIKSRVLREQLGDKI 601

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK-KNSSQKNGLSKQKKLATPVHRR 308
           +  A    D P+   +          + +       K K S+ ++   ++  +       
Sbjct: 602 IALAGAQFDKPVQEGDDAEAKLGRDGTPLRSKAANKKIKRSAIEDRKGRRVVVQRSGSDE 661

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRR 337
             A N   A G          QR  + +R
Sbjct: 662 ARARNEAEAGGYGP---PRRPQRRYHGKR 687


>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 =  287 bits (734), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKDNLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLIVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQL 232


>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 =  287 bits (734), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L +  +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++  
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELTPHEVKRL 233


>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 =  287 bits (734), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 117/232 (50%), Gaps = 1/232 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           LREG+NRE++++       V RL RI      L  L  G+ R ++   +   
Sbjct: 181 LREGRNREVRRMLAAVGHPVLRLRRIRLAFLTLRGLKPGTYRHLTPHEVERL 232


>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 =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+VI G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKVDPVKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKKDISKL 232


>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 =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 88/231 (38%), Positives = 134/231 (58%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AG+ASRR+ E+ +   RV+VNG  +        S D IEVDG  L +AE+ 
Sbjct: 5   ERLQKLIAQAGLASRRQAEQWLKDGRVRVNGRSVTLGDKADPSVDRIEVDGKALPRAEQK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP+G VTT  DP GR T+   L  I  RV  VGRLD+N+EGLLLLTNDG L + 
Sbjct: 65  LYLLLNKPLGYVTTLKDPQGRPTIRRFLKGIPQRVYPVGRLDVNSEGLLLLTNDGALTQH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  + YRV+ +G++       L++G+ ++        V        N+W  + +
Sbjct: 125 LLHPRHQVSKTYRVKVNGRISPQACRQLEQGVELEDGVTAPAVVRNVHHSPRNSWFDLEI 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           REG+NR+++++     ++V+ L RI  G  +LGTL  G  R ++ K +++ 
Sbjct: 185 REGRNRQVRRMCRGVGFEVSALKRIRIGSLELGTLAKGQCRSLTSKEIQDL 235


>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 =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 133/234 (56%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  G+ASRR+ E +IA  +V+VNG  +    V V    D + VDG  L   E+
Sbjct: 2   ERLQKFIASCGVASRRKAEELIASGKVRVNGRKVTELGVKVDPMKDKVMVDGQLL-AVEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ +DP GR TV D + +   R+  +GRLD++TEGLLLLTNDG LA+
Sbjct: 61  PVYYLMNKPKGVITSVTDPQGRETVMDYIKNEKRRIYPIGRLDLHTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V+   L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVNDTDLQVIADGVPLEDGVTAPATLVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE F ++++ L RI+YG   L  +  G  R+++++ +   
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYGGLTLSGVKRGGVRQLTQREVSAL 234


>gi|291544370|emb|CBL17479.1| ribosomal large subunit pseudouridine synthase B [Ruminococcus sp.
           18P13]
          Length = 242

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 86/236 (36%), Positives = 125/236 (52%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K+IA +G  SRR+ E  IA  +VK NG  ++       S D I V+G  +   
Sbjct: 1   MEKTRIQKIIADSGYCSRRKAESFIAAGQVKCNGRPVK-LGDKAGSRDLITVNGERIAIP 59

Query: 71  ERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           ++ +    + +KP G VTT SD   R  V D L  +  RV  VGRLD N+EGLLLLTNDG
Sbjct: 60  KKKQKLYLMLNKPRGYVTTMSDELDRRCVMDLLEDVPERVYPVGRLDRNSEGLLLLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + YRV     +   +L  L +G+ I G       V + T++     
Sbjct: 120 DFANSIMHPSRHVSKTYRVTVRPDITDQQLVQLSEGVEIDGKPTLPATVNVLTKEPGRVV 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + +REG+NR+I+++ E    +V RL RIS GP +LG L  G+ RE++ + LR  
Sbjct: 180 LLITIREGRNRQIRRMCEAVGLEVARLRRISIGPLKLGMLKPGTYRELTAEELRAL 235


>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 =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+VI G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVANKEVLRPLTRGVVIDGKKTKPAVYEIIKVDPVKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R+++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGNLDLTGLRPGEYRKLNKKDISKL 232


>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 =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 88/236 (37%), Positives = 134/236 (56%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AGI SRR+ E +I + RV+VNG +++   V V S D +EVDGVP+ + 
Sbjct: 1   MKMERLQKVIAHAGITSRRKAEGLITEGRVRVNGQVIKELGVQVGSKDVVEVDGVPIEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L++KP G+++  +D   R  V D    +  RV  VGRLD +T GLLLLTNDG L
Sbjct: 60  EPHVYYLFYKPRGVISAVTDDKKRKVVLDYFAEVPERVYPVGRLDYDTSGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           ++ L  P  +  +VY  +  G  D+ +L  L KGI I+G      +  + +  Q   ++ 
Sbjct: 120 SQTLMHPKHEVEKVYVAKVKGIADKKQLLPLTKGIRIEGRKTAPARFEILSTDQTAQSSI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + + EG+N ++K + +     V +L R +YGP  L  L  G  RE+SKK + + 
Sbjct: 180 VQLTIHEGRNHQVKNMLKAVGLPVQKLKRENYGPLDLKGLRPGEYRELSKKEVSQL 235


>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 =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 145/323 (44%), Positives = 194/323 (60%), Gaps = 1/323 (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 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +   +    D P+   E     R         D  ++ K S  ++   +   +      
Sbjct: 604 KIATMSGAQFDKPVREDEGPKVGRDGTPLRSKADNKKI-KRSKIEDRKGRTVVVQRSGSD 662

Query: 308 RNLASNVWMAKGIHSSFLSDSGQ 330
              A N   A G         G 
Sbjct: 663 EKRARNEAEANGYGPPRKPKRGY 685


>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 =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G        ++     + + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKENLRPLTRGVTIDGKKTKPATYEILKVDPEKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKKEISQL 232


>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 =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 81/235 (34%), Positives = 128/235 (54%), Gaps = 4/235 (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
               L++KP G++T+ SDP+GR  V D L  I  RV  VGRLD +TEGLL+LTNDG  A 
Sbjct: 63  I-YILFNKPKGVITSVSDPEGRRVVGDFLKGIKERVYPVGRLDYDTEGLLILTNDGEFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVT 190
           ++  P     + Y     G      L  L++G+ ++       +V           + ++
Sbjct: 122 MVTHPRHHVSKTYHATVKGVPHGSVLEKLREGVKLEDGMTAPAEVEYHDIDPDKKQSVIS 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EGKNR+++++FE   + V RL R+ +G   L  L  G  R + K+ ++  L
Sbjct: 182 ITIYEGKNRQVRRMFEAVGYPVTRLKRVKFGSIPLVGLPRGKFRRMRKEEVQALL 236


>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 =  286 bits (732), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 73/229 (31%), Positives = 122/229 (53%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  I  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKTILDLV-KIKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK +
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTKKEI 230


>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 =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 129/309 (41%), Positives = 178/309 (57%), Gaps = 2/309 (0%)

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 REQLGPHLLEEAQVNLDAPIYSSETLVRDR--PNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +QLG    E+       P   ++  ++         +        K+     N     +
Sbjct: 244 SDQLGLTDPEDDGHATAKPRLRAKPSMKRSGGGRYKGKTSSSQQDDKRGKDAHNRGPSSR 303

Query: 300 KLATPVHRR 308
                  RR
Sbjct: 304 HKTGQSGRR 312


>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 =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 80/358 (22%), Positives = 153/358 (42%), Gaps = 23/358 (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 ++ D    + D +     R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTN 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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT--- 303
             + E +    DA   ++    R R    +++ D     + +++++N    + +      
Sbjct: 234 --MCEGSVSTEDASKINA-KGQRIRKATDAKLFDSREENQASTARRNPKENRTRTYRGNN 290

Query: 304 -------PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  P  +R   S+    KG       ++   + N R   S    +S  R  A +
Sbjct: 291 ADEFRHAPNSKRGRNSSNGENKG---QSKGNTENWKSNSRSERSNSDNKSSDRNRAGR 345


>gi|330719107|ref|ZP_08313707.1| 16S rRNA uridine-516 pseudouridylate synthase [Leuconostoc fallax
           KCTC 3537]
          Length = 252

 Score =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 86/240 (35%), Positives = 132/240 (55%), Gaps = 2/240 (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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKG 184
           DG +A  L  P ++  +VY  +  G   ++ L  LKKG++I+G      +V++++  +  
Sbjct: 121 DGTIANELMHPKSKVDKVYIAKVKGMATENDLLPLKKGVMIEGHKTQPARVSVESVDKTK 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + V + + EGKN ++K +     + V +L R  Y    L  L  G  R+++   +   
Sbjct: 181 KTSMVKLIIHEGKNHQVKNMLAKVGFPVEKLKREQYAFLDLVGLQPGEYRKLTNAEVSRL 240


>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 =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 89/236 (37%), Positives = 126/236 (53%), Gaps = 1/236 (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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + + EGKNR ++++ E     V RL RI  G   +  +  G  R ++ K +RE 
Sbjct: 188 LEITVHEGKNRLVRRMCEKIGHPVLRLKRIKLGTLSIKGVKPGQYRLLNTKEIREL 243


>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 =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 127/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAAQDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L +  +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++  
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDARELTPHEVKRL 233


>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 =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 128/238 (53%), Gaps = 3/238 (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 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SN 186
                +  P  +  +VY  R  G  +++ L  L +G+VI+G         +       + 
Sbjct: 145 DFTDEMIHPRNEIDKVYVARVKGVANKEVLRPLTRGLVIEGKKTKPAVYEILKVDPVKNR 204

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + V + + EG+N ++KK+FE     V++L R  +G   L  L  G  R +SKK + + 
Sbjct: 205 SVVQLTIHEGRNHQVKKMFEAVGLPVDKLSRTQFGHLDLTGLKPGEARRLSKKEVSQL 262


>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 =  285 bits (731), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 122/229 (53%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKTILDLV-KVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK +
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTKKEI 230


>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 =  285 bits (731), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 127/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G   G  +  +   +     + V +
Sbjct: 120 MIHPRNEIDKVYLARLKGLATKENLRPLTRGVVIDGKKTGPARYKIIKVEPDKNRSLVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++K +F+     V++L R  +G   L  L  G +R +SKK + + 
Sbjct: 180 TIHEGRNHQVKNMFQAVGLLVDKLSRTQFGTLNLRGLQPGESRRLSKKEVSQL 232


>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 =  285 bits (731), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 83/232 (35%), Positives = 117/232 (50%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AGIASRR  E +I   RV+VNG ++      V S+ D +EVDG  +R  E 
Sbjct: 1   MRLQKYLAEAGIASRRASEELILAGRVRVNGEVVRELGTTVDSSRDRVEVDGQKIR-PEP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G VTT  DP GR  V D +     RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 60  KIYVLLYKPRGYVTTARDPQGRRKVTDLVAGAGGRVFPVGRLDYDSEGLLLLTNDGELAY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V          L  + +G+ +         V L  + G  A V + 
Sbjct: 120 RLTHPRFHVPKTYHVVLDRSPGPAALRAIARGVELDDGLTAPAGVRLVRRDGREALVEMT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R++++++    ++V RL R+     +LG L  G  R +    +RE 
Sbjct: 180 IHEGRKRQVRRMWAALGFEVQRLKRVRMAGLELGGLEPGRWRHLRTTEVREL 231


>gi|326692499|ref|ZP_08229504.1| ribosomal large subunit pseudouridine synthase B [Leuconostoc
           argentinum KCTC 3773]
          Length = 249

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 90/237 (37%), Positives = 137/237 (57%), Gaps = 2/237 (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 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNA 187
           +A  L  P ++  +VY  +  G    +KL  LK+G+VIQG      +V+++   +    +
Sbjct: 122 IANQLMHPKSRVDKVYMAKVEGIATDEKLAPLKRGVVIQGRKTAPARVSVERVDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V + EG+N ++K + +     V +L R  Y  F L  L +G  R+++   ++  
Sbjct: 182 MVRVIIHEGRNHQVKNMLQKVGLPVAKLTREQYAFFDLTGLQSGEYRKLTSAEVKRL 238


>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 =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 86/232 (37%), Positives = 120/232 (51%), Gaps = 1/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
            TP+R+ KV+ARAG+ SRR  E  IA  RV V+G  +    + V      I  DG PLR 
Sbjct: 1   MTPERLQKVLARAGVGSRRRAEEFIAAGRVTVDGRRVTEMGLRVDPEKQAITFDGRPLRF 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L +KP G VTT +DP GR  V   L     R+  VGRLD +TEG LLLTNDG 
Sbjct: 61  PENKVTVLLNKPAGYVTTMADPQGRPMVGSLLKEPGLRLFPVGRLDFDTEGALLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  R Y+    G      L  L++GI ++G       V    ++G    +
Sbjct: 121 LAHRLLHPSFEIKRTYQATVEGTPGAQALRALRQGIELEGRRTHPAMVKTLRRRGEQTVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EG+ R+++K+       V  L R++YG  +LG L  GS R ++ + +
Sbjct: 181 EIIIHEGRKRQVRKMLAAVGHPVLHLKRVAYGDLRLGRLPLGSYRRLNHEDI 232


>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 =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 87/235 (37%), Positives = 128/235 (54%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E++I   +V VN  ++      V   + IEV+GVPL++ E+ 
Sbjct: 2   ERLQKVIAQAGIASRRKAEQLILDGKVTVNDKVVRELGTKVTGKEKIEVEGVPLQR-EKK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP G V+T SD  GR TV D      S RV  VGRLD +T G+LL+TNDG  A 
Sbjct: 61  VYYVLHKPRGYVSTVSDELGRRTVLDFFADRVSERVYPVGRLDYDTSGVLLMTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            +  PS +  +VY  R  G V  + L    KGI I G        TL +    N  + V 
Sbjct: 121 KMMHPSGEIDKVYLARVKGIVLPENLKPFGKGIEIDGYKTKPASATLVSVDKKNQSSLVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EG+  ++KK+F+   + V +L R  +G   +  L AG  R ++   ++  L
Sbjct: 181 LTIHEGRYHQVKKMFDAIGFPVKKLRREQFGTIDVQGLAAGEFRPLTPHEVKTLL 235


>gi|332977338|gb|EGK14123.1| ribosomal large subunit pseudouridine synthase B [Desmospora sp.
           8437]
          Length = 236

 Score =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 127/232 (54%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV+ARAG+ASRR+ E  I   +V+VNG  + +    V    D IEV+G  +R  E+
Sbjct: 2   ERLQKVMARAGVASRRKSEEWILSGKVRVNGKTVTQLGTRVDPERDRIEVEGRLIR-PEQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP G++T+ SDPDGR  V D    +  RV  VGRLD +TEGLLLLTNDG L  
Sbjct: 61  KRYFLFYKPKGVITSLSDPDGRPVVTDWFREVEERVYPVGRLDYDTEGLLLLTNDGELTH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VY+    G   +  L  L+ G+ +        +V +       A + + 
Sbjct: 121 GLAHPRHEVDKVYQATVKGIPAKKSLRRLETGVKLTDGWTAPAKVRMLRSGKEQACLELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++ E     V  L+R+      L  L  G  RE+SK+ +R  
Sbjct: 181 IHEGRNRQVRRMCEAVGHPVVHLVRVQLAFLTLSGLQPGEYRELSKEEIRRL 232


>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 =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 133/234 (56%), Gaps = 5/234 (2%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVT 190
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +   V +D +K + + V 
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIVKVDPEK-NRSVVE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 179 LTIHEGRNHQVKKMFESVGLLVDKLSRTQFGTLDLAGLRPGESRRLNKKEISQL 232


>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 =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 103/355 (29%), Positives = 157/355 (44%), Gaps = 13/355 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
            +P+R+ KV+A AGIASRR+ E +IA  RV VNG ++      V    D + VDG PLR 
Sbjct: 1   MSPERLQKVLASAGIASRRDCEELIAAGRVTVNGRVVTVPGTRVDLEHDEVLVDGQPLRM 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +    + HKP G+V+T  DP GR TV D +  + +RV  VGRLD+++EGL+LLT+DG 
Sbjct: 61  PAKRTYIMLHKPAGVVSTAEDPHGRPTVVDLV-DVPARVFPVGRLDLDSEGLILLTDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  + YRV     +  D L   + G++++G       V L        WV
Sbjct: 120 LAYALTHPSFEVEKEYRVLLDRALTPDALRSWRNGVLLEGEMTAPAWVELLETTPEGVWV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + LREG+ R+I+ V +   ++V RL+R+  GP QLG L   + R ++ + +        
Sbjct: 180 RIVLREGRKRQIRAVAKLLGYEVRRLVRVREGPLQLGDLPPRAWRHLTDEEVAALRAHVS 239

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +  +  ++     +     R          D     ++ S      S  +        R 
Sbjct: 240 VRRSLADVPT-RSTDVVKSRALDEKPHRAGDSAPVTRQRSEHSERRSSDRSRREQRDERV 298

Query: 310 LASNVWMAKGIHSSFLSD----------SGQREENHRRSPSFPSKRSLRRTSAKK 354
                W      +                G   E   R+   P  R   R  A +
Sbjct: 299 TEGPTWGETDARAGRAPRGRQDSRGEAGRGAWGETDARAGRAPRGRQDSRGEAGR 353


>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 =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 118/229 (51%), Gaps = 1/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+ R+++++ +     +  L R   G   +  L  G  R +S++ +
Sbjct: 183 IHEGRKRQVRRMCDSIGHPIIELKRTQIGDISIKGLKPGEWRLLSQREI 231


>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 =  285 bits (730), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  D+D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIADKDNLRPLTRGVEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>gi|311068833|ref|YP_003973756.1| RluB protein [Bacillus atrophaeus 1942]
 gi|310869350|gb|ADP32825.1| RluB [Bacillus atrophaeus 1942]
          Length = 244

 Score =  285 bits (730), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 127/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKIITELGVKVTGSDQIEVNGMKIEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D    I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAADDDKGRKVVTDFFKEIPQRIYPIGRLDYDTSGLLLLTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  Q  + Y  +  G   ++ +  L++G+ ++       +  L +  ++   + + +
Sbjct: 121 LMHPKYQIDKTYVAKVKGIPSKELVRKLERGVQLEEGKTAPAKAKLLSLDKRKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE++   ++  
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLDLRGLHTGDARELTPHEVKRL 233


>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 =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 131/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKKEISQL 232


>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 =  285 bits (729), Expect = 8e-75,   Method: Composition-based stats.
 Identities = 87/291 (29%), Positives = 141/291 (48%), Gaps = 6/291 (2%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAERTRL 75
            K+++ AG+ASRR  E +I   RV V+G+ +         S   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 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ----LGPHLLE 251
           G+NR+++++F     +V RL R+ +    L  L  G+ R ++   + E      G H  E
Sbjct: 182 GRNRQVRRMFAAVGCRVQRLRRVRFAMLTLDGLPCGAFRHLTLDEIHELQKIAGGIHSEE 241

Query: 252 EAQVNLDA-PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
            ++            +    R    +   D   R + +   K  L + K+ 
Sbjct: 242 GSRRRRRTSGDDGGGSGGGTRRERNAARKDAARRPQDDDHGKRPLQRDKRR 292


>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 =  285 bits (729), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 121/229 (52%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKGRKTILDLV-KVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYLTAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G      L  G  R ++ K +
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTNKEI 230


>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 =  285 bits (729), Expect = 9e-75,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 134/234 (57%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLL-AQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG  A+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNETKRIYPIGRLDLYTEGLLLLTNDGEFAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  D L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++  
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKAL 234


>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 =  285 bits (729), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 127/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 8   ERLQKRIANSGYTSRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKMEQEDKI 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    + +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 68  -YILFHKPAQVITSVSDDHGRTVVTDYFKDLDTRIYPVGRLDYDTSGVLLLTNDGEFTNL 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P     + Y  +  G + ++++  L+ GI ++        V +  Q        V +
Sbjct: 127 MTHPRYHIPKTYVAKLKGYLMREEVKTLEAGIELEDGLTQPATVKIKRQDKDKNTTLVEI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE F   VN+L RI +G   L  L AG  R ++   ++
Sbjct: 187 TISEGRNRQVRRMFEHFGHSVNKLTRIQFGSLNLKGLNAGEGRVLTPHEVK 237


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 132/232 (56%), Positives = 166/232 (71%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV++RAGIASRRE ERMI   RV VNG  +   A+NV + D I VDG  + + E  R
Sbjct: 11  RIAKVLSRAGIASRREAERMIEDGRVSVNGKTITSPALNVTADDRIVVDGKQVGEPEPPR 70

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +WLYHKP GLVTT  D   R TVF +LP    RV+SVGRLD+N+EGLLLLTNDG + R L
Sbjct: 71  IWLYHKPAGLVTTERDEKDRPTVFASLPETMPRVMSVGRLDLNSEGLLLLTNDGEVKRKL 130

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPST WLR YRVR +G V + KL+ L++GI ++GI Y  M VT D Q+G+NAW+TV LR
Sbjct: 131 ELPSTGWLRRYRVRINGSVSEAKLDELREGITVEGIQYQPMVVTFDRQQGANAWLTVSLR 190

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           EGKNREI++        VNRLIR+SYGPFQL  L  G   E+ ++++R+QLG
Sbjct: 191 EGKNREIRRAMGEIGVTVNRLIRVSYGPFQLAALKQGEVEELKQRVVRDQLG 242


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      + T+     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYTIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQL 232


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKDNLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQL 232


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 80/353 (22%), Positives = 149/353 (42%), Gaps = 41/353 (11%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N      +  R++K I+ +G  SRRE +++I  QRV +NG ++      V+S D +
Sbjct: 1   MNTSNTSNTTVSSIRLNKFISDSGFCSRREADKLIDSQRVTING-VIPELGTKVLSGDEV 59

Query: 61  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
            VDG  ++ +           YHKP+G+  T ++   +  + D +     R+  +GRLD 
Sbjct: 60  RVDGNLIKASAENKSDRVYLAYHKPVGITCT-TERHVKGNIIDAI-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------------SDAVEGSTKTALKTDQKIAANVTD----------KNAPKT 271

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           +  + +   H R + S V  AK           +R+  +  +P+ PS+    +
Sbjct: 272 EPTRSSKRSHHRGIKSQVGEAK--------HGSRRQATNNTAPATPSRGRKPK 316


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 86/232 (37%), Positives = 120/232 (51%), Gaps = 1/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
            TP+R+ KV+ARAG+ SRR  E  IA  RV V+G  +    + V      I  DG PLR 
Sbjct: 1   MTPERLQKVLARAGVGSRRRAEEFIAAGRVTVDGRRVTEMGLRVDPEKQAITFDGRPLRL 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L +KP G VTT +DP GR  V   L     R+  VGRLD +TEG LLLTNDG 
Sbjct: 61  PENKVTVLLNKPAGYVTTMADPQGRPMVGSLLKEPGLRLFPVGRLDFDTEGALLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  R Y+    G      L  L++GI ++G       V    ++G    +
Sbjct: 121 LAHRLLHPSFEIKRTYQATVEGTPGAQALRALRQGIELEGRRTHPAMVKTLRRRGEQTVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EG+ R+++K+       V  L R++YG  +LG L  GS R ++ + +
Sbjct: 181 EIIIHEGRKRQVRKMLAAVGHPVLHLKRVAYGDLRLGRLPLGSYRRLNHEDI 232


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 145/329 (44%), Positives = 201/329 (61%), Gaps = 6/329 (1%)

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 HLLEEAQVNLDAPIYSSETLVRDRPNIIS----EVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            ++  A  +   P  S           +S     V D     KK  +++  +  +K    
Sbjct: 639 KVIALAGCDFAGPSPSETKPKPRAGKAVSAEEWAVADAAPAPKKTITKRGAVEDRKGRKV 698

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQRE 332
            V R   AS                G+R+
Sbjct: 699 KVER--TASEGGDRPLSRGPARRYHGKRD 725


>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 =  284 bits (728), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 131/233 (56%), Gaps = 3/233 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R+ KVIA AGIASRR+ E+MI   RV+V+G L+ +    V +   I VD  P+ + 
Sbjct: 1   MTLERLQKVIAEAGIASRRKAEKMIVAGRVRVDGKLVTKLGTKVDTFSTITVDDEPIER- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L++KP G+V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG L
Sbjct: 60  ESLHTYLFYKPRGVVSTAHDDKGRKTVVDYFDDLPYRLYPVGRLDYDTSGLLLMTNDGKL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A +L  P  +  +VY  +  G ++ D++  LKKG+ + G      +V +    QK +N  
Sbjct: 120 ANLLMHPKNEVPKVYVAKIEGILEPDQIMTLKKGVKVDGRKCAPAKVKILKTNQKKNNQI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + + EG   E+K++F+     V +L R  Y    L  L  G  RE++++ +
Sbjct: 180 VQLTIHEGHYHEVKRMFKAVGHPVEKLSRERYAFLDLHALTYGQYRELTREEV 232


>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 =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 127/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGEARRLNKKEVSQL 232


>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 =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 129/234 (55%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMIVAGRVKVDGHVVTKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTAEDDRGRKTVVDYFEDLPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  L +G+ +        +V +     K     V +
Sbjct: 122 LMHPKNEVAKVYVAKIKGILTPDEIKTLTQGVKLDHFKAAPAKVKVLKTDHKKDTQIVQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG   ++K++F+     V++L R  Y    L +L +G  RE+SK  + + +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVDKLAREKYAFLTLDSLTSGQYRELSKHEVDKLM 235


>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 =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 126/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  D++ L  L KG+ + G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVADKEVLRPLTKGVEVDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTQFGHLNLTGLRPGEARRLNKKEVSQL 232


>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 =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 128/234 (54%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKIIAEAGIASRRKAEKMITAGRVKVDGKVITKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T SD   R TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTASDDKDRKTVVDYFEDVPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ +        +V +    ++     V +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPEEIKTLTHGVKLDDFKAAPAKVKVLKTDKRKDTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKNEVDKLM 235


>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 =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 85/238 (35%), Positives = 129/238 (54%), Gaps = 4/238 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K++A+ G+ASRR  ERMIA+ RV VNG ++          D I VDG  +R+  
Sbjct: 3   EPIRLHKLLAQMGVASRRAAERMIAEGRVSVNGRIVNTPGAMASPEDEIRVDGKLVRQQP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + R  L +KP G+++T  D  GR TV D L    +RV  VGRLD ++EGL+LLTNDG LA
Sbjct: 63  KMRYILLNKPAGVLSTAKDERGRKTVIDLL-GQSNRVYPVGRLDKDSEGLMLLTNDGELA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  P     + Y V   G      L  L +G+ ++      +   + ++    + + +
Sbjct: 122 QRITHPRYGVHKQYMVEVEGYFSDRSLQDLLQGVELEDGFSKPLDAKIISRSRDKSKLLI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLG 246
            + EG+ R++++      +KV RL R++ GP  LG L  G  RE+S +    LR QLG
Sbjct: 182 TMGEGRKRQVRRTLAALGYKVKRLTRVALGPLSLGNLKPGEYRELSDQEAKWLRSQLG 239


>gi|158320609|ref|YP_001513116.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140808|gb|ABW19120.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 234

 Score =  284 bits (727), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 79/229 (34%), Positives = 118/229 (51%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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 VTT S+   R  V D +   + R+  VGRLD NT GLL+LTNDG L  
Sbjct: 61  KVYILLNKPTGYVTTVSEQFNRKKVTDLVDVPY-RIFPVGRLDYNTSGLLILTNDGELTY 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|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 =  284 bits (727), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 106/355 (29%), Positives = 163/355 (45%), Gaps = 18/355 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
            + +R+ KV+A AGIASRR+ E  IA  RV VNG ++      V    D I VDG P+ K
Sbjct: 1   MSAERLQKVLASAGIASRRDCEEYIAAGRVMVNGKVVRIPGTRVDPEHDEILVDGKPIGK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  + HKP G+V+T  DP GR TV D + ++  R+  VGRLD ++EGLLLLT+DG 
Sbjct: 61  IHHRTYVMLHKPAGVVSTTDDPHGRPTVVDLV-NLPQRLFPVGRLDYDSEGLLLLTDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L + L  PS Q  + Y+V  +     + L   + G+ + G+      V L  +    AWV
Sbjct: 120 LTQKLTHPSYQVEKEYQVLLNDAPSPNALRAWRTGVELDGVKTAPAWVELIERTPEGAWV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EG+ R+I++V     ++V RLIR+  GP  LG L +G+ R ++ + +       L
Sbjct: 180 RVILHEGRKRQIREVARLLGYEVRRLIRVREGPLALGDLPSGTWRFLTDEEV-----DML 234

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            E A+ N  A   +     R++  + +       R+  ++       K  +   P     
Sbjct: 235 REHAERN-AAVADAERPRRREQDEMKAVGGRRLRRINPSARLLQKGEKVTETTLPELDEA 293

Query: 310 LASNVWMAK---GIHSSFLSDSGQREEN-------HRRSPSFPSKRSLRRTSAKK 354
           + S   +             ++  R  +         R   F S R   R S  +
Sbjct: 294 IGSEKGIPSIGEEGRKVRDKEAPHRNASPARDFRRDDRGSGFRSDRRNDRGSGPR 348


>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 =  284 bits (727), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 145/329 (44%), Positives = 201/329 (61%), Gaps = 6/329 (1%)

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 HLLEEAQVNLDAPIYSSETLVRDRPNIIS----EVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            ++  A  +   P  S           +S     V D     KK  +++  +  +K    
Sbjct: 644 KVIALAGCDFAGPSPSETKPKPRAGKAVSAEEWAVADAAPAPKKTITKRGAVEDRKGRKV 703

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQRE 332
            V R   AS                G+R+
Sbjct: 704 KVER--TASEGGDRPLSRGPARRYHGKRD 730


>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 =  284 bits (727), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 135/234 (57%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLL-AQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNETKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  D L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGIEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++  
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKAL 234


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 135/234 (57%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLL-AQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNETKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  D L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDDDLQIIANGVELEDGITAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++  
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKAL 234


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/235 (35%), Positives = 130/235 (55%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG+++           D I V G P++  E+
Sbjct: 2   ERLQKILAQAGVASRRKCEELIQAGSVEVNGVIVTELGTKADPDQDMITVKGRPIK-TEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP+GR  V D L  +  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 61  KIYLMMNKPKGVITSASDPEGRKIVSDYLKGVKERVYPVGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  P     + Y     G     +L+ LKKGIV++       +V        G  + + 
Sbjct: 121 LLTHPKHHVPKTYVATVKGVPHGTELDKLKKGIVLEDGITAPAEVEYKDVDPNGKESVIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EG+NR+++++FE  +  V RL RI++G   L  L  G TR ++K  +   +
Sbjct: 181 ITIYEGRNRQVRRMFEAISHPVIRLKRIAFGDLLLQNLKRGLTRPLTKDEINRLI 235


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 85/231 (36%), Positives = 132/231 (57%), 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   ERLQKVIANSGVTSRRKAEQLIAAGRVTVNGEVVRELGTKVSPNDRIEVEGIELTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+V+  +D  GR TV D    I  R+  VGRLD  T GLLL+TNDG  A  
Sbjct: 61  RYFLFYKPRGVVSAVTDDKGRKTVADYFVDIPERLYPVGRLDYETSGLLLMTNDGDFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 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|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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 121/229 (52%), Gaps = 2/229 (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+ D +  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKTILDLV-KVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKISKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK +
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKNDLKLGEWRYLTKKEI 230


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQL 232


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 119/231 (51%), Gaps = 1/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++  G  SRR+ E  I   RV+VNG           S D + VDG  +  + + 
Sbjct: 6   MRLQKYLSECGETSRRKAEIWITAGRVQVNGRPARLGQSVHPSKDLVTVDGRAVAPSPK- 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G VTT  D   R  V D L  + +RV  +GRLD ++EGLLLLT+DG  A  
Sbjct: 65  VYIALNKPRGYVTTLHDELDRRCVTDLLKGVETRVYPIGRLDRDSEGLLLLTDDGAFANA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     ++Y V    +V ++++  L+ GI + G      +VT+       + + + L
Sbjct: 125 LTHPRHHVPKIYHVSVRPRVTEEQVARLQNGIELDGRMTAPAKVTVLRSGSDRSVLELVL 184

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+NR+I+++ E    +V RL R++ G  +LG L +G  RE++ K +R  
Sbjct: 185 YEGRNRQIRRMCEALGLEVARLSRVAVGTVKLGGLRSGQWRELTDKEVRAL 235


>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 =  283 bits (726), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 126/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  D++ L  L KG+ + G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVADKEVLRPLTKGVEVDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTQFGHLNLTGLRPGEARRLNKKEVSQL 232


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 140/259 (54%), Positives = 180/259 (69%), Gaps = 1/259 (0%)

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 AWLTVSLKEGKNREIRKVMAGMNLHVSRLIRTSYGPFQLGTLQRRELEEVSPRVLRDQL- 239

Query: 247 PHLLEEAQVNLDAPIYSSE 265
           P   E+A     AP   ++
Sbjct: 240 PKATEKAPPARRAPAKQAD 258


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 123/233 (52%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+   E  
Sbjct: 6   ERLQKVIANAGIASRRHAETLIASGHVKVNGHVTTEMGIKIGPHDTVEVDGVPI-GKEAK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G+++   D  GR  V D    +  R+  VGRLD +T GLL++TNDG LA  
Sbjct: 65  RYFLFYKPRGVISAVEDNKGRKVVTDYFEDVQERLYPVGRLDYDTSGLLVMTNDGELANH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P     + Y  +  G  ++  L  LK G+ I G      +V + +  +    A V +
Sbjct: 125 LMHPRYALEKKYVAKVEGIPNRPALAPLKTGVSIDGKMTAPAKVEILSTDKAKKTAIVAL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L + 
Sbjct: 185 TIHQGMNHQVKKMFKAVGFPVIKLSREAYGNLTLAGLQPGEHRPIKPQELHDL 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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 76/228 (33%), Positives = 120/228 (52%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A+ G+ASRR+ E +I Q RVKVNG  + +    +    D +EVDG  +     
Sbjct: 1   MRLQKFMAQCGVASRRKCEEIIQQGRVKVNGKTVNQLGFKIDPEKDIVEVDGERISLQSH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G++++  D  GR TV D +    + RV  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|229543960|ref|ZP_04433019.1| pseudouridine synthase [Bacillus coagulans 36D1]
 gi|229325099|gb|EEN90775.1| pseudouridine synthase [Bacillus coagulans 36D1]
          Length = 245

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 135/233 (57%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ SRR+ E++I + +VKVNG  +      V  +D IEV+G+PL + E+ 
Sbjct: 2   ERLQKVIAQAGVTSRRKAEQLILEGKVKVNGETVRTLGTKVSQSDKIEVEGIPLEREEK- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+++  SD  GR TV D      +RV  VGRLD +T GLL++TNDG  A +
Sbjct: 61  VYYLFYKPRGVISAVSDDKGRKTVSDYFRDAGARVYPVGRLDYDTSGLLVVTNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G   + +L  L+KGI ++       +  L +  ++   A V +
Sbjct: 121 LMHPRFEIDKTYIARLSGIPSRQELKQLEKGIRLKDGMTAPARAKLLSMDKRKKKAIVQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE   + V +L R +YG   L  L AG  RE++   ++  
Sbjct: 181 TIHEGRNRQVRRMFEHLGYPVEKLRREAYGMLTLKGLNAGEKRELTPHEVKTL 233


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 124/234 (52%), Gaps = 3/234 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           +  P     + Y  +  G      +  L++GI I G         + +   + +   V++
Sbjct: 121 MTHPKHHVEKKYIAKVKGVPTPRHMRQLERGIWIDGKKTSKAVARILSVDTEKNTGIVSL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG N ++KK+FE     V +L R  +G   L  L  G  RE+    +++ +
Sbjct: 181 TIHEGWNHQVKKMFEAVELPVQKLKREEFGFLTLENLRPGDYRELRAFEVQKLV 234


>gi|325690957|gb|EGD32957.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK115]
          Length = 242

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTQPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G        ++     + + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVTIDGKKTKPATYEILKVDVEKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKKEISQL 232


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G        ++     + + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVTIDGKKTKPATYEILKVDVEKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   +  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLLVDKLSRTQFGNLDVSGLRPGEYRRLNKKEISQL 232


>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 =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 124/233 (53%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +G  SRR+ E +I Q +V+VNG ++      V   D + V+G P+   E  
Sbjct: 2   ERLQKVIAASGYTSRRKAEDLIVQGKVEVNGQVVRELGTKVKKGDIVTVEGKPIVG-ENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G V T  D   R  V D    +  R+  VGRLD +T GL++++NDG  A +
Sbjct: 61  VYYVFYKPKGCVCTLDDEFDRPIVTDYFTDVKERIYPVGRLDFDTTGLIIMSNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P +   ++Y V   G ++   LN L+KGI ++G+     ++ +  +        + +
Sbjct: 121 IMHPRSHLEKIYEVSVKGLINGQTLNKLEKGIYLEGVKTLPCKIKVVNKDIEHKTTMLKI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L EGKNR++KK+FE     V RL R+S G   L  L  G  R +  + +++ 
Sbjct: 181 KLVEGKNRQVKKMFESVGHPVKRLHRVSIGCVNLKGLTPGKYRILKPQEVKDL 233


>gi|309389185|gb|ADO77065.1| ribosomal large subunit pseudouridine synthase B [Halanaerobium
           praevalens DSM 2228]
          Length = 236

 Score =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 124/232 (53%), Gaps = 2/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ KV+A AG+ASRR+ E +IA+ RVKVNG ++      +      + VDG  +   E+
Sbjct: 2   ERLQKVMAHAGVASRRKSEEIIAEGRVKVNGQVITEMGYKIDPAQAEVMVDGQVIS-EEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G +TT SDP+ R TV D +P +  R+   GRLD ++ GLL++TNDG L  
Sbjct: 61  KVYILLNKPEGYITTVSDPENRPTVMDLIPDLNQRLYPAGRLDFDSSGLLIMTNDGDLTY 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + YRV   G+++++     + G+VI G      +++    KG      + 
Sbjct: 121 KLTHPKKEVDKKYRVLIQGKLEEEDFEKFEAGMVIDGQETAPAEISNVDYKGEQTEFDIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++ +   + V  L RI +    L  +  G  R +++  +   
Sbjct: 181 IHEGRNRQVRRMAKIAGFSVISLKRIGFAFLTLTGVEEGKFRYLTEAEVENL 232


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQL 232


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 116/245 (47%), Gaps = 8/245 (3%)

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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLL 122
            P+    +    L +KP G+++   D     TV D     +    +  VGRLD +TEG L
Sbjct: 64  EPIVYQSQFYY-LLNKPAGVISATVD-SYEETVLDLFSEEAFREDLFPVGRLDKDTEGFL 121

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-- 180
           L+TNDGGLA  L  P     + Y  +  G +  +      KGI + G      ++ +   
Sbjct: 122 LITNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKTFAKGIKLDGEWTLPAELQILNV 181

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            +  + + + + L EGK  ++K++      +V  L RI  G   L   L  G  RE++ +
Sbjct: 182 DEDETRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTPE 241

Query: 240 ILREQ 244
            L + 
Sbjct: 242 ELAKL 246


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 121/229 (52%), Gaps = 2/229 (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+ D +  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKTILDLV-KVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYITAPATLEILKISKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G      L  G  R ++KK +
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKNDLKLGEWRYLTKKEI 230


>gi|327490097|gb|EGF21885.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1058]
          Length = 242

 Score =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 133/233 (57%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTQPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 124/229 (54%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYLCTAKDEKGRKTILDLV-KVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTMKKDHIELFKKGIDIGDYITAPAALEIFKTNKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G    G L  G  R ++KK +
Sbjct: 182 IHEGKNRQVRRMCKSIGHPVIDLDRISIGNISKGDLKLGEWRYLTKKEI 230


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 127/231 (54%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGEVVTELGTKVKPSDQVEVEGIKMEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    + +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILFHKPAQVITSVSDDRGRTVVTDYFKDLDTRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P     + Y  +  G + ++++  L+ GI ++        V +  Q        V +
Sbjct: 125 MTHPRYHIPKTYVAKLKGYLMREEVKALEAGIELEDGLTQPATVKIKRQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE F   VN+L RI +G   L  L AG  R ++   ++
Sbjct: 185 TISEGRNRQVRRMFEHFGHSVNKLTRIQFGSLNLKGLNAGEGRVLTPHEVK 235


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVITELGVKVTGSDQIEVNGLKVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAADDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  + +  ++   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPSKELLRKLERGIQLEEGKTAPARAKMLSLDKRKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  Y    L  L  G  RE++   ++  
Sbjct: 181 TIHEGRNRQVRRMFEAIGHDVLKLKREEYAFLDLRGLHTGDARELTPHEVKRL 233


>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 =  283 bits (725), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 153/376 (40%), Positives = 210/376 (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 EAQVNL----------DAP--------------------IYSSETLVRDRPNIISEVPDD 281
            A  +           +AP                    + +     R   +  + V D 
Sbjct: 268 AAGADFTGLLVERELEEAPPRVALRPAGKRQAAAEKGGTLKAPARRSRQDEDFDAPVEDV 327

Query: 282 FTRMKKNSSQKNGLSKQKKLATPVHRRNLAS----NVWMAKGIHSSFLSDSGQREENHRR 337
                  + ++       +    V  R   +     V   K    +  + +G R    + 
Sbjct: 328 IRPAGPRTRRRMSDENAVESRGSVADRKGRTVKVERVVAPKADAPTRGARTGARPGARKS 387

Query: 338 SPSFPSKRSLRRTSAK 353
                  R  RR  A+
Sbjct: 388 DRDEAGARPFRRGPAE 403


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+V+ G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLIRGVVLDGKKTQPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQL 232


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 90/259 (34%), Positives = 137/259 (52%), Gaps = 12/259 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++AR GIASRR  E++I   RV +NG  ++         D + VDG PL+  ER 
Sbjct: 3   ERVQKILARWGIASRRGAEKLILAGRVTLNGKPVQLGDQADPEGDRLCVDGKPLKATERP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           R   +L HKP G+V+T +DP GRSTV D LP    +   +  +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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EG+NR+I++V E   + V +L R++ G   LG L  G  R ++K  +++     
Sbjct: 183 IDIMLTEGRNRQIRRVAEQLGFPVVKLHRLAIGNLHLGDLQRGQARPLTKAEIKQL---- 238

Query: 249 LLEEAQVNLDAPIYSSETL 267
               +Q N + P +SS  +
Sbjct: 239 ---RSQYNSNFPFHSSAPV 254


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 70/229 (30%), Positives = 120/229 (52%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD++T G+++LTNDG +  
Sbjct: 63  KIYILLNKPKGYVCTAKDEKDRKTILDLV-KVKERIYPIGRLDMDTSGIIILTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y+ +  G + +D + L KKGI I         + +       + + + 
Sbjct: 122 KIIHPKFEKIKTYKAKVKGTIKKDHIELFKKGIDIGDYLTAPATLEILKINKDTSEIIIK 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+++++ +     V  L RIS G      L  G  R ++ K +
Sbjct: 182 IHEGKNRQVRRMCKSIGHAVIDLDRISIGNITKSDLKLGEWRYLTNKEI 230


>gi|154686561|ref|YP_001421722.1| RluB [Bacillus amyloliquefaciens FZB42]
 gi|154352412|gb|ABS74491.1| RluB [Bacillus amyloliquefaciens FZB42]
          Length = 244

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVITELGVKVTGSDQIEVNGLKVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D    +  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAADDDKGRKVVTDFFKEVPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L +  ++   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPSKELLRKLERGIQLEEGKTAPARAKLLSLDKRKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  Y    L  L  G  RE+S   ++  
Sbjct: 181 TIHEGRNRQVRRMFEAIGHDVLKLKREEYAFLDLRGLRTGDARELSPHEVKRL 233


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 87/231 (37%), Positives = 133/231 (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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+ R+I+K+ E     V RLIRI+    +LG L  G  R ++K+ + + 
Sbjct: 183 HEGRKRQIRKMLERVGHPVIRLIRIAIDGVKLGDLKPGQLRPLTKEEIEKL 233


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 120/229 (52%), Gaps = 2/229 (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 D +  +  R+  +GRLD ++ GLLLLTNDG +  
Sbjct: 62  KVYIALNKPVKYISSVKDEKGRKNVIDLI-DVKERIYPIGRLDYDSSGLLLLTNDGDIYN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y V  +G    +++  L+ GI I G      +V ++    + A + + 
Sbjct: 121 NLMHPSKEVYKTYLVTVNGIPTIEEIKKLETGIDIGGYITAPAKVKIEKLDYNKASLKIQ 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+I+K+ +     V  L RI+ G  +L  +  G  R ++K+ +
Sbjct: 181 IYEGKNRQIRKMCDSIGHSVIALKRIAIGDIKLKDIPQGKYRFLTKEEI 229


>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 =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 77/357 (21%), Positives = 152/357 (42%), Gaps = 20/357 (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 ++ D    + D +     R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTN 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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT--- 303
             + E +    DA    +    R R    +++ D     + +++++N    + +      
Sbjct: 234 --MCEGSVSTEDA-SKMNAKGQRIRKATDAKLFDSREENQTSTARRNQNENRTRTYRGNN 290

Query: 304 -------PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                  P  +R   S+   + G   ++ S+S     N  R+ S  ++        +
Sbjct: 291 ADEFRHAPNSKRGRNSSNGESGGNTENWKSNSRSERSNSDRNSSDRTRTDRNNNDRR 347


>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 =  283 bits (724), Expect = 4e-74,   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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 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|310642601|ref|YP_003947359.1| pseudouridine synthase [Paenibacillus polymyxa SC2]
 gi|309247551|gb|ADO57118.1| Pseudouridine synthase [Paenibacillus polymyxa SC2]
          Length = 252

 Score =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 83/235 (35%), Positives = 129/235 (54%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I    V+VNG+ +           D I V G P++  E+
Sbjct: 2   ERLQKILAQAGVASRRKCEELIQAGSVEVNGVTVTELGTKADPDQDMITVKGRPIK-TEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G++T+ SDP+GR  V D L  +  RV  VGRLD +TEGLLLLTNDG  A 
Sbjct: 61  KIYLMMNKPKGVITSASDPEGRKIVSDYLKGVKERVYPVGRLDYDTEGLLLLTNDGEFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
           +L  P     + Y     G     +L+ LKKGIV++       +V        G  + + 
Sbjct: 121 LLTHPKHHVPKTYVATVKGVPHGTELDKLKKGIVLEDGITAPAEVEYKDVDPDGKESVIQ 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + EG+NR+++++FE  +  V RL RI++G   L  L  G TR ++K  +   +
Sbjct: 181 ITIYEGRNRQVRRMFEAISHPVIRLKRIAFGDLLLQNLKRGLTRPLTKDEINRLI 235


>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 =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARIKGIATKENLRPLTRGVVIDGKKTKPARYNIIKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEQVGLLVDKLSRTQFGTLDLTGLRPGEARRLNKKEISQL 232


>gi|218660352|ref|ZP_03516282.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium etli IE4771]
          Length = 296

 Score =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 155/271 (57%), Positives = 188/271 (69%), Gaps = 11/271 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP
Sbjct: 32  TESEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVP 91

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R  ERTRLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLDINTEGLLLLTN
Sbjct: 92  IRGIERTRLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLDINTEGLLLLTN 151

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DGGLAR LELP+T WLR YRVR HG++DQ+ L+ LK GI + G+ YG ++ TLD  +GSN
Sbjct: 152 DGGLARALELPATGWLRRYRVRAHGEIDQEALDKLKDGIAVDGVLYGSIEATLDRTQGSN 211

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            W+T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV         G
Sbjct: 212 VWITMGLREGKNREIKNVMGALGLDVNRLIRISYGPFQLGDLPEGHVIEVR--------G 263

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           PH    A+    AP   S   +    + +  
Sbjct: 264 PH---AARSARPAPDRGSPRRISMHRSTMRR 291


>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 =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 79/234 (33%), Positives = 135/234 (57%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  G+ASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKFIASCGVASRRKAEELITEGKVQVNGRKVTELGVKIDPQKDKVKVNGQLL-AQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  +GRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNESKRIYPIGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  + L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDEDLQVIANGVKLEDGMTAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++  
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKAL 234


>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 =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 143/345 (41%), Positives = 188/345 (54%), Gaps = 8/345 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+K +ARAG+ASRREVER+I   RV +NG +L   AV V   D + VDG  + + E T
Sbjct: 35  ERVAKALARAGVASRREVERLIEAGRVAINGKVLTTPAVKVAPGDFLTVDGQLVAEREPT 94

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R++ YHKP GL+TTH+DP GR TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R 
Sbjct: 95  RIFRYHKPTGLMTTHNDPKGRPTVFGALPKDLPRLISVGRLDLNSEGLLLLTNDGELSRA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQKGSNAW 188
           LE PS  W+R YR R  G   Q KL+ LK G+ I+G+ YG ++  LD        G N W
Sbjct: 155 LETPSNAWVRRYRARAFGDTTQAKLDKLKDGVTIEGVTYGAIEAKLDKAHEKAGGGKNVW 214

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TV L EGKNRE++KV E    KVNRLIR+SYGPF LGTL AG   EV  +++RE L   
Sbjct: 215 ITVSLSEGKNREVRKVLESIGLKVNRLIRLSYGPFALGTLAAGQIEEVGPRVIRELLEGV 274

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +  E     D P ++        P       +   R    + +   L   +K   PV++ 
Sbjct: 275 VSPENMPTGDRPKFAGIANPTKAPGTEGG-GELQRRGAPRADRAVILDTPEKPEKPVYKP 333

Query: 309 NLASNVWMAK--GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             A     A   G          +     +R       + +    
Sbjct: 334 GWAKPKKKASPHGPPKGAGKGPAKGPAKAKRPAKSIESKFIDIGK 378


>gi|312277674|gb|ADQ62331.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 255

 Score =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K+  +      R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +
Sbjct: 2   LGRKDTAEAVEKRMRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIV 61

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EV+G P+   E    +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T G
Sbjct: 62  EVNGSPI-YNEEKVYYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVT 178
           LL+LTNDG     +  P  +  +VY  R  G   ++ L  L +G+VI G         + 
Sbjct: 121 LLILTNDGDFTDKMIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTQPAHYNII 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               + + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G +R +SK
Sbjct: 181 KVDHEKNRSVVELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLSK 240

Query: 239 KILREQ 244
           K + + 
Sbjct: 241 KEISQL 246


>gi|227498494|ref|ZP_03928640.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226903952|gb|EEH89870.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 246

 Score =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 86/240 (35%), Positives = 132/240 (55%), Gaps = 6/240 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A +G+ASRRE E++I Q RV VNG  +      V  TD I +DG PLRK ER 
Sbjct: 7   ERLQKMMAASGVASRRECEKIILQGRVTVNGKPVIELGTKVSPTDRILIDGRPLRK-ERH 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L +KP  ++TT  DP GR TV + +     RV  VGRLD  TEGLL++TNDG LA+ 
Sbjct: 66  RYFLLNKPPAVMTTMKDPRGRRTVAELMDKERERVYPVGRLDFMTEGLLIMTNDGALAQG 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           +  PS    + Y V   G V+++KL+ L+ GI +         V +     +   +   V
Sbjct: 126 MTHPSYHINKTYEVVVDGHVEEEKLDKLRTGIRLCDGMTAPALVEVKRYDSRRDQSIFEV 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPH 248
            + EG+NR+++++ E   + V +L R       L  +  G+ RE++      L++ +  H
Sbjct: 186 TIHEGRNRQVRRMCEAIGYPVRKLKRTQVAFLSLQGVKKGAYRELTDDEVVHLKKLVMHH 245


>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 =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSRETNKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSTSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|150390402|ref|YP_001320451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149950264|gb|ABR48792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 234

 Score =  282 bits (723), Expect = 5e-74,   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 D +  +  R+  VGRLD +T G LLLTNDG L  
Sbjct: 61  MIYILLNKPTGFVTTVSDQFDRKTVTDLV-GVSERIFPVGRLDYHTSGFLLLTNDGNLTF 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|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 =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 125/233 (53%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHH-EQH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D +    I  R+  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDDKGRRTVVDIIHDADIDERIYPVGRLDYDTTGILLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWV 189
             L  P  +  + Y  +  G V  D+L  L+ G+VI G      +  L    +    + V
Sbjct: 121 NKLMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVVIDGRKTKPAKSKLLNVDRAKKTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EG+N ++K +F+     V +L R +YGP  L  L  G  R +  + ++
Sbjct: 181 QLTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFRALKPEEVQ 233


>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 =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSRESNKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSTSSNTASGSKPTPRTGGTLSLRKSK 340


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

 Score =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 8/245 (3%)

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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLL 122
            P+    +    L +KP G+++   D     TV D     +    +  VGRLD +TEG L
Sbjct: 71  EPIAYQSQFYY-LLNKPAGVISATVD-SYEETVLDLFSEEAFREDLFPVGRLDKDTEGFL 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-- 180
           L+TNDGGLA  L  P     + Y  +  G +  +   +  KGI + G      ++ +   
Sbjct: 129 LITNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKIFAKGIKLDGEWTLPAELQILNV 188

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            +    + + + L EGK  ++K++      +V  L RI  G   L   L  G  RE++ +
Sbjct: 189 DEDEMRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTSE 248

Query: 240 ILREQ 244
            L + 
Sbjct: 249 ELAKL 253


>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 =  282 bits (723), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 149/346 (43%), Positives = 205/346 (59%), Gaps = 19/346 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + ++  +     +R++K +ARAG+ASRR+ E M+ Q RV VNG ++   A+++   D + 
Sbjct: 365 RREDAPKPKKAGERIAKALARAGLASRRDAEEMVTQGRVAVNGRVINSPALDITPNDVVT 424

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VDG PL   ERTRL+LYHKP GL+TTH DP+GR TVFDNLP    R+ISVGRLD NTEGL
Sbjct: 425 VDGKPLPPRERTRLFLYHKPRGLMTTHDDPEGRPTVFDNLPEGLPRLISVGRLDFNTEGL 484

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDGGLAR LELP T WLR YRVR HG V Q +L+ LK GI ++G+ YG +  TL+ 
Sbjct: 485 LLLTNDGGLARTLELPDTGWLRRYRVRAHGDVTQAQLDELKAGIEVEGVKYGPIDATLER 544

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G+N W+   +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   E+  ++L
Sbjct: 545 DQGANVWLVFAIREGKNREVRNVCAHLGLEVNRLIRVSYGPFQLGEVPEGQVEEIKSRVL 604

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           REQLG  ++E++    D P  ++ T             DD    +K  + K  +   +K 
Sbjct: 605 REQLGDKVIEKSGAQFDVPQKAAAT-------------DDGAPHEKKPASKRAVINDRKG 651

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
              + +R  +          +S      +R         +  KR L
Sbjct: 652 RRVLVQRTGSEEARERNEAEAS-GYGPPRRP-----KRGYHGKRDL 691


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 132/234 (56%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ K++A AG+ASRRE E++I   RV+VNG ++        +    I VDG P+   E 
Sbjct: 3   ERLQKILAAAGVASRREAEKIITAGRVRVNGKVVTELGCKFDADKVRISVDGKPI-AQEA 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++++KP G+VTT SDP  R ++ D + ++  RV  VGRLD NTEGLLLLTNDG LA+
Sbjct: 62  KAYYMFYKPRGVVTTMSDPQNRRSIADFVQNLPERVFPVGRLDFNTEGLLLLTNDGALAQ 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS +  + Y V+  G V Q+KL+ L+ G+ ++        V L             
Sbjct: 122 ALMHPSHEVNKTYFVKVPGIVPQEKLDQLRLGVKLEDGPTAPAIVNLRDYDHERGFTLFD 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+I+++ +   + V  L RI  GP QL  L  G  R +S++ L + 
Sbjct: 182 ITIHEGRNRQIRRMCDAIGFPVRDLKRIKLGPLQLQNLGRGKFRSLSEQELSQL 235


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 131/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGLATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKKEISQL 232


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 116/245 (47%), Gaps = 8/245 (3%)

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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLL 122
            P+    +    L +KP G+++   D     TV D     +    +  VGRLD +TEG L
Sbjct: 71  EPIAYQSQFYY-LLNKPAGVISATVD-SYEETVLDLFSEEAFREDLFPVGRLDKDTEGFL 128

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-- 180
           L+TNDGGLA  L  P     + Y  +  G +  +   +  KGI + G      ++ +   
Sbjct: 129 LITNDGGLAHQLLSPKKHVEKEYYAQVEGIMTAEDQKIFAKGIKLDGEWTLPAELQILNV 188

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            ++   + + + L EGK  ++K++      +V  L RI  G   L   L  G  RE++ +
Sbjct: 189 DEEEMRSEIKLILHEGKFHQVKRMVHAVGKEVVYLKRIRMGGLSLPDDLALGEYRELTSE 248

Query: 240 ILREQ 244
            + + 
Sbjct: 249 EMAKL 253


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 136/235 (57%), 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
            ++    L++KP  ++T+ SD  GR+ V D   ++ +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKI-YILFYKPTQVITSVSDDRGRTVVTDYFKNLEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
              ++  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +  
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|312622236|ref|YP_004023849.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202703|gb|ADQ46030.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 77/227 (33%), Positives = 120/227 (52%), Gaps = 2/227 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E +I Q RVKVNG L+ +    V    D +EVDG  +    + 
Sbjct: 6   RLQKFMAQCGVASRRKCEEIILQGRVKVNGELVNQLGFKVDPEKDVVEVDGKRISPQMQK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +    + RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 66  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   + ++   +KG++I G      +  +      NA V + 
Sbjct: 126 KVTHPKHDIEKTYIALIKGIPSKKEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIK 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+NR+I+K+ +    KV +L RI+ G  QLG L  G    + ++
Sbjct: 186 IHEGRNRQIRKMCDQIGHKVLKLKRIAIGKLQLGKLKEGEFVFLDRE 232


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSTSSNTASGSKPTPRTGGTLSLRKSK 340


>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 =  282 bits (722), Expect = 5e-74,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G  +L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLELTGLRPGESRRLNKKEISQL 232


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 81/236 (34%), Positives = 127/236 (53%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V VNG ++      V  +D + VDGVP+++ E  
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIAAGHVAVNGQVVTELGTKVTKSDQVTVDGVPIKR-EPL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
           + +L +KP G+V+T  D  GR TV D L       RV  VGRLD +T G+LLLTNDG LA
Sbjct: 61  KYYLLNKPRGVVSTAHDDKGRRTVVDILKDDDVEERVYPVGRLDYDTTGILLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
             L  P  +  + Y  +  G +    L  L++G+++ G    + +  L     +   + V
Sbjct: 121 NKLMHPKFEVEKTYIAKVKGVLSNHDLQKLRQGVIVDGRKTREAKSKLLEVADNRQSSRV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQ 244
            + + EG   ++K++ +     V +L R SYGP  L  L + G  RE+    +++ 
Sbjct: 181 RLTIHEGHYHQVKRMLKAVGHPVIKLHRESYGPLNLYGLASGGQWRELKPNEVKQL 236


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 129/234 (55%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMITAGRVKVDGKVITKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T SD  GR TV D    I  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTASDDKGRRTVVDYFEDIPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L  G+ +        +V +    ++     V +
Sbjct: 122 LMHPRNEVQKVYVAKIKGILTPEEIEGLTHGVKLDRFKAAPAKVKILKTDKRKDTQIVQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKNEVDKLM 235


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 148/322 (45%), Positives = 193/322 (59%), Gaps = 1/322 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T +R++KV+ARAG+ASRR+ E  + Q RV VNG ++   A++V S D I +DG PL +
Sbjct: 356 KKTGERIAKVMARAGVASRRDAEEWVTQGRVAVNGRVINSPALDVTSRDVITIDGQPLPE 415

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRL+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGG
Sbjct: 416 RERTRLFLYHKPRGLMTTHADPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDGG 475

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LAR LELP T WLR YRVR HG+V Q +L+ LK G+ + G+ YG +  TL+  +G+N W+
Sbjct: 476 LARALELPDTGWLRRYRVRAHGEVTQAQLDALKNGVEVDGVKYGSIDATLERDQGANVWL 535

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
              +REGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG  +
Sbjct: 536 VFAIREGKNREVRNVMAHLGLEVNRLIRVSYGPFQLAEIAEGQVEEVKTRVLREQLGDKI 595

Query: 250 LEEAQVNLDAPIYSSETLVR-DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
              A  N       +ET  +  R         D     K S  ++   +   +       
Sbjct: 596 AALANANFAGTAAEAETEPKLGRDGTPLRSKKDNKARAKRSLIEDRKGRNVVVQRTGSDE 655

Query: 309 NLASNVWMAKGIHSSFLSDSGQ 330
             A N   A G         G 
Sbjct: 656 ARARNEAEANGYGPPRRPKRGY 677


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 142/319 (44%), Positives = 193/319 (60%), Gaps = 3/319 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++KV++RAG+ SRR+ E  + Q RV VNG ++   A++V + D I VDG PL   E
Sbjct: 421 AGERIAKVVSRAGLCSRRDAEEWVTQGRVAVNGRIINSPALDVTTRDVITVDGKPLPLPE 480

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL++YHKP GL+TTH+DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLA
Sbjct: 481 RTRLFMYHKPRGLMTTHADPEGRPTVFDHLPDGLPRLISIGRLDFNTEGLLLLTNDGGLA 540

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELP T WLR YRVR HG+V Q +L+ LKKG+ + G+ YG +  TL+  +G+N W+  
Sbjct: 541 RTLELPDTGWLRRYRVRAHGEVTQGQLDELKKGVEVDGVKYGSIDATLERDQGANVWLVF 600

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            +REGKNRE++ V      +VNRLIR+SYGPFQLG L  G   EV  ++LREQLG  +  
Sbjct: 601 AIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLGELEEGQVEEVKTRVLREQLGEKIAA 660

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            +  +    I S   +  D   +   V   + R      +   +  Q+  +     RN A
Sbjct: 661 ASGADFARQIPSKGDVDLDPVVVKKPV---YKRGTVEDRKGRRVLVQRTGSEEARARNEA 717

Query: 312 SNVWMAKGIHSSFLSDSGQ 330
                      +      +
Sbjct: 718 EANGYGPPRRPTRGYKGKR 736


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYIARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGEARRLNKKEISQL 232


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 135/234 (57%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA  GIASRR+ E +I + +V+VNG  +    V +    D ++V+G  L   E+
Sbjct: 2   ERLQKYIASCGIASRRKAEELITEGKVQVNGRKVTELGVKINPQKDKVKVNGQLL-AQEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++T+ SDP GR TV D + +   R+  VGRLD+ TEGLLLLTNDG LA+
Sbjct: 61  PVYYLLNKPKGVITSVSDPQGRETVLDYIKNESKRIYPVGRLDLYTEGLLLLTNDGELAQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVT 190
            L  PS    + Y VR  G+V  + L ++  G+ ++        +        N    V 
Sbjct: 121 NLTHPSKGVEKTYEVRIKGRVRDEDLQVIANGVKLEDGMTAPATIVDLGFDDHNGVHEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE F ++++ L RI+Y    LG +  G++R+++ + ++  
Sbjct: 181 ITIHEGRNRQVRRMFEHFGYRIHNLKRIAYAGLTLGGVKRGASRQLTIREVKAL 234


>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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L KGIVI G      +  +    ++ + + V +
Sbjct: 120 MLHPRHEIDKVYVARVKGLASKDNLRPLTKGIVIDGKKTQPARYRIVKTDREKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLMVDKLSRTRFGTLDLSGLNPGEARRLNKKEISQL 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 =  282 bits (722), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 76/227 (33%), Positives = 120/227 (52%), Gaps = 2/227 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    + 
Sbjct: 6   RLQKYMAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRITLQMQK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +    + RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 66  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   +KG++I G      +  +      NA V + 
Sbjct: 126 KVTHPKHDIEKTYIALIRGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIK 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + EG+NR+I+K+ +    +V +L R++ G  QLG L  G    + K+
Sbjct: 186 IHEGRNRQIRKMCDQIGHEVLKLKRVAIGKLQLGKLKEGEFVFLDKE 232


>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 =  282 bits (722), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 79/247 (31%), Positives = 128/247 (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---QGICYG--DMQVTL 179
           TNDG  A+ L  P  +  + Y V+  G   +  L  L+ G+      G  Y     +   
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|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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIVKVDHEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGESRRLNKKEISQL 232


>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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 128/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +IA  RVKVNG ++      V   D I +D   L+  E  
Sbjct: 2   ERLQKAIAASGYTSRRKAEDLIAAGRVKVNGEVISELGFKVKKGDMIMIDDKALKG-ENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G + + SD  GRSTV D  P +  R+  VGRLD +T G+LL++NDG  A +
Sbjct: 61  VYYVFYKPKGCICSLSDELGRSTVIDYFPEVEERIYPVGRLDYDTTGVLLMSNDGEFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  PS+   +VY V   G V  + L+ L+KG+ ++G      ++ +  +  +     + +
Sbjct: 121 MMHPSSHLEKVYEVSVSGLVQGETLHKLEKGVYLEGTKTLPCKIKVTHKDVEHKTTILMI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L EGKNR++KK+FE    KV RL R+  G   L  L  G  R +  + ++E 
Sbjct: 181 KLVEGKNRQVKKMFEAMGHKVKRLHRLQVGTINLKGLTPGHYRLLKPQEVKEL 233


>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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 140/259 (54%), Positives = 180/259 (69%), Gaps = 1/259 (0%)

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 AWLTVSLKEGKNREIRKVMAGMNLHVSRLIRTSYGPFQLGTLLRRELEEVSPRVLRDQL- 239

Query: 247 PHLLEEAQVNLDAPIYSSE 265
           P   E+      AP   ++
Sbjct: 240 PKATEKTPTTQRAPAKQAD 258


>gi|323489657|ref|ZP_08094884.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323396788|gb|EGA89607.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 243

 Score =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 131/231 (56%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR+ E++I   +V+VNG  ++   V V ++D IEV+GV L K E+ 
Sbjct: 2   ERLQKVLAHAGVASRRKSEQLILDGKVRVNGKTIKELGVKVSNSDKIEVEGVQLEK-EQK 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 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|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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 340


>gi|325687113|gb|EGD29136.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK72]
          Length = 242

 Score =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 123/233 (52%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I Q +V+VNG ++      V   D I V+G PL   E  
Sbjct: 2   ERLQKAIAASGYTSRRKAEDLIVQGKVEVNGKVVTELGTKVKQGDLITVEGKPLVG-ENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G V T  D   R  + D    +  R+  VGRLD +T GL++++NDG  A +
Sbjct: 61  VYYVFYKPKGCVCTLDDEFDRPIITDYFTEVKERIYPVGRLDFDTTGLIIMSNDGEFANM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P +   ++Y V   G +    LN L+KG+ ++G+     ++ +  +  +     + +
Sbjct: 121 IMHPRSHLEKIYEVSIKGLITGPTLNKLEKGVYLEGVKTLPCKIKVVDKDTEHKTTMLKI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L EGKNR++KK+FE     V RL R+S G   L  L  G  R +  + +++ 
Sbjct: 181 KLVEGKNRQVKKMFESVGHPVKRLHRVSIGGINLKGLTPGRYRILKPQEVKDL 233


>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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 125/233 (53%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHH-EQH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D +    I  R+  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDDKGRRTVVDIIHDADIDERIYPVGRLDYDTTGILLLTNDGTLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWV 189
             L  P  +  + Y  +  G V  D+L  L+ G++I G      +  L    +    + V
Sbjct: 121 NKLMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVIIDGRKTKPAKSKLLNVDRAKKTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EG+N ++K +F+     V +L R +YGP  L  L  G  R +  + ++
Sbjct: 181 QLTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFRALKPEEVQ 233


>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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 80/246 (32%), Positives = 131/246 (53%), Gaps = 3/246 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K+  +      R++K IA AG+ASRR+ E +I + RV +NG  +   A  V + D +
Sbjct: 2   LGRKDTAEAVEKRMRINKYIAHAGVASRRKAEELIKEGRVTLNGKTVMELATIVKNGDIV 61

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EV+G P+   E    +L +KP G++++ SD   R TV D +P +  R+  VGRLD +T G
Sbjct: 62  EVNGSPI-YNEEKVYYLLNKPRGVISSVSDEKNRKTVIDLMPHVKERIYPVGRLDWDTTG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVT 178
           LL+LTNDG     +  P  +  +VY  R  G   ++ L  L +G+VI G         + 
Sbjct: 121 LLILTNDGDFTDKMIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTQPAHYNII 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               + + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G +R ++K
Sbjct: 181 KVDHEKNRSVVELTIHEGRNHQVKKMFESVGLIVDKLSRTRFGTLDLTGLRPGESRRLNK 240

Query: 239 KILREQ 244
           K + + 
Sbjct: 241 KEISQL 246


>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 =  282 bits (721), Expect = 7e-74,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLHPGESRRLNKKEISQL 232


>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 =  282 bits (721), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 84/246 (34%), Positives = 128/246 (52%), Gaps = 3/246 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK ++I+       R+ KV++  G+ SRR+ E  IAQ RV VNG   +       + D I
Sbjct: 1   MKTEDIMA-KVNGIRIQKVLSENGVMSRRKAEEAIAQGRVTVNGHPAQPGNPVDPARDVI 59

Query: 61  EVDGVPL--RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +DGV +  RK ++    + HKP G VTT SD  GR  V D +    + V  VGRLD N+
Sbjct: 60  AIDGVRVQLRKKKQNVYIMLHKPRGFVTTTSDELGRRCVTDLVKDAPAHVYPVGRLDRNS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLLLTNDG  A ++  PS    + YRV     V  ++   +  G+++ G       V 
Sbjct: 120 EGLLLLTNDGAFANLVMHPSNHISKTYRVTVRPDVSDEQAAKMSAGVMLDGRMTLPATVL 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +  ++     + + ++EG+NR+++++ E    +V RL R S GP +LG L  G  RE+  
Sbjct: 180 VLEKQDGRVVLQITIQEGRNRQVRRMCEAVGLEVARLKRTSVGPLKLGMLQPGQWRELRP 239

Query: 239 KILREQ 244
             +   
Sbjct: 240 GEVAAL 245


>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 =  282 bits (721), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 125/233 (53%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           L  P  +  +VY  +  G    D L  L++G+VI G      +  +   K +  NA V +
Sbjct: 121 LMHPRYEIDKVYVAKVKGYPSPDALKRLEEGLVIDGQKTAKARARIRKNKAAKENATVEL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+ E     V RL R  YG      L  G  R + K  +   
Sbjct: 181 TIHEGRNRQVRKMLEAVGHPVKRLNRERYGFLTTEGLGVGEYRPLLKAEVERL 233


>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 =  282 bits (721), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 99/341 (29%), Positives = 160/341 (46%), Gaps = 6/341 (1%)

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  K-PERLKYFVLNKPKGVLCTNHDPAGRTRVIDLFAKERVRLFPVGRLDEDSEGLLIVTND 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 FLEIVLGQGHNREIRRLFARIGHKVMSLQRIAFGPIRLGKQKVGQYRELTRNELEEL--R 261

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN--GLSKQKKLATPV 305
            +LE  +        S  +            P    + + +  +    G  +       +
Sbjct: 262 SILERNKKTPPKGPRSGGSGNSSPKRGSKGAPKGRRKPEGSGRKPEMAGSEEATPQKKRI 321

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            R N +  V  + G      S    R       P+   K++
Sbjct: 322 RRPNNSPTVGASGGKSGGRPSGGKSRSGYGSSKPAAGKKKT 362


>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 =  282 bits (721), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  282 bits (721), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTDQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSRETNKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 340


>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 =  282 bits (721), Expect = 8e-74,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 340


>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 =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 137/243 (56%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +V VNG ++      V ++D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVSVNGQVVTELGTKVSNSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR+ V D    I +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILFYKPTQVITSVSDDRGRTVVTDYFDDIETRIYPVGRLDYDTSGILLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEVKELEKGIQLEDGFTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F  +VN+L RI +GP  L  L AG  R ++   ++     HL E
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVNKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTL--RHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 NGK 245


>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 =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKENLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 135/235 (57%), 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
            ++    L++KP  ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKI-YILFYKPTQVITSVSDDRGRTVVTDYFKDLEARIYPVGRLDYDTSGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
              ++  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +  
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|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 =  281 bits (720), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 125/233 (53%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++I Q +V VNG ++      V   D I V+GVP+   E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLILQGKVAVNGKIVTELGTKVGVHDEIVVNGVPIHH-EQH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D +    I  R+  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDDKGRRTVVDIIHDAEIDERIYPVGRLDYDTTGILLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWV 189
             +  P  +  + Y  +  G V  D+L  L+ G+VI G      +  L    +    + V
Sbjct: 121 NKMMHPKYEVEKTYVAKVEGIVKNDELKQLRLGVVIDGRKTKPAKSKLLNVDRAKKTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EG+N ++K +F+     V +L R +YGP  L  L  G  R +  + ++
Sbjct: 181 QLTIHEGRNHQVKNMFKAVGHPVTKLHRETYGPLNLYGLQPGEFRALKPEEVQ 233


>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 =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 86/231 (37%), Positives = 129/231 (55%), Gaps = 2/231 (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 +KP G VTT SDP GR  V D L  I  R+  VGRLD++TEG LL+TNDG L  
Sbjct: 63  IYV-LLNKPAGYVTTLSDPQGRPMVSDLLADIPLRLFPVGRLDLDTEGALLMTNDGELGN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G    DKL  L+ GI I G+      V L  +      V + 
Sbjct: 122 AILHPRYEVNKTYEAEVSGSPSVDKLKRLESGIEIDGVMTRPAVVRLLRRHKGTTLVEIT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EGK R+++K+F+  N +V  L R +YG  +LG+L  G  R +++  L++
Sbjct: 182 IHEGKKRQVRKMFQAINHRVLHLRRTAYGNLRLGSLPLGKYRVLNQNDLKK 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 =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 143/284 (50%), Positives = 190/284 (66%), Gaps = 1/284 (0%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
              +   T +R++KV+ARAG+ASRR+ E M+ Q RV VNG ++   A++V   D I+VDG
Sbjct: 357 EAPKPRKTGERIAKVLARAGLASRRDAEEMVTQGRVSVNGRIINSPALDVTENDEIKVDG 416

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL + ERTRL+LYHKP GL+TTHSDP+GR TVFDNLP    R+IS+GRLD NTEGLLLL
Sbjct: 417 APLPERERTRLFLYHKPRGLMTTHSDPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLL 476

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGGLARVLELP T W R YRVR HG++ Q +L+ L  G+ + G+ YG ++ TL+  +G
Sbjct: 477 TNDGGLARVLELPDTGWTRRYRVRAHGEITQGQLDQLAAGVEVDGVKYGPIEATLERDQG 536

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +N W+ V +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G  +EV  ++LREQ
Sbjct: 537 ANVWLVVAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELPEGEVQEVKTRVLREQ 596

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           LG  ++ ++  +L  P  SS       P    +      R  + 
Sbjct: 597 LGEKVIAQSGADL-GPAGSSNREPLPDPKPKPKREIVADRKGRR 639


>gi|310828101|ref|YP_003960458.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308739835|gb|ADO37495.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 241

 Score =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/241 (33%), Positives = 121/241 (50%), Gaps = 8/241 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ G+ASRR+ E MIA  RV VNG  +    + V    D + VDG  +   ++
Sbjct: 1   MRLQKYMAQCGVASRRKSEEMIAAGRVCVNGEAVLTPGLQVDPEADTVTVDGKTI-AEDK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G+V+T +D     TV D LP I  R+ +VGRLD +TEGLL+LTNDG L  
Sbjct: 60  KIYVLLNKPKGVVSTSADRHADQTVMDRLP-IKERLFTVGRLDKDTEGLLILTNDGDLTF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-----CYGDMQVTLDTQKGSNA 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 H 248
            
Sbjct: 239 K 239


>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 =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/294 (27%), Positives = 137/294 (46%), Gaps = 6/294 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R+ K+++ AG+ASRR  E +I   RV V+G+ +          +H 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 AQVNLDAPIYSSETLVRDRPNIISEV-----PDDFTRMKKNSSQKNGLSKQKKL 301
           ++ +       S      R   +         D   R + +   K  L + K+ 
Sbjct: 243 SEEDCRRGCRPSGHDGSGRSRGMRRARPAPREDAACRPQDDDHGKRPLQRHKRR 296


>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 =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + + +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVIQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  281 bits (720), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + A V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRAVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>gi|242242766|ref|ZP_04797211.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233902|gb|EES36214.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 245

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/243 (33%), Positives = 139/243 (57%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA++G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIAKSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYIAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE+F  +VN+L+RI +GP  L  L AG  R ++   ++     HL E
Sbjct: 185 TISEGRNRQVRRMFEYFGHQVNKLVRIQFGPIDLKGLNAGEGRVLTPHEVKTL--RHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 NGK 245


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       S + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKSRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQL 232


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 120/233 (51%), Gaps = 4/233 (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
              + +KP G + T SD  GR TV D +P    R+ SVGRLD +T G+LLLTNDG     
Sbjct: 62  YYIM-NKPKGCLCTSSDDKGRKTVLDYMPKN-ERIFSVGRLDYDTSGVLLLTNDGEFCNH 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P     + Y V   G + +D +  L+KG+  +   Y   +V +  +    +     +
Sbjct: 120 MIHPRYHLEKTYVVNLQGILSEDDIKQLRKGLKTKTEKYQPAKVFVLQKDLTRNRTQFEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGKN ++K +      +V RL R+ +    +  L AG  R +    +++ 
Sbjct: 180 TISEGKNHQVKNMMLALGHEVRRLHRVKFAFLDVKDLRAGEYRRLKPYEIKQL 232


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/243 (33%), Positives = 137/243 (56%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     HL E
Sbjct: 185 TISEGRNRQVRRMFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVKIL--RHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 NGK 245


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLDIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 126/233 (54%), Gaps = 2/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+I+RAG+ASRR+ E +IA  RV V+G ++         ST  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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTV 191
            L  P     + YR +  G++  + L  L+ GI +        +V +    +   + V V
Sbjct: 123 ALLHPRFLVHKTYRAKVAGELTPEALKKLRSGIELADGMTAPAEVRVYGVTEKGLSDVEV 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L EG+NR+++++FE     V  L R  +    L  +  G++R ++K  +   
Sbjct: 183 TLHEGRNRQVRRMFEAVGCDVRALKRTRFAQLTLDGVKRGASRPLTKAEVEAL 235


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVNLKGLRPGEARRLNKKEISQL 232


>gi|322411180|gb|EFY02088.1| hypothetical protein SDD27957_02020 [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 240

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 130/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G  +L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTLELTGLRPGESRRLNKKEISQL 232


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 125/232 (53%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + + + 
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEINKL 234


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 74/229 (32%), Positives = 117/229 (51%), Gaps = 2/229 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+++ +A AGI SRR+ E +I   RVKVNG ++      +    D +E+DG  L + E  
Sbjct: 11  RLARYLAAAGITSRRKAETLIQAGRVKVNGRVVRELGFVINEEKDQVELDGWLLHREE-P 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G + T +D  GR TV D L  +  RV  VGRLD +TEGLLLL+NDG    +
Sbjct: 70  VYILLNKPSGYLCTLADTHGRPTVVDLLRGVTQRVYPVGRLDYDTEGLLLLSNDGDFTHL 129

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  +VY     G V +  +  L+ G++I  +     +V +  ++     + + +
Sbjct: 130 MTHPRFEIEKVYEAWVQGMVSRKAIERLRAGVIIDAVKTAPAKVRVLAKRKDRTLMEIRI 189

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+ R++KK+       V  L R  +G   L  L  G  R ++K  + 
Sbjct: 190 HEGRKRQVKKMCASVGHPVVALKRTRFGDLTLDGLRPGEFRYLTKDEVE 238


>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 =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 131/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +     + + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGLATKENLRPLTRGVVIDGKKTKPARYNIIKVDPEKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R ++G   L  L  G +R +SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFELVGLLVDKLSRTNFGTLDLSGLRPGESRRLSKKEISQL 232


>gi|327462027|gb|EGF08356.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score =  281 bits (719), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R+++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLNKKEVSQL 232


>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 =  280 bits (718), Expect = 1e-73,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 130/234 (55%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KVIA+AG+ASRR+ E  I + RVKVNG  +      V    D +EVDGVPL K E 
Sbjct: 2   ERLQKVIAKAGVASRRKAEEYIVEGRVKVNGETVTELGTKVNPSKDAVEVDGVPLDKEE- 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               L +KP G+V+T +D  GR  V D + S   R+  +GRLD +T GLLLLTNDG  A 
Sbjct: 61  PVYHLLYKPTGVVSTSNDEKGRKVVTDFIESE-QRIYPIGRLDYDTSGLLLLTNDGEFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           +L  P  +  + Y  +  G  ++ ++  L+ GIV++       +  + +  +K   A V 
Sbjct: 120 LLMHPRYKIEKEYIAKVKGIPERKRIKELETGIVLEDGKTAPAKAKVLSIDKKKQTAIVR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EGKNR+++++FE     V +L R  YG   LG L  G +R +    +++ 
Sbjct: 180 LIIHEGKNRQVRRMFEAIGHPVVKLKRERYGFLTLGHLHPGESRPLKPIEVKQL 233


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 123/231 (53%), Gaps = 3/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA+AGI SRR+ E  I   RVKVNG+++      V S D IEVD VP+ + E + 
Sbjct: 3   RLQKVIAQAGITSRRKAEVYILDGRVKVNGVVVNELGTKVSSKDTIEVDNVPISQ-EGSV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L++KP G+++  SD   R  V D    +  R+  +GRLD NT GLLLLTNDG  +++L
Sbjct: 62  YYLFYKPRGVISAVSDDKKRKVVTDFFTEVSERIYPIGRLDYNTSGLLLLTNDGEFSQLL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVG 192
             P  +  + Y  +  G      L  L +G+  +G  Y   +  + +   +   + V + 
Sbjct: 122 THPKNEIEKKYVAKVKGVALPHALKPLTRGLKYKGEKYAPAKYDILSTDTRAETSIVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + EGKN ++K + E     V +L R  YG   LG L  G  R + KK + +
Sbjct: 182 IHEGKNHQVKNMLEAVGLPVQKLKREQYGNLTLGNLKPGEYRPLLKKEINQ 232


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLLPLTRGVEIDGKKTKPAVYEIIKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLEVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           +  P  +  +VY  R  G   +D L  L KGIVI G      +  +    ++ + + V +
Sbjct: 120 MLHPRHEIDKVYVARVKGLASKDNLRPLTKGIVIDGKKTQPARYRIVKTDREKNRSVVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L +G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLMVDKLSRTRFGTLDLSGLNSGEARRLNKKEISQL 232


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 128/234 (54%), Gaps = 2/234 (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 D +P  + RV  VGRLDI+T GL+ LTNDG LA 
Sbjct: 61  KVYMILNKPIGVVTSASDEKDRPTVTDLVPDDY-RVYPVGRLDIDTTGLVFLTNDGQLAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           ++  P  +  + Y V   G  +  +L++L++G+ I+ +      V +      ++ + + 
Sbjct: 120 IMMHPRYKIGKKYIVTVDGTPNARELSILREGLDIRDLKTSPANVRILKSFKQDSILEIE 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+N ++K++F++   KV +L RIS G  QL  L  G+ R +S+K ++   G
Sbjct: 180 IFEGQNHQVKRMFDYIGHKVKKLKRISIGEIQLLDLEPGNYRYLSEKEVKYLKG 233


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 115/236 (48%), Gaps = 3/236 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD ++    P
Sbjct: 1   MTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEVKFHDEP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLT
Sbjct: 61  VS-IERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTTGVLLLT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++  ++   
Sbjct: 120 NDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISYASET-D 178

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 179 KSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQEV 234


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 97/270 (35%), Positives = 145/270 (53%), Gaps = 4/270 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
              +R+ K++ARAG+ASRR  E +IA  RV V+G ++ +        T  I +DG P+ +
Sbjct: 1   MAEERLQKILARAGVASRRAAEELIAAGRVAVDGQIVRQPGHKADPDTQSIAIDGKPIAR 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           AE    WL HKP G V+T  DP GR  V D LP     R+  VGRLD+++EGL+LLTNDG
Sbjct: 61  AEAKEYWLAHKPAGYVSTVHDPQGRPRVLDLLPPEIRARLYPVGRLDLDSEGLMLLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P     + YRV   G+ ++  L  L+ G+ I+G       +T+      ++ 
Sbjct: 121 DLALRLTHPRYGVPKTYRVWLSGRPNRADLEALRAGVEIEGRQTAPAMITVKAAADGHSK 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP- 247
           V++ LREG+ REIK +++     V RL+R+  GP +LG L  G+ R +S   ++      
Sbjct: 181 VSMVLREGRKREIKLMWKARGLNVIRLVRVGLGPLRLGDLPPGAVRRLSPAEIQALRRQC 240

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           H L   + + D  +  S    R+ P+  S 
Sbjct: 241 HALSGCKDSADG-VQKSARGARNAPSKKST 269


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 142/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 17  TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 75

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 76  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 134 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L      
Sbjct: 190 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDTEVSEILAMCEDS 249

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 250 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 309

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 310 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 340


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 126/233 (54%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQL 232


>gi|258591956|emb|CBE68261.1| Uncharacterized RNA pseudouridine synthase aq_1464 (RNA-uridine
           isomerase) (RNA pseudouridylate synthase) [NC10
           bacterium 'Dutch sediment']
          Length = 282

 Score =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 82/244 (33%), Positives = 123/244 (50%), Gaps = 2/244 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
             K   Q     +R+ + +ARAG+ SRR  E++I   RV+VNG +  +    V    D +
Sbjct: 13  PTKPARQTGGGEERLQRYLARAGLGSRRSCEQLILDGRVRVNGRIASQLGTKVSPGLDTV 72

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTE 119
             D  P+  ++     + HKP G++T+ SDP GR  + D LP     R+  VGRLD  TE
Sbjct: 73  TCDHKPVTSSQSLHYLILHKPAGVLTSLSDPRGRPVIGDLLPPRGLPRLFPVGRLDYQTE 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+LLTNDG LA  L  PS +  + Y  +  G    D L  LK G+V +G         +
Sbjct: 133 GLVLLTNDGVLAHGLMHPSFEVEKEYLAKVRGCPTPDDLARLKAGVVSEGEKLWATHAAI 192

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 +AW+ + + +G+  EI+++ +     V RL RI  GP  LG L  G  R+++  
Sbjct: 193 VKPGIGSAWLKLIVHQGRYHEIRRMCDAIGHPVLRLQRIRVGPIVLGKLPKGCWRQLTPA 252

Query: 240 ILRE 243
            L +
Sbjct: 253 ELAD 256


>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 =  280 bits (718), Expect = 2e-73,   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 D +  +  R+  +GRLD ++ G++LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTVLDLV-KVNERIYPIGRLDYDSSGIILLTNDGDIYN 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|327470426|gb|EGF15882.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK330]
          Length = 242

 Score =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLSKKEVSQL 232


>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 =  280 bits (718), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 139/344 (40%), Positives = 189/344 (54%), Gaps = 7/344 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV+K +ARAG+ASRREVER+I   RV +NG +L   A+ V   D + VDG  + + E T
Sbjct: 26  ERVAKALARAGVASRREVERLIEAGRVAINGKVLTTPAIKVKPGDFLTVDGQLVAEREPT 85

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R++ YHKP GL+TTH+DP GR TVF  LP    R+ISVGRLD+N+EGLLLLTNDG L+R 
Sbjct: 86  RIFRYHKPTGLMTTHNDPKGRPTVFQTLPKDLPRLISVGRLDLNSEGLLLLTNDGELSRA 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-----TQKGSNAW 188
           LE PS  W+R YR R  G   Q KL+ LK G+ I+G+ YG ++  LD        G N W
Sbjct: 146 LETPSNAWVRRYRARAFGDTTQAKLDTLKDGVTIEGVKYGSIEARLDKAHDKAGGGKNIW 205

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           +TV L EGKNRE++KV E    KVNRLIR+SYGPF LG L AG   EV  +++RE L   
Sbjct: 206 ITVSLSEGKNREVRKVLESVGLKVNRLIRMSYGPFALGALAAGQIEEVGPRVIRELLEGV 265

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           +  E     D P ++        P       D   R    + +    +  +K   PV++ 
Sbjct: 266 VPPENMPTGDRPKFAGIANPVKAPGTDGG-GDLQRRGVPRADRDLKPAAPEKPEKPVYKA 324

Query: 309 NLASNVWM-AKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             A      +    +   +   +       +     ++ + R  
Sbjct: 325 GWAKPKKKVSPHAPAKGAAKPKRAPAKSLETKFIDDRKPVARGK 368


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +G+VI G      +  +       + + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGIATKENLRPLTRGVVIDGKKTKPARYNIIRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG++ ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRHHQVKKMFESVGLLVDKLSRTRFGTLDLTGLRPGEARRLNKKEVSQL 232


>gi|296131694|ref|YP_003638941.1| pseudouridine synthase [Thermincola sp. JR]
 gi|296030272|gb|ADG81040.1| pseudouridine synthase [Thermincola potens JR]
          Length = 244

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 124/235 (52%), Gaps = 8/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QR+ KV+A  G+ +R+E +++I +++V+VNG L +   ++V    D I V+G P+   
Sbjct: 5   ERQRLDKVLAHMGLGTRKEAKKLIKERKVEVNGELAQDPGLHVRPGQDRIVVNGEPVEYR 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           +     + +KP G+++   D  G   V D L   +       VGRLD +TEGLLLLTNDG
Sbjct: 65  Q-FVYLMLNKPQGVLSATGDESG-QVVVDLLSPNYQSFHPFPVGRLDKDTEGLLLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y     G V Q+ + + ++G+++  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|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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 155/345 (44%), Positives = 205/345 (59%), Gaps = 12/345 (3%)

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 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            A  + + P+   E         +        R  + +  K  +SK  +      RR+  
Sbjct: 268 AAGADFNGPLVEREPEEEAPRRPLGLDKRKLPRAAEVADAKAAVSKPARR----ERRSA- 322

Query: 312 SNVWMAKGIHSSFLSDSG--QREENHRRSPSFPSKRSLRRTSAKK 354
                   I           +R ++  R        + R+  A K
Sbjct: 323 -----EPEIDPERPPRVPLRKRMQDEERKVVKVGTVADRKGRAVK 362


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 130/234 (55%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMITAGRVKVDGQVVTKLGTKVDTFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++++KP G+V+T  D  GR TV D    I  RV  +GRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYIFYKPRGVVSTADDDKGRKTVVDYFEDIPYRVYPIGRLDYDTSGLLLMTNDGELANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  +++  L KG+ +        +V +    ++ +   V +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPEEIKSLTKGVKLGRFKSAPAKVKVLKTDKRKNTQIVQI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKNEVDKLM 235


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 69/244 (28%), Positives = 116/244 (47%), Gaps = 6/244 (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  TVNGKRVEGKERPVLLAVNKPRGIVCTTSDKDRAENIVEFF-KYPVRIYPVGRLDKDSEG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL+TN G L   +        + Y V     V +  +  ++ G+ I G      +  + 
Sbjct: 119 LLLMTNQGDLVNRILRGRYGHEKEYLVTVDRPVTEAFIRQMRNGVEILGTRTKPCEAEIT 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++      ++ L +G NR+I+++ E   ++V  L R+     +LG L  G  RE++   
Sbjct: 179 GERS----FSIILTQGLNRQIRRMCEALGYQVKTLKRVRIMNVKLGNLKTGQYRELTPAE 234

Query: 241 LREQ 244
             E 
Sbjct: 235 WEEL 238


>gi|221310234|ref|ZP_03592081.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. 168]
          Length = 245

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 79/238 (33%), Positives = 130/238 (54%), Gaps = 3/238 (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    +L +KP G+++   D  GR  V D   +I  R+  +GRLD +T G
Sbjct: 65  EVNGLKVEREE-PVYFLLYKPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSG 123

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG  A  L  P  +  + Y  +  G   ++ L  L++GI ++       +  L 
Sbjct: 124 LLLLTNDGEFANKLMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLL 183

Query: 181 T--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +  +K   + + + + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 184 SLDKKKQTSIIQLTIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 241


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 76/230 (33%), Positives = 116/230 (50%), Gaps = 3/230 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R++K +A AG+ SRRE +  I    V VNG ++      VM TD ++  G  L   E+
Sbjct: 243 PVRLNKFLANAGVCSRREADEYIQAGSVTVNGQVVTELGTKVMRTDEVKF-GDNLVSLEK 301

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LLLTNDG LA
Sbjct: 302 KVYILINKPKDCVTTSDDPQQRKTVLDLVKNACPERIYPVGRLDRNTTGVLLLTNDGDLA 361

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY V     V Q+ L  + +GI ++       ++    ++     V +
Sbjct: 362 SKLTHPKFLKKKVYHVFLDKPVAQEDLQKIAEGIELEDGEIHADEIAYANEE-DKKQVGI 420

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K +
Sbjct: 421 EIHSGKNRIVRRIFEHLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEKEV 470


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  ++D L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKDNLRPLTRGLEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 IIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/342 (24%), Positives = 144/342 (42%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L      
Sbjct: 178 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILAMCEDS 237

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 238 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 297

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                        S  + SG R      +P      SLR++ 
Sbjct: 298 QRRP------SSPSSNTASGSRP-----TPRTGGTLSLRKSK 328


>gi|268610237|ref|ZP_06143964.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 247

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 128/238 (53%), Gaps = 3/238 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +     R+ K+IA +G+ SRR+ E +I++ RVK+NG  ++         D I +DG  
Sbjct: 1   MGDKVEKIRIQKMIADSGVCSRRKAEELISRGRVKLNGHPVK-LGDKCGYKDIITIDGER 59

Query: 67  LRKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           L   ++   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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               + + ++EG+NR+I+K+ E    +V RL R S GP +LG L  G+ R+++ + LR
Sbjct: 180 GRVVLLMTIKEGRNRQIRKMCEAVGLEVARLRRTSIGPIKLGMLKPGTYRDLTAEELR 237


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 134/245 (54%), Gaps = 3/245 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            KN  +++    R+ K +A AG+ASRR  E++I + RVKVNG++++     V   D IEV
Sbjct: 6   RKNNKEDHMAEVRLQKAMADAGVASRRASEKLILEGRVKVNGVVVKELGTKVKGDDAIEV 65

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           +G  + +      +L++KP G+++   D  GR  V D      +R+  +GRLD +T G+L
Sbjct: 66  NGTLIERERNKVYYLFYKPRGVISAVKDDKGRRVVTDYFEGEKNRIYPIGRLDYDTSGIL 125

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTL 179
           LLTNDG LA +L  P  +  + Y  +  G V  D L  L+KG+ ++   Y      +V  
Sbjct: 126 LLTNDGELANLLMHPRYKVDKTYVAKVEGLVQSDDLKRLRKGVKMKDGHYSARAKAKVIS 185

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +  +++ V++ + EG+N ++K +FE     V +L R +Y    L  L++G  RE+S +
Sbjct: 186 SDRAKNHSIVSLTIHEGRNHQVKNMFEAIGHPVMKLKRETYDFLTLKGLVSGQYRELSNE 245

Query: 240 ILREQ 244
            ++  
Sbjct: 246 EVKTL 250


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 126/232 (54%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG   ++K +F+  N  V++L R  Y    L +L++G  RE++ + + + 
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVDKLSRERYAFLTLKSLISGEYRELTHEEINKL 234


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 125/232 (53%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKIRGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + + + 
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEINKL 234


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 124/232 (53%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR  E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRNAEILITSGQVTVNGNLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKISGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + + + 
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEINKL 234


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 98/345 (28%), Positives = 151/345 (43%), Gaps = 14/345 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+IARAG+ASRR  E +I   RV+VNG ++    +      D IEVDG  L  +E 
Sbjct: 3   ERLQKIIARAGVASRRASEELILAGRVRVNGRVVTELGLKADRQKDRIEVDGKRLV-SEA 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL---REQLGPHL 249
           LREG+N++I+++ E   W V RL R ++       L  G  R ++   L   RE  G   
Sbjct: 182 LREGRNQQIRRMGEATGWPVMRLARTTFAGVSSEGLRPGEWRALTVDELLHIREAFGV-- 239

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
               +    A + +S   V  R    S         +     +       +   P   R 
Sbjct: 240 ---PKRIRGAVMGASSGPVDHRRTASSARSGAKASPR---PTQEAAGAAARSRGPAQPRV 293

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +     A        +    R      +PS P++    RT+  +
Sbjct: 294 RSRANADAPSAPGQGPAGRTARSRT-DAAPSTPARSPAGRTARSR 337


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 125/233 (53%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V   D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVITDLATTVKLGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G   ++ L  L +GIVI G      +  +       + + V +
Sbjct: 120 MTHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE     V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPGEARRLNKKEISQL 232


>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 =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 115/352 (32%), Positives = 167/352 (47%), Gaps = 28/352 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIEAGRVSVDGKIATLGDRVEVTPALKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    +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 ++          +DR  + +       R  K  SQ  G  +Q   A
Sbjct: 242 ELVGLPPETASKVAVE----------KDRRRMKAN---QIRRAVKRHSQTAGGPRQGSPA 288

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                R        A+   S+  +++ +   N  R+          R S  +
Sbjct: 289 -----RQGQGQAGAARPAGSARPAENTRAGNNTSRASGNARPGGNPRASGAR 335


>gi|218674407|ref|ZP_03524076.1| putative ribosomal large subunit pseudouridine synthase B
           [Rhizobium etli GR56]
          Length = 277

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 147/227 (64%), Positives = 175/227 (77%)

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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           T+GLREGKNREIK V       VNRLIRISYGPFQLG L  G   EV
Sbjct: 228 TMGLREGKNREIKNVLGALGLDVNRLIRISYGPFQLGDLPEGHVIEV 274


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 178 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 237

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 238 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 297

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 298 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 328


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 78/348 (22%), Positives = 146/348 (41%), Gaps = 14/348 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +++I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKYISETGFCSRREADKLIEQGRVTINGKQP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPVYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + +  +  G+ I        +VT +T+   
Sbjct: 116 NDGDIVNKILRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVTQETKFS- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L
Sbjct: 175 ---FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVTEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + E  V  +          R R    +++ D     + +++++N   +  K     
Sbjct: 232 A---MCEGSVGTEEASRVDAKGRRIRKATDAKLFDSREENQTSTARRNQKQRTFKGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R   +              D  + E+  R+  +  +KR     +AK
Sbjct: 289 EFR--HAPNSKKAQQRKQQDGDKPRFEKPKRQEQAGKAKRYDNPNAAK 334


>gi|319400836|gb|EFV89055.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           epidermidis FRI909]
          Length = 245

 Score =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 138/245 (56%), Gaps = 5/245 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+ K IA++G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + +
Sbjct: 4   EKERLQKRIAKSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQED 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG   
Sbjct: 64  KI-YILFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFT 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWV 189
            ++  P     + Y  +  G + ++++  L+KGI ++       QV +  Q  + +   V
Sbjct: 123 NLMTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTTLV 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     HL
Sbjct: 183 EITISEGRNRQVRRMFEYFGHQVNKLARIQFGPIDLKGLNAGEGRVLTPHEVKTL--RHL 240

Query: 250 LEEAQ 254
            E  +
Sbjct: 241 AENGK 245


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 127/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L    +G+ I+G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGVANKENLRPFTRGVEIEGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+FE    +V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFEAVGLQVDKLSRTRFGHLDLTGLRPGEARRLNKKEISQL 232


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 130/231 (56%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I   +VKVNG ++      V ++D +EV+G+ L + ++ 
Sbjct: 6   ERLQKRIASSGYTSRRKAETLITDGKVKVNGHVVTELGTKVSNSDTVEVEGIKLEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFNKPAQVITSVSDDRGRKVVTDYFKDIETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q        V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQPAQVKVKNQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE F  +V++L RI +GP  L  L AG  R ++   ++
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVSKLTRIQFGPLDLKGLNAGEGRVLTPHEVK 235


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 84/238 (35%), Positives = 126/238 (52%), Gaps = 5/238 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AG+ASRR  E +I   +VKVNG ++      V   D + V+G P+ + 
Sbjct: 1   MAKERLQKVIAHAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG 128
           E+   +L  KP G++++  D  GR TV D L +    +RV  VGRLD +T GLL++TNDG
Sbjct: 60  EQHEYYLLDKPRGVISSAHDDKGRKTVVDILKNEGVQTRVYPVGRLDYDTTGLLVMTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSN 186
            LA  L  P  +  +VY  +  G V  D++ LL++G+ I G      +  L    Q+   
Sbjct: 120 ELANRLMHPRFEVDKVYIAKVKGLVSNDEMRLLREGVKIDGKKSQPARTKLLEANQRQKT 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + V + + EG   ++KK+ E     V +L R SYGP  L  L  G  R++    +R  
Sbjct: 180 SVVKLTIHEGHYHQVKKMMEAVGHPVLKLHRESYGPLTLAGLNPGQFRKLKVDEVRAL 237


>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 =  280 bits (716), Expect = 3e-73,   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 D +  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTVLDLV-KVNERIYPIGRLDYDSSGLILLTNDGDIYN 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|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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 77/338 (22%), Positives = 139/338 (41%), Gaps = 23/338 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +D  PLR 
Sbjct: 3   TPTEKRLNKYISETGFCSRREADKLIEQGRVTINGQLP-EMGTKVSDDDEVCIDDKPLRS 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG 
Sbjct: 62  KEKPVYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    +  D +  +  G+ I        +VT +T+       
Sbjct: 120 IVNKILRAGNNHEKEYVVRVDKAITADFIKQMSSGVRILDTVTLPCKVTQETKFS----F 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E   ++V +L R+      L  +  G  R +++  + E L   +
Sbjct: 176 RIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTEAEVAEILA--M 233

Query: 250 LEEAQVNLDAPIYSSE----TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            E +    +A    S+        D     S   +  ++ ++N     G +  +    P 
Sbjct: 234 CEASSGTEEASRVDSQGQRIRKATDAKLFDSREENQPSKARRNPKTFRGHNADEFRHAPN 293

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            ++              S   DS + +    R P    
Sbjct: 294 SKKGKTR----------SERPDSSRADNRADRKPKSTG 321


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 113/242 (46%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ +D I
Sbjct: 257 IEYKEENFDPNEPLRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVNELGTKILRSDVI 316

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
              G P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 317 TFKGQPVTL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGICPERIYPVGRLDRNTT 375

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V          L  +  GI ++        +  
Sbjct: 376 GVLLLTNDGDLASKLTHPKFLKKKVYHVYLDKPATPQTLQQISDGIELEDGEIKADAIEY 435

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 436 -ADSLDQSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEQ 494

Query: 240 IL 241
            +
Sbjct: 495 EV 496


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 91/237 (38%), Positives = 134/237 (56%), Gaps = 2/237 (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 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNA 187
           +A  L  P ++  +VY  +  G    DKL  LK G+VI+G      +VT++   +    +
Sbjct: 122 IANQLMHPKSRVDKVYIAKVAGIATDDKLAPLKHGVVIKGRKTAPARVTIERIDKDKKTS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L EG+N ++K + +     V +L R  Y  F L  L +G  R+++   ++  
Sbjct: 182 MVRVILHEGRNHQVKNMLQKVGLPVEKLTREQYAFFDLTGLQSGEYRKLTSPEIKRL 238


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 142/294 (48%), Positives = 192/294 (65%), Gaps = 1/294 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++KV+ARAG+ASRR+ E M+ Q RV VNG ++   A++V   D I+VDG PL + ERTR
Sbjct: 375 RIAKVLARAGLASRRDAEEMVTQGRVTVNGRVINSPALDVTENDVIQVDGAPLPQRERTR 434

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+LYHKP GL+TTHSDP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTNDGGLARVL
Sbjct: 435 LFLYHKPRGLMTTHSDPEGRPTVFDNLPEGLPRLISIGRLDFNTEGLLLLTNDGGLARVL 494

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELP T W R YRVR HG++ Q +L+ L  G+ + G+ YG ++ TL+  +G+N W+ V +R
Sbjct: 495 ELPDTGWTRRYRVRAHGEITQAQLDQLAAGVEVDGVKYGPIEATLERDQGANVWLIVAIR 554

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           EGKNRE++ V  +   +VNRLIR+SYGPFQL  L  G  +EV  ++LREQLG  ++ ++ 
Sbjct: 555 EGKNREVRNVLAYLGLEVNRLIRVSYGPFQLLELPEGEVQEVKTRVLREQLGEKVIAQSG 614

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            +L  P           P    +      R  +    +   S++ +       R
Sbjct: 615 ADL-GPAGKGNREPLPDPKPKPKREVVADRKGRRVLVQRTGSEEARARHEAEAR 667


>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 =  280 bits (716), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVEINGKKTKPAVYEIIKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G +R ++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLEVDKLSRTRFGHLDLTGLRPGESRRLNKKEISQL 232


>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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 121/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K ++ +   P R++K ++ AG+ SRRE +  I +  V+VNG ++      +   D +
Sbjct: 1   MKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQEGVVQVNGQIVTELGTKITRQDTV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 61  LFKDQPVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 120 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVSIEDMEKIANGLELEDGEIHADAISY 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 180 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWRYLNER 238

Query: 240 ILREQ 244
            +   
Sbjct: 239 EVNAL 243


>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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 80/230 (34%), Positives = 127/230 (55%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A AG ASRR+ E +I + RVKVN  ++    + V    D + +DG  L     
Sbjct: 1   MRLQKFMAHAGAASRRKSEELIKEGRVKVNNNIVTEMGLEVDPNKDRVYLDGKRLNLENE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KPIG+VTT SD  GR  V D +     RV  VGRLDI+T GL+LLTNDG LA 
Sbjct: 61  NIYIILNKPIGVVTTSSDEKGRINVVDLVDET-KRVYPVGRLDIDTTGLVLLTNDGTLAN 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|332358327|gb|EGJ36153.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK355]
          Length = 242

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 132/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  L  G  R+++KK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTGLKPGEYRKLNKKEVSQL 232


>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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 125/232 (53%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KVIA AGIASRR+ E +I   +V VNG L+      V   D IEV+GVP+ K E+  
Sbjct: 4   RLQKVIAEAGIASRRKAEILITSGQVTVNGDLVTTLGTKVDDNDKIEVNGVPIHK-EQLH 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +V+T SD  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA  L
Sbjct: 63  TYLLYKPRNVVSTVSDNKGRKTVTDFFKDLPYRLYPVGRLDYDTSGLLLMTNDGELANRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
             P  +  +VY  +  G +   ++  LK G+ I G      +V +     +     V + 
Sbjct: 123 MHPKNEIEKVYVAKIRGFLTASEIYDLKHGVTIDGRKTAPAKVKIIKTDKNRNIQLVQLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG   ++K +F+  N  V +L R  Y    L +L++G  RE++ + + + 
Sbjct: 183 IHEGHYHQVKNMFKAVNHLVEKLSRERYAFLTLKSLISGEYRELTHEEINKL 234


>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 =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 73/229 (31%), Positives = 123/229 (53%), Gaps = 2/229 (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  KVYIMLNKPEGYISSVKDEKGRDTILDIV-KVNERIYPIGRLDYDSSGLLLLTNDGEIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ Y     G++        + GI I G      ++ + +     + + +G
Sbjct: 122 KIIHPRVEIIKRYVAVVKGEITDKDKMKFEIGIDIGGYITAPAELKVISYDKGVSTIEIG 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+I+K+    +  V  L RIS G  +LG L  G  R+++K+ L
Sbjct: 182 IHEGKNRQIRKMCAAIHHDVLSLKRISIGEIKLGYLKRGEYRKLNKEEL 230


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

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 77/338 (22%), Positives = 139/338 (41%), Gaps = 23/338 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +D  PLR 
Sbjct: 3   TPTEKRLNKYISETGFCSRREADKLIEQGRVTINGQLP-EMGTKVSDDDEVCIDDKPLRS 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG 
Sbjct: 62  KEKPVYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    +  D +  +  G+ I        +VT +T+       
Sbjct: 120 IVNKILRAGNNHEKEYVVRVDKAITADFIKQMSSGVRILDTVTLPCKVTQETKFS----F 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E   ++V +L R+      L  +  G  R +++  + E L   +
Sbjct: 176 RIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTEAEVAEILA--M 233

Query: 250 LEEAQVNLDAPIYSSE----TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
            E +    +A    S+        D     S   +  ++ ++N     G +  +    P 
Sbjct: 234 CEASSGTEEASRVDSQGQRIRKATDAKLFDSREENQPSKARRNPKTFRGHNADEFRHAPN 293

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            ++              S   DS + +    R P    
Sbjct: 294 SKKGKTR----------SERPDSSRADNRTDRKPKSTG 321


>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 =  279 bits (715), Expect = 4e-73,   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 ELLEGIVAEENMPKGDKPQFI-GVADPLKAVGTAGGGDMQRRGVPRTNKLTQVSIITPEE 316

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL-RRTSAKK 354
                + +    W       + +     R             + L  R +A K
Sbjct: 317 PVEEEKFVRKPGWAKPKKKPAIVGREPVRTAKKSIESKMIGPKPLSYRDAAAK 369


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 143/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTDQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 178 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 237

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 238 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 297

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 298 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 328


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 139/341 (40%), Positives = 194/341 (56%), Gaps = 3/341 (0%)

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 HL+
Sbjct: 186 VGIREGKNREVRKALDAVGLRVNRLIRIAYGPFQLGQLEKGEIKSVPSRVLHDQCG-HLI 244

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH--RR 308
           +         I       R       +      +       + GL K++   + +   R+
Sbjct: 245 DMGDTPTGQAIAKPRPANRAARKPGQKPDGKPGQRAMGGPGQPGLPKREVDDSLIEDARK 304

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               +    +         + +         +  S+    R
Sbjct: 305 GRPLDAKSTRARRGKDGKPTAKPAAGRAAPRATTSRSETPR 345


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 79/350 (22%), Positives = 147/350 (42%), Gaps = 25/350 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +++I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKYISETGFCSRREADKLIEQGRVTINGKQP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ +    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPVYIALNKPTGITCT-TERNIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + +  +  G+ I        +VT +T+   
Sbjct: 116 NDGDIVNKILRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVTQETKFS- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L
Sbjct: 175 ---FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVTEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + E  V  +          R R    +++ D     + +++++N   +  K     
Sbjct: 232 A---MCEGSVGTEEASRVDAKGRRIRKATDAKLFDSREENQTSTARRNQKQRTFKGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS-KRSLRRTSAKK 354
             R            H+     + QR++     P F   KR  +   AK+
Sbjct: 289 EFR------------HAPNSKKAQQRKQQDGDKPRFEKTKRPEQAGKAKR 326


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 144/347 (41%), Positives = 199/347 (57%), Gaps = 12/347 (3%)

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 ---EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
              E+ +      +       R RP             +++ +   G  K K      HR
Sbjct: 255 LGVEDGKPPRSERMAPKPGARRPRPEGGEGEERKGFGRQRDFAGAEGDRKPKSFGMKSHR 314

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                     +G    F        + + R      K    R   KK
Sbjct: 315 ---------EEGERKPFARREDGERKPYARREDGDRKPYAPRDGEKK 352


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 82/342 (23%), Positives = 142/342 (41%), Gaps = 20/342 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L      
Sbjct: 178 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILAMCEDS 237

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 238 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 297

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                           S S       + +P      SLR++ 
Sbjct: 298 QRRP-----------SSPSSNTASGSKPTPRTGGTLSLRKSK 328


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 83/241 (34%), Positives = 129/241 (53%), Gaps = 3/241 (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 +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LT
Sbjct: 61  PI-YNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQK 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 Q 244
            
Sbjct: 240 L 240


>gi|221314557|ref|ZP_03596362.1| pseudouridine synthase [Bacillus subtilis subsp. subtilis str. NCIB
           3610]
          Length = 229

 Score =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 77/225 (34%), Positives = 125/225 (55%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRRKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L +  +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 225


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 79/234 (33%), Positives = 128/234 (54%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K++A  G+ASRR+ E +I Q +VKVNG + +        TDH+ V G  +  +
Sbjct: 3   DQKIRLQKMLADCGVASRRKAEELIQQGKVKVNGHVAQIGDKVNPKTDHVTVAGRRIVAS 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +    + HKP G V+T SD  GR  V + +  I +RV  VGRLD ++EGLLL+TNDG  
Sbjct: 63  RQYYYIMLHKPRGYVSTMSDEMGRKCVAELVKDIPARVYPVGRLDRDSEGLLLMTNDGEF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A ++  PS    + YRV     + +++L L+  G+ I G+        + +++     + 
Sbjct: 123 ANLIMHPSKHVPKTYRVTVRPDISEEQLALMNVGMEIDGVRTAPADAWVISREPGRVVLE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + LREG+NR+I+K+ E    +V RL R++ G  +LG L  G  R ++   ++  
Sbjct: 183 IILREGRNRQIRKMCEQLGVEVARLKRVAVGQVKLGMLQPGKWRNLTLDEVKRL 236


>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 =  279 bits (715), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 77/348 (22%), Positives = 146/348 (41%), Gaps = 14/348 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +++I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKYISETGFCSRREADKLIEQGRVTINGKQP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ +    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPVYIALNKPTGITCT-TERNIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + +  +  G+ I        +VT +T+   
Sbjct: 116 NDGDIVNKILRAGNHHEKEYVVRVDKPITPEFIKAMSSGVNILDTVTLPCKVTQETKFS- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L
Sbjct: 175 ---FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVTEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + E  V  +          R R    +++ D     + +++++N   +  K     
Sbjct: 232 A---MCEGSVGTEEASRVDAKGRRIRKATDAKLFDSREENQTSTARRNQKQRTFKGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
             R   +              D  + E+  R+  +  +KR     +AK
Sbjct: 289 EFR--HAPNSKKAQQRKQQDGDKPRFEKPKRQEQAGKAKRYDNPNAAK 334


>gi|297570484|ref|YP_003691828.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
 gi|296926399|gb|ADH87209.1| pseudouridine synthase [Desulfurivibrio alkaliphilus AHT2]
          Length = 240

 Score =  279 bits (714), Expect = 4e-73,   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|312127407|ref|YP_003992281.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777426|gb|ADQ06912.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score =  279 bits (714), Expect = 4e-73,   Method: Composition-based stats.
 Identities = 76/226 (33%), Positives = 120/226 (53%), Gaps = 2/226 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A+ G+ASRR+ E +I Q RVKVNG L+ +    V    D +EVDG  +    + 
Sbjct: 6   RLQKFMAQCGVASRRKCEEIILQGRVKVNGKLVNQLGFKVDPEKDVVEVDGKRISLQRQK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +    + RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 66  VYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVNVRVFPVGRLDFDTTGLILLTNDGEFAY 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   +KG++I G      +  +      NA V + 
Sbjct: 126 KVTHPKHDIEKTYIALIKGIPSKEEIERFEKGLLIDGKMTAPAKFKILKLINGNALVEIK 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + EG+NR+I+K+ +    KV +L R++ G  QLG L  G    + +
Sbjct: 186 IHEGRNRQIRKMCDQIGHKVLKLKRVAIGKLQLGKLKEGKFVFLDR 231


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 87/233 (37%), Positives = 136/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQL 233


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 84/243 (34%), Positives = 128/243 (52%), Gaps = 2/243 (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 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVT 178
           GLL+LTNDG LA +L  PS    + Y  +  G V    +  L KGI +       D    
Sbjct: 121 GLLILTNDGELAHILAHPSFGVSKTYIAKVEGIVSAQTIAKLTKGIELDDGPIVADKARA 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L    G+   V + L  G+N  ++++ +     V  L+R  +GP  LG+L  G TR+++K
Sbjct: 181 LGRASGNETMVEITLHSGRNHIVRRMLDAVGHPVIDLVRRQFGPLTLGSLPVGRTRDLTK 240

Query: 239 KIL 241
             L
Sbjct: 241 AEL 243


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 137/243 (56%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILFYKPTQVITSVSDDLGRKVVTDYFEDIETRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQPAQVKIKRQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     HL E
Sbjct: 185 TISEGRNRQVRRMFEYFGHEVNKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTL--RHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 NGK 245


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 137/243 (56%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG ++      V  +D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQVVTELGTKVSHSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILFYKPTQVITSVSDDRGRKVVTDYFEDIETRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P     + Y  +  G + ++++  L++GI ++       QV +  Q  + +   V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREQVKELEQGIELEDGFTQPAQVKIKRQDKEKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     HL E
Sbjct: 185 TISEGRNRQVRRMFEYFGHEVNKLTRIQFGPLDLKGLNAGEGRVLTPHEVKTL--RHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 NGK 245


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 84/238 (35%), Positives = 126/238 (52%), Gaps = 5/238 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA AG+ASRR  E +I   +VKVNG ++      V   D + V+G P+ + 
Sbjct: 1   MVKERLQKVIAHAGVASRRAAEGLILAGKVKVNGQVVTELGTKVDGNDEVMVNGEPVEQ- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG 128
           E+   +L  KP G++++  D  GR TV D L +    +RV  VGRLD +T GLL++TNDG
Sbjct: 60  EQHEYYLLDKPRGVISSAHDDKGRKTVVDILKNEGVQTRVYPVGRLDYDTTGLLVMTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSN 186
            LA  L  P  +  +VY  +  G V  D++ LL++G+ I G      +  L    Q+   
Sbjct: 120 ELANRLMHPRFEVDKVYIAKVKGLVSNDEMRLLREGVKIDGKKSQPARTKLLEANQRQKT 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + V + + EG   ++KK+ E     V +L R SYGP  L  L  G  R++    +R  
Sbjct: 180 SVVKLTIHEGHYHQVKKMMEAVGHPVLKLHRESYGPLTLAGLNPGQFRKLKVDEVRAL 237


>gi|330830315|ref|YP_004393267.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805451|gb|AEB50650.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 230

 Score =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 109/230 (47%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R    ++I Q  V V+GI++++ A ++     IE DGV L   +R 
Sbjct: 1   MRLDKFLCDCSDLTRSLAGKLIRQGEVMVDGIVVKQPAFHINEQSQIEFDGVLLTLEQRN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V ++ DPD   TVF  +      ++  VGRLD++T GL+L+T+DG  + 
Sbjct: 61  RYFMLHKPEGYVCSNEDPDH-PTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V     V  D + L  +G+ ++          L+          + 
Sbjct: 120 RITSPRHECAKTYHVWLADPVSPDAIALFAEGVYLRNETDKTRPAQLEI--LGECEARLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L   L  G  RE++ + +
Sbjct: 178 IHEGKYHQVKRMFASIGNKVVGLHRERVGGLTLDDELAPGEYRELTAEEI 227


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 118/242 (48%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K ++ +   P R++K +A AGI SRRE +  I    V VNG ++      V  +D +
Sbjct: 5   IEYKELLTDPDEPIRLNKFLANAGICSRREADEFITAGVVSVNGEIVTELGTKVKRSDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  KFHDQPVN-IERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ + +GI +         ++ 
Sbjct: 124 GVLLLTNDGDLASKLTHPKFLKKKIYHVYCDKNVTKADLDQIVQGITLDDGEIHADAISY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 184 -ASDTDKSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>gi|332359120|gb|EGJ36941.1| ribosomal large subunit pseudouridine synthase B [Streptococcus
           sanguinis SK49]
          Length = 242

 Score =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 131/233 (56%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +GI I+G        ++       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGLANKEVLRPLTRGIEIEGRKTKPAVYEIIKVDPAKNRSVVQL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++KK+F+    +V++L R  +G   L  +  G  R++SKK + + 
Sbjct: 180 TIHEGRNHQVKKMFQAVGLQVDKLSRTRFGHLDLTDIKPGEYRKLSKKEVSQL 232


>gi|312135342|ref|YP_004002680.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775393|gb|ADQ04880.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 236

 Score =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 75/228 (32%), Positives = 120/228 (52%), Gaps = 2/228 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +E+DG  +    +
Sbjct: 1   MRLQKFMAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEIDGKRISLQRQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G++++  D  GR TV D +    + RV  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|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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 113/231 (48%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  +R+EV+  I +  V VNG + E+  + V   TD + V+G  +   E 
Sbjct: 1   MRLDKLLAHSGFGTRKEVKDFIKKGIVTVNGEIAEKDKMQVDPQTDEVCVNGEVITYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G V+   D +   TV D +   +   +  VGRLD++TEGLLL++NDG LA
Sbjct: 60  FVYYMLNKPAGYVSATED-NLYPTVVDLIDDYYRDDLFPVGRLDVDTEGLLLISNDGVLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY  + +G V    +     GI I        ++ + +   + + + V
Sbjct: 119 HQLLSPKKHCPKVYYAKINGIVTNQDVEAFFNGITIDDYQCQSAELKILSTSATTSEIEV 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + EGK  ++KK+F     +V  L RI      L   L  G  R ++ + L
Sbjct: 179 TIYEGKFHQVKKMFIAVGKEVTYLKRIRMKDLCLDNSLQLGEYRHLTDEEL 229


>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 =  279 bits (714), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 82/241 (34%), Positives = 129/241 (53%), Gaps = 3/241 (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 +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LT
Sbjct: 61  PI-YNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQK 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 Q 244
            
Sbjct: 240 L 240


>gi|330685968|gb|EGG97591.1| pseudouridine synthase B, ribosomal large subunit [Staphylococcus
           epidermidis VCU121]
          Length = 246

 Score =  278 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 130/231 (56%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I   +VKVNG ++      V ++D +EV+G+ L + ++ 
Sbjct: 6   ERLQKRIASSGYTSRRKAETLITDGKVKVNGQVVTELGTKVSNSDTVEVEGIKLEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFNKPAQVITSVSDDRGRKVVTDYFKDIETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q        V +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEVKALEKGIELEDGFTQPAQVKVKNQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE F  +V++L RI +GP  +  L AG  R ++   ++
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVSKLTRIQFGPLDIKGLNAGEGRVLTPHEVK 235


>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 =  278 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 82/241 (34%), Positives = 129/241 (53%), Gaps = 3/241 (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 +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LT
Sbjct: 61  PI-YNEEKVYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQK 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 Q 244
            
Sbjct: 240 L 240


>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 =  278 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 87/233 (37%), Positives = 136/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQL 233


>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 =  278 bits (713), Expect = 6e-73,   Method: Composition-based stats.
 Identities = 79/234 (33%), Positives = 128/234 (54%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGIASRR+ E+MI   RVKV+G ++ +    V +  +I VD  P+ + E  
Sbjct: 3   ERLQKVIAEAGIASRRKAEKMIVAGRVKVDGKVVTKLGTKVETFSNITVDDEPIER-ESL 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L++KP G+V+T  D  GR TV D    +  R+  VGRLD +T GLLL+TNDG LA +
Sbjct: 62  HTYLFYKPRGVVSTADDDKGRKTVVDYFEDVPYRLYPVGRLDYDTSGLLLMTNDGKLANL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G +  D++  L  G+ +        +V +    ++     + +
Sbjct: 122 LMHPRNEVSKVYVAKIKGILTPDEIKTLTTGVKLDRFKAAPAKVKILKTDKRKDTQIIQL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + EG   ++K++F+     V +L R  Y    L +L +G  RE+SK  + + +
Sbjct: 182 TIHEGHYHQVKRMFKAVGHLVEKLSREKYAFLTLDSLTSGQYRELSKHEVDKLM 235


>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 =  278 bits (713), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 114/335 (34%), Positives = 162/335 (48%), Gaps = 24/335 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIEAGRVSVDGKIATLGDRVEVTPALKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    +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      ++V ++          +DR  + +       R  K  SQ  G S+Q   A
Sbjct: 242 ELVGLEPETSSKVAVE----------KDRRRMKAN---QIRRAVKRHSQTAGASRQGAPA 288

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                   A     A+   ++   +S  R   + R
Sbjct: 289 RQGQA-GAARPAGSARAAENTRSGNSTSRASGNAR 322


>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 =  278 bits (713), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 83/234 (35%), Positives = 134/234 (57%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KVIA+AGIASRR+ E++I + +VKVNG +++   + V    D IEV+GVP+ K E 
Sbjct: 2   ERLQKVIAQAGIASRRKAEQLILEGKVKVNGQVVKELGIKVNPNQDDIEVEGVPVEKEE- 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++++  D  GR  V D L  I  RV  VGRLD +T GLLLLTNDG  A 
Sbjct: 61  PVYFLLYKPTGVISSVKDDKGRKVVTDFL-EIEQRVYPVGRLDYDTSGLLLLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           +L  P  +  +VY  +  G   +D+L LL +G+ ++       +V + +  ++   A V 
Sbjct: 120 LLMHPRHKIEKVYVAKVKGIPTRDQLKLLARGVKLEDGPTAPAKVKMLSVDRRKQTAIVK 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE    +V +L R  +    L  +  G  R +    ++  
Sbjct: 180 LTIHEGRNRQVRRMFETIGCEVMKLKREQFAFLDLSGMNPGDVRPLKPIEVKHL 233


>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 =  278 bits (713), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 80/362 (22%), Positives = 143/362 (39%), Gaps = 15/362 (4%)

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 ++      + D +     R+  +GRLD  ++G
Sbjct: 60  LIDDKPLRSKERPIYIALNKPTGITCT-TERHIEGNIVDFI-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 LREQ-------LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           + E         G     +          +++  + D     +            +    
Sbjct: 234 IGEINRLIAQSSGTEEASKVDAEGRKIAKATDAKLYDHRQQEARNEKRAQEKAFKTYSGT 293

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS-LRRTSA 352
           G   ++      +RRN  S     +       +    R  +    PSF  K + +++  +
Sbjct: 294 GEFTRRPGGQRQNRRNEESGESRQQRSQGRNDNRRPARTSDRDSKPSFGGKSTGIKKWKS 353

Query: 353 KK 354
           KK
Sbjct: 354 KK 355


>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 =  278 bits (712), Expect = 7e-73,   Method: Composition-based stats.
 Identities = 80/233 (34%), Positives = 128/233 (54%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P  +  +VY  R  G V ++ L  L +G+VI G      +  +   +     + V +
Sbjct: 146 MIHPRNEIDKVYLARVKGVVTKESLRPLTRGVVIDGKKTKPARYRIIRVEPDKNRSIVEL 205

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG++ ++KK+FE     V++L R  +G   +  L  G  R +SKK + + 
Sbjct: 206 TIHEGRHHQVKKMFEAVGHLVDKLSRTQFGSLDVRGLKPGEARRLSKKEVSQL 258


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 90/244 (36%), Positives = 132/244 (54%), Gaps = 2/244 (0%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D+          R+ K+IA +G  SRR+ E++I ++RVKVNG   +         D + V
Sbjct: 2   DRQNGGTQLEKIRLQKIIAESGFCSRRKAEQLIEERRVKVNGHPAKIGDKADPRKDVVTV 61

Query: 63  DGVPLRKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           D   +  A R   R  + HKP G VTT SD  GR  V D +  I  R+  VGRLD+N+EG
Sbjct: 62  DDERITVARRPTYRYVMLHKPRGYVTTMSDEKGRRCVADLVADIDERLYPVGRLDVNSEG 121

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL TNDG LA  +  PS    + YRV     +  ++   L +G+VI G      QV + 
Sbjct: 122 LLLFTNDGRLANDIMHPSRHVTKTYRVTVRPDITDEQAARLAEGVVIDGRKTAPAQVHVL 181

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T++ +   + V +REG+NR+I+K+ E    +V RL R S GP +LG L  G+ R+++ + 
Sbjct: 182 TKEPNRVVMEVVIREGRNRQIRKMMEAVGLEVARLKRTSLGPIKLGMLKPGAHRDLTAEE 241

Query: 241 LREQ 244
           L+  
Sbjct: 242 LKAL 245


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 73/338 (21%), Positives = 141/338 (41%), Gaps = 18/338 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AERT 73
           R++K I+  G  SRRE +R+I Q RV +NG +       V+  D + VD  P+    ++ 
Sbjct: 7   RLNKFISETGFCSRREADRLIEQGRVTINGKVP-EMGTKVLPGDDVCVDDKPISAVTDKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  VYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    + +  +  +  G+ I        +V+ +T+        + L
Sbjct: 124 ILRAGNNHEKEYVVRVDKPITEQFIKKMSSGVDILDTTTLPCKVSKETKFS----FRIVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L   + E +
Sbjct: 180 TQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGQWRYLSDDEIGEILA--MCESS 237

Query: 254 QVNLDAPIYSSE----TLVRDRPNIISEVPDDFTRMKKNSSQK--NGLSKQKKLATPVHR 307
               DA    +         D     S   +  ++ ++N  Q+   G + ++    P  +
Sbjct: 238 SGTEDASKVDARGRNIRKATDAKLFDSREENQESKARRNQKQRTFKGKNAEEFRHAPNSK 297

Query: 308 --RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             R   S+       +        + ++  +R  + P 
Sbjct: 298 KGRGGKSDSKSKPSTNKGKSVYKPKSDKPAQRPSNKPR 335


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 132/232 (56%), Positives = 167/232 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +ARAG+ASRR+ ERMI   RV +NG  +   A  V + D I +DG P+ +  RT
Sbjct: 11  ERIAKYLARAGVASRRDAERMIESGRVALNGTKVLHPATFVAAGDIILIDGSPVGEPSRT 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHK  GL+TTH DP+GR T+F+ +P    RV+SVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 71  RLWRYHKRAGLLTTHRDPEGRPTIFERMPPELPRVVSVGRLDLNSEGLLLLTNDGALARQ 130

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELP+T WLR YRVR HG VD  +L  LK GIV+ G+ YG +   +D+ KGSN+W+ VGL
Sbjct: 131 LELPTTGWLRRYRVRVHGTVDPARLAALKGGIVVDGVRYGPISAEIDSTKGSNSWLAVGL 190

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EGKNREI+KV      +  RLIRI+YGPFQLG L  G+  EV+ K+LREQL
Sbjct: 191 NEGKNREIRKVMAALGLETTRLIRIAYGPFQLGNLPRGAVAEVNPKVLREQL 242


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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|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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 84/239 (35%), Positives = 120/239 (50%), Gaps = 5/239 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R+ KV+A  G+ASRR  E +I   +V VNG   +       + D IE  G  L   
Sbjct: 1   MTTERLQKVLAHWGVASRRHAETLIRSGQVFVNGQRAKLGDKVDPARDRIEYKGERLNPP 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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            A + + L EG+NR+I++V +   + V  L RI+ GP  LG L   + R +S+  L   
Sbjct: 181 RALLEIILHEGRNRQIRRVADQLGYPVLALQRIAIGPVHLGHLRPRAVRPLSRHELAAL 239


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 132/231 (57%), Positives = 170/231 (73%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +AR+G+ASRR+ ERMIA+ RV++NG ++   A  V + D ++V+G  +   +RTR
Sbjct: 16  RIAKWLARSGVASRRDAERMIAEGRVQLNGAVVNHPATFVGAGDIVQVNGSVVGAPDRTR 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW YHKP GLVTTH DP+GR TVF++LP    RVISVGRLD+N+EGLLLLTNDG LAR L
Sbjct: 76  LWRYHKPDGLVTTHRDPEGRPTVFESLPPGLPRVISVGRLDLNSEGLLLLTNDGELARRL 135

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  W+R YRVR  G VD+  L  L +G    G+ YG ++  LD+ KG NAW+TV LR
Sbjct: 136 ELPSNGWIRRYRVRVFGVVDERMLASLARGSEFDGVRYGPIEAHLDSAKGDNAWLTVSLR 195

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGKNRE++KV +  N  V+RLIR SYGPFQLGTL  G   EV+ K++REQ+
Sbjct: 196 EGKNREVRKVMQGLNLHVSRLIRTSYGPFQLGTLTRGELEEVTGKVIREQV 246


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 116/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K I  +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD +
Sbjct: 201 IEYKEINYDPNEPLRLNKFLANAGVCSRREADEFIQAGVVSVNGEIVTELGTKILRTDVV 260

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   E+    L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 261 KFHDQPVN-IEKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNACPERIYPVGRLDRNTT 319

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V    L  + +GI ++        V  
Sbjct: 320 GVLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNVTAHDLAQIAEGIQLEDGEIKADDVQY 379

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 380 -AHPTDKKQVGIEIHSGKNRIVRRIFESLGYRVQKLDRVQFAGLTKKNLKRGDWRYLTEE 438

Query: 240 IL 241
            +
Sbjct: 439 EV 440


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 87/233 (37%), Positives = 137/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG +++   V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVKELGVKVSGTERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFADIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQL 233


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 88/233 (37%), Positives = 132/233 (56%), Gaps = 2/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ KV+A+AG+ASRR  E MI + RVKVNG  +    V V   D +EVDG P+   E+ 
Sbjct: 6   MRLQKVVAQAGLASRRGAETMITEGRVKVNGETVTTLGVKVGIHDTVEVDGAPIEGREKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+VTT SD  GR TV D L  I  RV  VGRLD +T G LLLTNDG +A  
Sbjct: 66  VYYLLNKPRGVVTTTSDEKGRKTVLDLLEDIDQRVYPVGRLDYDTTGALLLTNDGTIANQ 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P ++  ++Y  +  G    +KL  LK+G++I+G      +VT++   +    + V +
Sbjct: 126 LMHPKSRVDKIYLAKVSGIATVEKLAPLKQGVIIKGRKTAPARVTIERVDKDKKTSMVRI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+N ++K + +     V++L R  Y  F L  L +G  R+++   ++  
Sbjct: 186 IIHEGRNHQVKDMLQKVGLPVDKLTREQYAFFDLIGLQSGEYRKLTGVEVKRL 238


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 124/234 (52%), Gaps = 3/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+   E 
Sbjct: 5   TERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPI-GKEA 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG LA 
Sbjct: 64  KRYFLFYKPRGVISAVQDNKGRDVVTDYFKDIAERLYPVGRLDYDTSGLLVMTNDGDLAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            L  P     + Y  +  G  ++  L  LK G+ + G      +V + +  +    A V+
Sbjct: 124 HLMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTAIVS 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+  
Sbjct: 184 LTIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQAL 237


>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 =  278 bits (712), Expect = 8e-73,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 118/242 (48%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AG+ SRRE +  I    V VNG ++      V  TD +
Sbjct: 5   IEYKDILTDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKVKRTDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  KFHDQPVN-IERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ + +GI +         V+ 
Sbjct: 124 GVLLLTNDGDLASKLTHPKFLKKKIYHVYCDKNVTKADLDQIVQGITLDDGEIHADAVSY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++ 
Sbjct: 184 -ASDTDKSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEM 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  278 bits (712), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 143/327 (43%), Positives = 201/327 (61%), Gaps = 6/327 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R++KV+ARAG+ SRR+ E  I + RV VNG +++  A++V ++D I +DG PL +
Sbjct: 387 DKAGERIAKVVARAGLCSRRDAEAWITEGRVAVNGKVIDSPALDVKASDVITIDGKPLPE 446

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ERTRL+LYHKP GL+TTHSDP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGG
Sbjct: 447 RERTRLFLYHKPRGLMTTHSDPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGG 506

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LAR LELP T WLR YRVR HG++ Q +L+ L+ GI + G+ YG +   L+  + +N W+
Sbjct: 507 LARALELPETGWLRRYRVRAHGEITQAQLDELQNGIEVDGVQYGPIDAKLERDQSANVWL 566

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
              +REGKNRE++ V      +VNRLIR+SYGPFQL  L  G   EV  ++LR+QLG  +
Sbjct: 567 VFAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLELGEGEVDEVKTRVLRDQLGEKV 626

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIIS----EVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
           +  A  +   P  S          ++S     V +   + KK  +++  +  +K     V
Sbjct: 627 IALAGCDFAGPSPSETKPKPRAGKVVSAEEWSVVEGAAKPKKTITKRGAVEDRKGRRIKV 686

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQRE 332
            R   AS+               G+R+
Sbjct: 687 ER--TASDGGERPLSRGPARRYHGKRD 711


>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 =  278 bits (712), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
            L  P  +  + Y     G +  D++   + G+ I+       +  VT + ++ + +   
Sbjct: 121 KLTHPKHEIDKTYVASVKGIISDDEIRQFETGLKIEDYTTAPAKIRVTKENKEKNYSVCE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++  ++
Sbjct: 181 ITIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTEDEIK 232


>gi|410137|gb|AAA67493.1| ORFX13 [Bacillus subtilis subsp. subtilis str. 168]
          Length = 229

 Score =  278 bits (712), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 76/225 (33%), Positives = 124/225 (55%), Gaps = 3/225 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASR + E +I + +VKVNG ++    V V  +D IEV+G+ + + E  
Sbjct: 2   ERLQKVIAHAGVASRSKAEELIKEGKVKVNGKVVTELGVKVTGSDQIEVNGLKVEREE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G+++   D  GR  V D   +I  R+  +GRLD +T GLLLLTNDG  A  
Sbjct: 61  VYFLLYKPRGVISAAQDDKGRKVVTDFFKNIPQRIYPIGRLDYDTSGLLLLTNDGEFANK 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  +  G   ++ L  L++GI ++       +  L +  +K   + + +
Sbjct: 121 LMHPKYEIDKTYVAKVKGIPPKELLRKLERGIRLEEGKTAPAKAKLLSLDKKKQTSIIQL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EG+NR+++++FE    +V +L R  Y    L  L  G  RE+
Sbjct: 181 TIHEGRNRQVRRMFEAIGHEVIKLKREEYAFLNLRGLHTGDAREL 225


>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 =  278 bits (712), Expect = 9e-73,   Method: Composition-based stats.
 Identities = 71/331 (21%), Positives = 137/331 (41%), Gaps = 18/331 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG P+  
Sbjct: 3   SLTEKRLNKYISETGFCSRREADKLIEQGRVTINGQLP-PMGSKVTEHDQVCIDGKPVGY 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG 
Sbjct: 62  KEKPIYIALNKPTGITCT-TERDVPGNIVDFI-GHNKRIFPIGRLDKPSDGLIFLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR +  +  + +  +  G+ I        +V  +TQ       
Sbjct: 120 IVNKILRAGNNHEKEYVVRVNKPISAEFIRQMSAGVNILDTVTLPCKVVQETQYS----F 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--- 246
            + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L    
Sbjct: 176 RIILTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGQWRYLTDAEVNEILAMCE 235

Query: 247 --PHLLEEAQVNLDAPIYSSETLVR------DRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
                 E ++ +         T  +       +    SE P    + ++    ++  + +
Sbjct: 236 SSVSTEEASKTDSSGKQIRKATDAKLFDSRLAQSKTTSETPHKTYQGRQAHEFRHAPNSK 295

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           K         ++  N   A+    +    +G
Sbjct: 296 KGREQRQQHGDVKRNDNTARSARRNPTRKAG 326


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 116/359 (32%), Positives = 173/359 (48%), 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  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
             +R    +A+ TR+ LY+KP G + + +DP+GR TV+DNLP + S 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      +       D    +     RDR     E P      + N+   +  S+ 
Sbjct: 241 KELKELCQTADIP----VPDRKFSAGLQDFRDRQRRRLESPGSKRSSRPNTKVPDARSRP 296

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS---FPSKRSLRRTSAKK 354
                        +    A     +  S       +  R P      SK++  R   ++
Sbjct: 297 SSAHFDPEVTVGKAATPNAPKARMNTRSAPNFDNGSDTRQPKPRQQASKKTNSRNKDRR 355


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 106/348 (30%), Positives = 163/348 (46%), Gaps = 24/348 (6%)

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  DGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 -TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
                 +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  RE
Sbjct: 184 QQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRWRE 243

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +S+  +                D             P + ++  D   RM++ SS+  G 
Sbjct: 244 MSQYEV----------------DVLSAEVGLTPVAMPQLNAKSKDKLERMQRKSSRPVGK 287

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           S++ +   P +       V     I             +  R    P 
Sbjct: 288 SERVRTLRPANGSAATPRVSREPQIEGERPGRKPAARPDGERGSRAPR 335


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 116/229 (50%), Gaps = 2/229 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A  G+ASRR+ E +I Q RVKVNG  +      V    D + VDG  L   ++ 
Sbjct: 3   RLQKFMADCGVASRRKCEEIILQGRVKVNGRTITELGFKVDPQKDKVLVDGKKLVPVQKK 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++++  D  GR TV D +      RV  VGRLD +T GL+LLTNDG  A 
Sbjct: 63  IYIMLNKPFGVISSAKDEKGRKTVVDLVKDKVDVRVFPVGRLDFDTTGLILLTNDGEFAY 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y     G   ++++   KKG+ I G      +  +       + V + 
Sbjct: 123 KVTHPKHDIEKTYIALIEGVPTKEEIEQFKKGLFIDGKLTSPAKFRILKVFKGMSLVEIK 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+NR+++K+ +    +V +L R++ G  +LG L  G    + + ++
Sbjct: 183 IHEGRNRQVRKMCDAIGHRVLKLKRVAIGKLKLGKLKEGEFVFLDENMV 231


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 124/234 (52%), Gaps = 3/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+   E 
Sbjct: 5   TERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPI-GKEA 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG LA 
Sbjct: 64  KRYFLFYKPRGVISAVQDNKGRDVVTDYFKDITERLYPVGRLDYDTSGLLVMTNDGDLAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            L  P     + Y  +  G  ++  L  LK G+ + G      +V + +  +    A V+
Sbjct: 124 HLMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTAIVS 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+  
Sbjct: 184 LTIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQAL 237


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 124/234 (52%), Gaps = 3/234 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K+IA AGIASRR  E +IA   VKVNG +     + +   D +EVDGVP+   E 
Sbjct: 5   TERLQKIIANAGIASRRHAETLIATGHVKVNGQIETEMGIKIGPHDEVEVDGVPI-GKEA 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L++KP G+++   D  GR  V D    I  R+  VGRLD +T GLL++TNDG LA 
Sbjct: 64  KRYFLFYKPRGVISAVQDNKGRDVVTDYFKDITERLYPVGRLDYDTSGLLVMTNDGDLAN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            L  P     + Y  +  G  ++  L  LK G+ + G      +V + +  +    A V+
Sbjct: 124 HLMHPRYALEKKYVAKVQGVPNRPALAPLKTGVEVDGKMTAPAKVDIISTDKAKKTAIVS 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + +G N ++KK+F+   + V +L R +YG   L  L  G  R +  + L+  
Sbjct: 184 LTIHQGMNHQVKKMFKAVGFPVLKLSREAYGNLTLVGLQPGEHRPIKPQELQAL 237


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 81/339 (23%), Positives = 143/339 (42%), Gaps = 16/339 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQP-EVGSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT +TQ        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRIVLT 180

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

Query: 255 VNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
                   S +T+ R  D     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|168700584|ref|ZP_02732861.1| ribosomal large subunit pseudouridine synthase B [Gemmata
           obscuriglobus UQM 2246]
          Length = 271

 Score =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 92/279 (32%), Positives = 140/279 (50%), Gaps = 10/279 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
           +R++K +A AG+ SRR  +++I+  RVKVNG+ +    + +  + H I VD  P+R AE+
Sbjct: 2   ERLNKYLAHAGVGSRRHCDKLISAGRVKVNGVKVTELGLKIDPSAHQIAVDDQPVR-AEK 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 LTEGKNREIRRMLAKFGHKVMRLKRVAIGPVKLDKLPKGKARRISDEELKAL--KAFVTR 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           A+  + A        ++          D   R +K    
Sbjct: 239 ARQKITA------ARLKAADGGRKTSQDAPKRPRKTDGA 271


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 79/231 (34%), Positives = 119/231 (51%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++++ G+ASRR+ E+ I Q RV +NG + E      +  D I +DG  LR   R 
Sbjct: 3   ERLQKILSQLGVASRRQAEQWIQQGRVTINGRVAEIGQQADLKRDRIHLDGKRLRPKHRP 62

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R  L HKP+G+V+T  DP  R TV D + 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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+NR+I++V E     V RL R++ GP +LG+L  G  R ++   +
Sbjct: 183 VILHEGRNRQIRRVAEQLGHPVLRLTRVAIGPLRLGSLQPGEYRSLTAAEV 233


>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 =  278 bits (711), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 78/349 (22%), Positives = 143/349 (40%), Gaps = 14/349 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRREADRLIEQGRVTINGNKP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPIYIALNKPTGITCT-TERDVPGNIVDFI-GHQKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        +VT +T+   
Sbjct: 116 NDGDIVNKILRAGNSHEKEYVVRVDKPITVEFLKQMSSGVKILDTVTLPCKVTKETKFS- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L
Sbjct: 175 ---FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEVAEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + E  V  +    +       R    +++ D     + +++++N  ++  +     
Sbjct: 232 A---MCEGSVGTEEASKTDSRGRNIRKATDAKLFDSREENQDSTARRNQKTRTFRGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R   +              D G R            +RS  +    K
Sbjct: 289 QFR--HAPNSKKGQQKRRQCDDEGGRPAKEHYKAKPQGERSRPQGEHGK 335


>gi|291558038|emb|CBL35155.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           siraeum V10Sc8a]
          Length = 251

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 118/233 (50%), Gaps = 1/233 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RK 69
               R+ K+IA +G  SRR+ E  I Q  VKVNG  +          D + V+G  +   
Sbjct: 1   MEKVRLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPVSLGDKADPKNDIVTVNGEKIASS 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|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 =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 148/323 (45%), Positives = 193/323 (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 RNLASNVWMAKGIHSSFLSDSGQ 330
              A N   A G         G 
Sbjct: 603 EARARNEAEANGYGPPRRPKRGY 625


>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 =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 113/234 (48%), Gaps = 3/234 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG ++      V+ TD ++    P+ 
Sbjct: 252 DPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVTELGTKVLRTDEVKFHDNPVS 311

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTND
Sbjct: 312 L-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTGVLLLTND 370

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +A  L  P     +VY V     V    L  + +G+ ++        V    +    +
Sbjct: 371 GDMASKLTHPKFLKKKVYHVHLDKNVTAHDLEQIAQGVTLEDGEIHADAVEYADEH-DKS 429

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K +
Sbjct: 430 QVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFLTEKEV 483


>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 =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 112/232 (48%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R    ++I Q  V V+GI++++ A ++     +E DGV L   +R 
Sbjct: 1   MRLDKFLCDCSDLTRSLAGKLIRQGEVTVDGIVVKQPAFHINEQSQVEFDGVMLTLDQRN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V ++ DPD   TVF  +      ++  VGRLD++T GL+L+T+DG  + 
Sbjct: 61  RYFMLHKPEGYVCSNEDPDH-PTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V     V QD ++L   G+ ++          L+    +     + 
Sbjct: 120 RITSPRHECAKTYHVWLADPVHQDAISLFADGVFLRNETEKTRPAQLEI--LAECEARLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           + EGK  ++K++F     KV  L R   G   L   L  G  RE++ + + +
Sbjct: 178 IHEGKYHQVKRMFASIGNKVVGLHREQIGTLALDEALAPGEYRELTAEEIAQ 229


>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 =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 80/235 (34%), Positives = 123/235 (52%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V+VNG  +      V + D IEVDG+PL + E+ 
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIATGHVQVNGQTVTTLGTKVTAKDKIEVDGIPLHR-EKQ 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D L    I  R+  VGRLD +T GLLLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDEKGRRTVVDILREDEIEERIYPVGRLDYDTTGLLLLTNDGTLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWV 189
             +  P     + Y  +  G +  D L  L+ G+ + G      +  L    ++   + V
Sbjct: 121 NKMMHPKFAVDKTYVAKVKGLISNDDLKQLRTGVKVDGRRTKPAKTRLKGTDREKKTSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EG   ++K++       V +L R SYG   L  +  G  RE+  + ++  
Sbjct: 181 QLTIHEGHYHQVKRMLAAVGHPVIKLHRESYGFLNLQGVQPGDYRELRPEEVKRL 235


>gi|170288482|ref|YP_001738720.1| pseudouridine synthase [Thermotoga sp. RQ2]
 gi|170175985|gb|ACB09037.1| pseudouridine synthase [Thermotoga sp. RQ2]
          Length = 239

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 124/250 (49%), Gaps = 12/250 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++      V+  D + +DG  +R   + 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALDGEVVRF-HKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP G VT+  DP    T+ + LP     +  VGRLD + EGLL++TNDG  A  
Sbjct: 60  VYILFYKPSGYVTSTKDP-HSETIMEFLPP-LKGIFPVGRLDKDAEGLLIITNDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKC---VEKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  +IK++      K   L R   G   L   +  G  R +S++ ++      + E 
Sbjct: 175 TEGKYHQIKRMTAAVGLKTVHLKRTRIGGLVLPDDMKPGEYRFLSEEEVK-----KVFER 229

Query: 253 AQVNLDAPIY 262
                D P +
Sbjct: 230 EDQKEDTPRF 239


>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 =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 122/233 (52%), Gaps = 1/233 (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 HKP G +++ +DP GR  V D L ++ +RV  VGRLD +TEGLLLL+NDG  + +
Sbjct: 61  -YLLLHKPAGYISSLADPQGRPRVIDLLSAVNTRVFPVGRLDYDTEGLLLLSNDGEFSNL 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y     G V  D +  L++G+ ++       +V L + K   + + + +
Sbjct: 120 MTHPRYLIPKKYEAWVQGLVKPDTIRQLEQGVALEDGITAPARVRLLSSKKGQSLLELEI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGK R+IK++      +V +L R +     L  +  G  R ++   +   + 
Sbjct: 180 HEGKKRQIKRMCLAVGHRVTKLKRTALAFLTLEGVPRGQFRFLTASEVESLIM 232


>gi|291531258|emb|CBK96843.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           siraeum 70/3]
          Length = 251

 Score =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 118/233 (50%), Gaps = 1/233 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RK 69
               R+ K+IA +G  SRR+ E  I Q  VKVNG  +          D + V+G  +   
Sbjct: 1   MEKVRLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPVSLGDKADPKNDIVTVNGEKIASL 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|229916174|ref|YP_002884820.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
 gi|229467603|gb|ACQ69375.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
          Length = 252

 Score =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/240 (35%), Positives = 127/240 (52%), Gaps = 8/240 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AG+ASRR+ E MI   RV+VNG ++      V     IEVDGV + + E  
Sbjct: 2   ERLQKVIAQAGVASRRKAEEMILDGRVRVNGKVVRELGTKVGPKSEIEVDGVKIEQEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+T  D  GR  + D +P   +RV  VGRLD NT GL++LTNDG  + +
Sbjct: 61  VYYLLYKPSGYVSTVDDDKGRKVITDLVPPG-ARVFPVGRLDYNTTGLIILTNDGEFSNM 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDT--QKGSNAWVT 190
           +  P  +  + Y  +         +  L+ G+ +      G  +V + +  QK + A + 
Sbjct: 120 MTHPKYKIQKRYVAKVKNIPSYLAIKQLESGVELDDGFKTGSAKVKMKSVDQKKNTAILE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGP 247
           + + EG NR+I+++ E    +V +L R  +G   L  L  G  RE+S K    LRE   P
Sbjct: 180 IVISEGHNRQIRRMVEAIGSEVIKLKREQFGFLTLDGLNTGDWRELSHKEISKLRELANP 239


>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 =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 118/233 (50%), Gaps = 1/233 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RK 69
               R+ K+IA +G  SRR+ E  I Q  VKVNG  +          D + V+G  +   
Sbjct: 1   MEKVRLQKIIADSGYCSRRKAEEYIEQGCVKVNGRPVSLGDKADPKNDIVTVNGEKIASS 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 LANAVMHPSRHIKKRYRVTVRGEVTDDKLTTLASGVKIDTGVTLPCTVAVLAEEENRTVI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              + EGKNR+I+K+ E    ++ RL R + G  +LG L  G   +++ + L+
Sbjct: 181 EFTIAEGKNRQIRKMCEAVKLQIVRLKRNAVGNIKLGMLKPGEWADLTAEELK 233


>gi|313623106|gb|EFR93379.1| ribosomal large subunit pseudouridine synthase B [Listeria innocua
           FSL J1-023]
          Length = 244

 Score =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 136/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGVTSRRKAEKLIQEGKVTVNGKVVTELGVKVTGTERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLAREEYSFLNLRGLNAGERRELSHHEVKQL 233


>gi|295099584|emb|CBK88673.1| ribosomal large subunit pseudouridine synthase B [Eubacterium
           cylindroides T2-87]
          Length = 241

 Score =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 117/233 (50%), Gaps = 4/233 (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
              + +K  G + + +D   R TV D L  I  RV +VGRLD +T G+LLLTNDG     
Sbjct: 62  YYVI-NKTKGCICSSNDDRDRRTVLDYL-DIPQRVYTVGRLDYDTSGVLLLTNDGDFCNQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P     + Y V   G + QD + LL+KG+      +   +V + +           +
Sbjct: 120 MIHPRYHLPKTYVVNLQGTLTQDDIRLLRKGLKTNIGDFQPAKVKIISNDVTRDRTIFEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGKN ++K + E    +V +L R+ +G  ++  L  G  R +    +++ 
Sbjct: 180 TIMEGKNHQVKNMMEALGHQVRKLHRVRFGSIEVNDLKPGEYRRLKPYEVKQL 232


>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 =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 87/233 (37%), Positives = 137/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +  + A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKNKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQL 233


>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 =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 113/234 (48%), Gaps = 3/234 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG ++      V+ TD ++    P+ 
Sbjct: 252 DPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGEVVTELGTKVLRTDEVKFHDNPVS 311

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTND
Sbjct: 312 L-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTTGVLLLTND 370

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +A  L  P     +VY V     V    L  + +G+ ++        V    +    +
Sbjct: 371 GDMASKLTHPKFLKKKVYHVHLDKNVTAHDLEQIAQGVTLEDGEIHADAVEYADEH-DKS 429

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K +
Sbjct: 430 QVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFLTEKEV 483


>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 =  277 bits (710), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 107/237 (45%), Gaps = 3/237 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           LD  +     V + +
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLHNEKSLTKPAQLDVIEP--QRVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 123/234 (52%), Gaps = 6/234 (2%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
             L L +KP G VT+  D     TV + +     F ++  VGRLD + EGLLL+T DG L
Sbjct: 61  YYLVL-NKPAGYVTSTKDRQ--MTVMELVADIPRFDKLFPVGRLDKDAEGLLLMTTDGEL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y V+  G++ ++ +  L++GI ++       +V +       +   
Sbjct: 118 AHRLTHPKWKVPKTYVVKVEGRLTEEAVEPLRRGIELKDFKAKPAEVRILRSSEEESEAE 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EGK  ++K++F      V  L R+++GP +LG L  G  R ++++ LR  
Sbjct: 178 ITITEGKFHQVKRMFAAIGHPVKELKRVAFGPLKLGELPTGEYRHLTEEELRAL 231


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 3/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +
Sbjct: 34  KITHMRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQ 93

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG 
Sbjct: 94  QHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQ 153

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +  +  P     + Y V     V  D      KG+ +           L+    +   V
Sbjct: 154 WSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQV 211

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 212 RLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 264


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 126/237 (53%), Positives = 167/237 (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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           TVGLREGKNREI++  E+   +VNRLIR SYGPF+L  L  G   E+  K +++QLG
Sbjct: 182 TVGLREGKNREIRRAMEYVGLRVNRLIRTSYGPFKLDDLKPGDVEEIKAKTIKDQLG 238


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 77/349 (22%), Positives = 137/349 (39%), Gaps = 17/349 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG         V   D + VDG 
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRREADRLIEQGRVTINGQQP-EMGTKVQPGDDVCVDGN 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        +V    +K +
Sbjct: 116 NDGDIVNKILRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKV----EKET 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L
Sbjct: 172 KFSFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDNEVSEIL 231

Query: 246 G---PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK-- 300
                 +  E     DA   +       +     +   D T  +  +++    +   +  
Sbjct: 232 AMCEGSVGTEEASKRDAKGRNIRKATDAKLYDSRDENQDSTARRNQTARTFRGNNADEFR 291

Query: 301 ---LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
               +    +R    N               G+R ++H       SK  
Sbjct: 292 HAPNSKKGQQRRQRDNEGGRPASDHYRAKPQGERSKSHGEHNKTHSKSD 340


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/341 (24%), Positives = 146/341 (42%), Gaps = 20/341 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQP-EVGSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT +TQ        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   + E++ 
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA--MCEDSS 238

Query: 255 VNLDAPIYS----SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              +A   +    S     D     S   +  ++ ++N    +G + Q+    P  ++  
Sbjct: 239 GTEEASRVAQSGDSIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQ 298

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                      SS  + S   +   R +P      SLR++ 
Sbjct: 299 RHP-------KSSPSNSSTASKPASRPTPRTGGTLSLRKSK 332


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 135/233 (57%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I + +V VNG ++    V V  ++ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGITSRRKAETLIKEGKVTVNGKVVTELGVKVSGSERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKIRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQL 233


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 143/319 (44%), Positives = 187/319 (58%), Gaps = 3/319 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++KV++RAG+ SRR+ E  I + RV VNG ++   A++V   D I VDG PL   E
Sbjct: 465 AGERIAKVVSRAGLCSRRDAEDWITEGRVAVNGRIINSPALDVTERDVITVDGKPLPPPE 524

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RTRL+LYHKP GL+TTH+DP+GR TVFD+LP    R+IS+GRLD NTEGLLLLTNDGGLA
Sbjct: 525 RTRLFLYHKPRGLMTTHADPEGRPTVFDHLPEGLPRLISIGRLDFNTEGLLLLTNDGGLA 584

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R LELP T WLR YRVR HG+V Q +LN LK G+ + G+ YG +  TL+  +G+N W+  
Sbjct: 585 RTLELPDTGWLRRYRVRAHGEVTQAQLNELKDGVEVDGVKYGPIDATLERDQGANVWLVF 644

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            +REGKNRE++ V      +VNRLIR+SYGPFQLG +  G   EV  ++LREQLG  +  
Sbjct: 645 AIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLGEIEEGQVEEVKTRVLREQLGEKIAL 704

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            A  N    I S      D   +   V     R      +   +  Q+  +     RN  
Sbjct: 705 AAGANFARQIPSKGDTDLDPVVVKKPV---LKRSTVEDRKGRRVLVQRSGSEEARERNEL 761

Query: 312 SNVWMAKGIHSSFLSDSGQ 330
                             +
Sbjct: 762 EAAGFGPPKRPKRGYKGKR 780


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 130/248 (52%), Positives = 175/248 (70%), Gaps = 3/248 (1%)

Query: 1   MKDKNIVQ-ENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++ +   ++ TP  +R++K +ARAG+ASRR+ E+++   RV++N  ++   A  V S 
Sbjct: 1   MTEERMEDADSGTPRGERIAKWLARAGVASRRDAEKLVEDGRVRLNNQVVTHPATFVGSG 60

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D + V+G  +   +RTRLW YHK  G++TTH DP GR TVF+ LPS   RV+SVGRLD+N
Sbjct: 61  DLVTVNGALVEAPDRTRLWRYHKTDGVMTTHRDPQGRPTVFEKLPSSMPRVVSVGRLDLN 120

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLLLTNDG LAR LELP T W+R YRVR HG V Q  L+ L +G+ ++G+ YG ++ 
Sbjct: 121 SEGLLLLTNDGMLARRLELPQTGWIRRYRVRVHGDVTQAMLDSLARGVTVEGVRYGSIEA 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            LD+ KGSN+W+TV L+EGKNREI+KV       V RLIRI+YGPFQLG L  G   EV+
Sbjct: 181 GLDSSKGSNSWLTVSLKEGKNREIRKVMRHIGLHVTRLIRIAYGPFQLGQLGKGEVEEVT 240

Query: 238 KKILREQL 245
            K+LREQL
Sbjct: 241 GKVLREQL 248


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 124/233 (53%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A AGIASRR+ E++I + RVKVNG ++      V   D IEVD VP+   E   
Sbjct: 3   RLQKVLAHAGIASRRKAEQIILEGRVKVNGEIINELGRQVSKQDKIEVDNVPI-YQEAPV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L++KP G++T+ SD   R TV D       RV  VGRLD +T GLL++TNDG L + L
Sbjct: 62  YYLFYKPRGIITSVSDDKKRKTVADYFLHSNERVYPVGRLDYDTTGLLIVTNDGSLTQQL 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVG 192
             PS +  +VY  +  G   +  L  L KGI I+G        Q+     K   + V + 
Sbjct: 122 THPSHEIDKVYVAKVKGIALRKTLLPLTKGIKIKGRKTAPANFQILSVDTKKQTSLVQLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + EG+N ++K + +   + V +L R   G   L  L  G  R ++KK +   L
Sbjct: 182 IHEGRNHQVKDMLDTVGYPVQKLKRERIGDLTLEGLHPGEYRRLTKKEIHALL 234


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 86/233 (36%), Positives = 136/233 (58%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ SRR+ E++I + +V VNG ++    V V  T+ IEV+G+ L K E  
Sbjct: 2   ERLQKVIANAGVTSRRKAEKLIQEGKVTVNGKVVTELGVKVSGTERIEVEGIQLTKEE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R +L++KP G V+  +D  GR+TV D    I  R+  VGRLD +T GLLL+TNDG  A +
Sbjct: 61  RYFLFYKPRGTVSAVTDDKGRTTVADYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANL 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A V +
Sbjct: 121 LMHPKNEVSKTYIARIKGIPEREVIRELERGVVIDGRKTAPAKVKVRSSDKAKDKAIVEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 181 TIHEGRNRQVRKMFEAVGFEVQKLAREEYSFLNLRGLNAGERRELSHHEVKQL 233


>gi|255525211|ref|ZP_05392153.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255511074|gb|EET87372.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 234

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 121/230 (52%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD +T GL+LLTNDG +  
Sbjct: 63  KVYIALNKPKGYVSTVKDERGRKTILDLV-DVTERIYPIGRLDYDTSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  ++Y     G   ++ +   + GI I G      +  +  +      V + 
Sbjct: 122 KIIHPKQEKNKIYIALIKGIPTENDIKKFEIGINIDGYVTAPAKFKIIKKFKDYCEVEII 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + EG+NR+I+K+ +F N +V  L RI  G  +LG L  G  R +S K ++
Sbjct: 182 IHEGRNRQIRKMCDFINHQVLELKRIQIGDIKLGNLPLGKWRYLSNKEVK 231


>gi|31789454|gb|AAP58568.1| pseudouridylate synthase [uncultured Acidobacteria bacterium]
          Length = 317

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/237 (34%), Positives = 126/237 (53%), Gaps = 5/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
           F  +R+ K+IA AGIASRR  E++I    V VNG ++        +  DHI+V G  +  
Sbjct: 54  FMEERLQKIIATAGIASRRHAEQLITAGEVTVNGKVVTELGTKADAQNDHIKVRGKLINP 113

Query: 70  AERTR---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             +       L +KP G +++ SDP+GR TV + LP+   RV  VGRLD NTEGLLLLTN
Sbjct: 114 TLKRVEKNYILLNKPRGYLSSVSDPEGRPTVLELLPASLGRVYPVGRLDFNTEGLLLLTN 173

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG     +     +  +VY  +  G   +  +  L++G+ +  G+     ++ L  +  S
Sbjct: 174 DGDFTNFITSARNKVDKVYEAKVKGVPTEASVERLRRGVTLDDGVRTAPAKIRLLGETES 233

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           NAW  V L EGKN++I+++F+     V +L R   G  +   L  G  R +S+  ++
Sbjct: 234 NAWFEVLLHEGKNQQIRRMFDLIGHSVVKLRRSRIGGLRDDELKPGKWRRLSEYEVK 290


>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 =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V      + V G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKQLLKQKAVTVDGASVKDAAMHVDPEQQNVSVYGERVVYTE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D     TV D L  +        VGRLD +TEGLL+LTNDG L
Sbjct: 60  FVYFMMNKPPGVISATEDLRD-ETVIDLLEPLDQHFQPFPVGRLDKDTEGLLVLTNDGIL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY     G V ++ +    +G+ +  G      ++ +  +    + +
Sbjct: 119 AHKLLSPKKHVPKVYYAHIEGVVTEEDVEKFAEGVELDDGYMTKPGKLVIL-KSAPQSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++ + L
Sbjct: 178 ELTIQEGKFHQVKRMFESVGKRVTYLKRISMGNLKLDDHLALGEYRELTAEEL 230


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 112/242 (46%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    + VNG ++      VM TD +
Sbjct: 183 IEYKEENFDPNEPIRLNKYLANAGVCSRREADEFIQAGVITVNGEVVTELGTKVMRTDEV 242

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD N  
Sbjct: 243 KFHDQNVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNPT 301

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V    L  +  GI ++        +  
Sbjct: 302 GVLLLTNDGDLASKLTHPKFLKKKVYHVYLDKPVAAHDLQQIADGITLEDGEIHADAIEY 361

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +      V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +S+K
Sbjct: 362 ADEH-DKKQVGIEIHSGKNRIVRRIFEALGYRVTKLDRVQFAGLTKKNLRRGDWRFLSEK 420

Query: 240 IL 241
            +
Sbjct: 421 EV 422


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/341 (24%), Positives = 147/341 (43%), Gaps = 20/341 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQP-EVGSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T ++ D    + D + S   R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-SHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT +TQ        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   + E++ 
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA--MCEDSS 238

Query: 255 VNLDAPIYS----SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              +A   +    S     D     +   +  ++ ++N    +G + Q+    P  ++  
Sbjct: 239 GTEEASRVAQSGDSIKRATDAKLFDNREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQ 298

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                      SS  + S   +   R +P      SLR++ 
Sbjct: 299 RHP-------KSSPSNSSTASKPASRPTPRTGGTLSLRKSK 332


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 108/237 (45%), Gaps = 3/237 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           LD  +     V + +
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLHNEKSLTKPAQLDVIEP--QRVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
           REG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PHL
Sbjct: 179 REGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 125/232 (53%), Gaps = 1/232 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +IA  RV+V+G+ + R  V V   T  I VDG  +  A   
Sbjct: 33  RLQKVLAAAGVGSRRACEELIAAGRVEVDGVPVTRLGVRVDPQTAVIRVDGKRIPPATPF 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +  +KP G+VTT SDP GR  V D +  +  RV  VGRLD ++EGLLLLTNDG L   
Sbjct: 93  AYFALNKPRGVVTTMSDPRGRPCVGDLVADLPVRVFHVGRLDTDSEGLLLLTNDGRLTHR 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS    + Y     G++ +  ++LL+ G+ +         V +  + G+   V V +
Sbjct: 153 LTHPSHAVPKTYVADVEGRLGRTGVHLLRSGVDLADGPAQADAVRILERYGARTLVEVVV 212

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EG+   ++++       V RL+R + GP  LG L  G+ R+++ + L E L
Sbjct: 213 HEGRTHLVRRMLAAVGHPVRRLVRTAIGPVALGQLRPGARRQLTPRELGELL 264


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 80/349 (22%), Positives = 146/349 (41%), Gaps = 14/349 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRREADRLIEQGRVTINGNKP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPIYIALNKPTGITCT-TERDVPGNIVDFI-GHQKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        +VT +T+   
Sbjct: 116 NDGDIVNKILRAGNSHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVTKETKFS- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S + + E L
Sbjct: 175 ---FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDEEVAEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + E  V  +    +       R    +++ D     + +++++N  ++  +     
Sbjct: 232 A---MCEGSVGTEEASKTDSGGRNIRKATDAKLFDSREENQDSTARRNQKTRTFRGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+ A N    +        D G R            +RS  +    K
Sbjct: 289 EFRH-APNSKKGQQKRRQR-DDEGGRPAKEHYKAKPQGERSRPQGEHGK 335


>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 =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 84/233 (36%), Positives = 132/233 (56%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA++G+ SRR+ E+MI   +VKVNG  ++   V V + D I VDGVPL K E  
Sbjct: 6   ERLQKVIAQSGVTSRRKAEQMILDGKVKVNGETVQEMGVKVTANDEIVVDGVPLEK-ETP 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G++++  D  GR  V D   ++  R+  +GRLD +T G+LLLTNDG  A +
Sbjct: 65  VYFLLYKPRGVISSVKDDKGRKVVTDYFEAVEQRIFPIGRLDYDTSGVLLLTNDGDFANL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  +VY  +  G  ++ +L LL+KGI         +QV L +   +   + + +
Sbjct: 125 LMHPRHEIDKVYIAKVRGIPNKKELALLQKGIRSDKDVLKAVQVKLLSTDHQKKTSIIEL 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L EGKNR+++++ E   + V +L R  Y    L  L AG  R ++ K + + 
Sbjct: 185 TLHEGKNRQVRRMLEELGYPVMKLKRERYDFIGLEGLNAGEYRSLTPKEVNQL 237


>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 =  277 bits (708), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 79/349 (22%), Positives = 145/349 (41%), Gaps = 15/349 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKYISETGFCSRREADRLIEQGRVTINGQQP-EMGTKVLPGDDVCVDGN 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        +V    +K +
Sbjct: 116 NDGDIVNKILRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKV----EKET 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L
Sbjct: 172 KFSFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDDEVAEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + E  V  +    +       R    +++ D     + +++++N  ++  +     
Sbjct: 232 A---MCEGSVGTEEASKTDSRGRNIRKATDAKLYDSREENQGSTARRNQKTRTFRGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+  ++    KG       D G R            +RS  +    K
Sbjct: 289 EFRHAPNS---KKGQQRRQRDDEGGRPAKEHYKAKPQGERSRPQGEHGK 334


>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 =  277 bits (708), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 128/234 (54%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KVIA+AG+ SRR+ E++I + +V VNG  +      V    D + V+GVPL K E 
Sbjct: 5   ERLQKVIAQAGVTSRRKAEQLILEGKVIVNGNKVTELGTKVDLQHDEVIVEGVPLEKEE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++++  D  GR  V D +P    R+  +GRLD +T GL+LLTNDG  A 
Sbjct: 64  PIYFLLYKPTGVISSVDDEKGRKVVTDFIP-TDKRIFPIGRLDYDTSGLILLTNDGDFAN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           +L  P  +  + Y  +  G   ++ +  L+KGI ++       +V +    +K   + + 
Sbjct: 123 LLMHPKHEIYKTYIAKVEGVPLREDIKKLEKGIHLEDGRTAPAKVKVSRSDKKKGTSIIE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE     V +L R +YG   L  L AG  RE+    ++  
Sbjct: 183 ISIHEGRNRQVRRMFEAIGHPVMKLKRENYGFLNLKGLNAGDFRELKPHEVKRL 236


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 112/234 (47%), Gaps = 3/234 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    VKVNG ++      V+ +D +     P+ 
Sbjct: 13  DPTVPVRLNKYLANAGVCSRREADEFIQAGVVKVNGEVVTELGTKVLRSDEVVFHDQPVS 72

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E+    L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LL TND
Sbjct: 73  L-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNACPERIYPVGRLDRNTTGVLLFTND 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     +VY V     V    +  + +GI ++        +    +   N 
Sbjct: 132 GDLASKLTHPKFLKKKVYHVFLDKNVTAHDMQQIAEGIELEDGEIHADAIEYTNETEKN- 190

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++ + +
Sbjct: 191 QVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRYLTAQEV 244


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 144/355 (40%), Positives = 190/355 (53%), Gaps = 12/355 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            E    +R++K +ARAGIASRREVER+I   +V VNG +L+  A  V   D I VDG P+
Sbjct: 93  AEPKRSERIAKAMARAGIASRREVERLIGLGKVAVNGRILDTPATLVTRDDVITVDGKPI 152

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A+ TR+W Y+KP+GL+T+H+DP GR TVFD LPS   RVISVGRLDINTEGLLLLTND
Sbjct: 153 AAAQATRVWRYNKPVGLLTSHNDPQGRPTVFDALPSGLPRVISVGRLDINTEGLLLLTND 212

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------D 180
           G L+R LELP T  +R YR R  G+V Q  L+ LK G+ + G+ YG ++ ++       D
Sbjct: 213 GELSRALELPETALVRQYRARARGRVTQADLDKLKDGVTVDGVRYGPVEASIDKATTKED 272

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             + +N W++V + EGKNRE++KV E     VNRLIR++YGPFQLGTL  GS  EV  ++
Sbjct: 273 GSQAANLWISVQIAEGKNREVRKVLESVGLTVNRLIRLAYGPFQLGTLAVGSVEEVGPRV 332

Query: 241 LREQLGPH-----LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +RE LG H     L +   V   API    T              D +R           
Sbjct: 333 IRELLGEHIRPDNLPQGNTVETPAPIPGRRTGAPKVTGTSGSAMSDPSRKPSRVRAAATA 392

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +         +        A               E    +   P++    R 
Sbjct: 393 QVEGAERANRPPKKAGWAKAAAPNPRGPSTKKPWAPREGAAPTGDRPARVFKPRD 447


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 147/323 (45%), Positives = 193/323 (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 RNLASNVWMAKGIHSSFLSDSGQ 330
              A N   A G         G 
Sbjct: 648 EARARNEAEANGYGPPRRPKRGY 670


>gi|327484742|gb|AEA79149.1| Ribosomal large subunit pseudouridine synthase F LSU Psi2604
           [Vibrio cholerae LMA3894-4]
          Length = 328

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 76/304 (25%), Positives = 132/304 (43%), Gaps = 9/304 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTING-LQPEVGSKVTEQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L      
Sbjct: 178 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSDAEVSEILAMCEDS 237

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 238 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 297

Query: 310 LASN 313
               
Sbjct: 298 QRRP 301


>gi|327312548|ref|YP_004327985.1| pseudouridylate synthase [Prevotella denticola F0289]
 gi|326945115|gb|AEA21000.1| pseudouridylate synthase [Prevotella denticola F0289]
          Length = 507

 Score =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +
Sbjct: 259 IEYKEENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVV 318

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 319 LFQEKPVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTT 377

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V  + L  +  GI ++        +  
Sbjct: 378 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEY 437

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 438 ADPQ-DQTQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNVRRGDWRFLTEK 496

Query: 240 IL 241
            +
Sbjct: 497 EV 498


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +
Sbjct: 259 IEYKEENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVV 318

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 319 LFQEKPVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTT 377

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V  + L  +  GI ++        +  
Sbjct: 378 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEY 437

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 438 ADPQ-DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEK 496

Query: 240 IL 241
            +
Sbjct: 497 EV 498


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 79/225 (35%), Positives = 128/225 (56%), Gaps = 4/225 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLY 78
           ++  G+ASRR  E MIA  RV+VNG++++   V V    D I VDG  L K  + + +L+
Sbjct: 1   MSNCGVASRRASEEMIAAGRVRVNGVIVKTPGVKVDLQKDIIVVDGKRLEKPAK-QYYLF 59

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G++TT  D   R+TV D   ++  R+  VGRLD NTEGLL++TNDG LA +L  PS
Sbjct: 60  NKPKGVLTTVKDDRERNTVMDYFKNVKDRIYPVGRLDQNTEGLLIMTNDGALANILMHPS 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|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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 80/232 (34%), Positives = 118/232 (50%), Gaps = 2/232 (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 +L   + + G      +V    + G    +++ +
Sbjct: 123 LLHPSHQVEKEYLVWVTGDV-ETALPILSGPMELDGEPLAPAKVARGRESGGVTQLSITI 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            +GKNR+++++      +V RL RI  G   L   L  G  R ++ + L   
Sbjct: 182 CQGKNRQVRRMCAQAGLEVTRLKRIREGQVSLDRKLKPGQWRPLTAQELAAL 233


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 89/243 (36%), Positives = 125/243 (51%), Gaps = 10/243 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           + QR+ KV+A AG+ASRR  E++IA  RV V+GI +    V V   T  I VDG  +   
Sbjct: 76  SGQRLQKVLAHAGVASRRACEQLIADGRVSVDGITVTEPGVRVDPLTQEIRVDGSRILTN 135

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV----FDNLPSIFS-----RVISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV     D L          R++ 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 REQ 244
              
Sbjct: 316 AAL 318


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 82/274 (29%), Positives = 137/274 (50%), Gaps = 4/274 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD  P+ 
Sbjct: 201 EAGEPIRLNKFLSNSGLCSRRTADQYIAAGRVKVNGAVVSELGSQVLPTDQVMVDDKPVT 260

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E     L +KP   VTT +DP+GR TV D + +    R+  +GRLD NT G+LLLTND
Sbjct: 261 L-EAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTND 319

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P+ +  ++Y V    +V  + + ++  G  ++        ++  T + ++ 
Sbjct: 320 GDLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ-THD 378

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ-LG 246
            V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R   +G
Sbjct: 379 KVGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRMG 438

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               E+  V     +Y       D P    E+ D
Sbjct: 439 IKEQEDNGVAPTTKVYHKHQETPDHPFSSEEIED 472


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 77/229 (33%), Positives = 124/229 (54%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD +T GL+LLTNDG    
Sbjct: 62  KKYIALNKPTGYISSVKDDKGRKTILDLI-DVKERIYPIGRLDYDTSGLILLTNDGDFYN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY     G  +  +L   KKG+VI        ++ + + K +NA V + 
Sbjct: 121 KVIHPREEKEKVYVATIKGIPNSSELQDFKKGLVIDDYLTSPSKIKIISVKNNNAEVIIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+NR+++K+ E  N  V +L RIS G   LG L  GS R +++K +
Sbjct: 181 IMEGRNRQVRKMCEKINHPVIKLKRISVGHVGLGDLPIGSWRYLTQKEI 229


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 119/231 (51%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++     +V   D + +DG  +    R 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVNF-HRK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP G VT+  DP    T+ + LP     +  VGRLD + EGLL++TNDG  A  
Sbjct: 60  VYILFHKPSGYVTSTKDP-HSETIMEFLPP-LKGIFPVGRLDKDAEGLLIITNDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G++ +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VTSPKWSVEKEYIVKVEGEITEDKIEKLKNGVTLRDGFFAKAKC---VEKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            EG+  ++K++      +   L R   G   L   +  G  R +S++ +++
Sbjct: 175 TEGRYHQVKRMTAAVGLRTVHLKRTRIGELVLPDDMKPGEYRFLSEEEVKK 225


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 82/256 (32%), Positives = 128/256 (50%), Gaps = 5/256 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ + +ARAG+ASRR  E +++  RV+VNG++       V    D +EVDG+ +     
Sbjct: 1   MRLQRFLARAGVASRRGSEHLMSAGRVRVNGLVASELGTKVDVGADRVEVDGIEVVFGAP 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G +TT SDP GR  V + +P   F  +  VGRLD +T G+LL T DG LA
Sbjct: 61  PVYIVLNKPAGYLTTMSDPAGRPCVAELVPIRRFPGLFPVGRLDKDTTGVLLFTTDGDLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWV 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 LEEAQVNLDAPIYSSE 265
             +   +L  P  S +
Sbjct: 240 PADPPAHLGRPGASRK 255


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 82/341 (24%), Positives = 146/341 (42%), Gaps = 20/341 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQP-EVGSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT +TQ        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   + E++ 
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA--MCEDSS 238

Query: 255 VNLDAPIYS----SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              +A   +    S     D     S   +  ++ ++N    +G + Q+    P  ++  
Sbjct: 239 GTEEASRVAQSGDSIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQ 298

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                      SS  + S   +   R +P      SLR++ 
Sbjct: 299 RHP-------KSSPSNSSTASKPAPRPTPRTGGTLSLRKSK 332


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 114/335 (34%), Positives = 164/335 (48%), Gaps = 26/335 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I Q RV V+G +      V+V  +  I +DG  L   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIQQGRVSVDGKVATLGDRVDVTPSTKIRLDGRILPITE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDPDGR TVFD LP    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           V LD    S   + +DR  + +       R  K  ++  G  +     
Sbjct: 242 EL----------VELDVETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQQTAGRQ 288

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
               + +   N        +     SG+R    +R
Sbjct: 289 GSARKSSTRQNTGNTASSGAPV---SGRRRAPAKR 320


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 85/246 (34%), Positives = 126/246 (51%), Gaps = 11/246 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R++K +A+AG+ SRR+ +  IA  RV+VNG L+ +  V V    D + VDG  +   
Sbjct: 28  ESCRLNKFLAQAGVCSRRKADTYIAAGRVQVNGSLVTQLGVQVHPGQDEVRVDGRVVELP 87

Query: 71  ERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLL 124
           E         L HKP+ +VTT  DP GR TV D LPS     R+  VGRLD  +EGLLLL
Sbjct: 88  EAQSAGHDYILLHKPVQVVTTAKDPQGRRTVLDLLPSQTFTRRIFPVGRLDFMSEGLLLL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           T+DG LA  L  P     +VY V     V ++ +  +  G+ + +G     + V      
Sbjct: 148 TSDGELANRLTHPRWHVEKVYEVTLREAVTEEHMRQMSSGMRLSEGEQLAPVDVQRRKTA 207

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI--- 240
              + + + L +G NR+I+++       + RL RI  GP +LG L  G  R ++      
Sbjct: 208 ADTSSLELTLHQGVNRQIRRMCRDLGLTILRLKRIRQGPVRLGKLPQGHWRHLTATEITT 267

Query: 241 LREQLG 246
           L+++LG
Sbjct: 268 LKKRLG 273


>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 =  276 bits (707), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 126/234 (53%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  +R +V+R+I +  V VNG  ++  + NV    D + VDG  +   E+
Sbjct: 1   MRLDKLLADSGFGTRSQVKRLIKKGFVTVNGETIKDPSFNVDPQKDEVLVDGELVEY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G +T+  D     TV + +     F R+  VGRLD + EGLLL+TNDG L
Sbjct: 60  DYYLILHKPQGYITSTKDRQ--MTVMELIADIPRFERLFPVGRLDKDAEGLLLITNDGEL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  +VY V   G+++++ L  LKKGI ++       +V +   + S +   
Sbjct: 118 AHRLTHPKWKVPKVYFVVVEGKLNEENLEPLKKGIELKDFRAKPAKVRILKAEESESEAE 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EGK  ++K++FE     V  L RI +G  +LG L  G  R ++K+ L+E 
Sbjct: 178 IEITEGKYHQVKRMFEKIGHPVKYLRRIQFGNLKLGNLPVGEYRFLTKEELKEL 231


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 3/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R+ K IA+    SR    R I   RV V+G ++  AA  ++    +  DG PL +
Sbjct: 29  KITHMRLDKFIAQQLGVSRAIAGREIRGNRVTVDGEIVRNAAFKLLPEHDVAYDGNPLAQ 88

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG 
Sbjct: 89  QHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAWKLHAAGRLDIDTTGLVLMTDDGQ 148

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +  +  P     + Y V     V  D      KG+ +           L+    +   V
Sbjct: 149 WSHRITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQV 206

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 207 RLTISEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 259


>gi|297584469|ref|YP_003700249.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297142926|gb|ADH99683.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 239

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 131/234 (55%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+IA+AGI SRR+ E++I + RV VNG  ++         TD I VDGVPL+K E 
Sbjct: 2   ERLQKLIAQAGITSRRKAEKLIEEGRVYVNGNQVKEVGAKADLQTDEISVDGVPLQKEE- 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP G++++  D  GR TV D +P  F RV  VGRLD +T GL++LTNDG  A 
Sbjct: 61  PVYYLLYKPSGVISSAGDDKGRKTVIDLVPGEF-RVFPVGRLDFDTSGLIVLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
           +L  P  +  + Y  +  G   ++ L  L +GIV++       +  V    ++   A V 
Sbjct: 120 LLMHPKYRIHKTYIAKVKGLPLREDLKKLDRGIVLEDGKTAPAKTKVIKTDKRKGTAVVE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++F+   + V +L R  YG   L  L AG  RE+    ++  
Sbjct: 180 ITIHEGRNRQVRRMFDAIGFPVMKLKRERYGILDLKGLNAGDWRELKPHEVKTL 233


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 79/236 (33%), Positives = 129/236 (54%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KV+A AG+ASRR+ E++IA+  VKVNG +++     V   D IEVD VP+++ 
Sbjct: 1   MAEERLQKVMAEAGVASRRKSEKLIAEGHVKVNGRVVKELGTKVEQHDRIEVDEVPIQR- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   +L +KP G++T+ SD   R TV D  P +  R+  VGRLD +T G +L+TNDG L
Sbjct: 60  EQNVYFLLNKPRGVITSVSDDKNRKTVMDFFPDVTERIYPVGRLDYDTSGAVLMTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P  ++ + Y  +  G V+   L  L++G+VI        +  L +   +   + 
Sbjct: 120 ANRLMHPKFKFEKTYTAKVKGLVNGSALKRLEEGVVIDHRKTAKAKAKLISTDLEKKTSI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + + EG+N ++KK+F      V +L R SY    +  + +G  R +    ++  
Sbjct: 180 VQLTIHEGRNHQVKKMFMAVGHPVQKLHRNSYSFLSIDDVQSGKWRALKLSEVKRL 235


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 116/233 (49%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K ++ AG+ SRRE + +I    V VNG ++      +   D I+ DG  +  
Sbjct: 101 NEDAVRLNKYLSNAGVCSRREADVLIQTGVVSVNGEVITEMGYKIKPGDKIQYDGETIN- 159

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           AE  R  L +KP G +TT  DP GR TV    + +   R+  VGRLD +T GLLL TNDG
Sbjct: 160 AETKRYVLLNKPKGFITTMDDPLGRKTVMGLVIKACKERIYPVGRLDRDTTGLLLFTNDG 219

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +A+ L  P  +  ++Y V     V  + L  L  GI ++       +        S+  
Sbjct: 220 DMAKKLTHPRYEATKIYHVEVDKPVQSEHLEQLMSGIELEDGTIKADKAEYVKDGKSSRE 279

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V V +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K +
Sbjct: 280 VGVEIHSGKNRIVRRMFEKLGYEVVKLDRVQFASLTKKDLPRGYYRHLTEKEV 332


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 112/236 (47%), Gaps = 1/236 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR  E  +   RV V+G +             I VDG PL   
Sbjct: 1   MTRQRLQKLIAAAGLCSRRRAEEWLQAGRVTVDGQVARVGDQADPQQQTIHVDGQPLPSP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP+G++ +  DP GR TV D LP      +  VGRLD ++ G LLLT+ G 
Sbjct: 61  GMARVLLMNKPVGVICSCDDPQGRRTVLDLLPPEHRAGLHPVGRLDADSHGALLLTDLGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   +  L+  ++G+ + G      +V      G  + +
Sbjct: 121 LTLKLTHPRYSHAKTYRVWVQGVPSEPVLDRWRRGVPLDGRLTRPARVRQLRTWGDRSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + LREG+NR+I+++ E   + V  L R +     LG L  G    + +   +  L
Sbjct: 181 EIELREGRNRQIRRMAEALGYPVVDLQRTAIAGLPLGDLAEGCWIWLCEGEWKPLL 236


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ +D +
Sbjct: 261 IEYKEENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRSDVV 320

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 321 LFQEKPVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTT 379

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V  + L  +  GI ++        +  
Sbjct: 380 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEY 439

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 440 ADPQ-DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEK 498

Query: 240 IL 241
            +
Sbjct: 499 EV 500


>gi|317051704|ref|YP_004112820.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946788|gb|ADU66264.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 251

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 82/227 (36%), Positives = 119/227 (52%), Gaps = 5/227 (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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             V + EG+NR+I+K+FE   + V +L R+S G   LG +  G  R 
Sbjct: 183 YEVTITEGRNRQIRKMFEALKYDVRKLKRVSLGEILLGGVGVGKYRR 229


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 109/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +D       G+ +           L+  +     V + +
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLAEDTAQQFADGVQLHNEQSLTKPAQLEVIEP--QVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVLELHRERIGEIKLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 75/244 (30%), Positives = 118/244 (48%), Gaps = 5/244 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I+   V VNG ++      V+ +D +
Sbjct: 242 IEYKETHIDPNEPIRLNKYLANAGVCSRREADEFISAGVVSVNGTVVTELGTKVLRSDEV 301

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 302 KFHDQLVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTT 360

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           G+LLLTNDG LA  L  P     +VY V     V ++ L  +  GI +  G  + D    
Sbjct: 361 GVLLLTNDGDLASKLTHPKFLKKKVYHVHLDKNVAEEDLQKIASGIELEDGEIHADAIEY 420

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            D +      V + +  GKNR ++++FE   ++V RL R+ +       L  G  R +++
Sbjct: 421 ADDRDKK--QVGIEIHSGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLRRGDWRFLTE 478

Query: 239 KILR 242
           + + 
Sbjct: 479 QEVE 482


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 120/232 (51%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
            L  P  +  + Y     G +  D++   + G+ I+       +  VT + ++ + +   
Sbjct: 121 KLTHPKHEIDKTYVASVKGIISDDEIRQFETGLKIEDYTTAPAKIRVTKENKEKNYSVCE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++K+ +  N  V  L RIS G   L     G  R +++  ++
Sbjct: 181 ITIHEGRNRQVRKMCKAINHPVLNLRRISVGKIVLKDTKVGEYRYLTEDEIK 232


>gi|206601589|gb|EDZ38072.1| Pseudouridine synthase, Rsu [Leptospirillum sp. Group II '5-way
           CG']
          Length = 583

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 99/343 (28%), Positives = 160/343 (46%), Gaps = 12/343 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPL 67
           +     R+ K++A  G+ASRR  E MI    VKVNGI++      V   TD + VDG  +
Sbjct: 13  DEDGLIRLQKLLAHRGLASRRNAEEMIRGGLVKVNGIVVTVPGTKVHPETDRVTVDGKNV 72

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L+L++KP G+V+T  DPDG++T+ D  P I   +  VGRLDI +EG+LLLTN+
Sbjct: 73  PVEPEPFLFLFYKPKGVVSTLHDPDGKTTLKDFFPRINPLIH-VGRLDIQSEGVLLLTNN 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G LA+ +  P  +  R Y V+  G V  + L+ L+ G + + G     +++  +    +N
Sbjct: 132 GDLAQRILHPRYEIPRTYLVKVQGVVTPEHLDRLRSGKVRLDGRPVQPLELEQERLTETN 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +W  + L EG+NRE++++F+  ++ V +L RI++G   L  L  G  R V+ + +     
Sbjct: 192 SWYRITLTEGRNREVRRLFDALHYFVLKLTRIAFGNLDLTGLEPGEYRLVTPEEI----- 246

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
             LL  A+      I   E   R      +  PD   R  ++       +    +     
Sbjct: 247 DLLLSGARWKRKEAIPPPERSPRKPNFAAASSPDFRRRSVRSRPTFPDRAFSGPVDGNQE 306

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREEN----HRRSPSFPSKR 345
             +                S  G R ++    H R P    K+
Sbjct: 307 EDHFPRQARQGYSSRPDTRSRGGTRSDSEMFFHDRPPHRSDKK 349


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     VM TD +
Sbjct: 266 IEYKEENYDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVMRTDEV 325

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                 +   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 326 YFQDKLVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTT 384

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     +  + L  +  GI ++        +  
Sbjct: 385 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKAITANDLQKISDGIELEDGEIKADAIEY 444

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 445 ADPQ-DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEK 503

Query: 240 IL 241
            +
Sbjct: 504 EV 505


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 114/240 (47%), Gaps = 6/240 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           N   +     R++K ++ AGI SRRE +R+I   +V V+G       + V ++  I V+G
Sbjct: 2   NDNAKTDNGIRLNKYLSEAGICSRREADRLIEDGKVTVDGRTA-SMGMKVFTSQEITVNG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   ER  L   +KP G+V T SD D    + + L     R+  VGRLD ++EGLLL+
Sbjct: 61  KRVEGKERPVLLAVNKPRGIVCTTSDKDRAENIVEFL-KYPVRIYPVGRLDKDSEGLLLM 119

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TN G L   +        + Y V     V +  +  ++ G+ I G      +  +  ++ 
Sbjct: 120 TNQGDLVNRILRGRYGHEKEYLVTVDRPVTEAFIRQMRNGVEILGTRTKPCEAEITGKRS 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                ++ L +G NR+I+++ E   ++V  L R+     +LG L  G  RE++     E 
Sbjct: 180 ----FSIILTQGLNRQIRRMCEALGYQVKTLKRVRIMNVKLGNLKTGQYRELTPAEWEEL 235


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 82/341 (24%), Positives = 147/341 (43%), Gaps = 20/341 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG         V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNGAQP-EVGSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T ++ D +  + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVQGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT +TQ        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L   + E++ 
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILA--MCEDSS 238

Query: 255 VNLDAPIYS----SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
              +A   +    S     D     S   +  ++ ++N    +G + Q+    P  ++  
Sbjct: 239 GTEEASRVAQSGDSIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKAQ 298

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                      SS  + S   +   R +P      SLR++ 
Sbjct: 299 RRP-------TSSSSNSSTASKPTPRPTPRTGGTLSLRKSK 332


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 119/229 (51%), 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   ERLQKYMASCGVASRRKCEEIILNGEVKVNGVVITELGTRVNPVEDKVEYKGSLITKEEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G +T+  D  GR TV D +  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KVYIILNKPEGYITSAKDEKGRKTVLDLV-KVNERIYPIGRLDYDSSGLILLTNDGDVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y     G+V +  +++  KGI I G       + + +     + V V 
Sbjct: 122 KIIHPREELNKKYIAVVKGKVSKKDIDIFNKGIDIGGYITAPASLEVLSYANEKSTVEVC 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGKNR+I+K+    N +V  L R+S G  QL  L  G  RE++ + L
Sbjct: 182 IHEGKNRQIRKMCTAINHEVLSLNRVSIGEIQLKYLKKGEWRELTTEEL 230


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 122/235 (51%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K +A AG+ASRR  E++IA   V+VNG  +      V + D IEVDGVPL + E+ 
Sbjct: 2   ERLQKAMAEAGVASRRASEKLIATGHVQVNGQTVTTLGTKVAARDRIEVDGVPLHR-EKH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G++++  D  GR TV D L    I  R+  VGRLD +T GLLLLTNDG LA
Sbjct: 61  VYYLLNKPRGVISSAHDEKGRRTVVDILREDEIEERIYPVGRLDYDTTGLLLLTNDGALA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWV 189
             L  P     + Y  +  G V  D L  L+ G+ + G      +  L    ++   + V
Sbjct: 121 NKLMHPKFAVDKTYVAKVKGLVSNDDLKRLRTGVKVDGRRTQPAKARLKATDREKRTSIV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EG   ++K++       V +L R SYG   L  +  G  RE+  + ++  
Sbjct: 181 QLTIHEGHYHQVKRMLAAVGHPVIKLHRESYGFLTLQGVQPGDYRELRPEEVKRL 235


>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 =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 84/238 (35%), Positives = 121/238 (50%), Gaps = 4/238 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K++A  GIASRR+ E +I   +V VNG +++R    V    D IEV G PL   
Sbjct: 3   AAIRLQKLLAEHGIASRRKAEALIVSGQVCVNGTVVDRLGTRVDPQIDLIEVFGQPLHCM 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTND 127
                 L HKP+G ++T  DP GR TV D LP+ +     +  VGRLD ++ G L+++ND
Sbjct: 63  PPLLYVLLHKPVGWLSTCFDPRGRRTVLDLLPAEWRTGQGLHPVGRLDCDSSGALIVSND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G     L  P  Q  + YRV   G+     L   + G+V++G       VT+ ++     
Sbjct: 123 GEFTFRLTHPRHQLPKTYRVWVRGRPTAAVLGRWRAGVVLEGQKTLPAAVTVVSRAAEAT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + V L EG+NR+I+KV E     V RL R + GP  L  L  G+ R +S   +   L
Sbjct: 183 ELEVVLVEGRNRQIRKVAELLGHPVERLHRTAIGPVALAGLPPGAHRLLSASQIERLL 240


>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 =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 140/303 (46%), Positives = 192/303 (63%), Gaps = 2/303 (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 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            A  + + P+++      + P           R       ++   ++     P   R++ 
Sbjct: 268 AAGADFEGPLFN-HNDEDEAPKAGKPRG-AKARYAAAEGAEDRHRRRPIDVEPGEGRSVT 325

Query: 312 SNV 314
           + V
Sbjct: 326 AGV 328


>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 =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 117/242 (48%), 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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + +KP G +TT SDP GR TV + +P   F  +  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|332637861|ref|ZP_08416724.1| ribosomal large subunit pseudouridine synthase B [Weissella cibaria
           KACC 11862]
          Length = 255

 Score =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 124/241 (51%), Gaps = 11/241 (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  VYFLLNKPRGVVTTTNDDKGRQTVMDIVDEP-ERVYPVGRLDYDTTGVLLLTNDGELANR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------GICYGDMQVTLDTQK 183
           L  PS +  +VY  +  G    ++L  L+ G+ ++                 ++T    K
Sbjct: 122 LMHPSYRIDKVYVAKVKGIPTNEQLEQLRHGVTVRTKQNGRYTTFKAAPARAEITSTNTK 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              A V + + EGK  ++K++ +    +V +L R  YG   L  L  G  R +  + ++ 
Sbjct: 182 NHTAIVKLTIHEGKYHQVKEMMKAVGHEVLKLTRERYGMLDLAGLTPGEYRPLRYEEVQA 241

Query: 244 Q 244
            
Sbjct: 242 L 242


>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 =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 109/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D      +G+ +           L+  +     V + L
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAQQFTEGVQLHNEKSLTKPAQLEVIEP--QLVRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGDIKLDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 79/237 (33%), Positives = 117/237 (49%), Gaps = 1/237 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
                R+ K +A+AG+ASRR  E +I Q RV+V+G ++      V      I VDG  + 
Sbjct: 3   EEDGIRLQKALAQAGVASRRNAELLIEQGRVEVDGAVVTEFGTRVDPAVSVIRVDGERIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                   + +KP G+VTT SDP GR  + D +     R+  +GRLD +TEGLLLLTN G
Sbjct: 63  PVTAHVYLVLNKPRGVVTTMSDPQGRPCIADYVQERPERLFHIGRLDTDTEGLLLLTNHG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  L  PS +  + Y     G V    L  L  G+ ++        V + ++      
Sbjct: 123 EFAHRLAHPSYEVSKTYVAEVDGNVKPIVLRRLLDGVELEDGFAQADTVKVMSEIKGRTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + + L EG+NR ++++F+     V RL R + GP + G L  G  RE+  K L + L
Sbjct: 183 IQITLHEGRNRIVRRMFDAVGHPVKRLTRTAIGPVRRGNLHTGELRELDPKELGQLL 239


>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 =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 107/237 (45%), Gaps = 3/237 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           LD  +     V + +
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLYNEKSLTKPAQLDVIEP--QRVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTTEEIASVGAPHL 235


>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 =  276 bits (706), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 129/233 (55%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K I+R+G+ SRR+ E +I + RVKVNG ++    V +    D +EVD   ++  E+
Sbjct: 3   ERLQKFISRSGVTSRRKAEELILEGRVKVNGKVIRTLGVKIDPEKDVVEVDNKIIK-PEK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G +++  DP GR T+ D L     SRV  VGRLD ++EGLLL TNDG +A
Sbjct: 62  KLYIALYKPVGYLSSLYDPFGRRTIKDLLKDKLSSRVYPVGRLDFDSEGLLLCTNDGEIA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWV 189
             +  P  +  ++Y V  +G   +++L   ++G++++         +V     K   + +
Sbjct: 122 NFVIHPRYKIPKIYEVLVNGIPKEEELKKFREGVILEEGKTLPAEFEVVWKNSKTKRSLL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V L +G  R+I+++   F ++V +L RI  G  +LG L  G  R ++ + ++
Sbjct: 182 KVVLYQGWKRQIRRMLALFGYEVLKLKRIQIGEIRLGNLKPGEFRFLNDEEIK 234


>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 =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 108/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  +     V + +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQLHNEKSLTKPAQLEVIEP--QLVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVLELHRERIGDIKLDDDLAPGEYRPLTPEEIASVGAPHL 235


>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 =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 107/242 (44%), Gaps = 3/242 (1%)

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 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+L+T+DG  +  +  P     + Y V     V  D      KG+ +           L+
Sbjct: 121 LVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVAADTAEQFAKGVQLHNEKDLTKPAVLE 180

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
               +   V + + EG+  ++K++F      V  L R   G   L   L  G  R ++++
Sbjct: 181 V--ITPTQVRLTISEGRYHQVKRMFAAVGNHVVELHRERIGAIVLDDDLEPGEYRPLTEE 238

Query: 240 IL 241
            +
Sbjct: 239 EI 240


>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 =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 118/245 (48%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K ++ +   P R++K ++ AG+ SRRE +  I    V+VN  ++      +   D +
Sbjct: 1   MKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQAGVVQVNDQVVTELGTKITRQDKV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                 ++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 61  LFKDQQVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 119

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 120 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVSIEDMEKIANGLELEDGEIHADAISY 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 180 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVVKLDRVYFAGLTKKNLGRGKWRYLNER 238

Query: 240 ILREQ 244
            +   
Sbjct: 239 EVNAL 243


>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 =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 82/351 (23%), Positives = 147/351 (41%), Gaps = 16/351 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG +       VM  D + VD  
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRREADRLIEQGRVTINGQVP-EMGTKVMPGDDVRVDDK 57

Query: 66  PLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           P+    ++      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ L
Sbjct: 58  PINAVTDKPVYIALNKPTGITCT-TERDIPGNIVDFV-GHKKRIFPIGRLDKPSDGLIFL 115

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y VR    +  D +  +  G+ I        +VT +T+  
Sbjct: 116 TNDGDIVNKILRAGNNHEKEYVVRVDKPISDDFIKKMSSGVNILDTITLPCKVTKETKFS 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E 
Sbjct: 176 ----FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLTDAEVAEI 231

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-KKLAT 303
           L    + E   N +          R R    +++ D     + +++++N   +  K    
Sbjct: 232 LA---MCEGSSNTEEASKIDAKGKRIRKATDAKLFDSREENQDSTARRNQKQRTFKGRNA 288

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              R    S      G  S F    G  +      P+  S+ S R +  K+
Sbjct: 289 DEFRHAPNSKKGRHSGKQSEFKGKPGGNKGKTFHKPA--SENSQRPSKPKR 337


>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 =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 77/303 (25%), Positives = 130/303 (42%), Gaps = 27/303 (8%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVD 63
           N+    FT  R+ + +AR G+ASRR  E++I+  RV VNG++ +     V  + D + VD
Sbjct: 71  NLPSSTFT-MRLQRYLARCGVASRRGAEKLISAGRVTVNGVVQDVLGSKVDCAHDVVCVD 129

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLL 122
           G P    +     + +KP G++TT SDP G   V   +P   +  + +VGRLD +T GLL
Sbjct: 130 GTPCVLGDEHTYLILNKPQGVLTTMSDPFGHPCVAALVPKDTYPGLFAVGRLDGDTTGLL 189

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L + DG +   L  PS    + Y     G + +     L+ GI++         +T    
Sbjct: 190 LFSTDGNMGNRLLHPSHHVWKTYVCLLQGSLTRAAQKQLEAGIMLDDGPCAPSHITRLAP 249

Query: 183 KGSNAWV-------------------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
             +   +                   ++ +REG+  ++K++F+     V RL R  +GP 
Sbjct: 250 TDALCTLAPQCHILDGIPSARGYTICSISIREGRYHQVKRMFDAVGCPVVRLHRAQFGPL 309

Query: 224 QLGT-LLAGSTREVSKKILREQL----GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
            LG  L  G+ R  +   +   +        +  AQ N+    ++S           +  
Sbjct: 310 SLGDALPFGAWRMCTPAEVDALMRTVSSSDGIANAQTNVQTKAHTSALRYTQHGATPNVH 369

Query: 279 PDD 281
            D 
Sbjct: 370 NDK 372


>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 =  275 bits (705), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 108/357 (30%), Positives = 170/357 (47%), Gaps = 18/357 (5%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG +       V   
Sbjct: 1   MSEQDLQDTAITPPSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNG-VAATLGQRVDLH 59

Query: 58  DHIEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 GDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 KFTDIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G  RE+S+    IL  ++G   +    +NL A     + + R +      +         
Sbjct: 240 GRWREMSQGEIDILAAEVGLQPVALPALNLKA----KDKMERLQRKSSRPLGRGERVRNL 295

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
             + +   + ++    P        N   A     S +     + E  + +     K
Sbjct: 296 RPAHEGAAAGERPARQPREEAPRKGNRGSAVAERPSEMRKRPAKPEGDKPAGRGRGK 352


>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 =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ TD +
Sbjct: 266 IEYKEENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRTDEV 325

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                 +   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 326 YFQDKLVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTT 384

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V  + L  +  GI ++        +  
Sbjct: 385 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKAVTANDLQKISDGIELEDGEIKADAIEY 444

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 445 ADPQ-DQTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEK 503

Query: 240 IL 241
            +
Sbjct: 504 EV 505


>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 =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 237 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 296

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 297 KFHDEPVS-IERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 355

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++ 
Sbjct: 356 GVLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISY 415

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 416 ASET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 474

Query: 240 IL 241
            +
Sbjct: 475 EV 476


>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 =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 82/239 (34%), Positives = 129/239 (53%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QRV K++++ G+ASRR  E MI   RV++NG ++        + D +EVDG  ++  +R 
Sbjct: 3   QRVQKILSQWGVASRRHAEDMIVAGRVRLNGEIVTLGDKADPNCDRLEVDGKLIQPNQRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +    L +KPIG+V T +DP  RS V D LP  FS+   +  VGRLD N+ G LLLTNDG
Sbjct: 63  QLLYILMNKPIGVVCTCNDPQNRSIVLDFLPKAFSQGTGIHPVGRLDFNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G   +++L   ++G+++ G      QV +  +   +  
Sbjct: 123 ELTLRLTHPRYHLPKTYEVWVQGYPTEERLQQWREGVMLMGKKTLPAQVEVIRRSRQHTC 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
           + V L EG+NR+I+++ +   + V RL R + GP  L      +L +G  R ++   +R
Sbjct: 183 LKVVLTEGRNRQIRRIVQHLGFHVLRLHRTAIGPLVLSSPNESSLPSGQHRLLTPSEIR 241


>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 =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 108/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  +     V + +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQLHNEKSLTKPAQLEVIEP--QLVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVLELHRERIGAIKLDDDLAPGEYRPLTPEEIASVGAPHL 235


>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 =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 81/232 (34%), Positives = 129/232 (55%), Gaps = 1/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+NR+++++F     +V RL R+ +    L  L  G++R +S + +RE 
Sbjct: 183 IHEGRNRQVRRMFAAVGCRVLRLRRVRFAMLTLKDLPCGASRPLSAEEIREL 234


>gi|332093194|gb|EGI98254.1| ribosomal small subunit pseudouridine synthase A [Shigella boydii
           5216-82]
          Length = 231

 Score =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  275 bits (705), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 79/235 (33%), Positives = 130/235 (55%), Gaps = 1/235 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRK 69
              +R+ K++A AGIASRR  E MI   RV V+G+ +         +   I VDG+P++K
Sbjct: 1   MMEERLQKILANAGIASRRSAEEMIRAGRVTVDGVCVTELGRKYDAALHEIAVDGIPVQK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  L +KP+G ++T  D  GR TV D LP   +R+  VGRLD +TEGLLL+TNDG 
Sbjct: 61  ETERVYLLLNKPVGYLSTARDDRGRKTVLDLLPHTSARLYPVGRLDADTEGLLLITNDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + + L  P  +  +VYR    G +  +KL  L+ GI+++       ++ + +   +   +
Sbjct: 121 MTQGLLHPRYEIDKVYRAEIEGALTPEKLRHLRGGILLEDGITAPARMRILSADDTVTTI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EG+NR+++++F     +V RL R+ +    L  L  G++R +S + +RE 
Sbjct: 181 EIVIHEGRNRQVRRMFAAVGCRVLRLRRVRFAMLTLKDLPCGASRPLSAEEIREL 235


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 58/238 (24%), Positives = 110/238 (46%), Gaps = 3/238 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  +     V + L
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAQQFTDGVQLHNEESLTKPARLEVIEP--QLVRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLL 250
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +     PHLL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVLELHRERIGEIKLDDDLAPGEYRPLTEEEIASVGAPHLL 236


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 111/237 (46%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +D      +G+ +           L+  K  +  V + +
Sbjct: 121 VTSPKHHCEKTYLVTLEHPLAEDTAQQFAEGVQLHNEKDLTRPAQLE--KIEDTLVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAIVMDEDLAPGEYRPLTEEEIASVGAPHL 235


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V      + V G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKQLLKQKAVTVDGASVKDAAMHVDPEQQNVSVYGERVIYTE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D     TV D L  +        VGRLD +TEGLL+LTNDG L
Sbjct: 60  FVYFMMNKPPGVISATEDLRD-ETVIDLLEPVDQHFQPFPVGRLDKDTEGLLVLTNDGIL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY     G V ++ +     G+ +  G      ++ +  +    + +
Sbjct: 119 AHNLLSPKKHVPKVYYAHIEGVVTEEDVEKFANGVELDDGYMTKPGKLVIL-KSAPQSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++ + L
Sbjct: 178 ELTIQEGKFHQVKRMFEAVGKRVTYLKRISMGNLKLDDQLELGEYRELTVEEL 230


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 78/344 (22%), Positives = 137/344 (39%), Gaps = 23/344 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRR+ +R I Q  V +NG         V++ D + V+G  +  
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVFINGKRA-SVGDQVVAGDTVRVNGQIIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A+     + +KP+G+V+T    +  + V  +  S   R+  +GRLD +++GL+ LTN+
Sbjct: 62  QDADDFVFIVLNKPVGIVSTTESSEKNNIV--DFVSHGVRIFPIGRLDKDSQGLIFLTNN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V  +  +  D +  L  G+ I G       VT    K S  
Sbjct: 120 GDLVNKVLRAGNNHEKEYLVTVNKPITDDFIAGLAGGVPILGTMTKKCPVT----KVSPT 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++ K L   L  
Sbjct: 176 VFNITLVQGLNRQIRRMCEYFGYEVVKLERTRIMNVSLKGIPVGEWRDLTPKELSVLL-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             +E++     AP   S    R             +   K  S+  G +K          
Sbjct: 234 KSIEDSSSEASAPAKKSRNAPRKNTRTDGSSKPKVSSKPKAPSKPMGAAKGNTKHPKDDA 293

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
           R              +      +R     + P+           
Sbjct: 294 R------------KPAGSKSKDRRPFGDSKKPAGNGAGKRPTGK 325


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 75/354 (21%), Positives = 144/354 (40%), Gaps = 19/354 (5%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKYISETGFCSRREADRLIEQGRVTINGQQP-EMGTKVLPGDDVCVDGS 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVAAKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        +V    +K +
Sbjct: 116 NDGDIVNKILRAGNNHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKV----EKET 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L
Sbjct: 172 KFSFRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLSDDEVAEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN-------GLSKQ 298
               + E  V  +    +       R    +++ D     + +++++N       G +  
Sbjct: 232 A---MCEGSVGTEEASKTDSRGRNIRKATDAKLYDSREENQGSTARRNQKTRTFLGNNAD 288

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
           +    P  ++         +G   +      + +    R      K   +  ++
Sbjct: 289 EFRHAPNSKKGQQRRQRDDEGGRPAKEHYKAKPQGERSRPQGEHGKSQRKPDAS 342


>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 =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 86/231 (37%), Positives = 123/231 (53%), Gaps = 1/231 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AGI SRR  E ++ + RV VN +          S D IEVDG PL  A
Sbjct: 1   MTRQRLQKLIAAAGICSRRHAEELMREGRVTVNQVTAGLGDQADPSIDRIEVDGRPLSHA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
            R RL L +KP G++++ SDP GR TV D +P    R +  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|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 =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 131/239 (54%), Gaps = 2/239 (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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + V +  GKNR ++++FE   + V +L+R+  GP ++G+   G+ R +SK  +   L 
Sbjct: 295 LIEVTIHSGKNRIVRRLFEAVGYPVEKLVRVQMGPIRIGSQKQGTVRNLSKVEIGHLLA 353


>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 =  275 bits (704), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 240 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 299

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 300 KFHDEPVS-IERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 358

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++ 
Sbjct: 359 GVLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISY 418

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 419 ASET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 477

Query: 240 IL 241
            +
Sbjct: 478 EV 479


>gi|288556014|ref|YP_003427949.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
 gi|288547174|gb|ADC51057.1| pseudouridylate synthase [Bacillus pseudofirmus OF4]
          Length = 242

 Score =  275 bits (704), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 128/234 (54%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KVIA+AGI SRR+ E MI + +VKVNG ++    V V    D IEV+GVP+ K E 
Sbjct: 2   ERLQKVIAQAGITSRRKAETMITEGKVKVNGQVVRELGVKVNPNKDEIEVEGVPIDKEEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +Y KP G++++  D  GR  V D L  I  RV  +GRLD +T GL+LLTNDG  A 
Sbjct: 62  VYYLMY-KPQGVISSVKDEKGRKVVTDFL-EIEQRVFPIGRLDYDTSGLILLTNDGEFAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            L  P  +  +VY  +  G   ++ L  L+ G+V++       +V L +  +K   A V 
Sbjct: 120 QLMHPKFKIDKVYVAKVKGIPARESLKKLQHGVVLEDGKTAPAKVKLVSMDKKKQTAIVQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+++++FE     V +L R  Y    L ++  G  R +    ++  
Sbjct: 180 LTIHEGRNRQVRRMFEAIGHPVMKLKREQYSFLNLRSMNPGDVRPLKPIEVKHL 233


>gi|294775216|ref|ZP_06740740.1| pseudouridylate synthase [Bacteroides vulgatus PC510]
 gi|294450921|gb|EFG19397.1| pseudouridylate synthase [Bacteroides vulgatus PC510]
          Length = 488

 Score =  275 bits (704), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 240 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 299

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 300 KFHDEPVS-IERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 358

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++ 
Sbjct: 359 GVLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISY 418

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 419 ASET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 477

Query: 240 IL 241
            +
Sbjct: 478 EV 479


>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 =  275 bits (703), Expect = 8e-72,   Method: Composition-based stats.
 Identities = 87/237 (36%), Positives = 131/237 (55%), Gaps = 3/237 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R++K ++ AG+ASRR+ E++I + RVKVNG ++    V V    D +EVDG P++ 
Sbjct: 1   MMEVRINKFLSEAGVASRRKAEKLILEGRVKVNGEVVRSLGVKVNPEVDIVEVDGKPVK- 59

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +R R  + +KP   +T     PDGR T+ + +  I  RV  VGRLD NTEGLL+LTNDG
Sbjct: 60  PQRKRYIILNKPCCYLTQLGRSPDGRKTIEELIKDIPERVFPVGRLDYNTEGLLILTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  +  P  +  +VY     G+VDQ  L  +K+GI ++        + +   +G N  
Sbjct: 120 ELANRILHPRYKLPKVYLALVEGKVDQKTLKRMKQGIELEDGFAKPDNIRIVRYEGKNTL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + +   EG+   +K+    F  KV RL RI+ GP +LG L  G  RE+++  L +  
Sbjct: 180 LEITFHEGRKHLVKRFLGAFGHKVKRLKRIAIGPIKLGKLSPGKWRELNQGELAQLF 236


>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 =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 123/277 (44%), Gaps = 33/277 (11%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M + +  +    P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D 
Sbjct: 1   MGEVSDCESRIVPMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDE 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINT 118
           + VDG  +R A+     + HKP G VTT SDP GR TV + +P   +  +  +GRLD +T
Sbjct: 61  VAVDGAVVRLADGPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDT 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL + DG L   L  P     + Y     G+  +  L LL++GI +         V 
Sbjct: 121 TGLLLFSTDGELGNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVR 180

Query: 179 L-------------------------------DTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +                               + +    + V +G+REG+ R++K++   
Sbjct: 181 VVEGGAARHAERLLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAA 240

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V  L R S+GP +LG L  G+ R +  + +   
Sbjct: 241 VGHPVLALHRDSFGPLELGDLPRGAWRALDAEEVAAL 277


>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 =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 239 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 298

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 299 KFHDEPVS-IERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 357

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++ 
Sbjct: 358 GVLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISY 417

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 418 ASET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 476

Query: 240 IL 241
            +
Sbjct: 477 EV 478


>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 =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 82/274 (29%), Positives = 137/274 (50%), Gaps = 4/274 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD  P+ 
Sbjct: 199 EAGEPIRLNKFLSNSGLCSRRMADQYIAAGRVKVNGAVISELGSQVLPTDQVMVDDKPVS 258

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E     L +KP   VTT +DP+GR TV D + +    R+  +GRLD NT G+LLLTND
Sbjct: 259 L-EAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTND 317

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P+ +  ++Y V    +V  + + ++  G  ++        ++  T + ++ 
Sbjct: 318 GDLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ-THD 376

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ-LG 246
            V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R   +G
Sbjct: 377 KVGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRMG 436

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               E+  V     +Y       D P    E+ D
Sbjct: 437 VKEQEDNGVAPTTKVYHKHQETPDHPFASEEIED 470


>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 =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 131/239 (54%), Gaps = 2/239 (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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + V +  GKNR ++++FE   + V +L+R+  GP ++G+   G+ R +SK  +   L 
Sbjct: 295 LIEVTIHSGKNRIVRRLFEAVGYPVEKLVRVQMGPIRIGSQKQGTVRNLSKVEIGHLLA 353


>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 =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 110/242 (45%), Gaps = 7/242 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +K+ +     P R++K I+  G  SRRE +++I Q RV +NG         VM  D + 
Sbjct: 7   DNKDQLDTQNKPVRLNKFISDTGYCSRREADKLIDQGRVTINGTQP-EMGTKVMPDDEVL 65

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VD  PLR  ER      +KP G+  T ++   +  + D +     R+  +GRLD  ++GL
Sbjct: 66  VDDKPLRAKERPIYIALNKPTGVTCT-TERHVKDNIVDFI-GHRKRIFPIGRLDKPSDGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           + LTNDG +   +        + Y VR   Q+  + L  +  G+ I         V    
Sbjct: 124 IFLTNDGDIVNKILRAGNSHEKEYVVRVDHQITPEFLEKMASGVEILDTVTLPCTVK--- 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            K ++    + L +G NR+I+++ E   + V +L R+      +  L  G  R ++   +
Sbjct: 181 -KETDYSFRITLTQGLNRQIRRMCEALGYDVYKLRRVRIMNITIDGLPNGKWRYLTDAEI 239

Query: 242 RE 243
            E
Sbjct: 240 SE 241


>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 =  275 bits (703), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 77/246 (31%), Positives = 129/246 (52%), Gaps = 1/246 (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 ILREQL 245
            L E L
Sbjct: 241 ELGELL 246


>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 =  275 bits (703), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 109/230 (47%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R    ++I Q  V V+GI++++ A ++     +E DGV L   +R 
Sbjct: 1   MRLDKFLCDCSDLTRSLAGKLIRQGEVMVDGIVVKQPAFHINEQSQVEFDGVTLTLDQRN 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V ++ DPD   TVF  +      ++  VGRLD++T GL+L+T+DG  + 
Sbjct: 61  RYFMLHKPEGYVCSNEDPDH-PTVFFLMDEPAMGKLHVVGRLDLDTTGLVLVTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V     V  D + L  +G++++          L+          + 
Sbjct: 120 RITSPRHECAKTYHVWLADPVSPDAIALFAEGVLLRSETEKTRPAQLEI--LGECEARLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L   L  G  RE++   +
Sbjct: 178 IHEGKYHQVKRMFAAIGNKVVGLHRERVGGLTLDEELAPGEYRELTADEI 227


>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 =  275 bits (703), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/342 (24%), Positives = 141/342 (41%), Gaps = 22/342 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I Q RV +NG +       V   D + +DG PLR  ER  
Sbjct: 8   RLNKFISETGFCSRREADKLIEQGRVTLNG-VQPEVGSKVTEQDEVCIDGKPLRSKERPI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + +  +  G+ I        +VT +TQ        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITPEFIRQMASGVNILDTVTLPCKVTQETQYS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG-----PHL 249
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L         
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVNEILAMCEDSSGT 240

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
            E ++V          T  +   N  +       R  K    KN    +  L +   +R+
Sbjct: 241 EEASRVAQSGDSIKRATDAKLFDNREANKESKARRNPKTYHGKNAQEFRHALNSKKAQRH 300

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                       SS  + S   +   R +P      SLR++ 
Sbjct: 301 ----------PKSSPSNSSTASKPASRPTPRTGGTLSLRKSK 332


>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 =  275 bits (703), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGIMLDADLAPGEYRPLTEEEI 227


>gi|197122579|ref|YP_002134530.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172428|gb|ACG73401.1| pseudouridine synthase [Anaeromyxobacter sp. K]
          Length = 329

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/321 (27%), Positives = 136/321 (42%), Gaps = 4/321 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ K +A AGIASRR+ E +I+  RV+VN   +      V    D + VDG  + +
Sbjct: 1   MAEERLQKFLAGAGIASRRKAEALISAGRVRVNQRTVTELGTKVDPGRDLVTVDGALVSQ 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G VTT SDP GR T  + L  +  R   VGRLD + EG LLLT+DG 
Sbjct: 61  PEQRSYYLLYKPSGCVTTASDPQGRPTAMEYLRGVPGRPFPVGRLDYDAEGALLLTDDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     RVY V+  G    + L  +K G+ ++      ++V +      N W+
Sbjct: 121 LANRLAHPRYGHQRVYLVKVKGDPPAEALERMKAGVRLEDGPARALEVAVHEHADRNVWI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG+   +K++ E    +V RL R  +G   +G L  G  R +  + +R       
Sbjct: 181 RVVVGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGKFRRLEPEEVRALRQRVG 240

Query: 250 LEEAQVNLDAPIYSSETLVRDRP-NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           LE         +       R       +         +  + +    ++      P    
Sbjct: 241 LESGTPARGPSVRELPKAARRHGHGPPAAPGAVPPPAEPGADEVEPRARGASRGGPRPAG 300

Query: 309 NLASNVWMAKGIHSSFLSDSG 329
             A+      G  +S  S   
Sbjct: 301 PRATAPG--PGGRASRPSRPS 319


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 71/339 (20%), Positives = 136/339 (40%), Gaps = 14/339 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R++K I+  G  SRRE +R+I Q RV +NG +       V S D + VD  P+  A
Sbjct: 4   DTGKRLNKFISETGFCSRREADRLIEQGRVTINGKIP-EMGTKVQSGDDVRVDDKPIAAA 62

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG 
Sbjct: 63  SDKPIYIALNKPTGITCT-TERDIPGNIVDFV-GHKKRIFPIGRLDKPSDGLIFLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    +  D +  +  G+ I        +V    +K +    
Sbjct: 121 IVNKILRAGNNHEKEYVVRVDKPISDDFIKKMSSGVNILDTVTLPCKV----EKETKYSF 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L    
Sbjct: 177 RIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLTDAEVAEILA-MC 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNII-----SEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
            + +     + + +    +R   +        E  +   R  +      G +  +    P
Sbjct: 236 EDSSGTEEASKMDAKGKRIRRATDAKLFDSREENQESKARRNQKQRTFKGRNADEFRHAP 295

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             ++   S+         +      +   +    P+ P 
Sbjct: 296 NSKKGRNSDKQSEPKGKPAKGKTFYKPASDKAPRPAKPK 334


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 76/358 (21%), Positives = 151/358 (42%), Gaps = 20/358 (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 ++ D    + D +     R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSREKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTN 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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT--- 303
             + E +    DA    +    R R    +++ D     + +++++N    + +      
Sbjct: 234 --MCEGSVSTEDA-SKMNAKGQRIRKATDAKLFDSREENQTSTARRNQNENRARTYRGNN 290

Query: 304 -------PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  P  +R   S+   + G  ++    S  R E      +   +    R + ++
Sbjct: 291 ADEFRHAPNSKRGRNSSNGESSGGGNTENWKSNSRSERSNSDKNRSDRNRTDRDNNER 348


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 76/358 (21%), Positives = 151/358 (42%), Gaps = 20/358 (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 ++ D    + D +     R+  +GRLD  ++GL+ LTN
Sbjct: 60  VRSREKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTN 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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT--- 303
             + E +    DA    +    R R    +++ D     + +++++N    + +      
Sbjct: 234 --MCEGSVSTEDA-SKMNAKGQRIRKATDAKLFDSREENQTSTARRNQNENRTRTYRGNN 290

Query: 304 -------PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                  P  +R   S+   + G  ++    S  R E      +   +    R + ++
Sbjct: 291 ADEFRHAPNSKRGRNSSNGESGGGGNTENWKSNSRSERSNSDKNRSDRNRTDRDNNER 348


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 118/242 (48%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD +
Sbjct: 5   IEYKEENIDPTEPLRLNKFLANAGVCSRREADEFIQAGLVTVNGEVVTELGTKILRTDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  KFHDAPVTL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     +    ++ +++GI ++        V  
Sbjct: 124 GVLLLTNDGDLASKLTHPKFLKKKVYHVHLDKNLTAHDMDQIREGITLEDGEIKADAVEY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +   A V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +++K
Sbjct: 184 ADDR-DKAQVGIEIHSGKNRIVRRIFESLGYRVTKLDRVQFAGLTKKNLRRGDWRFLTEK 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+I+ +   P R++K +A AGI SRRE +  I    V VNG ++      +  TD +
Sbjct: 237 IEYKDILTDPNEPIRLNKFLANAGICSRREADEFITAGVVSVNGEVVTELGTKIKRTDEV 296

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 297 KFHDEPVS-IERKTYILLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 355

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  G+ +         ++ 
Sbjct: 356 GVLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIAAGVTLDDGEIHADAISY 415

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 416 ASET-DKSQVGIEIHSGKNRIVRRIFESLGYKVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 474

Query: 240 IL 241
            +
Sbjct: 475 EV 476


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 113/231 (48%), Gaps = 2/231 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A+ G+ASRR+ E +I    V VNG +++   + +    D + V G  +R    
Sbjct: 8   IRLHKYMAQCGVASRRKSEELIKSGAVSVNGHVVKDMGILIDPQKDEVRVYGRIIRLKSD 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G V+T  D  GR TV D +P +   R+  VGRLD +T GL+LLTNDG L 
Sbjct: 68  MIYIAVNKPRGYVSTVKDQFGRPTVLDLVPVADEYRLYPVGRLDYDTTGLILLTNDGDLT 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  ++Y     G  D   +   + G+V++G         L       + V +
Sbjct: 128 YRLTHPKHEIEKIYVAGLRGIPDNQDIFRFEHGLVLEGRLTAPAGFELIKADQRLSVVKI 187

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            LREG+NR+I+K+ +     V  L R + G  +L  L  G  R ++ K + 
Sbjct: 188 TLREGRNRQIRKMCDMIGHPVIWLRREAIGEVELCGLQPGQWRYLTPKEIE 238


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 78/351 (22%), Positives = 147/351 (41%), Gaps = 22/351 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + +R++K I+  G  SRRE +R+I Q RV +NG +       V+  D + VD  P+  A
Sbjct: 4   DSAKRLNKFISETGFCSRREADRLIEQGRVTINGRVP-EMGTKVLPGDDVRVDDKPISAA 62

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG 
Sbjct: 63  TDKPVYIALNKPTGITCT-TERDIPGNIVDFV-GHKKRIFPIGRLDKPSDGLIFLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    V  D +N +  G+ I         VT +T+       
Sbjct: 121 IVNKILRAGNNHEKEYVVRVDKPVSDDFINKMSSGVNILDTVTLPCTVTRETKFS----F 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L   +
Sbjct: 177 RIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLTDAEVAEILA--M 234

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN-------GLSKQKKLA 302
            E++    +A         R R    +++ D     + +++++N       G +  +   
Sbjct: 235 CEDSSGTEEA-SKVDGKGKRIRKATDAKLYDSREENQNSTARRNQKQRTFKGRNADEFRH 293

Query: 303 TPVHRRNLAS--NVWMAKGI--HSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            P  ++   +      AKG              + +    P      SL++
Sbjct: 294 APNSKKGRNNGGKHGEAKGKPNKGKTFFKPNSEQSSRPSKPKSGGTLSLKK 344


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 123/248 (49%), Gaps = 12/248 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++      V+  D + +DG  +R   + 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHPVLENDAVALDGEVVRF-HKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP G VT+  DP    T+ + LP     +  VGRLD + EGLL++TNDG  A  
Sbjct: 60  VYILFYKPSGYVTSTKDP-HSETIMEFLPP-LKGIFPVGRLDKDAEGLLIITNDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAK---RVEKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  +IK++      K   L R   G   L   +  G  R +S++ ++      + E 
Sbjct: 175 TEGKYHQIKRMTAAVGLKTVHLKRTRIGGLVLPDDMKPGEYRFLSEEEVK-----KVFER 229

Query: 253 AQVNLDAP 260
                D P
Sbjct: 230 EDQKEDTP 237


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 133/303 (43%), Gaps = 9/303 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+  G  SRRE +++I Q RV +NG L       V   D + +DG PLR  E
Sbjct: 5   TEKRLNKFISETGYCSRREADKLIEQGRVTLNG-LQPEVGSKVTDQDEVCIDGKPLRSKE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 64  RPIYIALNKPTGITCT-TERDVPGNIVDFI-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    +  + +  +  G+ I        +VT +TQ        +
Sbjct: 122 NKILRAGNNHEKEYVVRVDKPITPEFIRQMSSGVNILDTVTLPCKVTQETQYS----FRI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      L  +  G  R +S+  + E L      
Sbjct: 178 VLTQGLNRQIRRMCEALGYEVFKLRRVRIMNITLDGIPNGKWRYLSEAEVSEILAMCEDS 237

Query: 252 EAQVNLDAPIYSSETLVR--DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                      S +T+ R  D     S   +  ++ ++N    +G + Q+    P  ++ 
Sbjct: 238 SGTEEASRVAQSGDTIKRATDAKLFDSREANKESKARRNPKTYHGKNAQEFRHAPNSKKA 297

Query: 310 LAS 312
              
Sbjct: 298 QRR 300


>gi|320667979|gb|EFX34882.1| 16S rRNA pseudouridylate synthase A [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 231

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D  +   KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTADQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 71/349 (20%), Positives = 142/349 (40%), Gaps = 14/349 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRR  +++I + RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRRAADKLIEEGRVTINGKQP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVASKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y VR    +  + L  +  G+ I        +VT +T+   
Sbjct: 116 NDGDIVNKILRAGNNHEKEYVVRVDKPITDEFLKQMSSGVRILDTVTLPCKVTKETKFS- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L
Sbjct: 175 ---FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVAEIL 231

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + +  V  +    +       R    +++ D     + +++++N  ++  +     
Sbjct: 232 A---MCDGSVGTEEASKTDSRGRNIRKATDAKLFDSREENQGSTARRNQKTRTFRGNNAD 288

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             R+ A N    +        D   R            + +  +    +
Sbjct: 289 EFRH-APNSKKGQQKRRQR-DDESSRPAKEHYKAKTQGEHAKPQGEHGR 335


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 79/232 (34%), Positives = 124/232 (53%), Gaps = 1/232 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++F     +V RL R+ +    L  +  GS R ++   + E 
Sbjct: 183 IHEGRKRQVRRMFAAIGCRVQRLCRVRFAMLTLDGVSCGSFRHLTSDEIHEL 234


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 81/258 (31%), Positives = 122/258 (47%), Gaps = 13/258 (5%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E   P R+ + +ARAG+ASRR  E +++  RV VNG +       V    D + VDGVP
Sbjct: 22  DERVVPMRLQRFLARAGVASRRGSEALMSAGRVSVNGEVKTELGTKVDPAIDQVAVDGVP 81

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
           +         + +KP G++TT SDP GR  V D +P   +  +  VGRLD++T GLLL T
Sbjct: 82  VVLGVGAAYLMLNKPAGVLTTMSDPHGRPCVADIMPVRSYPGLFPVGRLDMDTTGLLLFT 141

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
            DG L   L  PS    + Y     G   +  L  L++GIV+        +  L  +   
Sbjct: 142 TDGDLGHALLHPSRHVWKTYVAVVDGVCREGDLEPLRRGIVLDDGPCQPARCALRDERDV 201

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                   +     V + +REG+  ++K++       V RL R+ +GP +L  L  GS R
Sbjct: 202 RDIAPRGLRAGTTAVRIEIREGRKNQVKRMLSKIGHPVLRLHRLRFGPLELNDLPCGSWR 261

Query: 235 EVSKKILREQLGPHLLEE 252
           E++   +        +EE
Sbjct: 262 ELTPTEVAALQSTPAVEE 279


>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 =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRYHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 109/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  +     V + L
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAQQFADGVQLHNEKSLTKPAQLEVIEP--QLVRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVLELHRERIGAIKLDDDLAPGEYRRLTAEEIASVGAPHL 235


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 119/235 (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+ D +  +  R+  +GRLD ++ GL+LLTNDG +  
Sbjct: 63  KLYIMLNKPEGYITSVKDEKGRKTILDLV-KVNERIYPIGRLDYDSSGLILLTNDGDIYN 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|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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEV 227


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 108/237 (45%), Gaps = 3/237 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 12  MRLDKFLSQQLGVSRALVARELRAKRVTIDGEIVKSGAIKLTPEQDVRFDGNPLQQTVGP 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 72  RYFMLNKPQGYVCSTEDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D       G+ +           L+  +     V + +
Sbjct: 132 ITSPRHHCEKTYLVTLEHPVADDTAQQFTDGVQLHNEKSLTKPAQLEVIEP--QLVRLTI 189

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 190 SEGRYHQVKRMFGAVGNRVLELHRERIGDIKLDDDLAPGEYRPLTAEEIASVGAPHL 246


>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 =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 88/292 (30%), Positives = 136/292 (46%), Gaps = 16/292 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
             R+ + +ARAG+ASRR  E ++   RV VNG++       V    DHIEVDGVP++  +
Sbjct: 29  TMRLQRFLARAGVASRRGSEDLMTAGRVTVNGLVATELGTKVDVDRDHIEVDGVPVKLNQ 88

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + +KP G +TT SDP  R  V D +P + F  +  VGRLD +T GLLL T DG L
Sbjct: 89  GAVYLMLYKPTGYLTTMSDPQERPCVADLVPRNRFPGLFPVGRLDRDTTGLLLFTTDGDL 148

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----------QVTL 179
           ++ L  PS    + Y+    GQ+    L+ L++GI +                    V  
Sbjct: 149 SQDLLHPSKHVHKTYQALVDGQLTDRDLDQLRRGIELDDGLCQPAICRVINAREAVAVAP 208

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              K     V V +REG+  ++K++    +  V RL R ++   +L  +  GS RE++ +
Sbjct: 209 QGVKPGTTAVEVIIREGRKNQVKRMLGKIHHPVIRLHRCNFAGLELEGVAKGSWRELTDR 268

Query: 240 I---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
               L+    P     A+ N D P  +  +  R   +  S    +  R +  
Sbjct: 269 EVQILKSGGIPPKQASAKRNGDKPQDTPASRTRHHGSHGSAPKRNTYRERYT 320


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  274 bits (701), Expect = 2e-71,   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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 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|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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 120/240 (50%), Gaps = 8/240 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAER 72
            R+ K++A  G  SR+EV++++ Q+ V V+G  ++ AA++V     I  V G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKQLLKQKAVTVDGAYVKDAALHVDPEQQIVSVFGERVVYTE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D     TV D L  +        VGRLD +TEGLLLLTNDG L
Sbjct: 60  FVYFIMNKPPGVISATEDLRD-ETVIDLLEPLHQHFQPFPVGRLDKDTEGLLLLTNDGHL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY  +  G V ++       GI +  G      ++ +  +    + +
Sbjct: 119 AHNLLSPKKHVPKVYYAQIEGVVTEEDAEKFANGIELDDGYVTKPGKLVIL-KSAQQSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++K++FE    +V  L RIS G  +L   L  G  RE++ + L +    H
Sbjct: 178 ELTIQEGKFHQVKRMFEAVGKRVTYLKRISMGSLKLDENLALGEYRELTAEELNDLQNNH 237


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/241 (34%), Positives = 127/241 (52%), Gaps = 11/241 (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  VYFLLDKPRGVVTTNSDDKGRQTVMDIVDEP-ERVYPVGRLDYDTTGALLLTNDGDLANK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------YGDMQVTLDT--QK 183
           L  P  +  +VY  +  G    ++L  L+ G+ ++ +                + +  +K
Sbjct: 122 LMHPKYRIDKVYVAKVKGIPTNEELEKLRHGVTVKTVQNGRHYTFNAAPAHAEILSTDKK 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              A V + + EGK  ++K++ +    +V +L R  YG   L  L  G  R +  + ++ 
Sbjct: 182 KHTAIVKLTIHEGKYHQVKEMLKSVGHEVIKLTRERYGMLDLTGLTPGEYRPLRHEEVQA 241

Query: 244 Q 244
            
Sbjct: 242 L 242


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 117/242 (48%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AGI SRRE +  I    V VNG ++      V+ +D +
Sbjct: 5   IEYKEDHIDPNEPLRLNKFLANAGICSRREADEFIQAGVVTVNGEVVTELGTKVLRSDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  KFRDQPVTL-EKKVYVLLNKPKNYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG +A  L  P     +VY V     +  + L  + +GI ++        V  
Sbjct: 124 GVLLLTNDGDMASKLTHPKFLKKKVYHVFLDKNIGVEDLQKIAEGIELEDGEIHADAVEY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +    + V + +  G+NR ++++FE   ++V RL R+ +       L  G  R ++++
Sbjct: 184 ANEN-DKSQVGIEIHSGRNRIVRRIFEALGYRVVRLDRVLFAGLTKKNLRRGDWRFLTEQ 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 106/229 (46%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D  +  + G+ + G        TL+  + S   V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPLAPDTADNFQAGVQLHGEKNLTRPATLE--QISEHQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++ + +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVALHRERIGAITLDDALEPGEYRPLTPEEV 227


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 129/233 (55%), Gaps = 3/233 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P  +  +VY  R  G V ++ L  L +G+VI G      +  +   +     + V +
Sbjct: 120 MIHPRNEIDKVYLARVKGVVTKESLRPLTRGVVIDGKKTKPARYRIIRVEPDKNRSIVEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG++ ++KK+FE     V++L R  +G   +  L  G  R +SKK + + 
Sbjct: 180 TIHEGRHHQVKKMFEVVGHLVDKLSRTQFGSLDVRGLKPGEARRLSKKEVSQL 232


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 84/241 (34%), Positives = 128/241 (53%), Gaps = 4/241 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E MI + RV+V+G++     + V  T   I VDG+ ++
Sbjct: 160 DVDGVRLQKVMAQAGVASRRVCEEMILEGRVEVDGVVTTELGMRVDPTSAVIHVDGIRIQ 219

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLT 125
             E     +++KP G+V+T  DP+GR  + D L +      R+  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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +  + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + ++ +   L
Sbjct: 340 HVLIEVVLHSGKNRIVRRMFDAVGFPVERLVRVKVGPIGLGDQRQGSIRNLGRQEVGHLL 399

Query: 246 G 246
            
Sbjct: 400 A 400


>gi|318606383|emb|CBY27881.1| ribosomal small subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
          Length = 235

 Score =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 108/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +           L+  +     V + +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPIADDTAQQFTDGVQLHNEKSLTKPAQLEVIEP--QLVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAAGNRVLELHRERIGDIKLDDDLAPGEYRPLTPEEIASVGAPHL 235


>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 =  274 bits (701), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 119/231 (51%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  GI SRRE +++I  +RV +NG L E  +  V S D + +DG PL   ++ 
Sbjct: 1   MRINKFISETGICSRREADKLIESKRVTINGQLAELGST-VASGDDVRIDGQPLGVKKKD 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T ++   +  + D + +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-TELHVKGNIIDFV-NHPERIFPIGRLDKDSQGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +  + L+ +  G+ I G      +VT    K S+    + L
Sbjct: 118 ILRAENNHDKEYIVTVDKPITANFLHGMANGVRILGTTTKPCKVT----KVSDRVFNIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G NR+I+++ + F ++V +L RI      LG L  G  R ++ K L + 
Sbjct: 174 TQGLNRQIRRMCQAFGYQVRKLERIRIMNIALGNLKLGQWRNLTAKELTDL 224


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 133/270 (49%), Gaps = 7/270 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLR 68
              QR+ KV+A  GI SRRE ER+IA  +VKVNG  +          D + +DG    + 
Sbjct: 1   MAEQRIQKVLADQGICSRREAERLIAAGKVKVNGRPVGLGDKMDPDYDKVSIDGKNVRIV 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  +    + HKP G +TT SD  GR TV D +  + + +  VGRLD ++EGLLL+T+DG
Sbjct: 61  RKRQYTYIMLHKPRGYLTTRSDDRGRKTVMDLVADVPAMLRPVGRLDKDSEGLLLMTDDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
               +L  PS    ++YRV  + +  ++++  +  G+V+  G+      + + T +    
Sbjct: 121 AFINLLTHPSGGVGKLYRVTVNPRATEEQVVQMASGVVLDDGVRTQPCVIHVVTDEPGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L EG+NR+I+++      +V RL R + GP +LG L  G  RE+ K  +      
Sbjct: 181 VLEITLHEGRNRQIRRMCSAVGLQVVRLKRSAEGPVKLGMLQPGEYRELKKSEVSALRN- 239

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
                 +    AP+       R  P    +
Sbjct: 240 ---AAQKNTRSAPVREENAPRRPGPLPRKK 266


>gi|310658781|ref|YP_003936502.1| rlub [Clostridium sticklandii DSM 519]
 gi|308825559|emb|CBH21597.1| RluB [Clostridium sticklandii]
          Length = 235

 Score =  273 bits (700), Expect = 2e-71,   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  YYYMLNKPIGYVSTAKDQFGRPSVVDFFDKK-QRIYPVGRLDYDSRGLLLMTNDGDLTYA 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     ++Y V     +   ++   K GI I G      ++T       N    V +
Sbjct: 120 LTHPKYHIEKIYEVIVSSTLSNSEIEKFKSGIDIGGYVTAKSRITFIG----NTSYEVII 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +EGKNR+I+K+F      V  L R+S G  +L  L  G+ R++  + + 
Sbjct: 176 KEGKNRQIRKMFSALGKDVLDLKRVSIGKLKLMDLKEGTYRKLINEEVE 224


>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 =  273 bits (700), Expect = 2e-71,   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+ D +  +  R+  +GRLD NT GLLL+TNDG +  
Sbjct: 63  KVYIALNKPEGYVSTVKDERNRKTIMDLV-EVEERIFPIGRLDYNTSGLLLMTNDGDIYN 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|328473478|gb|EGF44326.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 371

 Score =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 68/332 (20%), Positives = 141/332 (42%), Gaps = 10/332 (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 ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT +T+        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITDEFLKQMSSGVRILDTVTLPCKVTKETKFS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L    + +  
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVAEILA---MCDGS 237

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
           V  +    +       R    +++ D     + +++++N  ++  +       R+  ++ 
Sbjct: 238 VGTEEASKTDSRGRNIRKATDAKLFDSREENQGSTARRNQKTRTFRGNNADEFRHAPNSK 297

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
              +        +S   +E+++  P     + 
Sbjct: 298 KGQQKRRQRDDENSRPAKEHYKAKPQGERAKP 329


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 132/294 (44%), Gaps = 10/294 (3%)

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 ++ D    + D +     R+  +GRLD  ++GL+LLTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-GHKKRIFPIGRLDKPSDGLILLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    + +  ++ +  G+ I        +V  +T+        + L 
Sbjct: 125 LRAGNNHEKEYVVRVDKPITKKFVDQMSSGVEILDTKTLPCKVIQETKFS----FRITLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E L    + E+ 
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLSDHEVTEILS---MCESS 237

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            N +          + +    +++ D     K +++++N   +  K       R
Sbjct: 238 SNTEEASQRDAKGTQIKSATDAKLFDSREENKASTARRNQKQRTFKGRNADEFR 291


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 109/360 (30%), Positives = 170/360 (47%), Gaps = 30/360 (8%)

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  DHIEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 GDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 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+   +                P +  +  D   R+++ S+
Sbjct: 240 GRWREMSQGEIDILAAEVGLQPVAL----------------PEMKLKAKDKLERLQRKST 283

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +  G  ++ +   P            A+         SG+      R      + +    
Sbjct: 284 RPLGRGERVRTLRPAQEGQGERP---ARPAREEAPRKSGRGSTVAERPSEMRKRPARPEG 340


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 78/344 (22%), Positives = 132/344 (38%), 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 ++ D    + D +     R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 67  YIALNKPTGITCT-TERDVPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLTNDGDIVNKI 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        +VT +T+        + L 
Sbjct: 125 LRAGNSHEKEYVVRVDKPITGEFLKQMSSGVKILDTVTLPCKVTKETKFS----FRIVLT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL----GPHLL 250
           +G NR+I+++ E   ++V +L R+      L  +  G  R ++   + E L    G    
Sbjct: 181 QGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGKWRYLTDDEVAEILAMCDGSVGT 240

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

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


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAMLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLVSPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 89/243 (36%), Positives = 126/243 (51%), Gaps = 10/243 (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  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFS-----RVISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV     D L          R++ 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 REQ 244
              
Sbjct: 316 AAL 318


>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 =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 106/229 (46%), 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 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKYLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 107/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D       G+ +           L+  +     V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEHPVADDTAEQFAVGVQLHNEPTLTKPAQLEVIEP--QQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +     PHL
Sbjct: 179 SEGRYHQVKRMFGAVGNRVVALHRERIGAIVMDDDLAPGEYRPLTEEEIASVGAPHL 235


>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 =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 75/235 (31%), Positives = 122/235 (51%), Gaps = 4/235 (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  KVYIMLNKPEDVITSVKDEKDRKTVIDIV-KVNERIFPIGRLDYDSSGLILLTNDGELYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVT 190
            +  P  +  + Y     G+V  D     + GI I G      ++ +   + +   + + 
Sbjct: 122 KIIHPRVELDKKYVAVVKGEVSLDDKEKFESGIDIGGYITAPAKLKMLEYSHRKDLSTIE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V + EGKNR+I+K+    N +V  L R+S G  +LG L  G  R ++ + ++  +
Sbjct: 182 VCIHEGKNRQIRKMCSAINHEVISLKRVSIGNIRLGQLKKGEYRYLNDEEMKYLM 236


>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 =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 81/274 (29%), Positives = 136/274 (49%), Gaps = 4/274 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R++K ++ +G+ SRR  ++ IA  RVKVNG ++      V+ TD + VD   + 
Sbjct: 199 EAGEPIRLNKFLSNSGLCSRRMADQYIAAGRVKVNGAVISELGSQVLPTDQVMVDDKLVS 258

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E     L +KP   VTT +DP+GR TV D + +    R+  +GRLD NT G+LLLTND
Sbjct: 259 L-EAKVYVLLNKPKNCVTTLTDPEGRRTVMDLVHNACTERIYPIGRLDRNTTGILLLTND 317

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P+ +  ++Y V    +V  + + ++  G  ++        ++  T + ++ 
Sbjct: 318 GDLAVRLMHPAFRKKKIYEVALDKEVTVEHMQMIAHGFELEDGEIHADAISYITGQ-THD 376

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ-LG 246
            V + +  G+NR ++++FE   ++V  L R+ Y       L  G  R ++ + +R   +G
Sbjct: 377 KVGIEIHSGRNRIVRRIFEHLGYRVVHLDRVYYAGLTKKDLPRGRWRYLTPEEVRYLRMG 436

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               E+  V     +Y       D P    E+ D
Sbjct: 437 VKEQEDNGVAPTTKVYHKHQETPDHPFASEEIED 470


>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 =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 103/229 (44%), 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+ +          TL+        V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVTDDTAAQFAKGVQLHNEKELTKPATLEVVTP--VQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGAITLDEDLAPGEYRPLTEEEI 227


>gi|325497996|gb|EGC95855.1| 16S rRNA pseudouridylate synthase A [Escherichia fergusonii ECD227]
          Length = 231

 Score =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 101/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEV 227


>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 =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPDLAPGEYRPLTEEEI 227


>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 =  273 bits (699), Expect = 3e-71,   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  RYFMLNKPQGYVCATDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +    Y     TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKYLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 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 =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 111/370 (30%), Positives = 175/370 (47%), Gaps = 35/370 (9%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++++ +   TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+        V   
Sbjct: 1   MSEQDLKETEITPPSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEAT-LGQRVDLH 59

Query: 58  DHIEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 GDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 KFTDIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+++  +        L+   +                P +  +  D   R+++ S+
Sbjct: 240 GRWREMTQGEIDILAAEVGLQPVAL----------------PAMKLKAKDKMERLQRKST 283

Query: 291 QKNGLSKQKKLATPVH------RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP-S 343
           +  G  ++ +   P H       R        A     +  S   +R    R+ P  P  
Sbjct: 284 RPLGRGERVRNLRPAHEGAATGERPARQPREEAP-RKPTRGSTVAERPSEMRKRPGKPDG 342

Query: 344 KRSLRRTSAK 353
            +   R   K
Sbjct: 343 DKPAGRGRGK 352


>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 =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V+ TD +
Sbjct: 5   IEYKEENFDPNEPIRLNKYLANAGVCSRREADEFILSGAVTVNGEVVKELGSKVLRTDVV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  LFQDKPVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKGACPERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V  + L  +  GI ++        +  
Sbjct: 124 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKPVTANDLQKISDGIELEDGEIKADAIEY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +       V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 184 ASPD-DLTQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVQFAGLTKKNVRRGDWRFLTEK 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  273 bits (699), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 82/229 (35%), Positives = 122/229 (53%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++RAGIASRR+ E +I Q RV VNG ++ R    +   TD ++VDG P+ + E 
Sbjct: 1   MRLQKFMSRAGIASRRKSEELIQQGRVTVNGQVITRLGTKINPDTDTVKVDGEPITQEES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP   +T+  DP GR TV D +  +  RV  VGRLD ++ GL+LLTNDG LA 
Sbjct: 61  NVYIMLNKPKDYITSKDDPQGRKTVMDLI-QVKERVYPVGRLDYDSRGLVLLTNDGELAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V+      QDKL+ L  GI ++        V +   K  N  + + 
Sbjct: 120 RLMHPKYNIPKTYMVKVDKLPLQDKLDNLVNGIYLEEGLCKADHVEILDTK--NNILKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L EG+ R+I+++      +V  L R S G   L  L  G+ R+++K  +
Sbjct: 178 LSEGRKRQIRRMLASLGIEVKDLKRDSLGTLTLKDLSEGNYRKLTKDEI 226


>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 =  273 bits (699), Expect = 3e-71,   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|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 =  273 bits (698), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLII 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  273 bits (698), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L+ G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLVPGEYRPLTEEEI 227


>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 =  273 bits (698), Expect = 4e-71,   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|295098123|emb|CBK87213.1| ribosomal small subunit pseudouridine synthase A [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 235

 Score =  273 bits (698), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 106/229 (46%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     V  D      KG+ +           L+    ++  V + +
Sbjct: 121 ITSPRHHCDKTYRVMLESPVSDDTAEQFAKGVQLHNEKDLTKPAVLEILTPTD--VRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPDLAPGEYRPLTEEEI 227


>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 =  273 bits (698), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 110/237 (46%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D      +G+ +           L+  +  +  V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEHPLAADTAQQFAEGVQLHNEKDLTRPAQLE--QIEDKLVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVLELHRERIGAIVMDEDLAEGEYRPLTEEEIASVGAPHL 235


>gi|301062561|ref|ZP_07203199.1| pseudouridylate synthase [delta proteobacterium NaphS2]
 gi|300443326|gb|EFK07453.1| pseudouridylate synthase [delta proteobacterium NaphS2]
          Length = 295

 Score =  273 bits (698), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 75/244 (30%), Positives = 122/244 (50%), Gaps = 4/244 (1%)

Query: 5   NIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHI 60
           +  +  F P+   R++++++ AG+ SRR+ ++ I   R+ VNG  +           D I
Sbjct: 45  DFPEAPFNPEKPWRLNRILSSAGLTSRRKADQWILSGRITVNGKPVNAPGTTAFWGRDDI 104

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            VDG  +    +    + +KP G + +  DP+GR  V D    I  RV  VGRLD +T G
Sbjct: 105 RVDGQKIPLPPKKVYLMLNKPFGTICSLDDPEGRPLVTDLTKDIPIRVYPVGRLDFDTLG 164

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG  A  L  P     + Y+V   G +  + L  L+ GI +     G  +  L 
Sbjct: 165 LLLLTNDGEFAHRLTHPRFHVPKTYKVTVQGAISDEALKRLQTGITLNDGPAGRARTELI 224

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +    + + + + +GK+R+++++ E   + V  LIRIS+G  QLG L  G  R +  + 
Sbjct: 225 NRNNEKSILRMTITQGKSRQVRRMLEKVGFTVIHLIRISFGTLQLGDLKIGHHRHLDSEE 284

Query: 241 LREQ 244
           L + 
Sbjct: 285 LSKL 288


>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 =  273 bits (698), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 112/229 (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  KVYIALNKPEGYVSTVKDERGRKTILDIV-KVNERIFPIGRLDYNTSGLIILTNDGDVYN 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|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 =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 112/236 (47%), Gaps = 8/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVVY-QQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS--NAWV 189
            L  P     + Y     G  D++    +  G+ +  G      Q+ +  Q      + +
Sbjct: 121 QLLAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ L   
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEELAAL 236


>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 =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 112/236 (47%), Gaps = 1/236 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR  E  +   RV V+G++             I VDG PL   
Sbjct: 1   MTRQRLQKLIAAAGLCSRRRAEEWLQAGRVTVDGLVASVGDQADPQQQTIHVDGQPLPSR 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP+G++ +  DP GR TV D LP      +  VGRLD ++ G LLLT+ G 
Sbjct: 61  GVARVLLMNKPVGVICSCDDPQGRRTVLDLLPPEHRAGLHPVGRLDADSHGALLLTDLGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   +  L+  ++G+ + G      +V      G  + +
Sbjct: 121 LTLKLTHPRYSHAKTYRVWVKGVPPEPVLDRWRRGLPLDGCLTRPARVRRLRTWGDRSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + LREG+NR+I+++ E     V  L R +     LG L  G    +S+      L
Sbjct: 181 EIELREGRNRQIRRMAEALGHPVLDLQRTAIAGLPLGDLAEGCWIWLSEGEWEPLL 236


>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 =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 69/325 (21%), Positives = 137/325 (42%), Gaps = 10/325 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ +    +R++K I+  G  SRRE ++ I Q RV VNG       V V +TD + VDG 
Sbjct: 14  LLSDMTELKRLNKFISETGFCSRREADKYIEQGRVSVNGN-APEMGVKVAATDVVLVDGK 72

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL+   +     Y+KP+G+  T       + V     +   R+  +GRLD  +EGL+ LT
Sbjct: 73  PLKTPPKRVYIAYNKPVGITCTTERKIQSNIVKA--VNYPDRIFPIGRLDRPSEGLIFLT 130

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G +   +        + Y V     +++  ++ +  GI I        +VT    + +
Sbjct: 131 NEGDIVNKILRAGNNHEKEYVVTVDKPLNRQFVSKMANGIPILDTVTKKCKVT----QTA 186

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+  ++V  L R       L  L  G  R +S   + +  
Sbjct: 187 PKEFKIILTQGLNRQIRRMCEYLGYEVVTLKRTRIMNVTLKGLKVGQWRHLSDVEMAQI- 245

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               + ++    +  + +++ + ++               +    ++    K  +   P 
Sbjct: 246 -NDSIADSGKTQEHSLDTNKQVDKNAVISPKRDFQGENPRRNKQKERGDEQKNNRTNAPY 304

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQ 330
            +R+  + V   K   ++  S +  
Sbjct: 305 QKRS-TTYVGKPKTAKANSASSNKA 328


>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 =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 79/269 (29%), Positives = 120/269 (44%), Gaps = 33/269 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           +   P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D + VDG  +
Sbjct: 6   DRVVPMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDEVAVDGAVV 65

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
           R A+     + HKP G VTT SDP GR TV + +P   +  +  +GRLD +T GLLL + 
Sbjct: 66  RLADGPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDTTGLLLFST 125

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG L   L  P     + Y     G+  +  L LL++GI +         V +       
Sbjct: 126 DGELGNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVRVVEGGAAR 185

Query: 180 ------------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
                                   + +    + V +G+REG+ R++K++       V  L
Sbjct: 186 HAERLLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAAVGHPVLAL 245

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQ 244
            R S+GP +LG L  G+ R +  + +   
Sbjct: 246 HRDSFGPLELGDLPRGAWRALDAEEVAAL 274


>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 =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 85/248 (34%), Positives = 131/248 (52%), Gaps = 6/248 (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  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +  DG P+    R    L +KP G V T SD  GR T  D L   +S 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 AVNRRK----LRIVLVEGKNREIRRVLDSFNCTIKRLVRVRIGNLELGTLKAGEFRDLTV 236

Query: 239 KILREQLG 246
           +  +  LG
Sbjct: 237 QERQALLG 244


>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 =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 144/325 (44%), Gaps = 20/325 (6%)

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  YIAYNKPVGITCTTERKIQSNIVKA--VNYPDRIFPIGRLDRPSEGLIFLTNEGDIVNKI 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +++  +  +  G+ I        +VT   Q G+    T+ L 
Sbjct: 123 LRAGNNHEKEYVVTVDKPLNRQFVAKMGNGVPILDTITKKCKVT---QTGAQ-QFTIILT 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E+  ++V  L R+      L  L  G  R ++++ +   +  + + ++ 
Sbjct: 179 QGLNRQIRRMCEYLGYEVVTLKRVRIMNVTLKGLKVGQWRHLTEQEMA--IINNSISDSG 236

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK----------NSSQKNGLSKQKKLATP 304
              +  +Y     ++ +       P   +  K+          N  ++    K+++  TP
Sbjct: 237 KTQEHSVYDEANALQQQSPQAVAKPQKTSDKKRDFQGENPKRFNQGERTEERKKERSKTP 296

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSG 329
             +R+  + V   K I ++  SDS 
Sbjct: 297 YQKRS-TTYVGKPKSIKANKSSDSK 320


>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 =  272 bits (697), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 111/370 (30%), Positives = 176/370 (47%), Gaps = 35/370 (9%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+        V   
Sbjct: 1   MSEQDLQDTEITPPSGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEAT-LGQRVDLH 59

Query: 58  DHIEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 GDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 KFTDIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+++  +        L+   +                P +  +  D   R+++ S+
Sbjct: 240 GRWREMTQGEIDILAAEVGLQPVAL----------------PAMKLKAKDKMERLQRKST 283

Query: 291 QKNGLSKQKKLATPVH------RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP-S 343
           +  G  ++ +   P H       R        A    ++  S   +R    R+ P+ P  
Sbjct: 284 RPLGRGERVRNLRPAHEGAATGERPARQPREEAP-RKNTRGSTVAERPSEMRKRPAKPEG 342

Query: 344 KRSLRRTSAK 353
            +   R   K
Sbjct: 343 DKPAGRGRGK 352


>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 =  272 bits (697), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 115/236 (48%), Gaps = 3/236 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +   P R++K +A AG+ SRRE +  I+  ++ VNG ++      ++ TD I+  G  +
Sbjct: 287 TDPTEPLRLNKYLANAGVCSRREADNYISSGQITVNGEVVTELGTKILRTDEIKFKGQTV 346

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              E+    L +KP   VTT  DP  R  V D +      R+  VGRLD NT G+LL TN
Sbjct: 347 SL-EKKVYLLLNKPKDYVTTSDDPQQRKKVVDLVKDACPERIYPVGRLDRNTTGVLLFTN 405

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P     +VY V     V  + L  + +GI+++        +   +     
Sbjct: 406 DGDLASKLTHPKFLKKKVYHVFLDKPVAANDLQKIAEGIMLEDGEIKADAIEYASPD-DL 464

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K + 
Sbjct: 465 SQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVMFAGLTKKNVRRGDWRFLTQKEVE 520


>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 =  272 bits (697), Expect = 5e-71,   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 D +     R+  VGRLD +TEGL+LLTNDG   
Sbjct: 62  GKVYFMLYKPTGVISAAKDDRGRKTVVDLV-KYQERIYPVGRLDFDTEGLILLTNDGDFF 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|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 =  272 bits (697), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 86  IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 145

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +  P++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 146 TFNEKPVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 204

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 205 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISY 264

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 265 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNER 323

Query: 240 ILREQ 244
            +   
Sbjct: 324 EVNAL 328


>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 =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 85/239 (35%), Positives = 134/239 (56%), Gaps = 2/239 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI + RV VNG ++    V V  +   ++VDG+ ++
Sbjct: 136 DHDGVRLQKLLAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVDPSKVTVQVDGMTVQ 195

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             ++     ++KP G+V+T  DP+GR  + D L S  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            V V +  GKNR ++++F+   + V RL+R+  GP ++G+   G+ R +SK  +   L 
Sbjct: 316 LVEVTIHSGKNRIVRRLFDAVGYPVERLVRVEMGPIRIGSQKQGTVRNLSKVEIGHLLA 374


>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 =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE ++ I    VKVNG ++      V+ +D I
Sbjct: 261 IEYKEENIDPNEPLRLNKFLANAGVCSRREADQFIQSGMVKVNGNVVTELGTKVLRSDEI 320

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 321 IFHDQPVTL-EKKVYVLINKPKDYVTTSDDPQQRKTVMDLVKGVCPERIYPVGRLDRNTT 379

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V    +V +  L  +  G+ +         +  
Sbjct: 380 GVLLLTNDGDLASKLAHPKFLKKKVYHVFLDKEVTEHDLQQIATGVTLDDGEVHADAIEY 439

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    V + +  GKNR ++++FE   ++V RL R+ +       L  G  R +++K
Sbjct: 440 -ANDKDKTQVGIEIHSGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLKRGDWRFLTEK 498

Query: 240 IL 241
            +
Sbjct: 499 EV 500


>gi|257870825|ref|ZP_05650478.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804989|gb|EEV33811.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 241

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 73/245 (29%), Positives = 118/245 (48%), Gaps = 10/245 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G  SR+EV++ I +  V VNG  ++     V    D +   G  +R  ++
Sbjct: 1   MRLDKFLADMGYGSRKEVKQAIKKGVVAVNGQQVKSDKFQVAEQEDQVSFAGELVRY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++  +DP+   TV D          +  VGRLD +TEGLLL+TNDG L
Sbjct: 60  DFYYLLNKPAGVISATTDPE--KTVLDLFAAEDYRRDLFPVGRLDKDTEGLLLITNDGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     + Y     G + ++  +   +GI + G      Q+T+    ++   + 
Sbjct: 118 AHRLLSPKKHVEKEYYAEVRGIMTEEDRHQFLQGIELDGETLMPAQLTILKVDEQAETST 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           +T+ L EGK  ++K++ +    +V  L R   G  QL   L  G  R V++K L  QL  
Sbjct: 178 ITLILHEGKFHQVKRMVQAVGKEVTYLKRTRMGGLQLPKDLALGEYRSVTEKEL-AQLSA 236

Query: 248 HLLEE 252
              E+
Sbjct: 237 EPAED 241


>gi|291536218|emb|CBL09330.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis M50/1]
          Length = 235

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 80/235 (34%), Positives = 119/235 (50%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E 
Sbjct: 1   MRLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQKVDEKNDTVCFRGNPLTYTE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              +L+HKP G VT   D   R TV D L       +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 60  YEYYLFHKPAGCVTATEDNLHR-TVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVT 190
             L  P+    +VY  +  G+V ++ +NL K G+ I G         L+    G N+ + 
Sbjct: 119 HDLLSPAKHVSKVYYAKIDGRVTEEDVNLFKNGVDI-GEEKPAKPALLEVLHSGDNSEIR 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + + EG+  ++K++FE    KV  L R+  G   L   L  G  R ++++ L+E 
Sbjct: 178 LTITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEEELQEL 232


>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 =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 76/333 (22%), Positives = 133/333 (39%), Gaps = 26/333 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++ I Q RV VNG       V V +TD + VDG PL+   +  
Sbjct: 23  RLNKFISETGFCSRREADKYIEQGRVSVNGYSP-EMGVKVAATDVVLVDGKPLKATPKRV 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y+KP+G+  T        +      +  +R+  +GRLD  +EGL+ LTN+G +   +
Sbjct: 82  YIAYNKPVGITCTT--ESKIQSNIIRAVNYPTRIFPIGRLDRPSEGLIFLTNEGDIVNKI 139

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +++  +  +  G+ I        +VT    + +     + L 
Sbjct: 140 LRAGNNHEKEYVVTVDKPLNRQFVTKMANGVPILDTVTKKCKVT----QTAPKEFKIVLT 195

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL-----------RE 243
           +G NR+I+++ E+  ++V  L R       L  L  G  R +S   +           + 
Sbjct: 196 QGLNRQIRRMCEYLGYEVVTLKRTRIMNVTLKGLKVGQWRHLSDTEMAQINDSISDSGKT 255

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK-------NGLS 296
           Q       +   N             + P   ++      R  + +S +       NG  
Sbjct: 256 QEHSLDANKQSENNTPSAPKKRDFQGENPRRFNKGEQSGERSTERNSSRNSDRSNANGER 315

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           K ++   P  +R+  + V   K I  +  S S 
Sbjct: 316 KNERSKAPYQKRS-TTYVGKPKSIKENKSSQSK 347


>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 =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 114/234 (48%), Gaps = 3/234 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    VKVNG ++      VM TD +     P+ 
Sbjct: 248 DPTVPVRLNKFLANAGVCSRREADEFIQAGVVKVNGEVVTELGTKVMRTDEVVFHDQPVS 307

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             E+    L +KP   VTT  DP  R TV D + +    R+  VGRLD NT G+LLLTND
Sbjct: 308 L-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKNVCPERIYPVGRLDRNTTGVLLLTND 366

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P     +VY V     V    +  + +GI ++        +    +   N 
Sbjct: 367 GDLASKLTHPKYLKKKVYHVFLDKNVTAHDMQKIAEGIELEDGEVHADAIEYAHETDKN- 425

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++ +
Sbjct: 426 QVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNLRRGDWRFLTEEEV 479


>gi|291538915|emb|CBL12026.1| ribosomal small subunit pseudouridine synthase A [Roseburia
           intestinalis XB6B4]
          Length = 235

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 80/235 (34%), Positives = 119/235 (50%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E 
Sbjct: 1   MRLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQKVDEKNDTVCFRGNPLTYTE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              +L+HKP G VT   D   R TV D L       +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 60  YEYYLFHKPAGCVTATEDNLHR-TVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVT 190
             L  P+    +VY  +  G+V ++ +NL + G+ I G         L+    G N+ + 
Sbjct: 119 HDLLSPAKHVSKVYYAKIDGRVTEEDVNLFENGVDI-GEEKPAKPALLEVLHSGDNSEIR 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + + EG+  ++K++FE    KV  L R+  G   L   L  G  R +++K L+E 
Sbjct: 178 LTITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEKELQEL 232


>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 =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 99/344 (28%), Positives = 153/344 (44%), Gaps = 5/344 (1%)

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 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--EQ 244
           + + + L EGKNREI+++      KV  L R++ GP  L  L  G  R +    +   +Q
Sbjct: 299 SILELVLAEGKNREIRRMLARLGHKVMSLTRVAVGPITLKGLRTGEVRVLGTAEVDRLKQ 358

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +  +     + +LD+   SS    RDR    S    D +R      +  G ++    +  
Sbjct: 359 IARNPFPPTE-SLDSDAGSSAPAQRDRDYDRSAKRSDLSRRSAPGFRLGGGNRFGGGSNR 417

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
              R + +         S    +            + P  R + 
Sbjct: 418 PLGRPVYTPGNEPPEDRSDRRPNRLGGGNRFGEGGNRPLGRPVY 461


>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 =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 125/233 (53%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ASRR  E++IA   V+VNG  +    + V   D + VDGVPL + E  
Sbjct: 2   ERLQKVMAEAGVASRRASEKLIASGHVQVNGKTVTEMGIKVSEHDEVVVDGVPLHR-EAH 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP  ++T+  D  GR TV D L       RV  VGRLD +T G+LLLTNDG LA
Sbjct: 61  VYYLLNKPRSVITSAHDDKGRRTVVDILKEEGVAERVYPVGRLDYDTTGILLLTNDGELA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWV 189
             L  P  +  + Y  +  G V+ + L  L+ G+ + G      +  L     K   + V
Sbjct: 121 NRLMHPKFEVEKTYIAKVRGIVNNNDLKQLRIGVEVNGRLTKKAKSRLIETDHKKQTSLV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EG+  ++K +F+  +  V +L R +YGP  L  L +G  RE+ +  ++
Sbjct: 181 KLTIHEGRYHQVKLMFDAIHHPVIKLHRETYGPLDLNGLQSGEFRELKQDEVK 233


>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 =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKSYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 227


>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 =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 112/333 (33%), Positives = 165/333 (49%), Gaps = 25/333 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  L 
Sbjct: 25  KIVGEKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLS 84

Query: 69  KAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
             E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL
Sbjct: 85  IKESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLL 144

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +
Sbjct: 145 FTTDGELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGE 204

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK--- 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K   
Sbjct: 205 GINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATN 264

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LRE           V LD    S   + +DR  + +       R  K  ++ +G     
Sbjct: 265 YLREL----------VELDVETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVSGRQVAG 311

Query: 300 KLATPVHRRNLASNVWM-AKGIHSSFLSDSGQR 331
           +  +   + +   NV   A    +S  S   +R
Sbjct: 312 RQGS-ARKGSTRQNVGNAAPAATASRRSGPKKR 343


>gi|302333165|gb|ADL23358.1| ribosomal large subunit pseudouridine synthase B, RluB
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 245

 Score =  272 bits (696), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 80/243 (32%), Positives = 135/243 (55%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++  +  HL E
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVK--VMRHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 HGK 245


>gi|312876843|ref|ZP_07736820.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796358|gb|EFR12710.1| pseudouridine synthase [Caldicellulosiruptor lactoaceticus 6A]
          Length = 230

 Score =  272 bits (696), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 74/222 (33%), Positives = 117/222 (52%), Gaps = 2/222 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLY 78
           +A+ GIASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    +    + 
Sbjct: 1   MAQCGIASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRISLQMQKVYIML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G++++  D  GR TV D +    + RV  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|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 =  272 bits (696), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 122/233 (52%), Gaps = 3/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++ ++  G+ SRR+ +++I + RVKVNG ++    V +    D +EVDG  ++   R 
Sbjct: 4   RLNRYLSMCGVTSRRKADKLIEEGRVKVNGEVVRDLGVKIDPEVDRVEVDGKEVKPP-RK 62

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP   +T       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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             EG+   +K+    F   V +L RI+ G  +LG L  G  RE+S++ LR+  
Sbjct: 183 FHEGRKHIVKRFLASFGHPVIKLKRIALGTLKLGKLPPGKWRELSQRELRQLF 235


>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 =  272 bits (696), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 85/239 (35%), Positives = 134/239 (56%), Gaps = 2/239 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLR 68
           +    R+ K++A+AG+ASRR  E MI + RV VNG ++    V V  +   ++VDG+ ++
Sbjct: 144 DHDGVRLQKLLAQAGVASRRVCEEMITEGRVTVNGEVVTELGVRVDPSKVTVQVDGMTVQ 203

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             ++     ++KP G+V+T  DP+GR  + D L S  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            V V +  GKNR ++++F+   + V RL+R+  GP ++G+   G+ R +SK  +   L 
Sbjct: 324 LVEVTIHSGKNRIVRRLFDAVGYPVERLVRVEMGPIRIGSQKQGTVRNLSKVEIGHLLA 382


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 114/233 (48%), Gaps = 2/233 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ K +A  G+ASRR+ E +I+Q RVKVN  ++      V    D + VD V +  
Sbjct: 1   MLKERLQKYMAACGVASRRKCEEIISQDRVKVNCEIVNELGFKVDPEIDKVYVDSVLITL 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+      +KP G V+T  D  GR T+ D +  +  R+  +GRLD NT GL+LLTNDG 
Sbjct: 61  EEQKVYIALNKPEGYVSTVKDERGRKTILDIV-KVNERIFPIGRLDYNTSGLILLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +  P  +  +VY     G    D++     GI I G         +  +      V
Sbjct: 120 VYNKIIHPREEIDKVYIAVIKGIPSHDEIKNFCNGIDIGGYVTSKASFEILEKLNDKCKV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + + EGKNR+++++ E     V  L R+S G   L T+  G  R +++  ++
Sbjct: 180 KIIIHEGKNRQVRRMCEKIGHPVIALKRVSVGKISLNTIKRGEWRYLNESEIK 232


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K +  +   P R++K +A AG+ SRRE +  I    V VNG ++      V  +D +
Sbjct: 5   IEYKELNVDPDAPIRLNKFLANAGVCSRREADEFITAGVVSVNGTVVTELGTKVKRSDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 65  KFHEQPVS-IERKVYVLLNKPKDYVTTSDDPQNRKTVMDLVKNVCRERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL TNDG LA  L  P     ++Y V     V    +  + +GI ++        +  
Sbjct: 124 GVLLFTNDGELASKLTHPKFLKKKIYHVTTDKNVTAADMRQIAEGITLEDGEIKADAIEY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +       + + +  GKNR ++++FE   ++V +L R+ +       +  G  R ++++
Sbjct: 184 ASPT-DKKQIGIEIHSGKNRIVRRIFEALGYRVVKLDRVLFAGLTKKNVRRGDWRFLTEQ 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 112/236 (47%), Gaps = 8/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVVY-QQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS--NAWV 189
            L  P     + Y     G  D++    +  G+ +  G      Q+ +  Q      + +
Sbjct: 121 QLLAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLNILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ L   
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEELAAL 236


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +   +V VNG++ + +A  +   D I  DG PL   +  
Sbjct: 1   MRLDKFIAENTGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICFDGEPLAWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP   V +H D D   TVF        +++   GRLD +T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQNCVCSHDDGDY-PTVFQFFDYPLTTKLHCAGRLDADTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+        +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYATQFAEGILLRGEKTATKPAQLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVALHRWRIGDVVLDENLAEGEFRALTEDEI 227


>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 =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 112/333 (33%), Positives = 165/333 (49%), Gaps = 25/333 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  L 
Sbjct: 25  KIVGEKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLS 84

Query: 69  KAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
             E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL
Sbjct: 85  IKESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLL 144

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +
Sbjct: 145 FTTDGELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGE 204

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK--- 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K   
Sbjct: 205 GINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATN 264

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LRE           V LD    S   + +DR  + +       R  K  ++ +G     
Sbjct: 265 YLREL----------VELDVETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVSGRQVAG 311

Query: 300 KLATPVHRRNLASNVWMA-KGIHSSFLSDSGQR 331
           +  +   + +   NV  A     +S  S   +R
Sbjct: 312 RQGS-ARKGSTRQNVGNAVPAATASRRSGPKKR 343


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTRPAELEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVALHRERIGAIALDADLAPGEYRPLTEEEI 227


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 80/243 (32%), Positives = 135/243 (55%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYIMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++  +  HL E
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVK--VMRHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 HGK 245


>gi|271500910|ref|YP_003333935.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344465|gb|ACZ77230.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 232

 Score =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D     + G+ +          TL+    S   V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPLAADTAEKFQAGVQLHNEKNLTRPATLEV--LSEHQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 TEGRYHQVKRMFAAIGNHVVALHRERIGAITLDDTLEPGEYRPLTQEEV 227


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 76/356 (21%), Positives = 140/356 (39%), Gaps = 10/356 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +K+ +     P R++K I+  G  SRRE +++I Q RV +NG         VM  D + 
Sbjct: 7   DNKDQLDPQNKPVRLNKFISDTGYCSRREADKLIDQGRVTINGTQP-EMGTKVMPDDEVL 65

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           VD  PLR  ER      +KP G+  T ++   +  + D +     R+  +GRLD  ++GL
Sbjct: 66  VDDKPLRAKERPIYIALNKPTGVTCT-TERHVKDNIVDFI-GHRKRIFPIGRLDKPSDGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           + LTNDG +   +        + Y VR   Q+  + L  +  G+ I         V    
Sbjct: 124 IFLTNDGDIVNKILRAGNSHEKEYVVRVSHQITPEFLEKMASGVEILDTVTLPCIVK--- 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            K ++    + L +G NR+I+++ E   + V +L R+      +  L  G  R ++   +
Sbjct: 181 -KETDYSFRITLTQGLNRQIRRMCEALGYDVYKLRRVRIMNITIDGLPNGKWRYLTDAEI 239

Query: 242 RE---QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            E    +      E    +DA   +       +     +   +  + ++    ++   K 
Sbjct: 240 AEINTLISQSSGTEEASKVDAEGQAIAKATDAKLFDSRQQAAEERQRERERGMRDATYKT 299

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            K      R    ++         +  +  G    +  R       +S R + A +
Sbjct: 300 FKAKGEFTRTRRNTDRDDKSTDSRNGSARHGDSRPSQSRDHQSFRDQSARDSQAPR 355


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 105/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D     + G+ + G        TL+    S   V + +
Sbjct: 121 ITSPKHHCEKTYLVTLDQPLAPDTAEKFQAGVQLHGEQSLTRPATLEI--ISEHQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L AG  R ++ + +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVALHRERIGAITLDDALEAGEYRPLTPEEI 227


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 105/230 (45%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +   +V VNG++ + +A  +   D I  DG PL   +  
Sbjct: 1   MRLDKFIAENTGLTRSQASKALRAGQVTVNGVVEKNSATKISEQDEICFDGEPLAWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP   V +H D D   TVF        +++   GRLD +T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQNCVCSHDDGDY-PTVFQFFDYPLTTKLHCAGRLDADTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+        +GI+++G        TL+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYATQFAEGILLRGEKTLTKPATLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L  TL  G  R +++  +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVALHRWRIGNVVLDETLAEGEFRALTEDEV 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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 89/243 (36%), Positives = 126/243 (51%), Gaps = 10/243 (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  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFS-----RVISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV     D L          R++ 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 REQ 244
              
Sbjct: 316 AAL 318


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 112/333 (33%), Positives = 165/333 (49%), Gaps = 25/333 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  L 
Sbjct: 25  KIVGEKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLS 84

Query: 69  KAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
             E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL
Sbjct: 85  IKESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLL 144

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +
Sbjct: 145 FTTDGELANCLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGE 204

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK--- 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K   
Sbjct: 205 GINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATN 264

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LRE           V LD    S   + +DR  + +       R  K  ++ +G     
Sbjct: 265 YLREL----------VELDVETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVSGRQVAG 311

Query: 300 KLATPVHRRNLASNVWM-AKGIHSSFLSDSGQR 331
           +  +   + +   NV   A    +S  S   +R
Sbjct: 312 RQGS-ARKGSTRQNVGNAAPAATASRRSGPKKR 343


>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 =  272 bits (695), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 95/241 (39%), Positives = 140/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKSKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLAKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>gi|298694777|gb|ADI97999.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus ED133]
          Length = 245

 Score =  272 bits (695), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 80/243 (32%), Positives = 135/243 (55%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++  +  HL E
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIDYGPLNVVGLNAGEGRVLTPHEVK--VMRHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 HGK 245


>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 =  272 bits (695), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 107/351 (30%), Positives = 165/351 (47%), Gaps = 26/351 (7%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D+N  QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG       + V   D I
Sbjct: 4   QDQNDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-LGLRVDMHDAI 62

Query: 61  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD +P     R I++GRLD
Sbjct: 63  TIDGKVIKREEAAETVRRVIMYNKPDGEICTRDDPEGRPTVFDKMPRPKEGRWINIGRLD 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 QVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  +                D             P + ++  D   RM++ SS+  
Sbjct: 243 REMSQYEV----------------DILAAEVGLKPVAMPQMTAKSKDKLERMQRKSSRPM 286

Query: 294 GLSKQKKLATPVHRRNLASN-VWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           G +++ +   P                I     +      ++  R P  P 
Sbjct: 287 GKTERVRTLRPAAEGAPTGPRPSREPQIEGERPARKPAPRQDGERGPRTPR 337


>gi|330939561|gb|EGH42880.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. pisi str. 1704B]
          Length = 299

 Score =  272 bits (695), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 108/315 (34%), Positives = 159/315 (50%), Gaps = 31/315 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 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   + +                   P + ++  D   R+++ SS
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQ-------------------PQMNAKTKDKMERLQRQSS 283

Query: 291 QKNGLSKQKKLATPV 305
           +  G  ++ +   P 
Sbjct: 284 RPLGKGERVRTLRPA 298


>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 =  272 bits (695), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 95/241 (39%), Positives = 140/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLAKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  272 bits (695), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 96/354 (27%), Positives = 164/354 (46%), 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   ++ +KP G+++T+ DP GR+ V D +P    R+ ++GRLD 
Sbjct: 61  HQEILVDGQRLKFGKR-VYYMLNKPPGVLSTNFDPAGRTRVIDMVPQDV-RLFTIGRLDR 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 SKKILREQL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
                +        +   +     P  SS    R+ P           R     ++    
Sbjct: 239 KSAETKALRDAAFGVGAGKPKKPKPRKSSTPGEREGPIFPETKTIAKGRAGAKPTETGAK 298

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           S+     T    ++ ++    A    SS  +       +  R+ +  S  S  +
Sbjct: 299 SRATGKPTGAASKDRSTYKKSAGTGSSSRAAGKPAGSSSKDRASASKSSDSAPK 352


>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 =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 80/243 (32%), Positives = 136/243 (55%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIDARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++         +V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGLTQPADVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++  +  HL E
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVK--VMRHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 HGK 245


>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 =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 113/242 (46%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K +  +   P R++K +A AG+ SRRE +  I    V VNG ++      V  TD +
Sbjct: 5   IEYKELNVDPDAPIRLNKFLANAGVCSRREADEFITAGVVSVNGTVVTELGTKVKRTDEV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 65  KFHEQPVS-IERKVYVLLNKPKDYVTTSDDPQNRKTVMDLVKNVCRERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL TNDG LA  L  P     ++Y V     V    +  + +GI ++           
Sbjct: 124 GVLLFTNDGELASKLTHPKFLKKKIYHVTTDKNVTAADMRQIAEGITLEDGEIR-ADAID 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                    V + +  GKNR ++++FE   ++V +L R+ +       +  G  R ++++
Sbjct: 183 YASPTDKKQVGIEIHSGKNRIVRRIFEALGYRVVKLDRVLFAGLTKKNVRRGDWRFLTEQ 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 80/243 (32%), Positives = 135/243 (55%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++FE F  +V +L RI YGP  +  L AG  R ++   ++  +  HL E
Sbjct: 185 TITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVK--VMRHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 HGK 245


>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 =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 113/242 (46%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      ++ TD +
Sbjct: 233 IEYKEEHTDPNEPIRLNKYLANAGVCSRREADEFIQAGVVTVNGQVITELGTKIVRTDEV 292

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   E+    L +KP   VTT  DP  R TV + +      R+  VGRLD NT 
Sbjct: 293 KFHDQPVTL-EKKVYVLLNKPRDYVTTSDDPQQRKTVMELVKGACPERIYPVGRLDRNTT 351

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL TNDG LA  L  P     +VY V    +V    +  +  GI +         +  
Sbjct: 352 GVLLFTNDGDLASKLTHPKFLKKKVYHVFLDKEVTMHDMQQIATGITLDDGEIHADAIEY 411

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +      V + +  G+NR ++++FE   ++V RL R+ +       L  G  R +++K
Sbjct: 412 -AKDNDKKQVGIEIHSGRNRIVRRIFESLGYRVVRLDRVQFAGLTKKYLRRGDWRFLTEK 470

Query: 240 IL 241
            +
Sbjct: 471 EV 472


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 139/314 (44%), Gaps = 25/314 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++ + +N +  R++K I+ +G  SRRE +++I Q RVK+NG +       V   D + VD
Sbjct: 13  QDNIVDNNSEIRLNKFISDSGFCSRREADKLIEQNRVKINGDIP-ELGTKVQLGDLVLVD 71

Query: 64  GVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           G  +  + + +      +Y+KPIG+  T       + +  N      R+  +GRLD  +E
Sbjct: 72  GKRINASAQDKLDRIYIVYNKPIGITCTTERHIHGNII--NAIGHKKRIFPIGRLDKPSE 129

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+ LT+DG +   +        + Y V     + +  +  +++G+ I        +VT+
Sbjct: 130 GLIFLTSDGDIVNKILRAENAHDKEYLVTVDKPLSERFVERMQRGVPILDTITKPCKVTV 189

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D    S     + L +G NR+I+++ E   ++V +L R       LG L  G  R ++  
Sbjct: 190 D----SRFIFRIVLTQGLNRQIRRMCEHLGYEVLKLKRTRIMKVGLGNLKPGQWRNLTNI 245

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            L E             ++  + SS     D    +S+ P     +KK++   N     K
Sbjct: 246 ELAE-------------INQAVSSSSKTATDPAKPVSKAPQS-EAIKKSTGANNSHQPAK 291

Query: 300 KLATPVHRRNLASN 313
           K+    + +N  + 
Sbjct: 292 KIFINKNSKNTTTP 305


>gi|322715286|gb|EFZ06857.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
          Length = 231

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 60/229 (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  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNCVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 112/329 (34%), Positives = 165/329 (50%), Gaps = 25/329 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAER 72
           +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  L   E 
Sbjct: 3   EKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLSIKES 62

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL T D
Sbjct: 63  EENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D DK+  L +G+ ++        ++    +G N 
Sbjct: 123 GELANRLMHPSREVEREYAVRVFGQIDDDKIKQLSRGVQLEDGPAAFRTISYQGGEGINQ 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K    LRE
Sbjct: 183 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATNYLRE 242

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                      V LD    S   + +DR  + +       R  K  ++ +G     +  +
Sbjct: 243 L----------VELDVETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVSGRQVAGRQGS 289

Query: 304 PVHRRNLASNVWM-AKGIHSSFLSDSGQR 331
              + +   NV   A    +S  S   +R
Sbjct: 290 -ARKGSTRQNVGNAAPAATASRRSGPKKR 317


>gi|289624030|ref|ZP_06456984.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
          Length = 308

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 107/315 (33%), Positives = 158/315 (50%), Gaps = 31/315 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 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   + +                   P + ++  D   R+++  S
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQ-------------------PQMNAKTKDKMERLQRQPS 283

Query: 291 QKNGLSKQKKLATPV 305
           +  G  ++ +   P 
Sbjct: 284 RPLGKGERVRTLRPA 298


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 112/235 (47%), Gaps = 5/235 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D ++     + 
Sbjct: 2   DPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTVS 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTND
Sbjct: 62  -IERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G LA  L  P     ++Y V     + +  +  +  GI +  G  + D     D  K  +
Sbjct: 121 GDLASKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIHADAISYTDDFKKDD 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 181 --VGIEIHSGKNRIVRRIFESLGYKVMKLDRVYFAGLTKKGLRRGEWRYLTEQEV 233


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 111/332 (33%), Positives = 163/332 (49%), Gaps = 24/332 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ KV+ARAG  SRRE+E +I Q RV V+G +      V V     I +DG  L 
Sbjct: 24  KIVGEKLQKVLARAGHGSRREIEAIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLLS 83

Query: 69  KAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
             E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL
Sbjct: 84  ITESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLL 143

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++    +
Sbjct: 144 FTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQGGE 203

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK--- 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K   
Sbjct: 204 GLNQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATN 263

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            LRE           V LD+   S   + +DR  + +       R  K  ++  G     
Sbjct: 264 YLREL----------VELDSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQVAG 310

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
           +  +   + +   NV  A    ++    S +R
Sbjct: 311 RQGS-ARKGSTRQNVGNAAPAATAGRRGSNKR 341


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D   L  KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAALFAKGVQLNNEKDLTKPAQLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R +++  +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPELAPGEYRPLTEDEI 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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 128/236 (54%), Gaps = 3/236 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P  +  + Y  + +G+++ + L +L+ G+ I        +V +   K    N  V +
Sbjct: 122 ITHPKHKIKKTYVAKINGKLEDNHLRILRNGVRIDNYKTAKAEVNVVKNKNKSGNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGKNR+++++FE   ++V +L R S     L  L  G  R ++   ++  +  
Sbjct: 182 TIHEGKNRQVRRMFEALGYEVIKLKRESIEDLTLEGLKKGEYRPLTIHEVKRLINK 237


>gi|255012441|ref|ZP_05284567.1| ribosomal large subunit pseudouridine synthase B [Bacteroides sp.
           2_1_7]
          Length = 495

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +  P++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISY 425

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 426 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNER 484

Query: 240 ILREQ 244
            +   
Sbjct: 485 EVNAL 489


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 129/231 (55%), Gaps = 3/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG  +      V S+D +EV+G+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLITEGKVKVNGQTVTELGTKVKSSDTVEVEGIKIEQEDKM 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFYKPTQVITSVSDDRGRTVVTDYFKDLETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTV 191
           +  P     + Y  +  G + ++++  L+ GI ++       QV +  Q        V +
Sbjct: 125 MTHPRYHIQKKYVAKLKGYLMREEVKALENGIELEDGFTQPAQVKVKKQDKDKNITLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + EG+NR+++++FE F  +V++L RI +G   L  L AG  R ++   ++
Sbjct: 185 TISEGRNRQVRRMFEHFGHQVDKLTRIEFGNLNLKGLNAGEGRVLTPHEVK 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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 131/233 (56%), Gaps = 5/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K IA+AG+ SRR+ E++I + RVKVNG ++    V +    D +E+D   + K ++
Sbjct: 3   ERLQKFIAKAGVTSRRKAEKLILEGRVKVNGEVIRTLGVKIDPEKDIVEIDNK-IVKPDK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G +++  DP GR T+ D L      RV  VGRLD ++EGLLL TNDG +A
Sbjct: 62  KIYIALYKPVGYISSLYDPFGRRTIKDLLRDKVPFRVYPVGRLDFDSEGLLLCTNDGEIA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWV 189
            VL  P  +  +VY V   G   +++L  L++G++++         ++  + ++ + + +
Sbjct: 122 NVLIHPRYKIPKVYEVLIDGIPKEEELKKLREGVILEEGRTLPAGFEIIWENRRKNISLL 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + L +G  R+I+++   FN+KV  L R+  G  +LG L  G  R +    +R
Sbjct: 182 KITLYQGWKRQIRRMLALFNYKVLNLKRVQIGKIKLGDLKPGEIRFLRDDEIR 234


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 109/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V +D       G+ +           L+  +     V + L
Sbjct: 121 ITSPRHHCEKTYLVTLEHPVAEDTAQRFADGVQLHNETSLTKPAQLEIIEP--QLVRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFGAVGNRVLALHRERIGAMKLDDDLAPGEYRPLTAEEIASVGAPHL 235


>gi|330889215|gb|EGH21876.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 396

 Score =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 117/376 (31%), Positives = 172/376 (45%), Gaps = 28/376 (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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAP 302

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
              D         Q  G  + +       +R          G  +   +++  R      
Sbjct: 303 ATGDRA---PRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPAETNSRGTPVAE 359

Query: 338 SPSFPSKRSLRRTSAK 353
            PS  +KR  +    +
Sbjct: 360 RPSEMNKRPAKPGPKR 375


>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 =  271 bits (694), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 105/319 (32%), Positives = 161/319 (50%), Gaps = 14/319 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLR 68
            +++ KV+AR G+ SRRE++ +IA  RV+VNG +       V     +++DG     PL 
Sbjct: 2   SEKLQKVLARQGLGSRRELDALIAAGRVEVNGKVAA-VGDRVEGPLTVKIDGKVVLTPLS 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
           +  + R+ +Y+KP G VTT+ DP+ R TVFD+LP     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 QLGPHLLEEAQVNLDAPIYSS---ETLVRDRPNIISEVPDDFTRMKKNSSQK-NGLSKQK 299
            +G   LE +++   +    S   +  +       + +     +    S           
Sbjct: 241 AVGLKALESSEIARTSLASMSNDKKHALEKFAKHKANIKAAGRKALNASHNPFRKGRADD 300

Query: 300 KLATPVHRRNLASNVWMAK 318
           K   P   R+       AK
Sbjct: 301 KDRNPYGSRSGKYVYGDAK 319


>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 =  271 bits (694), Expect = 1e-70,   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+ D +  +  R+  +GRLD NT GLLL+TNDG +  
Sbjct: 63  NVYIALNKPEGYVSTVKDERDRKTIMDLV-EVEERIFPIGRLDYNTSGLLLMTNDGDVYN 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|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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +  P++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISY 425

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 426 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNER 484

Query: 240 ILREQ 244
            +   
Sbjct: 485 EVNAL 489


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +  P++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISY 425

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 426 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNER 484

Query: 240 ILREQ 244
            +   
Sbjct: 485 EVNAL 489


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/256 (33%), Positives = 136/256 (53%), Gaps = 12/256 (4%)

Query: 1   MKDKNIVQENFTPQ----------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERA 50
           M +K++ + +  P           R+ KV+A+AGIASRR  E +I + RV+VNG ++   
Sbjct: 16  MAEKDMSETHEPPIDQSAAKPEGIRLQKVLAQAGIASRRASEGLITEGRVEVNGHIVVEL 75

Query: 51  AVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              V    D I VDG  +    R    L +KP G+V+T  DP+GR T+ + +P    R+ 
Sbjct: 76  GTRVDPEHDSIRVDGARIPPPRRHMYLLLNKPRGVVSTMDDPEGRPTLAEYVPRH-QRLF 134

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            VGRLD  TEGL++LTNDG     L  PS +  + Y V   G +D   +  L+KG+ ++ 
Sbjct: 135 HVGRLDTETEGLIILTNDGEFGHRLSHPSYEVRKTYLVDAEGLMDNRTIRRLEKGLTLED 194

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 +V L ++   +  + + L  G+NR ++++ +     V +L RI  GP +LG L 
Sbjct: 195 GPIKPDRVKLVSRGPVHTMLQITLHSGRNRIVRRMMDSVGHPVRQLARIGIGPVRLGNLA 254

Query: 230 AGSTREVSKKILREQL 245
            G TRE+S++ L   L
Sbjct: 255 VGETRELSREELGTLL 270


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 107/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V +D       G+ +           L+  +     V + L
Sbjct: 121 ITSPRHHCEKTYLVTLEHPVAEDTAQRFADGVQLHNETSLTKPAQLEIIEP--QLVRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   L   L  G  R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFGAVGNRVLALHRERIGAMILDDDLAPGEYRPLTAEEIASVGAPHL 235


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 95/241 (39%), Positives = 140/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQEALNNLLKGVMLDDGLAKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLAMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>gi|330960474|gb|EGH60734.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 408

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 117/371 (31%), Positives = 176/371 (47%), 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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRD-RPNIIS 276
           RE+S+     L  ++G   + + Q+N                P+   E +VR  RP   +
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 277 EVPDDFTRMKKNSSQKNGLSK-QKKLATPVHRRNLASNVWMAK-GIHSSFLSDSGQREEN 334
              +   R  + +  +    +       P  R++       A     +S  +   +R  +
Sbjct: 303 PTGERAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAERPSD 362

Query: 335 HRRSPSFPSKR 345
             + P+ P  +
Sbjct: 363 MNKRPAKPGPK 373


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 97/327 (29%), Positives = 146/327 (44%), Gaps = 14/327 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--- 67
              +R+ K+++RAG+ASRR+VE  IA  R+ VNG           + D I +DG PL   
Sbjct: 1   MPAERLQKILSRAGVASRRQVEAWIAAGRLTVNGRPAVLGTRADPARDVIALDGRPLAGL 60

Query: 68  -RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT 125
             +  R R  L+HKP G+VTT  DP GR  V D         +  VGRLD ++EGLLLLT
Sbjct: 61  AERLSRKRYVLFHKPRGMVTTLRDPQGRPNVGDFCRRHGLQGLHPVGRLDFDSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG L   L  P  +  +VY V   G +D  +L  L+ G+++           +   +  
Sbjct: 121 DDGELTFALTHPRHEVDKVYHVLVRGDLDPARLRRLRDGVLLDDGPARARIARVLRPRPG 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             WV V LREG+ R+++++ +   W+V RL+R++ GP +LG L AG+ R +S++      
Sbjct: 181 GGWVEVVLREGRKRQVRRMCQAVGWQVVRLVRVAVGPLRLGRLAAGAWRPLSRQE----- 235

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               +E  +V    P    E   R R              ++  +   G           
Sbjct: 236 ----VESLRVAAGLPPRPDEPAPRHRQAGEGRPARGPAWGRRVPAGLAGRPPGPARPGAA 291

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQRE 332
            RR         +G           R 
Sbjct: 292 ARRVSEGPALQGQGPRGRVSRPPSGRN 318


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/364 (21%), Positives = 145/364 (39%), Gaps = 26/364 (7%)

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 ++      + D +     R+  +GRLD  ++G
Sbjct: 60  LIDDKPLRSKERPIYIALNKPTGITCT-TERHIEGNIVDFI-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 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           + E     L+ ++    +A      + V      I +  D      +    +N    Q+K
Sbjct: 234 IAEIH--RLISQSSGTEEA------SKVDGEGRKIEKATDAKLYDHRQQEARNEKRAQEK 285

Query: 301 -----------LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                         P  +R    N    +G       +   R + + +  +   +   RR
Sbjct: 286 KFKTYSGTGEFTRRPGGQRQNRRNEEGGEGRQQRGQRNGQGRNDRNSQDRNGNERNDNRR 345

Query: 350 TSAK 353
             ++
Sbjct: 346 QDSR 349


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 132/231 (57%), Positives = 167/231 (72%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K + R+G+ASRR+ ERMI + RV++NG ++   A  V   D ++VD   +   +RTR
Sbjct: 16  RIAKWLGRSGVASRRDAERMIEEGRVRLNGDIVRHPATFVSDGDIVQVDDKVIAAPDRTR 75

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           LW YHKP GLVTTH DPDGR TVF +LP    RVISVGRLD+N+EGLLLLTNDG LAR L
Sbjct: 76  LWRYHKPDGLVTTHRDPDGRPTVFASLPEGMPRVISVGRLDLNSEGLLLLTNDGELARKL 135

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
           ELPS  W+R YRVR  G V++D+L  L +G V +G+ YG ++  LD+ +G NAW+TV LR
Sbjct: 136 ELPSNGWIRRYRVRVFGVVNEDQLADLAQGSVFEGVHYGPIEAALDSSRGDNAWLTVSLR 195

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGKNREI+KV    N  V+RLIR SYGPFQLGTL      EV+ K+LREQ+
Sbjct: 196 EGKNREIRKVMRGLNLHVSRLIRTSYGPFQLGTLEREELEEVTGKVLREQV 246


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D       G+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAHGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGDIRLDDDLEPGEYRPLTEEEI 227


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 82/255 (32%), Positives = 135/255 (52%), Gaps = 4/255 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KVIA AG+ASRR+ E +IA   V +NG +++   + V ST  HIEVDGVPL + E+
Sbjct: 2   ERLQKVIANAGVASRRKAETLIATGHVTLNGKVVKEMGIKVDSTSAHIEVDGVPLTR-EK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +  +KP  +++  +D   R  V + L  I  RV  +GRLD +T GLLLLTNDG  A 
Sbjct: 61  KVYYALYKPRQVISAVTDDKKRRVVTEYLEDIQERVYPIGRLDYDTSGLLLLTNDGDFAN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 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 EEAQVNLDAPIYSSE 265
            E   + + P  S  
Sbjct: 241 NEKPKHKNRPKLSRH 255


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 60/229 (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  RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 109/333 (32%), Positives = 163/333 (48%), Gaps = 24/333 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL 67
           +    +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  L
Sbjct: 23  DKIVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLL 82

Query: 68  RKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
              E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLL
Sbjct: 83  SIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLL 142

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +     
Sbjct: 143 LFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTIKFQGG 202

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---K 238
           +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+     
Sbjct: 203 EGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLNAT 262

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             LRE           V LD+   S   + +DR  + +       R  K  ++  G    
Sbjct: 263 NYLREL----------VELDSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQVA 309

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
            +  +   + +   NV  A    ++    S +R
Sbjct: 310 GRQGS-ARKSSSRQNVGSAAPATTAGRRGSNKR 341


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 127/234 (54%), Gaps = 3/234 (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   R +V D +P+   RV  VGRLD  T G L+LTNDG  A  
Sbjct: 67  VYYILNKPRGIVSSANDDKDRESVVDLVPNDI-RVFPVGRLDRETTGALILTNDGDFAYY 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTV 191
           +  P     ++YRV   G++  +  N LK+GI I+G+ Y  ++++             ++
Sbjct: 126 MTHPKFDLSKIYRVSVRGRLSYEVTNSLKEGITIEGVEYKGVEISRVKYDAAKDKTQFSI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L EGKNR+I+K+F  F   V +L R   G   +  L  G  RE+    +++ L
Sbjct: 186 TLHEGKNRQIRKIFAHFGLPVLKLHRYQIGYLDIDELKIGQYRELKPFEVKKLL 239


>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 =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 129/236 (54%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KV+A AG+ASRR+ E++I +  V+VNG ++++    V + D IEVDGVPL++ 
Sbjct: 1   MEEERLQKVMAEAGVASRRKSEKLITEGHVRVNGKVIKQLGTKVTAHDKIEVDGVPLQR- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   +L +KP G++T+ SD   R TV D  P +  R+  VGRLD +T G +L+TNDG L
Sbjct: 60  EKMVYFLLNKPRGVITSVSDDKKRKTVMDFFPDVVERIYPVGRLDYDTSGAVLMTNDGTL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P  ++ + Y  +  G V+   L  L+ G+VI        +  L +   +   + 
Sbjct: 120 ANGLTHPKFKFEKTYTAKVKGIVNSLDLKKLENGLVIDHKKTAKAKAHLISTDDEKKTSI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V++ + EG+N ++K +F      V +L R SY    +  + +G  R +    +   
Sbjct: 180 VSLTIHEGRNHQVKNMFMAVGHPVQKLRRDSYSFLNIDGVQSGKWRALKVNEISRL 235


>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 =  271 bits (693), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 73/222 (32%), Positives = 118/222 (53%), Gaps = 2/222 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLY 78
           +A+ G+ASRR+ E +I Q RVKVNG  + +    V    D +EVDG  +    +    + 
Sbjct: 1   MAQCGVASRRKCEEIILQGRVKVNGKTVNQLGFKVDPEKDVVEVDGKRISLQMQKVYIML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP G++++  D  GR TV D +    + RV  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|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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/236 (34%), Positives = 126/236 (53%), Gaps = 2/236 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++ AG+ASRR  E  +   RV VNG             D I +DG P+R A   
Sbjct: 3   ERIQKILSAAGLASRRRAEEYLTAGRVTVNGRTAALGEKADPQRDDIRLDGKPVRPAGAH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G VTT SD  GR TV   +    +RV  VGRLD+++EGLLL+T+DG   + 
Sbjct: 63  TYLMLYKPRGYVTTLSDERGRRTVAQLVSGCGARVWPVGRLDLDSEGLLLMTDDGNFTQR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWVTVG 192
           L  PS Q  + Y V   G VD+  + +L   + + GI     ++ + +++G   A ++V 
Sbjct: 123 LIHPSHQVEKEYLVTVEGDVDRA-IPVLSGPMELDGIPLAPARIGVLSREGADRARLSVV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + EG+NR+++++      +V RL R+  G   LG L  G  R ++ + LR  LG  
Sbjct: 182 IHEGRNRQVRRMCALAGLEVKRLKRVREGGLALGRLRPGEWRRLTPQELRLALGER 237


>gi|288918462|ref|ZP_06412813.1| pseudouridine synthase [Frankia sp. EUN1f]
 gi|288350102|gb|EFC84328.1| pseudouridine synthase [Frankia sp. EUN1f]
          Length = 308

 Score =  270 bits (692), Expect = 2e-70,   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|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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 106/229 (46%), 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+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTVAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 115/329 (34%), Positives = 160/329 (48%), Gaps = 28/329 (8%)

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  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
            T    R+  Y+KP G + T  DP+GR TVFD LP    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-GTLLAGSTREV---SKKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLPLPKGLPRGGWAELPLNDINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V LDA   S   + R+R  + +       R  K   Q    +      
Sbjct: 242 EL----------VELDAETVSKLPVERERRRMKAN---QIRRAVKRHGQGGSAAAAA--- 285

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
              +RR+ ++N   +    S+    +  R
Sbjct: 286 --PNRRSGSANKGTSSTRGSAANKGTSNR 312


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 74/354 (20%), Positives = 135/354 (38%), Gaps = 20/354 (5%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRRE +R+I Q RV +NG +       V   D + VD  
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRREADRLIEQGRVTINGQVP-EMGTKVQLGDDVRVDDK 57

Query: 66  PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           P+  A ++      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ L
Sbjct: 58  PIAAATDKPVYIALNKPTGITCT-TERDIPGNIVDFV-GHKKRIFPIGRLDKPSDGLIFL 115

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +   +        + Y VR    +  D +  +  G+ I         VT +T+  
Sbjct: 116 TNDGDIVNKILRAGNSHEKEYVVRVDKPISDDFIKKMSSGVNILDTITLPCTVTKETKYS 175

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L +G NR+I+++ E   ++V +L R+      L  +  G  R +S   + E 
Sbjct: 176 ----FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRIMNISLDGIPNGQWRYLSDSEVTEI 231

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNII-----SEVPDDFTRMKKNSSQKNGLSKQK 299
           L     + +     + + +    +R   +        E  +   R  +      G +  +
Sbjct: 232 LA-MCEDSSGTEEASKMDNKGKRIRRATDAKLFDSREENQESKARRNQKQRTFKGRNADE 290

Query: 300 KLATPVHRRNLA----SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
               P  ++       S                          P      SL++
Sbjct: 291 FRHAPNSKKGRHGDKQSEFKGKPSGKGKSFHKPASDNGQRPSKPKSGGTLSLKK 344


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 111/328 (33%), Positives = 163/328 (49%), Gaps = 24/328 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAER 72
           +++ KV+ARAG  SRRE+E +I Q RV V+G +      V V     I +DG  L   E 
Sbjct: 28  EKLQKVLARAGHGSRREIETIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLLSITES 87

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL T D
Sbjct: 88  EEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTD 147

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++    +G N 
Sbjct: 148 GELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQGGEGLNQ 207

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K    LRE
Sbjct: 208 WYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATNYLRE 267

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                      V LD+   S   + +DR  + +       R  K  ++  G     +  +
Sbjct: 268 L----------VELDSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQVAGRQGS 314

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQR 331
              + +   NV  A    ++    S +R
Sbjct: 315 -ARKGSTRQNVGSAAPAATTNRRGSNKR 341


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 92/231 (39%), Positives = 141/231 (61%), Gaps = 5/231 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-RT 73
           R+ K +A  G+ SRRE E  I + RV +NG ++    V V   D + VDG  +     R 
Sbjct: 71  RLQKWLAEQGLCSRREGEVWIQEGRVSINGEVVTELGVKVAKRDRVAVDGQLVTPQRSRD 130

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP  ++ T SDP GR T+FD + +   SR+I+VGRLDIN+EGL++LT+DG LA 
Sbjct: 131 TAIILHKPKSIICTRSDPQGRRTIFDLIENHGSSRLITVGRLDINSEGLIILTSDGQLAH 190

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDT--QKGSNAWV 189
            L  PS +  RVYRV+ HG +   +L  ++  G+ ++    G +++ LD   ++G+N+W 
Sbjct: 191 GLMHPSREVPRVYRVKTHGILLASQLEQIRTVGVRLEDGPTGPLEIVLDRGREQGNNSWY 250

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T+ LREG+NRE++++F+ F  +V RL+R+ YG   LG L  G+ R V+   
Sbjct: 251 TITLREGRNREVRRIFDHFGLQVARLLRVGYGGISLGNLEPGAWRPVTVDE 301


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 115/233 (49%), Gaps = 9/233 (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  RLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP+G+  T   D +G    F N P+   R+  +GRLD +++GL++LTNDG +  
Sbjct: 60  EYLILNKPVGITCTTERDIEGNIIDFVNHPN---RIFPIGRLDKDSDGLIILTNDGDIVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     + +  +  +  G+ I G    +  V    ++  +    + 
Sbjct: 117 RILRAENNHDKEYIVTVDAPITETFIEGMAGGVDILGTTTKECVV----EQLESRTFRIV 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L +G NR+I+++ + F ++V RL R+     +LG L  G  R++++  ++   
Sbjct: 173 LTQGLNRQIRRMCKEFGYRVKRLQRVRIMNIELGDLPIGEWRDLTESEMKTLF 225


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 106/229 (46%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     +  D       G+ + G        TL+    +   V + +
Sbjct: 121 ITSPKHECDKTYLVTLEHPLADDTAEQFAHGVQLHGEKDLTKPATLEQLDAN--VVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAIELDEDLAPGEYRPLTEEEI 227


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 117/356 (32%), Positives = 173/356 (48%), Gaps = 38/356 (10%)

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----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLL 122
           ++ E T    R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLL
Sbjct: 65  KREEITGSVRRVLIYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLL 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDT 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 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +                   I S+E         +   P     MK+ + +K     Q+K
Sbjct: 245 V------------------DILSAE---------VGLAPQALPAMKEKTREKLDRL-QRK 276

Query: 301 LATPVHRRNLA--SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            A PV  R            G   +  S + +R++  +R+P  P K    R  + +
Sbjct: 277 SAKPVEVRGKRVLRPAKDEAGAEGARPSRAPRRDDGEQRAPRGPRKEGGERRESGR 332


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 97/349 (27%), Positives = 166/349 (47%), Gaps = 9/349 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 173 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 231

Query: 63  DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P++     +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 352 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 411

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK-KNSSQKNGLS 296
           +  +R+ +    L+    + +    +     R +P+ +       +R     +  +    
Sbjct: 412 EAQVRKLMATVGLKA--PSEEKGKRAGGQQERRQPDPMQTSMGFISREPVLTTHGQLDQP 469

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           ++             S         S + + SG R+ +  R+      +
Sbjct: 470 RRGGGRRGAPGLPGLSGYGSLPVAPSGYGNRSGGRDVDGNRASYGAGPK 518


>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 =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 115/254 (45%), Gaps = 22/254 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ + +ARAG+ASRR  E++I+  RV VNG  +      VM   DH+ VDG       
Sbjct: 24  TMRLQRFLARAGVASRRGSEKLISAGRVCVNGKQVRVLGTKVMPQYDHVTVDGKEYVLGN 83

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                L +KP  ++TT SDP G   V   +P   +  +  VGRLD +T G+LL T +G +
Sbjct: 84  DHVYLLLNKPSQVLTTMSDPFGFPCVASLVPCDDYPGLFPVGRLDSDTTGVLLFTTNGNM 143

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----- 185
              L  PS    + Y     G++   ++  L +GI+++        +   TQ        
Sbjct: 144 GNRLLHPSHHVWKTYVALIEGKLTSSQMQKLSQGIMLEDGMTSPCFIRTITQDEPCTHLD 203

Query: 186 --------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                         ++   + + EG+N ++K++ +     V +L R  +GP  L   +  
Sbjct: 204 KNHSLFDDMRLNAASSLCELKIHEGRNHQVKRMLQEIGHPVIKLHRFQFGPLCLNAQIPL 263

Query: 231 GSTREVSKKILREQ 244
           GS R  +++ + + 
Sbjct: 264 GSWRMCTQQEIHDL 277


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 60/229 (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+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKIYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNCVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 122/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K ++ +   P R++K ++ AG+ SRRE +  I +  VKVN +++      +   D +
Sbjct: 247 IKYKEVLADPNEPIRLNKFLSNAGVCSRREADEFIQKGAVKVNDVVVTELGTKITRQDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +  P++  E     + +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 307 TFNEKPVQ-IESKVYIVLNKPKNCVTTSDDPQERLTVMDLVKNACQERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  PS +  ++Y V     V  + +  +  G+ ++        ++ 
Sbjct: 366 GVLLLTNDGDLASKLTHPSFKKKKIYHVWLDKNVAIEDMEKIANGLELEDGEIHADAISY 425

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  G+NR ++++FE   + V +L R+ +       L  G  R ++++
Sbjct: 426 ASED-DKSQVGIEIHSGRNRIVRRIFESLGYHVTKLDRVYFAGLTKKNLGRGKWRYLNER 484

Query: 240 ILREQ 244
            +   
Sbjct: 485 EVNAL 489


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 78/363 (21%), Positives = 143/363 (39%), Gaps = 26/363 (7%)

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 ++      + D +     R+  +GRLD  ++G
Sbjct: 60  LIDDKPLRSKERPIYIALNKPTGITCT-TERHIEGNIVDFI-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 LREQLGPHLLEEAQVNLDAPIYSSE-----------------TLVRDRPNIISEVPDDFT 283
           + E     L+ ++    +A    +E                    R+      +    ++
Sbjct: 234 IGEI--NRLIAQSSGTEEASKVDAEGRKIAKATDAKLYDHRQQEARNEKRAQEKAFKTYS 291

Query: 284 RMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
              + + +  G  + ++       R         +  +    +D   +  N  R P+  S
Sbjct: 292 GTGEFTRRPGGQRQNRRNEEGGESRQQRGQGRNDRNSNGRNSNDRNGQGRNDNRRPARTS 351

Query: 344 KRS 346
            R 
Sbjct: 352 DRD 354


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 111/334 (33%), Positives = 166/334 (49%), Gaps = 24/334 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +     +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  
Sbjct: 29  KTKVVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHL 88

Query: 67  LRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           L   E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GL
Sbjct: 89  LSIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGL 148

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +T   
Sbjct: 149 LLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTITFQG 208

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
            +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K 
Sbjct: 209 GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKA 268

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LRE           V LD+   S  ++ +DR  + +       R  K  ++  G   
Sbjct: 269 TNYLREL----------VELDSETVSKLSVEKDRRRVKAN---QIRRAVKRHTEVAGRQV 315

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
             +  +   + +   NV  A    ++    S +R
Sbjct: 316 AGRQGS-ARKGSTRQNVGNAAPAAATGRRGSNKR 348


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 112/236 (47%), Gaps = 8/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVIY-QQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDSYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS--NAWV 189
            L  P     + Y     G  D++    +  G+ +  G      Q+ +  Q      + +
Sbjct: 121 QLLAPEYHVPKPYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ L   
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLAPGSYRPLTEEELAAL 236


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/235 (33%), Positives = 119/235 (50%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SR EV++ I    V VNG ++++    V    D +   G PL   E 
Sbjct: 5   MRLDKLLTELGTGSRSEVKKYIRSGLVTVNGEVVKKPEQRVDEKNDTVCFRGNPLTYTE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              +L+HKP G VT   D   R TV D L       +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 64  YEYYLFHKPAGCVTATEDNLHR-TVMDYLTDTARHDLFPVGRLDIDTEGLLLITNDGALA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVT 190
             L  P+    +VY  +  G+V ++ +NL + G+ I G         L+    G N+ + 
Sbjct: 123 HDLLSPAKHVSKVYYAKIDGRVTEEDVNLFENGVDI-GEEKPAKPALLEVLHSGDNSEIR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + + EG+  ++K++FE    KV  L R+  G   L   L  G  R ++++ L+E 
Sbjct: 182 LTITEGRFHQVKRMFEAVGKKVTYLKRVEMGSLVLPDELAPGEYRPLTEEELQEL 236


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 121/246 (49%), Gaps = 13/246 (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  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------------RVISVGRLDINT 118
                 L HKP G+VTT  DP GR TV D      S            R++ 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 KILREQ 244
           + +   
Sbjct: 314 EEITAL 319


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 98/331 (29%), Positives = 156/331 (47%), Gaps = 17/331 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--- 67
              QR+ K+++RAGIASRR+VE  IA  R+ VNG             D I VDG PL   
Sbjct: 1   MPAQRLQKLLSRAGIASRRQVENWIAAGRITVNGRPAVLGTRADPERDVIAVDGRPLADL 60

Query: 68  -RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLT 125
            ++  R R  + HKP G+VTT  DP GR +V D    +    +  VGRLD ++EGLLLLT
Sbjct: 61  RQRLARKRYVMLHKPRGMVTTLRDPQGRPSVGDFCRRAGLRGLHPVGRLDFDSEGLLLLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG L   L  P  +  +VY V   G ++  +L  L+ G+++           +   +  
Sbjct: 121 DDGELTFALTHPRHEVDKVYHVLVRGPLEPQRLRRLRDGVLLDDGPARARSARILRPRPG 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             WV V LREG+ R+++++     W V RL+R++ GP +LG L AG  R +S++      
Sbjct: 181 GGWVEVVLREGRKRQVRRMCRAVGWDVVRLVRVAVGPLRLGRLTAGQWRPLSRQE----- 235

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
               +E  +     PI+  E   R+     +       R     +     + + +  +  
Sbjct: 236 ----VEALRAAAGLPIHGDEPAPRE--GGAAPAITSRWRAASPRAGGGIAAGRAETGSAR 289

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHR 336
               + +    A G  +S    +G+++  +R
Sbjct: 290 TGGGVPATPGDA-GGKASGGRAAGRQQGRNR 319


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 111/229 (48%), Positives = 155/229 (67%), Gaps = 2/229 (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  RLWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNNGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            ELPS++  RVY VR +G  D   L    K + I GI Y    + L  +  +N+W+ V L
Sbjct: 121 FELPSSKLKRVYHVRAYGNPDP-LLKSNYKNLEIDGIFYNPQSIKLLRKNSTNSWLEVIL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EGKNREI+++FE F  KVN+LIR  YG F+L  L     REV+KK+ +
Sbjct: 180 FEGKNREIRRIFEHFGLKVNKLIRTEYGDFKLDNLKPNEYREVTKKLYK 228


>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 =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 86/239 (35%), Positives = 128/239 (53%), Gaps = 2/239 (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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+ +   L 
Sbjct: 344 LIEVVLHSGKNRIVRRLFDAVGFPVLRLVRVKVGPIGLGDQRQGSIRNLGKQEVGHLLA 402


>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 =  270 bits (691), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 90/331 (27%), Positives = 138/331 (41%), Gaps = 9/331 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ K +A AGIASRR+ E +I+  RV+VN   +      V    D + VDG  + +
Sbjct: 1   MAEERLQKFLAGAGIASRRKAEALISAGRVRVNQRTVTELGTKVDPGRDLVTVDGALVSQ 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G VTT SDP GR T  + L  +  R   VGRLD + EG LLLT+DG 
Sbjct: 61  PEQRSYYLLYKPSGCVTTASDPQGRPTAMEYLRGVPGRPFPVGRLDYDAEGALLLTDDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     RVY V+  G    + L  +K G+ ++      ++V +      N W+
Sbjct: 121 LANRLAHPRYGHQRVYLVKVKGDPPAEALERMKAGVRLEDGPARALEVAVHEHADRNVWI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG+   +K++ E    +V RL R  +G   +G L  G  R +  + +R       
Sbjct: 181 RVVVGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGRFRRLEPEEVRAL----- 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK-KLATPVHRR 308
               +V L++   +    VR+ P                +         +         R
Sbjct: 236 --RQRVGLESGTPARGPSVRELPKAARRHGHGPPAAPGAAPPPAEPDADEVGPRARGASR 293

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
                     G  +S  S   +      R  
Sbjct: 294 AGPRAAAPGPGGRASRPSRPSRPGRAGTRRR 324


>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 =  270 bits (691), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 60/229 (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+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>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 =  270 bits (691), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 127/236 (53%), Gaps = 3/236 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P  +  + Y  + +G+++ + L +L+ G+ I        +V +   K    N  V +
Sbjct: 122 ITHPKHKIRKTYVAKINGKLEDNHLRILRNGVRIDNYKTAKAEVNIVKNKNKSGNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGKNR+++++FE   ++V +L R S     L  L  G  R ++   ++  +  
Sbjct: 182 TIHEGKNRQVRRMFEALGYEVMKLKRESIEDLTLEGLKKGEYRTLTIHEVKRLINK 237


>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 =  270 bits (691), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 74/313 (23%), Positives = 138/313 (44%), Gaps = 17/313 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I QQR+ +NG +       V   D + VDG PL+  +   
Sbjct: 10  RLNKYISDTGYCSRREADKLIDQQRITINGNVP-EMGTKVAEGDDVLVDGKPLKAKQERI 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              ++KP+G+  T S+      + D + +   R+  +GRLD  ++GL+ LT+DG +   +
Sbjct: 69  YIAFNKPVGITCT-SERHVEGNIIDYI-NHEQRIFPIGRLDKPSDGLIFLTSDGDIVNKI 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  D L  +  G+ I        QV     + S     + L 
Sbjct: 127 LRAGNAHEKEYVVRVDKPITDDFLAQMAAGVPILDTVTLPCQVK----QESRFVFRITLT 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E+ +++V +L R+      LGTL +G  R ++   + EQ+   +   ++
Sbjct: 183 QGLNRQIRRMCEYLDYEVFKLKRVRIMNIDLGTLASGEWRYLTASEM-EQINNMIGTSSK 241

Query: 255 V--------NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                     +D  I + +     R +  +       R +           Q++      
Sbjct: 242 TEEASRKVKEVDGKIRTIKKASSGRNHHSNNTFSQKRREESKDRGFGKSYSQRRDEGKDQ 301

Query: 307 RRNLAS-NVWMAK 318
            +  ++  VW AK
Sbjct: 302 DKPQSTIKVWRAK 314


>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 =  270 bits (691), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 95/241 (39%), Positives = 140/241 (58%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG   +    +   +D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIDNGWVQVNGKPAK-LGDSAGPSDKISVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G V++  DP    TVFDNLP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKGKQNIRVLLYHKPVGEVSSRHDPKFEKTVFDNLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ LN L KG+++        ++     +G+
Sbjct: 120 NNGELANQLMHPKYGLEREYAVRVHGQVSQESLNNLLKGVMLDDGLGKFTKIQFRGGEGT 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + E 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLSRGQFYELTPKEVTEF 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 75/237 (31%), Positives = 119/237 (50%), Gaps = 2/237 (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 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y V   G +  +    L + G+ +        Q ++        
Sbjct: 136 ELSQHVMHPRYEVAKTYVVTLDGHLSGNVCRRLVRTGVQLDDGWIKLDQCSIIDANRETT 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S   +R  
Sbjct: 196 IVKVVLHSGKNRIVRRIFGAIGFPVRRLVRTQIGPIKLGDLKPGSYRVLSDAEVRSL 252


>gi|220912302|ref|YP_002487611.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859180|gb|ACL39522.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
          Length = 403

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/241 (36%), Positives = 128/241 (53%), Gaps = 4/241 (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  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLT 125
             E     +++KP G+V+T  DPDGR  + D L +      R+  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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +  + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+ +   L
Sbjct: 339 HVLIEVVLHSGKNRIVRRMFDAVGFPVQRLVRVKVGPIGLGDQRQGSIRNLGKQEVGHLL 398

Query: 246 G 246
            
Sbjct: 399 A 399


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 109/363 (30%), Positives = 170/363 (46%), Gaps = 30/363 (8%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++++     TP   +++ KV+AR G+ SRR+VE  I+Q R+KVNG+        V   
Sbjct: 1   MSEQDLQNTEITPPAGEKLQKVLARIGVGSRRDVEAWISQGRIKVNGVEAT-LGQRVDLH 59

Query: 58  DHIEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVG 112
           D I VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 GDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLA 230
               +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  
Sbjct: 180 KFTDIQKAPGGEGFNHWYHCVVMEGRNREVRRLWESQGMVVSRLKRVRFGPVFLNSDLPM 239

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  RE+++  +        L+   +                P +  +  D   R+++ S+
Sbjct: 240 GRWREMTQGEIDILAAEVGLQPVAL----------------PAMNLKAKDKMERLQRKST 283

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +  G S++ +   P      A                  +      R PS   KR  +  
Sbjct: 284 RPMGRSERVRSLRPAQEAAAAERPARQP--REEAPRKGSRGSAVAER-PSEMRKRPAKTD 340

Query: 351 SAK 353
             K
Sbjct: 341 GDK 343


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 146/342 (42%), Positives = 203/342 (59%), Gaps = 15/342 (4%)

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 EEAQVNLDAPIYSSETLVRDRPNII---------SEVPDDFTRMKKNSS---QKNGLSKQ 298
           E A V+   P   + T   + P             +   D  R +++S    +  G  + 
Sbjct: 265 EAAAVDFVGPAGDALTPPPEEPAPRPPRQKSLRNQKAFRDEERPRRDSGPFRKAEGGGRP 324

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                   RR      +       +  +   ++  +  R+ +
Sbjct: 325 AGAGLLARRRGPDPAAFDPAQPRKNKPAPGPRKHISSLRAEA 366


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 101/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L     R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGGITLDADLAPSEYRPLTEEEI 227


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 107/229 (46%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D   L  KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAALFAKGVQLNNEKDLTKPAQLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R +++  +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGAIELDPELAPGEYRPLTEDEI 227


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 119/375 (31%), Positives = 177/375 (47%), Gaps = 36/375 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRD-RPNIIS 276
           RE+S+     L  ++G   + + Q+N                P+   E +VR  RP   +
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------ 330
               D T       Q  G  + +       +R +  +     G  +   +D+ +      
Sbjct: 303 PATGDRT---PRQPQITGSERDRPRGGDSTQRPVRKDSGK-PGSRAPRPADNSRGTPVAE 358

Query: 331 REENHRRSPSFPSKR 345
           R  +  + P+ P  +
Sbjct: 359 RPSDMNKRPAKPGPK 373


>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 =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/250 (34%), Positives = 126/250 (50%), Gaps = 14/250 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
            + +R+ K++A+ GIASRR+ E+MI   RV +NG             D I+VDG  L+  
Sbjct: 2   DSGERLQKILAQWGIASRRQAEQMILDGRVWLNGEPATLGQKADPHCDRIQVDGRTLQSD 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTND 127
                  L +KP G+++T SDP GR T+ D LP  +  +    VGRLD  T G LL+TND
Sbjct: 62  RPDLLYLLLYKPTGVISTCSDPQGRPTILDLLPPHYRNLGLHPVGRLDSETTGALLITND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P  Q  +VY+V   G   +  L   + G+++ G      QV L  +    +
Sbjct: 122 GWLTHALTHPCHQVSKVYQVWVSGHPPESVLQQWRDGVMLAGRLTLPAQVRLLERTEIPS 181

Query: 188 ---WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSK- 238
               + V L EG+NR+I++V +   + V  L R   GP QL      TL  G  R ++  
Sbjct: 182 ALTCLEVILWEGRNRQIRRVAKKLGYPVVHLHRTGIGPVQLQATDQPTLAKGHYRHLTPG 241

Query: 239 --KILREQLG 246
             + LREQ+G
Sbjct: 242 ELEALREQVG 251


>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 =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 103/230 (44%), 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   MRLDKYLCDALGATRKEATKIIKSGDVTVNDIVQKSGAVKVTDDCIVEWQGREIQKP-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  +  KP G V +H D   ++            +   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLFKPDGFVCSHEDGFNQTAFMLLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 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|282860273|ref|ZP_06269343.1| pseudouridylate synthase [Prevotella bivia JCVIHMP010]
 gi|282586947|gb|EFB92182.1| pseudouridylate synthase [Prevotella bivia JCVIHMP010]
          Length = 555

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 116/243 (47%), Gaps = 3/243 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I   +V VNG ++      ++ TD +
Sbjct: 307 IEYKEEHIDPTEPLRLNKFLANAGVCSRREADDFILAGQVTVNGEVINELGTKILRTDEV 366

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 367 KFQDKLVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDACPERIYPVGRLDRNTT 425

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL TNDG LA  L  P     +VY V     +  ++L  +  GI ++        +  
Sbjct: 426 GVLLFTNDGDLASKLTHPKFLKKKVYHVFLDKPITANELQKISDGIELEDGEIKADAIEY 485

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +   A V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 486 ANPE-DQAQVGIEIHSGKNRIVRRIFESLGYRVVKLDRVMFAGLTKKNVRRGDWRFLTEK 544

Query: 240 ILR 242
            + 
Sbjct: 545 EVE 547


>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 =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 5   IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  KFHEEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 124 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +++ 
Sbjct: 184 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLTEA 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>gi|158320760|ref|YP_001513267.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140959|gb|ABW19271.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 228

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 117/232 (50%), Gaps = 7/232 (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 ++   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-TEKHVKGNIVDFV-HHKERIFPIGRLDKDSQGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  + +  +  G+ I G      +VT    K ++    + L
Sbjct: 118 ILRAENNHEKEYIVTVNKPITPEFIKGMSSGVKILGTKTKPCKVT----KINDTVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ + F +KV +L RI     +L  L  G  R+++K+ L   +
Sbjct: 174 TQGLNRQIRRMCQVFGYKVVKLQRIRIMNVKLKGLEIGQWRDLTKEELEGLI 225


>gi|227325901|ref|ZP_03829925.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 231

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 111/229 (48%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     + +D       G+ +          TL+  K ++  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPATLE--KITDYVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGIYLDSELEPGEYRELSAEEI 227


>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 =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 105/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V +D      +G+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVAEDTAEQFARGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGAIKLDDDLEPGEYRPLTEEEI 227


>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 =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 125/233 (53%), Gaps = 1/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           N    R+ KV+A AG+ SRR  E +IA  RV+V+G ++E   + V   T  IEVDG  + 
Sbjct: 7   NAEGVRLQKVLAAAGVGSRRHSEELIAAGRVRVDGRVVETQGMRVDPQTAIIEVDGERVV 66

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP+G+++  SD  GR TV D +      +  VGRLD+++EGLLL+TNDG
Sbjct: 67  TRAGLVHLALNKPVGVLSAMSDDRGRPTVADLVTDAGPGLFHVGRLDVDSEGLLLVTNDG 126

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  + Y V   G V +D    L++G+ +         V +    GS   
Sbjct: 127 ELAHRLSHPSFEVAKTYLVEVAGPVGRDVPRRLREGVELADGPVRADAVRIVGSAGSRVM 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + L EG+NR ++++ E  +  V RL+R   GP  LG+L  G TR +S+  +
Sbjct: 187 LEITLHEGRNRVVRRLMEAVDHPVRRLVRTRIGPVHLGSLRVGRTRHLSRGEV 239


>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 =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 115/242 (47%), Gaps = 9/242 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K    EN    R++K I+  GI SRRE + +I ++RV +NGI        V STD +++
Sbjct: 4   NKINHNENSDSMRINKFISEKGICSRREADTLIQEKRVTINGITA-ELGSRVKSTDEVKL 62

Query: 63  DGVPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           DG  L + E+        +KP+G++ T ++   ++ + D + +   R+  +GRLD ++EG
Sbjct: 63  DGKLLTEKEKDDKVYIALNKPVGIICT-TEKKIKNNIVDFV-NYPKRIFHIGRLDKDSEG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ LTNDG +   +        + Y V     +    L  +  G+ I        +V   
Sbjct: 121 LIFLTNDGDIVNKILRAGNNHEKEYIVTVDKCITNSFLKEMASGVSILNTVTKPCKVY-- 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K  +    + L +G NR+I+++ E   + V +L RI      L  +  G  R +S   
Sbjct: 179 --KEGSHIFRIILTQGLNRQIRRMCEALGYNVLKLKRIRIMNVTLKDIPVGKWRYLSPSE 236

Query: 241 LR 242
           L+
Sbjct: 237 LK 238


>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 =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 120/239 (50%), Gaps = 2/239 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V + L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R  
Sbjct: 220 TTMVKIVLHSGKNRIVRRIFGAVGFPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVRSL 278


>gi|213859463|ref|ZP_03385167.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 231

 Score =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 60/229 (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+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNRKSLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>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 =  269 bits (689), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 143/350 (40%), Positives = 191/350 (54%), Gaps = 13/350 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R++K +ARAGIASRREVER+I   +V VNG +L   AV V   D I VDG P+  A+ 
Sbjct: 80  TERIAKAMARAGIASRREVERLIGLGKVAVNGRILATPAVLVTRDDKITVDGKPIGAAQA 139

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+W YHKP GL+T+H+DP GR TVFD LPS   RVISVGRLD+ TEGLLLLTNDG L+R
Sbjct: 140 TRVWRYHKPAGLITSHNDPAGRPTVFDALPSGLPRVISVGRLDLATEGLLLLTNDGELSR 199

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------- 185
            LELP T  +R YR R  G++ Q++L+ LK G+V+ G+ YG ++ T+D  K         
Sbjct: 200 ALELPETALVRQYRARARGRITQEQLDKLKDGVVVDGVRYGPVEATIDKAKEKTEGEKSS 259

Query: 186 -NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            N W++V + EGKNRE++KV E     VNRLIR++YGPFQLGTL  GS  EV  +++RE 
Sbjct: 260 ANLWLSVSITEGKNREVRKVLESIGLTVNRLIRLAYGPFQLGTLPVGSVEEVGPRVIREM 319

Query: 245 LGPHLLEE-----AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           L  H+  E       V    PI    T              D +R           ++  
Sbjct: 320 LAEHIRPENLPTGNTVATPTPIPGRRTGTPIVRGKSGSAMSDPSRKPSRVRAAETAAEDG 379

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
                  R+   +          +F   +   ++        P +    R
Sbjct: 380 AEFGKPARKEGWAKAKPKFEHKKTFKPRARPGDDEGTEGGDRPRRPFTPR 429


>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 =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 126/247 (51%), Gaps = 16/247 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----------------GICYGDMQV 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 KKILREQ 244
           +  +R  
Sbjct: 241 EDEVRSL 247


>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 =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 119/375 (31%), Positives = 176/375 (46%), Gaps = 36/375 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRD-RPNIIS 276
           RE+S+     L  ++G   + + Q+N                P+   E +VR  RP   +
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------ 330
               D T       Q  G  + +       +R    +     G  +   +D+ +      
Sbjct: 303 PATGDRT---PRQPQITGSERDRPRGGDSTQRPARKDSGK-PGSRAPRPADNSRGTPVAE 358

Query: 331 REENHRRSPSFPSKR 345
           R  +  + P+ P  +
Sbjct: 359 RPSDMNKRPAKPGPK 373


>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 =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 127/234 (54%), Gaps = 6/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
              +R+ KV+A   I +R+EV+ ++ Q+ + V+G++     ++V      I VDG PL  
Sbjct: 1   MKRERLDKVLANMAIGTRKEVKALVKQRLIVVDGVVATDPGMHVIAEEQEILVDGEPLNF 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            +R    L +KP G+V+   D +   TV D LP  ++ +V  VGRLDI+TEGLLLLTNDG
Sbjct: 61  -KRWVYVLLNKPPGVVSATED-NVHETVVDLLPYEWAIKVHPVGRLDIDTEGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L+  L  P  +  + Y  R  G+V +  +    KG+ ++       ++ + +  G  + 
Sbjct: 119 HLSHSLLSPKKKVDKEYFARIEGRVTERHVQEFAKGVELEDFTTLPAKLEIIS-SGETSE 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + EGK  ++K++F  F+  V  L RI  GP  L  +L  G  RE++++ L
Sbjct: 178 IRVTIMEGKFHQVKRMFAAFDLHVVYLQRIRMGPLHLDPSLAPGEYRELTEEEL 231


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 83/236 (35%), Positives = 123/236 (52%), Gaps = 1/236 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T +R+ K+IA AG+ SRR+ E ++ QQRV+VNG ++          D I VDG PLR  
Sbjct: 1   MTGERLQKLIAAAGLCSRRKAEELLRQQRVRVNGQIVALGDRADPEQDRICVDGRPLRAP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
           E TRL L +KP+G++++  DP GR TV D +P+   R +  +GRLD ++ G LLLTN G 
Sbjct: 61  EATRLLLLNKPVGVISSCYDPRGRRTVLDLIPNHLRRGLHPIGRLDADSRGALLLTNRGQ 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G      L   + G+ + G       V    ++G    +
Sbjct: 121 LTLRLSHPRYAHSKTYRVWLEGDPSPQHLQSWRDGVWLDGQRTQPATVQRLRREGGRTLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V L+EG+NR+I++  +     V  L RI+     LG+L  G  R + +   R  +
Sbjct: 181 EVTLQEGRNRQIRRTADQLGHPVLDLQRIAIAGIPLGSLAEGEWRALHRGEWRHLM 236


>gi|325684334|gb|EGD26503.1| ribosomal small subunit pseudouridine synthase A [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 241

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 112/236 (47%), Gaps = 8/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + SR +V  +I   +V VNG +   A   V     + V+G  +   ++  
Sbjct: 3   RLDKFLANMKVGSRSQVHEIIKAGQVTVNGKVCRSAKQKVKEDAEVLVNGQAVIY-QQYH 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L +KP G+++   D   + TV D L     + ++  VGRLD +T GLLLLTNDG LA 
Sbjct: 62  YFLLNKPAGVLSATEDSR-QKTVLDLLKDQDRYQKIAPVGRLDKDTTGLLLLTNDGQLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS--NAWV 189
            L  P     + Y     G  D++    +  G+ +  G      Q+ +  Q      + +
Sbjct: 121 QLLAPEYHVPKTYYALLAGVADEETAKAIAAGLTLKDGTELKPGQLKILRQDKDQEQSEI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++F     KV +L R+S GP  L   L  GS R ++++ +   
Sbjct: 181 EITITEGKYHQVKRMFASQGMKVLKLKRLSMGPLTLPADLALGSYRPLTEEEMAAL 236


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 81/241 (33%), Positives = 123/241 (51%), Gaps = 2/241 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 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 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKG 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 L 245
           L
Sbjct: 241 L 241


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 127/233 (54%), Gaps = 3/233 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ + 
Sbjct: 1   MAEERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIER- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L++KP G+++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG L
Sbjct: 60  ESHHTYLFYKPRGVISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A +L  P  +  +VY  +  G +  D++  LKKG+ I        QV +           
Sbjct: 120 ANLLMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPAQVKVLKTNPRAQTQI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + + EG   ++K++F+  N  V++L R  Y    L  L +G  RE++ K +
Sbjct: 180 VQLTIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNHKEV 232


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 99/350 (28%), Positives = 168/350 (48%), Gaps = 15/350 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
            ++  V +     R+ K +A  G+ SRR  E  I   RV V+G ++      +   T  I
Sbjct: 11  PEEPSVDDESHLIRLQKFLAATGLGSRRHCEEYIETGRVSVDGDVITELGAKIDPETQFI 70

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           EVDG  +R   R R +L +KP G + T++DP GR  V D  P+   R+ +VGRLD N+EG
Sbjct: 71  EVDGERVRLQPR-RYYLLNKPSGFLCTNNDPAGRRRVVDLFPNDGQRLFTVGRLDENSEG 129

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+L+TNDG LA+ L  P  +  R Y V+  G   ++KL+ L+KG+  +   +    +   
Sbjct: 130 LILVTNDGELAQRLAHPRYRVARTYHVQVVGNPPREKLDELRKGVRFKEGVFRVSGLKYL 189

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++G +A++ + L EG+NREI+++      KV +L+RI +GP  LG L  G +R +S   
Sbjct: 190 KKQGKSAFLELTLHEGQNREIRRMMARIGHKVIQLVRIRFGPLNLGKLKTGESRRLSDTE 249

Query: 241 ---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LR+ L      + +        +       R ++     +      K+ S++    K
Sbjct: 250 LKKLRQLLNEKHSPDIRHRKGKKNAAPAKTRAPRKSVGKRSGERGAAAGKSVSERISGGK 309

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR---EENHRRSPSFPSK 344
           +        +R++++         SS    +G+R   +   +R+     K
Sbjct: 310 KTGG-----KRSVST--GRKPAADSSKPKTTGRRIIGDVAEKRTRQGKRK 352


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 116/374 (31%), Positives = 172/374 (45%), Gaps = 33/374 (8%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRP--AAG 300

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------R 331
            P           Q  G  + +       +R          G  +   +D+ +      R
Sbjct: 301 APATGGERAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAER 360

Query: 332 EENHRRSPSFPSKR 345
             +  + P+ P  +
Sbjct: 361 PSDMNKRPAKPGPK 374


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 128/233 (54%), Gaps = 3/233 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ + 
Sbjct: 1   MAEERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIER- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L++KP G+++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG L
Sbjct: 60  ESHHTYLFYKPRGVISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A +L  P  +  +VY  +  G +  D++  LKKG+ I        QV +           
Sbjct: 120 ANLLMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPAQVKVLKTNPRAQTQI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + + EG   ++K++F+  N  V++L R  Y    L  L +G  RE+++K +
Sbjct: 180 VQLTIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNRKEV 232


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 112/242 (46%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 83  IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEV 142

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 143 KFHDQAVS-IERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTT 201

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI +         ++ 
Sbjct: 202 GVLLLTNDGDLASKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIQADAISY 261

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 262 -TDDFKKDEVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 320

Query: 240 IL 241
            +
Sbjct: 321 EV 322


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 119/231 (51%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++  GI +R+EV  +I   RV VN   +   A  +   D ++VDG  +   E+ 
Sbjct: 1   MRLDRYLSNRGIGTRKEVRALIKHGRVTVNDRTVLDPAYKLSDKDVVKVDGKVIDLPEK- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP G VT+  DP    T+ + LP     +  VGRLD + EGLLL+TNDG  A  
Sbjct: 60  VYILFYKPAGYVTSTRDP-HSETIMEFLPD-IKGIFPVGRLDKDAEGLLLVTNDGEFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+  G++ +DKL  L++G+ ++   +   +     +K SN  V + +
Sbjct: 118 VISPRWKVEKEYVVKVEGEITEDKLEKLRRGVSLRDGFFAKAK---HVEKISNDTVKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            EGK  ++K++      K   L R+  G  +L   +  G  R +S++ +R+
Sbjct: 175 TEGKYHQVKRMMAAVGLKTIHLKRVRIGGLRLPQEMKPGEYRFLSEEEVRQ 225


>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 =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 98/246 (39%), Positives = 140/246 (56%), Gaps = 7/246 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ K++AR G+ SRRE+E  I   RV+VNG+  +     V   D + +DG P+      
Sbjct: 3   ERLQKILARGGLGSRREIEAWIKAGRVRVNGVPAQ-LGDKVSVKDRVTIDGRPISPKRLQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
              +++ +YHKP G V +  DP+GR  VF +LP     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 HLLEEA 253
             +E  
Sbjct: 242 AGMEPR 247


>gi|262091731|gb|ACY25320.1| ribosomal large subunit pseudouridine synthase B [uncultured
           actinobacterium]
          Length = 240

 Score =  269 bits (688), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 118/236 (50%), Gaps = 10/236 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 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+   RV  VGRLD ++EGLLL+TNDG 
Sbjct: 62  RPDLVYYLLNKPVDVISTAIDTHDRETVVDFVPAD-PRVYPVGRLDGDSEGLLLITNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHG---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 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|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 =  269 bits (688), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 76/232 (32%), Positives = 129/232 (55%), Gaps = 6/232 (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 + +P    R+  VGRLD ++ GL+LLTNDG LA  
Sbjct: 61  VVYALHKPAGVVSTAADTHGRRTVTELVPQG-RRLYPVGRLDADSTGLILLTNDGELANR 119

Query: 134 LELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + YR    G  +    L  L++G+ ++       +V    ++ S   + + 
Sbjct: 120 LTHPRFEVPKTYRATVGGPQIGDRTLRQLREGVRLEDGMTAPARV----RRLSAHVLELT 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + EG+ R+++++ E     V  L+R  +GP  LG L  G +R ++ + +RE 
Sbjct: 176 IHEGRKRQVRRMCEEVGHPVKSLVRTQFGPLSLGDLGTGRSRRLTAREVREL 227


>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 =  269 bits (688), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 110/318 (34%), Positives = 158/318 (49%), Gaps = 25/318 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL 67
           +    +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  L
Sbjct: 27  DKIVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLL 86

Query: 68  RKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
              E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLL
Sbjct: 87  SIKESEETVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLL 146

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +     
Sbjct: 147 LFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTIKFQGG 206

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK-- 239
           +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K  
Sbjct: 207 EGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKAT 266

Query: 240 -ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS-- 296
             LRE           V LD+   S   + +DR  + +       R  K  S+  G    
Sbjct: 267 NYLREL----------VELDSETVSKMPVEKDRRRVKAN---QIRRAVKRHSEVAGRQVA 313

Query: 297 KQKKLATPVHRRNLASNV 314
            ++  A     R   SN 
Sbjct: 314 GRQGSARKSSTRQNVSNA 331


>gi|291166791|gb|EFE28837.1| ribosomal large subunit pseudouridine synthase B [Filifactor alocis
           ATCC 35896]
          Length = 242

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 119/230 (51%), 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+  ++  SD  GR+TV +       R+  VGRLD  + GLLLLTNDG LA 
Sbjct: 61  KVYYMLNKPLRYISAVSDDRGRNTVLELF-RTKERIYPVGRLDYLSTGLLLLTNDGELAN 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|227112086|ref|ZP_03825742.1| 16S rRNA pseudouridylate synthase A [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 231

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 111/229 (48%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     + +D       G+ +          TL+  K ++  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPATLE--KITDYVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGIYLDSELEPGEYRELSAEEI 227


>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 =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 81/282 (28%), Positives = 131/282 (46%), Gaps = 3/282 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ +V+A  G+ASRR+ E +I   RV V+G ++    V V      I VDG  LR  ER
Sbjct: 2   ERLQRVLAAHGVASRRKAEELITAGRVTVDGQVVRELGVRVDPERQEIRVDGKRLR-PER 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + +KP G +TT SD  GR TV D +  +  RV+  GRLD  T GLLLLTNDG L  
Sbjct: 61  RRYIMLNKPPGYITTVSDERGRRTVMDLV-QVPERVVPAGRLDRPTAGLLLLTNDGDLLF 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 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           A      P     +   +R              +   S    
Sbjct: 240 ASAGRPLPEPGRRSDPGERRGEPRRSGPTRRGERPAPSGARP 281


>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 =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 120/244 (49%), Gaps = 6/244 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           + ++ +  R++K IA+ G+ SRR  + ++   RV VNG   +   + V    DH+ VDG 
Sbjct: 1   MSDDSSLMRLNKFIAQCGVTSRRGADDLVFGGRVAVNGEKADSPGIKVDPARDHVTVDGR 60

Query: 66  PLRKAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--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 LREQ 244
           L   
Sbjct: 241 LTAL 244


>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 =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 112/230 (48%), Positives = 150/230 (65%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            PQR++K++ARAG+ASRREVERMI + R+ +NG  +   A  + S   + VDG P+    
Sbjct: 64  EPQRIAKLLARAGVASRREVERMIEEGRITLNGEAVSTPATLLSSLHGVAVDGNPVAAPA 123

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RL+L+HKP G +TT  DP GR T++D LP    RV+ +GRLD+ TEGLLLLT DG   
Sbjct: 124 PARLFLFHKPSGFLTTERDPRGRPTIYDKLPPDLPRVMPIGRLDMMTEGLLLLTTDGEFK 183

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R +ELPST   R YR R  G+V Q++L  L  G+ I GI YG ++  L+ + G N W+ +
Sbjct: 184 RQMELPSTGVPRTYRARAFGEVSQNQLEDLFDGLEIDGIRYGRIEANLERRTGRNQWIEM 243

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EGKNRE+++V E    +VNRLIR SYGPF LG L +G+  EV +  L
Sbjct: 244 TLTEGKNREVRRVLEHLGLQVNRLIRTSYGPFHLGELASGAVEEVRQHDL 293


>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 =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 78/281 (27%), Positives = 147/281 (52%), Gaps = 10/281 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++ AG+ SRRE +R+I ++RV V+G    +  + V     I+VDG  +++ E+ 
Sbjct: 1   MRLNKYLSDAGVCSRREADRLIEEKRVLVDGKPAVQ-GMQVEDFQEIKVDGKAIKREEKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L ++HKP G+  T + P+ +  V   + +   RV   GRLD ++EGLLLLTN G L   
Sbjct: 60  VLLVFHKPKGIECTAN-PNVKKNVISYI-NYPIRVYYAGRLDKDSEGLLLLTNQGELVNQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +    +   + Y V     V ++ L  +++G+ + G      +V  +++K       + L
Sbjct: 118 IMKAGSYHEKEYLVTVDKPVTEEFLQSMREGVPVLGTITRKCKVEKESEK----VFRITL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++  +  ++V +L RI     +LG L  GS RE +K+ L ++L   + E+A
Sbjct: 174 TQGLNRQIRRMCNYLGYEVVKLKRIRIMNIELGNLPIGSYREATKEEL-DELKRQISEKA 232

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           +   +   +  +  V++     +  P    + K+  + +NG
Sbjct: 233 EKRQETDFHKGKKPVKNAGKYRN--PSKVRKQKRQEASRNG 271


>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 =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 85/235 (36%), Positives = 125/235 (53%), Gaps = 3/235 (1%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L +    RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 84  LVYLAMNKPRGVVSTMADEKGRTAIGDFLGNRVEQRVYHVGRLDADSEGLLLLTNDGTLA 143

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y     G + +     L  G+ +  G    D    +DT  G  A V 
Sbjct: 144 HRLMHPSYGVPKTYLCEVSGPIPRSLGRRLAAGVELTDGPATVDAFRVVDTL-GKTAQVE 202

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V L EG+   ++++F+     V+RL+R S GP +LG L AG TR ++   +    
Sbjct: 203 VTLHEGRKHIVRRLFDAVGHPVSRLVRTSIGPIRLGDLRAGRTRRLTNAEVAALF 257


>gi|330980378|gb|EGH78489.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 408

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 116/365 (31%), Positives = 170/365 (46%), Gaps = 42/365 (11%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 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   + +                   P + ++  D   R+++ SS
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQ-------------------PQMNAKTKDKMERLQRQSS 283

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS--KRSLR 348
           +  G  ++ +   P            A            Q   + R  P      +R  R
Sbjct: 284 RPLGKGERVRTLRPAAG---------APATGGERAPRQPQITGSERDRPRGGDSTQRPSR 334

Query: 349 RTSAK 353
           + S K
Sbjct: 335 KDSGK 339


>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 =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 105/353 (29%), Positives = 161/353 (45%), Gaps = 28/353 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K+  +     +++ KV+AR G+ SRR+VE  IA  R+KVNG       + V   D I
Sbjct: 4   INQKDDQEIGPAGEKLQKVLARIGVGSRRDVESWIAAGRIKVNGKDAT-LGLRVDMHDAI 62

Query: 61  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRW 242

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           RE+S+  +                D             P + ++  D   RM++ SS+  
Sbjct: 243 REMSQYEV----------------DVLSAEVGLTPVAMPQLNAKSKDKLDRMQRKSSRPM 286

Query: 294 GLSKQKKLATP---VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
             +++ +   P            V     I             +  R P  P 
Sbjct: 287 ARTERVRTLRPANGAPIGAGPRPV-REPQIEGERPGRKPAARPDGERGPRSPR 338


>gi|330866214|gb|EGH00923.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 408

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 114/371 (30%), Positives = 167/371 (45%), 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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA----------PIYSSETLVRDRPNIISEVPD 280
           RE+S+     L  ++G   + + Q+N             P        R R    +    
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQPSRPLGKGERVRTLRPAAGAP 302

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------REEN 334
                     Q  G  + +       +R          G  +   +D+ +      R   
Sbjct: 303 ATGDRAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAERPSE 362

Query: 335 HRRSPSFPSKR 345
             + P+ P  +
Sbjct: 363 MNKRPAKPGPK 373


>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 =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D     K G+ + G        TL+    +   V + +
Sbjct: 131 ITAPKHHCEKTYVVTLEQPIATDVAEKFKTGVQLNGEKELTKPATLEV--ITPTEVKLTI 188

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 189 SEGKYHQVKRMFAAVGNHVVALHRERIGDITLDDALAPGEYRPLTEEEI 237


>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 =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 82/238 (34%), Positives = 126/238 (52%), Gaps = 10/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ GIASRR  E+MIA  +V++NG  +         TD IEVDG P+   +R 
Sbjct: 3   ERVQKILSQWGIASRRRAEKMIAAGQVRLNGTTVHLGQKADPETDVIEVDGKPINPYQRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +    L +KP G+V+T  D   R TV D LP   ++   +  VGRLD ++ G LLLTNDG
Sbjct: 63  QSIYLLLNKPAGVVSTCRDSRNRPTVIDLLPDKLTKGQGIHPVGRLDADSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y+V   G   +  L   ++G+ + G      QV +  +KG +  
Sbjct: 123 ELTFRLTHPSHHIPKTYQVWVRGNPPESVLQTWREGVNLLGKKTLPAQVRVLKRKGQSTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
           + V L EG+NR+I++V +  ++ V  L R + GP +L       L  G  R ++   +
Sbjct: 183 LEVVLTEGRNRQIRRVAQLLSYPVIHLHRTAIGPIKLNLPGEPILPCGDYRALNDVEV 240


>gi|309810348|ref|ZP_07704183.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
 gi|308435661|gb|EFP59458.1| pseudouridylate synthase [Dermacoccus sp. Ellin185]
          Length = 303

 Score =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 77/228 (33%), Positives = 122/228 (53%), Gaps = 1/228 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ SRR  E +IA+ RV+V+G ++      +   +  I VDG  ++  +  
Sbjct: 67  RLQKVLAQAGVGSRRHCENLIAEGRVEVDGQVVTELGTRIDPESAVIHVDGDRIQLDDTL 126

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP G+V+T  D +GR  V + L     R+  VGRLD +TEGLLLLTNDG LA  
Sbjct: 127 VYLAFNKPTGVVSTMQDEEGRPCVGEYLEGRTERLFHVGRLDYDTEGLLLLTNDGNLANR 186

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L+ P     +VY     G V +D    +++GI ++          +   +   A V + L
Sbjct: 187 LQHPRYGVEKVYLATIPGPVPRDLGKRMREGIELEDGPAAVDSFKVVDSQPGMALVEIVL 246

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR ++++FE     V  L R   GP ++G L  G  R ++K+ +
Sbjct: 247 HEGRNRIVRRMFEEVGHPVIALARPQVGPVKVGDLRPGKMRPLNKREV 294


>gi|308272550|emb|CBX29154.1| Ribosomal large subunit pseudouridine synthase F [uncultured
           Desulfobacterium sp.]
          Length = 235

 Score =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 117/233 (50%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++ AG  SRR+ E+ I    VKVNG+++      V    D +EVDG  +   + 
Sbjct: 5   MRLQKYLSAAGFCSRRKGEKFILSGLVKVNGVVISELGTKVDPAKDVVEVDGNKIEAKDD 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G +TT S    R  +  +L +I  R+  VGRLD ++ GLLLLTNDG L  
Sbjct: 65  LIYIALNKPKGYITTCSRQRDRIVL--DLVNIPQRIYPVGRLDKDSTGLLLLTNDGRLHN 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  PS    + Y V     +  + L+ +K+G  + G      +++  + +       + 
Sbjct: 123 VLSHPSFDHEKEYEVSLKWPIADEALDKMKEGFFLMGSKTRPAEISRISPEK----FHIT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L+EG+NR+I+++ +    +V  L RI     +LG L  G+ R ++ K  +  L
Sbjct: 179 LKEGRNRQIRRMVDKVGNRVLELKRIRISDVKLGNLKEGAWRYLTDKEKKALL 231


>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 =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 84/245 (34%), Positives = 128/245 (52%), Gaps = 2/245 (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+T +D  GR ++ D +  +  R+  VGRLD +TE
Sbjct: 61  IHVDGLRVETRPEMRYYALNKPRGVVSTMADERGRKSLADYV-DVPERLFHVGRLDTDTE 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 ILREQ 244
            + E 
Sbjct: 240 EVGEL 244


>gi|256752686|ref|ZP_05493537.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
 gi|256748448|gb|EEU61501.1| pseudouridine synthase [Thermoanaerobacter ethanolicus CCSD1]
          Length = 240

 Score =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 79/236 (33%), Positives = 122/236 (51%), Gaps = 8/236 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I +  V VNG  ++ A + +   TD I  DG  +  
Sbjct: 1   MAKMRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIINTETDEILFDGKKIYY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G+++   DP    TV D LP          VGRLD +TEGLLL+TND
Sbjct: 61  KE-FIYIMMNKPKGVISATYDP-IEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G LA  L  P    ++ Y  +  G V++  +    +GIV++   Y  +   L+    S+ 
Sbjct: 119 GDLAHKLLSPKKNVIKKYYAKILGFVNESDIKAFNEGIVLEDG-YKTLPANLEILSSSDV 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V V +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 178 SKVYVYIREGKYHQIKRMFESVGKKVIYLKRLAMGNLTLDENLKPGEWRELSEEEL 233


>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 =  268 bits (687), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 117/236 (49%), Gaps = 7/236 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V   +D I  DG  +  
Sbjct: 1   MAKMRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTESDEILFDGEKINY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G+++   D +   TV D LP          VGRLD +TEGLLL+TND
Sbjct: 61  KE-FIYIMINKPKGVISATYD-EVEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G LA  L  P    ++ Y     G V++  +    +GI++  G       + +       
Sbjct: 119 GDLAHQLLSPKKNVIKKYYAEILGFVNESDIKAFNEGIILEDGYKTLPANLEILFSSSDV 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V V +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 179 SKVYVYIREGKYHQIKRMFESVGKKVIYLKRLAMGSLTLDENLKPGEWRELSEEEL 234


>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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 114/307 (37%), Positives = 157/307 (51%), Gaps = 27/307 (8%)

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  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T  DP+GR TVFD LP    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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K  SQ    S++    
Sbjct: 242 EL----------VELKAESTSKLPVERERRRMKAN---QIRRAVKRHSQHGSSSRR---- 284

Query: 303 TPVHRRN 309
            P  +R 
Sbjct: 285 APAAKRG 291


>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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 129/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V +   +
Sbjct: 53  VSNKNEIRDEV---RLNKYISETGFCSRREADKLIEQGRVKIDGVKATT-GMKVSNGQSV 108

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG PL+          +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 109 SIDGKPLKVENELVYIALNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 166

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 167 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLVKKE 226

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 227 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKE 282

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 283 LAEI--NRLTENSSKTEEASI 301


>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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 116/374 (31%), Positives = 171/374 (45%), Gaps = 34/374 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAP 302

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------R 331
              D         Q  G  + +       +R          G  +   +D+ +      R
Sbjct: 303 ATGDRA---PRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAER 359

Query: 332 EENHRRSPSFPSKR 345
                + P+ P  +
Sbjct: 360 PSEMNKRPAKPGPK 373


>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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 113/301 (37%), Positives = 156/301 (51%), Gaps = 23/301 (7%)

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  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T  DP+GR TVFD LP    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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K   Q +G S++    
Sbjct: 242 EL----------VELQAETASKLPVERERRRMKAN---QIRRAVKRHGQHSGGSRRAPTT 288

Query: 303 T 303
            
Sbjct: 289 K 289


>gi|148555617|ref|YP_001263199.1| pseudouridine synthase [Sphingomonas wittichii RW1]
 gi|148500807|gb|ABQ69061.1| pseudouridine synthase [Sphingomonas wittichii RW1]
          Length = 286

 Score =  268 bits (686), Expect = 8e-70,   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|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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 153/294 (52%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSHEVEREYSVRVFGQVDDAMLARLRKGVQLEDGLANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  268 bits (686), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 116/235 (49%), Gaps = 4/235 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K ++ AG  SRRE +R++   RV ++G +       V     + VDG  +   
Sbjct: 1   MMEERINKYLSEAGYCSRREADRLVEAGRVTIDG-VAAVCGSKVADGQKVCVDGKEVSGR 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L  ++KP G+V T +D  G + + D +     R+  VGRLD ++EGL+L+TNDG +
Sbjct: 60  SRHILLAFNKPAGIVCTTTDKQGSNNIVDFI-GYPERIYPVGRLDKDSEGLILMTNDGAM 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +   +    + Y VR +  V  + +  +  G+ ++ +           +K +     
Sbjct: 119 MDRILRSTNGHEKEYIVRVNKPVTDEFVKGMSDGVYLKELDRTTK--VCVVEKVTKFCFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L +G NR+I+++ E F +KV +L RI      LG L  G  R+V+ +   E +
Sbjct: 177 IVLTQGLNRQIRRMCENFGYKVMKLKRIRIMNIMLGDLKQGCYRDVTDEEYAELV 231


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 87/241 (36%), Positives = 129/241 (53%), Gaps = 4/241 (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  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLT 125
             E     +++KP G+V+T  DP+GR  + D L +      R+  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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +  + V L  GKNR ++++F+   + V RL+R+  GP  LG    GS R + K+ +   L
Sbjct: 336 HVLIEVVLHSGKNRIVRRLFDAVGFPVLRLVRVKVGPIGLGDQRQGSIRNLGKQEVGHLL 395

Query: 246 G 246
            
Sbjct: 396 A 396


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 79/236 (33%), Positives = 122/236 (51%), Gaps = 8/236 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I +  V VNG  ++ A + +   TD I  DG  +  
Sbjct: 1   MAKMRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIINTETDEILFDGKKIYY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G+++   DP    TV D LP          VGRLD +TEGLLL+TND
Sbjct: 61  KE-FIYIMMNKPEGVISATYDP-IEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G LA  L  P    ++ Y  +  G V++  +    +GIV++   Y  +   L+    S+ 
Sbjct: 119 GDLAHKLLSPKKNVIKKYYAKILGFVNESDIKAFNEGIVLEDG-YKTLPANLEILSSSDV 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V V +REGK  +IK++FE    KV  L R++ G   L   L  G  RE+S++ L
Sbjct: 178 SKVYVYIREGKYHQIKRMFESVGKKVIYLKRLAMGNLTLDENLKPGEWRELSEEEL 233


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 102/316 (32%), Positives = 151/316 (47%), Gaps = 13/316 (4%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            ++   F  +++ KV+A AGI SRR++E  IA+ R+ VNG         V  +D I  DG
Sbjct: 3   KLLTAPFANEKLHKVLADAGIGSRRDMEERIAEGRISVNGEPA-HVGQRVTPSDVIRFDG 61

Query: 65  VPLRK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
             +R+      +  ++ +YHKP G + +  DP+GR TVFD+LP I  +R I+VGRLD NT
Sbjct: 62  RIVRRSALENNDVPKVLIYHKPAGEIVSKDDPEGRPTVFDHLPRIGGARWIAVGRLDFNT 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL T+ G LA  L  P  +  R Y VR  G +  +  + L KGI +         + 
Sbjct: 122 EGLLLFTDSGNLANFLMHPRHEIEREYAVRVQGTMSPEAKDKLLKGIKLDDGIAKFTTLE 181

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               KG N W  V L EG+NRE++++FE     V+RLIR+ YG  +L   L  G TR +S
Sbjct: 182 EGGGKGFNRWYNVTLSEGRNREVRRMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMS 241

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +   + L     ++      AP     T         +  P    +  +        S 
Sbjct: 242 TEETEKWLDSISYKKGMSTAPAPRAPERTPRPAASRAPASAPKAGRKFGQRD-----TSS 296

Query: 298 QKKLATPVHRRNLASN 313
             + + P+  R     
Sbjct: 297 AIRSSRPMRSRGTRGP 312


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  + D +     R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TESHIRGNIVDFV-GHPQRIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  +  G+ I G      +VT    + S     + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVTPSFVQGMSSGVKILGHRTLPCEVT----RVSEYVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            EGKNR+I+++   F ++V +L R+     +LG+L  G+ R++++   +++LG  L
Sbjct: 174 TEGKNRQIRRMCAAFGYEVKKLQRLRIMNIRLGSLQKGAWRDLTEAE-KQELGQML 228


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 118/375 (31%), Positives = 173/375 (46%), Gaps = 35/375 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRD-RPNIIS 276
           RE+S+     L  ++G   + + Q+N                P+   E +VR  RP   +
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------ 330
               D         Q  G  + +       +R          G  +   +D+ +      
Sbjct: 303 PANSDRA---PRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAE 359

Query: 331 REENHRRSPSFPSKR 345
           R     + P+ P  +
Sbjct: 360 RPSEMNKRPAKPGPK 374


>gi|167587342|ref|ZP_02379730.1| pseudouridine synthase [Burkholderia ubonensis Bu]
          Length = 389

 Score =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 94/306 (30%), Positives = 152/306 (49%), Gaps = 7/306 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 66  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 124

Query: 63  DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P++     +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 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 +A         S     R +P+ +        R    ++  N    
Sbjct: 305 DAQVRKLMATVGL-KAPSEEKGKRGSGGQAERRQPDPMQTSMGFIGREPVLTTHGNLEQP 363

Query: 298 QKKLAT 303
           ++    
Sbjct: 364 RRGPRR 369


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 83/268 (30%), Positives = 128/268 (47%), Gaps = 8/268 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ K +A AGIASRR+ E +I+  RV+VN   +      V    D + VDG  + +
Sbjct: 1   MAEERLQKYLAGAGIASRRKAEALISAGRVRVNQRTVTELGTKVDPGRDLVTVDGALVSQ 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ++   +L +KP G VTT SDP GR T  + L  +  R   VGRLD + EG LLLT+DG 
Sbjct: 61  PDQRSYYLLYKPSGCVTTASDPQGRPTAMEYLRGVPGRPFPVGRLDYDAEGALLLTDDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P     RVY V+  G    + L  +K G+ ++      ++  +      N W+
Sbjct: 121 LANRLAHPRYGHQRVYLVKVKGDPPAEALERMKAGVRLEDGPARAIEAAVHDHADRNVWI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V + EG+   +K++ E    +V RL R  +G   +G L  G  R +  + +R       
Sbjct: 181 RVVVGEGRFHLVKRLCEAVGLQVQRLFRPEFGGIGVGGLRPGKFRRLQPEEVRAL----- 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISE 277
               +V L++   +    VR+ P     
Sbjct: 236 --RQRVGLESGTPARGPSVRELPKAARR 261


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 74/236 (31%), Positives = 127/236 (53%), Gaps = 3/236 (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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGKNR+I+++FE   ++V +L R +     L  L  G  R ++   ++  +  
Sbjct: 182 TIHEGKNRQIRRMFETLGYEVLKLKREAIEDLTLEGLKKGEYRVLTIHEVKRLINK 237


>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 =  268 bits (686), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 115/228 (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  KVYIMLNKPEGYVTTNKDEKNRKTILDIV-KVNERIYPIGRLDYDSSGLLLLTNDGDVYN 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|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 =  268 bits (686), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 130/349 (37%), Positives = 190/349 (54%), Gaps = 4/349 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +    +R++K +A AG+ SRRE ER+I +  V VNG +L+ AA  V   + I V+G  + 
Sbjct: 29  DWSKGERIAKWLAAAGVCSRREAERLIEEGLVAVNGQVLDSAAFKVTGNEKITVEGKRVG 88

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ++TRLW +HKP GLVTT+SDP+GR TVF++LP    RV+++GRLD+NTEGLLLLTNDG
Sbjct: 89  GPDKTRLWRFHKPKGLVTTNSDPEGRPTVFEHLPKKLPRVMTIGRLDLNTEGLLLLTNDG 148

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LAR LELP+T   R YR R  G++ Q +L+ L++G++ +G+ Y  +  TLD  KG N W
Sbjct: 149 ELARTLELPTTGLKRCYRARAFGKITQAELDKLQEGVLFEGVVYRSIIATLDKTKGDNNW 208

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L EGK RE ++  E     VNRLIR+SYGPF+LG L+ G   E+    L  + G  
Sbjct: 209 IDMTLTEGKKREARRALESVGLIVNRLIRVSYGPFELGDLVEGGVAEIPAGELLSEFGDS 268

Query: 249 LLEEAQVNLDA-PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
           +  + + +  + P    E   + R     +     T   K  +      + +K   P   
Sbjct: 269 ISRKRRPDPASVPQSYLEPDTKRRRTKGRDEDTSQTAPAKKPAATIKPLRGEKFEKPSSG 328

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRR---SPSFPSKRSLRRTSAK 353
           R  A      +  H       G       R    P+ P +  +  + AK
Sbjct: 329 REPAQRSHKRQTPHRYAALREGAETNPEPRDFSKPAKPGEAVVPASLAK 377


>gi|52424446|ref|YP_087583.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306498|gb|AAU36998.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 246

 Score =  268 bits (686), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 108/231 (46%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V+VNG +++  ++ +   D +  +G  L   E  
Sbjct: 17  MRLDKFLAENTGLTRSQAAKILRQGNVQVNGQVVKSGSLKITPQDEVLFEGESLEWLEDG 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G V +H D +   TV+       + ++ + GRLD +T GL+LLT+DG  + 
Sbjct: 77  VYIMLNKPQGYVCSHDDGEY-PTVYQFFDYPLAGKLHTAGRLDADTSGLVLLTDDGKWSH 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+ +     ++GI+++G         L+     N  V + 
Sbjct: 136 RVTSPKYHCQKTYLVTLADPVESNYRQACEQGILLRGEKEPTKPAILEIIDDYN--VNLT 193

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EG+  ++K++F     KV  L R   G  +L   L  G  R ++ + ++
Sbjct: 194 ISEGRYHQVKRMFAALGNKVVGLHRWKIGNIELDEDLPEGEFRVLTAEEIQ 244


>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 =  268 bits (686), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 73/339 (21%), Positives = 141/339 (41%), Gaps = 9/339 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R++K I+  G  SRRE +++I QQRV +NG +       V+S D++E+DG P+R  E
Sbjct: 6   EGKRLNKYISETGFCSRREADKLIEQQRVTINGKIP-EMGTKVLSGDNVEIDGKPVRSKE 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LTNDG + 
Sbjct: 65  KPVYIALNKPTGITCT-TERDVPGNIVDFV-GHHKRIFPIGRLDKPSDGLIFLTNDGDIV 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y VR    V +D L  +  G+ I        +V    ++ +     +
Sbjct: 123 NKILRAGNNHEKEYVVRVDKPVTRDFLKKMGSGVAILDTVTLPCRV----EQETKFSFRI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E   ++V +L R+      +  +  G  R ++ + + E     L E
Sbjct: 179 TLTQGLNRQIRRMCEALGFEVLKLRRVRIMNISIDGIPNGKWRYLTDQEVAEIH--RLCE 236

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
            +    +A    ++     +              ++     +G    +   +P   +   
Sbjct: 237 GSVSTEEASRKDAKGRHITKATDAKLHDARAEAKREKMKTFSGHGADEFRRSPNKNKRHK 296

Query: 312 SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                +    +       ++    +   S PSK   R  
Sbjct: 297 QEQGRSDKARNHHGKTQNRKPVAAKPDSSKPSKPRTRVG 335


>gi|302188863|ref|ZP_07265536.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 409

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 115/374 (30%), Positives = 170/374 (45%), Gaps = 33/374 (8%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRP--AAG 300

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------R 331
            P           Q  G  + +       +R          G  +     + +      R
Sbjct: 301 APATGGERAPRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPPKTSRGTPVAER 360

Query: 332 EENHRRSPSFPSKR 345
             +  + P+ P  +
Sbjct: 361 PSDMNKRPAKPGPK 374


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 97/342 (28%), Positives = 162/342 (47%), Gaps = 9/342 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 170 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 228

Query: 63  DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P++     +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 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 EAQVRKLMATVGLKAPSEEKGK--RGGGQAERRQPDPMQTSMGFISREPVLTTHGQLDQP 466

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           ++            S         S + + +G R+ +  R+ 
Sbjct: 467 RRGGRRGGPGLPGLSGYGSLPVA-SGYGNRAGGRDVDGNRAS 507


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 120/262 (45%), Gaps = 9/262 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           +  K  V       R+ K +A   + SR+EV++ I + +V VNG +       +    D 
Sbjct: 11  LSGKFFVLTRRKTMRLDKFLATMQLGSRKEVKQFIKKGKVTVNGEITRSDKAQINEYEDQ 70

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDIN 117
           I  +G  ++  ++   +L +KP G+++   D +   TV D L        +  VGRLD +
Sbjct: 71  ISFEGEVIQY-QKDYYYLLNKPAGVISATVD-NYDETVMDLLVDEDFREDLFPVGRLDKD 128

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQ 176
           TEGLL+LTNDG LA  L  P     + Y     G +  + + L  +G++I  G      +
Sbjct: 129 TEGLLVLTNDGQLAHRLLSPKKHVEKEYHATVAGVMTAEDVALFSEGLMIDQGEQCLPAK 188

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           +T+ +  +    + +++ L EGK  ++K++      +V  L RI  G   L  +L  G  
Sbjct: 189 LTILSVDESAQTSQISLILHEGKFHQVKRMVAAVGKEVVYLKRIRMGQLTLDESLALGEY 248

Query: 234 REVSKKILREQLGPHLLEEAQV 255
           R ++   +         + A++
Sbjct: 249 RALTALEVEALQQNPFSDNAEL 270


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/239 (34%), Positives = 125/239 (52%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QRV K++++ G+ASRR  E MI   RVK+NG ++        S D +EVDG  ++ ++R 
Sbjct: 3   QRVQKILSQWGVASRRHAEDMIIAGRVKLNGEIVTLGDKADPSCDRLEVDGRMIQPSQRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +    L +KP+G+V T  DP  RS V D LP   S+   +  VGRLD N+ G LLLTNDG
Sbjct: 63  QLLYILINKPVGVVCTCDDPQNRSIVLDLLPKQLSKGTGIHPVGRLDFNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G   +++L   ++G+++ G      QV +  +   N  
Sbjct: 123 ELTLRLTHPRYHLPKTYEVLIQGHPTEERLQQWREGVMLMGKKTLPAQVEVICRYRQNTR 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
           + V L EG+NR+I+ + +   + V RL R + G   L      +L  G  R ++   +R
Sbjct: 183 LKVILTEGRNRQIRHIVQHLGFHVLRLHRTAIGSLVLSSPNESSLPNGHYRLLTPSEIR 241


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 117/228 (51%), 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  KVYIMLNKPEGYVTTNKDEKNRKTILDIV-KVNERIYPIGRLDYDSSGLLLLTNDGDVYN 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|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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 121/235 (51%), Gaps = 1/235 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
              R++K +A  G+ASRR+ E +I++ +V VNG ++      +    D ++V G  +   
Sbjct: 3   EKMRINKYLASCGVASRRKCEEIISRGKVTVNGEVVRELGTIINVEKDLVKVYGKEVSLD 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +   ++ +KP G+++      G  TV D L     R+  VGRLD +T GL++LTNDG  
Sbjct: 63  TKKVYYMLNKPQGVISASKSKYGEETVVDLLGKKEHRLFPVGRLDKDTTGLIILTNDGDF 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y     G+VD   L+ LK+G+VI G      +V L    G N+ V 
Sbjct: 123 AYKLTHPKYEKEKTYEALVKGKVDSKSLDKLKQGVVIDGKKTSRAKVRLVKMIGVNSLVE 182

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L EG+ R++KK+ E    KV +L R       LG L  G  R+++K  + + L
Sbjct: 183 ITLIEGRKRQVKKMCEKVGHKVIKLNRTMENGLSLGDLEIGEYRKLTKNEVSKLL 237


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/238 (34%), Positives = 123/238 (51%), Gaps = 10/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
           +R+ K++A+ GIASRR+ E MI   RV+VNG  ++       ++D IEVDGV ++  +  
Sbjct: 3   ERLQKILAQWGIASRRQAEEMILAGRVRVNGNTVQLGQKANPASDRIEVDGVRVKSERRP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 128
           +    L +KP G+V+T SDP  R+TV D LP        +  VGRLD+ + G LLLTNDG
Sbjct: 63  QPVYLLLNKPAGVVSTCSDPAQRTTVLDLLPPKLRAGCGIHPVGRLDVESTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y+V   G   +  L    +G+++        QV +  + GS   
Sbjct: 123 NLTFALTHPRHCVPKTYQVWVEGDPPKSVLQTWSQGVLLSRRMTLPAQVRVQERNGSQTL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKIL 241
           + V L EG+NR++++V E   + V  L R + GP  L       L AG  R +    +
Sbjct: 183 LEVILYEGRNRQVRRVAEQLGYPVIHLHRTAIGPILLQPPGEPELPAGHYRPLLDSEI 240


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 97/342 (28%), Positives = 162/342 (47%), Gaps = 9/342 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 170 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 228

Query: 63  DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P++     +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 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 EAQVRKLMATVGLKAPSEEKGK--RGGGQAERRQPDPMQTSMGFISREPVLTTHGQLDQP 466

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           ++            S         S + + +G R+ +  R+ 
Sbjct: 467 RRGGRRGGPGLPGLSGYGSLPVA-SGYGNRAGGRDVDGNRAS 507


>gi|327480926|gb|AEA84236.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 375

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 118/361 (32%), Positives = 177/361 (49%), Gaps = 27/361 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
           +++ KV+AR GIASRR+VE+ I + RVKVNG +       V S D I VDG  L++ E  
Sbjct: 15  EKLQKVLARLGIASRRDVEKWIVEGRVKVNGAVAT-LGQRVDSHDAIAVDGRLLKREETS 73

Query: 73  ---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + T +DP+GR TVFD LP     R I++GRLDINT GLLL T DG
Sbjct: 74  QVVRRVLIYNKPDGEICTRNDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDG 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNA 187
            LA  L  PS +  R Y VR  G+VD + +  LK G++++        +      +G N 
Sbjct: 134 ELANRLMHPSYEMDREYAVRVRGEVDDEMIERLKTGVMLEDGPARFTDIQEAPGGEGFNH 193

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
           W    + EG+NRE+++++E     V+RL R+ +GP  +   L  G  RE+S+     L E
Sbjct: 194 WYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLPMGRWREMSQAEVDILSE 253

Query: 244 QLGPHLLE-------------EAQVNLDAPIYSSETLVR-DRPNIISEVP--DDFTRMKK 287
           ++G   +                Q  +  P+   E   R  RP   +++P  D     + 
Sbjct: 254 EVGLKPIALPSMKAKTKEKIDRMQRKVAKPLGRGERRSRVLRPAHEADMPVADKPRAARD 313

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           + S++      K   TPV  R   +     +       S   ++     + P F  +RS 
Sbjct: 314 DKSERKPRGSDKPRGTPVAERPGDTRKGGKRHEGGGRSSGPARKPAGEGQRPGFGRERSK 373

Query: 348 R 348
           R
Sbjct: 374 R 374


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQSKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPHLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSHEVEREYSVRVFGQVDDAMLARLRKGVQLEDGLANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 107/237 (45%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D  +    G+ +           L+  +     V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPLAADTASHFAAGVQLHNEKDLTRPAQLE--QLDEHRVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +     PHL
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVDLHRERIGAIRLDDDLAPGEYRPLTEEEIASVGAPHL 235


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 100/359 (27%), Positives = 166/359 (46%), Gaps = 9/359 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 176 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 234

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 355 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 414

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNGL 295
           +  +R+ +    L +A          S    R +P+ +       +R        Q +  
Sbjct: 415 EAQVRKLMATVGL-KAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQP 473

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +            L+    +            G R+ +  R+      +      AK+
Sbjct: 474 RRGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPKREGGAGAKR 532


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 100/359 (27%), Positives = 166/359 (46%), Gaps = 9/359 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 176 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 234

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 355 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 414

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNGL 295
           +  +R+ +    L +A          S    R +P+ +       +R        Q +  
Sbjct: 415 EAQVRKLMATVGL-KAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQP 473

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            +            L+    +            G R+ +  R+      +      AK+
Sbjct: 474 RRGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPKREGGAGAKR 532


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 116/228 (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  KVYIMLNKPEGYVTTNKDEKNRKTILDIV-KVNERIYPIGRLDYDSSGLLLLTNDGDVYN 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|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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 109/371 (29%), Positives = 175/371 (47%), Gaps = 24/371 (6%)

Query: 1   MKDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D++   +   P  +++ KV+AR G+ SRR+VE  I Q+R+KVNG+        V   D
Sbjct: 1   MNDQDHKDQEIGPAGEKLQKVLARIGVGSRRDVEAWITQKRIKVNGVEAT-LGQRVDLHD 59

Query: 59  HIEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGR 113
            I +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD +P     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 DMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG 231
              +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G
Sbjct: 180 FTDIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMG 239

Query: 232 STREVSKKI---LREQLGPHLLEEAQVNLDAP-------IYSSETLVRDRPNIISEVPD- 280
             RE+S+     L  ++G   +   Q+N  +          SS  + R      +  P  
Sbjct: 240 RWREMSQYEVDILSAEVGLTPVAMPQMNAKSKDKLERMQRKSSRPVARTERVARTLRPAL 299

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHR---RNLASNVWMAKGIHSSFLSDSGQREENHRR 337
           D        S++  +  +++   P  +   R   +      G  S+        +    +
Sbjct: 300 DAPATGGRISRQPQIEGERRPTAPSRQEGERAPRTPRPAPAGGRSNRGEADRPADNASTK 359

Query: 338 SPSFPSKRSLR 348
            P+ P+     
Sbjct: 360 RPAKPAANKRP 370


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 91/289 (31%), Positives = 149/289 (51%), Gaps = 6/289 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 174 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 232

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 353 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 412

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
              +R+ +    L+           ++    R +P+ +       +R  
Sbjct: 413 DAQVRKLMATVGLKAPSEEKGKRGGAAGPTERRQPDPMQTSMGFISREP 461


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 119/245 (48%), Gaps = 7/245 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEV 62
           + I +      R+ K +   G+ +R EV++++  +++ VNG ++ +    V    D I  
Sbjct: 15  QTIEKGKNELMRLDKFLTEMGLGTRSEVKKILKTKQITVNGEIVTKPETKVAPENDQISY 74

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGL 121
            G P+   E    +L++KP G VT   D     TV D L       +  VGRLDI+TEGL
Sbjct: 75  KGEPVTYCE-YEYYLFYKPAGCVTATED-QLHKTVMDYLTDTVRSDLFPVGRLDIDTEGL 132

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD 180
           LL+TNDG LA  L  P+    + Y     G V +  +N  + G+ I +       ++ + 
Sbjct: 133 LLITNDGALAHDLLSPAKHVEKTYYAVIDGVVTEKDVNSFENGVDIGEEKLTKPGKLRIL 192

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
            +    + + + + EG+  ++K++FE    KV  L RIS GP QL   L  G  R ++++
Sbjct: 193 -KSEPESEIELTITEGRFHQVKRMFEAVGKKVLYLKRISMGPLQLTDDLKPGEYRPLTEE 251

Query: 240 ILREQ 244
            +   
Sbjct: 252 EITAL 256


>gi|167738823|ref|ZP_02411597.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
          Length = 359

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 49  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 107

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 228 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 287

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 288 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 333


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 102/358 (28%), Positives = 163/358 (45%), Gaps = 19/358 (5%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
           +E    +R+ K++A AG+ASRR+ E +I   RV+VNG ++        + +DHI VDG  
Sbjct: 18  EEPRGGERLQKILASAGVASRRKAEELILAGRVQVNGQVVTEMGFKADAASDHIRVDGKL 77

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLL 123
           L+  E+ R ++ +KP G VTT SDP+GR TV +          R+  VGRLD  +EGLLL
Sbjct: 78  LQGPEKLRYFMLNKPKGYVTTVSDPEGRHTVMEFFHGRGKGGERLYPVGRLDYASEGLLL 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------ 177
           +TNDG LA  L   S+   +VY V+  G+  +++L  ++ GI+I     G+ +V      
Sbjct: 138 MTNDGALANTLTKASSHVEKVYLVKVSGRPTEEQLEQIRAGIMIDRGRPGEGRVMTAPAG 197

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +   N W  + L EG+NREI+K+FE     V ++ RI YGP  L  +  G  RE++
Sbjct: 198 VRMVRDAENPWFELTLIEGRNREIRKMFEETGHFVEKIRRIGYGPLVL-DVEPGEVRELN 256

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            + +        L  A     AP   + T  +    +    P   +       +      
Sbjct: 257 PEEV------DSLRRAAQRKRAPKPKAATKTKRLTMLPKAKPARKSATGGRPGRAGAGRP 310

Query: 298 QKKLATPVHR--RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
                    +  +N  S    A     +             R+ S    ++  + +A+
Sbjct: 311 AAGRPGRAGQGGQNARSGQGGASSERPARKLAPEGASRATERAGSRSGAKAGNKPAAR 368


>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 =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 3/242 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     +VYRV     +D   +     GI +          TL+      A +   +
Sbjct: 121 ITSPRHHCEKVYRVGVESPIDPSLVEKFAAGIQLHNEKDLTKPATLEIVGPQEALL--TI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEE 252
            EG+  ++K++F      V  L R   G   L   L  G  RE++++ +     P  L++
Sbjct: 179 SEGRYHQVKRMFAASGNHVVTLHRERIGDIVLDADLAEGEYRELTEEEVASIGLPDELKQ 238

Query: 253 AQ 254
            +
Sbjct: 239 PK 240


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 98/350 (28%), Positives = 163/350 (46%), Gaps = 9/350 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 31  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 89

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 210 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 269

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNGL 295
           +  +R+ +    L +A          S    R +P+ +       +R        Q +  
Sbjct: 270 EAQVRKLMATVGL-KAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQP 328

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
            +            L+    +            G R+ +  R+      +
Sbjct: 329 RRGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPK 378


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 116/242 (47%), Gaps = 8/242 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ E     ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG 
Sbjct: 4   LIYEKEQNMKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDDDVVTIDGQ 62

Query: 66  PLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            + K E+      +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LL
Sbjct: 63  VIAKEEKEKVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG +A  +     +  + Y V          ++ +  G+ I+       +VT   Q  
Sbjct: 121 TNDGAIANQILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVGQ-- 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             +   + L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   
Sbjct: 179 --STFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELHELEVGKWRSVTAEELEIL 236

Query: 245 LG 246
           +G
Sbjct: 237 IG 238


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 114/234 (48%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A  G  SR++V++++    V  NG  +  +  +V    D I V    +  + +
Sbjct: 1   MRIDKLLAHCGYGSRKDVKQLLKDGLVTSNGKKIRSSGAHVDPEKDEIYVGDEKINYS-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G V+   D +   TV D +      +  VGRLD++TEGLLL+TNDG LA 
Sbjct: 60  YVYYMLNKPDGYVSATED-NVYPTVIDLIKEYHPGLFPVGRLDVDTEGLLLITNDGQLAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P T   + Y V+  G++    +N   KGI ++        + +  +    +   V 
Sbjct: 119 RLLSPRTHVPKTYYVKVKGRLGIGDINAFTKGIPLEDFTCMPSYLKI-IKSDEISECEVT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EGK  ++K++F+    +V  L RIS G  +L   L  G  R ++ + +   L
Sbjct: 178 IYEGKFHQVKRMFQACGKEVVYLKRISMGELKLDENLKLGHYRPLTDEEINSIL 231


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 129/236 (54%), Gaps = 3/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA +G  SRR+ E++I + +V VNG ++++  V    +D I V+G+ L   E  
Sbjct: 3   ERLQKLIAASGYTSRRKAEQLILEGKVSVNGEVIKQLGVKAEPSDVIIVEGLRL-LKENK 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +L++KP  ++T+ SD   R  V D   ++  RV+ VGRLD +T G L+++NDG    +
Sbjct: 62  KYYLFYKPEKVITSMSDEKDRVCVKDFFEAVNERVVPVGRLDYDTSGALIMSNDGEFINL 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTV 191
           +  P  +  + Y  + +G++++  L +L+ G+ I        +V +   K    N  V +
Sbjct: 122 ITHPKHKIKKTYVAKINGKLEEHHLKILRSGVRIDNYKTSPAEVNIVKNKNKSGNTLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + EGKNR+++++FE   ++V +L R S     L  L  G  R ++   ++  +  
Sbjct: 182 TIHEGKNRQVRRMFEALGYEVMKLKRESIEDLTLDGLRKGEYRILTIHEVKRLINK 237


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 97/342 (28%), Positives = 164/342 (47%), Gaps = 9/342 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 157 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 215

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 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 EAQVRKLMATVGLKAPSEEKGK--RGAGQAERRQPDPMQTSMGFISREPVLTTHGQLDQP 453

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           ++            S         S + + +G R+ +  R+ 
Sbjct: 454 RRGGRRGGPGLPGLSGYGSLPVA-SGYGNRAGGRDVDGNRAS 494


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 106/305 (34%), Positives = 152/305 (49%), Gaps = 8/305 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ K++ARAG+ SRREVE  I   R+ +NG  +      V   D I++DG  L  A  
Sbjct: 22  PERIQKLLARAGVGSRREVESWIEAGRLSINGKPV-EPGQKVTVNDRIDLDGKRLDIAAG 80

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VTT  DP+GR TVFD+LP     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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L + L  G   E+ +K +     
Sbjct: 201 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLSVGKWEELDQKAVDSLSK 260

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  ++    P     TL R R       P      +         + +K    P  
Sbjct: 261 AVDLKPVEIPAKTPSEQK-TLDRKRRKQAGTGPRKSGGARWQVDSAGPSTGRKSSGKPPA 319

Query: 307 RRNLA 311
           R    
Sbjct: 320 RSGKR 324


>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 =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 116/374 (31%), Positives = 171/374 (45%), Gaps = 34/374 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAP 302

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------R 331
              D         Q  G  + +       +R          G  +   +D+ +      R
Sbjct: 303 ATGDRA---PRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAER 359

Query: 332 EENHRRSPSFPSKR 345
                + P+ P  +
Sbjct: 360 PSEMNKRPAKPGPK 373


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 79/246 (32%), Positives = 127/246 (51%), Gaps = 1/246 (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 ILREQL 245
            L   +
Sbjct: 241 ELGALM 246


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 91/242 (37%), Positives = 138/242 (57%), Gaps = 7/242 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG  ++    +    D I V G     P
Sbjct: 1   MSNERLQKILSQAGLGSRREMERWIENGWVQVNGKPVK-LGDSASEEDKITVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           L+  +  R+ LYHKP+G +++  DP    TVFD+LP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKVKKNVRILLYHKPVGEISSRHDPKFEKTVFDHLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N G LA  L  P   + R Y VR  GQV Q+ LN L KG+ +        ++     +G+
Sbjct: 120 NSGELANQLMHPKYGFEREYAVRVRGQVSQEVLNNLTKGVELDDGMAKFTRLEFRGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N+W  V L EG+NRE+++++E    +V+RLIRI YG   +   L  G   E++ K + + 
Sbjct: 180 NSWYHVTLNEGRNREVRRLWESQGLEVSRLIRIRYGTITMPRYLSRGQHYELTPKEVSDL 239

Query: 245 LG 246
           L 
Sbjct: 240 LA 241


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 74/259 (28%), Positives = 125/259 (48%), Gaps = 20/259 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +E   P R+ + +ARAG+ASRR  ER++   RV VNG ++      V     +     
Sbjct: 1   MTEERIVPMRLQRFLARAGVASRRGSERLMTSGRVTVNGQVVTELGSKVDPLVDVVAVDG 60

Query: 66  PL-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLL 123
            +   AE+    + +KP G +TT  DP GR T+ D +P   +  +  VGRLD++T GLL 
Sbjct: 61  VVCSIAEKPVYLMLNKPAGYLTTMKDPQGRPTIVDMVPTDTYPGLFPVGRLDMDTTGLLF 120

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG +A+ L  PS    + Y     G   +++LN L++GI ++       +V + +  
Sbjct: 121 FTTDGQMAQELLHPSKHVWKHYVAHVVGTPTEEQLNRLREGIELEDGPAAPAEVEIISDD 180

Query: 184 ------------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                               NA V+V +REG+  ++KK+    + +V  L R ++GP  L
Sbjct: 181 VKMKNLLAPQGLGKTGGGEPNALVSVTIREGRKHQVKKMLLAIHHRVLALHRDTFGPLHL 240

Query: 226 GTLLAGSTREVSKKILREQ 244
             +  G  R ++++ +   
Sbjct: 241 TRVKEGEWRLLTEEEVTAL 259


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 111/344 (32%), Positives = 162/344 (47%), Gaps = 13/344 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG + +           I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTITGKAS 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-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 P  +S    R R   I        R ++ ++   G S Q K   
Sbjct: 242 LVELQPEKETLLDLD-PANTSRKRERSRSQKIRR---AVKRHEERANAPKGRSNQTKRKK 297

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
           P  R     +   +    +     + + + N+ R       RS 
Sbjct: 298 PATRGTTTPDSGRSAPATNGKPQATKKPKLNNGRPAKPAKPRSR 341


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 87/235 (37%), Positives = 125/235 (53%), Gaps = 3/235 (1%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L +    RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYLAMNKPRGVVSTMADEKGRTAIADFLGNRVQERVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y     G + +     L  GI +  G    D    +DT  G  A V 
Sbjct: 138 HRLTHPSYGVPKTYLCEVSGPIPRTLGRRLAAGIELTDGPATVDAFRVVDTL-GRTAQVE 196

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V L EG+   ++++F+     V+RL+R S GP +LG L AG TR ++   +    
Sbjct: 197 VTLHEGRKHIVRRLFDAVGHPVSRLVRTSIGPIRLGDLRAGRTRRLTNAEVAALF 251


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 151/333 (45%), Positives = 208/333 (62%), Gaps = 9/333 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            ++ T  R++KV+ARAG+ SRR+ E  + + RV VNG++++  A++VM +D I VDG PL
Sbjct: 457 ADDKTGDRIAKVVARAGLCSRRDAETWVTEGRVAVNGLVIDSPALDVMPSDVITVDGKPL 516

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + ERTRL+LYHKP GL+TTH+DP+GR TVFDNLP    R+IS+GRLD NTEGLLLLTND
Sbjct: 517 PERERTRLFLYHKPRGLMTTHADPEGRPTVFDNLPEDLPRLISIGRLDFNTEGLLLLTND 576

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           GGLAR LELP T WLR YRVR HG+V Q +L+ LK GI + G+ YG+++  L+  +G+N 
Sbjct: 577 GGLARALELPETGWLRRYRVRAHGEVTQAQLDELKNGIEVDGVKYGEIEAKLERDQGANV 636

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+   +REGKNRE++ V      +VNRLIR+SYGPFQL  +  G   EV  ++LREQLG 
Sbjct: 637 WLVFAIREGKNREVRNVLAHLGLEVNRLIRVSYGPFQLLEIEEGEVEEVKTRVLREQLGD 696

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            +++ A  +   P   SE   + RP       +     KK +  K G  + +K       
Sbjct: 697 KIIQLAGADFGGP-SPSEARPKPRPGRPVAAAEAAPAPKKKAPTKRGAVEDRKGRKVKVE 755

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
           R  +       G     L+    R  + +R P+
Sbjct: 756 RTGSG------GDRG--LTRGPARRYHGKREPA 780


>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 =  267 bits (684), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 132/234 (56%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + +VKVNG  +      V  +D++EV+GV L + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLIVEGKVKVNGETVTELGTKVKPSDNVEVEGVKLEQEDKL 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L++KP  ++T+ SD  GR+ V D    + +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFYKPAQVITSVSDDRGRTVVTDYFDDLETRIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  P  +  + Y  +  G + +D++  L+KGI ++       +V +  Q  + +   V +
Sbjct: 125 MTHPRYKIKKKYVAKLKGYLMRDEVKALEKGIQLEDGKTHPAEVKIKNQNKEKNTTVVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGP-FQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE F  +V++L R+       L  L AG  R ++   +++ 
Sbjct: 185 TISEGRNRQVRRMFEHFGHEVSKLSRVELADFLTLKGLNAGEGRVLTPHEVKKL 238


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 127/233 (54%), Gaps = 3/233 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KVIA+AGIASRRE E+MI   RV+V+G ++ +    V S + + VD  P+ + 
Sbjct: 1   MAEERLQKVIAQAGIASRREAEKMILAGRVRVDGQVVTKLGTKVSSIEQVVVDNQPIER- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E    +L++KP G+++   D  GR TV D    +  R+  VGRLD +T GLLL+TNDG L
Sbjct: 60  ESHHTYLFYKPRGVISAVKDNKGRKTVADYFTDLPYRLYPVGRLDYDTSGLLLMTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A +L  P  +  +VY  +  G +  D++  LKKG+ I        +V +           
Sbjct: 120 ANLLMHPRNEVDKVYVAKIKGILQPDEIKALKKGVQIGRYKTKPARVKVLKTNPRAQTQI 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + + EG   ++K++F+  N  V++L R  Y    L  L +G  RE++ K +
Sbjct: 180 VQLTIHEGHYHQVKEMFKAVNHLVDKLSRERYSFLDLQGLTSGQYRELNHKEV 232


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 103/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +          TL+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 227


>gi|241764490|ref|ZP_04762511.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241366074|gb|EER60671.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 504

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 100/361 (27%), Positives = 155/361 (42%), Gaps = 17/361 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D +
Sbjct: 144 VPAKRVLLPQVETPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQV 202

Query: 61  EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
           +V+G P+R        R+  YHKP+G V +H DP  R TVF  LP +   +  SVGRLD+
Sbjct: 203 KVNGKPIRYRIDPPPARVIAYHKPVGEVVSHDDPQNRPTVFRKLPRLQQGKWQSVGRLDL 262

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ +         
Sbjct: 263 NTEGLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSNEEKQQLLDGVRLDDGMAAFGS 322

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
           +     +GSN W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E
Sbjct: 323 IEDGGGEGSNCWYRVTISEGRNREVRRMLEAVGHAVSRLIRIRYGAMVLPRGLKRGAWLE 382

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  +R  +        + +   P   +E                    +K +   NG 
Sbjct: 383 LGEGDIRALM--QAAGAGRPDAAGPRTEAEGGAARGNRERGRGSVRAGDGRKRTGGANGS 440

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTSAK 353
                      RR+       A G           G++ +  + S  +    SL R    
Sbjct: 441 MGSGGQGR-APRRS------DAPGARGGNAERPRGGEQPDPMKTSVGYIGADSLSRHRQD 493

Query: 354 K 354
           +
Sbjct: 494 Q 494


>gi|302533645|ref|ZP_07285987.1| pseudouridine synthase [Streptomyces sp. C]
 gi|302442540|gb|EFL14356.1| pseudouridine synthase [Streptomyces sp. C]
          Length = 239

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 78/231 (33%), Positives = 123/231 (53%), Gaps = 1/231 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V   D I+VDG+ +   
Sbjct: 1   MEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVTEQGKRVQPKDEIKVDGLTV-AT 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 60  QSFLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK+GI ++          +  Q G N  V 
Sbjct: 120 AHRLTHPKYGVQKTYVAAITGSLPRDIGKRLKEGIELEDGYARADNFRVVDQVGKNYLVE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V++L+R S+GP +LG   +G  R ++   +
Sbjct: 180 VTLHEGRKHIVRRMLAEAGFPVDKLVRTSFGPIELGDQKSGWLRRLTNTEV 230


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 141/355 (39%), Positives = 193/355 (54%), Gaps = 17/355 (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 LGPHLLEE-----AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           L  ++  E       V   API          P +        +   +  S+       +
Sbjct: 326 LADYIRPENLPTGNTVETPAPIPGRRVST---PIVKGRSGSAMSDPSRKPSRVRAAETAQ 382

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             A     R      W      +     S +  E        P++    R    +
Sbjct: 383 ADAVERRERPPKKEGWAKAAPKTGHPKKSFKPREGAPTDGERPARTYKPREEGDR 437


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 98/350 (28%), Positives = 163/350 (46%), Gaps = 9/350 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 31  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 89

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 210 DGGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 269

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK--KNSSQKNGL 295
           +  +R+ +    L +A          S    R +P+ +       +R        Q +  
Sbjct: 270 EAQVRKLMATVGL-KAPSEEKGKRGGSGPAERRQPDPMQTSMGFISREPVLTTHGQLDQP 328

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
            +            L+    +            G R+ +  R+      +
Sbjct: 329 RRGGGRRGGPGLPGLSGYGSLPVSPSGHGNRSGGGRDVDGNRASYGAGPK 378


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 114/233 (48%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R++K I+  G  SRRE ++++ Q RV +NG           ++D + VDG PL+  
Sbjct: 1   MEPVRINKFISETGFCSRREADKLVEQGRVMLNGRKA-VLGDKATTSDDVRVDGKPLKAK 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +      ++KP+G+  T ++   +  + D +     R+  +GRLD  +EGL+ LT+DG +
Sbjct: 60  KAGVYIAFNKPVGITCT-TERHIKGNIIDYI-RHKERIFPIGRLDKPSEGLIFLTSDGDI 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  +  + +  +  G+ I G+      V    +K S+   T
Sbjct: 118 VNKILRAGNNHEKEYVVTVNKPITPEFIQKMSSGVPILGVVTKKCFV----RKDSSYVFT 173

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + L +G NR+I+++ EF  + V +L R+      L  L  G  R+++   ++E
Sbjct: 174 IILTQGLNRQIRRMCEFLGYNVTKLKRVRIMNVTLKDLPVGKWRDLTAAEMQE 226


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 104/305 (34%), Positives = 154/305 (50%), Gaps = 14/305 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++AR+G  SRRE+E  I Q RV V+G +      + V     I +DG  L   E
Sbjct: 8   SEKLQKILARSGHGSRREIEGYIQQGRVSVDGKIATLGDRIEVQPATKIRLDGRILSIKE 67

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T 
Sbjct: 68  SQKAICRVLAYYKPEGELCTRHDPEGRPTVFDRLPKLLGSRWIAVGRLDVNTCGLLLFTT 127

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD  KL  L KGI ++        V     +G N
Sbjct: 128 DGELANRLMHPSREVEREYAVRVFGEVDDAKLKQLAKGIQLEDGPAAFRTVAFKGGEGIN 187

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    LR
Sbjct: 188 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIGLPKGLPRGGWAELGLEQTNYLR 247

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + +G H    ++V     +   +  ++      +         + ++ ++ G S+Q    
Sbjct: 248 QLVGLHEETVSKVA----VERDQRRMKANQIRRAVKRHAQVASRPSAGKRPGSSRQNAGR 303

Query: 303 TPVHR 307
           T   +
Sbjct: 304 TTAQK 308


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 91/289 (31%), Positives = 149/289 (51%), Gaps = 6/289 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 174 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 232

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 353 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 412

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
              +R+ +    L+           ++    R +P+ +       +R  
Sbjct: 413 DAQVRKLMATVGLKAPSEEKGKRGGAAGPTERRQPDPMQTSMGFISREP 461


>gi|304397506|ref|ZP_07379384.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304355124|gb|EFM19493.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 239

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 105/239 (43%), Gaps = 3/239 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     +  D       G+ +           L+    ++  V + L
Sbjct: 121 ITSPRHHCEKTYRVTLESPISDDTAAQFTAGVQLHNEKSLTKPAQLEVITPTD--VRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLE 251
            EG+  ++K++F     +V  L R   G   L   L  G  R +++  +     P  L+
Sbjct: 179 SEGRYHQVKRMFAAVGNRVIELHRERIGDIVLDEDLEPGEYRALTEDEIASIGLPKELQ 237


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 134/247 (54%), Gaps = 5/247 (2%)

Query: 5   NIVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIE 61
           N  Q+   P+  R+ KV+A AG+ASRR  E MI   RV+V+G ++    + V   T  I 
Sbjct: 95  NAGQDMHDPEGVRLQKVMAAAGVASRRVCEEMIEDGRVEVDGSIVTELGLRVNVETAVIS 154

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTE 119
           VDG+ L+  E     +++KP G+V+T  DP+GR  + D L + +   R+  VGRLD  TE
Sbjct: 155 VDGIRLQLKENMIYLVFNKPRGVVSTMDDPEGRRNISDFLKNKYAHERLFHVGRLDQATE 214

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG LA  L  PS +  + Y V+  G ++    N ++KGI ++          L
Sbjct: 215 GLLLLTNDGELANRLTHPSYEVPKTYLVQTKGPMETGVSNQMRKGIELEDGVTKIDAFKL 274

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 +  V V L  GKNR ++++F+   + V RL+R+  GP +LG    GS R + ++
Sbjct: 275 VDSTPGHVLVEVVLHSGKNRIVRRLFDAVGYPVERLVRLQVGPIRLGDQKQGSIRALGQQ 334

Query: 240 ILREQLG 246
            +   L 
Sbjct: 335 EVGHLLA 341


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G+ SR+EV++++  +R+ VN ++++ + ++V    D I VD   +   ++
Sbjct: 2   MRLDKLLSNMGVGSRKEVKQLLKSKRITVNEVIVKDSGMHVDPEYDQIFVDDQLISY-QK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+V+   D   R TV D L +   +     VGRLD +TEGLLL+TNDG L
Sbjct: 61  HIYLMMHKPPGVVSATVDNRDR-TVIDLLSADEKKFEPFPVGRLDKDTEGLLLITNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     +VY     G+  ++ +   ++G+ ++   Y      L+     +  V 
Sbjct: 120 AHRLTSPKKHVEKVYIAHISGEFPENIVEQFQEGLTLEDG-YQTKPAKLEILNKQSKEVK 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           V + EGK  +IK++F     KV  L R+     QL   L  G  R +++  L+
Sbjct: 179 VTITEGKYHQIKRMFIAVGCKVTYLKRVQMANLQLDDSLPIGDFRPLTEDELQ 231


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 67/261 (25%), Positives = 128/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V +   +
Sbjct: 53  VSNKNEIRDEV---RLNKYISETGFCSRREADKLIEQGRVKIDGVKATT-GMKVSNGQSV 108

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG  L+          +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 109 SIDGKSLKVENELVYIALNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 166

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 167 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLVKKE 226

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 227 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKE 282

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 283 LAEI--NRLTENSSKTEEASI 301


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 117/228 (51%), 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  KVYIMLNKPEGYVTTNKDEKNRKTILDIV-KVNERIYPIGRLDYDSSGLLLLTNDGDVYN 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|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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 112/229 (48%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     + +D       G+ +          TL+  K ++  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLEQPLAEDTAAQFTAGVQLHNEKNLTKPATLE--KITDHVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGDIWLDSELEPGEFRELSDEEI 227


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 116/374 (31%), Positives = 171/374 (45%), Gaps = 34/374 (9%)

Query: 2   KDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KDK   QE     +++ KV+AR G+ SRR+VE  I Q R+KVNG         V   D I
Sbjct: 4   KDKQDSQEIGPAGEKLQKVLARIGVGSRRDVEAWITQGRIKVNGKDAT-VGQRVDLHDAI 62

Query: 61  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAP 302

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------R 331
              D         Q  G  + +       +R          G  +   +D+ +      R
Sbjct: 303 ATGDRA---PRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAER 359

Query: 332 EENHRRSPSFPSKR 345
                + P+ P  +
Sbjct: 360 PSEMNKRPAKPGPK 373


>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 =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 112/369 (30%), Positives = 175/369 (47%), Gaps = 35/369 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            +DG  +++ E      R+ +Y+KP G + T  DP+GR TVFD +P     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 QVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRD-RPNI-- 274
           RE+S+     L  ++G   +   Q+N  +             P+  +E + R  RP +  
Sbjct: 243 REMSQYEVDILSAEVGLTPVAMPQMNAKSKDKLERMQRKSSRPVARTERVARTLRPALNA 302

Query: 275 ------ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
                 IS  P      +  +  +    +  +   P       SN   A     +  +  
Sbjct: 303 PATGGRISREPQIEGERRPTAPSRQEGERAPRTPRPAPAGGR-SNRGEADRPADNASTKR 361

Query: 329 GQREENHRR 337
             +   ++R
Sbjct: 362 PAKPAANKR 370


>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 =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 105/230 (45%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V +NG + +  A  V   D I  DG  L   E  
Sbjct: 1   MRLDKFLAETTGLTRSQAAKVLRQSAVTINGKIEKSGAAKVSPDDEIYYDGERLTWVENG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           +  + HKP G + +H D D   T++       S  + S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYIMLHKPQGYICSHEDGDH-PTIYQFFDYPLSTCLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P   + + Y V     V+ +      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHYPKTYLVTLADPVEANYAQACAEGILLRGEKEPTKPAELEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGNLVLDDDLGEGEFRPLTEEEI 227


>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 =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 153/294 (52%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 122/242 (50%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K + ++ +   P R++K ++ AG+ SRRE + +I +  + VNG ++      +   D +
Sbjct: 191 VKYREVLADPNEPIRLNKFLSNAGVCSRREADLLIEKGEITVNGEVVTELGRRITRQDEV 250

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTE 119
                 +   E     L +KP   VTT  DP+ R+TV D +  +   R+  VGRLD NT 
Sbjct: 251 IYKDKRVE-IESKVYVLLNKPKNCVTTSDDPECRTTVMDIVRYACPERIYPVGRLDRNTT 309

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LL+TNDG LA  L  PS +  ++Y V  +  V  + +  +  G+ +         ++ 
Sbjct: 310 GVLLITNDGDLASKLTHPSFKKKKIYHVWLNKDVSIEDMQKIADGVELDDGEIHADAISY 369

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++   + V + +  G+NR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 370 -VKEDDLSQVGIEIHSGRNRIVRRLFEHLGYRVVKLDRVYFAGLTKKNLPRGKWRYLNEQ 428

Query: 240 IL 241
            +
Sbjct: 429 EV 430


>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 =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 122/248 (49%), Gaps = 12/248 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +G+ +R+EV+++I Q RV VNG ++     +V   D + +DG  +    R 
Sbjct: 1   MRLDRYLSNSGVGTRKEVKKLIKQGRVTVNGRVVLDPGHSVSENDVVVLDGETVNF-HRK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP G VT+  DP    T+ + LP     +  VGRLD + EGLL++T+DG  A  
Sbjct: 60  VYILFHKPSGYVTSTKDP-HSETIMEFLPP-LKGIFPVGRLDKDAEGLLIITSDGDFAHR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V+  G+V +DK+  LK G+ ++   +   +     +K SN  + + +
Sbjct: 118 VISPKWSVEKEYIVKVEGEVTEDKIEKLKNGVTLRDGFFAKAKC---VEKLSNDTLKIVI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEE 252
            EGK  +IK++      +   L R   G   L   +  G  R +S++ ++      + E 
Sbjct: 175 TEGKYHQIKRMTVAVGLRTVHLKRTRIGRLVLPEDMKPGEYRFLSEEEVK-----KVFER 229

Query: 253 AQVNLDAP 260
                D P
Sbjct: 230 EDQKEDTP 237


>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 =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 129/233 (55%), Gaps = 3/233 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K +A  G+ SRRE++++I + +++VNG ++  A V V   D IEV G  + K 
Sbjct: 1   MEEIRINKYLASLGVGSRREIDKLIEEGKIRVNGEVI-SAGVKVTDKDIIEVKGKKISKD 59

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   ++ +KP+ ++++  D  GR TV D +     R+  +GRLD NT GL+LLTNDG 
Sbjct: 60  IEKKVYYMLNKPLEVLSSAKDDRGRKTVVDIV-KCKERIFPIGRLDYNTTGLILLTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P ++  + Y V+  G++    +  L+ G+ ++        V L +++   + +
Sbjct: 119 LFNRVIHPRSEVYKEYYVKVLGEIKDSSIKKLEDGVELEDGITLPAYVKLISRERGKSEL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            V +REG+NR+++++ E  N  V  L R   G   LG L  G  RE+++  ++
Sbjct: 179 MVSIREGRNRQVRRMLEAVNTPVLVLRRERIGKLSLGKLKVGEYRELTESEVK 231


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 102/316 (32%), Positives = 151/316 (47%), Gaps = 13/316 (4%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            ++   F  +++ KV+A AGI SRR++E  IA+ R+ VNG         V  +D I  DG
Sbjct: 45  KLLTAPFANEKLHKVLADAGIGSRRDMEERIAEGRISVNGEPA-HVGQRVTPSDVIRFDG 103

Query: 65  VPLRK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
             +R+      +  ++ +YHKP G + +  DP+GR TVFD+LP I  +R I+VGRLD NT
Sbjct: 104 RIVRRSALENNDVPKVLIYHKPAGEIVSKDDPEGRPTVFDHLPRIGGARWIAVGRLDFNT 163

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL T+ G LA  L  P  +  R Y VR  G +  +  + L KGI +         + 
Sbjct: 164 EGLLLFTDSGNLANFLMHPRHEIEREYAVRVQGTMSPEAKDKLLKGIKLDDGIAKFTTLE 223

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               KG N W  V L EG+NRE++++FE     V+RLIR+ YG  +L   L  G TR +S
Sbjct: 224 EGGGKGFNRWYNVTLSEGRNREVRRMFEAVGLPVSRLIRVKYGNLELPSDLPRGKTRRMS 283

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +   + L     ++      AP     T         +  P    +  +        S 
Sbjct: 284 TEETEKWLDSISYKKGMSTAPAPRAPERTPRPAASRAPASAPKAGRKFGQRD-----TSS 338

Query: 298 QKKLATPVHRRNLASN 313
             + + P+  R     
Sbjct: 339 AIRSSRPMRSRGTRGP 354


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 107/311 (34%), Positives = 151/311 (48%), Gaps = 23/311 (7%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHI 60
             K   + +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I
Sbjct: 12  PGKATPKGSSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKI 71

Query: 61  EVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLD 115
            +DG  +   E      R+  Y+KP G + T +DP+GR TVFD LP    +R I+VGRLD
Sbjct: 72  RIDGHLISVRESAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLD 131

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           +NT GLLL T DG LA  L  PS +  R Y VR  GQVD  KL  L +G+ ++       
Sbjct: 132 VNTCGLLLFTTDGELANRLMHPSREVEREYAVRVFGQVDDAKLRDLSRGVQLEDGPAAFK 191

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
            +     +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   
Sbjct: 192 TIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWT 251

Query: 235 EVS---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E+       LRE           V L     S   + +DR  + +       R  K  SQ
Sbjct: 252 ELDLAQTNYLREL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQ 298

Query: 292 KNGLSKQKKLA 302
            +G  +     
Sbjct: 299 VSGGRRSGGRN 309


>gi|227111426|ref|ZP_03825082.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 294

 Score =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 107/304 (35%), Positives = 151/304 (49%), Gaps = 23/304 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEGIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T +DPDGR TVFD LP    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-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWTEMPLEQLNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K  SQ N    ++   
Sbjct: 242 EL----------VQLPAETVSKLPVERERRRVKAN---QIRRAVKRHSQINTAPARRTSP 288

Query: 303 TPVH 306
            P  
Sbjct: 289 KPKR 292


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 120/245 (48%), Gaps = 7/245 (2%)

Query: 5   NIVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N   +   P+  R+   +A  G+ASRR  E  IA  RV VNG ++      V+  D + V
Sbjct: 13  NSSADQSQPESLRLQVYLAHCGVASRRSCETYIADGRVSVNGTVVTVPGTKVLPDDTVCV 72

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGL 121
           DG  +   E  R  L +KP G V + SD  GR T    L P    R+ +VGRLD+ + GL
Sbjct: 73  DGKRVTLEETKRYVLLNKPAGFVCSLSDEKGRQTAASLLEPHYSERLYNVGRLDMFSAGL 132

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +L TNDG  A  +  PS++  + Y V     V         KGI +  + Y         
Sbjct: 133 VLFTNDGEFAARVSHPSSEMEKEYVVDTSLPVPPALAEKFVKGIRVDNVFYRCKSA---- 188

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++ ++  + + L EGKNREI++VFE FN  V +L+RI  G   +  L  G  R+++   +
Sbjct: 189 ERLNSRRMRIVLIEGKNREIRRVFEAFNIGVKQLVRIRIGNLNIQGLGPGEFRDLTAAEV 248

Query: 242 REQLG 246
            + L 
Sbjct: 249 ADILA 253


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 55/229 (24%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D     K G+ + G        TL+    +   V + +
Sbjct: 121 ITAPKHHCEKTYVVTLEQPIATDVAEKFKTGVQLNGEKELTKPATLEV--ITPTEVKLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGKYHQVKRMFAAVGNHVVALHRERIGDITLDDALAPGEYRPLTEEEI 227


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 79/242 (32%), Positives = 132/242 (54%), Gaps = 11/242 (4%)

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  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           E     + +KP G+++   D   +  V D LP  +       VGRLD + EGLLLLTNDG
Sbjct: 65  E-YIYLMLNKPQGVLSATEDRYAK-VVVDLLPPRYRAFHPFPVGRLDKDAEGLLLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     ++Y     G V +  +   ++GI++  G      ++T+  + G+ +
Sbjct: 123 ELAHRLLSPKKHVSKMYYAVVDGIVTETDVEAFRQGIILNDGYRTMPGELTIL-RSGTES 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
            V + + EGK  ++K++FE  + +V  L RI+ GP +L   L  G  RE++++    LRE
Sbjct: 182 EVELTIYEGKYHQVKRMFEAVSKRVLYLKRIAMGPLRLDELLRPGEYRELTEEEIIKLRE 241

Query: 244 QL 245
            L
Sbjct: 242 LL 243


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 109/307 (35%), Positives = 155/307 (50%), Gaps = 25/307 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T +DPDGR TVFD LP    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-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWTEMPLEQLNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K  SQ    S   +  
Sbjct: 242 EL----------VQLPAETVSKLPVERERRRVKAN---QIRRAVKRHSQI--SSAPARRT 286

Query: 303 TPVHRRN 309
           +P  +RN
Sbjct: 287 SPKSKRN 293


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 135/294 (45%), Gaps = 12/294 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           +  R++K I+ +GI SRR+ +R I Q  V +NG       V V + D ++V+G  +    
Sbjct: 5   SSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAT-VGVQVSAGDVVKVNGQIIEPRN 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 64  EEDLILIALNKPVGVISTTEDGEQNNIV--DFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G      +V     + +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKVK----REATFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R+      L  L  G  R++++  L E     L
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERVRIMNISLKGLPQGEWRDLTEDELIELF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +  + + P+  +     +   +    P    +   N++ +   ++  +   
Sbjct: 236 IENSSSD-EKPVKKAPVKAVEAKRVSISGPKKTEKPDGNAASRKRFAQPGRKKK 288


>gi|325520892|gb|EGC99873.1| ribosomal large subunit pseudouridine synthase B [Burkholderia sp.
           TJI49]
          Length = 328

 Score =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 90/273 (32%), Positives = 144/273 (52%), Gaps = 6/273 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 38  NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRI 96

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 217 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELE 276

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           +  +R+ +    L+            +E    D
Sbjct: 277 EAQVRKLMATVGLKAPSEEKGRRGGETERRQPD 309


>gi|315166874|gb|EFU10891.1| conserved hypothetical protein [Enterococcus faecalis TX1341]
          Length = 257

 Score =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRNETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 108/310 (34%), Positives = 156/310 (50%), Gaps = 23/310 (7%)

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  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    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-GTLLAGSTREVSK---KILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWTELELPAINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + R+R  + +       R  K  +Q  G  ++    
Sbjct: 242 EL----------VELKPETVSKMPVERERRRVKAN---QIRRAVKRHTQVAGSGRRSAPG 288

Query: 303 TPVHRRNLAS 312
           +   + +  S
Sbjct: 289 SKSGKPSKRS 298


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 111/229 (48%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     + +D       G+ +          +L+  K ++  V + +
Sbjct: 121 ITSPKHECEKTYLVTLEQPLAEDTAAQFTAGVQLHSEKNLTKPASLE--KVTDYVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  RE+S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGISLDSELEPGEYRELSAEEV 227


>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 =  267 bits (682), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 73/243 (30%), Positives = 123/243 (50%), Gaps = 5/243 (2%)

Query: 2   KDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            +  I     TP   R++K IA AGI SRR  +  I+   V VNG ++      V  TD 
Sbjct: 163 NNAPIDYPTVTPAEVRLNKYIADAGICSRRNADMYISSGNVTVNGEVMTTLGYRVKPTDE 222

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           +  DG  L  +E+    L +KP G +TT +D  GR TV D + +   +R++ VGRLD  T
Sbjct: 223 VRFDGKLLS-SEKKEYILLNKPKGFITTTNDEKGRKTVMDLVANATSARILPVGRLDRAT 281

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG L + L  P+    ++Y V    ++D      ++ G+ ++       +++
Sbjct: 282 TGLLLLTNDGELTKKLTHPTHGVRKIYHVILDRKLDYKDFMKIQDGLELEDGFIEVDEIS 341

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               K  N  + + +  G+NR ++++FE   ++V +L R+ +       L  G  R +++
Sbjct: 342 YVNDKPKN-EIGIKIHSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQ 400

Query: 239 KIL 241
           + +
Sbjct: 401 QEV 403


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 115/234 (49%), Gaps = 8/234 (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 ++      + D +     R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAE-HIEDNIIDYI-DYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    + + +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVNQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELEILIG 227


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    V+++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVRIDGKPVKDAKFHVNIEKQEVTIYGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEGLLLLTNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DHHETVVDLLEFEDAIFNPFPVGRLDIDTEGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V +  +    KG+V+  G      ++T+       + +
Sbjct: 119 THQLLSPKKHVPKKYYAHIEGVVTEKDVEDFAKGVVLDDGYETKPGELTILNSD-DISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+  GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRVEMGPLTLDEELELGQYRELTDEEVE 231


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/269 (29%), Positives = 120/269 (44%), Gaps = 33/269 (12%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           +   P R+ K +ARAG ASRR  E ++   RV VNG ++      V    D + VDG  +
Sbjct: 25  DRVVPMRLQKFLARAGAASRRGSENLMTAGRVTVNGKVVTELGSKVDPLVDEVAVDGAVV 84

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
           R A+     + HKP G VTT SDP GR TV + +P   +  +  +GRLD +T GLLL + 
Sbjct: 85  RLADGPVTIMLHKPAGFVTTMSDPQGRRTVAELVPTERYPGLFPIGRLDFDTTGLLLFST 144

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG L   L  P     + Y     G+  +  L LL++GI +         V +       
Sbjct: 145 DGELGNGLLHPKHHVTKRYLACVEGRPTERDLALLRRGIELDDGPTQPADVRMVEGGAAR 204

Query: 180 ------------------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
                                   + +    + V +G+REG+ R++K++       V  L
Sbjct: 205 HAERLLEIPAAVPPRSSKEYAAVCEGRATRRSIVRLGIREGRKRQVKRMLAAVGHPVLAL 264

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQ 244
            R S+GP +LG L  GS R +  + +   
Sbjct: 265 HRDSFGPLELGDLPRGSWRALDAEEVAAL 293


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 72  IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 131

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 132 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 190

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++        ++ 
Sbjct: 191 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISY 250

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 251 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 309

Query: 240 IL 241
            +
Sbjct: 310 EV 311


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 105/236 (44%), Gaps = 3/236 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     +  D      +G+++ G  Y      L+    S   V + +
Sbjct: 121 ITSPKHHCEKTYRVELENDIADDVAKRFAEGVMLNGEKYPTKPAQLEV--ISPKEVLLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            EG+  ++K++F      V  L R   G   L   L  G  RE+++  +   + P 
Sbjct: 179 SEGRYHQVKRMFAAVGNHVCGLHRERIGDIWLDDDLAPGEYRELTEDEINSVIVPR 234


>gi|322832033|ref|YP_004212060.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167234|gb|ADW72933.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 235

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 106/229 (46%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D     + G+ +           L+  K  +  V + L
Sbjct: 121 ITSPRHHCEKTYLVTLEHPLADDTAAQFEAGVQLHNEDSLTKPAQLE--KIEDCLVRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   +   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVALHRERIGEIVMDEDLEPGQYRPLTEQEV 227


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 103/236 (43%), Gaps = 3/236 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ +    Y     TL+    S   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPLADDTAAQFTAGVQLHNEKYLTKPATLEV--VSECQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            EG+  ++K++F      V  L R   G   +   L  G  R ++ + +   + P 
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVALHRERIGAIVMDEDLGEGEYRPLTAEEIASVVVPR 234


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 129/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V     +
Sbjct: 50  VSNKNEIRDEV---RLNKYISETGFCSRREADKLIEQGRVKIDGVKATT-GMKVSKGQSV 105

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG PL+        + +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 106 FIDGKPLKVENELVYIVLNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 163

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 164 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLVKKE 223

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 224 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLTKKE 279

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 280 LAEI--NRLTENSSKTEEASI 298


>gi|227326052|ref|ZP_03830076.1| 23S rRNA pseudouridylate synthase B [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 294

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 110/307 (35%), Positives = 156/307 (50%), Gaps = 25/307 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEVIIQAGRVSVDGKIATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T +DPDGR TVFD LP    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-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWTEMPLEQLNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K  SQ N  S   +  
Sbjct: 242 EL----------VQLPAETVSKLPVERERRRVKAN---QIRRAVKRHSQIN--SAPARRT 286

Query: 303 TPVHRRN 309
           +P  +RN
Sbjct: 287 SPKPKRN 293


>gi|167719822|ref|ZP_02403058.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
          Length = 399

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 93/306 (30%), Positives = 151/306 (49%), Gaps = 8/306 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 97  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 155

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 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+      D          R +P+ +        R    ++       +
Sbjct: 336 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPR 393

Query: 299 KKLATP 304
           +    P
Sbjct: 394 RGRRGP 399


>gi|124515286|gb|EAY56796.1| Pseudouridine synthase, Rsu [Leptospirillum rubarum]
          Length = 616

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 96/348 (27%), Positives = 161/348 (46%), Gaps = 12/348 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPL 67
           +     R+ K++A  G+ASRR  E MI    VKVNGI++      V   TD + VDG  +
Sbjct: 13  DEDGLIRLQKLLAHRGLASRRNAEEMIRGGLVKVNGIVVTVPGTKVHPETDRVTVDGKTV 72

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                  L+L++KP G+V+T  DPD ++T+ D  P I   +  VGRLDI +EG+LLLTN+
Sbjct: 73  PVEPEPFLFLFYKPKGIVSTLHDPDEKTTLKDFFPQINPLIH-VGRLDIQSEGVLLLTNN 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G LA+ +  P  +  R Y V+  G V  + L+ L+ G + + G     +++  +    +N
Sbjct: 132 GDLAQRILHPRYEIPRTYLVKVQGVVKPEHLDRLRSGKVRLDGRPVQPLELEQERLTETN 191

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +W  + L EG+NRE++++F+  ++ V +L RI++G   L  L  G  R V+ + +   L 
Sbjct: 192 SWYRITLTEGRNREVRRLFDALHYFVLKLTRIAFGNLDLAGLEPGEYRLVTPEEIALLLS 251

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
               +  +         S       P   +         +++S +    S  +  + P  
Sbjct: 252 GARWKRKE---------SIPPPERSPRKPNPATPSSPDFRRHSFRSRTTSPDRTFSGPAD 302

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                       G       D+  R  +   S  F + R   R+  K+
Sbjct: 303 GDQEEDPFPRQTGQGHRSRPDTRSRGLSQSDSERFFNGRPRHRSDNKQ 350


>gi|311279823|ref|YP_003942054.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749018|gb|ADO48770.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 299

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 105/309 (33%), Positives = 153/309 (49%), Gaps = 23/309 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G +      V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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-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 +      E++V ++          +DR  + +       R  K  SQ N    +    
Sbjct: 242 ELVELKPETESKVAVE----------KDRRRMKAN---QIRRAVKRHSQVNSKPARSTGR 288

Query: 303 TPVHRRNLA 311
               R + +
Sbjct: 289 RASSRNSGS 297


>gi|291618129|ref|YP_003520871.1| RsuA [Pantoea ananatis LMG 20103]
 gi|291153159|gb|ADD77743.1| RsuA [Pantoea ananatis LMG 20103]
          Length = 239

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 106/241 (43%), Gaps = 3/241 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     V  D       G+ +           L+    +   V + L
Sbjct: 121 ITSPRHHCEKTYRVTLEAPVSDDTAAQFSAGVQLHNEKSLTKPAQLEV--ITPTEVLLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +     P  L++
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGEIVLDEALEPGEYRPLTEEEIASIGLPDELKQ 238

Query: 253 A 253
            
Sbjct: 239 K 239


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 101/278 (36%), Positives = 150/278 (53%), Gaps = 10/278 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             + +R+ KV+A+AG  SRRE+ER I   RV+VNG + +     V   D + +DG  +  
Sbjct: 2   TMSEERIQKVLAKAGQGSRREMERAIESGRVQVNGEVAK-LGDKVSEKDELRLDGKKISV 60

Query: 70  AERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T  DP+GR TVFD LP I   R I+VGRLDINT GLLL TN
Sbjct: 61  EAEKVRRVLIYNKPEGEICTRKDPEGRHTVFDRLPRIPGERWIAVGRLDINTSGLLLFTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS Q  R Y VR  G V Q+ ++ + +G+ ++        V     KGSN
Sbjct: 121 DGELANRLMHPSHQIEREYAVRVLGDVQQENIDAMCEGVELEDGPAKFTDVQFFDGKGSN 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ- 244
            W  V + EG+NRE+++++E   ++V+RL R+ YG   L   + AG+ +E++KK + +  
Sbjct: 181 LWFHVVIMEGRNREVRRLWESQGFQVSRLKRVRYGSVFLDSDVRAGTWQEMAKKDIDQLA 240

Query: 245 ----LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEV 278
               L P   +    +   P+       R R ++    
Sbjct: 241 KTVDLAPAPWKSIVKHKRDPMKRKMEKQRTRRSVGKTS 278


>gi|297170719|gb|ADI21742.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [uncultured actinobacterium
           HF0130_15N16]
          Length = 239

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 127/238 (53%), Gaps = 6/238 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E    +R+ K ++RAG+ASRR  E MI   RV +N  +       V  TD IE+DG+P
Sbjct: 1   MTEEEPLERLQKALSRAGVASRRVSEGMIEAGRVTINRRVAT-VGDRVSVTDRIELDGIP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + +      +L +KP+G+V+T  DP  R TV D + S   R+  VGRLD ++EGL++LTN
Sbjct: 60  VIRDPDLVHYLLNKPVGVVSTSKDPQKRRTVVDLV-SSNERIFPVGRLDADSEGLIILTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS    + Y V   G   +  L LL++G+ ++  C     V +      +
Sbjct: 119 DGELTHRLTHPSFGVSKEYLVHVEGVPSRSSLRLLREGVELEDGCTAPANVAM----PQD 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + + + EG+NR+++++       V RL+R+  G  +  +L  G+ R +S + +R  
Sbjct: 175 GVMRITIHEGRNRQVRRMCAAIGHPVQRLVRVRIGSIKDPSLRVGTARRLSVEEVRSL 232


>gi|152967064|ref|YP_001362848.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361581|gb|ABS04584.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
          Length = 322

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 119/238 (50%), Gaps = 1/238 (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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           V V L EG+   ++++ E   + V +L+R+  GP  LG L  G  R +++  +++ + 
Sbjct: 261 VEVVLHEGRKHIVRRMLEAEGYPVLKLVRVQMGPIVLGDLKPGKNRRLTRGEVQQLMA 318


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 71  IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 130

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 131 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 189

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++        ++ 
Sbjct: 190 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISY 249

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 250 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 308

Query: 240 IL 241
            +
Sbjct: 309 EV 310


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 131/232 (56%), Positives = 167/232 (71%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R++K +AR+G+ASRR+ ER++ + RV++NG  +   A  V + D ++V+G  +   ERT
Sbjct: 21  ERIAKWLARSGVASRRDAERLVEEGRVRLNGEPVTHPATFVAAGDIVQVNGAVVEAPERT 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RLW YHKP GLVTTH DP+ R TVF +LP    RVISVGRLD+N+EGLLLLTNDG LAR 
Sbjct: 81  RLWRYHKPDGLVTTHRDPEKRPTVFASLPPGMPRVISVGRLDLNSEGLLLLTNDGELARR 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           LELPS  WLR YRVR  G VD+ +L  L  G V +G+ YG ++  LD++KG NAW+TV L
Sbjct: 141 LELPSNGWLRRYRVRVFGVVDEARLAALAGGSVFEGVRYGPIEAGLDSRKGDNAWLTVAL 200

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           REGKNRE++KV    N  V+RLIR SYGPFQLGTL      EV  K+LREQ+
Sbjct: 201 REGKNREVRKVMRGLNLHVSRLIRTSYGPFQLGTLQRSELEEVPGKVLREQV 252


>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 =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 85/277 (30%), Positives = 138/277 (49%), Gaps = 3/277 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
              +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +  +
Sbjct: 18  MAEERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQ 77

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K ++      +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG
Sbjct: 78  KNQQLYYLALYKPRGYVTTASDELGRKTVMELVSDIPARLYPVGRLDKDSEGLLLMTNDG 137

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
             A+ +  PS    ++YRV    + D+ ++  +  G+V+  G       + + T +    
Sbjct: 138 AFAQAVTHPSGGISKLYRVTVQPRADESQILKMSSGVVLDDGTKTMPCAINVVTDEPGRT 197

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +      
Sbjct: 198 VMEMTLKEGKNREIRRMCEAVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEVSGLRAA 257

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
                AQ    A    +       P      P    +
Sbjct: 258 AAKGRAQTRSAALQSKAAARRPKGPVGSGNAPAKRRK 294


>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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 78/240 (32%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R+ K+++  G  +R+EV+  I +  V VNG  +    + +    D I  +   +  
Sbjct: 1   MAKMRIDKLLSNTGFGTRKEVKGFIKEGLVTVNGRTVNDPGLIIETDKDDIIFNDEKIFY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
             +    + +KP G+++   DP    TV D LP      +V   GRLD +TEGLLLLTND
Sbjct: 61  R-KYIYIMMNKPRGVISATYDP-SEKTVLDLLPDDIKARKVFPAGRLDKDTEGLLLLTND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  P     + Y     G +D+D ++L   GIV+    Y  M   L+    GS 
Sbjct: 119 GILAHKLLSPKKHVYKKYYAEISGFIDEDDISLFSNGIVLDDG-YKTMPAYLEIISSGSI 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + V V ++EGK  +IK++FE    KV  L R+S G   L   L  G  RE++   L+  L
Sbjct: 178 SKVYVSIKEGKYHQIKRMFESLGSKVIYLKRLSMGYLNLDENLKEGEWRELTDNELKLLL 237


>gi|148828349|ref|YP_001293102.1| methyltransferase [Haemophilus influenzae PittGG]
 gi|148719591|gb|ABR00719.1| predicted methyltransferase [Haemophilus influenzae PittGG]
          Length = 357

 Score =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPHLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGSANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFAGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|56478942|ref|YP_160531.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
 gi|56314985|emb|CAI09630.1| pseudouridylate synthase [Aromatoleum aromaticum EbN1]
          Length = 317

 Score =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 93/267 (34%), Positives = 139/267 (52%), Gaps = 7/267 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
            P+R+ KV+A+ G+ SRRE+E  +   R+ VNG+        +   D ++ +G  +    
Sbjct: 53  EPERLQKVLAQIGLGSRREIEEWVVAGRISVNGLPA-ELGQKIGPGDRVKYNGKLIPLRF 111

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G + +  DP+GR TVF+ LP +   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 PHLLEEAQVNLDAPIYSSETLVRDRPN 273
                + Q            L R  P 
Sbjct: 292 L-PKPQGQAARPGEQVRKTRLHRTTPR 317


>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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 153/294 (52%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQSKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPHLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGSANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLQNVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|301165765|emb|CBW25337.1| putative RNA pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 343

 Score =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 91/277 (32%), Positives = 137/277 (49%), Gaps = 3/277 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR-KAER 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L EG+NREI+K+ E     V++L R++     +  +  G  R ++KK L   +G      
Sbjct: 185 LGEGRNREIRKICEACGLTVDKLKRVAIEGLTVEGIAPGKFRYINKKQLLSLIGLSEDGR 244

Query: 253 AQVNLDAPIYSSETL-VRDRPNIISEVPDDFTRMKKN 288
              ++ A + S +T+ ++ +        DD   +K  
Sbjct: 245 KLESVKAWVSSKKTVNLKKKGVQPGTAADDEAWIKYR 281


>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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 99/308 (32%), Positives = 149/308 (48%), Gaps = 14/308 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  E   P ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+
Sbjct: 108 KYLNSEAVMP-KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVN 165

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+ +    +  R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTE
Sbjct: 166 GKPIARPNAKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTE 225

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A  +  P     R Y VR  G++D  +   L +GI ++           
Sbjct: 226 GLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEY 285

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
               GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G       
Sbjct: 286 LGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDIVLPRNLRRGRW----- 340

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS--SQKNGLS 296
           + L   L   L+ +  +  D          R   +  S +P  F  +++N     + G  
Sbjct: 341 EELDGSLVTALMVQLGLLRDGDESEGRRKSRQPQSHDSALPPGFGTLERNGMNGARIGRR 400

Query: 297 KQKKLATP 304
            + +   P
Sbjct: 401 GKLQGGRP 408


>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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 83/233 (35%), Positives = 132/233 (56%), Gaps = 3/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNG+++      V ++D IEV+GV L K E  
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLILEGKVKVNGVVVRELGTKVSNSDTIEVEGVKLEK-EDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G ++  +D  GR TV D    I  R+  VGRLD +T GLLLLTNDG  + +
Sbjct: 61  VYFLLYKPRGTISAVTDDKGRKTVTDLFHHIPQRIFPVGRLDYDTSGLLLLTNDGEFSYM 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTV 191
           L  P  +  + Y  R  G    + L  L++GI ++       +V++ +  +K   A   +
Sbjct: 121 LTHPKFKIDKTYIARVKGVPTIEGLKKLQRGIKLEDGKTAPAKVSMTSFDEKAGKAICEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EG+NR+++++FE     V +L R  +    L  L  G  RE+SK  +++ 
Sbjct: 181 TIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLFGLAPGEYRELSKHEVKQL 233


>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 =  266 bits (681), Expect = 4e-69,   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|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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE + +I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDCLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELDNLEVGKWRSVTSEELEILIG 227


>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 =  266 bits (681), Expect = 4e-69,   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|330989187|gb|EGH87290.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 408

 Score =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 115/374 (30%), Positives = 170/374 (45%), Gaps = 34/374 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VD   +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRDRPNIISE 277
           RE+S+     L  ++G   + + Q+N                P+   E +   RP   + 
Sbjct: 243 REMSQYEVDILAAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRPAAGAP 302

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------R 331
              D         Q  G  + +       +R          G  +   +D+ +      R
Sbjct: 303 ATGDRA---PRQPQITGSERDRPRGGDSTQRPSPRKDSGKPGSRAPRPADNSRGTPVAER 359

Query: 332 EENHRRSPSFPSKR 345
                + P+ P  +
Sbjct: 360 PSEMNKRPAKPGPK 373


>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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 118/356 (33%), Positives = 172/356 (48%), Gaps = 38/356 (10%)

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----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLL 122
           ++ E T    R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLL
Sbjct: 65  KREEITGSVRRVLIYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLL 124

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDT 181
           L T DG LA  L  PS Q  R Y VR  G+V ++ L  LK G++++        +     
Sbjct: 125 LFTTDGELANRLMHPSYQMDREYAVRVRGEVTEEMLENLKTGVMLEDGPAKFTDIKEAPG 184

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L     RE+ ++ 
Sbjct: 185 GEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMARWREMDQRE 244

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +                   I S+E         +   P     MK+ + +K     Q+K
Sbjct: 245 V------------------DILSAE---------VGLTPQALPAMKEKTREKLDRL-QRK 276

Query: 301 LATPVHRRNLA--SNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
            A PV  R            G  S+  S + +R+E  +R+P  P K    R    +
Sbjct: 277 SAKPVEVRGKRVLRPAKDEAGADSARPSRAPRRDEAEQRTPRGPRKEGGERRENGR 332


>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 =  266 bits (681), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 118/242 (48%), Gaps = 14/242 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ K++   G  SR ++++ + Q  + VNG  ++ + + V    D IEV+G  +   
Sbjct: 7   QTQRLDKILTHMGYGSRSDIKKQVKQGMITVNGRTIKDSGLQVHPYQDQIEVNGELVVFR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + HKP G+++   D   R TV D L +         VGRLD +TEGLLLLTNDG
Sbjct: 67  E-FIYIMLHKPPGVISATEDTRER-TVLDLLSAEERHFEPFPVGRLDKDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS-- 185
            LA  L  P     + Y     G V ++ +     G+ +  G      Q+T+   +    
Sbjct: 125 KLAHELLSPRRHVPKTYEATVSGHVTEEDILQFTAGVELDDGYVTLPAQLTILRHEQPHQ 184

Query: 186 -----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
                 +++++ + EGK  ++K++FE    KV  L R + GP +L   L  GS RE++ +
Sbjct: 185 ADGEVTSYISLVIHEGKFHQVKRMFEAIGKKVTYLKRTAMGPLKLDDQLPLGSYRELTSE 244

Query: 240 IL 241
            L
Sbjct: 245 EL 246


>gi|167562943|ref|ZP_02355859.1| RNA pseudouridylate synthase family protein [Burkholderia
           oklahomensis EO147]
          Length = 354

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 137/248 (55%), Gaps = 6/248 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 48  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 106

Query: 64  GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P++     +  R+ LYHKP G + +H+DP+GR +VFD LP++  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 227 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELEE 286

Query: 239 KILREQLG 246
             +R  + 
Sbjct: 287 AQVRRLMA 294


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 82/343 (23%), Positives = 149/343 (43%), Gaps = 18/343 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +G+ SRR  +R I Q  V +NG   +     V   D + V+G  +   E   
Sbjct: 7   RLNKYISESGLCSRRAADRYIEQGNVYINGKKAK-VGDKVFFGDIVTVNGQTIDPKEVEN 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L  Y+KP+G+ +T ++   +  + D++ +   RV  +GRLD +++GL+ LTN+G L  
Sbjct: 66  SVLIAYNKPVGITST-TEAGVKGNIVDHV-NHSERVFPIGRLDKDSQGLIFLTNNGDLVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +    +  + KG+ + G+     +V     K S     + 
Sbjct: 124 KILRAGNNHEKEYVVTVNKPLTDQFITGMAKGVPVLGVMTKKCKVV----KESPLIFKIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R+      L  +  G  RE++ + L      +++ +
Sbjct: 180 LIQGLNRQIRRMCEYFGYEVTKLERVRIMNIPLKGIPLGEWRELTPEELTGIF--NMVAK 237

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +    DA    +   V  +P    E           SS +N   K K  A P   R    
Sbjct: 238 SSAEADA----TPKRVSKKPKTPKEEDFLENVTPGRSSGRNAKPKSKGKAAPASVRREDR 293

Query: 313 NVWMAKGIHSSFLSDSGQREENHR--RSPSFPSKRSLRRTSAK 353
                KG      S + +             PSKR ++ T  +
Sbjct: 294 PAG-GKGKSGPKTSAAFKTTGAAGDWNKSGGPSKRPVKPTKGR 335


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 106/334 (31%), Positives = 162/334 (48%), Gaps = 24/334 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +     +++ KV+ARAG  SRRE+E +I Q RV V+G +      V V     I +DG  
Sbjct: 29  KTKVVGEKLQKVLARAGHGSRREIETIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHL 88

Query: 67  LRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           L   E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GL
Sbjct: 89  LSIKESEETVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGL 148

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  G +D +K+  L +G+ ++        ++   
Sbjct: 149 LLFTTDGELANRLMHPSREVEREYAVRVFGLIDDEKIKQLSRGVQLEDGPAAFRTISFQG 208

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
            +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K 
Sbjct: 209 GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKA 268

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LR+           V +D+   S   + +DR  + +       R  K  ++  G   
Sbjct: 269 TNYLRQL----------VEMDSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQV 315

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
             +  +   + +   N   A    ++    + +R
Sbjct: 316 AGRQGS-ARKGSTRQNTGNAAPAATAGRRGTNKR 348


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 116/236 (49%), Gaps = 7/236 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V   +D I  DG  +  
Sbjct: 1   MAKMRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTESDEILFDGEKINY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G+++   D +   TV D LP          VGRLD +TEGLLL+TND
Sbjct: 61  KE-FIYIMINKPKGVISATYD-EVEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G LA  L  P    ++ Y     G V++  +    +GI++  G       + +       
Sbjct: 119 GDLAHQLLSPKKNVIKKYYAEILGFVNESDIKAFNEGIILEDGYKTLPANLEILFSSSDV 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V V +REGK  +IK++FE    KV  L R++     L   L  G  RE+S+K L
Sbjct: 179 SKVYVYIREGKYHQIKRMFESVGKKVIYLKRLAMDNLTLDENLKPGEWRELSEKEL 234


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 78/326 (23%), Positives = 137/326 (42%), Gaps = 19/326 (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  YIAYNKPVGITCTTERKIQSNIVKA--VNYPERIFPIGRLDRPSEGLIFLTNEGDIVNKI 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +++  +N +  GI I        +VT   Q G+    ++ L 
Sbjct: 123 LRAGNNHEKEYVVTVDKPLNRQFVNKMANGIPILDTVTKKCKVT---QTGAQ-QFSIILT 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E+  ++V  L R+      L  L  G  R +S   +   +   + +  +
Sbjct: 179 QGLNRQIRRMCEYLGYEVVTLKRVRIMNVTLKGLKVGQWRHLSDAEM-AVINDSIADSGK 237

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTR-------MKKNSSQKNGLSKQKKLATPVHR 307
               +    +E       +  S       R        ++N+ ++   +K+    TP  +
Sbjct: 238 TQEHSLYDDTEQRKYTEQDKNSGAKSAHKRDFQGGKLRRENNDEQQKHAKKNSRNTPYQK 297

Query: 308 RNLA----SNVWMAKGIHSSFLSDSG 329
           R+      SN   A     +    SG
Sbjct: 298 RSTTYVGKSNTHKANTATGNKTRSSG 323


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 99/308 (32%), Positives = 149/308 (48%), Gaps = 14/308 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  E   P ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+
Sbjct: 115 KYLNSEAVMP-KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVN 172

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+ +    +  R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTE
Sbjct: 173 GKPIARPNAKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTE 232

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A  +  P     R Y VR  G++D  +   L +GI ++           
Sbjct: 233 GLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEY 292

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
               GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G       
Sbjct: 293 LGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDIVLPRNLRRGRW----- 347

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS--SQKNGLS 296
           + L   L   L+ +  +  D          R   +  S +P  F  +++N     + G  
Sbjct: 348 EELDGSLVTALMVQLGLLRDGDESEGRRKSRQPQSHDSALPPGFGTLERNGMNGARIGRR 407

Query: 297 KQKKLATP 304
            + +   P
Sbjct: 408 GKLQGGRP 415


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 99/308 (32%), Positives = 149/308 (48%), Gaps = 14/308 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  E   P ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+
Sbjct: 115 KYLNSEAVMP-KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVN 172

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+ +    +  R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTE
Sbjct: 173 GKPIARPNAKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTE 232

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A  +  P     R Y VR  G++D  +   L +GI ++           
Sbjct: 233 GLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDDAQRKSLTEGIELEDGKAAFGSFEY 292

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
               GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G       
Sbjct: 293 LGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDIVLPRNLRRGRW----- 347

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS--SQKNGLS 296
           + L   L   L+ +  +  D          R   +  S +P  F  +++N     + G  
Sbjct: 348 EELDGSLVTALMVQLGLLRDGDESEGRRKSRQPQSHDSALPPGFGTLERNGMNGARIGRR 407

Query: 297 KQKKLATP 304
            + +   P
Sbjct: 408 GKLQGGRP 415


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 92/250 (36%), Positives = 131/250 (52%), Gaps = 1/250 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
            T  R+ KV+A+AGIASRR  E +I Q RV VNGI++    V V    D I VD V +  
Sbjct: 1   MTKVRLQKVLAQAGIASRRGAEEVIRQGRVVVNGIVVTELGVKVDPHADRITVDRVTIAM 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L  KP   VTT  DP GR TVFD +P   +R+  VGRLD + EGLLLLTNDG 
Sbjct: 61  VESRVYLLLFKPRCCVTTARDPQGRKTVFDFVPDAGARLFPVGRLDFDAEGLLLLTNDGL 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L+ P     + Y V   G      L+ L+ G++++       +VT+      +  +
Sbjct: 121 LANRLQHPRYGVTKTYEVAAMGHPTPAALDRLRTGVMLEEGMTAPAEVTVIGSSPRSTRL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+IK++ E     V  + R+++GP +LG+L  G +R +    +        
Sbjct: 181 RIVLHQGWNRQIKRMGEAVGHPVLSIKRVAFGPLKLGSLKPGGSRHLKSGEVELLYKLVH 240

Query: 250 LEEAQVNLDA 259
           L++ Q N D 
Sbjct: 241 LDKEQRNADG 250


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 72/237 (30%), Positives = 118/237 (49%), Gaps = 2/237 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ K++A+AG  SRR+ E+MI   RV+V+G L+      V     HI VDG  + 
Sbjct: 16  NNEGIRLQKILAQAGFGSRRKCEQMITDGRVEVDGELVTELGTRVDPKKQHIRVDGSRVH 75

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP  +++   DP GR T+ D +   + RV  +GRLD ++EGL+L+TNDG
Sbjct: 76  LNPNHVTLALNKPKKVLSAMDDPKGRYTLADIIGDKYERVFHMGRLDYDSEGLILMTNDG 135

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++  +    L  +G+ +           +        
Sbjct: 136 ELSQHVMHPKYEVEKTYIATIDGKIGGNVCRRLVTQGVQLDDGLVKLDHCAIIDANRDQT 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+  +R  
Sbjct: 196 IVKVVLHSGKNRIVRRIFGAIGYPVRRLVRTQIGPIKLGDLKSGTYRVLSQVEVRSL 252


>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 =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 92/337 (27%), Positives = 148/337 (43%), Gaps = 18/337 (5%)

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     RV  VGRLD  ++G
Sbjct: 60  CADNIPVHKNEKKVLLLFNKPRGIVCSTKQQFDETTVTDYLDYPL-RVYPVGRLDKESQG 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 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
             E    HLLE +         +SET++R      +       R    + Q +       
Sbjct: 235 WEEL--NHLLESS---------TSETVIRTGEQNGNSSDHANERAGAKAGQGSKGVLPAG 283

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
                 +R + S+V  A G        SG++    RR
Sbjct: 284 YRDHKQQR-VRSDVRRASGSGERNRHCSGKQPNRKRR 319


>gi|309973338|gb|ADO96539.1| 23S rRNA pseudouridylate synthase RluB [Haemophilus influenzae
           R2846]
          Length = 357

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 111/294 (37%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  + L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDITLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 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 =  266 bits (680), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 107/304 (35%), Positives = 152/304 (50%), Gaps = 23/304 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEGIIQAGRVSVDGKVATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T +DPDGR TVFD LP    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-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGLPRGGWAEMPLEQLNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K  SQ +    ++   
Sbjct: 242 EL----------VQLPAETVSKLPVERERRRVKAN---QIRRAVKRHSQISTAPARRTSP 288

Query: 303 TPVH 306
            P  
Sbjct: 289 KPKR 292


>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 =  266 bits (680), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 80/238 (33%), Positives = 120/238 (50%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A+ G+ASRR  E MIA  RV VNG +++   V V   D + VDG  +   ER 
Sbjct: 1   MRLQKYMAQCGVASRRGSEAMIADGRVMVNGSVVDTPGVQVTPGDVVFVDGKLI-APERK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP G+VTT  D      + D + +   R+ ++GRLD +TEGLL+LTNDG L   
Sbjct: 60  VYLLLNKPRGVVTTSEDVHAERRILDLVAAEV-RLYAIGRLDKDTEGLLILTNDGDLTFR 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-------QGICYGDMQVTLDTQKGSN 186
           L  PS    +VY     GQ+    L  L++G+VI       +       +VT+  +K  +
Sbjct: 119 LTHPSYHLDKVYEAVVKGQLTAPALAALREGVVIPLDDAGTKTYRTQPAEVTVLRRKRGS 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             +++ L EGK R+I+K+     + V  L R + G     TL  G  R +    + + 
Sbjct: 179 TRLSITLCEGKKRQIRKMCAAVGYPVVALRRTAIGDIADDTLKPGEWRRLRPDEVAKL 236


>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 =  266 bits (680), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 110/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      + +  VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTDLFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +     GI +  G       + + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPASLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 NVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTEAEL 227


>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 =  266 bits (680), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEHFAKGVQLHNEKDLTRPAVLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G  +L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGAIELDPELAPGEYRPLTEEEI 227


>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 =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 81/235 (34%), Positives = 130/235 (55%), Gaps = 2/235 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
              +R+ K++++AG++SRR+ E+++ + RV VNG ++           DHI+VDG  L+ 
Sbjct: 1   MAEERLQKILSQAGVSSRRQAEKLMQEGRVTVNGSVITELGSKADLDRDHIKVDGRLLKA 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +       +KP G VTT  DP+GR TV D L  +  RV  VGRLD ++EGLLLLTNDG 
Sbjct: 61  PKHQIYIALNKPKGTVTTVHDPEGRETVMDLLHRVKERVYPVGRLDYHSEGLLLLTNDGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +   +T   + Y V+  G +  ++    + G+ + G       + L ++   N W 
Sbjct: 121 LANSIMSAATHLEKTYVVKVTGTLTAEQEEKFRTGVPLSGRRTLPAGLKLLSR-AENPWY 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V L EG+N +I+ +F  F   V +L R+  GP +LGTL  G+ R + ++ + + 
Sbjct: 180 EVKLTEGRNNQIRMMFRHFGKLVEKLKRVRIGPIELGTLKTGAFRYLDEEDVAKL 234


>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 =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 109/307 (35%), Positives = 155/307 (50%), Gaps = 25/307 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEGIIQAGRVSVDGKVATLGDRVEVTKATKIRIDGHVVTVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T +DPDGR TVFD LP    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-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+  +    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDITLPKGIPRGGWAEMPLEQLNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L A   S   + R+R  + +       R  K  SQ    S   +  
Sbjct: 242 EL----------VQLPAETVSKLPVERERRRVKAN---QIRRAVKRHSQI--SSAPARRT 286

Query: 303 TPVHRRN 309
           +P  +RN
Sbjct: 287 SPKPKRN 293


>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 =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 118/239 (49%), Gaps = 2/239 (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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++       L   G+ +           +      
Sbjct: 132 DGELSQHVMHPKYEVEKTYVATLEGKISGTVCRRLVTTGVQLDDGWIKLDHCAIIDSSRD 191

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +  V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S+  +R  
Sbjct: 192 HTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKPGSYRVLSQTEVRSL 250


>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 =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 105/358 (29%), Positives = 159/358 (44%), 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---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+
Sbjct: 250 EEGGGEGSNLWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLRRGAWMEL 309

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             + +R      L++ A  ++++      T  R RP   +         +   +Q+ G +
Sbjct: 310 DDRDIRA-----LMQAAGGSVESSEPGGGTSSRGRPGSGNAGGFKNGNGRPAGAQRQGGA 364

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             K                 A G         G + +  + S  +    S  R    K
Sbjct: 365 AGKS--------------GKAAGKSGRGAGGQGAQPDPMKTSQGYIGHDSFIRQRQDK 408


>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 =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 125/241 (51%), Gaps = 11/241 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E++++     V VNG +++ +   V    D+IEV+G  +   E  
Sbjct: 12  RLDKMLSHLGYGTRSELKKLAKNGGVTVNGKVVKDSGWKVYPDEDYIEVNGEQVIFRE-H 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              L +KP G+++   D   R TV D L        V  VGRLD +TEGLLLLTNDG LA
Sbjct: 71  VYVLLNKPAGVISATEDMRDR-TVVDLLDDHIRVFGVFPVGRLDKDTEGLLLLTNDGKLA 129

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----QKGSN 186
             L  P     + Y  R +G V ++ + +  +G+V+  G      Q+ +      ++   
Sbjct: 130 HNLLSPRKHVPKTYYARVNGDVTEEDVRIFSEGVVLDDGYMTMPAQLVVLDSGNPEEEKP 189

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           A + + + EGK  ++K++FE  + KV  L RIS G  +L  +L  G++RE++ K L    
Sbjct: 190 AEIELTIHEGKFHQVKRMFEAVHKKVVYLKRISMGSLKLDPSLSPGASRELTAKELEALQ 249

Query: 246 G 246
           G
Sbjct: 250 G 250


>gi|167824420|ref|ZP_02455891.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
          Length = 374

 Score =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 66  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 124

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 245 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 304

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 305 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 350


>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 =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>gi|184201169|ref|YP_001855376.1| pseudouridine synthase [Kocuria rhizophila DC2201]
 gi|183581399|dbj|BAG29870.1| pseudouridine synthase [Kocuria rhizophila DC2201]
          Length = 368

 Score =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 84/244 (34%), Positives = 129/244 (52%), Gaps = 2/244 (0%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
            +   +    R+ K++A+AG+ASRR  E MI   RV V+G ++    V V      + VD
Sbjct: 121 RLEVHDENGVRLQKLMAQAGVASRRVCEEMIQDGRVSVDGEIVTELGVRVDPALQAVHVD 180

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLL 122
           G+ ++  E+   + ++KP G+V+T  DPDGR  V D L P    RV  VGRLD+ TEGLL
Sbjct: 181 GMRIQTDEKLVYYAFNKPAGVVSTMEDPDGRRCVSDFLDPRKHQRVFHVGRLDVETEGLL 240

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG L   L  PS +  + Y V+ HG V++   N +K+GI ++          L   
Sbjct: 241 LLTNDGELTNRLTHPSYEVPKTYLVQVHGPVEKGIGNQMKQGIRLEDGIAKVDDFRLVDS 300

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              +  + V L  G+NR ++++F+  +  V +L R   GP  +G    G+ R++S   + 
Sbjct: 301 TPGHVLIEVVLHSGRNRIVRRMFDAVDHPVEKLARTHVGPIAIGDQKQGTVRKLSHTEVG 360

Query: 243 EQLG 246
             L 
Sbjct: 361 NLLA 364


>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 =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 112/229 (48%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V     + +D       G+ +          TL+  K ++  V + +
Sbjct: 121 ITSPKHECEKTYLVTLELPLAEDTAEQFTVGVQLHNEKNLTKPATLE--KITDHVVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L + L  G  RE+S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVELHRERIGGICLDSELEPGEFRELSAEEV 227


>gi|315149408|gb|EFT93424.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 257

 Score =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEDEL-QQLQPK 252


>gi|330966753|gb|EGH67013.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 408

 Score =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 119/375 (31%), Positives = 176/375 (46%), Gaps = 36/375 (9%)

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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G  
Sbjct: 183 DIKQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRW 242

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDA-------------PIYSSETLVRD-RPNIIS 276
           RE+S+     L  ++G   + + Q+N                P+   E +VR  RP   +
Sbjct: 243 REMSQYEVDILSAEVGLQPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVVRTLRPAAGA 302

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------ 330
               D T       Q  G  + +       +R    +     G  +   +D+ +      
Sbjct: 303 PATGDRT---PRQPQITGSERDRPRGGDSTQRPARKDSGK-PGSRAPRPADNSRGTPVAE 358

Query: 331 REENHRRSPSFPSKR 345
           R  +  + P+ P  +
Sbjct: 359 RPSDMNKRPAKPGPK 373


>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 =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 77/242 (31%), Positives = 125/242 (51%), Gaps = 2/242 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           + +   QE+    R+ KV+A+AG  SRR+ E MI   RV+V+G L+    V V      I
Sbjct: 7   RAQKAHQESHDGVRLQKVLAQAGFGSRRKCEVMITDGRVEVDGELVTELGVRVDPQHQEI 66

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            VDG  +  + +      +KP  +++T  DP GR T+ D +   + R+  +GRLD +TEG
Sbjct: 67  RVDGSRIHLSNKHITLALNKPRKVLSTMDDPKGRWTLRDIVGDRYERIFHMGRLDYDTEG 126

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTL 179
           L+L+T+DG LA+ +  P  +  + Y     G +     + L + G+ +        Q ++
Sbjct: 127 LILMTDDGELAQHVMHPKYEIEKTYIATVEGHIGGGVCHRLVRTGVQLDDGWIKLDQCSI 186

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            TQ    + + V L  G+NR ++++F    + V RLIR   GP  LG L +GS R +S  
Sbjct: 187 ITQNRERSVLKVVLHSGRNRIVRRIFGSIGFPVTRLIRTQIGPISLGELKSGSYRILSTH 246

Query: 240 IL 241
            +
Sbjct: 247 EV 248


>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 =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 111/294 (37%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  + L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDITLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 154/278 (55%), Gaps = 10/278 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
           ++ +N   +    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  
Sbjct: 48  IETENKANDKIVGEKLQKILARAGQGSRREIEEVIAAGRVSVDGKIATLGDRVQVSSSTK 107

Query: 60  IEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
           I +DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 REVSKK---ILREQLGPHLLEEAQVNLDAPIYSSETLV 268
            E+  +    LRE +G     E +V++      + T  
Sbjct: 288 EEMGLEQVNYLRELVGLKPETETKVDVTKARRRTSTRQ 325


>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 =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 109/230 (47%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+      L +GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAQMEIIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L  +L  G  R ++++ +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDESLEEGEYRPLTEQEI 227


>gi|152978349|ref|YP_001343978.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150840072|gb|ABR74043.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 231

 Score =  265 bits (679), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 111/234 (47%), Gaps = 5/234 (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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D D   TV+       + ++ + GRLD +T GL+LLT+DG  + 
Sbjct: 61  QYFMLNKPQGYVCSHEDGDY-PTVYQFFDYPLAGKLHTAGRLDADTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+ +  +  ++GI+++G         L+     N  V + 
Sbjct: 120 RVTSPKHYCEKTYLVTLADPVESNYQSACEQGILLRGEKEATKPAKLEIIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L   L  G  R ++++ +   L
Sbjct: 178 ITEGRYHQVKRMFAALGNKVVALHRWRVGTVVLDDDLEEGGFRALTQQEIEALL 231


>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 =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 119/237 (50%), Gaps = 1/237 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
              ++    R+ KV+A+AG+ASRR  E +IA  RV V+G+++      V   T  I VDG
Sbjct: 2   TTADSSEGVRLQKVLAKAGVASRRASEELIAAGRVSVDGVVVRELGRRVDPDTAVIHVDG 61

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           + ++  +       +KP G+ +T SD  GR  V D +     R+  VGRLD +TEGLLLL
Sbjct: 62  IRVQVRDDLVYLALNKPRGVHSTMSDAQGRPCVGDYVADRPERLFHVGRLDADTEGLLLL 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS    + Y     G V +     L+ G+ +           +   + 
Sbjct: 122 TNDGDLAHKLMHPSFHVTKTYLAEVEGAVARGLGKRLRAGVQLSDGPVTADAFRIKDVRP 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + V + L EG+   ++++       V +L+R + G  +LGT   G+ R ++++ +
Sbjct: 182 NRSLVEIVLHEGRKHIVRRLLAEVGHPVRKLVRTAIGEVRLGTTKPGTLRTLTQQEI 238


>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 =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 123/237 (51%), Gaps = 6/237 (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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +  + L EGKNREI+++     +++  L R+SY   QLG L AG  RE++   L + 
Sbjct: 181 FAELVLIEGKNREIRRMMRAIGYEIRDLKRVSYCQIQLGDLPAGEFRELTPNELNKL 237


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 109/230 (47%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +    V VNG + +  +  +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAGKALKSGLVTVNGKIEKSGSAKISETDEICYEGECLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+   +  L +GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYVEKLAEGILLRGEREPCLPAQMEIIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L  +L  G  R ++++ +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDESLEEGEYRLLTEQEI 227


>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 =  265 bits (678), Expect = 7e-69,   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|145631249|ref|ZP_01787022.1| predicted methyltransferase [Haemophilus influenzae R3021]
 gi|144983176|gb|EDJ90671.1| predicted methyltransferase [Haemophilus influenzae R3021]
          Length = 357

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 153/294 (52%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKVEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 130/312 (41%), Gaps = 12/312 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           N      +  R++K I+ +G  SRRE +++I   RV +NG ++      V+  D + VDG
Sbjct: 2   NTSNTTSSSIRLNKFISDSGFCSRREADKLIDSNRVTING-VIPELGTKVLPGDEVRVDG 60

Query: 65  VPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             ++ +           YHKP+G+  T ++   +  + D +     R+  +GRLD  +EG
Sbjct: 61  NLVKASAENKSDRVYLAYHKPVGITCT-TERHVKGNIIDAI-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 +   +    +   DA   +   +   R N +++   +         +++ + K   
Sbjct: 235 MHE-INSAVAGSTKTAEDAKHKTDTAVPDKRTNHVAKRSGNRGLKSDRGPERSQVRKHST 293

Query: 301 LATPVHRRNLAS 312
            A    RR    
Sbjct: 294 SAKTSSRRAPKR 305


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 84/236 (35%), Positives = 132/236 (55%), Gaps = 1/236 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + EG+NR I++ FE    +V RLIR +     LG L  G  R +    +++ L P 
Sbjct: 183 ISEGRNRVIRRAFEQLGHEVLRLIRTAVADLHLGNLREGDYRLLKGWEVQQLLTPR 238


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 123/239 (51%), Gaps = 2/239 (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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG LA+ +  P  +  + Y     G +     + L + G+ +        Q ++  Q   
Sbjct: 133 DGELAQHVMHPKYEVDKTYIATVEGHIGGSVCHRLVRTGVQLDDGWIKLDQCSIIDQNRD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + V V +  G+NR +++VF    + V +LIR   GP +LG L +GS R ++   +   
Sbjct: 193 RSVVKVVIHSGRNRIVRRVFGAIGFPVVKLIRTQIGPIKLGELKSGSYRVLTGAEVNAL 251


>gi|315146884|gb|EFT90900.1| conserved hypothetical protein [Enterococcus faecalis TX4244]
          Length = 257

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 67/269 (24%), Positives = 126/269 (46%), 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  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +  +        ++KP+G+V T      +  + D +     R+  +GRLD  +EGL+ LT
Sbjct: 58  ITERKTDFVYLAFNKPVGIVCTTDTRVEKDNIIDFI-KYPKRIFPIGRLDKPSEGLIFLT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG +   +   S    + Y V     + Q  +  +  GI ++ +     + T+  +K  
Sbjct: 117 DDGDIVNKILRASNNHEKEYIVTVDKPISQTFIKRMAGGIYLEDLDKTTKKCTV--RKID 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +   ++ L +G NR+I+++ E+  ++V  L R+     +L  +  G  RE + + L+   
Sbjct: 175 SQTFSIILTQGLNRQIRRMCEYLTYEVTSLKRVRIMNIKL-DVPIGEYREFTAEELKTL- 232

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
              LLE++  N      + +    +R   
Sbjct: 233 -NMLLEDSDKNYSETTPAKKVHKINRRKT 260


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 111/372 (29%), Positives = 176/372 (47%), Gaps = 19/372 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M D          +++ KV+AR G+ SRR+VE  IA+ RV VNG +       V S D I
Sbjct: 1   MNDTPENPHVPVGEKLQKVLARLGVGSRRDVEVWIAEGRVNVNGSVA-SLGQRVDSHDAI 59

Query: 61  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +R+ E      R+ +Y+KP G V T  DP+GR T+FD LP + + R I+VGRLD
Sbjct: 60  TVDGHLIRREEAAESVRRVLIYNKPEGEVCTRDDPEGRPTIFDRLPRLRTGRWINVGRLD 119

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLLL T DG LA  L  PS +  R Y VR  G+V ++ +  L  G++++       
Sbjct: 120 INTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVTEEMIERLLNGVMLEDGPAKFS 179

Query: 176 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 180 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMGRY 239

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKNS 289
           RE+ ++    L E++G   +    +   A   +  +   + RP   SE P+   +     
Sbjct: 240 REMDQREIDILSEEVGLKPVALPGMTTKAREKAERQQRKQARPLARSERPEAGRKRAPRR 299

Query: 290 SQKNGLSKQKKLATP-------VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFP 342
                 +++   + P         R+       +A+    S       +  + R + +  
Sbjct: 300 EDGENAARRAPASRPARGPQPSAERKGREQGTPVAERPRESNRKPRPSKPRDERPASAPG 359

Query: 343 SKRSLRRTSAKK 354
            K + R+   K+
Sbjct: 360 DKPAARKPQVKR 371


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 135/238 (56%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+ AG+ SRR+ E +I   RVKVNG  + +      S  D IEV+G  ++K ER
Sbjct: 3   ERLQKIISHAGVCSRRKAEELIKDGRVKVNGHTVTKLGTEADSVRDCIEVNGKVIKK-ER 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +L++KP  ++T+ +DP GR TV D    I  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 62  LKYFLFNKPDKVITSMTDPAGRRTVADYFSQIKERVFPVGRLDYHSEGLLLMTNDGDLDY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 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|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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 73/243 (30%), Positives = 123/243 (50%), Gaps = 5/243 (2%)

Query: 2   KDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            +  I     TP   R++K IA AGI SRR  +  I+   V VNG ++      V  TD 
Sbjct: 140 NNAPIDYPTTTPAEVRLNKYIADAGICSRRNADMYISAGNVTVNGEVMTTLGYRVKPTDE 199

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +  DG  L  +E+    L +KP G +TT +D  GR TV D + +  + R++ VGRLD  T
Sbjct: 200 VRFDGKLLS-SEKKEYILLNKPKGFITTTNDEKGRKTVMDLVANATNVRILPVGRLDRAT 258

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG L + L  P+    ++Y V    ++D      ++ G+ ++       +++
Sbjct: 259 TGLLLLTNDGELTKKLTHPTHGVRKIYHVILDRKLDYKDFMKVQDGLELEDGLIEVDEIS 318

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               K  N  + + +  G+NR ++++FE   ++V +L R+ +       L  G  R +++
Sbjct: 319 YVNDKPKN-EIGIKIHSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQ 377

Query: 239 KIL 241
           + +
Sbjct: 378 QEV 380


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 136/312 (43%), Gaps = 15/312 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE +++I QQR+ +NG +       V   D + VDG PL++ +   
Sbjct: 10  RLNKFISDTGYCSRREADKLIDQQRITINGKIP-EMGTKVADGDEVLVDGKPLKEKQDRI 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              ++KP+G+  T ++      + D + +   R+  +GRLD  ++GL+ LTNDG +   +
Sbjct: 69  YIAFNKPVGITCT-TERHVEGNIVDYI-NHEQRIFPIGRLDKPSDGLIFLTNDGDIVNKI 126

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y VR    +  + L  +  G+ I        ++     + S     + L 
Sbjct: 127 LRAGNAHEKEYVVRVDKPITDEFLQKMAAGVPILDTVTLPCKIK----QESRFVFRITLT 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG-------P 247
           +G NR+I+++ E+ +++V +L R+      LG L +G  R +S+  + +  G        
Sbjct: 183 QGLNRQIRRMCEYLDYEVFKLKRVRIMNIDLGKLASGEWRYLSQAEMDQLNGMIGTSSKT 242

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
                    +D  +   +     R +  +    +  R K    + +  + ++K       
Sbjct: 243 EEASRKVKEIDGKVRVLKKASSGRNHHSNNTFKENRREKAKEGRFSKSAPKRKNDRKEQG 302

Query: 308 RNLAS-NVWMAK 318
           +  +   VW  K
Sbjct: 303 KPQSEIKVWRPK 314


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 120/237 (50%), Gaps = 2/237 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ K++A+AG  SRR+ E+MI   RV+V+G L+      V  T   I VDG  +R
Sbjct: 15  NQEGIRLQKLLAQAGFGSRRKCEQMITDGRVEVDGELVTELGTRVDPTHQQIRVDGSRVR 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            + +      +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG
Sbjct: 75  ISNKHITLALNKPRKVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDG 134

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L   G+ +        +  +        
Sbjct: 135 ELSQHVMHPKYEVEKTYIATLEGRISGTVCRRLVTTGVQLDDGWIKLDRCAIIDATHDTT 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R  
Sbjct: 195 IVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKSGSYRVLSQTEVRSL 251


>gi|19879252|gb|AAK38326.1| hypothetical pseudouridine synthase [Flavobacterium johnsoniae
           UW101]
          Length = 304

 Score =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 65/275 (23%), Positives = 127/275 (46%), Gaps = 13/275 (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 ++ + ++ + D + +   R+  +GRLD  +EGL+ +T
Sbjct: 58  IVEKHEKLVYLAFNKPVGIECT-TNLEVKNNIVDYI-NYPKRIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  + +  +  +  G+ I        +V    ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYTVTVNKPITERFIQRMGNGVPILDTVTKKCKV----EQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+++   ++E  
Sbjct: 172 KYTFKIILTQGLNRQIRRMSEYLGYEVTALKRIRIINISL-DVPVGRYRDLTDAEIKEL- 229

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
              L+E +    +A +  +      R +      D
Sbjct: 230 -NKLIEPSSKTEEASLPKAAAPTPSRRSTFISKND 263


>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 =  265 bits (678), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 117/233 (50%), Gaps = 4/233 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR-KAE 71
            R++K IA +G+ASRR+ E +I + R++VN  +++  +  V    D +  D  P+  K 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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 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|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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 152/290 (52%), Gaps = 12/290 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 310 VNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|255099545|ref|ZP_05328522.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-63q42]
          Length = 240

 Score =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++  +D     TV D +   +       VGRLD +TEGLL+LTNDG L
Sbjct: 64  YIYLMMNKPAGYISATTD-KYDPTVLDLIDLSYLVFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  +    + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDG-YKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 235


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 122/249 (48%), Gaps = 8/249 (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 +KP G VT+  D DG  +V   L  +    + VGRLD +TEGLLL+
Sbjct: 61  EEVFYREFFHV-LLNKPAGYVTSTQDRDG-PSVTHLLEMVRDDWMPVGRLDKDTEGLLLI 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  P  +  + Y         Q  +     G  ++G      ++TL    G
Sbjct: 119 TTDGELAHRLTHPRWKVPKRYYAELAEPATQADVEAFAAGFELEGEPLQPAELTL----G 174

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            +  V + +REG+  ++K++F     +V  L R+++GP +L   L  G +R ++ +    
Sbjct: 175 KDRRVELVIREGRYHQVKRMFAARGNRVVYLKRVAFGPLELPEDLELGESRYLTAEEEHA 234

Query: 244 QLGPHLLEE 252
             G   LE 
Sbjct: 235 LYGAVGLEP 243


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGIPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 136/238 (57%), Gaps = 4/238 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K+I+ AG+ SRR+ E +I + RVKVNG  + +      S  D IEV+G  ++K ER
Sbjct: 3   ERLQKIISHAGVCSRRKAEELIKEGRVKVNGHTVTKLGTEADSVRDCIEVNGKVIKK-ER 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +L++KP  ++T+ +DP GR TV D    I  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 62  LKYFLFNKPDKVITSMTDPAGRRTVSDYFSQIKERVFPVGRLDYHSEGLLLMTNDGDLDY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 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|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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 119/249 (47%), Gaps = 14/249 (5%)

Query: 1   MKDKN------IVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           MK KN      I+  +  P+ R++K I+  G  SRRE +++I   RV V+GI        
Sbjct: 1   MKQKNNEDKFVIIHNDRGPEIRLNKFISETGFCSRREADKLIENGRVTVDGIKA-VMGTK 59

Query: 54  VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           V  +  ++VDG  ++K +       +KP+G+  T ++   +  + D + +   R+  +GR
Sbjct: 60  VKESADVKVDGKSIKKVDELVYIALNKPVGITCT-TEKKVKGNIVDFV-NHKKRIFPIGR 117

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD +++GL+LLTNDG +   +        + Y V     +D+  +  +  G+ I G    
Sbjct: 118 LDKDSQGLILLTNDGDVVNKILRAGNNHEKEYIVTVDKPIDEKFIKSMSSGVKILGTITK 177

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              VT    K +     + L +G NR+I+++ E   + V +L RI      +  L  G  
Sbjct: 178 KCIVT----KENKNTFRIILTQGMNRQIRRMCEALGYNVVKLNRIRIMNINIERLKIGEW 233

Query: 234 REVSKKILR 242
           R ++ K L+
Sbjct: 234 RNLTSKELK 242


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 128/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V     +
Sbjct: 50  VSNKNEIRDEV---RLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKGQSV 105

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG PL+          +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 106 SIDGKPLKVENELVYIALNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 163

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 164 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITDEFIKGMSNGVPILGTVTKKCLVKKE 223

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 224 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKE 279

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 280 LAEI--NRLTENSSKTEEASI 298


>gi|324328601|gb|ADY23861.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 242

 Score =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L RI  GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRIEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 92/240 (38%), Positives = 136/240 (56%), Gaps = 8/240 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+IA+AG+ASRR+ E +I + RVKVNG ++      V     +EVDGV L + E  
Sbjct: 2   ERLQKIIAQAGVASRRKAEELITEGRVKVNGKVITELGTKVGGRAEVEVDGVKLEREE-H 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G+V+T  D  GR TV D +P    RV  VGRLD NT GLLLLTNDG  + +
Sbjct: 61  VYYMLYKPTGVVSTVEDDKGRKTVVDLVPPG-HRVFPVGRLDYNTSGLLLLTNDGEFSNL 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAWVT 190
           L  P  +  + Y V+  G  D   +  L+KG+V+  G   G  +V +    +K + A + 
Sbjct: 120 LLHPKYKVPKRYIVKIKGVPDYYHVKGLEKGVVLPDGFKTGKARVEMRDIDKKKNTAILE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGP 247
           + + EG NR+++++ E    +V +L R  +G   L  L +G  RE+SKK    LRE   P
Sbjct: 180 MVIYEGHNRQVRQMVETLGAEVIKLKREQFGFLTLAGLTSGDWRELSKKEVNQLRELADP 239


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 72/293 (24%), Positives = 131/293 (44%), Gaps = 11/293 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
             R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYISESGICSRRDADRYIEQGNVFINGKRAA-VGDQVFAGDIVKVNGQLIEPRDE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L   +KP+G++TT  D + R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVLIALNKPVGIITTMEDSE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  +  G+ + G      +V    QK ++    
Sbjct: 123 VNKILRAGNNHEKEYVVTVNKPVTDEFIQGMSAGVPMLGTVTKKCKV----QKEASFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ + F ++V RL R       L  L  G  R+++   L E     L+
Sbjct: 179 ITLVQGLNRQIRRMCKHFGYEVTRLERTRIMNVNLKGLPQGEWRDLTDDELIELF--KLI 236

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           E +     +   +    V  +    +E  +       ++S+K      +K   
Sbjct: 237 ENSSSEEKSAKKAQTKHVTAKKTGFNEPKNAEKSDGNSASRKRFTQSGRKKKG 289


>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 =  265 bits (678), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 100/316 (31%), Positives = 155/316 (49%), Gaps = 11/316 (3%)

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  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  ++     +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 382 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 441

Query: 237 SKKILR---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           S + +R     LG  +   +           +   R         P       + + Q  
Sbjct: 442 SAEEVRVLMGLLGLKVPTASAGGGQGGQGGRQGNRRREAQPALTGPMSSGFTGEATFQSR 501

Query: 294 GLS-KQKKLATPVHRR 308
           G+  +    A P  RR
Sbjct: 502 GMGVENGNRALPAPRR 517


>gi|327394528|dbj|BAK11950.1| ribosomal small subunit pseudouridine synthase A RsuA [Pantoea
           ananatis AJ13355]
          Length = 239

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 106/241 (43%), Gaps = 3/241 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     V  D       G+ +           L+    +   V + L
Sbjct: 121 ITSPRHHCEKTYRVTLEAPVSDDTAAQFSAGVQLHNEKSLTKPAQLEV--ITPTEVLLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +     P  L++
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGEIVLDEALEPGEYRLLTEEEIASIGLPDELKQ 238

Query: 253 A 253
            
Sbjct: 239 K 239


>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 =  265 bits (677), Expect = 8e-69,   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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVIELHRERIGEIILDPALEPGEYRPLTEQEV 227


>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 =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGTLTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|167816044|ref|ZP_02447724.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
          Length = 358

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 60  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 118

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 239 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 298

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 299 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 344


>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 =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 89/274 (32%), Positives = 139/274 (50%), Gaps = 4/274 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
              +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +  +
Sbjct: 1   MAEERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQ 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K ++      +KP G VTT SD  GR TV D +  I +R+  VGRLD ++EGLLL+TNDG
Sbjct: 61  KNQQLYYLALYKPRGYVTTASDELGRKTVMDLVSDIPARLYPVGRLDKDSEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
             A+ +  PS    ++YRV    + D+  +  L  G+V+  G       + + T +    
Sbjct: 121 AFAQAVTHPSGGISKLYRVTVQPRADEATILKLSSGVVLDDGTKTMPCAINVVTDEPGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +      
Sbjct: 181 VMEMTLKEGKNREIRRMCESVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEVNGLRAA 240

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
            +   AQ    A   S     R R  +    P  
Sbjct: 241 AVKGRAQT-RSAAQQSKAAERRPRGPVGKNAPRK 273


>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 =  265 bits (677), Expect = 9e-69,   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 ++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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +      +KG+ + G         L+        V + +
Sbjct: 131 ITAPKHHCEKTYLVTLEEPIGEGVAEQFQKGVQLNGEKDLTKPAKLEILTP--TEVKLTI 188

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  ++K++F      V+ L R   G   L  TL  G  R ++++ +
Sbjct: 189 SEGKYHQVKRMFAAVGNHVSALHRERIGDITLDETLAEGEYRPLTEEEI 237


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 109/244 (44%), Positives = 149/244 (61%), Gaps = 3/244 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +    PQR++K++ARAG+ SRR+VERMI + R+ +NG ++ + A  + S + + VDG P
Sbjct: 42  TEREDGPQRIAKLLARAGVGSRRDVERMIEEGRIALNGEVVTQPAPLLASLEGLTVDGNP 101

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K   TRL+ +HKP G +T   DP GR T++D LP    R++ VGRLD NTEGLLLLTN
Sbjct: 102 VAKPVSTRLYRFHKPAGCLTAARDPKGRKTIYDVLPKGLPRLMPVGRLDYNTEGLLLLTN 161

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG   R LELP++   R YR R  G + Q +L  L  GI I GI YG +   L+ + G N
Sbjct: 162 DGAFKRQLELPASGVERTYRARAFGDISQAQLEELVMGIEIDGIRYGKIDANLERRTGRN 221

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL---RE 243
            W+ + L EGKNRE+++V E    +V+RLIR  YG F L  L  G+   V +  L   R 
Sbjct: 222 QWIEMTLTEGKNREVRRVLEHLGLQVSRLIRTRYGEFTLAGLDMGAVEVVPRDELFKFRR 281

Query: 244 QLGP 247
           QL  
Sbjct: 282 QLAK 285


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 99/309 (32%), Positives = 151/309 (48%), Gaps = 13/309 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGHGSRREMEALITAGRVSVDGKVAT-LGDRVEVNAVIRVDGHQVKTRAA 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + T  DP+GR TVFD LP +  +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-TLLAGSTREVSKKI---LRE 243
           W  V L EG+NRE+++++E    +V+RL+RI YG  +L   +  G  +E+       LR 
Sbjct: 181 WFNVTLTEGRNREVRRLWESQEVQVSRLMRIRYGDVKLDRGIPRGGWQELKLPEVNYLRG 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +      E++V+L     +S      +   I         M+    +    + ++K   
Sbjct: 241 LVNLPPETESKVDLQQDGKTSRHKQAAQ---IRRAVQRHKEMQGKEPRARATTARRKPQA 297

Query: 304 PVHRRNLAS 312
                   S
Sbjct: 298 STRNSGTGS 306


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPKGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 92/289 (31%), Positives = 149/289 (51%), Gaps = 7/289 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 172 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 230

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 351 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 410

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
              +R+ +    L +A          +    R +P+ +        R  
Sbjct: 411 DAQVRKLMATVGL-KAPSEEKGKRGGAGPTERRQPDPMQTSMGFIGREP 458


>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 =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 102/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN  + +  A  V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDAVQKSGAFKVTDECVVEWQGREIQKP-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  +  KP G V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLFKPDGFVCSHEDGFN-QTAFALLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     + +D      +GI ++      +   LD        V + 
Sbjct: 119 RITSPKHKCEKTYRVWLVDPIGEDYAEKFAQGIELRSEKEPTLPAQLDIVNQDENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ +
Sbjct: 179 ITEGKYHQVKRMFAALGNKVEHLHRERIGAIELDYSLEPGEYRFLTEEEI 228


>gi|145635048|ref|ZP_01790754.1| predicted methyltransferase [Haemophilus influenzae PittAA]
 gi|145267656|gb|EDK07654.1| predicted methyltransferase [Haemophilus influenzae PittAA]
          Length = 357

 Score =  265 bits (677), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 153/294 (52%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKIEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMLHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGEYRELTDEEVE 231


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 117/239 (48%), Gaps = 2/239 (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 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G++       L   G+ +           +      
Sbjct: 132 DGELSQHVMHPKYEVEKTYVATLEGKISGTVCRRLVTTGVQLDDGWIKLDHCAIIDASRD 191

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L  GKNR ++++F    + V RL+R   GP +LG L  GS R +S+  +R  
Sbjct: 192 YTMVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKPGSYRVLSQTEVRSL 250


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V+  +D     TV D +   +       VGRLD +TEGLL+LTNDG L
Sbjct: 64  YIYLMMNKPDGYVSATTD-KYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  +    + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDG-YKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEIK 235


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 124/235 (52%), Gaps = 7/235 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ K +A AG+ SRR  E +I+Q +V VNG ++ +  V +    D I V+G  +  
Sbjct: 1   MALERLQKYLAHAGVCSRRHAEELISQGKVAVNGEIVTQMGVKIDPDKDEIAVNGKKVEP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +     + +KP G +TT   P GR  V D +  +  R+  +GRLD N+ GLLLLT+DG 
Sbjct: 61  KQSRTYIMLNKPAGYLTTCKQP-GRKIVLDLI-DLPQRLFPIGRLDNNSTGLLLLTDDGR 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   L  PS    + Y V          L+ +++G++++G      +V    + G  +  
Sbjct: 119 IHHRLSHPSFDHEKEYEVETVKDAPDQALDAMRRGMILEGKKTRPAKVK---RTGPRS-F 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           T+ L+EG+NR+I+K+ E    KV RL R+     +LG L +G  R +++K ++  
Sbjct: 175 TIVLKEGRNRQIRKMVELTKNKVKRLHRVRMSTIRLGGLPSGKWRRLNEKEIQAL 229


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 119/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG +++     V  +D +
Sbjct: 189 IEYKQQFVDPNEPIRLNKYLANAGVCSRREADEFIETGAVTVNGEIVKELGTKVKRSDEV 248

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           + +G  +   E+    L +KP   VTT  DP  R TV D + +    R+  VGRLD  T 
Sbjct: 249 KFNGELVS-IEKKVYVLLNKPKDCVTTMDDPQERQTVMDFVKNACDERIYPVGRLDRKTT 307

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  L  + +GI ++       +V  
Sbjct: 308 GVLLLTNDGDLASKLTHPKYDKKKIYHVTLDRNIVKADLEKIAEGIELEDGLIKADEVGY 367

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +   N  V + +  GKNR ++++FE   ++V +L R+ +       L  G  R +S++
Sbjct: 368 TDEFKRN-QVGIEIHSGKNRIVRRIFESLGYRVTKLDRVYFAGLTKKGLRRGQWRYLSEQ 426

Query: 240 IL 241
            +
Sbjct: 427 EV 428


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ ++ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYLSEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 104/294 (35%), Positives = 152/294 (51%), Gaps = 13/294 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+A AG+ SRRE+E+ IA  R+ VNG +       V   D + VDG  +  A +
Sbjct: 2   SEKLQKVLANAGVGSRREMEKWIASGRISVNGKVAT-LGDRVEPLDQLRVDGNLITAAAK 60

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           +   R+ +Y+KP G + +  DP GR TVFD LP I + 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 SWYNVSLSEGKNREVRRLWESQGLQVSRLIRVRYGTLNLQNRLPQGGWIELPLTDL---- 236

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
              L +  Q++L+      +   +     +S +     + K N  +     K+K
Sbjct: 237 -NTLRKSVQLDLEQESLIEDKQTKLDHVRLSRMRRSVQKHKVNQGRAKARPKKK 289


>gi|295105527|emb|CBL03071.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii SL3/3]
          Length = 275

 Score =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 89/274 (32%), Positives = 139/274 (50%), Gaps = 4/274 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
              +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +  +
Sbjct: 1   MAEERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQ 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K ++      +KP G VTT SD  GR TV D +  I +R+  VGRLD ++EGLLL+TNDG
Sbjct: 61  KNQQLYYLALYKPRGYVTTASDELGRKTVMDLVSDIPARLYPVGRLDKDSEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
             A+ +  PS    ++YRV    + D+  +  L  G+V+  G       + + T +    
Sbjct: 121 AFAQAVTHPSGGISKLYRVTVQPRADEATILKLSSGVVLDDGTKTMPCAINVVTDEPGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +      
Sbjct: 181 VMEMTLKEGKNREIRRMCESVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEVNGLRAA 240

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
            +   AQ    A   S     R R  +    P  
Sbjct: 241 AVKGRAQT-RSAAQQSKAAERRPRGPVGKNTPRK 273


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 111/230 (48%), Positives = 158/230 (68%), Gaps = 2/230 (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   L    K + I GI Y    + L     +NAW  + L
Sbjct: 121 FELPSNKLKRVYHVRAYGNPDI-LLKSEYKNLEIDGILYNPYSIKLLRGNNTNAWFEIVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EGKNREI+++FE+F  KVN+LIR+ YG F +G L  G  +E++ KIL +
Sbjct: 180 FEGKNREIRRIFEYFGLKVNKLIRVQYGSFTIGNLKPGDYKEINNKILEK 229


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 82/234 (35%), Positives = 126/234 (53%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E MIAQ RV VNG ++      V   D +EVDG P+ K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEEMIAQGRVCVNGDIITEMGYKVKRGDVVEVDGNPIEK-ENK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP   + T +D   R+TV D +P    R+ +VGRLD +T G+LLLTNDG  A  
Sbjct: 61  VYFLMNKPKKTMCTSNDEFDRTTVIDLIP-CKERIFTVGRLDYDTSGVLLLTNDGEFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK--GSNAWVT 190
           +  P     +VY +  +G +  +++  +KKGIV+  G      ++ L  +    +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTPEEMIQIKKGIVLDDGKKTLPAKLKLTEKDVTKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+IK++ E   ++V RL R      +   L  G  R +    + + 
Sbjct: 180 LTIYEGRNRQIKRMMEALGYEVRRLHRKELAFLKCSDLRQGEYRILKPFEVAQL 233


>gi|167464456|ref|ZP_02329545.1| pseudouridine synthase [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 250

 Score =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 77/241 (31%), Positives = 125/241 (51%), Gaps = 11/241 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K+++  G  +R E++++     V VNG +++ +   V    D+IEV+G  +   E  
Sbjct: 6   RLDKMLSHLGYGTRSELKKLAKNGGVTVNGKVVKDSGWKVYPDEDYIEVNGEQVIFRE-H 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              L +KP G+++   D   R TV D L        V  VGRLD +TEGLLLLTNDG LA
Sbjct: 65  VYVLLNKPAGVISATEDMRDR-TVVDLLDDHIRVFGVFPVGRLDKDTEGLLLLTNDGKLA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT----QKGSN 186
             L  P     + Y  R +G V ++ + +  +G+V+  G      Q+ +      ++   
Sbjct: 124 HNLLSPRKHVPKTYYARVNGDVTEEDVRIFSEGVVLDDGYMTMPAQLVVLDSGNPEEEKP 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           A + + + EGK  ++K++FE  + KV  L RIS G  +L  +L  G++RE++ K L    
Sbjct: 184 AEIELTIHEGKFHQVKRMFEAVHKKVVYLKRISMGSLKLDPSLSPGASRELTAKELEALQ 243

Query: 246 G 246
           G
Sbjct: 244 G 244


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 122/241 (50%), Gaps = 10/241 (4%)

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 ++   +  + D +     RV ++GRLD +++GL+LLTNDG +   
Sbjct: 60  VYLALNKPVGITCT-TEKGVKGNIVDLVNHPL-RVFNIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +  + +  + KG+ I G      +VT    + S     + L
Sbjct: 118 ILRAENNHEKEYIVSVDKPITPEFIEKMSKGVRILGQKTLPCKVT----QISKYEFNIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLL 250
            +G NR+I+++ E   ++V RL R+      LG L  G  R+++KK    L ++L  H  
Sbjct: 174 TQGLNRQIRRMCEVLGYEVYRLQRVRIMNITLGNLPVGQWRDLTKKEKTRLFQELNYHPQ 233

Query: 251 E 251
           E
Sbjct: 234 E 234


>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 =  265 bits (677), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 117/237 (49%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 1   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDTVTYLGEIIAYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 61  FYYIL-HKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y    +G + ++ + L  +G++I G       ++ +D   Q+   +
Sbjct: 119 AHQLLSPKKHVEKEYLAEVNGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFCLPKDLNRGQYRPMTKEELEQ 235


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++ AG+ +R+EV+++I ++ V+VNG L+ +  ++V   D +++DG  +   E  
Sbjct: 1   MRLDKYLSHAGVGTRKEVKQLIRKKHVRVNGELVVKDDMHVEEDDLVQLDGEHI-YYEPF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G++    D +   TV D    +  +    VGRLD++TEGL+L++NDG LA 
Sbjct: 60  VYLMLNKPSGVICATQDSEH-ETVLDCFDVMLPKGCFPVGRLDMDTEGLVLISNDGKLAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     +D+  +  L  G +I       +   L+    ++ +  + 
Sbjct: 119 HLLSPKHHVRKTYYVEHQLCLDETAIKTLCNGSIILDEKTV-LCAALEVINETSCFFHIE 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
             EG+  +IK++F     +V  L R++ GP +L   L  G  R ++++ L   
Sbjct: 178 --EGRYHQIKRMFSAVGNEVLYLKRVAMGPLRLDDHLEVGEWRALTQEELAAL 228


>gi|167919194|ref|ZP_02506285.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei BCC215]
          Length = 408

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 99  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 157

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 278 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 337

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 338 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 383


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 148/271 (54%), Gaps = 10/271 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ KV+ARAG+ SRREVE +IA  RV VNG +      V V +   I VDG  + 
Sbjct: 13  KIVGEKLQKVLARAGVGSRREVETIIAAGRVSVNGKIASLGDRVEVKNDTKIRVDGGLVS 72

Query: 69  ----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLL 123
               + +  R+ +Y+KP G + T  DP+GR+TVF+ LP I  +R +SVGRLDINT GLLL
Sbjct: 73  LIAARKDICRVLMYYKPEGELCTRHDPEGRATVFERLPQISNARWVSVGRLDINTSGLLL 132

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  PS +  R Y VR  G V +  L  L+KG+ ++       +++    +
Sbjct: 133 FTTDGELANRLMHPSKEVEREYSVRVFGHVTEQMLAKLRKGVQLEDGPASFKKISAQGGQ 192

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK--- 239
           G N W +V L EG+NRE+++++E    +V+RLIR  YG   L   L  G   E+  +   
Sbjct: 193 GMNQWFSVTLTEGRNREVRRLWESQGIQVSRLIRTRYGNIDLMKGLPRGGWIELPLEKVN 252

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
            LR+ +   L  E++V+           +R 
Sbjct: 253 YLRQLVDLPLETESKVDTKNSRSFKSNQIRK 283


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 110/295 (37%), Positives = 152/295 (51%), Gaps = 19/295 (6%)

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  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E T    R+  Y+KP G + T +DP+GR TVFD LP    +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+       +
Sbjct: 181 NQWYTVTLTEGRNREVRRLWESVGVQVSRLIRTRYGDIQLPKGLPRGGWTEL-------E 233

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           L P       V+L   I S   + +DR    +       R  K  SQ    S++ 
Sbjct: 234 LAPTNYLRELVDLPPEITSKVAVEKDRRRTKAN---QIRRAVKRHSQVAPGSRRP 285


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMLHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDVSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGEYRELTDEEVE 231


>gi|254385863|ref|ZP_05001182.1| pseudouridine synthase [Streptomyces sp. Mg1]
 gi|194344727|gb|EDX25693.1| pseudouridine synthase [Streptomyces sp. Mg1]
          Length = 260

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 122/238 (51%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K         +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V   D I+VD
Sbjct: 15  KTFPGAEEEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVQPKDEIKVD 74

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ +   +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++L
Sbjct: 75  GLTV-ATQSYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIIL 133

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTN G LA  L  P     + Y     G + ++    LK GI ++          +  Q 
Sbjct: 134 LTNHGELAHRLTHPKYGVKKTYVAAITGPLPREIGKRLKDGIELEDGYARADHFRVVDQV 193

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G N  V V L EG+   ++++     + V +L+R S+GP +LG   +G  R ++   +
Sbjct: 194 GKNYLVEVTLHEGRKHIVRRMMAEAGFPVEKLVRTSFGPIELGDQKSGWLRRLTNTEV 251


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 97/248 (39%), Positives = 141/248 (56%), Gaps = 13/248 (5%)

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 DTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                         N W  V LREG+NRE+++++E    KV+RLIR+ YGP  L   L  
Sbjct: 183 VVDYRALGYEAPPGNEWYQVTLREGRNREVRRLWESQGLKVSRLIRVRYGPVSLPRGLRR 242

Query: 231 GSTREVSK 238
           G  R + +
Sbjct: 243 GEHRPLRE 250


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 66/223 (29%), Positives = 108/223 (48%), Gaps = 7/223 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+  GI SRRE ++ I   RV +NG++  +    V S D + +DG PLR   +   
Sbjct: 6   LNKYISETGICSRREADKFIEAGRVSLNGVVATK-GNRVASGDTVLLDGKPLRSNPKRIY 64

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
             +HKP GL  T +D   R+ V   + +   R+  +GRLD ++EGL+ LTNDG +   + 
Sbjct: 65  LAFHKPKGLTCT-TDLRDRTNVIAYI-NHPQRIFPIGRLDKDSEGLIFLTNDGDIVNKIL 122

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                  + Y V        D +  +  GI I G       V    ++   +   + L +
Sbjct: 123 RSRNGHEKEYIVVVDKPFAPDFIRRMSNGIPILGTTTKKCVV----EQKGQSTFRIILTQ 178

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           G NR+I+++ E+  ++V +L RI     +L  L  G  R  S+
Sbjct: 179 GLNRQIRRMCEYMGYEVKKLKRIRIMSIKLDDLAPGKWRYFSE 221


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 119/242 (49%), Gaps = 14/242 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ KV+   G  SR +++R + Q  + VNG + + + + V    D IEV+G  +   
Sbjct: 7   QTQRLDKVLTHMGYGSRSDIKRQMKQGMITVNGKITKDSGLQVHPYQDQIEVNGERVVFR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + HKP G+++   D   R TV D L +         VGRLD +TEGLLLLTNDG
Sbjct: 67  E-YIYIMLHKPPGVISATEDSRER-TVLDLLSAEERHFEPFPVGRLDKDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN- 186
            LA  L  P     + Y     G V ++ ++    G+ +  G      Q+T+   +    
Sbjct: 125 KLAHELLSPRRHVPKTYEATVSGHVTEEDIHQFTAGVELDDGYVTLPAQLTILRHEHPYQ 184

Query: 187 ------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK 239
                 +++++ + EGK  ++K++FE    KV  L R + GP +L   L  GS RE++ +
Sbjct: 185 ADGGVISYISLVIHEGKFHQVKRMFEAVGKKVTYLKRTAMGPLKLDEQLPMGSYRELTNE 244

Query: 240 IL 241
            L
Sbjct: 245 EL 246


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 84/234 (35%), Positives = 120/234 (51%), Gaps = 3/234 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +RV K++ARAG  SRR  E +I   RVK+NG      +    S D I VDG  +   
Sbjct: 1   MAEERVQKILARAGYGSRRACEELILAGRVKINGQTAVLGSKADPSRDQILVDGQKIPLQ 60

Query: 71  ERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 + HKP G+++      D R TV D +P +   + SVGRLD  +EGL+LLTNDG 
Sbjct: 61  PPPVYIMLHKPQGVLSDVEVHKDPRPTVRDLVP-VEGHLFSVGRLDYESEGLILLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
           LA  L  P     + YRV    + D+ +L   + G+V+  G      QV ++   G  AW
Sbjct: 120 LANRLTHPRYGHEKEYRVLVGTRPDERQLEAWRHGVVLEDGYRTAPAQVRVEGVAGKGAW 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + V LREG+ R+I+++       V R+IRI  G   LG L  G  R ++ + +R
Sbjct: 180 LRVILREGRKRQIREMGRLTGLPVLRIIRIRIGSLLLGDLKPGEWRYLTPQEVR 233


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 88/283 (31%), Positives = 134/283 (47%), Gaps = 9/283 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
             T QR+ +V+A  G+ASRR+ E +I   RV V+G+++      V      I VDG PL 
Sbjct: 4   TMTEQRLQRVLAAHGVASRRKAEELILAGRVTVDGVVVRELGRKVDPERQEICVDGKPLH 63

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +E  R  + HKP+G +TT +D  GR TV D +  +  RV+ VGRLD ++ GLLLLTNDG
Sbjct: 64  -SEPRRYIVLHKPVGYITTTADEYGRKTVLDLV-QVPERVVPVGRLDRDSSGLLLLTNDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +  P  +  + Y V   G    +    L++G+ + G      ++     +     
Sbjct: 122 DLIYRITHPRYELEKEYEVLVDGFPPPEVEEALRRGVPVDGRPVRIRRLEAIRVEPQGTV 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQL 245
             V + EG+NR I++VFE   + V RL R+  GP +LG L  G  R+++      LR  +
Sbjct: 182 YRVVIHEGRNRIIRRVFERVGYPVLRLQRVRVGPLRLGDLPPGRWRDLTASEVAALRRAV 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           G     E  V  +        +   R       P    +  + 
Sbjct: 242 GLPEFPEGAVGRERKARGGRGMPARRG---DRRPSGVRKEHRR 281


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 114/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T +D  D     + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAADHIDDNIIEYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 100/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN ++ +  +V V     +E  G  + K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDVVQKSGSVKVTDDCTVEWQGREIHKP-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  +  KP G V +H D   ++            +   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLFKPDGFVCSHEDGFNQTAFMLLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     V  D       GI ++      +   ++        V + +
Sbjct: 120 ITSPKHKCEKTYRVWLADPVQDDYAEKFANGIQLRNEKDLTLPAQMELVDAQENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G  +L  TL  G  R ++++ +
Sbjct: 180 TEGKYHQVKRMFAALGNKVEHLHRERIGDIELCDTLEPGEYRYLTQQEI 228


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 125/245 (51%), Gaps = 1/245 (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 REQLG 246
            +   
Sbjct: 418 GDLYA 422


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 107/341 (31%), Positives = 159/341 (46%), Gaps = 17/341 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E +I++ RV VNG +       V + D I VDG  +     
Sbjct: 2   SEKLQKVLARAGVGSRREMETVISEGRVSVNGKVAT-LGDRVEAKDVIRVDGHQISVPTL 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G V T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK---KILRE 243
           W  V L EG+NRE+++++E    +V+RL+RI YG  +L  TL  G   E+       LR+
Sbjct: 181 WFNVTLCEGRNREVRRLWESLEVQVSRLMRIRYGDIKLDKTLPRGGWAELELPQVNYLRK 240

Query: 244 QLGPHLLEEAQV----NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
            +     + ++V    +  +    +  + R               +   +        + 
Sbjct: 241 MVSLLPEDRSKVFGVEDRRSEFKQAAQIRRAVRRHRERTVLQGEEVAGEAPAMP--RPKV 298

Query: 300 KLATPVHRRNLASNV-WMAKGIHSSFLSDSGQREENHRRSP 339
             A P  +R     V W               R   + R  
Sbjct: 299 PRAAPPVKRERDDEVSWENARKRLRDGEPRKARPNANNRQR 339


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 104/308 (33%), Positives = 154/308 (50%), Gaps = 21/308 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V ++  I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETIIEAGRVSVDGKIAKLGDRVEVTASMKIRLDGHVVSIKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE-VPDDFTRMKKNSSQKNGLSKQKKL 301
           E           V L     S   + R+R  + +  +     R  + +      +   K 
Sbjct: 242 EL----------VELKPETVSKMPIERERRRVKANQIRRAVKRHTQVAGSGRRSTAGSKP 291

Query: 302 ATPVHRRN 309
                +R+
Sbjct: 292 GNKPSKRS 299


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 128/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V     +
Sbjct: 50  VSNKNEIRDKV---RLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKGQSV 105

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG PL+          +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 106 SIDGKPLKVENELVYIALNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 163

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 164 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITHEFIKGMSNGVPILGTVTKKCLVKKE 223

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 224 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKMGSWRYLTKKE 279

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 280 LAEI--NRLTENSSKTEEASI 298


>gi|167620251|ref|ZP_02388882.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis Bt4]
          Length = 431

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 95/311 (30%), Positives = 154/311 (49%), Gaps = 17/311 (5%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 129 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 187

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 308 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 367

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSET----LVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             +R  +       + V L AP+           R +P+ +        R    ++    
Sbjct: 368 AQVRRLM-------STVGLKAPVEEKGKRGGAAERRQPDPMQTSMGFINREPVLTTHGQL 420

Query: 295 LSKQKKLATPV 305
              ++    P 
Sbjct: 421 DQPRRGRRGPA 431


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 98/298 (32%), Positives = 150/298 (50%), Gaps = 8/298 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGHGSRREMEALITAGRVSVDGKVAT-LGDRVEVNAVIRVDGHQIKTRAA 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + T  DP+GR TVFD LP +  +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-TLLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL+RI YG  QL   +  G  +E+    +    G
Sbjct: 181 WFNVTLTEGRNREVRRLWESQEVQVSRLMRIRYGDVQLDRGIPRGGWQELKLPEVNYLRG 240

Query: 247 P-HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             +L  E +  +D       +  +    I   V        K    +   +++K  ++
Sbjct: 241 LVNLPNETESKVDLQQDGKTSRHKQAAQIRRAVKRHKEMQGKEPRARATTARRKPTSS 298


>gi|229163701|ref|ZP_04291648.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228619763|gb|EEK76642.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 242

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGVLTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|167570132|ref|ZP_02363006.1| RNA pseudouridylate synthase family protein [Burkholderia
           oklahomensis C6786]
          Length = 371

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 87/248 (35%), Positives = 138/248 (55%), Gaps = 6/248 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 60  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 118

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP++  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 239 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 298

Query: 239 KILREQLG 246
             +R  + 
Sbjct: 299 AQVRRLMA 306


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+ ++    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTI-SKSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 115/232 (49%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ +++   G+ +R+E++++I  ++V VNG L     +++    DHIEV G  +   E  
Sbjct: 8   RLDRLLNHMGLGTRKEIKKLIKAKQVMVNGELAMDPGLHIFPQRDHIEVQGEVIEYRE-Y 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP  +++   D   +  V D L   +       VGRLD +TEGLLLLTN+G LA
Sbjct: 67  IYLMLNKPQDVLSATEDASDK-VVIDLLDPTYHSFNPFPVGRLDKDTEGLLLLTNNGKLA 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G V ++ +    +G+ +  G      Q+ +  +    + + 
Sbjct: 126 HQLLSPKKHVPKTYYALVQGLVTEEDVAAFARGVELDDGYRTLPGQLKI-IRSAPQSEIE 184

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++FE    +V  L R+S GP  L   L  G  RE++ + +
Sbjct: 185 LTIYEGKYHQVKRMFEAVGKRVIYLKRLSMGPLVLDNNLKPGEYRELTDEEI 236


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV+    +  D      +G+++ G  Y      L+     +  V + +
Sbjct: 121 ITSPKHHCEKTYRVQLSDDIANDVAEQFAQGVMLNGEKYLTKPAKLEIISPRD--VRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L  TL  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVCGLHRERVGEIWLDETLEPGEYRPLTEEEI 227


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 75/235 (31%), Positives = 118/235 (50%)

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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V L EG+   ++++       V  L+R   GP +LG    G  R ++K  + + 
Sbjct: 246 EVILHEGRKHIVRRMLAEAGHPVLSLVRTQIGPIRLGDTKPGKFRRLTKGEVGDL 300


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 112/230 (48%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R++K ++  G  SRR  +++I Q RV +NG +       ++ TD + VDG  +    E  
Sbjct: 8   RINKYLSEVGYCSRRAADKLIDQGRVTINGKIP-EMGTKIIPTDEVRVDGELISESKEDF 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP+G+V T      +  + D + +   R+  +GRLD  +EGL+ LTNDG +   
Sbjct: 67  VYLAFNKPVGIVCTTDTRVEKDNIIDYI-NYPKRIFPIGRLDKPSEGLIFLTNDGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    +  D ++ +  GI I        +V    +K S     + L
Sbjct: 126 ILRARNHHEKEYIVKVDNIITDDFVHQMSNGIPILDTITRKCKV----EKLSKYEFRIIL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+  + V +L R+      L  +  G+ RE +K+ L+E
Sbjct: 182 TQGLNRQIRRMTEYLGYNVVKLKRVRIMNISL-DMPVGTYREFTKEELKE 230


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 113/230 (49%), Positives = 155/230 (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+     L    K + I GI Y    + L  Q  SN+W  V L
Sbjct: 121 FELPSNRLKRVYHVRAYGK-SDILLKSDYKNLEIDGIFYNPHSIKLLKQNKSNSWFEVVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EGKNREI+++FE+F  KV++LIRI YG F +  L  G+ +E++ KIL E
Sbjct: 180 FEGKNREIRRIFEYFGLKVHKLIRIQYGSFTIDNLKPGAYKEINNKILAE 229


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLQVGKWRDITGEELELLIG 227


>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 =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 120/237 (50%), Gaps = 8/237 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
            +  R+ K+++  G  SR+E++  I +  V +N ++++     V    D I      +  
Sbjct: 1   MSKMRIDKLLSNMGYGSRKEIKNFIKECLVAINDVIIDDPGFTVQPDKDVITFRNEKVSY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G++    DP  R TV D LP      +V   GRLD +TEGLLL+TND
Sbjct: 61  KE-YIYIMMNKPKGVICATYDPSER-TVVDLLPHHIKSRKVFPAGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G L+  L  P     + Y     G +D+D  +L  +GI++    Y  M  TL+     N 
Sbjct: 119 GELSHKLLSPKKHVFKKYYAEVLGFIDEDDASLFSEGILLDDG-YKTMPATLEIISSGNI 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + +REGK  +IK++FE  + KV  L R+S G  +L   L  G  RE++++ ++
Sbjct: 178 SKVYISIREGKYHQIKRMFEAIDSKVIYLKRLSIGKLKLDENLKEGEWRELNEEEIK 234


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+      L +GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EG+  ++K++F     KV  L R   G   L   L  G  R +S++ + 
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQEVE 228


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 114/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+ LTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLIFLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 123/229 (53%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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 D +    +R+  +GRLDI+T GL++LT+DG +  
Sbjct: 61  NTYIALNKPMGIVSTVKDEKDRKTVVDLIDGS-TRLYPIGRLDIDTTGLIILTDDGAITN 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|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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 107/309 (34%), Positives = 152/309 (49%), Gaps = 23/309 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K  ++ +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +
Sbjct: 2   KATLKGSSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRI 61

Query: 63  DGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +   E      R+  Y+KP G + T +DP+GR TVFD LP    +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---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                  LRE           V L     S   + +DR  + +       R  K  SQ +
Sbjct: 242 DLAQTNYLREL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVS 288

Query: 294 GLSKQKKLA 302
           G  +     
Sbjct: 289 GGRRSGGRN 297


>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 =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 116/237 (48%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 1   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKTQVNEFEDTVTYLGEIIAYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 61  FYYIL-HKPAGVISATQD-NHDQTVIDLLKDQDYREDLFPVGRLDKDTEGLLILTNDGIF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G       ++ +D   Q+   +
Sbjct: 119 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFWLPKDLNKGQYRPMTKEELEQ 235


>gi|223940522|ref|ZP_03632370.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890803|gb|EEF57316.1| pseudouridine synthase [bacterium Ellin514]
          Length = 235

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 84/232 (36%), Positives = 126/232 (54%), Gaps = 2/232 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR  ER+I   RV VNG  +      V    D I +DG PLR   + 
Sbjct: 3   RLQKFLAEAGVASRRASERIILGGRVSVNGDTVRELGTKVDPIHDSIALDGAPLRLKRKL 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   +KP G V +  D   R  + D LP+ +  + SVGRLD ++EGL+ LTNDG  +  
Sbjct: 63  YV-ALNKPRGYVCSRKDDRKRKVIGDLLPAEWDNLYSVGRLDSDSEGLIFLTNDGEFSLH 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  + L+ Y     G+V+Q+ L   K GIV +G      +    + + S + V + L
Sbjct: 122 LTHPRYRVLKKYLATVEGRVEQEMLQRFKHGIVHEGEKLKVDRARTLSVQNSTSLVELEL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EGKNREI+++FE     V+RL+R+  G  +LG L +G  R +++  ++  L
Sbjct: 182 TEGKNREIRRLFESQGLTVSRLVRMQIGKIKLGELRSGKWRMLTEAEIKSLL 233


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 109/233 (46%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +     GI +  G       + + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPASLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 NVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTEAEL 227


>gi|317970403|ref|ZP_07971793.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CB0205]
          Length = 235

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/233 (33%), Positives = 120/233 (51%), Gaps = 3/233 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ K+IA+AG+ SRR  E ++   RV VNG   +       ++D I +DG PL  +
Sbjct: 1   MAAERLQKLIAQAGVCSRRRAEELLRDGRVTVNGQRAQLGDKADPNSDAISLDGQPLGAS 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
               + L +KP G++++  DP+GR  V D LP   +R   +  VGRLD  + G LLL+ND
Sbjct: 61  AEPMVLLLNKPAGVLSSCFDPEGRPIVLDLLPPELARGQGLHPVGRLDFESRGALLLSND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + YRV   GQ  Q  L+   +G+ + G+    +QV   + +    
Sbjct: 121 GALTLQLTHPRYAHSKTYRVWVQGQPSQRVLDQWARGVSLDGLPSQPVQVRSLSSEQGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + + EGKNR+I++  E     V  L RI+ GP  LG L  G  R ++ + 
Sbjct: 181 LLELVMGEGKNRQIRRTAELLGHHVLDLQRIAIGPIHLGALPEGRWRRINDQE 233


>gi|310768104|gb|ADP13054.1| 16S rRNA pseudouridylate synthase A [Erwinia sp. Ejp617]
          Length = 234

 Score =  264 bits (675), Expect = 2e-68,   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|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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 114/240 (47%), Gaps = 7/240 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V V+G   +    +V   T  + V G P+    +
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMVDGKPAKDVKAHVDPDTQEVTVYGEPVDYR-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 60  FIYLMMNKPQGVLSATEDSR-QQTVIDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V    Q+  + ++ L+ G+ I+G       +  +      N  V
Sbjct: 119 AHRLLSPKKHVPKTYEVHLKSQISPEDISDLETGVYIEGGYKTKPAKAEIKANDNGNTVV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++ +    +V  L R+S GP  L   L  G  RE++++ L+    P 
Sbjct: 179 YLTITEGKFHQVKQMAKAVGNEVIYLKRLSMGPVSLDPALAPGEYRELTEEELKRLNEPQ 238


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/254 (30%), Positives = 123/254 (48%), Gaps = 1/254 (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 PHLLEEAQVNLDAP 260
                 AQ     P
Sbjct: 254 ISREARAQAGPATP 267


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 119/236 (50%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K+++ +G  SR+EV++M+    V+VN  L++ A  +V   +D I V G P+   E 
Sbjct: 1   MRLDKLLSNSGYGSRKEVKKMLKNGAVRVNDQLVKDAKKHVDPESDDITVYGAPVMYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L     R     VGRLD +TEGLLLLTNDG L
Sbjct: 60  FIYLMMNKPQGVLSATEDSR-QETVVDLLDPELLRFEPFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V  +  +DQ  L+ L+KG+ I +G      + +L   +     +
Sbjct: 119 AHQLLSPKKHVPKTYEVHVNKPIDQAALDQLEKGVDIGEGYVTKPAEASLLASENGVERL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++ +     V  L R+  G   L   LL G  RE+S+  L   
Sbjct: 179 LLTITEGKFHQVKRMLKAVGHDVIYLKRLKMGDVDLDEELLPGEYRELSEHELAAL 234


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>gi|315170764|gb|EFU14781.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 257

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGNVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 109/305 (35%), Positives = 153/305 (50%), Gaps = 20/305 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MIA  RV V+G +       V S+    I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIAAGRVSVDGKIAT-LGDRVESSKSLKIRIDGHLVSIA 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T SDP+GR TVFD LP    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+        
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITLPKGLPRGGWTELD------- 233

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L         V LD    +   + +DR    +       R  K  S+ +   +  +   P
Sbjct: 234 LPAVNYLRNLVELDDETVTKLVVEKDRRRTKAN---QIRRAVKRHSKVSSTPRAPRRN-P 289

Query: 305 VHRRN 309
             +RN
Sbjct: 290 GSKRN 294


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 122/234 (52%), Gaps = 3/234 (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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              L HKP+  V T +DP+GR TV   LP      R+  VGRLD  +EGLLLLTNDG LA
Sbjct: 61  YYLLLHKPVQTVCTVNDPEGRPTVMAYLPPEVRHLRLYPVGRLDYFSEGLLLLTNDGELA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
           + L  P     + Y V   G V +  L  +++G+ +  G     + V   T +  N  + 
Sbjct: 121 QRLTHPRHHQPKTYEVLIRGSVPETALAAMRRGMRLDEGQALLPVDVEAKTAENGNTLLR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + L +G NR+I+++       + RL R++ GP  LG L  G+ R ++   + + 
Sbjct: 181 MVLHQGVNRQIRRMCRDLGLTILRLRRVAQGPLALGNLKPGAARALTTGEVADL 234


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 120/239 (50%), Gaps = 2/239 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R  
Sbjct: 193 TTMVKVVLHSGKNRIVRRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVRSL 251


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 113/231 (48%), Gaps = 7/231 (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 ++   R  V D +     R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TESHIRGNVVDFV-GHPQRIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  +  G+ I G      +VT    + S     + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVIPSFVQGMSSGVKILGQRTLPCEVT----RVSEYVFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EGKNR+I+++   F ++V +L R+     +LG+L  G+ R +++    E 
Sbjct: 174 TEGKNRQIRRMCAAFGYEVKKLQRLRIMNIRLGSLQKGAWRNLTEAEKLEL 224


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 113/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE + +I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDHLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+ LTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLIFLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 72/228 (31%), Positives = 111/228 (48%), Gaps = 5/228 (2%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I+   V VNG ++      V+ +D ++     +   E+    
Sbjct: 2   NKYLANAGVCSRREADEFISAGVVSVNGTVVTELGTKVLRSDEVKFHDQLVSL-EKKVYV 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L 
Sbjct: 61  LLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTTGVLLLTNDGDLASKLT 120

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLR 194
            P     +VY V     V ++ L  +  GI +  G  + D     D +      V + + 
Sbjct: 121 HPKFLKKKVYHVHLDKNVAEEDLQKIASGIELEDGEIHADAIEYADDRDKK--QVGIEIH 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            GKNR ++++FE   ++V RL R+ +       L  G  R ++++ + 
Sbjct: 179 SGKNRIVRRIFESLGYRVVRLDRVQFAGLTKKNLRRGDWRFLTEQEVE 226


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 125/236 (52%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KV+A A +ASRR+ E +I ++R+KVNG ++      V S+D I +D  P+ KA   
Sbjct: 2   QRLQKVLAYANVASRRKAEILILEKRIKVNGKIISELGTKVSSSDIITLDDKPITKAT-Y 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +      R+  +GRLD NT GLLL+TNDG L +
Sbjct: 61  SYFLLNKPNGFLSTAKDKKNRPTVLDLIEEASIQRLYPIGRLDFNTTGLLLITNDGDLTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAW 188
            L  PS    + Y V+ +  + +  L+   KGI+I        +    + +      + W
Sbjct: 121 KLTHPSFCIPKEYHVKINACLQKKDLSTFCKGIIIDKKYLAVCKEIDILKISYMPKPSTW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + + EGKNR+++K+ +   ++V +L R  Y    +  L  G+ R +    +++ 
Sbjct: 181 LKLVITEGKNRQVRKMMQALGYQVLKLKRYRYSFLTIENLTIGAYRPLKIHEIKKL 236


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 86/239 (35%), Positives = 127/239 (53%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  + 
Sbjct: 3   DEQGIRLQKVLAQAGLASRRAAEEMIAAGRVEVNGELIVEQGRRVDPEHDEIRVDGSRIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTN 126
            A R   ++ +KP G+V+T  DP+ R  + D   +P    R+  VGRLD  T GL+LLTN
Sbjct: 63  TARRHVYYVLNKPRGVVSTMDDPESRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   +  L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGDEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++++ L + L
Sbjct: 182 SLVEVSLHEGRNRIVRRMMDSVAHPVRRLSRTAIGPVRLKRLSRGDMRELTREELGQLL 240


>gi|320663977|gb|EFX31164.1| 23S rRNA pseudouridylate synthase B [Escherichia coli O157:H7 str.
           LSU-61]
          Length = 290

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 107/300 (35%), Positives = 149/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTVEDCQLFAQGFALKDGEMVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 152/290 (52%), Gaps = 12/290 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 310 VNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 154/278 (55%), Gaps = 10/278 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
           ++ +N   +    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  
Sbjct: 48  IETENKANDKIVGEKLQKILARAGQGSRREIEEVIAAGRVSVDGKIAMLGDRVQVSSSTK 107

Query: 60  IEVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
           I +DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 REVSKK---ILREQLGPHLLEEAQVNLDAPIYSSETLV 268
            E+  +    LRE +G     E +V++      + T  
Sbjct: 288 EEMGLEQVNYLRELVGLKPETETKVDVTKARRRTSTRQ 325


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 152/290 (52%), Gaps = 12/290 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 310 VNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|296282690|ref|ZP_06860688.1| hypothetical protein CbatJ_03660 [Citromicrobium bathyomarinum
           JL354]
          Length = 252

 Score =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 109/240 (45%), Positives = 155/240 (64%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + ++     R++K++ARAG+ASRREVERMIA +R+ ++G  +E  A  + +   + VDG 
Sbjct: 1   MAEDERKGDRIAKLLARAGVASRREVERMIADKRIAIDGKTVETPATLLETLRGVTVDGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGL 121
           P+ K E TRL+ +HKP GL+T   DP GR T++D    +LP    RV+ +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|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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 104/315 (33%), Positives = 163/315 (51%), Gaps = 11/315 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVR 260

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEFDRQKLLQGVRLDDGEANFLRC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR---PNIISEVPDDFTRMKKNSSQKN 293
           S + +R  +G   L+    +      S     R R   P ++  +   FT      S+  
Sbjct: 441 SAEEVRVLMGSLGLKVPSASAGGGQGSRPQGGRRREAQPMLMGPMSSGFTGEATFQSRGQ 500

Query: 294 GLSKQKKLATPVHRR 308
           G+    + A P  RR
Sbjct: 501 GVENGNR-ALPAARR 514


>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 =  264 bits (675), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 112/233 (48%), 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 +KP G V+   D     TV + + S    +  VGRLD++TEGLLL++NDG L   
Sbjct: 61  YYIL-NKPQGYVSATED-MLYPTVMELIQSQRHDLYPVGRLDVDTEGLLLISNDGKLTHE 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V F G + ++ ++   + +  +       ++ +           + +
Sbjct: 119 VLSPKKHVDKKYYVEFDGTLPENAVDFFNQPMEFEEFTSAPSKLEIL----DTNKAYLTI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGK  ++K++FE  N  V  L RI +GP +L  L  G  R ++++ L    G
Sbjct: 175 HEGKFHQVKRMFEKANCTVTYLQRIEFGPLKLNDLPLGEFRALTQEELDALKG 227


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 123/232 (53%), Gaps = 3/232 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K +A  GIASRREV++MI +  +K+NG       + V   D I + G  + K 
Sbjct: 1   MEEMRINKYLASLGIASRREVDKMIEEGSIKINGEKAT-PGIKVSDKDEIYIRGKKIEKH 59

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   ++ +KP+ ++++  D  GR TV D + +   R+  +GRLD NT GL++LTNDG 
Sbjct: 60  TEKKVYYILNKPLEVLSSSKDDRGRKTVVDLI-NCKERIFPIGRLDYNTSGLIILTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + Y V+  G++ ++ + LLK G+ +         V +  ++     +
Sbjct: 119 LFNRIIHPKAEIFKEYYVKVLGEIKENNVELLKNGVELDDGITLPANVRILRREKGKTEL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V +REG+NR+++++ +  N  V  L R   G   LG L  G  RE++   +
Sbjct: 179 LVAIREGRNRQVRRMMDKINHPVITLRREKIGNLSLGNLKLGEYRELTNDEI 230


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 85/231 (36%), Positives = 126/231 (54%), Gaps = 1/231 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AGI SRR  E ++ Q RVKVNG L        +  D +EVDG PL++A
Sbjct: 1   MTRQRLQKLIAAAGICSRRRAEDLLRQHRVKVNGQLAAIGDQADLDQDDVEVDGRPLQRA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP G++ +  DP  R TV D +P+     +  VGRLD  + G LLL+N G 
Sbjct: 61  LVPRVLLLNKPPGVICSCRDPQQRKTVLDLVPAHLRDGLHPVGRLDAESRGALLLSNQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   + +L   ++G+V+ G      +VTL      ++ +
Sbjct: 121 LTLQLTHPRYNHCKTYRVTVAGLPPEKQLRQWRRGVVLDGTVTRPAEVTLLEGTTRSSVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V LREG+NR+I+++      +V  L RI+ G   LG++  G  RE+S++ 
Sbjct: 181 EVVLREGRNRQIRRIALSLGHRVLDLQRIAIGDLMLGSVAEGCWRELSRQE 231


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 118/241 (48%), Gaps = 8/241 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR++V++++    V VN   ++     V    D + ++G  +   E 
Sbjct: 1   MRIDKMLANLGYGSRKDVKKLLKDGAVTVNDEKVKDPKHQVDPEQDAVIINGEKVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L    +      VGRLD +TEGLLLLTNDG L
Sbjct: 60  FIYLMMNKPPGVISATEDSQF-ETVVDLLEMRDLVFSPFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y      +V  D +   KKG+++  G      ++ +  + G  + +
Sbjct: 119 AHRLLSPKKHVPKTYFAVIDREVTADDVAAFKKGVILDDGYETKPGELEIL-KSGITSDI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++FE    +V  L RIS GP +L  TL  G  RE++ + L + +   
Sbjct: 178 ELTITEGKFHQVKRMFEAVGKRVIYLKRISMGPLELDKTLELGEYRELTDEELDKLMNYE 237

Query: 249 L 249
           +
Sbjct: 238 V 238


>gi|167582090|ref|ZP_02374964.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis TXDOH]
          Length = 379

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 91/269 (33%), Positives = 143/269 (53%), Gaps = 13/269 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 73  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 131

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 252 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 311

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETL 267
             +R  +       + V L AP+      
Sbjct: 312 AQVRRLM-------STVGLKAPVEEKGKR 333


>gi|324117539|gb|EGC11445.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 299

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 107/309 (34%), Positives = 153/309 (49%), Gaps = 23/309 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K  ++ +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +
Sbjct: 2   KATLKGSSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRI 61

Query: 63  DGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +   E      R+ +Y+KP G + T +DP+GR TVFD LP    +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---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                  LRE           V L     S   + +DR  + +       R  K  SQ +
Sbjct: 242 DLAQTNYLREL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVS 288

Query: 294 GLSKQKKLA 302
           G  +     
Sbjct: 289 GGRRSGGRN 297


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 122/234 (52%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+  G+ SRRE ++ IA  RV +NG+  E  +  V   D I VDG PL + ++ 
Sbjct: 1   MRINKFISETGVCSRREADKWIAANRVTINGVPAELGST-VEEGDEIRVDGKPLGEKKKG 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T ++   +  + D + +   R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-TEKHVKGNIIDFV-NHPERIFPIGRLDKDSQGLILLTNDGDIVNQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR +  V  + +  +  G+ I G      +VT    + ++    + L
Sbjct: 118 ILRAENNHEKEYVVRVNKPVTDEFVKGMAGGVRILGTKTKPCKVT----RINDHVFRIIL 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|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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 116/246 (47%), Gaps = 8/246 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKFHVNVEEQEVTIHGEIVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LLLTNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVVDLLELEDAIFDPFPVGRLDIDTEGFLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V +  +    KG+++  G      ++T+  +    + +
Sbjct: 119 THQLLSPKKHVPKKYYAHVAGVVTEKDVEEFAKGVILDDGYETKPGELTIL-KSDDVSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + +       
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVEMLKTYQ 237

Query: 249 LLEEAQ 254
           +  E+Q
Sbjct: 238 VQTESQ 243


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V  + +     GI +  G      ++ + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTAEDVEAFAAGIELDDGYTCKPARLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKSVSYLKRISMGNLQLDESLALGEYRPLTEAEL 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 =  263 bits (674), Expect = 2e-68,   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|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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    I SR +V++ I +  V VNG     + + +   TD I+ +G  L  + +
Sbjct: 1   MRLDKFLVEMNIGSRSQVKQYIKKGMVSVNGTNAASSDMKINEDTDTIKYNGKQLCYS-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R +L +KP G V+   D +   TV D L       +  VGRLD++TEGLL++TNDG LA
Sbjct: 60  YRYFLLNKPAGCVSATKD-NVHQTVIDLLNGENTKDLFPVGRLDLDTEGLLIITNDGRLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AW 188
             L  P+    + Y     G VD   ++L K+GI I          + +     S   + 
Sbjct: 119 HHLLSPAHHIAKTYYADIDGYVDDQTISLFKQGIDIGDDTPTLPASLKIIEADRSTGSSR 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + + + EG+  ++K++F+  N  V  L RIS G   +   L  GS RE++ + +   
Sbjct: 179 IELTITEGRFHQVKRMFQAVNMSVTFLKRISMGNLHIADDLPTGSYRELTPEEVSAL 235


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/342 (27%), Positives = 158/342 (46%), Gaps = 24/342 (7%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +++  ++  P ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + +
Sbjct: 174 RRDLTADDDAP-KLHKVLAEAGLGSRRDMEELIIAGRVSVNGEPA-HIGQRILPTDQVRI 231

Query: 63  DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           +G  +++    +  R+ +YHKP G + + +DP+GR +VFD LP++  ++ ++VGRLD NT
Sbjct: 232 NGKLIQRKVSKKPPRVLVYHKPAGEIVSTNDPEGRPSVFDRLPTMKAAKWLAVGRLDFNT 291

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL T  G LA  L  P     R Y VR  G++++     L  G+ ++       ++ 
Sbjct: 292 EGLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMRQKLLAGVELEDGLAQFSKIA 351

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+ 
Sbjct: 352 DGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGLLTLPKNLKRGRWEEME 411

Query: 238 KKILREQLGPHLLEEAQVNLD-----------------APIYSSETLVRDRPNIISEVPD 280
           +  +R+ L    L++                       AP   +       P+       
Sbjct: 412 EHAVRDLLALSGLDKNTGEAGPANKGRAAGGDRVNGNRAPRVDNGLGQPRSPSQWQNTGT 471

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHS 322
              R +  +  K     Q++   P   +       M +   S
Sbjct: 472 GQGRSQGQNPGKPNRQGQQRSRQPDPLQTSLGFPGMGQPRRS 513


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 66/282 (23%), Positives = 125/282 (44%), Gaps = 10/282 (3%)

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 ++      V D +    +R+  +GRLD  +EGL+ LT
Sbjct: 60  PVKEKQKRIYIALNKPAGITCT-TERHIHGNVIDLI-DYSTRIFPIGRLDKPSEGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V+    V    L  + +G+ I        +VT + +   
Sbjct: 118 NDGDIVNKILRAGNAHEKEYIVKVDSTVTDKFLTGMARGVPILDTVTKPCKVTREGR--- 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G N++I+++ E F ++V  L R       +  L  G  R ++   + E  
Sbjct: 175 -FEFKIILTQGLNQQIRRMCEHFGFQVKSLTRTRIMNIDIKGLATGQWRLLTDNEMAEI- 232

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              ++E +    +A  Y  +   + +        +   R K+
Sbjct: 233 -NAMVEGSSSTEEASDY-GQVKPKVKGQHSKRGVNSAARQKR 272


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A + SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKLCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 101/315 (32%), Positives = 160/315 (50%), Gaps = 11/315 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 109 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVR 166

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD N
Sbjct: 167 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 226

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 227 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAESDRQKLLQGVRLDDGEANFLRC 286

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 287 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 346

Query: 237 SKKILREQ---LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           S + +R     LG  +   +                 +P ++  +   FT      S+  
Sbjct: 347 SAEEVRVLMGSLGLKVPSVSAGGGQGGRPQGGRRREAQPMLMGPMSSGFTGEATFQSRGQ 406

Query: 294 GLSKQKKLATPVHRR 308
           G+    + A P  RR
Sbjct: 407 GVENGNR-ALPAARR 420


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 133/236 (56%), Gaps = 4/236 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R++K IA++GI SRR+ + +I + +VKVNG  ++   + +    D +EV+G  ++  E+
Sbjct: 2   ERLNKYIAKSGICSRRKADELILEGKVKVNGKTVKNLGLKIDPKKDVVEVEGKIVKPTEK 61

Query: 73  TRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP+G ++    D  GR T+ D L    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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V +  GK R I++  + F  +V RLIR+  G   +G L     R +S+K +R  L
Sbjct: 182 LVEIHSGKKRIIRRFMDSFGHRVKRLIRVKIGSIDIGNLKPFDYRYLSEKEIRSIL 237


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 122/237 (51%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ KV+A  G  SR+EV++++    V VN   ++ A  +V    D I ++G  +   E 
Sbjct: 1   MRIDKVLANLGYGSRKEVKKLLKDGSVTVNDEKIKDAKQHVDPEKDLIRINGETVEYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D +   TV D L    +      VGRLD +TEGLLL+TNDG L
Sbjct: 60  FIYLMMNKPPGVISATED-NRDETVIDLLEAEDLIFEPFPVGRLDKDTEGLLLITNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y      +V ++ +   +KG+++  G      ++ +  + G  + +
Sbjct: 119 AHRLLSPKKHVPKTYFAVIDQEVTEEDVTAFRKGVILDDGYATKPGELNIL-KSGERSDI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            + + EGK  ++K++FE    KV  L R+S GP +L  TL  G  RE++++ L+  +
Sbjct: 178 ELTITEGKFHQVKRMFEAVGKKVVYLQRLSMGPLRLDETLELGEYRELTEEELQSLM 234


>gi|323439505|gb|EGA97226.1| ribosomal large subunit pseudouridine synthase B [Staphylococcus
           aureus O11]
          Length = 245

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 133/243 (54%), Gaps = 5/243 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ + KVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKAKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTV 191
           +  P  Q  + Y  +  G + ++++  L+KGI ++       +  V    +  +   V +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQPAEVKVKKQDKDKNTTLVEI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+NR+++++ E F  +V +L RI YGP  +  L AG  R ++   ++  +  HL E
Sbjct: 185 TITEGRNRQVRRMLEHFGHQVTKLSRIEYGPLNVVGLNAGEGRVLTPHEVK--VMRHLAE 242

Query: 252 EAQ 254
             +
Sbjct: 243 HGK 245


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 105/230 (45%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN ++ +  A  V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNDVMQKSGAFKVTDACVVEWQGREIQKP-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  +  KP G V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLFKPDGFVCSHEDGFN-QTAFALLDEVKMEDLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D  + L +G+ ++      +  T++        + + 
Sbjct: 119 RITSPKHKCEKTYRVWLVDPIGDDYADKLAQGVELRNEKEPTLPATMEVVNHDENELLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ +
Sbjct: 179 ITEGKYHQVKRMFAALGNKVEHLHRERIGAIELDYSLEPGEYRYLTEEEV 228


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 105/226 (46%), Gaps = 3/226 (1%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER    
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAVS-IERKIYV 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L 
Sbjct: 61  LLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLASKLT 120

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P     ++Y V     + +  +  +  GI +         ++  T       V + +  
Sbjct: 121 HPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIQADAISY-TDDFKKDEVGIEIHS 179

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 180 GKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQEV 225


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 110/290 (37%), Positives = 151/290 (52%), Gaps = 12/290 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 310 VNYLRELVG--LPAETETKLDVKQASRRLKSGQIRKAVKRYSEMNKRYKK 357


>gi|16801498|ref|NP_471766.1| hypothetical protein lin2436 [Listeria innocua Clip11262]
 gi|16414958|emb|CAC97663.1| lin2436 [Listeria innocua Clip11262]
          Length = 233

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVIYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NLSETVIDLLEQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V  + +     G+ +  G       + + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL   L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDDSLELGEYRPLTENEL 227


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 103/236 (43%), Gaps = 3/236 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +    L  KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVELESPLAEGTAELFAKGVQLHNEKDLTKPAVLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            EG+  ++K++F      V  L R   G   L   L  G  R +++  +     P 
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGDILLDDALAPGEYRPLTETEIASVGAPQ 234


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 112/294 (38%), Positives = 152/294 (51%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +
Sbjct: 66  KASNQPKIEGEKLQKVLARAGQGSRREIETMIASGRVSVEGKIAILGDRIDVHSGVKVRI 125

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    SR I+VGRLDIN
Sbjct: 126 DGQIINLSHAQKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGSRWIAVGRLDIN 185

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 186 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 245

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 246 KFTGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 305

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
             +    LRE +G  L  E    LD    S           +    +   R KK
Sbjct: 306 DLENVNYLRELVG--LPAETATKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>gi|289178586|gb|ADC85832.1| Ribosomal large subunit pseudouridine synthase B [Bifidobacterium
           animalis subsp. lactis BB-12]
          Length = 266

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 119/239 (49%), Gaps = 2/239 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           + +    R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + VDG  
Sbjct: 22  ENDGDGIRLQKLLAQAGFGSRRKCEEMITDGRVEVDGELVTELGTRVDPKRQQVRVDGSR 81

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R   R      +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 82  IRLNPRHITLALNKPRKVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 141

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G +       L + G+ +          ++      
Sbjct: 142 DGELSQHVMHPKYEVEKTYIATLEGHMSGTVCRRLVRTGVQLDDGWIKLDHCSIIDSNRD 201

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L  G+NR ++++F    + V RL+R   GP +LG + +GS R +S+  +R  
Sbjct: 202 QTIVKVVLHSGRNRIVRRIFGAIGFPVKRLVRTQIGPIKLGDIKSGSYRVLSQDEVRAL 260


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/343 (27%), Positives = 142/343 (41%), Gaps = 10/343 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
              +R+ K +ARAG+ASRR  E +I   RV VN   +      V   TD + VDG  +  
Sbjct: 1   MAAERLQKYLARAGVASRRHAEELITAGRVAVNNKTVTELGSRVEPGTDLVTVDGTLVTP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + +  +L +KP+G+VTT SDP GR TV + +     R+  VGRLD + EG LL T+DG 
Sbjct: 61  PDESSYFLLYKPVGVVTTLSDPQGRPTVANYVEETGKRLFPVGRLDYDAEGALLFTDDGA 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS Q  R Y  +  G  D   L+ L+ G+ ++      + V++      N W+
Sbjct: 121 LAHKLTHPSFQVPRTYLAKVKGAPDTATLDKLRGGVRLEDGMATPVSVSVFEAAERNTWL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EG+   IK++       V RL R SY    +  L  G  R +    +        
Sbjct: 181 KIVVAEGRPHLIKRLCAAVGHPVVRLFRPSYAGVGVEGLRPGELRPLKTSEVE------- 233

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           L  A  +  A   + E  +  R +  +    D     + S   +     K       R  
Sbjct: 234 LLNAVSDGKAAPPTGELRLPPRRHGRAAPGFDSDDEAELSMDDDAPVAAKPARKAPARAA 293

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             + V  +          +    +  RRS  F       R  +
Sbjct: 294 KTATVGGSSLARFGRPKGASAEGKPARRS--FGGDEGAPRGRS 334


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 69/228 (30%), Positives = 117/228 (51%), 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  KVYIMLNKPEGYVTTNKDEKNRKTILDIV-KVNERIYPIGRLDYDSSGLLLLTNDGDVYN 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|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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 104/315 (33%), Positives = 163/315 (51%), Gaps = 11/315 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 207 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVR 264

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD N
Sbjct: 265 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 324

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 325 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEFDRQKLLQGVRLDDGEANFLRC 384

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 385 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 444

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR---PNIISEVPDDFTRMKKNSSQKN 293
           S + +R  +G   L+    +      S     R R   P ++  +   FT      S+  
Sbjct: 445 SAEEVRVLMGSLGLKVPSASAGGGQGSRPQGGRRREAQPMLMGPMSSGFTGEATFQSRGQ 504

Query: 294 GLSKQKKLATPVHRR 308
           G+    + A P  RR
Sbjct: 505 GVENGNR-ALPAARR 518


>gi|186476490|ref|YP_001857960.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192949|gb|ACC70914.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 597

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 93/281 (33%), Positives = 144/281 (51%), Gaps = 13/281 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + ++
Sbjct: 191 KRVLSPDDDAPKLHKVLADAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRILPTDLVRIN 249

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 370 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIALPRGLKRGRWEELED 429

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +       A V L AP        R  P      P
Sbjct: 430 NQVRSLM-------ASVGLKAPAEEKGAGRRGEPERRQPDP 463


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 107/288 (37%), Positives = 154/288 (53%), Gaps = 12/288 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 88  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 147

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 268 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 327

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G  L  E +  +D       T +R     + +     T+ 
Sbjct: 328 VNYLRELVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 373


>gi|167894529|ref|ZP_02481931.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
          Length = 395

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 90  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 148

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 269 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 328

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 329 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 374


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 1/236 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              QR+ K+IA +G+ SRR  E+++ Q+RV +NG L +         D I VDG  L   
Sbjct: 1   MKQQRLQKLIAASGLCSRRHAEQLLLQERVTLNGHLAKLGDKADPELDKISVDGRVLNSN 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V LREG+NR+I++V E     V  L R +     L  L  G  R + ++     L
Sbjct: 181 KVVLREGRNRQIRRVAEQLGHPVLDLQRTAIANVALDALPEGCWRALDEREWTPLL 236


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 50/229 (21%), Positives = 101/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  +  +    G+ + G         L+  +       + +
Sbjct: 121 ITSPKHHCKKTYLVTLECPVAAETADKFLAGVQLNGEKTVTKPAQLEILEP--QIARLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVTALHRERIGEIILAPELEPGEYRSLTEQEI 227


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 89/260 (34%), Positives = 131/260 (50%), Gaps = 15/260 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ KV+A+ GIASRRE E MI + RV++NG L       V    D I VDG  +      
Sbjct: 30  RLQKVLAQWGIASRREAEEMIRRSRVQINGTLA-ELGQKVNPERDIITVDGKSVSAQRHH 88

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 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-----LLAGSTREVSKKILR- 242
           + + L+EG+NR+I++V E   + V +L R + G  QL T     L AG+ R +    +R 
Sbjct: 209 LEIVLQEGRNRQIRRVAEQLGYPVIKLHRTAIGSIQLQTSKQPLLRAGNYRILRDDEIRS 268

Query: 243 --EQLGPHLLEEAQVNLDAP 260
             EQL     +  +V    P
Sbjct: 269 LQEQLKHIPTQRIKVQNPQP 288


>gi|313622662|gb|EFR93029.1| RNA pseudouridine synthase family protein [Listeria innocua FSL
           J1-023]
          Length = 233

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 110/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPEKDQVTVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V  + +     G+ +  G       + + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  +IK++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQIKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTENEL 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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 99/229 (43%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     + +D       GI +           L+        V + +
Sbjct: 121 ITSPRHHCEKTYRVTLESPLAEDTAEQFAHGIQLHNEKALTKPAQLEVITA--TEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L   L  G  R +++  +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGAIALDPELEPGGYRPLTEDEI 227


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 90/290 (31%), Positives = 148/290 (51%), Gaps = 7/290 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A AG+ SRRE+E +I   RV VNG         ++ TD + 
Sbjct: 172 PQKRVLAPEDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRILPTDQVR 230

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           ++G P+++    +  R+ LYHKP G + +H+DP+GR++VFD LP +  ++ ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G+N W  V L EG+NRE++++FE     V+RLIR  +G   L   L  G   E+
Sbjct: 351 RDGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGSISLPRGLKRGRWEEL 410

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            +  +R+ +    L+ A  +       +    R +P+ +        R  
Sbjct: 411 DEAQVRKLMATVGLKVA-ADEKGGKRGAGAAERKQPDPMQTSMGFLNREP 459


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V VNG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTVNGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFGYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+      L +GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EG+  ++K++F     KV  L R   G   L   L  G  R +S++ + 
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQEVE 228


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 104/305 (34%), Positives = 153/305 (50%), Gaps = 23/305 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPL 67
           +    +++ K++ARAG  SRRE+E +I Q RV V+G +      V V     I +DG  L
Sbjct: 23  DKIVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKISTLGDRVEVTQATKIRLDGHLL 82

Query: 68  RKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
              E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLL
Sbjct: 83  SIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLL 142

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ +         ++    
Sbjct: 143 LFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLDDGPAAFRTISFQGG 202

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK-- 239
           +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K  
Sbjct: 203 EGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKAT 262

Query: 240 -ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             LRE           V L++   S   + +DR  + +       R  K  ++  G    
Sbjct: 263 NYLREL----------VELNSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQVA 309

Query: 299 KKLAT 303
            +  +
Sbjct: 310 GRQGS 314


>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 =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EGK  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 111/232 (47%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  GI SRR  ++ IA+ +V +NG         V   D + +DG  ++K ++ 
Sbjct: 1   MRINKYLSETGIISRRGADKWIAEGKVTINGEPAT-VGSQVQDGDIVCIDGKEVKKEQQL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T ++   +  V D +     R+  +GRLD  +EGLLLLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TERHIKGNVVDFVNHPL-RIFHIGRLDKESEGLLLLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    + +  +N +  G+ I         V    +K S+    + L
Sbjct: 118 ILRAENHHEKEYIVQVDKPITEQFINKMSAGVDILDTTTLPCYV----EKISDKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++     + V RL RI     +LG L  G  R+++ K   E  
Sbjct: 174 EQGLNRQIRRMCSALGYSVKRLQRIRIMNIKLGNLKVGQWRDLTDKEQTELF 225


>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 =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 115/235 (48%), Gaps = 5/235 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K ++ AG+ SRR  +R+I + RV VNG         V ++D + VDG  +   
Sbjct: 1   MEAVRINKYLSEAGVCSRRGADRLIEEGRVSVNGNHAF-LGSVVKNSDEVRVDGNLVTPV 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            +  L  ++KP G+V T +DP  +        +   R+  VGRLD  +EGL+LL+NDG L
Sbjct: 60  IKKILIAFNKPRGIVCTTADPKSKDVNIIEYINYPERIFPVGRLDKESEGLILLSNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +        + Y V      D + L  + +G+ I         +    +   N    
Sbjct: 120 SNKIMKARNFHEKEYEVEVDKPFDDEFLKKMSEGVPILDTITRKCTLKRTGKTSFN---- 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L +G NR+I+++ E+F +KV +L RI     +LG L +G+ R ++ K   E +
Sbjct: 176 IILTQGLNRQIRRMCEYFGYKVLKLKRIRIMNIKLGNLKSGTYRNITDKEYEELI 230


>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 =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 122/237 (51%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  +G+ SR +V++++ + +V VNG  +  A   +   +D I VDG  L   E+
Sbjct: 1   MRLDKFLVESGLGSRSQVKQLLKKGQVWVNGAAVTSAKTQINERSDQIVVDGQTLVY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLD++T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPKGVISATED-DRHKTVLDLLDDTARQKEVFPVGRLDVDTHGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAW 188
           +  +  P     +VY+ +  G +DQ  +    +GI ++       Q+ +  +      + 
Sbjct: 119 SHAMLSPKRHVAKVYQAQVAGLMDQADVERFAQGIELKDFTCQPAQLEILERDEGAKTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R+S GP QL  +L  G  R ++++ ++  
Sbjct: 179 VRITLSEGKFHQVKRMVLACGKEVTDLQRLSMGPLQLDPSLELGQWRRLTEEEMQSL 235


>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 =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 152/290 (52%), Gaps = 12/290 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 310 VNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 128/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V     +
Sbjct: 50  VSNKNEIRDKV---RLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKGQSV 105

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG PL+          +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 106 SIDGKPLKVENELVYIALNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 163

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 164 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKPITHEFIKGMSNGVPILGTVTKKCLVKKE 223

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 224 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLTKKE 279

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 280 LAEI--NRLTENSSKTEEASI 298


>gi|295100683|emb|CBK98228.1| ribosomal large subunit pseudouridine synthase B [Faecalibacterium
           prausnitzii L2-6]
          Length = 278

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 87/279 (31%), Positives = 140/279 (50%), Gaps = 4/279 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
              +R+ K+++  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +  +
Sbjct: 1   MAEERIQKIMSEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIQ 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K ++      +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG
Sbjct: 61  KNQQMYYLALYKPRGYVTTASDELGRKTVMELVADIPARLYPVGRLDKDSEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
             A+ +  PS    ++YRV    + D+ ++  L  G+V+  G       + + T +    
Sbjct: 121 AFAQAVTHPSGGISKLYRVTVQPRADEAQILKLSSGVVLDDGTKTMPCAINVVTDEPGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L+EGKNREI+++ E    +V RL R + G  +LG L  G  RE++K  +      
Sbjct: 181 VMEMTLKEGKNREIRRMCEAVGLEVIRLKRNAEGVVKLGMLQPGRYRELTKAEVNGLRAA 240

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
                AQ    A + S     R R  +         + K
Sbjct: 241 AAKGRAQT-RSAALQSRAAARRPRGPVGGNKAAAGKKHK 278


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 152/290 (52%), Gaps = 12/290 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           Q     +++ KV+ARAG  SRRE+E MIA  RV V G +      ++V S   + +DG  
Sbjct: 70  QPKAEGEKLQKVLARAGQGSRREIETMIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQI 129

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
              LRE +G  L  E +  LD    S           +    +   R KK
Sbjct: 310 VNYLRELVG--LPAETETKLDVKQASRRPKSGQIRKAVKRYSEMNKRYKK 357


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 107/309 (34%), Positives = 151/309 (48%), Gaps = 23/309 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   + +   +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +
Sbjct: 2   KATPKGSSMSEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRI 61

Query: 63  DGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +   E      R+  Y+KP G + T +DP+GR TVFD LP    +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---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                  LRE           V L     S   + +DR  + +       R  K  SQ +
Sbjct: 242 DLAQTNYLREL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVS 288

Query: 294 GLSKQKKLA 302
           G  +     
Sbjct: 289 GGRRSGGRN 297


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 114/234 (48%), Gaps = 8/234 (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      + D +     R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-HYPERIFPVGRLDKASEGLILLTNDGGIAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L +G  R+++ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNGLESGKWRDITAEELEILIG 227


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 121/239 (50%), Gaps = 2/239 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L  GKNR ++++F    + V RL+R   GP +LG L AGS R +S+  +R  
Sbjct: 193 ATIVKVVLHSGKNRIVRRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVRSL 251


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVMLESPVADDTAEQFTKGVQLHNEKDLTKPAVLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 179 IEGRYHQVKRMFAAVGNRVVGLHRERIGEIALDPELEPGEYRPLTEEEI 227


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 105/226 (46%), Gaps = 3/226 (1%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER    
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTVS-IERKIYV 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L 
Sbjct: 61  LLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLT 120

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P     ++Y V     + +  +  +  GI +         ++  T       V + +  
Sbjct: 121 HPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIQADAISY-TDDFKKDEVGIEIHS 179

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 180 GKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQEV 225


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 108/304 (35%), Positives = 151/304 (49%), Gaps = 13/304 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG + +           I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEGLIKSGRVSVNGQVAKLGERLEDENSVIRIDGHTVSGKAS 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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 P  +S    R R   I        R ++ ++   G S Q K   
Sbjct: 242 LVELKPEKETLLDLD-PSNTSRKRERSRSQKIRR---AVRRHEERANAPKGRSNQAKRKK 297

Query: 304 PVHR 307
           P  R
Sbjct: 298 PATR 301


>gi|257465549|ref|ZP_05629920.1| pseudouridine synthase [Actinobacillus minor 202]
 gi|257451209|gb|EEV25252.1| pseudouridine synthase [Actinobacillus minor 202]
          Length = 340

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 104/262 (39%), Positives = 148/262 (56%), Gaps = 10/262 (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  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           G  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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 KK---ILREQLGPHLLEEAQVN 256
            +    LRE +G     E +V+
Sbjct: 292 LEQVNYLRELVGLPAETETKVD 313


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 73/245 (29%), Positives = 116/245 (47%), Gaps = 10/245 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+K    E     R++K ++ AG  SRRE +R++ Q  VKVNG         V   D I
Sbjct: 7   LKEKKSADEQI---RLNKFLSDAGYCSRREADRLVEQGVVKVNGKTA-VMGQKVTINDSI 62

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V G  + + E   L   +KP+G+  T +D +    + D + +   RV  +GRLD N++G
Sbjct: 63  MVKGKNISREEEQILIALNKPVGIECT-TDLNNPDNIVDFI-NFDKRVYPIGRLDKNSQG 120

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLTNDG +   +   S    + Y V     V  D +  +  G+ I        +VT  
Sbjct: 121 LILLTNDGSIVNNILKGSNYHEKEYVVTVDKPVTDDFIKKMSTGVRILDQVTRPCKVT-- 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K       + L +G NR+I+++     + V +L RI     +LG L  G  R+V+   
Sbjct: 179 --KVKKHVFNIVLTQGLNRQIRRMCGELGYNVQKLKRIRIMNIELGNLPVGQYRKVTDSE 236

Query: 241 LREQL 245
           L+E +
Sbjct: 237 LKELM 241


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 74/236 (31%), Positives = 124/236 (52%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KV+A A +ASRR+ E +I ++R+KVNG ++      V S+D I +D  P+ K    
Sbjct: 2   QRLQKVLAYANVASRRKAEILILEKRIKVNGKIISELGTKVSSSDIITLDDKPITKTT-Y 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +      R+  +GRLD NT GLLL+TNDG L +
Sbjct: 61  SYFLLNKPNGFLSTAKDNKKRPTVLDLIEEANIQRLYPIGRLDFNTTGLLLITNDGDLTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAW 188
            L  PS    + Y V+ +  + +  L   +KGI+I        +    +    +   + W
Sbjct: 121 KLTHPSFCIPKEYHVKINACLQKKDLATFRKGIIIDKNYLAFCKEIDILKSSYKPKPSTW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + + EGKNR+++K+ +   ++V +L R  Y    +  L  G+ R +    +++ 
Sbjct: 181 LKLVITEGKNRQVRKMMQSLGYQVLKLKRYRYSFLTIENLTIGAYRPLKIHEIKKL 236


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     ++         GI + G         L+          + +
Sbjct: 121 ITSPKHHCEKTYLVALDRPIEPGTAEHFAAGIQLNGEKELTKPAVLEV--LDEQLARLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G   L  +L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVTALHRERIGAIVLDSSLEPGEYRALTQEEV 227


>gi|310767747|gb|ADP12697.1| 23S rRNA pseudouridylate synthase B [Erwinia sp. Ejp617]
          Length = 295

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 102/302 (33%), Positives = 147/302 (48%), Gaps = 22/302 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E +I+  RV V+G L       V       I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETLISAGRVSVDGKLAT-LGDRVEPGASLKIRIDGHVVPVS 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T SDP+GR TVFD LP    +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 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE +G          L     S   + +DR    +       +    +      S ++  
Sbjct: 241 RELVG----------LAPETVSKVPVEKDRRRTKANQIRRAVKRHTTTKVSKPGSGRRPS 290

Query: 302 AT 303
             
Sbjct: 291 KR 292


>gi|298490451|ref|YP_003720628.1| pseudouridine synthase ['Nostoc azollae' 0708]
 gi|298232369|gb|ADI63505.1| pseudouridine synthase ['Nostoc azollae' 0708]
          Length = 254

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 83/238 (34%), Positives = 125/238 (52%), 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 +KP G+V+T  DP GR TV D LP        +  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|251771881|gb|EES52455.1| Pseudouridine synthase, Rsu [Leptospirillum ferrodiazotrophum]
          Length = 638

 Score =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 106/360 (29%), Positives = 169/360 (46%), Gaps = 12/360 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
            D  I +E     R+ K++A  G+ASRR+ E++IA   V V+G ++      V      I
Sbjct: 14  DDSEIPEEADGRLRLHKILAHRGVASRRKSEQLIAAGSVTVDGEVVTEPGTRVDPKHQVI 73

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            VDG PL +   T L+L++KP G+V+T  DP+GR T+ D  P I   +  +GRLD  TEG
Sbjct: 74  LVDGRPLPREPETFLFLFYKPKGVVSTLFDPEGRPTLRDYFPGIDPLLH-IGRLDFQTEG 132

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTL 179
            LLLTN+G L++ +  P  +  R Y V+  G +    L  + +G I + G     +++  
Sbjct: 133 ALLLTNNGDLSQRILHPRFEIPRTYLVKIQGGMSPAHLERMARGEIRLDGRPVVPLELVP 192

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + Q  +NAW  + L EG+NRE++++FE  N+ V +L+R ++GP  L  L  G  R V+  
Sbjct: 193 ERQTSTNAWYRITLTEGRNREVRRLFETLNYFVLKLVRTAFGPLTLAGLEPGEYRTVTPH 252

Query: 240 ILREQLGPHLLEEAQVNLDAPIY-----SSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                L     +    NLD+                R +   E     +R  + ++ K+ 
Sbjct: 253 ETELLLAGTRPQSLPKNLDSRFSRRDDDGGAPRSEGRRSGREEKVGQGSREPRRTTGKSA 312

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ----REENHRRSPSFPSKRSLRRT 350
             + +    P   R+ AS       I  +           REE+ R + + P  RS    
Sbjct: 313 APRGEGFDRPSRPRSAASRGSAFPKIRRTEGEWPSGVRSPREESGREARTVPRTRSFEEG 372


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 111/234 (47%), Gaps = 8/234 (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      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R      +L  L  G  R ++   L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELDDLEVGKWRNITDGELEILIG 227


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 104/237 (43%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +    L  KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVALESPLAEGTAELFAKGVQLHNEKDLTKPALLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F      V  L R   G   L  +L  G  R +++  +     P  
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGDILLDESLAPGEYRPLTEAEIASVGAPQP 235


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 110/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +     GI +  G      ++ + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTAADVEAFAAGIELDDGYTCKPARLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKSVSYLKRISMGNLQLDESLALGEYRPLTEAEL 227


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 113/234 (48%), Gaps = 8/234 (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      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGIICTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 104/302 (34%), Positives = 147/302 (48%), Gaps = 22/302 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V       I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVEPGASLKIRIDGHVVPVS 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T SDP+GR TVFD LP    +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 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE +G          L     S   + +DR    +       +    +      S ++  
Sbjct: 241 RELVG----------LAPETVSKVPVEKDRRRTKANQIRRAVKRHTTTKVSKPGSGRRPS 290

Query: 302 AT 303
             
Sbjct: 291 KR 292


>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 =  263 bits (673), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 100/356 (28%), Positives = 166/356 (46%), Gaps = 10/356 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK-KNSSQKNGLSK 297
             +R  +    L+      D          R +P+ +        R     +  +    +
Sbjct: 412 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPR 469

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           + +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 470 RGRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 73/238 (30%), Positives = 128/238 (53%), Gaps = 7/238 (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  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLL 124
            ++  +R   +L++KP G V+   D +   TV D +  ++   +  VGRLDI+TEGLLL+
Sbjct: 65  IVKY-QRYEYYLFNKPSGCVSATCD-NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLI 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           TNDG L+  L  PS    + Y  R  G+V  D +   K+GI I +       ++ +  + 
Sbjct: 123 TNDGALSHELLSPSKHVAKTYYARIDGEVTLDDIIRFKEGIDIGEEKPTKPAELVI-KKS 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           GS + + + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++  
Sbjct: 182 GSVSEIELTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQAE 239


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 129/247 (52%), Gaps = 11/247 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +RV K++++ GIASRR+ E++I   RV++NG +           D +EVDG  ++   R
Sbjct: 2   TERVQKILSQWGIASRRQAEKLILAGRVRLNGNIASLGDKADPHQDLLEVDGTIIQPVNR 61

Query: 73  TR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
            R    L +KP+G+V+T  DP  R TV + LP+  ++   +  VGRLDIN+ G L+LTND
Sbjct: 62  PRPIYILLNKPLGVVSTCHDPQNRPTVLELLPATLNQGTGIHPVGRLDINSTGALVLTND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y+V   G   +  L   ++G+++ G      QV +  +     
Sbjct: 122 GELTLSLTHPRYHLPKTYQVWIDGNPGEQILQQWREGVMLMGKKTQPAQVKVVKRHHQQT 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKILR 242
            + V + EGKNR+I+++ +   + V +L R + G  QL      +L +G  R +    + 
Sbjct: 182 QLQVVITEGKNRQIRRIVQLLGFNVLKLHRTAIGLIQLNPANEPSLASGDYRFLKTFEI- 240

Query: 243 EQLGPHL 249
           + L  H+
Sbjct: 241 DYLRNHV 247


>gi|255305403|ref|ZP_05349575.1| putative RNA pseudouridine synthase [Clostridium difficile ATCC
           43255]
          Length = 240

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++  +D     TV D +   +       VGRLD +TEGLL+LTNDG L
Sbjct: 64  YIYLMMNKPDGYISATTD-KYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  +    + +
Sbjct: 123 SHRVLSPKKHVSKTYYAKIDGVVTEEDVEAFLEGVVLDDG-YKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 235


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 80/238 (33%), Positives = 117/238 (49%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++++ GIASRR  E MI   RV VNG +           D + VDG  ++   R 
Sbjct: 3   ERIQKLLSQWGIASRRHAEEMILAGRVSVNGKVANLGDKADPQQDFLSVDGKQIKADNRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           R    L +KP  +++T  DP GR TV D LP    R   +  VGRLD N+ G LLLTNDG
Sbjct: 63  RDIYLLVNKPRDVLSTCDDPRGRKTVLDLLPQDLQRGKGLHPVGRLDRNSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G    + L   + G+++ G       + + ++      
Sbjct: 123 ELTLRLTHPRYHLPKTYDVWLEGNPSDEDLEKWRSGMMLDGKKTLPATLEVISENKDQIH 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT----LLAGSTREVSKKILR 242
           + V L EG+NR+I+++ E     V +L R + GP QL T    L +G  R +S   +R
Sbjct: 183 LLVTLTEGRNRQIRRLAEELGLTVLKLHRRTIGPLQLHTRGKVLGSGQFRFLSPAEIR 240


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 150/290 (51%), Gaps = 12/290 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+A AG+ SRRE+E+ IA  R+ VNG +       V   D + VDG  +  A +
Sbjct: 2   SEKLQKVLANAGVGSRREMEKWIASGRISVNGKVAT-LGDRVEPVDQLRVDGNLITSAAK 60

Query: 73  T---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           +   R+ +Y+KP G + +  DP GR TVFD LP I + 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-LLAGSTREV---SKKILR 242
           +W  V L EGKNRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 181 SWYNVSLSEGKNREVRRLWESQGLQVSRLIRVRYGTLNLQNRLPQGGWIELPLTDLNTLR 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           + +   L +E+ V  D         +      + +   +  R K    +K
Sbjct: 241 KSVQLDLEQESLVE-DKQTKLDHVRLSRMRRSVQKHKVNQGRAKPRPKKK 289


>gi|271500649|ref|YP_003333674.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344204|gb|ACZ76969.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 296

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 107/307 (34%), Positives = 149/307 (48%), Gaps = 23/307 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   R+ V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T SDP+GR TVFD LP     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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + R+R  + +       R  K   Q    S+     
Sbjct: 242 EL----------VQLTPETVSKLPVERERRRVKAN---QIRRAVKRHGQTGAASRPSGNR 288

Query: 303 TPVHRRN 309
               +RN
Sbjct: 289 RSAPKRN 295


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 75/270 (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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGL 121
           V +    +    L +KP   +TT  D  GR TV D +   P   + +  VGRLD NT G+
Sbjct: 61  VRVVPQTQALYILMNKPHDTITTCDDERGRRTVLDLINLPPEQKNGLFPVGRLDRNTTGV 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG LA  L  P  +  ++Y  R    V  ++   L++G+ ++      +QV +  
Sbjct: 121 LLLTNDGELANRLMHPRYRVEKIYVARTARPVKPEEAEQLRRGVQLEDGPARAVQVAV-- 178

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                  + + + EG+NR+++++ E    +V +L R  Y       +  G  R ++   +
Sbjct: 179 NPADPHEIALMIYEGRNRQVRRMLEAIGHEVVQLKRTHYAGLTTKGVRPGKWRRLTDAEV 238

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
           R       L+  +     PI   +     R
Sbjct: 239 RRLYRLAGLKPPKTFKTMPIGHGDANAVKR 268


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 99/317 (31%), Positives = 154/317 (48%), Gaps = 23/317 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +  +    +++ K++AR+G  SRRE+E  + + R+ V+G +      + V     I +DG
Sbjct: 9   MSAKPQKTEKLQKILARSGHGSRREIETFLKEGRISVDGKIATLGDRIEVKPATKIRLDG 68

Query: 65  VPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             L   E      R+  Y+KP G + T  DP+GR TVF  LP  + +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 K---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    LRE +G     E +V ++          RD+  I +       R  K  SQ    
Sbjct: 249 QQTNYLRELVGLEAETETKVAVE----------RDQRRIKAN---QIRRAVKRHSQVAAR 295

Query: 296 SKQKKLATPVHRRNLAS 312
              K+ ++    +    
Sbjct: 296 PASKRQSSRPTAKRRTR 312


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 108/231 (46%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  R +    V +NG L +  +V +  TD I  +G  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAARALKSGLVTINGKLEKSGSVKIGDTDEICYEGERLEWVDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+      L +GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAKKLAEGILLRGEREPCLPAKMEVIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + EG+  ++K++F     KV  L R   G   L   L  G  R +S++ + 
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLEEGEYRPLSEQEVE 228


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 103/229 (44%), 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   MRLDKYLCDALGATRREATRIIKSGDVTVNDVVQKSGSVKVTDGCTVEWQGRELQKP-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  +  KP G V +H D   ++            +   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLFKPDGFVCSHEDGFNQTAFMLLDEVKIEELHFAGRLDVDTTGLVLITDDGKWSHR 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|299067338|emb|CBJ38535.1| Ribosomal large subunit pseudouridine synthase B [Ralstonia
           solanacearum CMR15]
          Length = 601

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 102/318 (32%), Positives = 156/318 (49%), Gaps = 14/318 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILPTDQVR 260

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPSKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +  
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELPESDRQKLLHGIRLDDGEANFLSC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLG------PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           S   +R  +G      P                       +P ++  +   FT      S
Sbjct: 441 SADDVRGLMGLLGLKVPSASAGGGQQGGQGGRQGNRRREAQPVLMGPMSSGFTGEATFQS 500

Query: 291 QKNGLSKQKKLATPVHRR 308
           +  G+    + A P  RR
Sbjct: 501 RGQGVENGNR-AMPAPRR 517


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 109/308 (35%), Positives = 152/308 (49%), Gaps = 22/308 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIDAGRVSVDGKIAKLGDRVEVNPAMKIRMDGHVVSVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + THSDP+GR TVFD LP    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-GTLLAGSTREVSKKILREQL 245
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+    +    
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIALPKGLPRGGWAELDLNAINYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK-----K 300
               L+   V       S   + R+R  + +       R  K   Q  G S ++     K
Sbjct: 242 ALVGLKPETV-------SKMPVERERRRMKAN---QIRRAVKRHIQVTGSSGRRNAPGSK 291

Query: 301 LATPVHRR 308
              P  RR
Sbjct: 292 SGRPSKRR 299


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 100/356 (28%), Positives = 166/356 (46%), Gaps = 10/356 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK-KNSSQKNGLSK 297
             +R  +    L+      D          R +P+ +        R     +  +    +
Sbjct: 412 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPR 469

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           + +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 470 RGRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>gi|240948952|ref|ZP_04753308.1| pseudouridine synthase [Actinobacillus minor NM305]
 gi|240296767|gb|EER47378.1| pseudouridine synthase [Actinobacillus minor NM305]
          Length = 340

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 109/283 (38%), Positives = 154/283 (54%), Gaps = 12/283 (4%)

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  GVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           G  +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    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 KK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            +    LRE +G  L  E +  +D       T VR     + +
Sbjct: 292 LEQVNYLRELVG--LPAETETKVDVTKNRRRTNVRQIRKAVKQ 332


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 105/239 (43%), Gaps = 3/239 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV     +  D       G+ +           L+    ++  V + L
Sbjct: 121 ITSPRHHCEKTYRVTLESPIGDDTAAQFTAGVQLHNEKDLTKPAQLEVITPTD--VRLTL 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLE 251
            EG+  ++K++F     +V  L R   G   L   L  G  R +++  +     P  L+
Sbjct: 179 SEGRYHQVKRMFAAVGNRVIELHRERIGDIALDDDLEPGDYRALTEDEIASIGLPKELQ 237


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 104/237 (43%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + +    L  KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVALENPLAEGTAELFAKGVQLHNEKDLTKPALLEV--ITPTEVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F      V  L R   G   L  +L  G  R +++  +     P  
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVGLHRERIGDILLDESLAPGEYRPLTEAEIASVGAPQP 235


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 126/232 (54%), Gaps = 1/232 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+++ +A  G+ SRR+VE  I   R+ VNG L++  +  ++   D + +DG P++ A+  
Sbjct: 41  RLNRYLADCGLGSRRKVEEFITTGRIAVNGNLVQDLSRQIIPGKDKVTLDGKPIQPAKEK 100

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G V + +D  GR TV+  LP    ++   GRLD  +EGLL  TND  L  +
Sbjct: 101 FYLILNKPRGYVVSQNDELGRKTVYSLLPPKGKQLAYAGRLDKESEGLLFFTNDTALINL 160

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VYRV  +  ++  +LN+L+KG+ I+G       + + ++  +   + + +
Sbjct: 161 LTHPKNKVEKVYRVDINRPLNNMELNMLRKGVEIEGGKTLPAGIFVKSKNANGMTLKIVI 220

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EG+ R+I+++ E    KV  L R+ +GP +L  L  G  R +    ++  L
Sbjct: 221 TEGRKRQIRQMIEAVGAKVTYLKRLQFGPLKLKDLPVGRWRLLEPGEVKALL 272


>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 =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 113/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV++++    ++V+G ++     +V      + + G P+   ++
Sbjct: 1   MRLDKLLSNMGAGSRKEVKQLLKSGAIQVDGEIVYDPKQHVDTENQQVLLYGEPVTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L     + +   VGRLD +TEGLLLLTNDG  
Sbjct: 60  FIYLMMNKPPGVISATEDKRD-QTVIDLLFDDVTYFKPFPVGRLDKDTEGLLLLTNDGSF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY     G + ++ +  + +G+ +  G      ++ +       + +
Sbjct: 119 NHALMSPKKHVEKVYYAEVIGTLTEEDVEEVAEGVTLEDGYKTKPGKLIILEATDETSTL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EGK  ++K++      +V  L R+S G   L  TL AG  RE+++  L
Sbjct: 179 ELTITEGKFHQVKRMMLALGKEVTYLKRLSIGQLPLDPTLEAGEYRELTRGEL 231


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 73/243 (30%), Positives = 123/243 (50%), Gaps = 5/243 (2%)

Query: 2   KDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            +  I     TP   R++K IA AGI SRR  +  I+   V VNG ++      V  TD 
Sbjct: 140 NNAPIDYPTTTPAEVRLNKFIADAGICSRRNADMYISAGNVMVNGEVMTTLGYRVKPTDE 199

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +  DG  L  +E+    L +KP G +TT +D  GR TV D + +  + R++ VGRLD  T
Sbjct: 200 VRFDGKLLS-SEKKEYILLNKPKGFITTTNDEKGRKTVMDLVANATNVRILPVGRLDRAT 258

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG L + L  P+    ++Y V    ++D      ++ G+ ++       +++
Sbjct: 259 TGLLLLTNDGELTKKLTHPTHGVRKIYHVILDRKLDYKDFMKVQDGLELEDGLIEVDEIS 318

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               K  N  + + +  G+NR ++++FE   ++V +L R+ +       L  G  R +++
Sbjct: 319 YVNNKPKN-EIGIKIHSGRNRIVRRIFEHLGYQVEKLDRVVFAGLTKKDLPRGHWRRLTQ 377

Query: 239 KIL 241
           + +
Sbjct: 378 QEV 380


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 78/242 (32%), Positives = 117/242 (48%), Gaps = 3/242 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              QR+ K+IA AG+ SRR  E ++ Q R++VNG             D I VDG PL + 
Sbjct: 1   MASQRLQKLIAAAGVCSRRHAEELLRQGRIQVNGAAARLGDSADPDRDSIAVDGRPLDRP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
            R  L L +KP+G++ + SDP GR TV D LP    +   +  +GRLD ++ G LLLTN 
Sbjct: 61  ARPVLLLLNKPLGVLCSCSDPQGRPTVLDLLPPELRQGQGLHPIGRLDADSRGALLLTNQ 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     ++YRV   G      L     G+ + G+    + V +  +     
Sbjct: 121 GDLTLRLTHPRYGHRKLYRVWVSGTPSATTLERWAAGVPLDGVASQPVDVRVLQRGKRGT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + + EG+NR+I++        V  L R+  GP +LG+L  G  R +  +  +    P
Sbjct: 181 RLELAMGEGRNRQIRRTAALLGHPVLDLQRVGIGPLRLGSLAEGCWRALDHQEWQALADP 240

Query: 248 HL 249
            L
Sbjct: 241 PL 242


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 117/235 (49%), Gaps = 8/235 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +    R++K ++ AG+ SRRE + +I Q RV V+G         V     I VD   +R+
Sbjct: 2   SMEKIRLNKYLSDAGVCSRREADSLILQGRVTVDGRKAVT-GEKVSVDQQIRVDNREIRQ 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L L +KP G++ T  +       F N P    RV  VGRLD++++GL+LLTN G 
Sbjct: 61  GQPKVLLLLNKPRGIICTAKNQKDNIVDFVNYPI---RVYPVGRLDVDSQGLILLTNQGE 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y+V     V ++ L+ + KG+ I G      Q+    +K      
Sbjct: 118 LVNKIMRAGNYHEKEYQVTVDHPVTKEFLSKMAKGVPILGTVTRPCQIKRTGEKS----F 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + L +G NR+I+++ E+F ++V RL R      +LG L  G+ REV+ +  RE 
Sbjct: 174 QIILTQGLNRQIRRMCEYFGYRVVRLNRTRIMNLKLGKLPVGAYREVTSEEWREL 228


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 128/261 (49%), Gaps = 12/261 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN +++     R++K I+  G  SRRE +++I Q RVK++G+      + V     +
Sbjct: 50  VSNKNEIRDKV---RLNKYISETGFCSRREADKLIEQGRVKIDGLKATT-GMKVSKGQSV 105

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG PL+          +KP+G+  T ++   +  + D + +   R+  +GRLD +++G
Sbjct: 106 SIDGKPLKVENELVYIALNKPVGITCT-TESKIKGNIVDFI-NHEKRIFPIGRLDKDSQG 163

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+ +TNDG +   +        + Y V  +  +  + +  +  G+ I G       V  +
Sbjct: 164 LIFMTNDGDIVNKILRAGNNHEKEYIVTVNKSITDEFIKGMSNGVPILGTVTKKCLVKKE 223

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++        + L +G NR+I+++ E+F ++V +L RI      LG L  GS R ++KK 
Sbjct: 224 SKNS----FRIILTQGLNRQIRRMCEYFGYEVKKLERIRIMNVSLGNLKIGSWRYLTKKE 279

Query: 241 LREQLGPHLLEEAQVNLDAPI 261
           L E     L E +    +A I
Sbjct: 280 LAEI--NRLTENSSKTEEASI 298


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 101/297 (34%), Positives = 148/297 (49%), Gaps = 10/297 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E  I   RV V+G +      V ++    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAKIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD DKL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           E +       ++V ++      +     R            R   NS++++    + 
Sbjct: 242 ELVELTPETSSKVAVEKDRRRMKANQIRRAVKRHSQTSANPRQGNNSNRRSSTRNKT 298


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 116/237 (48%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 17  MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKTQVNEFEDTVTYLGEIIAYQKD 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 77  FYYIL-HKPAGVISATQD-NHDQTVIDLLKDQDYREDLFPVGRLDKDTEGLLILTNDGIF 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G       ++ +D   Q+   +
Sbjct: 135 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETS 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 195 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFWLPKDLNKGQYRPMTKEELEQ 251


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 106/280 (37%), Positives = 153/280 (54%), Gaps = 12/280 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +     +++ K++ARAG  SRRE+E +IA  RV V+G +      V+V +T  I +DG  
Sbjct: 69  KTKIVGEKLQKILARAGQGSRRELEEVIAAGRVSVDGKIASLGDRVHVNATTKIRIDGTL 128

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T +DP+GR+TVFD LP    SR I+VGRLDINT GL
Sbjct: 129 INLVTAQKEICRVLMYYKPEGELCTRADPEGRATVFDRLPRLSGSRWIAVGRLDINTSGL 188

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       Q+    
Sbjct: 189 LLFTTDGDLANRLMHPSHEVEREYSVRVFGQVDDAMLQRLRKGVQLEDGPANFKQIKAVG 248

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 249 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 308

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
              LR+ +G  L  E +  +D       T +R     + +
Sbjct: 309 VNYLRDLVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQ 346


>gi|304396082|ref|ZP_07377964.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356451|gb|EFM20816.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 296

 Score =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 108/305 (35%), Positives = 153/305 (50%), Gaps = 20/305 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MIA  RV V+G +       V S+    I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIAAGRVSVDGKIAT-LGDRVESSKSLKIRIDGHLVSIA 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T SDP+GR TVFD LP    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+        
Sbjct: 181 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDITLPKGLPRGGWTELD------- 233

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           L         V LD    +   + +DR    +       R  K  ++ +   +  +   P
Sbjct: 234 LPAVNYLRNLVELDDETVTKLVVEKDRRRTKAN---QIRRAVKRHTKVSSTPRAPRRN-P 289

Query: 305 VHRRN 309
             +RN
Sbjct: 290 GSKRN 294


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 117/232 (50%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR-KAE 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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWV 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|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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 113/234 (48%), Gaps = 8/234 (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      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 92/289 (31%), Positives = 148/289 (51%), Gaps = 7/289 (2%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + +
Sbjct: 175 NKRVLSPDDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRI 233

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           +G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ 
Sbjct: 354 DGGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELD 413

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
              +R+ +    L +A          +    R +P+ +        R  
Sbjct: 414 DTQVRKLMATVGL-KAPSEEKGKRGGTGQAERRQPDPMQTSMGFIGREP 461


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 130/287 (45%), Gaps = 12/287 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + +EN T  R++K ++ AG  SRR  +++I Q RV +NG ++      +   D ++VDG 
Sbjct: 1   MAEENLT--RINKFLSEAGYCSRRAADKLIDQGRVTING-VVPEMGTKIAPGDEVKVDGE 57

Query: 66  PLRKAERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
            +   E+        ++KPIG+V T      ++ + D + +   R+  +GRLD  +EGL+
Sbjct: 58  LIATEEKEKPNVYIAFNKPIGIVCTTDTKREKNNIIDYI-NYPERIFPIGRLDKPSEGLI 116

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            LT+DG +   +        + Y V+ +  +  D +  + KGI I      +  V    +
Sbjct: 117 FLTSDGDIVNKILRARNNHEKEYIVKVNKPLQPDFVKKMSKGIPILDTVTRECFV----E 172

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +       + L +G NR+I+++ E+  + V +L RI      L  +  G  R ++K  L+
Sbjct: 173 QTGENEFRIILTQGLNRQIRRMCEYLGYAVTKLKRIRIMNVPL-DIPVGKWRHLTKAELK 231

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
           E                   +++  +     I  + P+   R +K S
Sbjct: 232 EIDRLVNTSSKTEEASQLSENNDNKIAKPKGIKPKNPNKHKRPRKKS 278


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGSRRSGGRN 288


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 71/288 (24%), Positives = 135/288 (46%), Gaps = 11/288 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+ +G+ SRRE E+ I + R+ +NG    +    V   D ++ DG  +     T  
Sbjct: 11  LNKYISSSGVCSRREAEKFIKEGRITINGK-ATQLGNRVGKKDVVKFDGRLVEPKNVTLY 69

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP+G+V+T  + +  + V     +   R+  +GRLD  +EGL+ LTNDG +   + 
Sbjct: 70  IALNKPVGIVSTTDEREPHNIVK--HVNYPERLFPIGRLDKPSEGLIFLTNDGDIVNKIL 127

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                  + Y V     +  D +  +  GI I G      +V    +K S+    + L +
Sbjct: 128 RAGNNHEKEYFVSVDKSITNDFITSMGNGIPILGTMTKRCKV----EKVSDKIFKIVLTQ 183

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV 255
           G NR+I+++ E+ +++V +L R       LG L +G  RE++++ +++ +   +   ++ 
Sbjct: 184 GLNRQIRRMCEYLDYEVTKLKRTRIMNVDLGYLQSGDWRELTEEEMKD-INKMIATSSKT 242

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              + I       R + N   + P      KK++S +    K K+  T
Sbjct: 243 EEASSIEEKPKQARPKRN---KAPTKNDFNKKSASFRKSSPKSKRSNT 287


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 113/229 (49%), Positives = 157/229 (68%), Gaps = 2/229 (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+     L    K + I GI Y    + L  Q  SN+W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDILLKSNYKNLEIDGIFYNPHSIKLLKQNKSNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           EGKNREI+++FE+F  KVN+LIRI YG F +G L  G  +E++ KIL +
Sbjct: 181 EGKNREIRRIFEYFGLKVNKLIRIQYGSFTIGNLKPGDYKEINNKILEK 229


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 119/249 (47%), Gaps = 10/249 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-K 69
               R++K ++  G  SRR  ++++ + R+K+NG +       V   D +EVDG P+R  
Sbjct: 1   MEKTRINKYLSEVGYCSRRAADKLLEEGRIKINGKIP-ELGTKVSDEDLVEVDGKPIREP 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+    +++KP+G+V T      ++ + D + +   R+  +GRLD  +EGL+LLT+DG 
Sbjct: 60  QEKPVYIVFNKPVGIVCTTDTKREKNNIVDYI-NHPKRIFPIGRLDKPSEGLILLTSDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y VR    +    L  ++ G+ I        +V    +K      
Sbjct: 119 IVNKILRARNNHEKEYLVRVDKPITPKFLEKMRNGVPILDTITRKCKV----EKIDEMNF 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+  ++V +L RI     +L  L  G  R+++   L       L
Sbjct: 175 RIILTQGLNRQIRRMCEYLGYEVKKLKRIRIMNIKL-DLPVGKWRDLTDDELNTL--NAL 231

Query: 250 LEEAQVNLD 258
           L ++    D
Sbjct: 232 LADSSKTFD 240


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 81/296 (27%), Positives = 139/296 (46%), Gaps = 10/296 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ + +ARAGIASRR+ E +I   RV +N   +      V   D + +DG  +R  
Sbjct: 1   MVGMRLQQFLARAGIASRRKAEDLIRAGRVTIN-EQVASIGAVVQPGDIVRLDGERVRMP 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++  +   HKP G  TTH D      V++ +P     + +VGRLD +TEGLLLLTNDG L
Sbjct: 60  QKKVVIALHKPKGYTTTHEDEHAEKIVYELVPKH-PGLHAVGRLDKDTEGLLLLTNDGHL 118

Query: 131 ARVLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            + L  P  Q  ++YR     G+V +     L +G+V+       ++        +   V
Sbjct: 119 TQHLTHPRNQVPKLYRAWCKNGRVSEKACQQLVQGVVLGDGLAQALEA-----HPTRNGV 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+ RE++++     + V RL+R++ GP +LG L AG  R ++   ++       
Sbjct: 174 KLVLTEGRKREVRRMLNKVGYPVERLVRLAVGPIELGELEAGEWRYLTPDEIKLLYTSAQ 233

Query: 250 L--EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           L   + Q     P   ++T  R + + +    +  +  ++  + +    +Q     
Sbjct: 234 LPRPKTQAQKPTPTPKAKTGTRPQKSTVESSSERLSTRQRQGTNRGSTDRQAHTRA 289


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 70/227 (30%), Positives = 108/227 (47%), Gaps = 5/227 (2%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++     +   ER    
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQAVS-IERKIYV 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L 
Sbjct: 61  LLNKPKDTVTTSDDPQARRTVMDLVKGACSERIYPVGRLDRNTTGVLLLTNDGDLASKLT 120

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLR 194
            P     ++Y V     + +  +  +  GI +  G  + D     D  K  +  V + + 
Sbjct: 121 HPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIHADAISYTDDFKKDD--VGIEIH 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            GKNR ++++FE   +KV +L R+ +       L  G  R ++++ +
Sbjct: 179 SGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQEV 225


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFMNEMSSGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVIKLKRERIMNIELNDLEVGKWRDITTEELELLIG 227


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 118/248 (47%), Gaps = 10/248 (4%)

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  EENVYIAFNKPVGIVCTTDTKREKNNIIDYI-KYPKRIFPIGRLDKPSEGLILLTSDGDI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y VR    +    L  ++ G+ I G      +V    ++       
Sbjct: 121 VNKILRARNNHEKEYIVRVDKPITNKFLEQMRAGVPILGTVTRKCEV----EQLDKMQFR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E+  ++V +L RI      L  L  G  RE++   ++     HL+
Sbjct: 177 IVLTQGLNRQIRRMCEYLGYEVKKLKRIRIMNIHL-DLPIGKWRELTPNEMKTL--NHLI 233

Query: 251 EEAQVNLD 258
           +++    D
Sbjct: 234 KDSAKTYD 241


>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 =  263 bits (672), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 77/236 (32%), Positives = 120/236 (50%), Gaps = 1/236 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K++A AG+ SRR  E  +   RV V+G +         ++  IEVDGVPL   
Sbjct: 1   MTRQRLQKLMAAAGLCSRRRGEDWLQAGRVTVDGRVASLGDQADPNSQLIEVDGVPLISV 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
           +  R++L +KP+G++ +  DP GR+TV D LP      +  VGRLD ++ G LLLT+ G 
Sbjct: 61  QEPRVFLLNKPVGVICSCRDPQGRATVLDCLPHQERSGLHPVGRLDADSRGALLLTDQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G      L   + G+++ G      +V     +G+++ +
Sbjct: 121 LTLRLTHPRYNHAKTYRVLVRGIPSSQALRRWRDGLLLDGRLTRPARVHCLRSRGASSLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V L+EG+NR+I++V E     V  L R++    +L  L  G  R +  +     L
Sbjct: 181 EVELKEGRNRQIRRVAELLGHPVIDLQRVAIDGIRLDDLAEGCWRRLDAREWSTIL 236


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 111/229 (48%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEN-NIIDYI-NYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RIDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEEL 222


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 101/316 (31%), Positives = 162/316 (51%), Gaps = 12/316 (3%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLIMQGRVSVNGLPA-HIGQRILPTDQVR 260

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPNKAPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +G+ +       ++ 
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAESDRQKLLQGVRLDDGEANFLRC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD----RPNIISEVPDDFTRMKKNSSQK 292
           S + +R  +G   L+    ++                 +P ++  +   FT      S+ 
Sbjct: 441 SAEEVRVLMGSLGLKVPSASVGGGQGGGRQQGGRRREAQPMLMGPMSSGFTGEATFQSRG 500

Query: 293 NGLSKQKKLATPVHRR 308
            G+    + A P  RR
Sbjct: 501 QGVENGNR-ALPAARR 515


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 110/320 (34%), Positives = 157/320 (49%), Gaps = 24/320 (7%)

Query: 1   MKDK-NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTD 58
           M DK    Q+    +++ K++ARAG  SRRE+E  I + R+ ++G        + V  + 
Sbjct: 1   MSDKTQKTQKTERTEKLQKILARAGHGSRREIEGYIQEGRISIDGKTATLGDRIEVKPSI 60

Query: 59  HIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGR 113
            I +DG  L   E      R+  Y+KP G + T  DP+GR TVFD LP +  +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 TREVSKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
             E+  +    LR+           V+L+    S   + RD+  I +       R  K  
Sbjct: 241 WTELGLEQTNYLRQL----------VDLNEETMSKVAVERDQRRIKAN---QIRRAVKRH 287

Query: 290 SQKNGLSKQKKLATPVHRRN 309
           SQ        K      R+N
Sbjct: 288 SQVGSSRPAGKRPASSSRQN 307


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 90/272 (33%), Positives = 141/272 (51%), Gaps = 6/272 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  +  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 185 KRALSADDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 243

Query: 64  GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P++     +  R+ +YHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 364 GGGEGTNRWYHVALAEGRNREVRRMFEAVGLTVSRLIRTRHGPIVLPRGLKRGRWEELED 423

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
             +R  +    L+    +      ++     D
Sbjct: 424 NQVRALMSAVGLKGPGEDKAERSKATPRRQPD 455


>gi|229175424|ref|ZP_04302937.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228608032|gb|EEK65341.1| Pseudouridine synthase [Bacillus cereus MM3]
          Length = 242

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FIYLMLHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+       + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTILKSDEI-SEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE+S + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELSDEEVE 231


>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 =  262 bits (671), Expect = 4e-68,   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 ITSPRHHCEKTYLVTLESAISDDTAQQFADGVQLHNEKTLTKPAMLAV--IAPNLVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G  +L   L  G  R +S + +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVALHRERIGAIRLDSDLQPGEYRPLSAEEI 227


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 412 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 457


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 147/288 (51%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D        + R +P+ +        R  
Sbjct: 412 AQVRRLMSTVGLKA--PTEDKGGKRGGPVERRQPDPMQTSMGFINREP 457


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 110/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG + + + + V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGYGSRREVKPLLKSGSVTVNGTIQKDSKLQVNPEKDQITVHGNPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +   + GI +  G       + + T     + +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIEGNVTVADIEAFQTGITLDDGYTCKPAHLEIITP----SEI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V  L RIS G  +L   L  G  R ++ + L
Sbjct: 175 NVTIQEGKFHQVKRMFAATGKTVTYLKRISMGKLKLDEALRLGEYRSLTDEEL 227


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTCRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|327330001|gb|EGE71755.1| ribosomal large subunit pseudouridine synthase B [Propionibacterium
           acnes HL097PA1]
          Length = 245

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 128/239 (53%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  + 
Sbjct: 3   NEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVDQGRRVDPERDEIRVDGSRIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTN 126
            A R   ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTN
Sbjct: 63  TARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLL 240


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 107/301 (35%), Positives = 153/301 (50%), Gaps = 25/301 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V ++    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 DGELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGIN 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 EQLGPHLLEEAQVNLDAPIYSSETLV-RDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           E +G            AP  +S+  V +DR  + +       R  K  SQ N   +    
Sbjct: 242 ELVGL-----------APETTSKVAVEKDRRRMKAN---QIRRAVKRHSQVNNNRRAGSR 287

Query: 302 A 302
            
Sbjct: 288 N 288


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 114/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDQIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDNKHR-TVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     + Y  +  G + Q+ ++   KGI ++       ++ L +   + + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVEGIMSQEDVDTFAKGIPLKDFTCQPAKLELVSVDPEKNQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLALDENLERGEWRRLTKEELEVLLA 237


>gi|229032362|ref|ZP_04188334.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228728970|gb|EEL79974.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 242

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+       + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHIAGVVTEEDVKEFAKGVILDDGYETKPGALTILKSDEI-SEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE+S + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDAELELGEYRELSDEEVE 231


>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 =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 101/297 (34%), Positives = 148/297 (49%), Gaps = 10/297 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E  I   RV V+G +      V ++    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAKIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  GQVD DKL  L +G+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           E +       ++V ++      +     R            R   NS++++    + 
Sbjct: 242 ELVELTPETSSKVAVEKDRRRLKANQIRRAVKRHSQTSANPRQGNNSNRRSSTRNKT 298


>gi|205374450|ref|ZP_03227246.1| pseudouridylate synthase (ribosomal small subunit pseudouridine
           synthase A) [Bacillus coahuilensis m4-4]
          Length = 236

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 111/236 (47%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV+ ++    V VNG   +    +V  + D + V G  +   E 
Sbjct: 1   MRIDKLLANMGYGSRKEVKSLLKSGNVVVNGTGCKDGKQHVNPSQDEVFVHGEKVVYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G+++   D     TV D L           VGRLD +TEGLL++TNDG L
Sbjct: 60  FIYLLMNKPQGVISATEDLRD-ETVIDLLEPDHRVFNPFPVGRLDKDTEGLLIITNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    +G+ +  G       + + +  G  + +
Sbjct: 119 SHQLLSPKKHVPKTYYAEVKGVVTEEDVAAFSEGVTLDDGYHTKPGDLVILS-SGEMSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++FE    KV  L RI  GP  L   L  G  RE+S++ + + 
Sbjct: 178 ELTITEGKFHQVKRMFESVGKKVVYLQRIKMGPILLDENLELGEYRELSQEEIDQL 233


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 119/239 (49%), Gaps = 2/239 (0%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           + +    R+ K++A+AG  SRR+ E MI   RV+V+G L+      V      + VDG  
Sbjct: 13  ENDGDGIRLQKLLAQAGFGSRRKCEEMITDGRVEVDGELVTELGTRVDPKRQQVRVDGSR 72

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R   R      +KP  +++T  DP GR T+ D +   + R+  +GRLD ++EGL+L+TN
Sbjct: 73  IRLNPRHITLALNKPRKVLSTMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTN 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
           DG L++ +  P  +  + Y     G +       L + G+ +          ++      
Sbjct: 133 DGELSQHVMHPKYEVEKTYIATLEGHMSGTVCRRLVRTGVQLDDGWIKLDHCSIIDSNRD 192

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L  G+NR ++++F    + V RL+R   GP +LG + +GS R +S+  +R  
Sbjct: 193 QTIVKVVLHSGRNRIVRRIFGAIGFPVKRLVRTQIGPIKLGDIKSGSYRVLSQDEVRAL 251


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 130/264 (49%), Gaps = 10/264 (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  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +  + +      ++KP+G+V T      +  + D + +   R+  +GRLD  +EGL+LLT
Sbjct: 58  IGERKQGFVYLAFNKPVGIVCTTDTRVEKDNIIDYI-NYPKRIFPIGRLDKPSEGLILLT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG +   +   S    + Y V     + Q  +  +  GI I+    G      + +K  
Sbjct: 117 DDGDIVNKILRASNNHEKEYIVTVDKPISQTFVARMAGGIYIE--ELGKRTKKCEVKKID 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
               ++ L +G NR+I+++ E+ N++V  L R+     +L  +  G  RE++K+  +   
Sbjct: 175 KFTFSIILTQGLNRQIRRMCEYLNYEVQTLKRVRIMNIKL-DMPLGKYRELTKEEFKTL- 232

Query: 246 GPHLLEEAQVNLDAPIYSSETLVR 269
             +L+ E++   +A  ++     R
Sbjct: 233 -SNLISESKKTFEAKQHTPRRNRR 255


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +  
Sbjct: 1   MKNVRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
            E     + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TND
Sbjct: 61  KE-FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN 186
           G L+  L  P     + Y     G V ++ +    KG+++  G       +T+  +    
Sbjct: 119 GKLSHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDI 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 SEIELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 234


>gi|311032169|ref|ZP_07710259.1| pseudouridine synthase F (ribosomal large subunit) [Bacillus sp.
           m3-13]
          Length = 235

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 120/241 (49%), Gaps = 7/241 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G+ASRR  +++I + +VK+NG + +     V   D + V+G  +R A   
Sbjct: 1   MRINKFISDSGVASRRGADKLIEEGKVKINGKVAQIGG-QVNPGDEVLVNGQIIRIARDN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KPIG+ +T ++   +  + D +     R+  +GRLD  +EGL+LLTNDG +   
Sbjct: 60  VYIALNKPIGITST-TEKKVKGNIIDLVNHPL-RLSHIGRLDKESEGLILLTNDGDIINE 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 Q 254
           +
Sbjct: 234 E 234


>gi|315103786|gb|EFT75762.1| conserved hypothetical protein [Propionibacterium acnes HL050PA2]
          Length = 245

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 128/239 (53%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  + 
Sbjct: 3   NEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTN 126
            A R   ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTN
Sbjct: 63  TARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQASEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLL 240


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 73/243 (30%), Positives = 115/243 (47%), Gaps = 5/243 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 246 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEV 305

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 306 KFHDQTVS-IERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTT 364

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI +  G  + D    
Sbjct: 365 GVLLLTNDGDLASKLTHPKYLKKKIYHVHLDKNLTKADMEQIAAGIQLDDGEIHADAISY 424

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            D  K  +  V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +++
Sbjct: 425 TDDFKKDD--VGIEIHSGKNRIVRRIFESLGYKVMKLDRVYFAGLTKKGLRRGEWRYLTE 482

Query: 239 KIL 241
           + +
Sbjct: 483 QEV 485


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++  +D     TV D +   +       VGRLD +TEGLL+LTNDG L
Sbjct: 64  YIYLMMNKPDGYISATTD-KYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWV 189
           +  +  P     + Y  +  G V ++ +    +G+V+    Y  M   L+  +    + +
Sbjct: 123 SHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDD-RYKTMPSQLNILKSDDESEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 235


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 112/230 (48%), Positives = 156/230 (67%), Gaps = 2/230 (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  RLWIYYKPVGLITTHKDPLSRKTVFEQLTG-LPRVISIGRLDLNSEGLLLLTNSGDLARQ 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            ELPS +  RVY VR +G+     L    K + I GI Y    + L  Q  SN+W  V L
Sbjct: 121 FELPSNRLKRVYHVRAYGK-SDILLKSDYKNLEIDGIFYNPHSIKLFKQNKSNSWFEVVL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            EGKNREI+++FE+F  KVN+LIRI YG F +  L  G+ +E++ KIL +
Sbjct: 180 FEGKNREIRRIFEYFGLKVNKLIRIQYGSFTIDNLKPGAYKEINNKILEK 229


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 100/353 (28%), Positives = 169/353 (47%), Gaps = 18/353 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +++  ++  P ++ KV+A AG+ SRR++E +I   RV VNG         ++  D + +
Sbjct: 167 RRDLTADDDAP-KLHKVLAEAGLGSRRDMEELIIAGRVSVNGEPA-HIGQRILPADQVRI 224

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           +G  +++    +  R+ +YHKP G + + +DP+GR +VF+ LP++  ++ ++VGRLD NT
Sbjct: 225 NGKLIQRKVSNKPPRVLVYHKPAGEIVSTNDPEGRPSVFERLPTMKAAKWLAVGRLDFNT 284

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL T  G LA  L  P     R Y VR  G++++     L  G+ ++       ++ 
Sbjct: 285 EGLLLFTTSGDLANRLMHPRYGIDREYAVRTLGELEEGMRQKLLAGVELEDGLAQFSKIA 344

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+ 
Sbjct: 345 DGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGTLTLPKNLKRGRWEEME 404

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ L    LE+  V+  AP   +    R   N    V D+   + ++ SQ   L  
Sbjct: 405 EHAVRDLLAMSGLEKKSVDG-APKGRNSPADRQNGNRAPRV-DNGMGLPRSPSQWGNLGG 462

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           Q +                  G          ++ +  + S  FP     RR+
Sbjct: 463 QGRPQG---------QNGKPAGGRQGQGQPRSRQPDPLQTSLGFPGMGQPRRS 506


>gi|332830420|gb|EGK03048.1| hypothetical protein HMPREF9455_01298 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 444

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 121/242 (50%), Gaps = 4/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K  +  N TP R++K +A AG+ SRRE +  I    VKVNG ++++    V   D +
Sbjct: 197 VKYKENIDPN-TPLRLNKYLANAGVCSRREADAYITSGVVKVNGEVVDQLGAKVTRGDLV 255

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+R  E     L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 256 TFQDKPVRL-ESKVYVLLNKPKNCVTTSDDPQNRLTVMDLVKNACPERIYPVGRLDRNTT 314

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P  +  ++Y+V     V  + +  +  G+ +         +  
Sbjct: 315 GVLLLTNDGDLASKLMHPKFKKKKIYQVTLDRDVAIEDMQAIADGVELDDGEIHADSIAY 374

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +   N  V + +  G+NR ++++FE   ++V +L R+ +       +L G  R +S+K
Sbjct: 375 QAEDVLN-VVGIEIHSGRNRIVRRIFEKLGYQVMKLDRVYFAGLTKKNVLRGKWRYLSEK 433

Query: 240 IL 241
            +
Sbjct: 434 EV 435


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 118/237 (49%), Gaps = 2/237 (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 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L   G+ +        +  +      N 
Sbjct: 135 ELSQHVMHPKYEVEKTYIATLEGRISGQVCRRLVTTGVQLDDGWIKLDRCAILDASRDNT 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R  
Sbjct: 195 LVKVVLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGSYRVLSQTEVRSL 251


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 150/300 (50%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +IA  RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIAAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +       ++V ++          +DR  + +       R  K  SQ  G  +    +
Sbjct: 242 ELVELKPETTSKVAVE----------KDRRRMKAN---QIRRAVKRHSQVGGSRRPGGRS 288


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 106/361 (29%), Positives = 172/361 (47%), Gaps = 14/361 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M D          +++ KV+AR G+ SRR+VE  IA+ RV VNG +       V S D I
Sbjct: 1   MNDTPENPHVPVGEKLQKVLARLGVGSRRDVEVWIAEGRVNVNGSVA-SLGQRVDSHDAI 59

Query: 61  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +R+ E      R+ +Y+KP G V T  DP+GR T+FD LP + + R I+VGRLD
Sbjct: 60  TVDGHLIRREEAAENVRRVLIYNKPEGEVCTRDDPEGRPTIFDRLPRLRTGRWINVGRLD 119

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           INT GLLL T DG LA  L  PS +  R Y VR  G+V ++ +  L  G++++       
Sbjct: 120 INTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVSEEMIERLLDGVMLEDGPAKFS 179

Query: 176 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
            +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  L   L  G  
Sbjct: 180 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFLTSELTMGRY 239

Query: 234 REVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           RE+ ++    L E++G   +    +   A    +E   R +   ++         K+   
Sbjct: 240 REMDQREIDILSEEVGLKPVALPGMTTKA-REKAERQQRKQARPLARSERPEAGRKRAPR 298

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
           +++G +  ++   P  R +        +         + +  E++R+      +      
Sbjct: 299 REDGDNAGRRT--PASRSSRGPQPGAERKGREQGTPVAERPRESNRKPRPSKPRDERPAG 356

Query: 351 S 351
           +
Sbjct: 357 A 357


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 111/232 (47%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  GI SRR  ++ IA+ +V +NG +       V + D + VDG  ++K ++ 
Sbjct: 1   MRINKYLSETGIISRRGADKWIAEGKVTINGEVAT-VGSQVEAGDIVCVDGKEVKKEQQL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+ +T ++   +  V D +     R+  +GRLD  +EGLLLLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TERHIKGNVVDFVNHPL-RIFHIGRLDKESEGLLLLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    +    +  +  G+ I         V    +K S     + L
Sbjct: 118 ILRAENHHEKEYIVQVDKPITAQFIQKMGAGVDILDTTTLPCHV----EKISEKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++     + V RL RI     +LG L  G  R++++K   E  
Sbjct: 174 EQGLNRQIRRMCSALGYSVKRLQRIRIMNIKLGNLKVGQWRDLTEKERTELF 225


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 123/241 (51%), Gaps = 3/241 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K++A AG+ SRR  E +I Q RV +NG +        +S+D +E+DG P+  A
Sbjct: 1   MTAQRLQKLLASAGLCSRRRAEELILQGRVTLNGAVARLGDQADLSSDRLELDGTPVAAA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
             T   L +KP G++ +  DP+GR+TV D LP   S    +  VGRLD  + G LLL+ND
Sbjct: 61  APTITVLLNKPRGVICSCHDPEGRTTVLDLLPPELSEATGLHPVGRLDGASRGALLLSND 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + YRV   G+   + L   ++G+ + G     + V    +     
Sbjct: 121 GALTLRLTHPRFGHRKHYRVWVTGEPAAEALEQWRRGVPLDGQPSQPVGVRELARGQRGT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + + EG+NR+I++  E     V  L R++ GP +LG L  G  R ++ +  R+    
Sbjct: 181 LLELEMVEGRNRQIRRTAELLGHPVRDLQRVAIGPLRLGELPEGRWRHLAPQEWRDLDAR 240

Query: 248 H 248
            
Sbjct: 241 R 241


>gi|602963|gb|AAB59990.1| ORF4 [Escherichia coli str. K-12 substr. W3110]
          Length = 243

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 96/242 (39%), Positives = 132/242 (54%), Gaps = 10/242 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQ 244
           E 
Sbjct: 242 EL 243


>gi|257900337|ref|ZP_05679990.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838249|gb|EEV63323.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 255

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 116/237 (48%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 17  MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDTVTYLGEIIAYQKD 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 77  FYYIL-HKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 134

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G       ++ +D   Q+   +
Sbjct: 135 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQESETS 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 195 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGNFCLPKDLNRGQYRPMTKEELEQ 251


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++      VKVNG ++    V V    D I  DG  +   E 
Sbjct: 22  QRIDKILSNLGYGSRSELKKFCKNGLVKVNGKVINNPGVQVDVENDEIIFDGEKVTYKE- 80

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++   D      V D +           VGRLD +TEGLL+LTNDG L
Sbjct: 81  FIYLMLNKPDGYISATFDKRD-PIVLDLIDKEDLVFEPFPVGRLDKDTEGLLVLTNDGQL 139

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           A  +  P     + Y  +  G V ++ +    KG+ +    Y  M   L   K    + +
Sbjct: 140 AHRVLSPKKHVPKTYYAKIEGIVTEEDIKAFAKGVTLDDG-YETMPAELIILKSDEISEI 198

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE  + KV  L R+S G  +L   L  G  RE++ + ++
Sbjct: 199 ELTIHEGKFHQVKRMFESVDKKVIYLKRLSMGKLKLDENLALGEYRELTDEEVK 252


>gi|313617518|gb|EFR89863.1| RNA pseudouridine synthase family protein [Listeria innocua FSL
           S4-378]
          Length = 233

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVIYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NLSETVIDLLEQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G+V  + +     G+ +  G       + + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGEVTAEDVEAFSAGVTLDDGYTCKPAHLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTENEL 227


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 78/254 (30%), Positives = 122/254 (48%), Gaps = 1/254 (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 PHLLEEAQVNLDAP 260
                 AQ     P
Sbjct: 259 ISREARAQAGPANP 272


>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 =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGKICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          ++ +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYIVTVDKPFTDWFIDEMSGGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVKKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|291524779|emb|CBK90366.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale DSM 17629]
          Length = 240

 Score =  262 bits (671), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 126/231 (54%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV+++I   ++ +NG +  +    V +  D + V+G  ++  +R
Sbjct: 2   IRLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNGRIVKY-QR 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +L++KP G V+  SD +   TV D +  ++   +  VGRLDI+TEGLLL+TNDG L+
Sbjct: 61  YEYYLFNKPSGCVSATSD-NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y  R  G+V  D +   K+GI I +       ++ +  + GS + + 
Sbjct: 120 HELLSPSKHVAKTYYARIDGEVTWDDIIRFKEGIDIGEERPTKPAELVI-KKSGSVSEIE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++  
Sbjct: 179 LTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQAE 229


>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 =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 117/235 (49%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V VNG L+++A   V  TD ++V    +   E+ 
Sbjct: 1   MRIDKYLANMKVGSRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKVADETIAY-EQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G++T   DP  + TV D +     +  +  VGRLD +T GLLLLTNDG L 
Sbjct: 60  YYFMLNKPAGVITATEDPQ-QKTVLDLIEHKDRYQGLSPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    +V  + +    KG+ +  G      Q+ +D       +  
Sbjct: 119 HNLLSPKKHVAKTYFVELDYEVSDELIVNFAKGVTLADGTKVSPSQLKIDKSNKKQGF-- 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EGK  +IK++F  F+  V RL RIS G   L   LL G  R+++K  +   
Sbjct: 177 ITIHEGKFHQIKRMFGLFDLGVVRLKRISMGNLSLDENLLLGKYRKLTKAEISAL 231


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 150/369 (40%), Positives = 197/369 (53%), Gaps = 29/369 (7%)

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 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LAR LE PS+ W+R YRVR  G   Q +L+ LK G  ++G+ YG M+ T+D   
Sbjct: 163 LTNDGELARSLEKPSSGWVRRYRVRALGHASQSRLDALKDGTTVEGVIYGPMEATIDKVA 222

Query: 184 GS-----NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                  N W+TV + EGKNRE++KV E    KVNRLIR++YGPFQLG L  G   EV  
Sbjct: 223 EKADGRANVWLTVAITEGKNREVRKVLESIGLKVNRLIRLAYGPFQLGNLETGEVEEVGP 282

Query: 239 KILREQLGPHL------LEEAQVNLDAPI-----------YSSETLVRDRPNIISEVPDD 281
           +++RE L   +       E A    DAP                           + PD 
Sbjct: 283 RVIRELLADVVSLKNLPPEGASQTGDAPRERPARGDARGEGFGGRRGGGDRFDKGDRPDR 342

Query: 282 FTRMKKNSSQKNGLS----KQKKLATPVHRRNLASNVWMAKGIHSSFLSDS---GQREEN 334
             R         G      K++       +R        A+        ++   G+R+  
Sbjct: 343 GDRTSSRPQNARGKPEFAEKREFKERDFDQRPRFEGDGEARDRKPERPFENRPFGERKSF 402

Query: 335 HRRSPSFPS 343
             R P    
Sbjct: 403 GDRKPYGAR 411


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 82/239 (34%), Positives = 126/239 (52%), Gaps = 10/239 (4%)

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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKIL 241
            + V L EGKNR+I+++ +   + V +L R + G  QL      +L +G  R +    +
Sbjct: 182 QLQVILTEGKNRQIRRIVQQMGFNVLKLHRTAIGLIQLTPSNDPSLASGHYRFLKSVEI 240


>gi|315648476|ref|ZP_07901575.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315276170|gb|EFU39516.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 253

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 76/240 (31%), Positives = 124/240 (51%), Gaps = 12/240 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           T QR+ KV++  G  SR E+++M  Q  + VNG +++    +V   TD IE +G  ++  
Sbjct: 7   TTQRLDKVLSNLGFGSRAELKKMAKQGSIVVNGTVMKDPGKHVDPYTDIIEFEGETIQYR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
           E     + HKP G+V+   D   R TV D L   +       VGRLD +TEGLLLLTNDG
Sbjct: 67  E-YVYIMLHKPPGVVSATEDLRDR-TVLDLLDKDYLVFEPFPVGRLDKDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN- 186
            LA  L  P     + Y     G+V ++   L   G+ +  G      ++ + + +  + 
Sbjct: 125 KLAHELLSPRKHIPKTYEAIVEGRVGEEDARLFAAGVTLDDGYATMPAELVIHSHEERDD 184

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
               + +++ + EGK  ++K++FE    KV  L R+S G  +L  +L  G+ RE++++ L
Sbjct: 185 GVILSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRVSMGELRLDKSLEIGTYRELTEEEL 244


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV ++G +    A+ V   D I +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAIDGEICTHGAL-VSDGDVITIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT   Q    +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVTRVGQ----STFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELHELEVGKWRSVTAEELEILIG 227


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD NT GLLL TNDG L
Sbjct: 61  YIYLMMNKPQGVVSATFD-NYDETVIDLLEDEDRIFEPFPVGRLDKNTVGLLLFTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGI++  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>gi|297520148|ref|ZP_06938534.1| 23S rRNA pseudouridylate synthase B [Escherichia coli OP50]
          Length = 281

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 106/292 (36%), Positives = 147/292 (50%), Gaps = 23/292 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E           V L     S   + +DR  + +       R  K  SQ +G
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSG 280


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 96/267 (35%), Positives = 136/267 (50%), Gaps = 7/267 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKA 70
            +R+ K++AR G  SRRE+ER I +  V VNG +           D + + G   PL  A
Sbjct: 2   TERLQKLLARLGHGSRREIERWIEEGLVTVNGKVA-SLGDQAGPDDKVAIRGRVVPLDVA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
            + R+  YHKP G +TT  DP+GR TVF++LP + + 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-TLLAGSTREVSKKILREQ--LG 246
            V LREG+NRE+++++E     V+RL R+ YGP  LG  L AG  R++    +     + 
Sbjct: 181 HVTLREGRNREVRRLWEAVGLTVSRLTRVRYGPISLGRDLRAGRWRDLEPGEMGALYAVA 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPN 273
                  ++  +            RP 
Sbjct: 241 GLPWTPPKIRREDRRPPKPPRTARRPK 267


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 123/237 (51%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  SR+EV+++I    V+VNG  ++  ++N+    D I V G  +    +
Sbjct: 2   ERIDKILANMGYGSRKEVKKLIKNNLVEVNGEKVKDPSINIDPEKDKILV-GDKVVNYRK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L   +       VGRLD +T GLLL+TNDG L
Sbjct: 61  FIYIMMNKPEGVVSATFD-NYDETVIDLLEEEYQVFNPFPVGRLDKDTVGLLLITNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P  +  +VY    + +V++  +   + GIVI  G      ++ +     + A V
Sbjct: 120 NHKLISPKWKVDKVYYAEINKEVNEKDIEAFQNGIVISDGYKCMPGKLEIIKSDENGAEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            V ++EGK  ++K++FE  + KV  L R+ +G   L  TL  G  RE++++ L   L
Sbjct: 180 YVTIQEGKFHQVKRMFEALDKKVVYLKRVKFGNINLDETLEEGEYRELTEEELENIL 236


>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 =  262 bits (670), Expect = 6e-68,   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|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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 102/339 (30%), Positives = 154/339 (45%), Gaps = 9/339 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
            + +R+ KV+A AGIASRR+ E  IA  RV VNG ++      V    D I VDG P+ K
Sbjct: 1   MSAERLQKVLASAGIASRRDCEEYIAAGRVMVNGKVVRIPGTRVDPEHDEILVDGRPIGK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  + HKP G+V+T  DP GR TV D + ++  R+  VGRLD ++EGLLLLT+DG 
Sbjct: 61  IHHRTYVMLHKPAGVVSTTDDPQGRPTVIDLV-NLEQRLFPVGRLDYDSEGLLLLTDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L + L  PS Q  + YRV  +       L   + G+ + G+      V L  +    AWV
Sbjct: 120 LTQKLTHPSYQVEKEYRVLLNEAPSPAALRAWRTGVELDGVKTAPAWVELIERTPDGAWV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            V L EG+ R+I++V     ++V RLIR+  GP  LG L +G+ R ++ + +       +
Sbjct: 180 RVILHEGRKRQIREVARVLGYEVRRLIRVREGPLTLGDLPSGTWRFLTDEEV------DM 233

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           L E      A   + +   R++            R+  ++       +      P     
Sbjct: 234 LREHAERNAAVAEAEQPRRREQGETQVSGGRRLRRITPSARLLQKGDQVTDTTLPDLDEA 293

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
           + S V     +     S   +R  +  R P         
Sbjct: 294 VES-VQPPPVVDERRSSRDNERIRHDERPPRDVRHSGRD 331


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 108/309 (34%), Positives = 155/309 (50%), Gaps = 25/309 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   RV V+G + +    V V+    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETMIEAGRVSVDGKIAKLGDRVEVVQGMKIRLDGHVVSIKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    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-GTLLAGSTREVSK---KILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   +  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGIPRGGWTELDLPAINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V+L     S   + R+R  + +       R  K  SQ +   +     
Sbjct: 242 EL----------VDLQPETVSKLPVERERRRVKAN---QIRRAVKRHSQVSTGRRSAAGG 288

Query: 303 TP--VHRRN 309
            P    +RN
Sbjct: 289 KPGKPSKRN 297


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 102/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    V V+G + +  +  V     +E DG  +  A   
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGEVLVDGEVQKSGSFKVPEGGVVEWDGREV-GAPGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPADFVCSHED-GYNPTAFVLLDEPKVENLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + 
Sbjct: 119 RITSPKHKCKKTYRVWLADAIQPDYVEKFAQGIELRNEREATLPAHLEIVNEAENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ +
Sbjct: 179 IVEGKYHQVKRMFAALGNKVELLHRERIGDIVLDDTLEPGDYRYLTQEEV 228


>gi|254496468|ref|ZP_05109345.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354324|gb|EET12982.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 252

 Score =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 92/242 (38%), Positives = 138/242 (57%), Gaps = 7/242 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----P 66
            + +R+ K++++AG+ SRRE+ER I    V+VNG  ++    +    D I V G     P
Sbjct: 1   MSSERLQKILSQAGLGSRREMERWIENGWVQVNGKPVK-LGDSASGDDKITVKGKLIPNP 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           L+  + TR+ LYHKP+G +++  DP    TVFD LP +   R + VGRLD+NT GLL+ T
Sbjct: 60  LKIKQNTRILLYHKPVGEISSRHDPKFEKTVFDRLPHLRQGRWVQVGRLDLNTSGLLIFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           N+G LA  L  P     R Y VR HGQV Q+ L +L+KG+ +        ++      G+
Sbjct: 120 NNGELANQLMHPRYGLEREYAVRVHGQVTQEMLTVLQKGVELDDGPAKFSRLESRGGDGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIRI YG   +   L    T E++ K + + 
Sbjct: 180 NTWYHVTLNEGRNREVRRLWESQGVEVSRLIRIRYGMLTMPRFLGRAQTYELTPKEVTDF 239

Query: 245 LG 246
           L 
Sbjct: 240 LA 241


>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 =  262 bits (670), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 127/240 (52%), Gaps = 3/240 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
               +R+ KV+ARAG  SRR  E +I+  RV+V+G +++   V +      + VDG  L+
Sbjct: 63  RADGERLQKVLARAGFGSRRACETLISTGRVRVDGAVVQEQGVRIDPAAQVVHVDGRRLQ 122

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E     + +KP G+V+  SDP+GR  + +   +   R+  VGRLD  TEGLLLLTNDG
Sbjct: 123 LDETKLTLVLNKPRGVVSAMSDPEGRRDLSEFTAAHSQRLYHVGRLDYETEGLLLLTNDG 182

Query: 129 GLARVLELPSTQWLRVYRVRFHGQ--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            LA  L  PS +  + Y  RF       +  +  L+ G+ ++       +  +  Q G  
Sbjct: 183 ELAHRLTHPSFEVAKTYVCRFDAPGGPPRGLVRTLRDGVELEDGPARADRARVLAQDGRE 242

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A V V L EG+NR ++++F    +++  LIR   GP  LG L  G+TRE+S + L   + 
Sbjct: 243 AVVEVTLHEGRNRIVRRMFASRGFELTALIRTRIGPVLLGDLAPGTTRELSGRELGTLMA 302


>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 =  262 bits (670), Expect = 6e-68,   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|308176960|ref|YP_003916366.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307744423|emb|CBT75395.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 373

 Score =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 78/241 (32%), Positives = 128/241 (53%), Gaps = 3/241 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +  V V L  G+NR ++++F+     V RL+R++ GP QLG    G+ R +  + +   +
Sbjct: 309 HVMVEVTLHSGRNRIVRRMFDEVGHPVQRLVRVAVGPVQLGDQKQGTIRSLGNQEVGHLM 368

Query: 246 G 246
            
Sbjct: 369 A 369


>gi|311693777|gb|ADP96650.1| pseudouridine synthase family 1 protein [marine bacterium HP15]
          Length = 312

 Score =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 71/314 (22%), Positives = 129/314 (41%), Gaps = 14/314 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +G+ SRRE +R I Q  V +NG         V+  D ++V+G  +     E 
Sbjct: 8   RLNKYISESGMCSRREADRYIEQGNVYINGKRAT-VGDQVLPGDTVKVNGQVIEPRAEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T    +  +           R+  +GRLD +++GL+ +T++G L  
Sbjct: 67  LVFIALNKPVGIVSTTDSAEKHN--IQRFVGHSERIFPIGRLDKDSQGLIFMTSNGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V ++ +  +  G+ I G      +V+    + S     + 
Sbjct: 125 KILRAGNNHEKEYLVTVDKPVTREFVEGMANGVPILGTMTKKCKVS----RESRFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L RI      L  L  G  R++S+K L           
Sbjct: 181 LVQGLNRQIRRMCEYFGYEVTKLERIRIMNVSLKGLAVGQWRDLSEKEL----AGLFDAI 236

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
              + +AP  + +   +         PD          +  G  +      P   +  AS
Sbjct: 237 RDSSSEAPPGAGKPAKKKSGTKAKPKPDRKPGSASTPGKPGGARRPGPKGKPAPGKKPAS 296

Query: 313 NVWMAKGIHSSFLS 326
                KG      S
Sbjct: 297 G-KRPKGGKPRQKS 309


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 71/244 (29%), Positives = 114/244 (46%), Gaps = 16/244 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
             R+ + +ARAG+ASRR  E +++  RV+VNG ++      V    D + VDGV  R ++
Sbjct: 11  TMRLQRFLARAGVASRRGSENLMSAGRVRVNGRVVSELGSKVTPGIDVVTVDGVECRLSD 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                + +KP G +TT SDP GR  V + +P + +  +  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|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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AG+ SR EV++++ +++V VNG L       +    D I   G  L   E+
Sbjct: 1   MRLDKFLVEAGVGSRTEVKQLLKKKQVLVNGKLETSPKTQIDEKLDKIVCQGQNLSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYMLNKPKGVISATED-DHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
           A  +  P     ++Y  +  G +  + +     GI ++       Q+ +    +K + + 
Sbjct: 119 AHAMLSPKKHVDKLYCAKVAGIMTDEDVKAFADGIELKDFTCQPAQLNIINADEKSNTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S GP +L   L  G  R +S   L   
Sbjct: 179 VEIVIKEGKFHQVKRMVLACGKEVTDLQRLSMGPLRLDDELALGEWRRLSPAELESL 235


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 110/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +     GI +  G      ++ + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTATDVEAFAAGIELDDGYTCKPARLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTETEL 227


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 128/239 (53%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  + 
Sbjct: 3   NEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTN 126
            A R   ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTN
Sbjct: 63  TARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   ++ L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIHRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLL 240


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 74/243 (30%), Positives = 114/243 (46%), Gaps = 5/243 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 253 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEV 312

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 313 KFHDQAVS-IERKIYVLLNKPKDTVTTSDDPQARRTVMDLVKGACEERIYPVGRLDRNTT 371

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT 178
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI +  G  + D    
Sbjct: 372 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKSDMEQIAAGIQLDDGEIHADAISY 431

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            D  K  +  V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+
Sbjct: 432 TDDFKKDD--VGIEIHSGKNRIVRRIFESLGYKVVKLDRVYFAGLTKKGLRRGEWRYLSE 489

Query: 239 KIL 241
             +
Sbjct: 490 AEV 492


>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 =  262 bits (670), Expect = 7e-68,   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|167845952|ref|ZP_02471460.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
          Length = 384

 Score =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 92/304 (30%), Positives = 150/304 (49%), Gaps = 8/304 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 84  KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 142

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 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+      D          R +P+ +        R    ++       +
Sbjct: 323 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPR 380

Query: 299 KKLA 302
           +   
Sbjct: 381 RGRR 384


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   LD    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLDV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 113/238 (47%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNFLKAGRVTVNGKKEKSAKLQIDEETDEICFDGKKLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   +P  + TV D +        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATENPKHK-TVLDLMDDYACAKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A  L  P     + Y  +  G +  + +    KGI ++       ++ L +   + + + 
Sbjct: 119 AHALLSPKRHVDKTYMAQVKGIMTDEDIETFAKGIPLKDFTCQPAKLELVSIDTEENKSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R +SK+ L   L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRVTMGTLTLDEELKRGEWRRLSKEELEGLL 236


>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 =  262 bits (670), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 1/236 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              QR+ K+IA +G+ SRR  E+++ Q+RV +NG L +         D I VDG  L   
Sbjct: 1   MKQQRLQKLIAASGLCSRRHAEQLLLQERVTLNGHLAKLGDKADPELDKISVDGRVLNSN 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V LREG+NR+I++V E     V  L R +     L  L  G  R + ++     L
Sbjct: 181 KVVLREGRNRQIRRVAEQLGHPVLDLQRTAIANVALNALPEGCWRALDEREWTPLL 236


>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 =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KAE 71
           R++K I+ +GI SRRE +R+I + RV +NG   +     V + D + VD   L+     E
Sbjct: 12  RLNKAISDSGICSRREADRLIEEGRVTINGKTAK-VGDRVSAFDEVIVDDRRLKLNKTGE 70

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R     ++KP G+V T ++PD +  + D + +   R+  +GRLD  +EGL+ LT+DG + 
Sbjct: 71  RPVYIAFNKPRGIVCT-TEPDVKDNIIDYI-NFPKRIFPIGRLDKPSEGLIFLTSDGNIV 128

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     +  + +  + KG+ I        QV  + +        +
Sbjct: 129 NKILRAGNNHEKEYIVTVDKPITDEFIKGMMKGVPILDTVTKKCQVFKEGEL----VFRI 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G  R+++K+ E+F + V +L R       L  L  G+ R ++ + L+  +   +++
Sbjct: 185 ILTQGLYRQVRKMCEYFGYHVTKLKRTRIMNISLAKLPLGTWRYLTPEELQGIM--DMVD 242

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
            +    +A   ++E   +     I   P D    K+
Sbjct: 243 SSSGTEEASFENTE--FKKEQKHIRSKPQDLKNKKR 276


>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 =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 83/240 (34%), Positives = 127/240 (52%), Gaps = 12/240 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A+ GIASRRE E MI   RV++NG L       V    D I +DG  L + +R
Sbjct: 3   ERLQKILAQWGIASRREAEEMIRHSRVQINGKLA-HLGQKVDPQKDAIAIDGKTLSEKQR 61

Query: 73  T--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---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|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 =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 104/230 (45%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V +NG + +  A  V   D I  DG  L      
Sbjct: 1   MRLDKFLAEMTDLTRSQATKVLRQSAVTINGKIEKSGAAKVGPNDEICYDGERLAWVAEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           +  + +KP G + +H D D   T++       S R+ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYIMLNKPQGYICSHEDGDH-PTIYQFFGYPLSARLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+ + +    +GI+++G        TL+     N  V + 
Sbjct: 120 RITSPKHHQPKTYLVTLADPVEANYVQACTEGILLRGEKDPTKPATLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EG+  +IK++F     KV  L R   G   L   L  G  R ++   +
Sbjct: 178 ISEGRYHQIKRMFAALGNKVVGLHRWKIGALVLDDSLEEGEYRALTAAEV 227


>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 =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 122/232 (52%), Gaps = 3/232 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
               R++K +A  GIASRREV++MI +  +KVNG       + V   D I + G  + K 
Sbjct: 1   MEEMRINKYLASLGIASRREVDKMIEEGAIKVNGEKAA-PGIKVSDEDEIYIKGKKIEKN 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   ++ +KP+ ++++  D  GR TV D +     R+  +GRLD NT GL++LTNDG 
Sbjct: 60  TEKKVYYILNKPLEVLSSSKDDRGRKTVVDLI-KCKERIFPIGRLDYNTSGLIILTNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +  P  +  + Y  +  G++ ++   LL+KG+ +         V +  ++     +
Sbjct: 119 LFNRIIHPKAEIFKEYYAKVFGEIKEENAELLRKGVELDDGMTLPANVKILRRERGKTEL 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V +REG+NR+++++ +  N  V  L R   G   LG L  G  RE++ + +
Sbjct: 179 LVAIREGRNRQVRRMLDKINHPVITLRREKIGDLSLGNLKLGEYRELTNEEV 230


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 73/238 (30%), Positives = 111/238 (46%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNFLKSGRVTVNGKKEKSAKLQIDEETDEICFDGQKLDYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  + TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDPKHK-TVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A  L  P     + Y  +  G +    +    KGI ++       ++ L +   +   + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTDTDVETFAKGIPLKDFTCQPAKLELVSIDTEKDQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R +SK+ L   L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLTLDEDLKRGEWRRLSKEELEVLL 236


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 110/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++    +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDPKFHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 THQLLSPKKHVPKKYYAHVSGVVTEEDVKEFAKGVILEDGYETKPGDLTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVAVNGQVETSPKTQIDENQDQIAFQGQVLTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATEDARHK-TVLDLLDDTARHKQVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A  +  P     ++Y+ +  G ++Q+ +   +KGI ++       ++ + +   +   + 
Sbjct: 119 AHAMLSPKKHVDKIYQAKVDGIMNQEDILAFEKGIELKDYTCQPAKLEIISVDRATGTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           V + + EGK  ++K++      +V  L R+S GP  L   L  G+ R ++++ L   
Sbjct: 179 VQITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSLPNDLEVGAWRRLTEEELEAL 235


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 75/240 (31%), Positives = 115/240 (47%), Gaps = 10/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDPKHR-TVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNA 187
           A  L  P     + Y  +  G + Q+ +    KGI ++       +   V++D +K + +
Sbjct: 119 AHALLSPKRHVDKTYLAQVEGIMSQEDVETFAKGIPLKDFTCQPAKLEFVSVDPEK-NQS 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V V + EGK  ++K++  F   +V  L R++ G   L   L  G  R ++K+ L     
Sbjct: 178 LVRVTIAEGKFHQVKRMVAFCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEELEVLFA 237


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 128/272 (47%), Gaps = 13/272 (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  LR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           ++ + E+     ++KP G+  T ++ D R  + D + +   R+  +GRLD  +EGL+ +T
Sbjct: 58  IQERTEKPIYLAFNKPAGIECT-TNLDVRDNIIDFI-NYPERIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  +    ++ +  GI I        +V    ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYIVTVNHPITDRFIDRMANGIPILETITKKCKV----EQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+ +++V  L R       L  +  G  R ++   + E  
Sbjct: 172 KFVFRIILTQGLNRQIRRMCEYLDYEVTALKRTRIINISL-DVAEGKYRNLTDAEVAEL- 229

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
              L+E +    +A + S++     + N    
Sbjct: 230 -NKLIEPSSKTEEASLPSNKGKFTGKRNYGER 260


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 107/288 (37%), Positives = 154/288 (53%), Gaps = 12/288 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G  L  E +  +D       T +R     + +     T+ 
Sbjct: 304 VNYLRELVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 104/302 (34%), Positives = 147/302 (48%), Gaps = 22/302 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V       I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVEPAASLKIRIDGHVVPVS 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP    +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 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           RE +G          L     S   + +DR    +       +    +      S ++  
Sbjct: 241 RELVG----------LAPETVSKVPVEKDRRRTKANQIRRAVKRHTTTKVSKPGSGRRPS 290

Query: 302 AT 303
             
Sbjct: 291 KR 292


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 70/226 (30%), Positives = 107/226 (47%), Gaps = 3/226 (1%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +   D ++    P+   ER    
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGAVVTELGTKIKRGDEVKFHDQPVS-IERKIYI 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L 
Sbjct: 61  LLNKPKDTVTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLT 120

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P     ++Y V     V +  ++ +  GI +         ++  T       V + +  
Sbjct: 121 HPKFLKKKIYHVHTDKNVTKADMDQIAAGIQLDDGEIHADAISY-TDDVRRDEVGIEIHS 179

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           GKNR ++++FE   +KV +L R+ +       L  G  R +S++ +
Sbjct: 180 GKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLSEQEV 225


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 105/230 (45%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  + + Q  V +NG + +  A  V   D I  DG  L   +  
Sbjct: 1   MRLDKFLAEHTGLTRSQATKALRQSAVTINGKIEKSGATKVSPQDAIYFDGELLTWLDVG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           +  +++KP G V +H D D   +++       S R+ S GRLDI+T GL+LLT+DG  + 
Sbjct: 61  QYLMFNKPQGYVCSH-DEDEHPSIYQFFDYPLSARLHSAGRLDIDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+ + +    +GI+++G         L+     N  V + 
Sbjct: 120 RVTSPKHHQPKTYLVTLADPVEANYVQACAEGILLRGEKDPTKPAVLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R ++ + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVLGLHRWKIGNLTLDDNLAEGDFRVLNAEEI 227


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 127/239 (53%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  + 
Sbjct: 3   NEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTN 126
            A R   ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTN
Sbjct: 63  TARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   +  L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + V V L EG+NR ++++ +     V RL R + GP +L  L  G  RE++ + L + L
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTAIGPVRLKRLGRGDMRELTHEELGQLL 240


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 91/234 (38%), Positives = 124/234 (52%), Gaps = 2/234 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE-R 72
           R+ KV+A+AGIASRR  E+MIA  RV V+G ++    V V   T  I VDG  L   E +
Sbjct: 12  RLQKVLAQAGIASRRASEQMIADGRVSVDGTVVRTQGVRVDPATQVIHVDGERLILDEAK 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +   +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y  R HG+V       L  GI ++          L    G    V + 
Sbjct: 132 RLTHPSYEIRKTYVARLHGEVKPGVRRRLLAGIELEDGPIAVDSFRLVDTYGDITTVEIV 191

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR +    L    G
Sbjct: 192 VHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRIKGNALTALYG 245


>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 =  262 bits (669), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 96/304 (31%), Positives = 145/304 (47%), Gaps = 12/304 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR-KAER 72
           R++K +A AG+ SRR  + +IA  RV VNG ++  A + +    D + VDG P+    E 
Sbjct: 10  RINKALASAGVCSRRHADDLIAAGRVTVNGAVVTEAGLRIDPARDALAVDGAPVNLAPEI 69

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
                 HK  G+VTT SDP+GR TVFD LP ++   R+  VGRLD  +EGLLLLT DG L
Sbjct: 70  PITLALHKKPGVVTTASDPEGRPTVFDGLPEVWRGKRLFPVGRLDFFSEGLLLLTTDGEL 129

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL-DTQKGSNAW 188
           A  L  P     + YRV   GQV  D L  + +G+ + +G     +   + +      + 
Sbjct: 130 ALRLTHPRWHVPKRYRVTVRGQVTPDMLGTMARGMRLAEGERLAPVAARVVEGPAQDRSI 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + L +G NR+I+++       V RL R+S GP  LG L  G+ RE++   L       
Sbjct: 190 LEMELHQGVNRQIRRMCRDLGLTVLRLARVSQGPVALGDLPLGACRELTPAEL------A 243

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
            L ++    DA +  +    R      ++ P    R  +   ++              RR
Sbjct: 244 TLRQSVGLDDADVAPAPPRPRPTAEGDTKRPPRPARPPQAGGKRPATKASGGETETGPRR 303

Query: 309 NLAS 312
           +  S
Sbjct: 304 DGQS 307


>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 =  262 bits (669), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 117/234 (50%), Gaps = 10/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++++ I++A   SRRE +R+I   RV +NG +    A+ V + D + +DG  + K  + 
Sbjct: 1   MKINQFISKALSCSRRETDRLIKANRVAINGEICTHGAL-VAADDIVSIDGKTIEKEAKE 59

Query: 74  R-LWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDG +A
Sbjct: 60  KIYIAFHKPVGITCTAAEHIEGNIIEYINHPE---RIFPVGRLDKASEGLILLTNDGAIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          ++ + +G+ I+       +VT       ++   +
Sbjct: 117 NQILHGDHEHEKEYIVTVDKPFTDWFIDSMSRGVKIKDGMTKPCKVT----GVDHSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G NR+I+++   F + V +L R+      L  L  G  R VS++ L E +
Sbjct: 173 VLTQGMNRQIRRMSRAFGYTVTKLKRVRIMNITLDGLEVGEWRNVSEQELIELM 226


>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 =  262 bits (669), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 104/300 (34%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKLLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>gi|291528900|emb|CBK94486.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           rectale M104/1]
          Length = 240

 Score =  262 bits (669), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 126/231 (54%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV+++I   ++ +NG +  +    V +  D + V+G  ++  +R
Sbjct: 2   IRLDKFLSEMGLGTRSEVKKLIKTGQIAINGTVAAKPETKVDTDADEVSVNGRIVKY-QR 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +L++KP G V+  SD +   TV D +  ++   +  VGRLDI+TEGLLL+TNDG L+
Sbjct: 61  YEYYLFNKPSGCVSATSD-NVHDTVMDYITDAVHDDLFPVGRLDIDTEGLLLITNDGALS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  PS    + Y  R  G+V  D +   K+GI I +       ++ +  + GS + + 
Sbjct: 120 HELLSPSKHVAKTYYARIDGEVTLDDIIRFKEGIDIGEERPTKPAELVI-KKSGSVSEIE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           + + EGK  ++K++FE    +V  L RIS GP +L   L  G+ R +++  
Sbjct: 179 LTITEGKFHQVKRMFEALGKRVIYLKRISMGPLKLPDDLKTGTYRALTQAE 229


>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 =  262 bits (669), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 143/328 (43%), Positives = 198/328 (60%), Gaps = 7/328 (2%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-----NAW 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
           +      + +     + T +R R       P    R   +        ++++   P+ R 
Sbjct: 286 IDPRNLPSEN--ETQTRTPMRLRRTDGEGAPRTGRRGGGDRFASKSEGREERRERPLSRD 343

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHR 336
                 + AK        +  + E + +
Sbjct: 344 EAFRRKYEAKEFGERDFDERPRFEGDGQ 371


>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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 147/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           +           V L     S   + +DR  + +       R  K  SQ  G  +     
Sbjct: 242 DL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQMAGGRRSGGRN 288


>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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 104/297 (35%), Positives = 145/297 (48%), Gaps = 17/297 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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-------L 234

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                    V L     S   + +DR  + +       R  K  SQ  G  +     
Sbjct: 235 AQTNYLRGLVELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQIAGGRRSGGRN 288


>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 =  261 bits (668), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 107/307 (34%), Positives = 152/307 (49%), Gaps = 23/307 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   R+ V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T SDP+GR TVFD LP     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-GTLLAGSTRE--VSK-KILR 242
            W  V L EG+NRE+++++E  + +V+RLIR+ YG  QL   L  G   E  ++    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVDVQVSRLIRVRYGDIQLPKGLPRGGWMEMGLTDVNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + R+R  + +       R  K  SQ    ++     
Sbjct: 242 EL----------VQLTPETVSKLPVERERRRVKAN---QIRRAVKRHSQVGVSNRPASGR 288

Query: 303 TPVHRRN 309
               +RN
Sbjct: 289 RSAPKRN 295


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 117/237 (49%), Gaps = 2/237 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ K++A+AG  SRR+ E +I   RV+++G L+      V      + VDG  +R
Sbjct: 15  NNEGIRLQKLLAQAGFGSRRKCEEIITDGRVEIDGELITELGTRVDPKHQEVRVDGSRVR 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG
Sbjct: 75  VNPNHVTLALNKPKRVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDG 134

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L   G+ +        +  +      + 
Sbjct: 135 ELSQHIMHPKYEVEKTYIATLDGRISGTVCRRLVTTGVQLDDGWIKLDRCAILDSSRDST 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+  +R  
Sbjct: 195 LVKVVLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGTYRVLSQVEVRSL 251


>gi|301156469|emb|CBW15940.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus parainfluenzae
           T3T1]
          Length = 232

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 109/229 (47%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     V+    +  ++GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLADPVENHYASACEEGILLRGEKEPTKPAKLEVLDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     KV  L R   G  +L  +L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGNVELDESLEEGEFRPLTQEEI 227


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/244 (33%), Positives = 128/244 (52%), Gaps = 7/244 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + EN +P R++K +A AGIASRR  + +I   RV VNG++       V+   D +  +G 
Sbjct: 1   MPEN-SPVRLNKYLADAGIASRRGADALIQGGRVCVNGLIQREPGTRVIPGQDTVLCNGA 59

Query: 66  PLRKAE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGL 121
           P+   +   +   + HKP+  VTT +DP GR TV D LP      R+  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 LREQ 244
           ++  
Sbjct: 240 IKTL 243


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 107/288 (37%), Positives = 154/288 (53%), Gaps = 12/288 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G  L  E +  +D       T +R     + +     T+ 
Sbjct: 304 VNYLRELVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 118/237 (49%), Gaps = 2/237 (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 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L   G+ +        +  +      + 
Sbjct: 135 ELSQHVMHPKYEVEKTYIATLEGRISGQVCRRLVTTGVQLDDGWIKLDRCAILDASRDST 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L +GS R +S+  +R  
Sbjct: 195 LVKVVLHSGKNRIVRRIFGSIGFPVKRLVRTQIGPIKLGDLKSGSYRVLSQTEVRSL 251


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 118/244 (48%), Gaps = 10/244 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   + TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATEDDQHK-TVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     + YR +  G + Q  +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKTYRAQVAGLMKQADVERFAAGIELKDFTCQPAQLKILELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL--REQL 245
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++++ +   E L
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLAMGPLQLDPALALGEWRRLTEEEILSLEIL 238

Query: 246 GPHL 249
           G  L
Sbjct: 239 GVEL 242


>gi|121533339|ref|ZP_01665167.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
 gi|121307898|gb|EAX48812.1| pseudouridine synthase [Thermosinus carboxydivorans Nor1]
          Length = 245

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/235 (33%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QR+ KV+A  G  SRRE+++M+  +RV VNG ++    ++V    D IEVDG P+   
Sbjct: 5   ERQRLDKVLAHLGYGSRREIKKMVKAERVIVNGAVVRDPELHVFPWQDRIEVDGEPIHYR 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP G+++   D  G+  V D L           VGRLD +TEGLLLLTNDG
Sbjct: 65  E-YIYLMMNKPQGVLSATEDAAGK-VVVDLLRPEHKAFAPFPVGRLDKDTEGLLLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y  R  G V  +     + GI +  G      ++T+    G  +
Sbjct: 123 QLAHRLLAPKKHVPKRYYARVKGVVTDEDKGAFQAGITLDDGYRTLPAELTIL-HAGPVS 181

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + + EGK  ++K++F      V  L R++ G   L   L  G  RE++   L
Sbjct: 182 EVELVIYEGKFHQVKRMFAARGKTVTYLKRLAMGALVLDEKLAPGEYRELTADEL 236


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 109/234 (46%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ K ++     SR +  + + Q  VKVN  L++  A+ V   D +E DG  L      
Sbjct: 3   QRLDKFLSEYTGLSRSQATKALRQNLVKVNQQLVKDGALKVSPEDVVEFDGETLEWVSGN 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + +L +KP G V +H D +   TV+        SR+ + GRLD++T GL+LLT+DG  + 
Sbjct: 63  QYFLLYKPEGYVCSHDDGEY-PTVYQFFDYPLSSRLHTAGRLDVDTTGLVLLTDDGQWSH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P   + + Y V     V+   L    +GI+++G         ++     N  + + 
Sbjct: 122 RITSPKYHYKKTYLVTLAAPVEDFYLEQCAQGILLRGEKQPTKPAQIEIIDDYN--LNLT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           + EGK  ++K++F     KV  L R   G   L   L  G  R ++   ++  L
Sbjct: 180 IVEGKYHQVKRMFAALGNKVIALHRWRIGQIILDPQLEEGQYRALTDAEVQSFL 233


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 59/228 (25%), Positives = 99/228 (43%), Gaps = 3/228 (1%)

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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V     V  D      KG+ +           L+    +   V + + 
Sbjct: 125 TSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTIS 182

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           EG+  ++K+ F      V  L R   G   L   L  G  R ++++ +
Sbjct: 183 EGRYHQVKRXFAAVGNHVVELHRERIGGITLDADLAPGEYRPLTEEEI 230


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/289 (35%), Positives = 144/289 (49%), Gaps = 17/289 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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-------L 234

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
                    V L     S   + +DR  + +       R  K  SQ  G
Sbjct: 235 AQTNYLRGLVELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQIAG 280


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 86/240 (35%), Positives = 125/240 (52%), Gaps = 11/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A  GIASRR+ E+MI  +RV+VNG +         S+D IEVDG P++ + R 
Sbjct: 3   ERLQKIMATWGIASRRQAEQMILAKRVRVNGNIAHLGQKANPSSDDIEVDGKPIKPSHRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KPIG+V+T +DP GR  V D LP    +   V  VGRLD+++ G LLLTNDG
Sbjct: 63  VPIYLLLNKPIGVVSTCADPGGRRNVLDLLPRRLQKGQGVHPVGRLDVDSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNA 187
            L   L  P     + Y+V   G   +  L   ++G+++        +V    Q   S  
Sbjct: 123 ELTFRLTHPRHHVPKTYQVWVQGHPPESVLQAWRQGVILSSRKTLSAEVRRLQQSIDSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKILR 242
            + V L EG+NR+I+KV E   + V +L R + G  QL       L  G  R ++   L 
Sbjct: 183 LLEVILFEGRNRQIRKVAEQLGYPVVKLHRSAIGSIQLNPPGKPELAPGRYRPLTPSELE 242


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 97/266 (36%), Positives = 140/266 (52%), Gaps = 7/266 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ K++AR G+ SRREVE  I   RV++NGI        V   D + V+G PL      
Sbjct: 3   ERLQKILARGGLGSRREVEEWIKAGRVRINGIPAR-LGDKVSDEDQVTVNGRPLSPRRLQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           A  +++ LYHKP G + +  DP+GR TVF +LP     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 HLLEEAQVNLDAPIYSSETLVRDRPN 273
             +E+          ++    + R  
Sbjct: 242 GGVEQRTTRFQPRSKNNRRGRQGRKQ 267


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 106/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +    V VN  + +  +V + + D I  DG  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDGELLEWMDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+       ++GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAQRFEEGILLRGEREPCLPAKMEVLDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDEDLQEGEFRPLTEDEM 227


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VK++G++++     V  +   + V G  +   E  
Sbjct: 4   RIDKMLANMGFGTRKEVKKLLKSGVVKIDGMIVKDPKTQVNPSEQVVTVRGEEVEYKE-F 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+++   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 63  IYLMMNKPPGVISATED-MAEETVIDLLEEEDRVFAPFPVGRLDKDTEGLLLLTNDGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G+V ++ +   + GIV+  G      ++ +  + G  + V 
Sbjct: 122 HQLLSPKKHVPKTYFAVIDGEVTEEDIESFRHGIVLDDGYKTKPAELIIL-KSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IK++F     +V  L RI  GP  L  +L  G  RE+++K ++
Sbjct: 181 VTITEGKFHQIKRMFRALGKRVVYLKRIQMGPLALDPSLEVGEYRELTEKEVK 233


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 101/295 (34%), Positives = 151/295 (51%), Gaps = 14/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  RV V+G L       V  +    I +DG  +  +
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLAT-LGDRVEPSVSLKIRIDGHVVPVS 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP    +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 REQLG--PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           RE +G  P  + +  V  D     +  + R      +         +++S ++ G
Sbjct: 241 RELVGLAPETVSKVPVEKDRRRTKTNQIRRAVKRHTTTKVSKPGSGRRSSKRQQG 295


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEEL 222


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNVEEQEVMIHGEIVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LLLTNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVVDLLELEDAIFDPFPVGRLDIDTEGFLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y     G V +  +    KG+++  G       +T+  +    + +
Sbjct: 119 AHQLLSPKKHVPKKYYAHVAGIVTEKDVEEFAKGVILDDGYETKPGALTIL-KSDDVSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVEKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 231


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/286 (35%), Positives = 147/286 (51%), Gaps = 10/286 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K++A AG+ SRR++E  I++ RV+VNG L +         D I VDG  +   
Sbjct: 15  DEPVRLQKLLAEAGLGSRRQIEGWISEGRVRVNGQLAK-LGDQATRADRIRVDGRDVTLK 73

Query: 71  ER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
            +    T++ +YHKP G + T  DP+ R TVF  LP     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-TLLAGSTREVS---KKIL 241
           N W  V LREG+NRE+++++E     V+RLIRI YG  +LG  L  G+ R ++   +  L
Sbjct: 194 NHWYNVVLREGRNREVRRLWEAAGCTVSRLIRIRYGNVELGRRLFPGNWRPLTDAERAEL 253

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
               G  +LE  ++   AP  +     +      S     + R  +
Sbjct: 254 MALAGLRVLERPRLRRPAPGAAKPRRPKPDDGSSSGEGLKWGRRSR 299


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 106/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + +    V VN  + +  +V + + D I  DG  L   +  
Sbjct: 1   MRLDKFIAENTGLTRSQAAKALKSGLVTVNQKVEKSGSVKISAQDEIRYDGELLEWMDEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYVCSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+       ++GI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAQRFEEGILLRGEREPCLPAKMEVLDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDENLQEGEFRPLTEDEM 227


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 105/306 (34%), Positives = 155/306 (50%), Gaps = 23/306 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +     +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  
Sbjct: 4   KTKVVGEKLQKILARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHL 63

Query: 67  LRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           L   E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GL
Sbjct: 64  LSIKESEEAVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS +  R Y VR  GQ+D +K+  L +G+ ++        ++   
Sbjct: 124 LLFTTDGELANRLMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTISFQG 183

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK- 239
            +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K 
Sbjct: 184 GEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKA 243

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              LRE           V LD+   S   + +DR  + +       R  K  ++  G   
Sbjct: 244 TNYLREL----------VELDSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQV 290

Query: 298 QKKLAT 303
             +  +
Sbjct: 291 AGRQGS 296


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/300 (34%), Positives = 149/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +IA  RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIAAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +       ++V ++          +DR  + +       R  K  SQ     +    +
Sbjct: 242 ELVELKPETTSKVAVE----------KDRRRMKAN---QIRRAVKRHSQVGSSRRPGGRS 288


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 103/305 (33%), Positives = 145/305 (47%), Gaps = 12/305 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++AR+G  SRRE+E  I Q RV V+G +      + V     I +DG  L   E
Sbjct: 8   SEKLQKILARSGHGSRREIEGYIQQGRVSVDGKIATLGDRLEVQPATKIRLDGRILNIKE 67

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T  DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T 
Sbjct: 68  SQKTVCRVLAYYKPEGELCTRHDPEGRPTVFDRLPKLLGSRWIAVGRLDVNTCGLLLFTT 127

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+VD  KL  L KGI ++        +     +G N
Sbjct: 128 DGELANRLMHPSREVEREYAVRVFGEVDDAKLKQLAKGIQLEEGPASFRTIAFKGGEGMN 187

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    LR
Sbjct: 188 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIGLPKGLPRGGWTELGLEQTNYLR 247

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + +   L EE    +                 +       +R        +   K  +  
Sbjct: 248 QLV--DLNEETVSKVAVGRDQRRLKANQIRRAVKRHAQVASRPSAGKRPGSSRQKAGRTT 305

Query: 303 TPVHR 307
            P  R
Sbjct: 306 APKGR 310


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 109/309 (35%), Positives = 151/309 (48%), Gaps = 16/309 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+RV K++ARAG+ SRREVE  I   R+ VNG+ ++       ++D  E+DG  L  +  
Sbjct: 21  PERVQKLLARAGVGSRREVEGWIEAGRLLVNGVPVQ-PGQKASTSDRFELDGKLLDVSSA 79

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VT+  DP+GR TVFD LP     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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L + L  G   E+ +K    L  
Sbjct: 200 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLTMGRWEELDQKGVDALSR 259

Query: 244 QLG------PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            +G      P      Q   D     S      R               K  S   G   
Sbjct: 260 AVGLGSVAVPQKTPGEQAAHDRKRRKSPGKSLQRTRKGGSWQVADGAPPKARSDSRGKPS 319

Query: 298 QKKLATPVH 306
             K   P  
Sbjct: 320 AGKGRKPAR 328


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 70/295 (23%), Positives = 139/295 (47%), Gaps = 9/295 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           ++K I+ +GI SRRE E+ I + RV +NG    +    V   D +++DG  ++  + T  
Sbjct: 17  LNKYISSSGICSRREAEKFIKEGRVTLNGK-ATQLGNRVTKKDVVKLDGRVVKPKDVTIY 75

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP+G+V+T    +  + V     +   R+  +GRLD  +EGL+ LTNDG +   + 
Sbjct: 76  IALNKPVGIVSTTDGREPNNIVKHI--NYPERLFPIGRLDKPSEGLIFLTNDGDIVNKIL 133

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                  + Y V  +  + +D +  +  GI I G       V    +K ++    + L +
Sbjct: 134 RAGNNHEKEYFVTVNKSITEDFIEKMGNGIPILGTVTQKCLV----EKVNDKIFKIILTQ 189

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV 255
           G NR+I+++ E+ +++V +L R      +LG L  G  RE++++ + E     ++  +  
Sbjct: 190 GLNRQIRRMCEYLDYEVTKLKRTRIMNVELGYLQTGDWRELTEEEMNEI--NKMISTSSK 247

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
             +A     +   +     ++   +DF R   +  + +  +K+K  +    R+  
Sbjct: 248 TEEASKIKEKPKAKKPKKKLAPTKNDFNRKSASFRKSSPKNKRKNTSFSSKRKRR 302


>gi|295090937|emb|CBK77044.1| ribosomal large subunit pseudouridine synthase F [Clostridium cf.
           saccharolyticum K10]
          Length = 271

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 73/270 (27%), Positives = 124/270 (45%), Gaps = 10/270 (3%)

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 +     RV  VGRLD ++EGL+L+TN
Sbjct: 65  ISGKDRPVVLLVNKPRGIVCTTSDRDRAENIVDFIGYPL-RVYPVGRLDKDSEGLILMTN 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G L   +        + Y V    ++ +  LN ++KG+ I         V    +K   
Sbjct: 124 QGELVNRILKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDTVTRPCTVEKTGEKS-- 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILRE 243
               + L +G NR+I+++ E   ++V  L R+     +L  L  G  RE+++   K L E
Sbjct: 182 --FRIILTQGLNRQIRRMCEALGYRVRTLKRVRIMNLRLDGLKTGEYREITRGEWKELTE 239

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L     E  + +       SE   R+   
Sbjct: 240 LLEGKG-ERRKADQKNAEKHSELGQREPEK 268


>gi|330911132|gb|EGH39642.1| ribosomal large subunit pseudouridine synthase B LSU [Escherichia
           coli AA86]
          Length = 291

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKTN---QIRRAVKRHSQVSGGRRSGGRN 288


>gi|229062392|ref|ZP_04199708.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228716863|gb|EEL68550.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 242

 Score =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNIEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V ++ +    KG+++  G      ++T+  +    + +
Sbjct: 119 THQLLSPKKHVPKKYYAHISGVVTEEDVKEFSKGVILEDGYETKPGELTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDQELELGQYRELTDEEVE 231


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 97/338 (28%), Positives = 155/338 (45%), Gaps = 9/338 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPL 67
           E    +R+ KV+A AG  SRR  E  I   RV ++G++ +   V V  S   + VDG  L
Sbjct: 32  EASAGERLQKVLASAGYGSRRACEEYIEMGRVTIDGVVAKELGVRVDLSRQKVAVDGEKL 91

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  E+ R +L+HKP G++ T+SDP GR+ V D  P    R+ +VGRLD  TEGLL++TND
Sbjct: 92  RVEEK-RYFLFHKPAGVLCTNSDPAGRTRVIDCFPPNVGRLFTVGRLDDGTEGLLIVTND 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 VLEITMREGQNREIRRLLARVGHKVMKLKRTHFGPIKLGDLERGAHRKLSEEELSKL--- 267

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               +  +       +     R R    +      TR   + +   G + + +L      
Sbjct: 268 ----QDVITGKWKEPAPRKPQRTRDAGKATSAGGVTRASSSRAGSAGATPRARLERTALP 323

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                 + +         S    + +      + P +R
Sbjct: 324 ATGLEPLTIPGSKLKRLGSSKALKSQVLNSPEANPKRR 361


>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 =  261 bits (668), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD NT GLLLLTNDG L
Sbjct: 61  YIYLMMNKPQGVVSATFD-NYDETVIDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGI++  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 97/300 (32%), Positives = 146/300 (48%), Gaps = 10/300 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV V+G +       V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGHGSRREMEALITAGRVSVDGKVAT-LGDRVEVNAVIRVDGHTVKTRAE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+  YHK  G + T  DP+GR TVFD LP + S 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-TLLAGSTREVSKKI---LRE 243
           W  V L EG+NRE+++++E    +V+RL+R+ YG   L   +  G  +E+       LR 
Sbjct: 181 WFNVTLTEGRNREVRRLWESQEVQVSRLMRVRYGDVTLDRGIPRGGWQELKLPEVNYLRG 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +      E++V+L     S+      +     +   D   M+  +       K      
Sbjct: 241 LVNMPPETESKVDLQQDGKSTRHKQAAQIRRAVKRHKDMQGMEPRARSTTARRKPTSSTR 300


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 110/229 (48%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D +     R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-HYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEEL 222


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 79/241 (32%), Positives = 117/241 (48%), Gaps = 6/241 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           E     R+ KV+++AGIASRR  E++I   RV+V+G ++      V   T  I VDGV +
Sbjct: 8   EQERGIRLQKVLSQAGIASRRAAEKLIIDGRVEVDGQVVTELGTRVDPDTSLIRVDGVRV 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLL 124
              +       +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LL
Sbjct: 68  ILDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGNKNLFHVGRLDADTEGLILL 127

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQK 183
           TNDG LA  L  PS +  + Y     G V +     L+ GI ++      D    +D   
Sbjct: 128 TNDGELAHRLMHPSHEVPKTYLATVAGTVPRGLGKKLRAGIELEDGPVRVDGFAVVDAIP 187

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G    V V L EG+NR ++++     + V  L+RI  G   LG    GS R + +  + +
Sbjct: 188 GKT-LVRVTLHEGRNRIVRRMLAAVGFPVQALVRIDIGGVSLGEQRPGSVRALRRDEIGQ 246

Query: 244 Q 244
            
Sbjct: 247 L 247


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 105/237 (44%), Gaps = 6/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +Q +    R+ K +  A   +R+E   ++    V V+ ++ +  A  +  T  +E  G  
Sbjct: 20  LQADEVSMRLDKFLCDALGTTRKEATMLLKSGEVTVDDLVQKSGAFKLKETSRVEWQGRE 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           +  A   R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T
Sbjct: 80  IT-AHGPRYIMMHKPDGVVCSHEDGFN-QTAFILLDEVNIQDLHFAGRLDVDTTGLLLIT 137

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG  +  +  P  +  + YRV     +  D       GI ++G     +   L+    S
Sbjct: 138 DDGQWSHRVTSPKHKCEKTYRVWLADPIQADYAEQFTNGIELRGERELTLPAQLEV--VS 195

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
              V + + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++ +
Sbjct: 196 ETEVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEEEI 252


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 101/238 (42%), Positives = 145/238 (60%), Gaps = 7/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ K++A AG+ SRRE+E+ I   RV VNG + +         D I VDG  +     
Sbjct: 2   SEKLQKILANAGLGSRREIEKWIEGGRVSVNGSIAK-LGERATDKDTIRVDGRIISIISA 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           +   TR+  Y+KP+G V+T  DP+GR+TVFDNLP+  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-LLAGSTREVSKKILREQ 244
           W  VGL EGKNRE++K++E    +V+RL+R+ YGP  L T L  G   ++ ++ + + 
Sbjct: 181 WYEVGLAEGKNREVRKLWESQGVEVSRLMRVQYGPISLPTRLSRGRWVDLEEQEINDL 238


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/297 (35%), Positives = 145/297 (48%), Gaps = 17/297 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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+         
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDFAQTNYLR 241

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           G        V L     S   + +DR  + +       R  K  SQ  G  +     
Sbjct: 242 GL-------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQIAGGRRSGGRN 288


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 114/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELEILLA 237


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 101/269 (37%), Positives = 140/269 (52%), Gaps = 12/269 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEITPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 E--QLGPHLLEEAQVNLDAPIYSSETLVR 269
           E  QL P    +  V  D     +  + R
Sbjct: 242 ELVQLAPETTSKVAVEKDRRRMKANQIRR 270


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 115/239 (48%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        +  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEIFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ + +  +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVEIFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELEILLA 237


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 107/288 (37%), Positives = 154/288 (53%), Gaps = 12/288 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G  L  E +  +D       T +R     + +     T+ 
Sbjct: 304 VNYLRELVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 100/237 (42%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     + ++       GI + G         L+  +     V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEQPISEETEEKFLAGIQLNGEKTLTKPAKLEIIEP--QIVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F      V  L R   G   L   L AG  R ++   +     P  
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGEIYLDPALEAGEYRALTDSEINSIQMPRF 235


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 99/279 (35%), Positives = 145/279 (51%), Gaps = 6/279 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            ++    ++ KV+A  G+ SRR++E +I Q RV VNG+       ++  TD + ++G P+
Sbjct: 23  ADDEDTMKLHKVLADVGMGSRRDMEDLIIQGRVSVNGLPA-HIGQSIGPTDQVRINGKPV 81

Query: 68  RKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
            +    +  R+ +YHKP G + + SDP+GR TVFD LP     R I+VGRLD NTEGLLL
Sbjct: 82  HRKIQTKPPRVIMYHKPAGEIVSQSDPEGRPTVFDRLPKPRQGRWIAVGRLDFNTEGLLL 141

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T  G LA  L  P     R Y VR  G + Q+   LLK GI +       +++ +   +
Sbjct: 142 FTTSGELANRLMHPRYGVEREYAVRILGDLSQENTVLLKSGITLDDGQAKFLRLAIGGGE 201

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           G+N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G   E+    + 
Sbjct: 202 GANRWYHVALSEGRNREVRRMFEAVGHTVSRLIRTRYGIFLLPPRLRRGKWEEIEAGDIY 261

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
             +    L+  Q        +S +  RDR  I  +   D
Sbjct: 262 NLMKSAGLKMPQPQDKGRNPNSNSNGRDRRPIGEDFQPD 300


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 123/234 (52%), Gaps = 7/234 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
            +R+ KV++ AG  SR++V+++I +  V+VNG ++  A   V    D I V G  L   E
Sbjct: 5   TERLDKVLSMAGYGSRKDVKKIIKRGEVEVNGRVVTDAGTPVAPAVDSISVSGELLIFKE 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
                + +KP G+++   D    +TV D L   FS   +  VGRLD + EGLLLLT+DG 
Sbjct: 65  HI-YIMMNKPQGVISATHDRRE-TTVIDLLEDEFSHRNLFPVGRLDKDAEGLLLLTDDGQ 122

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  +VY V   G++ ++ +   K+G+ +        ++ +  + G  +  
Sbjct: 123 LAHRLLSPRKKVEKVYYVEVKGRLVEEDVKAFKEGVFLGDYRALPAKLEIL-EAGEVSSA 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V + EGK  +IK++ +    +V  L R+S GP +L   L  G  RE++ + +R
Sbjct: 182 LVTIYEGKFHQIKRMMKARGKEVTYLKRLSMGPLKLDENLEPGEWRELTDEEIR 235


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   R  +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRACINGEVCTHGAL-VNEGDIVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++      + D +     R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAE-HIEDNIIDYI-DYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    + + +   + 
Sbjct: 118 QILHGDHEHEKEYVVAVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVNQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELEILIG 227


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/317 (32%), Positives = 163/317 (51%), Gaps = 13/317 (4%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K + +  E+  P ++ K++A AG+ SRR++E +I Q RV VNG+        ++ TD + 
Sbjct: 203 KVRELTAEDDAP-KLHKILADAGLGSRRDMEDLILQGRVSVNGLPA-HIGQRILPTDQVR 260

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD N
Sbjct: 261 VNGKLIQRKLPSKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFN 320

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+ T  G +A     P     R Y VR  G++ +     L +GI +       ++ 
Sbjct: 321 TEGLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELPESDRQKLLQGIRLDDGEANFLRC 380

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 381 ADGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 440

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR-----PNIISEVPDDFTRMKKNSSQ 291
           S + +R  +G   L+    +      S      +R     P ++  +   FT      S+
Sbjct: 441 SAEDVRGLMGLLGLKVPSASASGGQGSQGGRQGNRRREAQPVLMGPMSSGFTGEATFQSR 500

Query: 292 KNGLSKQKKLATPVHRR 308
             G+    + A P  RR
Sbjct: 501 GQGIENGNR-AMPAPRR 516


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD NT GLLLLTNDG L
Sbjct: 61  YIYLMMNKPQGVVSATFD-NYDETVIDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGI++  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGEYRELTDEEI 232


>gi|324328441|gb|ADY23701.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 229

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE + +I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDSLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T +D  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAADHIEGNIIDYINYPG---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRVFGFTVKKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>gi|284007498|emb|CBA72981.1| ribosomal large subunit pseudouridine synthase B [Arsenophonus
           nasoniae]
          Length = 322

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 98/300 (32%), Positives = 149/300 (49%), Gaps = 11/300 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+AR G  SRRE+E  I   R+ V+G L      + V +   I +DG  LR  E
Sbjct: 22  SEKLQKVLARCGYGSRREIESFIQSGRISVDGQLATLGDRIEVKANTKIRLDGHLLRIKE 81

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + TH DP+GR TVFD LP    SR I++GRLD+NT GLLL T 
Sbjct: 82  AEKSICRILAYYKPEGELCTHHDPEGRPTVFDRLPKLTGSRWIAIGRLDVNTCGLLLFTT 141

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P  +  R Y VR  G+++  K+  L KG+ ++        +     +G N
Sbjct: 142 DGELANRLMHPRHEVEREYAVRVFGEINDAKIRQLTKGVQLEDGEASFKTLKFRGGEGMN 201

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 202 QWFNVTLTEGRNREVRRLWEAVGIQVSRLIRVRYGDIYLPKGLPRGGWTELGLVQINYLR 261

Query: 243 EQLGPHLLEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           + +G      +++ ++          +R      ++V       K+ +    G +K  + 
Sbjct: 262 QLVGLSDETASKIAVEQDRRRIKANQIRRAVKRHTQVSSMRVANKRATGAAKGHNKPARK 321


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 72/248 (29%), Positives = 122/248 (49%), Gaps = 12/248 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + +    QR+ K++   G  +R E+++ + Q RV +NG++++ + +      D +E+DG 
Sbjct: 1   MSKGKKTQRLDKILGHLGYGTRSEIKKYVKQGRVTINGVVVKDSGIQCNPDVDVVELDGE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLL 123
            +   E     + HKP G+++   D     TV D LP  F       VGRLD +TEGLLL
Sbjct: 61  QIFYRE-FVYLMLHKPPGVISATED-MREKTVIDLLPVDFQVFSPFPVGRLDKDTEGLLL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT---- 178
           LTNDG LA  L  P     + Y     G V  ++    ++G+ +  G      ++     
Sbjct: 119 LTNDGQLAHDLLSPRKHVPKTYEAVVLGHVGDEEAARFREGVELDDGYVTLPAELKVLEH 178

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            +D      + V + + EGK  ++K++FE    +V  L R+S GP  L  +L  G+ RE+
Sbjct: 179 GIDADGTRISRVQLTISEGKFHQVKRMFEAVGSRVIYLKRLSMGPLVLDESLPLGAFREL 238

Query: 237 SKKILREQ 244
           ++  L+  
Sbjct: 239 TESELQSL 246


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/306 (33%), Positives = 152/306 (49%), Gaps = 12/306 (3%)

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----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLL 123
             E      R+  Y+KP G + T  DP+GR TVFD LP +  +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-GTLLAGSTREVSKK--- 239
           G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +   
Sbjct: 182 GINQWYNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDINLPKGLPRGGWTELGLEQTN 241

Query: 240 ILREQ--LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            LR+   LG  ++ +  V  D     +  + R              +   +SS++N   K
Sbjct: 242 YLRQLVGLGDEMVTKVAVERDQRRIKANQIRRAVKRHAKVASRPAGKRPASSSRQNAGRK 301

Query: 298 QKKLAT 303
                 
Sbjct: 302 TTPKGR 307


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/297 (35%), Positives = 145/297 (48%), Gaps = 17/297 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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-------L 234

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                    V L     S   + +DR  + +       R  K  SQ  G  +     
Sbjct: 235 SQTNYLRGLVELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQIAGGRRSGGRN 288


>gi|86130476|ref|ZP_01049076.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85819151|gb|EAQ40310.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 260

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 118/260 (45%), Gaps = 9/260 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AERT 73
           R++K ++ AG  SRR  +++I Q RV +NG +       +   D + V+G  +    E+ 
Sbjct: 8   RINKYLSEAGYCSRRAADKLIDQGRVTINGKVP-EMGTKITEGDEVRVNGELITSSTEKP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V T      +  + D + +  SR+  +GRLD  +EGL+ LTNDG +   
Sbjct: 67  VYIALNKPVGIVCTTDTRVEKDNIIDFI-NYPSRIFPIGRLDKPSEGLIFLTNDGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +    +  +  G+ I         V    ++ S     + L
Sbjct: 126 ILRARNNHEKEYEVWVDKPITPSFIQQMSNGVPILDTVTRKCHV----EQLSRFSFKIIL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E  +++V RL R      +L  +  G  R +S   + E++   + + A
Sbjct: 182 TQGLNRQIRRMCEALDYEVTRLKRNRIMNIEL-DVPVGKWRYISDTEM-EEINRLVEDSA 239

Query: 254 QVNLDAPIYSSETLVRDRPN 273
           + + DAP       +R   N
Sbjct: 240 KTHTDAPKEPRHPNLRRNRN 259


>gi|329576942|gb|EGG58425.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 257

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 75/255 (29%), Positives = 124/255 (48%), Gaps = 10/255 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M     ++E     R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD 
Sbjct: 1   MSQAIFLKERGMTMRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQ 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           I + G  L   ++   ++ HKP G+++   D     TV D L     R  +  VGRLD +
Sbjct: 61  IALMGEILTY-QKFFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ 176
           TEGLLLLTNDG LA  L  P     + Y     G V  +   L  +G  +  G      +
Sbjct: 119 TEGLLLLTNDGQLAHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSR 178

Query: 177 VTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
           + ++T  ++   + V + ++EG+  ++K++       V  L R+  G   L  TL  G  
Sbjct: 179 LVIETINEEEGTSVVRLVIQEGEFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEY 238

Query: 234 REVSKKILREQLGPH 248
           R +++  L +QL P 
Sbjct: 239 RPLTEAEL-QQLQPK 252


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 107/288 (37%), Positives = 155/288 (53%), Gaps = 12/288 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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-GTLLAGSTREVSKK- 239
             G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKSLPRGGWEEMGLEQ 303

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G  L  E +  +D       T +R     + +     T+ 
Sbjct: 304 VNYLRELVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>gi|229030086|ref|ZP_04186150.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228731256|gb|EEL82174.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 248

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 119/245 (48%), Gaps = 7/245 (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 S+   +  + D +     R+  +GRLD +++G
Sbjct: 60  RVNGEQLRIARDHVYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLTNDG +   +     +  + Y V     +  D L  +  G+ I G      ++T  
Sbjct: 118 LILLTNDGDIVNEILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT-- 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             + S     + L +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 176 --QLSKYEFNIILTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 233

Query: 241 LREQL 245
            R   
Sbjct: 234 KRRLF 238


>gi|221134960|ref|ZP_03561263.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Glaciecola sp. HTCC2999]
          Length = 331

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 104/311 (33%), Positives = 158/311 (50%), Gaps = 17/311 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           ++ KV+A  G+ SRRE+E  I Q R+ VNG +       V  +D I VDG  L++ ++  
Sbjct: 4   KLQKVLANQGVGSRREMETWIEQGRISVNGTIAT-LGDRVEPSDQIRVDGHLLKRDQKAP 62

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
             R+ +Y+KP G + + +DP GR TVFD LP+I S R I+VGRLD+NT GLLL TNDG L
Sbjct: 63  VCRVLMYNKPEGELCSRTDPLGRQTVFDRLPNIQSGRWIAVGRLDLNTAGLLLFTNDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
           A  L  P  +  R Y VR  G+V+   L LL+ G+ ++       ++      ++  NAW
Sbjct: 123 ANRLMHPRHEVEREYAVRVFGEVEPKTLKLLESGVELEDGLAKFTKIIARPNEEESINAW 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE---- 243
             V L EG+NRE+++++E    +V+RLIR+ YGP  L   L  G+  E+    +      
Sbjct: 183 YNVSLSEGRNREVRRLWESQGVQVSRLIRLRYGPLSLQKRLPQGAWIELELNDVNALRKQ 242

Query: 244 -QLGPHLLEEAQVNLDAPIYSS----ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            QL P       VN +   ++        V+   +  ++ P        +   K    ++
Sbjct: 243 VQLPPETETLVGVNDNKLNHTKLSRMRKSVKKHKDRNAKAPIKGEGESASDDTKRTSRRK 302

Query: 299 KKLATPVHRRN 309
                P   RN
Sbjct: 303 PNNGKPQANRN 313


>gi|295095683|emb|CBK84773.1| ribosomal large subunit pseudouridine synthase B [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 291

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 101/295 (34%), Positives = 152/295 (51%), Gaps = 19/295 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V ++    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 DGELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGIN 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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           + +G      ++V ++            R    +++     R  + SS +   S+
Sbjct: 242 DLVGLTPETTSKVAVEK---------DRRRMKANQIRRAVKRHSQVSSNRRSGSR 287


>gi|196233446|ref|ZP_03132289.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222442|gb|EDY16969.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 237

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 123/234 (52%), Gaps = 5/234 (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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            +G  R+I+ +     ++V RL RI  GP ++G +  G  R ++ K +    GP
Sbjct: 176 TQGIKRQIRLMLYDLGYEVERLARIRLGPLKIGEMRPGEWRLLTSKEIAALKGP 229


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 111/233 (47%), 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  + D +     R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TELHIRGNIVDFV-GHKERIFPIGRLDKDSEGLILLTNDGDVVNP 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V  + +  +  G+ I G      QVT   ++       + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPVTAEFVKGMSSGVRILGSMTLPCQVTRVAER----VFRIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EGKNR+I+++ E F + V +L RI      LG L  G  R++++    E  G
Sbjct: 174 TEGKNRQIRRMCEAFGYHVRKLQRIRIMNIHLGQLPTGKWRDLTETEKAELFG 226


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 147/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLVSVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQMSGGRRSGGRN 288


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 109/234 (46%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDEIYFEDQLLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLNKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYATACAEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  +   +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGNVVLDQSLDEGEYRPLTQSEIESLV 231


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 92/237 (38%), Positives = 133/237 (56%), Gaps = 4/237 (1%)

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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLG 246
           L EG+NR+++++ +     V  L RI YG   +  L  G  R ++++    LR+ + 
Sbjct: 183 LHEGRNRQVRRMCKAVGHPVLELTRIQYGNLTIDGLAPGEIRPLTEEEERILRQLVA 239


>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 =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 99/356 (27%), Positives = 165/356 (46%), Gaps = 10/356 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 173 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 231

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++ E     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 352 GGGEGTNHWYHVALAEGRNREVRRMLEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 411

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK-KNSSQKNGLSK 297
             +R  +    L+      D          R +P+ +        R     +  +    +
Sbjct: 412 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREPVLTTHGQLDQPR 469

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
           + +                A        S  G R+ +  R+ S+    + +R + K
Sbjct: 470 RGRRGPAGGGFGAGLGGGYAGLPGYGGASRQGGRDVDGNRA-SYGGAGANKRGAGK 524


>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 =  261 bits (667), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 74/348 (21%), Positives = 139/348 (39%), Gaps = 14/348 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   NDSTTRLNKYISESGICSRREADRYIEQGNVYINGKRA-EVGDRVAPGDTVKVNGQIIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E       +KP+G+V+T    +  + V        +R+  +GRLD +++GL+ LTN+
Sbjct: 62  QEPEDFVFIALNKPVGIVSTTESSERNNIV--RFVGHSTRIFPIGRLDKDSQGLIFLTNN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V  +  +  + +  +  G+ I G      +V     K S  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVEVNKPIRDNFIEGMANGVPILGTMTKKCKVK----KESPT 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L EG NR+I+++ E+F + V  L R+      L  L  G  R++++K L      
Sbjct: 176 VFRITLVEGLNRQIRRMCEYFGYDVVALERVRIMNVDLKGLATGDWRDLTQKELNGIF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             ++++     A   +++             P + T  KK +++ +    ++       +
Sbjct: 234 DAIKDSSSEAPAGRKTTQKRGGKPGGSGQNKPGNKTNSKKPAAKASKSGPKRGGPHKAKK 293

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF---PSKRSLRRTSA 352
            +   N            S     +      PS       +   +  A
Sbjct: 294 TSGNPNTKHPPKPPGGKPSGKPSPKGKAGGKPSGKPMKGGKPSPKGKA 341


>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 =  261 bits (667), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +     + V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGEL-VSDGDVVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 RILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  261 bits (667), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 91/269 (33%), Positives = 143/269 (53%), Gaps = 13/269 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 122 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 180

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 301 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 360

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETL 267
             +R  +       + V L AP+      
Sbjct: 361 AQVRRLM-------STVGLKAPVEEKGKR 382


>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 =  261 bits (667), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  261 bits (667), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 103/229 (44%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP G+V +H D   ++ +          +   GRLD++T GLLL+T+DG  +  
Sbjct: 60  RYIMMHKPDGVVCSHEDGFNQTALTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + +
Sbjct: 120 VTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 178 HEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 131/231 (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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSASSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|163942282|ref|YP_001647166.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
 gi|163864479|gb|ABY45538.1| pseudouridine synthase [Bacillus weihenstephanensis KBAB4]
          Length = 229

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   R  +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRACINGEVCTHGAL-VNEGDIVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++      + D +     R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAE-HIEDNIIDYI-DYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    + + +   + 
Sbjct: 118 QILHGDHEHEKEYVVAVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVNQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELEILIG 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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/239 (33%), Positives = 121/239 (50%), Gaps = 11/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
           +R+ K+I+  G+ASRR  E MI   RVKVNG             D IE+DG  L      
Sbjct: 3   ERLQKIISHWGVASRRHAEEMILSGRVKVNGDQAYLGQKADPKCDRIEIDGRALHPSSQP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 128
           +    L +KP+G+V+T ++P GR TV D LP        +  VGRLD ++ G LL+TNDG
Sbjct: 63  QPLYLLLNKPLGVVSTCAEPQGRKTVLDLLPRQLQVGQGLHPVGRLDTDSTGALLITNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNA 187
            L  +L  P     + Y+V   G   +  L   ++GI++ G      +V    + +GS  
Sbjct: 123 ELTFLLTHPRYHVAKTYQVLVQGCPPESVLEQWRQGILLSGKNTLPAKVRRIGKPRGSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKIL 241
            + V LREG+NR+I++V E   + V +L R + GP  L +     L +G  R +    +
Sbjct: 183 LLEVVLREGRNRQIRRVAEALGYPVVQLHRTAIGPIYLNSTGKPELASGEYRSLKNSEV 241


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 79/231 (34%), Positives = 114/231 (49%), Gaps = 1/231 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR  E  I   RVKV+G +          +  I VDG PL   
Sbjct: 1   MTRQRLQKLIAAAGLCSRRTAEDWIDAGRVKVDGRISSLGDQADPESQLIHVDGRPLSFR 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
               + L +KP G+++T  DP GRSTV D LP    + +  VGRLD ++ G LLLT+ G 
Sbjct: 61  GEPTVLLINKPAGVISTCRDPRGRSTVLDLLPQQLRQGLHPVGRLDADSRGALLLTDYGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G      L   ++G+ + G      +V +  ++     +
Sbjct: 121 LTLRLTHPRYDHAKTYRVWVEGTPLDTSLQRWRQGVTLDGTRTRSAEVRVLQRRSDRTLL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V L EG+NR+I++V E     V  L R++    +LG L  G  R +S+  
Sbjct: 181 EVVLLEGRNRQIRRVAELLGHPVVDLQRVAIAGLRLGALPEGRWRRLSRGE 231


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 73/245 (29%), Positives = 125/245 (51%), Gaps = 1/245 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           +  ++  ++    R+ K++A AGIASRR  E ++    V+VNG ++ R    V    D +
Sbjct: 6   ERDDLPLDDEGLIRLQKLLALAGIASRRGSEILMLNGEVEVNGEVVTRLGTKVDPGKDVV 65

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V G  L         + +KP G+V+T SDP+GR  + D +     R+  VGRLD +TEG
Sbjct: 66  RVGGKRLPPISGKVYLVLNKPRGVVSTMSDPEGRRNLSDLVADRPERLFHVGRLDTDTEG 125

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L++LTNDG  A  L  PS +  + Y     G++  +    L  G+ ++       +  + 
Sbjct: 126 LIILTNDGDFAHRLAHPSYEVDKTYVAEVKGEIFPNVRKRLLAGVTLEDGPVTVTKARIM 185

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +   + + + + EG+NR ++++ +     V RL R   GP +LG +  G  R++S++ 
Sbjct: 186 ETRKDKSIIELVIHEGRNRIVRRLLDHLGHPVTRLTRTRIGPVRLGAMKPGDMRDLSREE 245

Query: 241 LREQL 245
           L E L
Sbjct: 246 LGELL 250


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 119/247 (48%), Gaps = 16/247 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            R+ + +      SR EV++MI   RV V+G +   A   +  +   + +DG  +  A  
Sbjct: 10  MRLDRYLVEMKKGSRSEVKKMIKSGRVSVDGEICREAERKIQPSASEVSLDGTQVGYAA- 68

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G+V+   D   ++ V     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 69  YEYFMLNKPAGVVSATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGKLAH 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------ 186
            L  P     + Y  R  G++ ++ +   K+G+ ++      +   L  QK S       
Sbjct: 129 RLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDG-TRTLPARLVIQKASETAEDDG 187

Query: 187 ------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
                 + + + + EGK  ++K++FE    +V  L R+S G  +L  +L  G+ R ++++
Sbjct: 188 KADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLDESLAPGAYRRLTEE 247

Query: 240 ILREQLG 246
            + +  G
Sbjct: 248 EISKLQG 254


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 89/247 (36%), Positives = 134/247 (54%), Gaps = 6/247 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   DH++V+
Sbjct: 87  KRVLAPLAETPKLHKVLAQAGMGSRLEMEQLIMEGRITVNNEPA-HIGQRIQFGDHVKVN 145

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+R    A   R+  YHKP+G V TH DP  R TVF  LP +F  +  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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 266 GGGEGANCWYRVTIAEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWMELDE 325

Query: 239 KILREQL 245
             ++  +
Sbjct: 326 SDIKSLM 332


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 104/230 (45%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  + + Q  V +NG + +  A  V   D I  DG  L   +  
Sbjct: 1   MRLDKFLAEHTGLTRSQATKALRQSAVTINGKIEKSGATKVSPQDAIYFDGELLTWLDVG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           +  +++KP G V +H D D   +++       S R+ S GRLDI+T GL+LLT+DG  + 
Sbjct: 61  QYLMFNKPQGYVCSH-DEDEHPSIYQFFDYPLSARLHSAGRLDIDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+ +      +GI+++G         L+     N  V + 
Sbjct: 120 RVTSPKHHQPKTYLVTLADPVEANYAQACAEGILLRGEKDPTKPAVLEILDNYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R ++ + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVLGLHRWKIGNLTLDDNLAEGDFRVLNAEEI 227


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTDPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +     GI +  G      ++ + T       +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVTLADVEAFAAGIELDDGYTCKPARLEIITPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F     KV+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 NVTIQEGKFHQVKRMFAARGKKVSYLKRISMGNLQLDESLGLGEYRPLTESEL 227


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 88/257 (34%), Positives = 131/257 (50%), Gaps = 11/257 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ KV+A+ GIASRRE E MI + RV++NG L E         D I VDG  +      R
Sbjct: 4   RLQKVLAQWGIASRREAEEMIRRSRVQINGTLAELGQKVNPEKDIITVDGKSVSAQRHPR 63

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
               L +KP G+V+T  DP GR TV D LP    +   +  VGRLD ++ G L+LTNDG 
Sbjct: 64  LTYLLLNKPTGVVSTCYDPQGRKTVLDLLPEELRKGPGLHPVGRLDADSTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y+V   G   +  L + ++G+++ G      +V+L       + +
Sbjct: 124 LTFRLTHPSHSIPKTYQVLVKGHPPKAVLEMWREGVLLDGRKTRKAKVSLLESLAEKSRL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILRE- 243
            + L+EG+NR+I++V E   + V +L R + G  QL T     L AG+ R +    +R  
Sbjct: 184 EIVLQEGRNRQIRRVAEQLGYPVIKLHRTAIGSIQLQTSKQPLLRAGNYRILRDDEIRSL 243

Query: 244 QLGPHLLEEAQVNLDAP 260
           Q     +   ++N   P
Sbjct: 244 QEQVKNIPTKRINFQNP 260


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/330 (27%), Positives = 145/330 (43%), Gaps = 6/330 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D ++V+
Sbjct: 161 KRVLLPQVETPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRIQFGDQVKVN 219

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+R        R+  YHKP+G V +H DP  R TVF  LP +   +  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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 340 GGGEGANCWYRVTIAEGRNREVRRMLEAVGHAVSRLIRIRYGAMVLPRGLKRGTWLELDE 399

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +R            ++   P  +     R+R            R  +  +        
Sbjct: 400 RDIRALAQAAGARAPALSTRTPTDARAGKQRERSGPPMGNGPRRGRSPQGPAAGARAQNP 459

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDS 328
           ++           ++           +  S
Sbjct: 460 RRDGGGQGVGAGGNHAGPRAAAQPDPMQTS 489


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEANSCSRRETDRLIKAGRVAINGEICTHGAL-VNEGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                +HKP+G+  T ++  +G    + N P    R+  VGRLD  +EGL+LLTNDGG+A
Sbjct: 60  KVYIAFHKPVGITCTAAEHIEGNIIDYINYPE---RIFPVGRLDKASEGLILLTNDGGIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V          +N +  G+ I+       +VT    +   +   +
Sbjct: 117 NQILHGDHEHEKEYVVTVDKSFTDWFINEMSSGVKIKDGITKPCKVT----RVDKSTCRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R      +L  L  G  R+++ + L   +G
Sbjct: 173 VLTQGMNRQIRRMSRAFGFTVTKLKRERIMNIELNDLEVGKWRDITAEELELLIG 227


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/258 (34%), Positives = 134/258 (51%), Gaps = 6/258 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           R+ K++AR G+ SRRE+E MIA  RV +NG+  +         D I +DG  +R      
Sbjct: 35  RLQKLLARNGLGSRREIEDMIAAGRVSINGVTAK-PGDRAGPGDMIRIDGKIIRFRLAAL 93

Query: 73  -TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
             R+ +YHKP G + +  DP GR +VFD LP    S+ I++GRLD NT GLL+ T DG L
Sbjct: 94  LPRVIIYHKPEGEIVSVRDPQGRPSVFDKLPHIRSSKWIAIGRLDFNTSGLLIFTTDGTL 153

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  Q  R Y VR  G++  +++  L  GI ++       Q+  +   G+N W  
Sbjct: 154 ANHLMHPRYQMEREYAVRIVGELTPEQITRLTTGIELEDGLAKFDQLLDEGGTGTNHWYR 213

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHL 249
           + L+EG+NRE++++FE     V+RLIR+ +GP  L   L  G   E+    + + L    
Sbjct: 214 IMLKEGRNREVRRMFEALGLTVSRLIRVRFGPVNLPPRLKRGMWIELMDIEVEQLLKLVS 273

Query: 250 LEEAQVNLDAPIYSSETL 267
              A +    P   +   
Sbjct: 274 QPGAGIPDKPPSMQAGRR 291


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 136/260 (52%), Gaps = 2/260 (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 ++   L +KP G +TT+ DP+GR TV+  L  +   +  VGRLD++T 
Sbjct: 61  VTLEGKPLKAATKS-YILLYKPKGYLTTYRDPEGRPTVYALLGDVGKWLSPVGRLDLDTS 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 ILREQLGPHLLEEAQVNLDA 259
            + E  G    + +    D 
Sbjct: 240 EVHELRGQAAKKASGPARDK 259


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 134/243 (55%), Gaps = 5/243 (2%)

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
            ++    L++KP  ++T+ SD  GR  V D    I +R+  VGRLD +T GLLLLTNDG 
Sbjct: 62  EDKL-YILFYKPAQVITSVSDDRGRKVVTDYFKQIKTRIYPVGRLDYDTSGLLLLTNDGE 120

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

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--EQL 245
            V + + EG+NR+++++FE F  +V +L RI +GP  L  L AG  R ++   ++   Q+
Sbjct: 181 LVEITITEGRNRQVRRMFEHFGHQVTKLQRIEFGPLNLKGLNAGEGRVLTPHEVKMIRQI 240

Query: 246 GPH 248
             H
Sbjct: 241 AEH 243


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 105/301 (34%), Positives = 149/301 (49%), Gaps = 23/301 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV ++G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSIDGRIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288

Query: 303 T 303
           +
Sbjct: 289 S 289


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 114/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  L  P     + Y  +  G + Q+ +    KGI ++       ++ L     + + + 
Sbjct: 119 AHDLLSPKRHVDKTYLAQVKGIMTQEDVETFAKGIPLKDFTCKPARLELVSIDAEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELEVLLA 237


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 55/235 (23%), Positives = 101/235 (42%), Gaps = 3/235 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +D        +G+ + G         L+        V + +
Sbjct: 121 ITSPRHHCEKTYLVTLEQPLDPQTAEQFAQGVQLHGEKDLTKPARLEA--LDEHQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
            EG+  ++K++F     +V  L R   G   L   L  G  R +S   +   L P
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVALHRERIGAIALDAALAPGEYRALSDDEVASVLAP 233


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 101/287 (35%), Positives = 144/287 (50%), Gaps = 11/287 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           T +++ KV+ARAG+ SRRE+E  IA  RVKVNG +       V   D +  D  P+    
Sbjct: 4   TSEKLQKVLARAGLGSRREMETAIADGRVKVNGQVAT-LGDRVELRDKVAFDDRPVALRG 62

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLLL T 
Sbjct: 63  ADEVPRRVIMYNKPEGELCTRKDPEGRRTVFDRLPRLKGERWIAIGRLDINTSGLLLFTT 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PSTQ  R Y VR  G+V  D +  + +G+++         V     +G N
Sbjct: 123 DGELANRLMHPSTQIEREYAVRVMGEVTMDHIKAMVEGVMLDDGPARFTDVQEFGGEGIN 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V + EG+NRE+++++E  N  V+RL R+ YG   L     AG   E+ +  + +  
Sbjct: 183 TWFHVVIMEGRNREVRRLWESQNLTVSRLKRVRYGNIFLDKRAKAGEWVELGQDEIDDLA 242

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
               L   +V    P  + +   R   +     P    R  K+S  +
Sbjct: 243 EQAGLPSRKV----PELTPDEKNRWSRDKNKRRPVQGVRKPKSSRSR 285


>gi|323488402|ref|ZP_08093649.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
 gi|323397909|gb|EGA90708.1| pseudouridine synthase [Planococcus donghaensis MPA1U2]
          Length = 237

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 111/233 (47%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++  G  SR+EV+ ++  + V+VNG ++    V+V   TD + V G  +   E 
Sbjct: 1   MRLDKYLSNMGHGSRKEVKVLLKSKAVEVNGEIVRDPKVHVNEHTDLVSVGGEAVTYTE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               L +KP G+++   D     TV D L           VGRLD +TEG LLLTNDG L
Sbjct: 60  FIYLLMNKPQGVISATED-KYDKTVIDLLGKDEQHFEPFPVGRLDKDTEGFLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y     G V ++     KKG+V+  G       + +       + +
Sbjct: 119 AHELLSPKKHVDKTYFAHVEGVVTEEDTEAFKKGVVLDDGYETKPASLNILDSAVV-SKI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EGK  ++K++FE    +V  L R+S GP  L   L  G  R ++++ +
Sbjct: 178 ELTITEGKFHQVKRMFESVGKRVVYLKRLSMGPLSLDPELELGEYRHLTEEEM 230


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 100/347 (28%), Positives = 159/347 (45%), 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  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           G  +++     + R+  YHKP G V +  DP+GR TVF +LP    ++  +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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 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      +    D P         +  N      D     +    +  G  +Q
Sbjct: 401 SLVQALQGRSGEAPSGA-GDRPARR-----PNGQNQGGRRNDSRGSGRGGRGKGQGGDQQ 454

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +       R  + +    +  + S   S  G    +    P   S+R
Sbjct: 455 QPGPDSYARTTVEALFGKSPVVRSGGGSWGGAGNFSTGNKPGGQSRR 501


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 147/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIARLGDRVEVTPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETTSKVAVEKDRRRMKAN---QIRRAVKRHSQMSGGRRSGGRN 288


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 90/288 (31%), Positives = 150/288 (52%), Gaps = 7/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A AG+ SRRE+E +I   RV VNG         ++ TD + ++
Sbjct: 178 KRVLAPEDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRILPTDQVRIN 236

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR++VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +G   L   L  G   E+ +
Sbjct: 357 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGSIPLPRGLKRGRWEELDE 416

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R+ +    L+ A  +       +    R +P+ +        R  
Sbjct: 417 AQVRKLMATVGLKVA-ADEKGKRGGAGQAERRQPDPMQTSMGFLNREP 463


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 113/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDTKHR-TVLDLLDDYARAKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     + Y  +  G + Q+ ++   KGI ++       ++ L +   + + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTQEDVDAFAKGIPLKDFTCQPARLELVSVDPEKNQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L     
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEELEVLFA 237


>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 =  260 bits (666), Expect = 2e-67,   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|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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/256 (32%), Positives = 130/256 (50%), Gaps = 8/256 (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 D +P +   +  VGRLD ++EGLL+LT DG 
Sbjct: 61  PTPHVTYMLHKPAGFVTTAQDELGRRTVLDAMPPV-PGLHPVGRLDKDSEGLLILTTDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  +VYRV    +  + +L  L++G+ ++    G  +  ++   G    +
Sbjct: 120 LTLRLTHPRFEHEKVYRVWCFPEPGEQELAALRRGVELE---EGFARAEVEPAPGGALAL 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
              LREG+ R+++++F      V+RL+R   G   LG L  G   ++ ++ L   L P  
Sbjct: 177 ---LREGRKRQVRRMFAEVGCPVDRLLRYRVGGLWLGDLGPGEFVQLGEQELDWLLQPGT 233

Query: 250 LEEAQVNLDAPIYSSE 265
            +++    +    +  
Sbjct: 234 RQQSPAQREQEALTRR 249


>gi|322807584|emb|CBZ05159.1| ribosomal small subunit pseudouridine synthase A [Clostridium
           botulinum H04402 065]
          Length = 238

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD NT GLLLLTNDG L
Sbjct: 61  YIYLMMNKPQGVVSATFD-NYDETVVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGI++  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           QRV KV++  G  SR E+++   Q  V VNG  +    + V +  D I  +G  +   E 
Sbjct: 5   QRVDKVLSNLGYGSRAELKKFCKQGLVFVNGKAVSNPGLQVDTDIDEIVFNGEKINYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++   D      V D +   +       VGRLD +TEGLL+LTNDG L
Sbjct: 64  FIYLMMNKPDGYISATFD-KHDPIVLDLIDDEYLVFEPFPVGRLDKDTEGLLVLTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           A  +  P     + Y  +  G+V ++ +   K+G+V+    Y  M   L   K  + + +
Sbjct: 123 AHRVLSPKKHVPKTYYAKIDGKVTEEDIEAFKQGVVLDDG-YETMPSELVILKSDDISEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE     V  L R+S G  +L  TL  G  RE++ + ++
Sbjct: 182 ELTIHEGKFHQVKRMFESVGKTVVYLKRLSMGALKLDETLELGEYRELTDEEVK 235


>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 =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 117/235 (49%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V VNG L+++A   V  TD ++V    +   E+ 
Sbjct: 1   MRIDKYLANMKVGSRKEVHDLIKAKKVTVNGQLVKQAKQQVADTDIVKVADETIAY-EQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G++T   DP  + TV D +     +  +  VGRLD +T GLLLLTNDG L 
Sbjct: 60  HYFMLNKPAGVITATEDPQ-QKTVLDLIEHKDRYQGLSPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    +V  + +    KG+ +  G      Q+ +D       +  
Sbjct: 119 HNLLSPKKHVAKTYFVELDYEVSDELIVNFAKGVTLADGTKVSPSQLKIDKSNKKQGF-- 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EGK  +IK++F  F+  V RL RIS G   L   LL G  R+++K  +   
Sbjct: 177 ITIHEGKFHQIKRMFGLFDLGVVRLKRISMGNLSLDENLLLGKYRKLTKAEISAL 231


>gi|218512381|ref|ZP_03509221.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli 8C-3]
          Length = 244

 Score =  260 bits (666), Expect = 2e-67,   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|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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 117/239 (48%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGKVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A  L  P     + Y V+  G + Q  +++  +GI ++       ++ L +   + + + 
Sbjct: 119 AHALLSPKRHVNKTYLVQVKGIMTQGDVDIFAEGIPLKDFTCQPARLELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELENLLA 237


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 108/231 (46%), Positives = 153/231 (66%), Gaps = 2/231 (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  +   L    K + I GI Y    + L  Q  SN+W  V L 
Sbjct: 122 EMPASKLKRVYNVRAYGNPNI-LLKNNYKNLKIDGIFYNPHSIKLLRQNKSNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           EGKNREI+++FE+F  +VN+LIRI YG  ++G L  G+ +E+S KIL +QL
Sbjct: 181 EGKNREIRRIFEYFGLQVNKLIRIQYGALKIGNLKPGNYQEISNKILEKQL 231


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 73/226 (32%), Positives = 117/226 (51%), 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+T  D  GR+T+ D +  +  R+  +GRLD NT G+++LTNDG +   +  P 
Sbjct: 61  NKPTGYVSTVKDDRGRNTILDIV-KVKERIYPIGRLDYNTSGIIILTNDGEVYNKVAHPK 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|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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 80/239 (33%), Positives = 117/239 (48%), Gaps = 11/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
           +R+ K+I+  G+ASRR  E MI   RVKVNG             D IE+DG  L      
Sbjct: 3   ERLQKIISHWGVASRRHAEEMILSGRVKVNGDRAYLGQKADPKCDRIEIDGRALHPSSQP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 128
           +    L +KP+G+V T ++P GR  V D LP        +  VGRLD ++ G LL+TNDG
Sbjct: 63  QPLYLLLNKPLGVVCTCAEPQGRKAVLDLLPRQMRVGQGLHPVGRLDSDSTGALLITNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNA 187
            L  +L  P     + Y+V   G   +  L   ++GI++ G      QV    +   S  
Sbjct: 123 ELTFLLTHPRYHVAKTYQVLVQGCPPESVLEQWRQGILLSGKNTLPAQVRPIGKPSRSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKIL 241
            + V LREG+NR+I++V E   + V +L R + GP  L +     L +G  R +    +
Sbjct: 183 LLEVVLREGRNRQIRRVAEALGYPVVQLHRTAIGPIYLNSTGKPELASGEYRSLKNSEV 241


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 109/229 (47%), Positives = 150/229 (65%), Gaps = 2/229 (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+     L    K + I GI Y    + L  Q  SN+W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDILLKSHYKNLEIDGIFYNPHSIKLLKQNKSNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           EGKNREI+++FE+F  KVN+LIRI YG F +  L  G  +E++ KIL +
Sbjct: 181 EGKNREIRRIFEYFGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILEK 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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 88/239 (36%), Positives = 126/239 (52%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ KV+A+AG+ASRR  E MIA  RV+VNG L+      V    D I VDG  + 
Sbjct: 3   NEQGIRLQKVLAQAGLASRRAAEDMIAAGRVEVNGELIVEQGRRVDPERDEIRVDGSRIP 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTN 126
            A R   ++ +KP G+V+T  DP+GR  + D   +P    R+  VGRLD  T GL+LLTN
Sbjct: 63  TARRHVYYVLNKPQGVVSTMDDPEGRPCLSDLEGVPRGI-RLFHVGRLDTETSGLILLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  A  +  PS + L+ Y     G+VD   +  L KG+ ++        V L      +
Sbjct: 122 DGEFANRMTHPSYKVLKTYLADVEGRVDDKVIRRLSKGLTLEDGPVKPDAVRLVQAGEEH 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + V V L EG+NR ++++ +     V RL R   GP +L  L  G  RE++ + L + L
Sbjct: 182 SLVEVSLHEGRNRIVRRIMDSVAHPVRRLSRTVIGPVRLKRLGRGDMRELTHEELGQLL 240


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 105/237 (44%), Gaps = 6/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +Q +    R+ K +  A   +R+E   ++    V V+ ++ +  A  +  T  +E  G  
Sbjct: 20  LQADEVSMRLDKFLCDALGTTRKEATMLLKSGEVTVDDLVQKSGAFKLKETSCVEWQGRE 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           +  A   R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T
Sbjct: 80  IT-AHGPRYIMMHKPDGVVCSHEDGFN-QTAFILLDEVNIQDLHFAGRLDVDTTGLLLIT 137

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG  +  +  P  +  + YRV     +  D       GI ++G     +   L+    S
Sbjct: 138 DDGQWSHRVTSPKHKCEKTYRVWLADPIQADYAEQFTNGIELRGERELTLPAQLEI--VS 195

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
              V + + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++ +
Sbjct: 196 ETEVLLTIHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGDYRYLTEEEI 252


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 123/244 (50%), Gaps = 13/244 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K++++ G+ASRR+ E++I   +V++NG   E         D I ++G  L   +R 
Sbjct: 3   IRLQKLLSQWGVASRRQAEQLILAGQVQLNGHTAELGQKADPDQDQITLNGQILNPTDRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +    L +KP G+V+T  DP  R TV + LP  + +   +  VGRLD+ + G LLLTNDG
Sbjct: 63  QPLYLLVNKPKGVVSTCQDPQHRRTVLELLPKTYQQGQGLHPVGRLDVASTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSN 186
            L   L  P     + Y+V   G    + L+  ++GI + G      QV +    Q  +N
Sbjct: 123 QLTFALTHPRFHIAKTYQVWIEGCPPPEILDRWRQGIHLDGRTTLPAQVEILKPYQSHTN 182

Query: 187 AW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKI 240
           +  + V L+EG+NR+I+++ E   + V +L R   G   L +     L  G  R ++   
Sbjct: 183 SICLEVILQEGRNRQIRRIAEQLGYPVRKLHRTQIGSISLHSPSGKLLPQGRYRSLTASE 242

Query: 241 LREQ 244
           ++  
Sbjct: 243 MKNL 246


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD NT GLLLLTNDG L
Sbjct: 61  YIYLIMNKPQGVVSATFD-NYDETVVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGI++  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 115/231 (49%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AERT 73
           R++K ++  G  SRRE +RM+ Q R+ VNG +       V   D I VDGV +RK  E  
Sbjct: 4   RINKYLSEVGFCSRREADRMLEQGRITVNGNIP-EMGTKVSGEDEILVDGVSIRKVEEEH 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V T      R  + + + +   R+  +GRLD  +EGL+LLT+DG +   
Sbjct: 63  VYIALNKPVGIVCTTDTKRERDNIVEFV-NHPKRIFPIGRLDKPSEGLILLTSDGDIVNK 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y VR    +    L+ ++ G+ I GI     +V    ++       + L
Sbjct: 122 ILRARNNHEKEYIVRVDKPISPQFLHKMRNGVPILGIITNKCEV----EQIDTLSFRIIL 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G NR+I+++ E+  ++V +L RI     +L  L  G  R++S + L E 
Sbjct: 178 TQGLNRQIRRMCEYLGYEVKKLKRIRIMNIKL-DLPIGKWRDLSAQELAEL 227


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 87/246 (35%), Positives = 121/246 (49%), Gaps = 10/246 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-K 69
            + +R+ K +ARAGIASRR  E +I   RV VNG         V  TD + VDG  +   
Sbjct: 1   MSAERLHKRLARAGIASRRAAEELIRAGRVTVNGQTA-GLGQGVNDTDDVRVDGRLVELT 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              T  +  +KP+G VTT  D  GR  V D +P +   +  VGRLD ++EGLLLLTNDG 
Sbjct: 60  RPETVTYALYKPVGFVTTAHDEYGRRNVLDAMPDV-PGLHPVGRLDKDSEGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHG--QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           L   L  P     + YR    G     Q +L++L +GI +       +      + G+  
Sbjct: 119 LTLTLTHPRYGHEKAYRAWTEGREPPTQAELDVLVRGIAMDDGPAQALSA-APAEDGA-- 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              V L EG+NR+++++ E     V RL+R   G   LG L  G  RE+  + L + L P
Sbjct: 176 --YVVLGEGRNRQVRRMLEALGHPVGRLVRYRVGGLWLGDLNPGEYRELGPRDLEQLLHP 233

Query: 248 HLLEEA 253
           H    A
Sbjct: 234 HKTPRA 239


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 117/237 (49%), Gaps = 2/237 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           N    R+ K++A+AG  SRR+ E +I   RV+++G L+      V      + VDG  +R
Sbjct: 15  NNEGIRLQKLLAQAGFGSRRKCEEIITDGRVEIDGELITELGTRVDPKHQEVRVDGSRVR 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP  +++   DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG
Sbjct: 75  VNPNHVTLALNKPKRVLSAMDDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDG 134

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNA 187
            L++ +  P  +  + Y     G++       L   G+ +        +  +      + 
Sbjct: 135 ELSQHVMHPKYEVEKTYIATLDGRISGTVCRRLVTTGVQLDDGWIKLDRCAILDSSRDST 194

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V V L  GKNR ++++F    + V RL+R   GP +LG L +G+ R +S+  +R  
Sbjct: 195 LVKVVLHSGKNRIVRRIFGSIGFPVRRLVRTQIGPIKLGDLKSGTYRVLSQVEVRSL 251


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 107/226 (47%), Gaps = 3/226 (1%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           +K +A AG+ SRRE +  I    V VNG ++      +  +D ++    P+   ER    
Sbjct: 2   NKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVVKFHDEPVS-IERKVYV 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L +KP   VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L 
Sbjct: 61  LLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLT 120

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P     ++Y V     + +  +  +  GI ++        ++  T       V + +  
Sbjct: 121 HPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISY-TDDFKKDQVGIEIHS 179

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           GKNR ++++FE   +KV +L R+ +       L  G  R +S+  +
Sbjct: 180 GKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEAEV 225


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E ++   RV V+G + +    V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESILEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/233 (34%), Positives = 129/233 (55%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           N    R+ KV+A+AG+ SRR  E +IA  RV+VNG ++    + V   T  I VDG+ + 
Sbjct: 92  NEEGIRLQKVLAQAGVGSRRVSEDLIAAGRVEVNGEIVRHQGMRVDPETAVIRVDGMRIS 151

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            AE    + ++KP+G+V+   DPD R  + D +     R+  +GRLD++TEGL+LLTNDG
Sbjct: 152 TAEGIVHFAFNKPMGVVSAMDDPD-RPNLGDYVRGRNERLFHIGRLDVDTEGLILLTNDG 210

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS +  +VYR + +G V +D    L++G+ ++          L    G NA 
Sbjct: 211 ELAHRLAHPSYEIRKVYRAQVYGTVPKDLGRRLREGVDLEDGLARVDHFRLLDSVGRNAL 270

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + + EG+NR ++++ +     V  L+R  +GP  LG       R ++K+ +
Sbjct: 271 VEITIHEGRNRIVRRIMDAVGLPVRGLVRTKFGPISLGDQKPERMRPLNKEEV 323


>gi|217970106|ref|YP_002355340.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217507433|gb|ACK54444.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 379

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 93/266 (34%), Positives = 144/266 (54%), Gaps = 9/266 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRK 69
            P+R+ KV+A+AG+ASRRE+E  +   R+ VNG+        +   D ++V+G   PLR 
Sbjct: 115 EPERLQKVLAQAGVASRREIEEWVVAGRISVNGLPA-SLGQKIGPGDRVKVNGKLVPLRF 173

Query: 70  AER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
            +R  R+ +YHKP G + +  DP+GR TVF+ LP +   R ++VGRLD NT GLLL TND
Sbjct: 174 TQRSPRVLIYHKPEGEIVSRDDPEGRPTVFERLPILRKGRWLAVGRLDFNTSGLLLFTND 233

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  R Y VR  G++ ++++  L  GI ++        +  +  +G+N 
Sbjct: 234 GDLANKLMHPRYELEREYAVRILGELTEEQVKSLTDGIQLEDGPAKFNLLRDEGGEGANH 293

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LRE 243
           W  V + EG+NRE++++FE     V+RL+R+ YG  +L   L  G   E+ +     L  
Sbjct: 294 WYRVTISEGRNREVRRMFEAVGLTVSRLMRVRYGSVELPARLKRGMWMEMPEAEACALAG 353

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVR 269
              P    +  +    P+    T  R
Sbjct: 354 LPPPQQSRQQDLRDKRPVKLHRTQAR 379


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 76/326 (23%), Positives = 153/326 (46%), Gaps = 10/326 (3%)

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 +DP+ ++ +   + S   R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 63  YIAFNKPVGIVST-TDPNEKANIVKYI-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       +LE++ 
Sbjct: 177 QGLNRQIRRMCAYFDYEVLKLERTQIMNIELEGLGLGSWRDLNPGELEVLF--DMLEDSN 234

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
            ++D    S      ++   + ++  DF +   N+ +    +K +K  +P    +  S+ 
Sbjct: 235 KHVDDKGRSVSNKSINKQLELLDIQTDFRKSGLNA-KNRAATKNRKRQSPAQASSGTSSF 293

Query: 315 WMAKGIHSSFLSDSGQREENHRRSPS 340
              K      +      + +HR S +
Sbjct: 294 KPKKTGSGPRIGKQKASKVSHRGSRN 319


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 105/300 (35%), Positives = 148/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V +     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESIIEAGRVSVDGKIAKLGDRVEITPRLKIRIDGHLISVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 242 EL----------VELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 288


>gi|327394043|dbj|BAK11465.1| ribosomal large subunit pseudouridine synthase B RluB [Pantoea
           ananatis AJ13355]
          Length = 294

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 109/306 (35%), Positives = 152/306 (49%), Gaps = 20/306 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MIA  RV V+G L         S    I +DG  +  AE
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIAAGRVSVDGKLATLGDRIENSKALKIRIDGHLVSIAE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    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-------L 234

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                    V +D    +   + +DR    +       R  K  SQ +G   ++    P 
Sbjct: 235 PAVNYLRNMVGMDDETVTKLAVEKDRRRTKAN---QIRRAVKRHSQTSGRPARRN---PG 288

Query: 306 HRRNLA 311
            +RN  
Sbjct: 289 SKRNAT 294


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 118/240 (49%), Gaps = 7/240 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++      R+ K +A  G+ SR E++R I  +RV VNG+ +    + +   D I  D   
Sbjct: 1   MKAQVEKMRIDKYLANMGVGSRSEIKRYIKNKRVMVNGVYITDNGLIINLDDDIIFDEEK 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLL 124
           +    +    + +KP G+++   D   ++TV D L   +    +   GRLD +TEG LLL
Sbjct: 61  ISYR-KFVYIMMNKPQGVISATED-KYQNTVLDLLDPSYLHFDLFPAGRLDKDTEGFLLL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  +  P     + Y V   G +  + ++     I+I    Y  M   L+    
Sbjct: 119 TNDGKLAHNMLSPKKHVEKKYYVEVIGHLVNEDIDAFSGNIIIDDG-YECMPAKLEILDS 177

Query: 185 SN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ +   V ++EGK  +IK++FE    +V  L R++ GP +L   L  G  RE++++ ++
Sbjct: 178 NDISKAYVTIKEGKFHQIKRMFEAIGKEVTYLKRLTMGPLKLDENLELGEYRELTEQEMQ 237


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G  ++ A  +V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGTPVKDAKFHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V ++ +    KG+++  G      ++T+  +    + +
Sbjct: 119 THQLLSPKKHVPKKYYAHISGVVTEEDVIEFAKGVILEDGYETKPGELTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDEELELGQYRELTDEEVE 231


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 99/317 (31%), Positives = 156/317 (49%), Gaps = 23/317 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +  +    +++ K++AR+G  SRRE+E  + + R+ V+G +      V V ++  I +DG
Sbjct: 9   MSSKPQQTEKLQKILARSGHGSRREIEGFLKEGRISVDGKMATLGDRVEVTTSTKIRLDG 68

Query: 65  VPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             L   E      R+  Y+KP G + T  DP+GR TVF  LP    +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 K---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    LRE +G  +  E++V ++          RD+  + +       R  K  +Q    
Sbjct: 249 EQTNYLRELVGLSVETESKVAVE----------RDQRRLKAN---QIRRAVKRHTQVASR 295

Query: 296 SKQKKLATPVHRRNLAS 312
              K+ A+    +    
Sbjct: 296 PASKRQASRPTAKKRTR 312


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 218 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVV 277

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 278 KFHDETVS-IERKVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTT 336

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 337 GVLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIHADAISY 396

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +     V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 397 -SDEVKRDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 455

Query: 240 IL 241
            +
Sbjct: 456 EV 457


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   T+ D L           VGRLD NT GLLLLTNDG L
Sbjct: 61  YIYLMMNKPQGVVSATFD-NYDETIVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGIV+  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIEKFKKGIVLDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQYRELTDEEI 232


>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 =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 111/237 (46%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G  SR++V++++    V+V G  ++  + +V   ++ I V G  +   + 
Sbjct: 1   MRIDKFLANMGFGSRKDVKKLLKTGAVRVQGQPIKDPSTHVEPESESITVYGEEVEY-KP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGL 130
               + +KP G++    D +   TV D L           VGRLD +T GLLL+TNDG  
Sbjct: 60  YVYLMMNKPKGVICATEDLEH-ETVIDLLGEEERHYEPSPVGRLDKDTVGLLLITNDGKF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
              L  P     + YR    G V ++ +     G+V+  G       + +  + G+ + +
Sbjct: 119 NHWLMSPKHHVPKTYRALVEGHVTEEDVGAFSHGVVLDDGYVTKPATLHIL-EAGARSHI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            + L EGK  ++K++F+    +V  L RI  G   L   L  G  RE++K+ +   L
Sbjct: 178 ELILTEGKFHQVKRMFQAVGKRVLELERIKIGNLLLDPELARGEYRELTKEEIALLL 234


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/240 (34%), Positives = 119/240 (49%), Gaps = 8/240 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+   +ARAG+ SRR+ E +I Q RV+VNG +       V   D +EVDG P+     
Sbjct: 4   PLRLQAFLARAGVGSRRKAEELIRQGRVRVNGKVA-VLGQKVNPGDVVEVDGKPVEPPRE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +   HKP G  TT  DP  + TVFD LP     +  +GRLD ++EGLLLLTNDG L  
Sbjct: 63  RIVLALHKPRGYTTTRHDPHAQKTVFDLLPD-IPGLHPIGRLDRDSEGLLLLTNDGHLTL 121

Query: 133 VLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VYRV    G +       L +G+ ++              + +     +
Sbjct: 122 RLTHPRYGVRKVYRVYTERGTLPLAICQRLLEGVDLEDG-----PARALACRPAPGGALL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EG+ RE++++ +   + V RLIR+  GP  LG L  G  R++S + +   L    +E
Sbjct: 177 TLAEGRKREVRRMLKAVGYPVKRLIRLQVGPIHLGHLPPGKWRQLSPREVEALLRETPVE 236


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 246 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 305

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 306 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 364

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 365 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISY 424

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 425 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 483

Query: 240 IL 241
            +
Sbjct: 484 EV 485


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 116/237 (48%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 1   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDAVTYLGEIITYQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 61  FYYIL-HKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G       ++ +D   Q+   +
Sbjct: 119 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQETETS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 179 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQ 235


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 112/238 (47%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    + SR EV+  +   RV VNG   + A + +   TD I  DG  L   E 
Sbjct: 1   MRLDKYLVACAVGSRTEVKNFLKAGRVMVNGKKEKSAKLQINEETDEICFDGQKLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   + TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDSKHK-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  L  P     + Y  +  G + Q+ +    +GI ++        + L    ++ + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVGGIMTQEDVETFAQGIPLKDFTCQPAILELVSIDREKNQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLTLDEGLKRGEWRRLTKEELEALL 236


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 234 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 293

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 294 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 352

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 353 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISY 412

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 413 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 471

Query: 240 IL 241
            +
Sbjct: 472 EV 473


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 104/345 (30%), Positives = 154/345 (44%), Gaps = 20/345 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D I+
Sbjct: 111 PAKRVLLPQPETPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQIK 169

Query: 62  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+N
Sbjct: 170 VNGKPIRFRIAPPPVRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLN 229

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T+ G LA  L  P     R Y VR  G +  ++   L +G+ ++        V
Sbjct: 230 TEGLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSTEEKQRLLEGVPLEDGMASFGSV 289

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+
Sbjct: 290 EDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLEL 349

Query: 237 SKKILREQLGPHLLEEAQVNLDA----PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            ++ +R      L++ A   LD     P        R      +         +  +  +
Sbjct: 350 DERDIRA-----LMQAAGATLDGGGARPTSGQGRGGRKGDRRSAGPGKASGSGRDKTGGR 404

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            G       A P   +     +    G  S       QR    RR
Sbjct: 405 AGRPPS-PNAQPDPMKTSLGYI----GADSFSRHRQQQRNNGPRR 444


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 247 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 307 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++        ++ 
Sbjct: 366 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISY 425

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 426 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 484

Query: 240 IL 241
            +
Sbjct: 485 EV 486


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|294340472|emb|CAZ88853.1| putative Pseudouridine synthase [Thiomonas sp. 3As]
          Length = 562

 Score =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 100/347 (28%), Positives = 159/347 (45%), 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  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           G  +++     + R+  YHKP G V +  DP+GR TVF +LP    ++  +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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 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      +    D P         +  N      D     +    +  G  +Q
Sbjct: 404 SLVQALQGRSGEAPSGA-GDRPARR-----PNGQNQGGRRNDSRGSGRGGRGKGQGGDQQ 457

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           +       R  + +    +  + S   S  G    +    P   S+R
Sbjct: 458 QPGPDSYARTTVEALFGKSPVVRSGGGSWGGAGNFSTGNKPGGQSRR 504


>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 =  260 bits (665), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 247 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 306

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 307 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 365

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++        ++ 
Sbjct: 366 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISY 425

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 426 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 484

Query: 240 IL 241
            +
Sbjct: 485 EV 486


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 114/229 (49%), Gaps = 8/229 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R++K ++ AG  SRR  +++I Q+RV +NG++       +   D + VDG  +    E+ 
Sbjct: 8   RINKFLSEAGYCSRRAADKLIEQRRVTINGVVPA-MGTKIAPGDEVRVDGELISDPKEKP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KPIG+V T      +  + D + +  SR+  +GRLD  +EGL+ LT+DG +   
Sbjct: 67  VYLAFNKPIGIVCTTDTKVEKDNIIDYI-NYPSRIFPIGRLDKPSEGLIFLTSDGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  D +  +  GI I G      +V    ++ +     + L
Sbjct: 126 ILRARNNHEKEYEVTVNRPITSDFIQKMGNGIPILGTLTRKCKV----EQLTKYTFKIIL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ E+ +++V +L R       L  +  G  R ++++ L+
Sbjct: 182 TQGLNRQIRRMCEYLDYRVVKLKRTRIMNVSL-DIPVGKWRHLTEEELQ 229


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 111/230 (48%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R++K ++  G  SRR  +++I Q RV +NG +       ++S D + VDG  +    E+ 
Sbjct: 7   RINKYLSEVGYCSRRAADKLIDQGRVTINGKVP-EMGTKIISGDEVRVDGELISEPKEKP 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KPIG+V T      +  + D + +   R+  +GRLD  ++GL+ LTNDG +   
Sbjct: 66  VYLAFNKPIGIVCTTDTRVEKDNIIDFI-NYPKRIFPIGRLDKPSQGLIFLTNDGDIVNK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +++  L+ +  G+ I        ++T    + +     + L
Sbjct: 125 ILRARNHHEKEYLVTVDKPINKKFLDQMASGVPILDTVTRKCEIT----EVNKYQFKIIL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+  + V +L RI     +L  +  G  R ++   L+E
Sbjct: 181 TQGLNRQIRRMCEYLGYNVKKLKRIRIMNVKL-DMPIGKWRNLTNSELQE 229


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + TP R++K ++  G  SRR  +++I Q RV +NG +       + + D I VDG  + K
Sbjct: 3   DTTPTRINKYLSEVGYCSRRAADKLIDQGRVTINGKVP-EMGTKITAADEIRVDGELIGK 61

Query: 70  AE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            + +     ++KP+G+V T      +  + D + +   R+  +GRLD  +EGL+ LT+DG
Sbjct: 62  PKGKHTYLAFNKPVGIVCTTDTGVEKDNIIDFI-NYPKRIFPIGRLDKPSEGLIFLTDDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  ++ D L  +  G+ I        +V    ++     
Sbjct: 121 DIVNKILRARNNHEKEYIVSVNKPINSDFLRQMSSGVPILDTVTRPCKV----ERIDKYT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++ L +G NR+I+++ +   ++V RL R+     +L  L  G  R++++  L E
Sbjct: 177 FSIILTQGLNRQIRRMCDHLEYRVKRLQRVRIMNVEL-DLEVGKYRDLTEAELSE 230


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 138/278 (49%), Gaps = 8/278 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGV 65
           ++E     R+ K +A AG+ASRR+ E +I    V+VNG ++      V    D + V G 
Sbjct: 24  LREQRDGVRLQKFMASAGVASRRKAEELITAGVVRVNGQVVRELGTRVFPERDRVTVRGE 83

Query: 66  PLRKAERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           P++ AE    ++ +KP G+V++ +   D  GR TV   L  +  R+  VGRLD ++ G+L
Sbjct: 84  PIQ-AESKVYYVLNKPDGVVSSAAGSVDERGRPTVISLLHGVSERLYPVGRLDFHSRGVL 142

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGD-MQVTLD 180
           LLTNDGGLA  L  P    ++ Y V+F G++ +++  LL+ G+ +          ++   
Sbjct: 143 LLTNDGGLAEALTHPRHGVVKTYHVKFQGKLTEEQEQLLRDGVELDDGAITRPVAELFAF 202

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +  +N W  +G+REG NR+I+++ E     V +LIR++ G      +  G  R ++   
Sbjct: 203 RETATNVWYQIGIREGLNRQIRRMGEAIGHPVLKLIRVAIGDITADGVPEGEFRALNATE 262

Query: 241 LREQLGP-HLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           + + L    L  E +              RDRP     
Sbjct: 263 VGQLLANVKLAPEGRRGRSGGAGRPRGGQRDRPKAKKS 300


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 114/238 (47%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++  G  SR +V+++I +  VKVN  +++  + ++    D +E++   +   E 
Sbjct: 1   MRLDKFLSNQGFGSRSQVQKLIKKGFVKVNDEIVKDPSYHIDPMKDKVELEDEEILYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G +T   D +   TV D    +   S++  VGRLDI+TEGLL+LT DG  
Sbjct: 61  H-YFMLNKPAGYITATEDEEY-PTVLDLFSDLPIASKLFPVGRLDIDTEGLLILTTDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNA 187
              L  P     + Y     G +   D      KGI ++   Y     +V +       +
Sbjct: 119 GHRLSHPKWNIEKEYYAIVEGDISNIDFSESENKGIYLKKEKYQTKPFKVKVLNTSKDKS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + L EGK   +K++ +   + V  L RI  G  +L   LL G  RE+++K +++ 
Sbjct: 179 EILITLTEGKYHIVKRIMQELGYPVLYLKRIRIGNLKLDEDLLPGEFRELTEKEIKDL 236


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 118/243 (48%), Gaps = 7/243 (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 S+   +  + D +     R+  +GRLD +++GL+L
Sbjct: 69  GEQLRIARDHVYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLIL 126

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG +   +     +  + Y V     +  D L  +  G+ I G      ++T    +
Sbjct: 127 LTNDGDIVNEILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----Q 182

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            S     + L +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R 
Sbjct: 183 LSKYEFQIILTQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRR 242

Query: 244 QLG 246
              
Sbjct: 243 LFA 245


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 108/229 (47%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  Q  + Y V     V+    +  ++GI+++G         L+     N  V + +
Sbjct: 121 ITSPKHQCEKTYLVTLADPVENHYASACEEGILLRGEKEPTKPAKLEVLDDYN--VNLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     KV  L R   G  +L  +L  G  R ++++ +
Sbjct: 179 SEGRYHQVKRMFAALGNKVVALHRWRIGNVELDESLEEGEFRPLTQEEI 227


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/243 (31%), Positives = 119/243 (48%), Gaps = 7/243 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           +  +N    R+ KV+A+AG+ASRR  E +IA  RV V+G ++      V   T  + VDG
Sbjct: 1   MTTQNSDGVRLQKVLAQAGVASRRAAEELIAAGRVSVDGEIVREMGRRVDPDTAVVHVDG 60

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINT 118
             +   +       +KP G+++T SD  GR  V D +           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|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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  IE  G  +  A   
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDLVQKSGAFKLKETSRIEWQGREIT-AHGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFILLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D       GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQVDYAEQFTNGIELRGERELTLPAQLEV--VSETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  +L  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEEEI 226


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 105/317 (33%), Positives = 165/317 (52%), Gaps = 8/317 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  +  TP ++ KV+A AG+ SRRE+E +I   RV VNG         V + D + V+
Sbjct: 144 KYLNSDALTP-KLHKVLADAGVGSRREMEELIVAGRVSVNGEPA-HIGQRVGANDQVRVN 201

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+ +    +  R+ LYHKP G + +H DP+GR+TVF  LP +   + +SVGRLD+NTE
Sbjct: 202 GRPIVRPNAKKPPRIILYHKPAGEIVSHDDPEGRATVFARLPKMRVGKWLSVGRLDLNTE 261

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT  G LA  L  P     R Y VR  G++ +++ + L KGI ++        +  
Sbjct: 262 GLLILTTSGDLANRLMHPRYGAEREYAVRVLGELGEEQQDKLLKGIQLEDGLAQFGSLEY 321

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L   L  G   E+  
Sbjct: 322 LGGEGSNRWYRVTLKEGRNREVRRMFEAAGVTVSRLIRTRFGEVVLPRNLRRGRWEELDS 381

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            ++   L   L    + + D     S    R   +  S +P  F  +++N +    +S++
Sbjct: 382 SLVTA-LMLQLGLLREDDSDERGAGSGRGERQPVSHDSALPPGFGTLERNGTNGAKVSRR 440

Query: 299 KKLATPVHRRNLASNVW 315
            KL+    +R   +  +
Sbjct: 441 GKLSGGRPQRAATAQAY 457


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 87/274 (31%), Positives = 137/274 (50%), Gaps = 3/274 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
              +R+ K++A  G+ SRR  E++IA+ RVKVNG  ++       + D + VD   +  R
Sbjct: 1   MAEERIQKIMAEQGLCSRRAAEQIIAEGRVKVNGHPVKVGDKMDPNRDVLHVDDERIYIR 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K ++      +KP G VTT SD  GR TV + +  I +R+  VGRLD ++EGLLL+TNDG
Sbjct: 61  KDQQMYYLALYKPRGYVTTASDELGRKTVMELVSDIPARLYPVGRLDKDSEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
             A+ +  PS    ++YRV    + D+ ++  L  G+V+  G       + + T +    
Sbjct: 121 AFAQAVTHPSGGISKLYRVTVQPRADESQILKLSSGVVLDDGTKTMPCAINVVTDEPGRT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + L+EGKNREI+++ E    +V RL R + G  +LG L  G+ RE++K  +      
Sbjct: 181 VMEMTLKEGKNREIRRMCETVGLEVVRLKRNAEGVVKLGMLKPGTYRELTKAEINGLRAA 240

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
                AQ    A    +       P      P  
Sbjct: 241 AAKGRAQTRSAAVQSKAAERRPRGPVGKGTAPKK 274


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 109/322 (33%), Positives = 159/322 (49%), Gaps = 24/322 (7%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT----R 74
           +ARAG  SRRE+E +I Q RV V+G + +    V V     I +DG  L   E      R
Sbjct: 1   MARAGHGSRREIETIIQQGRVSVDGKISKLGDRVEVTQATKIRLDGHLLSIKESEEAVCR 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL T DG LA  
Sbjct: 61  VLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLLFTTDGELANR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS +  R Y VR  GQ+D +K+  L +G+ ++        +T    +G N W  V L
Sbjct: 121 LMHPSREVEREYAVRVFGQIDDEKIKQLSRGVQLEDGPAAFRTITFQGGEGINQWYNVTL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILREQLGPHL 249
            EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K    LRE      
Sbjct: 181 TEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATNYLREL----- 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                V LD+   S   + +DR  + +       R  K  ++  G     +  +   + +
Sbjct: 236 -----VELDSETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVAGRQVAGRQGS-ARKGS 286

Query: 310 LASNVWMAKGIHSSFLSDSGQR 331
              NV  A    ++    + +R
Sbjct: 287 TRQNVGNAAPAAATGRRGANKR 308


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      +VT    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 226


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 115/241 (47%), Gaps = 7/241 (2%)

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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R        E  
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFADLNYEPQ 233

Query: 254 Q 254
           +
Sbjct: 234 E 234


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 237 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 296

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 297 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 355

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  +  +  GI ++        ++ 
Sbjct: 356 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMEQIAAGIQLEDGEIHADAISY 415

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 416 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 474

Query: 240 IL 241
            +
Sbjct: 475 EV 476


>gi|262091774|gb|ACY25362.1| pseudouridine synthase family [uncultured actinobacterium]
          Length = 237

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 75/232 (32%), Positives = 115/232 (49%), Gaps = 5/232 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K+IA AGI SRR  + +I   RV VNGI++           D + VDG  + +
Sbjct: 1   MAQMRLNKIIADAGITSRRGADELIEDGRVAVNGIIVREMGSKFDPEMDKVMVDGETITR 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    HKP G+++T  DP+GR ++ D +     R+  VGRLD ++EGL+LLTNDG 
Sbjct: 61  TLTKSYLALHKPKGVLSTMFDPEGRPSLDDFIDLRKERLFHVGRLDKDSEGLILLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L      PS    + Y + F G +      +L KG+ ++          L  ++ S  W+
Sbjct: 121 LTFRATHPSFGLEKTYIIEFDGILPTGVDKVLLKGVELEDGMGR----VLTFKQLSPKWI 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + EG+   I+++ E     V RLIR  +GP  LG    G  R+++   L
Sbjct: 177 EVSIHEGRYHIIRRLMEAVGVNVLRLIRTKFGPISLGDTPEGRWRDLNDGEL 228


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 218 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVV 277

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 278 KFHDETVS-IERKVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTT 336

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 337 GVLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIHADAISY 396

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +     V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 397 -SDEVKRDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 455

Query: 240 IL 241
            +
Sbjct: 456 EV 457


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 114/231 (49%), Gaps = 4/231 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAE 71
           P R++K IA + I SRRE +  I    V VNG ++       V +TD +      +   E
Sbjct: 160 PMRLNKFIANSNICSRREADEFIQAGVVSVNGQVVTELGTKIVPATDKVHFHDQLVS-ME 218

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    L +KP  ++TT  DP  R TV D + +    RV  VGRLD NT G+LL+TNDG L
Sbjct: 219 KKIYILMNKPKNIITTLDDPKERRTVLDLIKNACSERVYPVGRLDRNTTGVLLITNDGDL 278

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  ++Y VR   + +   +  ++ GIV++        ++   ++ +   V 
Sbjct: 279 TSKLIHPKYEKKKIYHVRLDREFESQDMEAMRSGIVLEDGDIKADDISY-VKEDNKKEVG 337

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + +  GKNR ++++FE   +K+  L R+ +       L  G  R +S+  +
Sbjct: 338 IEIHSGKNRIVRRMFEHLGYKIVALDRVYFAGLTKKNLPRGKWRYLSESEV 388


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/231 (35%), Positives = 125/231 (54%), Gaps = 1/231 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T QR+ K+IA AG+ SRR+ E ++  +RV+VNG L        +  D IEVD  PL+ A
Sbjct: 1   MTRQRLQKLIASAGVCSRRKAEDLLRDRRVRVNGQLATLGDQADLDVDTIEVDDRPLQTA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
            + R+ L +KP G++ +  DP  R TV + +P      +  VGRLD  + G LLL+N G 
Sbjct: 61  PQARVLLLNKPPGVICSCRDPQRRRTVLELVPPDLREGLHPVGRLDAESRGALLLSNQGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + YRV   G   + +LN  ++G+V+ G      +V L  +    + +
Sbjct: 121 LTLQLTHPRYNHRKTYRVTVAGLPSEKQLNQWRRGVVLDGTVTRPAEVNLVKKSPQASVL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V LREG+NR+I++V      +V  L RI+ G   LG++  G  RE+S++ 
Sbjct: 181 EVILREGRNRQIRRVALSLGHRVLDLQRIAIGRLTLGSMREGCWRELSRQE 231


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 118/235 (50%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K++A  G  +R+ V+ ++  + V VNG++ +    +V   TD IEV G  ++  E 
Sbjct: 1   MRLDKLLANMGFGTRKTVKNVLKAKEVTVNGLVEKDGKTHVNPETDKIEVSGEVIQYQEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+V+  +D     TV D L           VGRLD +TEGLL+LTNDG L
Sbjct: 61  M-YFMLHKPQGVVSATTD-HVHKTVIDLLQPQDQVMDPFPVGRLDKDTEGLLILTNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI---CYGDMQVTLDTQKGSNA 187
           A  L  P     + Y     G VD+  +   + GI +          +++     +  ++
Sbjct: 119 AHNLLSPKKHVDKCYEAIIEGVVDEQDVQAFENGITLDDGFNCQSAKLEILSVDFEKESS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + V + EGK  ++K++FE  +  V  L R+S G  QL  TL  G  R+++K+ L
Sbjct: 179 VIQVTIHEGKFHQVKRMFEAVDKSVIYLKRLSMGSLQLDETLELGEYRQLTKEEL 233


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 123/251 (49%), Gaps = 6/251 (2%)

Query: 1   MKDKNIVQENFTP-----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M+  +   +   P     +R+ KV+A AG+ SRR  E +I ++RV VNG + +       
Sbjct: 1   MRRDDRAPKTDAPVFEGAERLQKVLAAAGVGSRRACEDLIFRRRVTVNGKVAQLGDKADP 60

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRL 114
           + D I VDG  L+   R      +KP G+V+T +D  GR+ + D + +    RV  VGRL
Sbjct: 61  TRDVILVDGERLQADTRLVYLALNKPRGVVSTMADEKGRAALSDFIGNRVEQRVYHVGRL 120

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D ++EGLLLLTNDG LA  L  PS    + Y     G + ++    L  GI ++      
Sbjct: 121 DADSEGLLLLTNDGDLAHRLTHPSYGVPKTYLCEVAGPIPRNLGKRLAAGIELEDGPVTV 180

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               +    G  A V + L EG+   ++++       V RL+R S GP +LG L AG TR
Sbjct: 181 DSFKVVDTLGKTAQVELTLHEGRKHIVRRLLGEVGHPVFRLVRTSIGPIRLGDLRAGRTR 240

Query: 235 EVSKKILREQL 245
            ++   +    
Sbjct: 241 RLTNAEVAALF 251


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 129/236 (54%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA A + SRR+VE +I Q+RVKVN  ++ +    V ++D + +D V ++K    
Sbjct: 2   ERLQKFIASANLVSRRKVEILILQKRVKVNNQVVSQLGTKVKASDVVTLDDVLIKKTT-L 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G ++T  D   R TV D +      R+ SVGRLD NT GL+L+TNDG + +
Sbjct: 61  FYYLLNKPQGYLSTTKDDKKRPTVLDLIKESQNQRLYSVGRLDFNTTGLILITNDGEMTQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQK---GSNAW 188
            L  P     + Y V+ +  + +  L+LL KG++I         ++ +  Q+     + W
Sbjct: 121 KLTHPCFGIPKEYHVKINVFLTKKDLSLLLKGVIIDHNYLSIPKEINILKQRYLPKPSTW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + + EGKNR+I+K+ E   ++V +L R SY    +  L  G+ R +    +++ 
Sbjct: 181 LKIVITEGKNRQIRKMMEALGYQVLKLRRYSYAFLTIEGLKTGAYRLLKIHEIKKL 236


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 118/260 (45%), Gaps = 11/260 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAERT 73
           R++K ++  G  SRRE +++I   R+ VNG +       V S D I VDG  +  + +  
Sbjct: 8   RINKFLSEVGYCSRREADKLIDAGRITVNGNIP-EMGTKVSSEDEIRVDGKIVGEQKDPP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              ++HKP+G+V T      +  + D + +  +R+  +GRLD  +EGL+ LTNDG +   
Sbjct: 67  VYLIFHKPVGIVCTTDTRVEKDNIIDYI-NYPTRIFPIGRLDKASEGLIFLTNDGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +D   +  +  GI I        +V    +K       + L
Sbjct: 126 ILRARNNHDKEYIVDVDKPIDASFVKRMSDGIPILDTITRKCEVEQLGKK----RFKIIL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E+ ++ V RL R+      L  +  G  R  +   L+E     LLE +
Sbjct: 182 TQGLNRQIRRMCEYLDYNVTRLKRVRIMNINL-DIPVGKYRAFTTAELKEL--NSLLEGS 238

Query: 254 QVNLDAPIYSSETLVRDRPN 273
               + P   +      RP+
Sbjct: 239 SKTFE-PESQTGNKPEIRPS 257


>gi|187928207|ref|YP_001898694.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187725097|gb|ACD26262.1| pseudouridine synthase [Ralstonia pickettii 12J]
          Length = 594

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 101/313 (32%), Positives = 158/313 (50%), Gaps = 9/313 (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  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  ++     +  R+ LYHKP G + + SDP+GR TVFD LP + + + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 380 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 439

Query: 237 SKKILREQLGPHLLE-EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           S + +R  +G   ++     +               P ++  +   F       S+  G+
Sbjct: 440 SAEDVRTLMGTLGMKVPTASSGGGQDRQGNRRRGPAPVLMGPMSSGFAGEANFQSRGMGV 499

Query: 296 SKQKKLATPVHRR 308
               + A P  RR
Sbjct: 500 ENGNR-AQPAQRR 511


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +   D +
Sbjct: 218 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRADVV 277

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +     +   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 278 KFHDETVS-IERKVYVLLNKPKDCVTTSDDPQARLTVMDLVKGACAERIYPVGRLDRNTT 336

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 337 GVLLLTNDGDLASKLTHPKYLKKKIYHVYLDKNLTKADMDQIAAGIQLEDGEIHADAISY 396

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            + +     V + +  GKNR ++++FE   +KV +L R+ +       L  G  R ++++
Sbjct: 397 -SDEVKRDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEQ 455

Query: 240 IL 241
            +
Sbjct: 456 EV 457


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 245 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 304

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 305 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 363

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  GI ++        ++ 
Sbjct: 364 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGIQLEDGEIHADAISY 423

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 424 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 482

Query: 240 IL 241
            +
Sbjct: 483 EV 484


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 123/244 (50%), Gaps = 4/244 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
            +K+    N   +R+ KV+A+AG+ASRR  E +I   RV+VNG +++R  V V    D I
Sbjct: 56  DEKSTQNPNTEGERLQKVLAKAGVASRRHAEVLIDAGRVEVNGKIIKRQGVRVNPNADVI 115

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDIN 117
            VDGV +   E    ++ +KP G+ +T  D  GR  V D +        R+  VGRLD +
Sbjct: 116 RVDGVRVNVNEDHEYFILNKPRGVQSTMQDDMGRPCVGDMVAEKTASGQRLFHVGRLDAD 175

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLL+LTNDG LA  L  P  +  + Y     G+ D+  +  LK GI +         V
Sbjct: 176 TEGLLILTNDGELANRLMHPKYEVSKTYLATVLGEADKSLVRTLKDGIELDDGMANADFV 235

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +  +    + + + L EG+   ++++ +   + V RL+R      QLG +  G  R ++
Sbjct: 236 QIVDKNQGMSLIRLELHEGRKHIVRRMLKAAGYPVQRLVRTKIHTVQLGDMKPGGIRALN 295

Query: 238 KKIL 241
              L
Sbjct: 296 SAEL 299


>gi|295095390|emb|CBK84480.1| ribosomal large subunit pseudouridine synthase F [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 290

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 74/292 (25%), Positives = 134/292 (45%), Gaps = 12/292 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V +NG         V+  D ++V+G  +    AE 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVVPGDVVKVNGQVIEPRDAED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  D + R  + D + +  SR+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVFIALNKPVGIVSTTEDGE-RDNIVDFV-NHSSRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V    +K +     + 
Sbjct: 125 KILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTVTKKCKV----RKEAPFAFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIELF--KLIEN 238

Query: 253 AQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +            +T    RP + +   ++  R K  + ++     +KK   
Sbjct: 239 SSSEAKPKAKAKPKTQAIKRPVVKAPQAEEKGRGKPGNGKRFTQPGRKKKGR 290


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 118/234 (50%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AGIASRR+ E +I Q RV VNG L+      V   D I VDG  + K E  
Sbjct: 2   ERLQKVMAAAGIASRRKCEELIVQGRVSVNGQLVSELGYKVKKGDQIAVDGKMIEK-EGK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP   + T +D  GR TV + +     R+ +VGRLD +T G+LLLTNDG  A  
Sbjct: 61  VYYLMNKPKKSMCTSNDEFGRKTVIELVEGT-ERIFTVGRLDYDTSGVLLLTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTLDTQKGSNAWVT 190
           +  P     +VY +  +G +  + +  LK GIV+           ++T    K +     
Sbjct: 120 IIHPRYHLPKVYNLTINGILKPEDMRKLKNGIVLDDGYKTMPAKFKITEKDLKKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+IK++ E   ++V RL R          L  G  R +    +++ 
Sbjct: 180 LTIYEGRNRQIKRMMEALGYEVRRLHRKQIAFLGCSDLRQGEYRTLKPFEVKKL 233


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 87/234 (37%), Positives = 126/234 (53%), Gaps = 2/234 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE-R 72
           R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    + V  T   I VDG  L   E +
Sbjct: 12  RLQKVLAQAGVASRRAAEQMIADGRVSVDGQVVRGQGMRVDPTAQVIHVDGERLILDETK 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +   +KP+G+V+T SDP+GR TV D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HVVLAINKPVGVVSTMSDPEGRPTVADIVAGYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS +  + Y  R HG+V       L  GI ++          +    G    V + 
Sbjct: 132 RLTHPSYEISKTYVARLHGEVRPGVKRRLMAGIELEDGPIAVDGFRVVDTYGDITTVEIV 191

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+NR ++++ +   + V  L+R  +GP +L  L  G++R V    L    G
Sbjct: 192 VHEGRNRLVRRMMDAVGFPVRELVRTGFGPIRLDHLQPGTSRRVKGNALTALYG 245


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 92/288 (31%), Positives = 146/288 (50%), Gaps = 8/288 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 132 KRVLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 190

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 311 GGGEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 370

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
             +R  +    L+      D          R +P+ +        R  
Sbjct: 371 AQVRRLMSTVGLKA--PTEDKGGKRGGPAERRQPDPMQTSMGFINREP 416


>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 =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 91/286 (31%), Positives = 146/286 (51%), Gaps = 8/286 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++  +    ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++G 
Sbjct: 1   MLSPDDDAPKLHKVLAEAGMGSRREMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRINGK 59

Query: 66  PLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGL 121
           P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+ +  
Sbjct: 180 GEGTNHWYHVALAEGRNREVRRMFEAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDEAQ 239

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
           +R  +    L+      D        + R +P+ +        R  
Sbjct: 240 VRRLMSTVGLKA--PTEDKGGKRGGPVERRQPDPMQTSMGFINREP 283


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 105/294 (35%), Positives = 149/294 (50%), Gaps = 10/294 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---KA 70
           +++ KV+ARAG+ SRRE+E  I + RV VNG +       V   D IE+DG P+      
Sbjct: 3   EKLQKVLARAGLGSRREMENRIREGRVVVNGEVAT-LGDRVGLEDQIELDGYPVSVSGAG 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           +  R+ +Y+KP G V T  DP+GR TVFD LP     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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            V L EG+NRE+++++E    KVNRL R+ +GP  L +    G   E+ +  +       
Sbjct: 182 YVCLMEGRNREVRRLWESQGLKVNRLKRVRFGPVFLPSKAKVGRWVEMEEAEVNGLCELV 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            ++ A +       + +     +     +VP    R K    Q +   + K   
Sbjct: 242 DIKPAPIKQ----KTKQEQEDLKRRRAKQVPGKARRTKGFDWQSSDKQEFKPRK 291


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 82/247 (33%), Positives = 119/247 (48%), Gaps = 10/247 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
            + +R+ K +ARAGIASRR  E MI   RV VNG++       V   D + VDG  +   
Sbjct: 1   MSGERLQKRLARAGIASRRAAEEMITAGRVTVNGVVA-HLGQTVTDADDVRVDGSLVDST 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A     +  +KP G VTT  D  GR  V D +P     +  VGRLD ++EGLLLLT DG 
Sbjct: 60  AVPAVTYALYKPRGYVTTARDEYGRRNVLDAMPE-IPGLHPVGRLDRDSEGLLLLTTDGQ 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQ--VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           L   +  P     + YR    G     Q +L+ L  G+ ++      +  +         
Sbjct: 119 LTLTMTHPRYGHEKAYRAWTEGPHDPTQGELDTLVSGVELEDGPARAVSASPAYGGAF-- 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              V L EG+NR+++++ E     V+RL+R   G   LG +  G  RE+++K L E + P
Sbjct: 177 ---VVLGEGRNRQVRRMLEAVGHPVSRLLRYRVGGLWLGDMEVGEYRELTRKDLDELVNP 233

Query: 248 HLLEEAQ 254
             +  A 
Sbjct: 234 ASIPRAS 240


>gi|167836825|ref|ZP_02463708.1| RNA pseudouridylate synthase family protein [Burkholderia
           thailandensis MSMB43]
          Length = 358

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 89/272 (32%), Positives = 142/272 (52%), Gaps = 6/272 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A AG+ SRRE+E +I   RV VNG         +M TD + ++
Sbjct: 60  KRVLSPEDDAPKLHKVLAEAGMGSRREMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 118

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++F+     V+RLIR  +GP  L   L  G   E+ +
Sbjct: 239 GGGEGTNHWYHVALAEGRNREVRRMFDAVGLMVSRLIRTRHGPIPLPRGLKRGRWEELDE 298

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
             +R  +    L+           ++E    D
Sbjct: 299 AQVRRLMSTVGLKAPTEEKGKRGGATERRQPD 330


>gi|158316819|ref|YP_001509327.1| pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112224|gb|ABW14421.1| pseudouridine synthase [Frankia sp. EAN1pec]
          Length = 259

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 119/242 (49%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 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|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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 104/300 (34%), Positives = 149/300 (49%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G +      V ++    I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIEAIIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 DGELANRLMHPSREVEREYAVRVFGQVDENKLRDLSRGVQLEDGPAAFKTIKFTGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + +DR  + +       R  K  SQ +   +     
Sbjct: 242 EL----------VELTPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSSNRRSGSRN 288


>gi|222110298|ref|YP_002552562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729742|gb|ACM32562.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 435

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 104/345 (30%), Positives = 154/345 (44%), Gaps = 20/345 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D I+
Sbjct: 99  PAKRVLLPQPETPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQIK 157

Query: 62  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+N
Sbjct: 158 VNGKPIRFRIAPPPVRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDLN 217

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T+ G LA  L  P     R Y  R  G +  ++   L +G+ ++        V
Sbjct: 218 TEGLLLFTSSGELANKLMHPRFGLEREYAARVLGALSTEEKQRLLEGVPLEDGMASFGSV 277

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+
Sbjct: 278 EDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLEL 337

Query: 237 SKKILREQLGPHLLEEAQVNLDA----PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
            ++ +R      L++ A   LD     P        R      +         +  +  +
Sbjct: 338 DERDIRA-----LMQAAGATLDGGGARPTSGQGRGGRKGDRRSAGPGKASGSGRDKTGGR 392

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
            G S     A P   +     +    G  S       QR    RR
Sbjct: 393 AGRSPS-PNAQPDPMKTSLGYI----GADSFSRHRQQQRNNGPRR 432


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 120/234 (51%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I++ RV VNG  +      V   D IEVDG P+ K E  
Sbjct: 2   ERLQKVIAAAGITSRRKAEVLISEGRVAVNGKTVTELGYKVKRGDLIEVDGKPIAK-EDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP   + T  D  GR TV D +     R+ +VGRLD +T GL++LTNDG  A  
Sbjct: 61  VYFLMNKPKRTMCTSEDEFGRQTVVDLI-DCEQRIFTVGRLDYDTSGLIILTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQ--VTLDTQKGSNAWVT 190
           +  P     +VY +  +G +  + +  +K GIV+  GI     +  +T    + +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTSEDMKKIKSGIVLDDGIKTLPAKYRITEKDPQKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+IK++ E   ++V RL R          L  G  R +    +++ 
Sbjct: 180 LTIVEGRNRQIKRMMEALGYEVRRLHRSKLAFLHCSDLRQGEYRVLKPFEVKQL 233


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      +VT    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 226


>gi|324326400|gb|ADY21660.1| RNA pseudouridine synthase family protein [Bacillus thuringiensis
           serovar finitimus YBT-020]
          Length = 235

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 226


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 226


>gi|327462777|gb|EGF09099.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 242

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++        + +    ++   + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEASL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ GP QL + L  G  R +++  +
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDSALALGEWRRLTEAEI 232


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 119/234 (50%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+++  G  SR+E++ ++ +  ++++G +++   + V      I+V G  +    +
Sbjct: 2   ERLDKILSNLGYGSRKEIKALVKKGEIEIDGKIIKDNGIKVDPNKSTIKVSGEEINYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L   ++      VGRLD +TEG LL+TNDG L
Sbjct: 61  YIYLMMNKPAGVVSATFD-NYDETVIDLLDYEYTVFDPFPVGRLDKDTEGFLLITNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y       VD+  +   +KGIV+  G      ++ + +   + + V
Sbjct: 120 NHRLTSPKWHVDKIYYAEIDKIVDEKDIRAFEKGIVLDDGYKCLPAKLEILSADENGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + ++EGK  ++K++FE    KV  L R+  G   L  +L  G  RE+++  ++
Sbjct: 180 NITIQEGKFHQVKRMFEAREKKVIYLKRLQMGNLVLDESLNEGEYRELTEDEIK 233


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 102/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++ + +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTAEEV 226


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 97/350 (27%), Positives = 153/350 (43%), Gaps = 24/350 (6%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D ++V+
Sbjct: 87  KRVLSPQPETPKLHKVLAQAGLGSRLEMEQLILEGRISVNAEPA-HIGQRIQFGDTVKVN 145

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+R        R+  YHKP G V TH DP  R TVF  LP +F  +  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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 266 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMLLPRGLKRGAFVELDE 325

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +          E++ +               P  +        R  +   ++N  S+ 
Sbjct: 326 RDIWALTNAVTRSESRAD--------PRGAPKHPGHVRGDEGGEFRPGRG-PRRNERSRG 376

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            +   P                     +D+   +E +   P      S  
Sbjct: 377 DRGRLPAPESGQ---------ADDFQPADADAEQEPNELQPPMHRTDSAP 417


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 93/273 (34%), Positives = 143/273 (52%), Gaps = 7/273 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  E+  P ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++  D + V+
Sbjct: 210 RELSAEDDAP-KLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPADQVRVN 267

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G  + +    +  R+ LYHKP G + + SDP+GR TVFDNLP I + + ++VGRLD NTE
Sbjct: 268 GKLIHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDNLPRIKTGKWVAVGRLDFNTE 327

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +++  
Sbjct: 328 GLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIAD 387

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +EV  
Sbjct: 388 GGGEGVNHWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQEVEP 447

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             ++  +    L+       AP  +++   R +
Sbjct: 448 NDVKALMTSVGLKVPGKGEQAPKGATKVGGRKQ 480


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 105/299 (35%), Positives = 147/299 (49%), Gaps = 9/299 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKA 70
           +++ KV+ARAG  SRRE+E  I + RV VNG +       V   D I +DG  +      
Sbjct: 3   EKLQKVLARAGQGSRREMETRIREGRVLVNGEVAT-LGDRVSVKDTITIDGYSIIATEAG 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G V T  DP+GR TVFD LP     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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            V L EG+NRE+++++E    KVNRL R+ +GP  L +    G   E+ +  +       
Sbjct: 182 YVCLMEGRNREVRRLWESQGVKVNRLKRVRFGPVFLPSKAKVGRWVEMEETDVNSLCAMV 241

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
            L+ +++    P    E L   R    +          K    ++    + K   P  R
Sbjct: 242 DLKLSEL---TPKTQQEKLELKRHKNKATAGGARRAPPKGFDWQSNDKPEFKPKKPGKR 297


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 117/237 (49%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++  ++V VNG +       +    D I V G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQINEKKDQIAVAGQVLSH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   R TV D L +   +  V  VGRLDI+T GLLLLTN G L
Sbjct: 60  FVYYLLNKPKGVISATEDDHHR-TVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNKGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++YR +  G + Q+ +     GI ++       Q+T+ +  +    + 
Sbjct: 119 AHAMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPAQLTILSTDEAKQTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + +REGK  +IK++ +     V  L R++ GP +L   L  G  R ++   L++ 
Sbjct: 179 VDITIREGKFHQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQL 235


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 107/301 (35%), Positives = 149/301 (49%), Gaps = 23/301 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+AR+G  SRRE+E +I Q RV V+G +      V+V     I +DG  +   E
Sbjct: 2   SEKLQKVLARSGHGSRREIESIIQQGRVSVDGKIATLGDRVDVTRATKIRIDGHVVTVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T SDP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V L     S   + R+R  + +       R  K  S         K  
Sbjct: 242 EL----------VQLSPETVSKLPVERERRRLKAN---QIRRAVKRHSLVGARRNAPKRN 288

Query: 303 T 303
            
Sbjct: 289 G 289


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 129/246 (52%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
             D   ++  +  R  L +KP+G V + SD  GR+T  D L   +  R+ ++GRLD+ + 
Sbjct: 53  CFDNQQIKFEKEKRYVLLNKPVGYVCSLSDEMGRATAADLLKEAYTERLYNIGRLDMYSG 112

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G +L TNDG  +  +E PS +  + Y +     +    +    +GI I+GI Y  +    
Sbjct: 113 GAILFTNDGDFSARIEHPSAEIEKEYLIETTQDIPDTLIERFTRGIRIEGIFYRCVSAKR 172

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              + +    ++ L EGKNREI+KVF+FF   + RLIR+  G  QL  L  G  R ++K+
Sbjct: 173 QASRKA----SIVLIEGKNREIRKVFDFFKIPIKRLIRVRIGGIQLNGLKPGEFRNLTKE 228

Query: 240 ILREQL 245
            + E L
Sbjct: 229 EIAELL 234


>gi|222640395|gb|EEE68527.1| hypothetical protein OsJ_26969 [Oryza sativa Japonica Group]
          Length = 1502

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 70/256 (27%), Positives = 121/256 (47%), Gaps = 19/256 (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   EVDGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
             VDG PLR        A R      +KP+G+  T ++   +  + D +     R+  +GR
Sbjct: 1311 LVDGQPLRARVARKPGARRHVYIALNKPVGVTCT-TETSVKGNIVDFV-GHEQRIFPIGR 1368

Query: 114  LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
            LD ++EGL+L+T++G +   +        + Y V  +  V  + L  + +G+ I      
Sbjct: 1369 LDKDSEGLILMTSNGDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRIHDQMTL 1428

Query: 174  DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              +    T + +     + L++G NR+I+ +   F ++V +L R+     ++G L  G  
Sbjct: 1429 PCK----TSRIAKFGFRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQW 1484

Query: 234  REVSKKILREQLGPHL 249
            R ++++ L+  L   L
Sbjct: 1485 RNLTEQELQGLLPKQL 1500


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 63/268 (23%), Positives = 121/268 (45%), Gaps = 12/268 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K +++ G  SRR  +++I Q R+ +N  +       V   D ++VDG P+ K E   
Sbjct: 6   RINKYLSQLGYCSRRAADKLIDQGRITINDKVP-EMGTKVTPGDLVKVDGKPVSKEELKE 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 ++KP+G+V T      +  + D + +   R+  +GRLD  +EGL+ LTNDG + 
Sbjct: 65  PNVYIAFNKPVGIVCTTDTRVEKDNIIDYI-NYPKRIFPIGRLDKPSEGLIFLTNDGDIV 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  V  + L  +  G+ I      + ++    +K  +    +
Sbjct: 124 NKILRARNNHEKEYVVSVNKPVSSEFLKKMSAGVPILDTVTRECEI----EKLGHHTFRI 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ--LGPHL 249
            L +G NR+I+++ EF +++V  L RI      L  +  G  R+++ + L+    L    
Sbjct: 180 VLTQGLNRQIRRMCEFLDYQVTSLKRIRIMNVSL-DIPVGEWRDLTSEELKTINNLTDES 238

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISE 277
            +  + +L +    +      RP     
Sbjct: 239 TKTEEGSLTSTAKKANLRTGKRPRKPKS 266


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 111/239 (46%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   R TV D L  I     V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDSKHR-TVLDLLDDIARTKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAW 188
           A  L  P     + Y     G + Q+ +    KGI ++       ++ + +     + + 
Sbjct: 119 AHALLSPKRHVDKTYLAHVEGIMTQEDVETFVKGIPLKDFTCQPAKLEIVSVDSVKNQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L     
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLVLDENLEQGEWRRLTKEELEVLFA 237


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 100/310 (32%), Positives = 153/310 (49%), Gaps = 12/310 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ K++ARAG+ SRRE+E  +   R+ VNG  +         +D  E+DG  L  A  
Sbjct: 56  PERIQKLLARAGVGSRREIEGWMDAGRLLVNGKPVT-PGQKATVSDVFELDGKRLEVAAA 114

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VTT  DP+GR TVFD LP     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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YG   L + L  G   E+ +K +   L 
Sbjct: 235 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGSIFLPSRLTVGKWEELDQKAVD--LL 292

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL---AT 303
              +  A++ +             +    + V +   R   +   K+G   +K     + 
Sbjct: 293 SRTVGLAKMAVPQQTPDEAAAQARQQRKAAPVTNRSNRAASSPGSKSGQGARKWAVADSK 352

Query: 304 PVHRRNLASN 313
           P      A N
Sbjct: 353 PQRSGGKARN 362


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 100/299 (33%), Positives = 152/299 (50%), Gaps = 18/299 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ K++A+AG+ SRRE+ER I Q RV++NG   +       + D I+VDG  +   +R
Sbjct: 2   SEKLQKILAQAGLGSRREMERWIEQGRVELNGSPAK-LGERAEAKDQIKVDGKVIEHGQR 60

Query: 73  T--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
              R+  Y+KP G V T  DP+GR TVFD LP     R I+VGRLDINT GLLL T DG 
Sbjct: 61  KARRVLAYNKPEGEVCTRHDPEGRPTVFDRLPKLHGERWIAVGRLDINTSGLLLFTTDGE 120

Query: 130 LARVLELPSTQ-WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           LA  L  PST    R Y VR  G+V  + +  + +G++++        V      G N W
Sbjct: 121 LANKLMHPSTNTVDREYAVRVAGEVTDEAVKAMTEGVLLEDGMAKFTDVQYFDGDGFNQW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V + EG+NRE+++++E   +KV+RL R+ YG   L   + AG   E+++    E    
Sbjct: 181 YHVCIMEGRNREVRRLWESQGFKVSRLKRVRYGCVFLPKRVSAGKWTELNQADTDEL--- 237

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                    +D P   S+ + +  P  +     +F R +      +  +K K  +    
Sbjct: 238 ------SALVDLP---SKPVAKLDPQEMKRYEREFRRQRTRQKAGDQPNKPKGPSRNAR 287


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 95/283 (33%), Positives = 148/283 (52%), Gaps = 15/283 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
              +++ KV+AR+G+ SRRE+ER I + RV+VNG +       +   D +EVDG      
Sbjct: 1   MADEKLHKVLARSGVGSRREMERWIKEGRVQVNGQVAT-LGDRISEGDQVEVDGRKTPLI 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
                  R+ +Y+KP+G + T  DP+GR TVF +LP +   R I++GRLDINT GLLL T
Sbjct: 60  FDNQAERRVLIYNKPVGEICTRHDPEGRPTVFRHLPPLKEGRWIAIGRLDINTSGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS Q  R Y VR  G VD+  L  LK G++++        V     +G+
Sbjct: 120 TDGELANALMHPSAQIDREYAVRVLGDVDEAMLQRLKDGVLLEDGMARFTDVQFFDGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W    + EG+NRE+++++E    +VNRL R+ +GP  L   + +G+ +E++ K +   
Sbjct: 180 NKWYHCVVMEGRNREVRRLWESQEIQVNRLKRVRFGPLFLPSDVRSGTWKELTVKEVNSL 239

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
               +LE        P  + +    ++            R ++
Sbjct: 240 --SKMLEL------KPKRAPKMTADEKQKYQRRFKKQKARRQE 274


>gi|325686573|gb|EGD28599.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 242

 Score =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++        + +    ++  ++ 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEDSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALALGEWRRLTTDELERL 235


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 114/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELEILLA 237


>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 =  259 bits (663), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>gi|332884211|gb|EGK04479.1| hypothetical protein HMPREF9456_00806 [Dysgonomonas mossii DSM
           22836]
          Length = 289

 Score =  259 bits (663), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 137/298 (45%), Gaps = 9/298 (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 +D D  + + D +     R+  +GRLD +++GL++LTN+G +   
Sbjct: 60  VFIAYNKPVGIVST-TDLDEPNNIIDAV-GHDERIFPIGRLDKDSQGLIILTNEGDMVNK 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 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +    AP   ++      P    +  + +   K  +  K   S  +   + V ++   
Sbjct: 233 KTE-SAPKKKTKPQEAKTPQPKGKSANSYKEKKTPTGYKESGSGMRNGKSSVKKKTRK 289


>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 =  259 bits (663), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 73/241 (30%), Positives = 124/241 (51%), Gaps = 3/241 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +  +  TP R++K +A +G+ SRR  +++I    V VNG ++ +   +V   D I VDG
Sbjct: 215 EMPVDPKTPLRLNKFLASSGVCSRRVADQLIVDGHVSVNGEIVTQLGKHVTREDFISVDG 274

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
            P+   E+    L +KP   VTT SDP+ R T  D + +    R+  VGRLD NT GLLL
Sbjct: 275 KPVS-IEKKIYVLLNKPRNCVTTSSDPEKRLTAIDLVRNACNERIYPVGRLDRNTTGLLL 333

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  P  +  ++Y+V     V  + +  +  GI ++        ++   + 
Sbjct: 334 LTNDGDLAAKLMHPKYEKKKIYQVTLDKPVSVEHMQQIASGIELEDGEIHADAISYVDEN 393

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + A V + +  G+NR ++++F+   ++V +L R+ +       L  G  R +++  +R 
Sbjct: 394 -NLAIVGIEIHSGRNRIVRRIFKHLGYRVYKLDRVYFAGLTKKDLPRGRWRYLTEDEVRN 452

Query: 244 Q 244
            
Sbjct: 453 L 453


>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 =  259 bits (663), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 113/230 (49%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   R  +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRACINGEVCTHGAL-VNEGDIVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++++  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKSFTDWFIDMMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L +G NR+I+++   F + V +L R+     +L  L AG  R+++ K L 
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELNELEAGKWRDITPKELE 223


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 118/237 (49%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I      L   E 
Sbjct: 1   MRLDKFLVDCGVGSRSQVKNFLKKKQVIVNGQVETSPKTQIDENKDRITYLDQELTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   DP  + TV D L       RV  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATEDPRHK-TVLDLLDDTARHKRVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +  +  S +W
Sbjct: 119 AHAMLSPKKHVDKIYQAKVAGVMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNESTSW 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           V + + EGK  ++K++      +V  L R+S GP  L   L  G+ R ++++ L   
Sbjct: 179 VQITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSLPNDLELGTWRRLTEEELEAL 235


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 226


>gi|301156161|emb|CBW15632.1| 23S rRNA pseudouridylate synthase [Haemophilus parainfluenzae T3T1]
          Length = 336

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 105/275 (38%), Positives = 151/275 (54%), Gaps = 10/275 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V S   + +
Sbjct: 45  KPSRQSTVEGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKMATLGDRIDVHSGVKVRI 104

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR TVFD LP    +R I+VGRLDIN
Sbjct: 105 DGRIINLQQAQKEVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRLNGARWIAVGRLDIN 164

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L+KG+ ++       ++
Sbjct: 165 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLARLRKGVQLEDGPANFKEI 224

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 225 KFAGGVGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 284

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLV 268
             +    LRE +G     E ++++  P    ++  
Sbjct: 285 DLENVNYLRELVGLPPETETKLDVTKPRRRPKSGQ 319


>gi|254818897|ref|ZP_05223898.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           intracellulare ATCC 13950]
          Length = 247

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 112/239 (46%), Gaps = 4/239 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  + + 
Sbjct: 183 KTLVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGPVSLGKQRPGSFRALGRDEIGQL 241


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 120/243 (49%), Gaps = 9/243 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV++ +      VNG +++     V   +D + V G  +   E 
Sbjct: 1   MRIDKLLSNMGYGSRKEVKKHLKGGGTVVNGEVVKDPKFQVDPESDTVTVHGEEVVYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D +G  TV D L           VGRLD +TEGLLL+TNDG L
Sbjct: 60  FIYLMMNKPPGVLSATEDAEG-ETVIDLLEMEDQIFNPFPVGRLDKDTEGLLLITNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G+V ++ ++   +G+ +  G      ++ + +  G  + +
Sbjct: 119 SHQLLSPKKHVPKTYFAVIEGEVTEEDVSAFAEGVTLDDGYETKPGELEIIS-SGIRSEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + + EGK  ++K++FE    +V  L RI+ G   L  TL  G  RE++ + + E L  H
Sbjct: 178 NLTITEGKFHQVKRMFESVGKRVIYLKRITMGLLPLDETLELGEYRELTDEEV-EGLKNH 236

Query: 249 LLE 251
            L+
Sbjct: 237 KLD 239


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREIML-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>gi|319949182|ref|ZP_08023271.1| pseudouridylate synthase [Dietzia cinnamea P4]
 gi|319437168|gb|EFV92199.1| pseudouridylate synthase [Dietzia cinnamea P4]
          Length = 252

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 121/239 (50%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +  P R+ K++A+AG+ASRR  E +IA+ RV+V+G ++    V V   T  I VDG  + 
Sbjct: 8   DGAPVRLQKILAQAGVASRRASEDLIARGRVEVDGKIVREMGVKVDPATAVIRVDGTRIV 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLT 125
             +       +KP G  TT SD  GR  V D +        R+  VGRLD +TEGLLL+T
Sbjct: 68  LDDTLVHLALNKPRGYHTTMSDEMGRPCVGDLVADRIDAGQRLFHVGRLDADTEGLLLVT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G V +     L++G+ ++       Q +L      
Sbjct: 128 NDGELAHRLMHPSYEVSKTYMATVTGVVGKGIGKQLREGVELEDGPAKVDQFSLLDVHDG 187

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + V V L EG+   ++++       V  L+R  +G   LG   AG+ R+++++ + + 
Sbjct: 188 RSLVKVVLHEGRKHIVRRLLAEVGHPVESLVRTRFGSVALGDQRAGTFRKLNRREVSDL 246


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 119/239 (49%), Gaps = 8/239 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +QE     R++K ++  G  SRR  +R+I + RV++NG+ +      V   D IEVDGV 
Sbjct: 1   MQEQTEGIRLNKYLSEIGHCSRRAADRLIEEGRVQINGVQVI-MGQKVTPLDRIEVDGVL 59

Query: 67  LR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +    ER     ++KPIG+V T      +  + D + +  +R+  +GRLD  +EGL+LLT
Sbjct: 60  VEDLQERNVYIAFNKPIGIVCTTDTRVEKDNIIDYI-NYPTRIFPIGRLDKPSEGLILLT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  V  + +  +  GI I         V    ++  
Sbjct: 119 NDGDIVNKILRARNNHEKEYIVTVNKPVTTEFVEKMANGIPILDTITRKCVV----EQIH 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                + L +G NR+I+++ E+ +++V +L RI     +L  +  G  R+++KK + E 
Sbjct: 175 KNQFRIILTQGLNRQIRRMCEYLDYRVVKLKRIRIMNIEL-NVGVGKYRDLTKKEMVEL 232


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 113/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  AG+ SR +V+ ++ +++V VNG+        V   TD++   G  L   E 
Sbjct: 1   MRLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNELTDNVTYQGQRLNY-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  + TV D L     +  V  VGRLD +T GLLLLTNDG L
Sbjct: 60  FVYYMLNKPKGVISATEDPSHK-TVLDLLDDTARQKAVFPVGRLDKDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + Q+ +    +GI ++          +    +    + 
Sbjct: 119 AHALLSPKKHVAKQYLAKVDGTMTQEDVKHFAQGITLKDHQCMPAYLDILEINESLKTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + + EGK  ++K++       V+ L RIS GP QL + L  G+ R ++   L   
Sbjct: 179 VKITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLTAAELETL 235


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 111/229 (48%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T ++      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAE-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTSEEL 222


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRVFGFTVTKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>gi|254361758|ref|ZP_04977893.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093293|gb|EDN74289.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 355

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 152/274 (55%), Gaps = 12/274 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR---- 68
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  I +DG  +     
Sbjct: 78  EKLQKILARAGQGSRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLMPA 137

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           + E  R+ +Y+KP G + T SDP+GRSTVFD LP    +R I+VGRLDINT GLLL T D
Sbjct: 138 QKEICRVLMYYKPEGELCTRSDPEGRSTVFDRLPRLSGARWIAVGRLDINTSGLLLFTTD 197

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G +D   L  L+KG+ ++       Q+ +    G N 
Sbjct: 198 GELANRLMHPSREVEREYSVRVFGNIDDAMLQRLRKGVQLEDGPANFKQIKVVGGTGLNQ 257

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  +    LRE
Sbjct: 258 WFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLDKGLPRGGWEEMGLEQVNYLRE 317

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            +G  L  E +  ++  +    T +R     + +
Sbjct: 318 LVG--LPPETETKVEVGVNRRRTNIRQIRKAVKQ 349


>gi|148827048|ref|YP_001291801.1| malic enzyme [Haemophilus influenzae PittGG]
 gi|148718290|gb|ABQ99417.1| malic enzyme [Haemophilus influenzae PittGG]
          Length = 232

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQKDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEKNYAEACAEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWLEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 125/238 (52%), Gaps = 10/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ G+ASRR  E MI  +RVK+NG ++        S D +EVDG  ++  +R 
Sbjct: 3   ERVQKILSQWGVASRRRAEDMILARRVKLNGKIVTLGDKADPSCDRLEVDGKLIQPNKRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
           +    L +KP+G+V+T  DP  RS V D LP   ++   +  VGRLD N+ G LLLTNDG
Sbjct: 63  KLIYILLNKPVGVVSTCDDPQNRSIVLDLLPKKLTQGTGIHPVGRLDFNSSGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G   ++ L   ++G+++ G      +V +  +      
Sbjct: 123 DLTLKLTHPRYHLPKTYEVLVKGHPPEETLQQWREGVILMGKKTLPAEVEVIRRSAQQTQ 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-----TLLAGSTREVSKKIL 241
           + V L EG+NR+I+++ E   ++V RL R +     L      +L +G  R ++   +
Sbjct: 183 LKVVLTEGRNRQIRRIVEQLGFRVLRLHRTAIDSLCLSPNHKNSLSSGHYRLLTPSEI 240


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 89/234 (38%), Positives = 123/234 (52%), Gaps = 2/234 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE-R 72
           R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    V V  T   I VDG  L   E +
Sbjct: 12  RLQKVLAQAGVASRRASEQMIADGRVSVDGTVVRNQGVRVDPTKQVIHVDGERLILDETK 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +   +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  R HG+V       L  GI ++          +    G    V + 
Sbjct: 132 RLTHPKYEIRKTYVARLHGEVKPGVKRTLMNGIELEDGPIKVDSFRIVDTYGDITTVEIV 191

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR V    L    G
Sbjct: 192 VHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRVKGNALSALYG 245


>gi|328944867|gb|EGG39027.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 242

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIAVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPRGVISATED-DRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++        + +    ++  ++ 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEDSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++++ +
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALALGEWRRLTEEEM 232


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 112/232 (48%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V      + V G  +   +  
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEY-KPF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 63  IYLMMNKPSGVVSATEDA-VEETVVDFLEEEDRAFSPFPVGRLDKDTEGLLLLTNDGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G+V +  +   ++G+V+  G      ++ +  + G  + V 
Sbjct: 122 HQLLSPKKHVPKTYFAVVDGEVTEADVAAFQRGVVLDDGYETKPAKLVVL-KSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + EGK  ++K++F+    +V  L RI  GP  L   L  G  RE++ + +
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLALDPDLAVGEYRELTDEEV 232


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 120/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     RV    VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRVDLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 104/230 (45%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSRVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL +G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLESGEYRYLTEEEV 226


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 87/238 (36%), Positives = 126/238 (52%), Gaps = 10/238 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R+ K++A+ GIASRRE E MI + RV++NG+L           D I VDG P+   +R  
Sbjct: 4   RLQKILAQWGIASRRESEEMIRRSRVRINGVLAHLGQKVDPERDKISVDGKPVYAQQRPP 63

Query: 74  -RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
               L HKP G+V+T  DP GR TV D LP    +   +  VGRLD  + G L+LTNDG 
Sbjct: 64  LIYLLLHKPAGVVSTCYDPQGRKTVLDLLPPELRKGSGLHPVGRLDAESTGALILTNDGD 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  PS    + Y+V   G   +  L + +KG+V++G      +V L      N+ +
Sbjct: 124 LTFGLTHPSHSIPKTYQVLVKGHPSEAVLEMWRKGVVLEGRKTRPAKVHLIESLAKNSHL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILR 242
            + L+EG+NR+I++V +   + V +L R S GP QL       L  G+ R +    +R
Sbjct: 184 EIVLKEGRNRQIRRVAQQLGYPVIQLHRTSIGPIQLQMPKLPFLGEGNYRSLKSAEIR 241


>gi|229169439|ref|ZP_04297147.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228614044|gb|EEK71161.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 248

 Score =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++G+ ++ A  +V      + + G  +   E 
Sbjct: 7   MRLDKLLANMGHGSRKEVKKLLKDGVVKIDGVPVKDAKFHVNVEEQEVMIHGEVVEYKE- 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 66  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKL 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y     G V ++ +    KG+++  G      ++T+  +    + +
Sbjct: 125 THQLLSPKKHVPKKYYAHISGVVTEEDVIEFAKGVILEDGYETKPGELTIL-KSDDISEI 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 184 ELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLMLDEELELGQYRELTDEEVE 237


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 123/238 (51%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K         +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VD
Sbjct: 171 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVD 230

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ +   +  + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD  TEG++L
Sbjct: 231 GLTV-ATQSYQFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDTETEGVIL 289

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q 
Sbjct: 290 LTNHGELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVEQT 349

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 350 GKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 407


>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 =  259 bits (662), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R   
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLF 225


>gi|318040247|ref|ZP_07972203.1| 16S rRNA pseudouridylate synthase [Synechococcus sp. CB0101]
          Length = 241

 Score =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 116/236 (49%), Gaps = 3/236 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ K+IA AG+ SRR  E ++   RV VNG   E         D I +DG PLR A
Sbjct: 1   MPEERLQKLIAAAGLGSRRYAETLLRAGRVSVNGRTAELGERADPERDAICIDGEPLRPA 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTND 127
           +     L +KP G++ +  DP+GR  V D LP        +  VGRLD ++ G LLL+N+
Sbjct: 61  QPPLALLLNKPAGVMCSCHDPEGRPIVLDLLPPELASGQGLHPVGRLDFHSRGALLLSNN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P  Q  + YR+   GQ  Q  L+   +G+ + G+    + +    Q+    
Sbjct: 121 GALTLQLTHPRFQHSKTYRIWVRGQPSQTVLDRWARGVPLDGLPSQPVTLHRLDQEHDAT 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + + + EG+NR+I++  E     V  L R++ G  +LG L  G  R +  +   +
Sbjct: 181 QLQLVMHEGRNRQIRRTAELLGHPVLDLQRVAIGSIELGELPEGRWRRLDPQEWPD 236


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 104/267 (38%), Positives = 150/267 (56%), Gaps = 10/267 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR-- 68
             +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V +   I +DG  +   
Sbjct: 62  EGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKIATLGDRIDVHAGVKIRIDGHLINLL 121

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
             + E  R+ +Y+KP G + T  DP+GR TVFD LP    SR I+VGRLDINT GLLL T
Sbjct: 122 HAQKEVCRVLMYYKPEGELCTRHDPEGRPTVFDRLPRLTGSRWIAVGRLDINTSGLLLFT 181

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD+  L+ LKKG+ ++       ++      G 
Sbjct: 182 TDGELANRLMHPSREVEREYSVRVFGQVDEAMLHRLKKGVQLEDGPANFKEIKFAGGVGM 241

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE--VSK-KIL 241
           N W  V L EG+NRE+++++E    +V+RLIR  YG   L  +L  G   E  ++    L
Sbjct: 242 NQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDLTNVNYL 301

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLV 268
           RE +G     E ++++  P   ++T  
Sbjct: 302 RELVGLPAEVETKLDVTKPRRRAKTGQ 328


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 104/274 (37%), Positives = 150/274 (54%), Gaps = 12/274 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR---- 68
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  +     
Sbjct: 68  EKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNLISLIPA 127

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +R ++VGRLDINT GLLL T D
Sbjct: 128 QKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLTGARWVAVGRLDINTSGLLLFTTD 187

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G +D+  L  L+KG+ ++       Q+      G N 
Sbjct: 188 GELANRLMHPSREVEREYSVRVFGNIDEAMLQRLRKGVQLEDGPANFKQIKTVGGTGLNQ 247

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  +    LRE
Sbjct: 248 WFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQVNYLRE 307

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            +G  L  E +  +D       T +R     + +
Sbjct: 308 LVG--LPAETETKVDVIKNRRRTNIRQIRKAVKQ 339


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQATKAIHQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEED 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 110/230 (47%), Gaps = 5/230 (2%)

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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           +  + +KP G V +H D D   T++       S ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYIMLYKPQGYVCSHDDGDY-PTIYQFFDYPLSTKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     ++ +     + GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPIESNYQQACEAGILLRGEKELTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G  +L  TL  G  R +S++ +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGCIELDETLEEGGYRSLSEQEI 227


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 95/297 (31%), Positives = 148/297 (49%), Gaps = 10/297 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++AR+G  SRRE+E  +   R+ V+G +      V V     I +DG  L   E
Sbjct: 42  TEKLQKILARSGHGSRREIETFLQAGRISVDGKIATLGDRVEVTPATKIRLDGRLLAIKE 101

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T  DP+GR TVF+ LP    +R I+VGRLD+NT GLLL T 
Sbjct: 102 PEKEICRVMAYYKPEGELCTRHDPEGRPTVFNRLPRLTGARWIAVGRLDVNTSGLLLFTT 161

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+++  K+  L +G+ ++        V+    +G N
Sbjct: 162 DGELANRLMHPSREVEREYAVRVFGEINDAKIRQLTQGVQLEDGPASFKTVSYRGGEGMN 221

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    LR
Sbjct: 222 QWFNVTLTEGRNREVRRLWESVGVQVSRLIRVRYGDIDLPKGLPRGGWTELGLEQTNYLR 281

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           E +   +  E++V ++      +     R              K+ SS+     + +
Sbjct: 282 ELVELPVETESKVAVERDQRRIKANQIRRAVKRHTQVASRPASKRQSSRPTAKRRTR 338


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 93/250 (37%), Positives = 131/250 (52%), Gaps = 6/250 (2%)

Query: 3   DKNIVQENFTPQ-----RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS- 56
           D++ V E  T +     R+ KV+A+AG+ASRR  E MI   RV V+G ++ R    V   
Sbjct: 368 DRDYVDERDTTEVPDGVRLQKVLAQAGVASRRACEDMIGDGRVTVDGQVVRRFGARVDPA 427

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
              I VDG  L           +KPIG+V+T SDPDGR ++ D +     R+  VGRLD 
Sbjct: 428 KQVIHVDGKRLPTMPDLVYLAINKPIGVVSTMSDPDGRPSLADFVADRTERLFHVGRLDT 487

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            TEGL+LLTNDG LA  L  PS    + Y  +  G++++D    LKKGI ++        
Sbjct: 488 ETEGLILLTNDGELANRLTHPSYGVQKKYWAKVPGRIERDLGRRLKKGIELEDGIAKADS 547

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            TL  + G  A V V L EG+   ++++ E     V  L RI +GP +LG L  G+ R +
Sbjct: 548 FTLVQEHGQQALVEVVLHEGRKHIVRRMLEEVGHPVIDLARIEFGPVKLGRLKPGTVRAL 607

Query: 237 SKKILREQLG 246
           + K + E   
Sbjct: 608 TVKEVGELYA 617


>gi|241662811|ref|YP_002981171.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864838|gb|ACS62499.1| pseudouridine synthase [Ralstonia pickettii 12D]
          Length = 594

 Score =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 101/313 (32%), Positives = 158/313 (50%), Gaps = 9/313 (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  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  ++     +  R+ LYHKP G + + SDP+GR TVFD LP + + + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 380 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 439

Query: 237 SKKILREQLGPHLLE-EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           S + +R  +G   ++     +               P ++  +   F       S+  G+
Sbjct: 440 SAEDVRTLMGTLGMKVPTASSGGGQDRQGNRRRGPAPVLMGPMSSGFAGEANFQSRGMGI 499

Query: 296 SKQKKLATPVHRR 308
               + A P  RR
Sbjct: 500 ENGNR-AQPAQRR 511


>gi|260905260|ref|ZP_05913582.1| pseudouridine synthase, Rsu [Brevibacterium linens BL2]
          Length = 238

 Score =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 116/233 (49%), Gaps = 1/233 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L  G+NR ++++ +     V RL+R  +GP  L     G  R +    + E  
Sbjct: 181 LHSGRNRIVRRLLKEVGHPVERLVRTKFGPITLDEQRQGKIRPLRSDEIGELF 233


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 121/233 (51%), Gaps = 6/233 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           P R+ K++A  G  SR++V+++I   +V +NG+++  A   V  + D I V G  +   E
Sbjct: 6   PARIDKILASCGYGSRKDVKKLIKSGQVSINGVIINDAGTLVNPSLDEIIVAGECIFY-E 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
                + +KP  +V++  D D  +TV D L   +   ++  VGRLD + EGL+ LT+DG 
Sbjct: 65  DNVYIMMNKPQDVVSSTYD-DFETTVIDLLEGEYFHRKLFPVGRLDKDAEGLIFLTDDGK 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +A  L  P  +  + Y V  +G++++  +     G+ ++       ++ +  +  + +  
Sbjct: 124 MAHRLLSPKNRVPKTYYVEVYGRLNESDVKAFAAGMELEDFTALPAELDILEKNNNISSA 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  +IK++ +    +V  L R+  GP +L   L  G  R+++K+ +
Sbjct: 184 YVTIYEGKFHQIKRMMKARGKEVTYLKRLFLGPLRLDEELEPGMWRKLTKEEV 236


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 104/275 (37%), Positives = 150/275 (54%), Gaps = 10/275 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
           K   Q     +++ KV+ARAG  SRRE+E MIA  RV V+G +      ++V S   + +
Sbjct: 45  KPSCQSTVEGEKLQKVLARAGQGSRREIEAMIADNRVSVDGKMATLGDRIDVHSGVKVRI 104

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T SDP+GR TVFD LP    +R I+VGRLDIN
Sbjct: 105 DGRIINLQQAQKEVCRVLMYYKPEGELCTRSDPEGRPTVFDRLPRLNGARWIAVGRLDIN 164

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  GQVD   L  L++G+ ++       ++
Sbjct: 165 TSGLLLFTTDGELANCLMHPSREVEREYSVRVFGQVDDAMLARLRRGVQLEDGPANFKEI 224

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+
Sbjct: 225 KFAGGIGINQWYDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKGLPRGGWEEM 284

Query: 237 SKK---ILREQLGPHLLEEAQVNLDAPIYSSETLV 268
             +    LRE +G     E ++++  P    ++  
Sbjct: 285 DLENVNYLRELVGLPPETETKLDVTKPRRRPKSGQ 319


>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 =  259 bits (662), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 103/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  +++    V VN  + +  AV V     IE  G  L   +  
Sbjct: 1   MRLDKFLCDALGATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVIEWQGREL-AMQGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGFNH-TAFVLLDEVKMDELHFAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D    L +G+ ++      +   +         V + 
Sbjct: 119 RITSPKHKCDKTYRVWLADPIGSDYAEKLAEGVQLRNEKELTLPAQMSIVNADENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV +L R   G  +L  +L  G  R ++++ +
Sbjct: 179 IHEGKYHQVKRMFAALGNKVEQLHRERIGAIELDESLEPGEYRYLTQEEI 228


>gi|257083600|ref|ZP_05577961.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256991630|gb|EEU78932.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 244

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEVVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMATGVKILGTKTLPCEIT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 226


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 106/308 (34%), Positives = 151/308 (49%), Gaps = 21/308 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI   R+ V+G +      V V     I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIESMIEAGRISVDGKIATLGDRVEVTRATKIRIDGHVVSVRE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+ +Y+KP G + T SDP+GR TVFD LP     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-GTLLAGSTRE--VSK-KILR 242
            W  V L EG+NRE+++++E    +V+RLIR+ YG  QL   L  G   E  ++    LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIQLPKGLPRGGWMEMKLTDVNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE-VPDDFTRMKKNSSQKNGLSKQKKL 301
           E           V L     S   + R+R  + +  +     R   +  Q  G ++    
Sbjct: 242 EL----------VQLTPETVSKLPVERERRRVKANQIRRAVKRHGGHGGQVGGNNRPAGS 291

Query: 302 ATPVHRRN 309
                +RN
Sbjct: 292 RRNAPKRN 299


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 114/229 (49%), Positives = 156/229 (68%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+
Sbjct: 452 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLK 500


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 77/237 (32%), Positives = 121/237 (51%)

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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V + L  GKNR ++++       V+ L R       L  L  G  R +  K L   
Sbjct: 216 IVQLTLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAAL 272


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 119/246 (48%), Gaps = 15/246 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            R+ + +      SR EV++MI   RV V+G +   A   +  +   + +DG  +  A  
Sbjct: 5   MRLDRYLVEMKKGSRSEVKKMIKSGRVSVDGEICREAERKIQPSASEVSLDGTQVGYAA- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G+V+   D   ++ V     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 64  YEYFMLNKPAGVVSATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGKLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            L  P     + Y  R  G++ ++ +   K+G+ ++      +   L  QK         
Sbjct: 124 RLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDG-TRTLPARLLIQKEAGTAEEGK 182

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
              S + + + + EGK  ++K++FE    +V  L R+S G  +L  +L  G+ R ++++ 
Sbjct: 183 ADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLYESLAPGAYRRLTEEE 242

Query: 241 LREQLG 246
           + +  G
Sbjct: 243 ISKLQG 248


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +     + V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGEL-VSDGDVVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKVSEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT    +   +   + 
Sbjct: 118 RILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQIIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +   + I+       QVT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSGVVKIKDGMTKQCQVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVTKLKRVRIMNIELDNLEVGKWRNVTSEELEILIG 227


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 88/234 (37%), Positives = 122/234 (52%), Gaps = 2/234 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE-R 72
           R+ KV+A+AG+ASRR  E+MIA  RV V+G ++    V V      I VDG  L   E +
Sbjct: 12  RLQKVLAQAGVASRRASEQMIADGRVSVDGTVVRNQGVRVDPAKQVIHVDGERLILDETK 71

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +   +KPIG V+T SDP+GR T+ D +     R+  VGRLDI+T GLLLLTNDG LA 
Sbjct: 72  HIVLAVNKPIGTVSTMSDPEGRPTIADLIADYPERLYHVGRLDIDTSGLLLLTNDGELAN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y  R HG+V       L  GI ++          +    G    V + 
Sbjct: 132 RLTHPKYEIRKTYVARLHGEVKPGVKRTLMNGIELEDGPIKVDSFRIVDTYGDITTVEIV 191

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + EG+NR ++++ E   + V  L+R  +GP  L  L  G+TR V    L    G
Sbjct: 192 VHEGRNRLVRRMMEAVGYPVRELVRTGFGPISLDHLKQGTTRRVKGNALSALYG 245


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 120/239 (50%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V++ I  Q+V+V+G L      NV  +   I V G  L  +  
Sbjct: 1   MRLDKLLGQAGFGSRGQVKKFIRSQQVRVDGELARTGNQNVDPSLQTITVSGKQLSYS-P 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP GLV+   D     TV D +  +  R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 60  HVYYILNKPAGLVSVVRD-QHYQTVIDLIAVVDRREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +  D +     GI  + G      ++ + +     +  
Sbjct: 119 GFRLLHPKYHVDKTYYVEVNGDLGIDAIAFFDNGIAFLDGTVCKSAKLQIISSSSEVSRA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+GPF+LG L  G  RE++ +    LR  L
Sbjct: 179 YITITEGKFHQVKKMFLAYGVKVTYLKRISFGPFELGDLSVGEYRELTAEEKNSLRNYL 237


>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 =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  SR+++++++AQ+ V +N  +  +    V    D + V G  +   +R
Sbjct: 1   MRIEKYLADTGWGSRKDIKQLLAQKIVTINDQVCSKGGTQVTPGSDCVAVGGQLVPY-QR 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D     TV D L   +  +    VGRLDI+T GLLLLTN+G L
Sbjct: 60  YHYYLLNKPEGILSATED-RHHQTVIDWLGEGYQHLDLFPVGRLDIDTTGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A  L  P  +  + Y     G VDQ  +   + G+ +        ++T+ +Q      + 
Sbjct: 119 AHQLLSPKKKVDKTYTATIRGLVDQADIAAFEAGLDLGDFTSLPAELTVLSQDVDQGTSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           + V ++EGK  ++K++F+    +V  L R++ GP +L   L  G  R ++++ 
Sbjct: 179 IQVIIQEGKFHQVKRMFQAVGKEVLSLHRLAMGPLRLESDLAHGQWRSLTEQE 231


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 102/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIML-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIQDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 116/237 (48%), Gaps = 9/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+ +I +  ++VNG +++     V    D +   G  +   + 
Sbjct: 7   MRLDKFLADMGLGSRKEVKGLIKKGTIEVNGQVVKSDKAQVNEFEDAVTYLGEIITYQKD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G+++   D +   TV D L     R  +  VGRLD +TEGLL+LTNDG  
Sbjct: 67  FYYIL-HKPAGVISATQD-NHDQTVIDLLEDQDYREDLFPVGRLDKDTEGLLILTNDGVF 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y     G + ++ + L  +G++I G       ++ +D   Q+   +
Sbjct: 125 AHQLLSPKKHVEKEYLAEVSGIMTEEDIRLFAEGLIIDGDEQTLPAKLQIDQVDQETETS 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            + + L EGK  ++K++ +    +V  L RI  G F L   L  G  R ++K+ L +
Sbjct: 185 IIRLILHEGKFHQVKRMVKAVGKEVLYLKRIRMGKFWLPKDLNKGQYRPMTKEELEQ 241


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGAIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ +  G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSSGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R ++ + L    G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELGVGKWRNIATEELEILKG 227


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 100/313 (31%), Positives = 159/313 (50%), Gaps = 9/313 (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---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           V+G  +++    +  R+ LYHKP G + + SDP+GR TVFD LP + + + ++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 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V L EG+NRE++++FE  N  V+RLIR  YG F L   L  G  +EV
Sbjct: 391 VDGGGEGVNHWYHVALTEGRNREVRRMFEAVNLTVSRLIRTRYGSFVLPRGLKRGRWQEV 450

Query: 237 SKKILREQLGPHLLE-EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           S + +R  +G   ++     +               P ++  +   F       S+  G+
Sbjct: 451 SAEDVRTLMGTLGMKVPTASSGGGQDRQGNRRRGPAPVLMGPMSSGFAGEANFQSRGMGI 510

Query: 296 SKQKKLATPVHRR 308
               + A P  RR
Sbjct: 511 ENGNR-AQPAQRR 522


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 104/303 (34%), Positives = 155/303 (51%), Gaps = 10/303 (3%)

Query: 4   KNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K  V+E+ +P  +++ KV+ARAGI SRRE+ER I + RVKVN  +       V  TD I 
Sbjct: 77  KPSVKESASPVDEKLQKVLARAGIGSRREMERAIEEGRVKVNDRIAT-LGDRVTLTDKIF 135

Query: 62  VDGVPL---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           V G  +    +A R R+ LY+KP G + +  DP+GR TV+D+LPS    R ISVGRLD N
Sbjct: 136 VGGQRVVLRTEAARRRVILYNKPEGEICSRHDPEGRPTVYDSLPSLKGERWISVGRLDFN 195

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL TNDG LA  L  PS+   R Y VR  G VD D    L +G+++         +
Sbjct: 196 TSGLLLFTNDGELANKLMHPSSVIDREYLVRIQGDVDDDMKERLLEGVLLDDGVARFTDI 255

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV 236
                +G N W    + EG+NRE+++++E    KV+RL R+ Y    + + +  G   E+
Sbjct: 256 VDGAGEGKNRWFYCVVMEGRNREVRRLWESQGVKVSRLKRVRYANIFIPSHVRVGQWTEL 315

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           +++ +R+       +    N    +  S   V        ++    +  K+        S
Sbjct: 316 TEQEIRDLCMTAGFDSN--NYTRIMRPSREEVAQIERHEKKLRSASSAPKRVKVDLRKRS 373

Query: 297 KQK 299
            +K
Sbjct: 374 PRK 376


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 113/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A   +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKFQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDINT GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDINTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++       ++ + +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPARLEILSTDAEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 103/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  +++    V VN  + +  AV V     +E  G  L   +  
Sbjct: 1   MRLDKFLCDALGATRKEATKILKSGEVTVNEQVQKSGAVKVTEECVVEWQGREL-AMQGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGFNH-TAFVLLDEVKMDELHFAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D    L +G+ ++      +   +         V + 
Sbjct: 119 RITSPKHKCDKTYRVWLADPIGSDYAEKLAEGVQLRNEKELTLPAQMTIVNADENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV +L R   G  +L  +L  G  R ++++ +
Sbjct: 179 IHEGKYHQVKRMFAALGNKVEQLHRERIGAIELDESLEPGEYRYLTQEEI 228


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 104/274 (37%), Positives = 152/274 (55%), Gaps = 12/274 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR---- 68
           +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S+  I +DG  +     
Sbjct: 78  EKLQKILARAGQGSRRELEEIIAAGRVSVDGKMATLGDRVQVSSSTKIRIDGHLVNLMPA 137

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +R I+VGRLDINT GLLL T D
Sbjct: 138 QKEICRVLMYYKPEGELCTRSDPEGRATVFDRLPRLSGARWIAVGRLDINTSGLLLFTTD 197

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  R Y VR  G +D   L  L+KG+ ++       Q+ +    G N 
Sbjct: 198 GELANRLMHPSREVEREYSVRVFGNIDDAMLQRLRKGVQLEDGPANFKQIKVVGGTGLNQ 257

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  +    LRE
Sbjct: 258 WFDVTLTEGRNREVRRLWESQGVEVSRLIRIRYGNIKLDKGLPRGGWEEMGLEQVNYLRE 317

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
            +G  L  E +  ++  +    T +R     + +
Sbjct: 318 LVG--LPPETETKVEVGVNRRRTNIRQIRKAVKQ 349


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 115/240 (47%), Gaps = 7/240 (2%)

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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R        E  +
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFADLNYEPQE 237


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 113/232 (48%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
            R++K I+  G  SRRE ++++   +V +NG+            D + V+G P+  K  +
Sbjct: 1   MRINKFISETGFCSRREADKLVESGQVTINGVKA-VLGSQAEPGDDVRVNGRPIAAKRSK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+  T ++   +  + D +     R+  +GRLD ++EGL+LLT+DG +  
Sbjct: 60  HVYIALNKPVGITCT-TETHVKGNIVDFV-GHPERIFPIGRLDKDSEGLILLTSDGDIVN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V     +    +  + +G+ I G      +VT    + S+    + 
Sbjct: 118 KILRAEGKHEKEYIVTVDRPITPSFVKAMSEGVKILGEMTLPCKVT----RVSDRVFRII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L EGKNR+I+++     ++V RL RI      LG    G+ R+++++  RE 
Sbjct: 174 LTEGKNRQIRRMCSALGYEVRRLQRIRIMNIHLGQQKVGTWRDLTEQEKREL 225


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 105/352 (29%), Positives = 153/352 (43%), Gaps = 19/352 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---E 71
           ++ KV+A  G+ SRR++E +I Q RV VNG+        +  TD + ++G P+ +    +
Sbjct: 198 KLHKVLADVGMGSRRDMEDLIIQGRVSVNGLPA-HIGQRIGPTDQVRINGKPVHRKIQTK 256

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
             R+ +YHKP G + + SDP+GR TVFD LP     R I+VGRLD NTEGLLL T  G L
Sbjct: 257 PPRVIMYHKPAGEIVSQSDPEGRPTVFDRLPKPRQGRWIAVGRLDFNTEGLLLFTTSGEL 316

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     R Y VR  G + Q+   LLK GI +       +++ +   +G+N W  
Sbjct: 317 ANRLMHPRYGVEREYAVRILGDLSQENTALLKSGITLDDGQAKFLRLAMGGGEGANRWYH 376

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHL 249
           V L EG+NRE++++FE     V+RLIR  YG F L   L  G       + +      +L
Sbjct: 377 VALSEGRNREVRRMFEAVGHTVSRLIRTRYGIFLLPPRLRRGKW-----EEIEAGGIYNL 431

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH--- 306
           ++ A + +  P                   +DF      +S     S+        H   
Sbjct: 432 MKSAGLKMPQP-SDKGRSPNPNNRDRRPAGEDFQPDPMQTSVSYWGSRDALTLASGHNGL 490

Query: 307 ----RRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
               R         A      F   +                +   R  AKK
Sbjct: 491 THQSRGGKPGGGGAASEGRGPFRGRTQGGRPGQGAGQGGQGGQGQNRNKAKK 542


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 75/234 (32%), Positives = 119/234 (50%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AGI SRR+ E +I++ RV VNG  +      V   D IEVDG  + K E  
Sbjct: 2   ERLQKVIAAAGITSRRKAEVLISEGRVAVNGETITELGYKVKRGDLIEVDGKAIEK-EDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP   + T  D  GR TV D +     R+ +VGRLD +T G+++LTNDG  A  
Sbjct: 61  VYFLMNKPKRTMCTSDDEFGRQTVVDLV-DCRQRIFTVGRLDYDTSGVIILTNDGDFANE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAWVT 190
           +  P     +VY +  +G +  + +  +K GIV+  GI     +  +  +  + +     
Sbjct: 120 IIHPRYHIPKVYNLTINGILTPEDMKKIKAGIVLDDGIKTLPAKYRMTEKDTEKNQCSFD 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+NR+IK++ E   ++V RL R          L  G  R +    +++ 
Sbjct: 180 LTIVEGRNRQIKRMMEALGYEVRRLHRSRLAFLHCSDLRQGEYRVLKPFEVKQL 233


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 114/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDSKHR-TVLDLLDDVARSKGVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A  L  P     + Y  +  G + Q+ +    KGI ++       ++ + +   + + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMSQEDVETFAKGIPLKDFTCQPARLEIISIDTEKNQSK 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + V + EGK  ++K++  +   +V  L R++ G   LG  L  G  R ++K+ L   L 
Sbjct: 179 IRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGTLALGENLERGEWRRLTKEELEVLLA 237


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 119/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I   G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIAFMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 75/332 (22%), Positives = 131/332 (39%), Gaps = 16/332 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  KN         R++K I+ +G+ SRRE +R I    V +NG    +    V+  D +
Sbjct: 1   MPGKNST-------RLNKYISESGMCSRREADRYIENGNVAINGK-AAQVGDQVLPGDKV 52

Query: 61  EVDGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            V+G  +     E       +KP+G+V+T    + R+ V  N      R+  +GRLD ++
Sbjct: 53  TVNGQLIEPRDEEDLIFIALNKPVGVVSTTDPAERRNIV--NHVGHGERIFPIGRLDKDS 110

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +GL+ LT++G L   +        + Y V  +  V  + +  +  G+ I G      +V 
Sbjct: 111 QGLIFLTSNGDLVNKILRAGNNHEKEYLVTVNKPVTTEFVQGMSAGVPILGTVTKRCKV- 169

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +K S     + L +G NR+I+++ EFF ++V +L R+      L  L  G  R++  
Sbjct: 170 ---EKVSRFVFRITLVQGLNRQIRRMCEFFGYEVTKLERVRIMNISLKGLSVGEWRDLGP 226

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           K L           ++V+ D    + +  V+         P         + Q     K 
Sbjct: 227 KELAGLFDMIRDSSSEVSPDNRSETKKPAVKRPSKKPGASPSGPRGKGAKTGQPGRPGKP 286

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
                   R    S       +     S   +
Sbjct: 287 TGKHGKPSRPGKPSKRGKPGKLRKPRQSSVKR 318


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 85/237 (35%), Positives = 133/237 (56%), Gaps = 7/237 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           T  R++K IA AGIASRR  + ++ + +VKVNG L +   + V    D +EV+G  ++  
Sbjct: 5   TTIRLNKYIASAGIASRRGADELVQKGKVKVNGELADSPGIQVDPDNDRVEVNGKLVQHD 64

Query: 71  ERTR--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTN 126
           E+++    L HK I  VTT  DP GR TV D LP      RV  VGRLD  +EG+LLLT 
Sbjct: 65  EKSKDLYILLHKTIETVTTAKDPQGRKTVLDLLPPDVINRRVFPVGRLDFYSEGMLLLTT 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKG 184
           DG L   +  P     ++Y V   G++ + +L++++ G+ ++  G     +++   ++ G
Sbjct: 125 DGELCNRMTHPKWHLPKIYHVTIRGKLSEKELSVMQNGMYLEDKGELLAPVKIKAISEVG 184

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 + LR+G NR+I+++F  F+  + RL R+  G  +LG L  G  RE+S K L
Sbjct: 185 ETTKYEMELRQGINRQIRRMFGEFDKTILRLKRVRQGRIELGALKPGKWRELSAKEL 241


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 101/331 (30%), Positives = 157/331 (47%), Gaps = 17/331 (5%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  ++  P ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+
Sbjct: 101 KYLNSDSVMP-KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVN 158

Query: 64  GVPL---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+      +  R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTE
Sbjct: 159 GKPIMRVNTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTE 218

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A  +  P     R Y VR  G++D+ +   L  GI ++        +  
Sbjct: 219 GLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGLAAFGALDY 278

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
               GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  TL  G   E+  
Sbjct: 279 LGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDVVLPRTLRRGRWEELDA 338

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            ++   +    ++   V  D     +    +   +  S +P  F  M +     NGL+  
Sbjct: 339 SLVTALM----VQLGLVRDDDEAGGNRRRSKQPQSHDSALPPGFGTMDR-----NGLNGA 389

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +       +     +   A     S    +G
Sbjct: 390 RIGRRGKLQGGRLGSAGQAA-ACPSDPFGTG 419


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 96/357 (26%), Positives = 164/357 (45%), Gaps = 11/357 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +++  E+  P ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + +
Sbjct: 187 RRDLTAEDDAP-KLHKVLADAGLGSRRDMEELIVAGRVSVNGEPA-HIGQRILPTDAVRI 244

Query: 63  DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +G  +++       R+ +YHKP G + +H+DP+GR++VFD LP++ + + ++VGRLD NT
Sbjct: 245 NGKLIQRKVSKRPPRVLVYHKPAGEIVSHADPEGRNSVFDRLPTMKAGKWLAVGRLDYNT 304

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL T  G LA  L  P     R Y VR  G++++     L  G+ +        ++ 
Sbjct: 305 EGLLLFTTSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLSGVELDDGPAQFSRIA 364

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G N W  V + EG+NRE++++FE     V+RLIR  YG   L  TL  G   E+ 
Sbjct: 365 DGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAMTLPQTLRRGRWEELE 424

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R  +    LE+          S       +       P       K   +  G + 
Sbjct: 425 ENAVRNLMAACGLEKQAGEG----KSGNGGHAGKGQGNGNGPRGNAMQNKGPQKGRGGNY 480

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +     ++     N     G  +       ++ +  + +  FP     R    ++
Sbjct: 481 GNQGGNYGNQGGNYGNQGGGYGGGNKGGQPKSRQPDPLQTALGFPDAGQRRNNRPQR 537


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 114/229 (49%), Positives = 156/229 (68%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+
Sbjct: 451 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLK 499


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 120/237 (50%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++  ++V VNG +       +    D I V G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQIDEKSDQIAVAGQVLSH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   R TV D L +   +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYVLNKPKGVISATEDDRHR-TVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A V+  P     ++YR +  G + Q+ +     GI ++ +     Q+T+ +  +    + 
Sbjct: 119 AHVMLSPKKHVDKLYRAQVDGIMTQEDVERFAAGIELKDLTCQPAQLTILSTDEAKQTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + +REGK  ++K++ +     V  L R++ GP +L   L  G  R ++   L++ 
Sbjct: 179 VDITIREGKFHQVKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQL 235


>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 =  258 bits (661), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 120/233 (51%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +    
Sbjct: 40  EPERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRIHTDT 99

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++W +HKP+G V++    D R  + D +  +  RV +VGRLD  T GLLLLTN+G LA
Sbjct: 100 VLQVWAFHKPVGTVSSMQPEDDRPCIGDWVTKLPERVYNVGRLDAATAGLLLLTNNGELA 159

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  PS +  + Y     GQV      +L++G+ ++       +  L   +  ++ V +
Sbjct: 160 NRIMHPSYEVPKTYVAVVQGQVKMGLGKVLRRGVELEDGKVKVDKFKLIEVRRGSSIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L  GKNR ++++       V+ L R       L  L  G  R +  K L   
Sbjct: 220 TLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAAL 272


>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 =  258 bits (661), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 129/294 (43%), Gaps = 11/294 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +   +
Sbjct: 5   SSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAT-VGEQVYAGDVVKVNGQLIEPRD 63

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +    L   +KP+G++ T  D +G + V  +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 64  QNDLVLIALNKPVGIICTTEDGEGDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 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     L
Sbjct: 178 SITLVQGLNRQIRRMCKYFGYEVTKLERTRIMNINLKGLPIGEWRDLRDDELIELF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +  +           V  +   IS           ++ +K      +K   
Sbjct: 236 IENSSSDEKPQKKPKAKPVVAKKPAISRSKPAEKSEANSAGRKRFTQPGRKKKG 289


>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 =  258 bits (661), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 115/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      +  +D +
Sbjct: 248 IEYKEQFVDPNEPIRLNKFLANAGVCSRREADEFITAGVVSVNGEVVTELGTKIKRSDVV 307

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 308 KFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMDLVKGACNERIYPVGRLDRNTT 366

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     + +  ++ +  G+ ++        ++ 
Sbjct: 367 GVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADMDQIAAGVQLEDGEIHADAISY 426

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            T       V + +  GKNR ++++FE   +KV +L R+ +       L  G  R +S+ 
Sbjct: 427 -TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFFAGLTKKGLRRGDWRYLSEA 485

Query: 240 IL 241
            +
Sbjct: 486 EV 487


>gi|332883058|gb|EGK03342.1| hypothetical protein HMPREF9456_01979 [Dysgonomonas mossii DSM
           22836]
          Length = 482

 Score =  258 bits (661), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 119/242 (49%), Gaps = 4/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K K  + +  TP R++K +A AG+ SRRE +  I    VKVNG ++++    V   D +
Sbjct: 235 VKYKENI-DPSTPLRLNKYLANAGVCSRREADAFITSGVVKVNGEVVDQLGAKVTRGDLV 293

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
                P+R  E     L +KP   VTT  DP  R TV D + +    R+  VGRLD NT 
Sbjct: 294 TFHDQPVRL-ESKVYVLLNKPKNCVTTSDDPQNRLTVMDLVKNACPERIYPVGRLDRNTT 352

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P  +  ++Y+V     V  + +  +  G+ +         +  
Sbjct: 353 GVLLLTNDGDLASKLMHPKFKKKKIYQVTLDRDVAIEDMQAIADGVELDDGEIHADSIAY 412

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +   N  V + +  G+NR ++++FE   ++V +L R+ +       +     R +++K
Sbjct: 413 QAEDVLN-VVGIEIHSGRNRIVRRIFEKLGYQVVKLDRVYFAGLTKKNIPRSKWRYLTEK 471

Query: 240 IL 241
            +
Sbjct: 472 EV 473


>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 =  258 bits (661), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 112/232 (48%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V      + V G  +   +  
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEY-KPF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 63  IYLMMNKPSGVVSATEDA-VEETVVDLLEEEDRAFCPFPVGRLDKDTEGLLLLTNDGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G+V +  +   ++G+V+  G      ++ +  + G  + V 
Sbjct: 122 HQLLSPKKHVPKTYFAVVGGEVTEADVAAFQRGVVLDDGYETKPAKLVVL-KSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + EGK  ++K++F+    +V  L RI  GP  L   L  G  RE++ + +
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLALDPDLAVGEYRELTDEEV 232


>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 =  258 bits (661), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 100/347 (28%), Positives = 164/347 (47%), Gaps = 13/347 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +  PQR+ K++A AG  SRRE+E +IA  R+ +NG        +V+ +D + +D  PL
Sbjct: 23  DPDAVPQRLHKLLALAGFGSRREMETLIASGRITINGKTA-EVGASVVPSDVVRLDSRPL 81

Query: 68  R---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
           R   + E  ++ LYHKP G + +H DP+ R++VFD LP I + + 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 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 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 ALL-------EWAELAVPKAVPRQLSPREKEKLGKVFTPKARKSRFDPEAHLESRGPRRV 314

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
           T      +   +   +    S      +  +   R  + P+++ + R
Sbjct: 315 TKAREEGMRQELGKQQAGRRSRHGAETEEAQRPSRQGAKPARKPVNR 361


>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 =  258 bits (661), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 71/278 (25%), Positives = 126/278 (45%), Gaps = 11/278 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G  SRRE ++ IA  RV +NG +       V  +D +E+DG PL+   +  
Sbjct: 6   RLNKYISDTGFCSRREADKYIADGRVTLNGKIP-EVGTKVTDSDVVEIDGKPLKAKPKAV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y+KP+G+  T ++ + RS +   + +   R+  +GRLD  +EGL+ LTN+G +   +
Sbjct: 65  FIAYNKPVGVTCT-TELNIRSNIISAI-NHPERIFPIGRLDRPSEGLIFLTNEGDIVNKI 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V     +    +  +  G+ I G      +VT  +  G N    + L 
Sbjct: 123 LRAGNNHEKEYLVTVDKAISPQFIKKMGAGVPILGTVTKQCKVTQVSSHGFN----IVLT 178

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLGPHLL 250
           +G NR+I+++ EF  ++V  L R+      L  L +G  R ++ K +    R   G    
Sbjct: 179 QGLNRQIRRMCEFLGYEVVTLKRVRIMNIDLTGLRSGQWRNLTDKEMAIINRSIEGSGKT 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           EE  V+ +      + + +        +     R+ K 
Sbjct: 239 EELSVDPNKNKNFKKPVKKQFDEPEQTMKTQAVRVIKK 276


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 117/235 (49%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I++ RV VNG + +     V   D I V G  LR A    
Sbjct: 5   RLNKFISESGKASRRGADKLISEGRVTVNGKVAK-VGDQVKPGDDIRVSGQQLRIARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T S+   +  + D +     R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITST-SEKKVKGNIIDLVNHPL-RIHHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + +  + +G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVAVDKPITPEFIKNMSEGVKILGTKTLPCKVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           +G NR+I+++ E   ++V RL R       L  L  G  R+++KK  R QL   L
Sbjct: 178 QGLNRQIRRMCEVLGYEVYRLQRTRIMNIHLNNLPVGQWRDLTKKE-RTQLFKEL 231


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 68/298 (22%), Positives = 123/298 (41%), Gaps = 11/298 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +   
Sbjct: 4   DESMRLNKYISESGICSRREADRFIEQGNVFINGKRA-GVGDQVFAGDLVKVNGQVIEPR 62

Query: 71  E--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E       + +KP+G+V+T    +  + V  +  +  +R+  +GRLD +++GL+ LTN G
Sbjct: 63  EADSLVFIVLNKPVGIVSTTEAGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V     V  + +  +  G+ I G      +V     K +   
Sbjct: 121 DLVNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGAVTKKCKVK----KEAPFV 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
             + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L E     
Sbjct: 177 FRITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIELF--K 234

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
           L+E++   +           +      S          K   + +      +   P  
Sbjct: 235 LIEDSSSEVKPAKGGQAAAGQGGKPKASAAQAGKPAPGKKPRRDDDHEIGGRPNVPGP 292


>gi|332830030|gb|EGK02658.1| hypothetical protein HMPREF9455_00908 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 342

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 144/318 (45%), Gaps = 16/318 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRRE +R I + RV +NG   +   + V+    ++V+G  +       
Sbjct: 4   RLNKYISNSGFCSRREADRFIEEGRVTINGKRAQ-VGMRVLPGQKVKVNGELIVNKIEPV 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              ++KP+G+V+T +DP  R  + + +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 63  YIAFNKPVGIVST-TDPQERDNIINFI-RHEQRIFPIGRLDKDSQGLILLTNDGDIVNKI 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V+ +  + +D L  + +G+ I        ++     + +     + L 
Sbjct: 121 LRAGNNHKKDYLVKVNRPITKDFLTRMAQGVPILDRVTRRCEIV----EINPYMFRISLI 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E+F+++V +L RI     +LG L  G+ R ++   L       +LE ++
Sbjct: 177 QGLNRQIRRMCEYFDYEVLKLERIQIMNIKLGDLGQGNWRNLTPTELEGLF--DMLENSE 234

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNV 314
                          ++    +    D     + +S      K+ K   P    + +SN 
Sbjct: 235 KT------QMSKAPSNKAFNKALEEFDIKTDYRKASIAAKYGKKDKTDKPGSTNSKSSNT 288

Query: 315 WMAKGIHSSFLSDSGQRE 332
             A     +      +R+
Sbjct: 289 -AAPSSDENEHKAKPKRK 305


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 63/260 (24%), Positives = 118/260 (45%), Gaps = 10/260 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERT 73
           R++K ++  G  SRR  +++I Q RV +NG +       +   D + V+G  +    E+ 
Sbjct: 8   RINKYLSEVGYCSRRAADKLIEQGRVTINGRIP-EMGTKISQGDEVHVNGELISAPTEKP 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP+G+V T      +  + D + +  SR+  +GRLD  +EGL+ LTNDG +   
Sbjct: 67  VYIAFNKPVGIVCTTDTRVEKDNIIDYI-NYPSRIFPIGRLDKPSEGLIFLTNDGDIVNK 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V     +    +  +  G+ I         V    ++ S     + L
Sbjct: 126 ILRARNNHEKEYEVWVDRPITPSFIQQMGNGVPILDTVTRTCHV----EQLSRFSFKIIL 181

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE-QLGPHLLEE 252
            +G NR+I+++ E  +++V RL R       L  +  G  R ++++ ++E  +     E+
Sbjct: 182 TQGLNRQIRRMCEALDYEVTRLKRNRIMNVSL-DVEEGKWRYITEEEMKEIYVLVADSEK 240

Query: 253 AQVNLDA-PIYSSETLVRDR 271
            Q   DA P +      R+R
Sbjct: 241 TQAEKDAEPKFKDLRSSRNR 260


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 103/316 (32%), Positives = 150/316 (47%), Gaps = 12/316 (3%)

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  LRKAER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLL 122
           + + +     R+ LYHKP G + T  DP  R+TVF  LP +  ++ +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 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI- 240
            GSN W  V + EG+NRE++++FE     V+RLIR  +G   L   L  G   E+     
Sbjct: 277 DGSNKWYRVTIEEGRNREVRRMFEALGLTVSRLIRSRFGDVHLPRNLKRGRWEELDPSQV 336

Query: 241 --LREQLG--PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
             L E LG      E+ +     P+     L       I    D F+  K   S      
Sbjct: 337 LGLMECLGLNKKNDEDGRKGRRGPVSHGNALPPGFEKSIDPSKD-FSIHKVRKSAGGPQR 395

Query: 297 KQKKLATPVHRRNLAS 312
                  P  RR  ++
Sbjct: 396 GLTGRGVPSQRRGRST 411


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 102/231 (44%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R++  ++I    V V+G + +  +  V     +E +G  +  A   
Sbjct: 1   MRLDKYLCDGLGATRKQATKIIKSGDVTVDGEVQKSGSFKVPEAGVVEWEGRLV-GAPGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   V +H D     T F  L      ++   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPADFVCSHED-GHNPTAFVLLDEPKVEKLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + 
Sbjct: 119 RITSPKHKCEKTYRVWLADAIQPDYIEKFAEGIELRNESGPTLPAHLEIVNEAENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ + 
Sbjct: 179 IVEGKYHQVKRMFAALGNKVEYLHRERIGSIVLDEALEPGDYRFLTEEEVE 229


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 80/350 (22%), Positives = 146/350 (41%), Gaps = 19/350 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+ +GI SRRE +R I Q +V +NG         V + D ++V+G  +   E
Sbjct: 5   ESMRLNKYISESGICSRREADRFIEQGQVFINGKRA-GIGDQVFAGDLVKVNGQVIEARE 63

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                  + +KP+G+V+T    +  + V  +  +  +RV  +GRLD +++GL+ LTN G 
Sbjct: 64  ADSLVFIVLNKPVGIVSTTEAGEKDNIV--DFVNHSTRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     V  D +  +  G+ I G      +V     K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPVTDDFIKGMGAGVPILGAVTKKCKVK----KEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L E     L
Sbjct: 178 RITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIELF--KL 235

Query: 250 LEEAQVNL-----DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +E++   +     D P  +   + +       + P      +          +  +   P
Sbjct: 236 IEDSSSEVKPAKGDKPKVAKAAVAQTGKAAQGKKPRRDDDHEIGGRPNVSGPEAFEKKIP 295

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           V +  +        G  ++    +G+   N  R P+    R+ +    KK
Sbjct: 296 VGKGAVGK---GGAGKAAAGKGSAGKGASNKGRKPAAAKPRAGQSGRQKK 342


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 121/234 (51%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV++  G  SR+E++ ++ +  ++++G +++   + V      I+V+G  +    +
Sbjct: 2   ERLDKVLSNLGYGSRKEIKALVKKGEIEIDGKVIKDNGLKVDPNKSIIKVNGEKINYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L   ++      VGRLD +TEGLL++TNDG L
Sbjct: 61  YIYIMMNKPAGVVSATFD-NYDETVIDLLDYEYTVFDPFPVGRLDKDTEGLLIITNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y      +VD+  +   +KGI +  G      ++ + +   + + V
Sbjct: 120 NHRLTSPKWHVDKIYYAEIDKRVDEKDVEKFEKGITLDDGYKCLPAKLEILSADENGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            V ++EGK  ++K++FE  + KV  L R+  G   L   L  G  RE+++K + 
Sbjct: 180 NVIIQEGKFHQVKRMFEARDKKVVYLKRLKMGNISLDNELEEGEYRELTEKEIE 233


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 125/233 (53%), Gaps = 4/233 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+IA +G+ SRR+ E  I Q RVKV+G ++    V       IEVDG  + + ++  
Sbjct: 3   RLQKIIAASGLTSRRKAEEWILQGRVKVDGQVVTELGVKPRKGALIEVDGKAIAREDKVY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP  ++ T +D   R TV D +  +  RV  VGRLD +T G+L++TNDG  A  +
Sbjct: 63  YVM-NKPKKVLCTLNDEHDRRTVVDLMMDVPQRVFPVGRLDYDTTGVLIMTNDGEFANEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK--GSNAWVTV 191
             P     +VY V  +G +  +++  L++G+V+  GI     ++ +  +          +
Sbjct: 122 IHPRYHIAKVYEVTINGILKTEEIKQLEQGVVLDDGIKTLPAKLWVTNKDFAHEQTMFEL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            ++EG+NR+IK++ E F ++V RL R S GP  +  L  G  R +    +++ 
Sbjct: 182 TIQEGRNRQIKRMLEVFGYEVRRLHRRSLGPITVRGLNPGEYRLMKPFEVKQL 234


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 117/235 (49%), Gaps = 8/235 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G ASRR  +++I++ RV VNG + +     V   D I V G  LR A    
Sbjct: 5   RLNKFISESGKASRRGADKLISEGRVTVNGKVAK-VGDQVKPGDDIRVSGQQLRIARNNV 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T S+   +  + D +     R+  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITST-SEKKVKGNIIDLVNHPL-RIHHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + +  + +G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVAVDKPITPEFIKNMSEGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           +G NR+I+++ E   ++V RL R       L  L  G  R+++KK  R QL   L
Sbjct: 178 QGLNRQIRRMCEVLGYEVYRLQRTRIMNIHLNNLPVGQWRDLTKKE-RTQLFKEL 231


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 102/344 (29%), Positives = 158/344 (45%), Gaps = 23/344 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D +
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HVGQRIQFGDIV 208

Query: 61  EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           +V+G P+R        R+  YHKP+G V TH DP  R TVF  LP     +  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 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
           V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 329 VEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWVE 388

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  ++      L+  A V   AP+  + +  R   N          R  ++  + NG+
Sbjct: 389 LDQADIQA-----LMSAAGVKERAPVERNNSGARGANNRGG-------RNSRSGGRGNGM 436

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
           +  +               W       +  + SG   +N R  P
Sbjct: 437 NADRAPQGRREGGGQRRGEW-----DGNRPAPSGMLGDNPRNKP 475


>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 =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 105/236 (44%), Gaps = 3/236 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV+    +  D     ++G+++ G         L+    S   V + +
Sbjct: 121 ITSPKHHCEKTYRVQLSEDIADDVTIQFEQGVMLNGEKSPTKPAQLEI--ISPREVLLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            EG+  ++K++F      V  L R   G   L   L  G  R +++  ++    P 
Sbjct: 179 SEGRYHQVKRMFAAVGNHVCGLHRERVGEIHLDEQLEPGEYRPLTEAEIKSITVPR 234


>gi|62261679|gb|AAX78007.1| unknown protein [synthetic construct]
          Length = 306

 Score =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 132/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 27  MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 84

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 85  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 144

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 265 LELNPSEVNRL 275


>gi|331270360|ref|YP_004396852.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329126910|gb|AEB76855.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 240

 Score =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 120/237 (50%), Gaps = 7/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
            T +R+ K+++  G  SR+E++ ++ +  ++++G  ++   V V      I+V G  +  
Sbjct: 1   MTMERLDKILSNLGYGSRKEIKVLVKKGEIEIDGEKIKDNGVKVDPNKSIIKVSGEEINY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
             +    + +KP G+V+   D +   TV D L   ++      VGRLD +TEG LL+TND
Sbjct: 61  R-KYIYLMMNKPAGVVSATFD-NYDETVIDLLDYEYTVFDPFPVGRLDKDTEGFLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   L  P     ++Y       VD+  +   +KGI++  G      ++ + +   + 
Sbjct: 119 GDLNHRLTSPKWHVDKIYYAEIDKIVDEKDIKAFEKGIMLEDGYRCLPAKLRVLSADENG 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + ++EGK  ++K++FE  + KV  L R+  G   L  +L  G  RE+++  ++
Sbjct: 179 SEVNITIQEGKFHQVKRMFEARDKKVIYLKRLQMGNLVLDESLSEGEYRELTEDEVK 235


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 72/294 (24%), Positives = 126/294 (42%), Gaps = 10/294 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFINGKRAT-IGDQVMPGDVVKVNGRLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE       +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVFIALNKPVGIVSTTEDSE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V  D +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPVTDDFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L      
Sbjct: 176 VFRITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGLPPGEWRDLTDDELIALFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVR-DRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    +   +        RP +  E  ++  R   N  +     ++KK
Sbjct: 236 IENSSSEAKPTSKAKAKPKTAGIKRPVVKIEKTNEKARPASNGKRFTSPGRKKK 289


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 125/244 (51%), Gaps = 8/244 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVD 63
           N+ ++     R+++ +A  GIASRR  ++M+ + RV +NG+L     V V+   D + VD
Sbjct: 4   NVEKKQNEAVRINRYLAMCGIASRRAADQMVLEGRVTINGVLASEPGVKVVPGKDEVIVD 63

Query: 64  GVPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           G    + E R    L++KP  ++TT SD   R  V D +  +  RV  VGRLD  T G+L
Sbjct: 64  GSKFAQPEGRKIYILFNKPRNVITTSSDERNREMVLDFI-DVNERVYPVGRLDRKTTGVL 122

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLD 180
           LLTNDG LA  L  PS+   + Y         Q  L LL  G+ +   G      Q  + 
Sbjct: 123 LLTNDGMLANKLMHPSSNVKKEYIAVLDAPFPQASLPLLTGGMRLSDTGEKVSPCQAKIM 182

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              GS  W  + + EGKN +++++F+   ++V RL R +Y    +G L  G  R +++  
Sbjct: 183 G-DGSQVW--ISIHEGKNHQVRRMFKTLGFEVTRLDRPTYAGLTVGDLRRGQWRHLTRTE 239

Query: 241 LREQ 244
           +++ 
Sbjct: 240 VQQL 243


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 77/237 (32%), Positives = 121/237 (51%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +    P+R+ KV++RAG+ASRR  E +IA+ RV++NG  +    V V+ TD I VDG  +
Sbjct: 36  EATSEPERLQKVLSRAGVASRRASEDLIARGRVQINGETVREMGVKVLPTDRITVDGQRI 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V + L  GKNR ++++       V+ L R       L  L  G  R +  K L   
Sbjct: 216 IVQLTLHSGKNRVVRRLLSAVGHPVSALTRTGIANLTLDGLKEGQFRLLHGKELAAL 272


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 114/229 (49%), Positives = 156/229 (68%)

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 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NRE+++V  +   +V+RLIRISYGPF LG L  G+  EV    L+
Sbjct: 452 HEGRNREVRRVLGYLGLQVSRLIRISYGPFLLGDLPVGAVEEVDPATLK 500


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR +V++++ +++V VNG +       +    D I   G  L   E+
Sbjct: 1   MRLDKFLVGAGIGSRNDVKQLLKKKQVTVNGEIETSPKTQIDEKIDKIVCQGENLSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D +   TV D L        V  VGRLDI+T GLL LTN+G L
Sbjct: 60  YVYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLFLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G +  + +    KGI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVDKLYRAKVAGIMTAEDVEHFAKGIELKDFTCQPAQLEILEIDEAAKTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S GP QL   L  G  R ++ + L + 
Sbjct: 179 VAITIKEGKFHQVKRMVLACGKEVTDLERLSMGPLQLDENLSLGEWRRLTAEELAKL 235


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 73/238 (30%), Positives = 116/238 (48%), Gaps = 3/238 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +  T  R++K IA +G+ SRRE +  I    V+VNG L+      V   D +  DG  +
Sbjct: 66  SDESTGIRLNKYIANSGVCSRREADTYIEHGSVEVNGNLVTEMGYKVQPDDVVRFDGTGI 125

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              E+ +  L +KP   +TT  D  GR TV D + +    R+  VGRLD NT GLLL TN
Sbjct: 126 T-PEQKKYILLNKPKNYITTMDDDRGRKTVMDLISNATKERIYPVGRLDRNTTGLLLFTN 184

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA+ L  P     ++Y      +++   L  L+  ++I+G     +           
Sbjct: 185 DGELAKKLTHPKHDVRKLYHASLDKKLELKDLEKLRGEVLIEG-KKVFIDAVSYVDGQPK 243

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + V + +  G+NR ++K+FE   +KV++L R+ +       L  G  RE++ + L   
Sbjct: 244 SEVGIEIHSGRNRIVRKIFEHLGYKVSKLDRVIFAELTKRNLPRGRWRELTNQELSNL 301


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 73/270 (27%), Positives = 123/270 (45%), Gaps = 10/270 (3%)

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 +     RV  VGRLD ++EGL+L+TN
Sbjct: 77  ISGKDRPVVLLVNKPRGIVCTTSDRDRAENIVDFIGYPL-RVYPVGRLDKDSEGLILMTN 135

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G L   +        + Y V    ++ +  LN ++KG+ I         V    +K   
Sbjct: 136 QGELVNRILKGRYGHEKEYLVSVDREITEQFLNRMRKGVKILDTVTRPCTVEKTGEKS-- 193

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK---KILRE 243
               + L +G NR+I+++ E   ++V  L R+     +L  L  G  RE+++   K L E
Sbjct: 194 --FRIILTQGLNRQIRRMCEALGYRVRTLKRVRIMNLRLDGLKTGEYREITRGEWKELTE 251

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L     E  + +       SE   R+   
Sbjct: 252 LLEGKG-ERRKADQKNAGKHSELGQREPEK 280


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 118/238 (49%), Gaps = 4/238 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +  +     R++K I+ AGI SRRE + +I   R+ VNG  +      V +TD ++   
Sbjct: 10  KVASDQINYVRLNKWISNAGICSRREADELIQAGRITVNGEKITTLGYQVKNTDIVKFRD 69

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
             L+   +    L +KP   +TT  DP+ R TV D +      RV  VGRLD NT GLL+
Sbjct: 70  KVLK-PNKHVYILLNKPRNCITTAFDPERRRTVLDFVKGACQERVYPVGRLDRNTTGLLV 128

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA+ L  PS Q  ++Y+V     +    L  +K GI ++        +++   +
Sbjct: 129 LTNDGDLAQKLAHPSYQIKKIYQVELASPIQPKDLAAIKAGICLKDGIVQVDSISIV--Q 186

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G  + + + +  GKNR I+++FE   +++  L R+ Y       L     R ++ + +
Sbjct: 187 GDESKLGIEIHSGKNRIIRRLFEHLGYQIINLDRVMYANLTKKELPRSKWRFLTNQEV 244


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 135/251 (53%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   EN TP+R+ K++A+ GI SRR++E  I Q RV+VNG +           D I
Sbjct: 1   MRRINQNIEN-TPERLQKLLAKYGIGSRRKIEEFIEQGRVRVNGKVAT-LGDKATDKDKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I +GRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVIIYHKREGEVCTSKDEKDRKTVFDSLPKLAKSRWIMIGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS +  R Y VR +G ++  + 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>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 =  258 bits (660), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 112/232 (48%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +  A   V      + V G  +   +  
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGAVKVDGAPVRDAKTKVRPDEQIVTVWGETVEY-KPF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 63  IYLMMNKPSGVVSATEDA-VEETVVDLLEEEDRAFSPFPVGRLDKDTEGLLLLTNDGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G+V +  +   ++G+V+  G      ++ +  + G  + V 
Sbjct: 122 HQLLSPKKHVPKTYFAVVDGEVTEADVAAFQRGVVLDDGYETKPAKLVVL-KSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + EGK  ++K++F+    +V  L RI  GP  L   L  G  RE++ + +
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRIQMGPLPLDPDLAVGEYRELTDEEV 232


>gi|301793545|emb|CBW35921.1| putative ribosomal small subunit pseudouridine synthase B
           [Streptococcus pneumoniae INV104]
          Length = 240

 Score =  258 bits (660), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 113/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVMDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  258 bits (660), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 95/314 (30%), Positives = 148/314 (47%), Gaps = 7/314 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  E+  P ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + ++
Sbjct: 160 RELRAEDDAP-KLHKVLADAGLGSRRDMEELIIAGRVSVNGEPA-HIGQRILPTDQVRIN 217

Query: 64  GVPLRKAER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           G  L++       ++ LYHKP G + +  DP+ R++VFDNLPS   S+ ++VGRLD NTE
Sbjct: 218 GKLLQRKVTKSLPKVMLYHKPAGEIVSRDDPEKRASVFDNLPSLKNSKWLAVGRLDFNTE 277

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL TN+G LA  L  P     R Y VR  G++++     L  G+ +         +  
Sbjct: 278 GLLLFTNNGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVDLGDGIGQFSSIAD 337

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+  
Sbjct: 338 GGGEGINKWYRVTIGEGRNREVRRMFESVGLTVSRLIRTRYGVITLPQNLKRGRWDELDD 397

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R  +    +E              +    R     +     +        +N  S+ 
Sbjct: 398 NAVRNLMRLSGMEPKGDKSATETAKGRSAGAKRQGQDRKGSFGRSETLSIHEFRNNDSRS 457

Query: 299 KKLATPVHRRNLAS 312
           KK  T   +    S
Sbjct: 458 KKGPTSAQKGAPRS 471


>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 =  258 bits (660), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 101/310 (32%), Positives = 155/310 (50%), Gaps = 11/310 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
             +++ KV+AR+G+ SRRE+ER I Q RV ++G         V++   IEVDG PL    
Sbjct: 18  DGEKLQKVLARSGLGSRREMERWIEQDRVTIDGKPA-SLGDRVVAGQRIEVDGRPLAAGD 76

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E+TR  LYHKP G V +  DP+GR TVF+ LP + S 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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL-- 245
             V L EG+NRE+++++E     V+RL R+ YG   + + +  G  +E++   +      
Sbjct: 197 YYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGDLFVPSKVKKGQYQELASNEINGLYRM 256

Query: 246 ----GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
                  +   ++ + +          R R N  ++        +K  S K      K  
Sbjct: 257 AGMPAKDVEPPSREDRNKHKRMEGKRGRVRGNKHAKDDFGSRDARKEKSGKGRKPGSKST 316

Query: 302 ATPVHRRNLA 311
           + P ++R   
Sbjct: 317 SAPKNKRRTR 326


>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 =  258 bits (660), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 77/232 (33%), Positives = 118/232 (50%), Gaps = 3/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R++K ++  G+ SRR+ +++I + RVKVNG+++      +    D +EVDG  L+   R 
Sbjct: 9   RLNKYLSMCGVTSRRKADQLIKEGRVKVNGLVVRELGYKIDPHRDTVEVDGKVLKPP-RK 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R    +KP   +T      G     D  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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              G+   +K+    F  KV RLIRI+ GP +LG L  G  R+++ + + E 
Sbjct: 188 FTIGRKHIVKRYCAHFGHKVLRLIRIAIGPIRLGKLSPGKWRDLTLQEVTEL 239


>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 =  258 bits (660), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 110/235 (46%), Gaps = 7/235 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N  P R++K ++ AG+ SRR+ +R + Q R+ V+G   +     V +   I VDG  +  
Sbjct: 32  NGEPMRLNKFLSDAGVCSRRQADRYVEQGRILVDGEPAQ-MGQKVHAGQDIRVDGKRVSV 90

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           + +  +   +KP G+V T    +  + V  +      R+  VGRLD ++EGL+L+TNDG 
Sbjct: 91  SRKQIVLAVNKPKGIVCTTEKREKDNIV--DFIGYPERIYPVGRLDKDSEGLILMTNDGE 148

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V    L  + +G+ I        +V            
Sbjct: 149 LMNEILKARNYHEKEYEVTINRPVTNVFLKQMSEGVEILDTVTRPCKVKRTGV----YTF 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + L +G NR+I+++ E   ++V  L R+      LG+L  G  RE++ + L + 
Sbjct: 205 RIILTQGLNRQIRRMCEACGYRVRELKRLRIMNIHLGSLPTGKYREITGEELSKL 259


>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 =  258 bits (660), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 135/251 (53%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   EN TP+R+ K++A+ GI SRR++E  I Q RV+VNG +           D I
Sbjct: 1   MRRINQNTEN-TPERLQKLLAKYGIGSRRKIEEFIEQGRVRVNGKVAT-IGDKATDKDKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I +GRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVIIYHKREGEVCTSKDEKDRKTVFDSLPRLAKSRWIMIGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS +  R Y VR +G ++  + 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +N  +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINSEICTHGAL-VSDGDRVTIDGQVIVKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D    + +  N  +   R+  VGRLD  +EGL+LLTNDGG+A 
Sbjct: 60  KVYIAFHKPVGITCTAADHIEDNII--NYINYPERIFPVGRLDKASEGLILLTNDGGIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          ++ + +G+ I+       +VT    +   +   + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 174 LTQGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 227


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V  + +     GI +  G      ++ +     +   +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGDVVAEDVTAFADGITLDDGYTCKPARLEI----INPNEI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLQLDESLELGEYRPLTETEL 227


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 130/268 (48%), Gaps = 10/268 (3%)

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  D    +FD++     R+  VGRLD +++GLLLLTNDG L+
Sbjct: 62  ETVILAYNKPLGLTCTAS-HDDPDNIFDHIKYPI-RLQYVGRLDKDSQGLLLLTNDGDLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             ++       + YRVR +  +  + L  +  G+ I        ++     K  N    +
Sbjct: 120 NSIQKSVNNHEKEYRVRVNKPITDEFLTQMAAGVPILDTVTKKCRLY----KIDNYSFKI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK---ILREQLGPH 248
            + +G NR+I+++ E+F +KV  L R+     +LG L  G  R ++K+    LR  +   
Sbjct: 176 IITQGLNRQIRRMCEYFGYKVVNLKRLRVINIRLGNLRPGEYRHLTKEEETELRRLVERK 235

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIIS 276
              + +     P   +E  V      +S
Sbjct: 236 EEVKTKREEAQPDNKNEQNVVGNKRYVS 263


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      +VT    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R   
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKRRLF 225


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 114/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        +  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEIFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ + +  +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVEIFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKETSCVEWQGREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLDI+T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDIDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRKRIGQITLDETLEPGEYRYLTEEEV 226


>gi|261408369|ref|YP_003244610.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261284832|gb|ACX66803.1| pseudouridine synthase [Paenibacillus sp. Y412MC10]
          Length = 253

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 75/240 (31%), Positives = 121/240 (50%), Gaps = 12/240 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           T QR+ KV++  G  SR E+++   Q  + VNG + +    +V    D IE +G  ++  
Sbjct: 7   TTQRLDKVLSNLGFGSRAELKKKAKQGSIVVNGTVTKDPGKHVDPYADIIEFEGETIQYR 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           E     + HKP G+V+   D   R TV D L + +       VGRLD +TEGLLLLTNDG
Sbjct: 67  E-YVYLMLHKPPGVVSATEDLRDR-TVLDLLDAEYRVFEPFPVGRLDKDTEGLLLLTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN- 186
            LA  L  P     + Y     G+VD++ +     G+ +  G      ++ + + +    
Sbjct: 125 KLAHELLSPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLDDGYVTLPGELAIHSHEERED 184

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
               + +++ + EGK  ++K++FE    KV  L RIS G  +L   L  G+ RE++++ L
Sbjct: 185 GVQLSRISLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYRELTEQEL 244


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 112/242 (46%), Gaps = 13/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   E 
Sbjct: 87  MRLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQE- 145

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV   L        +  VGRLD NTEGLL+LTNDG L
Sbjct: 146 YYYYLLNKPQGVVSATKD-NVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILTNDGAL 204

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL------DTQK 183
              L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ +      D+Q 
Sbjct: 205 GHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGDSQS 264

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + + 
Sbjct: 265 GWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTIEEIE 324

Query: 243 EQ 244
             
Sbjct: 325 NL 326


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 105/230 (45%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  +++    V VNG + +  A  +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENTGLTRSQAAKVLKSGVVTVNGNIEKSGAAKISQEDEIYYEDQKLEWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G + +H D +   TVF      + +++ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYICSHDDGEY-PTVFQFFDYPLMTKLHTAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+      L +GI+++G     +   L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEDFYAQRLAEGILLRGEKEPTLPAQLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L   L  G  R ++ + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVEALHRWRIGDVVLDERLEEGEFRSLTSEEI 227


>gi|295093016|emb|CBK82107.1| ribosomal small subunit pseudouridine synthase A [Coprococcus sp.
           ART55/1]
          Length = 241

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 118/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR +V++ + +  V VNG  ++ + V +    D I+ +G  L  + R
Sbjct: 1   MRLDKFLVEMGIGSRSQVKQYVKKGTVTVNGAPVKSSDVKIDENNDTIKYNGRILNYS-R 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R +L +KP G V+   D +   TV D L       +  VGRLDI+TEGLLLLTNDG L 
Sbjct: 60  YRYFLLNKPAGCVSATKD-NVHQTVIDLLKGENTKDLSPVGRLDIDTEGLLLLTNDGALT 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC---YGDMQVTLDTQKGSNAW 188
             L  P+    + Y     G V  D +NL   G+ I         D+++       + + 
Sbjct: 119 HHLLSPAHHIPKTYYAEIDGYVTDDTINLFATGVDIGDEKPTLPADLRILSSDSTAARSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + + EG+  ++K++FE    KV  L RI+ G  ++  +L  G+ R +S++ +
Sbjct: 179 IELIITEGRFHQVKRMFEAVGMKVTFLRRIAMGELKIDESLPTGAYRSLSEEEV 232


>gi|327438231|dbj|BAK14596.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 234

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 113/232 (48%), Gaps = 7/232 (3%)

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 D +     R+  +GRLD ++EGLLLLTNDG +   
Sbjct: 60  VYIVLNKPVGITST-TEKQIEGNVVDFVNHRL-RIFHIGRLDKDSEGLLLLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+    +    ++ +  G+ I        +V    +K S+    + L
Sbjct: 118 ILRAENHHEKEYVVQVDKPITDQFIHDMSSGVEILDTTTLPCRV----EKVSSKVFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++     + V RL RI      +G L  G  R+++ K   E  
Sbjct: 174 EQGLNRQIRRMCSALGYSVQRLQRIRIMNIHIGNLKVGQWRDLTDKERNELF 225


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 70/295 (23%), Positives = 129/295 (43%), Gaps = 12/295 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +    
Sbjct: 5   SSIRLNKYISESGICSRRDGDRYIEQGNVFINGKRAT-VGDQVFAGDVVKVNGQIIEPRD 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E       +KP G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G 
Sbjct: 64  EEDLVFIALNKPAGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGD 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       L
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNISLKGLPLGEWRDLTDDELLTLF--KL 235

Query: 250 LEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +         +  + +   RP I  +   + +     S ++     +KK   
Sbjct: 236 IENSSSEEKTVKKAPPKPVAAKRPGIQGQKKAEKSDDNTASRKRFTQPGRKKKGR 290


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 113/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 70/297 (23%), Positives = 138/297 (46%), Gaps = 12/297 (4%)

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  K--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
               E   L   +KP+G+V+T    +  + V  +  +  +R+  +GRLD +++GL+ LTN
Sbjct: 61  PRNEEDLVLIALNKPVGIVSTTESGEKDNIV--DYVNHSTRIFPIGRLDKDSQGLIFLTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            G L   +        + Y V  +  V  + +  +  G+ I G      +V     K + 
Sbjct: 119 HGDLVNKILRAGNSHEKEYLVTVNKPVTDEFIRGMGAGVPILGTMTKKCKVK----KEAP 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E   
Sbjct: 175 FVFRITLVQGLNRQIRRMCEHFGFEVTKLERVRIMNVRLTGIPVGEWRDLTDDELIELF- 233

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             ++E+++ ++  P  + +++  ++ N     P       +N ++K      +K   
Sbjct: 234 -DMMEKSESDI-KPKKAQKSVSANKGNTKQASPSKPKVKTENPTRKKFTQPGRKKKK 288


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 103/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    + V+G + +  A  V     +  +   +  A   
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPEGVEVMWEDRVI-GAPGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPADFVCSHED-GYNQTAFALLDEPKIENLHFAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D    L++GI+++      +   L+    +   V + 
Sbjct: 119 RITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +
Sbjct: 179 IVEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRYLTQEEI 228


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 114/230 (49%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R++  +++ ++RV V+G +++  A+ +     +E DG+ LR A   
Sbjct: 2   IRLDKFLCETVGVTRKQAAKILKEERVTVDGNIIKNGAIKIAEEADVEFDGMSLRLA-GP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G V +H DP    TVF  L  I   ++   GRLD +T GLLLLT+DG  + 
Sbjct: 61  RYYMMNKPAGYVCSHDDP-YNPTVFVLLDEIGAEKLHIAGRLDCDTTGLLLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VYRV     V  +      +GI ++G     +   +  Q+     V + 
Sbjct: 120 RVTSPKHKCDKVYRVWLDDPVSPETEQCFAEGIKLRGERTETLPAQM--QRVGEKEVLLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R S G   L   L  G  RE++ + +
Sbjct: 178 IHEGKYHQVKRMFAAVGNKVVGLHRESVGGLVLDEALEPGEYRELTDEEI 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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 101/339 (29%), Positives = 153/339 (45%), Gaps = 20/339 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D +
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HVGQRIQFGDIV 208

Query: 61  EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           +V+G P+R        R+  YHKP+G V TH DP  R TVF  LP     +  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 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
           V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 329 VEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWVE 388

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  ++      L+  A V   AP+  S    R   N          R  ++  + NG+
Sbjct: 389 LDQADIQA-----LMSAAGVKERAPVERSSGGARGANNRGG-------RNNRSGGRGNGM 436

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
           +  +               W   G   +     G    N
Sbjct: 437 NADRAPQGRREGGGQRRGEWD--GNRPAPSGMLGDNPRN 473


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 110/232 (47%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ER 72
            R+ K + +    SR +  +++   R+ VN ++++  A +V   D + +D  PL    E+
Sbjct: 1   MRLDKHLHQCLGISRSQASQLLKAGRISVNSLIIKSGAQHVTEQDSVLLDDKPLDTPGEK 60

Query: 73  TRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G V  + D    G + +FD      S + + GRLD +T GL+L+TNDG  
Sbjct: 61  LYYFMLHKPQGYVCANGDASHPGITRLFDL--PCASELHAAGRLDADTTGLVLVTNDGQW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P  Q  + YRV     +  +   +  KGI+++          L+T   +   V 
Sbjct: 119 SHRVTSPRKQCDKTYRVWLAEPISPETEEIFAKGILLRSETQVTRPAQLET--ITPQEVL 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++F      V RL R   G   L   L  GS RE++ + +
Sbjct: 177 LTIHEGKYHQVKRMFAAVGNHVERLHRERIGELVLDADLPEGSYRELTPEEI 228


>gi|54112711|gb|AAV28989.1| NT02FT0029 [synthetic construct]
          Length = 271

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N + +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQINDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>gi|260685750|ref|YP_003216883.1| pseudouridine synthase [Clostridium difficile R20291]
 gi|260211766|emb|CBE02116.1| pseudouridine synthase [Clostridium difficile R20291]
          Length = 258

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 114/251 (45%), Gaps = 24/251 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYREY 64

Query: 73  TRLWL-----------------YHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGR 113
             L +                  +KP G ++  +D     TV D +   +       VGR
Sbjct: 65  IYLIMQNSVKQEPCDFSHGRFRMNKPDGYISATTD-KYDPTVLDLIDLSYLAFEPFPVGR 123

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD +TEGLL+LTNDG L+  +  P     + Y  +  G V ++ +    +G+V+    Y 
Sbjct: 124 LDKDTEGLLVLTNDGKLSHRVLSPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDG-YK 182

Query: 174 DMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
            M   L+  +    + + + + EGK  ++K++FE    KV  L R+S G  +L  +L  G
Sbjct: 183 TMPSQLNILKSDDESEIELTIHEGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELG 242

Query: 232 STREVSKKILR 242
             RE++ + ++
Sbjct: 243 EYRELTDEEVK 253


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 101/234 (43%), Gaps = 3/234 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +      L  +GI++ G         L+        V + +
Sbjct: 121 ITSPRHHCEKSYLVTLEQPLAPQTAALFAQGIMLNGETDLTKPAQLEA--FDEHHVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            EG+  ++K++F     +V  L R   G   L   L  G  R +S   +   L 
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGAIALDAALAPGEYRALSDDEVASALA 232


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 119/233 (51%), Gaps = 1/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +       + D I VDG  L+   R 
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQLGDKADPARDVIVVDGERLQADVRL 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+VTT +D  GR+ + D + +    RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 79  VYVAMNKPRGVVTTMADEKGRTELADFIGARLEQRVYHVGRLDADSEGLLLLTNDGTLAH 138

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS + L+ Y     G + ++    L  G+ ++          +    G  A V + 
Sbjct: 139 KLMHPSYEVLKTYLAEVAGPIPRNLGKRLTAGVELEDGPVKVDGFKVVDTLGKTAQVELT 198

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L EG+   ++++       V+RLIR S GP +LG L  G  R ++   +    
Sbjct: 199 LHEGRKHIVRRLMAEVGHPVSRLIRTSIGPIKLGDLRTGRMRRLTNAEVAALF 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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 93/293 (31%), Positives = 149/293 (50%), Gaps = 13/293 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ KV+ARAG  SRR+VE  I + +V  NG         +   D +++D   L      
Sbjct: 3   ERIQKVLARAGYGSRRQVETWIKEGKVSCNGETAT-LGDQISEGDRLKLDNKLLSPKRLW 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            +  ++ LY+KP+G V T SDP+GR T+F  LP+    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-GTLLAGSTREVSKKILREQ--- 244
             V ++EG+NRE+++++E    +V+RL+R+ YGP  +   L  G   +V    L      
Sbjct: 182 YHVVIQEGRNREVRRLWESQGVQVSRLMRVRYGPIIIPNNLRMGHWTKVEGADLEHLYEQ 241

Query: 245 --LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
             + P   E+       P+ +  T  ++ P    +   D     K S +  G 
Sbjct: 242 AGMKPQQTEKTGKRQQKPVRNQATAKKESPYRGKKQTQD-KATGKRSPRIRGR 293


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 113/231 (48%), Gaps = 7/231 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R   
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLF 228


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 70/295 (23%), Positives = 128/295 (43%), Gaps = 12/295 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +    
Sbjct: 5   SSIRLNKYISESGICSRRDGDRYIEQGNVFINGKRAT-VGDQVFAGDVVKVNGQIIEPRD 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E       +KP G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G 
Sbjct: 64  EEDLVFIALNKPAGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGD 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       L
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNISLKGLPLGEWRDLTDDELLTLF--KL 235

Query: 250 LEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +         +  + +   RP I  +   + +     S +      +KK   
Sbjct: 236 IENSSSEEKTVKKAPPKPVAAKRPGIQGQKKAEKSDDNTASRKHFTQPGRKKKGR 290


>gi|262182363|ref|ZP_06041784.1| putative pseudouridylate synthase [Corynebacterium aurimucosum ATCC
           700975]
          Length = 286

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 127/245 (51%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           ++ KN        +R+ KV+A+AG+ASRR  E +I + RV+VNG ++ +    V    D 
Sbjct: 33  VEGKNKKNSQNQGERLQKVLAKAGVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDV 92

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDI 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|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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 102/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIML-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 103/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    + V+G + +  A  V     +  +   +  A   
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEVMWEDRVI-GAPGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPADFVCSHED-GYNQTAFALLDEPKIENLHFAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D    L++GI+++      +   L+    +   V + 
Sbjct: 119 RITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +
Sbjct: 179 IVEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRYLTQEEI 228


>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 =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 106/229 (46%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YRV+    +  D +   + G+++ G         L+    S   V + +
Sbjct: 121 ITSPKHHCEKTYRVQLSEDITDDVIQKFEIGVMLNGEKSPTKPAQLEI--ISPREVLLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  ++K++F      V  L R   G  +L   L  G  R +++  +
Sbjct: 179 SEGRYHQVKRMFAAVGNHVCGLHRERVGEIRLDEQLEPGEYRPLTEDEI 227


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 92/285 (32%), Positives = 145/285 (50%), Gaps = 10/285 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 202 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 260

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 KILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +         EE      AP       ++     I+  P
Sbjct: 441 NQVRALMASVGLKAPTEERGSRNAAPERKQPDPMQTSMGFINREP 485


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 108/294 (36%), Positives = 154/294 (52%), Gaps = 12/294 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEV 62
             +   +   +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV S   + +
Sbjct: 37  NEMKTTSAEGEKLQKVLARAGQGSRREIESIIAENRVSVDGKIATLGDRINVNSGVKVRI 96

Query: 63  DGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           DG  +     + E  R+ +Y+KP G + T  DP+GR+TVFD LP    +R I+VGRLDIN
Sbjct: 97  DGNLINLTQAQKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGARWIAVGRLDIN 156

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL T DG LA  L  PS +  R Y VR  G VD   LN LKKG+ ++       ++
Sbjct: 157 TSGLLLFTTDGELANRLMHPSREVEREYSVRVFGAVDDAMLNRLKKGVQLEDGPANFKEI 216

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                 G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G  +E+
Sbjct: 217 KFVGGVGMNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKNLPRGGWQEM 276

Query: 237 SKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
                  LRE +G  L  E +  LD      +         +    +   R KK
Sbjct: 277 ELADVNYLRELVG--LPPETETKLDMNKQRRKPKTGKIRKAVKRYSELSKRYKK 328


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 123/239 (51%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ K++ARAG  SRR  E +I Q RV+VNG ++      V    D ++V
Sbjct: 67  KTFPGAEQEGERLQKILARAGYGSRRSCEELIEQARVEVNGEIVLEQGKRVDPEKDEVKV 126

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  D +GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 127 DGLTV-ATQSYQFFSLNKPAGVVSTMEDNEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 185

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     +VY     G + +D    LK GI ++          +  Q
Sbjct: 186 LLTNHGELAHRLTHPKYGVKKVYLAHIVGPIPRDLGKQLKDGIQLEDGYARADHFRVVQQ 245

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 246 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 304


>gi|46370355|gb|AAS89963.1| hypothetical protein [Agrobacterium vitis]
          Length = 240

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 136/217 (62%), Positives = 162/217 (74%)

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 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           RLIRISYGPFQLG L     +EV  ++LR+QLGP L+
Sbjct: 181 RLIRISYGPFQLGDLPESQVQEVRGRMLRDQLGPRLI 217


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMATGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>gi|327484245|gb|AEA78652.1| Ribosomal small subunit pseudouridine synthase A [Vibrio cholerae
           LMA3894-4]
          Length = 231

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 102/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +     +E  G  +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKSGEVTVDDVVQKSGAFKLKEASRVEWQGREIML-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGIVCSHEDGFN-QTAFTLLDEVNVEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYAEQFNRGIELRGERELTLPAQLEV--ISETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  TL  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 226


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 126/244 (51%), Gaps = 8/244 (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+ + +    SRV   GRLD ++EGL
Sbjct: 76  VEGEQAVRSQERILLVVNKPRGVVCTTDKTWGDTTLEELV-DYPSRVFYAGRLDKDSEGL 134

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTL 179
           +L+TNDG L   +   + +  + Y V+    VD   L  + KG+ ++         +V  
Sbjct: 135 ILMTNDGELQDKIMRAANRHEKEYLVKVDRTVDDTFLKKMAKGVYLRELDTVTRPCRVEK 194

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++       + L +G NR+I+++     ++V  L R+     +LG L AG  RE + +
Sbjct: 195 TGRRA----FRIVLTQGLNRQIRRMCAALGYQVQELRRVRIMNIRLGGLPAGQYREATDE 250

Query: 240 ILRE 243
            LRE
Sbjct: 251 ELRE 254


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 114/237 (48%), Gaps = 11/237 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  +R E+++++ Q +V V G +++ +   V    D +  DG  +   E 
Sbjct: 5   MRIDKLLSHTGYGTRSEIKKLVKQGKVTVAGKVVKDSGQLVDPELDEVAFDGELVLYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   R TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 64  VIYLMMNKPPGVISATEDRRER-TVIDLLEQEDQLMDPFPVGRLDKDTVGLLLLTNDGQL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK----GS 185
           A  L  P     + Y     G V ++     K G+ +  G       + +  +     G 
Sbjct: 123 AHELLSPRKHVPKTYEAVVQGDVGEEDQEQFKAGVTLDDGYVTMPSDLKILKKDSGEGGV 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + +++ + EGK  ++K++FE    KV  L RIS GP +L   L  G+ RE++ + L
Sbjct: 183 TSVISLTIMEGKFHQVKRMFEAVGKKVVFLKRISMGPLELDADLEEGTYRELTDEEL 239


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG + +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRVEKSPKTQIDETADEIIVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G + Q  ++    GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMKQADVDRFAAGIELKDFTCQPAQLKVLELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ GP QL   +  G  R ++++ +
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPAVALGEWRRLTEEEM 232


>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 =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 110/239 (46%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 61  VYYIM-NKPKGVISATEDSKHR-TVLDLLDDLARTKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAW 188
           A  L  P     + Y  +  G + Q+ +    KGI ++       ++ + +       + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMSQEDVETFAKGISLKDFTCQPAKLEILSVDSGKDESQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 VRVTIAEGKFHQVKRMVSYCGKEVVDLQRLTMGTLALDENLERGEWRRLTKEELEVLLA 237


>gi|315506751|ref|YP_004085638.1| pseudouridine synthase [Micromonospora sp. L5]
 gi|315413370|gb|ADU11487.1| pseudouridine synthase [Micromonospora sp. L5]
          Length = 256

 Score =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 119/233 (51%), Gaps = 1/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A AG+ SRR  E +I ++RV VNG + +       + D I VDG  L+   R 
Sbjct: 19  ERLQKVLAAAGVGSRRACEDLIFRRRVTVNGRVAQLGDKADPARDVIVVDGERLQADVRL 78

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G+VTT +D  GR+ + D + +    RV  VGRLD ++EGLLLLTNDG LA 
Sbjct: 79  VYVAMNKPRGVVTTMADEKGRTELADFIGARLEQRVYHVGRLDADSEGLLLLTNDGTLAH 138

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS + L+ Y     G + ++    L  G+ ++          +    G  A V + 
Sbjct: 139 KLMHPSYEVLKTYLAEVAGPIPRNLSKRLTAGVELEDGPVKVDGFKVVDTLGKTAQVELT 198

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L EG+   ++++       V+RLIR S GP +LG L  G  R ++   +    
Sbjct: 199 LHEGRKHIVRRLMAEVGHPVSRLIRTSIGPIKLGDLRTGRMRRLTNAEVAALF 251


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 89/240 (37%), Positives = 134/240 (55%), Gaps = 8/240 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P R+ KV+A AG+ SRRE+E  IA  +V VNG++      +V+++D +++ G  +  
Sbjct: 82  EAKPVRLQKVLAEAGVGSRREMEEWIAAGKVSVNGVVAT-VGQSVVNSDKVKIGGRLINI 140

Query: 70  A-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
                    R+ +YHKP G + +  DPDGR +VF  LP +   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 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           G+N W  V + EG+NRE++++FE     V+RLIR+ YGPF L   L  G  RE+ +  ++
Sbjct: 261 GANHWYRVTISEGRNREVRRMFEAVGCTVSRLIRVRYGPFILPPQLKRGMARELKEAEIK 320


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 108/352 (30%), Positives = 159/352 (45%), Gaps = 10/352 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K +++      ++ KV+A++GI SRR++E+ I   +V VN  +     + +   D I 
Sbjct: 223 STKRVLRPEPEAPKLHKVLAQSGIGSRRDMEQFILDGKVTVNDEVA-HVGMRISYGDRIA 281

Query: 62  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDIN 117
           VDG P+R   +    RL  YHKP G V T +DP+GR TVF  LP +   +  SVGRLDIN
Sbjct: 282 VDGKPVRLRIQPGPARLLAYHKPTGEVVTLNDPEGRPTVFRRLPRLQQGKWQSVGRLDIN 341

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL TN G LA  L  P     R Y VR  G +++++   L +G+ I G   G   +
Sbjct: 342 TEGLLLFTNSGELANQLMHPRFGVEREYAVRVLGSLNEEQRAKLLEGVEIDGQTAGFKSI 401

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G+N W  V + EG+NRE++K+F+     V+RLIRI YG   L   L  G   E+
Sbjct: 402 EEGGGEGANRWYRVVITEGRNREVRKLFDKVGLAVSRLIRIRYGTVVLPRGLKRGVWVEL 461

Query: 237 SKKILR--EQL--GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             + LR   QL  G         + DA     +     R            +    +  +
Sbjct: 462 DDQDLRAIRQLASGNRGAAAQSESRDAQGNREQRRNNGRNGKPERNARGPQQGGARAQGQ 521

Query: 293 NGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            G  +  +      R   A+      G        +   +   RR    P +
Sbjct: 522 GGGERGPRREPRESRFGEAAPDTDGAGEEDFGRIPNPLEQTFDRRFAKGPRR 573


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 112/233 (48%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G  +      V      + V G  +   +  
Sbjct: 4   RIDKLLAHMGYGTRKEVKKLLKSGLVKVDGAAVYDPKTKVRPDEQTVTVWGETVEYKQ-F 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+++   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 63  IYLMMNKPPGVISATEDA-VEETVVDLLEEEDRLFDPFPVGRLDKDTEGLLLLTNDGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G+V +D +   ++G+V+  G      ++ +  + G  + V 
Sbjct: 122 HQLLAPKKHVPKTYFAVIDGEVTEDDVEAFRRGVVLDDGYETKPAELVVL-KSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++F+    +V  L R+  GP  L   L  G  RE++ + + 
Sbjct: 181 VTITEGKFHQVKRMFQAVGKRVVYLKRVQMGPLSLDPNLAVGEYRELTDEEVE 233


>gi|156340515|ref|XP_001620471.1| hypothetical protein NEMVEDRAFT_v1g223077 [Nematostella vectensis]
 gi|156205434|gb|EDO28371.1| predicted protein [Nematostella vectensis]
          Length = 275

 Score =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 117/235 (49%), Gaps = 3/235 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
                  R++K IA +G+ SRRE +  IA   V VNG ++      V  TD I  DG  +
Sbjct: 37  SSPEDGIRLNKYIANSGVCSRREADTYIASGNVVVNGKVITEMGFKVKPTDDIRFDGTAI 96

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
              E+ +  L +KP   +TT  D  GR TV D + +    R+  VGRLD NT GLLL TN
Sbjct: 97  SPEEK-KYVLLNKPKNYITTMDDDRGRKTVMDLVQNAARERIYPVGRLDRNTTGLLLFTN 155

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA+ L  P     ++Y      +++   L+ ++  ++I+G      +V     +   
Sbjct: 156 DGDLAKKLTHPKHNVQKLYHASLDRKLEVKDLHKMRDEVIIEGKRVFIDEVDYVAGEKKT 215

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             V + +  G+NR ++K+FE F +KV +L R+ +       L  G  RE++ + +
Sbjct: 216 -EVGIKIHSGRNRIVRKIFEHFGYKVVKLDRVIFAGLTKKNLPRGRYRELTTQEV 269


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 96/266 (36%), Positives = 142/266 (53%), Gaps = 7/266 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           +R+ K++AR G+ SRREVE  I   RV++NGI  +     V   D + ++G PL      
Sbjct: 3   ERLQKILARGGLGSRREVEAWIKAGRVRINGIPAQ-LGDKVSDEDQVTINGRPLSPRRLQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
           A  +++ LYHK  G + +  DP+GR TVF +LP     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 HLLEEAQVNLDAPIYSSETLVRDRPN 273
             +E     L +   ++    + R  
Sbjct: 242 GGVERRITGLQSRSKNNRRGRQGRKQ 267


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/239 (33%), Positives = 122/239 (51%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K++++ GIASRR+ E +I   RVKVNG L++         D +EVDG  +   +R 
Sbjct: 3   ERVQKILSQWGIASRRKAESLILAGRVKVNGNLVKLGDKVDPYCDRLEVDGKRIEPTQRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KP+G+V+T  DP  R TV + LP    +   +  VGRLD N+ G LLLTNDG
Sbjct: 63  EFLYILVNKPLGVVSTCDDPQNRPTVLELLPQELRKGTGIHPVGRLDFNSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y V   G + +  L   ++G+++ G      QV +  +      
Sbjct: 123 ELTLRLTHPRYHLPKTYEVSISGDISETSLQQWREGVMLMGKKTLPAQVEVIHRCRQQTC 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
           + V L EG+NR+I+++ E   + V RL R + G   L      +L +G  R +    +R
Sbjct: 183 LKVILIEGRNRQIRRIVEHLGFSVLRLHRTAVGSIALHRPHEPSLPSGHYRLLKASEIR 241


>gi|291522303|emb|CBK80596.1| ribosomal large subunit pseudouridine synthase F [Coprococcus catus
           GD/7]
          Length = 261

 Score =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 127/255 (49%), Gaps = 9/255 (3%)

Query: 4   KNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+I+ EN      R+++ ++ AG  SRRE +R+I   RV V+G         V     ++
Sbjct: 6   KDILHENEDKSDVRLNRFLSDAGFCSRREADRLIEAGRVTVDGTKA-ELGTRVRPGQVVK 64

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V    +R+ +R  L  ++KP G+V T      ++ + D +     R+  +GRLD ++EGL
Sbjct: 65  VGSKVVRQNDRMVLIAFNKPRGIVCTTDRVREKNNIIDYI-HYPERIYPIGRLDKDSEGL 123

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +LLTNDG +   +   S    + Y VR + ++  + +  + KG+ I         +    
Sbjct: 124 ILLTNDGTIVNHILKASQYHEKEYIVRVNKKITDEFIQGMSKGVPILDTVTRPCTL---- 179

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++  +   ++ L +G NR+I+ +   F++ V +L R+     +LG+L  G  R+V+ + L
Sbjct: 180 RRIDDYTFSIILTQGLNRQIRYMCRHFDYHVTKLKRVRIMNIRLGSLPVGKWRDVTAEEL 239

Query: 242 REQLGPHLLEEAQVN 256
            EQL    +   + N
Sbjct: 240 -EQLKRQFIANDRRN 253


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTVEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGEYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 119/238 (50%), Gaps = 9/238 (3%)

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  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           + +K E+     +HKP G+V T         + + + +  +R+  +GRLD  +EGL+ LT
Sbjct: 59  ISKKKEKPVYIAFHKPTGIVCTTDTRVEPDNIIEYI-NYPTRIFPIGRLDKMSEGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V     +D   ++ +  GI I        +V    ++  
Sbjct: 118 NDGDIVNKILRSRNNHGKEYIVTVDHSIDDRFISRMASGIPILDTVTKKCEV----EQIG 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                + L +G NR+I+++ E+ N++V +L RI     +L  +  G+ R+++K+ L E
Sbjct: 174 RKTFRIVLTQGLNRQIRRMCEYLNYRVTKLKRIRIMNVEL-DIPKGTYRDLTKEELDE 230


>gi|295676258|ref|YP_003604782.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295436101|gb|ADG15271.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 589

 Score =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 98/355 (27%), Positives = 158/355 (44%), Gaps = 15/355 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 188 KRVLSPDDDAPKLHKVLAEAGMGSRRDMEELIIAGRVSVNGEPA-HIGQRIMPTDQVRIN 246

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V L EG+NRE++++FE     V+RLIR  +GP  L   L  G   E+  
Sbjct: 367 GGGEGTNHWYHVALAEGRNREVRRMFEAAGLMVSRLIRTRHGPISLPRGLKRGRWEELED 426

Query: 239 KILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP-----DDFTRMKKNS 289
             +R  +         EE      AP       ++     I+  P       F +  +  
Sbjct: 427 NQVRALMASVGLKAPTEERGSRNAAPERRQPDPMQTSMGFINREPVLMSHSRFEQQPRGQ 486

Query: 290 SQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSK 344
            ++                  A     A G       D  +    +        K
Sbjct: 487 GRRGAAGGGFGAGMGGGAGFGAGAGNRAPGGQRGRDVDGNRAPSPNGNRARTGGK 541


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 107/228 (46%), Positives = 146/228 (64%), Gaps = 2/228 (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+     L    K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDILLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILE 228


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 94/342 (27%), Positives = 148/342 (43%), Gaps = 8/342 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D ++
Sbjct: 137 PAKRVLPPQVEMPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRVQYGDQVK 195

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP     +  SVGRLD+N
Sbjct: 196 VNGRPIRYRIDPPAPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLAHGKWQSVGRLDLN 255

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ ++        +
Sbjct: 256 TEGLLLFTSAGELANKLMHPRFGLEREYAVRVLGALSNEEKQRLLDGVQLEDGMAAFGSI 315

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +GSN W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+
Sbjct: 316 EDGGGEGSNCWYRVTISEGRNREVRRMLESVGHAVSRLIRIRYGSMMLPRGLKRGAWLEL 375

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++ +R  +     +  +                R               +         
Sbjct: 376 DERDIRALMQAAGADMPRPAGPGAAAGDRKGGGPRKGGGRGQGGPGGPAPRGDYFNPPAG 435

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            + K A P    +    +  + G   S      ++++  +R 
Sbjct: 436 GRGKRAAPSS--SQPDPMKTSVGYIGSDSLARHRQDQKQKRK 475


>gi|111221683|ref|YP_712477.1| pseudouridylate synthase [Frankia alni ACN14a]
 gi|111149215|emb|CAJ60900.1| Pseudouridylate synthase [Frankia alni ACN14a]
          Length = 254

 Score =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 120/234 (51%), Gaps = 3/234 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R+ KV+A AGI SRR  E +IA+ RV V+G+++      V   T  IEVDG  +  
Sbjct: 12  DEGIRLQKVLASAGIGSRRRGEELIAEGRVSVDGVVVREQGRRVNPETAIIEVDGDRIVT 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTND 127
                    +KP G+++  SD  GR T+ D L        +  VGRLD ++EGLLL+TND
Sbjct: 72  RTGLVHLALNKPRGVLSAMSDDRGRPTIADLLTEFDGGGGLFHVGRLDGDSEGLLLVTND 131

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y V   G + ++    L+ G+ ++        V L  Q     
Sbjct: 132 GELAHRLTHPSFEVPKTYLVEVSGPLRREVPRTLRTGVELEDGPARADSVQLVDQANGRV 191

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + + EG+NR ++++ E   + V+RL+R   G   LGTL +G  R +++  +
Sbjct: 192 MLEIVIHEGRNRIVRRMMETVGYPVHRLVRTRLGAVHLGTLRSGRARHLTRGEV 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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 108/228 (47%), Positives = 148/228 (64%), Gaps = 2/228 (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   L    K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGKYDI-LLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGNFTIDNLKPGDYKEINNKILE 228


>gi|257086025|ref|ZP_05580386.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994055|gb|EEU81357.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 244

 Score =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEMVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>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 =  257 bits (658), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 106/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R +  +++ Q  V VNG + +  A  V  TD I ++G  L      
Sbjct: 1   MRLDKFLAENTGLTRSQANKVLKQSAVTVNGHVEKNGAQKVSQTDEICLEGEHLPWVSAG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           +  + +KP G V +H D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYLMLYKPQGYVCSHEDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGKWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+        +G++++G        TL+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVESHYQQACAEGMLLRGEKTPTKPATLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G  +L   L  G  R +S + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGQIELDDRLAEGEYRSLSAEEI 227


>gi|295115835|emb|CBL36682.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SM4/1]
          Length = 346

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 118/247 (47%), Gaps = 16/247 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            R+ + +      SR EV++MI   RV V+G     A   +  +   + +DG  +  A  
Sbjct: 5   MRLDRYLVEMKKGSRSEVKKMIKSGRVSVDGETCREAERKIQPSASEVSLDGTQVGYAA- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G+V+   D   ++ V     +    +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 64  YEYFMLNKPAGVVSATEDGRHKTVVSLIEDAKRRDLFPVGRLDIDTEGLLLITNDGKLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------ 186
            L  P     + Y  R  G++ ++ +   K+G+ ++      +   L  QK S       
Sbjct: 124 RLLSPKKHVDKTYFARVEGRLPENAIEQFKEGLTLEDG-TRTLPARLVIQKASGTAEDDG 182

Query: 187 ------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
                 + + + + EGK  ++K++FE    +V  L R+S G  +L  +L  G+ R ++++
Sbjct: 183 KADSSLSEIELTIHEGKFHQVKRMFEAVGCRVVYLKRLSMGSLRLDESLAPGAYRRLTEE 242

Query: 240 ILREQLG 246
            + +  G
Sbjct: 243 EISKLQG 249


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 103/230 (44%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R++  ++I    + V+G + +  A  V     +  +   +  A   
Sbjct: 1   MRLDKYLCDALGATRKQATKIIKSGDITVDGEVQKSGAFKVPKGAEVMWEDRVI-GAPGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPADFVCSHED-GYNQTAFALLDEPKIENLHFAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D    L++GI+++      +   L+    +   V + 
Sbjct: 119 RITSPKHKCEKTYRVWLVDAIQPDYAEKLEQGIILRNESEATLPARLEIVNEAENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +
Sbjct: 179 IVEGKYHQVKRMFAALGNKVEYLHRERIGSIELDEALEPGDYRHLTQEEI 228


>gi|303242956|ref|ZP_07329414.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
 gi|302589505|gb|EFL59295.1| pseudouridine synthase [Acetivibrio cellulolyticus CD2]
          Length = 250

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 125/235 (53%), Gaps = 8/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             QRV ++++  G  +RRE+++++    VKV+G +++ + ++V   T  IE+ G  L   
Sbjct: 3   ETQRVDRILSNFGFGTRREIKQLVKNGEVKVDGEVIKDSGMHVDPKTSKIEISGQVLNYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           +   + + +KP G+++   D +   TV D LP  +       VGRLDI+TEGLLL+TNDG
Sbjct: 63  QFIYVMM-NKPAGVISATFD-NRHETVVDILPEEYKCFDPFPVGRLDIDTEGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y     G+V    + + ++GI++  G      ++ +  Q  S++
Sbjct: 121 QLAHELLSPRKHVPKKYFAYIEGEVSAGDVKMFEEGILLDDGYKTLPAELHILEQGESSS 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V V + EGK  ++K++FE    KV  L RI+ G   L   L  G  RE+++  L
Sbjct: 181 -VEVIIFEGKFHQVKRMFEAVGKKVKYLKRITMGNLVLDEALATGECRELTENEL 234


>gi|218663826|ref|ZP_03519756.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli IE4771]
          Length = 267

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/257 (31%), Positives = 132/257 (51%), Gaps = 5/257 (1%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TD 58
           +++  +  +   +R  + + +++ G  SR + ER+IA+ RV V+G  +   +  V   T 
Sbjct: 11  RERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAEGRVSVDGRTVNDPSAWVDLVTA 70

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            I VDG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  
Sbjct: 71  EIRVDGLVI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLKDFEIPHLSPVGRLDKA 129

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G       V
Sbjct: 130 SEGLLLFTNDTEFAQILLDPITHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAV 189

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 190 RRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALT 249

Query: 238 KKILREQLGPHLLEEAQ 254
              L+        E A+
Sbjct: 250 AAELQALHRSAGTERAR 266


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 132/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKRAGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/234 (34%), Positives = 124/234 (52%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G +++ SD  GR TV D LP +  R+  VGRLD +T G+L+LTNDG     
Sbjct: 60  VYYLLNKPRGAISSVSDDKGRKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDT 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK-LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVT 190
           +  P  +  +V   R    + + K L  L +GIVI G      +  +       + + V 
Sbjct: 120 MIHPRNEIDKVIW-RVSKVLQRKKNLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + EG+N ++KK+FE     V++L R   G   L  L  G  R ++KK + + 
Sbjct: 179 LTIHEGRNHQVKKMFESVGLLVDKLSRTRLGTVDLKGLRPGEARRLNKKEISQL 232


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 105/303 (34%), Positives = 156/303 (51%), Gaps = 21/303 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV--PLR 68
             +++ KV+AR+G  SRRE+E +I Q RV V+G +      V+V ST  I +DG    ++
Sbjct: 3   ESEKLQKVLARSGQGSRREIEAVIEQGRVSVDGKVATLGDRVDVTSTTKIRIDGRIIAIK 62

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
             E    R+  Y+KP G + T  DP+GR TVFD LP    +R ++VGRLDINT GLLL T
Sbjct: 63  PVEDAVCRVLTYYKPEGELCTRRDPEGRPTVFDRLPRLNNARWVAVGRLDINTSGLLLFT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y +R  G+VD+DK   L +G+ +         +T    +G 
Sbjct: 123 TDGELANRLMHPSCKIEREYALRVFGEVDEDKQRQLTRGVQLDDGPAAFRSLTFQGGEGL 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---IL 241
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  +    L
Sbjct: 183 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDVTLPKGLPRGGWTELPLEQTNYL 242

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS-EVPDDFTRMKKNSSQKNGLSKQKK 300
           RE          +V L     +   + RDR  + + ++     R  + +  + G    K+
Sbjct: 243 RE----------KVQLPLESVTKLPVERDRRRLKATQIRRVVKRNSQRAPSRRGGQSIKR 292

Query: 301 LAT 303
              
Sbjct: 293 NNG 295


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 8/235 (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 ++ + +  + D +     RV ++GRLD +++GL+LLTNDG +   +
Sbjct: 64  YLALNKPVGITST-TEKNVKGNIVDLVNHPL-RVFNIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                Q  + Y V     +  + L  + +G+ I G      +V    ++ S     + L 
Sbjct: 122 LRAENQHEKEYIVSVDKPITPEFLTQMSEGVKILGTKTLPCKV----EQLSKFDFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           +G NR+I+++ E   ++V RL R+      LG L  G  R+++KK  ++QL   L
Sbjct: 178 QGLNRQIRRMCEALGYEVFRLQRVRIMNIHLGNLPVGQWRDLTKKE-KQQLFREL 231


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 102/296 (34%), Positives = 157/296 (53%), Gaps = 23/296 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +++ KV+ARAG+ SRRE+ER+I+  +V VNG         V + D IE DG  ++ 
Sbjct: 7   EPQGEKLQKVLARAGLGSRREMERLISLGKVSVNGATAR-LGDRVGAEDKIEYDGKRIQA 65

Query: 70  A----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
           A    +RTR+ LY+KP G + + +DP+GR TV+DNLP I  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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            N W    + EG+NRE+++++E    +V+RL R+ YG   + + + AG   E+++K + E
Sbjct: 186 KNRWFYCVVMEGRNREVRRLWESQEVRVSRLKRVRYGNIFIPSHVRAGQWVELTEKDVGE 245

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                              ++      +P    E+     R ++   + N    ++
Sbjct: 246 L----------------CDTAGLAPPPKPKYSPELRRSRERHQRKLRKANTSRTRR 285


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 121/241 (50%), Gaps = 8/241 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
             N    R+++ +A  GIASRR  ++++ + RV VNG ++ +    V    D + VDG  
Sbjct: 4   STNSEEVRINRFLALCGIASRRAADQLVLEGRVMVNGTVITQPGTKVNPDKDEVIVDGQK 63

Query: 67  LRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             + E R    L++KP  +++T SD   R  V D +  +  RV  VGRLD  T GL+LLT
Sbjct: 64  YAQPESRKVYILFNKPRNVISTSSDEKNREMVLDYI-DVKERVFPVGRLDRKTTGLILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQK 183
           NDG LA  L  PS+   + Y      +     L  L  G+ ++  G      +  L  + 
Sbjct: 123 NDGTLANKLMHPSSNVKKEYIAVLGEKFPASMLPQLTGGMRLKDTGEKVRPCRAKLLDEG 182

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                V + + EGKN +++++FE   ++V RL R++Y    +G L  G  R +S+  +RE
Sbjct: 183 ---MQVLLSIHEGKNHQVRRMFETLGYEVKRLERVAYAGLTIGELRRGEWRYLSRNEVRE 239

Query: 244 Q 244
            
Sbjct: 240 L 240


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 115/229 (50%), 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
               + HKP G+++   D   ++ +   +      +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYY-MLHKPAGVISATEDAREKTVIDLIVSRKRKDLFPVGRLDKDTEGLLLITNDGELAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y  +  G V Q+ +    +G+ I         V    + G  + + + 
Sbjct: 122 RLLSPKKHVDKTYYAKVQGIVTQEDVRKFAEGVDIHEKKLTAPAVLEVVKSGEVSEILLT 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           + EGK  ++K++FE    KV  L R+S GP QL  TL+ G  RE+++K 
Sbjct: 182 ICEGKFHQVKRMFEAVGKKVIYLKRLSMGPLQLDETLMPGEYRELTEKE 230


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 92/285 (32%), Positives = 145/285 (50%), Gaps = 10/285 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 207 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 265

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 KILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +         EE      AP       ++     I+  P
Sbjct: 446 NQVRALMASVGLKAPTEERGSRNAAPERKQPDPMQTSMGFINREP 490


>gi|332359960|gb|EGJ37774.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 242

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIVVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAQLKIVELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ G  QL + L  G  R ++++ +
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLTMGSLQLDSALALGEWRRLTEEEM 232


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 118/229 (51%), Gaps = 2/229 (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      V D +    +RV  VGRLD ++ GLL+LTNDG     
Sbjct: 61  IYIAINKPIGYASTVKDKFADKKVVDLI-KSDTRVYPVGRLDKDSHGLLILTNDGEFTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V +
Sbjct: 120 LTHPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+NR+I+++F+F N  V  L R+  G +++   L +G  + +  K L
Sbjct: 180 FEGRNRQIRRMFDFINHPVLDLKRVQIGNYKMDNSLKSGEYKLLKSKDL 228


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKSGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     + Y  +  G + Q+      KGI ++       ++ L +   K + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTQEDAETFAKGIPLKDFTCQPARLELVSVDTKKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L + 
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELEDL 235


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 113/233 (48%), Gaps = 7/233 (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 S+   +  + D +     R+  VGRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RINHVGRLDKDSDGLILLTNDGDIINE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLKEMAAGVKILGTKTLPCEIT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +G NR+I+++ E   ++V  L R      QL  L  G  R+++KK  +    
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIQLNNLPVGQWRDLTKKEKKRLFA 226


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 115/240 (47%), Gaps = 1/240 (0%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E    +R+ K+IA AG+ SRR  E ++   RVKVN  + +         D I +DG PL 
Sbjct: 8   ETVKAERLQKLIAAAGVCSRRHAEELLRAGRVKVNDRMAQLGDRAEPGLDRITIDGTPLP 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
             +  RL L +KP G++++  DP GR  V D +P    R +  VGRLD  + G LLLTN 
Sbjct: 68  ANDPPRLLLLNKPRGVISSCQDPQGRPIVLDLVPKHLRRGLHPVGRLDAESRGALLLTNQ 127

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + YRV   G+     L   ++G+ +        +V       +  
Sbjct: 128 GELTLQLTHPRYSHAKTYRVWVQGRPSHGALEHWRRGLRLDQRLTQPAEVRELHHNANRT 187

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + V LREG+NR+I++V E     V  L R +     LG+L  G  RE+++   R    P
Sbjct: 188 LLEVVLREGRNRQIRRVAELLGHPVLDLQRTAIATVVLGSLQEGRWRELTEGEWRALTRP 247


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 120/234 (51%), Gaps = 1/234 (0%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P+R+ KV+A AG+ SRR  E +I +++V VNG + +       +T  I V+G  L+   R
Sbjct: 18  PERLQKVLAAAGVGSRRACEDLIFRRKVTVNGRVAQLGDKVDPATAVIHVNGERLQADTR 77

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP G+V+T +D  GR+ + D L +    RV  VGRLD ++EGLLLLTNDG LA
Sbjct: 78  LVYLAMNKPRGVVSTMADERGRTALADFLNNRVEQRVYHVGRLDADSEGLLLLTNDGTLA 137

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y     G + ++    L  GI ++          +    G  A V +
Sbjct: 138 HRLMHPSYGVQKTYLCEVAGPIPRNLGKRLAAGIELEDGPVSVDAFRVVDSLGRTAQVEL 197

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L EG+   ++++       V+RL+R + GP +LG L +G TR ++   +    
Sbjct: 198 SLHEGRKHIVRRLLAEVGHPVSRLVRTAIGPIRLGDLRSGRTRRLTNAEVAALF 251


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+
Sbjct: 1   MRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTLSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D +   TV D L           VGRLDI+T GLLLLTN+G L
Sbjct: 60  YVYYMLNKPKGVISATED-NHHKTVLDLLDKIAWDKEAFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     + YR +  G +    +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSV 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + ++EGK  ++K++ +    KV  L R+S GP QL   L  G  R ++   L
Sbjct: 179 VEITIKEGKFHQVKRMVQACGKKVTDLQRLSMGPLQLDKQLALGEWRRLTDDEL 232


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 76/234 (32%), Positives = 119/234 (50%), 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  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             ER    + +KP G V T++DP       D +      R+ S GRLD ++EGL+L +ND
Sbjct: 62  AEERKVYIMLNKPRGYVCTNADPHADLKAVDLIRLTPPLRLFSAGRLDKDSEGLILFSND 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G     L  P  + L+VY+VR   +    +L  +++G++ +G       V+    +  + 
Sbjct: 122 GDYVARLTHPRHEILKVYQVRVRREFKPAELEQMRRGVLERGELLKVHAVS----RCGDC 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L EGKNREI+++         RL R+  G  +LG L  G+ RE++   +
Sbjct: 178 TYLITLNEGKNREIRRLTAALGSPTRRLKRLQIGALRLGGLPVGNWRELTPAEI 231


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 105/315 (33%), Positives = 161/315 (51%), Gaps = 15/315 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
             +++ KV+AR+G+ SRRE+ER I Q+RV ++G    R    V++   IEVDG PL  + 
Sbjct: 18  DGEKLQKVLARSGLGSRREMERWIEQERVTIDGK-AARLGDRVVAAQRIEVDGRPLVASD 76

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E+TR  LYHKP G V +  DP+GR TVF+ LP + S 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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL-- 245
             V L EG+NRE+++++E     V+RL R+ YG   + + +  G  +E++   +      
Sbjct: 197 YYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGDLFVPSKVKKGQWQELAPNEINGLYRM 256

Query: 246 ----GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ--- 298
                  +   ++ +            R R N  ++   D T      S+K   S++   
Sbjct: 257 AGMQAKDVEPPSREDRSKHKRMEGKRGRVRGNRHAKSARDKTGAPDKGSRKPSRSRKPGS 316

Query: 299 -KKLATPVHRRNLAS 312
            K+ + PV  +  + 
Sbjct: 317 GKRESAPVKNKGRSR 331


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 70/229 (30%), Positives = 123/229 (53%), Gaps = 3/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+++ I+  G+ASRR+ +++I + +VKVNGI ++     V    D +EV+G  ++   R 
Sbjct: 9   RLNRFISMCGVASRRKADKLIKEGKVKVNGITIKEMGYRVDPQKDVVEVEGRVIKAP-RY 67

Query: 74  RLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   +++ ++  DG+ ++ + + +I  RV   GRLD N EGLL+LTNDG LA 
Sbjct: 68  RYVILNKPCCYLSSLAEGKDGKKSIKELIKNIPERVYPAGRLDYNAEGLLVLTNDGELAN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V   G+V+   L  + KG  ++       +V +   +  +  + V 
Sbjct: 128 RIMHPRYKLKKTYLVWVEGRVNPKTLKEMAKGAHLEDGFARPDKVRIVKMQKDSTLLEVV 187

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             EG+   +K+    F  KV  L R + GP +LG L  G  R+++ + L
Sbjct: 188 FHEGRKHIVKRFMAKFGHKVKALKRTAIGPIKLGKLPPGKWRDLTAEEL 236


>gi|159026975|emb|CAO86693.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 248

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 90/239 (37%), Positives = 127/239 (53%), 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--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 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|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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 100/290 (34%), Positives = 148/290 (51%), Gaps = 11/290 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +++ KV+ARAG  SRRE+E  IA  RVKVNG +       + + D +  D  P+  
Sbjct: 2   NTPTEKLQKVLARAGFGSRREMETAIADGRVKVNGQVAT-LGDRIETRDRVTFDERPVNL 60

Query: 70  AE----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
            +      R+ +Y+KP G + T  DP+GR TVF+ LP     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 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
                 L   +V    P  + +   R   +     P +  R  K+S +  
Sbjct: 241 LAQLADLPARKV----PELTPDEQNRWSRDKNKRRPVNAMRKPKSSRRSR 286


>gi|332365802|gb|EGJ43559.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 242

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLIY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISVTED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFICQPAQLKIVELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R+  GP QL + L  G  R +++  +
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLRMGPLQLDSALSLGEWRRLTEAEI 232


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 120/242 (49%), Gaps = 10/242 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  GI SR+E+++++ ++ V VNG +++ A   V   TD I + G  L   ++
Sbjct: 1   MRLDKFLADVGIGSRKEIKQLLKKKVVTVNGDVVKEAKTQVNEETDQIALMGEILTY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L     R  +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FFYYMLHKPQGVISATED-QRDETVIDLLTDQDYRADLFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V  +   L  +G  +  G      ++ ++T  ++   +
Sbjct: 119 AHQLLSPKKHVDKEYLAEVEGLVTAEDCQLFAQGFALKDGEIVKPSRLVIETINEEEGTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            V + ++EGK  ++K++       V  L R+  G   L  TL  G  R +++  L +QL 
Sbjct: 179 VVRLVIQEGKFHQVKRMLATVGKPVTYLKRLRMGELWLDETLELGGYRPLTEAEL-QQLQ 237

Query: 247 PH 248
           P 
Sbjct: 238 PK 239


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     RV  VGRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RVNHVGRLDKDSDGLILLTNDGDIINEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLKQMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      QL  L  G  R+++KK  +    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIQLNNLPVGQWRDLTKKEKKRLFA 229


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 109/237 (45%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  AG+ SR +V+ ++ +++V VNG+        V   TD +   G  L   E 
Sbjct: 1   MRLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEMTDEVSYQGQRLNY-EA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D     TV D L     +  V  VGRLD +T GLLL+TNDG L
Sbjct: 60  FVYYMLNKPKGVISATED-SSHKTVLDLLDDTARQKAVFPVGRLDKDTHGLLLVTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y     G + Q+ +    +GI ++          +    +    + 
Sbjct: 119 AHALLSPKKHVAKQYLAVVDGMMTQEDVKHFAQGITLKDHQCMPAHLDILEINESLKTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + + EGK  ++K++       V+ L RIS GP QL + L  G+ R ++   L   
Sbjct: 179 VKITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLTAAELEAL 235


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 107/228 (46%), Positives = 147/228 (64%), Gaps = 2/228 (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+     L    K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDVLLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILE 228


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/243 (32%), Positives = 116/243 (47%), Gaps = 9/243 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDHIEVDGVPLRKAER 72
            R+ K +A  G  SR+EV++ + +  V VNG  ++      V ++D + V    +   E 
Sbjct: 1   MRLDKFLAHHGYGSRKEVKQFLKKTEVTVNGKRVQDGKQAIVPTSDIVRVQDEVILYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              W+ HKP G ++   D     TV D L        V  VGRLD +TEGLLLLT+DG L
Sbjct: 60  YVYWMLHKPSGYISATEDQA--KTVLDLLKPKDAGRAVFPVGRLDKDTEGLLLLTDDGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY     G V  D ++  KKGIV+         ++ +    G    +
Sbjct: 118 AHELLSPKKHVNKVYEATIEGVVTGDDVHAFKKGIVLEDDYQCKPAKLEILQVNGVKTDI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
            + ++EGK  +IK++F   + KV  L RI  G  QL   L  G  R ++ + L EQL   
Sbjct: 178 RITIQEGKYHQIKRMFLAVDKKVIYLKRIQMGSLQLDENLARGEYRPLTVEEL-EQLSKK 236

Query: 249 LLE 251
            LE
Sbjct: 237 RLE 239


>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 =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 68/299 (22%), Positives = 133/299 (44%), Gaps = 16/299 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +     E 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGHVFINGKRA-GIGDQVSAGDVVKVNGQLIEPRNEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T    +  + V  +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTESGEKDNIV--DYVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V     K +     + 
Sbjct: 125 KILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTMTKKCKVK----KEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E    +L+E+
Sbjct: 181 LVQGLNRQIRRMTEHFGYEVTKLERVRIMNVRLTGIPVGEWRDLTDDELIELF--NLIEK 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           ++ ++       +   + +    +              + N    +KK   P  ++   
Sbjct: 239 SESDV-----KPKKAAKPQARASNNKSSGKQGSGSQKPKVNAEPPKKKFTQPGRKKKKR 292


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 107/228 (46%), Positives = 147/228 (64%), Gaps = 2/228 (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+     L    K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDVLLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILE 228


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 110/237 (46%), Gaps = 3/237 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  +       G+ +         V L+  K ++  V + +
Sbjct: 121 VTSPKHHCEKTYLVTLEHSLAANTAQRFAAGVQLHNEKSLTRPVQLE--KINDRQVRLAI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
            EG+  ++K++F     +V  L R   G   +   L +G+ R ++ + +     PHL
Sbjct: 179 SEGRYHQVKRMFAAIGNRVIALHRERIGTIVMDKDLASGAYRPLTAEEIASVGAPHL 235


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 106/228 (46%), Positives = 147/228 (64%), Gaps = 2/228 (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+     L    K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDILLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILE 228


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+ +I + +V V+G +++   + +    + I V G  L   ++
Sbjct: 2   ERLDKILANLGYGTRKEVKALIKKGQVDVDGEVVKDNGMQIDPEKNKIFVFGKELVY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD NT GLLLLTNDG L
Sbjct: 61  YIYLIMNKPQGVVSATFD-NYDETVVDLLEDEDRIFEPFPVGRLDKNTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y  + + +V  + +   KKGI++  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKIYYAKINKKVTDEDIKKFKKGIILDDGYECFPAKLEIIKSFNEESEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++FE  + KV  L R  +GP +L  +L  G  RE++ + +
Sbjct: 180 RVTIHEGKFHQVKRMFESVDKKVIYLKREEFGPLKLDESLEEGQCRELTDEEI 232


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 10/235 (4%)

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-LWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +    +HKP+G+  T +   +G    + N P    R+  VGRLD  +EGL+LLTNDG +A
Sbjct: 60  KVYIAFHKPVGITCTAAKHIEGNIIAYINYPE---RIFPVGRLDKASEGLILLTNDGKIA 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V          ++ +  G+ I+       +VT    +  ++   +
Sbjct: 117 NQILHGDHGHEKEYVVTVDKSFTDGFIHGMSCGVKIKDGMTKPCKVT----RVDDSTFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++   F + V +L R+     +LG L  G  R ++ + L+E  G
Sbjct: 173 VLTQGMNRQIRRMSRAFGYTVTKLKRVRIMNIKLGELEVGKWRYLTDEELQELRG 227


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 94/308 (30%), Positives = 147/308 (47%), Gaps = 7/308 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D I
Sbjct: 118 VPHKRVLLPQPESPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HIGQRVQFGDQI 176

Query: 61  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
           +V+G P+R       TR+  YHKP+G V TH DP  R TVF  LP +   +  SVGRLD+
Sbjct: 177 KVNGKPIRFRVAPPPTRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQQGKWQSVGRLDL 236

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           NTEGLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ ++        
Sbjct: 237 NTEGLLLFTSSGELANKLMHPRFGLEREYAVRVLGALSDEERQRLLDGVSLEDGMAAFGS 296

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
           +     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 297 IEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWLE 356

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  +R  +    +            +     R +P       +   +    + + +G 
Sbjct: 357 LDEHDIRALMQAAGVPADAGGGARAGRNGRRGER-KPMGAKMQGEGRGKAAGRAGRSSGS 415

Query: 296 SKQKKLAT 303
           S+   + T
Sbjct: 416 SQPDPMKT 423


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 114/229 (49%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGI SRRE +  IA   V VNG  +      V  TD +  DG  L++ ER 
Sbjct: 70  IRLNKYIANAGICSRREADTYIAAGNVTVNGKTITEMGYKVQPTDEVRFDGRLLQR-ERK 128

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  D  GR TV + +  +  +R++ VGRLD NT GLLL TNDG LA+
Sbjct: 129 EYVLLNKPRNFITTTRDEKGRRTVMELISRASNARLVPVGRLDRNTTGLLLFTNDGELAK 188

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y V          L  L++G+ ++       + +      S   V V 
Sbjct: 189 KLTHPKHGVRKIYHVELDKTFKSADLGKLREGLELEDGRIEVDEASYIDG-ASKKEVGVE 247

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L  G+NR ++++FE   ++V +L R+         L  G  R ++++ +
Sbjct: 248 LHSGRNRIVRRIFEHLGYQVVKLDRVVLAGLTKKDLPRGHWRHLTEQEV 296


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 89/239 (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   ERVQKILAQWGIASRRRAEEMIVAGRVRRNGKIVQLGEKADPEKDHLEIDGKKIEPANRP 62

Query: 74  R--LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 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|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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 120/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  ++VNG +++   + +    D I V+G  +    +
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVRKGLIEVNGEIVKDNGMQIDPEVDKILVNGEEIFYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  YIYLMMNKPDGVVSATFD-NRDETVIDLLEIEHQVFEPFPVGRLDKDTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P  +  +VY  +   +V +  +   K GI +  G    + ++ +     S + V
Sbjct: 120 NHRLISPKWKVDKVYYAKIDKKVTEADIKKFKNGITLDDGYTCKEAKLEILESSDSGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + ++EGK  ++K++FE  +  V  L R+ +G  QL   L  G  RE++++ +
Sbjct: 180 MITIQEGKFHQVKRMFEAVDKSVVYLKRVEFGTLQLDEDLEEGEYRELTEEEV 232


>gi|317402968|gb|EFV83508.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 469

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 100/331 (30%), Positives = 154/331 (46%), Gaps = 17/331 (5%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  E   P ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+
Sbjct: 104 KYLNSEAVMP-KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVN 161

Query: 64  GVPL---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+      +  R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTE
Sbjct: 162 GKPIMRANTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTE 221

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A  +  P     R Y VR  G++D+ +   L  GI ++        +  
Sbjct: 222 GLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGVAAFGALDY 281

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
               GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  +L  G   E+  
Sbjct: 282 LGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDVVLPRSLRRGRWEELDA 341

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            ++   +         V L       E+    R +   +  D        +  +NG++  
Sbjct: 342 SLVTALM---------VQLGLLREDDESGGNRRRSKQPQSHDSALPPGFGTMDRNGMNGA 392

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
           +       +   A +   A     S    +G
Sbjct: 393 RIGRRGKIQGGRAGSAGQAA-ACPSDPFGTG 422


>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 =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 113/231 (48%), Gaps = 7/231 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R   
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKRRLF 228


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 122/239 (51%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG  SRR  E +I Q RV+VNG ++      V    D ++V
Sbjct: 112 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEVKV 171

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 172 DGLTV-ATQSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 230

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q
Sbjct: 231 LLTNHGELAHRLTHPKYGVRKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQ 290

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 291 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 349


>gi|283850767|ref|ZP_06368054.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283574010|gb|EFC21983.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 285

 Score =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 92/296 (31%), Positives = 142/296 (47%), Gaps = 19/296 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M DK ++       R++K +A AG+ SRR+ + +I   RV V+G ++      +    + 
Sbjct: 1   MDDKALL-------RLNKALADAGVCSRRQADALITAGRVTVDGAVVTELGNKIDPARNR 53

Query: 60  IEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRL 114
           + VDG P+R    A+     L +K  G VTT +DP+GR TVFD LP+ +   R+  VGRL
Sbjct: 54  LAVDGRPVRLSGAADAPLTLLLNKRPGCVTTANDPEGRPTVFDELPAAYRARRLFPVGRL 113

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYG 173
           D  +EGLLLLT DG LA  L  P     + Y V   G V+   L+ + KG+ + +G    
Sbjct: 114 DYFSEGLLLLTTDGELANRLAHPRWHVDKRYLVTVRGTVNGQTLDTMAKGMTLAEGEQLA 173

Query: 174 DMQVTLDTQ-KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            ++  +  +       + + L +G NR+I+++    +  V +L RI+ GP  LG L AG 
Sbjct: 174 PVRARITARLAADRFVLEMELSQGVNRQIRRMCRDLDLTVLKLCRIAQGPVSLGGLPAGK 233

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
            RE++   L        L  +     AP   S       P   SE P      ++ 
Sbjct: 234 CRELAASELAALRRSVGLPSS----AAPAKPSVKAPGKAPRKASESPSGKAPGRRR 285


>gi|187923621|ref|YP_001895263.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187714815|gb|ACD16039.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 626

 Score =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 93/285 (32%), Positives = 148/285 (51%), Gaps = 10/285 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 202 KRVLAADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 260

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR++VFDNLP +  ++ ++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 KILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +         EE     +AP       ++     I   P
Sbjct: 441 NQVRALMASVGLKAPTEEKGGRREAPERKQPDPMQTSMGFIGREP 485


>gi|158520075|ref|YP_001527945.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158508901|gb|ABW65868.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
          Length = 241

 Score =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 117/233 (50%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++ AG+ SRR  E  IA+ RV VNG ++      V   +D +  DG  +  AE 
Sbjct: 10  IRLQKFLSGAGVCSRRRAEVYIAEGRVAVNGQVVTELGTKVDPESDDVMFDGHRVTLAES 69

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP G VT+       +TV + + ++  RV  VGRLD  + GLLL+T+DGGL +
Sbjct: 70  HVYIALNKPPGYVTSCLQKQE-TTVMELV-AVDQRVFPVGRLDKPSCGLLLMTSDGGLHQ 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS    + Y V     V    L+ +++G+VI G      +V     + S+    + 
Sbjct: 128 RLSHPSFDHEKEYDVACDRPVSDADLDAMRRGMVITGRKTRPAKVK----RLSDRRFLII 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L+EG+NR+I+++ E    +V  L RI      LG L  G  R ++++  +  L
Sbjct: 184 LQEGRNRQIRRMAEMLGNRVVLLRRIRIAHIHLGDLAEGRWRYLTEEEKKALL 236


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 124/242 (51%), Gaps = 6/242 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K +++AG+ SRR+ +  + Q +V V+G         V     +  +G P+R   
Sbjct: 7   SAVRINKFLSQAGLCSRRQADFYVEQGKVTVDGKTA-EPGTKVCEGQEVCFNGKPVRMDT 65

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T    Y+KP G+V T S  +  + +  +     SR+  VGRLD +++GL+LLTNDG  A
Sbjct: 66  QTVYLAYNKPKGIVCTSSKEEANNII--DAVGYPSRIYPVGRLDKDSQGLILLTNDGEAA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  + ++  D +  ++ G+ +  +     + T+  +   +    +
Sbjct: 124 NEIMKARNYHEKEYEVTVNKRITNDFIQGMRNGVPLSELDTVTRKCTVKKEGPDS--FRI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+F ++V +L R+     +LG L  GS R+++ + ++  L   L+ 
Sbjct: 182 ILTQGLNRQIRRMCEYFGYRVTKLRRVRVMNIRLGNLKEGSYRKLTPEEIK-MLKEELIR 240

Query: 252 EA 253
           E 
Sbjct: 241 ER 242


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 130/231 (56%), 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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+
Sbjct: 1   MRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADQIRCQGQTLSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D +   TV D L           VGRLDI+T GLLLLTN+G L
Sbjct: 60  YVYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKETFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     + YR +  G +    +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVDKTYRAKVAGLMTTTDVAAFANGIDLKDFTCQPAQLVILEINEAERTSV 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + ++EGK  +IK++ +    KV  L R+S GP QL   L  G  R ++   L
Sbjct: 179 VEITIKEGKFHQIKRMVQACGKKVTDLQRLSMGPLQLDKQLALGEWRRLTDDEL 232


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 110/286 (38%), Positives = 156/286 (54%), Gaps = 12/286 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR-- 68
             +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV +   + +DG  +   
Sbjct: 39  EGEKLQKVLARAGQGSRREIEAIIAENRVSVDGKIATLGDRINVYAGVKVRIDGHLINLT 98

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
             + E  R+ +Y+KP G + T  DP+GR+TVFD LP    +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-GTLLAGSTREVSKKI---L 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+       L
Sbjct: 219 NQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMELADVNYL 278

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           RE +G  L  EA+  L A     +         +    +   R KK
Sbjct: 279 RELVG--LPPEAETKLGANKTRHKPKFGRIRKAVKRYSELNKRYKK 322


>gi|226943690|ref|YP_002798763.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
 gi|226718617|gb|ACO77788.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
          Length = 382

 Score =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 105/361 (29%), Positives = 168/361 (46%), Gaps = 17/361 (4%)

Query: 1   MKDKNIVQENF-TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++          +++ KV+AR G+ SRR++E  IA+ RV VNG +       V   D 
Sbjct: 1   MSEREENSPPAAQGEKLQKVLARMGLGSRRDIEARIAEGRVMVNGTVAT-LGQRVGRHDA 59

Query: 60  IEVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRL 114
           I +DG  LR+ E      R+ +Y+KP G + T +DP+GR TVFD LP +   R +++GRL
Sbjct: 60  IALDGRLLRREEGAELVRRVLIYNKPDGEICTRNDPEGRPTVFDRLPRLKEGRWVNIGRL 119

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DINT GLLL T DG LA  L  PS +  R Y VR  G+V ++ L  LK+G++++      
Sbjct: 120 DINTTGLLLFTTDGELANRLMHPSYEMDREYAVRVRGEVTEEMLETLKRGVMLEDGPARF 179

Query: 175 MQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
             +      +G N W    + EG+NRE+++++E     V+RL R+ +GP  +   L  G 
Sbjct: 180 TDIQEAPGGEGLNHWFHCVVMEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLAMGR 239

Query: 233 TREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSE-TLVRDRPNIISEVPDDFTRMKKN 288
            RE+++     L  ++G   L   ++ L              +P       +   R    
Sbjct: 240 WREMTQDEVDILSREVGLEPLALPEMKLRFREKMERLQRKSAKPVGRGGARERVLRPAHE 299

Query: 289 SSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
            ++       ++       R   + V        S     G+      RSP+   +R  R
Sbjct: 300 GAEAQERRAPRRPKEERAPRGRGTPVAERPA--ESVRKRPGR--PAGERSPAESGERPAR 355

Query: 349 R 349
           +
Sbjct: 356 K 356


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 107/228 (46%), Positives = 147/228 (64%), Gaps = 2/228 (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+     L    K + I GI Y    + L  Q  +N W  V L 
Sbjct: 122 ELPSSRLKRVYHVRAYGK-SDILLKSNYKNLEIDGIFYNPHSIKLLKQNKTNCWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           EGKNREI+++FE+   KVN+LIRI YG F +  L  G  +E++ KIL 
Sbjct: 181 EGKNREIRRIFEYCGLKVNKLIRIQYGSFTIDNLKPGDYKEINNKILE 228


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 101/317 (31%), Positives = 155/317 (48%), Gaps = 23/317 (7%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           +  +    +++ K++AR+G  SRRE+E ++ + R+ V+G +      V V +T  I +DG
Sbjct: 9   MSSKPQQTEKLQKILARSGHGSRREIEGLLKEGRISVDGKMATLGDRVEVKATTKIRLDG 68

Query: 65  VPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             L   E      R+  Y+KP G + T  DP+GR TVF+ LP    +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 K---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +    LRE           V LD    S  ++ RD+  I +       R  K  +Q    
Sbjct: 249 EQTNYLREL----------VELDVETESKVSVERDQRRIKAN---QIRRAVKRHTQVASR 295

Query: 296 SKQKKLATPVHRRNLAS 312
              K+ ++    +    
Sbjct: 296 PAAKRQSSRPTAKRRTR 312


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 76/234 (32%), Positives = 113/234 (48%), Gaps = 7/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K++A  G  +R EV+  I + RV VNG + + A   V    D I +DG P+  
Sbjct: 1   METIRLDKLLAATGAGTRSEVKNAIRKGRVTVNGAVCKSADSKVDADKDVICLDGAPVVY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDG 128
             R    + +KP G VT   D     TV D +  +    +  VGRLD++TEGLLL+TNDG
Sbjct: 61  T-RYEYHMLYKPAGCVTAVRDARY-PTVMDYISSARKKDLFPVGRLDLDTEGLLLITNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNA 187
            LA  L  P     + Y  R  G+V  + +   ++GI I G     M   L+    G  +
Sbjct: 119 ELAHRLLAPGWHVDKTYYARVQGEVTAEDIRRFQEGIDI-GEKRPTMPAELEILAAGQES 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            V V + EGK  ++K++F      V  L R+  G   L   L AG +R ++++ 
Sbjct: 178 EVRVTIHEGKYHQVKRMFAAIGKPVLYLKRLRMGSLTLDENLQAGGSRLLTQEE 231


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 82/240 (34%), Positives = 118/240 (49%), Gaps = 6/240 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
                R+ KV+++AGIASRR  ERMI   RV+V+G ++      V      I VDG  + 
Sbjct: 3   EEQGVRLQKVLSQAGIASRRVAERMIIDGRVEVDGQIVTELGTRVDPAVADIRVDGSRII 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             +       +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGLLLLT
Sbjct: 63  LDDTMVYLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKG 184
           NDG LA  L  PS +  + Y     G V +     LK G+ +     + D    +DT  G
Sbjct: 123 NDGELAHRLMHPSFEVPKTYVATVMGTVPRGLGKKLKAGVELDDGPAHVDDFAVVDTVPG 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V V L EG+NR ++++    ++ V  L+R   G   LG    GS R +++K + E 
Sbjct: 183 KT-MVKVTLHEGRNRIVRRLLAAVDFPVQELVRTEIGSVSLGDQRPGSIRALTRKEVGEL 241


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/294 (23%), Positives = 132/294 (44%), Gaps = 12/294 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           +  R++K I+ +GI SRR+ +R I Q  V +NG       V V   D ++V+G  +    
Sbjct: 5   SSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAA-VGVQVFPGDVVKVNGQTIEPRN 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 64  EEDLVLIALNKPVGVISTTEDGEQNNIV--DFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K S    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTK----KCKVKKESTFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R+      L  L  G  R++++  L E     L
Sbjct: 178 RITLVQGLNRQIRRMTKHFGYEVTKLERVRIMNISLKGLPQGEWRDLTEDELIELF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +  + + P   +     +   +    P    +   N++ +   ++  +   
Sbjct: 236 IENSSSD-EKPAKKAPVKRVEAKRVSISGPKKAEKPDSNAAARKRFAQPGRKKK 288


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 123/246 (50%), Gaps = 9/246 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
            R++K +A  G+ SRRE ++ I   RV +NG + E  A+ V   D + +DG  +   +  
Sbjct: 1   MRLNKFLASIGVCSRREADKAIEAGRVMINGEVAELGAM-VGEEDLVSLDGRYIATGKDV 59

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  +  ++KP G+V T SD DG + V D +  +  R+  VGRLD ++ GLLLLTN G
Sbjct: 60  EKVKPIIIAFNKPEGIVCTTSDNDGATNVVDYI-GMKERIYPVGRLDKDSSGLLLLTNQG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L   +    + Y V+ +  +D D +N +  GI +  +     +  +  +K +   
Sbjct: 119 SLTNSLLRAANYHEKEYIVKVNKDIDDDFINKMSNGIYLYELKTKTRKCKV--KKLNKNT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            ++ L +G NR+I+++      KV +L R+     +L  L  G+ R +S + +++     
Sbjct: 177 FSIVLTQGLNRQIRRMCLACGMKVQKLNRVRIVNIKLDGLALGAYRNLSDEEIKKLYKEL 236

Query: 249 LLEEAQ 254
            + E  
Sbjct: 237 GIRENG 242


>gi|325068740|ref|ZP_08127413.1| pseudouridine synthase family protein [Actinomyces oris K20]
          Length = 303

 Score =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 85/228 (37%), Positives = 119/228 (52%), Gaps = 10/228 (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  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFS-----RVISVGRLDINTEGL 121
                 + HKP G+VTT  DP+GR TV     D L          R++ 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 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                + V + L  GKNR ++++ +     V RL R   GP +LG L 
Sbjct: 256 SGPRGSIVEITLHSGKNRIVRRMLDAVGHPVTRLARTRLGPLRLGNLR 303


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 100/339 (29%), Positives = 153/339 (45%), Gaps = 20/339 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D +
Sbjct: 150 MPAKRVLAPQVDSPKLHKVLAQAGMGSRLEMEQLILEGRISVNNEPA-HVGQRIQFGDIV 208

Query: 61  EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           +V+G P+R        R+  YHKP+G V TH DP  R TVF  LP     +  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 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
           V     +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E
Sbjct: 329 VEDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMMLPRGLKRGAWVE 388

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           + +  ++      L+  A V   AP+  +    R   N          R  ++  + NG+
Sbjct: 389 LDQADIQA-----LMSAAGVKERAPVERNNGGARGANNRGG-------RNSRSGGRGNGM 436

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
           +  +               W   G   +     G    N
Sbjct: 437 NADRAPQGRREGGGQRRGEWD--GNRPAPSGMLGDNPRN 473


>gi|21324194|dbj|BAB98819.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Corynebacterium glutamicum
           ATCC 13032]
          Length = 252

 Score =  257 bits (656), Expect = 3e-66,   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|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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 118/231 (51%), Gaps = 8/231 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ K++AR G+ SR+EV R++   +V+V G ++   A +V     +EVDG PL   
Sbjct: 1   MRGERLDKLLARLGLGSRKEVARLVRSGQVQVEGQVVRDPAFHVPPGARLEVDGEPLVLR 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
                 L HKP G VT+  +     +V+  L    +R +  VGRLD +TEGLLL T DG 
Sbjct: 61  CHHH-ILLHKPAGYVTSRREG---PSVYALLEGFPTRDLSPVGRLDKDTEGLLLFTTDGE 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  + Y V       ++     ++G+V++G      +++ D        V
Sbjct: 117 LLHRLTHPRHKVEKRYLVHLERPATREDQEAFREGLVLEGTRLLPAELSWD---QDPTRV 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + LREG+  ++K++F+    +V  L R+S GP  LG L  G  R +S++ 
Sbjct: 174 ELVLREGRFHQVKRMFQARGNRVLYLKRLSLGPLTLGDLPVGQARYLSQEE 224


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 113/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDINT GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDINTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVGKTYLAQVKGIMTQEDVETFAEGIPLKDFTCKPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  257 bits (656), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 130/283 (45%), Gaps = 13/283 (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 ++ + ++ + D + +   R+  +GRLD  +EGL+ +T
Sbjct: 58  IVEKHEKLVYLAFNKPVGIECT-TNLEVKNNIVDYI-NYPKRIFPIGRLDKASEGLIFMT 115

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +   +        + Y V  +  + +  +  +  G+ I        +V    ++ S
Sbjct: 116 NDGDIVNKILRARNNHEKEYTVTVNKPITERFIQRMGNGVPILDTVTKKCKV----EQIS 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+++   ++E  
Sbjct: 172 KYTFKIILTQGLNRQIRRMSEYLGYEVTALKRIRIINISL-DVPVGRYRDLTDAEIKEL- 229

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
              L+E +    +A +  +      R +      D   R + N
Sbjct: 230 -NKLIEPSSKTEEASLPKAAAPTPSRRSTFISKNDPRFRKRGN 271


>gi|254775517|ref|ZP_05217033.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           avium subsp. avium ATCC 25291]
          Length = 247

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 109/236 (46%), 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  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 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|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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 97/304 (31%), Positives = 148/304 (48%), Gaps = 11/304 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---E 71
           ++ KV+A AGI SRRE+E +I   RV VNG         V + D + V+G  + +    +
Sbjct: 3   KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAANDQVRVNGKLISRPNAKK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
             R+ LYHKP G + +H DP+GR+ VF  LP + + + +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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           V L+EG+NRE++++FE     V+RLIR  +G   L  +L  G       + L   L   L
Sbjct: 182 VTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDLVLPRSLRRGRW-----EELDASLVSAL 236

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           + +  +  D          R   +  S +P  F  M++N      + ++ KL       +
Sbjct: 237 MVQLGLLRDEEESGGRRKSRQPQSHDSALPPGFGTMERNGMNGARIGRRGKLQGGRSASS 296

Query: 310 LASN 313
             S 
Sbjct: 297 ATSP 300


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 130/238 (54%), Gaps = 7/238 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  ++  P ++ KV+A AGI SRRE+E +I   RV VNG         V   D + V+
Sbjct: 106 KYLNSDSVMP-KLHKVLADAGIGSRREMEELIVAGRVSVNGEPA-HIGQRVAPNDQVRVN 163

Query: 64  GVPL---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+      +  R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTE
Sbjct: 164 GKPIMRTNTKKPPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTE 223

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A  +  P     R Y VR  G++D+ +   L  GI ++        +  
Sbjct: 224 GLLIFTTSGDMANRIMHPRYGTEREYAVRVLGEMDEAQRQSLVDGIELEDGVAAFGALDY 283

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
               GSN W  V L+EG+NRE++++FE     V+RLIR  +G   L  TL  G   E+
Sbjct: 284 LGGDGSNRWYRVTLQEGRNREVRRMFEAVGVTVSRLIRTRFGDVVLPRTLRRGRWEEL 341


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACAEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>gi|329939210|ref|ZP_08288584.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
 gi|329302095|gb|EGG45988.1| pseudouridine synthase [Streptomyces griseoaurantiacus M045]
          Length = 364

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 121/239 (50%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           K         +R+ KV+ARAG  SRR  E +I   RV+VNG ++      V    D I+V
Sbjct: 118 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEDARVEVNGEIVLEQGKRVDPEHDEIKV 177

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 178 DGLTV-ATQSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 236

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q
Sbjct: 237 LLTNHGELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQ 296

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 297 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 355


>gi|145636895|ref|ZP_01792560.1| malic enzyme [Haemophilus influenzae PittHH]
 gi|145269976|gb|EDK09914.1| malic enzyme [Haemophilus influenzae PittHH]
          Length = 232

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDMDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>gi|325697447|gb|EGD39333.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 242

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 113/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIVVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAQLKIVELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLTMGPLQLDPALALGEWRRLTADELERL 235


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 101/300 (33%), Positives = 152/300 (50%), Gaps = 23/300 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E +I   RV V+G + +    V V++   I +DG  +   E
Sbjct: 2   SEKLQKVLARAGHGSRREIETIIEAGRVSVDGKIAKLGDRVEVVAGMKIRLDGHVISVKE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +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 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E +       ++V ++          +DR  + +       R  K  SQ +   +     
Sbjct: 242 ELVELKPETTSKVAVE----------KDRRRVKAN---QIRRAVKRHSQVSPTRRSGSRN 288


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 132/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>gi|291522211|emb|CBK80504.1| ribosomal small subunit pseudouridine synthase A [Coprococcus catus
           GD/7]
          Length = 250

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 121/236 (51%), Gaps = 8/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV+ +I +  V VNG ++ +    V    D +   G P+   +  
Sbjct: 6   RLDKYLADMSVGTRSEVKNLIKKGLVTVNGEVIRKPEYKVDIEKDDLVCRGEPVAY-QTL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+++  +DP  + TV D +       +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 65  VYYMLNKPAGVISATNDPK-QKTVLDLITDKSRKDLFPVGRLDKDTEGLLLITNDGDLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDT-QKGSNAWV 189
            L  P     +VYR R  GQV  +   L  KG+ I      +  M   L+    G  + +
Sbjct: 124 QLLSPKKHVDKVYRARIEGQVTAEDAALFAKGLGIDDEDGAWRAMPAKLNILSSGPESEI 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + +REGK  +IK++FE  + KV  L R+S G  +L  TL  G  RE+++  ++  
Sbjct: 184 EITIREGKFHQIKRMFEAVDKKVVYLKRLSMGSLRLDETLALGEYRELTEDEVQAL 239


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 136/296 (45%), Gaps = 14/296 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFINGKRA-GIGDQVSAGDIVKVNGQLIEPRDEDD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T    +  + V  +  +   R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTESGEKGNIV--DYVNHSKRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V     K +     + 
Sbjct: 125 KILRAGNDHEKEYVVTVNKPVTDEFIQGMASGVPILGTMTKKCKVK----KEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R+     +L  +  G  R+++   L E    +L+E+
Sbjct: 181 LVQGLNRQIRRMTEHFGYEVTKLERVRIMNVKLTGIPVGEWRDLTDDELIELF--NLIEK 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
           ++ ++  P  +++   R+  +         T  K  ++ +    K  +      +R
Sbjct: 239 SESDV-KPKKAAKPQARNTGS--KTAGKQGTSSKPKANAEPPKKKFTQPGRKKKKR 291


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 114/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A VL  P     + Y  +  G + Q+ +    KGI ++       ++ + +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 103/234 (44%), Gaps = 2/234 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R+E  R+I    V V+G+  +  +V V     +E DG  L+     
Sbjct: 1   MRLDKFLCETLGATRKEATRIIKSGTVTVDGVKTKVTSVKVTDDSTVEWDGRELKF-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  +  KP G V +H D    S +         ++   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLFKPDGYVCSHEDSTHPSALSLLDEVNLEKLHFAGRLDVDTTGLVLITDDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +  D    L+ GI ++      M   ++        + + +
Sbjct: 120 ITSPKRKCAKTYRVWLADPIGADYAEKLEAGIQLKSEKDLTMPAVMEIVDEEEHELLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            EGK  ++K++F     KV  L R   G   L  +L  G  R ++++ +    G
Sbjct: 180 HEGKYHQVKRMFAALGNKVEGLHRAQIGGLGLDYSLEPGEYRYLTEEEVEAVFG 233


>gi|323525722|ref|YP_004227875.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323382724|gb|ADX54815.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 618

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 93/285 (32%), Positives = 145/285 (50%), Gaps = 10/285 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 208 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 266

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 KILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +         EE      AP       ++     IS  P
Sbjct: 447 NQVRALMASVGLKAPSEERGGRNAAPERKQPDPMQTSMGFISREP 491


>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 =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 79/245 (32%), Positives = 130/245 (53%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M++   V++     R+ KVI++AG+ASRR  E++I   RVKV+G ++    + V  +   
Sbjct: 1   MRNDPHVEDGV---RLQKVISQAGVASRRHAEKLIISGRVKVDGNIVRTLGIRVDPSVQT 57

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           I VDG  +    ++     +KP G+V+T  DPDGR  + + +     R+  VGRLD +T 
Sbjct: 58  IHVDGNQIMLDTKSLTIALNKPAGVVSTMDDPDGRPCLAEFVEQYNQRLYHVGRLDTDTA 117

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+LLTNDG L+  L  PS +  + Y    HG+V +     L +GI ++          +
Sbjct: 118 GLILLTNDGELSHRLMHPSWEVPKTYVATVHGEVPRGLGRKLARGITLEDGPVKVEDFQI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    V + L EG+NR ++++ +   + V  L+R  +GP  +G L +G TR +   
Sbjct: 178 TDHYGEMTLVQLTLHEGRNRIVRRIMDHVGFPVIELVRTQFGPVHIGRLHSGVTRRIEGP 237

Query: 240 ILREQ 244
           +L+E 
Sbjct: 238 VLQEL 242


>gi|229060031|ref|ZP_04197402.1| Pseudouridine synthase [Bacillus cereus AH603]
 gi|228719250|gb|EEL70858.1| Pseudouridine synthase [Bacillus cereus AH603]
          Length = 227

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 62/227 (27%), Positives = 111/227 (48%), 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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RINHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I        ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEIT----QLSKYEFEIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK 
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKE 220


>gi|229161332|ref|ZP_04289317.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228622146|gb|EEK78987.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 238

 Score =  256 bits (655), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 113/231 (48%), Gaps = 7/231 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFNIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R   
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKRRLF 228


>gi|312863597|ref|ZP_07723835.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101133|gb|EFQ59338.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 243

 Score =  256 bits (655), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 117/237 (49%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG L       +    D I      L   E 
Sbjct: 1   MRLDKFLVDCGVGSRSQVKNFLKKKQVTVNGQLETSPKTQIDENKDRIAYLDQELTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   +P  + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATENPRHK-TVLDLLDDTARHKQVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +  +  S +W
Sbjct: 119 AHAMLSPKKHVDKIYQAKVAGVMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNESTSW 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           V + + EGK  ++K++      +V  L R+S GP  L   L  G+ R ++++ L   
Sbjct: 179 VQITIAEGKFHQVKRMVAACGKEVTELQRLSMGPLSLPNDLELGTWRRLTEEELEAL 235


>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 =  256 bits (655), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 121/231 (52%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +  A
Sbjct: 196 EGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTV-AA 254

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V++  DPDGR  + D + +  +R+  VGRLD  TEG+++LTN G L
Sbjct: 255 QSYLFFALNKPAGVVSSMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIIMLTNHGEL 314

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +    G N  V 
Sbjct: 315 AHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYLVE 374

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 375 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 425


>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 =  256 bits (655), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 114/234 (48%), Gaps = 5/234 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K ++ AG+ SRRE +R +    V ++G++       V+    +   G P++K E
Sbjct: 3   EPVRINKYLSEAGVCSRREADRQVEAGNVTIDGVVA-SMGAKVLPDQTVLFCGKPVKKEE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L  +HKP G+V T    +  + V  +  +   R+  +GRLD ++EGLLL+TN+G + 
Sbjct: 62  EMILLAFHKPTGIVCTAEKREKNNVV--DYINYPKRIYPIGRLDKDSEGLLLMTNNGDIV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  V    L  L  G+ +  +                    +
Sbjct: 120 NRIMRAGNMHEKEYIVTVNKPVTDSFLRGLAGGVPL--VELNATTRKCKVWGIGKRQFGI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G NR+I+++ E+F ++V +L+R      +LG L AG+ REV+ +  +E +
Sbjct: 178 ILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLKAGTYREVTPQEYKELM 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 =  256 bits (655), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 121/236 (51%), Gaps = 8/236 (3%)

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 ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TESHIKGNIVDFV-GHNERIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V +  L  +  G+ I G      +VT  +++       + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPVTESFLRGMAGGVKILGEMTLPCEVTRMSER----VFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            EGKNR+I+++   F ++V +L RI     +LG+   GS R+++ K  +E+LG  L
Sbjct: 174 TEGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRIGSWRDLNDKE-KEELGRLL 228


>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 =  256 bits (655), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 77/245 (31%), Positives = 122/245 (49%), Gaps = 10/245 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K  VQE     R++K +A  G+ASRR  ++++ + +V VNG + +     V    D + V
Sbjct: 2   KKQVQE--EKVRINKYLAMCGVASRRAADQLVLEGKVSVNGHIADEPGFKVDPRNDEVIV 59

Query: 63  DGVPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           DG  +   E R    L++KP  ++TT+ D   R  + D +  +  RV  VGRLD  + GL
Sbjct: 60  DGRLMATPEARKVYILFNKPRNVITTNHDERDRQQILDFI-DVPERVFPVGRLDRKSTGL 118

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTL 179
           LLLTNDG LA  L  PS+Q  + Y      +     L  L  G+ ++  G      +  +
Sbjct: 119 LLLTNDGTLAHRLMHPSSQVQKEYLAALDAKFPPAMLQKLTGGMRLKDTGEKVSPCRAKI 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                S   V V + EGKN +++++F    ++V RL R++Y    LG L  G  R +S+ 
Sbjct: 179 LDDGMS---VLVSIHEGKNHQVRRMFSTLGFEVKRLDRVAYAGLTLGELRRGEWRFLSRN 235

Query: 240 ILREQ 244
            + + 
Sbjct: 236 EVEKL 240


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 115/239 (48%), Gaps = 13/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++ +  V VN  L++     +  + DHIEV G  +   + 
Sbjct: 1   MRIDKLLSNTGFGSRKEVKGLLKKGGVTVNSELIKDGKRQIDPSEDHIEVFGEVIEY-KP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L           VGRLD +T G +LLTNDG L
Sbjct: 60  FIYLMMNKPKGVISATEDVTDK-TVVDLLATEHALYDPFPVGRLDKDTTGFMLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P  +  + YRV     +       L  G+ +  G      ++T       N  +
Sbjct: 119 AHQLTSPKKKVDKTYRVHIDAPLTSADEASLIAGVELDDGYITKPAKLTY---GNDNTVI 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQ 244
            + + EGK  ++K++F+    KV  L R + GP +L  +LL G  RE++ +    LREQ
Sbjct: 176 FLTITEGKFHQVKRMFQALGRKVINLKRETIGPLKLDPSLLLGEYRELTDEEVAGLREQ 234


>gi|310765941|gb|ADP10891.1| 23S rRNA pseudouridine synthase F [Erwinia sp. Ejp617]
          Length = 292

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 66/293 (22%), Positives = 124/293 (42%), Gaps = 9/293 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
             R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRA-SVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   +   +KP+G+++T  + + R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVVIALNKPVGIISTTEEGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G      +V     K S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTKKCKV----NKESTFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V++L R       L  L  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYEVSKLERTRIMNISLKGLPPGEWRDLTDDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             ++           T  +      ++     T     + +K      +K   
Sbjct: 239 SSSEDGTAKKAKPKATTAKKPAASGAKGGAKVTGNANAAPRKRFAQPGRKKKG 291


>gi|291617615|ref|YP_003520357.1| RluB [Pantoea ananatis LMG 20103]
 gi|291152645|gb|ADD77229.1| RluB [Pantoea ananatis LMG 20103]
          Length = 294

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 108/306 (35%), Positives = 153/306 (50%), Gaps = 20/306 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MIA  RV V+G L         S    I +DG  +  AE
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIAAGRVSVDGKLATLGDRIENSKALKIRIDGHLVSIAE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T SDP+GR TVFD LP    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-------L 234

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                    V +D    +   + +DR    +       R  K  SQ +G   ++    P 
Sbjct: 235 PAVNYLRNMVGMDDETVTKLAVEKDRRRTKAN---QIRRAVKRHSQTSGRPARRN---PG 288

Query: 306 HRRNLA 311
            +RN  
Sbjct: 289 SKRNAT 294


>gi|295110375|emb|CBL24328.1| ribosomal large subunit pseudouridine synthase F [Ruminococcus
           obeum A2-162]
          Length = 310

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/306 (24%), Positives = 134/306 (43%), Gaps = 10/306 (3%)

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  DGKPVEKEEREVLLLFYKPRGIVCSTKKQRRETTVTEYI-DYPTRIYPVGRLDKDSEGLL 119

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+TN G L   +        + Y+V    +V  + +  ++ G+ I G         +  +
Sbjct: 120 LMTNQGELVNRIMRAGNYHEKEYQVTVDHEVTDEFVRHMQTGVPILGTVTRPC---IVRK 176

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            G N+  T+ L +G NR+I+++ E+  + V  L R+      L  L  G+ RE+ +    
Sbjct: 177 TGRNS-FTIVLTQGLNRQIRRMCEYHGYHVRTLKRVRIMNLTLDGLKCGAYREIRRDEWS 235

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E     L+  +         +       R N       +  R  K          +++  
Sbjct: 236 EL--KELIRNSSSE--TITETGGHHGNSRSNPNERTGSEAERGGKGILSGRQRDHEQQGV 291

Query: 303 TPVHRR 308
               +R
Sbjct: 292 RRAVQR 297


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 123/239 (51%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           K         +R+ K++ARAG  SRR  E +I Q RV+VNG ++      V    D ++V
Sbjct: 68  KTFPGAEQEGERLQKILARAGYGSRRSCEELIEQARVEVNGEIVLEQGKRVDPERDEVKV 127

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  D +GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 128 DGLTV-ATQSYQFFSLNKPAGVVSTMEDNEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 186

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     +VY     G + +D    LK GI ++          +  Q
Sbjct: 187 LLTNHGELAHRLTHPRYGVKKVYLAHIVGPIPRDLGKQLKDGIQLEDGYAKADHFRVVEQ 246

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 247 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 305


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 121/231 (52%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +  A
Sbjct: 195 EGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTV-AA 253

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V++  DPDGR  + D + +  +R+  VGRLD  TEG+++LTN G L
Sbjct: 254 QSYLFFALNKPAGVVSSMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIIMLTNHGEL 313

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +    G N  V 
Sbjct: 314 AHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYLVE 373

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 374 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 424


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 137/341 (40%), Positives = 187/341 (54%), Gaps = 3/341 (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---SFPSKRSLRRTS 351
                    +  +   +R     R+       S + +R   
Sbjct: 322 KRHEAEAARTEEAKPARRGGASGRATLTLGGASAKPVRSGK 362


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 106/288 (36%), Positives = 154/288 (53%), Gaps = 12/288 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVP 66
           +E    +++ K++ARAG  SRRE+E +IA  RV V+G +      V V S   I +DG  
Sbjct: 64  KEKVVGEKLQKILARAGQGSRRELEEIIAAGRVSVDGKIASLGDRVQVSSATKIRIDGNL 123

Query: 67  LR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +     + E  R+ +Y+KP G + T SDP+GR+TVFD LP    +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-GTLLAGSTREVSKK- 239
             G N W  V L +G+NRE+++++E    +V+RLIRI YG  +L   L  G   E+  + 
Sbjct: 244 GTGLNQWFDVTLTKGRNREVRRLWESQGVEVSRLIRIRYGNIKLEKGLPRGGWEEMGLEQ 303

Query: 240 --ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
              LRE +G  L  E +  +D       T +R     + +     T+ 
Sbjct: 304 VNYLRELVG--LPAETETKVDVTKNRRRTNIRQIRKAVKQHSKYRTKA 349


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 133/299 (44%), Gaps = 17/299 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R++K I+ +G  SRRE +++I + RVK+NG +       V+  D + VDG  +    
Sbjct: 5   TGKRLNKYISDSGFCSRREADKLIEKSRVKINGTIP-ELGTKVLPGDIVLVDGRAINAVA 63

Query: 72  RTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             +       Y+KPIG+  T ++ D R  + D +     R+  +GRLD  +EGL+ LT+D
Sbjct: 64  ENKSDRIYIAYNKPIGITCT-TERDVRGNIIDAI-RHKKRIFPIGRLDKPSEGLIFLTSD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V     + +  +  +++G+ I         V +     S  
Sbjct: 122 GDIVNKILRAENAHDKEYLVTVDKPLSERFVERMQRGVPILDTITKPCIVKVQ----SRF 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE--QL 245
             ++ L +G NR+I+++ E+  ++V  L R       L  L  G  R +S + ++E  Q 
Sbjct: 178 VFSIILTQGLNRQIRRMCEYLGYEVQALQRTRIMQVTLKNLKPGQWRNLSVQEMQEINQA 237

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
             H  + AQ+   A    +    R   N        F  +KK  S+ +  S+   L   
Sbjct: 238 VSHSSKTAQITTPA----NPPNTRKIYNQSGSTKKIFVNVKKTKSKPSANSRTLSLKRK 292


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/247 (30%), Positives = 127/247 (51%), Gaps = 4/247 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 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 KKILREQ 244
            + + E 
Sbjct: 363 SQEVSEL 369


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 112/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RINHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I        +VT    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVT----QLSKYEFEIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  +   
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKKRLF 225


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 105/344 (30%), Positives = 163/344 (47%), Gaps = 25/344 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ KV+ARAG+ SRRE+E MI   RV VNG++ +           I VDG  +     
Sbjct: 2   SEKLQKVLARAGLGSRREIESMIQAGRVSVNGVVAKLGDRLEDLNAAIRVDGHHVSVSAS 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             +  R+  Y+KP G + T SDP+GR TVFD LP    +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-GTLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVITEGRNREVRRLWETQGVTVSRLKRVRYGDIYLSKELPRGGWMELELKDVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN-SSQKNGLSKQKKLA 302
            +      E  +N +A         + R + + ++     R ++   S +    + ++  
Sbjct: 242 MVELRPESETLINPEA---------KKRKSRVQKIRRAVRRYEERVESGETRKPRNRRGG 292

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRS 346
            P   R          G  S     S   + ++R+  S  ++  
Sbjct: 293 QPAGNRTRVG------GGRSGKPGASRPGQSSNRQKKSGGNRNP 330


>gi|239828089|ref|YP_002950713.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239808382|gb|ACS25447.1| pseudouridine synthase [Geobacillus sp. WCH70]
          Length = 240

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 116/233 (49%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VK++G++++     V  T   + V G  +   E  
Sbjct: 4   RIDKMLANMGYGTRKEVKKLLKSGVVKIDGVVVKDPKTQVNPTEQVVTVRGKEVEYKE-F 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 63  IYLMMNKPPGVVSATEDV-VEETVVDLLEEEDRVFSPFPVGRLDKDTEGLLLLTNDGQLA 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y     G+V ++ +   ++GIV+  G      ++ +  + G  + V 
Sbjct: 122 HQLLSPKKHVPKTYFAVIDGEVTEEDIASFRRGIVLDDGYETKPAELVVL-KSGLRSDVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  ++K++F     +V  L RI  GP  L  +L  G  RE++ + + 
Sbjct: 181 VTITEGKFHQVKRMFRAIGKRVIYLKRIQMGPLVLDPSLDLGEYRELTDEEVE 233


>gi|307730031|ref|YP_003907255.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307584566|gb|ADN57964.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 614

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 94/285 (32%), Positives = 146/285 (51%), Gaps = 10/285 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 205 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 263

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 KILREQLGPHLL----EEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +    L    EE      AP       ++     IS  P
Sbjct: 444 NQVRALMASVGLKAPNEERGGRGAAPERKQPDPMQTSMGFISREP 488


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 119/240 (49%), Gaps = 1/240 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +A V + L EG+NR ++++ +     V RL R   GP  LG L  G+TR +  + L   +
Sbjct: 181 SAVVELVLHEGRNRIVRRLLDAAGHPVQRLTRTRVGPVLLGQLRPGATRVIDGEELGRLM 240


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 132/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>gi|325688986|gb|EGD30994.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 242

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDETADEIIVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A V+  P     ++YR +  G ++Q        GI ++       Q+ +    +    + 
Sbjct: 119 AHVMLSPKKHVEKIYRAQVAGLMNQADEERFAAGIELKDFTCQPAQLKILELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R +++K +
Sbjct: 179 VEITLAEGKFHQVKRMVASCGKEVTDLQRLTMGPLQLDPALALGEWRRLTEKEI 232


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 99/229 (43%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +         +GI++ G         L+        V + +
Sbjct: 121 ITSPRHHCEKSYLVTLEQPLAPQTAAQFAEGILLNGETDLTKPAQLEA--FDEHHVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R +S   +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVGLHRERIGAIALDAALAPGEYRALSDDEV 227


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 118/232 (50%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+EV++++    VKV+G +++ A  +V      + V G  +   +  
Sbjct: 3   RIDKLLANMGYGTRKEVKKLLKAGVVKVDGTIIKDAKTHVDPKAQVVTVWGEEVEY-KPF 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+++   D     TV D L           VGRLD +TEGLLLLTNDG LA
Sbjct: 62  IYLMMNKPKGVISATEDA-VEETVVDLLEEEDRIFDPFPVGRLDKDTEGLLLLTNDGQLA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     ++Y     G+V +D +   ++G+V+  G      ++ +  + G  + V 
Sbjct: 121 HQLLSPKKHVPKIYEAIIDGEVTEDDVVAFQRGVVLDDGYETKPAELVV-IRTGLRSDVR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  +IK++F+    +V  L RI  GP  L  TL  G  RE++ + +
Sbjct: 180 ITITEGKFHQIKRMFQAVGKRVIYLKRIQMGPIPLDETLELGEYRELTDEEI 231


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 72/240 (30%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  + 
Sbjct: 8   EKDIEMRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKIA 67

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTN 126
             ++   +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTN
Sbjct: 68  Y-QQYHYFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTN 125

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG LA  L  P+    +VYR +  G  D +      +G+++  G      ++ +  Q   
Sbjct: 126 DGALAHELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQD 185

Query: 186 N--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           N  + + + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+    ++
Sbjct: 186 NNLSQIEIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEIDLAEIK 245


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 100/289 (34%), Positives = 155/289 (53%), Gaps = 10/289 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           + Q+    +R+ KV+ARAG  SRR +E MI+  R+ ++G +      V++ S   I +DG
Sbjct: 37  VNQQKVEGERLQKVLARAGQGSRRTIEAMISANRISIDGKMATLGDRVDIHSGVKIRIDG 96

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +     + E  R+ LY+KP G + T  DP+GR+TVFD LP    SR I+VGRLDINT 
Sbjct: 97  HIVNLTQAQKEVCRVLLYYKPEGELCTRHDPEGRATVFDRLPRLNGSRWIAVGRLDINTS 156

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  P  +  R Y VR  G+VD   +  L+KG+ ++        +  
Sbjct: 157 GLLLFTTDGELANRLMHPRHEVEREYAVRVFGEVDDAMIARLRKGVQLEDGPANFTSIKA 216

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE--V 236
              +G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E  +
Sbjct: 217 TGGQGMNQWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLTKSLPRGGWEEMDL 276

Query: 237 SK-KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           +    LR+ +G     +++++   P       +R      +E+   + +
Sbjct: 277 TNINYLRKLVGLPPETDSKIDTKKPRRIKTGQIRKAVKRYAELNKRYKK 325


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 115/234 (49%), Gaps = 5/234 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K ++ AG+ SRRE +R +    V ++G++       V+    +   G P++K E
Sbjct: 3   EPVRINKYLSEAGVCSRREADRQVEAGNVTIDGVVA-SMGAKVLPDQTVLFCGKPVKKEE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L  +HKP G+V T    +  + V  +  +   R+  +GRLD ++EGLLL+TN+G + 
Sbjct: 62  EMILLAFHKPTGIVCTAEKREKNNVV--DYINYPKRIYPIGRLDKDSEGLLLMTNNGDIV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V  +  V    L  L  G+ +  +            +       +
Sbjct: 120 NRIMRAGNMHEKEYIVTVNKPVTDSFLRGLAGGVPL--VELNATTRKCKVWRIGKRQFGI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G NR+I+++ E+F ++V +L+R      +LG L AG+ REV+ +  +E +
Sbjct: 178 ILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLKAGTYREVTPQEYKELM 231


>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 =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 117/237 (49%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ +  V VNG   +    ++  T D I V G  L   E+
Sbjct: 1   MRLDKFLVENGLGSRSQVKEVLKKGLVLVNGRAEKSPKTHINETADEIVVSGQKLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G ++   D   + TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPKGYISATEDERHK-TVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +    +GI ++       Q+ +    ++   + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQSDVEQFARGIELKDFTCQPAQLKIVELDEEKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++K+ ++  
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDSGLALGEWRRLTKEEMKSL 235


>gi|253996068|ref|YP_003048132.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982747|gb|ACT47605.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 374

 Score =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 100/339 (29%), Positives = 161/339 (47%), Gaps = 22/339 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---K 69
            QR+ K++A AG+ SRR++E +IA  RV VNG +       V   D + +D  PLR   +
Sbjct: 36  TQRLHKLLALAGLGSRRDMEELIASGRVTVNGKVA-EVGAGVTEHDVVRLDSRPLRLPFE 94

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
            E  ++ +YHKP G + +  DP+GR++VFD LP     + 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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI------- 240
             V LREG+NRE++++FE F   V+RL+R+ +GP  L   +  G   ++ +K        
Sbjct: 215 YQVILREGRNREVRRLFEAFQLPVSRLMRVRFGPVNLPPRVKRGKMLKLEQKEVVGLLEW 274

Query: 241 ---------LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
                    LR+      L+   V          + +   P   +E      R K  S++
Sbjct: 275 ADLPVPKAPLRQLTQREKLKSTAVFTPKVRKQRVSALDRPPRDAAEGEAGGYRGKPGSAR 334

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ 330
                K        +RR   S+   A  +      + G+
Sbjct: 335 GPATKKPIARKPAANRRVRQSSDLNAPQMQKKSDRNRGR 373


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 97/251 (38%), Positives = 133/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +        +  D I
Sbjct: 1   MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKAIEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             DG  L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDGKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 67/291 (23%), Positives = 129/291 (44%), Gaps = 12/291 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R + Q  V +NG         V + D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYVEQGNVFINGKRAA-VGDQVYAGDVVKVNGQLIEPRDEDD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIISTTEDGEHDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  L  G+ + G            +K S     + 
Sbjct: 125 KILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTK----KCKVKKESTFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPQGEWRDLTDDELIELF--KLIEN 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +  + +AP+  S          +   P    +   N++ +   ++  +   
Sbjct: 239 SSSD-EAPVKKSPPKSVTNKKPVINGPKKTEKPDGNAAARKRFAQPGRKKK 288


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 117/239 (48%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V++ I  Q+V+V+  L      NV      I V G  L  +  
Sbjct: 1   MRLGKLLGQAGFGSRGQVKKFIRSQQVRVDDELARTGNQNVDPNLQTITVSGKQLSYS-P 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP GLV+   D     TV D +  +  R  +  VG LD +TEGL+L+TN+G L
Sbjct: 60  HVYYILNKPAGLVSVVRD-QHYQTVIDLIAVVDRREGLYPVGCLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +  D +     GI  + G      ++ + +     +  
Sbjct: 119 GFRLLHPKYHVDKTYYVEVNGDLGIDAIAFFDNGIAFLDGTVCKPAKLQIISSSSEVSRA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+GPF+LG L  G  RE++ +    LR  L
Sbjct: 179 YITITEGKFHQVKKMFLAYGVKVTYLKRISFGPFELGDLPVGEYRELTAEEKNSLRNYL 237


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 81/357 (22%), Positives = 149/357 (41%), Gaps = 24/357 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           T  R++K I+ +G+ SRRE +R I Q  V +NG         V   D ++V+G  +    
Sbjct: 5   TSIRINKYISESGLCSRREADRFIDQGSVFINGKRAGT-GDQVSPGDLVKVNGQIIEPQE 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE       +KP+G+V+T    +  + V        +R+  +GRLD +++GL+ LTN+G 
Sbjct: 64  AEDLIFIALNKPVGIVSTTESSEPANIVS--FVKHGARIFPIGRLDKDSQGLIFLTNNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +   +    + Y V  +  + Q  ++ +  G+ I G      +V     K S    
Sbjct: 122 LVNKILRAANNHEKEYLVTVNKPITQAFIDGMSGGVPILGQVTKKCKVV----KESTYVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V RL RI      L  L  G  R++++K L+  +   L
Sbjct: 178 NITLVQGLNRQIRRMAEHFGYEVTRLERIRIMNVSLKGLALGDWRDLTQKELQTLV--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-KKLATPVH-R 307
            E++    + P  +                    R      + NG +++  + + P   +
Sbjct: 236 TEDSDTT-NPPAKNPRKPKPQGNRHSGNRESGNRRSDTRDGKNNGGARRGGRPSAPGKGK 294

Query: 308 RNLASNVWMAKGIHSSFLSDSGQREENHRRSP----------SFPSKRSLRRTSAKK 354
              +       G      S     + N + +P            P+ RS  + + K+
Sbjct: 295 PGSSKPSNSKPGSSRPGSSKPPHSKGNGKPAPKGKTGTGGKGRAPAGRSAPKPAGKR 351


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKSITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 117/235 (49%), Gaps = 7/235 (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    +  + +     +  +R+  +GRLD ++EGLLL+TN+G 
Sbjct: 61  GNEMVLLAVNKPAGIVCTEEKKEKHNIIRFL--NYPTRITYIGRLDKDSEGLLLMTNNGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y+V  +  V ++ +  + +G+ I        +V    +   N   
Sbjct: 119 IINKMMRAGNRHEKEYKVTVNKPVTREFIEKMGQGVPILDTVTRPCKVKAIGKYKFN--- 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + L +G NR+I+++ E+F +KV RL R+     QLG+L  G  REV+   +RE 
Sbjct: 176 -IVLTQGLNRQIRRMCEYFGYKVTRLERVRVMNIQLGSLKPGEYREVTDDEIREL 229


>gi|327468371|gb|EGF13856.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK330]
          Length = 242

 Score =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 113/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDEAADDIVVSGQRLIY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++        + +    ++   + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEASL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPALALGEWRRLTADELERL 235


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 132/247 (53%), Gaps = 20/247 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           QR+ KV+ARAG+ASRR  E++IA+ RV V+G L+    + V   T  +EVDG  +   +R
Sbjct: 19  QRLHKVLARAGVASRRGAEQLIAEGRVVVDGRLVVEQGMQVDPATAVVEVDGKRVAVDDR 78

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +L +KP G+VT  SD   R  V D L   P + + +  VGRLD +T GLLL++NDG 
Sbjct: 79  HATYLLNKPKGVVTAMSDQRER-CVGDLLREQPDLPAGLFHVGRLDADTTGLLLVSNDGE 137

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------- 182
           LA  L  PS +  + Y     G V +  L+ L++G+ ++        V +  +       
Sbjct: 138 LAHRLAHPSYEIPKTYLATVRGAVGKGALDALRRGVSLEDGPARADAVAVKGEARPAPLR 197

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                    G+ + V + L EG+NR ++++F+     V  L R+  GP +LG L AG+ R
Sbjct: 198 KAQTGHASGGARSVVEITLHEGRNRIVRRMFDAVGHPVVELARLRIGPIRLGGLQAGALR 257

Query: 235 EVSKKIL 241
            ++ + +
Sbjct: 258 ALAPEEV 264


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 121/233 (51%), Gaps = 1/233 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ KV+A AG+ SRR  E +I   RV V+ + +    V +    + + VDG+ ++     
Sbjct: 27  RLQKVLATAGLGSRRACENLITAGRVTVDDVPVHELGVRIDPDKNVVHVDGLRIQLDMSL 86

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+V+T  DP+GR T+   +     R+  VGRLD ++EGLLLLTNDG LA  
Sbjct: 87  LTLALNKPLGVVSTMHDPEGRPTLAQFVADRPERLFHVGRLDADSEGLLLLTNDGELANR 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  + Y V+  G+V  +    L KGI ++       +  L       + + V L
Sbjct: 147 LTHPKYKITKTYTVQVEGRVPANLGTTLLKGIELEDGVATVDKYRLVDATPQASLIEVEL 206

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EG+NR I+++FE   + V +L+R   GP +LG L  G  R + +  L   + 
Sbjct: 207 HEGRNRIIRRMFETAGYPVTQLVRTKIGPIRLGDLRQGRVRVIGQTELGTLMA 259


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 117/233 (50%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ KV+A  G  +R+EV+ ++ +  V++NG+  + + V V  + D I+V+G  +    +
Sbjct: 2   ERLDKVLANLGYGTRKEVKVLVKKGAVEINGVQAKNSDVKVDTNEDIIKVNGETINYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  FIYLMMNKPAGVVSATFD-NYDETVIDLLDPEEQIFEPFPVGRLDKDTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY       VD   +   +KGIV+  G      ++ +       + V
Sbjct: 120 NHKLISPKYHVDKVYYAEIDKPVDDKDVKCFEKGIVLDDGYKTMPGKLEILKATEHGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++FE    KV  L RIS+G   L   L  G  RE+S+  L
Sbjct: 180 YVTIQEGKFHQVKRMFESLGKKVVFLKRISFGGIILDEDLEEGQYREISEDEL 232


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 62/238 (26%), Positives = 115/238 (48%), Gaps = 12/238 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  +R E+++M  Q  V VNG  +++   ++    D + ++G  +R  E 
Sbjct: 1   MRLDKMLSNLGYGTRSEIKKMCRQGMVTVNGQEVKKPDHHIDPDQDQVCLNGQAVRYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V+   D     TV D +   +       VGRLD +TEGLL++TNDG L
Sbjct: 60  YIYLMMNKPAGCVSATYD-KYDQTVIDLIDPEYLAFEPFPVGRLDKDTEGLLVITNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL----DTQKGS 185
           +  +  P     ++Y      +V    +    KG+ I         ++ +    + + G+
Sbjct: 119 SHRVLSPKKHVPKIYYAEIDHEVLARDIEAFSKGVYIGDDYTTKPAKLEVIKSFEAEDGA 178

Query: 186 -NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            ++ + V + EGK  ++K++FE     V  L RI  G  +L  +L  G  RE++++ +
Sbjct: 179 IHSEIYVTISEGKFHQVKRMFEAVGKSVLYLKRIQMGGLKLDESLGLGEYRELTEEEI 236


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 121/236 (51%), Gaps = 8/236 (3%)

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 ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TESHIKGNIVDFV-GHNERIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V +  L  +  G+ I G      +VT  +++       + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPVTESFLRGMAGGVKILGEITLPCEVTRMSER----VFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            EGKNR+I+++   F ++V +L RI     +LG+   GS R+++ K  +E+LG  L
Sbjct: 174 TEGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRIGSWRDLNDKE-KEELGRLL 228


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 117/234 (50%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KVI+  G  SR++V+  + +  ++V+G++++   ++V      I+++G  +    +
Sbjct: 2   ERLDKVISNLGYGSRKDVKAFVKKGLIEVDGVIVKDNGLSVDPEKSVIKINGEEVFYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D +   TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  YIYLMMNKPAGVISATHD-NRDETVIDLLYVDHQVFEPFPVGRLDKDTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
              L  P     +VY  +   +VD+  +   K GI +    Y  M+  L+    S   + 
Sbjct: 120 NHRLISPKWHVDKVYYAKIDKKVDEKDIQAFKSGITLDDG-YKCMEAKLEIISASEEGSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V ++EGK  ++K++FE    KV  L R  +G   L   L  G  RE+S + L
Sbjct: 179 IRVTIQEGKFHQVKRMFEAVGKKVEYLKREEFGGLSLDTDLEEGEYRELSDEEL 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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 106/326 (32%), Positives = 159/326 (48%), Gaps = 13/326 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E    +++ KVIAR G+ASRRE E  I+  RV+VNG +       V + D I VDG  + 
Sbjct: 7   EKAQGEKLQKVIARQGLASRREAEEWISGGRVRVNGKVA-HLGDRVTAEDKISVDGHKIA 65

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
              AE T + +Y+KP G VT+  DP+GR TVF  LP + S 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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V L+EG+NRE+++++E     V+RL R+ YG   L + +  G+     +K +   
Sbjct: 186 NRWFHVVLQEGRNREVRRLWESQGVTVSRLKRVRYGYMFLPSRVRLGNWEMAGQKDV--- 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
               L E A +    P   +      R  I  +         K S+ + G     +    
Sbjct: 243 --NVLYEMAGMQ---PKTVASLTPHTREKIQRQQGKSGASKPKPSNGRTGARAPARKPAA 297

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQ 330
                 ++ +  + G          Q
Sbjct: 298 ASDERRSAPLRHSTGRKPGPGRRKPQ 323


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 123/235 (52%), Gaps = 4/235 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +E     R++K I+ AGI SRRE ++ IA  +VKVN  ++      V   D +  +G P+
Sbjct: 48  KELKEGIRLNKFISNAGICSRREADKHIADGKVKVNNKVVTELGFKVKPMDDVAFEGKPI 107

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTN 126
           ++ E+    L +KP G +TT  DP GR TV D +  +   R+  VGRLD NT GLLL TN
Sbjct: 108 KR-EKLVYVLLNKPKGFITTMDDPKGRKTVMDLIATAGDERIYPVGRLDRNTTGLLLFTN 166

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA+ L  P  +  ++Y+V     + ++    +++GI ++        + + T    +
Sbjct: 167 DGELAKKLTHPKHKIKKIYQVELDKPITEEDFLKIQEGITLEDGEVKVDNLAILTPDAKS 226

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + + +R G+NR +++ FE   + V +L R ++       L  G  R + +K +
Sbjct: 227 --IGMEIRMGRNRIVRRTFEHLGYDVVKLDRTTFAGLTKKDLARGKWRFLKEKEV 279


>gi|320011602|gb|ADW06452.1| pseudouridine synthase [Streptomyces flavogriseus ATCC 33331]
          Length = 389

 Score =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 120/231 (51%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             +R+ K++ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +   
Sbjct: 151 EGERLQKILARAGMGSRRACEELIEQARVEVNGEIVLEQGMRVDPQKDEIKVDGLTV-AT 209

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 210 QSYLFFALNKPAGVVSTMGDPDGRQNLGDYVNNRETRLFHVGRLDTETEGIILLTNHGEL 269

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +    G N  V 
Sbjct: 270 AHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYLVE 329

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 330 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 380


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>gi|13472018|ref|NP_103585.1| hypothetical protein mlr2177 [Mesorhizobium loti MAFF303099]
 gi|14022763|dbj|BAB49371.1| mlr2177 [Mesorhizobium loti MAFF303099]
          Length = 250

 Score =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 82/228 (35%), Positives = 124/228 (54%), Gaps = 3/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +IA+ RV+V G ++  AA+ V  + D I VDG P+  AER  
Sbjct: 19  LNRALSKLGLCSRTQAELLIAEGRVRVGGKVVRDAALRVDLNRDRIVVDGEPV-IAERKV 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP  R TV+  L       V  VGRLD  +EGLLL+TND   A  
Sbjct: 78  YVMLNKPRGLVTTRDDPQQRDTVYACLEGLDLPFVSPVGRLDKASEGLLLMTNDTHFANR 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y V+     D+  L  L+ G+ + G       + L    G  AW+ + L
Sbjct: 138 LMDPASHLPKTYHVQVGTVPDEAMLETLRAGVSVDGETLTANSIVLLRSGGRTAWLEIVL 197

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR I+++      +V RLIRI+ G   LG L  G+ R ++ + L
Sbjct: 198 DEGRNRHIRRLLAAHGIEVKRLIRIAIGRLPLGDLAKGTARHLTPEEL 245


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 77/229 (33%), Positives = 125/229 (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 D +     R+  VGRLD ++ GLLLLTNDG LA  
Sbjct: 60  KYYLLNKPIGYSSTAKAQFQEKIVLDLI-DSKERIYPVGRLDKDSFGLLLLTNDGDLAFR 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS    + Y V+    + +  L  L  GI+++G      +  +   K +   V V L
Sbjct: 119 LTHPSHNVEKEYIVKVDKTLKESDLKKLSSGIMLEGKITRKARFEMLDFKSN--IVKVFL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +EG+NR+I+K+F+  ++ V  L RI++G  +LG L  G+ RE+SK+ + 
Sbjct: 177 KEGRNRQIRKMFKTLDYNVISLERIAFGKIKLGKLKVGNYRELSKEEIE 225


>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 =  256 bits (654), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 117/235 (49%), Gaps = 4/235 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +E     R+++ IA AGI SRRE + +I+  ++ VNG ++      V  TD ++  G   
Sbjct: 317 KEETDEIRLNRYIANAGICSRREADDLISSGQISVNGKIVTEMGYKVRPTDVVKY-GKKA 375

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              E+    L +KP   +TT  DP+ R TV D +      RV  VGRLD NT GLLLLTN
Sbjct: 376 LNPEKMVYILINKPKDYITTTDDPEERKTVLDIIAGACSERVYPVGRLDRNTTGLLLLTN 435

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS+   ++Y+      +  +    LK G+ ++       +V L T     
Sbjct: 436 DGELAEKLTHPSSGIKKIYQAELDKPITTEDFEQLKAGVELEDGFIRPDEVGLVTPDA-- 493

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             V + +  G+NR ++++FE   ++V +L R  +       L  G  R +++K +
Sbjct: 494 QVVGLEIHSGRNRIVRRMFEHLGYEVQKLDRTVFAGLNKKDLPRGKWRFLTEKEV 548


>gi|332365597|gb|EGJ43357.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 242

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 113/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++ + +  V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQFLKKGLVLVNGRAEKSPKTQIDETADEIAVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKAFTCQPAQLKILELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTNLQRLTMGPLQLDPALALGEWRRLTTDELERL 235


>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 =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 135/318 (42%), Positives = 182/318 (57%), Gaps = 7/318 (2%)

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 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE--TLVRDR 271
           RLIRIS+GPF LG L  G   EV   +L++QLGP L     V  +         T  R +
Sbjct: 181 RLIRISFGPFMLGDLEPGQVEEVKTSVLKDQLGPRLARSLGVRREVVREEKRLSTPSRGK 240

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
           P  +     +  R ++   +       ++        + A  V +          D G+R
Sbjct: 241 PTYLRRKEAEPERPRRAFEEPQ----MRRRRVLSEDASEAPIVELVPVPKPPRA-DRGER 295

Query: 332 EENHRRSPSFPSKRSLRR 349
            E    +P    +RS  R
Sbjct: 296 GEKRDFAPRDRGERSFDR 313


>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 =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 118/236 (50%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ K+++  G  +R+E++ ++ Q  V+++  +++ + + +   D  I V G  +   + 
Sbjct: 2   ERLDKILSNLGYGTRKEIKALVKQGLVEIDNEVVKDSGMKIDPDDKEIRVSGEMVNYRQN 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G+V+   D +   TV D L       +   VGRLD +T GLLLLTNDG L
Sbjct: 62  IYLIM-NKPNGVVSATFD-NYDETVVDLLDPEHQAFKPFPVGRLDKDTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y       VDQ+ +   K GI +  G      ++ +     + + V
Sbjct: 120 NHRLISPKWHVDKIYYAEIDKPVDQNDVEKFKIGITLDDGYKCLPGKLKILESDENGSKV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            V ++EGK  ++K++F   +  V  L RI +GP +L   L  G  RE+S+  ++  
Sbjct: 180 EVTIQEGKFHQVKRMFNALDKNVVYLKRIKFGPMELDLDLEEGEYRELSEDEIKSL 235


>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 =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 112/231 (48%), Gaps = 7/231 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RINHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  R   
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKRRLF 228


>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 =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV++++ +  VKVN  + +     V    D I VDG  +     
Sbjct: 1   MRLDKFLSNMGVGTRTEVKQLLKKNSVKVNDKVEKSPKSQVDPEQDEITVDGKIIEYI-N 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G V+   D D   TV D +       +  VGRLD +TEGLLL+TNDG   
Sbjct: 60  HVYIMLNKPKGYVSATYD-DINQTVIDLIADYCHLDLFPVGRLDKDTEGLLLITNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y+V     +  + +   K GI +        Q+       S     V
Sbjct: 119 HNLMSPSKHVSKTYKVTSKYPIKNEDIIAFKNGIELSDGKVKPAQLEKLDHNVS----LV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++F   + +V  L R+      L   L +G  R ++ + L+
Sbjct: 175 TIYEGKYHQVKRMFHSIDNEVLELKRLKIANLTLDENLKSGEYRLLTSEELK 226


>gi|297161649|gb|ADI11361.1| putative pseudouridine synthase [Streptomyces bingchenggensis
           BCW-1]
          Length = 333

 Score =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 122/239 (51%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+V
Sbjct: 87  KTFPGAEQEGERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPEKDEIKV 146

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++
Sbjct: 147 DGLTV-ATQSYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGII 205

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G L+  L  P     + Y     G + +D    LK GI ++          +   
Sbjct: 206 LLTNHGELSHRLTHPRYGVTKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVQN 265

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++   +
Sbjct: 266 TGKNYLVEVSLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPIALGDQKSGWLRRLTNTEV 324


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 107/338 (31%), Positives = 153/338 (45%), Gaps = 26/338 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAILGERLEEDNAVVRIDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKK---ILRE 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+ AP  ++    R R            R  +   ++      +    
Sbjct: 242 LVELRPEKETVLNM-APDAATRKRERTRS-------QKIRRAVRRHEERISTPAGRSGKA 293

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
           P  R+          G   S   +    ++   R P  
Sbjct: 294 PARRK---------PGSGESSTRNKVANQQQSSRKPRG 322


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 104/306 (33%), Positives = 153/306 (50%), Gaps = 21/306 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV +NG +       V +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSINGEIA-NLGDRVDADAKVRLDGRLVSIKSA 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    +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-GTLLAGSTREVSKK---ILRE 243
           W  VGLREG+NRE+++++E    +V+RLIR+ YG  +L  TL  G   E+  +    LR+
Sbjct: 181 WWHVGLREGRNREVRRLWESQEVQVSRLIRVRYGMIELPKTLPRGGWIELPLEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
             G      + +  D    +  + VR              R  + S  K G +   K   
Sbjct: 241 LAGMDPETRSMIGTDKHSVARASQVRSA---------KIRRAVRKS--KVGAATGSKRPK 289

Query: 304 PVHRRN 309
           P   R+
Sbjct: 290 PTRTRS 295


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 121/231 (52%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
             +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +  A
Sbjct: 189 EGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVVEQGMRVDVHKDEIKVDGLTV-AA 247

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V++  DPDGR  + D + +  +R+  VGRLD  TEG+++LTN G L
Sbjct: 248 QSYLFFALNKPAGVVSSMEDPDGRQCLGDYVNNRETRLFHVGRLDTETEGIIMLTNHGEL 307

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +    G N  V 
Sbjct: 308 AHRLTHPKYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYLVE 367

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 368 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 418


>gi|327439180|dbj|BAK15545.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 240

 Score =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 66/226 (29%), Positives = 113/226 (50%), Gaps = 8/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV+ ++ Q+ V V+G+ ++ +A++V     ++ V G  +   E 
Sbjct: 5   MRLDKLLANMGYGSRKEVKLLLKQKAVTVDGVTVKDSAMHVNPEKQNVSVFGERVEYVE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L   +       VGRLD +TEGLLL+TNDG L
Sbjct: 64  FIYLMMNKPPGVISATED-RYDQTVIDLLDPEYQHFEPFPVGRLDKDTEGLLLITNDGNL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V +  +    +G+ +  G      ++ +    G  + +
Sbjct: 123 AHNLLSPKKHVPKWYYAKIDGVVTEADIEAFAQGVTLEDGYHTKPGELKILV-SGEQSEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + ++EGK  ++K++FE    KV  L R+S G  +L   L  G  R
Sbjct: 182 ELMIQEGKFHQVKRMFEAVGKKVTYLKRLSMGTLKLDEELALGEYR 227


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 67/271 (24%), Positives = 127/271 (46%), Gaps = 13/271 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN T  R++K ++  G  SRRE ++++ + R+ +NG ++      V   D + VDG  
Sbjct: 1   MEENLT--RINKFLSETGHCSRREADKLLDEGRITING-IVPEMGTKVSHHDEVRVDGKL 57

Query: 67  LR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +R K E+     ++KP+G+  T ++ D R  + D + +   R+  +GRLD  +EGL+ +T
Sbjct: 58  VREKTEKPVYLAFNKPVGIECT-TNLDVRYNIVDFI-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-DIPVGRYRDLTDAEITEL- 229

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
             +L+E +    +A     E   R    I  
Sbjct: 230 -NNLIEPSSKTEEASFPKVEAPKRRIEFIKR 259


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 121/249 (48%), Gaps = 13/249 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
           +R+ K +ARAG+ASRR  E +I   RV VNG +       VM  D + VDG  +   A+ 
Sbjct: 6   ERLQKRLARAGVASRRAAEDLITAGRVTVNGQIAT-LGRTVMPDDEVRVDGRLIEAPAQE 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +  +L +KP G VTT  D  GR  V   +P     +  VGRLD ++EGLLLLT DG L  
Sbjct: 65  SVTFLLYKPAGYVTTARDEYGRRNVLSAMPP-IPGLHPVGRLDKDSEGLLLLTTDGQLTL 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + YR    GQ    +L +L+ GI +       +               V 
Sbjct: 124 TLTHPRYGHEKAYRAWTAGQPVAAELRVLETGIELADGPARALSARPARGGA-----LVT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP----- 247
           L EG+NR+++++ +   + V+RL+R   G   LG L  G  R +S + L + L P     
Sbjct: 179 LTEGRNRQVRRMLDAIGYPVHRLLRYRVGGLWLGDLEPGEYRLLSPRDLHDLLHPAQVPR 238

Query: 248 HLLEEAQVN 256
           H+ E A+  
Sbjct: 239 HVWERAERE 247


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 115/233 (49%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++A +GI SR+EV++++    V ++G   +    +V  ++H + V G P+   E 
Sbjct: 1   MRLDKLLANSGIGSRKEVKKIVKAGAVSIDGKQAKDVKTHVDPSEHEVTVYGEPIEYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L     R      GRLD +T GLLLLTNDG L
Sbjct: 60  FIYLMMNKPQGVLSATEDSR-QKTVIDLLAPDDMRFEPFPAGRLDKDTVGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V     + ++ +  L+ G+ I+G       +V        +  +
Sbjct: 119 AHRLLSPKKHVPKTYEVHLRSGLSEEDIANLESGVFIEGGYKTKPAKVETIANSEEHTEI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EGK  ++K++ +    +V  L R+S G   L  +L  G  RE++++ L
Sbjct: 179 RLTITEGKYHQVKQMAKAVENEVIFLKRLSMGSLLLDPSLEPGEYRELTEEEL 231


>gi|327440834|dbj|BAK17199.1| 16S rRNA uridine-516 pseudouridylate synthase [Solibacillus
           silvestris StLB046]
          Length = 247

 Score =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 78/232 (33%), Positives = 129/232 (55%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA AG+ASRR+ E++I + +VKVNG++++     V ++D IEV+GV L K E  
Sbjct: 2   ERLQKVIAYAGVASRRKAEQLIVEGKVKVNGVVVKELGTKVSNSDTIEVEGVKLEK-EDK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP   ++  +D  GR TV D        R+  VGRLD +T GLLLLTNDG  + 
Sbjct: 61  VYFLLYKPRAYISAVTDDKGRKTVTDIFKKHVHQRIFPVGRLDYDTTGLLLLTNDGEFSN 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           ++  P  +  + Y  R  G   +  L  L+ GI ++       +V++ +  +K   A   
Sbjct: 121 LMTHPKFKIDKTYIARVKGIPTKQGLMKLQSGIKLEDGKTAPAKVSMTSFDEKAGKAICE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + EG+NR+++++FE     V +L R  +    L  L  G  R+++K  ++
Sbjct: 181 ITIHEGRNRQVRRMFEAIGTPVVKLKRERFAFLDLTGLSPGEYRQLTKHEVK 232


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 96/342 (28%), Positives = 161/342 (47%), Gaps = 19/342 (5%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +++  ++  P ++ KV+A AG+ SRR++E +I   RV VNG         +++ D + +
Sbjct: 197 RRDLTADDDAP-KLHKVLAEAGLGSRRDMEELIISGRVSVNGEPA-HIGQRILAQDQVRI 254

Query: 63  DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +G  +++    +  R+ +YHKP G + +H DPDGR +VF+ LP++ + + ++VGRLD NT
Sbjct: 255 NGKLIQRRVSKKPPRVLVYHKPAGEIVSHDDPDGRPSVFERLPNMKAGKWLAVGRLDFNT 314

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL T  G LA  L  P     R Y VR  G++++     L  G+ +        +V 
Sbjct: 315 EGLLLFTTSGDLANRLMHPRYNIDREYAVRTLGELEEGMRQKLLAGVELDDGVAQFSRVA 374

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
               +G N W  V + EG+NRE++++FE     V+RLIR  YG   L   L  G   E+ 
Sbjct: 375 DGGGEGVNKWYRVTIGEGRNREVRRMFEAIGLTVSRLIRTRYGAMVLPPNLKRGRWEEMD 434

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +  +R+ L    LE+     +     S     +  +      +   R    ++ ++G   
Sbjct: 435 EHSVRDLLKISGLEKTVGKSE----PSRGRSDEHDSEGGVNGNRIERAP--ATARHGAPN 488

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSP 339
             +   P   +      W  KG         G   +   R P
Sbjct: 489 GNRANAPEPGQ------WQGKGRSGPARGPGGFAGQGQPRGP 524


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 109/236 (46%), Gaps = 4/236 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
                R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  + 
Sbjct: 4   EAQGIRLQKVLSQAGIASRRAAEKLIVDGRVEVDGQVVTELGTRVDPDAAVIRVDGARVV 63

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             E       +KP G+ +T SD  GR  + D +         +  VGRLD  TEGL+LLT
Sbjct: 64  LDESQVYLALNKPRGVHSTMSDDRGRPCIGDLIERRVRGNKNLFHVGRLDAETEGLILLT 123

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G + +     L+ GI +        +  +      
Sbjct: 124 NDGELAHRLMHPSHEVPKTYLATVTGSIPRGLGKTLRAGIELDDGMARVDEFAVVDAIPG 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  +
Sbjct: 184 KTLVRVTLHEGRNRIVRRLLAAAGFPVESLVRTDIGPISLGKQRPGSIRALGRDEV 239


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 108/237 (45%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +  AG+ SR +V+ ++ +++V VNG+        V    D +   G  L   E 
Sbjct: 1   MRLDKFLVDAGLGSRSQVKLLLKKKQVSVNGVSQTSPKYQVNEMADEVSYQGQRLNY-EA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D     TV D L     +  V  VGRLD +T GLLL+TNDG L
Sbjct: 60  FVYYMLNKPKGVISATED-SSHKTVLDLLDDTARQKAVFPVGRLDKDTHGLLLVTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y     G + Q+ +    +GI ++          +    +    + 
Sbjct: 119 AHALLSPKKHVAKQYLAVVDGMMTQEDVKHFAQGITLKDHQCMPAYLDILEINESLKTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + + EGK  ++K++       V+ L RIS GP QL + L  G+ R ++   L   
Sbjct: 179 VKITIEEGKFHQVKRMVAACGKTVSDLQRISMGPLQLDSALAPGAYRRLTAAELETL 235


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 118/229 (51%), Gaps = 2/229 (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      V D +    +RV  VGRLD ++ GLL+LTNDG     
Sbjct: 61  IYIAINKPIGYASTVKDKFADKKVVDLI-KSDTRVYPVGRLDKDSHGLLILTNDGEFTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V +
Sbjct: 120 LTHPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENVKNDTKYRVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+NR+I+++F+F N  V  L R+  G +++   L +G  + +  K L
Sbjct: 180 FEGRNRQIRRMFDFINHPVLDLKRVQIGNYKMENSLKSGEYKLLKSKDL 228


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 113/238 (47%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A   I SR +V++ I +  + VNGI+ +     +    D I  +G  +   ++
Sbjct: 1   MRIDKFLANQDIGSRSQVKQYIKKGMISVNGIVCKSPEQKIDENADQISYNGKVIGY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G V+  +D +   TV D L +      +  VGRLDI+TEGLLL+T+DG L
Sbjct: 60  HHYYMLNKPSGCVSATND-NLHITVLDLLKASVPVKNLFPVGRLDIDTEGLLLITDDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS--NA 187
           +  L  PS    + Y  R  G   ++ +   K+G+ I          + +     +   +
Sbjct: 119 SHNLLSPSKHVAKTYFARIDGLATEEHIKAFKEGLDIGDDKPTKPGTLVIKNTDLNTQTS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + + + EG+  ++K+ FE    KV  L R+S G   L   L  G  RE++   L+  
Sbjct: 179 EILLTITEGRYHQVKRSFEALGMKVTYLKRLSMGSLTLDEALAPGEFRELTDIELQAL 236


>gi|311694421|gb|ADP97294.1| RNA-binding S4 domain protein [marine bacterium HP15]
          Length = 327

 Score =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 107/301 (35%), Positives = 149/301 (49%), Gaps = 15/301 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
           P+R+ K++ARAGI SRRE+E  +   R+ VNG  +          D  E+DG  L     
Sbjct: 22  PERIQKLLARAGIGSRREIEGWMEAGRLLVNGQPVA-PGQKATVEDRFELDGKRLEVSGA 80

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +Y+KP G VTT  DP+GR TVFD LP     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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  V L EG+NRE+++++E    +V+RL R+ YGP  L + L  G   E+ ++ +     
Sbjct: 201 WFHVTLLEGRNREVRRLWESQGVRVSRLKRVRYGPIFLPSRLTVGKWEELDQRAVDTLSR 260

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              LE  ++    P   +E    DR    S       R  K +          K A P  
Sbjct: 261 TVGLEAVEIPQKTP---NEKAAHDRQRRKSP-----GRSGKKTPGNKWAVSDTKPAKPAG 312

Query: 307 R 307
           R
Sbjct: 313 R 313


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++  + V VNG L ++   +V    D + V G  +   E 
Sbjct: 1   MRLDKLLASSGFGSRKDVKKLVKARAVTVNGELAKQVKDHVDPSNDEVLVHGERVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G+++   D    + V    P   +R    VGRLD +T GLLLLTNDG LA
Sbjct: 60  FIYLMMNKPDGVISATEDVRDETVVDLLEPEDIAREPFPVGRLDKDTVGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V     +    +N L++G+ ++        +V +D  +  +  + 
Sbjct: 120 HQLLSPKKHVPKTYEVHLKYPLGDQDINRLEEGVIILDDYRTKPAKVEVDANESEDTRIR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K + +    +V  L R S G   L   L  G  RE++ + L
Sbjct: 180 LTITEGKYHQVKLMAQAVGNEVIFLKRRSMGSLSLDEDLAPGEYRELTDEEL 231


>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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 109/236 (46%), 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  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 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|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 =  255 bits (653), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 94/322 (29%), Positives = 148/322 (45%), Gaps = 13/322 (4%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D ++V+
Sbjct: 86  KRVLSPQPETPKLHKVLAQAGLGSRLEMEQLILEGRISVNAEPA-HIGQRIQFGDTVKVN 144

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+R        R+  YHKP G V TH DP  R TVF  LP +F  +  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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 265 GGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLKRGAFVELDE 324

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETL-------VRDRPNIISEVPDDFTRMKKNSSQ 291
             +          E++ +                   R  P           R +   + 
Sbjct: 325 NDIHALTSAVSRSESRPDPRGEAAGPGQSEGEGGVQQRRGPRRNERPRSGAGRPRNLDAG 384

Query: 292 KNGLSKQKKLATPVHRRNLASN 313
           ++G+ +    + P   R  ++ 
Sbjct: 385 QSGVQQPLDDSQPPMNRTDSAP 406


>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 =  255 bits (653), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 118/229 (51%), Gaps = 2/229 (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      V D +    +RV  VGRLD ++ GLL+LTNDG     
Sbjct: 61  IYIAINKPIGYASTVKDKFADKKVVDLI-KSDTRVYPVGRLDKDSHGLLILTNDGEFTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++Y V   G+ ++ ++  LK GI++ G      ++       ++    V +
Sbjct: 120 LTHPKFEHKKIYEVLVKGKPNKTEIKQLKDGILLDGYKLKKSKIEFIENIKNDTKYRVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+NR+I+++F+F N  V  L R+  G +++   L +G  + +  K L
Sbjct: 180 FEGRNRQIRRMFDFINHPVLDLKRVQIGNYKMENSLKSGEYKLLKSKDL 228


>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 =  255 bits (653), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 71/296 (23%), Positives = 132/296 (44%), Gaps = 24/296 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           P+R++K I+ +G  SRR  ++MI   RV +N  +       V++ D ++VDG  +     
Sbjct: 12  PKRLNKYISDSGFCSRRSADKMIEANRVTINDKVP-ELGTKVLAGDVVKVDGYDIAPISD 70

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                    Y+KPIG+  T ++   R  + D +     R+  +GRLD  +EGL+ LT+DG
Sbjct: 71  DKSDRIYIAYNKPIGITCT-TEKHVRGNIIDAI-GHKKRIFPIGRLDKPSEGLIFLTSDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V     + +  +  + +G+ I G       V +     S   
Sbjct: 129 DIVNKILRAENAHDKEYIVTVDKPISERFIERMSRGVPILGTITKPCIVQV----KSRFE 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            T+ L +G NR+I+++ E+ +++V +L R      +LG L  G  RE++           
Sbjct: 185 FTIILTQGLNRQIRRMCEYLDYEVLKLKRSRIMKVELGDLTPGQWRELT----------- 233

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           + E A++N      S   +   +P   +   +D   +  ++S  N  +K +    P
Sbjct: 234 ITEMAEINQAVEGSSKTAINTAQPKQTTSSMNDLEEL--SASLNNADNKSESKTEP 287


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 113/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ M+   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNMLKSGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L  I     V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDIARSKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     + Y  +  G + Q+      KGI ++       ++ L +   K + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTQEDAETFAKGIPLKDFTCQPARLELVSVDTKKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQVKRMVGYCGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELE 233


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 74/241 (30%), Positives = 121/241 (50%), Gaps = 8/241 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
           + N    R+++ +A  GIASRR  ++++ + RV +NG ++    V V  + D + +DG  
Sbjct: 7   KSNNDGMRINRFLAMCGIASRRAADQLVQEGRVCINGKIVTTPGVKVNPSRDEVIIDGKR 66

Query: 67  LRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             + E R    L +KP  ++TT SD   R  V D +  +  R+  VGRLD  T G++LLT
Sbjct: 67  FAQPENRKVYILLNKPRNVITTSSDERQREMVLDFI-DVPERIFPVGRLDRKTTGVILLT 125

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQK 183
           NDG LA  L  PS+   + Y      +     L  L  G+ ++  G      +  L    
Sbjct: 126 NDGELAHKLMHPSSGVKKEYIAELSERFPAAMLGKLTNGMRLKDTGEKVSPCRAKLLD-- 183

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                V + + EGKN +++++F+   ++V RL R++Y   Q G L  G  R +S+  +RE
Sbjct: 184 -DGMRVLLSIHEGKNHQVRRMFDTLGFEVKRLDRVAYAGLQAGELRRGEWRYLSRNEVRE 242

Query: 244 Q 244
            
Sbjct: 243 L 243


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 112/237 (47%), Gaps = 8/237 (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      ++ + D +     R+  +GRLD ++EGL+ LT++
Sbjct: 61  KPIQDHVYIAFNKPVGIVSTTDTKAEKNNMIDYI-GHQQRIFPIGRLDKDSEGLIFLTSE 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V     +    +  +  GI I        +V    +K S  
Sbjct: 120 GDIVNKILRSKNNHEKEYIVTVDKPITDRFIQKMGAGIPILDTVTDPCKV----EKISKV 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + L +G NR+I+++ E+  ++V +L RI      L  +  G  R+++   L+E 
Sbjct: 176 KFRIILTQGLNRQIRRMCEYLGYEVRQLKRIRIMNVHL-DIPVGKWRDLTASELKEL 231


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 91/273 (33%), Positives = 143/273 (52%), Gaps = 7/273 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  ++  P ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++  D + V+
Sbjct: 215 RELSADDDAP-KLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPADQVRVN 272

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G  + +    +  R+ LYHKP G + + SDP+GR TVFD+LP I + + ++VGRLD NTE
Sbjct: 273 GKLIHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRIKTGKWVAVGRLDFNTE 332

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +++  
Sbjct: 333 GLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIAD 392

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +EV  
Sbjct: 393 GGGEGVNQWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQEVEP 452

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
             ++  +    L+       AP  +++   R +
Sbjct: 453 NDVKALMAGVGLKVPGKGEQAPKGATKVGGRKQ 485


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLAQSKEVFPVGRLDIDTHGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A VL  P     + Y+ +  G + Q+ +    KGI ++       ++ + +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYQAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 105/311 (33%), Positives = 150/311 (48%), Gaps = 11/311 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-LLAGSTREVSKK---ILRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ-KKLA 302
            +     +E  +N+ AP  ++    R R   I             +  ++G +   +K  
Sbjct: 242 LVELRPEKETVLNM-APDAATRKRERTRSQKIRRAVRRHEERISATPGRSGKAPACRKPG 300

Query: 303 TPVHRRNLASN 313
                RN  +N
Sbjct: 301 GESSTRNKVAN 311


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 111/232 (47%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+ ++ + +V VN  + +    ++  T D + V+G  +     
Sbjct: 1   MRLDKFLANMGVGTRTEVKHLLKKGKVTVNTSVEKSPKSHINPTEDIVHVNGKQVEFVNN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D   R TV D +P      +  VGRLD +TEGLLL+TNDG  +
Sbjct: 61  -VYIMLNKPKGYISATHDESNR-TVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGQFS 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y V     V +  ++  KKGI++        Q+T   +  S+    V
Sbjct: 119 HDLMSPSKHVSKTYEVTSKKPVTKVDIDAFKKGIILSDGPVKPAQLTRINETISH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++F     +V  L R+      L   L +G  + +S K L+
Sbjct: 175 TIYEGKYHQVKRMFHAIENEVLELKRLKIANLALDENLKSGEYKLLSDKELK 226


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 118/230 (51%), Gaps = 11/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ + +A +G  +R EV+R+I +  VKVNG   +   + +    D ++V G  + + ++
Sbjct: 1   MRLDRFLAHSGFGTRSEVKRLIKKGLVKVNGKQAKSPDLKIDEDKDVVQV-GEEIVELQK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ DP    T+F  +P    +  + +VGRLD + EGLL++TN+G  
Sbjct: 60  RVYIMMNKPQGYVCSNDDPLS-PTIFSLIPENLKYRNLHTVGRLDKDAEGLLIITNNGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V+   +++++K+ + + G+V+  G      + T+      +  V
Sbjct: 119 THKVISPKKHIEKEYIVKLEKELNREKIKVFEDGVVLDDGYKTLPAKYTIL----DDFTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           ++ + EGK  +IK++FE    KV  L R+  G  +L   L  G  + + +
Sbjct: 175 SLTIYEGKYHQIKRMFESIGNKVVYLKRVRIGRLKLDENLNPGEYKVLDE 224


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 105/273 (38%), Positives = 152/273 (55%), Gaps = 10/273 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           + +     +++ KV+ARAG  SRRE+E MIA+ RV V+G +      ++V S   + +DG
Sbjct: 69  VKKPKVEGEKLQKVLARAGQGSRREIEAMIAENRVSVDGKMATLGDRIDVRSGVKVRIDG 128

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +     + E  R+ +Y+KP G + T  DP+GR+TVFD LP    SR I+VGRLDINT 
Sbjct: 129 HIVNLMHAQKEVCRVLMYYKPEGELCTRHDPEGRATVFDRLPRLTGSRWIAVGRLDINTS 188

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  PS +  R Y VR  GQVD   LN LKKG+ ++       ++  
Sbjct: 189 GLLLFTTDGELANRLMHPSREVEREYSVRVFGQVDDAMLNRLKKGVQLEDGPANFKEIKF 248

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE--V 236
               G N W  V L EG+NRE+++++E    +V+RLIR  YG   L  +L  G   E  +
Sbjct: 249 AGGVGMNQWFDVTLMEGRNREVRRLWESQGVQVSRLIRTRYGNISLMKSLPRGGWEEMDL 308

Query: 237 SK-KILREQLGPHLLEEAQVNLDAPIYSSETLV 268
           +    LRE +G     E ++++  P   ++T  
Sbjct: 309 TNVNYLRELVGLPPEMETKLDVTKPRRRAKTSQ 341


>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 =  255 bits (652), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 113/235 (48%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR+EV+++I    V VN   +E  + ++    D +E++G  +   E 
Sbjct: 1   MRLDKFLVNQGFGSRKEVQKLIKAGIVYVNNFPVEDPSFHINPEKDVVEIEGQEIEYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G +T   D +   TV D      I S++  VGRLD++TEGLL++T+DG L
Sbjct: 61  -YYFMLNKPKGYITATYD-ENYPTVMDLFASEPIVSKLFPVGRLDVDTEGLLIITSDGVL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICY--GDMQVTLDTQKGSNA 187
           A  L  P     + Y V   G +   D     K+G+ ++   Y     +V +       +
Sbjct: 119 AHRLSHPKWNVEKEYFVIVEGDISDIDFSKYEKEGMYLKKEKYKTKPFKVKVLKTSFEES 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + + EGK   +KK+      +V  L R+  GP  L   L  G  RE++K+ +
Sbjct: 179 ELLITITEGKYHIVKKIMYAVGHEVKYLKRVRIGPLILDEDLEVGEYRELTKEEI 233


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 112/235 (47%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  L  P     + Y  +  G + Q+ +    KGI ++        + L     + + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVKGIMTQEDVETFAKGISLKDFTCQPAILELVSIDPEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  ++K++  +   +V  L R++ G   L  +L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQVKRMVTYCGKEVVDLQRLTMGTLVLDESLQRGEWRRLTKEELE 233


>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 =  255 bits (652), Expect = 8e-66,   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  TRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                ++KP G++T       D R  V D   +   R+  VGRLD NTEGLL++TNDG L
Sbjct: 61  FVYIAFNKPQGVLTAMERAPGDKRPIVADYFRNYPVRLFPVGRLDYNTEGLLIMTNDGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTLD--TQK 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|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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 114/232 (49%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A A + +R+EV+++I  +RV+VN  +  +    +   D + VD   L   E  
Sbjct: 1   MRLDKYLAHAQLGTRKEVKKLIRSKRVRVNDEICTKEDRQLQKEDCVYVDDELLVYDE-L 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+++   D    +TV D   +   +    VGRLDI++EGLLL+TNDG LA 
Sbjct: 60  VYLMLYKPQGVISATED-RVHTTVMDIFDAPLPKNCFPVGRLDIDSEGLLLITNDGQLAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V     +  + L LL+ G I +        Q    +       + +
Sbjct: 119 QLLSPKKHVDKTYYVECEKTLSSEDLQLLESGTIQLDKEHVLPAQAKRISANS----LYL 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++EGK  ++K++ +    KV  L RIS G  QL  +L  G  R +S++ +R
Sbjct: 175 TIQEGKFHQVKRMLQACGNKVCYLKRISMGSLQLDKSLAPGEWRYLSEEEIR 226


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 112/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RINHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + L  +  G+ I        +VT    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVT----QLSKYEFQIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  +   
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKKRLF 225


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 107/235 (45%), Positives = 152/235 (64%), Gaps = 2/235 (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  +   L      + I GI Y    + L  Q  +N+W  V L 
Sbjct: 122 EMPSSKLKRVYNVRAYGNAN-FLLKNNYNNLKIDGIFYNPYSIKLLRQNKNNSWFEVVLF 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           EGKNREI+++FE+F  KVN+LIR+ YG  ++G L  G  +E+S KIL++ +   L
Sbjct: 181 EGKNREIRRIFEYFGLKVNKLIRVQYGALKIGNLKPGDYKEISNKILKKIISNKL 235


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 112/235 (47%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLL NDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLANDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A VL  P     + Y  +  G + Q+ +    +GI ++        + L +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYLAQVKGIMTQEDVETFAEGIPLKDFTCQPAILELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>gi|254495132|ref|ZP_05108056.1| pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85819482|gb|EAQ40639.1| pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 282

 Score =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 74/232 (31%), Positives = 115/232 (49%), Gaps = 3/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G+ SRRE +  I    VKVNG L+      V   D ++ DG  +   E+ 
Sbjct: 49  IRLNKYIANSGVCSRREADTYIEHGSVKVNGKLVTEMGYKVQPDDVVQFDGTSIT-PEQK 107

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP   +TT  D  GR TV D + +    R+  VGRLD NT GLLL TNDG LA+
Sbjct: 108 RYILLNKPKNYITTMDDDRGRKTVMDLVSNASKERIYPVGRLDRNTTGLLLFTNDGDLAK 167

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     ++Y      ++D   L  L+  ++I+G       V+    +     + + 
Sbjct: 168 KLTHPKHNVRKLYHASLDRKLDLKDLEKLRGEVIIEGRKVFIDAVSYVDGQ-PKTEIGIE 226

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +  G+NR ++K+FE   +KVN+L R+ +       L  G  R ++ + +   
Sbjct: 227 IHSGRNRIVRKIFEHVGYKVNKLDRVIFAELTKKNLPRGRWRALTNQEVSNL 278


>gi|313636574|gb|EFS02285.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL S4-171]
          Length = 233

 Score =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 109/233 (46%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG++ + + + V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKLQVNPEKDQITVHGNPVIYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +   + GI +  G       + +         +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDDGYTCKPAHLEIMAPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V  L R+S G   L  +L  G  R +++  L
Sbjct: 175 RVTIQEGKFHQVKRMFAATGKTVTYLKRLSMGKLMLDESLGLGEYRSLTEDEL 227


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 115/233 (49%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + + + V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKMQVNPDKDEITVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G+V  + +    +GIV+  G      ++ +     +   +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIDGEVLLEDVKAFAEGIVLDDGYICKPARLEI----INPNEI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 175 KVTIQEGKFHQVKRMFAARGKTVSYLKRISMGQLQLDESLELGEYRPLTETEL 227


>gi|240173130|ref|ZP_04751788.1| ribosomal large subunit pseudouridine synthase B [Mycobacterium
           kansasii ATCC 12478]
          Length = 250

 Score =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 78/236 (33%), Positives = 113/236 (47%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KV+++AGIASRR  E+MI   RV+V+G L+      V      I VDG  +   E 
Sbjct: 10  IRLQKVLSQAGIASRRAAEKMIIDGRVEVDGKLVTELGTRVDPDVSVIRVDGARVVLDES 69

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP G+ +T +D  GR  + D +         +  VGRLD +TEGL+LLTNDG 
Sbjct: 70  LVYLALNKPRGMHSTMADDRGRPCIGDLIERKVRGNKNLFHVGRLDADTEGLILLTNDGE 129

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAW 188
           LA  L  PS +  + Y     G V +     L+ GI +       D    +D   G    
Sbjct: 130 LAHRLMHPSHEVPKTYLATVAGTVPRGLGKKLRTGIELDDGLARVDGFAVVDAIPGKT-L 188

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V V L EG+NR ++++     + V  L+R   GP  LG    GS R + +  + + 
Sbjct: 189 VRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGPVTLGKQRPGSVRALGRDEIGQL 244


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 101/231 (43%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R++  ++I    + V+G + +  A  V     +E +G  +  A   
Sbjct: 1   MRLDKYLCDGLGATRKQATKIIKSGEITVDGEVQKSGAFKVPEGGVVEWEGREV-GAPGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPADFVCSHED-GHNPTAFVLLDEPKVENLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D +    +GI ++      +   L+    +   V + 
Sbjct: 119 RITSPKHKCEKTYRVWLVDAIQPDYVEKFAEGIELRNEREPTLPAHLEIVNEAENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EGK  ++K++F     KV  L R   G   L   L  G  R ++++ + 
Sbjct: 179 IVEGKYHQVKRMFAALGNKVEHLHRERIGSIVLDEALEPGDYRFLTEEEVE 229


>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 =  255 bits (652), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R    
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLTKKEKRRLFA 229


>gi|170696462|ref|ZP_02887588.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170138615|gb|EDT06817.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 639

 Score =  255 bits (652), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 92/285 (32%), Positives = 145/285 (50%), Gaps = 10/285 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++  +    ++ KV+A AG+ SRR++E +I   RV VNG         +M TD + ++
Sbjct: 213 KRVLSADDDAPKLHKVLAEAGMGSRRDMEELIVAGRVSVNGEPA-HIGQRIMPTDQVRIN 271

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTE 119
           G P+++    +  R+ LYHKP G + +H+DP+GR +VFD LP +  ++ ++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 KILREQLG----PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
             +R  +         EE      AP       ++     I+  P
Sbjct: 452 NQVRALMASVGLKAPSEERGGRNAAPERKQPDPMQTSMGFINREP 496


>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 =  255 bits (652), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 105/311 (33%), Positives = 150/311 (48%), Gaps = 11/311 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-LLAGSTREVSKK---ILRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-SKQKKLA 302
            +     +E  +N+ AP  ++    R R   I             +  ++G    ++K  
Sbjct: 242 LVELRPEKETVLNM-APDAATRKRERTRSQKIRRAVRRHEERISATPGRSGKAPARRKPG 300

Query: 303 TPVHRRNLASN 313
                RN  +N
Sbjct: 301 GEPSTRNKVAN 311


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 123/241 (51%), Gaps = 5/241 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +   ++     R++K +++AGI SRR+ +  + + RV+V+G +       V+    +  D
Sbjct: 7   QETKRKTEDAVRINKYLSQAGICSRRQADTYVEEGRVEVDGEVAVS-GTKVLPGQSVTFD 65

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P++  E      +HKP G+V T S  + +  + D + +  +R+  VGRLD +++GL+L
Sbjct: 66  GKPVKIQEDLIFLAFHKPRGIVCTASKEE-KDNIIDYI-NYPTRIYPVGRLDKDSQGLIL 123

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG  A  +        + Y V  + ++  + ++ ++  + +  I     +  +  + 
Sbjct: 124 LTNDGEAANQIMKARNYHEKEYEVTVNKRITNEFIHDMRNPVPLDEINAVTRRCKVIKEG 183

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +     + L +G NR+I+++ E F ++V +L R+     +LG L  G  R+++   LRE
Sbjct: 184 PNE--FRIILTQGLNRQIRRMCEHFGYRVTKLKRVRVMNIKLGDLKEGRYRKLTPDELRE 241

Query: 244 Q 244
            
Sbjct: 242 L 242


>gi|322833321|ref|YP_004213348.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321168522|gb|ADW74221.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 439

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 106/299 (35%), Positives = 148/299 (49%), Gaps = 17/299 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKA 70
             +++ KV+ARAG  SRREVE MI   RV V+G +      V V     I +DG  L   
Sbjct: 149 QSEKLQKVLARAGHGSRREVEAMIQAGRVSVDGKISTLGDRVEVTGGTKIRLDGHVLSVM 208

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP +  SR I+VGRLD+NT GLLL T
Sbjct: 209 ESQDTVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKMRGSRWIAVGRLDVNTSGLLLFT 268

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  GQVD +K+  L +G+ ++        +     +G 
Sbjct: 269 TDGELANRLMHPSREVEREYAVRVFGQVDDEKIKQLSRGVQLEDGPAAFRSIKFQGGEGL 328

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G  +E+        
Sbjct: 329 NQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDLNLPKGLPRGGYKELD------- 381

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           L         V++     S   + RDR  + +       R  K  +Q     +    A 
Sbjct: 382 LPDINYLRTLVDMTEETVSKLPVERDRRRVKAN---QIRRAVKRHTQVAPTRRTTGPAK 437


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 115/234 (49%), Gaps = 10/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
            R++K I++ G  SRRE  R+IA  R+ +NG + E+ A  V   D + +DG  +   +  
Sbjct: 1   MRINKYISQTGFCSRRETNRLIASGRITINGKVCEKGA-EVEPEDIVLIDGQEIPHNDSE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KP+G+V T ++  +G    + N P   SR+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 60  PVYLALNKPMGIVCTAAEEVEGNIIRYVNYP---SRIFAIGRLDKASEGLILLTNDGDIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  + +  + +G+ I  +     +V     + S A   +
Sbjct: 117 NKMMRSEHDHEKEYVVTVDRPVTDEFMRRMSQGVEILDVVTKPCEVF----RQSEAVFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G N +I+++ +   ++V +L RI      L  L  G  R + ++ L + L
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERIRIMNITLDQLERGKWRHLEERELHKLL 226


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLNKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 78/247 (31%), Positives = 123/247 (49%), Gaps = 3/247 (1%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-T 57
           M +      + + +  R+ KV+++AG+ASRR  E+MI + RV+VNG ++      V   T
Sbjct: 1   MSEHRSPTNSPSAEGVRLQKVLSQAGVASRRAAEQMIVEGRVEVNGEIVLELGTRVDPDT 60

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
             I VDG  +         L +KP G++ T SD  GR  + D L     R+  VGRLD++
Sbjct: 61  AVIHVDGNRIMVNADLTHLLLNKPKGILCTMSDDQGRPCIGDYLRERQGRLYHVGRLDVD 120

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL+TNDG LA  L  PS + L+ Y     G + ++    L+ GI ++         
Sbjct: 121 SEGLLLITNDGELAHRLMHPSYRILKTYLAEVPGPIPKNLGRELRNGIELEDGPVKVDSF 180

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            L       A V V L EG+   ++++ +     V RL+R + G  +L T   G+ R + 
Sbjct: 181 KLVDVNEGRALVEVVLHEGRKHVVRRLLKQVGHPVLRLVRTAVGDVRLTTERQGAIRPLD 240

Query: 238 KKILREQ 244
           +K +   
Sbjct: 241 RKEISSL 247


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 67/292 (22%), Positives = 131/292 (44%), Gaps = 10/292 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +   +   
Sbjct: 18  RLNKYISESGICSRREADRYIEQGLVLINGKRA-SIGDQVFAGDEVKVNGRLIEAQDNSE 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T  D +  + V  +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 77  LVLIALNKPVGIVSTTDDGEKDNIV--DYVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 134

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +  + ++ +  G+ I G            +K +     + 
Sbjct: 135 KILRAGNDHEKEYLVTVNKPITDEFIHGMGAGVPIMGQKTK----KCKVKKEAPMVFRIT 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 AQVNLDAPIYSSETLVRDRPNIIS-EVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++    A     +  +      +   +P   T+  +N+S+K      +K   
Sbjct: 251 SEAPPKAKQNKPKKQISSNAKALGIHIPQTKTKETENNSRKRFAQPGRKKKK 302


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 81/305 (26%), Positives = 123/305 (40%), Gaps = 1/305 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A AG+ASRR+ E +I   RVKVN   +      V    D + VDG  + ++E  
Sbjct: 13  RLQKYLAEAGVASRRKAEELILAGRVKVNARAVTVLGSKVDPARDLVTVDGRLVSRSETR 72

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G VTT SDP+GR T  + L  +  RV SVGRLD + EG +L T+DG LA  
Sbjct: 73  SYYLLYKPPGCVTTASDPEGRPTALEYLRGVKERVFSVGRLDFDAEGAVLFTDDGELANR 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     R Y V+  G+     L  L  G+ ++      ++     +   N W+ V +
Sbjct: 133 LAHPRYGHRRTYLVKVRGEPPPAALERLVAGVRLEDGPARALEAVPHERAERNVWIRVVV 192

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EG+   +K++ E    +V RL R  +G   +  L  G  R ++   +R       L   
Sbjct: 193 GEGRFHLVKRLCEAVGLQVQRLYRPEFGGITVEGLRPGQFRPLAPVEVRALKTAVGLAGG 252

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
              +                          R  +         K+         R    +
Sbjct: 253 APAVAPRELPRAARRHGHGPPAPPELAPARREGERGEPGRREGKELPPRGEPRVRGRGED 312

Query: 314 VWMAK 318
                
Sbjct: 313 AGRGP 317


>gi|40062484|gb|AAR37436.1| RNA pseudouridylate synthase, putative [uncultured marine bacterium
           105]
          Length = 255

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 85/236 (36%), Positives = 122/236 (51%), Gaps = 5/236 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ KV+A AGI+SRR  ER+I   RV VNG  + +         D I VDG  ++     
Sbjct: 7   RLQKVLASAGISSRRAAERLIEVGRVTVNGRSVTKLGAKADPDLDDIRVDGRKVKTGRPR 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L  KP G VTT  DP+GR T+ + + ++   V  VGRLD ++EGL++LTNDG LA  
Sbjct: 67  IYLLVCKPRGYVTTRFDPEGRRTILNLISNVREYVYPVGRLDYDSEGLVILTNDGTLAAR 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAWV 189
           L  P     RVY VR  G   Q  ++ L+ G++I G       V     L  +   NA +
Sbjct: 127 LTHPRYGVERVYEVRVRGVPSQAAIDSLRHGVLINGRRTASSSVKFLRRLKAKSSENALL 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            V +REG+NR+++K+ E     V RL R   GP +  +L  G  R ++   +   +
Sbjct: 187 RVAIREGRNRQVRKMCEAIGHPVIRLRRTQIGPLRDSSLKVGKHRLLTTSEVAALM 242


>gi|295100099|emb|CBK89188.1| ribosomal small subunit pseudouridine synthase A [Eubacterium
           cylindroides T2-87]
          Length = 230

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 109/229 (47%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++  G  +R +V+ +I    V + G  +++A   V     + VD  P+   +  
Sbjct: 1   MRLDKFLSHMGYGTRNKVKNIIKNGWVTIEGKTIKKADHQVKEDQIVYVDDTPVSYIQ-Y 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G V+   D +   T+ + +PSI   +  VGRLDI+TEGLLL+ NDG L   
Sbjct: 60  EYYILNKPSGYVSATED-NVHPTIMELIPSIRKDLYPVGRLDIDTEGLLLVCNDGQLTHD 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V F G + ++ + +  + + +         + +           + +
Sbjct: 119 LLSPKKHVQKKYYVEFEGTLPENAVEIFNQPMDLDDFIAKPSTLEIL----DTNKAYLTI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EGK  ++K++F+    +V  L R+S+GP +L  L  G  R +S   + 
Sbjct: 175 SEGKFHQVKRMFQKIGCEVTYLQRVSFGPLELKNLEIGQARALSPDEIE 223


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 97/299 (32%), Positives = 149/299 (49%), Gaps = 17/299 (5%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +   ++   +++ KV+AR G+ SRRE+ER I Q RV ++G         V   + I VDG
Sbjct: 12  DAPAKSLPGEKLQKVLARTGLGSRREMERWIEQGRVSIDGKPAT-LGDRVTHRERISVDG 70

Query: 65  VPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGL 121
            P+    A+ TR  LYHKP G V +  DP GR TVF+ LP + S R IS+GRLD NT GL
Sbjct: 71  RPVNTTPAQETRCILYHKPTGEVCSRKDPQGRRTVFERLPKLKSGRWISIGRLDYNTSGL 130

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG LA  L  PS+   R Y VR  G+  +D L  L  G++++        +    
Sbjct: 131 LLFTTDGDLANKLMHPSSNIEREYMVRVMGEWKEDMLQRLLDGVMLEDGVARFSDIQDGG 190

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
             G N W  V + EG+NRE+++++E     V+RL R+ YG   + + +  G   E++ K 
Sbjct: 191 GDGINHWFYVVIMEGRNREVRRLWESQGLTVSRLKRVRYGEVFIPSKVKQGQWVELAGKE 250

Query: 241 LREQLGPHLLEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           ++               D P+       +++R  +  +      +    SS ++G   +
Sbjct: 251 IKSLY---------RMADLPLKDMKRGTIKEREKMERQF--SKRKGPGGSSARSGRKPR 298


>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 =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 105/311 (33%), Positives = 150/311 (48%), Gaps = 11/311 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNAVVRIDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-LLAGSTREVSKK---ILRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWMELDLKQVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-SKQKKLA 302
            +     +E  +N+ AP  ++    R R   I             +  ++G    ++K  
Sbjct: 242 LVELRPEKETVLNM-APDAATRKRERTRSQKIRRAVRRHEERISATPGRSGKAPARRKPG 300

Query: 303 TPVHRRNLASN 313
                RN  +N
Sbjct: 301 GESSTRNKVAN 311


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 116/230 (50%), Gaps = 5/230 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAE 71
            +R++K ++  GI SRRE +RMI + R+ ++G +       V     I VDG  +     
Sbjct: 10  SERINKYLSAHGICSRREADRMIQEGRITIDGRIAA-MGEMVDDNTIICVDGRKVDNSTP 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +  ++KP+G+V T +D  G++ + D +     R+  VGRLD  ++GL+LLTNDG + 
Sbjct: 69  PQVVIAFNKPVGIVCTTTDKQGKNNIVDFI-GYKERIYPVGRLDKESDGLILLTNDGDMM 127

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L        + Y V  +  +++D +  +  GI ++ +     +  ++  K S+    +
Sbjct: 128 DRLLRSVNGHEKEYIVSVNKPINKDFIKRMSGGIYLKELDRTTRKCVVE--KISDRTFRI 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L +G NR+I+++     + V +L RI     +LG L  G  RE+  K L
Sbjct: 186 ILTQGLNRQIRRMCAECGYSVTKLTRIRIMNVELGDLKTGEYRELDGKEL 235


>gi|301169983|emb|CBW29587.1| 16S rRNA pseudouridylate 516 synthase [Haemophilus influenzae
           10810]
          Length = 232

 Score =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 110/234 (47%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIHQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++G         L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRGEKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRSLTQSEIEKLV 231


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/245 (33%), Positives = 127/245 (51%), Gaps = 4/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           ++ KN        +R+ KV+A+AG+ASRR  E +I + RV+VNG ++ +    V    D 
Sbjct: 52  VEGKNKKNSQNQGERLQKVLAKAGVASRRHAEILIDEGRVEVNGQVIIKQGTRVDPNKDV 111

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDI 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|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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 117/239 (48%), Positives = 159/239 (66%), Gaps = 7/239 (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  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTE 119
           G P+ +AE TRL+ +HKP GL+T   DP GR T++    + LP    RV+ 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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   G N W+ + LREGKNRE+++V E F  +VNRL+RI YGPF LG L  G   E+ +
Sbjct: 181 ERGSGRNRWIEMTLREGKNREVRRVLEHFGLEVNRLLRIGYGPFHLGDLPRGQAVELKQ 239


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 114/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V +N  L+++A   V   D ++VD   +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQTITY-QQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G++T   DP  + TV D +     +  +  VGRLD +T GLLL+TNDG L 
Sbjct: 60  HYFMLNKPTGVITATEDPQ-QKTVLDLIASKDRYPDLAPVGRLDKDTTGLLLITNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    ++  +  +   KG+ +  G   G  Q+ +D          
Sbjct: 119 HNLLSPKKHVAKTYFVELDQEIANEVDSAFAKGVALADGTQVGSAQLIIDKSNKKQGL-- 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EGK  +IK++F  F+  V +L RI  G   L   L  G  RE+++  +   
Sbjct: 177 ITIHEGKFHQIKRMFGLFDLGVVKLKRIKMGNLSLDENLPQGKYRELTEAEISAL 231


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 132/293 (45%), Gaps = 14/293 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I  +GI SRR+ +R I Q  V +NG         V S D ++V+G  +       
Sbjct: 8   RLNKYIGESGICSRRDADRYIEQGHVFINGKRAA-VGDQVYSGDVVKVNGQLIEPRNEND 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+++T  + +  + V  +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIISTTEEGESDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V ++ +  L  G+ + G      +V+    K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTEEFILGLGAGVPMMGTVTKKCKVS----KVATFVFNIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPMGEWRDLTDDELIELF--KLIEN 238

Query: 253 AQVNLDAPIYS--SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +  + + P+    ++++   +P +      + +       ++     +KK   
Sbjct: 239 SSSD-EKPVKKVQAKSVADKKPRVNGVKKPEKSDSNSAPRKRFAQPGRKKKGR 290


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/297 (25%), Positives = 128/297 (43%), Gaps = 12/297 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 30  PDSSIRLNKYISESGICSRREADRFIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGRLIEP 88

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE       +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 89  REAEDLVFIALNKPVGIVSTTEDSE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 146

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  D +  +  G+ I G            +K +  
Sbjct: 147 GDLVNKILRAGNDHEKEYLVTVDKPITDDFIRGMGAGVPILGTVTK----KCKVKKEAPF 202

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V RL R       L  L  G  R+++   L E    
Sbjct: 203 VFRITLIQGLNRQIRRMCEHFGYEVTRLERTRIMNVGLSGLPLGEWRDLTDDELIELF-- 260

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +            +T    RP +  E   +  + +  ++ K   S  +K   
Sbjct: 261 KLIENSSSEAKPKAKAKPKTAGIKRPVVKIEKSAEKEKSRPAANGKRFTSPGRKKKG 317


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 72/318 (22%), Positives = 136/318 (42%), Gaps = 10/318 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +G+ SRR  +R I Q  V +NG   +     V   D + V+G  +   E   
Sbjct: 7   RLNKYISESGLCSRRAADRYIEQGNVYINGKKAK-VGDKVFFGDLVMVNGQTIEPKEVEH 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L  Y+KP+G+ +T ++   +  + D++ +   RV  +GRLD +++GL+ LTN+G L  
Sbjct: 66  SVLIAYNKPVGITST-TEAGVKGNIVDHV-NHSERVFPIGRLDKDSQGLIFLTNNGDLVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  + +  +  + KG+ I GI     +VT    K S     + 
Sbjct: 124 KILRAGNNHEKEYLVTVNKPLTEQFITNMSKGVPILGIMTKKCKVT----KESPFVFKIT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  RE++ +   +         
Sbjct: 180 LIQGLNRQIRRMCEHFGFEVTKLERTRIMNIGLKGIPLGEWRELTAEEQTDIYNMVAKSS 239

Query: 253 AQVNLDAPIYSSETLVRD-RPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +     AP  S++   ++     ++   +      K S+      ++K           A
Sbjct: 240 SLEAASAPKKSAKKPEQELTEKPVARKKNSRPAGAKPSAAGKARPERKSGPASRGASASA 299

Query: 312 SNVWMAKGIHSSFLSDSG 329
           +  W      S       
Sbjct: 300 APDWNKSNGPSRRPVKPS 317


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 123/241 (51%), Gaps = 5/241 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +   ++     R++K +++AGI SRR+ +  + + RV+V+G +       V+    +  D
Sbjct: 2   QETKRKTEDAVRINKYLSQAGICSRRQADTYVEEGRVEVDGEVAVS-GTKVLPGQSVTFD 60

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P++  E      +HKP G+V T S  + +  + D + +  +R+  VGRLD +++GL+L
Sbjct: 61  GKPVKIQEDLIFLAFHKPRGIVCTASKEE-KDNIIDYI-NYPTRIYPVGRLDKDSQGLIL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG  A  +        + Y V  + ++  + ++ ++  + +  I     +  +  + 
Sbjct: 119 LTNDGEAANQIMKARNYHEKEYEVTVNKRITNEFIHDMRNPVPLDEINAVTRRCKVIKEG 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +     + L +G NR+I+++ E F ++V +L R+     +LG L  G  R+++   LRE
Sbjct: 179 PNE--FRIILTQGLNRQIRRMCEHFGYRVTKLKRVRVMNIKLGDLKEGRYRKLTPDELRE 236

Query: 244 Q 244
            
Sbjct: 237 L 237


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 101/230 (43%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++ +  V V+ ++ +  A  +  T  +E     +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKRGEVTVDDVVQKSGAFKLKETSCVEWQDREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D       GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLAEPIQADYAEQFTNGIELRGERELTLPAQLEI--VSETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  +L  G  R +++  +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEDEV 226


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 118/230 (51%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G  +R+EV +++  ++V+VNG++++    N+   TD + V G  ++  + 
Sbjct: 1   MRIDKFLAHMGFGTRKEVRKLLKARKVEVNGVVVKDPGYNLNVDTDKVIVKGEEVKY-KP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G V+   D     TV D +P +  ++  VGRLDI+TEGLL+LT+DG LA 
Sbjct: 60  FVYFMLNKPKGYVSATVDRRY-PTVVDLVP-VHRKIFPVGRLDIDTEGLLILTDDGQLAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y       ++++  + +K GI ++   Y      L  + G     T+ 
Sbjct: 118 HLTSPKKEVEKEYYFELDKPLEEEDFSKIKTGIRLED-NYLTKPARLLGKVGDKHG-TIV 175

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F      V  L RI  G   L   L  G  RE++ + +
Sbjct: 176 ITEGKYHQVKRMFLALGKTVVYLKRIRIGGLILDNKLSPGEYRELTPEEI 225


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 98/299 (32%), Positives = 153/299 (51%), Gaps = 13/299 (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---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + +  DP+GR TVFD LP+    R I+VGRLD+NT GLLL TNDG
Sbjct: 61  QPICRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRLGRWITVGRLDMNTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------LDTQ 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 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
              L  H+    +      +   +        +   V     R ++  +++ G   ++K
Sbjct: 241 NA-LRNHVQLPDETQTMVNVRQGKLDHARLSRMRRSVKKHKVRKQQGLNKRAGRPAKRK 298


>gi|312196764|ref|YP_004016825.1| pseudouridine synthase [Frankia sp. EuI1c]
 gi|311228100|gb|ADP80955.1| pseudouridine synthase [Frankia sp. EuI1c]
          Length = 285

 Score =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 77/233 (33%), Positives = 122/233 (52%), Gaps = 3/233 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ KV+A AG+ SRR  E +I   RV+V+G ++      V   T  IEVDG  +   
Sbjct: 44  EGIRLQKVLASAGVGSRRHNEELIDAGRVRVDGKVVREQGRRVDPETAVIEVDGERVVTR 103

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG 128
                   +KP G+V+T SDP+ R T+ D L      + +  VGRLD+++EGLLL+TN+G
Sbjct: 104 TGLVHLALNKPRGVVSTMSDPEDRPTISDLLTEFGASAGLFHVGRLDVDSEGLLLVTNNG 163

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  PS Q  + Y+V+ +G + ++ +  L   + +           +  Q GS   
Sbjct: 164 DLAHRLTHPSYQVPKTYQVQINGPLRKETMRRLHTRVELSDGPVRVDSARIIDQVGSQIL 223

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + L EG+NR ++++ E     V RL+R  +G   LGTL +G  R ++   +
Sbjct: 224 LEIVLHEGRNRIVRRMMEEVGHPVVRLLRTEFGAVHLGTLRSGRARHLTLHEV 276


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/252 (30%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRK 69
              QR+ +++A  G+ SRR++++M     ++V+G ++  A+++V     +  V G P+  
Sbjct: 1   MAKQRLDRILAEMGVGSRRDIKKMARSGLIEVDGRVVRDASLHVDPGQQVLCVAGHPVHY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
            +    W+ +KP G+V+   DP  R TV D L       R+   GRLDI+TEG +L+T+D
Sbjct: 61  -QPFHYWMMNKPPGVVSAVIDPRHR-TVIDLLDESDRTPRLFPAGRLDIDTEGFVLITDD 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSN 186
           G LA  +  P     + YR    G+V    +    +G+V+    Y  +   L  +  G  
Sbjct: 119 GQLAHAILSPKRHVSKTYRATVQGRVSDADVAAFARGLVLGDG-YRALPAHLQIRDAGER 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LR 242
           + V + LREGK  +IK++F      V  L R++ G   L   L  G  R ++      LR
Sbjct: 178 SEVEIVLREGKFHQIKRMFAALGKPVLYLKRVAIGGVPLDPALPPGGYRALADDEVARLR 237

Query: 243 E---QLGPHLLE 251
           E   +L PH  E
Sbjct: 238 ETDPRLPPHPAE 249


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 71/213 (33%), Positives = 115/213 (53%), Gaps = 2/213 (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 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTVGLREGKNREIKKVFEFFNWK 211
            ++KL  LK+G+V++G      +V+++  + +   + V + + EG+N ++K +       
Sbjct: 121 TEEKLAPLKRGVVLKGRKTAPARVSIERIEPTKRTSMVRLTIHEGRNHQVKNMLAKVGLP 180

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V +L R  Y  F +  L  G  R+++   ++  
Sbjct: 181 VQKLKREQYAFFDVTGLQPGEYRKLTSVEIKRL 213


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 133/305 (43%), Gaps = 19/305 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
            R++K I+ +G  SRRE +R+I + RV +NG   +     V   D +EVDG  ++  + +
Sbjct: 1   MRLNKFISDSGFCSRREADRLIEEGRVLINGRRCKT-GQQVEDKDFVEVDGQRIKAKRQK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 ++KP G+  T ++   +  + D + +   ++  +GRLD  + GL+ +TNDG + 
Sbjct: 60  ERVYLAFNKPEGITCT-TEGSVKGNIVDFI-NYPEKIFPIGRLDKFSNGLIFMTNDGDIV 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  + L  +  GI I        +VT    K S     +
Sbjct: 118 NKILRAGNAHEKEYVVTIDRPVTDEFLRKMSNGIPILDTVTKKCKVT----KVSKNTFRI 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I+++ E+   +V  L R       LG L  G+ R ++ K + E     ++E
Sbjct: 174 ILTQGLNRQIRRMCEYLACRVLSLQRTRIMKVDLGKLKPGTWRHLNPKEMAEI--NQMIE 231

Query: 252 EAQVNLDAPI---YSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL-----SKQKKLAT 303
            +    +A           +  RP     +       KK+S ++ G      SKQ   + 
Sbjct: 232 SSSNTQEASKDSNKQGRRSLPKRPVARQNMKTSSQSHKKSSPKRRGQTSGRPSKQNSKSR 291

Query: 304 PVHRR 308
           P  +R
Sbjct: 292 PQRKR 296


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 102/306 (33%), Positives = 143/306 (46%), Gaps = 9/306 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  K ++       ++ KV+A+AGI SRR++E+MI + R+ VNG         + + D I
Sbjct: 41  LPAKRVLAPEPDAPKLHKVLAQAGIGSRRDMEQMILEGRITVNGEPA-HIGQRIAAGDRI 99

Query: 61  EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G P+R       TR+  YHKP G V TH DP  R TVF  LP +   +  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 VSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           +S++    LR   G     E +              R +       P+   R  +   ++
Sbjct: 280 LSEQDVRTLRRMTGVGERPEGEAREAREAGGDRRGKRGKRGRGGNAPEGAPRAARPQRRE 339

Query: 293 NGLSKQ 298
            G    
Sbjct: 340 GGEGPA 345


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-T 73
           R++K ++ AG  SRR  +++I +  V +NG +       V   D + V G  + +     
Sbjct: 7   RINKFLSEAGYCSRRNADKLIEEGAVTINGKIP-EMGTKVGPDDEVRVKGELITEPNSNF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP G+V T      +  + D + +   R+  +GRLD  +EGL+LLTNDG +   
Sbjct: 66  VYLAFNKPRGIVCTTDTRREKDNIIDYI-NYPERIFPIGRLDKYSEGLILLTNDGDIVNK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V  +  +  D +  +  G+ I         V    ++   +   + L
Sbjct: 125 ILRARNNHEKEYIVHLNKPIKGDFIQKMGDGVPILDTVTKKCFV----EQIGKSSFKIIL 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +G NR+I+++ E+F++KV  L RI     +L T   G  R ++   L+E
Sbjct: 181 TQGLNRQIRRMCEYFDYKVAGLKRIRIMNVKLDT-EKGKWRHLTPNELKE 229


>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 =  255 bits (651), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATEDSRHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +  +  S + 
Sbjct: 119 AHAMLSPKKHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           V + + EGK  ++K++      +V  L R+  GP  L   L  G  R ++++ L
Sbjct: 179 VQITIAEGKFHQVKRMVAACGKEVADLQRLKMGPLSLPNDLELGDWRRLTQEEL 232


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 121/241 (50%), Gaps = 7/241 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +    R++K IA AG+ SRR+ + ++ Q RV ++G  +++    V     + VDG  +
Sbjct: 5   SSDREGMRINKYIAHAGVCSRRDADDLVEQGRVHIDGERVDQHGTCVREGQTVTVDGEEV 64

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLL 124
              E     L +KP   ++T  DP  R TV D +       S +  VGRLD NT G+LL+
Sbjct: 65  YPLE-FEYLLLNKPKDTISTTDDPKDRRTVLDAIGVPEDNPSGLFPVGRLDRNTTGVLLV 123

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           +NDG LA  L  P  +  ++Y VR    V   +L+ LK+G+ +  G    D    LD Q+
Sbjct: 124 SNDGDLAHRLMHPRYEIPKIYYVRVQDDVKPHQLDQLKRGVELSDGAAAADQVAYLDPQR 183

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++  + + L EG+NR+I+++ E     + +L R  Y     G L  G  R +  + +RE
Sbjct: 184 KTD--IALELHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRLEPEEVRE 241

Query: 244 Q 244
            
Sbjct: 242 L 242


>gi|327390694|gb|EGE89034.1| hypothetical protein SPAR5_0271 [Streptococcus pneumoniae GA04375]
          Length = 240

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDQIHFDGQKLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAW 188
           A  L  P     + Y+ +  G + ++ +    +GI ++       ++ L +   + + + 
Sbjct: 119 AHTLLSPKRHVDKTYQAQVKGMMTREDVETFAEGIPLKDFTCQPAKLELVSIDTEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L   
Sbjct: 179 IRVTIAEGKFHQIKRMVAYCGKEVMDLQRLTMGTLVLDENLGRGEWRRLTKEELENL 235


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 93/303 (30%), Positives = 149/303 (49%), Gaps = 12/303 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  ++  P ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++ TD + V+
Sbjct: 226 RELSADDDAP-KLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPTDQVRVN 283

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G  + +    +  R+ LYHKP G + + SDP+GR TVFD+LP I + + ++VGRLD NTE
Sbjct: 284 GKLIHRKVTTKPPRVLLYHKPSGEIVSQSDPEGRPTVFDSLPRIKNGKWVAVGRLDFNTE 343

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +++  
Sbjct: 344 GLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIQLDDGEANFLRIAD 403

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +E+  
Sbjct: 404 GGGEGVNQWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQELDP 463

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             +R      L+    +   +    S      +     +  +         +  +GL + 
Sbjct: 464 TDVR-----GLMANIGLKAPSKEAQSGGKGVTKVGGRKQREEAALAGMPMHTGMDGLPRY 518

Query: 299 KKL 301
           +K 
Sbjct: 519 EKS 521


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 107/231 (46%), Positives = 150/231 (64%), Gaps = 6/231 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++     R++K++ARAG+ASRRE+ERMIA  R+ +N  ++E  A  + S   + VDG P+
Sbjct: 9   EDRPEGDRIAKLLARAGVASRREIERMIADGRITLNDKVVETPATFLTSLQGVAVDGKPV 68

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLL 123
            K E  +L+ +HKP GL+T   DP GR+T++    + LP    R++ +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 -KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             G N WV + + EGKNRE+++V E+   KVNRLIR +YGPF LG L  G 
Sbjct: 189 AGGKNQWVEMTITEGKNREVRRVLEYLGLKVNRLIRTAYGPFGLGDLPRGQ 239


>gi|315644423|ref|ZP_07897556.1| pseudouridine synthase [Paenibacillus vortex V453]
 gi|315280173|gb|EFU43466.1| pseudouridine synthase [Paenibacillus vortex V453]
          Length = 233

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 65/236 (27%), Positives = 121/236 (51%), Gaps = 8/236 (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 ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALYKPVGITST-TELHIKGNIVDFV-GHKERIFPIGRLDKDSEGLILLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +    L  +  G+ I G      +VT  +++       + L
Sbjct: 118 ILRSEGKHEKEYIVTVDRPLTDTFLRGMSSGVKILGEMTLPCEVTRMSER----VFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            EGKNR+I+++   F ++V +L RI     +LG+   GS R++++K  RE+LG  L
Sbjct: 174 TEGKNRQIRRMCSAFGYEVRKLQRIRIMNIRLGSQRVGSWRDLNEKE-REELGRLL 228


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I  ++V +N  L+++A   V   D ++VD   +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKAKKVTINEKLVKQAKQQVTENDMVKVDNQTITY-QQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +KP G++T   DP  + TV D +     +S +  VGRLD +T GLLL+TNDG L 
Sbjct: 60  HYFMLNKPTGVITATEDPQ-QKTVLDLIASKDRYSDLAPVGRLDKDTTGLLLITNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V    ++  +  +   KG+ +  G   G  Q+ +D          
Sbjct: 119 HNLLSPKKHVAKTYFVELDQEIANEVDSAFAKGVALADGTQVGSAQLIIDKSNKKQGL-- 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EGK  +IK++F  F+  V +L RI  G   L   L  G  RE+++  +   
Sbjct: 177 ITIHEGKFHQIKRMFGLFDLGVVKLKRIKMGNLSLDENLPQGKYRELTEAEISAL 231


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 118/237 (49%), Gaps = 7/237 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           Q   T  R++K ++ AG+ SRRE +R+I   +V V+G       + V  +  + V    +
Sbjct: 5   QTTETTVRLNKFLSEAGVCSRREADRLIENGKVTVDGKRA-EMGMRVSPSQRVCVGKKEV 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+     L   +KP+G+V T    +  + +     +  +RV  +GRLD ++EGLLL+TN+
Sbjct: 64  RQKNEMVLLAVNKPVGIVCTEEKKEKNNIIRFL--NYPTRVTYIGRLDKDSEGLLLMTNN 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     Q  + Y+V  +  V ++ +  + +G+ I        +V +  +     
Sbjct: 122 GDIINKMMRAGNQHEKEYKVTVNKPVTKEFIEKMAEGVPILDTVTRKCKVEMLGK----Y 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + L +G NR+I+++ E+  +KV RL RI      LG L  G  R+V++  +++ 
Sbjct: 178 KFRIILTQGLNRQIRRMCEYLGYKVTRLERIRVMNITLGELKPGEYRKVTEAEIQKL 234


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 102/309 (33%), Positives = 149/309 (48%), Gaps = 10/309 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLR 68
            +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG      ++
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKIQ 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +    R+  Y+KP G + T  DP+GR TVFD LP I  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+    +S    R R   I                ++    ++K   
Sbjct: 242 LVELRPEKETMLDLNKD-NTSRKRERARSQKIRRAVKRHEERVNTPKGRSNNPSRRKPKK 300

Query: 304 PVHRRNLAS 312
               +   S
Sbjct: 301 TAGDQGARS 309


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 123/238 (51%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K         +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VD
Sbjct: 210 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVD 269

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ +   +  + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD  TEG++L
Sbjct: 270 GLTV-ATQSYQFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDTETEGVIL 328

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q 
Sbjct: 329 LTNHGELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVEQT 388

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 389 GKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 446


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 121/241 (50%), Gaps = 7/241 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             +    R++K IA AG+ SRR+ + ++ Q RV ++G  +++    V     + VDG  +
Sbjct: 17  SSDREGMRINKYIAHAGVCSRRDADDLVEQGRVHIDGERVDQHGTRVREGQTVTVDGEEV 76

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLL 124
              E     L +KP   ++T  DP  R TV D +       S +  VGRLD NT G+LL+
Sbjct: 77  YPLE-FEYLLLNKPKDTISTTDDPKDRRTVLDAIGVPEDNPSGLFPVGRLDRNTTGVLLV 135

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQK 183
           +NDG LA  L  P  +  ++Y VR    V   +L+ LK+G+ +  G    D    LD Q+
Sbjct: 136 SNDGDLAHRLMHPRYEIPKIYYVRLQDDVKPHQLDQLKRGVELSDGAAAADQVAYLDPQR 195

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++  + + L EG+NR+I+++ E     + +L R  Y     G L  G  R +  + +RE
Sbjct: 196 KTD--IALELHEGRNRQIRRMMEALGHTIVQLERAKYATLTTGRLQRGEWRRLEPEEVRE 253

Query: 244 Q 244
            
Sbjct: 254 L 254


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/246 (33%), Positives = 130/246 (52%), Gaps = 17/246 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV K+I++ GIASRR+ E+MI   RV++NG +++        TD IEV+G  L+ + R 
Sbjct: 3   ERVQKIISQWGIASRRQAEKMIVAGRVRLNGTVVQLGQKANPETDLIEVNGQRLKPSNRP 62

Query: 74  R--LWLYHKPIGLVTTHSD-------PDGRSTVFDNLPSIFSR---VISVGRLDINTEGL 121
           +    L +KP+G+V+T  +        + R TV D LPS   +   +  VGRLD+ + G 
Sbjct: 63  QAIYLLLNKPVGVVSTCRNYRVCNTILEKRRTVLDLLPSTIRQGQGIHPVGRLDMESTGA 122

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG L   L  P     + YRV   G   +  L+  ++G+ + G      QV +  
Sbjct: 123 LILTNDGTLTYKLTHPRHHVPKTYRVWVKGHPPESILSAWRQGVDLSGRTTLPAQVRVLK 182

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREV 236
           Q+     + + L EG+NR+I++V +   + V  L R + GP QL       LL+G  R +
Sbjct: 183 QQPDKTLLEIVLTEGRNRQIRRVADLLGYPVIHLHRTAIGPIQLQRPGEPILLSGHYRYL 242

Query: 237 SKKILR 242
            +  +R
Sbjct: 243 EEFEIR 248


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 104/302 (34%), Positives = 148/302 (49%), Gaps = 14/302 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             I +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIKSGRVSVNGQVARLGERLEDENAVIRIDGHTVSAKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E++ K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIYLDKKLPRGGWMELTLKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +   L  E +  LD    +S    R R   I        R ++ ++   G S Q++   
Sbjct: 242 LV--ELRPEKETMLDLSQNTSRQRERSRSQKIRR---AVRRHEERANAPKGRSNQQRRNK 296

Query: 304 PV 305
             
Sbjct: 297 KS 298


>gi|302518236|ref|ZP_07270578.1| pseudouridine synthase [Streptomyces sp. SPB78]
 gi|302427131|gb|EFK98946.1| pseudouridine synthase [Streptomyces sp. SPB78]
          Length = 447

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 78/238 (32%), Positives = 123/238 (51%), Gaps = 1/238 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K         +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V  +D I+VD
Sbjct: 202 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGLRVKPSDEIKVD 261

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G+ +   +  + +  +KP G+V T  DP+GR  + D + +  +R+  VGRLD  TEG++L
Sbjct: 262 GLTV-ATQSYQFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRLDTETEGVIL 320

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q 
Sbjct: 321 LTNHGELAHRLTHPRYGVRKTYLAHIVGPIPRDLGKRLKDGIELEDGWARADHFRVVEQT 380

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 381 GKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 438


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 73/289 (25%), Positives = 127/289 (43%), Gaps = 10/289 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E   
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGQLIEPREADD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +         
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIENSS 240

Query: 253 AQVNLDA-PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++    A P   + T    RP +  E  +D  R   N  +     ++KK
Sbjct: 241 SEAKPKARPKAKAATPGIKRPVVKMENSNDKGRPAGNGKRFTQPGRKKK 289


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 88/243 (36%), Positives = 137/243 (56%), Gaps = 12/243 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 69
           +R+ K +A  G+ SRRE+E  I + R++VNG L       +   + + +DG PLR    +
Sbjct: 6   ERIQKWLAARGLGSRREIEGWIREGRLRVNGKLA-ELGQRISGYERLSLDGKPLRVSPER 64

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               ++ +YHKP G + + +DPDGR TVF +LP +   R +S+GRLD+NT GLLL TNDG
Sbjct: 65  EAPRQILMYHKPPGEICSRNDPDGRPTVFRHLPKLRQGRWVSIGRLDLNTAGLLLFTNDG 124

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-----GDMQVTLDTQK 183
            LA  L  PS +  R Y VR  G+V++D L  L+ G+ ++           +Q   +   
Sbjct: 125 ELANRLMHPSAEIEREYWVRVAGEVNEDTLQALRNGLELEDGFACFDDVQPLQALHEDDT 184

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
             N + +V L+EG+NRE+++++E    +V+RL RI +G   L   L AG  R ++   + 
Sbjct: 185 QYNRYFSVVLKEGRNREVRRLWEAVGCQVSRLKRIRFGNLWLPKNLAAGRWRPLTAGEVN 244

Query: 243 EQL 245
             L
Sbjct: 245 ALL 247


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR EV++++ +++V VNG +       +    D I   G  L   E+
Sbjct: 1   MRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISCQGQTLSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D +   TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  YVYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     + YR +  G +    +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVILETNEAERTSV 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + ++EGK  ++K++ +    KV  L R+S  P QL   L  G  R ++   L
Sbjct: 179 VEITIKEGKFHQVKRMVQACGKKVTDLQRLSMVPLQLDKQLALGEWRRLTDDEL 232


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 93/342 (27%), Positives = 148/342 (43%), Gaps = 8/342 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          V   D ++
Sbjct: 139 PAKRVLPPQVEMPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HIGQRVQYGDQVK 197

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP     +  SVGRLD+N
Sbjct: 198 VNGRPIRYRIDPPAPRVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLAHGKWQSVGRLDLN 257

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T+ G LA  L  P     R Y VR  G +  ++   L  G+ ++        +
Sbjct: 258 TEGLLLFTSAGELANKLMHPRFGLEREYAVRVLGALSNEEKQRLLDGVQLEDGMAAFGSI 317

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +GSN W  V + EG+NRE++++ E     V+RLIRI YG   L   L  G+  E+
Sbjct: 318 EDGGGEGSNCWYRVTISEGRNREVRRMLESVGHAVSRLIRIRYGSMMLPRGLKRGAWLEL 377

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            ++ +R  +     +  +                R               +         
Sbjct: 378 DERDIRALMQAAGADMPRPAGPGAAAGDRKGGGPRKGGGRGQGGPGGPAPRGDYFNPPAG 437

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
            + + A P    +    +  + G   S      ++++  +R 
Sbjct: 438 GRGQRAAPPS--SQPDPMKTSVGYIGSDSLARHRQDQKQKRK 477


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 102/289 (35%), Positives = 145/289 (50%), Gaps = 12/289 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAE 71
            +++ KV+ARAG  SRRE+E MI+  RV V+G L              I +DG  +  AE
Sbjct: 2   SEKLQKVLARAGHGSRREIETMISAGRVSVDGKLATLGDRIENDKSLKIRIDGHLVSIAE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
            T    R+  Y+KP G + T +DP+GR TVFD LP    SR I+VGRLD+NT GLLL T 
Sbjct: 62  STTEVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPRLRGSRWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G+V  DK+  L KG+ ++        +     +G N
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGEVGDDKIRQLSKGVQLEDGPAAFKTLRFAGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK---KILR 242
            W  V L EG+NRE+++++E    +V+RL+R+ YG  QL   L  G   E+       LR
Sbjct: 182 QWYNVTLTEGRNREVRRLWEAVGVQVSRLMRVRYGDIQLPKGLPRGGWMELELPAVNYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             +G  + EE    +        T        +          +++S +
Sbjct: 242 TLVG--MPEETVTKVAVEKDRRRTKANQIRRAVKRHSQVSNSPRRSSKR 288


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG+ +R+EV+  I + RV VNG +  +    +    D + +D   +   E 
Sbjct: 1   MRLDKYLAHAGLGTRKEVKLAIRKGRVSVNGEVCRKDDRKIQEGVDVVCLDKEEI-YYEA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
               + +KP  +V+  SDP    TV D + +   +    VGRLD++TEGLLL+TNDG LA
Sbjct: 60  VVYIMLNKPQDVVSATSDPTY-ETVLDCIDAFLPKDCFPVGRLDMDTEGLLLITNDGKLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V     + +     L+ G IV+        +V +      +  + 
Sbjct: 119 HRLLSPKHHVEKTYLVDLAQPLQEGDQKKLENGSIVLDEEPVLPARVEIL----EDTQIL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           + ++EG+  ++K++      +V  L RI+ GP +L   L +G  R +S++ +   
Sbjct: 175 LHIQEGRFHQVKRMLHAIGNEVVHLKRIAMGPLRLDEALASGEWRYLSEEEITAL 229


>gi|311899116|dbj|BAJ31524.1| putative ribosomal large subunit pseudouridine synthase B
           [Kitasatospora setae KM-6054]
          Length = 428

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 120/231 (51%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             +R+ KV+ARAG+ SRR  E +IAQ RV VNG  +      V    D I+VDG+ +   
Sbjct: 190 DGERLQKVLARAGMGSRRACEELIAQGRVDVNGETVLEQGRRVDPVKDEIKVDGLTV-AT 248

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 249 QSYLFFALNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGEL 308

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    L KG+ ++          + +  G N  V 
Sbjct: 309 AHRLTHPKYGVTKTYLAAIQGPLPRDLGKTLAKGVELEDGWARADSFKVISNLGKNYLVE 368

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V++L+R ++GP  LG   +G  R ++   +
Sbjct: 369 VTLHEGRKHIVRRLLAEVGFPVDKLVRTAFGPITLGDQKSGWLRRLTNPEV 419


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 112/232 (48%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  + K  R
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIREGIVTVNGKRIVEVDFKINPEEDVVEVDGR-VAKFSR 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ DP    TVF  +     +  + +VGRLD + EGLL++T+DG  
Sbjct: 60  QIYIMMNKPKGYVCSNDDP-ASLTVFSLISDDLKYRDLHTVGRLDKDAEGLLIITDDGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P  +  + Y VR   +VD++KL   + GI++  G      + T+      +  V
Sbjct: 119 THRVISPKKRIEKEYLVRLEKEVDEEKLKEFENGIILDDGYKTLPAKYTI----IDSTTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++K++FE    KV  L R+  G   L   L  G  + + ++ 
Sbjct: 175 KLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDQNLKPGEYKVIDREE 226


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 72/351 (20%), Positives = 139/351 (39%), Gaps = 27/351 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAERT 73
           ++K I+  G  SRRE + +I   RV +N              D +EVDG  +   K E+ 
Sbjct: 7   LNKFISDTGYCSRREADNLITSGRVLLNDRPAA-LGNRYKPGDTVEVDGSLITAAKKEKR 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G +TT ++   +  +   + +   R+  +GRLD ++EGL+ LTNDG +   
Sbjct: 66  VYLALNKPPG-ITTTTELHIKDNIISFV-NYPQRIFPIGRLDKDSEGLIFLTNDGDIINK 123

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   +    + Y VR +  +D + L+ + +G+ I        +V +  ++       + L
Sbjct: 124 ILRAANNHEKEYVVRVNKPIDTNFLHQMSQGVPILDTRTLPCKVQMTGRQ----TFRITL 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            +G NR+I+++ E+  + V  L R+     +L  L  G  R +S+  +        ++E+
Sbjct: 180 TQGLNRQIRRMCEYLGYTVVGLQRVRIMNVRLDKLPLGKWRYLSEAEI------AFIKES 233

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
             +    +         R      V +       ++ +    +  K++A P   R     
Sbjct: 234 VAD-STKVSGESKPSGARRKTAKPVEEKEHLRTGSTPKNKPATGHKRVAAPAKHREEQEP 292

Query: 314 VWMAKGIHSSFLSDSGQREENHRR----------SPSFPSKRSLRRTSAKK 354
            +M K    S   +       HR             S    +   + S  +
Sbjct: 293 AFMPKN-KPSAGHNRAAAPAKHREQQEPAFTPKNKSSTHKHKPADKDSKPQ 342


>gi|313632172|gb|EFR99245.1| ribosomal small subunit pseudouridine synthase A [Listeria
           seeligeri FSL N1-067]
          Length = 233

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG++ + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKSQVNPEKDQITVHGNPVIYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +   + GI +  G       + +         +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDDGYTCKPAHLEIMAPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V  L R+S G   L  +L  G  R +++  L
Sbjct: 175 RVTIQEGKFHQVKRMFAATGKTVTYLKRLSMGKLMLDESLGLGEYRSLTEDEL 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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 108/233 (46%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K+++  G  SRREV+ ++    V VNG++ + +   V    D I V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRREVKPLLKSGSVVVNGVIQKDSKSQVNPEKDQITVHGNPVIYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP  +V+   D +   TV D L      +    VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYFMLHKPQNVVSATED-NLSETVIDLLAQEDTLTNPFPVGRLDKDTEGLLIITNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G V    +   + GI +  G       + +         +
Sbjct: 119 AHNLLSPKKHIDKTYYAKIEGDVTATDVEAFRTGITLDDGYTCKPAHLEIMAPN----EI 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++F      V  L R+S G   L  +L  G  R +++  L
Sbjct: 175 RVTIQEGKFHQVKRMFAATGKTVIYLKRLSMGKLMLDESLGLGEYRSLTEDEL 227


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 88/235 (37%), Positives = 136/235 (57%), Gaps = 3/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AGIASRR+ E +I   +VKVNG+++      V   D I V+GV L+K E+ 
Sbjct: 2   ERLQKTIAKAGIASRRKAEELIVSGKVKVNGVVVTELGTQVSPDDDISVNGVVLKKEEK- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  ++++ SD  GR TV   L  +  R+  VGRLD +T G+LLLTNDG  A  
Sbjct: 61  VYYLLNKPRRVISSVSDEKGRETVLAYLSDVRERIYPVGRLDYDTSGILLLTNDGDFANA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTV 191
           +  PS+   + Y V   G +  D LN L +GI++        +V L  +  K +   + +
Sbjct: 121 MMHPSSHLPKTYEVAVTGVLTDDMLNRLARGIMLSDGKTLPAEVVLLERSTKKNKTVLHI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            ++EG+NRE++++ E+F+ +V RL RI YG   LG L  G  R++    +R+ L 
Sbjct: 181 TIQEGRNREVRRMMEYFHCEVTRLNRIGYGFLDLGNLRQGQYRKLRSFEVRKLLA 235


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 123/239 (51%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG  SRR  E +I + RV++NG ++      V    D I+V
Sbjct: 126 KTFPGAEQEGERLQKVLARAGFGSRRACEELIEEARVEINGEIVLEQGRRVDPEKDEIKV 185

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 186 DGLTV-ATQSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 244

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q
Sbjct: 245 LLTNHGELAHRLTHPKYGVKKTYLAHIVGPIPRDLGKQLKDGIQLEDGYARADHFRVVQQ 304

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 305 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 363


>gi|295105192|emb|CBL02736.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii SL3/3]
          Length = 233

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 111/232 (47%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + M+A+ RV+VNG + ++    +   D + VDG PLR  ++ 
Sbjct: 1   MRLDKYLAETAQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDNDTVTVDGAPLRY-QKF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DGG A
Sbjct: 60  VYLMLNKPEGVVSASTDKRD-TTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V     + Q+       G+ +  G      +VT  +  G    V 
Sbjct: 119 HDILSPRHHVSKTYTVTIDTPLTQEMRTGFAAGVTLADGTALSPAEVTALSPDG--CTVR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V LR+G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 177 VVLRQGVYHQIKRMFGVYGAGVNALHREAIGGLALDAQLAPGQWRELSDEEV 228


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 122/231 (52%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             +R+ KV+ARAG  SRR  E +I   RV+VNG ++    + V    D I+VDG+ +   
Sbjct: 113 EGERLQKVLARAGYGSRRACEELIEDARVEVNGEIVLEQGLRVDPENDEIKVDGLTV-AT 171

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  + +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 172 QSYQFFSLNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGEL 231

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +  Q G N  V 
Sbjct: 232 AHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYLVE 291

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   +
Sbjct: 292 VTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEV 342


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 117/237 (49%), Gaps = 4/237 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
           VQ++    R+++ I+ +GI SRR+ + +I    V VNG ++      +    D +  +G 
Sbjct: 230 VQKDDGLIRLNRYISNSGICSRRKADELIEAGVVSVNGEVVSELGHKIDPVKDQVRYNGE 289

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLL 124
            L++ E+    L +KP   +TT  DP  R TV   +      R+  VGRLD NT GLLL+
Sbjct: 290 LLKR-EKKIYVLLNKPKDYITTTDDPQERRTVMQLVEKASRERIYPVGRLDRNTTGLLLM 348

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  P     ++Y V     + Q  LN ++ G+ ++        V+  T  G
Sbjct: 349 TNDGDLADKLSHPKNGITKIYHVELSRSLSQGDLNKIQFGLELEDGIIKPDSVSYVTG-G 407

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           S   V + +  GKNR ++++FE   + V +L R+ YG      L  G  R + +  L
Sbjct: 408 SKREVGIQIHSGKNRIVRRIFEHLGYDVVKLDRVVYGNLTKKDLPRGRWRYLEEHEL 464


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 112/236 (47%), Gaps = 7/236 (2%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 62  IYVMM-NKPQGVLSATEDSR-QQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y VR    +  + +  L++G+VI+G        V   T+      +
Sbjct: 120 AHRLLSPKKHVPKTYEVRLTSPLSPEDIIDLERGVVIEGGYKTKPAAVKTITESPDETVI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K + +    +V  L R+S G   L   L  G  RE++++ L   
Sbjct: 180 HLTITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPELKPGEFRELTEEELAAL 235


>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 =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 110/233 (47%), Gaps = 5/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K IA     +R +  + I Q  VK+NG +++  +V +   D I  +   L   E  +
Sbjct: 4   RLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGSVQISQEDEIYFEDELLTWIEEGQ 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G V ++ D D   T++       + ++ S GRLD++T GL+LLT+DG  +  
Sbjct: 64  YFMLNKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGLVLLTDDGQWSHR 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V+++      +GI+++G         L+     N  V + +
Sbjct: 123 ITSPKHHCEKTYLVTLADPVEENYSAACAEGILLRGEKEPTKPAKLEILDDYN--VNLTI 180

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 181 SEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 233


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/233 (32%), Positives = 122/233 (52%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           +   +R+ KV+ARAG+ SRR  E +I   RV+VNG ++    V V    D I+VDG+ + 
Sbjct: 128 DQEGERLQKVLARAGMGSRRACEELIDAGRVEVNGKIVIEQGVRVDPEQDEIKVDGLTV- 186

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 187 ATQSHLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 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|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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 104/301 (34%), Positives = 149/301 (49%), Gaps = 13/301 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLR 68
            +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG      ++
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKIQ 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +    R+  Y+KP G + T  DP+GR TVFD LP I  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+    +S    R R   I        R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNKD-NTSRKRERARSQKIRR---AVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 P 304
           P
Sbjct: 298 P 298


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 125/242 (51%), Gaps = 7/242 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+ + +++ G+A+RR+ E +I    V VNG  +      V+   D + V G  +  
Sbjct: 2   DEAIRLQRYLSQCGVAARRKAEELITSGVVSVNGQRVTELGTKVVPGRDRVSVRGEAV-Y 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E     L +KP G +T  +DP+ R TV + L  + +RV+ VGRLD  +EG+LLLTNDG 
Sbjct: 61  PEEPFYVLLNKPKGCLTAVTDPENRPTVMEYLHGLPARVVPVGRLDFYSEGVLLLTNDGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNA- 187
           L+  L+ P     + Y V+   QV +  L +L++G+ ++        Q+ +     S   
Sbjct: 121 LSARLQSPRHHVEKTYHVKVRDQVTERHLEVLRQGVRLEDGTVTRPAQIDMLGGTKSRHD 180

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQ 244
           W+ + L EGK+R+I ++     + V +L R+++G      L  G  RE+++     LRE 
Sbjct: 181 WLVITLTEGKSRQIHRMLGVLGYTVMKLQRVAFGGLTFHGLRVGDARELTQAEVNDLREL 240

Query: 245 LG 246
           +G
Sbjct: 241 VG 242


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 73/295 (24%), Positives = 129/295 (43%), Gaps = 23/295 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E   
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGRLIEPREADD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +     L+E 
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLF--KLIEN 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVP---DDFTRMKKNSSQKNGLSKQKKLATP 304
           +         SSE   + RP   +  P       +M+ ++ +       K+   P
Sbjct: 239 S---------SSEAKPKARPKAKAATPGIKRPVVKMENSNDKGRPAGNGKRFTQP 284


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/240 (30%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  + 
Sbjct: 3   EKDIEMRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKIA 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTN 126
             ++   +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTN
Sbjct: 63  Y-QQYHYFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG LA  L  P+    +VYR +  G  D +      +G+++  G      ++ +  Q   
Sbjct: 121 DGALAHELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQD 180

Query: 186 N--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           N  + + + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+    ++
Sbjct: 181 NNLSQIEIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEIDLAEIK 240


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 121/244 (49%), Gaps = 7/244 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR---KA 70
           R++K IA AG+ SRR+ + +I Q  V+VNG +++     V+   D IEV G  L      
Sbjct: 7   RLNKAIAGAGVCSRRQADDLIQQGVVRVNGEVVDTPGARVVPGRDRIEVRGQLLELDAAP 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
                 + HKP+ +V+T  DP GR TV   LP      R+  VGRLD  +EGLL+LT+DG
Sbjct: 67  AAFTYVMLHKPVQVVSTVRDPQGRPTVLGILPPDLRGGRLYPVGRLDYFSEGLLILTDDG 126

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            L   L  P     +VY V+  G V +  L  +++G+ + +G     + V L       +
Sbjct: 127 DLTNRLTHPRYHLPKVYMVKVRGHVTESTLAPMRQGMTLAEGEKLAPVDVRLLQSDRQAS 186

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++       V  L R+  GP +LG L  G+ R ++   +      
Sbjct: 187 LFEMTLHQGVNRQIRRMCRDLGLTVLLLRRVRQGPLELGELPKGAARRLTPHEVAALRRA 246

Query: 248 HLLE 251
             LE
Sbjct: 247 AGLE 250


>gi|160881056|ref|YP_001560024.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429722|gb|ABX43285.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 477

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/352 (20%), Positives = 139/352 (39%), Gaps = 10/352 (2%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  +      R++K ++ +GI SRRE +  IA+  V ++G +       V+    + +  
Sbjct: 10  DTEETGEKAVRINKYLSESGICSRREADTRIAKGEVTIDGEVA-VMGSKVLPGQKVVLGK 68

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             + + E+  L  +HKP G+V T ++      + D +     R+  +GRLD ++EGL+ L
Sbjct: 69  KEVSREEKMVLIAFHKPKGIVCT-TEKREPDNIIDYI-KYSQRIYPIGRLDKDSEGLIFL 126

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TN+G +   +        + Y V  +  +    L  +  G+ I         +    +  
Sbjct: 127 TNNGDIVNKILRAGNHHEKEYIVTVNKPITAAFLKGMAGGVPILDTVTKPCTL----EAI 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL--- 241
                 + L +G NR+I+++ E F++KV +L+RI      LG L  G  R ++ K L   
Sbjct: 183 DKVTFRIILTQGLNRQIRRMCEHFDYKVTKLVRIRIMNVNLGRLKVGGYRNLTDKELEGI 242

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           +EQ+     E   +  D         V +             R  K+         +K+ 
Sbjct: 243 KEQIELSNNEALNLEPDDEFPIERVNVANIAKTHGNNVATGKRRTKDKYFAEKKDDKKRS 302

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAK 353
               ++  +       K   + F S +           SF   +   + S++
Sbjct: 303 DATRNKAEVNKFASKNKSEGNKFGSKNSSEGNKFGSKNSFEGNKFGSKNSSE 354


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 116/235 (49%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R+EV++ I Q +V VNG +++ A   +  T D + + G  +     
Sbjct: 2   MRLDKYLAEMGVGTRQEVKKQIRQGKVTVNGTVVKAADTKIDETCDEVTIGGRNISYV-S 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D    +TV D +     + +  VGRLD +TEGLLL+TNDG LA
Sbjct: 61  YEYYMLNKPGGVVSATEDRRD-TTVIDLIKDKKRKDLFPVGRLDKDTEGLLLITNDGDLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAW 188
             L  P     +VY  +  G V ++ +    +GI I   +       ++ +  +    + 
Sbjct: 120 HRLLAPKKHVDKVYYAKIDGMVTEEDVKRFAEGIDIGAEEEEMTRPAKLDIM-KSAEESE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + + EGK  ++K++F     +V  L R   GP  L   L  G  R ++++ + 
Sbjct: 179 IRLTIHEGKFHQVKRMFLAVGKEVTYLKRERMGPLCLDENLKPGEYRLLTEEEIE 233


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQIDEKIDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   DP  R TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYMMNKPKGVISATEDPKHR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A VL  P     + Y+ +  G + Q+ +    KGI ++       ++ + +   + + + 
Sbjct: 119 AHVLLSPKRHVDKTYQAQVKGIMTQEDVETFIKGIPLKDFTCQPARLEILSTDAEKNQSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + V + EGK  +IK++  +   +V  L R++ G   L   L  G  R ++K+ L 
Sbjct: 179 IRVTIAEGKFHQIKRMVGYCGKEVVDLQRLTMGTLVLDENLERGEWRRLTKEELE 233


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/243 (31%), Positives = 125/243 (51%), Gaps = 7/243 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K K   +++ T  R++K IA AGI+SRRE + +I    V VNG ++      V  TD + 
Sbjct: 53  KLKPAPKDDGT-IRLNKYIANAGISSRREADELILTGVVTVNGKVITEMGYKVQPTDEVR 111

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEG 120
            DG  +  AE+   ++ +KP G +TT  D   R TV D +     +R+  VGRLD  T G
Sbjct: 112 FDGKKIS-AEKNVYFILNKPKGYITTTKDEKNRQTVLDLMEGATTARIFPVGRLDRQTTG 170

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVT 178
           +LL TNDG L + L  PS    +VY V    ++    +  ++KGI +  +G+   D    
Sbjct: 171 VLLFTNDGFLTKKLTHPSHDVKKVYHVTLDRKLSSHDMAEIRKGIRLIPEGVATVDEVSF 230

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +D +   +  + + L  G NR ++++FE   ++V +L R+S+       L  G  R ++ 
Sbjct: 231 IDGR--PHNEIGLELHIGWNRVVRRIFESLGYQVEKLDRVSFAGLTKSKLRQGQYRALTP 288

Query: 239 KIL 241
           + +
Sbjct: 289 QEV 291


>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 =  254 bits (649), Expect = 2e-65,   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  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDI 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|288553832|ref|YP_003425767.1| pseudouridine synthase [Bacillus pseudofirmus OF4]
 gi|288544992|gb|ADC48875.1| pseudouridine synthase [Bacillus pseudofirmus OF4]
          Length = 233

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 114/225 (50%), Gaps = 8/225 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWLY 78
           ++  G  SR+EV++++    V++N  +++  +  V      + V G  +   +     + 
Sbjct: 2   LSNMGYGSRKEVKKVLKSGSVRINEKVIKDGSYKVDPDQSDVTVHGELVEY-KPYVYLML 60

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G+++   D +   TV D L   +       VGRLD +TEG+LLLTNDG  +  L  
Sbjct: 61  NKPQGVISATED-NHHKTVIDLLDESYLLYDPFPVGRLDKDTEGMLLLTNDGKFSHSLMS 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLRE 195
           P     + Y  +  G V ++ + L KKG+ +  G       +T+ T  G  + V + + E
Sbjct: 120 PKKHVKKTYYAKVKGTVTEEDIGLFKKGVTLDDGYVTKPADLTIITA-GEQSEVELTITE 178

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
           GK  ++K++FE  + KV  L RIS G  +L  +L  G  RE++++
Sbjct: 179 GKFHQVKRMFEAVDKKVTFLKRISIGGLKLDPSLEKGMVRELTEE 223


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 118/230 (51%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K++++AG+ASRR  E +I + RV+V+G  +    + V+ +  I V+G  +    
Sbjct: 40  EPVRLQKLLSQAGVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQRIHTDA 99

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++W ++KP+G V+T    D R  + D    +  RV  VGRLD+ T GL+LLTN+G LA
Sbjct: 100 ALQVWAFNKPVGTVSTMQPEDDRPCLGDWATKLPQRVFHVGRLDVATSGLILLTNNGDLA 159

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y     GQV      +L++G+ ++          L   +  ++ V +
Sbjct: 160 NRLVHPRYEVPKTYVAMVQGQVKPGLGKVLRRGVELEDGVTKVDTFKLVEVRRGSSIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L  GKNR ++++       V+ L R + G  +LG L  G  R ++   L
Sbjct: 220 TLHSGKNRVVRRLLSEVGHPVSALTRTAIGTLRLGDLKEGHFRLLTGSDL 269


>gi|328554622|gb|AEB25114.1| 16S pseudouridylate synthase [Bacillus amyloliquefaciens TA208]
          Length = 239

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 112/236 (47%), Gaps = 7/236 (2%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 61  IYVMM-NKPQGVLSATEDSR-QQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y VR    +  + +  L++G+VI+G        V   T+      +
Sbjct: 119 AHRLLSPKKHVPKTYEVRLTSPLSPEDIIDLERGVVIEGGYKTKPAAVKTITESPDETVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K + +    +V  L R+S G   L   L  G  RE++++ L   
Sbjct: 179 HLTITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPELKPGEFRELTEEELAAL 234


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/244 (32%), Positives = 126/244 (51%), Gaps = 2/244 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG  SRR  E +I Q RV+VNG ++    + V    D I+V
Sbjct: 110 KTFPGAEQEGERLQKVLARAGYGSRRSCEELIEQARVEVNGEIVLEQGLRVDPEKDEIKV 169

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  D +GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 170 DGLTV-ATQSYQFFSLNKPAGVVSTMEDTEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 228

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     +VY     G + +D    LK GI ++          +  Q
Sbjct: 229 LLTNHGELAHRLTHPKYGVKKVYLAHIVGPIPRDLGKRLKDGIQLEDGYAKADHFRVVEQ 288

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            G N  V V L EG+   ++++     + V++L+R+++GP  LG   +G  R +S   + 
Sbjct: 289 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRVAFGPITLGDQKSGWLRRLSNTEVG 348

Query: 243 EQLG 246
             +G
Sbjct: 349 MLMG 352


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSSSSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 86/291 (29%), Positives = 142/291 (48%), 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   ++ +KP G+VTT+ D  GR+ V D +P    RV +VGRLD  +EG
Sbjct: 82  RVDGEALRKPQRL-YFVVNKPEGVVTTNYDQAGRTRVIDLVP-TDERVFAVGRLDRASEG 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


>gi|297585561|ref|YP_003701341.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297144018|gb|ADI00776.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 237

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 113/231 (48%), Gaps = 8/231 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRR  +++I + +V +NG   +     V   D + V+G P+   +   
Sbjct: 4   RINKYVSETGKTSRRGADKLIQEGKVTINGKPAQ-LGDQVEPGDDVIVNGEPVHIVKENV 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
               +KP+G+ +T ++   +  + D +     R+  +GRLD ++EGL+LLTNDG +   +
Sbjct: 63  YIALNKPVGITST-TERKVKGNIIDLVNHPL-RIFHIGRLDKDSEGLILLTNDGDIVNEI 120

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V  +  +  + L  + +G+ I        +V     K S     + L 
Sbjct: 121 LRAENKHEKEYIVTVNKPITPEFLKQMSEGVDILDTTTLPCKVK----KLSKYEFNITLT 176

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ +   + V RL+R       LG L  G  R++SKK  R QL
Sbjct: 177 QGLNRQIRRMCDALGYDVQRLLRTRIMNIHLGKLPPGQWRDLSKKE-RTQL 226


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 107/310 (34%), Positives = 151/310 (48%), Gaps = 11/310 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKK---ILRE 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  AP  ++    R R   I             +  ++G S ++K   
Sbjct: 242 LVELRPEKETVLN-TAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGRSG-SARRKPGG 299

Query: 304 PVHRRNLASN 313
               RN  +N
Sbjct: 300 ESSTRNKVAN 309


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 96/348 (27%), Positives = 158/348 (45%), Gaps = 18/348 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              +  PQR+ K++A AG+ SRRE+E +I   R+ +NG + E  A  V   D +  D  P
Sbjct: 22  TDPDAVPQRLHKLLALAGLGSRREMEELILSGRITINGKVAEVGAAVV-PGDVVRFDSRP 80

Query: 67  LRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
           +      E  ++ +YHKP G + +  DP+ R+TVFD LP    ++ I++GRLDINT GLL
Sbjct: 81  VHLPFEAELAQVLIYHKPEGEIVSQDDPEKRATVFDKLPRVRGAKWIAIGRLDINTSGLL 140

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T  G LA     P  +  R Y VR  G++ + ++  L +GI ++        +     
Sbjct: 141 IFTTSGELANRFMHPRYEVEREYAVRIFGELTEGEMLQLTQGIELEDGPASFDSIRPQGG 200

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           +G+N W  V LREG+NRE++++F+ F   V+RL+R+ +GP  L   L  G    +  K +
Sbjct: 201 EGANHWYQVILREGRNREVRRLFDAFQKPVSRLMRVRFGPVNLPPRLKRGQMLNLDPKEV 260

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDR------PNIISEVPDDFTRMKKNSSQKNGL 295
              L    L   +    AP+       +++      P      P+   R +  + +    
Sbjct: 261 LGLLEWAGLPLPK----APLRQRTAREKEKAGQVFTPKARRAAPEREPRAEGTTGRPAYG 316

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           ++         R+   S         S  +           R P+   
Sbjct: 317 ARPDAAGRADGRKTSTSPARKP--AQSRRIRQDADIPAPRSRRPATKR 362


>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 =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 105/301 (34%), Positives = 147/301 (48%), Gaps = 13/301 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG++ +        +  + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGVVAKLGERLEDESSVVRIDGHIVSAKVQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---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     +S    R R   I        R ++  S   G S       
Sbjct: 242 LVELRPEKETMLDLSKD-NTSRKRERARSQKIRR---AVKRHEERVSTSKGRSNNPARRK 297

Query: 304 P 304
           P
Sbjct: 298 P 298


>gi|163857448|ref|YP_001631746.1| pseudouridine synthase [Bordetella petrii DSM 12804]
 gi|163261176|emb|CAP43478.1| pseudouridine synthase [Bordetella petrii]
          Length = 588

 Score =  254 bits (649), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 95/304 (31%), Positives = 145/304 (47%), Gaps = 6/304 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---E 71
           ++ KV+A AGI SRRE+E +I   RV VNG         V  +D + V+G P+ +    +
Sbjct: 124 KLHKVLADAGIGSRREMEELITAGRVSVNGEPA-HIGQRVAPSDQVRVNGKPVARPNTKK 182

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
             R+ LYHKP G + +H DP GR++VF  LP + + + +SVGRLD+NTEGLL+ T  G +
Sbjct: 183 PPRVILYHKPAGEIVSHDDPGGRASVFARLPKLRTGKWLSVGRLDLNTEGLLIFTTSGDM 242

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P     R Y VR  G++D      L +GI ++        +      GSN W  
Sbjct: 243 ANRIMHPRYGTEREYAVRVLGEMDDATRKSLVEGIELEDGQAAFGALDYLGGDGSNRWYR 302

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           V L+EG+NRE++++FE     V+RLIR  +G   L  TL  G   E+   ++   +    
Sbjct: 303 VTLQEGRNREVRRMFESVGVTVSRLIRTRFGDLVLPRTLRRGRWEELDSSLVTALMVQLG 362

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           L     + D    + +    D          D   M      + G  +     +  H  +
Sbjct: 363 LLRDDDDADGGRNARQPRSHDSALPPGFGTMDRNGMNGARIGRRGKLQGGGPGSAGHVAS 422

Query: 310 LASN 313
             S+
Sbjct: 423 SPSD 426


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 80/240 (33%), Positives = 124/240 (51%), Gaps = 11/240 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR---- 68
            R++K +A AG+ SRR+ + ++    V VNGI      + V    D + V G P+     
Sbjct: 1   MRLNKALAMAGVCSRRKADELVFAGNVAVNGITASSPGIQVDPQNDIVTVFGKPVAFLPQ 60

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLL 124
             +A     ++ +KP+ +VTT SDP GR TV + LP      RV  VGRLD  +EGLLLL
Sbjct: 61  EGQATEHAYYMLNKPVEVVTTASDPQGRRTVLEILPEEVRKRRVFPVGRLDFFSEGLLLL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVT-LDTQ 182
           T+DG L   +  P     +VY V   G+V +DKL  +++G+ + +G     ++V  LD Q
Sbjct: 121 TSDGDLTYRMTHPRYHLPKVYEVLVRGEVTRDKLEAMRRGMTLAEGEKLAPVEVKVLDKQ 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 + + L +G NR+I+++       V +L R   GP  LG L  G  R ++   ++
Sbjct: 181 MLGKTLLELTLIQGINRQIRRMCRDLGLTVLKLRRTCEGPLSLGALPTGKLRTLTPAEVK 240


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 102/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++ +  V V+ ++ +  A  +  T  +E     +      
Sbjct: 1   MRLDKFLCDALGTTRKEATQLLKRGEVTVDDVVQKSGAFKLKETSRVEWQDREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D      KGI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQGDYAEQFTKGIELRGERELTLPAQLEV--VSETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  +L  G  R +++  +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDESLEPGEYRYLTEDEV 226


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 73/328 (22%), Positives = 133/328 (40%), Gaps = 20/328 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V++NG         V+ TD + V+G  +     E 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVRINGKRA-SVGDQVLPTDTVMVNGQIIEPRAEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T +D   R  +   +     R+  +GRLD +++GL+ +T++G L  
Sbjct: 67  QVFIALNKPVGIVST-TDSAERDNIQRFV-GHTVRIFPIGRLDKDSQGLIFMTSNGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     + +  ++ +  G+ I G      +V+    + S     + 
Sbjct: 125 KILRAGNNHEKEYLVTVDKPITKTFIDGMAGGVPILGTVTKKCRVS----QESRFVFRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F + V RL R       LG L  G  R+++ K L   L   + + 
Sbjct: 181 LVQGLNRQIRRMAEHFGFDVTRLERQRIMNISLGNLPVGQWRDLTSKEL-AVLMDSIRDS 239

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +     AP   +                      K   +    S  +    P +R     
Sbjct: 240 SSDAPAAPQKPAGKTKPANAPAQKRESHKPRAGNKTPPRPGAKSAGQPGGRPDNR----- 294

Query: 313 NVWMAKGIHSSFLSDSGQREENHRRSPS 340
                 G   +    S  +++  R +  
Sbjct: 295 -----PGSKPAARPKSKPKKQRQRSTKR 317


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 112/231 (48%), Gaps = 7/231 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKAVKGNIIDLVNHPL-RINHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  + L  +  G+ I        +VT    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPEFLEKMAAGVKILDTKTLPCEVT----QLSKYEFQIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ E   ++V  L R      +L  L  G  R++SKK  +   
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQWRDLSKKEKKRLF 228


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 113/239 (47%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
           +    R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      I VDG  + 
Sbjct: 3   DNDGIRLQKVLSQAGIASRRVAEKMIRDGRVEVDGRIVTELGTRVDPAASVIRVDGARIT 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             +       +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGLLLLT
Sbjct: 63  VDDTLVYLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G V +     L++G+ ++          +      
Sbjct: 123 NDGELAHRLMHPSFEVPKSYVATVLGSVPKGLGRKLREGVELEDGPVQVDDFAVVDTTPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L EG+   ++++     + V  L+R   G   LG    GS R +++K + E 
Sbjct: 183 RTLVRVTLHEGRKHIVRRLLAEVGFPVQELVRTDIGTVSLGDQRPGSIRVLTQKEIGEL 241


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 93/295 (31%), Positives = 144/295 (48%), Gaps = 14/295 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       + +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-NLGDRIEADVKIRIDGRAISIKSA 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
              L+E        +  ++     R  +         R  +          +K+ 
Sbjct: 241 TAGLKEETRT----VLGTDKHSVARSKVKG---SKIRRAVRKHKAVASKPGRKRT 288


>gi|328881450|emb|CCA54689.1| Ribosomal large subunit pseudouridine synthase B [Streptomyces
           venezuelae ATCC 10712]
          Length = 453

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 121/239 (50%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++      V    D I+V
Sbjct: 207 KTFPGAEQEGERLQKVLARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEIKV 266

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++
Sbjct: 267 DGLTV-ATQSYLFFALNKPSGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGII 325

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + ++    LK GI ++          +  Q
Sbjct: 326 LLTNHGELAHRLTHPKYGVKKTYLAAITGPLPREVGKRLKDGIQLEDGYARADHFRVVEQ 385

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V +L+R ++GP  LG   +G  R ++   +
Sbjct: 386 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVEKLVRTAFGPIALGDQKSGWLRRLTNTEV 444


>gi|322434202|ref|YP_004216414.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
 gi|321161929|gb|ADW67634.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX9]
          Length = 312

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 139/286 (48%), Gaps = 24/286 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           +R+ K++A+AG+ASRR+ E +I   RV+VNG ++        +T DHI VDG  ++  E+
Sbjct: 24  ERLQKILAQAGLASRRKAEEIILDGRVQVNGTVVTELGTRADATKDHIRVDGKLIKGPEQ 83

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTN 126
            + ++ +KP G VTT  DP  R TV   +           R+  VGRLD  +EGLLL+TN
Sbjct: 84  QKYYMVNKPRGYVTTLDDPQHRPTVMQLMTPKSGPHETQVRLYPVGRLDYLSEGLLLMTN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-------------YG 173
           DG LA  L   ST   + Y V+  G      L+ +++GI+I                   
Sbjct: 144 DGDLANALSKASTGVEKTYLVKTSGVPPDSALDQIRRGIMIDRGRLDEVRAGRRDRILTA 203

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V L  ++G N W  V L EG+NR+++K+FE     V ++ RI YG  +L  +  G  
Sbjct: 204 PAKVEL-VRRGDNPWYEVTLTEGRNRQLRKMFEEVGHHVEKIRRIGYGALRL-DVAPGEF 261

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYS--SETLVRDRPNIISE 277
           RE+    +         ++ +   + P +S     +   RP     
Sbjct: 262 RELKPGEVMALDRASKGKKVEPKRNLPEFSKLKAPVKPKRPGAGKS 307


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 69/292 (23%), Positives = 127/292 (43%), Gaps = 12/292 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     E 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRA-SVGAQVFAGDEVKVNGQLIEPRDEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ + G            +K S     + 
Sbjct: 125 KILRAGNNHEKEYVVTVDKPITDEFITGMGAGVPMLGTVTK----KCKVKKESTFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMTKHFGYEVTKLERTRIMNVNLKGLPLGEWRDLTDDELIELF--KLIEN 238

Query: 253 AQV-NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +   +  A    ++T    +P        +       S ++     +KK   
Sbjct: 239 SSSEDKPAKKGQAKTTPAKKPAASGAKTSEKPNANPASRKRFTQPGRKKKGR 290


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 100/230 (43%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+GI+ +  +  V     +E  G  L  +   
Sbjct: 1   MRLDKFLCDALGTTRKESTQLLKSGDVTVDGIVRKSGSCQVTELSQVEWQGRALTLS-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G V +H D     T F  L     R +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLHKPQGYVCSHEDSFN-QTAFVLLDEANQRDLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + YRV     +  +      KGI ++G         L+        V + 
Sbjct: 119 RVTSPKHHCEKTYRVWLADPIAAEYTEQFAKGIELRGERDLTRPAQLEI--IDQQQVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L   L  G +R +++  +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVVGLHRERVGDIVLDPGLEPGESRYLTESEI 226


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 111/232 (47%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++  + V VNG L ++   +V    D + V G  +   E 
Sbjct: 1   MRLDKLLASSGFGSRKDVKKLVKARAVTVNGELAKQVKDHVDPSNDEVLVHGERVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G+++   D    + V    P   +R    VGRLD +T GLLLLTNDG LA
Sbjct: 60  FIYLMMNKPDGVISATEDLRDETVVDLLEPEDIAREPFPVGRLDKDTVGLLLLTNDGQLA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V     +    +  L++G+V +        +V +D  +  +  + 
Sbjct: 120 HQLLSPKKHVPKTYEVHLKYPLGDQDIKRLEEGVVILDDYRTKPAKVEVDANESEDTRIR 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K + +    +V  L R S G   L   L  G  RE++ + L
Sbjct: 180 LTITEGKYHQVKLMAQAVGNEVIFLKRRSMGAVSLDEDLAPGEYRELTDEEL 231


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 114/238 (47%), Gaps = 6/238 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E   P R+   +A +   +R+E +++I+   V V      +A + +     + + G  ++
Sbjct: 10  ETVLPMRLDYFLAHSAGLTRKEAKKLISGGAVTVADEAKPKANLQLRPDQVVMLHGEVVQ 69

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R  + HKP+ +V +  DP+ R TV D LP++   +V   GRLD +T GL+LLT+D
Sbjct: 70  LP-GHRYLMLHKPVDVVCSTDDPEHR-TVLDLLPAVLRTQVHPAGRLDRDTTGLVLLTSD 127

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  +  L  P+    + YRV     V  + L  L++GI+++G     +      ++ +  
Sbjct: 128 GQWSHRLTSPNHACGKCYRVICADPVSDEDLQALREGILLRGEDSPTLPA--LAERVNTH 185

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + + EG+  ++K++      KV  L R   G   L   L  G  R ++++ +R  
Sbjct: 186 TLRLTITEGRYHQVKRMLAARGNKVVGLHREQIGDIVLDADLAPGEFRALTEEEIRSL 243


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/229 (33%), Positives = 118/229 (51%), Gaps = 2/229 (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      V D +    +RV  VGRLD ++ GLL+LTNDG L   
Sbjct: 61  IYIAINKPIGYTSTVKDKFADKKVVDLI-KFKTRVYPVGRLDKDSHGLLILTNDGELTYE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY V   G+  +DK+  LK GIV+ G       +        N    V +
Sbjct: 120 LTHPKFEHKKVYEVLVKGRPTKDKIQELKNGIVLDGYKLKKSSIEFIANVKDNTKYMVTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EG+NR+I+K+F++ N  V  L R+  G +++   L +G    +  + L
Sbjct: 180 YEGRNRQIRKMFDYINHPVLDLKRVQIGYYKMEDNLKSGEYVLLKNEDL 228


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 142/328 (43%), Gaps = 21/328 (6%)

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 ++   +  + D +     R+  +GRLD  +EGL+LL
Sbjct: 61  GSAPGKSDRVYIAYNKPVGITCT-TERSVQGNIVDAI-DHHQRIFPIGRLDKPSEGLILL 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 LGPHLLEEAQVNLDAPIYSSETLVRDR-PNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                +  +      P  SS++  + R P    +      +  + S++    S + K + 
Sbjct: 235 ----NIAISGSTGSPPKKSSQSAAKKRKPQHRLKGTGSDAKPARKSTKSRHSSSKNKDSG 290

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQR 331
              RR+         G   S  S   ++
Sbjct: 291 SDSRRSARK-----PGSRKSPTSSKRRK 313


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 88/341 (25%), Positives = 151/341 (44%), Gaps = 10/341 (2%)

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+  +P +   +  VGRLD ++EGLLLLTNDG L   
Sbjct: 60  VVIALHKPVGVTTTKSDPHAERTVYQLVPDV-PGLHPVGRLDKDSEGLLLLTNDGDLTLK 118

Query: 134 LELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     +VYR    HG+V +     L +G+ +       ++    TQ+G+     + 
Sbjct: 119 LTHPRYGVRKVYRAWCKHGRVSEADCRRLVEGVALDDGLAQALEAE-PTQEGA----RIV 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           + EGK RE++++     + V RL+R+  GP +LG L  G  R ++ + +    G   L+ 
Sbjct: 174 MAEGKKREVRRMLGRLGYPVTRLVRLQVGPIKLGKLNPGEWRYLTPEEIGLLQGQKPLKP 233

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH--RRNL 310
            +    A    ++   +   +   + P    + +   + +         A      R   
Sbjct: 234 RKKEGWAKAKPAKFAQQREESRAIKPPSRTEQGRAGFTVRTKSPGDTPQAGTDRWARWAR 293

Query: 311 ASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
            S+    +           Q +      P     +S   T 
Sbjct: 294 ESDRSAQRSGRWGTSRRPYQGKRTAELEPKGLGSKSTSSTK 334


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG + +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRVEKSPKTQIDETADEIVVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q        GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQTDEERFAAGIELKDFTCQPAQLKILELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ GP Q    L  G  R +++  +
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQSDPALALGEWRRLTEVEM 232


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 116/235 (49%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG L+      V  TD + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTIPKQQVKETDLVAVDGNKIAY-QQY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTNDG LA
Sbjct: 60  HYFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKDTTGLLLLTNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AW 188
             L  P+    +VYR +  G  D +      +G+++  G      ++ +  Q   N  + 
Sbjct: 119 HELLAPNKHVAKVYRAKIAGVPDPETAKKFAQGLILGDGTKLKPAKLKILKQDQDNNLSQ 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + ++EGK  +IK++F     KV  L R+S G   L   L  G  +E+    ++
Sbjct: 179 IEIQIQEGKYHQIKRMFGAVGMKVLELDRVSMGKLHLPADLKRGEYKEIDLAEIK 233


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/240 (32%), Positives = 115/240 (47%), Gaps = 6/240 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
           +    R+ KV+++AGIASRR  E++I   RV+V+G ++      V      I VDG  + 
Sbjct: 3   DTEGIRLQKVLSQAGIASRRAAEKLIIDGRVEVDGRVVTELGTRVDPDASVIRVDGARVV 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             E       +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLT
Sbjct: 63  LDESLVYLALNKPRGMHSTMSDDRGRPCIGDLVERKVRGNKNLFHVGRLDADTEGLILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKG 184
           NDG LA  L  PS +  + Y     G V +     LK GI +       D    +D   G
Sbjct: 123 NDGELAHRLMHPSHEVPKTYLATVTGSVPRGIGKKLKAGIELDDGPARVDDFAVVDAIPG 182

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V V L EG+NR ++++     + V  L+R   GP  LG    GS R +++  + + 
Sbjct: 183 KT-LVRVVLHEGRNRIVRRLLGAAGFPVEALVRTDIGPVSLGKQRPGSIRALNQGEVGQL 241


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATEDSRHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +  +  S + 
Sbjct: 119 AHAMLSPKRHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           V + + EGK  ++K++      +V  L R+  GP  L   L  G  R ++++ L
Sbjct: 179 VQITIAEGKFHQVKRMVAACGKEVADLQRLKMGPLSLPNDLELGDWRRLTQEEL 232


>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 =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 121/231 (52%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             +R+ KV+ARAG  SRR  E +I Q RV+VNG ++      V    D ++VDG+ +   
Sbjct: 121 EGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGKRVDPEKDEVKVDGLTV-AT 179

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 180 QSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVILLTNHGEL 239

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +  Q G N  V 
Sbjct: 240 AHRLTHPKYGVKKTYLAAIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQTGKNYLVE 299

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 300 VTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 350


>gi|195952397|ref|YP_002120687.1| pseudouridine synthase [Hydrogenobaculum sp. Y04AAS1]
 gi|195932009|gb|ACG56709.1| pseudouridine synthase [Hydrogenobaculum sp. Y04AAS1]
          Length = 239

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 117/230 (50%), Gaps = 2/230 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+++ ++ AG+ SRR+ +  I +  VKVN  +++     +    D +E  G  + KA++
Sbjct: 1   MRLNRFLSLAGVCSRRKADEYIEKGYVKVNNNIVKELGTTINPDEDIVEFRGR-IVKAQK 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|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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 73/289 (25%), Positives = 127/289 (43%), Gaps = 10/289 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E   
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGRLIEPREADD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +         
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIENSS 240

Query: 253 AQVNLDA-PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++    A P   + T    RP +  E  +D  R   N  +     ++KK
Sbjct: 241 SEAKPKARPKAKAATPGIKRPVVKMENSNDKGRPAGNGKRFTQPGRKKK 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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

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    + ++ +     +  +R+  +GRLD ++EGLLL+TN+G + 
Sbjct: 73  RMVLLAVNKPTGIVCTEEKREKKNIIRFL--NYPTRITYIGRLDKDSEGLLLMTNNGDII 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y+V  + +V ++ +  + +G+ I        +V    +K       +
Sbjct: 131 NKMMRAGNCHEKEYKVTVNKEVTKEFVRKMSEGVPILDTVTRPCKV----EKTGKYKFRI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L +G NR+I+++ E+F ++V RL R+     +LG L +G  REV+ + L E 
Sbjct: 187 ILTQGLNRQIRRMCEYFGYQVTRLERVRVMNIELGNLKSGEYREVTGRELDEL 239


>gi|205374821|ref|ZP_03227614.1| tRNA pseudouridine synthase A [Bacillus coahuilensis m4-4]
          Length = 235

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 118/236 (50%), Gaps = 8/236 (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 ++   +  + D +     R+ ++GRLD  ++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITST-TEKGVKGNIIDLVNHPL-RIFNIGRLDKESDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     + Q+ L+ +  G+ I G      ++    ++ S     + L
Sbjct: 118 ILRAENKHEKEYFVSVDKPITQEFLDNMASGVKILGTKTLPCKI----EQISKYDFQITL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            +G NR+I+++ E   ++V RL R       LG L  G  R++SKK  + QL   L
Sbjct: 174 TQGLNRQIRRMCEALGYEVYRLQRTRIMNIHLGNLPVGQWRDLSKKE-KTQLFKEL 228


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 86/244 (35%), Positives = 128/244 (52%), Gaps = 6/244 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
                  R+ K++AR G+ SRRE+E MIA  RV +N    +         D I +DG  +
Sbjct: 27  APPAETDRLQKLLARNGLGSRREIEAMIAAGRVSINNTTAK-LGDRAGLGDKIRIDGRII 85

Query: 68  RKAER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
           R +      R+ +YHKP G + +  DP GR +VFD LP    S+ I++GRLD NT GLL+
Sbjct: 86  RLSMPALLPRIIIYHKPEGEIVSARDPQGRLSVFDKLPHIQSSKWIAIGRLDFNTSGLLI 145

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T DG LA  L  P  Q  R Y VR  G++  +++  L  GI ++       Q+  +   
Sbjct: 146 FTTDGALANRLMHPRYQMEREYAVRIVGELSPEQITHLTTGIELEDGSAKFDQLLDEGGL 205

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           G+N W  + L+EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E+    + 
Sbjct: 206 GTNHWYRIVLKEGRNREVRRMFEALGITVSRLMRVRFGPVNLPPRLKRGMWLELVDTEVE 265

Query: 243 EQLG 246
             L 
Sbjct: 266 RLLA 269


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 90/259 (34%), Positives = 139/259 (53%), Gaps = 7/259 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
           P+R+ K++A++GI SRRE+E +IA  R+ +NG           + D ++V+G  ++    
Sbjct: 66  PERLHKLLAQSGIGSRREMEELIAAGRISINGETA-SVGQTASAGDRVKVNGKLVQLRFS 124

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
               R+ LYHKP G + + +DP+ R  VF ++P I + R ++VGRLD NT GLLLLT  G
Sbjct: 125 DRLPRVILYHKPEGEIVSRNDPEHRPNVFTSMPRISAGRWVAVGRLDFNTSGLLLLTTSG 184

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA  L  P  Q +R Y VR  G++ ++    L  GI +               +G+N W
Sbjct: 185 DLANRLMHPRYQLVREYAVRILGELTEEVRRQLLDGIDLDDGPAQFASFQEAGGEGANRW 244

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
             V L EG+NRE++++FE     V+RL+R+ YGPF L   L  G   E+S+  +++ L  
Sbjct: 245 YRVSLHEGRNREVRRMFEAVGVVVSRLMRVRYGPFALPPGLKRGQVLELSEADVKKLLAD 304

Query: 248 HLLEEAQVNLDAPIYSSET 266
             +   +    AP    E 
Sbjct: 305 FGMANPEAGR-APRRPRER 322


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 95/349 (27%), Positives = 152/349 (43%), Gaps = 13/349 (3%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            + +  E+  P ++ KV+A AG+ SRR++E +I   RV VNG         ++ TD + +
Sbjct: 164 RRELTAEDDAP-KLHKVLADAGLGSRRDMEELIVAGRVSVNGEPA-HIGQRILPTDQVRL 221

Query: 63  DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINT 118
           +G  +++       R+  YHKP G + +  DP+ R +VFD LP    S+ ++VGRLD NT
Sbjct: 222 NGKLIQRKIAKSLPRVLTYHKPAGEIVSRDDPEKRPSVFDRLPLLKNSKWLAVGRLDFNT 281

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL TN G LA  L  P     R Y VR  G++++     L  G+ +        ++ 
Sbjct: 282 EGLLLFTNSGDLANRLMHPRYNIEREYAVRTLGELEEGMRQKLLAGVDLGDGIGQFSKIV 341

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
               +G N W  V + EG+NRE++++FE     V+RLIR  YG   L  +L  G   E+ 
Sbjct: 342 DGGGEGVNKWYRVTIGEGRNREVRRMFEAVGLTVSRLIRTRYGAVVLSQSLKRGRWDELE 401

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR------MKKNSSQ 291
           +  +R  L    L+            S       P+                  +K S  
Sbjct: 402 ENAVRNLLRLSGLDNKDDKKTQGKTRSRNASGQYPDFPKSQSLSIRELQLQGQHQKKSPG 461

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
               S + +   P+      + +        +     G+ +   RR   
Sbjct: 462 GQKGSPRNRQPDPLQTAFGYAGMGQNPPKGGTGQRARGRGQPGQRRRAR 510


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 106/309 (34%), Positives = 151/309 (48%), Gaps = 10/309 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKK---ILRE 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  AP  ++    R R   I             +  ++G +++K    
Sbjct: 242 LVELRPEKETVLN-TAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGRSGSARRKPGGE 300

Query: 304 PVHRRNLAS 312
              R  +AS
Sbjct: 301 SSTRNKVAS 309


>gi|332993044|gb|AEF03099.1| RNA pseudouridine synthase family protein [Alteromonas sp. SN2]
          Length = 246

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 115/234 (49%), Gaps = 11/234 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+  G+ SRRE +++I Q RV +N  L       V   D ++VDG  ++     +
Sbjct: 8   RLNKYISDTGLCSRREADKLIEQNRVTINDKLP-ELGTKVAQGDKVKVDGKLVKAVAEDK 66

Query: 75  ----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 +Y+KPIG+  T ++   +  + D +     R+  VGRLD  +EGL++LT+DG +
Sbjct: 67  SDRIYLVYNKPIGITCT-TERHVKGNIIDAI-KHKQRIFPVGRLDKPSEGLIILTSDGDI 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  + +  +  + KG+ I G      +V    +       +
Sbjct: 125 VNKILRAENSHDKEYEVTVNQPISERFVQKMAKGVPILGTVTKPCKVNARGK----FQFS 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + L +G NR+I+++ EF  ++V +L R      +LG L  G  R +++K L + 
Sbjct: 181 IILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELGNLKPGQWRNLTEKELNQL 234


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 110/301 (36%), Positives = 159/301 (52%), Gaps = 22/301 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+ARAG  SRR +E MI Q+R+ ++G +      V+V  +  I +DG  L   E
Sbjct: 2   SEKLQKVLARAGHGSRRAIETMIMQRRISLDGKIATLGDRVDVRQSTKIRLDGRVLAITE 61

Query: 72  R----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T  DP GR TVFD LP    SR ++VGRLD+NT GLLL T 
Sbjct: 62  SNAAICRVLAYYKPEGELCTLHDPQGRPTVFDRLPKLRTSRWVAVGRLDVNTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P  +  R Y VR  GQ+D+DK+  L KGI ++       +++    +G N
Sbjct: 122 DGELANRLMHPRHEVEREYAVRVFGQIDEDKIKQLNKGIQLEDGPASFHKISFQGGEGIN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILR 242
            W  V L EG+NRE+++++E  + KVNRLIRI YG   L   L  G   E+  K    LR
Sbjct: 182 QWYHVTLTEGRNREVRRLWEAVDVKVNRLIRIRYGDINLPKGLPRGGWTELDLKAINYLR 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           E           V+L A   S   + ++R  + +        +K++S +K   ++Q K  
Sbjct: 242 EL----------VSLPAETVSKLPVEQERRRMKAN--QIRRAVKRHSEKKRADTRQIKKR 289

Query: 303 T 303
            
Sbjct: 290 R 290


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 99/290 (34%), Positives = 145/290 (50%), Gaps = 12/290 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       + +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-SLGDRIEADAKIRIDGRAISIKSE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVTLSEGRNREVRRLWESQEVQVSRLIRIRYGSIELPKSLPRGGWIELELEQVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             G  +  E +  L    +S          I   V        KN+ Q+ 
Sbjct: 241 TAGLDI--ENRTMLGTDKHSVARSKVKSAKIKRAVHKHKATGGKNTRQRT 288


>gi|315617385|gb|EFU97991.1| ribosomal large subunit pseudouridine synthase F [Escherichia coli
           3431]
          Length = 290

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 127/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D  GR  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTED-GGRDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     + ++ +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/240 (33%), Positives = 125/240 (52%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           +V +N   +R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDG
Sbjct: 39  LVGDNPKGERLQKVLAKAGVASRRHAEIMIDAGRVEVNGKIVMQQGVRVDPNVDVIRVDG 98

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 121
           V +   E TR ++ +KP GL +T SD  GR  + D +        R+  VGRLD +TEGL
Sbjct: 99  VRINVNEETRYFILNKPRGLQSTMSDELGRPCIGDLIGDRVAAGQRLFHVGRLDADTEGL 158

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +L+TNDG LA  L  P  +  + Y     G+     +  LK+G+ ++        V +  
Sbjct: 159 ILITNDGELANRLMHPKYEVRKTYLATVLGEAGNGLVRTLKEGVELEDGLAKADYVQIVD 218

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +    + V V L EG+   ++++ +   + V RL+R      QLG +  G  R ++   L
Sbjct: 219 KNQGYSLVRVELHEGRKHIVRRMLKEAGFPVQRLVRTKLHTLQLGEMKPGILRALNSNEL 278


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 73/289 (25%), Positives = 127/289 (43%), Gaps = 10/289 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E   
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDLVKVNGRLIEPREADD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +         
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLTGIPLGEWRDLTDDELIDLFKLIENSS 240

Query: 253 AQVNLDA-PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           ++    A P   + T    RP +  E  +D  R   N  +     ++KK
Sbjct: 241 SEAKPKARPKAKAATPGIKRPVVKMENSNDKGRPAANGKRFTQPGRKKK 289


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 120/231 (51%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             +R+ KV+ARAG+ SRR  E +I   RV+VNG ++    V V    D I+VDG+ +   
Sbjct: 138 EGERLQKVLARAGVGSRRACEELIEAGRVEVNGSIVIEQGVRVDPENDEIKVDGLTV-AT 196

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 197 QSYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGEL 256

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + ++    LK GI ++          +    G N  V 
Sbjct: 257 AHRLTHPRYGVKKTYLAAIQGPLPRELGKRLKDGIALEDGYARADHFRVVENTGKNYLVE 316

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V+RL+R ++GP  LG   +G  R +S   +
Sbjct: 317 VTLHEGRKHIVRRMLAEAGFPVDRLVRTAFGPIGLGDQKSGWLRRLSNTEV 367


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 114/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVNGEEIAY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  ++ VGRLD +T GLLLLTNDG L 
Sbjct: 60  HYFLLNKPKGVLSATED-RSQKTVISLLDPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAW 188
             L  P+    +VYR    G  D++       G+++  G      ++ +  Q  + + + 
Sbjct: 119 HELVAPNKHVAKVYRAEIAGVADEETAKAFASGMMLGDGTKLKPAKLKILKQDRENATSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + + + EGK  +IK++F     KV  L R+S G   L   L  G   E+S   ++
Sbjct: 179 IEIEISEGKYHQIKRMFGAVGMKVTALDRLSMGNLHLQSDLKRGKYVELSLDEIK 233


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 82/243 (33%), Positives = 126/243 (51%), Gaps = 14/243 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
           + QR+ KV+ARAG+ASRR  E++IA+ RV+V+G L+    V V   T  +EVDG  +   
Sbjct: 17  SAQRLHKVLARAGVASRRGSEQLIAEGRVRVDGRLVTEQGVLVDPHTAVVEVDGKRIAVD 76

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------------VISVGRLDINT 118
           +R   +  +KP G++T  SD   R  V D L                  +  VGRLD +T
Sbjct: 77  DRHATYALNKPKGVLTAMSDTRER-CVGDLLREAGPDFAADGRAGLPAGLFHVGRLDADT 135

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLL++NDG LA  L  PS +  + Y     G V +  +  L+ G+V++       +V 
Sbjct: 136 TGLLLVSNDGELAHRLAHPSYEIPKTYIATVRGVVAKRAVEQLRAGVVLEDGPAKADEVC 195

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L   +     V + L EG+NR ++++F+     V  L R+  GP +LG L +G+ R +S 
Sbjct: 196 LRGSQRDRTVVEITLHEGRNRIVRRMFDEVGHPVIELARLRIGPIRLGDLRSGALRALSS 255

Query: 239 KIL 241
             +
Sbjct: 256 SEV 258


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 122/239 (51%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG  SRR  E +I Q RV+VNG ++      V    D ++V
Sbjct: 101 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEVNGEIVLEQGRRVDPEKDEVKV 160

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 161 DGLTV-ATQSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 219

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q
Sbjct: 220 LLTNHGELAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQ 279

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V++L+R ++GP  LG   +G  R +S   +
Sbjct: 280 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDKLVRTAFGPITLGDQKSGWLRRLSNTEV 338


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 72/240 (30%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R+ K +A   + SR+EV  +I ++ V VNG L+      V   D + VDG  + 
Sbjct: 11  EKDIEMRIDKYLANMNVGSRKEVHSLIKKKVVTVNGELVTAPKQQVKEDDLVVVDGNEIA 70

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTN 126
             ++   +L +KP G+++   D   + TV   L     +  +  VGRLD NT GLLLLTN
Sbjct: 71  Y-QQYHYFLLNKPKGVISATED-RSQQTVISLLKTKDRYQGIAPVGRLDKNTTGLLLLTN 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG LA  L  P+    +VYR +  G   ++ +     GI +  G      ++ +  Q   
Sbjct: 129 DGALAHELLAPNKHVTKVYRAKISGVASEETIKTFASGITLGDGTKLKPAKLEILAQDKV 188

Query: 186 N--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +  + + + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E+++  ++
Sbjct: 189 HDLSQIEIQIQEGKYHQIKRMFGAVGMKVLELDRISMGKLSLPTDLKRGQYQEITRDKIK 248


>gi|320106004|ref|YP_004181594.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319924525|gb|ADV81600.1| pseudouridine synthase [Terriglobus saanensis SP1PR4]
          Length = 301

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 96/306 (31%), Positives = 147/306 (48%), Gaps = 24/306 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M  K  ++      R+ K++A AGIASRR+ E +I + RV+VNG ++           DH
Sbjct: 1   MAKKPELKAGPEGVRLQKILADAGIASRRKSEEVILEGRVQVNGKVVTELGTRANPEKDH 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLD 115
           I VDG  L+  E  R +L +KP G VTT  DP+ R T+ D L         R+  VGRLD
Sbjct: 61  IRVDGKLLQGPEEHRYYLVNKPRGYVTTMHDPEKRPTIVDLLIKDGKMPDVRLYPVGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ------- 168
            N+EGLLL+TNDG LA  L   S    + Y V+  GQ  +  ++ L++G++I+       
Sbjct: 121 YNSEGLLLMTNDGELANALSKASNSVEKTYLVKVAGQPSEQAIDQLRRGVMIERGRLQET 180

Query: 169 ------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                  +     +V L  + G N W  V L EG+NR+++K+FE  +  V ++ RI YG 
Sbjct: 181 QGARRNRVMTAPAKVKL-VRAGLNPWFEVSLTEGRNRQLRKMFEEIDHHVEKIRRIGYGA 239

Query: 223 FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
             L  +  G  RE+    +         ++ +     P  +  T+    P   +     +
Sbjct: 240 LVL-DVAPGEFRELKPGEVTALGRAATGKKVERRRTMPEAAKLTV----PGKKTGSRKAY 294

Query: 283 TRMKKN 288
            R +K 
Sbjct: 295 KRPRKE 300


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 99/290 (34%), Positives = 139/290 (47%), Gaps = 7/290 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V S   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIA-SLGDRVESDAKIRIDGRTVSIRSE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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|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 =  253 bits (647), Expect = 3e-65,   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|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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 110/232 (47%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + M+A+ RV+VNG + ++    +  TD + VDG  L   ++ 
Sbjct: 1   MRLDKYLAETAQCTRSEAKTMLAKGRVQVNGAVCKKGDTQLKDTDTVAVDGALLTY-QKF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DGG A
Sbjct: 60  VYLMLNKPEGVVSASTDKRD-TTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V     + Q+       G+ +  G      +VT  +  G    V 
Sbjct: 119 HDILSPRHHVSKTYTVTIDTPLTQEMCTGFAAGVTLADGTALSPAEVTALSPDGLT--VR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V LR+G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 177 VVLRQGVYHQIKRMFGVYGAGVNALHREAIGGLALDAQLAPGQWRELSDEEV 228


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 118/234 (50%), Gaps = 7/234 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           P R+ + +A  G  +R +V+ M+ + RV++NG  ++ A   V   +D +EVD   +  A 
Sbjct: 16  PMRLDRFLAEMGYGTRTQVKDMVKKGRVRMNGEAVKDADRKVNPESDIVEVDRSRVAYA- 74

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           R   ++ +KP G+V+   D    + V     ++   +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 75  RMEYYMLNKPQGVVSATEDRKYPTVVGLIREALRKDLFPVGRLDIDTEGLLLITNDGELA 134

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN---A 187
             L  P     +VY     G + +D +   ++GI +  G      ++ +    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|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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 127/294 (43%), Gaps = 12/294 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
              R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +    
Sbjct: 5   QSIRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVMPGDVVKVNGQLIEPRD 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE       +KP+G+V+T  D + R  + D + +  SR+  +GRLD +++GL+ LTN G 
Sbjct: 64  AEDLVFIALNKPVGIVSTTEDGE-RDNIVDFV-NHSSRIFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  +  G+ I G      +V  +         
Sbjct: 122 LVNKILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTVTKKCKVKKEAPFA----F 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E     L
Sbjct: 178 RITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIELF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +         +       +   + + P    + +   + K      +K   
Sbjct: 236 IENSSSEAKPKAKAKPKTQAIK-RPVVKAPQSEEKGRGKPAGKRFTQPGRKKKG 288


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 128/303 (42%), Gaps = 11/303 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRR+ +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVYLNGKRAA-VGDQVVAGDTVKVNGQLIEP 61

Query: 70  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E       + +KP+G+V+T    +  + V  +      R+  +GRLD +++GL+ LTN+
Sbjct: 62  KEADDFVFIVLNKPVGIVSTTESSEKNNIV--DFVRHSVRIFPIGRLDKDSQGLIFLTNN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V  +  +    +  L  G+ + G       VT    K +  
Sbjct: 120 GDLVNKVLRAGNNHEKDYVVTVNKPITDSFIEGLAGGVPMLGKMTKKCPVT----KVAPN 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L     G  R+++ + L   L  
Sbjct: 176 VFNITLVQGLNRQIRRMCEHFGYEVVKLERTRIMNVSLKGTPVGDWRDLTPQELSVLL-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             +E++      P   S    R      +      +   K +++ N    +     P   
Sbjct: 234 KSIEDSSSESSTPAKKSRNTPRKNARTDTSEKPKVSSKPKGAAKGNAKHPKDGARKPAGS 293

Query: 308 RNL 310
           +  
Sbjct: 294 KGK 296


>gi|119898401|ref|YP_933614.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119670814|emb|CAL94727.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 356

 Score =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 92/271 (33%), Positives = 142/271 (52%), Gaps = 9/271 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
            P+R+ KV+A+AG+ASRRE+E ++   R+ VNG+        +   D ++++G  +    
Sbjct: 89  EPERLQKVLAQAGVASRREIEELVVAGRISVNGLPA-SLGQKIGPGDRVKLNGKLIPLRF 147

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G + +  DP+GR TVF+ LP +   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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  V L EG+NRE++++FE     V+RL+R+ YGP +L   L  G   E+ +    +   
Sbjct: 268 WYRVTLAEGRNREVRRMFEAVGLTVSRLMRVRYGPVELPARLKRGMWMELPEA---DACA 324

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
              L   +V+  A     E   R    +  E
Sbjct: 325 LAGLPPPRVDPSARGARREKAPRLHHTLPHE 355


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 99/298 (33%), Positives = 152/298 (51%), Gaps = 17/298 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV ++G++       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGVIA-NLGDRIEADAKVRIDGRAISLKSA 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V LREG+NRE+++++E    +V+RLIR+ YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRVRYGMVELPKSLPRGGWVELPIEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             G  L  E +  L A  +S          I   V     R  K ++       +++ 
Sbjct: 241 LAG--LEPETRTMLAADKHSVARAQVKSAKIRRAV-----RKHKVTATPKAKPTRQRS 291


>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 =  253 bits (647), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+  I +  V+VNG ++++    V    D I  DG  +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSYIRKGFVEVNGEIIKKDDYKVDYQKDEIIFDGELIEYR-P 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G V+   D +   TV D +    +  +  VGRLDI+TEGLLL++NDG  A
Sbjct: 62  YVYLMLNKPKGYVSATKD-NVHPTVIDLIVGYENYDLFPVGRLDIDTEGLLLISNDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P+    +VY  R  G +++  +   K G+++  G       + +      +  V 
Sbjct: 121 HRLMSPNRNHAKVYVARIAGIMNEFDILAFKDGVILDNGYKCKPANLKILEVFDDSCEVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           + + EGK  ++KK+ E  N KV  L RIS     +  +L  G  RE++K+ 
Sbjct: 181 IEIFEGKFHQVKKMVEACNKKVTYLKRISIKGLTIDRSLQLGDFRELTKEE 231


>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 =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 102/229 (44%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +  D       G+ + G         L+  +     V + +
Sbjct: 121 ITSPKHHCEKTYLVTLEYPISDDTEMKFLAGVQLNGEKTLTKPAKLEIIEP--HRVRLSI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           REG+  ++K++F      V  L R   G   L  TL  G  R ++K  +
Sbjct: 179 REGRYHQVKRMFAAVGNHVVELHRERVGQIYLDSTLEPGEYRALTKHEI 227


>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 =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 135/247 (54%), Gaps = 7/247 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +  ++  P ++ KV+A  G+ SRRE+E +I Q RV VNG+        ++ TD + V+
Sbjct: 209 RELSADDDAP-KLHKVLAEGGLGSRREMEELILQGRVSVNGLPA-HIGQRILPTDQVRVN 266

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G  + +    +  R+ LYHKP G + + SDP+GR TVFD+LP + + + ++VGRLD NTE
Sbjct: 267 GKLIHRKVSTKPPRVLLYHKPAGEIVSQSDPEGRPTVFDSLPRMKTGKWVAVGRLDFNTE 326

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+ T  G +A     P     R Y VR  G++ +     L  GI +       +++  
Sbjct: 327 GLLIFTTSGDIANRFMHPRYGVEREYAVRTLGELAEADRQRLLHGIKLDDGEANFLRIAD 386

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +G N W  V L EG+NRE++++FE     V+RLIR  YG F L   L  G  +E+  
Sbjct: 387 GGGEGVNQWYHVALTEGRNREVRRMFEAVGLTVSRLIRTRYGQFLLPRGLKRGRWQELEA 446

Query: 239 KILREQL 245
             ++  +
Sbjct: 447 NEVKSMM 453


>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 =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K ++  GI SRR  ++ I   RV +NG L       + S+D ++VDG  + +  + 
Sbjct: 1   MRINKFLSETGITSRRGADKFIEAGRVTINGNLA-ELGSKIESSDEVKVDGKVIEQPNQQ 59

Query: 74  RLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++L  +KP+G+ +T ++      + D + +   R+  +GRLD ++EGL+LLTNDG +  
Sbjct: 60  YVYLALNKPVGITST-TERHIEGNIVDFV-NHAERIFHIGRLDKDSEGLILLTNDGDIVN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V+    + +  L+ +++G+ I        +     +K S+    + 
Sbjct: 118 EILRVENEHEKEYVVKVDMPITESFLSKMEEGVEILDTKTLPAKA----EKLSSYTFKLT 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           LR+G NR+I+++     ++V  L R+      LG L  G  R+++     E  
Sbjct: 174 LRQGLNRQIRRMCTALGYEVRSLKRVRIINIFLGDLPVGEWRDLTDVERTELF 226


>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 =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 71/297 (23%), Positives = 127/297 (42%), Gaps = 12/297 (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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  VGRLD +++GL+ LTN 
Sbjct: 80  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPVGRLDKDSQGLIFLTNH 137

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V  + +  +  G+ I G            +K +  
Sbjct: 138 GDLVNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 193

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F + V +L R       L  +  G  R+++   L +    
Sbjct: 194 VFRITLVQGLNRQIRRMCEHFGYDVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 251

Query: 248 HLLEEAQVNLDAPIYSS-ETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         ++ +         +  +     + +  SS K   S  +K   
Sbjct: 252 KLIERSSSEAKTKTKATPKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKKG 308


>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 =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 77/237 (32%), Positives = 116/237 (48%), Gaps = 4/237 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ KV+A+AG+ASRR  E MI + RV+VNG ++ +  V V    D I VDGV +   
Sbjct: 76  DGIRLQKVLAQAGVASRRHSEVMIDEGRVEVNGKIVRQQGVRVDPNVDIIRVDGVRVNVN 135

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTND 127
           E  + +  +KP G+ TT  D  GR  V D +        R+  VGRLD +TEGLLLLTND
Sbjct: 136 EDQQYFALNKPRGVHTTMEDELGRPCVGDFVADRVAAGQRLFHVGRLDADTEGLLLLTND 195

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L+  L  P     + Y     G+     +  LKKGI ++          +       +
Sbjct: 196 GELSNRLMHPKYGVEKTYLATVLGEAKPALVRELKKGIELEDGVAKADYAQIVDTHQGQS 255

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + + EG+   ++++ +   + V RL+R      QLG L  G+ R ++   L   
Sbjct: 256 LIRLVIHEGRKHVVRRMLKEAGYPVQRLVRTKIHTVQLGELKPGAMRALNDSELTAL 312


>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 =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 120/233 (51%), Gaps = 5/233 (2%)

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  D   ++ +   L     R+   GRLD  +EGLL++T+DG L   
Sbjct: 60  TVLAVHKPAGIVCT-EDKRVKNNIIRFL-KYPERITYAGRLDKESEGLLIMTDDGELING 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y+V  +  V ++ +N +  G+ +     G  +VT   + ++      T+
Sbjct: 118 MMRSRYGHEKEYKVWVNKPVTEEFVNRMSSGVRLVDKEKGLDEVTRPCEVRQCGTYIFTI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L +G NR+I+++ E   +KV RL+RI     +LG L  G+ R+++++ L E 
Sbjct: 178 ILTQGLNRQIRRMCEALGYKVKRLVRIRIMNIELGNLKPGAYRKLTEQELNEL 230


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 117/234 (50%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +    + SR EV++ I Q R+ V+G    +    +   +  + VD   +   E 
Sbjct: 2   MRLDKYLCEMNVGSRSEVKKYIRQGRITVDGKTAVKPEEKIDEHSQKVCVDSRVIGY-EA 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+  +D   + TV D +     + +  VGRLD +TEGLLL+TNDG +A
Sbjct: 61  FEYYMLYKPSGVVSATTDRKEK-TVLDLIEEKKRKDLFPVGRLDKDTEGLLLITNDGEMA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VY  +  G+V + ++ +  +G+ I    Y         ++G+ + + +
Sbjct: 120 HRLLSPKKHVDKVYYAKIDGKVTEREVQIFSEGLSIGNDEYAKPSALKILKEGNISEIEL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            ++EGK  ++K++F     +V  L RIS G   L  +L  G  R +++K + + 
Sbjct: 180 TIQEGKFHQVKRMFHAVGMEVIYLKRISMGNLVLDESLKKGEYRRLTEKEVEQL 233


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 122/235 (51%), Gaps = 1/235 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKA 70
              R+ KV+A AG+ SRRE E +I Q RV+V+G ++    V V  T H+  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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V L  G+NR ++++F+     V RL+R S GP +LG L  G TR +++  +   +
Sbjct: 206 VQLHSGRNRIVRRIFDSLGHPVTRLVRTSIGPIKLGDLKQGRTRVLNRTEVATLM 260


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 103/372 (27%), Positives = 158/372 (42%), Gaps = 22/372 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K +++      ++ KV+A+AG+ SRR++E++I + +V VNG +     + +   D I+
Sbjct: 278 PGKRVLRPEPEAPKLHKVLAQAGVGSRRDMEQLIQEGQVSVNGEVA-HIGMRIAQGDQIK 336

Query: 62  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           + G P++        R+  YHKP+G V TH DP+GR TVF  LP +   + +SVGRLDIN
Sbjct: 337 IAGRPIKVRIAPPPARVLAYHKPVGEVVTHHDPEGRPTVFRRLPRLPVGKWLSVGRLDIN 396

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL TN G LA  L  P     R Y VR  G +D+     L +G+ I+G       +
Sbjct: 397 TEGLLLFTNSGELANQLMHPRFGVEREYAVRVLGSLDEAARARLLEGVEIEGQRAMFKSI 456

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G N W  V + EG+NRE++++F+     V+RLIRI Y    L   L  G   E+
Sbjct: 457 DDGGGEGINHWYRVVITEGRNREVRRLFDAVGLTVSRLIRIRYATVVLPRGLKRGVWVEL 516

Query: 237 SKKILREQL----GPHLLEEAQVNLDAPIYSSETLVRDRPNI----------ISEVPDDF 282
               +R+      GP      +         +E   RD                      
Sbjct: 517 DDNDVRQIRQIANGPRAERGEREERGPRADRAERGPRDGQQPGRGAGKGKGGGQGQGQGP 576

Query: 283 TRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWM--AKGIHSSFLSDSGQREENHRRSPS 340
              +   +   G   Q++   PV +       +               G    + R +  
Sbjct: 577 QMSQGGQNAPGGRGNQQRGNKPVGKGGQGGQGFERRGPDGRPGAPRSGGAEWRDERPARD 636

Query: 341 FPSKRSLRRTSA 352
               R   R   
Sbjct: 637 GNVSREPPRERE 648


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 73/292 (25%), Positives = 130/292 (44%), Gaps = 12/292 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V +NG         V+  D ++V+G  +    AE 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVVPGDVVKVNGQLIEPRDAED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  D + R  + D + +  SR+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVFIALNKPVGIVSTTEDGE-RDNIVDFV-NHSSRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V  +          + 
Sbjct: 125 KILRAGNDHEKEYIVTVNKPVTDEFIRGMGAGVPILGTVTKKCKVKKEAPFA----FRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F + V +L R       L  +  G  R+++   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMCEHFGYDVTKLERTRIMNVSLSGIPLGEWRDLTDDELIELF--RLIEN 238

Query: 253 AQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +            +T    RP + +   ++  R K  + ++     +KK   
Sbjct: 239 SSSEAKPKAKAKPKTQAIKRPVVKAPPAEEKGRGKPANGKRFAQPGRKKKGR 290


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 113/246 (45%), Gaps = 11/246 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRR  + +I + +V +NG +       V   D +EV+G  + K     
Sbjct: 4   RINKYLSEVGYCSRRVADSLIEEGKVTINGEIP-EMGTKVEEGDQVEVEGQRIEKSMKHE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +++KP+G+V T         + D +    +R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  KIYLVFNKPVGIVCTTDRRVESDNIIDFI-KYPTRIFPIGRLDKPSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +++D +  +  G+ I G    +  V     K       + 
Sbjct: 122 KILRARNNHEKEYIVSVNRPINRDFIQSMSNGVEILGTITKNCFVKQLGPKK----FRII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K+ L E     LLE 
Sbjct: 178 LTQGLNRQIRRMCESLGFRVKSLKRVRIMNIKL-DVSIGEYREFTKEELFEL--NKLLEN 234

Query: 253 AQVNLD 258
           +    D
Sbjct: 235 SSKTYD 240


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 127/303 (41%), Gaps = 11/303 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N +  R++K I+ +GI SRR+ +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   NASSTRLNKYISESGICSRRDADRFIEQGNVYLNGKRAA-VGDQVVAGDTVKVNGQLIEP 61

Query: 70  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E       + +KP+G+V+T    +  + V  +      R+  +GRLD +++GL+ LT++
Sbjct: 62  KEADDFVFIVLNKPVGIVSTTESSEKNNIV--DFVRHSVRIFPIGRLDKDSQGLIFLTSN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V  +  +    +  L  G+ + G       VT    K +  
Sbjct: 120 GDLVNKVLRAGNNHEKEYLVTVNKPLTDSVIEGLAGGVPMLGKMTKKCPVT----KVAPN 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L     G  R+++ K L   L  
Sbjct: 176 VFNITLVQGLNRQIRRMCEHFGYEVVKLERTRIMNVSLKGTPVGDWRDLTPKELSVLL-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
             +E++      P   S    R  P          +     +++ N    +     P   
Sbjct: 234 KSVEDSSSQDSKPAKKSRNAPRKNPRTDDSSKAKSSSKTAGAAKGNKKHSKDGARKPAGS 293

Query: 308 RNL 310
           +  
Sbjct: 294 KGK 296


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 70/244 (28%), Positives = 114/244 (46%), Gaps = 8/244 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV 62
           KN+        R+ K +  AGI SR EV++++ +++V VNG +       +    D I  
Sbjct: 2   KNVRIGKGKKMRLDKFLVEAGIGSRTEVKQLLKKKQVLVNGKVEISPKTQIDEKADRISC 61

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEG 120
            G  L   E+   ++ +KP G+++   D +   TV D L        V  VGRLDI+T G
Sbjct: 62  QGQTLSY-EKYVYYMLNKPKGVISATED-NHHKTVLDLLDKTAWDKEVFPVGRLDIDTHG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTN+G LA  +  P     + YR +  G +    +     GI ++       Q+ + 
Sbjct: 120 LLLLTNNGKLAHAMLSPKKHVDKTYRAKVAGLMTTADVAAFANGIDLKDFTCQPAQLVIL 179

Query: 181 T--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS 237
              +    + V + ++EGK  ++K++ +    KV  L R+S  P QL   L  G  R ++
Sbjct: 180 ETNEAERTSVVEITIKEGKFHQVKRMVQACGKKVTDLQRLSMVPLQLDKQLALGEWRRLT 239

Query: 238 KKIL 241
              L
Sbjct: 240 DDEL 243


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 95/276 (34%), Positives = 148/276 (53%), Gaps = 6/276 (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---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
            AE+    R+ +Y+KP G + + SDP+GR TVF+ LP    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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           +N W  V L EG+NRE+++++E    +V+RL R+ +G   L + L  G  +E+  K ++E
Sbjct: 184 ANHWYYVALMEGRNREVRRLWESQEIQVSRLKRVRFGGVFLPSKLRQGQWQEMPYKEVQE 243

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
                 +E  +     P        + R N   + P
Sbjct: 244 LYKMAGMEALKPQKMMPKELQSMERQQRKNRGIKHP 279


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 110/229 (48%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V+VN   ++    ++    DH+ V+G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGAVEVNDKKIKTPKTHINPNEDHVTVNGSTISYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G+++   D D   TV D +P      +  VGRLD +TEGLLLLTNDG   
Sbjct: 61  -VYIMLNKPKGVISATED-DSHKTVIDLIPEYSHLGIFPVGRLDKDTEGLLLLTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + Q  +   + G+ +        ++     KG++    V
Sbjct: 119 HELMNPNKHVSKTYEVVSKYPIKQADIEAFESGVELSDGKVKPAKLI----KGNDHLSYV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     +V  L RI     +L  +L  G  R ++++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIANLELDQSLNDGEFRFLNEQ 223


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 130/249 (52%), Gaps = 8/249 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK +          R+++ +A  G+ASRR  ++++   RV +NG ++    + V  + D 
Sbjct: 1   MKKRTAENREERLVRINRYLAMCGVASRRASDQLVEAGRVMINGSIILEPGLKVDPSVDE 60

Query: 60  IEVDGVPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           + VDG  L   E +    L++KP  ++TT+SD   R TV + + S+  R+  VGRLD  T
Sbjct: 61  VIVDGSMLALPEGKKVYILFNKPKNVITTNSDEKNRETVLNYI-SVKERIYPVGRLDRKT 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQ 176
            G+LLLTNDG LA  L  PS+   + Y      +     L  L  G+ ++  G      Q
Sbjct: 120 TGVLLLTNDGNLAHKLMHPSSNVKKEYIAVLDKKFPHTLLLQLTGGMRLKDTGEKVSPCQ 179

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +  + G   W++  + EGKN +++++FE   ++V++L R++Y   ++G L  G  R +
Sbjct: 180 AKILDE-GFQVWLS--IHEGKNHQVRRMFETLGFEVDKLERVAYAGLKVGDLRRGEWRAL 236

Query: 237 SKKILREQL 245
            +K +++  
Sbjct: 237 DRKEIQQLF 245


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 106/310 (34%), Positives = 149/310 (48%), Gaps = 11/310 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKK---ILRE 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  AP  ++    R R   I             +  +   S ++K   
Sbjct: 242 LVELRPEKETVLN-TAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGR-SSSARRKPGG 299

Query: 304 PVHRRNLASN 313
               RN  +N
Sbjct: 300 ESSTRNKVAN 309


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 113/243 (46%), Gaps = 7/243 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             I  E     R++K I+ +G  SRR+ +R IA+  V ++G+        V+    + V+
Sbjct: 16  NPIQHEARESLRLNKYISDSGYCSRRQADRFIAEGVVAIDGVTAT-VGQQVLPGQRVTVE 74

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           G  +   +       +KP G+  T     +G  + F N P +   +  +GRLD ++ GL+
Sbjct: 75  GNHVTIDDEKVYIALNKPRGITCTTDGAIEGNISDFMNYPKM---IFPIGRLDKDSSGLI 131

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LD 180
           LLTNDG +   +        + Y V  +  +D+D +  + KG+ I       MQVT   D
Sbjct: 132 LLTNDGDIVNKILREEYGHDKEYIVSVNKTIDEDFITKMSKGVEIYNQQTHRMQVTNPSD 191

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++ +     + L +G NR+I+++ +   +KV  L R+      LG L  G  R +S   
Sbjct: 192 VEQVAPKTFRIVLNQGLNRQIRRMTKALGFKVTTLNRVRIMNINLGDLKVGEWRYLSVHE 251

Query: 241 LRE 243
           L E
Sbjct: 252 LEE 254


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 96/251 (38%), Positives = 131/251 (52%), Gaps = 9/251 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             D   L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDSKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD 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 REVSKKILREQ 244
            E++   +   
Sbjct: 239 LELNPSEVNRL 249


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 120/238 (50%), 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   IRLDKFLSEMGVGTRQEVKQYIRKGKVEVDGEIAKRPELKVDETKANVTLDGERIGYA-S 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D   + TV D +     + +  VGRLD +T GLLL+TNDG LA
Sbjct: 66  YVYYMLNKPSGVVSATEDKREK-TVIDLIKGQKRKDLFPVGRLDKDTVGLLLITNDGNLA 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN-AW 188
             L  P     + Y  +  G V +D      +G+ I  +      M   LD  K  + + 
Sbjct: 125 HRLLSPKHHVDKCYFAKVQGNVTKDDAEKFAEGVNIGTEDEPEITMPGKLDIIKSDDLSE 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           + + ++EGK  ++K++F+    +V  L R   G   L   L  G  R ++++ L+  L
Sbjct: 185 IRLTIQEGKFHQVKRMFQAVGKEVVYLKRERMGSLILDDNLAEGEYRMLTEEELKNLL 242


>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 =  253 bits (646), Expect = 4e-65,   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|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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 117/238 (49%), Gaps = 8/238 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ K +   G+ SR EV++++ +++++VNG +     +++    D +   G  L 
Sbjct: 2   KEASMRLDKYLVDCGVGSRTEVKQVLKKKKIQVNGKVETSPKIHIDPDKDQVTYLGESL- 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
             E    +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN
Sbjct: 61  FHEEFVYYLLNKPKGVISATED-DHHQTVLDLLDDTARHKEVFPVGRLDIDTHGLLLLTN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKG 184
           +G LA  +  P     +VYR +  G + Q+ ++  K+GI ++       ++ +    Q+ 
Sbjct: 120 NGKLAHAMLSPKKHVDKVYRAQVAGIMTQEDIDRFKEGIELKDFTTLPAELEMLEVDQEA 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           ++  V + + EGK  ++K++      +V  L RIS GP  L   L  G  R +    L
Sbjct: 180 NSCLVQIRIAEGKFHQVKRMVAACGKEVTDLERISMGPLSLDPALKLGQWRRLQSSEL 237


>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 =  253 bits (646), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 107/308 (34%), Positives = 147/308 (47%), Gaps = 15/308 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVSVKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIYLDKKLPRGGWMELELKDVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  + L+    SS    R R   I        R ++  S   G S       P
Sbjct: 243 VELRPEKETMIELN---NSSRKRDRARSQKIRR---AVKRHEERVSTPKGRSNNAARRKP 296

Query: 305 VHRRNLAS 312
                  S
Sbjct: 297 SKAAGQTS 304


>gi|311281430|ref|YP_003943661.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308750625|gb|ADO50377.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 292

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 74/307 (24%), Positives = 127/307 (41%), Gaps = 25/307 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +    AE 
Sbjct: 8   RLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVAPGDVVKVNGQLIEPRDAED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  D +  + V  +  +  SR+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVFIALNKPVGIVSTTEDGERNNIV--DFVNHSSRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G      +V  +          + 
Sbjct: 125 KILRAGNDHEKEYVVTVNKPVTDEFIRAMGAGVPILGTVTKKCKVKKEAPFA----FRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L E     L+E 
Sbjct: 181 LIQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLAGIPPGEWRDLTDDELIELF--KLIEN 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
           +                +        P       K  +   G +  K  A   +R+   S
Sbjct: 239 SSS--------------EAKPKAKAKPKTAAGAVKKPAGNGGKNMAKTPAEMANRKRFTS 284

Query: 313 NVWMAKG 319
                KG
Sbjct: 285 PGRKKKG 291


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 77/236 (32%), Positives = 121/236 (51%), Gaps = 1/236 (0%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
              +   +R+ KV+ARAG+ SRR VE M+ Q R+ VNG  +    + V    D I VDGV
Sbjct: 36  TDASAEGERLQKVLARAGVGSRRVVENMVDQGRISVNGKTVAVQGMRVDPERDKIAVDGV 95

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   +    +  +KP G++T  SD   R TV D +  +   ++ VGRLD +TEGLLL+T
Sbjct: 96  RIELRDDRVTYALNKPPGVITAMSDDRNRPTVGDMVGDLAPGLVHVGRLDQDTEGLLLVT 155

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y  +  G V +D    L+ G+ ++          +      
Sbjct: 156 NDGELAHRLAHPSYEVKKTYLAQVSGSVPRDMARRLRSGVELEDGPVKVDSFRVVDTHAG 215

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V V L EG+   ++++       V+RL R + GP +L  + +GS R +S+  +
Sbjct: 216 QSVVEVVLHEGRKHIVRRLLASVGLPVSRLTRTAVGPVKLERMRSGSIRRLSRAEV 271


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 104/301 (34%), Positives = 148/301 (49%), Gaps = 13/301 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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+    +S    R R   I        R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNKD-NTSRKRERARSQKIRR---AVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 P 304
           P
Sbjct: 298 P 298


>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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 119/234 (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  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D   ++ +   N 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|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 =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 83/242 (34%), Positives = 124/242 (51%), Gaps = 8/242 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+   +ARAG+ASRR+ E +I + RV+VNG +       V   D +EVDG  +   
Sbjct: 1   MKALRLQAFLARAGVASRRKAEDLIREGRVRVNGKVA-VLGQKVGPEDLVEVDGKRVELP 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++  +   HKP G  TT  DP  R TVFD LP     +  VGRLD ++EGLLLLTNDG L
Sbjct: 60  QKRLVLALHKPKGYTTTRHDPHARRTVFDLLPK-IPGLHPVGRLDRDSEGLLLLTNDGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VYRV   G  + ++    L  G+ ++      +        G+    
Sbjct: 119 THRLTHPRFGVRKVYRVWTEGGTLPKEVCRRLLLGVDLEDGPARAL-ACCPAPGGA---- 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S++ ++  L    
Sbjct: 174 VLVLAEGRKREVRRMLQRVGYPVRRLLRLQVGPIRLGDLPPGKWRRLSEREVKALLRLVG 233

Query: 250 LE 251
           LE
Sbjct: 234 LE 235


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 94/292 (32%), Positives = 145/292 (49%), Gaps = 11/292 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +++ K++A AGI SRR++E +I   RV VNG+        V + D I V+G PL +
Sbjct: 286 SPDAEKLHKILADAGIGSRRDMEELIIAGRVSVNGLPA-HVGQRVGTEDVIRVNGKPLSR 344

Query: 70  A-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
                 +  ++ LYHKP G + T  DP  R  VFD LP    +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 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           G+N W  V + EG+NRE++++F+     V+RL+RI +GP  L   L  G    +++  +R
Sbjct: 465 GANHWYRVVILEGRNREVRRLFDAVGLTVSRLVRIRFGPIALPPRLQRGRLHALTEAEVR 524

Query: 243 ---EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
              +Q+  H+ E      DA   +     + R        D   R  + + +
Sbjct: 525 QLQQQMRRHVAEMTDGAADAARETRSGNAQGRGKGAGRGNDAPRRQGRGAGK 576


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 99/298 (33%), Positives = 152/298 (51%), Gaps = 17/298 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV ++G++       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGVIA-NLGDRIEADAKVRIDGRAVSLKSA 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V LREG+NRE+++++E    +V+RLIR+ YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRVRYGMVELPKSLPRGGWVELPIEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             G  L  E +  L A  +S          I   V     R  K ++       +++ 
Sbjct: 241 LAG--LEPETRTMLAADKHSVARAQVKSAKIRRAV-----RKHKVTATPKAKPTRQRS 291


>gi|312622542|ref|YP_004024155.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203009|gb|ADQ46336.1| pseudouridine synthase [Caldicellulosiruptor kronotskyensis 2002]
          Length = 233

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 113/232 (48%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ + +
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIREGIVTVNGKQIVEVDFKINPEEDIVEVDGRVVKFS-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ +     TVF  +     +  + +VGRLD + EGLL++T+DG  
Sbjct: 60  QIYIMMNKPKGYVCSNEEL-ASLTVFSLISDDLKYRDLHTVGRLDKDAEGLLIITDDGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P  +  + Y VR   +VD++KL   + GI++  G      + T+      +  V
Sbjct: 119 THRVISPKKRIEKEYLVRLEKEVDEEKLKEFENGIILDDGYKTLPAKYTI----IDSTTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++K++FE    KV  L R+  G   L  +L  G  R + ++ 
Sbjct: 175 KLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDQSLKPGEYRVMKEEE 226


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 118/234 (50%), Gaps = 7/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  G+ +R ++++ I++ +V VNG + + A   +    D +   G  +  AE  
Sbjct: 4   RLDKYLADMGLGTRSQIKKDISKGQVLVNGTVSKDAGTRIDTEKDQVSYLGQTVTYAE-Y 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D   R TV D +       +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYYMLNKPAGVVSATEDRHDR-TVLDLIDTKQRKDLFPVGRLDKDTEGLLLITNDGALAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTV 191
            L  P +   +VY  R  G+V  + + L +KG+ I G     +   L+       + + +
Sbjct: 122 RLLSPKSHVDKVYFARIEGKVTAEDVFLFQKGVDI-GEQALTLPARLEILSSDTVSEIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + EGK  ++K++FE    KV  L R+S G   L   L  G+ R ++   +R  
Sbjct: 181 TICEGKFHQVKRMFESVGKKVLYLKRLSMGTLILDDLLPPGAYRTLTAGEIRSL 234


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 80/238 (33%), Positives = 122/238 (51%), Gaps = 12/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK--AE 71
           RV K+I++ GIASRR+ E MI Q RV+VNG L       V    D I +DG P+ +    
Sbjct: 4   RVQKIISQWGIASRRQAEEMIGQSRVRVNGNLAR-LGQKVDPKVDMISIDGKPVTQGSPP 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KP G+V+T +DP GR+TV D LP+   +   +  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-----LAGSTREVSKKIL 241
           + + L+EG+NR+I++V +   + V  L R + G  +L          G  R +    +
Sbjct: 183 LEIILQEGRNRQIRRVAQQLGYPVVHLDRRAIGTIELHNSDGKFTDVGKYRHLITSEI 240


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 106/310 (34%), Positives = 149/310 (48%), Gaps = 11/310 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + VDG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDDNALVRVDGHVVSVKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKK---ILRE 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  AP  ++    R R   I             +  +   S ++K   
Sbjct: 242 LVELRPEKETVLN-TAPDAATRKRERTRSQKIRRAVRRHEERVSTAPGR-SASARRKPGG 299

Query: 304 PVHRRNLASN 313
               RN  +N
Sbjct: 300 ESSTRNKVAN 309


>gi|254525127|ref|ZP_05137182.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722718|gb|EED41243.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 240

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 79/235 (33%), Positives = 118/235 (50%), Gaps = 5/235 (2%)

Query: 14  QR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKA 70
            R  +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG PL   
Sbjct: 1   MRHGLARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIGQPAPPIEVDGQPLAAP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGG 129
           +R    + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND  
Sbjct: 61  QRL-YLMLNKPRGVVTTVQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQ 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  L  P T   + Y V+  G  D   L  L+ G+  +G       V +       AW+
Sbjct: 120 WAARLTDPQTGPDKTYHVQVDGMPDHATLAALQAGVEDEGEFLAAHAVRVLRSGDKTAWL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V L EG+NR I+++   F+ +V RL+R++ G   LG L  G  R +    L+  
Sbjct: 180 EVVLDEGRNRHIRRLLAAFDLQVLRLVRVAIGGLVLGDLGKGQWRVLEVSDLQRL 234


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 116/234 (49%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR++V+++I   RVKV+G +++     +      I V+G  +   ++
Sbjct: 2   ERLDKIISNMGYGSRKDVKKIIKDGRVKVDGEVVKDNNKQLDPQKSKIIVNGEEISY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++  SD D   TV D L           +GRLD +T GLL LTNDG  
Sbjct: 61  YIYLMMNKPDGVISATSD-DYDKTVIDLLEVEDQVFEPFPIGRLDKDTVGLLFLTNDGDF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY  +    V  + +   K+GIV+  G      ++ +       + V
Sbjct: 120 NHRLISPKWHVDKVYYAKIDKDVTSEDVVAFKEGIVLDDGYKCMSAKLEVLNNSKEGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V +REGK  ++K++FE    KV  L RIS+   +L   L  G  RE+++  ++
Sbjct: 180 KVTVREGKYHQVKRMFEAQGKKVVYLKRISFAGIKLDENLEEGEYRELTEDEMK 233


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 58/230 (25%), Positives = 101/230 (43%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E  +++    V V+ ++ +  A  +  T  +E     +      
Sbjct: 1   MRLDKFLCDALGTTRKESTQLLKSGEVTVDDVVQKSGAFKLKETSRVEWQEREITL-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G+V +H D     T F  L       +   GRLD++T GLLL+T+DG  + 
Sbjct: 60  RYIMMHKPDGVVCSHEDGFN-QTAFTLLDEVNIEDLHFAGRLDVDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     +  D  +   +GI ++G     +   L+    S   V + 
Sbjct: 119 RVTSPKHKCEKTYRVWLADPIQADYADQFTQGIELRGERELTLPAQLEV--VSETEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L   L  G  R +++  +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVIGLHRERIGQITLDEALEPGEYRYLTEDEV 226


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 107/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V    D I V+   +   ++
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D +   T+ D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-EVHPTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P+    + Y V     + Q  ++  K GI +              +K  N    V
Sbjct: 119 HEVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSDGKLKPA----ILKKVDNYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYRLLTQ 222


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 75/244 (30%), Positives = 124/244 (50%), Gaps = 7/244 (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  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDIN 117
            ++  G  +   E+    L +KP   +TT  DP+GR TV + +  +   R+  VGRLD  
Sbjct: 313 VVKY-GRKILNPEKLVYVLLNKPKDFITTTEDPEGRRTVMELVAKAGPERIYPVGRLDRA 371

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLL TNDG LA  L  PS +  ++Y+V     + ++    L +G+ ++       QV
Sbjct: 372 TTGLLLFTNDGELAEKLSHPSNEIRKIYQVEIDKPLAKEDFEKLIEGVELEDGFIKPDQV 431

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++ T       + + +  GKNR ++++FE   ++V +L R +Y       L  G+ R ++
Sbjct: 432 SIVT--PDQQVIGIEIHSGKNRVVRRIFEHLGYEVTQLDRTTYAGLTKKDLPRGNWRFLT 489

Query: 238 KKIL 241
           +K +
Sbjct: 490 EKEV 493


>gi|297583540|ref|YP_003699320.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297141997|gb|ADH98754.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 236

 Score =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            RV K++A  G  SR++V++++ +    VNG +++ A  +V   TD +   G P+   E 
Sbjct: 1   MRVDKLLAHVGYGSRKDVKQLLKKGLFTVNGEVVKSAKAHVDPETDDLAFGGEPILYREH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + + HKP G+++   D   R TV D L       +   VGRLD +T GLLLLTNDG  
Sbjct: 61  LYVMM-HKPAGVLSATEDVSER-TVVDLLEEEDRLFQPFPVGRLDKDTTGLLLLTNDGKW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P+ +  + Y V     V  +  + L++G+ +    Y      +     S + + 
Sbjct: 119 AHGITSPARKIPKTYEVLTAEPVTDEMADQLQQGVTLDDG-YETRPAGVAFPDESRSRLY 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + EGK  ++K++       V+ L RI  G   L  +L AG+ RE+++K + 
Sbjct: 178 LTIDEGKYHQVKRMLAAVGNHVDGLKRIRIGGLPLDESLEAGTYRELTEKEIE 230


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 118/242 (48%), Gaps = 4/242 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
             KN+  ++    R+++ IA +GI SRR+ + +IA   V VNG ++      +    D +
Sbjct: 216 SRKNVAVKDDGLIRLNRYIANSGICSRRKADELIAAGVVSVNGEVVSELGHKIDPAKDQV 275

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
             +G  L++ E+    L +KP   +TT  DP  R TV   +      R+  VGRLD NT 
Sbjct: 276 RYNGELLKR-EKKVYVLLNKPKDYITTTDDPQERRTVMQLVEKASRERIYPVGRLDRNTT 334

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL+TNDG LA  L  P     ++Y V     + Q  LN ++ G+ ++        V+ 
Sbjct: 335 GLLLMTNDGELADKLSHPKNGITKIYHVELSRSLSQGDLNKIQFGLELEDGIIKPDSVSY 394

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               GS   V + +  GKNR ++++FE   + V +L R+ YG      L  G  R + + 
Sbjct: 395 VAG-GSKREVGIQIHSGKNRIVRRIFEHLGYDVVKLDRVVYGNLTKKDLPRGRWRFLEEH 453

Query: 240 IL 241
            L
Sbjct: 454 EL 455


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 75/245 (30%), Positives = 121/245 (49%), Gaps = 3/245 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M D++   ++    R+ KV+A AG+ASRR+ E +I   RVKV+GI++      +      
Sbjct: 1   MSDRSEAADD--GVRLQKVLASAGVASRRKAEELIRDGRVKVDGIVVREMGTRIDPENAV 58

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + VDG  +           +K  G+++T SD  GR  +   L     R+  VGRLD+ +E
Sbjct: 59  VHVDGNRITTRTDLVYLALNKERGVLSTMSDELGRPHIGQMLEDRSERLFHVGRLDMESE 118

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG LA  L  PS    + Y     G + +D    LK G+ ++          +
Sbjct: 119 GLLLLTNDGDLAHRLTHPSYGVAKTYVAEVPGPIPKDLGRRLKAGVELEDGPAKVDSFDV 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                + A V V + EG+   ++++ E  +  V+RL+R   GP QLG    G+ R+++  
Sbjct: 179 MDLHHNRAVVEVVIHEGRKHIVRRLLEAVDRPVSRLVRTQIGPVQLGHQRPGTLRKLNPV 238

Query: 240 ILREQ 244
            + + 
Sbjct: 239 EVSQL 243


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 118/249 (47%), Gaps = 9/249 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RK 69
             P R++K     G  SRR+ +++I    V VNG   E       + D + V+G  + ++
Sbjct: 1   MEPIRINKYFTTIGFCSRRKADKLIEAGYVTVNGKRPEMGQKIDPAKDKVRVNGKLVGQE 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+    +++KP+G+V T      +  + D + +  SR+  +GRLD  +EGL+ LTNDG 
Sbjct: 61  EEKPVYLVFNKPVGIVCTTDTHVEKDNIIDYI-NYPSRIFPIGRLDKPSEGLIFLTNDGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +        + Y V     +  D +N +K GI I      + +V    +K ++   
Sbjct: 120 IVNKILRARNHHEKEYIVTVDRVISDDFVNRMKSGIPILDTVTRECEV----EKITDYMF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+  ++V  L RI      L  +  G  R+ + +  +E     L
Sbjct: 176 KIVLTQGLNRQIRRMCEYLGYEVLTLKRIRIMNVTL-DIPVGEYRDFTDQEFKEL--QDL 232

Query: 250 LEEAQVNLD 258
           LE+++    
Sbjct: 233 LEDSEKTAP 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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 82/242 (33%), Positives = 123/242 (50%), Gaps = 8/242 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+   +ARAG+ASRR+ E +I + RV+VNG +       V   D +EVDG  +   
Sbjct: 1   MKALRLQAFLARAGVASRRKAEDLIREGRVRVNGKVA-VLGQKVGPEDLVEVDGKRVELP 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++  +   HKP G  TT  DP  R TVFD LP     +  VGRLD ++EGLLLLTNDG L
Sbjct: 60  QKRLVLALHKPKGYTTTRHDPHARRTVFDLLPK-IPGLHPVGRLDRDSEGLLLLTNDGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VYRV   G  + ++    L  G+ ++              + +    
Sbjct: 119 THRLTHPRFGVRKVYRVWTEGGTLPKEVCRRLLLGVDLEDG-----PARALACRPAPGGA 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S++ ++  L    
Sbjct: 174 VLVLAEGRKREVRRMLQRVGYPVRRLLRLQVGPIRLGDLPPGKWRRLSEREVKALLRLVG 233

Query: 250 LE 251
           LE
Sbjct: 234 LE 235


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 100/229 (43%), Gaps = 2/229 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  A+R+E  ++I    V VN  + +  A  V     +E  G  ++K    
Sbjct: 1   MRLDKYLCDALGATRKEATKIIKSGDVTVNEQVQKSGAFKVDDHSIVEWQGREVQKP-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  +  KP G V +H D   ++            +   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLFKPDGFVCSHEDGFNQTAFMLLDEVRIEDLHFAGRLDVDTTGLVLITDDGQWSHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +     +   KGI ++      +   L+        V + +
Sbjct: 120 ITSPKHKCDKTYRVWLADPIQPHYADEFTKGIQLRNEKGLTLPAKLELVDAQENEVLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G  +L  +L  G  R ++++ +
Sbjct: 180 NEGKYHQVKRMFAALGNKVEHLHRERIGQIELCESLEPGDYRYLTQEEV 228


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 75/235 (31%), Positives = 118/235 (50%), Gaps = 1/235 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ KV+A+AG+ SRR  E+++A+  V+VNG +  +  + V   TD I VDG  L   
Sbjct: 8   DGIRLQKVLAQAGLGSRRRCEQLMAEGHVEVNGEITTQMGIRVDPATDVIHVDGRRLPPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                 L +KP G+VT+ +D  GR  +   L     R+  VGRLD +T GLL++TNDG L
Sbjct: 68  SDHVYVLLNKPRGVVTSMADERGRPDLRSLLADRTERLFHVGRLDTDTSGLLMMTNDGDL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS ++ + Y     G VD      LK G+ +        +  +       + V 
Sbjct: 128 AHRLAHPSFEFTKTYVALVEGVVDPAVGTRLKSGVELDDGPATVDRFRIKDTSQGRSLVE 187

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L  G+NR ++++       V  L R ++GP +L  L +G  R++++  L   L
Sbjct: 188 LDLHMGRNRIVRRLLAEVGHPVVELTRTAFGPLRLAGLGSGRARDLTRDELGALL 242


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 108/230 (46%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R+E  +++  + V+VNG +++  A+ V     +E  G  L   +  
Sbjct: 1   MRLDKFLCTTLGITRKEAGKILKDKLVEVNGEIVKNGALKVTDDCDVEFSGRTLSL-QGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G V +H D D   TVF     +   R+   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYYMLNKPSGYVCSHVD-DFNPTVFILFDEVAPERMHVAGRLDGDTTGLVLVTDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     +++  +   ++G+ ++G     +   L+  +   A +   
Sbjct: 119 RITSPRHVCEKTYYVETADPIEESYIQAFEEGVQLRGEKELTLPAKLEILEEKVALL--T 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  +L   L  G  R +++  +
Sbjct: 177 ITEGKYHQVKRMFAAMGNKVELLHRERVGAIELDDDLEPGEYRPLTEDEI 226


>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 =  252 bits (645), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 75/297 (25%), Positives = 129/297 (43%), Gaps = 12/297 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +  
Sbjct: 3   PDSSIRLNKYISESGICSRREADRFIEQGNVFLNGKRAT-IGDQVMPGDVVKVNGRLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE       +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVFIALNKPVGIVSTTEDSE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V  D +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPVTDDFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L +    
Sbjct: 176 VFRITLIQGLNRQIRRMCEHFGYEVTKLERTRIMNVGLSGLPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +            +T    RP +  E   +  + +  ++ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTAGIKRPVVKIEKSAEKEKSRPAANGKRFTSPGRKKKG 290


>gi|324989740|gb|EGC21683.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 242

 Score =  252 bits (645), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 112/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V++++ +  V VNG   +     +    D I V G  L   E+
Sbjct: 1   MRLDKFLTENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDEAADDIVVSGQRLIY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DHHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++        + +    ++   + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADVERFAAGIELKDFTCQPAHLKILELDEEKEASL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDPALALGEWRRLTADELERL 235


>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 =  252 bits (645), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 98/353 (27%), Positives = 157/353 (44%), Gaps = 11/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ KV+ARAG  SRRE+E MI   RV V+G + +        T  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGDVAKLGDRLEDMTASVRIDGRRIELVAS 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T  DP+GR TVFD LP + + 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-GTLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++      V+RL R+ YG   L   L  G   E+       LRE
Sbjct: 182 TFYVVITEGRNREVRRLWASQGVTVSRLKRVRYGDIYLSKELPRGGWMELELNDVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRP-NIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +G     E ++ ++            R      E  D+    ++N  +    +   + A
Sbjct: 242 LVGLQPETETELTVEGQKRKRNVRQIRRAVRRFEERADNTNSRRRNDRRSTTRNSDVEKA 301

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF-PSKRSLRRTSAKK 354
                R  ++         +        R     ++ +  P ++  +  +  K
Sbjct: 302 GNDKPRRPSTRSSDVDKAGNQKPRRPSTRNSGADKAENNKPRRQPRQNDADNK 354


>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 =  252 bits (645), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 124/236 (52%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K+++ + +ASRR+ E++I ++RVKVNG L+ +  V V   D I VD   ++ +E  
Sbjct: 2   ERLQKILSYSNVASRRKSEKLILEKRVKVNGKLVTKLGVKVSKKDIILVDDQIIKNSENC 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP G ++T  D   R TV D +      R+  VGRLD NT GLLL+TNDG L +
Sbjct: 62  YY-LINKPSGCISTVKDEKNRPTVIDLIKDTEKKRIYPVGRLDFNTTGLLLITNDGQLTK 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKGSNAW 188
            L  PS+   + Y V+ +  +   +L  L++G++I      +      +        + W
Sbjct: 121 KLTHPSSLIEKEYHVKINYCLSSLELKKLQQGVIIDENYLSVPKKIKILKKRLLPKPSTW 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + + EGKN +I+K+ E   + + +LIR  Y    +  +  G  R +    +++ 
Sbjct: 181 LQIIITEGKNHQIRKMMEKLGFHILKLIRYRYAFLTIKGIKKGQYRILKIHEIKKL 236


>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 =  252 bits (645), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I   G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRSQVKTFLKKKQVTVNGQVETSPKTQIDEDKDQIAYLGQELTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATEDSRHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++Y+ +  G +D++ +   +KGI ++       ++ + +  +  S + 
Sbjct: 119 AHAMLSPKKHVDKIYQAKVAGIMDEEDILAFEKGIKLKDHTCQPAKLEIVSVDRNASTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           V + + EGK  ++K++      KV  L R+  GP  L   L  G+ R ++++ L
Sbjct: 179 VQITVAEGKFHQVKRMVAACGKKVADLQRLKMGPLSLPNDLELGAWRRLTQEEL 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 =  252 bits (645), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 74/297 (24%), Positives = 129/297 (43%), Gaps = 12/297 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K I+ +GI SRRE +R I Q  V +NG         VM  D ++V+G  +  
Sbjct: 3   PDASIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVMPGDVVKVNGRLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE       +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEELVFIALNKPVGIVSTTEDSE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G      +V  +       
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTKKCKVKKEAP----F 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  L  G  R+++   L      
Sbjct: 176 VFRITLIQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLAGLPPGEWRDLTDDELITLF-- 233

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +            +T    RP +  E P +  + +  ++ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTAGIKRPVVKIEKPKEKEKARPAANGKRFTSPGRKKKG 290


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 127/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     + ++ +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 118/235 (50%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  +R E++++I   RV V+G  +++  + +  T   + ++G  +  A++
Sbjct: 2   MRIDKYLAEMGQGTRSEIKKLIRSGRVMVDGETVKKPELKIDETTQKVSLEGKQIGYAKK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
               LY KP G+++   D D   TV D +       +  VGRLD +TEGLLL+TNDG LA
Sbjct: 62  EYYMLY-KPAGVISATKD-DRDKTVLDLITDKKRNDLFPVGRLDKDTEGLLLITNDGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY  +  G+VD+  +     G+ I          + +  + G  + + 
Sbjct: 120 HRLLSPKKHVDKVYYAKVQGKVDESDVKAFADGVDIGDDTPAKSADLRIL-KSGEESEIE 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EG+  ++K++F     +V  L R+S G   L  TL  G  R ++++ +++ 
Sbjct: 179 LTITEGRFHQVKRMFHAVGKEVIYLKRLSMGSLALDKTLTKGEYRSLTEEEIKKL 233


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 108/376 (28%), Positives = 169/376 (44%), Gaps = 38/376 (10%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRK 69
            + +R+ K+IA AG+ASRR+ E ++   RV VNG +           TD I VDG PL+ 
Sbjct: 1   MSSERLQKIIAAAGMASRRKAEELVTAGRVTVNGEVKNELGSKADPETDDIRVDGKPLK- 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE+    L HKP G VTT SDP+GR TV D +  I +R+  VGRLD  +EGLLLLTNDG 
Sbjct: 60  AEQLVYVLLHKPKGYVTTVSDPEGRETVMDLVKGIPARLYPVGRLDYLSEGLLLLTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------QG-------- 169
           +A  L   ST   + Y V+  G+  ++++  L+ G+ +            +G        
Sbjct: 120 MAAKLTHASTHVPKKYLVKVSGEPTEEQIQELRNGVQLPPEQGHIHADPREGGRFGGEKR 179

Query: 170 ----ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
               +     ++ L T++G N W  V L EG+NR+I+++F+F    V ++ R+ YGP +L
Sbjct: 180 RSTAVKTAPCKIEL-TREGDNPWYEVTLNEGRNRQIRRMFDFIGHHVEKIKRVEYGPLKL 238

Query: 226 GTLLAGSTREVSKKIL----REQLGPHLLEEAQVNLDAPIYS-SETLVRDRPNIISEVPD 280
             +  G  R ++   +    +   G H    A+        +  E     R       P 
Sbjct: 239 -DVENGEFRLLNPAEVARLKKAAEGKHEAPRARDEKPRFAKARGERPAFGRGRSDDRAPF 297

Query: 281 DFTRMKKNSSQKNGLSKQKKLAT-----PVHRRNLASNVWMAKGIHSSFLSDSGQREENH 335
                K  S  ++   ++ + A                    K    +  +  G+R++  
Sbjct: 298 QKGSYKDRSELESEKGERTRTARFDADGKRMEEAPRERRERPKFDRGARPAFRGKRDDAR 357

Query: 336 RRSPSFPSKRSLRRTS 351
              P+F  KR   R  
Sbjct: 358 GERPAFRGKRDDARGE 373


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 120/236 (50%), Gaps = 8/236 (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 ++   +  + D +     R+ ++GRLD ++EGL+L+TNDG +   
Sbjct: 60  VYIAVHKPVGITST-TEKKVKGNLVDMVNHPL-RIFNIGRLDKDSEGLILMTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  + +  ++ G+ I G      +V   ++   N    + L
Sbjct: 118 ILRAEGEHEKEYIVSVDKPITPEFVEQMEAGVKILGQKTLPCKVRPLSKFDFN----ITL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            +G NR+I+++ E   ++V RL R+      LG L  G  R++SKK  REQL   L
Sbjct: 174 TQGLNRQIRRMCEALGYEVFRLQRVRVMNITLGKLPPGQWRDLSKKE-REQLFREL 228


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 118/230 (51%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K++++AG+ASRR  E +I + RV+V+G  +    + V+ +  I V+G  +    
Sbjct: 40  EPVRLQKLLSQAGVASRRASEDLIKRGRVQVDGETVTEMGLKVLPSARITVNGQRIHTDA 99

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++W ++KP+G V+T    D R  + D    +  RV  VGRLD+ T GL+LLTN+G LA
Sbjct: 100 ALQVWAFNKPVGTVSTMQPEDDRPCLGDWATKLPQRVFHVGRLDVATAGLILLTNNGDLA 159

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y     GQV      +L++G+ ++          L   +  ++ V +
Sbjct: 160 NRLVHPRYEVPKTYVAMVQGQVKPGLGKVLRRGVELEDGVTKVDTFKLVEVRRGSSIVQL 219

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L  GKNR ++++       V+ L R + G  +LG L  G  R ++   L
Sbjct: 220 TLHSGKNRVVRRLLSEVGHPVSALTRTAIGTLRLGDLKEGHFRLLTGSDL 269


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 76/234 (32%), Positives = 115/234 (49%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ KV+A+AG+ASRR  E MI Q RV+VNG  +    + V  + D I VDG  +   
Sbjct: 53  EGVRLQKVLAQAGVASRRHAEIMITQGRVEVNGTRVTTQGMRVDPSRDVIRVDGTRINVN 112

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
           E    ++++KP G+ +T  D   R++V   L        R+  VGRLD +TEGLLLLTND
Sbjct: 113 EELEYFVFNKPRGVQSTMKDEMDRTSVGSYLSERTASGQRLFHVGRLDADTEGLLLLTND 172

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  + Y     G+     +  L++GI +         V +       +
Sbjct: 173 GELANRLMHPRYEIAKTYMATVLGEAKPALVKKLREGIELDDGPAKADYVQIVDTHNGQS 232

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V L EG+   ++++ +     V RL+R      QLG +  GS R ++   L
Sbjct: 233 IIRVELHEGRKHIVRRMLKAAGHPVQRLVRTKVHTVQLGDMKPGSLRALNAAEL 286


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 76/252 (30%), Positives = 120/252 (47%), Gaps = 24/252 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ K +A AG  +R EV++ I + +V+VNG   ++  + V    D + + G  +  A   
Sbjct: 6   RLDKFLADAGKGTRSEVKKFIQKGQVQVNGAPAKKPELKVDPEKDTVILSGETVGVAPEF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+   D + R TV + +PS    +  VGRLD +TEGLLL+T+DG LA  
Sbjct: 66  VYYLLNKPAGCVSATEDRNDR-TVMEYVPSDRKGIFPVGRLDKDTEGLLLITDDGMLAHE 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-------- 185
           L  P     + Y VR  G++  +K+  L+ G+ I G     M   ++   GS        
Sbjct: 125 LLAPGKHVDKTYFVRVEGKLTVEKIEKLENGVDI-GEKKLTMPAKVEIVGGSWEGAGEPE 183

Query: 186 ------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGS 232
                          + + + EGK  ++K++ E     V  L RIS GP  L   L  G 
Sbjct: 184 PGRVRRENLPEVYTELHLTIHEGKFHQVKRMMEAVGTPVIYLKRISMGPLILPDDLKKGE 243

Query: 233 TREVSKKILREQ 244
            R ++ + LR+ 
Sbjct: 244 CRSLTDEELRKL 255


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 127/231 (54%), Gaps = 1/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             +R+ KV+A AG+ SRR  E+MIA  RV+V+G+ +    V +  +   + VDG+P++  
Sbjct: 45  QGERLQKVLAAAGLGSRRACEQMIADGRVEVDGVPVTELGVRIDPSRQKVAVDGLPVQLD 104

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +     +++KP+G+++T  D +GR +V D   +   R+  VGRLD +T GLLLLTNDG L
Sbjct: 105 DSKVYLVFNKPVGVISTMEDEEGRLSVGDYTYTRKERLFHVGRLDQDTSGLLLLTNDGEL 164

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L+ PS    + Y  +  G V +   NLL++G+ ++         ++   +   A V 
Sbjct: 165 AHRLQHPSYSVPKTYVAKVPGPVKKGLGNLLREGVELEDGVVKVDDFSVVASQPGWAMVQ 224

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+   ++++ E   + V  L+R   G  ++G L  G+ R V+   L
Sbjct: 225 LVIHEGRKHVVRRLLEEVGYPVEELVRTQVGEIRMGDLRPGNLRAVTPDEL 275


>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 =  252 bits (644), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 85/245 (34%), Positives = 136/245 (55%), Gaps = 8/245 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
                  Q++ KV+A+AG+ SRRE+E +IA  +V +NG   +     + + D + V G  
Sbjct: 66  TSPQPVTQKLHKVLAQAGLGSRREMEELIASGQVTINGKTAQ-VGDRIAARDVVRV-GKR 123

Query: 67  L----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGL 121
           +          R+ LYHKP G + +  DP GR++VFD LP    S+ I++GRLD NT GL
Sbjct: 124 VVHFRSARRLPRVMLYHKPEGEIVSQDDPQGRTSVFDKLPQLRSSKWIAIGRLDYNTSGL 183

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+ T DG LA  L  P  +  R Y VR  G++  ++  LL  G+ ++        ++ + 
Sbjct: 184 LVFTTDGELANRLMHPRFEVEREYAVRIIGRLTPEQATLLTSGVELEDGAAKFDYLSDEG 243

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            +GSN W  V L+EG+NRE++++FE     V+RL+R+ +GP  L + L  G + E+++  
Sbjct: 244 GEGSNHWYRVILKEGRNREVRRMFEAVGMTVSRLMRVRFGPINLPSRLKRGKSMELNEAE 303

Query: 241 LREQL 245
           +   L
Sbjct: 304 IGRLL 308


>gi|291513764|emb|CBK62974.1| pseudouridine synthase family [Alistipes shahii WAL 8301]
          Length = 455

 Score =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 125/250 (50%), Gaps = 10/250 (4%)

Query: 2   KDKNIVQENFTPQ------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
            DK      F P+      R+++ IA++GI SRRE +  I    V VNG ++      V+
Sbjct: 203 DDKPASYPKFNPEKQTGEMRLNRFIAQSGICSRREADDFITAGVVSVNGKIVTELGTKVL 262

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
            TD +  +  P++  E+    + +KP G VT+  DP    TV + +      R+  VGRL
Sbjct: 263 PTDEVRFNDEPVQ-GEKKVYLVLNKPKGYVTSLDDPHAGKTVMELVSGACTERIYPVGRL 321

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D N+ GLLL TNDG L + L  PS +  ++Y+V     + +  ++ + +G+ ++      
Sbjct: 322 DKNSLGLLLFTNDGDLTKQLTHPSYKKKKIYQVTLDKPLTRADMDRIAEGVTLEDGEIFA 381

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +++    K +   V + +  G+NR ++++FEF  + V +L R+ Y       L  G+ R
Sbjct: 382 DEISYV--KENKQEVGIEIHSGRNRIVRRIFEFLGYTVTKLDRVYYAGLTKKNLKRGAWR 439

Query: 235 EVSKKILREQ 244
            ++++ +   
Sbjct: 440 FLTREEVERL 449


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 103/235 (43%), Gaps = 2/235 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +     A+R E  R++    V VNG+  +  +V V     +E DG  L+     
Sbjct: 1   MRLDKFLCETTGATRSEATRIVKSGTVTVNGVKTKVTSVKVTDDSTVEWDGRELKF-HGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  +  KP G V +H D    S +         ++   GRLD++T GL+L+T+DG  +  
Sbjct: 60  RYIMLFKPDGYVCSHEDSTHPSALTLLDEVNLEKLHFAGRLDVDTTGLVLITDDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + YRV     +       L +GI ++      M  T++        + + +
Sbjct: 120 ITSPKRKCPKTYRVWLDEPIGAYYAEQLTEGIQLKSETGLIMPATMEVVNEEEHELLLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           +EGK  ++K++F     KV  L R   G   L  +L  G  R ++ + ++  L  
Sbjct: 180 QEGKYHQVKRMFAALGNKVEGLHRSQIGGLGLDYSLEPGEYRYLTAEEVKAVLSK 234


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 102/309 (33%), Positives = 146/309 (47%), Gaps = 9/309 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---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 VHRRNLASN 313
             +      
Sbjct: 303 GEQGARNKQ 311


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 108/234 (46%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R +  + I Q  VK+NG +++  AV +   D I  +   L   E  
Sbjct: 1   MRLDKFIAENVGLTRSQATKAIRQSAVKINGEIVKSGAVQISQEDKIYFEDELLTWVEEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ HKP G V ++ D D   T++       + ++ S GRLD++T G +LLT+DG  + 
Sbjct: 61  QYFMLHKPQGCVCSNDDGDY-PTIYQFFDYPLAGKLHSAGRLDVDTTGFVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+++      +GI+++          L+     N  V + 
Sbjct: 120 RITSPKHHCEKTYLVTLADPVEENYAAACSEGILLRREKEPTKPAKLEILDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EG+  ++K++F     KV  L R   G   L  +L  G  R +++  + + +
Sbjct: 178 ISEGRYHQVKRMFAALGNKVVGLHRWKIGDVVLDESLEEGEYRPLTQSEIEKLV 231


>gi|269467788|gb|EEZ79546.1| 16S rRNA uridine-516 pseudouridylate synthase [uncultured SUP05
           cluster bacterium]
          Length = 241

 Score =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 88/237 (37%), Positives = 137/237 (57%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----K 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   SR + VGRLD+NT GLLL TN+G 
Sbjct: 61  EEETKVIILNKQAGVICSNKDKEGRKSAYDLLPKE-SRWVMVGRLDLNTSGLLLFTNNGD 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            V L+EGK RE+++++E   +KV+RLIRI +G  +L  +L A     +  K ++  L
Sbjct: 180 KVVLKEGKKREVRRLWEALGFKVSRLIRIRFGEIRLPDSLRANQYEYLKSKQVQSLL 236


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 116/235 (49%), Gaps = 1/235 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKA 70
           T +R+ KV+AR G+ SRR  E +IAQ RV V+G ++      V      I VDG+ ++  
Sbjct: 8   TGERLQKVLARNGVGSRRACEGLIAQGRVSVDGHVVRELGTRVDPVASVIHVDGIRVQTD 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                   +KP G+V+T  D  GR  +   +     R+  VGRLD +TEGL+LL+NDG L
Sbjct: 68  SSLLTLALYKPPGVVSTMYDDMGRPGLAQYVEDRPERLYHVGRLDQDTEGLILLSNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  + Y  R  G V +    +L++GI ++       +  L      N+ V 
Sbjct: 128 THRLTHPKYEVPKTYIARVEGSVTRGLGRVLERGITLEDGPARVDRFILRESAPRNSIVE 187

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L  G+NR ++++       V  L+R+ +G   +G L  G TR V+   L   +
Sbjct: 188 ITLHSGRNRIVRRMMAEVGHPVMELVRMKFGTVVVGHLKPGKTRVVAGSELGALM 242


>gi|254743404|ref|ZP_05201089.1| ribosomal large subunit pseudouridine synthase F [Bacillus
           anthracis str. Kruger B]
          Length = 235

 Score =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 7/232 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     +  D L  +  G+ I G      ++T    + S     + L
Sbjct: 118 ILRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R   
Sbjct: 174 TQGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQRRDLTKKEKRRLF 225


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 76/241 (31%), Positives = 123/241 (51%), Gaps = 8/241 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVP 66
            E+    R+++ +A  GIASRR  ++++A  RV VNG + +   + ++   D + VDG  
Sbjct: 4   TEDEGGIRINRYLAMCGIASRRAADKLVADGRVTVNGKIADEPGLRILPFKDEVIVDGRK 63

Query: 67  -LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +    +    L +KP  ++TT  D   R T+ D + S+  RV  VGRLD  T G++LLT
Sbjct: 64  FVVPEAKKVYILLNKPRNVITTSHDEKDRETILDLV-SVEERVYPVGRLDRKTTGVILLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQK 183
           NDG LA  L  PS+   + Y      +  Q  L+ L  G+ ++  G      Q  L    
Sbjct: 123 NDGILAHRLMHPSSNVKKEYVAELDKRFPQGLLSQLVGGMKLKDTGEKVSPCQAKLLD-D 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G   W  + + EGKN +++++ E   + V +L R++Y   + G L  G+ R +SK  +RE
Sbjct: 182 GMRIW--ISIHEGKNHQVRRMLETLGFDVTKLERVAYAGLKAGDLRRGAWRHLSKNEVRE 239

Query: 244 Q 244
            
Sbjct: 240 L 240


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 112/241 (46%), Positives = 157/241 (65%), Gaps = 8/241 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     R++K++ARAG+ASRREVERMI   RV ++G  +E  A  + S   + VDG P+ 
Sbjct: 14  DRPDGDRIAKLLARAGVASRREVERMITDGRVALHGKPVETPATFLESLRGVTVDGKPVG 73

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLL 124
           KAE TRL+ ++KP GL+T  +DP GR+T++D L +       RV+ +GRLD NTEGLLLL
Sbjct: 74  KAEPTRLFAFNKPTGLLTAENDPKGRATIYDALKNALPKDAGRVMPIGRLDFNTEGLLLL 133

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDGGL R +ELPS+   R YR R  G + Q++L  L +GI I G+ YG +   L+ +  
Sbjct: 134 TNDGGLKRRMELPSSGIPRTYRARAFGDITQEQLESLIEGIEIDGVRYGRIDANLEQKTK 193

Query: 184 ---GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              G N W+ + + EGKNRE+++V E F  +V+RL+R++YGPFQLG L  G   E+ K  
Sbjct: 194 SAGGRNQWIEMTITEGKNREVRRVLEHFGLEVSRLMRVAYGPFQLGDLPRGQAVEIRKGD 253

Query: 241 L 241
           L
Sbjct: 254 L 254


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 99/298 (33%), Positives = 150/298 (50%), Gaps = 17/298 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV ++G +       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIA-SLGDRIEADAKVRIDGRAISLKSA 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V LREG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVELPKSLPRGGWVELPVEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
             G  L  E +  L A  +S          I   V     R  K +        +++ 
Sbjct: 241 LAG--LEPETRTMLAADKHSVARAQVKSAKIRRAV-----RKHKVTGAGKAKPTRQRS 291


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 101/296 (34%), Positives = 151/296 (51%), Gaps = 16/296 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV ++G +       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIA-SLGDRIEADAKVRIDGRAISLKSA 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V LREG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVELPKSLPRGGWVELPMEQVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             G  L  E +  L A  +S          I         + K   S K   S+Q+
Sbjct: 241 LAG--LEPETRTMLAADKHSVARAQVKSAKIRR----AVRKHKVTGSGKPKPSRQR 290


>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 =  252 bits (644), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 120/231 (51%), Gaps = 6/231 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+   +A++G  SRR  E++I   RVKVN  ++      V   D + VDGV     ER
Sbjct: 6   PIRLQSFLAKSGWGSRRSCEQLIIDGRVKVNSQVVRELGTKVDKDDAVYVDGVLAEPNER 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
           T  +  HKP G V +++DP+      D +       + ++GRLD  + GL+L TNDG ++
Sbjct: 66  TYYYALHKPAGYVCSNADPNESYFARDLIDVPERNLLFNIGRLDKESTGLVLFTNDGEIS 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
           +++  PS +  + Y V     +  + L   + GI I     Y   +  L+T++    WV 
Sbjct: 126 QLITHPSYEIEKEYLVNTDRTIMIEDLQEARHGIRIDDGRPYRISRYKLETKR----WVR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+NREI+K+F +  + V +LIRI  G  +LG L     R V+K  +
Sbjct: 182 IILTEGRNREIRKIFTYLGYDVKKLIRIRIGTLELGDLAPAQFRRVTKDEI 232


>gi|299139090|ref|ZP_07032266.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
 gi|298598770|gb|EFI54932.1| pseudouridine synthase [Acidobacterium sp. MP5ACTX8]
          Length = 307

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 89/303 (29%), Positives = 138/303 (45%), Gaps = 36/303 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A+AGIASRR  E +I + RV+VNG ++        +T DHI VDG  L   E  
Sbjct: 14  RLQKILAQAGIASRRAAETIILEGRVQVNGQVVTELGTRADATRDHIRVDGKLLHGPEPQ 73

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-----------PSIFSRVISVGRLDINTEGLL 122
           R ++ +KP G VTT  DP+ R TV   L            +   R+  VGRLD  +EGLL
Sbjct: 74  RYFMVNKPRGYVTTLDDPEHRPTVMQLLGQDAQKKSVGEHNKLPRLYPVGRLDYLSEGLL 133

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC----------- 171
           L+TNDG LA  L   +    + Y V+  G    + ++ L++GI+I               
Sbjct: 134 LMTNDGELANKLSKAAAGVEKTYLVKVSGSPTDEAIDQLRRGIMIDRGRLNEVRSGRRDR 193

Query: 172 --YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 ++    ++G N W  V L EG+NR+++K+FE     V ++ RI YG   L  + 
Sbjct: 194 VLTSPAKIE-QVRRGENPWFEVTLTEGRNRQLRKMFEEIGHHVEKIRRIGYGALVL-DIP 251

Query: 230 AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            G  RE++   ++                      +  + +   +   VP      KK  
Sbjct: 252 PGGFRELTTGEVQAL---------GRAAAGKKVERKKTLPEAAQLKKPVPPKKRAFKKAV 302

Query: 290 SQK 292
            ++
Sbjct: 303 RKR 305


>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 =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 127/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVNPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPVTDEFVTGMAAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L E    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIELFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                +     A      T ++     + +  +  +R   N  +     ++KK
Sbjct: 236 IENSSSGTKPKAKAKPKTTGIKRPVVKMEKTAEKGSRPASNGKRFTSPGRKKK 288


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 112/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+  + +++V VNG +       +    D I      L   E 
Sbjct: 1   MRLDKFLVDCGLGSRSQVKIYLKKKQVTVNGQVETSPKTQIDEKKDQIAYQSQELTH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPKGVISATEDARHK-TVLDLLDETARHKQVFPVGRLDIDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     ++Y+ +  G +D+  +   +KGI ++       ++ + +  Q    + 
Sbjct: 119 AHAMLSPRKHVDKIYQAKVAGVMDEADMQAFEKGIELKDHTCQPAKLEILSVDQAVKTST 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           V V + EGK  ++K++      +V  L R+S G   L   L  G+ R ++++ L
Sbjct: 179 VQVTIAEGKFHQVKRMVAACGKEVTDLQRLSMGSLVLPDDLEIGTWRRLTQEEL 232


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG  SRR  E +I Q RV++NG ++      V    D ++V
Sbjct: 125 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEINGEIVLEQGRRVDPEKDEVKV 184

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 185 DGLTV-ATQSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 243

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q
Sbjct: 244 LLTNHGELAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQ 303

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V+ L+R ++GP  LG   +G  R +S   +
Sbjct: 304 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDNLVRTAFGPITLGDQKSGWLRRLSNTEV 362


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 104/301 (34%), Positives = 147/301 (48%), Gaps = 13/301 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRREIESLIKSGRVSVNGIVAKLGERLEDENSVVRIDGHIVSAKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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+    +S    R R   I        R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNKD-NTSRKRERARSQKIRR---AVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 P 304
           P
Sbjct: 298 P 298


>gi|332993790|gb|AEF03845.1| pseudouridine synthase [Alteromonas sp. SN2]
          Length = 298

 Score =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 108/310 (34%), Positives = 152/310 (49%), Gaps = 27/310 (8%)

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---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + +  DP+GR TVFD LP+    R I+VGRLD+NT GLLL TNDG
Sbjct: 61  QPVCRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRMGRWIAVGRLDMNTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------Q 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 --LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
             LR+ +   L EE Q  +D      +     R            R  K    +      
Sbjct: 241 NSLRDIV--QLPEETQTMVDVRQGKLDHARLSR----------MRRSVKKHKVRKENGGV 288

Query: 299 KKLATPVHRR 308
           KK      +R
Sbjct: 289 KKRVARTPKR 298


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 113/230 (49%), Gaps = 3/230 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+++ +A +G+ SRR+ ++ I    VK NGI +      V  TD+I      +R +E 
Sbjct: 54  PIRLNRYLANSGLCSRRKADKYIQTGLVKKNGIPVTEFGTRVNRTDNITFCNSLVR-SEH 112

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L +KP   VTT +DP GR TV D +  +   ++  VGRLD NT G+LLLTNDG L+
Sbjct: 113 KVYLLLNKPKNCVTTTNDPQGRLTVMDLIKTACKEQIFPVGRLDRNTTGVLLLTNDGKLS 172

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     ++Y V  +  +D   +  L KGI ++        ++    K     + +
Sbjct: 173 AKLTHPRHMKKKIYHVWLNRGIDAADIKKLSKGIQLEDGGIWADDISYVNDK-DKTQINI 231

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  G+N  I+++FE   + V +L R+ +       L  G    ++ + +
Sbjct: 232 EIHSGRNHIIRRMFESLGYHVVKLDRVYFAGLTKKKLKKGQWCFLNDREV 281


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 74/241 (30%), Positives = 119/241 (49%), Gaps = 5/241 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K K     + T  R+++ IA +G+ SRRE + +IA   + VNG ++      V   D ++
Sbjct: 394 KGKRTPANDGTT-RLNRFIANSGVCSRREADELIAHGDISVNGKIVTEMGYKVKEGDTVK 452

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEG 120
             G  +   ER    L +KP   +TT  DP+ R TV + +      R+  VGRLD NT G
Sbjct: 453 Y-GTKVLNPERFVYVLLNKPKDYITTTEDPEERKTVMELVADAGKFRMYPVGRLDRNTTG 511

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL+TNDG LA  L  PS    ++Y+V     +  +    +KKGI ++        +++ 
Sbjct: 512 LLLITNDGELADKLTHPSNNIRKIYQVELDKPITDEHFEAIKKGIELEDGPIKPDAISIV 571

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T       V + +  G+NR ++++FE F ++V +L R +Y       L  G  R +  K 
Sbjct: 572 TPDA--YVVGIEIHSGRNRIVRRIFESFGYEVTKLDRTTYAGLTKKELPRGKWRFLDPKE 629

Query: 241 L 241
           +
Sbjct: 630 V 630


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 121/233 (51%), Gaps = 5/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + +R EV++MI +  V V+G+++++    V     + V    +    +  
Sbjct: 7   RLDKYLADMQVGTRSEVKQMIRKGLVTVDGLIVKKPEEKVDCEKQVVVCSGAIVSYHQYE 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   DP  + TV D +     + +   GRLD +TEGLLL+TNDG LA  
Sbjct: 67  YYMLNKPAGVVSATEDPRDK-TVIDLIEDRRRKDLFPAGRLDKDTEGLLLITNDGALAHD 125

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y  +  G V ++ + L  KGI I +        +T+ +  G  + +T+ 
Sbjct: 126 LLSPKKHVDKKYYAKIEGTVTEEDVELFGKGIDIGEKRVTLPAVLTILS-SGEESEITLT 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           +REGK  ++K++FE    KV  L R+S G   L   LL G  R+++++ L + 
Sbjct: 185 IREGKFHQVKRMFEAVGKKVTYLKRLSMGSLVLDEKLLPGEYRKLTEQELTQL 237


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 113/237 (47%), Gaps = 13/237 (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  + D + +   R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  VYIALNKPVGITCT-TERHIRGNIIDFI-NHPERIFPIGRLDKDSEGLILLTNDGSIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNA 187
           +     +  + Y V  + ++    +  + KG+ I      +       ++     + ++ 
Sbjct: 118 ILAEENKHEKDYIVTVNKKITPSFIEGMSKGVKIYNPVKNKDTMTKRCKLV----RINDR 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + L +G NR+I+++   F ++V +L R+      L  L  G  R ++++ +++ 
Sbjct: 174 TFKITLCQGLNRQIRRMCTHFGYRVVKLKRVRIMNLTLKDLTIGKWRNLTEEEVKDL 230


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 90/266 (33%), Positives = 143/266 (53%), Gaps = 12/266 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + ++N   QR+ K +A  G+ SRR++E  I + R+KV+G +       +   + + +DG 
Sbjct: 1   MNKKNDDAQRIQKYLAARGVGSRRQIETWIKEGRLKVDGRVA-ELGQKISGNERLSLDGK 59

Query: 66  PLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEG 120
           PLR A   +    + +YHKP G + T  DP+GR +VF +LP I   R +++GRLD+NT G
Sbjct: 60  PLRIAVEHKNPHMILMYHKPAGEICTRKDPEGRVSVFQHLPKISHGRWVAIGRLDLNTSG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL- 179
           LLL TNDG LA  L  PS +  R Y VR  G+V ++ L  L++GI +        ++   
Sbjct: 120 LLLFTNDGALANQLMHPSAEIEREYWVRVAGEVTEEMLTALRQGIPLDDGLARFTEICPL 179

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
               +     N + +V L+EG+NRE+++++E    KV+RL RI YG   L  +L AG  R
Sbjct: 180 KTLHEDDTQFNRYFSVTLKEGRNREVRRLWEAVGCKVSRLKRIRYGTISLPPSLSAGRHR 239

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAP 260
            ++       +     +  + N   P
Sbjct: 240 LLTAGEQASLISLVSEKNRRDNSPKP 265


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLTDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 63/226 (27%), Positives = 112/226 (49%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV++  G  SR+E++  + +  ++V+G +++   + V      I+V+G  +    +
Sbjct: 2   ERLDKVLSNLGYGSRKEIKAFVKKGEIEVDGKVVKDNGIKVDPNKSIIKVNGEEINYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L   ++      VGRLD +TEGLLL+TNDG L
Sbjct: 61  YIYIMMNKPAGVVSATFD-NYDETVIDLLDYEYTVFDPFPVGRLDKDTEGLLLITNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y       VD+  +   KKGI +  G      ++ + +   + + V
Sbjct: 120 NHRLTSPKWHVDKTYYAEIDKMVDEKDVEKFKKGITLDDGYKCLPAKLEILSSDENGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + ++EGK  ++K++FE     V  L R++ G   L   L  G+ R
Sbjct: 180 NITIQEGKFHQVKRMFEARGKNVVYLKRLTMGNISLDEELDEGTYR 225


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 122/236 (51%), Gaps = 8/236 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I    V+VNG ++   +  V    D +  DG  +  
Sbjct: 1   MAKMRLDKLLSNMGIGTRKEVKKYIKDGLVEVNGEIVLDPSKTVDTEKDEVLFDGEKVEY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTND 127
            E   + + +KP G+++   D     TV D LP      +V  VGRLD +TEGLL++TND
Sbjct: 61  KEFIYVMM-NKPQGVISATHD-KSEETVIDLLPEEIALRKVFPVGRLDKDTEGLLIITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G LA  L  P  + ++ Y     G++ +      K+G++++   Y  M   L+  + S+ 
Sbjct: 119 GELAHKLLSPKKKVVKKYYAEVLGKITEKDAEKFKEGVILEDG-YRTMPSQLEIIESSDI 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V V L EGK  ++K++FE    KV  L R+  G  QL   L  G  RE++++ +
Sbjct: 178 SKVYVYLTEGKYHQVKRMFEAIGKKVLYLKRLCMGKLQLDENLEPGEWRELTEEEV 233


>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 =  252 bits (643), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 81/251 (32%), Positives = 132/251 (52%), Gaps = 12/251 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
           +R+ K++++ GIASRR+ E+MI   RVKVNG +++         D+IEVDG+P+R   R 
Sbjct: 3   ERLQKILSQWGIASRRQAEQMIIAGRVKVNGKIVQLGEKAQPDLDNIEVDGLPIRPEARP 62

Query: 73  -TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KP+G+++T S+P  RS V D L +       +  VGRLD ++ G LLLTNDG
Sbjct: 63  SPIYLLLNKPMGVISTCSEPRKRSKVLDILNAELRNGKGIHPVGRLDADSTGALLLTNDG 122

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSNA 187
            +   L  P     + Y+V   G   +  L L ++GI++ G      +V +  +   S  
Sbjct: 123 RVTYCLTHPKYCLSKTYQVLVEGHPQESILKLWRQGIILSGKKTLPAEVKVLKECNSSQT 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKILR 242
            + V + EG+NR+I++V +    +V +L R + G  +L       L  G  R++    + 
Sbjct: 183 LLEVVISEGRNRQIRRVADKLGHRVLKLHRTAIGQIKLQLPGESVLPIGHYRQLKDFEI- 241

Query: 243 EQLGPHLLEEA 253
           E L   ++E  
Sbjct: 242 EFLDDQIIESK 252


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 117/235 (49%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ ++  +++ VN   ++   + +    D ++ +   +   + 
Sbjct: 1   MRLDKFLANSGIGTRKEVKEILKNKKISVNDAFVKDGKIQIDEEKDIVKYEDNII-YYKP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   R TV D L   +    +  VGRLDI+TEGLLLLTNDG L
Sbjct: 60  FVYIMMNKPAGVISATEDNHHR-TVIDLLNDEYRTYDIFPVGRLDIDTEGLLLLTNDGIL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNA 187
           +  L  P     + Y V+    + ++ +  L+ GI + +       +V +     + +  
Sbjct: 119 SHNLLSPKKHVDKKYYVKISNPLTEEDIKTLENGIKLEENFVTKKAKVKIICNNSEKNEN 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
              + + EGK  ++K++F+  N +V  L R+  G   L   L  G  RE++++ L
Sbjct: 179 LAYITISEGKFHQVKRMFKAVNNEVLYLKRVKMGSLSLDEKLKLGEYRELTEEEL 233


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 121/239 (50%), Gaps = 2/239 (0%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           K         +R+ KV+ARAG  SRR  E +I Q RV++NG ++      V    D ++V
Sbjct: 125 KTFPGAEQEGERLQKVLARAGYGSRRACEELIEQARVEINGEIVLEQGRRVDPEKDEVKV 184

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           DG+ +   +  + +  +KP G+V+T  DP+GR  + D + +  +R+  VGRLD  TEG++
Sbjct: 185 DGLTV-ATQSYQFFSLNKPAGVVSTMEDPEGRQCLGDYVTNRETRLFHVGRLDTETEGVI 243

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTN G LA  L  P     + Y     G + +D    LK GI ++          +  Q
Sbjct: 244 LLTNHGELAHRLTHPRYGVKKTYLAHIVGPIPRDLGKRLKDGIQLEDGYARADHFRVVEQ 303

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N  V V L EG+   ++++     + V+ L+R ++GP  LG   +G  R +S   +
Sbjct: 304 TGKNYLVEVTLHEGRKHIVRRMLAEAGFPVDNLVRTAFGPITLGDQKSGWLRRLSNTEV 362


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 77/229 (33%), Positives = 114/229 (49%), Gaps = 8/229 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V    D I  DG  +  
Sbjct: 1   MAKMRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTEFDEILFDGEKINY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G+++   DP    TV D LP          VGRLD +TEGLLL+TND
Sbjct: 61  KE-FIYIMMNKPKGVISATYDP-IEKTVIDLLPQELKARNPFPVGRLDKDTEGLLLITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G LA  L  P    ++ Y     G V++  +   K+GIV++   Y  +   L+    S  
Sbjct: 119 GNLAHKLLSPKKNVIKKYYAEILGFVNERDIKAFKEGIVLEDG-YKTLPADLEILLSSEV 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           + V V +REGK  +IK++FE    KV  L R++ G   L   L  G  R
Sbjct: 178 SKVYVYIREGKYHQIKRMFESVGKKVVYLKRLAMGSLTLDENLKPGQWR 226


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 77/251 (30%), Positives = 132/251 (52%), Gaps = 21/251 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK-AER 72
           R++K +A AG+ SRR  + +IA  RV VNG  +    + V   TD +EVDG P++  A+ 
Sbjct: 6   RINKALADAGVCSRRRADELIAAGRVSVNGEPVASPGLQVTPGTDKLEVDGKPVQPIAQA 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP+ +V+T  DP+GR+TV D +P+ +   R+   GRLD  +EGL+LLT+DG L
Sbjct: 66  PCYLLLNKPVRVVSTAYDPEGRTTVLDLVPAKWKARRLYPAGRLDFFSEGLVLLTDDGEL 125

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--- 186
              +  P     RVY V   G V    L +++KG+ + +G     +++ +   +  +   
Sbjct: 126 TNRVVHPRHHMPRVYHVLIRGGVSDRALEVMRKGMTLAEGEKLAPVEIRVLPGQVHDLSG 185

Query: 187 -------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                          + + L +G NR+I+++    +  + RL+R++ GP +LG +  G  
Sbjct: 186 VSRNAGPPAGQRGTLLEMTLHQGLNRQIRRMCRDLHLTILRLVRVAQGPLRLGVMKPGEA 245

Query: 234 REVSKKILREQ 244
           RE++   +   
Sbjct: 246 RELTPAEVAAL 256


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 117/236 (49%), Gaps = 8/236 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K +++AG  SRRE ++++ Q RV +NG  +      V S D + VDG  + K
Sbjct: 2   NKESIRINKYLSQAGFCSRREADKLMEQGRVTINGEYI-EMGTKVNSGDKVYVDGKLVEK 60

Query: 70  A-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E       +KP G+V T +    ++ + D +    +R+  +GRLD  +EGL+L+TNDG
Sbjct: 61  ETEEKVYLAVYKPKGVVCTTNSKVEKNNIVDFV-DYPTRIFPIGRLDKMSEGLILMTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +        + Y V  +  +  D +  ++KG+ I        +V    +K  +  
Sbjct: 120 EIVNHILRARHFHDKEYLVTVNKTITDDFIEKMRKGVPILDTMSRRCEV----EKLGDRS 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + L +G NR+I+++ E  +++V  L R       L  +  G+ R ++++ +++ 
Sbjct: 176 FKIVLTQGLNRQIRRMCEALDYRVRTLKRTRIKNITL-DVEKGNYRNLTEEEIKDL 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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 100/289 (34%), Positives = 154/289 (53%), Gaps = 10/289 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDG 64
           I Q+    +R+ KV+AR G  SRR +E MI+  R+ ++G +      V++ S   I +DG
Sbjct: 60  INQQKVEGERLQKVLARVGQGSRRTIEAMISANRISIDGKMATLGDRVDIHSGVKIRIDG 119

Query: 65  VPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
             +     + E  R+ LY+KP G + T  DP+GR+TVFD LP    SR I+VGRLDINT 
Sbjct: 120 HIVNLTQAQKEVCRVLLYYKPEGELCTRHDPEGRATVFDRLPRLNGSRWIAVGRLDINTS 179

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL T DG LA  L  P  +  R Y VR  G+VD   +  L+KG+ ++        +  
Sbjct: 180 GLLLFTTDGELANRLMHPRHEVEREYAVRVFGEVDDTMIARLRKGVQLEDGPANFTSIKA 239

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE--V 236
              +G N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E  +
Sbjct: 240 TGGQGMNQWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLTKSLPRGGWEEMDL 299

Query: 237 SK-KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           +    LR+ +G     +++++   P       +R      +E+   + +
Sbjct: 300 TNINYLRKLVGLPPETDSKIDTKKPRRIKTGQIRKAVKRYTELNKRYKK 348


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 94/295 (31%), Positives = 149/295 (50%), Gaps = 16/295 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       + +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-NLGDRIEADVKIRIDGRTVSIKSE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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 WWHVTLAEGRNREVRRLWESQEVQVSRLIRIRYGKIELPKSLPRGGWVELTMEQV----- 235

Query: 247 PHLLEEAQVNLDA-PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            +L + A +N +   +  ++     R  +         R  +          +K+
Sbjct: 236 NYLRKTAGLNEETRTVLGTDKHSVARSKVKG---SKIRRAVRKHKAVASKPGRKR 287


>gi|302387646|ref|YP_003823468.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302198274|gb|ADL05845.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 262

 Score =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 110/238 (46%), Gaps = 15/238 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
              R++K ++ AGI SRRE +R I   +V +NG         V+    + ++G  ++   
Sbjct: 4   EGIRLNKFLSEAGICSRREADRFIEAGKVSINGKAAAT-GQKVLPGQSVTINGRTVQAGK 62

Query: 69  ----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                 E       HKP G+V T S  D    + D +     R+  VGRLD ++EGL+L+
Sbjct: 63  GDQSHKEEPVFLAVHKPRGIVCTTSHKDRAPNIVDMV-DYPVRIYPVGRLDKDSEGLILM 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQ 182
           TN G L   +        + Y V+ +  V  D +  +KKG+ +    +      VT   +
Sbjct: 122 TNQGSLVNKMMRSGNAHEKEYLVKVNRPVTDDFIRTMKKGVFLPELNVTTKPCFVTKAGE 181

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           K       + L +G NR+I+++     ++V  L R+     +LG L  G+ RE+SK+ 
Sbjct: 182 KA----FRIVLTQGLNRQIRRMCSQLGFEVRMLKRMRIMNIELGDLKPGAYRELSKRE 235


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 101/274 (36%), Positives = 143/274 (52%), Gaps = 17/274 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ K++AR+G  SRRE+E  I +  V VNG +      V+VM +  I +DG  L   E
Sbjct: 2   SEKLQKILARSGYGSRREIEEKIQRGLVSVNGKISTLGDRVSVMPSTQIRLDGRILPITE 61

Query: 72  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+K  G + T  DP GR TVFD LP    SR I +GRLDINT GLLL T 
Sbjct: 62  PQKIPCRVLAYYKIEGEICTRKDPKGRPTVFDRLPKLHHSRWIGIGRLDINTSGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y  R  GQV++  +  L +GI ++       +VT    +G N
Sbjct: 122 DGELAHRLMHPSQEIEREYASRIFGQVNEPSIKQLTQGIQLEDGMAAFRRVTFGGGEGLN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV---SKKILR 242
            W  V L EG+NRE+++++E    +V+RLIRI YG  +L   L  G  +E+   +   LR
Sbjct: 182 HWYNVILTEGRNREVRRLWEAIGVQVSRLIRIRYGDIKLPKGLPRGGWKEMDISTIHYLR 241

Query: 243 EQLGPH-------LLEEAQVNLDAPIYSSETLVR 269
           E +G         L+E+ +     P      + R
Sbjct: 242 ELVGLKKDITNTLLIEKKEQRFFKPRQIRRAVKR 275


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV++++ +  VKVN  + +     V    D I VDG  +     
Sbjct: 1   MRLDKFLSNMGVGTRTEVKQLLKKNSVKVNDKVEKSPKSQVDPEQDEITVDGKIIEYI-N 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G V+   D D   TV D +       +  VGRLD +TEGLLL+TNDG   
Sbjct: 60  HVYIMLNKPKGYVSATYD-DINQTVIDLIADYRHLDLFPVGRLDKDTEGLLLITNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS    + Y+V     +  + +   K GI +        Q+       S     V
Sbjct: 119 HNLMSPSKHVSKTYKVTSKYPIKNEDIIAFKNGIELSDGKVKPAQLEKLDHNVS----LV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++F   + +V  L R+      L   L +G  R ++ + L+
Sbjct: 175 TIYEGKYHQVKRMFHSIDNEVLELKRLKISNLTLDENLKSGEYRLLTSEELK 226


>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 =  252 bits (643), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 132/300 (44%), Gaps = 15/300 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           T  R++K I+ +GI SRRE +R + +  V +NG   +     V + D ++V+G  +    
Sbjct: 5   TTTRLNKYISESGICSRREADRFVEKGSVFINGKRAK-VGDQVSAGDTVKVNGQIIDPRD 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            ER  L   +KP+G+V T    +  + V  +  +   R+  +GRLD +++GL+ LTN+G 
Sbjct: 64  EERLVLIALNKPVGVVCTTEGSEKNNIV--DYVNHGERIFPIGRLDKDSQGLIFLTNNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +     +  + Y V     +    +  + KG+ I G      ++     K +    
Sbjct: 122 LVNKILRAGNRHEKEYLVTVDKPITDTFIRDMAKGVPILGEVTRKCKIV----KETPTLF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F + + RL R+      +  L  G  R+ S+  L   L    
Sbjct: 178 RITLVQGLNRQIRRMCDHFGYDIVRLERVRIMNVSMKGLGVGEWRDFSQNELAGIL--ES 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS----QKNGLSKQKKLATPV 305
             ++Q               DRP    +    ++  KK+ S     KNG +   K + P 
Sbjct: 236 TADSQSAAAPSKKRKPAKTGDRPWYPEKPKSAYSSRKKSPSGTPKAKNGGASGDKPSRPP 295


>gi|332359298|gb|EGJ37119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 242

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 116/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKGLVLVNGRAEKSPKTQIDERADEIVVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++       Q+ +    ++  ++ 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMEQADVERFAAGIELKDFTCQPAQLKILELDEEKESSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL  TL  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVAACRKEVTDLQRLTMGPLQLDPTLALGEWRRLTTDELERL 235


>gi|312127717|ref|YP_003992591.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
 gi|311777736|gb|ADQ07222.1| pseudouridine synthase [Caldicellulosiruptor hydrothermalis 108]
          Length = 233

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 113/232 (48%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I    V VNG  +      +    D +EVDG  ++ + R
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIRGGIVTVNGKRIVEVDFKINPEEDVVEVDGRIVKFSRR 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ DP    TVF  +     +  + +VGRLD + EGLL++T+DG  
Sbjct: 61  I-YIMMNKPKGYVCSNDDP-ASLTVFSLISDNLKYRDLHTVGRLDKDAEGLLIITDDGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P  +  + Y VR   +VD+++L   + GI++  G      + T+      +  V
Sbjct: 119 THRVISPRKRIEKEYLVRLEKEVDEERLKEFENGIILDDGYKTLPAKYTI----IDSTTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++K++FE    KV  L R+  G   L  +L  G  R + ++ 
Sbjct: 175 KLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDESLKPGEYRVMKEEE 226


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 74/246 (30%), Positives = 119/246 (48%), Gaps = 4/246 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           +K      ++    R+++ I+ AGI SRR+ + +I    + VNG ++      V    D 
Sbjct: 194 VKQATSDYDDNGMIRLNRYISNAGICSRRKADELITAGVISVNGEVVTELGSKVDPAKDE 253

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           I+ +G  L++ E+    L +KP   +TT  DP  R TV   + +    R+  VGRLD NT
Sbjct: 254 IKYNGERLKR-EKMVYVLLNKPKDYITTTDDPQERRTVMQLVANATKERIYPVGRLDRNT 312

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG LA  L  P     ++Y V     ++Q   N +  G+ ++        ++
Sbjct: 313 TGLLLLTNDGNLAEKLSHPRNNISKIYNVELDKSLNQGDFNKIVFGLELEDGFVKPDDLS 372

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q GS   V + +  GKNR ++++FE   + V +L R+ Y       L  G  R + +
Sbjct: 373 Y-VQGGSKREVGIQIHSGKNRIVRRIFESLGYDVVKLDRVVYANLTKKDLPRGRWRYLEE 431

Query: 239 KILREQ 244
           K L + 
Sbjct: 432 KELIQL 437


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 121/242 (50%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K+++ +   P R++K +A AGI SRRE +  I    V VNG+++      V  TD I
Sbjct: 5   IEYKDVLTDPDEPIRLNKFLANAGICSRREADEFITAGVVSVNGVVVTELGTKVKRTDEI 64

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 65  KFHDQPVN-IERKVYVLLNKPKDCVTTSDDPQERKTVMDFVKGACKERIYPVGRLDRNTT 123

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  GI +         V+ 
Sbjct: 124 GVLLLTNDGDLASKLTHPKYLKKKIYHVYCDKNVTKADLDQIVSGITLDDGEIHADAVSY 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++    + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 184 ASET-DKSQVGIEIHSGKNRIVRRIFEALGYRVIKLDRVYFAGLTKKGLRRGDWRYLTEQ 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 98/290 (33%), Positives = 149/290 (51%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKA 70
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V     I +DG    ++ A
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIAT-LGDRVEVDAKIRIDGRTTSIKTA 60

Query: 71  ERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           +    R+  YHKP G + +  DP+GR TVF+ LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V L+EG+NRE+++++E    +V+RLIR+ YG  +L  TL  G   E+       LR+
Sbjct: 181 WWHVTLKEGRNREVRRLWESQEIQVSRLIRVRYGMVELPKTLPRGGWIELPLDQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             G      + +  D    +   +   +     +     +   K S Q++
Sbjct: 241 LAGLEAETRSMLGSDKHSVARSKVKSSKIRRAVQKHKVISSRAKPSRQRD 290


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 117/235 (49%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +     
Sbjct: 1   MRLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPEVDVIRVDGVRVNVNNN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGG 129
            + ++ +KP G+ +T SD  GR  + D +    S    +  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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V L EG+   ++++ +   + V  L+R      QLG    G+ R ++   LR  
Sbjct: 181 RVQLHEGRKHIVRRMLKAAGYPVQYLVRTKLHTVQLGEQKPGTIRALNDNELRSL 235


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 99/290 (34%), Positives = 147/290 (50%), Gaps = 12/290 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV ++G + +     + +   + +DG  +     
Sbjct: 7   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIAK-LGDRIEADAKVRIDGRTVSIKSE 65

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG   L  +L  G   E+  +    LR+
Sbjct: 186 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIDLPKSLPRGGWVELPIEQVNYLRK 245

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             G  + EE +  L    +S          I   V    T   K   Q++
Sbjct: 246 LAG--MDEETRTLLGTDKHSVARAKVKSAKIRRAVRKHKTTAGKTPRQRS 293


>gi|325695507|gb|EGD37407.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 242

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ ++ V VNG   +     +  T D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQLLKKELVLVNGRAEKSPKTQIDETADEIIVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHKTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A  +  P     ++YR +  G ++Q        GI ++       Q+ +     +   + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMNQADEERFAAGIELKDFTCQPAQLKILELDAAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + L EGK  ++K++      +V  L R++ GP QL   L  G  R ++   L   
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQLDFALALGEWRRLTTDELERL 235


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPGKDRVTFMGEDLVH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPAGVISATED-DHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
           A  +  P     ++YR +  G +D+  +   + GI ++       ++ +     +N  ++
Sbjct: 119 AHAMLSPKKHVSKIYRAQVAGIMDEADVARFEAGIALKDFTTLPARLQILEVNEANASSY 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + + EGK  ++K++      +V  L RIS GP  L  +L  G  R +    L
Sbjct: 179 VEIEIAEGKFHQVKRMVAACGKEVADLERISMGPLTLDPSLKLGEWRRLQPSEL 232


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 98/293 (33%), Positives = 145/293 (49%), Gaps = 11/293 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ V+G +       V S   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISVDGEIA-SLGDRVESDVKVRIDGRAISIKSE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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+      EQ+ 
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKSLPRGGWIELP----IEQVN 236

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                         I  ++     R  +         R  K ++  N  S+ +
Sbjct: 237 YLRQTAGMDEETRSILGTDKHSVARAKVRGAKIRRAVRKHKATATPNKPSRSR 289


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 106/301 (35%), Positives = 146/301 (48%), Gaps = 15/301 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKSGRVSVNGIVAKLGERLEDEQAVVRIDGHVVSVKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKKI---LREQ 244
             V + EG+NRE+++++E  +  V+RL R+ YG   L   L  G   E+  K    LRE 
Sbjct: 183 FYVVINEGRNREVRRLWESQDCTVSRLKRVRYGDIYLDKKLPRGGWMELELKDVNYLREL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +     +E  + L+    SS    R R   I        R ++  S   G S       P
Sbjct: 243 VELRPEKETMIELN---NSSRKRDRARSQKIRR---AVKRHEERVSTPKGRSNNAARRKP 296

Query: 305 V 305
            
Sbjct: 297 S 297


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 116/231 (50%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I+  GI SRRE + +I Q++VKVNG +       V S D IEV+G  L+K +  
Sbjct: 1   MRLNNFISSTGICSRREADELIKQKKVKVNGEIA-PLGYIVNSKDKIEVNGKLLQKKKND 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T ++   +  + D + +   R+  +GRLD ++EGL+LLTNDG +   
Sbjct: 60  IYIALNKPVGITCT-TERHIKGNIIDFI-NHTERIFPIGRLDKDSEGLILLTNDGSIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           +        + Y V  +  +    +N + KG+ I         +T      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|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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 62/285 (21%), Positives = 109/285 (38%), Gaps = 17/285 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
              R++K I+ +G  SRRE +++I    V VNG             D + V+G  ++   
Sbjct: 3   DGIRLNKFISDSGYCSRREADKLIEDDLVLVNGQPPT-LGTRCHPGDVVYVEGKRIKSRA 61

Query: 70  ----AERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                       Y+KP  +  T   D  G      +      R+  +GRLD  +EGL+LL
Sbjct: 62  NAGSQADREYIAYNKPTHITCTTEADVVGN---IISAVGYKKRIFPIGRLDKMSEGLILL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG +   +        + Y V     +    +  +  G+ I G      ++ +  +  
Sbjct: 119 TSDGDIVNKILRAENAHDKEYLVTVDKPITDKFIEKMGNGVPILGTKTLPCKINMQGE-- 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L EG NR+I+++ E+F ++V +L R+      LG L  G  R+++   L + 
Sbjct: 177 --FMFKIILTEGLNRQIRRMCEYFGYEVTKLKRVRIMNITLGNLKPGEWRKLTANQLTDI 234

Query: 245 LG--PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
                H   +A       I         +   I        R  +
Sbjct: 235 NNAIEHSSGDAAPKGAKLIRRKPKKPSQQERAIKSKTPKVVRTPR 279


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 122/241 (50%), Gaps = 4/241 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K++          R+++ I+ +G+ SRRE +++I    + VNG ++      V  TD ++
Sbjct: 147 KERTQRHNEPEKMRLNRFISNSGVCSRREADKLIEMGMISVNGKVITEMGFQVSPTDTVK 206

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEG 120
             G  L K E+    L +KP   +TT +DP  R TV D + +    R+  VGRLD NT G
Sbjct: 207 Y-GKRLLKREKFVYVLLNKPKDFITTTNDPQDRKTVMDLIKNSCDERIYPVGRLDRNTTG 265

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL TNDG +A+ L  PS    +VY+V     +  + L+ + +G++++       ++ + 
Sbjct: 266 LLLFTNDGEVAKKLSHPSHDVKKVYQVELDKPLKDEDLDSIAEGVILEDGYAAVDEIAIL 325

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                   V V +  G+NR ++++F   +++V +L R  Y       +  G  R +S+K 
Sbjct: 326 --NPERTLVGVEIHIGRNRIVRRIFNHLDYEVVKLDRTMYAGLNKKNIDRGDWRYLSEKE 383

Query: 241 L 241
           +
Sbjct: 384 V 384


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 82/241 (34%), Positives = 129/241 (53%), Gaps = 3/241 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV V+G  +  A+  V  ST  I VDG+ +  AE   
Sbjct: 72  LPRALSKLGYCSRTQAERLIAESRVAVDGRTVSDASAWVDLSTARISVDGLVI-AAEAKI 130

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L +     +  VGRLD  +EGLLL TND   A+ 
Sbjct: 131 YLMLNKPRGLVTTRQDPEGRPTVYDCLKNFDIPHLSPVGRLDKASEGLLLFTNDTEFAQT 190

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D +++  +  GI   G            Q   N+W+ V L
Sbjct: 191 LLDPLTHVTKTYHVQIDRLMDDEEIAAMTSGIRHDGELLTAAATRRLRQGDRNSWIEVEL 250

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++  L+       +E A
Sbjct: 251 DEGRNRQIRRMLEALGAECLRLVRVAIGGLELGELPKGAVRALTEGELQGLRRRAGMERA 310

Query: 254 Q 254
           +
Sbjct: 311 R 311


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/252 (29%), Positives = 120/252 (47%), Gaps = 6/252 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           + K+    +    R+++ I+ AGI SRR+ + +I    V VNG ++      V    D I
Sbjct: 270 RKKSTTDADKGKIRLNRYISNAGICSRRKADELIVAGVVSVNGQVISELGFKVDPYKDEI 329

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
             +G  L++ E+    L +KP   +TT  DP  R TV   +      R+  +GRLD NT 
Sbjct: 330 RYNGETLKR-EKMVYVLLNKPKDYITTTEDPQERRTVMHLVDKASKERIYPIGRLDRNTT 388

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL+TNDG LA  L  P +   ++Y V     + Q  LN +  GI ++        V+ 
Sbjct: 389 GLLLMTNDGDLADKLSHPKSNISKLYHVELDKSLSQGDLNKIAYGIELEDGLIKPDSVSY 448

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             Q  S   V + +  GKNR ++++FE   + V +L R  Y       L  G  R + ++
Sbjct: 449 -VQGASKREVGIQIHSGKNRVVRRIFESLGYDVVKLDRAIYAGLTKKDLPRGRWRYLEEQ 507

Query: 240 ILREQLGPHLLE 251
            + +    HL++
Sbjct: 508 EVIQL--KHLIK 517


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 121/229 (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   R+ + GRLD  TEG++L++NDG     
Sbjct: 60  EYYLLYKPKKVICTNSDNFARRLAVDFIRSK-KRLFTYGRLDYMTEGIILVSNDGDTYNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +    ++   L  L+KGI+I G      ++     K  +A V V +
Sbjct: 119 VMHPRKKLFKTYIAKLDKPIEDKDLARLEKGILIDGQKTAPAKIK----KTDDAEVKVSI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+FE  ++ V  L R++ G F++G L  G  R++++  + 
Sbjct: 175 FEGRNRQIRKMFENLHYNVKELKRVTIGEFKIGNLKPGEYRKLTEDEIE 223


>gi|329725501|gb|EGG61981.1| pseudouridylate synthase [Staphylococcus epidermidis VCU144]
          Length = 230

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V    D I V+   +   ++
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     T+ D LP      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATEDELH-PTIIDLLPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P+    + Y V     + Q  ++  K GI +              +K  +    V
Sbjct: 119 HEVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSDGKLKPA----ILKKVDDYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYRLLTQ 222


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 91/346 (26%), Positives = 138/346 (39%), Gaps = 13/346 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K +ARAG+ASRR  E +I   RV VN   +      V   TD + 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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--EQLGPHLL 250
           + EG+   IK++       V RL R +Y    +  +  G  R ++   +R  + +     
Sbjct: 183 VAEGRPHLIKRLCAAVGHPVVRLFRPAYAGVGVSGVRPGELRPLTSTEVRLLQDVAEART 242

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT---RMKKNSSQKNGLSKQKKLATPVHR 307
              +  L+ P                    +           S+    +K  +       
Sbjct: 243 APPEGELNLPPRRHGRAAPGFEEDEDGEGFEVEGAAAAPAKPSRSPAAAKTGRARPAAAG 302

Query: 308 RNLASNVWMAKG-------IHSSFLSDSGQREENHRRSPSFPSKRS 346
           R        +               S +   EE   R      K+S
Sbjct: 303 RPERKPAGKSPRTEGGTGLARFGRTSSAAVSEEGSERPRRSEWKKS 348


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 105/334 (31%), Positives = 161/334 (48%), Gaps = 20/334 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E +IA+ RV VNG ++      V   D I +DG P+   + 
Sbjct: 2   SEKLQKVLARAGLGSRREMEAVIAEGRVSVNGEMVT-LGTRVEEVDRIRLDGNPVSVVKE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + T  DP+GR TVFD LP + S 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 EQ-----LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK---NSSQKNG 294
                  L P     +    +  I         + N   + P    R+ K    +++  G
Sbjct: 241 YLRTLVSLPPETTARSLERKETRIRQGRIRRSLKNNDARQKPTRSGRLGKEIEETTESRG 300

Query: 295 LSKQKKLATPVH-RRNLASNVWMAKGIHSSFLSD 327
            S+ K   + +   R         +G  +   + 
Sbjct: 301 KSRTKPTGSGIPLHRGKKGPAKQQRGPKAKKRTR 334


>gi|220929584|ref|YP_002506493.1| pseudouridine synthase [Clostridium cellulolyticum H10]
 gi|219999912|gb|ACL76513.1| pseudouridine synthase [Clostridium cellulolyticum H10]
          Length = 245

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 122/236 (51%), Gaps = 8/236 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
             QR+ KV++  G  SR  ++  + +  V V+G +++ + ++V      IE+DG  L   
Sbjct: 3   QKQRLDKVLSNFGFGSRNYIKGAVKKGLVTVDGRIIKDSGIHVDPEVSIIEIDGERLNYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
            +    + +KP G+++  SD   + TVFD LP  +    +   GRLDI+TEGL+L+TNDG
Sbjct: 63  -KYIYIMLNKPQGVISATSDRK-QKTVFDILPEEYKCFDLFPAGRLDIDTEGLVLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-A 187
            L+  +  P     + Y  +  G+V+Q+      +G+ +    Y  +   L+  K  + +
Sbjct: 121 QLSHEILSPKKHVPKQYYAKVMGRVNQEDAEAFSRGVTLDDG-YQTLPAVLEILKSDDLS 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + + EGK  ++K++FE    KV  L R+S G  +L  +L  G  +E+ +  + 
Sbjct: 180 EIKLTIVEGKFHQVKRMFEAVGKKVIYLKRLSMGNLRLDESLQLGECKELGESDIE 235


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 126/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSIRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDVVKVNGRLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSTSEVKPKAKAKPKTAGIKRPVVKMEKTSEKGGRPASNGKRFTSPGRKKK 288


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 101/296 (34%), Positives = 151/296 (51%), Gaps = 16/296 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV ++G +       + +   + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSIDGEIA-SLGDRIEADAKVRIDGRSISLKSA 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V LREG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVCLREGRNREVRRLWESQEVQVSRLIRIRYGMVELPKSLPRGGWVELPMEQVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             G  L  E +  L A  +S          I         + K   S K   S+Q+
Sbjct: 241 LAG--LEPETRTMLAADKHSVARAQVKSAKIRR----AVRKHKVTGSGKPKPSRQR 290


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 78/248 (31%), Positives = 123/248 (49%), Gaps = 12/248 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           MK  N   E     R+++ +A  GIASRR  ++++   RV VNG ++    + V  T D 
Sbjct: 1   MKKSNKDDE----VRINRYLASCGIASRRAADQLVLDGRVMVNGTVITTPGIKVSPTRDE 56

Query: 60  IEVDGVPLRKAE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           + VDG    + E R    L++KP  ++TT+SD   R  V D +  +  RV  VGRLD  T
Sbjct: 57  VIVDGEKFAQPEHRKVYILFNKPRNVITTNSDEKNREMVLDFI-DVEERVFPVGRLDRKT 115

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQ 176
            G++LLTNDG LA  L  PS+   + Y      +   + L  L  G+ ++  G      +
Sbjct: 116 TGVILLTNDGTLAHKLMHPSSNVKKEYIAELSEKFTPNLLPQLTGGMRLKDTGEKVSPCR 175

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +         V V + EGKN +++++FE   ++V RL R++Y     G L  G  R +
Sbjct: 176 AKIL---EDGMQVLVSIHEGKNHQVRRMFETLGFEVKRLERVAYAGLLAGELRRGEWRYL 232

Query: 237 SKKILREQ 244
           S+  ++  
Sbjct: 233 SRNEVQAL 240


>gi|332752067|gb|EGJ82460.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           4343-70]
          Length = 290

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 124/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R ++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRYLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 103/300 (34%), Positives = 146/300 (48%), Gaps = 13/300 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVSAKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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  ++ +    +S    R R   I        R ++  S   G S       P
Sbjct: 243 VELRPEKETLLDENK-ANTSRKRERSRSQKIRR---AVKRHEERVSSGGGRSNNPSRRKP 298


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 112/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  +R EV++ + +  V VNG + + A   +    D +++ G  +   E 
Sbjct: 2   MRLDKFLAHMGQGTRTEVKQSLKKGNVTVNGKVEKSAKTQIDPHHDVVQIHGHQIDYVE- 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
           T   + +KP G ++   DP  ++TV D +    +  +  VGRLD +TEGLLL+TNDG  +
Sbjct: 61  TVYLMLNKPKGYISATEDPK-QATVIDLIKDYKYLDLFPVGRLDKDTEGLLLITNDGQFS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     V +D   + K+G+++        ++T+     S     V
Sbjct: 120 HNLMNPNKHVAKTYLVTSKYPVTKDNQYMFKQGVMLSDGLTKPAELTIIDDYHS----KV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + EG+  +IK++F     +V  L RI     +L   L  G  R +++  + + 
Sbjct: 176 TIYEGRYHQIKRMFHSIENEVLELKRIQIANLRLDEELDEGQYRVLTQTDIEQL 229


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 66/223 (29%), Positives = 105/223 (47%), Gaps = 3/223 (1%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A AGI SRR+ ++ I    + VNG ++      V+ +D I     P+R  E+    L +
Sbjct: 1   MANAGICSRRDADKYIQAGVITVNGKVVTELGTKVLRSDDILFHESPVRL-EKKVYVLLN 59

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           KP G +TT  DP  R TV + +      R+  VGRLD NT G+LLLTNDG LA  L  P 
Sbjct: 60  KPKGCITTSEDPQERKTVMNLVKGACQERIYPVGRLDRNTTGVLLLTNDGELAAKLTHPQ 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               ++Y V     V    L  +  GI +         +   ++      + + +  GKN
Sbjct: 120 FMKKKIYHVYLDKNVSGVDLQKIADGITLDDGEIKADDIQYASET-DKKQIGIEIHSGKN 178

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           R ++++FE   + V +L R+ +       L  G  R +++  +
Sbjct: 179 RIVRRIFESLGYHVVKLDRVYFAGLTKKHLRRGDWRYLTQDEV 221


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 79/234 (33%), Positives = 120/234 (51%), Gaps = 4/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E +IAQ RV+VNG ++ R  V V   T  I VDGV ++  E  
Sbjct: 110 RLQKVLAQAGVASRRMSEELIAQGRVEVNGEIVMRQGVRVDPDTAVIRVDGVRVKVNEDL 169

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
                +KP+G+ +T  D  GR  V D +         +  VGRLD  TEGLLLLTNDG L
Sbjct: 170 VYIALNKPLGVQSTMKDDMGRPCVGDIVGEKVDAGLHLFHVGRLDAKTEGLLLLTNDGEL 229

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G+ D++ +  L++G+ ++        V +       + + 
Sbjct: 230 ANRLMHPKYHVSKTYLATVLGEADRELVKKLREGVDLEDGIAKADYVQIVDTYEGRSLIR 289

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V L EG+   ++++ +   + V +L+R      QLG L  G+ R ++   LR  
Sbjct: 290 VELHEGRKHIVRRMLKELGFPVQQLVRTKIHTVQLGELTPGAIRHLNDSELRAL 343


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 104/229 (45%), Gaps = 3/229 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V     +  +       GI+++G         L T   S   V + +
Sbjct: 121 LTSPRHHCEKDYLVTLEQPLAAEITAQFAAGILLRGEKLPTRPARLAT--LSPLKVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++   +
Sbjct: 179 SEGRYHQVKRMFAAVGNRVVALHRERIGAIVLDAHLQPGEYRALTAGEV 227


>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 =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 107/296 (36%), Positives = 155/296 (52%), Gaps = 13/296 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +++ KV+AR G+ SRR +E  IA  RV VNG + +     V + D I VDG  LR     
Sbjct: 3   EKLQKVLARFGLGSRRLMEEWIAAGRVVVNGQIAK-LGDRVTAQDKIAVDGETLRIPSWV 61

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
             R R+  YHKP G +TT +DP GR TVFD LP    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+  +  R+ L  
Sbjct: 182 YHVTLAEGRNREVRRLFEAVGLTVSRLIRVRYGVVEMPRLLKTGYFDELPDEE-RDAL-- 238

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L     VN   P   S+++ R    +     ++  R  + +  +    + ++   
Sbjct: 239 -LASVQWVNPATP--PSDSVERVTAPLPDARKNNSRREARQTPSRGRPGQGRRTVR 291


>gi|332999092|gb|EGK18679.1| ribosomal large subunit pseudouridine synthase F [Shigella flexneri
           K-218]
          Length = 291

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 67/295 (22%), Positives = 125/295 (42%), Gaps = 9/295 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R ++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRYLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                ++    A        ++     + +  +   R   N  +     ++++ A
Sbjct: 236 IENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKRRDA 290


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 104/351 (29%), Positives = 157/351 (44%), Gaps = 18/351 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +          T  + +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAILGERLEDETAVVRIDGHAVSAKAP 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK---ILRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LR+
Sbjct: 182 TFYVVINEGRNREVRRLWESQGTTVSRLKRVRYGDIFLDKKLPRGGWVELDLKQVNYLRD 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +E  ++      +S    R R            R  K   ++   +  K  + 
Sbjct: 242 LVELRPEKETMLDESKD-NTSRKRERSRS-------QKIRRAVKRHEERITTTTAKPKSR 293

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
             +      +   A    +     S  R     +S    ++    +  A +
Sbjct: 294 VTNGTTTGGSTGNAP-TRARRKPGSSTRNSAQEQSSRQGTRAPSGKAKAPR 343


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 74/246 (30%), Positives = 119/246 (48%), Gaps = 4/246 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           +K      ++    R+++ I+ AGI SRR+ + +I    + VNG ++      V    D 
Sbjct: 194 VKQATSDYDDNGMIRLNRYISNAGICSRRKADELITAGVISVNGEVVTELGSKVDPAKDE 253

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINT 118
           I+ +G  L++ E+    L +KP   +TT  DP  R TV   + +    R+  VGRLD NT
Sbjct: 254 IKYNGERLKR-EKMVYVLLNKPKDYITTTDDPQERRTVMQLVANATKERIYPVGRLDRNT 312

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLLTNDG LA  L  P     ++Y V     ++Q   N +  G+ ++        ++
Sbjct: 313 TGLLLLTNDGNLAEKLSHPRNNISKIYNVELDKSLNQGDFNKIVFGLELEDGFVKPDDLS 372

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q GS   V + +  GKNR ++++FE   + V +L R+ Y       L  G  R + +
Sbjct: 373 Y-VQGGSKREVGIQIHSGKNRIVRRIFESLGYDVVKLDRVVYANLTKKDLPRGRWRYLEE 431

Query: 239 KILREQ 244
           K L + 
Sbjct: 432 KELIQL 437


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 127/293 (43%), Gaps = 11/293 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
             R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     
Sbjct: 6   SIRLNKYISESGICSRRDADRYIEQGNVFINGKRVA-LGDRVFPGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +       +KP+G+V+T  D +  + V  +  +  +R+  +GRLD +++GL+ LTN G L
Sbjct: 65  DNLIFIALNKPVGVVSTTEDGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + ++ L  G+ + G            +K +     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTDEFIHGLGAGVPMLGTVTK----KCKVKKVAPFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E     L+
Sbjct: 179 IVLVQGLNRQIRRMCEHFGYEVTKLERTRIMNVGLAGLPLGEWRDLTDDELVELF--KLI 236

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           E++         +   + +   +   +   D       + ++     +KK   
Sbjct: 237 EDSSSEAKPAKKAKPAVKKPASSGNGQRTADKPSGNPAARKRFTQPGRKKKGR 289


>gi|310659128|ref|YP_003936849.1| pseudouridylate synthase [Clostridium sticklandii DSM 519]
 gi|308825906|emb|CBH21944.1| pseudouridylate synthase [Clostridium sticklandii]
          Length = 236

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 107/237 (45%), Gaps = 13/237 (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  VYIALYKPVGITCTTEEHIEGNIV--DYVNYKERIFPIGRLDKDSEGLILLTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------ICYGDMQVTLDTQKGSNA 187
           +        + Y V     +D   L  + +G+ I              ++     K S  
Sbjct: 118 ILREENHHEKEYIVTVDKPLDSKTLKQMSQGVRIYNPVKNTYTTTKPCKI----HKISEK 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + L +G NR+I+++ + F +KV +L R+      L  L  G  R +++  +   
Sbjct: 174 SFKIVLSQGLNRQIRRMCQHFGYKVRKLKRVRILNITLDGLSYGKWRFLNQAEVSSL 230


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 129/248 (52%), Gaps = 9/248 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKA 70
             QR+ KVI+  G  SR +++  + +  V V+G +++ + ++V      IE++G  L   
Sbjct: 3   QKQRLDKVISNFGFGSRNDIKSAVKKGLVTVDGAIVKDSGIHVDPEASIIEINGERLNYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
            +    + +KP G+++  SD   R TVFD LP  +    +   GRLDI+TEGL+L+TNDG
Sbjct: 63  -KFIYIMMNKPQGVISATSDRKQR-TVFDILPEEYKCFELFPAGRLDIDTEGLVLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-A 187
            L+  +  P     + Y  +  G+V+Q+  +  ++G+ +    Y  +   L+  K    +
Sbjct: 121 QLSHEILSPKKHVPKQYYAKVLGRVNQEDADAFRQGVTLDDG-YSTLPAVLEVLKSDELS 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            + + + EGK  ++K++FE    KV  L R+S G  +L   L  G  +E+ +  + E L 
Sbjct: 180 EIKLTIVEGKFHQVKRMFEAVGKKVIYLKRLSMGNLRLDENLKLGECKELGESDI-ELLK 238

Query: 247 PHLLEEAQ 254
             ++ + +
Sbjct: 239 QAVIPDNK 246


>gi|239997156|ref|ZP_04717680.1| RNA pseudouridine synthase family protein [Alteromonas macleodii
           ATCC 27126]
          Length = 252

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 113/234 (48%), Gaps = 11/234 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---- 67
            P+R++K I+  G+ SRRE +++I Q RV VN          V   D ++VDG  +    
Sbjct: 5   APKRLNKYISDTGLCSRREADKLIEQNRVTVNNQPP-ELGTKVGPGDTVKVDGKVVGAVA 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                    +Y+KPIG+  T ++   +  + D +     R+  VGRLD  +EGL++LT+D
Sbjct: 64  SDKSDRVYIVYNKPIGITCT-TERHVKGNIIDAI-GHKERIFPVGRLDKPSEGLIILTSD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  + +  +N + +G+ I G       V    +     
Sbjct: 122 GDIVNKILRAENAHDKEYEVTVNQPISERFVNRMSRGVPILGTVTKPCVVKPTGKN---- 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             T+ L +G NR+I+++ EF  ++V +L R      +LG+L  G  R ++ + L
Sbjct: 178 TFTIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELGSLKPGQWRNLTSREL 231


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 121/233 (51%), Gaps = 5/233 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A   + +R EV++MI +  V V+G+++++    V     + V    +    +  
Sbjct: 3   RLDKYLADMQVGTRSEVKQMIRKGLVTVDGLIVKKPEEKVDCEKQVVVCSGAIVSYHQYE 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   DP  + TV D +     + +   GRLD +TEGLLL+TNDG LA  
Sbjct: 63  YYMLNKPAGVVSATEDPRDK-TVIDLIEDRRRKDLFPAGRLDKDTEGLLLITNDGALAHD 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P     + Y  +  G V ++ + L  KG+ I +        +T+ +  G  + +T+ 
Sbjct: 122 LLSPKKHVDKKYYAKIEGTVTEEDVELFGKGVDIGEKRVTLPAVLTILS-SGEESEITLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           +REGK  ++K++FE    KV  L R+S G   L   LL G  R+++++ L + 
Sbjct: 181 IREGKFHQVKRMFEAVGKKVTYLKRLSMGSLVLDEKLLPGEYRKLTEQELTQL 233


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 126/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  251 bits (641), Expect = 1e-64,   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|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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 106/347 (30%), Positives = 164/347 (47%), Gaps = 19/347 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----LR 68
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      + 
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSVNGQVAQ-VGERIEPGDELRIDGRKVSFQIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD LP+I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKNDIDNLTK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +    T  R +   ++     F R ++  ++  G  + K    P  
Sbjct: 241 AVELKPRQGTGLYGMAKRRT-ERMQEKPMAARRGGFLRQQRRDNEDEGQQQAK----PAF 295

Query: 307 RRNLASNVWMAKGIHSSFLSD---SGQREENHRRSPSFPSKRSLRRT 350
            R    N       HS    D   +G  +   R++  +  + S    
Sbjct: 296 NRERREN----PNGHSQRRQDNAQTGYGQREPRQNSGYAQRDSRPEN 338


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + +++++ GIASR + +  I   RV++N  L+      +    D + +D  P+ +    +
Sbjct: 3   LDRLLSKLGIASRSQAQEWIRAGRVRINRRLVRMPDTWIDWPGDAVTLDDRPIEQR-PPQ 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             L+HKP G+VTTH D  GR T+FD LP     + +VGRLD  T GLLLLTND  L+  L
Sbjct: 62  FILFHKPKGVVTTHQDEKGRPTIFDVLPPELKGLHAVGRLDQATSGLLLLTNDSTLSSFL 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 VNLDAP 260
           V    P
Sbjct: 242 VPQAKP 247


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   ++
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  YIYLMMNKPAGVISATYDKRD-ETVIDLLYMEDQVFEPFPVGRLDKDTVGLLLLTNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY    +  + +  +   + G+ +  G      ++ +      ++ V
Sbjct: 120 NHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSRV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+  L
Sbjct: 180 EVTVQEGKYHQVKRMFEARGKKVIYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>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 =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 128/290 (44%), Gaps = 18/290 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K I+ +G  SRR+ +++I + +V +NG  +       M  D I V+G  + +     
Sbjct: 9   RLNKAISDSGYCSRRQADKLIEEGKVTLNGNPV-SLGDRAMPDDVIHVEGNLITENNNLV 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP+G+  T +D      V D +     R+  VGRLD  +EGLLL+TNDG +   +
Sbjct: 68  YIILNKPVGITCT-TDLRVEGNVVDYI-DHKERIFHVGRLDKPSEGLLLMTNDGDIVNKI 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V+    +  + +  +  GI ++ +     +  ++  + S     + L 
Sbjct: 126 LRAGNSHEKEYFVKVDRPITTEFIRRMGNGIPLEELETTTKKCFVE--QVSRFVFRIILV 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +G NR+I+++ E+ +++V  L R      +LG L  G  R+++K+ L+            
Sbjct: 184 QGLNRQIRRMCEYLDYEVMELKRERIMNIELGDLPYGEWRDLTKEELQGL---------- 233

Query: 255 VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
              DA   S      DR       P       +N  +     ++ +L  P
Sbjct: 234 --KDAVAKSENDSFIDREEKRKAAP-KTGDANRNRPRNEAPKRESRLKNP 280


>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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 143/304 (47%), Gaps = 13/304 (4%)

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  LRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +   +         +KP+G+V+T  + + R  + D + +   RV  +GRLD +++GL+ L
Sbjct: 58  IAPRDEADLVFIALNKPVGIVSTTENTE-RDNIVDFV-NHSERVFPIGRLDKDSQGLIFL 115

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T++G L   +        + Y V  +  + +  L  ++ G+ + G+     +V    ++ 
Sbjct: 116 TSNGDLVNKILRAGNNHDKEYVVTVNKPITEAFLQGMRAGVPMLGVITKKCKV----EQV 171

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           S     + L +G NR+I+++ E FN++V +L R S     L  L  G  R++ ++ L   
Sbjct: 172 STFVFKIILVQGLNRQIRRMCEHFNFEVTKLERQSIMNVSLKGLPVGEWRDLDEQELSTL 231

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +   L+E +   +      ++           E P+ F + +    +K   +K K   + 
Sbjct: 232 M--KLIEHSSSEVKNAPKKAKKKPTQSLRDKIEGPEHFMQGRGAKPKKPAANKGKPSHSR 289

Query: 305 VHRR 308
             +R
Sbjct: 290 KPKR 293


>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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 126/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 115/231 (49%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ + +V+VNG   +++  ++   TD I VDG  +   ++
Sbjct: 1   MRLDKYLANMGVGTRSEVKQLLKKNKVQVNGKNEKQSKAHINPDTDEITVDGNLIEYVDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G ++   D +  + V         ++  VGR+  +TEGL+LLTNDG    
Sbjct: 61  -VYIMLNKPAGYISATEDEEQSTIVSLIKDFQHMKIFPVGRVGKDTEGLILLTNDGQFNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    ++YRV     +  D +    +G+ +        Q+    +  +     V 
Sbjct: 120 DIMSPNKHVSKIYRVEAKNPITDDDIKQFAEGVELSDGKTKPAQLE---RTENEKVAFVS 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +REG+  ++K++F   + +V  L R+  G  +L   L  GS RE++++ + 
Sbjct: 177 IREGRYHQVKRMFHAIDNEVLNLKRVQIGKLKLDSNLPKGSYRELTQEEIE 227


>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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   ++
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  YIYLMMNKPAGVISATYDKRD-ETVIDLLYMEDQVFEPFPVGRLDKDTVGLLLLTNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY    +  + +  +   + G+ +  G      ++ +      ++ V
Sbjct: 120 NHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSRV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+  L
Sbjct: 180 EVTVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSESEL 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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 112/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  +R EV++ + +  V VNG + + A   +    D +++ G  +   E 
Sbjct: 2   MRLDKFLAHMGQGTRTEVKQSLKKGNVTVNGKVEKSAKTQINPHHDVVQIHGHQIDYVE- 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
           T   + +KP G ++   DP  ++TV D +    +  +  VGRLD +TEGLLL+TNDG  +
Sbjct: 61  TVYLMLNKPKGYISATEDPK-QATVIDLIKDYKYLDLFPVGRLDKDTEGLLLITNDGQFS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     V +D   + K+G+++        ++T+     S     V
Sbjct: 120 HNLMNPNKHVAKTYLVTSKYPVTKDNQYMFKQGVMLSDGLTKPAELTIIDDYHS----KV 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + EG+  +IK++F     +V  L RI     +L   L  G  R +++  + + 
Sbjct: 176 TIYEGRYHQIKRMFHSIENEVLELKRIQIANLRLDEELDEGQYRVLTQTDIEQL 229


>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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 109/234 (46%), Gaps = 8/234 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +R+ K +ARAG+ASRR+ E +I    V VNG+        V + D + V G  +     
Sbjct: 2   SERLQKFLARAGVASRRKAEALILSGAVTVNGVRA-ELGQRVAAGDEVRVRGERVAPPAA 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + L EG+NR+++++      +V RL+R   G   LG +  G  R +S   L + 
Sbjct: 176 LVLSEGRNRQVRRMLAALGCEVTRLLRTRIGGLSLGAMRPGELRRLSDAELAQL 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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>gi|225621236|ref|YP_002722494.1| pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225216056|gb|ACN84790.1| pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 229

 Score =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 112/236 (47%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA   +ASRRE +R+I    VKVNGI+    A  V   D IE      +  E  
Sbjct: 1   MRLNKYIASLNLASRREADRLIQNGNVKVNGIINTNPATQVDENDKIECSIE--QYKENK 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G V + +  +G+  +++ +   F  +  VGRLD ++ GL+L TNDG  A+ 
Sbjct: 59  IYIKLNKPRGYVVSSNKNEGKP-IYNLIKKDFDNIYPVGRLDKDSSGLILFTNDGVFAKQ 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   +T   + Y VR    +    L  L+ GI + G      +V    +        + L
Sbjct: 118 IIGENTNCEKEYYVRVDDNIPDGALQKLEYGISLDGQKLKPAKVKRVNKNS----FHIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            EGKNR+I+++ +   ++V  L R+      L  L  G+ + ++K+ +   L   L
Sbjct: 174 TEGKNRQIRRMCQKVGFEVIILKRLRISGILLEDLKEGTFKSLTKEEIESILKNEL 229


>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 =  251 bits (641), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 123/240 (51%), Gaps = 8/240 (3%)

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  D   ++ +   L     RV   GRLD ++EGLL++TNDG L   
Sbjct: 61  VVLAVNKPAGIVCTG-DMKVKNNIIRFL-HYPVRVTYAGRLDKDSEGLLIMTNDGELINS 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +        + Y VR   ++  + +  + +G+ IQ +      +    + ++      ++
Sbjct: 119 MMRARYHHEKEYHVRVDKEITSEFVRQMSEGVHIQDVEKNLDAVTRPCEVKQIGKYTFSI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR---EQLGPH 248
            L +G NR+I+++ E   +KV +L+RI     +LG+L +G+ R++  + L+   EQ G H
Sbjct: 179 ILTQGLNRQIRRMCEALGYKVTKLVRIRIMNVELGSLKSGAVRKIEGQELKKLYEQAGTH 238


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 94/232 (40%), Positives = 126/232 (54%), Gaps = 5/232 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAE 71
           +++ KV+ARAG+ SRRE+E+ I+  RVK++G +       V     IEVDG  L    AE
Sbjct: 32  EKLQKVLARAGLGSRREMEKWISDGRVKLDGRIA-ELGDRVCDNAAIEVDGQALSRAPAE 90

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
             R  LYHKP G V T  DP+GR TVF+ LP     R IS+GRLD NT GLLL T DG L
Sbjct: 91  AVRCLLYHKPTGEVCTRKDPEGRRTVFERLPKVKGGRWISIGRLDYNTSGLLLFTTDGEL 150

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS    R Y VR  G+ D D L  L  G+ +         +      G N W  
Sbjct: 151 ANALMHPSAVIEREYMVRVMGEWDTDTLQRLIHGVELDDGFARFTDIQDGGGDGINHWFY 210

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V L EG+NRE+++++E     V+RL R+ YG   + + +  G   E+ +K +
Sbjct: 211 VVLMEGRNREVRRLWESQGLTVSRLKRVRYGEVFIPSKVKQGKWMELDQKDV 262


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP I  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVIAIEKSNEKARPASSGKRFTSPGRKKK 287


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVSILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP I  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVIAIEKSNEKARPASSGKRFTSPGRKKK 287


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 119/246 (48%), Gaps = 9/246 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
            R++K +A  G+ SRRE +R I   RV +NG         V   D + +DG  +   +  
Sbjct: 1   MRLNKFLASIGVCSRREADRAIEANRVMINGETA-ELGAIVGEEDLVSLDGRYIATGKDV 59

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  +  ++KP G+V T SD DG + V D +  +  R+  VGRLD ++ GLLLLTN G
Sbjct: 60  EKVKPIIIAFNKPEGVVCTTSDNDGATNVVDYI-GMKERIYPVGRLDKDSSGLLLLTNQG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L   +    + Y V+ +  +D + +N +  GI +  +     +  +  +K +   
Sbjct: 119 SLTNSLLRAANYHEKEYIVKVNKDIDDEFINKISNGIYLYELKTKTRKCKV--RKLNKNT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            ++ L +G NR+I+++      KV +L R+     +L  L  G  R +S + +++     
Sbjct: 177 FSIVLTQGLNRQIRRMCAACGRKVQKLNRVRIVNIKLDGLAVGDYRNLSDEEIKKLYKEL 236

Query: 249 LLEEAQ 254
            +++  
Sbjct: 237 GIKDNG 242


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 113/231 (48%), Gaps = 7/231 (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 S+   +  + D +     R+  +GRLD +++GL+LLTNDG +   +
Sbjct: 64  YIALNKPVGITCT-SEKSVKGNIIDLVNHPL-RISHIGRLDKDSDGLILLTNDGDIVNEI 121

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V     +  D L  +  G+ I G      ++T    + S     + L 
Sbjct: 122 LRAENKHEKEYIVSVDKPITPDFLEKMAAGVKILGTKTLPCEIT----QLSKYEFKIILT 177

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +G NR+I+++ E   ++V  L R      +L  L  G  R+++KK  R   
Sbjct: 178 QGLNRQIRRMCEALGYQVYTLKRTRIMNIELNNLPVGQRRDLTKKEKRRLF 228


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 111/239 (46%), Gaps = 12/239 (5%)

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  RPRPVLLAVNKPKGIVCTTTDKDRAENIVDFL-GYPERIYPVGRLDKDSEGLLLMTNQGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
           L   +        + Y V     V +  L  +  GI +          +V     K    
Sbjct: 121 LVNKIMRSGNAHEKEYIVTIDKPVTERFLEQMAGGIRLPELDQVTRPCKVK----KVERN 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             ++ L +G NR+I+++ E    +V RL+R+     +LG L  G+ R+++K+   E  G
Sbjct: 177 TFSIILTQGLNRQIRRMCEACGCQVKRLVRVRIMNIRLGNLRTGAYRQITKEEYEELTG 235


>gi|295692648|ref|YP_003601258.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030754|emb|CBL50233.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 236

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 115/235 (48%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGVVAVNGKTVKTLKEKINENDVVTVNGEEIAY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  ++ VGRLD +T GLLLLTNDG L 
Sbjct: 60  HYFLVNKPKGVLSATED-RNQKTVISLLDLQDQYQGIVPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAW 188
             L  P+    +VYR +  G  D++       G+++  G      ++ +  Q  + + + 
Sbjct: 119 HELLAPNKHVAKVYRAQIAGVADEETAKAFASGMMLGDGTKLKPAKLKILKQDRENATSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + + + EGK  +IK++F     KV  L R+S G   L   L  G   E+S   ++
Sbjct: 179 IEIEISEGKYYQIKRMFGAVGMKVTALDRLSMGNLHLPSDLKRGKYVELSLDEIK 233


>gi|225620831|ref|YP_002722089.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
 gi|225215651|gb|ACN84385.1| pseudouridine synthase [Brachyspira hyodysenteriae WA1]
          Length = 359

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/345 (27%), Positives = 157/345 (45%), Gaps = 31/345 (8%)

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
           ++  + R    +KPIG+V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 64  KRQTK-RYMALYKPIGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 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 KIRLTINEGKNREIRKIFDHLGYKVIDLERISVGCVSKYDEVSGTLEAGHIRDLTKKEI- 241

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                          D      +  ++D  +I   +PDD        S  N  +  K+  
Sbjct: 242 ---------------DFFFKQKDKKLKDIESIFENIPDDIEDENYEDSILNSSNNDKEEN 286

Query: 303 TPVHRRNLASN---------VWMAKGIHSSFLSDSGQREENHRRS 338
             VH R+  +             +          S + E +  R 
Sbjct: 287 KKVHDRSKWAKAKHKKKRLITKKSSTFKGKMQKKSSKSEFSENRK 331


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 104/301 (34%), Positives = 147/301 (48%), Gaps = 13/301 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  I   RV VNGI+ +           + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRREIESFIKSGRVSVNGIVAKLGERLEDENSVVRIDGHVVSAKIQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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+    +S    R R   I        R ++  +   G S       
Sbjct: 242 LVELRPEKETMLDLNKD-NTSRKRERARSQKIRR---AVKRHEERVNTPKGRSNNPSRRK 297

Query: 304 P 304
           P
Sbjct: 298 P 298


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 116/254 (45%), Gaps = 11/254 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH- 59
           + D +   +     R+ K +A +G+ SR EV+ ++ + RV V G +       V      
Sbjct: 19  LTDLSAKSDIIKDMRLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQ 78

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +  DG  L   E    +L +KP GLV+   D   ++ V       F   +  VGRLD NT
Sbjct: 79  VAFDGEILDYQE-YYYYLLNKPQGLVSATKDNLFKTVVQLLSEKDFREDIFPVGRLDKNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQV 177
           EGLL+LTNDG L   L  P     + Y  R  G+V  + +N   +G+ ++ G      ++
Sbjct: 138 EGLLILTNDGALGHDLTQPKKHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGEL 197

Query: 178 TL------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
            +      ++Q G  + + V + EGK  ++K++FE     V  L RI  G   L   L  
Sbjct: 198 FIENIYEGESQSGWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLAL 257

Query: 231 GSTREVSKKILREQ 244
           G+ R ++ + +   
Sbjct: 258 GAYRPLTTEEIENL 271


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 82/259 (31%), Positives = 135/259 (52%), Gaps = 5/259 (1%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STD 58
           +++    +N   +R  + + +++ G  SR + ER+IA+ RV V+G  +  A+  V  +T 
Sbjct: 11  RERTKPADNAAAKRVTLPRALSKLGYCSRTQAERLIAENRVAVDGRTVSDASAWVDLATA 70

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            I +DG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  
Sbjct: 71  SISIDGLVI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKA 129

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G        
Sbjct: 130 SEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRIMDDEDIAAMTAGIRHDGELLTATAA 189

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 190 RRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALT 249

Query: 238 KKILREQLGPHLLEEAQVN 256
           +  L+       +E  + N
Sbjct: 250 EPELQALRRKTGMERTRRN 268


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 114/236 (48%), Gaps = 11/236 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +  P+R++K I+  G+ SRRE +++I Q+RV VN          +   D ++VDG  +  
Sbjct: 3   DQAPKRLNKYISDTGLCSRREADKLIEQKRVSVNNHPP-ELGTKIGPNDIVKVDGKIVGA 61

Query: 70  AER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             +        +Y+KPIG+  T ++   +  + D +    +R+  VGRLD  +EGL++LT
Sbjct: 62  VAKDKSDRVYIVYNKPIGITCT-TERHVKGNIIDAI-GHKARIFPVGRLDKPSEGLIILT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG +   +        + Y V  +  + +  +  + +G+ I G       V    +   
Sbjct: 120 SDGDIVNKILRAENAHDKEYEVTVNQPISERFVKRMARGVPILGTVTKPCVVKPTGKN-- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               T+ L +G NR+I+++ EF  ++V +L R      +L  L  G  R +++  L
Sbjct: 178 --TFTIILTQGLNRQIRRMCEFLGYEVTKLKRTRIMHLELKALKPGQWRNLTQHEL 231


>gi|327538428|gb|EGF25099.1| ribosomal large subunit pseudouridine synthase B [Rhodopirellula
           baltica WH47]
          Length = 395

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/337 (28%), Positives = 160/337 (47%), Gaps = 4/337 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++++A AG  SRR+ E +I + RV V+G  +      V      + VDG  LR  ++ 
Sbjct: 26  RINQLLASAGFGSRRQCEELIREGRVDVDGETITELGTTVDPDLQKVRVDGNYLR-PQKL 84

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+G+VTT+ DP GR  V D +P    RV  VGRLDI++EGL+LLTNDG LA+ 
Sbjct: 85  VYYVVNKPVGIVTTNRDPRGRPRVIDLVPPT-ERVFPVGRLDISSEGLILLTNDGDLAQK 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++++  + ++L   +    
Sbjct: 204 KEGKNREIRRILARFGHKVQQLRRVAIGPLKLGDVPRGAYRKLTRDEV-DKLRRSIDAAE 262

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           +    AP     +    +        +   +         G  K  K +     R+ A+ 
Sbjct: 263 KAAKTAPPARPASKQSIKRRPGGASRNVAAKGTGGRPAFKGGRKAVKNSRTTETRSSATG 322

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              +K +    LS  G             S++   R 
Sbjct: 323 PKTSKPVKKRTLSSGGSTGTVIGADAPKESRKKTERG 359


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/290 (32%), Positives = 145/290 (50%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEI-SGLGDRVEADAKIRIDGRAVSLKSA 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR+TVF+ LP    +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-GTLLAGSTREVSKK---ILRE 243
           W  V LREG+NRE+++++E  + +V+RLIR+ YG  +L  TL  G   E+       LR+
Sbjct: 181 WWHVTLREGRNREVRRLWESQDVQVSRLIRVRYGKVELPKTLPRGGWIELPMDQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
             G      + +  D    +   +   +               K + Q++
Sbjct: 241 LAGLEAETRSVLGSDKHSVARSKVKSAKIRRAVHKHKVVGNHGKPTRQRS 290


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN  +++   ++V    D I V+   +   ++
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGSVKVNQNIVKLPKLHVNPNSDEIMVNDEVVSYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     T+ D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATEDELH-PTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P+    + Y V     + Q  ++  K GI +              +K  +    V
Sbjct: 119 HEVMNPNKHVSKTYEVYSKHPITQFDIDKFKSGIELSDGKLKPA----ILKKVDDYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAQLELDHNLDLGSYRLLTQ 222


>gi|323975348|gb|EGB70451.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
          Length = 290

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 126/293 (43%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSTSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 112/239 (46%), Gaps = 4/239 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
           +    R+ KV+++AGIASRR  E+MI   RV+V+  ++      V   +  I VDG  + 
Sbjct: 3   DNDGVRLQKVLSQAGIASRRVAEKMIRDGRVEVDDRIVTELGTRVDPAESVIRVDGARIT 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLT 125
             +       +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGLLLLT
Sbjct: 63  VDDTLVHLAINKPRGMHSTMSDDRGRPCVGDLVEHRVRGNKKLFHVGRLDADTEGLLLLT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  + Y     G V +     L++G+ +           L      
Sbjct: 123 NDGELAHRLMHPSYEVPKSYVATVLGSVPRGLGRKLREGVELDDGPVQVDDFALVDTTPG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              V V L EG+   ++++     + V  L+R   G   LG    GS R +++K + E 
Sbjct: 183 RTLVRVTLHEGRKHIVRRLLAEVGFPVQNLVRTDIGGVSLGDQRPGSIRALTQKEIGEL 241


>gi|150391402|ref|YP_001321451.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
 gi|149951264|gb|ABR49792.1| pseudouridine synthase [Alkaliphilus metalliredigens QYMF]
          Length = 243

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 75/235 (31%), Positives = 116/235 (49%), Gaps = 8/235 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
            QR+ K++A  G  SR ++ R+  Q  V VNG +++ ++ +V    D I V G       
Sbjct: 4   TQRLDKILANLGHGSRSDIRRLCRQGVVTVNGAVVKSSSQHVEPENDKITV-GEEEIYYR 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGG 129
                + +KP  +++   D   + TV D L S +    V  VGRLD +TEGLL+LTNDG 
Sbjct: 63  EFVYIMMNKPQDVISATEDFKEK-TVVDLLESKYQAFDVFPVGRLDKDTEGLLMLTNDGK 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AW 188
           LA  L  P     + Y  +  G V    +   +KGI I+      M   L   K    + 
Sbjct: 122 LAHQLLSPKKHVPKTYYAKIEGVVTDADVEAFEKGIFIE-ENLQTMPSQLKILKADEISE 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           V V + EGK  ++K++F+  + +V  L R+S G   L   L  G+ RE+S++ L+
Sbjct: 181 VEVTIYEGKYHQVKRMFQATDKEVVYLKRLSMGSLMLDNSLDLGTYRELSEEELQ 235


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 112/232 (48%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ + R
Sbjct: 1   MRLDKFLTHCGFGSRTQVKKLIREGIVTVNGKQIVEVDFKINPEEDVVEVDGRIVKFS-R 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ DP    TVF  +        + +VGRLD + EGLL++T+DG  
Sbjct: 60  WIYIMMNKPKGYVCSNEDPMS-LTVFSLISDDLKHRDLHTVGRLDKDAEGLLIITDDGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P  +  + Y VR   +VD+++L   + GI++  G      + T+      +  V
Sbjct: 119 THRVISPKKRIEKEYLVRLEKEVDEERLKEFENGIILDDGYKTLPAKYTI----IDSTTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++K++FE    KV  L R   G   L  +L  G  R + ++ 
Sbjct: 175 KLCIYEGKYHQVKRMFEAIGNKVVDLKRRRIGGLNLDESLKPGEYRLMKEEE 226


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 102/309 (33%), Positives = 146/309 (47%), Gaps = 10/309 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNG++             + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVARLGERLEDENAVVRIDGHIVSAKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN-GLSKQKKLAT 303
           +     ++  ++ +    S +        I   V     R+       N      KK A 
Sbjct: 243 VELRPEKQTLLDENKANSSRKRERSRSQKIRRAVKRHEERVNSGGRSNNPARRNPKKGAG 302

Query: 304 PVHRRNLAS 312
             + R+   
Sbjct: 303 KANTRSKQR 311


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/228 (31%), Positives = 123/228 (53%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
            R++K IA     SRR+ + +I  ++VK+NG +LE  A  V   D +E+DG  +   + +
Sbjct: 1   MRINKFIATKTAYSRRKADELIKDKKVKINGEVLENLAYTVNDDDEVELDGRIISDIKVK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L++KP  +V+T SD  GR  + D  P   S V  VGRLD ++ GL+++TNDG LA 
Sbjct: 61  KYYYLFNKPKNVVSTVSDEFGRYCITDFFPPDIS-VFPVGRLDYDSTGLIIVTNDGDLAN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS    + Y     G++ + ++ +  +G+VI        ++ L     S     + 
Sbjct: 120 KIAHPSHHVKKTYIATLDGRLSEAQMKIFSEGVVIDSKKTLPAEIEL--YDFSETQYKIS 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EG+NR+I+K+ +     V  L RIS G  +LG ++ G  R+++++ 
Sbjct: 178 IYEGRNRQIRKMIDVLGRNVRELKRISIGKIKLGRIVEGKYRKLTEEE 225


>gi|283471019|emb|CAQ50230.1| RNA pseudouridine synthase family protein [Staphylococcus aureus
           subsp. aureus ST398]
          Length = 231

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + ++ +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEEDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>gi|324996011|gb|EGC27922.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK678]
          Length = 242

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 113/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR +V++++ +  V VNG   +     +    D I V G  L   E+
Sbjct: 1   MRLDKFLAENGLGSRAQVKQILKKGLVLVNGRAEKSPKTQIDERADEIVVSGQRLTY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVISATED-DRHQTVLDLLDETARQKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAW 188
           A  +  P     ++YR +  G ++Q  +     GI ++       Q+ +    +    + 
Sbjct: 119 AHAMLSPKKHVEKIYRAQVAGLMEQADVERFAAGIELKDFTCQPAQLKILELDEAKETSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V + L EGK  ++K++      +V  L R++ GP Q    L  G  R +++  +
Sbjct: 179 VEITLAEGKFHQVKRMVAACGKEVTDLQRLTMGPLQSDPALALGEWRRLTEVEM 232


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 112/232 (48%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D IEVDG  + K  +
Sbjct: 1   MRLDKFLTHCGFGSRSQVKKLIREGIVTVNGKQIVEVDFKINPEEDIIEVDGR-VAKFSK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ +     TVF  +     +  + +VGRLD + EGLL++T+DG  
Sbjct: 60  QIYIMMNKPKGYVCSNEEL-ASLTVFSLISDDLKYRDLHTVGRLDKDAEGLLIITDDGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P  +  + Y VR   +VD++KLN  + GI++  G      + T+      +  V
Sbjct: 119 THRVISPKKRIEKEYLVRLEKEVDEEKLNEFENGIILDDGYKTLPAKYTI----IDSTTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++K++FE    KV  L R+  G   L  +L  G  R +  + 
Sbjct: 175 KLCIYEGKYHQVKRMFEAIGNKVVDLKRLRIGGLNLDQSLKPGEYRVMKVEE 226


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 103/349 (29%), Positives = 157/349 (44%), Gaps = 8/349 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG  SRRE+E MI   RV V+G++ +        T ++ VDG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDMTANVRVDGHRIELISS 61

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T  DP+GR TVFD LP + + 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+  K + E   
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYLTKDMPRGGWSELELKEVNELRA 241

Query: 247 P-HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
              L  E +  L       +  +R     +    +       N+  + G +  ++     
Sbjct: 242 TVELPPETETALTVEGQKRKKGIRQIRRAVRRHEERIETGNGNARGRRGRNNDRRNPGAS 301

Query: 306 HRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
              ++ S     +G   S     G+   N    P    KR     +A +
Sbjct: 302 RNADVESQQNERRGSGRSQPVK-GRDNRNDSGKPQSSGKRKPSGNAANR 349


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L   E 
Sbjct: 1   MRLDKFLVDCGMGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPGKDRVTFMGEDLVH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPAGVISATED-DHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
           A  +  P     ++YR +  G +D+  +   + GI ++       ++ +     +N  ++
Sbjct: 119 AHAMLSPKKHVSKIYRAQVAGIMDEADVARFEAGIALKDFTTLPARLQILEVNEANASSY 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + + EGK  ++K++      +V  L RIS GP  L  TL  G  R +    L+  
Sbjct: 179 VEIEIAEGKFHQVKRMVAACGKEVVDLERISMGPLMLDPTLQLGEWRRLQPSELKSL 235


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 116/254 (45%), Gaps = 11/254 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH- 59
           + D +   +     R+ K +A +G+ SR EV+ ++ + RV V G +       V      
Sbjct: 19  LTDLSAKSDIIKDMRLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQ 78

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +  DG  L   E    +L +KP GLV+   D   ++ V       F   +  VGRLD NT
Sbjct: 79  VAFDGEILDYQE-YYYYLLNKPQGLVSATKDNLFKTVVQLLSEKDFREDIFPVGRLDKNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQV 177
           EGLL+LTNDG L   L  P     + Y  R  G+V  + +N   +G+ ++ G      ++
Sbjct: 138 EGLLILTNDGALGHDLTQPKKHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGEL 197

Query: 178 TL------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
            +      ++Q G  + + V + EGK  ++K++FE     V  L RI  G   L   L  
Sbjct: 198 FIENIYKGESQSGWISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLAL 257

Query: 231 GSTREVSKKILREQ 244
           G+ R ++ + +   
Sbjct: 258 GAYRPLTTEEIENL 271


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 107/290 (36%), Positives = 155/290 (53%), Gaps = 12/290 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR-- 68
             +++ KV+ARAG  SRRE+E +IA+ RV V+G +      +NV +   + +DG  +   
Sbjct: 39  EGEKLQKVLARAGQGSRREIEAIIAENRVSVDGKIATLGDRINVYAGVKLRIDGHLINLT 98

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
             + E  R+ +Y+K  G + T  DP+GR+TVFD LP    +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-GTLLAGSTREVSKKI---L 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+       L
Sbjct: 219 NQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMELADVNYL 278

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           RE +G  L  E +  L A     +         +    +   R K + + 
Sbjct: 279 RELVG--LPPETETKLGANKTRHKPKFGQIRKAVKRYSELNKRYKNSKNS 326


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + ++ +   K+GI +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEEDIQAFKEGITLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 70/336 (20%), Positives = 137/336 (40%), Gaps = 14/336 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K I+ +G+ SRRE +R I Q  V +N          V   D + V+G  +   E
Sbjct: 5   TSTRLNKYISESGMCSRREADRFIEQGNVFINKKRA-EVGDQVNPGDVVRVNGAKIEPPE 63

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    +KP+G+V+T    +  + V     +  SR+  +GRLD +++GL+ LT++G 
Sbjct: 64  AEDLVFIALNKPVGIVSTTEMEEPDNMVS--FVNHSSRIFPIGRLDKDSQGLIFLTSNGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     + +D +N +  G+ + G      +V     + +    
Sbjct: 122 LVNKILRAGNNHEKEYVVTVDKPLTEDAINTMASGVPMLGTKTKKCKVV----QEAPNVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ EF  ++V  L R+      L  L  G  R++++K + E     +
Sbjct: 178 RIFLVQGLNRQIRRMCEFCGYQVTELERVRIMNISLKGLPVGDWRDLTEKEMTEL--SKM 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           +E +     +    +    + +    S+           S ++   S +         R+
Sbjct: 236 IEHSSSEDTSKQKPAPAKAKSKGRSNSKSFSKSKAQAAESRKEKSQSSKPASKGKSDGRS 295

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                   K       ++ G+ +    RS S    +
Sbjct: 296 RP---GEGKNESGRGKNEGGRGKAPLNRSRSGEGGK 328


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 80/242 (33%), Positives = 121/242 (50%), Gaps = 8/242 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+  ++ARAG+ASRR+ E +I Q  V+VNG +       V   D +EV G  +   
Sbjct: 1   MKAMRLQALLARAGVASRRQAEVLIRQGLVRVNGEVA-HLGQKVGPDDLVEVAGRRVEWP 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +   HKP G  TT SDP  R TVF+ LP +   + +VGRLD  +EGLLL TNDG L
Sbjct: 60  RERLVLALHKPRGYTTTRSDPHARRTVFELLPEV-PGLQAVGRLDRESEGLLLFTNDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VYRV    G + +     L +G+ ++            + + +    
Sbjct: 119 LFRLTHPRYGVKKVYRVWTERGTLPEAVCRKLVEGVALEDG-----PARALSCRPAQGGA 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+ RE++++ +   + V RL+R+  GP +LG L  G  R +S + ++  L    
Sbjct: 174 ILTLGEGRKREVRRMLQAVGYPVKRLLRLQVGPIRLGNLPPGRWRRLSPEEVQALLKEVG 233

Query: 250 LE 251
           LE
Sbjct: 234 LE 235


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 110/231 (47%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR EV+ ++   RV VNG   + A + +    D I  DG  L   E 
Sbjct: 1   MRLDKFLVACAVGSRTEVKNLLKAGRVTVNGKKEKSAKLQINEERDEIRFDGQVLEYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D   R TV D L        V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYYMMNKPQGVISATEDSKHR-TVLDLLDDVARSKEVFPVGRLDIDTHGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     + Y  +  G + Q+ +    +GI ++       ++ L +   + + + 
Sbjct: 119 AHALLSPKRHVDKTYLAQVEGIMTQEDVETFAEGIPLKDFTCQPARLELVSVDPEKNQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
           V V + EGK  ++K++  +   +V  L R++ G   L   L  G  R ++K
Sbjct: 179 VRVTIAEGKFHQVKRMVAYCGKEVVDLQRLTMGALILDEKLKRGEWRRLTK 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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 114/229 (49%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVNY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L  
Sbjct: 60  HYFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWV 189
            L  P+    ++YR +  G  D + +     G+ +  G      ++ +  Q   +  + +
Sbjct: 120 ELLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILAQDEEHDSSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + +REGK  +IK++F     KV  L RIS G  +L   L  G+  E+S
Sbjct: 180 EIKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELS 228


>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 =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPASSGKRFTSPGRKKK 287


>gi|329929427|ref|ZP_08283175.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
 gi|328936514|gb|EGG32959.1| pseudouridylate synthase [Paenibacillus sp. HGF5]
          Length = 243

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRL 75
            KV++  G  SR E+++   Q  + VNG + +    +V    D IE +G  ++  E    
Sbjct: 2   DKVLSNLGFGSRAELKKKAKQGSIVVNGTITKDPGKHVDPYADIIEFEGETIQYRE-YVY 60

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARV 133
            + HKP G+V+   D   R TV D L + +       VGRLD +TEGLLLLTNDG LA  
Sbjct: 61  LMLHKPPGVVSATEDLRDR-TVLDLLDAEYRVFEPFPVGRLDKDTEGLLLLTNDGKLAHE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN-----A 187
           L  P     + Y     G+VD++ +     G+ +  G      ++ + + +        +
Sbjct: 120 LLSPRKHIPKTYEATVEGRVDEEDVRRFAAGVTLDDGYVTLPGELAIHSHEEREDGDQLS 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +++ + EGK  ++K++FE    KV  L RIS G  +L   L  G+ RE++++ L
Sbjct: 180 RISLTIHEGKFHQVKRMFEAVGKKVVYLKRISMGELRLDENLEIGTYRELTEQEL 234


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 98/230 (42%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  ++R+E  +++    V V+G + +  +V V     +      L      
Sbjct: 1   MRLDKFLCDALGSTRKEATQILKSGDVTVDGKVQKSGSVQVTEASVVAWQERQLSLT-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGFN-QTAFVLLDEVNMRGLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     V  D    L  GI ++      +   ++        V + 
Sbjct: 119 RITSPKHKCDKTYRVWLADAVQADYAEKLAHGIELRNERELTLPAHMELVNADENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  +L  G  R +++  +
Sbjct: 179 IHEGKYHQVKRMFAALGNKVEALHRERVGDIVLDESLEPGEYRYLTEAEV 228


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 121/233 (51%), Gaps = 2/233 (0%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
               +R+ KV+ARAG+ SRR  E +I Q RV+VNG ++    + V    D I+VDG+ + 
Sbjct: 126 EVEGERLQKVLARAGMGSRRACEELIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTV- 184

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G
Sbjct: 185 ATQSYLFFALNKPAGVVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHG 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|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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 102/309 (33%), Positives = 148/309 (47%), Gaps = 9/309 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNG++ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGVVAKLGERLEDENAIVRIDGHTVSAKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKK---ILREQ 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 VHRRNLASN 313
             + + A  
Sbjct: 303 GEQGSRAKQ 311


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 77/246 (31%), Positives = 123/246 (50%), Gaps = 5/246 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M   N  ++     R+ + +A+ G+ASRR  E +I   RV VNG ++      V   D +
Sbjct: 1   MPVNNSKEKKEDVMRLQQYMAKCGVASRRASEAIICAGRVTVNGTVVTELGTKVDVQDKV 60

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
            VD   +   E+    L +KP G V + SD  GR    D L   +S R+ +VGRLD+ + 
Sbjct: 61  CVDEKEIHLEEKKCYVLLNKPSGYVCSASDEKGRPVAADLLKEAYSERLYNVGRLDMFSS 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL++ TNDG  A  L  PS +  + Y V     + +   +    GI I G+ Y       
Sbjct: 121 GLIIFTNDGDFAAKLSHPSAELEKEYIVDTSLPMPRFLADDFMDGIRIDGVFYRCK---- 176

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D ++ ++  + + L EGKNREI++VFE +   +  L+RI  G   +G L  G  R++++ 
Sbjct: 177 DARELNSHRMRIVLVEGKNREIRRVFEKYEVGIKSLMRIRIGCVGVGELQFGQFRDLTQD 236

Query: 240 ILREQL 245
            ++  L
Sbjct: 237 EVKALL 242


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 120/236 (50%), Gaps = 11/236 (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 +G      D D +S++   LP+   R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  GAEALSYWIFNKAVGTDCRLLDAD-KSSLLHLLPTT-PRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y V+     +   +  +  G+  + +     QVT    + S+  
Sbjct: 119 ELTHKLMHPSFAHSKTYHVQLDRPFNDAFIEQMASGVQYKEVRTLPCQVT----RLSDVS 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + L +G NR+I+++     +KV  L R++     LG+L  G  R +S + +   
Sbjct: 175 FEIVLTQGLNRQIRRMSNALGYKVVDLQRVALMTLTLGSLAEGEMRPLSPEEVTAL 230


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/302 (22%), Positives = 140/302 (46%), Gaps = 10/302 (3%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E     R++K I+ +G  SRRE ++ I  ++V VNG + +    +V   D + V+ + ++
Sbjct: 2   ERKETIRLNKFISDSGYCSRREADQYIENRQVYVNGRIAK-VGQHVQLHDQVVVNNIEIK 60

Query: 69  KAERT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             ++        +KP+G+  T +DP+  + + D L S   R+  +GRLD +++GL+LLT+
Sbjct: 61  PRDKEMAIYIALNKPVGITCT-TDPNDPTNIIDFL-SFGERIFPIGRLDKDSQGLILLTS 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +     +  + Y V     +  D    ++ G+ I G+      V    +K + 
Sbjct: 119 DGDIVNKILRAGNKHEKEYIVTVDKPITDDFCTKMENGVPILGVNTKKCTV----EKLNT 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L +G NR+I+++ E+F+++V +L R       L  +  G  R+++K+ L E   
Sbjct: 175 NTFKIILIQGLNRQIRRMCEYFDYRVTKLERTRIMNIDL-NVPIGQYRDLTKEELMELKR 233

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                E      A   +++     +  ++ +      R+ +    +  + K K    P  
Sbjct: 234 LTAQSEQHEKAKANKKTAKKKSTTKKTVLEKDTTPKKRITRKPKSQPRIGKSKPPEKPKR 293

Query: 307 RR 308
           +R
Sbjct: 294 KR 295


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/337 (28%), Positives = 160/337 (47%), Gaps = 4/337 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+++++A AG  SRR+ E +I + RV V+G  +      V      + VDG  LR  ++ 
Sbjct: 26  RINQLLASAGFGSRRQCEELIREGRVDVDGETITELGTTVDPDLQKVRVDGNYLR-PQKL 84

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP+G+VTT+ DP GR  V D +P    RV  VGRLDI++EGL+LLTNDG LA+ 
Sbjct: 85  VYYVVNKPVGIVTTNRDPRGRPRVIDLVPPT-ERVFPVGRLDISSEGLILLTNDGDLAQK 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++++  + ++L   +    
Sbjct: 204 KEGKNREIRRILARFGHKVQQLRRVAIGPLKLGDVPRGAYRKLTRDEV-DKLRRSIDAAE 262

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           +    AP     +    +        +   +         G  K  K +     R+ A+ 
Sbjct: 263 KAAKTAPPARPASKQSIKRRPGGASRNVAAKGTGGRPAFKGGRKAVKKSRTTETRSSATG 322

Query: 314 VWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
              +K +    LS  G             S++   R 
Sbjct: 323 PKTSKPVKKRTLSSGGSTGTVIGADAPKESRKKTERG 359


>gi|315179963|gb|ADT86877.1| 16S rRNA uridine-516 pseudouridylate synthase [Vibrio furnissii
           NCTC 11218]
          Length = 233

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 98/230 (42%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A  ++R+E  +++    V V+G + +  +V V     +      L      
Sbjct: 1   MRLDKFLCDALGSTRKEATQILKSGDVTVDGKVQKSGSVQVTEASVVAWQERQLSLT-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D     T F  L       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGFN-QTAFVLLDEVNMRGLHFAGRLDVDTTGLVLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     V  D    L  GI ++      +   ++        V + 
Sbjct: 119 RITSPKHKCDKTYRVWLADAVQADYAEQLAHGIELRNERELTLPAHMELVNADENEVLLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G   L  +L  G  R +++  +
Sbjct: 179 IHEGKYHQVKRMFAALGNKVEALHRERVGEIVLDESLEPGEYRYLTEAEV 228


>gi|239993811|ref|ZP_04714335.1| pseudouridine synthase (makes pseudouridine2605 in 23 S RNA)
           [Alteromonas macleodii ATCC 27126]
          Length = 298

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 96/299 (32%), Positives = 152/299 (50%), Gaps = 13/299 (4%)

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---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
               R+ +Y+KP G + +  DP+GR TVFD LP+    R I+VGRLD+NT GLLL TNDG
Sbjct: 61  QPICRVLMYNKPEGELCSRHDPEGRDTVFDRLPAIRLGRWITVGRLDMNTSGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------LDTQ 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 ESMNRWYNVTLKEGRNREVRRLWESQGVQVSRLIRVKYGPIELQKRLPQGAWVELGLEDV 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
              L  H+    +      +   +        +   V     R ++  +++ G   ++K
Sbjct: 241 NA-LRSHVQLPDETQTMVNVRQGKLDHARLSRMRRSVKKHKVRKQQGLNKRAGRPAKRK 298


>gi|300214283|gb|ADJ78699.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 240

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 119/234 (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  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KPIG+V+   D   ++ +   N 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|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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 75/229 (32%), Positives = 112/229 (48%), Gaps = 8/229 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K+++  GI +R+EV++ I +  V VNG  ++ A + V    D I  DG  +  
Sbjct: 1   MAKMRIDKLLSNIGIGTRKEVKKFIKEGLVLVNGNTVKDAGLIVDTEFDEILFDGEKINY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            E     + +KP G+++   DP    TV D LP           GRLD +TEGLL +TND
Sbjct: 61  KE-FIYIMMNKPKGVISATYDP-IEKTVIDLLPQELKARNPFPAGRLDKDTEGLLFITND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           G LA  L  P    ++ Y     G V++  +   K+GIV++   Y  +   L+    S  
Sbjct: 119 GNLAHKLLSPKKNVIKKYYAEILGFVNERDIKAFKEGIVLEDG-YKTLPADLEILLSSEV 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           + V V +REGK  +IK++FE    KV  L R++ G   L   L  G  R
Sbjct: 178 SKVYVYIREGKYHQIKRMFESVGKKVVYLKRLAMGSLTLDENLKPGQWR 226


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 95/288 (32%), Positives = 157/288 (54%), Gaps = 10/288 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             ++V KV+ARAG  SRRE+E MI++ RV ++G +       +  T+ I +DG  ++   
Sbjct: 69  DSEKVQKVLARAGKGSRREMETMISEGRVSIDGKVAF-LGDRITGTEQIRLDGHHVKLTA 127

Query: 72  R----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
           +     R+ +Y+KP G + T  DP+GR TVFD LP + + R ++VGRLDINT G+LL T 
Sbjct: 128 QDEDICRVLVYNKPEGEMCTRKDPEGRPTVFDRLPPLDAGRWVAVGRLDINTSGMLLFTT 187

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS +  R Y VR  G++++  L  L+ G+ ++       ++T    +G N
Sbjct: 188 DGELANRLMHPSQKVEREYAVRVFGEINEAMLQTLRAGVKLEDGMARFQKITYRGGEGRN 247

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL---R 242
            W  V L EG+NRE+++++E  + +V+RLIR+ YG  ++   L  G  RE++ K +   R
Sbjct: 248 HWFHVVLSEGRNREVRRLWESQDVQVSRLIRVRYGDMEMQRQLPMGGWRELALKEVNYYR 307

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           + +      E++V +D     +    R R ++           ++   
Sbjct: 308 QLVNLTPEAESKVKVDEKAMDNAKSRRIRRSVKKHQQRHQQSTRRRHK 355


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 101/289 (34%), Positives = 146/289 (50%), Gaps = 12/289 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  R+ ++G +       V +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRISIDGEIA-NLGDRVEADVKIRIDGRAVSIKSE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+  +    LR+
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKSLPRGGWVELELEQVNYLRQ 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             G  L  E +  L    +S          I   V        KN+ Q+
Sbjct: 241 TAG--LAIENRTLLGTDKHSVARAKVKSAKIKRAVNKHKVNAAKNTRQR 287


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 114/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   ++
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  YIYLMMNKPAGVISATYDKRD-ETVIDLLYMEDQVFEPFPVGRLDKDTVGLLLLTNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY    +  + +  +   + G+ +  G      ++ +      +A V
Sbjct: 120 NHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSARV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+  L
Sbjct: 180 EVTVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 98/288 (34%), Positives = 142/288 (49%), Gaps = 24/288 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E  IA  RV V+G +       V +   I +DG  +     
Sbjct: 2   SEKLQKVLARAGHGSRREMEAWIAAGRVSVDGEIA-SLGDRVETDAKIRIDGRTVSIRSE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + +  DP+GR TVFD LP    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-GTLLAGSTREVS--------- 237
           W  V L EG+NRE+++++E    +V+RLIRI YG  +L  +L  G   E+          
Sbjct: 181 WWHVSLAEGRNREVRRLWESQEVQVSRLIRIRYGMIELPKSLPRGGWIELPIEQVNYLRK 240

Query: 238 ----KKILREQLG--PHLLEEAQVNLDAPIYS--SETLVRDRPNIISE 277
                +  R  LG   H +   +V       +     +   RP    +
Sbjct: 241 TAGMDEETRSILGTDKHSVARNKVRSAKIKRAVHKHKVASGRPKPSRQ 288


>gi|322835106|ref|YP_004215133.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321170307|gb|ADW76006.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 290

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 69/295 (23%), Positives = 130/295 (44%), Gaps = 12/295 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +    
Sbjct: 5   SSIRLNKYISESGICSRRDADRYIEQGNVFINGRRAA-VGAQVFAGDVVKVNGQIIEPRD 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L   +KP+G++TT  + + R  + D + +   RV  +GRLD +++GL+LLTN G 
Sbjct: 64  EEDLVLIALNKPVGIITTMEEGE-RDNIRDFV-NHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +  + +  +  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYIVTVNKPITDEFIAGMGAGVPMLGTVTK----KCKVKKEAPMVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F + V +L R+      L  L  G  R+++   L E     L
Sbjct: 178 RITLVQGLNRQIRRMTKHFGFDVTKLERVRIMNINLKGLPLGEWRDLTDDELIELF--KL 235

Query: 250 LEEAQV-NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +   +  A    S+     +P +      +       S ++     +KK   
Sbjct: 236 IENSSSEDKPAKKGPSKPAQAKKPAVTKTKNSEKPEANSASRKRFAQPGRKKKGR 290


>gi|118595131|ref|ZP_01552478.1| pseudouridylate synthase [Methylophilales bacterium HTCC2181]
 gi|118440909|gb|EAV47536.1| pseudouridylate synthase [Methylophilales bacterium HTCC2181]
          Length = 280

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 90/263 (34%), Positives = 146/263 (55%), Gaps = 8/263 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
           +R+ K++A++G  SRRE+E+ I + +V VN    +     +  +D I  +G  +      
Sbjct: 20  ERIHKLLAQSGYGSRREIEKAILEDKVLVNNQNAK-IGQLITPSDKIIFNGKAIFLNNDN 78

Query: 73  --TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
              R+ +YHKP G + T +DP GRSTVF+ LP I   + +S+GRLD NT GLL+ T+ G 
Sbjct: 79  NLPRVLIYHKPEGEIVTENDPGGRSTVFEKLPRIKKGKWMSIGRLDFNTSGLLIFTSYGE 138

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  P  +  R Y VR  G++ +D++   K GI I G       +  +  +G+N W 
Sbjct: 139 LANRLMHPKYEIEREYSVRILGELSEDQIKEFKSGIDIDGGKAKFESIYFEGGEGANKWY 198

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            V L+EG+NRE++++FE+F+  V+RLIR+ +G   L + L  G   E+++  +   L  H
Sbjct: 199 RVVLKEGRNREVRRMFEYFDLTVSRLIRVRFGIVILPSHLKRGMHTELTQAEVTRLLQKH 258

Query: 249 LLEEAQVNLDAPIYSSETLVRDR 271
            +E    + + P  S++     R
Sbjct: 259 DIEPN--DFNKPQLSNQRKRNKR 279


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRFTSPGRKKK 287


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 125/239 (52%), Gaps = 9/239 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + +L +KP G+V+  SD +   TV D +       ++  VGRLD +TEGLLL+TN+G L
Sbjct: 61  -KYFLLNKPAGVVSAVSDKEH-QTVIDLIKEADCVPKLYPVGRLDRSTEGLLLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+           ++ + T     +  
Sbjct: 119 GYRMLHPKYHVAKTYYVEVNAFLADDVPAFFENGVSFDDGTICKPAKLEIITASPEKSSA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQL 245
            V + EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   K+IL+  L
Sbjct: 179 YVTISEGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTEKEILKNYL 237


>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 =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 98/288 (34%), Positives = 145/288 (50%), Gaps = 8/288 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
              +++ K +AR G+ SRR++E +I + RV VNG +       V   D I VDG  LR  
Sbjct: 1   MKDEKLQKALARLGLGSRRQMEDVIREGRVSVNGTVAT-IGDRVGQGDEIRVDGRLLRYT 59

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
               +R R+ +Y+KP G + +  DP+GR TVF+ LP     R + VGRLDIN+ GLLL T
Sbjct: 60  AENEKRRRILMYYKPEGEICSAHDPEGRPTVFERLPPLNHDRWVMVGRLDINSTGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  R Y VR  G+V  + +  LK+G++++        +     +G 
Sbjct: 120 NDGELAHRLMHPSNEIEREYAVRVMGEVTPEIMLNLKRGVMLEDGMAQFDDIVEKGGEGI 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           N W  V L+EG+NRE++++FE    KV+RL+RI YG   L   L  G   E+ ++ +   
Sbjct: 180 NKWYQVKLKEGRNREVRRLFESQGLKVSRLLRIRYGSVSLPRELRTGRYLELDRREIDTL 239

Query: 245 LGPHLLEEAQ-VNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            G   +   Q   L       +     +P           R K+  S 
Sbjct: 240 AGLVNIRPRQGTGLYGIAKRRQERFEKKPLKARRGGHYLRRDKEKRSS 287


>gi|313159346|gb|EFR58710.1| pseudouridylate synthase [Alistipes sp. HGB5]
          Length = 423

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 127/250 (50%), Gaps = 10/250 (4%)

Query: 2   KDKNIVQENFTPQ------RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
            DK      FTP+      R+++ +A++G+ SRRE +  I    V VNG ++ +    V+
Sbjct: 171 DDKPASYPKFTPEKQIGEMRLNRFLAQSGLCSRREADDFITAGLVTVNGQIVTQLGTKVL 230

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
            TD ++ +   ++  E+    + +KP G VT+  DP    TV + +      R+  VGRL
Sbjct: 231 PTDEVKFNDSRVQ-GEKKVYLVLNKPKGYVTSLDDPHAGKTVMELVQGACTERIYPVGRL 289

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D N+ GLLL TNDG L + L  P+ +  ++Y+V     + +  ++ + +GI ++      
Sbjct: 290 DKNSLGLLLFTNDGDLTKQLTHPAFRKKKIYQVSLDKPLTRADMDRIAEGITLEDGEIFA 349

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +++    K +   V + +  G+NR ++++FEF  + V +L R+ Y       L  G+ R
Sbjct: 350 DEISYV--KDNKQEVGIEIHSGRNRIVRRIFEFLGYTVTKLDRVYYAGLTKKNLKRGAWR 407

Query: 235 EVSKKILREQ 244
            +S++ +   
Sbjct: 408 FLSREEVERL 417


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 118/231 (51%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MIA  RV+++G ++    + +   T  I VDG  +   E  
Sbjct: 90  RLQKVLAQAGVASRRGAEEMIAAGRVEIDGEIVTEQGLRIDPDTAIIRVDGARVIIDETR 149

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGL 130
           +    +KP G  +T +D  GR  V D +        R+  VGRLD +TEGLLLLTNDG L
Sbjct: 150 QYLALNKPRGWQSTMADDQGRPCVGDIVAERVMAGQRLFHVGRLDADTEGLLLLTNDGEL 209

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y     G+V +    +L+ G+ +        ++T+       + + 
Sbjct: 210 AHRLMHPSYEVPKTYLATVRGEVPRSLSRMLRDGVELDDGPVAVDKLTIVDVHEGQSLLR 269

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+NR ++++ +   + V  L+R   G   LG    GS R + +  +
Sbjct: 270 ITLHEGRNRIVRRMMDEVGFPVVELVRTHVGSVALGEQRPGSLRVLGRDEV 320


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 114/229 (49%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVNY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L  
Sbjct: 60  HYFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWV 189
            L  P+    ++YR +  G  D + +     G+ +  G      ++ +  Q   +  + +
Sbjct: 120 ELLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILVQDEEHDSSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + +REGK  +IK++F     KV  L RIS G  +L   L  G+  E+S
Sbjct: 180 EIKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELS 228


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 92/238 (38%), Positives = 136/238 (57%), Gaps = 7/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            +++ KV+ARAGI SRR +E  IA  RV VNG   +     V   D + VDG  +  +  
Sbjct: 2   SEKLQKVLARAGIGSRRSMEDWIASGRVSVNGKKAK-VGDRVERGDVLRVDGRSMDYSGE 60

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             +  R+ +Y+KP G V T +DP+GR TVFD LP     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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           W  V ++EG+ RE+++++E    +V+RLIR+ YG   L   L AG   E+S+  + E 
Sbjct: 181 WYHVIIKEGRRREVRRMWETQGVQVSRLIRVRYGCVTLPRGLKAGRWEELSEDQISEL 238


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 124/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++             ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKVKAKPKTAGIKRPLVKMEKTSEKGGRPASNGKRFTSPGRKKK 288


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 116/233 (49%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++V +      ++++G  +    +
Sbjct: 2   ERLDKIISNLGYGSRKEAKVLARKGLIEVDGKIIKDSSVTIDPEKSIVKINGEEIFYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG  
Sbjct: 61  YIYLMMNKPTGVISATHDSKD-ETVIDLLELDHQIFNPFPVGRLDKDTVGLLLLTNDGEF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     +VY  +   +V++      KKG+V+  G    + ++ + +     + V
Sbjct: 120 NHRMISPKWHVDKVYYAKIDKEVNEKDQQAFKKGVVLDDGYKCLEAKLDIISASPEGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + ++EGK  ++K++FE  + KV  L R  +G   L   L  G  RE+S + L
Sbjct: 180 RITIQEGKYHQVKRMFEACDKKVVYLKREEFGGLILDENLEEGEYRELSDEEL 232


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 112/234 (47%), Gaps = 4/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ KV+++AGIASRR  E+MI   RV+V+G ++      V  T   I VDG  +   +  
Sbjct: 8   RLQKVLSQAGIASRRVAEKMILDGRVEVDGHIVTELGTRVDPTAADIRVDGTRVLLDDTL 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  + D +         +  VGRLD +TEGL+LLTNDG L
Sbjct: 68  VHLAINKPRGMHSTMSDDRGRPCIGDLVEHRVRGNKGLFHVGRLDADTEGLMLLTNDGEL 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y     G V +     L+ G+ +           +       + V 
Sbjct: 128 AHRLMHPSYEVPKTYVATVLGTVPRGLGKKLRAGVELDDGPARVDDFAVVDAMPGRSMVR 187

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V L EG+ R ++++     + V  L+R   G   LG    GS R +++K + E 
Sbjct: 188 VTLHEGRKRIVRRLLAAVGFPVQELVRTDIGAVSLGEQRPGSIRVLTRKEIGEL 241


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 124/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++             ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKVKAKPKTAGIKRPLVKMEKTSEKGGRPASNGKRFTSPGRKKK 288


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 93/255 (36%), Positives = 141/255 (55%), Gaps = 10/255 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRR++E +I + RV V+G ++      V     I VDG  ++    
Sbjct: 2   SEKLQKVLARAGLGSRRKMEVVIQEGRVSVDGKVV-GLGERVTDVQVIRVDGHIVKNLTP 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T SD +GR+TVF+ LPS   +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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
           W  V L EG+ RE+++++E    +V+RL+R+ YG   L   L  G   E++ K    LR+
Sbjct: 181 WFHVVLTEGRTREVRRLWESQGLQVSRLMRVRYGNITLSKQLPQGGWHELNLKEVNYLRK 240

Query: 244 QLGPHLLEEAQVNLD 258
            +      E++V +D
Sbjct: 241 LVDMPKETESKVKVD 255


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 120/240 (50%), Gaps = 9/240 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR-- 68
           T  R++K +A AG+ SRR V++ I    V +NG  + +  + +    D I + G  +   
Sbjct: 22  TSIRINKALANAGVCSRRNVDKYILNGEVTINGKSVTQPGIYIHPDKDIIALHGRRVDIQ 81

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT 125
            K ++      +KPI ++++  DP  R TV D +P  +   R+  VGRLD  +EGLLL+T
Sbjct: 82  LKNKKYYYLSMYKPIKVISSVKDPQNRLTVLDFIPFPWKNYRLYPVGRLDFFSEGLLLIT 141

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ-- 182
           NDG L + L  P     +VY V    ++    L  + KGI +  G      +V + +   
Sbjct: 142 NDGELTQRLTHPRYHISKVYHVLIRERILNTTLKNISKGITLSDGTKLPPAKVRVLSSIT 201

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +  W+ + L++G NR+I+++ +     + +LIR+  G   L  L  G  R +    ++
Sbjct: 202 ETNTTWLEITLQQGINRQIRRMCKELGLTILKLIRVKQGNINLSNLQPGEVRPLKNDEIK 261


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 107/228 (46%), 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      ++ + D + +   R+ +VGRLD ++EGLLLLTNDG +   
Sbjct: 60  IYLLLHKPTGIVCTAQ-RQVKNNLIDYM-NYRERIFAVGRLDKDSEGLLLLTNDGDIVNK 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V          L  +  G+ I         VT    +       + L
Sbjct: 118 IMRVENGHEKEYIVTVDRPYPDTFLKSMASGVEILDQVTEPCTVT----RIDEMTFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++G NR+I+++ + F + V RL R+      +  L  G  RE++ + L
Sbjct: 174 KQGLNRQIRRMTKEFGYYVTRLRRVRIMNLSIDRLPYGQWRELTDEEL 221


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 123/236 (52%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +   E 
Sbjct: 1   MRLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVAL-EG 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           +  +L HKP G+V+  +D +   TV D +    SR  +  VGRLD +TEGL+L+TN+G L
Sbjct: 60  SAYYLLHKPAGVVSAVTDQEH-QTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              +  PS    +VY V  +G + +D       G+  + G       +T+      ++  
Sbjct: 119 GYRMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSRA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           T+ L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++   +    
Sbjct: 179 TIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGTYRQLTPNEMEHLF 234


>gi|260463018|ref|ZP_05811221.1| pseudouridine synthase [Mesorhizobium opportunistum WSM2075]
 gi|259031139|gb|EEW32412.1| pseudouridine synthase [Mesorhizobium opportunistum WSM2075]
          Length = 259

 Score =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 79/228 (34%), Positives = 122/228 (53%), Gaps = 3/228 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +I + RV+V G ++   A+ V  + D I VDG  +  AER  
Sbjct: 28  LNRALSKLGLCSRTQAELLITEGRVRVGGKVVRDPALRVDLNRDSIVVDGEKV-IAERKV 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP  R TV+  L +     +  VGRLD  +EGLLL+TND   A  
Sbjct: 87  YVMLNKPRGLVTTRDDPQQRDTVYACLEALDLPFISPVGRLDKASEGLLLMTNDTRFANR 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y V+     D   L  L+ G  + G       + L    G  AW+ V L
Sbjct: 147 LMDPASHLPKTYHVQVATVPDAAMLETLRAGATVDGEILTANSIDLLRSGGRTAWLEVVL 206

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR I+++    + +V RLIRI+ G  +LG L  G+ R ++ + L
Sbjct: 207 DEGRNRHIRRLLAAHDIEVLRLIRIAIGGLRLGDLAKGTARHLTAEEL 254


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 125/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  250 bits (639), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 103/310 (33%), Positives = 147/310 (47%), Gaps = 13/310 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDENAVVRIDGHAVSAKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIFLDKKLPRGGWMELDLKDVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +   +++     +S    R R   I        R ++  +   G S   +   
Sbjct: 242 LVELKPEKTTMLDVSKD-NTSRKRERSRSQKIRR---AVRRHEERVTAPAGRSGSSRRKD 297

Query: 304 PVHRRNLASN 313
              R+   +N
Sbjct: 298 AASRQKAGNN 307


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 124/250 (49%), Gaps = 9/250 (3%)

Query: 2   KDKNIVQENFTP-----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
             KN  Q++ TP      R+++ IA +GI SRR+ + +I    + VN +++      V  
Sbjct: 144 SRKNTSQQSSTPKEPDQIRLNRYIANSGICSRRKADELITSGAITVNDVVVSELGAKVNP 203

Query: 57  T-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
           T D ++ +G  L++ E+    L +KP   +TT  DP  R TV + + +    R+  VGRL
Sbjct: 204 TTDKVKYNGQLLKR-EKMVYVLLNKPKDFITTTEDPQERKTVMELVKNATSERIYPVGRL 262

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D NT GLLLLTNDG LA  L  P     ++Y V     + Q   N +  G+ ++      
Sbjct: 263 DRNTTGLLLLTNDGDLAEKLSHPRNNITKIYNVELSKNLTQGDFNKIAFGVELEDGFIKP 322

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             V+  +  G+   + + +  GKNR ++++FE   ++V +L R+ Y       L  G  R
Sbjct: 323 DAVSYVSG-GTKKEIGIQIHSGKNRIVRRIFESLGYEVEKLDRVIYANLTKKDLTRGKWR 381

Query: 235 EVSKKILREQ 244
            +++  + + 
Sbjct: 382 FLTENEIIQL 391


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 107/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKAHIEPKNDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + ++ +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEEDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G+ R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVIHLKRIKIADLELDSNLESGNYRLLTE 222


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 125/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 124/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++             ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKVKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>gi|329297659|ref|ZP_08254995.1| 23S rRNA pseudouridylate synthase B [Plautia stali symbiont]
          Length = 292

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 102/302 (33%), Positives = 149/302 (49%), Gaps = 25/302 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MI+  R+ V+G L       + +     I +DG  +  A
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMISAGRISVDGKLAT-LGDRIENDKTLKIRIDGHLVSIA 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
           E      R+  Y+KP G + T +DP+GR TVFD LP    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-GTLLAGSTREVSK---KIL 241
           N W  V L EG NRE+++++E    +V+RL+R+ YG  QL   L  G   E+       L
Sbjct: 181 NQWYNVTLTEGCNREVRRLWEAVGVQVSRLMRVRYGDIQLPKGLPRGGWMEMELPAVNYL 240

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ +G          L     +   + +DR    +       R  K  S  +  S ++  
Sbjct: 241 RKLVG----------LPEETVTKVAVEKDRRRTKAN---QIRRAVKRHSAVSNNSPRRNS 287

Query: 302 AT 303
             
Sbjct: 288 NK 289


>gi|315170843|gb|EFU14860.1| conserved hypothetical protein [Enterococcus faecalis TX1342]
          Length = 320

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 135/270 (50%), Gaps = 7/270 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E     R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G
Sbjct: 53  LIPEWSGTMRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKG 112

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
             +        ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLL
Sbjct: 113 QLISHKT-HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLL 170

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDT 181
           LLT++G L   L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+  
Sbjct: 171 LLTDNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLA 230

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
              + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 231 ATETESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 290

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           L+  L    +E+ Q +   P        R 
Sbjct: 291 LQLLLPYFFIEKQQTSKALPSNLKREEERK 320


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 77/226 (34%), Positives = 116/226 (51%), Gaps = 9/226 (3%)

Query: 11  FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               R+ K +A+AG+AS RR+ E +I   RV +NG +       V   D + VDG P+  
Sbjct: 1   MEAIRLQKYLAQAGVASSRRKAEALIRAGRVTINGQVAA-LGAKVTPGDEVCVDGRPVAP 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R  +   HKP G+ TT  D     TVF+ +P+    + +VGRLD ++EGLLLLTNDG 
Sbjct: 60  TARRVVLALHKPPGVTTTRRDRFAERTVFELVPA-IPGLHTVGRLDRDSEGLLLLTNDGR 118

Query: 130 LARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           L + L  P     +VYRV    G+V    L  L+KG+ ++      ++            
Sbjct: 119 LTQRLTHPRYGVPKVYRVWTAKGEVPPFILKRLEKGVRLEDGPARALKARPKVGG----- 173

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             + L EG+ RE++++     + V RL+R+  GP +LG L  G+ R
Sbjct: 174 CVLTLAEGRKREVRRMLRAVGYPVVRLLRVKIGPIRLGGLKPGAWR 219


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 126/296 (42%), Gaps = 11/296 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 289


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 68/291 (23%), Positives = 126/291 (43%), Gaps = 12/291 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +     E 
Sbjct: 8   RLNKYISESGICSRREADRYIEQGNVFINGKRAA-IGDQVAPGDVVKVNGQLIEPRNEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  D + R  + D + +  SR+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVFIALNKPVGIVSTTEDGE-RDNIVDFV-NHSSRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +  D +  +  G+ I G      +V  +          + 
Sbjct: 125 KILRAGNDHEKEYVVTVNKPITDDFIRGMGAGVPILGTVTKKCKVKKEAPFA----FRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMCEHFGFEVTKLERTRIMNVSLSGIPLGEWRDLNGDELIELF--KLIEN 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +  +       ++   +     +   P    + +   + K  +   +K   
Sbjct: 239 SSSDAKP-KTKAKPKTQGIKRPVVNAPASAEKERNKPAGKRFVQPGRKKKG 288


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 69/293 (23%), Positives = 125/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 115/249 (46%), Gaps = 6/249 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDH 59
           M  +          R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      
Sbjct: 1   MMAEPEESREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPPVAV 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDI 116
           + VDG  +   +       +KP G+ +T SD  GR  + D +        ++  VGRLD 
Sbjct: 61  VRVDGARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDA 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDM 175
           +TEGL+LLTNDG LA  L  PS +  + Y     G V +     L+ GI +     + D 
Sbjct: 121 DTEGLMLLTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDD 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +D   G    V V L EG+NR ++++     + V  L+R   G   LG    GS R 
Sbjct: 181 FAVVDAIPGKT-LVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRA 239

Query: 236 VSKKILREQ 244
           +    + + 
Sbjct: 240 LRSNEIGQL 248


>gi|289810128|ref|ZP_06540757.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 256

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 120/263 (45%), Gaps = 12/263 (4%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRD 270
            L+E +      P   SE   R 
Sbjct: 234 KLIEGSSSE-AKPKGQSEAEDRG 255


>gi|282864458|ref|ZP_06273514.1| pseudouridine synthase [Streptomyces sp. ACTE]
 gi|282560945|gb|EFB66491.1| pseudouridine synthase [Streptomyces sp. ACTE]
          Length = 382

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 77/231 (33%), Positives = 119/231 (51%), Gaps = 2/231 (0%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
             +R+ K++ARAG+ SRR  E +I Q RV+VNG ++      V    D I+VDG+ +   
Sbjct: 144 EGERLQKILARAGMGSRRACEELIEQARVEVNGEIVLEQGKRVDPQKDEIKVDGLTV-AT 202

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +    +  +KP G+V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G L
Sbjct: 203 QSYLFFALNKPAGVVSTMGDPDGRQNLGDYVTNRETRLFHVGRLDTETEGIILLTNHGEL 262

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y     G + +D    LK GI ++          +    G N  V 
Sbjct: 263 AHRLTHPRYGVKKTYLAAIQGPLPRDLGKRLKDGIQLEDGYARADHFRVVENTGKNYLVE 322

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V L EG+   ++++     + V RL+R S+GP  LG   +G  R ++   +
Sbjct: 323 VTLHEGRKHIVRRMLAEAGFPVERLVRTSFGPIPLGDQKSGWLRRLTNTEV 373


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 100/309 (32%), Positives = 145/309 (46%), Gaps = 9/309 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VHRRNLASN 313
             +      
Sbjct: 303 GQQGARNKQ 311


>gi|188996649|ref|YP_001930900.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931716|gb|ACD66346.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 244

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 125/232 (53%), Gaps = 4/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA++GI SRR+ + +I + +VKVNG +++     +    D +EV+G  ++  E+ 
Sbjct: 4   RLNKYIAQSGICSRRKADELIKEGKVKVNGEIIKDLGAKINPEKDIVEVEGNIIKPVEKK 63

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP+G ++    D  GR T+ D L   +I   +  VGRLD N+EGLL+LTNDG  
Sbjct: 64  IYIKIYKPVGYLSAVGKDKFGRKTLTDLLKELNIKENLFPVGRLDYNSEGLLILTNDGEF 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  +VY V    +VD++ LN +KKG +++   +   +V +      + W+ 
Sbjct: 124 ANKIAHPKHKIKKVYHVEVVPKVDEETLNQMKKGAILEDGFFKPDKVEILKHTKDSTWLL 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             +  GK R +++    FN KV RL+R+      +  L     + ++ K +R
Sbjct: 184 FEIHSGKKRILRRYVSKFNHKVKRLVRVKIDSISIENLKPHQFKHLTDKEVR 235


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 79/249 (31%), Positives = 116/249 (46%), Gaps = 3/249 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             QR+ KV+++AG+ SRR  E ++ Q RV +NG             D I VDG  +    
Sbjct: 4   ERQRLQKVLSQAGVCSRRRAEELMRQGRVLLNGRPASPGDQGDPLRDRILVDGELVSPPA 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDG 128
                L HKP G+ +T  DP GR TV D LP+       +  VGRLD ++ G LLL+N+G
Sbjct: 64  EELTVLLHKPRGVHSTCFDPRGRRTVLDLLPAELAEGQGLHPVGRLDCDSRGALLLSNNG 123

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + YR+   G      L   + G+++ G       V    Q   ++ 
Sbjct: 124 ALTLALTHPRFSHRKSYRIWVSGHPSSAVLQQWRHGVLLDGRPTRSADVRELQQDAEHSQ 183

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + + +REG+NR+I++V E     V  L+R+S GP QLG L +G  R +            
Sbjct: 184 LELVMREGRNRQIRRVAEQLGHPVRDLLRVSIGPVQLGDLPSGQWRRLHPDEQAALKAVT 243

Query: 249 LLEEAQVNL 257
           L    Q + 
Sbjct: 244 LAASRQESR 252


>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 =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 71/294 (24%), Positives = 131/294 (44%), Gaps = 12/294 (4%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            L+E +            +T    RP +  E  ++  R   +  +     ++KK
Sbjct: 234 KLIEGSSSEAKPKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKK 287


>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 =  250 bits (638), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 75/328 (22%), Positives = 131/328 (39%), Gaps = 14/328 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
            +  R++K I+ +G  SRRE +++IA  RVK+NG LL      V S D + VD  PLR  
Sbjct: 4   DSAVRLNKFISDSGHCSRREADKLIASDRVKING-LLPELGAVVESGDVVTVDDQPLRAS 62

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                      Y+KP G+  T +D   +  + D +     R+  +GRLD  +EGL+LLT+
Sbjct: 63  AADKTDRIYIAYNKPFGITCT-TDQTVKGNIVDAI-DHDERIFPIGRLDKPSEGLILLTS 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG +   +        + Y V  +  +  +    + +G+ I G      +V +  +    
Sbjct: 121 DGDIVNKILRAENAHDKEYIVTVNKNLAPNFAEKMSRGLPILGTITKPCKVRVIGK---- 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 +         +      +    S   K      
Sbjct: 237 ATSQSSKTAIKGANAKSSASPTATKPRVAKPKVKKEPKDLDKHGRPKNKSTGVKRGAKSK 296

Query: 307 R---RNLASNVWMAKGIHSSFLSDSGQR 331
                    N    +G      +  G++
Sbjct: 297 NLTTGGRTGNKGAGRGNAGRPTAPRGRK 324


>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 =  250 bits (638), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 114/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV++  G  +R+E+++++ +  V VN   ++ + + +    D I ++G  +   ++
Sbjct: 2   ERLDKVLSNLGYGTRKEIKQVVKKGFVTVNDEKVKDSGLQIDPEKDTIVINGEKVEY-KK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG L
Sbjct: 61  YIYLMMNKPAGVISATYDKRD-ETVIDLLYMEDQVFEPFTVGRLDKDTVGLLLLTNDGDL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY    +  + +  +   + G+ +  G      ++ +      ++ V
Sbjct: 120 NHKLISPKYHVDKVYYAEINAPITEKDIKAFENGVTLDDGYKCMSAKLKVIENLEDSSRV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V ++EGK  ++K++FE    KV  L R S+G   L  +L  G  +E+S+  L
Sbjct: 180 EVTVQEGKYHQVKRMFEARGKKVVYLKRTSFGNLPLDESLEEGEYKELSESEL 232


>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 =  250 bits (638), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 112/232 (48%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K++  +G  +R+E++ +     V VNG ++  ++V V     + V G  +   E  
Sbjct: 2   IRLDKLLGHSGYGTRKEIKSLCKSGDVTVNGEIVRDSSVKVDEGATVIVAGEKVEY-EAV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + HKP G+V+   D   R TV D LPS +  SRV  VGRLDI+T GLLLL+NDG  A
Sbjct: 61  SYLMLHKPAGVVSATQDSRVR-TVLDILPSRYAASRVAPVGRLDIDTTGLLLLSNDGTWA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     +VY  +  G +  D       GIV+  G+     +     +K +   + 
Sbjct: 120 HKVISPKKHVPKVYEAQVEGVIPADVGERFAAGIVLEDGVECLPARA----EKTAEGRLQ 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++       V  L R   G   L   L AG  R+++K+ +
Sbjct: 176 ITVCEGKFHQVKRMCSVVGLTVTSLHRSRIGGLALDKNLQAGEYRKLTKEEI 227


>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 =  250 bits (638), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 115/249 (46%), Gaps = 6/249 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M  +          R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      
Sbjct: 1   MMAEPEESREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAV 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDI 116
           + VDG  +   +       +KP G+ +T SD  GR  + D +        ++  VGRLD 
Sbjct: 61  VRVDGARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDA 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDM 175
           +TEGL+LLTNDG LA  L  PS +  + Y     G V +     L+ GI +     + D 
Sbjct: 121 DTEGLMLLTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDD 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +D   G    V V L EG+NR ++++     + V  L+R   G   LG    GS R 
Sbjct: 181 FAVVDAIPGKT-LVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRA 239

Query: 236 VSKKILREQ 244
           +    + + 
Sbjct: 240 LRSNEIGQL 248


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IEHSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPASSGKRFTSPGRKKK 287


>gi|323466841|gb|ADX70528.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 246

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 68/229 (29%), Positives = 114/229 (49%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++ 
Sbjct: 11  MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEVNY-QKY 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L  
Sbjct: 70  HYFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNH 129

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--AWV 189
            L  P+    ++YR +  G  D + +     G+ +  G      ++ +  Q   +  + +
Sbjct: 130 ELLAPNKHVDKIYRAKIAGVADDETVKTFASGMTLGDGTKLKPAELKILAQDEEHDSSEI 189

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + +REGK  +IK++F     KV  L RIS G  +L   L  G+  E+S
Sbjct: 190 EIKIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGNYIELS 238


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 126/296 (42%), Gaps = 11/296 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  RESEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +  P     + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRPGNDHEKEYLVTVDKPITDEFIRGMGPGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 289


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 109/232 (46%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + ++++ RV+VNG + ++    +  +D + VDG  L   ++ 
Sbjct: 1   MRLDKYLAETAQCTRSEAKALLSKGRVQVNGAVCKKGDTQLKESDTVAVDGRALSY-QQF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DG  A
Sbjct: 60  VYIMLNKPEGVVSASTDKRD-TTVVDLVGDAYPRRQLFPAGRLDKTSTGFVLLTDDGTFA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V     + ++       G+ +  G      +VT  +  G    V 
Sbjct: 119 HDILAPKRHVSKTYTVVLDTPLTEEMRTGFAAGVTLADGTALSPAEVTALSADG--CTVR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V L++G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 177 VVLKQGVYHQIKRMFGVYGAGVNGLHRDAIGGLALDPALAPGQWRELSAEEV 228


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVKLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP   ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKDYISATED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 134/293 (45%), Gaps = 10/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-- 67
             T  R++K I+ +GI SRRE +R I Q  V +NG         V++ D ++V+G  +  
Sbjct: 3   TDTSIRLNKYISESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIES 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+A+   L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRFTSPGRKKK 287


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 93/365 (25%), Positives = 156/365 (42%), Gaps = 20/365 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
           +   +++ KV+ARAG  SRRE+E MI   RV ++G++ +        +  + +DG  +  
Sbjct: 2   SIMSEKLQKVLARAGQGSRREIELMIQSGRVSIDGVVAKLGDRLDDFSVLVRIDGHKIDL 61

Query: 69  ---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLL 124
                E  R+  Y+KP G + T  DP+GR TVFD LP + S R +SVGRLD NT GLLL 
Sbjct: 62  VSPSEEVCRVLAYNKPEGELCTRHDPEGRRTVFDRLPRLSSGRWVSVGRLDANTSGLLLF 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T DG LA  L  PS    R Y VR  G+++++ +  L +G+ ++        V     +G
Sbjct: 122 TTDGELANRLMHPSRSVEREYMVRVFGEINENMVKNLVQGVELEDGMARFEDVVYSGGEG 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI--- 240
            N    V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+  K    
Sbjct: 182 MNHTFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDIYLTKDMPRGGWMELELKEVNY 241

Query: 241 LREQLGPHLLEEAQVNLDAPIYSS-----ETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           LRE +     E   + ++              VR     ++E P           ++   
Sbjct: 242 LREVVELEAEENTMLTVEGLKRKRGVRQIRRAVRRHEERVTETPRGRRGRTNTPDERRSS 301

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS------FPSKRSLRR 349
           ++  +                      +    S  +     R  +         ++    
Sbjct: 302 TRNSEAEGQNVPVGKRKPSGKPSTAKPTRGKPSAGKPAQGNRRKTDDCNEPAGKRKPSGN 361

Query: 350 TSAKK 354
            + ++
Sbjct: 362 GAQRR 366


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 125/296 (42%), Gaps = 11/296 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  RESEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 289


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 112/232 (48%), Gaps = 11/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  SR +V+++I +  V VNG  +      +    D +EVDG  ++ + R
Sbjct: 1   MRLDKFLTHCGFGSRTQVKKLIREGIVTVNGKQIVEVDFKINPEEDVVEVDGRVVKFS-R 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V ++ DP    TVF  +        + +VGRLD + EGLL++T++G  
Sbjct: 60  WIYIMMNKPKGYVCSNEDPMS-LTVFSLISDDLKHRDLHTVGRLDKDAEGLLIITDNGEY 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P  +  + Y VR   +VD+++L   + GI++  G      + T+      +  V
Sbjct: 119 THRVISPKKRIEKEYLVRLEKEVDEERLKEFENGIILDDGYKTLPAKYTI----IDSTTV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++K++FE    KV  L R   G   L  +L  G  R + ++ 
Sbjct: 175 KLCIYEGKYHQVKRMFEAIGNKVVDLKRRRIGGLNLDESLKPGEYRVMKEEE 226


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 125/239 (52%), Gaps = 9/239 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + +L +KP G+V+  SD +   TV D +       ++  VGRLD +TEGLLL+TN+G L
Sbjct: 61  -KYFLLNKPAGVVSAVSDKEH-QTVIDLIKEADRVPKLYPVGRLDRSTEGLLLVTNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+           ++ + T     +  
Sbjct: 119 GYRMLHPKYHVAKTYYVEVNAFLADDAPAFFENGVSFDDGTICKPAKLEIITASPETSSA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQL 245
            V + EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   K+IL+  L
Sbjct: 179 YVTISEGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTEKEILKNYL 237


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 68/292 (23%), Positives = 126/292 (43%), Gaps = 12/292 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRAA-IGDQVYAADVVKVNGQLIEPRDEDD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIISTTEDGEQDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  L  G+ + G            +K +     + 
Sbjct: 125 KILRAGNDHEKDYVVTVNKPVTDEFILGLSAGVPMLGTVTK----KCKVKKEATFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++   F ++V +L R       L  L  G  R+ +   L E     L+E 
Sbjct: 181 LVQGLNRQIRRMCSHFGYEVTKLERTRIMNINLKGLPQGEWRDFTDDELIELF--KLIEH 238

Query: 253 AQV-NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +   +       S+     +P+I      + +     S ++     +KK   
Sbjct: 239 SSSEDKPTKKAQSKPAAEKKPSIKRPKVAEKSDGNAASRKRFAQPGRKKKGR 290


>gi|326407871|gb|ADZ64942.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. lactis CV56]
          Length = 273

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 112/241 (46%), Gaps = 11/241 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   E 
Sbjct: 32  MRLDKFLAESGLGSRSEVKILLKKGRVTVAGEVQRDGRFQVDKNSRQVAFDGEILDYQE- 90

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
              +L +KP GLV+   D   ++ V       F   +  VGRLD NTEGLL+LTNDG L 
Sbjct: 91  YYYYLLNKPQGLVSATKDNLFKTVVQLLSEKDFREDIFPVGRLDKNTEGLLILTNDGALG 150

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL------DTQKG 184
             L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ +      ++Q G
Sbjct: 151 HDLTQPKRHVEKEYFARIDGKVTDEIVNKFAEGLTLKNGEKARPGELFIENIYKGESQSG 210

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
             + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + +  
Sbjct: 211 WISEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTTEEIEN 270

Query: 244 Q 244
            
Sbjct: 271 L 271


>gi|315180431|gb|ADT87345.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 315

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 102/304 (33%), Positives = 144/304 (47%), Gaps = 13/304 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E +I   RV VNG +             + +DG  +    +
Sbjct: 2   SEKLQKVLARAGHGSRRELEALIRAGRVSVNGKVAVLGERLEDENAVVRIDGHAVSAKAQ 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G + T  DP+GR TVFD LP I  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-TLLAGSTREVSKKI---LRE 243
              V + EG+NRE+++++E     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWESQETTVSRLKRVRYGDIFLDKKLPRGGWMELDLKDVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     +   +++     +S    R R   I        R ++  +   G S   +   
Sbjct: 242 LVELKPEKTTMLDVSKD-NTSRKRERSRSQKIRR---AVRRHEERVTAPAGRSGSSRRKD 297

Query: 304 PVHR 307
              R
Sbjct: 298 AASR 301


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 67/293 (22%), Positives = 124/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++             ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKTKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 121/241 (50%), Gaps = 2/241 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + +    E+    R++K +A  G+ASRRE   ++ Q  + VN ++       + + D ++
Sbjct: 26  ERRPSAPESTEGMRLNKYVAHCGVASRREAAEIVKQGHITVNSVVETEPFYQIKTGDIVK 85

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEG 120
             G  +R   R   +L +KP  ++TT SD  GR TV D +      RV  VGRLD +T G
Sbjct: 86  YKGQVIRPEVRRVYYLMNKPKNVITTTSDEKGRKTVLDLVADRVEERVFPVGRLDRDTTG 145

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTNDG LA  +  PS +  ++Y    +  V ++ L  ++ G+ ++      +     
Sbjct: 146 LLLLTNDGELALKMTHPSYKIKKIYHATLNKTVSKEDLEKIRAGLELEDGP-APVDAADY 204

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +  ++ V + +  G+NR ++++FE   ++V +L R+  G      L  G  R ++ + 
Sbjct: 205 IIERPHSEVGLTVHIGRNRIVRRIFEHLGYEVLKLDRVYLGGLTKKDLPRGFVRRLTSQE 264

Query: 241 L 241
           L
Sbjct: 265 L 265


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 135/270 (50%), Gaps = 7/270 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E     R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G
Sbjct: 53  LIPEWSGTMRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKG 112

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
             +        ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLL
Sbjct: 113 QLISHKT-HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLL 170

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDT 181
           LLT++G L   L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+  
Sbjct: 171 LLTDNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLA 230

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
              + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 231 ATETESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 290

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           L+  L    +E+ Q +   P        R 
Sbjct: 291 LQLLLPYFFIEKQQTSKALPSNLKREEERK 320


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 71/297 (23%), Positives = 128/297 (43%), Gaps = 12/297 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLNGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +            +T    RP +  E   +      ++ ++     +KK   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGCPASNGKRFTSPGRKKKGR 290


>gi|320179014|gb|EFW53973.1| 23S rRNA pseudouridine synthase F [Shigella boydii ATCC 9905]
          Length = 290

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 125/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSSSEAKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 288


>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 =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 123/236 (52%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +   E 
Sbjct: 1   MRLDKCLEKAKVGSRKQVKKLFKAQQIKINGHAAQSLSQIVDPELQTIQVSGKKVAL-EG 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           +  +L HKP G+V+  +D +   TV D +    SR  +  VGRLD +TEGL+L+TN+G L
Sbjct: 60  SAYYLLHKPAGVVSAVTDQEH-QTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              +  PS    +VY V  +G + +D       G+  + G       +T+      ++  
Sbjct: 119 GYRMLHPSHHVDKVYYVEVNGCLAEDASKFFASGVTFLDGTRCQPADLTVLEASLDHSRA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           T+ L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++   +    
Sbjct: 179 TIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGAYRQLTPNEMEHLF 234


>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 =  249 bits (637), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 116/241 (48%), Gaps = 17/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A AG  +R EV++ I + +V+VNG+  +++ + V   D + +DG  + +A    
Sbjct: 6   RLDKFLADAGAGTRSEVKKFIQKGKVQVNGVPAKKSEIKVSEEDEVVLDGNRISQAPEFV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L HKP G V+   D   + TV + + S    +  VGRLD +TEGLLL+T+DG LA  L
Sbjct: 66  YYLLHKPAGYVSATEDKRDK-TVMELVASDRKDLFPVGRLDKDTEGLLLITDDGALAHEL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------- 181
             P     + Y     G + ++ +     G+ I G     M   L               
Sbjct: 125 LSPKKHVDKTYYAVTDGCMTKEDVQRFADGLEI-GEKNPTMPAKLKILSTRKVEETELEQ 183

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
              G ++ + + ++EGK  ++K++ E    KV  L RIS G   L   L  G  R+++ +
Sbjct: 184 YPSGWSSEIQLTIKEGKFHQVKRMTEAVGKKVVYLKRISMGVLTLPDDLKKGECRQLTAE 243

Query: 240 I 240
            
Sbjct: 244 E 244


>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 =  249 bits (637), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 117/241 (48%), Gaps = 10/241 (4%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPL 67
           E     R+ K +A  GI +R+EV+R I Q RV ++GI  +     +      I  DG  +
Sbjct: 2   EAMLMIRLDKYLADMGIGTRQEVKRYIRQGRVSIDGIPAKSPETKIEEKARKITFDGREV 61

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTN 126
             A+    ++ +KP G+V+   D    +TV D +     + +  VGRLD +TEGLLL+TN
Sbjct: 62  DYAD-YEYYMLNKPSGVVSATEDAR-CTTVVDLIRDKKRKDLFPVGRLDKDTEGLLLITN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L+  L  P     + Y  +  G+V ++     ++G+ I    +        V    +
Sbjct: 120 DGQLSHRLLSPKKHVDKTYYAKVAGKVTKEDAKAFREGVNIGTEEKEEWTRPG-VLDILK 178

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
               + + + ++EGK  ++K++F+    +V  L R S G  +L  TL  G  R ++KK L
Sbjct: 179 SEEVSEIRLTIQEGKYHQVKRMFQAVGKEVLYLKRESMGCLKLDETLKPGEYRPLTKKEL 238

Query: 242 R 242
            
Sbjct: 239 E 239


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 72/231 (31%), Positives = 131/231 (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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFMLNKPLEVLSASSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 115/235 (48%), Gaps = 10/235 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
               + +KP  +V+  SDP    TV D + +I  R    VGRLDI+TEGLLL+TNDG LA
Sbjct: 60  VVYIMLNKPQDVVSATSDPTH-ETVLDCIDAILPRDCFPVGRLDIDTEGLLLITNDGKLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVT 190
             L  P    ++ Y V+    + +     L+ G IV+        +V L  +      + 
Sbjct: 119 HRLLSPKNHVVKTYFVQLAKPLQEADKKRLEDGSIVLDEEPVQCARVELLEE----TQIL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           + ++EG+  ++K++      +V  L RI+ GP QL   L  G  R + ++ L   
Sbjct: 175 LHIQEGRFHQVKRMLHAVGNEVVYLRRIAMGPLQLDEQLAPGDWRYLYEEELAAL 229


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 111/232 (47%), Gaps = 9/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRR+ +R+I + +V +NG +       V   D +EV+G  ++K   ++
Sbjct: 4   RINKYLSEVGYCSRRKADRLIEEGKVTINGKIP-EIGAKVEDGDQVEVEGQRIKKSTKQK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KPIG+V T         + D +     R+  +GRLD ++EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPIGVVCTTDRGVEPDNIIDFI-KYPKRIFPIGRLDKSSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  ++++ +  +  G+ I      +  V     K       + 
Sbjct: 122 KILRARNNHEKEYIVSVNRPINREFIQTMSNGVEILETKTKNCFVKKLGPKK----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L +G NR+I+++ E   ++V  L R+     +L  L  G  RE +K+ + + 
Sbjct: 178 LTQGLNRQIRRMCESLGYRVQSLKRVRIMNIKL-DLPIGKYREFTKEEISDL 228


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 77/244 (31%), Positives = 117/244 (47%), Gaps = 8/244 (3%)

Query: 8   QENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           +E+  P   R+ KV+++AGIASRR  E+MI   RV+V+G ++      V      + VDG
Sbjct: 5   EESREPRGIRLQKVLSQAGIASRRAAEKMIVDGRVEVDGHVVTELGTRVDPQVAVVRVDG 64

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGL 121
             +   +       +KP G+ +T SD  GR  + D +        ++  VGRLD +TEGL
Sbjct: 65  ARVVLDDSLVYLALNKPRGMHSTMSDDRGRPCIGDLIERKVRGTKKLFHVGRLDADTEGL 124

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLD 180
           +LLTNDG LA  L  PS +  + Y     G V +     L+ GI +     + D    +D
Sbjct: 125 MLLTNDGELAHRLMHPSHEVPKTYLATVTGSVPRGLGRTLRAGIELDDGPAFVDDFAVVD 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              G    V V L EG+NR ++++     + V  L+R   G   LG    GS R +    
Sbjct: 185 AIPGKT-LVRVTLHEGRNRIVRRLLAAAGFPVEALVRTDIGAVSLGKQRPGSVRALRSNE 243

Query: 241 LREQ 244
           + + 
Sbjct: 244 IGQL 247


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A   + +R EV+ +I ++RV VN  ++ +    +    D + VDG  +   E 
Sbjct: 3   IRLDKYLADMQVGTRSEVKELIRKKRVTVNDNIVTKPESKINTDGDSVNVDGNAVGYHE- 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+  +D +  +TV D + +   + +  VGRLD +TEGLL++TNDG +A
Sbjct: 62  YEYFMLNKPAGVVSA-TDDNTCTTVIDLIKNKNRKDLFPVGRLDKDTEGLLIITNDGAMA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDT--QKGSNAW 188
             L  P     + Y  +  G++   ++     G+ +          + + +       + 
Sbjct: 121 HDLLSPKKHVDKTYYAKVKGKISDMEVKQFADGLFVDEELTALPAILKVLSYNSDKDYSE 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + V + EGK  ++K++F     +V  L RI++G   L  +L  G  R ++K+ +
Sbjct: 181 IHVTIHEGKFHQVKRMFTAIGSEVLFLKRITFGALPLDESLKTGEYRALTKEEI 234


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDMISVRGELIEYVEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISGTED-HHSKTVIDLIPEYQHLNIFPVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  249 bits (636), Expect = 5e-64,   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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 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|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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 91/235 (38%), Positives = 133/235 (56%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN   L +    +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVN-QRLAQLGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+ R+TVF+ LP     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-GTLLAGSTREVSKKILREQ 244
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++  
Sbjct: 182 VVVVEGRHRLVRRLWESQGLKVSRLIRVRFGPIVLPKSLRRGAWKELESPEIKSL 236


>gi|325002515|ref|ZP_08123627.1| ribosomal large subunit pseudouridine synthase B [Pseudonocardia
           sp. P1]
          Length = 253

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 76/242 (31%), Positives = 114/242 (47%), Gaps = 7/242 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGV 65
              +    R+ KV+ARAG+ASRR  E +IAQ RV+V+G  +      +   T  + VDG 
Sbjct: 3   TAHDPDGVRLQKVLARAGVASRRAAEELIAQGRVQVDGETVREMGRRIDPETAVLHVDGA 62

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTE 119
            +   +       +KP+GL +T SD  GR  V D L           R+  VGRLD +TE
Sbjct: 63  RVTLRDDQVYLALNKPVGLHSTMSDDLGRPCVGDLLADRVELMNSAQRLFHVGRLDADTE 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG L   L  PS +  + Y     G++ +D    L+ GI ++          L
Sbjct: 123 GLLLLTNDGELGHRLMHPSYEVPKTYLAEVEGKIARDLGRRLRDGIELEDGIARVDAFKL 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + L EG+   ++++       V RL+R + G  +LG    G  R + + 
Sbjct: 183 VDAVPGRSTVQLILHEGRKHIVRRMLSEVGHPVQRLVRTAVGEVRLGNQKPGKLRPLDRV 242

Query: 240 IL 241
            +
Sbjct: 243 EV 244


>gi|257482791|ref|ZP_05636832.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. tabaci ATCC
           11528]
          Length = 241

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 96/238 (40%), Positives = 131/238 (55%), 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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG 231
            +      +G N W    + EG+NRE+++++E     V+RL R+ YGP  L   L  G
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMG 240


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 82/233 (35%), Positives = 123/233 (52%), Gaps = 3/233 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR + E +IA+ RV+V G ++  AA+ V    D I VD  P+  AER  
Sbjct: 19  LNRALSKLGLCSRTQAEVLIAEGRVRVGGKVVRDAALRVDLDRDRIVVDDRPVV-AERKV 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP  R TV+  L       V  VGRLD  +EGLLL+TND   A  
Sbjct: 78  YLMLNKPRGLVTTRDDPQQRDTVYACLEGLDLPFVSPVGRLDKASEGLLLMTNDTRFANR 137

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P++   + Y V+     D   L  L+ G+++ G       + L    G  AW+ + L
Sbjct: 138 LMDPASHLPKTYHVQIGTVPDAPMLETLRAGVIVDGEVLTANAIELLRSGGRTAWLEIVL 197

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            EG+NR I+++      +V RLIRI+ G   LG L  G+ R ++ + L    G
Sbjct: 198 DEGRNRHIRRLLAAHGVEVLRLIRIAIGRLPLGDLAKGTARHLTAEELALLRG 250


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPASSGKRFTSPGRKKK 287


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 119/232 (51%), Gaps = 8/232 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ +++A A + SR EV++++ ++RV+VNG + + + + V   T  I VD +P+   E+ 
Sbjct: 3   RLDRILANARVGSRSEVKKLVKEKRVRVNGEIAKSSDMRVDENTAEIFVDDIPVTY-EKY 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP G ++  ++     TV D +   +  +   GRLD +TEGLL++TNDG LA  
Sbjct: 62  VYYMLNKPAGYISA-TEGKNCPTVLDLITEDYKGMFPCGRLDKDTEGLLMITNDGPLAHE 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V     + ++ +  ++ G+   G+ Y          K S+   T+ +
Sbjct: 121 LLSPKKHVEKEYYVEHTLPLTEEDIAKIESGVTYNGVSYKPAVYK----KISDTSCTLTI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           +EGK  EIK +F     KV  L R+      L  TL  G  R ++K+ L + 
Sbjct: 177 QEGKYHEIKFIFNSVGDKVVYLKRLRMKNLVLDETLKPGEYRPLTKEELEDL 228


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPASSGKRFTSPGRKKK 287


>gi|40063061|gb|AAR37917.1| RNA pseudouridylate synthase family protein [uncultured marine
           bacterium 560]
          Length = 244

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 87/238 (36%), Positives = 135/238 (56%), Gaps = 7/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +R+ K+IA AG  SRR  ER+I Q RV +N   ++     V+  D + +DG  +     
Sbjct: 2   SERLQKLIANAGYGSRRWAERLIEQGRVSLNNHDVKLGDKAVL-NDKVRIDGKLIDLKRY 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               T++ + +K  G + +  DP+GR +VFD LP   SR I +GRLD+N+ GLLL TN+G
Sbjct: 61  AKTETKVLILNKQAGFICSTKDPEGRKSVFDLLPEN-SRWIMIGRLDLNSSGLLLFTNNG 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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
             V +REG+ RE+++++EF ++KV+RLIRI +G   L   L +  +  +  K L+  L
Sbjct: 180 YRVVIREGRKREVRRLWEFLDFKVSRLIRIRFGDICLPDKLRSNQSEYLKPKQLKTLL 237


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 101/293 (34%), Positives = 150/293 (51%), 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  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
              R+ +Y+KP G V T  DP+GR TVFD LP     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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 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|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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 128/294 (43%), Gaps = 11/294 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R + Q  V +NG         V   D ++V+G  +   +
Sbjct: 5   SSIRLNKYISESGICSRRDADRYVEQGNVFINGKRAA-VGDQVYVGDVVKVNGQLIEPRD 63

Query: 72  RTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + L L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 64  ESDLILIALNKPVGIISTTEDGESDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 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     L
Sbjct: 178 SITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPIGEWRDLRDDELIELF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +  +           V  +   IS           ++ +K      +K   
Sbjct: 236 IENSSSDEKPQKKPKAKPVVAKKPAISRSKPAEKSETNSAGRKRFTQPGRKKKG 289


>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 =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 127/296 (42%), Gaps = 11/296 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 289


>gi|312868136|ref|ZP_07728340.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
 gi|311096540|gb|EFQ54780.1| pseudouridylate synthase [Streptococcus parasanguinis F0405]
          Length = 242

 Score =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV++++ Q+++ VNG       + +    D +   G  L   E 
Sbjct: 1   MRLDKFLVDCGVGSRTEVKQLLKQKKIAVNGKKETAGKLQIDPDKDQVTFMGEDLVH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D D   TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPAGVISATED-DHHQTVLDLLDETARHKEVFPVGRLDIDTHGLLLLTNNGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     + YR +  G +D+  +   ++GI ++       ++ +    +  ++++
Sbjct: 119 AHAMLSPKKHVSKNYRAQVAGIMDEADVARFEEGIALKDFTTLPARLQILEVNEASASSY 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + + EGK  ++K++      +V  L RIS GP  L  TL  G  R +    L+  
Sbjct: 179 VEIEIAEGKFHQVKRMVAACGKEVVDLERISMGPLTLDPTLQLGEWRRLHTSELKSL 235


>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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 84/238 (35%), Positives = 125/238 (52%), Gaps = 12/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           RV K+I++ GIASRRE E MI Q RV++NGIL       V    D I +DG P+ +  R 
Sbjct: 4   RVQKIISQWGIASRREAEEMIGQSRVRINGILAR-LGQKVDPRVDIISIDGKPVIQGNRP 62

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDG 128
                L +KP G+V+T +DP GR+TV D LP+   +   +  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|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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 96/351 (27%), Positives = 164/351 (46%), Gaps = 19/351 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ KV+ARAG  SRRE+E MI   RV ++G++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQSGRVSIDGVVAKLGDRLDDLSVLVRLDGHKIDLVSP 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T  DP+GR TVFD LP + S 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-GTLLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   +  G   E+  K    LRE
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDIYLTKDMPRGGWMELELKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +     E   + ++          + R   + ++     R ++  ++     ++ + + 
Sbjct: 242 VVELEAEENTMLTVEG---------QKRKRGVRQIRRAVRRHEERVTE-TPRGRRGRTSN 291

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
           P  RR+   N  +      +       +    + +   PS     + + +K
Sbjct: 292 PDERRSSTRNSEVEGQNAPAGKRKPSGKPSTAKPTRGKPSAGKPAQGNRRK 342


>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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 71/207 (34%), Positives = 119/207 (57%), Gaps = 3/207 (1%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           VKVNG +++   + V S+D +EVDG+P+ + E     L +KP G++++ +D  GR  V D
Sbjct: 6   VKVNGKVVKELGLKVSSSDRVEVDGIPVEREE-PVYILLYKPRGVISSVTDEKGRKVVTD 64

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
            LP I  RV  VGRLD +T GLLL+TNDG  A +L  P  +  +VY  +  G   ++KL 
Sbjct: 65  LLPQIKERVYPVGRLDFDTSGLLLMTNDGEFANLLMHPKNEVEKVYVAKIKGIPAREKLK 124

Query: 160 LLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
            L++G+ ++       +V + +  ++ + A V + + EG+NR+++++ E     V +L R
Sbjct: 125 SLERGVRLEDGKTAPARVKVLSIDKQKNTAIVELVIHEGRNRQVRRMLEAIGHPVMKLKR 184

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQ 244
             YG   L  L AG  RE++   +++ 
Sbjct: 185 ERYGFLTLQGLSAGDARELTAHEVKQL 211


>gi|298707966|emb|CBJ30337.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 468

 Score =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 84/341 (24%), Positives = 145/341 (42%), Gaps = 16/341 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL--RKA 70
           +R+ K ++ AG+ SRR+ E+MI   RV+VNG +++   V V    D + VDG  +  R  
Sbjct: 35  ERLQKFLSHAGLDSRRQCEQMILDGRVRVNGKMVKELGVKVNPRRDQVHVDGNRVSMRPD 94

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
              +    +KP G++ T SD  GR T   ++P     R++ VGRLD ++ GLLLLTN+  
Sbjct: 95  SEIKWVALNKPKGVICTVSDELGRPTAVASIPRGLEMRLVPVGRLDRDSCGLLLLTNENS 154

Query: 130 LARVLELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-- 186
               L  PS    + YRV    G    ++ ++L +G+++ G         ++        
Sbjct: 155 WINPLTHPSYGHEKTYRVALTSGYPTTEEWDVLTQGMLLDGDPNPTRPCIVEVVNYDRRT 214

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               V + +REGKNR+I+++FE    +V  + R+S+GP +L  L  G  RE+ +  +   
Sbjct: 215 RVTTVDIIIREGKNRQIRRMFEGIGHEVKSITRVSHGPIRLKNLRPGEWRELEQWEIE-- 272

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
               L       L +P                +         + +SQ+     + +    
Sbjct: 273 ---KLKNLTTKTLKSPAKQLAPTPTRAEGRHRQAAAAGRMSSRMTSQQQYHGSEYRRDAL 329

Query: 305 VHRRNLASNV--WMAKGIHSSFLSDSGQREENHRRSPSFPS 343
               +  + V  W   G+  +    +         S     
Sbjct: 330 DEEEDEWNQVGAWDRSGVRKAVAPSARAGAPATTASARGGG 370


>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 =  249 bits (636), Expect = 6e-64,   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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 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|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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 76/223 (34%), Positives = 117/223 (52%), Gaps = 3/223 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG P+   +R  
Sbjct: 33  LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIASPAPPIEVDGQPMAAPQRL- 91

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  
Sbjct: 92  YLMLNKPRGVVTTAQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAH 151

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+     D+D L  L+ G+  +G     + V +       AW+ V L
Sbjct: 152 LTDPETGPQKTYHVQVDRLPDEDTLAALRAGVEDEGEFLVALAVRVLRSGDKTAWLEVVL 211

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            EG+NR I+++   F+ +V RL+R++ G   LG L  G  R +
Sbjct: 212 DEGRNRHIRRLLAAFDLQVLRLVRVAIGELTLGDLGKGQWRVL 254


>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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 82/241 (34%), Positives = 128/241 (53%), Gaps = 10/241 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R++K +A AG+ +RR+VE +I Q RV VNG ++E  AV V    D + VDG  +R  +R
Sbjct: 1   MRLNKFLAYAGLGARRKVEELIKQGRVTVNGEVVENPAVEVDPKKDEVRVDGERVRLPKR 60

Query: 73  TRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 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 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G N +V +    GKNR +++ F+ F+  V +L RI+ GP +LG L  G  RE++ + +++
Sbjct: 181 GRNTYVQISFDIGKNRVVRRFFDRFDHGVLKLKRIAIGPLKLGNLPKGMYRELTPEEVKK 240

Query: 244 Q 244
            
Sbjct: 241 L 241


>gi|319745443|gb|EFV97749.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 240

 Score =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 116/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   E+
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   DP  + TV D L        V  VGRLDI+T G LLLTN+G L
Sbjct: 60  FVYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGFLLLTNNGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  +  P     + Y  +  G + +D +    KGI+++         ++    Q  + + 
Sbjct: 119 AHKILSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKNQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + + 
Sbjct: 179 VKITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEIEKL 235


>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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 110/230 (47%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     +R    + +    + VNG +++  A+ + S D +  +G  L   E  
Sbjct: 1   MRLDKFIAENIGLTRSLANKALKSSLITVNGQVVKSGAMKITSADGVCYEGNRLTWLESG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G + ++ D +   TVF         R+ + GRLD++T GL+LLT+DG  + 
Sbjct: 61  QYFMLYKPQGYICSNDDSEY-PTVFQFFDYRLMVRLHTAGRLDVDTTGLVLLTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     V+QD    L KGI+++G     +   ++     N  V + 
Sbjct: 120 RITSPKYHCEKSYLVTLADPVEQDYALKLAKGILLRGERDPCLPAAMEIIDDYN--VNLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     KV  L R   G   L  TL  G+ R ++K+ +
Sbjct: 178 ICEGRYHQVKRMFAALGNKVQALHRWRIGEIILDETLQEGTFRHLTKQEI 227


>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 =  249 bits (636), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRFTSPGRKKK 287


>gi|304403869|ref|ZP_07385531.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304346847|gb|EFM12679.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 260

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 71/251 (28%), Positives = 118/251 (47%), Gaps = 16/251 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
                R+ K++A  G  +R E+++ + Q +V V+G +++ + + +      +   G  + 
Sbjct: 11  TDKRMRLDKLLANMGYGTRSEIKKAVKQGKVTVDGRVVKDSGLQIKPNEQQVAFSGELVV 70

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
             +     + HKP G+V+   D     TV D L +     +   VGRLD +TEGLLLLTN
Sbjct: 71  YRD-VVYLMLHKPPGVVSATEDSRD-ETVIDLLDADDRILQPFPVGRLDKDTEGLLLLTN 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHG--QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           DG LA  L  P     + Y  R  G   V Q        G+ +    Y  M   L+ ++ 
Sbjct: 129 DGQLAHDLLSPRKHVPKTYFARVLGEEPVGQADRERFAAGVELDDG-YVTMPAELEVEQA 187

Query: 185 SN------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
                   + + + ++EGK  +IK++F+    +V  L R+S GP  L  TL  G+ RE++
Sbjct: 188 EQSDDGWVSLIRITIQEGKFHQIKRMFQAVGKQVIYLKRLSMGPLHLDETLPIGAYRELT 247

Query: 238 KKILREQLGPH 248
           +  + E L  H
Sbjct: 248 EDEI-ELLRSH 257


>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 =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRFTSPGRKKK 287


>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 =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 74/239 (30%), Positives = 118/239 (49%), Gaps = 5/239 (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
           +   E+ R  + HKP G+V+   D     TV D +      +  VGRLD +TEGLLLLTN
Sbjct: 61  VTY-EKYRYIMLHKPAGVVSATEDAQ-CQTVLDLITEGRKGLFPVGRLDKDTEGLLLLTN 118

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P     + Y     G+V + +  L  +G+ I       +   L+    +N
Sbjct: 119 DGALAHNLLSPRKHVDKTYFAILDGEVGEKEQELFLQGLDIGDEK-KTLPAKLEITDKAN 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
             V + ++EG+  ++K++ E    KV  L RIS GP  L   L  G  R + ++ L + 
Sbjct: 178 -EVFITVQEGRFHQVKRMAEAVGRKVEYLKRISMGPLVLDKELKKGEYRPLFEEELAKL 235


>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 =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 71/296 (23%), Positives = 127/296 (42%), Gaps = 11/296 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V S D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKSGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 289


>gi|323254500|gb|EGA38311.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 289

 Score =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NYSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRLTSPGRKKK 287


>gi|324112367|gb|EGC06345.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 290

 Score =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 68/293 (23%), Positives = 125/293 (42%), Gaps = 9/293 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSIRLNKYISESGICSRREADRFIEQGNVFINGKRAT-IGDQVKPGDVVKVNGRLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +K +G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKSVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 236 IENSTSEVKPKAKAKPKTAGIKRPVVKMEKTSEKGGRPASNGKRFTSPGRKKK 288


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 70/293 (23%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVAVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRFTSPGRKKK 287


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 106/353 (30%), Positives = 161/353 (45%), Gaps = 14/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV V+G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHVVSVKES 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           T    R+  YHKP G + T  DP+GR TVFD LP    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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---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 ---PVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTS 351
              P  +R   +      G   S       GQ+    + SP+  + +S  R  
Sbjct: 302 SSLPSAKRGSNNGDSQPSGKPQSKGKKPAAGQKPVRSKFSPNGKAPKSKPRQR 354


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 114/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR++V+    +  ++V+G++++ +A+ V      I+++G  +    +
Sbjct: 2   ERLDKIISNLGYGSRKDVKSFAKKGIIEVDGLIVKDSAMLVDPEKSVIKINGEEVLYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D +   TV D L           +GRLD +T GLLLLTNDG L
Sbjct: 61  YIYIMMNKPDGVISATHD-NRDETVIDLLNLEHQVFDPFPIGRLDKDTVGLLLLTNDGEL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY       VD+  +   K GI +  G    +  + + +     + +
Sbjct: 120 NHRLISPKWHVDKVYYAEIDKSVDEKDIKAFKDGITLDDGYKCLEANLEILSSSNDGSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + ++EGK  ++K++FE    KV  L R  +G   L   L  G  RE++ + L
Sbjct: 180 RLTIQEGKFHQVKRMFEAVGKKVTYLKREEFGGLLLDPDLEEGEYRELTDEEL 232


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 125/288 (43%), Gaps = 12/288 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +   E
Sbjct: 5   ESMRLNKYISESGICSRREADRFIEQGHVFINGKRA-GIGDQVQVGDLVKVNGQVIEPRE 63

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L   +KP+G+V+T    +  + V  +  +  +RV  +GRLD +++GL+ LTN G 
Sbjct: 64  ADSLVLIALNKPVGIVSTTEAGEKDNIV--DFVNHSTRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     V  + +  +  G+ I G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYLVTVDKPVTDEFVRGMAAGVPILGTVTK----KCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E F ++V +L RI      L  L  G  R+++   L +     L
Sbjct: 178 RITLVQGLNRQIRRMCEHFGFEVTKLERIRIMNVSLKGLPVGEWRDLTDDELIDLF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +E++   +  P    +      P   S  P    + +++   + G   
Sbjct: 236 IEDSSSEV-KPAKGDKPKAAKAPAAQSAKPGQGKKPRRDDDHEIGGRP 282


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 78/243 (32%), Positives = 117/243 (48%), 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  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINT 118
           VDG+ +   +       +KP G  +T SD  GR  + D +    S   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|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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 68/301 (22%), Positives = 126/301 (41%), Gaps = 18/301 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
             R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRA-SVGDRVFAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   +   +KP+G+++T  + + R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVVIALNKPVGIISTTEEGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G            +K S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTK----KCKVKKESTFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V++L R       L  L  G  R+++   L E     L+
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYEVSKLERTRIMNVSLKGLPPGEWRDLTDDELIELF--KLI 236

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNL 310
           E +            T  + +P   +      +  K  +      +   +       R  
Sbjct: 237 ENSSSE-------DGTAKKTKPKATTAKKPAASGAKGGAKATGNANPAPRKRFAQPGRKK 289

Query: 311 A 311
            
Sbjct: 290 K 290


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 106/353 (30%), Positives = 161/353 (45%), Gaps = 14/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV V+G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHVVSVKES 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           T    R+  YHKP G + T  DP+GR TVFD LP    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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---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 ---PVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFPSKRSLRRTS 351
              P  +R   +      G   S       GQ+    + SP+  + +S  R  
Sbjct: 302 SSLPSAKRGSNNGDSKPSGKPQSKGKKPAAGQKPVRSKFSPNGKAPKSKPRQR 354


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 92/235 (39%), Positives = 134/235 (57%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN   L +    +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVN-QRLAQLGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+GR+TVF+ LP     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-GTLLAGSTREVSKKILREQ 244
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++  
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLSKSLRRGAWKELESPEIKSL 236


>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 =  248 bits (635), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 109/239 (45%), Gaps = 13/239 (5%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPL 67
           E  T  R+ ++IA  G  S+R+V+ MI   RV + +G +L+       + D I VDG PL
Sbjct: 10  EGHTDMRLIRLIANLGYGSQRDVKAMIKAGRVTLADGTVLDD-GTK-AAHDDIRVDGEPL 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLL 123
                  + + HKP G   + SDP     V++ LP  F      V  VGRLD ++ GLLL
Sbjct: 68  DPPPGL-VLMLHKPEGYTCSTSDPG--RIVYELLPERFMHRNPIVAPVGRLDRDSTGLLL 124

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQ 182
           LT+DG LA  +  P     + Y V     +  ++  +   G ++++          L   
Sbjct: 125 LTDDGPLAHRITSPKRHVPKTYEVTLARPLSGEEGAVFASGTLMLRSESTPLAPAELVVS 184

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               A   + + EG+  ++K++F      V RL R + G   LG L  G  R +S   +
Sbjct: 185 GPQTA--RITITEGRYHQVKRMFAAVGNHVERLHRAAIGGLDLGDLAEGQWRPLSPAEI 241


>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 =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 122/236 (51%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K + +A + SR++V+++   Q++K+NG   +  +  V      I+V G  +   E 
Sbjct: 1   MRLDKCLEKAKVGSRKQVKKLFKAQQIKINGQAAQSLSQIVDPELQTIQVSGKKVAL-EG 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           +  +L HKP G+V+  +D +   TV D +    SR  +  VGRLD +TEGL+L+TN+G L
Sbjct: 60  SAYYLLHKPAGVVSAVTDQEH-QTVIDLISPQDSREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D       G+  + G       +T+      ++  
Sbjct: 119 GYRMLHPSHHVDKFYYVEVNGCLAEDASKFFASGVTFLDGTRCQPAVLTVLEASLDHSRA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           T+ L EGK  ++KK+F  +  KV  L RIS+G F+LG L  G+ R+++   +    
Sbjct: 179 TIKLAEGKFHQVKKMFLAYGVKVTYLKRISFGGFELGDLERGAYRQLTPNEMEHLF 234


>gi|121308590|dbj|BAF43685.1| hypothetical protein [Vibrio fischeri]
          Length = 354

 Score =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 104/353 (29%), Positives = 166/353 (47%), Gaps = 14/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV V+G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSVDGQRAKLGDRLENVDAKIRIDGHVVSVKES 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           T    R+  YHKP G + T  DP+GR TVFD LP    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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   L  G   E+  K    LRE
Sbjct: 182 TFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKALPRGGWMELELKEVNYLRE 241

Query: 244 QLGPHLLEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +     +E+ +++D      +++  +     +    +  T  +   + + G S +K + 
Sbjct: 242 MVELPAEKESLLDVDKESRKRAKSKTQKIRRAVKRYDERSTEERNTPAGRRGRSNKKPVG 301

Query: 303 TPVHRRNLASNVWMAKGIHSSFLSD----SGQREENHRRSPSFPSKRSLRRTS 351
           + +      SN   ++             +GQ+    + SP+  + +S  R  
Sbjct: 302 SSLPSAKRGSNNGESQSSGKPQSKGKKPVAGQKPVRSKFSPNGKAPKSKPRQR 354


>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 =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 78/245 (31%), Positives = 126/245 (51%), Gaps = 11/245 (4%)

Query: 7   VQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           ++++ T +   R++K +A  GIASRRE +R++    V +NG +     V V    D + V
Sbjct: 1   MKKDMTTEEGIRINKYLALCGIASRRESDRLVEAGEVMINGRIARTQGVKVHPGKDEVVV 60

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
            G  L    E+    L +KP  ++TT+ D   R TV D + S+  R+  VGRLD  + GL
Sbjct: 61  KGRILALPEEKKVYILLNKPRNIITTNRDEKDRETVLDIV-SVPQRIFPVGRLDRKSTGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTL 179
           LLLTNDG LA  L  PS+   + Y  +      + +L  L  G+ ++  G      +  L
Sbjct: 120 LLLTNDGDLAHRLMHPSSLVEKEYLAQLEKPFLEKELKNLTGGMRLKDTGEKVSSCKAKL 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +       V V + EGKN +++++F    + V +L R+SY   ++G L  G  R ++KK
Sbjct: 180 LS---DGMQVLVTIHEGKNHQVRRMFWSLGYDVKKLDRVSYAGLKVGRLRRGEWRFLNKK 236

Query: 240 ILREQ 244
            ++E 
Sbjct: 237 EVKEL 241


>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 =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 92/235 (39%), Positives = 134/235 (57%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN   L +    +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVN-QRLAQLGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+GR+TVF+ LP     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-GTLLAGSTREVSKKILREQ 244
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++  
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGAWKELESPEIKSL 236


>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 =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 92/235 (39%), Positives = 133/235 (56%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN   L +    +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVN-QRLAQLGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+GR+TVF+ LP     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-GTLLAGSTREVSKKILREQ 244
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G  +E+    ++  
Sbjct: 182 VVVVEGRHRFVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGDWKELESPEIKSL 236


>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 =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 112/235 (47%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     +   D + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGLVDVNGKTVKTPKEKINEDDVVTVNGEKVAY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTNDG L 
Sbjct: 60  HYFLLNKPTGVLSATED-RSQKTVISLLKPEDRYQGIAPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAW 188
             L  P+    +VYR +  G  D + +     G+ +  G      ++ +  Q  + + + 
Sbjct: 119 HELLAPNKHVAKVYRAQIAGVADDETVKTFASGMTLGDGTKLKPAKLRILKQDRENATSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + + EGK  +IK++F     KV  L R++ G   L   L  G   E+S   + 
Sbjct: 179 IEIEISEGKYHQIKRMFGAVGMKVMALDRLAMGKLCLPADLKRGKYVELSLDEIE 233


>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 =  248 bits (635), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 120/257 (46%), Gaps = 12/257 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V   D ++V+G  +   +
Sbjct: 5   SSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAA-VGDQVYVGDVVKVNGQLIEPRD 63

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 64  ENDLVLIALNKPVGIISTTEDGESDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G      +V  +         
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFILGLGAGVPMLGTVTKKCKVKKEAA----FVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           ++ L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E     L
Sbjct: 178 SITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPQGEWRDLTDDELTELF--KL 235

Query: 250 LEEAQVNLDAPIYSSET 266
           +E +  + + P   +E+
Sbjct: 236 IENSSSD-EKPYKKAES 251


>gi|297538013|ref|YP_003673782.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257360|gb|ADI29205.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 374

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 93/340 (27%), Positives = 171/340 (50%), Gaps = 12/340 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
            QR+ K++A AG+ SRR++E +I+  RV VNG    +    V   D + +D  P++    
Sbjct: 36  TQRLHKLLALAGLGSRRDMETLISSGRVTVNGAPATQ-GQGVTQFDTVRLDSRPVKLPFI 94

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E  ++ +YHKP G + +  DP+GR++VFD LP + + + 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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL-- 245
             V LREG+NRE++++FE F   V+RL+R+ +GP  L   +  G+  ++ +K +   L  
Sbjct: 215 YQVILREGRNREVRRLFEAFQLPVSRLMRVRFGPVNLPPRVKRGTMLKLEQKEVVGLLEW 274

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS----SQKNGLSKQKKL 301
               +  A +         +      P +  +      R+ +      S+K  +++++  
Sbjct: 275 ADLPVPSAPLRQLTQREKLKATTVFMPKVRKQRISALDRVPRTDGEPYSKKPSVARKEAP 334

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSF 341
             P  R++    V     + +     +G ++++ R     
Sbjct: 335 KKPAPRKSENRRVRQTSDLPAPDAQKAGMQKKSDRNRGRG 374


>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 =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 106/228 (46%), Positives = 144/228 (63%), Gaps = 4/228 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++ARAGIASRREVERMI + RVK+   ++   A  + S   + VDG P+      R
Sbjct: 30  RIAKLLARAGIASRREVERMIEEGRVKIGDEVVTTPATLLTSLKGVSVDGKPVAPMAPPR 89

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L+ +HKP GL+T   DP GR T++    + LP    RV+ VGRLD+NTEGLLL+TNDG L
Sbjct: 90  LFRFHKPSGLITAERDPTGRPTIYTALRNALPQGTPRVMPVGRLDVNTEGLLLMTNDGEL 149

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            R LELPST   R YR R  G + Q +L  L +GI I G+ YG +   L+   G N W+ 
Sbjct: 150 KRALELPSTGIPRTYRARTFGDISQARLEELMEGIEIDGVRYGSINANLERSAGRNKWIE 209

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + L EGKNRE+++V E    +V+RL+R  YGPF+L  L  G+  E+ +
Sbjct: 210 LTLTEGKNREVRRVLEHLGLQVSRLLRTKYGPFELADLPRGAAEEIPQ 257


>gi|329667573|gb|AEB93521.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           johnsonii DPC 6026]
          Length = 233

 Score =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVAY-QQY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTNDG LA
Sbjct: 60  HYFLLNKPKGVISATED-RSQKTVLSLLKPKDRYKGIAPVGRLDKDTTGLLLLTNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAW 188
             L  P+    + YR +  G  D++ + +   G+ +  G      ++ +  Q  +   + 
Sbjct: 119 HELLAPNKHVTKKYRAKIAGVADEETVEIFASGMTLGDGTKLKPAELKILIQDKEADRSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + + ++EGK  +IK++F     KV  L RIS G   L T L  G  +E+S K ++
Sbjct: 179 IEIEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPTSLKRGEYKEISLKEIK 233


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 91/309 (29%), Positives = 141/309 (45%), Gaps = 7/309 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K ++       ++ KV+A+AG+ SR E+E++I + R+ VN          +   D I+
Sbjct: 101 PAKRVLLPQVDSPKLHKVLAQAGLGSRLEMEQLILEGRISVNNEPA-HVGQRIQFGDQIK 159

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           V+G P+R        R+  YHKP+G V TH DP  R TVF  LP     +  SVGRLD+N
Sbjct: 160 VNGQPIRFRIDPPPARVIAYHKPVGEVVTHDDPQNRPTVFRKLPRLQHGKWQSVGRLDLN 219

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLL T+ G LA  L  P     R Y  R  G + +++   L  G+ ++        +
Sbjct: 220 TEGLLLFTSSGELANSLMHPRFGLEREYAARVLGALSKEEKQRLTDGVQLEDGVAAFGSI 279

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                +G+N W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+
Sbjct: 280 EDGGGEGANCWYRVTISEGRNREVRRMFEAVGHAVSRLIRIRYGAMVLPRGLKRGAWVEL 339

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSET-LVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
            +  ++       ++        P          DR  +  E    +    + +      
Sbjct: 340 DQADIQSLASAAGMQARAPAAPKPPAGGRRGGPADRNTVRREGGGRYFDGNRPAPNAMLD 399

Query: 296 SKQKKLATP 304
             + K A  
Sbjct: 400 GPRAKPAAK 408


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 131/293 (44%), Gaps = 10/293 (3%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NYSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRVGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 235

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++    A      T ++ RP +  E  ++  R   +  +     ++KK
Sbjct: 236 IERSSSEAKPKAKAKPKTTGIK-RPVVAIEKSNEKARPTSSGKRFTSPGRKKK 287


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 103/314 (32%), Positives = 148/314 (47%), Gaps = 9/314 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +++ KV+ARAG  SRRE+E +I   RV VNGI+ +           + +DG  +    + 
Sbjct: 3   EKLQKVLARAGHGSRRELEALIKAGRVSVNGIVAKLGERLEDENAVVRIDGHTVSAKAQE 62

Query: 74  ----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
               R+  Y+KP G + T  DP+GR TVFD LP I  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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK---ILREQ 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 VHRRNLASNVWMAK 318
             + + A      +
Sbjct: 303 GEQGSRAKQGGKPQ 316


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 129/315 (40%), Gaps = 10/315 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +K I  +  T  R++K ++ AG+ SRRE +++    RV V G  +      + +   +
Sbjct: 1   MDEKRITTDQ-TTIRINKYLSAAGVCSRREADQLTDAGRVTVAGKEIGT-GERIPADAEV 58

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            +DG P++   R  L L++KP G+V +       +TV + L     RV  VGRLD ++EG
Sbjct: 59  FLDGRPVKAETRQVLLLFYKPRGIVCSTKKQRQETTVTEFL-DYPVRVYPVGRLDKDSEG 117

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLLLTN G L   +        + Y V    ++ +  +  +  G+ I G       V   
Sbjct: 118 LLLLTNQGDLVNRIMRAGNYHEKEYEVTVDKKITETFIRKMSSGVPILGTVTRPCTVY-- 175

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV---S 237
            + G  +  ++ L +G NR+I+++ E+  + V  L RI      L  L  G  RE+    
Sbjct: 176 -KTGDKS-FSIILTQGLNRQIRRMCEYLGYHVCTLKRIRIMNLTLDGLKCGEYREICGDE 233

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
            K L E +     E            S    +                +    ++  + +
Sbjct: 234 WKKLNELIRDSSSETVIRTGGQHGKISGRTNKRTGAEAERSGKGILSGRPGDHEQQRVRR 293

Query: 298 QKKLATPVHRRNLAS 312
             +      +RN   
Sbjct: 294 TVRSTGKNGKRNRNR 308


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 67/228 (29%), Positives = 114/228 (50%), 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 + +  +G+ T+++ L +    V  VGRLD ++ GL+LLTNDG  A+ 
Sbjct: 57  IYIKLNKPRGYVVSTNKDEGK-TIYELLNNKLKGVYPVGRLDKDSNGLILLTNDGVFAKK 115

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +   ++   + Y V+ +  +    L  L+ GI + G      +    T+   N    + L
Sbjct: 116 IIGENSNCEKEYYVKVNDNIPDGALKKLEYGISLDGKKLKPAKTKRITKNSFN----IIL 171

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR+I+++ E   ++V  L R+      L  L  G    ++K+ +
Sbjct: 172 TEGRNRQIRRMCEKVGFEVIILKRLRINNIFLNELKEGKFEYLTKEEI 219


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 110/239 (46%), Gaps = 12/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++   G  +R E+++   Q  V+VNG   +++ V+V    D I  +G  +   E 
Sbjct: 1   MRLDKLLGNLGYGTRSEIKKYCKQGFVRVNGAEAKKSDVHVDPENDEIVFNGELVNYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               L +KP G V+   D     TV D +   +       VGRLD +TEGLL++TNDG L
Sbjct: 60  FVYLLLNKPAGYVSATFD-KYDPTVIDLIGEEYLPFEPFPVGRLDKDTEGLLVITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--- 186
           +  +  P     + Y      +VD   + + +KG+ I +       ++ +          
Sbjct: 119 SHRVLSPKNHVPKKYYAIIDKEVDDMDVRIFEKGVYIGEDYTTKPSKLEVLNPFEFEDGS 178

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
             + V V + EGK  ++K++FE    +V  L RI  G  +L   L  G  RE++ + + 
Sbjct: 179 LGSEVHVTISEGKFHQVKRMFEAVGKEVVYLQRIQMGGLELDEELDLGEYRELTPEEVE 237


>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 =  248 bits (634), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 114/229 (49%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG +++     V  +D + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHVLIKKGIVTVNGDVVKTPKQQVKESDEVLVDGQEINY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G+++   D   R+ +    P   +  +  VGRLD +T GLLLLTNDG L  
Sbjct: 60  HYFLMNKPKGVLSATEDRSQRTVISLLKPQDQYQGITPVGRLDKDTTGLLLLTNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSN--AWV 189
            L  P+    ++YR +  G  D + + +   G+ +         ++ + +Q   +  + +
Sbjct: 120 KLLAPNKHVDKIYRAKIAGVADDETVKIFASGMTLGDSTKLKPAELKILSQDEEHDSSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            + +REGK  +IK++F     KV  L RIS G  +L   L  G   E++
Sbjct: 180 EIRIREGKYHQIKRMFGAVGMKVVELERISMGKLKLPKDLKRGEYIELN 228


>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 =  248 bits (634), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 74/244 (30%), Positives = 124/244 (50%), 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  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
             +  A RT  ++ +KP G+V+   D     TV + +       +  VGRLDI+TEGLLL
Sbjct: 61  AAVAYA-RTEYYMLNKPQGVVSATEDGRY-QTVTELITGALRGDIFPVGRLDIDTEGLLL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTNDG LA  L  P     +VY  R  GQ+ +D +     G+V++      +   L+  +
Sbjct: 119 LTNDGSLAHNLLSPRKHVDKVYFARIEGQLPEDAVGRAAAGLVLEDG-TKTLPARLEILE 177

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
                V + +REGK  ++K++FE    +V  L R+S GP  L   L  G  R ++++ ++
Sbjct: 178 PG--QVRLTIREGKFHQVKRMFEAMGCRVTYLKRLSMGPLVLDPALAPGEYRPLTEQEIQ 235

Query: 243 EQLG 246
           +  G
Sbjct: 236 DLQG 239


>gi|311031252|ref|ZP_07709342.1| ribosomal small subunit pseudouridine synthase A [Bacillus sp.
           m3-13]
          Length = 236

 Score =  248 bits (634), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 112/226 (49%), Gaps = 8/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A +G  +R+EV++++    VKV+G +++ A V+V      + V    +   E 
Sbjct: 1   MRLDKMLANSGFGTRKEVKKLLKTGVVKVDGNVVKDAKVHVDPEVQEVTVHDDIVEYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + HKP GL++   D   + TV D L           VGRLD +TEGLLLLTNDG L
Sbjct: 60  FIYLMMHKPPGLLSATEDHR-QETVVDILQEEDKMFEPFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  +  G+V  + +   KKG+ +  G      ++ +  + G  + +
Sbjct: 119 AHQLLSPKKHVPKTYYAKIDGEVTTEDMEAFKKGVTLDDGYETLPAELVIL-EAGPESQI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + EGK  ++K++F+     V  L R+S G  +L   L  G  R
Sbjct: 178 EITIVEGKFHQVKRMFQAVGKTVTYLKRLSMGELKLDEDLELGEYR 223


>gi|242243012|ref|ZP_04797457.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242233613|gb|EES35925.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 230

 Score =  248 bits (634), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 105/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  VKVN   ++   ++V    D I V+   +   ++
Sbjct: 1   MRLDKFLANMGVGTRSEVKQLLKKGAVKVNQNKVKSPKLHVNPNSDEIMVNDEVVSYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D     T+ D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKGYISATEDELH-PTIIDLIPEYAHLNIFPVGRLDKDTEGLLLVTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P+    + Y V     + Q  ++  K GI +              +K  +    V
Sbjct: 119 HEVMNPNKHVSKTYEVYSKHPITQFDIDEFKSGIELSDGKLKPA----ILKKVDDYVSHV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L  GS R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRIKIAELELDHNLDLGSYRLLTQ 222


>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 =  248 bits (634), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 81/229 (35%), Positives = 129/229 (56%), Gaps = 3/229 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + ER+IA+ RV V G      ++ +    D I VDG P+  AE   
Sbjct: 28  LARALSKLGYCSRTQAERLIAEGRVSVGGRKTTDLSLWIDIDRDRITVDGTPV-AAEARI 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-SVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TVFD L  + +R +  VGRLD  +EGLLL TND  LA+ 
Sbjct: 87  YLMLNKPRGLVTTRDDPEGRPTVFDCLGKVDARFMSPVGRLDKASEGLLLFTNDTVLAQR 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P+T   + Y V+  G  D+     +  G+   G     + V        N+W+ V L
Sbjct: 147 LLDPATHLGKTYHVQVRGLFDEAAARAMMDGVSEGGEMLKAIDVRRLRSGDKNSWIEVEL 206

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +S+  ++
Sbjct: 207 QEGRNRQIRRMLDALGFECLRLVRVSIGEIRLGDLPKGASRPLSEAEVQ 255


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 95/266 (35%), Positives = 147/266 (55%), Gaps = 16/266 (6%)

Query: 2   KDKNIVQENFTPQ---RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           K+++ +     P+   ++ KV+A +G+ SRRE+E +I   RV VN          V+ TD
Sbjct: 54  KNRSKLNVRLDPELAPKLHKVLADSGMGSRREMEELIVAGRVSVNAEPA-HLGQRVLPTD 112

Query: 59  HIEVDGVPLRKAER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRL 114
            + V+G  +++  +    R+ +YHKP G + +  DP GR+TVF  LP I + + 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 LYVDAAGGEGANRWYKVGLKEGRNREVRRMFEACNLTVSRLIRTRFGDIMMPSTLKRG-- 290

Query: 234 REVSKKILR-----EQLGPHLLEEAQ 254
           R +  + L      + LG  + E AQ
Sbjct: 291 RHMEMEALEAMSYMQSLGLKVDESAQ 316


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 91/235 (38%), Positives = 133/235 (56%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN   L +    +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVN-QRLAQLGDRITEQDLVYIDGQLSSLSAPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+ R+TVF+ LP     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-GTLLAGSTREVSKKILREQ 244
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++  
Sbjct: 182 VVVVEGRHRLVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGAWKELESPEIKSL 236


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 81/257 (31%), Positives = 134/257 (52%), Gaps = 5/257 (1%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TD 58
           +++  +  +   +R  + + +++ G  SR + ER+IA+ RV ++G  +   +  V   T 
Sbjct: 11  RERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAESRVSIDGRTVNDPSAWVDLVTA 70

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            I VDG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  
Sbjct: 71  KIRVDGLVI-AAEAKIYLILNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKA 129

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL TND   A++L  P T   + Y V+    +D +++  +  GI   G       V
Sbjct: 130 SEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRVLDDEEIAAMTSGIRHDGELLTATAV 189

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 190 RRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAARALT 249

Query: 238 KKILREQLGPHLLEEAQ 254
              L+       +E A+
Sbjct: 250 AAELQALRRSAGMERAR 266


>gi|300072082|gb|ADJ61482.1| ribosomal small subunit pseudouridine synthase A [Lactococcus
           lactis subsp. cremoris NZ9000]
          Length = 242

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 112/242 (46%), Gaps = 13/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   E 
Sbjct: 1   MRLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV   L        +  VGRLD NTEGLL+LTNDG L
Sbjct: 60  YYYYLLNKPQGVVSATKD-NVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILTNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL------DTQK 183
              L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ +      D+Q 
Sbjct: 119 GHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGDSQS 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + + 
Sbjct: 179 GWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTIEEIE 238

Query: 243 EQ 244
             
Sbjct: 239 NL 240


>gi|52425093|ref|YP_088230.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52307145|gb|AAU37645.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 402

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 149/289 (51%), Gaps = 12/289 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ KV+ARAG  SRRE+E +I Q RV V+G +      V V     I +DG  + 
Sbjct: 116 TVEGEKLQKVLARAGQGSRREIESIIEQGRVSVDGKIATLGDRVTVHDGLKIRIDGHLVN 175

Query: 69  ----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
               + E  R+ +Y+KP G + T  DP+GR+TVFD LP    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-GTLLAGSTREVSKK--- 239
           G N W  V L EG+NRE+++++E    +V+RLIRI YG  QL  TL  G   E+      
Sbjct: 296 GLNQWFDVTLMEGRNREVRRLWESQGIQVSRLIRIRYGNIQLMKTLPRGGWEEMDLAKVN 355

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
            LRE +G  L  E +  LD                +    +   R KK+
Sbjct: 356 YLRELVG--LPPETETKLDVTNLRRRAKTGQIRKAVKRYSEMNKRYKKS 402


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 118/236 (50%), Gaps = 6/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+ +I +  VKVNG+++++    V    D I  D   +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSLIRKGFVKVNGMIIKKDDFKVDHEIDEIVFDDELIEYR-P 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D +   TV + +    +  +  VGRLD++TEGLLL+TNDG  +
Sbjct: 62  YVYIMLNKPAGYISATKD-NLHPTVLELIEGYENYDLFPVGRLDLDTEGLLLITNDGDFS 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  PS    ++Y     G +D+  +   K GI++  G       + +  +   +  V 
Sbjct: 121 HKLLAPSRNHSKIYFANIAGVMDEQDIQAFKDGIILNTGYHCKPANLEIINKNNDSCDVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + + EGK  ++KK+ E    +V  L R+S    +L  +L  G  RE+S + L + +
Sbjct: 181 IEIFEGKFHQVKKMVEVCGKEVIYLKRLSIRNLELDRSLSLGDFRELSNEELVDLM 236


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 74/242 (30%), Positives = 116/242 (47%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AG+ SRRE +  I    V VNG ++      V+  D +
Sbjct: 242 IEYKETHIDPNEPIRLNKYLANAGVCSRREADEFILAGVVTVNGNVVTELGTKVLRADEV 301

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   E+    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 302 KFHDQPVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMDLVKDVCPERIYPVGRLDRNTT 360

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V +D L  +  GI ++        +  
Sbjct: 361 GVLLLTNDGDLASKLTHPKFLKKKVYHVHLDKNVTEDDLQKIASGIELEDGEIHADAIEY 420

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++     V + +  GKNR ++++FE   ++V RL R+ +       L  G  R ++++
Sbjct: 421 ADER-DKKQVGIEIHSGKNRIVRRIFESLGYRVLRLDRVQFAGLTKKNLRRGDWRFLTEQ 479

Query: 240 IL 241
            +
Sbjct: 480 EV 481


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 91/235 (38%), Positives = 133/235 (56%), Gaps = 5/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
           +R+ KV+AR+G  SRRE+E+MIA+ R+KVN   L +    +   D + +DG    L   E
Sbjct: 3   ERIQKVLARSGYGSRREIEKMIAEGRIKVN-QRLAQLGDRITEQDLVYIDGQLSSLSVPE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
           + R+ LYHKP G + T  DP+ R+TVF+ LP     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-GTLLAGSTREVSKKILREQ 244
           V + EG++R +++++E    KV+RLIR+ +GP  L  +L  G+ +E+    ++  
Sbjct: 182 VVVVEGRHRLVRRLWESQGVKVSRLIRVRFGPIVLPKSLRRGAWKELEAPEIKSL 236


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 99/296 (33%), Positives = 155/296 (52%), Gaps = 14/296 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N   +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++ 
Sbjct: 2   NIQGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDLIRVDGHTVKI 60

Query: 70  AERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
            E+     R+ +Y+KP G ++T  DP+GR TVFD LP I   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-LLAGSTREVSKKILRE 243
            N W  V L EG+NRE++++++  + +V+RLIRI YG  +L   +  G   E   + +  
Sbjct: 181 INRWFNVTLNEGRNREVRRLWQSQDVEVSRLIRIRYGKLELDKRVPQGGWVEYDLETVNY 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                      V L     +  +++ ++        +   +  K  +Q+   +K+K
Sbjct: 241 L-------RKTVKLGRETQTKLSVMPEKRKDKRAKINQIRKAVKKHNQRVKSTKRK 289


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 81/259 (31%), Positives = 134/259 (51%), Gaps = 5/259 (1%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STD 58
           +++    +N   +R  + + +++ G  SR + ER+IA+ RV V+G ++   +  V  +T 
Sbjct: 11  RERTKPTDNAAAKRVTLPRALSKLGYCSRTQAERLIAENRVAVDGRIVNDTSAWVDLATA 70

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            I +DG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  
Sbjct: 71  RISIDGLVI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKA 129

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G        
Sbjct: 130 SEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRIMDDEDIAAMTSGIRHDGELLTATAA 189

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +S
Sbjct: 190 RRLRHGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALS 249

Query: 238 KKILREQLGPHLLEEAQVN 256
           +  L+       +E  + N
Sbjct: 250 EPELQALRRKTGMERTRRN 268


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 135/270 (50%), Gaps = 7/270 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E     R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G
Sbjct: 53  LIPEWSGTMRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKG 112

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
             +        ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLL
Sbjct: 113 QLISHKT-HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLL 170

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDT 181
           LLT++G L   L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+  
Sbjct: 171 LLTDNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLA 230

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
              + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 231 ATETESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 290

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           L+  L    +E+ Q +   P        R 
Sbjct: 291 LQLLLPYFFIEKQQTSKALPSNLKREEERK 320


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 118/234 (50%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++VN+      ++++G  +    +
Sbjct: 2   ERLDKIISNLGYGSRKEAKLLAKKGLIEVDGKIIKDSSVNIDPEKSIVKINGEEIFYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG  
Sbjct: 61  YIYLMMNKPTGVISATHDSKD-ETVIDLLELDHQIFDPFPVGRLDKDTVGLLLLTNDGDF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
              +  P     +VY  +   +V++      KKG+V+    Y  ++  LD    S   + 
Sbjct: 120 NHRMISPKWHVDKVYYAKIDKEVNEKDQEAFKKGVVLDDG-YKCLEAKLDIISASTEGSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V + ++EGK  ++K++FE  + KV  L R  +G   L  TL  G  RE+S + L
Sbjct: 179 VRITIQEGKYHQVKRMFEARDKKVVYLKREEFGGLILDETLEEGEYRELSDEEL 232


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 65/227 (28%), Positives = 112/227 (49%), 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 VTT ++P  R  +   +    +R+  +GRLD ++ GL+LLTNDG +   
Sbjct: 60  VYLKYHKPVG-VTTTTEPHVRRNIIAEI-GHTARIFPIGRLDKDSSGLILLTNDGDIVNE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        R YRV    + D+  L  + +G+ I G+      +     +       + L
Sbjct: 118 ILRVEHGHEREYRVEVDREFDETFLARMARGVTILGVPTRPCTLARLGPR----RFRIIL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+++ +   ++V  L R+      +  L AG   +++   
Sbjct: 174 TEGRNRQIRRMCQALGYRVVSLHRVRIMHITIDGLHAGQWMDLTHDE 220


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 99/296 (33%), Positives = 156/296 (52%), Gaps = 14/296 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++ 
Sbjct: 2   SIQGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDLIRVDGHTVKI 60

Query: 70  AERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
            E+     R+ +Y+KP G ++T  DP+GR TVFD LP I   R I+VGRLD+NT GL+L 
Sbjct: 61  EEKADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  R Y  R  G+V  + +  L +G+ ++        VT    +G
Sbjct: 121 TNDGELANRLMHPSYEVEREYSARVFGEVTNETVKNLLRGVELEDGPAKFTTVTPMGGEG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            N W  V L EG+NRE++++++  + +V+RLIRI YG  +L   +  G   E   + +  
Sbjct: 181 VNRWFNVTLNEGRNREVRRLWQSQDAEVSRLIRIRYGKLELDKRVPQGGWMEYDLETVNY 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                      V L     +  +++ ++        +   +  K  +Q+   +K+K
Sbjct: 241 L-------RKTVKLGRETQTKLSVMPEKRKDKRAKINQIRKAVKKHNQRVKPTKRK 289


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 69/336 (20%), Positives = 135/336 (40%), Gaps = 20/336 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+ +G+ SRRE ++ I Q  V +NG         V   D + ++G  +   E
Sbjct: 3   EKIRLNKFISDSGVCSRREADKYIEQGHVFINGRRAT-VGAQVSKHDKVTLNGNLIEAKE 61

Query: 72  RT--RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            T      ++KP+G+++T ++   + ++ D +     R+  +GRLD  ++GL+ LTN+G 
Sbjct: 62  GTDFAFIAFNKPVGIIST-TEIGVKDSIIDYI-GYHERIFPIGRLDKESQGLIFLTNNGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V  +  +  + +  +  G+ I G       V     K S    
Sbjct: 120 IVNKILRAGNKHEKEYLVTVNKPITDEFILKMGNGVPILGEMTKKCSVI----KESVFSF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F ++V +L RI      L  +  G  R++  + + E +    
Sbjct: 176 RIVLIQGLNRQIRRMCEYFEYEVVKLERIRIMNIGLKGIPLGEWRQLEAEEMNEIMMAIK 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
              +     +    S+   ++      + P   ++  K     N   K K+L        
Sbjct: 236 DSSSTAKPKSNGGESKIQHQEPRRKTMDRPMSGSKPSKTDRTSNPNPKSKELRG------ 289

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
                  A                   R+   P KR
Sbjct: 290 -----GYAGQAGKKTNPSRSASNAKGNRTSGKPGKR 320


>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 =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 114/237 (48%), Gaps = 11/237 (4%)

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  RKPKPVLLVVNKPRGIVCTTSDKDRAMNIVEYL-DYPERIYPVGRLDKDSEGLLLMTNQG 153

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +        + Y V     +  D ++ + KGI ++ +        +    G    
Sbjct: 154 DLVNKIMRSGNAHEKEYIVTVDRPLTDDAMDRMAKGIYLRELETVTRPCKVKRVDGKT-- 211

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            ++ L +G NR+I+++ E     V RL+R+     +L  L  G++REV ++  RE +
Sbjct: 212 FSIILTQGLNRQIRRMCEACGCHVERLVRVRIMNIRLDGLETGASREVGQEEYRELM 268


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 120/241 (49%), Gaps = 5/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
            + +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +   
Sbjct: 1   MSLERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNKLVLSD 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLLL+TNDG
Sbjct: 61  SNNQKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT--QKGS 185
            L+  +  P  ++L+ Y+    GQV++ ++N L KG+ I            L    +  +
Sbjct: 121 VLSNFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKN 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    ++   
Sbjct: 181 TSIVELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIADLKPGQYRELKTHEVKRLY 240

Query: 246 G 246
           G
Sbjct: 241 G 241


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 63/322 (19%), Positives = 133/322 (41%), Gaps = 21/322 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
              R++K I+ +G  SRRE ++ I Q  V +NG+  +     V   D + V+G  L++  
Sbjct: 3   ESIRLNKFISDSGYCSRREADKYIEQGSVFINGVRAK-IGTQVTRRDKVVVNGHTLQQKS 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E       +KP G+ +T ++      + D +     R+  +GRLD +++GL+ LT++G 
Sbjct: 62  QEEEIYIALNKPPGVTST-TEKGVVDNIVDYV-GHPQRIFPIGRLDKDSQGLIFLTSNGD 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y V     +  D +  +  G+ I G+      V    ++ S+   
Sbjct: 120 IVNKILRAGNEHQKEYLVTVDKPITPDFIAKMATGVPILGVVTKKCIV----EQISSNVF 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ E+F + V +L R      +L  +  G  RE+++  +R      +
Sbjct: 176 KIVLIQGLNRQIRRMCEYFQYNVTKLERTRIMNIELKGIPLGEWRELTESEMRIL--NDM 233

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
           L++++   D     +  + +   +  +          K +              P    +
Sbjct: 234 LKDSKSETDRVSQKASAVGQKPKSKPTPPKKKPIVAAKKTG----------TQKPRSFGS 283

Query: 310 LASNVWMAKGIHSSFLSDSGQR 331
                  +        +  G+R
Sbjct: 284 KPGTGGKSASSRGKKSTSRGRR 305


>gi|315151609|gb|EFT95625.1| conserved hypothetical protein [Enterococcus faecalis TX0012]
          Length = 320

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 135/270 (50%), Gaps = 7/270 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++QE     R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G
Sbjct: 53  LIQEWSGTMRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKG 112

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
             +        ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLL
Sbjct: 113 QLISHKT-HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLL 170

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDT 181
           LLT++G L   L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+  
Sbjct: 171 LLTDNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLA 230

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
              + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 231 ATETESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 290

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           L+  L    +E+ Q +            R 
Sbjct: 291 LQLLLPYFFIEKQQTSKALLSNLKREEERK 320


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 106/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V VN  +++    ++    D I V G  +   E 
Sbjct: 1   MRIDKFLANMGVGTRNEVKQLLKKGLVNVNEQVIKSPKTHIEPENDKITVRGELIEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP   ++   D     TV D +P      + +VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPKDYISATED-HHSKTVIDLIPEYQHLNIFTVGRLDKDTEGLLLITNDGDFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     + +D +   K+G+ +         +T    + S+    V
Sbjct: 119 HELMSPNKHVSKKYEVISANPITEDDIQAFKEGVTLSDGKVKPAILTYIDNQTSH----V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            + EGK  ++K++F     +V  L RI     +L   L +G  R +++
Sbjct: 175 TIYEGKYHQVKRMFHSIQNEVLHLRRIKIADLELDSNLDSGEYRLLTE 222


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 83/248 (33%), Positives = 134/248 (54%), Gaps = 8/248 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+  +      P R+ K ++ +G+ SRRE+E  I    V VNG         V   D +
Sbjct: 199 LKEVRVDHAEIEPVRLQKALSSSGVGSRREMEEWIEAGLVTVNGKKA-SLGDKVGPQDKV 257

Query: 61  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
            V G  + L+  +R  R+ +YHK  G + T  DP+GR TVFD LP    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 V--TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
           +  T   ++ +N W  V ++EG+NRE++++FE F   V+RL+R+ +G   L   L  G  
Sbjct: 378 IFQTGGQEESANQWYNVVIKEGRNREVRRMFEHFGLTVSRLMRVRFGNIGLPPRLKRGQF 437

Query: 234 REVSKKIL 241
            E++   +
Sbjct: 438 YELNAAEV 445


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 106/233 (45%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++   + +R+ ++ ++   RV+V   +++ A   V     + VD  P+R     
Sbjct: 1   MRIDRFLSHMNVGTRKTLKPLLKAGRVRVADKVIKEAKYQVTPETVVYVDDEPIRYQTNF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             WL +KP G+++  +DP    TV D          +  VGRLD +T GLLL+TNDG LA
Sbjct: 61  -YWLLNKPAGVISATTDPQ--KTVMDLFAPADYREDLFPVGRLDKDTTGLLLITNDGDLA 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWV 189
             L  P     + YR +  G V          G+ ++       Q+T+     +   + +
Sbjct: 118 HDLLSPKKHVAKTYRAKIAGVVTAADQAQFAAGLKLRDFDAQPAQLTILRTDTARQESLI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + EGK  ++K++F     +V  L RI  GP  L   L  G  R ++   +
Sbjct: 178 EVEIHEGKFHQVKRMFHAVGKEVLTLERIKMGPLSLPADLKRGQYRALTTTEI 230


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 116/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   E+
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLLTNNGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  +  P     + Y V+  G + +D +    KGI+++         ++    Q    + 
Sbjct: 119 AHKMLSPKKHVDKCYEVKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+  G  QL   L +G  R ++ K + + 
Sbjct: 179 VKITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQLDKQLESGQWRRLTIKEIEKL 235


>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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 118/234 (50%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +++ G  +R E +++I  +RV++N  +++   + +   +D I +DG  L    +
Sbjct: 3   MRLDKFLSQTGKFTRAEAKKVIKAKRVRLNDEVVKDGKIKINEESDKIFLDGELLALNNK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D   ++ +   N P     +  VGRLD  T GLL++TNDG  A
Sbjct: 63  EVYYMLNKPAGVVSATRDDKDKTVIDLINFPGRKEDLFPVGRLDKETTGLLIITNDGKFA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNAW 188
             +  P     + Y     G++ + ++ +  +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|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 =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 66/291 (22%), Positives = 129/291 (44%), Gaps = 9/291 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--R 72
           R++K I+ +GI SRRE +R I Q  V +NG         V + D ++V+G  +   +   
Sbjct: 8   RLNKYISESGICSRREADRYIEQGLVLINGKRA-GIGDRVTAGDEVKVNGRLIEAQDNSE 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T +D   +  + D + +  +RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVST-TDEGEKDNIVDYV-NHSTRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ I G      +V  +          + 
Sbjct: 125 KILRAGNSHEKEYLVTVDKPITDEFIRGMGAGVPILGQKTKKCKVKKEAA----MVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L RI      L  L  G  R+++   L +         
Sbjct: 181 LVQGLNRQIRRMCEYFGYEVTKLERIRIMNVSLAGLPVGEWRDLTDDELIKLFDAIEASS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++          + +  +   +   +P    +  +N+++K      +K   
Sbjct: 241 SEAPKQKQNKPKKQISSNAKALGIHIPKTKAKETENNTRKRFAQPGRKKKK 291


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 113/263 (42%), Gaps = 37/263 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
              R++K IA  GIASRR  + ++A  R+ +NG       +    +D IE+DG PL+   
Sbjct: 29  AKIRINKYIAGLGIASRRAADELLADGRITINGETAGLGEMVDPQSDRIELDGRPLKVEC 88

Query: 71  ----------------------------ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNL 101
                                        +      +KP G+V T    +    T + N 
Sbjct: 89  APLPYAPYGKASPPRLTSKDDNQATSNYPQRVYIALNKPKGIVCTTDSREPENITEYMNF 148

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
           P    R+  +GRLD  + GLLLLTNDG +   +        + YRV     + +  L  +
Sbjct: 149 PI---RIFPIGRLDKASSGLLLLTNDGSIVNRILRAHNHHEKEYRVEVDKPLTEAALQTM 205

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + G+ I G+     ++ L     +   +T+ L +G NR+I+++ E+  +KV +L R    
Sbjct: 206 RTGVPILGVVTLPCRIKLL----NPTTMTIILTQGLNRQIRRMCEYCGYKVVKLERRRIM 261

Query: 222 PFQLGTLLAGSTREVSKKILREQ 244
              LG +  G+ R ++   L + 
Sbjct: 262 NITLGKMPVGAWRYLTYPELSQL 284


>gi|213424484|ref|ZP_03357281.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 267

 Score =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 116/249 (46%), Gaps = 11/249 (4%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN 256
            L+E +   
Sbjct: 234 KLIEGSSSE 242


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 119/238 (50%), Gaps = 8/238 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A  GIASRR  ++++ + RV VNG + ++  + +    D + VDG  + +
Sbjct: 7   DEKVRINKYLAMCGIASRRAADQLVLEGRVMVNGHVADQPGLQIDPKHDEVIVDGRHMAQ 66

Query: 70  AE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E +    L++KP  ++TT  D   R  + D +  +  RV  VGRLD  + GLL+LTNDG
Sbjct: 67  PEHKKVYILFNKPRNVITTSHDERDRQQILDFV-DVPERVFPVGRLDRKSTGLLILTNDG 125

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSN 186
            LA  L  PS+   + Y      +     L+ L  G+ ++  G      +  +     S 
Sbjct: 126 TLAHRLMHPSSLVQKEYLAELDAKFPGSMLSKLTSGMRLKDTGEKVSPCRAKILDDGMS- 184

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             V V + EGKN +++++F    ++V RL R++Y     G L  G  R +S+K +   
Sbjct: 185 --VLVSIHEGKNHQVRRMFSTLGFEVKRLDRVAYAGLTPGELRRGEWRYLSRKEVEHL 240


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 112/239 (46%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +  AGI SR +V+ ++ ++ V VNG    +A + +    D +   G  L   E 
Sbjct: 1   MRLDKFLVEAGIGSRTQVKSILKKKEVFVNGKPESQAKLQIKPNQDQVSFGGQVLVYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L +KP G+V+   D     TV D L     R  V  VGRLD +T GLLLLTNDG L
Sbjct: 61  LYY-LLNKPQGVVSATED-KVHQTVLDLLDDTARRKSVFPVGRLDKDTHGLLLLTNDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA--W 188
           A  L  P     +VY  R  G + +  +    KGI +        Q+ ++          
Sbjct: 119 AHRLLSPKKHVDKVYMARVDGIMTEQDVEAFAKGITLSDHQCLPAQLQIEEVDVERTCCK 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           V + +REGK  +IK++      +V  L RIS GP QL   L  G+ R +++  ++  L 
Sbjct: 179 VRITIREGKFHQIKRMVLACGKEVTDLQRISMGPIQLDDSLALGAFRRLNETEMKALLA 237


>gi|327188988|gb|EGE56177.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli CNPAF512]
          Length = 267

 Score =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 81/257 (31%), Positives = 134/257 (52%), Gaps = 5/257 (1%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TD 58
           +++  +  +   +R  + + +++ G  SR + ER+IA+ RV ++G  +   +  V   T 
Sbjct: 11  RERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAESRVSIDGRTVNDPSAWVDLVTA 70

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            I VDG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  
Sbjct: 71  KIRVDGLVI-AAEAKIYLILNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKA 129

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL TND   A++L  P T   + Y V+    +D +++  +  GI   G       V
Sbjct: 130 SEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRLLDDEEIAAMTSGIRHDGELLTATAV 189

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++
Sbjct: 190 RRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAARALT 249

Query: 238 KKILREQLGPHLLEEAQ 254
              L+       +E A+
Sbjct: 250 AAELQALRRSAGMERAK 266


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 99/319 (31%), Positives = 154/319 (48%), Gaps = 19/319 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
           M DK     +   +++ K++AR+G  SRRE+E  + + R+ ++G+  +    ++  ST  
Sbjct: 1   MSDK-----SQRTEKLQKILARSGHGSRREIEGYLQEGRISIDGVKAKLGDRIDANSTAK 55

Query: 60  IEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
           I +DG  L   E      R+  Y+KP G + T SDP GR TVF  LP    +R I+VGRL
Sbjct: 56  IRLDGRILSIREAQKDVCRVLAYYKPEGELCTRSDPQGRPTVFQRLPRLNSARWIAVGRL 115

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D+NT GLLL T DG LA  L  PS +  R Y VR  G++D  K+  L +G+ ++      
Sbjct: 116 DVNTSGLLLFTTDGELANRLMHPSREVEREYAVRVFGEIDDAKIRQLTRGVQLEDGPASF 175

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
             V+    +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G  
Sbjct: 176 RSVSYRGGEGINQWYNVSLTEGRNREVRRMWEAVGVQVSRLIRVRYGDIDLPKGLPRGGW 235

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            E+        L         V L+    +   + +D+  I +       +     S + 
Sbjct: 236 VEL-------GLNQINYLRQLVELNDETVTKVAVEKDQRRIKANQIRRAVKRHTKISART 288

Query: 294 GLSKQKKLATPVHRRNLAS 312
             S  K+ ++        S
Sbjct: 289 STSPAKRASSRRQSAGSKS 307


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 120/241 (49%), Gaps = 5/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
            + +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +   
Sbjct: 1   MSLERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNKLVLSD 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLLL+TNDG
Sbjct: 61  SNNQKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT--QKGS 185
            L+  +  P  ++L+ Y+    GQV++ ++N L KG+ I            L    +  +
Sbjct: 121 VLSNFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKN 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    ++   
Sbjct: 181 TSIVELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIADLKPGQYRELKTHEVKRLY 240

Query: 246 G 246
           G
Sbjct: 241 G 241


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/230 (31%), Positives = 117/230 (50%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K IA +GI SRRE + +IA+  V VNG ++    + V   D +   G  +   E+  
Sbjct: 203 RLNKYIANSGICSRREADDLIAKGLVSVNGKVVTELGLKVSKFDRVVYQGKKIN-PEKPV 261

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             L +KP   +TT  DP  R TV   + +    R+  VGRLD NT GLLL TNDG LA  
Sbjct: 262 YVLLNKPKDFITTTDDPLERKTVMALVGNACEERIFPVGRLDRNTTGLLLFTNDGELAAK 321

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTV 191
           L  PS Q  ++Y+V     +  +    + +G+ ++   +   DMQV    +K     + +
Sbjct: 322 LSHPSNQIKKIYQVTLDKPLTHNDEKDILEGLTLEDGEVEVDDMQVLSVDRKI----LGL 377

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +  GKNR ++++F    ++V  L R+ Y       L  G+ R +S++ +
Sbjct: 378 EIHVGKNRIVRRIFAHLGYEVTALDRVMYAGLDKKDLKRGNYRFLSEQEV 427


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 119/242 (49%), Gaps = 4/242 (1%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           N  +      R+ KV+A AG+ASRR  E++IA  RV+VNG ++ +    +  + D + VD
Sbjct: 41  NKPESEKAQVRLQKVLASAGVASRRMSEKLIAAGRVEVNGEVVVKMGTRIDPSVDIVRVD 100

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEG 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 LR 242
           L+
Sbjct: 281 LQ 282


>gi|332346017|gb|AEE59351.1| 23S rRNA pseudouridylate synthase F YjbC [Escherichia coli UMNK88]
          Length = 277

 Score =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 114/249 (45%), Gaps = 11/249 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN 256
            L+E +   
Sbjct: 234 KLIENSSSE 242


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 119/239 (49%), Gaps = 5/239 (2%)

Query: 5   NIVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +  E+   + R+++ I+  G+ SRR+ + +I   RVKVNG +++   + V   D +EVD
Sbjct: 166 RLKNEDENAELRLNRYISMGGVCSRRDADELIVAGRVKVNGEVVQTVGLKVRKKDKVEVD 225

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
            V +   E+    + +KP   VTT  DP  R TV   +      R+  VGRLD  T G+L
Sbjct: 226 DVQI-FPEKKVYLVLNKPKDYVTTVEDPLERKTVMALVEGACKERIYPVGRLDRQTTGVL 284

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L TNDG LA+ L  P     ++Y V     + ++    +  G+ ++       +++  + 
Sbjct: 285 LFTNDGDLAKKLTHPKYDHKKIYHVFLDRVLTEEDFQAIANGVQLEDGFIKADEISYTS- 343

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 V + +  GKNR ++++FE F +++ +L R+ +       L  G+ R ++ K +
Sbjct: 344 -PDCTEVGIEIHSGKNRIVRRIFEHFGYQIIKLDRVYFAGITKKNLPRGTWRFLTPKEV 401


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 115/234 (49%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+++I Q +V V+G + +     +  S   +   G  +   E 
Sbjct: 8   IRLDKYLADMGVGTRTEVKKLIRQGKVTVDGSIEKSPERKIDISHQKVCCMGEAVSY-ET 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G+V+  +D   ++ V          +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 67  HEYYMLNKPAGVVSATTDRQDKTVVELISSKKRRDLFPVGRLDKDTEGLLLITNDGELAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +  G VD+    +   G+ I  G      ++ +    G  + + V
Sbjct: 127 RLLSPKKHVDKVYYAKVQGIVDEVDQEIFAVGMSIGNGETALPSKLEILY-SGEISEIRV 185

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            ++EGK  ++K++F     +V  L R+S G   L  TL +G  R ++K+ L+  
Sbjct: 186 TIQEGKFHQVKRMFHAVGKEVIYLKRLSMGTLLLDETLKSGEYRALTKEELKRL 239


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 81/243 (33%), Positives = 129/243 (53%), Gaps = 3/243 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + ER+IA+ RV V+G  +   +  V  +T  I VDG+ +  AE   
Sbjct: 27  LPRALSKLGYCSRTQAERLIAESRVAVDGRTISDISAWVDLATARISVDGLVI-AAEAKI 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +EGLLL TND   A++
Sbjct: 86  YLMLNKPRGLVTTRDDPEGRPTVYDCLREFDIPHLSPVGRLDKASEGLLLFTNDTEFAQI 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+    +D + +  +  GI   G            Q   N+W+ V L
Sbjct: 146 LLDPVTHVTKTYHVQIDRIMDDEGIAAMTSGIRHDGELLTATAARRLRQGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
            EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R +++  L+       +E+A
Sbjct: 206 DEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTEAELQSLRRKTGIEKA 265

Query: 254 QVN 256
           + N
Sbjct: 266 RRN 268


>gi|331268777|ref|YP_004395269.1| pseudouridine synthase [Clostridium botulinum BKT015925]
 gi|329125327|gb|AEB75272.1| pseudouridine synthase [Clostridium botulinum BKT015925]
          Length = 226

 Score =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 114/231 (49%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR+E  R+I + R+ VNG +       V   D I +D  P++K E+ 
Sbjct: 1   MRINKLLSNYGICSRKEANRIIEENRIIVNGEVCI-PGQWVEEYDEILMDNEPIKKKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T +  + +  + D L +    +  VGRLD ++EGL+L+TNDG L+  
Sbjct: 60  -YIALNKPVGITCTAA-REVKDNIIDFL-NYPEYIFPVGRLDKDSEGLILMTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     Q  + Y V      D   +  + +G+ + G       VT    + +N    + L
Sbjct: 117 ILESENQHEKEYIVTVDKPFDDLFIKAMSEGVQLNGPKTRPCIVT----RINNDTFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G NR+I+++   F + V +L RI     ++  +  G  + ++ + + E 
Sbjct: 173 TQGLNRQIRRMTRAFGYTVIKLERIRILNIKINGIDNGKWKYLTDEEITEL 223


>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 =  247 bits (632), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 115/230 (50%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVAY-QQY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTNDG LA
Sbjct: 60  HYFLLNKPKGVISATED-KSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAW 188
             L  P+    + YR +  G  D++ + +   G+ +  G      ++ +    ++   + 
Sbjct: 119 HELLAPNKHVTKKYRAKIAGVADEETVKVFASGMTLGDGTKLKPAELKILMQDKESDQSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           + + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E++
Sbjct: 179 IEIEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPANLKRGQYQEIT 228


>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 =  247 bits (632), Expect = 2e-63,   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  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTND 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|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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 104/231 (45%), Positives = 150/231 (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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSRVISVGRLDINTEGLLLLTND 127
             RL+ +HKP GL+T   DP GR T+++ L    P+   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|295692663|ref|YP_003601273.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|295030769|emb|CBL50248.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
          Length = 234

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I +  V VNG+ ++     V  +D + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHLLIKKGIVAVNGVTVKTPKQQVKESDQVTVNGDAVAY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  ++ VGRLD +T GLLLLTNDG L 
Sbjct: 60  HYFLLNKPKGVLSATED-RSQPTVISLLAPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAW 188
             L  P+    ++YR +  G  D + +     G+ +  G      ++ + +Q  + + + 
Sbjct: 119 HELLAPNKHVDKIYRAKIAGVADDETVKTFAAGMTLGDGTKLQPAELKILSQDEEHNRST 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + +REGK  +IK++F     KV  L RIS G   L   L  G   E+  + +
Sbjct: 179 TEIKIREGKYHQIKRMFGAVGMKVVELERISMGDLTLPANLKRGEYLELKLEDI 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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 123/239 (51%), Gaps = 7/239 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K ++ AG+ SRRE +R +    + ++G + E  A  V+    +   G  
Sbjct: 1   MEEN--GIRINKFLSEAGVCSRREADRQVELGNITIDGKVAETGA-RVLPGQTVLFQGKK 57

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           + K E   L  +HKP+G+V T ++   ++ V D + +   R+  +GRLD ++EGLLLLTN
Sbjct: 58  VSKEEEMILIAFHKPVGIVCT-AEKREKNNVIDYI-NYPKRIYPIGRLDKDSEGLLLLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G +   +        + Y V  +  V +  ++ L  G+ +       M      ++   
Sbjct: 116 NGDIVNKMMRSGNMHEKEYIVTVNRPVTESFIHGLANGVPL--AELNTMTRKCHVKQIGK 173

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
               + L +G NR+I+++ E+F ++V +L+R      +LG L  G+ R+V+ +  R+ L
Sbjct: 174 KQFKIILTQGLNRQIRRMCEYFGYRVEKLVRTRIMNIELGDLPVGTYRDVTTEEYRQLL 232


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 99/302 (32%), Positives = 158/302 (52%), Gaps = 11/302 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
             +++ K++AR G  SRREVE++I+Q  VKVNG +          TD ++V+   +++  
Sbjct: 16  AGEKLQKILARGGFGSRREVEKLISQGLVKVNGKVAT-LGDRAFPTDTLKVNDQLVKETR 74

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTN 126
              + T++ LY+KP G V +  D  GR T+F +LP I  SR ISVGRLDINT GLL+LTN
Sbjct: 75  LEKQPTQVILYNKPEGQVCSRKDEKGRETIFTSLPRIINSRWISVGRLDINTSGLLILTN 134

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD---MQVTLDTQK 183
           +G LA  L  PS +  R Y VR  G+V  + L+ LKKG+ ++          ++    + 
Sbjct: 135 NGELANRLMHPSYEMEREYSVRVFGEVSDEILDRLKKGVKLEDGFAKFESIGKIPQQEED 194

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
             N W  V ++EG+NRE+++++E    +V+RL+R  YG F L   L  G +  ++ K + 
Sbjct: 195 SINQWYRVVIKEGRNREVRRIWESQGVQVSRLVRTRYGQFSLPRNLRRGKSEPLTWKQIN 254

Query: 243 EQLGP-HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           + L    L EE + +L      ++ +         +        +K  + +   SK K  
Sbjct: 255 QLLKSVDLPEEPRPDLRNNPAKAKKMAARHAEPFKKETGRVKYKEKGENHREEKSKPKSA 314

Query: 302 AT 303
             
Sbjct: 315 RR 316


>gi|126173147|ref|YP_001049296.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996352|gb|ABN60427.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 236

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 113/233 (48%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDESLNCLDSIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLAYWILNKAVGTDCRLLEQDE-TSLIRLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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|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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 120/231 (51%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   GI SR +V+ +I  Q+VKVN  ++     NV  +   I   G P++ AE 
Sbjct: 1   MRIDKLLEEEGIGSRNQVKTLIKSQQVKVNEKVITDGKTNVDPSLQVITASGTPIQ-AEG 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD     TV D L     ++++  +GRLD +TEGL+LLT++G L
Sbjct: 60  HHYFILNKPNGVVSARSDGLH-QTVIDCLSVEDRYAKLYPIGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y VR +GQ+  D L   ++GIV   G       + +  +    +  
Sbjct: 119 GFRMLHPSHHVSKTYLVRVNGQLKDDALVFFEEGIVFHDGTKCKPAHLQILKKDEKCSEA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V + EGK  ++KK+F  +  KV  L RIS+    LG L  G  R++++  
Sbjct: 179 VVTISEGKFHQVKKMFLAYGLKVIYLKRISFAGLTLGELPVGQYRKLTELE 229


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 79/248 (31%), Positives = 123/248 (49%), Gaps = 12/248 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M +K   +E     R+++ +A  GIASRR  ++M+ + RV VNG ++    + +    D 
Sbjct: 1   MTEKRRGEE----VRINRYLAMCGIASRRAADQMVIEGRVMVNGQVVIEPGLQIKMGKDE 56

Query: 60  IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           + VDG       ER    L++KP  ++TT SD   R  V D +  +  RV  VGRLD  T
Sbjct: 57  VIVDGQKYALPEERKVYILFNKPRNVITTSSDERDREMVLDYI-KVKERVFPVGRLDRKT 115

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQ 176
            G LL TNDG LA  L  PS+   + Y         Q  L LL  G+ ++  G      Q
Sbjct: 116 TGALLFTNDGILANKLMHPSSNVKKEYLAVLDTAFPQSSLPLLTGGMRLKDTGEKVRPCQ 175

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +    G   W  + L EGKN +++++F    ++V RL R++Y   + G L  G  R +
Sbjct: 176 AKILDG-GMQVW--MSLHEGKNHQVRRMFWTLGFEVTRLERVTYAGLKTGDLRRGEWRYL 232

Query: 237 SKKILREQ 244
           +++ +R+ 
Sbjct: 233 NREEVRQL 240


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 75/237 (31%), Positives = 115/237 (48%), Gaps = 3/237 (1%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
            +  R+   +AR+G A SRR+ E MI   RV+VNG +         S+D + +DG  +  
Sbjct: 1   MSAVRLQAFLARSGAAPSRRKAEEMIRAGRVRVNGRVASLGERVDPSSDRVSLDGRRVEP 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                 +  HKP G +TT  D  GR TV   +P     ++ VGRLD +T GLLLLTNDG 
Sbjct: 61  PSGYAYYALHKPRGYLTTMRDDFGRRTVASLMP-RIPGLVPVGRLDRDTSGLLLLTNDGR 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  +  PS++  + Y +   G   Q+ L  L  G  ++       +++   +       
Sbjct: 120 LAHRIAHPSSRVEKEYELVVRGDPPQEALRRLAAGPTLEDGPMLPPRLSHLRRGPRATTF 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + + EG+ R I++       ++  L R+  GP  LG L  G  R +S++ L E LG
Sbjct: 180 HLTIHEGRKRIIRRACAATGLELLSLRRVRVGPVLLGDLAPGRYRPLSEEEL-EGLG 235


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 110/226 (48%), Gaps = 8/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    VKV+G  ++ A V+V      I V G  +   E 
Sbjct: 1   MRLDKLLSTIGYGSRKEVKGLLKTGAVKVDGTAVKDAKVHVNPDEQEITVHGEAVSYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L           VGRLD +TEGLLLLTNDG L
Sbjct: 60  FVYFMLHKPQGVISATEDSLH-ETVLDLLELDDAVYDPFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  + +  V ++     ++G+ +  G      ++ + T  G  + +
Sbjct: 119 AHQLLSPKKHVPKTYFAKINAPVTEEDAEAFRQGVTLDDGYVTKSAELKILT-SGVESEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + EGK  ++K++FE    KV  L R+S G   L  +L  G  R
Sbjct: 178 ELTIVEGKFHQVKRMFEARGKKVTYLKRLSMGALLLDESLDLGEYR 223


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 127/231 (54%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 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 +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKIYFMLNKPLEVLSSSSDDRGRKTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGDLF 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|283769102|ref|ZP_06342007.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283104288|gb|EFC05666.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 242

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 86/234 (36%), Positives = 136/234 (58%), Gaps = 3/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR+ KVIA+AGIASRR+ E +IAQ +VKVNG +++   V V   D I V+G  ++K E+ 
Sbjct: 2   QRLQKVIAQAGIASRRKAEELIAQGKVKVNGKVVKEMGVQVSFDDEIMVNGQSIQKEEK- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP  +++T  D   R+T+ D    +  R+  VGRLD  T GLLL+TNDG  A  
Sbjct: 61  VYFLLNKPKKMISTVHDDLKRATIMDCFRDVKQRIFPVGRLDYETTGLLLVTNDGEFANA 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTV 191
           +  PS    ++Y V  +G ++   L  LKKGI ++        V +   ++K +   + +
Sbjct: 121 MMHPSHHMDKIYEVYVNGYLEDHMLTKLKKGIPLEDGMTLPASVEVLERSRKTNKTRIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            ++EGKNRE++++  +F ++V+ L RI Y    LG L  G  R + K  +++ L
Sbjct: 181 TIQEGKNREVRRMMAYFGFEVHTLQRIGYSFLNLGNLRQGEYRRLKKFEVKKLL 234


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 116/239 (48%), Gaps = 3/239 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  V +   P R++K +A AGI SRRE +  I    + VNG ++    V V+ TD +   
Sbjct: 269 KKTVVDLTKPIRLNKFLANAGICSRREADEYIQAGVISVNGEIVTEMGVKVLLTDKVMFH 328

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
              +R +ER    L +KP   VTT  D   R TV D + +    R+  VGRLD NT G+L
Sbjct: 329 EQTVR-SERKVYLLLNKPKDCVTTSEDTHDRLTVLDLVKNACSERIYPVGRLDRNTTGVL 387

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG LA  L  P     ++Y       +++     +  G+ +  +      +    +
Sbjct: 388 LLTNDGDLASKLTHPKYDKKKIYHATLDKPLEKADFETILAGVPLDDVNIAADALEF-VK 446

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +G    V + +  G+NR ++++FE   +K+ RL R+ +       L  G  R +S++ +
Sbjct: 447 EGDLKQVGIEIHSGQNRVVRRIFEKLGYKIIRLDRVYFAGLTKKQLPRGKYRFLSEREV 505


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 75/246 (30%), Positives = 120/246 (48%), Gaps = 3/246 (1%)

Query: 3   DKNIVQENFT--PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
            K    +  T    R+ KV+A AG+ SRR  E+MI   RV+V+G ++      +  T   
Sbjct: 21  QKQTTSDPHTHSGVRLQKVMADAGLGSRRACEQMILDGRVEVDGHIVIELGTRIDPTKQR 80

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           + VD +P+  +     +  +KP  +V++  DP+GR  + + +     R+  VGRLD  TE
Sbjct: 81  LVVDSMPIETSTEKVYFALNKPAKVVSSMGDPEGRRNLDEFVRDRTERLFHVGRLDYETE 140

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLTNDG +A  L  P  +  + Y  +  G V +D    L++GI +           L
Sbjct: 141 GLLLLTNDGDMANRLTHPRYEIPKKYLAQVKGPVAKDVGARLREGIELDDGISRVDSFKL 200

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              +   A V V L  GKNR ++++       V RL+R  +GP +L     G  R++  +
Sbjct: 201 IDSQPGVALVEVILHSGKNRIVRRLLSAVGNPVLRLVRTEFGPIELAEQRQGKMRQLRPE 260

Query: 240 ILREQL 245
            + E +
Sbjct: 261 EVSELM 266


>gi|330685516|gb|EGG97168.1| putative 16S pseudouridylate 516 synthase [Staphylococcus
           epidermidis VCU121]
          Length = 230

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 110/235 (46%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  GI +R EV++ + +  VKVN  + +     +    D I V+G  +   ++
Sbjct: 1   MRLDKFLANMGIGTRNEVKQSLKKGYVKVNDKVNKSPKTQINPDEDIITVNGEKIIYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP  +V+   D D   TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPSDVVSATED-DKHQTVIDLIPEYKHLGIFPVGRLDKDTEGLLLITNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     V Q  +   K+G+ +        Q+ +   + S     V
Sbjct: 119 HNLMSPNKHVPKTYEVVSKNDVTQSDVERFKEGLELSDGLLKPAQLEIIENRRS----RV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            + EGK  ++K++F     +V +L RI     +L T L  G  R ++++  +  L
Sbjct: 175 TIYEGKYHQVKRMFHEIENEVLQLKRIKIANLELDTSLKLGEFRLLTEEDFKLLL 229


>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 =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 131/242 (54%), Positives = 167/242 (69%)

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 PH 248
             
Sbjct: 241 RR 242


>gi|152979359|ref|YP_001344988.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841082|gb|ABR75053.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 373

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 151/286 (52%), Gaps = 12/286 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR-- 68
             +++ KV+ARAG  SRRE+E +IA+ RV V+G +      V V S   I +DG  +   
Sbjct: 90  AGEKLQKVLARAGQGSRREIEAVIAEGRVSVDGKIAALGDRVIVHSGLKIRIDGHLVNLT 149

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
             + +  R+ +Y+KP G + T  DP+GR+TVF+ LP    SR ++VGRLDINT GLLL T
Sbjct: 150 GVQKDVCRVLMYYKPEGELCTRHDPEGRATVFERLPRLTGSRWVAVGRLDINTSGLLLFT 209

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG LA  L  PS +  R Y VR  G VD   L  L+KG+ ++        +      G 
Sbjct: 210 TDGELANRLMHPSREVEREYSVRVFGNVDDAMLARLQKGVQLEDGPANFTAIKPAGGTGM 269

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---IL 241
           N W  V L EG+NRE+++++E    +V+RLIRI YG  +L  TL  G  +E+  +    L
Sbjct: 270 NRWFDVTLIEGRNREVRRLWESQGIQVSRLIRIRYGNIKLMKTLPRGGWQEMDLENVNYL 329

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           RE +G  L  E +  LD    +           +    D   R +K
Sbjct: 330 RELVG--LPPETETRLDVTQSNRRAKTGQIRRAVKRYSDVTRRYRK 373


>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 =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 74/234 (31%), Positives = 119/234 (50%), Gaps = 2/234 (0%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+ KV+A AG  SRR+ E++I   RV V+G ++    V V    + I VDG+ L+     
Sbjct: 6   RLQKVLADAGYGSRRKAEQLIEDGRVSVDGQIIIELGVRVDPAKNVIHVDGLRLQLDTNK 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+++  SD  GR T+ D + +   R+  VGRLD+++EGL+LLTNDG L   
Sbjct: 66  VTLAVNKPAGVISAMSDEKGRPTLADLVRNREERLFHVGRLDLDSEGLILLTNDGELGNR 125

Query: 134 LELPSTQWLRVYRVRFH-GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  + Y V    G V    +  L  G+ ++       +V +         V V 
Sbjct: 126 LAHPKYEVPKTYLVTVSGGDVFPRIVRALLDGVDLEDGPARMDRVKIVQALEGMTMVEVV 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L +G+NR ++++F+  +  V RL+R   GP  LG    G+ R +S+  +   + 
Sbjct: 186 LHDGRNRVVRRMFDAVDRPVERLVRTKIGPIALGDQRPGTHRVLSRTEVGSLMA 239


>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 =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 58/234 (24%), 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  TRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KPIG+++   D   ++ +   N 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|284007248|emb|CBA72545.1| ribosomal small subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 231

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 100/230 (43%), Gaps = 3/230 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  +  +    GI ++G         L     S+  V + +
Sbjct: 122 MISPKHHCEKTYLVTLAQPVSTELADKFLAGIWLKGEKLPTKPAKLSI--VSSKQVRLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            EG+  ++K++F      V  L R   G   L   L AG  R ++++ ++
Sbjct: 180 SEGRYHQVKRMFAAVGNHVCALHRERIGGIYLDPALRAGEYRSLTQEEIK 229


>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 =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 118/235 (50%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVNGEKVAY-QQY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTNDG LA
Sbjct: 60  HYFLLNKPKGVISATED-RSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL--DTQKGSNAW 188
             L  P+    + YR +  G  D++ + +   G+ +  G      ++ +    ++   + 
Sbjct: 119 HELLAPNKHVTKKYRAKIAGVADEETVKIFAIGMTLGDGTKLKPAELKILMQDKESDQSE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           + + ++EGK  +IK++F     KV  L RIS G   L   L  G  +E++ K ++
Sbjct: 179 IEIEIQEGKYHQIKRMFGAVGMKVIELDRISMGKLVLPANLKRGQYQEITLKEIK 233


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 65/233 (27%), Positives = 111/233 (47%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +       R    +   D IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDELLNCLDRIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E    W+++K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  QTETLAYWVFNKAVGTDCRLLEQDE-TSLVHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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|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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 115/230 (50%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A  G  +R++V+ ++ +  V VN  ++  A + +    D + V G  +   ++
Sbjct: 1   MRLDKFLAHNGFGTRKDVKILVKKGMVTVNHDVVRDAGMVLNLEKDEVFVKGESVSY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP G +  H+ P+   +V + + S    ++ VGRLD +TEGLLL+TNDG  + 
Sbjct: 60  DIYFMMNKPAGYICEHN-PEMYPSVLELIESYHRDLVFVGRLDADTEGLLLITNDGQFSH 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|58220684|gb|AAW67949.1| putative rRNA pseudouridine synthase B [Desulfovibrio gigas]
          Length = 253

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 84/250 (33%), Positives = 123/250 (49%), Gaps = 16/250 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
               R++KV+A+AG+ASRR  + ++   RV+VNG + E   + V   D IEVDG P    
Sbjct: 1   MDAIRLNKVLAQAGVASRRGADELVFAGRVRVNGAVAESPGMRVTPDDRIEVDGAPMPRK 60

Query: 67  -LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLL 122
            L         L HKP+ +V+T  DP GR TV D LP       R+  VGRLD  +EGLL
Sbjct: 61  DLAAGHALNYILLHKPVEVVSTVRDPQGRRTVLDLLPQALRANTRLYPVGRLDYFSEGLL 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGD 174
           LLT+DG LA  L  P     + Y V   G V    L  ++ G+ +         G     
Sbjct: 121 LLTDDGDLANRLMHPRHHVPKRYEVLVRGDVPTTALQTMRSGMTLPPQAGDPPAGTRLQT 180

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +   +   K     + + L +G NR+++++ E     + RL R+  G  +LGTL  GS R
Sbjct: 181 VPARILGIKDGKTLLELVLHQGVNRQVRRMCEALGLTILRLTRVGLGSLELGTLEKGSWR 240

Query: 235 EVSKKILREQ 244
            ++K  ++  
Sbjct: 241 RLTKDEVQAL 250


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 66/225 (29%), Positives = 108/225 (48%), Gaps = 8/225 (3%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E     + HKP
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGIPVKDAKVHVNVEEQEVMIHGEVVEYKE-FVYLMMHKP 59

Query: 82  IGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 60  QGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y     G V ++ +    KG+++  G       +T+  +    + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 114/239 (47%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  +R+ V+ ++  + V VNG + +     V    D I V G  +   E 
Sbjct: 1   MRLDKLLANMGFGTRKTVKNVLKAKEVTVNGTMEKDGKTQVDPDKDVIVVSGEAVHYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+V+   D +   TV D L           VGRLD +TEGLLLLTNDG L
Sbjct: 60  FVYFMMHKPQGVVSATID-NLHETVIDLLQPQDQVFDPFPVGRLDKDTEGLLLLTNDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDT--QKGSNA 187
           A  L  P     + Y     G V++  +   K GI +  G      ++ + +   +    
Sbjct: 119 AHNLLSPKKHVDKCYEAIIEGLVNEQDIQAFKDGITLNDGFICQSAKLEILSTDLEKEQT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            + V + EGK  ++K++FE  +  VN L R+S G  QL  T+  G+ R ++ + L   +
Sbjct: 179 LIHVTIHEGKFHQVKRMFEAVDKSVNYLKRLSMGKLQLDETVEIGNYRPLTNEELESLI 237


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 110/235 (46%), Gaps = 9/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++ + +  VKVN  +++     +    D I V+   +   ++
Sbjct: 1   MRLDKFLANMGVGTRNEVKQSLKKGYVKVNNEVIKSPKTQIDPNEDIITVNDEKIIYIDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G+V+   D D   TV D +P      +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYIMLNKPSGVVSATED-DKHQTVIDLIPEYQHLEIFPVGRLDKDTEGLLLITNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V     V Q  +   K+G+ +        Q+ +   + S     V
Sbjct: 119 HDLMSPNKHVPKTYEVVSKNDVTQSDVERFKEGLELSDGLVKPAQLEIIENRRS----RV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            + EGK  ++K++F     +V +L RI     +L T L  G  R +++   +  L
Sbjct: 175 TIYEGKYHQVKRMFHEIENEVLQLKRIKIANLELDTSLKLGEFRLLTENDFKLLL 229


>gi|325473332|gb|EGC76527.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 234

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 119/234 (50%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +AR G+ASRR  E +I   RV V+G ++      V   + I +DG  +      
Sbjct: 5   IRLQVYLARCGVASRRASENLILNGRVSVDGKIITELGTKVSGKEKICLDGKQIFPEAEK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP G V + +D   R      L   +  R+ ++GRLD+ + G +L TNDG  + 
Sbjct: 65  RYILLNKPEGYVCSLADEKDRPIAASLLKDTYTERLYNIGRLDMLSGGAILFTNDGDFSA 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +E PS++  + Y V    +   + L    +G+ I+G+ Y      L  ++ +   + + 
Sbjct: 125 KVEHPSSEIEKEYEVITVFEYPDEVLQKFLRGVRIEGVFYKA----LSAERIAKNKMRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L EGKNREI++V +FFN K+ +L R+  G   L  L +G  R ++ + ++  LG
Sbjct: 181 LIEGKNREIRRVLKFFNIKIKKLTRVRIGCVYLADLPSGKHRPLTSEEIKGLLG 234


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 81/244 (33%), Positives = 122/244 (50%), Gaps = 4/244 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
             K    E     R+ KV+A+AG+ASRR  E++I + RV+V+G ++ R  V V   T  I
Sbjct: 72  SGKRAHSEAGEGVRLQKVLAQAGVASRRMAEKLIDEGRVEVDGKIVTRQGVRVDPNTSVI 131

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDIN 117
            VDG  +   E  + ++ +KP G+ +T  D  GR  V D +    S   R+  VGRLD  
Sbjct: 132 RVDGSRVIVNEDMQYFVLNKPRGVQSTMHDDMGRPCVGDIIGEKISAGQRLFHVGRLDAA 191

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLLLTNDG LA  L  PS +  + Y     G+VD   +  L+KGI +          
Sbjct: 192 TEGLLLLTNDGELANRLMHPSYEVTKTYMATVVGEVDSKVMRELEKGIELDDGIAKADMA 251

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + V + L EG+   ++++ +   + V RL+R      QLG    G+ R ++
Sbjct: 252 QIIDVWQGRSIVRIELHEGRKHIVRRMLKTAGFPVERLVRTKIHTVQLGEQTPGALRALN 311

Query: 238 KKIL 241
           +  L
Sbjct: 312 RAEL 315


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 116/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   E+
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLL+TN+G L
Sbjct: 60  FVYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  +  P     + Y  +  G + +D +    KGI+++         ++    Q    + 
Sbjct: 119 AHKMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + + 
Sbjct: 179 VKITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEIEKL 235


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 115/240 (47%), Gaps = 10/240 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLR 68
           N   +R+ KV+   G+ SR+E+ R+     + +NG ++  A      +  HIEV G PL 
Sbjct: 15  NMAYERLDKVLGHLGVGSRKEIHRLARAGLITINGKIVADAGFKFDPSQAHIEVAGEPLV 74

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
             ++    L +KP G +T+  DP G   +   LP  F R   + VGRLD +TEGLLLLT 
Sbjct: 75  Y-QKFFYLLLNKPAGYITSTKDPSGTP-ITALLPEEFWRNDWMPVGRLDKDTEGLLLLTT 132

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   L  P  +  + Y V        + + +   G + ++G      ++ L      
Sbjct: 133 DGELLHRLTHPRWKVTKRYYVELASPATPEDVAVFAAGTLELEGEPLQPAELYL---GPD 189

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKILREQ 244
              V + LREG+  ++K++F     +V  L R+++G       L  G++R+++   ++  
Sbjct: 190 PRKVELVLREGRFHQVKRMFAARGNQVTYLKRLAFGPLQLPPNLPPGASRQLTPDEIKAL 249


>gi|315126449|ref|YP_004068452.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
 gi|315014963|gb|ADT68301.1| pseudouridine synthase [Pseudoalteromonas sp. SM9913]
          Length = 289

 Score =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 97/296 (32%), Positives = 154/296 (52%), Gaps = 14/296 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++ 
Sbjct: 2   SIQGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDLIRVDGHTVKI 60

Query: 70  AERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLL 124
            E+     R+ +Y+KP G ++T  DP+GR TVFD LP I   R I+VGRLD+NT GL+L 
Sbjct: 61  EEKADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGDRWIAVGRLDVNTSGLMLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS +  R Y  R  G+V  + +  L +G+ ++        +     +G
Sbjct: 121 TNDGELANRLMHPSYEVEREYSARVFGEVTDETMKNLLRGVELEDGPAKFTGIKPMGGEG 180

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
            N W  V L EG+NRE++++++  + +V+RLIRI YG  +L   +  G   E     +  
Sbjct: 181 INRWYNVTLNEGRNREVRRLWQSQDVEVSRLIRIRYGKLELDKRVPQGGWIEYDLDTVNY 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                      V L     +  +++ ++        +   +  K  +Q+   +K+K
Sbjct: 241 L-------RKTVKLGKETQTKLSVIPEKRKDKRAKINQIRKAVKKHNQRVKPTKRK 289


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 112/230 (48%), Positives = 151/230 (65%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            PQR++K++ARAG+ASRREVERMI + R+ +NG  +   A  + S   + VDG P+    
Sbjct: 27  EPQRIAKLLARAGVASRREVERMIEEGRITLNGEAITTPATLLASLHGVAVDGAPVAAPA 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             RL+L+HKP G +TT  DP GR T++D LP+   RV+ +GRLD+ TEGLLLLT DG   
Sbjct: 87  PARLFLFHKPSGFLTTERDPRGRPTIYDKLPADLPRVMPIGRLDMTTEGLLLLTTDGEFK 146

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           R +ELPST   R YR R  G V Q++L  L +GI I GI YG ++  L+ + G N W+ +
Sbjct: 147 RQMELPSTGVPRTYRARAFGDVSQNQLEDLFEGIEIDGIRYGQIEANLERRTGRNQWIEM 206

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EGKNRE+++V E    +V+RLIR SYGPF LG L +G+  EV +  L
Sbjct: 207 TLTEGKNREVRRVLEHLGLQVSRLIRTSYGPFHLGELPSGAVEEVRQHDL 256


>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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 114/232 (49%), 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  IYIKLNKPRGYVVSSNKKEGKP-IYSLIKNDFNNIYPVGRLDKDSSGLIILTNDGVFSRK 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|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 =  247 bits (630), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++ AG+ SRRE +R+I   +V V+G       + V     ++V    +R      
Sbjct: 3   RLNKYLSDAGVCSRREADRLIESGQVSVDGQRA-VPGMKVADGQEVKVGKKVIRSNTEKI 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   +KP G+V T  D   +  +   L     RV   GRLD ++EGLL++TNDG L   +
Sbjct: 62  VLAVNKPAGIVCT-EDVREKKNIIRYLKYPI-RVTYAGRLDKDSEGLLIMTNDGDLINGM 119

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNAW 188
                   + Y+V  +  V QD ++ +K+GI I        +     +     +K     
Sbjct: 120 MRARHGHEKEYKVTVNKPVTQDFISKMKEGIRIVDKEKRLDVATRPCKA----EKLGKYT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            ++ L +G NR+I+++ E   +KV RL+R+     +LG+L  G+ R+++++ L+E 
Sbjct: 176 FSITLTQGLNRQIRRMCEALGYKVERLVRVRIMNIELGSLKPGAYRKLTEQELKEL 231


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 118/233 (50%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K+I+  G  SR+E + +  +  ++V+G +++ ++VN+      ++++G  +    +
Sbjct: 2   ERLDKIISNLGYGSRKEAKLLAKKGLIEVDGKIIKDSSVNIDPEKSIVKINGEEIFYR-K 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L           VGRLD +T GLLLLTNDG  
Sbjct: 61  YIYLMMNKPTGVISATHDSKD-ETVIDLLELDHQIFDPFPVGRLDKDTVGLLLLTNDGDF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     +VY  +   +V++      KKG+V+  G    + ++ + +     + V
Sbjct: 120 NHRMISPKWHVDKVYYAKIDKEVNEKDQEAFKKGVVLDDGYKCLEAKLDIISASPEGSEV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + ++EGK  ++K++FE  + KV  L R  +G   L  TL  G  RE+S + L
Sbjct: 180 RITIQEGKYHQVKRMFEARDKKVVYLKREEFGGLILDETLEEGEYRELSDEEL 232


>gi|110835398|ref|YP_694257.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110648509|emb|CAL17985.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 229

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 113/231 (48%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +A +   +R+E +++I++  V V G    +A + +     + V G  ++     
Sbjct: 1   MRLDYFLAHSAGLTRKEAKQLISRGAVTVEGEAKPKANLQLRPDQAVTVHGERVQPP-GH 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP+ +V +  DP  R TV D LP     +V   GRLD +T GL+LLT+DG  + 
Sbjct: 60  RYLMLHKPVDVVCSTEDPGHR-TVLDLLPPELRAQVHPAGRLDRDTTGLVLLTSDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+    + YRV+    V  + +  L++G++++G     +   ++  +   A + + 
Sbjct: 119 RLTSPNHACGKRYRVQCADPVSDEDMQALREGVLLRGEDKPTLPAQVE--RLDEACLLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +REG+  ++K++      KV  L R   G  QL   L  G  R +++  + 
Sbjct: 177 IREGRYHQVKRMLAACGNKVLGLHREQIGEIQLDAALAPGEYRALTEDEVE 227


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 62/224 (27%), Positives = 104/224 (46%), Gaps = 10/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
            R++K I+  G  SRRE  R+IA  R+ +NG +   A   V   D + +DG P+      
Sbjct: 1   MRINKYISETGFCSRRETNRLIAAGRITINGSVC-EAGAEVEPLDIVLIDGKPIPINHSE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KPIG+V T ++  +G    + N P   SR+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 60  PVYLALNKPIGIVCTAAEQVEGNIIRYVNYP---SRIFAIGRLDKASEGLILLTNDGSIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  +    + +G+ I  +     +V     + S     +
Sbjct: 117 NQMMRSEHGHEKEYVVTVDKPVTDEFTQTMSRGVEILNVITKPCKV----DRISEYEFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            L +G N +I+++ +   ++V +L R+      L  L  G  R 
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERVRIMNITLDHLERGQWRH 216


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 107/341 (31%), Positives = 165/341 (48%), Gaps = 13/341 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP----LR 68
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG      + 
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSVNGQIAQ-VGERIEPGDELRIDGRKVAFQIE 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + SDP+ R TVF+ LP+I   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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WFQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWIELDKNDIDNLTK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK---NGLSKQKKLAT 303
              L+  Q      + +     R +   ++     F R ++  S +   N   ++++   
Sbjct: 241 AVELKPRQGTGLFGM-AKRRNERMQDKPMAARRGGFLRQQRRDSDEQPQNNTGRERRDEN 299

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDS--GQREENHRRSPSFP 342
              RR+ A N    + +      D   G+REE    +P  P
Sbjct: 300 AYGRRDRAENQNGTQFVRRENRPDQGFGRREERDENAPRRP 340


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 17/229 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++++  G  SR+E   ++   RV V G   +  A  V +   + VDG PL   E   
Sbjct: 41  RLDQLLSNLGYCSRKEARYLLKDNRVTVAGEYAKSPAQKVDAA-TVRVDGEPLDFPEGI- 98

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           L + +KP+G V +H   +G   ++D LP  +     +++SVGRLD +T GL+L+T+D  L
Sbjct: 99  LVMLNKPLGYVCSHDSGEGMR-IYDLLPERWEFRNPKIVSVGRLDKDTTGLILVTDDTKL 157

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAW 188
              L  P     ++Y+V  +  +  D +    KG+V+          +V + ++  +N  
Sbjct: 158 VHQLTSPKHHVDKLYKVTVNSPLQPDIIEAFAKGVVLGDGAEQCLPAKVEIISENMAN-- 215

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL----GTLLAGST 233
             V L EGK  +++++F    + V  L R  +GP+ L      L  G  
Sbjct: 216 --VTLNEGKYHQVRRMFAACGYHVEALHRSQFGPYSLHDLGQDLPQGDW 262


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 65/287 (22%), Positives = 122/287 (42%), Gaps = 9/287 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRVA-LGDRVFPGDVVKVNGQLIEPRNEDN 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  + +  + V  +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LIFIALNKPVGIVSTTEEGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + YRV  +  V  D +  L  G+ + G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYRVTVNKPVTDDFIRGLGAGVPMLGTVTK----KCKVKKEAPFVFRIV 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|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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/230 (33%), Positives = 128/230 (55%), Gaps = 5/230 (2%)

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 KP+G +T++ DP     + + L  +  R  + GRLD ++EGLL++TNDG     
Sbjct: 62  YLKLY-KPVGFITSNFDPYNDKDLNNLL-DLDKRFFAAGRLDKDSEGLLIITNDGDFTNE 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  + Y V+    ++  +++L +KGI I  G    D ++ L  +K       V 
Sbjct: 120 IIHPSKKLDKTYIVKVSKLLNNKEISLFEKGIDIGNGEVTSDSKIVLIDKK--TNKYKVT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+I+++FE+F+ KV  L RIS GP QL  +    TR+ +   L 
Sbjct: 178 IHQGYNRQIRRMFEYFSSKVINLKRISIGPIQLSNMKPYETRQFTADELE 227


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 77/234 (32%), Positives = 117/234 (50%), Gaps = 4/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ KV+A+AG+ASRR  E MI   RV+VNG ++ +  V V    D I VDGV +      
Sbjct: 46  RLQKVLAQAGVASRRNAEIMIDSGRVEVNGAVVMQQGVRVNPKVDVIRVDGVRVNVNNNH 105

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
           + ++ +KP G+ +T SD  GR  + D +    S    +  VGRLD +TEGL+LLTNDG L
Sbjct: 106 QYFVLNKPRGIHSTMSDDLGRPCIGDLVSERISAGQGLFHVGRLDADTEGLILLTNDGEL 165

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y     G+ D+  +  LK G+ +         V +       + V 
Sbjct: 166 ANRLSHPKYEVSKTYIAEVLGEADRSLVTTLKNGVELDDGPAAADYVQIVDVHQGRSLVR 225

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V L EG+   ++++ +   + V  L+R      QLG    G+ R ++   LR  
Sbjct: 226 VQLHEGRKHIVRRMLKAAGYPVQYLVRTKLHTVQLGEQKPGTIRALNDNELRSL 279


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 115/237 (48%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +   G  +R +++ M+ + RV+VNG +++     +   TD + VD   +    R
Sbjct: 1   MRLDKFLGEMGYGTRTQIKEMVRKGRVQVNGQVIKAPESKLAPETDQVMVD-QSVVGYAR 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +KP  +V+  +D    + V     ++   +  VGRLD++TEGLL++TNDG +A 
Sbjct: 60  MEYYMLNKPKDVVSATTDSRYPTVVGLIGDALRKDLFPVGRLDVDTEGLLIITNDGEMAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN---AW 188
            L  P     +VY  R  G++  +      +GIV+  G+      +  +           
Sbjct: 120 NLLSPKKHVDKVYMARLSGRLPVNAKERFSEGIVLDDGVKTLPALLEYEGCGNGTEGLTE 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + +REGK  ++K++FE     V  L R+S GP  L   L  G  R ++++ +R  
Sbjct: 180 VLLTIREGKFHQVKRMFEALGCHVEYLKRMSMGPLGLDPELEPGQYRPLTEEEIRSL 236


>gi|326564224|gb|EGE14460.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis 12P80B1]
          Length = 328

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 96/304 (31%), Positives = 151/304 (49%), Gaps = 13/304 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
               +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R 
Sbjct: 20  KPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRL 78

Query: 69  ---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
              + +R R+  Y+KP G + + SDP GR TVFD LP     R + VGRLDIN+ GLLL 
Sbjct: 79  KAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLF 138

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +      G
Sbjct: 139 TNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFDDIKEGGGIG 198

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+    + +
Sbjct: 199 VNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIELDASDIGK 258

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +    L + Q              +++   I + P     +++   + +   +++K  T
Sbjct: 259 LVDSVGLRQRQGT------GLNHATKEKQARIHKKPLKSREIRRQKHEAHERREERKKHT 312

Query: 304 PVHR 307
           P HR
Sbjct: 313 PKHR 316


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 112/242 (46%), Gaps = 6/242 (2%)

Query: 6   IVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
           I  E  + +  R+ KV+++AGIASRR  ERMI   RV+V+G ++      +    + + V
Sbjct: 13  IRTETMSEEGIRLQKVLSQAGIASRRVAERMIYDGRVEVDGEIVTEQGRRIDPAVNVVRV 72

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTE 119
           DG  +           +KP G+++T SD  GR  V   +         V +VGRLD +T 
Sbjct: 73  DGARVIMNTDLVYLALNKPFGMLSTMSDDRGRPCVGKLIEERVRGNQGVRNVGRLDADTV 132

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL+LLTNDG L   L  PS +  + Y     G + +     L+ G+ +        +   
Sbjct: 133 GLILLTNDGELTHRLMHPSYEVPKTYIATVAGTIPRGLGRQLRDGVELADGPAKVDEFKF 192

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + L EG+NR ++++ +     V  L+R   G   LG    GS R + + 
Sbjct: 193 LGTTDGQSMVQLTLHEGRNRIVRRMMDAAGHPVVELVRTKIGDVTLGNQRPGSLRALGRD 252

Query: 240 IL 241
            +
Sbjct: 253 EI 254


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 137/249 (55%), 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 +  +   V S+GRLD++TEGLL+LT+DG L R
Sbjct: 102 HTYILYNKPKGQLCSRLDKKKRPLIYDFI-DVAPNVQSIGRLDMDTEGLLMLTDDGALTR 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|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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 96/304 (31%), Positives = 151/304 (49%), Gaps = 13/304 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
               +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R 
Sbjct: 20  KPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRL 78

Query: 69  ---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
              + +R R+  Y+KP G + + SDP GR TVFD LP     R + VGRLDIN+ GLLL 
Sbjct: 79  KAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLF 138

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +      G
Sbjct: 139 TNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFDDIKEGGGIG 198

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+    + +
Sbjct: 199 VNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIELDASDIGK 258

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +    L + Q              +++   I + P     +++   + +   +++K  T
Sbjct: 259 LVDSVGLRQRQGT------GLNHATKEKQARIHKKPLKSREIRRQKHEAHERREERKKHT 312

Query: 304 PVHR 307
           P HR
Sbjct: 313 PKHR 316


>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 =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 93/289 (32%), Positives = 146/289 (50%), Gaps = 10/289 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+AR+G  SRRE+E  I+  R++VNG + +     + +   + +DG  ++    
Sbjct: 2   TEKLQKVLARSGHGSRREIETKISAGRIRVNGKVAQ-LGERIDADAKVRIDGHEVQIKPE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G + T  DP+GR TV+D LP +  +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   +     
Sbjct: 181 WFHVTISEGRNREVRRLWESQEVQVSRLIRVRYGDIPLEPGLPQGGWAEMSLPQVNALRA 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
              L   + +   P +      + R            R+ K  S++ G 
Sbjct: 241 QVNLPAEKESFLDPRHE---ESKQRRFAKIRKATARHRLDKKQSKRRGK 286


>gi|224369318|ref|YP_002603482.1| RluB [Desulfobacterium autotrophicum HRM2]
 gi|223692035|gb|ACN15318.1| RluB [Desulfobacterium autotrophicum HRM2]
          Length = 230

 Score =  246 bits (629), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 113/234 (48%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL--RKA 70
            R+ K +A AG+ SRR  E  I + RV VN  ++      +    D +EVD  P+     
Sbjct: 1   MRLQKFLAHAGVCSRRRGEVYILEGRVSVNHKVVISLGTKIDPEIDLVEVDKKPIVLASE 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +       +KP G+V++ S P G   V D +  I  RV  +GRLD ++ GLLLLT+DG L
Sbjct: 61  KAKIYIALNKPAGVVSSCSHP-GEKVVVDLI-DIKDRVYPIGRLDKDSVGLLLLTDDGNL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  PS    + Y V     ++ + L  +  GIV+ G      +V    ++ S+    
Sbjct: 119 HNRLSHPSFDHEKEYVVETTAPINDEALAQMAAGIVLDGKITRKARV----RRLSDNRFN 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + L++G NR+I+++      +V  L R+  G  +LG L  G  R ++   +R  
Sbjct: 175 IVLKQGINRQIRRMVTAVGNRVKLLKRVRMGSVRLGNLGTGKWRYLTDTEVRAL 228


>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 =  246 bits (629), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 121/291 (41%), Gaps = 9/291 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +    A+ 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGHVFINGKRA-GIGDQVFAGDVVKVNGQLIEPRDADD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T  + +  + V  +  +  +RV  +GRLD +++G++ LTN G L  
Sbjct: 67  LVLIALNKPVGIVSTTENGEKDNIV--DYVNHSTRVFPIGRLDKDSQGIIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  + +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVSLSGLPLGEWRDLTDDELIELFKAIEDSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++                +                ++S +   ++  +   
Sbjct: 241 SEAKPTKKAKPKAKPAAAKSPPNKGAKPAGKSSSADASSRKRFTQPGRKKK 291


>gi|297521296|ref|ZP_06939682.1| 16S rRNA pseudouridylate synthase A [Escherichia coli OP50]
          Length = 207

 Score =  246 bits (629), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 55/209 (26%), Positives = 93/209 (44%), Gaps = 2/209 (0%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +           L+    +   V + +
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAEQFAKGVQLHNEKDLTKPAVLEV--ITPTQVRLTI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGP 222
            EG+  ++K++F      V  L R   G 
Sbjct: 179 SEGRYHQVKRMFAAVGNHVVELHRERIGG 207


>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 =  246 bits (629), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 107/225 (47%), Gaps = 8/225 (3%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++G  ++ A V+V      + + G  +   E     + HKP
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGTPVKDAKVHVNVEEQEVMIHGEVVEYKE-FVYLMMHKP 59

Query: 82  IGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 60  QGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y     G V ++ +    KG+++  G       +T+  +    + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>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 =  246 bits (629), Expect = 4e-63,   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  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDI 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|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 =  246 bits (629), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 106/235 (45%), Gaps = 12/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K ++ +G  SR+EV  +  Q RV VNG +    A  V +  D ++VD  P+   E  
Sbjct: 6   RLDKWLSHSGQGSRKEVRDLCRQGRVLVNGEICRDGAQLVETGVDRVQVDRQPVCYEE-F 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + HKP G+++  +D   R TV D LP       V  VGRLD +T GLLLLTNDG  A
Sbjct: 65  YYIMLHKPRGVISATTDAACR-TVLDFLPPPCRTGGVFPVGRLDKDTTGLLLLTNDGVWA 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     +VY     G + +D        IV+  G      +      +     V 
Sbjct: 124 HRILSPKKHCYKVYEATVSGSIPEDLTVRFASRIVLADGTVCLPARAL----RIDGQTVE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           + + EG+  ++K++      +V  L R   G   L   L  G  R++++   RE 
Sbjct: 180 ITVYEGRYHQVKRMCAAVGLQVLSLHRHKIGALGLDPALSPGQWRKLTEVE-REL 233


>gi|194477231|ref|YP_002049410.1| Pseudouridine synthase, Rsu [Paulinella chromatophora]
 gi|171192238|gb|ACB43200.1| Pseudouridine synthase, Rsu [Paulinella chromatophora]
          Length = 242

 Score =  246 bits (629), Expect = 4e-63,   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|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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 120/234 (51%), Gaps = 5/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +AR G+ASRR  E +I   RV V+G ++    + V   + I +DG  +      
Sbjct: 5   IRLQVYLARCGVASRRASENLILNGRVSVDGKIITELGIKVSGKEKICLDGKQIFPEAEK 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP G V + +D   R      L   +  R+ ++GRLD+ + G +L TNDG  + 
Sbjct: 65  RYILLNKPEGYVCSLADEKDRPIAASLLKDTYTERLYNIGRLDMLSGGAILFTNDGDFSA 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +E PS++  + Y V    +   + L    +G+ I+G+ Y      L  ++ S   + + 
Sbjct: 125 KVEHPSSEIEKEYEVITVFEYPDEILQKFLRGVRIEGVFYKA----LSAERISKNKMRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           L EGKNREI++V +FFN K+ +L R+  G   L  L +G  R ++ + ++  LG
Sbjct: 181 LIEGKNREIRRVLKFFNIKIKKLTRVRIGCVYLADLPSGKHRPLTSEEIKGLLG 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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 112/242 (46%), Gaps = 13/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A +G+ SR EV+ ++ + RV V G +       V      +  DG  L   E 
Sbjct: 1   MRLDKFLAESGLGSRSEVKVLLKKGRVTVAGEIQRDGRFQVDKNSRQVAFDGQILDYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV   L        +  VGRLD NTEGLL+L+NDG L
Sbjct: 60  YYYYLLNKPQGVVSATKD-NVFKTVVQLLSEKDFRKDIFPVGRLDKNTEGLLILSNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTL------DTQK 183
              L  P     + Y  R  G+V  + +N   +G+ ++ G      ++ +      D+Q 
Sbjct: 119 GHDLTQPKKHVEKEYFARIDGKVTDEIINKFAEGLTLKNGEKARPGELFVEKTYKGDSQS 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           G  + + V + EGK  ++K++FE     V  L RI  G   L   L  G+ R ++ + + 
Sbjct: 179 GWVSEIRVIIHEGKFHQVKRMFEAVEMYVLYLKRIRMGNLALDSDLALGAYRPLTIEEIE 238

Query: 243 EQ 244
             
Sbjct: 239 NL 240


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 83/239 (34%), Positives = 130/239 (54%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR---- 68
            R++K +ARAGI SRR  + ++   RVKVN  ++    + V    D I VDG P++    
Sbjct: 5   MRLNKALARAGICSRRRADGLVFSGRVKVNDEVVREPGIRVDPEKDSIIVDGRPVKIETE 64

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTN 126
           +       + +KP+ +VTT SDP GR+ V D LP    R  +  VGRLD  + GLL+LTN
Sbjct: 65  QERELVHVMLNKPVQVVTTTSDPGGRAKVTDLLPDRLRRMRLFPVGRLDYFSRGLLILTN 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG LA  L  PS +  +VYRV+  G + + KL ++++G+V+ +G     ++V +  Q   
Sbjct: 125 DGDLAHSLTHPSRKIPKVYRVKMRGDLSKKKLQIMRRGMVLSEGEKLAPVEVKILQQTRD 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +    + L +G NR+I+++    +  V  L+RI  GP  LG L  G  R +    + + 
Sbjct: 185 SVLAEMTLVQGINRQIRRMCRDLDMVVLSLVRIRQGPLALGELKPGEWRYLEPGEVSQL 243


>gi|193782973|gb|ACF20459.1| pseudouridine synthase [Serratia symbiotica]
          Length = 300

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 90/234 (38%), Positives = 129/234 (55%), Gaps = 10/234 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAE 71
            +++ KV+AR G  SRRE+E MI   RV +NG + +    + +     I +DG  +   +
Sbjct: 2   SEKLHKVLARTGYGSRREIEAMINACRVSINGKIAKLGDRIEIHPMMKIRIDGNIISIKK 61

Query: 72  RT----RLWLYHKPIGLVTTHSDP---DGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
                 R+  Y+KP G + T S+P   +GR TVFD+LP + + 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-GTLLAGSTREV 236
           G N W  V L EG+NRE+++++E    +V+RLIRI YG   L   L  GS  E+
Sbjct: 182 GLNQWYHVTLTEGRNREVRRLWEAVGIQVSRLIRIRYGNIVLPKGLPRGSWAEL 235


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 115/237 (48%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VNG       V V    D I+ +G  +   E+
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNGNSETSPKVQVDEYRDEIKYNGTLVSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLL+TN+G L
Sbjct: 60  FVYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  +  P     + Y  +  G + +D +    KGI+++         ++    Q    + 
Sbjct: 119 AHKMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+  G  QL   L +G  R ++ K + + 
Sbjct: 179 VKITIKEGKFHQVKRMVAACGKEVLELKRLRMGNLQLDKQLESGQWRRLTIKEIEKL 235


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 64/291 (21%), Positives = 122/291 (41%), Gaps = 9/291 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRA-SVGAQVFAGDVVKVNGQLIEPRDEDD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ + G            +K +     + 
Sbjct: 125 KILRAGNNHEKEYVVTVDKPITDEFIAGMSAGVPMLGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E         
Sbjct: 181 LVQGLNRQIRRMCKHFGFEVTKLERTRIMNVNLKGLPLGEWRDLTDDELVELFKLLENSS 240

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++        +    V  +    S            +S+K  +   +K   
Sbjct: 241 SEDKPAKKAKAPAKAVAAKKPQKSAAKPAEKADAAGASRKRFVQPGRKKKG 291


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 114/231 (49%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+    A  N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNGEITVNGMSYILAKDNIDENSDTIEYNGERLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDFKED-TVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHKLLSPKNHIDKVYYVEIEKNILDEDILKLEQGVDIGNYITQPAKV----EKISDNKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KV  L R S+G   L  L  G  +EVS + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVCYLRRESFGKLTLNDLTLGEVKEVSLEDI 225


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 102/233 (43%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-AER 72
            R+ K ++     +R E  + I + RV VNG++  +A   V     I VDG PL    ++
Sbjct: 2   MRLDKYLSERTGLTRSESRKAITKGRVAVNGMVCRKADTQVAEDAAIAVDGTPLAGSYQK 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D    +TV D + + F R  +   GRLD  + G +LLT+DG L
Sbjct: 62  YVYIMLNKPEGVVSASRDKRD-TTVVDLVAADFPRRALFPAGRLDKTSTGFVLLTDDGAL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P+    + Y V     +          G+ +  G      +     +      V
Sbjct: 121 AHDLLSPAHHVDKQYLVTLDTPLTDAMRAGFAAGVTLADGETMAPAEAEPAGEDP--CVV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V L +G   +IK++F  +   VN L R + G   L   L  G  RE++ + L
Sbjct: 179 KVTLHQGVYHQIKRMFGVYGAGVNALHRYAIGGVALDAALAPGQWRELTAEEL 231


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 122/241 (50%), Gaps = 5/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + +R+ KVI+  G  SRR  E++I + RVKVN  ++ +  V +     I +D   +   
Sbjct: 1   MSLERLQKVISSRGYCSRRTAEKLILENRVKVNNQIINKLGVKIDPKAEIIIDNKLVTSD 60

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLL++TNDG
Sbjct: 61  SNNQKYYYLFYKPRLVLTTMYDPKKRKTVADYFKDLNHRVYPVGRLDYDVSGLLIMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGS 185
            L+  +  P  ++L+ Y+    GQV++ ++N L KG+ I           ++    +  +
Sbjct: 121 ELSNFIMHPKYEFLKTYQGLCQGQVNKQQVNQLIKGVYIDNNYLTKAYSSKLIKYDKLKN 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    +++  
Sbjct: 181 VSIVELTINEGKKHHVKKMFESIQAQLLKLKRTRIEFLEIDNLKPGQYRELKVHEIKKLY 240

Query: 246 G 246
           G
Sbjct: 241 G 241


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 75/239 (31%), Positives = 125/239 (52%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K++ +AG  SR +V+++I  ++V V+G L E   +NV  S   I V G  ++++  
Sbjct: 1   MRLDKLLGQAGFGSRNQVKKLIRSRQVYVDGRLAEADNLNVETSLQKITVSGKQVKQSSE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + +L +KP G+V+  SD +   TV D +       ++  VGRLD +TEGLLL+TN+G L
Sbjct: 61  -KYFLLNKPAGVVSAVSDKEH-QTVIDLIKESDRVPQLYPVGRLDRSTEGLLLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+           ++ + T     +  
Sbjct: 119 GYRMLHPKYHVAKTYYVEVNAFLADDAPAFFENGVSFDDGTICKPAKLEIITASTEESSA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQL 245
            V + EGK  +IKK+F  +  KV  L R+++G FQLG L +G  RE++   K+IL+  L
Sbjct: 179 YVTISEGKFHQIKKMFLAYGVKVTYLKRLTFGEFQLGDLPSGQYRELTSTEKEILKNYL 237


>gi|213163156|ref|ZP_03348866.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 289

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 70/294 (23%), Positives = 130/294 (44%), Gaps = 12/294 (4%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E+F ++V +L R       L  +  G   +++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWHDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            L+E +            +T    RP +  E  ++  R   +  +     ++KK
Sbjct: 234 KLIEGSSSEAKPKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKK 287


>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 =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 61/247 (24%), Positives = 117/247 (47%), Gaps = 9/247 (3%)

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    +  S V     +   RV  +GRLD ++ GLLL+TN+G
Sbjct: 70  RQDEMIVLAVNKPKGIVCTEERRERDSIVRFL--NYPVRVTYIGRLDKDSRGLLLMTNNG 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 FKIILTQGLNRQIRRMCEALGYEVKDLLRVRVMNITLDGLKEGKYRKLTDRELNEL--DQ 241

Query: 249 LLEEAQV 255
           LLE++  
Sbjct: 242 LLEQSSS 248


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 112/232 (48%), Gaps = 7/232 (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    + +S V     +   RV  VGRLD ++ GLLL+TN+G 
Sbjct: 71  SEEMIVLAVNKPAGIVCTEETRERKSIVRFL--NYPVRVTYVGRLDKDSRGLLLMTNNGD 128

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +   +     +  + Y+V     +  + L  +  G+ I G      +V    QK      
Sbjct: 129 IINKMMRAGNRHEKEYKVTVDKALTPEFLEKMSSGVAILGTVTRPCRV----QKIGKYTF 184

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           T+ L +G NR+I+++ E   ++V  L+R      +LG L  G  R+++ K L
Sbjct: 185 TIILTQGLNRQIRRMCEVLGYEVKDLVRTRIMNIELGKLKEGEYRKLTDKEL 236


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 106/234 (45%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R+E  +++  + V+VNG ++   +V V     +E +G  L   +  
Sbjct: 1   MRLDKFLGTTLGITRKEAGKILKDRMVEVNGEVVRNGSVQVSDDCDVEFNGRSLSL-QGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G V +H D D   T+F     I    + V GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYYMLNKPQGFVCSHVD-DFNPTIFVLFDEISPEKMHVAGRLDGDTTGLVLVTDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     + +D +     G+ ++          L+    + A +   
Sbjct: 119 RITSPRHVCEKTYYVETADPITEDYIQQFADGVQLRSEKELTRPAKLEILGENEALL--T 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +   L
Sbjct: 177 ITEGKYHQVKRMFAAMGNKVVGLHRERVGAVELDEELEPGEYRPLTEEEIASFL 230


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 100/309 (32%), Positives = 146/309 (47%), Gaps = 8/309 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
              +++ K +AR G+ SRR++E +I   RV VN          V   D I VDG  ++  
Sbjct: 1   MKDEKLQKALARMGLGSRRQMEEVIKAGRVTVNNGPAT-IGDRVEQGDEIRVDGRQIKYT 59

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
               +R R+  Y+KP G V + +DP+GR TVF+ LP     R + VGRLDIN+ GLLL T
Sbjct: 60  AENEKRRRVLAYYKPEGEVCSANDPEGRPTVFERLPKLTHDRWVMVGRLDINSTGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +A  L  PS++  R Y VR  G V  D    +  G++++        +     +G 
Sbjct: 120 NDGEMAHRLMHPSSEVTREYAVRVLGDVTPDMARAMTTGVMLEDGMAKFEDIKEGGGEGV 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L+EG+NRE++++FE    KV+RL+R SYG   L   L  G   E+ +K +   
Sbjct: 180 NKWHHVKLKEGRNREVRRLFESQGLKVSRLLRTSYGNIALPKELRTGRFLELDRKDINIL 239

Query: 245 LGPHLLEEA-QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                L       L       +  +R++P                SS  N  +K K   +
Sbjct: 240 TDLVSLRPRYGTGLHGAAKEKQERIRNKPLKARRTDTRSDNRNSTSSSANSSTKPKTSGS 299

Query: 304 PVHRRNLAS 312
           P  R    S
Sbjct: 300 PASRGTRNS 308


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 130/294 (44%), Gaps = 12/294 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RK 69
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +  R 
Sbjct: 4   SSIRLNKYISESGICSRRDADRYIEQGNVFINGKRA-VIGDQVYAGDVVKVNGQLIDARD 62

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L + +KP+G+++T  D +  + V  +  +   R+  +GRLD +++GL+ LTN G 
Sbjct: 63  EDDLVLIVLNKPVGIISTTEDSEHNNIV--DFVNHSKRIFPIGRLDKDSQGLIFLTNQGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V ++ +  L  G+ + G            +K S    
Sbjct: 121 LVNKVLRAGNDHEKEYVVTVNKPVTEEFILGLGAGVPMLGTVTK----KCKVKKVSTFVF 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 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           L E   +        +T         S  P    +   NS+ +   ++  +   
Sbjct: 234 LIENSSSEGKTAKKVQTKSVTHKKTNSNGPKKAEKPDGNSASRKRFAQPGRKKK 287


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           +  +    +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V    D I VDG
Sbjct: 55  VDDDKPKGERLQKVLAKAGVASRRHAEILIDAGRVEVNGNVILKQGVKVNPAVDVIRVDG 114

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 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|91070007|gb|ABE10933.1| putative pseudouridylate synthase specific to ribosomal small
           subunit [uncultured Prochlorococcus marinus clone
           ASNC3046]
          Length = 240

 Score =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 118/246 (47%), Gaps = 11/246 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           R++K ++  G  SRRE +++I + +V +NG +       V   D +EV G  + K++R  
Sbjct: 4   RINKYLSEVGYCSRREADKLILEGKVTINGKIP-EIGAKVEEIDQVEVKGQRIEKSDRQE 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  KIYLAFNKPLGIVCTTDRKVEPNNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ +  ++ + +  +  G+ I      +  V     +       + 
Sbjct: 122 KILRARNNHEKEYIVKVNRPINSEFIQKMSNGVEILDTITKNCSVKQLGPRK----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E   ++V  L R+     +L  + +G  RE S++ L+E  G  LL+ 
Sbjct: 178 LTQGLNRQIRRMCETLGYRVRSLKRVRIMNIKL-DMPSGKYREFSREELQELNG--LLQN 234

Query: 253 AQVNLD 258
           +    D
Sbjct: 235 SSKTYD 240


>gi|315022583|gb|EFT35609.1| Ribosomal large subunit pseudouridine synthase B [Riemerella
           anatipestifer RA-YM]
          Length = 311

 Score =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 118/239 (49%), Gaps = 3/239 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             +VQ+     R++K IA +GI SRRE + +I Q  V++NG ++      V  TD +  D
Sbjct: 69  NKLVQQPKDTIRLNKYIANSGICSRREADELIQQGLVEINGKVVTELGYQVQKTDKVVFD 128

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLL 122
           G  +   E+    L +KP G ++T  D   R TV D   +    R+  VGRLD  T G++
Sbjct: 129 GQSIT-PEKPVYVLLNKPKGYISTTKDEKARKTVMDLTANASPYRIFPVGRLDRQTTGVI 187

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG L + L  PS    ++Y V    ++  + + ++ KGI ++        ++    
Sbjct: 188 LLTNDGHLTKKLTHPSFNIKKIYHVTLDRKLTGEDMAIIAKGIRLEEGVAEVDSISYIDG 247

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           K  N  + + +  G NR I+++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 248 KPKN-EIGIEIHIGWNRVIRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 305


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 118/239 (49%), Gaps = 3/239 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
             +VQ+     R++K IA +GI SRRE + +I Q  V++NG ++      V  TD +  D
Sbjct: 69  NKLVQQPKDTIRLNKYIANSGICSRREADELIQQGLVEINGKVVTELGYQVQKTDKVVFD 128

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLL 122
           G  +   E+    L +KP G ++T  D   R TV D   +    R+  VGRLD  T G++
Sbjct: 129 GQSIT-PEKPVYVLLNKPKGYISTTKDEKARKTVMDLTANASPYRIFPVGRLDRQTTGVI 187

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG L + L  PS    ++Y V    ++  + + ++ KGI ++        ++    
Sbjct: 188 LLTNDGHLTKKLTHPSFNIKKIYHVTLDRKLTGEDMAIIAKGIRLEEGVAEVDSISYIDG 247

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           K  N  + + +  G NR I+++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 248 KPKN-EIGIEIHIGWNRVIRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 305


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 117/233 (50%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  +R+E++ ++    VK+NG +++ +++ +      IEV G  +   ++ 
Sbjct: 9   RIDKILANLGFGTRKEIKAVVKNGEVKINGTVIKDSSMKIDPDKSTIEVGGNVVEY-KKN 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              L +KP G+V+   D +   TV D L   +   +   VGRLD +TEGLLL+TNDG L 
Sbjct: 68  IYLLMNKPQGVVSATFD-NYDETVIDILEPEYQAFKPFPVGRLDKDTEGLLLITNDGELN 126

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     +VY       +D+  +N  KKGI +  G      ++ +       A V 
Sbjct: 127 HRMISPKNHVDKVYYAEIDKYLDERDVNRFKKGIQLKDGYKCLPGKLHIIESDEDGAKVE 186

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V ++EGK  ++K++F      V  L RI +GP  L   L  G  RE+SK  + 
Sbjct: 187 VTIQEGKFHQVKRMFNALGKNVVYLKRIKFGPIDLDKDLNLGQYRELSKNEIE 239


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 114/230 (49%), Gaps = 7/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K IA AG+ SRR+  R+I Q  V VNG + +     V + D I V+   L    
Sbjct: 3   DGIRLAKYIANAGLCSRRQASRLIDQGLVTVNGGIADHICF-VGTDDVITVNDELLVYQT 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +L++KP+G+ +    P+  +++   LPS   R+  +GRLD ++ GL++LTNDG L 
Sbjct: 62  EQVYYLFNKPVGIDSRLL-PNDSASLIHLLPSEI-RIYPIGRLDKDSYGLMILTNDGELY 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + YRV     +D +  N + +GI + G       V     + +     +
Sbjct: 120 HQMNHPDHHQEKEYRVSVERPIDANFCNKMAQGIPVDGQLTQPCSVW----QTAENEFHI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L +G NR+I+K+ +   +KV  L RI      +G L AG  + ++K  +
Sbjct: 176 VLTQGLNRQIRKMAKHCGYKVVDLERIRIANLAIGDLSAGEFKTLTKADI 225


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 113/243 (46%), Gaps = 14/243 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K +A   + +R +V+  I ++ V VNG+ + +  V V    D I V G  +  
Sbjct: 1   MANIRLDKYLADMQVGTRSQVKEQIRKKLVSVNGVTVTKPDVKVDTDRDKIMV-GSDIIG 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +   ++ +KP G+++  +DP  ++ V     +I   +  VGRLD +TEGL+L+TNDG 
Sbjct: 60  YTQFEYFMLNKPKGVLSAANDPKAQTVVDLITDNICRDLFPVGRLDKDTEGLMLITNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA-- 187
           LA  L  P     + Y VRF G +  + +    KGI I      D +V  + ++  +   
Sbjct: 120 LAHKLLSPRKHVDKSYYVRFEGIIADNTVESFAKGIDINIAKCADDEVDNNPKEIYHTKP 179

Query: 188 ---------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
                       + + EGK  +IK++F     +V  L RIS G  QL   L  G  R ++
Sbjct: 180 AKLRLMSADEAVITISEGKFHQIKRMFMAAGCRVTYLKRISMGTLQLDFDLKPGQYRRLT 239

Query: 238 KKI 240
              
Sbjct: 240 DSE 242


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 72/222 (32%), Positives = 108/222 (48%), Gaps = 1/222 (0%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A AG+ SRR  E  +   RV V+G +             I VDG+PL      R++L +
Sbjct: 1   MAAAGLCSRRRGEDWLQAGRVTVDGRVASLGDQADPDCQLIAVDGIPLISVREPRVFLLN 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           KP+G++ +  DP GRSTV D LP      +  VGRLD ++ G LLLT+ G L   L  P 
Sbjct: 61  KPVGVICSCRDPQGRSTVLDCLPHQERPGLHPVGRLDADSRGALLLTDQGELTLRLTHPR 120

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               + YRV   G  +   L   ++G+ + G       V     +G+++ + V LREG+N
Sbjct: 121 YSHAKTYRVLVKGIPNALVLRRWREGLQLDGRLTRPALVRCLRSRGTSSLLEVELREGRN 180

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           R+I++V E     V  L R++     L  L  G  R +  + 
Sbjct: 181 RQIRRVAELLGHPVIDLQRVAIDGIHLDDLAEGCWRRLDARE 222


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 66/225 (29%), Positives = 108/225 (48%), Gaps = 8/225 (3%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E     + HKP
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE-FVYLMMHKP 59

Query: 82  IGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 60  QGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y     G V ++ +    KG+++  G       +T+  +    + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>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 =  246 bits (628), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 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 +     R+  VGRLD  T GL+LLTNDG L 
Sbjct: 60  KKVYFMLNKPLEVLSSSSDNRGRKTVVDLI-KTDKRIFPVGRLDYMTSGLILLTNDGELF 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|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 =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 117/234 (50%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ KV+A+AG+ASRR  E +I   RV+VNG ++    + V    D I VDGV +   
Sbjct: 79  EGIRLQKVLAQAGVASRRHAEILIDAGRVEVNGKIVMTQGMRVNPNVDVIRVDGVRVNVN 138

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTND 127
           E  + ++ +KP GL +T SD  GR  V D +    S   R+  VGRLD  TEGLLLLTND
Sbjct: 139 ENLQYFVLNKPRGLQSTMSDDMGRPCVGDIVGERISAGQRLFHVGRLDAATEGLLLLTND 198

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  P  +  + Y     G+ D+  +  L+ GI +         V +       +
Sbjct: 199 GELANRLMHPRYEVSKTYLATVLGEADKRLVKQLRDGIELDDGPAKADLVQIIDTFQGKS 258

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + L EG+   ++++ +   + V RL+R      QLG    G+ R ++   L
Sbjct: 259 LIRIELHEGRKHIVRRMLKTAGFPVQRLVRTKIHTIQLGEQTPGAIRALNSSEL 312


>gi|326575652|gb|EGE25575.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis CO72]
          Length = 328

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 96/304 (31%), Positives = 151/304 (49%), Gaps = 13/304 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
               +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R 
Sbjct: 20  KPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRL 78

Query: 69  ---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
              + +R R+  Y+KP G + + SDP GR TVFD LP     R + VGRLDIN+ GLLL 
Sbjct: 79  KAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLF 138

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +      G
Sbjct: 139 TNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTTGVELEDGVAKFDDIKEGGGIG 198

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+    + +
Sbjct: 199 VNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIELDASDIGK 258

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +    L + Q              +++   I + P     +++   + +   +++K  T
Sbjct: 259 LVDSVGLRQRQGT------GLNHATKEKQARIHKKPLKSREIRRQKHEAHERREERKKHT 312

Query: 304 PVHR 307
           P HR
Sbjct: 313 PKHR 316


>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 =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 66/225 (29%), Positives = 108/225 (48%), Gaps = 8/225 (3%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRLWLYHKP 81
            G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E     + HKP
Sbjct: 1   MGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE-FVYLMMHKP 59

Query: 82  IGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
            G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L+  L  P  
Sbjct: 60  QGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKLSHQLLSPKK 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y     G V ++ +    KG+++  G       +T+  +    + + + + EGK 
Sbjct: 119 HVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEIELVITEGKF 177

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 178 HQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 222


>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 =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 69/296 (23%), Positives = 124/296 (41%), Gaps = 11/296 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   RV  +GRLD + +GL+ LTN 
Sbjct: 62  RESEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDFQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 289


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 79/232 (34%), Positives = 124/232 (53%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   +   E  
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKIN-EESF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+++     + +V + +    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 64  EYYLLNKPAGYVSSNRSYPNQPSVIELI-KTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGKN EIKK+ +F    V +L R  +    +G L  G  R +S++ + +
Sbjct: 183 TIAEGKNHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQYRALSEQEVEK 234


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 110/226 (48%), Gaps = 9/226 (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  LW--LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T         + D + +  +R+  +GRLD N+EGL+ LTNDG +  
Sbjct: 63  YIYLAFNKPVGIVCTTDRRVEPDNIIDFI-NYSTRIFPIGRLDKNSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +++D ++ +  G+ I      +  V     K       + 
Sbjct: 122 KILRARNNHEKEYIVSVNRPINRDFIHNMSNGVKILDTITKNCFVKQLGVKK----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L +G NR+I+++ E   ++V  L RI     +L  +  G  RE +K
Sbjct: 178 LTQGLNRQIRRMCESLGYRVQSLKRIRIMNIKL-DIPTGKYREFTK 222


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 99/295 (33%), Positives = 154/295 (52%), Gaps = 14/295 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +++ KV+ARAG+ SRRE+E+ I   RV VNG + +     V  TD I VDG  ++  
Sbjct: 4   IQGEKLQKVLARAGVGSRREMEKYIDANRVSVNGKVAK-LGDRVEETDSIRVDGHTVKIE 62

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLT 125
           E+     R+ +Y+KP G ++T  DP+GR TVFD LP I   R I+VGRLDINT GL+L T
Sbjct: 63  EKADRICRVIMYNKPEGELSTRKDPEGRRTVFDRLPRIDGERWIAVGRLDINTAGLMLFT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA  L  PS +  R Y  R  G+V ++ +  L +G+ ++      + V     +G 
Sbjct: 123 NDGELANRLMHPSYEVEREYSARVFGEVTKETIKNLTRGVELEDGPAKFLTVNPMGGEGI 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V L EG+NRE++++++    +V+RLIRI YG  +L   +  G   E     +   
Sbjct: 183 NRWYNVTLNEGRNREVRRLWQSQEVEVSRLIRIRYGKLELDKRVPQGGWIEYDLDTVNYL 242

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
                     V L     +  +++ ++        +   +  K  +Q+   +K+K
Sbjct: 243 -------RKTVKLGRETQTKLSVMPEKRKDKRAKINQIRKAVKKHNQRVKPTKRK 290


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 114/231 (49%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR+E  R+I + R+ VNG +       V   D I +D  P++K E+ 
Sbjct: 1   MRINKLLSNYGICSRKEANRIIEENRIIVNGEVCI-PGQWVEEYDEILMDNEPIKKKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T +  + +  + D L +    +  VGRLD ++EGL+L+TNDG L+  
Sbjct: 60  -YIALNKPVGITCTAA-REVKDNIIDFL-NYPEYIFPVGRLDKDSEGLILMTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V      D   +  + +G+ + G+      VT    + +N    + L
Sbjct: 117 ILESENHHEKEYIVTVDKPFDDSFIKGMSEGVQLNGVKTRPCIVT----RINNDTFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G NR+I+++   F + V +L RI     ++  +  G  R ++ K + E 
Sbjct: 173 TQGLNRQIRRMTRAFRYTVIKLERIRILNIKINEIDVGKWRYLTHKEIDEL 223


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 69/226 (30%), Positives = 110/226 (48%), Gaps = 8/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    VKV+G  ++ A V+V      I V G  +   E 
Sbjct: 1   MRLDKLLSTIGYGSRKEVKGLLKTGAVKVDGSAVKDAKVHVNPDEQEITVHGEAVSYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   D     TV D L           VGRLD +TEGLLLLTNDG L
Sbjct: 60  FVYFMLHKPQGVISATEDSLH-ETVLDLLELDDAVYDPFPVGRLDKDTEGLLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  + +  V ++     ++G+ +  G      ++ + T  G  + +
Sbjct: 119 AHQLLSPKKHVPKTYFAKINAPVTEEDAEAFRQGVTLDDGYVTKSAELKILT-SGVESEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + EGK  ++K++FE    KV  L R+S G   L  +L  G  R
Sbjct: 178 ELTIVEGKFHQVKRMFEARGKKVTYLKRLSMGALLLDESLDLGEYR 223


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 93/290 (32%), Positives = 148/290 (51%), Gaps = 10/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+AR+G  SRRE+E MI   R++VNG + +     + +   + +DG  +     
Sbjct: 2   TEKLQKVLARSGYGSRREIEAMIGAGRIRVNGKVAQ-VGERIDADASVRIDGHEVVIKSE 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
                R+  YHKP G + T  DP+GR TV++ LP +  +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 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
            W  V L+EG+NRE+++++E    +V+RLIR+ YG  +L   L  G   E+    + E  
Sbjct: 181 RWYHVTLKEGRNREVRRLWESQEVQVSRLIRVRYGDIKLESGLPQGGWSELELDQVNELR 240

Query: 246 GPHLLEEAQVNLDAPIY--SSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
               L+    +   P +  S +          S+  D     ++ +  K 
Sbjct: 241 AKVGLQPEDKSFVDPRHQESKQRKFAKIRKATSKRKDRLREAQRVNKNKR 290


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 116/231 (50%), Gaps = 3/231 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K IA +GI SRRE + +I Q  V+VNG ++      V  TD +  DG  +   E
Sbjct: 159 DSIRLNKYIANSGICSRREADELITQGLVEVNGKVVTEMGYQVQKTDRVVFDGQSIT-PE 217

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           +    L +KP G ++T  D   R TV D + +    R+  VGRLD +T G++LLTNDG +
Sbjct: 218 KPVYVLLNKPKGYISTTKDDKARKTVMDLVANASPYRLFPVGRLDRSTTGVILLTNDGHM 277

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            + L  PS    ++Y V    ++  + L L+ +GI +        Q++    K  N  V 
Sbjct: 278 TKKLTHPSFDAKKIYHVTLDKKLTGEDLRLIAEGIRLDEGVAVVDQISYIEGKPKN-EVG 336

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + +  G NR I+++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 337 IEIHIGWNRVIRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 387


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 116/231 (50%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNGI    A  N+    D IE +   L   ++
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNNEITVNGISNISAKDNIDENSDIIEYNEEKLEY-KK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKSGYITATEDFKEN-TVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHKLLSPKNHVDKVYYVEIKNNISDEDIFKLEQGVDIGNYITQPAKV----EKISDNEIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  +IKK+ E  N KV  L R+S+G  +L  L  G  REV+ + +
Sbjct: 175 LTIKEGKFHQIKKMLEAINNKVCYLKRVSFGRLKLNDLALGEVREVNLEDI 225


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 75/238 (31%), Positives = 131/238 (55%), Gaps = 4/238 (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 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           L +G  R+I+ +     +KVNRL R++ GP  L  +  G  R ++++ ++   G   L
Sbjct: 186 LSQGMKRQIRTMLSLLGYKVNRLRRVALGPLTLKRMKPGELRSLTEREIKSLYGAFEL 243


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 84/241 (34%), Positives = 136/241 (56%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 1   MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 59

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT 
Sbjct: 60  WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 120 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   
Sbjct: 180 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANI 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  245 bits (627), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 80/236 (33%), Positives = 129/236 (54%), Gaps = 6/236 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-- 72
           ++ K++A+ G+ SRRE+E +IA  +VK+N  +           D + +    +R  E   
Sbjct: 38  KLQKLLAQKGLGSRREMEALIASGQVKLNDHIA-VIGDRAGPGDIVRIGRRVIRIHEEEE 96

Query: 73  -TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
             ++ LYHKP G + + +DP  R +VFD LP    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 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           V L+EGKNRE++++F      V+RL+R+ +GP  L   +  G   E+ +K  R  L
Sbjct: 217 VILKEGKNREVRRMFGAIGLTVSRLMRVRFGPINLPPRIKRGQWLELDEKETRRLL 272


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 108/232 (46%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + IA +   SR+E +R IA   V+VNG + + +A  V +   + + G  +      
Sbjct: 1   MRLDQFIATSSELSRKEAKRAIAAGDVQVNGDVWKNSATAVPANAEVMLQGELVALPAE- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G ++   D D + T  D LP+  +R +   GRLD +T GLLLLT+DG  + 
Sbjct: 60  RYLMLNKPAGFISATRDSD-QPTALDLLPAELTRNLHIAGRLDADTTGLLLLTSDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  + Y+V     + Q  +  L+ G+++          QVT+   +     V 
Sbjct: 119 RVTSPRVECPKTYQVALSVPISQAAIAALETGVMLRNDTKPTKPAQVTVLQSQ----LVE 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++       V  L R   G   L   L AG  R ++   +
Sbjct: 175 LTISEGRYHQVKRMLAAVGNHVTALHRSRIGGVTLDPALAAGEHRFLTSAEI 226


>gi|332969784|gb|EGK08795.1| ribosomal large subunit pseudouridine synthase B [Psychrobacter sp.
           1501(2011)]
          Length = 354

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 89/306 (29%), Positives = 148/306 (48%), Gaps = 10/306 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ K +AR G+ SRR++E +I   RV +N          V  +D I VDG  ++    
Sbjct: 46  TEKLQKALARMGLGSRRQMEEVIKAGRVSINQKPAT-IGDRVEQSDEIRVDGRLIKYKSE 104

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             +R R+  Y+KP G + + +DP+GR+TVF+ LP     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
              +   +   D  ++      ++R               ++       + +    +  +
Sbjct: 285 LVGIRPRE---DMGVHGKAKEKKERFQKKPLKARTIRTSSRSGRAGTTATGRNSNPSSSN 341

Query: 307 RRNLAS 312
            R   +
Sbjct: 342 TRGRDT 347


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 135/270 (50%), Gaps = 7/270 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDG 64
           ++ E     R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G
Sbjct: 53  LIPEWSGTMRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKG 112

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLL 122
             +        ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLL
Sbjct: 113 QLISHKT-HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYRVGRLDGDTEGLL 170

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDT 181
           LLT++G L   L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+  
Sbjct: 171 LLTDNGQLGYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLA 230

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
              + + V + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 231 ATETESHVFLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 290

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
           L+  L    +E+ Q +   P        R 
Sbjct: 291 LQLLLPYFFIEKQQTSKALPSNLKREEERK 320


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VN ++++     V  +D + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGIVAVNDVIVKTPKQQVKESDQVTVNGDAVAY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  ++ VGRLD +T GLLLLTNDG L 
Sbjct: 60  HYFLLNKPKGVLSATED-RNQPTVISLLAPQDRYQGIVPVGRLDKDTTGLLLLTNDGQLN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAW 188
             L  P     +VYR    G  +   +     G+ +  G      ++ + +Q  +   + 
Sbjct: 119 HELLAPGKHVDKVYRAEIAGVANDATVKTFASGMTLGDGTKLQPAELKILSQDEEHDRST 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + + EGK  +IK++F     KV  L RIS G   L   L  G   E+  + +
Sbjct: 179 TEIKICEGKYHQIKRMFGAVGMKVVELERISMGKLSLPANLKRGEYLELKLEDI 232


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 70/245 (28%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A  GI SRRE +  I Q  VKV+G +       V+   HIE+D    +  
Sbjct: 1   MEPVRLSKRLAELGICSRREADSYIEQGWVKVDGQVA-VLGFKVLPHQHIELDPRAKKAQ 59

Query: 71  ERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLD 115
                 L +KP+G V+  ++                +G  +     P+    +   GRLD
Sbjct: 60  LERVTILLNKPVGYVSGQAEKGYKPAAMLAVPANHWEGDKSGIRFSPNHLKGLAPAGRLD 119

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L   ++   + Y VR  G++  + L LL  G+ + G      
Sbjct: 120 IDSVGLLVLTQDGVVAKRLIGENSTVEKEYLVRVTGELSPEGLKLLNHGLSLDGQPLRPA 179

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+   +      +   LREGK R+I+++ E     V  L R+  G   LG L  G  R 
Sbjct: 180 KVSWQNED----QLRFILREGKKRQIRRMCEQVGLYVVGLKRVRIGNVMLGDLPTGQWRY 235

Query: 236 VSKKI 240
           + +  
Sbjct: 236 LREDE 240


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 103/229 (44%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR E +R+I   RV+V G ++     NV +   I V+G  LR A   
Sbjct: 1   MRLDKYLSQVTDYSRSEGKRLIRSGRVRVAGHVVIDPRENVDNNAVIVVNGQQLRSA-SP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HKP G ++   D    + +         ++   GRLDI+T GLLL+++DG     
Sbjct: 60  RYFMLHKPDGYISATKDRQHLTALELFDEDNVDQLHIAGRLDIDTTGLLLVSDDGQWCHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P +   + YRV     +  + +  +++GI +       +   LD      A   + +
Sbjct: 120 VTSPKSDCKKTYRVEAVDPITPEAIKNIEQGIHLSQEKKPTLPADLDLLDEHTA--RLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            EGK  ++K++F     KV  L R   G   L   L  G  R ++   +
Sbjct: 178 TEGKYHQVKRMFAAVGNKVECLHRERIGNIVLDDDLAPGEYRSLTAAEI 226


>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 =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 93/305 (30%), Positives = 148/305 (48%), Gaps = 10/305 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ K +AR G+ SRR++E +I   RV +N          V   D I VDG  ++    
Sbjct: 42  TEKLQKALARMGLGSRRQMEEVIKAGRVSINQKPA-SIGDRVEQGDEIRVDGRLIKYKSE 100

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             +R R+  Y+KP G + + +DP+GR+TVF+ LP     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-GTLLAGSTREVSKKI---LRE 243
           W  V L+EG+NRE++++ E    KV+RL+R SYG   L   L  G   E+ +K    L +
Sbjct: 221 WYHVKLKEGRNREVRRLIESQGLKVSRLLRTSYGSVDLPKELRTGRFIELDRKDIHRLID 280

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +G    E+  V+  A         +              R   ++ +    ++ +    
Sbjct: 281 LVGIRPREDMGVHGKAKEKKERFQKKPMKARTIRTSSRSGRASTSTGKNTSATRGRDTGN 340

Query: 304 PVHRR 308
              +R
Sbjct: 341 RGSKR 345


>gi|222084363|ref|YP_002542892.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221721811|gb|ACM24967.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 278

 Score =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 77/243 (31%), Positives = 130/243 (53%), Gaps = 3/243 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + + +++ G  SR + E +IA  RV V+G  +      +      I VDG  +  AE+  
Sbjct: 27  LPRALSKLGYCSRTQAEALIAAGRVTVDGREITDPTAWIDLDRARIAVDGEAI-AAEKKL 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP GLVTT  DP+GR TV+D L  I    +  VGRLD  +EGLLL TND  LA+ 
Sbjct: 86  YFMLNKPRGLVTTRDDPEGRPTVYDCLRDIDARHLAPVGRLDKASEGLLLFTNDTVLAQA 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P +   ++Y V+ +  ++Q+ L+ +++G++  G         L      N W+ V L
Sbjct: 146 LLDPISHVGKIYHVQVNTIMEQELLDRMERGVIDDGELLTATAARLLRSGDRNGWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           +EG+NR+I+++ E    +  RL+R+++G   LG L  G+ R +++  +        +E+ 
Sbjct: 206 KEGRNRQIRRMLEVLGVECLRLVRVAFGDIALGDLAKGAVRALTEAEVLGLRRRAGMEKT 265

Query: 254 QVN 256
             N
Sbjct: 266 GRN 268


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 97/306 (31%), Positives = 150/306 (49%), Gaps = 15/306 (4%)

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  HIEVDGVPLR--KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLD 115
            + +DG P+   + ER R  LYHKP+G V +  DP+GR TVFD+LP     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 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            +      G N W  V L EG+NRE+++++E     V+RL R+ YG   + + L  G   
Sbjct: 187 DIVDGGGDGINRWFYVVLMEGRNREVRRLWESQGLTVSRLKRVRYGEVFIPSKLKKGEWT 246

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E+  + +    G   + +       P+        +R    S        +++ +S K G
Sbjct: 247 ELPDRDVEVLYG---MAKLPAKPIMPLGDKSRAKLERLAKKS----GRETVRRLASGKGG 299

Query: 295 LSKQKK 300
             +++K
Sbjct: 300 FQRRRK 305


>gi|291619766|ref|YP_003522508.1| RluF [Pantoea ananatis LMG 20103]
 gi|291154796|gb|ADD79380.1| RluF [Pantoea ananatis LMG 20103]
          Length = 297

 Score =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 121/291 (41%), Gaps = 12/291 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     + 
Sbjct: 15  RLNKYISESGICSRRDADRFIEQGNVFINGKRAA-VGAQVFAGDVVKVNGQLIEPRDEDD 73

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 74  LVLIALNKPTGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 131

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V  + +  +  G+ + G            +K +     + 
Sbjct: 132 KILRAGNNHEKEYVVTVDKPVTDEFIAGMASGVPMLGTVTK----KCKVKKEAPYVFRIT 187

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  +  G  R+++     E     LLE 
Sbjct: 188 LVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGIPLGEWRDLTDDERVELF--KLLEN 245

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +    D P   +                   + +   + +   ++  +   
Sbjct: 246 SSSE-DKPAKKTPQKSPAAKKPAKNAVKQGEKSEDKPASRKRFTQPGRKKK 295


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 107/234 (45%), Gaps = 7/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KV+   G  +R +V++ I Q  VKVNG++++     +  TD +      L + 
Sbjct: 1   MAKERLDKVLGNYGFGTRSDVKKEIYQGNVKVNGLVVKDPGYKITLTDIVVYYDETLNRK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
           E    ++ +K    +T   DP  + TV D L        +  +GRLD  TEGLLL T DG
Sbjct: 61  E-FYYFMMNKAPDCITATEDPREK-TVMDYLSERHRNMNLFPIGRLDKETEGLLLFTTDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-A 187
            LA     P     + Y       V    ++  + GI +    Y  +   L     SN  
Sbjct: 119 TLAHYYTSPKHFVEKEYYAEISAPVTAFDISQFESGITLDDG-YKTLPARLAIPDPSNPH 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
             TV LREGK R+I+++F+    +V  L R+  G  +L   L  GS RE+++  
Sbjct: 178 IATVWLREGKYRQIRRMFQSLGKEVQYLKRVKMGNLELDRDLEVGSYRELTEAE 231


>gi|153001970|ref|YP_001367651.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366588|gb|ABS09588.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 242

 Score =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 114/241 (47%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D+IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPVRLGESLNCLDNIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLAYWVLNKAVGTDCRLLEQDE-TSLIHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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

Query: 244 Q 244
            
Sbjct: 235 L 235


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 72/231 (31%), 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+    K     +
Sbjct: 149 FANRVIHPSANIHKEYLVKTNEEVEAEHLSALSSGTLVEKTFVRPIRVS----KVRRGTL 204

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGK REI+ + E     V  L RI  G   LG L  G  RE++ + 
Sbjct: 205 KITIAEGKKREIRLLMESAKLPVLELTRIRIGGLHLGPLQPGEWREMTARE 255


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 116/233 (49%), 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 +G      D D +S++   LP+   R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  GAEALSYWIFNKAVGTDCRLLDAD-KSSLLHLLPTT-PRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS    + Y V+     +   +  +  G+  + +     QVT  +       
Sbjct: 119 ELTHKLMHPSFAHSKTYHVQLDRPFNDAFIAQMASGVQYKEVRTLPCQVTRLSAD----R 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + L +G NR+I+++     +KV  L R++     L +L  G  R +S + +
Sbjct: 175 FEIVLTQGLNRQIRRMSNALGYKVIDLQRVALMTLTLASLAEGEMRPLSPEEI 227


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 78/242 (32%), Positives = 125/242 (51%), Gaps = 7/242 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R++K +A AG+ SRR+ + +IA  RV V+G ++      +      + VDG  + 
Sbjct: 3   DDNGVRLNKALAEAGVCSRRQADALIAAGRVAVDGSVVTELGRKIDPARSRLSVDGKDVV 62

Query: 69  KAE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLL 124
           K +   T   + HK  G VTT  DP+GR TVFD LP  +   R+ SVGRLD  +EGLLLL
Sbjct: 63  KPDTAGTLTLMLHKKPGCVTTARDPEGRPTVFDALPDPYRKRRLFSVGRLDFFSEGLLLL 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ- 182
           T DG LA  L  P     + Y V   G V  + +  + +G+ + +G     +   +  + 
Sbjct: 123 TTDGELAYRLAHPRWHAPKRYLVTVRGHVGPEAIEAMGRGMRLAEGEPLAPVAARIVKRL 182

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 + + LR+G NR+++++       V +L+R++ GP +LG L  G  RE++ + L 
Sbjct: 183 AADRFVLEMELRQGINRQVRRMCRDLGLTVLKLVRVAQGPLELGGLAPGKCRELAGEELA 242

Query: 243 EQ 244
             
Sbjct: 243 AL 244


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 116/229 (50%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G  SRR+ + +I + RV VN        ++V   D + +DG  ++   R 
Sbjct: 1   MRLNKFIAETGFCSRRKADELINEGRVTVNKHEAI-IGMDVKPEDVVRIDGERVKLNTRY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++ ++ D  GR    D + S  +R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYILNKPKRVICSNEDKFGRRLAVDFIKSR-ARLFTYGRLDFMTEGLIIISNDGEVYNH 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +   +++   +  L+ G+VI G      +V     K     + + +
Sbjct: 119 VMHPRKKLYKSYIAKVSREIEDKDIEALQHGVVIDGKRTAPAKVK----KIDKKELRIAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+ E   + VN L RI  G   LG L  G  R +++  ++
Sbjct: 175 FEGRNRQIRKMLETLGYNVNSLKRIKVGELTLGNLQVGEYRALNEDEIK 223


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 73/236 (30%), Positives = 126/236 (53%), Gaps = 10/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ +I  +++ VN  ++  + + +  T D I+ +   +    +
Sbjct: 1   MRLDKFLANSGIGTRKEVKEIIKNRKIFVNDKIVMSSDLKIDETKDIIKYENNVINYT-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
            R  + +KP G ++  +D + + TV D +    + ++  VGRLDI+TEGLLLLTNDG LA
Sbjct: 60  FRYIMLNKPKGYISATND-NKQKTVLDLITDFKTYKLFPVGRLDIDTEGLLLLTNDGDLA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V     +  D ++ ++KGI I +GI     ++     K  +  + 
Sbjct: 119 HNLLSPKKHVEKKYYVELSQDISSDDISNIEKGIDIGEGIITRLSKII----KVDDNKLY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           + + EGK  ++K++F+  N +V  L RIS G   L   L  G  RE++ + LR  L
Sbjct: 175 IIITEGKFHQVKRMFKAVNNEVKYLKRISMGSLILDEKLNLGEYRELTYEELRSLL 230


>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 =  245 bits (626), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 119/246 (48%), Gaps = 11/246 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRRE +R+I + +V +NG + +     V  +D +EV G  ++K   ++
Sbjct: 4   RINKYLSEVGYCSRREADRLIHEGKVTINGKIPK-IGSKVEESDQVEVKGQRIKKITGQK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDRKVEPNNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ + Q++ D +  +  G+ I      +  V     K       + 
Sbjct: 122 KILRARNNHEKEYIVKVNRQINSDFIQSMSSGVEILDTITKNCFVKQLGPKK----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K+ L E     LL++
Sbjct: 178 LTQGLNRQIRRMCESLGYRVRSLKRVRIMNIEL-DVSTGKYREFTKEELFEL--NRLLKK 234

Query: 253 AQVNLD 258
           +    D
Sbjct: 235 SSKTYD 240


>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 =  245 bits (626), Expect = 9e-63,   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 KPARVSWQNED----QLRFILNEGKKRQIRRMCEIVGLKVVGLKRVRIGRVMLGDLPVGQ 332

Query: 233 TREVSKKI 240
            R ++ + 
Sbjct: 333 WRLLTPEE 340


>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 =  245 bits (626), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 110/234 (47%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +RRE  +++  + ++V+G ++  A+ +V   + +E +G PL+  +  
Sbjct: 1   MRLDKFLGTTLGITRREAGKLLRDKMIEVDGEIVRSASFSVSDDNDVEFNGRPLKL-QGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G V +H D D   TVF     +    + V GRLD +T GL+LLT+DG  + 
Sbjct: 60  RYFMLNKPEGFVCSHVD-DFNPTVFVLFDEVSPEKMHVAGRLDGDTTGLVLLTDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     + +D +   + G+ ++          L+      A +   
Sbjct: 119 RITSPRHLCSKTYFVEAADPITEDYIKQFEAGVQLRSEKELTRPAKLEILGEREALL--T 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EGK  ++K++F     KV  L R   G  +L   L  G  R ++++ +   L
Sbjct: 177 ISEGKYHQVKRMFAAMGNKVVGLHRERIGTVELDEDLAPGEYRPLTEEEIASFL 230


>gi|326565822|gb|EGE15984.1| ribosomal large subunit pseudouridine synthase B [Moraxella
           catarrhalis BC1]
          Length = 328

 Score =  245 bits (626), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 96/304 (31%), Positives = 151/304 (49%), Gaps = 13/304 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
               +++ K++AR G+ SRR +E +I   R+ +NG +       V+ TD I +DG  +R 
Sbjct: 20  KPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINGKVAT-LGDRVILTDEIRIDGRQVRL 78

Query: 69  ---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
              + +R R+  Y+KP G + + SDP GR TVFD LP     R + VGRLDIN+ GLLL 
Sbjct: 79  KAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLF 138

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +      G
Sbjct: 139 TNDGELAHRLMHPSSGIIREYAVRVLGEVTSQIASQLTAGVELEDGVAKFDDIKEGGGIG 198

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+    + +
Sbjct: 199 VNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIELDASDIGK 258

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +    L + Q              +++   I + P     +++   + +   +++K  T
Sbjct: 259 LVDSVGLRQRQGT------GLNHATKEKQARIHKKPLKSREIRRQKHEAHERREERKKHT 312

Query: 304 PVHR 307
           P HR
Sbjct: 313 PKHR 316


>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 =  245 bits (626), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 81/246 (32%), Positives = 134/246 (54%), Gaps = 6/246 (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  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            + G  ++        R+ LY+K  G + +  DP GR ++FD LP   S R +++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 VSKKIL 241
           ++   +
Sbjct: 329 LNPMEV 334


>gi|189499452|ref|YP_001958922.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
 gi|189494893|gb|ACE03441.1| pseudouridine synthase [Chlorobium phaeobacteroides BS1]
          Length = 254

 Score =  245 bits (626), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 77/250 (30%), Positives = 116/250 (46%), Gaps = 7/250 (2%)

Query: 1   MKDKNIVQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK K+      TP    R++K +A  GIASRR  +R++    V VNG ++ +    V   
Sbjct: 1   MKKKSSNAHVETPGAAVRINKYLALCGIASRRAADRLVESGEVMVNGRIMMKKGATVRPG 60

Query: 58  -DHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D + V    L    E+    L +KP   +TT SD   R TV D +  +  RV  VGRLD
Sbjct: 61  VDEVVVSNRLLALPEEKKVYILLNKPRNYITTSSDEKERETVLDLV-DVRERVFPVGRLD 119

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             T G+LLLTNDG LA  L  PS++  + Y         +  L  L  G+ ++       
Sbjct: 120 RKTTGMLLLTNDGALAHRLMHPSSEVEKEYLAELETPFSEKDLPSLTGGMRLKDTGEKTS 179

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                  +G    + V + EGKN +++++F    + V RL R +Y   + G L  G  R 
Sbjct: 180 PCKGKIMQGGLRVL-VTIHEGKNHQVRRMFRSLGYDVKRLDRTAYAGLRAGKLRRGEWRY 238

Query: 236 VSKKILREQL 245
            + K + + +
Sbjct: 239 ATSKEVEQLM 248


>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 =  245 bits (626), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 110/234 (47%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R+E  R+++ + ++VNG +++ A++ +     +E +G  L   +  
Sbjct: 1   MRLDKFLATTLGITRKEAGRLLSNKMIEVNGNVVKSASLKITDDCDVEFNGKKLAL-QGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D D   TVF     +    + V GRLD +T GL LLT+DG  + 
Sbjct: 60  QYFMLNKPEGFVCSHVD-DHNPTVFVLFDEVSPEKMHVAGRLDGDTTGLTLLTDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     +VY V     V ++ +    +G+ ++G         L+      A +   
Sbjct: 119 RVTSPRHVCEKVYHVELADPVPEETIQTFLEGVQLRGEKDITRPAKLEILSEREAIL--T 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EGK  ++K++F     +V  L R   G   L   L  G  R ++++ +   L
Sbjct: 177 ITEGKYHQVKRMFAAVGNRVVGLHREQVGAVVLDENLEPGEYRRLTEEEIASFL 230


>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 =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 107/226 (47%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V ++G   +    +V   T  + V G P+   E 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKEHVDPDTQEVTVYGEPVDYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 60  FIYLMMNKPQGVLSATEDSR-QQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V    Q+ ++ ++ L+ G+ I+G       +  + T    N  +
Sbjct: 119 AHRLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPAKAEIKTNDSGNTVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + + EGK  ++K++ +    +V  L R+S G   L   L  G  R
Sbjct: 179 YLTITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALAPGEYR 224


>gi|291485437|dbj|BAI86512.1| hypothetical protein BSNT_04375 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 239

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 107/226 (47%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V ++G   +    +V   T  + V G P+   E 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKAHVDPDTQEVTVYGEPVDYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 60  FIYLMMNKPQGVLSATEDSR-QQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V    Q+ ++ ++ L+ G+ I+G       +  + T    N  +
Sbjct: 119 AHRLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPARAEIKTNDSGNTVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + + EGK  ++K++ +    +V  L R+S G   L   L  G  R
Sbjct: 179 YLTITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALAPGEYR 224


>gi|332974446|gb|EGK11370.1| ribosomal large subunit pseudouridine synthase B [Kingella kingae
           ATCC 23330]
          Length = 390

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 82/250 (32%), Positives = 135/250 (54%), Gaps = 6/250 (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  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  ++        R+ LY+K  G + +  DP GR ++FD LP   S R +++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 VSKKILREQL 245
           ++   +   L
Sbjct: 366 LNPAEVANIL 375


>gi|218289710|ref|ZP_03493918.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
 gi|218240167|gb|EED07351.1| pseudouridine synthase [Alicyclobacillus acidocaldarius LAA1]
          Length = 242

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 117/239 (48%), Gaps = 8/239 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
               RV K +  AG  +R E +++    RV++NG  ++ AA +     D +EVDG  +  
Sbjct: 1   MATIRVDKWLTTAGYGTRSEAKKLCRAGRVRLNGETVKDAAKHADPAVDVLEVDGE-IVP 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
            E    ++ +KP G V++  DP     V + L    I+  V  VGRLD + EGLLLLTND
Sbjct: 60  YEPLVYFMMYKPPGYVSSTEDPRD-PVVIELLDEEDIWRDVFPVGRLDKDAEGLLLLTND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  P     + Y VR  G + +D    L +G+V+    Y  M   L+  + G+ 
Sbjct: 119 GPLAHRLLAPKRHVPKRYFVRVRGALGEDDARALAEGVVLDDG-YKAMPAELEILRSGAE 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           +   + + EGK  ++K++F     +V  L RIS GP  L   L  G  R +++  +   
Sbjct: 178 SEAIIQVYEGKYHQVKRMFASLGKRVTFLKRISMGPLSLDPALKPGEYRRLTEGEIEAL 236


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/241 (34%), Positives = 136/241 (56%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+
Sbjct: 1   MEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 59

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT 
Sbjct: 60  WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 120 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   
Sbjct: 180 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANI 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>gi|325128449|gb|EGC51330.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis N1568]
          Length = 256

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 135/237 (56%), Gaps = 7/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 1   MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 59

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT 
Sbjct: 60  WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 120 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQIRVLTEEGVMLEDGLAKVERIREQGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +
Sbjct: 180 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEV 236


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 116/229 (50%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA  G  SRR+ + +I + RV VN        ++V   D + +DG  ++   R 
Sbjct: 1   MRLNKFIAETGFCSRRKADELINEGRVTVNKHEAI-IGMDVKPEDVVRIDGERVKLNTRY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++ ++ D  GR    D + S  +R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYILNKPKRVLCSNEDKFGRRLAVDFIKSR-ARLFTYGRLDFMTEGLIIISNDGEVYNH 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +   +++   +  L+ G+VI G      +V     K     + + +
Sbjct: 119 VMHPRKKLYKSYIAKVSREIEDKDIEALQHGVVIDGKRTAPAKVK----KIDKKELRIAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+ E   + VN L RI  G   LG L  G  R +++  ++
Sbjct: 175 FEGRNRQIRKMLETLGYNVNSLKRIKVGELTLGNLQVGEYRALNEDEIK 223


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 109/234 (46%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAE 71
            R++K ++ AGI SRR  ++ I   R+K+NG+        V   D +EVD   +     +
Sbjct: 1   MRINKFLSEAGICSRRGADKWIEAGRIKINGVKA-ELGSKVTEGDSVEVDNKVVTLNTDK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                  +KP G+ +T ++   +  + D +     R+  +GRLD ++EGL+LLTNDG + 
Sbjct: 60  GYVYIKLNKPRGITST-TERHIKGNIVDFV-GHSERIFHIGRLDKDSEGLILLTNDGDIV 117

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +     +  + Y V     +  D +  + +G+ I        +V    +K +     +
Sbjct: 118 NEILRKEGRHEKEYIVTVDKPITDDFVKQMSEGVAILDTVTLPAEV----EKLNTKTFKI 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L +G NR+I+++ E   ++V +L RI      +  L  G  +++++    E  
Sbjct: 174 ILTQGLNRQIRRMTEALGYEVKQLRRIRVMNILVDDLKLGEWKDLTEAEKDELF 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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 110/242 (45%), Gaps = 13/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R E ++++    V+VN  + + AA+ V   + I +DG  L  A  +
Sbjct: 1   MRLDKFICKSTELTRTEAKKVLKSGEVRVNNEVAKNAAMQVHENNLITIDGQQLS-ARGS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ HK +  + ++ D    S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 60  RYYILHKIVDTICSNVDEIYPSVLHSLEVDKAFDLHIAGRLDADTTGLVLITDDGRWSHN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGICYGDMQVTLDTQKGSN--- 186
           +  P  Q  + YRV    ++D DKL         G+ +QG         L   +  N   
Sbjct: 120 VISPKKQCQKTYRVWLRSEIDDDKLSALVARFDSGLQLQGEDSLTRPAILTRVEIDNLVD 179

Query: 187 -----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + + EGK  ++K++F     +V  L R   G   LG L  G  RE+++  +
Sbjct: 180 EASYRSEVLLTITEGKYHQVKRMFAAVGNRVVGLHREQIGKITLGDLAPGEWRELTEDEI 239

Query: 242 RE 243
            +
Sbjct: 240 TQ 241


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 68/294 (23%), Positives = 125/294 (42%), Gaps = 12/294 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N T  R++K I+ +G+ SRR+ +R I Q  V +NG   +     V+  D ++V+G  +  
Sbjct: 3   NRTSTRLNKYISESGMCSRRDADRFIEQGNVHINGRRAQ-VGDQVLPGDVVKVNGQVVEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E       +KP+G+V+T    +  +           R+  +GRLD +++GL+ LT++
Sbjct: 62  RDEEDLVFIALNKPVGIVSTTDSAEKDN--IQRFVGHSERIFPIGRLDKDSQGLIFLTSN 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     V ++ +  +  G+ I G      +V    +K S  
Sbjct: 120 GDLVNKILRAGNNHEKEYLVTVDKPVTREFVEGMSNGVPILGTMTKRCKV----EKVSRF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR---EQ 244
              + L +G NR+I+++ E+F ++V RL R+      L  L  G+ R++++K L    + 
Sbjct: 176 VFRITLVQGLNRQIRRMAEYFGYEVARLERVRIMNVSLQGLPVGAWRDLTEKELAVLFDA 235

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           +     E  +     P          RP    +      +    S    G    
Sbjct: 236 IRDSSSEATEPAGSKPRKKPAGARGARPGPGGKPARAGAKAGGKSPAGKGRKGP 289


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 111/230 (48%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNELN-VHGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D   R T F+ L  I   ++   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGSNR-TAFELLDEIKMDKLHFAGRLDVDTTGLVLMTDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  ++YRV     V+ D +   K+GI ++      +   L+ +  +   V + 
Sbjct: 119 RITSPKHKCEKMYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEVR--AEREVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQEEV 226


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 119/246 (48%), Gaps = 9/246 (3%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++ + +   T +  R++K ++ AG+ SRRE +R+I   RV V+G   +   + ++   
Sbjct: 1   MNNRILQEYQKTKEEVRLNKYLSEAGVCSRREADRLIESGRVSVDGKRAQT-GMKIVPGQ 59

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            ++V    + K +   +   +KP G+V T    +  S V         R+  VGRLD ++
Sbjct: 60  VVKVGKKVVSKQDEMVVLAVNKPAGIVCTEERRERNSIVRFL--DYPIRITYVGRLDKDS 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 KILREQ 244
             L E 
Sbjct: 234 AELNEL 239


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 109/233 (46%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRVT-LGDQVFPGDVVKVNGQLIEPRNEDN 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  + +  + V  +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LIFIALNKPVGIVSTTEEGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  V  D +  L  G+ + G            +K +     + 
Sbjct: 125 KILRAGNDHEKEYLVTVNKPVTDDFIRGLGAGVPMLGTVTK----KCKVKKEAPFVFRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L +G NR+I+++ E F ++V +L R       +  L  G  R+++   L E  
Sbjct: 181 LVQGLNRQIRRMCEHFGYEVTKLERTRIMNVGMAGLPPGEWRDLTDDELVELF 233


>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 =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 79/240 (32%), Positives = 122/240 (50%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDG 64
           +  +    +R+ KV+A+AG+ASRR  E +I   RV+VNG ++ +  V V    D I VDG
Sbjct: 55  VDDDKPKGERLQKVLAKAGVASRRHAEILIDGGRVEVNGNVVLKQGVKVNPAVDVIRVDG 114

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 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|327396520|dbj|BAK13941.1| ribosomal large subunit pseudouridine synthase F [Pantoea ananatis
           AJ13355]
          Length = 290

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 63/291 (21%), Positives = 121/291 (41%), Gaps = 12/291 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRFIEQGNVFINGKRAA-VGAQVFAGDVVKVNGQLIEPRDEDD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPTGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     V  + +  +  G+ + G            +K +     + 
Sbjct: 125 KILRAGNNHEKEYVVTVDKPVTDEFIAGMASGVPMLGTVTK----KCKVKKEAPYVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  +  G  R+++     E     LLE 
Sbjct: 181 LVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGIPLGEWRDLTDDERVELF--KLLEN 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +    D P   +                   + +   + +   ++  +   
Sbjct: 239 SSSE-DKPAKKTPQKSPAAKKPAKNAVKQGEKSEDKPASRKRFTQPGRKKK 288


>gi|304395011|ref|ZP_07376895.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304357264|gb|EFM21627.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 292

 Score =  245 bits (625), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 67/294 (22%), Positives = 126/294 (42%), Gaps = 14/294 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRA-SVGAQVFAGDVVKVNGQLIEPRDEDD 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G++TT  + + R  + D + +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIITTMEEGE-RDNISDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ + G            +K +     + 
Sbjct: 125 KILRAGNNHEKEYVVTVDKPITDEFIAGMSAGVPMLGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ + F ++V +L R       L  L  G  R+++   L E     LLE 
Sbjct: 181 LVQGLNRQIRRMCKHFGFEVTKLERTRIMNVNLKGLPLGEWRDLTDDELVELF--KLLEN 238

Query: 253 AQVN---LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +             ++     +P   +  P +       S ++     +KK   
Sbjct: 239 SSSEDKPAKKAKAPAKAAAASKPQKRAAKPAEKADANGASRKRFVQPGRKKKGR 292


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 120/237 (50%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR EV+R++ +++V VNG +   A + +    D I V+   L   ER
Sbjct: 5   MRLDKFLVEMGLGSRTEVKRLLKKKQVLVNGKIETSAKIQIDENQDEISVNNQVLIY-ER 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+++   D   R TV D L     +  V  VGRLDI+T GLLLLTN+G L
Sbjct: 64  FVYYLLNKPKGVISATEDDKHR-TVLDLLNENARQKEVFPVGRLDIDTHGLLLLTNNGAL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  +  P     +VYR +  G + +  +   + GI ++       ++T+    ++   + 
Sbjct: 123 AHAMLSPKKHVAKVYRAKVDGIITEKDVEHFEAGIELKDFTCQPAKLTILEVNEEQQTSL 182

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + + EGK  ++K++ +     V  L R+S GP  L   L   + R ++K+ L + 
Sbjct: 183 VEIIISEGKFHQVKRMVQACGKTVTDLERLSMGPLMLDERLELVTFRRLTKEELEKL 239


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 111/230 (48%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      
Sbjct: 17  MRLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNELN-VHGP 75

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D   R T F+ L  I   ++   GRLD++T GL+L+T+DG  + 
Sbjct: 76  RYIMLYKPEGFVCSHEDGSNR-TAFELLDEIKMDKLHFAGRLDVDTTGLVLMTDDGKWSH 134

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  ++YRV     V+ D +   K+GI ++      +   L+ +  +   V + 
Sbjct: 135 RITSPKHKCEKMYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEVR--AEREVLLT 192

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++ +
Sbjct: 193 IHEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQEEV 242


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 107/226 (47%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR+EV+ ++    V ++G   +    +V   T  + V G P+   E 
Sbjct: 1   MRLDKLLANSGYGSRKEVKAVVKAGAVMIDGKPAKDVKAHVNPDTQEVTVYGEPVDYRE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 60  FIYLMMNKPQGVLSATEDSR-QQTVVDLLTPEEMRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V    Q+ ++ ++ L+ G+ I+G       +  + T    N  +
Sbjct: 119 AHRLLSPKKHVPKTYEVHLKSQISREDISDLETGVYIEGGYKTKPARAEIKTNDSGNTVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
            + + EGK  ++K++ +    +V  L R+S G   L   L  G  R
Sbjct: 179 YLTITEGKYHQVKQMAKAVGNEVVYLKRLSMGRVSLDPALAPGEYR 224


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 119/232 (51%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV+ ++  +++ VNG ++    V V   TD I  DG  ++  E 
Sbjct: 1   MRIDKCLADCGLGTRSEVKSLLKSKKITVNGKVVTNGKVQVNPETDEILFDGEKIQYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D +  ++    V  VGRLDI+T GLLLLTNDG L
Sbjct: 60  FVYIMMNKPKGVVSATED-NLHKTVLDLINPLYFKKGVFPVGRLDIDTHGLLLLTNDGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     ++Y+ R  G +  +     ++GIV+  G      ++ + +     + V
Sbjct: 119 AHRLLSPKKHVTKIYQARVEGVMTPEDAAAFERGIVLSDGTECMPARLDILSTTQDESIV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + L+EGK  ++K++ +     V  L R++ G  +L   L  G +R ++++ 
Sbjct: 179 QIHLKEGKFHQVKRMVKACGKNVVDLQRLTMGTLKLDERLALGESRPLTEEE 230


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 74/232 (31%), Positives = 117/232 (50%), Gaps = 1/232 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              QR+ K+IA +GI SRR+ E +I Q +V VNG   +         D I V+G  + K 
Sbjct: 1   MIKQRLQKIIAESGICSRRKAEELIIQHKVLVNGFAAKIGDKANPENDQIIVNGYRIPKV 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
              R+ L +KP G++++ +D  GR TV   +PS   + +  +GRLD  + G +LLTN+G 
Sbjct: 61  IFNRVILLNKPRGIISSCNDQFGRKTVLSLIPSDIRKGLYPIGRLDYESRGAILLTNNGD 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     + Y V   G      L+  ++G V+ G      +V L       + +
Sbjct: 121 LTLKLTHPKFNHTKSYFVWVKGLPSSSTLSEWRQGTVLDGKITMKAKVNLIKSLKHQSLI 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + ++EG+NR+I+++ E F   V  L R++    +LG L  G  REV +  L
Sbjct: 181 QIEMKEGRNRQIRRISEKFGHPVIDLKRVAISKIKLGNLQEGCWREVKEDEL 232


>gi|300934025|ref|ZP_07149281.1| putative pseudouridylate synthase [Corynebacterium resistens DSM
           45100]
          Length = 335

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 122/234 (52%), Gaps = 4/234 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ KV++ AG+ASRR  E++IA  RV+VNG ++++  + +  + D + VDG  ++  E  
Sbjct: 96  RLQKVLSSAGVASRRMSEKLIAAGRVEVNGEVVQQMGLRIDPSVDVVRVDGTRVQVNEEM 155

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGL 130
             +  +KP G+ +T  D  GR  V + + + F++   +  VGRLD  TEGLLLLTNDG L
Sbjct: 156 VYFALNKPRGVHSTMHDDLGRPHVGELIEAKFNQGQGLFHVGRLDAATEGLLLLTNDGEL 215

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  + Y     G+ D+  +  LK G+ ++        V +       + + 
Sbjct: 216 ANRLMHPKYEVSKTYMATVLGEADRGLIRTLKDGVDLEDGMARADYVQIVDVWQGKSLIK 275

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V L EG+   ++++ +   + V  L+R      QLG    G+ R +++  L+  
Sbjct: 276 VELHEGRKHIVRRMLKAAGFPVQALVRTKIHTVQLGEQKPGTVRALNRSELQSL 329


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 123/230 (53%), 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: 10  MRINKYIAKAGLASRRKSEEYIKKGLVFVNGKKLDDLSYQVKENDEVKVMGKLLEIKEKF 69

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KPIG ++++ DP  +  +   +  I  R    GRLD ++ GL+L+TNDG +   
Sbjct: 70  YYKL-NKPIGFISSNYDPHNKKDLNSLV-KIDQRFFCAGRLDKDSHGLMLITNDGKITNK 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS +  + Y V+    +++D   L +KGI +       D ++ L  +  +     V 
Sbjct: 128 LIHPSKKIEKTYIVKVDKLLNKDDEALFRKGIKLSDNEKTSDAKINLIDE--NRKIYEVI 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+++++F +F  KV  L RI  G  +LG L  G  ++++KK L 
Sbjct: 186 IHQGFNRQVRRMFLYFGSKVIDLKRIKIGQIELGKLEDGKYKKLNKKELE 235


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 119/242 (49%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ K ++ +   P R++K +A AG+ SRRE +  I    V VNG+++      V  +D +
Sbjct: 183 MEYKEVLADPNEPIRLNKFLANAGLCSRREADEFITAGVVSVNGVVVTELGTKVKRSDEV 242

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P++  ER    L +KP   VTT  DP  R TV D +      R+  VGRLD NT 
Sbjct: 243 KFHDQPVK-IERKVYVLLNKPKDCVTTSDDPQERKTVLDLVKDACTERIYPVGRLDRNTT 301

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     ++Y V     V +  L+ +  GI +         ++ 
Sbjct: 302 GVLLLTNDGDLASKLTHPKYLKKKIYHVFLDKNVTKADLDQIASGITLDDGEIHADAISY 361

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + V + +  GKNR ++++FE   ++V +L R+ +       L  G  R ++++
Sbjct: 362 -ASDTDKSQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVYFAGLTKKGLRRGDWRYLTER 420

Query: 240 IL 241
            +
Sbjct: 421 EV 422


>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 =  244 bits (624), Expect = 1e-62,   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   +  ++ E
Sbjct: 1   MRINKFLSSLGIASRRAIDKYIEEGRIKVNGAIP-SIGIDVNEDDEIYIDNKKIETKRIE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               ++ +KP+ +++  SD  GR TV D +     R+  +GRLD  T GL+LLTNDG L 
Sbjct: 60  EKVYFILNKPLEVLSASSDDRGRRTVVDLI-KTDKRIFPIGRLDYMTSGLILLTNDGELF 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|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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 108/235 (45%), Gaps = 6/235 (2%)

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  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ +KP G+V+   D    ST  D +    S  +   GRLDI+T GLLL+T+DG     
Sbjct: 62  YFMLNKPAGVVSATKD-SNNSTALDLIFEHRSDELQIAGRLDIDTTGLLLITDDGQWNHR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P +   ++YRV     +  D    L  G+ ++G  +  +  T++  +  +  V + +
Sbjct: 121 LTSPRSDCQKIYRVTLGIPITPDYAEKLANGVWLKGEKHPCLPATME--QIDDETVLLSI 178

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
            EGK  ++K++F      V  L R   G   L  +L  G  R ++   +   + P
Sbjct: 179 AEGKYHQVKRMFAALGNHVEALHRTQVGGIILDESLEPGDYRALTDAEVASIMAP 233


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 64/294 (21%), Positives = 128/294 (43%), Gaps = 12/294 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R I Q  V +NG         V   + ++V+G  +   +
Sbjct: 5   SSIRLNKYISESGICSRRDADRYIEQGNVFINGKRAA-VGDQVYVGNVVKVNGQLIEPRD 63

Query: 72  R--TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L   +KP+G+++T  + +  + V  +  +   RV  +GRLD +++GL+LLTN G 
Sbjct: 64  ENDLVLIALNKPVGIISTTEEGESDNIV--DFVNHSKRVFPIGRLDKDSQGLILLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFIVGLAAGVPMMGTVTK----KCKVKKIAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  R++    L E     L
Sbjct: 178 NITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVTLKGLPQGEWRDLLDDELIELF--KL 235

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           +E +  + + P+  ++          +  P    +    S+ +   ++  +   
Sbjct: 236 IENSSSD-EKPVKKTQAKPVAVKKPSTSGPKKAEKSDGISASRKRFAQPGRKKK 288


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 142/251 (56%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 324 ELNPAEVANIL 334


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 107/229 (46%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V+VN   ++     +   TD + VDG  +   + 
Sbjct: 1   MRIDKFLANMGLGTRTEVKQLLKKGLVEVNEKKIKTPKSQIDPETDKVVVDGEEISYVDN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP   ++   D +   TV D +P      +  VGRLD +TEGLLLLTNDG   
Sbjct: 61  -VYMMLNKPKDYISATED-NAHQTVLDLIPEFSHLGIFPVGRLDKDTEGLLLLTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + Q  +   K G+ +        ++     KG++    V
Sbjct: 119 HELMSPKKHVSKTYEVISKYPIKQSDIEAFKLGVELSDGKVKPAELI----KGNDRLSYV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     +V  L R+     +L  TL +G  R ++++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRVKIANLELDETLNSGEYRFLNEQ 223


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/230 (36%), Positives = 120/230 (52%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERT 73
           R+   +AR G  SRR  E +I + RV+VNG ++   A  V    D + +DG  +    + 
Sbjct: 17  RLHVFLARCGEGSRRACEELIKKGRVRVNGRVITNPAHRVDPQEDRVTLDGRDVHLVGKF 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
               +HKP G + T SDP GR  V+D +  +   +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|154687141|ref|YP_001422302.1| YtzF [Bacillus amyloliquefaciens FZB42]
 gi|154352992|gb|ABS75071.1| YtzF [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 65/226 (28%), Positives = 106/226 (46%), Gaps = 7/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K++A +G  SR++V++++    V ++G   +    +V      I V G P    E 
Sbjct: 1   MRLDKLLANSGFGSRKDVKKIVKAGAVMIDGEPAKDVKTHVDPEKQDITVYGEPADYREF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G+++   D   + TV D L     R      GRLD +TEG LLLTNDG L
Sbjct: 61  IYVMM-NKPQGVLSATEDSR-QQTVVDLLTPEEQRFEPFPAGRLDKDTEGFLLLTNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y VR    +  + +  L++G+VI+G        V + T+      +
Sbjct: 119 AHRLLSPKKHVPKTYEVRLTSPLSPEDIVHLERGVVIEGGYKTKPAAVEIITESPDETVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + EGK  ++K + +    +V  L R+S G   L   L  G  R
Sbjct: 179 HLTITEGKYHQVKLMAKAVGNEVAYLKRLSMGAVSLDPDLKPGEFR 224


>gi|292559208|gb|ADE32209.1| Pseudouridine synthase, Rsu [Streptococcus suis GZ1]
          Length = 235

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 69/229 (30%), Positives = 113/229 (49%), Gaps = 8/229 (3%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHK 80
             G+ SR EV++++  ++V VNG +       +    D I V G  L   E    +L +K
Sbjct: 2   DCGVGSRTEVKKLLKNKQVTVNGQVETSPKQQINEKKDQIAVAGQVLSH-ETFVYYLLNK 60

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           P G+++   D   R TV D L +   +  V  VGRLDI+T GLLLLTN G LA  +  P 
Sbjct: 61  PKGVISATEDDHHR-TVLDLLDNTARQKEVFPVGRLDIDTHGLLLLTNKGQLAHAMLSPK 119

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLREG 196
               ++YR +  G + Q+ +     GI ++       Q+T+ +  +    + V + +REG
Sbjct: 120 KHVDKLYRAQVDGIMTQEDVERFAAGIELKDFTCQPAQLTILSTDEAKQTSLVDITIREG 179

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           K  +IK++ +     V  L R++ GP +L   L  G  R ++   L++ 
Sbjct: 180 KFHQIKRMVQACGKTVTDLQRLTMGPLRLDPKLALGEYRRLTAAELKQL 228


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 114/231 (49%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+       N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNDEITVNGMSDILPKDNIDENSDIIEYNGERLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDFKEN-TVMDLLPEWVIRKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHRLLSPKNHIDKVYYVEIENNILDEDILKLEQGVNIGNYITQPAKV----EKISDNKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KV  L R+S+G   L  L  G  +EV+ + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVCYLKRVSFGKLTLNDLTLGEVKEVNLEDI 225


>gi|291563383|emb|CBL42199.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SS3/4]
          Length = 265

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 75/244 (30%), Positives = 124/244 (50%), Gaps = 15/244 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  +R E++ MI + R+ VNG+++++    +    D I +D  P+   E 
Sbjct: 22  IRLDKYLADMGKGTRTELKEMIRRGRITVNGVIVKKPETKIKKGEDTICLDNAPVEYVE- 80

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
              +L +KP G+++   D   R TV D +     + +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 81  LEYYLLNKPQGVISATEDRR-RETVVDLIDEKSRKDLFPVGRLDIDTEGLLLITNDGALA 139

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG------ 184
             L  P     +VY  R  G V  + +   ++G+ +  G+     ++ +  +K       
Sbjct: 140 HRLLAPGHHVDKVYEARCKGFVPDEAVQRFREGMTLADGLSCMPSELEILERKPEDPETG 199

Query: 185 --SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
             + + V + L EGK  ++K++ E     V  L R+S GP +L   L  G  R+++ K  
Sbjct: 200 TAAESLVRLTLHEGKFHQVKRMMEETGCPVLHLKRLSMGPLKLDDALKTGEYRKLTDKE- 258

Query: 242 REQL 245
           RE L
Sbjct: 259 RELL 262


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 102/224 (45%), Gaps = 10/224 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-KAER 72
            R++K I+  G  SRRE  R+IA  R+ +NG +   A   V   D + +DG  +   +  
Sbjct: 1   MRINKYISETGFCSRRETNRLIAAGRITINGNVC-EAGAEVEPQDIVLIDGEAIPLNSSE 59

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 +KPIG+V T ++   G    + N P   SR+ ++GRLD  +EGL+LLTNDG + 
Sbjct: 60  PVYLALNKPIGIVCTAAEQVAGNIISYVNYP---SRIFAIGRLDKASEGLILLTNDGSIV 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     V  +    +  G+ I  +     +V     + S     +
Sbjct: 117 NQMMRSEHGHEKEYVVTVDKPVTNEFTQAMSCGVEILNVITKPCKV----DRTSEYEFRI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            L +G N +I+++ +   ++V +L R+      L  L  G  R 
Sbjct: 173 ILTQGLNLQIRRMCKALGYRVLKLERVRIMNITLDHLERGQWRH 216


>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 =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 92/298 (30%), Positives = 146/298 (48%), Gaps = 7/298 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP+I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWIELDKADIDNLTK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
              L+  Q      +    T       + +       + ++ +      +  +K  +P
Sbjct: 241 SVELKPRQGTGLYGMAKRRTERMAEKPMAARRGGYLRQQRRENEGTEQTAAPRKPYSP 298


>gi|323466661|gb|ADX70348.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 216

 Score =  244 bits (624), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 66/214 (30%), Positives = 111/214 (51%), Gaps = 3/214 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI   RVKV+G ++ +    V +  +I VD  P+ + E    +L++KP G+V+T  D  G
Sbjct: 1   MIVAGRVKVDGKVVTKLGTKVETFSNITVDDEPIER-ESLHTYLFYKPRGVVSTADDDKG 59

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TV D    +  R+  VGRLD +T GLLL+TNDG LA +L  P  +  +VY  +  G +
Sbjct: 60  RKTVVDYFEDVPCRLYPVGRLDYDTSGLLLMTNDGKLANLLMHPRNEVSKVYVAKIKGIL 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             D++  L  G+ +        +V +    ++     + + + EG   ++K++F+     
Sbjct: 120 TPDEIKTLTTGVKLDRFKAAPAKVKILKTDKRKDTQIIQLTIHEGHYHQVKRMFKAVGHL 179

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           V +L R  Y    L +L +G  RE+SK  + + +
Sbjct: 180 VEKLSREKYAFLTLDSLTSGQYRELSKHEVDKLM 213


>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 =  244 bits (624), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 69/245 (28%), Positives = 114/245 (46%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  IA+  VKV+G ++      V+ T  I ++     K 
Sbjct: 1   MEKIRLSKLMSEQGLCSRREADDFIAKGWVKVDGEIVSELGTKVLPTQKITLEKAAQAKQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
           +     L +KP+G V+  ++   +  +           D  P  F R     +   GRLD
Sbjct: 61  QGRVTILLNKPVGYVSGQAEEGHKPAILLLDAATRWEQDTAPHRFHRSQLLGLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L    +   + Y VR  G++  + LNLL  G+ + G      
Sbjct: 121 IDSTGLLVLTQDGRIAKQLIGEDSPIEKEYLVRVQGKLVGNGLNLLNHGLSLDGKKLKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+   +      +   L EGK R+I+++ E    KV  L R+  G  +LG L  G  R 
Sbjct: 181 KVSWQNED----QLRFILNEGKKRQIRRMCEMVGLKVTALKRVRIGKVRLGDLPQGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRADE 241


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 107/229 (46%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A  G+ +R EV++++ +  V+VN   ++     +   TD + VDG  +   + 
Sbjct: 1   MRIDKFLANMGLGTRTEVKQLLKKGLVEVNEKKIKTPKSQIDPETDKVVVDGEEISYVDN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D +   TV D +P      +  VGRLD +TEGLLLLTNDG   
Sbjct: 61  -VYMMLNKPKGYISATED-NAHQTVLDLIPEFSHLGIFPVGRLDKDTEGLLLLTNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + Q  +   K G+ +        ++     KG++    V
Sbjct: 119 HELMSPKKHVSKTYEVISKYPIKQSDIEAFKLGVELSDGKVKPAELI----KGNDRLSYV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EGK  ++K++F     +V  L R+     +L  TL +G    ++++
Sbjct: 175 TIYEGKYHQVKRMFHSIENEVLELKRVKIANLELDKTLNSGEYCFLNEQ 223


>gi|319638171|ref|ZP_07992934.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400444|gb|EFV81102.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 352

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 143/247 (57%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 146 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRISIFDRLPQAASSRWVAIGRLDI 205

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 326 ELNPAEV 332


>gi|301320594|gb|ADK69237.1| pseudouridylate synthase [Mycoplasma mycoides subsp. mycoides SC
           str. Gladysdale]
          Length = 252

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 119/241 (49%), Gaps = 5/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
            + +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +   
Sbjct: 1   MSLERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNRLVLSD 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLLL+TNDG
Sbjct: 61  SNNQKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGLLLMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT--QKGS 185
            L   +  P  ++L+ Y+    GQV++ ++N L KG+ I            L    +  +
Sbjct: 121 VLFNFIMHPKYEFLKTYQGLCQGQVNKQQINQLIKGVYIDNDYLTKAYSAKLVKYDKLKN 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + V + + EGK   +KK+F+    ++ +L R      ++  L  G  RE+    ++   
Sbjct: 181 TSIVELTINEGKKHHVKKMFDSIQAQLLKLKRTKIEFLEIADLKPGQYRELKTHEVKRLY 240

Query: 246 G 246
           G
Sbjct: 241 G 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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 144/275 (52%), Gaps = 9/275 (3%)

Query: 1   MKDKNIVQE--NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++ I  E      +++ KV+A+AG  SRR +E  IA  RV VNG       + V+  D
Sbjct: 1   MIEQEIEAEYQPEAGEKLQKVLAQAGFGSRRNMEEWIAAGRVSVNGEPAT-LGMRVVPGD 59

Query: 59  HIEVDGVPLRKAER---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRL 114
            ++ +   +R  ER    R+ LYHKP G + +  DP+ R++VFD LP     + I+VGRL
Sbjct: 60  LVKTERRTIRVGERDHTARVLLYHKPEGEIVSRDDPEKRASVFDKLPKLRGQKWIAVGRL 119

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYG 173
           D NT GLL+ T  G LA  L  P  +  R Y VR  G + +D++   LK+G++++     
Sbjct: 120 DFNTSGLLIFTTSGELANRLMHPRFEVEREYAVRVQGSMTEDQITQVLKEGVMLEDGPVT 179

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGS 232
             ++  +  +G N W  V L+EG+NR +++ F+     V+RLIR+ +G   L   L  G 
Sbjct: 180 FDKLEDNGGEGFNHWYKVMLKEGRNRIVRRTFDALALPVSRLIRVRFGIINLPPRLKRGM 239

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETL 267
           + E+ +  + + L    +   +V   AP + +   
Sbjct: 240 SAELGEGEIAQVLDWVGISTDEVEPPAPKFVAPKP 274


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 84/241 (34%), Positives = 136/241 (56%), Gaps = 7/241 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 1   MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 59

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT 
Sbjct: 60  WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 120 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +   
Sbjct: 180 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVANI 239

Query: 245 L 245
           L
Sbjct: 240 L 240


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 71/213 (33%), Positives = 111/213 (52%), Gaps = 3/213 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           MI Q  V +NG ++   A  V S D +E++G P+   E    +L +KP G +++ SD  G
Sbjct: 1   MIKQGLVTLNGQVITDLATTVKSGDVVEIEGSPI-YNEEKVYYLLNKPRGAISSVSDDKG 59

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R TV D LP +  R+  VGRLD +T G+L+LTNDG     +  P  +  +VY  R  G  
Sbjct: 60  RKTVLDLLPQVKERIYPVGRLDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIA 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            ++ L  L +GIVI G      +  +       + + V + + EG+N ++KK+FE     
Sbjct: 120 TKENLRPLTRGIVIDGKKTKPARYNIVRVEADKNRSIVELTIHEGRNHQVKKMFESVGLL 179

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V++L R  +G   L  L  G  R ++KK + + 
Sbjct: 180 VDKLSRTRFGTVDLKGLRPGEARRLNKKEISQL 212


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 88/241 (36%), Positives = 134/241 (55%), Gaps = 9/241 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E  I+  RV VNG +       V S D + VDG  ++    
Sbjct: 2   SEKLQKVLARAGLGSRRELETWISDGRVSVNGTVAT-LGDRVGSEDTLRVDGRMIKVKAE 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G V + +DP+GR TVFDNLP     R + VGRLDINT G++L T D
Sbjct: 61  EDTVQRVIMYHKPPGEVCSRNDPEGRPTVFDNLPRLQGMRWVQVGRLDINTTGMMLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGS 185
           G LA  L  PS  ++R Y VR  G + Q+K   +  G++++        +      ++G+
Sbjct: 121 GELAHRLMHPSNGFVREYAVRVRGGMTQEKRQAMLDGVLLEDGVSKFDSIEDAGGAEEGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W  V L  GK RE++++F+  + +V RL+RI +G   L   L  G   E+  + ++  
Sbjct: 181 NHWYKVTLTGGKYREVRRLFQSQDLEVARLMRIRFGDLNLPPQLRQGRWMELEPEQMKAL 240

Query: 245 L 245
           +
Sbjct: 241 I 241


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 109/230 (47%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +RRE   ++  + V VN ++ +  ++ V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGVTRREATHLLKSKAVTVNDVIQKSGSLKVTEECVVEWQGNELN-VHGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D   R   F+ L  I   ++   GRLDI+T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGANR-IAFELLDEIKMDKLHFAGRLDIDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     V+ D +   K+GI ++      +   L+ +  +   V + 
Sbjct: 119 RITSPKHKCEKTYRVWLVEPVEDDYVEKFKEGIQLKSEDGLTLPAHLEVR--AEREVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVEGLHRERIGEIEMDESLELGEYRYLTQEEV 226


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 74/229 (32%), Positives = 131/229 (57%), 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 LMHPRFKIRKTYLVKTKGPIKTETLKAMSKGVNLEDGFFRPIRIK---KTNSPNWVLISI 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             G+NR I++  + F+ K+++L RI+ G  +LG L  G  RE++K+ + 
Sbjct: 177 DTGRNRIIRRFLKKFDIKIDKLKRIAIGNIELGNLRNGEFRELTKQEIE 225


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 9/239 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + ++ +KP G+V+  SD +   TV D +       ++  VGRLD +TEG LL+TN+G L
Sbjct: 61  -KYFILNKPAGVVSAVSDKEH-QTVIDLIVESDRVPKLYPVGRLDRDTEGFLLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G++  D     + G+           ++ +       +  
Sbjct: 119 GYRMLHPKYHVTKTYYVEVNGRLADDTPAFFENGVTFDDGTVCKPAKLEIIESSSEKSSA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQL 245
            + + EGK  ++KK+F  +  KV  L R+++G F+LG L  G  RE++   K+IL+  L
Sbjct: 179 YITIAEGKFHQVKKMFLAYGVKVTYLKRMTFGEFELGDLPTGHYRELTINEKEILKNYL 237


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 99/287 (34%), Positives = 139/287 (48%), Gaps = 7/287 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +++ KV+AR G+ SRR++E  I   RV++N          V S D + VDG PLR     
Sbjct: 3   EKLQKVLARHGLGSRRQMEAWIRAGRVQINDRPAT-IGDRVTSRDRLSVDGKPLRVPSWV 61

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
             R R+  YHKP G + T  DP+GR TVFD LP    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 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 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|325201930|gb|ADY97384.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M01-240149]
          Length = 256

 Score =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 135/237 (56%), Gaps = 7/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    V VNG   +     V   DH+ V G  + L+
Sbjct: 1   MEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 59

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT 
Sbjct: 60  WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 120 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           N W  V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +
Sbjct: 180 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEV 236


>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 =  244 bits (623), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 324 ELNPAEVANIL 334


>gi|323697859|ref|ZP_08109771.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457791|gb|EGB13656.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 251

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 82/232 (35%), Positives = 118/232 (50%), Gaps = 6/232 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL--RKAE 71
           R++K IA+ G+ASRR  + M+   RV VNG   +   + V    D + VDG  +  + + 
Sbjct: 10  RLNKFIAQCGVASRRGADEMVFAGRVTVNGATADSPGLQVDPARDEVAVDGKVIGQKASA 69

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGG 129
                L HKP+  VTT SDP GR TV D LP      R   VGRLD  +EGLLLLT DG 
Sbjct: 70  GDLTLLLHKPVETVTTASDPQGRKTVLDLLPPEIRKKRPFPVGRLDFFSEGLLLLTTDGD 129

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAW 188
           L   L  P     +VY V   G V Q  +  +++G+ + +G      +V L         
Sbjct: 130 LCYRLTHPKYHLPKVYVVTIRGSVPQKAVQTMRQGMTLREGDRLAPAKVRLLKPIAGTQQ 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + + L +G NR+I+++ E     + RL R+  GP  LG L  G+ RE++ + 
Sbjct: 190 LEITLIQGVNRQIRRMCEELGLTILRLRRVRQGPVALGDLKPGAWRELTSEE 241


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 115/228 (50%), Gaps = 6/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A AG+ SRR+ + MI + RV VN        + + S D + VDG  ++     
Sbjct: 1   MRLNKYMADAGVCSRRKADEMIKEGRVTVNKKEA-VLGMEISSGDIVRVDGEKIKLNTVY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP  ++ ++ D  GR    D + S   R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYMLNKPKRVICSNEDRFGRRLAIDYIKSK-KRLFTYGRLDYMTEGLIIISNDGEVYNH 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +   +V++  +   K G+VI G      +V     K     + + +
Sbjct: 119 VMHPRKKLYKSYIAKLSREVEEKDMEAWKHGVVIDGKRTAPAKVK----KIDKKEIRIAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+NR+I+K+ E   + V  L R+  G   LG L  G  R ++++ +
Sbjct: 175 FEGRNRQIRKMVEILGYTVESLKRVKVGELTLGYLQPGDYRALTEEEV 222


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 71/299 (23%), Positives = 139/299 (46%), Gaps = 20/299 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG  +      V   D ++V+G  +     + 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRVT-LGDRVFPGDVVKVNGQVIEPRNEDN 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                 +KP+G+V+T  D +  + V  +  +  +R+  +GRLD +++GL+ LTN G L  
Sbjct: 67  LIFIALNKPVGIVSTTEDGEKDNIV--DFVNHSTRIFPIGRLDKDSQGLIFLTNQGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + YRV  +  +  D +  L  G+ + G      +V  +T         + 
Sbjct: 125 KILRAGNGHEKEYRVTVNKPLTDDVIRGLGDGVPMLGTVTKKCKVKKETPL----VFRIV 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R       L  L  G  R+++    R QL   L+E+
Sbjct: 181 LVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLIGLPLGEWRDLTDDE-RGQL-FKLIED 238

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLA 311
           +   +       +++ + +P + +   ++  R    S     L+ +K+   P  ++   
Sbjct: 239 SSSEV-------KSVKKAKPAVKNLAGNNGPRNGNRSGS--SLAARKRFTQPGRKKKGR 288


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 68/292 (23%), Positives = 129/292 (44%), Gaps = 12/292 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K I+ +GI SRR+ +R I Q  V +NG         V S D ++V+G  +     E 
Sbjct: 8   RLNKYISESGICSRRDADRYIEQGNVFINGKRAA-IGDQVFSGDVVKVNGQLIEPRNEED 66

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L   +KP+G+V+T ++   R  + D + +   RV  +GRLD +++GL+ LTN G L  
Sbjct: 67  LVLIALNKPVGIVST-TESGERDNIVDYV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLVN 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V  +  +  D +  +  G+ I G            +K +     + 
Sbjct: 125 KILRAGNEHEKEYLVTVNKPITDDFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R+      L  +  G  R+++   L +     ++E+
Sbjct: 181 LVQGLNRQIRRMCEYFGFEVTKLERVRIMNVNLSGIPLGEWRDLTDDELIKLF--EMIEK 238

Query: 253 AQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           ++           +T    +             M   +S+K      +K   
Sbjct: 239 SESEAKPKKSAKPKTSTAGKTGSKPNAGSKPKGMADTASRKRFTQPGRKKKR 290


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 116/231 (50%), Gaps = 8/231 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R+ KV+AR G+ SR+EV R++ Q +V+V G +++     V     +EV+G PL   
Sbjct: 1   MKGERLDKVLARLGLGSRKEVARLVRQGKVRVLGQVVKDPGFRVPEGAALEVEGRPLEVR 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGG 129
               + L HKP G VT+ ++     +V+  L    +R +  VGRLD + EGLLL T DG 
Sbjct: 61  RHLHV-LLHKPPGFVTSRTEG---PSVYALLQGFPTRDLSPVGRLDKDAEGLLLFTTDGL 116

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P  +  + Y V     V        ++GI++ G      ++T         W 
Sbjct: 117 LLHRLTHPRHKVAKRYLVHLERPVGPKDQEAFREGILLDGKKTLPAELTPL---EDPTWA 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V L+EG+  +IK++F     +V RL R++ GP +LG L  G  R +++  
Sbjct: 174 EVVLKEGRFHQIKRMFRARGNRVLRLKRLALGPLELGDLPPGKARPLTEAE 224


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 95/304 (31%), Positives = 150/304 (49%), Gaps = 13/304 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
               +++ K++AR G+ SRR +E +I   R+ +N  +       V+ TD I +DG  +R 
Sbjct: 20  KPAGEKLQKLLARLGLGSRRGLEEIIKSGRISINDKVAT-LGDRVILTDEIRIDGRQVRL 78

Query: 69  ---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLL 124
              + +R R+  Y+KP G + + SDP GR TVFD LP     R + VGRLDIN+ GLLL 
Sbjct: 79  KAEREKRRRVIAYYKPEGEICSASDPQGRPTVFDRLPKLTNDRWVMVGRLDINSSGLLLF 138

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG LA  L  PS+  +R Y VR  G+V     + L  G+ ++        +      G
Sbjct: 139 TNDGELAHRLMHPSSGIIREYAVRVLGEVTPQIASQLTAGVELEDGVAKFDDIKEGGGIG 198

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
            N W  V ++EG+ RE++++FE    KV+RLIR  YG   L   L  G   E+    + +
Sbjct: 199 VNKWYHVTIKEGRKREVRRMFESQTLKVSRLIRTRYGTVILPKELRTGRFIELDASDIGK 258

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +    L + Q              +++   I + P     +++   + +   +++K  T
Sbjct: 259 LVDSVGLRQRQGT------GLNHATKEKQARIHKKPLKSREIRRQKHEAHERREERKKHT 312

Query: 304 PVHR 307
           P HR
Sbjct: 313 PKHR 316


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 97/307 (31%), Positives = 150/307 (48%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +       + R   ++E P    R      Q+    K+    T   
Sbjct: 241 SVELKPRQGTGLFGM------AKRRTERMTEKPMAARRGGYLRQQRRDDEKEAPANTSNQ 294

Query: 307 RRNLASN 313
           R++   N
Sbjct: 295 RKSTGFN 301


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 79/233 (33%), Positives = 121/233 (51%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SRR V+R++  ++V+VNG  +   ++NV      + V GVP+   + 
Sbjct: 1   MRLDKLLFETGFGSRRTVKRLLKSKQVQVNGQTIMVDSLNVDPQLQEVTVAGVPIDY-QP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+V+  SD     TV D +        +  VGRLD +TEGLLLLTN+G L
Sbjct: 60  HVYYMLHKPAGVVSAVSDA-VNQTVIDLIEPSQRVPGLFPVGRLDKDTEGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L +P  +  + Y V  + +V  D       GIV  G +     Q+T+ +Q  + + V
Sbjct: 119 GYQLLIPKKEVTKCYEVVVNERVTDDDQLAFTAGIVFDGGVICKPAQLTILSQSDTESRV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EGK  ++KK+F     KV  L R+S GP QL  TL  GS R +  + L
Sbjct: 179 LLEISEGKFHQVKKMFLSVGKKVIYLKRLSMGPLQLDKTLSLGSYRPLHAEEL 231


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 117/232 (50%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  G  SR+EV R I  +R+ VNG L E+    V  +D I +DG  ++  E+ 
Sbjct: 1   MRINKLLSNYGYCSRKEVSRWIEDKRIIVNGKLCEQ-GQWVEESDEILLDGEKIKPKEK- 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP G+V T S  +  + + D L +    V  VGRLD +++GL+L+TNDG LA  
Sbjct: 59  VYIALNKPPGIVCT-SAREIDNNIIDFL-NYKDYVFPVGRLDKDSQGLILMTNDGELANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +    +   + Y V      D+  +  +  G+ I G      ++    ++      ++ L
Sbjct: 117 ILSSDSYHEKEYIVTIDRDFDESFIEGMSNGVEILGTITRPCKL----RRIDKNIFSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++ + F + V +L RI         +  G  + ++K+++ + +
Sbjct: 173 TQGLNRQIRRMTKAFGYNVIKLERIRIMNIMSNDIELGQWKFINKEVISKLI 224


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 103/228 (45%), Gaps = 4/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R E   +I    V VNG  +  A+  V   + I +DG  L     +
Sbjct: 1   MRLDKFLCKSTELTRIEATALIVAGEVLVNGQTVTSASTQVHENNRITLDGQVLT-PRAS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKP+  ++++ D D  S +          +   GRLD +T GL+L+T+DG  +  
Sbjct: 60  RYIMMHKPLDTLSSNVDGDYPSVMNCLDVDKVCDLHIAGRLDADTTGLVLVTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     +VYRV     ++ D       G+ +QG     +   L+    S   V + +
Sbjct: 120 IINPKYHCEKVYRVSLRDPINDDVAGKFACGVQLQGEASLTLPAKLEV--VSPTEVLLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EG+  ++K++F     +VN L R   G  +L  +  G  R ++ + +
Sbjct: 178 TEGRYHQVKRMFAAVGNRVNGLHRQQVGDIKL-DIGLGQWRYLTTEEI 224


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 103/353 (29%), Positives = 163/353 (46%), Gaps = 14/353 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E MI   RV ++G   +           I +DG  +   E 
Sbjct: 2   SEKLQKVLARAGLGSRRELETMIQAGRVSIDGQKAKLGDRLENVDARIRIDGHVVSVKES 61

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           T    R+  YHKP G + T  DP+GR TVFD LP I  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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LRE 243
              V + EG+NRE++++++     V+RL R+ YG   L   L  G   E+  K    LR+
Sbjct: 182 TFYVVINEGRNREVRRLWDSQGVTVSRLKRVRYGDIFLEKALPRGGWMELELKEVNYLRD 241

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDR-PNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +     +E+ +++D            +    +    +  T  +  +  + G + +K + 
Sbjct: 242 MVELPHEKESLLDVDKESRKRAKSKSQKIRRAVKRHDERTTEDRNTAGGRRGRNNKKPVG 301

Query: 303 TPVHRRNLASNVWMA----KGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             +      +++  A    KG      S +G +    + SP+  + +S  R  
Sbjct: 302 GSLPTAKKPTSIESAKPAGKGKPKGKPSANGAKPIRTKFSPNGKAPKSAPRQR 354


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 131/247 (53%), Gaps = 10/247 (4%)

Query: 8   QENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            E   P +R+ KV+A+AGI SRRE+E  I+  RV VNG +     + V   D ++VDG  
Sbjct: 5   AETSQPGERLQKVLAQAGIGSRREMEEWISAGRVTVNGTVAT-LGMRVAEGDKVQVDGRN 63

Query: 67  LR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEG 120
           +R     +    R+ LYHK  G + +  DP  R++VFD LP     + I++GRLD NT G
Sbjct: 64  VRLQLQTEQTMPRILLYHKQEGEIVSRDDPGERASVFDALPKLRGQKWIAIGRLDFNTSG 123

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTL 179
           LL+ T  G LA  L  P  +  R Y VR  GQ+  + +  + K+GI +        Q++ 
Sbjct: 124 LLIFTTSGELANRLMHPRFEVEREYAVRVQGQMTPEHMRQVTKEGIELDDGVVRFEQLSD 183

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
           +  +G N W  + L+EG+NR +++ FE     V+RL+R+ +G   L   +  G   E+  
Sbjct: 184 EGGEGFNHWYRLVLKEGRNRVVRRTFEALGLPVSRLMRVRFGIIGLPPRIKRGMMAELGD 243

Query: 239 KILREQL 245
             +R  L
Sbjct: 244 NEVRSIL 250


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 103/351 (29%), Positives = 162/351 (46%), Gaps = 14/351 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG  SRRE+E MI   RV V+G++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDLSVSVRIDGHNIELISS 61

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T  DP+GR TVFD LP + + 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+  K + E   
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYLTKDMPRGGWSELELKEVNELRA 241

Query: 247 P-HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT-------RMKKNSSQKNGLSKQ 298
              L  E +  L       +  +R     +    +          R + N  +  G S+ 
Sbjct: 242 TVELPPETETALTVEGQKRKKGIRQIRRAVRRHEERVETGGGRGRRGRGNDRRNPGSSRN 301

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            ++    + R        AKG  +    D+G+ + + R   S   + S +R
Sbjct: 302 AEVEAQSNERRGNGRSQPAKGRDNRDSRDNGKPQSSGRPQTSGKPQSSGKR 352


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 97/307 (31%), Positives = 151/307 (49%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +       + R + ++E P    R      Q+    K+    T   
Sbjct: 241 SVELKPRQGTGLFGM------AKRRTDRMTEKPMAARRGGYLRQQRRDDEKEAPTNTGNQ 294

Query: 307 RRNLASN 313
           R++   N
Sbjct: 295 RKSTGFN 301


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 114/231 (49%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    I SR +V+++I  +R+ ++  +      NV      I VDG  L+ A+ 
Sbjct: 1   MRLDKLLETCQIGSRGQVKKLINAKRITIDDKVAIDGRQNVDPGLQRIGVDGNILQ-AKG 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+   D +   TV D L     F  +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HHYFILNKPRGVVSALKDKEH-PTVIDCLIEADRFPNLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P+    + Y V  +G +D D  +  + G+V   G       V + +     +  
Sbjct: 119 GFRMLHPNHHVDKSYYVVVNGFLDDDLPSFFRAGVVFFDGTVCKAAAVEILSAGEKQSVA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V L EGK  +IKK+F  +  KV  L R+++  F LG L  G  R ++ + 
Sbjct: 179 KVTLSEGKFHQIKKMFLAYGVKVIYLKRMTFAEFTLGNLAEGEYRTLTDQE 229


>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 =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 61/240 (25%), Positives = 109/240 (45%), Gaps = 11/240 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
             R+ K ++     +R +V+  I + RV  NG++++     V    D I +DG P+   E
Sbjct: 4   TIRLDKYLSDMTSETRSKVKEYIRKGRVTANGVVIKSPETKVDTDNDEICIDGKPVGYVE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------IFSRVISVGRLDINTEGLLLLT 125
               ++ +KP G++T+ ++     TV D           F+ +  VGRLD +TEGLLL+T
Sbjct: 64  -YYYYMMNKPQGVITS-TEKGRTKTVMDVFKETGTGCPRFNELSPVGRLDKDTEGLLLIT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   L  P     +VY       V    + +   G+ +        ++ +      
Sbjct: 122 NDGELNHKLLSPKNHVDKVYYAELKSPVKVSDIEIFAGGLDLGDFICKPARLEI-CDDVK 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
                + + EGK  ++K++FE    +V  L R+S G  +L   L  G  R ++++ + + 
Sbjct: 181 KFAAKITISEGKFHQVKRMFEAVENEVIYLKRLSMGSLKLDDNLELGEVRALTEEEIGQL 240


>gi|313665476|ref|YP_004047347.1| pseudouridylate synthase [Mycoplasma leachii PG50]
 gi|312949302|gb|ADR23898.1| pseudouridylate synthase [Mycoplasma leachii PG50]
          Length = 252

 Score =  243 bits (622), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 122/242 (50%), Gaps = 7/242 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + +R+ KVI+  G  SRR  E++I + R+KVN  ++ +  V +     I +D   +   
Sbjct: 1   MSLERLQKVISSRGYCSRRTAEKLILENRIKVNNQIINKLGVKIDPKAEIIIDNKLVTSD 60

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GLL++TNDG
Sbjct: 61  SNNQKYYYLFYKPRLVLTTMYDPKKRKTVADYFKDLNHRVYPVGRLDYDVSGLLIMTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKG 184
            L+  +  P  ++L+ Y+    GQV + ++N L KG+ I        Y    V  D  K 
Sbjct: 121 ELSNFIMHPKYEFLKTYQGLCQGQVSKQQVNQLIKGVYIDNNYLTKAYSAKLVKYDKLK- 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + V + + EGK   +KK+FE    ++ +L R      ++  L  G  RE+    +++ 
Sbjct: 180 NVSIVELTINEGKKHHVKKMFESIQAQLLKLKRTKIEFLEIDNLKPGQYRELKIHEIKKL 239

Query: 245 LG 246
            G
Sbjct: 240 YG 241


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 116/230 (50%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +GI SRRE +++I +  VKVNGI++      V   D ++ +   L   E++
Sbjct: 329 IRLNKYISNSGICSRREADQLIIEGTVKVNGIVVTELGYKVKPGDSVKYNNKVLN-PEKS 387

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP   +TT  D + R TV   + +    R+  VGRLD NT GLLL TNDG LA+
Sbjct: 388 VYVLLNKPKDFITTMEDENDRKTVMQLVANATKERIYPVGRLDRNTTGLLLFTNDGELAQ 447

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  PS +  ++Y V     +  +  + +  G I +        +  + +   S   + +
Sbjct: 448 KLTHPSNKVKKIYEVELDKPITAEDFDKIVDGKIHLFDGPVKVDEAAIIS--PSKKIIGI 505

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG+NR ++++FE   + V +L R+ Y       +  GS R ++   +
Sbjct: 506 EIHEGRNRIVRRIFESLGYDVLKLDRVMYAGLTKKNIPRGSWRYLTATEV 555


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   LY KP G+V+   D + + TV D +        +  +GRLD +TEGLL++TN+G L
Sbjct: 61  SYYLLY-KPSGVVSAVRDSEHK-TVIDLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +  
Sbjct: 119 GYRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 179 RITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D  P      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L LP ++  +VY V     +DQ  ++    G+  +      +   L+      A   + 
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPIGPRCA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 178 LHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 115/242 (47%), Gaps = 9/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A AG  +R+ V+ ++ + RV+VNG  +++    +    D I+VDG  +   E 
Sbjct: 2   MRLDKFLAHAGFGTRKAVKELVRKGRVEVNGQRVKKDDQKIDERQDQIQVDGRIVTY-ET 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KP G+V+   D     TV D L +  S +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 61  EVYIMLNKPQGVVSATEDSRY-ETVLDCLETNRSDLFPVGRLDIDTEGLLLITNDGALAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     + Y V      D      ++ GI I          +    ++ +   + +
Sbjct: 120 DLLSPKKHVDKTYEVHLERPWDPQYEAAIQMGIRISDEEVCLPATL----RQTAEHIILL 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|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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 103/351 (29%), Positives = 161/351 (45%), Gaps = 14/351 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+ARAG  SRRE+E MI   RV V+G++ +        +  + +DG  +     
Sbjct: 2   SEKLQKVLARAGQGSRREIELMIQNGRVSVDGVVAKLGDRLEDLSVSVRIDGHNIELISS 61

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
             E  R+  Y+KP G + T  DP+GR TVFD LP + + 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+  K + E   
Sbjct: 182 TFYVVITEGRNREVRRLWDSQGVTVSRLKRVRYGDVYLTKDMPRGGWSELELKEVNELRA 241

Query: 247 P-HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT-------RMKKNSSQKNGLSKQ 298
              L  E +  L       +  +R     +    +          R + N  +  G S+ 
Sbjct: 242 TVELPPETETALTVEGQKRKKGIRQIRRAVRRHEERVETGAARGRRGRGNDRRNPGSSRN 301

Query: 299 KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRR 349
            ++    + R        AKG  +    D+G+ +   R   S   + S +R
Sbjct: 302 AEVEAQSNERRGNGRSQPAKGRDNRDSRDNGKPQSAGRPQTSGKPQSSGKR 352


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 97/307 (31%), Positives = 150/307 (48%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +       + R   ++E P    R      Q+    K+    T   
Sbjct: 241 SVELKPRQGTGLFGM------AKRRTERMTEKPMAARRGGYLRQQRRDDEKEAPANTGNQ 294

Query: 307 RRNLASN 313
           R++   N
Sbjct: 295 RKSTGFN 301


>gi|91200876|emb|CAJ73931.1| conserved hypothetical protein [Candidatus Kuenenia
           stuttgartiensis]
          Length = 260

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 123/259 (47%), Gaps = 2/259 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ KV+A AGI SRRE E +I   RV V+G  +      V +    I  DG+P+R  E 
Sbjct: 3   ERLQKVLASAGIGSRRECENVILAGRVTVDGERVTALGATVDAGKSVIYCDGMPIR-PEA 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP   + T+ D   R    D + ++  R+ ++GRLD  +EGL+++TNDG L+ 
Sbjct: 62  KIYYLLNKPKDCLCTNYDELNRLRAIDIIKNVKQRLYTIGRLDKQSEGLIIITNDGELSN 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|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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 135/237 (56%), Gaps = 7/237 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLR 68
             P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+ V G  + L+
Sbjct: 1   MEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHVTVKGSIIKLK 59

Query: 69  KAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
            A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT 
Sbjct: 60  WADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTT 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGS 185
            G L +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+
Sbjct: 120 SGELVQRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGA 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           N W  V ++EG+NRE++++FE     V+RL+RI +GP  L   L  G   E++   +
Sbjct: 180 NKWYNVVIKEGRNREVRRIFESQGLTVSRLVRIGFGPIGLPNRLKRGQFYELNPAEV 236


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 72/240 (30%), Positives = 123/240 (51%), Gaps = 7/240 (2%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + ++ +KP G+V+  SD +   TV D +       R+  VGRLD +TEGLLL+TN+G L
Sbjct: 61  -KYFILNKPAGVVSAVSDKEH-QTVIDLIAEADRVPRLYPVGRLDRDTEGLLLITNNGLL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G + +D     + G+            + +       +  
Sbjct: 119 GFRMLHPKYHVTKTYYVEVNGLLAEDAPAFFENGVTFDDGTVCKPANLEIIEASSEKSSA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + + EGK  ++KK+F  +  KV  L R+++G F+LG L  G  RE++ K  +E L  +L
Sbjct: 179 YISIAEGKFHQVKKMFLAYGVKVIYLKRMTFGDFELGDLPRGQYRELNTKE-KEILKNYL 237


>gi|323167301|gb|EFZ53010.1| ribosomal large subunit pseudouridine synthase F [Shigella sonnei
           53G]
          Length = 291

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 70/297 (23%), Positives = 125/297 (42%), Gaps = 12/297 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF-- 233

Query: 248 HLLEEAQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            L+E +            +T    RP +  E        ++ +         K+   
Sbjct: 234 KLIENSSSEAKPKAKAKPKTAGIKRPVVKMEKRRKKAVARRPTVSVLPRRGVKRRGA 290


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 117/231 (50%), Gaps = 3/231 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K IA +GI SRRE + +I Q  V+VNG ++      V  TD +  DG  +   E
Sbjct: 137 ETIRLNKYIANSGICSRREADELITQGLVQVNGAVVTEMGYQVQKTDKVIFDGQGIT-PE 195

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGL 130
           +    L +KP G ++T  D   R TV D + +    RV  VGRLD +T G++LLTNDG +
Sbjct: 196 KPVYVLLNKPKGYISTTKDEKARKTVMDLVANASPYRVFPVGRLDRSTTGVILLTNDGHM 255

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
            + L  PS    ++Y V    ++D+  LN + +G+ ++        ++    K  N  V 
Sbjct: 256 TKKLTHPSFNMKKIYHVTLDRKLDRADLNAIAEGVRLEEGVAEVDSISYIEGKPKN-EVG 314

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + +  G NR ++++F+   ++V  L R+ +       +  G  R +++  +
Sbjct: 315 IEIHIGWNRVVRRIFQRLGYEVEALDRVMFAGLTKKNIKRGHWRILTELEV 365


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 119/241 (49%), Gaps = 16/241 (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 +G      D D +S++   LP+   R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  GVEALSYWLFNKAVGTDCRLLDAD-KSSLLHLLPAT-PRLYPVGRLDKDSRGLLLLTNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQK 183
            L   L  PS    + Y V+     +   +  +  G+       + +     QVT    +
Sbjct: 119 ELTHKLMHPSFAHSKTYHVQLDSPFNDAFIEQMACGVQYKEVRNKEVRTLPCQVT----R 174

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            S+    + L +G NR+I+++     +KV  L R++     LG+L  G  R +S + +  
Sbjct: 175 LSDVSFEIVLTQGLNRQIRRMSNALGYKVIDLQRVALMTLTLGSLAEGEMRPLSPEEVTA 234

Query: 244 Q 244
            
Sbjct: 235 L 235


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 87/286 (30%), Positives = 136/286 (47%), Gaps = 6/286 (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+GR TV D + S  +R+  VGRLD ++EGLLLLT+DG L  
Sbjct: 62  LHYVLLHKPSSVMTTLHDPEGRQTVADLVKSH-NRLFPVGRLDYDSEGLLLLTDDGDLTF 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 ++   + ++L  H    
Sbjct: 181 IHEGRNRQIRRVAEALGLEVRRLIRLREGPLTLGELQAGQWRALTPTEI-DRLRMHG--- 236

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            Q     P+   E     +P       D   ++ +  +      ++
Sbjct: 237 KQSKAWTPVRPQENAEGGKPRRQVRRIDRSGQLVERRADVEPRLQR 282


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 141/251 (56%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 324 ELNPAEVANIL 334


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 62/218 (28%), Positives = 99/218 (45%), Gaps = 3/218 (1%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGL 84
           + SRRE +  I    V VNG ++      +   D ++     +   ER    L +KP   
Sbjct: 1   MCSRREADEFITAGVVSVNGEVVTELGTKIKRGDEVKFHDQTVS-IERKIYVLLNKPKDT 59

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           VTT  DP  R TV D +      R+  VGRLD NT G+LLLTNDG LA  L  P     +
Sbjct: 60  VTTSDDPQARRTVMDLVKGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKYLKKK 119

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +Y V     + +  +  +  GI +         ++   +   +  V + +  GKNR +++
Sbjct: 120 IYHVHLDKNLTKADMEQIAAGIQLDDGEIQADAISYTDEFKKD-EVGIEIHSGKNRIVRR 178

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +FE   +KV +L R+ +       L  G  R +++  +
Sbjct: 179 IFESLGYKVVKLDRVFFAGLTKKGLRRGEWRYLTEPEV 216


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 114/231 (49%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+    A  N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNGEIAVNGMSDILAKDNIDENSDTIEYNGERLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDFKED-TVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHKLLSPKNHIDKVYYVEIEKNILDEDILKLEQGVDIGNYITQPAKV----EKISDNKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KV  L R S+G   L  L  G  +EVS + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVCYLRRESFGKLTLNDLTLGEVKEVSLEDI 225


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 114/227 (50%), 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  D   R ++   L +   RV   GRLD ++ GLLL+TN+G + 
Sbjct: 78  EMIVLAVNKPKGIVCT-EDQRERDSIVRFL-NYPVRVTYAGRLDKDSRGLLLMTNNGDII 135

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   + +  + Y+V    ++ +  +  + +G+ I         V     K      ++
Sbjct: 136 NQMMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPILDTVTRPCTVK----KIGKYTFSI 191

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++ 
Sbjct: 192 ILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLTD 238


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 81/236 (34%), Positives = 129/236 (54%), Gaps = 7/236 (2%)

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   SR + VGRLD+NT GLLL TN+G L
Sbjct: 63  QEIKVIILNKQAGVICSNLDDKGRKSVYSLLPKE-SRWVMVGRLDLNTSGLLLFTNNGDL 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-GTLLAGSTREVSKKILREQL 245
           V L+EG+  E+++++E   +KV+RLIRI +G  +L   L A     +  + ++  L
Sbjct: 182 VVLKEGRKHEVRRLWEELGFKVSRLIRIRFGEIRLPNNLKANQYDYLKPRQVKLLL 237


>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 =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 57/234 (24%), Positives = 108/234 (46%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +RRE  +++  + ++V+G ++  A+  V   + +E +G PL+  +  
Sbjct: 1   MRLDKFLGTTLGITRREASKLLRDKMIEVDGEIVRSASFAVSDDNDVEFNGRPLKL-QGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G V +H D D   TVF     +    + V GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYFMLNKPEGFVCSHVD-DFNPTVFVLFDEVSPEKMHVAGRLDGDTTGLVLVTDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     + +D +   + G+ ++          L+      A +   
Sbjct: 119 RITSPRHLCSKTYFVEAADPITEDYIKQFEAGVQLRSEKELTRPAKLEILSEREALL--T 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + EGK  ++K++F     +V  L R   G  +L   L  G  R ++ + +   L
Sbjct: 177 ISEGKYHQVKRMFAAMGNRVVGLHRERIGTVELDEDLAPGEYRLLTAEEIASFL 230


>gi|308389478|gb|ADO31798.1| putative pseudouridine synthase [Neisseria meningitidis alpha710]
          Length = 349

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 85/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>gi|239815173|ref|YP_002944083.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239801750|gb|ACS18817.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 604

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 89/305 (29%), Positives = 142/305 (46%), Gaps = 11/305 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E +I Q R+ VN          +   D ++++
Sbjct: 188 KRVLLPEADSPKLHKVLAQAGLGSRLEMEALILQGRISVNNEPA-HIGQRIQYGDQVKIN 246

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 367 GGGEGSNHWYRVTISEGRNREVRRLFESVGHAVSRLIRIRYGAMVLPRGLKRGAWMELDE 426

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + +       L + +      P        ++         +   R  +N+       + 
Sbjct: 427 RDISA-----LFQASGGGAPRPPQQQRGPGQEGAGGGRNGRNKKRRGNRNAGGGQQQPRD 481

Query: 299 KKLAT 303
            +   
Sbjct: 482 MRDDG 486


>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 =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 116/231 (50%), Gaps = 3/231 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           +++ +++ G+ SR E  R IA  RV V+G ++      ++     + +DG PL  +ER  
Sbjct: 34  LARTLSKLGLCSRTEAVRWIAAGRVAVDGRIVTDPEFPILRGRHRLALDGAPLSASERL- 92

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  D  GR TV+          +  VGRLD  +EGLLL TND   A  
Sbjct: 93  YLMLNKPRGLVTTAQDERGRETVYRCFDGAGLPWLAPVGRLDKASEGLLLFTNDPQWAAR 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P T   + Y V+     D   L  ++ G++  G      QV L  Q   +AW+ + L
Sbjct: 153 VTDPGTGPDKTYHVQVDVLPDAALLQRMRAGVMADGEALCAKQVRLLRQGERHAWLEIVL 212

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+NR+I+++   F   V RL+R++ G   LG L  G+ R +S   +   
Sbjct: 213 DEGRNRQIRRLLAAFGVDVVRLVRVAIGTLVLGELGKGAWRTLSAAEVSAL 263


>gi|309378850|emb|CBX22555.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 349

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 86/251 (34%), Positives = 141/251 (56%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 104/345 (30%), Positives = 160/345 (46%), Gaps = 15/345 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
            +P+R+ KV+A AGIASRR+ E +IA  RV VNG ++      V    D + VDG PL+ 
Sbjct: 1   MSPERLQKVLASAGIASRRDCEALIAAGRVMVNGRVVVVPGTRVDLDHDEVLVDGQPLQM 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             +    + HKP G+V+T  D  GR TV D + ++ +RV  VGRLD+++EGL+LLT+DG 
Sbjct: 61  PTKRTYIMLHKPAGVVSTAEDTHGRPTVLDLV-NVPARVFPVGRLDMDSEGLILLTDDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           LA  L  PS +  + YRV     +  + L   + G+++ G       V L        WV
Sbjct: 120 LAYALTHPSFEVEKEYRVLLDRALTPEALRSWRNGVLLDGEMTAPAWVELIGTAPEGVWV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + LREG+ R+I+ V +   ++V RLIR+  G   LG L   + R ++ + +        
Sbjct: 180 RIVLREGRKRQIRAVAKLLGYEVRRLIRVREGDLVLGDLPPRAWRHLTDEEVAALRTHIA 239

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRN 309
                V     +  S    RD        PD  +R  ++   +           P  RR+
Sbjct: 240 KRRPPVERSPGVAPSSVRNRDDERPSYRTPDIRSRGDRDDRGREF------EREPRARRD 293

Query: 310 LASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSAKK 354
                W        F  +   R ++  R   F  +   RR S ++
Sbjct: 294 SGERGWE-------FEREPRARRDSGERGREFEREPRARRDSGER 331


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 101/232 (43%), Gaps = 6/232 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I  Q   VNG ++      V   D +     PL    +
Sbjct: 4   PCRLDKFISHLAELPRSKARAAIKSQAATVNGEVITAFDFQVSQQDDVLFYDEPLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R ++ +KP+G V  +SD   + TVFD L     S     GRLDI+T GL+L+TNDG  +
Sbjct: 64  -RYFMLNKPVGYVCANSDELHK-TVFDLLDEPNLSDFHVAGRLDIDTTGLVLITNDGDWS 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     +    L  L+ G+ +      D+      ++  N  + +
Sbjct: 122 HKITSPKKNKFKTYLVETQEPITDAALQQLRDGVQLHNE--KDLTRPAIAERLGNYGLRL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++    + KV  L R      +LG  L AG  R ++   ++
Sbjct: 180 SISEGKYHQVKRMLAAVDNKVVELHREQIAGIKLGEDLAAGEYRPLTAAEIK 231


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   LY KP G+V+   D + + TV D +        +  +GRLD +TEGLL++TN+G L
Sbjct: 61  SYYLLY-KPSGVVSAVRDSEHK-TVIDLISEKDRVEGLYPIGRLDRDTEGLLIITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +  
Sbjct: 119 GYRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 179 RITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 119/242 (49%), Gaps = 9/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++++ VN        V V    D I+ +G  +   E+
Sbjct: 1   MRLDKFLVECGLGSRTQVKLILKKKQISVNSNSETSPKVQVDEYRDEIKYNGTLVSY-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+++   DP  + TV D L        V  VGRLDI+T GLLL+TN+G L
Sbjct: 60  FVYYMLHKPKGVISATDDPSHK-TVLDLLDKTARDKAVFPVGRLDIDTTGLLLITNNGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  +  P     + Y  +  G + +D +    KGI+++         ++    Q    + 
Sbjct: 119 AHKMLSPKKHVDKCYEAKISGIMTEDDILAFDKGIILKDFTCLPALLEIVEVNQVKKQSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGP 247
           V + ++EGK  ++K++      +V  L R+S G  QL   L +G  R ++ K + E+L  
Sbjct: 179 VKITIKEGKFHQVKRMVAACGKEVLELKRLSMGNLQLDKQLESGQWRRLTIKEI-EKLEK 237

Query: 248 HL 249
           H+
Sbjct: 238 HM 239


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 94/312 (30%), Positives = 149/312 (47%), Gaps = 7/312 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV +NG + +     +  TD + +DG  ++    
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSINGKIAQ-VGERIEPTDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 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 RRNLASNVWMAK 318
           R+ +  N    K
Sbjct: 301 RKTIGLNKGFKK 312


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 117/242 (48%), Gaps = 14/242 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R++K IA  G  SRRE +R+IA +RV VNG      AV V   D + VDG PLR      
Sbjct: 4   RLNKHIADTGFCSRREADRLIAARRVTVNGHPAGTGAV-VGEEDQVLVDGQPLRARVARK 62

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A R      +KP+G+  T ++   +  + D +     R+  +GRLD  +EGL+L+T++
Sbjct: 63  PGARRHVYIALNKPVGVTCT-TETSVKGNIVDFV-GHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  V  + L  + +G+ I        +    T + +  
Sbjct: 121 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRIHDQMTLPCK----TSRIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L  
Sbjct: 177 GFRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLLPK 236

Query: 248 HL 249
            L
Sbjct: 237 QL 238


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 101/231 (43%), Gaps = 6/231 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I  +   +R   ++ + +  +  +G++++ +   V+    + +DG P+     
Sbjct: 6   PVRLDKFICESTSLTRSLAKKALHRGEITCDGVVVKDSGFKVLEGMQVCLDGEPISLV-G 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  + +KP+  + +  D +   +V   L       +   GRLD +T GL+L+T+DG  +
Sbjct: 65  ERYLMLNKPVDTICSTID-EAYPSVLSLLDIEKPETLHIAGRLDADTTGLVLITSDGQWS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     VD+  + +   G+ ++          L+  +     V +
Sbjct: 124 HRITSPKKDCGKRYLVALADPVDESLVGIFAAGVELRNEDGLTKPAVLEIIEP--QLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 182 TITEGKYHQVKRMFAAVGNHVVGLHRESIGRIELDSDLAPGEWRYLTSEEI 232


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 116/242 (47%), Gaps = 8/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    + SR +V+ ++ ++ V+VNG +       +    D + + G  L+  E 
Sbjct: 1   MRLDKFLVDCTVGSRSQVKAILKKKEVQVNGQIESSPKRQIDEKKDRVTLAGQLLKH-ET 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D     TV D L  P+   +V  VGRLDI+T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPQGVVSATEDSQH-QTVLDLLDEPAHQKQVFPVGRLDIDTTGLLLLTNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
           A  +  P     +VY+ +  G +  + +    +GI ++       Q+ +     +     
Sbjct: 119 AHAMLSPKKHVAKVYQAKVEGLMTDEDVVAFGQGIRLKDFVCRPAQLQILESDQAQGSCL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           V + + EGK  ++K++      KV  L RIS GP  L   L  G  R +S + L +  G 
Sbjct: 179 VQIEIAEGKFHQVKRMVASRGKKVLELKRISMGPLHLPHDLSEGHYRRLSAQELADLSGF 238

Query: 248 HL 249
           H+
Sbjct: 239 HV 240


>gi|295100310|emb|CBK97855.1| ribosomal small subunit pseudouridine synthase A [Faecalibacterium
           prausnitzii L2-6]
          Length = 234

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 107/232 (46%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + ++A+ RV VNG +  +    +   D + VDG  L   +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKALLAKGRVTVNGAVCRKGDTQLKEADAVAVDGKALAYRQ-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+  +D    +TV D +   + R  +   GRLD  + G +LLT+DGG A
Sbjct: 60  VYLMLNKPEGVVSASADKRD-TTVVDLVGDAYPRRELFPAGRLDKTSTGFVLLTDDGGFA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V     + ++       G+ +  G      +V+  T  G    V 
Sbjct: 119 HDILAPKRHVSKTYTVVIDTPLTEEMKAGFAAGVTLADGTALSPAEVSALTPDGLT--VR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V LR+G   +IK++F  +   VN L R + G   L  +L AG  RE++   +
Sbjct: 177 VLLRQGVYHQIKRMFGVYGAGVNALHRDAIGGLALDESLAAGQWRELTADEV 228


>gi|229916458|ref|YP_002885104.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
 gi|229467887|gb|ACQ69659.1| pseudouridine synthase [Exiguobacterium sp. AT1b]
          Length = 237

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 117/234 (50%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A  G  SR++V+ ++ Q  V+V+  L++ A  +V  + + + V G  +     
Sbjct: 1   MRIDKLLANMGYGSRKDVKILLKQGAVRVDEALVKDAKRHVDPSSEKVTVFGEVVEYR-P 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+++   D    +TV + + S ++   +  VGRLD +T GLLL+TNDG  
Sbjct: 60  YIYFMMNKPEGVISATED-QVETTVIELIDSEYAHYDLFPVGRLDKDTTGLLLITNDGAF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY     G++  + +     G+ +  G      ++ + ++ G  + +
Sbjct: 119 NHALMSPRKHVDKVYIAEVDGEMTVEDIKTFANGVELEDGYTTKPARLEILSRSGRRSVI 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKILR 242
            + L EGK  ++K++       V RL R+  G      TL  G+ RE++++ ++
Sbjct: 179 RLTLSEGKYHQVKRMVAAVGKHVERLERVQIGELELDETLELGAYRELTEEEVQ 232


>gi|291550320|emb|CBL26582.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           torques L2-14]
          Length = 241

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 121/240 (50%), Gaps = 7/240 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +A  GI +R EV++ I + +V+VN   ++R  + +    DH+   G  +  AE  
Sbjct: 4   RLDKYLADMGIGTRTEVKKAITKGQVRVNEETVKRPEIKIDTEKDHVFYQGQMVAYAE-Y 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D    STV D +     + +  VGRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYYMLNKPAGVVSATED-KNDSTVLDLIDEKQRKDLFPVGRLDKDTEGLLLITNDGELAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTV 191
            L  P     +VY  R  G+V ++ +    +G+ I G     +   L+  ++   + + +
Sbjct: 122 QLLSPKKHVDKVYFARIDGKVTEEDVRRFAEGLEI-GEEKPTLPAHLEILKREEISEIRL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
            +REGK  ++K++F     +V  L R+  G   L   L  G  RE++ + L       LL
Sbjct: 181 TIREGKFHQVKRMFHAVGKEVIYLKRLQMGSLVLDPRLALGEYRELTGQELEALRDRSLL 240


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 97/307 (31%), Positives = 150/307 (48%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRIAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQGLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +       + R   ++E P    R      Q+    K+    T   
Sbjct: 241 SVELKPRQGTGLFGM------AKRRTERMTEKPMAARRGGYLRQQRRDDEKEAPANTGNQ 294

Query: 307 RRNLASN 313
           R++   N
Sbjct: 295 RKSTGFN 301


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 13/242 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
                R++K IA  G  SRRE +R+IA++RV VNG      AV V   D + VDG PL+ 
Sbjct: 2   TEEAVRLNKHIAGTGFCSRREADRLIAERRVTVNGQPAGVGAV-VGEGDEVRVDGQPLKL 60

Query: 69  -----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                   R      +KP+G+  T ++   +  + D +     R+  +GRLD ++EGL+L
Sbjct: 61  RAARPGKRRHVYIALNKPVGITCT-TESSVKGNIVDFV-GHEQRIFPIGRLDKDSEGLIL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LT++G +   +        + Y V  +  V  + L  + +G+ I        + +   + 
Sbjct: 119 LTSNGDIVNEILRAENGHQKEYLVAVNKPVTDEFLRGMSRGVRIHNQMTLPCRASRIAKF 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           G      + L++G NR+I+ +   F+++V +L R+     +LGTL  G  R ++ + LR 
Sbjct: 179 G----FRIVLQQGLNRQIRLMAAAFDYRVTQLRRVRIDNIRLGTLKPGQWRNLTPEELRG 234

Query: 244 QL 245
            L
Sbjct: 235 LL 236


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 97/230 (42%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  V  +G +++ ++  V +   I +DG  +      
Sbjct: 1   MRLDKFICESTELTRSFAKKALHRGDVTCDGEVVKSSSFKVKAGQIICLDGKVISVV-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   +    D     TV D L       +   GRLDI+T GL+L+T DG  + 
Sbjct: 60  RFLMLNKPADTICATFDI-VHPTVIDLLDIEKADTLHIAGRLDIDTTGLVLITTDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V    ++D   +    +G+ ++          L+     +A   + 
Sbjct: 119 KITSPKKDCGKCYLVTLTDELDASLVETFAQGVELRNEDGLTKPAVLEIIDSHHA--RLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R S G   L   L  G  R ++ + +
Sbjct: 177 ITEGKYHQVKRMFAAVGNKVVGLHRESVGKIVLDDDLAPGEWRFLTDEEI 226


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 86/242 (35%), Positives = 128/242 (52%), Gaps = 8/242 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAE 71
            +R+ K +ARAG+ASRR  E +I   RV VNG+  +     V   D + VDG P+ ++  
Sbjct: 2   TERLQKRLARAGVASRRAAEALITSGRVTVNGVTAQ-LGQTVTEADEVLVDGQPIAQRPT 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +  +KP G VTT  D  GR TV D +P++   +  VGRLD ++EGLLLLT DG L 
Sbjct: 61  QHVTFALYKPRGFVTTARDELGRRTVLDAMPNV-PGLHPVGRLDRDSEGLLLLTTDGDLT 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VYR    GQ D+  L  L +G+ ++    G  +V         AW  V
Sbjct: 120 LTLTHPRYGHEKVYRAWTDGQPDEAALGRLARGMNLEDGPTGPAEVRAA---PDGAW--V 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            +REG+NR+++++ +   + V RL+R   G   L  L  G  RE+ ++ L+E L   L+ 
Sbjct: 175 TIREGRNRQVRRMLDAVGYPVTRLVRTRVGGLWLEDLGPGEYRELDERALQELLNVSLVP 234

Query: 252 EA 253
             
Sbjct: 235 HR 236


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 120/268 (44%), Positives = 156/268 (58%), Gaps = 1/268 (0%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
              +    +R++K +ARAG+ASRREVER+I    V VNG  L   A  V   + I+V   
Sbjct: 30  TPADWSEGERIAKYLARAGVASRREVERLIEAGEVTVNGQKLTSPAFKVTGREAIKVGRK 89

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            ++  + +RLW YHKP GL+TT +DP GR T+FD LP    R ++VGRLD+ TEGLLLLT
Sbjct: 90  VIQAPDASRLWRYHKPSGLITTTNDPAGRRTIFDELPKSLPRTVTVGRLDLTTEGLLLLT 149

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LAR LELP +   R YRVR  G V Q K++ L  GI ++G+ Y  ++   D + G+
Sbjct: 150 NDGELARFLELPKSALERTYRVRAKGTVTQLKIDELASGITVEGVKYQPIKAVFDREMGA 209

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           N+W+TV L EGKNRE++K  E     VNRLIR+SYGPF L  L  G   EV   +L   L
Sbjct: 210 NSWLTVTLTEGKNREVRKALESVGLTVNRLIRVSYGPFLLADLKPGQVDEVPPDLLETAL 269

Query: 246 GPHLLE-EAQVNLDAPIYSSETLVRDRP 272
                E +      AP   S    R   
Sbjct: 270 ALLGHEVDTAPEKPAPAAKSRLGRRGPS 297


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   LY KP G+V+   D + + TV D +        +  +GRLD +TEGLL++TN+G L
Sbjct: 61  SYYLLY-KPSGVVSAVRDSEHK-TVIDLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +  
Sbjct: 119 GYRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 179 RITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>gi|150376249|ref|YP_001312845.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
 gi|150030796|gb|ABR62912.1| pseudouridine synthase [Sinorhizobium medicae WSM419]
          Length = 260

 Score =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 76/229 (33%), Positives = 126/229 (55%), Gaps = 3/229 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  +R + E++IA+ RV V G  +   A  V    D I VDG  +  A+   
Sbjct: 25  LARALSKLGYCTRTQAEKLIAEGRVSVGGRRVTDLAHWVDIEADRIAVDGTVI-AAQPKV 83

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TVF  L ++    +  VGRLD  +EGLLL TND  LA+ 
Sbjct: 84  YLMLNKPRGLVTTRDDPEGRPTVFTCLETVDAPSLSPVGRLDKASEGLLLFTNDTVLAQR 143

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+  G + +     + +G+   G      +V L      N+W+ V L
Sbjct: 144 LLDPQTHLGKRYHVQVRGFLGEAMAARMVEGVTEGGELLRAARVALLRGGDRNSWIEVEL 203

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+++ +   ++  RL+R++ G  +LG L  G++R +++  +R
Sbjct: 204 TEGRNRQIRRMLDALGFECLRLLRVAIGEVRLGDLPKGASRPLAEAEIR 252


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 116/238 (48%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K ++ +G+ SR+EV++++ Q+ +KVNG L +     +   D  +   G  +   ++
Sbjct: 1   MRLDKFLSDSGLGSRKEVKQLLKQKCIKVNGTLAKDGKQQISQIDDYVTHAGEKIVY-QK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP  ++++  DP  R TV D L        +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  YFYYVLNKPKNVISSTKDPIER-TVVDLLAKKHYRKDIFPVGRLDKDTEGLLLLTNDGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN--A 187
           A  L  P     + Y     G V +  + L  KG  ++ G      ++ +D     +   
Sbjct: 119 AHQLLSPKKHVDKEYLAEIDGIVTEQDIKLFAKGFTLKNGEAVKPARLIIDQMDEGHQMT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            V + ++EGK  ++K+VFE    +V  L R+  G   L   L  G  R ++   L + 
Sbjct: 179 IVHLTIQEGKFHQVKRVFETIGKRVTYLKRLKMGSLSLDSDLPLGKYRPLTTVELAQL 236


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 85/251 (33%), Positives = 139/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>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 =  243 bits (620), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 72/240 (30%), Positives = 117/240 (48%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDG 64
             +++    R+ KV+++AG+ASRR  E +IA  RV+V+G ++      V   +  I VDG
Sbjct: 2   TSEQHPDGIRLQKVLSQAGVASRRAAEDLIAAGRVEVDGEVVTELGRRVHPDEAVIHVDG 61

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 121
             +   +      ++KP G+ +T SD  GR  V D L   +     V+ VGRLD NTEGL
Sbjct: 62  TRVNLRDDLVYLAFNKPKGVHSTMSDDRGRPCVGDYLRGRWEETPGVVHVGRLDENTEGL 121

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG L   L  PS + L+ Y     G V +     L+ G  +        Q  +  
Sbjct: 122 LLLTNDGDLGHRLMHPSYRVLKTYFAEVEGLVPRGLGKELRAGWELPDGIVKVDQFRVKD 181

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + + + + EG+   ++++       V +L+R + G  QLG    G+ R +++  +
Sbjct: 182 MHSGRSMIELVIHEGRKHIVRRLMAATGHPVRKLVRTAVGDVQLGNQRQGTIRRLNRGEV 241


>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 =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 110/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +++A   SR++ ++++    V VNG +++ A++++    D IE  G PL  A  
Sbjct: 1   MRLDKFLSKATELSRKDCKKILHAGEVTVNGEVVKDASLHIDEVGDDIEWAGEPLSVAMG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  L +KP G   T   P     V D +       +   GRLD++T G LLL++DGG  
Sbjct: 61  NRYLLLYKPEGFECTLK-PKEWPIVTDLIDVPQLGSLRIAGRLDVDTTGALLLSDDGGFL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P     +VY +     + + +    +  L KGI+++          L     ++A
Sbjct: 120 HRVTSPKHHVAKVYELTLADPMTEAQQAFAIKELAKGIMLEDEYDKTKPAELSFSDATHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L EGK  ++K++  +F  KV  L R S G   L  L  G +R ++ + +
Sbjct: 180 --KLVLTEGKYHQVKRMMGYFGNKVIELHRASIGNITLAGLEKGESRFLTAEEI 231


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 108/232 (46%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R E + ++ + RV VNG + ++    +   D + VDG PL   +  
Sbjct: 1   MRLDKYLAETAQCTRSEAKTLLNRGRVTVNGAVCKKGDTQLREGDSVAVDGAPLAYRQ-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V+  +D    +TV D +   + R  +  VGRLD  + G +LLT+DGG A
Sbjct: 60  VYLMLNKPEGVVSASTDKRD-TTVVDLIGDAYPRRELFPVGRLDKTSTGFVLLTDDGGFA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             +  P     + Y V     + ++      +G+ +  G      +V   T  G    V 
Sbjct: 119 HEILAPKRHVSKTYTVVIDTPLTEEMRRGFAEGVTLADGTALSPAEVEALTPDGLT--VK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V LR+G   +IK++F  +   VN L R + G   L   L  G  RE+S + +
Sbjct: 177 VRLRQGVYHQIKRMFGVYGAGVNALHRDAIGGLALDPALAPGQWRELSAEEV 228


>gi|312863475|ref|ZP_07723713.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
 gi|311101011|gb|EFQ59216.1| pseudouridylate synthase [Streptococcus vestibularis F0396]
          Length = 239

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 75/241 (31%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+  SD +   TV D +     R  +  VGRLD NTEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPAGVVSARSDKEH-QTVIDLIKPEDQRDGLYPVGRLDRNTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPGYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTICKSAQLEILSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 RITISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRVLTEAEKVILRTYL 238

Query: 246 G 246
           G
Sbjct: 239 G 239


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 143/247 (57%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 146 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 205

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 326 ELNPAEV 332


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 116/242 (47%), Gaps = 14/242 (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 ++   +  + D +     R+  +GRLD  +EGL+L+T++
Sbjct: 63  PGTRRHVYIALNKPVGVTCT-TETSVKGNIVDFV-GHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +        + Y V  +  V  + L  + +G+ I        +    T + +  
Sbjct: 121 GDIVNQILRAENGHQKEYLVAVNKPVTDEFLRGMARGVRIHDQMTLPCK----TSRIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L++G NR+I+ +   F ++V +L R+     ++G L  G  R ++++ L+  L  
Sbjct: 177 GFRITLQQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKIGALKPGQWRNLTEQELQGLLPK 236

Query: 248 HL 249
            L
Sbjct: 237 QL 238


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 143/247 (57%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 146 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 205

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G++  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 326 ELNPAEV 332


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 122/230 (53%), 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 +KPIG ++++ DP  +  +   +  I  R    GRLD ++ GL+L+TNDG +   
Sbjct: 61  YYKL-NKPIGFISSNYDPHNKKDLNSLV-KIDHRFFCAGRLDKDSHGLMLITNDGKITNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS +  + Y V+    +++D   L +KGI +       D ++ L  +        V 
Sbjct: 119 LIHPSKKIEKTYIVKVDKLLNKDDEALFRKGIKLSVNEKTSDAKINLIDENSK--IYEVI 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+++++F +F  KV  L RI  G  +LG L  G  ++++KK L 
Sbjct: 177 IHQGFNRQVRRMFLYFGSKVIDLKRIKIGQIELGKLEDGKYKKLNKKELE 226


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   LY KP G+V+   D + + TV D +        +  +GRLD +TEGLL++TN+G L
Sbjct: 61  SYYLLY-KPSGVVSAVRDSEHK-TVIDLISEKDKVEGLYPIGRLDRDTEGLLIVTNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +  
Sbjct: 119 GYRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 179 RITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 125/232 (53%), Gaps = 4/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R++K IA++GI SRR+ + +I +  VKVNG +++     +    D +EV+G  ++  E+ 
Sbjct: 4   RLNKYIAQSGICSRRKADELIKEGIVKVNGEIIKDLGAKINPEKDVVEVEGNIIKPVEKK 63

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP+G ++    D  GR T+ D L   +I   +  VGRLD N+EGLL+LTNDG  
Sbjct: 64  IYIKIYKPVGYLSAVGKDKFGRKTLTDLLKELNIKENLFPVGRLDYNSEGLLILTNDGEF 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P  +  ++Y V    +V++++LN +KKG +++   +   +V +      + W+ 
Sbjct: 124 ANKIAHPRHEIRKIYHVEVVPKVNEERLNQMKKGAILEDGFFKPDKVEILKHTKDSTWLL 183

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             +  GK R +++    FN KV RL+R+      +  L     + ++ K ++
Sbjct: 184 FEIHSGKKRILRRYVSKFNHKVRRLVRVKIDSISIENLKPHQFKHLTDKEVK 235


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 76/240 (31%), Positives = 114/240 (47%), Gaps = 4/240 (1%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDG 64
              E+    R+ KV+++AG+ASRR  E +I   RV+V+G ++      V      I VDG
Sbjct: 2   TSSEHPDGVRLQKVLSQAGVASRRAAEDLIVAGRVEVDGEVVTELGRRVDPDAAIIHVDG 61

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 121
             +   +       +KP G+ +T SD  GR  V D L   +     V+ VGRLD NTEGL
Sbjct: 62  TRVNLRDDLIYLALNKPKGVHSTMSDDRGRPCVGDYLRGRYEETPGVVHVGRLDENTEGL 121

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLLTNDG L   L  PS + L+ Y     G V +     L+ G  +        Q  +  
Sbjct: 122 LLLTNDGDLGHRLMHPSYRVLKTYLAEVDGLVPRGLGKELRNGWELPDGIVKVDQFRVKD 181

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + V + + EGK   ++++ +     V +L+R + G  QLG    GS R ++K  +
Sbjct: 182 MHSGKSLVELVIHEGKKHIVRRLLKDTGHPVLKLVRTAVGDVQLGNQRVGSIRRLTKTEV 241


>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 =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 105/276 (38%), Gaps = 47/276 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K +A  G+ SRRE +  IA   VKVNG       V V  +D IEVD   
Sbjct: 1   MTDAPAPIRLNKRMAELGLCSRREADEWIANGWVKVNGKPA-EMGVKVTPSDRIEVDKAA 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISV 111
             +       L +KPIG V+  ++      V               F   P     +   
Sbjct: 60  KGQQANQVTILINKPIGYVSGQAEDGHEPAVTLFTPQNRWAEDNARFFFSPQQLRGLAPC 119

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-------------------HGQ 152
           GRLDI++ GLL++T DG +AR L    +   + Y VR                       
Sbjct: 120 GRLDIDSIGLLVMTQDGRIARQLIGEDSVMEKEYLVRVAYHGLGQPAPTGQLVRMDDDDP 179

Query: 153 VD--------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           V            L  L+ G+ + G      +V     +     +   L EGK R+I+++
Sbjct: 180 VTTNVQAVFPPAMLARLRHGLSLDGQPLKPARVEWQNPE----QLRFVLTEGKKRQIRRM 235

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            E    KV  L R+  G   LG L  G  R +    
Sbjct: 236 CELVGLKVVGLKRVRIGKVMLGNLPVGQWRYLGPHE 271


>gi|295108497|emb|CBL22450.1| ribosomal small subunit pseudouridine synthase A [Ruminococcus
           obeum A2-162]
          Length = 257

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 115/238 (48%), Gaps = 22/238 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           R+ K +A AG  +R EV+++I + +V+VNG+  ++  + V    D + + G  +  A   
Sbjct: 6   RLDKFLADAGKGTRSEVKKIIQKGQVQVNGVPAKKPEMKVVPENDVVVLSGETVGAAPEF 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+   D + R TV + +PS    +  VGRLD +TEGLLL+T+DG LA  
Sbjct: 66  VYYLLNKPAGCVSATEDRNDR-TVMEYVPSDRKGLFPVGRLDKDTEGLLLITDDGMLAHE 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL---------DTQK 183
           L  P     + Y VR  G++  + +  L+ G+ I +       +V +         D+Q 
Sbjct: 125 LLAPGKHVDKTYFVRVEGKLTVENIRNLENGVDIGEEKMTMPAKVEIVGGSWEGAGDSQS 184

Query: 184 GS---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAG 231
           G             + + + EGK  ++K++       V  L RIS GP  L   L  G
Sbjct: 185 GRVRIENLPEVYTELHLTIHEGKFHQVKRMMAAVGNPVIYLKRISMGPLTLPDNLKKG 242


>gi|289668818|ref|ZP_06489893.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 285

 Score =  242 bits (619), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 76/238 (31%), Positives = 124/238 (52%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +  H  I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQHSSITVDGSPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      +G+     +V++  +   NA
Sbjct: 158 TVTDPTTGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPEGEGMLLRAKRVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RLIR++ GP  +G L  G+ R +S + +R  L
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLIRVAIGPLAMGELCKGAWRMLSAEEVRALL 275


>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 =  242 bits (619), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 75/223 (33%), Positives = 114/223 (51%), Gaps = 3/223 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R IA+ RV+V+G ++      +      IEVDG P+   +R  
Sbjct: 42  LARVLSKAGVCSRSEAARWIAEGRVRVSGRIVRDPEFPIGQPAPPIEVDGQPMGAPQRL- 100

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  
Sbjct: 101 YLMLNKPRGVVTTAQDERGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAR 160

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   + Y V+     D   L  L+ G+  +G       V +       AW+ V L
Sbjct: 161 LTDPETGPQKTYHVQVDRLPDDATLAALQAGVDDEGEFLVAQAVRVLRSGDKTAWLEVVL 220

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            EG+NR I+++   F+ +V RL+R++ G  QL  L  G  R +
Sbjct: 221 DEGRNRHIRRLLAAFDLQVLRLVRVAIGGLQLADLGKGQWRML 263


>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 =  242 bits (619), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D  P      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L LP ++  +VY V     +DQ  ++    G+  +      +   L+      A   + 
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPIGPRCA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 178 LHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>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 =  242 bits (619), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 58/226 (25%), Positives = 108/226 (47%), Gaps = 9/226 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRR  +R+I + +V +NG + E+    V   D ++VDG  + K   ++
Sbjct: 4   RINKYLSEVGYCSRRVADRLIEEGKVVINGKIPEK-GTKVEEGDQVKVDGQRIEKSTKQK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T         + D +    +R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDRRVEHDNIIDFI-KYPTRIFPIGRLDKPSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V  +  +++D +  +  G+ I      +  V     K       + 
Sbjct: 122 KILRARNNHEKEYIVSVNRPINRDFIQSMSNGVEILETITKNCFVKQLGAKK----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +K
Sbjct: 178 LTQGLNRQIRRMCESLGYRVESLKRVRIMNIKL-DVPIGKYREFTK 222


>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 =  242 bits (619), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 78/232 (33%), Positives = 124/232 (53%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   +   E  
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKIN-EESF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+++     + +V + +    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 64  EYYLLNKPAGYVSSNRSYPNQPSVIELI-KTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGKN EIKK+ +F    V +L R  +    +G L  G  R +S++ + +
Sbjct: 183 TIAEGKNHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQHRALSEQEVEK 234


>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 =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 122/246 (49%), Gaps = 12/246 (4%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K   +E      R+ K ++ A I +R EV+++I + RV VN  ++     +V   D 
Sbjct: 1   MSKKISKKESEIKSIRLDKFLSNAHIGTRNEVKKIIKEGRVSVNFEIIRNPDFHVKLDDI 60

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           IE+DG  +    +    ++HKP G V+T SD +   +V + +   + + +   GRLD + 
Sbjct: 61  IELDGNRIE-PHKNVYIIFHKPSGFVSTTSDRE--PSVLNLIDHPYLNELHIAGRLDKDV 117

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG--QVDQDKLNLLKKGIVIQ-GICYGDM 175
           EGLL+LTNDG     L  P     + Y +      +V Q+ + ++ +GI ++ G      
Sbjct: 118 EGLLILTNDGEFTHNLISPKKHIEKEYWIYTKENVEVTQNMVKMVSEGIELEKGTKTLPG 177

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           ++    +K S   +++ + EGK  ++KK+      +  +++R+  G   L  L  G  +E
Sbjct: 178 KI----RKVSEKIISLTIVEGKYHQVKKMCISLGIEWEKIVRVRIGNLTLEGLEKGKWKE 233

Query: 236 VSKKIL 241
           +SK+ +
Sbjct: 234 LSKEEI 239


>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 =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 90/284 (31%), Positives = 140/284 (49%), Gaps = 14/284 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG+ SRRE+E  I+  RV VNG +       V S D + VDG  ++    
Sbjct: 2   SEKLQKVLARAGLGSRRELETWISDGRVSVNGTVAT-LGDRVGSEDTLRVDGRIIKVKTE 60

Query: 73  ----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G V + +DP+GR TVFDNLP     R + VGRLDINT G++L T D
Sbjct: 61  EDTVQRVIMYHKPPGEVCSRNDPEGRPTVFDNLPRLQGMRWVQVGRLDINTTGMMLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGS 185
           G LA  L  PS  ++R Y VR  G +  +K   +  G++++        +      ++G+
Sbjct: 121 GELAHRLMHPSNGFVREYAVRVRGVMTPEKRQAMLDGVLLEDGVSKFDSIEDAGGAEEGA 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           N W    L  GK RE++++F+  + +V RL+RI +G   L   L  G   E+  + ++  
Sbjct: 181 NHWYKATLTGGKYREVRRLFQSQDLEVARLMRIRFGDLTLPPQLRQGRWMELEPEQMKA- 239

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
               L+E+  +                    ++ P    R    
Sbjct: 240 ----LIEKVDLKGKKYTGLYGRARLRHQRGGNKPPRKARRGPYR 279


>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 =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 324 ELNPAEV 330


>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 =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 121/233 (51%), Gaps = 9/233 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +   G+ SRREV++++   +++VN I+++    N+  + D IE DG  L   
Sbjct: 3   DKMRLDKFLTECGLGSRREVKKLLDNGKIRVNDIIVKNPQANIKESIDKIEYDGNKLEYK 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG 128
           E  R ++ +K  G +T   DP  + TV + LP       +  VGRLD +TEGLLL TNDG
Sbjct: 63  E-FRYYIMNKKGGYITATEDPKEK-TVMELLPEWVIKKDLAPVGRLDKDTEGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P     + Y  +   ++ + ++  L++G+ I G      +  +  +K     
Sbjct: 121 KLGHSLLSPKKHVDKTYYAKLEKEIGEVEIKKLEEGVDIGGYITQPAKAKIVGEK----E 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + +REGK  ++KK+ E  N KV  L R+++G  +L  +  G  RE++ + +
Sbjct: 177 IELTIREGKFHQVKKMLEAVNNKVVYLKRVTFGKLELKDMELGEVREINLEDI 229


>gi|301336267|ref|ZP_07224469.1| ribosomal large subunit pseudouridine synthase B [Chlamydia
           muridarum MopnTet14]
          Length = 241

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 108/233 (46%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A AG+ASRR+ + ++    V VNG +     V V    D +EV+G  +  
Sbjct: 1   MAKVRLNKFLASAGVASRRKCDEIVFAGAVTVNGKVAAGPFVIVDEELDSVEVEGQRI-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E+   ++ HKP+G + +      G   V D L     R+ +VGRLD  T GL+L+TNDG
Sbjct: 60  TEKKVYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +  +  PS    + Y ++    V    L  L  G+VI G     + V     K     
Sbjct: 120 EFSNRVIHPSFGITKEYLLKVSRDVSARDLETLMAGVVIDGRIVRPVSVK----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L
Sbjct: 176 IKIIVNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGQYRELTDAEL 228


>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 =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 86/269 (31%), Positives = 134/269 (49%), Gaps = 6/269 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +         +R+ K +A AG+ SRRE+E  IA+ RV+VNG         V   D ++V 
Sbjct: 24  QQATAPEAASERLHKALASAGLGSRREMEEWIAEGRVQVNGETAT-VGSKVGPRDVVKVS 82

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           G  +      +RTR+ +YHK  G + +  DP GR+TVFD LP    S+ I+VGRLD NT+
Sbjct: 83  GRRVYLRFDEKRTRILIYHKSEGEIVSRDDPGGRATVFDALPRLRGSKWIAVGRLDYNTD 142

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL++ T  G LA  L  P  +  R Y VR  G++ +D +  L  G+ +            
Sbjct: 143 GLMIFTTSGDLANRLMHPRFEVEREYAVRVLGELTEDMIAELLAGVELDDGPAQLQSCFA 202

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSK 238
              +G+N W  V ++EG+ RE++++FE     V+RL RI +GP  L   L  G   E+  
Sbjct: 203 AGGEGANRWYRVVIKEGRKREVRRLFEHLGLTVSRLTRIRFGPIVLPPQLRRGQKTELDD 262

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETL 267
            ++ + +    +E +       +    T 
Sbjct: 263 DLVAQVMRWAGMEASPRRKTRGVPDKHTR 291


>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 =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 120/244 (49%), Gaps = 1/244 (0%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           + ++   +     R+ K +A AG+ASRR  E MIA  RV V+G ++ R    V   +  I
Sbjct: 445 EARDTYTDVENGIRLQKALAAAGVASRRASEEMIAAGRVSVDGQVVRRFGARVDPESSEI 504

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            VDG+ +  A     +  +KP G+V+T  DP+GR T+ D       R+  VGRLD  TEG
Sbjct: 505 RVDGMRVVTAPDKLYFALNKPRGVVSTMWDPEGRPTLADYTGQTEERIFHVGRLDTETEG 564

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLTNDG LA  L  P  + ++ Y  +  G V    +  ++KG+ ++          + 
Sbjct: 565 LILLTNDGELANRLTHPRYKVVKTYIAKVPGPVPHRVVREVQKGVELEDGPVEVDSFRVV 624

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +   A V + L EG+   ++++ E     V  L R   GP  L  L  G+ R ++ + 
Sbjct: 625 DNEPPKALVEIRLHEGRKHIVRRLMEAVGHPVADLARTQVGPIDLNALKLGTMRALTSRE 684

Query: 241 LREQ 244
           + E 
Sbjct: 685 VSEL 688


>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 =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 111/232 (47%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A++   SR+EV R +    V VN + ++  A+++   D + + G P+      
Sbjct: 1   MRLDKYLAQSTGFSRKEVRRFMKAGEVVVNDLEIKDPALHISDEDDVYLSGYPVEAP-GE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           +  + HKP+G V ++ D     TV   L       +   GRLD++T GL+L+T++G  A 
Sbjct: 60  KYLMLHKPLGCVCSNDDSTH-PTVLSLLDLPRAEELTICGRLDVDTTGLVLITSNGKWAH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  + Y+V     + QD +    KG+++  +       ++T+  +  +     
Sbjct: 119 KVTSPKHKTGKRYQVTTADPIPQDAITKFAKGLMLINEKERTKPAELTIIGEYEA----E 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           V L EG+  ++K++F     KV  L R+S G   L   L  G  R ++ + +
Sbjct: 175 VVLTEGRYHQVKRMFAAIGNKVEELHRVSIGAISLDEDLEPGEFRFLTDEEI 226


>gi|319744819|gb|EFV97158.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           agalactiae ATCC 13813]
          Length = 239

 Score =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   LY KP G+V+   D + + TV D +        +  +GRLD +TEGLL++TN+G L
Sbjct: 61  SYYLLY-KPSGVVSAVRDSEHK-TVIDLISEKDKVEGLYPIGRLDRDTEGLLIITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +++D +   ++G+V   G      ++T+DT     +  
Sbjct: 119 GYRMLHPKHHVAKTYYVEVNGFLERDAITFFEEGVVFDDGTKCKPAELTIDTANNDKSTA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L RIS+G  +L   L  G  R +    
Sbjct: 179 RITITEGKFHQVKKMFLAYGVKVIYLRRISFGDLRLDMNLKPGQYRRLRDSE 230


>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 =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 138/247 (55%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R  ++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWGAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 324 ELNPAEV 330


>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 =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 85/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>gi|325132446|gb|EGC55139.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M6190]
          Length = 349

 Score =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 323 ELNPAEVANIL 333


>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 =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 116/231 (50%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG+    A  N+    D IE +   L   ++
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNNEITVNGMSNISAKDNIDENSDIIEYNEEKLEY-KK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKSGYITATEDFKEN-TVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY V     +  + +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHKLLSPKNHVDKVYYVEIKNNISDEDIFKLEQGVDIGNYISQPAKV----EKISDNKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  +IKK+ E  N KV  L R+S+G  +L  L  G  REV+ + +
Sbjct: 175 LTIKEGKFHQIKKMLEAINNKVCYLKRVSFGRLKLNDLALGEVREVNLEDI 225


>gi|254672143|emb|CBA04924.1| conserved hypothetical protein [Neisseria meningitidis alpha275]
          Length = 349

 Score =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 85/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 118/230 (51%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ +R+IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQRLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP+   TV + L P     +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPEH-PTVLELLPPDHRDDLHIGGRLDYNTTGLMLLTNDGRWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L LP ++  +VY V     +DQ  ++    GI  +      +   L+     +A   + 
Sbjct: 120 RLTLPGSRRDKVYYVETEEPIDQRYVDAFAAGIHFRFEDLVTLPAQLEPLGPRSA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           L EG+  ++K++F  F+ +V RL R   G  QL  TL  G+ R ++ + +
Sbjct: 178 LHEGRYHQVKRMFGHFDNRVLRLHRERMGDIQLDPTLPPGAWRPLNAEEI 227


>gi|42523444|ref|NP_968824.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
 gi|39575650|emb|CAE79817.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
          Length = 245

 Score =  242 bits (618), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 114/239 (47%), Gaps = 17/239 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++A  GI SRRE +  I++  V VNG ++ +    V     I ++   L++ +R  
Sbjct: 8   RLSKLMAEKGICSRREADDYISRGLVMVNGEVVSQLGTKVSPDVKITLEAQALKQQKRLA 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-------------SIFSRVISVGRLDINTEGL 121
             L +KP+G V+   +P  +  +    P               F  +   GRLDI+++GL
Sbjct: 68  TILLNKPVGYVSAQPEPPYQPAIKLITPQNQFGNSKTRLKEEHFKGLAVAGRLDIDSQGL 127

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LL T DG +A+ +    ++  + Y VR  G +  DKL LL  G+ + G      +V    
Sbjct: 128 LLFTQDGRIAKKIIGEESKVEKEYIVRVQGTLPPDKLKLLNFGLSLDGKKLKPAKVEWLN 187

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +      +   L+EGK R+I+++ E    KV  L R+  G  +LG L  G  R + +  
Sbjct: 188 ED----QLRFILQEGKKRQIRRMCELVGLKVTGLKRVRIGKIRLGQLPEGQWRFLEEDE 242


>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 =  242 bits (618), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 114/227 (50%), 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  D   R ++   L +   RV   GRLD ++ GLLL+TN+G + 
Sbjct: 73  EMIVLAVNKPKGIVCT-EDQRERDSIVRFL-NYPVRVTYAGRLDKDSRGLLLMTNNGDII 130

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +   + +  + Y+V    ++ +  +  + +G+ I         V     K      ++
Sbjct: 131 NQMMRAANRHEKEYKVTVDKEITEQFIKKMSEGVPILDTVTRPCTVK----KIGKYTFSI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L +G NR+I+++   F ++V  L+RI     +LG+L  G+ R+++ 
Sbjct: 187 ILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLKEGAYRKLTD 233


>gi|254670545|emb|CBA06380.1| conserved hypothetical protein [Neisseria meningitidis alpha153]
          Length = 349

 Score =  242 bits (618), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  242 bits (618), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 61/237 (25%), Positives = 114/237 (48%), Gaps = 7/237 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + I+  +F+  R++K+I++AG+ S+++ +  I Q RV VNG +       V   D + +D
Sbjct: 22  QKIIATDFSSMRLNKLISQAGLGSKKQADAWIMQNRVTVNGQVA-SVGQKVNQHDQVLLD 80

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P+  +    L  YHKP+G+V TH      + V      +     ++GRLD  +EGL++
Sbjct: 81  GRPVAWSSEVLLMAYHKPVGVVCTHDLSVANNLVVST--GLMQHFSAMGRLDKASEGLMI 138

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LTN G L   +  P     + Y V     + +  L  +++G+ I G      ++    + 
Sbjct: 139 LTNQGDLTNHILQPGFAHEKEYWVEVDQPLTEYFLTNMQQGVEIMGQVTRPCEIEATGE- 197

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                  + L +G N++I+++ +   ++V RL R+      L  L   + RE++   
Sbjct: 198 ---HCFRIVLTQGLNKQIRRMCKSLGYRVLRLQRVRIAQVWLDDLPVNTLRELNDVE 251


>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 =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 68/248 (27%), Positives = 110/248 (44%), Gaps = 22/248 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +R I    V V+G  +      +  T  I+++     + 
Sbjct: 1   MEKIRLSKLMSEQGLCSRREADRYIELGWVFVDGEQISELGTKIYPTQKIKLNKAAQAQQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------------------DNLPSIFSRVISVG 112
                 L +KP+G V+   +P  R  +                      PS    +   G
Sbjct: 61  ISLVTILLNKPVGYVSGQPEPGYRPAIVLIKPENQFIPKQPAQPNKRFQPSHLKNLAPAG 120

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLDI+++GLL+LT DG +A+ +    +   + Y VR  G + ++KL LL  G+ + G   
Sbjct: 121 RLDIDSQGLLVLTQDGRIAKQMIGEDSNIEKEYLVRVEGVLPREKLALLNHGLSLDGQPL 180

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
               VT   Q      +   L+EGK R+I+++ E  N KV  L R+  G  +LG L  G 
Sbjct: 181 KPANVTWQNQD----QLRFILQEGKKRQIRRMCELVNLKVTGLKRVRIGKVKLGNLPEGQ 236

Query: 233 TREVSKKI 240
            R +    
Sbjct: 237 WRYLEDGE 244


>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 =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 114/225 (50%), Gaps = 13/225 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++++  G  SR+E   ++  +RV V G   +  A+ V     + VDG  L   +   
Sbjct: 15  RLDQLLSNLGYCSRKEARYLLKGKRVTVKGEFAKSPALKVDPA-TVRVDGEALDAPDGI- 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           L + +KP+G V +H + +G   ++D LP  +     +++SVGRLD +T GL+L+T+D  L
Sbjct: 73  LVMLNKPLGYVCSHDNNEGMR-IYDLLPERWEFRNPKIVSVGRLDKDTSGLILVTDDTKL 131

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QG-ICYGDMQVTLDTQKGSNAW 188
              L  P     +VY+V     +  D ++   KG+V+ +G       ++ + ++  +N  
Sbjct: 132 VHQLTSPKHHVDKVYQVSVDCPLQSDIIDSFAKGVVLGEGAEQCLPAKIEIVSENVAN-- 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             V L EGK  +++++F    + V  L R  +G ++L  L  G  
Sbjct: 190 --VTLNEGKYHQVRRMFAACGYHVEALHRSQFGQYRLQDLAQGEW 232


>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 =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 97/308 (31%), Positives = 143/308 (46%), Gaps = 8/308 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK- 69
              +++ K +AR G+ SRR++E +I   RV VN          V   D I VDG  ++  
Sbjct: 1   MKDEKLQKALARMGLGSRRQMEEVIKAGRVTVNNGPAT-IGDRVEQGDEIRVDGRQIKYT 59

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
               +R R+  Y+KP G V + +DP+GR TVF+ LP     R + VGRLDIN+ GLLL T
Sbjct: 60  SENEKRRRVLAYYKPEGEVCSANDPEGRPTVFERLPKLTHDRWVMVGRLDINSTGLLLFT 119

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG +A  L  PS++  R Y VR  G V  D    +  G++++        +     +G 
Sbjct: 120 NDGEMAHRLMHPSSEVTREYAVRVLGDVTPDMARAMTTGVMLEDGMAKFEDIKEGGGEGV 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           N W  V L+EG+NRE++++FE    KV+RL+R SYG   L   L  G   E+ +K +   
Sbjct: 180 NKWHHVQLKEGRNREVRRLFESQGLKVSRLLRTSYGNITLPKELRTGRFLELDRKDINTL 239

Query: 245 LGPHLLEEA-QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                L       L       +  +R++P                SS K   S       
Sbjct: 240 TDLVSLRPRYGTGLHGAAKEKQERIRNKPLKARRTDTRGDNRNSTSSAKPKSSASPVSRG 299

Query: 304 PVHRRNLA 311
             + R+  
Sbjct: 300 TRNTRDRN 307


>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 =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 75/239 (31%), Positives = 116/239 (48%), Gaps = 8/239 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
               RV K +  AG  +R E +++    RV++NG  ++ AA +     D +EVDG  +  
Sbjct: 1   MASIRVDKWLTTAGYGTRSEAKKLCRAGRVRLNGETVKDAAKHADPAVDVLEVDGELVPY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTND 127
            E    ++ +KP G V++  DP     V + L    I+  V  VGRLD + EGLLLLTND
Sbjct: 61  -EPLVYFMMYKPPGYVSSTEDPRD-PVVIELLDEEDIWRDVFPVGRLDKDAEGLLLLTND 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSN 186
           G LA  L  P     + Y VR  G + +     L +G+V+    Y  M   L+  + G+ 
Sbjct: 119 GPLAHRLLAPKRHVPKRYFVRVRGALGEGDARALAEGVVLDDG-YKAMPAELEILRSGAE 177

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           +   + + EGK  ++K++F     +V  L RIS GP  L   L  G  R +++  +   
Sbjct: 178 SEAIIQVYEGKYHQVKRMFASLGKRVTFLKRISMGPLSLDPALKPGEYRRLTEGEIEAL 236


>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 =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 108/228 (47%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  SR+EV+++I    V VN + ++  + ++   TD +E++G  +   E 
Sbjct: 1   MRLDKFLVNQGFGSRKEVQKLIKAGIVYVNDVPVKDPSFHIDPNTDVVEIEGQEVEYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G +T   D +   TV D      I +++  +GRLDI+TEGLL++T+DG L
Sbjct: 61  -YYFMLNKPKGYITATYD-ENYPTVMDLFSAEPIVNKLFPIGRLDIDTEGLLIITSDGVL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
           A  L  P     + Y V   G V   D     K+GI +          +V +       +
Sbjct: 119 AHRLSHPKWNVEKEYFVIVEGDVSDIDFSKYEKEGIYLKKDKYKTKPFKVNVLKTSFEES 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
            + + + EGK   IKK+    + +V  L R+  GP  L   L  G  R
Sbjct: 179 ELLITITEGKYHIIKKIMYALDHEVKYLKRVRIGPLTLDEDLDVGEYR 226


>gi|322412052|gb|EFY02960.1| Ribosomal small subunit pseudouridine synthase A [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 243

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 113/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR +V+ ++ ++ + VN  +     V +    D +   G PL   E 
Sbjct: 1   MRLDKFLVETGVGSRSQVKSLLKKKAILVNQEVETSPKVQINEHKDVVTYLGKPLTY-EA 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G ++   D   ++TV D L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 60  FVYYVLNKPAGFLSATKD-RAQATVIDLLDETARQKDVFPVGRLDKDTRGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAW 188
           A  L  P     + Y  +  G + +   +   KGI ++       ++ +  +  S     
Sbjct: 119 AHDLLSPKKHVTKEYLAKVAGIMTEADKDDFAKGISLKDYQCLPAKLEVLDKDVSQETCV 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V++ ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 179 VSITIQEGKFHQVKRMVAACGKEVLELQRLSMGPLRLDPSLAEGDFRRLTSEELQSL 235


>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 =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 116/244 (47%), Gaps = 14/244 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +   P RV+K + + G+ SRRE E +IA+  V ++G  +  A   +     + ++   
Sbjct: 6   TYDGDEPVRVNKWLGQTGVCSRREAESLIAEGLVSIDGETISDAGRKIEPGQTLTLNDTA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------LPSIFSRVISVGRLDI 116
            +        + HKP+G V+   DP     V              P+  + +  +GRLD 
Sbjct: 66  QQALASGMTLVLHKPVGYVSGQPDPGKIPAVRLLKIPNRIGEGETPARDASLPPIGRLDE 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLLLL++DG +A+ +  P+++  + Y V   G + + KL+ L+ G+V+        +
Sbjct: 126 DSRGLLLLSSDGVVAKAVIGPASELDKEYLVVVDGVITEAKLSRLRHGLVLNDKPLKPAR 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           VT    +     +   L EGK R+I+++ E    +V  L RI  GP ++G L  G  R +
Sbjct: 186 VT----QIEPQRLRFVLTEGKYRQIRRMCELVGLEVVDLYRIRIGPLEIGDLPEGRWRHL 241

Query: 237 SKKI 240
           + + 
Sbjct: 242 TDQE 245


>gi|304405744|ref|ZP_07387402.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
 gi|304344987|gb|EFM10823.1| pseudouridine synthase [Paenibacillus curdlanolyticus YK9]
          Length = 235

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 115/232 (49%), Gaps = 7/232 (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 ++   +  + D +     R+  +GRLD ++EGL+L+TNDG +   
Sbjct: 60  VYIALNKPVGITST-TESQIKGNIVDFV-GHSERIFPIGRLDKDSEGLILMTNDGDIVNR 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V     V    +  + +G+ I G      QVT   ++       + L
Sbjct: 118 ILRAEGKHEKEYIVTVDRPVTPMFIKGMSEGVRILGTMTLPCQVTRIAERI----FKIVL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            EGKNR+I+++ E F ++V RL R+      LG L  G  R++ +  L E  
Sbjct: 174 TEGKNRQIRRMCEVFGYRVVRLRRVRIMNIHLGDLANGRWRDLHQDELDELF 225


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 74/241 (30%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+  SD     TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPAGVVSARSDKKH-QTVIDLIKPEDQREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPRYHVAKTYYVEVNDILGPDTPAFFESGVVFEDGTICKSAQLEILSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 RITISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRALTEAEKVILRTYL 238

Query: 246 G 246
           G
Sbjct: 239 G 239


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 83/246 (33%), Positives = 136/246 (55%), Gaps = 6/246 (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  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  ++        R+ LY+K  G + +  DP GR ++FD LP   S R +++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 VSKKIL 241
           ++   +
Sbjct: 338 LNPMEV 343


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 86/246 (34%), Positives = 132/246 (53%), Gaps = 6/246 (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  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
              G P+R        R+ LYHK  G + T  DP+GR T+FD LP    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 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
           +     +G N W  V ++EG+NRE++++FE F   V+RLIR+ +G   L   L  G   E
Sbjct: 414 IVEQGGEGVNHWYRVVIKEGRNREVRRIFEHFGLTVSRLIRVRFGNIGLPARLKRGQFYE 473

Query: 236 VSKKIL 241
           ++   +
Sbjct: 474 LNSAEV 479


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 94/231 (40%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  V  +G +++ +   V     I +DG  +      R
Sbjct: 14  RLDKFICESTELTRSFAKKALHRGDVTCDGEVVKNSGFKVKVGQTICLDGKVISVV-GPR 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP   +    D     TV D L       +   GRLDI+T GL+L+T DG  +  
Sbjct: 73  FLMLNKPADTICATFDI-VHPTVIDLLDIEKADTLHIAGRLDIDTTGLVLITTDGQWSHK 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V+   ++D   +    +G+ +  +        + +           +
Sbjct: 132 ITSPKKDCSKCYLVKLTDELDASLVETFAQGVELRNEDGLTKPAVLEI----IDTHTARL 187

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + EGK  ++K++F     KV  L R S G   L   L  G  R ++ + +
Sbjct: 188 TITEGKYHQVKRMFAAVGNKVVGLHRESVGKIVLDDDLAPGEWRYLTDEEV 238


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 107/233 (45%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A AG+ASRR+ + +I    V VNG +     V V    D +EV G  +  
Sbjct: 1   MAKVRLNKFLASAGVASRRKCDEIIFAGSVTVNGRVATGPFVTVDEEFDSVEVGGQRI-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           AE+   ++ HKP+G + +      G   V D L     R+ +VGRLD  T GL+L+TNDG
Sbjct: 60  AEKKVYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++    V    L  L  G VI G     + V     K     
Sbjct: 120 EFANRVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSVK----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L
Sbjct: 176 IKIIVNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDSEL 228


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 91/238 (38%), Positives = 134/238 (56%), Gaps = 8/238 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ K +A AG+ SRRE+ER+I    V VNG   +     V + D I V+G  +R+   
Sbjct: 40  TEKLQKALADAGMGSRREMERLIESGIVTVNGNPAK-LGDRVSAEDVIRVEGRLVRRLSP 98

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
             A+  R+ LYHKP G + +  DP+GR +VF++LP +   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-GTLLAGSTREVSKKILRE 243
            W  V +REG+NRE++++FE  N  V+RLIR+ YG  +L   L+ G   E+    +R 
Sbjct: 219 HWYVVTIREGRNREVRRLFESVNLTVSRLIRVRYGAVELPPGLVRGKREEMDPADVRR 276


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 110/244 (45%), Gaps = 15/244 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDH 59
           M  K  +      +R+ KVIA     SRR+V+R++ + ++ VNG  +++A + +   TD 
Sbjct: 1   MPQKQKL------ERLDKVIAAQTKLSRRDVQRLVGRGQISVNGTPVKKADLKIDPDTDV 54

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDIN 117
           + V G  L   +R    + +KP G+V   SD     TV D +P    R  +   GRLD +
Sbjct: 55  VMVSGKTLAL-KRHVYIMLNKPRGVVCATSDA-ALPTVLDLVPDSLMRRGLFPAGRLDKD 112

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEG +L+T+DG  A  +  P +   + Y  R    V Q  +     G+ + G      ++
Sbjct: 113 TEGFVLITDDGAFAHRILAPKSHVPKTYTARLDAPVTQQMIEAFAAGVQLDGAVCMPAEL 172

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            +     +     V +R+G   +IK++F      V  L R   G   L   L  G  RE+
Sbjct: 173 CVLDTPDT---ARVVIRQGMYHQIKRMFAACGAHVLALRRDRIGGLSLDIALGPGECREL 229

Query: 237 SKKI 240
           S   
Sbjct: 230 SAAE 233


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 96/312 (30%), Positives = 150/312 (48%), Gaps = 7/312 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGQIAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 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 RRNLASNVWMAK 318
           R+ +A N    K
Sbjct: 301 RKTVAVNKGFKK 312


>gi|268596680|ref|ZP_06130847.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
 gi|268550468|gb|EEZ45487.1| pseudouridine synthase [Neisseria gonorrhoeae FA19]
          Length = 416

 Score =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 210 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 269

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 390 ELNPAEVANIL 400


>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 =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 68/232 (29%), Positives = 114/232 (49%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D LP      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLLPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVT 190
            L LP ++  +VY V     +DQ  ++    G+    + +     Q+     + +     
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLITLPAQLEPIGPRCA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 176 LTLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>gi|319794363|ref|YP_004156003.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315596826|gb|ADU37892.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 601

 Score =  242 bits (617), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 86/247 (34%), Positives = 129/247 (52%), Gaps = 6/247 (2%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K ++       ++ KV+A+AG+ SR E+E +I Q R+ VN          +   D ++++
Sbjct: 175 KRVLLPEADSPKLHKVLAQAGLGSRLEMEALILQGRISVNNEPA-HIGQRIQYGDQVKIN 233

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           G P+R        R+  YHKP+G V TH DP  R TVF  LP +   +  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 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
              +GSN W  V + EG+NRE++++FE     V+RLIRI YG   L   L  G+  E+ +
Sbjct: 354 GGGEGSNCWYRVTISEGRNREVRRLFESVGHAVSRLIRIRYGAMVLPRGLKRGAWMELDE 413

Query: 239 KILREQL 245
           + +R   
Sbjct: 414 RDIRALF 420


>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 =  242 bits (617), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 110/236 (46%), Gaps = 10/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     +R+E  R++  + ++VNG +++  ++ +     +E +G  L   +  
Sbjct: 1   MRLDKFLATTLGITRKEAGRLLNNKMIEVNGDVVKSISLKITDDCDVEFNGKKLTL-QGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLAR 132
           + ++ +KP G V +H D D   TVF     +    + V GRLD +T GL LLT+DG  + 
Sbjct: 60  QYFMLNKPEGFVCSHVD-DHNPTVFVLFDEVSPEKMHVAGRLDGDTTGLTLLTDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P     +VY V     V ++ +    +G+ ++G        ++ +  ++ +     
Sbjct: 119 RVTSPRHVCEKVYHVELADPVPEETIQTFLEGVQLRGEKDITRPAKLEILGEREA----I 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           + + EGK  ++K++F     +V  L R   G   L   L  G  R ++ + +   L
Sbjct: 175 LTITEGKYHQVKRMFAAVGNRVVGLHREQVGAVVLDENLKPGEYRRLTDEEIASFL 230


>gi|296390923|ref|ZP_06880398.1| putative pseudouridylate synthase [Pseudomonas aeruginosa PAb1]
          Length = 230

 Score =  242 bits (617), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D  P      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLFPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L LP ++  +VY V     +DQ  ++    G+  +      +   L+      A   + 
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLTTLPAQLEPIGPRCA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 178 LHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>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 =  242 bits (617), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 210 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 269

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 390 ELNPAEVANIL 400


>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 =  242 bits (617), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 110/238 (46%), Gaps = 8/238 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE 71
             R+ K +   G+ SR +V+ ++ ++ + VN  +     V +    D +   G PL   E
Sbjct: 2   TMRLDKFLVETGVGSRSQVKSLLKKKAILVNQEVETSPKVQINEHKDVVTYLGKPLTY-E 60

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
               ++ +KP G ++   D   ++TV D L     +  V  VGRLD +T GLLLLTN+G 
Sbjct: 61  AFVYYILNKPAGFLSATKD-RAQATVIDLLDETARQKDVFPVGRLDKDTRGLLLLTNNGQ 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NA 187
           LA  L  P     + Y  +  G +     +   KGI ++       ++ +  +  S    
Sbjct: 120 LAHDLLSPKKHVTKEYLAKVAGIMTDADKDDFAKGISLKDHQCLPAKLEVLDKDLSQETC 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            V++ ++EGK  ++K++      +V  L R+S GP +L   L  G  R ++   L+  
Sbjct: 180 VVSITIQEGKFHQVKRMVAACGKEVLELQRLSMGPLRLDPGLAEGDFRRLTSDELQSL 237


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A A I +R EV ++I +  + VNG +++  + ++  TD +E  G  +    R 
Sbjct: 1   MRLDRFLANAKIGTRSEVRKIIKKGEISVNGEIVKNISFHINETDIVEYMGKTVVPY-RK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              +++KP G V+  +  + + +VFD +   F  ++   GRLD + EGLL+LTNDG    
Sbjct: 60  IYLIFNKPAGFVSDKT--NAQPSVFDLIDHPFIDQMHVAGRLDRDVEGLLILTNDGLFTH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y + F G +  +K+ +++ GIV+    +   ++ L +        T+ 
Sbjct: 118 RLISPKFHVEKEYMIWFEGNLTAEKIQIVENGIVLAQNRFKPAKIKLLSSNIM----TLT 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + EGK  ++KK+ +       ++ RI  G   LG +  G+ RE+ +  L E +
Sbjct: 174 ITEGKYHQVKKMIKIMGLTYRKIKRIRIGNINLGNMSTGNYRELDENELNELM 226


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 113/232 (48%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA  R++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGRLRVDGQVVRDGTHEVRVFSRVELDEQLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D  P      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLFPEDQRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVT 190
            L LP ++  +VY V     +DQ  ++    G+    + +     Q+     + +     
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLITLPAQLEPIGPRCA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 176 LTLHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 138/247 (55%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 112/231 (48%), Gaps = 6/231 (2%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-LW 76
           K +  AG  SRRE+   +   RV VNG   E  +  +   D I +D  P+  AE  R   
Sbjct: 10  KALRDAGCGSRRELAEAVKAGRVAVNGTTAESFSAAITPADVITLDSRPVVTAESARVYL 69

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +KP+G++TT  DP GR TV D LP  +   R+  VGRLD NT GL++LTNDG L   L
Sbjct: 70  LLNKPLGVITTTEDPQGRPTVIDLLPPDWQQKRLFPVGRLDENTTGLIILTNDGELTNRL 129

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     + Y V     ++ +    +K G + +        +++       N    + +
Sbjct: 130 THPRYGVEKEYLVGIDRSLNSEDFEKIKSGGLELDDGPASPARISPVNAAPFN--YRISI 187

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EG+ R ++++F     +V  L RI  G  +LG L  G+ R+++   LR  
Sbjct: 188 HEGRKRIVRRLFAALGHQVRVLRRIRVGSLELGNLKEGNWRQLTPLELRRL 238


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 106/235 (45%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       R+ KV+A AGI SRR  E +IA  RV VNG   +           I VDG  
Sbjct: 1   MTAEPEGVRLQKVMAAAGIGSRRACENLIAAGRVTVNGKKAQLGNRVDPQHAVIHVDGER 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +    +   +  +KP G V+T  D   R  + +    I  RV  VGRLD  +EGLLLLTN
Sbjct: 61  VITDTKLVHFALNKPRGYVSTMDDELKRPDLNEFTAGISERVFHVGRLDTESEGLLLLTN 120

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  + YR +  G         L  G+V++          +  +    
Sbjct: 121 DGELGNRLTHPSYEIAKTYRCQVTGYAGPAIARRLAAGVVLEDGPVTVDDFKVIDEHADQ 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A V + + EG+   ++++       VNRL+R + G  +L  L  G+ R++    +
Sbjct: 181 ALVEIVVHEGRKHVVRRLLAEVGLPVNRLVRTAIGDIRLANLKPGTLRKLRPDEI 235


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 130/231 (56%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 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 +     R+  VGRLD  T GL+LLTNDG L 
Sbjct: 60  KKVYFMLNKPLEVLSSSSDNRGRKTVVDLI-KTDKRIFPVGRLDYMTSGLILLTNDGELF 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|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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 115/246 (46%), Gaps = 11/246 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
             R++K I  +GI SRR+ +R I Q  V +NG         V++ D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRA-SVGDRVLAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   +   +KP+G+V+T  + + R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  EDLVVIALNKPVGIVSTTEEGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V ++ +  L  G+ + G            +K S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTEEFIRGLGAGVPMLGTVTK----KCKVKKESTFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  L  G  R+++   L E     L+
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYEVTKLERTRIMNVSLKGLPPGEWRDLTDDELIELF--KLI 236

Query: 251 EEAQVN 256
           E +   
Sbjct: 237 ENSSSE 242


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 115/238 (48%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    + +R ++ ++I ++ V VN ++ +   V V    D + + G  +   ++
Sbjct: 1   MRVDKFLHDMNVGTRSQIRKLIKEKAVFVNDVVAKSGRVKVDPVVDQVRL-GEQVITYQQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP+G+VT   D   + TV D          +  VGRLD +TEGLLL+TN+G L
Sbjct: 60  YFYFMMNKPLGVVTATEDRK-QKTVMDLFNKVDFRKDLFPVGRLDKDTEGLLLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNA 187
           A  L  P     + Y     GQ+    +     GIV+  G       +T+          
Sbjct: 119 AHQLLAPERHVQKTYEAVVTGQITDPAVKQFADGIVLKDGTQLKPADLTILNYSALDEQT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
            V V L+EGK  +++++F     +V  L RIS+GP QL   LL G+ RE+S + + + 
Sbjct: 179 LVHVTLKEGKYHQVRRMFGSLGERVVSLKRISFGPLQLEEGLLPGTYRELSDEEIEKL 236


>gi|161870231|ref|YP_001599401.1| pseudouridine synthase [Neisseria meningitidis 053442]
 gi|161595784|gb|ABX73444.1| pseudouridine synthase [Neisseria meningitidis 053442]
          Length = 416

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 210 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 269

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 390 ELNPAEV 396


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 116/237 (48%), Gaps = 10/237 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ ++ ++R+ VN  ++  A  ++    D +  DG  +   E 
Sbjct: 1   MRIDKFLANSGIGTRKEVKELLKKKRISVNDEVVTEAKTHIDEDNDFVAFDGKRIEFKEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP  +++   D   R TV D L    ++V    VGRLD +TEGLL+LTNDG +
Sbjct: 61  L-YIMLNKPQDVISATDDERHR-TVLDLLEEPLTKVGLFPVGRLDKDTEGLLVLTNDGKM 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y V     + +++  +L+ G+ ++       +V   T+      V 
Sbjct: 119 AHELLSPKKHVPKRYYVELKKTLSKEEAAILENGVELETFTTKPAKVEFITEDK----VY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + + EGK  ++K++F+    +V  L R   G   L   L  G  RE++   L +  G
Sbjct: 175 IIISEGKYHQVKRMFKCVGNRVLFLKRTGMGNLGLDENLAPGEYRELTSDELEQLQG 231


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 141/251 (56%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 193 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 252

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 373 ELNPAEVANIL 383


>gi|291043642|ref|ZP_06569358.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|291012105|gb|EFE04094.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 399

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/251 (33%), Positives = 140/251 (55%), Gaps = 7/251 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 193 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 252

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKILREQL 245
           E++   +   L
Sbjct: 373 ELNPAEVANIL 383


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 85  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 143

Query: 61  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 144 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 203

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 324 ELNPAEV 330


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 78/235 (33%), Positives = 122/235 (51%), Gaps = 7/235 (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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R WL +KP G VT + D     T+FD      + + + +VGRLD +TEGL+L+T +G L
Sbjct: 60  -RYWLMNKPAGYVTANHD-KVVPTIFDLFATDDLVAGLYAVGRLDRDTEGLVLVTTNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y VR + ++ +  +    +GIV  G       Q+ L +     +  
Sbjct: 118 GYQLLHPTKKVDKKYSVRVNARLTEKDVQAFSEGIVFHGGTRCLPAQLLLKSCHDQESEA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V L EGK  ++KK+F     KV  L RIS+GP +L TL  G  R ++K  L   
Sbjct: 178 EVVLSEGKFHQVKKMFLACGKKVTFLKRISFGPLELKTLPVGEYRSLTKHELEAL 232


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 117/234 (50%), Gaps = 9/234 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRR+ +R + Q  V +NG   +   + V   D ++V+G  +  
Sbjct: 2   TDSAIRLNKYISESGICSRRDADRYVEQGNVFINGRRAQVGDL-VSIGDKVKVNGQDIEP 60

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE       +KP+G+V+T ++   R  + D + +  SR+  +GRLD +++GL+ LTN+
Sbjct: 61  RDAENLVFIALNKPVGIVST-TEGSERDNIVDFV-NHSSRIFPIGRLDKDSQGLIFLTNN 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V  +  +  D +  +  G+ I G+      V    ++ S  
Sbjct: 119 GDLVNKILRAGNNHDKEYVVTVNKPITDDFIKGMGAGVPILGVVTKKCVV----EQVSPF 174

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +G NR+I+++ E+F ++V +L R       L  L  G  R++ K+ L
Sbjct: 175 AFKIVLVQGLNRQIRRMCEYFGFEVTKLERQQIMNVSLKGLPIGEWRDLDKQEL 228


>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 =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 100/230 (43%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     SR   ++ I    V  +G++++  A  V     +   G  L      
Sbjct: 1   MRLDKYLAETTALSRGLAKKAINSGDVSCDGVVMKDPAFKVPQGARVCFQGEVLALV-GV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP+  + +  D +   +V   L  +   ++   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYLMLHKPVDTICSTQD-EYYPSVLSLLDIARPDKLHIAGRLDADTTGLVLITDDGLWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + YRV+    +  D +    +G+ + G         L+    + A +++ 
Sbjct: 119 KVTSPKRDCAKRYRVQLAESLTDDLIAQFAEGVQLNGEDGLTKPAKLELLSDTEALLSIT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
             EGK  ++K++F     KV  L R + G  +L   L  G  R +++  +
Sbjct: 179 --EGKYHQVKRMFAAVGNKVIGLHREAVGAIELDPQLAPGEWRYLTEAEI 226


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 59/243 (24%), Positives = 111/243 (45%), Gaps = 18/243 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA     SR EV+R+I  + V V+  +    +  V + + + +DG  +    + 
Sbjct: 1   MRLDKFIANNSSYSRTEVKRLIKNKTVCVDKKITTDPSFTVTNLNTVRIDGEIIEAI-KP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------------VISVGRLDINTEG 120
              + +KP G V  + D      V D +    +R             +   GRLD++T G
Sbjct: 60  LYIMLNKPTGYVCANKDNIHSPVV-DLITEQHARQSDQTPPKYRAQSLQIAGRLDVDTTG 118

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+LLT++G     +  P+    + YRV+    +D   + LL +G+++ G     +  T++
Sbjct: 119 LVLLTDNGEWNHRVTSPNKACFKRYRVKLEKPLDDAAIKLLSEGVMLHGEKAATLPATVE 178

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
               SN  V + ++EG+  ++K++F      V +L R + G  +L   L  G  R ++ +
Sbjct: 179 L--ISNTEVLLSIQEGRFHQVKRMFVKVGTCVVKLHREAIGAIELDTNLKPGQWRHLTNE 236

Query: 240 ILR 242
            + 
Sbjct: 237 EIE 239


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 114/231 (49%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   GI SR+EV+++I+   + VNG     A  N+    D IE +G  L   E 
Sbjct: 1   MRLDKFLVECGIGSRKEVKKLISNDEITVNGFNDISAKDNIDENSDIIEYNGEKLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDFKEN-TVMDLLPEWVIRKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY +     +    +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHRLLSPKNHIDKVYYIEIENNILDKDILKLEQGVDIGNYITQPAKV----EKISDNKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KV  L R+S+G  +L  L  G  +EV+ + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVCYLKRVSFGKLKLDDLALGEVKEVNLEDI 225


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 108/347 (31%), Positives = 166/347 (47%), Gaps = 25/347 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG        A
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQT-GMSVKSGDKIELDGRGFVATALA 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP    +R I+VGRLDINT GLLL T DG 
Sbjct: 87  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAVGRLDINTTGLLLATTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR         V    ++ L +G+ ++       ++       
Sbjct: 147 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIIDRLGRGVALEDGPAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK---KI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   L  G + E+     + 
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVTLPRELARGHSVELGSAQVEA 266

Query: 241 LREQLGPHLLEEAQVNLDAPI---YSSETLVRDRPNIISEV------PDDFTRMKKNSSQ 291
           LR QL       + + L   I    +++T VR R               D  R  +    
Sbjct: 267 LRAQLKLEEGAPSALTLQPVIGQRRAAKTTVRVREGGRGNAYVNGHNTADEGRELRRFDN 326

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                 + +       +   +    A    S       QR + + RS
Sbjct: 327 VREDRGRGRGGKGGGFKGGLTVSGEAAAKQSQKPFK--QRAQKNDRS 371


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 115/238 (48%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    + +R ++ ++I ++ V VN ++ +   V V    D + + G  +   ++
Sbjct: 1   MRVDKFLHDMNVGTRSQIRKLIKEKVVFVNDVVAKSGRVKVDPVVDQVRL-GEQVITYQQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP+G+VT   D   + TV D          +  VGRLD +TEGLLL+TN+G L
Sbjct: 60  YFYFMMNKPLGVVTATEDRK-QKTVMDLFNKVDFRKDLFPVGRLDKDTEGLLLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNA 187
           A  L  P     + Y     GQ+    +     GIV+  G       +T+          
Sbjct: 119 AHQLLAPERHVQKTYEAVVTGQITDPAVKQFADGIVLKDGTQLKPADLTILNYSALDEQT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
            V V L+EGK  +++++F     +V  L RIS+GP QL   LL G+ RE+S + + + 
Sbjct: 179 LVHVTLKEGKYHQVRRMFGSLGERVVSLKRISFGPLQLEEGLLPGTYRELSDEEIEKL 236


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 61/230 (26%), Positives = 106/230 (46%), Gaps = 7/230 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLER--AAVNVMSTDHIEVDGVPLRKAERT 73
           + +++ + G   R+E  ++I    V+VNG +++   A   +     + VDG P       
Sbjct: 3   LYRLLQQQGFGGRKECRQLIEYGLVEVNGEVVDDYRAQFELADIASLAVDGEPWPLVTGP 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGLA 131
              L HKP    T+H  P    +V+  LP  F+R+   +VGRLD++T GL+LL+NDG   
Sbjct: 63  LYLLLHKPANYETSHK-PQCHPSVYRLLPDQFARLDVSAVGRLDVDTTGLILLSNDGQFI 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     +VYRV    +   + +  L+ G+ +              ++     + +
Sbjct: 122 HALSSPKKLVPKVYRVTLKHEATPELIAKLQSGVYLNDEAREFA--ADSVEQIDPHTILL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK  ++K++    + +V  L R S G   LG L  G  R ++ + L
Sbjct: 180 TITEGKYHQVKRMVAAASNRVEALHRESLGAIVLGDLPVGEWRHLTAEEL 229


>gi|49081896|gb|AAT50348.1| PA0733 [synthetic construct]
          Length = 231

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 111/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA   ++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGHLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D  P      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L LP ++  +VY V     +DQ  ++    G+  +      +   L+      A   + 
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPIGPRCA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 178 LHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 95/291 (32%), Positives = 143/291 (49%), Gaps = 13/291 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKA 70
            +++ KV+ARAG  SRRE+E MIA  RV ++G + +     V       + +DG  +   
Sbjct: 2   SEKLQKVLARAGHGSRREIEAMIAAGRVSIDGQVAK-LGDRVDGRAELKVRIDGHAVSLK 60

Query: 71  ERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLT 125
                  R+  Y+KP G + + SDP GR TVF+ LP    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-GTLLAGSTREVSKK---IL 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      +  ++    I   V     R  K    K
Sbjct: 241 RDLVGLERESRTLLAQDKLGARRQKTLK-AGKIRRAVHKHRARPAKGRPNK 290


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 66/290 (22%), Positives = 121/290 (41%), Gaps = 9/290 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--A 70
             R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +     
Sbjct: 6   SIRLNKYIGESGICSRRDADRYIEQGNVFINGKRAA-VGDRVFAGDVVKVNGQLIEPRNE 64

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   +   +KP+G+V+T ++   R  + D + +   RV  +GRLD +++GL+ LTN G L
Sbjct: 65  DDLVIIALNKPVGIVST-TEGGERDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V  +  V  + +  L  G+ + G            +K S     
Sbjct: 123 VNKILRAGNDHEKEYLVTVNKPVTAEFIRGLGAGVPMLGTVTK----KCKVKKESTFVFR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F + V +L R       L  L  G  R+++   L E       
Sbjct: 179 ITLVQGLNRQIRRMSEHFGYDVTKLERTRIMNVSLKGLPPGEWRDLTDDELIELFKLIEN 238

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
             ++           T  +      ++V        +    + G  K+ +
Sbjct: 239 SSSEDAAVKKAKPKATAAKKPAASGAKVTSSANAAPRKRFAQPGRKKKGR 288


>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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 114/230 (49%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AG  SRR+ + +I + +VK+N  ++    ++V   D +EV+G  L   E+ 
Sbjct: 1   MRINKFIAHAGYTSRRKADELILKGKVKINDEVILEPGIDVCDDDRVEVEGKVLS-IEKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G +T++ DP     + + +  I  R  + GRLD ++EGLL++TNDG     
Sbjct: 60  FYIKLYKPVGFITSNFDPYNEKDLNELV-DIDKRFFAAGRLDKDSEGLLIITNDGEFTNN 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|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 =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 107/347 (30%), Positives = 166/347 (47%), Gaps = 25/347 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG        A
Sbjct: 24  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQT-GMSVKSGDKIELDGRGFVATALA 82

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP    +R I++GRLDINT GLLL T DG 
Sbjct: 83  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAIGRLDINTTGLLLATTDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR         V    ++ L +G+ ++       ++       
Sbjct: 143 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLARGVALEDGPAKFDEIERIGGTD 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK---KI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   L  G + E+     + 
Sbjct: 203 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELARGHSVELGTAQVEA 262

Query: 241 LREQLGPHLLEEAQVNLDAPI---YSSETLVRDRPNIISEV------PDDFTRMKKNSSQ 291
           LR QL       + + L   I    +++T VR R               D  R  +    
Sbjct: 263 LRAQLKLEEGAPSALTLQPVIGQRRAAKTTVRVREGGRGNAYVNGHNTADEGRELRRFDN 322

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                 + +       +   +    A    S       QR + + RS
Sbjct: 323 VREDRGRGRGGKGGGFKGGLTVSGEAAAKQSQKPFK--QRTQKNDRS 367


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 102/243 (41%), Positives = 156/243 (64%), Gaps = 9/243 (3%)

Query: 2   KDKNIVQENFT----PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMS 56
           KDK I  E        +R++KV++R+G+ASRR+ + MI + RVKVNG++        V  
Sbjct: 94  KDKIIENEQDEIKGHKERLNKVLSRSGVASRRKADEMIREGRVKVNGVVTTLENDHFVSI 153

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRL 114
            D +EVDG  ++K    R+W++ K   ++ THS+ +GR ++   L  +     +I+VGRL
Sbjct: 154 IDEVEVDGKIIKKP-MPRMWMHFKKPKVLVTHSEVEGRESLVPILKKVLKKDHLITVGRL 212

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D  +EGL+LLTNDG L+R LE P  ++ R YRVR  G++ Q+  ++  KGIVI  I Y  
Sbjct: 213 DYYSEGLILLTNDGNLSRYLEHPDNEFERTYRVRIFGKITQEMQDIFTKGIVIDNIKYKP 272

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
           ++V +D +  +N+WV + ++EGKNREI+K+ E+FN KV RLIR+ YGP++L  +L  G T
Sbjct: 273 IEVIVDKESKNNSWVVIKIKEGKNREIRKILEYFNIKVLRLIRVGYGPYELPESLKHGET 332

Query: 234 REV 236
            E+
Sbjct: 333 IEI 335


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 139/247 (56%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 109/230 (47%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +   G+ SRREV+ ++    + VNG + +   +N+   D          + ++ 
Sbjct: 1   MRLDKFLTECGLGSRREVKELLNTGEITVNGAVADNPQMNIKENDDEVFYQERKLEYKKF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLA 131
           R ++ +K  G +T   D     TV D LP       +  VGRLD +TEGLLLLT+DG L 
Sbjct: 61  RYYILNKKAGYITAVGDARD-QTVMDLLPDWVIKKDLAPVGRLDKDTEGLLLLTSDGALN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y      ++ +  L  L+ G+ I G      +      K  +  + +
Sbjct: 120 HKLLSPKNHVEKTYYAELEKEISEADLERLRNGVDIGGYITMPGKAV----KIDSCKIHL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            ++EGK  ++KK+ E    KV  L R+S+G  +L  L  G+ +EVS + +
Sbjct: 176 TIKEGKFHQVKKMLEAVGNKVTFLRRVSFGKLKLEDLELGAVKEVSIEDI 225


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 100/252 (39%), Positives = 144/252 (57%), Gaps = 13/252 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---VPLR 68
             +++ KV+ARAG+ SRRE+E  I   RV++ G   +         DH+E+DG     + 
Sbjct: 10  AGEKLQKVLARAGLGSRREMEAAIQAGRVRIEGRTAK-LGDRARPRDHVELDGRTVQRVH 68

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +    R+ LY+KP G VTT SDP+GRSTVF+ LP    R I+VGRLDIN++GLLL TNDG
Sbjct: 69  REPPRRVLLYNKPEGEVTTRSDPEGRSTVFERLPRTPGRWIAVGRLDINSQGLLLFTNDG 128

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----LDTQK 183
            LA  L  PST   R Y  R HG+V ++ ++ L  G+ ++        V       + Q+
Sbjct: 129 ELANALMHPSTGVEREYACRIHGEVTEEMVHRLVDGVELEDGPAHFEVVESGMPVDEPQE 188

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS---KK 239
           G+NAW  V + EG+ RE+++++E     V+RLIR+ YGP  +   L  G  RE+    K+
Sbjct: 189 GTNAWYHVIVTEGRRREVRRLWESQGVTVSRLIRVRYGPMVMPRDLRRGQLRELDEAGKR 248

Query: 240 ILREQLGPHLLE 251
            L E +G    E
Sbjct: 249 ELYEHVGLTPPE 260


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 99/270 (36%), Positives = 150/270 (55%), Gaps = 12/270 (4%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            ++   +R+ KV+AR G+ SRRE+ER I + R+K+NG  +      + + DH+ ++   +
Sbjct: 11  NQSVDGERIQKVLARGGVGSRREIERWIDEGRLKINGKPV-GLGDRLKAGDHLLINDRVV 69

Query: 68  RKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLL 122
                  + TR+ LYHKP+G V T  DP+GR  VF  LP    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
                  L E A +  + P++ ++  V+  
Sbjct: 250 E-----LLFEFAGMAGEKPVHITKPEVKAH 274


>gi|289664226|ref|ZP_06485807.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 285

 Score =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 76/238 (31%), Positives = 124/238 (52%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +  H  I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQHSSITVDGSPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      +G+     +V++  +   NA
Sbjct: 158 TVTDPTTGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPEGEGMLLRAKRVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RLIR++ GP  +G L  G+ R +S + +R  L
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLIRVAIGPLAMGELCKGAWRMLSAEEVRALL 275


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 112/239 (46%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A  GI +R+EV++ I Q +VKV+  +++     V   +   + G    + E  
Sbjct: 7   IRLDKYLADMGIGTRQEVKKHIRQGKVKVDAAVVKSPEYKVNEKESTVLYGDSPVRYEAF 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+++   D   + TV D +       +   GRLD +TEGLLL+TNDG LA 
Sbjct: 67  VYYMLNKPAGVISATEDRREK-TVVDLIKTKERKDLFPAGRLDKDTEGLLLITNDGKLAH 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAW 188
            L  P     + Y  R  G V ++      +GI I             + + +  G  + 
Sbjct: 126 SLLSPKKHVDKTYYARVKGIVTEEDARAFAEGIDIGTSALPEWTRPAVLEIIS-SGQESA 184

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           V + ++EGK  ++K++F     +V  L R   G   L  +L  G  R+++ + LR   G
Sbjct: 185 VRLTIQEGKFHQVKRMFLARGKEVVYLKRERMGGLVLDSSLKPGEYRKLTDEELRNIYG 243


>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 =  241 bits (615), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 111/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     SRR+ + +IA   ++V+G ++      V     +E+D   L+  +  
Sbjct: 1   MRLDRFLANLPELSRRDAQMLIAGGHLRVDGQVVRDGTHEVRVFSRVELDERLLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP+G V+   DP    TV D  P      +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYYMLHKPMGCVSATRDPQH-PTVLDLFPEDLRDDLHIGGRLDYNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L LP ++  +VY V     +DQ  ++    G+  +      +   L+      A   + 
Sbjct: 120 RLTLPGSRRDKVYYVETEAPIDQRYVDAFAAGLHFRFEDLVTLPAQLEPIGPRCA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  ++K++F  F+ KV RL R   G   L   L  G+ R ++ + +
Sbjct: 178 LHEGRYHQVKRMFGHFDNKVLRLHRERMGDICLDPQLPPGAWRPLNAEEI 227


>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 =  241 bits (615), Expect = 2e-61,   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|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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 119/233 (51%), Gaps = 7/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ KV+A  G  +R+EV+ ++    VK++G++++  ++ +   +  IEV+   + + ++ 
Sbjct: 3   RLDKVLANLGYGTRKEVKAIVKSGAVKIDGLVVKDNSMKIDPDECKIEVE-ETVVEYKKN 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              L +KP G+V    D + + TV D L   +   +   VGRLD +T+GLLL+TNDG L 
Sbjct: 62  IYILMNKPEGVVCATFD-NYQETVIDILEPKYQAFKPFPVGRLDKDTKGLLLITNDGELN 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVT 190
             L  P     +VY      +VD D +   K GIV++        ++ +     + A V 
Sbjct: 121 HRLISPKNHVDKVYYAEIDKKVDMDDIRKFKMGIVLKDEYTCMPAELKIIESDENGARVE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           V ++EGK  +IK++F      V  L RI +GP  L   L  G  RE+  + + 
Sbjct: 181 VTVQEGKFHQIKRMFNSLGKNVIYLERIKFGPLSLDDNLQEGEYRELYGEEIE 233


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 81/259 (31%), Positives = 127/259 (49%), Gaps = 9/259 (3%)

Query: 1   MKDKNIVQENFTP--QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST- 57
           ++ K   ++N      R++K IA  G ASRR+ + MI Q  V VNG ++      V    
Sbjct: 28  LRRKIKTEQNINDPIIRLNKFIALCGEASRRKADEMIEQGEVMVNGKVVMELGYKVDRRA 87

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           D + V+G  L +  +    L +KP  +VTT SD   R TV + +  +  RV  VGRLD +
Sbjct: 88  DEVVVNGKKLHENTQKIYILLNKPKDVVTTSSDEKSRKTVVELV-GLKDRVFPVGRLDRD 146

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDM 175
           T G+LLLTNDG L   L  P+    + Y      ++    L  +KKG  ++  G      
Sbjct: 147 TTGVLLLTNDGDLTYRLTHPTFGVQKQYVATLDKKITSVDLQNIKKGFRLKDTGEKVSPC 206

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +    G   W  V + EGKN +I ++F  F + V +L+R++YG  ++GT+  G  R 
Sbjct: 207 NARILD-DGYTIW--VAIHEGKNHQIHRMFWSFGYNVKKLVRVAYGGLEVGTMRRGEWRF 263

Query: 236 VSKKILREQLGPHLLEEAQ 254
           +++  + +      LE  Q
Sbjct: 264 LTQLEVSKLYKQVQLEGKQ 282


>gi|325205871|gb|ADZ01324.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M04-240196]
          Length = 349

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 139/247 (56%), Gaps = 7/247 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    + VNG   +     V   DH+
Sbjct: 84  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWITNGWITVNGKTAQ-LGDKVTPDDHV 142

Query: 61  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++ +L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 72/235 (30%), Positives = 117/235 (49%), Gaps = 6/235 (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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
           T  +  +KP G V T+ DP+ +    D +       +  +GRLD  + GL+L TNDG +A
Sbjct: 66  TYYYALYKPRGYVCTNYDPNEKLYARDLIDIADKNLLFHIGRLDKESSGLILYTNDGDVA 125

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
           + +  PS +  + Y V    +V ++ L    KGI I     Y   +  + ++K    WV 
Sbjct: 126 QKIMHPSREIEKEYLVSCSTEVRREDLEEALKGIYIDIPQPYRIKRFEILSKK----WVR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L EGKNREI+K+F ++ + V +L+R+  G  +LG +  G  R +    +   L
Sbjct: 182 IILTEGKNREIRKIFSYYGYDVKQLVRMRIGCIELGEMQPGQYRALFSSEIEAML 236


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 106/232 (45%), Gaps = 6/232 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I ++ V VNG ++      +   D +   G PL    +
Sbjct: 4   PCRLDKFISHLAEIPRTQARASIKRKEVSVNGEVITSHNFQLAQQDEVLHQGTPLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R ++ +KP+G V  +SD   + TVFD L     S     GRLDI+T GL+++TNDG  +
Sbjct: 64  -RYYMLNKPVGYVCANSDELHK-TVFDLLDEPNMSDFHVAGRLDIDTTGLVIITNDGDWS 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     +  + L  L+ G+++      D+      ++ +N  + +
Sbjct: 122 HKITSPKNNKFKTYLVETQEPITDEALEQLRTGVMLHNE--KDLTRPAIAERLANYGLRL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++    + KV  L R       L   L +G  R ++ + ++
Sbjct: 180 SISEGKYHQVKRMLYAVDNKVVELHREQIAGITLDENLASGEYRLLTPEEIK 231


>gi|152981336|ref|YP_001353751.1| pseudouridylate synthase [Janthinobacterium sp. Marseille]
 gi|151281413|gb|ABR89823.1| pseudouridylate synthase [Janthinobacterium sp. Marseille]
          Length = 248

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 114/248 (45%), Gaps = 23/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK ++  G+ SRRE +  IA+  V+V+G ++      V+ T  + V+     +  
Sbjct: 3   EPLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGSKVLPTQRVTVERQAAAEQS 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDI 116
           +    L +KP+G V+  ++   +  V                   P+    ++  GRLDI
Sbjct: 63  KRVTVLINKPMGYVSGQAEDGYKPAVALVNASTRWSEDQAATQFHPTQLRSLVPAGRLDI 122

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L    T   + Y VR      G++ +  L  L  G+++ G   
Sbjct: 123 DSVGLLVLTQDGRIAKHLIGEDTSVEKEYLVRVQYSKPGKLPEADLKRLNHGLMLDGKKL 182

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V    +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G 
Sbjct: 183 LPAKVKWQNED----QLSFILREGKKRQIRRMCDMVGLKVIGLKRVRIGNVKLGDLPVGQ 238

Query: 233 TREVSKKI 240
            R + +  
Sbjct: 239 WRYLREDE 246


>gi|329571723|gb|EGG53404.1| pseudouridine synthase B, ribosomal large subunit [Enterococcus
           faecalis TX1467]
          Length = 205

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 66/201 (32%), Positives = 102/201 (50%), Gaps = 3/201 (1%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           ++     V   D +EVDGVP+   E    +L++KP G+++  SD  GR  V D    +  
Sbjct: 2   VKELGTQVSKQDTVEVDGVPI-YQEEYGYYLFYKPRGVISAVSDDKGRKVVTDYFTDVTE 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 LGTLLAGSTREVSKKILREQL 245
           L  L  G  R+++KK + + L
Sbjct: 181 LQGLRPGQYRDLTKKEISQLL 201


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 72/230 (31%), Positives = 115/230 (50%), Gaps = 9/230 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLWL 77
           +++ G+ SR E  R IA+ RV V+  ++      + +  H  I VDG PL    R    +
Sbjct: 2   LSKLGVCSRTEAARWIAEGRVSVDARVIHDPEFPIRADQHEAITVDGQPLAGPAR-VYLM 60

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  +  
Sbjct: 61  LNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAAAVTD 120

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTV 191
           P+    + Y V+   +   ++L  L+ G++       G      QV L  +   NAW+ +
Sbjct: 121 PAIGPDKTYHVQVDCRPGAEQLAQLQAGVIDPAPDGDGALLRAKQVRLLREGERNAWLEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S   +
Sbjct: 181 VLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAAEV 230


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 118/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + ++ + V+G +    A N+ +    +   G  ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKKEILVDGQVAISLAQNIDTGLQELIFQGRKIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT   D     TV D LP      +V ++GRLD +T GLLLLTN+G L
Sbjct: 60  T-YLMLHKPNGVVTASKDKK-LPTVMDLLPQHLQSDQVYAIGRLDRDTTGLLLLTNNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K GIV + G      Q+ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQQFKNGIVFLDGTICKPAQLEILSSSPSISRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           T+ + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++++ L+
Sbjct: 178 TITISEGKFHQVKKMFLSVGVKVTALKRVQFGDFLLDPDLAEGQYRLLNQEELK 231


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 114/228 (50%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR+E  R+I Q R+ VNG L       V  +D I +D   ++  ++ 
Sbjct: 1   MRINKLLSNYGICSRKEANRIIEQNRIIVNGKLCI-PGQWVEESDEILLDNKRIK-PKKK 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP+G+  T S  D ++ + D + +    +  VGRLD  +EGL++LTNDG L+  
Sbjct: 59  VYILLNKPVGITCTSS-KDIKANIIDFV-NYRDYIFPVGRLDKKSEGLIILTNDGELSNK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V+     D + +  + KG+ ++G+      V    ++       + L
Sbjct: 117 ILESENMHEKEYVVKVDKPFDDEFIENMSKGVQLKGVKTRTCIV----RRIDECTFKIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G NR+I+K+   F + V +L RI     ++  +  GS R  ++  L
Sbjct: 173 TQGLNRQIRKMTRAFGYTVVKLKRIRIMNLKIDGIDIGSFRHFTEDEL 220


>gi|319442276|ref|ZP_07991432.1| putative pseudouridylate synthase [Corynebacterium variabile DSM
           44702]
          Length = 282

 Score =  240 bits (614), Expect = 2e-61,   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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDIN 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|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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 109/252 (43%), Gaps = 20/252 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  +   P R+SK +A  G+ SRRE +  IA   VKVNG +++     V     IEV 
Sbjct: 132 KPVPSQPELP-RLSKRMAELGLCSRREADEFIANGWVKVNGEVVDVLGTRVAPDAKIEVS 190

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRV 108
               +    T   L HKP+G V+  ++      V    P                    +
Sbjct: 191 KEAHQHQAETVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNQWKEDPSQTVFKRGHLRGL 250

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLDI++ GLL+LT DG +AR L    +   + Y VR  G + ++ L  L  G+ + 
Sbjct: 251 APAGRLDIDSTGLLVLTQDGRVARRLIGEDSTVEKEYLVRVTGTLSEEGLRKLNHGLSLD 310

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+     +V+   +      +   LREG+ R+I+++ E     V  L R+  G   LG L
Sbjct: 311 GVKLKPAKVSWQNED----QLRFVLREGRKRQIRRMCELVGLTVVGLKRVRIGSVTLGKL 366

Query: 229 LAGSTREVSKKI 240
             G  R +    
Sbjct: 367 PVGMWRYLRPGE 378


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 118/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +   G  ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQGRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LP       + +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPTGVVTANKDRE-LPTVMDLLPPDIQSDMLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ + EGK  ++KK+F     KV  L RI +G F L   L  G  R ++++ L+
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTSLKRIQFGEFTLDPELAEGQYRPLNQEELK 231


>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 =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/237 (32%), Positives = 121/237 (51%), Gaps = 10/237 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
              +R+ K++A  G  SR+EV+ +IA+ RV V+G    R        +  I+VDG  +  
Sbjct: 1   MAMERLDKLLASTGRWSRKEVKELIARGRVLVDGRPAGRPEDKCEPQSACIQVDGEIVDC 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTND 127
           A      + HKP GL++   D   +STV D LP    R  +  VGRLD +TEGLLLLT+D
Sbjct: 61  A-PCVYIMLHKPAGLLSATQDKK-QSTVLDLLPEHLRRRGLFPVGRLDKDTEGLLLLTDD 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN 186
           G L   L  P     +VY  R  GQ+D++ + +L +G+ +  G+      +      G  
Sbjct: 119 GPLGHDLLSPRKHVDKVYYARVDGQIDKEDVQVLAQGMTLGDGLVCLPAGLEPL---GDG 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           +   V LREGK  ++K++       V  L R+S GP +L   L  G  R ++++ ++
Sbjct: 176 SECLVTLREGKYHQVKRMLAARGKPVLYLKRLSMGPLKLDEKLEKGQWRFLTEREVQ 232


>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 =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITILAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 124/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++A+  I SR+ +++ + ++ + V+G+     A N  +    +   G+ ++  E 
Sbjct: 1   MRLDKLLAQEKI-SRKAMKQALLKKEILVDGLPASSLAQNTDTGLQELMFQGIRIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT   D     TV D LP      ++ ++GRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPNGVVTASKDKK-LPTVMDLLPQHLQSDQLYAIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K GI+ + G      Q+ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGPLTPDHIQEFKDGIIFLDGTICKPAQLEILSSSPSLSKA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           T+ + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++K+ L  QL  +
Sbjct: 178 TITISEGKFHQVKKMFLSVGVKVTALKRVQFGNFILNPDLAEGDFRLLNKEEL--QLIKN 235

Query: 249 LLEEAQ 254
            LE + 
Sbjct: 236 YLENSG 241


>gi|254525039|ref|ZP_05137094.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722630|gb|EED41155.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 546

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 107/347 (30%), Positives = 166/347 (47%), Gaps = 25/347 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA+  VKVNG + +   ++V S D IE+DG        A
Sbjct: 24  ERLHKVLAQAGLGSRRALEQRIAEGLVKVNGEVAQT-GMSVKSGDKIELDGRGFVATALA 82

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP    +R I++GRLDINT GLLL T DG 
Sbjct: 83  EPSRVLVYNKPEGEVTTREDPEGRPTVFESLPPLKGARWIAIGRLDINTTGLLLATTDGE 142

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR         V    ++ L +G+ ++       ++       
Sbjct: 143 LANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLSRGVALEDGPAKFDEIERIGGTD 202

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK---KI 240
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   L  G + E+     + 
Sbjct: 203 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELARGHSVELGTAQVEA 262

Query: 241 LREQLGPHLLEEAQVNLDAPI---YSSETLVRDRPNIISEV------PDDFTRMKKNSSQ 291
           LR QL       + + L   I    +++T VR R               D  R  +    
Sbjct: 263 LRAQLKLEEGAPSALTLQPVIGQRRAAKTTVRVREGGRGNAYVNGHNTADEGRELRRFDN 322

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRS 338
                 + +       +   +    A    S       QR + + RS
Sbjct: 323 VREDRGRGRGGKGGGFKGGLTVSGEAAAKQSQKPFK--QRAQKNDRS 367


>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 =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 6/232 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I ++ V VNG ++      +   D +  +G PL    +
Sbjct: 4   PCRLDKFISHLAEVPRTQARASIKRKEVSVNGEVITAHNFQLAKDDVVLHNGEPLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R ++ +KP+G V  +SD D   TVFD L     S     GRLDI+T GL+++TNDG  +
Sbjct: 64  -RYFMLNKPVGYVCANSD-DLHKTVFDLLDEPNMSDFHVAGRLDIDTTGLVIITNDGDWS 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P +   + Y V     +  + L  L++G+++      D       ++ +N  + +
Sbjct: 122 HKITSPRSNKFKTYLVETQEPITDEALEQLREGVMLHNE--KDATRPAIAERLANYGLRL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++    + KV  L R      +L   L  G  R +++  ++
Sbjct: 180 SISEGKYHQVKRMLYAVDNKVVELHREQIAGIKLDEDLAPGEYRLLTENEIK 231


>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 =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/232 (33%), Positives = 123/232 (53%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA+AG+ASRR+ E MI   +VKVNG ++ +    V S D + VD   +   E  
Sbjct: 5   ERLQKRIAQAGVASRRKAEEMIVNGQVKVNGKIITKLGKKVSSDDIVYVDNKKIN-EESF 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             +L +KP G V+++     + +V + +    +R+ SVGRLD +T G+LLLTNDG L + 
Sbjct: 64  EYYLLNKPAGYVSSNRSYPNQPSVIELI-KTKTRIFSVGRLDQDTTGVLLLTNDGELTQK 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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + EGK  EIKK+ +F    V +L R  +    +G L  G  R +S++ + +
Sbjct: 183 TIAEGKTHEIKKILDFIGHPVIKLNRDMFDGITIGNLKKGQYRALSEQEVEK 234


>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 =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 75/227 (33%), Positives = 123/227 (54%), Gaps = 3/227 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V    D I VDG  +    R  
Sbjct: 85  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEADRIAVDGTVIAAQAR-V 143

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TVF  L ++    +  VGRLD  +EGLLL TND  LA+ 
Sbjct: 144 YLMLNKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQR 203

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   +VY V+  G   +     + +G+   G     ++V        N+W+ + L
Sbjct: 204 LLDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKGGDRNSWIEIEL 263

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++  
Sbjct: 264 DEGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTEAE 310


>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 =  240 bits (613), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 82/238 (34%), Positives = 132/238 (55%), Gaps = 7/238 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR---- 68
            +++ K++A  G+ SRRE+ER I   RV +NG   +   + +     + +D   +R    
Sbjct: 2   SEKIQKILAHFGLGSRREIERWIHDGRVHINGQPAK-LGMRIHLKAKVTIDNQRIRLTTN 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
           K    R+ +YHKP+G + + SDP    TVF++LP     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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           W  V L+EG+NRE+++++E     V+RL+RI +G   L   L  G   E+  K +++ 
Sbjct: 181 WYHVVLKEGRNREVRRLWETQGVTVSRLMRIRFGNVSLPHDLKKGHFFELKTKAIKKL 238


>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 =  240 bits (613), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 107/233 (45%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A AG+ASRR+ + +I    V VNG +     V V    D +EV G  +  
Sbjct: 1   MAKVRLNKFLASAGVASRRKCDEIIFAGSVTVNGRVAAGPFVTVDEEFDSVEVGGQRI-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           AE+   ++ HKP+G + +      G   V D L     R+ +VGRLD  T GL+L+TNDG
Sbjct: 60  AEKKVYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++    V    L  L  G VI G     + V     K     
Sbjct: 120 EFANRVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSVK----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L
Sbjct: 176 IKIIVNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDSEL 228


>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 =  240 bits (613), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 97/307 (31%), Positives = 153/307 (49%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE  + KV+RL+R  YG   L   L  G   E+ K  +     
Sbjct: 181 WYQVVVKEGRNREVRRIFESQDLKVSRLLRTRYGTVILPRELRTGRWMELDKTDIDNLAK 240

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              L+  Q      +       + R + ++E P    R      Q+    K+  + T   
Sbjct: 241 SVELKPRQGTGLFGM------AKRRTDRMTEKPMAARRGGYLRQQRRDDEKEAPVNTGNQ 294

Query: 307 RRNLASN 313
           R++   N
Sbjct: 295 RKSTGFN 301


>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 =  240 bits (613), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 116/236 (49%), Gaps = 7/236 (2%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           T  WL HKP G++T  +D D  +TV D L        +  VGRLD +T GL+ LT +G L
Sbjct: 61  T-YWLLHKPQGVLTAVTD-DRFTTVIDCLAPQDQAPGLYPVGRLDRSTTGLVFLTTNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y+V  +G + QD +    +GI+I          + ++      +  
Sbjct: 119 GYRMLHPQYHVEKEYQVVVNGPLTQDHVASFAQGILIDQNRPCAPAHLVIEASGPQESRA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + +REGK  ++KK+F     KV +L R+  G   L   L  G+ R +  + L + 
Sbjct: 179 RLTIREGKFHQVKKMFLSVGVKVTQLHRLRMGHLVLDQDLAPGAYRPLKPEELDQL 234


>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 =  240 bits (613), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 108/245 (44%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  GI SRRE +  I Q  V V+G  +      +     I +D     + 
Sbjct: 1   MEKVRLSKLMSARGICSRREADVYIEQGSVYVDGQPVRELGTKIYPWQEIVLDRAAQIRQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLD 115
            +    L +KP+G V+   +P  +S +                  +P     +   GRLD
Sbjct: 61  NQQVTILLNKPVGYVSGQPEPGYKSAISLVNNDSHFHQDRSSLRFVPQHLKNIAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+ T DG +A+ L    +Q  + Y VR  G + ++ L LL  G+ + G      
Sbjct: 121 IDSQGLLVFTQDGRIAKQLIGEYSQIEKEYLVRVSGNLTREGLALLNHGLQLDGQALKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+   Q      +   L+EGK R+I+++ E     V  L R+  G  +L  L  G  R 
Sbjct: 181 RVSRLNQD----QLRFILQEGKKRQIRRMCELVGLNVTGLKRVRIGQIRLADLPEGKWRY 236

Query: 236 VSKKI 240
           + K  
Sbjct: 237 LGKNE 241


>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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 112/243 (46%), Gaps = 14/243 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--------NVMSTD 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 +G  +     D  S++   LP+   R+  VGRLD ++
Sbjct: 61  QLTFDGAPISAVEEKEYWAFHKAVGTDSRLL-IDDSSSLLHLLPAT-PRLYPVGRLDKDS 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 RLAKD----QFEITLTQGLNRQIRRMSQALGFKVIDLKRVKIQSLALGDLKEGEMRQLTS 234

Query: 239 KIL 241
             L
Sbjct: 235 SEL 237


>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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 112/231 (48%), Gaps = 5/231 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R+SKV+A AGIASRR  E +I Q  VKVNG +++     V    D I V    + +
Sbjct: 1   METNRLSKVLAAAGIASRRACEELIFQGLVKVNGEVIKVPQTKVNPEIDTITVRDEVINR 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E    +L +KP G + +         + D       R+ +VGRLD +T+GLL++TNDG 
Sbjct: 61  KEDKVYYLLNKPPGYICSARKSGQTKIILDLFQDEDHRLFTVGRLDKDTQGLLIVTNDGH 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS    + Y  +   ++  + L  +  G +++G+    ++V    QK     +
Sbjct: 121 FANQIIHPSANIQKEYLAKTDQEISHEHLIAIANGTLVEGVFVKPIRV----QKVRKGTI 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGK RE++ +      KV  L RI  G   LG L  G+ R +++  
Sbjct: 177 KIIIGEGKKREVRMLLSAAGLKVQELTRIRLGGLHLGRLPIGNWRPLTETE 227


>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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 66/235 (28%), Positives = 111/235 (47%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K ++   IA+R + + M+   RV VNG  ++ A + V    D I VDG      E 
Sbjct: 3   IRIDKFLSTQAIATRSQAKEMLRAGRVLVNGTPVKAADLKVDPEGDEIRVDGRVYGYQEH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D   R TV D +P    R  +   GRLD +T G +L+T+DG  
Sbjct: 63  L-YLMLNKPQGVVSATDDKVHR-TVLDLVPPELRRRGLFPAGRLDRDTVGFVLITDDGEF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  +  P     + Y     G + +++L++L +G+V+  G      ++T+  Q G    +
Sbjct: 121 AHNILSPRHHVPKTYEAGLDGPIGENELSVLAQGVVLGDGTKCRPAELTVL-QSGERPLI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            + + EG+  +IK++F     +V  L R   G   L  +L  G    +S   L +
Sbjct: 180 QIVIVEGRYHQIKRMFAAVGRRVLTLKRTKIGGLALDPSLKEGDCIAISPSNLEK 234


>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 =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 95/236 (40%), Positives = 141/236 (59%), Gaps = 7/236 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +++ KV+ARAG+ SRR++E  I   R++VNG +       V     I VDG PLR+  
Sbjct: 3   ETEKLQKVLARAGMGSRRQMEHWIRDGRIRVNGRIAR-LGERVAPRMQITVDGRPLRRRS 61

Query: 72  R---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
                R+ LYHKP+G+VTT SDP GR TVF +LP I   R I+VGRLDINT GLLL T D
Sbjct: 62  LSGLPRMLLYHKPVGVVTTRSDPAGRPTVFQHLPRIKKGRWIAVGRLDINTCGLLLFTTD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN 186
           G LA  L  PS + +R Y VR +G+V  + +  L++G+ ++       ++ +  + + +N
Sbjct: 122 GELANRLMHPSFRLVREYAVRVYGEVTAEMITRLQQGVELEDGRGAFDRIEVLCEAQAAN 181

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            W  V L EG+ RE+++++E    +V+RLIR+ YGP +L   L  G  R++    +
Sbjct: 182 GWYRVSLAEGRRREVRRLWESQGVRVSRLIRLRYGPVRLPPGLRQGQIRKLGPAEI 237


>gi|157371821|ref|YP_001479810.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157323585|gb|ABV42682.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 266

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 60/253 (23%), Positives = 111/253 (43%), Gaps = 10/253 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           +  R++K I+ +GI SRR+ +R I   +V +N          V   D + V+G  +    
Sbjct: 5   SSIRLNKYISDSGICSRRQADRYIKLGKVFINDNQA-EVGAPVFIGDVVSVNGQRIEPRN 63

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                L   +KP+G++T+            +  +   R   VGRLD +++GL+ LTN G 
Sbjct: 64  DADLVLIALNKPVGIITSM--GKHVPNNIGDFVNHSQRTFPVGRLDKDSQGLIFLTNRGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V     +  + +  +  G+ I G      QV    ++ +   +
Sbjct: 122 LVNKILRAGNNHQKEYLVTVDKPLTDEFIQGMGAGVPILGKVTHKCQV----EQEAPQVL 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ ++F ++V +L R+      L  L  G  R++S+   R +L   L
Sbjct: 178 RITLVQGLNRQIRRMCKYFGYQVTKLERVRIMNISLQGLALGEWRDLSEDE-RTELFKLL 236

Query: 250 LEEAQVNLDAPIY 262
              +    D P  
Sbjct: 237 EHSSSEEPDLPQR 249


>gi|257462423|ref|ZP_05626837.1| ribosomal small subunit pseudouridine synthase A [Fusobacterium sp.
           D12]
          Length = 231

 Score =  240 bits (612), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 118/231 (51%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR+EV+ ++ +++++VN  ++      +    D +  +   L   ++
Sbjct: 1   MRMDKFLVECGLGSRKEVKELLKKRKIQVNASIVTSGQQIIDEEKDEVFYEKEKLVY-KK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G VT   D   R TV + LP       ++ VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYILYKKAGYVTALEDSKER-TVMELLPEWVIRKDLVPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P +   + Y V     + ++ +  L++G+ I        QV    ++     ++
Sbjct: 119 NHQLLSPKSHVDKTYHVCLEKIITEEAIEQLRQGVRIGDYTTLPAQV----EQLEEQKIS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  + KV+ L R+S+G   LG L  G  REVS + +
Sbjct: 175 LTIQEGKFHQVKKMLEAVDNKVSYLKRVSFGRLVLGDLKPGEVREVSLEDI 225


>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 =  240 bits (612), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 110/232 (47%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A+ G+ +R EV+ ++ +  V  NG  ++ +   +    D +EV G  +   E 
Sbjct: 1   MRIDKFLAQMGVGTRTEVKALLKKGHVLHNGAKIKSSKTQIDPEHDVVEVKGRVIAY-EP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP  +++   D     TV D +       +  VGRLD +TEGLLL+TNDG   
Sbjct: 60  FVYLMMNKPQNVISATVDDQH-QTVIDIIEGYRHLDLFPVGRLDKDTEGLLLITNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y V+    +  +     ++GI ++        + +       A+  V
Sbjct: 119 HALMNPNKHVSKTYWVKAKYALKTNDPKRFEEGITLKEGRLQPAHLEILD-DSMTAF--V 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            ++EGK  ++K++F   + +V  L R+S G   L  +L  G+ R +++  L+
Sbjct: 176 TIQEGKYHQVKRMFHAIDNEVVGLKRVSIGDLTLDSSLSPGAYRSLTEDELK 227


>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 =  240 bits (612), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 110/243 (45%), Gaps = 15/243 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---- 67
              R++K ++ AGI SRRE +R+I + +V V G         +   + +  +G  +    
Sbjct: 4   DGIRLNKFLSGAGICSRREADRLIEEGKVTVGGRTA-VPGQKIKKGETVVCNGRTIAAGS 62

Query: 68  ---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               K     L   HKP G+V T SD D    + D +     R+   GRLD  +EGL+L+
Sbjct: 63  RGAEKKPERVLLAVHKPCGIVCTTSDKDRAPNIVDMV-DCPVRIYPAGRLDKESEGLILM 121

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQ 182
           TN G L   +   S+   + Y V     V  + +  ++KG+ +    +           +
Sbjct: 122 TNQGDLVNRMMRGSSGHEKEYLVWIDRPVKPEFIQKMRKGVFLPELDVTTKPCFAEKTGE 181

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           K       + L +G NR+I+++ E    KV +L R+     +LG L AG +R VSKK   
Sbjct: 182 KS----FRIVLTQGLNRQIRRMCEQLGCKVRKLKRVRIMNIELGDLKAGESRPVSKKEYA 237

Query: 243 EQL 245
           E +
Sbjct: 238 ELM 240


>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 =  240 bits (612), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 99/232 (42%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R   ++ + +  +  +G++++ A   V     I ++G P+      
Sbjct: 1   MRLDKFICESTSLTRSLAKKALHRGDITCDGVVIKDAGFKVTEGMQICLEGEPIVLV-GE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP+  + +  D +   +V   L       +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYVMLNKPVDTICSTID-EAYPSVLSLLDIPKPETLHIAGRLDADTTGLVLITSDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  + Y V+    VD   + +  KG+ +  +        + +         V 
Sbjct: 119 KITSPKKECGKRYLVQLADPVDDGLIEVFAKGVALRNEDGLTKPAVLEI----IDPQQVR 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++F      V  L R   G  +L   L  G  R ++ + +
Sbjct: 175 LTITEGKYHQVKRMFAAVGNLVVGLHRERIGQIELDPDLALGEWRYLTAEEI 226


>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 =  240 bits (612), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR+E +++++  RVKV+G    +A   V +   + +DG P+      
Sbjct: 1   MRLDQYLSNGTELSRKEAKKVVSAGRVKVDGETCRQANRQVEAEQSVHLDGKPVNPP-GD 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+++  +D   + T  D LP    SRV   GRLD +T GLLLLT+DG  + 
Sbjct: 60  IYLMMHKPAGVLSATTD-SSQPTALDLLPRGLASRVHIAGRLDKDTTGLLLLTSDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + YRV     + +     L+KG+++ G         +     +N  + + 
Sbjct: 119 AVTSPRRECRKSYRVWLAEAIPEQACRALEKGVMLNGETTETRPAEVRVH--NNQLIDLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + EG+  ++K++      +V  L R   G  +L   L  G  R ++ + +R
Sbjct: 177 IGEGRYHQVKRMLAAVGNRVEALHRFRIGSIELDDKLAPGEFRALTYQEIR 227


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 74/233 (31%), Positives = 106/233 (45%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A AG+ASRR+ + +I    V VNG       V V    D +EV G  +  
Sbjct: 1   MAKVRLNKFLASAGVASRRKCDEIIFAGSVTVNGRAATGPFVTVDEEFDSVEVGGQRI-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           AE+   ++ HKP+G + +      G   V D L     R+ +VGRLD  T GL+L+TNDG
Sbjct: 60  AEKKVYFMVHKPLGYLCSSERKFPGSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++    V    L  L  G VI G     + V     K     
Sbjct: 120 EFANRVIHPSFGITKEYLLKVSRDVTARDLETLMAGTVIDGKVVRPVSVK----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L
Sbjct: 176 IKIIVNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDSEL 228


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 106/232 (45%), Gaps = 6/232 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R +    I +Q   VNG ++      +   D +   G  L    +
Sbjct: 4   PCRLDKFISHLAELPRSKARASIKRQAALVNGEVVTAFDFQIKQQDEVVFQGEQLVFLGK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R ++ +KP+G V+ +SD   + TVFD +     S     GRLDI+T GL++LTNDG  +
Sbjct: 64  -RYFMLNKPVGYVSANSDELHK-TVFDLIDEPNMSDFHVAGRLDIDTTGLVILTNDGDWS 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     +  + L+ L++G+ +              ++ +N  + +
Sbjct: 122 HKITSPKNNKFKTYLVETQEPITDESLDALREGVQLHNEKALTRPAK--AERLANYGLRL 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++    + KV  L R   G  +L   L AG  R ++ + ++
Sbjct: 180 SICEGKYHQVKRMLAAVDNKVVELHREQIGNIKLDENLAAGEYRLLTAEEIK 231


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 138/247 (55%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 143 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 202

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 323 ELNPAEV 329


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G  +R  V+++I  ++VKV+G ++ +    V S T  +EV+G  +   E 
Sbjct: 6   IRLDKYLVHVGYGTRSTVQKIIRGKKVKVDGQVIIKPETAVNSLTSVVEVNGERMDYQE- 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G +T   D     TV D L        V  VGRLD +TEGLL+LTNDG +
Sbjct: 65  FYHFILNKPRGYITATEDGRD-QTVLDLLEERDQNKEVFPVGRLDKDTEGLLILTNDGKM 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     +VY  R  G++ ++ + +  +GI +  G  Y   ++ +  +    + +
Sbjct: 124 AHGLLSPKRHVDKVYYARVAGKMTEEDIKMFAEGIALTDGTKYAPGKLEI-IRSDEESEI 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            V + EGK  ++K++ +    +V  L RI  G  +L   L  G+ R ++K+ L
Sbjct: 183 YVTIHEGKFHQVKRMVQAVGKEVVYLKRIKMGGLELPEDLSLGTYRTLTKEEL 235


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 84/247 (34%), Positives = 138/247 (55%), Gaps = 7/247 (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  EVDG--VPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  + L+ A+R  R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 142 TVKGSIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 201

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    PS +  R Y VR  G +  +++  L ++G++++       
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 EVSKKIL 241
           E++   +
Sbjct: 322 ELNPAEV 328


>gi|269302650|gb|ACZ32750.1| RNA pseudouridine synthase [Chlamydophila pneumoniae LPCoLN]
          Length = 235

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 107/232 (46%), Gaps = 6/232 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K +A AG+ASRR+ + +I    V VNG + E   V V   D ++V G  +   
Sbjct: 1   MTKVRLNKFLASAGVASRRKCDEIIFSGSVTVNGRVAEGPFVLVDPEDKVQVGGTSVHLT 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   ++ HK IG + +      G   V D    +  RV +VGRLD  T GL+L+TNDG 
Sbjct: 61  -KKVYFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS+   + Y ++    V    L  L +G  I G     + VT    K     V
Sbjct: 120 FANKIIHPSSGITKEYLLKVSRDVSAKDLEKLMEGTFIDGKHVRPVSVT----KIRRGTV 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EGK  EI+   +     +  L RI  G   LG L  G  RE++   L
Sbjct: 176 KIVVSEGKKHEIRLFADAAGLPILELKRIRIGSLVLGGLRYGEYRELTDAEL 227


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 114/229 (49%), Gaps = 4/229 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              +R++K +A  GIASRR+ E +I   +V VNG ++ +  + V  ++ I V G  + + 
Sbjct: 1   MNKKRIAKHLASCGIASRRKCEDLIFAGKVSVNGEVVRQPQLLVDGSEKITVSGKKVNRQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   ++ +KP+  + + +   G   V D    +  R+ +VGRLD  T GLL++TNDG  
Sbjct: 61  EKKVYFMLNKPLNTLCSPNGKKGSKLVTDLFEGVKERLFTVGRLDKETTGLLIVTNDGEF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  PS+   + Y  +   ++  D L  +  G  ++G+    + V     K   A + 
Sbjct: 121 TNQVIHPSSNIQKEYIAKTDCEISNDHLKAIAAGTSVEGVFVQPLSVK----KVRKATLK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           V + EGK RE++ +      +V  L R   G   LG+L  G  R ++++
Sbjct: 177 VVVGEGKKREVRLLIAAAGLEVRALKRTRIGSLTLGSLPIGHWRSLTER 225


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 68/236 (28%), Positives = 120/236 (50%), Gaps = 3/236 (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-QGICYGDMQVTLD--TQKGSNAWVT 190
           +  P  ++ + Y+    G+V + ++N L KG+ I        +Q  L    Q+   + + 
Sbjct: 122 VMHPRYEFFKTYQGLCKGKVSKQQVNQLLKGVKIEDDYFTKAIQAELLNYDQEKDQSIIE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + EGK   +K++F      + +L R      ++  L  G  RE+    +++  G
Sbjct: 182 MTIAEGKKHHVKQMFSAIEANLMKLKRTKIEFLEVDDLEVGRYRELKPHEVKKFYG 237


>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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 112/231 (48%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SRREV+ ++    + VNGI+     +N+    D I      L   ++
Sbjct: 1   MRLDKFLTECGLGSRREVKEILNTGEITVNGIIANNPQMNIKENSDEIFYQERKLEY-KK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D     TV + LP       +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FRYYILNKKAGYITAVEDSRD-QTVMELLPDWVIKKDLAPVGRLDKDTEGLLLLTNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y       + +D+L  L+ G+ I G      +      +  +A + 
Sbjct: 119 NHKLLSPKNHVEKTYYAELEKDISEDELVKLRNGVDIGGYITMPAKA----DRIDSAKIH 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E    KV  L RIS+G  +L  L  G+ +EV+ + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVGNKVIFLKRISFGKLKLDNLELGAVKEVNIEDI 225


>gi|300121522|emb|CBK22041.2| Pseudouridine synthase [Blastocystis hominis]
          Length = 271

 Score =  239 bits (611), Expect = 4e-61,   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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 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|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 =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 115/238 (48%), Gaps = 8/238 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK 69
               R+ K +A  G+ +R EV+R I + R+ VNG +++     +   TD +  DG  +  
Sbjct: 1   MGKIRLDKYLADMGLGTRTEVKRDIKKGRISVNGEIVKSPEYKIDIQTDVVLADGKEIAY 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDG 128
            E    ++ +KP G+V+   D   + TV D +       +  VGRLD +TEGLLL+TNDG
Sbjct: 61  EE-LVYYMLNKPQGVVSATEDRRDK-TVLDLISEKKRKDLFPVGRLDKDTEGLLLITNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y VR    + ++    L++G+ I +        V +  +K   A
Sbjct: 119 ELAHNLLSPKKHVDKKYFVRLRDALSEEDKKHLEEGVDIGEDKLTLPSHVFVLNEKRDEA 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
              + +REGK  +IK++F     +V  L R+S G   L   LL G  R ++ + +   
Sbjct: 179 --EIVIREGKFHQIKRMFHAVGNEVVFLKRLSMGSLTLDEALLTGEYRLLTPQEIERL 234


>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 =  239 bits (611), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 118/232 (50%), Gaps = 7/232 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPSGVVSARRDKEH-QTVIDLIKPEDQREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +  +  +     + G+V +         + + +     +  
Sbjct: 119 GFALLHPRYHVAKRYYVEVNDVLGPEAPAFFESGVVFEDGTVCKPAHLKILSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L RIS+G F L   L  GS R ++++ 
Sbjct: 179 HITISEGKFHQVKKMFLAYGVKVTYLKRISFGDFVLDEKLPRGSYRPLTEEE 230


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 112/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E 
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 61  FVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + +   +   +GI ++         +V     +   + 
Sbjct: 120 AHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 180 VKITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 236


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 70/244 (28%), Positives = 113/244 (46%), Gaps = 9/244 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G+ SR+EV+++I   +++VN + + +    V    D +   G  L   + 
Sbjct: 2   MRLDKFLATLGLGSRKEVKKLITSGQIQVNDVTVTKVNHGVDEDHDQVAYLGQELVY-QA 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP GLV+   D     TV D +   F  V    VGRLDI+T GLLLLTN+G L
Sbjct: 61  YYYVMLNKPDGLVSATED-KMHETVIDWVALDFDHVDLFPVGRLDIDTTGLLLLTNNGQL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
           A  L  P     + Y+    GQV +  +     GI ++       ++ +         + 
Sbjct: 120 AHQLLSPKKHVAKTYQALVTGQVSEVDIAAFAAGIRLKDFTAQAAELEILDYDPDKDQSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKILREQLGP 247
             V + EGK  ++K++F   + +V  L R+S G       L  G  RE++     + L P
Sbjct: 180 TKVTIHEGKFHQVKRMFLARDHEVLHLHRVSMGPLDLDPDLDLGQYRELTAAEC-DLLRP 238

Query: 248 HLLE 251
           + LE
Sbjct: 239 YGLE 242


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 97/307 (31%), Positives = 151/307 (49%), Gaps = 13/307 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 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      +       + R + ++E P    R      Q+    K+    T   
Sbjct: 241 SVELKPRQGTGLFGM------AKRRTDRMTEKPMAARRGGYLRQQRRDEEKEAPANTGNQ 294

Query: 307 RRNLASN 313
           R++   N
Sbjct: 295 RKSTGFN 301


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 51/230 (22%), Positives = 101/230 (43%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR++V R + ++RV ++  ++   AV ++    +  D   L+     
Sbjct: 1   MRLDRFLSHQLGKSRKQVTRALKEKRVILDSKVITNGAVKLLPEQKVLFDQQLLKYPITG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G + +  DP     V D      S  + + GRLDI+  GL+L+T+DG  + 
Sbjct: 61  RYFMLNKPKGYLCSTRDP-HHPVVNDFFDETVSGELHAAGRLDIDATGLVLMTDDGQWSH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     +  D       G+ ++          L      +  + + 
Sbjct: 120 RLTSPKYHCKKTYWVTLASPISHDPTQNFLDGLRLKNEKTLTRPAQLKIVTPQS--MELT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EG+  ++K++F      V  L R+  G  +L   L+ G  R ++K+ +
Sbjct: 178 ITEGRYHQVKRMFAAIGHHVTELHRMQIGSIKLDEALMPGQYRLLTKQEI 227


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 112/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E 
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 61  FVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKTVFPVGRLDKDTRGLLLLTNNGQL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + +   +   +GI ++         +V     +   + 
Sbjct: 120 AHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 180 VKITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 236


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 112/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E 
Sbjct: 1   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ES 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + +   +   +GI ++         +V     +   + 
Sbjct: 119 AHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 179 VKITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 235


>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 =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 103/229 (44%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +A     SR+E +R IA+ +++VNG ++ +   +V     +E  G  +    + 
Sbjct: 1   MRLDYFLAHTTSWSRKEAKRFIAKGKIRVNGDVVTKPNASVTEDCKVESHGEVILWR-KE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           + +  +KP   V+   D +    + D + P     +  VGRLD +T GL+ LT DG    
Sbjct: 60  KYFALYKPADYVSALEDSES-PVLIDLIEPEERKNLKIVGRLDKDTTGLIFLTTDGQWLH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + YRV     + +     L+ G+++ G         ++  + S+  + + 
Sbjct: 119 RITSPKHDCYKTYRVYCADPISEANCKSLETGVMLNGEDLPTSPAKVE--RVSDTEILLS 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++EGK  ++K++      +V +L R +     L  L  G  R +++  +
Sbjct: 177 IKEGKYHQVKRMLAAVGNRVEKLHREAISDVNLDGLQEGQYRILTEDEI 225


>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 =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 112/237 (47%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E 
Sbjct: 1   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ES 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 60  FVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKTVFPVGRLDKDTRGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + +   +   +GI ++         +V     +   + 
Sbjct: 119 AHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSL 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++      +V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 179 VKITIQEGKFHQVKRMVAACGKEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 235


>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 =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 109/241 (45%), Gaps = 16/241 (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 +G      + D ++++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  ETEALAYWIFNKAVGTDCRLLEQD-KTSLLHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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

Query: 244 Q 244
            
Sbjct: 235 L 235


>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 =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 108/238 (45%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +  AGI SR +V+ ++ ++ V VNG +   A   +    D I   G  L   E 
Sbjct: 1   MRLDKFLVDAGIGSRSQVKSLLKKKEVLVNGQVESSAKRQIDSDKDQIVFQGQKLVYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D +   TV D L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 61  LYY-MLNKPAGVVSATED-NLHQTVVDLLDDRARQKEVFPVGRLDKDTHGLLLLTNNGEL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAW 188
           A  L  P     ++Y     G + +      + GI +         + +    +      
Sbjct: 119 AHQLLTPKKHVDKIYLAHIEGMMTKKDQEAFENGIQLSDHHCLPATLEVLETDEHKQTCK 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           V + L+EGK  ++K++ +    +V  L R++ GP +L   L  G  R ++ + +   +
Sbjct: 179 VKITLKEGKFHQVKRMVKACGKEVTDLQRLTMGPLKLDNQLQLGQFRRLTDEEITSLM 236


>gi|332202557|gb|EGJ16626.1| hypothetical protein SPAR69_0668 [Streptococcus pneumoniae GA41317]
          Length = 241

 Score =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>gi|237745528|ref|ZP_04576008.1| pseudouridylate synthase [Oxalobacter formigenes HOxBLS]
 gi|229376879|gb|EEO26970.1| pseudouridylate synthase [Oxalobacter formigenes HOxBLS]
          Length = 249

 Score =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 116/248 (46%), Gaps = 23/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK ++  GI SRRE +  I +  VKV+G  + +    V+    I ++    ++  
Sbjct: 4   EPVRLSKRMSELGICSRREADEWIERGWVKVDGKTVSQLGSKVLPHQKISIEKQASQEQA 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDI 116
           R    L +KP+G V+  ++   +  V                   PS    ++  GRLDI
Sbjct: 64  RRVTILINKPVGYVSGQAEDGYKPAVSLISEATRWKGDPSKEKFKPSQLRSLVPAGRLDI 123

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L   ++   + Y VR      G++ ++ L LL+ G+ + G   
Sbjct: 124 DSVGLLVLTQDGRIAKRLIGENSATDKEYLVRVKYLKPGKLPENDLQLLRHGLKLDGKPL 183

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V       ++  +   LREGK R+I+++ E    KV  L RI  G  +LG L  G 
Sbjct: 184 LPAKVNWQ----NDDQLRFVLREGKKRQIRRMCEAVGLKVIGLKRIRIGQIKLGDLPPGQ 239

Query: 233 TREVSKKI 240
            R +  + 
Sbjct: 240 WRYLRPEE 247


>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 =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 120/238 (50%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 17  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSITVDGQPLAGPARC 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 77  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDMQVTLDTQKGSNA 187
            +  P+    + Y V+   +    +L  L+ G+       +G+     QV++  +   NA
Sbjct: 136 TVTDPARGPDKTYHVQIDCRPSAAQLTQLQAGVADTDPEGEGVLLRAKQVSVLREGERNA 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +
Sbjct: 196 WLEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVRTLV 253


>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 =  239 bits (610), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+SK +A  G+ SRRE +  I Q  VKV+G +       V+  + IE+D       
Sbjct: 1   MEPVRLSKRMAELGLCSRREADSYIEQGWVKVDGEVA-VLGQKVLPHNQIEIDKKAQDAQ 59

Query: 71  ERTRLWLYHKPIGLVTTHSD-----------PDGRS----TVFDNLPSIFSRVISVGRLD 115
                 L +KP+G V+  ++           P+ R     +     PS    +   GRLD
Sbjct: 60  SARVTILLNKPVGYVSGQAEDGYLPAAALIKPENRWAEDGSRKRFQPSHLRGLAPAGRLD 119

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A+ L    ++  + Y VR  G++    L LL  G+ + G      
Sbjct: 120 IDSVGLLVLTQDGRIAKQLIGEHSEVEKEYLVRVEGELTPSGLALLNHGLELDGKKLLPA 179

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V    +      +   LREGK R+I+++ E    +V  L RIS G  +LG L  G  R 
Sbjct: 180 KVGWQNED----QLRFVLREGKKRQIRRMCELVGLRVVGLKRISIGKVKLGNLPTGQWRY 235

Query: 236 VSKKI 240
           +    
Sbjct: 236 LRDDE 240


>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 =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 108/233 (46%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
               R++K +A AG+ASRR+ + +I    V +NG +     V V    D+IEV G  +  
Sbjct: 1   MAKVRLNKFLASAGVASRRKCDEIIFAGSVTINGKVAAGPFVTVDEEFDYIEVGGQRI-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           AE+   ++ HKP+G + +      +   V D L     R+ +VGRLD  T GL+L+TNDG
Sbjct: 60  AEKKVYFMVHKPLGYLCSSERKFPQSKLVIDLLSHCPYRLFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++    V    L  L  G +I G     + V     K     
Sbjct: 120 EFANRVIHPSFGITKEYLLKVSRDVTAKDLESLMSGTMIDGRIVRPVSVK----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   L
Sbjct: 176 IKIIVNEGKKHEIRLFAEAAGLQLLELKRIRIGSLVLGGLPYGKYRELTDAEL 228


>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 =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 77/212 (36%), Positives = 111/212 (52%), 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  RSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           R TV D L S F R   +  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|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 =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 111/229 (48%), Gaps = 8/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++  G+ +R EV++ + +++V ++  +       +    + ++V+   +    +
Sbjct: 1   MRLDKFLSNMGVGTRTEVKQRLKKKQVTIDDKVETSPKKQINPELEIVKVNDQKIDFVNK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP   ++  +D   + TV D +    +  +  VGRLD +TEGLLL+TNDG   
Sbjct: 61  -VYLMLNKPKDYISATTDEQHK-TVLDLIEDYRYLDLFPVGRLDKDTEGLLLITNDGQFN 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     + ++ +N  K GI +        ++ +   + + ++  V
Sbjct: 119 HELMSPGKHVAKTYEVISQKNITKNDINAFKVGIELNEGLAKPAKL-VQGDELNKSF--V 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK 239
            + EG+  ++K++F   + +V  L RI  G  QL  TL +G  R ++++
Sbjct: 176 TIYEGRYHQVKRMFHAIDNEVLALKRIRIGDLQLDSTLASGEYRHLTQQ 224


>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 =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 91/288 (31%), Positives = 145/288 (50%), Gaps = 8/288 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV VNG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARIGLGSRRYMEEVIAAGRVSVNGRVAQ-VGERIEPGDELRIDGRKVQFQIE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           W  V ++EG+NRE++++FE    KV+RL+R  YG   L   L  G   E+ K  + + L 
Sbjct: 181 WYQVVVKEGRNREVRRIFESQELKVSRLLRTRYGTVILPRELRTGRWMELDKTDI-DNLA 239

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             +  + +        +     R     ++     F R ++   +K  
Sbjct: 240 KSVELKPRQGTGLFGMAKRRTDRMTEKPMAARRGGFLRQQRRDDEKEA 287


>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 =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 101/232 (43%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I+ +   +R   ++ + +  V V+G +++  +  +  +  + +DG P+      
Sbjct: 1   MRLDKFISESTQLTRSLAKKALHRGEVTVDGQVIKDGSFKLNESQQVCLDGEPISLI-GP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP   + +  D +   +V + L       +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RFIMLHKPADTLCSTVD-EVYPSVLNLLDLPHKEDLHIAGRLDADTTGLVLITSDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  + Y V+    +  + +     G+ +  +        + L      +    
Sbjct: 119 RVTSPKRECGKTYLVQLADPLKAEWVEQFATGLALRSEEGLTKPATLELLG----SHEAR 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++F     KV  L R S G   L  +L  G  R +++  +
Sbjct: 175 LTITEGKYHQVKRMFAAVGNKVVGLHRESVGEIVLDESLAPGEWRYLTEAEI 226


>gi|226941109|ref|YP_002796183.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
 gi|226716036|gb|ACO75174.1| Pseudouridine synthase [Laribacter hongkongensis HLHK9]
          Length = 703

 Score =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 85/252 (33%), Positives = 136/252 (53%), Gaps = 8/252 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
            R+ K +A AG+ SRR+++ ++A  RV +NG +       V   D + VD  P  +R  +
Sbjct: 453 MRLQKALALAGLGSRRDMDELVAAGRVSINGAVA-ELGARVRPGDKVRVDSKPVLIRWPD 511

Query: 72  R-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           R  R+ +YHK  G + T  DP+GR+TVFD LP    S+ +++GRLD+NT GLL+ T  G 
Sbjct: 512 RLPRVIVYHKQEGEIVTRDDPEGRTTVFDRLPQTRSSKWVAIGRLDVNTSGLLIFTTSGD 571

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NA 187
           LA  +  PS +  R Y VR  G++  +++     G+ +         +  D  K    N 
Sbjct: 572 LANRMTHPSFEVEREYAVRVLGKLTPEQMKETTAGVQLDDGPASFQFIREDDDKEDSVNH 631

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLG 246
           W  VG+REG+NRE++++FE F   V+RL+R+ +G   L + L  G   E+++  + + + 
Sbjct: 632 WYRVGIREGRNREVRRMFEHFGLTVSRLMRVRFGIVTLPSRLKRGQFYELNELEVSKLMH 691

Query: 247 PHLLEEAQVNLD 258
              L  A    D
Sbjct: 692 WSGLTMAGTRAD 703


>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 =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 100/231 (43%), Gaps = 6/231 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I  +   +R   ++ + +  +  +GI+++ +   V+    + ++G P+     
Sbjct: 6   PVRLDKFICESTSLTRSLAKKALHRGEITCDGIVVKDSGFKVLEGMQVCLEGEPISLV-G 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  + +KP+  + +  D +   +V   L       +   GRLD +T GL+L+T+DG  +
Sbjct: 65  ERYLMLNKPVDTICSTID-EAYPSVLSLLDIEKPETLHIAGRLDADTTGLVLITSDGQWS 123

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     + Y V     VD   + +   G+ ++          L+  +     V +
Sbjct: 124 HRITSPKKDCGKRYLVTLADPVDGSLVGIFAAGVELRNEDGLTKPAVLEIIEP--QLVRL 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 182 TITEGKYHQVKRMFAAVGNHVVGLHRESIGRIELDSDLAPGEWRYLTSEEI 232


>gi|160880922|ref|YP_001559890.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160429588|gb|ABX43151.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 240

 Score =  238 bits (609), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 113/233 (48%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A   + +R EV++MI + RV VNG         V S  D I VD   L      
Sbjct: 9   RLDKYLADLSVGTRTEVKQMIRKGRVMVNGNTETSPETKVDSNHDKIFVDSRELSYVT-L 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+  +D   ++TV D +     + +  VGRLD +TEGLL++TNDG LA 
Sbjct: 68  EYFMLNKPAGVVSASNDKK-QTTVVDLIDEAKRKDLFPVGRLDKDTEGLLIITNDGDLAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY  +    + ++       G+ I       +   L+      A+  V 
Sbjct: 127 QLLSPKKHVDKVYFAKLRDPLKKEDEEAFAAGLKIDEEFTA-LPAKLERISEQEAY--VT 183

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           +REGK  +IK++FE    +V  L RIS G   L  +L  G  RE++++ +   
Sbjct: 184 IREGKFHQIKRMFEATRNEVIYLKRISMGSLVLDESLSLGEYRELTEEEIEAL 236


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 99/287 (34%), Positives = 137/287 (47%), Gaps = 23/287 (8%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT----RLWLYHK 80
             RRE+E +I   RV V+G + +    V V     I +DG  +   E      R+  Y+K
Sbjct: 1   GPRREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYK 60

Query: 81  PIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           P G + T +DP+GR TVFD LP    +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 EVRRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLREL----------V 230

Query: 256 NLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            L     S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 231 ELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 274


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGIKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>gi|324018876|gb|EGB88095.1| hypothetical protein HMPREF9542_02380 [Escherichia coli MS 117-3]
          Length = 277

 Score =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 99/285 (34%), Positives = 137/285 (48%), Gaps = 23/285 (8%)

Query: 28  RREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT----RLWLYHKPI 82
           RRE+E +I   RV V+G + +    V V     I +DG  +   E      R+  Y+KP 
Sbjct: 4   RREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE 63

Query: 83  GLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G + T +DP+GR TVFD LP    +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 L
Sbjct: 184 RRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLREL----------VEL 233

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 234 PPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 275


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 114/236 (48%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I+     SR E +++I +  V +N IL++     V   +D + V+G  L   ++
Sbjct: 1   MRLDKFISTTTTLSRAEAKKIIKKG-VLINNILVKSPDYKVDELSDQVIVNGERLVY-QK 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP  +V+   D     TV D L       +V  VGRLD +TEGL+LLTNDG L
Sbjct: 59  YIYIMMNKPKNVVSATEDA-VEKTVVDILEEKDRIHKVFPVGRLDKDTEGLMLLTNDGEL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V   G++  + + L++ GI+I G       ++ +       +  
Sbjct: 118 AHKLISPKKDVEKKYYVEVSGKLKDEYIELVENGIIIDGGYKCKSARLEILESNEEKSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           ++ + EGK  ++K++ +     V  L R+S G  +L   L  G  R +++K L+  
Sbjct: 178 SIFITEGKFHQVKRMMKALGTTVTYLKRLSIGSLKLDENLKLGEYRYLTEKELKNL 233


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 73/227 (32%), Positives = 112/227 (49%), Gaps = 3/227 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           +++V+++AG+ SR E  R I   RV+V+G ++      +      + VDG      ER  
Sbjct: 26  LARVLSKAGLCSRTEAARWIEAGRVQVDGRIVRDPEYPMRHGLRGVLVDGRAPAGPERI- 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
               +KP GLVTT  D  GR TV+  L       +  VGRLD  +EGLLL +ND   A  
Sbjct: 85  YLALNKPRGLVTTARDEQGRDTVYRCLDGSGLPWLAPVGRLDRASEGLLLFSNDPAWAAR 144

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P +   + Y V+     DQ  L  L+ G+   G     +  ++      NAW+ + L
Sbjct: 145 VLDPDSGPDKTYHVQVDAIPDQTLLQALRTGVDADGEHLRAVSASVLRTGTRNAWLEIVL 204

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+++   F+  V RL+R++ G  QLG L  G  R +    
Sbjct: 205 DEGRNRQIRRLLAAFDLSVLRLVRVAIGALQLGDLGKGQWRMLQPAE 251


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 115/229 (50%), 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  ++ ++ D  GR T+  +L     R+ + GRLD  TEGL++++NDG +   
Sbjct: 60  EYYILNKPKRVLCSNEDRQGR-TLAVSLIKSKKRLFTYGRLDYMTEGLIIISNDGDIYNN 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y  +    +  D +  LK G+VI G+     +V   T++     V V +
Sbjct: 119 VMHPKKKLYKSYIAKIDSDITDDHIEALKYGVVIDGVRTLPAKVKTITKR----EVRVAI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            EG+NR+I+K+FE   + V  L R+  G   L  L  G  R+++   ++
Sbjct: 175 HEGRNRQIRKMFEVLGYTVKTLRRVKVGELSLKGLEVGKYRKMTDDEIK 223


>gi|332075974|gb|EGI86440.1| hypothetical protein SPAR68_0695 [Streptococcus pneumoniae GA41301]
          Length = 241

 Score =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 127/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 84/256 (32%), Positives = 130/256 (50%), Gaps = 20/256 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPL 67
           E   P R+ + +ARAG+ASRR  ER++ + RV+VNG+++      V  T D +EVDG  +
Sbjct: 4   ERIVPMRLQRFLARAGVASRRGSERLMTEGRVRVNGVVVSELGSKVDPTRDTVEVDGHIV 63

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
             A+     + +KP G +TT SDP GR T+   +P   +  +  VGRLD++T GLLL T 
Sbjct: 64  GIADAPVYLMLNKPEGYLTTMSDPQGRPTIKTMVPTKRYPGLFPVGRLDMDTSGLLLFTT 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---- 182
           DG +A+ L  PS    + Y     G   + +L  L++GI++        +V L       
Sbjct: 124 DGTMAQELLHPSRHVWKHYLALVLGVPTEAELERLRRGIMLDDGMAQPAKVELRDDLLEL 183

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                      K  NA V + + EG+  ++KK+      +V  L R ++GP +L  +  G
Sbjct: 184 HGTSRYPQNPNKPQNAIVGIWIHEGRKHQVKKMMSAIGHRVLVLHRDAFGPLRLTNVEEG 243

Query: 232 STREVSKKI---LREQ 244
             RE+  +    LREQ
Sbjct: 244 CWRELRDEEIAALREQ 259


>gi|315159966|gb|EFU03983.1| conserved hypothetical protein [Enterococcus faecalis TX0312]
          Length = 260

 Score =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIRGKQVTVDGIVTLNESHNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 93/302 (30%), Positives = 146/302 (48%), Gaps = 7/302 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV +NG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSINGRIAQ-VGERIEPGDELRIDGRKVQFQVE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 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 RR 308
            R
Sbjct: 301 GR 302


>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 =  238 bits (609), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 103/246 (41%), Gaps = 19/246 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I Q  V V+G         +     I +D     K 
Sbjct: 1   MEKVRLSKLMSAQGMCSRREADVYIEQGWVYVDGQPARELGTKIYPWQEITLDRTAQIKQ 60

Query: 71  ERTRLWLYHKPIGLV---------------TTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            +    L +KP+G V                  S      +           +   GRLD
Sbjct: 61  NQQVTILLNKPVGYVSGQPELGYKPAASLICHDSRFHRDRSSLKFTSQHLKNLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+ T DG +A+ L    ++  + Y VR  G + +  L LL  G+ + G      
Sbjct: 121 IDSQGLLVFTQDGRVAKQLIGEYSRIEKEYLVRVIGNLTRKGLALLNHGLQLDGQVLKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+L  Q      +   L+EGK R+I+++ E     V+ L R+  G  +L  L  G  R 
Sbjct: 181 KVSLLNQD----QLRFILQEGKKRQIRRMCELVGLNVSGLKRVRIGQIRLADLPEGKWRY 236

Query: 236 VSKKIL 241
           + K  L
Sbjct: 237 LGKNEL 242


>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 =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 127/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 94/282 (33%), Positives = 137/282 (48%), Gaps = 10/282 (3%)

Query: 28  RREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT----RLWLYHKPI 82
           RRE+E  I   RV V+G +      V ++    I +DG  +   E      R+  Y+KP 
Sbjct: 9   RREIEAKIEAGRVSVDGKIATLGDRVEIVPGLKIRIDGHLISVKESAEQICRVLAYYKPE 68

Query: 83  GLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G + T +DP+GR TVFD LP    +R I+VGRLD+NT GLLL T DG LA  L  PS + 
Sbjct: 69  GELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            R Y VR  GQVD DKL  L +G+ ++        +     +G N W  V L EG+NRE+
Sbjct: 129 EREYAVRVFGQVDDDKLRQLSRGVQLEDGPAAFKTIKFTGGEGINQWYNVTLTEGRNREV 188

Query: 202 KKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS---KKILREQLGPHLLEEAQVNL 257
           ++++E    +V+RLIR+ YG   L   L  G   E+       LRE +       ++V +
Sbjct: 189 RRLWEAVGVQVSRLIRVRYGDILLPKGLPRGGYTELDLAQTNYLRELVELTPETSSKVAV 248

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           +      +     R            R   NS++++    + 
Sbjct: 249 EKDRRRLKANQIRRAVKRHSQTSANPRQGNNSNRRSSTRNKT 290


>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 =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 121/237 (51%), Gaps = 10/237 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV K++++ GIASRR  E +I ++R+K+NG ++        + D +E+DG  ++  ++T+
Sbjct: 4   RVQKILSQLGIASRRHAEILILEKRLKLNGQIVLLGDKADPNHDLLELDGKIIKSHKKTQ 63

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGG 129
               L +KP+G++ +  D   RS V D LPS   +   +  VGRLD+N+ G LLLTNDG 
Sbjct: 64  LFYILVNKPVGIICSCKDSQNRSIVMDLLPSNLRKGMGIHPVGRLDMNSSGALLLTNDGN 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   L  P     ++Y V   G   Q  L   ++G+V+ G       + +         +
Sbjct: 124 LTLRLTHPRYHLPKIYEVLVRGNFTQAILKDWRQGVVLDGKKTLPAYLEVINNNRQYTNL 183

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-----GTLLAGSTREVSKKIL 241
            + L EGKNR I+++ + F   V +L R + GP  L       +  G  R +S   +
Sbjct: 184 KIILTEGKNRHIRRIAQKFELDVIKLHRTAIGPISLSTSKVDNVKLGHYRLLSSSEI 240


>gi|88859932|ref|ZP_01134571.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88817926|gb|EAR27742.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 293

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 100/299 (33%), Positives = 152/299 (50%), Gaps = 16/299 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+ARAG  SRRE+E+ I   RV V+G +       V     I +DG  ++  E 
Sbjct: 2   SEKLQKVLARAGKGSRREIEKFIEAHRVSVDGNVAR-LGDRVEPHQLIRLDGHIVKIEEP 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+ +YHKP G + T  DP+GR TVFD L      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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK---ILRE 243
           W  V L EG+NRE++++++    +V+RLIR+ YG  +L   L  G   E+       LR+
Sbjct: 181 WYNVLLTEGRNREVRRLWQSQGVEVSRLIRVRYGDLELNKRLPQGGWEELELDKVNYLRK 240

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            +G          L+  +       +D+   I+++     + K+ ++ K    K KK  
Sbjct: 241 LVGL------DRELETKLSVIPEKRKDKRAKIAQIRKAVNKHKQRTTGKKTDPKAKKRT 293


>gi|160876850|ref|YP_001556166.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862372|gb|ABX50906.1| pseudouridine synthase [Shewanella baltica OS195]
          Length = 256

 Score =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 29  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 87

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T DG  +  
Sbjct: 88  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 146

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 147 ITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 204

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 205 TEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 253


>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 =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 111/230 (48%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +  A   +R+E   ++  + V VN ++ +  +V V     +E  G  L      
Sbjct: 1   MRLDKFLCDALGITRKEATHLLKTKTVTVNDVMQKSGSVKVTEQCVVEWQGNELN-VHGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V +H D   R T F+ L  I   ++   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMLYKPEGFVCSHEDGSNR-TAFELLDEIKMDKLHFAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  ++YRV     V+ D +   K+GI ++      +   L+ +  +   V + 
Sbjct: 119 RITAPKHKCEKMYRVWLVDPVEPDYVEKFKEGIQLKSEDGLTLPAHLEVR--AEREVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R   G  ++  +L  G  R ++++ +
Sbjct: 177 IHEGKYHQVKRMFAALGNKVEALHRERIGEIEMDESLELGEYRYLTQEEV 226


>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 =  238 bits (608), Expect = 9e-61,   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  RTRLWLYHKPIGLVTTHSDPDGRSTVF----------------DNLPSIFSRVISVGRLD 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 KVAWQNAD----QLRFSLKEGRKRQIRRMCELVGLRVVGLKRVRIGAVRLGDLPLGRWRY 238

Query: 236 VSKKI 240
           ++   
Sbjct: 239 LAPGE 243


>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 =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 75/243 (30%), Positives = 122/243 (50%), 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  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINT 118
           +   G P+    +      +KP+  + TH D +GR    D +   F  R+ +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 I----ISPVKVKIVLREGKNREIRKLFTSKNIKVKRLHRVRIGPVQIAGMHPGEFRNLKP 236

Query: 239 KIL 241
           K +
Sbjct: 237 KEI 239


>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 =  238 bits (608), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESRNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 99/285 (34%), Positives = 137/285 (48%), Gaps = 23/285 (8%)

Query: 28  RREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT----RLWLYHKPI 82
           RRE+E +I   RV V+G + +    V V     I +DG  +   E      R+  Y+KP 
Sbjct: 1   RREIESIIEAGRVSVDGKIAKLGDRVEVTPGLKIRIDGHLISVRESAEQICRVLAYYKPE 60

Query: 83  GLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G + T +DP+GR TVFD LP    +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 L
Sbjct: 181 RRLWEAVGVQVSRLIRVRYGDIPLPKGLPRGGWTELDLAQTNYLREL----------VEL 230

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                S   + +DR  + +       R  K  SQ +G  +     
Sbjct: 231 PPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQVSGGRRSGGRN 272


>gi|46202419|ref|ZP_00053237.2| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 236

 Score =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 108/241 (44%), Gaps = 13/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ ++IA  G  S+R+V+ MI    V   +G +L+  +  V   D I VDG PL     
Sbjct: 1   MRLIRLIANLGYGSQRDVKAMIKDGLVTRADGSVLDDTS-KVAHED-IRVDGEPLDPPPG 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDG 128
             + + +KP G   + SDP     V++ LP  F      V  VGRLD ++ GLLLLT+DG
Sbjct: 59  L-VLMLNKPEGYTCSTSDPG--RVVYELLPPRFMHRNPIVAPVGRLDRDSSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            LA  +  P     + Y V     +  ++  +   G ++++          L       A
Sbjct: 116 PLAHRVTSPKRHVPKTYEVTLARPLTGEEGAVFASGTLMLRSENTPLAPAELMVTGPQTA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + + EG+  ++K++F      V RL R + G   LG L  G  R ++   +   + P
Sbjct: 176 --RITITEGRYHQVKRMFAAVGNHVERLHRAAIGGLDLGDLPEGQWRMLTPDEITLVIAP 233

Query: 248 H 248
            
Sbjct: 234 Q 234


>gi|217974541|ref|YP_002359292.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499676|gb|ACK47869.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 242

 Score =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 113/241 (46%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D+IE+D  P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLGESLNCLDNIELDSAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLSYWILNKAVGTDCRLLEQDE-TSLIHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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

Query: 244 Q 244
            
Sbjct: 235 L 235


>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 =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 113/231 (48%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR+EV+ ++  ++++VNG+ +     N+    D +      L   E 
Sbjct: 1   MRIDKFLVECGVGSRKEVKELLKSRKIRVNGLFITSPKENIEEEKDEVYYGEKKLSYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ HK  G VT   D    +TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYILHKKAGYVTALEDSRE-ATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P +   + Y       + ++ L  L++G++I        +     +K  +  + 
Sbjct: 119 NHRLLSPKSHVDKTYHASLECDITEEALEKLREGVMIGEYKTLPAKA----EKLEDRKIA 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + +REGK  ++KK+ E    KV  L RIS+G   LG L  G  +EVS + +
Sbjct: 175 LTIREGKFHQVKKMLEAVGNKVIYLKRISFGKLVLGDLELGEVKEVSLEDI 225


>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 =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 108/232 (46%), Gaps = 6/232 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K +A AG+ASRR+ + +I    V VNG + E   V V   D ++V G  +   
Sbjct: 1   MTKVRLNKFLASAGVASRRKCDEIIFSGSVTVNGRVAEGPFVLVDPEDKVQVGGTSVHLT 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   ++ HK IG + +      G   V D    +  RV +VGRLD  T GL+L+TNDG 
Sbjct: 61  -KKVYFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS+   + Y ++    V    L  L +G  I G     + VT    K     V
Sbjct: 120 FANKIIHPSSGITKEYLLKVSRDVSAKDLGKLMEGTFIDGKHVRPVSVT----KIRRGTV 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EGK  EI+   +   + +  L RI  G   LG L  G  RE++   L
Sbjct: 176 KIVVSEGKKHEIRLFADAAGFPILELKRIRIGSLVLGGLRYGEYRELTDAEL 227


>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 =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 136/247 (55%), Gaps = 7/247 (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  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G P++        R+ LY+K  G + +  DP GR ++FD LP   S R +++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 EVSKKIL 241
           E++   +
Sbjct: 344 ELNPAEV 350


>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 =  238 bits (608), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 106/238 (44%), Gaps = 9/238 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            QR+   I+     +R +++R+I   RV ++   + + A  +  T+ + VDG  +     
Sbjct: 2   SQRLDAFISNNSDFTRSQIQRLIKAGRVHIDDKPVSQGAQKLNGTESVRVDGELIEPL-S 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            R  + HKP G V  ++D +   TV D +     + +   GRLD++T GL+LLT+DG   
Sbjct: 61  LRYLMLHKPQGYVCANTDSEH-PTVLDLIDLPRKQTLQIAGRLDLDTTGLVLLTDDGQWN 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P  +  + YRV     +  D  +    GI + G  +      L+     NAW+  
Sbjct: 120 HRITSPRRECSKRYRVTTAEPIAADTAHYFTDGIQLHGEKHKTRPAHLELIDDYNAWLD- 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + EGK  ++K++F     KV  L R   G   L   L     R ++   +   LG H
Sbjct: 179 -IHEGKYHQVKRMFAATGNKVIALHRTRIGSITLDNQLTPAHWRPLTPAEI---LGIH 232


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 112/235 (47%), Gaps = 5/235 (2%)

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  D   +  +   L +   RV   GRLD ++EGLL++TNDG L   
Sbjct: 61  TVLAVYKPAGIVCT-EDKREKKNIIRFL-NYPLRVTYAGRLDKDSEGLLIMTNDGDLING 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           +        + Y+V  + ++  + +  + +G+ I+        +      +K      ++
Sbjct: 119 MMRARFSHEKEYKVTVNKEITPEFIEKMSRGVHIRDREKNLDAVTRPCKVRKNGKYTFSI 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            L +G NR+I+++ E   +KV  L RI     +LG L  G  R ++++ L+E  G
Sbjct: 179 ILTQGLNRQIRRMCEALGYKVTTLKRIRIMNVELGNLKPGEVRGLTEQELKELYG 233


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 55/222 (24%), Positives = 105/222 (47%), Gaps = 9/222 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +++I + +V +NG +       V   D +EV G  + K++R +
Sbjct: 4   RINKYLSEVGYCSRREADKLILEGKVTINGEIP-EIGTKVEDNDQVEVKGQRIEKSKRQK 62

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDKKLEPNNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ +  ++ + +  +  G+ I      +  V     +       + 
Sbjct: 122 KILRARNNHEKEYIVKVNRPINSNFIKSMSNGVEILDTITKNCFVEQLGPRN----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           L +G NR+I+++ E   ++V  L R+     +L  +  G  R
Sbjct: 178 LTQGLNRQIRRMCEALGYRVRSLKRVRIMNIKL-DVPTGEYR 218


>gi|313904278|ref|ZP_07837656.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
 gi|313470828|gb|EFR66152.1| pseudouridine synthase [Eubacterium cellulosolvens 6]
          Length = 256

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 112/256 (43%), Gaps = 27/256 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++   + +R+E++  I +    VNGI +     ++   + +  DG P+R  E  
Sbjct: 1   MRLDKYLSDMNVGTRKELKTKIRKGAATVNGIRITDPGFSIKGDEDVTFDGKPIRYNE-Y 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G++T   D   + TV D L       +  VGRLD NT GLLL+TNDG L  
Sbjct: 60  EYYMLNKPAGVITATEDRK-QQTVLDLLGKDRRKDLFPVGRLDKNTVGLLLITNDGDLNH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSN----- 186
            L  P     + Y  +  G+V    +    KG+ I         ++ + + + +      
Sbjct: 119 KLLSPKKHTDKKYYAKIDGRVTDADVEAFAKGLRIDDELTALPAKLEILSFRETATDADR 178

Query: 187 -----------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TL 228
                            + + V + EGK  +IK++F     +V  L R+S G   L  +L
Sbjct: 179 EDLLTAEHPESSLSSGVSEICVTIHEGKFHQIKRMFHAVEKEVLYLKRLSMGSLVLDPSL 238

Query: 229 LAGSTREVSKKILREQ 244
             GS R +++  +R  
Sbjct: 239 PEGSWRPLTEDEIRNL 254


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 116/248 (46%), Gaps = 23/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK ++  G+ SRRE +  IA+  V+V+G ++      ++ T  + V+     +  
Sbjct: 3   EPLRLSKRMSELGLCSRREADEWIARGWVRVDGKVVSELGTKILPTQRVTVERQAAAEQS 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDI 116
           +    L +KP+G V+  ++   +  V                   P+    ++  GRLDI
Sbjct: 63  KRVTILINKPMGYVSGQAEDGYKPAVALVKAESRWKEDTSPTQFHPTQLRSLVPAGRLDI 122

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L   ++   + Y VR      G++ +  L  L  G+++ G   
Sbjct: 123 DSVGLLVLTQDGRIAKHLIGENSSVEKEYLVRVQYIKPGKLPEADLQRLNHGLMLDGKKL 182

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              QV    +      ++  LREGK R+I+++ +    KV  L R+  G  +LG L  G 
Sbjct: 183 LPAQVKWQNED----QLSFILREGKKRQIRRMCDIVGLKVVGLKRVRIGRVKLGDLPVGE 238

Query: 233 TREVSKKI 240
            R +++  
Sbjct: 239 WRYLAEGE 246


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 93/302 (30%), Positives = 146/302 (48%), Gaps = 7/302 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
            +++ KV+AR G+ SRR +E +IA  RV +NG + +     +   D + +DG  ++    
Sbjct: 2   SEKLQKVLARVGLGSRRYMEEVIAAGRVSINGRIAQ-VGERIEPGDELRIDGRKVQFQVE 60

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
              R R+ +Y+KP G + + +DP+ R TVFD+LP I + 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 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 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 RR 308
            R
Sbjct: 301 GR 302


>gi|295113966|emb|CBL32603.1| pseudouridine synthase family [Enterococcus sp. 7L76]
          Length = 260

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I++ G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKLKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETKSHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 112/239 (46%), Gaps = 10/239 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A     +R +V+  + + RV V+G +   +          + +DG P+  A R
Sbjct: 5   IRLDKFLAEMKKGTRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVSYA-R 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D +   TV   +  +    +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 64  MEYFMLNKPQGVVSATED-NLHPTVISLIGDAKRKDLFPVGRLDIDTEGLLLITNDGKLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQ----KGSN 186
             L  P     +VY  +  G + +D +     GI +         ++ +++         
Sbjct: 123 HELLSPKKHVDKVYFAKVKGTLREDIVQAFAGGITLADQTTVLPAELLIESSYEEAGEPV 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
               + + EGK  ++K++FE    +V  L R+S GP  L   L  G +R ++ K ++  
Sbjct: 183 CEARLTIHEGKFHQVKRMFEAAGGQVVFLKRLSMGPLTLDPKLKPGESRLLTGKEIKAL 241


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 107/237 (45%), 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 +G      + D ++++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  ETEALAYWIFNKAVGTDCRLLEQD-KTSLLHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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|291518121|emb|CBK73342.1| ribosomal small subunit pseudouridine synthase A [Butyrivibrio
           fibrisolvens 16/4]
          Length = 234

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 102/234 (43%), Gaps = 14/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K++    I +R EV+ ++ +  + V+G    +    V      I   G      ++
Sbjct: 2   MRLDKLLVELNIGTRSEVKALLKKGLIFVDGEKATKPEQKVDENSVVITYQGKEYTY-QK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              ++ +KP G++T   D     TV D      P     +  VGRLD +T GLLL+TNDG
Sbjct: 61  FSYYVINKPKGVITATEDA-HEKTVMDVFYSLCPDAPKGLAPVGRLDKDTTGLLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  +  P     + Y V   G++ ++ +  L+ G+ I +G       V  +  K    
Sbjct: 120 QLAHDMLSPKKHVDKTYFVTLDGELSEEDVAALEAGVHIGEGEPTAPATVKYEGGK---- 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKK 239
              + + EGK  ++K++F      V  L R ++GP  L    +  G    ++ +
Sbjct: 176 TCYITIHEGKFHQVKRMFFAVGKTVLELKRTAFGPLVLDEEKVPEGHFITLNPE 229


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 107/232 (46%), Gaps = 6/232 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R++K +A AG+ASRR+ + +I    V VNG + E   V V   D ++V G  +   
Sbjct: 1   MTKVRLNKFLASAGVASRRKCDEIIFSGSVTVNGRVAEGPFVLVDPEDKVQVGGTSVHLT 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   ++ HK IG + +      G   V D    +  RV +VGRLD  T GL+L+TNDG 
Sbjct: 61  -KKVYFMVHKAIGYLCSSEKKFPGTKLVIDLFAHLPYRVFTVGRLDKETSGLILVTNDGE 119

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  PS+   + Y ++    V    L  L +G  I G     + VT    K     V
Sbjct: 120 FANKIIHPSSGITKEYLLKVSRDVSAKDLGKLMEGTFIDGKHVRPVSVT----KIRRGTV 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + + EGK  EI+   +     +  L RI  G   LG L  G  RE++   L
Sbjct: 176 KIVVSEGKKHEIRLFADAAGLPILELKRIRIGSLVLGGLRYGEYRELTDAEL 227


>gi|307301432|ref|ZP_07581192.1| pseudouridine synthase [Sinorhizobium meliloti BL225C]
 gi|306903489|gb|EFN34077.1| pseudouridine synthase [Sinorhizobium meliloti BL225C]
          Length = 262

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 76/227 (33%), Positives = 123/227 (54%), Gaps = 3/227 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V    D I VDG  +    R  
Sbjct: 27  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEADRIAVDGTVIAAQAR-V 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TVF  L ++    +  VGRLD  +EGLLL TND  LA+ 
Sbjct: 86  YLMLNKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQR 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   +VY V+  G   +     + +G+   G     ++V        N+W+ V L
Sbjct: 146 LLDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKSGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++  
Sbjct: 206 DEGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTEAE 252


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 74/238 (31%), Positives = 123/238 (51%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQQFAITVDGQPLTGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NA
Sbjct: 158 TVTDPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGMLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVRALV 275


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 74/238 (31%), Positives = 123/238 (51%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRADQQFSITVDGQPLTGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NA
Sbjct: 158 TVTDPATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGMLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVRALV 275


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/230 (32%), Positives = 118/230 (51%), Gaps = 2/230 (0%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAERTR 74
           +++V+++ G  SR     +I    V+VNG +          + D +EV  + +R A R  
Sbjct: 15  LARVLSKLGYCSRARAFELIRADEVRVNGKVERNPERPTDPARDRVEVAHIAIRAA-RFL 73

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP GL+TT SD  GR T++  LP     V  VGRLD  +EGLLLLTND   A  +
Sbjct: 74  YYVVNKPRGLITTASDEKGRETIYSLLPPDSPWVAPVGRLDKASEGLLLLTNDSEWAAKI 133

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P++   + Y V+      +  +  L +GI   G      +V++    G N W+ + L 
Sbjct: 134 TDPNSHLDKTYHVQVSTLPSEQMVEALSRGIRSDGELLLAKRVSILRAGGKNGWLEIVLE 193

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EGKNR+I+++      +V RLIR++ GP  LG L  G  R ++ +   E 
Sbjct: 194 EGKNRQIRRMVAALQIEVLRLIRVAIGPLTLGELPKGGCRALTAEEKAEL 243


>gi|307316843|ref|ZP_07596285.1| pseudouridine synthase [Sinorhizobium meliloti AK83]
 gi|306897465|gb|EFN28209.1| pseudouridine synthase [Sinorhizobium meliloti AK83]
          Length = 262

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 76/227 (33%), Positives = 123/227 (54%), Gaps = 3/227 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++ +++ G  SR + E++IA+ RV V G  +   +  V    D I VDG  +    R  
Sbjct: 27  LARALSKLGYCSRTQAEKLIAEGRVSVAGRKITDLSHWVDIEVDRIAVDGTVIAAQAR-V 85

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP GLVTT  DP+GR TVF  L ++    +  VGRLD  +EGLLL TND  LA+ 
Sbjct: 86  YLMLNKPRGLVTTRDDPEGRPTVFSCLDNVDVPSLSPVGRLDKASEGLLLFTNDTVLAQR 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P T   +VY V+  G   +     + +G+   G     ++V        N+W+ V L
Sbjct: 146 LLDPETHLGKVYHVQVRGIFGEAMAARMVEGVTEGGELLRALRVERLKSGDRNSWIEVEL 205

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            EG+NR+I+++ +   ++  RL+R+S G  +LG L  G++R +++  
Sbjct: 206 DEGRNRQIRRMLDVLGFECLRLLRVSIGEIRLGDLPKGASRPLTEAE 252


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 127/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDQIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LP      ++ ++GRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPPDIQSDKLYALGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +G +  D + + +KGIV + G      ++ +     S++  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNGLLTPDHIQVFQKGIVFLDGTVCKPARLKILAASPSHSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  ++KK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTSLKRIQFGDFTLKPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>gi|268608512|ref|ZP_06142239.1| 16s pseudouridylate synthase [Ruminococcus flavefaciens FD-1]
          Length = 255

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 114/253 (45%), Gaps = 16/253 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K I+     +R +++ + A+  V VNG  ++R+   + +  D + V G  +  +ER
Sbjct: 4   IRLDKFISERTEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAIS-SER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
            R  L +KP G V++  D DG  TV   +P       +   GRLD ++ G LL+T+DG L
Sbjct: 63  FRYILLNKPKGYVSSTDDKDG-ETVIKLVPPEMRSKGLFPAGRLDKDSTGALLITDDGAL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  +  P+    ++Y        +Q+ +    KGIV+  G      +V     + ++   
Sbjct: 122 AHRICSPNNHISKIYAAELSRPFEQEYVEKFAKGIVLANGEACSPCKV--QKAENADNLA 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
            V L EG   ++K++F      V  L RIS G   L   L  G    +  K + +     
Sbjct: 180 FVELHEGMYHQVKRMFAAVGNHVENLKRISIGGLILPKDLPLGKCMYLLPKDIEQMF--- 236

Query: 249 LLEEAQVNLDAPI 261
                +++ DA +
Sbjct: 237 ----TKIDFDAIL 245


>gi|307304763|ref|ZP_07584513.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|306912165|gb|EFN42589.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 250

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T DG  +  
Sbjct: 82  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPDTLHIAGRLDADTTGLVLITTDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 198

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 199 TEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 67/266 (25%), Positives = 127/266 (47%), Gaps = 13/266 (4%)

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 ++   ++ V D L +   R+  +GRLD ++EGLLLLTN
Sbjct: 58  VSKEEEMILIALNKPAGIVCT-AEKREKNNVIDYL-NYPKRIYPIGRLDKDSEGLLLLTN 115

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKG 184
           +G +   +     +  + Y V  +  +    +  L  G+ +   G+      V     K 
Sbjct: 116 NGEIVNKMMRSGNRHEKEYIVTVNKTISDSFIRGLAGGVPLVELGVTTRKCHVK----KL 171

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           S+    + L +G NR+I+++ E+F ++V +L R+     +LG L  G  R V+    +  
Sbjct: 172 SSKQFKIILTQGYNRQIRRMCEYFGYRVVKLERVRIMNIELGDLPRGKYRAVTPLEYKGL 231

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRD 270
               L+ ++      P  + +   + 
Sbjct: 232 --KRLIADSSNQPVIPDTNKDHSDKK 255


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 114/236 (48%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I    + SR E +++I +  V VNG +++     +    D + V+   L   ++
Sbjct: 1   MRLDKYIGHTTLLSRAESKKIIKKG-VLVNGNIVKAPDFKIDELNDEVIVNEKKLIY-QK 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D   R TV D L           VGRLD +TEGL+LLTNDG L
Sbjct: 59  YIYIMMNKPKGVISATEDSISR-TVIDLLEEKDCIFEPFPVGRLDKDTEGLMLLTNDGNL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +  + +  LK+GI++  G      ++ + T   S +  
Sbjct: 118 GHQLTSPKKDVEKQYYVEVNGVLKVEHIPYLKEGIILEDGYKCKSAKLDILTSDVSKSTA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++ +    +V  L R+S G   L  TL  G  R ++++ L++ 
Sbjct: 178 YIYVTEGKFHQVKRMMKALGCEVTYLKRLSIGELVLDETLELGKYRYLTEQELKKL 233


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 109/250 (43%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++++ G+ SRRE +  I +  V V+G  ++     V     I++D           
Sbjct: 78  RLSKLMSKLGLCSRREADEWIEKGWVMVDGERVDTLGTKVFPDQRIDIDPAAEAFQSSQV 137

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINTE 119
             + HKP+GLV+  ++   +  +    P                   ++   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 ALKPAQVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVVGLKRVRMGQVMLGALPP 313

Query: 231 GSTREVSKKI 240
           G  R +S+  
Sbjct: 314 GQWRYLSEDE 323


>gi|217974709|ref|YP_002359460.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499844|gb|ACK48037.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 250

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T DG  +  
Sbjct: 82  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDASLIAIFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 198

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 199 TEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>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 =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 102/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I Q  V V+G  ++     V     IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEQGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 60

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYEPAAVLITRANQWSGDRSQIRFSPQHLHALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VPLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCEMVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 237 QGQWRYLSPDE 247


>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 =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 111/237 (46%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E 
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 61  FVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + +   +   +GI ++         +V     +   + 
Sbjct: 120 AHDLLSPKKHVTKEYLAKVAGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++       V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 180 VKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 236


>gi|261855955|ref|YP_003263238.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836424|gb|ACX96191.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 369

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 108/354 (30%), Positives = 170/354 (48%), Gaps = 13/354 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            + QR+ K++A  G+ SRR +E  I+   VK+NG++ +       + D ++V G  +  +
Sbjct: 1   MSKQRLQKILATQGLGSRRMIEGWISAGEVKLNGVVAQ-LGDVAEAGDVLDVRGQKITVS 59

Query: 71  ERT---RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
           + T   R+ +YHKP G +T+ SDP+GR TVF +LP+I   R I+VGRLD NT GLLL TN
Sbjct: 60  DETPIRRVIIYHKPEGEITSTSDPEGRPTVFGSLPAIRQGRWITVGRLDFNTSGLLLATN 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  PS Q  R Y VR  G + +D++  L   + +        Q++     G N
Sbjct: 120 DGELANRLMHPSHQIERTYAVRVLGGLTEDQVKQLTTEVQLDDGPAHFDQLSDAGGTGVN 179

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI---LR 242
            W  V LREG+NREI+++ E     V+RLIRISY    L   L  G  +++  ++   L 
Sbjct: 180 RWYHVTLREGRNREIRRMIEAVGAVVSRLIRISYAGIPLPPRLKPGRAQDLPPEMEDALV 239

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDR---PNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           + +G       +V  +     +    R R     +     + F    +  SQ+   +  +
Sbjct: 240 KLVGLRPETRRKVQDEDTKRRALKPYRARVQTGTVAKRPAEPFRVPVRAESQEGADTAGR 299

Query: 300 KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR-SPSFPSKRSLRRTSA 352
             + P+ R    S+         S        E + +R  P+    + +RR   
Sbjct: 300 PTSRPIERATTRSSRPGEPRPVLSRARPQMTEEGSDKRGKPARAGGKPIRRERQ 353


>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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 118/244 (48%), Gaps = 14/244 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   P R++K + ++G+ SRRE + +IA   V ++G ++  A   +     + +    
Sbjct: 6   LYDGPEPSRINKWLGQSGVCSRREADALIADGLVSIDGEVVTDAGRKIEPGQTLTLSDRA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVISVGRLDI 116
                     + HKP+G V+   +PD    V              P+  + +  +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 VS----RMESFRLKFILREGRNRQIRRMCAMVDLEVVDLIRVRIGPLKLDNLPEGHWRML 241

Query: 237 SKKI 240
           + + 
Sbjct: 242 TAEE 245


>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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 70/218 (32%), Positives = 110/218 (50%), Gaps = 2/218 (0%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIG 83
           + SRR  E +I Q RV+VNG ++    + V    D I+VDG+ +   +    +  +KP G
Sbjct: 1   MGSRRACEDLIDQARVEVNGKIVTEQGLRVDPEKDEIKVDGLTV-ATQSYLFFALNKPAG 59

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           +V+T  DPDGR  + D + +  +R+  VGRLD  TEG++LLTN G LA  L  P     +
Sbjct: 60  VVSTMEDPDGRQCLGDYVTNRETRLFHVGRLDTETEGIILLTNHGELAHRLTHPRYGVKK 119

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
            Y     G + +D    LK GI ++          +    G N  V V L EG+   +++
Sbjct: 120 TYLAAIQGPLPRDLGKQLKNGIELEDGYARADHFKVVQNTGKNYLVEVSLHEGRKHIVRR 179

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +     + V +L+R S+GP  LG   +G  R ++   +
Sbjct: 180 MLSEAGFPVEKLVRTSFGPIPLGDQKSGWLRRLTNTEV 217


>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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 70/238 (29%), Positives = 114/238 (47%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A AG  SR +V+ ++  ++V VNG    +A   +    D +EV+G  +   E 
Sbjct: 1   MRLDKFLAEAGFGSRSQVKNLLKTKKVCVNGKNESQAKKQINPNLDRVEVEGQEVLYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+   D     TV D L +   +  V  VGRLD +T GLLLLTN+G L
Sbjct: 60  FVYYMLNKPKGVVSATQD-KVHQTVLDLLDATAKQKAVFPVGRLDKDTHGLLLLTNNGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW 188
           A  L  P     +VY     G +    +   +KGI +         + +    +    + 
Sbjct: 119 AHRLLSPKKHVNKVYVAEVDGLMTSQDIEAFEKGIQLSDHQCQPAVLEILASDRDKFQSR 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           V + ++EGK  ++K++      +V  L R+  GP QL  TL  G+ R++ K  +   L
Sbjct: 179 VKIVIKEGKFHQVKRMVLACGKEVRDLQRLEMGPLQLDSTLDLGAFRKLEKSEIEALL 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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 112/232 (48%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            R+ KV+A+AG+ASRR  E +I+Q RV+V+G ++    + +   + +          ++ 
Sbjct: 1   MRLQKVLAQAGVASRRAAEELISQGRVEVDGRIVIEQGLRIDPENAVVRVDGVRVVVQKD 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 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|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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 117/232 (50%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+++  GI SR +  ++I   RVKVNG L       V  TD I +D  P+++ ER 
Sbjct: 1   MRINKLLSNKGICSRSQAHQLIVAGRVKVNGQLCI-PGQWVEETDEILLDDRPVKEKERL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP+G+V T +  +G         +  + +  VGRLD +++GL+LLTNDG LA  
Sbjct: 60  -YIILNKPVGIVCTAA--EGVKDNIIRYMNYPAYLFPVGRLDKDSQGLILLTNDGDLASD 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +        + Y V+     ++D L+ + +G+ +  G+     QV+   +        + 
Sbjct: 117 ILEAEKGHEKEYMVQVDRPYEEDFLHKMSQGVNLGDGVITRICQVSAINED----TFRII 172

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L +G NR+I+++ + F + V RL RI      LG L  G  R+++   +   
Sbjct: 173 LTQGMNRQIRRMTKAFGYNVVRLERIRLLNIALGPLAYGEWRKLTNLEVETL 224


>gi|166710887|ref|ZP_02242094.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 245

 Score =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 73/234 (31%), Positives = 119/234 (50%), Gaps = 9/234 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRLWL 77
           +++ G+ SR E  R IA  RV V+  ++      + +     I VDG PL    R    +
Sbjct: 2   LSKLGVCSRTEAARWIADGRVSVSTRVVRDPEFPIRADQQSSITVDGQPLTGPARC-YLM 60

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A  +  
Sbjct: 61  LNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAATVTD 120

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTV 191
           P+T   + Y V+     +  +L  L+ G+V      +G+     QV++  +   NAW+ +
Sbjct: 121 PATGPDKTYHVQIDCLPNVAQLAQLQAGVVDPDPEGEGVLLRAKQVSVLREGERNAWLEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +
Sbjct: 181 VLDEGRNRQIRRLLAAVDIGVLRLMRVAIGPLAMGELGKGAWRMLSAEEVRALV 234


>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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPSGVVSARKDKEH-QTVIDLIRPEDRREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEILSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 RITISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYL 238

Query: 246 G 246
           G
Sbjct: 239 G 239


>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 =  237 bits (606), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 58/221 (26%), Positives = 104/221 (47%), Gaps = 9/221 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K ++  G  SRRE +R+I   +V +NG +       V  +D +EV G  + K++R +
Sbjct: 4   RINKYLSEVGYCSRREADRLILDGKVTINGKIP-EIGTKVEDSDQVEVKGQRIEKSKRQK 62

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T         V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDRKVEPDNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ +  ++ D +  +  G+ I G    +  V     +       + 
Sbjct: 122 KILRARNNHEKEYIVKVNRPINNDFIQSMSNGVEILGTITKNCFVKQLGPRN----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           L +G NR+I+++ E   ++V  L RI     +L  +  G  
Sbjct: 178 LTQGLNRQIRRMCEALGYRVQSLKRIRIMNIKL-DVPTGEY 217


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 118/242 (48%), Gaps = 3/242 (1%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ K    +   P R++K +A AGI SRRE +  I    V VNG ++      V+ +D +
Sbjct: 231 IEYKEEHIDPNEPIRLNKYLANAGICSRREADEFIQAGVVTVNGNVVTELGTKVLRSDEV 290

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTE 119
           +    P+   E+    L +KP   VTT  DP  R TV + +      R+  VGRLD NT 
Sbjct: 291 KFHEQPVSL-EKKVYVLLNKPKDYVTTSDDPQQRKTVMELVKGACEERIYPVGRLDRNTT 349

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG LA  L  P     +VY V     V ++ +  + +GI ++        +  
Sbjct: 350 GVLLLTNDGDLASKLTHPKFLKKKVYHVFLDKAVTEEDMQKIAEGIELEDGEIHADAIEY 409

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             ++     V + +  GKNR ++++FE   ++V +L R+ +       +  G  R +++K
Sbjct: 410 ADER-DKKQVGIEIHSGKNRIVRRIFESLGYRVIKLDRVQFAGLTKKNVRRGDWRYLTEK 468

Query: 240 IL 241
            +
Sbjct: 469 EV 470


>gi|315269053|gb|ADT95906.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 250

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T DG  +  
Sbjct: 82  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 198

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 199 TEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 59/225 (26%), Positives = 109/225 (48%), Gaps = 9/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R++K ++  G  SRRE +R+I + +V +NG + +     V  +D +EV G  ++K   ++
Sbjct: 4   RINKYLSEVGYCSRREADRLIHEGKVTINGKIPK-IGSKVEESDQVEVKGQRIKKITGQK 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                ++KP+G+V T       + V D +     R+  +GRLD  +EGL+ LTNDG +  
Sbjct: 63  NIYLAFNKPVGIVCTTDRKVEPNNVIDFI-KYPKRIFPIGRLDKLSEGLIFLTNDGDIVN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V+ + Q++ D +  +  G+ I      +  V     K       + 
Sbjct: 122 KILRARNNHEKEYIVKVNRQINSDFIQSMSSGVEILDTITKNCFVKQLGPKK----FKII 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           L +G NR+I+++ E   ++V  L R+     +L  +  G  RE +
Sbjct: 178 LTQGLNRQIRRMCESLGYRVRSLKRVRIMNIEL-DVSTGKYREFT 221


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 76/231 (32%), Positives = 122/231 (52%), Gaps = 4/231 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R++K IA  G+ SRR+ E ++ +  + +N   +   +  V    D +     PL   E+
Sbjct: 1   MRIAKFIAACGVCSRRKAEELVNEGHITINNHRVTELSTQVDVDNDEVRYRRKPLVL-EK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP+G V T+ DP       D LP    R+ +VGRLD  +EGL++LTNDG LA+
Sbjct: 60  KLYYLLNKPVGYVCTNDDPFAEKKAIDLLPDK-GRLYTVGRLDKPSEGLIVLTNDGDLAK 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           ++  PS +  + YRV   G+V Q KL+ L + G+  +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|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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 100/230 (43%), Gaps = 4/230 (1%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     +D   + +   G+ ++          LD     +  V + +
Sbjct: 120 ITSPKKDCGKRYWVELAEPIDDSLIQVFADGVELRNEDGLTKPALLDI--IDSTHVRLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            EGK  ++K++F     +V  L R + G  +L   L AG  R ++   ++
Sbjct: 178 SEGKYHQVKRMFAAVGNRVVNLHREAVGAIELNADLAAGEWRFLTDAEVK 227


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/236 (31%), Positives = 120/236 (50%), Gaps = 7/236 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SRR V+R+I  ++V+VNG++     +NV      + V G  +R  + 
Sbjct: 1   MRLDKLLFETGFGSRRTVKRLIKSKQVQVNGLIALVDNLNVDPQLQEVIVSGELIRF-QP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKP G+V+  SD     TV D +        +  VGRLD +TEGLLLLTN+G L
Sbjct: 60  HVYYMLHKPAGVVSAVSDVLN-QTVIDLIEPSQRVPGLFPVGRLDKDTEGLLLLTNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L +P  + ++ Y    + +V  +       GIV  G +     ++T+ ++  + + V
Sbjct: 119 GYQLLIPKKEVIKCYEAVVNERVTSEDQFAFASGIVFNGGVKCKPAKLTILSESDAESKV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++KK+F     KV  L R+S GP QL  TL  GS R +  + L   
Sbjct: 179 LLEISEGKFHQVKKMFLSVGKKVIYLKRLSMGPLQLDKTLPLGSYRALHSEELAAL 234


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 74/250 (29%), Positives = 108/250 (43%), 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  LWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++      V                   P     +   GRLDI++ 
Sbjct: 77  TILLHKPMGYVSGQAEDGHTPAVALINPRTHWREDPSRQRFSPPQLRGLAPCGRLDIDSV 136

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFH-GQV--------DQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L    ++  + Y VR H G +           +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 ALKPAKVEWQNPE----QLRFVLKEGKKRQIRRMCELVGLKVVGLKRIRIGRVVLGNLPV 252

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 253 GQWRYLGPNE 262


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/226 (33%), Positives = 112/226 (49%), Gaps = 5/226 (2%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           ++ARAG  SRR +E  I   RV++NG +    A      D +E DG+ +   E+   WL 
Sbjct: 11  LLARAGCGSRRVLEDAIRDGRVRINGEVATIGARVRPGVDRVEFDGLEIATEEQREYWLL 70

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G+V++  DP+GR TV   + +  SRV  VGRLD+++EGLL+LTNDG L   L  P 
Sbjct: 71  NKPRGVVSSVVDPEGRPTVRSLV-ATTSRVYPVGRLDVDSEGLLILTNDGPLTYQLTHPR 129

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               + Y V     V +     L++G+ + G       V           V + L EG+N
Sbjct: 130 FHVPKEYLVWVDRPVPRRLGRELREGVEVDGELLRASSV----GTVGPRLVRIVLTEGRN 185

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           R+I+++       V RL+R+  GP     L  G  R +  + L   
Sbjct: 186 RQIRRMVGAVGLSVERLVRVRIGPLVDPHLPPGVARRLEPRELARL 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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 111/236 (47%), Gaps = 7/236 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R+ K +      +R E  +MI Q RV     ++++    V    D I  DG  L  
Sbjct: 6   MKTLRLDKFLCDVLGCTRSEARKMIRQGRVLAGDEIIKKPEYKVNPEEDEITADGQRLNF 65

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
             +    + +KP G+VT   D   + TV D L     + +   GRLD +TEGLLL+TNDG
Sbjct: 66  R-KYEYLMMNKPKGVVTATKDGRDK-TVMDLLTGRHRKGLFPAGRLDKDTEGLLLITNDG 123

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y V   G++ +++  + + G+ I         ++ + T  G  +
Sbjct: 124 ELAHRLLSPKHHVTKCYSVTVTGEIGREQQEIFESGMDIGDDKPLKPAKLVILT-SGEVS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              V + EG+  +IK++FE    KV  L R+S G   L   LL G  RE++++ ++
Sbjct: 183 QAEVFITEGRFHQIKRMFEAVGSKVLELKRLSMGSLVLDPELLPGQVRELTEEEIK 238


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 66/248 (26%), Positives = 116/248 (46%), Gaps = 15/248 (6%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL--------ERAAVNVMST 57
           + Q+N +  R++K +A  G+ SRR   R I   ++ ++G L           +    +S 
Sbjct: 1   MTQDNPS-IRLAKYLAMTGLCSRRAATRYIRDGQITLDGRLANHIDTISLTDSDSGFISQ 59

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDIN 117
           + ++ DGV ++  E  + W+ +K +G       P   S++   LP+   R+  VGRLD +
Sbjct: 60  EILKFDGVLIQGIESKQYWMLNKSVGTDCRLL-PHDPSSLLHLLPAS-PRLYPVGRLDKD 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 T----RLDDDKFEIILTQGLNRQIRRMSQALGYKVIDLKRVQIQTLKLGELEEGEMRELT 233

Query: 238 KKILREQL 245
              L   L
Sbjct: 234 TNELALLL 241


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 112/237 (47%), Gaps = 10/237 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAER 72
            R+ K +A     +R +V+  + + RV V+G +   +          + +DG P+  A R
Sbjct: 5   IRLDKFLAEMKKGTRSQVKEAVRKGRVTVDGAVCRSSDFKFDPEVSGVCMDGEPVSYA-R 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+   D +   TV   +  +    +  VGRLDI+TEGLLL+TNDG LA
Sbjct: 64  MEYFMLNKPQGVVSATED-NLHPTVISLIGDAKRKDLFPVGRLDIDTEGLLLITNDGKLA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQ----KGSN 186
             L  P     +VY  +  G + +D +     GI +         ++ +++         
Sbjct: 123 HELLSPKKHVDKVYFAKVKGTLREDIVQAFAGGITLADQTTVLPAELLIESSYEEAGEPV 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
               + + EGK  ++K++FE    +V  L R+S GP  L   L  G +R ++ K ++
Sbjct: 183 CEARLTIHEGKFHQVKRMFEAAGGQVVFLKRLSMGPLTLDPKLKPGESRLLTGKEIK 239


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 120/230 (52%), 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 +KPIG ++++ DP     +   L +I  R    GRLD ++ GL+++TNDG +   
Sbjct: 61  YYKL-NKPIGYISSNYDPHNEKDLNKLL-NIDERFFCAGRLDKDSHGLMIITNDGKITNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  ++Y V+   ++   +      G+ + Q     D +++L  ++       V 
Sbjct: 119 IIHPSKKIDKIYIVKVDKKLTAYQEKNFMDGLKLSQKEITSDAKISLIDKEKIT--YKVT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+I+++FE+F  KV  L RI  G   L  L  G  +++SKK + 
Sbjct: 177 IHQGYNRQIRRMFEYFKIKVIDLKRIKIGQICLDDLKDGDYKKLSKKEVE 226


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 118/231 (51%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ + +   GI SR+EV+++I+ + +KVNG     A  N+   +D IE +G  L   E 
Sbjct: 1   MRLDRFLVECGIGSRKEVKKIISAKEIKVNGSYDISAKDNIDEYSDVIEYNGERLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D    +TV D LP       +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDIR-EATVMDLLPEWVIRKDLAPVGRLDKDTEGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V     + Q+ +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHKLLSPKNHVDKTYYVEIENNISQEDILKLEEGVDIGNYITLPAKV----EKISDTKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KVN L R ++    L  L  G  +EV+ + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVNYLQRTTFAKLSLDGLALGEVKEVNLEDI 225


>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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 102/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 60

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 237 QGQWRYLSPDE 247


>gi|153002130|ref|YP_001367811.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151366748|gb|ABS09748.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 246

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + ++G P+      R
Sbjct: 19  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLEGEPIALV-GVR 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T DG  +  
Sbjct: 78  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLITTDGQWSHK 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 137 ITSPKKECGKRYLVQLADPVDAGLIAVFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 194

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 195 TEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 243


>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 =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 111/236 (47%), Gaps = 7/236 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
               R+ K +      +R E  +MI Q RV     ++++    V    D I  DG  L  
Sbjct: 1   MKTLRLDKFLCDVLGCTRSEARKMIRQGRVLAGDEIIKKPEYKVNPEEDEITADGQRLNF 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
             +    + +KP G+VT   D   + TV D L     + +   GRLD +TEGLLL+TNDG
Sbjct: 61  R-KYEYLMMNKPKGVVTATKDGRDK-TVMDLLTGRHRKGLFPAGRLDKDTEGLLLITNDG 118

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            LA  L  P     + Y V   G++ +++  + + G+ I         ++ + T  G  +
Sbjct: 119 ELAHRLLSPKHHVTKCYSVTVTGEIGREQQEIFESGMDIGDDKPLKPAKLVILT-SGEVS 177

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              V + EG+  +IK++FE    KV  L R+S G   L   LL G  RE++++ ++
Sbjct: 178 QAEVFITEGRFHQIKRMFEAVGSKVLELKRLSMGSLVLDPELLPGQVRELTEEEIK 233


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 111/235 (47%), Gaps = 10/235 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K IA   + SR+EV+++I  +R+ VN  +  R  + +   TD I +DG  +   E 
Sbjct: 1   MRLDKFIANFTLYSRKEVKKLIKAKRITVNDSIASRPEMQIDEETDTISLDGQWIGY-EP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGG 129
              +L +KP   ++T   P   S V D LP+    +     VGRLD +TEGLLLLTNDG 
Sbjct: 60  YIYYLLNKPQNCLSTTR-PGPTSIVTDFLPANEVEIYQPFPVGRLDKDTEGLLLLTNDGD 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKG--SN 186
            A  L  P     + Y     G V ++ +    KG+ I  G      Q+ +       + 
Sbjct: 119 FAHDLLSPKKLVSKEYYAEIEGIVTEEDVKAFAKGLTIDQGDHCAPSQLDILATDPAKNR 178

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
           + +TV L EGK  ++K++F+    +V  L R   G   L   L  G+  ++  + 
Sbjct: 179 SEITVTLTEGKYHQVKRMFQAVGKEVIYLQRFRIGSLYLPEELELGTAFKLLPEE 233


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 71/221 (32%), Positives = 113/221 (51%), Gaps = 10/221 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I   RV VNG ++ +   ++    D I VDGV +   ++
Sbjct: 1   MRLDKLLANKAFGSRKEVHQIIRDGRVTVNGAVILKKDQSIHIDDDIIAVDGVQISTKQQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
                +HKP G +T   DP     V D LP  F +  V  VGRLD +TEGLLLLTNDG  
Sbjct: 61  -YYIKFHKPAGYITAVEDPTH-PVVMDLLPPEFKKMGVFPVGRLDKDTEGLLLLTNDGIW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  +        +VY V F+G++ +D L  ++ GIV+  G       + + +++     +
Sbjct: 119 AHSIINGHKHVPKVYYVEFNGKLTKDGLERIETGIVLGDGTQCKPANIDVLSEQS----L 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
            + + EGK  ++K++      +V  L R+S G   L  + A
Sbjct: 175 HITIEEGKYHQVKRMIGAAGGEVTYLKRLSIGHITLNGIEA 215


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 56/229 (24%), Positives = 108/229 (47%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R E  ++I    + VN  ++   A  V   + + +DG+ L  A  +
Sbjct: 5   MRLDKFICKSTDLTRTEATQLINAGNIIVNNEVVSNEATQVHENNDVLLDGIKL-IARAS 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP+  + ++ D +   ++F+ +       +   GRLD +T GL+L+T+DG  + 
Sbjct: 64  RYILMHKPLNTICSNID-EVYPSLFNYIDVEKADDLHIAGRLDADTTGLVLITDDGRWSF 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+ Q  + YRV     + +D      +G+ +QG     +   LD    +   V + 
Sbjct: 123 NIITPNKQCEKTYRVGLRNPIAEDAAEKFAQGVKLQGEKQLTLPAKLDVVTSNE--VLLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  +L  +  G  R ++ + +
Sbjct: 181 ITEGKYHQVKRMFSAIGNRVVTLHREQIGNIKL-DVEVGKWRFLTPEEI 228


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 105/250 (42%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 3   RLSKLMSELGMCSRREADEWIEKGWVMVDGERIDTLGTKVRPDQRIEIDPAAEAAQMSQV 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINTE 119
             L HKP+GLV+  ++   +  +    P                   ++   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 PLKPAQVNWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPP 238

Query: 231 GSTREVSKKI 240
           G  R +S   
Sbjct: 239 GQWRYLSPDE 248


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 120/238 (50%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSITVDGQPLAGPARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDMQVTLDTQKGSNA 187
            +  P+    + Y V+   +    +L  L+ G+       +G+     QV++  +   NA
Sbjct: 158 TVTDPARGPDKTYHVQIDCRPSAAQLTQLQAGVADTDPEGEGVLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +R  +
Sbjct: 218 WLEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVRTLV 275


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 119/240 (49%), Gaps = 11/240 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRK 69
               R+ K +A AG  +R EV++ I++ +V+VNG  +   A  +   +  +   G  +  
Sbjct: 1   MKKIRLDKYLADAGAGTRSEVKKYISKAQVQVNGKTVLNPAEKIEPEEVEVCCLGQVVH- 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +R   +L HKP G V+   D   R TV + +PS    +  VGRLD +TEGLLL+TNDG 
Sbjct: 60  VDRYEYYLLHKPAGCVSATEDVRER-TVMEFVPSRRKDLFPVGRLDKDTEGLLLITNDGE 118

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---QKGSN 186
           LA  L  P     + Y  +  G++ Q+     ++G+ I G     +   L+    + G  
Sbjct: 119 LAHRLLAPRRHVPKQYFAQIKGKMTQEDAQKFRQGVEI-GEKNPTLPAKLEILSVENGEE 177

Query: 187 AWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            W++   + + EGK  +IK++ +    +V  L RIS GP  L   L  G  R +++K + 
Sbjct: 178 GWISCINLTIEEGKFHQIKRMVQAVGKEVIYLKRISMGPLYLDENLERGQCRPLTEKEIE 237


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 122/241 (50%), Gaps = 10/241 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPSGVVSARKDKEH-QTVIDLIRPEDQREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEILSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 RITISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYL 238

Query: 246 G 246
           G
Sbjct: 239 G 239


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 73/250 (29%), Positives = 106/250 (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  LWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++      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 ALKPAKVDWQNPE----QLRFVLQEGKKRQIRRMCELVGLKVVGLKRIRIGRVVLGNLPV 335

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 336 GQWRYLGPNE 345


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 115/244 (47%), Gaps = 14/244 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +   P R++K + ++G+ SRRE E +IA   V ++G ++  A   +     + ++   
Sbjct: 6   TYDGPEPVRINKWLGQSGVCSRREAEGLIADGLVSIDGEVVRDAGRKIEPGQTLTLNDTG 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------LPSIFSRVISVGRLDI 116
                     L HKP+G V+   +P     V              P+  + +  VGRLD 
Sbjct: 66  EAALAAGVAILLHKPVGYVSGQPEPGKIPAVRLLTTANRVGDGETPARDASLPPVGRLDE 125

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+L++DG +A+ +  P +   + Y VR  G V + KL  L+ G+ + G      +
Sbjct: 126 DSRGLLMLSSDGVVAKAVIGPQSDLDKEYLVRVAGTVTEAKLTKLRHGLELDGRQLKPAR 185

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           VT    +     +   LREG+NR+I+++ E    +V  L RI  GP +LG L  G  R +
Sbjct: 186 VT----QMEPQRLRFILREGRNRQIRRMCELVGLEVVDLYRIRIGPVKLGDLPEGRWRML 241

Query: 237 SKKI 240
           +   
Sbjct: 242 TADE 245


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 113/241 (46%), Gaps = 16/241 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVPLR 68
            R++K +A+ GI SRRE  R+I   R+ +NG +       R   ++   D IE+DG P+ 
Sbjct: 1   MRLAKYLAQCGIGSRREACRLIEAGRITLNGHIARHTDPIRLDESLNCLDRIELDGAPIT 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K E    W+ +K +G      + D  +++   LP    R+  VGRLD ++ GLLLLTNDG
Sbjct: 61  KTETLAYWILNKAVGTDCRLLEQDE-TSLIHLLPKA-PRLYPVGRLDKDSRGLLLLTNDG 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

Query: 244 Q 244
            
Sbjct: 235 L 235


>gi|158319769|ref|YP_001512276.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158139968|gb|ABW18280.1| pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
          Length = 242

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 66/223 (29%), Positives = 111/223 (49%), Gaps = 6/223 (2%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            QR+ K+++  G  SR+++ ++     VKV+G +++ ++ +V   +   + G  +     
Sbjct: 4   TQRIDKILSNLGYGSRKDIRQICKNGLVKVDGKVVKDSSAHVDPENSQIIIGNEVVNYRE 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D +   TV D L   +    V  VGRLD +TEGLLLLTNDG L
Sbjct: 64  FVYLMMHKPQGVISATED-NRDQTVVDLLDEEYLPFSVFPVGRLDKDTEGLLLLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWV 189
           A  L  P     + Y  +  G V +  +   K+G+ I+   Y  +   L+  K    + +
Sbjct: 123 AHNLLSPKKNVPKTYYAKVLGTVTRSDIESFKEGVFIE-EDYKTLPAELNILKSDEISEI 181

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
            + + EGK  ++K++FE  +  V  L R+S G   L  TL  G
Sbjct: 182 ELTIYEGKFHQVKRMFEAVDKTVVYLKRLSMGTLNLDPTLPLG 224


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 95/305 (31%), Positives = 148/305 (48%), Gaps = 21/305 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            +++ KV+AR+G+ SRR++E +I + RV V+G ++      V     + VDG  ++    
Sbjct: 2   SEKLQKVLARSGLGSRRKMETVIQEGRVSVDGQVV-GLGTRVTVEQILRVDGHTVKYITE 60

Query: 73  T----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
                R+  Y+KP G V T SD  GR TVF+ LP    +R IS+GRLDINT GLLL T D
Sbjct: 61  ENTICRILAYNKPEGEVCTRSDEAGRKTVFERLPRLNGARWISIGRLDINTSGLLLFTTD 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----K 183
           G  A  +  PS +  R Y VR  G VD   LN L+ G+ ++      + +    +    +
Sbjct: 121 GEFANRMMHPSREVEREYAVRIFGNVDDAMLNRLRMGVKLEDGEAKFLSIKESGKEAGGE 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           G N W  V L EG+ RE+++++E    +V+RL+R+ YG   L   L  G   E++ K + 
Sbjct: 181 GINRWYHVVLTEGRTREVRRLWESQGVQVSRLMRVRYGHLHLDKQLPQGGWIELNLKEVN 240

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                 L++ ++         +ET VR   N          R  K  +Q      +++  
Sbjct: 241 --YFRKLVDLSK--------ETETKVRVDDNKTKNTQARIRRAVKKHTQHRKAGVRRRST 290

Query: 303 TPVHR 307
                
Sbjct: 291 ARTRH 295


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + + G P+      R
Sbjct: 19  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVCLQGEPIALV-GVR 77

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T+DG  +  
Sbjct: 78  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLVTSDGQWSHK 136

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 137 ITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 194

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 195 TEGKYHQVKRMFAAVGNHVQELHRESVGQIELDPALALGEWRYLTAEEI 243


>gi|227872023|ref|ZP_03990406.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227842134|gb|EEJ52381.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 239

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 120/237 (50%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            R+ K ++  G+ SR  ++R I +  VK+NG +++  ++ V   +  I     P+   E 
Sbjct: 1   MRLDKYLSDMGVESRSVLKREIRKGLVKINGEIVKDPSMEVQPGNSEIVYKDEPIHYEEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   + +KP+G++++  D   + TV D         +  VGRLD ++EGLLL+ NDG LA
Sbjct: 61  SYYMM-NKPVGVLSSTEDRK-QKTVLDLFSDKHRKDLFPVGRLDKDSEGLLLIMNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V   G++ +++L+ L++GI     +     +    +     + V 
Sbjct: 119 HKLLSPKMHIEKKYLVEIPGKISEEELDRLRQGIQYDTDLIAMPAKARCLSSTEEGSRVE 178

Query: 191 VGLREGKNREIKKVFEFF--NWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           V + EGK  +IKK+F     ++ V +L R+S GP  L   L  G  R++S++ ++  
Sbjct: 179 VIIMEGKFHQIKKMFLALSTDYVVTKLQRLSMGPLHLDPALAPGEYRKLSEEEVQAL 235


>gi|312277957|gb|ADQ62614.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 239

 Score =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 73/241 (30%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPSGVVSARKDKEH-QTVIDLIRPEDQREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCQSAQLEVLSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            V + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 RVTISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYL 238

Query: 246 G 246
           G
Sbjct: 239 G 239


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 97/230 (42%), Gaps = 4/230 (1%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I  +   +R   ++ + +  +  +G +++ A   V+    + ++G  +     
Sbjct: 6   PVRLDKFICESTSLTRSLAKKALHRGDITCDGAVIKDAGFKVLEGMQVCLEGEFISLV-G 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + +KP+  + +  D    S +          +   GRLD +T GL+L+T+DG  + 
Sbjct: 65  ERYLMLNKPVDTICSTIDEVYPSVLSLLDIEKPETLHIAGRLDADTTGLVLITSDGQWSH 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + Y V     VD+  + +   G+ ++          L+  +     V + 
Sbjct: 125 RITSPKKDCGKRYLVTLAEPVDESLIGVFAAGVELRNEDCLTKPALLEIIEP--QLVRLT 182

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 183 ITEGKYHQVKRMFAAVGNHVVGLHRESIGKIELDAELALGEWRYLTSEEI 232


>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 =  237 bits (604), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 76/236 (32%), Positives = 113/236 (47%), Gaps = 10/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
           +R+ K++A  G  SRREV+ ++   RV  NG ++             + VDG  +   ER
Sbjct: 2   ERLDKILASTGRWSRREVKELVRAGRVTANGAVVRSPEEKYQREGLDLRVDGQSV-LCER 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + HKP GLV+   DP  ++TV + LP    ++     GRLD +TEGLLLLTNDG L
Sbjct: 61  YTYLMLHKPAGLVSATEDPR-QATVLELLPEHLRKIGLFPAGRLDRDTEGLLLLTNDGAL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y V+  GQ+DQ  +   + G+ +  G+      + L          
Sbjct: 120 AHDLLSPRKHVDKTYFVQVEGQLDQSDVEAFQGGMTLGDGLVCLPAGLKLLEAPD---EA 176

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            V LREGK  +IK++       V  L R++ GP  L   L  G  R ++++ L   
Sbjct: 177 LVTLREGKYHQIKRMLAARGKPVRYLKRLTMGPLVLDEGLEKGQWRPLTEEELSRL 232


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 107/249 (42%), Gaps = 19/249 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       R+SK +A  G+ SRRE +  IA+  V V+G ++      V     I +D   
Sbjct: 1   MDSQSDKIRLSKRMAELGLCSRREADDYIARGWVSVDGQIISELGSKVSPDQRITLDARA 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISV 111
                     L HKPIG V+  ++   +      +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 LKPARVWWQNRD----QLRFVLVEGKKRQIRRMCELVGLRVVGLKRIRIGRIMLGDLPQG 236

Query: 232 STREVSKKI 240
             R ++   
Sbjct: 237 QWRYLAPGE 245


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 116/228 (50%), Gaps = 9/228 (3%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRL 75
            K +   G+ SR+EV+ ++ +++++VN  ++      +    D +  +   L   ++ R 
Sbjct: 2   DKFLVECGLGSRKEVKELLKKRKIQVNASIVTSGQQIIDEEKDEVFYEKEKLVY-KKFRY 60

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +K  G VT   D   R TV + LP       ++ VGRLD +TEGLLL TNDG L   
Sbjct: 61  YILYKKAGYVTALEDSKER-TVMELLPEWVIRKDLVPVGRLDKDTEGLLLFTNDGKLNHQ 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P +   + Y V     + ++ +  L++G+ I        QV    ++     +++ +
Sbjct: 120 LLSPKSHVDKTYHVCLEKIITEEAIEQLRQGVRIGDYTTLPAQV----EQLEEQKISLTI 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +EGK  ++KK+ E  + KV+ L R+S+G   LG L  G  REVS + +
Sbjct: 176 QEGKFHQVKKMLEAVDNKVSYLKRVSFGRLVLGDLKPGEVREVSLEDI 223


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 111/237 (46%), Gaps = 8/237 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ +R +V+ ++ ++ + VN  +   A  ++    D +   G PL   E 
Sbjct: 2   MRLDKFLVATGVGTRSQVKLLLKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ES 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G V+   D   ++TV + L     +  V  VGRLD +T GLLLLTN+G L
Sbjct: 61  FVYYLLNKPSGYVSATQDRQ-QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     + Y  +  G + +   +   +GI ++         +V     +   + 
Sbjct: 120 AHDLLSPKKHVTKEYLAKVVGIMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQRTSL 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           V + ++EGK  ++K++       V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 180 VKITIQEGKFHQVKRMVAACGKGVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 236


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 120/232 (51%), Gaps = 6/232 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++++++AG+ SR      I   RV+V+G  +         S   I +DG+ +  + R +
Sbjct: 26  LARILSKAGLCSRTVAVEWIRAGRVEVDGRRILDPEARFPLSGPGIRIDGLDITASTR-Q 84

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L HKP G++TT  D  GR+TV+D LP     +  VGRLD  + GLLL +ND   A+ L
Sbjct: 85  VLLLHKPRGVLTTRQDERGRATVYDLLPGS-PWLAPVGRLDQASSGLLLFSNDPHWAQRL 143

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+    +  D +  L    V+ G     MQ+      G   W+   L+
Sbjct: 144 LDPDQHVAKTYHVQIRPPLSTDTVVQLAADSVLDGEPCLPMQIRELRCGGKTQWLEFILQ 203

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV---SKKILRE 243
           EG+NR+I+++    + +V RLIR++ G   LG L AG  R +    +++LR+
Sbjct: 204 EGRNRQIRRLLAACDREVLRLIRVAVGNLPLGELRAGEWRWLHSGEEELLRQ 255


>gi|167645656|ref|YP_001683319.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167348086|gb|ABZ70821.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 255

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 121/251 (48%), Gaps = 15/251 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + +   PQRV++ +A+ G+ SRRE E +I Q  V ++G+ ++     +     + +    
Sbjct: 6   LYDEAEPQRVNRWLAQNGVCSRREAEALILQGLVSIDGLRVDDVGRKIEPGQTLVLSDRA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-----------LPSIFSRVISVGRLD 115
             + E     + HKPIG+V+   D      V              +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 QVEVVGRQ----QLKFILQEGRNRQIRRMCELVELTVVDLLRIRIGNVMLGDLPEGRWRP 241

Query: 236 VSKKILREQLG 246
           +S       +G
Sbjct: 242 LSAAERSSLIG 252


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 111/234 (47%), Gaps = 7/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  I++ G+ASRR  + +I   R+KVNG+      + +   D + +D   +   E  
Sbjct: 1   MRLNLYISKTGVASRRGADSLIEHGRIKVNGVTA-VLGMQITKNDVVTLDNNIIEPLEEK 59

Query: 74  RLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP+G+V+T  +   G    F N      ++  VGRLD ++ GL+LLTNDG +  
Sbjct: 60  FYILLNKPVGIVSTTNTAISGNMITFMNFKE---KIFPVGRLDKDSHGLILLTNDGSIVN 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
            +        + Y V  +   D   +  +  G+ I      + Q+T+ +  +       +
Sbjct: 117 KILRVENGHDKEYHVTLNKPYDDYFIETMTSGVEIYNPVAHEKQMTMPSILKPLDERTFS 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + +R+G NR+I+++ +   ++V  L R+      LG L  G  R ++   L+E 
Sbjct: 177 LTIRQGLNRQIRRMADSLGYRVESLERVRIMHLTLGDLPVGYWRYLTSDELKEL 230


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 113/236 (47%), Gaps = 10/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++     R++V  ++A+ RV V+G ++  A   +     + +DG  LR+ E+  
Sbjct: 7   RLDRFISQHCQIPRKQVRLILAKGRVSVDGQVVRDADCQIDQFSQVMLDGQALRQ-EQPI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+G+V+   D + + TV D LP      +  VGRLD+NT GLLLLTND   ++ 
Sbjct: 66  YLMLHKPVGVVSATKDDEHK-TVMDLLPDYQDKGLHIVGRLDLNTSGLLLLTNDSRWSKR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           +  P  +  + Y V     + Q  +    +G     + I     Q+ +           V
Sbjct: 125 IMSPEHKVAKQYLVTLKAPLTQAYVKAFAEGFYFAFENITTQPAQLEILEP----HLARV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            L EG+  +IK++F  F  +V  L R+S G   L  TL  G  R ++ + +    G
Sbjct: 181 TLHEGRYHQIKRMFGRFRNQVMALHRLSVGNLILDETLAVGQYRPLTPQEVASIFG 236


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 74/238 (31%), Positives = 120/238 (50%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 17  LARVLSKLGVCSRTEAARWIAAGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 77  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDDAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L  G+V      QG+     QV++  +   NA
Sbjct: 136 TVTDPATGPDKTYHVQIDCRPSAAQLVQLHAGVVDPDPQGQGLLLRAKQVSVLREGERNA 195

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +   +
Sbjct: 196 WLEIVLDEGRNRQIRRLLAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVSALV 253


>gi|304410666|ref|ZP_07392284.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|304351150|gb|EFM15550.1| pseudouridine synthase [Shewanella baltica OS183]
          Length = 250

 Score =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 100/229 (43%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  +  +GI+++ +   V     + + G P+      R
Sbjct: 23  RLDKFICESTPLTRSLAKKALHRGDITCDGIVVKDSGFKVTEGMRVYLQGEPIALV-GVR 81

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+  + +  D +   +V   +       +   GRLD +T GL+L+T+DG  +  
Sbjct: 82  YLMLNKPVDTICSTID-ETYPSVLSLVDVPKPETLHIAGRLDADTTGLVLVTSDGQWSHK 140

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P  +  + Y V+    VD   + +   G+ ++G         L+  +     V + +
Sbjct: 141 ITSPKKECGKRYLVQLADPVDAGLIAIFAAGVELRGEDGLTKPALLEIIEP--QLVRLTI 198

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R S G  +L   L  G  R ++ + +
Sbjct: 199 TEGKYHQVKRMFAAVGNHVQGLHRESVGQIELDPALALGEWRYLTAEEI 247


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/235 (29%), Positives = 116/235 (49%), Gaps = 10/235 (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   +    +RV   GRLD ++EGLL+L+NDG L   
Sbjct: 60  VVLAYYKPVGVVCTEKDTHAERTVTSEV-KYPTRVTYAGRLDKDSEGLLILSNDGNLINA 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTV 191
           +   S +  + Y V    ++  D LN +  G+ ++         +VT   +K       +
Sbjct: 119 MMKSSNKHEKEYEVSVDREISGDFLNRMSNGVYLEELDRTTRGCKVTRTGKKS----FRI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILREQ 244
            L +G NR+I+++     + V  L RI     +L    ++ G   E+ KK +   
Sbjct: 175 ILTQGLNRQIRRMCNALGYNVESLKRIRVMTVKLSDYDIMPGQYVELDKKSIESL 229


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 74/238 (31%), Positives = 121/238 (50%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      QG+     QV++  +   NA
Sbjct: 158 AVTDPATGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPQGQGVLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L  G+ R +S + +   +
Sbjct: 218 WLEIVLDEGRNRQIRRLVAAVDIGVLRLVRVAIGPLAMGELGKGAWRMLSAEEVSALV 275


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 79/237 (33%), Positives = 114/237 (48%), Gaps = 8/237 (3%)

Query: 10  NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                R+ K +  AG A SRR+ E +I   RV VNG ++      V   D + V G    
Sbjct: 3   RMDGIRLQKYLVLAGAAPSRRKAEDLIRAGRVSVNGAVV-GLGARVYPGDEVRVGGRRAE 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             ER  +   HKP G  TT     G  TV++ LP     +  VGRLD ++EGLLL TNDG
Sbjct: 62  LPERRVVLALHKPKGYETTRQSRSGAPTVYELLPD-LPGLHPVGRLDRDSEGLLLFTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRF-HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
            L + L  P     +VYRV    G    D L  L++G+V++      ++V     +  + 
Sbjct: 121 ALTQRLTHPRYGVKKVYRVWSRKGTPPPDLLRKLERGLVLKSG----VRVQALKARPKDG 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + L EGK RE++ +     + V RL+R+  GP +LG    G+ RE+S   L+  
Sbjct: 177 GAVITLTEGKKREVRYMMAAIGYPVERLVRVKMGPIRLGGQKPGTWRELSASELKAL 233


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 112/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +RR+V  ++ ++RV V+G+ +     +V     + VD   ++  +  
Sbjct: 1   MRIDRFLSNLPRLNRRQVRLLLVERRVSVDGVAVSDPHHDVRDFSCVCVDDEVIQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SDP    TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATSDPQH-PTVLDLLDEPDKDELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P+T+  +VYRV     +  +       G+    + +     ++ L           
Sbjct: 120 RLTQPTTKLPKVYRVHTEDTIGPEYAPTFAAGLYFAFEDLTTQPAELALLGP----TTAR 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           + + EG+  ++K++F  FN KV  L R   GP +L + L  G  R +S + +R 
Sbjct: 176 LSIIEGRYHQVKRMFGHFNNKVIGLHRERMGPLELDSALAPGEYRALSLEEIRR 229


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 117/229 (51%), 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 KLAHPKHNIKKIYHVGLNKPLTKAHFENILQGVTLEDGV-ANVDALGYVEAGDKTQVGIE 460

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  GKNR ++++FE   ++V +L R++Y       +  G  R +++K +
Sbjct: 461 IHSGKNRIVRRIFEHLEYEVEKLDRVTYAGLTKKNINRGKWRFLTEKEI 509


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 73/241 (30%), Positives = 123/241 (51%), Gaps = 10/241 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPSGVVSARKDKEH-QTVIDLIRPEDRREGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPRYHVAKTYYVEVNDILGPDAPAFFESGVVFEDGTVCKSAQLEVLSSASDKSCA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            V + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 RVTISEGKFHQVKKMFLAYGVKVTYLKRISFGEFKLDEGMAVGSYRTLTEAEKTILRTYL 238

Query: 246 G 246
           G
Sbjct: 239 G 239


>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 =  236 bits (603), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 100/229 (43%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R + +++I Q R+  +G ++      V+    I  DG  +     T
Sbjct: 1   MRLDKYICESTTMTRSQAKKVIIQGRITSDGTVMRNTGYKVLENTPICFDGNLIN-VRGT 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + +KP   + +  D    S +         ++   GRLD +T GL L+T+DG  +  
Sbjct: 60  RYIMLNKPKDFICSTVDEQFPSIINLIKVDKPDQLCIAGRLDADTTGLALITDDGQWSHK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + YR      V+Q+ + L K+GI ++      +  TL+    ++  V + +
Sbjct: 120 ITSPRRNCSKRYRATLAQPVEQNAVTLFKEGIQLKSENVPCLPATLEI--LTDNEVLLTI 177

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EGK  ++K++F      V  L R   G  +L   L  G  R ++   +
Sbjct: 178 HEGKYHQVKRMFAAIGNLVVELHREQIGEIKLDTDLKLGEWRYLTTDEV 226


>gi|300714626|ref|YP_003739429.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299060462|emb|CAX57569.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 292

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/294 (22%), Positives = 121/294 (41%), Gaps = 9/294 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           +  R++K I  +GI SRR+ +R I Q  V +NG         V + D ++V+G  +    
Sbjct: 5   SSIRLNKYIGESGICSRRDADRYIEQGNVFINGKRAA-VGDQVYAGDVVKVNGQLIEPRN 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   L   +KP+G+++T  + +  + V  N  +   RV  +GRLD  ++GL+ LTN G 
Sbjct: 64  EDDLVLIALNKPVGIISTTEEGERDNIV--NFVNHSKRVFPIGRLDKESQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  V  + +  L  G+ + G            +K +    
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKLVTDEFIAGLGAGVPMLGTVTK----KCKVKKEAPFVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ + F ++V +L R       L  L  G  RE +   L E      
Sbjct: 178 RITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVSLKGLPIGEWREFTDDELIELFKLIE 237

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
              ++ N +            +   I+            +++K  +   +K   
Sbjct: 238 HSSSEENPEKKAKPKAKPAAVKKPTIAGPKTAEKPTANGAARKRFVQPGRKKKG 291


>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 =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 113/233 (48%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
            T  R++K ++ AGIASRR+ + +I    V +NG + +   V V    D + V G P+  
Sbjct: 1   MTKVRLNKFLSAAGIASRRKCDEIIFAGEVTINGRVAQGPFVQVDDQHDRVLVRGKPI-A 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + +   ++ HKP+G V T      G   V D    +  RV +VGRLD  T GL+L+TNDG
Sbjct: 60  STKKVYFMVHKPLGFVCTSERKFPGTKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  PS    + Y ++ +  V +  LN L +G +I G     + V+    K     
Sbjct: 120 DFANKIIHPSYGITKEYLLKVNRDVIEKDLNSLMQGTMIDGKRVRPVAVS----KVRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E    ++  L RI  G   LG L  G  RE++   +
Sbjct: 176 IKIVVNEGKKHEIRLFAEAAGLQILELKRIRIGSLVLGGLRYGEYRELTDAEI 228


>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 =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/220 (31%), Positives = 108/220 (49%), Gaps = 10/220 (4%)

Query: 34  MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           M+   RV VNG   + A + +    D I  DG  L   E    ++ +KP G+++   DP 
Sbjct: 1   MLKAGRVTVNGKKEKSAKLQIDEERDEIIFDGQVLEYEE-FVYYMMNKPKGVISATEDPK 59

Query: 93  GRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            R TV D L        V  VGRLDI+T GLLLLTNDG LA  L  P     + Y+ +  
Sbjct: 60  HR-TVLDLLDDLARSKEVFPVGRLDIDTHGLLLLTNDGQLAHALLSPKRHVDKTYQAQVK 118

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G + Q+ + +  KGI ++       +   V++DT+K   + + V + EGK  ++K++  +
Sbjct: 119 GIMTQEDVEIFAKGIPLKDFTCQPAKLEIVSIDTEKI-QSQIRVTIAEGKFHQVKRMVAY 177

Query: 208 FNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
              +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 178 CGKEVVDLQRLTMGTLVLDENLQRGEWRRLTKEELEALLA 217


>gi|227517791|ref|ZP_03947840.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
 gi|227074752|gb|EEI12715.1| pseudouridylate synthase [Enterococcus faecalis TX0104]
          Length = 260

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 78/262 (29%), Positives = 132/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+Q GI     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPVRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 73/232 (31%), Positives = 120/232 (51%), Gaps = 6/232 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           +++++++AG+ SR      I   RV+V+G  +         S   I +DG+ +  + R +
Sbjct: 22  LARILSKAGLCSRTVAVEWIRAGRVEVDGRRILDPEARFPLSGPGIRIDGLDITASTR-Q 80

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L HKP G++TT  D  GR+TV+D LP     +  VGRLD  + GLLL +ND   A+ L
Sbjct: 81  VLLLHKPRGVLTTRQDERGRATVYDLLPGS-PWLAPVGRLDQASSGLLLFSNDPHWAQRL 139

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     + Y V+    +  D +  L    V+ G     MQ+      G   W+   L+
Sbjct: 140 LDPDQHVAKTYHVQIRPPLSTDTVVQLAADSVLDGEPCLPMQIRELRCGGKTQWLEFILQ 199

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV---SKKILRE 243
           EG+NR+I+++    + +V RLIR++ G   LG L AG  R +    +++LR+
Sbjct: 200 EGRNRQIRRLLAACDREVLRLIRVAVGNLPLGELRAGEWRWLHSGEEELLRQ 251


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 92/297 (30%), Positives = 146/297 (49%), Gaps = 13/297 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
           +R+ K +A+ G+ SRR++E  I   ++ VNG + +     +  +D + +DG  +   +  
Sbjct: 3   ERIQKRLAQLGMGSRRQIEHWIRDGKITVNGKVAQLGDT-LEWSDRVTLDGKAIDLEQVD 61

Query: 72  --RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
                + LYHKP G V T SDP GR+TVF+ LP + + R ISVGRLD+NT GLLL T DG
Sbjct: 62  TIPKEVLLYHKPEGEVCTRSDPQGRTTVFERLPRLRAGRWISVGRLDVNTAGLLLFTTDG 121

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--- 185
            LA  L  PS +  R Y VR  G V  + LN L +G+ ++       ++ +   +     
Sbjct: 122 ELANRLMHPSREIDREYAVRVLGDVSDEMLNQLVEGVQLEDGAAKFSEIVIGDHEYDSDR 181

Query: 186 -NAWVTVGLREGKNREIKKVFEFF-NWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            N W  V L+EG+NRE+++++E F    V+RL R+ Y    L  TL  G  +       +
Sbjct: 182 ANRWYYVCLQEGRNREVRRLWESFSGVTVSRLKRVRYANIFLPKTLARGQWKRAEYDEFQ 241

Query: 243 EQL-GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           E      L   +Q          +     R   I++        ++++SQ    + +
Sbjct: 242 ELYRSVELTPPSQKTYAESGGKRKEKHTRRARDINQKRRQQQNRRRSASQMRRRNPR 298


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 114/238 (47%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR  E   
Sbjct: 24  RLNKHIAETGFCSRREADRLIGERRVTVNGVIAGTGAV-VGEDDTVLVDGQPLRVREAKK 82

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R      +KP+G+ +T       + V         R+  +GRLD ++EGL+L+T++
Sbjct: 83  PGTRRHVYIALNKPVGITSTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMTSN 140

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ +        +    T + +  
Sbjct: 141 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRLHDETTLPCR----TARIAKF 196

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R ++ + L+  L
Sbjct: 197 GFRIVLEQGLNRQIRLMAAAFGFRVTQLRRVRIDNIKLAALKPGQWRNLTDQELQGLL 254


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 127/238 (53%), Gaps = 2/238 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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  KVYILLNKPRGYISSVKDDRGRKTLLDIV-KVNERVYPIGRLDYNTSGAIILTNDGEVYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   ++Y     G    +++   + GI I G      +    +    ++ V + 
Sbjct: 122 NIAHPGSNKSKIYIAAIKGIPSSEEIKRFENGIDIGGYITAKAKFDFISSNKESSKVKIE 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + EGKNR+++K+ +     V  L+RI+ G  +LG L  G+ R +++K ++   G  LL
Sbjct: 182 IHEGKNRQVRKMCDAIGHPVITLMRIAIGDIKLGNLKEGAWRYLTEKEIQYIKGGKLL 239


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 113/255 (44%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 89/235 (37%), Positives = 128/235 (54%), Gaps = 4/235 (1%)

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  TRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
              WL YHKP+G + + SDP+GR  VF +LP     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-TLLAGSTREVSKKILREQ 244
           V + EG+NR ++++++     V+RLIR+ YGP  LG  L  G++R++  + +   
Sbjct: 181 VVVSEGRNRLVRRLWDAVGVTVSRLIRVRYGPVVLGRGLKTGASRDLEVREVEAL 235


>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 =  236 bits (602), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 127/238 (53%), Gaps = 2/238 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 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  KVYILLNKPRGYISSVKDDRGRKTLLDIV-KVNERVYPIGRLDYNTSGAIILTNDGEVYN 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P +   ++Y     G    +++   + GI I G      +    +    ++ V + 
Sbjct: 128 NIAHPGSNKSKIYIAAIKGIPSSEEIKRFENGIDIGGYITAKAKFDFISSNKESSKVKIE 187

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + EGKNR+++K+ +     V  L+RI+ G  +LG L  G+ R +++K ++   G  LL
Sbjct: 188 IHEGKNRQVRKMCDAIGHPVITLMRIAIGDIKLGNLKEGAWRYLTEKEIQYIKGGKLL 245


>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 =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 115/232 (49%), Gaps = 10/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K+++  G  SRREV  +I +  +     L  ++   V S D I  +G PL   +   
Sbjct: 6   RLDKLLSSLGYCSRREVALLIREGIITHAHNLPLKSDTKV-SHDEILCEGEPLDPPQGI- 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           + L HKP GLV +H D +G+  V+D LP  +     ++ +VGRLD +T GLLLLT+DG L
Sbjct: 64  VILMHKPAGLVCSHDDGEGK-LVYDLLPERWRLRDPKISTVGRLDKDTSGLLLLTDDGAL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P  +  +VY  R    +  D+  +   G +++ G     +   L      +  V
Sbjct: 123 LHRLTSPKHKVPKVYEARLDRALKGDEAEIFASGTLMLNGEKTPCLPAKLTV--IDDTHV 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           T+ + EG+  +++++F      V  L R S+G   LG L AG  R +  + L
Sbjct: 181 TLEIVEGRYHQVRRMFAAVGNHVTALHRCSFGTLTLGDLKAGEYRLIDAQSL 232


>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 =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 124/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGAVTANKDKE-LPTVMDLLPSNIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV +        ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDDTVCKPAKLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 115/231 (49%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    I SR +V+++I+ +++ V+  +      NV      I VDG  LR A+ 
Sbjct: 1   MRLDKLLETCQIGSRGQVKKLISAKKIIVDDRVAIGGQQNVDPGLQTIIVDGKVLR-AKG 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +  +KP G+V+   D +   TV D L     F  +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HHYFFLNKPRGVVSALKDREH-PTVIDCLTEADRFPSLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +  D L+  + G+V + G       V + + +   +  
Sbjct: 119 GFRMLHPKHHVDKSYYVVVNGFLGDDLLSFFRSGVVFLDGTVCKAAAVEILSAREKQSVA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V L EGK  +IKK+F  +  KV  L R+++  F +G L AG  R ++   
Sbjct: 179 KVTLSEGKFHQIKKMFLAYGVKVIYLKRLTFAEFSVGNLAAGEYRTLTAHE 229


>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 =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 102/239 (42%), Gaps = 6/239 (2%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             N   QR+ + ++++G  SR    + I    V +NG L   A+  +   D +      +
Sbjct: 9   TPNQERQRLDRFLSQSGRLSRSMARKAILAGEVTINGTLCRDASTKIGPNDTVHHH-HDI 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTN 126
             A      + HKP G+V    D   R TV D L     S +   GRLDI+T GL+LLT+
Sbjct: 68  VVAPSHHYLMLHKPEGVVCATEDGRHR-TVIDLLGEPWRSDLHIAGRLDIDTTGLVLLTS 126

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG  +  +  P     + Y V     +        ++G+++ G         L+     +
Sbjct: 127 DGDWSHRVTSPRHNKAKRYHVTTADPIASSWCASFEQGVMLDGETKLTRPAQLEILDEFH 186

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           A   + L+EG+  ++K++F     +V +L R + G   L   L  G  R ++   ++  
Sbjct: 187 A--NLCLQEGRYHQVKRMFAAMGTRVVKLHRYAIGELILDNTLPLGHYRALTDCEIQRL 243


>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 =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 76/243 (31%), Positives = 129/243 (53%), Gaps = 9/243 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I +E F   R++  ++ AGI SRRE +++I    ++VNG ++ +    V   D I
Sbjct: 5   MNQKKIEEEKF--IRLNHYLSNAGITSRREADKLIQSGLIEVNGKIVTKFGTVVHKNDVI 62

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTE 119
           +  G  ++  ++    L +KP G +T+  DP  R TV + +P+  + R+  VGRLD  T 
Sbjct: 63  KFHGSRIK-NKKKIYILLNKPKGYITSTRDPFNRKTVMNLIPNFQNYRIYPVGRLDRLTT 121

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           G+LLLTNDG +   L  P  +  ++Y V  +  +    L+ +++G     I   + +V +
Sbjct: 122 GVLLLTNDGFITEKLTHPKYKIQKIYLVVLNKTIHYQDLDKIRQG----KIYLNEGRVKI 177

Query: 180 D-TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           D   K +   V +GL  G NR I+++F+   ++V +L RI +G F    L  GS   +SK
Sbjct: 178 DFLHKYAKNIVKIGLHIGWNRVIRRIFKKLTYQVIKLERIHFGGFTNKNLKIGSWCFLSK 237

Query: 239 KIL 241
           + +
Sbjct: 238 QEV 240


>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 =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGDILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  235 bits (601), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 112/255 (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-VLGQKVSPADRI 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E+D     +       L +KP+G V+  ++                +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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  235 bits (601), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 116/234 (49%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   ++  E+ 
Sbjct: 6   RLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDHKLIQF-EQF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+V+   D     TV D +   +  R+  VGRLD +TEGLLLLT+DG LA 
Sbjct: 65  HYLMLHKPQGVVSATKD-HHDQTVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGMLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +  GQ  ++++   K+G+ I  G      ++ +       + V +
Sbjct: 124 ELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDIGNGEKSKQARLQILKADVQESEVLI 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E 
Sbjct: 184 TIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQEL 237


>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 =  235 bits (601), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 113/240 (47%), Gaps = 14/240 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             R++K IA +G  SRRE +R+I ++RV VNG+     AV V + D + VDG PLR  E 
Sbjct: 15  TIRLNKYIAESGFCSRREADRLIGERRVTVNGVPAGTGAV-VGAEDTVLVDGQPLRIREA 73

Query: 72  ------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 +      +KP+G+  T       + V         R+  +GRLD ++EGL+L+T
Sbjct: 74  KKLGGRKHVYIALNKPVGITCTTESSVKGNIVK--FVGHEQRIFPIGRLDKDSEGLILMT 131

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +
Sbjct: 132 SNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIA 187

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 188 KFGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 247


>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 =  235 bits (601), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 88/227 (38%), Positives = 128/227 (56%), Gaps = 7/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           R+ K+IA AG  SRR VER+I Q R++VN  +          T  +++DG  +       
Sbjct: 4   RLQKLIANAGYGSRRWVERLIEQGRIEVNNKIAI-IGDKTEITSLVKIDGRKINLSRYVE 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ + +K  G++ ++ D  GR +V+  LP   SR I VGRLD+NT GLLL+TN+G L
Sbjct: 63  QETKVIILNKQAGVICSNRDDKGRKSVYSLLPKE-SRWIMVGRLDLNTSGLLLVTNNGDL 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-GTLLAGSTREV 236
           V LREGK RE+++++E   +KV+RLIRI +G  +L   L A     +
Sbjct: 182 VVLREGKKREVRRLWEVLGFKVSRLIRIRFGEIRLPDNLKANQYDYL 228


>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 =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 63/245 (25%), Positives = 108/245 (44%), Gaps = 20/245 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              RVSK+++  G+ SRRE +  I Q  V V+G ++    V       IE+      +  
Sbjct: 3   EKVRVSKLLSELGLCSRREADSYIEQGLVTVDGEVVNELGVRAYRHQKIELQSGAKAQQA 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIF---------------SRVISVGRLD 115
                + +KP+G ++   D          + P  +                 +   GRLD
Sbjct: 63  SRITVILNKPVGYISHFDDEQEYQPAASLITPDNYFASPLDKGRNPRFNTKGLAPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+LT DG +A++L   ++   + Y VR  G++  + L+ L+ G+ +  +     
Sbjct: 123 IDSTGLLVLTQDGRIAKLLIGENSPIEKEYLVRVEGKLSFEDLDKLRHGLTLDDVVLKPA 182

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV+   +      +   LREG+ R+I+++ E    KV  L R+  G   LG L  G  R 
Sbjct: 183 QVSWQNED----QLRFVLREGRKRQIRRMCEMVGLKVIGLKRVRIGRISLGPLPPGQWRF 238

Query: 236 VSKKI 240
           V  + 
Sbjct: 239 VRPEE 243


>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 =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 115/239 (48%), Gaps = 3/239 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K    +     R++K IA AGI +RRE +R IA   V+VNG  +      V  TD ++ D
Sbjct: 85  KPNATDQSKGIRLNKYIANAGICARREADRYIAAGNVEVNGKPMTELGYRVQPTDVVKFD 144

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLL 122
           G  +  AE+    L +KP G +TT  D  GR TV D +       +  VGRLD  T GLL
Sbjct: 145 GKNIS-AEKKEYILLNKPKGFITTTQDEKGRKTVMDLVAGAAEGNIKPVGRLDRLTTGLL 203

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           LLTNDG L + L  PS    ++Y V    ++     + +++G+ ++        +     
Sbjct: 204 LLTNDGDLMKKLTHPSHGVRKIYHVILDKKLALADFHKIQEGLTLEDGFIQVDDINFVDG 263

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              N  + V +  G+NR ++++FE   + V +L R+ +       L  G  R ++ + +
Sbjct: 264 APHN-EIGVKIHSGRNRIVRRIFESLGYVVEKLDRVVFAGLTKKDLPRGHWRTLTAQEI 321


>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 =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 108/231 (46%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-T 73
           R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V   + +          ++  
Sbjct: 28  RLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVVEQGLRVDPENAVVRVDGVRVVVQKDL 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
                +KP G   T SD  GR  V D +        R+  VGRLD +TEGLLL TNDG L
Sbjct: 88  VYLAMNKPRGWQCTMSDDLGRPCVGDIVSERVQSGQRLFHVGRLDADTEGLLLFTNDGDL 147

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y    HG V++     L+ G+ +          T+         V 
Sbjct: 148 AHRLMHPSFEVPKTYLATVHGVVERSTGKQLRDGVTLDDGPAKVDAFTVLEINEGKTLVK 207

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+   ++++ +     V RL+R + G   LG    G+ R + +  +
Sbjct: 208 LVLHEGRKHIVRRLLDAVGHPVVRLVRTNVGVVALGDQRPGTQRVLGRSEV 258


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 69/252 (27%), Positives = 108/252 (42%), Gaps = 20/252 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  +   P R+SK +A  G+ SRRE +  I    V+VNG +++     V    +IEV 
Sbjct: 207 KPVASQPDLP-RLSKRMAELGLCSRREADEWIVNGWVRVNGQVVDELGSRVEPDANIEVS 265

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRV 108
               +        L HKP+G V+  ++      V    P                    +
Sbjct: 266 KEAEKHQSEIVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNHWAEDPVQKEFRRGFLKGL 325

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLDI++ GLL+LT DG +AR L    +Q  + Y VR  G +  + L  L  G+ + 
Sbjct: 326 APAGRLDIDSTGLLVLTQDGRVARQLIGEDSQTEKEYLVRVEGTLSDEGLRKLNHGLSLD 385

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+     +V+   +      +   LREG+ R+I+++ E     V  L R+  G   LG L
Sbjct: 386 GVQLKPAKVSWQNED----QLRFVLREGRKRQIRRMCELVGLHVVGLKRVRIGSVALGKL 441

Query: 229 LAGSTREVSKKI 240
             G  R +    
Sbjct: 442 PPGQWRYLRPGE 453


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 71/271 (26%), Positives = 103/271 (38%), Gaps = 47/271 (17%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +A   + SRRE +  IA   VKVNG       V V  +D IE+D     +  
Sbjct: 10  APVRLNKRMAELKMCSRREADEWIANGWVKVNGKPA-EMGVKVTPSDRIEIDKAAKGQQA 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
                L +KPIG V+  ++      V               F   P     +   GRLDI
Sbjct: 69  NQVTILINKPIGYVSGQAEDGHEPAVTLFTPQNRWAEDNARFFFSPQQLRGLAPCGRLDI 128

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-------------------HGQVDQ-- 155
           ++ GLL++T DG +AR L    +   + Y VR                       V Q  
Sbjct: 129 DSIGLLVMTQDGRVARQLIGEDSVMEKEYLVRVAYYGPGQSAPTGQLIRMDDDDPVTQNV 188

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                   L  L+ G+ + G      +V     +     +   L EGK R+I+++ E   
Sbjct: 189 QAVFPPAMLARLRHGLSLDGQQLKPARVEWQNPE----QLRFVLTEGKKRQIRRMCELVG 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            KV  L R+  G   LG L  G  R +    
Sbjct: 245 LKVVGLKRVRIGKVMLGNLPVGQWRYLGPHE 275


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 75/231 (32%), Positives = 116/231 (50%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ + +   GI SR+EV+++I+ + VKVNG     A  N+   +D IE +G  L   E 
Sbjct: 1   MRLDRFLVECGIGSRKEVKKIISTKEVKVNGSYDISAKDNIDEYSDIIEYNGKKLEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D    +TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDTR-EATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V     + Q+ +  L++G+ I        +V     K S+  + 
Sbjct: 119 NHRLLSPKNHVDKTYYVEIENNISQEDILKLEEGVDIGSYVTLPAKVK----KISDTKIF 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KV  L R S+   +L  L  G  +EV+ + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVIYLQRTSFAKLKLADLALGEVKEVNLEDI 225


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 66/222 (29%), Positives = 115/222 (51%), Gaps = 11/222 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRR  +  I   +V +NG         VM  D +   G  +++ +
Sbjct: 3   DGIRLNKYLSEAGVCSRRAADTHIENGKVTINGETA-VMGQKVMPGDVVTFMGRKVQQKD 61

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RT +  Y+KPIGL  T S  DPD    +FD++     R+  VGRLD +++GLLLLTNDG 
Sbjct: 62  RTVILAYNKPIGLTCTASKADPDN---IFDHI-DYPIRLQYVGRLDKDSQGLLLLTNDGD 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L+  ++       + YRVR + ++ +D +  + +G+ I        +V    +K  +   
Sbjct: 118 LSNAIQKSVNNHEKEYRVRVNREITEDFIRKMSEGVPILDTVTKKCKV----RKIDDRSF 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + L +G NR+I+++ +   ++V  L R+     +LG +  G
Sbjct: 174 MIVLTQGLNRQIRRMCDALGYRVVNLKRVRVCNVKLGNMRPG 215


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 74/230 (32%), Positives = 114/230 (49%), Gaps = 8/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ SRR+ E +I   RVKV+G +     + V ++ ++EVDG  +    + 
Sbjct: 16  IRLNKYLAMCGLGSRRKTEALIVSGRVKVDGEIAAGPWIMVNTSYNVEVDGK-IVAPLKN 74

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP   V    D    +TV D LP      R+  VGRLD N+ GLL+LTNDG  A
Sbjct: 75  LYLVMNKPRNCVCAVVDSRY-TTVIDLLPKDLIGHRLFPVGRLDKNSSGLLILTNDGDFA 133

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  P     + YRV  +  +    L   +KG+ +         V +     S+ W  +
Sbjct: 134 QDIIHPRNGITKTYRVMLNKPMTSGDLEKWRKGVYLDDRLIKPKDVKIL----SDKWCVI 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EGK REI+++ E   +KV  L+RI  G  +L TL  G   + SK  L
Sbjct: 190 EIYEGKKREIRRMAECLGYKVVELVRIKIGRLELKTLDEGCFLKFSKDKL 239


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 119/231 (51%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +   G+ +RR+V+ +I++  + +N   +      +    D I++ G  + K ++
Sbjct: 1   MRLDKFLTECGVGTRRDVKNIISKNEITINDKKVNSPKEKIDLENDVIKI-GERVLKYKK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D   + TV + LP       +  VGRLD +TEGLLL TN+G +
Sbjct: 60  DRFYIMNKTSGFITATEDTREK-TVMELLPEWVIKKDLFPVGRLDKDTEGLLLFTNNGKI 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P     + Y V+   ++D+  +NLL++G+ I G      +V +     +N  + 
Sbjct: 119 AHELLSPKKHVDKTYLVKLLKEIDKKSVNLLEEGVDIGGYITKPSKVQI----INNTEIL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EGK  ++KK+ E    KV  L R+S+G  +LG L  G  +EV  K +
Sbjct: 175 LTICEGKFHQVKKMLEAVGNKVIYLKRLSFGNLELGDLPLGEVKEVDLKDI 225


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 116/234 (49%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   ++  E+ 
Sbjct: 9   RLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDHKLIQF-EQF 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+V+   D     TV D +   +  R+  VGRLD +TEGLLLLT+DG LA 
Sbjct: 68  HYLMLHKPQGVVSATKD-HHDQTVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGMLAH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +  GQ  ++++   K+G+ I  G      ++ +       + V +
Sbjct: 127 ELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDIGNGERSKQARLQILKADVQESEVLI 186

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E 
Sbjct: 187 TIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQEL 240


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 112/240 (46%), Gaps = 14/240 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V + D + VDG PLR  E 
Sbjct: 15  TIRLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGAEDTVLVDGQPLRIREA 73

Query: 72  ------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 +      +KP+G+  T       + V         R+  +GRLD ++EGL+L+T
Sbjct: 74  KKLGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMT 131

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +
Sbjct: 132 SNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIA 187

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 188 KFGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 247


>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 =  235 bits (600), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 114/238 (47%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRRE +R+I ++RV VNG++    AV V   D + VDG PLR  E   
Sbjct: 4   RLNKHIAETGFCSRREADRLIGERRVTVNGVIAGTGAV-VGEDDTVLVDGQPLRVREAKK 62

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R      +KP+G+ +T       + V         R+  +GRLD ++EGL+L+T++
Sbjct: 63  PGTRRHVYIALNKPVGITSTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ +        +    T + +  
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRLHDETTLPCR----TARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R ++ + L+  L
Sbjct: 177 GFRIVLEQGLNRQIRLMAAAFGFRVTQLRRVRIDNIKLAALKPGQWRNLTDQELQGLL 234


>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 =  235 bits (600), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 104/230 (45%), Gaps = 9/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA+    S+ +V  +IA+ RV VN  +       +   D + +D   L+K     
Sbjct: 7   RLDRFIAKHTDHSKNDVRILIAKGRVYVNQTVAVSVDQIIKQFDEVILDDEVLQKNT-PI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP G+V+  SDP   +TV D L   +  +   GRLD  + GLLLLTNDG  +  L
Sbjct: 66  YLMLNKPAGVVSATSDPQH-TTVIDLLDDHYKDLHIAGRLDRFSTGLLLLTNDGEWSNSL 124

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     +     +   KG+    + I     Q+     + +     V 
Sbjct: 125 SHPDNRVAKRYIVELKEPITDAYGDAFAKGMHFAYEDITTQPAQLKQLEPRVA----EVT 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|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 =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDQIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HK  G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKSAGVVTANKDRE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>gi|332971035|gb|EGK10006.1| ribosomal large subunit pseudouridine synthase F [Kingella kingae
           ATCC 23330]
          Length = 243

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 70/244 (28%), Positives = 110/244 (45%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A   I SRRE +  I Q  VKVNG +       V+  D I++D    ++  
Sbjct: 3   EPIRLSKRMAELKICSRREADSYIEQGWVKVNGAVA-VLGQKVLPNDRIDLDKRAHQQQT 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
           +    L +KP+G V+   + D R+ +                   PS    +   GRLDI
Sbjct: 62  QRVTILLNKPVGFVSGQPEKDYRAAIELITESNHWQGDTSRIAFHPSQLRGLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L    +   + Y VR  G +    L LL  G+ + G      +
Sbjct: 122 DSVGLLVLTQDGRIAKQLIGEQSDSEKEYLVRVKGTLSPQGLALLNHGLSLDGEKLRPAK 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R +
Sbjct: 182 VEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGALPTGQWRYL 237

Query: 237 SKKI 240
            +  
Sbjct: 238 GENE 241


>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 =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 91/248 (36%), Positives = 139/248 (56%), Gaps = 7/248 (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----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
           ++G  +     +   +RL +YHKP G + +HSDP  + TVF  LP + + + 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 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
                 +G+N W  + L+EG+NREI+++ E  N KV+RLIR  YGP  L + L  G   E
Sbjct: 182 FEHTGGEGANQWFRIILKEGRNREIRRLVESQNLKVSRLIRTRYGPLNLPSHLKRGQFME 241

Query: 236 VSKKILRE 243
           + KK L +
Sbjct: 242 LEKKNLEK 249


>gi|295093348|emb|CBK82439.1| ribosomal large subunit pseudouridine synthase F [Coprococcus sp.
           ART55/1]
          Length = 234

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 66/222 (29%), Positives = 114/222 (51%), Gaps = 11/222 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K ++ AG+ SRR  +  I   +V +NG         VM  D +   G  +++ +
Sbjct: 3   DGIRLNKYLSEAGVCSRRAADTHIENGKVTINGETA-VMGQKVMPGDVVTFMGRKVQQKD 61

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RT +  Y+KPIGL  T S  DPD    +FD++     R+  VGRLD +++GLLLLTNDG 
Sbjct: 62  RTVILAYNKPIGLTCTASKADPDN---IFDHI-DYPIRLQYVGRLDKDSQGLLLLTNDGD 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L+  ++       + YRVR + ++ +D +  +  G+ I        +V    +K  +   
Sbjct: 118 LSNAIQKSVNNHEKEYRVRVNREITEDFIRKMSDGVPILDTVTKKCKV----RKIDDRSF 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            + L +G NR+I+++ +   ++V  L R+     +LG +  G
Sbjct: 174 MIVLTQGLNRQIRRMCDALGYRVVNLKRVRVCNVKLGNMRPG 215


>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 =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 113/246 (45%), Gaps = 20/246 (8%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              P R+SK +A   + SRRE +  I Q  VKVNG++       V+ TD I++D +  ++
Sbjct: 3   EIQPIRLSKRMAELKMCSRREADHYIEQGWVKVNGVVA-VLGQKVVPTDRIDLDKIAHQQ 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRL 114
             +    L +KP+G V+   + D R+ +                   P     +   GRL
Sbjct: 62  QAQRVTILLNKPVGFVSGQPEKDYRAAIELIAADNHWNGDTSKIPFHPKQLKGLAPAGRL 121

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ GLL+LT DG +A+ L    +   + Y VR  G + ++ L LL  G+ + G     
Sbjct: 122 DIDSVGLLVLTQDGRIAKQLIGEHSDSEKEYLVRVKGNLIENGLALLNHGLSLDGEKLRP 181

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R
Sbjct: 182 AKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRIGKVKLGALPVGQWR 237

Query: 235 EVSKKI 240
            +    
Sbjct: 238 YLGANE 243


>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 =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 113/231 (48%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +   G+ SR+EV+ ++  ++++VNG+ +      +    D +      L   E 
Sbjct: 1   MRIDKFLVECGVGSRKEVKELLKSRKIRVNGLFITSPKETIEEEKDEVYYGEKKLSYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ HK  G VT   D    +TV D LP       +  VGRLD +TEGLLL TNDG L
Sbjct: 60  FRYYILHKKAGYVTALEDSRE-ATVMDLLPEWVIKKDLAPVGRLDKDTEGLLLFTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P +   + Y       + ++ L  L++G++I        +     +K  +  + 
Sbjct: 119 NHRLLSPKSHVDKTYHASLECDITEEALEKLREGVMIGEYKTLPAKA----EKLEDRKIA 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + +REGK  ++KK+ E    KV  L RIS+G   LG L  G+ +EVS + +
Sbjct: 175 LTIREGKFHQVKKMLEAVGNKVIYLKRISFGKLVLGDLELGAVKEVSLEDI 225


>gi|325479564|gb|EGC82660.1| pseudouridylate synthase [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 233

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 73/230 (31%), Positives = 122/230 (53%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA++G  SRR+ + +I   +VKVNGIL+      V   D +E+DG  L   E+ 
Sbjct: 1   MRINKYIAKSGYTSRRKADDLIKASKVKVNGILINEPGYEVTDDDILEIDGKRL-YIEKN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G VT++ DP     +   +  +  R  + GRLD ++EGLL++TNDG     
Sbjct: 60  FYKKLYKPVGYVTSNYDPHNEKDLNSLI-DMKERFFAAGRLDKDSEGLLIITNDGHFTNG 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  + Y V    ++ + +    +KGI I +G    + ++ L   K       V 
Sbjct: 119 IIHPSNELEKTYIVTVSRKLSKSQEKKFEKGIDIGRGEITSNSKIKLLDSK--TNKYEVK 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +G NR+I+++F +F+ KV  L RIS GP +L  +     R+ S+K + 
Sbjct: 177 IHQGYNRQIRRMFAYFSSKVINLKRISIGPIKLDDMKEYEIRDFSEKEME 226


>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 =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 67/219 (30%), Positives = 104/219 (47%), Gaps = 8/219 (3%)

Query: 34  MIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD 92
           M+   RV VNG   + A + +    D I +DG  L   E    ++ +KP G+++   DP 
Sbjct: 1   MLKAGRVTVNGKKEKSAKLQIDEERDEIRLDGQVLEYEE-FVYYMMNKPQGVISATEDPK 59

Query: 93  GRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
            R TV D L        V  VGRLDI+T GLLLLTNDG LA  L  P     + Y  +  
Sbjct: 60  HR-TVLDLLDDLARTKEVFPVGRLDIDTHGLLLLTNDGQLAHALLSPKRHVDKTYLAQVK 118

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFF 208
           G + Q+ +    KGI ++       ++ L +     + + + V + EGK  ++K++  + 
Sbjct: 119 GIMTQEDVETFAKGIPLKDFTCQPARLELVSIDTAKNQSQIRVTIAEGKFHQVKRMVAYC 178

Query: 209 NWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
             +V  L R++ G   L   L  G  R ++K+ L   L 
Sbjct: 179 GKEVVDLQRLTMGTLMLDENLQRGEWRRLTKEELENLLA 217


>gi|291561019|emb|CBL39819.1| ribosomal small subunit pseudouridine synthase A
           [butyrate-producing bacterium SSC/2]
          Length = 242

 Score =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 116/234 (49%), Gaps = 6/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +  +   +R+E +  + + +V VNG  +++    V    D +E D   ++  E+ 
Sbjct: 6   RLDKFLCDSLNMTRKEAKESVKKGKVVVNGEAIKKPEYKVDAEQDQVEFDHKLIQF-EQF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G+V+   D     TV D +   +  R+  VGRLD +TEGLLLLT+DG LA 
Sbjct: 65  HYLMLHKPQGVVSATKD-HHDQTVLDLIHEDYKDRLFPVGRLDKDTEGLLLLTDDGMLAH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  +  GQ  ++++   K+G+ I  G      ++ +       + V +
Sbjct: 124 ELLSPRKHVDKVYFAKVSGQFGENEIARFKEGLDIGNGERSKQARLQILKADVQESEVLI 183

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + EGK  ++K++ +    +V  L R+S G  +L   L  G  R ++K  L+E 
Sbjct: 184 TIMEGKFHQVKRMVKAVGSEVLYLKRLSMGSLKLDEELKLGEYRRLTKAELQEL 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 =  235 bits (599), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 108/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      +R++V  ++A +RV+V+G++       V     +EVD   ++     
Sbjct: 1   MRLDRFLGNLPCYNRQQVRLLLASKRVRVDGVVASDPLHEVREFSRVEVDDQVVQAGYPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G V+  SDP    TV D LP+     +   GRLD NT GL++LTNDG  +R
Sbjct: 61  RYLMLHKPTGCVSATSDPLH-PTVLDLLPAELRDGLHIAGRLDYNTTGLMILTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P T+  +VY V    ++    ++  ++G              LD      A   + 
Sbjct: 120 HLTQPRTKLPKVYLVHTEDEIGAHYVDKFREGFYFAFEDLTTQPAQLDILGPREA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F +F  KV  L R   G   L   L  G  RE+S + +
Sbjct: 178 IVEGRYHQVKRMFGYFQNKVVGLHRERMGAIALDPGLAPGEYRELSAEEI 227


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 115/261 (44%), Gaps = 30/261 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A A + SR+ V   I +  VKVN  L+   A+ +    D IE     +  A +
Sbjct: 1   MRLDKFLAEAAVGSRKNVRIYIKEGMVKVNKELVTEPAIEIDENCDVIEYLNEIVSYAGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +++KP G +T  +D +   TVFD L  +    +  VGRLD +TEGLLL TNDG   
Sbjct: 61  LYY-MFNKPAGCITAKTD-EIHKTVFDFLGEAGTKGIFHVGRLDKDTEGLLLFTNDGEFE 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLD--------- 180
             +  P     + Y     G + ++    L++G  I    I     ++ +D         
Sbjct: 119 HKIMYPEKHVEKTYFFWALGSLSEEDKKQLEQGTYIGQCKILTKPAKIEVDKFGIYEELK 178

Query: 181 ------------TQKGSNAWVT--VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                       +  G+   V+  + + EG+  ++K++ +     V  L RIS G   L 
Sbjct: 179 HEMATDNVNNINSNHGTQPVVSGYLTISEGRKHQVKRMLKSVGCYVVYLKRISIGGLALD 238

Query: 227 -TLLAGSTREVSKKILREQLG 246
            +L  G  R +++  +++ LG
Sbjct: 239 KSLKKGQYRPLTELEIQKVLG 259


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 114/239 (47%), Gaps = 10/239 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G  SR+EV  ++   RV+V+G  +  A   V      + +DG  L      
Sbjct: 5   RLDKLLAGQGQGSRKEVHTLLRGGRVQVDGQTVTDAGQKVDPDRQRVTLDGHALLWRAHL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+++   DP  R TV D LP+   R  +   GRLD +TEG LL+T+DG  A
Sbjct: 65  -YLMMNKPAGVISASRDPKAR-TVLDLLPADLCRPGLFPAGRLDKDTEGFLLITDDGAFA 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P     ++Y        D    +    G+ ++   +  +   L   +G++A+  V
Sbjct: 123 HDILAPRRHVEKIYLATLDRPADTADTDAFATGLTLEDGLH-CLPARLWLGEGTDAYAAV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
             REGK  +++++F     +V  L RI  G   L  +L  G  RE++    R+++G  L
Sbjct: 182 --REGKFHQVRRMFAARGKQVVHLRRIQIGGLALDESLAPGEARELTPAE-RDRIGLRL 237


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 121/240 (50%), Gaps = 10/240 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+V+   D +   TV D +     R  +  VGRLD +TEGL+L+TN+G L
Sbjct: 61  -VYYLMNKPAGVVSARKDKEH-QTVIDLITPEDQRDGLYPVGRLDRDTEGLVLITNNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +  +  D     + G+V +        Q+ + +     +  
Sbjct: 119 GFAMLHPRYHVAKTYYVEVNDVLGPDAPAFFESGVVFEDGTVCKSAQLEILSSARDKSSA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
            + + EGK  ++KK+F  +  KV  L RIS+G F+L   +  GS R +++     LR  L
Sbjct: 179 HITISEGKFHQVKKMFLAYGVKVTYLKRISFGAFKLDEGIAVGSYRTLTETEKTILRTYL 238


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 99/232 (42%), Gaps = 8/232 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+ K I+      R + +  I ++  KVNG ++      V  +D +      L     
Sbjct: 4   PCRLDKFISHLTELPRTKTKAGIKRKYAKVNGTVITSFDYQVTESDVVLWQDKQLEVL-G 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KP G V   SD   ++ +      + S++   GRLD++T GL+L+TNDG  + 
Sbjct: 63  DRYFMLNKPEGYVCATSDELHQTVLELLDEPVMSKLHIAGRLDLDTTGLVLITNDGEWSH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P  Q  + Y V     +  D L  L+ G+ + G         V L  +      V 
Sbjct: 123 KVTSPKYQKYKTYLVETLEPMTDDALQELRDGVQLHGEKGLTQPAIVELLAEYS----VR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++F     KV  L R       L   L  G  R ++ + +
Sbjct: 179 ISICEGKYHQVKRMFAAVGNKVEVLHREKIAGITLDQDLAPGQYRLLTAEEI 230


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 112/255 (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-VLGQKVSPADRI 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVIGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>gi|213618826|ref|ZP_03372652.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 276

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 125/283 (44%), Gaps = 12/283 (4%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--RTRLWLY 78
           + +GI SRRE +R I Q  V +NG         V++ D ++V+G  +   E     L   
Sbjct: 1   SESGICSRREADRFIEQGNVFINGKRAA-IGDQVVAGDVVKVNGRLIEPREADDLVLIAL 59

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN G L   +    
Sbjct: 60  NKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNHGDLVNKILRAG 117

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               + Y V     +  + +  +  G+ I G            +K +     + L +G N
Sbjct: 118 NDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRITLVQGLN 173

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN-L 257
           R+I+++ E+F ++V +L R       L  +  G  R+++   L +     L+E +     
Sbjct: 174 RQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF--KLIEGSSSEAK 231

Query: 258 DAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                  +T    RP +  E  ++  R   +  +     ++KK
Sbjct: 232 PKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKK 274


>gi|309379383|emb|CBX21950.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 252

 Score =  234 bits (598), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 112/255 (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-VLGQKVSPADRI 59

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR---------------STVFDNLPSIF 105
           E++     +       L +KP+G V+  ++   +               ++     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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT+ G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDSGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 80/249 (32%), Positives = 124/249 (49%), Gaps = 19/249 (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-------------ICYGDMQVTLD 180
           L    +   RVY V+  G+V       +++G+ ++              + +        
Sbjct: 121 LM--ESDIPRVYNVKIKGEVTPKMEEAMREGLELEDATAGGHEKSRVTSMKFAPFFAYRI 178

Query: 181 TQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +     + + V L EGKNREI++ F  F   V  L R+ YG  +L  L  G TR +SKK
Sbjct: 179 DKNAPTFSKLKVALTEGKNREIRRFFAHFGKDVVDLKRVEYGWIKLNALPTGKTRYLSKK 238

Query: 240 I---LREQL 245
               LRE L
Sbjct: 239 EYEKLREFL 247


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 112/247 (45%), Gaps = 18/247 (7%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R+SK+++  G+ SRRE + +I +  V V+G  +    + +     I +     
Sbjct: 70  TDAPEGVRLSKIMSERGLCSRREADEIIERGWVFVDGQRVSELGIRIDPNAEITLAAQAK 129

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTV--------FD------NLPSIFSRVISVGR 113
           R+       L HKP+G V+   +P     V        FD        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 PAKVEWLNED----QLRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGRVKLGDLPLGQW 305

Query: 234 REVSKKI 240
           R + +  
Sbjct: 306 RFLREDE 312


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 107/245 (43%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK++A  G+ SRRE +  I +  V+V+G+++            I +D    R+ 
Sbjct: 1   MEKIRISKLMAERGLCSRREADAYIERGWVRVDGVVVSELGSKAWPDQKITLDKQAQRRQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLD 115
                 L +KP+G V+  ++   R  V                   P     +   GRLD
Sbjct: 61  TSRVTILLNKPVGYVSGQAEQGYRPAVSLISASTRYRVDKSPLKFEPGHLRGLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +AR L    ++  + Y VR  G++  + L  L  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIARQLINEDSEIDKEYLVRVQGKIAGNGLAQLNFGLSLDGKPLRRA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            V    +      +   L+EGK R+I+++ E    KV  L R+  G   LG L  G  R 
Sbjct: 181 HVEWQNED----QLRFVLQEGKKRQIRRMCEQVGLKVIGLKRVRMGRIVLGDLPPGQWRY 236

Query: 236 VSKKI 240
           + +  
Sbjct: 237 LKEGE 241


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 112/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGDKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 83/247 (33%), Positives = 132/247 (53%), Gaps = 7/247 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++++        P R+ K +A +G+ SRRE+E  I    V VNG + +     V   D +
Sbjct: 61  LQEQRSDLSGIEPVRLQKALAASGVGSRREMEEWIQNGWVTVNGKVAQ-LGDKVQPEDQV 119

Query: 61  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  ++        R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 120 LVKGSVIKLKWPDRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 179

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G LA     PS +  R Y VR  G++  D++ LL  +G++++       
Sbjct: 180 NTSGLLILTTSGELANRFAHPSFEVEREYAVRVLGELGMDEMRLLTSEGVMLEDGLARVE 239

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
           ++     +G N W  V L+EG+NRE++++FE F   V+RL+R  +GP  L   L  G   
Sbjct: 240 RIHSQGGEGVNKWYNVVLKEGRNREVRRIFEHFGLTVSRLVRTGFGPIGLPNRLKRGQFY 299

Query: 235 EVSKKIL 241
           E++   +
Sbjct: 300 ELNAAEV 306


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/231 (31%), Positives = 117/231 (50%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ + +   GI SR+EV+++I+   +KVNG     A  N+   +D IE +G  L   ++
Sbjct: 1   MRLDRFLVECGIGSRKEVKKIISANEIKVNGSYDISAKDNINEYSDVIEYNGERLEY-KK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D    +TV D LP       +  VGRLD +TEGLLLLTNDG L
Sbjct: 60  FRYYIMNKKAGYITATEDIR-EATVMDLLPEWVIRKDLAPVGRLDKDTEGLLLLTNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V     + Q+ +  L++G+ I        +V    +K S+  + 
Sbjct: 119 NHRLLSPKNHVDKTYYVEIENNISQEDVLKLEEGVDIGNYITLPAKV----EKISDTKIY 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++EGK  ++KK+ E  N KV  L R ++    L  L  G  +EV+ + +
Sbjct: 175 LTIKEGKFHQVKKMLEAVNNKVTYLQRTTFAKLSLADLALGEVKEVNLEDI 225


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 78/253 (30%), Positives = 130/253 (51%), Gaps = 15/253 (5%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------ICYGDMQVTLDT 181
           L   ++   RVY+++  G++    +  ++ G+ +              +    +   +  
Sbjct: 121 LM--NSDLPRVYKLKIKGEITDKMIEAMQNGVEVGDAGAHEENEIKKMVLKPFLSAQIIK 178

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + + V + EGKNRE+++ F  F  +V  L R+SYG   L  L  G TR   KK  
Sbjct: 179 NTPKYSTLKVAIGEGKNRELRRFFANFGSEVVDLKRLSYGWVSLNALPTGKTRYFDKKEY 238

Query: 242 REQLGPHLLEEAQ 254
           +  L   L +EA+
Sbjct: 239 K-LLKEFLHKEAE 250


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 98/234 (41%), Gaps = 10/234 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++A   V VNGI  E     V +   + +VDG       R  
Sbjct: 36  LYRILQSQGFGTRRYCKDLVAAGLVHVNGIEAEDPDAQVDTAGLVLDVDGERWAYHARA- 94

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 95  YLMLHKPAGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVH 153

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAWVTV 191
            L  P  Q  +VY +     V   ++  L +G+++      D  V     ++     + +
Sbjct: 154 TLTSPRHQVPKVYEITTADPVTDAQVAQLCRGVLLDDE---DATVAAAWAERVDTCHLRM 210

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            L +GK  ++K++       V  L R + G   L   L  G  R + +  L   
Sbjct: 211 ALTQGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLAPGQWRWLERDDLTAL 264


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 74/237 (31%), Positives = 125/237 (52%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLL 235


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 112/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/208 (35%), Positives = 117/208 (56%), Gaps = 3/208 (1%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           +V VNG ++    V V  ++ IEV+G+ L K E  R +L++KP G V+  +D  GR+TV 
Sbjct: 1   KVTVNGKVVTELGVKVSGSERIEVEGIQLTKEE-HRYFLFYKPRGTVSAVTDDKGRTTVA 59

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
           D    I  R+  VGRLD +T GLLL+TNDG  A +L  P  +  + Y  R  G  +++ +
Sbjct: 60  DYFTDIPERLYPVGRLDYDTSGLLLMTNDGDFANLLMHPKNEVAKTYIARIKGIPEREVI 119

Query: 159 NLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
             L++G+VI G      +V + +  +    A V + + EG+NR+++K+FE   ++V +L 
Sbjct: 120 RELERGVVIDGRKTAPAKVKIRSSDKAKDKAIVEITIHEGRNRQVRKMFEAVGFEVQKLS 179

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQ 244
           R  Y    L  L AG  RE+S   +++ 
Sbjct: 180 REEYSFLNLRGLNAGERRELSHHEVKQL 207


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 84/242 (34%), Positives = 126/242 (52%), Gaps = 6/242 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               QR+ K+IA AG+ SRRE ER+I   +V+VNG + +        +D I V+  PL K
Sbjct: 3   EVEKQRIQKLIANAGLCSRREAERLIEDGKVRVNGKIAQ-LGDKARISDDIFVNNKPLNK 61

Query: 70  A-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTN 126
             ER+   L +KP G++ T+SDP    TVFD LP      R+   GRLD ++EGLL+LTN
Sbjct: 62  HVERSVTVLMNKPKGVLCTNSDPHADRTVFDLLPLDLQRQRMFCAGRLDKDSEGLLVLTN 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKG 184
           DG LA  +  P++  ++ YRV  H   D+  +  L  G+  +G      +V       +G
Sbjct: 122 DGDLAHRITHPTSNVVKRYRVVLHRDFDKADIPKLLNGVDYEGDFLKAEKVIPAPAVGEG 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
               + V L  GK REI+++FE   + V +L+R+  G   L  +  G  + + KK +   
Sbjct: 182 HLRRLEVHLHHGKKREIRRLFEANRYYVKKLVRVQIGGMVLKNMPKGGIKVLGKKDIERL 241

Query: 245 LG 246
             
Sbjct: 242 FA 243


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 114/255 (44%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E+D     +       L +KP+G V+  ++                +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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 115/228 (50%), 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
               ++KP+G+  T  +   ++ + D + +    +  VGRLD  ++GL++LTNDG LA  
Sbjct: 60  -YIAFNKPVGITCTL-EKTVKNNIGDYI-NFSDYIFPVGRLDKESQGLIILTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V  +   +   +N + +G+ I G+     QV+    K S+    + L
Sbjct: 117 ILESENKHEKEYIVTLNRPFNDSFINGMSEGVEICGVKTRKCQVS----KISDNVFRIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     ++  +  G  R ++ + L
Sbjct: 173 TQGLNKQIRRMSKTFGYTVIKLERIRILNIKIDGIDIGKWRVLTDEEL 220


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>gi|237747726|ref|ZP_04578206.1| pseudouridylate synthase [Oxalobacter formigenes OXCC13]
 gi|229379088|gb|EEO29179.1| pseudouridylate synthase [Oxalobacter formigenes OXCC13]
          Length = 248

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 68/248 (27%), Positives = 118/248 (47%), Gaps = 23/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK ++  GI+SRRE +  I +  VKV+G ++ +    V+    I ++    ++  
Sbjct: 3   EPVRLSKRMSELGISSRREADEWIEKGWVKVDGKVVSQLGSKVLPHQKITIEKQASQEQS 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDI 116
           R    L +KP+G V+  ++   +  V                   PS    ++  GRLDI
Sbjct: 63  RRVTILINKPMGYVSGQAEDGYKPAVALISEDTHWKDDPSKEKFRPSQLRSLVPAGRLDI 122

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L   ++   + Y VR      G++   +LN+L+ G+ + G   
Sbjct: 123 DSVGLLVLTQDGRIAKHLIGENSPTDKEYLVRVKYTRPGRLPDSELNMLRHGLKLDGKAL 182

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V       ++  +   LREGK R+I+++ E    +V  L RI  G  +LG L  G 
Sbjct: 183 LPAKVEWQ----NDDQLRFVLREGKKRQIRRMCEAVGLRVIGLKRIRIGNVRLGDLPTGQ 238

Query: 233 TREVSKKI 240
            R +  + 
Sbjct: 239 WRYLRPEE 246


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLKGDILVDGCPARSLAQNIDTGLQELLFQEQIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LP      ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPPDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + YRV  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYRVEVNGLLTLDHIQAFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           ++ + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDENLQAGDYRPLNSEEL 230


>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 =  233 bits (596), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 107/245 (43%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK ++  G+ SRRE +  I +  V V+G  +      V     I +        
Sbjct: 1   MEKIRLSKRMSELGLCSRREADSYIEKGWVDVDGETVSLLGTKVYPNQQITLRTAAQVVQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGR---------------STVFDNLPSIFSRVISVGRLD 115
                 L +KP+G V+  ++   +                +      S F  +   GRLD
Sbjct: 61  HERVTILINKPVGYVSGQAEHGYKPASALLDEATHWKDDPSPIKFHRSQFIGLAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A+ L    ++  + Y VR  G+++   L LL +G+ + G      
Sbjct: 121 IDSQGLLILTQDGRVAKQLIGEDSKVDKEYLVRVQGKLESSGLALLCQGLKLDGEYLKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +V+   +      +   LREGK R+I+++ E     V  L RI  G  +LG L AG  R 
Sbjct: 181 KVSWQNED----QLRFVLREGKKRQIRRMCELVGLTVTGLKRIRIGKIKLGLLPAGQWRY 236

Query: 236 VSKKI 240
           + +  
Sbjct: 237 LGEHE 241


>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 =  233 bits (596), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPTSSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+VT   D     TV D +P      ++ ++GRLD +T GLLLLT++G L
Sbjct: 60  I-YLMLHKPNGVVTASKDKK-LPTVMDLVPKNIQSGQLYAIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K+GIV + G      Q+ + +   + +  
Sbjct: 118 GFQLLHPQYHVDKSYQVVVNGPLTSDHIQKFKEGIVFLDGTTCKPAQLEILSSSPTESRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTSLKRVQFGDFTLDPELAEGQYRPLNPEELE 231


>gi|319792471|ref|YP_004154111.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315594934|gb|ADU36000.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 249

 Score =  233 bits (596), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 98/245 (40%), Gaps = 15/245 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
             +  ++   G  +RR    ++ Q  V ++G  +     +V     +  V G P    E+
Sbjct: 1   MHLQDILYTQGFGTRRVCAGLVQQGHVTIDGKAVTDPFADVDPEGLLYTVQGTPWAYHEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLL 123
               + HKP G   +   P    +++  LPS             V ++GRLD +T GLLL
Sbjct: 61  A-YLMLHKPAGTECSQK-PSTYPSIYTLLPSPLRLRPNKGAVQGVQAIGRLDQDTTGLLL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           +T+DG     +  P     +VY V     VD+ ++  L  G+V+            ++  
Sbjct: 119 MTDDGQFIHKMGSPKHHVPKVYEVTAKHPVDEAQIAKLLAGVVLDDDPKPVRAAACESDS 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
             +  + + L EGK  ++K++      +V  L R   G   L   L  G  R ++ + + 
Sbjct: 179 PLH--LRLTLTEGKYHQVKRMLAAVGNRVEGLHRSRIGELSLPADLAPGQWRWLTAEEVA 236

Query: 243 EQLGP 247
               P
Sbjct: 237 ALRAP 241


>gi|325193088|emb|CCA27453.1| RNA pseudouridine synthase putative [Albugo laibachii Nc14]
          Length = 285

 Score =  233 bits (596), Expect = 3e-59,   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  GVPLRKAER-------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--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|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 =  233 bits (596), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 111/237 (46%), Gaps = 7/237 (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  PLRKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            +    +   ++ HKP+G + +      G   V D    +  RV +VGRLD  T GL+L+
Sbjct: 64  RV-GMTKKVYFMVHKPLGYLCSSERKFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILV 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG  +  +  PS    + Y ++    V    L  L  G +I G     + V    +K 
Sbjct: 123 TNDGEFSNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMGGTIIDGKRVRPVSV----EKI 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               + + + EGK  EI+   E     +  L RI  G F LG L  G  RE++   +
Sbjct: 179 RRGTIKIIVNEGKKHEIRLFAEAAGLPILELSRIRIGSFVLGGLRYGEYRELTDAEI 235


>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 =  233 bits (596), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 111/228 (48%), Gaps = 6/228 (2%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRL 75
            K++ +A I SR EV++MI  Q+V ++G + +  + NV +    + VDG  +        
Sbjct: 2   DKLLEKARIGSRTEVKKMIKNQKVVLDGKIAQSISQNVDTGFQELIVDGKKIEGY-SHHY 60

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L HKP G VT   D     T+FD L        +  VGRLD +TEGL+L+T++G L   
Sbjct: 61  FLIHKPAGYVTARLD-QNHPTLFDLLKPEDRVEGLYPVGRLDRDTEGLVLVTDNGPLGFR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS    + Y V  +G + +D     + GIV + G       + +   + + +   + 
Sbjct: 120 MLHPSHHVEKTYYVEVNGFLGEDAPLFFRSGIVFLDGTVCKPAVLEVINCQQNLSKAYLT 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + EGK  ++KK+F  +  KV  L R+S+    LG L  G  R +    
Sbjct: 180 ISEGKFHQVKKMFLSYGLKVTYLRRVSFAGLSLGNLPLGKYRPLDWNE 227


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 134/260 (51%), Gaps = 20/260 (7%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK++   +E  T  R++K I+     SRRE + +IA+ RVKVN   +   +  V+ +D +
Sbjct: 1   MKNQPEAKEENT--RLNKFISHNSKYSRREADAIIAEGRVKVNKKTITDLSTKVLDSDIV 58

Query: 61  EVDGVPLRKAERTRL--WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +D  P++  +       +Y+KP G + T +DP GR  +FD L + +   + +GRLD  +
Sbjct: 59  AIDNKPIKFEKNKMYTVLVYNKPKGELVTKNDPQGRRIIFDTLGAKYKHFLPIGRLDYAS 118

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDM 175
           EG+LLLT+   +A  L    +   RVY+++  G +++   + +  G+ ++      + D 
Sbjct: 119 EGVLLLTDSVDVANGLMH--SDLQRVYKIKVSGPINKQVEDAMLHGLELEDATKGAWKDS 176

Query: 176 QVT-----------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           +V            +D+ K + + + V + EGKNRE+++ F  F   V  L R+ YG   
Sbjct: 177 KVKSMSFAPFLGYKIDSVKDTFSKLKVAITEGKNRELRRFFAHFGLDVMDLKRVEYGGIS 236

Query: 225 LGTLLAGSTREVSKKILREQ 244
           L  L  G +R ++++  +  
Sbjct: 237 LNNLPTGKSRYLTREEYKNL 256


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 69/232 (29%), Positives = 119/232 (51%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K 
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKE 229


>gi|302187757|ref|ZP_07264430.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 230

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 110/232 (47%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDGEILQAGKAP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    +G+     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGLTTQPAQLTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRENIGALALDPGLRPGSYRALNAGEI 227


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 127/234 (54%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++  ++ AGI+SRR+ ++ I    ++VNG  + R    + + D +   G  ++   + 
Sbjct: 6   IRLNHYLSNAGISSRRKADQFIQSGAIEVNGKPVRRLGTVIHTNDLVTFYGEKIKIQNKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP G +TT  DP  R TV + +P++   R+  VGRLD +T G+LLLTNDG +A 
Sbjct: 66  -YLLLNKPKGFITTTKDPFNRKTVMNLIPNLSKYRIFPVGRLDRSTTGVLLLTNDGSIAE 124

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P +   ++Y V    ++  + L+ ++KG I ++    G ++V    +  S   + +
Sbjct: 125 KLTHPKSHVQKIYHVLLDKEIKNEDLDQIRKGKIYLK---EGKVKVIFVNKGHSKYQIKI 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           GL  G NR IK++F+  N++V +L R+++G      +  G+   +++K +   L
Sbjct: 182 GLYIGWNRIIKRIFKKLNYQVIQLDRVNFGGLSKKNIQIGNWCFLNQKEVENIL 235


>gi|167586851|ref|ZP_02379239.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 298

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 103/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 50  MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERASAAQAAQ 109

Query: 74  RLWLYHKPIGLVTTHSDPDGRS-TVFD--------------NLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++      TV                  P     +   GRLDI++
Sbjct: 110 VTILLHKPVGYVSGQAEDGYEPATVLITRENHWSGDRSALRFSPQHLHSLAPAGRLDIDS 169

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 285

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 286 QGQWRYLSADE 296


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 71/251 (28%), Positives = 116/251 (46%), Gaps = 13/251 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDH 59
           M +K   +     QR+ K ++     SR +V+ +I +  + VNG + ++    V  + D 
Sbjct: 1   MTNKKAGKNT---QRLDKFVSSMTPYSRSDVKTLIKKSAIYVNGSVAKKPNQPVNVTEDK 57

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDI 116
           +EVDG  L   E     + HKP G+++   D +   TV D LP       +   VGRLD 
Sbjct: 58  VEVDGQELVY-EPYVYIMMHKPDGVISATED-NRWETVIDLLPEDLILTYQPFPVGRLDK 115

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDM 175
           +T GLLL+TNDG     L  P     + Y V   G +    ++  +KG+ I QG      
Sbjct: 116 DTTGLLLITNDGQFNHALMAPKKHVEKEYAVLVDGLLSDKHIDQFEKGLDIGQGEKTKPA 175

Query: 176 QVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGS 232
           Q+ +D   ++   +   V + EGK  ++K++F   + +V +L R   G   L   L  G 
Sbjct: 176 QLFIDQVDEEAGQSLARVVIAEGKYHQVKRMFHAVDCEVVQLHRQRIGQLILPDALTEGE 235

Query: 233 TREVSKKILRE 243
             +V  + L +
Sbjct: 236 FVQVDYQDLYD 246


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+       A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+ R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAEGNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 102/260 (39%), Positives = 153/260 (58%), Gaps = 14/260 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+ K++ARAGIASRR+ E +I   RVKVNG +++   + V   D I VD  P++ 
Sbjct: 134 KIGTERIQKILARAGIASRRKAEELIIDGRVKVNGKIIKMEEILVKPHDIITVDDKPIK- 192

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
            ++ ++W++ K   ++T+  DPDGR  +   +  +     +ISVGRLD  TEGL+L TND
Sbjct: 193 VDKPKIWMHFKNPQVLTSEYDPDGRDCLLPIIRKVIGIDHLISVGRLDYYTEGLILFTND 252

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LAR L LP   + RVY+VR  G+   +    L KG+VI  + Y  + V ++++  SN 
Sbjct: 253 GELARYLTLPQNLFFRVYKVRIFGKFTDEMKFSLAKGMVINEVFYRPVSVQVESETDSNT 312

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVS-KKILR--- 242
           W+ + L+EGK REI+ + E+FN KV RLIR++YGP+ L   L  G T EV  K  L+   
Sbjct: 313 WLRITLQEGKKREIRTLLEYFNVKVLRLIRVAYGPYVLPNSLKHGETIEVPIKDELKPFI 372

Query: 243 ------EQLGPHLLEEAQVN 256
                 E+L   L E+ ++ 
Sbjct: 373 NKYNSTERLKKTLQEQKKIE 392


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 69/252 (27%), Positives = 108/252 (42%), Gaps = 20/252 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +  +   P R+SK +A  G+ SRRE +  I    V+VNG +++     V    +IEV 
Sbjct: 177 KPVASQPDLP-RLSKRMAELGLCSRREADEWIVNGWVRVNGQVVDELGSRVEPDANIEVS 235

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRV 108
               +        L HKP+G V+  ++      V    P                    +
Sbjct: 236 KEAEKHQSEIVTILLHKPVGYVSGQAEDGYEPAVVLVHPDNHWAEDPVQKEFRRGFLKGL 295

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLDI++ GLL+LT DG +AR L    +Q  + Y VR  G +  + L  L  G+ + 
Sbjct: 296 APAGRLDIDSTGLLVLTQDGRVARQLIGEDSQTEKEYLVRVEGTLSDEGLRKLNHGLSLD 355

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+     +V+   +      +   LREG+ R+I+++ E     V  L R+  G   LG L
Sbjct: 356 GVQLKPAKVSWQNED----QLRFVLREGRKRQIRRMCELVGLHVVGLKRVRIGSVALGKL 411

Query: 229 LAGSTREVSKKI 240
             G  R +    
Sbjct: 412 PPGQWRYLRPGE 423


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/230 (30%), Positives = 120/230 (52%), Gaps = 3/230 (1%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           +++V+++ G+ SR    + I   RV V+G ++          D  I +DG+P ++  R +
Sbjct: 6   LARVLSKWGLCSRTVAAQWIRAGRVAVDGRIVRDPEAPQRGLDLWISIDGIP-QQRARRQ 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + + HK  G+V + SD  GR TVF ++P     +  +GRLD  + GLLL +ND   ++ L
Sbjct: 65  VLMLHKKRGVVVSRSDERGRPTVFADIPQE-PWLAPIGRLDRASSGLLLFSNDPIWSQRL 123

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P+    + YRV+    +  + L+ +    V+ G     M+V      G   W+   L+
Sbjct: 124 LDPAGHLPKTYRVQIRPPLAAEALHHIATASVLDGRPCLPMEVRAVACGGKTQWLEFVLQ 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           EG+NR+I+++ E    +V RLIRI++G   LG L  GS R +S+  +   
Sbjct: 184 EGRNRQIRRLLEAQGVEVLRLIRIAFGSVILGDLAPGSWRWLSEAEITAL 233


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 107/226 (47%), Gaps = 9/226 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +   G+ SR+++++++ + RVK+NG++     + +    D I +D   L     
Sbjct: 1   MRLEKYLVNCGVGSRKDIKKIVEEGRVKINGLVTLNFGLWIEEDRDDITLDNRHLEFKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +K  G +T   D D   T+ + LP       +  VGRLD +TEGLLL TNDG  
Sbjct: 60  LRYYILYKTKGYITAVKD-DRHPTIMELLPGWLETKDLFPVGRLDKDTEGLLLFTNDGDT 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P  +  + Y V     + +  +  L+KG+ I        +V    Q      + 
Sbjct: 119 NYKMTHPDKKISKKYYVELDKPISEGDIKDLEKGVDIGTHICLPAKVQYIEQNK----IF 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + ++EGK  ++KK+      KV+ L R+ +G   L  +  G  RE+
Sbjct: 175 LTIQEGKYHQVKKMVGSIKNKVSYLKRVKFGNLTLEDMKPGELREI 220


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+   +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTNLKRIQFGDFTLNPDLAEGNYHPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 93/224 (41%), Positives = 130/224 (58%), Gaps = 10/224 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KA 70
            +++ KV+A AG+ SRRE+E+ I+  RV VNG + +       + D I VDG  ++    
Sbjct: 2   SEKLQKVLATAGLGSRRELEKWISAGRVSVNGSIAK-LGDRAAADDRILVDGRLIKIVTD 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
           +  R+ +Y KP G V T SDPDGR TVFD LP +   R I++GRLDINT GLLL TN G 
Sbjct: 61  DSPRVLMYSKPEGEVCTTSDPDGRPTVFDRLPRLSRGRWIAIGRLDINTSGLLLFTNHGE 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------DTQK 183
           LA  L  PS +  R Y  R HG+VD+  +  L  G+V++        V        +   
Sbjct: 121 LANRLMHPSYEVQREYMARIHGEVDEAMIKRLTDGVVLEDGLASFKSVKAQHARSSEDLG 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           G N W  V L EG+ RE+++++E  + +VNRL RISYGP +L +
Sbjct: 181 GRNRWFKVILAEGRTREVRRLWESQDVEVNRLKRISYGPIELPS 224


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 117/239 (48%), Gaps = 9/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    + +R ++ +MI  + + VN  +++   V V    D + +    +   ++
Sbjct: 1   MRVDKFLHDMNMGTRTQIRKMIKDKLIFVNDTVVKTGRVKVDPVVDEVRLKDQVIEY-QQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP+G++T   D   + TV D      + + +  VGRLD +T+GLLL+TN+G L
Sbjct: 60  YFYFMMNKPLGVLTATEDRK-QKTVMDLFNKVDLRNDLFPVGRLDKDTQGLLLITNNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD--TQKGSNA 187
           A  L  P     + Y     G++    +   +KGI +  G      Q+ ++  ++     
Sbjct: 119 AHDLLAPERHVDKTYEAVVTGKITDQAVEEFQKGITLRDGTTLKPAQLIIEHYSELDDQT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            V V L+EGK  +++++F     KV  L R S+GP +L   LL G+ RE++   +   +
Sbjct: 179 VVKVVLKEGKYHQVRRMFGSLGEKVVTLRRTSFGPLELDVGLLPGTYRELTDDEINRLV 237


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 103/229 (44%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R E   +I    V VN  +    A  V   + + +D   L  A  +
Sbjct: 1   MRLDKFICKSTDLTRNEATLLINAGNVTVNNEVASNEATQVHENNDVLLDEKKL-IARAS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP+G + ++ D +   ++F+ +       +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYILMHKPLGTICSNID-EVYPSLFNYIDVEKADDLHIAGRLDADTTGLVLITDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+ Q  + YRV     + +D       G+ +QG         LD    +   V + 
Sbjct: 119 NIITPNKQCEKTYRVGLRNPIAEDAAEKFALGVQLQGEKQLTFPAKLDVVTSNE--VLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  +L  +  G  R ++ + +
Sbjct: 177 ITEGKFHQVKRMFSAIGNRVVTLHREQIGNIKL-DVEVGKWRFLTPEEI 224


>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 =  233 bits (594), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 118/234 (50%), Gaps = 11/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  QRV +NG +  +  ++V   +D I VDG  +   ++
Sbjct: 1   MRLDKLLANKAYGSRKEVHQLIKDQRVTINGEVARKKDIHVDIESDVIAVDGQIVN-TKQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
                +HKP G VT   D      V D LP  +    V+ VGRLD +TEGLLLLTNDG  
Sbjct: 60  HYYIKFHKPKGYVTAVEDASH-PVVMDLLPPEYIKMGVVPVGRLDKDTEGLLLLTNDGVW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           +  +   +    +VY V F G++ +D +  +K+GIV+  G       + + + K     V
Sbjct: 119 SHSIINGNKHVEKVYYVEFEGELTEDGIQRIKEGIVLGDGTHCKPALIDILSSKS----V 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
            + + EGK  ++K++       V  L R++ G   L  +   GS +++S   + 
Sbjct: 175 HITIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLTGIEEVGSAQDLSSDDIE 228


>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 =  233 bits (594), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 111/236 (47%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I+     SR E +++I +  + +N  L++     V    D + +DG  L   ++
Sbjct: 1   MRLDKFISTTTTLSRAEAKKVIKKG-ILINDKLIKSPDYKVDEINDQVILDGKRLVY-QK 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP   ++   D     TV D L       +V  VGRLD +TEGL+LLTNDG L
Sbjct: 59  YVYIMMNKPQDTISATEDA-IEKTVVDILKEEDRIHKVFPVGRLDKDTEGLMLLTNDGEL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P    ++ Y V   G++ ++ L +++ G+ +  G      ++ +       +  
Sbjct: 118 AHRLISPKKDVVKKYYVEVSGELKEEHLPIIEAGVTLEDGYKCKAAKLEILESNEDESKA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++ +     V  L R+S G  +L   L  G  R ++++ L + 
Sbjct: 178 NIYITEGKFHQVKRMMKSLGTTVTYLKRLSIGSLKLDENLKLGDYRYLTEEELNKL 233


>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 =  233 bits (594), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 112/228 (49%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR++  ++I + R+ VNG+   +    V   D I +D  PL   E+ 
Sbjct: 1   MRINKLFSNLGICSRKDTSKLIEENRIIVNGLPCIQ-GQWVELEDEILLDNKPLPIKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T +D    + +  N  +    +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 60  -YIALNKPVGVTCTAADEVEHNII--NFMNYNEYIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  +  G+ I  +     +V    ++ S     + L
Sbjct: 117 ILESENEHEKEYIVTLDRPFNDEFILGMTSGVEICNVKTRQCKV----RRISEDTFNIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     +LG L  G  R +S++ L
Sbjct: 173 TQGLNKQIRRMSKAFGYNVKKLERIRIVNIELGNLEYGKWRYLSEEEL 220


>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 =  233 bits (594), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+VT   D     TV D LP      ++ ++GRLD +T GLLLLT++G L
Sbjct: 60  N-YLMLHKPNGVVTASKDKK-LPTVMDLLPPDIQSDQLYAIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K GIV + GI     Q+ + +   + +  
Sbjct: 118 GFQLLHPQYHVDKSYQVVVNGLLTSDHIQKFKDGIVFLDGITCKPAQLEILSSSPTESRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L+
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTALKRVQFGDFTLDPELAKGQYRPLNPEELK 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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 107/250 (42%), 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  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------------DNLPSIFSRVISV 111
              +  +    L HKP+G V+   +P     V                  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 LKPARVEWL----NDDQLRFVLREGRKRQIRRMCELVGLRVTGLKRVRIGAVRLADLPLG 294

Query: 232 STREVSKKIL 241
             R +    +
Sbjct: 295 QWRFLRPDEV 304


>gi|283769551|ref|ZP_06342447.1| pseudouridylate synthase [Bulleidia extructa W1219]
 gi|283103819|gb|EFC05205.1| pseudouridylate synthase [Bulleidia extructa W1219]
          Length = 231

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 119/233 (51%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +V+A A + SR +V+ M+   RV VNG +   +++ V    D I +D   L+ A +
Sbjct: 1   MRLDRVLANASVGSRTQVKNMVKNGRVSVNGKIALASSMMVDPNQDVIRIDDEILQYA-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +  + +KP G ++  ++     TV + +P+ +  +   GRLD +TEGLLL+TNDG LA 
Sbjct: 60  YQYLMLYKPAGYISA-TEGRYDPTVLELVPN-YKGLFPCGRLDKDTEGLLLMTNDGRLAH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V     + Q+ +  +++GI  + I Y   ++ +      +   T+ 
Sbjct: 118 NLLSPKKHVEKEYYVEHQLPLSQEDVLCIERGIRYKNITYKGAKLKIL----DDLQCTII 173

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           L+EGK  EIK +F   + KV  L RI      L  TL  G  R +S++ + + 
Sbjct: 174 LQEGKYHEIKNIFLAIDNKVTYLKRIRMKNLILDETLKKGEYRPLSEEEIGDL 226


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 112/242 (46%), Gaps = 14/242 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV--------NVMSTD 58
           + ++    R++K +A  G+ SR+   R I    + ++G L               + S +
Sbjct: 1   MTQDKPSMRLAKYLAMTGLCSRKAATRYIRDGHITLDGRLANHIDTISLIESPSGLTSLE 60

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            ++ DGV ++  E  + W+ +K +G        D  S++   LP    R+  VGRLD ++
Sbjct: 61  ILKFDGVLIQGVESKQYWMLNKSVGTDCRLLAHD-PSSLLHLLPDN-PRLYPVGRLDKDS 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 ----RLNDNKFEIILTQGLNRQIRRMSQALGYKVVDLKRVNIQSLALGDLKEGEMRQLTA 234

Query: 239 KI 240
             
Sbjct: 235 LE 236


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 109/233 (46%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
               R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG  +  
Sbjct: 1   MGKIRLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDGRRV-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   ++ HKP+G + +      G   V D    +  RV +VGRLD  T GL+L+TNDG
Sbjct: 60  MTKKVYFMVHKPLGYLCSSERTFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +  +  PS    + Y ++    V    L  L +G VI G     + V    +K     
Sbjct: 120 EFSNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMEGTVIDGKRVRPVSV----EKIRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E     +  L RI  G F LG L  G  RE++   +
Sbjct: 176 LKIIVNEGKKHEIRLFAEAAGLPILELSRIRIGSFVLGGLRYGEYRELTDAEI 228


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 104/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 60

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 237 QGQWRYLSADE 247


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 121/249 (48%), Gaps = 23/249 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +A +GI +R+EV+ ++  ++V VN + ++   ++V    D ++ +   +   + 
Sbjct: 1   MRLDKFLANSGIGTRKEVKEILKNKKVSVNNVFVKDGKIHVDEEKDIVKYENKIINY-KP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D     TV D L   +    +  VGRLDI+TEGL+LLTNDG L
Sbjct: 60  FVYIMMNKPAGVISATED-SHHKTVIDLLNDEYRTYDIFPVGRLDIDTEGLILLTNDGIL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLD---TQKGSN 186
           +  L  P     + Y V+    + +D +  L+ GI + +     + +V +    ++K S 
Sbjct: 119 SHNLLSPKKHVDKKYYVKITKSLSEDDIKTLENGIKLEENFITKNAKVEIICNNSEKESE 178

Query: 187 AW-------------VTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGS 232
            +             V + + EGK  ++K++F+    +V  L R+  G       L  G 
Sbjct: 179 DFDFGENENNKNENSVYITISEGKFHQVKRMFKAVGNEVLYLKRVKMGNLLLDENLELGG 238

Query: 233 TREVSKKIL 241
            RE+++K L
Sbjct: 239 YRELTQKEL 247


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 68/257 (26%), Positives = 107/257 (41%), Gaps = 29/257 (11%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D    
Sbjct: 39  DDRPGAVRINKRIADMGMCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQ 97

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVG 112
            + ++    L +KP+G V+  ++      V                    S    +   G
Sbjct: 98  ERQDQQVTILLNKPMGYVSGQAEDGHEPAVVLITNENRWNEDRSKTRFNFSQLKGLAPCG 157

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKK 163
           RLDI++ GLL+LT DG +AR +    ++  + Y VR               ++KL LL+ 
Sbjct: 158 RLDIDSVGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRH 217

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ +        QV     +     +   L EGK R+I+++ E    KV  L RI  G  
Sbjct: 218 GLSLDEQPLKPAQVDWQNPE----QLRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGV 273

Query: 224 QLGTLLAGSTREVSKKI 240
            LG L  G  R ++   
Sbjct: 274 TLGNLPTGQWRYLAAHE 290


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 61/224 (27%), Positives = 105/224 (46%), Gaps = 9/224 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     + ++ +  +  G+ I G            +K +  
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITEEFIRGMSAGVPILGTVTK----KCKVKKEAPF 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
              + L +G NR+I+++ E F ++V +L R       L  +  G
Sbjct: 176 VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLG 219


>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 =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 120/241 (49%), Gaps = 9/241 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLKGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D     TV D LP      ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKK-LPTVMDLLPLDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
           ++ + EGK  ++KK+F     KV  L R+ +G F L T L  G  R ++ + L E +  H
Sbjct: 178 SITISEGKFHQVKKMFLSIGVKVTSLKRVQFGDFTLDTELTEGHYRPLNPEEL-EIIKNH 236

Query: 249 L 249
           L
Sbjct: 237 L 237


>gi|254670635|emb|CBA06652.1| pseudouridylate synthase [Neisseria meningitidis alpha153]
          Length = 252

 Score =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 112/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 103/246 (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  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--------------------IFSRVISVGRL 114
             + HKP+G V+  ++   +  +    P                     +   +   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 AKVSWQNED----QLRFVLREGKKRQIRRMCEMVGLHVVGLKRIRMGSITLGKLPVGQWR 419

Query: 235 EVSKKI 240
            +    
Sbjct: 420 YLRSDE 425


>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 =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 118/245 (48%), 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  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFSRVISVGRLD 115
               +     +YHKP+G+V+   +      V               P+  S++  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
            V    Q+     +   L+EG+NR+I+++ +    +V  L R   GP ++G L  G  R 
Sbjct: 188 VV----QQVGEQTLRFVLKEGRNRQIRRMCDMCELRVLDLYRSRIGPVEIGDLPEGQWRL 243

Query: 236 VSKKI 240
           ++ + 
Sbjct: 244 LTLEE 248


>gi|302386350|ref|YP_003822172.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
 gi|302196978|gb|ADL04549.1| pseudouridine synthase [Clostridium saccharolyticum WM1]
          Length = 241

 Score =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 114/233 (48%), Gaps = 8/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERT 73
           R+ K +   G  +R +++ M  + R+ V+G   ++    +      + VDG P+    R 
Sbjct: 5   RLDKYLTEMGEGTRSQIKEMARKGRIFVDGQPEKKTERKIHPEQNQVSVDGRPVSYV-RY 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D     TV   + S     +  VGRLDI+TEGLLL+TNDG LA 
Sbjct: 64  EYYMLNKPQGVVSATEDSRYD-TVISLIKSRKRDDLFPVGRLDIDTEGLLLITNDGDLAH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  P     +VY  R  G++  D    +++G+V+  G       + +  Q    + + +
Sbjct: 123 QLLSPKKHVDKVYFARIQGELPPDAKEQMEEGLVLSDGTPTMPAHLEVLKQGREESSLEI 182

Query: 192 --GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
              +REGK  ++K++FE    +V  L R++ G   L   L  G  R +S++ +
Sbjct: 183 LLTIREGKFHQVKRMFETLGCRVIYLKRMTMGSLTLDEALAPGEYRPLSEEEI 235


>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 =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + + ++ V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGKILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSISQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTILKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 112/228 (49%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR++  ++I + R+ VNG+   +    V   D I +D   L   E+ 
Sbjct: 1   MRINKLFSNLGICSRKDTSKLIEENRIIVNGLPCIQ-GQWVELEDEILLDNKLLPIKEKI 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
                +KP+G+  T +D    + +  N  +    +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 60  -YIALNKPVGVTCTAADEVEHNII--NFMNYNEYIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  ++ G+ I  +     +V    ++ S     + L
Sbjct: 117 ILESENEHEKEYIVTLDRPFNDEFILGMENGVEICNVKTRQCKV----RRISEDTFNIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     +LG L  G  R +S++ L
Sbjct: 173 TQGLNKQIRRMSKAFGYNVEKLERIRIVNIELGDLEYGKWRYLSEEEL 220


>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 =  232 bits (593), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 116/236 (49%), Gaps = 3/236 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             ++    R++K IA AGI +RRE +R I    V+VNG  +      V   D ++ DG  
Sbjct: 53  TTDDSKGIRLNKYIANAGICARREADRYITAGNVEVNGKPMTELGYRVQPNDIVKFDGKN 112

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           +  AE+    L +KP G +TT  D  GR TV + +       +  VGRLD  T GLLLLT
Sbjct: 113 IS-AEKKEYILLNKPKGFITTTQDEKGRKTVMELVVGAAQGNIKPVGRLDRLTTGLLLLT 171

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L + L  PS    ++Y V    ++     + +++G+ ++        ++   +   
Sbjct: 172 NDGDLIKKLTHPSHGVRKIYHVILDKKLALPDFHKIQEGLTLEDGFIQVDDISF-VEGAP 230

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  + V +  G+NR ++++FE   + V +L R+ +       L  G  R ++++ +
Sbjct: 231 HNEIGVKIHSGRNRIVRRIFESLGYTVEKLDRVVFAGLTKKDLPRGHWRPLTQQEV 286


>gi|289668229|ref|ZP_06489304.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 240

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 111/238 (46%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR  E   
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVSAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +      +KP+G+  T       + V         R+  +GRLD ++EGL+L+T++
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +  
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 177 GFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSFSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 110/250 (44%), Gaps = 14/250 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL---LERAAVNVMST-----DHIEVDGV 65
            R++K +A  G  SRR   R+I   +V++N  L   ++  ++          + I V+  
Sbjct: 1   MRLAKYLALTGCCSRRAATRLIRDGQVRINDRLANHVDSVSLIDTPEGQRSAEQIYVNDE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   E    WL++K +G  +        +++   LP    R+  +GRLD ++ GLL+LT
Sbjct: 61  LVCPIEAKAYWLFNKSVGTDSRLL-AHLPNSLIHLLPET-PRLYPIGRLDKDSRGLLILT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   L  P     + Y V+     D   L  +  G+  + +           Q+ +
Sbjct: 119 NDGELTHKLMHPDFGHAKTYHVQLDRDFDDAFLASMAAGVSYKDVTTLPC----IMQRLA 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+++ +   +KV  L R+S    QLG L  GS R +S   L + L
Sbjct: 175 ADKYQITLTQGLNRQIRRMSQALGFKVIDLKRVSIQSLQLGDLAEGSMRPLSSAELADLL 234

Query: 246 GPHLLEEAQV 255
                 E+  
Sbjct: 235 ASVACPESSA 244


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 64/259 (24%), Positives = 117/259 (45%), Gaps = 31/259 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERT 73
           R+ K +   G  +R +V++ I +  V VNG + ++A   V    D I   G  +  A   
Sbjct: 4   RLDKYLTEMGCGTRSQVKKEILKGSVSVNGEIAKKAERKVDTEKDEIIFKGEKIFYA-GY 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G+V+   D   R TV D +     + +   GRLD +TEGLLL+TNDG LA 
Sbjct: 63  EYFMLNKPAGVVSATEDKKER-TVIDLIKESKRKDLFPAGRLDKDTEGLLLITNDGQLAH 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTL------------ 179
            L  P     ++Y  +  G V ++ + L +KG+ I          + +            
Sbjct: 122 RLLSPKKHVDKIYYAKIKGIVTEEDVRLFEKGVHIGDEKPTMPAALEILSVQKERRKEKI 181

Query: 180 -------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        D ++   + + + ++EG+  ++K++F     +V  L RI +G   L 
Sbjct: 182 KEQKILPETKNETDEKEDGYSEIYLTIKEGRFHQVKRMFRAVGKEVVYLKRIQFGTLTLD 241

Query: 227 -TLLAGSTREVSKKILREQ 244
            +L  G  R+++++ + + 
Sbjct: 242 PSLKPGQYRKLTEEEVEQL 260


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 106/231 (45%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V    HI++D   + +A    
Sbjct: 28  RLDRYLCTQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSHIQLD-EQILQANVPV 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKPIG+V+   D   + TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 87  YVMLHKPIGVVSATKDTQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDA 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     + ++ +     G+    + I     ++ +     +     V
Sbjct: 146 LMSPTHKVDKVYRVTLANPITEEYIAAFAAGMYFGFEDITTQPAKLVILADNVA----EV 201

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 202 TLHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTAAEV 252


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 63/236 (26%), Positives = 114/236 (48%), Gaps = 8/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K I+   + SR E +++I +  V VN +L+++    V    D + +DG  L   ++
Sbjct: 1   MRLDKYISSITVYSRAETKKIIKKG-VLVNNVLVKQPDYQVDEENDQVVIDGKSLFY-QK 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP  +++   D    +TV D L       +   VGRLD +TEGL+LLTNDG L
Sbjct: 59  HVYIMMNKPGNIISATEDKKD-TTVIDILNEKDRLFKPFPVGRLDKDTEGLMLLTNDGEL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P    ++ Y V   G++  + + +++ G+V+  G       + + T     +  
Sbjct: 118 AHKLISPKKDVIKKYYVEVDGELKVEHVTIIRDGVVLEDGYKTKCAALEILTSNTEKSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + EGK  ++K++ +     V  L R+S G   L  +L  G  R ++   L++ 
Sbjct: 178 YISITEGKFHQVKRMMKSLGVNVTYLKRLSIGSLVLDESLKLGEYRYLTDTELKKL 233


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 114/250 (45%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   +F   R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDFETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTELDRIDLNKQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVI----------S 110
              K       + +KP+G V+  ++   +S     T  ++     SR+            
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 KLRPAKVEWQNED----QLRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 115/229 (50%), 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
                +KP+G+V T ++ + ++ + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  -YIALNKPVGVVCTAAE-EVKNNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++     + +    ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMERGVEILGQVTKPCKLK----RINENTYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVIKLERIRILNITLEDIEYGKWRYINREEIE 221


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 109/242 (45%), Gaps = 16/242 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDG 64
            R++K +A  G  SRR   R+I   +V  N  L       V   D         H+ V+G
Sbjct: 1   MRLAKYLAITGCCSRRAATRLIRDGQVIFNDRLANHVDS-VTLIDTPEGQRCQEHVIVNG 59

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++  E    WL++K +G  +     +  +++   LP +  R+  VGRLD ++ GLLLL
Sbjct: 60  ELIQAVEAKAYWLFNKAVGTDSRLL-AELPNSLIHLLP-VSPRLYPVGRLDKDSHGLLLL 117

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDG L   L  P     + Y V+     D+  L  +  G+  +G+      +T      
Sbjct: 118 TNDGELTHQLMHPDFGHSKTYHVQVDRPFDEVFLANMAAGVSYKGVTTLPCTITRLDVD- 176

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                 + L +G NR+I+++     +KV  L RIS    QLG LL GS R +S   L + 
Sbjct: 177 ---RYEIILTQGLNRQIRRMSHALGFKVIDLKRISIQSLQLGNLLEGSMRPLSSTELADL 233

Query: 245 LG 246
           L 
Sbjct: 234 LA 235


>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 =  232 bits (592), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 112/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  231 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 105/239 (43%), Gaps = 13/239 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
           P  + +++   G  +RR    +IA   V+VNG L E         D   + VDG      
Sbjct: 15  PMTLDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQ-FEVDGLRLTVDGEEWLAC 73

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
            +    + +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG
Sbjct: 74  TKA-YLMLNKPAGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDG 131

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NA 187
                   P  +  +VY V     V Q++++ L+ G+ +       + +  +  + +   
Sbjct: 132 QFIHAQTSPKRKVPKVYEVTTAEPVTQEQVDALRTGVKLDDE---PVPIAAEGCEITGEC 188

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKILREQ 244
            + + L +GK  ++K++       VN L R + G  +L    L  G  R ++ + L   
Sbjct: 189 SLRLTLLQGKYHQVKRMVAAAGNHVNALHRSAVGGLRLDPAALPEGEWRWLTAEDLAAL 247


>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 =  231 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 114/229 (49%), 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
                +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  -YIALNKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++     + +    ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILGQVTKPCKLK----RINENTYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      +  +  G  R +++K + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITIDNIEYGKWRYINRKEIE 221


>gi|152999616|ref|YP_001365297.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151364234|gb|ABS07234.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 256

 Score =  231 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 108/231 (46%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV+V+G++++     V    HI++D   + +A    
Sbjct: 28  RLDRYLCTQLHTHRKAVRELLLSGRVRVDGLIVKDMDRQVDEFSHIQLD-EHILQANAPV 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKPIG+V+   D   + TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 87  YVMLHKPIGVVSATKDIQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDA 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V
Sbjct: 146 LMSPTHKVDKVYRVTLANPITEEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EV 201

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 202 TLHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTAAEV 252


>gi|126173257|ref|YP_001049406.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996462|gb|ABN60537.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 256

 Score =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V     I++D   + +A    
Sbjct: 28  RLDRYLCSQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSRIQLD-EQILQANAPV 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKPIG+V+   D   + TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 87  YVMLHKPIGVVSATKDTQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDA 145

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V
Sbjct: 146 LMSPTHKVDKVYRVTLANPITEEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EV 201

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 202 TLHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTVAEV 252


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 62/228 (27%), Positives = 109/228 (47%), 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
            +  ++KP G +T++ DP GR  + D      +++   GRLD ++EGL+  +NDG +   
Sbjct: 61  YVK-FYKPRGFLTSYGDPYGRKNLDDFEFFKKTKLAYSGRLDNDSEGLIFFSNDGSIIHR 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           ++ P     + Y V     +  ++   ++ G+ I G  +    V    +K       V +
Sbjct: 120 MQTPKYDVEKEYIVYTKRPLGDEEKLAMENGLEIDGYKFKKCSV----EKIGRNKYRVII 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            EGK R+I+ +F+ FN +V RL+RI      LG L  G  + ++K  +
Sbjct: 176 TEGKKRQIRNMFKHFNIEVERLVRIRIANITLGELKPGDFKFLTKDEI 223


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 73/238 (30%), Positives = 120/238 (50%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERT 73
           +++V+++ G+ SR E  R IA  RV V+  ++      +       I VDG PL    R 
Sbjct: 39  LARVLSKLGVCSRTEAARWIADGRVSVSARVVRDPEFPIRGDQQSSIAVDGQPLAGLARC 98

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 99  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWIAPVGRLDKASEGLLLFSNDPQWAA 157

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   +    +L  L+ G+V      QG+     QV++  +   NA
Sbjct: 158 AVTDPATGPDKTYHVQIDCRPSAAQLAQLQAGVVDPDPQGQGVLLRAKQVSVLREGERNA 217

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W+ + L EG+NR+I+++    +  V RL+R++ GP  +G L   + R +S + +   +
Sbjct: 218 WLEIVLDEGRNRQIRRLVAAVDIGVLRLVRVAIGPLAMGELGKSAWRMLSAEEVSALV 275


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 112/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGDKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRIVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQE-MVSRKAMKQALLKKEILVDDCPARSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G VT   D  G  TV D LP      ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPNGSVTASKD-KGLPTVMDLLPPDIQSDQLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K+GIV + G      ++ + +   + +  
Sbjct: 118 GFQLLHPQYHVDKSYQVVVNGLLTPDHIQYFKEGIVFLDGTTCKPAKLDILSASPTESRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTTLKRVQFGDFTLDSELAEGQYRPLNPEELE 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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 103/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   D     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATVDTQH-PTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+        G+    + I     Q+TL     +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPHSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 176 LTIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 96/234 (41%), Gaps = 10/234 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNGI  E     V +   + +VDG       R  
Sbjct: 10  LYRILQSQGFGTRRYCKDLVLAGLVHVNGIEAENPDAQVDTAGLVLDVDGERWAYHARA- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 69  YLMLHKPAGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVH 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAWVTV 191
            L  P  Q  +VY +     V   +L  L +G+++      D  V     ++     + +
Sbjct: 128 TLTSPRHQVPKVYEITTADPVTDAQLAQLCQGVLLDDE---DATVAAAWAERVDTCHLRM 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            L +GK  ++K++       V  L R + G   L   L  G  R +    L   
Sbjct: 185 ALTQGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLAPGQWRWLEHDDLTAL 238


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 65/254 (25%), Positives = 112/254 (44%), Gaps = 27/254 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A + +  R+ V   I    VKVNG ++   ++++    D +E     +    +
Sbjct: 1   MRLDKFLAESAVGRRKIVRTYIKDGMVKVNGEIITEPSIDINEKLDDVEYLEKKVVHTGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++++KP G +T   D   R TVFD      + V  VGRLD +TEGLLLLTNDG    
Sbjct: 61  -VYYMFNKPSGCITATKDNIHR-TVFDYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEFEH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-- 190
            +  P     + Y     G +D +    L++G+ I           +D  K S +++   
Sbjct: 119 KVMHPEKHVEKTYFFWALGSLDDEDKKQLQEGVFIGSNEALTKPAKIDIHK-SGSYIEFK 177

Query: 191 --------------------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                               + + EG+  ++K++ +     V  L RIS G  +L  +L 
Sbjct: 178 EEIPINSLKNKDHQPVVSGYLTISEGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLK 237

Query: 230 AGSTREVSKKILRE 243
            G  R+++KK ++ 
Sbjct: 238 MGDYRDLTKKEIKR 251


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 105/229 (45%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R +   MI    V VN  ++   A  V   +HI  +G  L  A  +
Sbjct: 1   MRLDKFVCKSTELTRVDATAMITGGCVSVNHDVILDVATQVHENNHISFNGEVLT-ARPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP   + ++ D +   ++F+ +     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYILLHKPADTICSNID-EAYPSLFNYIDVENASELHVAGRLDADTTGLVLVTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+    +VYRV     +  D +     G+ +QG         L+    S+  V + 
Sbjct: 119 NIITPTKHCQKVYRVGLSRPIGDDVVAKFAHGVQLQGEQQLTRPAILEV--VSSKEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  QL  +  G  R ++ + +
Sbjct: 177 ITEGKFHQVKRMFSAVGNRVVSLHREKIGAIQL-DVEVGQWRYLTDREV 224


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 116/233 (49%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      +R  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLKGEILVDGRPARSLAQNIDTGLQELLFQDQIIRGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D L       ++ +VGRLD +T GLLL+T++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDRE-LPTVMDLLSPDIQSDKLYAVGRLDRDTTGLLLVTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + YRV  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYRVEVNGLLTPDHIQAFQKGIVFLDGTVCKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           ++ + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDENLQAGDYRPLNSEEL 230


>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 =  231 bits (591), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 80/245 (32%), Positives = 127/245 (51%), Gaps = 8/245 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVP 66
            E     R++K +A AG+ SRR  + ++AQ  V VNG++++   V V+   D + V G  
Sbjct: 42  HEAEQSVRINKALADAGVCSRRAADELVAQGVVTVNGVVVDTPGVKVVPDRDELCVRGKK 101

Query: 67  L----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEG 120
           +      +      + HKP+ +VTT SDP+GR TV D LP +    R+  VGRLD  +EG
Sbjct: 102 IFLKSSSSRSHTYLMMHKPVEVVTTVSDPEGRRTVIDILPPLHRKKRLFPVGRLDFFSEG 161

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL 179
           LLLLT+DG L   L  PS    + Y V+  G V  + L  ++KG+ + +G     ++V +
Sbjct: 162 LLLLTDDGVLTHRLTHPSWHLPKTYLVKVRGVVQDNDLQAMRKGMTLAEGEKLAPVEVEV 221

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            ++      + + L +G NR+I+++       V  L R+  GP  LG L  G  RE++  
Sbjct: 222 LSRHHDWLLLEMTLFQGINRQIRRMCRDAGLTVLSLHRVRQGPLSLGELRTGEVRELTDS 281

Query: 240 ILREQ 244
            +   
Sbjct: 282 EIAAL 286


>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 =  231 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 111/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++V  M+AQ+RV+V+G +      +V     +E+D   L+     
Sbjct: 1   MRLDRFLANLPSYNRQQVRLMLAQRRVRVDGKVASDPLTDVREFSRVELDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V+   DP  R TV D LP+     +   GRLD NT GL++LTNDG  +R
Sbjct: 61  RYLMLYKPTGCVSATHDPQHR-TVLDLLPTALRDDLHIAGRLDFNTTGLMILTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+T+  + Y V    ++ +  +   ++G              LD      A + + 
Sbjct: 120 RLTQPATKLPKHYLVDTEDEIGEHYVAKFREGFYFAFEDLTTQPAQLDILGPHRARLAIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             EG+  ++K++F  FN KV  L R S G  +L   L  G  RE++   +
Sbjct: 180 --EGRYHQVKRMFGHFNNKVVGLHRESMGAIRLDPGLAPGEYRELTANEI 227


>gi|313500364|gb|ADR61730.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 230

 Score =  231 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 68/230 (29%), Positives = 111/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R+ V  M+AQ+RV+V+G ++     +V     +E+D   L+     
Sbjct: 1   MRLDRFLANLPSYNRQHVRLMLAQRRVRVDGQVVSDPLTDVREFSRVELDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G V+   DP  R TV D LP+     +   GRLD NT GL++LTNDG  +R
Sbjct: 61  RYLMLYKPTGCVSATHDPQHR-TVLDLLPAALRDDLHIAGRLDFNTTGLMILTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+T+  + Y V    ++ +  +   ++G              LD      A + + 
Sbjct: 120 RLTQPATKLPKHYLVDTEDEIGEHYVAKFREGFYFAFEDLTTQPAQLDILGPHRARLAIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             EG+  ++K++F  FN KV  L R S G  +L   L  G  RE++   +
Sbjct: 180 --EGRYHQVKRMFGHFNNKVIGLHRESMGAIRLDPGLAPGEYRELTANEI 227


>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 =  231 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  231 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 114/229 (49%), 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
                +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  -YIALNKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++     + +    ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMERGVEILGQVTKPCKLK----RINENTYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINREEIE 221


>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 =  231 bits (591), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 106/245 (43%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     + 
Sbjct: 1   MEKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGAKAFPDQVITLERAAQARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
                 L +KP+G V+  ++      V           D  P  F R     +   GRLD
Sbjct: 61  TSRVTILINKPVGYVSGQAEKGYTPAVALIDARSRFANDRHPQRFERAHLEGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A+ L    +   + Y VR  G++    L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIAKHLIGEDSSVDKEYLVRVQGELSDRGLQLLNHGLSLDGKALKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R 
Sbjct: 181 QVRWQNHD----QLRFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVSLGDLPLGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRDDE 241


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR---------------STVFDNLPSIF 105
           E++     +       L +KP+G V+  ++   +               ++     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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 103/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   D     T+ D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATVDTQH-PTILDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P  +  +VY V     +D+        G+    + I     Q+TL   + +     
Sbjct: 120 RLTQPQNKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 176 LTIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 68/255 (26%), Positives = 112/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIF 105
           E++     +       L +KP+G V+  ++                +  ++     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 SLDGEKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPPGKWRYLAPGE 250


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 109/235 (46%), Gaps = 5/235 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLR 68
           +    R+ K +A  G  SR E++  I +  V +NG  ++ A     +  D +      ++
Sbjct: 2   DVMKIRIDKYLADMGAGSRTEIKDDIRKGLVYINGNKVKSAGEKADTLNDEVAYKENIIK 61

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E     L +KP G+V+   D   + TV D + S    +  VGRLD +TEGLLLLTNDG
Sbjct: 62  YIE-FEYILLNKPAGVVSATEDRKEK-TVLDIIDSKRKDLFPVGRLDKDTEGLLLLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKGSNA 187
            LA  L  P     + Y V   G +  +   L K GI +       + ++ + +     +
Sbjct: 120 MLAHELLSPKKHVDKKYYVETDGLLTDEHRKLFKNGIKVDDEFTAKEAELQILSSGDKGS 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              + +REGK  ++K++ E     V  L RIS GP  L   +  G++R ++   +
Sbjct: 180 KAYLTIREGKYHQVKRMMEAVGNTVTYLKRISMGPLTLPEDMETGTSRMLTDSEI 234


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   D     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATVDTQH-PTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+        G+    + I     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 176 LTIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>gi|313200941|ref|YP_004039599.1| pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440257|gb|ADQ84363.1| pseudouridine synthase [Methylovorus sp. MP688]
          Length = 237

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 101/238 (42%), Gaps = 10/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAE 71
             + +++   G  SR+    +I    V VNG   +        TD +   V+  P    E
Sbjct: 1   MHLERILHAQGFGSRKNCRILIRHHAVTVNGEPCDNP-FADFDTDKLAFTVNDEPWEYRE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
           +    + +KP     +H  P    +VF  LP       V  +GRLD +T GL+LL++DG 
Sbjct: 60  KA-YLMLNKPANYECSHK-PQHHPSVFALLPHPLLERGVQCIGRLDEDTTGLILLSDDGQ 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P  +  ++Y V     VD D++  L++G+ +           L  ++ S+  +
Sbjct: 118 FIHRMSSPKWKVPKIYEVGAKHAVDADQIRQLQEGVQLVDEPAP--IAALACEQISDQVL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + L EGK  ++K++      +V  L RI  G   L   L  G  R +++  L    G
Sbjct: 176 HLTLAEGKYHQVKRMLAAVGNRVESLKRIRIGELVLPDDLAEGQWRWLTESELASLNG 233


>gi|311695566|gb|ADP98439.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 232

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 107/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++S++++     SRR+   +IA  RV VN +    AA  V     + +DG  +++AE  
Sbjct: 1   MKLSRILSNRNDISRRQANFLIASGRVAVNDVTCRDAAAEVDRFSCVRMDGDIIQEAEAC 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + HKP G ++   D   R TV + + P +   +   GRLD  + GLL+LTNDG  +R
Sbjct: 61  HHLMLHKPAGFLSATLDDTHR-TVMELISPELREDLHIAGRLDRASTGLLILTNDGRWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  +VYRV     +  +  +   +GI  +          LD    S     V 
Sbjct: 120 QLTEPRIKIPKVYRVSTAYPISPETPHRFAEGIWFEFEQLTTSPADLDL--LSPCEARVT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + EG+  ++K++F     +V  L R   G  +L   L AG  R ++ + +
Sbjct: 178 IYEGRYHQVKRMFHAVGNRVTALHREQMGNIRLDDDLAAGEYRSLTAEEI 227


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 114/229 (49%), 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
                +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  -YIALNKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++     + +    ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILGQVTKPCKLK----RINENTYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLKDIEYGKWRYINREEIE 221


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 77/262 (29%), Positives = 131/262 (50%), Gaps = 7/262 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRIIRGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TE LLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTERLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L   
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYF 238

Query: 249 LLEEAQVNLDAPIYSSETLVRD 270
            +E+ Q +   P        R 
Sbjct: 239 FIEKQQTSKALPSNLKREEERK 260


>gi|257870927|ref|ZP_05650580.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257805091|gb|EEV33913.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 237

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 76/235 (32%), Positives = 125/235 (53%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I      SR+E++R+  Q +V V+  +    + NV S    I+V GV L+   R
Sbjct: 1   MRIDKLIEERLATSRKEMKRLFQQGKVLVDQQIERNPSRNVDSRLHEIKVAGVLLQ--TR 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              +L +KP G+VT + D    +TV D L     +  + +VGRLD +TEGL+LLT +G L
Sbjct: 59  DVYYLLNKPAGVVTANIDHQH-ATVIDLLQPEDRQATLYAVGRLDRDTEGLVLLTTNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V  +G V  + +    +GIV  G +     ++T++   G  ++V
Sbjct: 118 GYELLHPNKKVPKRYDVIVNGPVTAEDVAAFAQGIVFHGGVVCQPAKLTIEMTSGRRSFV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + + EGK  ++KK+F     KV  L R++ GP +LG LL+G  R +++  L   
Sbjct: 178 HLEIAEGKFHQVKKMFLARGKKVIALKRVAIGPLELGDLLSGEYRNLTQFELESL 232


>gi|152995917|ref|YP_001340752.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150836841|gb|ABR70817.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 238

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 109/234 (46%), Gaps = 10/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R+E  + I    V VNG ++   A  V   + + ++G  L+  +  
Sbjct: 5   MRLDKFVCKSTELTRKEAVQCIHSGEVCVNGEVVTSEATQVHENNTVLLNGDRLKTRD-F 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP G V ++ D +   +VF+ L     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 64  RYILMNKPAGTVCSNID-EVYPSVFNYLDVDKASELHIAGRLDADTTGLVLITDDGRWSF 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            + LPS    +VYRV+    +      + +   K+G+ +QG         LD        
Sbjct: 123 NITLPSNDCCKVYRVQLSQAIPAERSGELVTQFKQGLQLQGEQGLTRPAKLDIITPKE-- 180

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + + EGK  ++K++F     +V  L R   G   L  L  G  R +SK  + 
Sbjct: 181 VLLTITEGKFHQVKRMFSAVGNRVVGLHREQIGEVYL-DLDVGQWRYLSKSEVE 233


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 102/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 1   MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQ 60

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 61  VTILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VPLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 236

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 237 QGEWRYLGPDE 247


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 71/240 (29%), Positives = 111/240 (46%), Gaps = 4/240 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
            +    R+ KV+A+AG+ASRR  E MIA  RV+V+G ++    + V  +  +        
Sbjct: 74  PDGEKIRLQKVLAQAGVASRRVAEEMIADGRVEVDGEIVTEQGLRVDPSVAVVRVDGVRV 133

Query: 69  KA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLL 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 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + V V L EG+   ++++       V RL+R   G   LG    GS R + +  +   
Sbjct: 254 GKSTVRVVLHEGRKHIVRRLLAEVGHPVQRLVRTHVGTVALGDQRPGSLRVLGRDEVESL 313


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++   G  SR +V+++I  + V ++G        +V S    I V+G  ++    
Sbjct: 1   MRLDKLLEVTGFGSRNQVKQLIKGRSVLIDGQPARAGCQSVDSGLQVIMVNGRQIKAFA- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R +L HKP G+V+  SD     TV D +      + +  +GRLD +T GL+LLT++G L
Sbjct: 60  HRYYLLHKPAGVVSACSDRKH-QTVIDLIRKEDRVANLYPIGRLDRDTTGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G +  D +   + G+  + G       + +       +  
Sbjct: 119 GFRMLHPKHHVNKTYLVTVNGSLAADAVPFFENGVTFLDGTRCKSAALRIIKADQMESQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            V L EGK  +IKK+F  +  KV +L RI +    LG L  G+ R+++ K 
Sbjct: 179 EVTLSEGKYHQIKKMFLSYGLKVTQLKRIGFAEIALGDLAEGAYRQLTVKE 229


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 114/229 (49%), 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
                +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  -YIALNKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++     + +    ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIEKMEQGVEILGQVTKPCKLK----RINENTYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINREEIE 221


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 60/244 (24%), Positives = 109/244 (44%), Gaps = 18/244 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE ++ I    V ++G  +         T  +E+        
Sbjct: 1   MEKVRISKILSEQGLCSRREADKFIELGLVLLDGKTVSELGTKACRTQKVELKDRAQIAQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSR-------------VISVGRLDI 116
                 + +KP+G ++   D    +     + P  F +             +   GRLDI
Sbjct: 61  SAKATIILNKPVGFISHLDDDKEFTPAASLVTPDKFYQTNDTRRPTFNTDGLAPAGRLDI 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ +   +    + Y VR  G +  + L+LL  G+ + G      +
Sbjct: 121 DSSGLLVLTQDGRIAKQIIGENVIVEKEYLVRIEGTLTDEALSLLNHGLTLDGYELKPAK 180

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V       ++A ++  L EG+NR+I+K+ +    KV  L R+  G  +LG + +GS R +
Sbjct: 181 VLWQ----NDAQLSFTLIEGRNRQIRKMCQLVGVKVTALKRVRIGNVRLGNIPSGSWRFL 236

Query: 237 SKKI 240
               
Sbjct: 237 GADE 240


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 60/234 (25%), Positives = 98/234 (41%), Gaps = 10/234 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++A   V VNGI  E     V +   + +VDG       R  
Sbjct: 36  LYRILQSQGFGTRRYCKDLVAAGLVHVNGIEAEDPDAQVDTAGLVLDVDGERWAYHARA- 94

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 95  YLMLYKPAGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVH 153

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAWVTV 191
            L  P  Q  +VY +     V   ++  L +G+++      D  V     ++     + +
Sbjct: 154 TLTSPRHQVPKVYEITTADPVTDAQVAQLCRGVLLDDE---DATVAAAWAERVDTCDLRM 210

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            L +GK  ++K++       V  L R + G   L   L  G  R + +  L   
Sbjct: 211 ALTQGKYHQVKRMVAAAGNHVTALHRSAIGALTLDAGLAPGQWRWLERDDLTAL 264


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 111/232 (47%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            RV + ++     +R++V  ++ ++RV+++G  +      V     +EVD   L+     
Sbjct: 1   MRVDRFLSNLPRFNRQQVRLLLVERRVRIDGQTVSDPHAQVREFSRVEVDDDVLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   DP    TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPPGCVSATRDPQH-PTVLDWLDEPDKNDLHIAGRLDFNTTGLMLITNDGSWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +  +  +   +G+    + +     ++TL   + +     
Sbjct: 120 RLTQPQTKLPKVYYVETEQIITAEYADTFARGLYFAFEDLTTQPAELTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R   GP  L   L  G  R +S + +
Sbjct: 176 LSIVEGRYHQVKRMFGHFNNKVLRLHRERMGPLTLDAHLEPGQYRALSPEEV 227


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 72/250 (28%), Positives = 119/250 (47%), Gaps = 18/250 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
            R++K ++  G+ SRRE +R IA+ RV++NG         V   D +E+DG  ++KA   
Sbjct: 1   MRINKCLSELGLCSRREADRWIAEGRVRLNGETA-EMGQQVEEKDRLELDGKLVKKAGKA 59

Query: 71  -----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 R  L   +KP G+V + SD D    + + + +   RV  +GRLD ++EGL+LLT
Sbjct: 60  VRAQAPRRVLLACYKPRGVVCSCSDKDRAKNIVELV-NYPERVYPIGRLDKDSEGLILLT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQK 183
           N G L   +        + Y V     + ++ L+ L  G+ +          +V  D + 
Sbjct: 119 NQGELVNRINRGGRN-EKEYVVTVDRPLTREALDRLADGVELSELNQKTRPCEVWQDLRL 177

Query: 184 GS---NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE--VSK 238
                     + L +G NR+I+++ E   ++V RL R+     +L  L  G  RE  +S+
Sbjct: 178 PPGRRQRQFHIVLSQGLNRQIRRMCEALGYEVKRLKRVRILSLRLEGLRPGEFREIGLSE 237

Query: 239 KILREQLGPH 248
             L E+L P 
Sbjct: 238 LGLSEELWPE 247


>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 =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 116/278 (41%), Gaps = 26/278 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I++  VKV+G ++      V     I +D     +     
Sbjct: 10  RLSKRMSELGLCSRREADEWISKGWVKVDGQVVSELGSKVRPDQKITIDRKAKDQQNERV 69

Query: 75  LWLYHKPIGLVTTHSDPDG---------RSTVFD------NLPSIFSRVISVGRLDINTE 119
             + +KP+G V+  ++            R+   D        PS    ++  GRLDIN+ 
Sbjct: 70  TIILNKPLGYVSGQAEDGHEPARILITPRNRWIDDPSPRRFNPSQLKSLVPAGRLDINST 129

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-------HGQVDQDKLNLLKKGIVIQGICY 172
           GLL+LT DG +A+ +   ++   + Y VR        + +    KL LL  G+ + G   
Sbjct: 130 GLLVLTQDGRIAKTIIGENSSVEKEYIVRVAMTDGRSNSEFPPAKLALLNHGLELDGKPL 189

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   LREG+NR+I+++ +    KV  L R+  G   LG L  G 
Sbjct: 190 EKAEVSWLNED----QLKFVLREGRNRQIRRMCDLVGLKVLALKRVRVGNIPLGNLPVGK 245

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
            R +          P     ++    AP        R 
Sbjct: 246 WRYLEDGESFTGSAPKRAPSSRPAAGAPRRPKTFKPRK 283


>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 =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 114/232 (49%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            RV + ++     +R++V  ++ ++RV+++G ++      V+    +EVD   L+  +  
Sbjct: 1   MRVDRFLSNLPRYNRKQVRLLLVEKRVRIDGKVVSDPHSEVLEFSRVEVDDEVLQPGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G V+   DP+   TV D +       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLNKPQGCVSATRDPEH-PTVLDLIHEPDKDDLHIAGRLDFNTTGLMLITNDGSWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V    ++  +      +GI    + +     Q+ +   + +     
Sbjct: 120 RLTQPQTKLPKVYYVETEQEIGPEYAIKFAEGIYFAFEDLTTQPAQLQVLGPRTA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R S GP  L   L  G  R +  + +
Sbjct: 176 LSIVEGRYHQVKRMFGHFNNKVLRLHRESMGPLALDHALKPGEYRALRTEEI 227


>gi|238809688|dbj|BAH69478.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 269

 Score =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 75/248 (30%), Positives = 122/248 (49%), Gaps = 11/248 (4%)

Query: 1   MKDKNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M + N + E F      RV K+IA+ G  SRR+ E  I ++ VKVNG +++         
Sbjct: 12  MNEINFLVERFAMKELIRVQKLIAQTGYCSRRKAEEYIEKKLVKVNGKIVQ-LGDKASEN 70

Query: 58  DHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           D I+++   +  +      +L +KP   ++T  DP GR TV D + +   R+  VGRLD 
Sbjct: 71  DEIKINNQLISLQKPNFVYFLLNKPKKTISTVKDPKGRKTVVDLI-NYSERIAPVGRLDY 129

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T G LLLTND  +   L  P  + LR YRVR    +   +  L+  G+++ G     + 
Sbjct: 130 DTTGALLLTNDWEMINKLTHPKYEILRTYRVRIDSPLSLKEFKLINAGLIVNGKFSKQIV 189

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +DT+        V L  G    IK++F+  N +V  L R+S+    +  +  GS R +
Sbjct: 190 DQVDTKS-----YLVTLHVGSYHHIKELFKALNHEVINLKRVSFANLTVEKMPEGSYRTL 244

Query: 237 SKKILREQ 244
           + K +++ 
Sbjct: 245 TLKEIKDL 252


>gi|149198178|ref|ZP_01875225.1| RsuA protein [Lentisphaera araneosa HTCC2155]
 gi|149138780|gb|EDM27186.1| RsuA protein [Lentisphaera araneosa HTCC2155]
          Length = 239

 Score =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 106/235 (45%), Gaps = 8/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA 70
              R+ K+IA+    +R E  R +    VKVN I  +     +  + D +  DG  L   
Sbjct: 6   AKIRLDKMIAKCTDLTRSEATRALKNGFVKVNDIPQKVGKSTIDLANDVVTFDGEVLEYR 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDG 128
           E T  ++ +KP G V    D     TV D LP   +       GRLDI+T GL++LT+DG
Sbjct: 66  E-TIYFMLNKPKGYVCAAKDER-LKTVLDLLPPALASREPFSCGRLDIDTTGLVILTDDG 123

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             A  +  P  +  + Y V    ++  + +  L++G+ + G         ++  K     
Sbjct: 124 TWAHGITSPKRKCEKSYLVGSVSELSDEDMRNLEQGVYLDGDDKITAPAKIE--KIDEKT 181

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
             + + EG+  ++K++FE  +  V  L R   G   L   L  G+ R+++ + ++
Sbjct: 182 YRLKITEGRYHQVKRMFEAVDNMVKSLHREQIGGLSLDDDLDEGNWRDLTAEEVK 236


>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 =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 14/240 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VD  PLR  E 
Sbjct: 2   TIRLNKYIAETGFCSRREADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDDQPLRIREA 60

Query: 72  ------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 +      +KP+G+  T       + V         R+  +GRLD ++EGL+L+T
Sbjct: 61  KKLGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +
Sbjct: 119 SNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIA 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 175 KFGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  231 bits (589), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 105/229 (45%), Gaps = 4/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++ +++      SRR+ + ++A  RV V+G       +++     + VD   ++ A  +
Sbjct: 1   MKLLRILTNQNGISRRQAKALLAAGRVHVDGERCHDPDLDIPRFREVCVDQRIIQSAAPS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G ++   D     TV + +  +    V   GRLD  + GLL+LT+DG  +R
Sbjct: 61  YYLMLNKPSGYLSATRDDQH-PTVMELIDPLLRPHVHIAGRLDRASTGLLILTSDGVWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+ +  +VYRV     +  +  +  ++GI  +         +L+        V + 
Sbjct: 120 RLTEPAVKIPKVYRVTTAYAISPETEDRFREGIWFEYEQLRTSPASLE--PLGEREVRLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+  ++K++F     +V  L R S G   +  L  GS R +S + +
Sbjct: 178 IYEGRYHQVKRMFHAVGNRVTSLHRESMGGLTVDGLEPGSYRHLSAQEV 226


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 84/249 (33%), Positives = 126/249 (50%), Gaps = 6/249 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ KV+A AG+ASRR  E MI   RV+VNG+++      +   TD ++VDG  ++    
Sbjct: 1   MRLQKVLANAGVASRRVSEEMIVAGRVRVNGVVVTELGSRIHPETDLVDVDGTAIQLDTS 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + +KP G+V++ SD  GR  +         R+ +VGRLD +T GLL+LTNDG LA 
Sbjct: 61  KRYVILNKPTGVVSSMSDDRGRPDLRQYTKDWDERLFNVGRLDADTSGLLVLTNDGDLAH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  PS    +VY  +  GQV    +  L KG+ ++       +  L       + V + 
Sbjct: 121 VLAHPSFGVTKVYIAKVEGQVLPQTIQHLLKGVDLEDGRIAADKARLLDSSRGESLVELT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L  GKNR ++++       V  L+R  +GP  LGTL  G  RE++           LL  
Sbjct: 181 LHSGKNRIVRRLMAEVGHPVIELVRRQFGPLHLGTLPVGKARELTTVE-----RGALLTL 235

Query: 253 AQVNLDAPI 261
           ++ + D P 
Sbjct: 236 SRRDGDTPA 244


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/192 (34%), Positives = 107/192 (55%), Gaps = 3/192 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTV 191
           +  P  +  +VY  R  G  +++ L  L +G+ I G         +       + + V +
Sbjct: 120 MIHPRNEIDKVYVARVKGIANKENLRPLTRGVEIDGKKTKPAVYEILKVDPVKNRSVVQL 179

Query: 192 GLREGKNREIKK 203
            + EG+N ++KK
Sbjct: 180 TIHEGRNHQVKK 191


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 116/233 (49%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+       A N+ +    +   G  ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQGRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D     TV D LP      ++ +VGRLD +T GLLL+T++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKK-LPTVMDFLPPDIQSDKLYAVGRLDRDTTGLLLVTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTVCKAARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           ++ + EGK  ++KK+F     KV  L R  +GP+ L   L AG  R ++ + L
Sbjct: 178 SITISEGKFHQVKKMFLSVGVKVTSLKRTHFGPWSLDDNLQAGDYRPLNSEEL 230


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 120/229 (52%), Gaps = 5/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +G  SRR+ + ++ + +VKVNG       +++  +D +E+DG  L   E+ 
Sbjct: 1   MRINKYIASSGYTSRRKADDLVKKGKVKVNGETTHELGLDIKDSDVVEIDGKVLEIEEKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            + LY KP G +T++ DP     + D +  +  R  + GRLD ++EGLL++TNDG     
Sbjct: 61  YIKLY-KPRGYITSNFDPYNDRDLNDLV-KLDQRFFAAGRLDKDSEGLLIITNDGIFTNQ 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVG 192
           +  PS +  + Y VR    +++++    + GI I       D ++ L  +        V 
Sbjct: 119 IIHPSKKLDKTYIVRVSRLLNKEECQQFESGIDIGDSEMTSDSRIELIDKTSKT--YKVT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + +G NR+I+++F +F+ +V  L RIS GP +L  +     R   +  +
Sbjct: 177 IHQGYNRQIRRMFAYFSSEVKMLKRISIGPIKLDGMKPYEKRNFDQAEM 225


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/233 (30%), Positives = 109/233 (46%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRK 69
               R++K +A +G+ASRR+ + +I    V VNG +     V V   TD ++VDG  +  
Sbjct: 1   MGKVRLNKFLASSGVASRRKCDEIIFSGHVTVNGRVAPGPFVLVDEETDTVKVDGRRV-G 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             +   ++ HKP+G + +      G   V D    +  RV +VGRLD  T GL+L+TNDG
Sbjct: 60  MTKKVYFMVHKPLGYLCSSERKFPGDKLVIDLFSHLPYRVFTVGRLDKETSGLILVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +  +  PS    + Y ++    V    L  L +G VI G     + V    +K     
Sbjct: 120 EFSNKIIHPSFGITKEYLLKVSRDVTAKNLEDLMEGTVIDGKRVRPVSV----EKIRRGT 175

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + + EGK  EI+   E     +  L RI  G F LG L  G  RE++   +
Sbjct: 176 LKIIVNEGKKHEIRLFAEAAGLSILELSRIRIGSFVLGGLRYGEYRELTDAEI 228


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +  +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNELLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 115/235 (48%), Gaps = 9/235 (3%)

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  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+VTT  D  GR TV+          +  VGRLD  +EGLLL +ND   A 
Sbjct: 97  -YLMLNKPRGVVTTVRDEQGRDTVYRCFDGAGLPWLAPVGRLDKASEGLLLFSNDPQWAA 155

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDMQVTLDTQKGSNA 187
            +  P+T   + Y V+   + D  +L  +  G+        G      QV +  +   NA
Sbjct: 156 AVTDPATGPDKTYHVQVDCRPDALQLARMHDGVADTDPESDGSLLRAKQVRVLREGERNA 215

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           W+ + L EG+NR+I+++       V RL+R++ GP  +G L  GS R +S   +R
Sbjct: 216 WLEIVLDEGRNRQIRRLLAALEIGVLRLVRVAIGPLAMGELGKGSWRLLSAAEVR 270


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVREFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   D     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATVDTQH-PTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+        G+    + I     Q+TL   + +     
Sbjct: 120 RLTQPKTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 176 LTIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 107/238 (44%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K +    I +R +V R+I    +  NG  +      +    D + +D V +R  + 
Sbjct: 1   MRVDKFLHAMRIGTRTQVRRLIKDGHITANGEPVISGKQQINPGSDTVFLDDVQVRYQQY 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP+G++T  +D   + TV D          +  VGRLD +TEG+L++TNDG L
Sbjct: 61  FYYVM-NKPVGVITATTDSAAK-TVMDLFNTTDFRDDLFPVGRLDKDTEGILVITNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTL-DTQKGSN-A 187
           +  L  P+    +VY     G++   +L     GI +  G      Q  +    +  N  
Sbjct: 119 SHDLLSPNHHVTKVYEAEVTGEITAAQLANFNDGITLKDGTELQPAQAEIVQFHEIENFT 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + + EGK  ++K++      +V  L RI +G   L   LLAG+ R ++   L   
Sbjct: 179 TIRIMIHEGKYHQVKRMVGTLGERVVGLRRIKFGSLTLPVGLLAGNYRALTDDELTAL 236


>gi|289663281|ref|ZP_06484862.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 240

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 109/238 (45%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR  E   
Sbjct: 4   RLNKYIAETGFCSRREADRLIGERRVTVNGVSAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +      +KP+G+  T       + V         R+  +GRLD  +EGL+L+T++
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V    L  + +G+ I        +    T + +  
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDQFLRGMARGVRIHNETTLPCR----TARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 177 GFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A N+ +    +   G  +R  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNIDTGLQELLFQGRIIRGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LP       + +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPPDIQSDSLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K+GIV +  I     ++ + +   + +  
Sbjct: 118 GFQLLHPQYHVDKSYQVVVNGPLTSDHIQQFKEGIVFLDEITCKPAKLDILSASPTESRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ + EGK  ++KK+F   + KV  L R+ +G F L   L  G  R +++K L+
Sbjct: 178 SITISEGKFHQVKKMFLSVSVKVTALKRVQFGDFTLDSELAEGQYRPLNQKELQ 231


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 108/231 (46%), Gaps = 6/231 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DH 59
           M+ KN         R+++ +A  G+ SRR+ E +I + ++ +NG  +      +    D 
Sbjct: 1   MQSKNDSNARDE-IRLNRFLADCGLGSRRKTEELILRGQITINGKRVTDLGTKIKPGSDV 59

Query: 60  IEVDGVPLRKAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +   G  +    +  R+ + +KP+G + +H D     TVF  LP  +      GRLD+N+
Sbjct: 60  VSYLGNVVEPTRKPKRILILNKPVGYLCSHGDRFHEKTVFSLLPLTYKNFKIAGRLDLNS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQV 177
            GLL+LTNDG LA+ +  PS    + Y V  +    +  +    +KGI+  G       V
Sbjct: 120 RGLLILTNDGELAQKISHPSNGSEKEYLVTLNHDPGEKWIQAAFQKGILDAGEILRAKMV 179

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            L    G N    V L EGK R+I+++F      V  L RI  G  QL  L
Sbjct: 180 KLV--PGKNCVYRVILAEGKKRQIRRMFHASGASVIDLQRIRIGSIQLEKL 228


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 81/247 (32%), Positives = 135/247 (54%), Gaps = 7/247 (2%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K++        P+R+ KV+A +G+ SRRE+E  I    V VNG   +     +   D +
Sbjct: 82  LKERRSDLSRMEPERLQKVLAASGVGSRREMEEWINNGWVTVNGKTAQ-LGDKITPDDQV 140

Query: 61  EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDI 116
            V G  ++        R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDI
Sbjct: 141 LVKGNIIKLKWADRLPRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDI 200

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDM 175
           NT GLL+LT  G L +    P  +  R Y VR  G +  +++ +L ++GI+++       
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 EVSKKIL 241
           E++   +
Sbjct: 321 ELNPAEV 327


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/234 (28%), Positives = 117/234 (50%), Gaps = 6/234 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV ++I +  V VNG  ++     V  TD + V+G  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHQLIKKGIVSVNGQTVKTPKEKVAETDEVTVNGEKIVY-QKY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             +L +KP G+++   D   R+ +   +L   +  ++ VGRLD +T GLLLLTNDG L  
Sbjct: 60  HYFLMNKPKGVLSATEDRSQRTVISLLDLKDQYQGIVPVGRLDKDTTGLLLLTNDGQLNH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQ--KGSNAWV 189
            L  P+    +VYR +  G  D++ +     G+ +         ++T+  Q  +  ++ +
Sbjct: 120 ELLAPNKHVAKVYRAKIAGVADENTVKTFASGMTLGDETKLKPAKLTVLKQDLEHDSSEI 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            + + EGK  +IK++F     KV  L RIS G  +L   L  G   E+    ++
Sbjct: 180 EIEISEGKYHQIKRMFGAVGMKVVELERISMGKLKLPNNLKRGQYIEIDVDEIK 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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 110/236 (46%), Gaps = 9/236 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +++A   SR++ ++++    + VNG +++ ++ +V  + D I   G  L  A+ 
Sbjct: 1   MRLDKFLSKATELSRKDAKKVLHAGEITVNGTIIKDSSHHVDLANDEILWAGEALSVADG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  L +KP G   T   P     V D +     + +   GRLD++T G LLL++DG   
Sbjct: 61  NRYILLYKPDGFECTLK-PKEYPMVTDLIAVPEVANLRIAGRLDVDTTGALLLSDDGAWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P     + Y++     +D+D     +  +  GI+++G         L     ++A
Sbjct: 120 HRVTSPKRHQPKQYQLTLADAMDKDAQAYAIKQIANGILLEGETEKTRPAVLSFIDETHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +   L EGK  ++K++  +F  KV +L R S G   L  L  G  R ++   + +
Sbjct: 180 VL--TLTEGKYHQVKRMMAYFGNKVIKLHRASIGHISLEGLQMGECRFLTPDEINQ 233


>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 =  230 bits (587), Expect = 2e-58,   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|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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 120/233 (51%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
           +R+ K+++  G+ SR+E   +I +  V VNGIL  R         D I ++G PLR  +R
Sbjct: 6   ERLDKILSSQGVGSRKEAGILIRRGLVHVNGILATRPETKTDPERDQITIEGKPLRF-QR 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D   + TV D +P + SR  +   GRLD +T GLL+LT+DG L
Sbjct: 65  HVYLMMNKPAGVVSASRDSREK-TVVDLVPPVLSRRDLFPAGRLDRDTTGLLILTDDGEL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  +  P     ++Y     G V  +++     G+ ++      +   L   K   AW T
Sbjct: 124 AHRMLSPKKHVYKLYEASVDGPVGAEEIEKFAAGVALEDG-TVCLPAGLTVVKQGTAWET 182

Query: 191 VG-LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +  +REGK  ++KK+F     +V RL R+  G  +L  TL  G  RE++K+ L
Sbjct: 183 LVEIREGKFHQVKKMFLAVGRRVLRLKRVRIGGLELDKTLKEGECRELTKEEL 235


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 119/241 (49%), Gaps = 9/241 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       + NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDNCPASSLSQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   L HKP G+VT   D     TV D LP      ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLLLHKPNGVVTASKDKK-LPTVMDLLPPDIKSYQLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y++  +G +  + +   K GIV + G      Q+ + +   + +  
Sbjct: 118 GFQLLHPQYHVDKSYQMVVNGPLTSEHIQKFKDGIVFLDGTTCKPAQLEILSSSPTESHA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L R+ +G F L   L  G  R ++ + L E +  H
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRVQFGDFTLDPELSEGQFRSLNPEEL-ELIKKH 236

Query: 249 L 249
           L
Sbjct: 237 L 237


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 75/248 (30%), Positives = 122/248 (49%), Gaps = 11/248 (4%)

Query: 1   MKDKNIVQENF---TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M + N + E F      RV K+IA+ G  SRR+ E  I ++ VKVNG +++         
Sbjct: 1   MNEINFLVERFAMKELIRVQKLIAQTGYCSRRKAEEYIEKKLVKVNGKIVQ-LGDKASEN 59

Query: 58  DHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           D I+++   +  +      +L +KP   ++T  DP GR TV D + +   R+  VGRLD 
Sbjct: 60  DEIKINNQLISLQKPNFVYFLLNKPKKTISTVKDPKGRKTVVDLI-NYSERIAPVGRLDY 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T G LLLTND  +   L  P  + LR YRVR    +   +  L+  G+++ G     + 
Sbjct: 119 DTTGALLLTNDWEMINKLTHPKYEILRTYRVRIDSPLSLKEFKLINAGLIVNGKFSKQIV 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +DT+        V L  G    IK++F+  N +V  L R+S+    +  +  GS R +
Sbjct: 179 DQVDTKS-----YLVTLHVGSYHHIKELFKALNHEVINLKRVSFANLTVEKMPEGSYRTL 233

Query: 237 SKKILREQ 244
           + K +++ 
Sbjct: 234 TLKEIKDL 241


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 109/234 (46%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            RV + ++     +R++V  ++ ++RV ++G+ +      V +   + VD   L+  +  
Sbjct: 1   MRVDRFLSNLPRFNRKQVRLLLVERRVSIDGVAVSDPHHEVRTFSRVCVDDEVLQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  +DP    TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATADPQH-PTVLDLLDEPDKDELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +  +       G+    + +     ++ L           
Sbjct: 120 RLTQPQTKLPKVYHVETEQDIGPEYATTFAGGLYFAFEDLTTQPAELELLGP----TTAR 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + + EG+  ++K++F  F+ KV  L R   GP  L  TL  G  R ++   +R+
Sbjct: 176 LSIIEGRYHQVKRMFGHFDNKVIGLHRERMGPLVLDATLAPGQYRALTDDEIRQ 229


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 100/232 (43%), 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 ITSPKKECGKRYLLETAEPLKQEWVEEFAAGLQLNNEDGLTKPATLEILG----SHQARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++       V +L R S G  +L  +L +G  R +++  ++
Sbjct: 176 TITEGKYHQVKRMLAAVGNCVTQLHRESVGEIELDESLASGEWRYLTEAEIK 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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/244 (29%), Positives = 110/244 (45%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A  GI SRRE +  I +  V+VNGI        V   D I+++     +  
Sbjct: 3   DPVRLSKRMAELGICSRREADSYIEKGWVRVNGIPA-VLGQKVSPADRIDLNKQAHEQQA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
                L +KP+G V+   + D R+ V                   PS    +   GRLDI
Sbjct: 62  NRVTILLNKPVGFVSGQPEKDYRAAVELITAENQWEGDTSRIAFHPSHTRNLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L   +    + Y VR  G + ++ L LL  G+ + G      Q
Sbjct: 122 DSVGLLVLTQDGRIAKQLIGDNGNSEKEYLVRVKGSLKENGLALLNHGLSLDGEKLRPAQ 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+   Q      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R +
Sbjct: 182 VSWQNQD----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRVGRIKLGALPQGKWRYL 237

Query: 237 SKKI 240
               
Sbjct: 238 QANE 241


>gi|71894432|ref|YP_278540.1| 16S rRNA uridine-516 pseudouridylate synthase family protein
           [Mycoplasma synoviae 53]
          Length = 232

 Score =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 115/232 (49%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA + + +R E++++I++  VKVN ++++++       D I ++G+ L   E  
Sbjct: 1   MRIEKFIADSTLYTRNEIKKLISKGLVKVNDLIIKKSQSIDPKLDKIYLEGILLEAREEF 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + +KP G +  + D   +  VF+    L        ++GRLDI+TEGLL++TNDG L
Sbjct: 61  SYIMMNKPAGYICANFD-WNKQVVFELLLDLEMNLKDFFTIGRLDIDTEGLLIITNDGKL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P     + Y V     ++++   LL+K ++I  I Y            SN    
Sbjct: 120 SHNLLSPKKHIPKTYYVELDKPLEKNIKELLEKELLIDEIKYK----KSILNNISNNKWE 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  +IK +F  F +KV  L RI      L   L  G  + ++K+ L
Sbjct: 176 ITIFEGKFHQIKIIFAHFGYKVTYLKRIKMNNLSLDENLKPGEYKFLTKEEL 227


>gi|226360073|ref|YP_002777851.1| pseudouridine synthase [Rhodococcus opacus B4]
 gi|226238558|dbj|BAH48906.1| pseudouridine synthase [Rhodococcus opacus B4]
          Length = 350

 Score =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/243 (29%), Positives = 114/243 (46%), Gaps = 4/243 (1%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D+          R+ KV+A+AG+ASRR  E +I+Q RV+V+G ++    + +   + +  
Sbjct: 99  DRPAGPPQGDGMRLQKVLAQAGVASRRAAEELISQGRVEVDGRIVIEQGLRIDPENAVVR 158

Query: 63  DGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINT 118
                   ++       +KP G  +T SD  GR  V D +        R+  VGRLD +T
Sbjct: 159 VDGVRVVVQKDLVHLALNKPRGWQSTMSDDLGRPCVGDIVSERVAAGQRLFHVGRLDADT 218

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLLLTNDG LA  L  PS +  + Y     G +++     LK+G+ +          T
Sbjct: 219 EGLLLLTNDGDLAHRLMHPSFEVSKTYLATVSGALERGVGKKLKEGVELDDGPAKVDTFT 278

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L       + V V L EG+   ++++F+     V RL+R   G   LG    G+ R + +
Sbjct: 279 LLDINEGKSLVRVTLHEGRKHIVRRLFDAVGHPVIRLVRTDIGAVALGDQRPGTLRVLGR 338

Query: 239 KIL 241
             +
Sbjct: 339 GEV 341


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 68/245 (27%), Positives = 121/245 (49%), Gaps = 19/245 (7%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +   P R++K +A++G+ SRRE + +I +  V + G  +  A   ++    + +D   
Sbjct: 6   TYDGAEPVRLNKWLAQSGVCSRREADTLIEEGCVAIAGETVRDAGRKILPGQTVTLD--- 62

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFSRVISVGRLD 115
            R        +Y+KPIG+V+   +P     V            D  P   S++  +GRLD
Sbjct: 63  -RGETLPMTVIYNKPIGIVSGQPEPGETPAVRMIRRANVFGPADVYPDQTSKLAPIGRLD 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLL+L+ DG LA+ +  P ++  + Y V+  GQ+ + KL  L+ G+ + G      
Sbjct: 122 KDSHGLLVLSEDGVLAKAVIGPDSELDKAYHVQVRGQIIEAKLAWLRHGLELDGRKLKPA 181

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           ++T   Q G  + +T  L+EG+ R+I+++ +    +V  L R   GP QLG L  G  R 
Sbjct: 182 EIT---QTGPQS-LTFVLKEGRKRQIRRMCDMVELRVTDLYRDRIGPLQLGDLPEGQWRF 237

Query: 236 VSKKI 240
           ++   
Sbjct: 238 MTPDE 242


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 74/220 (33%), Positives = 114/220 (51%), Gaps = 8/220 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +AR G+ SRR+VE +I   RVK+NG+++      V   DH+EVDG  +   ++ 
Sbjct: 1   MRLNQYLARCGLGSRRKVEALIVTGRVKLNGLVVSDLGCRVEEGDHVEVDGCSVHPLDKI 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+V    D   R TV D LP      R   VGRLD  ++GLL+LTNDG   
Sbjct: 61  YIVM-NKPRGVVCAVEDRRYR-TVLDLLPPQIRALRPFPVGRLDKESQGLLILTNDGDFC 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P    ++ Y V     V  + L+ LK G+   G     + V+L   +     V V
Sbjct: 119 DAILHPRRGIIKTYEVTVDRDVPSESLDRLKGGVWSDGEILEPLMVSLMGPR----TVRV 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            ++EGK RE++++     +KV  L+R   G  +L  L AG
Sbjct: 175 DIQEGKKREVRRMMAALGFKVLSLLRRRIGKMELRRLRAG 214


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 111/250 (44%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  ++    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MEHDSNETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTAA-LGQKVTERDRIDLNRQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVIS 110
              K       L +KP+G V+  ++                +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 KLRPAKVKWQNED----QLRFVLKQGKKRQIRRMCELVGLRVIGLKRIRMGKVKLGKLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  I SR+ +++ + +  + V+       A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKI-SRKAMKQALLKGDILVDSCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV D LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMDLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V+ +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVQVNGLLTPDHIQAFQKGIVFLDGTVCKPAKLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L   + R +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTSLKRIQFGDFTLNPDLAESNYRPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 111/249 (44%), Gaps = 11/249 (4%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RK 69
           +  R++K I+ +GI SRR  +R I    V +N  L       V S D + V+   +  R 
Sbjct: 5   SSIRLNKYISDSGICSRRHADRHIKLGNVFINDRLAA-VGAQVFSGDRVRVNDRQIAPRD 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A+   L   +KP+G++T+    + R  + D + +   R   +GRLD  ++GL+ LTN G 
Sbjct: 64  ADDLVLIALNKPVGVLTSMGKHE-RDNIGDFV-NHSQRTFPIGRLDKASQGLIFLTNQGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L   +        + Y V  +  +    +  +  G+ I G       V    +K ++   
Sbjct: 122 LVNKILRAGNNHEKEYLVTVNKPLTDAFIQGMGAGVPILGKVTHPCLV----EKEASQVF 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L +G NR+I+++ ++F ++V +L R+      L  L  G  R+ +     E     L
Sbjct: 178 RITLVQGLNRQIRRMCKYFGYEVTKLERVRIMNVDLTGLALGEWRDFTADERLELF--KL 235

Query: 250 LEEAQVNLD 258
           +E +     
Sbjct: 236 IEHSSSEEP 244


>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 =  230 bits (587), Expect = 3e-58,   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|330889469|gb|EGH22130.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. mori str. 301020]
          Length = 230

 Score =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G         V     + +DG  L+  +  
Sbjct: 1   MRLDRFLSNLPSLNRKSVRLALASGRVQVDGQTTSDPHHEVRDFSRVALDGEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   D     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATVDTQH-PTVLDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+        G+    + I     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAATFAAGMYFSFENITTQPAQLTLLRPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  FN KV RL R + G   L   L  G  R +    +
Sbjct: 176 LTIVEGRYHQVKRMFGHFNNKVLRLHRENIGALALDPALAPGGYRALHAAEI 227


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 77/235 (32%), Positives = 127/235 (54%), Gaps = 8/235 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKA 70
             QR+ K+++ +G  +R+E++++I    VKV+G++++ +A+ V   +  IEV G  L+  
Sbjct: 3   DTQRIDKILSNSGFGTRKEIKKLIKNGEVKVDGVVVKDSAMQVNPKESVIEVAGEILKYR 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           E     + +KP G+++   D   R TV D LP  +    +  VGRLDI+TEGLLLLTNDG
Sbjct: 63  E-YIYIMMNKPQGVISATYDNRHR-TVIDILPDEYKFFNLFPVGRLDIDTEGLLLLTNDG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNA 187
            LA  L  P     + Y     G V    +++ ++G+V+    Y  +   L   + G  +
Sbjct: 121 QLAHELLSPRKHVPKKYYALIDGIVTTKDVDVFREGVVLDDG-YKTLPSELFILKSGPYS 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + + EGK  ++K++FE    KV  L RI  G  +L  TL  G  RE++ + +
Sbjct: 180 EVEIVIYEGKFHQVKRMFEAVGKKVKYLRRIGMGKLKLDETLEPGDVRELTDEEM 234


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 118/243 (48%), Gaps = 15/243 (6%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +   PQRV+K +A++G+ SRRE E +IA   V ++G  +  A   ++    + +     
Sbjct: 12  YDEAEPQRVNKWLAQSGVCSRREAEALIADGLVSIDGETIADAGRKILPGQTLTLADRA- 70

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVISVGRLDIN 117
             +      + +KP+G V+   +P     V              P   + +  +GRLD +
Sbjct: 71  AASLGGFTAVLNKPVGYVSGQPEPGHVPAVRLLTAANLSGEGAAPDARASLPPLGRLDED 130

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           + GLL+L++DG LA+ +  P +   + Y VR  GQVD+ KL  L+ G+ + G       V
Sbjct: 131 SRGLLILSDDGVLAKAVIGPQSDLDKEYVVRVAGQVDERKLARLRHGLELDGRKLKPATV 190

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           ++         +   L+EG+ R+I+++ +    +V  L+R+  GP +LG L  G  R ++
Sbjct: 191 SVIQGN----TLRFVLKEGRKRQIRRMCDLVGLRVVDLLRVRIGPLKLGDLPEGRWRVLT 246

Query: 238 KKI 240
            + 
Sbjct: 247 PQE 249


>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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 123/244 (50%), 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 ++   R  + + L +   RV   GRLD N+EGLL+LTNDG L + 
Sbjct: 60  IYLKMYKPVGIVCT-AEKRERDNLIEYL-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|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 =  230 bits (587), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 114/230 (49%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     SR E  + + Q+RV VNG L++  +  V + D + +DG  +      
Sbjct: 1   MRLDKFLANYSSLSRTEATKALKQKRVLVNGDLVKTGSHKVANDDQVWLDGRRIEMNT-A 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP   +  ++DP   + VFD +    + V  +VGRLD++T GLLL+T+DG  + 
Sbjct: 60  VYFMMNKPANYLCANADPQH-ALVFDLIDEASTYVLHTVGRLDLDTTGLLLITDDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + YRV     +  D     ++G++++      +   L   + ++  V + 
Sbjct: 119 RLTSPKHHIPKTYRVWLDEPLVADAEIQCEQGLLLRSESKPTLPAEL--NRITDTEVLIT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EG+  ++K++F     +V RL R   GP +L   L  G  R ++++ L
Sbjct: 177 ISEGRYHQVKRMFAAMGNRVVRLHRERIGPLELDPNLAPGEYRSLTQQEL 226


>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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 101/238 (42%), Gaps = 10/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAE 71
             + +++   G  SR+    +I    V VNG   +        TD +   V+  P    E
Sbjct: 1   MHLERILHAQGFGSRKNCRILIRHHAVTVNGEPCDNP-FADFDTDKLAFTVNEEPWEYRE 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
           +    + +KP     +H  P    +VF  LP       V  +GRLD +T GL+LL++DG 
Sbjct: 60  KA-YLMLNKPANYECSHK-PQHHPSVFALLPHPLLERGVQCIGRLDEDTTGLILLSDDGQ 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P  +  ++Y V     VD D++  L++G+ +           L  ++ S+  +
Sbjct: 118 FIHRMSSPKWKVPKIYEVGAKHAVDADQIRQLQEGVQLVDEPAP--IAALACEQISDQVL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
            + L EGK  ++K++      +V  L RI  G   L   L  G  R +++  L    G
Sbjct: 176 HLTLAEGKYHQVKRMLAAVGNRVESLKRIRIGELVLPDDLAEGQWRWLTESELASLNG 233


>gi|254804685|ref|YP_003082906.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
 gi|254668227|emb|CBA05021.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
          Length = 252

 Score =  230 bits (586), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 111/255 (43%), 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  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR---------------STVFDNLPSIF 105
           E++     +       L +KP+G V+  ++   +               ++     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 SLDGEKLRPAQVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKL 235

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  R ++   
Sbjct: 236 GRLPLGKWRYLAPGE 250


>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 =  230 bits (586), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 107/245 (43%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     + 
Sbjct: 1   MEKVRISKLMSERGLCSRREADTYIERGWVRVDGVVVSELGARAYPDQVITLERAAQARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
                 L +KP+G V+  ++      V           D  P  F R     +   GRLD
Sbjct: 61  TSRVTILINKPVGYVSGQAEKGYTPAVALIDSRSRYAGDRAPQRFERAHLDGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A+ L    +   + Y VR  G +  + L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIAKHLIGEDSSVDKEYLVRVQGNLSDNGLALLNHGLSLDGKALKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R 
Sbjct: 181 QVRWQNSD----QLRFVLREGKKRQIRRMCELVGLKVIGLKRVRIGRVSLGDLPLGQWRY 236

Query: 236 VSKKI 240
           + +  
Sbjct: 237 LREDE 241


>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 =  230 bits (586), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 67/230 (29%), Positives = 108/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++   M+AQ+RV+V+G ++      V     +E+D   L+     
Sbjct: 1   MRLDRFLANLPSHNRQQARLMLAQRRVRVDGQVVSDPLAEVREFSRVELDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G V+   DP    TV D LP+     +   GRLD NT GL++LTNDG  +R
Sbjct: 61  RYLMLHKPTGCVSATQDPQH-PTVLDLLPAALRDDLHIAGRLDFNTTGLMILTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+T+  + Y V    ++ +  +   ++G              LD      A + + 
Sbjct: 120 RLTQPATKLPKHYLVDTEDEIGEHYVARFREGFYFAFENLTTQPALLDILGPRQARLAIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             EG+  ++K++F  FN KV  L R S G   L   L  G  RE++   +
Sbjct: 180 --EGRYHQVKRMFGHFNNKVVGLHRESMGAICLDPGLAPGEFRELTADEI 227


>gi|241662183|ref|YP_002980543.1| pseudouridine synthase [Ralstonia pickettii 12D]
 gi|240864210|gb|ACS61871.1| pseudouridine synthase [Ralstonia pickettii 12D]
          Length = 248

 Score =  230 bits (586), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 97/232 (41%), Gaps = 7/232 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V +NG+ +E     V +   + +VDG       R  
Sbjct: 9   LYRILQSQGFGTRRYCKDLVLAGLVCINGVEMESPDALVDTAGLVLDVDGERWAYHARA- 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G+  +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 68  YLMLNKPAGVECSQK-PKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  Q  +VY +     V + ++  L  G+++              ++     + + 
Sbjct: 127 TITSPRHQVPKVYEITTAEPVTEAQIAQLCAGVLLADENEN--VAAAWAERVGTHHLRMA 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L +GK  ++K++       V  L R + G   LG L  G  R +    L   
Sbjct: 185 LTQGKYHQVKRMVAAAGNHVVGLHRSAIGGLSLGDLAPGEWRWLEAADLEAL 236


>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 =  230 bits (586), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+  + SR+ +++ + +  + V+G      A N+ +    +      ++  E 
Sbjct: 1   MRLDNLLAQEKV-SRKAMKQALLRGEILVDGCPARSLAQNIDTGLQELLFQDRIIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT + D +   TV + LPS     ++ +VGRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPAGVVTANKDKE-LPTVMNLLPSDIQSDKLYAVGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   +KGIV + G      ++ + +   S +  
Sbjct: 118 GFQLLHPQYHVDKTYQVEVNGLLTPDHIQTFQKGIVFLDGTICKPARLEILSASPSLSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  +IKK+F     KV  L RI +G F L   L  G+   +++K L  Q+  +
Sbjct: 178 SITISEGKFHQIKKMFLSIGVKVTNLKRIQFGDFTLNPDLAEGNYHPLNQKEL--QIIKN 235

Query: 249 LLEEAQ 254
            LE ++
Sbjct: 236 YLEMSR 241


>gi|218682423|ref|ZP_03530024.1| pseudouridine synthase [Rhizobium etli CIAT 894]
          Length = 538

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 73/224 (32%), Positives = 117/224 (52%), Gaps = 5/224 (2%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STD 58
           +++     +   +R  + + +++ G  SR + ER+IA+ RV V+G  +   +  V  +T 
Sbjct: 6   RERTKPAADAAAKRVTLPRALSKLGYCSRTQAERLIAESRVAVDGRTISDTSAWVDLATA 65

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDIN 117
            I VDG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  
Sbjct: 66  KISVDGLVI-AAETKIYLMLNKPRGLVTTRHDPEGRPTVYDCLRDFDIPHLSPVGRLDKA 124

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G        
Sbjct: 125 SEGLLLFTNDTEFAQILLDPVTHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAA 184

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
               Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G
Sbjct: 185 RRLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIG 228


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 120/232 (51%), Gaps = 10/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           RV K+++  G  SR+E+++ +   ++K+N   +++    + S  D I  DG  +   E  
Sbjct: 4   RVDKILSELGFGSRQEIKKYVKAGKIKINDRTVKKPEEKINSKNDIIYFDGKEIEVEEFE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G V    D   R TV + + S    ++ VGRLD++TEG+L+LTNDG L   
Sbjct: 64  TYILY-KPAGYVCATKDNVHR-TVMELIDSKRKNIVPVGRLDLDTEGILILTNDGDLNHR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P++   + Y   F G++D + + + + G+ I +G      ++ + ++      + + 
Sbjct: 122 LVSPASHVDKSYYAVFDGKLDSNAIEMTQAGLDIGEGEFSKPAELKILSEN----EILLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVSKKILR 242
           + EGK  ++K++ +    +V  L R+++G  +L  L    G +R+++   + 
Sbjct: 178 IHEGKFHQVKRMVKALGGEVTYLKRVAFGGLKLDDLKLEKGESRKITGDEME 229


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 68/225 (30%), Positives = 110/225 (48%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK-AE 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 RVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           + +  PS    + Y V       +  +    +KGI+  G       V L    G      
Sbjct: 135 QKITHPSNGSEKEYLVTLKHDPGEKLIQAAFQKGILDAGEILHAKMVKLV--PGKKCVYR 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
           V L EGK R+I+++F +F   V  L RI  GP +L    L  G  
Sbjct: 193 VILEEGKKRQIRRMFRWFGVSVVDLQRIRIGPLKLEKFNLEEGQY 237


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 56/232 (24%), Positives = 97/232 (41%), Gaps = 7/232 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNG+ +E     V +   + +VDG       R  
Sbjct: 9   LYRILQSQGFGTRRYCKDLVLAGLVFVNGVEMESPDALVDTAGLVLDVDGERWAYHARA- 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G+  +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 68  YLMLNKPAGVECSQK-PKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  Q  +VY +     V + ++  L  G+++              ++     + + 
Sbjct: 127 TITSPRHQVPKVYEITTAEPVTEAQIAQLCAGVLLADENEN--VAAAWAERVGTHHLRMA 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L +GK  ++K++       V  L R + G   LG L  G  R +    L   
Sbjct: 185 LTQGKYHQVKRMVAAAGNHVAGLHRSAIGGLSLGDLAPGEWRWLEAADLEAL 236


>gi|325529283|gb|EGD06232.1| putative RNA pseudouridylate synthase [Burkholderia sp. TJI49]
          Length = 306

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 104/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +  HIE+D          
Sbjct: 58  MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQHIEIDERAQAAQAAQ 117

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 118 VTILLHKPVGYVSGQAEDGYEPAAVLITRDNHWSGDRSPLRFSPQHLRTLAPAGRLDIDS 177

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 293

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 294 QGQWRYLSADE 304


>gi|213619052|ref|ZP_03372878.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 270

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 93/276 (33%), Positives = 129/276 (46%), Gaps = 17/276 (6%)

Query: 34  MIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTH 88
           +I   RV V+G +      V V     I +DG  +   E      R+  Y+KP G + T 
Sbjct: 2   IIEAGRVSVDGKIATLGDRVEVTPGLKIRIDGHLISVKESAEQICRVLAYYKPEGELCTR 61

Query: 89  SDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
           +DP+GR TVFD LP    +R I+VGRLD+NT GLLL T DG LA  L  PS +  R Y V
Sbjct: 62  NDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTTDGELANRLMHPSREVEREYAV 121

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           R  GQVD+ KL  L +G+ ++        +     +G N W  V L EG+NRE+++++E 
Sbjct: 122 RVFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEA 181

Query: 208 FNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
              +V+RLIR+ YG   L   L  G   E+        L         V L     S   
Sbjct: 182 VGVQVSRLIRVRYGDIPLPKGLPRGGWTELD-------LAQTNYLRGLVELPPETSSKVA 234

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
           + +DR  + +       R  K  SQ  G  +     
Sbjct: 235 VEKDRRRMKAN---QIRRAVKRHSQIAGGRRSGGRN 267


>gi|240047413|ref|YP_002960801.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239984985|emb|CAT04978.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 233

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 114/232 (49%), Gaps = 8/232 (3%)

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  VWYLLNKPAGYITTVRDQFNRPTVMDFFDNK-THLFPVGRLDYNTTGLLLITNDGELANK 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L  P  +  R+Y  +    +   +L+ L    + + G+           +K S+    + 
Sbjct: 123 LLHPRNKIERIYLAKLDYSLADWELDFLNTTSLNLDGVISKQK-----IEKVSSRKYKIT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + +G N  +KK+F     +V  L RI +   +L  L  G  R++S   +++ 
Sbjct: 178 IWQGSNHHVKKIFAIAKKQVIELKRIGFANLELANLPEGQFRKLSDLEIKKL 229


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 98/230 (42%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  A   SR   ++ + +  V  +G++++ +   V     + ++G  L      
Sbjct: 1   MRLDKFITEASELSRSLAKKALHRGDVTCDGVIVKDSGFKVEPGTKVCLEGRELSLF-GV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP+  + +  D +   +V   +     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYLMLNKPVDTICSTID-EVYPSVLSLIDVEKASNLHIAGRLDADTTGLVLITSDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P     + Y V     +D+  +    +GI ++         TL+     +A   + 
Sbjct: 119 RATSPKKDCGKRYLVEVAEPLDESLIETFAEGIALRNEDGLTKPATLEIIDSHHA--RLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++F      V  L R   G  +L   L  G  R +++  +
Sbjct: 177 ITEGKYHQVKRMFAATGNAVINLHRECVGSIELDPGLALGEWRYLTQAEI 226


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 68/256 (26%), Positives = 111/256 (43%), Gaps = 27/256 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++   + +R E++R I +  V+VNG  +      V   D I   G P+    R 
Sbjct: 18  MRLDKFLSDMNMGTRTELKRDIRKGAVQVNGEKITDPGFMVNENDEIIFAGEPVPYF-RY 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ +KP G++T   D   + TV D       + +  VGRLD +T GLLL+TNDGG   
Sbjct: 77  EYYMLNKPAGVITATED-RYQKTVLDFFGERRRKDLSPVGRLDKDTVGLLLVTNDGGFHH 135

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSN----- 186
            L  P     + Y  R  G+VD+      +KGI +  I      ++ +D  + +      
Sbjct: 136 RLLSPKKHIDKEYYARIDGRVDEADREKFEKGIYVDEIFTALPAKLMIDGYRENALESDF 195

Query: 187 -----------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TL 228
                            + + V ++EGK  +IK++F     +V  L RI  G   L  TL
Sbjct: 196 MDLANSRAPKSALENGVSEIRVVVQEGKFHQIKRMFHALGKEVIYLKRIRIGSVVLDPTL 255

Query: 229 LAGSTREVSKKILREQ 244
             G+ R ++   +   
Sbjct: 256 EEGTYRRLTAGEVAAL 271


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 65/252 (25%), Positives = 108/252 (42%), Gaps = 25/252 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A + +  R+ V   I    VKVNG ++   ++N+    D +E  G  +    +
Sbjct: 1   MRLDKFLAESAVGRRKIVRTYIKDGMVKVNGKIITEPSININEKLDDVEYLGKKVIHNGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++++KP G +T   D +   TVFD      + V  VGRLD +TEGLLLLTNDG    
Sbjct: 61  -VYYIFNKPAGCITATRD-NIHKTVFDYFDEDMNGVFHVGRLDKDTEGLLLLTNDGEFEH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------TQ 182
            +  P     + Y     G +D +    L+ GI I           +D           +
Sbjct: 119 KVMYPEKHVEKTYFFWALGSLDDEDKKQLEAGIFIGNNESLTKPAKIDLYKSGLYKEFKE 178

Query: 183 KGSNAWVT-----------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
           +     +            + + EG+  ++K++ +     V  L RIS G  +L  +L  
Sbjct: 179 EIPIKNLENKDHQPVVSGYLTISEGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLKM 238

Query: 231 GSTREVSKKILR 242
           G  R ++KK + 
Sbjct: 239 GDYRNLTKKEIE 250


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 109/238 (45%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRR+ +R+I ++RV VNG+     AV V   D + VDG PLR  E   
Sbjct: 4   RLNKYIAETGFCSRRQADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +      +KP+G+  T       + V         R+  +GRLD  +EGL+L+T++
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I             T + +  
Sbjct: 121 GNIVNEILRAENRHKKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPC----HTARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 177 GFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 109/238 (45%), Gaps = 14/238 (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       + V         R+  VGRLD  +EGL+L+T++
Sbjct: 63  PGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPVGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +  
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 177 GFRIVLEQGLNRQIRLMASEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 68/225 (30%), Positives = 110/225 (48%), Gaps = 7/225 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK-AE 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 RVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           + +  PS    + Y V       +  +    +KGI+  G       V L    G      
Sbjct: 135 QKITHPSNGSEKEYLVTLKHDPGEKLIQAAFQKGILDAGEILHAKMVKLV--PGKKCVYR 192

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
           V L EGK R+I+++F +F   V  L RI  GP +L    L  G  
Sbjct: 193 VILEEGKKRQIRRMFRWFGVSVVDLQRIRIGPLKLEKFNLEEGQY 237


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 13/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K++A  G  SR++V   + +    +NG+     A ++  T D + V+G+ ++    
Sbjct: 1   MRVDKILASNGYGSRKDVRVFLKKNNCCINGVRCINPAQHIDPTKDTVTVNGISVQLRT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           +   + HKP G V++  DP    TV D LP+ F+   +  +GRLDI+TEGLL++TNDG L
Sbjct: 60  SVYIMLHKPAGCVSSTKDP-IHKTVMDFLPAPFNAMDLFPIGRLDIDTEGLLIITNDGNL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQ-GICYGDMQVTL-DTQKG 184
              +  P +  ++ Y +     + + ++      L +GI++  G       + L +    
Sbjct: 119 THSITAPKSNCVKTYYLELERPLTETEIHNFTEKLAQGILLHTGYTCLPAALELTENIHT 178

Query: 185 SNAW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            NA    + + EGK  +IKK+   F  K+  L R+S    +L  +L AG+ RE++ + +
Sbjct: 179 KNAQAFLIHITEGKYHQIKKMCTAFGVKLTYLKRVSMAGLELDPSLAAGNCRELTSEEI 237


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 117/278 (42%), Gaps = 26/278 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I++  VKV+G ++      V     I +D     +     
Sbjct: 10  RLSKRMSELGLCSRREADEWISKGWVKVDGQVVSELGSKVRPDQKITIDRKAQDQQNERV 69

Query: 75  LWLYHKPIGLVTTHSDPDG---------RSTVFD------NLPSIFSRVISVGRLDINTE 119
             + +KP+G V+  ++            R+   D        PS    ++  GRLDIN+ 
Sbjct: 70  TIILNKPLGYVSGQAEDGHEPARILITPRNRWIDDPSPRRFNPSQLKSLVPAGRLDINST 129

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-------HGQVDQDKLNLLKKGIVIQGICY 172
           GLL+LT DG +A+ +   ++   + Y VR        + +    KL LL  G+ + G   
Sbjct: 130 GLLVLTQDGRIAKTIIGENSSVEKEYIVRVAMTDGRSNSEFPPAKLALLNHGLELDGKPL 189

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   LREG+NR+I+++ +    KV  L R+  G  +LG L  G 
Sbjct: 190 EKAEVSWLNED----QLKFVLREGRNRQIRRMCDLVGLKVLALKRVRVGNVRLGKLPVGK 245

Query: 233 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
            R +          P     ++    AP        R 
Sbjct: 246 WRYLEDGESFTGPAPKRASSSRPAAGAPRRPKTFKPRK 283


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 72/237 (30%), Positives = 126/237 (53%), Gaps = 5/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K +A  G+ASRR+++  I + ++ VNGIL       V + D I V+G  
Sbjct: 1   MEEN--KIRINKFLASKGVASRRQIDLWIEEGKILVNGILATS-GQKVSAEDKILVNGKM 57

Query: 67  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +  K E+   ++ +K   +++   D  GR TV D +P+  +R+  VGRLD  T GL+LLT
Sbjct: 58  ISEKEEKKVYYILYKEEEVLSAVKDERGRKTVVDCIPTK-ARIFPVGRLDYRTSGLILLT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   +  P  +  + Y V   G + +++L  L++G+ ++     +  V     +  
Sbjct: 117 NDGELFNRVMHPRAEIFKTYEVLAKGHLTREQLKTLEEGVELEEGKTLEALVAKVKYEKG 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           N +  + +REG+NR+I+++ E    +V RL R   G   L  L  G  R + ++ + 
Sbjct: 177 NTFFEISIREGRNRQIRRMVEAVGSRVYRLRRTKIGRLSLEGLKLGQYRRLQEEEIE 233


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 130/253 (51%), Gaps = 20/253 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             F   R++K ++     SRRE +++I + +++VN  ++   A  V STD +E+ G  L 
Sbjct: 15  PKFELIRLNKFLSHNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEI-GKKLI 73

Query: 69  KAERTRLW---LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           K E+ +L+   +Y+KP G + +  DP GR T++D L   +   +SVGRLD ++EGLLLL+
Sbjct: 74  KEEKNKLYTVIVYNKPKGEIVSKKDPQGRKTIYDGLEHKYKHFLSVGRLDYSSEGLLLLS 133

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT---- 178
           +   +   L    +   RVY+++ +G +       ++ GI I+      Y   ++     
Sbjct: 134 DSVDIVNALMH--SDLERVYKIKLNGVITPAVEQAMQSGITIEDATSGAYKGTKIKSMSF 191

Query: 179 -------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  + T    ++ + V + EGKNRE+++ F  FN  V  L R+ YG   L  L  G
Sbjct: 192 APFLAYDIQTNGTKHSKIKVVINEGKNRELRRFFAHFNLDVLDLKRLEYGGISLNNLPTG 251

Query: 232 STREVSKKILREQ 244
            +R ++K+  +  
Sbjct: 252 KSRYLTKEEYKNL 264


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 110/238 (46%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRR+ +R+I ++RV VNG+     AV V   D + VDG PLR  E   
Sbjct: 4   RLNKYIAETGFCSRRQADRLIGERRVTVNGVPAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               +      +KP+G+  T       + V         R+  +GRLD  +EGL+L+T++
Sbjct: 63  LGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +  
Sbjct: 121 GNIVNEILRAENRHKKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 177 GFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>gi|217974432|ref|YP_002359183.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499567|gb|ACK47760.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 235

 Score =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V    HI++D   + +A    
Sbjct: 7   RLDRYLCTQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSHIQLD-EQILQANAPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKPIG+V+   D   + TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YVMLHKPIGVVSATKDIQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V
Sbjct: 125 LMSPTHKVDKVYRVTLANPITEEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 181 TLHEGKYHQIKRMFGRFRNPVVGLHRLSIGDIVLDEKLAPGESRALTAAEV 231


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 109/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P ++  +VY V     +D+       +G+    +GI     Q+TL   + +     
Sbjct: 120 RLTQPQSKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGITTQPAQLTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALLLDPDLRPGSYRALNAGEI 227


>gi|330937693|gb|EGH41591.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 230

 Score =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 108/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVGEFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPDLCPGSYRALNAGEI 227


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 96/233 (41%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNG+  E     V +   + +VDG       R  
Sbjct: 10  LYRILQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDTQVDTAGLVLDVDGERWAYHARA- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G   +   P    +V+  LP+      V  VGRLD +T GLLLLT+DG    
Sbjct: 69  YLMLHKPAGFECSQK-PRHHPSVYTLLPAPLRERGVQCVGRLDQDTTGLLLLTDDGQFVH 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  Q  +VY +     V   ++  L +G+++            +     +  + + 
Sbjct: 128 TLTSPRHQVPKVYEITTAEPVTDAQVAQLCQGVLLDDEDVSVAAAWAERVDALH--LRMA 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           L +GK  ++K++       V  L R + G   L   L  G  R + +  L   
Sbjct: 186 LTQGKYHQVKRMVAAAGNHVAALHRSAIGALTLDAGLAPGQWRWLERDDLTAL 238


>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 =  229 bits (585), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 93/240 (38%), Positives = 156/240 (65%), Gaps = 9/240 (3%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ + + ++    +R+SK ++R+G+ SRR+ E+MI    +KV+G +     + V   ++I
Sbjct: 163 IQYERLRKQVMNEERLSKYLSRSGVCSRRQAEKMIKDGLIKVDGKVATS-NLPVTPKNNI 221

Query: 61  EV---DGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----FSRVISVG 112
           E+    G      ++  ++W+++KP G++ +H DP  R +VF+ + +        +I+VG
Sbjct: 222 EIFTQRGEKFAPVKQNAKIWIFYKPRGMICSHDDPLKRPSVFNYIYNNTKIKEPHIIAVG 281

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD N+EGL+LLTNDG +A+ LE P +   R YRVR  G++D+ KL  L++G VI G+ Y
Sbjct: 282 RLDYNSEGLILLTNDGDIAQCLEQPESNIYRQYRVRVQGELDERKLLKLRQGTVINGVQY 341

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           G   V +D ++ SN W+TVGL  GKNREI+KV + F+ +V+RL R+SYGP+++G++L G 
Sbjct: 342 GPFNVEIDKRQSSNTWLTVGLYTGKNREIRKVMQKFDLRVSRLKRLSYGPYKIGSMLPGQ 401


>gi|119897119|ref|YP_932332.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669532|emb|CAL93445.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 500

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 110/247 (44%), Gaps = 18/247 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E  +  R+SKV+A  GI SRRE + +I +  V V+G  +      +     + +     +
Sbjct: 257 EAPSGVRLSKVMADRGICSRREADELIERGWVFVDGRRVSELGTRIDPDARVVLAPEAKK 316

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTV--------FD------NLPSIFSRVISVGRL 114
              +    L HKP+G V+   +P     V        FD        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 AKVEWINED----QLRFVLKEGRKRQIRRMCELVGLRVVGLKRVRIGRVKLGDLPLGEWR 492

Query: 235 EVSKKIL 241
            +    +
Sbjct: 493 YLRDDEV 499


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 60/209 (28%), Positives = 109/209 (52%), Gaps = 3/209 (1%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            I+   V VNG ++      V  TD +  DG  L  +E+    L +KP G +TT +D  G
Sbjct: 2   YISAGNVTVNGEVMTTLGYRVKPTDEVRFDGKLLS-SEKKEYILLNKPKGFITTTNDEKG 60

Query: 94  RSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           R TV D + +   +R++ VGRLD  T GLLLLTNDG L + L  P+    ++Y V    +
Sbjct: 61  RKTVMDLVANATNARILPVGRLDRATTGLLLLTNDGELTKKLTHPTHGVRKIYHVILDRK 120

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           ++      +++G+ ++       +++   QK  N  + + +  G+NR ++++FE   ++V
Sbjct: 121 LEYKDFIAIEQGLELEDGFIQVDEISYVDQKPKN-EIGIKIHSGRNRIVRRIFEHLGYQV 179

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           ++L R+ +       L  G  R ++++ +
Sbjct: 180 DKLDRVVFAGLTKKDLPRGHWRRLTQQEV 208


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 104/233 (44%), Gaps = 5/233 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  ++S++++     SR++   +IA  +V VN +    A  +V     + V+G  L++
Sbjct: 12  TMSAMKLSRIVSNQPDISRKQANWLIATGQVYVNDLSCRTADADVDEFAAVSVNGKTLQQ 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
                  + HKP G ++   D D   TV   LP   S+ +   GRLD  T GL++LTN+G
Sbjct: 72  GHCAHYIMLHKPAGYLSATED-DTHPTVLQLLPPGLSQCLHIAGRLDRATTGLMILTNNG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +R L LP     +VYRV     +  D      +GI  +         TL+  +     
Sbjct: 131 TWSRQLTLPGMGIAKVYRVTTAYPIGPDTPQRFAEGIWFEYEQLTTAPATLELLEP--TL 188

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
             + + EG+  ++K++F     +V  L R   G  QL   L  G+ R ++   
Sbjct: 189 ARLTIYEGRYHQVKRMFHAVGNRVIALHREQIGHLQLNSDLAEGNFRMLTGSE 241


>gi|166711386|ref|ZP_02242593.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 240

 Score =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 110/238 (46%), Gaps = 14/238 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R++K IA  G  SRR+ +R+I ++RV VNG+     AV V   D + VDG PLR  E   
Sbjct: 4   RLNKYIAETGFCSRRQADRLIGERRVTVNGVSAGTGAV-VGEEDTVLVDGQPLRVREAKK 62

Query: 72  ----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
               R      +KP+G+  T       + V         R+  +GRLD  +EGL+L+T++
Sbjct: 63  LGGRRHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKESEGLILMTSN 120

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +  
Sbjct: 121 GNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIAKF 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 177 GFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 110/245 (44%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G+++       +    I ++     + 
Sbjct: 1   MEKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARALPDQVITLERAAAARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
                 L HKP+G V+  ++      V           D  P  F R     +   GRLD
Sbjct: 61  TARVTILLHKPVGYVSGQAEKGYTPAVALIDARSRYAGDRAPQRFERGQLQGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    +V  L R+  G   LG L AG  R 
Sbjct: 181 QVRWQNAD----QLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPAGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRADE 241


>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 =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 100/235 (42%), Gaps = 12/235 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAERT 73
           + +++   G  +RR    ++A   V+VNG L E         D   + VDG       + 
Sbjct: 5   LDRILQSQGFGTRRYCGDLVAAGLVEVNGELCEDPGAR-FEVDGLRLMVDGEEWLACTKA 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG   
Sbjct: 64  YV-MLNKPTGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFI 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVT 190
                P  Q  ++Y V     V  +++  L+ G+ +         +  D  + +    + 
Sbjct: 122 HAQTSPKKQVPKIYEVTTFDPVTPEQVEALRTGVKLDDE---PAPIAADACEATGERSLR 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           + L +GK  ++K++       V  L R + G   L   L  G  R ++ + L   
Sbjct: 179 LTLLQGKYHQVKRMVAAVGNHVTALHRSAIGGLVLDPALGPGEWRWLTPEDLAAL 233


>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 =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 112/240 (46%), Gaps = 14/240 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR+ E 
Sbjct: 2   TIRLNKYIAETGSCSRREADRLIGERRVTVNGMPAGTGAV-VGEEDTVLVDGQPLRRREA 60

Query: 72  ------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 +      +KP+G+  T       + V         R+  +GRLD ++EGL+L+T
Sbjct: 61  KRLGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +
Sbjct: 119 SNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRRMARGVRIHNETTLPCR----TARIA 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 175 KFGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 60/252 (23%), Positives = 119/252 (47%), Gaps = 10/252 (3%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +  + QR++K +  AG+ SRRE +  I   +V ++G         V+    + V+G  +
Sbjct: 18  ADPASGQRLNKFLTNAGVCSRREADHRIRAGQVTIDGQTA-ELGQRVLPGQRVAVNGRII 76

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              E   + L+HKP G+V T    +  + V  +     SRV  VGRLD  + GL+L+TN 
Sbjct: 77  EGKEEEIILLFHKPRGIVCTAEKREKNNIV--DFIGYPSRVYPVGRLDKESRGLILMTNQ 134

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGS 185
           G +   +   + +  + Y+V  +  + +  +  ++ GI ++  G      Q+     +  
Sbjct: 135 GDIVNRMMRAANRHEKEYQVTVNRGISETFVRRMRAGIYLKELGETTRPCQI----HQTG 190

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +   T+ L +G NR+I+++     ++V  L+R+     +L  +  G  R++ ++  RE+L
Sbjct: 191 DRTFTIILTQGLNRQIRRMCHTLGYEVTDLLRVRIMNLRLDGIPEGEYRKIGRRE-REEL 249

Query: 246 GPHLLEEAQVNL 257
              L     ++ 
Sbjct: 250 NRLLAASPSISR 261


>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 =  229 bits (584), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 109/253 (43%), Gaps = 25/253 (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
              ++++KP G VT   D +   TVFD      + V  VGRLD +TEGLLLLTNDG    
Sbjct: 61  -VYYMFNKPAGCVTATRD-NVHKTVFDYFHEDMNGVFHVGRLDKDTEGLLLLTNDGEFEH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------- 183
            +  P     + Y     G  D +    L++GI I           +D  K         
Sbjct: 119 KVMYPEKHVEKTYFFWALGSFDDEDKKQLEEGIFIGNNESLTKPAKIDVHKSGLYKEFKE 178

Query: 184 --------GSNAWV----TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                     +  +     + + EG+  ++K++ +     V  L RIS G  +L  +L  
Sbjct: 179 EIPIKNLENKDHQLVVSGYLTISEGQKHQVKRMLKAVGCYVIYLKRISIGGLKLDESLKM 238

Query: 231 GSTREVSKKILRE 243
           G  R+++KK +  
Sbjct: 239 GDYRDLTKKEIER 251


>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 =  229 bits (584), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 69/244 (28%), Positives = 109/244 (44%), Gaps = 22/244 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST------------DHIE 61
            R++K +A  G  SRR   R+I    V+++    ER A +V S             + I 
Sbjct: 1   MRLAKYLALTGCCSRRAATRLIRDGLVRID----ERLANHVDSVTLIDTPIGQRSIEQIY 56

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           V+  P+R  E    WL++K +G  +         ++   LP    R+  VGRLD ++ GL
Sbjct: 57  VNDEPIRVVEAKAYWLFNKAVGTDSRLLAHLPN-SLLHLLPES-PRLYPVGRLDKDSRGL 114

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+LTNDG L   L  P     + Y V+     D   L  +  G+  + +           
Sbjct: 115 LILTNDGELTHKLMHPDFGHAKTYHVQVDRPFDDAFLVNMAAGVSYKDVVTLPC----IM 170

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           Q+ +     + L +G NR+I+++ +   +KV  L R+S    QLG L  GS R +S   L
Sbjct: 171 QRLAADKYEITLTQGLNRQIRRMSQALGFKVIDLKRVSIQSLQLGDLPEGSMRPLSSAEL 230

Query: 242 REQL 245
            + L
Sbjct: 231 ADLL 234


>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 =  228 bits (583), Expect = 7e-58,   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  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------------DNLPSIFSRVISVGR 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 PAWVKQLNED----QLHIILKEGKKRQIRRMCELVGLQVIGLKRVRIGRIRLGDLPMGQW 370

Query: 234 REVSKKI 240
           R +    
Sbjct: 371 RFLRADE 377


>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 =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 106/239 (44%), Gaps = 14/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--------VNVMSTDHIEVDGV 65
            R+++ +A  G  SRR   R+I   RV +   L +               ++  + VDG 
Sbjct: 1   MRLAQYLALTGRCSRRAASRLIRNGRVSLGDRLAKHTDSIELIETPTGTQASLSVCVDGE 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           PL        W+++K +G        D  +++   LP    R+  VGRLD ++ GLLLLT
Sbjct: 61  PLPPIADKAYWIFNKAVGTDCRLLAED-TTSLIHLLPRQ-PRLYPVGRLDKDSRGLLLLT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L + L  PS    + Y VR     D D +  +  G+  + +     QVT   Q   
Sbjct: 119 NDGELTQRLMHPSFAHHKRYHVRLDRPFDDDFVVKMAAGVSYKDVTTQPCQVTRLGQDS- 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
                + L +G NR+I+++ +    KV  L R++     LG L  G  R +++  L E 
Sbjct: 178 ---FEIVLTQGLNRQIRRMSKTLGHKVIDLKRVAIESLTLGDLPEGEMRPLTQAELDEL 233


>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 =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 77/240 (32%), Positives = 129/240 (53%), 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
            +  + R    +KP+G+V+T     GR  + +    I  R+   GRLD  + G++++TND
Sbjct: 64  ERQTK-RYMALYKPLGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 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|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 =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 108/234 (46%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ + +   GI SR E+++ +   RVK+NG   + +   V    D I  D   +   E 
Sbjct: 3   IRIDRFLCHMGIGSRSEIKKYLKTCRVKLNGKFEKNSNTQVDIEKDEILFDDEIVIYKEF 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           T   + +KP   ++   D     TV D L   +S   +  VGRLDI+T G L+LTNDG  
Sbjct: 63  T-YLMLNKPKDFISATFDTK-LPTVLDLLEFPYSNMELFPVGRLDIDTTGFLILTNDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P  +  + Y V    ++  +++  L+ GI  +   +      ++  K S   + 
Sbjct: 121 SYNVTNPKKKVNKKYFVTLRDEIISEQIEKLENGIYFEKEDFTTENAKVE--KISEKEIN 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILRE 243
           + + EGK  ++K++ E+   +V  L ++  G   L   L  G  RE++   L E
Sbjct: 179 LTISEGKFHQVKRMLEYVENEVVELKKVCIGNLNLDDSLKLGEYREITNSELEE 232


>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 =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 111/250 (44%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +  ++    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MEHDSNETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNRQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVIS 110
              K       L +KP+G V+  ++                +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 KLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGKLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 69/269 (25%), Positives = 103/269 (38%), Gaps = 48/269 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  +    VKVNG +       V   D IEVD     +     
Sbjct: 37  RLNKRMAELGLCSRREADAWVENGWVKVNGRVA-EMGQQVSPADRIEVDPQAQNQQATQV 95

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIF-----SRVISVGRLDINTE 119
             L HKPIG V+  ++      V           D  P  F       +   GRLDI++ 
Sbjct: 96  TILLHKPIGYVSGQAEDGHEPAVVLVQAQNRWREDRAPHRFNGGQLRGLAPAGRLDIDST 155

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRV----------------------------RFHG 151
           GLL+LT DG +AR L    ++  + Y V                                
Sbjct: 156 GLLVLTQDGRVARQLIGEDSEIEKEYLVRVVYLGTPAAASAPTELQPIHANDPVSANVQA 215

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 L  L+ G+ + G      +V  +    +   +   L+EGK R+I+++ E    K
Sbjct: 216 VFPPAMLAKLRHGLSLDGQALKPARVDWE----NTEQLRFVLKEGKKRQIRRMCELVGLK 271

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           V  L R+  G   LG L  G  R ++   
Sbjct: 272 VVGLKRVRIGRVMLGQLPQGQWRYLAPHE 300


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 113/250 (45%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDSETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNKQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVI----------S 110
              K       L +KP+G V+  ++   +S     T  ++     SR+            
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 KLRPAKVEWQNED----QLRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRTDE 245


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 63/238 (26%), Positives = 108/238 (45%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K +A     +R EV+ ++  +RV VNG+        +   +D + +D   L   + 
Sbjct: 1   MRLDKFLAECNQGTRSEVKVLLKSKRVTVNGVTENSGKRQINEVSDVVCLDEKKLTY-QS 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP  ++T   D   + TV D +        +  VGRLD +T GL+LLTNDG L
Sbjct: 60  FAYYMLNKPKDVITATED-SVQKTVLDLIDKKDRIKGLFPVGRLDKDTTGLVLLTNDGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGD--MQVTLDTQKGSNA 187
           A  L  P     +VY  +  G V + ++ L  K I ++ G       + V    +    +
Sbjct: 119 AHNLLAPKKHVEKVYEAKIEGIVTEAEVELFSKPIELKNGEVTKPSRLVVKKADEDAGMS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + + + EGK  +IK++F      V  L R+  G  +L   L  G  R +++  + E 
Sbjct: 179 EIEITISEGKYHQIKRMFASTGMHVLELKRLKMGSLELDDRLDPGKYRALTQTEIEEL 236


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 106/241 (43%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVSDLKKQFAPENFEFSVFGQNYQYREKI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP       V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L+        +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLIQGVNLHQEKGVFAATDVALLE-----THQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEDGDWVYLSEQE--KQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>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 =  228 bits (583), Expect = 8e-58,   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 ITSPKKECGKRYLLETADPLTEELIGKFATGLQLNNEDGLTKPAKLELLG----THQARL 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + EGK  ++K++      KV +L R   G  +L  +L  G  R +++  ++
Sbjct: 176 TITEGKYHQVKRMLAAVGNKVTKLHREVVGEIELDSSLELGQWRFLTEAEIK 227


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 67/226 (29%), Positives = 112/226 (49%), 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 T  D   R  V D +     ++  VGRLD +T G+LLLTNDG L+ +L  
Sbjct: 61  VLNKPKNTVCTLKDNFNRVKVTDLI-DTDKKIFPVGRLDYDTTGVLLLTNDGKLSNLLTH 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           PS++  R+YR R    +   ++ +L K ++I          T +          V L +G
Sbjct: 120 PSSEIKRIYRARISAPLTDKEMEILSKPVIINNQRS-----TQEIYPADTKSYYVVLHQG 174

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               +KK+FE  + KV  L R+ +    +  +  G  R ++   L+
Sbjct: 175 SYHHVKKLFELVDKKVLDLNRVEFANITVKNMQKGQYRRLTLHELK 220


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 67/235 (28%), Positives = 119/235 (50%), Gaps = 10/235 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAERT 73
           RV K+++  G  SR E++R +   +V++N   +++    +    D +  DG  +   E  
Sbjct: 7   RVDKILSELGFGSRTEIKRYVKAGKVRINENPVKKPEEKINTEIDRLYFDGKDVVIEEFE 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              LY KP G V    D +   TV + + S    ++ VGRLD++TEGLL+LTNDG L   
Sbjct: 67  TYVLY-KPAGYVCATFD-NVHKTVMELIDSNRKNIVPVGRLDLDTEGLLILTNDGNLNHR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVG 192
           L  PS+   +VY  +F G +  D + +  KG+ I  G      ++ + ++      V + 
Sbjct: 125 LVSPSSHVDKVYYAKFDGVLADDAIEMTAKGLDIGDGEVSKPAKLEIVSKN----EVLLT 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKILREQL 245
           + EGK  ++K++ +    +V  L R ++G   L    L  G +R++S + +R+ +
Sbjct: 181 IHEGKFHQVKRMIKALGGEVTYLKRTAFGGLGLDDLNLKRGESRKISMEEMRKLI 235


>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 =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 130/253 (51%), Gaps = 20/253 (7%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             F   R++K ++     SRRE +++I + +++VN  ++   A  V STD +E+ G  L 
Sbjct: 15  PKFELIRLNKFLSHNSNYSRREADKLIEEGKIRVNNKVVTDLATKVKSTDKVEI-GKKLI 73

Query: 69  KAERTRLW---LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           K E+ +L+   +Y+KP G + +  DP GR T++D L   +   +SVGRLD ++EGLLLL+
Sbjct: 74  KEEKNKLYTVIVYNKPKGEIVSKKDPQGRKTIYDGLEHKYKHFLSVGRLDYSSEGLLLLS 133

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT---- 178
           +   +   L    +   RVY+++ +G +       ++ GI I+      Y   ++     
Sbjct: 134 DSVDIVNALMH--SDLERVYKIKLNGLITPAVEQAMQSGITIEDATSGAYKGTKIKSMSF 191

Query: 179 -------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  + T    ++ + V + EGKNRE+++ F  FN  V  L R+ YG   L  L  G
Sbjct: 192 APFLAYDIQTNGTKHSKIKVVINEGKNRELRRFFAHFNLDVLDLKRLEYGGISLNNLPTG 251

Query: 232 STREVSKKILREQ 244
            +R ++K+  +  
Sbjct: 252 KSRYLTKEEYKNL 264


>gi|325524840|gb|EGD02796.1| ribosomal small subunit pseudouridine synthase A [Burkholderia sp.
           TJI49]
          Length = 238

 Score =  228 bits (583), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 96/236 (40%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G           +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIDAGRVAIAGAPATDPDARFDTDGLVFTVDGTPWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G       V  D +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRTGVQLHGEPRPIAAVAADAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R   G F L   L  G+ R +    L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRERIGGFTLPDDLAPGAWRWLDDADLSALRNP 234


>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 =  228 bits (583), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 89/238 (37%), Positives = 140/238 (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 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           N W+ + L+EGKNREI+++    + +VN+L R+ +GPF++  L  G  +    K +R+
Sbjct: 181 NFWIEMELKEGKNREIRELMRSIDLRVNKLTRLEFGPFKISNLKPGEIKTAEPKEIRQ 238


>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 =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 61/215 (28%), Positives = 103/215 (47%), Gaps = 7/215 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+EV++++    VK++GI ++ A V+V      + + G  +   E 
Sbjct: 1   MRLDKLLANMGYGSRKEVKKLLKDGVVKIDGISVKDAKVHVNVEEQEVMIHGEVVEYKE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG L
Sbjct: 60  FVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFNPFPVGRLDIDTEGFLLITNDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + Y     G V ++ +    KG+++  G       +T+  +    + +
Sbjct: 119 SHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGALTIL-KSDDISEI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
            + + EGK  ++K++FE    K + L     G   
Sbjct: 178 ELVITEGKFHQVKRMFEAVGEKSSLLKENRDGTVS 212


>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 =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 126/237 (53%), Gaps = 5/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K +A  G+ASRR+++  I + ++ VNGIL       V + D I V+G  
Sbjct: 1   MEEN--KIRINKFLASKGVASRRQIDLWIEEGKILVNGILATS-GQKVSAEDKILVNGKM 57

Query: 67  L-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +  K E+   ++ +K   +++   D  GR TV D +P+  +R+  VGRLD  T GL+LLT
Sbjct: 58  ISEKEEKKVYYILYKEEEVLSAVKDERGRKTVVDCIPTK-ARIFPVGRLDYRTSGLILLT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   +  P  +  + Y V   G + +++L  L++G+ ++     +  V     +  
Sbjct: 117 NDGELFNRVMHPRAEIFKTYEVLAKGHLTREQLKTLEEGVELEEGKTLEALVAKVKYEKG 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           N +  + +REG+NR+I+++ E    +V +L R   G   L  L  G  R + ++ + 
Sbjct: 177 NTFFEISIREGRNRQIRRMVEAVGSRVYQLRRTKIGRLSLEGLKLGQYRRLQEEEIE 233


>gi|193077698|gb|ABO12547.2| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 234

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 103/238 (43%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP       V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V  +  V  +++ +L +G+ +     G      D        +T+ 
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGGFA--ATDVALLGTHQLTMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  +++
Sbjct: 179 IHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE--KQLAQNII 234


>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 =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 112/240 (46%), Gaps = 14/240 (5%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE- 71
             R++K IA  G  SRRE +R+I ++RV VNG+     AV V   D + VDG PLR+ E 
Sbjct: 2   TIRLNKYIAETGSCSRREADRLIGERRVTVNGMPAGTGAV-VGEEDTVLVDGQPLRRREA 60

Query: 72  ------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
                 +      +KP+G+  T       + V         R+  +GRLD ++EGL+L+T
Sbjct: 61  KRLGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKDSEGLILMT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +
Sbjct: 119 SNGNIVNEILRAENRHQKEYLVAVNKPVTDEFLRGMARGVRIHNETTLPCR----TARIA 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F ++V +L R+     +L  L  G  R +S   LR  L
Sbjct: 175 KFGFRIVLEQGLNRQIRLMAAEFGYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELRGLL 234


>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 =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 108/233 (46%), Gaps = 6/233 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
           T  R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +   
Sbjct: 15  TNMRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP 74

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDG 128
            +    + +KP G+V+   D     T+ D L        +  VGRLD +TEGL+LLT++G
Sbjct: 75  -KHSYIILNKPSGVVSAKKDT-NYLTIIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNG 132

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            L   +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +
Sbjct: 133 PLGFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQS 192

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++  
Sbjct: 193 QASLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTESE 245


>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 =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/222 (30%), Positives = 115/222 (51%), Gaps = 6/222 (2%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIG 83
           + SRRE++++I  + V ++GI     + NV +T   I V+G  +   +  + ++ +KP G
Sbjct: 5   VLSRREMKKLIKNEAVLIDGIPATHVSNNVDATLQVITVNGTRIH-DDSQKYYMLNKPQG 63

Query: 84  LVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           L++  +D +  +TV D   +     +  +GRLD +TEGLLL+TN+G L   +  P     
Sbjct: 64  LISATTDKEH-TTVIDLFANENVEGLYPLGRLDGDTEGLLLVTNNGPLGYRMLNPDQHIE 122

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           + Y V  +G +D D +   K+G+   G        +T+     +    TV + EGK  ++
Sbjct: 123 KEYYVEVNGPLDNDAVETFKRGVTFHGGYQCKPSMLTIIESSDNLGRATVTISEGKFHQV 182

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           KK+F     KV  L RI +G F L  +L  G  RE+++  L+
Sbjct: 183 KKMFLCVGVKVTYLKRIRFGEFVLDESLAPGEYRELNEAELQ 224


>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 =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 59/229 (25%), Positives = 109/229 (47%), Gaps = 9/229 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++ A + SR+EV+R+I    VK+NG ++      V   D + V+  P+      
Sbjct: 1   MRLDKFLSNAKVGSRKEVKRLIKFGIVKINGEIITNVDFKVKENDIVTVNNTPITPYHN- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              +++KP G  ++ S+ +     F + P     +   GRLD + EGLLL+TNDG     
Sbjct: 60  VYIIFNKPTGYTSSKSEFERNIFEFIDHP-YVENLHIAGRLDKDVEGLLLITNDGIFTHK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVG 192
           +  P ++  + Y V+   ++  + +   K GIV++ G  +         ++  + ++++ 
Sbjct: 119 ITSPKSKIEKEYIVKVDKEISDEMIQKAKDGIVLKNGTRFKPA----IIKRLKDNFISIT 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKK 239
           + EGK  EIK + +F      ++ RI  G  +L    L  G   E+  K
Sbjct: 175 ITEGKYHEIKLIVKFLGLSYKKIERIRIGKLKLEDFNLKRGEWSEIDYK 223


>gi|170720236|ref|YP_001747924.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169758239|gb|ACA71555.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 233

 Score =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/230 (28%), Positives = 107/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++V  ++ Q+RV+V+G  +      V     IEVD   L+     
Sbjct: 1   MRLDRFLANLPSYNRQQVRLLLVQRRVRVDGETVADPRAEVREFSRIEVDDQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP+G V+   D   R TV D LP      +   GRLD NT GL++LTNDG  +R
Sbjct: 61  RYLMLHKPVGCVSATHDSQHR-TVLDLLPEPLRADLHIAGRLDYNTTGLMILTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+T+  + Y V    ++    +   + G          +   LD      A + + 
Sbjct: 120 RLTQPATKLPKHYLVETEDEIGAHYIEKFRAGFYFAFEDLTTLPAQLDILGPRTARLAII 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             EG+  ++K++F +F+ KV  L R + G  QL   L  G  R ++   +
Sbjct: 180 --EGRYHQVKRMFGYFDNKVVGLHRETMGAIQLDPGLAPGEFRALTAAEI 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 =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 113/250 (45%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDSETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNKQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVI----------S 110
              K       L +KP+G V+  ++   +S     T  ++     SR+            
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 KLRPAKVEWQNED----QLRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>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 =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 93/229 (40%), Gaps = 4/229 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K I  +   +R   ++ + +  V  +G +++ +   V     I +DG  L      R
Sbjct: 28  RLDKFICESTSLTRSLAKKAMHRGDVTCDGEIIKNSGFKVTDAHTICLDGEVLSII-GPR 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP+  + +  D +  S +          +   GRLD +T GL+L+TNDG  +  +
Sbjct: 87  FIMINKPVDTICSTIDEEYPSVLGLIDVIKPEELHIAGRLDADTTGLVLITNDGQWSHKI 146

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  + Y +     +    +     G+ +           LD      A   + + 
Sbjct: 147 TSPKKECGKRYLLETAEPLADSLVEQFATGLQLNNEDGLTKPAILDILGAHEA--RLTIT 204

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           EGK  ++K++      +V RL R   G  +L   L  G  R ++ + ++
Sbjct: 205 EGKYHQVKRMLAAVGNRVTRLHRECVGTIELDADLDLGEWRYLTDEEIK 253


>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 =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 63/217 (29%), Positives = 107/217 (49%), Gaps = 7/217 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K IA AG+ SR++  R+I +  V VN         +V   D I V+G  ++ A 
Sbjct: 3   TKIRLAKYIAHAGVCSRKQASRLIDEGVVTVNNRPANHID-HVDEQDDIIVNGQVVKGAA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + YHKP+G+    ++ D  +++  +LP   +RV  +GRLD ++ GLL+LTNDG   
Sbjct: 62  DLVYFAYHKPVGIDCKLNEND-PASLIHHLP-TLTRVYPIGRLDKDSRGLLILTNDGDFC 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     ++      +  GI +        +VT    K ++   ++
Sbjct: 120 NQLIHPDFHQPKRYLVTVDKPINNAFCEKMAAGIPVDKQITLPCEVT----KIADNQFSI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            L++G NR+I+K+  +  +KV  L R+ +    L  L
Sbjct: 176 ILKQGLNRQIRKMAHYCGFKVIDLFRVQFSELALSNL 212


>gi|239501492|ref|ZP_04660802.1| hypothetical protein AbauAB_04211 [Acinetobacter baumannii AB900]
          Length = 234

 Score =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 105/241 (43%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVGDLKKQFSPENFEFSVFGQNYQYREKI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP       V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L         +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALL-----GTHQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE--KQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>gi|144575100|gb|AAZ43829.2| 16S rRNA uridine-516 pseudouridylate synthase and related
           Pseudouridylate synthase [Mycoplasma synoviae 53]
          Length = 234

 Score =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 115/232 (49%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K IA + + +R E++++I++  VKVN ++++++       D I ++G+ L   E  
Sbjct: 3   IRIEKFIADSTLYTRNEIKKLISKGLVKVNDLIIKKSQSIDPKLDKIYLEGILLEAREEF 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + +KP G +  + D   +  VF+    L        ++GRLDI+TEGLL++TNDG L
Sbjct: 63  SYIMMNKPAGYICANFD-WNKQVVFELLLDLEMNLKDFFTIGRLDIDTEGLLIITNDGKL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P     + Y V     ++++   LL+K ++I  I Y            SN    
Sbjct: 122 SHNLLSPKKHIPKTYYVELDKPLEKNIKELLEKELLIDEIKYK----KSILNNISNNKWE 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  +IK +F  F +KV  L RI      L   L  G  + ++K+ L
Sbjct: 178 ITIFEGKFHQIKIIFAHFGYKVTYLKRIKMNNLSLDENLKPGEYKFLTKEEL 229


>gi|327479891|gb|AEA83201.1| pseudouridylate synthase [Pseudomonas stutzeri DSM 4166]
          Length = 230

 Score =  228 bits (582), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 111/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      SR++V R+++  R +VNG +       V   D +E+DG  L+  +  
Sbjct: 1   MRLDRYLGSRAQLSRQDVRRLVSDGRARVNGEVTRTLDREVRIFDCVELDGQVLQPGKVA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G V+   D   R TV D +       +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYLMLHKPPGCVSATRDAAHR-TVIDLIDEPDKDDLHIAGRLDFNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P++   +VY V    ++D   +    +G+    + +     ++ L   + +     
Sbjct: 120 RLTQPTSLQGKVYLVETEDEIDPGCVEAFARGLYFRFEDLTTLPAELVLLGPRRA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + L EG+  ++K++F  F  KV  L R S GP  L  +L  G  R ++   + +
Sbjct: 176 LTLHEGRYHQVKRMFGHFGNKVTALHRESMGPLLLDASLSPGCYRPLTDNEIAQ 229


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 119/238 (50%), Gaps = 5/238 (2%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           ++    R  K++A AGI SRR  E  I    V +NG   E  +    + D + ++G  ++
Sbjct: 2   DSPQLIRTQKLLADAGICSRRVAEEYIKNGEVTINGKTAELGSKVDPAIDDVRLNGRRIK 61

Query: 69  KAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLT 125
             +  + +   +KP G + ++ DP    TVFD LP+ +   R+   GRLD ++EGLL+LT
Sbjct: 62  VVKHKQLVIALNKPKGFICSNDDPHNDRTVFDLLPTDYNRERLFCAGRLDKDSEGLLILT 121

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQK 183
           NDG LA  L  PS    + Y V       + K+  L +G+ ++G      +     D  K
Sbjct: 122 NDGDLANRLMHPSNLVTKRYHVSLKQPFPKAKIFRLMRGVTVEGEKLKVEKAVFAGDKNK 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             +  + + +  GK REI+++F+  ++ V +L R   G + +  +  G++  +S + +
Sbjct: 182 AESTELDLAMHHGKKREIRRLFQALHYDVKKLKRYQIGRYSIKGMPKGASIGLSPRDI 239


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 51/209 (24%), Positives = 89/209 (42%), Gaps = 4/209 (1%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
               V V+G + +  A  V     +E +G  +  A   R  + +KP   V +H D     
Sbjct: 15  KSGEVTVDGEVQKSGAFKVPEGGVVEWEGREV-GAPGPRYIMLYKPADFVCSHED-GHNP 72

Query: 96  TVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
           T F  L       +   GRLD++T GL+L+T+DG  +  +  P  +  + YRV     + 
Sbjct: 73  TAFVLLDEPKVENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKCEKTYRVWLVDAIQ 132

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            D +    +GI ++      +   L+    +   V + + EGK  ++K++F     KV  
Sbjct: 133 PDYVEKFAEGIELRNEREATLPAHLEIVNEAENEVLLTIVEGKYHQVKRMFAALGNKVEH 192

Query: 215 LIRISYGPFQLGT-LLAGSTREVSKKILR 242
           L R   G   L   L  G  R ++++ + 
Sbjct: 193 LHRERIGSIVLDEALEPGDYRFLTEEEVE 221


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 112/251 (44%), Gaps = 22/251 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MDNTSEETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNRQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----------------VI 109
              +       L +KP+G V+  ++  G  +  + + +                    + 
Sbjct: 60  AHERQAERVTILLNKPVGYVSAQAE-KGYKSAAELITADNRWESDDSHIPFSEKHKFGLA 118

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
             GRLDI++ GLL+LT DG +A+ L   ++   + Y VR  G++D+  L LL  G+ + G
Sbjct: 119 PAGRLDIDSVGLLVLTQDGRIAKQLIGENSGSEKEYLVRVRGKLDEKGLALLNHGLSLDG 178

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 +V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L 
Sbjct: 179 EKLRPAKVEWQNED----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGKLP 234

Query: 230 AGSTREVSKKI 240
            G  R +    
Sbjct: 235 PGKWRYLRADE 245


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 111/249 (44%), Gaps = 20/249 (8%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       R+SK +A  G+ SRRE +  I +  V VNG         V   D IE+    
Sbjct: 1   MTTPDNTVRLSKRMAELGLCSRREADAYIERGWVSVNGEKA-VLGQKVGEGDRIELHRAA 59

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPS----------IFSRVISV 111
             +       L HKP+G V+  ++   RS     T  ++ P               +   
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 LRPAKVSWQNQD----QLRFVLKQGKKRQIRRMCELVGLRVVGLKRIRIGKVKLGALPPG 235

Query: 232 STREVSKKI 240
             R ++   
Sbjct: 236 QWRYLAPHE 244


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  + SR+ +++ + ++ + V+       A NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKV-SRKAMKQALLKKEILVDDCPASSLAQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G VT   D     TV D LP      ++ ++GRLD +T GLLLLT++G L
Sbjct: 60  N-YLMLHKPNGAVTASKDKK-LPTVMDLLPPDIQSDQLYAIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K+GIV + G      Q+ + +   S +  
Sbjct: 118 GFQLLHPQYHVNKSYQVVVNGPLTSDHIQSFKEGIVFLDGTTCKPAQLEILSSSPSESHA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ + EGK  +IKK+F     KV  L R+ +G F L   L  G  R ++ + L 
Sbjct: 178 SITISEGKFHQIKKMFLSVGVKVTALKRVQFGDFTLDPELAEGQYRPLNPEELE 231


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 111/234 (47%), Gaps = 11/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQLIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKVVSTTQ- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
                +HKP G VT   D      V D LP  F    V+ VGRLD +TEGLLLLTNDG  
Sbjct: 60  LYYVKFHKPKGYVTAVED-SNHPVVMDLLPLEFIKMGVVPVGRLDKDTEGLLLLTNDGVW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +   +    +VY V F G +  + +  +K+GI++  G      ++   +       V
Sbjct: 119 GHSIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGDGTQCKPAEIEFVSLHS----V 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
            V + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 175 HVTIEEGKYHQVKRMISAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 119/237 (50%), Gaps = 13/237 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT- 73
           R++K IA +G  SRRE +R+IA +RV VN +     +V     D ++VDG PLR   +  
Sbjct: 17  RLNKHIAESGFCSRREADRLIAARRVTVNDLPGGVGSVV-GEGDEVKVDGQPLRARAKHK 75

Query: 74  -----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                     +KP+G+  T ++ + +  + D +     R+  +GRLD ++EGL+L+T++G
Sbjct: 76  GGRHHVYIALNKPVGVTCT-TEREVKGNIVDFV-GHEQRIFPIGRLDKDSEGLILMTSNG 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +   +     +  + Y V  +  V  + L  + +G+ +        +    T + +   
Sbjct: 134 DIVNEILRAENRHQKEYLVAVNKPVTDEFLRGIARGVRVHDQMTLPCR----TARIAKFG 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             + L +G NR+I+ +   F+++V +L R+     +LG L  G  R ++++ LR  L
Sbjct: 190 FRIVLEQGLNRQIRLMAAAFDYRVTQLRRVRIDNIKLGALKPGQWRNLTEQELRGLL 246


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 107/234 (45%), Gaps = 7/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLRK 69
            T  R+S  +A  G+ASRR+  R+I   RV +N  L +    VN    + I VD  P+  
Sbjct: 1   MTSMRLSHYLAVCGVASRRQAARLIDTGRVSINHQLAKHTDRVNFCEIETILVDDKPILA 60

Query: 70  AERTRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +  + WLYHKP+G+       DP     V   LP    R+   GRLD ++ GLLLLTND
Sbjct: 61  VQDKQYWLYHKPVGIDCRLLVDDPHSLLHVLPELP----RLYPAGRLDKDSRGLLLLTND 116

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L + L  P     + Y V+    +    L+++  G+    +      +   +      
Sbjct: 117 GQLTQALMHPDYYHPKTYVVQVDKPISTSFLSMMANGVSYGDVQTRSCDIRPLSLTAEED 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +G NR+I+++ +   +KV  L+R      ++  L   + R ++   L
Sbjct: 177 RFEIVLTQGLNRQIRRMCQTLGYKVIDLMRTQLLDIRIDELAEKTMRPLTAAEL 230


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 108/231 (46%), Gaps = 4/231 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER-T 73
           R+ KV+A+AG+ASRR  E +I Q RV+V+G ++    + V   + +          ++  
Sbjct: 115 RLQKVLAQAGVASRRAAEELIDQGRVEVDGRIVVEQGLRVDPENAVVRVDGVRVVVQKDL 174

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGL 130
                +KP G   T SD  GR  V D +        R+  VGRLD +TEGLLL TNDG L
Sbjct: 175 VYLAMNKPRGWQCTMSDDLGRPCVGDIVSERVQSGQRLFHVGRLDADTEGLLLFTNDGDL 234

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  PS +  + Y    HG V++     L+ G+ +          T+         V 
Sbjct: 235 AHRLMHPSFEVPKTYLATVHGVVERSTGKQLRDGVTLDDGPAKVDAFTVLEINEGKTLVK 294

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + L EG+   ++++ +     V RL+R + G   LG    G+ R + +  +
Sbjct: 295 LVLHEGRKHIVRRLLDAVGHPVVRLVRTNVGVVALGDQRPGTQRVLGRSEV 345


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 105/241 (43%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP       V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L         +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALL-----GTHQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE--KQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 95/238 (39%), Positives = 151/238 (63%), Gaps = 9/238 (3%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +N++Q    P R+SK +A+  + SRRE E+MI    + V+G  +E   + V S + I+V 
Sbjct: 28  QNLIQP--EPMRLSKYLAQTSVCSRREAEKMIESGMILVDGKKVES-NIPVTSENKIQVF 84

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDIN 117
             +G  +   + T++W+++KP+G++ +H+DP  R + +D           +ISVGRLD N
Sbjct: 85  TKNGEKMPTKQSTKVWIFYKPVGMICSHNDPFKRPSFYDFAKLRLKTDQHIISVGRLDFN 144

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +EGL+++TNDG LAR +ELP T+  R+YRVR +G   ++KL  ++ GI I G+ YG   V
Sbjct: 145 SEGLIVVTNDGELARCMELPETKLQRIYRVRVYGTFTEEKLKKIRNGITIAGVNYGPYWV 204

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            ++ ++  N W+ + L +GKNREI+KV + F+ +VNRLIR SYGP++L  L  G   E
Sbjct: 205 NVENRQSRNTWLIMRLEQGKNREIRKVMQKFDLRVNRLIRQSYGPYKLMGLKPGDFYE 262


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 79/258 (30%), Positives = 129/258 (50%), Gaps = 17/258 (6%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQ--------- 182
           L    +   RVY++R  G +  +    +++G+ I  +G      Q  +  +         
Sbjct: 121 LM--KSDLPRVYKLRIKGNITPEIEKAMQEGVEIGVEGAHEKTKQEKIKLKPFYSYQIIK 178

Query: 183 -KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI- 240
                + + V + EGKNRE+++ F  F   V  L R+SYG   L  L  G TR   K+  
Sbjct: 179 NDPKYSTLKVAITEGKNRELRRFFAHFGRDVLDLKRLSYGWVALNALPTGKTRYFDKREY 238

Query: 241 --LREQLGPHLLEEAQVN 256
             L+E L     +    N
Sbjct: 239 KLLKEFLKERDAKAKNKN 256


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 106/241 (43%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V V+G + +         +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSVDGEVADDLKKQFSPENLEFSLFGETYQYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP I     V ++GRLD +T GLLLLT+DG   +
Sbjct: 62  YLALKKPKGFECSHQ-PHHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V     V  +++ +L +G+ +   +GI        L+        +
Sbjct: 121 ALTHPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGIFAATDVAILEM-----HQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV  L R   G   L  L  G    +S++  ++QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDGEWVYLSEE--QKQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>gi|289677892|ref|ZP_06498782.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae FF5]
          Length = 230

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 108/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPGLRPGSYRALNAGEI 227


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 56/235 (23%), Positives = 99/235 (42%), Gaps = 12/235 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAERT 73
           + +++   G  +RR    +IA   V+VNG L E         D   + VDG       + 
Sbjct: 3   LDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQ-FEVDGLRLTVDGEEWLACTKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG   
Sbjct: 62  -YLMLNKPTGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFI 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVT 190
                P  +  ++Y V     V  ++   L  G+ +         +  +  + +    + 
Sbjct: 120 HAQTSPKRKVPKIYEVTTAEPVTPEQAEALCSGVQLLDE---PAPIAAEACEITGERSLR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
           + L +GK  ++K++       V+ L R + G  +L   L  G  R ++ + L   
Sbjct: 177 LTLVQGKYHQVKRMVAAAGNHVSALHRSAIGGLRLDPALAEGEWRWLTAQELAAL 231


>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 =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 100/362 (27%), Positives = 169/362 (46%), Gaps = 16/362 (4%)

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  ER-QRKRYMALYKPLGVVSTTKYLPGRRIITEFFKGIKERLFYAGRLDSESRGIMIITND 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A ++  PS + L+VY V  +G++D +KL    KGI I+ I Y   +  + ++    +
Sbjct: 123 GEFANIITHPSYEILKVYDVTVNGKIDSEKLYEASKGITIKNITYSPFKFKILSKGRVQS 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF-----QLGTLLAGSTREVSKKILR 242
            + + + EGKNREI+K+F++  +KV  L RIS G         GTL AG  R+++KK + 
Sbjct: 183 KIRLTINEGKNREIRKIFDYLGYKVIDLERISVGCVSKYDETSGTLEAGHIRDLTKKEIE 242

Query: 243 ---EQLGPHL--LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
              +Q    L  +E    N+     +         N  S++ +   + +K   + +    
Sbjct: 243 FFFKQKDKKLKDIENIFANVSEYDDNIIDDDYAEDNTYSDISNKTEQDEKKEKKHDKSKW 302

Query: 298 QKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQRE-----ENHRRSPSFPSKRSLRRTSA 352
            K             N + AK   S  L  + ++      EN     +   KRS  +   
Sbjct: 303 AKAKPKKKRLVTKRENTYKAKTNKSKTLKSANKKNNFNSFENKEYKKNDSKKRSFNKERT 362

Query: 353 KK 354
            K
Sbjct: 363 DK 364


>gi|327473408|gb|EGF18828.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK408]
          Length = 241

 Score =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I      +     
Sbjct: 1   MRLGQLLA-ANHISRKKMKQSLLQKQIFVDGKPACKLSQNVDTGLQQITFQSKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGSVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +     +  ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPKDKSSFQEGIRFLDGTTCQPAQLSILSTNSSLSCA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R +++K L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLATGDYRPLNQKEL 230


>gi|330723277|gb|AEC45647.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyorhinis MCLD]
          Length = 242

 Score =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 113/229 (49%), 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
               ++KP  +V T  D   R  + D  P     +  VGRLD NT G++LLTNDG LA  
Sbjct: 62  YY-AFYKPKRVVCTREDNFNRKKIIDFFPKK-EYLFPVGRLDFNTTGIILLTNDGELANK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  R Y V  +G +  +++N   K ++         Q+    +K +     V L
Sbjct: 120 LIHPKFQIERTYLVHTNGDLSDEQINFANKNVIKLNNEINSRQI---IKKKATNKYIVKL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           ++G N  +K++F+ F  +V  L R+ +    L  L  G  R+++ K ++
Sbjct: 177 KQGSNHHVKRLFDHFQIEVLDLKRVQFASINLANLSLGQYRKLTPKEIK 225


>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 =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 108/245 (44%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     + 
Sbjct: 1   MEKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARAFPDQAITLERAAAARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
                 L HKP+G V+  ++      V           D  P  F R     +   GRLD
Sbjct: 61  TARVTILLHKPVGYVSGQAEKGYTPAVALIDARSRYAGDRAPLRFERGQLQGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R 
Sbjct: 181 QVRWQNAD----QLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPVGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRADE 241


>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 =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (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 LARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYGDMQVTL------DTQ 182
             + +  P  +  + Y +     V   K+      G+   G     + V         T 
Sbjct: 121 FIQKVTHPKNKIDKEYIISLKQPVSWKKIAEEFMLGVREGGETLRALAVKPANVFPEKTP 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKI 240
            G  +++++ 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|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 =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 105/241 (43%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP       V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHQ-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V  +  V  +++ +L +G+ +   +G+        L         +
Sbjct: 121 ALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGVFAATDVALL-----GTHQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQE--KQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>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 =  227 bits (580), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 112/234 (47%), Gaps = 11/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKVVSTTQ- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
                +HKP G VT   D      V D LP  F    V+ VGRLD +TEGLLLLTNDG  
Sbjct: 60  LYYVKFHKPKGYVTAVED-SNHPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGVW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +   +    +VY V F G +  + +  +K+GI++  G      ++    +  S   V
Sbjct: 119 GHSIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGDGTQCKPAEI----ESVSLHSV 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
            V + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 175 HVTIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 113/229 (49%), 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
                +KP+G+V T ++ + +  + D L  I   V  +GRLD +++GL++LTNDG LA  
Sbjct: 60  -YIALNKPVGVVCTAAE-EVKDNIIDYL-GIDDYVFPIGRLDKDSQGLIILTNDGDLANE 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +        + Y V        D +  +++G+ I G      ++     + +    ++ L
Sbjct: 117 VLAAENNHEKEYIVTLDQPFYDDFIKKMERGVEILGQVTKPCKLK----RINENTYSIIL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            +G NR+I+++ + F + V +L RI      L  +  G  R ++++ + 
Sbjct: 173 TQGLNRQIRRMSKVFGFNVVKLERIRILNITLEDIEYGKWRYINREEIE 221


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 76/244 (31%), Positives = 125/244 (51%), Gaps = 4/244 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
            ++          R+ KV+A AG+ASRR  E++IA  RV+VNG +++R  V +    D +
Sbjct: 39  SEQKAAPAAEDKVRLQKVLAAAGVASRRMSEKLIAAGRVEVNGKVVDRMGVRIDPNKDVV 98

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDIN 117
            VDGV ++  +    ++++KP G+ +T SD  GR +V + +     +   +  VGRLD  
Sbjct: 99  RVDGVRVQVNDEMHYYIFNKPRGVQSTMSDDMGRPSVGNFIDERLKQGQGLFHVGRLDAQ 158

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           TEGLLLLTNDG LA  L  PS +  + Y     G+  +  ++ LKKGI +         V
Sbjct: 159 TEGLLLLTNDGELANRLMHPSYEVSKTYMATVLGEAKKGLVHELKKGIELDDGIAKADDV 218

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + + L EG+   ++++ +   + V  L+R      QLG    GS R ++
Sbjct: 219 QIVDVWQGKSLIKLELHEGRKHIVRRLLKAAGFPVQALVRTKIHTVQLGDQKPGSVRALN 278

Query: 238 KKIL 241
           +  L
Sbjct: 279 RSEL 282


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 105/238 (44%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G ++          +    V G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP       V +VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           VL  P     +VY V  +  V  +++ +L +G+ +      ++    D        +T+ 
Sbjct: 121 VLTHPRKHVPKVYHVTTYDPVTPEQIEMLIQGVNLH--QEKEVFAATDVALLGTHQLTMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  +++
Sbjct: 179 IHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEDGDWVYLSEQE--KQLAQNII 234


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 124/247 (50%), Gaps = 17/247 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +   PQRV+K +A++G+ SRRE E++I+   V ++G ++E     +     + +    
Sbjct: 6   TYDEAEPQRVNKWLAQSGVCSRREAEQLISDGLVSIDGEVVEDVGRKIQPGQTLVLADRA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-------------LPSIFSRVISVGR 113
             K + T  +L HKP G+V++  DP                      +P     +  VGR
Sbjct: 66  TAKLDGTPTYLIHKPRGVVSSQPDPGQVPAARLLTRANLWGDARGVAIPQSGDLIPPVGR 125

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD ++ GLLLL+ DG +A+ +  P +   + YRV   G++ ++KL LL+ G+ + G    
Sbjct: 126 LDKDSRGLLLLSQDGVVAKAVIGPQSDLEKEYRVAVMGELTEEKLELLRFGLELDGRELR 185

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V +     S+  ++  LREG+NR+I+++ +  + KV  L R+  GP  LG +  G  
Sbjct: 186 PAEVEV----ISDQRLSFVLREGRNRQIRRMCDLVDLKVVDLFRVRIGPLDLGDMPEGRW 241

Query: 234 REVSKKI 240
           R ++   
Sbjct: 242 RPLTSAE 248


>gi|110004423|emb|CAK98761.1| probable ribosomal large subunit pseudouridine synthase b protein
           [Spiroplasma citri]
          Length = 267

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 79/259 (30%), Positives = 123/259 (47%), Gaps = 10/259 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA  G  SRR+ E +I Q RVKVN +++      V   D I  + + + +    
Sbjct: 2   ERLQKVIAAKGYCSRRKAEELIIQGRVKVNNVVVTTLGTKVGKNDQIN-NQILMNENSNK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +K    V+T  DP  R TV   +  I  R+  VGRLD +T GLLLLTNDG    +
Sbjct: 61  IYLMLNKRRNCVSTMYDPQHRKTVLTYVKGISERIYPVGRLDYDTSGLLLLTNDGEFTNI 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT-QKGSN-AWVT 190
           +  PS    + Y V   G + + +L  L  GI I+ GI     Q  L   ++  N + + 
Sbjct: 121 ITHPSHIINKTYHVLLSGYLSKQQLQQLATGIEIEPGIIRSQAQAKLVKYEEVKNVSILL 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           + + E    ++KK+ +    +V +L RI+ G  QL  TL  G  R +  K ++      +
Sbjct: 181 LTIHEVTKHQVKKMIQSLGHEVIKLKRIAIGFLQLDETLKPGEWRYLKPKEIKRFFWNSI 240

Query: 250 -----LEEAQVNLDAPIYS 263
                ++E + N D    S
Sbjct: 241 TLKNKIKERKNNADYISRS 259


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 108/233 (46%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   SR E  ++I  +RV VNG+ +   A  V   +HI +DG  L      
Sbjct: 1   MRLDKFVCKSTPLSRTEAVQVIHHERVLVNGVAIVDEAAQVHENNHIILDGKHLV-PRPF 59

Query: 74  RLWLYHKPIGLVTTH----SDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDG 128
           R  L HKP   ++ +    S      +VFD L     S +  VGRLD +T GLLL T+DG
Sbjct: 60  RYLLLHKPANCLSANISEPSKSTKYPSVFDVLNIDNSSELHLVGRLDADTTGLLLATDDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +  +  P++   +VYRV     +  +  +    GI++QG     +   L+    S   
Sbjct: 120 RWSFTITSPNSDCSKVYRVGLAKPLGPEVADKFLAGILLQGEHELTLPAKLEV--ISPNQ 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L +GK  ++K++F     KV  L R   G   L  +  G  R +++  +
Sbjct: 178 VLLTLTQGKFHQVKRMFAAVGNKVVSLHREKIGAISL-DVPQGQWRALTEAEV 229


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 106/241 (43%), Gaps = 15/241 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            T  R+SK+++  G+ SRRE +  I    V V+GI +            IE+ G   R  
Sbjct: 1   MTLVRISKLLSNQGVCSRREADHFIELGFVYVDGIKVTELGAKANPEQKIELRGEGHRLQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-----------LPSIFSRVISVGRLDINTE 119
           +  +  L +KPIG V+   D     +               L  +  ++   GRLDI++ 
Sbjct: 61  KSKKTILLNKPIGFVSHADDEGKYKSSLSLILKENFFGDEKLDKLSFKLAPAGRLDIDST 120

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +A+ +    ++  + Y VR  G +  + L LLK G+ +         V+ 
Sbjct: 121 GLLVLTEDGVIAKKIIQEDSEIEKEYLVRVSGNLIPNGLKLLKHGLFLDNKPLKKAIVSW 180

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +      +   L+EGK R+I+++ E    KV  L R+  G  +L  L  G  R +   
Sbjct: 181 INED----QLKFILKEGKKRQIRRMCELVGLKVVGLKRVRIGKIRLSNLPIGKWRFLQGN 236

Query: 240 I 240
            
Sbjct: 237 E 237


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 110/233 (47%), Gaps = 5/233 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE-RT 73
           + KV+  A + SRR++   I Q  V +NG   E  +  V    D +  +G P+  +  R 
Sbjct: 11  LVKVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQQDKVTFEGKPVELSRIRR 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGK R ++++F    +++  L R      +LG L  G TRE++   +   
Sbjct: 190 IIHEGKKRIVRRMFAHLGYQIKALKRSRIATLRLGKLEEGKTRELTPGEIAAL 242


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/231 (32%), Positives = 121/231 (52%), 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 +  V    ++ S+    V L 
Sbjct: 123 QRAEEKVEKEYIVTVNRVLKKGEMDDLRKGIVYEGIRYRECIV----EQHSHDRYQVVLH 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|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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 111/234 (47%), Gaps = 11/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDGKVVSTTQ- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
                +HKP G VT   D      V D LP  F    V+ VGRLD +TEGLLLLTNDG  
Sbjct: 60  LYYVKFHKPKGYVTAVED-SNHPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGVW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +   +    ++Y V F G +  + +  +KKGI++  G      ++   +       V
Sbjct: 119 GHSIINGNKHVPKIYYVEFEGTLSDEGIQRIKKGILLGDGTQCKPAEIEFVSLHS----V 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
            V + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 175 HVTIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>gi|187927714|ref|YP_001898201.1| pseudouridine synthase [Ralstonia pickettii 12J]
 gi|187724604|gb|ACD25769.1| pseudouridine synthase [Ralstonia pickettii 12J]
          Length = 248

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 55/232 (23%), Positives = 98/232 (42%), Gaps = 7/232 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V +NG+ +E     V +   + +VDG       R  
Sbjct: 9   LYRILQSQGFGTRRYCKDLVLAGLVFINGVEMESPDALVDTAGLVLDVDGERWAYHARA- 67

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G+  +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 68  YLMLNKPAGVECSQK-PKHHPSVYTLLPVPLRERAVQCVGRLDQDTTGLLLLTDDGQFVH 126

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  Q  +VY +     V + ++  L  G+++              ++     + + 
Sbjct: 127 TITSPRHQVPKVYEITTAEPVTEAQIAQLYAGVLLADENEN--VAAAWAERVDTHHLRMA 184

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L +GK  ++K++       V+ L R + G   LG L  G  R +    L   
Sbjct: 185 LTQGKYHQVKRMVAAAGNHVDGLHRSAIGGLSLGDLAPGEWRWLEAADLEAL 236


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              RVSK+++  G+ SRRE +  I Q  V ++G ++    V       IE+      +  
Sbjct: 3   EKVRVSKLLSELGLCSRREADSYIEQGLVTIDGEVVNELGVRAYRHQKIELQSGAKAQQA 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIF---------------SRVISVGRLD 115
                + +KP+G ++ + D          + P+ +                 +   GRLD
Sbjct: 63  SRITVILNKPVGYISHYDDEQEYQPAASLITPANYFASPLDKGKSPRFNTKGLAPAGRLD 122

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ G+L+LT DG +A++L   ++   + Y VR  G++  + L+ L+ G+ +  +     
Sbjct: 123 IDSTGMLVLTQDGRIAKLLIGENSPIEKEYLVRVAGRLSFEGLDRLRHGLSLDEVELKPA 182

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV+   ++     +   LREG+ R+I+++ E    KV  L R+  G   LG+L  G  R 
Sbjct: 183 QVSWQNEE----QLRFVLREGRKRQIRRMCEIVGLKVLGLKRVRMGRISLGSLPPGQWRY 238

Query: 236 VSKKI 240
           V    
Sbjct: 239 VGPHE 243


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 60/230 (26%), Positives = 108/230 (46%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR++   +I+  R++V+G ++     ++     +E+D   L+     
Sbjct: 1   MRLDRFLSNFSRFSRQDSRLLISAGRLRVDGEIIIDPRFDIRDFQRVELDDELLQAGRSA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R W+ HKP+G+V+     + R TV D L       +   GRLD+NT GLLL+TNDG  +R
Sbjct: 61  RYWMLHKPVGVVSATEHDEHR-TVLDLLDEPDKHELHLAGRLDLNTSGLLLITNDGLWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY V     + ++   +  +G+         +   LD     +A   + 
Sbjct: 120 RITQPQQRKPKVYHVTTEQPITEEYAEVFARGLYFAFEDLTTLPAQLDVLDSHHA--RLT 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           L EG+  ++K++F  F  +V  L R S G   L   L  G  R ++   +
Sbjct: 178 LFEGRYHQVKRMFGHFRNRVVALHRESMGEIVLDPQLAPGQYRALTAAEI 227


>gi|221133423|ref|ZP_03559728.1| pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 226

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 52/225 (23%), Positives = 105/225 (46%), Gaps = 6/225 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++++ + +  +V  +IA+  + VN  + +  +  V   + +      L      
Sbjct: 1   MRLDKYVSKSTVLTAAQVLEVIARGEISVNDSVTDDPSYQVHKNNTVHWLDTRLECR-PF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP  ++ ++ D +   +VF+ +       +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYIMLNKPPNMICSNID-EHYPSVFNLVDIPHQHELHIAGRLDADTTGLVLITDDGSWSY 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VYRV     +  D +  L+KG+++QG     +   +D    +   V + 
Sbjct: 119 RLTHPDNHCPKVYRVCLAKPISDDMIMRLEKGVLLQGESAPTLPAAIDVVGANE--VLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           + +GK  ++K++F     +V  L R + G   L  +  G  R +S
Sbjct: 177 ITQGKFHQVKRMFAAVGNRVKALHREAIGEINL-DVEVGQWRYIS 220


>gi|171910347|ref|ZP_02925817.1| Pseudouridine synthase, Rsu [Verrucomicrobium spinosum DSM 4136]
          Length = 229

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 63/227 (27%), Positives = 115/227 (50%), Gaps = 10/227 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++A  G  +RREV  M+ +  VKV G++ E     V  T  + V G PL       
Sbjct: 6   RLDQLLASLGYGTRREVRNMVDRGLVKVGGVVAEDFDARVDPT-TVTVKGEPLDAP-FGL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
           + ++HKP+G V +H+  +G  T++D LP  +         VGRLD +T G+LLLT+ G L
Sbjct: 64  VAVFHKPVGYVCSHASDEG-PTIYDLLPKRWPFRNPTVTSVGRLDKDTSGILLLTDQGKL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
            +    P ++  +VY V     +++  + +  +G ++++      +   L+     +A  
Sbjct: 123 VQKWTSPKSEMDKVYEVTVDRPLEERLIGVFAEGTLLLESENKPCLPAKLEIVDALHA-- 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + L+EG+  +++++F    W V  L R  +G ++L  L  G  R +
Sbjct: 181 RLTLQEGRYHQVRRMFASQGWHVEALHRSRFGEYELEGLEVGQWRVL 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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 124/247 (50%), Gaps = 17/247 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +   PQRV+K +A++G+ SRRE E++I+   V ++G ++E     +     + +    
Sbjct: 6   TYDEAEPQRVNKWLAQSGVCSRREAEQLISDGLVSIDGEVVEDVGRKIQPGQTLTLADRA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-------------LPSIFSRVISVGR 113
             K +    +L HKP G+V++  DP                      +P     +  +GR
Sbjct: 66  TAKLDAVPTYLVHKPRGVVSSQPDPGQVPAARLLTRANLWGDARGVAIPQSGDLIPPIGR 125

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD ++ GLLLL+ DG +A+ +  P ++  + YRV   G++ ++KL LL+ G+ + G    
Sbjct: 126 LDKDSRGLLLLSQDGVVAKAVIGPQSELEKEYRVAVMGELTEEKLELLRFGLELDGRELR 185

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             +V +     S+  ++  LREG+NR+I+++ E  + KV  L R+  GP  LG +  G  
Sbjct: 186 PAEVEV----ISDQRLSFVLREGRNRQIRRMCELVDLKVVDLFRVRVGPLDLGDMPEGHW 241

Query: 234 REVSKKI 240
           R ++   
Sbjct: 242 RLLTAAE 248


>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 =  227 bits (579), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 108/245 (44%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G+++            I ++     + 
Sbjct: 1   MEKVRISKLMSERGLCSRREADSYIERGWVRVDGVVVSELGARAFPDQAITLERAAAARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
                 L HKP+G V+  ++      V           D  P  F R     +   GRLD
Sbjct: 61  TARVTILLHKPVGYVSGQAEKGYTPAVALIDARSRHAGDRAPLRFERGQLQGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIAKKLIGEDSEVDKEYLVRVQGRLSEAGLALLNHGLSLDGKPLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    +V  L R+  G   LG L  G  R 
Sbjct: 181 QVRWQNAD----QLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVSLGDLPVGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRADE 241


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 113/250 (45%), Gaps = 20/250 (8%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +   +    R+SK +A+ G+ SRRE +  I Q  VKVNG         V   D I+++  
Sbjct: 1   MQNNDSETMRLSKRMAQLGLCSRREADSYIEQGWVKVNGQTA-VLGQKVTERDRIDLNKQ 59

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVI----------S 110
              K       L +KP+G V+  ++   +S     T  ++     SR+            
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 KLRPAKVEWQNED----QLRFILRQGKKRQIRRMCELVGLRVVGLKRIRMGKVKLGRLPP 235

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 236 GKWRYLRADE 245


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 57/206 (27%), Positives = 101/206 (49%), Gaps = 10/206 (4%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-LWLYHKPIGLVTTHSDP-DGRSTVFD 99
           +NG +       V   D + +DG  + K ++ +    +HKP+G+  T +D  DG    + 
Sbjct: 3   INGEVCTH-GTIVTENDIVTIDGKTIEKEDKEKIYIAFHKPVGITCTAADHIDGNIIEYI 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           N P    R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++
Sbjct: 62  NHPE---RIFPVGRLDKASEGLILLTNDGRIANQILHGDHEHEKEYIVTVDKPFTDWFID 118

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            + +G+ I+       +VT    + +++   + L +G NR+I+++   F + V +L R+ 
Sbjct: 119 GMSRGVKIKDGITKQCKVT----RVNSSTFRIILTQGMNRQIRRMSRAFGYTVTKLKRVR 174

Query: 220 YGPFQLGTLLAGSTREVSKKILREQL 245
               +L  L AG  R V+ + L+E L
Sbjct: 175 IMNIKLDGLEAGEWRNVTVQELQELL 200


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 84/281 (29%), Positives = 122/281 (43%), Gaps = 17/281 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K +A AGI SRR  E +IA   V VNG         +    D I V G  +R   + 
Sbjct: 8   RLQKFLADAGICSRRAAETLIADGEVWVNGQPAT-LGQKITPDVDKITVRGKNVRTVAQP 66

Query: 74  RL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
           +L    HKP GLV ++ DP    TVFD LP      R    GRLD ++EGLL+LT DG L
Sbjct: 67  KLTLAMHKPRGLVCSNDDPHNPETVFDLLPREMARHRFFCAGRLDKDSEGLLILTTDGDL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
           A  L  PST  ++ Y V         +L  L +G+ I+G         L     +     
Sbjct: 127 ANRLMHPSTVVVKRYHVVLAEPFPAKRLGALLRGVTIEGERLKVEYAALVNPNAAELSTS 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + V L  GK REI+++F    ++V RL R   G F L  +   + + ++ + +       
Sbjct: 187 LDVHLHHGKKREIRQLFMALGFEVRRLRRYQIGAFPLRGIPVRAMKLLTPREIATLFAQP 246

Query: 249 LLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
            ++ A          + T    RP   + V     +  + S
Sbjct: 247 GIQPA----------ATTRRYGRPQARNAVSQKKLQSSRQS 277


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/231 (29%), Positives = 109/231 (47%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+GI  +   + V    HI  DG  L+ A +  
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLTERVYVDGIPAKALDLLVDEFSHIVFDGQVLQ-ANKPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+G+V+   D + R TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YLMLHKPVGVVSATKDTEHR-TVIDLLDCDARHELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VYRV     + ++ +    +G+    + I     ++T+           V
Sbjct: 125 LMSPDQKVDKVYRVTLANPLSEEYIAAFAQGMYFGFEDITTQPAKLTIL----DTHIAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            LREGK  +IK++F  F   V  L R S G   L   L  G +R ++ + +
Sbjct: 181 TLREGKYHQIKRMFGRFRNPVVGLHRHSIGEITLDDGLKPGESRMLTAQEV 231


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 111/232 (47%), Gaps = 9/232 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K IA AG+ SR++  R+I +  V VN         +V   D I V+G  ++   
Sbjct: 3   TKIRLAKYIAHAGVCSRKQASRLIDEGAVIVNNRPANHID-HVDEQDQITVNGQIIKGTA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + YHKP+G+     D +  ++++ +LP   +RV  +GRLD ++ GLL+LTNDG L 
Sbjct: 62  ELIYFAYHKPVGIDCKL-DQNDPASLYHHLP-TITRVYPIGRLDKDSRGLLILTNDGELC 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V  +  +D +    +  G+ +         V    +K ++   ++
Sbjct: 120 NQLIHPDFHQPKRYLVSVNKSIDAEFCTKMAAGVPVDKQITLPCSV----EKIADKQFSI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            L++G NR+I+K+  +  +KV  L R       L    L  G    ++K  +
Sbjct: 176 ILKQGLNRQIRKMAHYCGYKVIDLYREQISELTLQTLNLAQGQYIAINKSDI 227


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/229 (31%), Positives = 113/229 (49%), 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
               ++KP  +V T  D   R  + D  P     +  VGRLD NT G++LLTNDG LA  
Sbjct: 62  YY-AFYKPKRVVCTREDNFNRKKIIDFFPKK-EYLFPVGRLDFNTTGIILLTNDGELANK 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  Q  R Y V  +G +  +++N   K ++         Q+    +K +     V L
Sbjct: 120 LIHPKFQIERTYLVHTNGDLSDEQINFANKNVIKLNNEINSRQI---IKKKATNKYIVKL 176

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           ++G N  +K++F+ F  +V  L R+ +    L  L  G  R+++ K ++
Sbjct: 177 KQGSNHHVKRLFDHFQIEVLDLKRVQFASINLANLSLGQYRKLTPKEIK 225


>gi|222624207|gb|EEE58339.1| hypothetical protein OsJ_09447 [Oryza sativa Japonica Group]
          Length = 1194

 Score =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 120/238 (50%), 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  IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
           I V+G  + K       +  +KP G + +  +P    ++FD+    ++++          
Sbjct: 125 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVPKPRLF 184

Query: 111 -VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            VGRLD+ T GL+++TNDG  A+ L  PS+  ++ Y V   G V ++ L  + +G  I G
Sbjct: 185 TVGRLDVATSGLIIITNDGEFAQKLSHPSSNIMKEYVVTIDGPVHRNHLIAISEGTKIDG 244

Query: 170 ICY-GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +    D+   LD Q       + + + EG+N E++++ +    +V  L R+  G F+L
Sbjct: 245 VKCIPDLVEPLDVQSNTKRTRIRIAVHEGRNHEVRELVQNAGLEVYALKRVRIGRFRL 302


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 105/229 (45%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   ++ E    I    + VN  ++   A  V  ++ + +DG  L   E  
Sbjct: 1   MRLDKFICKSTQLTKAEAIERIHDGDISVNDAVIINEATQVHESNTVIMDGKRLIARE-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F+ L     + +   GRLD +T G++L+T++G  + 
Sbjct: 60  RYILMHKPAGTICSNID-EVYPSLFNYLDIENTAELHIAGRLDADTTGMVLITDNGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+ +  +VYRV    ++  D     K GI +QG         L         V + 
Sbjct: 119 NITSPNQKCSKVYRVGLSREIAADVAEKFKAGIKLQGEQKLTAPALLTVISAKE--VLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R + G  +L  L  G  R +++  +
Sbjct: 177 ITEGKFHQVKRMFAAVGNRVVSLHREAIGEVRL-DLEVGQWRYLTQDEV 224


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 114/238 (47%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A +GIA+R +V+ ++ Q+RV+ N   +    V +    D I +D   +   E+
Sbjct: 1   MRLDKFLADSGIATRSQVKLILKQKRVRKNQETVTNGKVQIDEKLDEIYLDDERV-YYEK 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+   D    +TV D +        V  VGRLDI+T G LLLTN+G L
Sbjct: 60  YLYYVMNKPKGVVSATEDTKH-ATVLDLIGELAQKRGVFPVGRLDIDTHGFLLLTNNGAL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSN--A 187
           +  +  P     + Y  +  G + Q+     +KGI +  G       + + +   ++  +
Sbjct: 119 SHAMLSPKKHVEKTYVAKIEGIMTQEDQVSFEKGITLDDGYECMPAHLEILSVDKNHQAS 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            V + ++EGK  ++K++ +     V  L RIS GP  L  +L  G  R +    L   
Sbjct: 179 LVQIKIKEGKFHQVKRMVKACGKTVIDLQRISMGPLHLDKSLKLGEFRSLKDSELEAL 236


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 117/235 (49%), Gaps = 4/235 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--E 71
           +R+ K+I+ +GI SR++ E +I Q+RV +N  +             I      +     +
Sbjct: 3   ERLQKIISNSGICSRKKAEALIDQKRVFINNEIA-SLGEKADILIDIIRIDDYIIPKNIK 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGL 130
            +++ L +KP G+++T  D  GR TV D LP    + +  VGRLD ++ G L+++N+G L
Sbjct: 62  SSKVILLNKPTGVISTCRDTHGRKTVLDLLPDNLQKGMHPVGRLDKDSRGALIISNNGLL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V   G   ++ L   + GI I         V +  ++G+N  + 
Sbjct: 122 TLHLTHPRFNHKKRYSVLITGVPSKNTLKKWRNGIEIDKKTTRKALVNIVKRQGNNTLLE 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L EG+NR+I+KV +     V  LIRI  G  +L  L  G+ RE+++    + +
Sbjct: 182 IVLFEGRNRQIRKVADKLGHPVIDLIRIEIGNIKLNGLKEGAWREINELEWNQLI 236


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 111/234 (47%), Gaps = 11/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +   ++    D + VDG  +    +
Sbjct: 1   MRLDKLLANKAYGSRKEVHQIIKDRRVTINGSITTKKDTHIDIDVDIVAVDGK-IVSTTQ 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
                +HKP G VT   D      V D LP  F    V+ VGRLD +TEGLLLLTNDG  
Sbjct: 60  LYYVKFHKPKGYVTAVED-SSHPVVMDLLPPEFIKMGVVPVGRLDKDTEGLLLLTNDGVW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +   +    +VY V F G +  + +  +K+GI++  G      ++   +       V
Sbjct: 119 GHSIINGNKHVPKVYYVEFEGTLSDEGIQRIKEGILLGDGTQCKPAEIEFVSLHS----V 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
            V + EGK  ++K++       V  L R++ G   L  +   GS  E++ + + 
Sbjct: 175 HVTIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHIDLSGIEEVGSAMELTVEQIE 228


>gi|299067788|emb|CBJ38998.1| 16S rRNA pseudouridylate 516 synthase [Ralstonia solanacearum
           CMR15]
          Length = 239

 Score =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 94/226 (41%), Gaps = 8/226 (3%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTRLWLY 78
           +   G  +RR  + ++    V VNG+  E     V +   + +VDG       R    + 
Sbjct: 1   MQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDAQVDTAGLVLDVDGERWAYHARA-YLML 59

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLEL 136
           HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG     L  
Sbjct: 60  HKPTGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVHTLTS 118

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           P  Q  +VY +     V   ++  L +G++++        V    ++     + + L +G
Sbjct: 119 PRHQVPKVYEITTAEPVTDAQVTQLCQGVLLEDEDVP--VVAAWAERVDACHLRMALTQG 176

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           K  ++K++       V  L R + G   LG  L  G  R +    L
Sbjct: 177 KYHQVKRMVAAAGNHVVALHRSAIGGLTLGADLAPGQWRWLEGDDL 222


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IAQ RV+VNG +     + V ++D I VD        +  
Sbjct: 59  RLNKRMAELGLCSRREADDWIAQGRVRVNGQVA-PIGLRVTASDRIAVDKQARGAQRQRV 117

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++   R  V                   P+    +   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 PLKPAVVDWQNPE----QLRFVLTEGRKRQIRRMCALVGLTVVGLKRVRIGRVRLGLLPA 293

Query: 231 GSTREVSKKI 240
           G  R ++   
Sbjct: 294 GQWRYLAADE 303


>gi|239814633|ref|YP_002943543.1| pseudouridine synthase [Variovorax paradoxus S110]
 gi|239801210|gb|ACS18277.1| pseudouridine synthase [Variovorax paradoxus S110]
          Length = 249

 Score =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 98/245 (40%), Gaps = 15/245 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
             +  ++   G  +RR    ++ Q  V + G  +     ++   D +  V G      E+
Sbjct: 1   MHLQDILYSQGFGTRRVCAGLVQQGHVSIAGAAVTDPFADLDPEDLLFTVQGTEWAYHEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLL 123
               + HKP G   +   P    +++  LPS             V ++GRLD +T GLLL
Sbjct: 61  A-YLMLHKPAGTECSQK-PSTYPSIYTLLPSPLRLRPNKGAVQGVQAIGRLDQDTTGLLL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           LT+DG     +  P     +VY V     VD  ++  L  G+V+            ++  
Sbjct: 119 LTDDGQFIHKMGSPKHHVPKVYEVTAKHPVDAAQIEKLLAGVVLDDDPKPVRAAACESDS 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
             +  + + L EGK  ++K++      +V  L R   G   L G L AG  R ++ + + 
Sbjct: 179 PLH--LRLTLTEGKYHQVKRMLAAVGNRVEGLHRSRIGDLALPGDLAAGQWRWLTAEQVA 236

Query: 243 EQLGP 247
               P
Sbjct: 237 ALRAP 241


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 73/237 (30%), Positives = 122/237 (51%), Gaps = 5/237 (2%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++EN    R++K +A  G+ASRR+V+  I + R+ VNG L       V   D I V+G  
Sbjct: 1   MEEN--KIRINKFLASKGLASRRQVDLWIEEGRISVNGSLATS-GQKVSEEDDIVVNGKS 57

Query: 67  LRKAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           + + ++    +L +K   +++   D  GR TV D + S + R+  VGRLD  T GL+LLT
Sbjct: 58  ISQKKQKKVYYLLYKEEEVLSAVKDDRGRRTVVDCVLSPY-RIFPVGRLDYRTSGLILLT 116

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L   +  P  +  + Y V   G + +++L  L++G+ ++        +     +  
Sbjct: 117 NDGDLFNRMMHPRAEIFKSYEVLAKGHLTKEQLKTLEEGVELEEGKTLAALIAKVKYEKG 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           N +  + +REGKNR+I+++ E    +V RL R   G   L  L  G  R + +K + 
Sbjct: 177 NTFFEISIREGKNRQIRRMVEAVGSRVYRLRRTKIGKLSLDGLSLGEYRALEEKEIE 233


>gi|325122669|gb|ADY82192.1| 16S rRNA synthase [Acinetobacter calcoaceticus PHEA-2]
          Length = 234

 Score =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 107/241 (44%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G + +       S +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGYVSIDGEVADDLKKQFSSENLEFSLFGETYQYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP I     V ++GRLD +T GLLLLT+DG   +
Sbjct: 62  YLALKKPKGFECSHQ-PHHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V     V  +++ +L +G+ +   +G+        L+        +
Sbjct: 121 ALTHPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGLFAATDVAILE-----THQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV  L R   G   L  L  G    +S++  ++QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDGEWVYLSEQ--QKQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>gi|217969527|ref|YP_002354761.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217506854|gb|ACK53865.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 234

 Score =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 103/235 (43%), 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  KPIGLVTTHSDPDGRSTVF--------------DNLPSIFSRVISVGRLDINTEGLLLLT 125
           KP+G V+   +P     V                  PS    +   GRLDI++ GLL+LT
Sbjct: 61  KPVGYVSGQPEPGYSPAVSLIGPDNQADRDVAQRFHPSHLKNLAPAGRLDIDSTGLLVLT 120

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            DG +AR L    ++  + Y VR  G + ++ L LL  G+ +        +V       +
Sbjct: 121 QDGRIARQLIGEDSKVEKEYIVRVEGTLAENGLALLNHGLWLDDRPLRPAEVEW----IN 176

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +  +   LREG+ R+I+++ E    KV  L R+  G  +LG L  G  R + +  
Sbjct: 177 DDQLRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGHVKLGDLPLGQWRFLREDE 231


>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 =  226 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 112/229 (48%), Gaps = 6/229 (2%)

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  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           + + HKP+G+V+   D   R TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 81  V-MLHKPVGVVSATIDDKHR-TVIDLLEQDDKESLHIVGRLDLNTSGLLLLTNDGRWSKR 138

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++YRV     +  D ++   +G+  +      +   L+      A   V L
Sbjct: 139 LMDPEHKVGKLYRVHLQNPLTPDYISGFAQGMYFEFEDITTLPAELEIIDSYTAL--VTL 196

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  +IK++F  F   V  L RIS G   L   L  G +R ++ K +
Sbjct: 197 YEGRYHQIKRMFGRFRNPVIGLHRISVGNIVLDNNLKPGESRVLTPKEI 245


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 73/251 (29%), Positives = 105/251 (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  RLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINT 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 QQLKPAVVEWQNPE----QLRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGQVLLGKLP 347

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 348 PGQWRYLAPGE 358


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 112/240 (46%), Gaps = 23/240 (9%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V+V+G ++      V+ + H+ ++     +  +    L +
Sbjct: 1   MSELGLCSRREADVWIEKGWVRVDGKVVSELGSKVLPSQHVTIERQAAAEQSKLVTILIN 60

Query: 80  KPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V+  ++   +  V                   P+    ++  GRLDI++ GLL+L
Sbjct: 61  KPMGYVSGQAEDGYQPAVTLIKPENRWAEDQATTQFHPTQLRSLVPAGRLDIDSIGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           T DG +A+ L   +T+  + Y VR      G++ +++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 NED----QLSFILREGKKRQIRRMCDMVGLKVLGLKRVRIGNIKLGDLPVGEWRYLGADE 236


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 107/231 (46%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADIDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++  
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTESE 229


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 103/229 (44%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   ++ E    I    + VN  ++   A  V  ++ + +DG  L   E  
Sbjct: 1   MRLDKFICKSTQLTKAEAIERIHAGDINVNSAVIINEATQVHESNTVIMDGKRLIARE-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F+ L     + +   GRLD +T G++L+T++G  + 
Sbjct: 60  RYILIHKPAGTICSNID-EVYPSLFNYLDVDNIAELHIAGRLDADTMGMVLITDNGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P+ +  +VYRV     +  D     K GI +QG         L         V + 
Sbjct: 119 NITSPNQKCSKVYRVGLSRDITADVAEKFKAGIKLQGAQKLTAPALLTIISAKE--VLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R + G   L  L  G  R ++K  +
Sbjct: 177 ITEGKFHQVKRMFASVGNRVVSLHREAIGEVTL-DLEVGQWRYLTKDEV 224


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 72/227 (31%), Positives = 114/227 (50%), Gaps = 9/227 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +++     R+ V  M+AQ RV ++G+L   AA  +     I VDGV L       
Sbjct: 91  RLDKHLSKQTGVPRKAVRLMLAQARVTIDGVLARDAAEVINPFSRIAVDGVGL-PTNTPH 149

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V    D   R TV D L   F   +  VGRLDI + GL+LLTNDG  +R 
Sbjct: 150 YIMLNKPSGVVCATRDARHR-TVIDILDLPFQHTLHIVGRLDIQSTGLVLLTNDGQWSRR 208

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L LP +++ + YRV     +  +++   + GI    +G+     ++ L     +N    V
Sbjct: 209 LSLPQSKFAKHYRVTTEQAITSEQIAGFEAGIFFAYEGLTTRPARLHLINSHEAN----V 264

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            L EG+  +I+++F  +  +V  + R + GP+ L  L  G  RE+S 
Sbjct: 265 TLTEGRYHQIRRMFGRYGNRVLSIHRYATGPYVLSNLRPGQYREISP 311


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 69/217 (31%), Positives = 106/217 (48%), Gaps = 4/217 (1%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
           E +IAQ RV+VNG ++ R  V V   T  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 FNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + V +L+R      QLG L  G+ R ++   LR  
Sbjct: 183 LGFPVQQLVRTKIHTVQLGELTPGAIRHLNDSELRAL 219


>gi|317403818|gb|EFV84295.1| pseudouridylate synthase [Achromobacter xylosoxidans C54]
          Length = 243

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 107/245 (43%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G ++            I ++     + 
Sbjct: 1   MEKVRISKLMSERGLCSRREADSYIERGWVRVDGEVVSELGARAFPNQVITLERAAQARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFSR-----VISVGRLD 115
                 L +KP+G V+  ++      V           D  P  F R     +   GRLD
Sbjct: 61  TSRVTILINKPVGYVSGQAEKGYTPAVALIDARSRFAGDRSPQRFERGHLDGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +A++L    +   + Y VR  G + ++ L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRVAKLLIGEDSSIDKEYLVRVQGDLSENGLALLNHGLSLDGKALKPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    KV  L R+  G   LG L  G  R 
Sbjct: 181 QVRWQNHD----QLRFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVALGELPLGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRDDE 241


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 112/276 (40%), Gaps = 47/276 (17%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR-- 68
              +R++K+++  G+ SRRE +R+I   +V V+G+  +     V     +   G  +   
Sbjct: 1   MMEERLNKLLSAMGVCSRREADRLIESGKVLVDGVPAK-MGQKVRMDQTVVCRGKVVGRG 59

Query: 69  -------------------------------------KAERTRLWLYHKPIGLVTTHSDP 91
                                                K  R  L   +KP G+V T SD 
Sbjct: 60  EAAAGAGNGKTARRVGSGRADGTAAQDARPASLPRSMKKPRPVLLAVNKPKGVVCTASDK 119

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           D    + D +     RV  VGRLD ++EGL+L+TN G L   +        + Y+V    
Sbjct: 120 DKAPNIVDMI-QYPVRVYYVGRLDKDSEGLVLMTNQGDLVNKIMRSGNAHEKEYQVVVDR 178

Query: 152 QVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            V  + L  ++KG+ ++         +V    +K  +   ++ L +G NR+I+++ E   
Sbjct: 179 PVTAEFLARMEKGVRLKELDRTTLPCKV----RKTGDKRFSIVLTQGLNRQIRRMCEACG 234

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             V  L R+      LG L +G  R+V     RE +
Sbjct: 235 CHVRSLKRVRVMNICLGDLKSGEYRQVEGAEYREFM 270


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 109/229 (47%), Gaps = 9/229 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T  R++K IA AGI SR++  R+I +  V VN         +V   D I V+   ++ A 
Sbjct: 3   TKIRLAKYIAHAGICSRKQASRLIDEGVVTVNNRPANHID-HVDEQDTIIVNEKEIKGAA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               + YHKP+G+    +  D  +++  +LP   +RV  +GRLD ++ GLL+LTNDG   
Sbjct: 62  DLVYFAYHKPVGIDCKLN-IDDPASLIHHLP-TLTRVYPIGRLDKDSRGLLILTNDGDFC 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V  +  +D      +  G+ +        +V     K ++   ++
Sbjct: 120 NQLIHPDFHQPKHYLVTVNKPLDDAFCKKMAAGVPVDKHITLPCEV----NKIASNQFSI 175

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSK 238
            L++G NR+I+K+  +  +KV  L R+ +    L    L      +++K
Sbjct: 176 VLKQGLNRQIRKMAHYCGYKVIDLFRVQFSDLTLSKLNLPENQYIQINK 224


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 104/242 (42%), Gaps = 24/242 (9%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SKV+A  GI SRRE +  I    V V+G++++     +     I +          T 
Sbjct: 169 RLSKVMAERGICSRREADEWIMNSWVMVDGVIIDTLGTRINPDAEIVISSYAHEVQAETV 228

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS--------------------IFSRVISVGRL 114
             + HKP+G V+  ++   +  +    P                       + +   GRL
Sbjct: 229 TIILHKPVGYVSGQAEDGYQPAIVLVHPDNEWLDDPELNQLHEREFQRRYLNGLAPAGRL 288

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           DI++ G+L+LT DG +AR L    +   + Y VR  G +D D L  L  G+ + G     
Sbjct: 289 DIDSTGMLVLTQDGRVARHLIGEDSTVEKEYLVRVEGSLDDDGLKRLNHGLSLDGEKLKP 348

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +V+   +      +   LREGK R+I+++ E     V  L R+  G   LG L  G  R
Sbjct: 349 AKVSWQNED----QLRFVLREGKKRQIRRMCEMVGLHVVGLKRVRIGSVNLGKLPVGQWR 404

Query: 235 EV 236
            +
Sbjct: 405 YL 406


>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 =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 60/228 (26%), Positives = 111/228 (48%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR++  ++I + R+ VNG    +    V   D I +D  PL   ++ 
Sbjct: 1   MRINKLFSNLGICSRKDTSKLIEENRIIVNGFPCIQ-GQWVELEDEILLDNKPL-PIKKK 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KPIG+  T +D    + +  N  +    +  VGRLD  ++GL+LLTNDG LA  
Sbjct: 59  IYIVLNKPIGITCTAADEVENNII--NFMNYPEYIFPVGRLDKASQGLILLTNDGDLANK 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +     +  + Y V      + + +  +  G+ I  +     +V    ++ S     + L
Sbjct: 117 ILESENKHEKEYIVTLDKPFNDEFILGMTSGVEICNVKTRQCKV----RRISEDTFNIVL 172

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +G N++I+++ + F + V +L RI     +LG L  G  R + ++ L
Sbjct: 173 TQGLNKQIRRMSKTFGYTVKKLERIRIVNIELGDLEYGKWRYLLEEEL 220


>gi|254251646|ref|ZP_04944964.1| Pseudouridine synthase [Burkholderia dolosa AUO158]
 gi|124894255|gb|EAY68135.1| Pseudouridine synthase [Burkholderia dolosa AUO158]
          Length = 238

 Score =  226 bits (577), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VDG       R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVGGATATDPDTAFDTDGLVFTVDGTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLTLNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +   +L+ L+ G+ + G     +       + ++  V + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLSDTQLHTLRTGVQLHGEP-KPIAAVAADARDAHTLV-LT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V+ L R S G   L   L  G+ R + +  L     P
Sbjct: 179 VVEGKYHQVKRMVAAVSNRVDALHRESIGGLTLPDNLAPGTWRWLDEAELAALRNP 234


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/244 (28%), Positives = 108/244 (44%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A   + SRRE +  I Q  VKVNG         V  +D IE+         
Sbjct: 5   EPVRLSKRMAELKLCSRREADGYIEQGWVKVNGQTA-VLGQKVTPSDRIELAKQAHETQA 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
           +    L +KP+G V+   + D R+ V                    S    +   GRLDI
Sbjct: 64  QRVTVLLNKPVGYVSGQPEKDYRAAVELITAENRWDGDTSRIPYRDSHKKGLAPAGRLDI 123

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L    +   + Y VR  G++ ++ L LL  G+ + G      +
Sbjct: 124 DSVGLLVLTQDGRIAKQLIGGDSGIEKEYLVRVKGRLSEEGLRLLNYGLSLDGEKLRPAK 183

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   L++GK R+I+++ E    +V  L RI  G  +LG L  G  R +
Sbjct: 184 VEWQNED----QLRFILKQGKKRQIRRMCELVGLRVIGLKRIRMGQVKLGALPPGKWRYL 239

Query: 237 SKKI 240
            K  
Sbjct: 240 GKDE 243


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 102/230 (44%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I  +   +R + +++I+Q R+  +  ++   A        I  DG  +      
Sbjct: 1   MRLDKTICESTTLTRSQAKKVISQGRITCDDKIIRSCAFKPRKDAVIVFDGKTI-AIRGP 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP   + ++ D     ++F+ +       +   GRLD +T GL L+T+DG  + 
Sbjct: 60  RYMMLNKPENFICSNVDEQ-LPSLFNLVDVDKKELLFIAGRLDADTTGLTLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  + ++ YRV     + +D + L K GI ++      +   L+    S+  V + 
Sbjct: 119 KITSPRNKCIKRYRVGLDAPICEDAVALFKAGIQLKSENQPCLPAELNI--LSSTEVILS 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + EGK  ++K++F      V  L R   G  +L   L  G  R ++ K +
Sbjct: 177 ISEGKYHQVKRMFGAIGNVVIELHREKIGDIELDNTLALGEWRYLTDKEV 226


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 103/239 (43%), Gaps = 13/239 (5%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDG 128
               L HKP G   +  D      +++ LP  F      +  VGRLD +T G+LL+T+DG
Sbjct: 59  FS-LLLHKPSGYTCSTKDTG--RLIYELLPPRFRSRAPVLAPVGRLDRDTSGMLLMTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L   +  P +   +VY V     +  D+  L   G ++++G     +   L+      A
Sbjct: 116 ALLHRIISPKSALDKVYEVSLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGPRQA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              + L EG+  +++++F      V  L R   G   L  L AG  R +    L    G
Sbjct: 176 --RLTLHEGRYHQVRRMFAAAGNHVAALHRSRIGGLSLDALPAGQWRALDASDLEVLFG 232


>gi|330898470|gb|EGH29889.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 230

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 108/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAIKFAEGLYFAFENLTTQPAQLTLLGPQSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPGLRPGSYRALNAGEI 227


>gi|167824765|ref|ZP_02456236.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 9]
          Length = 300

 Score =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 53  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 112

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 113 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 172

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 173 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 232

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 233 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 288

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 289 GEWRYLGPDE 298


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 103/238 (43%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++G + +         +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIDGEVADDLKKQFSPENLEFSLFGETYQYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP I     V ++GRLD +T GLLLLT+DG   +
Sbjct: 62  YLALKKPKGFECSHQ-PHHHQSVFSLLPEILIQRGVQAIGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     V  +++ +L +G+ +            D +      +T+ 
Sbjct: 121 ALTHPRKHVPKVYHVTTIDPVTPEQIEMLSQGVSLHQEKGVFA--ATDVKILETHQLTMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + +G   ++K++      KV  L R   G   L  L  G    +S++  ++QL  +++
Sbjct: 179 IHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPELEDGEWVYLSEQ--QKQLAQNII 234


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 114/243 (46%), Gaps = 18/243 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               RVSK+++  GI SRRE +  I +  VK +G ++      V+    + +D   L   
Sbjct: 1   MEKVRVSKLLSEQGICSRREADVFIERGWVKADGNVV-SLGTKVLPNAKLTLDKKALESK 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV--------FDNLPSIF-----SRVISVGRLDIN 117
            +    + +KP+G V++  + + +S +        +D + + F       + + GRLDI 
Sbjct: 60  SKQVTIILNKPVGYVSSQPEKNYKSALSLITKANQYDRVHNEFSESHLKGLATAGRLDIE 119

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           ++GLL++T DG +A+ L    ++  + Y VR  G++ +  L LL  G+ + G    D +V
Sbjct: 120 SQGLLVMTQDGSIAKQLIGEDSEVEKEYIVRVEGKLSERGLQLLNHGLSLDGQPLRDAEV 179

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                  ++  +   L EGK R+I+++ E    KV  L R+  G   L  L  G  R + 
Sbjct: 180 EW----INDDQLRFILWEGKKRQIRRMCELVGLKVIGLKRVRMGNVTLADLPTGKWRYLK 235

Query: 238 KKI 240
              
Sbjct: 236 PFE 238


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 103/306 (33%), Positives = 176/306 (57%), Gaps = 15/306 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +  +N++Q    P R+SK +A+  + SRRE E+MI    + V+G  +  + + V S + I
Sbjct: 25  LTKQNLIQS--EPMRLSKYLAQTSVCSRREAEKMIESGMILVDGKKV-DSNIPVTSENKI 81

Query: 61  EV---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRL 114
           +V   +G  +   + T++W+++KPIG++ +H+DP  R + +D           +ISVGRL
Sbjct: 82  QVFTKNGERMPVKQSTKVWIFYKPIGMICSHNDPFKRPSFYDFAKLRLKTDQHIISVGRL 141

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D N+EGL+++TNDG LAR +ELP T+  R+YRVR +G   ++KL  ++ G+ I G+ YG 
Sbjct: 142 DFNSEGLIVVTNDGELARCMELPETKLQRIYRVRVYGTFTEEKLKKIRNGLTIAGVNYGP 201

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             V ++ ++  N W+ + L  GKNREI+KV + F+ +VNRLIR SYGP++L  L  G   
Sbjct: 202 YWVNVENRQSRNTWLIMRLESGKNREIRKVMQKFDLRVNRLIRQSYGPYKLMGLKPGDFY 261

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           E     +  ++   L  +A+  L       E +  ++  +  +  D+ ++ +K   ++  
Sbjct: 262 E---AQIEPEIKRKLYLQARKKL---QNVQEQIQLEQTKLNIKALDEQSKNEKQIEKQEN 315

Query: 295 LSKQKK 300
              QKK
Sbjct: 316 DQVQKK 321


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 118/233 (50%), Gaps = 5/233 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+++G+ SRR  +++I +  V +NG++ E     V   D + +D   +   
Sbjct: 1   MEEIRINKYISKSGVCSRRAADKLINEGHVTINGVVAET-GSKVTEKDIVRIDDDIINLI 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  +++ ++KP+G +++ SD  G + +   LP     +  VGRLD ++EGL+L+TNDG L
Sbjct: 60  KDIKVYAFYKPVGYISSLSDEQG-TGIASFLPQGM-GLFPVGRLDKDSEGLMLITNDGNL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAW 188
              +   S    + Y V    + + D L  + KG+ I     G   +T    T+   +  
Sbjct: 118 MNEILNASNGHEKEYIVTTRQKFNNDFLVKMAKGVPITNRATGKKIITAPCKTEALEDNS 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + + +G NR+I+++  +F+  V  L R+      LG +  G  +E+S+  L
Sbjct: 178 FKITIIQGLNRQIRRMCGYFDIDVVSLKRVRIMNIMLGNMRPGELKELSQSEL 230


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 66/227 (29%), Positives = 110/227 (48%), Gaps = 9/227 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           +R+ K++A  G  +R+EV+R++    V+V+G ++    + +      +EV G  +     
Sbjct: 6   ERIDKILAHLGFGTRKEVKRLLRAGGVRVDGRVVRDPGMKLDPARARLEVAGEVVVWQRH 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             + LY KP G+VT   D    +TV D LP+  +R  ++ VGRLD +TEGLLLLT DG L
Sbjct: 66  HHVMLY-KPAGVVTATRDARH-ATVLDCLPASLARKDLLPVGRLDRDTEGLLLLTTDGAL 123

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  +VY          +      +G+V+        ++ L         V 
Sbjct: 124 LHRLTHPRWKVPKVYYAELEQPARPEDAQAFAEGLVLSEGRCLPAELELL---EDPRRVR 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           + L EG+  ++K++F     +V  L R++ GP +L   L  G  R +
Sbjct: 181 LVLWEGRYHQVKRMFAARGNRVTYLKRLAVGPLELDPKLKPGEARAL 227


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 66/238 (27%), Positives = 107/238 (44%), Gaps = 17/238 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  GI SRRE +RMI +  V+ NG ++      V     IE+     +      
Sbjct: 5   RLSKLMSLRGICSRREADRMIEKGLVRANGKVISELGTKVPENAEIELLPHAKKWQAEKV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSRVISVGRLDINTEGLL 122
             + +KPIG V+T     G     D +            P    ++   GRLDI+++G+L
Sbjct: 65  TIILNKPIGYVSTQ-PEKGYKQALDLITPERQWNSKSFDPKHLRKLSVAGRLDIDSKGIL 123

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +LT DG +A+ +    ++  + Y VR  G V    +  L  G+V+         +    Q
Sbjct: 124 ILTQDGVIAKKIIGNESEIEKEYLVRVDGAVTPGIIKRLSFGLVLDNTPLKKANI----Q 179

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +     +   L EGK R+I+++ E    KV  L R+  G  +LG L  G  R + K  
Sbjct: 180 QLDEHLMKFTLIEGKKRQIRRMCELVGLKVVDLKRVRIGKIRLGDLPTGYWRYLKKSE 237


>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 =  226 bits (576), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 106/241 (43%), Gaps = 15/241 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V V+G + +         +    + G   +  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSVDGEIADDLKKQFSPENLEFSLFGQTYQYREQ-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H  P    +VF  LP I     V ++GRLD +T GLLLLT+DG   +
Sbjct: 62  YIALKKPKGFECSHQ-PQHHQSVFSLLPEIMIHRGVQAIGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWV 189
            L  P     +VY V     V  +++ +L +G+ +   +GI        L+        +
Sbjct: 121 ALTHPRKHVPKVYHVTTLDPVTPEQIAMLSEGVSLHQEKGIFAATDVAMLE-----THQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           T+ + +G   ++K++      KV  L R   G   L  +  G    +S++  ++QL  ++
Sbjct: 176 TMTIHQGVYHQVKRMIAAVGNKVEALHRHQVGQLVLPEIADGEWVYLSEQ--QKQLAQNI 233

Query: 250 L 250
           +
Sbjct: 234 I 234


>gi|46449495|gb|AAS96146.1| ribosomal large subunit pseudouridine synthase B [Desulfovibrio
           vulgaris str. Hildenborough]
          Length = 267

 Score =  226 bits (576), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 123/239 (51%), Gaps = 9/239 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE-- 71
           R++K ++ AG+ SRR+ + +IA  +V+VNG ++      V   TD IEV+G  L   E  
Sbjct: 22  RLNKALSGAGVCSRRQADTLIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGEAL 81

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
              R    + +KP+ +V+T  DP GR+T+ D LP      R+  VGRLD  +EGLLLLT+
Sbjct: 82  NRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLLTD 141

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  +   
Sbjct: 142 DGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRSEY 201

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + + L +G NR+I+++       V RL+RI  GP +LG L  G+ R +    ++  
Sbjct: 202 GVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGACRRLEDHEVKAL 260


>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 =  226 bits (576), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 120/255 (47%), Gaps = 17/255 (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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVT 178
            L   ++   R+Y+V+  G+V  +    +  G+ +     G               +   
Sbjct: 123 ALM--NSNLERIYKVKIKGEVTPEIEAAMMNGLELLDATAGGHSHSKVTSMTFAPFLGYK 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   + + + + + + EG+NREI++ F  F  +V  L RIS+   +L  L  G  R +S+
Sbjct: 181 IQKNEHNYSVLKIAISEGQNREIRRFFAHFGTEVADLKRISFAEVELNNLPTGKVRFLSR 240

Query: 239 KILREQLGPHLLEEA 253
                       EE 
Sbjct: 241 SEYSALFTFMKAEEK 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 =  226 bits (576), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 57/232 (24%), Positives = 106/232 (45%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R E   +I   +V+VNGI++      V   + I + G  L  A  +
Sbjct: 1   MRLDKFLCKSTDFTRVESIDLIEAGKVRVNGIVIITPQTQVHENNSIMLSGQRLV-ARPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKPI  + ++ D D  S +          +   GRLD +T GLLLLT+DG  +  
Sbjct: 60  RYIMLHKPINTLCSNVDGDYPSVMNYIHMDRAEDLHITGRLDADTTGLLLLTDDGRWSFN 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P     + YRV     ++++ ++      ++G+ +QG     +   L+    +   V
Sbjct: 120 IINPKYHCEKTYRVTLRDPIEEEDIDELVSRFEQGLQLQGEKSLTLAAKLEV--IAPHQV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + L EG+  ++K++F     +V  L R   G   L  +  G  R +++  +
Sbjct: 178 LLTLSEGRYHQVKRMFFTVGNRVVGLHRQQVGKLSL-DIELGEWRYLTEDEV 228


>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 =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 112/230 (48%), Gaps = 5/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +A     +R++   M+AQ+RV+++G ++      V     +++D   L+     
Sbjct: 1   MRLDRFLANLPHCNRQQARLMLAQRRVRLDGQVISDPLAEVREFSRVQLDEQLLQAGRPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G V+   DP    TV + LP+     +   GRLD NT GL++LTNDG  +R
Sbjct: 61  RYLMLHKPAGCVSATHDPQH-PTVLELLPAALRADLHIAGRLDFNTTGLMILTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P+T+  + Y V    ++ +  +   ++G              LD      A + + 
Sbjct: 120 RLTQPATKLPKQYLVETEDEIAEHYVAKFREGFYFAFENLTTQPAQLDILGPRQARLAIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             EG+  ++K++F FF+ KV  L R S G  +L   L  G+ R+++ + +
Sbjct: 180 --EGRYHQVKRMFGFFDNKVVGLHRESMGAIRLDPGLAPGAFRQLTPEEI 227


>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 =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 62/216 (28%), Positives = 103/216 (47%), Gaps = 8/216 (3%)

Query: 35  IAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           + +  V VNG   +     +  T D + V G  L   E+   +L +KP G ++   D   
Sbjct: 17  LEKGLVLVNGRAEKSPKTQINETEDEVVVSGQKLTY-EKFVYYLLNKPKGYISATEDERH 75

Query: 94  RSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           + TV D L        V  VGRLDI+T GLLLLTN+G LA  +  P     ++YR +  G
Sbjct: 76  K-TVLDLLDETALQKEVFPVGRLDIDTHGLLLLTNNGKLAHAMLSPKKHVEKIYRAQVAG 134

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            ++Q  +    +GI ++       Q+ +    ++   + V + L EGK  ++K++     
Sbjct: 135 LMNQSDVEQFARGIELKDFTCQPAQLKILEVDEEKETSLVEISLAEGKFHQVKRMVAACG 194

Query: 210 WKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            +V  L R++ GP QL   L  G  R ++++ L+  
Sbjct: 195 KEVTDLQRLTMGPLQLDPELALGEWRRLTEEELKSL 230


>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 =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 74/269 (27%), Positives = 113/269 (42%), Gaps = 48/269 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ASRRE +  IA+  VKVNG++     + V+    IE+D     +  +  
Sbjct: 39  RLNKRMAELGLASRREADDWIAKGWVKVNGVVAT-MGMQVLPDVRIEIDKQAQGQQAKQV 97

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
             L HKPIGLV+  ++      +               F   PS    ++  GRLDI++ 
Sbjct: 98  TVLVHKPIGLVSGQAEDGHLPAITLVQPQNRWAQDNARFFFHPSQLKSLVPAGRLDIDST 157

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF--------------------HGQV------ 153
           GLL+LT DG +AR L        + Y VR                        V      
Sbjct: 158 GLLVLTQDGRVARQLIGEDAVMEKEYLVRVVYNADQGAATSTGQLSRIDDDDPVSTDVQS 217

Query: 154 --DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++KL LL+ G+ + G      +V     +     +   L EGK R+I+++ E    K
Sbjct: 218 VFPREKLALLRHGLSLDGQALQPAKVDWQNPE----QLRFILTEGKKRQIRRMCELVGLK 273

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           V  L R+  G   LG L  G  R ++   
Sbjct: 274 VVGLKRVRIGKVMLGNLPLGQWRYLAPHE 302


>gi|332976275|gb|EGK13136.1| ribosomal small subunit pseudouridine synthase A [Psychrobacter sp.
           1501(2011)]
          Length = 234

 Score =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 110/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K I++A   SR+E ++++    + VN  +++  +++V    D +   G PL  A  
Sbjct: 1   MRLDKFISKATELSRKEAKKVLHASEITVNDEVVKDGSLHVDVLNDEVMWAGEPLSVATG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +R  L +KP G   T   P     V D +       +   GRLD++T G LLL++DGG  
Sbjct: 61  SRYLLLYKPEGFECTLK-PKEYPMVTDLIAVPELGNLRIAGRLDVDTTGALLLSDDGGWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P     +VY +     +D+      +  + +GI++ G        TL+    ++A
Sbjct: 120 HRVTSPRHLHEKVYELTLAEPMDEAEQAHAVKKVAQGILLDGDYEPTKPATLEFIDETHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L EGK  ++K++  +F  KV  L R S G   L  L  G +R +++  +
Sbjct: 180 --RLILTEGKYHQVKRMMGYFGNKVIELHRASIGGVTLEGLEKGESRFLTEDEI 231


>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 =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 112/232 (48%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ +++   G  SR+E+  ++   RV V+G  +      V   T  + VDG P+R    
Sbjct: 1   MRLDRLLGHMGFGSRKELRALLKAGRVTVDGRPVTDPGTLVDPGTSSVAVDGEPVRFQRH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             + L HKP G++T  +DP  R TV D LP    R  ++ VGRLD +TEGLLLLT DG L
Sbjct: 61  FHV-LLHKPAGVITATADPRQR-TVMDVLPEDLRRRDLVPVGRLDKDTEGLLLLTTDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
           A  L  P     + Y  R    +D         G+ +  G      ++ + + +      
Sbjct: 119 AHRLMAPRWHQPKRYLARVDRPLDPADQEAFAAGVPLADGYVTLPARLEILSPQEG---- 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V +REGK  +++++F     +V  L R+S GP  LG L  G+ R ++   +
Sbjct: 175 IVTVREGKYHQVRRMFAARGKRVVYLKRLSMGPLSLGDLPPGAARPLTAAEV 226


>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 =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 101/229 (44%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +      +R   ++++ +  V+ +G +++     V     + ++GVPL     T
Sbjct: 1   MRLDKYLCSCTDLTRSMAKKLLHKGEVQCDGEVVKDPGFKVTDDTQVVLEGVPL-GPVAT 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP   + ++ D +   +V + +       +   GRLD++T GL+LL+ DG    
Sbjct: 60  RYIMLHKPAEFLCSNVD-ELYPSVLNLIELPKRETLRIAGRLDVDTTGLVLLSEDGQWCH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  Q  + YR      +  D    L +G+ +           L   + S+  V + 
Sbjct: 119 QITSPRRQCSKRYRAWLAEPLVADAEQQLAQGVQLHNEEGLTRPAELV--RISDTEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           + EGK  ++K++F     KV  L R + G  +L  TL  G  R +S+  
Sbjct: 177 IEEGKYHQVKRMFAALGNKVVALHREAIGAIELDETLEPGEWRLLSEDE 225


>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 =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 118/242 (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 ALM--ESNLERIYKIKIKGEVTSEMEAAMLNGMMLDDATAGGHSHSKVTSMEFKPFIGYK 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|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 =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 106/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQQVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>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 =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 80/238 (33%), Positives = 126/238 (52%), Gaps = 5/238 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+ K+++ AG+ SRR+ E +I   RV+VNG ++          TD IE  G  + K E 
Sbjct: 3   ERLQKILSHAGVCSRRKAEELILAGRVRVNGRVVRELGTEADVCTDKIEALGE-IVKPEP 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R +L+HKP  ++T+ SDP GR TV D    +  RV  VGRLD ++EGLLL+TNDG L  
Sbjct: 62  LRYYLFHKPDCVITSVSDPAGRRTVMDYFRRVRERVFPVGRLDYHSEGLLLVTNDGQLDF 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVT 190
           +L  P  +  + Y V   G+  +     ++KG+ I        ++ +     + +   + 
Sbjct: 122 ILTHPCHEVQKEYEVVVRGKFSEKLAKKMEKGVKIDSGVTAPCEIEVLGYDAEKNKTRLR 181

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
           + L EGKNREI+K+ E F++ V  L RI Y    L  +  G  R ++   +++    H
Sbjct: 182 MVLHEGKNREIRKMMEIFHYPVFELKRIRYSFLTL-DVNRGQYRRLTAAEVKKLYELH 238


>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 =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 54/206 (26%), Positives = 96/206 (46%), Gaps = 8/206 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +    A+ V   D + +DG  + K E+      +HKP+G+  T +D      + D 
Sbjct: 3   INGEICTHGAL-VSDGDRVTIDGQVIVKEEKEKVYIAFHKPVGITCTAAD-HIEDNIIDY 60

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           + +   R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++ 
Sbjct: 61  I-NYPERIFPVGRLDKASEGLILLTNDGAIANQILHGDHEHEKEYVVTVDKPFTDWFIDE 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I+       +VT    +   +   + L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSSGVKIKDGMTKPCKVT----RVDQSTFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILREQLG 246
              +L  L  G  R V+ + L   +G
Sbjct: 176 MNIELNELEVGKWRSVTAEELEILIG 201


>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 =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 99/231 (42%), Gaps = 10/231 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  +RR  + ++    V VNG+  E     V +   + +VDG       R  
Sbjct: 10  LYRILQSQGFGTRRYCKDLVFAGLVHVNGVEAEDPDAQVDTAGLVLDVDGERWAYHARA- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G   +   P    +V+  LP       V  VGRLD +T GLLLLT+DG    
Sbjct: 69  YLMLHKPTGFECSQK-PRHHPSVYTLLPVPLRERGVQCVGRLDQDTTGLLLLTDDGQFVH 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTV 191
            L  P  Q  +VY +     V   ++  L +G++++     D+ V     ++     + +
Sbjct: 128 TLTSPRHQVPKVYEITTAEPVTDAQVTQLCQGVLLEDE---DVPVAAAWAERADACHLRM 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            L +GK  ++K++       V  L R + G   LG  L  G  R +    L
Sbjct: 185 ALTQGKYHQVKRMVAAAGNHVAALHRSAIGGLTLGADLAPGQWRWLESDDL 235


>gi|167911508|ref|ZP_02498599.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 112]
          Length = 298

 Score =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 51  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 110

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 111 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 170

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 171 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 230

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 231 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 286

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 287 GEWRYLGPDE 296


>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 =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 111/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      SR++V R+++  R +VNG +       V   D +E+DG  L+  +  
Sbjct: 1   MRLDRYLGSRAQLSRQDVRRLVSDGRARVNGEVTRTLDREVRIFDCVELDGQVLQPGKVA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP G V+   D   R TV D +       +   GRLD NT GL+LLTNDG  +R
Sbjct: 61  RYVMLHKPPGCVSATRDAAHR-TVIDLIDEPDKDDLHIAGRLDFNTTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P++   +VY V    ++D   +    +G+    + +     ++ L   + +     
Sbjct: 120 RLTQPTSLQGKVYLVETEDEIDPGCVGAFARGLYFRFEDLTTLPAELVLLGPRRA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           + L EG+  ++K++F  F  KV  L R S GP  L  +L  G  R ++   + +
Sbjct: 176 LTLHEGRYHQVKRMFGHFGNKVTALHRESMGPLLLDASLTPGCYRPLTDNEIAQ 229


>gi|323127651|gb|ADX24948.1| Putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. equisimilis ATCC 12394]
          Length = 238

 Score =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 111/231 (48%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SRR+V+++I  Q V+++  +      NV      IE+ G  +    +
Sbjct: 1   MRLDKLLEVVTDGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEISGKRISHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYFILNKPAGVVSARSDI-NHVTVLDQLSEKDRHPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G +D+D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVAKTYMVTVNGFLDEDAPDFFAAGIKFPTGEQCRPAQLTILQASQEKSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R V+   
Sbjct: 179 RLVISEGKFHQVKKMFLTYGLKVISLKRTSFAGLELGELASGAYRSVTDAE 229


>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 =  225 bits (575), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 108/238 (45%), Gaps = 14/238 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A     SR +V  ++  +R++VNG      +  + S D + +D  PL+     
Sbjct: 1   MRLDKFVADNTSYSRSQVRGLLKAKRIRVNGQTALAPSAALKSDDEVTLDDAPLQARSD- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--------FSRVISVGRLDINTEGLLLLT 125
              + HKP G V  ++D +   TVFD LP           +R+   GRLD++T GL+L+T
Sbjct: 60  VYLMLHKPAGYVCANTDAEH-PTVFD-LPGFSARYSNADIARLQIAGRLDLDTTGLVLIT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG     +  P  +  + Y V     +  +  +   +G+++ G     +   L+    +
Sbjct: 118 SDGQWNHRITSPRQKCRKAYYVECAAPIAAETKSAFAEGVLLHGEKRPTLPAELELLSAN 177

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            A + +   +G   ++K++F     KV RL R   G   L   LL G  R ++   +R
Sbjct: 178 TANLYIE--QGIYHQVKRMFASTGNKVLRLHRFQIGALALETDLLPGDMRALTSDEIR 233


>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 =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 72/232 (31%), Positives = 122/232 (52%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +     
Sbjct: 1   MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHKT- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L
Sbjct: 60  HVYYMLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V
Sbjct: 119 GYQLIRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHV 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
            + ++EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ 
Sbjct: 179 FLTIQEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREE 230


>gi|167646666|ref|YP_001684329.1| pseudouridine synthase [Caulobacter sp. K31]
 gi|167349096|gb|ABZ71831.1| pseudouridine synthase [Caulobacter sp. K31]
          Length = 245

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 111/233 (47%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           R+ +++A  G  SRR+V+ +++  +V ++G+ ++ A   +  T  +     + GVP+   
Sbjct: 8   RLDRLLANLGYGSRRDVQALVSTGKVTLDGVAIKDAGQKIAVTADLPLRMRIRGVPVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
               L + HKP+G+V +H +   R  ++D LP  +      + SVGRLD +T GLLL+T+
Sbjct: 68  APLVLLM-HKPLGVVCSHREDGER--IYDLLPKRWQIRDPALSSVGRLDKDTSGLLLITD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     +VYR      ++  +      G ++++G     +  TLD     
Sbjct: 125 DGDFLHRVISPKRHVPKVYRATLDRPLNGTEGAAFASGALMLEGEEKPLLPATLDV--LG 182

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
           +    + + EG+  +++++F      V  L R   G   L   L  G  R ++
Sbjct: 183 DHEARLTITEGRYHQVRRMFAAVGNHVVGLHRERIGGIDLPEDLAPGEHRILT 235


>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 =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 95/236 (40%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VD           
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVTVAGASATDPDATFDTDGLVFSVDDTAWPFHAHA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +LN L+ G+ + G       V  D +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLNTLRTGVQLHGEPKPIAAVAADAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G F L G L  G+ R +    L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESIGGFTLPGDLAPGAWRWLDDADLSALRNP 234


>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 =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 102/236 (43%), Gaps = 13/236 (5%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDG 128
             +   HKP+G   +  DP     V+D LPS F         VGRLD +T GLLL+T+DG
Sbjct: 59  L-ILALHKPVGYTCSTKDPG--RIVYDLLPSRFRLRSPLMSTVGRLDRDTSGLLLMTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L   +  P ++  ++Y       +  D+      G +++ G     + V L+       
Sbjct: 116 ALLHRIVSPKSRLAKIYEATLAEDLRGDEAAQFASGTLLLDGETTPLLPVQLEVLGPR-- 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            V V L EG+  +++++F      V  L R   G   L  L AG  R +    L +
Sbjct: 174 QVRVVLHEGRYHQVRRMFAAVGNHVLALHRSRIGGLALDALPAGQWRALEPMELAQ 229


>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 =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 100/245 (40%), Gaps = 28/245 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V V+G  ++     V     IE+D             L H
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQVTVLIH 60

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINTEGLLLL 124
           K +G V+  ++   +  +    P                   ++   GRLDI++ GLL+L
Sbjct: 61  KTVGFVSGQAEDGYQPAITLVTPENRWEGDRSNIRFSVAHLRQLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGICYGDM 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 QVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALPPGQWRY 236

Query: 236 VSKKI 240
           ++   
Sbjct: 237 LAADE 241


>gi|299115182|emb|CBN74013.1| RNA pseudouridylate synthase domain-containing protein (C-terminal)
           RNA pseudouridylate synthase dom [Ectocarpus
           siliculosus]
          Length = 490

 Score =  225 bits (574), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 119/345 (34%), Positives = 169/345 (48%), Gaps = 35/345 (10%)

Query: 3   DKNIVQENFTP----QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           D+  +Q+  T      R+S+ IAR+GIASRRE ERM+    V VNG  ++  A+NV   D
Sbjct: 98  DEEALQQPPTKDPSVMRLSRRIARSGIASRREAERMVEAGVVMVNGATVQTPALNVGPRD 157

Query: 59  HIEVD------------------GVPLRKAER--TRLWLYHKPIGLVTTHSDPDGRSTVF 98
            ++V+                  G  L + E    +LW+ HK    + T  DP+GR TVF
Sbjct: 158 IVKVNVGLFQQPGNGTDCFTFVQGKVLERPESHTPKLWMVHKMRNELVTRHDPEGRPTVF 217

Query: 99  DNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           D L  +     ++ VGRLD NTEGLLLLTNDG LAR +ELPS+  +R Y VR +G + ++
Sbjct: 218 DRLTKLKLPDTLMPVGRLDYNTEGLLLLTNDGDLARKMELPSSNIVRTYSVRVYGNITEE 277

Query: 157 KLNLLKKGIVIQGICYG-----DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           KL  ++ G  I G+ Y              ++G NAW+T+   EGKNR+I+K+ ++    
Sbjct: 278 KLRAMRSGCTIDGVRYKGMFVRVEGGGGKGREGRNAWLTIECTEGKNRQIRKICKYLCLT 337

Query: 212 VNRLIRISYGPFQLGTLLAGST--REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
           VNRL R  YGPF LG + AG     E+ K  +R                +   SS   V 
Sbjct: 338 VNRLARTRYGPFSLGKVRAGGVAAVEIPKAFMRRLEDGGGSPGGAGGGGSGSGSSRRRVG 397

Query: 270 DRP--NIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLAS 312
             P   +  E+     ++ + SS   GLS           R  +S
Sbjct: 398 PGPGNGMRREMEAGGMKVSEVSSPGTGLSNTVGGGRDTGDRAGSS 442


>gi|167739176|ref|ZP_02411950.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 14]
          Length = 313

 Score =  225 bits (574), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 66  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 125

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 126 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 185

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 186 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 245

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 246 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 301

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 302 GEWRYLGPDE 311


>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 =  225 bits (574), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+G   +   + V    HI  DG  L+ A +  
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLAERVYVDGAPAKSLDLLVDEFSHIVFDGQVLQ-ANQPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+V+   D + R TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YLMLYKPVGVVSATKDKEHR-TVIDLLDCDTRQELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VYRV     +  + +    +G+    + I     ++ +           V
Sbjct: 125 LMSPEQKVDKVYRVTLANPLSDEYIAAFAQGMYFGFEDITTQPAKLVILAP----HVAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            LREGK  +IK++F  F   V  L R+S G   L   L  G +R ++ + +
Sbjct: 181 TLREGKYHQIKRMFGRFRNPVLGLHRLSIGEITLDEALKPGESRMLTAQEV 231


>gi|144900938|emb|CAM77802.1| Ribosomal small subunit pseudouridylate synthase [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 230

 Score =  225 bits (574), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 107/235 (45%), Gaps = 15/235 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNG-ILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ ++IA  G  S+R++  ++   RV+  +G  L+E   V   + D I VDG PL    
Sbjct: 1   MRLVRLIANLGYGSQRDIRFLLRDGRVRHADGRELVESDKV---AHDDIRVDGEPLDPPA 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
              + + HKP G   + SDP     V++ LP  F      +  VGRLD +T GLLLLT+D
Sbjct: 58  GL-VIMLHKPAGYTCSSSDPG--RIVYELLPPRFMHRNPVLAPVGRLDRDTTGLLLLTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   L  P     + Y V     ++  +  +   G ++++          L     + 
Sbjct: 115 GKLLHRLTSPRHHVPKTYDVTLDRPLEGTEAEIFASGTLMLRSEKTPLAPAQLQVLGPNQ 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A   + L EG+  ++K++F      V  L R   GP  LG L  G  R ++ + L
Sbjct: 175 A--RLTLHEGRYHQVKRMFAAVGNHVVSLHRAGLGPLTLGDLPEGQWRVMAAEEL 227


>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 =  225 bits (574), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 65/240 (27%), Positives = 119/240 (49%), Gaps = 8/240 (3%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGV 65
           + E     R+ +++A     +R+++++++A++++ V+ +  ++ + N+      I++ G 
Sbjct: 4   ISEKEPSMRLDQLMANHQY-TRKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI-GE 61

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLL 123
            + +  R   ++ HKPIG VT   D     TV D +     +  +  +GRLD +T GLLL
Sbjct: 62  RIIQEPRHHYYMLHKPIGAVTAKRDA-HHPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLL 120

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ 182
           LT++G L   L  P     +VY V  +G +    +   + GI    G       +T+   
Sbjct: 121 LTDNGPLGFQLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILES 180

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
             S +   V + EGK  ++KK+F     KV  L R+S+GPF L   L  G +R +++  L
Sbjct: 181 TPSYSKAQVRISEGKYHQVKKMFLAIGVKVMTLKRLSFGPFTLDPQLAPGESRPLNEVEL 240


>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 =  225 bits (574), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 67/238 (28%), Positives = 106/238 (44%), Gaps = 24/238 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +++K +A  G  SR+E+E  I + RV   G               +E DG PL       
Sbjct: 6   KLAKYLASLGYGSRKEMEVAIRRGRVTGWGE-------------DVEFDGEPLDPGPGM- 51

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           + L HKP G   +H D      V+D LP  F     ++ SVGRLD +T GLLL T+DG L
Sbjct: 52  VILMHKPAGYTCSHQDQG--KLVYDLLPPRFLKRDPKISSVGRLDADTTGLLLFTDDGAL 109

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P +   + Y       ++  +      G ++++G     +   L+      A  
Sbjct: 110 LHRLISPKSDIPKTYEATLARPLEGFEKEFFASGSLILRGEDKPCLPAELEVTGERTA-- 167

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + L EG+  +++++F      V  L R  +GP +LG L  G+ R +++   R  L P
Sbjct: 168 RLTLSEGRYHQVRRMFAAAGNHVEALHRSRFGPLELGDLSEGAWRLLTEAE-RAGLAP 224


>gi|330981482|gb|EGH79585.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 230

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 108/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKVP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RHFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + +     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENLTTQPAQLTLLGPQSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALALDPNLRPGSYRALNAGEI 227


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 106/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQQVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 60/218 (27%), Positives = 103/218 (47%), Gaps = 7/218 (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+    +  D  S++  +LP   +RV  +GRLD ++ GL++LTNDG  
Sbjct: 61  ADLVYFAYHKPVGIDCKLNHHD-PSSLIHHLPQ-LTRVYPIGRLDKDSRGLIILTNDGDF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V  +  +D      +  G+ +        +V     K ++   +
Sbjct: 119 CNQLIHPDFHQPKRYLVTVNKPLDAHFCEKMAAGVPVDKQITRPCEVV----KIASNQFS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           + L++G NR+I+K+  +  + V  L R+      L  L
Sbjct: 175 IVLKQGLNRQIRKMAHYCGYTVIDLYRVQISELLLDNL 212


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +L      NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMLARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|330950091|gb|EGH50351.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 230

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 64/228 (28%), Positives = 107/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R++V   +A  RV+V+G         V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRQQVRLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + I     Q+TL   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQPIDERYAAKFAEGLYFAFENITTQPAQLTLLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
           + + EG+  ++K++F  F+ KV RL R + G   L   +  GS R ++
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRENIGALALDHDVPPGSYRALN 223


>gi|163857342|ref|YP_001631640.1| pseudouridylate synthase [Bordetella petrii DSM 12804]
 gi|163261070|emb|CAP43372.1| pseudouridylate synthase [Bordetella petrii]
          Length = 243

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 105/245 (42%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK++A  G+ SRRE +  I +  VKV+G+++            I ++     + 
Sbjct: 1   MEKIRISKLMAERGLCSRREADSYIERGWVKVDGVVVAELGARAFPDQVITLERAAQARQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLD 115
                 L +KP+G V+  ++                    +      +    +   GRLD
Sbjct: 61  TARVTILINKPVGYVSGQAEKGYTPASALVDARSRYARDRSPLRFTRAHLQGLAVAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I+++GLL+LT DG +AR L    +   + Y VR  G++D   L LL  G+ + G      
Sbjct: 121 IDSQGLLVLTQDGRIARQLIGEDSSVDKEYLVRVQGRLDAGGLALLNHGLSLDGKPLRPA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           QV           +   LREGK R+I+++ E    KV  L R+  G  +LG L  G  R 
Sbjct: 181 QVRWQNAD----QLCFVLREGKKRQIRRMCELVGLKVVGLKRVRIGRVKLGDLPPGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRDDE 241


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 99/233 (42%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            ++ +++   G  SR+    MI    V VNG + +           +  V G      E+
Sbjct: 1   MQLERILHSQGFGSRKICRSMIRHGEVAVNGEVCDFPFTEFDPEHLVFTVRGETWTYREK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP     +H  P    ++F  LP+      V S+GRLD +T GLLLL++DG  
Sbjct: 61  A-YLMLNKPAHYECSHK-PQHHPSIFSLLPAPLLERGVQSIGRLDEDTTGLLLLSDDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWV 189
              +  P  +  +VY V     +D+ ++  L  G+ +         V   + K   +  +
Sbjct: 119 IHRMSSPKWKVPKVYEVTTKHPLDETQVTSLLSGVQLLDE---PAPVAALSAKIVGDHVL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + L EGK  ++K++    + +V  L RI  G   L   L  G+ R +   +L
Sbjct: 176 HLTLAEGKYHQVKRMLAAVSNRVEALKRIRIGSLDLPEDLAPGAWRWLDAAML 228


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 57/206 (27%), Positives = 102/206 (49%), Gaps = 10/206 (4%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-LWLYHKPIGLVTTHSDP-DGRSTVFD 99
           +NG + +     V   D + +DG  + K ++ +    +HKP+G+  T +D  DG    + 
Sbjct: 3   INGEVCKH-GTIVTENDIVMIDGKTIEKEDKEKIYIAFHKPVGITCTAADHIDGNIIEYI 61

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           N P    R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++
Sbjct: 62  NHPE---RIFPVGRLDKASEGLILLTNDGRIANQILHGDYEHEKEYIVTVDKPFTDWFID 118

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            + +G+ I+       +VT    + +++   + L +G NR+I+++   F + V +L R+ 
Sbjct: 119 GMSRGVKIKDGITKQCKVT----RVNSSTFRIILTQGMNRQIRRMSRAFGYTVTKLKRVR 174

Query: 220 YGPFQLGTLLAGSTREVSKKILREQL 245
               +L  L AG  R V+ + L+E L
Sbjct: 175 IMNIKLDGLEAGEWRNVTVQELQELL 200


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 114/241 (47%), Gaps = 5/241 (2%)

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 +KP G V +        TV+D LP     +  VGRLD ++EG
Sbjct: 61  KVDGRHMTPMEEVVV-LLNKPRGYVCSREAQGAIGTVYDLLPPRLRHLNYVGRLDADSEG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL++TN G L +VL  P+    + Y V      D   L    +G+ I         V   
Sbjct: 120 LLIMTNKGELTQVLSHPTGGIEKEYWVTVDQNFDNSVLMQFLRGVRIPEGNAKAKYV--- 176

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             + S     + L +G  R+++++F+    +V +L+R+  G    G L  G  + +    
Sbjct: 177 -CRASARRACIVLEQGLKRQVRQMFQCLGLRVRKLVRVRIGSLWGGDLEPGGWKFLDDAD 235

Query: 241 L 241
           +
Sbjct: 236 V 236


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 114/235 (48%), Gaps = 6/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K+++RAGIASRR  E++I + RV+V+G L+      V      + VDGV +   +  
Sbjct: 18  RLQKILSRAGIASRRAAEKLIIEGRVEVDGQLVRELGTRVDPDVSVVRVDGVKVVVDDSL 77

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 78  VYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGEL 137

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L  G+ +     + D    +D   G    V
Sbjct: 138 AHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKT-LV 196

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+ 
Sbjct: 197 RLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQL 251


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 111/234 (47%), Gaps = 12/234 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           + +R+  +++R G  SR EV  ++ + RV+V G LL +A+  V +   + VD  P+    
Sbjct: 4   SAERMDHLLSRLGYCSRSEVRDLLREGRVRVAGELLRKASAKVNAA-EVWVDEEPIDHPH 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTND 127
                LYHKP+G V  H DP     ++ + P  +         VGRLD  T G+LLLT+D
Sbjct: 63  AF-YLLYHKPLGKVCAHDDPRA---IYQDFPLRWRYRRPALSSVGRLDRETSGVLLLTDD 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G        P     RVYRV     +  D  ++L  G +++ G         L     + 
Sbjct: 119 GDWLHHWTSPRRAIPRVYRVTLQEPLRSDAADILAAGTLMLDGEDTPCRPAALHC--LTE 176

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             V + L EG+  E++++F   +  V  L R +YGPF L  L AG  RE++   
Sbjct: 177 REVRLTLTEGRYHEVRRMFAALDNLVLTLHREAYGPFLLDDLPAGQWRELTVAE 230


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 109/261 (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  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRV 108
                        L HK +G V+  ++   +  +    P                   ++
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 LLRHGLSLDDVPLKPAQVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVR 323

Query: 220 YGPFQLGTLLAGSTREVSKKI 240
            G   LG L  G  R ++   
Sbjct: 324 MGRVVLGALPPGQWRYLAADE 344


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 54/229 (23%), Positives = 101/229 (44%), Gaps = 12/229 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TD-HIEVDGVPLRKAERT 73
           + K++   G  SR+  +++I    V +   + +     +   TD + +V        E+ 
Sbjct: 7   LEKMLQSQGFGSRKYCQQLIKNGAVSIQDEIQKDLKYRIHDLTDFNFQVFDQNYVYREK- 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G   +H  P    +VF  LP +     + +VGRLD +T GLLLLT+DG   
Sbjct: 66  VYIILNKPKGFECSHQ-PHHHQSVFSLLPDLLIQRNIAAVGRLDQDTTGLLLLTDDGQYL 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWV 189
             L  P     +VY V     +  D+++ L++G+ +      +    VTL  +      +
Sbjct: 125 HTLTHPKKHVPKVYHVATIDPITVDQMHQLEQGVELHNEKGVFAATNVTLLNE----TQL 180

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           ++ + +G   ++K++      KV  L R   G  +L  L  G    +++
Sbjct: 181 SMTIHQGVYHQVKRMIAAVGNKVTALHRHKIGQLELPNLAEGEWMYLTE 229


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 109/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     SR++   +I+  R++V+G  +     +V     +E+D   L+     
Sbjct: 1   MRLDRFLSNFPRFSRQDSRLLISAGRLRVDGETVRDPRFDVRDFQRVELDDELLQAGRSA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R W+ HKP+G+V+  +  + R TV D L       +   GRLD+NT GLLL+TNDG  +R
Sbjct: 61  RYWMLHKPVGVVSATAHDEHR-TVLDLLDEPDRHDLHLAGRLDLNTSGLLLITNDGRWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  +VY V     +  +   + ++G+    + +     ++ L     +     
Sbjct: 120 RITQPQQRKPKVYHVSTEQPITAEYAEVFERGLYFAFEDLTTLPARLELLGSHSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + L EG+  ++K++F  F  +V  L R S G   L   L  G  R ++   +
Sbjct: 176 LTLFEGRYHQVKRMFGHFRNRVVALHRESMGEIVLDPQLAPGQYRALTAAEI 227


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 375 MRLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQ 434

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                    +     P     +   GRLDI++
Sbjct: 435 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 494

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 610

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 611 QGQWRYLSADE 621


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/222 (31%), Positives = 111/222 (50%), Gaps = 13/222 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
           +R+ +V+A  G+ +R+EV ++I    V+V+G ++      +      IEV G P+R A R
Sbjct: 3   ERLDRVLAHLGLGTRKEVGKLIRAGAVRVDGAVVRDRGYKLDPEAARIEVRGEPVRYA-R 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               L HKP G++T     +  +TV D LP    R  +  VGRLD +TEGLLLLTN G L
Sbjct: 62  HFYVLLHKPAGVLTATR-SERETTVLDLLPDALWRDDLRPVGRLDRDTEGLLLLTNHGEL 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P  +  +VY      ++ +D      +G++     +   ++     + +     
Sbjct: 121 LHRLTHPRWKVAKVYFAELASELPEDAARRFAEGVL----DFAPAELEALGPRAA----R 172

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
           V L EGK+R+++++F      V  L R  +GP +LG L  G 
Sbjct: 173 VTLYEGKHRQVRRMFAALGAPVAYLRRERFGPLELGGLEPGQ 214


>gi|218296286|ref|ZP_03497042.1| pseudouridine synthase [Thermus aquaticus Y51MC23]
 gi|218243358|gb|EED09888.1| pseudouridine synthase [Thermus aquaticus Y51MC23]
          Length = 245

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 71/232 (30%), Positives = 115/232 (49%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++AR G+ SR+EV R+I   +V+V G ++     +V     +EV+G PL    R 
Sbjct: 13  ERLDKLLARLGLGSRKEVGRLIRSGKVRVGGGVVLDPGFHVPEGAALEVEGRPL-AVRRH 71

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
              L HKP G VT+  +     +V+  L    +R +  VGRLD +TEGLLL T DG L  
Sbjct: 72  LHLLLHKPAGYVTSRKEG---PSVYALLEGFPTRDLSPVGRLDKDTEGLLLFTTDGELLH 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y V          +   ++GI++ G      ++ L        WV + 
Sbjct: 129 RLTHPRHKVEKRYLVHLLHPATAADVRAFQEGILLSGEKTLPARLHL---GEDPTWVELT 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L EG+  ++K++F+    +V  L R++ GP  L  L  G+ R ++ +  R  
Sbjct: 186 LLEGRFHQVKRMFQARGNQVLYLKRLALGPLTLEDLPLGAARPLTPEEERAL 237


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+A I SR+ ++R + +  + ++       + NV +    I  D   +  A  
Sbjct: 1   MRLDRLLAQASI-SRKSMKRALLRGAILIDQTPARSLSQNVDTGLQEILFDKQKV-PAPA 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G +T +SD   + TV D +        + S+GRLD +T GLLL+T++G L
Sbjct: 59  HRYFMMNKPRGYITANSDA-SKETVIDLIQKEDYSGELYSIGRLDRDTTGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V+ +G ++   +   ++G+  + G      Q+T+ +     +  
Sbjct: 118 GFQLLHPQYHVDKTYYVQVNGLLNNQAIEAFQQGVRFLDGKVCKPAQLTIHSTTPVLSTA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +V + EGK  ++KK+F     KV  L R  +G FQL  +L  G  R +++  L+
Sbjct: 178 SVTISEGKFHQVKKMFLAIGVKVTYLKRTHFGDFQLDPSLAEGDYRSLNQDELK 231


>gi|167720171|ref|ZP_02403407.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei DM98]
          Length = 305

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 58  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 117

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 118 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 177

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 178 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 237

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 238 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 293

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 294 GEWRYLGPDE 303


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 106/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|167563192|ref|ZP_02356108.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           EO147]
          Length = 321

 Score =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 100/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 74  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 133

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++      V                   P     +   GRLDI++ 
Sbjct: 134 TILLHKPVGYVSGQAEDGYAPAVTLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 193

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G 
Sbjct: 194 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERMADIDQHFPAESLAKLRHGLELDGA 253

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 254 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 309

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 310 GEWRYLGPDE 319


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 75/239 (31%), Positives = 116/239 (48%), Gaps = 3/239 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K     N    R++K I+ +GI SRRE +  I+   V VNG ++      V  TD +  D
Sbjct: 50  KQKTSSNPNEIRLNKYISNSGICSRREADMHISVGSVTVNGKVVTEMGYKVQLTDEVRFD 109

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLL 122
           G  +   E+    L +KP G + T  D  GR TV D +  +  +R++ VGRL+  T GLL
Sbjct: 110 GRIIN-PEKATYILLNKPKGFLVTTKDEKGRKTVMDLVATATTARIVPVGRLERQTTGLL 168

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L TNDG LAR L  P     +++ V     + Q   N +K G+ I+G  YG  +++   Q
Sbjct: 169 LFTNDGELARKLTDPHQNVRKIFHVELDRNLSQTDFNKIKDGVNIRGDIYGVDEISW-IQ 227

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             S   V + +  G N  +K +FE  ++ V RL R+ +       L     R ++ + +
Sbjct: 228 GASKREVGIKVSTGSNGLVKAIFEHLSYTVARLDRVVFAGLTKKDLPRSHWRHLTAQEV 286


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 110/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K I++A   SR+E ++++    + VN  +++  +V+V    D +   G PL  A  
Sbjct: 1   MRLDKFISKATELSRKEAKKVLHASEITVNDEVVKDGSVHVDVLNDEVMWAGEPLSVATG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +R  L HKP G   T   P     V + +     S +   GRLD++T G L+L++DG   
Sbjct: 61  SRYILLHKPEGFECTLK-PKEYPIVTELIAVPELSNLRIAGRLDVDTTGALILSDDGSWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P     +VY +     +D++     +  + +GI++ G         L+    ++A
Sbjct: 120 HRVTSPRHLHEKVYELTLADAMDEEAQAHAIKKVGQGILLDGDYEPTKPALLEFIDETHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L EGK  ++K++  +F  KV  L R S G   L  L  G +R +++  +
Sbjct: 180 --RLILTEGKYHQVKRMMAYFGNKVVELHRASIGGITLEGLEKGDSRFLTEDEV 231


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 114/235 (48%), Gaps = 6/235 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K+++RAGIASRR  E++I + RV+V+G L+      V      + VDGV +   +  
Sbjct: 17  RLQKILSRAGIASRRAAEKLIIEGRVEVDGQLVRELGTRVDPDVSVVRVDGVKVVVDDSL 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGL 130
                +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGL+LLTNDG L
Sbjct: 77  VYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTNDGEL 136

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWV 189
           A  L  PS +  + Y     G V +     L  G+ +     + D    +D   G    V
Sbjct: 137 AHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKT-LV 195

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+ 
Sbjct: 196 RLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQL 250


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 7/230 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K ++     SR EV+R++    + VN +  + AA+ +    D I +   PL     
Sbjct: 1   MRLDKYVSSVTDYSRAEVKRLLKNGSITVNDVSTKNAALQLDTQKDIICLFDEPLSAPA- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
            R ++ +KPI  +    D     TV D L      ++   GRLD +T GL+L+T+DG  +
Sbjct: 60  PRYFMLNKPIDTICATED-SMHPTVIDLLDEPNTQQLHIAGRLDKDTTGLVLITDDGQWS 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +  P+   ++ YRV       +     L++G+++          T++    +   + +
Sbjct: 119 HQITSPNKHCIKTYRVELEEAFTETAKKALEEGVLLHNEKKPTRSSTVNI--INKYCIEL 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++       V +L R   G  QL  +L  G  R ++   
Sbjct: 177 AISEGKYHQVKRMLAAVGNHVKQLHRQQIGHIQLDSSLSLGQYRALTTDE 226


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 112/232 (48%), 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P T+  ++Y V    ++  + +     G+    + +     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|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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SRR+V+++I  Q V+++  +      NV      IE+ G  +    +
Sbjct: 1   MRLDKLLEVVTDGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEISGKRISHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYFILNKPAGVVSARSDI-NHVTVLDQLSEKDRHPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G +D D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVAKTYMVTVNGFLDADAPDFFAAGIKFPTGEQCRPAQLTILQASQEKSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R ++   
Sbjct: 179 RLVISEGKFHQVKKMFLTYGLKVISLKRASFAGLELGELASGAYRSLTDAE 229


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/232 (30%), Positives = 124/232 (53%), Gaps = 4/232 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+++ IAR+G  SRR+ +++I   +VKVNG +++     V    D +E+DG  ++   +
Sbjct: 3   MRLNRFIARSGYCSRRKADQLIEMGKVKVNGKVVKDFGYRVDTEKDRVEIDGKLIKLELK 62

Query: 73  TRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGG 129
                 +KP G +T    D  GR T+ D      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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + +  GK R I++  ++F + V RLIR   G  +LG+L     + + +KI+
Sbjct: 183 EITIHSGKKRIIRRFTKYFGYPVERLIRTRIGSIELGSLKEKEWKYIDEKII 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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/234 (29%), Positives = 119/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            R+ K++A AG  +R EV++ + Q  V+V+G +++   ++V      +   G P+R    
Sbjct: 1   MRLDKMLANAGYGTRNEVKKALKQGVVEVDGAVVKDGKLHVQPERQSVCYAGTPVRYKAE 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+VT   D   + TV D + + +  +    VGRLD +T GLLLLT DG  
Sbjct: 61  L-YLMLNKPAGVVTATEDAR-QKTVLDLMKNEWGHMKPFPVGRLDKDTTGLLLLTTDGAF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P     + YR    G+V Q  +   K G+V+  G C    Q+ ++ + G  + +
Sbjct: 119 SHELMAPKKHIAKEYRALVEGKVTQADVEAFKNGVVLDDGYCTKPAQLEIE-ESGPLSAI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           ++ L EGK  ++K++F     KV +L RI  G   L  +L  G  RE++   ++
Sbjct: 178 SLELTEGKFHQVKRMFAAVGKKVIKLERIRIGSLLLDSSLPKGGYRELTPAEIQ 231


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 111/237 (46%), Gaps = 13/237 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R E   +I   +V VNG  +   +  V   +HI ++G     A  +
Sbjct: 1   MRLDKFLCKSTQLTRHEACELILAGKVLVNGESVVSPSAQVHENNHIRLEGGQRLTARAS 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP   ++++ D D   +VF+ +     S +   GRLD +T GLLL+T+DG  + 
Sbjct: 61  RYIMLHKPADTLSSNVDGDH-PSVFNFINLEHTSELHIAGRLDADTTGLLLITDDGRWSF 119

Query: 133 VLELPSTQWLRVYRVRFH--------GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
            +  P     +VYRV           G++D +     K+G+ +QG     +   L+    
Sbjct: 120 NVFNPKYHCEKVYRVYLRDSIEGEIAGEIDAELKARFKQGLDLQGEQALTLPAKLEFVSP 179

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               V + + EG+  ++K++F     +VN L R   G  +L  +  G  R ++++ +
Sbjct: 180 KE--VLLTITEGRYHQMKRMFARVGNRVNALHREQVGKIKL-DMPVGQWRYLTREEI 233


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 111/240 (46%), Gaps = 14/240 (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       + V         R+  +GRLD  +EGL+L+T
Sbjct: 61  KKPGGRKHVYIALNKPVGITCTTESSVKGNIV--EFVGHEQRIFPIGRLDKESEGLILMT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++G +   +     +  + Y V  +  V  + L  + +G+ I        +    T + +
Sbjct: 119 SNGNIVNEILRAENRHQKEYLVAVNKAVTDEFLRGMARGVRIHNETTLPCR----TARIA 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
                + L +G NR+I+ +   F+++V +L R+     +L  L  G  R +S   L   L
Sbjct: 175 KFGFRIVLEQGLNRQIRLMAAEFDYRVTQLRRVRIDNIKLAALKPGQWRNLSDAELHGLL 234


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 100/239 (41%), Gaps = 12/239 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAERT 73
           + +++   G  +RR    +IA   V+VNG L E         D   + VDG       + 
Sbjct: 3   LDRILQSQGFGTRRYCGDLIAAGLVEVNGELCEDPRAQ-FEVDGLRLTVDGEEWLACTKA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G   +   P    +V++ LP    +  V +VGRLD +T GLLLLT+DG   
Sbjct: 62  -YLMLNKPAGYECSQR-PRHHPSVYNLLPVPLRQREVQAVGRLDHDTTGLLLLTDDGQFI 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVT 190
                P  +  ++Y V     V  ++   L+ G+ +         +  +  + +    + 
Sbjct: 120 HAQTSPKRKVPKIYEVTTAEPVTPEQAEALRSGVQLLDE---PAPIAAEACEITGERSLR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPH 248
           + L +GK  ++K++       V+ L R + G   L   L  G  R ++ + L    G  
Sbjct: 177 LTLVQGKYHQVKRMVVAAGNHVDALHRSAIGSLPLDPALAEGEWRWLTAQELAALTGKE 235


>gi|332362872|gb|EGJ40665.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK49]
          Length = 241

 Score =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 119/233 (51%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+T+ + + S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPQDKIAFQEGIRFLDGTVCQPAQLTIFSSRSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           +V + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 178 SVRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>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 =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 108/242 (44%), Gaps = 20/242 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK +A  G+ SRRE +  I++  V VNG+        V   D IE++ V  R   R 
Sbjct: 1   MRLSKRMAELGLCSRREADEYISRGLVSVNGVPA-VLGQKVTERDRIEMNRVAERDQSRR 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINT 118
              L HKP+G V+  ++   R       P                    ++  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 WQ----NDDQLRFVLQQGKKRQIRRMCALVGLEVLALKRVRVGSVRLGALPPGQWRYLLP 235

Query: 239 KI 240
           + 
Sbjct: 236 EE 237


>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 =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 108/247 (43%), Gaps = 23/247 (9%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK+++  G+ SRRE +  I +  V+V+G ++            I ++       
Sbjct: 1   MEKVRISKLMSEQGLCSRREADSYIERGWVRVDGEVVSELGAKAYPHQKITLERAARAAQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV-----------------FDNLPSIFSRVISVGR 113
                 L +KP+G V+  ++   +  V                 FD   +    +   GR
Sbjct: 61  TSLATILINKPVGYVSGQAEDGYKPAVALVDARSQYEGDRSGRRFDR--ANLRGLAVAGR 118

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LDI+++GLL+LT DG +A+ L    +   + Y VR  G++ +  L LL  G+++ G    
Sbjct: 119 LDIDSQGLLVLTQDGRVAKQLIGEDSLVDKEYLVRVEGRLSERGLALLNHGLMLDGKPLK 178

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              V    +      +   LREGK R+I+++ E    +V  L R+  G  +LG L  G  
Sbjct: 179 PANVCWQNED----QLRFVLREGKKRQIRRMCELVGLRVVGLKRVRIGRVRLGDLPVGQW 234

Query: 234 REVSKKI 240
           R + +  
Sbjct: 235 RYLREDE 241


>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 =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 102/236 (43%), Gaps = 17/236 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDH--IEVDGVPLRKA 70
            ++ K +A  G  SR+EV  M  + RV   +G +L          DH  + VDG PL   
Sbjct: 1   MKLVKHLANLGYGSRKEVAWMFREGRVTDADGEVL----YQDDPLDHDNVRVDGEPLDPP 56

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTN 126
           +   L + HKP G   +  D      V+D LP  F     V    GRLD  T GLLL+T+
Sbjct: 57  QGL-LLMLHKPAGYTCSTKDKG--RIVYDLLPPRFRLRDPVLSTVGRLDRETTGLLLMTD 113

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P ++  +VY       +  D+  L   G ++++      +   ++     
Sbjct: 114 DGQLLHRIVSPKSKLAKVYEADLAEDLRGDEAQLFASGTLMLESETTPLLPAQMEVLGPR 173

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            A   V L EG+  +++++F      V  L R   G   LG L  G  R++ +  L
Sbjct: 174 RA--RVVLHEGRYHQVRRMFAAVGNNVVALHRPRIGGLALGDLAEGQWRQLGQDDL 227


>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 =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 107/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G +      +V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVAFDMQILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  +D    +TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATTDAQH-ATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + I     Q+T+   + +     
Sbjct: 120 RLTQPHTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV +L R S G   L   L  G  R +    +
Sbjct: 176 LSIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPALPPGGYRSLQAAEI 227


>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 =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 86/245 (35%), Positives = 121/245 (49%), Gaps = 11/245 (4%)

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 D + +   R++ VGRLD NT G+LLLT D  L  
Sbjct: 65  FKYFLLNKPKNSITTSNDPKGRRTVIDLI-NTNERIVPVGRLDRNTTGVLLLTTDYELVN 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      L+E+
Sbjct: 179 LHVGSYHHVKKLFEKIGHKVLTLKRVSYANLTVDKLPEGMYRELTLKEVRNL--KLLVEK 236

Query: 253 AQVNL 257
            + NL
Sbjct: 237 QEKNL 241


>gi|323526492|ref|YP_004228645.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323383494|gb|ADX55585.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 243

 Score =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 100/245 (40%), Gaps = 28/245 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V V+G  ++     V     IE+D             L H
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQVTVLIH 60

Query: 80  KPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           K +G V+  ++                +G  +      +   ++   GRLDI++ GLL+L
Sbjct: 61  KTVGYVSGQAEDGYQPAITLVTPENRWEGDRSDIRFSVAHLRQLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGICYGDM 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 QVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPPGQWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LGPDE 241


>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 =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/251 (28%), Positives = 104/251 (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  RLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINT 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 QQLKPALVEWQNPE----QLRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGQVLLGKLP 235

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 236 PGQWRYLAPGE 246


>gi|324990675|gb|EGC22611.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK353]
          Length = 241

 Score =  224 bits (572), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKYVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++++ Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQILLQKQILVDGNPACKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKITFQEGIRFLDGTVCQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R +++K L  ++   
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQKEL--EIIKE 235

Query: 249 LLEEAQ 254
            LE+++
Sbjct: 236 YLEKSR 241


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 80/234 (34%), Positives = 117/234 (50%), Gaps = 5/234 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRR+VE++I   RV VNG L+      V   D + VD V +    +T 
Sbjct: 4   RLNKYLASCGVGSRRKVEQLITAGRVTVNGYLVSDLGHQVEDGDAVAVDDVEVHVEAKT- 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             +  KP G +   ++PD    V D LP  +   R+  VGRLD+ +EG+L+LTNDG  A 
Sbjct: 63  YIVIRKPRGYICAVTNPDY-PVVLDLLPRSYDRLRLFPVGRLDLQSEGILILTNDGDFAN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTV 191
            L  PS    + Y VR +  +    L  L+ G V +G     + V  L  ++    W T 
Sbjct: 122 DLIHPSNGVTKTYEVRMNRVLTAADLENLRGGTVFEGRRLVPLSVDLLPDRRPEGQWATF 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L EG  REI+ + E     V  L R + G  +L TL +G   EV+ K L + +
Sbjct: 182 VLGEGVKREIRLMAEGCGMTVEVLFRRAIGRMELRTLKSGEFVEVTLKDLWKMI 235


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 106/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPIHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R +++  
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTESE 229


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 96/236 (40%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  +DG       R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIESGRVTVAGASATDPDAAFDTDGLVFTLDGTAWPYHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLLARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D+ +LN L+ G+ + G       V    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDETQLNALRSGVQLHGEPKPIAAVAAVAR--DTHTLALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R   G F L   L  GS   +++  L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRERIGGFALPAGLAPGSWCWLAEAELAALRNP 234


>gi|167894879|ref|ZP_02482281.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 7894]
          Length = 307

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 60  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 119

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 120 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 179

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 180 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 239

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 240 PLKPAMVSWQNGE----QLCFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 295

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 296 GEWRYLGPDE 305


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 98/245 (40%), Gaps = 28/245 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D             L H
Sbjct: 1   MSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQVTILLH 60

Query: 80  KPIGLVTTHSDPDGRS-TVFD--------------NLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V+  ++      TV                  P     +   GRLDI++ GLL+L
Sbjct: 61  KPVGYVSGQAEDGYEPATVLITRENHWSGDRSPLRFSPQHLRTLAPAGRLDIDSTGLLVL 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGICYGDM 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 MVSWQNGE----QLRFVLREGRKRQIRRMCELVGLDVIGLKRVRMGRVMLGALPQGQWRY 236

Query: 236 VSKKI 240
           +S   
Sbjct: 237 LSADE 241


>gi|72080505|ref|YP_287563.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 7448]
          Length = 237

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 111/231 (48%), Gaps = 6/231 (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        I    ++     +K S+    V +
Sbjct: 119 LLHPSSKIERTYLVKTDFSLSDKEIRFLND----NKIQLDSVKSIQKIKKCSSRTYLVTV 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++ + ++  
Sbjct: 175 WQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTNQEIKSL 225


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 54/206 (26%), Positives = 95/206 (46%), Gaps = 8/206 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +       V   D + ++G  + K E+      +HKP+G+  T +D      + D 
Sbjct: 3   INGEICTH-GTRVRDGDIVTINGQVIEKEEKEKVYIAFHKPVGITCTAAD-HIEDNIIDY 60

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           + +   R+  VGRLD  +EGL+LLTNDG +A  +     +  + Y V          ++ 
Sbjct: 61  I-NYPERIFPVGRLDKASEGLILLTNDGTIANQILHGDHEHEKEYVVTVDKPFTDWFIDE 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I+       +VT    +   +   V L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSGGVKIKDGMTKPCKVT----RIDQSTFRVVLTQGMNRQIRRMSRAFGFTVTKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILREQLG 246
              +L  L AG  R+++ K L    G
Sbjct: 176 MNIELNELEAGKWRDITPKELEILTG 201


>gi|332363998|gb|EGJ41777.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK355]
          Length = 241

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 119/233 (51%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+     + + NV ++   I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDDKPACKLSQNVDTSLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDEEVEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +     +  ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPKDKSSFQEGIRFLDGTTCQPAQLSILSTSSSLSCA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPELATGDYRPLNQEEL 230


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 105/238 (44%), Gaps = 9/238 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V + G ++          +    + G   R  E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGSVSIEGEIVTDLKKQFSPENLEFSLFGETYRYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
                KP G   +H+ P    +VF  LP I     V ++GRLD +T GLLLLT+DG   +
Sbjct: 62  YLALKKPQGFECSHN-PQHHQSVFSLLPEIMIQRGVQAIGRLDQDTTGLLLLTDDGKYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY V     V  +++ +L +G+ +      D+    D     +  +T+ 
Sbjct: 121 ALTHPRKHVPKVYHVTTIDSVTPEQIEMLTQGVNLH--QEKDVFAATDVALLGSHQLTMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + +G   ++K++      KV +L R   G   L  +  G    +S++   +QL  +++
Sbjct: 179 IHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGDWVYLSEQE--KQLAQNII 234


>gi|325697062|gb|EGD38949.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK160]
          Length = 241

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKQVSDPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKLAFQEGIRFLDGTICQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 178 TVKISEGKFHQIKKMFLALGVKVTYLKRIQFGNFTLDPDLATGDCRPLNQEEL 230


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 122/231 (52%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+IA +G  SRRE +R+I    V VNG+++   A      DH+ V+G  L    + 
Sbjct: 9   IRLNKLIASSGKYSRREADRLIQNGFVLVNGVVITNPAEKFSINDHVVVNGEKLDFN-KK 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KPI ++T++     + ++ D      +R+   GRLD  +EGL++ TNDG L   
Sbjct: 68  VYIKFYKPIKVLTSYDKYRDKKSLLDIEFFKKNRLGYSGRLDYESEGLIIFTNDGDLIYK 127

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           ++ PS++  + Y V     +++ +L L++ G+  + I Y   ++        N    + L
Sbjct: 128 IQHPSSRIEKEYIVAVDKILEEKELELIRAGLKTKEIKYLPCKINYLG----NYTYNIVL 183

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            EGK REI+ +F+FF   V +L R+  GP ++  L  G  + +SKK + E 
Sbjct: 184 YEGKKREIRNIFKFFKINVKKLKRVRIGPIRIVDLKPGEYKHLSKKEIEEL 234


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 55/206 (26%), Positives = 98/206 (47%), Gaps = 8/206 (3%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +NG +    A+ V   D + +DG  + K E+      +HKP+G+  T +D      + D 
Sbjct: 3   INGEICTHGAL-VSDGDRVTIDGQVIVKEEKEKVYIAFHKPVGITCTAAD-HIEDNIIDY 60

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           + +   R+  VGRLD  +EGL+LLTNDGG+A  +     +  + Y V          ++ 
Sbjct: 61  I-NYPERIFPVGRLDKASEGLILLTNDGGIANQILHGDHEHEKEYVVTVDKPFTDWFIDE 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           + +G+ I+       +VT    +   +   + L +G NR+I+++   F + V +L R+  
Sbjct: 120 MSRGVKIKDGMTKPCKVT----RVDQSTFRIVLTQGMNRQIRRMSRAFGFTVIKLKRVRI 175

Query: 221 GPFQLGTLLAGSTREVSKKILREQLG 246
              +L  L  G  R V+ + L   +G
Sbjct: 176 MNIELNELEVGKWRSVTAEELEILIG 201


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 59/232 (25%), Positives = 100/232 (43%), Gaps = 11/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERT 73
           +  ++   G  SRR+   ++A  RV + G + +    +   TD +E  VDG      +  
Sbjct: 3   LETILFSQGFGSRRQCRALVAAGRVAIGGAICDDPEQS-FPTDGLEFDVDGTRWLYRQHA 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G   +  +P    +VF  LP       V  VGRLD +T GLLLL++DG   
Sbjct: 62  -YLVLNKPAGYECSR-EPQHHESVFALLPPQLATRGVQCVGRLDQDTTGLLLLSDDGQFV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  + Y       +D  +L  L+ G+++ G         LD Q      + +
Sbjct: 120 HAYTSPKRKVPKTYLATLKHPLDAAQLTALRDGVLLHGEPKP--IAALDAQARGTHQLEM 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL--GTLLAGSTREVSKKIL 241
            ++EGK  ++K++      +  +L R   G F L    L  G+ R + +  L
Sbjct: 178 TVQEGKYHQVKRMIAAAGNRCEQLHRERIGGFALPADALPPGAWRWLDEADL 229


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 106/231 (45%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +       R+ V  ++   RV V+G++++     V     I++D   + +A    
Sbjct: 7   RLDRYLCTQLHTHRKAVRELLLSGRVCVDGLIVKDMDRQVDEFSRIQLD-EHILQANAPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKPIG+V+   D   + TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YVMLHKPIGVVSATKDTQHK-TVIDLLDCEARDELHIAGRLDLNSSGLLLLTNDSRWSDA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     + ++ +    +G+    + I     ++ +     +     V
Sbjct: 125 LMSPTHKVDKVYRVTLANSITKEYIAAFAEGMYFGFEDITTQPAKLVILADNVA----EV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 181 TLHEGKYHQIKRMFGRFRNPVVGLHRLSIGEIVLDEKLAPGESRALTAAEV 231


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 10/231 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ ++ +R G  SR E+   +   RV V    +   ++ V     +++DG PL   E  
Sbjct: 6   ERLDRLFSRLGYGSRSELREWLRAGRVSVGSRPVGSPSLRVDPK-LVQIDGQPLDHPEGL 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
              LYHKP G V  H +P    +V+ + P+ +      + +VGRLD +T G+LL+T+DGG
Sbjct: 65  -YLLYHKPRGKVCAHGEP---RSVYGDFPAAWSVRRPAINTVGRLDADTSGVLLVTDDGG 120

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
                  P     R YRV     +    L  L+ G ++         +  D +  +   +
Sbjct: 121 WLHRWTHPRRAVPRTYRVGLAEPITDGALAQLRSGKLLLAGETSPC-LPADVEVLAPRHL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + LREG+  E++++      +V+ L R ++GPF++  L +GS R +    
Sbjct: 180 RLTLREGRYHEVRRMLAALGNRVDTLHREAFGPFRVDDLPSGSWRLLDPHE 230


>gi|227874423|ref|ZP_03992604.1| RluF protein [Oribacterium sinus F0268]
 gi|227839739|gb|EEJ50188.1| RluF protein [Oribacterium sinus F0268]
          Length = 240

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 114/240 (47%), 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  KEKPKPVLLKYYKPRGIICTTGEKDRGKNVIEAI-GYKERIYPIGRLDKDSEGLLLLTNQ 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-----DTQ 182
           G L   +   S    + Y V     V ++ L  +  G+ +  +     +  L       +
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|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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/251 (25%), Positives = 102/251 (40%), Gaps = 32/251 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      +    
Sbjct: 1   MRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARSEQGER 60

Query: 74  RLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                +   T           +   GRLDI++
Sbjct: 61  VTVLLHKPMGYVSGQAEDGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDIDS 120

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQV--------DQDKLNLLKKGI 165
            GLL+LT DG +AR L    +   + Y VR       G V         ++ L  L+ G+
Sbjct: 121 TGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRHGL 180

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G   L
Sbjct: 181 SLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSVVL 236

Query: 226 GTLLAGSTREV 236
           G L  G  R +
Sbjct: 237 GDLPVGKWRFL 247


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 119/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A A I SR+E+++ +  +++ ++G      + NV S    I + G  L     
Sbjct: 17  MRLDKFLALAKI-SRKEMKQKLRLRQIVIDGQAARSLSQNVDSGLQSISLAGKTLNHLA- 74

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R +L +KP G VT +SD D + TV + +       ++ ++GRLD +T GLLL+T++G L
Sbjct: 75  HRYFLMNKPAGAVTANSDAD-KLTVLELIAPEDFNDQLYAIGRLDRDTRGLLLITDNGPL 133

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +DQ+     ++GIV + G      Q+ + T    ++  
Sbjct: 134 GFQLLHPQYHIAKTYYVEVNGPLDQEATIAFQQGIVFLDGTRCKPAQLQIHTTSPEHSTA 193

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +V + EGK  ++KK+F     KV  L R  +G FQL   L  GS R ++   L 
Sbjct: 194 SVTISEGKFHQVKKMFLAVGVKVTYLKRTHFGDFQLDPNLTEGSYRPLNPSELE 247


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 116/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++ +  + SR+ +++ + ++ + V+ +     A NV +    +   G  ++  E 
Sbjct: 1   MRLDKLLTQEKV-SRKAIKQALLKKEILVDELPATSLAQNVDTGLQELIFQGRKIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           T   + HKP G+VT   D     TV D LP       + ++GRLD +T GLLLLT++G L
Sbjct: 60  T-YLMLHKPNGVVTASKDKK-LPTVMDLLPQSLQSEELYAIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + YRV  +G +  DK+   K GIV + G      Q+ + +   S++  
Sbjct: 118 GFQLLHPQYHVDKTYRVEVNGPLTPDKVQEFKDGIVFLDGTVCKPAQLDILSSSSSHSKA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  ++KK+F     KV  L RI +G F L   L  G  R ++++ L 
Sbjct: 178 IITIAEGKFHQVKKMFLSIGVKVTSLKRIQFGDFTLDSELAEGQYRSLNQEELE 231


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 58/235 (24%), Positives = 93/235 (39%), Gaps = 12/235 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+  +++R G  SRRE    I +  +   G         V +   I +DG P+   +  
Sbjct: 1   MRLDALLSRYGYCSRREAPGWIKRHSITFKGKPCSSPTDKVQAE-GILLDGEPVEFPDGL 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGG 129
                +KP G   +H D +G   ++D LP  +         VGRLD  T GLLLLT+DG 
Sbjct: 60  -YAALYKPEGYTCSHDDGEGN-LIYDLLPFQWRHRNPAVSSVGRLDKETSGLLLLTDDGK 117

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
               +  P     +VY       +  + + L   G + + G         L+ ++   A 
Sbjct: 118 FIHRMTSPRHHVAKVYEAVTEEDIPTEAVELFASGTLTLNGETRPCAPALLEIREPRRAL 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           +   L EGK  +++++       V  L R+S G   L    L  G    +    L
Sbjct: 178 L--TLTEGKYHQVRRMLAAVGAPVLSLCRVSIGSLHLDSLNLKPGEWAPIRPDAL 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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  ++  +RV V+G   +   + V    HI  DG  L+ A +  
Sbjct: 7   RLDRYLAVKLQIHRKAVRELLLAERVYVDGAPAKALDLLVDEFSHIVFDGQVLQ-ANQPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+V+   D + R TV D L       +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YLMLYKPVGVVSATKDKEHR-TVIDLLDCDTRQELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VYRV     +  + +    +G+    + I     ++ +           V
Sbjct: 125 LMSPEQKVDKVYRVTLANPLSDEYIAAFAQGMYFGFEDITTQPAKLVILAP----HVAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            LREGK  +IK++F  F   V  L R+S G   L   L  G +R ++ + +
Sbjct: 181 TLREGKYHQIKRMFGRFRNPVLGLHRLSIGEITLDEALKPGESRMLTAQEV 231


>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 =  223 bits (570), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 117/242 (48%), Gaps = 13/242 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +    I +R++++  +   R  VNG ++ R  ++V    D I  DG  LR + +
Sbjct: 1   MRLDKFLGLFDIGTRKQIKEYLKNGRCSVNGEVVTRPDIHVDENNDEISFDGKTLRYS-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              ++ +KP G+V+  +D    +TV D L       +   GRLDI+TEGLLLLT+DGGL 
Sbjct: 60  YHYYMLYKPQGVVSATTDGRN-TTVLDLLQEENVKGLSPAGRLDIDTEGLLLLTDDGGLI 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------YGDMQVTLDTQK 183
             L  P     +VY V     +    +  L+KG+ I                 V +D   
Sbjct: 119 HRLLSPKKHVDKVYEVHLRKDLSDKDIESLEKGVNIGDTKDNGEIDYTLPARVVRMDEDD 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            +   V + + EG+  ++K++ E    +V  L R+S GP  L  TL  G  R+++++ L+
Sbjct: 179 ENRPVVHLIIHEGRFHQVKRMMEAVGNEVLFLKRLSMGPLILDETLEPGEYRQLTQEELK 238

Query: 243 EQ 244
           + 
Sbjct: 239 QL 240


>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 =  223 bits (570), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 115/234 (49%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+  I SR+ +++ + ++ + V+       + NV +    +   G  ++  E 
Sbjct: 1   MRLDRLLAQEKI-SRKAMKQALLKKEILVDECPARFLSQNVDTGLQKLVFQGRQIQGYEH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G+VT   D     TV D L       ++ ++GRLD +T GLLLLT++G L
Sbjct: 60  N-YLMLHKPNGVVTASRD-KNLPTVMDLLSPDIQSDQIYAIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y+V  +G +  D +   K+GIV + G       + + +   S++  
Sbjct: 118 GFQLLHPQYHVDKSYQVVVNGPLTPDHIQRFKEGIVFLDGTTCKPATLEILSSSPSSSQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           T+ + EGK  ++KK+F     KV  L R+ +G F L   L  G  R ++++ L 
Sbjct: 178 TITISEGKFHQVKKMFFSVGVKVVSLKRVQFGDFTLDSELAEGQYRFLNQEELE 231


>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 =  223 bits (570), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 111/234 (47%), Gaps = 12/234 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           + +R+  +++R G  SR EV  ++ + RV+V G LL +A+  V +   + VD  P+    
Sbjct: 18  SAERMDHLLSRLGYCSRSEVRDLLREGRVRVAGELLRKASAKVNAA-EVWVDEEPIDHPH 76

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTND 127
                LYHKP+G V  H DP     ++ + P  +         VGRLD  T G+LLLT+D
Sbjct: 77  AF-YLLYHKPLGKVCAHDDPRA---IYQDFPLRWRYRRPALSSVGRLDRETSGVLLLTDD 132

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G        P     RVYRV     +  D  ++L  G +++ G         L     + 
Sbjct: 133 GDWLHHWTSPRRAIPRVYRVTLQEPLRSDAADILAAGTLMLDGEDTPCRPAALHC--LTE 190

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             V + L EG+  E++++F   +  V  L R +YGPF L  L AG  RE++   
Sbjct: 191 REVRLTLTEGRYHEVRRMFAALDNLVLTLHREAYGPFLLDDLPAGQWRELTVAE 244


>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 =  223 bits (570), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 105/243 (43%), Gaps = 23/243 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-------STDHIEVDGVP 66
            R+ K++A  G  +R EV++++  +       +     V          S   + V    
Sbjct: 1   MRLDKLLAHTGYGTRTEVKKLLKSK------EVKVDGVVVKDAKVKVDLSKQCVTVFDEV 54

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLL 124
           +   E     + +KP   ++   D   R TV D L   +    V   GRLD +TEGL+LL
Sbjct: 55  VEYRE-FVYLMMNKPQDCLSATRDQRYR-TVIDLLDDYYLMFDVAPAGRLDRDTEGLVLL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-----YGDMQVTL 179
           TNDG LA  +  P     + Y     G++  +KLN L+ G+ I             +V +
Sbjct: 113 TNDGKLAHEIISPKKDVYKRYVAHVTGELTDEKLNQLETGVEILDGTGEVFSTKPAKVKI 172

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
             +      V + + EGK  ++K++F     KV  L R++ G  +L  +L  G  RE++ 
Sbjct: 173 LQKNDEWTEVEICITEGKFHQVKRMFASVGGKVIYLKRLAIGGLELDESLELGEYRELTD 232

Query: 239 KIL 241
           + L
Sbjct: 233 EEL 235


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 68/226 (30%), Positives = 120/226 (53%), Gaps = 10/226 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +++    SR  +  ++A  RV+VNG+ +      +   D +E+DG PL+ +E  R
Sbjct: 7   RLDRFLSQVLQVSRSGLRPVLAAGRVRVNGVPVRDRQQRIGPFDRVELDGQPLQ-SEAPR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V+  SD    +TV D LP+   + +   GRLD N+ GL+LLTNDG  +R 
Sbjct: 66  YLMVNKPAGVVSATSDDQH-TTVMDLLPASQRQGLHLAGRLDFNSTGLVLLTNDGAWSRQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P +Q  + YRV     + +  +    +G+    +GI     ++ + +   ++ W   
Sbjct: 125 LSQPQSQVRKHYRVTVEQPLTEAYVAAFSEGMWFAFEGIKTRPAEIKIRSAYEADVW--- 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
            L EG+  +IK++F  F+ KV  L R++ G   L  +L  G +R++
Sbjct: 182 -LCEGRYHQIKRMFGRFDNKVLTLHRLAIGHLVLDESLAPGESRDL 226


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 107/235 (45%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            ++ +++ + G  SRRE   +I + RV VNG + +   V + +   +  VDGV    AE 
Sbjct: 1   MQLERILQKHGFGSRRECRGLIRRDRVAVNGQVCDDPFVELDTEGLVFTVDGVDWPYAEF 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G   +   P   + V + LP       V  +GRLD +T GLLL+TNDG L
Sbjct: 61  A-TLMLHKPAGYECSRK-PKHHAGVLELLPIPLRERDVQPIGRLDEDTTGLLLITNDGQL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L     +  +VY       +DQ +++ L  G+++    Y  +        G    + 
Sbjct: 119 NHQLSSAKRKVPKVYLATTKHPLDQAQIDQLVAGVLLADE-YEPISAAAAEIVGEK-LLR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + L EGK  ++K++    + +V  L R + G   L   L  G  R +S   L++ 
Sbjct: 177 LTLTEGKYHQVKRMVAAVSNRVEALHREAVGELTLPPDLKPGEWRWLSAADLQKL 231


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 110/233 (47%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++ +    SR++++++I+   V ++       + NV      I V G  +    +
Sbjct: 1   MRLEHLLMKHFDISRKQMKKLISSGEVLIDSTPATHVSNNVDPQIQVITVQGSRMEDNSQ 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + +L +KP G++T  +D     TV D   +     +  +GRLD +TEGLL++TN+G L 
Sbjct: 61  -KYYLLNKPKGVITATTDSQ-LPTVIDLFKNENIEGLYPIGRLDRDTEGLLIITNNGPLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVT 190
             L  P     + Y V  +G +D   +     GI+   G      ++++     S +  T
Sbjct: 119 YRLLNPIQHIEKEYYVEVNGPLDNSCIQRFYDGIMFHDGTICKPAKLSILESSPSFSKAT 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           V + EGK  +IKK+F     KV  L RI +G F L  +L  G  R ++   L+
Sbjct: 179 VTISEGKFHQIKKMFLCVGVKVTFLKRIRFGEFLLDESLSPGEYRPLNFSELQ 231


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVTVAGASATDPDASFDTDGLVFTVDDTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +LN L+ G+ + G       V    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + ++ L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESIGGFTLPEDLAPGAWRWLGERELSALRDP 234


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 105/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  P     + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPIHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 100/230 (43%), Gaps = 12/230 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K I   G+ SR++ + +I    + +NG +  RA  ++  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVP 60

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 61  MPYFYILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
                +  P  +  ++YRV      +      LK G+++          +  L       
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPANDTLCATLKNGVLLHDDNETVAAAEAVL----ADP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V +L R  +G + +  L AG  + +
Sbjct: 176 TTLMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLAAGEWKFI 225


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 81/230 (35%), Positives = 120/230 (52%), Gaps = 4/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ASRR+VE  +   RV +NG ++   +  V  TD + +DG  +   E  
Sbjct: 3   IRLNKYLASCGLASRRKVEEFVLSGRVALNGRVVRDLSTTVEETDTVTLDGKEVS-PESR 61

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V    D     TV D LP  +S  R+  VGRLD  +EGLL+LTNDG  A
Sbjct: 62  VYIVMNKPQGVVCAVEDRFD-MTVIDVLPPAYSKFRLFPVGRLDKESEGLLVLTNDGDFA 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  PS+   R Y V  + ++  +K+ L  KG  I+G     + V    +     WVTV
Sbjct: 121 HFLMHPSSNIKRDYEVLLNEELTVEKMKLWLKGFEIEGGFVRPLSVQPLCRPPYGRWVTV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG+ RE++ + E   +KV  LIR   G  +L  L  G T ++S+  L
Sbjct: 181 SITEGQKREVRLMAEHLGYKVMVLIRRRIGRMELRNLNKGQTVKLSQDEL 230


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 108/232 (46%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G+        V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGLTTSDPHHEVREFSCVMFDTEILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  +D     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPPGCVSATTDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D   +    +G+    + I     Q+ +   + ++    
Sbjct: 120 RLTQPQTKMPKVYYVETEQLIDDRYVLKFAEGLYFSFENITTQPAQLNVLGPRSAH---- 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV RL R S G   L  TL AGS R +    +
Sbjct: 176 LSIVEGRYHQVKRMFGHFDNKVLRLHRESIGALTLDPTLAAGSYRALHAAEI 227


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 106/234 (45%), Gaps = 5/234 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    ++S++++     SR+    +IA   V V+G +    A  +     +  +G  ++ 
Sbjct: 12  NIATMKLSRILSNQNGVSRKRANALIAAGTVTVDGCICRETAREIDRFSTVACNGRVIQH 71

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDG 128
            ++    + +KP G ++  +D     TV + + P +   +   GRLD  + GLL+LTNDG
Sbjct: 72  GDQAHYLMLNKPAGYLSATAD-KVHKTVMELIDPELRKDLHIAGRLDRASTGLLILTNDG 130

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
             +R L  P  +  +VYRV     V  + +    +GI  +          L+    + + 
Sbjct: 131 AWSRRLTEPRIKLPKVYRVTTVEPVSTNAIERFAQGIWFEYERLTTSPARLEPLSANES- 189

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             V + EG+  +IK++F     +V+ L R   G   L  TL  G +R ++ + +
Sbjct: 190 -RVTIYEGRYHQIKRMFHATGNRVSSLHREQMGAITLDPTLEPGESRPLTSREI 242


>gi|312601099|gb|ADQ90354.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae 168]
          Length = 236

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 112/234 (47%), Gaps = 6/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K ++  G+ SRR+ E++I Q R+K+N    +     V   D IE+D   + K 
Sbjct: 1   MKKIRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIVSQNDVIELDQQKITKK 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG  
Sbjct: 60  PPIFWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTSGLILITNDGKT 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  PS++  R Y V+    +   ++  L        I    ++     +K S+    
Sbjct: 119 TNKLLHPSSKIERTYLVKTDFSLSDKEIRFLND----NKIQLDSVKSIQKIKKCSSRTYL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++K+ ++  
Sbjct: 175 VTVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTKQEIKSL 228


>gi|71893518|ref|YP_278964.1| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae J]
          Length = 237

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 111/231 (48%), Gaps = 6/231 (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        I    ++     +K S+    V +
Sbjct: 119 LLHPSSKIERTYLVKTDFSLSDKEIRFLND----NKIQLDSVKSIQKIKKCSSRTYLVTV 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G N  IKK+F   + KV +L R+S+   +L  +  G  R+++ + ++  
Sbjct: 175 WQGSNHHIKKLFLSISKKVLKLKRVSFANIKLDNISEGKYRKLTNQEIKSL 225


>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 =  223 bits (569), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 73/228 (32%), Positives = 116/228 (50%), Gaps = 3/228 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-RKAER 72
            RV + +AR G  SRRE ++ +A+ RV+VNG       +   + D I +DG P+  +   
Sbjct: 1   MRVQRALARVGAVSRREADKAVAEGRVQVNGTTAIVGQLVDPARDRITLDGTPVATQVTA 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  + HKP  ++TT  DP+GR+TVFD +      ++ VGRLD  TEG+LLLT DG  A 
Sbjct: 61  HRWIVLHKPAAVMTTRKDPEGRATVFDLVDDA-PGLVYVGRLDFMTEGVLLLTTDGTAAH 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|325688213|gb|EGD30232.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK72]
          Length = 241

 Score =  223 bits (569), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 127/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPSGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           TV + EGK  +IKK+F     KV  L RI +G F+LG  L  G  R ++++ L  ++   
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIRFGNFKLGPELTTGEYRPLNQEEL--EIIKE 235

Query: 249 LLEEAQ 254
            LE+++
Sbjct: 236 YLEKSR 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 =  223 bits (569), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 70/250 (28%), Positives = 124/250 (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 TDNPEVADVLM--GSKLPRTYNLKIDKPLTPEMEKAMKEGLILEDAREGGHKESEITRME 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|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 =  223 bits (568), Expect = 4e-56,   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  HKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVLE 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|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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 113/241 (46%), Gaps = 3/241 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             K   + +    R+++ I+ +G+ SRRE +  IA   +KVNG  +      V  +D + 
Sbjct: 89  PAKPAKKGDDNSIRLNRYISNSGVCSRREADIFIAAGSIKVNGKAVVEMGYKVALSDVVS 148

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEG 120
            DGV L   E+    L +KP    ++ +D     +    + +   S++  VGRLD +  G
Sbjct: 149 FDGVVLN-PEKRAYILLNKPKDFDSSATDASQPKSALGLVANATKSKIKPVGRLDKSASG 207

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LLL TNDG L   L  P   + ++Y       +  D L  ++KGIV++       +++ +
Sbjct: 208 LLLFTNDGELQTKLTKPKNGFRKIYHATLSKSLKADDLEKVRKGIVLEDGPVRVHEIS-N 266

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +      V + +   KN  IK++F+   +++ +L R+ Y       L  G  R ++++ 
Sbjct: 267 IEGSPATEVGIEILSAKNNIIKRLFDHLGYELIKLDRVVYAGLTKKDLPRGQWRTLTEQE 326

Query: 241 L 241
           +
Sbjct: 327 I 327


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 76/239 (31%), Positives = 123/239 (51%), Gaps = 9/239 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE-- 71
           R++K ++ AG+ SRR+ + +IA  +V+VNG ++      V   TD IEV+G  L   E  
Sbjct: 47  RLNKALSGAGVCSRRQADTLIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGEAL 106

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
              R    + +KP+ +V+T  DP GR+T+ D LP      R+  VGRLD  +EGLLLLT+
Sbjct: 107 NRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLLTD 166

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  +   
Sbjct: 167 DGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRSEY 226

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + + L +G NR+I+++       V RL+RI  GP +LG L  G+ R +    ++  
Sbjct: 227 GVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGACRRLEDHEVKAL 285


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 112/232 (48%), Gaps = 7/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
            R+ K +   G  +R+EV+ ++ +  VKVN ++++++ +  V   D + V    +   E 
Sbjct: 1   MRLDKFLGNHGFGTRKEVKLLVKRGAVKVNDVVVKKSDIKIVPENDTVTVYDEVVMY-EP 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G +++  D     TV + +       +  VGRLD +TEGLL+LTNDG  +
Sbjct: 60  FVYIMLNKPAGYISSTKDYKD-ETVLELIEGFEHYDLHPVGRLDKDTEGLLILTNDGQFS 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVT 190
             +  P     + Y  R  G V  D + L K GI +    Y  M   L     G  + + 
Sbjct: 119 HDVLSPRKHVNKTYFARVDGYVTDDTVELFKAGITLDDG-YKAMPAELQIISAGEISEIE 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + ++EGK  ++K++F   +  V  L RI  G   L  +L  G+ R+++ + +
Sbjct: 178 LVIQEGKFHQVKRMFIAVDMIVIYLKRIKMGGLPLDESLTPGAYRKLTLEEI 229


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 71/357 (19%), Positives = 137/357 (38%), Gaps = 37/357 (10%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
                 P R++K +A+ G+ SRRE + +I +  ++++G  +  A   V     + +    
Sbjct: 6   TYTGDEPLRINKWLAQEGVCSRREADALIEKGLIQLDGKPVTVAGERVTKGQTLSLTDAA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFSRVISVGRLD 115
            R+ +     + +KP+G V+   +P     +              +P   +++  +GRLD
Sbjct: 66  SRRLDNQLSVILNKPVGYVSGTPEPGEIPAIRLISEENLSGSAHAIPQRSNKMAPLGRLD 125

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLL+L+ DG LA+ +  P +   + Y V+  G +   K+ LL+ G+ + G      
Sbjct: 126 KDSHGLLILSEDGVLAKAIIGPLSDMDKEYLVKVRGDITTAKVALLRHGLELDGRQLRPA 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           +VT +  +     +   L+EG+NR+I+++ E    +V  L RI  GP  L  L  G  R 
Sbjct: 186 EVTQERGQ----VLRFVLKEGRNRQIRRMCELVELRVLDLQRIRVGPILLAGLPQGKWRP 241

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           +  K                        +  L       +   P       + S      
Sbjct: 242 LGAKE----------------------RAALLAAGAGEEVRSSPARREDRLRTSDGPRRE 279

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTSA 352
             +     P   R+ +       G        +G + +     P+ P  +  R  + 
Sbjct: 280 RSETGRDQPRTDRDRSGQFGTKPGQGRPDKPRTGPKPDRAGAKPARPGAKPARPGAK 336


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 125/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPSGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L  ++   
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEEL--EIIKE 235

Query: 249 LLEEAQ 254
            LE+++
Sbjct: 236 YLEKSR 241


>gi|254673145|emb|CBA07952.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha275]
          Length = 256

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+++            D    + 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLENP 201

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 202 TTLLLTITEGKYHQVKRMIAAVGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 107/233 (45%), Gaps = 5/233 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE-RT 73
           + KV+  A + SRR++   I Q  V +NG   E  +  V    D +  +G  +  +  R 
Sbjct: 11  LVKVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQKDKVTFEGKLVVLSRVRR 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGK R ++++F      +  L R      +LG L  G TRE++   +   
Sbjct: 190 IIHEGKKRIVRRMFARLGHPIKALKRSRIATLRLGKLEEGKTRELTPGEIAAL 242


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 82/264 (31%), Positives = 132/264 (50%), Gaps = 10/264 (3%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--RKAERTRLWLYHKPIGLVTTH 88
           +ER I Q R++++G +       +     ++VDG  L   + E  R  LYHKP+G V + 
Sbjct: 1   MERWIEQGRIEIDGRVAT-LGDRIYPDQRLKVDGRRLDLERKEEVRCLLYHKPVGEVCSR 59

Query: 89  SDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
            DP+GR TVFD+LP++ + 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 FNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
               V+RL R+ +G   + + L  G   E+ +K +       L + A++     +  +  
Sbjct: 180 QGLTVSRLKRVRFGEVFIPSKLKKGQWMELPEKDVE-----VLYQMAKLPAKPVVPLTAR 234

Query: 267 LVRDRPNIISEVPDDFTRMKKNSS 290
               +  +  +      R  K   
Sbjct: 235 EQEKQERLTKKSGRRIQRPGKGGK 258


>gi|323527102|ref|YP_004229255.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323384104|gb|ADX56195.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 239

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 101/232 (43%), Gaps = 10/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +  + D      VDGV     ER
Sbjct: 3   LESILFSQGFGSRRQCRALIVDARVSIDGTVCADADADFPAGDAAFCFSVDGVVWPYRER 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  +VY       +D  +L LL+ G+++ G       V  D +      + 
Sbjct: 121 VHTFTSPKRKVPKVYVATTRHPLDDAQLGLLRHGVLLHGESKPVAAV--DAEARGEHSLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++      +   L R   G   L  TL  G+ + + +  +
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPATLAPGAWQWLDETEI 230


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 55/231 (23%), Positives = 109/231 (47%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++ +   +R   ++ + +  V+VNG +++ AA  +     +   G PL +    
Sbjct: 1   MRLDRFLSESTELTRSLAKKALHRGEVEVNGDVVKNAAFKLGDEHVVRWLGEPLARI-GV 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G   T   P    +V + L  +   R+   GRLD++T GL+L+T DG  + 
Sbjct: 60  RYLMLNKPAGYECTTR-PGRYPSVIELLDVAKRGRLHIAGRLDVDTTGLVLITEDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTV 191
            L  P  +  + Y V     + +     L +G++++G     +   L+    ++   V +
Sbjct: 119 RLTSPRRRCDKHYLVTLARPLAEGAETALAEGLMLEGEDKPTLPARLERLDDADGVRVRL 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            ++EG+  +IK++F   + +V  L R   G   L   L AG  RE+++  +
Sbjct: 179 VIQEGRFHQIKRMFAALDNEVVALHRERIGEIALDPALAAGEWRELTQAEI 229


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A   I  R+E+++ +A++++ V+G+   + + NV +    +      L     
Sbjct: 1   MRLDQLLAHYQI-PRKEIKQSLAKRQILVDGLAATKLSQNVDTGLQEVRWKDQVLTDC-S 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L HKP GLVT   D    STV D L       +   +GRLD +T GLLLLT++G L
Sbjct: 59  HHYFLLHKPQGLVTATKDAQH-STVLDLLRTEDRTPKTYPIGRLDRDTTGLLLLTDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y    +G ++   +   ++GI  + G      ++ + +   + +  
Sbjct: 118 GFQLLHPQYHIEKEYAATVNGPLEPAHIEKFQEGITFLDGTTCKPAKLEILSSSLTESQA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            V L EGK  ++KK+      KV  L RI +G F L   L  G  R +++  L+
Sbjct: 178 LVTLSEGKFHQVKKMLLSVGVKVTSLKRIKFGDFSLDPNLAEGQYRPLNQDELQ 231


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 65/245 (26%), Positives = 108/245 (44%), Gaps = 19/245 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+SK++++ G+ SRRE +  I +  V V+G  + +  + V  T  I++  +   + 
Sbjct: 1   MEKIRLSKLMSQKGLCSRREADDYIERGWVFVDGERISQLGIKVFPTQEIKLARMAQAQQ 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLD 115
                 L HKP+G V+   +   +  +                   P     +   GRLD
Sbjct: 61  CDQITVLLHKPVGYVSGQPERGYKPAISLINRESEFQDSKASSSFSPLNLKGMAPAGRLD 120

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           I++ GLL+ T DG +AR L    ++  + Y VR  G+V Q  LNLL  G+ + G      
Sbjct: 121 IDSSGLLVFTQDGRIARKLIGAESEIEKEYLVRAEGEVSQRTLNLLSHGLSLDGQALKRA 180

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            V    +      +   L+EG+ R+I+++ E    KV  L R+  G  +LG L  G  R 
Sbjct: 181 VVVQQNKD----QLRFILKEGRKRQIRRMCELVGLKVTGLKRVRIGKVRLGELPLGKWRY 236

Query: 236 VSKKI 240
           +    
Sbjct: 237 LRPGE 241


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 64/234 (27%), Positives = 111/234 (47%), Gaps = 6/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K ++  G+ SRR+ E++I Q R+K+N    +     V   D IE+D   + K 
Sbjct: 1   MKKIRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIVSQNDVIELDQQKITKK 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG  
Sbjct: 60  PPIFWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTTGLILITNDGKT 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  PS++  R Y V+    +   ++  L        I    ++     +K S+    
Sbjct: 119 TNKLLHPSSKIERTYLVKTDFSLSDKEIRFLND----NKIQLDSVKSIQKIKKCSSRTYL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + +G N  IKK+F   N KV +L R+S+   +L  +  G  R+++ + ++  
Sbjct: 175 VTVWQGSNHHIKKLFLSINKKVLKLKRVSFANIKLNNISEGKYRKLTNQEIKSL 228


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 76/234 (32%), Positives = 116/234 (49%), Gaps = 4/234 (1%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA 70
              R+ KV+A AG+ASRR  E +IA  RV+V+G ++    + +   T  I+VDG  +   
Sbjct: 120 DGMRLQKVLAAAGVASRRGAEELIAAGRVEVDGEVVVEQGLRIDPDTAIIKVDGARVVID 179

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTND 127
           E  +    +KP G  +T SD  GR  + D +        R+  VGRLD +TEGLLLLTND
Sbjct: 180 ESKQYLALNKPKGWHSTMSDDQGRPCIGDIIAERVMAGQRLFHVGRLDADTEGLLLLTND 239

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS +  + Y     G+V++     L++G+ ++          L       +
Sbjct: 240 GELAHRLMHPSYEVPKTYLATVRGEVNRGLGRELRQGVELEDGPVAVDSFALLEVNQGKS 299

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            V + L EG+ R ++++     + V  L+R   GP  LG    GS R +  K +
Sbjct: 300 LVRLTLHEGRKRVVRRLLAEVGFPVVGLVRTDIGPVTLGKQRPGSLRVLDNKEI 353


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 106/233 (45%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R      I    V VNG++    A+ V   + + ++G PL     +
Sbjct: 1   MRLDKFLCKSTDLNRDAASVAILSGSVTVNGVIATDCAMQVHENNAVSLNGKPL-APRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP   + ++ D     ++F  L       +  VGRLD +T GL+LLT+DG  + 
Sbjct: 60  RYFVLHKPADTLCSNVD-GAYPSLFHLLDIERAFDLHIVGRLDADTTGLVLLTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  Q  +VYRV+    +D +           G+ +QG     +  TL  Q+  +  
Sbjct: 119 NIISPQYQCKKVYRVQLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDDKT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 177 VLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL-DVDVGEWRELTLTEI 228


>gi|307578345|gb|ADN62314.1| RNA-binding S4 domain-containing protein [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 519

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 104/357 (29%), Positives = 167/357 (46%), Gaps = 24/357 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K +   +     +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D I
Sbjct: 14  LKRETATEAPKLEERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKI 72

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E  R+ +Y+KP G VTT  DP+GR TVF+ LP    +R I++GRLDI
Sbjct: 73  ELDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDI 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS++  R Y VR         V  + L  L +G++++   
Sbjct: 133 NTTGLLLLTTDGELANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGT 192

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                +       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 193 AKFDTIERIGNTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLR 252

Query: 231 GSTREVSK---KILREQLG----------PHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           G + E+ K   + LR QL              +   + +  A ++ +           + 
Sbjct: 253 GQSTELPKTQVEALRTQLKLEKDMPLALTLQPVIGQRRSAKATLHVNRNDNNKHAYHNNH 312

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
              D +R  +          + +       R   S    AK  H  F     + + +
Sbjct: 313 STADESRELRRFDTLRDDRGRGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRS 369


>gi|328868084|gb|EGG16464.1| Putative synthase [Dictyostelium fasciculatum]
          Length = 444

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 91/237 (38%), Positives = 138/237 (58%), Gaps = 19/237 (8%)

Query: 7   VQENFTP---QRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV 62
           ++E   P   +R+ K ++R+G+ SRR+ ERMI + RV VNG +   +  + V  TD + V
Sbjct: 154 IEEKIDPNQVERLQKRLSRSGVTSRRQSERMIMEGRVCVNGKVASMKNDLFVKPTDIVTV 213

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEG 120
           D   + ++              +    DP+ + T+   L  + +   ++SVGRLD  +EG
Sbjct: 214 DNKIIEESVPK-----------ICNLQDPE-KDTLIPILQKMLNKDHLMSVGRLDYYSEG 261

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L+L+TNDG L+R LELP + + + YRVR  G+V  D    L +G+ I GI Y  M+++++
Sbjct: 262 LILITNDGELSRYLELPQSGFEKTYRVRIFGKVTPDMNMALTRGLTIDGIRYAPMKISVE 321

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
            +  SN WV   L EGKNREI+++FE FN KV R+IR  +GP+ L  TL  G T EV
Sbjct: 322 RETDSNTWVICTLTEGKNREIRRIFEHFNVKVLRIIRTQFGPYTLPETLKPGETVEV 378


>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 =  223 bits (568), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 68/257 (26%), Positives = 107/257 (41%), Gaps = 29/257 (11%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D    
Sbjct: 447 DDRPGAVRINKRIADMGLCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQ 505

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVG 112
            + ++    L +KP+G V+  ++      V                    S    +   G
Sbjct: 506 DRQDQQVTILLNKPMGYVSGQAEDGHEPAVVLITNENRWNEDRSKTRFNFSQLKGLAPCG 565

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKK 163
           RLDI++ GLL+LT DG +AR +    ++  + Y VR               ++KL LL+ 
Sbjct: 566 RLDIDSVGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRH 625

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ +        QV     +     +   L EGK R+I+++ E    KV  L RI  G  
Sbjct: 626 GLSLDEQPLKPAQVDWQNPE----QLRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGV 681

Query: 224 QLGTLLAGSTREVSKKI 240
            LG L  G  R ++   
Sbjct: 682 TLGNLPTGQWRYLAAHE 698


>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 =  223 bits (568), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 60/239 (25%), Positives = 100/239 (41%), Gaps = 8/239 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+    ++   RV++ G +       + + D    VDG      E+  
Sbjct: 5   LEKILQSQGFGSRKFCRNLVLGHRVEIAGKICTDPDRKLETDDLAFRVDGETWEYREKL- 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G   +   P    +VF  LP  F    +  VGRLD +T GLLLLT+DG    
Sbjct: 64  YLVLNKPAGYECSRQ-PQHHPSVFALLPEPFVQRGLQCVGRLDQDTTGLLLLTDDGHFIH 122

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  ++Y V      +  +L  L  G+ ++          L  Q      + + 
Sbjct: 123 QYTSPRKKVPKIYTVTGVSPFEATQLEKLVTGVQLKDEKTLTS--ALACQLIDEYRLRLS 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHLL 250
           + EGK  ++K++      +V  L R + G F L  TLL G  R +++  L+    P   
Sbjct: 181 ITEGKYHQVKRMIAAAGNRVETLHRSAIGGFTLEETLLPGHWRFLNENDLKRLSEPFPA 239


>gi|167619584|ref|ZP_02388215.1| pseudouridine synthase family protein [Burkholderia thailandensis
           Bt4]
          Length = 364

 Score =  223 bits (568), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 103/250 (41%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 117 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 176

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 177 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDST 236

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 237 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDGV 296

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 297 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 352

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 353 GQWRYLGPDE 362


>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 =  223 bits (568), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 122/245 (49%), Gaps = 11/245 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV K+IA++G+ SRR+ E+MI++  V VNGI            D I+V+G  +   + T 
Sbjct: 6   RVQKLIAQSGLMSRRDAEKMISKGLVFVNGIK-SSIGDKASINDEIKVNGKIINLTKNTV 64

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP   +TT  DP GR TV D + +   R++ VGRLD NT G+LLLT D  L  
Sbjct: 65  FKYYLLNKPKNTITTSKDPKGRHTVIDLI-NTSERIVPVGRLDRNTTGVLLLTTDYELVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  RVYR R    +   +   L  GI I G     M   +  Q  + +++ + 
Sbjct: 124 KLTHPKYEIERVYRARIDSPLTLKEFKELNAGIEIDG----KMSYQIVDQVDTKSYL-IS 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L  G    +KK+FE     V  L R+SY    +  L  G  RE++ K ++      L+E+
Sbjct: 179 LHVGSYHHVKKLFEKIGHSVLTLKRVSYANLTVDKLPEGMYRELTIKEVKNL--KLLVEQ 236

Query: 253 AQVNL 257
            +  L
Sbjct: 237 QEKKL 241


>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 =  223 bits (568), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 103/233 (44%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG +    A+ V   + + ++G PL     +
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAIINGSVTVNGTIATDCAMQVHENNAVCLNGKPL-APRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP   + ++ D     ++F  L       +  VGRLD +T GL+LLT+DG  + 
Sbjct: 60  RYFMLHKPADTLCSNVD-GAYPSLFHLLDIEHAFDLHIVGRLDADTTGLVLLTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  Q  +VYRV+    +D +           G+ +QG     +  TL  Q+     
Sbjct: 119 NIISPQYQCEKVYRVQLRDPLDSEATAAIATTFAAGLQLQGETALTLPATL--QQVDEKT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 177 VLLTLTEGKFHQVKRMFAAVGNKVIALHRAQIGAVVL-DVDIGEWRELTLAEI 228


>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 =  223 bits (568), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 123/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDTGLQQITFQGKQVSGPAH 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 60  HYY-MLNKPAGAVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+T+ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPQDKIAFQEGIRFLDGTVCQPAQLTIFSSCFSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           +V + EGK  +IKK+F     K+  L RI +G F L   L  G  R ++++ L  ++   
Sbjct: 178 SVRISEGKFHQIKKMFLVVGVKIIYLKRIQFGNFTLDPDLATGDCRPLNQEEL--EIIKE 235

Query: 249 LLEEAQ 254
            LE++Q
Sbjct: 236 YLEKSQ 241


>gi|330964551|gb|EGH64811.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 230

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 106/231 (45%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G +      +V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVAFDTEILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  +D    +TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATTDAQH-ATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + I     Q+T+   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           + + EG+  ++K++F  F+ KV +L R S G   L   L  G  R +    
Sbjct: 176 LSIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPALPPGGYRSLQAAE 226


>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 =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 82/235 (34%), Positives = 129/235 (54%), Gaps = 8/235 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAE 71
            +++ K+++  G  SRR +E MI    V +NG  ++    +N  + + I + G  +   +
Sbjct: 2   SEKIQKILSHLGYGSRRNIENMIKFGDVSINGKKIVIGQRLNNKNIEVITIKGETVSIKK 61

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
              +T++ +Y+KP G + T +D   R  VFD LP     R IS+GRLDINT GLLL TN+
Sbjct: 62  TDFKTKIIIYNKPEGEICTRNDYKKRPIVFDKLPLLNIHRWISIGRLDINTRGLLLFTNN 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLD-TQKGS 185
           G LA  L  PS +  R Y +R  G+++++ +N+LK G+ I+        + T+D      
Sbjct: 122 GNLANELMHPSNKIEREYYIRVFGKINKNTMNILKNGVKIKDGYAAFKSIQTIDHACSKK 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           N W    L EG+NREI+ +++    +V+RLIRI YG   L   L  G   E+S +
Sbjct: 182 NKWFKGVLCEGRNREIRSMWQAVQCQVSRLIRIRYGNIFLPKNLKLGDWSELSSE 236


>gi|167846297|ref|ZP_02471805.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           B7210]
          Length = 334

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 87  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 146

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 147 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 206

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 207 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 266

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 267 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 322

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 323 GEWRYLGPDE 332


>gi|167581475|ref|ZP_02374349.1| pseudouridine synthase family protein [Burkholderia thailandensis
           TXDOH]
          Length = 324

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 103/250 (41%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 77  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 136

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 137 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDST 196

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 197 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDGV 256

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 257 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 312

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 313 GQWRYLGPDE 322


>gi|327458771|gb|EGF05119.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1057]
          Length = 241

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 124/246 (50%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV      I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDIGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L  ++   
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGDFTLDPDLAKGDYRALNQEEL--EIIKE 235

Query: 249 LLEEAQ 254
            LE+++
Sbjct: 236 YLEKSR 241


>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 =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 58/235 (24%), Positives = 97/235 (41%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            R+S+V+   G  +RR+   +I    V+V G +++     + + D +  V G      ++
Sbjct: 1   MRISQVLFSQGFGTRRDCAGLIHAGAVEVAGRVVDDPDEELPTEDLVFSVQGRAWPFHDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             L L HKP     +   P     V   LP+      +  VGRLD +T G LLLT+DG L
Sbjct: 61  A-LVLLHKPTHYECSQK-PRHHPGVLSLLPTPLRVRGLQPVGRLDEDTTGALLLTDDGTL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY +     +  +++  L +G+V+       ++     + G    + 
Sbjct: 119 IHRLTSPKHHVPKVYEITAKHALADEQIARLTEGVVLDDDP-QPVRAAAAERTG-EFTLR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L EGK  ++K++      +   L R   G   L  L  G  R V        L
Sbjct: 177 LTLTEGKYHQVKRMLAAVGNRCEALHRSRIGALALDDLPVGQWRWVGPDERARLL 231


>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 =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++      R+ V  ++   RV+V+G +++     V    HI++D   L+ A    
Sbjct: 7   RLDRYLSAKMQMPRKLVRDLLLSGRVQVDGQIVKEMDRQVDEFSHIQLDDQVLQ-ANTPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+G+V+   D   + TV D L + +   +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YMMLHKPVGVVSATKDNQHK-TVIDLLDNEYRHELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     +  D +    +G+    + I     ++ +      +    V
Sbjct: 125 LMSPTEKVDKVYRVTLANPLTHDYVTAFAEGMYFGFEDITTQPAKLVIL----DSHLAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L+EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 181 TLKEGKYHQIKRMFGRFRNPVIGLHRLSIGDIVLDEQLQPGESRTLTAAEI 231


>gi|167570375|ref|ZP_02363249.1| pseudouridine synthase family protein [Burkholderia oklahomensis
           C6786]
          Length = 414

 Score =  222 bits (567), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 100/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 167 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 226

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++      V                   P     +   GRLDI++ 
Sbjct: 227 TILLHKPVGYVSGQAEDGYAPAVTLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 286

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G 
Sbjct: 287 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERMADIDQHFPAESLAKLRHGLELDGA 346

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 347 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 402

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 403 GEWRYLGPDE 412


>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 =  222 bits (567), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 100/230 (43%), Gaps = 12/230 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K I   G+ SR++ + +I    + +NG +  RA  N+  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDNIDPSQVHTLSVDGEEIAAVP 60

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 61  MPHFYILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
                +  P  +  ++YRV      D      LK G+++          +  L       
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVL----TDP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V +L R  +G + +  L AG  + +
Sbjct: 176 TTLMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLAAGEWKFI 225


>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 =  222 bits (567), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 104/244 (42%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A  G+ SRRE +  I +  V+VNG         V   D I++         
Sbjct: 5   EPLRLSKRMAELGLCSRREADAYIERGWVRVNGQTA-VLGQKVSPADRIDLAREAHETQA 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
           R    L +KP+G V+   +   R+ V                   P     +   GRLDI
Sbjct: 64  RRVTVLLNKPVGYVSGQPEKGYRAAVELFTPENRWEGDQSRIPFDPRHLRGLAPAGRLDI 123

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG  A+ L        + Y VR  G++ ++ L LL  G+ + G      +
Sbjct: 124 DSVGLLVLTQDGRTAKQLVGADGGSEKEYLVRVRGRLKENGLALLNHGLSLDGEPLRPAK 183

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V    +      +   LR+GK R+I+++ E     V  L RI  G  +LG L  G  R +
Sbjct: 184 VEWQNRD----QLRFVLRQGKKRQIRRMCELVGLTVVGLKRIRIGRVKLGALPPGKWRYL 239

Query: 237 SKKI 240
           +   
Sbjct: 240 ASDE 243


>gi|167816387|ref|ZP_02448067.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei 91]
          Length = 351

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 104 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 163

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 164 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 223

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 224 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 283

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 284 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 339

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 340 GEWRYLGPDE 349


>gi|330877468|gb|EGH11617.1| ribosomal small subunit pseudouridine synthase A [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 230

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 62/231 (26%), Positives = 107/231 (46%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A  RV+V+G +      +V     + +D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKSVRLALASGRVQVDGQITTDPHYDVREFSCVALDAEILQPGKAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+  +D    +TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATTDAQH-ATVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + I     Q+T+   + +     
Sbjct: 120 RLTQPQTKMPKVYYVETEQLIDERYALTFAEGLFFSFENIITQPAQLTVLGPRSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           + + EG+  ++K++F  F+ KV +L R S G   L   L  G  R +    
Sbjct: 176 LSIIEGRYHQVKRMFGHFDNKVLQLHRESIGALILDPALPPGGYRSLQAAE 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 =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 103/233 (44%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG++    A+ V   + +  +G  L     +
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAILSGSVTVNGVIATDCAMQVHENNAVCFNGKSLV-PRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP   + ++ D     ++F  L       +  VGRLD +T GL+LLT+DG  + 
Sbjct: 60  RYFMLHKPADTLCSNVD-GAYPSLFHLLDIERAFDLHIVGRLDADTTGLVLLTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  Q  +VYRV+    +D +           G+ +QG     +  TL  Q+  +  
Sbjct: 119 NIISPQYQCKKVYRVQLRDPLDSEATAAIAATFTAGLQLQGETALTLPATL--QQVDDKT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 177 VLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL-DVDVGEWRELTLAEI 228


>gi|322412114|gb|EFY03022.1| Putative 16S pseudouridylate synthetase [Streptococcus dysgalactiae
           subsp. dysgalactiae ATCC 27957]
          Length = 238

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 110/231 (47%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++      SRR+V+++I  Q V+++  +      NV      IEV    +    +
Sbjct: 1   MRLDKLLELVANGSRRQVKQLIKGQDVRIDHEIAWSGRQNVDPGLQLIEVSRKRISHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+  SD     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYFILNKPAGVVSARSDI-NHVTVLDQLAEKDRHPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G +D+D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVAKTYMVTVNGFLDEDAPDFFASGIKFPTGEQCRPAQLTILQASQEKSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            + + EGK  ++KK+F  +  KV  L R S+   +LG L +G+ R ++   
Sbjct: 179 RLVISEGKFHQVKKMFLTYGLKVISLKRTSFAGLELGELASGAYRSLTDAE 229


>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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 63/203 (31%), Positives = 94/203 (46%), Gaps = 3/203 (1%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           VKVNG ++      V+ TD +     P+   E+    L +KP   VTT  DP  R TV D
Sbjct: 2   VKVNGNVVTELGTKVLRTDEVIFHEQPVTL-EKKVYVLINKPKDYVTTSDDPQQRKTVMD 60

Query: 100 NLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +      R+  VGRLD NT G+LLLTNDG LA  L  P     +VY V    +V +  L
Sbjct: 61  LVKGVCPERIYPVGRLDRNTTGVLLLTNDGDLASKLAHPKFLKKKVYHVFLDKEVTEHDL 120

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
             +  G+ +         +           V + +  GKNR ++++FE   ++V RL R+
Sbjct: 121 QQIATGVTLDDGEVHADAIEY-ANDKDKTQVGIEIHSGKNRIVRRIFESLGYRVVRLDRV 179

Query: 219 SYGPFQLGTLLAGSTREVSKKIL 241
            +       L  G  R +++K +
Sbjct: 180 QFAGLTKKNLKRGDWRFLTEKEV 202


>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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 110/232 (47%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+I  +G+ +R+ +++   +  + VNG +++  A  V    D +   G  +   E 
Sbjct: 1   MRLDKMIGNSGLDTRKNIKKNAKKGAILVNGEVVKDTATQVDPEVDEVYYMGHFVDYFEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             + + +KP G ++   D D   TV D L   +    +   GRLD +T GLLLL+ DG  
Sbjct: 61  IYVMM-NKPAGFLSATEDKD--PTVIDLLDDFYKVIDLSIAGRLDKDTTGLLLLSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y V    ++D+  ++L K+G+ I+   Y      L+  +   A V 
Sbjct: 118 IHKVTSPNSNIEKTYLVECRDKIDESLIDLFKEGVYIKEDDYTARSAKLEILEEKKAIVK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V   EGK   +K++F     KV +L RI+ G   L   L  G  RE+S   +
Sbjct: 178 VT--EGKFHLVKRLFSNCCNKVEKLKRIAIGDLSLDEHLAEGEYRELSDDEI 227


>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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A    A R+++++++A++++ V+ +  ++ + N+      I++ G  + +  R
Sbjct: 1   MRLDQLMADHQYA-RKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI-GERIIQEPR 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKPIG VT   D     TV D +     +  +  +GRLD +T GLLL+T++G L
Sbjct: 59  HHYYMLHKPIGAVTAKRDA-HHPTVIDLVDPQQEYPDLYPLGRLDRDTSGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY V  +G +    +   + GI    G       +T+     S +  
Sbjct: 118 GFQLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTPSYSKA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V + EGK  ++KK+F     KV  L R+S+GPF L   L  G +R +++  L
Sbjct: 178 QVRISEGKYHQVKKMFLAIGVKVMTLKRLSFGPFTLDPQLAPGESRPLNEVEL 230


>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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 82/245 (33%), Positives = 122/245 (49%), Gaps = 11/245 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV K+IA++G+ SRR+ E+MI++  V VNGI            D I+V+G  +   + T 
Sbjct: 6   RVQKLIAQSGLMSRRDAEKMISKGLVFVNGIK-SSIGDKASMNDEIKVNGKIINLTKNTV 64

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L +KP   +TT  DP GR TV D + +   R++ VGRLD NT G+LLLT D  L  
Sbjct: 65  FKYYLLNKPKNTITTSKDPKGRHTVIDLI-NTSERIVPVGRLDRNTTGVLLLTTDYELVN 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  RVYR R    +   +   L  GI I G     M   +  Q  + +++ + 
Sbjct: 124 KLTHPKYEIERVYRARIDSPLTLKEFRELNAGIEIDG----KMSYQIVDQVDTKSYL-IS 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L  G    +KK+FE     V  L R+SY    +  L  G  RE++ K ++      L+E+
Sbjct: 179 LHVGSYHHVKKLFEKIGHSVLTLKRVSYANLTVDKLPEGMYRELTIKEVKNL--KLLVEQ 236

Query: 253 AQVNL 257
            +  L
Sbjct: 237 QEKKL 241


>gi|260222138|emb|CBA31404.1| hypothetical protein Csp_F37360 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 282

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 69/285 (24%), Positives = 109/285 (38%), Gaps = 63/285 (22%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ASRRE +  IA+  VKVNG +     + V+    IE+D     +    
Sbjct: 1   MRLNKRMADLGMASRREADEWIAKGWVKVNGKVA-EMGMQVLPDVRIEIDKQAQGQQANQ 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINT 118
              L +KP+G+V+  ++      +               F    S    ++  GRLDI++
Sbjct: 60  VTILLNKPLGIVSGQAEDGHEPAIKLIQPQNRWRDDNARFFFHGSQLKSLVPAGRLDIDS 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF----------------------------- 149
            GLL+LT DG +AR L    +   + Y VR                              
Sbjct: 120 TGLLVLTQDGRVARQLIGEDSVMEKEYLVRVAYTGVENPGAANSPAATYPALAGRGKPQQ 179

Query: 150 ------HGQVD--------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                    V          +KL LL+ G+++        +V     +     +   L E
Sbjct: 180 LIRLDDDDPVTSDVQSVFPPEKLQLLRHGLILDDQRLKPAKVEWQNPE----QLRFVLTE 235

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           GK R+I+++ E    KV  L R+  G   LG L  G  R +    
Sbjct: 236 GKKRQIRRMCELVGLKVVGLKRVRVGKVMLGNLPVGQWRYLLPHE 280


>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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 79/266 (29%), Positives = 125/266 (46%), Gaps = 9/266 (3%)

Query: 34  MIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDP 91
           MI +  V VNG  +    + V   +D I VDG PLRK   +    + +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 +           T
Sbjct: 181 KIGFDVMRLQRVAIGRLRMGAVKTGELVYLNDAAVQRVFLADDPEEIKTKRT--YKGRAT 238

Query: 267 LVRDRPNIISEVPDDFTRMKKNSSQK 292
             +      S+V       K  + +K
Sbjct: 239 SEKKTAKPASKVKTTKKPSKYKNGKK 264


>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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 83/264 (31%), Positives = 123/264 (46%), 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   SFEPIRLQKYLADAGVCSRRAAEALIASGEVWVNGAPAQ-VGQKVTPGVDRVTTGGKPVR 61

Query: 69  KAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT 125
              + R+    HKP GLV T+ DP    T+F  LP  F+  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|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 =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 64/231 (27%), Positives = 106/231 (45%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLDPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           ++ + EGK  ++KK+F  +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 SLTISEGKFHQVKKMFLTYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 229


>gi|167919518|ref|ZP_02506609.1| pseudouridine synthase family protein [Burkholderia pseudomallei
           BCC215]
          Length = 361

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 114 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 173

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 174 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 233

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 234 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 293

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 294 PLKPAMVSWQNGE----QLCFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 349

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 350 GEWRYLGPDE 359


>gi|144227495|gb|AAZ44253.2| ribosomal large subunit pseudouridine synthase B [Mycoplasma
           hyopneumoniae J]
          Length = 240

 Score =  222 bits (566), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 111/234 (47%), Gaps = 6/234 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K ++  G+ SRR+ E++I Q R+K+N    +     +   D IE+D   + K 
Sbjct: 1   MKKIRINKFLSEMGVCSRRQSEKLILQGRIKINNETAK-IGQIISQNDVIELDQQKITKK 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
                +  +KP   +T+  DP+ R T+ +        +  VGRLD  T GL+L+TNDG  
Sbjct: 60  PPIFWYALNKPKNYITSRFDPENRPTIMEFFSKN-EYLFPVGRLDFQTTGLILITNDGKT 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  PS++  R Y V+    +   ++  L        I    ++     +K S+    
Sbjct: 119 TNKLLHPSSKIERTYLVKTDFSLSDKEIRFLND----NKIQLDSVKSIQKIKKCSSRTYL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V + +G N  IKK+F   + KV +L R+S+   +L  +  G  R+++ + ++  
Sbjct: 175 VTVWQGSNHHIKKLFLSISKKVLKLKRVSFANIKLDNISEGKYRKLTNQEIKSL 228


>gi|319425419|gb|ADV53493.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 236

 Score =  222 bits (566), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 110/231 (47%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++      R+ V  ++   RV+V+G +++     V    HI++D   L+ A    
Sbjct: 7   RLDRYLSAKMQMPRKLVRDLLLSGRVQVDGQIVKEMDRQVDEFSHIQLDDQVLQ-ANTPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+G+V+   D   + TV D L + +   +   GRLD+N+ GLLLLTND   +  
Sbjct: 66  YMMLHKPVGVVSATKDNQHK-TVIDLLDNEYRHELHIAGRLDLNSSGLLLLTNDSRWSEA 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P+ +  +VYRV     +  D +    +G+    + I     ++ +      +    V
Sbjct: 125 LMSPTEKVDKVYRVTLANPLTHDYVTAFAEGMYFGFEDITTQPAKLVIL----DSHLAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L+EGK  +IK++F  F   V  L R+S G   L   L  G +R ++   +
Sbjct: 181 TLKEGKYHQIKRMFGRFRNPVIGLHRLSIGAIVLDEQLQPGESRTLTAAEI 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 =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 77/239 (32%), Positives = 122/239 (51%), Gaps = 9/239 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAE-- 71
           R++K ++ AG+ SRR+ +  IA  +V+VNG ++      V   TD IEV+G  L   E  
Sbjct: 47  RLNKALSGAGVCSRRQADTFIAGGKVRVNGEVVTEMGRRVFPATDRIEVEGRLLACGEAL 106

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
              R    + +KP+ +V+T  DP GR+T+ D LP      R+  VGRLD  +EGLLLLT+
Sbjct: 107 NRHRHTYVMLNKPVQVVSTVRDPQGRTTILDILPDDLKTVRLYPVGRLDFFSEGLLLLTD 166

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGS 185
           DG L   L  P     + YRV     +    L  ++ G+ + +G     ++  +  +   
Sbjct: 167 DGDLTHRLTHPKWHLPKYYRVLVREDIPPAALTAMRSGMTLAEGDRVAPVEAYIIDRSEY 226

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + + L +G NR+I+++       V RL+RI  GP +LG L  GS R +    ++  
Sbjct: 227 GVELEMVLHQGINRQIRRMCRDLGLTVLRLLRIQQGPVELGNLSRGSCRRLEDHEVKAL 285


>gi|170693595|ref|ZP_02884753.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170141377|gb|EDT09547.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 239

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 104/237 (43%), Gaps = 11/237 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + GI+      +  + D      VDGVP    E 
Sbjct: 3   LESILFSQGFGSRRQCRALIADARVAIGGIVCTDPDADFATDDASFSFSVDGVPWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L+ G+++ G         +D        + 
Sbjct: 121 VHMFTSPKRKVPKVYVATTRHPIDDRQLSALRDGVMLHGES--KAVAAIDAHARGEHSLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
           + + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L+  LG
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERVGGLALPATLAPGAWQWLDETELK-LLG 234


>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 =  221 bits (565), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 95/233 (40%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVSVAGASATDPDASFDTDGLVFTVDDTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPTPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +LN L+ G+ + G       V    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L   
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESIGGFTLPDDLAPGAWRWLGEGELSAL 231


>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 =  221 bits (565), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 117/238 (49%), Gaps = 4/238 (1%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL 67
           E     R+++ IA +G+ SRR+ + +I    V VNG+++      V +  D I  +G  L
Sbjct: 181 EENGLIRLNRYIANSGVCSRRKADELIQAGVVTVNGVVVTELGTKVDAAKDEIRYNGEKL 240

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
           ++ E+    L +KP   +TT  DP  R TV   +      R+  VGRLD NT GLLLLTN
Sbjct: 241 KR-EKMVYVLLNKPKDYITTTDDPQERKTVMHLVEKASRERIYPVGRLDRNTTGLLLLTN 299

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG LA  L  P    +++Y V  +  + Q   N +  G+ ++       +V+   Q  S 
Sbjct: 300 DGNLAEKLSHPRNNIMKIYHVELNKSLTQGDFNKIGYGVELEDGFIKPDEVSY-IQGASK 358

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             + + +  G+NR ++++FE   + V +L R+ Y       L  G  R + +K + + 
Sbjct: 359 REIGIQIHSGRNRIVRRIFESLGYDVIKLDRVIYANLTKKDLPRGRWRYLEEKEIIQL 416


>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 =  221 bits (565), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 101/228 (44%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLENPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAVGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|167837045|ref|ZP_02463928.1| pseudouridine synthase family protein [Burkholderia thailandensis
           MSMB43]
          Length = 325

 Score =  221 bits (565), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 101/246 (41%), Gaps = 28/246 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 78  RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 137

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 138 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 197

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G 
Sbjct: 198 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGA 257

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 258 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 313

Query: 231 GSTREV 236
           G  R +
Sbjct: 314 GQWRYL 319


>gi|289665762|ref|ZP_06487343.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 527

 Score =  221 bits (565), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 105/367 (28%), Positives = 174/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSATEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV+++    LR +L       + + L  P+       +   ++  +   +      
Sbjct: 254 GQSVEVAQEKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGH 312

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR----RSPSFPS 343
            S    G   ++       R               +   ++  R+   R    R P+   
Sbjct: 313 TSGADEGRELRRFDNLREDRGRGGRGKPGGFKGGLTVSGEAAARQSQQRPFKQRGPAKGD 372

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 373 RGALPEG 379


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 100/230 (43%), Gaps = 12/230 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K I   G+ SR++ + +I    + +NG +  RA  ++  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVP 60

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 61  MPHFYILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
                +  P  +  ++YRV      D      LK G+++          +  L       
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVL----ADP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V +L R  +G + +  L AG  + +
Sbjct: 176 TTLMMTITEGKYHQVKRMIAAAGNRVEQLHREKFGDWNVDDLAAGEWKFI 225


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 100/230 (43%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 10  TIMKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTV 69

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 70  VPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+ +            D    + 
Sbjct: 129 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAA--DAVLENP 186

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 187 TTLLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 236


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 116/241 (48%), Gaps = 10/241 (4%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A      SR +V+++  ++++ VNG L+ R+   V + D I V+G  L   ++
Sbjct: 5   MRLDKLVASQFSDVSRADVKKLCLKKKISVNGKLMARSDAKVDTDDEIFVNGERLVY-KK 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V +  + D   TV D +P    R  +   GRLD +TEG +LLT+DG L
Sbjct: 64  HVYIMLNKPAGVVCSTKEGDS-MTVLDLVPPELMRNGLFPAGRLDKDTEGFVLLTDDGEL 122

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSN 186
           +  +  P T   + Y VR       +  +++  G+ I+    G     +         ++
Sbjct: 123 SHRMLSPKTHVPKTYFVRLEKPYQPEYADIMAAGMTIKGLDGGEDEKCLPAQFSGSDEND 182

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQL 245
              T+ L EGK  ++K++F     KV  L R + G   L G L +G   E+  K + + L
Sbjct: 183 CECTLILHEGKFHQVKRMFAELGNKVVYLKRTAIGEMPLNGELASGKCLEILHKDVEKLL 242

Query: 246 G 246
            
Sbjct: 243 A 243


>gi|309379227|emb|CBX22184.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 230

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 103/228 (45%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NGI ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGICMDDTDADIDSSSVETLDIDGKAVTVIP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPTDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P+ +  ++Y V       +     LK G+++      +     D    S + 
Sbjct: 120 HLNHKLTSPNHKIPKLYEVTLKHPAGETLCETLKNGVLLHDE--NETVYAADAVLESPSA 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|152995450|ref|YP_001340285.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150836374|gb|ABR70350.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 229

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 108/230 (46%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++     +R+  +   ++ RV VNG ++++A   V   D I +D + L      
Sbjct: 1   MRLDFYLSHVTELARKAAKIAASKGRVTVNGEVVKKANYTVQEGDQICLDDILLAWPSEG 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              L HKP G V    DPD   TV D LPS     +  VGRLD +T GLLLLT DG    
Sbjct: 61  YY-LLHKPAGYVCATQDPDH-PTVLDLLPSHLGQELKIVGRLDKDTTGLLLLTTDGQWLH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + YR+     +  + L  L++G+++ G     +      ++ S+  + + 
Sbjct: 119 RITSPRNACNKRYRMMLADPISDEDLKQLEEGVMLNGESQPTLPAI--AERISDCDIYLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           ++EGK  ++K++      KV  L R   G   L   + AG  RE++++ +
Sbjct: 177 IQEGKYHQVKRMLAAVGNKVEELHRDQIGLLSLDADIQAGEFRELTEEEV 226


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 101/233 (43%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A  +  +T  + EVDG+      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGIAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   S+VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G       +    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVAALAAVARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L   
Sbjct: 179 IAEGKYHQVKRMVAAASNRVEALHRSRIGGFALPEDLAEGAWRWLDERDLAAL 231


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 101/233 (43%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A  +  +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   S+VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G       +    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVAALAAVARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L   
Sbjct: 179 IAEGKYHQVKRMVAAASNRVEALHRSRIGGFALPEDLAEGAWRWLDERDLAAL 231


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 107/248 (43%), Gaps = 24/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              RVSK+I   G+ASRRE +  I    VKV+G +         +   IE+D     +  
Sbjct: 10  EGVRVSKLITERGLASRREADAWIEAGWVKVDGKMA-VLGQRAAADCRIEIDPRARNEQA 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDI 116
           R    L HKP+G V+  ++   +                T     P     +   GRLDI
Sbjct: 69  RRVTVLLHKPMGFVSGQAEDGYKPAATLVIPANRWKDDPTRLAFHPGQLRGLAPAGRLDI 128

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L    T+  + Y VR      G++    L  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 RPARVSWQNED----QLRFVLREGRKRQIRRMCELVGLKVVGLKRVRIGSVSLGQLPPGQ 244

Query: 233 TREVSKKI 240
            R + +  
Sbjct: 245 WRYLGENE 252


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA+  V VNG         V     IEVD    ++  +  
Sbjct: 20  RLNKRMAELGLCSRREADDWIARGWVLVNGAPA-VMGQPVAPDARIEVDRQAEQQQRQQV 78

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
             L +KP+G V+  ++      V                   P     +   GRLDI++ 
Sbjct: 79  TILINKPVGYVSGQAEDGHEPAVVLVQPQNRWRECNSRMRWGPEQLRGLAPAGRLDIDSI 138

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRV---------RFHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L   +++  + Y V                ++KL LL+ G+ + G 
Sbjct: 139 GLLVLTQDGRVARQLIGENSEIEKEYLVRVSYGAETSNVQAVFPREKLALLRHGLSLDGQ 198

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV     +     +   L+EGK R+I+++ E     V  L R+  G   LG L  
Sbjct: 199 ALRPAQVDWQNPE----QLRFVLKEGKKRQIRRMCEQVGLFVTGLKRVRIGRVNLGHLPV 254

Query: 231 GSTREVSKKI 240
           G  R ++   
Sbjct: 255 GQWRYLAAHE 264


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 109/250 (43%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G+++++    V     I++D       ++  
Sbjct: 377 RLSKLMSELGLCSRREADEWIEKGWVTVDGVVVDKLGTKVRPDADIQIDPAAQAAQQKQV 436

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                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 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLHVVGLKRVRMGHVMLGALPP 612

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 613 GQWRYLGPDE 622


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 110/229 (48%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E  + I    V VN +++   +  V  ++ I ++G  L   E  
Sbjct: 10  MRLDKYLCKSTELTKLEAVQRIQNGEVSVNSVVVLDESTQVHESNAILLNGDALTLRE-F 68

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F+ L     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 69  RYILMHKPAGTICSNID-EVYPSLFNYLELEKASELHIAGRLDADTTGLVLITDDGRWSF 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            + LP+    +VYRV     +  D  +  K GI +QG         L+    ++  V + 
Sbjct: 128 NITLPTKSCKKVYRVILSRDIKDDVADKFKAGIQLQGEQKLTRPAELEV--ITSKEVLLT 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K  +
Sbjct: 186 ITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEAGQWRYLTKAEV 233


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 101/233 (43%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A  +  +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHASFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   S+VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G       +    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVAALAAVARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L   
Sbjct: 179 IAEGKYHQVKRMVAAASNRVEALHRSRIGGFALPENLAEGAWRWLDERDLAAL 231


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 109/229 (47%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G PL+  E  
Sbjct: 1   MRLDKYLCKSTDLTKPEAIERIHNGEVNVNSETVTDESAQVHESNTILLNGTPLKLRE-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F+ +     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYLLMHKPAGTICSNID-EVYPSLFNYIEIDKASELHIAGRLDADTTGLVLITDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            + LP+    +VYRV     +  D  +  K GI +QG         L+    ++  V + 
Sbjct: 119 NITLPTKSCKKVYRVTLSRGIKDDVADKFKAGIQLQGEQKPTRPAELEV--ITSKQVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K  +
Sbjct: 177 ITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEAGQWRYLTKAEV 224


>gi|51922071|gb|AAU14148.1| rluB [Mycoplasma mobile 163K]
          Length = 235

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 74/235 (31%), Positives = 117/235 (49%), Gaps = 6/235 (2%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K+I++AGI+SRR  E +I ++RVK+NG++ +         D I VD   + K 
Sbjct: 1   MEKIRIQKLISQAGISSRRAAEDLILKKRVKINGVIAK-IGDKASLEDVILVDEKVISKE 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+   +L +KP  +VTT  D   RS + D +     ++  VGRLD +T G+++LTNDG  
Sbjct: 60  EK-VYYLLNKPKNVVTTLKDNFNRSIITDFIDEKKYKIFPVGRLDYDTTGIIILTNDGET 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A  L  P  +  R+Y V    ++  +++  L      Q +     +   +  K SN    
Sbjct: 119 ANKLLHPKYEIPRIYEVIIDKELSLEEIKYLNS----QEVFLNSKKSFQEVSKISNYKYK 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           + L +G    IKK+FE    KV  L R  Y  F L  L  G+ R+++K  +   L
Sbjct: 175 IKLHQGSYHHIKKLFEIVGKKVKDLNRTEYAFFNLENLSIGNYRKLNKHEIDRLL 229


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 100/229 (43%), Gaps = 11/229 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++    +    N  + D   +V G   +  E   
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGAVSIDSQTCDNPKQNFSTEDLSFQVFGEQYQYRE-YV 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G   +H     R +VF  LP I     V  VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIVLHKPQGYECSHQATHHR-SVFSLLPEILVHRGVQCVGRLDQDTTGLLLLTDDGQYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            L  P     +VY V     V  ++   L+ G+ ++     Y    + L +++     + 
Sbjct: 121 ALTHPKKHVPKVYCVSTADPVTTEQKQQLELGVELRNEKGIYAATDIKLISER----QLA 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + +G   ++K++      KV RL R   G  +L  L  G    ++ +
Sbjct: 177 MTIHQGVYHQVKRMIAAVGNKVERLHRQQIGLLELPNLEEGHWDYLTPQ 225


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 102/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D          
Sbjct: 442 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 501

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 502 VTILLHKPVGYVSGQAEDGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 561

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 677

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 678 QGQWRYLSPDE 688


>gi|167844683|ref|ZP_02470191.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei B7210]
          Length = 240

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 100/233 (42%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++    V V G     A     +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGHVAVGGATCADAHAPFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   S+VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-EPQHHSSVFALLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G       +    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVAALAAVARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R   G F L   L  G+ R + ++ L   
Sbjct: 179 IAEGKYHQVKRMVAAASNRVEALHRSRIGGFALPEDLAEGAWRWLDERDLAAL 231


>gi|328945586|gb|EGG39737.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1087]
          Length = 241

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRIDQLLA-ANHISRKKMKQSLLQKQILVDGKPACKLSQNVDTGLQQINFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPQDKIAFQEGIRFLDGTICQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L
Sbjct: 178 TVKISEGKFHQIKKMFLAIGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQEEL 230


>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 =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 123/262 (46%), Gaps = 28/262 (10%)

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  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGRLDINTE 119
           PL   E+   ++ +K  G V +    D R TVF+ + S  +R         VGRLD +TE
Sbjct: 61  PLT-VEQNAYFMMNKASGAVCSTK-SDRRKTVFEYIFSEDNRKYPGGNLSTVGRLDADTE 118

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-DKL---NLLKKGIVIQGI----- 170
           GLL++T+DG L   +  P  +  + Y V     VD  +KL     L  G+ I+       
Sbjct: 119 GLLIITSDGNLIHRVTFPKYEVPKTYLVYLRDSVDDSEKLSYEKKLAAGVHIEAEGKDGE 178

Query: 171 -CYGDMQVTLDTQKGSNA--------WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                  +    +   +            + + EGK  E+K++F+    +V  L RI   
Sbjct: 179 ADCRPAVIEWKEKNQYHTKTSECPSEVCCLTVTEGKFHEVKRIFKALGNEVVYLKRIRIN 238

Query: 222 PFQLG-TLLAGSTREVSKKILR 242
              L  TL  GS R ++K+ +R
Sbjct: 239 NLFLDETLKEGSYRPLTKEEIR 260


>gi|186475366|ref|YP_001856836.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184191825|gb|ACC69790.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 234

 Score =  221 bits (563), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 104/230 (45%), Gaps = 8/230 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  V+   G  SRR+   MIA  RV + G  L+   ++V +   + EVDG      ER  
Sbjct: 3   LESVLFSQGFGSRRQCRAMIADGRVSIGGATLDDPDIDVDAKALVFEVDGTVWPYHERAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  DP    +VF+ LP+ F    +  VGRLD +T GLLLL++DG    
Sbjct: 63  V-LLNKPAGYECSR-DPQHHLSVFNLLPAQFATRGIQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L  L++G+++ G         +     S   + + 
Sbjct: 121 AYTSPKRKVPKRYLATTRHPLDDAQLAALREGVLLHGEAKRIA--AVAAHARSAHELELT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + EGK  ++K++      +V  L R   G   L   L  G+ + + +  L
Sbjct: 179 VLEGKYHQVKRMVAAAGNRVEALHRERIGGLALPAELAEGAWQWLDEAGL 228


>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 =  221 bits (563), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 53/229 (23%), Positives = 106/229 (46%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   ++ + +  I    VK+N  ++      V + + + +D   L      
Sbjct: 1   MRLDKFICKSTNLNKEQAQAQIQAGIVKINNDIVCDIKAQVHANNQVRLDNRLL-YLRPF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L+HKP   + ++ D +   ++F+ L       +  VGRLD++T G++L+T+DG  + 
Sbjct: 60  RYILFHKPANTICSNLD-ENYPSLFNFLDIEYLDELHIVGRLDVDTTGMVLITDDGHWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  Q ++ YRV     +D+  +   K G+ +QG     +   L      N  + + 
Sbjct: 119 NITRPEKQCVKEYRVSLSQTLDESAIEQFKYGLKLQGEAELTLPARLTFIDDKNVVLGIT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             +GK  ++K++F     +V RL R + G   L  +  G  R +++  +
Sbjct: 179 --QGKFHQVKRMFAALGNRVVRLHRQAIGSVTL-DVAEGQWRYLTEAEV 224


>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 =  221 bits (563), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 104/233 (44%), Gaps = 11/233 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDG 128
             + + HKP G + +  D      V+D LP+ F         VGRLD +T GLLLLT+DG
Sbjct: 59  LMV-MLHKPSGYICSTKDAG--RLVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +  P T   +VY       +  D+  L   G ++       +Q  +    G    
Sbjct: 116 ALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-CQ 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 175 VRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 73/258 (28%), Positives = 125/258 (48%), Gaps = 20/258 (7%)

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-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------SR 107
            V+G  + K       +  +KP G + +  + + + +V                     R
Sbjct: 210 YVNGNRIPKKLPPKVYFALNKPKGYICSSGEKEIK-SVISLFDEYLSSWDKRNPGTPKPR 268

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           + +VGRLD+ T GL+++TNDG  A+ L  PS+   + Y     G + +  L  + +G ++
Sbjct: 269 LFTVGRLDVATTGLIVVTNDGDFAQKLSHPSSSLPKEYITTVVGDIHKRHLMAISEGTIV 328

Query: 168 QGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +G+      V L  ++     A + + + EG+N E++++ +    +V+ L R+  G F+L
Sbjct: 329 EGVHCVPDSVELMPKQHDIPRARLRIVVHEGRNHEVRELVKNAGLEVHSLKRVRIGGFRL 388

Query: 226 -GTLLAGSTREVSKKILR 242
              L  G   E+ +  L+
Sbjct: 389 PSDLGLGKHVELKQSELK 406


>gi|241766432|ref|ZP_04764306.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241363374|gb|EER58885.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 237

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 97/240 (40%), Gaps = 29/240 (12%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGL 84
           + SRRE +  IAQ  VKVNG +     + V +TD IEVD       E+    L HKP+G 
Sbjct: 1   MCSRREADDWIAQGWVKVNGQVA-PMGLQVHATDRIEVDKKAQGFQEQRVTILLHKPMGY 59

Query: 85  VTTHSDPDGRSTVF---------------DNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           V+  ++      V                   P     +   GRLDI++ GLL+LT DG 
Sbjct: 60  VSGQAEDGHTPAVALINPRTHWREDPSRNRFSPPQLRGLAPAGRLDIDSVGLLVLTQDGR 119

Query: 130 LARVLELPSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +AR +    +   + Y VR                 +L  L  G+ + G      +V   
Sbjct: 120 VARQIIGEDSSMDKEYLVRVQYGDVATNVQAVFPAQQLARLCHGLSLDGQALKPARVEWQ 179

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             +     +   L EGK R+I+++ E    +V  L RI  G   LG L  G  R +    
Sbjct: 180 NPE----QLRFVLTEGKKRQIRRMCELVGLRVVGLKRIRIGRVTLGNLPVGQWRYLGPHE 235


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 102/238 (42%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R+     I +  V VNG ++      V  ++ +   G  L  A  +
Sbjct: 1   MRLDKFICKSTELNRKHASDCIERAEVSVNGEVITDVRFQVHESNEVRYKGQRLV-ARPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKPI  ++++ D D  S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 60  RYIMLHKPIHTLSSNVDGDYPSLFRCIDIDRVEDLHIVGRLDADTTGLVLLTDDGRWSFD 119

Query: 134 LELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  Q  + YRV       G V  D +   + G+ +Q      +   L+    +   V
Sbjct: 120 IIRPDKQCAKTYRVMLRDPIAGDVAADVIARFEAGLQLQNEQALTLPAKLEI--VAPREV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            + + EGK  ++K++F     +V  L R   G   L  L  G  R +S   ++    P
Sbjct: 178 LLTITEGKYHQVKRMFAAVGNRVIGLHREQIGDLSL-DLKVGEWRYLSDTEVKRLSTP 234


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVSVAGASATDPDASFDTDGLVFTVDDTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +LN L+ G+ + G       V    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + ++ L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESIGGFTLPVDLAPGAWRWLGERDLSALRDP 234


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+++            D    + 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLENP 201

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 202 TTLLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+++            D    + 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNP 201

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 202 TTLLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 81/235 (34%), Positives = 129/235 (54%), Gaps = 8/235 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAE 71
            +++ K+++  G  SRR +E MI    + +NG  ++    +N  + + I + G  +   +
Sbjct: 2   SEKIQKILSHLGYGSRRNIENMIKFGDISINGKKIVIGQRLNNKNIEVITIKGETVSIKK 61

Query: 72  ---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
              +T++ +Y+KP G + T +D   R  VFD LP     R IS+GRLDINT GLLL TN+
Sbjct: 62  TDFKTKIIIYNKPEGEICTRNDYKKRPIVFDKLPLLNIHRWISIGRLDINTRGLLLFTNN 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLD-TQKGS 185
           G LA  L  PS +  R Y +R  G+++++ +N+LK G+ I+        + T+D      
Sbjct: 122 GNLANELMHPSNKIEREYYIRVFGKINKNTMNILKNGVKIKDGNAAFKSIQTIDHACSKK 181

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
           N W    L EG+NREI+ +++    +V+RLIRI YG   L   L  G   E+S +
Sbjct: 182 NKWFKGVLCEGRNREIRSMWQAVQCQVSRLIRIRYGNIFLPKNLKLGDWSELSSE 236


>gi|325130337|gb|EGC53103.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis OX99.30304]
          Length = 230

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 101/228 (44%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVLHLHRRRFAHLETENLKPGEWKFI 225


>gi|291001465|ref|XP_002683299.1| predicted protein [Naegleria gruberi]
 gi|284096928|gb|EFC50555.1| predicted protein [Naegleria gruberi]
          Length = 362

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 101/241 (41%), Positives = 147/241 (60%), Gaps = 12/241 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA-- 70
           +RVSK +AR G+ S+++   +I   +VKVNGIL+  +   +    D + V GV + K   
Sbjct: 83  ERVSKFLARVGVCSKQQGVDLIKAGQVKVNGILITESGQKMNPFYDVVTVKGVNITKKDV 142

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSI-FSRVISVGRLDINTEGLLLL 124
               E  +L+ YHKP G++ +  D  G R T++  L  + 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 L 245
            
Sbjct: 320 F 320


>gi|126172676|ref|YP_001048825.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125995881|gb|ABN59956.1| pseudouridine synthase [Shewanella baltica OS155]
          Length = 233

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 101/233 (43%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG +    A+ V   + + ++  PL     +
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAIINGSVTVNGAIATDCAMQVHENNAVCLNEKPL-MPRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP   + ++ D     ++F  L       +  VGRLD +T GL+LLT+DG  + 
Sbjct: 60  RYFMLHKPADTLCSNVD-GAYPSLFHLLDIEHAFDLHIVGRLDADTTGLVLLTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  Q  +VYRV     +D +           G+ +QG     +  TL  Q+     
Sbjct: 119 NIISPQYQCEKVYRVTLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDEKT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EGK  ++K++F     KV  L R   G   L  +  G  RE++   +
Sbjct: 177 VLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAVTL-DVDVGEWRELTLAEI 228


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 73/229 (31%), Positives = 112/229 (48%), Gaps = 6/229 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     SR+ V  ++A+  VKV+G +       V    HI ++G  L+ A    
Sbjct: 7   RLDRFISATKRVSRKHVRVLLAKGLVKVDGEIARDIDQIVDEFSHITLEGEVLQ-ANTPI 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+G+V+   D D   TV D L      ++  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 66  YLMLHKPVGVVSATVD-DKHKTVIDLLSHPDKQQLHIVGRLDLNTSGLLLLTNDGRWSKR 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  ++YRV     +D   +    +G+  +      +   L+      A   V L
Sbjct: 125 LMSPEHKVAKLYRVSLENPIDASYIQAFHEGMYFEFEDITTLPAKLEIVDPHTAL--VTL 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            EG+  +IK++F  F   V  L RIS G   L + LLAG +R +S   +
Sbjct: 183 MEGRYHQIKRMFGRFRNPVIGLHRISVGEIVLDSQLLAGQSRVLSTAEI 231


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 103/233 (44%), Gaps = 11/233 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDG 128
             + + HKP G + +  D      V+D LP+ F         VGRLD +T GLLLLT+DG
Sbjct: 59  LMV-MLHKPSGYICSTKDAG--RLVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +  P T   +VY       +  D+  L   G ++       +Q  +    G    
Sbjct: 116 ALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-CQ 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 175 VRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>gi|308389419|gb|ADO31739.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha710]
          Length = 256

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 102/230 (44%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTV 84

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+++            D    + 
Sbjct: 144 DGKLNHSLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNP 201

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 202 TTLLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>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 =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 104/229 (45%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G  L      
Sbjct: 1   MRLDKYLCKSTDLTKSEAIERIHNGEVSVNSEFVLDESTQVHESNTILLNGDALTLRA-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F+ L     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYILMHKPAGTICSNID-EVYPSLFNYLELDKVSELHIAGRLDADTTGLVLITDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            + LP+    +VYRV     +  D  +  K G+ +QG         L+    S   V + 
Sbjct: 119 NITLPTKSCKKVYRVTLSRDIKDDVADKFKAGVPLQGEKNLTRPAELEV--ISPKEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  +L  +  G  R +++  +
Sbjct: 177 ITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEEGHWRYLTEDEV 224


>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 =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 75/251 (29%), Positives = 115/251 (45%), Gaps = 17/251 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +S+ +AR G  SR++V+ +I Q RV   +G+ L          D + VDG PL   E   
Sbjct: 3   LSRYLARLGYGSRKQVDILIRQHRVTTRDGVALRDG--ECPPHDTLAVDGEPLDPPEGAV 60

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
           + L HKP+G V + +D      V++ LPS F      + +VGRLD +T GLLLLT+DG L
Sbjct: 61  V-LLHKPLGYVCSTNDR--PPIVYELLPSRFLSRSPVMATVGRLDADTSGLLLLTDDGAL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              +  P T   + YRV     +  D+      G ++++G        TL         V
Sbjct: 118 NHRITSPRTHVPKTYRVTLAESLHGDEAAQFASGTLMLKGEDAPLRPATLFVHDART--V 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
            + L EG+  +++++F      V  L RI+ G   L  L  G  R +S   +        
Sbjct: 176 DLSLVEGRYHQVRRMFAATGNHVVTLQRIALGSLTLEGLAEGEWRVLSAAEVETL----R 231

Query: 250 LEEAQVNLDAP 260
           L   +   +AP
Sbjct: 232 LAARRSGGEAP 242


>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 =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 108/229 (47%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    I    V VN   +   +  V  ++ I ++G PL+  E  
Sbjct: 1   MRLDKYLCKSTDLTKPEAIERIHNGEVNVNSETVTDESTQVHESNTILLNGTPLKLRE-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F  +     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYLLMHKPAGTICSNVD-EVYPSLFKYIEIDKASELHIAGRLDADTTGLVLITDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            + LP+    +VYRV     +  D  +  K G+ +QG         L+    ++  V + 
Sbjct: 119 NITLPTKSCKKVYRVTLSRDIKDDVADKFKAGVKLQGEQNLTRPAELEV--ITSKEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     +V  L R   G  +L  + AG  R ++K  +
Sbjct: 177 ITEGKFHQVKRMFAAVGNRVVGLHREQIGDVRL-DVEAGQWRYLTKAEV 224


>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 =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 71/251 (28%), Positives = 114/251 (45%), Gaps = 29/251 (11%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R++K +AR G+ SRRE +  I+Q  V++NG  +      VM  D +EV      +
Sbjct: 24  PPEGERLNKHLARTGVCSRREADDWISQGWVRINGRPV-EMGQKVMPGDVVEVRQAARAR 82

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRS--TVFD-------------NLPSIFSRVISVGRL 114
            +     L +KP+G V+  ++   R   T+ D                +    +   GRL
Sbjct: 83  QQDKVTILLNKPVGYVSGQAEDGYRPAVTLIDAQSRWAGDTNPRRFERNQLRGLAVAGRL 142

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-GQV--------DQDKLNLLKKGI 165
           DI++ GLL+LT DG +AR L    +   + Y VR   G+V          D+L LL+ G+
Sbjct: 143 DIDSVGLLVLTQDGRVARQLIGEDSSTTKEYLVRVRYGEVERNVQAAFPPDRLKLLRHGL 202

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G      QV  +  +     +   L+EG++R+I+++ E     V  L RI  G   L
Sbjct: 203 SLDGHKLKPAQVDWENPE----QLRFVLQEGRHRQIRRMCELVGLAVTGLKRIRVGNVLL 258

Query: 226 GTLLAGSTREV 236
           G L  G  R +
Sbjct: 259 GRLPPGQWRYL 269


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/316 (24%), Positives = 140/316 (44%), Gaps = 23/316 (7%)

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+   +A 
Sbjct: 62  FTVIVYNKPRGELVTKKDPQGRKTIYDSLAKQYRHYIPIGRLDFASEGLLLLTDASRVAT 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VT 178
            L   +++  RVY+++  G V +     + +G+ ++    G  +                
Sbjct: 122 ALM--TSKMERVYKIKIKGPVTEAMKVAMGEGLELEDASAGAHEHAEAGPMSFAPFYAYQ 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---LRE---QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
                LRE    L     ++ +    AP    ++  +       E      +        
Sbjct: 240 SEYASLREFLDALEKAEKQKQKSEKKAPRAEGKSEFKPAKTFTKEKSKAKPKSSNEPFGT 299

Query: 293 NGLSKQKKLATPVHRR 308
           N    +KK A   H++
Sbjct: 300 NKYKPEKKFAKGEHKK 315


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 112/249 (44%), Gaps = 32/249 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ASRRE +  I Q  V+V+G ++++    V     I +D     +  +  
Sbjct: 171 RLSKRMSELGLASRREADEWIEQGYVRVDGEVVDQLGARVRPEQQITIDPQARLEQAQRV 230

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS----------------IFSRVISVGRLDINT 118
             L HKP+G V+  ++ DG +  F  + +                    ++  GRLD+++
Sbjct: 231 TILLHKPLGYVSGQAE-DGHAPAFTLVTAANRWATDGSKQRFNASQLKHLVPAGRLDLDS 289

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVI 167
            GLL+LT DG +A++L    +   + Y VR                  + L  L+ G+ +
Sbjct: 290 TGLLVLTQDGRVAKLLIGEDSPVEKEYVVRVQWTARPELTDLKQHFPPEALARLRHGLAL 349

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G      +V+   ++     +   LREGK R+I+++ E    KV  L RI  G   LG 
Sbjct: 350 DGEKLKPAKVSWQNEQH----LRFVLREGKKRQIRRMCELVGLKVESLKRIRIGRVGLGE 405

Query: 228 LLAGSTREV 236
           L  G  R +
Sbjct: 406 LPPGQWRYL 414


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 104/357 (29%), Positives = 167/357 (46%), Gaps = 24/357 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K +   +     +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D I
Sbjct: 14  LKRETATEAPKLEERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKI 72

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E  R+ +Y+KP G VTT  DP+GR TVF+ LP    +R I++GRLDI
Sbjct: 73  ELDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDI 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS++  R Y VR         V  + L  L +G++++   
Sbjct: 133 NTTGLLLLTTDGELANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGT 192

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                +       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 193 AKFDTIERIGNTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLR 252

Query: 231 GSTREVSK---KILREQLG----------PHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           G + E+ K   + LR QL              +   + +  A ++ +           + 
Sbjct: 253 GQSTELPKTQVEALRTQLKLEKDMPLALTLQPVIGQRRSAKATLHVNRNDNNKHAYHNNH 312

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
              D +R  +          + +       R   S    AK  H  F     + + +
Sbjct: 313 STADESRELRRFDTLRDDRGRGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRS 369


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 104/357 (29%), Positives = 167/357 (46%), Gaps = 24/357 (6%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K +   +     +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D I
Sbjct: 14  LKRETATEAPKLEERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKI 72

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E  R+ +Y+KP G VTT  DP+GR TVF+ LP    +R I++GRLDI
Sbjct: 73  ELDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDI 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS++  R Y VR         V  + L  L +G++++   
Sbjct: 133 NTTGLLLLTTDGELANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGT 192

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                +       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 193 AKFDTIERIGNTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLR 252

Query: 231 GSTREVSK---KILREQLG----------PHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           G + E+ K   + LR QL              +   + +  A ++ +           + 
Sbjct: 253 GQSTELPKTQVEALRTQLKLEKDMPLALTLQPIIGQRRSAKATLHVNRNDNNKHAYHNNH 312

Query: 278 VPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREEN 334
              D +R  +          + +       R   S    AK  H  F     + + +
Sbjct: 313 STADESRELRRFDTLRDDRGRGQGKHHFKDRLTVSGEAAAKQAHKPFKQYKPKNDRS 369


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 102/228 (44%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  P+ +  ++Y V       +     LK G+++      +     D    S + 
Sbjct: 120 HLNHKLTSPNHKIPKLYEVTLKHPAGETLCETLKNGVLLHDE--NETVYAADAVLESPSA 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 58/229 (25%), Positives = 100/229 (43%), Gaps = 11/229 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V ++    +    N  + D   +V G   +  E   
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKNGAVSIDSQTCDHPKQNFSTEDLSFQVFGEQYQYREHI- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP G   +H     R +VF  LP I     V  VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIVLHKPQGYECSHQATHHR-SVFSLLPEILIHRGVQCVGRLDQDTTGLLLLTDDGQYLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            L  P     +VY V     V  ++   L+ G+ ++     Y    + L +++     + 
Sbjct: 121 ALTHPKKHVPKVYCVSTADPVTTEQKQQLELGVELRNEKGIYAATDIKLISER----QLE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + + +G   ++K++      KV RL R   G  +L  L  G    ++ +
Sbjct: 177 MTIHQGVYHQVKRMIAAVGNKVERLHRQQIGLLELPNLEEGHWDYLTLE 225


>gi|303233542|ref|ZP_07320201.1| pseudouridylate synthase [Finegoldia magna BVS033A4]
 gi|302495346|gb|EFL55093.1| pseudouridylate synthase [Finegoldia magna BVS033A4]
          Length = 235

 Score =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 119/231 (51%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +    +
Sbjct: 1   MRLDKMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENNDVVKIYDEVIEYR-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  ++ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 60  FLYFVMNKRKGVTSHSKDPMHKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P  +  + Y+V    +VD+   +  +KGI +           ++     N ++   
Sbjct: 120 NLISPKKEVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIITKPAKMEIIDDYNCYL--T 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 178 IKEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>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 =  220 bits (561), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 103/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD +T G+LL+T+D
Sbjct: 58  GFS-LLLHKPSGYTCSTKDTG--RLIYELLPPRFRSRAPVLAPVGRLDRDTSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY +     +  D+  L   G ++++G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDITLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGLRE 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLLLDGLPSGQWRALEASDLEVLFG 232


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 76/259 (29%), Positives = 130/259 (50%), Gaps = 18/259 (6%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  + D I
Sbjct: 148 RRFYNENFKEQPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDII 207

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIF---------SRV 108
            V+G  + K       +  +KP G + +  + + +S  ++FD   S +          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 GTLLAGSTREVSKKILREQ 244
             L  G   E+ +  L+  
Sbjct: 388 SDLGLGKHVELKQSELKAL 406


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 109/251 (43%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V+V+G +++     V +  HI+V         R 
Sbjct: 274 MRLSKRMSELGLCSRREADEWIEKGWVRVDGQIVDTLGAKVTAAQHIDVLPNARAAQARQ 333

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINT 118
              + +KP+G V+   + D    V    P+                   +   GRLDI++
Sbjct: 334 VTIVLNKPVGYVSGQPEGDYPPAVALITPANRWSDDPAPTRFSATHLRSLAPAGRLDIDS 393

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRV---------RFHGQVDQDKLNLLKKGIVIQG 169
            GLL+LT DG +A+ L    ++  + Y V         +       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 VRLKPAQVDWQNGE----QLRFVLREGRKRQIRRMCELVGLEVVGLKRVRIGQLVLGALP 509

Query: 230 AGSTREVSKKI 240
           +G  R +    
Sbjct: 510 SGKWRYLRADE 520


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 102/230 (44%), Gaps = 12/230 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K I   G+ SR++ + +I    + VNG +   A  ++   +   + +DG P+    
Sbjct: 1   MQLLKYIQAQGLGSRKQCQWLIDNGCIAVNGEIRSDAKSSIKPEEVETLAIDGEPIFAVP 60

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L +KP    T+H  P    +VF   P+    +   +VGRLD +T G+LL+TNDG
Sbjct: 61  LPYFYILLNKPANYETSHK-PQQYPSVFSLFPNHMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
                +  P  +  ++YRV      D      LK G+++          +  L+      
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHAADNRLCETLKNGVLLHDDNETVAADEAVLE----KP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V RL R  +G +    L +GS + +
Sbjct: 176 TVLLMTITEGKYHQVKRMVAAAGNRVERLHREKFGDWSADDLPSGSWKFI 225


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 49/231 (21%), Positives = 100/231 (43%), Gaps = 7/231 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    V +   +++     +     + EV G      E+  
Sbjct: 3   LEKMLQSQGFGSRKHCQQLIKNGAVSIQDEVIDNPKHKLDLNHLNFEVYGKSQTYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +H       +VFD    I     +  VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALNKPQGYECSHQ-ATHHFSVFDLFDDILLNRGIQCVGRLDHDTTGLLLLTDDGQFLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VY+++    V  +++  L++G+ ++      +    +  + +   + + 
Sbjct: 121 ALTHPKKHVAKVYQMQTADPVTDEQIQQLEQGVELRNE--KGIFAATEVARLAENRLQMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           + +G   ++K++      KV +L R   G   L  L  G    ++ + + +
Sbjct: 179 IHQGVYHQVKRMLAAVGNKVEQLHRAQIGALALPELAEGEWLYLNAEQVAQ 229


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 104/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 264 MRLSKRMSELGLCSRREADEWIEKGWVIVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 323

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 324 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 383

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 499

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 500 QGQWRYLSADE 510


>gi|322379744|ref|ZP_08054054.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321147815|gb|EFX42405.1| pseudouridine synthase [Helicobacter suis HS5]
          Length = 257

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 118/245 (48%), Gaps = 17/245 (6%)

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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC------------YGDMQVTL 179
             L    +   RVY V+  G + Q  L  ++ G+ +QG+                M   +
Sbjct: 125 NALMH--SSLERVYLVKIQGNITQTMLEAMQTGLELQGLEGAHPKSKYTRMHIAPMACQI 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                + + + + L+EG NREI++ F  F  +V  L R+S+G   L  L  G TR ++ K
Sbjct: 183 LKNHRNYSKIKITLQEGHNREIRRFFAHFKKEVLDLRRVSFGFVSLNALPVGKTRYLNPK 242

Query: 240 ILREQ 244
             ++ 
Sbjct: 243 EYKQL 247


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 94/258 (36%), Positives = 144/258 (55%), Gaps = 14/258 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K +   +     +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D I
Sbjct: 14  LKRETATEAPKLEERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKI 72

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E  R+ +Y+KP G VTT  DP+GR TVF+ LP    +R I++GRLDI
Sbjct: 73  ELDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDI 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS++  R Y VR         V  + L  L +G++++   
Sbjct: 133 NTTGLLLLTTDGELANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGT 192

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                +       S+ W  + ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 193 AKFDTIERIGNTDSHDWFRIVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLR 252

Query: 231 GSTREVSK---KILREQL 245
           G + E+ K   + LR QL
Sbjct: 253 GQSTELPKTQVEALRTQL 270


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 103/357 (28%), Positives = 167/357 (46%), Gaps = 21/357 (5%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +D +  ++    +R+ KV+A+AG+ SRR +E+ IA   VKVNG + +   +++ S D IE
Sbjct: 17  RDASAAEQPKLEERLHKVLAQAGLGSRRALEQRIADGLVKVNGEVAQT-GMSIKSGDRIE 75

Query: 62  VDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
           +DG         E  R+ +Y+KP G VTT  DP+GR T+F+ LP+   +R I++GRLDIN
Sbjct: 76  LDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTIFEALPALKGARWIAIGRLDIN 135

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICY 172
           T GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G+V++    
Sbjct: 136 TTGLLLLTTDGELANAMMHPSYEIEREYVVRVRAPEGEESVPDSMIERLARGVVLEDGSA 195

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAG 231
              ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   +L G
Sbjct: 196 KFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVALPREVLRG 255

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            + E+++  +        LEE       P   +   V  +      V           + 
Sbjct: 256 QSMELAQDKVEALRAELKLEEG-----TPSALTLQPVIGQRKAAKAVVQVGRGGNAYVNG 310

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFL-----SDSGQREENHRRSPSFPS 343
            N   + ++L      R         K  H         +    ++   +R+P  P 
Sbjct: 311 HNAADEGRELRRFDTFREDRGRGRGGKKPHGGLTVSGEMAAKQAQKPFKQRTPKGPK 367


>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 =  220 bits (560), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 377 MRLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQ 436

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                    +     P     +   GRLDI++
Sbjct: 437 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 496

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 612

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 613 QGQWRYLSADE 623


>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 =  220 bits (560), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 82/238 (34%), Positives = 123/238 (51%), Gaps = 5/238 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   QR+++ +AR G+ASRR+ E +I   RV++NG ++   AV V   D +EVDG P+  
Sbjct: 2   SEDSQRLNQYLARCGVASRRKAEALILGGRVRLNGCVVLDLAVRVQGEDRVEVDGEPVLP 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
                  + HKP G+++   D     TV D LPS F   R   VGRLD ++EGLLLLTND
Sbjct: 62  RVAL-YLVLHKPRGVLSAVEDRR-EQTVVDLLPSRFRPERPFPVGRLDKDSEGLLLLTND 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G  A+ L  PS   ++ Y V+    +  +    + +G+  +G     + +          
Sbjct: 120 GDFAQRLLHPSAGIVKSYEVQLDRPLAPEHRERMLEGLWSEGEFLRPLSIRSLGV-PDRR 178

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           W    L EGK REI+++   F + V RLIR   G  +L  L  G  +E+S + L  Q+
Sbjct: 179 WTVFDLVEGKKREIRRLAALFEYGVLRLIRRRVGKLELRRLETGVAQELSGEALWRQI 236


>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 =  220 bits (560), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 94/258 (36%), Positives = 144/258 (55%), Gaps = 14/258 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K +   +     +R+ KV+A+AG+ SRR +E+ I+   +KVNG + +   ++V S D I
Sbjct: 14  LKRETATEAPKLEERLHKVLAQAGLGSRRALEQRISNGLIKVNGDIAQ-LGMSVKSGDKI 72

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E  R+ +Y+KP G VTT  DP+GR TVF+ LP    +R I++GRLDI
Sbjct: 73  ELDGRSFVASALTEPARVLIYNKPEGEVTTREDPEGRPTVFETLPVLKGARWIAIGRLDI 132

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS++  R Y VR         V  + L  L +G++++   
Sbjct: 133 NTTGLLLLTTDGELANAMMHPSSEIEREYVVRVRSPEGEEHVQDELLEQLTRGVMLEDGT 192

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
                +       S+ W  + ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 193 AKFDTIERIGNTDSHDWFRIVVKEGRNREVRRLWESQGCQVSRLKRTRYGSVLLPRELLR 252

Query: 231 GSTREVSK---KILREQL 245
           G + E+ K   + LR QL
Sbjct: 253 GQSTELPKTQVEALRTQL 270


>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 =  220 bits (560), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 421 MRLSKRMSELGMCSRREADEWIEKGWVLVDGARIDTLGTKVRADQKIEIDERASAAQAAQ 480

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                    +     P     +   GRLDI++
Sbjct: 481 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 540

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPALVSWQNGE----QLRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 656

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 657 QGQWRYLSADE 667


>gi|317055194|ref|YP_004103661.1| pseudouridine synthase [Ruminococcus albus 7]
 gi|315447463|gb|ADU21027.1| pseudouridine synthase [Ruminococcus albus 7]
          Length = 246

 Score =  220 bits (560), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 117/245 (47%), Gaps = 13/245 (5%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ K++A    A  SR +V+++  ++++ VNG L+ R+   V + D I +DG  L   +
Sbjct: 5   MRLDKLVASQ-FADISRADVKKLCLKKKIMVNGKLMARSDAKVDTDDEIIIDGRKLTY-K 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGG 129
           +    + +KP G+V +  +    +TV D +P    R  +   GRLD +TEG +L+T+DG 
Sbjct: 63  KHIYIMLNKPAGVVCSTKE-GASTTVLDLVPDELRRDGLFPAGRLDKDTEGFVLITDDGE 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQKG 184
           L+  +  P T   + Y VR     +    +++  G+ I G+  GD               
Sbjct: 122 LSHRVLSPKTHVPKTYFVRLEKPWEDSYKDIMAAGMTIDGLHEGDSEEKCQPAQFLASDE 181

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           +    T+ + EGK  ++K++FE    KV  L R++ G   L   L  G   E+  K + +
Sbjct: 182 NVCECTLIIHEGKFHQVKRMFEKLGNKVVYLKRVAIGEMPLDRGLELGECLEIMHKDVEK 241

Query: 244 QLGPH 248
            L   
Sbjct: 242 LLARK 246


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 125/239 (52%), Gaps = 15/239 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAER 72
           R+ +++A +G+ SR +V++MI ++   V+G+ +   +  ++ TD   I +DG PL     
Sbjct: 4   RLDRILALSGLGSRSDVKKMIRKKNCCVDGVRIVSPSF-ILDTDLNKITIDGEPLVLRTN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               +++KP G VT+ SDP    TV D + + F R  +  +GRLDI+TEGLL++T+DG +
Sbjct: 63  -VYLMFNKPQGCVTSTSDP-VHKTVMDYIKAPFDRMTLFPIGRLDIDTEGLLIITDDGEI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQ-GICYGDMQ-VTLDTQKG 184
              +  P +  ++ Y +    +   ++        +KGIV++ G      +    + + G
Sbjct: 121 THKITSPKSGTVKTYYLELSREPSDEEFKNYCEEFEKGIVLKNGYKCLPAKFEKCENKTG 180

Query: 185 S-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           S  +   + + EGK  ++KK+      ++  L RI+ G   L  TL  G  RE+S + +
Sbjct: 181 SFRSGFLMHITEGKFHQVKKMCLSAGNELCYLRRIAVGSIVLDETLKTGEYRELSAEEI 239


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 68/248 (27%), Positives = 112/248 (45%), Gaps = 24/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
             +R+SK +A  G+ASRRE +  I    V+V+G +       V     I VD    ++  
Sbjct: 171 EGERLSKRMAALGLASRREADEWIEAGWVRVDGKMA-VLGQRVGPQAKIHVDPAAHKQQA 229

Query: 72  RTRLWLYHKPIGLVTTHSD-----------PDGRSTV----FDNLPSIFSRVISVGRLDI 116
           +    L +KP+G V+  ++           P+ R +      +  P     +   GRLDI
Sbjct: 230 QRVTILVNKPVGYVSGQAEDGYEPAAALIRPENRWSEDSSGVNWHPGQLRGLAPAGRLDI 289

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF----HGQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A++L    +   + Y VR      G++    L LL  G+ + G   
Sbjct: 290 DSVGLLVLTQDGRVAKLLIGDESLVEKEYLVRVAYQGQGRLPDSALALLNHGLELDGQAL 349

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V+   +      +   LREGK R+I+++ E    +V  L R+  G   LG L AG 
Sbjct: 350 RPAKVSWQNED----QLRFVLREGKKRQIRRMCEAVGLQVLGLKRVRIGSVSLGHLPAGQ 405

Query: 233 TREVSKKI 240
            R + +  
Sbjct: 406 WRYLRRDE 413


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 100/228 (43%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  ++ A  ++ S     +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCIDDADADIHSASVHTLDIDGKAVTVIP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPADYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V      D      LK G+++            D    S   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPADGILCETLKNGVLLHDENETVCAA--DANLESPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRQFAHLETENLKPGEWKFI 225


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 121/243 (49%), Gaps = 4/243 (1%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K KN  +++     R++K IA AGI SRR+ +  IA   V VNG ++      V  TD 
Sbjct: 38  IKRKNTALEKREDGMRLNKYIANAGICSRRDADIYIASGNVSVNGEVVTEMGYKVQLTDE 97

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINT 118
           ++ DG  +   ++   ++ +K  G+  T S   G  TV D +  +  S++  +G+LD  T
Sbjct: 98  VKFDGRSIT-PDKPEYFVLNKSKGVFVTGSVHKGGLTVMDIMAKASKSKLDPIGKLDTQT 156

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLL+ TNDG LA+ L  P     ++Y ++    + QD L  +++G+ I+        V+
Sbjct: 157 TGLLVFTNDGALAKKLANPKNGIRQIYHIKLDHALSQDDLEKIREGVYIESKKINVTDVS 216

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +      V + L   K   ++K+F+  ++++  L R+ YG      L  G  R ++K
Sbjct: 217 Y-VKDRPKTEVGMELTSTKPHIVQKIFKSLSYEILNLDRVVYGGLTKKDLPRGRFRTLTK 275

Query: 239 KIL 241
           + +
Sbjct: 276 QEV 278


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 98/232 (42%), Gaps = 12/232 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    + +N  +           +   EV G      E+  
Sbjct: 3   LEKILQSQGFGSRKYCQQLIKSGAISINHEICADTKAKFDLKNFTFEVHGEEFEYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +H       +VFD          +  VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALNKPQGYECSHQ-AQYHFSVFDLFDPALLNRGIQCVGRLDQDTTGLLLLTDDGQFLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            L  P     +VY +     +  +++ LL++G+ +   GI         + ++ S+  ++
Sbjct: 121 ALTHPRKHVAKVYDLITVDPITPEQIRLLEQGVELRNDGIFKA-----SNIKQTSSHQLS 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + + +G   ++K++      KV +L R   G  +L  L  G    + +  + 
Sbjct: 176 LAIHQGVYHQVKRMLAAVGNKVEKLHRSKIGELELPMLAEGEWTYLDQTEIE 227


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 105/233 (45%), Gaps = 11/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKAER 72
            ++ K IA  G  SR+EV R+  + R+  + G +L  A  +V  T  +  DG PL     
Sbjct: 1   MKLLKYIANLGYGSRKEVARIFREGRITNDEGEVLY-ADDHVQHTA-VRFDGEPLDPPPG 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDG 128
             + + HKP G + +  D      V+D LP+ F         VGRLD +T GLLLLT+DG
Sbjct: 59  LMV-MLHKPSGYICSTKDAG--RLVYDLLPARFRLRSPLLSTVGRLDGDTSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   +  P T   +VY       +  D+  L   G ++       +Q  +    G    
Sbjct: 116 ALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLGP-CQ 174

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 175 VRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>gi|325473314|gb|EGC76509.1| pseudouridine synthase [Treponema denticola F0402]
          Length = 245

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 124/239 (51%), Gaps = 15/239 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAER 72
           R+ +++A +G+ SR +V++MI ++   V+G+ +   +  ++ TD   I +DG PL     
Sbjct: 4   RLDRILALSGLGSRSDVKKMIRKKNCCVDGVRIVSPSF-ILDTDLNKITIDGEPLVLRTN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               +++KP G VT+ SDP    TV D + + F R  +  +GRLDI+TEGLL++T+DG +
Sbjct: 63  -VYLMFNKPQGCVTSTSDP-VHKTVMDYIKAPFDRMTLFPIGRLDIDTEGLLIITDDGEI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQ-GICYGDMQ-VTLDTQKG 184
              +  P +  ++ Y +    +   ++        +KGI+++ G      +      + G
Sbjct: 121 THKITSPKSGTVKTYYLELSREPSDEEFTNYCEEFEKGIMLKNGYKCLPAKFEKCGNKTG 180

Query: 185 S-NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           S  +   + + EGK  ++KK+      ++  L RI+ G   L  TL  G  RE+S + +
Sbjct: 181 SFRSGFLMHITEGKFHQVKKMCLSAGNELCYLRRIAVGSIVLDETLKTGEYRELSAEEI 239


>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 =  219 bits (559), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 101/228 (44%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  219 bits (559), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 116/233 (49%), Gaps = 6/233 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA++GI SRRE +  I    V VNG+++      V  TD ++ +   +   E+ 
Sbjct: 217 IRLNRFIAQSGICSRREADDFIQAGLVTVNGVVVTTLGTKVQPTDEVKFNDSRVE-GEKK 275

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G VT+  DP    TV + +      R+  VGRLD N+ GLLL TNDG L R
Sbjct: 276 VYLVLNKPKGYVTSLDDPHADKTVMELVKDACTERIYPVGRLDKNSVGLLLFTNDGDLTR 335

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            L  PS Q  ++Y+V     + +  +  + +GI +  G  Y D    +   K     V +
Sbjct: 336 QLTHPSFQKKKIYQVSLDKPLTKADMEQIAQGITLEDGEIYAD---EIAYVKEDKTEVGI 392

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +  G+NR ++++FE   + V +L R+ Y       L  G  R ++++ ++  
Sbjct: 393 EIHSGRNRIVRRIFEHLGYAVKKLDRVYYAGLSKKNLKRGQWRFLTREEVQRL 445


>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 =  219 bits (559), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 57/228 (25%), Positives = 99/228 (43%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  +  A  ++ S     +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVSINGTCMNDADADIDSASVHTLDIDGKAVTIIP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPADYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLVTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V      D      LK G+++            D    S   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPADGILCETLKNGVLLHDENETVCAA--DANLESPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRQFAHLETKNLKPGEWKFI 225


>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 =  219 bits (559), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 228 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 287

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 288 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 347

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 348 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 407

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 408 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 463

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 464 GEWRYLGPDE 473


>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 =  219 bits (559), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 102/232 (43%), Gaps = 10/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G +   A  +  + D      VDGV     E 
Sbjct: 28  LESILFTQGFGSRRQCRALIADARVSIGGAVCTDADADFPTGDTTFSFTVDGVDWPYREH 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 88  A-YLLLNKPAGYECSR-DPQHHLSVFSLLPPQFAGRGVQCVGRLDQDTTGLLLLSDDGKF 145

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L+ G+++ G       V ++ +   +  + 
Sbjct: 146 VHLFTSPKRKVPKVYVATTRHPIDDAQLSALRDGVLLNGEARPIAAVDVEARG--DHTLA 203

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           + + EGK  ++K++      +   L R   G   L   L  G+ + + +  L
Sbjct: 204 LTVMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPEALARGAWQWLDETDL 255


>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 =  219 bits (559), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 110/236 (46%), Gaps = 9/236 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A AG+ASRR   R+I   RV ++G     +   V  ++ + VDG PL  A+   
Sbjct: 11  RLCKYLAEAGVASRRGASRLIETGRVCIDGQQASHSD-RVFDSNRVTVDGAPLCPAQAKA 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +LYHKP+G+       D   ++   LP    R+   GRLD ++ GLLLLTNDG L + L
Sbjct: 70  YFLYHKPVGIDCRLRAEDPH-SLIHCLPGDL-RLFPAGRLDKDSRGLLLLTNDGELTQRL 127

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------DTQKGSNAW 188
             P     + Y +  +     D +  +  G            V         T+ G+   
Sbjct: 128 MHPDFHHQKGYLITLNKAPQPDDIAAIAAGFDYGEGPTRPCVVEAAIDCGYATEDGNPRK 187

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + L EGK R+I++++    ++V  L+R S     +G L  G  R ++   LR+ 
Sbjct: 188 LRMRLTEGKKRQIRRLWRARGYRVLDLLRESIQQLNIGKLEQGEIRSLTASELRQL 243


>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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 65/232 (28%), Positives = 117/232 (50%), Gaps = 4/232 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++    +R+ V  M+A+ +V+V+G L     + V    HI V+   ++  + + 
Sbjct: 7   RLDRFISQHLKINRKNVRLMLAKGQVRVDGELARDIDLIVDEFSHICVNDEVIQAKQAS- 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + HKP+G+V+   D   ++ +        + +  VGRLD+NT GLLLLTNDG  ++ L
Sbjct: 66  YIMLHKPVGVVSATVDDKHKTVIELLKCDDRNSLHIVGRLDLNTSGLLLLTNDGRWSKQL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P  +  ++YRV     +  + ++   KG+  +      +   L+      A   V L 
Sbjct: 126 MDPEYKVGKLYRVELQNPLTVEYISAFAKGMYFEFEDITTLPAELEIVDSHTAL--VTLY 183

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           EG+  +IK++F  F   V  L RIS G   L  TL +G +R ++ + ++ +L
Sbjct: 184 EGRYHQIKRMFGRFRNPVVGLHRISVGQIVLDKTLASGQSRPLTPEEIKHKL 235


>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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 92/224 (41%), Positives = 133/224 (59%), Gaps = 3/224 (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  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 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 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           E++K        V +LIR+ YGP++L  L +G+  EV  K L +
Sbjct: 182 EVRKALAHVRLVVKQLIRVQYGPYRLADLPSGAVLEVRPKSLEK 225


>gi|218533320|ref|YP_002424135.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
 gi|218525623|gb|ACK86207.1| pseudouridine synthase [Methylobacterium chloromethanicum CM4]
          Length = 320

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 89/299 (29%), Positives = 143/299 (47%), Gaps = 11/299 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLR 68
           + +P  + +V+++ G  SRR  E +I   RV+V+G ++  A V V      I VDG  L 
Sbjct: 21  SPSPVSLPRVLSKFGFCSRRSAEVLIESGRVRVDGRVVRNAGVRVDPQRAAICVDGRRLV 80

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
            A +    L +KP GL+TT+ DP GR TV+D L       +  VGRLD  +EGLLL+TND
Sbjct: 81  SAAK-VYLLLNKPRGLLTTYGDPQGRKTVYDCLAGHDLPFLAPVGRLDCASEGLLLMTND 139

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
              A  L  P++   +VY V+   + D+  L  L++G+   G       V        NA
Sbjct: 140 TRWAHRLLDPASNVDKVYHVQIDRRPDEALLTGLREGVAHDGERLAAKSVAPLRVGERNA 199

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           W+ V L EG+NR+I+++      +V RL+R++ G  +LG +  G+ R ++          
Sbjct: 200 WLEVVLSEGRNRQIRRMMALNGAEVLRLVRVAVGGVRLGDVRKGAFRHLTDAE------- 252

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                A    D+ I  S T  R      +   +   +    +S     +++ +L  P+ 
Sbjct: 253 RACLAAGGRTDS-IRRSPTAGRAENGRETFSAERLLQRSVATSSIRSDTERDQLRMPIE 310


>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 =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 101/228 (44%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHSLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|224100741|ref|XP_002311995.1| predicted protein [Populus trichocarpa]
 gi|222851815|gb|EEE89362.1| predicted protein [Populus trichocarpa]
          Length = 397

 Score =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 123/260 (47%), Gaps = 20/260 (7%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF    QR+SKV+A AG+ASRR  E +I + +V VNG +       V    D I
Sbjct: 135 RRFYNENFRDQAQRLSKVLAAAGVASRRSSEALIFEGKVTVNGSVCNTPQTRVDPGRDSI 194

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------SR 107
            V+G  L K          +KP G + +  + + + +V   L   F             R
Sbjct: 195 YVNGNRLPKKLPPKIYIALNKPKGYICSLGEKESK-SVMCLLDDYFQSWDKRNPGLPKPR 253

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           + +VGRLD+ T GL+++TNDG  A+ +  PS+   + Y     G V +  L  + +G VI
Sbjct: 254 LFTVGRLDVATTGLIIVTNDGDFAQQIAHPSSNLSKEYIATVDGVVSKRHLFAVSEGTVI 313

Query: 168 QGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           +G+      V L  Q+       + + + EG+N E++++ +    +++ L R+  G F+L
Sbjct: 314 EGVRCVPDSVELLPQQPDRPRPRLRIVVHEGRNHEVRELVKNAGLEIHSLKRVRIGGFRL 373

Query: 226 -GTLLAGSTREVSKKILREQ 244
              L  G   E+ +  L+  
Sbjct: 374 PSDLGLGKHAELKQTDLKTL 393


>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 =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 101/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 402 MRLSKRMSELGMCSRREADEWIEKGWVLVDGERIDTLGTKVRADQKIEIDERASAAQAAQ 461

Query: 74  RLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                    +     P     +   GRLDI++
Sbjct: 462 VTILLHKPVGYVSGQAEDGYEPAAVLITRANRWSGDHSPVRFSPQHLHALAPAGRLDIDS 521

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPALVSWQNGE----QLRFVLREGKKRQIRRMCELVGLDVIGLKRVRMGRVMLGALP 637

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 638 QGQWRYLSADE 648


>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 =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 121/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 102/239 (42%), Gaps = 13/239 (5%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTNDG 128
               L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+DG
Sbjct: 59  FS-LLLHKPSGYTCSTKDTG--RLIYELLPLRFRSRAPVLAPVGRLDRETSGMLLMTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L   +  P +   +VY V     +  D+  L   G ++++G     +   LD      A
Sbjct: 116 ALLHRIISPKSALDKVYDVTLAEDLRGDEAALFSSGTLLLEGETKPLLPAELDVLGPREA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 176 --RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLEGLPSGQWRTLEAPDLEVLFG 232


>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 =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 58/254 (22%), Positives = 107/254 (42%), Gaps = 17/254 (6%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+ K+++  G  +R++V   I    + V G   E  A  V ++D + ++G PL  
Sbjct: 3   DQKSERLDKLLSNLGYGARKDVRHWIKAGWITVQGEAAESPAQKVFASD-VLLEGEPLDH 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLT 125
            +     +YHKP+  V +    +G   ++D+LP+ +         VGRLD +T GLL++T
Sbjct: 62  PDGL-TIIYHKPLDTVCSRK--EGGRLIYDDLPARWLDRKPPFSPVGRLDKDTSGLLIVT 118

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLDTQ 182
           +DG L   L  P     + Y V     +   +  ++  G ++           ++ +   
Sbjct: 119 DDGQLNHCLTSPKQHISKTYSVTLAEPLQGREAEIMAAGTLLLENDDRPCLPAELIV--- 175

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKI 240
             S    ++ L EG+  + +++F      V  L R   G   L    L  G  +  +   
Sbjct: 176 -HSPTQASLTLHEGRYHQARRMFVALGNHVTALQRTHIGALALKDTGLKPGEYQVTTSAE 234

Query: 241 LREQLGPHLLEEAQ 254
           L   + P     AQ
Sbjct: 235 LMAMIQPVAPSSAQ 248


>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 =  219 bits (558), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 111/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +++A   SR+E ++++    V VN  +++   V+V    D ++  G PL  A  
Sbjct: 1   MRLDKFLSKATELSRKESKKILHAGEVTVNEQVIKDPGVHVDIVNDDVQWAGEPLSVATG 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  L HKP G   T    +    V D +       +   GRLD++T G LL+++DGG  
Sbjct: 61  NRYILLHKPEGFECTLKAKEY-PIVTDLIAVPELGSLRIAGRLDVDTTGALLISDDGGWL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P  +  +VY +     +D D     +  + +GI+++G        TL+    ++A
Sbjct: 120 HRVTSPKHEHAKVYELTLADAMDSDAQANAIKEVAEGILLEGDHEETKPATLEFIDETHA 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +GK  ++K++  +F  +V  L R S G   L  L  G +R ++ + +
Sbjct: 180 --RLTLEQGKYHQVKRMMGYFGNRVVELHRASVGHITLDGLEKGDSRFLTPEEV 231


>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 =  219 bits (558), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 117/241 (48%), Gaps = 8/241 (3%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
               E     ++ K I++ G  SRR+ E +I Q+R+K+N  +       V++ D I +DG
Sbjct: 3   ETKDEFEKTIKIQKAISQVGYCSRRQAEELIKQKRIKINHQVAT-LGQRVLADDQIFIDG 61

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             L         +++KP   + T  DP+ R T+++ +  +     SVGRLD N+ G++L+
Sbjct: 62  KKLNIKPPKFYLVFNKPKNTICTLKDPEKRKTIYEYM-GLKEYAYSVGRLDFNSTGIILV 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQK 183
           TNDG  A ++  PS    RVY V    ++ +   N L    +++ G      + +    K
Sbjct: 121 TNDGDFANLIAHPSANIKRVYEVVLEKELSEGDFNYLNSNKVILNG-----KKSSQSLSK 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            +    +V L EG+N  +K +F   N  V  L R+SYGP     L  G TR +S+  ++ 
Sbjct: 176 LAPFKYSVSLYEGRNHHVKNLFLLVNNYVKELHRVSYGPITDANLKIGKTRHLSESEVQN 235

Query: 244 Q 244
            
Sbjct: 236 L 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 =  219 bits (558), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 54/228 (23%), Positives = 99/228 (43%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+ +            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAA--DAVLENPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>gi|325694128|gb|EGD36046.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK150]
          Length = 241

 Score =  219 bits (558), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 116/233 (49%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++   Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSHLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANHDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 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|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 =  219 bits (558), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 110/243 (45%), Gaps = 17/243 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRK 69
            T  R++  +A+ G+ASRR+  R+I   RV +NG                + VDG  +  
Sbjct: 1   MTSIRLAHYLAQCGVASRRQASRLIEAGRVLLNGNQASHTDYIDEHNASSLRVDGKAI-A 59

Query: 70  AERTRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E    WLY+KPIG+       DP   +++   LPS   R+   GRLD ++ GLLLLTND
Sbjct: 60  PEAKAYWLYNKPIGIDCRLLAQDP---ASLIHQLPSA-PRLYPAGRLDKDSRGLLLLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   L  P     + Y V+ +  +  + +  L  G+   G+     +V    ++ ++ 
Sbjct: 116 GDLTHKLMHPDFYHPKTYHVQVNQPLKDEDIMALSTGVAYPGVLTRRCEV----RRLADD 171

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-----LLAGSTREVSKKILR 242
              + L +G NR+I+++ +   +KV  L R +    +L +     L     R +    L 
Sbjct: 172 KFEMILTQGLNRQIRRMCKALGYKVIDLQRTAIMKLELNSKEFEQLADNKMRPLEAAELI 231

Query: 243 EQL 245
             L
Sbjct: 232 SLL 234


>gi|325204300|gb|ADY99753.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis M01-240355]
          Length = 230

 Score =  219 bits (558), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 100/228 (43%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 55/228 (24%), Positives = 103/228 (45%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +IA   V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIAGGYVFINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++      +     D    S + 
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPAGETLCETLKNGVLLHDE--NETVYAADAVLESPSA 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 119/231 (51%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ ++++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +    +
Sbjct: 1   MRLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENNDVVKIYDEVIEYR-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  ++ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 60  YLYFVMNKRKGVTSHSKDPMYKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y+V    +VD+   +  +KGI +          T++     N ++   
Sbjct: 120 NLISPKKDVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIVTKPATMEIIDDYNCYL--T 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 178 IKEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>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 =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 56/239 (23%), Positives = 106/239 (44%), Gaps = 13/239 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+E++  I    +   +G  ++  +   +  + I  D  PL   E 
Sbjct: 1   MRLVKLLANLGYGSRKEMQAAIRNGWITDKDGNAIKADSK--LPHEEILFDDEPLDPPEG 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDG 128
           + + L +KP+G   +  D      VFD LP  +         VGRLD +T GLLL T+DG
Sbjct: 59  S-VILLNKPLGYTCSMKDRG--RLVFDLLPDRYRVRKPALSFVGRLDKDTTGLLLFTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
            L   +  P     ++Y V     +   + +L   G ++++          L+    ++A
Sbjct: 116 KLLHRIISPKADVAKIYEVELDRPMTGGEGDLFASGEMMLENETNPLKPAELEVLSETSA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
              + L EG+  +++++F      V  L R   G   L  +  G+ + ++++ + +  G
Sbjct: 176 --RLTLHEGRYHQVRRMFAATGNHVTNLHRAQLGGLTLEGVEEGTWKLLAQEEIAKIFG 232


>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 =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 61/222 (27%), Positives = 111/222 (50%), Gaps = 6/222 (2%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           +R++K +A + G+ SRR+ + +IA+Q+V +N    +     +  +D I ++   +     
Sbjct: 15  ERLNKFLAFQLGV-SRRQADNLIAKQKVYINNQPAQ-LGARIGESDTITINNHIVGGRSS 72

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               + +KPI  V +        T++  LP  F  +  VGRLD N+ GLLLLTNDG  A 
Sbjct: 73  YTYLMLNKPINYVCSRKQQGKTPTIYSLLPDKFHNLKPVGRLDANSSGLLLLTNDGDFAF 132

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  + Y V    ++      ++   GI +       + ++  + +  + W+ V
Sbjct: 133 RMTHPKFKKNKQYNVTLDKELAPLHQQMIADFGIQLNDG-LSKLGLSRQSNQDRHNWI-V 190

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            + EG+NR+I++ F    + V +L R  +G ++LGTL AG  
Sbjct: 191 TMSEGRNRQIRRTFAALGYTVIKLHRTHFGTYKLGTLGAGDY 232


>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 =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 102/251 (40%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D          
Sbjct: 398 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDERASAAQAAQ 457

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 458 VTILLHKPVGYVSGQAEDGYEPASVLITRANQWSGDRSPLRFSPQHLHALAPAGRLDIDS 517

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALP 633

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 634 QGQWRYLSPDE 644


>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 =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 69/252 (27%), Positives = 123/252 (48%), Gaps = 19/252 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+     SRRE + +I Q +V VNG ++   A +V   D ++++G  +R  
Sbjct: 1   MQKSRLNKFISHNTSYSRREADELIKQGKVSVNGRVISELATSVSDEDKVKINGRIVRLK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + +YHK  G + +  D  GR T++D+L   F++ +S+GRLD  +EGLLLLT+   +
Sbjct: 61  KEFTMIVYHKQKGELVSKKDDRGRKTIYDSLDRQFAKFVSIGRLDYASEGLLLLTDAPAI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQ 176
           A  L   ++   R Y ++  G++  + +  + +G                        + 
Sbjct: 121 ATALM--NSDVEREYYLKVKGEITPEVITAMNEGFFAADATKGAHAKTAIKSMEFKPFLD 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +    G    + V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R  
Sbjct: 179 YKIFGSSGGFTKLKVVINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWRYF 238

Query: 237 SK---KILREQL 245
                + LR+ L
Sbjct: 239 ENGEYEALRDFL 250


>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 =  218 bits (557), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 104/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 364 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 423

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 424 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 483

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 599

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 600 QGQWRYLSADE 610


>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 =  218 bits (557), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 80/263 (30%), Positives = 127/263 (48%), Gaps = 18/263 (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  IEVDGVPLRKA-ERTRLWLYHKPIGLVTTH-SDPDGRSTVF-DNLPSIF--------SRV 108
           I V+G  + K       +  +KP G + +   D     ++F D 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 GI-CYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           GI C  D+  +LD Q  +    + + + EG+N E++++ +    +V  L R+  G F+L 
Sbjct: 325 GIMCIPDLVESLDAQSDTRKTRLKIVVHEGRNHEVRELVQNAGLQVYALKRVRIGRFRLP 384

Query: 227 -TLLAGSTREVSKKILREQLGPH 248
             L  G   E+ +  ++   G  
Sbjct: 385 ADLGIGKFVELKQADIKALEGNK 407


>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 =  218 bits (557), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 69/236 (29%), Positives = 117/236 (49%), Gaps = 10/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----A 70
           R+ K+++  GI SRR+ E +I   ++ +N  + +     V   D I+++   ++     A
Sbjct: 7   RIQKILSEQGICSRRKAEELILSGKILINNKIAK-LGECVTINDEIKINNRIIKLNNNIA 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +  + +KP+  + T SDP  R T+++ L +   R+ S+GRLD NT G++L+TNDG  
Sbjct: 66  NNFKYIVLNKPMNTICTASDPQNRKTIYEYLKAK-ERLFSIGRLDFNTTGIILITNDGEF 124

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           A +L  PS++  R+Y      ++   +LNLL    V+        +VT    K S     
Sbjct: 125 ANLLSHPSSEIPRIYIATLEREMLDGELNLLNSNHVLLNGKISKQKVT----KLSAFKYE 180

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           V L EG+N  +K +F   N  V +L R S+G      L  G  R ++   + + L 
Sbjct: 181 VLLYEGRNHHVKNLFLLVNNYVKKLHRKSFGCIDDSNLKIGQYRNLTSSEINKLLA 236


>gi|295677418|ref|YP_003605942.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295437261|gb|ADG16431.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 236

 Score =  218 bits (557), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 100/235 (42%), Gaps = 10/235 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD-HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +  V S      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIGDGRVGIDGAICTDADADFAVDSGALRFSVDGVEWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP+G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPVGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  ++Y       +D  +L  L+ G+++ G         LD +      + 
Sbjct: 121 VHQFTSPKRKVPKLYVATTRHPLDDAQLAALRDGVLLHGETKP--SAALDAEARDTHTLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L   
Sbjct: 179 LTVLEGKYHQVKRMIAASGNRCEALHRERIGGLVLPATLAPGAWQWLDEAGLAAL 233


>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 =  218 bits (557), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 89/253 (35%), Positives = 144/253 (56%), Gaps = 11/253 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---A 70
           +R+ KV+A+AG+ SRR +E+ IA   VKVNG + +    ++ S D +E+DG         
Sbjct: 29  ERLHKVLAQAGLGSRRALEQRIADGLVKVNGEVAQ-VGQSIRSGDRVELDGKAFVASALT 87

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E  R+ +Y+KP G VTT  DP+GR T+F++LP    +R I++GRLDINT GLLLLT DG 
Sbjct: 88  EPARVLVYNKPEGEVTTREDPEGRPTIFESLPRLKGARWIAIGRLDINTTGLLLLTTDGE 147

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           +A  +  PS +  R Y VR         V  + ++ L +G+ ++       Q+       
Sbjct: 148 IANAMMHPSYEVEREYVVRVRAPEGQESVPDNIVDRLARGVALEDGPAKFDQIERIGGTD 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R+ YG   L   LL G ++E+ ++ +  
Sbjct: 208 SHDWFKVVVKEGRNREVRRLWESQGCQVSRLKRVRYGKVSLPRELLRGQSQELPQEQVEA 267

Query: 244 QLGPHLLEEAQVN 256
                 LE++  +
Sbjct: 268 LRKELKLEDSAAS 280


>gi|167903268|ref|ZP_02490473.1| RNA pseudouridine synthase family protein [Burkholderia
           pseudomallei NCTC 13177]
          Length = 444

 Score =  218 bits (557), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 197 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 256

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 257 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 316

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 317 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 376

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 377 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 432

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 433 GEWRYLGPDE 442


>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 =  218 bits (557), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 108/229 (47%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ E    IA+ RVKVN  ++   +  V   +H+ ++G  L  A   
Sbjct: 1   MRLDKFVCKSTTLTKNEALECIAEGRVKVNAKIVTVESTQVHENNHVTLNGDLLT-ARPF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP   + ++ D +   ++F+ +     S +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYLLMNKPANTICSNID-EAYPSLFNYIKEGNNSELHIAGRLDSDTTGLVLITDDGRWSY 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS +  +VYRV     +  + +  ++ G+ +QG         L     +   V + 
Sbjct: 119 NIITPSKKCEKVYRVGLRNIITSEAIIKIELGVQLQGEVELTRPAKLKI--ITEREVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EGK  ++K++F     KV  L R  +G   L  +  G  R ++   +
Sbjct: 177 IIEGKFHQVKRMFSAVGNKVILLHREQFGEISL-DVNEGEWRYLTDYEV 224


>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 =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 57/231 (24%), Positives = 119/231 (51%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ ++++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +    +
Sbjct: 1   MRLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENKDVVKIYDEVIEYR-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  R+ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 60  YLYFVMNKRKGVTSHSKDPMHRTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y+V    +VD+   +  +KGI +          T++     N ++   
Sbjct: 120 NLISPKKDVSKKYKVTLRYKVDEKYNDTFEKGIKLMPEDIITKPATMEIIDDYNCYL--T 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + L+
Sbjct: 178 IKEGKYHQVKRMFEKVGNEVVELQRVQIGSFKLPEDLEEGDFRELTDEELK 228


>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 =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 73/285 (25%), Positives = 128/285 (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 LM--GSDLERTYNLKIDKPVTQEMVAAMNEGLVLDDARAGGHEKSKIYGMEFAPFAHFEI 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 EYDDLH--KFMKQLKAEKKVEVKNRANALKQEEANKKAKKSDRRD 281


>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 =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 69/235 (29%), Positives = 116/235 (49%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A   + SR+EV  +I ++ V VNG +++     V   D + VDG  +   ++ 
Sbjct: 1   MRIDKYLANMNVGSRKEVHNLIKKKIVTVNGEVVKTPKEQVKEEDQVAVDGEKVAY-QQY 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G+++   D   + TV   L     +  +  VGRLD +T GLLLLTNDG LA
Sbjct: 60  HYFLLNKPKGVISATED-RSQKTVLSLLKPKDRYKDIAPVGRLDKDTTGLLLLTNDGALA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAW 188
             L  P+    + YR +  G  D++ + +   G+ +  G      ++ +  Q      + 
Sbjct: 119 HELLAPNKHVTKKYRAKIAGVADEETVKIFASGMTLGDGTKLKPARLKILMQDKESDESE 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + + ++EGK  +IK++F     KV  L RIS     L T L  G  +E+  K ++
Sbjct: 179 IEIEIQEGKYHQIKRMFGAVGMKVIELDRISMEKLVLPTSLKRGEYKEIRLKEIK 233


>gi|167582947|ref|ZP_02375821.1| ribosomal small subunit pseudouridine synthase A [Burkholderia
           thailandensis TXDOH]
          Length = 240

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   ++VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G     +       +G    + + 
Sbjct: 121 AYTSPKRKVPKTYVAAVRHPLDDAQLDALRAGVLLHGEP-KPIAALAAAARG-ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V+ L R   G F L   L  G+ R + ++ L   
Sbjct: 179 IAEGKYHQVKRMVAAVSNRVDALHRSRIGGFALPEDLAEGAWRWLDERDLAAL 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 =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 105/230 (45%), Gaps = 10/230 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +A+     ++ V  ++  +RV V+G +    A+ +     I +    LR A+  R
Sbjct: 7   RLDSFLAKTLNIPKKAVRELLKAERVTVDGKVALEMALQIGPFSQIYLGDTALR-ADTPR 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+V+   D + + TV D +P      +  VGRLD+NT GL+LL+ND   +  
Sbjct: 66  YLMLNKPVGVVSATKDKEHK-TVLDLIPEALRAGLHIVGRLDLNTSGLVLLSNDSRWSES 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           +  P     + Y V     + +D +   ++G     +GI     ++ +  ++ +     V
Sbjct: 125 MMQPGAHVPKEYWVTLEHPLTEDYIAAFERGFYFETEGITTLPARLAILGEREA----RV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            L EGK  +IK++F  F   V  L R   G   L   L  G  R ++   
Sbjct: 181 ELCEGKYHQIKRMFGRFQNPVVALHRHRIGALMLDPGLAPGQWRPLTDDE 230


>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 =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 56/231 (24%), Positives = 118/231 (51%), Gaps = 5/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ ++++   IA+R+E+++M+ +  + VN + +++++ ++    D +++    +    +
Sbjct: 1   MRLDRMLSEMKIATRKEIKQMVKKGIITVNDVTVKKSSEHIDENNDVVKIYDEVIEYR-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              ++ +K  G+ +   DP  ++ + D        +  VGRLD++T GLL++TNDG  A 
Sbjct: 60  FLYFVMNKRKGVTSHSKDPMHKTVIDDMGELCVFDLNPVGRLDLDTTGLLIITNDGKFAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y+V    +VD+   +  +KGI +           ++     N ++   
Sbjct: 120 NLISPKKDVSKKYKVTLRDKVDEKYNDTFEKGIKLMPEDIVTKPAKMEIIDDYNCYL--T 177

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           ++EGK  ++K++FE    +V  L R+  G F+L   L  G  RE++ + LR
Sbjct: 178 IKEGKYHQVKRMFEKVGNEVVELQRVQIGDFKLPEDLEEGDFRELTDEELR 228


>gi|332361775|gb|EGJ39579.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1056]
          Length = 241

 Score =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 117/234 (50%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++   Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSHLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPSGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +        ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQDKIAFQEGIRFLDGTICQPAQLSILSSSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++++ L 
Sbjct: 178 TVKISEGKFHQIKKMFLAVGVKVIYLKRIQFGNFTLDPDLAKGDCRPLNQEELE 231


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G        ++ +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDADLDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  DP    +VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-DPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G         +         + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGE--PKPVAAVAADARDPHTLALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G   L   L  G+ R + +  L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESVGGLALPADLAPGAWRWLGEAELAALRNP 234


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 98/312 (31%), Positives = 162/312 (51%), Gaps = 15/312 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLR 253

Query: 231 GSTREVSKK---ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + E++++    LR +L       + + L  P+       +   ++  +   +     +
Sbjct: 254 GQSVELAQEKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQ 312

Query: 288 NSSQKNGLSKQK 299
            S    G   ++
Sbjct: 313 TSGADEGRELRR 324


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 312 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 371

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 372 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 431

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 432 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 491

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 492 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 547

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 548 GEWRYLGPDE 557


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 130/245 (53%), Gaps = 10/245 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+A I SR+++++ + ++++ V+     + + NV +    I ++  P+   + 
Sbjct: 10  MRLDILLAQAHI-SRKKMKQALLKKKILVDDCPARKLSQNVDTGLQTITLEEQPV-LGKP 67

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + ++ +KP+G+VT +SD     TV D +        + SVGRLD +T GLLL+T++G L
Sbjct: 68  HQYFMMNKPLGVVTANSDAKF-QTVLDLIRPEDFSEDLYSVGRLDRDTSGLLLITDNGPL 126

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
             +L  P     + Y V  +G +D   +   +KGIV + G       +T+ +   + +  
Sbjct: 127 GFLLLHPQYHVTKTYEVEVNGLLDDQAVQSFQKGIVFLDGTICKPATLTIRSSSSNKSRA 186

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           TV + EGK  +IKK+F     KV  L RI +G F+L   L  G  R +++  L  ++  H
Sbjct: 187 TVTISEGKFHQIKKMFLTVGVKVTSLKRIHFGDFELEPNLATGEYRVLNQAEL--EIVRH 244

Query: 249 LLEEA 253
            LE++
Sbjct: 245 YLEKS 249


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/252 (26%), Positives = 123/252 (48%), Gaps = 19/252 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+     SRRE + +I Q +V +NG ++   A +V   D ++++G  +R  
Sbjct: 1   MQKSRLNKFISHNTSYSRREADELIKQGKVSINGRVVSELATSVSDEDKVKINGRIVRLK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + +YHK  G + +  D  GR T++D+L   F++ +S+GRLD  +EGLLLLT+   +
Sbjct: 61  KEFTVIVYHKQKGELVSKKDDRGRKTIYDSLDRQFAKFVSIGRLDYASEGLLLLTDAPAI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQ 176
           A  L   ++   R Y ++  G++  + +  + +G                        + 
Sbjct: 121 ATALM--NSDVEREYYLKVKGEITPEVITAMNEGFFAADATKGAHAKTAIKSMEFRPFLD 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +    G    + V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R  
Sbjct: 179 YKIFGSSGGFTKLKVVINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWRYF 238

Query: 237 SK---KILREQL 245
                + LR+ L
Sbjct: 239 ENGEYEALRDFL 250


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 111/234 (47%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K +++A   SR+E ++++    V VN  +++   V+V    D ++  G PL  A  
Sbjct: 6   MRLDKFLSKATELSRKESKKILHAGEVTVNEQVIKDPGVHVDIVNDDVQWAGEPLSVATG 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R  L HKP G   T    +    V D +       +   GRLD++T G LL+++DGG  
Sbjct: 66  NRYILLHKPEGFECTLKAKEY-PIVTDLIAVPELGSLRIAGRLDVDTTGALLISDDGGWL 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +  P  +  +VY +     +D D     +  + +GI+++G        TL+    ++A
Sbjct: 125 HRVTSPKHEHAKVYELTLADAMDSDAQANAIKEVAEGILLEGDHEETKPATLEFIDETHA 184

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              + L +GK  ++K++  +F  +V  L R S G   L  L  G +R ++ + +
Sbjct: 185 --RLTLEQGKYHQVKRMMGYFGNRVVELHRASVGHITLDGLEKGDSRFLTPEEV 236


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 98/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G        ++ +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDADLDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  DP    +VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 63  VVL-NKPAGYECSR-DPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G         +         + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGE--PKPVAAVAADARDPHTLALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G   L   L  G+ R + +  L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESVGGLALPADLAPGAWRWLGEAELAALRNP 234


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 312 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 371

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 372 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 431

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 432 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 491

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 492 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 547

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 548 GEWRYLGPDE 557


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 63/220 (28%), Positives = 101/220 (45%), Gaps = 8/220 (3%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLW 76
           +++   G  +R E   +I Q R +VNG  +     ++ + D   EVDGV     E+  + 
Sbjct: 5   QILFSQGFGTRHECTGLIVQGRFRVNGTAVTDPDEDIPTEDLTFEVDGVQWPFFEKA-II 63

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +KP     +   P    +V   LP      +V  VGRLD +T GLLLLT+DG L   L
Sbjct: 64  LLNKPEHYECSLK-PIHHPSVLSLLPPPLRVRKVQPVGRLDEDTTGLLLLTDDGKLIHRL 122

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++YRV     V + ++  L KG+ +      D+   +   K S   + +G+ 
Sbjct: 123 THPKKHVTKIYRVTLKHPVTEKQIAQLLKGVQLAD--SPDIVKAVSCDKVSELVIDLGIT 180

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGST 233
           +GK  ++K++    + +V  L RI +G   L   L  G  
Sbjct: 181 QGKYHQVKRMMAAVSNRVVALERIRFGNLSLPEDLKPGEW 220


>gi|325478230|gb|EGC81349.1| putative 16S pseudouridylate 516 synthase [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 232

 Score =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 111/232 (47%), 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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++   D D   TV D L   +    +   GRLD +T GLLLL+ DG  
Sbjct: 61  I-YIMMNKPQGYLSATEDKD--PTVIDLLDDFYRVLDLSIAGRLDKDTTGLLLLSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y  +    +D+  ++L K+G+ I+   Y      L+    + A VT
Sbjct: 118 IHRVTSPNSNIEKTYIAKTRDPIDESLIDLFKEGVYIKEDDYTARSAKLEIIGKNEAKVT 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V   EGK   +K++F     +V  L R++ G  +L + L  G  RE+S   +
Sbjct: 178 VT--EGKFHLVKRLFSNSGNEVVDLKRVAIGDLKLDSHLGLGEYRELSDDEV 227


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 100/228 (43%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     + +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYIMLNKPEDYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLENPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  218 bits (556), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 58/233 (24%), Positives = 93/233 (39%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G        +  +   +  VD           
Sbjct: 3   LESILYTQGFGSRRQCRGLIETGRVNVAGASATDPDASFDTDGLVFTVDDTAWPFHAHA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +LN L+ G+ + G       V    +      + + 
Sbjct: 121 GYTSPKRKVPKTYVATVRHPLDDTQLNALRAGVQLHGEPKPIAAVAAHAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R S G F L   L  G+ R +    L   
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESIGGFTLPDDLAPGAWRWLGASELSAL 231


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 103/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+D
Sbjct: 58  GFS-LLLHKPGGYTCSTKDTG--RLIYELLPPRFRSRAPVLAPVGRLDRETSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY +    ++  D+  L   G ++++G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDITLAEELRGDEAALFASGSLLLEGETKPLLPAELEVLGPRE 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLEVLFG 232


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 99/230 (43%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +  
Sbjct: 10  TIMKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTV 69

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 70  VPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+ +            D    + 
Sbjct: 129 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAA--DAVLENP 186

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +   L R  +   +   L  G  + +
Sbjct: 187 TTLLLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAHLETENLKPGEWKFI 236


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 316 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 375

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 376 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 435

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 436 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 495

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 496 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 551

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 552 GEWRYLGPDE 561


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 104/367 (28%), Positives = 174/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 35  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQT-GMSVRSGDKI 93

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 94  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 153

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 154 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 213

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 214 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 273

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +      
Sbjct: 274 GQSVEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGH 332

Query: 288 NSSQKNGLSKQK----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            S    G   ++    +       R    +      +     +   Q+    +R P+   
Sbjct: 333 TSGADEGRELRRFDNLREDRGRGGRGKPGDFKGGLTVSGEAAARQSQQRPFKQRGPAKGD 392

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 393 RGALPEG 399


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 104/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 362 MRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 421

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 422 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 481

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 597

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 598 QGQWRYLSADE 608


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV + G         + +   +  VDG P     R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAIGGAPATDPDAELDTDGLVFTVDGTPWPFHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  DP    +VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 63  VVL-NKPAGYECSR-DPQHHPSVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G         +         + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHALDAAQLDALRGGVQLHGE--PKPVAAVAADARDPHTLALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G   L   L  G+ R + +  L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVEALHRESVGGLALPADLAPGAWRWLGQAELAALRNP 234


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 74/252 (29%), Positives = 121/252 (48%), Gaps = 19/252 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K+I+     SRRE + +I    VKV+G +++  +  V   + IE++G  L + 
Sbjct: 1   MELTRLNKMISHNTHYSRREADELIKAGHVKVDGNVVQDLSTQVSFKNKIELNGKALFEK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +YHK  G + +  D  GR T++D LPS F+  +SVGRLD  +EGLLLL +   +
Sbjct: 61  HGYSVIVYHKQKGELVSKKDDRGRKTIYDTLPSKFAHYLSVGRLDFASEGLLLLCDSPSV 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------------YGDMQ 176
              L        RVY V+ +G V       +++G+ ++                    + 
Sbjct: 121 VSALMHGD--LERVYYVKINGLVSPAMEKAMQEGLSLEDARRGGHAKSEIHAMDFAPFVN 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +     + + + V + EGKNRE+++ F +F+  V  L R+SYG   LG L  G  R  
Sbjct: 179 YRIIKNSPTFSTIKVTINEGKNRELRRFFGYFDVDVVDLKRVSYGKIDLGMLKPGKHRFF 238

Query: 237 SKKI---LREQL 245
           S      LR+ L
Sbjct: 239 SASEYTALRDYL 250


>gi|167835760|ref|ZP_02462643.1| RNA pseudouridine synthase family protein [Burkholderia
           thailandensis MSMB43]
          Length = 240

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/235 (26%), Positives = 104/235 (44%), Gaps = 8/235 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV   G     A  +  +T  + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAAVGATCTDAHASFDTTQLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  +P   ++VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  VVL-NKPAGYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G       +    +      + + 
Sbjct: 121 AYTSPKRKTPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPVAALAAVARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLG 246
           + EGK  ++K++    + +V+ L R   G F L G L  G+ R + +  L    G
Sbjct: 179 IAEGKYHQVKRMVAAASNRVDALHRSRIGGFALPGDLAEGAWRWLDEHDLAALRG 233


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 102/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+D
Sbjct: 58  GFS-LLLHKPGGYTCSTKDTG--RLIYELLPPRFRSRAPVLAPVGRLDRETSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY +     +  D+  L   G ++++G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDITLAEDLRGDEAALFASGSLLLEGETKPLLPAELEVLGPRE 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLEVLFG 232


>gi|297538780|ref|YP_003674549.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297258127|gb|ADI29972.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 245

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 98/230 (42%), Gaps = 8/230 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAERTR 74
           + ++I   G  +R+    +I  Q V VNG + +   AV         V G      E++ 
Sbjct: 11  LERIICNQGFGARKLCRILILNQEVTVNGEICDDPDAVFDTENLQYTVKGEAWDYREKS- 69

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP     +H       T++  LP       V  +GRLD +T GL+L+++DG    
Sbjct: 70  YLMLHKPSNYECSHK-TQHHPTIYSLLPHPLVVRDVQCIGRLDEDTTGLILISDDGQFIH 128

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY V     +  +++  + KG+ +           L   + +   + + 
Sbjct: 129 RMSSPKHKVPKVYEVTCKHPMSDEQIAHILKGVQLVDEDAP--IAALACTRITQNIIHMT 186

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           L EGK  ++K++    + +V  L RI  G  +L   L  G  R +++  L
Sbjct: 187 LAEGKYHQVKRMVAAISNRVEGLKRIQIGEVKLPDDLAVGEWRWLTESEL 236


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 96/239 (40%), Gaps = 16/239 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAER 72
            ++  ++   G  +RR    +I Q  V V GI     A+  ++ D    V GV     E+
Sbjct: 1   MQLQDILFSQGFGTRRVCAGLIQQGFVAVAGIPCTEPAMEFVAEDLRFTVQGVAWEYHEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--------RLDINTEGLLLL 124
               + HKP G   +   P    +++  LPS   +             RLD +T GLLLL
Sbjct: 61  A-YLMLHKPAGYECSQK-PSTYPSIYTLLPSPIRQRGGGAAAGVQAVGRLDQDTTGLLLL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QK 183
           ++DG     +  P     +VY V     VD  ++  L  G+V+         V     +K
Sbjct: 119 SDDGKFIHRMSSPRHHVPKVYEVTAKHAVDDRQVQKLLAGVVLDD---DPKPVRAAACEK 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
                +++ L EGK  ++K++      +V  L R   G   L   L  G  R ++ + L
Sbjct: 176 TGELQLSLTLTEGKYHQVKRMIAAVGNRVEDLHRSQLGGLMLPEDLKPGQWRWLTAQDL 234


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 62/240 (25%), Positives = 101/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+D
Sbjct: 58  GLS-LLLHKPSGYTCSTKDTG--RLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY +     +  ++  L   G +++ G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDITLAEDLHGEEAALFASGSLLLDGETKPLLPAELEVLGPRQ 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEANDLEVLFG 232


>gi|325128404|gb|EGC51287.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis N1568]
          Length = 230

 Score =  218 bits (555), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 100/228 (43%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDLDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPEDYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+++            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLENPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 111/233 (47%), Gaps = 3/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K IA +G+ SRR+ +  IA   V VNG  +      V   D +  DG  L  
Sbjct: 59  NSDGIRLNKYIANSGVCSRRDADMYIAAGNVTVNGKSITEMGYRVKLEDDVRFDGRRLN- 117

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
            E+    L +KP G   T +   G  TV + +    S +V  VG+LD   +GLLL TNDG
Sbjct: 118 PEKPEYILLNKPAGFFVTGNPEKGGKTVMELVARTTSAKVSPVGKLDNQAKGLLLFTNDG 177

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            LA+ L  P     ++Y+V  +  + ++ L  ++KG+ I+G       ++   +   +  
Sbjct: 178 TLAKKLAKPKNGIRQIYQVTLNKNLTKEDLEGIEKGVYIEGSKVLITSISF-IEDKPHNE 236

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L   K   + ++F+   ++V  L R+ +G      L  G  R ++K+ +
Sbjct: 237 VGIELYSIKEHIVTRIFKSLGYEVESLDRVVFGGLTKKDLPRGRHRNLTKQEV 289


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 70/245 (28%), Positives = 129/245 (52%), Gaps = 10/245 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+  ++A+A I SR+++++ + ++++ V+     + + NV +    I ++  P+   + 
Sbjct: 1   MRLDVLLAQAHI-SRKKMKQALLKKKILVDDCPARKLSQNVDTGLQTITLEEQPV-LGKP 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
            + ++ +KP+G+VT +SD     TV D +       ++ SVGRLD +T GLLL+T++G L
Sbjct: 59  HQYFMMNKPLGVVTANSDAKS-QTVLDLIKPEDFNDKLYSVGRLDRDTSGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +D   +   +KGIV + G       +T+ +   + +  
Sbjct: 118 GFQLLHPQYHVTKTYEVEVNGLLDDRAVQSFQKGIVFLDGTSCKPAILTIHSSSSNKSCA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           TV + EGK  +IKK+F     KV  L R  +G F+L     AG  R +++  L  ++  H
Sbjct: 178 TVTISEGKFHQIKKMFLTVGVKVTSLKRTHFGDFELEPNSAAGEYRALNQAEL--EIVRH 235

Query: 249 LLEEA 253
            LE++
Sbjct: 236 YLEKS 240


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 108/234 (46%), Gaps = 13/234 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            ++S+V+   G  +RRE E +I    V V G+++E  +  V     +  V+G       +
Sbjct: 1   MKLSQVLFSQGFGARRECEGLICAGLVSVGGVVIEEPSHEVAPEGLLFTVEGQTWAYHAK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G   +   P    ++++ LP+ F R  + +VGRLD +T GLLL T+DG L
Sbjct: 61  A-LIVMNKPAGFECSKK-PRHHPSIYNLLPAQFKRRDMQTVGRLDEDTTGLLLFTDDGNL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----DMQVTLDTQKGSN 186
                 P     ++Y       VD+ ++  L  G+V+            ++T   +  ++
Sbjct: 119 IHRWTSPKHHVPKIYEAGCKHPVDEAQVARLLAGVVLHDDPLPVQALAAEITGAFEHPTH 178

Query: 187 ---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
                + + L EGK  ++K++    + +V  L R  +G ++L   L  G  R +
Sbjct: 179 GTLHGLRLTLAEGKYHQVKRMLAAVSNRVETLHRSGFGAYRLPDDLKLGEWRWL 232


>gi|167561885|ref|ZP_02354801.1| RNA pseudouridine synthase family protein [Burkholderia
           oklahomensis EO147]
          Length = 240

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 64/233 (27%), Positives = 102/233 (43%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A A    +    EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCTDAHASFDTARLAFEVDGVAWPYHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  +P   S+VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  VVL-NKPAGYECSR-EPQHHSSVFRLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G       V    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEPKPIAAVAAHARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + ++ L   
Sbjct: 179 VAEGKYHQVKRMVAAASNRVEALHRASIGGFTLPADLAEGAWRWLDERDLAAL 231


>gi|254670490|emb|CBA06210.1| ribosomal small subunit pseudouridine synthase A [Neisseria
           meningitidis alpha153]
          Length = 256

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 53/230 (23%), Positives = 100/230 (43%), Gaps = 8/230 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK 69
           T  ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++D   +  
Sbjct: 25  TIMKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDEEAVTV 84

Query: 70  -AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTN 126
             E     + +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TN
Sbjct: 85  VPEPYFYIMLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITN 143

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG L   L  PS +  ++Y V       +     LK G+++            D    + 
Sbjct: 144 DGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVLLHDENETVCAA--DAVLKNP 201

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             + + + EGK  ++K++      +V  L R  +   +   L  G  + +
Sbjct: 202 TTLLLTITEGKYHQVKRMIAAAGNRVQHLHRRRFAHLETENLKPGEWKFI 251


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 104/251 (41%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D          
Sbjct: 362 MRLSKRMSELGLCSRREADEWIEKGWVIVDGERIDTLGTKVRADQRIEIDERAQAAQAAQ 421

Query: 74  RLWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++                 G  +     P     +   GRLDI++
Sbjct: 422 VTILLHKPVGYVSGQAEDGYEPASVLITRENHWSGDRSPLRFSPQHLRALAPAGRLDIDS 481

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQG 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 VALKPAMVSWQNGE----QLRFVLREGRKRQIRRMCELVGLEVIGLKRVRMGRVTLGALP 597

Query: 230 AGSTREVSKKI 240
            G  R +S   
Sbjct: 598 QGQWRYLSADE 608


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 104/367 (28%), Positives = 174/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +      
Sbjct: 254 GQSVEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGH 312

Query: 288 NSSQKNGLSKQK----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            S    G   ++    +       R    +      +     +   Q+    +R P+   
Sbjct: 313 TSGADEGRELRRFDNLREDRGRGGRGKPGDFKGGLTVSGEAAARQSQQRPFKQRGPAKGD 372

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 373 RGALPEG 379


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 96/239 (40%), Gaps = 16/239 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAER 72
            ++ +++   G  +RR    ++ Q  V V G+     A+  +       V GV     E+
Sbjct: 1   MQLQEILFSQGFGTRRVCAGLVQQGFVTVAGVPCTEPAMEFIAVGLRFTVQGVAWEYHEK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--------RLDINTEGLLLL 124
               + HKP G   +   P    +++  LP+   +             RLD +T GLLLL
Sbjct: 61  A-YLMLHKPAGHECSQK-PSTYPSIYTLLPAPIRQRGGGAAAGVQAVGRLDQDTTGLLLL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QK 183
           ++DG     +  P     +VY V     VD  ++  L  G+V+         V     ++
Sbjct: 119 SDDGKFIHRMSSPRHHVPKVYEVTAKHPVDAQQVQKLLAGVVLDD---DPKPVRAAACEQ 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            S   +++ L EGK  ++K++      +V  L R   G   L   L  G  R ++ + L
Sbjct: 176 TSELQLSLTLTEGKYHQVKRMIAAVGNRVEGLHRSRIGSLALPADLKPGEWRWLTVQDL 234


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 121/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVGKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 99/312 (31%), Positives = 161/312 (51%), Gaps = 15/312 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +     +
Sbjct: 254 GQSIEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQ 312

Query: 288 NSSQKNGLSKQK 299
            S    G   ++
Sbjct: 313 TSGADEGRELRR 324


>gi|325690206|gb|EGD32210.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK115]
          Length = 241

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 126/246 (51%), Gaps = 10/246 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+++++   Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLDQLLA-ANHISRKKMKQSHLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEIEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +  +  +  ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTPNDSSSFQEGIRFLDGTVCQPAQLSILSTSSSLSRA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           +V + EGK  +IKK+F     KV  L RI +G F L   L  G  R +++K L  ++   
Sbjct: 178 SVRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNQKEL--EIIKE 235

Query: 249 LLEEAQ 254
            LE+++
Sbjct: 236 YLEKSR 241


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 89/219 (40%), Positives = 124/219 (56%), Gaps = 7/219 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            +++ KV+AR G+ SRRE+E  I + RVKVN  +       V   D I V+   +R+   
Sbjct: 2   TEKLQKVLARVGLGSRREIETWIEEGRVKVNQYIAT-LGARVSPHDEIRVNERRIRQSDL 60

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
               R ++  YHKPIG V T  D +GR+T+F+ LP     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|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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 65/309 (21%), Positives = 123/309 (39%), Gaps = 16/309 (5%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +   PQR++K + ++G+ SRRE E ++ Q  + ++G+ +      +   + + +    
Sbjct: 6   TYDGEEPQRINKWLGQSGVCSRREAEGLVEQGLISIDGVKVTEPGRKIEKGETLTLADAA 65

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-----------LPSIFSRVISVGRLD 115
             K       + +KPI  V+ H +      V              +P   +R+  VGRLD
Sbjct: 66  TDKLASAMSVILNKPIDYVSAHPNEGEVPAVRLLTKANLSGQSETIPDRDTRLAPVGRLD 125

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            ++ GLL+LT DG L + +  P     + Y V  +G +  +K+  L  G+ + G      
Sbjct: 126 KDSRGLLILTEDGVLTKAVIGPDADSEKEYLVTVNGTITHEKIRRLCHGLRMDGRALKPA 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            VT +  +     +   L EG+NR+I+++ E     V  L RI  G   +G L  G  R 
Sbjct: 186 IVTHEGGQ----VLRFILTEGRNRQIRRMAELVQLHVVDLFRIRIGHVHIGELPEGKWRT 241

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++    R+ L      +  +  D    +     +    +  +           ++     
Sbjct: 242 MTTHE-RDGLIDKSKADKSLKPDPISSTFVPPEKPEKPVRRQGTSAKKLDPYRNADGYSK 300

Query: 296 SKQKKLATP 304
              K  + P
Sbjct: 301 RNYKAKSRP 309


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 99/234 (42%), Gaps = 15/234 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            R+ K++A  G  SR+EV++ I    V  +  G LL   A    + + I  +  PL  A 
Sbjct: 1   MRLIKLLANLGYGSRKEVQKYIRMGIVT-DAEGNLLNDDAK--TAHEDIRFNERPLDPAH 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTND 127
              + + +KP G V +  D      V++ LP  FS    V    GRLD +T GLLL T+D
Sbjct: 58  G-VVLMLNKPTGYVCSLKDTG--KLVYELLPHRFSERKPVLSTVGRLDADTSGLLLFTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G     +  P     ++Y V     +   +  +   G ++++          ++      
Sbjct: 115 GDYLHRIISPKNHVAKIYEVTLARPLQGHEAAIFASGELMLESEKTPLKPAAMEQTGEKT 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           A   + L EG+  +++++F      V  L R   G   LG L  G  R ++ + 
Sbjct: 175 A--RLTLYEGRYHQVRRMFAAVGNHVEALHRSQMGDLTLGELRPGKWRLLTTEE 226


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 106/233 (45%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R   +R IA+  VK+NG ++ +A   V +   +   G  L +    
Sbjct: 1   MRLDKFICQSTNLTRTLAKREIARSNVKINGEVVRKADHKVTADMDVWFSGKSLSQRA-P 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP+ ++ +  D +   +V + +       +   GRLD++T GL+L+T+DG  + 
Sbjct: 60  RYIMMHKPLDVICSTVDEEH-PSVMNLIEADKREELHIAGRLDVDTTGLVLITDDGKWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P     + YRV+    +    +   + GI +  +       ++ + ++K     V 
Sbjct: 119 RVTSPKRACNKRYRVQLAEAIAPTAVADFEAGIHLRSEDKPCLPAKLEILSEK----EVL 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + ++EGK  ++K++F      V  L R   G   L   L  G  R ++ +  +
Sbjct: 175 LTIQEGKYHQVKRMFASQGNSVVGLHREQIGEIVLDPALELGEWRYLTDEEAK 227


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 105/367 (28%), Positives = 174/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +     +
Sbjct: 254 GHSVEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQ 312

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR----RSPSFPS 343
            S    G   ++       R               +   ++  R+   R    R P+   
Sbjct: 313 TSGADEGRELRRFDNLREDRGRGGRGKPGGFKGGLTVSGEAAARQSQQRPFKQRGPAKGD 372

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 373 RGALPDG 379


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 105/233 (45%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G +L+ A   +       + + + G P+   
Sbjct: 8   RLDRLLANLGYGSRKEVQALVAGGKVVLDGAILKDAGARIAVDATLPERMTIRGAPVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
               L + HKP+G+V +H +   +  ++D LP  +         VGRLD +T GL+L+T+
Sbjct: 68  APLVLIM-HKPLGVVCSHKEDGEK--IYDLLPRRWRLRDPGLSTVGRLDKDTSGLILITD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     + Y       ++  +  +   G +++       +   LD     
Sbjct: 125 DGDFLHRVISPKRHVPKTYLATLDRPLNGSEGEVFAAGTLMLDSEEKPLLPARLDVVNAH 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            A   + + EG+  +++++F      V  L R   G   L   L AG  R ++
Sbjct: 185 AA--RLTITEGRYHQVRRMFAAVGNHVVALHRERIGGIALPDDLAAGQHRILT 235


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 61/233 (26%), Positives = 101/233 (43%), Gaps = 8/233 (3%)

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 LELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P  +  + Y  R    ++ D     +    +GIV++G         L      +  V
Sbjct: 120 ITSPRRRCPKAYVARLARPLEGDEARRAMQAFAEGIVLEGEDAPTRPAELTC--LDDHRV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + + EG+  +++++       V  L R S G   L   L  G  RE++ + +
Sbjct: 178 RLVIDEGRYHQVRRMLAAIGNHVETLHRESVGALVLDDTLEPGEWRELTPEEV 230


>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 =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 68/257 (26%), Positives = 107/257 (41%), Gaps = 29/257 (11%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +     R++K IA  G+ SRRE +  +    V VNG +      NV+  D IE+D    
Sbjct: 389 DDRPGAVRINKRIADMGMCSRREADEWVENGWVTVNGEVAT-MGQNVVPGDRIEIDQKAQ 447

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---------------DNLPSIFSRVISVG 112
            + ++    L +KP+G V+  ++      V                    S    +   G
Sbjct: 448 ERQDQQVTILLNKPMGYVSGQAEDGHEPAVVLITNENRWNEDRSKTRFNFSQLKGLAPCG 507

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKK 163
           RLDI++ GLL+LT DG +AR +    ++  + Y VR               ++KL LL+ 
Sbjct: 508 RLDIDSVGLLVLTQDGRVARQIIGEDSEVDKEYLVRVTFGDRDVDVQSVFPEEKLALLRH 567

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+ +        QV     +     +   L EGK R+I+++ E    KV  L RI  G  
Sbjct: 568 GLSLDEQPLKPAQVDWQNPE----QLRFVLTEGKKRQIRRMCEQVGLKVVGLKRIRIGGV 623

Query: 224 QLGTLLAGSTREVSKKI 240
            LG L  G  R ++   
Sbjct: 624 TLGNLPTGQWRYLAPHE 640


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 323 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 382

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 383 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 442

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 443 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 502

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 503 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 558

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 559 GEWRYLGPDE 568


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 103/250 (41%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 310 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 369

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 370 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDST 429

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 430 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDGV 489

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 490 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 545

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 546 GQWRYLGPDE 555


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 102/229 (44%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   +R     ++A   V VNG ++  A   V   + +   G  L  A  +
Sbjct: 1   MRLDKFLCKSTKLTRSAATEVLALGEVSVNGSIVTEARFQVHENNSVLWRGERL-IARPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKP+  ++++ D D   ++F  +       +  VGRLD +T GL+LLT+DG  + 
Sbjct: 60  RYIMLHKPLNTLSSNVDGDY-PSLFHCIDIERAEDLHIVGRLDADTSGLVLLTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P     + YRV     +  D       G+ +Q          L     +   V + 
Sbjct: 119 EIIRPDKLCPKTYRVTLRDPIAADVAEKFNVGVQLQNESKLTAPAMLKV--INEREVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + EG+  ++K++F     +VN L R   G  QL  +L G+ R +S + +
Sbjct: 177 ITEGRYHQVKRMFAAVGNRVNGLHREQIGDLQLDVVL-GNWRFLSPQEV 224


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 324 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 383

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 384 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 443

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 444 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 503

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 504 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 559

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 560 GEWRYLGPDE 569


>gi|225448976|ref|XP_002270186.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 393

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 80/259 (30%), Positives = 128/259 (49%), Gaps = 18/259 (6%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I + RV VNG +       V    D I
Sbjct: 131 RRFYNENFRDPPQRLSKVLAAAGVASRRNSEELIFEGRVTVNGSVCNTPQTRVDPARDMI 190

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIF--------SRV 108
            V+G  L K          +KP G + +  + + +S +    D L S           R+
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 GICYGDMQVTLDTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L   + + +   + V + EG+N E++++ +    +++ L RI  G F+L 
Sbjct: 311 GVHCTPDSVELLPPQPNISKPRLRVVVHEGRNHEVRELVKSAGLQIHSLKRIRIGGFRLP 370

Query: 226 GTLLAGSTREVSKKILREQ 244
             L  G   E+ +  L+  
Sbjct: 371 SDLGHGKHVELKQGDLKAL 389


>gi|322378546|ref|ZP_08052993.1| Pseudouridine synthase [Helicobacter suis HS1]
 gi|321149023|gb|EFX43476.1| Pseudouridine synthase [Helicobacter suis HS1]
          Length = 257

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 118/245 (48%), Gaps = 17/245 (6%)

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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC------------YGDMQVTL 179
             L    +   RVY V+  G + Q  L  ++ G+ +QG+                M   +
Sbjct: 125 NALMH--SSLERVYLVKIQGNITQTMLEAMQTGLELQGLEGAHPKSKYTRMHIAPMACQI 182

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                + + + + L+EG NREI++ F  F  +V  L R+S+G   L  L  G TR ++ K
Sbjct: 183 LKNHRNYSKIKITLQEGHNREIRRFFAHFKKEVLDLRRVSFGFVSLNALPVGKTRYLNPK 242

Query: 240 ILREQ 244
             ++ 
Sbjct: 243 EYKQL 247


>gi|257138757|ref|ZP_05587019.1| pseudouridine synthase family protein [Burkholderia thailandensis
           E264]
          Length = 547

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 103/250 (41%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D     +     
Sbjct: 300 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAEQAAQV 359

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 360 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWGGDRSPLRFSPQHLRALAPAGRLDIDST 419

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 420 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTTDIERHFPAESLAKLRHGLELDGV 479

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 480 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 535

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 536 GQWRYLGPDE 545


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 113/239 (47%), Gaps = 8/239 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++R G  SRR+  ++I   RV+VNG  +      +     I +DG  +    + 
Sbjct: 1   MRLDTFLSRFGGISRRQSRKLIKTGRVEVNGAKIRNPEFKIPENSSIFLDGNRIVPYGKL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP+G V + S  +G  +V+D +  +F S++   GRLD N+ GLLLL+NDG    
Sbjct: 61  -YIAMNKPVGYVCSKSRTEG-LSVYDLINEVFSSKLSIAGRLDKNSRGLLLLSNDGNFVH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  + Y V+   ++  ++L +L + + I    Y   +     Q       ++ 
Sbjct: 119 EIISPRKKIEKEYIVKVEEKILPEQLQILLQHVDIGKGEYARAE---SVQFIDIVTFSIV 175

Query: 193 LREGKNREIKKVFE-FFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPHL 249
           L EGK  EI+++ +      V  L RI  G + L G L  G  R ++++ ++   G  L
Sbjct: 176 LTEGKYHEIRRMVKSALKNNVVDLKRIRIGGYHLPGDLHEGEWRILTEEEIKAATGKIL 234


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 100/237 (42%), Gaps = 19/237 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-----EVDGVPLR 68
            ++ K IA  G  SR+EV R+  + R+  NG         + + D +       DG PL 
Sbjct: 1   MKLLKYIANLGYGSRKEVARIFREGRIT-NGE-----GEVLYADDQVQHIAVRFDGEPLD 54

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLL 124
                 + + HKP   + +  D      V+D LP  F         VGRLD +T GLLLL
Sbjct: 55  PPPGLMV-MLHKPSDYICSTKDAG--RLVYDLLPPRFRLRSPLLSTVGRLDGDTSGLLLL 111

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           T+DG L   +  P T   +VY       +  D+  L   G ++       +Q  +    G
Sbjct: 112 TDDGALLHRMISPKTHLPKVYEATLVQALRGDEATLFASGTLLLDGDTKPLQPAVLEVLG 171

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
               V + L EG+  +++++F     +VN L R + G   L  L  G  R +  + L
Sbjct: 172 P-CQVRLTLYEGRYHQVRRMFGATGNRVNTLHRSAIGGLVLDGLPEGQWRVLEAQDL 227


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 117/248 (47%), Gaps = 21/248 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +AR+G ASRR  E +IA  RV V+G  +      V + + + VDG  ++     R
Sbjct: 11  RLQVYLARSGCASRRACEALIASGRVTVDGQTVTTQGRTVCAQNVVCVDGTVVQLERVQR 70

Query: 75  LWLYHKPIGLVTTHSD----------------PDGRSTVFDNL-PSIFSRVISVGRLDIN 117
             L +KP+G + + +                     +   D + 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 ----RHLAAQCVQLVLVEGKKREIRVVFEAWGQDVVRLVRVRIGRVRLGPLRPGAFRTMR 246

Query: 238 KKILREQL 245
            + + + L
Sbjct: 247 LQEVAQLL 254


>gi|163851700|ref|YP_001639743.1| pseudouridine synthase [Methylobacterium extorquens PA1]
 gi|163663305|gb|ABY30672.1| pseudouridine synthase [Methylobacterium extorquens PA1]
          Length = 242

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 108/241 (44%), Gaps = 15/241 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVP 66
               R+ +++A  G  SRREVE +     V+++G  L  A+  V     +     V G  
Sbjct: 1   MKALRLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRVPLEPDLSARMTVQGEA 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLL 122
           L         + HKP+G+  +H +      V+  LP  + R       VGRLD  T GLL
Sbjct: 61  LDPLPG-VCLMLHKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLL 117

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+T+DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T
Sbjct: 118 LMTDDGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMET 177

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
              ++   TV L EG+  +++++F      V+ L R   G   L   L AG  R +    
Sbjct: 178 DDPTHC--TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFRILGPGE 235

Query: 241 L 241
           +
Sbjct: 236 I 236


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 118/230 (51%), Gaps = 3/230 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R++K ++ +G+ SRR+ E +I   +V+VN  ++   +  V    D ++V+G  ++  ++
Sbjct: 1   MRINKFLSFSGLTSRRKAEDLILSGKVEVNDKVISDLSYKVDPNKDVVKVNGRLVKIRKK 60

Query: 73  TRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               L++KP  ++T    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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              EG    +K+  +   + V RLIR++ G F+L  +  GS R +S++ +
Sbjct: 181 AFHEGMKHLVKEYLKKMGYSVKRLIRVAIGDFRLTGV-PGSYRWLSEEEV 229


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 101/229 (44%), Gaps = 10/229 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G +   A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVSIGGAVCTDADADFPTGDTTFSFTVDGVVWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L  G+++ G       V ++ +   +  + 
Sbjct: 121 VHLFTSPKRKVPKVYVATTRHPIDDVQLSALHDGVLLHGESKPIAAVNVEARG--DHTLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
           + + EGK  ++K++      +   L R   G F L G L  G  + + +
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERIGGFALPGALAPGGWQWLDE 227


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 69/234 (29%), Positives = 111/234 (47%), Gaps = 11/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-AAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A     SR+EV ++I  +RV +NG +  +      +  D + VDG  +   + 
Sbjct: 1   MRLDKLLANKAFGSRKEVHQIIKDRRVTINGEITTKKDIHIDIDIDTVAVDGQTVNTTQ- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
                +HKP G VT   D      V D LP  +    V+ VGRLD +TEGLLLLTNDG  
Sbjct: 60  LYYVKFHKPKGYVTAVEDSTH-PVVMDLLPPEYLKMGVVPVGRLDKDTEGLLLLTNDGVW 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +        +VY V F G++ ++ +  +K+GIV+  G       + L     SN   
Sbjct: 119 GHSIINGHKHVPKVYYVEFEGELSEEGIQRIKEGIVLGDGTQCKPALIELL----SNQSA 174

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILR 242
           T+ + EGK  ++K++       V  L R++ G   L  +   GS  +++   + 
Sbjct: 175 TITIEEGKYHQVKRMIGAAGGTVTYLKRLTIGHVDLSGIEEVGSVMDLTIDEVE 228


>gi|166712399|ref|ZP_02243606.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 553

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 108/368 (29%), Positives = 172/368 (46%), Gaps = 21/368 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGTVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G + EV++  +        LEE      A         R        V  D       + 
Sbjct: 254 GQSVEVAQDKVDALRAELKLEEG--APSALTLQPVIGQRRAAKSTVHVTRDGRSNAYVNG 311

Query: 291 QKNGLSKQKKLATPVHRRNLASNVWMAKGIH----SSFLSDSGQREENHR----RSPSFP 342
             +G  + ++L    + R         K        +   ++  R+   R    R P+  
Sbjct: 312 HTSGADEGRELRRFDNLREDRGRGGRGKPGDFMGGLTVSGEAAARQSQQRPFKQRGPAKG 371

Query: 343 SKRSLRRT 350
            + +L   
Sbjct: 372 DRGALPEG 379


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 105/233 (45%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G +L+ A   +       + + + G P+   
Sbjct: 3   RLDRLLANLGYGSRKEVQALVAGGKVVLDGAILKDAGARIAVDATLPERMTIRGAPVDPP 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
               L + HKP+G+V +H +   +  ++D LP  +         VGRLD +T GL+L+T+
Sbjct: 63  APLVLIM-HKPLGVVCSHKEDGEK--IYDLLPRRWRLRDPGLSTVGRLDKDTSGLILITD 119

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     + Y       ++  +  +   G +++       +   LD     
Sbjct: 120 DGDFLHRVISPKRHVPKTYLATLDRPLNGSEGEVFAAGTLMLDSEEKPLLPARLDVVNAH 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            A   + + EG+  +++++F      V  L R   G   L   L AG  R ++
Sbjct: 180 AA--RLTITEGRYHQVRRMFAAVGNHVVALHRERIGGIALPDDLAAGQHRILT 230


>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 =  217 bits (553), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 104/348 (29%), Positives = 168/348 (48%), Gaps = 16/348 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDINT GLLLLT DG 
Sbjct: 87  EPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR         V    +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEDKVSDAIIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKK---I 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  P+       +   ++  +   +     + S    G   ++ 
Sbjct: 267 LRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRRF 325

Query: 301 LATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR-RSPSFPSKRSL 347
                 R               +   ++  R+   R   P  P K   
Sbjct: 326 DNPRDDRGGRGRGKPGGFKGGLTVSGEAAARQSQQRPFKPRAPGKGDR 373


>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 =  217 bits (553), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 72/254 (28%), Positives = 121/254 (47%), Gaps = 35/254 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL 77
           +VI++ G  SR + E ++ + RV + G ++          D I VDG P++ +E    ++
Sbjct: 32  RVISKRGFCSRSQAENLVREGRVSLRGKIVRDPDTPARENDEICVDGKPVKASE-FVYFM 90

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLLLTNDG 128
            +KP G VTT SD  GR+TV D     +           +  VGRLD  +EGLLL TND 
Sbjct: 91  MNKPRGYVTTASDEKGRATVMDLFREQYAKMFPGKPVPHISPVGRLDAASEGLLLFTNDT 150

Query: 129 GLARVLELPSTQ------------------WLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
             A  L     +                    ++YRV+ +G    ++L+ ++ G  +   
Sbjct: 151 QWADALLKTKDERRKTRDDKCVERESRGPIHTKIYRVQVNGHPTAEELSQMEAGFNVPPR 210

Query: 171 CYGDMQ-------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            +G+ +         L +    N W+ + L EGKNREI+++     ++V RL+RI +  +
Sbjct: 211 VFGEPEEFMHAVSAKLYSAGEKNCWLEITLDEGKNREIRRMLAKLGYEVLRLVRIKFCNY 270

Query: 224 QLGTLLAGSTREVS 237
           +LG L  G  R+++
Sbjct: 271 ELGDLKQGEIRKIN 284


>gi|296085982|emb|CBI31423.3| unnamed protein product [Vitis vinifera]
          Length = 296

 Score =  217 bits (553), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 80/259 (30%), Positives = 128/259 (49%), Gaps = 18/259 (6%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I + RV VNG +       V    D I
Sbjct: 34  RRFYNENFRDPPQRLSKVLAAAGVASRRNSEELIFEGRVTVNGSVCNTPQTRVDPARDMI 93

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIF--------SRV 108
            V+G  L K          +KP G + +  + + +S +    D L S           R+
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 GICYGDMQVTLDTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL- 225
           G+      V L   + + +   + V + EG+N E++++ +    +++ L RI  G F+L 
Sbjct: 214 GVHCTPDSVELLPPQPNISKPRLRVVVHEGRNHEVRELVKSAGLQIHSLKRIRIGGFRLP 273

Query: 226 GTLLAGSTREVSKKILREQ 244
             L  G   E+ +  L+  
Sbjct: 274 SDLGHGKHVELKQGDLKAL 292


>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 =  217 bits (553), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 113/243 (46%), Gaps = 11/243 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR- 68
              P  +S+ +ARAG+  ++E E  I   RV +NG + + A   V     ++VDG+ +  
Sbjct: 20  KEKPDWLSRALARAGVFPQKEAEDAIRAGRVSINGRVAKMALTPVPPGATVKVDGLVVSL 79

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSR-----VISVGRLDINTEGLL 122
           +A  TR+  +HKP GL+++        TVF+  LP +          +VGRLD+++ GLL
Sbjct: 80  EAPPTRVLAFHKPAGLLSSTERQHRTGTVFEALLPQLPPELAGYTWHAVGRLDVDSTGLL 139

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L TND  L      P     + Y          +++  L++G+ +        +V +  +
Sbjct: 140 LFTNDDKLVAHATSPDAHLPKRYVATVFSTASDERVEPLRRGMTLDDGPARPAKVNVRDE 199

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V V L EG++ ++K++       V  L R + G   L  +  G+ R ++   +R
Sbjct: 200 ----HTVEVTLTEGRHHQVKRMLGAVGLPVRALHREAVGSVDLEGIPEGTFRLLTDDEVR 255

Query: 243 EQL 245
           E L
Sbjct: 256 EGL 258


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 60/203 (29%), Positives = 94/203 (46%), Gaps = 3/203 (1%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V VNG ++      +  +D ++    P+   ER    L +KP   VTT  DP  R TV D
Sbjct: 2   VSVNGEVVTELGTKIKRSDVVKFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMD 60

Query: 100 NLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +      R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     + +  +
Sbjct: 61  LVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADM 120

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
             +  GI ++        ++  T       V + +  GKNR ++++FE   +KV +L R+
Sbjct: 121 EQIAAGIQLEDGEIHADAISY-TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRV 179

Query: 219 SYGPFQLGTLLAGSTREVSKKIL 241
            +       L  G  R +S+  +
Sbjct: 180 FFAGLTKKGLRRGDWRYLSEAEV 202


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 60/203 (29%), Positives = 95/203 (46%), Gaps = 3/203 (1%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V VNG ++      +  +D ++    P+   ER    L +KP   VTT  DP  R TV D
Sbjct: 2   VSVNGEVVTELGTKIKRSDVVKFHDEPVS-IERKVYVLLNKPKDTVTTSDDPQERRTVMD 60

Query: 100 NLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +      R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     + +  +
Sbjct: 61  LVKGACNERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHLDKNLTKADM 120

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           + +  GI ++        ++  T       V + +  GKNR ++++FE   +KV +L R+
Sbjct: 121 DQIAAGIQLEDGEIHADAISY-TDDFKKDQVGIEIHSGKNRIVRRIFESLGYKVVKLDRV 179

Query: 219 SYGPFQLGTLLAGSTREVSKKIL 241
            +       L  G  R +S+  +
Sbjct: 180 FFAGLTKKGLRRGDWRYLSEAEV 202


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 98/232 (42%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
            ++ +++   G  +RR    ++    V+V G +++  + +  +   + EVDG      + 
Sbjct: 1   MKLEQILFTQGFGTRRVCAGLVDCGAVRVGGQVVDDPSADFDTAGLVFEVDGREWPFRQP 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             L + HKP G   +   P    +V   LP       V  VGRLD +T GLLL T+DG L
Sbjct: 61  A-LVMLHKPAGYECSQK-PRHHPSVMSLLPPPLRTRGVQPVGRLDEDTTGLLLFTDDGKL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY       VD+  +  L  G+V+       ++       G N  + 
Sbjct: 119 IHRLTSPKHHVPKVYEATTKHPVDEAVVQRLLAGVVLDDDP-QPVRALQAQCTGPNT-LR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + L EGK  ++K++      +V  L R ++G   L   L  G    V  + +
Sbjct: 177 LVLAEGKYHQVKRMVAAAGNRVEALHRSAFGALTLPADLAPGRWCWVEPEAI 228


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 105/230 (45%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + I ++    + +  ++I    V VNG+++   AV V   + I ++G  L  A   
Sbjct: 1   MRLDRFICKSTELVKYDAIQLIHNGEVFVNGVVVRNEAVQVHENNDISLNGQKL-AARAF 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L +KP   + ++ D     ++F  +     S +   GRLD NT GL+L+T+DG    
Sbjct: 60  RYMLINKPANTLCSNVD-GVYPSLFSLIDVERPSELHIAGRLDANTTGLVLITDDGRWTF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  PS Q  +VYRV+    +  D      +GI +QG     +   L     +   V + 
Sbjct: 119 AITSPSGQCHKVYRVKLAKPIAADAGESFLQGIALQGEQELTLPAQLQI--ITPQEVLLT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           L EGK  ++K++F     KV  L R S G   +  +  G  R +S   ++
Sbjct: 177 LTEGKFHQVKRMFAAVGNKVVSLHRESIGAVSV-DVAEGEWRYLSVDEVQ 225


>gi|149377680|ref|ZP_01895416.1| pseudouridylate synthase [Marinobacter algicola DG893]
 gi|149358033|gb|EDM46519.1| pseudouridylate synthase [Marinobacter algicola DG893]
          Length = 234

 Score =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 106/233 (45%), Gaps = 10/233 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R+   +A A   SRR+ ++ I+  RV+V+G    + A  V     + +D  PL   E 
Sbjct: 4   SMRLDYFVANATTLSRRDAKKAISAGRVRVDGETCRKPASPVAKDTRVSLDDQPLSLPEE 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            R  + +KP G+++  +D   + T  D LP+     +   GRLD +T GLLLLT DG  +
Sbjct: 64  -RYLMLYKPAGVISATTDSQ-QPTALDLLPADVRHGLHIAGRLDADTTGLLLLTTDGQWS 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWV 189
             +  P  +  + YRV     +D   +  L++G+++ G         V L         +
Sbjct: 122 HRITSPRLKCHKTYRVTLAEPIDDFAITQLQQGVLLHGESRPTRPADVHLLNAG----EI 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + L EG+  ++K++       V  L R   GP  L   L  G  RE++ + +
Sbjct: 178 DLTLSEGRYHQVKRMLAAVGNHVTGLHRWRVGPLILDDSLAPGDYRELTAEEV 230


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 117/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A    A R+++++++A++++ V+ +  ++ + N+      I++ G  + +  R
Sbjct: 1   MRLDQLMADHQYA-RKDIKQLLARRQILVDHLPAQKLSQNIDPGLQQIQI-GDRIIQEPR 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
              ++ HKPIG VT   D     TV + +     +  +  +GRLD +T GLLL+T++G L
Sbjct: 59  HHYYMLHKPIGAVTAKRDA-HHPTVIELVDPQQEYPDLYPLGRLDRDTSGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              L  P     +VY V  +G +    +   + GI    G       +T+     S +  
Sbjct: 118 GFQLLHPQYHVEKVYEVEVNGPLYAAHIEQFQNGISFTDGPICKPASLTILESTLSYSKA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            + + EGK  ++KK+F     KV  L R+S+GPF L   L  G +R +++  L
Sbjct: 178 QIRISEGKYHQVKKMFLAIGVKVMTLNRLSFGPFTLDPQLAPGESRPLNEVEL 230


>gi|291543398|emb|CBL16507.1| pseudouridine synthase family [Ruminococcus sp. 18P13]
          Length = 255

 Score =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 105/235 (44%), Gaps = 6/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            R+ K IA     SR+EV+ ++ +  V+VNG   +     V    D I + GV L     
Sbjct: 1   MRLDKCIADHSAYSRKEVKELLRRGSVRVNGAPEQDPGRQVDPEGDEIMLAGVIL-PTAL 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R ++ +KP G +++      ++ V    P +   +   GRLD++TEG+LLLTNDG LA 
Sbjct: 60  HRTYMLNKPKGCISSTRTGKTKTVVEFLPPELRKGIFPAGRLDVDTEGMLLLTNDGDLAH 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V+    V +  +   + G+V+  G      +V       + A V  
Sbjct: 120 RILSPRRHIPKYYLVQLAKPVVEKTVETFENGVVLEDGTRCLPARVAALPGVENTALVE- 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            L EGK  ++K++F      V +L+R+  G   +   L  G    +  K +    
Sbjct: 179 -LHEGKFHQVKRMFAAVENHVEQLLRVQMGGLPIDVKLGKGDYLLLLHKDIERLF 232


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 70/251 (27%), Positives = 118/251 (47%), Gaps = 14/251 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLR 68
              PQR++KV+A AG+ASRR  E +I Q +V VNG +       V  S D I V+G  + 
Sbjct: 152 EHEPQRLAKVLAAAGVASRRTSEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRIS 211

Query: 69  KA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINT 118
           K       +  +KP G + +  +     ++ D+    ++++           VGRLD+ T
Sbjct: 212 KKLPPKLYFAVNKPKGYICSSGEEKSVISLLDDYLKGWNKLQPGVPKPRLFTVGRLDVAT 271

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL+++TNDG  A+ +  PS+   + Y V   G V +  L  +  G VI G+      V 
Sbjct: 272 TGLIIVTNDGEFAQKVSHPSSNITKEYVVTIDGAVHKKHLVAISGGTVIDGVKVVPDLVE 331

Query: 179 LDTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
               +       + + + EG+N E++++ +    KV  L R+  G F+L   L  G   E
Sbjct: 332 PLDTQADTKRMRLKIVVHEGRNHEVRELVQNAGLKVYALKRVRIGRFRLPSDLGIGKMVE 391

Query: 236 VSKKILREQLG 246
           + +  ++   G
Sbjct: 392 LKEADIKALDG 402


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 58/232 (25%), Positives = 112/232 (48%), 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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G ++   D D   TV D L   +    +   GRLD +T GL+LL+ DG  
Sbjct: 61  I-YIMMNKPAGFLSATEDKD--PTVIDILDDFYKGLDLSIAGRLDKDTTGLILLSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y+V    ++  D + + ++G+ I+   Y      L+  +   A V 
Sbjct: 118 IHKVTSPNSNIEKTYQVETRDEIKNDLIKIFEEGVYIKEDDYTARPAKLEILEEKKALVR 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|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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 101/305 (33%), Positives = 157/305 (51%), Gaps = 13/305 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR         V    +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E++++ +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKVDA 266

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LEE      A         R        V  D       + Q +G  + ++L  
Sbjct: 267 LRAELKLEEG--APSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRR 324

Query: 304 PVHRR 308
             + R
Sbjct: 325 FDNLR 329


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 105/367 (28%), Positives = 173/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP    SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +     +
Sbjct: 254 GHSVEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQ 312

Query: 288 NSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHR----RSPSFPS 343
            S    G   ++       R               +   ++  R+   R    R P+   
Sbjct: 313 TSGADEGRELRRFDNLREDRGRGGRGKPGGFKGGLTVSGEAAARQSQQRPFKQRGPAKGD 372

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 373 RGALPDG 379


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 68/252 (26%), Positives = 120/252 (47%), Gaps = 19/252 (7%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+     SRRE + +I   ++ VN  L+   A +V   D +++ G  ++  
Sbjct: 1   MQKMRLNKFISHNTSYSRREADELIKSGKISVNNKLVSELATSVSDEDKVKIGGRLVKPK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + +YHK  G + T  D  GR T++D LP  F++ +S+GRLD  +EGLLLLT+   +
Sbjct: 61  KDFTMIVYHKQKGELVTKKDDRGRKTIYDALPEGFAKFVSIGRLDYASEGLLLLTDAPAI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---ICYGDMQVT--------- 178
           A  L    +   R Y ++  G++  +    +++G          +   ++          
Sbjct: 121 ATALMS--SDIEREYYLKVKGEITDEVKTAMREGFFAADASKGAHAKSKIKSMEFKPFVA 178

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +    G      V + EG+NRE+++ F +F+ +V  L R+S+G   LG L  G  R  
Sbjct: 179 FDIFGSSGGYTKFRVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVDLGMLKPGKWRYF 238

Query: 237 SK---KILREQL 245
                + LR+ L
Sbjct: 239 ENGEYEDLRDFL 250


>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 =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 73/235 (31%), Positives = 125/235 (53%), Gaps = 7/235 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGV----PLR 68
           +++ K++AR G  SRR +E +I    VK+N  +++    +++     + ++       L 
Sbjct: 3   EKIQKILARHGYGSRRYIESLIKSHSVKINDEVVKVGQRISINVIQKVIINNNNYKPKLN 62

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTND 127
             +  ++ LY+KP G + T  D   R T+F+ LP    +R I++GRLD+N+ GLLL T D
Sbjct: 63  INKSLKVLLYNKPEGEICTRKDQRNRRTIFEKLPKLSNARWINIGRLDLNSSGLLLFTTD 122

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G LA  L  PS    R+Y+VR  GQ  ++ L  L   + +         +     +G N 
Sbjct: 123 GELAYRLTHPSFNIERIYKVRVFGQFTENILKQLNVRVKLLDGYANFKSIQFKYGEGKNK 182

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           W  V L EG++R +++++E   ++VN+L+RISY    L  TL  G+   ++K  +
Sbjct: 183 WFNVSLCEGRHRIVRRIWEKLGFQVNKLVRISYAHLTLPKTLFPGTWITLNKHDI 237


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   ++VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  V-ALNKPAGYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G     +       +G    + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEP-KPIAALAAAARG-ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V+ L R   G F L   L  G+ R + ++ L   
Sbjct: 179 IAEGKYHQVKRMVAAASNRVDALHRSRIGGFALPEDLAEGAWRWLDERDLAAL 231


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 115/248 (46%), Gaps = 16/248 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+     SRRE + +I   +V + G ++   A +V   D + ++G  ++  
Sbjct: 1   MEKTRLNKFISHNTNYSRREADELIKAGKVSIAGRVVSDLATSVDEDDKVRINGRLIKLK 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + +YHK  G + +  D  GR T++D L   F++ +SVGRLD  +EGLLLLT+   +
Sbjct: 61  KEFTVIVYHKQKGELVSKKDDRGRKTIYDTLDKKFAKFVSVGRLDYASEGLLLLTDAPAI 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQ 176
           A  L   ++   R Y ++  G++ ++ +  +  G   +                    + 
Sbjct: 121 ATALM--NSDLEREYYLKVKGEISKEVIEAMTNGFFAKDATKGAHAKTTIKSMEFKPFLA 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +    G    + V + EG+NRE+++ F +F+ +V  L R+S+G   L  L  G  R  
Sbjct: 179 YKVFGSSGGYTKLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDMLKPGKWRYF 238

Query: 237 SKKILREQ 244
                 + 
Sbjct: 239 ENSEYEDL 246


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 338 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 397

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 398 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 457

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 458 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 517

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 518 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 573

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 574 GEWRYLGPDE 583


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 103/233 (44%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A  +  +   + EVDGV      R  
Sbjct: 15  LESILFTQGFGSRRQCRALVEAGRVAVGGATCADAHTSFDTARLVFEVDGVAWPYRARAY 74

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           +   +KP G   +  +P   ++VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 75  V-ALNKPAGYECSR-EPQHHASVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 132

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+++ G     +       +G    + + 
Sbjct: 133 AYTSPKRKVPKTYVATVRHPLDDAQLDALRAGVLLHGEP-KPIAALAAAARG-ERLLEMT 190

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V+ L R   G F L   L  G+ R + ++ L   
Sbjct: 191 IAEGKYHQVKRMVAAASNRVDALHRSRIGGFALPEDLAEGAWRWLDERDLAAL 243


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 77/260 (29%), Positives = 124/260 (47%), Gaps = 18/260 (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 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------------VT 178
            L    +   R+Y+++  G+V  D  + +  GI +     G                   
Sbjct: 122 SLM--ESDLERIYKLKIKGEVTPDMEDAMLNGIYLDDASAGAHSHSKITSMDIKPFIGYK 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 KILREQLGPHLLEEAQVNLD 258
                 L   L EE +   D
Sbjct: 240 SEYSA-LYKFLKEEKKRARD 258


>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 =  216 bits (551), Expect = 4e-54,   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  RLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINT 118
              L HKP+G V+  ++      V                   P+    +   GRLDI++
Sbjct: 118 VTILLHKPMGYVSGQAEDGHTPAVALVNARSHWQGDASRMRFAPAQLKGLAPCGRLDIDS 177

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-GQVDQDKLNLL--------KKGIVIQG 169
            GLL+LT DG +AR L    +   + Y VR   G+  QD   +           G+++ G
Sbjct: 178 VGLLVLTQDGRVARQLIGEDSAVDKEYLVRVQYGERTQDVRAVFPADRLALLCHGLLLDG 237

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                 QV     +     +   LREGK R+I+++ E    KV  L RI  G   LG L 
Sbjct: 238 QPLKPAQVDWQNPE----QLRFVLREGKKRQIRRMCELVGLKVVGLKRIRIGRVLLGNLP 293

Query: 230 AGSTREVSKKI 240
            G  R ++   
Sbjct: 294 VGQWRYLAPGE 304


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 327 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 386

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 387 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 446

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 447 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 506

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 507 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 562

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 563 GEWRYLGPDE 572


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 104/236 (44%), Gaps = 14/236 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD------HIEVDGV 65
            R++K +A  G+ SRR   R I    + + G           + S D       +  DG+
Sbjct: 23  IRLAKYLALTGLCSRRAATRYIRDGLIMIEGRQANHIDTVTLIESPDGLICKELLLFDGM 82

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +   E  +  + +K +G       PD   ++   LP+   R+  VGRLD ++ GLLLLT
Sbjct: 83  AVEGIEPKQYRMLNKCVGTDCRLL-PDDSDSLLHLLPAS-PRLYPVGRLDKDSRGLLLLT 140

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG L + L  P     + YRVR       + L  + +G+  + +      +T  ++   
Sbjct: 141 NDGELTQHLMHPDFGHTKTYRVRVDRPYGDEFLQKMAQGVSYRDVTTLPCTMTRLSED-- 198

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                + L +G NR+I+++ +   +KV  L R+      L  L  G  RE++ + +
Sbjct: 199 --QFEIVLTQGLNRQIRRMSQALGFKVIDLKRVKIQTLMLEDLNEGEMRELTVEEI 252


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 95/230 (41%), Gaps = 10/230 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K +   G+ SRR+ ER+     V+VNG  +  A   +       + + G  +    
Sbjct: 1   MQLVKYLQAQGVGSRRQCERLAECGGVEVNGETVSGAKTEIAPDSVRTLRIGGAAVCVVP 60

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 + +KP G  T+H  P     VF   P+    +   +VGRLD +T G+LL+TNDG
Sbjct: 61  LPYFYIVLNKPAGYETSHK-PRDWPGVFTLFPANLRNLDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
                +  P     ++YR       D      L+ G+++               +     
Sbjct: 120 QFNHRMTSPKHHVAKLYRATLKHAADAALCETLQNGVLLHDDNETVAADA---AELADPH 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + + + EGK  ++K++      +V +L R+ +G +    L  G  R VS
Sbjct: 177 TLLLTIGEGKYHQVKRMVAAAGNRVEKLHRLRFGSWSAEDLAVGEWRFVS 226


>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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 89/232 (38%), Gaps = 11/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + +++   G  +R+    +I    V +NG++++     V +TD    +     R  E   
Sbjct: 6   LDRILQSQGFGTRKYCRGLIEDGEVSINGVVVDNFKTAVDTTDLEFTIFDEVWRYRE-HV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP     +   P     V   LP  F    +  VGRLD +T G+LL+++DG    
Sbjct: 65  YIVLNKPANFECSRK-PSHHPGVLTLLPEQFTWRDLQPVGRLDHDTTGMLLMSDDGPFIH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVTV 191
               P     ++Y    H  V  + +  L  G+ +         +   T +  +   + +
Sbjct: 124 AQSSPKRHIPKIYVATTHDPVTPELIAQLLGGVQLHDE---PAPLAAQTCRMLAEHQIEI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            L +GK  ++K++        + L R   G   L    L  G    +  + L
Sbjct: 181 VLEQGKYHQVKRMLAAAGNHCSALNRAEIGELTLESLGLEEGEWTYLDAEQL 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 =  216 bits (551), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 108/241 (44%), Gaps = 15/241 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVP 66
               R+ +++A  G  SRREVE +     V+++G  L  A+  +     +     V G  
Sbjct: 1   MKALRLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEA 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLL 122
           L         + HKP+G+  +H +      V+  LP  + R       VGRLD  T GLL
Sbjct: 61  LDPLPG-VCLMLHKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLL 117

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+T+DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T
Sbjct: 118 LMTDDGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMET 177

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
              ++   TV L EG+  +++++F      V+ L R   G   L   L AG  R +    
Sbjct: 178 DDPTHC--TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFRILGPGE 235

Query: 241 L 241
           +
Sbjct: 236 I 236


>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 =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 104/367 (28%), Positives = 173/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP    SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +     +
Sbjct: 254 GHSVEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQ 312

Query: 288 NSSQKNGLSKQK----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            S    G   ++    +       R           +     +   Q+    +R P+   
Sbjct: 313 TSGADEGRELRRFDNLREDRGRGGRGKPGGFRGGLTVSGEAAAKQSQQRPFKQRGPAKGD 372

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 373 RGALPDG 379


>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 =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 327 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 386

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 387 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 446

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 447 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 506

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 507 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 562

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 563 GEWRYLGPDE 572


>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 =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 121/249 (48%), Gaps = 20/249 (8%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------ 181
           L    +   R Y ++  G +D++ +  ++ G+ IQ    G    T  T            
Sbjct: 120 LMH--SDLEREYYLKVKGNIDKNVIEAMQNGLEIQNEKKGAHAKTKITSMSFAPFLGFEI 177

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L AG  R +   
Sbjct: 178 FGSSGGYTKLKVIINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKAGKYRYLENG 237

Query: 240 I---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 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 =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 108/241 (44%), Gaps = 15/241 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVP 66
               R+ +++A  G  SRREVE +     V+++G  L  A+  +     +     V G  
Sbjct: 1   MKALRLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEA 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLL 122
           L         + HKP+G+  +H +      V+  LP  + R       VGRLD  T GLL
Sbjct: 61  LDPLPG-VCLMLHKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLL 117

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+T+DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T
Sbjct: 118 LMTDDGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMET 177

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
              ++   TV L EG+  +++++F      V+ L R   G   L   L AG  R +    
Sbjct: 178 DDPTHC--TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLVLPTDLPAGEFRILGPGE 235

Query: 241 L 241
           +
Sbjct: 236 I 236


>gi|209517428|ref|ZP_03266269.1| pseudouridine synthase [Burkholderia sp. H160]
 gi|209502082|gb|EEA02097.1| pseudouridine synthase [Burkholderia sp. H160]
          Length = 236

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 100/232 (43%), Gaps = 10/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMSTD-HIEVDGVPLRKAER 72
           +  ++   G  SRR+   +I   RV ++G +   A  +  V S      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIGDARVSIDGAICTDADADFAVESGALRFSVDGVEWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP+G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPVGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
                 P  +  ++Y       +D  +L  L+ G+++ G         LD Q      + 
Sbjct: 121 VHQFTSPKRKVPKLYVATTRHPLDDAQLTALRHGVLLHGETRP--SAALDAQARDTHTLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L
Sbjct: 179 LTVLEGKYHQVKRMIAASGNRCEALHRERIGGLALPATLAPGAWQWLDEAGL 230


>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 =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 108/241 (44%), Gaps = 15/241 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVP 66
               R+ +++A  G  SRREVE +     V+++G  L  A+  +     +     V G  
Sbjct: 1   MKALRLDRLLANLGYGSRREVEGLARAGLVRLDGQALRDASQRIPLEPDLSARMTVQGEA 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLL 122
           L         + HKP+G+  +H +      V+  LP  + R       VGRLD  T GLL
Sbjct: 61  LDPLPG-VCLMLHKPLGVTCSHKEVG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLL 117

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+T+DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++T
Sbjct: 118 LMTDDGALLHRIISPKAKVSKRYRVTLARPLQGDETAILASGEMMLEGEDKPLLPVEMET 177

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
              ++   TV L EG+  +++++F      V+ L R   G   L   L AG  R +    
Sbjct: 178 DDPTHC--TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLVLPADLPAGEFRILGPGE 235

Query: 241 L 241
           +
Sbjct: 236 I 236


>gi|217974985|ref|YP_002359736.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217500120|gb|ACK48313.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 233

 Score =  216 bits (550), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 104/233 (44%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++    R      I    V VNG +    A+ V   + + ++  PL     +
Sbjct: 1   MRLDKFLCKSTDLDRDAASVAIINGSVTVNGAIATDCAMQVHENNAVCLNEKPL-MPRPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP   + ++ D     ++F  L       +  VGRLD++T GL+LLT+DG  + 
Sbjct: 60  RYFMLHKPADTLCSNVD-GAYPSLFHLLDIERAFDLHIVGRLDVDTTGLVLLTDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P  Q  +VYRV     +D +           G+ +QG     +  TL  Q+  +  
Sbjct: 119 NIISPQYQCKKVYRVTLRDPLDSEATAAIAATFAAGLQLQGETALTLPATL--QQVDDKT 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EGK  ++K++F     KV  L R   G F L  +  G  RE++   +
Sbjct: 177 VLLTLTEGKFHQVKRMFAAVGNKVVALHRAQIGAFIL-DVDIGEWRELTLAEI 228


>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 =  216 bits (550), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/249 (27%), Positives = 123/249 (49%), Gaps = 19/249 (7%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQVTL 179
           L    +   R Y ++  G++  + +  +++G   +                    +   +
Sbjct: 121 LM--GSDIEREYYLKIKGEITPNVIAAMQEGFFAKDATKGAHARTKQISMEFKPFLAYKI 178

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +  G    + V + EG+NRE+++ F +F+ +V  L R+S+G   L  L  G  R  +  
Sbjct: 179 ISFSGGYTRLKVIINEGQNRELRRFFGYFDLEVMDLKRVSFGRVSLDQLGEGKWRYFTNS 238

Query: 240 I---LREQL 245
               LR+ L
Sbjct: 239 EYDDLRDFL 247


>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 =  216 bits (550), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  216 bits (550), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 324 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 383

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 384 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 443

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 444 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 503

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 504 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 559

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 560 GEWRYLGPDE 569


>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 =  216 bits (550), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 104/367 (28%), Positives = 173/367 (47%), Gaps = 19/367 (5%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP    SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPVLKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVPDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSK---KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           G + EV++     LR +L       + + L  P+       +   ++  +   +     +
Sbjct: 254 GHSVEVAQDKVDALRAELKLEEGAPSALTL-QPVIGQRRAAKSTVHVSRDGRSNAYVNGQ 312

Query: 288 NSSQKNGLSKQK----KLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
            S    G   ++    +       R           +     +   Q+    +R P+   
Sbjct: 313 TSGADEGRELRRFDNLREDRGRGGRGKPGGFRGGLTVSGEAAAKQSQQRPFKQRGPAKGD 372

Query: 344 KRSLRRT 350
           + +L   
Sbjct: 373 RGALPDG 379


>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 =  216 bits (550), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 62/236 (26%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +++ + +AG+  R + E  I + RV ++G +       V     + VDG+          
Sbjct: 31  LARALGKAGVMPRAQAEAAIREGRVTLDGRVEHEPFAPVRPEMEVRVDGLVRNLEAPVLT 90

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGG 129
            ++HKP GLV   SD +G  TVF+ L    ++       ++VGRLD +T GLLL TND  
Sbjct: 91  LMFHKPAGLVVHGSDAEGVGTVFECLRERLTQPLRDYEWLAVGRLDRDTTGLLLFTNDER 150

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L +    P     + Y     G   +D L  L++G+V++          L         V
Sbjct: 151 LVQHGTSPERHLPKRYVAGVVGPPPEDALRRLREGLVLEDGPTRPAGARLRAPD----VV 206

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            + L EG+N ++K++       V  L R + G   L  +  G+ R ++ + + + L
Sbjct: 207 ELTLTEGRNHQVKRMLAAVGHPVRTLHREAVGGVTL-DVPEGAWRLLTDEEVSQGL 261


>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 =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 116/236 (49%), Gaps = 10/236 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++      R+++  M+AQ RV+V+GI+ +     V    H+ VD   L+   R  
Sbjct: 7   RLDRFLSSELKIKRKDIRLMLAQNRVRVDGIVAKDIQQLVDEFSHVSVDDAVLKNN-RPS 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP+G+V+   D D   TV D L       +  VGRLD+NT GL+LLTNDG  +R 
Sbjct: 66  YVMLNKPVGVVSATKD-DKHKTVIDLLDHPAKSELHIVGRLDLNTSGLMLLTNDGRWSRK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P ++  + YRV     +  + ++   KG     + I     ++ + ++  +     V
Sbjct: 125 LMSPESKVEKRYRVTLQNPLSTEYIDAFAKGFYFEFEDITTQAAKLEIISEHIA----EV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLG 246
            L EGK  +IK++F  F   V  L R S G   L   L  G +RE+S + + +  G
Sbjct: 181 TLTEGKYHQIKRMFGRFRNPVIGLHRYSVGELLLDPDLDEGGSRELSVEEVNDIFG 236


>gi|226939001|ref|YP_002794072.1| RsuA [Laribacter hongkongensis HLHK9]
 gi|226713925|gb|ACO73063.1| RsuA [Laribacter hongkongensis HLHK9]
          Length = 231

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 93/231 (40%), Gaps = 7/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAER 72
            ++ +++ R G +SR+    +I Q RV V G + +   + V        VD       E 
Sbjct: 1   MQLERLLHREGWSSRKGCRILINQGRVCVAGEVADDPGLEVEPEGLAYSVDDEAAIAREH 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP+ L  +   P  R+ V    P  +    V  VGRLD +T GLLLL++DG  
Sbjct: 61  L-YLILNKPLDLECSRK-PTVRTGVLTLFPPRYSERGVQPVGRLDADTSGLLLLSDDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P     + Y       V+ + L  L  G+V+         V    +      + 
Sbjct: 119 IHRITSPKHLVPKTYVATCARPVEPEHLRQLLAGVVLNDDPAP--VVARSARTLDEHTLE 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EG+  +++++        + L R   G   L  L  G  RE++   L
Sbjct: 177 LVVTEGRYHQVRRMIAAVGNHCDALHRSRIGELVLDGLAPGQWRELTAAEL 227


>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 =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 114/234 (48%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A+A I SR+ +++ + ++ + V+       + NV +    I      +     
Sbjct: 1   MRLDRLLAQASI-SRKSMKQALLRRAILVDQTPARNLSQNVDTGLQDILFYKQKISAPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G +T +SD   ++TV D +        + S+GRLD +T GLLL+T++G L
Sbjct: 59  HRYFMMNKPRGYITANSDA-SKATVIDLIQKEDFSEELYSIGRLDRDTTGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V+ +G +D   +   ++G+  + G      Q+ + +     +  
Sbjct: 118 GFQLLHPQYHVDKTYFVQVNGLLDNQAIEAFQQGVRFLDGKVCKPAQLIIHSATPVLSTA 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           +V + EGK  ++KK+F     KV  L R   G FQL   L  G  R +++  L+
Sbjct: 178 SVTISEGKFHQVKKMFLAIGVKVTYLKRTHLGDFQLDPNLDEGDYRSLNQDELK 231


>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 =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 52/228 (22%), Positives = 98/228 (42%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAE 71
            ++ K I   G+ SR++ + +I    + +NG +  RA  ++  +    + VDG  +    
Sbjct: 1   MQLLKYIQSQGLGSRKQCQWLIDNDCIAINGEIHNRAKDDIDPSQVHTLSVDGEEIAAVP 60

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L HKP    T+H  P    ++F   P     +   +VGRLD +T G++L+TNDG
Sbjct: 61  MPHFYILLHKPADYETSHK-PQQYPSIFSLFPDHMRNIDMQAVGRLDADTTGIILITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
                +  P  +  ++YRV      D      LK G+++                 +   
Sbjct: 120 QFNHRVTSPKHKVPKLYRVTLKHPADDTLCTTLKNGVLLHDDNETVAAAEAVLAAPTT-- 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +V +L R  +G + +  L  G  + +
Sbjct: 178 LMMTITEGKYHQVKRMVAAAGNRVEQLHREKFGDWNVDDLATGEWKFI 225


>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 =  215 bits (549), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 53/228 (23%), Positives = 98/228 (42%), Gaps = 8/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSYVETLDIDGEAVTVVP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L   L  PS +  ++Y V       +     LK G+ +            D    +   
Sbjct: 120 KLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNGVPLHDENETVCAA--DAVLENPTT 177

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + + EGK  ++K++      +   L R  +   +   L  G  + +
Sbjct: 178 LLLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAHLETENLKPGEWKFI 225


>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 =  215 bits (549), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 99/241 (41%), Gaps = 15/241 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTND 127
              + L +KP+G   +  D      V+D LP  F     V    GRLD +T G LL T+D
Sbjct: 58  GM-VLLLNKPVGYTCSTKDRG--RLVYDLLPDRFRLRKPVLSTVGRLDRDTSGALLFTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P ++  +VY       +  D+      G +++ G         L+      
Sbjct: 115 GVLLHRIIAPKSEVPKVYEAELDRPLKGDEAAQFASGTLMLDGEDKPLKPAELEVLGERR 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L RI  G   L  L  G+ R + ++ + +   
Sbjct: 175 A--RLTLHEGRYHQVRRMFAATGNHVTALARIRIGALTLDGLAEGTWRLLDERDVAKIFA 232

Query: 247 P 247
           P
Sbjct: 233 P 233


>gi|332366092|gb|EGJ43848.1| ribosomal small subunit pseudouridine synthase A [Streptococcus
           sanguinis SK1059]
          Length = 241

 Score =  215 bits (549), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 118/233 (50%), Gaps = 8/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ +++A A   SR+ +++ + Q+++ V+G    + + NV +    I   G  +     
Sbjct: 1   MRLEQLLA-ANHISRKNMKQSLLQKQILVDGKPAYKLSQNVDTGLQQITFQGKHVSGPA- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G VT + D + + TV D L     +  + S+GRLD +TEGLLL+T++G L
Sbjct: 59  HRYYMLNKPAGAVTANRDAE-KLTVLDLLDKEVEKENLYSIGRLDRDTEGLLLITDNGPL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V  +G +   K    ++GI  + G      Q+++ +   S +  
Sbjct: 118 GFQLLHPQYHVEKTYYVEVNGPLTSQKKISFQEGIRFLDGTVCQPAQLSILSTSSSLSRT 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           TV + EGK  +IKK+F     KV  L RI +G F L   L  G  R ++K+ L
Sbjct: 178 TVRISEGKFHQIKKMFLAVGVKVTYLKRIQFGDFTLDPDLAKGDYRALNKEEL 230


>gi|167569105|ref|ZP_02361979.1| RNA pseudouridine synthase family protein [Burkholderia
           oklahomensis C6786]
          Length = 240

 Score =  215 bits (549), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 63/227 (27%), Positives = 99/227 (43%), Gaps = 8/227 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G     A A    +    EVDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRALVEAGRVAVGGATCTDAHASFDTARLAFEVDGVAWPYHARAY 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + L +KP G   +  +P   S+VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 63  VVL-NKPAGYECSR-EPQHHSSVFRLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D   L+ L+ G+++ G       V    +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDALLDALRAGVLLHGEPKPIAAVAAHARG--ERLLEMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + +
Sbjct: 179 VAEGKYHQVKRMVAAASNRVEALHRASIGGFTLPADLAEGAWRWLDE 225


>gi|291059845|gb|ADD72580.1| RNA pseudouridine synthase superfamily [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 284

 Score =  215 bits (549), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 117/248 (47%), Gaps = 21/248 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   +AR+G ASRR  E +IA  RV V+G  +      V + + + VDG  ++     R
Sbjct: 34  RLQVYLARSGCASRRACEALIASGRVTVDGQTVTTQGRTVCAQNVVCVDGTVVQLERVQR 93

Query: 75  LWLYHKPIGLVTTHSD----------------PDGRSTVFDNL-PSIFSRVISVGRLDIN 117
             L +KP+G + + +                     +   D + 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 ----RHLAAQCVQLVLVEGKKREIRVVFEAWGQDVVRLVRVRIGRVRLGPLRPGAFRTMR 269

Query: 238 KKILREQL 245
            + + + L
Sbjct: 270 LQEVAQLL 277


>gi|188581487|ref|YP_001924932.1| pseudouridine synthase [Methylobacterium populi BJ001]
 gi|179344985|gb|ACB80397.1| pseudouridine synthase [Methylobacterium populi BJ001]
          Length = 242

 Score =  215 bits (549), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 110/246 (44%), Gaps = 15/246 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVP 66
               R+ +++A  G  SRREVE +     V+ +G  L  A+  +      +  + V G P
Sbjct: 1   MKAVRLDRLLANLGYGSRREVEGLARAGLVRRDGEALRDASQRIALEPDLSARMTVQGAP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLL 122
           L         + HKP+G+  +H +      ++  LP  + R       VGRLD  T GLL
Sbjct: 61  LDPLPG-VCLMLHKPLGVTCSHKEAG--PLIYSLLPERWRRRDPALSTVGRLDKETSGLL 117

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDT 181
           L+T+DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V ++ 
Sbjct: 118 LMTDDGALLHRIIAPKAKVAKRYRVTLARPLQGDEAAILASGELMLEGEDKPLLPVEMEG 177

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           +  ++   TV L EG+  +++++F      V+ L R   G   L   L AG  R +    
Sbjct: 178 EDATHC--TVTLHEGRYHQVRRMFAALGNHVDALHRDRVGGLALPADLPAGEFRILGPGE 235

Query: 241 LREQLG 246
           +    G
Sbjct: 236 IAAVFG 241


>gi|307730739|ref|YP_003907963.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307585274|gb|ADN58672.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 239

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 101/235 (42%), Gaps = 10/235 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV +   +   A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVTIGDTVCTDADADFPAEDTSFCFSVDGVTWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       VD  +L+LL+ G+++ G       V  D Q      + 
Sbjct: 121 VHLFTSPKRKVPKVYVASTRHPVDDTQLSLLRNGVLLHGESKPVAAV--DAQLRGERSLA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L   
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERVGGLALPATLAPGAWQWLDEAALEAL 233


>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 =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 332 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 391

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 392 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 451

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 452 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 511

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 512 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 567

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 568 GEWRYLGPDE 577


>gi|330957838|gb|EGH58098.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 230

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 64/232 (27%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + ++     +R+ V   +A   VKV+G+        V     +  D   L+  +  
Sbjct: 1   MRLDRFLSNLPRFNRKNVRLALAGGHVKVDGLTSTDPHHEVREFSCVVFDEEILQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ HKP G V+   D     TV D L       +   GRLD NT GL+L+TNDG  +R
Sbjct: 61  RYFMLHKPQGCVSATVDAQH-PTVIDLLDEPDRHELHIAGRLDFNTTGLMLITNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            L  P T+  +VY V     +D+       +G+    + I     Q+TL   + +     
Sbjct: 120 RLTQPQTRLAKVYYVETEQIIDERYAARFAEGLYFSFENITTQPAQLTLLGPRCA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F  F+ KV  L R S G   L  TL  G+ R +    +
Sbjct: 176 LSITEGRYHQVKRMFGHFDNKVVTLHRESVGELLLDPTLEPGNYRALHAPEI 227


>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 =  215 bits (548), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 60/241 (24%), Positives = 123/241 (51%), Gaps = 3/241 (1%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+K  V+      R++K IA AGI SRR+ +  I    V VNG  +      V  +D ++
Sbjct: 15  KNKPKVETVDGGIRLNKYIANAGICSRRDADIYITAGNVTVNGKTITEMGYKVKLSDEVK 74

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEG 120
            DG  +   ++   +L +KP  +  + S  +   TV D +  +  +R+  +G+L+ +  G
Sbjct: 75  FDGRSIT-PDKKEYYLLNKPKDVFVSGSLNESGMTVLDIVGRATKARLSPIGKLERSAMG 133

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L++LTNDG L++ L  P     ++Y V+ + ++ Q  L  +++GI ++      + ++  
Sbjct: 134 LVVLTNDGTLSKSLANPRHGIRQIYHVQLNKELSQVDLEKIRQGITLEDGEIKVVDISY- 192

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +  S   V + ++  K+  ++++F+  N+++  L R+ +G      L  G  R ++K+ 
Sbjct: 193 VENKSKREVGIEIKSTKSHIVQRLFKSLNYEIKYLDRVVFGTLTKKDLPRGMFRHLTKQE 252

Query: 241 L 241
           +
Sbjct: 253 I 253


>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 =  215 bits (548), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 119/241 (49%), Gaps = 9/241 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KVI +    SR+E++R+  Q +V V+  +  R   NV S    I V G  L   E 
Sbjct: 1   MRLDKVIEQQLNTSRKEMKRLFQQGKVLVDQRIEGRPERNVDSAIHQIIVAGRQLETQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R ++ +KP G+VT + D     TV D +        + +VGRLD +TEGL+L+T +G L
Sbjct: 60  -RYYIVNKPNGVVTANVDQQH-QTVIDLIAPKDQHPDLYAVGRLDRDTEGLVLVTTNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
              L  P+ +  + Y V  +  V  + +     GI    G+      +T+   + + ++V
Sbjct: 118 GYDLLHPTKKVTKRYEVVVNDLVTPEDVAAFATGITFHGGVTCKPAALTIIDARAARSFV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGPH 248
           ++ + EGK  ++KK+F     KV +L R + G   L   L  GS R ++++ L+  L  H
Sbjct: 178 SLEIAEGKFHQVKKMFLARGKKVIQLKRTAMGSLVLPDDLAVGSYRSLTQEELK-GLAAH 236

Query: 249 L 249
            
Sbjct: 237 F 237


>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 =  215 bits (548), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 120/247 (48%), 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------------L 179
           L    +   R Y ++  G++  +    +K G   +    G    T              +
Sbjct: 120 LM--QSNIEREYYLKVKGEITDEIKTAMKDGFFAKDATKGAHPKTEIKSMNFAPFVAFDI 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|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 =  215 bits (548), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 102/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V +   IE+D           
Sbjct: 327 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRADQRIEIDSNARAAQAAQV 386

Query: 75  LWLYHKPIGLVTTHSDPD---------------GRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                 G  +     P     +   GRLDI++ 
Sbjct: 387 TILLHKPVGYVSGQAEDGYAPAATLVTRENHWSGDRSPLRFSPQHLRALAPAGRLDIDST 446

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT +G +A+ L    +   + Y VR                + L  L+ G+ + G+
Sbjct: 447 GLLVLTQNGRVAKQLIGEQSDIDKEYLVRVRFGERTADIERHFPAESLAKLRHGLELDGV 506

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 507 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGRVMLGALPQ 562

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 563 GEWRYLGPDE 572


>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 =  215 bits (548), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 105/235 (44%), Gaps = 15/235 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEVDGVPLRKAE 71
            ++ K++A  G  SR+E++++I +  +  +  G  L+  +   ++ D I + G PL  A+
Sbjct: 1   MKLIKLLANLGYGSRKEMQQLIRRGTIT-DAAGQPLDDDSA--IAHDDIRLRGKPLDPAQ 57

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTND 127
              + L HKP G V +  D      V++ LP  FS    V    GRLD +T GLLL+T+D
Sbjct: 58  GM-ILLLHKPTGFVCSTKDRG--RLVYELLPERFSLRKPVISTVGRLDSDTSGLLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G     +  P     ++Y V     +    + +   G ++++          ++    + 
Sbjct: 115 GDFLHKVISPRNHVAKIYEVTTARPISPTYVPVFASGELMLESEKEPLKPAQMEITGETT 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           A   + L EG+  +++++F      V  L R   G   L  L  G  R ++   +
Sbjct: 175 A--RLTLYEGRYHQVRRMFAAVGNHVEALHRAQMGELTLDDLAPGKWRLMTPDDI 227


>gi|217968594|ref|YP_002353828.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|217505921|gb|ACK52932.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 245

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 91/241 (37%), Gaps = 14/241 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-------IEVDGVP 66
            ++ +++   G  SR++   +I    V V G + +                    VD  P
Sbjct: 1   MQLERLLHAQGFGSRKDCRALIRAGYVSVAGEVCDDPTEEFDPGSRDGSPGLEFTVDDQP 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLL 124
            R   +  + L HKP G   +   P    +VF  LP       V  VGRLD +T GLLLL
Sbjct: 61  WRFRAQAYVVL-HKPAGYECSQK-PTFHPSVFTLLPPQLLARGVQCVGRLDQDTTGLLLL 118

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           ++DG           +  +VY V     V+QD  + L  G+ +            +    
Sbjct: 119 SDDGQFIHQWSSGKKRTPKVYEVTLKHAVEQDFADRLVAGVELNDEPVPIAAAACELLSP 178

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           +   + + + EGK  ++K++      +V  L R   G   L   L  G  R +  + L  
Sbjct: 179 TT--LRLTICEGKYHQVKRMVGAAGNRVEVLHRSRVGGLDLPAGLAPGQWRWLEAEDLAR 236

Query: 244 Q 244
            
Sbjct: 237 L 237


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 101/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+D
Sbjct: 58  GFS-LLLHKPGGYTCSTKDTG--RLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY V    ++  D+  L   G ++++G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDVTLAEELRGDEAALFASGSLLLEGETKPLLPAELEVLGPRQ 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 175 T--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLPSGQWRALEASDLDVLFG 232


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 97/231 (41%), Gaps = 12/231 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVPLRKAE 71
            ++ K +   GI SR++ + +I    V++N  +      ++       + +DG  +    
Sbjct: 1   MQLIKYLQSQGIGSRKQCQWLIQNDCVEINDTIRNDTKADIDPAEVQTLRIDGEDIVVVP 60

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  MPYFYILLNKPADYETSHK-PQQYPSVFSLFPDHMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
                +  P  +  ++YRV      D      LK G+++          +  L+    + 
Sbjct: 120 QFNHRVTSPKHKVPKIYRVTLKHPADDSLCETLKNGVLLHDDNETVRAAEAVLE----NP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + + + EGK  ++K++      +V  L R  +    +  L +G  + ++
Sbjct: 176 TTLLMTITEGKYHQVKRMVAAAGNRVEHLHRDEFNGRTVENLASGEWKFIT 226


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 55/233 (23%), Positives = 105/233 (45%), Gaps = 10/233 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   SR E   +I   +V+VN +++  A   V   + I + G  L  A  +
Sbjct: 1   MRLDKFLCKSTDFSRAESIDLIEAGQVRVNELVIVTAQTQVHENNCIMLAGRRLV-ARPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + HKPI  + ++ D D   +V + +       +   GRLD +T GL+L+T+DG  + 
Sbjct: 60  RYIMLHKPIDTLCSNVDGDY-PSVMNYIQVDRAEDLHITGRLDADTTGLVLITDDGRWSF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +  P     + YRV     ++   ++      ++G+ +QG     +   L+    +   
Sbjct: 119 NIINPKYHCEKTYRVTLRDPIEDGDIDELVSRFEQGLQLQGEKKLTLAAKLEV--ITPHQ 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L EG+  ++K++F     +V  L R   G   L  +  G  R ++   +
Sbjct: 177 VLLTLSEGRYHQVKRMFFTVGNRVVGLHRQQVGKLSL-DIELGEWRHLTADEV 228


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 118/241 (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 LM--ESELERVYLLKLSGLIKDSVFDAMESGITLEDASAGGHSKSKIKAMEFAPFVGYTC 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|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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 53/225 (23%), Positives = 98/225 (43%), Gaps = 10/225 (4%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGV-PLRKAERTR 74
           K +   GI SR+  + +I    V++NG ++      +   +     +DG   +       
Sbjct: 5   KYLQAQGIGSRKMCQTLIRCGLVQINGEIINNEKAEITPENVQTMNIDGEDAVVIPLPYY 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             L +KP    T+H  P    +VF   P       + ++GRLD +T G+LL+TNDG    
Sbjct: 65  YILLNKPENYETSHK-PRDYPSVFMLFPDHLRATDIQAIGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWVTV 191
            +  P  +  ++YRV      ++     LK G+++         V+ +  +  S   + +
Sbjct: 124 KMTSPKHKVAKIYRVTLKHSANESICETLKNGVLLHDDNE---TVSAENAELTSPTELIL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + EGK  ++K++      +V  L R+ +G +    L AG  R +
Sbjct: 181 TISEGKYHQVKRMVAAAGNRVEALHRLQFGDWGTEDLAAGEWRFI 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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 110/234 (47%), Gaps = 10/234 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K + ++   ++ +  + I    V VNG ++   +  V   + + + GV L   +  
Sbjct: 1   MRLDKFVCKSTQLTKADAVQCIHLGEVGVNGEVITSESTQVHENNTVTLRGVKLIARD-F 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  L HKP G + ++ D +   ++F++L     S +   GRLD++T GL+L+T+DG    
Sbjct: 60  RYILMHKPAGTICSNID-EVYPSLFNSLDVENVSELHIAGRLDVDTTGLVLITDDGRWTF 118

Query: 133 VLELPSTQWLRVYRVRFHGQVD----QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            + +PS Q  + YRV     +      D ++    G+ +QG     +  TL  Q  +   
Sbjct: 119 DITVPSKQCAKTYRVTLSRGIAADGVDDLVSRFAAGVKLQGEQQLTLPATL--QVITPTE 176

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V + + EGK  ++K++F     +V  L R   G   L  +  G  R ++ + ++
Sbjct: 177 VLLTITEGKFHQVKRMFAAVGHRVVALHRERIGDICL-DVDVGQWRYLTDEEVK 229


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/233 (29%), Positives = 115/233 (49%), Gaps = 9/233 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I++  + S  +  R++AQQR+ V+G L       V    H+ +DG  L       
Sbjct: 7   RLDRFISQNSVYSLSDTRRLLAQQRIFVDGHLAYSIQQQVTQFTHVVLDGNCLN-DSTAV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V+  +DP    TV D +       +  VGRLD NT GL+LLTNDG  +R 
Sbjct: 66  YMMLNKPKGFVSATTDPKH-PTVLDLIQHPQKNELHIVGRLDFNTTGLVLLTNDGAWSRK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           + LP T+  ++Y V     ++ + + + +KGI    + I      + +     S     +
Sbjct: 125 ISLPETKLAKIYEVTLSKPLNDEYIEVFRKGIYFSYENITTQPAYLEIL----SEYQARL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L EGK  ++K++F FF  +V  L R + GP  L  L  G ++ ++K+ +  Q
Sbjct: 181 SLIEGKYHQVKRMFGFFQNEVLALHRTAVGPISLDGLTVGHSKLLTKQTIEGQ 233


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 53/232 (22%), Positives = 103/232 (44%), Gaps = 15/232 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRKA 70
           R+ +++A  G  SR+EV+ ++A  +V ++G  L+ A + +       + + + GV +   
Sbjct: 8   RLDRLLANLGYGSRKEVQALVAAGKVVLDGKPLKDAGLRIAVDATLPERMTIRGVAVDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
               + + HKP+G+V +H +   +  ++D LP  +         VGRLD  T GL+L+T+
Sbjct: 68  APL-VLMMHKPLGVVCSHKEDGEK--IYDLLPRRWRLRDPALSTVGRLDKETSGLILITD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG     +  P     + Y  R    +   +      G ++++G     +   L+     
Sbjct: 125 DGDFLHRVISPKRHVPKTYLARLDRPLSGSEGETFAAGTLMLEGEEKPLLPARLEIVDER 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
            A   + + EG+  +++++F      V  L R   G   L   L  G  R +
Sbjct: 185 TA--RLTITEGRYHQVRRMFAAVGNHVTDLHRERIGRLVLPDDLEPGQHRIL 234


>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 =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 106/239 (44%), Gaps = 15/239 (6%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLR 68
             R+ +++A  G  SRRE++ +    R++++G  L  A   + +T      + V G PL 
Sbjct: 6   TIRLDRLLANLGYGSRREIQALARAGRIRLDGEALREADGRIAATADLPARLTVSGEPLD 65

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLL 124
                   + HKP G+  +H +      V+  LP  + R       VGRLD +T GLLL+
Sbjct: 66  PPAPLA-LMLHKPTGVTCSHKEAG--PLVYGLLPERWRRREPALSTVGRLDKDTSGLLLV 122

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQK 183
           T+DG L   +  P  +  + YRV     +  D+  +L  G ++++G     + V    Q 
Sbjct: 123 TDDGALLHRIISPKAKIEKQYRVELDRPLRGDEGAILVSGTLMLEGEEAPLLPVGFTAQG 182

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
              A   V L EG+  +++++F      V  L R   G   L   L  G+ R +    L
Sbjct: 183 PRQA--RVVLTEGRYHQVRRMFAALGNHVTALHRDRVGGLTLPEDLAPGAYRILDAAAL 239


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/220 (34%), Positives = 121/220 (55%), Gaps = 6/220 (2%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAER-TRLWLYHKPIGLVTT 87
           +E  I    V+VNG   +     V   D + V G  + L+ A+R  R+ LY+K  G + +
Sbjct: 1   MEEWIGNGWVQVNGKTAQ-LGDKVSPDDQVTVKGSAIKLKWADRLPRILLYYKQEGEIVS 59

Query: 88  HSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
             DP GR +VFD LP   S R +++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-LLAGSTREVSKKILREQL 245
                V+RL+R+ +GP  L   L  G   E++   +   L
Sbjct: 180 HIGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEVAAIL 219


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 97/235 (41%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            ++ + +   G+ SRR    ++    V  NG+        V      + VDG      ++
Sbjct: 1   MKLYRALQSQGLGSRRGCAALVRAGAVLANGLACADPEAEVDPVGLELTVDGTVWAYRDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
             L + HKP G   +H  P    +VF  LP+      V  VGRLD +T GLLL ++DG  
Sbjct: 61  AYLVM-HKPEGYECSHH-PRHHPSVFSLLPAPLVQRGVQCVGRLDQDTTGLLLFSDDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P  +  +VYR R    V+   L  L+ G+ +           L  +   +  + 
Sbjct: 119 IHRMTSPKKRVGKVYRARCAEPVNAATLAALRAGVQLNDEPAP--LAALACEAVDDRTLR 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + L EGK  +++++       V RL R + G + L   L  G  R +    L+  
Sbjct: 177 LVLAEGKYHQVRRMIAAAGNHVARLHREAVGEYPLPDDLPPGGWRWLEAGDLQRL 231


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 50/231 (21%), Positives = 97/231 (41%), Gaps = 12/231 (5%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS--TDHIEVDGVPLRKAE 71
            ++ K +   GI SR++ + +I    V++N  +      ++       + +DG  +    
Sbjct: 1   MQLIKYLQSQGIGSRKQCQWLIQNDCVEINDTVRNDTKADIDPAEVQTLRIDGEDIVVVP 60

Query: 72  RTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
                 L +KP    T+H  P    +VF   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  MPYFYILLNKPADYETSHK-PQQYPSVFSLFPDHMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
                +  P  +  ++YRV      D      LK G+++          +  L+    + 
Sbjct: 120 QFNHRVTSPKHKVPKIYRVTLKHPADDSLCETLKNGVLLHDDNETVHAAEAVLE----NP 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + + + EGK  ++K++      +V  L R  +    +  L +G  + ++
Sbjct: 176 TTLLMTITEGKYHQVKRMVAAAGNRVEHLHRDEFNGRTVENLASGEWKFIT 226


>gi|315059155|gb|ADT73484.1| Putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni S3]
          Length = 253

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ ++    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEVKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/244 (28%), Positives = 112/244 (45%), Gaps = 20/244 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A+ G+ SRRE +  I Q  VKVNG +       V+  D I++D    ++  
Sbjct: 3   EPIRLSKQMAQLGLCSRREADHYIEQGWVKVNGEVA-VLGQKVLPGDRIDLDKNAHQQQA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
                L +KP+G V+   +   ++ V                   P     +   GRLDI
Sbjct: 62  GRVTVLLNKPVGYVSGQPEKGYKAAVELITPENHWEGDQSRIAFQPQHLRGLAPAGRLDI 121

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++ GLL+LT DG +A+ L        + Y VR  G++ ++ LNLL  G+ + G      +
Sbjct: 122 DSVGLLVLTQDGRVAKQLVGEQDSREKEYLVRVRGKIIENGLNLLNHGLHLDGQSLRPAK 181

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           V+   +      +   L +GK R+I+++ E    +V  L R+  G  +LG L  G  R +
Sbjct: 182 VSWQNED----QLRFILTQGKKRQIRRMCELVGLRVVGLKRVRIGRIKLGALPPGKWRYL 237

Query: 237 SKKI 240
           S   
Sbjct: 238 SPDE 241


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 102/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD  T GLLL+T+D
Sbjct: 58  GLS-LLLHKPSGYTCSTKDTG--RLIYELLPPRFRLRAPVLAPVGRLDRETSGLLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY +     +  D+  L   G ++++G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDITLAEDLRGDEAALFASGSLLLEGETKPLLPAELEVLGPRQ 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L R   G   L  L +G  R +    L    G
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGSHVVALHRSRIGGLSLDGLPSGQWRALEASDLEVLFG 232


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 100/307 (32%), Positives = 156/307 (50%), Gaps = 26/307 (8%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSAPEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G V T  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVITREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L      
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLP----- 248

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
                     RE L  H +E AQ  +DA + +   L    P+ ++  P    R    S+ 
Sbjct: 249 ----------RELLRGHSVEVAQDKVDA-LRAELKLEEGAPSALTLQPVIGQRRAAKSTV 297

Query: 292 KNGLSKQ 298
                 +
Sbjct: 298 HVSRDGR 304


>gi|121606483|ref|YP_983812.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
 gi|120595452|gb|ABM38891.1| pseudouridine synthase [Polaromonas naphthalenivorans CJ2]
          Length = 278

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  IA+  V+VNG+        V +   IEV     ++  +  
Sbjct: 32  RLNKRMADLGLCSRREADDWIARGWVRVNGLPA-VMGQPVAANARIEVAREAEQQQRQQV 90

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------------VISVGRLDINTE 119
             L +KP+G V+  ++      V    P    R               +   GRLDI++ 
Sbjct: 91  TILINKPVGYVSGQAEDGHEPAVALVQPENRWRECNSRMRWGFEQLRGLAPAGRLDIDSI 150

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRV---------RFHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +AR L    +   + Y V                ++KL LL  G+ + G 
Sbjct: 151 GLLVLTQDGRVARQLIGEDSDMEKEYLVRVSYGAENVNVQAAFPREKLALLCHGLSLDGQ 210

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV+    +     +   L+EGK R+I+++ E     V  L R+  G   LG L  
Sbjct: 211 LLRPAQVSWQNPE----QLRFVLKEGKKRQIRRMCEQVGLFVTGLKRVRIGRVNLGHLPI 266

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 267 GQWRYLMPHE 276


>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 =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 71/231 (30%), Positives = 112/231 (48%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++++AGIASRR  E +I +  VK+N  +           D I V+G  +   E+ 
Sbjct: 2   ERIQKLLSQAGIASRRSSEELIKKGLVKINDKVA-LVGQKASFNDKITVNGKEI-LQEKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP   V T+ D   R  V D LP+   R+  VGRLD +T G+LLLTNDG L+  
Sbjct: 60  VYYILNKPAKYVCTNKDNFDRKKVIDLLPNDV-RIFPVGRLDYDTTGVLLLTNDGELSNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  PS + LR YR R    + +  LN L K  +I G        +   ++  N    V L
Sbjct: 119 LIHPSFKILRKYRARLDEPLSRQDLNELNKDQIINGKLS-----SQSVEQLDNKTYLVSL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G    +K++F      V  L R+ +    +  +  G  R ++ K ++  
Sbjct: 174 HQGTYHHVKELFSKVGRLVINLKRVEFAGLGVEKIPVGEFRSLTMKEIKSL 224


>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 =  214 bits (546), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 105/236 (44%), Gaps = 8/236 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           P  + K++   G  +RR    ++  + VKVNG+L E     +      + V+G      E
Sbjct: 4   PISLEKILFSQGFGTRRYCSDLVYAELVKVNGVLAEDPEERIATENLMLNVEGKDWEYHE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
           +     ++KP     +H       +V+  LPS F    +  VGRLD +T GLLL+++DG 
Sbjct: 64  KA-YLAFNKPANYECSHKTI-HHPSVYSLLPSPFVERGLQCVGRLDYDTTGLLLISDDGQ 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     +VYR+     + Q +++ L  G+V+          T   ++ S+  +
Sbjct: 122 FIHKMTTPKKNIGKVYRITTSEPITQKQIDHLLNGVVLDDDP-KPCFATA-CKQVSDHVL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            + + +G+  ++K++       V +L R   G +Q+   L  G  R +    L++ 
Sbjct: 180 AMTIVDGRYHQVKRMMAAVGNHVTQLHRTEIGAYQMPVDLAEGEWRWLYPDDLKQL 235


>gi|187925109|ref|YP_001896751.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716303|gb|ACD17527.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 236

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 63/232 (27%), Positives = 103/232 (44%), Gaps = 10/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAER 72
           +  ++   G  SRR+   +IA  RV + G+    A  +  + D      VDGV     E 
Sbjct: 3   LESILFTQGFGSRRQCRALIADARVSIGGVACTDADADFPTGDTAFFFSVDGVDWPYREH 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               L +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG  
Sbjct: 63  A-YLLLNKPAGYECSR-DPQHHLSVFSLLPPQFAERGVQCVGRLDQDTTGLLLLSDDGKF 120

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +   P  +  +VY       +D  +L+ L+ G+++ G     +       +G+N  + 
Sbjct: 121 VHLFTSPKRKVPKVYIATTRHPLDDAQLSALRDGVLLHGEP-KPIAAVDAAARGANT-LA 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
           + + EGK  ++K++      +   L R   G   L  TL  G+ + + +  L
Sbjct: 179 LTVMEGKYHQVKRMIAAAGNRCEALHRERIGGLALPETLAPGAWQWLDETDL 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 =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 100/237 (42%), Gaps = 7/237 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K I ++   +R +    I    + VNG  +   +  V  ++ +   G  L  A  +
Sbjct: 1   MRLDKFICKSTELNRAQASECIECAEISVNGETITEVSFQVHESNSVVFKGQRLV-ARPS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R  + HKPI  ++++ D D  S            +  VGRLD +T GL+LLT+DG  +  
Sbjct: 60  RYIMLHKPIHTLSSNVDGDYPSLFRCINIERAEELHIVGRLDADTTGLVLLTDDGRWSFD 119

Query: 134 LELPSTQWLRVYRVRFHGQVDQ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  P  Q  + YRV     +     D +     G+ +Q      +   L+    +   V 
Sbjct: 120 IIRPDKQCEKTYRVTLRDAIRDDVADMVARFAHGLQLQNEPALTLPAKLEV--VTEKEVL 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           + + EGK  ++K++F     +VN L R   G   L  L  G  R +S+  +     P
Sbjct: 178 LTITEGKYHQVKRMFAAVGNRVNGLHRERIGGLSL-ELDVGCWRHLSEDEVNRLSTP 233


>gi|293363190|ref|ZP_06610074.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
 gi|292553049|gb|EFF41798.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
          Length = 237

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 67/231 (29%), Positives = 111/231 (48%), Gaps = 8/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K++A+AGIASRR+ E +I +  VK+NG +           D I V+G  + + E+ 
Sbjct: 2   ERIQKLLAQAGIASRRKAEELITKGLVKINGDVAT-IGQKATFNDKISVNGKEIVQ-EKK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ +KP   V T  D   R  V D + +   R+  VGRLD +T G+L+LTNDG L+  
Sbjct: 60  VYFVLNKPSKTVCTLKDNFNRRKVVDLIETNL-RIFPVGRLDYDTTGVLILTNDGELSNK 118

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P    +R YR R    + +D +  L    +I G     +   +DT+        V L
Sbjct: 119 LIHPKYNIIRKYRARLDEPLSKDDIKELNNEQLINGKPSKQVVEQIDTKS-----YLVTL 173

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            +G    +K++F      V  L R+ +    +  +  G  R ++ K ++  
Sbjct: 174 TQGTYHHVKELFSKVGRLVINLKRVEFAGIGVDKIPMGEYRSLNMKEIKTL 224


>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 =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 106/237 (44%), Gaps = 10/237 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAERT 73
           + K++ R G  SR+    ++ Q RV    ++          TD  H  VDG      E  
Sbjct: 8   LEKILQRQGFGSRKLCRTLVRQGRVHAGDVVCTDPDRR-FETDALHFSVDGEDWVYREHL 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G   +H  P   S+VF   P+ F    +  VGRLD +T GLLLL++DG   
Sbjct: 67  -YIVLNKPSGFECSHQ-PQHHSSVFTLFPTQFIQRGLQCVGRLDQDTTGLLLLSDDGDFI 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P  +  +VY +  + ++D+ +L  LK G+ ++      M   L  +      + +
Sbjct: 125 HRYTSPKKKVPKVYEISTNAEIDESQLEKLKNGVQLKDETG--MTKALSCESFDEYRMRL 182

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQLGP 247
            + EGK  ++K++      +V +L R + G F L  +L AG  R +    L +   P
Sbjct: 183 VIAEGKYHQVKRMVAAAGNRVEKLHRSAIGGFALEESLPAGEWRYLDVNDLNKLDEP 239


>gi|323253055|gb|EGA36888.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
          Length = 171

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 42/169 (24%), Positives = 77/169 (45%), Gaps = 3/169 (1%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G V +  DPD  + ++     +  ++ + GRLDI+T GL+L+T+DG  +  
Sbjct: 1   RYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYKLHAAGRLDIDTTGLVLMTDDGQWSHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P     + Y V     V  D      KG+ +          TL+    +   V + +
Sbjct: 61  ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVRLTI 118

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 119 SEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 167


>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 =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 101/305 (33%), Positives = 157/305 (51%), Gaps = 13/305 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---PLRKA 70
           +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D IE+DG         
Sbjct: 28  ERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKIELDGRSFVASALT 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDINT GLLLLT DG 
Sbjct: 87  ESSRVLVYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDINTTGLLLLTTDGE 146

Query: 130 LARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           LA  +  PS +  R Y VR         V    +  L +G++++       ++       
Sbjct: 147 LANAMMHPSYEVEREYVVRVRAPEGEEKVPDSMIERLSRGVLLEDGGAKFDEIERIGGTD 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
           S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL G + E++++ +  
Sbjct: 207 SHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRTRYGKVSLPRELLRGQSVELAQEKVDA 266

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
                 LEE      A         R        V  D       + Q +G  + ++L  
Sbjct: 267 LRAELKLEEG--APSALTLQPVIGQRRAAKSTVHVSRDGRSNAYVNGQTSGADEGRELRR 324

Query: 304 PVHRR 308
             + R
Sbjct: 325 FDNLR 329


>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 =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 111/247 (44%), Gaps = 29/247 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K++A+ G+ SRRE E  I    V V+G  ++   + V     + +D    R   +  
Sbjct: 45  RLAKLMAQKGLCSRREAEAYIQAGDVLVDGERVQADWLKVPVDSDVSLDFRAQRHQNKKV 104

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV----FDNLPSIFSRVIS--------------VGRLDI 116
             + +KP+G V++  + +    V    F+N     SRV                 GRLD+
Sbjct: 105 TLVLNKPLGYVSSQPELNKTPAVRLLTFENECQELSRVKPRQNVEPVALWKMAVCGRLDV 164

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH---GQVDQD---KLNLLKKGIV-IQG 169
           N+ GLLL T DG +A+ L  P     + Y VR       +      K+ +L+ G+   +G
Sbjct: 165 NSTGLLLFTQDGTVAKKLLDPKGGIEKEYLVRVDLNLDPLTDKIRRKIEVLQAGVTSDEG 224

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
           I Y    V +         + V L EGKNR I+++ E    +V  L R+  G  +LG+L 
Sbjct: 225 ITYRAKSVEILNAN----QLRVVLTEGKNRHIRRMCEHVGLRVMALKRVRIGGVKLGSLP 280

Query: 230 AGSTREV 236
            G  R +
Sbjct: 281 VGQWRYL 287


>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 =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 102/240 (42%), Gaps = 15/240 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
              + L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+D
Sbjct: 58  GFSV-LLHKPSGYTCSTKDTG--RLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY V     +  D+  L   G ++++G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDVTLAEDLRGDEAALFASGTLLLEGETKPLLPAELEVLGARQ 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A   + L EG+  +++++F      V  L R   G   L  L AG  R +    L    G
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLDAGHWRPLGPDDLEVLFG 232


>gi|330720777|gb|EGG98994.1| Ribosomal small subunit pseudouridine synthase A [gamma
           proteobacterium IMCC2047]
          Length = 239

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 67/233 (28%), Positives = 111/233 (47%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     S++ V  ++AQ RV V+G +       + +   I +DG  L+      
Sbjct: 7   RLDRFISSKMAISQKAVRPILAQGRVAVDGCVCRDRQQIINTFSRITLDGQILQANTPL- 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V+   D     TV D L      ++  VGRLD N+ GLLLLTND G ++ 
Sbjct: 66  YLMMNKPKGVVSATRDNQY-QTVIDLLDHPERSKLHLVGRLDFNSTGLLLLTNDSGWSQQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  + YRV  +  +DQ  ++    G+    +        + +     ++    V
Sbjct: 125 LMKPDQKVSKRYRVTVNNPLDQQTVDAFAAGMYFAYEDATTRPAGLNI----INDYEAEV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            L EG+  +IK++F   N KV  L RI+ G   L  +L AG +RE+S   + +
Sbjct: 181 TLTEGRYHQIKRMFARCNNKVLALHRIAIGNLLLDPSLSAGQSRELSAAEVTD 233


>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 =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 91/255 (35%), Positives = 131/255 (51%), Gaps = 12/255 (4%)

Query: 43  NGILLERAA-VNVMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           +G +      +NV S+  + +DG  +     + E  R+ +Y+KP G + T  DP+GR+TV
Sbjct: 2   DGKIATLGDRINVHSSVKVRIDGNLINLTQAQKEVCRVLMYYKPEGELCTRHDPEGRATV 61

Query: 98  FDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           FD LP    +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  L  E +  LD      ++      
Sbjct: 182 RIRYGNIKLMKTLPRGGWQEMPLDEVNYLRDLVG--LAPETETKLDVNKQRRQSKAGQIR 239

Query: 273 NIISEVPDDFTRMKK 287
             +    +   R KK
Sbjct: 240 KAVKRYSELSRRYKK 254


>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 =  213 bits (544), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 112/245 (45%), Gaps = 5/245 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTR 74
           + ++I  AG  +R+  +R++    V V+G ++ + A  V  +   I VD + + +     
Sbjct: 3   LGQLIMDAGQVTRKACKRLLKDGHVTVDGQVVTQFATVVDPSWQEIAVDQIVIDRHFGHT 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L HKP G ++ + D     TV D +        +   GRLD +  GL+ +TN+G L  
Sbjct: 63  YYLVHKPKGYLSANKD-QTHPTVIDLIQPADNPGDLAITGRLDRDAHGLVFVTNNGQLHY 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
           + + P     + YR+  +G +D+  +   + G++   G      ++ + +    ++   V
Sbjct: 122 IFQQPKFDIPKTYRITVNGLIDKKMVAQFQAGVIFQDGTICKAARLEIISASPQSSTGLV 181

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            + EG+  ++KK+F     KV  L R   G  ++  L  G  R +++  ++      LL 
Sbjct: 182 TISEGRRHQVKKMFLACGVKVTDLYRQKIGDLRIDDLAVGDYRRLNEAEIQSLKSIFLLY 241

Query: 252 EAQVN 256
           + +  
Sbjct: 242 DKRKE 246


>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 =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 101/250 (40%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  ++     V    +IE+D           
Sbjct: 489 RLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPEQNIEIDQRAQAAQAAQV 548

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++      V                   P     +   GRLDI++ 
Sbjct: 549 TILLHKPVGYVSGQAEDGYEPAVTLITRENHWSGDHSALRFSPQHLRTLAPAGRLDIDST 608

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L    +   + Y VR                + L  L+ G+ + G 
Sbjct: 609 GLLVLTQDGRIAKQLIGEQSDIDKEYLVRVRFGERLTDIDQHFPAESLAKLRHGLELDGA 668

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                 V+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 669 PLKPAMVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALPQ 724

Query: 231 GSTREVSKKI 240
           G  R +S   
Sbjct: 725 GEWRYLSPDE 734


>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 =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 110/242 (45%), Gaps = 8/242 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ +++      S+ + + +  ++ V V+  ++   ++NV     I   G  L    + 
Sbjct: 1   MRIDRLLQVNDFGSKSDRKHLFQRKIVTVDQRVITDGSINVDPGLQIIKVGNHLITGPQE 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             W+ +KP G VT + D   +  VFD L        + S+GRLD  TEGLL+LT +G L+
Sbjct: 61  YYWMMNKPAGYVTANKDIT-KPVVFDLLQAQDRHPDLYSLGRLDRFTEGLLILTTNGPLS 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVT 190
           R L  P     + Y V  +G +  D++    +GIVI         Q+ +     S +   
Sbjct: 120 RRLLQPHQHVAKTYAVEVNGFLGYDQVQAFAQGIVIDQSYQCQPAQLQIIQAGSSASRAQ 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL---REQLG 246
           V L EGK  ++KK+F     KV +L R+S+    L   L  G  R +    L   +  LG
Sbjct: 180 VTLHEGKFHQVKKMFLSLGVKVTQLKRLSFAGIDLDPDLAPGQYRVLKADELALIKAFLG 239

Query: 247 PH 248
           P 
Sbjct: 240 PQ 241


>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 =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 94/236 (39%), Gaps = 8/236 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLR 68
            F    +  ++   G  SRRE   ++ +  V +     +           +  VDGV   
Sbjct: 22  EFQRMNLENILFSQGFGSRRECRALVIRGAVTIGEQRCDDPDAVFEPAGLVFHVDGVRWA 81

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTN 126
              +    + HKP G   +H+ P    +V+  LP       V  VGRLD +T GLLLL++
Sbjct: 82  YRHQA-YLVLHKPPGYECSHA-PQHHPSVYSLLPPALITRGVQCVGRLDADTTGLLLLSD 139

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           DG     L  P  +  + Y       V   +L+ L++G+ + G     + V    +    
Sbjct: 140 DGAFIHRLSSPKHKIPKTYVATTRHPVRDAQLDALRQGVQLHGE--PAVSVARSARLRDE 197

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             + + L EGK  ++K++      +V +L R + G   L   L  G    +    L
Sbjct: 198 HTIELVLTEGKYHQVKRMIAAAGNRVEQLHREAIGALVLPAALAPGQWWWLEADEL 253


>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 =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 61/236 (25%), Positives = 100/236 (42%), Gaps = 15/236 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
                L HKP G   +  D      +++ LP  F      +  VGRLD  T G+LL+T+D
Sbjct: 58  GLS-LLLHKPSGYTCSTKDTG--RLIYELLPPRFRLRAPVLAPVGRLDRETSGMLLMTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G L   +  P +   +VY +     +  ++  L   G +++ G     +   L+      
Sbjct: 115 GALLHRIISPKSALDKVYDITLAEDLRGEEAALFASGSLLLDGETKPLLPAELEVLGPRQ 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           A   + L EG+  +++++F      V  L R   G   L  L +G  R +    L 
Sbjct: 175 A--RLTLHEGRYHQVRRMFAAAGNHVVALHRSRIGGLSLDGLSSGQWRALEANDLE 228


>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 =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 113/232 (48%), Gaps = 10/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +++ V  ++A+ +V V+G +       +    H+ +DG  L+    + 
Sbjct: 7   RLDRFISAKTGINKKHVRLLLAKGQVLVDGEVARDIDQIIDEFSHVCLDGKVLQANAPSY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           + LY KP+G+V+   D   R TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  VMLY-KPVGVVSATVDDKHR-TVIDLLERDDKHSLHIVGRLDLNTSGLLLLTNDGRWSKK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VYRV     +D+  +     G+    + I     ++ +  +        V
Sbjct: 125 LMSPDHKVGKVYRVTLKNPIDESYIAAFAGGMYFAFEDITTQPAKLEIVDE----HTALV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
            L EG+  +IK++F  F   V  L R+S G  +L   L  G +R++S   ++
Sbjct: 181 TLVEGRYHQIKRMFGRFRNPVIGLHRLSVGAIELDPQLAVGQSRDLSMTEIQ 232


>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 =  213 bits (543), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 67/254 (26%), Positives = 105/254 (41%), Gaps = 31/254 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVK--------------VN---G-ILLERAAVNVMS 56
           R+ ++++  G  SRRE    +    V               VN   G   L   +  V  
Sbjct: 4   RLDQLLSSLGYCSRREARDFLRAHTVTISPPPPPPPSAGNSVNVSVGLQPLRDPSAKVNP 63

Query: 57  TDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVI 109
            D    + VDG  L       L + HKP G V +H + +G   V+D LP  +     +V 
Sbjct: 64  LDPARPVFVDGEALDHP-GGLLLMLHKPTGFVCSHDEREG-PRVYDLLPPRWRARNPQVT 121

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQ 168
           S+GRLD +T GLL+LT+   L      P  +  ++YR      V    ++L   G + + 
Sbjct: 122 SIGRLDKDTSGLLILTDRTELVHTYTSPRHKVPKLYRATLDRDVPASLVDLFAAGTLQLD 181

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF-EFFNWKVNRLIRISYGPFQLGT 227
           G        TL  +  +     + L EGK  +++++F       V  L R  +G   LG 
Sbjct: 182 GEKAPCAPATL--RLPAPRVAELVLVEGKYHQVRRMFAAAAGATVLTLHRECFGRLTLGD 239

Query: 228 LLAGSTREVSKKIL 241
           L  G  RE+S+  +
Sbjct: 240 LKPGEYREISESEI 253


>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 =  213 bits (543), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 107/237 (45%), Gaps = 15/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----MSTDHIEVDGVPLRKA 70
           R+ K++A  G  SRRE++ +     ++++G  L  A   V       + + VDG  L   
Sbjct: 8   RLDKLLANLGYGSRREIQALARAGAIRLDGAELADAGDRVALAPDLPERLTVDGESLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
                 + HKP+G+  +H +      V+  LP  + R       VGRLD  T GLLLLT+
Sbjct: 68  PGL-CLMLHKPLGVTCSHKEAG--PLVYGLLPERWRRRDPPLSTVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  Q  + YRV     +   +  +   G +V++G     + V LD +  +
Sbjct: 125 DGALLHRIISPKAQVAKRYRVTLDRPLTGREAEVFAAGTLVLEGEERPLLPVRLDVEDAT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
                V L EG+  +++++F      V  L R   G   L   L AG+ R ++ + +
Sbjct: 185 RC--AVTLTEGRYHQVRRMFAAVGNHVAALHRDRVGGLALPADLPAGAHRVMTAEDV 239


>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 =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 71/248 (28%), Positives = 110/248 (44%), Gaps = 20/248 (8%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
              +R+ K+++  G  SR++V +++    V VNG +     V+V    D + VDG  +  
Sbjct: 1   MKTERLDKILSHHGFGSRKDVRKLLHAGSVAVNGTVCVSPDVHVDPDADELTVDGSSV-P 59

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLL 123
             R    + +K  G+V +  D   R TVFD L   + +      +  VGRLDI+TEGLLL
Sbjct: 60  MRRHIYIMMNKCAGVVCSARDGLHR-TVFDLLDDSYRQEFLGGSLHMVGRLDIDTEGLLL 118

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVI----QGICYGDM 175
           LT DG L   L  P T   + Y +R    V  +           GI I        Y   
Sbjct: 119 LTTDGTLTHRLTSPKTHVTKTYTIRLKNCVPDEAQPLITRRFSDGIHIAPDGDDGEYDCK 178

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTR 234
              L    G+    ++ + EG+  ++K++      +V  L RI+ G   L   L  G+ R
Sbjct: 179 PADLHWFSGTEC--SLVITEGRFHQVKRMIAAAGNEVVYLKRIAIGALLLDPALENGAYR 236

Query: 235 EVSKKILR 242
           E+S + L 
Sbjct: 237 ELSLRELE 244


>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 =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 61/232 (26%), Positives = 100/232 (43%), Gaps = 15/232 (6%)

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  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTND 127
              + L +KP+G V +  D      V+D LP  F     V    GRLD  T G LL T+D
Sbjct: 58  G-VVILMNKPLGYVCSTKDQG--RLVYDLLPDRFRMRKPVLSTIGRLDKETSGALLFTDD 114

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
           G     +  P +   +VY V     ++  +  L   G ++++          LD    ++
Sbjct: 115 GTFLHQVISPKSNVPKVYEVTLDRPMNGSEAALFASGEMMLENEQKPLKPAELDVIDETH 174

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           A   + L EG+  +++++F      V  L R   G   L  +  G  + +S+
Sbjct: 175 A--RLTLHEGRYHQVRRMFAATGNHVTDLARSRIGTLTLEGVDEGQWKILSE 224


>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 =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 94/302 (31%), Positives = 137/302 (45%), Gaps = 13/302 (4%)

Query: 55  MSTDHIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVI 109
                I +DG  +          R+  Y+KP G + T  DP+GR TVFD LP I  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 LAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             G  +E+  +    LRE +     +E  ++LD P  +S    R R   I        R 
Sbjct: 187 PRGGWKELDLQEVNYLRELVELQPEKETLLDLD-PANTSRKRERSRSQKIRR---AVKRH 242

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           ++ ++   G S Q K   P  R     +   +    +     + + + N+ R       R
Sbjct: 243 EERANAPKGRSNQTKRKKPATRGTTTPDSGRSAPATNGKPQATKKPKLNNGRPAKPAKPR 302

Query: 346 SL 347
           S 
Sbjct: 303 SR 304


>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 =  213 bits (542), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 114/267 (42%), Gaps = 39/267 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  ++I Q+R+K+NG         V   D I  DG  ++  E+ 
Sbjct: 1   MRINKLFSNLGICSRKETNKLIEQKRIKINGEYC-VLGQWVEDNDEILFDGERVKSMEK- 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
               ++KP G+  T  + + +  + + + +    V  VGRLD ++EGL++LTNDG  +  
Sbjct: 59  VYLAFYKPKGITCTL-EKNAQGNIGEYI-NYNQYVFPVGRLDKDSEGLIILTNDGVFSNH 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------------QGICYGDMQ--- 176
           +     +  + Y V+     D + L  ++ G+ I              +GI   D +   
Sbjct: 117 ILECDNKHEKEYIVKVDKPFDDNFLLSMRTGVEISAKSGSGVKRISDSEGIVIKDGKDEI 176

Query: 177 ------------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                                  ++ +     + L +G NR+I+K+     +KV  L RI
Sbjct: 177 IMLDEAKNGKMKKDIVKTRPCKVERINEDTFKIILTQGLNRQIRKMSSVLGYKVISLKRI 236

Query: 219 SYGPFQLGTLLAGSTREVSKKILREQL 245
                 L  L  G  R + K+ + E +
Sbjct: 237 RIMNIHLDYLECGEYRLIPKEHIDELM 263


>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 =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 119/249 (47%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT------------ 181
           L    +   R Y ++  G V +  +  ++ G+ I+    G    T  T            
Sbjct: 120 LMH--SDLEREYYLKVKGIVTKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIGFEI 177

Query: 182 --QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L  G  R +   
Sbjct: 178 FGSSGGYTKLRVIINEGKNRELRRFFGHFDVEVMDLKRVAFGVLDLGMLKPGKHRYLENG 237

Query: 240 I---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  212 bits (541), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 101/232 (43%), Gaps = 10/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + K++   G  SR+  +++I    ++++G ++      +     + +V G      E+  
Sbjct: 3   LEKMLQSQGFGSRKHCQQLIKNAAIEIDGQIITDPKYKLKLDALNYKVHGKSFEYREK-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +H       +VFD    +     +  VGRLD +T GLLLLT+DG   +
Sbjct: 62  YIALNKPQGYECSHQ-ATHHFSVFDLFDDVLLNRGIQCVGRLDQDTTGLLLLTDDGQFLQ 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VYR++    V  +++  L++G+ ++           D ++ +   + + 
Sbjct: 121 ALTHPKKHVAKVYRMKTADPVTDEQVQQLEQGVELRNEKGSFA--ATDVKRLAECELQMT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL---GTLLAGSTREVSKKIL 241
           + +G   ++K++      KV  L R   G   L     L+ G    ++ + +
Sbjct: 179 VHQGVYHQVKRMLAAVGNKVESLHRQQIGALDLTGIPDLVEGHWIYLNAEQV 230


>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 =  212 bits (541), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 110/235 (46%), Gaps = 3/235 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           + +    R++K I+ +GI SRR+ +  I    V VNG  +      V  TD ++ DG  +
Sbjct: 88  KPDDGTIRLNKYISNSGICSRRDADIYIKAGSVTVNGKPVSEMGYRVKLTDEVKFDGQNI 147

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTN 126
           +  ++ +  L +KP G +          TV D +  +  + +  VGRL   + GL+L TN
Sbjct: 148 QPYQK-QYLLLNKPKGFIAPRKGERASKTVLDLMQSAGVANLHYVGRLGRQSVGLMLFTN 206

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           D  +A  L  P+ +  ++Y+V        + L  L+ GI I G    D++     + G N
Sbjct: 207 DLEMANKLNNPNLEMRKIYQVALDRSFKHEDLMQLRNGIAINGEVI-DVKEINYVEDGRN 265

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             + + +  GK+  ++ +FE   +++  L R+  G      L  G  R ++++ +
Sbjct: 266 NEIGIEIHSGKDNIVQALFEAVKYEIKVLDRVVLGGLTKKDLPRGHYRALTEQEI 320


>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 =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 56/228 (24%), Positives = 105/228 (46%), Gaps = 3/228 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +A +G+ SRRE +  IA   V VNG  +      V  +D +  DG  L   ++  
Sbjct: 48  RLNRYVANSGVCSRREADIYIAAGSVTVNGKPVIEMGYKVQLSDEVRFDGRLLNPIKKEY 107

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
           + L +KP    T+  D  G  T    + +    +++ VG++D ++ GLLL TNDG L   
Sbjct: 108 VVL-NKPKDFATSTRDGAGNRTAMGLVSNASKAKLLPVGKMDKSSTGLLLFTNDGDLTAR 166

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     +++ V     +    L  +K+GI I+        ++   +      V V +
Sbjct: 167 LNSPKNGLRKIFHVELTKPLKSTDLKRIKEGIEIEESVVRIQDISY-IENAPKTQVGVEI 225

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
              +N  ++++FE  ++ V +L  + Y       L  G  R ++++ +
Sbjct: 226 FSTRNNIVRRLFEKLDYDVVKLDLVVYAGLTKKDLPRGHWRPLTEQEI 273


>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 =  212 bits (540), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 114/241 (47%), Gaps = 10/241 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + ++     SR  +  ++A  RV+VNG +       +   D +  DG  L+ A R R
Sbjct: 14  RLDRFLSARLQMSRSNLRLLLAAGRVRVNGQVERDRQRRIGLFDAVVCDGEILQ-ANRPR 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V+   D +   TV + LP      +   GRLD N+ GL+LLTNDG  +R 
Sbjct: 73  YLMINKPAGVVSATRD-EHHPTVLELLPRGQREGLHLAGRLDFNSTGLVLLTNDGAWSRR 131

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTV 191
           L LP T   + YRV     +  + +    + +            ++T+ +   ++ W   
Sbjct: 132 LSLPETGLWKHYRVSVDKPLSDEDVVSFSQRMWFDFEQIYTQPARLTIRSSFEADVW--- 188

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLL 250
            L EGK  +IK++F     KV  L R++ G  QL   L  G +RE+++   +  L P  +
Sbjct: 189 -LHEGKYHQIKRMFGRTGKKVTALHRLAVGRIQLDAYLAPGESRELTQAEQQTALDPEPV 247

Query: 251 E 251
           E
Sbjct: 248 E 248


>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 =  212 bits (540), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 59/201 (29%), Positives = 93/201 (46%), Gaps = 3/201 (1%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           VNG+++      +   D ++     +   ER    L +KP   VTT  DP  R TV D +
Sbjct: 1   VNGVVVTELGTKIKRADEVKFHDQMVS-IERKIYILLNKPKDTVTTSDDPQARRTVMDLV 59

Query: 102 PS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                 R+  VGRLD NT G+LLLTNDG LA  L  P     ++Y V     V +  ++ 
Sbjct: 60  KGACDERIYPVGRLDRNTTGVLLLTNDGDLASKLTHPKFLKKKIYHVHTDKNVTKADMDQ 119

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  GI +         ++  T       V + +  GKNR ++++FE   +KV +L R+ +
Sbjct: 120 IAAGIQLDDGEIHADAISY-TDDVRRDEVGIEIHSGKNRIVRRIFESLGYKVVKLDRVFF 178

Query: 221 GPFQLGTLLAGSTREVSKKIL 241
                  L  G  R +S++ +
Sbjct: 179 AGLTKKGLRRGEWRYLSEQEV 199


>gi|289671226|ref|ZP_06492301.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 291

 Score =  212 bits (540), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 95/262 (36%), Positives = 147/262 (56%), Gaps = 11/262 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K  +  +     +R+ KV+A+AG+ SRR +E+ IA   +KVNG + +   ++V S D I
Sbjct: 15  LKRDSATEAPKLEERLHKVLAQAGLGSRRALEQRIADGLIKVNGAVAQT-GMSVRSGDKI 73

Query: 61  EVDGV---PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDI 116
           E+DG         E +R+ +Y+KP G VTT  DP+GR TVF++LP+   SR I++GRLDI
Sbjct: 74  ELDGRSFVASALTEPSRVLIYNKPEGEVTTREDPEGRPTVFESLPALKGSRWIAIGRLDI 133

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGIC 171
           NT GLLLLT DG LA  +  PS +  R Y VR         V    +  L +G++++   
Sbjct: 134 NTTGLLLLTTDGELANAMMHPSYEVEREYVVRVRAPEGEEKVSDAIIERLSRGVLLEDGG 193

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++       S+ W  V ++EG+NRE+++++E    +V+RL R  YG   L   LL 
Sbjct: 194 AKFDEIERIGGTDSHDWFRVVVKEGRNREVRRLWESQGCQVSRLKRSRYGKISLPRELLR 253

Query: 231 GSTREVSKKILREQLGPHLLEE 252
           G + EV+++ +        LEE
Sbjct: 254 GQSVEVAQEKVDALRAELKLEE 275


>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 =  212 bits (540), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 59/225 (26%), Positives = 102/225 (45%), Gaps = 8/225 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV ++GI+L+ A  +  + D H +VDG       +  
Sbjct: 3   LETILYSQGFGSRRQCRALVEAGRVSIDGIVLDDADADFATDDLHFDVDGTRWPYRAQA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G   +  DP    +VF  LP  F    V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLVLNKPAGYECSR-DPQHHLSVFSLLPPQFGARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L  L++G+++ G       V    ++  +  + + 
Sbjct: 121 AYTSPKKKVPKTYLAEVKHALDDRQLAALREGVLLHGEPKPIAAVAARARELRS--LELT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           + EGK  ++K++      +V  L R   G + L   L  G  R +
Sbjct: 179 VLEGKYHQVKRMVAASGNRVEALHRERVGGYTLPADLAPGGWRWL 223


>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 =  212 bits (540), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 120/249 (48%), Gaps = 20/249 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 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---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>gi|218459923|ref|ZP_03500014.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli Kim 5]
          Length = 199

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 68/196 (34%), Positives = 102/196 (52%), Gaps = 2/196 (1%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINT 118
           I VDG+ +  AE     + +KP GLVTT  DP+GR TV+D L       +  VGRLD  +
Sbjct: 4   IRVDGLVI-AAEAKIYLMLNKPRGLVTTRHDPEGRPTVYDCLKDFEIPHLSPVGRLDKAS 62

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           EGLLL TND   A++L  P T   + Y V+    +D + +  +  GI   G       V 
Sbjct: 63  EGLLLFTNDTEFAQILLDPITHVTKTYHVQIDRIMDDEAIAAMTSGIRHDGELLTATAVR 122

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              Q   N+W+ V L EG+NR+I+++ E    +  RL+R++ G  +LG L  G+ R ++ 
Sbjct: 123 RLRQGDRNSWIEVELDEGRNRQIRRMLEALGTECLRLVRVAIGGLELGELPKGAVRALTA 182

Query: 239 KILREQLGPHLLEEAQ 254
             L+       +E A+
Sbjct: 183 AELQALHRSAGMERAR 198


>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 =  211 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 104/230 (45%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G++T   DP  +STV D +        +  VGRLD +T GLLLLT DG L 
Sbjct: 61  DYLM-NKPAGVITATEDPT-QSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y       +  D    L+ GI ++       QV +         + +
Sbjct: 119 HALLSPNRHIAKTYAATLAKTLTADMKQQLETGIDLKDFTTAPAQVVVLPDTDGK-RIQI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++    + +V  L RI+ GP  L   L AG  R ++   
Sbjct: 178 TITEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYRALTDDE 227


>gi|171914565|ref|ZP_02930035.1| putative pseudouridylate synthase [Verrucomicrobium spinosum DSM
           4136]
          Length = 235

 Score =  211 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 66/234 (28%), Positives = 109/234 (46%), Gaps = 11/234 (4%)

Query: 16  VSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +S++IAR  G+  R    + IA +RVKV   ++      V     + +D   +++ E   
Sbjct: 3   LSRLIARHKGMG-RTAAMQAIAGKRVKVEDQVVTDGQHEVDRFSTVWLDDTLVQEGESAL 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
             + HKP+G ++   DP    TV D +       +   GRLD ++ GLLLLTNDG  +R 
Sbjct: 62  YIMLHKPVGYLSATRDPQH-PTVIDLIDHPARETLHIAGRLDRSSSGLLLLTNDGRWSRR 120

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VY V     +  + + L  KG     + +     ++ +  ++ +     V
Sbjct: 121 LTEPGEKVDKVYLVETAEPIAPEAVELFAKGFYFHTEDLTTLPAELGILGERLA----RV 176

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            L EG+  +IK++F     +V  L R S G   L   L  G  RE+ + +LR Q
Sbjct: 177 TLHEGRYHQIKRMFHRVGNRVISLHRESIGSLVLPVELFPGQWREIRRDVLRSQ 230


>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 =  211 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 71/263 (26%), Positives = 117/263 (44%), Gaps = 22/263 (8%)

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  IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------S 106
           I V+G  + K       +  +KP G + +  +     +V                     
Sbjct: 204 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEES--KSVVSLFNDYLKGWNKIQPGLPKP 261

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           R+ +VGRLD+ T GL+++TNDG  A+ L  PS+   + Y V   G V +  L  + +G  
Sbjct: 262 RLFTVGRLDVATAGLIIVTNDGEFAQKLAHPSSNVTKEYVVTIDGAVHKKHLIAISEGTK 321

Query: 167 IQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           I G+      V     +       + + + EG+N E++++ +    +V  L R+  G F+
Sbjct: 322 IDGVMCIPDLVEPLAAQSDTRKTRLRIVVHEGRNHEVRELVQNAGLQVYALKRVRIGRFR 381

Query: 225 LG-TLLAGSTREVSKKILREQLG 246
           L   L  G   E+ +  ++   G
Sbjct: 382 LPADLGIGKFVELKQADIKALDG 404


>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 =  211 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 112/233 (48%), Gaps = 3/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K +A +G+ SRR+ +  I+   V VNG  +      V  TD ++ DG  L  
Sbjct: 41  NPDLIRLNKYVANSGVCSRRDADIYISAGNVTVNGKPITEMGYKVRKTDEVKFDGRLLN- 99

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDG 128
            E+    L +KP    TT  D  G+  V   +  +  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|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 =  211 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 90/237 (37%), Gaps = 10/237 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTR 74
           + +++   G  +R+    +I    V +NG  +        ++D    +     R  +   
Sbjct: 6   LDRILQSQGFGTRKYCRNLIEDGEVSINGESVTDYRAAFDTSDLEFTIFDEVWRYRQ-HV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP     +   P     V   LP  F    +  VGRLD +T G+LL+++DG    
Sbjct: 65  YIVLNKPANFECSRK-PSHHPGVLTLLPEQFTWRELQPVGRLDHDTTGMLLMSDDGPFIH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P     +VY    H  V  + +  L  G+ +       +        G+N  + + 
Sbjct: 124 AQSSPKRHIPKVYVATTHDPVTPELIAQLLGGVQLHDEP-APLAAQTCRMLGAN-ELEIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVSKKILREQLGP 247
           L +GK  ++K++        + L R++ G   L +L    G    ++   L   L P
Sbjct: 182 LEQGKYHQVKRMLAAAGNHCSALRRVAIGALTLESLELDEGEWAYLTDAQL-ALLAP 237


>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 =  211 bits (539), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 56/230 (24%), Positives = 101/230 (43%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + +A      R+ V  M+   RV V+ ++++   + +     + VDG  L+  +   
Sbjct: 7   RLDQFLAGKLQVPRKSVRFMLLAGRVSVDNMIIKDMDLQLDEFSQVCVDGAALQNNQPC- 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP+G+V+   D   ++ +          +   GRLD+N+ GLLL+TND   +  L
Sbjct: 66  YLMLNKPVGVVSATKDDIHKTALELLHGIKLEMLHIAGRLDLNSSGLLLITNDARWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     +D+  ++    G+    +GI        +     S     V 
Sbjct: 126 MSPDNKVSKKYLVTLANPIDETYISAFAGGMYFAFEGITTQAAGFEIL----SEYQARVS 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           L+EGK  +IK++F  F   V  L R + G   L  TL  G  R ++   +
Sbjct: 182 LKEGKYHQIKRMFGRFRNPVIGLHREAIGELVLDETLAPGEFRHLTPAEI 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 =  211 bits (539), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPEKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+V  + +V    +   + GIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQVVVNERVTPADVTAFENGIVFADGYQCKPADLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVTALKRLSMGPLELDEQLGVGEYRSLTLAEMKKL 233


>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 =  211 bits (539), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 65/237 (27%), Positives = 105/237 (44%), Gaps = 15/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----VDGVPLRKA 70
           R+ +++A  G ASRRE++ +    R++++G     A   +  T  +E    VDG  L   
Sbjct: 8   RLDRLLANMGYASRREIQMLARNGRIQLDGAAFHDADKRIALTPDLETRLVVDGEALDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
                 + HKP+G+  +H +      V+D LP  + R       VGRLD  T GLLL+T+
Sbjct: 68  PGFA-LMLHKPLGVTCSHKEAG--PLVYDLLPQRWRRRDPAISTVGRLDKETSGLLLMTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P     + YRV     +  D+  L   G ++++G         L+     
Sbjct: 125 DGKLLHRIISPKRHVAKRYRVHLARSMTGDEAALFAAGTLMLEGEEKPLAPAELEVVGPQ 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            A + V   EG+  +++++F      V  L R S G   L   L  G+ R +    L
Sbjct: 185 EALLEV--HEGRYHQVRRMFAATGNHVEALHRESVGGLSLPADLAPGAIRRLDDADL 239


>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 =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 54/225 (24%), Positives = 97/225 (43%), Gaps = 10/225 (4%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGV-PLRKAERTR 74
           K +   GI +R+  + ++    V++NG  +     ++       + +DG   +       
Sbjct: 5   KYLQAQGIDTRKGCQWLVKHGLVQINGATVPDEKADIAPDSVQTLTIDGEDAVVIPLPYF 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             L +KP G  T+H  P    +VF  LP       + +VGRLD +T G+LL+TNDG    
Sbjct: 65  YILLNKPAGYETSHK-PRDYPSVFSLLPDQVRAADIQAVGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P  +  ++YR       D      L+ G+++         Q     +      + +
Sbjct: 124 RMTSPKHKVDKIYRATLKHAADPSLCAQLQAGVLLHDDNETVSAQA---AELHDAHTLIL 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +REGK  ++K++      +V  L R+ +GP+    L AG  R +
Sbjct: 181 TIREGKYHQVKRMVAAAGNRVEHLHRLQFGPWDTQDLQAGEWRFI 225


>gi|167585734|ref|ZP_02378122.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 238

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 96/231 (41%), Gaps = 10/231 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAERTR 74
           +  ++   G  SRR+   ++   RV V G                + VDGV      R  
Sbjct: 3   LESILFTQGFGSRRQCRGLVDAARVAVAGAPCTDPDAEFDTDGLVVSVDGVAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPTPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTV 191
               P  +  + Y       +D  +L+ L+ G+ + G       +  +         + +
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDAQLHALRTGVQLHGE---PKPIAAVAADARDAHVLAL 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + EGK  ++K++    + +V  L R S G F L   L  G+ R +S+  L
Sbjct: 178 TVLEGKYHQVKRMVAAASNRVEALHRESIGGFALPADLEPGAWRWLSEADL 228


>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 =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 102/234 (43%), Gaps = 15/234 (6%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAERT 73
           + K++   G  SR+  +++I    V +   + +    N   T+H+  EV G      E  
Sbjct: 3   LEKILQSQGFGSRKYCQQIIKNGSVTIENQICDNPKQN-FPTEHLCFEVFGEEYLFREN- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G   +H       +VF   P I     +  VGRLD +T GLLLLT+DG   
Sbjct: 61  VYIVLNKPKGYECSHQ-ATHHKSVFSLFPEILLHRGIQCVGRLDQDTTGLLLLTDDGQYL 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWV 189
           + L  P     +VY V     + Q++   L++G+ ++     Y    V L     S   +
Sbjct: 120 QALTNPRKHVPKVYHVTTADPITQEQKQALEQGVELRNEKGIYAATDVHLF----SEHQL 175

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV--SKKIL 241
           ++ + +G   ++K++      KV  L R   G F+L  +  G    +  ++K L
Sbjct: 176 SMTIHQGIYHQVKRMLAAVGNKVEDLHRHQVGLFELPKIPEGEWLYLSATQKQL 229


>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 =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 95/233 (40%), Gaps = 17/233 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K+IA  G  SR+E++  I    V   +G  L+  A +    + I  D  PL  A  
Sbjct: 1   MRLVKLIANLGYGSRKEIQTAIKNGWVTDRDGNTLK--ATSQTPHEDILFDDEPLDPAPG 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDG 128
             L + +KP+G   + +D      V+D LP  +     V    GRLD  T GLLL T+DG
Sbjct: 59  MVLAM-NKPLGYTCSTNDQG--KLVYDLLPDRYRMRKPVLSTIGRLDKETSGLLLFTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---IVIQGICYGDMQVTLDTQKGS 185
                +  P     +VY V     +  ++  L   G   +  +        + +      
Sbjct: 116 TFLHKVISPKANVGKVYEVTLDRPMKGNETALFASGEMMLESEDKPLKPAMLEVL----D 171

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +    V L EG+  +++++F      V  L R   G   LG L  G  R + +
Sbjct: 172 DTHARVILHEGRYHQVRRMFAATGNHVTNLSRTQIGGLSLGCLEDGQWRMLDE 224


>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 =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLTLAEMKKL 233


>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 =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 113/238 (47%), Gaps = 8/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A  G  SR +V+ ++  ++V VNG    +A   +    D +EV+G  +   E 
Sbjct: 1   MRLDKFLAETGFGSRTQVKSLLKTKKVCVNGKKESQAKKQINPNLDRVEVEGQEVLYEE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
              ++ +KP G+V+   D     TV D L +   +  V  VGRLD +T GLLLLTN+G L
Sbjct: 60  FVYYMLNKPKGVVSATQD-KVHQTVLDLLDATAKQKEVFPVGRLDKDTHGLLLLTNNGNL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAW 188
           A  L  P     +VY     G +    +   KKGI +          ++     + S + 
Sbjct: 119 AHRLLSPKKHVNKVYVADVDGLMTNQDIEAFKKGIHLSDHQCQPALLEILALDYEKSQSR 178

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
           V + ++EGK  ++K++      +V  L R+  GP QL + L  G+ R++    +   L
Sbjct: 179 VKIVIKEGKFHQVKRMVLACGKEVRDLQRLEMGPLQLDSKLALGAFRKLENTEIEALL 236


>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 =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 70/233 (30%), Positives = 113/233 (48%), Gaps = 2/233 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ +A  G+ASRR  E +I   RVKV  +     A+++   D + VDG  +   +++
Sbjct: 1   MRLNRYLALCGVASRRRSEDIIRTGRVKVENVTATDPAMDISEEDQVSVDGKSVCF-QKS 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G V    D    + V    P     R+  VGRLD  +EGLL+LTNDG    
Sbjct: 60  VYIVMNKPKGYVCAVEDRFYPTVVGLLSPDLRAKRIYPVGRLDRQSEGLLVLTNDGDFCN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  PS  + + Y V     + ++ L   +KG+ I G     + + +  +K +  WV++ 
Sbjct: 120 SLIHPSAGYQKTYEVLLGEALTEENLFSWRKGVPINGKVVSPVSIRVMDRKPARRWVSIV 179

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           L+EG  REI+ +   F+  VN L R   G  +L  L +G    V  + L   +
Sbjct: 180 LQEGLKREIRIMASHFSLSVNVLFRRKVGRMELRKLKSGEYCVVELQRLWRLI 232


>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 =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/232 (28%), Positives = 116/232 (50%), Gaps = 10/232 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +++ V  ++A+ +V V+G +     + +    H+ +DG  L+    + 
Sbjct: 7   RLDRFISVKTGINKKYVRLLLAKGQVLVDGEIARDIDLIIDQFSHVSLDGQVLQANAPSY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           + LY KP+G+V+   D D   TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  VMLY-KPVGVVSATID-DKHKTVIDLLDREDKHSLHIVGRLDLNTSGLLLLTNDGRWSKK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  +VYRV     +D+  +     G+    + I     ++ +      +    V
Sbjct: 125 LMSPQHKVDKVYRVTLKNPIDESYIVAFAAGMYFAFEDITTQPAKLEIV----DDHTALV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            L EG+  +IK++F  F   V  L R+S G  +LG  L  G +R++S+  ++
Sbjct: 181 TLVEGRYHQIKRMFGRFRNPVIGLHRLSVGTIELGLQLAVGESRDLSESEIQ 232


>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 =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 57/227 (25%), Positives = 111/227 (48%), Gaps = 3/227 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +++  ++++GI+SRR  + +I    +KVNG ++++    + + D ++     L   E+  
Sbjct: 8   KLNSYLSKSGISSRRNADNLIKSGNIKVNGKIIKKLGYIISNNDIVKYKDKRL-YPEKKI 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP G V++    D  + V D +   +  + S+GRLDI T G+LL TNDG L+  L
Sbjct: 67  YLILNKPKGYVSSMKKQDNNNIVLDLIKINYK-IFSIGRLDIETSGVLLFTNDGYLSNKL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             P     ++Y V  + +++   L  +K     +        ++   +   N  + + L 
Sbjct: 126 THPKFNIKKIYHVVLNKKINNKDLLKIKNSFSFKEGKLKIYNISYIKKLPKNN-IKLELH 184

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            G N+ +K++F    +KV  L RI++G   +  L  G  R + K  +
Sbjct: 185 IGWNKIVKRIFNKIKYKVLYLKRINFGGITIKGLKIGEYRYLKKNEI 231


>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 =  211 bits (537), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 64/238 (26%), Positives = 117/238 (49%), Gaps = 9/238 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKAE 71
            R+ + ++  GI+SR E+++ I + +V +NG      ++ V   +   +   G      E
Sbjct: 1   MRLDRFLSEMGISSRSELKKEIRRGQVLLNGEEARDPSLFVDPENPPVVLYRGREFHY-E 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGL 130
               ++ +KP G+++   D   +STV D +     R +  VGRLD + EGLLL++NDG L
Sbjct: 60  AFSYYMMNKPAGILSASRDKK-QSTVLDLIQEDRRRDLFPVGRLDKDCEGLLLISNDGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV 189
           +  L  P +   ++Y VR  G++ +    L ++G+     +     ++T+ + +   +  
Sbjct: 119 SHRLLRPKSHVPKLYFVRVSGRLTESDAELFRRGLRYDEDLTALPAELTILSAEDIISEA 178

Query: 190 TVGLREGKNREIKKVFEFFNWK--VNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            V + EGK  +IKK+F     K  V  L RI+ GP +L   L  G  R++ +  +   
Sbjct: 179 CVRITEGKFHQIKKMFLALPKKKEVLFLKRIALGPLRLDEALKPGEYRKLKEAEISAL 236


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 62/248 (25%), Positives = 110/248 (44%), Gaps = 23/248 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK ++  G+ SRRE +  I +  V+V+G+++      V+    + V+     +  
Sbjct: 3   EPVRLSKRMSELGLCSRREADEWIEKGWVRVDGVVVSVLGSKVLPHQKVTVERQASAEQA 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDI 116
           +    L +KP+G V+  ++   +  V                   P     ++  GRLDI
Sbjct: 63  QRVTILLNKPMGYVSGQAEDGYKPAVVLVNEQSRWAEDQTEMRFHPRQLKSLVPAGRLDI 122

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH----GQVDQDKLNLLKKGIVIQGICY 172
           ++ GLL+LT DG +A+ L    +   + Y VR      G++ +  L  L  G+++ G   
Sbjct: 123 DSVGLLVLTQDGRIAKQLIGEDSAVDKEYLVRVQYTRPGKLPESDLKRLNHGLIMDGKPL 182

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
              +V    +      +   LREGK R+I+++ +    KV  L R+  G  +LG L  G 
Sbjct: 183 RPAKVVWQNED----QLRFTLREGKKRQIRRMCDMVGLKVIGLKRVRIGGVKLGELPTGQ 238

Query: 233 TREVSKKI 240
            R +    
Sbjct: 239 WRYLRPDE 246


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 99/234 (42%), Gaps = 8/234 (3%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE 71
           P  + K++   G  +RR    ++    VKVNG+L E     +      + V+       E
Sbjct: 4   PISLEKILFSQGFGTRRYCSDLVYADLVKVNGVLAEDPEERIATEGLVLTVEDRDWEYHE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGG 129
           +     ++KP     +H       +V+  LPS F    +  VGRLD +T GLLL+++DG 
Sbjct: 64  KA-YIAFNKPENYECSHK-TTHHPSVYSLLPSPFVERGLQCVGRLDFDTTGLLLISDDGQ 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
               +  P     +VY +     + Q +++ L  G+V+         V     + +   +
Sbjct: 122 FIHKMTTPKKNIGKVYEITTPEPITQSQIDHLLNGVVLDDDPKPCFAVAC--NQLTEYTL 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EG+  ++K++       V +L R   G + +   L  G  R +  + L+
Sbjct: 180 AMTIVEGRYHQVKRMMAAVGNHVAKLHRTEIGAYLMPTDLAEGEWRWLYPQDLQ 233


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 65/230 (28%), Positives = 104/230 (45%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G++T   DP  +STV D +        +  VGRLD +T GLLLLT DG L 
Sbjct: 61  DYLM-NKPAGVITATEDPT-QSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y       +  D    L+ GI ++       QV +         + +
Sbjct: 119 HALLSPNRHIAKTYAATLAKTLTADMKQRLETGIDLKDFTTAPAQVVVLPDTDGK-RIQI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++    + +V  L RI+ GP  L   L AG  R ++   
Sbjct: 178 TITEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYRALTDDE 227


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 106/240 (44%), Gaps = 18/240 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
             R++K++A  G  SRRE  R I Q  VKVNG++   A   V  TD +E+    +    +
Sbjct: 7   SIRLNKLLAHQGWCSRREANRFIEQGLVKVNGVVSRDA--RVAPTDTVELLPQAVTVQAQ 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +  L HKP+G V++  + D        +     P       + GRLDIN+ GLL+LT  
Sbjct: 65  QKTILVHKPVGYVSSQPETDSIPQEQASSRRLFHPRTQLGWATAGRLDINSTGLLVLTQS 124

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQV-------DQDKLNLLKKGIVIQGICYGDMQVTLD 180
           G +A+ L  P  +  + Y VR                L  L+ GI   G     + V   
Sbjct: 125 GRVAKTLIGPDVRVDKEYLVRVRPSPFFDRNQSTAAVLERLRDGIRDAGELLHAVSV--- 181

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            ++ +   +   L EGK+R I+++      +V+ L R+  G   LG L  G  R ++   
Sbjct: 182 -ERVNTDQLRFVLHEGKHRHIRRMCRAVGLEVDGLKRVRIGEIVLGNLPVGQWRYLAPHE 240


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLTLAEMKKL 233


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 102/244 (41%), Gaps = 19/244 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
            ++  ++   G  +RR    +I Q RV ++        +   +T  I+V+G+ LR     
Sbjct: 1   MQLQDILYSQGFGTRRICAGLIQQGRVAIHATGTLEPTICQDATQDIDVEGLVLRVQGVD 60

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINT 118
              +     + HKP G   +   P    +++  LP+   +         V +VGRLD +T
Sbjct: 61  WPYQPRAYVMLHKPAGTECSQK-PSAYPSIYTLLPAPLRQRPSKGSVDGVQAVGRLDQDT 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG     +  P     +VYRV     V +++++ L +G+V+           
Sbjct: 120 TGLLLLSDDGQFIHRMSSPKKHVPKVYRVTAKHPVTKEQIDRLLEGVVLDDDPRPVRAAA 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
                     + + L EGK  ++K++      +V  L R   G   L   +  G  R + 
Sbjct: 180 CALVDA--HVLDLTLTEGKYHQVKRMIAAVGNRVEALHRSHIGRLALPADMQPGEWRWLG 237

Query: 238 KKIL 241
           ++ L
Sbjct: 238 EEEL 241


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/234 (31%), Positives = 110/234 (47%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K +A  G+ SRR+VE  I   RV   G  +     +V   + + VD V +R  ER 
Sbjct: 1   MRLNKYLALCGVGSRRKVEEFIFAGRVVCGGYQVTEPGYDVPDGEIVTVDDVEVR-PERK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + HKP G +   SD      + D LP  +   R+  VGRLD+ +EGLL+LTNDG  +
Sbjct: 60  IYMVLHKPRGYICAVSD-RNYPVILDLLPREYDYYRLFPVGRLDLQSEGLLMLTNDGDFS 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  P     + Y V      ++ ++  L+ G V +G     + V    ++    W+  
Sbjct: 119 QEMIHPRAGITKEYEVLLDRMPNEREMRQLRDGTVFEGKRLHPVGVDFLQREPEGRWLRF 178

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            L EG  REI+ + E    KV  L R   G  +L  L +G  RE S   LR  +
Sbjct: 179 VLNEGVKREIRLIAEGAGLKVQVLFRRRIGRMELRHLKSGCAREYSADQLRRMI 232


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 109/264 (41%), Gaps = 27/264 (10%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  +L L +KP  ++   +D  GR T+ D +      + + GRLD ++EGLLLL
Sbjct: 35  KPELAPEDRKLLLLNKPYMVLCQFTDEAGRETLKDYIKE--PGIYAAGRLDRDSEGLLLL 92

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  + Y V+  G   ++KL  L+ G+ +           +     
Sbjct: 93  TNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEKLAALRAGVELNDGMTLPAGARIMDEPA 152

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + ++   +W+ + + EG+NR+++++         RLIR + G + L  L  
Sbjct: 153 VWPRNPPIRERKEIPTSWLEIKIIEGRNRQVRRMTAHIGHPTLRLIRYAIGDWTLDGLAP 212

Query: 231 GSTREVSKKIL-----------REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           G +R +    L             + G H  + A+   DAP  +S+    +RP       
Sbjct: 213 GESRSLPAPELTPSSSRSPRPASSRSGAHTAKPAKPAGDAPRRASQPRQDERPRSTHPTE 272

Query: 280 DDFTRMKKNSSQKNGLSKQKKLAT 303
              T       + +G    ++ A 
Sbjct: 273 RAATNPTGGKHRSSGRGTARRPAR 296


>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 =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 62/250 (24%), Positives = 105/250 (42%), Gaps = 28/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++  G+ SRRE +  I +  V V+G  ++     V     IE+D           
Sbjct: 402 RLSKLMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQRIEIDPAAEAAQASQV 461

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINTE 119
             L HK +G V+  ++   +  +    P                   ++   GRLDI++ 
Sbjct: 462 TVLIHKTVGFVSGQAEDGYQPAITLVTPENRWEGDRSNIRFSVAHLRQLAPAGRLDIDST 521

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKGIVIQGI 170
           GLL+LT DG +A+ L    ++  + Y VR                + L LL+ G+ +  +
Sbjct: 522 GLLVLTQDGRIAKRLVGGHSEIDKEYLVRVAFGEHTTDVESHFPPESLALLRHGLSLDDV 581

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                QV+    +     +   LREGK R+I+++ E    +V  L R+  G   LG L  
Sbjct: 582 PLKPAQVSWQNGE----QLRFVLREGKKRQIRRMCELVGLEVIGLKRVRMGHVMLGALPP 637

Query: 231 GSTREVSKKI 240
           G  R ++   
Sbjct: 638 GQWRYLAADE 647


>gi|294340758|emb|CAZ89150.1| putative ribosomal large subunit pseudouridine synthase [Thiomonas
           sp. 3As]
          Length = 300

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 63/265 (23%), Positives = 103/265 (38%), Gaps = 38/265 (14%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---MSTDHIEVDGV 65
           +     R+SK ++  G+ASRRE +  I +  V ++G         V   +    I +   
Sbjct: 39  DPAAEVRLSKRMSELGLASRREADDWIERGWVLLDGTPA-VLGTKVAGNLPASRIVIRKA 97

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD---------------NLPSIFSRVIS 110
              +       L HKP+G V+  ++      V                   P+    +  
Sbjct: 98  AQHRQAAQVTILLHKPVGYVSAQAEHGYTPAVALIKAENRWAECEAPQPFSPAHLRHLAV 157

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------HGQVDQ 155
            GRLDI++ GLL+LT DG +AR L    +   + Y VR                     +
Sbjct: 158 AGRLDIDSTGLLVLTQDGRIARQLIGEDSAVEKEYLVRVSLTDAPARNGAEEDVQAAFTE 217

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
            +L LL+ G+ +        QV       +   +   LREGK R+I+++ E    +V  L
Sbjct: 218 SRLALLRHGLKLDDQPLRPAQVEW----INPQQLRFVLREGKKRQIRRMCELVGLRVTGL 273

Query: 216 IRISYGPFQLGTLLAGSTREVSKKI 240
            R+  G  +LG L  G  R + +  
Sbjct: 274 KRVRIGGLRLGALPLGQWRYLREDE 298


>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 =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 61/221 (27%), Positives = 100/221 (45%), Gaps = 13/221 (5%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89
           E   +I    V+VN  ++      V   D I V G  +  ++    ++ +KP G +  + 
Sbjct: 27  ECRTLIKHGFVEVNNQVINDHRYVVHDDDKINVFGKAIH-SQPFVYYMMNKPKGYICANY 85

Query: 90  DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
           D      V D +    +  I VGRLD +T G LLLTND  + + L LP     + Y V  
Sbjct: 86  D-KNHLCVVDLIER--NDCICVGRLDKDTTGFLLLTNDKSIVKALLLPQNHQPKTYLVTT 142

Query: 150 HGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
              +D++ +   + GIVI   IC    Q+ L     +     + L EGK  ++KK+F   
Sbjct: 143 RFPIDENSIYRFEMGIVIDQDICCLPAQLEL----INTHQCYLTLHEGKYHQVKKMFLSC 198

Query: 209 NWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI---LREQL 245
             +V  L RI++    L  +L  G  R++++     L+E +
Sbjct: 199 QNEVVDLKRIAFAGLVLDASLGYGEYRQLNQDEFQKLKELV 239


>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 =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 105/250 (42%), Gaps = 29/250 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A  G+ SRRE +  + +  V+VNG L      NV++ D I V+     + ++  
Sbjct: 345 RINKRLADMGLCSRREADEWVDKGWVRVNGELA-VMGQNVVAADRITVEREARERQDQQV 403

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINTE 119
             L HKP+G V+  ++      V    P                    +   GRLDI++ 
Sbjct: 404 TILIHKPMGYVSGQAEDGHEPAVVLVTPQNHWNQDTSRTRFNFAQLKGLAPCGRLDIDSV 463

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF---------HGQVDQDKLNLLKKGIVIQGI 170
           GLL++T DG +AR +    ++  + Y VR                ++L  L  G+ + G 
Sbjct: 464 GLLVMTQDGRVARQIIGEDSEMDKEYLVRVTYGDRDIDVQSVFPAEQLARLCHGLSLDGE 523

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +V     +     +   L EGK R+I+++ E    +V  L RI  G   LG L  
Sbjct: 524 ALKPAKVDWQNPE----QLRFVLTEGKKRQIRRMCELVGLRVVGLKRIRIGRVTLGNLPV 579

Query: 231 GSTREVSKKI 240
           G  R +    
Sbjct: 580 GQWRYLGAHE 589


>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 =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 136/288 (47%), Gaps = 19/288 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           +       R+++ I+     SRRE + +I   RV +    +E  A  V   + + +DG  
Sbjct: 4   IDPKEPTMRLNQYISHHSKYSRREADELIKAGRVNIEKRKIENLATQVKEDERVFIDGKF 63

Query: 67  LRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 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 TDSPKVAKALM--ESELERVYHLKIDKRVSPEMIKAMEEGLVLEDASAGGHEKSEIKSMS 181

Query: 174 ---DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +     +++ + V ++EGKNRE+++ F  F  KV  L R+SYG   L  L  
Sbjct: 182 FSPFAGFEVAKDSPTHSKIKVAIKEGKNRELRRFFAHFGAKVLDLKRVSYGWVSLNALPD 241

Query: 231 GSTREVSKKILREQLG-PHLLEEAQVNLDAPIYSSETLVRDRPNIISE 277
           G  R +++    +       L++++     P  +S        +  + 
Sbjct: 242 GKNRYLNRSEYNKLHAFMKELQKSEEKEKKPRKASYRSATKSDSARAP 289


>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 =  210 bits (535), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 72/236 (30%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDERLAVGEYRSLTLAEMKKL 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 =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 59/283 (20%), Positives = 110/283 (38%), Gaps = 60/283 (21%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K+ +  GI SR+E  R+I ++R+ +NG         V  +D I  DG P+   E+ 
Sbjct: 1   MRINKLFSNYGICSRKETNRLIEEKRIIINGRYCVE-GQWVNDSDEIIFDGKPISTVEK- 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP+G+  T  +    + +          +  VGRLD +++GL+L+TNDG +A  
Sbjct: 59  VYIVLNKPVGITCTAENKVSDNIIS--YMKYPHYIFPVGRLDKDSQGLILMTNDGEVANR 116

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------------------ 169
           +        + Y V+ +   D + L  +  G+ I G                        
Sbjct: 117 ILESDNMHEKEYLVQVNKNFDDEFLKRMSNGVEITGNKSSGVRRISDKLGLYKKIEDKEI 176

Query: 170 ----------------------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                                       +     QV    ++  +    + L +G N++I
Sbjct: 177 LLGEEDPGDSSIVQLKELKNIEREQNKFVKTRPCQV----ERVDDNTFKIILTQGMNKQI 232

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +K+     +KV +L RI     +L  L  G  R + +  ++  
Sbjct: 233 RKMSGALGYKVIKLERIRIMNIKLNDLETGKWRYLEENEMKSL 275


>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 =  210 bits (534), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEHLAVGEYRSLTLAEMKKL 233


>gi|289677286|ref|ZP_06498176.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
           syringae pv. syringae FF5]
          Length = 208

 Score =  210 bits (534), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 84/205 (40%), Positives = 112/205 (54%), 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  EVDGVPLRKAER----TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
            VDG  +++ E      R+ +Y+KP G + T  DP+GR TVFD LP     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 QV-TLDTQKGSNAWVTVGLREGKNR 199
            +      +G N W    + EG+NR
Sbjct: 183 DIQQAPGGEGFNHWYHCVVMEGRNR 207


>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 =  210 bits (534), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 107/230 (46%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G++T   DP  +STV D +        +  VGRLD +T GLLLLT DG L 
Sbjct: 61  DYLM-NKPAGVITATEDPT-QSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y  +    +  +  + L+ G+ ++        V +      N  + +
Sbjct: 119 HTLLAPNHHVPKTYAAKLAKALTTEMKHQLEHGVALKDFTTAPADVQVVPAT-DNKEIHI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            + EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++   
Sbjct: 178 TITEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALTDDE 227


>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 =  210 bits (534), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 66/231 (28%), Positives = 111/231 (48%), Gaps = 10/231 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +R+ V  ++A+  V+V+G +       +     + ++G  L+    + 
Sbjct: 7   RLDRFISVKTGINRKNVRLLLAKGLVEVDGDIARNIDQIIDEFSDVSLEGEVLQSNSPSY 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
           + + HKP+G+V+   D D   TV D L       +  VGRLD+NT GLLLLTNDG  ++ 
Sbjct: 67  V-MLHKPVGVVSATVD-DKHKTVIDLLTDKSKHDLHIVGRLDLNTSGLLLLTNDGRWSKK 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTV 191
           L  P  +  ++YRV     +D   +    +GI    + I     Q+ L      +    V
Sbjct: 125 LMSPHHKVGKLYRVTLQNPIDDSYVKAFAEGIYFEFEDIITKPAQLALV----DSHTALV 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            L EG+  +IK++F  F   V  L RIS G   L + L  G +R ++ + +
Sbjct: 181 TLVEGRYHQIKRMFGRFRNPVIGLHRISVGKILLDSQLTPGMSRSLTAQEI 231


>gi|253996871|ref|YP_003048935.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253983550|gb|ACT48408.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 245

 Score =  210 bits (534), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 54/233 (23%), Positives = 97/233 (41%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTR 74
           + +++   G  SR+    ++  + V VNG L +           H  + G      E++ 
Sbjct: 10  IERILHNQGFGSRKLCRILVINEEVTVNGELCDDPDTTFELENLHYTIKGEAWVYHEKS- 68

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
             + HKP     +H       T++  LP       V  +GRLD +T GL+L+++DG    
Sbjct: 69  YLMMHKPSNYECSHK-TQHHPTIYSLLPHPLVERGVQCIGRLDEDTTGLILISDDGQFIH 127

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P  +  +VY V     V  +++  + KG+ +           L   K ++  + + 
Sbjct: 128 RMSSPKHKVPKVYEVTCKHAVSDEQIAHILKGVQLVDEDAP--IAALACTKINDHVIHMT 185

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           L EGK  ++K++    + +V  L RI  G  +L   L  G  R +S   L   
Sbjct: 186 LAEGKYHQVKRMVAAISNRVEALKRIKIGRLELPQDLKVGEWRWLSASDLNAL 238


>gi|311696250|gb|ADP99123.1| pseudouridine synthase, Rsu [marine bacterium HP15]
          Length = 230

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 57/229 (24%), Positives = 104/229 (45%), Gaps = 6/229 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + IA +   SR+E +R I +  V +N  + + A   +   + + + G PL      
Sbjct: 1   MRLDQFIANSTELSRKEAKRAIGRGEVTINEQICKGANTRLAGDERVALSGTPLSLP-GE 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  + +KP G+V+  +D D   T  D LP+     +   GRLD +T GLLLLT DG  + 
Sbjct: 60  RYLMMNKPAGVVSATTDSDH-PTALDLLPAEITRHLHIAGRLDADTTGLLLLTTDGQWSH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +  P T   + YRV  +  +       L++G+ +           +   +  +  + + 
Sbjct: 119 RVTSPRTDCPKTYRVTLNEPLSDAAAQQLERGVDLHNDPRPTRPARVHFLE--DRIIELT 176

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           + EG+  ++K++       V  L R+  G  +L   L+ G  RE++ + 
Sbjct: 177 ISEGRYHQVKRMMAAVGNHVEALHRVRIGQVELDDALMPGEYRELTAEE 225


>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 =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 108/230 (46%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G++T   DP  +STV D +        +  VGRLD +T GLLLLT DG L 
Sbjct: 61  DYLM-NKPAGVITATEDPT-QSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y  +    +  +  + L++G+ ++        V +      N  + +
Sbjct: 119 HTLLAPNHHVPKTYAAKLAKALTTEMKHQLEQGVALKDFTTAPADVQVVPAT-DNKEIHI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            + EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++   
Sbjct: 178 TITEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALTDDE 227


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 114/242 (47%), Gaps = 18/242 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RKAE 71
           +R+SKV+A AG+ASRR  E +I   RVKVNG +       V    D I +DG  L +K  
Sbjct: 242 ERLSKVLAAAGVASRRGSEDIIFAGRVKVNGKVCTVPQTPVNPLKDTIFLDGRSLPKKPP 301

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTE 119
               +  +KP G + + S  D        L   +             R+ +VGRLD+ T 
Sbjct: 302 PKFYFALNKPKGYICS-SAKDAPKPALSLLEDYWKIWDKKNPGVSRPRLFTVGRLDVATS 360

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLL+TNDG  A+ +  PS+   + Y      +V + +L L+  G  +Q +     +V L
Sbjct: 361 GLLLITNDGDFAQRVSHPSSGLTKEYIATVTERVTKRQLQLIAGGTKVQDVHCVPTEVEL 420

Query: 180 DTQKGSNA--WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
              +  +A   + + + EG+NRE++++      +V  L R+  G   L   L  G    +
Sbjct: 421 LPPEPGDARNRIRIVVCEGRNREVRELVANAGLEVLALKRVRIGGLSLSRKLSPGKFEVL 480

Query: 237 SK 238
           ++
Sbjct: 481 TE 482


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 102/233 (43%), Gaps = 3/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +    R++K +A +G+ SRRE +  IA   V VNG ++      V   D ++ DG  L  
Sbjct: 39  DPNSIRLNKYVANSGVCSRREADVFIAAGSVTVNGKVVSEMGYKVKLDDVVKFDGRHLN- 97

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
            E+    L +KP    TT  +  G+  V   + S     ++ V ++   + GLLL TND 
Sbjct: 98  PEKREYVLLNKPKDFSTTVRNEHGKRNVAGLISSASKATLLPVDKMAKASTGLLLFTNDK 157

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            L R L  P     ++Y V     +    L  ++ G+ I         ++       N  
Sbjct: 158 ELTRRLLNPKNGLRKIYHVELSKALSPADLKKIQDGLAIDEKVVNVHDISYVDNAPKN-Q 216

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           V + L   ++  + K+FE   ++V +L R+ YG      L  G  R ++K+ +
Sbjct: 217 VGIELFSSRSNIVTKIFEHLGYEVAKLDRVVYGGLTKKDLPRGHWRYLTKQEV 269


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 51/231 (22%), Positives = 89/231 (38%), Gaps = 9/231 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           + +++   G  SR+    +I    V +NG +++       + D +  +        E   
Sbjct: 6   LDRILQSQGFGSRKYCRELIEDGEVVINGEVVDDYRATPDTKDLVLTIFEEEWEYRE-HV 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP  +  +   P     V   LP  F    V  VGRLD +T GLLL+++DG    
Sbjct: 65  YIAINKPPNIECSRK-PSHHPGVLTLLPEQFTWRDVQPVGRLDHDTTGLLLMSDDGAFIH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P     +VY       V +  +  LK G+ +       +  T   Q G N  + + 
Sbjct: 124 AQSSPKRHVPKVYAATTAEPVTEALIAQLKAGVQLHDEP-APLAATRCRQLGEN-LLEIV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
           L +GK  ++K++        + L R + G  QL    L  G    +  + +
Sbjct: 182 LEQGKYHQVKRMLAAAGNHCSALQRTAIGGLQLEALALEEGEWTYLDAEQM 232


>gi|296136628|ref|YP_003643870.1| pseudouridine synthase [Thiomonas intermedia K12]
 gi|295796750|gb|ADG31540.1| pseudouridine synthase [Thiomonas intermedia K12]
          Length = 300

 Score =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 63/265 (23%), Positives = 103/265 (38%), Gaps = 38/265 (14%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---MSTDHIEVDGV 65
           +     R+SK ++  G+ASRRE +  I +  V ++G         V   +    I +   
Sbjct: 39  DPAAEVRLSKRMSELGLASRREADDWIERGWVLLDGTPA-VLGTKVAGNLPASRIVIRKA 97

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD---------------NLPSIFSRVIS 110
              +       L HKP+G V+  ++      V                   P+    +  
Sbjct: 98  AQHRQAAQVTILLHKPVGYVSAQAEHGYTPAVALIKAENRWAECEAPQPFSPAHLRHLAV 157

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF---------------HGQVDQ 155
            GRLDI++ GLL+LT DG +AR L    +   + Y VR                     +
Sbjct: 158 AGRLDIDSTGLLVLTQDGRIARQLIGEDSAVEKEYLVRVSLTDAPARNGAEEDVQAAFPE 217

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
            +L LL+ G+ +        QV       +   +   LREGK R+I+++ E    +V  L
Sbjct: 218 SRLALLRHGLKLDDQPLRPAQVEW----INPQQLRFVLREGKKRQIRRMCELVGLRVTGL 273

Query: 216 IRISYGPFQLGTLLAGSTREVSKKI 240
            R+  G  +LG L  G  R + +  
Sbjct: 274 KRVRIGGLRLGALPLGQWRYLREDE 298


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 62/230 (26%), Positives = 107/230 (46%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV++ G L+     N++    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRIAGELVTDPGYNILPGVAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G++T   DP  +STV D +        +  VGRLD +T GLLLLT DG L 
Sbjct: 61  DYLM-NKPAGVITATEDPT-QSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y  +    +  +  + L+ G+ ++        V +      N  + +
Sbjct: 119 HTLLAPNHHVPKTYAAKLAKALTTEMKHQLEHGVALKDFTTAPADVQVVPAT-DNKEIYI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI 240
            + EGK  +IK++    + +V  L RI+ GP +L   L AG  R ++   
Sbjct: 178 TITEGKYHQIKRMLLAVDNEVVALTRIAMGPLRLPEDLDAGEYRALTDDE 227


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 98/245 (40%), Gaps = 21/245 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN--G----ILLERAAVNVMSTDHI-EVDGVP 66
            ++  ++   G  +RR    +I Q  V V+  G    ++    A N+     +  V G  
Sbjct: 1   MQLQDILYSQGFGTRRICAGLIQQGWVAVHSAGSLEPVVCLEPAQNLKEQGLVLRVQGQD 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
                +  + + +KP G   +   P    +V+  LP+   +         V +VGRLD +
Sbjct: 61  WPYHAKAYV-MLNKPAGTECSQK-PSAYPSVYTLLPAPLRQRPGKSAVSGVQAVGRLDQD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T GLLLL++DG     +  P     +VY+V     VD  ++  L  G+V+         V
Sbjct: 119 TTGLLLLSDDGQFIHRMSSPKKHVPKVYQVTVRHPVDAAQVECLLAGVVLDDDPKPVRAV 178

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
               +      + + L EGK  ++K++      +V  L R   G  +L   +  G  R +
Sbjct: 179 ACVQRDA--HRIDLTLTEGKYHQVKRMIAAVGNRVEALHRARIGGLELPADMAPGQWRWL 236

Query: 237 SKKIL 241
               L
Sbjct: 237 GLDEL 241


>gi|56807363|ref|ZP_00365352.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 228

 Score =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 57/216 (26%), Positives = 100/216 (46%), Gaps = 8/216 (3%)

Query: 35  IAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           + ++ + VN  +   A  ++    D +   G PL   E    +L +KP G V+   D   
Sbjct: 7   LKKKAIFVNQKVETSAKAHIDEYKDLVTYQGTPLVY-ESFVYYLLNKPSGYVSATQDRQ- 64

Query: 94  RSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           ++TV + L     +  V  VGRLD +T GLLLLTN+G LA  L  P     + Y  +  G
Sbjct: 65  QATVMELLDDTARQKAVFPVGRLDKDTRGLLLLTNNGQLAHDLLSPKKHVTKEYLAKVAG 124

Query: 152 QVDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + +   +   +GI ++         +V     +   + V + ++EGK  ++K++     
Sbjct: 125 IMTEADKDYFARGISLKDHQCLPAHLEVLASDLQQQTSLVKITIQEGKFHQVKRMVAACG 184

Query: 210 WKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            +V  L R+S GP +L  +L  G  R ++ + L+  
Sbjct: 185 KEVLDLQRLSMGPLKLDPSLAEGEFRRLTPEELQSL 220


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 102/256 (39%), Gaps = 28/256 (10%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +     R+SK ++  G+ SRRE +  I +  V V+G  ++     V     IE+D   + 
Sbjct: 290 DEAGMMRLSKRMSELGLCSRREADEWIEKGWVLVDGERIDTLGTKVRPDQKIEIDDQAIA 349

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGR 113
                   L HKP+G V+  ++      V                   P     +   GR
Sbjct: 350 AQAAQVTILLHKPVGYVSGQAEDGYEPAVTLITRENHWSGDRSALRLSPLHLRTLAPAGR 409

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR---------FHGQVDQDKLNLLKKG 164
           LDI++ GLL+LT DG +A+ L    +   + Y VR                + L  L+ G
Sbjct: 410 LDIDSTGLLVLTQDGRIAKQLIGEQSDIDKEYLVRVRFGEHVIDVDQHFPAESLAKLRHG 469

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + + G+      V+    +     +   LREGK R+I+++ E    +V  L R+  G   
Sbjct: 470 LELDGVPLKPAMVSWQNSE----QLRFVLREGKKRQIRRMCELVGLEVVGLKRVRMGRVM 525

Query: 225 LGTLLAGSTREVSKKI 240
           LG L  G  R +    
Sbjct: 526 LGALPQGQWRYLGADE 541


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 52/235 (22%), Positives = 93/235 (39%), Gaps = 8/235 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAER 72
             + +++   G  SR+    +I   RV ++G + +    ++ + D +  VD    R  ++
Sbjct: 1   MHIERILHSQGFGSRKVCRALIRAGRVTISGQIQDNPFADLPTADLVFTVDRETWRFRDK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + HKP G   +   P   + VF  LP       V  +GRLD +T GLLLL++DG  
Sbjct: 61  A-YLMLHKPSGYECSRQ-PQFHAPVFALLPEPLVNRGVQPIGRLDQDTTGLLLLSDDGQF 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             V      +  ++Y V     V++     L  G+ +            +     +  + 
Sbjct: 119 IHVWSSGRKRVPKIYEVAVRHPVNETMTEALLAGVQLHDDPEPVAAAACERTGERS--LK 176

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           + + EGK  ++K++      +V  L R   G   L   L  G  R +    L   
Sbjct: 177 LTITEGKYHQVKRMVAAAGNRVESLHRSGIGGLMLPDDLAPGQWRWLDDGDLARL 231


>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 =  209 bits (533), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 64/237 (27%), Positives = 102/237 (43%), Gaps = 10/237 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ +++A  G  SRRE    I   RV + G     +     + D + +DG PL   +   
Sbjct: 3   RLDQLLANLGYCSRREARSWIEAGRVTIGGEAANDSGQKAAAAD-VRIDGEPLDHPDGLL 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
           L L+  P+GLV +H + +G   ++  LP  + R       VGRLD  T GLLLLT+   L
Sbjct: 62  LLLHK-PLGLVCSHDEREG-PNIYSLLPERWRRRNPAVTSVGRLDKETSGLLLLTDQSLL 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P  +  +VYR      +  D + L   G + ++G  +      L       A  
Sbjct: 120 VHRLTSPKHKVPKVYRASVDRDLSPDLVPLFASGTLQLEGEAHPCAPAELRLLGPREA-- 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + L EG+  +++++       V  L R  +G   L  L  G+ RE+       + G
Sbjct: 178 ELTLTEGRYHQVRRMLAACGLTVLTLHRARFGHLALDDLAPGAWRELPLDEFAARFG 234


>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 =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 100/247 (40%), Gaps = 24/247 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV---NGILL----ERAAVN-VMSTDHIEVDGV 65
            ++  ++   G  +RR    MI Q  V V   N  L      +AA   +     + V GV
Sbjct: 1   MQLQDILYSQGFGTRRVCAGMIQQGLVGVYESNQALAPVIYTQAATEFIAEGLRLRVQGV 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDI 116
                E+  + + HKP     +   P    +V+  LPS             V +VGRLD 
Sbjct: 61  DWPYHEKAYV-MLHKPSATECSQK-PSTYPSVYTLLPSALRLRPQKGAVQGVQAVGRLDQ 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T GLLLLT+DG     +  P     +VY V     +D  ++  L  G+V+         
Sbjct: 119 DTTGLLLLTDDGQFIHRMNSPRHHVPKVYEVTVKHPLDDTQVARLLAGVVLDD---DPKP 175

Query: 177 VTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
           V     +  S+  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R
Sbjct: 176 VRAAAAEAVSSHHLRLTLTEGKYHQVKRMVAAVSNRVEALHRSQIGGLRLPDDLAPGQWR 235

Query: 235 EVSKKIL 241
            +S   L
Sbjct: 236 WLSAADL 242


>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 =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 123/241 (51%), 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------------L 179
           L    ++  R+Y ++  G++ ++    ++ G+ +Q    G  + +              +
Sbjct: 121 LM--ESKMERIYLLKLSGKIQEEVFEAMENGLSLQDARAGGHKESKIQSMEFAPFLGYWV 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|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 =  209 bits (532), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 109/241 (45%), Gaps = 7/241 (2%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V +    +R+ K +++    SR+E   +I + RV V+G     AA+ +     I +D  
Sbjct: 1   MVSDKVQKERLDKCVSKLTGLSRKEASALIKEGRVLVDGQAALEAALKIPVNSIITIDDD 60

Query: 66  PLRKAE---RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGL 121
            +   E   + R+++ +KP  +V    D + R      +  +    +   GRLDI+T GL
Sbjct: 61  EISLYEEGFKKRVYMLNKPSDMVCADRDRNHRIVTSLFVEELRPDTLHCAGRLDIDTTGL 120

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L++T+DG L   +  P  +  ++YR      + +  ++   KGI      +      L  
Sbjct: 121 LIVTDDGELIHEITHPKKEITKLYRAVTDKPIPEKAVSAFLKGIKHPEEKFPYKSAKLTI 180

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           +  +   V V  +EG+  E+K++FE    +V  L R+  G  +L   L  G  R +S   
Sbjct: 181 ESANVGLVEV--KEGRFHEVKRLFECVGCEVIELTRLKIGSLELDDSLEEGEYRLLSDDE 238

Query: 241 L 241
           +
Sbjct: 239 V 239


>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 =  209 bits (532), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 113/231 (48%), Gaps = 18/231 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RKAE 71
           +R+SKV+A AG+ASRR  E +I   +V VNG +      +V    D I +DG P+ R+  
Sbjct: 20  ERLSKVMAAAGVASRRACEEIIFAGKVVVNGKVCRTPETHVDPLKDLIYIDGKPIPRRLP 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTE 119
              ++  +KP G + +    D + TV+  L                 R  +VGRLD+ T 
Sbjct: 80  PKMVFALYKPKGYICS-DAKDDKKTVYLLLEKYLKTWEKNNPGLTKPRFFTVGRLDVATT 138

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVT 178
           GL+ +TNDG  A+ +  PS+   + Y V    + V + +L  +  G  I G+    + V 
Sbjct: 139 GLIFVTNDGEFAQKVSHPSSGITKEYLVTVDSESVTKRQLKRIASGTEIDGVMCVPISVE 198

Query: 179 LDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           L   +   S   + V + EG+N E++++ E    KV+ L R+  G  +L +
Sbjct: 199 LVKSEPGDSRHRIRVVVTEGRNHEVRQLVESAFLKVHALKRVRVGGLRLPS 249


>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 =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 87/238 (36%), Positives = 134/238 (56%), Gaps = 8/238 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDHIEVDGVPL---RKA 70
           ++ K+++  G  SRR +E MI   ++ +NG         N  +   I +D   +   R  
Sbjct: 4   KIQKILSDLGYGSRRFIECMIKCGKISINGEKAIIGQYLNKKNPGEILIDKKKIIVKRNK 63

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
              ++ +Y+KPIG V T  D   R TVFD LP    +R +SVGRLDINT+GLLL TNDG 
Sbjct: 64  NLPKVLIYNKPIGEVCTRDDFQKRLTVFDKLPKLNLNRWVSVGRLDINTKGLLLFTNDGT 123

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQG-ICYGDMQVTLDTQKGSNA 187
           LA  L  P +Q  R Y +R  G+++++K+N+L+KG+ +I G + + ++    D ++G N 
Sbjct: 124 LANKLMHPRSQIEREYNIRIFGEMNKNKINILRKGVKIIHGYVSFKEIVPLYDKKEGKNK 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
           W    L EGKNREI+ +F+    +VN+LIR+ YG   L   L  G    ++   L++ 
Sbjct: 184 WFKGILCEGKNREIRLMFKSIQCQVNQLIRVRYGNIILPKNLKEGQWMMLNSIFLKKL 241


>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 =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 55/220 (25%), Positives = 101/220 (45%), Gaps = 10/220 (4%)

Query: 51  AVNVMSTDHIEVDGVPL--RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
              V   D + V+G P+  RKAE   L   +KP+G++T+      R+ + D + +   R 
Sbjct: 5   GEQVFVGDSVSVNGQPIAPRKAEDLVLIALNKPVGVITSMG-KQVRNNIGDWV-NHSQRT 62

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             +GRLD +++GL+ LTN G L   +        + Y V     +  + +  +  G+ I 
Sbjct: 63  FPIGRLDKDSQGLIFLTNHGELVNKILRAGNNHQKEYLVSVDRPITDEFIQAMGAGVPIL 122

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G       V    +K ++  + + L +G NR+I+++ ++F ++V +L R+      L  L
Sbjct: 123 GTVTKPCLV----EKIASQILRITLVQGLNRQIRRMCKYFGYQVTKLERVRIMNINLHGL 178

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
             G  R+ + +  RE     L+E +      P  +S   V
Sbjct: 179 ALGEWRDFTDEERRELF--RLIEHSSSEASQPATTSIPPV 216


>gi|291532977|emb|CBL06090.1| ribosomal large subunit pseudouridine synthase B [Megamonas
           hypermegale ART12/1]
          Length = 173

 Score =  208 bits (531), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 54/167 (32%), Positives = 90/167 (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 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLR 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|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 =  208 bits (531), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 69/231 (29%), Positives = 113/231 (48%), Gaps = 18/231 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPL-RKAE 71
           +R+SKV+A AG+ASRR  E +I   +V VNG +      +V    D I +DG P+ R+  
Sbjct: 20  ERLSKVMAAAGVASRRACEEIIFAGKVVVNGKVCRTPETHVDPLKDLIYIDGKPIPRRLP 79

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTE 119
              ++  +KP G + +    D + TV+  L                 R  +VGRLD+ T 
Sbjct: 80  PKMVFALYKPKGYICS-DAKDDKKTVYLLLEKYLKTWEKNNPGLTKPRFFTVGRLDVATT 138

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVT 178
           GL+ +TNDG  A+ +  PS+   + Y V    + V + +L  +  G  I G+    + V 
Sbjct: 139 GLIFVTNDGEFAQKVSHPSSGITKEYLVTVDNESVTKRQLKRIASGTEIDGVMCVPISVE 198

Query: 179 LDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           L   +   S   + V + EG+N E++++ E    KV+ L R+  G  +L +
Sbjct: 199 LVKSEPGDSRHRIRVVVTEGRNHEVRQLVESAFLKVHALKRVRVGGLRLPS 249


>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 =  208 bits (531), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 94/200 (47%), Gaps = 12/200 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            ++++ I+ A   SRRE +R+I   RV +NG +    A+ V   D + +DG  + K E+ 
Sbjct: 1   MKINQYISEAKSCSRRETDRLIKAGRVAINGEICTHGAL-VSDGDVVTIDGQVIAKEEKE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                +HKP+G+  T +D      + D +     R+  VGRLD  +EGL+LLTNDG +A 
Sbjct: 60  KVYIAFHKPVGITCTAAD-HIEDNIIDYI-HYPERIFPVGRLDKASEGLILLTNDGTIAN 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +     +  + Y V          +N +  G+ I+       +VT          + + 
Sbjct: 118 QILHGDHEHEKEYVVTVDKPFTDWFINEMSSGVKIKDGMTKPCKVTRVRS------INIS 171

Query: 193 --LREGKNREIKKVFEFFNW 210
             L +G NR+I+++     +
Sbjct: 172 YHLTQGMNRQIRRMSRAIGY 191


>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 =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 111/237 (46%), Gaps = 11/237 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +++ + RAG+  ++E E+ I   RVKV G L       V    ++ VDG   R      +
Sbjct: 29  LARALGRAGVMPQQEAEQAIRDGRVKVEGRLELEPFAPVRLGSNVFVDGWAHRLEAPLHV 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            + L EG++ ++K++       V  L R + G   L  +  G  R +S   +   LG
Sbjct: 205 ELVLTEGRHHQVKRMLAAVGHPVRTLHRQAVGTVSL-DVPVGDWRSLSPGEVTGGLG 260


>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 =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 108/239 (45%), Gaps = 15/239 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST----DHIEVDGVPLRKA 70
           R+ +++A  G  SRRE++ +     + ++G  L  A   +  T    + + V GV L   
Sbjct: 8   RLDRLLANLGYGSRREIQALARAGAIILDGARLRAADERIPVTRDLPERLTVGGVALDPP 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
               + + HKP G+  +H +      V+  LP  + R       VGRLD  T GLLLLT+
Sbjct: 68  PGL-VLMLHKPTGVTCSHKEAG--PLVYGLLPERWRRRDPPLSTVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+  L   G ++++G     + V L  +  +
Sbjct: 125 DGALLHRIISPKAKVAKRYRVELARPLAGDEGALFASGTLMLEGEDKPLLPVELVAEGPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILRE 243
            A  +V L EG+  +++++F      V  L R   G   L   L  G+ R + +  L +
Sbjct: 185 RA--SVTLTEGRYHQVRRMFAAVGNHVTALHRDRVGRLDLPADLAPGAYRILGEAELAQ 241


>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 =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 123/249 (49%), Gaps = 20/249 (8%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           L    +   R Y ++  GQ+ +  +  ++ G+ IQ    G    T               
Sbjct: 120 LMH--SDLEREYYLKIKGQISKKVIEAMQNGLEIQNSTKGAHAKTKINSMKFAPFLDFEI 177

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EG+NRE+++ F +F+ +V  L R+++G  +LG L AG  R + + 
Sbjct: 178 FGWSGGYTKLRVVINEGQNRELRRFFGYFDLEVMDLKRVAFGIVELGMLKAGKYRFLERG 237

Query: 240 I---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 115/241 (47%), Gaps = 2/241 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++ K +   G A RR+ ++ I   RV VNG ++++   +V   D + +D   L+  ++ 
Sbjct: 8   IKLQKYLQMCGFA-RRKADQYIIAGRVTVNGKVVDKPWFDVKDDDIVMLDNKKLKINQKF 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ HKP G  TT  DP  + T+ + +  I + V   GRLD +  G+L+LTNDG L  +
Sbjct: 67  EYYVLHKPKGYATTLYDPKQKKTIKELIKHIKTPVKPAGRLDKDATGVLILTNDGKLIDI 126

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L        + Y V+  G V  + L  LKKGI  +          +  +    + + V L
Sbjct: 127 LTNAKYGVKKEYIVKVSGSVSFNDLLKLKKGIYDERDFLKLEYFDILEKGFDYSIIKVVL 186

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKKILREQLGPHLLEE 252
            +GK  EIK++F+    KV  L RI++GP  +  +   G   ++  K L   L     EE
Sbjct: 187 IKGKKHEIKRLFKSIGHKVLELKRIAHGPISISIVPNEGDLTKLKGKDLERLLKLKKGEE 246

Query: 253 A 253
            
Sbjct: 247 K 247


>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 =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 117/236 (49%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPEKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+V  + +V    +   + GIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQVVVNERVTSADVTAFENGIVFADGYQCKPADLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R  +   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVTALKRLSMGPLELDEQLGVGEYRSFTLAEMKKL 233


>gi|241765880|ref|ZP_04763813.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241364178|gb|EER59374.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 249

 Score =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 98/250 (39%), Gaps = 24/250 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRV-KVNGIL------LERAAVNVMSTD-HIEVDGV 65
            ++  ++   G  +RR    ++ Q  V   +G           A+      D  ++V GV
Sbjct: 1   MQLQDILYSQGFGTRRVCAGLVQQGWVETASGDPDAAFSACTEASAEFDVDDLRLKVQGV 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDI 116
                 +    + HKP G   +   P    +++  LP+   +         V +VGRLD 
Sbjct: 61  LWPYHAKA-YIMLHKPAGTECSQK-PSTYPSIYTLLPAPLRQRPCKGAIQGVQAVGRLDQ 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T GLLLL++DG     +  P     +VY+V     VD+ ++  L  G+V+         
Sbjct: 119 DTTGLLLLSDDGQFIHRMSSPKKHVPKVYQVTTKHPVDERQIAALLAGVVLDD---DPKP 175

Query: 177 VTLDTQK-GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTR 234
           V         +  +++ L EGK  ++K++      +V  L R   G   L   L  G   
Sbjct: 176 VRAAACSVVDSHRLSLTLTEGKYHQVKRMLAAVGNRVEALHRSRIGTLDLPADLAPGQWL 235

Query: 235 EVSKKILREQ 244
            +S   L + 
Sbjct: 236 WLSDADLHKL 245


>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 =  208 bits (530), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 19/241 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R+++ I+ +G+ SRR+ +  I    VKVNG ++      V  TD ++ DGV +  
Sbjct: 60  NPDEIRLNRYISNSGMCSRRDADIYIQSGNVKVNGEVITEMGYRVKLTDSVQFDGVNIT- 118

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
            E+    L +KP    T   D  G + V D + +   + ++ VGR+D  T GLLL TND 
Sbjct: 119 PEKKEYILLNKPKNFSTAGDDSAGSANVLDLVRNATKANLMPVGRMDKTTTGLLLFTNDT 178

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--------YGDMQVTLD 180
            + +   +P+ +  +VY+V     +  + L  ++KG+ I              D   +  
Sbjct: 179 EIVQKFTVPNQRSSKVYQVTLDKNLKFEDLEKIQKGLTIDDHKVFVEEVTYIQDQPKSEI 238

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
             K   + V V         ++K+FE F + V ++ R+++       L  G  R ++++ 
Sbjct: 239 GIKMKTSNVKV---------VRKIFEHFKYDVLKVDRVTFAGLTKKNLPRGDWRFLTEQE 289

Query: 241 L 241
           +
Sbjct: 290 I 290


>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 =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 71/240 (29%), Positives = 113/240 (47%), Gaps = 11/240 (4%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P  +S+ +ARAG    +E E  I + RV VNG ++ +    V     + VDG  +R+   
Sbjct: 29  PDWLSRALARAGALPLQEAEDAIQEGRVTVNGRVVRQPLAPVPEGAVLRVDGTEVRREVE 88

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSR--VISVGRLDINTEGLLLLTN 126
           TR+  +HKP  L+T+        TV++     LPS  +R    +VGRLD  T GLLL TN
Sbjct: 89  TRVLAFHKPADLLTSTVSQHRTGTVYEVLLPQLPSELARYTWHAVGRLDRGTTGLLLFTN 148

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           D  L      P T   + Y     G  D+ ++  L++G+ ++       QV +       
Sbjct: 149 DEKLVAHATSPETHLAKRYVATVQGTADEARVAPLRQGVQLEDGPTRPAQVRIRDA---- 204

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
             V V + EG+N ++K++       V  L R + G   L  +  G+ R ++ + + E LG
Sbjct: 205 HTVEVIVTEGRNHQVKRMLGAVGLPVRALHREAIGGVAL-DVPVGTFRLLTPEEVTEGLG 263


>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 =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 104/230 (45%), Gaps = 6/230 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     SR+EV+ +I  +RV+V G L+     NV+    +EV+          
Sbjct: 1   MRLDKYLSHLQFGSRKEVKALIRDKRVRVAGDLITDPGYNVLPGIAVEVNDAQADGPLEV 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G++T   DP  +STV D +        +  VGRLD +T GLLLLT DG L 
Sbjct: 61  DYLM-NKPAGVITATEDPT-QSTVLDLIRPHDYRPGLYPVGRLDKDTTGLLLLTTDGNLG 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P+    + Y       +  D    L+ GI ++       QV +         + +
Sbjct: 119 HALLSPNRHIAKTYAATLAKTLTADMKQRLETGIDLKDFTTAPAQVVVLPDTDGK-RIQI 177

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
            + EGK  ++K++    + +V  L RI+ GP  L   L AG  + ++   
Sbjct: 178 TITEGKFHQVKRMLLAVDNEVTALTRIAMGPLSLPADLAAGEYQALTDDE 227


>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 =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 107/242 (44%), Gaps = 20/242 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K    R  L++KP G++T  +DP+GR T+ D +P     V   GRLD+++EGLL L+ND
Sbjct: 6   EKQGTYRYILFYKPYGVLTAFTDPEGRPTLKDWIP--VPDVYPAGRLDMDSEGLLFLSND 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G L   +  P  Q  + Y V+  G V  + L  L++G+ ++G      QV +  +     
Sbjct: 64  GDLMHRITDPRYQHPKTYLVQVEGVVSGEALAKLRRGVEVKGRQTQRCQVMVIPEPDLPP 123

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                   G   W+ + L EGK R+++ +         RL+R++ GP  L  L  G  R+
Sbjct: 124 RAKPVTPHGPTTWLRMVLTEGKKRQVRHMTAAVGHPTLRLVRVAIGPLSLEGLTPGEWRD 183

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGL 295
           ++ + L       LL+ +    D  I +            +       R  + S   + +
Sbjct: 184 LTPQEL------ALLKRSLRLTDGRIPAMSAGNARESRYRNAARQSSNRGSRPSGADDPV 237

Query: 296 SK 297
            +
Sbjct: 238 QE 239


>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 =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/231 (30%), Positives = 113/231 (48%), Gaps = 17/231 (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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               G    + V + EGKNRE+++ F  F+ +V  L R+++G   LG L A
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFFGHFDLEVMDLKRVAFGALDLGMLKA 228


>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 =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 64/202 (31%), Positives = 110/202 (54%), Gaps = 5/202 (2%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
             +D IEV+G+ +   ++    L+HKP  ++T+ SD  GR+ V D    I +R+  VGRL
Sbjct: 2   KPSDTIEVEGIKIELEDKI-YILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRL 60

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D +T GLLLLTNDG    ++  P  Q  + Y  +  G + ++++  L+KGI ++      
Sbjct: 61  DYDTSGLLLLTNDGEFTNLMTHPRYQIKKKYVAKLKGYLMREEVKALEKGIELEDGMTQP 120

Query: 175 MQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            +  V    +  +   V + + EG+NR+++++FE F  +V +L RI YGP  +  L AG 
Sbjct: 121 AEVKVKKQDKDKNTTLVEITITEGRNRQVRRMFEHFGHQVTKLSRIEYGPLNVVGLNAGE 180

Query: 233 TREVSKKILREQLGPHLLEEAQ 254
            R ++   ++  +  HL E  +
Sbjct: 181 GRVLTPHEVK--VMRHLAEHGK 200


>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 =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 68/233 (29%), Positives = 110/233 (47%), Gaps = 5/233 (2%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRKAE-RT 73
           + KV+  A + SRR++   I Q  V +NG   E  +  V    D +  +G P+  +  R 
Sbjct: 11  LVKVLVEARLGSRRKMAEAIKQGLVTLNGQKAESYSQPVNTQQDKVTFEGKPVELSRIRR 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 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 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + EGK R ++++F    +++  L R      +LG L  G TRE++   +   
Sbjct: 190 IIHEGKKRIVRRMFAHLGYQIKALKRSRIATLRLGKLEEGKTRELTPGEIAAL 242


>gi|257899452|ref|ZP_05679105.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257837364|gb|EEV62438.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 238

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 71/236 (30%), Positives = 118/236 (50%), Gaps = 8/236 (3%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              + LP  +  + Y+   + +V    +   +KGIV   G       + +       + V
Sbjct: 118 GYEMLLPEKKVSKTYQAVVNERVTSADVAAFEKGIVFADGYQCQSANLKILKADKHQSTV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
            + ++EGK  ++KK+F     KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 178 LLTIQEGKFHQVKKMFLAQGKKVIALKRLSMGPLELDEQLAVGEYRSLTLAEMKKL 233


>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 =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 109/256 (42%), Gaps = 28/256 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +A++ I +R+ V + +    VK+NGI +  AAV +   + I      + + +  
Sbjct: 1   MRLDKFLAQSQIGTRKIVRQYVKDGLVKINGITIFEAAVEINEIEDIIEYNGQITEYKEK 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++++KP G +T   D D + TVFD         V  VGRLD +TEGLLL TNDG    
Sbjct: 61  VYYMFNKPSGCITARKDADDK-TVFDYFKEINMDGVFHVGRLDKDTEGLLLFTNDGDFNN 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQV------TLDTQKG 184
            L  P     + Y     G +D+     L+ G+ I          ++      T +  K 
Sbjct: 120 KLMSPKFHVDKKYFFIALGSIDEKNKKNLESGVSIGENEPITKPAKIENLKNGTYEELKD 179

Query: 185 S---------NAWV--------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|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 =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 61/234 (26%), Positives = 123/234 (52%), Gaps = 9/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++++   SR+E + +I + RVKV+G ++++A   V   + +EV+G  ++  ++ 
Sbjct: 1   MRLDKYLSKSLHISRKEAKELIREGRVKVSGKVVKQAEYRVKEGEEVEVEGKSVK-PKKN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G ++T  +     +  + +   F   ++ S GRLD++ EGLLL+T+DG LA
Sbjct: 60  VYLMLYKPKGYLSTTEEDKKYPSFLELIREHFPSRKLFSAGRLDVDAEGLLLITDDGELA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P  +  + Y VR    +  ++L  L + + ++      +Q+ +  +K S   V  
Sbjct: 120 HRLTHPKWKVEKEYIVRLDRDIGDEELKKLYE-VKLE---EKPVQL-VKAEKLSGDTVKA 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            L EG++  +K++F+     V  L R   G  +L   +  G  RE++++ ++E 
Sbjct: 175 ILTEGRHHVVKRLFKAVGHNVVYLKRTRVGNLRLDENMEPGEWRELTEEEVKEL 228


>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 =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 122/249 (48%), Gaps = 20/249 (8%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           L    +   R Y ++  GQ+ +  +  ++ G+ IQ    G    T               
Sbjct: 120 LMH--SDLEREYYLKIKGQISKKVIEAMQNGLEIQNSTKGAHAKTKINSMKFAPFLDFEI 177

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               G    + V + EG+NRE+++ F +F+ +V  L R+++G  +LG L  G  R + + 
Sbjct: 178 FGWSGGYTKLRVVINEGQNRELRRFFGYFDLEVMDLKRVAFGIVELGMLKVGKYRFLERG 237

Query: 240 I---LREQL 245
               LR+ L
Sbjct: 238 EYEKLRDFL 246


>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 =  207 bits (527), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 67/225 (29%), Positives = 113/225 (50%), 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  IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
           I V+G  + K       +  +KP G + +  +P    ++FD+    ++++          
Sbjct: 220 IYVNGNRISKKLPPKLYFAVNKPKGYICSCGEPKSIISLFDDYLKGWNKIQPGVPKPRLF 279

Query: 111 -VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            VGRLD+ T GL+++TNDG  A+ L  PS+  ++ Y V   G V ++ L  + +G  I G
Sbjct: 280 TVGRLDVATSGLIIITNDGEFAQKLSHPSSNIMKEYVVTIDGPVHRNHLIAISEGTKIDG 339

Query: 170 ICY-GDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +    D+   LD Q       + + + EG+N E++++ +    +V
Sbjct: 340 VKCIPDLVEPLDVQSNTKRTRIRIAVHEGRNHEVRELVQNAGLEV 384


>gi|295111666|emb|CBL28416.1| pseudouridine synthase family [Synergistetes bacterium SGP1]
          Length = 244

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 71/230 (30%), Positives = 109/230 (47%), Gaps = 5/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R++  +A  G+ASRR  E +I   RV+V   ++      V    D +  DG  L+  E  
Sbjct: 7   RLNAFLAACGVASRRRAEEVIRAGRVRVGDRIVLAPFFQVDPEVDEVTCDGRTLKATEPV 66

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + + +KP G+V   SD      V D LP      RV   GRLD  +EGLL+LTNDG L 
Sbjct: 67  YVVM-NKPGGVVCAVSD-KYDPVVVDLLPEAVKSRRVYPAGRLDRESEGLLILTNDGALT 124

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           + +  PS    + Y    +  +++ +L   + G  I+G     + VTL  ++    WV+V
Sbjct: 125 QEVMHPSKGLHKEYEALLNVPINERQLARWRGGFEIEGRRAVPISVTLMDREPEGRWVSV 184

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + EG  RE++ +     + V RL+R   G   L  L  G   ++S   L
Sbjct: 185 VIGEGLKREVRVMANLAGFSVERLVRRRLGKMVLEKLRPGEFVDLSFSEL 234


>gi|302327988|gb|ADL27189.1| ribosomal small subunit pseudouridine synthase A [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 231

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 109/238 (45%), Gaps = 12/238 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRK 69
            T +R+   +A  G  SR++   ++    V+++G +L+   +   +    I V+G     
Sbjct: 1   MTLERL---LASMGFGSRKDARGLVRMGLVELDGKVLDDPFMEFKTRPEFITVNGEEAPT 57

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
            E+  + LY KP  +  +H+  D +  V+D LP  F+   + SVGRLD ++ GLLLL+N 
Sbjct: 58  VEKLYVMLY-KPTDVECSHNARDHKP-VYDLLPERFTAMGIQSVGRLDADSSGLLLLSNQ 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G     +E P     + YRV         +   L  G++++      +   ++    +  
Sbjct: 116 GDFIHKVESPKKGLWKKYRVTLARPFTDAQKAELLAGVMLKDERRPVLAREIEVSGDA-- 173

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            V + + EG   +++++F      V  L RI+ GP  L  TL  G  R ++ + +   
Sbjct: 174 -VDISIGEGLYHQVRRMFAAVGNHVETLERIAIGPVVLDRTLGEGGWRFLTDEEVAAL 230


>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 =  206 bits (525), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 55/189 (29%), Positives = 91/189 (48%), Gaps = 17/189 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R  L+HKP G+++  S  +G  T+ D +    + V  VGRLD ++EGL+LLTN G L 
Sbjct: 2   HYRYLLFHKPYGVLSQFSGGEGPPTLKDYI--TVADVYPVGRLDRDSEGLMLLTNHGELQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------- 184
             L  P     R Y V+  G    + L  L  G+++QG C    QV +   +        
Sbjct: 60  HRLSDPRFAHPRTYWVQVEGCPTPEALEQLATGVMVQGKCTRPAQVEVLAAEPDLPPRDP 119

Query: 185 --------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+++ LREG+NR+++++     +   RL+R++     LG+L  G  R++
Sbjct: 120 PIRFRLSIPTTWLSLTLREGRNRQVRRMTAAVGFPTLRLVRVAIAHLNLGSLAPGQWRDL 179

Query: 237 SKKILREQL 245
           +    +  L
Sbjct: 180 TPVEQQTLL 188


>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 =  206 bits (525), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 65/216 (30%), Positives = 107/216 (49%), Gaps = 7/216 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKA 70
              R+ K +   G  SR EV+R++ +++V VNG +   A + +    D I V+   L   
Sbjct: 3   EKMRLDKFLVEMGFGSRTEVKRLLKKKQVLVNGKIETSAKIQIDENQDEISVNNQVLIY- 61

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
           +R   +L +KP G+++   D   R TV D L     +  V  VG LDI+T GLLLLTN+G
Sbjct: 62  KRFVYYLLNKPKGVISATEDDKHR-TVLDLLDENARQKEVFPVGWLDIDTHGLLLLTNNG 120

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSN 186
            LA  +  P     +VYR +  G + +  +   + GI ++       ++T+    ++   
Sbjct: 121 TLAHAMLSPKKHAAKVYRAKVDGIITEKDVEHFEAGIELKDFTCRPAKLTILEVNEEPQT 180

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           + V + + EGK  + K++ +    KV  L R S GP
Sbjct: 181 SLVEITISEGKFHQEKRMVQACGKKVTDLERFSMGP 216


>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 =  206 bits (525), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 106 RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 162

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 163 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 222

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  206 bits (525), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 70/244 (28%), Positives = 114/244 (46%), Gaps = 16/244 (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 SALMH--SALERVYLLKIQGPITPEILEGMQNGICSHKGAHPNNPKQSLELPPFAHCHII 177

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                 + + + L EGKNRE+++ F  F+  V  L R+SYG   L  L  G TR ++ K 
Sbjct: 178 KNHPHFSKLKITLTEGKNRELRRFFAHFDRAVLDLQRVSYGFTHLNALPEGKTRYLNPKE 237

Query: 241 LREQ 244
            +  
Sbjct: 238 YQHL 241


>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 =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 109/236 (46%), Gaps = 3/236 (1%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           ++      R++K I+ +G+ SRR+ +  I    V VNG ++     +V   D ++ DG  
Sbjct: 33  IKNPSAGMRLNKYISNSGVCSRRDADIYIKSGNVTVNGEVIIEMGHHVKLEDEVKFDGRR 92

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLT 125
           +   E     L +KP     T S   G+ T  D + +    ++  VG+LD +  GL+L T
Sbjct: 93  IN-PEPKAYVLLNKPKSFYVTGSYEKGKLTALDLVQNASKSKLAPVGKLDTSAMGLILFT 151

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           NDG LA+ L        ++Y+V     + +  L ++K G  I+G      +      +  
Sbjct: 152 NDGTLAKKLSGHKNGIRQIYQVELTKPLRESDLEVIKDGPFIEGSKVKIEEAAFVDNRPK 211

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           N  V + LR  +   ++++F+   +++ ++ R+ Y       L  G  R ++++ +
Sbjct: 212 N-IVGLELRSQRAHIVQRIFKKLGYEIEKMDRVIYANLDKKNLPRGHYRHLTRQEV 266


>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 =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 108/233 (46%), Gaps = 9/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-IEVDGVPLRKAERTR 74
           + +++A  G  SR++   ++    V+++G +L+   +   +    I V+G      E+  
Sbjct: 6   LERLLASMGFGSRKDARGLVRMGLVELDGKVLDDPFMEFKTRPEFITVNGEEAPTVEKLY 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
           + LY KP  +  +H+  D +  V+D LP  F+   + SVGRLD ++ GLLLL+N G    
Sbjct: 66  VMLY-KPTDVECSHNARDHKP-VYDLLPERFTAMGIQSVGRLDADSSGLLLLSNQGDFIH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +E P     + YRV         +   L  G++++      +   ++    +   V + 
Sbjct: 124 KVESPKKGLWKKYRVTLARPFTDAQKAELLAGVMLKDERRPVLAREIEVSGDA---VDIS 180

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + EG   +++++F      V  L RI+ GP  L  TL  G  R ++ + +   
Sbjct: 181 IGEGLYHQVRRMFAAVGNHVETLERIAIGPVVLDRTLGEGGWRFLTDEEVAAL 233


>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 =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 76/233 (32%), Positives = 118/233 (50%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
            ++ K IA  G  SRR+ E +I Q +VKVN          V   D IE++G  L + E  
Sbjct: 1   MKIQKRIAHLGYCSRRQAEALILQNKVKVNSSFAT-IGQIVSDQDIIEINGKILVEKENE 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              +L HKP   +++  D   R  V D + S  SRV  VGRLD NT G+L+LTNDG L +
Sbjct: 60  KEYYLLHKPPKTISSTKDEKNRQVVTDLVKSK-SRVYPVGRLDYNTTGVLILTNDGDLTQ 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            L  P  Q  R+Y  +    +++ +L  L ++ I I       + +    Q    +++ V
Sbjct: 119 KLLHPKYQIKRLYHCKLDIPLEEKELIYLNEEKIYID----KKLSIHKVLQVEKKSYL-V 173

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            L +G    +KK+FE  N KV +L R+++GP  +  L  G  R+++ K ++  
Sbjct: 174 ELHQGSYHHVKKIFEKVNRKVVKLKRLAFGPITIDNLPEGYFRKLTFKEIKTL 226


>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 =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 56/188 (29%), Positives = 91/188 (48%), Gaps = 20/188 (10%)

Query: 73  TRLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            R  L++KP  ++T  +D    + RST+ D +P  F  +  VGRLD ++EGLLLLT+DG 
Sbjct: 3   YRYILFYKPYDVLTQFTDAESENKRSTLKDYIPISF--IYPVGRLDRDSEGLLLLTDDGQ 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           +   L  P     R Y V+      +D +  L+ GI IQ       +V L          
Sbjct: 61  MQHRLSDPKFAHPRTYWVQVEKIPSEDAIAHLRSGITIQNYRTRPTKVQLLSTEPLLPPR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    AW+ + L EGKNR+++++     +   RL+R++    +L  L  G  R
Sbjct: 121 NPPIRFRKNIPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVAIAHLRLDGLEPGQWR 180

Query: 235 EVSKKILR 242
           E++ + L+
Sbjct: 181 ELNPEELK 188


>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 =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 84/232 (36%), Gaps = 11/232 (4%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERT 73
           + +++   G  +R+    +I    V V G  +     +   TD++E  V G   R  E  
Sbjct: 6   LDRILQSQGFGTRKWCRELIEDGEVLVAGDSITDY-RHAFETDNLEFSVYGESWRFRE-H 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
                +KP     +   P     V   LP  F    V  VGRLD +T GLLL+++DG   
Sbjct: 64  VYIALNKPADYECSRK-PSHHPGVLSLLPEQFALRDVQPVGRLDHDTTGLLLMSDDGAFI 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P     +VY    H  V    +  L  G+ +         V  +        + +
Sbjct: 123 HAQSSPKRHIPKVYVATTHDPVTPQLVRQLMSGVKLHDEPAPLAAVVCNM--LDTCQLKI 180

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            L +GK  ++K++          L R   G  +L    L  G    + +  L
Sbjct: 181 VLEQGKYHQVKRMLAAAGNHCTALRRTEIGKLRLEALGLAEGEWCYLGEAEL 232


>gi|224826005|ref|ZP_03699108.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224601642|gb|EEG07822.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 236

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 107/233 (45%), Gaps = 7/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRKAERT 73
           + +++ + G  SR+E  +++    V+++G +++   + +     D + +DG P       
Sbjct: 3   LYRLMQQQGFGSRKECRKLVEHGLVELDGAVVDDYRLEIDPAAIDELVIDGEPWEILMLP 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
              L HKP G  T+H  P    +VF  LP  FS+  + +VGRLD++T GLLLLT DG   
Sbjct: 63  LYILLHKPAGYETSHK-PMHNPSVFTLLPWQFSQLGIAAVGRLDVDTTGLLLLTTDGQFV 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L  P     + Y V     V +  +  LK G+ ++        V    +      + +
Sbjct: 122 HALTSPKKHVPKCYEVTLKHPVSEALVKHLKAGVFLKDDNEK--VVADQVEVVDEITIRM 179

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            + +GK  ++K++      +V  L R++ G  QLG L  G  R +    L E 
Sbjct: 180 TITQGKYHQVKRMIAAAGNRVQELHRVALGTLQLGELDEGEWRHLDAAELAEL 232


>gi|23007931|ref|ZP_00049587.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 179

 Score =  206 bits (524), Expect = 6e-51,   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|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 =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 54/231 (23%), Positives = 103/231 (44%), Gaps = 6/231 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K ++     SR+E++ M+    VKV  + ++ + V +    D I V+G  +   E 
Sbjct: 1   MRLDKFLSNLNYGSRKEIKLMVKNGLVKVGNLTVKSSDVKIDPNYDKIFVNGTEVIYKEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             +  ++KP G +++H   +   ++F+ +  P     +   GRLD ++EGL++LT  G L
Sbjct: 61  -VILSFYKPAGYLSSHK-AEIYPSLFELIGAPYNQYDLKIAGRLDYDSEGLVILTTSGDL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P  +  +VY  +     ++     L +G+ I G                     
Sbjct: 119 VHQITHPKKKIRKVYEAKLDKHFNESSKLKLLQGVEIMGEDGMPYIGIALDLHYKEDVAY 178

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + EGK  ++KK+F    + V  L RI  G   L  L  G+ +E+ +  +
Sbjct: 179 ITIDEGKFHQVKKMFLEVGFLVTNLKRIQIGALTL-DLEPGTYKEIEENDI 228


>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 =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 89/187 (47%), Gaps = 18/187 (9%)

Query: 72  RTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             R  +++KP G+++    D    ST+ D +      V  VGRLD ++EGLLLLTNDG L
Sbjct: 4   HYRYIIFYKPYGVLSQFTKDAPTHSTLKDYID--VPDVYPVGRLDWDSEGLLLLTNDGQL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
              L  P     R Y V+     D+D +  L+ G+ IQ       QV L +++       
Sbjct: 62  QHRLAHPRFGHKRTYWVQVERIPDEDAIKRLQTGVKIQDYRTQPAQVRLLSKEPELPERT 121

Query: 185 ---------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                      AW+ + L EGKNR+++++     +   RL+R+S    QL  L  G  R+
Sbjct: 122 PPIRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVSIAHLQLDDLQLGEWRD 181

Query: 236 VSKKILR 242
           ++   L+
Sbjct: 182 LTTSELQ 188


>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 =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 67/216 (31%), Positives = 103/216 (47%), Gaps = 2/216 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               ++ K +   G A RR+ +  I  +RV VNG  ++     V   D++ VDG  L+  
Sbjct: 23  DENIKLQKYLQLCGFA-RRKADEYITSKRVIVNGKTVDEPWFEVNEDDNVLVDGKILKPN 81

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +     L HKP   VTT  DP  + T+ + +  I + +   GRLD +  G+L+LTNDG L
Sbjct: 82  QFEYYVL-HKPKDYVTTLFDPKQKKTIGELIKHIKTPLKPAGRLDKDATGVLILTNDGEL 140

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             +L     +  + Y V+    V  ++L  LKKGI  +G         +  +    + V 
Sbjct: 141 IDILTNAKYRVKKEYIVKVKSVVSAEELVKLKKGIYDKGEFLKLEHFKIIEKSSEYSIVR 200

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           V L +GK  EIK++F      V  L RIS+GP  + 
Sbjct: 201 VELIKGKKHEIKRLFSSIGHNVLELKRISHGPISIS 236


>gi|222110316|ref|YP_002552580.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221729760|gb|ACM32580.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 245

 Score =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 101/247 (40%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
            ++  ++   G  +RR    +I Q RV ++        +   +T  I+V+ + LR     
Sbjct: 1   MQLQDILYSQGFGTRRICAGLIQQGRVAMHATGTLEPTICQDATQDIDVESLVLRVQGVD 60

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINT 118
              +     + HKP G   +   P    +++  LP+   +         V +VGRLD +T
Sbjct: 61  WPYQPKAYVMLHKPAGTECSQK-PSAYPSIYTLLPAPLRQRPSKGAVDGVQAVGRLDQDT 119

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG     +  P     +VYRV     V +++++ L  G+V+           
Sbjct: 120 TGLLLLSDDGQFIHRMSSPKKHVPKVYRVTAKHPVTKEQVDRLLAGVVLDDDPRPVRAAA 179

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVS 237
                     + + L EGK  ++K++      +V  L R   G   L   +  G  R + 
Sbjct: 180 CALVDA--HVLDLTLTEGKYHQVKRMIAAVGNRVEALHRSHIGRLALPADMQPGEWRWLG 237

Query: 238 KKILREQ 244
           ++ L + 
Sbjct: 238 EEELAQL 244


>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 =  205 bits (523), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 66/254 (25%), Positives = 110/254 (43%), Gaps = 32/254 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      +     IE+      +     
Sbjct: 356 RLSKRMSELGLCSRREADEWIPRGWVLVDGKPVTELGSRIRPDAEIEILQEARSEQGERV 415

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L +KP+G V+  ++                +G  T     P     +   GRLDI++ 
Sbjct: 416 TVLLNKPVGYVSGQAEDGYEPAAALFAPENQWEGDPTRKRFAPWQRKNLAPAGRLDIDST 475

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQVDQ--------DKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR      HG V++        D L LL+ G+ 
Sbjct: 476 GLLVLTQDGRVARALIGEDSTVEKEYLVRVVWHSPHGPVERNISAEFPADDLELLRHGLS 535

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L R+  G   LG
Sbjct: 536 LDGVPLKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLQVVGLKRVRMGRVVLG 591

Query: 227 TLLAGSTREVSKKI 240
            L  G  R + +  
Sbjct: 592 DLPPGKWRFLGQFE 605


>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 =  205 bits (523), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 95/188 (50%), Gaps = 17/188 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   SD +GRST+ D +    + V  VGRLD ++EGLLLLTN+G + 
Sbjct: 40  QTQVILFNKPFDVLCQFSDENGRSTLKDFID--IAEVYPVGRLDRDSEGLLLLTNNGEIQ 97

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y ++  G  D+  L  L++G+ ++       +V L            
Sbjct: 98  HRLAEPKFKMEKTYWMQVEGVPDETALEQLRRGVQLKDGMTKPAKVRLISEPDCLWQRVP 157

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RLIR     F L  L   + R +
Sbjct: 158 PIRERKNIPTSWLEIKIYEGRNRQVRRMTAHIGFPTLRLIRCQLAGFTLQNLAPKTYRTL 217

Query: 237 SKKILREQ 244
           ++  L++ 
Sbjct: 218 TQDELKQL 225


>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 =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 60/203 (29%), Positives = 96/203 (47%), Gaps = 8/203 (3%)

Query: 48  ERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                 +    D I V G  L   E    +L +KP G+++   D   R TV D L +   
Sbjct: 26  TSPKQQINEKKDQIAVAGQVLSH-ETFVYYLLNKPKGVISATEDDHHR-TVLDLLDNTAR 83

Query: 107 R--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           +  V  VGRLDI+T GLLLLTN G LA  +  P     ++YR +  G + Q+ +     G
Sbjct: 84  QKEVFPVGRLDIDTHGLLLLTNKGQLAHAMLSPKKHVDKLYRAQVDGIMTQEDVERFAAG 143

Query: 165 IVIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           I ++       Q+T+ +  +    + V + +REGK  +IK++ +     V  L R++ GP
Sbjct: 144 IELKDFTCQPAQLTILSTDEAKQTSLVDITIREGKFHQIKRMVQACGKTVTDLQRLTMGP 203

Query: 223 FQLG-TLLAGSTREVSKKILREQ 244
            +L   L  G  R ++   L++ 
Sbjct: 204 LRLDPKLALGEYRRLTAAELKQL 226


>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 =  205 bits (522), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 54/189 (28%), Positives = 91/189 (48%), Gaps = 16/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +      ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 90  KRVISPSERKVVLFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVEIIPEPE 207

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  205 bits (522), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 56/225 (24%), Positives = 108/225 (48%), Gaps = 12/225 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  +R E ++ +    + +N   +   ++     D I+++G  L   + T 
Sbjct: 7   RVDAHLSSLGYCTRSEAKKFLRMNEICINDNRVYNTSIKAY-HDDIKINGEVLD--DETL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
           L L +KP G + +H+D      ++  LP  +SR       +GRLDI+T G++LLT+DG L
Sbjct: 64  LILLNKPQGYICSHNDSG--KLIYSLLPQRYSRRNPKISTIGRLDIDTTGVILLTDDGVL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
           +  L  P     ++Y       +  D++ +   G +++ G     +   L+    +  +V
Sbjct: 122 SHRLTSPKKDISKIYEATLEKPLKGDEVEIFASGTLMLNGEEKPLLPAKLEI--ITPTFV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + + EGK  ++K++F   + KV +L R  +  F+L  L  G  +
Sbjct: 180 KIEIVEGKYHQVKRMFAAVSNKVIKLHRTKFADFELEDLKEGEFK 224


>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 =  205 bits (522), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 63/254 (24%), Positives = 105/254 (41%), Gaps = 32/254 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I    V V+G  +      +     IE+      +     
Sbjct: 332 RLSKRMSELGLCSRREADEWIPHGWVLVDGKPVTELGSRIRPDAEIEIMQEARSEQGERV 391

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L +KP+G V+  ++                +G  T     P     +   GRLDI++ 
Sbjct: 392 TVLLNKPVGYVSGQAEDGYEPAAVLFTPENQWEGDPTRKRFAPWQRKSLAPAGRLDIDST 451

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-------------QVDQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR                +   D L LL+ G+ 
Sbjct: 452 GLLVLTQDGRVARALIGEDSTVEKEYLVRVIWHSPQGVVERNISAEFPADDLELLRHGLS 511

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G+     +V+   ++     +   LREG+ R+I+++ E    +V  L R+  G   LG
Sbjct: 512 LDGVPLKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLQVVGLKRVRMGRVVLG 567

Query: 227 TLLAGSTREVSKKI 240
            L  G  R + +  
Sbjct: 568 DLPPGKWRFLGQFE 581


>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 =  205 bits (522), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 113/229 (49%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G+ SRR+ +  I    VKVNG+ +      V   D +  DGV L   E+ 
Sbjct: 70  IRLNKYISNSGVCSRRDADLYIQSGNVKVNGVPVTEMGYLVKLNDVVNFDGVTLT-PEKK 128

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP    T   +      V + +  +  +++  +GR+D NT GLLL TND  + R
Sbjct: 129 EYILLNKPKNFTTALDEGQEYRNVLELVRAATNAKIAPIGRMDKNTTGLLLFTNDTDMIR 188

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
              LP+ +  ++Y+V     +  + L  + KG+V+ G      +++   +K   + V + 
Sbjct: 189 KFSLPNQKSPKIYQVSLDKNLKFEDLEKISKGLVLDGHRVSVEEISY-IEKEPKSEVGLK 247

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           LR    + ++ +FE F++ V R+ R+S+       L  G+ R ++ + +
Sbjct: 248 LRSSNVKVVRAIFENFDYNVLRIDRVSFAGLTKKNLPRGNWRFLTDQEV 296


>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 =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 5   RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 61

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 62  TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 121

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|396661|emb|CAA79503.1| unknown open reading frame [Buchnera aphidicola]
          Length = 258

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 87/239 (36%), Positives = 131/239 (54%), Gaps = 9/239 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-NVMSTDHIEVDGVPL----RK 69
           ++ K+++  G  SRR +E MI   ++ +NG         N  +   I +D   +     K
Sbjct: 4   KIQKILSDLGYGSRRFIECMIKCGKISINGEKAIIGQYLNKKNPGEILIDKKKIIVKRNK 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
                L   +KPIG V T  D   R TVFD LP    +R +SVGRLDINT+GLLL TNDG
Sbjct: 64  NLPKVLIYNNKPIGEVCTRDDFQKRLTVFDKLPKLNLNRWVSVGRLDINTKGLLLFTNDG 123

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQG-ICYGDMQVTLDTQKGSN 186
            LA  L  P +Q  R Y +R  G+++++K+N+L+KG+ +I G + + ++    D ++G N
Sbjct: 124 TLANKLMHPRSQIEREYNIRIFGEMNKNKINILRKGVKIIHGYVSFKEIVPLYDKKEGKN 183

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILREQ 244
            W    L EGKNREI+ +F+    +VN+LIR+ YG   L   L  G    ++   L++ 
Sbjct: 184 KWFKGILCEGKNREIRLMFKSIQCQVNQLIRVRYGNIILPKNLKEGQWMMLNSIFLKKL 242


>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 =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 102/240 (42%), Gaps = 11/240 (4%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEV 62
           +  N  P R+ K+++  G  +R+E++ +   QR+ +     +  +  V   +     + +
Sbjct: 1   MSGNAKPVRLDKLLSNMGYGTRKEIDALARYQRILLGDKGFKSGSDKVTPNEDLQNRLTI 60

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSIFSRVISVGRLDINTEG 120
           D  P+       + + +KP G+  +  D     T             +  +GRLD  T G
Sbjct: 61  DDKPVDPLPGFAV-MLNKPAGVTCSRKDSGTLITELFPSRWDKRDPLLSPIGRLDKETSG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTL 179
           LLLLT+DG L   +  P TQ  + Y V     ++ D+ ++   G ++++      +   L
Sbjct: 120 LLLLTDDGQLNHRVSSPKTQTPKRYHVILDRDLNGDEDSIFAAGELMLESETKPLLPAEL 179

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSK 238
                  A +   L EG+  +++++F      VN L R S G   L   L  G  R +S+
Sbjct: 180 SALGKREAIL--TLHEGRYHQVRRMFAAVGNHVNALHRESIGGLTLPEDLQQGQWRIMSE 237


>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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 66/232 (28%), Positives = 109/232 (46%), Gaps = 10/232 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   +A A   SR+E +  IA+ RV VNG    +A   V     + +D  PL   ++ 
Sbjct: 1   MRLDYYLAHAANLSRKEAKIAIAKGRVLVNGESKLKANSPVTDLCDVILDKSPLSF-QQN 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           R ++ +KP G+V    D +    V D LP    + +  VGRLD +T GLLLLT DG    
Sbjct: 60  RYYMMYKPAGVVCALQDDEHD-VVLDLLPHEIQKELKIVGRLDKDTTGLLLLTTDGQWLH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVT 190
            +  P     + Y V    ++ +D +  L+KG++++G        +V   T+K     ++
Sbjct: 119 KITSPKHDCPKTYLVDLADEITKDAIEALEKGVLLKGEIDLTKPAKVVSHTEK----QIS 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EGK  ++K++      KV  L R   G   L   +  G   E+S + +
Sbjct: 175 LTISEGKYHQVKRMLAAVGNKVEALHRTQIGEVCLSQDMALGEFTELSPEQV 226


>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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 58/227 (25%), Positives = 106/227 (46%), Gaps = 12/227 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  SR E ++ +   +V+VNG  +      V   D I +D + L     T 
Sbjct: 7   RVDAHLSSLGYCSRSEAKKFLKIFQVRVNGERVFDTNKKVYHNDII-IDEIVLDPETLTV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
             L HKP G++ +H D      ++  LP  + +       +GRLD +T G +LLT+DG L
Sbjct: 66  --LMHKPSGIICSHDDVGV--LIYSLLPERWQKRNPKLSTIGRLDGDTTGAILLTDDGAL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P +   ++Y V     +  ++  +   G ++++G     +   ++    S + V
Sbjct: 122 NHRLTSPKSDISKLYEVTLAQPLKGNEAEIFTSGTLILRGEKKPLLPAKMNV--ISESVV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            + + EGK  ++K++F     KV  L R+S+G + +  L  G  + +
Sbjct: 180 HLEISEGKYHQVKRMFAAVGNKVTALHRVSFGKYSIENLAIGEYKIL 226


>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 =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 100/233 (42%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+     +RR+V   IAQ+R+ VNG         V    HI  D   L+ A    
Sbjct: 7   RLDRFISLNSNLNRRDVRLAIAQKRILVNGKHASTIHQVVSQFCHITFDNQTLQ-ANAPV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G V+   D     TV   LP      +  VGRLD N+ GL+LLTN+G  +R 
Sbjct: 66  YIMLNKPAGRVSATKDSTH-PTVVGCLPQQLQANIHIVGRLDFNSTGLMLLTNNGAWSRH 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L  P  +  ++Y V     ++ D+    ++    G+             L+    + A  
Sbjct: 125 LTSPENKVNKIYEVELERTINDDEWPQYISAFASGMYFAFEDLTTQPAKLERLTATRA-- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
            V L EG+  +IK++F  F  KV  L R   G   L   L  G  R ++   +
Sbjct: 183 RVTLVEGRYHQIKRMFGRFRNKVIALHRTQLGALPLDPALQPGEHRLLNDDEI 235


>gi|213023264|ref|ZP_03337711.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 244

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 86/250 (34%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 59  HIEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGR 113
            I +DG  +   E      R+  Y+KP G + T +DP+GR TVFD LP    +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 TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
             E+        L         V L     S   + +DR  + +       R  K  SQ 
Sbjct: 182 WTELD-------LAQTNYLRGLVELPPETSSKVAVEKDRRRMKAN---QIRRAVKRHSQI 231

Query: 293 NGLSKQKKLA 302
            G  +     
Sbjct: 232 AGGRRSGGRN 241


>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 =  204 bits (520), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 106/240 (44%), Gaps = 17/240 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           RV +++A  G   RRE + ++ + RV   +G  L+     V   D + +D   L      
Sbjct: 80  RVERLLANLGYGKRRECQVLVKKGRVTRRDGGKLK-VGDKVCWGDVV-LDEEDLDPPSPL 137

Query: 74  RLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTND 127
            L   HKP G V T  D +      V+D LP  F+R    +  VGRLD +T GLLLLT+D
Sbjct: 138 -LLALHKPGGYVVTSPDDENITDPVVYDLLPYRFARRRPFLAPVGRLDKDTSGLLLLTDD 196

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK----KG-IVIQGICYGDMQVTLDTQ 182
           G L   +  P     +VY       +  ++          G +V++G     +   LD  
Sbjct: 197 GALLHRINSPRRGIWKVYEATLAEPMSTNQAAAAARRFASGSLVLEGDHTPLLPAKLDLI 256

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
               A   V + EGK  +++++F      V  L R+S G   LG+L  G  R +  + L+
Sbjct: 257 GARTA--RVAICEGKYHQVRRMFAAVGSHVVALHRVSVGGLTLGSLPEGEWRYLQPQELQ 314


>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 =  204 bits (520), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 62/262 (23%), Positives = 105/262 (40%), Gaps = 32/262 (12%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            + + +      R+SK ++  G+ SRRE +  I +  V V+G  +      +     IE+
Sbjct: 347 RQPVSEHEDGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGKPVTELGTRIRPEAEIEI 406

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR---------------STVFDNLPSIFSR 107
                 +       L +KP+G V+  ++                    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 DDLLERLRHGLSLDGVALKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLKVVG 582

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           L R+  G   LG L  G  R +
Sbjct: 583 LKRVRMGRVVLGDLPPGQWRFL 604


>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 =  204 bits (520), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 105/233 (45%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
            RV K+I   G+ +R+ ++R   +  + +NG +++ ++V V    D +   G  +   E 
Sbjct: 1   MRVDKMIGNTGLDTRKNIKRNAKKGALVINGEIVKDSSVKVDPLVDEVFYMGHFVEYIEN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+++   D +   TV D L   +    +   GRLD +T GL++L+ DG  
Sbjct: 61  L-YLILNKPSGVLSATQDAE--ETVIDLLDDFYKNYDLSIAGRLDKDTTGLIILSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y V+    + ++     KKG+ I+   Y      L       A V 
Sbjct: 118 IHKITSPNSHITKTYEVKTRDPIAENLKEEFKKGVYIKEDDYTARPAELTITGEKEAIVK 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           V   EGK   +K++F     +V  L R + G   L   L  G  RE+++  L 
Sbjct: 178 VT--EGKYHLVKRLFSNLGNEVVGLKRTAIGKLVLDPYLKEGDYRELTEAELE 228


>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 =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 66/228 (28%), Positives = 109/228 (47%), Gaps = 9/228 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R+ + I++    S  +   +IAQ+R+ ++G +       V    ++E+DG  L+ 
Sbjct: 2   KSTTNRLDRFISQNSPFSISDTRLLIAQKRILLDGHVAHSNQQKVTKFTYVELDGNCLQ- 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
                  + +KP G+V+   D    STV D +       +  VGRLD NT GL+LLTNDG
Sbjct: 61  DNNPLYIMLNKPKGVVSATKDIKH-STVLDLIQHPQKNELHIVGRLDFNTTGLVLLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
             +R + LP T+  +VY V     + ++ + + ++GI    + I      + +     S 
Sbjct: 120 AWSRKISLPETKLAKVYEVTLSKPLTEEYVAVFREGIYFGYEDITTKPACLEIL----SE 175

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + L EGK  ++K++F FF  +V  L R S G   L  L  G +R
Sbjct: 176 YTARLSLVEGKYHQVKRMFGFFQNEVLELHRASVGNISLEGLEEGHSR 223


>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 =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 121/241 (50%), 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------------L 179
           L    ++  RVY ++  G++ ++    ++ G+ +Q    G  Q +              +
Sbjct: 121 LM--ESKLERVYLLKLSGEIKEEVFEAMENGLSLQDARLGGHQKSKIKAMEFSPFMGYWV 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|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 =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 66/268 (24%), Positives = 118/268 (44%), 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  LRKAER-------------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVIS 110
           +                   +  + HKP GL+ T+ D   R +VF   P       R++S
Sbjct: 100 INIQNIKNILNNYNINNNSYKWIVLHKPKGLICTNQDEKDRKSVFSIFPEDLLQKYRIVS 159

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG- 169
           VGRLD NT G+LL TN+      L  P  + +R Y +   G V  D L +L  G+ ++  
Sbjct: 160 VGRLDRNTSGILLFTNEYAWVNKLTHPKYERVRKYMIHIEGPVRMDALKMLANGVYLKDE 219

Query: 170 ---------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                              +  V +  Q    + + + ++EG+NR+I+K+F+  N  + +
Sbjct: 220 DNDKKKNKKTQPALIEVLREENVKIQNQIKKISVLNISIKEGRNRQIRKMFQQINQPIIK 279

Query: 215 LIRISYGPFQLGTL-LAGSTREVSKKIL 241
           + R ++    L  + L    RE++KK +
Sbjct: 280 IKRTAFENITLKNIHLPKQYRELTKKEI 307


>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 =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/195 (33%), Positives = 98/195 (50%), Gaps = 8/195 (4%)

Query: 52  VNVMSTD-HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RV 108
           + V   +  IEV G  L+  E     + +KP G+++   D   R TV D LP  +    +
Sbjct: 1   MQVNPKESVIEVAGEILKYRE-YIYIMMNKPQGVISATYDNRHR-TVIDILPDEYKFFNL 58

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
             VGRLDI+TEGLLLLTNDG LA  L  P     + Y     G V    +++ ++G+V+ 
Sbjct: 59  FPVGRLDIDTEGLLLLTNDGQLAHELLSPRKHVPKKYYALIDGIVTTKDVDVFREGVVLD 118

Query: 169 GICYGDMQVTL-DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG- 226
              Y  +   L   + G  + V + + EGK  ++K++FE    KV  L RI  G  +L  
Sbjct: 119 DG-YKTLPSELFILKSGPYSEVEIVIYEGKFHQVKRMFEAVGKKVKYLRRIGMGKLKLDE 177

Query: 227 TLLAGSTREVSKKIL 241
           TL  G  RE++ + +
Sbjct: 178 TLEPGDVRELTDEEM 192


>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 =  203 bits (518), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 57/220 (25%), Positives = 110/220 (50%), Gaps = 9/220 (4%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           ++ A + SR++V+++I ++RVKVNG ++ +   NV   D + VD + +         +++
Sbjct: 1   MSNAKVGSRKQVKKLIKEKRVKVNGSIVTKPEFNVDENDEVFVDDIEI-IPHHNVYIVFN 59

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           KP G  ++ S+ +     F + P     +  VGRLD + EGL+L+TNDG     +  P +
Sbjct: 60  KPSGFTSSKSEYERNIFEFIDHP-YLDELHIVGRLDKDVEGLILITNDGNFTHKVISPKS 118

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
              + Y V+  G + ++ + +   GI +  GI +   ++T    K  +  +++ + EGK 
Sbjct: 119 NIEKEYIVKIEGILTKEMIEIASNGITLNNGIKFKPAKIT----KIDDETISLVITEGKF 174

Query: 199 REIKKVFEFFNWKVNRLIRISYG--PFQLGTLLAGSTREV 236
            E+K +  F   K  ++ R+  G        L  G  +E+
Sbjct: 175 HEVKLIVGFLGLKYKKIKRVRIGKLNLNDFNLNLGEWKEI 214


>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 =  203 bits (518), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 59/204 (28%), Positives = 101/204 (49%), Gaps = 9/204 (4%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           M+AQ+R+ V+G +    +  +     +++DG    +       + +KP G+V    DP  
Sbjct: 1   MLAQRRIMVDGKVASDMSQTIDKFSRVQLDGE-WTQNHTAHYLMLNKPQGVVCATKDPLH 59

Query: 94  RSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           R T+ D L      ++  VGRLD N+ GL+LLTNDG  +R L  P ++ ++ YRV     
Sbjct: 60  R-TILDLLELPDKEQLHIVGRLDYNSTGLVLLTNDGQWSRKLSHPDSKLIKRYRVTTEQT 118

Query: 153 VDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + ++ +   + G+     GI      +T+   K +     V L EG+  +IK++F  F  
Sbjct: 119 ITEEYVQAFQSGMYFDFEGITTRPAPLTILDSKTAQ----VDLTEGRYHQIKRMFGRFQN 174

Query: 211 KVNRLIRISYGPFQLGTLLAGSTR 234
           KV  + R + G ++LG L  G  +
Sbjct: 175 KVLSIHRFAVGSYELGELSPGEYK 198


>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 =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 105/235 (44%), Gaps = 4/235 (1%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           +++    R++K IA +GI SRRE +  I+  +V VNG ++      V   D +  DG  +
Sbjct: 59  KKDDGTMRLNKYIANSGICSRREADMYISIGQVTVNGKVVNEMGYQVKLEDDVRFDGRRI 118

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
              E     L +KP G  TT S+  G  TV D +     SR+  +GRL  N  GLLL TN
Sbjct: 119 N-PEAKAYVLLNKPKGFATTTSNDKGN-TVMDLVAGSTKSRIQPIGRLGRNAMGLLLFTN 176

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           D  L +          ++Y V     +    +  + +G+ I G      +++        
Sbjct: 177 DDELVQKFTNSKKGVDKLYHVELSNNLKGADIERINEGLKIDGKTITVDEISYVDG-APK 235

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             V + +R   N  I+ +FE  N++V R+  ++        L  G  R ++K+ +
Sbjct: 236 KEVGLRIRNTGNSVIRTIFEHLNYEVVRVDCVTIAGLTKKDLPRGHWRYLTKQEV 290


>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 =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 55/225 (24%), Positives = 107/225 (47%), Gaps = 12/225 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  +R E ++ +    + +N   +   ++     D I+++G  L   + T 
Sbjct: 7   RVDAHLSSLGYCTRSEAKKFLRMNEICINDNRVYNTSIKAY-HDDIKINGEVLD--DETL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
           L L +KP G + +H+D      ++  LP  ++R       +GRLDI+T G++LLT+DG L
Sbjct: 64  LILLNKPQGYICSHNDSG--KLIYSLLPQRYNRRNPKISTIGRLDIDTTGVILLTDDGVL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     ++Y       +  D++ +   G +++ G     +   L+    +  +V
Sbjct: 122 NHKLTSPKKDISKIYEATLEKPLKGDEVEIFASGTLMLNGEEKPLLPAKLEI--ITPTFV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + + EGK  ++K++F   + KV +L R  +  F+L  L  G  +
Sbjct: 180 KIEIVEGKYHQVKRMFAAVSNKVIKLHRTKFADFELEDLKEGEFK 224


>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 =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 55/185 (29%), Positives = 91/185 (49%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L +KP  ++T  +D DGR+T+ D +P     V   GRLD ++EGLLLLTNDG
Sbjct: 26  PPAEPRLLLLNKPFDVLTQFADADGRATLKDFVP--VPGVYPAGRLDRDSEGLLLLTNDG 83

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P  +  + Y V+  G+VD+ +L  L++G+ +        +     +      
Sbjct: 84  RLQARIADPKHKLPKTYWVQVEGEVDETQLERLRQGVELNDGMTLPAEARQLDEPELWPR 143

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 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|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 =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 61/195 (31%), Positives = 94/195 (48%), Gaps = 20/195 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R  L +KP  ++    D  GRST+ D +P     V   GRLD ++EGL+LLTNDG L  
Sbjct: 3   YRYILLYKPYRVLCQFQDQKGRSTLKDYVP--IPDVYPAGRLDYDSEGLVLLTNDGWLQH 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------- 183
            L  P     R Y V+  G+ D   L+ L  G+VIQG      +V +  Q          
Sbjct: 61  RLTDPRYGHPRTYWVQVEGKPDTAALSQLAAGVVIQGYRTRPARVEVLDQDPPLPPRYPP 120

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE-- 235
                   + W+++ LREG+NR+++++     +   RL+R++    QLG L  G  RE  
Sbjct: 121 IRYRRHIPSQWLSLTLREGRNRQVRRMTAAVGFPTLRLVRVAIANLQLGNLAPGQWREIL 180

Query: 236 -VSKKILREQLGPHL 249
            + +++L +  G   
Sbjct: 181 PLERQVLWQSCGRRP 195


>gi|255084639|ref|XP_002508894.1| predicted protein [Micromonas sp. RCC299]
 gi|226524171|gb|ACO70152.1| predicted protein [Micromonas sp. RCC299]
          Length = 248

 Score =  203 bits (517), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 103/242 (42%), Gaps = 32/242 (13%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE---------------- 71
           RRE +  ++  RV+VNG L++  +  V S D + +DG  L                    
Sbjct: 1   RREADEAVSAGRVRVNGALVK-PSFRVRSGDVVTLDGKALDWEPFAAATEGSIGAHAGSN 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
                 Y+KP G+  T                  +RV  VGRLD ++ GL+LLT+DG + 
Sbjct: 60  GFFYLKYNKPRGVTCTMESSQRTKPAKGV---GSARVFPVGRLDRDSSGLVLLTDDGRVP 116

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGI----CYGDMQVTLDT 181
             L  PS +  + Y V        D +  L+ G+VI       G+          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 IL 241
            L
Sbjct: 237 EL 238


>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 =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 92/185 (49%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              + RL L +KP  ++T  +D  GR+T+ D +      V   GRLD ++EGLLLLTNDG
Sbjct: 5   PPAQPRLLLLNKPFDVLTQFNDEQGRATLKDFVD--VPGVYPAGRLDRDSEGLLLLTNDG 62

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P  +  + Y V+  G+  +++L  L+ G+++        +     +      
Sbjct: 63  RLQARIADPKHKLAKTYWVQVEGEPSEEQLQQLRTGVMLNDGPTLPAEARRLDEPELWER 122

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       +W+ + +REG+NR+++++         RL+R++ GP++L  L  G  R
Sbjct: 123 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVAIGPWRLDGLQPGQWR 182

Query: 235 EVSKK 239
           E++ +
Sbjct: 183 ELAAR 187


>gi|207091745|ref|ZP_03239532.1| hypothetical protein HpylHP_01046 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 257

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKCSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  203 bits (516), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 61/189 (32%), Positives = 94/189 (49%), Gaps = 17/189 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR  ++HKP  ++   +DPDGR T+ D +      V + GRLD ++EGLLLLT+DG LA 
Sbjct: 7   TRTLVFHKPYDVLPCFTDPDGRPTLGDYID--VPGVYAAGRLDRDSEGLLLLTSDGALAH 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|217978386|ref|YP_002362533.1| pseudouridine synthase [Methylocella silvestris BL2]
 gi|217503762|gb|ACK51171.1| pseudouridine synthase [Methylocella silvestris BL2]
          Length = 255

 Score =  202 bits (515), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 60/229 (26%), Positives = 101/229 (44%), Gaps = 15/229 (6%)

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  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
               +   +KP G+  +  +      VFD LP  F         VGRLD +T GLLL+T+
Sbjct: 72  PGM-VIALNKPRGVTCSRKEAG--PLVFDLLPPRFRLREPALSTVGRLDKDTSGLLLITD 128

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   L  P     + Y  +    +  D+  +   G +++       +   L     +
Sbjct: 129 DGALLHRLISPKHNIAKRYCAKLARPLRGDEAEIFASGEMMLDDEAKPLLPAVLRVLSPT 188

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            A V+V   EG+  +I+++F      V  L R+S G F L  TL  G  
Sbjct: 189 EAEVSVT--EGRYHQIRRMFAATGNHVLELHRMSIGDFALPLTLAPGDF 235


>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 =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 55/217 (25%), Positives = 101/217 (46%), Gaps = 9/217 (4%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89
           + + +I   R++VN  +++     V   D I  DGV L+       ++ +KP G +  + 
Sbjct: 10  KCKNLIKSSRIRVNNQIIKDIRYQVDIDDVIVFDGVELKWP--FVYYMLNKPKGYICANH 67

Query: 90  DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
           D   +  V D +         +GRLDI+T GLLL+TND  L++ L LP     + Y V  
Sbjct: 68  DKKYK-CVIDLIGRD--DCYCLGRLDIDTTGLLLITNDKTLSKRLLLPENHIDKKYYVTV 124

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
             ++  D + +   GI+I           L+     + ++   + EG+  +IKK+F   N
Sbjct: 125 KNKLTDDLIEIFNNGIIID-QKVKCKPSYLEIIDDYHCYL--TINEGRYHQIKKMFLSCN 181

Query: 210 WKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
            KV  L R+ +    L   L   + R+++ + +++ +
Sbjct: 182 NKVLELKRVMFASINLDNNLSLANYRKLNNQEIKQLI 218


>gi|126640866|ref|YP_001083850.1| putative ribosomal large subunit pseudouridine synthase B
           [Acinetobacter baumannii ATCC 17978]
          Length = 279

 Score =  202 bits (514), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 84/279 (30%), Positives = 130/279 (46%), Gaps = 13/279 (4%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAE----RTRLWLYHKPIGLVTTHSDPDGRST 96
            VNG + +     +   D + +DG  ++       R R+ +Y+KP G + + +DP+ R T
Sbjct: 2   SVNGRVAQ-VGERIEPGDELRIDGRKVQFQIEDEIRRRVLIYYKPEGEICSRNDPEKRPT 60

Query: 97  VFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           VFD+LP I + 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 IRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
           +R  YG   L   L  G   E+ K  +        L+  Q      +       + R   
Sbjct: 181 LRTRYGTVILPRELRTGRWMELDKTDIDNLAKSVELKPRQGTGLFGM------AKRRTER 234

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
           ++E P    R      Q+    K+    T   R++   N
Sbjct: 235 MTEKPMAARRGGYLRQQRRDDEKEAPANTGNQRKSTGFN 273


>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 =  202 bits (514), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 54/187 (28%), Positives = 93/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  + L++KP   ++  +D DGR T+ + +      V + GRLD ++EGLL+L
Sbjct: 91  RAISPSERKVV-LFNKPYDTLSQFTDGDGRKTLANYI--QIKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L++G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGVPQESDLEALRQGVTLKDGPTLPAKVEIMPEPE 207

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 68/235 (28%), Positives = 116/235 (49%), Gaps = 14/235 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ ++I+ +   +R++V  ++AQ+RV V+G+L    A  V    H+ +D   L+ A +T 
Sbjct: 7   RLDRLISDSRQINRKKVRLILAQKRVYVDGVLATDIAQLVDQFSHVVMDNEVLQ-ANQTH 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGG 129
             + +KPIG+V    D   + TV D L   F +     +  VGRLD+NT GL+LLTND  
Sbjct: 66  YIMLNKPIGVVCATKDKKHK-TVIDLLAEQFDQDVLDSLHIVGRLDLNTSGLVLLTNDSR 124

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNA 187
            +  L  P  +  + Y+V     +  D ++   KG+    + I      + + +   +  
Sbjct: 125 WSERLTSPEHKVSKGYQVTLENALTTDYIDAFAKGMYFPYENITTKPAILHIVSLFEAQ- 183

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
              V L EG+  +IK++F  F   V  L R S G  +L  +L  G +R ++   +
Sbjct: 184 ---VSLTEGRYHQIKRMFGRFRNPVIALHRYSIGSLRLDESLKDGESRVLNVSEV 235


>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 =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 118/239 (49%), Gaps = 15/239 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  G+ S++++ R++ ++  ++NG  +  A   +    D +  +G  L      
Sbjct: 4   RIDKILAANGLGSQKDIRRLLRKEDFRINGTRVTDAGTLLDPEHDALSRNGETLHLRT-C 62

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA 131
              + +KP G+VT+ +DP   STV + LP  F    +  +GRLD++TEGLL++TNDG L 
Sbjct: 63  CYLMLNKPAGVVTSTADPLH-STVMELLPPPFPAMELFPIGRLDLDTEGLLIITNDGALT 121

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLK----KGIVIQGICYGDMQVTLDT---QKG 184
             L  P +  ++ Y +       +      +    +G+ + G  +  +  T +    Q+ 
Sbjct: 122 HRLTAPKSACIKSYYLETAEPFTESTFTAARIACAEGLPL-GKNFTCLPATFERTTSQRV 180

Query: 185 SNAW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
              W   + + EGK  ++KK+ +    +V  L RI+ G   L   L AGS RE++   +
Sbjct: 181 KTEWAFLMHICEGKYHQVKKMVKALGNEVVYLKRIAMGGVTLDPKLPAGSCRELTPDEI 239


>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 =  201 bits (513), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLTNDG
Sbjct: 5   PPSEPKLLLFNKPFDVLTQFNDEQGRSTLKDFIP--VPGVYPAGRLDRDSEGLLLLTNDG 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|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 =  201 bits (513), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 53/176 (30%), Positives = 87/176 (49%), Gaps = 16/176 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   VLFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLILTNDGILQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------------ 183
            P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +             
Sbjct: 60  QPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPTLWPRNPPVRFR 119

Query: 184 --GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                 W+ + L EG+NR+++++     +   RLIR S G + LG L  G  REV+
Sbjct: 120 AAIPTTWLAITLMEGRNRQVRRMTAHIGFPTLRLIRYSMGDWNLGDLQPGEWREVT 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 =  201 bits (513), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 56/189 (29%), Positives = 94/189 (49%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  + L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RAISPSERKVV-LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V + ++  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGVPQESDLEALRHGVTLKDGPTLPAKVEIMSEPE 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (513), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 59/214 (27%), Positives = 97/214 (45%), Gaps = 6/214 (2%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHS 89
           ++++I  Q V V+ +       NV      IEV G  +    +    + +KP G+V+   
Sbjct: 1   MKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-KHSYIILNKPSGVVSAKK 59

Query: 90  DPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
           D     TV D L        +  VGRLD +TEGL+LLT++G L   +  PS    + Y V
Sbjct: 60  DT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPLGFRMLDPSHHVSKTYLV 118

Query: 148 RFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
             +G + +D  +    GI    G      Q+T+       +  ++ + EGK  ++KK+F 
Sbjct: 119 TVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQASLTISEGKFHQVKKMFL 178

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +  KV  L R  +   +LG L +G  R ++   
Sbjct: 179 TYGLKVTSLKRTHFAGLELGHLASGEYRYLTASE 212


>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 =  201 bits (513), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (513), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 68/234 (29%), Positives = 110/234 (47%), Gaps = 11/234 (4%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
            ++++  G   R+EV  ++AQ R+ ++G   +     V     + +D   L+ A + R  
Sbjct: 2   DRLVSERGGVHRKEVRLLLAQGRIHIDGRPADSINQAVGPFTRVTLDARVLQ-ANKARYV 60

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           + HKP G+V+   D   + TV D L     S +  VGRLD N+ GL+LLTNDG  +R L 
Sbjct: 61  MLHKPSGVVSATRDKQHK-TVIDLLSVPYSSELHIVGRLDFNSTGLMLLTNDGRWSRSLS 119

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGL 193
            P     + YRV     +D   +     G+     G+     ++ +  Q  +     V L
Sbjct: 120 DPQNNIAKTYRVLLEKALDDSYVKAFADGMYFDFEGVTTRPAELRILGQYEA----EVDL 175

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA-GSTREVSKKILREQLG 246
            EG+  +IK++F  F+ +V  L R S G   +    A G  RE++   L + LG
Sbjct: 176 IEGRYHQIKRMFGRFDNRVKALHRTSVGSLSMAAGPALGQWRELTLSEL-DLLG 228


>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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 93/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  + L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAERKVV-LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 103/230 (44%), Gaps = 6/230 (2%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I      +RREV+ ++    + VN  +  +  +++   D + V G  +    + R
Sbjct: 4   RLDRYIGNNTELTRREVKFLLKAGEITVNDEVPSKPGLHLKEGDVVAVQGRVVE-PRQPR 62

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARV 133
            ++ HKP   ++  S  +      D +   F   +  VGRLD++T GLLL+T+DG  ++ 
Sbjct: 63  YFMLHKPPECISARSTEEH-LGALDLIEEPFHDELHIVGRLDLDTTGLLLVTDDGQWSQR 121

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P  +  +VY V     +        + GI ++   +      LD    +     + +
Sbjct: 122 LRSPRHKVPKVYWVTTAKPIASTVAARFEAGIYLKTEDHTTAPAQLDV--VAECRARLTI 179

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            EGK  ++K++F   + +V  L R S G   L   L  G  R ++ + ++
Sbjct: 180 TEGKFHQVKRMFAAVDNEVTALHRASVGEIVLDEDLEPGEYRALTAQEIQ 229


>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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 103/250 (41%), Gaps = 32/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      +     
Sbjct: 376 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQSARSEQGERV 435

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                +G  T     P     +   GRLDI++ 
Sbjct: 436 TVLMHKPVGYVSGQAEDGYQPAVSLFVPENQWEGDPTRKRFAPWQRRALAPAGRLDIDST 495

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFH-------------GQVDQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR                   ++ +  L+ G+ 
Sbjct: 496 GLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVEHDISKVFPEELMEKLRFGLS 555

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   LG
Sbjct: 556 LDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGSIVLG 611

Query: 227 TLLAGSTREV 236
            L  G  R +
Sbjct: 612 DLPVGQWRFL 621


>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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 52/176 (29%), Positives = 82/176 (46%), Gaps = 6/176 (3%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDG 128
           +     + HKP G+++   D D   TV D L           VGRLDI+TEG LL+TNDG
Sbjct: 4   KEFVYLMMHKPQGVISATED-DNHETVIDLLELEDAIFDPFPVGRLDIDTEGFLLITNDG 62

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNA 187
            L+  L  P     + Y     G V ++ +    KG+++  G       +T+  +    +
Sbjct: 63  KLSHQLLSPKKHVPKKYYAHVAGVVTEEDVKEFAKGVILDDGYETKPGTLTIL-KSDDIS 121

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + + EGK  ++K++FE    KV  L R   GP  L   L  G  RE++ + + 
Sbjct: 122 EIELVITEGKFHQVKRMFEAVGKKVVYLKRTEMGPLVLDEELELGQYRELTDEEVE 177


>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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (512), Expect = 1e-49,   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|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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 101/251 (40%), Gaps = 22/251 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-------ILLERAAVNVMSTDHIEVDGVP 66
            ++  ++   G   RR    ++ Q  V++          +L+             V GV 
Sbjct: 1   MQLQDMLYSQGFGIRRVCSGLVQQGWVELWNPQTSDWEKVLDSTQQVDPEGLRFRVQGVE 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
               E   + L +KP G   +   P    +++  LP+   +         V +VGRLD +
Sbjct: 61  WEYHELGYV-LLNKPAGTECSQK-PSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+       ++ 
Sbjct: 119 TTGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDDDP-KPVKA 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
               ++  +  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R +
Sbjct: 178 AA-CEQVDSHVLDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMELPADLEPGQWRWL 236

Query: 237 SKKILREQLGP 247
           +   L E   P
Sbjct: 237 TAHEL-ELFKP 246


>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 =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 90/186 (48%), Gaps = 16/186 (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 GSTREV 236
           G  RE+
Sbjct: 227 GEWREI 232


>gi|315185613|gb|EFU19381.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 214

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 72/204 (35%), Positives = 105/204 (51%), Gaps = 6/204 (2%)

Query: 41  KVNGILLERAAVNVMS-TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           +VNG ++   A  V    D + +DG  +    +     +HKP G + T SDP GR  V+D
Sbjct: 2   RVNGRVITNPAHRVDPQEDRVTLDGRDVHLVGKFLYLAFHKPPGYLCTRSDPQGRPLVYD 61

Query: 100 NLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            +  +   +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|302135159|ref|ZP_07261149.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. tomato NCPPB 1108]
          Length = 222

 Score =  201 bits (512), Expect = 1e-49,   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: 39  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|317181142|dbj|BAJ58928.1| hypothetical protein HPF32_1346 [Helicobacter pylori F32]
          Length = 257

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 123/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRCVIYESLEKKYTHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLKRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/295 (22%), Positives = 120/295 (40%), Gaps = 57/295 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGV 65
             E+    R++K+I+     SRR+ +  I   +VK+N  ++     +V    D + +   
Sbjct: 39  TNEDANIIRLNKLISMKRNISRRKSDEFIKDGKVKINNKIITNPGTHVHIGKDSLRIYDK 98

Query: 66  PLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISV 111
            ++           + +  +  + HKP GL+ T +D   R +++   P       R+++V
Sbjct: 99  KIKLTNIINMIKQNENKLHKWIVLHKPKGLLCTSNDEKNRKSIYTLFPEEMLQKYRLVTV 158

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGI 170
           GRLD NT G+LLLTND      L  P  Q +R YRV   G V  + L  L +GI + +  
Sbjct: 159 GRLDRNTSGVLLLTNDYAWVNKLTHPKYQRIRTYRVHIEGPVKMNALKELARGIYLEEDE 218

Query: 171 CYGDM----------------------------------------QVTLDTQKGSNAWVT 190
                                                        ++ +         + 
Sbjct: 219 KTQPKKIYNYKESREKSNIDDKKKKKMSKMKKKTNPAFIEILREEKIKIKEDTKKITVLN 278

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKKILREQ 244
           + ++EG+NR+I+K+F+  N  V ++ R S+    L  +      RE+++K + + 
Sbjct: 279 ISIKEGRNRQIRKMFQQINQPVIKIKRTSFENITLKNIYFPKQYRELNQKEVNDL 333


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 60/215 (27%), Positives = 104/215 (48%), Gaps = 9/215 (4%)

Query: 30  EVERMIAQQRVKVNGILLERAAVN-VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTH 88
           +   M+ + +V +NG  ++    N V+ +DHI V+G  L++      + Y+KP G+  T 
Sbjct: 75  KASNMVLENQVFING--VKALQRNDVLKSDHIVVNGEVLQEGRNFTYYAYYKPRGIECTL 132

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           +     + +   LP     V  VGRLD  +EGLLLLTNDG L + +        + Y V 
Sbjct: 133 N-AAIENNLLHTLP-FGEHVYPVGRLDKESEGLLLLTNDGKLYKDIAFSDNFKEKEYLVE 190

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +  + +  L  GIVI G      +V++ T+        + L +G NR+I+++    
Sbjct: 191 VDKPLTDEAVEQLSSGIVIMGQKTRPARVSMVTEHS----FRIILTQGLNRQIRRMCYKL 246

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            ++V  L RI     +LG L  G+ R +++  + +
Sbjct: 247 RYEVTMLKRIRITSIELGDLKPGAYRVLTRAEIFD 281


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEVQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 209

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 210 SGEYRVLDEKEKRQLF 225


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 54/230 (23%), Positives = 97/230 (42%), Gaps = 21/230 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RL L +KP   +   S     +T+ D +P   + V   GRLD ++EG++LLT+ G L  
Sbjct: 2   PRLILLNKPFDTICQFSASPPHATLADWVP--VAGVYPAGRLDTDSEGMVLLTDHGPLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            +  P+ +  + Y V+  G  + ++L  L++G+ +         V +  +          
Sbjct: 60  AIAHPAAKAPKTYWVQVEGTPEAEQLEQLRQGVDLGDFVTQPASVRILPEPELWPRQPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                    W+ + + EGKNR+++++         RL+R++ G  +LG L  G  RE++K
Sbjct: 120 RFRKTVPTHWLEIIISEGKNRQVRRMTAKVGLPTLRLVRVAVGSLKLGELQPGEWREIAK 179

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             L     P + ++A     AP           P   S       R +  
Sbjct: 180 GEL-----PAVWQQAWSQTAAPKPHRAPQSSRAPRFKSTGAGRTARQRPK 224


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLTNDG
Sbjct: 5   PPSEPKLLLFNKPFDVLTQFNDEQGRSTLKDFIP--VPGVYPAGRLDRDSEGLLLLTNDG 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|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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 91  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 207

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 209 SGEYRVLDEKEKRQLF 224


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/263 (24%), Positives = 106/263 (40%), Gaps = 32/263 (12%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
             +    E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE
Sbjct: 349 PRQAAQTESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIE 408

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFS 106
           +      +       L HKP+G V+  ++                +G  T     P    
Sbjct: 409 IHQSARSEQGERVTVLMHKPVGYVSGQAEDGYQPAVSLFVPENQWEGDPTRKRFAPWQRR 468

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH-------------GQV 153
            +   GRLDI++ GLL+LT DG +AR L    +   + Y VR                  
Sbjct: 469 ALAPAGRLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVEHDISKVF 528

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            ++ +  L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V 
Sbjct: 529 PEELMEKLRFGLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVV 584

Query: 214 RLIRISYGPFQLGTLLAGSTREV 236
            L RI  G   LG L  G  R +
Sbjct: 585 GLKRIRMGSIVLGDLPVGQWRFL 607


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 59/195 (30%), Positives = 90/195 (46%), Gaps = 29/195 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               L++KP G++   +D D     R T+ D +P     + SVGRLD ++EGLLLLTN+G
Sbjct: 2   YEYILFNKPYGVLCQFTDTDNPNAPRPTLKDYIP--LPDIYSVGRLDFDSEGLLLLTNNG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L        R Y V+     D+  L+ L++G++I+  C    QV L         
Sbjct: 60  RLKHRLSHREFSHPRTYWVQVERIPDEIALDRLRQGVLIKDYCTRPAQVKLLATEPNLSP 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP--------FQL 225
                   +    AW+ + L EG+NR+++++     +   RLIRIS G           L
Sbjct: 120 RNPPIRYRKTVPTAWLEITLTEGRNRQVRRMTAAIGYPTLRLIRISMGFKIGKTLEKLSL 179

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  RE ++  
Sbjct: 180 GDLKPGEWREATQLE 194


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 91  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 147

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 148 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 207

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|221134604|ref|ZP_03560907.1| RNA pseudouridine synthase family protein [Glaciecola sp. HTCC2999]
          Length = 211

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 48/204 (23%), Positives = 89/204 (43%), Gaps = 11/204 (5%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           VNG L       +  +D + + G  +             LYHKP+G+  T ++   +  +
Sbjct: 2   VNGQLP-LLGTKITPSDTVSIQGKVISAVAADKSDRVYVLYHKPVGITCT-TERHIKGNI 59

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
            D +    +R+  VGRLD  +EGL++LT+DG +   +        ++YRV     +    
Sbjct: 60  IDAI-GHKTRIFPVGRLDKPSEGLIILTSDGDIVNKILRAENAHDKLYRVTVDKPITSKF 118

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           + ++  G+ I        +V     +       + L +G NR+I+++ E+  + V RL+R
Sbjct: 119 IEIMSGGVPILDTVTKPCKVK----QIGKFSFDITLTQGLNRQIRRMCEYCGYDVKRLVR 174

Query: 218 ISYGPFQLGTLLAGSTREVSKKIL 241
                  L  L  G  R ++ + L
Sbjct: 175 TRIMHLTLAKLPVGQWRNLTNEEL 198


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 58/186 (31%), Positives = 90/186 (48%), Gaps = 17/186 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R   ++KP G++T  +D  GR T+   +P    +V  VGRLD ++EGLLLLT+DG L   
Sbjct: 2   RYLKFYKPYGVLTQFTDRQGRPTLKSFIP--VPKVYPVGRLDRDSEGLLLLTDDGRLNAR 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 KILREQ 244
             L   
Sbjct: 180 AELARL 185


>gi|301155121|emb|CBW14585.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 228

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 51/190 (26%), Positives = 96/190 (50%), Gaps = 17/190 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+T + L++KP  ++T  +D +GR+T+ D +      V + GRLD ++EGLL+LTN+G +
Sbjct: 32  EQTIVILFNKPFDVLTQFTDENGRATLKDFI--TIPNVYAAGRLDRDSEGLLILTNNGEV 89

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L+ L+KG+ ++       +V L           
Sbjct: 90  QHRLADPKFKTEKTYFVQVEGIPEETDLDKLRKGVELKDGMTKPAKVRLISEPDFLWPRN 149

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + Q  + +W+ + + EG+NR+++++     +   RLIR       L  L  G  R 
Sbjct: 150 PPIRERQSITTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMSHLTLDGLGNGEYRC 209

Query: 236 VSKKILREQL 245
           ++K+ +R   
Sbjct: 210 LNKEEMRALF 219


>gi|282876081|ref|ZP_06284948.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
 gi|281295106|gb|EFA87633.1| pseudouridylate synthase [Staphylococcus epidermidis SK135]
          Length = 194

 Score =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 59/187 (31%), Positives = 102/187 (54%), Gaps = 4/187 (2%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +     L++KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG 
Sbjct: 10  KKTKIYILFYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGE 69

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
              ++  P  +  + Y  +  G + ++++  L+KGI ++       QV +  Q  + +  
Sbjct: 70  FTNLMTHPRYRIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKNTT 129

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
            V + + EG+NR+++++FE+F  +VN+L RI +GP  L  L AG  R ++   ++     
Sbjct: 130 LVEITISEGRNRQVRRMFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVKIL--R 187

Query: 248 HLLEEAQ 254
           HL E  +
Sbjct: 188 HLAENGK 194


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEVQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 209 SGEYRVLDEKEKRQLF 224


>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 =  201 bits (511), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 62/233 (26%), Positives = 108/233 (46%), Gaps = 9/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ + +      +RR    ++A  RV+V+G ++      +     IEVDG  L+     
Sbjct: 1   MRLDRFLGNLPDFNRRNSRLLLASGRVRVDGQVVRDGCSEIREFSRIEVDGRILQPGRAA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
             ++ HKP G+V+       R TV D L     + +   GRLD+ T GLLLLTNDG  +R
Sbjct: 61  LYFMLHKPAGVVSATRHERHR-TVLDLLDEPDRQGLHLAGRLDLGTTGLLLLTNDGHWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  +VY V     + ++ +    +G+    + +      + L     +     
Sbjct: 120 RITHPRYKLAKVYYVETAEPIGEEYIETFARGLYFAFEDLVTQPAHLELLGSHSA----R 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
           + L EG+  ++K++F +F   V RL R S GP +L   L  G  R ++ + ++
Sbjct: 176 LTLFEGRYHQVKRMFGYFRNPVLRLHRESMGPLRLESELPPGHYRPLTSEEIQ 228


>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 =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 94/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTRPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|170718088|ref|YP_001785122.1| pseudouridine synthase [Haemophilus somnus 2336]
 gi|168826217|gb|ACA31588.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 227

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 90/187 (48%), Gaps = 16/187 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   +D  GR+T+ D +      +  VGRLD ++EGLLLLTN+G L 
Sbjct: 35  QTKVILFNKPFDVLCQFTDEQGRATLKDFIK--IPHIYPVGRLDRDSEGLLLLTNNGELQ 92

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y V+  G   +  L  L+KGI +        +V L            
Sbjct: 93  HRLTNPKFKMEKTYWVQIEGIPVETDLAQLRKGIELNDGLTKPAKVRLISEPNIWQRHPP 152

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EG+NR+++++     +   RLIR       L  L  G  RE++
Sbjct: 153 IRERKTVPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYETAGLTLTNLANGQFRELT 212

Query: 238 KKILREQ 244
              L++ 
Sbjct: 213 LTELQDL 219


>gi|330953605|gb|EGH53865.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 343

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 87/297 (29%), Positives = 134/297 (45%), Gaps = 27/297 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
           R+ +Y+KP G + T  DP+GR TVFD LP     R I++GRLDINT GLL+ T DG LA 
Sbjct: 14  RVIMYNKPDGEICTRDDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLMFTTDGELAN 73

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTV 191
            L  PS +  R Y VR  G+VD D L  LK G++++        +      +G N W   
Sbjct: 74  RLMHPSFEMDREYAVRVRGEVDDDMLLRLKNGVILEDGPARFTDIQQAPGGEGFNHWYHC 133

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LREQLGP 247
            + EG+NRE+++++E     V+RL R+ YGP  L   L  G  RE+S+     L  ++G 
Sbjct: 134 VVMEGRNREVRRLWESQGLVVSRLKRVRYGPVFLNSDLPMGRWREMSQYEVDILAAEVGL 193

Query: 248 HLLEEAQVNLDA-------------PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
             + + Q+N                P+   E +   RP   +  P           Q  G
Sbjct: 194 QPVAQPQMNAKTKDKMERLQRQSSRPLGKGERVRTLRP--AAGAPATGGERAPRQPQITG 251

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQ------REENHRRSPSFPSKR 345
             + +     + +R          G  +   +D+ +      R  +  + P+ P  +
Sbjct: 252 SERDRPRGGDLTQRPSPRKDSGKPGSRAPRPADNSRGTPVAERPSDMNKRPAKPGPK 308


>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 =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 118/272 (43%), Gaps = 37/272 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE-- 71
           R++K+I+     SRR+ +  I    VK+N  +++    ++  S D I++ G  +      
Sbjct: 57  RLNKIISMEKKISRRKSDEFIKDGNVKLNNKVVKNPGTHIDVSKDKIKISGKLVNIVRTQ 116

Query: 72  ---------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTE 119
                      + ++ HKP G + T +D   R++++   P       R++SVGRLD NT 
Sbjct: 117 KMINRNDNNFYKWFVLHKPKGFLCTSNDEKDRASIYSLFPQDIMDNYRLVSVGRLDRNTS 176

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG---------- 169
           G+LLLTN+      L  P  Q +R YRV   G      L  L  GI +Q           
Sbjct: 177 GVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGPAQMKVLKQLATGIYLQDDNRGKENKKI 236

Query: 170 ---ICYGDMQVTLDTQK--------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                     + +  ++           + + + +REG+NR+I+K+FE  N  V ++ R 
Sbjct: 237 VKKKRTQPAFIEILREETIKVKDQVKKVSVLNISVREGRNRQIRKMFEQINQPVIKIKRT 296

Query: 219 SYGPFQLGTL-LAGSTREVSKKILREQLGPHL 249
           ++    L  +      RE++++ +       L
Sbjct: 297 AFENITLKDVFFPKQYRELTQREISNLKARRL 328


>gi|298492438|ref|YP_003722615.1| pseudouridine synthase ['Nostoc azollae' 0708]
 gi|298234356|gb|ADI65492.1| pseudouridine synthase ['Nostoc azollae' 0708]
          Length = 195

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 53/187 (28%), Positives = 85/187 (45%), Gaps = 18/187 (9%)

Query: 72  RTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             +  ++HKP G+++  + +     T+ D +      +  VGRLD ++EGL+LLTNDG L
Sbjct: 4   DFKYIIFHKPYGVLSQFTQESPKHITLKDYID--VPEIYPVGRLDWDSEGLMLLTNDGQL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P     R Y V+     D + +N L  G+ IQ       QV L           
Sbjct: 62  QHRLANPRFGHKRTYWVQLEHIPDGEAINKLCTGVEIQNYQTRPAQVKLFLEEPTVSERN 121

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +    AW+ + L EGKNR+++++     +   RLIR+S    QL  L  G  R 
Sbjct: 122 PPIRFRKNIPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLIRVSITNLQLNGLQPGEWRY 181

Query: 236 VSKKILR 242
           ++   ++
Sbjct: 182 LTAPEIQ 188


>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 =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 50/179 (27%), Positives = 91/179 (50%), Gaps = 16/179 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP   +   +D +GR+T+ + LP   +      GRLD+++EGLL+LTN+G L   
Sbjct: 4   LLLINKPYNTLCQFTDGEGRNTLANLLPDGKYKDYYPAGRLDLDSEGLLILTNNGSLQHR 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------------- 178
           +  PS +  + Y V+  G + Q+ +  L+ G+ ++       +                 
Sbjct: 64  ISHPSQKLEKTYWVQVEGDITQEAIAQLEAGVELKDGKTKPAKAKKIAPPQNLWERNPPV 123

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            + +    +W+ + + EGKNR+++++    N+   RLIR + GP+QL  L  GS +E +
Sbjct: 124 RERKNIPTSWLRLTISEGKNRQVRRMTAAVNYPTLRLIRAAIGPWQLDNLAPGSYKEET 182


>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 =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 58/195 (29%), Positives = 90/195 (46%), Gaps = 29/195 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               L++KP G++   +D D     R T+ D +P     + SVGRLD ++EGLLLLTN+G
Sbjct: 2   YEYILFNKPYGVLCQFTDTDNPNSPRPTLKDYIP--LPDIYSVGRLDFDSEGLLLLTNNG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L        R Y V+     D+  L+ L++G++I+  C    Q+ L         
Sbjct: 60  RLKHRLSHREFSHPRTYWVQVERIPDEIALDRLRQGVLIKDYCTRPAQIKLLATEPNLSP 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP--------FQL 225
                   +    AW+ + L EG+NR+++++     +   RLIRIS G           L
Sbjct: 120 RNPPIRYRKTVPTAWLEITLTEGRNRQVRRMTAAIGYPTLRLIRISMGFKIGKTLEKLSL 179

Query: 226 GTLLAGSTREVSKKI 240
           G L  G  RE ++  
Sbjct: 180 GDLKPGEWREATQLE 194


>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 =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 55/190 (28%), Positives = 93/190 (48%), Gaps = 17/190 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLLTN+G +
Sbjct: 38  EDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLLTNNGEI 95

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y  +  G      L  L+KG+ ++       +              
Sbjct: 96  QHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPNYEWQTA 155

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L +G  R 
Sbjct: 156 PKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELNSGEYRV 215

Query: 236 VSKKILREQL 245
           + +K  R+  
Sbjct: 216 LDEKEKRQLF 225


>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 =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 51/182 (28%), Positives = 87/182 (47%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              + RL L +KP  ++T  +D  GR+T+ D +      V   GRLD ++EGLLLLTNDG
Sbjct: 22  PPAQPRLILLNKPFDVLTQFNDEQGRATLKDFVE--VPGVYPAGRLDRDSEGLLLLTNDG 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|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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 57/196 (29%), Positives = 93/196 (47%), Gaps = 18/196 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AE T L L +KP  ++T  +D  GR T+ D +      +  VGRLD ++EGLLLL
Sbjct: 27  RPLTFAETT-LVLLNKPYDVLTQFTDEQGRKTLKDFI--TMPNIYPVGRLDRDSEGLLLL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P     + Y V+  G    + L  L KG+ ++       +V       
Sbjct: 84  TNNGEIQHRLAHPKFDKQKTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATPD 143

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIR+  G F+LG L 
Sbjct: 144 FAWNIAPQIRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTLRLIRVGIGQFRLGNLG 203

Query: 230 AGSTREVSKKILREQL 245
            G  + +S+   R+  
Sbjct: 204 CGEFQVLSENEKRKLF 219


>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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 53/212 (25%), Positives = 99/212 (46%), Gaps = 18/212 (8%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +R  + V +   +      +     T++ L++KP  ++T  SD +GR+T+ D +P   S+
Sbjct: 25  KRPNLKV-AKSAVNFYEKKVISFAETKVILFNKPYDVLTQFSDENGRATLKDFIP--VSQ 81

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V   GRLD ++EGL+LLTN+G +   L  P  +  + Y  +      +  L  L++G+V+
Sbjct: 82  VYPAGRLDRDSEGLVLLTNNGEIQHRLAEPKFKTEKTYFAQVEAIPQEVDLEQLRQGVVL 141

Query: 168 QGICYGDMQVTL---------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                   +V L               + +    +W+ + + EG+NR+++++     +  
Sbjct: 142 NDGKTLPAKVRLVSEPNWLWERNPPIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPT 201

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            RLIR     F L  L  G  R++S+  L   
Sbjct: 202 LRLIRYQMALFTLDNLPQGQYRQLSEAELTAL 233


>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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 57/196 (29%), Positives = 93/196 (47%), Gaps = 18/196 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AE T L L +KP  ++T  +D  GR T+ D +      +  VGRLD ++EGLLLL
Sbjct: 27  RPLTFAETT-LVLLNKPYDVLTQFTDEQGRKTLKDFI--TMPNIYPVGRLDRDSEGLLLL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P     + Y V+  G    + L  L KG+ ++       +V       
Sbjct: 84  TNNGEIQHRLAHPKFDKQKTYWVQVEGVPQPEDLAKLAKGVELKDGLTKPAKVRAIATPD 143

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIR+  G F+LG L 
Sbjct: 144 FAWHIAPQIRERKTIPTSWIELIISEGKNRQVRRMTAHIGFPTLRLIRVGIGQFRLGNLG 203

Query: 230 AGSTREVSKKILREQL 245
            G  + +S+   R+  
Sbjct: 204 CGEFQVLSENEKRKLF 219


>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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 101/252 (40%), Gaps = 22/252 (8%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNG------ILLERAAVNVMSTD-HIEVDGV 65
             ++  ++   G   RR    ++ Q  V++          +  +   V        V GV
Sbjct: 2   SMQLQDMLYSQGFGIRRVCSGLVQQGWVELWNPQTSDWEKILDSTQQVDPGGLRFRVQGV 61

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDI 116
                E   + L +KP G   +   P    +++  LP+   +         V +VGRLD 
Sbjct: 62  EWEYHELGYV-LLNKPAGTECSQK-PSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQ 119

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+       ++
Sbjct: 120 DTTGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDDDP-KPVK 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
                ++  +  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R 
Sbjct: 179 AAA-CEQVDSHVLDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMELPAELEPGQWRW 237

Query: 236 VSKKILREQLGP 247
           ++   L E   P
Sbjct: 238 LTADEL-ELFKP 248


>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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 94/233 (40%), Gaps = 13/233 (5%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERT 73
           + +++   G  +R+   ++IA   +++ G  +      +  TD +E  VD       ER 
Sbjct: 6   LDRILHTQGFGTRKYCRQLIAAGAIRIGGDTITDTNTPI-ETDGLEFSVDDEHCIYRERI 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            +   +KP  +  +   P     V   LP  F+R  V  VGRLD +T GLLL+++DG   
Sbjct: 65  YV-ALNKPANIECSRK-PSHHPGVLSILPDQFTRRDVQPVGRLDHDTTGLLLMSDDGAFI 122

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSNAWVT 190
                P     +VY    +  V  + +  L  G+ +         ++    +   +  + 
Sbjct: 123 HTQSSPKHHVPKVYVATTYAPVTGELIERLLAGVKLHDEPGTLAAEI---CRMIDDHHLE 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVSKKIL 241
           + L +GK  ++K++    +     L R   G  +L    L  G    ++   L
Sbjct: 180 IVLEQGKYHQVKRMLAAADNHCTALNRSQIGNLKLAELALAPGEWCYLNDAQL 232


>gi|10304093|gb|AAG16128.1|AF261151_1 pseudouridylate synthase-like protein [Vibrio cholerae]
          Length = 241

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 93/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P       + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDGYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 107/262 (40%), Gaps = 32/262 (12%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D      +    R+SK ++  G+ SRRE +  I +  V V+G  +      V +  +IE+
Sbjct: 431 DAPETSHDDGLIRLSKRMSELGLCSRREADEWIPRGWVIVDGKPVTELGSRVRADANIEI 490

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS---------------TVFDNLPSIFSR 107
                 +       L HKP+G V+  ++                    T     P     
Sbjct: 491 HQAARSEQGERVTVLLHKPMGYVSGQAEDGYEPAAVLFTAENQWSEDPTRKRFAPWQRKS 550

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-------------VD 154
           +   GRLDI++ GLL+LT DG +AR L    +   + Y VR                   
Sbjct: 551 LAPAGRLDIDSTGLLVLTQDGRVARALIGEDSNVEKEYLVRVQWHSPDGVVERNVSEVFP 610

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            DKL LL+ G+ + G+     +V+   ++     +   LREG+ R+I+++ E    +V  
Sbjct: 611 ADKLELLRHGLSLDGVVLKPAKVSWQNEE----QLRFVLREGRKRQIRRMCEQVGLEVVG 666

Query: 215 LIRISYGPFQLGTLLAGSTREV 236
           L R+  G   LG L  G  R +
Sbjct: 667 LKRVRMGRIVLGDLPPGQWRFL 688


>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 =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 54/187 (28%), Positives = 93/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  + L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RAISPSERKVV-LFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V + ++  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGVPQESDLEALRHGVTLKDGPTLPAKVKIMSEPE 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 88/196 (44%), Gaps = 27/196 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  R  L++KP G++   +D   + R T+ D +P     V SVGRLD ++EGLL LTN+G
Sbjct: 4   KNYRYLLFNKPYGVLCQFTDNTENPRPTLKDYIP--VPDVYSVGRLDRDSEGLLFLTNNG 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|308062723|gb|ADO04611.1| hypothetical protein HPCU_07355 [Helicobacter pylori Cuz20]
          Length = 257

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRCVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  200 bits (508), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 86/182 (47%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  200 bits (508), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 209 SGEYRVLDEKEKRQLF 224


>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 =  200 bits (508), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 56/188 (29%), Positives = 96/188 (51%), 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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  +VY V+  G  D+D L+ L+ GI ++          L     
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGLPDEDALSQLRTGITLKDGPTLPAGAELVSEPA 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|119896376|ref|YP_931589.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119668789|emb|CAL92702.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 248

 Score =  200 bits (508), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 85/236 (36%), Gaps = 14/236 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-------HIEVD 63
               ++ +++   G  SR++   ++    V V G+  +                    VD
Sbjct: 1   MQAMQIERLLHSQGFGSRKDCRALLRAGYVSVAGVPCDDPRAEFDPGSKDGSPGLEFTVD 60

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGL 121
                   +    + HKP G   +H  P    +VF  LP       V  +GRLD +T GL
Sbjct: 61  DEIWHFRAQA-YLMLHKPAGYECSHK-PTFHPSVFTLLPPQLLNRGVQCIGRLDQDTTGL 118

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           LLL++DG           +  +VY +      D   +  L  G+ +            + 
Sbjct: 119 LLLSDDGQFIHQWSSGKKRTPKVYEIGLKHAADDALVAALLAGVELHDEPTPIAAAACEI 178

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREV 236
              ++  + + + EGK  ++K++      +V  L R   G   L   L  G  R +
Sbjct: 179 --TASHALRLTITEGKYHQVKRMVAAAGNRVETLHRSRVGGLTLDPALKPGEWRWL 232


>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 =  200 bits (508), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 64/230 (27%), Positives = 107/230 (46%), Gaps = 8/230 (3%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + IA      ++ V  ++   +V V+G   +   + V    HIE +GV LR+ ++ +
Sbjct: 7   RLDQFIAGTLQIPKKAVRLLLVTNKVLVDGQFAKSPDLQVDEFTHIECNGVVLRQYQK-Q 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            ++ +KP G+V+   D    + +          +   GRLD+++ GLLLLTND   +  L
Sbjct: 66  YYMLNKPDGVVSATIDDKHATALGLITGVNTDMLHIAGRLDLHSTGLLLLTNDAKWSEAL 125

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVG 192
             P  +  + Y V     ++Q+ +    KG+    + I     Q+TL     S+    V 
Sbjct: 126 MDPQHKVDKQYLVTLANPLEQEYVEAFSKGMYFGFEDITTLPAQLTLL----SSHRARVV 181

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           LREGK  +IK++F  F   V  L R S G   L   L  G  R ++K  +
Sbjct: 182 LREGKYHQIKRMFGRFRNPVVALHRESIGKIVLDKQLELGEFRSLTKAEV 231


>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 =  200 bits (508), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 57/196 (29%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    +V  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQVYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKIIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 209

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 210 SGEYRVLDEKEKRQLF 225


>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 =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 100/252 (39%), Gaps = 24/252 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG-------ILLERAAVNVMSTDHIEVDGVP 66
            ++  ++   G   RR    ++ Q  V++          +L+             V GV 
Sbjct: 1   MQLQDMLYSQGFGIRRVCSGLVQQGWVELWNPQTSDWEKVLDSTQQVDPEGLRFRVQGVE 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
               E   + L +KP G   +   P    +++  LP+   +         V +VGRLD +
Sbjct: 61  WEYHELGYV-LLNKPAGTECSQK-PSAYPSIYTLLPAPLRQRPNKGAVQGVQAVGRLDQD 118

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           T G+LLL++DG     +  P     +VYRV     VD  ++  L  G+V+         V
Sbjct: 119 TTGMLLLSDDGQFIHRMSSPKKHVSKVYRVTCKHPVDAKQIQRLLDGVVLDD---DPKPV 175

Query: 178 TLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTRE 235
                ++  +  + + L EGK  ++K++    + +V  L R   G  +L   L  G  R 
Sbjct: 176 RAAACEQVDSHVLDLTLTEGKYHQVKRMIAAVSNRVEGLHRRRIGGMELPAELEPGQWRW 235

Query: 236 VSKKILREQLGP 247
           ++   L E   P
Sbjct: 236 LTADEL-ELFKP 246


>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 =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 86/175 (49%), Gaps = 16/175 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L   L 
Sbjct: 2   IIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------------- 182
            P ++  + Y V+  G   ++ L  L+KG+ ++       ++ +  +             
Sbjct: 60  QPQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGMTLPAKIEVMPEPEIWERTPPVRFR 119

Query: 183 -KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                 W+ + + EG+NR+++++     +   RL+R S G   L  L  G  RE+
Sbjct: 120 ANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGIALDDLKPGEWREI 174


>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 =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 58/187 (31%), Positives = 95/187 (50%), Gaps = 1/187 (0%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
             +D I+VDG+ +   +  + +  +KP G+V T  DP+GR  + D + +  +R+  VGRL
Sbjct: 2   KPSDEIKVDGLTV-ATQSYQFFSLNKPAGVVATMEDPEGRQNLGDYVNNRETRLFHVGRL 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|325181472|emb|CCA15906.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 246

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 61/235 (25%), Positives = 107/235 (45%), Gaps = 25/235 (10%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V++  +P  +  +               +   P   S++   GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVT 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 VLNAN----QLQFILTEGKKRHIRYMCEAVGIKVIALKRVRIGNIRLGALPVGNF 231


>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 =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 55/247 (22%), Positives = 100/247 (40%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKAE 71
            ++  ++   G   RR    ++ Q  V++           + ST  I+ +G+   ++  E
Sbjct: 3   MQLQDILYSQGFGIRRVCSGLVQQGWVELWDTEANDWVRCLDSTQDIDPEGLRYRVQGVE 62

Query: 72  RTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVGRLDINT 118
                    L HKP G   +   P    +++  L               V +VGRLD +T
Sbjct: 63  WAYHALGYVLLHKPAGTECSQK-PSTYPSIYSLLPLPLRLRPNKGAVQGVQAVGRLDQDT 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG     +  P     ++YRV     VD  ++  L  G+V+       ++  
Sbjct: 122 TGLLLLSDDGQFIHRMSSPKKHVPKIYRVTTKHPVDASQVQRLLDGVVLDDDP-KPVKAA 180

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              ++ S   + + L EGK  ++K++      +V  L R   G  +L   L  G  R ++
Sbjct: 181 A-CEQVSEHVLDLTLTEGKYHQVKRMIAAVGNRVEGLHRWKIGELELTEDLQPGQWRWLT 239

Query: 238 KKILREQ 244
            + L + 
Sbjct: 240 AEDLAKL 246


>gi|318606116|emb|CBY27614.1| ribosomal large subunit pseudouridine synthase E; LSU Psi2457
           [Yersinia enterocolitica subsp. palearctica Y11]
          Length = 208

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 56/188 (29%), Positives = 96/188 (51%), 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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  +VY V+  G  D+D L+ L+ GI ++          L     
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGLPDEDALSQLRTGITLKDGPTLPAGAELVSEPA 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|308805586|ref|XP_003080105.1| unnamed protein product [Ostreococcus tauri]
 gi|116058564|emb|CAL53753.1| unnamed protein product [Ostreococcus tauri]
          Length = 405

 Score =  199 bits (507), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 112/250 (44%), Gaps = 20/250 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK----A 70
           ++K +A  G+ASRR  + +I   RVKVNG  +      V  +TD + VDG  +       
Sbjct: 145 LNKALASLGVASRRGADDLIFGGRVKVNGTTITAPQTKVNLNTDVVMVDGKVVEGGVSFV 204

Query: 71  ERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSI------------FSRVISVGRLDIN 117
           +    ++ +KP G V +     +   TV D                   R+ +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|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 =  199 bits (507), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 71/224 (31%), Positives = 104/224 (46%), Gaps = 10/224 (4%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KAERTR 74
            +A  G+ SRR  E +I +  VK+NG L +     V   D +E           K E   
Sbjct: 14  FLAEKGMGSRRFCEELIRKNLVKINGTLAK-LGDKVFLGDRVEYRRQVFVLRDLKIESKI 72

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
               HKP   + ++ DP+GR      +  +F  R+ S+GRLD  + GLLL TNDG  A  
Sbjct: 73  YIALHKPKNYLCSNFDPEGRKLAISLVQPLFKERLFSIGRLDFKSSGLLLFTNDGQFANS 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           +  P ++  + Y V     V++D L   K GI I+   +      +      N  V + L
Sbjct: 133 IVHPRSEVEKEYIVESKKDVNEDLLINFKHGIKIEREIFKLKSYEMLG----NNSVKLVL 188

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            EGKNREI+KVF   N  + ++ RI  G  +L  L  G  + +S
Sbjct: 189 TEGKNREIRKVFLSKNIFLKKVHRIRIGNIKLDNLKEGQIKVLS 232


>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 =  199 bits (507), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 62/232 (26%), Positives = 104/232 (44%), Gaps = 9/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ +++ +    +RR V  ++ Q RV VN +++      V + D +  DG   +  +  
Sbjct: 1   MRLDRLLCQHPKWNRRHVLGLLVQGRVTVNEVVVTNPTHEVSAFDTVHADGELCQAGKPA 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP G+++  SDP    TV   LP      +   GRLD  + GL+LLTNDG  +R
Sbjct: 61  HYLMLNKPAGILSATSDP-VHPTVMQLLPEALAKDLHIGGRLDRASTGLMLLTNDGQWSR 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVT 190
               P  +  +VYRV     +  D   +  +GI    + I     Q+    +        
Sbjct: 120 RATDPDKRSPKVYRVTLANPIHPDTEQVFAEGIYFPFEAITTSPAQLERLGE----CECR 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  +IK++F  F   V  L R S G   L  TL  G  R ++ + +
Sbjct: 176 LTIYEGRYHQIKRMFGRFRNPVVALHRESMGAITLDPTLAPGQYRALTAEEI 227


>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 =  199 bits (507), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 95/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G++++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVILKDGPTLPAKVDIMPEPT 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|261840134|gb|ACX99899.1| pseudouridylate synthase [Helicobacter pylori 52]
          Length = 257

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 123/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRHVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 121/236 (51%), Gaps = 11/236 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+SKVIA+AG ASRR+ E +I + +VKVN  ++      V   D I V+G PL K E  
Sbjct: 2   ERLSKVIAQAGCASRRKAENLITEGKVKVNDEVINVLGYKVSPKDIITVEGKPLVK-EPL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L +KP G ++T +D   R  + D +       R+  + +L+ +T GLLL+TNDG L 
Sbjct: 61  VYYLLNKPTGYLSTTADIHKRRNILDLILKEDQNVRLFPIHKLEYDTSGLLLVTNDGELT 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
           + L   S    + Y +R  G + ++++  +K+GI ++      + + +     ++    V
Sbjct: 121 KKLTSQSESIQKEYVIRTKGIMIKERIREIKRGIKVENKIIKPVDIAIVELDKAHQSTLV 180

Query: 190 TVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + +    N   +E+K +F+    +V  + RI +    L  +  GS R++    ++
Sbjct: 181 KMIIT---NESAKELKTMFKQLGHEVKNMTRIRFDSLTLEGVNRGSYRKLKSHEVK 233


>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 =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 56/185 (30%), Positives = 92/185 (49%), Gaps = 17/185 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A   R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG
Sbjct: 25  PAAPRRVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDG 82

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P+ +  +VY V+  G  D D L  LK+G+ ++          L         
Sbjct: 83  KLQARLTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWP 142

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 143 RHPPIRERKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEW 202

Query: 234 REVSK 238
           +E++ 
Sbjct: 203 KEITD 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 =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 92/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER  + L++KP   ++  +D DGR T+ D +      V + GRLD ++EGLL+L
Sbjct: 60  RPLSPAERKVV-LFNKPYDTLSQFTDGDGRKTLADYI--QIKDVYAAGRLDRDSEGLLIL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 117 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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 =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 90/188 (47%), Gaps = 17/188 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P R     ++ +++KP  ++   +D  GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 22  KPSRPRGERKVIIFNKPFDVLVQFTDDSGRKTLKDFIP--IPDIYAAGRLDRDSEGLLVL 79

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  +VY  +  G   +  L   ++G+ ++       ++       
Sbjct: 80  TNDGKLQAKLTQPNKKTGKVYYAQVEGIPTEIALQQFREGLNLKDGKTLPAKIERVEQPT 139

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|86132523|ref|ZP_01051117.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|85817084|gb|EAQ38268.1| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 296

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 108/242 (44%), Gaps = 6/242 (2%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +   +++    R++K IA +G+ SRRE +  I+  +V VNG ++      V   D + 
Sbjct: 53  KKQTQRKKDDGTMRLNKYIANSGVCSRREADMYISIGQVTVNGKVINEMGYQVKIEDDVR 112

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEG 120
            DG  +   E     L +KP G  TT S+  G  TV D +     SR+  +GRL  N  G
Sbjct: 113 FDGRRIN-PEAKAYVLLNKPKGFATTTSNDKGN-TVMDLVAGSTKSRIQPIGRLGRNAMG 170

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-L 179
           LLL TND  L +          ++Y +     +       +++G+ I G      +++ +
Sbjct: 171 LLLFTNDDELVQRFTNSKKGVDKLYHIELSNNLKAADAERIREGLKIGGKTIMVEEISFV 230

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D        + +    G N  I+ +FE  N++V R+  ++        L  G  R ++K+
Sbjct: 231 DGAPKKEVGLRIKNT-G-NSIIRTIFEHLNYEVVRVDCVTIAGLTKKDLPRGHWRHLTKQ 288

Query: 240 IL 241
            +
Sbjct: 289 EV 290


>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 =  199 bits (506), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 71/234 (30%), Positives = 103/234 (44%), Gaps = 12/234 (5%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL-- 67
           N    RV   +A  GI SRR  E +I +  +KVNGI  +     V   D +E  G  +  
Sbjct: 5   NSKGLRVHVFLAEKGIGSRRFCEELIRKNLIKVNGIFAK-LGDKVFLGDRVEY-GKQVFV 62

Query: 68  ---RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLL 123
               K         +KPI  + ++ DP GR      +  +F  R+ S+GRLD  + GLLL
Sbjct: 63  FQDSKVVNKIYIALNKPINYLCSNFDPMGRKLAISLVQPLFRERLFSIGRLDFKSSGLLL 122

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            TNDG  A  +  P  +  + Y +     V +D L   K GI +    +      +    
Sbjct: 123 FTNDGRFANSIVHPKNEIEKEYIIESKRVVSEDLLVNFKNGIKVDNELFKLKSYVMLG-- 180

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             N    + L EGKNREI+KVF   N  + ++ R+  G   L  L  G  + +S
Sbjct: 181 --NNTARLILTEGKNREIRKVFLSRNIFLKKVHRVRIGNITLSNLKEGQIKVLS 232


>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 =  199 bits (506), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 60/233 (25%), Positives = 109/233 (46%), Gaps = 10/233 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ + I+R    + + V  ++ ++++ V+G +       V     + VDG  +++ +   
Sbjct: 7   RLDRFISRRLSVTNKAVRELLVRKKIIVDGEVASLMNQTVGPFTFVVVDGEVIQQRQ-PV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
             + +KP G+V+   D D  + V D +       +   GRLD NT GLLLLTNDG  ++ 
Sbjct: 66  YLMMNKPKGVVSATKD-DKHTIVLDLIDHPLKEELHIAGRLDFNTTGLLLLTNDGAWSKQ 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           L LP    ++ YRV     +    +        +G+ +          TL     S+  V
Sbjct: 125 LSLPENNIMKKYRVTLKDHLFSSDVLIYQKKFSEGVFLSSENITTRPATLLA--LSSNIV 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKIL 241
            + + EG+  ++K++F FF  +V  L R+S G  ++ G L  G  R ++ K +
Sbjct: 183 ELSICEGRYHQVKRMFGFFQNEVLELHRLSVGSLEMEGGLALGRYRVLTPKEI 235


>gi|170023963|ref|YP_001720468.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|169750497|gb|ACA68015.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
          Length = 208

 Score =  199 bits (506), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 56/185 (30%), Positives = 92/185 (49%), Gaps = 17/185 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A   R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG
Sbjct: 25  PAAPRRVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDG 82

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P+ +  +VY V+  G  D D L  LK+G+ ++          L         
Sbjct: 83  KLQARLTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWP 142

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 143 RHPPIRERKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEW 202

Query: 234 REVSK 238
           +E++ 
Sbjct: 203 KEITD 207


>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 =  199 bits (506), Expect = 7e-49,   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  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  199 bits (506), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 90/187 (48%), Gaps = 16/187 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++   +D  GR+T+ D +      +  VGRLD ++EGLLLLTN+G L 
Sbjct: 23  QTKVILFNKPFDVLCQFTDEQGRATLKDFIK--IPHIYPVGRLDRDSEGLLLLTNNGELQ 80

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y V+  G   +  L  L+KGI +        +V L            
Sbjct: 81  HRLTNPKFKMEKTYWVQIEGIPVETDLAQLRKGIELNDGLTKPAKVRLISEPNIWQRHPP 140

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + + EG+NR+++++     +   RLIR       L  L+ G  RE++
Sbjct: 141 IRERKTVPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYETAGLTLTNLVNGQFRELT 200

Query: 238 KKILREQ 244
              L+  
Sbjct: 201 LTELQNL 207


>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 =  199 bits (506), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 78/198 (39%), Positives = 102/198 (51%), Gaps = 8/198 (4%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+  N   +   P+R+ K++A+ GI SRR++E  I Q RVKVNG +           D I
Sbjct: 1   MRRANQNNDK-NPERLQKLLAKYGIGSRRKIEEYIEQGRVKVNGKVAT-LGDKASEADKI 58

Query: 61  EVDGVPL----RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLD 115
             D   L    +   R R+ +YHK  G V T  D   R TVFD+LP +   R I VGRLD
Sbjct: 59  SFDSKALHSYGQPMTRPRVVIYHKREGEVCTSKDEKDRQTVFDSLPKLAKSRWIMVGRLD 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGD 174
           INT GLLL T DG LA  L  PS Q  R Y VR  G Q+  + +N LK+GI ++      
Sbjct: 119 INTTGLLLFTTDGDLANRLMHPSYQIEREYAVRVFGQQLSDETINKLKEGIQLEDGIAKF 178

Query: 175 MQVTLDTQKGSNAWVTVG 192
             +     +G+N W  V 
Sbjct: 179 NSIKFSGGEGANLWYYVT 196


>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 =  199 bits (506), Expect = 7e-49,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|329737424|gb|EGG73678.1| S4 domain protein [Staphylococcus epidermidis VCU028]
          Length = 180

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 59/176 (33%), Positives = 95/176 (53%), Gaps = 1/176 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I + RVKVNG  +      VM +D +EVDG+ + + ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAEVLITEGRVKVNGQTVTELGSKVMPSDLVEVDGIKIEQEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L +KP  ++T+ SD  GR  V D    + SR+  VGRLD +T G+LLLTNDG    +
Sbjct: 66  -YILLYKPTQVITSVSDDRGRRVVTDYFDDLESRIYPVGRLDYDTSGVLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           +  P     + Y  +  G + ++++  L+KGI ++       QV +  Q      +
Sbjct: 125 MTHPRYHIKKKYVAKLKGYLMREEIKQLEKGIELEDGYTQPAQVKIKKQDKEKIRL 180


>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 =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 105/248 (42%), Gaps = 22/248 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV---NGI----LLERAAVNVMSTD-HIEVDGV 65
            ++ +++   G  +RR    +I    V++   N      +   A++++        V G 
Sbjct: 1   MQLQEILYSQGFGTRRVCAGLIQHGHVQLRKKNDTGDAWVCTDASLDIDPEGLTFHVQGK 60

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDI 116
             +  ER  + + +KP  +  +   P    +V+  LP    +         V ++GRLD 
Sbjct: 61  VWQWHERAYVMM-NKPAAVECSQK-PSTYPSVYTLLPDPLRQRPGPGKILGVQTIGRLDQ 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +T GLLLL++DG     +  P  Q  + YRV     + Q + + L KG+V+       + 
Sbjct: 119 DTTGLLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQLLKGVVLNDDPKPVIA 178

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTRE 235
                Q+G  +   + + EGK  +IK++      +V +L RI  G   L   L AG  R 
Sbjct: 179 ADCVLQEG--SVFDLTVTEGKYHQIKRMVAAVGNRVEQLHRIRIGGLHLPDDLQAGDWRW 236

Query: 236 VSKKILRE 243
           +    +R 
Sbjct: 237 LGDDDVRR 244


>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 =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 54/185 (29%), Positives = 89/185 (48%), Gaps = 18/185 (9%)

Query: 74  RLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  ++HKP G+++  + +     T+ D +      V  VGRLD ++EGLLLLTN+G L  
Sbjct: 6   RYIIFHKPYGVLSQFTQESPKHITLKDYID--VPNVYPVGRLDWDSEGLLLLTNNGRLQH 63

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P     R Y V+     D++ +N L+ G+ IQ       +V L             
Sbjct: 64  RLSDPRFGHERTYWVQVERIPDEEAINRLQAGVEIQDYRTRPAKVRLLPEYPPVGDRQPP 123

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    AW+ + L EGKNR+++++     +   RL+R+S G  +L  L  G  R+++
Sbjct: 124 IRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLLRVSIGHLRLDGLALGEWRDLT 183

Query: 238 KKILR 242
              L+
Sbjct: 184 SLELK 188


>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 =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 63/271 (23%), Positives = 119/271 (43%), 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  LRKAERTRL----------------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SR 107
           +      ++                 + HKP GL+ T+ D   R ++F   P       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--------CYGDMQVTLDTQK--------GSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +                + +  ++             + + ++EG+NR+I+K+F+  N  
Sbjct: 220 KDEDNNKKKKKKTQPAFIEVLREENVKIQNQIKKITVLNISIKEGRNRQIRKMFQQINQP 279

Query: 212 VNRLIRISYGPFQLGTL-LAGSTREVSKKIL 241
           + ++ R ++    L  + L    RE++KK +
Sbjct: 280 IVKIKRTAFENITLKNIHLPKQYRELTKKEI 310


>gi|317013226|gb|ADU83834.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori Lithuania75]
          Length = 257

 Score =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L        + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAD--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>gi|327483844|gb|AEA78251.1| Ribosomal large subunit pseudouridine synthase E LSU Psi2457
           [Vibrio cholerae LMA3894-4]
          Length = 241

 Score =  198 bits (505), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 95/187 (50%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G++++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGSPQESDLEALRHGVILKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  198 bits (505), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 55/196 (28%), Positives = 93/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D   R T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 31  KPQLSFEDTVVVLFNKPFDVLTQFTDEQRRQTLKDFIP--IPQIYPVGRLDRDSEGLLLL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 89  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 149 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRIGLGQFQLGELN 208

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 209 SGEYRVLDEKEKRQLF 224


>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 =  198 bits (505), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  198 bits (505), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 78/175 (44%), Gaps = 17/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L++KP G++   S      T+ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   RILLFNKPYGVICQFSRDGMHPTLADYI--AVPDVYPAGRLDTDSEGLLLLTDDGKLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G  D   L  L++GI ++       +  L              
Sbjct: 61  ITDPKHKQPKTYWVQVEGIPDATALEQLRRGIQLKDGMTLPAEANLMAEPQGLWLRDPPV 120

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              +     W+ + + EGKNR+++++     +   RLIR S G + +  L  G  
Sbjct: 121 RFRKDIPTCWLWLTIHEGKNRQVRRMTAAVGFPTLRLIRYSIGKWTIDGLAPGKW 175


>gi|52426397|ref|YP_089534.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52308449|gb|AAU38949.1| RsuA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 247

 Score =  198 bits (505), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 93/188 (49%), Gaps = 17/188 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T++ L++KP  ++T  +D +GR+T+ D +      V + GRLD ++EGLL+LTN+G + 
Sbjct: 53  ETQVILFNKPFDVLTQFTDENGRATLKDFI--HIPDVYAAGRLDRDSEGLLILTNNGEIQ 110

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y V+  G+  +  L  L++G+ ++       +V L            
Sbjct: 111 HRLADPKFKMEKTYFVQVEGEPTETDLAKLRQGVELKDGMTRPAKVRLIAQPDFIWQRTP 170

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EGKNR+++++     +   RLIR +   F L  L  GS R +
Sbjct: 171 PIRERKSIPTSWLEIKISEGKNRQVRRMTANIGFPTLRLIRYAVSSFTLDNLANGSYRLL 230

Query: 237 SKKILREQ 244
           +   L   
Sbjct: 231 TDNELERL 238


>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 =  198 bits (505), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 51/184 (27%), Positives = 93/184 (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 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P+ +  +VY V+  G   ++ L  L++G++++          L         
Sbjct: 83  KLQAKLTQPAQKTGKVYFVQVEGVPTEEALTQLQRGVILKDGPTLPAGAELVCEPEWLWP 142

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 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|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 =  198 bits (505), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 52/185 (28%), Positives = 89/185 (48%), Gaps = 18/185 (9%)

Query: 74  RLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R  ++HKP G+++  + +     T+ D +      V  VGRLD ++EGLLLLTN+G L  
Sbjct: 6   RYIIFHKPYGVLSQFTQESPKHITLKDYID--VPDVYPVGRLDWDSEGLLLLTNNGRLQH 63

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P     R Y V+     D++ ++ L+ G+ I+       +V L             
Sbjct: 64  RLSDPRFGHERTYWVQVERIPDEEAISKLQTGVEIRDYRTRPAKVGLLPEYPPVGDRQPP 123

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +    AW+ + L EGKNR+++++     +   RL+R+S G  +L  L  G  R+++
Sbjct: 124 IRFRKNVPTAWLEMTLTEGKNRQVRRMTAAVGFPTLRLVRVSIGHLRLDGLALGEWRDLT 183

Query: 238 KKILR 242
              L+
Sbjct: 184 SLELK 188


>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 =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 67/258 (25%), Positives = 107/258 (41%), Gaps = 32/258 (12%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + E+    R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+    
Sbjct: 372 LAESSGLVRLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAA 431

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISV 111
             +       L HKP+G V+  ++                +   T           +   
Sbjct: 432 RSEQGERVTVLLHKPVGYVSGQAEDGYEPAAALFTAENQWEEDPTRKHFAAWQHKGLAPA 491

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQV--------DQDKL 158
           GRLDI++ GLL+LT DG +AR L    +   + Y VR       G V         +D L
Sbjct: 492 GRLDIDSTGLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWNAPQGPVEHDISKVFPEDLL 551

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            +L+ G+ + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI
Sbjct: 552 EMLRHGLSLDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRI 607

Query: 219 SYGPFQLGTLLAGSTREV 236
             G   LG L  G  R +
Sbjct: 608 RMGSVVLGDLPVGKWRFL 625


>gi|317182664|dbj|BAJ60448.1| hypothetical protein HPF57_1374 [Helicobacter pylori F57]
          Length = 257

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  + +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTKEMESAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 94/189 (49%), Gaps = 17/189 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +++ L++KP  ++T  +D +GR+T+ D +  I   V + GRLD ++EGLL+LTN+G + 
Sbjct: 35  ESQVILFNKPFDVLTQFTDENGRATLKDFI--IIPNVYAAGRLDRDSEGLLILTNNGEVQ 92

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y  +  G  ++  L+ L++G+ ++       +V L            
Sbjct: 93  HRLADPKFKTEKTYFAQVEGIPEESDLDKLRQGVELKDGMTKPAKVRLISEPDFLWPRNP 152

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + Q    +W+ + + EG+NR+++++     +   RLIR       L  L  G  R +
Sbjct: 153 PIRERQSIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLIRYQMSHLTLDGLSNGEYRRL 212

Query: 237 SKKILREQL 245
           +++ +R   
Sbjct: 213 NEEEMRALF 221


>gi|330963493|gb|EGH63753.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 210

 Score =  198 bits (504), Expect = 1e-48,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 103/246 (41%), Gaps = 22/246 (8%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKV------NGI-LLERAAVNVMSTD-HIEVDGVPL 67
           +  ++   G  +RR    +I    V++       G      A ++V        V G   
Sbjct: 8   LQDILYSQGFGTRRVCAGLIQHGHVQLREKGDAGGAWTCTDAGLDVDPEGLTFYVQGTAW 67

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINT 118
           +  ER  + + +KP  +  +   P    +V+  LP    +         V ++GRLD +T
Sbjct: 68  QWHERAYVMM-NKPAAVECSQK-PSTYPSVYTLLPDPLRQRPGPGKILGVQTIGRLDQDT 125

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GLLLL++DG     +  P  Q  + YRV     + Q + + L KG+V+       + V 
Sbjct: 126 TGLLLLSDDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQLLKGVVLNDDPKPVIAVD 185

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
              Q+G      + + EGK  +IK++      +V +L RI  G   L   L AG  R + 
Sbjct: 186 CVLQEGP--VFDLTVTEGKYHQIKRMVAAVGNRVEQLHRIRIGGLHLPDDLQAGDWRWLR 243

Query: 238 KKILRE 243
           ++ +R 
Sbjct: 244 EEDVRR 249


>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 =  198 bits (504), Expect = 1e-48,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 56/188 (29%), Positives = 91/188 (48%), Gaps = 16/188 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P       RL L++KP  ++T  +D  GRST+ D +P     V   GRLD ++EGLLLLT
Sbjct: 2   PKAPPSEPRLLLFNKPFDVLTQFNDERGRSTLKDFIP--VPGVYPAGRLDRDSEGLLLLT 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|330987630|gb|EGH85733.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 210

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|330873550|gb|EGH07699.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
          Length = 210

 Score =  198 bits (504), Expect = 1e-48,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 112/229 (48%), Gaps = 3/229 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K I+ +G  SRR+ +  I    VKVNGI +      V   D +  DG  L   E+ 
Sbjct: 70  IRLNKYISNSGACSRRDADIYIQSGNVKVNGIPVIEMGYMVKPGDVVNFDGSVLT-PEKK 128

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP    T   +      V + +     S++ +VGR+D NT GLLL TND  + R
Sbjct: 129 EYILLNKPKNFTTAFDEGQENRNVLELVRGSTNSKIAAVGRMDKNTTGLLLFTNDTDMIR 188

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
              LPS +  ++Y+V     +  + L  + KG+VI G      +++   +K + + V + 
Sbjct: 189 RFSLPSQKSSKIYQVSLDKNLKFEDLEKISKGLVIDGHRVFVEEISY-IEKEAKSEVGLK 247

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           L+    + ++ +FE F + V R+ R+S+       L  G+ R ++++ +
Sbjct: 248 LKTANVKVVRAIFESFKYDVLRIDRVSFAGLTKKNLPRGNWRFLTEQEI 296


>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 =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    ++  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQIYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIRI  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPPLRLIRIGLGQFQLGELN 209

Query: 230 AGSTREVSKKILREQL 245
           +G  R + +K  R+  
Sbjct: 210 SGEYRVLDEKEKRQLF 225


>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 =  198 bits (504), Expect = 1e-48,   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  PTAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|332674227|gb|AEE71044.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 262

 Score =  198 bits (504), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--KAER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++  K ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKSLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>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 =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 103/250 (41%), Gaps = 32/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      +     
Sbjct: 423 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVKPDAIIEIHQAARSEQGERV 482

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS---------------IFSRVISVGRLDINTE 119
             L HKP+G V+  ++   +  V   +P                    +   GRLDI++ 
Sbjct: 483 TVLMHKPVGYVSGQAEDGYQPAVSLFVPENQWEADPTRKRFAPWQRRALAPAGRLDIDST 542

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFH-------------GQVDQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR                   ++ +  L+ G+ 
Sbjct: 543 GLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWHSPDGVVERDISKVFPEELMEKLRFGLS 602

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   LG
Sbjct: 603 LDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGSIVLG 658

Query: 227 TLLAGSTREV 236
            L  G  R +
Sbjct: 659 DLPVGQWRFL 668


>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 =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 72/245 (29%), Positives = 107/245 (43%), Gaps = 9/245 (3%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-FSRVISVGR 113
                I VDG  L  A +    L +KP GL+TT+ DP GR TV+D L       +  VGR
Sbjct: 3   PQRAVICVDGRRLVSAAK-VYLLLNKPRGLLTTYGDPQGRKTVYDCLAGHDLPFLAPVGR 61

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           LD  +EGLLL+TND   A  L  P++   +VY V+     D+  L  L++G V  G    
Sbjct: 62  LDCASEGLLLMTNDTRWAHRLLDPASNVDKVYHVQIDRTPDEALLTGLREGAVHDGERLA 121

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              V        NAW+ V L EG+NR+I+++      +V RL+R++ G  +LG +  G+ 
Sbjct: 122 AKSVAPLRVGERNAWLEVVLSEGRNRQIRRMMALNGAEVLRLVRVAVGGLRLGDVRKGAF 181

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           R ++               A    D+   S      +             R    SS ++
Sbjct: 182 RHLTDAE-------RACLAAGGRTDSIRRSPTAGRAENGRETFSAERLLQRSVATSSIRS 234

Query: 294 GLSKQ 298
              + 
Sbjct: 235 DTGRD 239


>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 =  198 bits (503), Expect = 1e-48,   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  KPVRPRGERKVVIFNKPFDVLVQFTDENGRKTLKDFIP--IRDIYAAGRLDRDSEGLLVL 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|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 =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 78/234 (33%), Positives = 131/234 (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 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
            + L+EGK  EI+ +F+  N +VN+L R+SYGPF+L  +L G  ++ SK  L +
Sbjct: 182 EMNLKEGKKNEIRNIFKELNLQVNKLKRVSYGPFKLDNMLPGDLKKPSKIELEK 235


>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 =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 55/188 (29%), Positives = 94/188 (50%), 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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  +VY V+  G    D L+ L+ G+ ++          L     
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGVPGDDTLSQLRTGMTLKDGPTLPAGAELVSEPE 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|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 =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 55/196 (28%), Positives = 94/196 (47%), Gaps = 17/196 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E T + L++KP  ++T  +D  GR T+ D +P    +V  VGRLD ++EGLLLL
Sbjct: 32  KPQLSFEDTVVVLFNKPFDVLTQFTDEQGRQTLKDFIP--IPQVYPVGRLDRDSEGLLLL 89

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  +  + Y  +  G      L  L+KG+ ++       +        
Sbjct: 90  TNNGEIQHRLANPKFEKQKTYLAQVEGIPQAADLAKLEKGVELKDGLTKPAKAKAISAPN 149

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIR+  G FQLG L 
Sbjct: 150 YEWQTAPKIRERKTIPTSWIELKIHEGKNRQVRRMTAHIGFPTLRLIRVGLGQFQLGDLD 209

Query: 230 AGSTREVSKKILREQL 245
           +G  R +++   R+  
Sbjct: 210 SGEYRILNETGKRQLF 225


>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 =  198 bits (503), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 57/196 (29%), Positives = 96/196 (48%), Gaps = 20/196 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +     ++  VGRLD ++EGLLLLTN+G +
Sbjct: 29  EETIIVLFNKPYDVLTQFTDEQGRKTLKDFID--IPKIYPVGRLDRDSEGLLLLTNNGEI 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---LREQLGPH 248
           +S      L +QLG  
Sbjct: 207 LSLSEKSRLFKQLGLR 222


>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 =  198 bits (503), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 46/172 (26%), Positives = 82/172 (47%), Gaps = 6/172 (3%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              +HKP+G+  T +D      + D + +   R+  VGRLD  +EGL+LLTNDGG+A  +
Sbjct: 2   YIAFHKPVGITCTAAD-HIEDNIIDYI-NYPERIFPVGRLDKASEGLILLTNDGGIANQI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                +  + Y V          ++ + +G+ I+       +VT    +   +   + L 
Sbjct: 60  LHGDHEHEKEYVVTVDKPFTDWFIDEMSRGVKIKDGMTKPCKVT----RVDQSTFRIVLT 115

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +G NR+I+++   F + V +L R+     +L  L  G  R V+ + L   +G
Sbjct: 116 QGMNRQIRRMSRAFGFTVIKLKRVRIMNIELNELEVGKWRSVTAEELEILIG 167


>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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 54/178 (30%), Positives = 89/178 (50%), 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 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P+ +  +VY V+  G  D D L  LK+G+ ++          L               +
Sbjct: 59  QPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWPRHPPIRE 118

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E++ 
Sbjct: 119 RKTIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRFSMGNLSLGNLQPGEWKEITD 176


>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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 57/187 (30%), Positives = 93/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL  AER ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 57  RPLSPAER-KVILFNKPYDTLSQFTDGDGRKTLADYIP--IKDVYAAGRLDRDSEGLLIL 113

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 114 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 173

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 94/189 (49%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T + L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETTVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 53/197 (26%), Positives = 95/197 (48%), Gaps = 17/197 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P      T + L++KP  +++  SD  GR+T+ D +P     V  VGRLD ++EGLLLL
Sbjct: 29  KPKVSFAETIVLLFNKPYNVLSQFSDQQGRATLKDFIP--IENVYPVGRLDRDSEGLLLL 86

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G +   L  P  + ++ Y  +  GQ     L  L  G+ ++       +V++     
Sbjct: 87  TNNGEIQHRLAHPKFEKVKTYLAQLEGQPQAVDLAKLTCGVELKDGLTRPAKVSVIAPPN 146

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + + EGKNR+++++     +   RLIR++   F+LG L 
Sbjct: 147 YNWHTAPNIRERKTIPTSWLELKIYEGKNRQVRRMTAHIGFPTLRLIRVALSGFELGNLA 206

Query: 230 AGSTREVSKKILREQLG 246
            G  R +++   R+   
Sbjct: 207 TGEYRLLTEIEKRQLFA 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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 30  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 87

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 88  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 147

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 148 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 207

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 208 SLDEIKALF 216


>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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 85/188 (45%), Gaps = 21/188 (11%)

Query: 76  WLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L++KP  ++   +D D     R T+ D +      V  VGRLD ++EGLLLLTN G + 
Sbjct: 6   ILFYKPYDVLCQFTDNDPTTSPRKTLKDFI--SIPGVYPVGRLDRDSEGLLLLTNQGKIQ 63

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             L        R Y V+     D+  LN L+ G+ I+       QV L            
Sbjct: 64  HRLSHRKFNHPRTYWVQVEHIPDETALNALRAGVQIKDYQTRSAQVQLLPTEPALPPRDP 123

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +    AW+ + L EG+NR+I+++     +   RL+R++   F+L  L  G  R++
Sbjct: 124 PIRFRKTVPTAWLEITLTEGRNRQIRRMTAAVGFPTLRLVRVAIADFRLDGLKPGQWRDL 183

Query: 237 SKKILREQ 244
           ++  +   
Sbjct: 184 TQIEVHNL 191


>gi|317014873|gb|ADU82309.1| hypothetical protein HPGAM_07680 [Helicobacter pylori Gambia94/24]
          Length = 257

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLIYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKARFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>gi|317010168|gb|ADU80748.1| ribosomal large subunit pseudouridinesynthase B [Helicobacter
           pylori India7]
          Length = 257

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 123/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDRVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+L+L++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLILSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREIENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>gi|302185134|ref|ZP_07261807.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae 642]
          Length = 210

 Score =  197 bits (502), Expect = 2e-48,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 61/206 (29%), Positives = 97/206 (47%), Gaps = 9/206 (4%)

Query: 47  LERAAVNVMSTDH--IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS- 103
           +      + +     I VDG PL    R    + +KP G+VTT  D  GR TV+      
Sbjct: 2   VHDPEYPIRADQQSSITVDGQPLAGPARC-YLMLNKPRGVVTTVRDEQGRDTVYRCFDGA 60

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
               +  VGRLD  +EGLLL +ND   A  +  P+T   + Y V+   +   ++L  L+ 
Sbjct: 61  GLPWIAPVGRLDKASEGLLLFSNDPQWAAAVTDPATGPDKTYHVQIDCRPSAEQLAQLRA 120

Query: 164 GIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           G+V       G       V +  +   NAW+ + L EG+NR+I+++       V RL+R+
Sbjct: 121 GVVDPDPEGDGALLRAKHVGVLREGERNAWLEIVLDEGRNRQIRRLLAALEIGVLRLVRV 180

Query: 219 SYGPFQLGTLLAGSTREVSKKILREQ 244
           + G   +G L  G+ R +S + +R  
Sbjct: 181 AIGALAMGELGKGAWRMLSAEEVRAL 206


>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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 56/188 (29%), Positives = 96/188 (51%), 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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  +VY V+  G  D+D L+ L+ GI ++          L     
Sbjct: 79  TNDGKLQARLTQPAQKTGKVYFVQVEGLPDEDALSQLRIGITLKDGPTLPAGAELVSEPA 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|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 =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 81/176 (46%), 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G  D   L+ L+ G++++          L              
Sbjct: 61  ITDPKHKLPKTYWVQVEGVPDSAALDALRAGVLLKDGMTQPAGAALIDTPPGLWPRTPPV 120

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +    +W+ + +REGKNR+++++     +   RLIR   G + L  L  G+ +
Sbjct: 121 RARKAIPTSWLELTIREGKNRQVRRMTAAVGFPTLRLIRYRIGAWTLDGLDQGTWK 176


>gi|146282670|ref|YP_001172823.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
 gi|145570875|gb|ABP79981.1| pseudouridine synthase [Pseudomonas stutzeri A1501]
          Length = 297

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 89/295 (30%), Positives = 138/295 (46%), Gaps = 22/295 (7%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL 134
            +Y+KP G + T +DP+GR TVFD LP     R I++GRLDINT GLLL T DG LA  L
Sbjct: 2   LIYNKPDGEICTRNDPEGRPTVFDRLPRPKEGRWINIGRLDINTTGLLLFTTDGELANRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVGL 193
             PS +  R Y VR  G+VD + +  LK G++++        +      +G N W    +
Sbjct: 62  MHPSYEMDREYAVRVRGEVDDEMIERLKTGVMLEDGPARFTDIQEAPGGEGFNHWYHCVV 121

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKI---LREQLGPHL 249
            EG+NRE+++++E     V+RL R+ +GP  +   L  G  RE+S+     L E++G   
Sbjct: 122 MEGRNREVRRLWESQGLVVSRLKRVRFGPVFMTSDLPMGRWREMSQAEVDILSEEVGLKP 181

Query: 250 -------------LEEAQVNLDAPIYSSETLVR-DRPNIISEVP--DDFTRMKKNSSQKN 293
                        ++  Q  +  P+   E   R  RP   +++P  D     + + S++ 
Sbjct: 182 VALPSMKAKTKEKIDRMQRKVAKPLGRGERRSRVLRPAHEADMPVADKPRAARDDKSERK 241

Query: 294 GLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLR 348
                K   TPV  R   +     +       S   ++     + P F  +RS R
Sbjct: 242 PRGSDKPRGTPVAERPGDTRKGGKRHEGGGRSSGPARKPAGEGQRPGFGRERSKR 296


>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 =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 114/248 (45%), Gaps = 17/248 (6%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R++K I+     SRRE + +I Q +V +NG ++    + V   + I +    ++  
Sbjct: 1   MQKMRLNKFISHNTAYSRREADELIKQGKVSINGRVVSD-FIEVSGEEKIRIGSRLIKPK 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +Y+K  G + T  D  GR T++D+LP  FSR +SVGRLD  +EGLLLLT+   +
Sbjct: 60  TEFTMIVYNKRKGELVTKKDDRGRRTIYDSLPEGFSRFVSVGRLDFASEGLLLLTDAPAI 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--------------ICYGDMQ 176
           A  L   ++   R Y ++  G+V ++ +  +++G                        + 
Sbjct: 120 ATALM--NSDIEREYYLKVKGEVKEEVVTAIREGFFAADASKGAHAKSKIKSMEFKPFLG 177

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +    G    +   + EG+NRE+++ F +F+  V  L R ++G   LG L  G  R  
Sbjct: 178 YRIMPSSGGYTKIKAIINEGQNRELRRFFGYFDLDVVELKRTAFGRMTLGMLKPGKWRYF 237

Query: 237 SKKILREQ 244
                 + 
Sbjct: 238 DHSEYEDL 245


>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 =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L        + Y ++  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAD--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 117/245 (47%), Gaps = 17/245 (6%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+++ IA     SRRE +++I   RV +        +V +     + +DG  +   E+ 
Sbjct: 1   MRLNQYIAHHTKYSRREADKLIESGRVNIEKSKASLQSV-LREGMSVFIDGKRIVPKEQF 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 LM--ESHLERVYLVKINGEITKEIIEAMEKGLVSEDARAGGHIKSNIVAMEFAPFAHYEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 ++ + V + EGKNRE+++ F  F  +V  L RI+YG   L  L  G  R  +K+
Sbjct: 178 LKNDKRHSKLKVSITEGKNRELRRFFGVFGREVLDLRRIAYGFVNLNALPCGKKRYFTKE 237

Query: 240 ILREQ 244
             +  
Sbjct: 238 EYKSL 242


>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 =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>gi|330960137|gb|EGH60397.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 210

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 86/182 (47%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEGGRATLKDFID--IPGIYPAGRLDRDSEGLLLLTNDG 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|330952996|gb|EGH53256.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 210

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  197 bits (501), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 75/251 (29%), Positives = 117/251 (46%), Gaps = 28/251 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEV--DGVPLRKA 70
           +RVSK++AR G  SRRE E++IA  RV+VNG ++         ++D +E+  DG     +
Sbjct: 84  ERVSKILARRGACSRREAEQLIADGRVRVNGTVITEQGHKCDVNSDRVEITSDGSAWLSS 143

Query: 71  ERTRLWLYHKPIGLV-----------TTHSDPDG------RSTVFDNLP---SIFSRVIS 110
                   +KP GLV            +  +P        +    D+L    S  SR   
Sbjct: 144 --KLTLAVNKPPGLVSNLPSADEVAACSIVEPSNAWMRSMKWVAMDDLRRATSDPSRFNV 201

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLD ++ GLL+LT DG LAR +       ++ Y V     V +  +  L   +++ G+
Sbjct: 202 CGRLDKDSRGLLILTEDGALARSVIG-GNGVVKRYVVTTDADVRESHMQSLNGTVMLDGV 260

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
               M V    +      +   LREGKNR+I++V E F  +V  L R+  G   +G L  
Sbjct: 261 ELLPMNVKRLGRGSRT--LEFNLREGKNRQIRRVCEKFGLRVVDLHRVQIGEIDIGDLPE 318

Query: 231 GSTREVSKKIL 241
           G+ R +S+  +
Sbjct: 319 GAWRILSEDEV 329


>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 =  197 bits (501), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 75/263 (28%), Positives = 119/263 (45%), Gaps = 22/263 (8%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-- 71
            R+++ IA     SRRE + +IAQ RV V           +     + VDG  LR+ +  
Sbjct: 1   MRLNQYIAHHSKYSRREADGLIAQGRVNVEKKKA-VLGQELKEGQRVFVDGKQLREKKDG 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + + +YHKP G + T SD  GR ++FD+L   ++    VGRLD  +EGLLLL++D  +A
Sbjct: 60  PSTVIVYHKPKGELVTRSDDRGRRSIFDSLGRRYAHFTPVGRLDFASEGLLLLSDDKKIA 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQV 177
             L    +   R Y ++  G V +     ++ G+ ++    G                  
Sbjct: 120 HFLM--QSDLEREYILKISGAVTEKMKEAMENGLELEDARAGGHEKSKIQKMSFKPFAFY 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +     + + + V + EGKNRE+++ F  F  +V  L R+ YG   L  L  G  R +S
Sbjct: 178 QIQKNDRNFSKLKVRITEGKNRELRRFFAHFKAEVLDLRRVGYGFVTLSALPVGKVRFLS 237

Query: 238 KKI---LREQLGPHLLEEAQVNL 257
           K+    L + L  H       N 
Sbjct: 238 KEEYKKLHQLLKEHAKNPEGRNA 260


>gi|327482354|gb|AEA85664.1| pseudouridine synthase [Pseudomonas stutzeri DSM 4166]
          Length = 177

 Score =  197 bits (501), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 52/178 (29%), Positives = 88/178 (49%), Gaps = 16/178 (8%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L +KP  ++T  +D DGR+T+ D +      V   GRLD ++EGLLLLTNDG L   + 
Sbjct: 1   MLLNKPFDVLTQFADADGRATLKDFV--SVPGVYPAGRLDRDSEGLLLLTNDGRLQARIA 58

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------- 184
            P  +  + Y V+  G+VD+ +L  L++G+ +        +     +             
Sbjct: 59  DPKHKLPKTYWVQVEGEVDETQLERLRQGVELNDGMTLPAEARQLDEPELWPRNPPVRFR 118

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                +W+ + +REG+NR+++++         RL+R+  GP+ L  L  G  REV  +
Sbjct: 119 KSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGPWALDGLQPGEWREVPAQ 176


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 121/247 (48%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 STLMHAN--LEKEYLVKIQGFVTKEMENAMQEGLKLENATKGAHQKTSIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 122/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRHVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKARFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 58/189 (30%), Positives = 95/189 (50%), 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 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P+ +  +VY V+  G    D L  L++GI ++          L    
Sbjct: 78  LTNDGKLQAKLTQPAQKTGKVYFVQVEGVPGDDALMQLRRGISLKDGPTLPAGAELVDEP 137

Query: 180 -----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 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|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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 122/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+L+L++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLILSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>gi|145355123|ref|XP_001421818.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582057|gb|ABP00112.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 238

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 68/239 (28%), Positives = 102/239 (42%), Gaps = 26/239 (10%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------- 74
           RRE +  ++  RV VNG L+   +  V + D + +DG  +      R             
Sbjct: 1   RREADAAVSAGRVLVNGELVR-PSQRVKAGDVVTLDGKVMLWEAYARRVEEEIANDATSS 59

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTNDG 128
               LY+KP G+V T       S  F            R+  VGRLD ++ GL+LLTNDG
Sbjct: 60  FVYLLYNKPRGVVCTMEPHQRTSLHFALERERARMKKIRIFPVGRLDKDSSGLVLLTNDG 119

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------LDTQ 182
            ++  L  PS +  + Y V     V    +  L  G+VI  +    M  T       + +
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|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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +      V   GRLD ++EGLLLLTNDG
Sbjct: 29  APVEPKLILFNKPFDVLTQFSDGEGRATLKDFI--AVPGVYPAGRLDRDSEGLLLLTNDG 86

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L++G+ +        +            
Sbjct: 87  QLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLREGVQLNDGMTLPAEARQLEEPTLWPR 146

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  +
Sbjct: 147 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLEQGQWK 206

Query: 235 EVSKK 239
           EV+ +
Sbjct: 207 EVAAR 211


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 98/295 (33%), Positives = 145/295 (49%), Gaps = 35/295 (11%)

Query: 15  RVSKVIA---RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPL 67
           R+SKV++      + SRRE ERMI    V + G +L    + +   D     ++V+G  +
Sbjct: 38  RLSKVLSLHTENLVISRREAERMIRSGDVTLAGNVLTSPMMMLKEEDLNDGALKVNGKVV 97

Query: 68  RKA---------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--------SI 104
                              +TR+W+ HK  G +   +DP  R ++   L           
Sbjct: 98  NLRSSKGPRSVAGEENSVHKTRVWIAHKLPGEIVADNDPYDRPSLLQRLIRGGVGKVGKT 157

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
              + SVGRLD+NTEGL+L+TNDG  AR +ELPS +  R YRVR HG +   KL  ++KG
Sbjct: 158 RLHLKSVGRLDMNTEGLILVTNDGKYAREMELPSNKLHRTYRVRVHGLLTDHKLARIRKG 217

Query: 165 IVIQGICYGDMQVTLDTQKGS---NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           + ++GI Y  M++  ++ + S   N W+ V   EGKNR+I+ VF++    V RLIRISYG
Sbjct: 218 VTVEGIRYPPMRIIPESTRQSQSTNKWLKVTCTEGKNRQIRNVFKYLGLTVTRLIRISYG 277

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
            ++L T+  G   EV  K +  Q   H     +    AP  S E         + 
Sbjct: 278 DYRLQTIPPGMAIEVPAKHIENQ--KHRGRLIRPTKPAPKRSDEAESSKAVQWVR 330


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|300691607|ref|YP_003752602.1| pseudouridine synthase [Ralstonia solanacearum PSI07]
 gi|299078667|emb|CBJ51325.1| Pseudouridine synthase [Ralstonia solanacearum PSI07]
          Length = 641

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 103/250 (41%), Gaps = 32/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      +     
Sbjct: 390 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARSEQGERV 449

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                +   T           +   GRLDI++ 
Sbjct: 450 TVLLHKPVGYVSGQAEDGYEPAAALFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDIDST 509

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQV--------DQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR       G V         ++ L  L+ G+ 
Sbjct: 510 GLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDVSKVFPEELLEKLRHGLS 569

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   LG
Sbjct: 570 LDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGRVVLG 625

Query: 227 TLLAGSTREV 236
            L  G  R +
Sbjct: 626 DLPVGKWRFL 635


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 85/181 (46%), Gaps = 16/181 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L  
Sbjct: 61  PVIVLFNKPFDVLCQFTDEQGRKTLKDYIP--VPGVYAAGRLDRDSEGLLLLTNDGKLQS 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            +  P  +  + Y  +  G  D   L  L++G+ ++       ++++             
Sbjct: 119 QITEPKKKTYKTYWAQVEGAPDDSDLEKLRQGVELKDGMTLPAKISIMDNPAIWPRTPPI 178

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +       W+ + + EG+NR+++++     +   RLIR   G + L  L  G  R++  
Sbjct: 179 RERANIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLQNGEYRQLDM 238

Query: 239 K 239
           K
Sbjct: 239 K 239


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 90/183 (49%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +         V L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVTEPEWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYTLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 105/234 (44%), Gaps = 4/234 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA +GI SRRE +  I+  +V VNG ++      V   D +  DG  +   E  
Sbjct: 53  IRLNKYIANSGICSRREADLYISTGQVTVNGEIINEMGFKVNLDDDVRFDGRRIN-PEAK 111

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              L +KP G   T S+  G  TV D +  S  SR+  VGRL  N  GLLL TND  + +
Sbjct: 112 AYVLLNKPKGFSVTTSNAKG-MTVMDLVASSTKSRIQPVGRLGRNATGLLLFTNDDKVMK 170

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L    T   R++ +     +  + L+ +KKG+ + G       ++          V + 
Sbjct: 171 KLTNSKTGLPRLFHIELDKNLKAEDLDKIKKGLTVDGKRLEIEDLSYVDG-APKKEVGLK 229

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           +R   N  I+ +FE   ++V R+  +  G      L  G  R + ++ +   + 
Sbjct: 230 MRNVGNSIIRSIFEHLGYQVVRVDCVILGTLTKKDLPRGKYRHLKEQEIHNLMM 283


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 56/185 (30%), Positives = 92/185 (49%), Gaps = 17/185 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A   R+ L++KP  ++   +D  GR+T+   +P  F  V + GRLD ++EGLL+LTNDG
Sbjct: 25  PAAPRRVLLFNKPFDVLPQFTDESGRTTLQGFIP--FKDVYAAGRLDRDSEGLLVLTNDG 82

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P+ +  +VY V+  G  D D L  LK+G+ ++          L         
Sbjct: 83  KLQARLTQPAQKTGKVYFVQVEGVPDNDALTQLKRGVTLKDGLTLPAGAELVAEPEWLWP 142

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 143 RHPPIRERKTIPTSWLKITLYEGRNRQVRRITAHVGFPTLRLIRFSIGNLSLGNLQPGEW 202

Query: 234 REVSK 238
           +E++ 
Sbjct: 203 KEITD 207


>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 =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 54/187 (28%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +  +ER  + L++KP   ++  +D DGR T+ D +      V + GRLD ++EGLL+L
Sbjct: 58  RAISPSERKVV-LFNKPYDTLSQFTDGDGRKTLADYI--SIKDVYAAGRLDRDSEGLLIL 114

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+ G+ ++       +V +  +  
Sbjct: 115 TNDGILQARLTQPQSKAPKTYWVQVEGAPQESDLEALRHGVTLKDGPTLPAKVDIMPEPT 174

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|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 =  196 bits (500), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 51/193 (26%), Positives = 90/193 (46%), Gaps = 16/193 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +   + L+L HKP  +++  +D  GR+T+ + +      +   GRLD ++EGLLLLT DG
Sbjct: 56  RPPMSSLYLLHKPYQMLSQFTDTRGRATLAEAID--VPDIYPAGRLDYDSEGLLLLTGDG 113

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            LA  +  P  +  + Y V+  G+ +   L  L++G+ ++       +V           
Sbjct: 114 ALAHRISHPRHKQPKTYWVQVEGEPEPAALQALRQGVTLRDGPTRPAKVRRLESPDVAPR 173

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    AW+ + L EG+NR+++++         RLIR++ G + L  L  G  R
Sbjct: 174 HPPVRHREAVPTAWLELTLSEGRNRQVRRMTAHVGHPTLRLIRVAIGSWHLAGLAPGEWR 233

Query: 235 EVSKKILREQLGP 247
             +    R Q  P
Sbjct: 234 RETLHAPRAQAAP 246


>gi|153000988|ref|YP_001366669.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|151365606|gb|ABS08606.1| pseudouridine synthase [Shewanella baltica OS185]
          Length = 282

 Score =  196 bits (500), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 101 PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 158

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 159 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIWPRNPPV 218

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 219 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSGEHK 274


>gi|317179635|dbj|BAJ57423.1| hypothetical protein HPF30_1326 [Helicobacter pylori F30]
          Length = 262

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 122/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLVKIQGFVTREMENAIQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>gi|308064218|gb|ADO06105.1| hypothetical protein HPSAT_07015 [Helicobacter pylori Sat464]
          Length = 257

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y ++  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>gi|217973052|ref|YP_002357803.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217498187|gb|ACK46380.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 282

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 101 PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 158

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 159 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIGPRNPPV 218

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 219 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSGEHK 274


>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 =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 88/183 (48%), Gaps = 16/183 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + E   + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG
Sbjct: 52  RPENPVIVLFNKPFDVLCQFTDEAGRQTLKDFIP--VADVYAAGRLDRDSEGLLLLTNDG 109

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  PS +  + Y V+  G+   + +N L  G+ ++       +V +         
Sbjct: 110 QLQAKLTQPSQKTFKTYWVQVEGEPSDEAINALCNGVGLKDGMTLPAKVCVMASPDIWPR 169

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +     W+ V + EG+NR+++++         RLIR   G + L  L  G  +
Sbjct: 170 TPPVRERKAIPTTWLEVQICEGRNRQVRRMTAHVGHPTLRLIRYKIGQWCLDDLPNGEYK 229

Query: 235 EVS 237
            +S
Sbjct: 230 VIS 232


>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 =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 103/243 (42%), 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  RTRLWLYHKPIG----------LVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDIN 117
            +   +++KPIG           + T   PD       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 SWLSEQ----QLRFVVHENRKRQIQRQCELVGLQVTDIKRVRIGGVSLGKLPPGQWRYLR 410

Query: 238 KKI 240
              
Sbjct: 411 PDE 413


>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 =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 101 PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 158

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 159 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIWPRNPPV 218

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 219 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSGEHK 274


>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 =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 53/184 (28%), Positives = 92/184 (50%), Gaps = 17/184 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                R+ L++KP  ++   +D  GR T+ + +P  FS V + GRLD ++EGLL+LTNDG
Sbjct: 25  PVTPRRVLLFNKPFDVLPQFTDESGRRTLKEFIP--FSDVYAAGRLDRDSEGLLVLTNDG 82

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P+ +  +VY V+  G   ++ L  L++G+ ++          L         
Sbjct: 83  KLQAKLTQPAQKTGKVYFVQVEGVPGEEALTQLQRGVTLKDGPTLPAGAELVAEPEWLWP 142

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  
Sbjct: 143 RHPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEW 202

Query: 234 REVS 237
           +E++
Sbjct: 203 KEIN 206


>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 =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 101 PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 158

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 159 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIGPRNPPV 218

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 219 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSGEHK 274


>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 =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 57/189 (30%), Positives = 88/189 (46%), Gaps = 18/189 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           A   R  +++KP G+++  + +    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|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 =  196 bits (499), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 54/183 (29%), Positives = 90/183 (49%), Gaps = 16/183 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  ++T  SD +GR+T+ D +      V   GRLD ++EGLLLLTNDGGL   
Sbjct: 1   RLILFNKPFDVLTQFSDGEGRATLKDFID--IPGVYPAGRLDRDSEGLLLLTNDGGLQAR 58

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  +  + Y V+  G+   ++L  L+ G+ +        +     +           
Sbjct: 59  IADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLAEPALWPRNPPVR 118

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  +W+ + +REG+NR+++++         RL+R+  G + L  L  G  REV  K
Sbjct: 119 FRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWREVPAK 178

Query: 240 ILR 242
           + R
Sbjct: 179 LQR 181


>gi|240950257|ref|ZP_04754536.1| pseudouridylate synthase [Actinobacillus minor NM305]
 gi|240295234|gb|EER46035.1| pseudouridylate synthase [Actinobacillus minor NM305]
          Length = 224

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 56/196 (28%), Positives = 96/196 (48%), Gaps = 20/196 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E T + L++KP  ++T  +D  GR T+ D +     ++  VGRLD ++EGLLLLTN+G +
Sbjct: 29  EETIIVLFNKPYDVLTQFTDEQGRKTLKDFID--IPKIYPVGRLDRDSEGLLLLTNNGEI 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---LREQLGPH 248
           +S      L +QLG  
Sbjct: 207 LSLSEKSRLFKQLGLR 222


>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 =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 122/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 TLMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>gi|299067456|emb|CBJ38655.1| Pseudouridine synthase [Ralstonia solanacearum CMR15]
          Length = 687

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 104/250 (41%), Gaps = 32/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     +E+      +     
Sbjct: 436 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEVEILPAARSEQGERV 495

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                +   T           +   GRLDI++ 
Sbjct: 496 TVLLHKPVGYVSGQAEDGYEPAAALFTAENQWEEDPTRKHFAAWQHKGLAPAGRLDIDST 555

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQV--------DQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR       G V         +D L +L+ G+ 
Sbjct: 556 GLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWNAPQGPVEHDISKVFPEDLLEMLRHGLS 615

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   ++     +   LREGK R+I+++ E    +V  L RI  G   LG
Sbjct: 616 LDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLEVVGLKRIRMGSIVLG 671

Query: 227 TLLAGSTREV 236
            L  G  R +
Sbjct: 672 DLPVGKWRFL 681


>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 =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y ++  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLIKIQGFVTREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 121/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDRVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L        + Y ++  G V ++  N +++G+ ++    G  Q T              
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 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>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 =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 48/184 (26%), Positives = 92/184 (50%), Gaps = 16/184 (8%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +R     +L  ++KP G++   SD  GR T+ D +P   + V   GRLD ++EGL+LLT+
Sbjct: 6   IRPRAGKKLLRFNKPYGVLCQFSDQQGRKTLKDFVP--VADVYPAGRLDYDSEGLVLLTD 63

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--- 183
           DG L   +  P ++  + Y V+  G + ++ +  L  G+ ++       +  + T+    
Sbjct: 64  DGRLQARIAQPHSKLPKTYWVQVEGMITENAVRQLAAGVRLKDGMTQPARARILTKPTLW 123

Query: 184 -----------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                         +W+ + L EG+NR+++++     +   RL+R++ G ++L  L  G+
Sbjct: 124 AREPPVRFRKTIPTSWLELTLYEGRNRQVRRMTAAVGFPTLRLVRVAIGMWRLNDLALGA 183

Query: 233 TREV 236
             EV
Sbjct: 184 YEEV 187


>gi|261838734|gb|ACX98500.1| pseudouridine synthase B [Helicobacter pylori 51]
          Length = 262

 Score =  196 bits (498), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 63/246 (25%), Positives = 122/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A   + SRRE E+++ + RVK+N    + ++V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTMHSRREAEKLVLEGRVKINHEHAKLSSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+    V ++  + +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLVKIQSFVTKEMESAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>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 =  196 bits (498), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 44/173 (25%), Positives = 83/173 (47%), Gaps = 16/173 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L+HKP G++   S    R T+ + +      + + GRLD ++EGLL+LTNDG L + +
Sbjct: 79  ILLFHKPFGVICQFSRDGTRPTLANYI--SLPDIYAAGRLDQDSEGLLVLTNDGKLQQRI 136

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--------------TLD 180
             P  +  + Y  +  G + ++ L+ L+ GI ++       +                 +
Sbjct: 137 THPKHKLEKTYLAQVEGIISEEALHQLRTGIALKDGKTLPAKAQRIEPPNFAERIPPIRE 196

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +    +W+ + + EG+NR+++++     +   RLIR   G +QLG L  G  
Sbjct: 197 RKNIPTSWLELRICEGRNRQVRRMTAATGFPTLRLIRTRIGEWQLGELQPGEW 249


>gi|330976863|gb|EGH76892.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aptata str.
           DSM 50252]
          Length = 210

 Score =  196 bits (498), Expect = 6e-48,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|307638112|gb|ADN80562.1| Ribosomal large subunit pseudo uridine synthase B [Helicobacter
           pylori 908]
          Length = 257

 Score =  196 bits (498), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 126/261 (48%), Gaps = 20/261 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  + +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMESAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQLGPHLLEEAQVNLD 258
           ++    QL   +   A    D
Sbjct: 238 RQE-YNQLHAFMANRANTKGD 257


>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 =  196 bits (498), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 46/178 (25%), Positives = 86/178 (48%), Gaps = 16/178 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L  
Sbjct: 62  PIIVLFNKPFDVLCQFTDEQGRQTLKDFIP--IPGVYAAGRLDRDSEGLLLLTNDGKLQS 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            +  P  +  + Y  +  G  ++D L  L++G+ ++       ++++             
Sbjct: 120 QITEPKKKTYKTYWAQVEGAPNEDDLEKLRQGVELKDGMSLPAKISIMNNPDIWPRTPPI 179

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +       W+ + + EG+NR+++++     +   RLIR   G + L  L  G  R++
Sbjct: 180 RERANIPTTWLEIKICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLKNGEYRQL 237


>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 =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 53/181 (29%), Positives = 92/181 (50%), Gaps = 17/181 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L++KP  ++   +D  GR+T+ + +P  F+ V + GRLD ++EGLL+LTNDG L 
Sbjct: 28  PRRVLLFNKPFDVLPQFTDESGRTTLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQ 85

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P+ +  +VY V+  G    D L  L++G+ ++          L            
Sbjct: 86  ARLTQPAKKTGKVYFVQVEGVPSDDALLQLQRGMTLKDGPTLPAGAELVSEPEWLWPRNP 145

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E+
Sbjct: 146 PIRERKSIPTSWLKITLFEGRNRQVRRMTAHIGFPTLRLIRFSMGNLSLGDLQPGEWKEI 205

Query: 237 S 237
           +
Sbjct: 206 N 206


>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 =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 124/247 (50%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRMIYESLERKYAHFVPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y ++  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLIKIQGFVTKEMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN +V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKIRVVINEGKNRELRRFFAFFNARVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>gi|330938238|gb|EGH41915.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 210

 Score =  195 bits (497), Expect = 6e-48,   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  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 55/185 (29%), Positives = 95/185 (51%), 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 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  +VY V+  G  D+  L+ L+ GI+++        V L        
Sbjct: 84  GKLQAQLTQPHKKTAKVYYVQVEGVPDEISLDKLRNGIILKDGPTLPAGVELVHEPTWLW 143

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   LG +  G 
Sbjct: 144 SRHPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGNLPLGKMKPGE 203

Query: 233 TREVS 237
            +E++
Sbjct: 204 WKEIN 208


>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 =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 59/230 (25%), Positives = 97/230 (42%), Gaps = 15/230 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--VMST--DHIEVDGVPLRKA 70
           R+ +++   G  SR ++ RM     + ++   +  A     V       + V   PL   
Sbjct: 8   RIDQLLGSLGYGSRGDIARMAKSGWITLDDARIWDATTRIAVTPDLPARMVVSREPLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTN 126
               + L HKP+G+  +H +      V+D LP  + R   V    GRLD  T GLLLLT+
Sbjct: 68  AGM-VILLHKPLGMTCSHKEDG--PLVYDILPDRWKRRQPVISTVGRLDKQTSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P     + YR      ++ ++  +   G +V+QG         L     +
Sbjct: 125 DGPLLHRIISPKQHIKKTYRATLARPLEGNEAAIFAAGDLVLQGEDKPLAPAELRVISPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTR 234
            A +TV   EG+  +++++F      V  L R + G   L   L+ G  R
Sbjct: 185 EAVLTVT--EGRYHQVRRMFAATGNHVTALHRDALGGLVLPDDLMPGQWR 232


>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 =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 48/185 (25%), Positives = 89/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              +  L+L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 29  AEPKLILFLFNKPFDVLTQFSDEGGRATLKDFID--IPGIYPAGRLDRDSEGLLLLTNDG 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 EVSKK 239
           EV+ +
Sbjct: 207 EVAAQ 211


>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 =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 94/189 (49%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 30  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 87

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 88  QHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKPAKVRLISEPNLWERNP 147

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+  G   +  L  GS R +
Sbjct: 148 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVGMGSLSINGLANGSFRLL 207

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 208 SLDEIKALF 216


>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 =  195 bits (497), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 51/186 (27%), Positives = 95/186 (51%), Gaps = 16/186 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       QV L           
Sbjct: 94  QHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKQAQVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSIDGLANGSFRLL 213

Query: 237 SKKILR 242
           S   ++
Sbjct: 214 SLDEIK 219


>gi|293363560|ref|ZP_06610316.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
 gi|292552909|gb|EFF41663.1| pseudouridylate synthase [Mycoplasma alligatoris A21JP2]
          Length = 230

 Score =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 111/234 (47%), Gaps = 8/234 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++ K I+     +R ++++++ +++V +N  L+   ++N    + + +D       +  
Sbjct: 1   MKLEKFISNVTDLTRSQIKKLLKEKKVFINDNLVTSDSINFK-VEKLVID-QIAYNTDEY 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
              + +KP   +T+H D +   ++F+ +  +    +I+ GRLD++TEGLLL+++D   + 
Sbjct: 59  VYIMLNKPQNYITSHKD-ELYPSLFNLVSDAKRKNLIAYGRLDVDTEGLLLISDDTESSH 117

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     + Y V    ++    + +   G +I      D  +       S+    + 
Sbjct: 118 KLLSPKHHVEKKYYVEVDKKIPTSLVEIFLNGFIID---KNDKVLPSKLLIISDNKCYLT 174

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQL 245
           ++EGK  ++K++F+     V  L RI +   +L  TL  G  R ++KK +   L
Sbjct: 175 IKEGKFHQVKRMFKTHYLNVTFLKRIEFNNLKLDETLKPGQWRYLTKKEVELLL 228


>gi|104783740|ref|YP_610238.1| pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95112727|emb|CAK17455.1| pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 209

 Score =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 52/186 (27%), Positives = 90/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       RL L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLL
Sbjct: 22  QPKAPPAEPRLILFNKPFDVLTQFSDGEGRATLKDFID--IPGIYPAGRLDRDSEGLLLL 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|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 =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 106/240 (44%), Gaps = 13/240 (5%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDG 128
                 HKP G   +  D      ++D LP  +     V    GRLD +T GLLLLT+DG
Sbjct: 59  LS-IALHKPAGYTCSTKDKG--RLIYDLLPPRYRDRDPVLSTVGRLDRDTSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
           GL   +  P ++  +VY V     +  D++ L   G ++++      +   L+      A
Sbjct: 116 GLLHRIISPKSKLPKVYEVELSDDLRGDEVALFASGTLMLESEKTPLLPAELEVLDARRA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L EG+  +++++F      V  L R   G   L  L  G  R+++   L     P
Sbjct: 176 --RLVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTPTDLDTLFAP 233


>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 =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 89  PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 146

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 147 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGITLPAKVKIMDSPDIWPRNPPV 206

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 207 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSGEHK 262


>gi|224004838|ref|XP_002296070.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209586102|gb|ACI64787.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 365

 Score =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 88/246 (35%), Positives = 135/246 (54%), Gaps = 16/246 (6%)

Query: 2   KDKNIVQENF----TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-S 56
           K K+I   N        R++ ++ +    SRR+ ERM+   RV + G +++  +     S
Sbjct: 63  KRKDITNTNLSNGTEGVRITTLLCKHLGLSRRQSERMVLLGRVTLFGKVVDSPSFEFSAS 122

Query: 57  TDH----IEVDGVPLRKAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNLP-----SIFS 106
           TD     I+VDG  +  AE+T R+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 IQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           ++G     +Q T  D    +N W+ +   EGKNR+++++       V RLIRISYG + L
Sbjct: 243 VRGASGEVVQSTGKDVNGSTNTWLQITCTEGKNRQLRRILGSMGLDVTRLIRISYGDYDL 302

Query: 226 GTLLAG 231
            ++  G
Sbjct: 303 NSIPPG 308


>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 =  195 bits (497), Expect = 8e-48,   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  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 113/233 (48%), Gaps = 7/233 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++     +R E++ ++   RV +NG L +   +     + + +DG+     ++ 
Sbjct: 1   MRIEKWLSDVTDYTRSEIKNLLKNNRVYINGRLYDE-TIKYNEFNSLRIDGID-YATDKY 58

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              + +KP G +T++ D +   +VF+ +      +I+ GRLD++TEGLL+L+++  L   
Sbjct: 59  VYIMLNKPQGYITSNKD-ELYPSVFNLIDVPRKNLIAYGRLDVDTEGLLVLSDNHKLCHE 117

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L  P     + Y V+   Q++ + +++ K+G  I G     +   L+       ++   +
Sbjct: 118 LLAPKKHVFKKYLVQVDKQLEPNLIDIFKQGFSI-GEDKNTLPSKLEIIDNFTCYL--TI 174

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            EGK  ++K++F+   + V  L R+S+    L   L     R +S   + + +
Sbjct: 175 SEGKFHQVKRMFKTNGYNVIFLKRVSFKNIILDEKLKPSQWRFLSSDEINDLI 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 =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 59/228 (25%), Positives = 103/228 (45%), Gaps = 12/228 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           RV   ++  G  +R E +R +    V V    +      V  +  I V+G  L       
Sbjct: 7   RVDAHLSSLGYCTRSEAKRFLTTNNVSVYNERIFDVTKKVHHS-EIRVNGELLDAE--RL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
           + L +KP G+V +HSD      ++  LP  + R       +GRLDI+T G +LL++DG L
Sbjct: 64  VILMNKPHGVVCSHSDSGV--LIYSLLPPRWQRRNPKVSTIGRLDIDTTGAILLSDDGAL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P ++  ++Y V     +  D+  +   G +++ G     +   ++     +  V
Sbjct: 122 NHKLTSPKSEVTKIYEVTLAQALRGDEAEIFASGELLLNGEKKPLLPAKMEVIGPIH--V 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            V + EG+  ++K++F     +V  L R S+G F +  L     RE+S
Sbjct: 180 RVEICEGRYHQVKRMFASVGNRVTALHRASFGDFSVEDLKPSEFREIS 227


>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 =  195 bits (497), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 54/248 (21%), Positives = 102/248 (41%), Gaps = 28/248 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RL L +KP G++   +D  GR T+ + +P     V + GRLD ++EGLL L++DG L  
Sbjct: 24  PRLILLNKPYGVLPQFTDDQGRPTLAELVP--VKGVYAAGRLDRDSEGLLALSDDGPLIA 81

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------- 183
            +  P+++  + Y V+  G    + L  L++G+ ++       +V    +          
Sbjct: 82  RIAAPASKMPKTYWVQVEGVPTDEALEALRRGVTLKDGPTLPAEVRRMEEPDPLWPRDPP 141

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    +W+ + LREG+NR+++++     +   RLIR S G + L  L  G  REV 
Sbjct: 142 VRYRAAIPTSWIALTLREGRNRQVRRMTAAVGFPTLRLIRWSIGDWTLDGLAPGQWREVP 201

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR---PNIISEVPDDFTRMKKNSSQKNG 294
           +        P     ++        + + L   +   P   +          + +     
Sbjct: 202 Q--------PPATPSSRQKSSGQKSTGQKLTGQKLTGPKAPAPTGKRGPIKPRRTVAPRS 253

Query: 295 LSKQKKLA 302
              + +  
Sbjct: 254 APSRPRNR 261


>gi|309751708|gb|ADO81692.1| 23S rRNA U2457 pseudouridine synthase [Haemophilus influenzae
           R2866]
          Length = 227

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 94/189 (49%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNHGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 54/186 (29%), Positives = 90/186 (48%), Gaps = 16/186 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G P       RL L++KP  ++T     DGR+T+ D +P     V   GRLD ++EGLLL
Sbjct: 22  GPPEAPQAAPRLILFNKPFDVLTQFRGGDGRATLKDFIP--VPGVYPAGRLDRDSEGLLL 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|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 =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 94/189 (49%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN G L
Sbjct: 30  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNHGEL 87

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 88  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 147

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 148 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFRLL 207

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 208 SLDEIKALF 216


>gi|301169411|emb|CBW29011.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 240

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 94/189 (49%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN G L
Sbjct: 49  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNHGEL 106

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 107 QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 166

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 167 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFRLL 226

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 227 SLDEIKALF 235


>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 =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 71/237 (29%), Positives = 106/237 (44%), 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  PLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEG 120
                  K E       HKP   + ++ DP+GR      +  +F  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 G----NNSVKLVLTEGKNREIRKVFLSKNIFLKKIHRIRIGNIKLDDLKEGQIKVLS 232


>gi|284920961|emb|CBG34024.1| ribosomal large subunit pseudouridine synthase E (rRNA
           pseudouridylate synthase E) [Escherichia coli 042]
          Length = 217

 Score =  195 bits (496), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 53/189 (28%), Positives = 91/189 (48%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L
Sbjct: 31  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +         V L     
Sbjct: 89  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPA 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 208

Query: 230 AGSTREVSK 238
            G  REV+ 
Sbjct: 209 NGEWREVTD 217


>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 =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 94/189 (49%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T + L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETTVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       QV L           
Sbjct: 94  QHRLSDPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGMTKQAQVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGSLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 55/185 (29%), Positives = 94/185 (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 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P+ +  +VY V+  G    D L+ L++G+V++          L        
Sbjct: 82  GKLQAKLTQPAQKTGKVYFVQVEGTPGDDALSQLRQGMVLKDGPTLPAGAELVDEPEWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 126/260 (48%), Gaps = 20/260 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y V+  G V ++  + +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLVKIQGFVTREMESAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQLGPHLLEEAQVNLD 258
           +    QL   +   A    D
Sbjct: 244 QE-YNQLHAFMANRANTKGD 262


>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 =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 93

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 94  QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKPAKVRLISEPNLWERNP 153

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 154 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFRLL 213

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 214 SLDEIKALF 222


>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 =  195 bits (496), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAQLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y ++  G + ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLIKIQGFITREMENAMQEGLKLKNATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 122/247 (49%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y ++  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLIKIQGFVTREIENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EIIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 54/190 (28%), Positives = 92/190 (48%), Gaps = 17/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 55  KPRKENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVL 112

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  ++Y V+  G  D + L  L+ G+ +         + +     
Sbjct: 113 TNDGALQARLTQPDKRTGKIYYVQVEGIPDHEALQALRAGVTLNDGPTLPAGIEIVAEPD 172

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 56/180 (31%), Positives = 91/180 (50%), Gaps = 17/180 (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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  +VY V+  G  D+  LN L+ G+ ++          L            
Sbjct: 105 AKLTQPHKKTAKVYYVQVEGIPDESTLNKLRNGVTLKDGPTLSAGAELVEEPEWLWERTP 164

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + L EG+NR+++++     +   RLIR S G  QLG L  G  RE+
Sbjct: 165 PIRERKNIPVSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRFSIGSLQLGQLSPGEWREI 224


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 92/187 (49%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D + L  L+ G+ +         + +        
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 44/182 (24%), Positives = 86/182 (47%), Gaps = 16/182 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG L
Sbjct: 84  QNPIIVLFNKPFDVLCQFTDEQGRQTLKDFIP--IQDVYAAGRLDRDSEGLLLLTNDGQL 141

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------ 178
              +  P  +  + Y V+  G    + +  L+ G+ ++       +V             
Sbjct: 142 QSRITEPKKKTDKTYWVQVEGIPSDEAIQALRDGVTLKDGPTLPAKVERIAEPDVWPRNP 201

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + ++   +W+ + + EG+NR+++++     +   RLIR   G + L  +  G  + +
Sbjct: 202 PVRERKQIPTSWLAITICEGRNRQVRRMTAHVGYPTLRLIRYKIGQWSLNGVANGEYKVL 261

Query: 237 SK 238
            +
Sbjct: 262 PQ 263


>gi|271500470|ref|YP_003333495.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270344025|gb|ACZ76790.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 218

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 53/188 (28%), Positives = 88/188 (46%), Gaps = 18/188 (9%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P+   +R R+ L +KP  +++  +D  GR T+ D +P  F  + + GRLD ++EGLL+
Sbjct: 31  NEPVVVTQR-RIVLLNKPFDVLSQFTDEGGRPTLKDYVP--FRDIYAAGRLDRDSEGLLI 87

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-------- 175
           LTNDG L   L  P  Q  ++Y  +  G  D+D L   + G+V+                
Sbjct: 88  LTNDGKLQARLTQPGKQTPKIYYAQVEGIPDEDALRAFRTGLVLNDGPTLPAGAECVDEP 147

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                        +    +W+ + L EG+NR+++++     +   RLIR S     L  L
Sbjct: 148 VWLWPRQPPIRQRKNIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMANLTLDGL 207

Query: 229 LAGSTREV 236
           L G  +E+
Sbjct: 208 LPGDWKEI 215


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 48/185 (25%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDEGGRATLKDFID--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 88/189 (46%), Gaps = 18/189 (9%)

Query: 65  VPLRKA--ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
            P+ K       + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL
Sbjct: 34  KPISKPSVANPVMVLFNKPFDVLCQFTDEAGRKTLKDFIP--VPGVYAAGRLDRDSEGLL 91

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--- 179
           LLTNDG     L  P  +  + Y V+  G+ +Q  ++ L  G+ ++       +V L   
Sbjct: 92  LLTNDGKFQSKLTEPKQKTFKTYWVQVEGEPNQAAIDALCAGVELKDGMTLPAKVRLMAT 151

Query: 180 -----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      + Q    AW+ V + EG+NR+++++         RLIR   G + L  L
Sbjct: 152 PDVWPRTPPVRERQSIPTAWLEVQICEGRNRQVRRMTAHVGHPTLRLIRYKIGQWSLDDL 211

Query: 229 LAGSTREVS 237
             G  + ++
Sbjct: 212 NNGDYKLLN 220


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 90/187 (48%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++L
Sbjct: 49  KPRIAPKDRKVVIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVL 106

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   ++ L  L+KG+ ++        V +  +  
Sbjct: 107 TNDGILQAKLTQPQSKSPKTYWVQVDGAPTEEDLEKLRKGVELKDGITLPAIVEVMPEPE 166

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RL+R S G   L  L  
Sbjct: 167 IWERNPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGSIVLDNLKP 226

Query: 231 GSTREVS 237
           G  RE++
Sbjct: 227 GEWREIN 233


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 95/188 (50%), Gaps = 16/188 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P   A+  ++ +++KP   ++  +D +GR T+ D +P     + + GRLD ++EGL++
Sbjct: 44  NKPRISAQDRKVVVFNKPFDTLSQFTDGEGRKTLADYIP--IKDIYAAGRLDRDSEGLMV 101

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ- 182
           LTNDG L   L  PS++  + Y V+  G  ++  L+ L+KG+ ++       +V +  + 
Sbjct: 102 LTNDGILQARLTQPSSKSPKTYWVQVDGAPNEADLDKLRKGVELKDGMTLPAKVEVMAEP 161

Query: 183 -------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                             W+ + + EG+NR+++++     +   RLIR S G   LG L 
Sbjct: 162 SVWERNPPVRFRANIPTTWIAITIVEGRNRQVRRMTANIGFPTLRLIRYSMGDVTLGDLQ 221

Query: 230 AGSTREVS 237
            G  +E++
Sbjct: 222 PGEWKEIT 229


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 102/250 (40%), Gaps = 32/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      +     
Sbjct: 426 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARSEQGERV 485

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                +   T           +   GRLDI++ 
Sbjct: 486 TVLLHKPMGYVSGQAEDGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDIDST 545

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQV--------DQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR       G V         ++ L  L+ G+ 
Sbjct: 546 GLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRHGLS 605

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G   LG
Sbjct: 606 LDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSVVLG 661

Query: 227 TLLAGSTREV 236
            L  G  R +
Sbjct: 662 DLPVGKWRFL 671


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 110/245 (44%), Gaps = 9/245 (3%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ +N    R+ ++++  GI  R  V R + ++RV ++G     ++    S D + +DG 
Sbjct: 1   MIIKNSKKLRIDRLLSNLGIVERSSVPRFLNEKRVTISGKKATLSSK--ASPDEVRIDGK 58

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGL 121
            +           HKP G + +  +      V+D LP  F     +    GRLD    GL
Sbjct: 59  LIENPSALH-LALHKPSGYICSTVNDGDHKVVYDLLPKDFQSRKPIPSIAGRLDKWVTGL 117

Query: 122 LLLTNDGGLARVLELP-STQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTL 179
           ++ + DG L   +  P      + Y V    ++  D++ + + G ++++G         L
Sbjct: 118 VIFSQDGKLVERIITPKDDGCGKDYEVVLKNKLGGDEIGVFESGGLMLRGEEAPCKPAKL 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +    S   V V L EG+  +++++F   + K   + R   GP +LG L  G  R +++K
Sbjct: 178 EILDESKNKVKVTLFEGRYHQVRRMFAANDNKALEIHRTRIGPVELGDLPVGKWRHLTEK 237

Query: 240 ILREQ 244
            +++ 
Sbjct: 238 EIQDL 242


>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 =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 53/183 (28%), Positives = 90/183 (49%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +         V L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>gi|319426627|gb|ADV54701.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 270

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 89  PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 146

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 147 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGITLPAKVKIMDSPDVWPRNPPV 206

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 207 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDNLPSGEHK 262


>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 =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 92/187 (49%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D + L  L+ G+ +         + +        
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|313500758|gb|ADR62124.1| Pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 210

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +      V   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDGEGRATLKDFID--IPGVYPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
           GL   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  GLQARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLEEPELWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWR 204

Query: 235 EVSKK 239
           EV  K
Sbjct: 205 EVPAK 209


>gi|170719828|ref|YP_001747516.1| pseudouridine synthase [Pseudomonas putida W619]
 gi|169757831|gb|ACA71147.1| pseudouridine synthase [Pseudomonas putida W619]
          Length = 209

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 54/189 (28%), Positives = 91/189 (48%), Gaps = 16/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       RL L++KP  ++T  SD DGR+T+ D +      +   GRLD ++EGLLLL
Sbjct: 22  QPKAPPAEPRLILFNKPFDVLTQFSDSDGRATLKDYID--IPSIYPAGRLDRDSEGLLLL 79

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           TNDGGL   +  P  +  + Y V+  G+ + ++L  L++G+ +        +     +  
Sbjct: 80  TNDGGLQARIADPRHKLAKTYWVQVEGEPNDEQLKRLREGVELNDGPTLPAEARRLDEPE 139

Query: 185 --------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 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|300704234|ref|YP_003745837.1| pseudouridine synthase [Ralstonia solanacearum CFBP2957]
 gi|299071898|emb|CBJ43227.1| Pseudouridine synthase [Ralstonia solanacearum CFBP2957]
          Length = 677

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 102/250 (40%), Gaps = 32/250 (12%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK ++  G+ SRRE +  I +  V V+G  +      V     IE+      +     
Sbjct: 426 RLSKRMSELGLCSRREADEWIPRGWVLVDGEPVTELGSRVRPDAEIEILPAARSEQGERV 485

Query: 75  LWLYHKPIGLVTTHSDP---------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
             L HKP+G V+  ++                +   T           +   GRLDI++ 
Sbjct: 486 TVLLHKPMGYVSGQAEDGYEPAATLFTAENQWEEDPTHKRFAAWQHKGLAPAGRLDIDST 545

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRF-----HGQV--------DQDKLNLLKKGIV 166
           GLL+LT DG +AR L    +   + Y VR       G V         ++ L  L+ G+ 
Sbjct: 546 GLLVLTQDGRVARHLIGEDSTVEKEYLVRVVWDAPQGPVEHDISKVFPEELLEKLRHGLS 605

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           + G      +V+   ++     +   LREGK R+I+++ E     V  L RI  G   LG
Sbjct: 606 LDGEALKPAKVSWQNEE----QLRFVLREGKKRQIRRMCEQVGLTVVGLKRIRMGSVVLG 661

Query: 227 TLLAGSTREV 236
            L  G  R +
Sbjct: 662 DLPVGKWRFL 671


>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 =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLSPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>gi|297380685|gb|ADI35572.1| conserved hypothetical protein [Helicobacter pylori v225d]
          Length = 262

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 121/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>gi|317178163|dbj|BAJ55952.1| hypothetical protein HPF16_1355 [Helicobacter pylori F16]
          Length = 262

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 120/246 (48%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++ 
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNH 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>gi|322833615|ref|YP_004213642.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321168816|gb|ADW74515.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 208

 Score =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 90/183 (49%), Gaps = 17/183 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                ++ L++KP  ++   +D  GR+T+ D +P   + + + GRLD ++EGLL+LTNDG
Sbjct: 25  PKGPVKVILFNKPFDVLPQFTDEAGRATLKDYIP--LTDIYAAGRLDRDSEGLLVLTNDG 82

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------- 175
            L   L  P  +  ++Y V+  G+ D   +  L++GI ++                    
Sbjct: 83  KLQAALTQPGKRTGKIYYVQVEGEPDDAAVKSLREGITLKDGPTLPAGAAIVPEPEWLWA 142

Query: 176 --QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    AW+ + L EG+NR+++++     +   RLIR S G F LG L  G  
Sbjct: 143 RNPPIRERKSIPTAWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYSMGEFTLGDLQPGQW 202

Query: 234 REV 236
           +E+
Sbjct: 203 KEI 205


>gi|315585848|gb|ADU40229.1| RNA pseudouridine synthase [Helicobacter pylori 35A]
          Length = 262

 Score =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 122/246 (49%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    +  +V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLVSV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKIRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>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 =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 48/181 (26%), Positives = 86/181 (47%), Gaps = 16/181 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 78  KPQGDPMIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IPGVYAAGRLDRDSEGLLLLTND 135

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  + Y V+  G+  +  L  L++G+ ++       +V+L        
Sbjct: 136 GQLQAKLTEPKKKTFKTYWVQVEGEPTEADLAKLRQGVELKDGMTLPAKVSLMATPNVWP 195

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EG+NR+++++     +   RLIR   G + L  L  G  
Sbjct: 196 RNPPIRERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLATGEH 255

Query: 234 R 234
           +
Sbjct: 256 K 256


>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 =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 85/181 (46%), Gaps = 16/181 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 83  KPQGEPMIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IPGVYAAGRLDRDSEGLLLLTND 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 R 234
           +
Sbjct: 261 K 261


>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 =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 54/169 (31%), Positives = 87/169 (51%), Gaps = 2/169 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 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+ D +  +  R+  +GRLD +T GL+LLTNDG +  
Sbjct: 63  KVYIALNKPKGYVSTVKDERGRKTILDLV-DVTERIYPIGRLDYDTSGLILLTNDGDIYN 121

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
            +  P  +  ++Y     G   ++ +   + GI I G      +  +  
Sbjct: 122 KIIHPKQEKNKIYIALIKGIPTENDIKKFEIGINIDGYVTAPAKFKIIK 170


>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 =  194 bits (494), Expect = 2e-47,   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|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 =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/186 (27%), Positives = 90/186 (48%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+
Sbjct: 34  HENQPTRVILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNN 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G   QD L  L+ G+ +           L        
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGE 211

Query: 233 TREVSK 238
            REV+ 
Sbjct: 212 WREVTD 217


>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 =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 96/226 (42%), Gaps = 12/226 (5%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGV-PLRKAERTR 74
           K +   GI +R+  + ++  Q V++NG  +      V   +   + ++G   L       
Sbjct: 5   KYLQAQGIDTRKGCQWLVKHQLVQINGDTIASDKAEVQPENVRSLSIEGEDALIIPLPHF 64

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
             L +KP     +H  P    +VF  LP       + ++GRLD +T G+LL+TNDG    
Sbjct: 65  YILLNKPADYEVSHK-PRDYPSVFTLLPDQIRAADIQAIGRLDADTTGVLLITNDGQFNH 123

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVT 190
            +  P  +  ++YR+           + LK G+++          +  L T       + 
Sbjct: 124 RMTSPKHKVAKIYRITLKHPASDTLCSSLKNGVLLHDDNETVAAQEAILQTP----TTLL 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + + EGK  ++K++      +V +L R  +G +    L AG  R +
Sbjct: 180 MTISEGKYHQVKRMIAAAGNRVAQLHRQQFGDWDTQDLAAGEWRFI 225


>gi|301510575|ref|ZP_07235812.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii
           AB058]
          Length = 210

 Score =  194 bits (494), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/219 (23%), Positives = 93/219 (42%), Gaps = 15/219 (6%)

Query: 38  QRVKVNGILLERAAVNVMSTD-HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
             V ++G ++          +    V G   +  E+       KP G   +H  P    +
Sbjct: 1   GSVIIDGEVVSDLKKQFSPENFEFSVFGQNYQYREKI-YIALRKPQGFECSHQ-PQHHQS 58

Query: 97  VFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
           VF  LP       V +VGRLD +T GLLLLT+DG   + L  P     +VY V  +  V 
Sbjct: 59  VFSLLPETMIHRGVQAVGRLDQDTTGLLLLTDDGKYLQALTHPRKHVPKVYHVTTYDPVT 118

Query: 155 QDKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +++ +L +G+ +   +G+        L         +T+ + +G   ++K++      K
Sbjct: 119 PEQIEMLTQGVNLHQEKGVFAATDVALL-----GTHQLTMTIHQGVYHQVKRMIAAVGNK 173

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           V +L R   G   L  +  G    +S++   +QL  +++
Sbjct: 174 VEKLHRHQIGQLVLPEIEEGGWVYLSEQE--KQLAQNII 210


>gi|145580106|pdb|2OML|A Chain A, Crystal Structure Of E. Coli Pseudouridine Synthase Rlue
          Length = 189

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 9   QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 66

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 67  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 126

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 127 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 186

Query: 236 VSK 238
           V+ 
Sbjct: 187 VTD 189


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 66/227 (29%), Positives = 91/227 (40%), Gaps = 11/227 (4%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRK 69
              +R+   +   G  SR E   ++   RV V G +     A          VDG P   
Sbjct: 1   MELERL---LRSQGFGSRAECRGLVCTGRVSVEGRVCNDPLAQFEPEGLSFAVDGQPWAY 57

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTND 127
             R      +KP G   +   P    +VF  LP    R  V +VGRLD +T GLLLLT+D
Sbjct: 58  R-RFVYLALNKPAGHECSRR-PIHYPSVFSLLPIPLVRRGVQAVGRLDADTTGLLLLTDD 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G        P     +VY V     VD  ++  L  G+V+       M    D Q   + 
Sbjct: 116 GAFIHACTSPRRMVPKVYEVSTRHAVDDGQVAALLSGVVLHDESQAIMAAACDRQGERSL 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGST 233
            +TV L  GK   +K++      +V  L R++ G   L  TL AG  
Sbjct: 176 RLTVTL--GKYHLVKRMVAAAGNRVEALHRVAIGGLALPATLAAGRW 220


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/178 (29%), Positives = 83/178 (46%), Gaps = 17/178 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L L +KP G+++  S      T+ D +P   S V   GRLD ++EGL+LLTNDG    
Sbjct: 19  PKLVLLNKPYGVLSQFSGEPDDVTLKDFVPH--SNVYPAGRLDKDSEGLMLLTNDGVYQA 76

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--------------- 177
            L  P  +  + Y V+  G  D+ +L  L+ G  +        Q                
Sbjct: 77  RLANPKYKVAKTYWVQVEGIPDEAQLTALRNGCELNDGLTKPAQAFAIDAPIGLWPRNPP 136

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             + +   ++W+++ + EGKNR+++++         RLIR   GPF+L  L  G  RE
Sbjct: 137 VRERKTVPDSWLSLSITEGKNRQVRRMTAHVGLPTLRLIRAQIGPFKLAGLQPGEWRE 194


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 49/169 (28%), Positives = 85/169 (50%), Gaps = 6/169 (3%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +KP G ++  +D     TV D +   +       VGRLD +TEGLL+LTNDG L+  + 
Sbjct: 1   MNKPDGYISATTD-KYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKLSHRVL 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLR 194
            P     + Y  +  G V ++ +    +G+V+    Y  M   L+  +    + + + + 
Sbjct: 60  SPKKHVPKTYYAKIDGVVTEEDVEAFLEGVVLDDG-YKTMPSQLNILKSDDESEIELTIH 118

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
           EGK  ++K++FE    KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 119 EGKFHQVKRMFESVGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEVK 167


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PSIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 91/188 (48%), Gaps = 17/188 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T++ L++KP  ++T  SD +GR+T+   +P     V   GRLD ++EGL+LLTN+G + 
Sbjct: 48  ETQVILFNKPYDVLTQFSDEEGRATLKAFIP--IPHVYPAGRLDRDSEGLVLLTNNGEIQ 105

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L +P     + Y  +  G   +  L  L++G+V+        +V L            
Sbjct: 106 HRLAVPKFNTEKTYFAQVEGIPQETDLAQLRQGVVLNDGKTLPAKVRLVPEPNWLWQRNP 165

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + ++   +W+ + + EG+NR+++++     +   RLIR     F L  L  G  R++
Sbjct: 166 PIRERKQIPTSWLEIKIHEGRNRQVRRMTAHIGFPTLRLIRYQMALFNLANLEQGQYRQL 225

Query: 237 SKKILREQ 244
           S+  L   
Sbjct: 226 SEVELTAL 233


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 54/188 (28%), Positives = 86/188 (45%), Gaps = 18/188 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           A   +  ++HKP G+++  + +     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|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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 99/263 (37%), Gaps = 17/263 (6%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       +L L +KP  ++   +D  GR T+ D +      + + GRLD ++EGLLLL
Sbjct: 49  KPAPAPADRKLLLLNKPYMVLCQFTDEAGRETLKDYITE--PGIYAAGRLDRDSEGLLLL 106

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  + Y V+  G   ++KL  L  G+ +           +     
Sbjct: 107 TNDGKLQARLTQPGEKTPKTYWVQVEGVPSEEKLAALCAGVELNDGMTLPAGARIMEEPA 166

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + ++    W+ + + EG+NR+++++         RLIR + G + L  L  
Sbjct: 167 VWPRNPPIRERKEIPTCWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDWSLDGLAP 226

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET-LVRDRPNIISEVPDDFTRMKKNS 289
           G +R +    L     P   +        P  + +    R       +  +      + S
Sbjct: 227 GESRALPAPELAPAPRPATTQGKAQTSAKPQGAGQRGAPRAARRPQHQGQEQAPGQGRGS 286

Query: 290 SQKNGLSKQKKLATPVHRRNLAS 312
            +       +       RR   S
Sbjct: 287 REAEPHPGHRSGGRGTARRPARS 309


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 50/178 (28%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD L  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+ 
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 177


>gi|237735675|ref|ZP_04566156.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229381420|gb|EEO31511.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 235

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 98/224 (43%), Gaps = 8/224 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           V+ +  + + +  + +I    ++VN  ++      V + D I    + L  A+    ++ 
Sbjct: 12  VLMKNKLGNHKICKTLIRHGEIRVNDQVITDVRYPVKADDIIMYHHIQLN-AQPFVYYMM 70

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP   +  + D      V D +         +GRLDI+T GLL++TND  L++ L LP 
Sbjct: 71  NKPADYLCANHD-KYHQCVIDLI--GREDCYCLGRLDIDTTGLLIITNDTSLSKKLLLPQ 127

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               + Y V     +  + +     G+VI       +   L+     +    V + EG+ 
Sbjct: 128 NHVNKKYYVTTKFPLKDELIKKFSDGVVID-HKVQCLPSLLEILDEYHCL--VTINEGRY 184

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +IKK+F+    +V  L RI++   +L   L  G  R+++   L
Sbjct: 185 HQIKKMFKSCQNEVCTLKRIAFAGIELDQKLALGEYRDLTSTEL 228


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>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 =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 59/295 (20%), Positives = 109/295 (36%), Gaps = 42/295 (14%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       +L L +KP  ++   +D  GR T+ D +      + + GRLD ++EGLLLL
Sbjct: 49  KPQVAPADRKLLLLNKPYMVLCQFTDEAGRETLKDYIKE--PGIYAAGRLDRDSEGLLLL 106

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  + Y V+  G   +++L  L+ G+ +        +  L     
Sbjct: 107 TNDGKLQARLTQPGEKTPKTYWVQVEGIPSEEELAALRAGVELNDGLTLPAEARLMDEPN 166

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--- 227
                    + ++    W+ + + EG+NR+++++         RLIR + G + LG    
Sbjct: 167 VWPRNPPIRERKEVPTRWLEIKIVEGRNRQVRRMTAHIGHPTLRLIRYAIGDWTLGNWQE 226

Query: 228 --LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRM 285
             L  G +R +    L                 AP+  +      +P   S         
Sbjct: 227 DGLAPGESRSLPAPEL-----------------APVSPARPR---KPQTGSSTAKPANDR 266

Query: 286 KKNSSQKNGLSKQKKLATPVHRRNLASNVWMA-KGIHSSFLSDSGQREENHRRSP 339
            + ++Q N  +  +    P   +  +     +         +    R    + S 
Sbjct: 267 PRRTAQSNRKNPPRSAGKPAIDQAGSRPPAESKPRSSGRGTARRPARHTTDKESS 321


>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 =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 55/208 (26%), Positives = 100/208 (48%), Gaps = 22/208 (10%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           ++KP  ++T  SD  GR T+ D +P   S V + GRLD ++EGLLLLT+DG L   +  P
Sbjct: 6   FNKPFEVLTQFSDGAGRQTLADFIP--VSGVYAAGRLDRDSEGLLLLTDDGPLQNRISHP 63

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQ 182
             +  +VY V+  G +  + +  L+ G+ ++       +V++                  
Sbjct: 64  LHKLKKVYWVQVDGAISDEAVERLRHGVELKDGMTSPARVSVMEAPATLWPRNPPIRTRA 123

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +   +W+++ + EG+NR+++++     +   RLIR + GP  L  L  G+  EV  + L 
Sbjct: 124 QIPTSWISLEISEGRNRQVRRMTAAVGFPTLRLIRYAIGPITLDGLQPGTYDEVDAQQLW 183

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRD 270
                +L       +D P+ S+    + 
Sbjct: 184 -----NLFPTQGSGVDRPVVSAGNSHKK 206


>gi|330722223|gb|EGH00111.1| Ribosomal large subunit pseudouridine synthase E [gamma
           proteobacterium IMCC2047]
          Length = 220

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 99/232 (42%), Gaps = 27/232 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L L++KP  +++  +D  GR T+ D +      V + GRLD N+EGLLLLT++G L  
Sbjct: 2   PTLILFNKPYDVLSQFTDDKGRPTLADFITQ--KGVYAAGRLDYNSEGLLLLTDNGQLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---------- 182
            +  P  +  + Y V+  G + +  +  L+ GI ++       +V    +          
Sbjct: 60  HIAHPRHKQEKTYWVQVEGDISEQAVKQLRTGIQLKDGLTRPAKVQKLPEPELWPRNPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               +   +WV + + EG+NR+++++     +   RL+R++ G ++L  L  G  + ++ 
Sbjct: 120 RFRAEIPTSWVEIKISEGRNRQVRRMTAAVGFPTLRLVRVAIGNWELENLQPGEYKVLT- 178

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
                     +   A+    A   +    ++       +      + +K   
Sbjct: 179 ----------VDAPAEPKKHASKKTRIPTLKPTVRYSKKRTKQALKRQKAKP 220


>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 =  193 bits (492), Expect = 2e-47,   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|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 =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 51/186 (27%), Positives = 90/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   A RT++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 8   KPKTPASRTKIVLFNKPFNVLTQFTDATGRQTLKDFIP--IPDIYASGRLDKDSEGLLVL 65

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDG L   L  P  +  + Y V+  G   + +L  L+ G+ ++       +V       
Sbjct: 66  TNDGKLQSKLTDPKKKTSKTYWVQVEGIPQERQLQALRDGVELKDGLTRPAKVESMPEPA 125

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      Q    +W+++ + EGKNR+++++     +   RL+R   G + L  +  
Sbjct: 126 LWPRTPPVRFRQSIPTSWLSITISEGKNRQVRRMTAHIGFPTLRLVRYRIGNWTLDGIDT 185

Query: 231 GSTREV 236
           G   E+
Sbjct: 186 GQYVEL 191


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 90/189 (47%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L
Sbjct: 26  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +         V L     
Sbjct: 84  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPA 143

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 144 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 203

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 204 NGEWREATD 212


>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 =  193 bits (492), Expect = 3e-47,   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|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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 50/178 (28%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD L  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+ 
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVTD 177


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 214

Query: 236 VSK 238
            ++
Sbjct: 215 ATE 217


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 52/212 (24%), Positives = 92/212 (43%), Gaps = 22/212 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDG------RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L L++KP G++   +D  G      R+T+ D L      +   GRLD ++EGLLLLT++G
Sbjct: 4   LILFNKPFGVLCQFTDEKGGTNGNPRATLADWL--TIPAIYPAGRLDYDSEGLLLLTDNG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV----------- 177
            L   +  P  +  + Y V+  G++++  L  L++G+ ++        V           
Sbjct: 62  QLQHRIASPRLKMPKTYWVQVEGEINESALTKLREGVELKDGKTRPADVATMTPPEIWPR 121

Query: 178 ---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +WV + + EGKNR+++++     +   RLIR   G + L  L  G  R
Sbjct: 122 NPPVRYRESIPTSWVRITITEGKNRQVRRMTAAVGFPTLRLIRYGIGDWTLDGLTPGEYR 181

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
            +S             + A++   AP      
Sbjct: 182 AISVHAPAPPPEKAARKPAKLRKHAPRRRPRP 213


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 52/186 (27%), Positives = 90/186 (48%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+
Sbjct: 24  HENQPTRVILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNN 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G   QD L  L+ G+ +           L        
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 142 PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGE 201

Query: 233 TREVSK 238
            REV+ 
Sbjct: 202 WREVTD 207


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 86/181 (47%), Gaps = 16/181 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +      + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 78  KPQGDPMIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IPGVYAAGRLDRDSEGLLLLTND 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 R 234
           +
Sbjct: 256 K 256


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 48/181 (26%), Positives = 87/181 (48%), Gaps = 19/181 (10%)

Query: 74  RLWLYHKPIGLVTTHSDP---DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +L L++KP  +++  +D      R+T+ D +      V   GRLD ++EGLLLLT+ G L
Sbjct: 3   KLILFNKPFHVLSQFTDERASHPRATLADWIDQ--PGVYPAGRLDYDSEGLLLLTDQGAL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P+ +  + Y V+  G++  + L+ L+KG+V++       +              
Sbjct: 61  QHRIASPTNKMPKTYWVQVEGELTDEALHKLRKGVVLKDGITRPARAERLETPDLWPRNP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                Q     W+ + + EGKNR+++++     +   RLIR+  G + L  L  G  R V
Sbjct: 121 PVRFRQNVPTTWLALTITEGKNRQVRRMTAAVGYPTLRLIRVRIGDWTLDNLKPGEYRSV 180

Query: 237 S 237
           +
Sbjct: 181 T 181


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDILPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 73/239 (30%), Positives = 106/239 (44%), Gaps = 18/239 (7%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
            GI S  E  R+I + R+ +NG  + +     +  D I V+G PL    R    L HKP 
Sbjct: 1   MGIPSGTEAGRLIERGRISINGRPIVQNRWVDVRKDSILVNGTPLEATCRL-TLLMHKPA 59

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           G V +  DP  R TVF  LP     + + GRLD +T GLLLLTND  L   L  P  +  
Sbjct: 60  GYVVSRDDPLNRDTVFQLLPDPSVYIGASGRLDKDTTGLLLLTNDTYLQSSLVDPVYKVP 119

Query: 143 RVYRVRFHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------------AW 188
           +VYRV   G  ++  +L  L+ G+ ++        V      G                 
Sbjct: 120 KVYRVVVKGAALNGAQLMALRSGVSLEDGPTLPALVEPLDVNGDPLPLEMSEYDRYKCKQ 179

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL---GTLLAGSTREVSKKILREQ 244
           + + L EG+NR+++++ E     V  L RI  GPF L   G    G  R+++   +   
Sbjct: 180 LNITLWEGRNRQVRRMVEAVGSTVRDLCRIQLGPFSLHAAGVPNPGDVRQLTIDEVETL 238


>gi|254496292|ref|ZP_05109179.1| pseudouridine synthase [Legionella drancourtii LLAP12]
 gi|254354480|gb|EET13128.1| pseudouridine synthase [Legionella drancourtii LLAP12]
          Length = 240

 Score =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 54/179 (30%), Positives = 84/179 (46%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP  +V   +      T+ + +        + GRLD N+EGLLLLTNDG L   L
Sbjct: 55  LILFNKPFAVVCQFTGEKHEHTLAEFIDK--PDFYAAGRLDKNSEGLLLLTNDGALQHQL 112

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P     + Y V+  G      L  LKKG+V++ I +   +V                 
Sbjct: 113 THPKFNKKKYYWVQVEGIPTAADLEPLKKGLVLKDITFLPAEVRCIEEPALWPRTPPVRF 172

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            Q    +W+ + LREGKN +++++     +   RL+R   G +QLG L  G  R V+++
Sbjct: 173 RQSIPTSWLEIILREGKNHQVRRMTAAMGFPTLRLVRHRIGDWQLGDLQPGEFR-VTQQ 230


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 65/246 (26%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AER 72
           R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    ++
Sbjct: 7   RINQFLAHYTKHSRREAEKLVLEGRVKINHEHAQLASV-VKENDKVFLDKRLIKPLKNKK 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +YHKP G + + +DP  R  ++++L   ++  + VGRLD  +EG+LLL++   +  
Sbjct: 66  FSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFVPVGRLDFASEGVLLLSDSKAVVS 125

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L   +    + Y ++  G V ++  N +++G+ ++    G  Q T              
Sbjct: 126 ALMHAN--LEKEYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGYE 183

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R +++
Sbjct: 184 IIKNHAKYSKLRVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLNR 243

Query: 239 KILREQ 244
           +   E 
Sbjct: 244 QEYNEL 249


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 100/264 (37%), Gaps = 32/264 (12%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRK 69
             P ++  ++   G  +RR    ++ Q RV V G       A       H+ V+G+  R 
Sbjct: 1   MPPMQLQDILFGQGFGARRVCAGLVQQGRVSVAGAACIDPLAEFEPEGLHLRVEGLEGRT 60

Query: 70  AERT----------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------------ 107
             R            L + +KP G   +   P    +V+  LP    +            
Sbjct: 61  GLREGGLDWVCHLSALIMLNKPAGYECSQK-PSAWPSVYTLLPLPLRQRPAQGKKGATAG 119

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVD----QDKLNLLKK 163
           V +VGRLD +T GLLLLT+DG L   L  P  +  +VY V     V        +  L  
Sbjct: 120 VQAVGRLDQDTTGLLLLTDDGQLIHKLASPRHKVSKVYEVGLKHPVPSPAEASFVQRLLD 179

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G+V+    +       +     +  + + L +GK  ++K++      +V  L R   G  
Sbjct: 180 GVVLDDDPHPVRAAACELLTPQH--LRLTLTDGKYHQVKRMVAAVGNRVETLHRSRIGAL 237

Query: 224 QL-GTLLAGSTREVSKKILREQLG 246
           QL   L  G  R +     R  LG
Sbjct: 238 QLPDDLAPGQWRWLEVAD-RALLG 260


>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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRE 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 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|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 =  193 bits (492), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 49  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 106

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 107 QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKSAKVRLISEPNLWERNP 166

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 167 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFRLL 226

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 227 SLDEIKALF 235


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 53/183 (28%), Positives = 90/183 (49%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +         V L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGRTLPAGVELVDEPTWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 54/188 (28%), Positives = 91/188 (48%), Gaps = 16/188 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +    + V   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDCEGRATLKDFID--IAGVYPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
           GL   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  GLQARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVELNDGPTLPAEARRLEEPELWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLEQGCWR 204

Query: 235 EVSKKILR 242
           EV  K+ R
Sbjct: 205 EVPAKLKR 212


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 49/178 (27%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD L  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE ++
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREATE 177


>gi|317011592|gb|ADU85339.1| hypothetical protein HPSA_06915 [Helicobacter pylori SouthAfrica7]
          Length = 254

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 121/247 (48%), Gaps = 19/247 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   +     VGRLD  +EG+LLL++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKNDPLKRRVIYESLEKKYVHFAPVGRLDFASEGVLLLSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    R Y ++  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEREYLIKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFVGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +       + + V + EGKNRE+++ F FFN  V  L R+ YG   L  L  G  R ++
Sbjct: 178 EILKNHAKYSKLKVIINEGKNRELRRFFAFFNAGVLDLRRVRYGFVNLNALPVGKMRFLN 237

Query: 238 KKILREQ 244
           ++   E 
Sbjct: 238 RQEYNEL 244


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 52/189 (27%), Positives = 90/189 (47%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
               + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L
Sbjct: 26  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVL 83

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN+G L   L  P  +  ++Y V+  G   QD L  L+ G+ +         V L     
Sbjct: 84  TNNGALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGSTLPAGVELVDEPA 143

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 144 WLWPRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLA 203

Query: 230 AGSTREVSK 238
            G  RE + 
Sbjct: 204 NGEWREATD 212


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 53/182 (29%), Positives = 91/182 (50%), Gaps = 17/182 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L +KP  ++   +D  GR+T+   +P  F+ V + GRLD ++EGLL+LTNDG L 
Sbjct: 28  PRRIVLLNKPFDVLPQFTDEAGRATLKGLVP--FNDVYAAGRLDRDSEGLLVLTNDGKLQ 85

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L  P  +  +VY V+  G+ D++ L  L++G++++                       
Sbjct: 86  ARLTQPGQKTAKVYYVQVEGEPDEEALRHLRQGVILKDGPTLPADAEKVEQPEWLWPRNP 145

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +     W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +E+
Sbjct: 146 PIRERKSIPTHWLKMTLYEGRNRQVRRMTAHIGFPTLRLIRFSMGNLTLGNLQPGEWKEI 205

Query: 237 SK 238
           S 
Sbjct: 206 SD 207


>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 =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 87/183 (47%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 39  KEVKDPIIVLFNKPFDVLCQFTDEQGRKTLKDFIP--IQEVYAAGRLDRDSEGLLLLTND 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 REV 236
           R++
Sbjct: 217 RKL 219


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 48/185 (25%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDGEGRATLKDFID--VPGIYPAGRLDRDSEGLLLLTNDG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 86  QLQARIADPKHKLAKTYWVQVEGEPSAEQLQRLRDGVELNDGMTLPAEARSLDEPQLWPR 145

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +WV + +REG+NR+++++         RL+R+  G + +  L  G  +
Sbjct: 146 NPPVRFRKSVPTSWVELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWK 205

Query: 235 EVSKK 239
           EV  +
Sbjct: 206 EVPAR 210


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T + L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTHVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 49/184 (26%), Positives = 92/184 (50%), Gaps = 17/184 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GRST+ D +P     + + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRSTLKDFIP--VPGIYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L+ L+ G+ +         + +        
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGEPTAEALDALRNGVTLNDGPTLPAGIEVVEEPVWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 142 PRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLENLANGE 201

Query: 233 TREV 236
            RE+
Sbjct: 202 WREL 205


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 204

Query: 236 VSK 238
           V+ 
Sbjct: 205 VTD 207


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 51/186 (27%), Positives = 90/186 (48%), Gaps = 17/186 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            + + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+
Sbjct: 24  HENQPTRVILFNKPYDVLPQFTDETGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNN 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G   QD L  L+ G+ +           L        
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 142 PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGE 201

Query: 233 TREVSK 238
            RE ++
Sbjct: 202 WREATE 207


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 105/240 (43%), Gaps = 13/240 (5%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDG 128
                 HKP G   +  D      ++D LP  F     V    GRLD  T GLLLLT+DG
Sbjct: 59  LS-IALHKPAGYTCSTKDTG--RLIYDLLPPRFRDRDPVLSTVGRLDRETSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
           GL   +  P ++  +VY V     +  D++ L   G ++++      +   L+      A
Sbjct: 116 GLLHRIISPKSKLPKVYEVELSDDLRGDEVALFASGTLMLESEKTPLLPAELEVLDARRA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L EG+  +++++F      V  L R   G   L  L  G  R+++   L     P
Sbjct: 176 --RLVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTSTDLDTLFAP 233


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 46/181 (25%), Positives = 86/181 (47%), Gaps = 16/181 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ L++KP  ++   +D  GR T+ D +      + + GRLD ++EGLL+LTNDG L 
Sbjct: 42  EQKIVLFNKPFDVLCQFTDEAGRQTLADFID--IKDIYAAGRLDRDSEGLLVLTNDGQLQ 99

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y V+  G    + +  L +G+ ++       QV L            
Sbjct: 100 NKLASPKHKTSKTYWVQVEGIPSAEAIKSLCQGVELKDGPTLPAQVELMHAPDIWPRNPP 159

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+++ L EG+NR+++++         RLIR   G + +  +  G  + V+
Sbjct: 160 IRERKNIPTSWLSITLTEGRNRQVRRMTAHIGHPTLRLIRYRIGHWTIDGIENGQFKSVA 219

Query: 238 K 238
           K
Sbjct: 220 K 220


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPEWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 95/189 (50%), Gaps = 16/189 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G L
Sbjct: 47  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNGEL 104

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L           
Sbjct: 105 QHRLADPKFKTEKTYWVQVEGIPEETDLAQLRKGVELKDGVTKSAKVRLISEPNLWERNP 164

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + + EG+NR+++++     +   RL+R+S G   +  L  GS R +
Sbjct: 165 PIRERKNIPTSWLEIKISEGRNRQVRRMTAHIGFPTLRLVRVSMGLLSINGLENGSFRLL 224

Query: 237 SKKILREQL 245
           S   ++   
Sbjct: 225 SLDEIKALF 233


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 51/178 (28%), Positives = 87/178 (48%), Gaps = 17/178 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           TR+ L +KP  ++   +D DGR+T+ D +P     V + GRLD ++EGL++LT+DG L  
Sbjct: 7   TRVILLNKPYDVLCQFTDADGRATLKDFVP--VPGVYAAGRLDRDSEGLVVLTDDGALTA 64

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            +  P  +  + Y  +  G  +   L  L++G+V+        +V               
Sbjct: 65  RIADPRHKMAKTYWAQVEGIPEDAALEALRRGVVLNDGPTLPAEVRAIPEPPGLWPRTPP 124

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               +    AW+ + LREG+NR+++++         RL+R + GP+ L  L  G  RE
Sbjct: 125 VRFRKSIPTAWLELTLREGRNRQVRRMTAAVGLPTLRLVRRAVGPWTLEGLAPGEWRE 182


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 47/176 (26%), Positives = 85/176 (48%), Gaps = 16/176 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLLLLTNDG L  
Sbjct: 89  PIIVLFNKPFDVLCQFTDEQGRKTLKDYIP--IADVYAAGRLDRDSEGLLLLTNDGQLQA 146

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G   +D L  L++G+ +        +V +             
Sbjct: 147 RLTEPKKKTFKTYWVQVEGVPTEDALTKLRQGVELNDGMTLPAKVKIMDSPDIWPRNPPV 206

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + +     W+ + + EG+NR+++++     +   RLIR   G + +  L +G  +
Sbjct: 207 RERKNIPTTWLEIQIHEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSIDNLPSGEHK 262


>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 =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>gi|320184392|gb|EFW59203.1| 23S rRNA pseudouridine synthase E [Shigella flexneri CDC 796-83]
          Length = 207

 Score =  193 bits (491), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>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 =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +         V L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD +  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 214

Query: 236 VSK 238
            ++
Sbjct: 215 ATE 217


>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 =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 48/178 (26%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD +  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE ++
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWREATE 177


>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 =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 53/185 (28%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                RL L++KP  ++T  SD +GR+T+ D +      V   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPRLILFNKPFDVLTQFSDGEGRATLKDFID--IPGVYPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
           GL   +  P  +  + Y V+  G+   ++L  L+ G+ +        +            
Sbjct: 85  GLQARIADPKHKLAKTYWVQVEGEPSDEQLQRLRDGVALNDGPTLPAEARRLEEPELWPR 144

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +    +W+ + +REG+NR+++++         RL+R+  G + L  L  G  R
Sbjct: 145 NPPVRFRKSVPTSWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWALDGLGQGCWR 204

Query: 235 EVSKK 239
           EV  K
Sbjct: 205 EVPAK 209


>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 =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRE 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 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 =  193 bits (490), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 50/184 (27%), Positives = 89/184 (48%), Gaps = 17/184 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     + + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRKTLKDFIP--VPGIYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V +        
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGEPTPEALEALRTGVALNDGPTLPAGVEVVEEPAWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  193 bits (490), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +         V L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  193 bits (490), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 83/178 (46%), Gaps = 16/178 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+  + L++KP  ++   +D + R T+ D +      + + GRLD ++EGLLLLTNDG L
Sbjct: 23  EKQIVVLFNKPFDVLCQFTDENNRRTLKDFI--TIPGIYAAGRLDRDSEGLLLLTNDGKL 80

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              +  P  +  + Y V+  G   +  L  L++G+ ++       +V +           
Sbjct: 81  QHQIANPVKKTEKTYWVQIEGAPSEQDLAKLRQGVELKDGMTKPAKVAIMLEPNVWPRNP 140

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +       W+ + + EG+NR+++++     +   RLIR   G + L  +  G  +
Sbjct: 141 PIRERASIPTTWLEITITEGRNRQVRRMTANIGFPTLRLIRYRIGNWTLDNINNGEYK 198


>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 =  193 bits (490), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 52/183 (28%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD +TEGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDTEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>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 =  193 bits (490), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDCDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 116 GVLQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  193 bits (490), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
            ++
Sbjct: 215 ATE 217


>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 =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 73/269 (27%), Positives = 120/269 (44%), Gaps = 27/269 (10%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE------------RTRL 75
           RRE +  ++  RV VNG L+   +  V+  D + +DG  +                R   
Sbjct: 106 RREADDAVSAGRVLVNGELVR-PSRRVVHGDVVTLDGKAMDWEPYAQSVESELGDARFVY 164

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
             Y+KP G+V T SD + R+++F  L           R+  VGRLD ++ GL+LLTNDG 
Sbjct: 165 LKYNKPRGVVCTMSDTE-RTSMFHALHHERKALGKDVRLFPVGRLDKDSSGLVLLTNDGR 223

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------DTQK 183
           ++  L  P  +  + Y V     V +     L +G+VI      D++ T+      +  K
Sbjct: 224 VSDALLDPERKAEKTYDVDVDRIVSEADARTLARGVVISTTQQRDLKETVAATLPCEVTK 283

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
                +   L+EG+NR+I+K+ E  ++ V RL R       LG L  G    + +  +  
Sbjct: 284 TGEKSLRFVLKEGRNRQIRKMCEVLSYDVERLHRTRIDDVALGDLEVGGVAPLDEDEVNA 343

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
            L   +   A    ++  ++SE+  R R 
Sbjct: 344 -LSARVDARASTPRESSKHTSESRRRRRA 371


>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 =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQLKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  192 bits (489), Expect = 6e-47,   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  KPKVAPKDRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--IKNVYAAGRLDRDSEGLMVL 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|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 =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 49/186 (26%), Positives = 91/186 (48%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                  R+++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+L
Sbjct: 8   KRKAPIRRSKIVLFNKPFNVLTQFTDATGRQTLKDFIP--IPDIYAAGRLDKDSEGLLVL 65

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TNDG L   L  P  +  + Y V+  G+  + +L  L+ G+ ++       +V       
Sbjct: 66  TNDGKLQHKLTDPKKKTSKTYWVQVEGEPQEYQLQALRDGVALKDGMTRPAKVERMQEPS 125

Query: 181 ----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                      Q    +W+ + + EGKNR+++++     +   RL+R   G + L  + +
Sbjct: 126 LWARNPPVRFRQSIPTSWLAITISEGKNRQVRRMTAHIGFPTLRLVRYRVGNWTLDGIAS 185

Query: 231 GSTREV 236
           G+ RE+
Sbjct: 186 GTYREL 191


>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 =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 53/233 (22%), Positives = 101/233 (43%), Gaps = 15/233 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM----STDHIEVDGVPLRKA 70
           R+ +++   G  SR E+ ++   +R+ ++G  +   A  +      T+ + V G PL   
Sbjct: 8   RIDRLLGSLGYGSRGEIAQIARARRIVLDGARVANVAKRIPMSPDLTERMTVHGAPLDPL 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINTEGLLLLTN 126
               + + +KP G + +  D      V+D LP  +      +  VGRLD  T GLLLLT+
Sbjct: 68  LGMVVMM-NKPAGYICSRKDSG--PLVYDLLPDRWRHRKPMLSPVGRLDKETSGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
            G L   +  P+    + YR      ++  ++N+   G +++ G         L     +
Sbjct: 125 HGDLLHRITSPNLAVEKTYRASLARPLEGHEVNVFASGELMLSGEKKPLHPAKLSVLSPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVS 237
            A + +   EG+  +++++F      V  L R + G   L   L A +   ++
Sbjct: 185 EARLNIT--EGRYHQVRRMFAAVGNHVEALHREALGDLTLPDNLQAAAWCLLN 235


>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 =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 49/178 (27%), Positives = 85/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD L  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE ++
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREATE 177


>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 =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 96/236 (40%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVAGAAATDPDAPFDTAGLVFSVDDTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G       V  D +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLAPGAWRWLDEADLAALRNP 234


>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 =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 57/233 (24%), Positives = 110/233 (47%), Gaps = 4/233 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K +A +G+ SRRE +  IA   V VNG ++      V  TD +  DG  +  
Sbjct: 44  NPDEIRLNKYVANSGMCSRREADENIAIGLVSVNGKVVTEMGYKVKRTDEVRFDGQRIT- 102

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
            E     L +KP G  TT ++  GR TV D + +   + V  +GRL  N+ GLLL TND 
Sbjct: 103 PEAKVYVLLNKPKGFATTTAEGKGR-TVMDLVANATNANVKPIGRLGRNSLGLLLFTNDD 161

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            + +          R+++V     +  + L  +K+G  ++G       ++    +  N  
Sbjct: 162 KIVQKFTNSKNGVARLFQVELDKNLKYEDLKKIKEGFKVEGKLITVEDISYIEGESKNK- 220

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + + ++   N  ++ +F+ FN+ + ++  ++ G      +  G  + ++++ +
Sbjct: 221 IGLKIKNTGNTILRTIFDNFNYDIVKIDCVAIGHLTKKDIPRGHWKHLTEQEV 273


>gi|332342737|gb|AEE56071.1| ribosomal pseudouridine synthase, large subunit [Escherichia coli
           UMNK88]
          Length = 207

 Score =  192 bits (489), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD +  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>gi|218192109|gb|EEC74536.1| hypothetical protein OsI_10056 [Oryza sativa Indica Group]
          Length = 279

 Score =  192 bits (489), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 63/234 (26%), Positives = 109/234 (46%), Gaps = 14/234 (5%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA-ERTRLWLYHKPIGLVT 86
           R  E +I Q +V VNG +       V  S D I V+G  + K       +  +KP G + 
Sbjct: 46  RTCEELIFQGKVTVNGSVCTAPQTKVDISKDSIYVNGNRISKKLPPKLYFAVNKPKGYIC 105

Query: 87  THSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP 137
           +  +     ++FD+    ++++           VGRLD+ T GL+++TNDG  A+ L  P
Sbjct: 106 SCGERKSIISLFDDYLKGWNKIQPGVPKPRLFTVGRLDVATSGLIIITNDGEFAQKLSHP 165

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-GDMQVTLDTQKG-SNAWVTVGLRE 195
           S+  ++ Y V   G V ++ L  + +G  I G+    D+   LD Q       + + + 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|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 =  192 bits (489), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 54/191 (28%), Positives = 97/191 (50%), Gaps = 16/191 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           RK   T+L L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTND
Sbjct: 16  RKPAVTQLVLFNKPFDVLCQFTDEAGRQTLKDFIP--LPGVYAAGRLDRDSEGLLLLTND 73

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------- 178
           G L   L  P  Q  + Y V+  G  D+  L+ L++G+ ++       +V          
Sbjct: 74  GQLQSRLTEPKKQTYKTYWVQVEGIPDESALDKLREGVELKDGPTLPARVRRIDAPQIWP 133

Query: 179 -----LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +   + W+ + + EG+NR+++++     +   RL+R + G  +LG L +G  
Sbjct: 134 RNPPVRERKSIPDCWLEIQICEGRNRQVRRMTAHIGYPTLRLVRAAIGEIRLGHLGSGEY 193

Query: 234 REVSKKILREQ 244
           R++++  +   
Sbjct: 194 RKLNRDEISSL 204


>gi|152978114|ref|YP_001343743.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150839837|gb|ABR73808.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 243

 Score =  192 bits (489), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 50/188 (26%), Positives = 94/188 (50%), Gaps = 16/188 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T++ L++KP  ++T  +D  GR T+ D +P     + + GRLD ++EGLL+LTN+G L 
Sbjct: 52  QTQVVLFNKPFDVLTQFTDESGRKTLKDFIP--VPGIYAAGRLDRDSEGLLILTNNGELQ 109

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L  P  +  + Y V+  GQ  +  L  L++G+ ++       +V              
Sbjct: 110 HRLANPKFKLPKTYWVQVEGQPTEADLERLRRGVELKDGMTKPAKVRSIAEPDLWQRVPP 169

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    AW+ + L EGKNR+++++     +   RL+R +     L  L +G  RE++
Sbjct: 170 IRERKNIPTAWLEIQLGEGKNRQVRRMTAHIGFPTLRLVRAATAGLTLHGLPSGQYRELT 229

Query: 238 KKILREQL 245
           +  ++   
Sbjct: 230 ESEIKRLF 237


>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 =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 90/185 (48%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           K     + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG
Sbjct: 47  KTVEPVIVLFNKPFDVLCQFTDEQGRQTLKDFIP--IPGVYAAGRLDRDSEGLLLLTNDG 104

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P  +  + Y  +  G  D+ +L+LL+KG+ ++       ++++         
Sbjct: 105 KLQSKLTEPKKKTFKTYWAQVEGAPDEAQLDLLRKGVELKDGMTLPAKISIMSQPTVWER 164

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +     W+ + + EG+NR+++++     +   RLIR   G + L  L  G  +
Sbjct: 165 VPPIRERKAIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDLSPGQYQ 224

Query: 235 EVSKK 239
            +  K
Sbjct: 225 SIDMK 229


>gi|224008973|ref|XP_002293445.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
 gi|220970845|gb|EED89181.1| pseudouridylate synthase [Thalassiosira pseudonana CCMP1335]
          Length = 253

 Score =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 114/251 (45%), Gaps = 22/251 (8%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +KN+    F P R++KV  +    SRR+ ++++A  R+ +N   +  A   V +    
Sbjct: 3   VSNKNVT---FQPIRINKVFKKTH--SRRQADQLVADGRITINDEPVHSAGQRVSNG--- 54

Query: 61  EVDGVPLRKAERT-RLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFSRVISVGRLD 115
              G     + +      Y KP+G+  T +D      + D L        SR+  VGRLD
Sbjct: 55  ---GANSESSTQVFEYIKYWKPLGVTCT-TDRRIYDNLIDALQQDGCRPKSRIFPVGRLD 110

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
             T G++L+T+DG L         +  + Y V+ +  V  D +  L++G+ +        
Sbjct: 111 KETSGIILMTSDGRLPNAALRGKYKHPKTYVVKANRPVANDDIKRLREGVPLT-APTLPC 169

Query: 176 QVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AG 231
           +V    L T   S+ ++ + L EG+NR+I+K+ E   ++V  L R S+    L  L   G
Sbjct: 170 KVKAVQLSTLDLSSRYLEITLVEGRNRQIRKMLEAIGYRVMELHRKSFMNLTLENLEGEG 229

Query: 232 STREVSKKILR 242
               ++ + + 
Sbjct: 230 DWAHLTNREME 240


>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 =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 73/233 (31%), Positives = 106/233 (45%), Gaps = 20/233 (8%)

Query: 30  EVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTH 88
           E  R+I + R+ +NG  +++   VNV   D I V+G PL    R    L HKP G V + 
Sbjct: 8   EAGRLIERGRISINGRPIVQNRWVNVH-KDSILVNGTPLEATCRL-TLLMHKPAGYVVSR 65

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
            DP  R TVF  LP     + + GRLD +T GLLLLTND  L   L  P  +  +VYRV 
Sbjct: 66  DDPLNRDTVFQLLPDPSVYIGASGRLDKDTTGLLLLTNDTYLQSSLVDPVYKVPKVYRVV 125

Query: 149 FHG-QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------------AWVTVGLR 194
             G  ++  +L  L+ G+ ++        V      G                 + + L 
Sbjct: 126 VKGAALNGAQLMALRSGVSLEDGPTLPALVEPLDVNGDPLPLEMSEYDRYKCKQLNITLW 185

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQL---GTLLAGSTREVSKKILREQ 244
           EG+NR+++++ E     V  L RI  GPF L   G    G  R+++   +   
Sbjct: 186 EGRNRQVRRMVEAVGSTVRDLCRIQLGPFSLHAAGVPNPGDVRQLTIDEVETL 238


>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 =  192 bits (488), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 98/224 (43%), Gaps = 8/224 (3%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           V+ +  + + +  + +I    ++VN  ++      V + D I    + L  A+    ++ 
Sbjct: 12  VLMKNKLGNHKICKTLIRHGEIRVNDQVITDVRYPVKADDIIMYHHIQLN-AQPFVYYMM 70

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP   +  + D      V D +         +GRLDI+T GLL++TND  L++ L LP 
Sbjct: 71  NKPADYLCANHD-KYHQCVIDLI--GREDCYCLGRLDIDTTGLLIITNDTSLSKKLLLPQ 127

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
               + Y V     +  + +     G+VI       +   L+     +    V + EG+ 
Sbjct: 128 NHVNKKYYVTTKFPLKDELIKKFFDGVVID-HKVQCLPSLLEILDEYHCL--VTINEGRY 184

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            +IKK+F+    +V  L RI++   +L   L  G  R+++   L
Sbjct: 185 HQIKKMFKSCQNEVCTLKRIAFAGIELDQKLALGEYRDLTSTEL 228


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 88/174 (50%), Gaps = 16/174 (9%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG L   L  
Sbjct: 1   MFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLTNDGILQAKLTQ 58

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-------------- 182
           P ++  + Y V+  G   +  L+ L+KG+ ++       +V +  +              
Sbjct: 59  PKSKSPKTYWVQVDGAPSESDLDKLRKGVELKDGMTLPAKVEVMAEPNVWERTPPVRFRA 118

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                W+ + + EG+NR+++++     +   RLIR S G  +LG L  G  +E+
Sbjct: 119 NIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIKLGELQPGEWKEI 172


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 95/233 (40%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVAGAAATDPDATFDTDGLVFSVDDTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G       V  D +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L   
Sbjct: 179 VLEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLAPGAWRWLDEADLAAL 231


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 70/258 (27%), Positives = 121/258 (46%), Gaps = 26/258 (10%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEV---D 63
             N +  R++KV+A  G+ASRR  E +I++ RV+VNG ++      +  T D +E+    
Sbjct: 70  ATNESRPRLAKVLAACGVASRRACEELISEGRVRVNGRVVSEQGTTIDPTTDRVELLVKY 129

Query: 64  GVPLRKAERTR--LWLYHKP-IGLVTTHSDPDGRSTVFDNLPSIF--------------- 105
            V L +  R R    +Y +P  G + + SD  GR  +   L + +               
Sbjct: 130 SVNLHRGHRVRRHNLIYPEPDKGYICSSSDVSGRGKLAVQLLNPWLEQWRRNSKDTKRLP 189

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            R  +VGRLD+ + GL+ +TNDG  A  +  PS+   + Y V       + +L  L  G 
Sbjct: 190 PRFFTVGRLDVASSGLIFITNDGHWANRVIHPSSGLTKEYVVGLGRDASRPQLQALAAGT 249

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + G     ++V +    G +  + + ++EGK  E++++ +    ++  L R+  G F+L
Sbjct: 250 EVAGTFVSPVEVEVL---GDSRRLRIVVQEGKKHEVRELVKAAGLELTSLKRVRIGGFRL 306

Query: 226 G-TLLAGSTREVSKKILR 242
              L  G  RE+    LR
Sbjct: 307 PRDLGIGGFRELKPSDLR 324


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 61/228 (26%), Positives = 107/228 (46%), Gaps = 9/228 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   ++R G  SR E  R+I    V +NG+L    +  V  TD + VDG PL      
Sbjct: 1   MRLDAFVSRFGRFSRSESRRIIRSNGVSLNGVLTNNPSEVVDETDTVIVDGRPLEAFWN- 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR 132
                +KP G V +    +GR +VF+ + + FS  + + GRLD +  GLL+L+NDG    
Sbjct: 60  VYIALNKPEGYVCSRERSEGR-SVFELIDANFSADLSTGGRLDKDATGLLILSNDGKFIH 118

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            +  P     + Y V    ++ + +++++ +G+ I          V    ++  +  + +
Sbjct: 119 EVISPRKLVEKEYLVETAKEITKKEISMISQGLFIGNNEFSKPTHV----EQIDHFHMRI 174

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSK 238
            L EG+  E+K++      KV +L R   G + L   L  G  + +S+
Sbjct: 175 VLTEGRYHEVKRLVSASGNKVIQLHRRRIGSYCLSEELRPGDWQLLSE 222


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 51/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 204

Query: 236 VSK 238
            ++
Sbjct: 205 ATE 207


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 87/180 (48%), Gaps = 16/180 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG L 
Sbjct: 54  ERKIIIFNKPYDTLSQFTDGEGRKTLADFIP--VKEVYAAGRLDRDSEGLMVLTNDGILQ 111

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             L  P ++  + Y V+  G   + +L  L+ G+ ++       QV +            
Sbjct: 112 AKLTQPKSKSPKTYWVQVEGAPTEAQLEPLRSGVELKDGLTLPAQVEIIQDPQLWERNPP 171

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + + EG+NR+++++     +   RL+R S G   L  L  G  +E+S
Sbjct: 172 VRFRAAIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGMTLQDLQPGEWKEIS 231


>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 =  192 bits (488), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 85/184 (46%), Gaps = 16/184 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P       ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 36  KPQIAQSDKKVILFNKPYDVLCQFTDEQNRQTLANFIP--IKDVYAAGRLDRDSEGLLLL 93

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN G L   L  P  +  + Y V+  G   +  ++ L +G+ ++       QV L     
Sbjct: 94  TNCGKLQNTLTAPGKKTNKTYWVQVEGVPTEASIDALSQGVELKDGLTLPAQVKLIDEPA 153

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+++ + EGKNR+++++         RLIR S G + L  +  
Sbjct: 154 LWPRTPPVRERKSIPTSWLSITINEGKNRQVRRMTAHIGHPTLRLIRYSIGKYTLDGIET 213

Query: 231 GSTR 234
           G  +
Sbjct: 214 GQYK 217


>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 =  192 bits (488), Expect = 8e-47,   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  IKNKPKVAPEDRKVVVFNKPFDTLSQFTDGDGRKTLADYI--TVKDVYAAGRLDRDSEGL 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|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 =  192 bits (488), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 52/179 (29%), Positives = 94/179 (52%), Gaps = 17/179 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++  + L++KP  ++T  +D +GR T+ D +      V + GRLD ++EGLLLLT+DG L
Sbjct: 5   KKIMIILFNKPYDVLTKFTDGEGRKTLKDYIK--IPNVYAAGRLDKDSEGLLLLTDDGKL 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
             +L  P ++  + Y V+  G+   +    L+KG++++       +V L           
Sbjct: 63  NHLLTDPKSKSYKTYLVQVEGEFSPEAAQKLQKGLLLKDGKTLPAKVKLIDEPDWLWERT 122

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 123 PPIRERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYSLGNLKSGEYK 181


>gi|324113926|gb|EGC07900.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 217

 Score =  192 bits (488), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   +D L  L+ G+ +                       
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + + EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITIYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  191 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRD 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 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 =  191 bits (487), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 88/180 (48%), Gaps = 16/180 (8%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ +++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++LTNDG L 
Sbjct: 54  ERKIIIFNKPYDTLSQFTDGEGRKTLADFIP--VKEVYAAGRLDRDSEGLMVLTNDGILQ 111

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             L  P ++  + Y V+  G   + +L  L++G+ ++       QV +            
Sbjct: 112 AKLTQPKSKSPKTYWVQVEGAPTEAQLEPLRRGVELKDGLTLPAQVEIIQDPQLWERNPP 171

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                     W+ + + EG+NR+++++     +   RL+R S G   L  L  G  +E+S
Sbjct: 172 VRFRAAIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGGMTLQDLQPGEWKEIS 231


>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 =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 54/200 (27%), Positives = 85/200 (42%), Gaps = 29/200 (14%)

Query: 69  KAERTRLWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +     L++KP  ++   +D     + R T+ D +      V SVGRLD ++EGLL L
Sbjct: 2   AKKNRHYLLFNKPYNVLCQFTDNSNLENPRPTLKDYIK--VPDVYSVGRLDKDSEGLLFL 59

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           TN+  L   L        R Y V+     DQ  LN L++G+ I+       +V L     
Sbjct: 60  TNNAQLKHRLSHRQFAHPRTYLVQVERIPDQVALNQLRQGVRIKDYKTRPAKVKLLDSPP 119

Query: 181 -----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-------- 221
                       +    AW+ + L EG+NR+++++     +   RLIRI+ G        
Sbjct: 120 SVPPRDPPIRYRKTVPTAWLEMTLTEGRNRQVRRMTAAVGYPTLRLIRIAIGVQRKGKII 179

Query: 222 PFQLGTLLAGSTREVSKKIL 241
              L  L  G  RE++   L
Sbjct: 180 NLTLEGLKPGQWRELTPSEL 199


>gi|242239490|ref|YP_002987671.1| pseudouridine synthase [Dickeya dadantii Ech703]
 gi|242131547|gb|ACS85849.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 208

 Score =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 86/187 (45%), Gaps = 17/187 (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 AGSTREV 236
            G  +E+
Sbjct: 199 PGEWKEI 205


>gi|323187623|gb|EFZ72930.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           RN587/1]
          Length = 177

 Score =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 49/178 (27%), Positives = 84/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD L  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE + 
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREATD 177


>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 =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 89/189 (47%), Gaps = 16/189 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L++KP   +   +  +G ST+ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   KLVLFNKPFNTLCQFTGENGDSTLADYID--IPEVYPAGRLDKDSEGLLLLTDDGQLQNQ 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           +  P  +  + Y V+  G  + ++L  L+ G++IQ       +V L              
Sbjct: 61  IASPKHKMEKTYWVQVEGVPEDNELEPLRLGVIIQNYKTKPAKVRLLETPEVWPRNPPIR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +    +W+ + + EGKNR+++++     +   RLIR   G +QL  L  G  + +   
Sbjct: 121 ERKNIPTSWLEITISEGKNRQVRRMTAAVGFPTLRLIRAQIGQWQLDDLKVGEYKVIEVS 180

Query: 240 ILREQLGPH 248
             +   GP 
Sbjct: 181 TPKAMAGPR 189


>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 =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--IQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   +D L  L+ G+ +                       
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRD 214

Query: 236 VSK 238
           V+ 
Sbjct: 215 VTD 217


>gi|160901833|ref|YP_001567414.1| pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359477|gb|ABX31091.1| pseudouridine synthase [Petrotoga mobilis SJ95]
          Length = 220

 Score =  191 bits (487), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 67/215 (31%), Positives = 112/215 (52%), Gaps = 10/215 (4%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVP------LRKAERTRLWLYHKPIGLVTTHSDPDGR 94
           KVNG L++     +   + IE +          +KAE    +L +KP G++ T  D  GR
Sbjct: 2   KVNGKLVKEPWYELKENNFIEFNNKKYGLSDLQKKAENKVYYLLNKPKGILCTFKDDFGR 61

Query: 95  STVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            T+ D +      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|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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 49/186 (26%), Positives = 93/186 (50%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ L++KP   ++  +D +GR T+ D +P     V + GRLD ++EGL++L
Sbjct: 59  KPKVALEDRKVILFNKPFDTLSQFTDGEGRKTLADFIP--VKDVYAAGRLDRDSEGLMVL 116

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG     L  P+++  + Y V+  G   ++ L+ L+KG+ ++       Q+ + ++  
Sbjct: 117 TNDGIFQAKLTQPNSKSPKTYWVQVEGAPSEEDLDKLRKGVELKDGMTLPAQIEVMSEPV 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMNVGQLQP 236

Query: 231 GSTREV 236
           G  +E+
Sbjct: 237 GEWKEI 242


>gi|309792033|ref|ZP_07686509.1| pseudouridine synthase [Oscillochloris trichoides DG6]
 gi|308225926|gb|EFO79678.1| pseudouridine synthase [Oscillochloris trichoides DG6]
          Length = 637

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 83/298 (27%), Positives = 126/298 (42%), Gaps = 4/298 (1%)

Query: 56  STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
             D IEVDG P+RK       + +KP+G V+T  DP GR TV D +  + +RV  VGRLD
Sbjct: 4   DADVIEVDGQPVRKPTTRTYLVLNKPVGFVSTVDDPQGRPTVVDLV-DVPARVYPVGRLD 62

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           +++EGLLLLT+DG L   L  P  +  + YR      +D + L   ++G+++ G      
Sbjct: 63  VDSEGLLLLTDDGELTHQLTHPRFEIEKEYRALLDRPLDTEALRQWREGVLLNGEPTAPA 122

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            V L        W  V LREG+ R+I++V     ++V RLIR+  G   LG L   + R 
Sbjct: 123 WVDLLETTAEGPWFRVVLREGRKRQIREVARLLGYEVLRLIRVREGDLLLGDLPLRAWRP 182

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI-ISEVPDDFTRMKKNSSQKNG 294
           +++  +   L  H+    +      +         R      E   D +  ++      G
Sbjct: 183 LTEDEVAA-LRAHVAVRRESGERMDVGGKRQAAAGRGEPRREESRRDDSSPRREDGPPRG 241

Query: 295 LSKQKKLATPVHRRNLASNVWMAKGIHSSFLS-DSGQREENHRRSPSFPSKRSLRRTS 351
             + ++   P   R               F   D   R     R    P +R   R S
Sbjct: 242 RGEFRREDGPPRGRGEFRREDGPPRGRGEFRREDGPPRGRGEFRREDGPPRRDEGRGS 299


>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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 47/178 (26%), Positives = 86/178 (48%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +++KP  ++   +D  GR+T+   +P   + + + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   VIFNKPFDVLPQFTDEQGRTTLKQYIP--LTGIYAAGRLDRDSEGLLVLTNDGQLQAQLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  +VY V+  G+  +  L   ++G+ ++       Q                  +
Sbjct: 60  QPGKRTGKVYYVQVEGEPTEHDLARFRQGLTLKDGPTLPAQAERVAEPEWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR S G   L  L +G  RE+  
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMGSITLEDLASGCWREIDW 177


>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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 59/233 (25%), Positives = 95/233 (40%), Gaps = 8/233 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVAGAAATDPDAPFDTAGLVFSVDDTAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G       V  D +      + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEPKPIAAVAADAR--DTHALALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L   
Sbjct: 179 VLEGKYHQVKRMVAAASNRVELLHRESIGGFALPADLAPGAWRWLDEADLAAL 231


>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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 92/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             ++     R+ L++KP  ++   +D  GR T+ + +P  F+ V + GRLD ++EGLL+L
Sbjct: 21  KQVKPVGPRRVLLFNKPFDVLPQFTDESGRRTLKEFIP--FNDVYAAGRLDRDSEGLLVL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  ++Y V+  G  + D L+ L+ G+V++          L     
Sbjct: 79  TNDGKLQAKLTQPTAKTGKIYFVQVEGVPEDDALDKLRHGVVLKDGPTLPAGAELVSEPE 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+++++     +   RLIR S G   L  L 
Sbjct: 139 WLWPRVPPIRERKNIPTRWLQITLYEGRNRQVRRMTAHIGFPTLRLIRFSVGNLSLADLQ 198

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 199 PGEWKEI 205


>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 =  191 bits (486), Expect = 1e-46,   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  KPRPAPKDRKVIIFNKPFDVLSQFTDDQHRQTLADFI--SVKDVYAAGRLDRDSEGLLIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +D L+ L++G+ ++       +V +  +  
Sbjct: 79  TNDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLDKLRQGVELKDGMTLPAKVEIIPEPN 138

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 139 VWERNPPVRFRAAIPTTWISITITEGRNRQVRRMTANIGFPTLRLIRYSMGDWTIKDVAH 198

Query: 231 GSTREVS 237
           G+ +EVS
Sbjct: 199 GTWKEVS 205


>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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 104/240 (43%), Gaps = 13/240 (5%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDG 128
                 HKP G   +  D      ++D LP  F     V    GRLD  T GLLLLT+DG
Sbjct: 59  LS-IALHKPAGYTCSTKDTG--RLIYDLLPPRFRDRDPVLSTVGRLDRETSGLLLLTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNA 187
           GL   +  P ++  +VY V     +  D++ L   G ++++      +   L+      A
Sbjct: 116 GLLHRIISPKSKLPKVYEVELSEDLRGDEVALFASGTLMLESEKTPLLPAELEVLDARRA 175

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L EG+  +++++F      V  L R   G   L  L  G  R+++   L     P
Sbjct: 176 --RLVLHEGRYHQVRRMFAATGNHVQALHRSRVGGLDLQGLDEGQWRQLTSTDLDTLFAP 233


>gi|159028310|emb|CAO87208.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 194

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 54/187 (28%), Positives = 87/187 (46%), Gaps = 22/187 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  L++KP  ++   +D +GRST+ D +P     + SVGRLD ++EGLLLLT++G L   
Sbjct: 3   KYILFYKPYDVLCQFTDENGRSTLKDYIP--IPNIYSVGRLDRDSEGLLLLTDNGQLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L        R Y V+     D + L  L++G+ IQ        V +              
Sbjct: 61  LGHRQFAHPRTYWVQVERIPDLNALEKLRQGLAIQDYRTRPAIVNILDFEPDLPPREPPI 120

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY-----GPFQLGTLLAGST 233
              +    AW+ + L EG+NR+++++     +   RLIR +          L  L  G  
Sbjct: 121 RYRKSIPTAWLEITLTEGRNRQVRRMTAAVGYPTLRLIRTAITIDKNNKLCLTGLQPGQW 180

Query: 234 REVSKKI 240
           REV++K 
Sbjct: 181 REVTEKE 187


>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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTNDG L
Sbjct: 37  PPKRVILFNKPYDVLPQFTDEAGRSTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G+   + L  L+ G+ +                       
Sbjct: 95  QASLTQPGKRTGKIYYVQVEGEPTDETLAALRHGVELNDGPTLPAGVERVSEPEWLWPRN 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    AW+ + L EG+NR+++++     +   RLIR + G + L +L  G  R+
Sbjct: 155 PPIRERKSIPTAWLKITLYEGRNRQVRRMTAHVGYPTLRLIRYAMGHYTLDSLANGEWRD 214

Query: 236 VSK 238
            ++
Sbjct: 215 ATE 217


>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 =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 47/185 (25%), Positives = 85/185 (45%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDGEGRATLKDYID--IPGIYPAGRLDRDSEGLLLLTNDG 85

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----- 183
            L   +  P  +  + Y V+  G    ++L  L+ G+ +        +     +      
Sbjct: 86  QLQARIADPRHKLAKTYWVQVEGLPTAEQLQRLRDGVELNDGMTLPARARQLDEPELWPR 145

Query: 184 ---------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                        W+ + +REG+NR+++++         RL+R+  G + +  L  G  +
Sbjct: 146 NPPVRFRATIPTTWLELVIREGRNRQVRRMTAAVGLPTLRLVRVRIGDWTIEGLDQGQWK 205

Query: 235 EVSKK 239
           EV  +
Sbjct: 206 EVPAR 210


>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 =  191 bits (486), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 90/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 58  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 115

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 116 GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 175

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 54/188 (28%), Positives = 85/188 (45%), Gaps = 18/188 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           A   +  ++HKP G+++  + +     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|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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 84/189 (44%), Gaps = 17/189 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
            R  L++KP  +++  +D          L    S   V  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 VSKKILREQ 244
           ++   ++  
Sbjct: 186 LNLSEIQSL 194


>gi|323967074|gb|EGB62500.1| RNA pseudouridylate synthase [Escherichia coli M863]
          Length = 217

 Score =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   QD L  L+ G+ +                       
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 103/236 (43%), Gaps = 9/236 (3%)

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  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGL 130
               HKP G + +  +      ++D LP  F +        GRLD    GL++L+ DG L
Sbjct: 68  -IAVHKPSGYICSTVNDHDHKIIYDILPKEFFKRKPTLSIAGRLDKWVTGLVVLSQDGKL 126

Query: 131 ARVLELP-STQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAW 188
              +  P      + Y V    ++  D+  + + G I+++G         L         
Sbjct: 127 VDRIISPKDDGCGKDYEVVLKDKLVGDEAEVFESGKIMLRGESTPCKPAKLQVLDKEKNK 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           V V L EG+  +I+++F     K   + R   GP +LG L  G  R ++++ L+E 
Sbjct: 187 VKVTLYEGRYHQIRRMFASTENKAVEIHRTRIGPVELGDLGLGKWRHLTEQELKEL 242


>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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   +D L  L+ G+ +                       
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--IQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   Q+ L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQEALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRD 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 51/194 (26%), Positives = 90/194 (46%), Gaps = 16/194 (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 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P ++  + Y V+  G   ++ L  L+KG+ ++        V +    
Sbjct: 82  LTNDGILQARLTQPKSKQPKTYWVQVEGAPSEESLQALRKGVELKDGMTLPAGVEVMSEP 141

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++         RLIR     + +  L 
Sbjct: 142 NIWPRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYKMADWTVDDLE 201

Query: 230 AGSTREVSKKILRE 243
            G  RE++ + L +
Sbjct: 202 PGQWREITLETLPQ 215


>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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 53/186 (28%), Positives = 87/186 (46%), Gaps = 19/186 (10%)

Query: 76  WLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L++KP G+++  +D       T+ + +P     +  VGRLD ++EGLLLL+N GGL   
Sbjct: 6   ILFYKPYGVLSQFTDRQETSHPTLKEFIP--IPDIYPVGRLDRDSEGLLLLSNHGGLQHQ 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L  P     R Y V+     DQ  L  LK+G+ I+       Q +L              
Sbjct: 64  LCNPKFGHPRTYWVQVENIPDQIALQKLKQGVTIRNYRTRPTQASLLSEPPLLPPRTPPV 123

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    AW+T+ L EG+NR+++++     +   RL+R++    QL  L  G  R +S 
Sbjct: 124 RFRKHIPTAWMTMTLYEGRNRQVRRMTAAVGFPTLRLVRVAIAHLQLQDLQPGQWRHLSP 183

Query: 239 KILREQ 244
             + + 
Sbjct: 184 AEIEQL 189


>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 =  191 bits (485), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 63/222 (28%), Positives = 107/222 (48%), Gaps = 11/222 (4%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
           + +++AQ R+ ++G+  E  +  V    H+ +D   + +AE+ R  + +KP G+V+   D
Sbjct: 1   MHQLLAQGRILLDGLAAESISQVVGPFTHVVLD-QRVLQAEQPRYIMLNKPPGMVSATCD 59

Query: 91  PDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRF 149
               STV D + +  ++ +  VGRLD N+ GLLLLTNDG  +R +  P    ++ YRV+ 
Sbjct: 60  EQH-STVLDLVSAPNAKSLHIVGRLDFNSTGLLLLTNDGRWSRGVSSPQKGVVKTYRVQL 118

Query: 150 HGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                 D       G+    + I     ++   +       V     EG+  +IK++F +
Sbjct: 119 EQPFRSDYREAFAAGLYFAFENITTRPAEIRRLSDLSRGRSV-----EGRYHQIKRMFGY 173

Query: 208 FNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPH 248
           FN +V  L R+S G   L   L  G+ RE++   L      H
Sbjct: 174 FNNRVLNLHRLSIGALSLDPKLHQGAWRELTLSELNALGVEH 215


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 52/179 (29%), Positives = 94/179 (52%), Gaps = 17/179 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++  + L++KP  ++T  +D +GR T+ D +      V + GRLD ++EGLLLLT+DG L
Sbjct: 5   KKIMIILFNKPYDVLTKFTDGEGRKTLKDYIK--IPNVYAAGRLDKDSEGLLLLTDDGKL 62

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
             +L  P ++  + Y V+  G+   +    L+KG++++       +V L           
Sbjct: 63  NHLLTDPKSKSYKTYLVQVEGEFSSEAAQKLQKGLLLKDGKTLPAKVKLIDEPDWLWERT 122

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
               + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 123 PPIRERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYSLGNLKSGEYK 181


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 55/187 (29%), Positives = 87/187 (46%), Gaps = 22/187 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  L++KP  ++   +D +GRST+ D +P     + SVGRLD ++EGLLLLT++G L   
Sbjct: 3   KYILFYKPYDVLCQFTDENGRSTLKDYIP--IPNIYSVGRLDRDSEGLLLLTDNGQLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L        R Y V+     D + L  L++G+ IQ        V L              
Sbjct: 61  LGHRQFAHPRTYWVQVERIPDLNALEKLRQGLPIQDYRTRPAIVNLLDFEPDLPPREPPI 120

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY-----GPFQLGTLLAGST 233
              +    AW+ + L EG+NR+++++     +   RLIR +          L  L  G  
Sbjct: 121 RYRKSVPTAWLEITLTEGRNRQVRRMTAAVGYPTLRLIRTAITIDKNNKLCLTGLQPGQW 180

Query: 234 REVSKKI 240
           REV++K 
Sbjct: 181 REVTEKE 187


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 52/225 (23%), Positives = 104/225 (46%), Gaps = 12/225 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+   ++  G  +R + ++ +    + VN   +   +      D I ++G  L     T 
Sbjct: 7   RIDAHLSSLGYCTRGDAKKFLKINELLVNENRVFNPSTKAY-HDDITINGEKLDPE--TL 63

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGL 130
             L +KP G++ +H+D      ++  LP  +     ++ +VGRLD++T G ++LT+DG L
Sbjct: 64  TILLNKPSGVICSHNDAGV--LIYSLLPYRWTQRNPKISTVGRLDVDTTGAIILTDDGTL 121

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P  +  ++Y       +  D+  +   G +++ G     +   L+    S   V
Sbjct: 122 NHKLANPKKEISKIYEAHLKVPLKGDEEKIFASGELLLNGEDKPLLPAKLEV--LSPTCV 179

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + + EGK  ++K++F   + +V +L RIS+  F +  L  G  +
Sbjct: 180 RLEIVEGKYHQVKRMFAAVDNRVVKLHRISFDNFTVEDLKEGEYK 224


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 47/178 (26%), Positives = 83/178 (46%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLD 180
            P  +  ++Y V+  G   +D L  L+ G+ +                           +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE + 
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREATD 177


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 52/190 (27%), Positives = 91/190 (47%), Gaps = 17/190 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              R+ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+L
Sbjct: 31  KRRRENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  ++Y V+  G    + LN L+ G+ +         V L     
Sbjct: 89  TNDGALQARLTQPGKRTGKIYFVQVEGDPTAEALNALRNGVTLNDGPTLPAGVELVAEPD 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+++++     +   RLIR + G + L  L 
Sbjct: 149 WLWPRNPPIRERKTIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYTLDNLA 208

Query: 230 AGSTREVSKK 239
            G  R+++ +
Sbjct: 209 NGEWRDITGE 218


>gi|281178245|dbj|BAI54575.1| conserved hypothetical protein [Escherichia coli SE15]
          Length = 217

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRD 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 60/237 (25%), Positives = 100/237 (42%), Gaps = 15/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           R+ K++A  G  SRREV+ +     + ++G  + +A   +  T  +    +VDG PL   
Sbjct: 6   RLDKLLANMGYGSRREVQALARAGAITLDGAPVPKADTRIALTPDLPARMQVDGRPLDPL 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
                 + HKP G+  +H +      V+  LPS +         VGRLD  T GLLLLT+
Sbjct: 66  PGMA-LMLHKPTGVTCSHKETG--ELVYSLLPSRWRMREPPLSTVGRLDKETSGLLLLTD 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P     + Y       +  D+  +   G ++++G         L+    S
Sbjct: 123 DGDLLHRIISPRRHVAKRYVATLARPLRGDEGAIFAAGELMLEGEDKPLAPAVLE--PLS 180

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
                + + EG+  +++++F      V  L R   G   L   L  G  R +  + L
Sbjct: 181 PTLARLTITEGRYHQVRRMFAAVGNHVEALHRDRIGGLDLPADLAPGRYRLMGAEDL 237


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 103/225 (45%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           RV   +A  G+ SRR  E +I ++ V+VNG + +     V   D I            ++
Sbjct: 8   RVQVFLAEKGVGSRRFCEELIKKKLVRVNGSIAK-LGDKVALGDRITYKKQIYVFTDFQS 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
           +       +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KSKIYLALNKPKNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  +    
Sbjct: 127 FANYIIHPKGKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLREGQVK 227


>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 =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 87/181 (48%), Gaps = 16/181 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG 
Sbjct: 3   PQERQVVIFNKPFDTLSQFTDGDGRKTLADFIP--VKEVYAAGRLDRDSEGLMVLTNDGI 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------ 183
           L   L  P ++  + Y V+  G   +  L+ L+ G+ ++        V +  +       
Sbjct: 61  LQAKLTQPQSKSPKTYWVQVEGAPQEADLDKLRNGVELKDGPTLPAIVEIMPEPEVWERH 120

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                       W+ + + EG+NR+++++     +   RLIR S G   LG L  G  + 
Sbjct: 121 PPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIVLGDLQPGEWKH 180

Query: 236 V 236
           +
Sbjct: 181 I 181


>gi|330910949|gb|EGH39459.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           AA86]
          Length = 207

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--IQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   Q+ L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQEALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRD 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 207


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   QD L  L+ G+ +                       
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGVDLVEEPEWLWPRN 144

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 207


>gi|315179854|gb|ADT86768.1| pseudouridine synthase family 1 protein [Vibrio furnissii NCTC
           11218]
          Length = 183

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 86/181 (47%), Gaps = 16/181 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
               ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG 
Sbjct: 3   PHERQVVIFNKPFDTLSQFTDGDGRKTLADFIP--VKDVYAAGRLDRDSEGLMVLTNDGI 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------ 183
           L   L  P ++  + Y V+  G   +  L+ L+ G+ ++        V +  +       
Sbjct: 61  LQAKLTQPQSKSPKTYWVQVEGAPQEADLDKLRNGVELKDGPTLPAIVEIMPEPEVWERH 120

Query: 184 --------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                       W+ + + EG+NR+++++     +   RLIR S G   LG L  G  + 
Sbjct: 121 PPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDIVLGDLQPGEWKH 180

Query: 236 V 236
           +
Sbjct: 181 I 181


>gi|327253839|gb|EGE65468.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           STEC_7v]
          Length = 207

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   QD L  L+ G+ +                       
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 144

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  RE
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRE 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 207


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 46/185 (24%), Positives = 84/185 (45%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 28  PPAEPKLILFNKPFDVLTQFSDEGGRATLKDFID--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRD 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 92/187 (49%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D + L  L+ G+ +         + +        
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPDNEALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|319794805|ref|YP_004156445.1| pseudouridine synthase [Variovorax paradoxus EPS]
 gi|315597268|gb|ADU38334.1| pseudouridine synthase [Variovorax paradoxus EPS]
          Length = 182

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 83/181 (45%), Gaps = 17/181 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLTNDG 
Sbjct: 4   PNTSRLIRFNKPYGVLSQFTPEGRWRGLKDFID--IPDVYVAGRLDADSEGLLLLTNDGQ 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------- 179
           L   +  P  +  + Y V+  G   ++ L  L++G+ +        + +L          
Sbjct: 62  LQARIADPRFKMEKTYWVQVEGVPTEEALAALRQGVQLNDGLTRPARASLLDPPPDVWPR 121

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    AW+ + + EG+NR+++++         RLIR + GP  L  L  G+ R
Sbjct: 122 QPPIRERKSIPTAWLELAISEGRNRQVRRMTAAVGLPTLRLIRAAIGPHTLDGLAPGTWR 181

Query: 235 E 235
           E
Sbjct: 182 E 182


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 46/179 (25%), Positives = 81/179 (45%), Gaps = 19/179 (10%)

Query: 74  RLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R+ L +KP G+++  +D   P  R T+   +      V   GRLD ++EGLL+LT+DG L
Sbjct: 3   RILLLNKPYGVLSQFTDARSPSPRPTLSGFV--TVPGVYPAGRLDRDSEGLLVLTDDGAL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G      L LL+ G+ +        QV             
Sbjct: 61  QARIADPRHKLPKTYLVQVEGAPTDADLALLRHGVTLNDGPTRPAQVQRIAPPALWERDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                +   + W+ + + EG+NR+++++     +   RL+R   G + L  L  G+ R+
Sbjct: 121 PVRFRKSVPDQWIEITIHEGRNRQVRRMTAHIGFPTLRLVRWQIGDWTLDGLAPGAWRD 179


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 48/180 (26%), Positives = 88/180 (48%), Gaps = 16/180 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG L
Sbjct: 59  QNRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDGIL 116

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +           
Sbjct: 117 QAKLTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAKVEVIDAPTIWERNP 176

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                      W+ + + EG+NR+++++     +   RL+R S G   LG L  G  +E+
Sbjct: 177 PVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGDLQPGQWKEI 236


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   +D L  L+ G+ +                       
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 154

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRD 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  190 bits (483), Expect = 3e-46,   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  NKPRVDLKNRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--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 TIWERNPPVRFRANIPTTWLAITIVEGRNRQVRRMTAHIGFPTLRLVRYSMGDITLGGLQ 223

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 224 PGQWKEI 230


>gi|320195863|gb|EFW70488.1| Ribosomal large subunit pseudouridine synthase E [Escherichia coli
           WV_060327]
          Length = 177

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 48/178 (26%), Positives = 84/178 (47%), Gaps = 17/178 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G   QD L  L+ G+ +           L               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+ + 
Sbjct: 120 RKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRDATD 177


>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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 54/182 (29%), Positives = 90/182 (49%), Gaps = 19/182 (10%)

Query: 77  LYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP  +++  +D +   R T+ D +P   S V  VGRLD ++EGLLLLTN G L   L
Sbjct: 1   MFYKPYDVLSQFTDREDSPRRTLKDYIP--VSEVYPVGRLDRDSEGLLLLTNHGRLQHRL 58

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  R Y V+     D+  LN L++G+VI+       QV   +Q+           
Sbjct: 59  SNPRFRHPRTYWVQVERIPDEAALNQLRQGVVIKDYQTRKAQVQRLSQEPDLPPRDPPIR 118

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                   W+ + L EG+NR+++++     +   RLIR++    +L  L  G  R+++  
Sbjct: 119 FRKTVPTCWLEITLTEGRNRQVRRMTAVVGFPTLRLIRVAIAHLRLDGLQPGQWRDLTPP 178

Query: 240 IL 241
            L
Sbjct: 179 EL 180


>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 =  190 bits (483), Expect = 3e-46,   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     V + GRLD ++EGLL+L
Sbjct: 30  KRKPENQPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVL 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|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 =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 111/231 (48%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I  A + +R+ ++R   +  + +NG +++ ++V V    D +   G  +   + 
Sbjct: 3   MRVDKMIGNANLDTRKNIKRNAKKGELIINGQIVKDSSVKVDPNLDEVIYMGELVDYFDN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGL 130
               + +K  GL+   ++ DG  TV  +L   +  +     GRLD +T GLLLL+ DG  
Sbjct: 63  I-YIMMNKREGLICQSNELDG--TVMSDLDEFYLNLDLAIAGRLDKDTTGLLLLSTDGKF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y V    ++D   +   K G+ I+   Y      LD      A+V 
Sbjct: 120 IHKVISPNSHIWKKYEVETSKKIDPSLVENFKDGVYIKEDDYYARSAKLDIIGEKKAYVY 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           V   EGK   +K++F   + +V +L R++ G  +L  +L  G  RE+S++ 
Sbjct: 180 VT--EGKFHLVKRLFSNNDNEVIKLKRLAIGDLELDQSLNPGQYRELSEEE 228


>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 =  190 bits (483), Expect = 3e-46,   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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG     L  P+++  + Y V+  G   ++ L+ L+KG+ ++       +V L  +  
Sbjct: 117 TNDGIFQAKLTQPNSKSPKTYWVQVEGAPSEEDLDKLRKGVELKDGMTLPAKVELMAEPE 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWDRNPPVRFRAAIPTTWLVITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDMNVGQLQP 236

Query: 231 GSTREV 236
           G  +E+
Sbjct: 237 GEWKEI 242


>gi|145355350|ref|XP_001421926.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144582165|gb|ABP00220.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 287

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 66/245 (26%), Positives = 108/245 (44%), Gaps = 16/245 (6%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG----ILLERAAVNVMSTDH 59
           K         +R+  +++R G+ SR +  R IA++ V  +G           +   + D 
Sbjct: 38  KTSGAATAKAERLDALLSRLGLTSRADAARFIAERVVTTDGARATERATSGKLKARAAD- 96

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLD 115
           + VDG  L   +   L + HK  G+V +H   +G ++V+D LP  + R       VGRLD
Sbjct: 97  VRVDGETLEDVDGL-LIVMHKARGVVCSHDVREG-TSVYDALPERWRRRKPSIESVGRLD 154

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGD 174
            +T GLLLLT+DG L   L  P  +  + YRV+    + +D + +   G + + G     
Sbjct: 155 KDTSGLLLLTDDGALVHALTTPKKEIGKWYRVKTDRPIPRDAVEVFASGELTLDGETRAC 214

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL---LAG 231
                +          + L EGK  ++K++F FF   V  L R S+G   L        G
Sbjct: 215 KPAVCELMD-DETEARLRLTEGKFHQVKRMFAFFGCTVIGLHRESFGSLTLERAGVSEPG 273

Query: 232 STREV 236
             + +
Sbjct: 274 DFKTL 278


>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 =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 90/187 (48%), Gaps = 19/187 (10%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPD--GRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           L  A    L  ++KP  ++   +D     R T+      +  RV + GRLD ++EGLLLL
Sbjct: 4   LPTAVPAMLIAFNKPFNVLCQFTDRSVPPRPTLAGF--GLPPRVYAAGRLDHDSEGLLLL 61

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           T++G LA  L  P  +  + Y V+  G    ++L  L+ G+V+        ++       
Sbjct: 62  TDNGTLAHKLTDPKHKADKTYWVQVEGMPSDEQLQQLRTGVVLNDGPTLPAKIERLDPAP 121

Query: 181 -----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                       +   ++W+ + +REG+NR+++++    N    RL+R+S GP++L  L 
Sbjct: 122 SLWTRDPPVRFRKTVPDSWLAITIREGRNRQVRRMTAAVNLPTLRLVRVSMGPYRLDDLQ 181

Query: 230 AGSTREV 236
            G  R++
Sbjct: 182 PGQWRQI 188


>gi|328473240|gb|EGF44088.1| pseudouridine synthase family 1 protein [Vibrio parahaemolyticus
           10329]
          Length = 232

 Score =  190 bits (482), Expect = 4e-46,   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|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 =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 53/184 (28%), Positives = 90/184 (48%), Gaps = 17/184 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R     ++ +++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 24  RPRGPRKVVIFNKPFDVLPQFTDEAGRSTLKDFIP--LTDVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  +VY V+  G  D   L   ++G+ ++        + +        
Sbjct: 82  GKLQAQLTQPGQKTGKVYYVQVEGVPDDAALAQFRQGLELKDGMTLPAGIEIVAEPEWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    AW+ V L EG+NR+++++     +   RLIR S G + L  L  G 
Sbjct: 142 PRNPPIRERKSIPTAWIKVILFEGRNRQVRRMTAHIGFPTLRLIRYSMGDYTLDNLANGE 201

Query: 233 TREV 236
            RE+
Sbjct: 202 WREM 205


>gi|162138450|ref|YP_540277.2| 23S rRNA pseudouridine synthase E [Escherichia coli UTI89]
          Length = 207

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWRD 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 207


>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 =  190 bits (482), Expect = 4e-46,   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  KPKVDPKDRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVL 105

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           TNDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +  +  
Sbjct: 106 TNDGILQAKLTQPKSKSPKTYWVQVDGAPLEQDLEKLRKGVELKDGMTLPAEVEVIPEPQ 165

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   L  L+ 
Sbjct: 166 VWDRTPPVRFRANIPTTWLAITIIEGRNRQVRRMTAHIGFPTLRLIRHSMGDIVLKDLMP 225

Query: 231 GSTREVS 237
           G  RE+S
Sbjct: 226 GEWREIS 232


>gi|332993406|gb|AEF03461.1| ribosomal large subunit pseudouridine synthase E [Alteromonas sp.
           SN2]
          Length = 180

 Score =  190 bits (482), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 45/178 (25%), Positives = 87/178 (48%), Gaps = 16/178 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           A  +++ L++KP  +++  +D DGR T+ D +      V + GRLD ++EGLL+LTNDG 
Sbjct: 2   ANESKIVLFNKPFQVLSQFTDADGRETLKDYID--IPGVYAAGRLDRDSEGLLVLTNDGK 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   L  P  +  + Y V+  G  ++  L+ L+ G+ ++       +V            
Sbjct: 60  LQHKLAHPEAKTSKTYWVQVEGIPNEAALDALRNGVELKDGMTKPAKVVAIDPPELWDRI 119

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 Q    +W+++ + EG+NR+++++     +   RL+R   G + +  +  G  
Sbjct: 120 PPVRFRQAIPTSWLSITISEGRNRQVRRMTAHIGFPTLRLVRYRVGNWTIDGIDNGKY 177


>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 =  190 bits (482), Expect = 4e-46,   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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG     L  P+++  + Y V+  G   +  L+ L+KG+ ++       +V +  +  
Sbjct: 117 TNDGIFQAKLTQPNSKSTKTYWVQVEGAPSEKDLDKLRKGVELKDGMTLPAEVEVMQEPQ 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMNVGQLQP 236

Query: 231 GSTREV 236
           G  +EV
Sbjct: 237 GEWKEV 242


>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 =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 49/186 (26%), Positives = 92/186 (49%), Gaps = 16/186 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    E  ++ +++KP   ++  +D +GR T+ D +      V + GRLD ++EGLL+L
Sbjct: 41  KPKIAPEERKVIIFNKPFDTLSQFTDGEGRKTLADYI--SIKGVYAAGRLDRDSEGLLVL 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|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 =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++    +L L +KP G+++  +  +G  T+   +P   + V   GRLD ++EGLLLLTND
Sbjct: 6   KRPANPKLVLLNKPYGVLSQFTGEEGDQTLKPFIPH--NDVYPAGRLDKDSEGLLLLTND 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------- 177
           G     L  P  +  + Y V+  G   +++L  L+ G+ +        +           
Sbjct: 64  GVYQARLANPKYKVWKTYWVQVEGDPSEEQLEQLRNGVELNDGMTRPAEAFVMPEPMNLW 123

Query: 178 -----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +   ++W+ + +REGKNR+++++         RLIR + GPFQL T+  G 
Sbjct: 124 PRNPPVRERKSVPDSWLCLKIREGKNRQVRRMTAHVGLPTLRLIRAAVGPFQLKTMQPGE 183

Query: 233 TR 234
            R
Sbjct: 184 WR 185


>gi|312945697|gb|ADR26524.1| 23S rRNA pseudouridine synthase E [Escherichia coli O83:H1 str. NRG
           857C]
          Length = 207

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------------- 175
              L  P  +  ++Y V+  G   +D L  L+ G+ +                       
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTEDALEALRNGVTLNDGPTLPAGAEMVEEPEWLWPRN 144

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRD 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 207


>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 =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 85/182 (46%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R A   ++ +++KP  ++   +D  GR+T+ D +      + + GRLD ++EGLL+LTND
Sbjct: 29  RPAAPRQVVIFNKPFDVLPQFTDEQGRATLKDYI--SLQGIYAAGRLDRDSEGLLVLTND 86

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  +VY V+  G+ D+  L    +G+ ++                   
Sbjct: 87  GRLQAQLTQPGKRTGKVYYVQVEGEPDEADLRRFCQGLTLKDGPTLPALAERVAQPEWLW 146

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S G   L  L  G 
Sbjct: 147 PRNPPIRERKNIPTSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMGSLTLQDLAPGE 206

Query: 233 TR 234
            R
Sbjct: 207 WR 208


>gi|145342798|ref|XP_001416276.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144576501|gb|ABO94569.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 249

 Score =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 75/252 (29%), Positives = 111/252 (44%), Gaps = 24/252 (9%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           E+   +RVSK++AR G  SRRE ER+I   RV V+G  +        +   IE+ G   R
Sbjct: 2   EDDELERVSKILARRGTCSRREAERLIEDGRVLVDGETI-ELGFKARANARIEITGEGTR 60

Query: 69  KAERTRLWLYHKPIGLVT-----------THSDPDGRS------TVFDNLPSIFSRV--- 108
                   + +KP G V+              +P          T  D+L  +   V   
Sbjct: 61  WLREKLTVIVNKPPGYVSNLPAEGEIAAAACVEPRNAWMRAMEGTPMDDLKRVTRDVSSF 120

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
              GRLD ++ GLL+LT DG LAR +       L+ Y V     V +  +  L   + + 
Sbjct: 121 NVCGRLDKDSRGLLILTEDGALARSVIG-GNGVLKKYVVTTDADVRESHMRSLNGRVQLD 179

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           G+    M V           +   LREGKNR+I++V E F  +V  L R+  G  Q+G L
Sbjct: 180 GVELLPMNVQRLGHGSRT--LEFNLREGKNRQIRRVCEKFGLRVVDLHRVQIGDVQIGDL 237

Query: 229 LAGSTREVSKKI 240
             G+ R +S++ 
Sbjct: 238 PEGAWRLMSERE 249


>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 =  189 bits (481), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 54/190 (28%), Positives = 95/190 (50%), 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 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--- 179
           +LTNDG L   L  P  +  ++Y V+  G  D+  LN L+ GI ++          L   
Sbjct: 78  VLTNDGKLQARLTQPHKKTAKIYYVQVEGIPDESALNKLRNGITLKDGPTLPAGAELVKE 137

Query: 180 ------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 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|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 =  189 bits (481), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 50/189 (26%), Positives = 89/189 (47%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              ++ +  R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+L
Sbjct: 31  KRRKENQPKRVVLFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  ++Y V+  G+   + L  L+ G+ +         + +     
Sbjct: 89  TNDGALQARLTQPGKRTGKIYYVQVEGEPTAEALEALRNGVTLNDGPTLPAGIEVVDEPE 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|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 =  189 bits (481), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  189 bits (481), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 44/177 (24%), Positives = 80/177 (45%), Gaps = 17/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R+ L +KP G+++  +D      T+ D +      V + GRLD ++EGLL+LT+DG L  
Sbjct: 3   RVILLNKPFGVLSQFTDEGTNHPTLKDYVK--IPGVYAAGRLDRDSEGLLVLTDDGRLQN 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            +  P  +  + Y  +  G  D   L  L+ G+ ++       +  +             
Sbjct: 61  RIASPKFKQPKTYWAQVEGTPDDAALEALRAGVKLKDGMTKPARARIIDAPDVWERDPPI 120

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +   + W+ + L EG+NR+++++         RLIR S G + +  L  G  R+
Sbjct: 121 RVRKAIPDTWIELVLTEGRNRQVRRMTAAVGHPTLRLIRYSIGDWTIDNLALGQWRD 177


>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 =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 54/181 (29%), Positives = 93/181 (51%), Gaps = 17/181 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   SD  GR T+ D +P   S + + GRLD ++EGL++LTNDG L   L
Sbjct: 60  VVLFNKPFDVLPQFSDEAGRRTLKDFIPQ--SGIYAAGRLDRDSEGLMILTNDGTLQARL 117

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  +VY V+  G   ++ L  L+ G+ ++       +V +               
Sbjct: 118 TQPGKRTGKVYFVQVEGCPHENDLVPLRAGVDLKDGPTLPAEVEIVAAPDWLWDRHPPVR 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +    +W+ + L EG+NR+++++     +   RLIR S G  QL TL  G  R++S +
Sbjct: 178 ERKAIPTSWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGTLQLQTLAPGEWRDISSE 237

Query: 240 I 240
           I
Sbjct: 238 I 238


>gi|237653664|ref|YP_002889978.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237624911|gb|ACR01601.1| pseudouridine synthase [Thauera sp. MZ1T]
          Length = 229

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 52/206 (25%), Positives = 93/206 (45%), Gaps = 17/206 (8%)

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
               +  ++           TRL L +KP G++   +D  GR T+ D +      V + G
Sbjct: 9   KCEPSSGVKKSDTSAEGRAETRLLLLNKPFGVLCQFTDEAGRRTLKDYVE--VPGVYAAG 66

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           RLD ++EGL+LLT DG L   +  P  +  + Y V+  G++D+  L +L+ G+ +     
Sbjct: 67  RLDADSEGLVLLTGDGALQHRIADPRHKLAKTYLVQVEGEIDEAALAILRAGVDLGDFRS 126

Query: 173 GDMQVTLD---------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
                                   +    +W+ + L EGKNR+++++    +    RL+R
Sbjct: 127 LPCAARRMPAPDWLWPRDPPVRFRKSVPTSWIEIVLCEGKNRQVRRMTAKVDHPTLRLVR 186

Query: 218 ISYGPFQLGTLLAGSTREVSKKILRE 243
           ++ GP+ L  L  G  RE++   + E
Sbjct: 187 VAIGPWTLAGLGVGEWRELAGAEIAE 212


>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 =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 57/235 (24%), Positives = 98/235 (41%), Gaps = 17/235 (7%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K++A  G  SR+E++  I    V  + G  L+  A    + + I  D  PL  A  
Sbjct: 1   MRLVKLLANLGYGSRKEMQVAIRNGWVTDLKGNRLKADAK--TAHEDILFDDEPLDPAHG 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDG 128
             + L +KP+G   +  D      V+D LP  F     V    GRLD  T G LL T+DG
Sbjct: 59  -VVILMNKPLGYTCSIKDQG--RLVYDLLPDRFRMRKPVLSTIGRLDKETSGALLFTDDG 115

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---IVIQGICYGDMQVTLDTQKGS 185
                +  P ++  ++Y V     +  D+  L   G   +  +       ++ +  +  +
Sbjct: 116 TFLHRVISPKSEVPKIYEVALDRPMKGDEGALFASGDMMLESEDKPLKPAELEVIDETHA 175

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + L EG+  +++++F      V  L R   G   L  L  G  + +S++ 
Sbjct: 176 ----RLTLHEGRYHQVRRMFAATGNHVTDLTRSHIGGLGLEGLEEGQWKVLSEEE 226


>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 =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 87/188 (46%), 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 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+ ++        V +    
Sbjct: 82  LTNDGVLQARLTQPKSKQAKVYWVQVEGAPTEADLQALRDGVELKDGMTLPAGVEVIESP 141

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++     +   RLIR     + +  L 
Sbjct: 142 QIWDRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGFPTLRLIRYKMAQWTVDDLA 201

Query: 230 AGSTREVS 237
            G  REV+
Sbjct: 202 PGEWREVT 209


>gi|328870986|gb|EGG19358.1| hypothetical protein DFA_02145 [Dictyostelium fasciculatum]
          Length = 534

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 65/286 (22%), Positives = 116/286 (40%), Gaps = 17/286 (5%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K+++  G+ +R +V++ I   +V   G  +      V   D I V G  +   
Sbjct: 2   IERVRLDKLLSNLGLCTRSKVQQFINANKVTYQGQKV-SPKAKVDVED-IRVMGRKVDHP 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLT 125
           E       HKPIG V ++S  DG    ++D LP  F+         GRLD    GL++++
Sbjct: 60  E-LLTIAVHKPIGYVCSNSREDGDHKIIYDLLPKEFADRSPTLSIAGRLDKWVTGLVVMS 118

Query: 126 NDGGLARVLELP-STQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQK 183
            +G +   +  P   +  +VY V    + +  + + +  G + ++           +   
Sbjct: 119 QNGKIVERIITPKDDKMGKVYEVVCESKFNGTEADEMASGRVQLRSEDGPCKPAHFEVVD 178

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             N    + L EGK  +++++      K   + R   GP QLG L  G  R +SK+ +  
Sbjct: 179 QENKMARLTLYEGKYHQVRRMMSAVGNKAIGIHRTQVGPIQLGDLEVGKWRILSKEEM-- 236

Query: 244 QLGPHLLEEAQVNLDAPIYS-SETLVRDRPNIISEVPDDFTRMKKN 288
                LLE  QV+  A   +      ++     +E+ D  T     
Sbjct: 237 ----ELLEAIQVSKPAITKNLYRRKAKEDARDEAELDDKMTMKPGQ 278


>gi|221134863|ref|ZP_03561166.1| pseudouridine synthase, Rsu [Glaciecola sp. HTCC2999]
          Length = 196

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 85/177 (48%), Gaps = 16/177 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+  + L++KP  ++T  +D  GR T+ D +      + + GRLD ++EGLL+LTNDG L
Sbjct: 19  EKKLVVLFNKPFNVLTQFTDQAGRQTLKDYID--IPNIYAAGRLDRDSEGLLVLTNDGKL 76

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------ 178
              L  P+ +  + Y V+  G +  + +  L  G+ ++       +V             
Sbjct: 77  QHALAHPTQKTTKTYWVQVEGDITDEAIEQLSNGVNLKDGMTAPAKVEKMAAPAIWPRTP 136

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              +      +WV++ + EG+NR+++++    N+   RLIR   G + +  +  G  
Sbjct: 137 PIRERASIPTSWVSITISEGRNRQVRRMTAHVNYPTLRLIRYRVGQWTIDNIANGEF 193


>gi|157370266|ref|YP_001478255.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157322030|gb|ABV41127.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 178

 Score =  189 bits (480), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 52/176 (29%), Positives = 86/176 (48%), Gaps = 17/176 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR+T+ + +P  F  V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   VLFNKPFDVLPQFTDEAGRATLKEFIP--FPDVYAAGRLDRDSEGLLVLTNDGKLQAQLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  +VY V+  G    + L  L+ G+ ++        V L               +
Sbjct: 60  EPGKRTGKVYYVQVEGAPQDNDLVSLRNGVTLKDGPTLPAGVELVAEPQWLWPRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +    AW+ + L EG+NR+++++     +   RLIR S G   LG L  G  + +
Sbjct: 120 RKSIPTAWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYSMGNISLGELQPGEWKCL 175


>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 =  189 bits (480), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L N+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLANNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 154

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 155 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRD 214

Query: 236 VSK 238
            + 
Sbjct: 215 ATD 217


>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 =  189 bits (480), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 88/183 (48%), Gaps = 17/183 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 34  KERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V +        
Sbjct: 92  GALQAKLTQPGKRTGKIYYVQVEGEPTAEALAALRNGVTLNDGPTLPAGVEVVEEPAWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKSIPTCWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGE 211

Query: 233 TRE 235
            R 
Sbjct: 212 WRR 214


>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 =  189 bits (480), Expect = 7e-46,   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  KPRPAPKDRKVIIFNKPFDVLSQFTDDQHRQTLADFI--SVKDVYAAGRLDRDSEGLLIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +D L+ L++G+ ++       +V +  +  
Sbjct: 79  TNDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLDKLRQGVELKDGMTLPAKVEIIPEPN 138

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 139 VWERNPPVRFRAAIPTTWISITIIEGRNRQVRRMTANIGFPTLRLIRYSMGDWTIKDVAH 198

Query: 231 GSTREVS 237
           G+ +EVS
Sbjct: 199 GTWKEVS 205


>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 =  189 bits (480), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 93/187 (49%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              ++++  R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+L
Sbjct: 31  RRPQESQPKRVILFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------- 175
           TNDG L   L  P  +  ++Y V+  G+ D++ L  L+ G+ +                 
Sbjct: 89  TNDGALQAKLTQPGKRTGKIYFVQVEGEPDEEALAALRNGVTLNDGPTLPAGIERVNEPE 148

Query: 176 ------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L 
Sbjct: 149 WLWPRNPPIRERKSIPTSWLKITLFEGRNRQVRRMTAHVGFPTLRLIRYAMGSYTLDSLA 208

Query: 230 AGSTREV 236
            G  R+V
Sbjct: 209 NGEWRDV 215


>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 =  189 bits (480), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 88/187 (47%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              +     RL L++KP  ++   +D  GR T+ D +P   + V + GRLD ++EGLL+L
Sbjct: 31  KRRKPEGPKRLILFNKPYDVLPQFTDEAGRQTLKDFIP--VAGVYAAGRLDRDSEGLLVL 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 AGSTREV 236
            G  R+V
Sbjct: 209 CGQWRDV 215


>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 =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 97/236 (41%), Gaps = 8/236 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           +  ++   G  SRR+   +I   RV V G           +   +  VD        R  
Sbjct: 3   LESILYTQGFGSRRQCRGLIEAGRVAVAGAAATDPDAAFDTDGLVFSVDDAAWPFHARA- 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
               +KP G   +  DP   ++VF  LP+      V  VGRLD +T GLLLL++DG    
Sbjct: 62  YLALNKPAGYECSR-DPQHHASVFSLLPAPLVARGVQCVGRLDQDTTGLLLLSDDGQFVH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
               P  +  + Y       +D  +L+ L+ G+ + G     +       +  +A + + 
Sbjct: 121 AYTSPKRKVPKTYVATVRHPLDDTQLHALRTGVQLHGEP-KPIAAVAADARAPHA-LALT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGP 247
           + EGK  ++K++    + +V  L R S G F L   L  G+ R + +  L     P
Sbjct: 179 VLEGKYHQVKRMVAAASNRVELLHRESIGGFTLPADLAPGAWRWLDEADLAALRNP 234


>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 =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 52/175 (29%), Positives = 92/175 (52%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR T+ D +      V + GRLD ++EGLLLLT+DG L  +L
Sbjct: 2   IILFNKPFDVLTKFTDSEGRKTLKDYIE--IPNVYAAGRLDKDSEGLLLLTDDGKLNHLL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 60  TDPKSKSFKTYLVQVEGEFSIEAAQKLEKGVLLKDGKTLPAKVKLIDEPEWLWERTPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 120 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYTLGNLKSGDYK 174


>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 =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 52/175 (29%), Positives = 92/175 (52%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR T+ D +      V + GRLD ++EGLLLLT+DG L  +L
Sbjct: 2   IILFNKPFDVLTKFTDGEGRKTLKDYIE--IPNVYAAGRLDKDSEGLLLLTDDGKLNHLL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P ++  + Y V+  G+   +    L+KG++++       +V L               
Sbjct: 60  TDPKSKSFKTYLVQVEGEFSIEAAQKLEKGVLLKDGKTLPAKVKLIDEPEWLWERTPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           + +    +WV + ++EGKNR+I+++     +   RLIR S G + LG L +G  +
Sbjct: 120 ERKAIPTSWVEISIKEGKNRQIRRMTAAVGFPTLRLIRWSIGQYTLGNLKSGDYK 174


>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 =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 42/161 (26%), Positives = 72/161 (44%), Gaps = 5/161 (3%)

Query: 83  GLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G V +H D     T F  L       +   GRLD++T GL+L+T+DG  +  +  P  + 
Sbjct: 1   GFVCSHEDGFNH-TAFVLLDEVKMENLHFAGRLDVDTTGLVLITDDGQWSHRITSPKHKC 59

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            + YRV     V  + +   ++GI ++      +   L+        V + + EGK  ++
Sbjct: 60  AKTYRVWLADPVQDNYIKAFEEGIELRNEKAPTLPAQLEI--IDEKEVLLTIHEGKYHQV 117

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           K++F     KV  L R S G   L   L  G  R ++++ +
Sbjct: 118 KRMFAALGNKVEGLHRESVGDIVLDEMLEPGEYRYLTQEEI 158


>gi|329577701|gb|EGG59128.1| pseudouridylate synthase [Enterococcus faecalis TX1467]
          Length = 197

 Score =  188 bits (479), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 62/198 (31%), Positives = 101/198 (51%), Gaps = 5/198 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134
           + +KP G+V+  SD   + TV D +     R  +  VGRLD +TEGLLLLT++G L   L
Sbjct: 1   MLNKPKGVVSAVSDA-SKKTVIDLIAPQDRRPGLYPVGRLDGDTEGLLLLTDNGQLGYQL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGL 193
             P+ +  + Y V+ +G V  +     K GIV+QG I     ++T+     + + V + +
Sbjct: 60  IRPNKEVAKCYEVKVNGLVSAEDCAKFKDGIVLQGGIQCKPAKITVLAATETESHVFLTI 119

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEE 252
           +EGK  ++KK+F     KV  L R + GP +L   L  G+ R ++++ L+  L    +E+
Sbjct: 120 QEGKFHQVKKMFLSVGKKVTALKRQTMGPLRLDPQLPLGAYRSLTREELQLLLPYFFIEK 179

Query: 253 AQVNLDAPIYSSETLVRD 270
            Q +   P        R 
Sbjct: 180 QQTSKALPSNLKREEERK 197


>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 =  188 bits (479), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 50/179 (27%), Positives = 90/179 (50%), Gaps = 18/179 (10%)

Query: 74  RLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           R+ +++KP G++T  +D   GR+T+ D +P     V   GRLD ++EGL++LT+DG L  
Sbjct: 3   RIIVFNKPYGVLTQFTDREHGRATLADFIP--IPGVRPAGRLDRDSEGLIVLTDDGRLQA 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------- 183
            +  P  +  + YRV+  G  D+  LN L++G+ +        +  +  +          
Sbjct: 61  RIADPRHKMAKTYRVQVEGLPDEAALNRLRRGVRLNDGLTLPAEANIIPEPAWLWPRDPP 120

Query: 184 ------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     W+ + +REG+NR+++++     +   RLIR + G + L  L  G  RE+
Sbjct: 121 VRFRATIPTTWLELVIREGRNRQVRRMTAAVGFPTLRLIRWAIGAWTLEGLAPGEWREL 179


>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 =  188 bits (479), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 45/175 (25%), Positives = 80/175 (45%), Gaps = 17/175 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+ L +KP  ++   +D +GR T+   +P     V + GRLD ++EGL++LT+DG L  
Sbjct: 2   PRIILLNKPFDVLCQFTDREGRRTLAVYVPE--PGVYAAGRLDRDSEGLVVLTDDGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            +  P  +  + Y V+  G  D   L  L +G+ ++       +V +             
Sbjct: 60  RISDPKHKMSKTYWVQVEGVPDAQALKALAEGVELKDGLTLPARVKIIDEPPGLWPRDPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
               Q    +W+ + + EG+NR+++++         RLIR   G + L  L  G 
Sbjct: 120 IRVRQSIPTSWLELTISEGRNRQVRRMTAAVGHPTLRLIRYRVGSWTLDGLGPGE 174


>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 =  188 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 51/175 (29%), Positives = 85/175 (48%), Gaps = 5/175 (2%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLE 135
           + +KP G+++  SD +   TV D L     + +  VGRLD +TEGLLL+TNDG L+  L 
Sbjct: 1   MLNKPAGVLSAVSD-NNCKTVIDLLDVTPKKGLFPVGRLDKDTEGLLLITNDGELSHNLL 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            P+    + Y V  +G +    + L +KG+ I G         L   +   +   + + E
Sbjct: 60  SPAKHVDKTYYVELNGDLIDSDIELFEKGLDI-GEKNLTKPAILKILE-KRSTALITITE 117

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHL 249
           GK  ++K++F+     V  L R++ GP +L   L  G  R+++   +   L    
Sbjct: 118 GKYHQVKRMFQAIGLTVTFLKRLTMGPLKLDENLKPGEYRKLTVSEVEALLNNKP 172


>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 =  188 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P R  E  R+ L++KP  +++  +D   R+T+ D +      V + GRLD ++EGLLLL
Sbjct: 25  RPDRPREARRIVLFNKPFDVLSQFTDGGNRATLADYIQE--PGVYAAGRLDRDSEGLLLL 82

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P  +  + Y V+  G+ D+  L  L+ G+ +        +V       
Sbjct: 83  TNDGALQAKLTQPGKKTSKTYYVQVEGEPDEAALQALRDGVTLNDGPTLPAKVERIDEPH 142

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +    +W+++ + EG+NR+++++     +   RLIR   G + L  L 
Sbjct: 143 WLWPRNPPIRERKAIPTSWLSISIIEGRNRQVRRMTAHIGYPTLRLIRYRIGSWTLDGLA 202

Query: 230 AGSTREV 236
            G  R +
Sbjct: 203 NGEYRVL 209


>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 =  188 bits (479), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 50/179 (27%), Positives = 88/179 (49%), Gaps = 17/179 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            R+ L++KP G++   +   G  ++ D +P  F+     GRLD ++EGL+LLT++G L  
Sbjct: 2   PRIILFNKPYGVICQFTPTCGHRSLQDFIP--FAGFYPAGRLDADSEGLVLLTDNGKLQD 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            +  P  +  + Y V+  G+ D   LN +++GIV+        QV+L             
Sbjct: 60  KICSPKYKLSKTYWVQVEGKPDDVALNAMRRGIVLSDFKTKSAQVSLMNEPSFIWDRQPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +     W+++ L+EGKNR+I+++     +   RLIR + G   L  +  G  R +
Sbjct: 120 IRFRKSIPTTWLSLILKEGKNRQIRRMTAAVFFPTLRLIRYAIGLHTLKGIAPGEWRML 178


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 49/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+L N+G L
Sbjct: 27  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLANNGAL 84

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              L  P  +  ++Y V+  G   QD L  L+ G+ +           L           
Sbjct: 85  QARLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEPAWLWPRN 144

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 145 PPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGNYSLDNLANGEWRD 204

Query: 236 VSK 238
            + 
Sbjct: 205 ATD 207


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 49/185 (26%), Positives = 87/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A+   + L++KP  ++   +D  GR T+ D +      V + GRLD ++EGLLLLTNDG
Sbjct: 54  AAKDPVILLFNKPFDVLCQFTDEQGRKTLKDFI--AVKDVYAAGRLDRDSEGLLLLTNDG 111

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------- 178
            L   +  P+ +  + Y V+  G  DQ  L  L+ G+ ++       ++T          
Sbjct: 112 KLQSKITEPNKRTFKTYWVQVEGTPDQADLQALRDGVKLKDGMTLPAKITSISEPKVWDR 171

Query: 179 ----LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +     W+ + + EG+NR+++++     +   RLIR   G + L  +  G  R
Sbjct: 172 EPPIRERKNIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDIDIGQYR 231

Query: 235 EVSKK 239
            +  K
Sbjct: 232 ILDMK 236


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 56/173 (32%), Positives = 84/173 (48%), Gaps = 16/173 (9%)

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           ++T  S  +GR T+ D +      V  VGRLD ++EGLLLLT+DG LA  L  P     R
Sbjct: 1   MLTQFSGGEGRHTLKDYID--IPGVYPVGRLDRDSEGLLLLTDDGALAHRLTDPRFAHPR 58

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------------TQKGSNAWV 189
            Y V+  G  D + L  L  G+ IQGI                         +    +W+
Sbjct: 59  TYWVQVEGTPDGEALGRLAAGVEIQGIRTRPATAVAIAEPDLPERPVPIRVRKSIPTSWI 118

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            + L EG+NR+++++     +   RL+R++ G   LG L  G  RE+S++ LR
Sbjct: 119 ALTLTEGRNRQVRRMTAAVGYATLRLVRVAIGALSLGDLAPGRWRELSERELR 171


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 112/231 (48%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I  A + +R+ ++R   +  + +NG +++ ++V V    D +   G  +   + 
Sbjct: 1   MRVDKMIGNANLDTRKNIKRNAKKGELIINGQIVKDSSVKVDPNLDEVIYMGELVDYFDN 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGL 130
               + +K  GL+   ++ DG  TV  +L   +  +     GRLD +T GLLLL+ DG  
Sbjct: 61  I-YIMMNKREGLICQSNELDG--TVMSDLDEFYLNLDLAIAGRLDKDTTGLLLLSTDGKF 117

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y V    ++D   + + K G+ I+   Y      LD   G  A+V 
Sbjct: 118 IHKVISPNSHIWKKYEVETSKKIDPSLVEIFKDGVYIKEDDYYARSAKLDIIGGKKAYVY 177

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           V   EGK   +K++F   + +V +L R++ G  +L  +L  G  RE+ ++ 
Sbjct: 178 VT--EGKFHLVKRLFSNNDNEVIKLKRLAIGDLELDQSLNPGQYRELIEEE 226


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 81/177 (45%), Gaps = 17/177 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+   +P   + V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   ILFNKPFDVLPQFTDEQGRDTLKKYIP--ITDVYAAGRLDRDSEGLLILTNDGKLQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLD 180
            P     +VY  +  G  D   L   ++G+ ++                          +
Sbjct: 60  QPQKNTNKVYYAQVEGIPDDAALVKFRQGLTLKDGPTRPAGIERVNEPDWLWPRTPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +    +W+ + L EG+NR+++++     +   RLIR   G + L  L  G  +E++
Sbjct: 120 RKNIPTSWLKITLSEGRNRQVRRMTAHIGYPTLRLIRYQIGEYTLNNLAPGEWKEIT 176


>gi|255081278|ref|XP_002507861.1| predicted protein [Micromonas sp. RCC299]
 gi|226523137|gb|ACO69119.1| predicted protein [Micromonas sp. RCC299]
          Length = 257

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 65/253 (25%), Positives = 107/253 (42%), Gaps = 30/253 (11%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-MSTDHIEVDGVPLRK 69
              QR+SK +A  G+ASRR  E +I   RV+VNG+ +      V  S D I VDG  ++ 
Sbjct: 1   DEGQRLSKALAALGVASRRASEELIFAGRVQVNGVTVTMPQHAVSTSRDVIAVDGKVVQG 60

Query: 70  ------AERTRLWLYHKPIGLVTTHSDPDG-------RSTVFDNLPSIF----------- 105
                       +L HKP G + +                V D                 
Sbjct: 61  GLESLGDGGHLYFLLHKPKGYLCSSKPAGAGARASGQDRLVLDLFEDWREGWRKRHPGQL 120

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R+ +VGRLD+NT G+LL+T DG   + +  PS+Q  + Y V    +  + ++  + +G
Sbjct: 121 APRLFTVGRLDVNTTGMLLVTTDGQWCQRVAHPSSQIPKSYIVTAATRPTKAQIKKMAEG 180

Query: 165 IVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             + G+    ++V         G    + V + +G+NRE++ +       V +L R+  G
Sbjct: 181 CEVDGVHVTPLRVESMEGARDGGPAHRILVDVVDGRNREVRVLSASAGVDVKKLKRVRVG 240

Query: 222 PFQL-GTLLAGST 233
             ++   L  G  
Sbjct: 241 GLRMPSELPIGKY 253


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 87/187 (46%), Gaps = 17/187 (9%)

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 AGSTREV 236
            G  REV
Sbjct: 209 CGQWREV 215


>gi|251789551|ref|YP_003004272.1| pseudouridine synthase [Dickeya zeae Ech1591]
 gi|247538172|gb|ACT06793.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 218

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 45/184 (24%), Positives = 85/184 (46%), Gaps = 17/184 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             A + R+ L++KP  +++  +D   R+T+ D +P     + + GRLD ++EGL++LTND
Sbjct: 34  TAAAQARIVLFNKPFDVLSQFTDEGSRATLKDYVP--LRDIYAAGRLDRDSEGLMILTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y  +  G  D + L+  + G+ +                    
Sbjct: 92  GQLQARLTQPGKKTPKIYYAQVEGIPDDEALHAFRTGLQLNDGTTLPAGAERVEEPAWLW 151

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR S     L  L  G 
Sbjct: 152 PRQPPIRERKNIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMANQTLDGLSPGE 211

Query: 233 TREV 236
            +E+
Sbjct: 212 WKEI 215


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 46/185 (24%), Positives = 88/185 (47%), Gaps = 16/185 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            A+   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG
Sbjct: 54  AAKDPVILLFNKPFDVLCQFTDEQGRKTLKDFIP--VKDVYAAGRLDRDSEGLLLLTNDG 111

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   +  P  +  + Y V+  G  ++  L  L+ G+ ++       ++++         
Sbjct: 112 KLQSKITEPKKKTFKTYWVQVEGAPNEAALQTLRNGVKLKDGMTLPAKISILSEPNIWDR 171

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +     W+ + + EG+NR+++++     +   RLIR   G + L  +  G  +
Sbjct: 172 EPPIRERKNIPTTWLEIQICEGRNRQVRRMTAHIGFPTLRLIRYKIGQWSLDDIDIGQYQ 231

Query: 235 EVSKK 239
            +  K
Sbjct: 232 ILDMK 236


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 48/180 (26%), Positives = 83/180 (46%), Gaps = 20/180 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L L +KP G+++  +D       R+T+ D +     RV   GRLD ++EGLLLLT+DG L
Sbjct: 2   LILLNKPYGVLSQFTDKGNADSPRATLSDYVE--VPRVYPAGRLDRDSEGLLLLTDDGAL 59

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G    D+L  L++G+ +         V             
Sbjct: 60  QARIAHPKFRKPKTYLVQVEGDPTDDQLAQLRRGVSLNDGPTRPATVRRLPPPDLWPRVP 119

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +AW+ + + EG+NR+++++         RL+R S G + +  L  G  R +
Sbjct: 120 PVRFRKSVPDAWLELTITEGRNRQVRRMTAHVGLPCLRLVRWSIGDWSVAGLAPGEWRGL 179


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 115/231 (49%), Gaps = 9/231 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            RV K+I  A + +R+ +++   +  + +NG +++ ++V V    D +   G  +   E 
Sbjct: 3   MRVDKMIGNANLDTRKNIKKNAKKGGLVINGEIIKDSSVKVDPNIDEVIYMGELVDYFEN 62

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGL 130
               + +K  GL+   ++ DG  TV  +L   +  +     GRLD +T GLLL++ DG  
Sbjct: 63  I-YIMMNKREGLICQSNELDG--TVMSDLDEFYLNLDLAIAGRLDKDTTGLLLMSTDGKF 119

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +  P++   + Y V    ++D D + + K+G+ I+   Y      L+  +   A+V 
Sbjct: 120 IHRVISPNSNIWKKYEVETSKKIDPDLVEIFKEGVYIKEDDYYARSAKLEIIEDKKAYVY 179

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKI 240
           V   EGK   +K++F   + +V +L R++ G  QL  TL  G  RE++++ 
Sbjct: 180 VT--EGKFHLVKRLFSNNDNEVVKLKRLAIGKLQLDKTLNPGDYRELTQEE 228


>gi|224824759|ref|ZP_03697866.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224603252|gb|EEG09428.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 225

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 48/179 (26%), Positives = 87/179 (48%), Gaps = 17/179 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L L++KP G++   S  +   T+ D++      V   GRLD ++EGLLLLT DG L  
Sbjct: 2   PQLILFNKPYGVICQFSQHELHPTLKDHID--IPGVYPAGRLDTDSEGLLLLTGDGELQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
            +  P  +  + Y V+  G   +++L  L+ G+ +        +V L ++          
Sbjct: 60  RISDPRWKQSKTYWVQVEGTPVEEQLEALRAGVNLGDFITQPAEVRLLSEPPQLWERKPP 119

Query: 185 -------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                   +AW+ + + EGKNR+++++         RL+R++ GP++L  L  G  R +
Sbjct: 120 VRFRKTVPDAWLEIIISEGKNRQVRRMTAKVGLPTLRLVRVAVGPWRLDGLQPGEFRRL 178


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 64/245 (26%), Positives = 117/245 (47%), Gaps = 17/245 (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    +  LR Y ++ +G + Q+ ++ ++ G++ +                        +
Sbjct: 120 LM--ESDLLRTYILKINGFITQEIISAMENGLISEDTRVGAHSKSHITSMEFAPFNSYKI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                  + + V + +GKNRE+++ F  F  +V  L RISYG   L  L  G  R  + +
Sbjct: 178 LKNDRRYSKIKVSIAQGKNRELRRFFGAFGREVLDLRRISYGFVHLNALPCGKKRFFTHE 237

Query: 240 ILREQ 244
             R+ 
Sbjct: 238 EYRDL 242


>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 =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 102/225 (45%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----KA 70
           RV   +A  G+ SRR  E +I ++ ++VNG + +     V   D I            ++
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNGSIAK-LGDKVSPGDRIIYKKQIYVFKGFQS 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
           +       +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KNKIYLALNKPRNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y V     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRRKVEREYIVESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>gi|321223855|gb|EFX48918.1| Ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
          Length = 181

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 51/179 (28%), Positives = 86/179 (48%), Gaps = 17/179 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   VLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G  D   L  L+ G+ +         + +               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +    +W+ V L EG+NR+++++         RLIR S G + L  L  G  RE++++
Sbjct: 120 RKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWREIAQE 178


>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 =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 49/175 (28%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +++KP+ ++T  +D  GR+T+ D +      V + GRLD ++EGLLLLT+DG +   +
Sbjct: 4   LVVFNKPMNVLTQFNDSQGRATLSDFIDK--PGVYAAGRLDYDSEGLLLLTDDGAIQARI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------D 180
             P  +  + Y V+  G + +  L  L+KG+++          +L               
Sbjct: 62  SQPKFKLPKTYWVQVEGVIGEAALRRLEKGVMLNDGPTRPAHASLISPPEVWERDPPIRQ 121

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
            +    +W+ + L EG+NR+++++     +   RLIR S GP+ +  L  G  RE
Sbjct: 122 RKNIPTSWIALTLFEGRNRQVRRMTAAVGFPTLRLIRYSIGPWSINGLQPGEWRE 176


>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 =  188 bits (477), Expect = 1e-45,   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  KPRPAPEDRKVLIFNKPFDVLSQFTDDQHRQTLADFI--SVKDVYAAGRLDRDSEGLLIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG L   L  P ++  + Y V+  G   +D L  L++G+ ++       +V + T+  
Sbjct: 79  TNDGVLQARLTQPESKSPKTYWVQVEGAPTEDDLEKLRQGVELKDGMTLPAKVEVMTEPE 138

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ V + EG+NR+++++     +   RLIR S G + +  +  
Sbjct: 139 LWERNPPVRFRAAIPTTWIAVTIIEGRNRQVRRMTAHIGFPTLRLIRYSMGDWTIKDVPH 198

Query: 231 GSTREVS 237
              +EV+
Sbjct: 199 REWKEVT 205


>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 =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 88/187 (47%), Gaps = 16/187 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   A+  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 38  KPAIAAQDIKIVLFNKPFDVLCQFTDDANRKTLAEFIP--IKEVYAAGRLDRDSEGLLLL 95

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TN G L   L  P  +  + Y V+  G+   + +  L  G+ ++       +V++ ++  
Sbjct: 96  TNCGKLQNTLTAPGKKTSKTYWVQVEGEPSSESIAALCTGVELKDGLTLPAKVSIISEPT 155

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+++ + EG+NR+++++         RLIR S G + L  +  
Sbjct: 156 VWTRNPPVRERKLIPTTWLSITISEGRNRQVRRMTAHIGHPTLRLIRYSIGKYTLDGIKN 215

Query: 231 GSTREVS 237
           G  + ++
Sbjct: 216 GEYKVMT 222


>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 =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 54/194 (27%), Positives = 85/194 (43%), Gaps = 24/194 (12%)

Query: 73  TRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L+HKP  ++   S  D   + T+ D +      V  VGRLD ++EGLLLLTN+G L
Sbjct: 3   YRYLLFHKPYDVLCQFSPSDRPDQQTLKDYID--VPEVYPVGRLDRDSEGLLLLTNNGAL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P     R Y V+   +  +  L  L++G+ IQ       +V             
Sbjct: 61  QHRLCHPRFGHDRTYWVQVEREPTEAALQALRQGVQIQDYRTRPAKVQRLDDPQIPERDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLA 230
                +    AW+ + L+EG+NR+++++         RLIR +        P QL  L  
Sbjct: 121 PIRFRKTVPTAWLALTLQEGRNRQVRRMTAAVGHPTLRLIRAAIATHPDQPPLQLQGLAP 180

Query: 231 GSTREVSKKILREQ 244
           G+ R+++    R  
Sbjct: 181 GTWRDLTAIECRRL 194


>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 =  188 bits (477), Expect = 1e-45,   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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK- 183
           TNDG     L  P+++  + Y V+  G   +  L+ L+KG+ ++       +V +  +  
Sbjct: 117 TNDGIFQAKLTQPNSKSTKTYWVQVEGAPSEKDLDKLRKGVELKDGMTLPAEVEVMQEPQ 176

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                            W+ + + EG+NR+++++     +   RLIR S G   +G L  
Sbjct: 177 VWERTPPVRFRAAIPTTWLAITIIEGRNRQVRRMTANIGFPTLRLIRYSMGNMDVGQLQP 236

Query: 231 GSTREV 236
           G  +++
Sbjct: 237 GEWKDI 242


>gi|303286517|ref|XP_003062548.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456065|gb|EEH53367.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 230

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 59/225 (26%), Positives = 99/225 (44%), Gaps = 11/225 (4%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGL 84
             SRR  +R++A   V VNG ++  A   V   D +E+ G  +R  E      Y KP G+
Sbjct: 9   FTSRRNADRLVASGAVTVNGAVVA-AGAMVFPGDVVELRGERVRW-ETLNYVKYWKPRGV 66

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
             T +D   R+ + D +    +R+  VGRLD ++ GL+LLT+DG L         +  + 
Sbjct: 67  TCT-TDARDRTNIVDAVNYPDARLFPVGRLDKDSTGLILLTSDGRLPNAALRSGRKRDKK 125

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQ--------GICYGDMQVTLDTQKGSNAWVTVGLREG 196
           Y V     V  + + +L+ G+VI                 +  +        + + LREG
Sbjct: 126 YLVVVDAVVRPEDVRMLRDGVVISTPVQRDRVDRVLTARTLPCEIDVVGARTLEITLREG 185

Query: 197 KNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +NR+I+++ +   ++V  L R       L     G   E  ++ L
Sbjct: 186 RNRQIRRMLDAVGYRVINLHRTEIMGIGLRGTREGRWVECDEEEL 230


>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 =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 100/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ ++VNG + +     V   D I          +   
Sbjct: 8   RVQVFLAEKGVGSRRFCEELIRKKLIRVNGSIAK-LGDKVSPGDRIIYKKQIYVFKDFQS 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D +GR      +  +F  R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KNKIYLALNKPKNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRRKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>gi|254521474|ref|ZP_05133529.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219719065|gb|EED37590.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 179

 Score =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 47/179 (26%), Positives = 88/179 (49%), Gaps = 19/179 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD--GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L  ++KP  ++   +D     R T+      +  RV + GRLD ++EGLLLLT++G LA 
Sbjct: 2   LIAFNKPFNVLCQFTDRSVPPRPTLAGF--GLPPRVYAAGRLDHDSEGLLLLTDNGTLAH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P  +  + Y V+  G    ++L  L+ G+++        ++               
Sbjct: 60  KLTDPKHKADKTYWVQVEGTPSDEQLQQLRDGVLLNDGPTLPAKIERLDPAPSLWTRDPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   +AW+ + +REG+NR+++++    N    RL+R++ GP++L  L  G  R++
Sbjct: 120 VRFRKTVPDAWLAITIREGRNRQVRRMTAAVNLPTLRLVRVAMGPYRLDDLQPGQWRQI 178


>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 =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 89/187 (47%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 44/180 (24%), Positives = 86/180 (47%), Gaps = 21/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L++KP G+++  +D       R T+   +          GRLD ++EGL++LT++G 
Sbjct: 3   RVILFNKPFGVLSQFTDKGTEGSPRPTLSGFIDE--KGFYPAGRLDRDSEGLIVLTDNGA 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  D   +N L++G+ ++       +V+L          
Sbjct: 61  LQARISHPKYKLAKTYWVQVEGTPDDAAINALRQGVTLKDGKTAPAKVSLIDTPAGLWDR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   +AW+++ + EG+NR+++++         RLIR   G +QL  +  G+ R
Sbjct: 121 DPPVRFRKSVPDAWLSITITEGRNRQVRRMTAHVGLPTLRLIRAQIGDWQLNAMRPGTWR 180


>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 =  188 bits (477), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 47/179 (26%), Positives = 87/179 (48%), Gaps = 19/179 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD--GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L  ++KP  ++   +D     R T+      +  RV + GRLD ++EGLLLLT++G LA 
Sbjct: 2   LIAFNKPFNVLCQFTDRSVPARPTLAGF--GLPPRVYAAGRLDHDSEGLLLLTDNGTLAH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P  +  + Y V+  G    ++L  L+ G+ +        ++               
Sbjct: 60  KLTDPRHKADKTYWVQVEGTPSDEQLQQLRDGVELNDGPTLPAKIERLDPAPSLWTRDPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   +AW+ + +REG+NR+++++    N    RL+R++ GP++L  L  G  R++
Sbjct: 120 VRFRKTVPDAWLAITIREGRNRQVRRMTAAVNLPTLRLVRVAMGPYRLDDLQPGQWRQI 178


>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 =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 54/189 (28%), Positives = 88/189 (46%), Gaps = 21/189 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            R  L++KP  +++  +D D     R T+ D +P     V SVGRLD+++EGLLLLT+D 
Sbjct: 3   YRYILFYKPYNVLSQFTDRDSHAQSRQTLKDYIP--IPSVYSVGRLDLDSEGLLLLTDDR 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L  P     R Y V+         L  L++GI IQ       +V L         
Sbjct: 61  KLKYRLGQPEFAHPRTYWVQVERIPTTQALEQLRQGITIQNYRTRTARVQLLLTEPLLPP 120

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   Q    AW+ + L EG+NR+++++     +   RL+R++     L +L  G  
Sbjct: 121 RIPPIRFRQNVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRVAIAHLTLNSLEPGHW 180

Query: 234 REVSKKILR 242
           R++  + ++
Sbjct: 181 RDLHPQEIQ 189


>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 =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 51/194 (26%), Positives = 87/194 (44%), Gaps = 8/194 (4%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRL 114
            D + V+   +   E    ++ +KP+G +T   D +   TV   L       ++  +GRL
Sbjct: 2   KDKVSVEDEDVNYQENF-YFMLNKPLGYITATYD-ENFPTVISLLDDETVKDKLFPIGRL 59

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVI--QGIC 171
           D++TEGLL+LT DG LA  L  P     + Y     G V +   +  +K GI +      
Sbjct: 60  DLDTEGLLILTTDGQLAHRLAHPKWNIEKEYYAIVEGDVSKIDFSPFEKEGIYLKKDKYK 119

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               +V + +     + V + + EGK   +KK+ E     V  L R+  G  +L   L  
Sbjct: 120 TKPFKVKVLSALEEESKVLITVSEGKYHIVKKIMESLGHPVKYLKRVRMGNLKLDENLQP 179

Query: 231 GSTREVSKKILREQ 244
           G  R ++++ +R+ 
Sbjct: 180 GDYRPLTEEEIRKL 193


>gi|312172141|emb|CBX80398.1| ribosomal large subunit pseudouridine synthase [Erwinia amylovora
           ATCC BAA-2158]
          Length = 218

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 51/181 (28%), Positives = 86/181 (47%), Gaps = 17/181 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   SD  GR T+ D +P     + + GRLD ++EGL++LTNDG L   L
Sbjct: 40  VVLFNKPFDVLPQFSDEAGRRTLKDYIPH--PGIYAAGRLDRDSEGLMVLTNDGALQAQL 97

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  +VY V+  G   +  L  L+ G+ ++        V                 
Sbjct: 98  TQPGKRTGKVYFVQVEGCPQESDLQPLRDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIR 157

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +
Sbjct: 158 ERKAIPTCWLKITLYEGRNRQVRRMTAHIGYPTLRLIRFSMGNLGLRALAPGEWRDISHE 217

Query: 240 I 240
           I
Sbjct: 218 I 218


>gi|304397253|ref|ZP_07379132.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304355402|gb|EFM19770.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 184

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 50/181 (27%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L++KP  ++   +D  GR T+ D +    + V + GRLD ++EGL++LTNDG L 
Sbjct: 2   PRRVILFNKPFDVLPQFTDEAGRRTLKDFV--SVAEVYAAGRLDRDSEGLMVLTNDGALQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L  P  +  +VY V+  G+  +  L  L+ G+ ++                       
Sbjct: 60  AALTQPGKRTGKVYYVQVEGEPQEADLQPLRDGVNLKDGMTLPAGIEKVPEPQWLWPRQP 119

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +     W+ V L EG+NR+++++     +   RLIR + G + L  L  G+ RE+
Sbjct: 120 PIRERKNIPTQWLKVTLYEGRNRQVRRMTAHIGFPTLRLIRYAMGQYSLDDLAPGAWREL 179

Query: 237 S 237
           S
Sbjct: 180 S 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 =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 85/186 (45%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P R     ++ L++KP  ++T  S   G  T+ D +      +   GRLD ++EGLL+LT
Sbjct: 26  PKRPRGPQKIILFNKPFNVLTQFSGEPGDKTLADYI--SIKDIYPAGRLDKDSEGLLVLT 83

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------ 179
           NDG L   L  P ++  + Y V+  G    D L  L+KG+ ++        +        
Sbjct: 84  NDGILQARLTQPQSKQPKTYWVQVEGVPSDDDLEQLRKGVTLKDGLTLPADIERMEQPVI 143

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   + +     W+ + LREG+NR+++++     +   RLIR     + +  L  G
Sbjct: 144 WDRTPPIRERKNIPTTWLALTLREGRNRQVRRMTAHIGFPTLRLIRYKMADWTVDDLAPG 203

Query: 232 STREVS 237
             REV+
Sbjct: 204 EWREVT 209


>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 =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 100/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R+   +A  G+ SRR  E +I ++ V+VNG + +     V   D I          +   
Sbjct: 8   RIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAK-LGDKVALGDRIIYKKQIYVFKDLQS 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D +GR      + P    R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KSRVYLALNKPRNYLCSNFDANGRKLAISLVQPLFKERLFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLKEGQVK 227


>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 =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 50/186 (26%), Positives = 85/186 (45%), Gaps = 16/186 (8%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P R     ++ L++KP  ++T  S   G  T+ D +      +   GRLD ++EGLL+LT
Sbjct: 26  PKRPRGPQKIILFNKPFNVLTQFSGEPGDKTLADYI--SIKDIYPAGRLDKDSEGLLVLT 83

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------ 179
           NDG L   L  P ++  + Y V+  G    D L  L+KG+ ++        +        
Sbjct: 84  NDGILQARLTQPQSKQPKTYWVQVEGAPSDDDLEQLRKGVTLKDGLTLPADIERMEQPVI 143

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   + +     W+ + LREG+NR+++++     +   RLIR     + +  L  G
Sbjct: 144 WDRTPPIRERKNIPTTWLALTLREGRNRQVRRMTAHIGFPTLRLIRYKMADWTVDDLAPG 203

Query: 232 STREVS 237
             REV+
Sbjct: 204 EWREVT 209


>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 =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 47/183 (25%), Positives = 86/183 (46%), Gaps = 16/183 (8%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  +  ++  ++KP   ++  +D  GR T+ D +      + + GRLD ++EGL++LTND
Sbjct: 45  RSPDERKVIAFNKPYDTLSQFTDGQGRQTLADFI--TIKDIYAAGRLDRDSEGLMILTND 102

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G L   L  P  +  + Y V+  G+  +  L  L++G+ ++       +V +        
Sbjct: 103 GVLQARLTQPKAKAPKTYWVQVEGEPQEADLEQLRRGVTLKDGPTLPAKVEIIKPPQVWE 162

Query: 184 ----------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                         W+ + + EG+NR+++++     +   RLIR S G   L TL  G  
Sbjct: 163 RNPPVRFRAAIPTTWLAMTIIEGRNRQVRRMTACIGFPTLRLIRYSIGNTTLETLQPGEW 222

Query: 234 REV 236
           RE+
Sbjct: 223 REI 225


>gi|6689331|emb|CAB65436.1| hypothetical protein [Synechococcus elongatus PCC 6301]
          Length = 199

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 55/194 (28%), Positives = 84/194 (43%), Gaps = 24/194 (12%)

Query: 73  TRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            R  L+HKP   V   S  D   + T+ D +      V  VGRLD ++EGLLLLTN+G L
Sbjct: 3   YRYLLFHKPYDAVCQFSPSDRPDQQTLKDYID--VPEVYPVGRLDRDSEGLLLLTNNGAL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              L  P     R Y V+   +  +  L  L++G+ IQ       +V             
Sbjct: 61  QHRLCHPRFGHDRTYWVQVEREPTEAALQALRQGVQIQDYRTRPAKVQRLDDPQIPERDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLA 230
                +    AW+ + L+EG+NR+++++         RLIR +        P QL  L  
Sbjct: 121 PIRFRKTVPTAWLALTLQEGRNRQVRRMTAAVGHPTLRLIRAAIATHPDQPPLQLQGLAP 180

Query: 231 GSTREVSKKILREQ 244
           G+ R+++    R  
Sbjct: 181 GTWRDLTAIECRRL 194


>gi|238910944|ref|ZP_04654781.1| ribosomal large subunit pseudouridine synthase E [Salmonella
           enterica subsp. enterica serovar Tennessee str.
           CDC07-0191]
          Length = 211

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 52/187 (27%), Positives = 91/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 24  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAEGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 82  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 86/188 (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 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+ ++        V +    
Sbjct: 82  LTNDGVLQARLTQPKSKQAKVYWVQVEGTPTEANLQALRDGVELKDGMTLPAGVEVIESP 141

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++         RLIR     + +  L 
Sbjct: 142 IVWDRNPPIRERKSIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYQMAQWTVNDLA 201

Query: 230 AGSTREVS 237
            G  REV+
Sbjct: 202 PGEWREVT 209


>gi|150020316|ref|YP_001305670.1| pseudouridine synthase [Thermosipho melanesiensis BI429]
 gi|149792837|gb|ABR30285.1| pseudouridine synthase [Thermosipho melanesiensis BI429]
          Length = 243

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/228 (29%), Positives = 113/228 (49%), Gaps = 5/228 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++ +++   G A RR+ + +I  ++VKVNG ++ +   +V   D I V+G       + 
Sbjct: 7   IKLQRILQICGFA-RRKADELIFSKKVKVNGKIVTKPWFDVKVDDEITVEGKKFTLP-KF 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
             ++ HKP G VT+  DP  ++T+ +        +   GRLD +  G+L+LTNDG L  V
Sbjct: 65  EYYVLHKPKGYVTSLYDPKEKNTIKEFFKD--KPLKPAGRLDKDVSGVLILTNDGDLIDV 122

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           L        +VY  +  G+V  + L  LKKGI  +G         +  Q  + + V V +
Sbjct: 123 LTNAKYGVKKVYIAKITGRVKFEDLLSLKKGIYDKGDFLKLEHFDILEQGFNYSTVKVEM 182

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-AGSTREVSKKI 240
            +GK  E+K++FE    KV  L RI +GP  +      G  R++  +I
Sbjct: 183 IKGKKHEVKRLFEKIGHKVLELRRIKHGPVSISLAPNPGDMRKIEGEI 230


>gi|311279960|ref|YP_003942191.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749155|gb|ADO48907.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 215

 Score =  187 bits (475), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 87/179 (48%), Gaps = 17/179 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTNDG L 
Sbjct: 38  PKRVILFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVLTNDGPLQ 95

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L  P  +  ++Y V+  G+  ++ L  L+ G+ +                        
Sbjct: 96  ARLTQPGKRTGKIYFVQVEGEPGEEALAALRSGVTLNDGPTLPAGAERVAEPTWLWPRNP 155

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L +G  R+
Sbjct: 156 PIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLASGEWRD 214


>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 =  187 bits (475), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 88/180 (48%), Gaps = 20/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL L++KP G+++  +D       R+T+ D++      V   GRLD ++EGLLLLT+DG 
Sbjct: 3   RLLLFNKPFGVLSQFTDRGTADSPRATLSDHI--NIPGVYPAGRLDRDSEGLLLLTDDGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G+ D   L  L++G+ ++       Q             
Sbjct: 61  LQARISHPKFKAPKTYLVQVEGEPDDAALAALRRGVTLKDGPTRPAQAERIAPPDLWPRD 120

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   ++W+ + + EG+NR+++++     +   RL+R S G + L  +  G+ +E
Sbjct: 121 PPVRYRKSVPDSWLRLTITEGRNRQVRRMTAHVGYPTLRLVRWSVGDWTLDGIAPGTWQE 180


>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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 100/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R+   +A  G+ SRR  E +I ++ V+VNG + +     V   D I          +   
Sbjct: 8   RIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAK-LGDKVTLGDRIIYKKQVYLFKDFQS 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D +GR      + P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  KDRVYLALNKPKNYLCSNFDANGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  +    
Sbjct: 127 FANDIIHPRLKVEREYIIESKKDIDENLLISFKSGIKIKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   +  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKSVFLKKIHRIRIGNINLDSLKEGQVK 227


>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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 109/238 (45%), Gaps = 23/238 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             +L + +KP  +++  +  DG+ T+ + +      V + GRLD ++EGLLLLTN+G L 
Sbjct: 2   PEKLIILNKPFHVLSQFTADDGKDTLANYIDD--ENVYAAGRLDYDSEGLLLLTNNGSLQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--------- 182
            ++  P  +  + Y V+  G++  D +  L +G+ ++       +     Q         
Sbjct: 60  HLIASPKFKMPKTYWVQVEGEITDDAIGSLCRGVELKDGMTKPAECRKIDQPNIWDRTPA 119

Query: 183 -----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--E 235
                    +WV + + EGKNR+++++     +   RLIR S GP+ + +L +G ++  E
Sbjct: 120 VRYRANIPTSWVALTITEGKNRQVRRMTAAVGFPTLRLIRYSIGPYTVDSLRSGESKIAE 179

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
           ++ + LREQ+     E  Q     P   S    + +     +      R  +++ +  
Sbjct: 180 LTSQ-LREQVS----EFEQKKRATPPNRSRHRSKGQSLPDGKGNTRRHRSAQSARRPR 232


>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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 49/182 (26%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 34  KERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V +        
Sbjct: 92  GALQAKLTQPGKRTGKIYYVQVEGEPTPEALAALRDGVTLNDGPTLPAGVEVVEEPAWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGE 211

Query: 233 TR 234
            R
Sbjct: 212 WR 213


>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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 51/187 (27%), Positives = 90/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+     D   L  L+ G+ +         + +        
Sbjct: 92  GALQARLTQPGKRTGKIYYVQVESIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 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|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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 52/202 (25%), Positives = 89/202 (44%), Gaps = 31/202 (15%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            R  +++KP  ++   +D       R T+ D +      V  VGRLD+++EGLLLLT+DG
Sbjct: 3   YRYIVFYKPYNVLCQFTDEGNSTTSRQTLKDYI--NIPNVYPVGRLDLDSEGLLLLTDDG 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L        R Y V+     D+  LN L++G+ I+        V +         
Sbjct: 61  QLQHRLAHRKFAHPRTYWVQVENIPDEPALNRLREGVKIKDYQTRKAWVKVFPTEPPLPP 120

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP--------FQL 225
                   +     W+ + L EG+NR+++++     +   RL+R++ G           L
Sbjct: 121 RNPPIRYRKNIPTCWLEITLTEGRNRQVRRMTAAVGYPTLRLVRVAMGIGKGKNGFQLDL 180

Query: 226 GTLLAGSTREVS--KKILREQL 245
             L  G  R+V+  ++ + EQL
Sbjct: 181 KGLEPGQWRDVTDIERKVLEQL 202


>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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 55/184 (29%), Positives = 96/184 (52%), Gaps = 17/184 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +K + TR+ L++KP  ++   +D  GRST+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 34  KKTQPTRVILFNKPYDVLPQFTDEAGRSTLKDYIP--VQGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+ D+D L  L+ G+ +         V L        
Sbjct: 92  GALQATLTQPGKRTGKIYFVQVEGEPDEDALAKLRTGVTLNDGPTLSAGVELVSEPEWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ + L EG+NR+++++     +   RLIR + G + L +L  G+
Sbjct: 152 PRNPPIRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGRYTLDSLANGA 211

Query: 233 TREV 236
            R++
Sbjct: 212 WRDI 215


>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 =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 62/225 (27%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ ++VNG + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNGSIAK-LGDKVSPGDRIIYKKQIYVFKDFQS 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D +GR      + P    R+ S+GRLD  + GLLL TNDG 
Sbjct: 67  KNKIYLALNKPRNYLCSNFDVNGRKLAISLVQPLFKERIFSIGRLDFKSSGLLLFTNDGE 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI ++   +      +  +  +    
Sbjct: 127 FANDIIHPRGKVEREYIIESKKDIDENLLISFKSGIKVKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L  L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNIFLKKIHRIRIGNINLDNLKEGQVK 227


>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 =  186 bits (474), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 84/179 (46%), Gaps = 19/179 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L L++KP G++   +D      R T+ D++      V   GRLD ++EGLLLLT+DG L 
Sbjct: 3   LILFNKPYGVLCQFTDERTGPPRPTLADHI--HRPGVYPAGRLDHDSEGLLLLTDDGRLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y  +  G  D+  L  L+KG+ ++       +  L            
Sbjct: 61  ARIADPRHKMPKTYLAQVEGVPDEAALASLRKGVRLKDGMTLPAEAALIEDPALWPRDPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   ++W+ + +REG+NR+++++         RL+R   G + L  L  G  REV
Sbjct: 121 IRVRKTVPDSWLRLTIREGRNRQVRRMTAAVGHPTLRLVRWQVGDWSLDGLRPGEWREV 179


>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 =  186 bits (474), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 85/180 (47%), Gaps = 20/180 (11%)

Query: 75  LWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L L +KP G+++  +D       R+T+ D +     +V   GRLD ++EGLLLLT+DG L
Sbjct: 2   LILLNKPYGVLSQFTDKGTADSPRATLSDYVD--VPKVYPAGRLDRDSEGLLLLTDDGRL 59

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G    +++  L++G+ ++       QV             
Sbjct: 60  QARIAHPKFKKPKTYLVQVEGDPSDEQIARLRRGVTLKDGPTRPAQVRRLPPPDLWPRVP 119

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +AW+ + + EG+NR+++++         RL+R S G + +  L  G  R +
Sbjct: 120 PVRFRKSVPDAWLEMTITEGRNRQVRRMTAHVGLPCLRLVRWSIGDWSVEGLAPGEWRNI 179


>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 =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 48/225 (21%), Positives = 87/225 (38%), Gaps = 8/225 (3%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERTR 74
           ++ ++ + G  +R +   + A   V ++G  L     +      +    G+    ++   
Sbjct: 3   LADILFKQGFGTRYDCRSIAASGAVSIDGRELTDPDEDFDPEGLVLTWRGMQWPVSDN-V 61

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLAR 132
           L   +KP G   +   P    +V + LP       V  VGRLD +T GLLL T++G L  
Sbjct: 62  LIAMNKPTGYECSLK-PSAHPSVMNLLPGPLRTRGVQPVGRLDWDTTGLLLFTDNGALLH 120

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            L  P     +VYR              L  G+V+       +          +  + + 
Sbjct: 121 RLTHPKKHVNKVYRATLSHPAANGTCEKLLSGVVLDDDP-KPVFAKAAELMAPD-VLMLT 178

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
           + +GK  ++K++      +V  L RI  G ++L   L  G    +
Sbjct: 179 ISQGKYHQVKRMVAACGNRVVALHRIKVGAYELPADLKPGEWCWL 223


>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 =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 99/231 (42%), Gaps = 6/231 (2%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K I+ +GI SRRE +  I    V VNG ++      V   D +  DG  +   E
Sbjct: 58  EGIRLNKYISNSGICSRREADTYIETGLVSVNGKIVNEMGYKVKLEDDVRFDGRRIN-PE 116

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGL 130
                L +KP G  TT S+  G  TV D + +   SR+  +GRL  N  GLLL TND  L
Sbjct: 117 PMTYVLLNKPKGFATTTSESKGN-TVMDLVANASNSRITPIGRLGRNATGLLLFTNDDKL 175

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L        R++ V     +    +  +++G  I G      ++    +  +   + 
Sbjct: 176 KEKLS--KKGMSRLFHVELDKNLKAADIQKIREGFTIAGKKIEIEEINY-VEGKTKKEIG 232

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           + ++   N  I+ +F  F + + RL  ++        L  G  + ++ + L
Sbjct: 233 LKIKNLGNSVIRDIFAHFEYDIVRLDCVALAHLTKKDLPRGKWKILTTQEL 283


>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 =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 47/207 (22%), Positives = 93/207 (44%), Gaps = 20/207 (9%)

Query: 44  GILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           G   +  +V     + I    +P       ++ L++KP  +++  +D D R T+ D +  
Sbjct: 20  GNAAKHPSVK----NKINTQQLPPVSDATRKILLFNKPFNVLSQFTDQDNRQTLKDYID- 74

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
               V + GRLD ++EGLLLLTNDG L   +  P+ +  + Y V+  G+  +  L  L+ 
Sbjct: 75  -IPEVYAAGRLDRDSEGLLLLTNDGKLQAKITEPNAKTSKTYWVQVEGRPTEADLQKLRD 133

Query: 164 GIVIQGICYGDMQVTL--------------DTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           G+ ++        + L              +       W+++ + EG+NR+++++     
Sbjct: 134 GVNLKDGLTLPAGIELMEQPAIWARVPPIRERANIPTTWLSITISEGRNRQVRRMTAHIG 193

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREV 236
           +   RLIR   G + +  +  G  + +
Sbjct: 194 FPTLRLIRYRIGDWTIDDIDNGQYKLL 220


>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 =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 34  KEHQPKTVILFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V +        
Sbjct: 92  GALQAKLTQPGKRTGKIYYVQVEGEPTAEALAALRDGVTLNDGPTLPAGVEVVEEPAWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ V L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKSIPTRWLKVTLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGE 211

Query: 233 TR 234
            R
Sbjct: 212 WR 213


>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 =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 49/175 (28%), Positives = 88/175 (50%), Gaps = 16/175 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            T++++++KP  ++T  +D D R T+ D +      + + GRLD ++EGLLLLTN+G L 
Sbjct: 57  PTQVYVFNKPYMVLTQFTDADNRETLKDYIK--VPDIYAAGRLDRDSEGLLLLTNNGRLQ 114

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  + Y V+  G+   +KL+ L+ GI+++       +V +            
Sbjct: 115 AKLTQPGEKTEKTYWVQVEGEPSPEKLSDLRYGIILKDGPTLPAKVEIMTEPSVWPRVPP 174

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             + Q     W+ + + EG+NR+I+++         RLIR   GP+ L  +  G 
Sbjct: 175 IRERQNIPTTWLAITIIEGRNRQIRRMTAHIGHPTLRLIRYRIGPWTLDNIQPGE 229


>gi|330973498|gb|EGH73564.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 173

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 54/173 (31%), Positives = 84/173 (48%), Gaps = 9/173 (5%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
            R ++ HKP G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +
Sbjct: 3   PRYFMLHKPEGCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWS 61

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWV 189
           R L  P ++  +VY V     +D+       +G+    +GI     Q+TL   + +    
Sbjct: 62  RRLTQPQSKMPKVYYVETEQPIDERYAAKFAEGLYFAFEGITTQPAQLTLLGPRRA---- 117

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            + + EG+  ++K++F  F+ KV RL R + G   L   L  GS R ++   +
Sbjct: 118 RLSIVEGRYHQVKRMFGHFDNKVLRLHRETIGALLLDPDLRPGSYRALNAGEI 170


>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 =  186 bits (473), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 79/176 (44%), Gaps = 17/176 (9%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
            +KP  ++   +D  GR+T+ D +P     V + GRLD ++EGLL+LTNDG L   L  P
Sbjct: 1   MNKPFDVLPQFTDEQGRATLKDYIP--LQGVYAAGRLDRDSEGLLVLTNDGRLQAQLTQP 58

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLDTQ 182
             +  +VY V+  G+  +  L    +G+ ++                          + +
Sbjct: 59  GKRTGKVYYVQVEGEPSEADLQRFCQGLTLKDGPTLPALAERVAQPDWLWPRNPPIRERK 118

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               +W+ + L EG+NR+++++     +   RLIR S     L  L  G  R +  
Sbjct: 119 NIPTSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMDSLTLQDLAPGEWRRIDW 174


>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 =  186 bits (473), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 84/177 (47%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+V   S  +   T+ D +      V + GRLD ++EGLL+LT+DG L   +
Sbjct: 2   LILFNKPFGVVCQFSAHENHPTLKDYI--AMPDVYAAGRLDTDSEGLLILTDDGRLQHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  + +++Y  +  G  D + L+ L++G+ +        QV +               
Sbjct: 60  AHPKHKEIKIYWAQVEGAPDDEALSPLRRGVDLGDFVTQPAQVKIIAEPANLWARVPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + +     W+ + + EGKNR+++++     +   RLIR + G   L  L  G  + +
Sbjct: 120 ERKAIPTTWLEIRISEGKNRQVRRMTAKIGFPTLRLIRYAIGAHTLAGLQPGEFKIL 176


>gi|171911201|ref|ZP_02926671.1| ribosomal large subunit pseudouridine synthase B [Verrucomicrobium
           spinosum DSM 4136]
          Length = 345

 Score =  186 bits (473), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 136/317 (42%), Gaps = 7/317 (2%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           M+   RV +NG +    +  V  +D + VDG  +R   +  + + HKP GLV +  D   
Sbjct: 1   MVRDGRVILNGKICTNLSTTVTDSDDVVVDGNKVR-PHKGVVIVLHKPRGLVCSRRDERD 59

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
           R T++  LP  F  +  VGRLD  +EGLLL+TN G +++ L  PS    + Y V    + 
Sbjct: 60  RDTIYSLLPEKFHTLHHVGRLDKESEGLLLMTNRGEVSQRLLHPSQGVEKEYEVILETRF 119

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D + L  L KG   +       +  +      +  + + L++G  R+I+ +  F  ++V 
Sbjct: 120 DPENLTRLTKGFHTEDGYAKAERAWMIG----DYKIGMVLKQGLKRQIRMMLYFLGYEVK 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 KEAKRSSRKTGARKRTGGTSPASGAGAGSSFGGDRGQSAGEGAARGPRGG--SIRGRERD 293

Query: 334 NHRRSPSFPSKRSLRRT 350
              +    P   S  R+
Sbjct: 294 GGSKGSRGPKSESGPRS 310


>gi|144897678|emb|CAM74542.1| 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 195

 Score =  186 bits (473), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 50/181 (27%), Positives = 86/181 (47%), Gaps = 18/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            RL L++KP  ++T  +D + GR+T+ D +      V   GRLD ++EGLL+L++DG L 
Sbjct: 2   PRLILFNKPYDVLTQFTDREAGRATLADYVD--VPGVYPAGRLDRDSEGLLVLSDDGPLI 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-------- 183
             +  P  +  + Y  +  G      L  L++G++++          L  +         
Sbjct: 60  ARIAQPRHKLAKTYFAQVEGIPTAAALAQLRQGVMLKDGPTLTAGAELVAEPDWLWPRHP 119

Query: 184 -------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     AWV + L EG+NR+++++     +   RLIR + G + L  L  G  REV
Sbjct: 120 PIRWRAAIPTAWVKLTLHEGRNRQVRRMTAAVGFPTLRLIRWAVGDWNLAGLAPGQWREV 179

Query: 237 S 237
           +
Sbjct: 180 T 180


>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 =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 81/205 (39%), Gaps = 35/205 (17%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
           +   +  +  +++KP G++   +D     R T+ D +      +  VGRLD ++EGLLLL
Sbjct: 33  IALNKTPQTIVFYKPYGVLCQFTDNSAHPRPTLKDYI--NLPDLYPVGRLDQDSEGLLLL 90

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
           T++G L   L        R Y  +  G    + L  L++GI             + T+  
Sbjct: 91  TSNGKLQHRLAHREFAHQRTYFAQVEGSPTDEDLEPLRRGITFADYPTRPAIAKIITEPD 150

Query: 183 ------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY---------G 221
                           +W+++ L EG+NR+++++     +   RL+R+           G
Sbjct: 151 FPPRNPPIRYRASIPTSWLSITLTEGRNRQVRRMTAAVGFPTLRLVRVQIQVTGRSPQQG 210

Query: 222 P--------FQLGTLLAGSTREVSK 238
                      L  L  G  R ++ 
Sbjct: 211 KGKSAATWCLTLEGLSPGQWRPLTP 235


>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 =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 111/238 (46%), Gaps = 5/238 (2%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    R++K +A AGI SRR+ +  IA   V VNG ++      V   D +  DG  +  
Sbjct: 51  NSNEIRLNKYVANAGICSRRDADVHIATGLVTVNGKVVTEMGYKVKLEDEVRYDGARIN- 109

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
            E+    L +KP G  TT S+  G+ TV D + +   SR+  +GRL  N+ GLLL TND 
Sbjct: 110 PEKKAYVLLNKPKGFATTTSEYKGK-TVMDLVANATSSRIKPIGRLGRNSTGLLLFTNDD 168

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            +       +   +R++ +     +  + L  +++G+ I+G         +D        
Sbjct: 169 KVVDRFTNSNKGVVRLFHLELDKNLKLEDLKKIREGLRIEGKQIN--VEEIDYVDNRKNE 226

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           + + ++   N  +  +F++F +++ ++  +         +  G+ + ++++ ++  + 
Sbjct: 227 IGIKIKNTGNTILHTIFDYFKYELVKIDCVQIAHLTKKDIPRGNWKILTEQEVQTLMM 284


>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 =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 53/182 (29%), Positives = 94/182 (51%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E  ++ L++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++LTNDG
Sbjct: 52  PIEERKVILFNKPYDTLSQFTDGDGRKTLADYIP--VKDVYAAGRLDRDSEGLMVLTNDG 109

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L  P ++  + Y V+  G   +D L+ L++G+V++       +V+L         
Sbjct: 110 ILQARLTQPKSKSEKTYWVQVDGAPSEDDLDKLRRGVVLKDGPTLPAKVSLMDTPDVWER 169

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                        W+++ + EG+NR+++++     +   RLIR S   F++G LL G   
Sbjct: 170 HPPVRFRANIPTTWLSITIIEGRNRQVRRMTANIGFPTLRLIRASMAGFEIGGLLPGDWL 229

Query: 235 EV 236
           E+
Sbjct: 230 EI 231


>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 =  186 bits (472), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 46/199 (23%), Positives = 92/199 (46%), Gaps = 20/199 (10%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P  + E+ ++ L++KP  ++T  +D  GR T+ + +      +   GRLD ++EGLLLL
Sbjct: 18  KPKLQLEQIKVVLFNKPYDVLTQFTDEQGRKTLKNFI--HIPDIYPCGRLDRDSEGLLLL 75

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN G +   L  P+ +  + Y V+  G   +  L  L++G++++        V       
Sbjct: 76  TNCGEIQHRLTTPAFKSKKTYWVQVEGVPSEQDLEALRQGVILKDGKTLPALVKFIPPPQ 135

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-- 227
                     + +    +W+ + + EG+NR+++++     +   RLIRI+     L    
Sbjct: 136 NLWQRDPPIRERKTIPTSWLEIAIHEGRNRQVRRMTAHIGYPTLRLIRIATAGLNLFDFP 195

Query: 228 -LLAGSTREVSKKILREQL 245
            L  G +  ++   + + L
Sbjct: 196 QLQLGCSYSLNSNEIEQLL 214


>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 =  186 bits (472), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 85/188 (45%), Gaps = 17/188 (9%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V   P  + E TRL  +HKP G+++  +       + D +      V   GRLD ++EG
Sbjct: 29  TVVRQPAPRPEVTRLLCFHKPYGVLSQFTPEGKWQGLKDWID--VPGVYVAGRLDADSEG 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|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 =  186 bits (472), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 43/177 (24%), Positives = 79/177 (44%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP+ +++  +       + D +      V + GRLD ++EGLLLLT+DG L   +
Sbjct: 2   LIAFNKPMNVLSQFTSEGKWRGLKDWID--VPGVYAAGRLDRDSEGLLLLTDDGRLQARI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  + Y     G+  QD +N L +G+ ++       +V                 
Sbjct: 60  TDPRAKMPKTYYALVEGRPSQDAINRLCEGVSLKDGPTRPAKVAAVPAPDWLWPRDPPVR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +   +AW+ + + EG+NR+++++         RLIR   G + L  L  G  R +
Sbjct: 120 LRKTVPDAWLRLTITEGRNRQVRRMCAAVGLPCLRLIRTQIGDWTLDGLAPGQWRRI 176


>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 =  186 bits (472), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 86/188 (45%), Gaps = 16/188 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
             P R     ++ L++KP   +T  S   G ST+ D +P     V   GRLD ++EGLL+
Sbjct: 24  NKPKRSRGPQKIILFNKPFNTLTQFSGEPGDSTLADFIP--VKDVYPAGRLDKDSEGLLV 81

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P ++  +VY V+  G   +  L  L+ G+ ++        V +    
Sbjct: 82  LTNDGVLQARLTQPKSKQAKVYWVQVEGAPTETNLQALRDGVELKDGMTLPAGVEVIESP 141

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L+EG+NR+++++         RLIR     + +  L 
Sbjct: 142 IVWDRNPPIRERKNIPTTWLAITLKEGRNRQVRRMTAHIGHPTLRLIRYQMAQWTVSDLA 201

Query: 230 AGSTREVS 237
            G  REV+
Sbjct: 202 PGEWREVT 209


>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 =  186 bits (472), Expect = 6e-45,   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|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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 68/253 (26%), Positives = 115/253 (45%), Gaps = 30/253 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-----------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    +   R Y ++    + +  +  +++G+ +Q    G       
Sbjct: 120 LLILSDSKEVVSKLMH--SNLPRTYILKIDSHITKQMIKAMEEGLTLQNAKAGGHRLSKI 177

Query: 174 ------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                  M+  +  +  S + + V + EGKNRE+++ F  FN  V  L R+SYG   L  
Sbjct: 178 KTMEFMPMEYEI-IKSASISKLKVRISEGKNRELRRFFAHFNANVLDLRRVSYGFINLNA 236

Query: 228 LLAGSTREVSKKI 240
           L  G TR  +K+ 
Sbjct: 237 LPVGKTRFFTKQE 249


>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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 43/182 (23%), Positives = 89/182 (48%), Gaps = 21/182 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           ++ L++KP  +++  +D       R T+ + +      V + GRLD ++EGLL+LTNDG 
Sbjct: 3   KVILFNKPFNVLSQFTDKGTEASERKTLSEFID--MPGVYAAGRLDKDSEGLLVLTNDGV 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------ 183
           L + +  P  +W + Y V+  G   QD + +L+ G+ ++       +  +  +       
Sbjct: 61  LQQEISNPKHKWPKTYVVQVEGTPTQDDIKVLESGVTLKDGITKPAEAEIIDKPEGLWDR 120

Query: 184 ---------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                      ++W+ + + EG+NR+++++     +   RLIR S G F +  +  G  +
Sbjct: 121 LPPIRYRKAIPDSWLMITITEGRNRQVRRMTAAIGFPTLRLIRYSIGNFTIDDIPNGQWK 180

Query: 235 EV 236
           ++
Sbjct: 181 QL 182


>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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 89/178 (50%), Gaps = 16/178 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L +KP  +++  +D +GR+T+ D +     ++   GRLD ++EGLLLLT++G +   
Sbjct: 3   KIILLNKPFNVLSQFTDSEGRATLADFVTE--KKLYPAGRLDYDSEGLLLLTDNGTVQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P T+  + Y V+  G   +  +  L+ G +++        V L  +           
Sbjct: 61  ISHPRTKMPKTYWVQVEGAPTEQDIEPLRVGAILKDGPCLPAMVELIPEPNIWKREPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                   W+ + + EG+NR+++++     +   RLIR+  G + + TL  G TR+++
Sbjct: 121 ARKAIPTTWLQLVITEGRNRQVRRMTASLGFPTLRLIRVKIGEWSIDTLKPGETRQIT 178


>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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 24  KERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTND 81

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V L        
Sbjct: 82  GALQAKLTQPGKRTGKIYYVQVEGEPTPEALTALRDGVTLNDGPTLPAGVELVEEPVWLW 141

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 142 PRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGD 201

Query: 233 TR 234
            R
Sbjct: 202 WR 203


>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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 87/180 (48%), Gaps = 17/180 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +T + L++KP  +++  +D  GR+T+ D +P     + S GRLD ++EGL++LTNDG L 
Sbjct: 28  KTHIVLFNKPFDVLSQFTDEGGRATLKDYVP--LRDIYSAGRLDRDSEGLMILTNDGKLQ 85

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------Q 176
             L  P  +  ++Y  +  G  D++ L+  + G+++                        
Sbjct: 86  ARLTQPGKKTPKIYYAQVEGVPDKEALHAFRTGLILSDGPTLPAGVEQVEEPAWLWPRQP 145

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + L EG+NR+++++     +   RLIR S     L  L  G  RE+
Sbjct: 146 PIRERKTIPVSWLKITLYEGRNRQVRRMTAHIGYPTLRLIRYSMAGQTLDGLHPGEWREI 205


>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 =  185 bits (471), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 87/183 (47%), Gaps = 17/183 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ + +RL L++KP G+++  +       + D +      V   GRLD ++EGLLLL ND
Sbjct: 28  QRHDASRLILFNKPYGVLSQFTPEGRWRGLKDFI--AIPGVYVAGRLDADSEGLLLLAND 85

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   +  P  +  ++Y V+  G   +  L  L++G+ +        +  L        
Sbjct: 86  GKLQAHIADPRFKMEKIYWVQVEGTPGEAALQALREGVALNDGPTRPARARLMDAPAALW 145

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                    Q    AW+ +G+REG+NR+++++     +   RL+R + G + L  L  GS
Sbjct: 146 QREPPVRVRQSIPTAWIELGIREGRNRQVRRMTAAVGFPTLRLVRAAIGNWSLDGLAPGS 205

Query: 233 TRE 235
            R+
Sbjct: 206 WRD 208


>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 =  185 bits (471), Expect = 8e-45,   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  IHAISNMPLILFNKPFQTMCQFSPHPTRKSLADHID--IPNIYPAGRLDADSEGLLLLND 76

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------- 178
           DG L   +  P  +  + Y V+  G  D D L  L+  + +      + +V         
Sbjct: 77  DGKLQHAISHPDRKHTKTYLVQVEGVPDADALARLRAPLDLGDFVTQECEVKRVAEPDWL 136

Query: 179 -------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--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|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 =  185 bits (471), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 51/181 (28%), Positives = 86/181 (47%), Gaps = 17/181 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   SD  GR T+ D +P     + + GRLD ++EGL++LTNDG L   L
Sbjct: 40  VVLFNKPFDVLPQFSDEAGRRTLKDYIPH--PGIYAAGRLDRDSEGLMVLTNDGALQAQL 97

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  +VY V+  G   +  L  L+ G+ ++        V                 
Sbjct: 98  TQPGKRTGKVYFVQVEGCPQESDLLPLRDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIR 157

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +
Sbjct: 158 ERKAIPTCWLKITLYEGRNRQVRRMTAHIGYPTLRLIRFSMGNLGLRALAPGEWRDISHE 217

Query: 240 I 240
           I
Sbjct: 218 I 218


>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 =  185 bits (471), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 100/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           R+   +A  G+ SRR  E +I ++ V+VNG + +     V   D I          +   
Sbjct: 8   RIHVFLAEKGVGSRRFCEELIRKKLVRVNGSIAK-LGDKVALGDRIIYKKQIYVFKDLQS 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D +GR      + P    RV S+GRLD  + GLLL TNDG 
Sbjct: 67  KSRVYLALNKPRNYLCSNFDANGRKLAISLVQPLFKERVFSIGRLDFKSSGLLLFTNDGK 126

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            A  +  P  +  R Y +     +D++ L   K GI I+   +      +  +  +    
Sbjct: 127 FANDIIHPRQKVEREYIIESKKDIDENLLISFKLGIKIKKEFFKLKSYEILNKNSA---- 182

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            + L EGKNREI+KVF   N  + ++ RI  G   L +L  G  +
Sbjct: 183 RLILDEGKNREIRKVFLSKNVFLKKIHRIRIGNINLDSLKEGQVK 227


>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 =  185 bits (471), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 84/179 (46%), Gaps = 19/179 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L  ++KP G++   +D      R T+   +      V   GRLD+++EGLLLLT+DG L 
Sbjct: 2   LIAFNKPYGVLCQFTDESTGPARPTLATFID--VPGVYPAGRLDLDSEGLLLLTDDGRLQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G+ D+D L  L++G+ ++       QV              
Sbjct: 60  ARIADPRYKAPKTYLVQVEGEPDEDALAALRRGVRLKDGMTLPAQVERIEAPDLWPRNPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   + W+ + LREG+NR+++++         RL+R   G + L  +  G  REV
Sbjct: 120 VRFRKSVPDCWLKLILREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLEGIAPGEWREV 178


>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 =  185 bits (471), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   SD  GR T+ D +P +   + + GRLD ++EGL++LTNDG L   L
Sbjct: 40  VVLFNKPFDVLPQFSDGSGRRTLKDYVPQL--GIYAAGRLDRDSEGLMVLTNDGELQAQL 97

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  +VY V+  G   +  L  L+ G+ ++        V                 
Sbjct: 98  TQPGKRTGKVYYVQVEGCPQEGDLQPLRDGVNLKDGPTLPAVVEKVAAPDWLWDRQPPIR 157

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +
Sbjct: 158 ERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGSLGLRALAPGEWRDISDE 217

Query: 240 I 240
           I
Sbjct: 218 I 218


>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 =  185 bits (471), Expect = 8e-45,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 87/184 (47%), Gaps = 16/184 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   A+  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 38  KPQIDAKDKKIVLFNKPFDVLCQFTDDADRKTLAEFIP--IKDVYAAGRLDRDSEGLLLL 95

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN G L   L  P+ +  + Y V+  G+   + +  L KG+ ++        V +     
Sbjct: 96  TNCGKLQNTLTAPNKKTNKTYWVQVEGEPSTESIQALCKGVELKDGLTLPANVKMIEEPN 155

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +    +W+++ + EGKNR+++++         RLIR S G + L  +  
Sbjct: 156 IWQRTPPVRERKSIPTSWLSITINEGKNRQVRRMTAHIGHPTLRLIRYSIGNYTLDDINT 215

Query: 231 GSTR 234
           G  +
Sbjct: 216 GEYK 219


>gi|310767366|gb|ADP12316.1| Ribosomal large subunit pseudouridine synthase E [Erwinia sp.
           Ejp617]
          Length = 218

 Score =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 17/181 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   SD  GR T+ D +P +   + + GRLD ++EGL++LTNDG L   L
Sbjct: 40  VVLFNKPFDVLPQFSDGSGRRTLKDYVPQL--GIYAAGRLDRDSEGLMVLTNDGELQAQL 97

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  +VY V+  G   +  L  L+ G+ ++        V                 
Sbjct: 98  TQPGKRTGKVYYVQVEGCPQEGDLQPLRDGVNLKDGPTLPAVVEKVAAPDWLWDRQPPIR 157

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +
Sbjct: 158 ERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFSMGSLGLRALAPGEWRDISNE 217

Query: 240 I 240
           I
Sbjct: 218 I 218


>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 =  185 bits (470), Expect = 9e-45,   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|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 =  185 bits (470), Expect = 9e-45,   Method: Composition-based stats.
 Identities = 45/189 (23%), Positives = 90/189 (47%), Gaps = 6/189 (3%)

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
             + V +   ++V    + K +   +   +KP G+V T  D   R ++   L +   RV 
Sbjct: 1   MGMRVTAGQIVKVGKKTVSKQDEMIVLAVNKPKGIVCT-EDQRERDSIVRFL-NYPVRVT 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 TVTRPCTVK----KIGKYTFSIILTQGLNRQIRRMCAAFGYEVKDLVRIRIMNIRLGSLK 174

Query: 230 AGSTREVSK 238
            G+ R+++ 
Sbjct: 175 EGAYRKLTD 183


>gi|291617070|ref|YP_003519812.1| RluE [Pantoea ananatis LMG 20103]
 gi|291152100|gb|ADD76684.1| RluE [Pantoea ananatis LMG 20103]
          Length = 219

 Score =  185 bits (470), Expect = 1e-44,   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|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 =  185 bits (470), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 48/174 (27%), Positives = 88/174 (50%), Gaps = 16/174 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L+HKP  +++  +D +GR T+ D +    +   + GRLD ++EGLLLL NDG L + +
Sbjct: 4   LILFHKPYRVLSQFTDSEGRGTLGDFITK--AGFYAAGRLDYDSEGLLLLCNDGRLQQRI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------D 180
             P  +  + Y V+  G + +  L  L+ G+ ++       + ++              +
Sbjct: 62  ADPRFKLWKSYAVQLEGDITEAALCSLRDGVELKDGATLPARASIIRTPAFWPRNPPIRE 121

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +  + +WV + +REG+NR+++++     + V RLIR   G + L  L  G  R
Sbjct: 122 RKTQTTSWVEISIREGRNRQVRRMCAKVGFPVLRLIRTRIGDWGLDDLAPGEYR 175


>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 =  185 bits (470), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 34  KERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V L        
Sbjct: 92  GALQAKLTQPGKRTGKIYYVQVEGEPTPEALTALRDGVTLNDGPTLPAGVELVEEPVWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGD 211

Query: 233 TR 234
            R
Sbjct: 212 WR 213


>gi|167470950|ref|ZP_02335654.1| ribosomal small subunit pseudouridine synthase A [Yersinia pestis
           FV-1]
          Length = 165

 Score =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 39/165 (23%), Positives = 76/165 (46%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +  P     + Y V     +  D       G+ +           
Sbjct: 121 VTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLYNEKSLTKPAQ 165


>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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 81/176 (46%), Gaps = 18/176 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L++KP G+++  +D   G+ T+ + +      V   GRLD ++EGLL+LT+DG     
Sbjct: 3   LILFNKPYGVLSQFTDEGSGKRTLKEFI--ALPGVYPAGRLDFDSEGLLILTDDGREQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  +  + Y  +  G   ++ L  L+KG+ ++          L  +           
Sbjct: 61  IADPKHKIPKTYLAQVEGIPSEEALQALRKGVDLKDGRTRPATARLAAEPENLWPRDPPI 120

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  + W+ + + EG+NR+++++         RLIR+  G + L  L  G+ R
Sbjct: 121 RYRKSVPDTWIELTITEGRNRQVRRMTAAAGHPTLRLIRLRIGDWDLENLPPGAWR 176


>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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 54/189 (28%), Positives = 87/189 (46%), Gaps = 21/189 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            R  L++KP  +++  +D D     R T+ D +P     V SVGRLD+++EGLLLLT+D 
Sbjct: 3   YRYILFYKPYNVLSQFTDRDSHTPSRQTLKDYIP--IPSVYSVGRLDLDSEGLLLLTDDR 60

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L  P     R Y V+         L  L++GI IQ       +V L         
Sbjct: 61  KLKYRLGQPEFAHPRTYWVQVERIPTTQALEQLRRGITIQNYRTRTARVQLLLTEPLLPP 120

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   Q    AW+ + L EG+NR+++++     +   RL+R++     L +L  G  
Sbjct: 121 RIPPIRFRQNVPTAWLEITLTEGRNRQVRRMTAAVGFPTLRLVRVAIAHLTLNSLQPGDW 180

Query: 234 REVSKKILR 242
           R++    ++
Sbjct: 181 RDLHPHEIQ 189


>gi|239994883|ref|ZP_04715407.1| ribosomal large subunit pseudouridine synthase E [Alteromonas
           macleodii ATCC 27126]
          Length = 180

 Score =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 47/174 (27%), Positives = 85/174 (48%), Gaps = 16/174 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP  +++  +D DGR T+ D +      V + GRLD ++EGLL+LTNDG L   
Sbjct: 6   KVVLFNKPFQVLSQFTDADGRETLKDYID--VPGVYAAGRLDRDSEGLLVLTNDGKLQHK 63

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L  P  +  + Y V+  G +D+  +  L+ G+ ++       +V                
Sbjct: 64  LANPKAKTSKTYWVQVEGIMDEKAMQALRDGVELKDGMTRPAKVKAMEAPSVWPRNPPVR 123

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             Q    +WV + + EG+NR+++++     +   RLIR   G + +  +  GS 
Sbjct: 124 FRQSIPTSWVEITITEGRNRQVRRMTANVGYPTLRLIRYRVGNWTIDGIDNGSY 177


>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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 103/246 (41%), Gaps = 21/246 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +++KP  +++  +  + ++T+   +    +     GRLD ++EGLLLLT+ G L  
Sbjct: 2   PSIIVFNKPFQVLSQFTTDEEKATLSSFIDK--ANFYPAGRLDYDSEGLLLLTDHGALQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
           ++  P  +  + Y V+  G++ ++ +  L+ G+ ++       +  +             
Sbjct: 60  LIASPQHKMPKTYLVQVEGELTKEAVEQLRVGVELKDGLTKPAEAKIASDFEPWPRHPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ + + EGKNR+++++     +   RLIR   GP+ L  +  G   E   
Sbjct: 120 RERKNIPTSWLELTITEGKNRQVRRMTAAVGFPTLRLIRTQIGPYSLTDIELGHWLE--- 176

Query: 239 KILREQLGPHL--LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           K + E L   L   E+ +        SS    R             +  ++  + + G  
Sbjct: 177 KPIDEMLAMELEKFEKNRARQKPRGTSSNNRRRSHSAKNKLSRSPVSNGQRKKTGQAGTQ 236

Query: 297 KQKKLA 302
             ++  
Sbjct: 237 PTRRTR 242


>gi|327393520|dbj|BAK10942.1| ribosomal large subunit pseudouridine synthase E RluE [Pantoea
           ananatis AJ13355]
          Length = 219

 Score =  184 bits (469), Expect = 1e-44,   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|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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 51/181 (28%), Positives = 86/181 (47%), Gaps = 17/181 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   SD  GR T+ D +P     + + GRLD ++EGL++LTNDG L   L
Sbjct: 30  VVLFNKPFDVLPQFSDEAGRRTLKDYIPH--PGIYAAGRLDRDSEGLMVLTNDGALQAQL 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  +VY V+  G   +  L  L+ G+ ++        V                 
Sbjct: 88  TQPGKRTGKVYFVQVEGCPQESDLLPLRDGVNLKDGPTLPAVVERVAAPGWLWDRQPPIR 147

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +     W+ + L EG+NR+++++     +   RLIR S G   L  L  G  R++S +
Sbjct: 148 ERKAIPTCWLKITLYEGRNRQVRRMTAHIGYPTLRLIRFSMGNLGLRALAPGEWRDISHE 207

Query: 240 I 240
           I
Sbjct: 208 I 208


>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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 100/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D DGR      +  +F  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|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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 84/177 (47%), Gaps = 21/177 (11%)

Query: 75  LWLYHKPIGLVTTHSDP----DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L L++KP  ++   +D     D R T+ D +        + GRLD ++EGLLLLTNDG L
Sbjct: 4   LLLFNKPFNVLCQFTDEPEFKDQRQTLADFI--NQPGFYAAGRLDRDSEGLLLLTNDGKL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------ 178
            + +  P  +  + Y V+  G ++++ +  L++G+ ++       +              
Sbjct: 62  QQHIANPKHKQPKTYLVQVEGDINKEAIKQLQQGVTLKDGLTRPAKARKIPEPKWLWPRN 121

Query: 179 ---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
               + +    +WV + + EGKNR+++++     +   RLIR   G +QL  L  G 
Sbjct: 122 PPIRERKNIPTSWVELIITEGKNRQVRRMTAAVGFPTLRLIRTQIGDYQLKNLQPGE 178


>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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 49/177 (27%), Positives = 85/177 (48%), Gaps = 17/177 (9%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +++KP  ++   +D  GR T+ + +P   S V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   IIFNKPFDVLPQFTDEQGRETLKNYIP--VSDVYAAGRLDRDSEGLLVLTNDGKLQAELT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTLD 180
            P  +  +VY  +  G  D+  L   ++G+ +                           +
Sbjct: 60  QPQKKTGKVYYAQVEGVPDETALAKFRQGLTLNDGPTLPAGIERVDEPEWLWVRNPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +    +W+ + L EG+NR+++++     +   RLIR S G F L  L +G  +EV+
Sbjct: 120 RKNIPTSWLKITLYEGRNRQVRRMTANIGFPTLRLIRYSMGSFTLNNLSSGEWKEVT 176


>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 =  184 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 46/178 (25%), Positives = 81/178 (45%), Gaps = 19/178 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L L++KP G++   +D      R T+   +      V   GRLD+++EGLLLLT+DG L 
Sbjct: 3   LILFNKPYGVLCQFTDESTGPPRPTLAAFIKR--PGVYPAGRLDLDSEGLLLLTDDGRLQ 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|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 =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 46/186 (24%), Positives = 88/186 (47%), Gaps = 20/186 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL L++KP G+++  +D       R+T+ D++      V   GRLD ++EGLLLLT+DG 
Sbjct: 3   RLILFNKPYGVLSQFTDKGMADSKRATLSDHID--LPGVYPAGRLDRDSEGLLLLTDDGK 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  ++Y V+     D   +  L +G+ ++       +V+           
Sbjct: 61  LQERIASPRFKTEKIYLVQVERIPDDAAIEALCRGVTLKDGPTRPARVSRIAPPDLWERD 120

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   + W+++ + EG+NR+++++         RL+R   G + L  L  G+ R+
Sbjct: 121 PPVRFRKSVPDCWLSITISEGRNRQVRRMTAHVGHPTLRLVRWRIGAWSLDGLAPGTWRD 180

Query: 236 VSKKIL 241
              + L
Sbjct: 181 APPETL 186


>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 =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 52/178 (29%), Positives = 87/178 (48%), Gaps = 17/178 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ L++KP  ++   +D  GR+T+ + +P  F+ V + GRLD ++EGLL+LTNDG L 
Sbjct: 28  PRRVILFNKPFDVLPQFTDEAGRATLKEFIP--FNDVYAAGRLDRDSEGLLVLTNDGKLQ 85

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  +VY V+  G    D +  L+ G+ ++        V L            
Sbjct: 86  AQLTQPGKRTGKVYYVQVEGAPQDDDVAPLRAGVTLKDGPTLPAGVELVDEPTWLWPRHP 145

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              + +     W+ + L EG+NR+++++     +   RLIR S G   LG L  G  +
Sbjct: 146 PIRERKAIPTRWLKITLYEGRNRQVRRMTAHIGFPTLRLIRYSMGELALGELQPGEWK 203


>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 =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 46/178 (25%), Positives = 80/178 (44%), Gaps = 19/178 (10%)

Query: 75  LWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L L++KP G++   SD      R T+   +          GRLD+++EGLLLLT+DG L 
Sbjct: 3   LILFNKPYGVLCQFSDERTGPPRPTLAAYIDR--PGFYPAGRLDLDSEGLLLLTDDGRLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G  D+  L  L+ G+ ++       QV              
Sbjct: 61  ARIADPRFKMPKTYLVQVEGDPDEAALAALRHGVRLKDGPTLPAQVERIEAPALWPRDPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               +   + W+ + +REG+NR+++++         RL+R   G + L  +  G  R+
Sbjct: 121 VRFRKSVPDRWLRLTIREGRNRQVRRMTAAIGHPTLRLVRWRIGDWTLDGIPQGQWRD 178


>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 =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 58/186 (31%), Positives = 93/186 (50%), Gaps = 17/186 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R   ++KP G++T  +D +GR T+   +P    RV  VGRLD ++EGLLLLT+DG L   
Sbjct: 29  RYLKFYKPYGVLTQFTDREGRPTLQSFIP--VPRVYPVGRLDRDSEGLLLLTDDGRLNAR 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 KILREQ 244
             L + 
Sbjct: 207 VELAQL 212


>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 =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 66/233 (28%), Positives = 116/233 (49%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K IA     SR EV+  + ++ +KVNGI+L +       +D++EVD V ++  
Sbjct: 1   MAQIRIEKFIADLTGLSRNEVKAKLKKKAIKVNGIVLSKLIKIDPESDYVEVDNVVVKY- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+ + ++++KP   V  +SDP   +T+FD +     +  S GRLD +TEGLL+L+NDG +
Sbjct: 60  EKFQYYMFNKPANFVCANSDP-NEATIFDIVGLPNKKFFSFGRLDKDTEGLLILSNDGEM 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V+   +++ D L    + I I       +    + +        
Sbjct: 119 CHKLLSPKNHIPKKYYVKVDKKINSDVLLN-NRPIKISD---DFIVSKYELEPIDEKSCF 174

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILR 242
           + + EGK  ++K++F  F   V  L R+ +G  +L   L  G  R++S+  + 
Sbjct: 175 LTIYEGKFHQVKRMFGAFGISVLYLKRVQFGNLKLDNSLKLGEIRKLSELEVE 227


>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 =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 50/182 (27%), Positives = 88/182 (48%), Gaps = 17/182 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +   + L++KP  ++   +D  GRST+ D +P   + V + GRLD ++EGLL+LTND
Sbjct: 34  KERQPKTVILFNKPYDVLPQFTDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLLVLTND 91

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G+   + L  L+ G+ +         V L        
Sbjct: 92  GALQAKLTQPGKRTGKIYYVQVEGEPTPEALTALRDGVPLNDGPTLPAGVELVEEPVWLW 151

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G + L  L  G 
Sbjct: 152 PRNPPIRERKSIPTRWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGGYTLDGLANGD 211

Query: 233 TR 234
            R
Sbjct: 212 WR 213


>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 =  184 bits (468), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D DGR      + 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|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 =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 65/225 (28%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D DGR      + 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|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 =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ V+VN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVRVNNTIAK-LGDKVTLGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D DGR      + 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|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 =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 45/182 (24%), Positives = 89/182 (48%), Gaps = 16/182 (8%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +A+   + L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLLLLTNDG
Sbjct: 52  RAKDPIIVLFNKPFDVLCQFTDEQGRQTLKDYIP--IPDVYAAGRLDRDSEGLLLLTNDG 109

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   +  P  +  + Y  +  G+ ++  ++ L+ G+ ++       +V +         
Sbjct: 110 KLQSKITEPKKKTFKTYWAQVEGEPNEADVDKLRHGVELKDGMTLPAKVMIMTQPDVWPR 169

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +     W+ + + EG+NR+++++     +   RLIR   G + L  L +G  +
Sbjct: 170 TPPIRERKGIPTTWLEIQICEGRNRQVRRMTANIGFPTLRLIRYKIGQWSLNDLQSGEYQ 229

Query: 235 EV 236
            +
Sbjct: 230 RI 231


>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 =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 87/179 (48%), Gaps = 19/179 (10%)

Query: 74  RLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R+ L++KP G+++  +D   P  R T+   +      V   GRLD ++EGLL+LT+DG L
Sbjct: 3   RVILFNKPFGVLSQFTDAKSPTPRPTLSAFID--VPGVYPAGRLDRDSEGLLVLTDDGKL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G+  +  L+LL+ G+ ++       ++ L           
Sbjct: 61  QARIAAPKNKMSKTYFVQVEGEPTEKDLSLLRDGVTLKDGPTRPAKLRLIDPPQLWDRDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                +   + W+ + + EG+NR+++++     +   RL+R   G + L  + +G+  E
Sbjct: 121 PVRFRKSVPDTWIEITISEGRNRQVRRMTAHIGFPTLRLVRWRIGNWTLDGIESGTWIE 179


>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 =  184 bits (467), Expect = 2e-44,   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   LILFNKPFQVMCQFSPHPTRASLADYLD--IPDIYPAGRLDADSEGLLLLTDDGKLQHAI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y  +  G    + L  L+  + +        +V                 
Sbjct: 61  SHPDHKQTKTYLAQVEGIPHTEALARLRAPLNLGDFITQGCEVKRVQEPDWLWPRNPPIR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--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|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 =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 46/178 (25%), Positives = 85/178 (47%), Gaps = 16/178 (8%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L L +KP G++   S+     T+   +P   + V   GRLD ++EGLLLLT DG L  
Sbjct: 25  PQLILLNKPYGVICQFSEHPTHPTLKSCVPQ--AGVYPAGRLDTDSEGLLLLTGDGALQH 82

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            +  P  +  + Y V+  G   +++L +L++G+ +        +V               
Sbjct: 83  RIADPRWKLPKTYWVQVEGDPKEEQLEMLRRGVDLGDFVTRPAEVRRIETPELWPRNPPV 142

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              +   + W+ + + EGKNR+++++         RL+R++ GP++L  L  G  R +
Sbjct: 143 RFRKTVPDCWLEIIISEGKNRQVRRMTAKAGLPTLRLVRVAIGPWKLDGLQPGEMRAI 200


>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 =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 50/184 (27%), Positives = 84/184 (45%), Gaps = 17/184 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P  + E TRL  +HKP G+++  +       + D + +    V   GRLD ++EGLLLL
Sbjct: 33  QPAPRPEVTRLLCFHKPYGVLSQFTPEGKWQGLKDWIDA--PGVYVAGRLDADSEGLLLL 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|303275424|ref|XP_003057006.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226461358|gb|EEH58651.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 305

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 13/243 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P+R+ ++++R G  +R E +R     RV ++G  + RA   V   D + +DG P    +
Sbjct: 53  APERLDRLLSRLGYCTRAEAKRWARDGRVLLHGEPVARAEAKVTPRD-VLIDGEPAEAPD 111

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTND 127
              L L HKP G V  H   +G  +V+D LP  +         +GRLD +T GLLLLT+D
Sbjct: 112 GL-LALMHKPRGRVCGHDASEG-PSVYDLLPERWRARRPGVETIGRLDKDTTGLLLLTDD 169

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTL---DTQK 183
           G L   L  P  +  +VY +     + +D ++L   G + + G     +   L   +   
Sbjct: 170 GDLLHRLASPKKRVEKVYELVVDAPIPRDAVDLFASGSLTLTGEKKPCLPAKLIVSERAD 229

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKIL 241
            +    ++ + EGK  ++K++      +V  L R S+G   L    L  G  R +S++  
Sbjct: 230 HNRTRASLSVTEGKFHQVKRMMRAVGCEVTALHRESFGGMALSRMELREGEVRVLSRETA 289

Query: 242 REQ 244
            E 
Sbjct: 290 LEL 292


>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 =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 50/187 (26%), Positives = 86/187 (45%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
             +   +  R+ L++KP  ++   +D  GR+T+   +P  F+ V + GRLD ++EGLL+L
Sbjct: 16  KHVAAQDLYRVVLFNKPFDVLPQFTDAAGRTTLKAFIP--FTDVYAAGRLDRDSEGLLVL 73

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
            N+G L   L  P  +  +VY V+  G      L  L+ G+ ++        V       
Sbjct: 74  NNEGKLQAQLTQPGKRIGKVYFVQVEGVPQDRDLTPLRHGVTLKDGPTLPAIVERVDEPQ 133

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +     W+ + L EG+NR+I+++     +   RLIR S G   LG L 
Sbjct: 134 WLWPRNPPIRERKSIPTTWLKITLFEGRNRQIRRMTAHIGFPTLRLIRYSMGNLSLGELQ 193

Query: 230 AGSTREV 236
            G  + +
Sbjct: 194 PGEWKNL 200


>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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 62/217 (28%), Positives = 102/217 (47%), Gaps = 9/217 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             T  R+ + I++    S  +   +IAQ+R+ V+G +       V    ++E+DG  L+ 
Sbjct: 29  KSTTNRLDRFISQNSTFSISDTRLLIAQKRILVDGHVAHSNQQKVTKFTYVELDGNCLQ- 87

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
                  + +KP G+V+   D    STV D +       +  VGRLD NT GL+LLTNDG
Sbjct: 88  DNNPVYIVLNKPKGVVSATKDIKH-STVLDLIQHSQKNELHIVGRLDFNTTGLVLLTNDG 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN 186
             +R + LP T+  +VY V     +  + + + ++GI    + I      + +     S 
Sbjct: 147 AWSRKISLPETKLAKVYEVTLSKPLSDEYITVFREGIYFGYEDITTKPACLEIL----SE 202

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
               + L EGK  ++K++F FF  K    I   +G F
Sbjct: 203 YTARLSLVEGKYHQVKRMFGFFKTKCWNFIEFLWGIF 239


>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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 49/175 (28%), 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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  + Y V+  G    ++L  L+ G+V+        QV +  Q            
Sbjct: 62  TDPRHKQPKTYWVQVEGAPQPEQLQALRDGVVLNDGPTRPAQVRMLDQAPQLWPRDPPVR 121

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDALAPGQWR 176


>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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 80/187 (42%), Gaps = 21/187 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++KP  ++   +D       RST+ D +      V   GRLD ++EGL+LLT++G L
Sbjct: 8   FIRFNKPFDVLPQFTDRQNTDSPRSTLSDFID--LPGVYPAGRLDRDSEGLMLLTDNGRL 65

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              +  P  +  + Y V+  G  D   +  L+ G+ +        +  L           
Sbjct: 66  QSHISDPKHKMPKTYWVQVEGIPDAAAIRALRDGVELNDGMTRPAKARLIDEPEGLWPRT 125

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +   + W+ + LREG+NR+++++         RLIR   G + L  L  GS   
Sbjct: 126 PPIRERKTVPDCWLELTLREGRNRQVRRMTAAVGHPTLRLIRARIGDWTLDDLAPGSWDS 185

Query: 236 VSKKILR 242
           +   +L 
Sbjct: 186 LPMPVLE 192


>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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 47/179 (26%), Positives = 79/179 (44%), Gaps = 20/179 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL L++KP  +++  +D       R+T+ D +     RV   GRLD ++EGLLLLT+DG 
Sbjct: 3   RLILFNKPYDVLSQFTDRGSEGSPRATLSDFID--IPRVYPAGRLDRDSEGLLLLTDDGQ 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y  +  G  D   L  L+ G+ +        +V            
Sbjct: 61  LQARIANPRFKTEKTYYAQVEGLPDDTALAALRAGVTLSDGPTRPARVERTEPPTLWPRT 120

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 +   + W+ + + EG+NR+++++         RLIR   G + L  L  G  R
Sbjct: 121 PPVRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTLRLIRWRIGDWTLDGLGPGEWR 179


>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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/218 (27%), Positives = 96/218 (44%), Gaps = 20/218 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLE-RAAVNVMS-TDHIEVDGVPLRKAERTR----LWLYHK 80
           SRRE +++I   RV VN I ++ +    V+   D I +DG+P+              Y K
Sbjct: 1   SRREADKLIEAGRVSVNDIPVKSKGGFKVVPFHDKITLDGIPVTGTSDATINFDYVKYWK 60

Query: 81  PIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           P+G+  T +D      + D L         R+  VGRLD  T GL+LLT+DG +   +  
Sbjct: 61  PVGVTCT-TDRKIAGNIIDALEEAGFDSSKRIFPVGRLDKETSGLILLTSDGRVPNAVLR 119

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDMQVT---LDTQKGSNA 187
              +  ++Y+V     V    +  L+ G++I       G     +         Q     
Sbjct: 120 GRHKQPKIYQVWVDRPVLAKDVAQLRDGVIITTVAQRDGNRAEPLTARTKSCAVQVLGRE 179

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            + + L EG+NR+I+K+    N+ V RL R+ +    L
Sbjct: 180 KLQLTLVEGRNRQIRKMLGALNYTVKRLHRVQFMELTL 217


>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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 84/188 (44%), Gaps = 17/188 (9%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            V   P  +   TRL  +HKP G+++  +       + D +      V   GRLD ++EG
Sbjct: 29  TVVRQPAPRPGVTRLLCFHKPYGVLSQFTPEGKWQGLKDWID--VPGVYVAGRLDADSEG 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|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 =  183 bits (466), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 48/182 (26%), Positives = 85/182 (46%), Gaps = 19/182 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL L++KP  +++  +D      R T+ D +     RV   GRLD ++EGLLLLT+DG L
Sbjct: 3   RLILFNKPYDVLSQFTDSSIGADRRTLSDFID--VPRVYPAGRLDRDSEGLLLLTDDGRL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G V  D L  L+ G+ ++       +              
Sbjct: 61  QARISNPRFKTPKTYLVQVEGDVTSDALACLRAGVSLKDGPTLPAEAERIDPPALWPRDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   + W+++ +REG+NR+++++         RL+R   G + L  +  G+ R+ 
Sbjct: 121 PVRFRKTVPDCWISLTIREGRNRQVRRMTAAVGHPTLRLVRWRIGDWTLDGVAPGTWRDA 180

Query: 237 SK 238
           S 
Sbjct: 181 SP 182


>gi|312148012|gb|ADQ30671.1| hypothetical RNA pseudouridine synthase [Borrelia burgdorferi JD1]
          Length = 249

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ V+VN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVRVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D DGR      + 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|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 =  183 bits (465), Expect = 4e-44,   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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           +  P  +  + Y  +  G +  + +  L+ G+ ++       +                 
Sbjct: 61  MMNPRFKTPKTYLAQVEGDITDEAIRRLESGLQLKDGPTLPAKARRVSEPAWLWPRQPPI 120

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 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|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 =  183 bits (465), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 47/185 (25%), Positives = 85/185 (45%), Gaps = 23/185 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRS-------TVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            RL L++KP G+++  +D  G         T+ D +      V   GRLD ++EGLL+LT
Sbjct: 2   PRLILFNKPYGVLSQFTDRGGADGTGGGRATLSDYID--VPGVYPAGRLDKDSEGLLVLT 59

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           +DG L   +  P  +  + Y  +  G+ D   L+ L +G+ +         V        
Sbjct: 60  DDGALQARISSPKHKMPKTYLAQVEGEPDDAALDALARGVTLNDGPTRPATVRRIGAPKL 119

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                     +   ++W+ + + EG+NR+++++         RL+R   G +++G L  G
Sbjct: 120 WDRDPPVRYRKSVPDSWLELTITEGRNRQVRRMTAAVGHPTLRLVRWRIGGWEIGDLAVG 179

Query: 232 STREV 236
           + REV
Sbjct: 180 AWREV 184


>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 =  183 bits (465), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 51/195 (26%), Positives = 85/195 (43%), Gaps = 29/195 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +  L++KP  ++   +D  G    R T+ D +      V SVGRLD+++EGLLLLT++G
Sbjct: 2   YKYILFYKPYNVLCQFTDNSGDKTNRQTLKDFID--IPHVYSVGRLDLDSEGLLLLTDNG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   L        R Y V+     D+  LN L++G+ I+        V           
Sbjct: 60  PLQHRLGHRQFAHPRTYWVQVENIPDEAALNRLREGVKIEDYWTRKASVIKLPTEPVLPP 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP--------FQL 225
                   +     W+ + L EG+NR+++++     +   RL+R++ G           L
Sbjct: 120 RNPPIRYRKSIPTCWLEITLTEGRNRQVRRMTAAVGYPTLRLVRVAMGIGKGKNEFQLGL 179

Query: 226 GTLLAGSTREVSKKI 240
             L  G  REV++  
Sbjct: 180 EGLEPGQWREVTEIE 194


>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 =  183 bits (465), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 50/185 (27%), Positives = 92/185 (49%), Gaps = 17/185 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           + +   ++ +++KP  ++   +D  GR T+ + +P   S V + GRLD ++EGLL+LTND
Sbjct: 39  KPSTPRKVIIFNKPFDVLPQFTDEQGRETLKNYIP--ISDVYAAGRLDRDSEGLLVLTND 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|261821431|ref|YP_003259537.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
 gi|261605444|gb|ACX87930.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 209

 Score =  183 bits (465), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 47/190 (24%), Positives = 87/190 (45%), Gaps = 17/190 (8%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           G         R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++
Sbjct: 21  GKRQPDNAPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIP--ISGIYAAGRLDRDSEGLMI 78

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
           LTNDG L   L  P+ +  ++Y V+  G  D+  L   + G+ +           +    
Sbjct: 79  LTNDGKLQARLTQPTEKTAKIYYVQVEGIPDEAALTHFRTGLELNDGKTLPAGAEIVPEP 138

Query: 180 -----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      + +   + W+ + L EG+NR+++++     +   RLIR       +  L
Sbjct: 139 DWLWPRNPPIRERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENL 198

Query: 229 LAGSTREVSK 238
           L G  +E++ 
Sbjct: 199 LPGEWKEITD 208


>gi|329297161|ref|ZP_08254497.1| 23S rRNA pseudouridine synthase E [Plautia stali symbiont]
          Length = 222

 Score =  183 bits (465), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 53/187 (28%), Positives = 90/187 (48%), Gaps = 17/187 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R     R+ L++KP  ++   SD  GR T+ D +P   S V + GRLD ++EGL++LTND
Sbjct: 37  RSKGPRRVILFNKPFDVLPQFSDEAGRRTLKDFVP--VSEVYAAGRLDRDSEGLMILTND 94

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------------ 175
           G L   L  P  +  ++Y V+  G   +  L+ L++GI +                    
Sbjct: 95  GALQAQLTQPGKRTGKIYYVQVEGVPQESDLSRLRRGIPLNDGPTLPAGAEVVPEPAWLW 154

Query: 176 ---QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +     W+ + L EG+NR+++++     +   RLIR + G +QL  L  G 
Sbjct: 155 PRTPPIRERKAIPTCWLKITLYEGRNRQVRRMTAHIGFPTLRLIRFAMGDYQLQDLAPGE 214

Query: 233 TREVSKK 239
            R++S +
Sbjct: 215 WRDISDQ 221


>gi|326692342|ref|ZP_08229347.1| ribosomal large subunit pseudouridine synthase E [Leuconostoc
           argentinum KCTC 3773]
          Length = 177

 Score =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 83/175 (47%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D DGR T+ D +     RV + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IVLFNKPYNVLTKFTDADGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHAL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G   + +L  L+ G+ ++       +                  
Sbjct: 60  TDPENKAYKTYVVQVEGVPTKAQLKQLENGVELKDGWTLPAKAKRIPYPKWLWPRENPIR 119

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +    +++ + ++EG+NR+++++         RLIR   G + L  L  G  R
Sbjct: 120 VRKNQPTSFIQLKIKEGRNRQVRRMTAAVGLPTLRLIRTHIGDYHLADLKPGEYR 174


>gi|213620819|ref|ZP_03373602.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 165

 Score =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 46/165 (27%), Positives = 76/165 (46%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +  P     + Y V     V  D      KG+ +          T
Sbjct: 121 ITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPAT 165


>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 =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 83/179 (46%), Gaps = 19/179 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L  ++KP  ++   +D +   R T+      +   V   GRLD ++EGLLLLT+DG LA 
Sbjct: 2   LIAFNKPFNVLCQFTDRNASPRRTLAGF--GLPGGVYVAGRLDYDSEGLLLLTDDGALAH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P  +  + Y V+  G    ++L  L  G+ +        QV+              
Sbjct: 60  RLTDPRHKQPKTYWVQVEGVPQPEQLQRLGDGVALNDGPTAPAQVSRLDAAPALWPRDPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   +AW+ + LREG+NR+++++         RL+R++ G  +L  L  GS R +
Sbjct: 120 VRFRKTVPDAWLQIVLREGRNRQVRRMTAAVGLPTLRLVRVAMGTHRLDGLAPGSWRAL 178


>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 =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 50/181 (27%), Positives = 88/181 (48%), Gaps = 18/181 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            RL L +KP  +++  +D  +GR+T+   +P     V   GRLD ++EGLLLLT++G L 
Sbjct: 2   PRLILLNKPYDVLSQFTDRAEGRATLASLVP--IPGVYVCGRLDRDSEGLLLLTDNGPLQ 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|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 =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 99/241 (41%), Gaps = 16/241 (6%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++     R++K ++ AG+ SRRE +  I    V VNG ++      V  TD ++ DG  +
Sbjct: 17  EKPSETVRLNKFLSNAGLCSRREADSHIEMGLVHVNGKIITEMGYQVKPTDEVKFDGARV 76

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTN 126
           ++       L +KP G V T        +V D + S     V +VG +     GLL  TN
Sbjct: 77  QQT-PPVYLLLNKPKGFVATSQGGKIVKSVQDLIRSAVKTPVPAVGDMGRPMTGLLFFTN 135

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-LDTQKGS 185
           D  + R     S     +Y+V     V  D +  LK+G ++        +V+ +D +   
Sbjct: 136 D-EVLRKKLNNSKSIPMIYQVLLDKNVTTDMMRQLKEGQMVFEKMQKINEVSHMDGKSKK 194

Query: 186 NAWVTVGLREGKNR-----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
              + V              I K+F     KV  L RI+Y       L  G+ R ++ K 
Sbjct: 195 EVGIEV-------HSLSPAIIVKLFAAVGCKVVLLDRITYAGLTKKELPRGNWRRLNTKE 247

Query: 241 L 241
           +
Sbjct: 248 V 248


>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 =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 63/225 (28%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ ++VN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLIRVNNTIAK-LGDKVTLGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D DGR      + 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|261856640|ref|YP_003263923.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837109|gb|ACX96876.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
          Length = 180

 Score =  183 bits (464), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 81/176 (46%), Gaps = 19/176 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L  ++KP  +++  +   G +  T+ D +      V + GRLD ++EGLLLLT+DG L  
Sbjct: 2   LIAFNKPFDVLSQFTVEPGSAAGTLADYIDQ--PNVYAAGRLDRDSEGLLLLTDDGRLQA 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P  +  + Y  +  G V    L  L+ G+V++       +  +             
Sbjct: 60  QLTQPDAKQPKTYLAQVDGDVTAQALAQLRAGVVLKDGKTRPAEAHVVPEPDWLWPRTPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
               +    +W+ + + EGKNR+++++     +   RLIR++ G   LG+L  G  
Sbjct: 120 IRVRKNIPTSWIELTITEGKNRQVRRMTAAVGFPTLRLIRVAVGSHNLGSLQPGQW 175


>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 =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 85/180 (47%), Gaps = 21/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L++KP G+++  +D       R T+   +          GRLD ++EGL++LT+DG 
Sbjct: 3   RVILFNKPYGVLSQFTDKGSEGSPRPTLSAYIDQ--PGFYPAGRLDRDSEGLMVLTDDGK 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V+  G  +  +L +L+ G+ ++       + TL          
Sbjct: 61  LQARISNPKHKMAKTYLVQVEGTPEPQQLEVLRAGVRLKDGMTKPAKATLACPPENLWER 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   ++W+ + + EG+NR+++++         RLIR+  G + L  L+ G+ R
Sbjct: 121 TPPVRYRKTVPDSWLQISISEGRNRQVRRMTAHVGLPCLRLIRMRVGDWALNDLVPGAWR 180


>gi|89092944|ref|ZP_01165896.1| RsuA protein [Oceanospirillum sp. MED92]
 gi|89082969|gb|EAR62189.1| RsuA protein [Oceanospirillum sp. MED92]
          Length = 223

 Score =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 98/239 (41%), Gaps = 31/239 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP  ++T  +  D + T+ D +        + GRLD ++EGLL+LTNDG    
Sbjct: 2   PSILLFNKPFQVLTQFTTDDDKQTLADYIE--LPDYYAAGRLDYDSEGLLILTNDGPTQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------------- 178
            L  P  +  + Y  +  G+V ++ L  L  G+ ++       +                
Sbjct: 60  YLANPQFKMEKTYWAQVEGEVTEEALETLSSGVELKDGMTRPAKAKKINEPAIWQRTPPI 119

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +    +W+ + + EGKNR+++++     +   RL+R + G + L  L  G       
Sbjct: 120 RERKNIPTSWIELKITEGKNRQVRRMTAAVGFPTLRLVRYAIGEWTLDNLKPGQ------ 173

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
                     L+E           +  T  R       E P + +R K+++ +  G ++
Sbjct: 174 --------SSLIESDIKIPKRKPKNRSTTARSLSGKRKERPGE-SRQKRSAPKNKGYNR 223


>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 =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 54/193 (27%), Positives = 88/193 (45%), Gaps = 18/193 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  +  +L L++KP G++T  +      T+   +   F    + GRLD  +EGLL+LT+D
Sbjct: 16  RNHKMPQLILFNKPYGVLTQFTGELPEQTLSAFIK--FPGFYAAGRLDKQSEGLLVLTDD 73

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L        
Sbjct: 74  GKLQHRLTHPKFEKKKHYWVQVEGAPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWP 133

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + LREGKN +I+K+     +   RLIR   G ++L  L  G  
Sbjct: 134 RIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRHQIGDWRLDQLQPGEY 193

Query: 234 R--EVSKKILREQ 244
           +   ++   L E 
Sbjct: 194 KLINLTNDKLNEL 206


>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 =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 88/232 (37%), Positives = 130/232 (56%), Gaps = 8/232 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILL----ERAAVNVMSTDHIEVDGVPLRK 69
           +++ K+++  G+ SRR +E+ I  + +K+NG ++         N+ S    +       K
Sbjct: 3   EKIQKILSNCGVDSRRNIEKHILNKSLKINGKIVHIGERFLKKNIKSIFLKKK--KIFIK 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDG 128
            E+T++ +YHKP+G + T  D   R TVF  LP   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-LLAGSTREVSKK 239
             V L +GKNRE++ ++   N KVNRLIRI +G   L   L +G   E+S +
Sbjct: 181 FKVSLFQGKNREVRLLWNAINIKVNRLIRIKFGIITLPKFLKSGCFFELSYQ 232


>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 =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 50/183 (27%), Positives = 89/183 (48%), Gaps = 17/183 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R+ +++KP  ++   SD  GRST+ D +P   + V + GRLD ++EGL++LTNDG L 
Sbjct: 27  PRRVIIFNKPFDVLPQFSDEAGRSTLKDFIP--VAGVYAAGRLDRDSEGLMVLTNDGALQ 84

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------ 179
             L  P  +  ++Y V+  G  D   +  L+ G+ ++          L            
Sbjct: 85  ATLTQPGKRTGKIYYVQVEGIPDISHIQALRDGVNLKDGPTLPAGAELVAEPEWLWPRNP 144

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + +    +W+ + L EG+NR+++++     +   RLIR + G   L  L  G  R+V
Sbjct: 145 PIRERKAIPTSWLKITLYEGRNRQVRRMTAQIGFPTLRLIRFAMGTQMLQDLPPGEWRDV 204

Query: 237 SKK 239
           + +
Sbjct: 205 TAE 207


>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 =  182 bits (463), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 81/180 (45%), Gaps = 21/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L++KP G+++  +D       R T+   +          GRLD ++EGL++LT+ G 
Sbjct: 3   RVILFNKPFGVLSQFTDKGTEGSPRPTLSAYIDE--KGFYPAGRLDRDSEGLMVLTDSGP 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|253995971|ref|YP_003048035.1| pseudouridine synthase [Methylotenera mobilis JLW8]
 gi|253982650|gb|ACT47508.1| pseudouridine synthase [Methylotenera mobilis JLW8]
          Length = 184

 Score =  182 bits (463), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 45/184 (24%), Positives = 85/184 (46%), Gaps = 23/184 (12%)

Query: 75  LWLYHKPIGLVTTHSDPD------GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + L++KP  +V   S  D        +T+ D +P     V + GRLD ++EGLL+LT+DG
Sbjct: 2   IILFNKPFNVVCQFSPHDSPNPDNRHATLKDFIP--IPDVYAAGRLDTDSEGLLILTDDG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P  + ++ Y V+  G    + L  L+ G+ +        +V++         
Sbjct: 60  ALQHRLSHPKHKEIKTYWVQVEGAPSDEALQPLRVGVDLGDFITQPAEVSVMNEPAGIWL 119

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + + EGKNR+++++     +   RLIR + G + L  +  G  
Sbjct: 120 RNPPIRERKAIPTTWLQIKISEGKNRQVRRMTAKVGFPTLRLIRYAIGRYTLDGIANGEY 179

Query: 234 REVS 237
           + ++
Sbjct: 180 KVLT 183


>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 =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 42/180 (23%), Positives = 84/180 (46%), Gaps = 21/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L++KP G+++  +D       R T+   + +        GRLD ++EGL++LT+DG 
Sbjct: 3   RVILFNKPFGVLSQFTDKGSEGSPRPTLSAFIDA--PGFYPAGRLDRDSEGLMVLTDDGK 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y  +  G  +   +  L+ G+ ++       QV++          
Sbjct: 61  LQARISNPKHKMTKTYLAQIEGTPEPQHIEALRAGVRLKDGMTRPAQVSVATPPDTLWER 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   +AW+ + + EG+NR+++++         RLIR+  G + L  L+ G+ R
Sbjct: 121 SPPVRFRKTVPDAWLQISISEGRNRQVRRMCAHVGLPCLRLIRMRIGDWALNDLVPGAWR 180


>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 =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 85/179 (47%), Gaps = 19/179 (10%)

Query: 74  RLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           R+ L++KP G+++  +D   P  R T+   +      V   GRLD ++EGLL+LT+DG L
Sbjct: 3   RVILFNKPFGVLSQFTDTRSPTERPTLSRYVD--VPAVYPAGRLDRDSEGLLVLTDDGRL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  +VY  +  G  D D L  L++G+ ++          L           
Sbjct: 61  QARIASPKARTEKVYLAQVEGDPDDDALAPLRRGLELKDGPTRPAVARLIEPPALWERDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                +   + WV V + EG+NR+++++     + V RL+R   G + L  L  G+ R+
Sbjct: 121 PVRFRKSVPDRWVEVTITEGRNRQVRRMCAAIGFPVLRLVRWRVGDWTLEGLAPGAWRD 179


>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 =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 44/184 (23%), Positives = 84/184 (45%), Gaps = 16/184 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P   ++  ++ L++KP  ++   +D   R T+ + +P     V + GRLD ++EGLLLL
Sbjct: 39  KPQIASKDRKIVLFNKPFDVLCQFTDDADRKTLAEFIP--IKEVYAAGRLDRDSEGLLLL 96

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TN G L   L  P  +  + Y  +  G+   + +N L  G+ ++        V +     
Sbjct: 97  TNCGKLQNSLTAPDKKTNKTYWAQVEGEPTSESINDLCNGVELKDGLTLPANVKIIDEPT 156

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    + +     W+++ + EG+NR+++++         RLIR S G + L  +  
Sbjct: 157 IWARNPPVRERKAIPTTWLSITINEGRNRQVRRMTAHIGHPTLRLIRYSIGNYTLDDINC 216

Query: 231 GSTR 234
           G  +
Sbjct: 217 GEYK 220


>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 =  182 bits (462), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 53/193 (27%), Positives = 86/193 (44%), Gaps = 18/193 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R  +  +L L++KP G++T  +      T+   +        + GRLD  +EGLL+LT+D
Sbjct: 19  RNHKMPQLILFNKPYGILTQFTGELPEQTLSAFIK--LPGFYAAGRLDKQSEGLLILTDD 76

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L        
Sbjct: 77  GKLQHRLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKIWP 136

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +     W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  
Sbjct: 137 RIPPIRERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEY 196

Query: 234 R--EVSKKILREQ 244
           +   ++   L E 
Sbjct: 197 KLINLTNDKLNEL 209


>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 =  182 bits (462), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 53/188 (28%), Positives = 85/188 (45%), Gaps = 18/188 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L L++KP G++T  +      T+   +   F    + GRLD  +EGLL+LT+DG L  
Sbjct: 2   PQLILFNKPYGVLTQFTGELPEQTLSAFIK--FPGFYAAGRLDKQSEGLLILTDDGKLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L             
Sbjct: 60  RLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWPRIPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EV 236
            + +     W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  +   +
Sbjct: 120 RERKHIPTTWLGIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEYKLINL 179

Query: 237 SKKILREQ 244
           +   L E 
Sbjct: 180 TNDKLNEL 187


>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 =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 64/225 (28%), Positives = 99/225 (44%), Gaps = 10/225 (4%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--- 71
           RV   +A  G+ SRR  E +I ++ VKVN  + +     V   D I          +   
Sbjct: 8   RVHVFLAEKGVGSRRFCEELIRKKLVKVNNTIAK-LGDKVALGDRIIYKKQIFVFKDFQI 66

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   +KP   + ++ D +GR      + 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|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 =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 80/179 (44%), Gaps = 17/179 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+ G 
Sbjct: 2   KARARLIRFNKPYGVLSQFTPEGRWRGLKDFID--LPGVYVAGRLDADSEGLLLLTDSGP 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------ 177
           L   +  P  +  + Y V+  G  D   L  L++GI +        +V            
Sbjct: 60  LQARISDPRHKMEKTYWVQVEGIPDDAALAALQRGITLNDGPTRPARVHRLEPPPALCPR 119

Query: 178 ---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                  +   ++W+ + +REG+NR+++++         RL+R + GP+ L  L  G+ 
Sbjct: 120 DPPIRVRRNIPDSWIELVIREGRNRQVRRMTAAVGHPTLRLVRTAIGPYTLDGLAPGAW 178


>gi|126642165|ref|YP_001085149.1| 16S rRNA pseudouridylate 516 synthase [Acinetobacter baumannii ATCC
           17978]
          Length = 201

 Score =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 50/191 (26%), Positives = 84/191 (43%), Gaps = 8/191 (4%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTE 119
           V G   +  E+       KP G   +H  P    +VF  LP       V +VGRLD +T 
Sbjct: 17  VFGQNYQYREKI-YIALRKPQGFECSHH-PQHHQSVFSLLPETMIHRGVQAVGRLDQDTT 74

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLLLLT+DG   + L  P     +VY V  +  V  +++ +L +G+ +     G      
Sbjct: 75  GLLLLTDDGKYLQALTHPRKHVPKVYHVTTYDPVTPEQIEMLTQGVNLHQEKGGFA--AT 132

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           D        +T+ + +G   ++K++      KV +L R   G   L  +  G    +S++
Sbjct: 133 DVALLGTHQLTMTIHQGVYHQVKRMIAAVGNKVEKLHRHQIGQLVLPEIEEGGWVYLSEQ 192

Query: 240 ILREQLGPHLL 250
              +QL  +++
Sbjct: 193 E--KQLAQNII 201


>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 =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 53/188 (28%), Positives = 86/188 (45%), Gaps = 18/188 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L L++KP G++T  +      T+   +   F    + GRLD  +EGLL+LT+DG L  
Sbjct: 2   PQLILFNKPYGVLTQFTGELPEQTLSAFIK--FPGFYAAGRLDKQSEGLLVLTDDGKLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L             
Sbjct: 60  RLTHPKFEKKKHYWVQVEGAPTDKDLQPLRKGLVIKDITFLPAEAKLISEPKIWPRIPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EV 236
            + +     W+ + LREGKN +I+K+     +   RLIR   G ++L  L  G  +   +
Sbjct: 120 RERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRHQIGDWRLDQLQPGEYKLINL 179

Query: 237 SKKILREQ 244
           +   L E 
Sbjct: 180 TNDKLNEL 187


>gi|269468805|gb|EEZ80409.1| 16S rRNA uridine-516 pseudouridylate synthase [uncultured SUP05
           cluster bacterium]
          Length = 174

 Score =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 40/174 (22%), Positives = 76/174 (43%), Gaps = 19/174 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G++   S      T+ D +      +   GRLD ++EGL++LT+DG L   +
Sbjct: 2   IVLFNKPFGVLCQFSGEG--KTLSDYID--IKNIYPAGRLDKDSEGLIVLTDDGKLQHQI 57

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P     + Y V+  G +  + +  L +G+ ++       +  +               
Sbjct: 58  SHPKFDKEKTYVVQVEGSITDNAITQLCRGVALKDGMTKPAKAKIITKPSWVWDRIPPIR 117

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             Q    +W+ + + EGKNR+++++     +   RLIR   G + L  L  G  
Sbjct: 118 KRQNIPTSWIELSITEGKNRQVRRMSAHVGFPTLRLIRTEIGSWSLKRLPLGKY 171


>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 =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 81/177 (45%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G++   S  +   T+ D +      V + GRLD ++EGLL+LT+DG L   +
Sbjct: 2   LILFNKPYGVICQFSPHEKHKTLKDYI--AVPGVYAAGRLDTDSEGLLILTDDGRLQHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G    + L  L+ G+ +        +V                 
Sbjct: 60  SHPRHKEFKTYWVQVEGDPSDEALEPLRHGMDLGDFVTQPAKVRRIEEPAGLWPRHPPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + +    AW+ V + EGKNR+++++     +   RL+R + G   L  +  G  R++
Sbjct: 120 ERKAIPTAWLEVIIAEGKNRQVRRMTAKAGFPTLRLVRYAVGQHTLEGIAPGEWRQL 176


>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 =  181 bits (461), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 45/188 (23%), Positives = 88/188 (46%), Gaps = 18/188 (9%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
            ++   L   E   + L +KP G+++  ++     T+ + +      V  +GRLD ++EG
Sbjct: 14  RINNAKLTFDETIVV-LVNKPYGVLSQFTNNQACKTLKEFI--SIPNVYPIGRLDKDSEG 70

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL- 179
           LLLLTN+G +   L  P  +  + Y V+  G    + LN L  G++++       +V + 
Sbjct: 71  LLLLTNNGQIQHRLANPKFEKEKTYWVQIEGIPQPEDLNRLASGVILKDGLTKPAKVKII 130

Query: 180 --------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                         + +    +W+ + + EGKNR+++++     +   RL+R+    F+L
Sbjct: 131 PDPHFKWQSAPKIRERKNIPTSWIELKIVEGKNRQVRRMTAHIGFPTLRLVRVGVSYFKL 190

Query: 226 GTLLAGST 233
           G+L  G  
Sbjct: 191 GSLAPGEY 198


>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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 53/191 (27%), Positives = 81/191 (42%), Gaps = 19/191 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L HKP G ++  +          +L      V  VGRLD ++EGLLLL+ND  L   
Sbjct: 3   HYILLHKPFGYLSQFTPETPGQLTLADLGPFPPEVYPVGRLDQDSEGLLLLSNDSRLNVQ 62

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLD--------- 180
           L  P     R Y V+  G  D+  L  L+ G+ I    +       +  L          
Sbjct: 63  LLDPRHAHWRTYWVQVEGIPDEAALAHLRSGVEIRFNKKTYHTLPARAQLLDPQPTVAER 122

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                        W+ + L+EGKNR+++++     + V RLIR++    QLG L  G+ R
Sbjct: 123 NPPIRYRANIPETWLELSLQEGKNRQVRRMCAKVGYPVLRLIRVNIENLQLGDLAVGAWR 182

Query: 235 EVSKKILREQL 245
             ++K +   L
Sbjct: 183 ACTQKEIYTYL 193


>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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 81/180 (45%), Gaps = 21/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L++KP G+++  +D       R T+   +          GRLD ++EGL++LT+ G 
Sbjct: 3   RVILFNKPFGVLSQFTDKGTEGSPRPTLSAYIDE--KGFYPAGRLDRDSEGLMVLTDSGP 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|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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 84/176 (47%), Gaps = 17/176 (9%)

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           ++   +D  GRST+ D +    + V  +GRLD ++EGLLLLTN+G +   L  P  +  +
Sbjct: 1   MLCQFTDEAGRSTLKDFI--NVAGVYPIGRLDRDSEGLLLLTNNGDIQHRLAEPKFKMEK 58

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQKGSNAW 188
            Y V+  G  D+  L  L++G+ +        +V L               + +    AW
Sbjct: 59  TYWVQVEGVPDEIALERLRRGVELNDGMTLPAKVRLISEPNFLWPRVPPIRERKNIPTAW 118

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           + + + EG+NR+++++     +   RLIR     F L  L   + R +++  L++ 
Sbjct: 119 LEIKIYEGRNRQVRRMTAHIGFPTLRLIRYQQAGFSLQHLAPKTYRTLTQDELKQL 174


>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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 46/181 (25%), Positives = 81/181 (44%), Gaps = 21/181 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R  L++KP  +++  +D       R T+ D +      V   GRLD ++EGL++LT+DG 
Sbjct: 3   RTILFNKPFDVLSQFTDAGTAGTPRRTLSDFID--LPGVYPAGRLDRDSEGLMILTDDGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y  +  G  D   L  L++G+ ++       +V            
Sbjct: 61  LQARIAHPRYKAAKTYLAQVEGLPDHAALEALRRGVTLKDGPTRPARVRRIDVPEDLWDR 120

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   + W+ + L EG+NR+++++         RLIRI  G +QL  L  G  R
Sbjct: 121 DPPVRYRKSVPDCWIELTLTEGRNRQVRRMTAHVGHPTLRLIRIRIGDWQLDHLPPGHWR 180

Query: 235 E 235
           +
Sbjct: 181 D 181


>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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 103/241 (42%), Gaps = 24/241 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           +R+  V  R GI++ R V R++ +  V VNG  +  +   +  +TD + +DG+  +    
Sbjct: 7   ERLDTVFIRRGISTHRRVRRLLQKHNVCVNGTRVLESGFGLNLATDELSIDGIK-KNLAP 65

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLL 123
               + +K  G + +  D     TV+  +P  +          ++ +VGRLD +TEGLL+
Sbjct: 66  DIYLMMNKKSGTICSTKDDGLYKTVYSFIPQKYFYYAKENSLQKIHTVGRLDTDTEGLLI 125

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--------- 174
            T +G  +  L  P     + Y V       +++   L+K    +G              
Sbjct: 126 FTTNGDFSHSLANPLFHVKKTYYVELEKSEPEEQRKFLEKKFS-EGFFIPPEKNEREFIS 184

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGST 233
               L+    ++    + + EGK  ++K++F     KV  L RIS G   L   L  G +
Sbjct: 185 RPAILEWNSANSC--RLTITEGKFHQVKRMFSAQGNKVIFLKRISIGSLALDEKLAPGDS 242

Query: 234 R 234
           R
Sbjct: 243 R 243


>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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 47/175 (26%), 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+         V +               
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQEAQLQALRDGVVLNDGPTRPASVRMLDPAPELWPRTPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTASVGLPTLRLVRVAIGDWRLDGLAPGQWR 176


>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 =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 65/305 (21%), Positives = 119/305 (39%), Gaps = 70/305 (22%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER- 72
           R++K+I+     SRR+ ++ I    VK+N  +++    ++    D I++ G  +   +  
Sbjct: 23  RLNKIISLEKKMSRRKSDQFIKDGNVKLNNKIVKNPGTHIDVKKDKIKICGKTVNILKTQ 82

Query: 73  ----------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTE 119
                      + ++ HKP GL+ T  D   R++++   P       R++SVGRLD NT 
Sbjct: 83  KMISPNDSSMYKWFVLHKPKGLLCTSDDEKERASIYSLFPQDILDNYRLVSVGRLDRNTS 142

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------ 167
           G+LLLTN+      L  P  Q +R YRV   G      L  L  G+ +            
Sbjct: 143 GVLLLTNEYAWVNKLTHPKYQRIRTYRVHIEGAAQMKVLRELAAGVYLPDDDRGGKVKKG 202

Query: 168 ----------------------------------QGICYGDMQVTLDTQKGSN------- 186
                                             +G       + +  Q+          
Sbjct: 203 MQKGMQKGMQKGMQKGMQKGVPKGIQKGFPTGMQKGFPTQPAFIEILRQETIKVKDQVKR 262

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL-LAGSTREVSKKILREQ 244
            + + + +REG+NR+I+K+FE  N  V ++ R ++    L  +      RE++ + + + 
Sbjct: 263 VSVLNISVREGRNRQIRKMFEQINQPVIKIKRTAFENITLKDVFFPKQYRELTPREVSDL 322

Query: 245 LGPHL 249
                
Sbjct: 323 KARRF 327


>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 =  181 bits (460), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 86/187 (45%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GRST+ D +P   S + + GRLD ++EGL++L
Sbjct: 31  KRQPDNTPRRIVLFNKPFDVLPQFTDEAGRSTLKDYIP--ISGIYAAGRLDRDSEGLMIL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +           +     
Sbjct: 89  TNDGKLQAQLTQPTKKTAKIYYVQVEGIPDDAILTRFRTGLELNDGKTQPAGAEIVPEPD 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR S     +  LL
Sbjct: 149 WLWPRNPPIRERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYSMANQTVENLL 208

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 209 PGEWKEI 215


>gi|289664922|ref|ZP_06486503.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 190

 Score =  181 bits (460), Expect = 2e-43,   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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G+   ++L  L+ G+V+        QV                 
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTLPAQVRSLDPAPQLWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDTLAPGQWR 176


>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 =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 46/182 (25%), Positives = 83/182 (45%), Gaps = 17/182 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +RL  ++KP G+++  +       + + +      V + GRLD ++EGLLLLTNDG L 
Sbjct: 31  PSRLLCFNKPYGVLSQFTPEGRWRGLKEYID--VPGVHAAGRLDADSEGLLLLTNDGPLQ 88

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G  D+  L  L++G+ +        Q               
Sbjct: 89  ARIADPRFKMEKTYWVQVEGLPDEAALQALRQGVQLNDGMTLPAQARRLEPPPVLWQRDP 148

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  ++V
Sbjct: 149 PIRVRQNIPDCWIELVIREGRNRQVRRMTAAIGHPTLRLVRAAIGPYTLDGLEPGQWKDV 208

Query: 237 SK 238
             
Sbjct: 209 EP 210


>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 =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 52/188 (27%), Positives = 84/188 (44%), Gaps = 18/188 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            +L L++KP G++T  +      T+   +        + GRLD  +EGLL+LT+DG L  
Sbjct: 2   PQLILFNKPYGILTQFTGELPEQTLSAFIK--LPGFYAAGRLDKQSEGLLILTDDGKLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  + Y V+  G      L  L+KG+VI+ I +   +  L             
Sbjct: 60  RLTHPKFEKKKHYWVQVEGVPTDKDLQPLRKGLVIKDITFLPAEARLISEPKIWPRIPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR--EV 236
            + +     W+ + LREGKN +I+K+     +   RLIR   G + L  L  G  +   +
Sbjct: 120 RERKHIPTTWLEIILREGKNHQIRKMTAAIGFPTLRLIRYQIGDWHLDQLQPGEYKLINL 179

Query: 237 SKKILREQ 244
           +   L E 
Sbjct: 180 TNDKLNEL 187


>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 =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 43/181 (23%), Positives = 78/181 (43%), Gaps = 21/181 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++KP  ++   +D       RST+ D +      V   GRLD ++EGL++LT+ G L
Sbjct: 4   FIRFNKPYDVLPQFTDRANADSPRSTLSDFID--LPGVYPAGRLDRDSEGLMVLTDHGRL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P  +  + Y V+  G+ D   L  L+ G+ ++       +  +           
Sbjct: 62  QAQISDPRHKMAKTYWVQVEGRPDAAALKALQDGVELKDGLTRPAKALMINEPKGLWPRN 121

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 Q   ++W+ + LREG+NR+++++         RLIR   G + L  L  G    
Sbjct: 122 PPIRVRQTIPDSWIELTLREGRNRQVRRMTAAVGHPTLRLIRARIGDWSLDGLAPGQWES 181

Query: 236 V 236
           +
Sbjct: 182 L 182


>gi|289669952|ref|ZP_06491027.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 190

 Score =  181 bits (459), Expect = 2e-43,   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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G+   ++L  L+ G+V+        QV                 
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTLPAQVRSLDPVPQLWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDTLAPGQWR 176


>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 =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 86/179 (48%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++   +D  GR T+ D +    + V + GRLD ++EGL++LTNDG L   L
Sbjct: 44  VILFNKPFDVLPQFTDEAGRRTLKDFV--SVADVYAAGRLDRDSEGLMVLTNDGALQAAL 101

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------------QVTL 179
             P  +  +VY V+  G   +  L  L+ G+ ++                          
Sbjct: 102 TQPGKRTGKVYYVQVEGDPQEADLQPLRDGVNLKDGMTLPAGVEKVAEPAWLWPRQPPIR 161

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           + +     W+ V L EG+NR+++++     +   RLIR + G + L  L +G  RE+S+
Sbjct: 162 ERKNIPTQWLKVTLYEGRNRQVRRMTAHIGFPTLRLIRYAMGSYSLDDLASGMWREISE 220


>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 =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 49/174 (28%), Positives = 85/174 (48%), Gaps = 7/174 (4%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +++KP G +T   D     TV D         ++  VGRLDI+TEGLL++T+DG LA  +
Sbjct: 1   MFNKPSGYITAVKDERY-PTVMDFFADLPFSKKLFPVGRLDIDTEGLLIITDDGQLAHRI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICY--GDMQVTLDTQKGSNAWVTV 191
             P  +  + Y     G +    L+  +K GIV++   Y     ++ + +     + + +
Sbjct: 60  AHPKWEIEKEYYAVVKGDISDLDLSRFEKEGIVLKKEKYRTKPFKINIISTSEERSEIYI 119

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            +REGK   +K++ E     V  L R+  GP +L   L  G  RE++ + + + 
Sbjct: 120 TVREGKYHIVKRIMEELGHPVLYLKRVRIGPLRLDEDLEEGDFRELTDEEIEKL 173


>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 =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 59/222 (26%), Positives = 98/222 (44%), Gaps = 27/222 (12%)

Query: 72  RTRLWLYHKPIGLVTTHSD--PDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +    L HKP  ++   +D  P G  R T+ D +P     + SVGRLD+++EGLLLLTND
Sbjct: 2   QHSYVLLHKPYNVLCQFTDNSPQGSQRQTLKDFVP--VPDIYSVGRLDLDSEGLLLLTND 59

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
             L   L  P     R Y V+     D   L  L++G+++QG         L T +    
Sbjct: 60  APLKHYLCEPKFAHSRTYWVQVENIPDGQALEQLRQGVMVQGKKTRPAIANLLTPEPTVP 119

Query: 185 ------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG----PFQLGTL 228
                         AW+ + L EG+NR+++++         RL+R++ G       L  L
Sbjct: 120 AREPPIRFRKNVPTAWLELTLTEGRNRQVRRMTAAVGHPTLRLMRVAIGAGPAKLTLTGL 179

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
             G  R ++   +      +L+++A+ N  +P   + +    
Sbjct: 180 GPGEWRHLTTAEIGAL--QNLVKKAKPNQRSPHKKTASRKPK 219


>gi|289209534|ref|YP_003461600.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288945165|gb|ADC72864.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
          Length = 180

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 84/180 (46%), Gaps = 16/180 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R+ L+HKP G++   +DP+GR T+ D +      V   GRLD ++EGL++LT+DG L   
Sbjct: 3   RIVLFHKPWGVLPQFTDPEGRPTLADYID--IPGVYPAGRLDRDSEGLMVLTDDGRLNAR 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|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 =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 86/175 (49%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR+T+ D +     RV + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IVLFNKPYNVLTKFTDTEGRATLADYID--IPRVYAAGRLDMDSEGLLLLTDQGHLNHAL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G   + +L  L++G+ ++       +V                 
Sbjct: 60  TDPDNKAYKTYVVQVEGIPTKAQLKQLEQGVDLKDGLTLPAKVKRIPYPKWLWAREKPIR 119

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             Q    +++ + ++EG+NR+++++         RLIR   G + L  L  G  R
Sbjct: 120 TRQNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGDYHLADLQPGQYR 174


>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 =  180 bits (458), Expect = 2e-43,   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|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 =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 83/176 (47%), Gaps = 19/176 (10%)

Query: 76  WLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L++KP G++T  +D   P  R T+     ++   V + GRLD ++EGLL+LT+DG L  
Sbjct: 31  ILFNKPFGVLTQFTDAKSPTERPTLSGF--NLPKGVYAAGRLDRDSEGLLVLTDDGKLQA 88

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P+ +  + Y V+  G      L  L+  + ++       QV L             
Sbjct: 89  QLSKPTFKTPKTYLVQIEGDPTDADLAPLRTRVTLKDGPTLPAQVRLIDPPDVWHRDPPV 148

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +   +AW+ V + EG+NR+++++     +   RL+R S G + L  +  G  R
Sbjct: 149 RVRKSIPDAWIEVTITEGRNRQVRRMCAHIGFPCLRLVRWSVGAWTLDGIDQGQWR 204


>gi|56475798|ref|YP_157387.1| pseudouridine synthase [Aromatoleum aromaticum EbN1]
 gi|56311841|emb|CAI06486.1| Pseudouridine synthase [Aromatoleum aromaticum EbN1]
          Length = 230

 Score =  180 bits (458), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 46/176 (26%), Positives = 76/176 (43%), Gaps = 17/176 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L +KP G++   S      T+   +P     V   GRLD ++EGLLLLT+DG L   
Sbjct: 30  RLILLNKPYGVICQFSGDGVHVTLKAFVP--VPGVYPAGRLDTDSEGLLLLTDDGALQHR 87

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y  +  G+  +  L  L+ G+ +                          
Sbjct: 88  IADPRHKLPKTYLAQVEGEPGETALTALRGGLDLGDFVTRPCSARRVAEPDWLWPRDPPV 147

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +    +W+ + L EGKNR+++++     +   RLIR++ G + L  L  G  R
Sbjct: 148 RFRKNVPTSWLEIVLHEGKNRQVRRMTAKAGFPTLRLIRVAIGDWSLAGLAPGQWR 203


>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 =  180 bits (458), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 49/175 (28%), Positives = 86/175 (49%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +DPDGR T+ D +     RV + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IILFNKPYNVLTKFTDPDGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHDL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G   + +L  L++GI ++       +V                 
Sbjct: 60  TDPENKAYKTYVVQVEGIPTKAQLKALEQGIELKDGMTLPAKVKRIPYPKWLWEREKPIR 119

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             Q    +++ + ++EG+NR+++++         RLIR     + +G L  G  R
Sbjct: 120 VRQNQPTSFLQIKIKEGRNRQVRRMTAAVGIPTLRLIRTHIDAYHIGDLKPGMYR 174


>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 =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 45/175 (25%), Positives = 85/175 (48%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D  GR+T+ D +     RV + GRLD+++EGLLLLT++G L   L
Sbjct: 2   IVLFNKPYNVLTKFTDDQGRATLADFID--IPRVYAAGRLDMDSEGLLLLTDNGQLNHAL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G   + ++  L+ G+ ++       +V                 
Sbjct: 60  TDPENKAYKTYIVQVEGVPTKAQIKTLETGVELKDGMTLPAKVKRIPYPKWLWEREKPIR 119

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             Q    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R
Sbjct: 120 VRQNKPTSFLQIKIKEGRNRQVRRMTAAVGVPTLRLIRTHIGDYHIADLKPGQYR 174


>gi|110834141|ref|YP_693000.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110647252|emb|CAL16728.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 206

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 54/221 (24%), Positives = 95/221 (42%), Gaps = 33/221 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L +KP  +++  SD  GR T+ + +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   QLILLNKPFRVLSQFSDDQGRRTLREFV--CVPGVYPAGRLDWDSEGLLLLTDDGALQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  GQ    +L  L++GI ++       +V+L              
Sbjct: 61  ISDPRFKLPKTYLVQVEGQPGPQELQKLRQGIRLKDGPTRPAKVSLIDDPCLWPRTPPVR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +   ++W+++ + EG+NR+++++         RLIR   G + L  L  G +R +   
Sbjct: 121 SRKTVPDSWLSLTIDEGRNRQVRRMTAAIGHPTLRLIRWQIGDWSLADLAPGESRSM--- 177

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
                          V+   P  +     R R       P+
Sbjct: 178 --------------MVHAPKPATAKHRRPRHRSGGPGPKPN 204


>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 =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 46/177 (25%), Positives = 82/177 (46%), Gaps = 16/177 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
           R+ L +KP  +++  +D + R+T+                GRLD ++EGLLLLT++G L 
Sbjct: 3   RIILVNKPYNMLSQFTDSENRATLRQLFTDAAAVEGFYPAGRLDYDSEGLLLLTDEGSLQ 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G+ D + L  L+ G+ ++       QV L            
Sbjct: 63  HRISEPKMKLAKTYWVQVEGEPDSEALAQLRGGVDLKDGRTHPAQVKLLETPTLWERTPP 122

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +   +W+ + + EG+NR+++++         RLIR + G +QL  L  G  R
Sbjct: 123 VRHRAQIPTSWLELKISEGRNRQVRRMTAAVGHPTLRLIRYAIGSWQLAGLQPGEHR 179


>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 =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 107/245 (43%), Gaps = 15/245 (6%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EV 62
           + +     RV +++   G  SR E+ R+     + ++G  L   +  +  T  +    E+
Sbjct: 1   MSKKIPTSRVDQLLGSMGYGSRAEMARLGKAGGIVLDGADLTDVSKRIPVTPDLPGRMEI 60

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINT 118
           DG PL       + L +KP+G+  +H +      V+D LP  + R       +GRLD  T
Sbjct: 61  DGEPLDPVAGLVV-LLNKPLGMTCSHKEDGA--LVYDVLPDRWRRRDPAISTIGRLDKQT 117

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQV 177
            GLLLLT+DG L   +  P     +VYR      ++  +  L   G +V++G        
Sbjct: 118 SGLLLLTDDGDLLHRVISPKRHVAKVYRATLARPLNGTEGALFASGELVLEGEDKPLAPA 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREV 236
            L+    + A +TV   EG+  +++++F      V  L R   G   L   L  G  R +
Sbjct: 178 VLEVVSPTEALLTVT--EGRYHQVRRMFAAAGNHVEALHRERLGGLVLPDELAPGEWRLL 235

Query: 237 SKKIL 241
           ++  +
Sbjct: 236 TEDEI 240


>gi|319762719|ref|YP_004126656.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117280|gb|ADU99768.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 188

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 80/179 (44%), Gaps = 17/179 (9%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
             R RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+ G 
Sbjct: 2   KARARLIRFNKPYGVLSQFTPEGRWRGLKDFID--LPGVYVAGRLDADSEGLLLLTDSGP 59

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------ 177
           L   +  P  +  + Y V+  G  D   L  L++GI +        +V            
Sbjct: 60  LQARISDPRHKMEKTYWVQVEGIPDDAALAALQRGITLNDGPTRPARVHRLEPPPALCPR 119

Query: 178 ---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                  +   ++W+ + +REG+NR+++++         RL+R + GP+ L  L  G+ 
Sbjct: 120 DPPIRVRRNIPDSWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYTLDGLAPGAW 178


>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 =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 45/176 (25%), Positives = 81/176 (46%), Gaps = 19/176 (10%)

Query: 76  WLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            L++KP G++T  +D   P  R T+      +   V + GRLD ++EGLL+LT+DG L  
Sbjct: 4   ILFNKPFGVLTQFTDAKCPTERPTLSGF--DLPKGVYAAGRLDRDSEGLLVLTDDGKLQA 61

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P  +  + Y V+  G      L+ ++  + ++       +V L             
Sbjct: 62  QLSSPKFKTPKTYLVQVEGDTTDADLDPMRASLSLKDGPTLPARVHLIDPPDLWLRDPPV 121

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              +   + W+ V + EG+NR+++++     +   RL+R S G + L  +  G  R
Sbjct: 122 RVRKSIPDTWIKVTITEGRNRQVRRMCAALGFPCLRLVRWSVGSWTLDGISQGQWR 177


>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 =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 63/233 (27%), Positives = 115/233 (49%), Gaps = 7/233 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K IA     SR EV+  + ++ +KVNG++L +        D +E+D   L+  
Sbjct: 1   MAQIRIEKYIADLTNLSRNEVKNKLKKKAIKVNGVILTKLIKIDPEKDVVELDNGILKY- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+ + ++++KP   +  +SD +  +T+FD +     +  S GRLD +TEGLL+L+NDG +
Sbjct: 60  EKFQYYMFNKPANFICANSDSEE-ATIFDIVGLPAEKFFSFGRLDKDTEGLLILSNDGQM 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     + Y V+   ++D + L      I I        +  L+     + ++ 
Sbjct: 119 CHRLLSPKNHVPKKYYVKVDKKIDSEILLN-NSPIKINDDFVV-SKYILELIDDKSCFL- 175

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
             + EGK  +IK++F    + V  L R+ +G  +L   L  G  R++S+  ++
Sbjct: 176 -TIYEGKFHQIKRMFGSLGFSVLYLKRVEFGKLKLDNNLKLGQVRKLSEDEVK 227


>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 =  179 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 49/175 (28%), Positives = 81/175 (46%), 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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G     +L  L+ G+V+        +V                 
Sbjct: 62  TDPRHKQPKTYWVQVEGTPAPSQLQALRDGVVLNDGPTRPAKVRSIDPSPQVWPRDPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RLIR++ G + L TL  G  R
Sbjct: 122 VRKTVPDAWLELQITEGRNRQVRRMTASVGLPTLRLIRVAIGDWTLDTLAPGQWR 176


>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 =  179 bits (456), Expect = 4e-43,   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|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 =  179 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 77/217 (35%), Gaps = 17/217 (7%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER--- 72
           + +++   G  +R+   ++I    V V G ++               DG+  R  +    
Sbjct: 6   LDRLLQSQGFGTRKWCRQLIDDGEVSVAGTVVTDYRTAFEP------DGLTFRLFDEDWD 59

Query: 73  ---TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
                    HKP     +   P     V   LP  F    V  VGRLD +T GLLL+++ 
Sbjct: 60  FHEHVFVALHKPPNFECSRK-PSHHPGVLSILPENFTWRDVQPVGRLDHDTTGLLLMSDH 118

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G        P +   +VY       V  + + LL  G+ +         V        + 
Sbjct: 119 GPFIHAQSSPKSHIPKVYIATTAEAVTPELVALLLAGVQLHDEPAPLAAVRCSM--VDSH 176

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
            + + L +GK  ++K++          L R++ G   
Sbjct: 177 RIEIVLEQGKYHQVKRMLAAAGNHCAALQRVAIGQLT 213


>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 =  179 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 46/184 (25%), Positives = 89/184 (48%), Gaps = 21/184 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + L++KP  +++  +D       R T+   +      V + GRLD ++EGLL+LT+DG L
Sbjct: 4   ILLFNKPFNVLSQFTDAGNEASSRRTLSHFID--VPNVYAAGRLDKDSEGLLVLTDDGKL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  PS +  + Y V+  G  D+  L+LL+ G++++       +V L           
Sbjct: 62  QHRISDPSNKMEKSYWVQVEGIPDETALDLLRAGVLLKDGMTKPAKVKLMDQPVDLWVRE 121

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   ++W+ + + EG+NR+++++     +   RLIR   G + +  + +G    
Sbjct: 122 PPVRYRKSVPDSWIEITISEGRNRQVRRMTACVGFPTLRLIRYRVGNWTIDGIESGDWIM 181

Query: 236 VSKK 239
            SKK
Sbjct: 182 HSKK 185


>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 =  179 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 90/186 (48%), Gaps = 18/186 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP G+++  +  DG+ T+ + +      V + GRLD ++EGLL+LT+DG L   
Sbjct: 3   KVVLFNKPCGVLSQFTAQDGQRTLAEFIDQ--PGVYAAGRLDKDSEGLLVLTDDGALQHR 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 ERKSIPTAWIELSLSEGRNRQVRRMTAAVGFPTLRLVRWSVGPWDLEGLAPGELRVITAP 180

Query: 238 KKILRE 243
             +LRE
Sbjct: 181 DSMLRE 186


>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 =  179 bits (456), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 112/259 (43%), Gaps = 41/259 (15%)

Query: 73  TRLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           TRL  ++KP  ++   +D       R T+   +      V + GRLD ++EGL+LLT++G
Sbjct: 2   TRLIRFNKPYDVLPQFTDSGSQGSARPTLSAYI--NCPGVYAAGRLDRDSEGLMLLTDNG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   +  P  +  + Y V+  G+ D   L  L++G+ ++       +  L         
Sbjct: 60  RLQAWISDPQHKMAKTYWVQVEGEPDSRALAALQQGVALKDGMTRPAKAHLMEAPAQLWQ 119

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +    +W+++ L+EGKNR+++++     +   RLIR S G + L  L  GS 
Sbjct: 120 REPPIRTRKSIPTSWISLTLKEGKNRQVRRMTAAVGFPTLRLIRYSIGVWTLDGLPQGSW 179

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            ++                   ++  P   S+   R      ++   D    + N S++N
Sbjct: 180 EDL----------------EVPSIPGPAKPSQLPNRRAQQKRNKEGQD---QEGNPSERN 220

Query: 294 GLSKQKKLATPVHRRNLAS 312
             ++QK+   P  RR+ ++
Sbjct: 221 ATARQKQRGKP-RRRSRST 238


>gi|325181473|emb|CCA15907.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 241

 Score =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 56/219 (25%), Positives = 99/219 (45%), Gaps = 25/219 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V++  +P  +  +               +   P   S++   GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVT 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 VLNAN----QLQFILTEGKKRHIRYMCEAVGIKVIALKR 215


>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 =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 57/129 (44%), Positives = 75/129 (58%), Gaps = 1/129 (0%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRK 69
            +P R+ K +A +GI SRR+ E++I   RV +NG  +      +    D I VDG  +++
Sbjct: 97  MSPVRLQKFLAASGICSRRKAEQLILDGRVTLNGETVLILGTKITPDIDKITVDGKLVKE 156

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E+   +L +KP G VTT SDP GR  V D L  I  RV  VGRLD +TEG LLLTNDG 
Sbjct: 157 EEQKVYYLLNKPKGYVTTLSDPQGRPVVTDLLHGINERVFPVGRLDFDTEGALLLTNDGD 216

Query: 130 LARVLELPS 138
           LA+    P 
Sbjct: 217 LAQKTLPPQ 225


>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 =  179 bits (455), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 53/187 (28%), Positives = 84/187 (44%), Gaps = 19/187 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP  +++  S    R T+ D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LILLNKPFQVMSQFSAHPERQTLADYID--IPNVYPAGRLDADSEGLLLLTDDGKLQHAI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P  +  + Y  +  GQ   + L+ L++ + +        Q  L  + G          
Sbjct: 61  AHPRRKLPKTYLAQVEGQPSPEALDKLRQPLDLGDFVTQGSQARLIQEPGWMWPRNPPIR 120

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL--AGSTREVS 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|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 =  179 bits (455), Expect = 5e-43,   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|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 =  179 bits (455), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 108/241 (44%), Gaps = 19/241 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +   G+ SRRE +  I    VKV+G+++      V     IE+    +       
Sbjct: 6   RLSKRMTELGLCSRREADEFIEMGLVKVDGVVVNVLGSRVRPEQTIELTRQAMALQAERV 65

Query: 75  LWLYHKPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTE 119
            +L +KP+G  +  S+   R                  +  L    + +   G+LD+++ 
Sbjct: 66  TFLLNKPVGYGSGPSEAGERPAWQLIKPETRSPRDRSGYTFLKKHLNYLAPAGKLDVDSS 125

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT DG +AR L   +  + + + V   G+V    L  L+ G+ + G     ++V+ 
Sbjct: 126 GLLVLTQDGRIARALMAKAADFEQEFLVWVEGEVSDAMLEQLRHGLSLDGEALKPVKVS- 184

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              + S++ +   LR+   R+I+++ E    +V  + RI  G   LG L  G  R +++ 
Sbjct: 185 ---RQSDSQLRFVLRDPVRRQIRRMAELVGLRVTAVRRIRIGRIALGDLEQGQWRYLTEH 241

Query: 240 I 240
            
Sbjct: 242 E 242


>gi|213024491|ref|ZP_03338938.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           404ty]
          Length = 182

 Score =  179 bits (455), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 48/176 (27%), Positives = 83/176 (47%), Gaps = 17/176 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 4   KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTND 61

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G L   L  P  +  ++Y V+  G  D   L  L+ G+ +         + +        
Sbjct: 62  GALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLW 121

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  + +    +W+ V L EG+N +++++         RLIR S G + L  L
Sbjct: 122 PRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLRLIRYSMGDYTLNGL 177


>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 =  179 bits (454), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 105/255 (41%), Gaps = 34/255 (13%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           T+L L++KP  ++T  +D  GR T+ D++     +V   GRLD ++EGLLLLT+ G L  
Sbjct: 2   TQLILFNKPYDVLTQFTDSAGRRTLKDHID--LEQVYPAGRLDRDSEGLLLLTDSGPLQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
           ++  P  +  + Y V+     D+  L  L+ G+ ++       +  L             
Sbjct: 60  LIANPKFKLEKTYWVQVENIPDETALQQLRDGVELKDGLTLPAKARLIDPPPVWPRTPPI 119

Query: 180 -DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            + +     W+ + ++EG+NR+++++         RLIR S   + L  L  G       
Sbjct: 120 RERKSIPTQWLELKIQEGRNRQVRRMTAAIGCPTLRLIRYSIDIWTLDNLSQGQW----- 174

Query: 239 KILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
                        +A  + D   + ++   ++               ++ + +K  L   
Sbjct: 175 -------------QAAPDADMIKWRNDLETKNNRRRRDPTQRSVPAGRRRNPRKTDLKPA 221

Query: 299 KKLATPVHRRNLASN 313
           ++ +    + N  S+
Sbjct: 222 RRSSRTRRKLNRGSD 236


>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 =  179 bits (454), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 46/187 (24%), Positives = 84/187 (44%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++L
Sbjct: 31  KRQPDNAPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIP--VSGIYAAGRLDRDSEGLMIL 88

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +           +     
Sbjct: 89  TNDGKLQARLTQPTQKTAKIYYVQVEGIPDDAALTRFRTGLDLNDGKTLPAGAEIVPEPS 148

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR       +  LL
Sbjct: 149 WLWPRNPPIRERKSIPDCWLKITLYEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLL 208

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 209 PGEWKEI 215


>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 =  179 bits (454), Expect = 7e-43,   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|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 =  178 bits (453), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 79/179 (44%), Gaps = 17/179 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 30  LLRFNKPYGVLSQFTPEGRWRGLQDFID--VPGVYVAGRLDADSEGLLLLTDDGALQARI 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|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 =  178 bits (453), Expect = 1e-42,   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|227111561|ref|ZP_03825217.1| putative RNA pseudouridylate synthase [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 208

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 46/187 (24%), Positives = 84/187 (44%), Gaps = 17/187 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++L
Sbjct: 21  KRQPDNAPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIP--ISGIYAAGRLDRDSEGLMIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +           +     
Sbjct: 79  TNDGKLQARLTQPTQKTAKIYYVQVEGIPDAAALTRFRTGLDLNDGKTLPAGAEIVPEPS 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR       +  LL
Sbjct: 139 WLWPRNPPIRERKSIPDCWLKITLHEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLL 198

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 199 PGEWKEI 205


>gi|325205754|gb|ADZ01207.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M04-240196]
          Length = 186

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 45/178 (25%), Positives = 80/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +   F      GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFI--NFPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPGEW 179


>gi|166714192|ref|ZP_02245399.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 200

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 82/175 (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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G+   ++L  L+ G+V+        QV                 
Sbjct: 72  TDPRHKQPKTYWVQVEGEPQAEQLQALRDGVVLNDGPTRPAQVRSLDPAPPLWPRDPPVR 131

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 132 VRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 186


>gi|290977401|ref|XP_002671426.1| predicted protein [Naegleria gruberi]
 gi|284084995|gb|EFC38682.1| predicted protein [Naegleria gruberi]
          Length = 244

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 103/244 (42%), Gaps = 19/244 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRV--KVNGILLERAAVNVMSTD--HIEVDGVPLRKA 70
           R+ +V++  GI SR +V   I +  V   +    +      +       + V+G P    
Sbjct: 3   RIDRVLSGMGICSRSDVIHYIRKNEVMDTIKKQRILSLKHKISEHQLESLMVNGKPFPFP 62

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLT 125
                   +KP   +  T  +      ++D LP  F         VGRLD+++ GLL++T
Sbjct: 63  TLNLTIALNKPESYLCSTQRESSNHKIIYDLLPPEFLNRNPTLGNVGRLDLDSCGLLIMT 122

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDT--- 181
            DG L   +        + Y V F   ++ D +LN +K+      +       TL     
Sbjct: 123 QDGDLHHRILSAD--VEKTYLVEFVPPIESDVELNQMKELFFSGDLQLRSEDSTLKPITN 180

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL---AGSTREVS 237
            +  + + +++ + EGK  +++++F   + +V  L RI  G   L  L    +G+   +S
Sbjct: 181 FEYINPSTISISIVEGKYHQVRRMFAACSKRVVGLKRIKIGDLTLEGLNIETSGAWCVLS 240

Query: 238 KKIL 241
           K++L
Sbjct: 241 KEVL 244


>gi|227327062|ref|ZP_03831086.1| putative RNA pseudouridylate synthase [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 208

 Score =  178 bits (451), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 46/189 (24%), Positives = 85/189 (44%), Gaps = 17/189 (8%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
                    R+ L++KP  ++   +D  GR T+ D +P   S + + GRLD ++EGL++L
Sbjct: 21  KRQPDNTPRRIVLFNKPFDVLPQFTDEAGRRTLKDYIP--VSGIYAAGRLDRDSEGLMIL 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----- 179
           TNDG L   L  P+ +  ++Y V+  G  D   L   + G+ +           +     
Sbjct: 79  TNDGKLQAQLTQPTKKTAKIYYVQVEGIPDDAALTRFRTGLDLNDGKTLPAGAEIVPEPD 138

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   + W+ + L EG+NR+++++     +   RLIR       +  LL
Sbjct: 139 WLWPRNPPIRERKSIPDCWLKITLNEGRNRQVRRMTANIGYPTLRLIRYGMANQTVENLL 198

Query: 230 AGSTREVSK 238
            G  +E++ 
Sbjct: 199 PGEWKEITD 207


>gi|222110563|ref|YP_002552827.1| pseudouridine synthase [Acidovorax ebreus TPSY]
 gi|221730007|gb|ACM32827.1| pseudouridine synthase [Acidovorax ebreus TPSY]
          Length = 216

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 44/174 (25%), Positives = 78/174 (44%), Gaps = 17/174 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 30  LLRFNKPYGVLSQFTPEGRWRGLQDFID--VPGVYVAGRLDADSEGLLLLTDDGALQARI 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G  D+  L  L++G+ +        +V                 
Sbjct: 88  SDPRHKMEKTYWVQVEGIPDEAALQALRQGVQLGDGPTLPARVRRLEPPPALWERDPPIR 147

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
             Q   + W+ + +REG+NR+++++         RL+R + GP+ L  L  G  
Sbjct: 148 VRQNIPDCWIELIIREGRNRQVRRMTAAVGHPTLRLVRAAIGPYALDGLEPGCW 201


>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 =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 55/196 (28%), Positives = 90/196 (45%), Gaps = 6/196 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K++    + SR +V+++I  Q V V+ +       NV      IEV G  +    +
Sbjct: 1   MRLDKLLEGTKVGSRSQVKKLIKAQGVWVDHMPARNGRQNVDPGLQLIEVTGQRVTHP-K 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+V+   D     TV D L        +  VGRLD +TEGL+LLT++G L
Sbjct: 60  HSYIILNKPSGVVSAKKDT-NYLTVIDQLAEEDKSPDLYPVGRLDRDTEGLVLLTDNGPL 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWV 189
              +  PS    + Y V  +G + +D  +    GI    G      Q+T+       +  
Sbjct: 119 GFRMLHPSHHVSKTYLVTVNGLLAEDASDFFAAGICFPTGEQCQPAQLTILKADTDQSQA 178

Query: 190 TVGLREGKNREIKKVF 205
           ++ + EGK  ++KK F
Sbjct: 179 SLTISEGKFHQVKKCF 194


>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 =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 57/230 (24%), Positives = 97/230 (42%), 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+   D     T +D+LP  +     VGRLD + EGLLLLT++G L  
Sbjct: 61  HHYLVYNKAAGQVSAKKDA-HWPTPYDHLPECYQGTSIVGRLDRDVEGLLLLTDNGQLHY 119

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTV 191
            LE       + Y+V  +G +  D +   + G+    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|318042073|ref|ZP_07974029.1| pseudouridine synthase, Rsu [Synechococcus sp. CB0101]
          Length = 232

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 54/191 (28%), Positives = 89/191 (46%), Gaps = 24/191 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRS--TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L++KP G+++  +   G     + D++P     V + GRLD ++EGLLLLT +G L + 
Sbjct: 11  LLFYKPYGVLSQFTPEPGSRWGCLADHIP--VPDVYTAGRLDADSEGLLLLTANGRLQQR 68

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L  P+    R Y V+  G  D  +L  L++G+VIQG      +                 
Sbjct: 69  LTDPAWGHWRRYWVQVEGIPDAAQLQQLEQGLVIQGQRTLPARANAIADPDLPPRDPPIR 128

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQLGTLLAGST 233
             Q+   +W+ V LREG+NR+++++         RL+R++        P  L  L  G  
Sbjct: 129 SRQQIPTSWLAVELREGRNRQVRRMTAAVGLPTLRLLRVAIDLMDGGAPLSLDGLEPGQW 188

Query: 234 REVSKKILREQ 244
           R V+ +  R  
Sbjct: 189 RAVTPEEERRL 199


>gi|315929678|gb|EFV08855.1| conserved hypothetical protein [Campylobacter jejuni subsp. jejuni
           305]
          Length = 204

 Score =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 61/206 (29%), Positives = 99/206 (48%), 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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG--------------DMQVTL 179
           L    +   R Y ++  G V +  +  ++ G+ I+    G               +   +
Sbjct: 120 LMH--SDLEREYYLKVKGTVSKQVIEAMQNGLEIKNEKKGAHAKTKITSMSFAPFIDFEI 177

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVF 205
               G    + V + EGKNRE+++ F
Sbjct: 178 FGSSGGYTKLRVVINEGKNRELRRFF 203


>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 =  177 bits (449), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 44/183 (24%), Positives = 82/183 (44%), Gaps = 21/183 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           TRL  ++KP  ++   +D       R+T+ D +      V   GRLD ++EGL+LLT+ G
Sbjct: 2   TRLIRFNKPYDVLPQFTDRGSDSSPRATLSDWID--LPGVYPAGRLDRDSEGLMLLTDHG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G  D   +  L  G+ ++       +  L         
Sbjct: 60  RLQAWISDPQHKMPKTYWVQVEGTPDAAAIQALANGVELKDGMTRPAKAALIEEPEGIWA 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +   ++W+ + +REG+NR+++++         RLIR + G + L  L  G+ 
Sbjct: 120 RNPPIRVRKSVPDSWIALTIREGRNRQVRRMTAAVGHPTLRLIRAAIGIWTLDGLSPGTW 179

Query: 234 REV 236
            ++
Sbjct: 180 EDL 182


>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 =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 87/179 (48%), Gaps = 19/179 (10%)

Query: 74  RLWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           RL L++KP  +++  +D   P  R+T+ D +     +V   GRLD ++EGLLLLT+DG L
Sbjct: 3   RLILFNKPFDVLSQFTDTKSPSPRATLSDYID--VPKVYPAGRLDRDSEGLLLLTDDGRL 60

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------- 180
              +  P ++  + Y  +  G      L+ L+KG+ ++       +V L           
Sbjct: 61  QARISSPKSRTPKTYLAQVEGAPTDADLDPLRKGVTLKDGLTRPAEVHLIDPPDLWERDP 120

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                +   + W+ + + EG+NR+++++     +   RL+R   G + +  +  G+ R+
Sbjct: 121 PVRYRKSVPDRWIELTITEGRNRQVRRMTAAVGFPTLRLVRWRVGDWSVEGIAPGTWRD 179


>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 =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/203 (28%), Positives = 107/203 (52%), Gaps = 5/203 (2%)

Query: 48  ERAAVNVMS-TDHIEVDGVPLRKAERTRL-WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                 +    D I +DG  +R  ++ R+ +  +KP G +++ SD  GR T+ D +    
Sbjct: 2   TEPWFEIDPVKDSITLDGKKVRPRKQQRVVYALNKPRGYLSSMSDDRGRKTIADLIKGKI 61

Query: 106 S-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             +V  VGRLD++TEGL++LTNDG LAR L  PS++  + Y  R  G++   ++  L+ G
Sbjct: 62  PEKVFHVGRLDMDTEGLIILTNDGELARKLSHPSSKIRKTYVARVTGKLSHHEIKRLENG 121

Query: 165 IVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           +V+  G       + +      +  V + + EG  REI+++F+ F+  V  L R + G  
Sbjct: 122 VVLRDGFKTSGASIRVIRASLRDTLVEIIIHEGHKREIREMFKVFDKHVLYLKRTAIGSL 181

Query: 224 QLGTLL-AGSTREVSKKILREQL 245
           ++  +   G  ++++ + +++ L
Sbjct: 182 KVDIVPNPGDIKKLTGQEIQKLL 204


>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 =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 50/180 (27%), Positives = 89/180 (49%), Gaps = 18/180 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           TRL +++KP  ++T  +D +G R+T+ D +      V + GRLD ++EGLL+LT+ G LA
Sbjct: 16  TRLIVFNKPYDVLTQFTDREGGRATLKDFIK--VPGVYAAGRLDRDSEGLLVLTDSGPLA 73

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-------- 183
             +  P  +  + Y  +  G   +  L+ L++GIV++             +         
Sbjct: 74  ARISDPKHKLAKTYWAQVEGVPTEADLDRLRRGIVLKDGPTLPAGARAMAEPDNLWPRDP 133

Query: 184 -------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+ + LREG+NR+++++     +   RLIR + G + L  L  G  R+V
Sbjct: 134 PIRYRAAIPTSWIELTLREGRNRQVRRMTAAMGFPTLRLIRWAVGEWNLEGLAPGEWRDV 193


>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 =  176 bits (448), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 81/177 (45%), Gaps = 16/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP  +++  +D  GR T+   +          GRLD ++EGLLLL ++G L + +
Sbjct: 4   LILLNKPYQVLSQFTDSAGRDTLAKFI--RTPGFYPAGRLDYDSEGLLLLCDEGRLQQRI 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|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 =  176 bits (448), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 45/175 (25%), Positives = 85/175 (48%), Gaps = 17/175 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP  ++T  +D +GR T+ D +     RV + GRLD+++EGLLLLT+ G L   L
Sbjct: 2   IVLFNKPYNVLTKFTDAEGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLNHEL 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G   + +L  L++G+ ++       +V                 
Sbjct: 60  TDPDNKAYKTYVVQVEGVPTKSQLKQLEQGVALKDGLTLPAKVKRIPYPKWLWEREKPIR 119

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R
Sbjct: 120 IRKNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGEYHIADLKPGQYR 174


>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 =  176 bits (448), Expect = 4e-42,   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   LIAFNKPYGVICQFSPHEKHKSLKDFI--NLPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPGEW 179


>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 =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 97/252 (38%), Gaps = 32/252 (12%)

Query: 73  TRLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           TRL  ++KP  ++   +D       R+T+ D +      V   GRLD ++EGL+LLT+ G
Sbjct: 2   TRLIRFNKPYDVLPQFTDRGSTDSPRATLSDWID--LPGVYPAGRLDRDSEGLMLLTDQG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---- 184
            L   +  P  +  + Y V+  G  D   +  L +G+ ++       +  L  +      
Sbjct: 60  RLQAWISDPQHKMPKTYWVQVEGTPDAAAITALAEGVELKDGLTRPAKARLIAEPEGLWA 119

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       ++W+ + +REG+NR+++++         RLIR + G + L  L  G  
Sbjct: 120 RNPPIRVRKSVPDSWIELTIREGRNRQVRRMTAAVGHPTLRLIRAAIGAWTLNGLGQGQW 179

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
            ++    +    GP             + + + + R      +E   +    +    +  
Sbjct: 180 EDL---EVPNIPGPP--------RPKHVPNRQAIARRHAREEAEAKQEARVSRPKPGKST 228

Query: 294 GLSKQKKLATPV 305
           G       A   
Sbjct: 229 GTKAGSAKAGSA 240


>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 =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 43/177 (24%), Positives = 79/177 (44%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +       + + +      V   GRLD ++EGLL+LT+DG L   +
Sbjct: 4   LVFFNKPYGVLSQFTPEGKWRALNEFI--TVKDVYVAGRLDADSEGLLILTDDGKLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  +  + Y  +  G  D+  L+ L+ GI +        +V L  +            
Sbjct: 62  ADPRHKLEKTYWAQVEGVPDEAALDRLRAGIELSDFTAKPAKVRLIDEPAGLWQRDPPIR 121

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  +W+ + + EGKNR+++++     +   RLIR + G   L  L  G  R++
Sbjct: 122 FRAAIPTSWLEIRISEGKNRQVRRMTAAIGYPTLRLIRAAIGAATLDGLALGQWRKI 178


>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 =  176 bits (447), Expect = 5e-42,   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   LVLLNKPYGVLSQFSDRSTPPKRTLAEFGLPPQVYAAGRLDHDSEGLLLLTDDGPLAHRL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y V+  G  D  +L  L  G+++         V                 
Sbjct: 62  TDPRHKQPKTYWVQVEGDPDTSQLQALCDGVLLNDGPTRPANVRRLECAPTLWPRDPPVR 121

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ V + EG+NR+++++         RL+R++ G + L +L  G  R
Sbjct: 122 VRKTVPDAWLEVQITEGRNRQVRRMTASVGLPTLRLVRVAIGAWSLASLQPGQWR 176


>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 =  176 bits (447), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 49/189 (25%), Positives = 82/189 (43%), Gaps = 18/189 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
            +L +KP  +++  S    +ST+ +      + V  VGRLD ++EGLLLLTND  L   L
Sbjct: 7   YFLIYKPYLMLSQFSKEGDKSTLANLDFDFPTDVYPVGRLDADSEGLLLLTNDKQLNHRL 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGSN------ 186
             P  +  R Y V+  G +  +    L  G+ I   G  Y  +       +  N      
Sbjct: 67  LNPKFRHNRTYYVQVDGALTDEACQQLSAGVTISVDGKAYDTLPAKAILIEAPNLPERNP 126

Query: 187 ----------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +W+++ L EGKNR+++K+     +   RL+R +        +  G  R +
Sbjct: 127 PIRFRASIPTSWLSITLHEGKNRQVRKMTAAVGFPTLRLVRWAIESLTAEEMAPGEVRLL 186

Query: 237 SKKILREQL 245
           S+  +   L
Sbjct: 187 SRAEVLRGL 195


>gi|46203293|ref|ZP_00208890.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 187

 Score =  176 bits (447), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 49/179 (27%), Positives = 90/179 (50%), Gaps = 18/179 (10%)

Query: 73  TRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           TRL +++KP  ++T  +D +G R+T+ D +      V + GRLD ++EGLL+LT+ G LA
Sbjct: 2   TRLIVFNKPYDVLTQFTDREGGRATLKDFI--NVPGVYAAGRLDRDSEGLLVLTDSGPLA 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-------- 183
             +  P  +  + Y  +  G   +D L+ L++G+V++        V    +         
Sbjct: 60  ARISDPKHKLAKTYWAQVEGIPSEDDLDKLRRGVVLKDGPTLPAGVRTMPEPDNLWPRDP 119

Query: 184 -------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                     +W+ + +REG+NR+++++     +   RLIR + G + L  L  G  R+
Sbjct: 120 PIRYRAAIPTSWIELTIREGRNRQVRRMTAAMGFPTLRLIRWAVGEWTLAGLAPGEWRD 178


>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 =  176 bits (447), Expect = 5e-42,   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   LIIFNKPYGVITQFSEHEVYPSLKEFI--SHKNVYPAGRLDADSEGLVILTDNGALQNKL 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|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 =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 45/192 (23%), Positives = 79/192 (41%), Gaps = 6/192 (3%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             A ++    + +++DG  +    E     L +KP    T+H  P    +VF   P    
Sbjct: 4   TDADIDSSYVETLDIDGEAVTVVPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMR 62

Query: 107 RV--ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            +   +VGRLD +T G+LL+TNDG L   L  PS +  ++Y V       +     LK G
Sbjct: 63  NIDMQAVGRLDADTTGVLLITNDGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNG 122

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + +            D    +   + + + EGK  ++K++      +V  L R  +   +
Sbjct: 123 VPLHDENETVCAA--DAVLENPTTLLLTITEGKYHQVKRMVAAAGNRVQHLHRRRFAHLE 180

Query: 225 LGTLLAGSTREV 236
              L  G  + +
Sbjct: 181 TENLKPGEWKFI 192


>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 =  176 bits (446), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 80/179 (44%), Gaps = 22/179 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDG------RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L L++KP  +++  +D         R+T+ D +      +   GRLD ++EGLLLLT+DG
Sbjct: 4   LILFNKPFQVLSQFTDERRPTDKPRRATLADWI--NQPGIYPAGRLDYDSEGLLLLTSDG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G ++   L  L++G+ ++                    
Sbjct: 62  QLQHCIASPRGKMEKTYWVQVEGTINPQTLRQLEQGVQLKDGLTRPALARAMDEPVIWLR 121

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                  Q    +W+ + + EG+NR+++++     +   RLIR   G + LG L  G  
Sbjct: 122 TPPVRFRQNIPTSWLELTICEGRNRQVRRMTAALGFPTLRLIRYRIGDWSLGLLEPGQY 180


>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 =  176 bits (446), Expect = 6e-42,   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   LIIFNKPCGVICQFSPHEKHPSLKDHIDA--PGFYPAGRLDTDSEGLLLLTDDGQLQARI 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|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 =  176 bits (446), Expect = 6e-42,   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   LIIFNKPYGVICQFSPHEKHKSLKDFI--NLPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI +         V L               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRLLEHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLKPGEW 179


>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 =  176 bits (446), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 89/180 (49%), Gaps = 20/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDG----RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L++KP+G+++  +D       RST+ + +      V   GRLD ++EGLL+LT+DG 
Sbjct: 3   RVILFNKPMGVLSQFTDKGNADSPRSTLSEFVD--VKGVYPAGRLDRDSEGLLVLTDDGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLD-------- 180
           L   +  P  +  + Y V+  G   +D++  L+ G+ +        + V +D        
Sbjct: 61  LQARIASPKFKRPKTYLVQVEGTPSEDQIRALRAGVDLNDGPTRRAECVAIDPPDLWPRN 120

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   +AW+++ + EG+NR+++++         RL+R S G + +  L  G  R+
Sbjct: 121 PPVRFRKSVPDAWLSLTISEGRNRQVRRMTAHVGLPCLRLVRWSVGDWSVEGLAPGEWRD 180


>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 =  176 bits (446), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 79/179 (44%), Gaps = 20/179 (11%)

Query: 74  RLWLYHKPIGLVTTH----SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL L++KP  +++      S    R+T+ D +     RV   GRLD ++EGLL+LT+DG 
Sbjct: 3   RLILFNKPYDVLSQFTGRGSADSPRATLSDFID--VPRVYPAGRLDRDSEGLLVLTDDGQ 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------ 177
           L   +  P  +  + Y  +  G  D   L  L++G+ +        +V            
Sbjct: 61  LQARIANPRFKTEKTYFAQVEGLPDDATLAALRQGVTLNDGPTRPARVDRMEPPTLWPRT 120

Query: 178 --TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 +   + W+ + + EG+NR+++++         RLIR   G + L  +  G  R
Sbjct: 121 PPVRFRKSVPDCWLKLTISEGRNRQVRRMTAHIGHPTLRLIRWRIGDWTLDGIGPGQWR 179


>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 =  175 bits (445), Expect = 7e-42,   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   RLILFNKPYGVLSQFTPEGRWQGLRDHL--ALPGVYAAGRLDADSEGLLILTDDGPTQAR 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|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 =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 57/210 (27%), Positives = 93/210 (44%), Gaps = 17/210 (8%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
             ++VN  +++   +++  TD   +    +      + ++ HKP G V  + D      +
Sbjct: 25  GLIQVNNEIVDE-DMDI--TDETVIYDSKILDPHPLKYYIIHKPSGYVCANKD-SHDPCL 80

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
              LP     +  VGRLD NT GL++LTND  L + L LP     R Y       +    
Sbjct: 81  ISLLPDD--NLHYVGRLDRNTTGLVILTNDLKLRKRLTLPEFHIPRTYAFTCLNPL--KD 136

Query: 158 LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVT--VGLREGKNREIKKVFEFFNWKVNR 214
           +   K+GI I G +      V +       +     + L EG+  EIKK+F   N K+  
Sbjct: 137 ITPFKEGITIDGDVKCLPAIVEM------TSEYEGVITLEEGRYHEIKKMFLSLNNKITS 190

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L RI YG   LG L +G+ R ++++ +   
Sbjct: 191 LHRIMYGDISLGDLPSGTYRTLTQEEINHL 220


>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 =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 47/175 (26%), Positives = 81/175 (46%), Gaps = 15/175 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP G+++  SD             +   V + GRLD ++EGLLLLT+DG LA  +
Sbjct: 2   LVLLNKPYGVLSQFSDRSQPPKRTLAEFGLPPDVYAAGRLDHDSEGLLLLTDDGALAHRV 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G+    +L  L+ G+V+        QV                 
Sbjct: 62  TDPRHKQPKTYWVQVEGEPQAGQLQALRDGVVLNDGPTRTAQVRSLDPAPPLWPREPPVR 121

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 122 VRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 176


>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 =  175 bits (445), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 48/184 (26%), Positives = 87/184 (47%), Gaps = 21/184 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L +KP G+++  +D       R T+   +          GRLD ++EGLL+LT+ G 
Sbjct: 4   RVILLNKPYGVLSQFTDKGTEGSSRPTLSTYIDE--KGFYPAGRLDRDSEGLLVLTDHGP 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLD-------- 180
           L   +  P  +  + Y V+  G  D   L  L+KG+ ++       +V  +D        
Sbjct: 62  LQARIAHPKYKRPKTYLVQVEGTPDAAALEALRKGVDLKDGLTKPAEVDQIDAPETLWPR 121

Query: 181 ------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                  +   +AW+ + +REG+NR+++++    +    RLIR S G ++L  L  G+ R
Sbjct: 122 DPPVRFRKTVPDAWLRITIREGRNRQVRRMTAHVDLPTLRLIRASVGDWELAGLQPGAWR 181

Query: 235 EVSK 238
             ++
Sbjct: 182 WSTE 185


>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 =  175 bits (445), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 47/175 (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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------------L 179
             P  +  + Y V+  G+    +L  L+ G+V+        QV                 
Sbjct: 72  TDPRHKQPKTYWVQVEGEPQAGQLQALRDGVVLNDGPTRTAQVRSLDPAPPLWPREPPVR 131

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +   +AW+ + + EG+NR+++++         RL+R++ G ++L  L  G  R
Sbjct: 132 VRKTVPDAWLELRITEGRNRQVRRMTAAVGLPTLRLVRVAIGDWRLDMLAPGQWR 186


>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 =  175 bits (445), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 46/182 (25%), Positives = 87/182 (47%), Gaps = 22/182 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP  ++   +D  GR+T+ D +     RV   G LD ++EGL++LT+DG L   +
Sbjct: 8   LILFNKPFNVLCQFTDKSGRATLADFVD--VPRVYPAGLLDYDSEGLVVLTDDGRLQARI 65

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------CYGDMQVTLDTQKG---- 184
             P  + ++ Y V+  G  D+  L  L+ G+ ++              V +  +      
Sbjct: 66  ADPRFKLVKTYWVQVEGVPDEAALVQLRAGVWLKDKGKREAQRTLPAAVRVIAEPPLWPR 125

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       AW+ + +REG+NR+++++         RL+R+  G + L  L +G+ +
Sbjct: 126 VPPVRFRLSVPTAWLELSIREGRNRQVRRMTAAVGLPTLRLVRVQVGDWSLRGLQSGAWK 185

Query: 235 EV 236
           +V
Sbjct: 186 KV 187


>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 =  175 bits (445), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 44/166 (26%), Positives = 76/166 (45%), Gaps = 16/166 (9%)

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
           +T  +   G +T+ D +P     V   GRLD ++EGLL+LTNDG L   L  P ++  + 
Sbjct: 1   MTQFTGEPGDATLADFIP--VKDVYPAGRLDKDSEGLLVLTNDGILQARLTQPKSKSAKT 58

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------------SNAWVT 190
           Y V+  G   ++ L  L+ G+ ++        V +  +                   W++
Sbjct: 59  YWVQVEGIPSENALKSLRNGVELKDGWTLPAIVEIMDEPAIWDRNPPIRHRPSVPTTWLS 118

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           + L EG+NR+++++         RL+R   G + +  L  G  REV
Sbjct: 119 ITLTEGRNRQVRRMTAAVGHPTLRLVRYQMGHWTVDGLQPGEWREV 164


>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 =  175 bits (444), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 46/171 (26%), Positives = 78/171 (45%), Gaps = 15/171 (8%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           +KP G+++  SD             +  +V + GRLD ++EGLLLLT+DG LA  L  P 
Sbjct: 42  NKPYGVLSQFSDRSTPPKRTLAEFGLPPQVYAAGRLDHDSEGLLLLTDDGPLAHRLTDPR 101

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------------TQK 183
            +  + Y V+  G  D  +L  L  G+++         V                   + 
Sbjct: 102 HKQPKTYWVQVEGDPDTSQLQALCDGVLLNDGPTRPANVRRLECAPTLWPRDPPVRVRKT 161

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             +AW+ V + EG+NR+++++         RL+R++ G + L +L  G  R
Sbjct: 162 VPDAWLEVQITEGRNRQVRRMTASVGLPTLRLVRVAIGAWSLASLQPGQWR 212


>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 =  175 bits (444), Expect = 1e-41,   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 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLKPGEW 179


>gi|119897392|ref|YP_932605.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669805|emb|CAL93718.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 201

 Score =  175 bits (444), Expect = 1e-41,   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   RLILLNKPYGVLCQFSGEPGRATLKDHVP--IPEVYPAGRLDTDSEGLLLLTDDGALQAR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  G+ D   L  L+ G+ +                          
Sbjct: 61  IADPRHKLPKTYLVQVEGEPDDAALAALRAGVDLGDFRTRPCSARRVVEPDWLWPRDPPV 120

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
              +    +WV + LREGKNR+++++     +   RL+R++ GP++L  L  G+ REV  
Sbjct: 121 RYRKSVPTSWVEIVLREGKNRQVRRMTAKVGFPTLRLLRVAIGPWRLDGLAPGAWREVEP 180

Query: 239 K 239
           +
Sbjct: 181 R 181


>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 =  175 bits (444), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 45/178 (25%), Positives = 86/178 (48%), Gaps = 17/178 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + L++KP  ++T  +D +GR T+ D +     RV + GRLD+++EGLLLLT+ G L 
Sbjct: 7   KNMIVLFNKPYNVLTKFTDAEGRPTLADYID--IPRVYAAGRLDMDSEGLLLLTDSGKLN 64

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L  P  +  + Y V+  G   + +L  L++G+ ++       +V              
Sbjct: 65  HGLTDPDNKAYKTYVVQVEGVPTKSQLKQLEQGVALKDGLTLPAKVKRIPYPKWLWEREK 124

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +    +++ + ++EG+NR+++++         RLIR   G + +  L  G  R
Sbjct: 125 PIRIRKNQPTSFIQLKIKEGRNRQVRRMTAAVGIPTLRLIRTHIGEYHIADLKPGQYR 182


>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 =  174 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 53/160 (33%), Positives = 86/160 (53%), Gaps = 17/160 (10%)

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
           GR+T+ D +P  FS V + GRLD ++EGLL+LTNDG L   L  P  +  +VY V+  G 
Sbjct: 2   GRTTLKDFIP--FSDVYAAGRLDRDSEGLLILTNDGKLQAQLTQPGKKTAKVYYVQVEGV 59

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQKGSNAWVTVGLREGK 197
            D++ L+ L+KGI+++        V L               + +    +W+ + L EG+
Sbjct: 60  PDEESLDKLRKGIILKDGLTLPAGVELVNEPTWLWVRHPPIRERKSIPVSWLKITLYEGR 119

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
           NR+++++     +   RLIR S G  QLG +  G  +E++
Sbjct: 120 NRQVRRMTAHIGFPTLRLIRFSMGTLQLGEIKPGEWKEIN 159


>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 =  174 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 70/180 (38%), Positives = 102/180 (56%), Gaps = 2/180 (1%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
           R    TR+ LYHKP+G + +  DP+GR  +F  LP     R ++VGRLD+NT+GL+LLTN
Sbjct: 12  RLQAFTRVLLYHKPVGELVSRRDPEGRPLIFSRLPRLELGRWVAVGRLDVNTQGLILLTN 71

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +G LA  L  PS    R Y VR  G V +  +  L  G+ ++        V     +G+N
Sbjct: 72  NGELAHRLMHPSHAVEREYAVRILGTVSEAVIERLLDGVQLEDGPARFESVAEAGGEGAN 131

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQL 245
            W  V +REG+NR +++++E  N  V+RLIR+ YG   L   L AG++ E+  + L   L
Sbjct: 132 RWFHVVVREGRNRLVRRLWESQNLVVSRLIRVRYGDIVLPPRLRAGASIELEGEALDGLL 191


>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 =  174 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 89/214 (41%), Gaps = 41/214 (19%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R  L +KP  +++  +D  GR T+ D +      V +VGRLD ++EGLLLLT+DG + 
Sbjct: 2   PYRYLLLYKPYDVLSQFTDESGRRTLKDLV--AVPNVYAVGRLDRDSEGLLLLTDDGPMQ 59

Query: 132 RVLELPSTQWLRVYRVRFHGQVD----QDKLNLLKKGIVIQGICYGDMQVTLD------- 180
             L  P     R Y V+          +  ++ L+ G+ I+G      QV++        
Sbjct: 60  HRLSHPRFGHRRQYWVQVECGPKSQPIEAAIDQLRAGVTIRGYRTRPAQVSVIPDPDLPP 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI--------------- 218
                   ++ + AW+ + L EGKNR+++++     +   RL+R                
Sbjct: 120 RNPPIRYRKQIATAWLEIALTEGKNRQVRRMTAAVGFPTLRLVRSALFLPTPEKRQKQRQ 179

Query: 219 ---SYG---PFQLGTLLAGSTREVSKKILREQLG 246
                G      L  L  G  R ++   +R   G
Sbjct: 180 TKKRAGAALALTLSGLSPGQWRSLTATEIRSLPG 213


>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 =  174 bits (442), Expect = 2e-41,   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|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 =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/235 (24%), Positives = 100/235 (42%), Gaps = 24/235 (10%)

Query: 73  TRLWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            RL  ++KP  ++   +D       R T+ D +      V   GRLD ++EGL+LLT+ G
Sbjct: 2   PRLIRFNKPYDVLPQFTDRGSQESSRKTLSDFIDC--PGVYPAGRLDRDSEGLMLLTDFG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   +  PS +  + Y V+  GQ D+  L  L KG+ ++          L         
Sbjct: 60  RLQAWISDPSHKMAKTYWVQVEGQPDRAGLEALSKGVELKDGLTLPASAHLMEEPAMLWA 119

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+++ ++EGKNR+++++         RLIR S G + L  L  GS 
Sbjct: 120 RTPPIRERKNIPTSWISLTIKEGKNRQVRRMTAAIGHPTLRLIRYSIGTWTLEGLSQGSW 179

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
            ++    +  +  P  L +++     P     +  R  P    E  D   R +K 
Sbjct: 180 EDLEVPRVPGRPKPSGLPKSRTEKTVPSTKPNSKKRKSP---PEKRDSARRKRKT 231


>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 =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 100/244 (40%), Gaps = 38/244 (15%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL  ++KP  ++   +D       R+T+ D +      V   GRLD ++EGL+LLT++G 
Sbjct: 3   RLIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDC--PGVYPAGRLDRDSEGLMLLTDNGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------- 179
           L   +  P  +  + Y  +  G  D+D LNLL++G+ ++       +  L          
Sbjct: 61  LQAWISDPKHKLEKTYWAQVEGIPDEDALNLLRQGVELKDGMTRPAKARLINEPAQLWAR 120

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    AW+ + + EGKNR+++++         RLIR + G + L  L  G  +
Sbjct: 121 TPPIRERKSVPTAWLELKITEGKNRQVRRMTAAVGHPTLRLIRYAIGAWTLDGLAQGKWQ 180

Query: 235 EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
           ++                    +  P   S+   R +P+      +  +R      +   
Sbjct: 181 DLD----------------PPRVPGPPKPSQKPPRRKPHA-QNTENGASRSPSKRRKPRS 223

Query: 295 LSKQ 298
            S +
Sbjct: 224 KSTR 227


>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 =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 15/237 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           RV +++   G  SR E+ RM     + ++G  L   +  +  T  +    E+DG PL   
Sbjct: 8   RVDRLLGSMGYGSRAEMARMAKAGGIVLDGADLTDVSRRIPVTRDLPTRMEIDGEPLDPV 67

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
           +   + L +KP+G+  +H +      V+D LP  +         +GRLD  T GLLLLT+
Sbjct: 68  QGL-VILLNKPLGMTCSHKEEGA--LVYDILPGRWRSRDPAISTIGRLDKQTTGLLLLTD 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P     +VYR      +   + +L   G +V++G         L+    +
Sbjct: 125 DGDLLHRVISPKRHVAKVYRAGLARPLMGTEGDLFASGELVLEGEDKPLAPAVLEVVSPT 184

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            A +TV   EG+  +++++F      V  L R   G   L   L  G  R ++ + +
Sbjct: 185 EALLTVT--EGRYHQVRRMFAAAGNHVETLHRERLGGLVLPADLAPGQWRLLTPEEI 239


>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 =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 78/175 (44%), Gaps = 16/175 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            ++ L++KP G+V+  S  +   T+   +        + GRLD N+EGLLLLT+ G L  
Sbjct: 2   PQIVLFNKPYGVVSQFSGEEHEHTLAAFID--IPNFYAAGRLDKNSEGLLLLTDSGALQH 59

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------ 180
            L  P     + Y V+  G      L++L+ G+V++ I +      L             
Sbjct: 60  RLTAPKFNKRKYYWVQVEGTPCNQDLDILRNGLVLKDISFLPAGARLIDEPHLWPRNPPI 119

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
              +    +W+ + L EGKN +I+K+     +   RL+R     ++L  L  G  
Sbjct: 120 RFRKNIPTSWLEIILSEGKNHQIRKMTAAIGFPTLRLVRHRISDWRLDNLQPGEY 174


>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 =  174 bits (442), Expect = 2e-41,   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   LIIFNKPYGVICQFSPHEKHKSLKDFI--NLPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI +         V +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRVLEHGETNPLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLRPGEW 179


>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 =  174 bits (442), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 41/181 (22%), Positives = 81/181 (44%), Gaps = 21/181 (11%)

Query: 75  LWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              ++KP  +++  +D       R+T+ D++      V   GRLD ++EGL+LLT+ G L
Sbjct: 4   FIRFNKPYDVLSQFTDRGSADSPRATLSDHID--LPGVYPAGRLDRDSEGLMLLTDVGRL 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              +  P  +  + Y V+  G  D   L  L +G+ ++       +              
Sbjct: 62  QARIADPRHKLAKTYWVQVEGVPDAAALRALAEGVELKDGLTRPARARAMPEPPGLWPRN 121

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               + +   ++W+ + +REG+NR+++++         RLIR   G + L  L+ G  + 
Sbjct: 122 PPIRERKSVPDSWIELTIREGRNRQVRRMTAAVGHPTLRLIRARIGDWTLDGLVPGEWQS 181

Query: 236 V 236
           +
Sbjct: 182 L 182


>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 =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 44/153 (28%), Positives = 73/153 (47%), Gaps = 16/153 (10%)

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
           D +P     V + GRLD ++EGLL+LTNDG L   L  P ++  + Y V+  G   +  L
Sbjct: 3   DYIP--IKDVYAAGRLDRDSEGLLILTNDGILQARLTQPQSKAPKTYWVQVEGAPQESDL 60

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQK--------------GSNAWVTVGLREGKNREIKKV 204
             L+ G+ ++       +V +  +                   W+ + L EG+NR+++++
Sbjct: 61  EALRHGVTLKDGPTLPAKVEIMPEPTLWPRNPPVRFRAAIPTTWLAITLMEGRNRQVRRM 120

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +   RLIR S G + LG L  G  +EV+
Sbjct: 121 TAHIGFPTLRLIRYSMGDWNLGDLQPGEWQEVT 153


>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 =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 58/182 (31%), Positives = 87/182 (47%), Gaps = 11/182 (6%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
            +L   HKP G V T SD  GR TV+D LP     +  + VGRLD++++GLLL T DG +
Sbjct: 9   PKLLALHKPKGYVVTRSDELGRKTVYDLLPDWAFENGWMPVGRLDMDSKGLLLFTTDGKI 68

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              L  P     +VY +   G V  + +   KKG+  +      + V      G+   + 
Sbjct: 69  GDALTRPGN-CKKVYEIWVRGYVTDEHIAAAKKGVESKQGLLKALSVEKLGTGGAKTKLR 127

Query: 191 VGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V + EGKNR I+++F            KV  L R+  G F L  + +G  R ++K+  + 
Sbjct: 128 VVIDEGKNRHIRRLFGALKDPKFSTPLKVLDLKRVRIGTFDL-DIESGQWRFLTKEEEKR 186

Query: 244 QL 245
            L
Sbjct: 187 LL 188


>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 =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 51/184 (27%), Positives = 85/184 (46%), Gaps = 19/184 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP  ++   S   GR T+ D+L      +   GRLD ++EGL+LLT+DG L   +
Sbjct: 3   LILFNKPYLVLCQFSPQAGRRTLADHL--AIPDIYPAGRLDADSEGLMLLTDDGRLQHDI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG---------- 184
             P+ +  + Y V+  G  D   LN L+ G+ +        +V                 
Sbjct: 61  SDPTHKQPKAYLVQIEGIPDPVALNTLRTGVFLGDFTSKAAKVIEVATPAWLWPRNPPIR 120

Query: 185 -----SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTREVS 237
                   W+ + + EGKNR+++++         RL+R++ GP+ L +  LL G +R V 
Sbjct: 121 QRAVTPTRWLLLTITEGKNRQVRRMTAAVGLPTLRLVRVAIGPYSLESHPLLPGESRVVD 180

Query: 238 KKIL 241
              L
Sbjct: 181 AAEL 184


>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 =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 52/182 (28%), Positives = 89/182 (48%), Gaps = 21/182 (11%)

Query: 75  LWLYHKPIGLVTTHSDPD-----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           + L +KP  +++  +D +      R T+ D L          GRLD ++EGLLLLTNDG 
Sbjct: 4   IILINKPFRVLSQFTDREQTSRGPRKTLADYL--SAPGFRVAGRLDYDSEGLLLLTNDGV 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L + +  P  +  + Y V+  G V+ + L  L KG+ ++       + T           
Sbjct: 62  LQQRIANPRHKQWKTYWVQIEGAVNNEILGQLMKGVELKDGPTQPCKATAISEPALWSRD 121

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   ++W+ + LREG+NR+I+++     +   RL+R + GP+QL TL  G  R 
Sbjct: 122 PPVRYRRNVPDSWIEMSLREGRNRQIRRMTAAVGFPTLRLVRRAIGPWQLDTLRPGEHRR 181

Query: 236 VS 237
           ++
Sbjct: 182 LT 183


>gi|309378696|emb|CBX22646.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 186

 Score =  173 bits (440), Expect = 3e-41,   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   LIVFNKPYGVICQFSPHEKHKSLKDFI--NLPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI +         V +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDETRLESLRKGIDLGDFVTRPASVRVLEHGETNPLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLKPGEW 179


>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 =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 46/178 (25%), Positives = 78/178 (43%), Gaps = 19/178 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP   ++  S    R+T+ D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPYQTMSQFSAHPSRATLADCVD--VPGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G  D+  L  L+ G+ +        +  +  +            
Sbjct: 61  ADPRHKLVKTYLAQVEGVPDEAALATLRTGVDLGDFKTLPAKARVVDEPAWLWERHPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTRE 235
                   W+ + +REGKNR+++++         RL+RIS G  +L    L+ G   E
Sbjct: 121 YRAAIPTTWIELSIREGKNRQVRRMTAAVGLPTLRLVRISIGNLKLPELGLMPGQWCE 178


>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 =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/229 (27%), Positives = 112/229 (48%), Gaps = 12/229 (5%)

Query: 43  NGILLERAAVNV-MSTDHIEVDG-VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           NG +     ++V   +  I +DG   +  +E   ++L +KPIG ++  SD  GR T+ D 
Sbjct: 2   NGRIETYPRLDVFSESSEILLDGNRLIFSSEEKVVYLVNKPIGYLSAMSDDRGRKTLSDL 61

Query: 101 LPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
           +      RV  VGRLD ++ GL+L+TNDG L+ ++  P+++  + Y V   G++    L 
Sbjct: 62  VSDRIKERVFHVGRLDQDSCGLILMTNDGDLSNLVSHPASEIEKTYVVGIKGKLTDRDLE 121

Query: 160 LLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
            +K G+ +  G      ++ L    G  +   + + EG  REI+++F   N  V+ L+R+
Sbjct: 122 AVKGGLTLGDGFKTSPAKIRLVRSDGDFSKYAITIHEGHKREIREIFRVLNKSVSSLVRV 181

Query: 219 SYGPFQLGTLL-AGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
           S GP  +  +   G  + +S+K +        L E   +  AP  +   
Sbjct: 182 SIGPLSISLVPSPGDIKRLSRKEI-------ALLENGAHRKAPKKAQRK 223


>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 =  173 bits (440), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 50/198 (25%), Positives = 84/198 (42%), Gaps = 27/198 (13%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
            +A+     L +KP G ++  +   G     + D +P    RV + GRLD ++EGLL+LT
Sbjct: 3   TQADDFTTLLLNKPYGFLSQFTPEPGSQWRCLADLIP--IPRVYAAGRLDADSEGLLVLT 60

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----- 180
           + G L   L  P     RVY V+  G   + +L  L  G++I+G        +       
Sbjct: 61  SHGRLQHRLTNPHLSHWRVYWVQVEGSPSESQLQKLASGVIIKGKRTRPALASWLKGNVA 120

Query: 181 ------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------P 222
                        Q    +W+ + L+EG+NR+++++         RLIR          P
Sbjct: 121 PIVREREPPIRVRQSIPTSWLELKLKEGRNRQVRRMTAAVGLPTLRLIRHRIELMDGEPP 180

Query: 223 FQLGTLLAGSTREVSKKI 240
             +  +  G  R+VS + 
Sbjct: 181 LSIEGMDPGQWRQVSSRE 198


>gi|299472407|emb|CBN77595.1| conserved unknown protein [Ectocarpus siliculosus]
          Length = 390

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 72/234 (30%), Positives = 109/234 (46%), Gaps = 13/234 (5%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK++A   I +R EV+ ++ + RVKV+G +++     +     IEV+G          
Sbjct: 137 RLSKLLADRAIGTRSEVDTLVRRGRVKVDGAVVKSPKTKLPVDCVIEVNGEV--HGPVPL 194

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
           L  +HKP G++TT SD   R  + D LP     +   VGRLD ++ GLLLL++DG L   
Sbjct: 195 LVAFHKPKGVITTLSDDWDREDLSDVLPKSLLLKHHPVGRLDADSSGLLLLSSDGALTHR 254

Query: 134 LELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           L  P  +  R Y        + ++     +  LK+GI      Y      +  +      
Sbjct: 255 LLNPRFEVEREYVASVDVPPEGEEPGDSLVTALKEGITTADGVYKADVPAISGRD----- 309

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           V V +REGKNR ++++     + V  L R  YG   LG L  G    VS   L 
Sbjct: 310 VGVVVREGKNRMVRRMLANAGYPVLELRRERYGKILLGDLPEGEHVPVSGDALE 363


>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 =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 47/176 (26%), Positives = 81/176 (46%), Gaps = 19/176 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + L +KP  +++  SD D    R T+ + L          GRLD ++EGL LLT+DG L 
Sbjct: 26  IILLNKPFRVLSQFSDRDNDPPRLTLANLL--SAPEFRVAGRLDYDSEGLTLLTDDGKLQ 83

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
           + +  P  +  + Y V+  G   Q  +  L  G+V+        +V              
Sbjct: 84  QQIANPKFKVWKTYWVQVEGAPKQQAIEQLTSGVVLNDGLTKPAKVRAIDPPDLWERSPS 143

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +AW+ + ++EG+NR+I+++    N    RL+RI+ G +++G L  G  
Sbjct: 144 VRFRAHIPDAWLEISIQEGRNRQIRRMTAAVNLPTLRLVRIAIGDWEIGNLQPGEY 199


>gi|330751986|emb|CBL80499.1| ribosomal large subunit pseudouridine synthase F [uncultured
           Polaribacter sp.]
          Length = 164

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 44/162 (27%), Positives = 75/162 (46%), 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 +  + V     +   R+  +GRLD  +EGL+ LT
Sbjct: 60  LVEPKNITLYIALNKPVGIVSTTDDREPNNIV--QHVNYPERLFPIGRLDKPSEGLIFLT 117

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           NDG +   +        + Y V     +  D +  +  GI I
Sbjct: 118 NDGDIVNKILRAGNNHEKEYFVSVDKSITDDFIASMGNGIPI 159


>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 =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 42/178 (23%), Positives = 84/178 (47%), Gaps = 19/178 (10%)

Query: 74  RLWLYHKPIGLVTTHSDP---DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           ++ L++KP  ++   +D      R T+ D +      V + GRLD ++EGLLLLTNDG L
Sbjct: 37  KIILFNKPFDVLCQFTDDAEQGQRRTLADYIEE--KEVYAAGRLDRDSEGLLLLTNDGKL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL----------- 179
              +  P+ +  + Y V+  G      L+ L++G++++       ++             
Sbjct: 95  QAQITQPNKKTDKTYWVQVEGAPTDADLDKLRQGVILKDGLTLPAKIEFLKDAKIWPRVP 154

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                +     W+++ + EG+NR+++++     +   RLIR S G + +  +  G  +
Sbjct: 155 PIRQRENIPTTWLSITICEGRNRQVRRMTANIGFPTLRLIRYSIGQWNIEGIDNGHYK 212


>gi|330818088|ref|YP_004361793.1| Pseudouridine synthase [Burkholderia gladioli BSR3]
 gi|327370481|gb|AEA61837.1| Pseudouridine synthase [Burkholderia gladioli BSR3]
          Length = 192

 Score =  173 bits (439), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 45/191 (23%), Positives = 77/191 (40%), Gaps = 19/191 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWV--RTPGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G  D   L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGTPDDAALKALARGVDLGDYVTRPCRADYVEPPETLWPRNPPVR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--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|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 =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 47/180 (26%), Positives = 82/180 (45%), Gaps = 20/180 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           R+ L +KP G+++  +D       R T+   +     +V   GRLD ++EGLL+LT+DG 
Sbjct: 3   RVILLNKPFGVLSQFTDKGLEGTTRPTLSAYVD--VPQVYPAGRLDRDSEGLLVLTDDGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------- 180
           L   +  P  +  + Y V       +D L  L+KGI ++       QV            
Sbjct: 61  LQAQIADPKFKKPKTYLVLVERIPSEDALQSLRKGITLKDGMTRPAQVERVEPPELWERD 120

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +   + W+   +REG+NR+++++         RL+R S G + L  + +G  R+
Sbjct: 121 PPVRFRKSVPDCWLKFTIREGRNRQVRRMTAAVGHPTLRLVRWSVGEWTLDGIASGVWRD 180


>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 =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 48/233 (20%), Positives = 93/233 (39%), Gaps = 21/233 (9%)

Query: 73  TRLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           TRL  ++KP  ++   +D       R+T+ D +      V   GRLD ++EGL+LLT+ G
Sbjct: 2   TRLIRFNKPYDVLPQFTDRGSDSSPRATLSDWID--LPGVYPAGRLDRDSEGLMLLTDHG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------- 180
            L   +  P  +  + Y V+  G  D   +  L  G+ ++       +  L         
Sbjct: 60  RLQAWISDPQHKMPKTYWVQVEGTPDAAAIQALANGVELKDGMTRPAKAALIEEPEGIWA 119

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +   ++W+ + +REG+NR+++++         RLIR + G + L  L  G+ 
Sbjct: 120 RNPPIRVRKSVPDSWIALTIREGRNRQVRRMTAAVGHPTLRLIRAAIGIWTLDGLSPGTW 179

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            ++    +     P      Q        +S++   +    +        R +
Sbjct: 180 EDLEAPTIPGPPKPKPAPNRQAIARRKAAASKSARPEPDAGLKLRKPRKPRKR 232


>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 =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 45/182 (24%), Positives = 84/182 (46%), Gaps = 21/182 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           RL  ++KP  ++   +D       R+T+ D +      V   GRLD ++EGL+LLT++G 
Sbjct: 3   RLIRFNKPFDVLPQFTDRGSEGSPRATLSDYVDC--PGVYPAGRLDRDSEGLMLLTDNGR 60

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------- 179
           L   +  P  +  + Y V+  G   +D L  L++G+ ++       +  L          
Sbjct: 61  LQAWISDPKHKLEKTYWVQVEGIPTEDALKALRQGVDLKDGMTRPAKAELISEPAQLWAR 120

Query: 180 -----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                + +    AW+ + + EGKNR+++++     +   RLIR + G + L  L  G   
Sbjct: 121 TPPIRERKSVPTAWLELKISEGKNRQVRRMTAAMGYPTLRLIRYAIGAWTLDGLAQGKWD 180

Query: 235 EV 236
           ++
Sbjct: 181 DL 182


>gi|238028429|ref|YP_002912660.1| Pseudouridine synthase [Burkholderia glumae BGR1]
 gi|237877623|gb|ACR29956.1| Pseudouridine synthase [Burkholderia glumae BGR1]
          Length = 192

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 79/190 (41%), Gaps = 19/190 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LVALNKPFGTICQFSPHETRPSLGDWV--RAPGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G  D   L  L +G+ +        + +L               
Sbjct: 61  AEPRHKLVKRYWAQVEGAPDAAALKALARGVDLGDYVTRPCRASLVEPPATLWPRTPPVR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   L    L  G T E+ 
Sbjct: 121 FRAAIPTTWIELAISEGKNRQVRRMTAAVGFPTLRLVRVGIGALDLFALGLAPGETIELP 180

Query: 238 KKILREQLGP 247
            +   +   P
Sbjct: 181 PRAPWDGFAP 190


>gi|319638581|ref|ZP_07993343.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317400330|gb|EFV80989.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 186

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 81/179 (45%), Gaps = 21/179 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L   +
Sbjct: 4   LIILNKPYGVICQFSAHEKHPCLKDFVEK--PGFYPAGRLDTDSEGLLLLTNNGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +               
Sbjct: 62  ADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTRPAEVRVLEEGEADVLWPRVPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTR 234
               +   + WV + + EGKNR+++++     +   RL+R++ G   L    L  G  R
Sbjct: 122 IRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQWR 180


>gi|325204476|gb|ADY99929.1| ribosomal large subunit pseudouridine synthase E [Neisseria
           meningitidis M01-240355]
          Length = 185

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 79/178 (44%), Gaps = 22/178 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G++   S  +   ++ D +   F      GRLD ++EGLLL T+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFI--NFPGFYPAGRLDTDSEGLLL-TDDGRLQAQI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 61  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L    L  G  
Sbjct: 121 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPGEW 178


>gi|291545735|emb|CBL18843.1| pseudouridine synthase family [Ruminococcus sp. SR1/5]
          Length = 610

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 48/192 (25%), Positives = 87/192 (45%), Gaps = 11/192 (5%)

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           TV + L     R+  +GRLD ++EGLLLLTN+G L   +        + Y+V  +  V +
Sbjct: 2   TVTEYL-DYPVRIYPIGRLDKDSEGLLLLTNEGDLVNRIMKAGNYHEKEYQVTVNKPVTE 60

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           + +  +  G+ I        +VT   + G N+   + L +G NR+I+++ E+F +KV  L
Sbjct: 61  EFIRGMGGGVPILDTVTRPCKVT---KTGKNS-FRIILTQGLNRQIRRMCEYFGYKVVTL 116

Query: 216 IRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNII 275
            R+      +  L  G  RE+  +  +E      LEE   +  +   +  +  R     +
Sbjct: 117 KRVRIMNLYIDGLEEGKYREIRPEERKE------LEEMLSSEKSEKRTGGSHERIIHKKM 170

Query: 276 SEVPDDFTRMKK 287
            E+ +      +
Sbjct: 171 KELGEKLREASR 182


>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 =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 54/235 (22%), Positives = 95/235 (40%), Gaps = 38/235 (16%)

Query: 73  TRLWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           TRL  ++KP  ++   +D       R+T+   +      V + GRLD ++EGLLLLT++G
Sbjct: 2   TRLIRFNKPYDVLPQFTDSGSQDSPRATLSKYIDC--PGVYAAGRLDRDSEGLLLLTDNG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   +  P  +  + Y V+  G  DQ+ L  L +G+ ++       +V L         
Sbjct: 60  RLQAWITDPKHKMDKTYWVQVEGIPDQEALKNLAEGVELKDGITRPAKVRLMPEPTGLWA 119

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +   ++W+ + LREG+NR+++++         RLIR S G + L  L  G+ 
Sbjct: 120 RTPPVRVRKTVPDSWIALTLREGRNRQVRRMTAAVGHPTLRLIRYSIGAWTLDGLAQGAW 179

Query: 234 REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                            E+ +                RP   +  P    R ++ 
Sbjct: 180 -----------------EDVEPPRVPGPPKPSQKPPRRPKPSAARPPKGDRPRRR 217


>gi|325181474|emb|CCA15908.1| ribosomal large subunit pseudouridine synthase F put [Albugo
           laibachii Nc14]
          Length = 248

 Score =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 53/213 (24%), Positives = 96/213 (45%), Gaps = 25/213 (11%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +A   + SRR+ ER I+   V VNG  +++  + +     +E  G  ++  ++    + +
Sbjct: 1   MAERKMCSRRDAERYISAGDVYVNGEQIQQDWIKIPRDSCVEFSGKAVKAEKQKVSVILN 60

Query: 80  KPIGLVTTHSDPDGRSTV---------------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           KP+G V++  +P  +  +               +   P   S++   GRLDIN+ GLLL 
Sbjct: 61  KPLGYVSSQPEPMRKPAIELLSIQNAFQLTARWYGKEPKSLSKLAVCGRLDINSTGLLLF 120

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVT 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 VLNAN----QLQFILTEGKKRHIRYMCEAVGIK 209


>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 =  173 bits (438), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 43/175 (24%), Positives = 87/175 (49%), Gaps = 16/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ L++KP  +++  SD +GR T+ D L        + GRLD ++EGLLLLT++G L + 
Sbjct: 12  KIILFNKPFRVLSQFSDTEGRRTLADFL--SAPEFRAAGRLDYDSEGLLLLTDNGQLQQQ 69

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 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|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 =  172 bits (437), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 44/192 (22%), Positives = 78/192 (40%), Gaps = 6/192 (3%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             A ++    + +++DG  +    E     L +KP    T+H  P    +VF   P    
Sbjct: 4   TDADIDSSYVETLDIDGEAVTVVPEPYFYILLNKPEDYETSHK-PKHYRSVFSLFPDNMR 62

Query: 107 RV--ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
            +   +VGRLD +T G+LL+TNDG L   L  PS +  ++Y V       +     LK G
Sbjct: 63  NIDMQAVGRLDADTTGVLLITNDGKLNHNLTSPSRKIPKLYEVTLKHPTGETLCETLKNG 122

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           + +            D    +   + + + EGK  ++K++      +   L R  +   +
Sbjct: 123 VPLHDENETVCAA--DAVLENPTTLLLTITEGKYHQVKRMVAAAGNRAQHLHRRRFAHLE 180

Query: 225 LGTLLAGSTREV 236
              L  G  + +
Sbjct: 181 TENLKPGEWKFI 192


>gi|326623646|gb|EGE29991.1| RNA pseudouridine synthase family protein [Salmonella enterica
           subsp. enterica serovar Dublin str. 3246]
          Length = 172

 Score =  172 bits (437), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 47/171 (27%), Positives = 80/171 (46%), Gaps = 17/171 (9%)

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   L  P  +  +
Sbjct: 1   MLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGK 58

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------DTQKGSNAW 188
           +Y V+  G  D   L  L+ G+ +         + +               + +    +W
Sbjct: 59  IYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSW 118

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + V L EG+NR+++++         RLIR S G + L  L  G   E++++
Sbjct: 119 LKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQWCEIAQE 169


>gi|281202742|gb|EFA76944.1| hypothetical protein PPL_09696 [Polysphondylium pallidum PN500]
          Length = 614

 Score =  172 bits (437), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 97/247 (39%), Gaps = 18/247 (7%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL------- 75
           +G+ SR +    I   RV V G  +      V   D + + G  L       L       
Sbjct: 116 SGLCSRSKALSYIGINRVTVLGQKV-SPKTKVNVED-VRIMGKKLENTNPYILYYYYYSK 173

Query: 76  ---WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDG 128
                 HKP G + +++       ++D LP  F++ +      GRLD    GL+L++ DG
Sbjct: 174 RLTIAVHKPNGYICSNAREGDHKIIYDLLPPEFAKRLPTLSVAGRLDKWVTGLVLMSQDG 233

Query: 129 GLARVLELPSTQ-WLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGSN 186
            +   +  P    + ++Y V        ++    + G ++++           +      
Sbjct: 234 KIVERIITPKDDSFGKIYDVVCKAPFKGNEAEAFESGTMMLRSEEEPCKAAKFEVLDNDR 293

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
               + L EG+  +++++    + K   + RI  GP  LG L AG  R ++++ + +   
Sbjct: 294 NLARLTLYEGRYHQVRRMMAALDNKAMEIHRIKVGPIDLGDLPAGKWRYLTEEEMEKIKA 353

Query: 247 PHLLEEA 253
             + + A
Sbjct: 354 IQVTKSA 360


>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 =  172 bits (437), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 62/234 (26%), Positives = 113/234 (48%), Gaps = 9/234 (3%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
               R+ K IA     SR EV+  + ++ +KVN ++L +        D +E+D   L+  
Sbjct: 1   MAQIRIEKYIADLTNLSRNEVKNKLKKKAIKVNRVILTKLIKIDSEKDVVELDNSILKY- 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E+ + ++++KP   +  +SD +  +T+FD +     +  S GRLD +TEGLL+L+NDG +
Sbjct: 60  EKFQYYMFNKPANFICANSDSEE-ATIFDIVGLPAEKFFSFGRLDKDTEGLLILSNDGQM 118

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWV 189
              L  P     + Y V+   ++D + L  L    I I       +      +   +   
Sbjct: 119 CHRLLSPKNHVPKKYYVKVDKKIDSEIL--LNHSPIKIND---DFIVSKYILELIDDKGC 173

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
            + + EGK  +IK++F    + V  L R+ +G  +L   L  G  R++S+  ++
Sbjct: 174 FLTIYEGKFHQIKRMFGSLGFSVLYLKRVEFGKLKLDNNLKLGQVRKLSEDEVK 227


>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 =  172 bits (436), Expect = 8e-41,   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 +   F      GRLD ++EGLLLLT+DG L   +
Sbjct: 4   LIAFNKPYGVICQFSPHEKHKSLKDFI--NFPGFYPAGRLDTDSEGLLLLTDDGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI + G       + +               
Sbjct: 62  TDPKFKHPKTYWAQLEGVPDESRLESLRKGIDLGGFVTRPASIRILKHGEADSLWERIPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RLIR++ G  +L    L     
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLIRVASGRLKLFDLDLKPREW 179


>gi|323527142|ref|YP_004229295.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
 gi|323384144|gb|ADX56235.1| pseudouridine synthase [Burkholderia sp. CCGE1001]
          Length = 189

 Score =  172 bits (436), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 79/189 (41%), Gaps = 19/189 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLLALNKPFGTICQFSPHETRASLADWVK--VPGVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------------T 178
           +  P  + ++ Y  +  G VD   L  L +G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGTVDAAALKKLARGVDLGDYVTKPCRADYVEPGDTLWTRTPPI 119

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EGKNR+++++     +   RL+R+  G   +    L  G   EV
Sbjct: 120 RYRAAIPTSWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLGLQPGEYVEV 179

Query: 237 SKKILREQL 245
                 E L
Sbjct: 180 PPNAPWEGL 188


>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 =  172 bits (436), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 47/154 (30%), Positives = 80/154 (51%), Gaps = 4/154 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
            R+ K++A  GI +R+EV+ +I +  VKVNG+++++    V    D I  D   +     
Sbjct: 3   MRLDKLLANYGIGTRKEVKSLIRKGFVKVNGMIIKKDDFKVDHEIDEIVFDDELIEYR-P 61

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
               + +KP G ++   D +   TV + +    +  +  VGRLD++TEGLLL+TNDG  +
Sbjct: 62  YVYIMLNKPAGYISATKD-NLHPTVLELIEGYENYDLFPVGRLDLDTEGLLLITNDGDFS 120

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             L  PS    ++Y     G +D+  +   K G+
Sbjct: 121 HKLLAPSRNHSKIYFANIAGVMDEQDIQAFKDGL 154


>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 =  172 bits (436), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 53/194 (27%), Positives = 83/194 (42%), Gaps = 24/194 (12%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD--GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                   L HKP G+++  S       ST+   +P     V + GRLD ++EGLLLLT+
Sbjct: 10  ARPAPTTLLLHKPYGVLSQFSPEPLSPWSTLAPLVP--VPGVYAAGRLDADSEGLLLLTS 67

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG L + L  P     R Y V+  G      L  L++G+++QG      Q          
Sbjct: 68  DGPLQQRLTDPRWGHWRRYWVQVEGTPSDAALQQLREGVMVQGRRTLSAQAIALADPGLA 127

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLG 226
                    +    +W+ +GLREG+NR+++++         RL+R++        P  L 
Sbjct: 128 ERVPPIRQRRSIPTSWLELGLREGRNRQVRRMTAAVGLPTLRLLRVAIDLMDGEPPLSLE 187

Query: 227 TLLAGSTREVSKKI 240
            L  G  R V+   
Sbjct: 188 GLAPGQWRPVTAAE 201


>gi|187925144|ref|YP_001896786.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
 gi|187716338|gb|ACD17562.1| pseudouridine synthase [Burkholderia phytofirmans PsJN]
          Length = 189

 Score =  171 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 46/190 (24%), Positives = 80/190 (42%), Gaps = 19/190 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   HLLALNKPFGTICQFSPHETRASLADWVK--VPDVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G VD   L  L +G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGAVDAATLKKLARGVDLGDYVTRPCRAEYVEPTDALWTRTPPI 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+
Sbjct: 120 RFRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLGLQPGESVEL 179

Query: 237 SKKILREQLG 246
           S K   E + 
Sbjct: 180 SPKAPWEGIA 189


>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 =  171 bits (435), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 81/179 (45%), Gaps = 21/179 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L   +
Sbjct: 4   LIILNKPYGVICQFSAHEKHQCLKDFVEK--PGFYPAGRLDTDSEGLLLLTNNGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +               
Sbjct: 62  ADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTRPAEVRVLEEGEADVLWPRVPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTR 234
               +   + WV + + EGKNR+++++     +   RL+R++ G   L    L  G  R
Sbjct: 122 IRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQWR 180


>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 =  171 bits (435), Expect = 1e-40,   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|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 =  171 bits (434), Expect = 1e-40,   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   LIAFNKPYGVICQFSPHEKHKSLKDFID--LPSFYPAGRLDTDSEGLLLLTDDGWLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ +L  L+KGI +         V +               
Sbjct: 62  TDPKFKHPKTYWAQLEGLPDESRLESLRKGIDLGDFVTRPALVRVLNPGEAERLWERVPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R++ G  +L    L  G  
Sbjct: 122 IRVRKTVPDFWIEITISEGKNRQVRRMTAKAGYPCLRLVRVASGRLKLFDLDLRPGEW 179


>gi|295677452|ref|YP_003605976.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
 gi|295437295|gb|ADG16465.1| pseudouridine synthase [Burkholderia sp. CCGE1002]
          Length = 189

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 44/180 (24%), Positives = 78/180 (43%), Gaps = 19/180 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL  ++KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLLAFNKPFGTICQFSPHETRASLADWVK--VPGVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G +D   L  L +G+ +        Q                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGALDDAALKKLARGVDLGDFVTRPCQANYVEPSSSLWTRTPPI 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+
Sbjct: 120 RYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFSLGLQPGESIEL 179


>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 =  171 bits (434), Expect = 1e-40,   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   IVLFNKPFGVVCQFSKHEIHPTLKDYL--NIPNIYPAGRLDTDSEGLLVLTDNGKIQHEI 59

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P++   + Y V+  G +  + +  L+ GI ++       +V                 
Sbjct: 60  SSPNSHKYKGYWVQVEGDIKNEAIQKLQNGIKLKDFTSLPARVEKINEPEIWERSTPIRF 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +    +WV + +REGKNR+++K+     +   RLIR     + L  LL G  
Sbjct: 120 RKNLPTSWVKIQIREGKNRQVRKMTAAVGFPTLRLIRYHVDDYYLNKLLPGDY 172


>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 =  171 bits (434), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 45/172 (26%), Positives = 80/172 (46%), Gaps = 7/172 (4%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +KP  +++   D   R TV   L     +  +  VG LD +T GLLLLTNDG L   L 
Sbjct: 1   MNKPKDVLSATEDRSQR-TVISLLKNTDRYQGISPVGCLDKDTTGLLLLTNDGQLNHELL 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQ--KGSNAWVTVG 192
            P     ++YR +  G ++++ +     G+ +          + + +Q  K   + + + 
Sbjct: 60  APGKHVDKIYRAKIAGPINEETVKTFASGMTLGDDTKLKPATLKILSQDEKEDTSQIEIK 119

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKKILRE 243
           ++EGK  +IK++F     K   L RI+ G  +L   L  G    +S + +++
Sbjct: 120 IQEGKYHQIKRIFAAVGMKAIELDRIAMGNLRLPPDLKRGEYCTLSPERIQQ 171


>gi|332971549|gb|EGK10499.1| ribosomal large subunit pseudouridine synthase E [Kingella kingae
           ATCC 23330]
          Length = 203

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 81/187 (43%), Gaps = 21/187 (11%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            K +   L   +KP G++   S  +   T+ D +      V   GRLD ++EGLLLLT+D
Sbjct: 14  TKKQPAMLIALNKPYGIICQFSPHEKHRTLKDLV--NVPNVYPAGRLDTDSEGLLLLTDD 71

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G     +  P  +  + Y  +  G  D DKL  L++ + +        Q+ L        
Sbjct: 72  GKQQARIADPRNKITKTYWAQLEGSPDADKLARLQQPLDLGDFVAQPAQIRLLNENEIAQ 131

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--L 228
                    + +   + W+ + +REGKNR+++++     +   RLIR+  G   L    L
Sbjct: 132 IWTRNPPIRERKTVPDFWLQIQIREGKNRQVRRMTAKAGYPCLRLIRVGIGRVNLFDLGL 191

Query: 229 LAGSTRE 235
             G  +E
Sbjct: 192 ELGQWQE 198


>gi|209517462|ref|ZP_03266303.1| pseudouridine synthase [Burkholderia sp. H160]
 gi|209502116|gb|EEA02131.1| pseudouridine synthase [Burkholderia sp. H160]
          Length = 204

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 19/179 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R+++ D +      V   GRLD ++EGL+LLT+DG L   +
Sbjct: 18  LLALNKPFGTICQFSPHETRASLADWVK--VPGVYPAGRLDSDSEGLVLLTDDGALQARI 75

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G VD   L  L +G+ +        Q T                
Sbjct: 76  AEPRHKLVKRYWAQVEGAVDDAALKKLARGVDLGDYVTRPCQATYVEPDSSLWARTPPIR 135

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+
Sbjct: 136 YRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFSLGLQPGESIEL 194


>gi|467162|gb|AAA50926.1| u0247g [Mycobacterium leprae]
          Length = 186

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 52/178 (29%), Positives = 80/178 (44%), Gaps = 5/178 (2%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTND 127
           +       +KP G+ +T SD  GR  V D +        ++  VGRLD +TEGL+LLTND
Sbjct: 4   DSLVYLALNKPRGMYSTMSDDRGRPCVGDLIERRVRGNKKLFHVGRLDADTEGLILLTND 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC-YGDMQVTLDTQKGSN 186
           G LA  L  PS +  + Y     G V +     L  G+ +     + D    +D   G  
Sbjct: 64  GELAHRLMHPSHEVSKTYLATVKGAVPRGLGKKLSVGLELDDGPAHVDDFAVVDAIPGKT 123

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
             V + L EG+ R ++++     + V  L+R   G   LG    G  R + +  +R+ 
Sbjct: 124 -LVRLTLHEGRKRIVRRLLTAAGFPVEMLVRTDIGAVSLGDQRPGCLRALLRDEIRQL 180


>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 =  170 bits (432), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 53/231 (22%), Positives = 88/231 (38%), Gaps = 31/231 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G ++  S+   R T+   +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTMSQFSEHPTRPTLASCV--SVPGVYPAGRLDADSEGLLLLTDDGVLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D D L  L+ G+ +        +V                 
Sbjct: 61  ADPRHKLEKTYLAQVEGIPDADALARLRAGVDLGDFVTRPAKVRAVEAPDWLWPRHPPVR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                  +W+ + +REGKNR+++++         RLIR+  G   L    L  G + EV 
Sbjct: 121 FRAAIPTSWLELKIREGKNRQVRRMTAAVGLPTLRLIRVGIGALDLRSLNLAPGESCEV- 179

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
                       L E+ + L      +    R   +   +      R++  
Sbjct: 180 -----------PLAESGMALATSNGRAAPAPRIHVSKTRQANGTKRRLRYK 219


>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 =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 92/229 (40%), Gaps = 6/229 (2%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN G L 
Sbjct: 13  DLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNHGDLV 70

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             +        + Y V     + ++ +     G+ I G            +K +     +
Sbjct: 71  NKILRAGNDHEKEYLVTVDKPITEEFIRGXSAGVPILGTVTK----KCKVKKEAPFVFRI 126

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L +G NR+I++  E F ++V +L R       L  +  G  R+++   L +        
Sbjct: 127 TLVQGLNRQIRRXCEHFGYEVKKLERTRIXNVSLSGIPLGEWRDLTDDELIDLFKLIENS 186

Query: 252 EAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
            ++V   A        ++       +  +   R   N  +     ++KK
Sbjct: 187 SSEVKPKAKAKPKTAGIKRPVVKXEKTAEKGGRPASNGKRFTSPGRKKK 235


>gi|171909920|ref|ZP_02925390.1| Pseudouridine synthase, Rsu [Verrucomicrobium spinosum DSM 4136]
          Length = 189

 Score =  170 bits (431), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 48/191 (25%), Positives = 87/191 (45%), Gaps = 22/191 (11%)

Query: 75  LWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L   HKP G+++  T   P  R+     LP   + V  +GRLD ++EGLLLL+++    +
Sbjct: 2   LIAIHKPYGVLSQFTKEHPSHRTLAEFGLP---AGVYPIGRLDSDSEGLLLLSDEARWNQ 58

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P+    R Y V+  G    + +  L +G+ +        +V L             
Sbjct: 59  QLLHPTRGHERTYHVQVEGIPTAEAITRLTRGVQLPDFYTLACKVQLLEPAPLYPARVPP 118

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTRE 235
             + +    +W+ + L EGKNR+++++     +   RLIR + G  +L    L  G  +E
Sbjct: 119 IRERKSIPTSWLAMKLVEGKNRQVRRMTAAVGYPTLRLIRAAMGRLELARLDLEPGKWQE 178

Query: 236 VSKKILREQLG 246
           +++  ++  L 
Sbjct: 179 LTEGQIKLLLA 189


>gi|291550526|emb|CBL26788.1| pseudouridine synthase family [Ruminococcus torques L2-14]
          Length = 194

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 48/190 (25%), Positives = 81/190 (42%), Gaps = 28/190 (14%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             ++++KP G VT   D     TV D         +  VGRLD  T GLLL+T+DG   +
Sbjct: 3   HYYMFNKPFGCVTARRDSLY-PTVMDYFSELNNDNLNPVGRLDRETTGLLLITDDGVFNQ 61

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV- 189
            L  PS    + Y     G + +D+   L+KGI+++G  +     ++ +  Q   +  + 
Sbjct: 62  KLTHPSYHKEKTYHFTVLGDLTEDRCQQLEKGILLKGSPVLTSPAKLKVFRQDILSNIID 121

Query: 190 ----------------------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG- 226
                                  + + EG+ R+I+++ +  +  V  L RIS     L  
Sbjct: 122 TLHPEVQNAVCHNLPTHPVTYGEITISEGRKRQIRRMMKAVHCCVIELKRISIEDIILDE 181

Query: 227 TLLAGSTREV 236
           TL  G  +E+
Sbjct: 182 TLSPGEWKEI 191


>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 =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 108/238 (45%), Gaps = 11/238 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K ++  G  SR + E +I ++++ VNG         V   + I ++G  L + +  
Sbjct: 1   MRLQKFLSDIGYCSRGQAEDLIRKRKIMVNGKQAT-LGDKVRGNEKIVIEGRLLERKKGP 59

Query: 74  --RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ L+HKP  +  + +      T+ D       RV  VG LD  +EG+LLLTNDG +A
Sbjct: 60  AKKVLLFHKPEAVDCSLAPSKTTKTLLD-FDFGTDRVFPVGYLDQASEGILLLTNDGEIA 118

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             L LP  +    Y +    ++D + +  L +            +  +D ++     + +
Sbjct: 119 NKLSLPEFRPEDEYLLTSPEEIDAEMIEKLTQ-----ARKAEKNKSVVDIEQIDAKHLRI 173

Query: 192 GLRE-GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPH 248
            L++ G++++IKK+ E     + +L+R+  G   L  L  G    +  + L+  L   
Sbjct: 174 -LQQGGRSKDIKKMCEAVELVIEQLVRVRVGNITLEGLEKGIYIPLDPEQLKRLLKKQ 230


>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 =  169 bits (430), Expect = 4e-40,   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   LIAFNKPCGVICQFSPHETHPSLKDHIDA--PGFYPAGRLDTDSEGLLLLTNDGRLQARI 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P     + Y  +  G  D+ KL LL++ + +        +  L               
Sbjct: 65  AEPRHGKEKTYWAQVEGAPDEHKLALLRRPMDLGDFITQPARTRLLAADETERLWPRQPP 124

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGSTRE 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|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 =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 83/180 (46%), Gaps = 17/180 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L++KP G+++  +D  G  TV   L        V   GRLD ++EGLLLL +DG L 
Sbjct: 3   RLLLFNKPFGVLSQFTD-RGSPTVRSTLSDFIAVKGVYPAGRLDRDSEGLLLLCDDGRLQ 61

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-------------- 177
             +  P  +  + Y V+  G   + +L  L++G+ ++        V              
Sbjct: 62  ARIADPRFKMPKTYLVQVEGDPQEPELERLRQGVQLKDGMTLPADVARIDEPDLWLRDPP 121

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               +   + W+ + +REG+NR+++++         RL+R S G + +  +  G   ++S
Sbjct: 122 IRQRKAIPDNWLKLTIREGRNRQVRRMTAAVGLPTLRLVRWSIGDWSVAGIAPGRFEQLS 181


>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 =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/195 (28%), Positives = 85/195 (43%), Gaps = 28/195 (14%)

Query: 76  WLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L HKP G+++  +   G     + D +P    +V + GRLD ++EGLLLLT +G L + 
Sbjct: 8   LLLHKPYGVLSQFTPEPGSRWRCLADLVP--VPQVYAAGRLDADSEGLLLLTTEGRLQQR 65

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------------- 177
           L  P     R Y V+  G     +L  L  G+++QG      Q                 
Sbjct: 66  LTDPRFGHWRTYWVQVEGTATDKQLQQLCDGVLVQGRQTLPAQAQRLRHDQIQPWPDRVP 125

Query: 178 -TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLA 230
              + +     W+ + LREG+NR+++++         RLIR +        P  L  L  
Sbjct: 126 PIRERRSIPTDWLELSLREGRNRQVRRMTAAVGLPTLRLIRSAIDLMDGGLPLNLNGLAP 185

Query: 231 GSTREVSKKI-LREQ 244
           GS R VS +  LR Q
Sbjct: 186 GSWRPVSTEEHLRLQ 200


>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 =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 46/158 (29%), Positives = 79/158 (50%), Gaps = 1/158 (0%)

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             DP GR T+ D +   + R+  +GRLD ++EGL+L+TNDG L++ +  P  +  + Y  
Sbjct: 1   MEDPKGRYTLRDIVGDKYERIFHMGRLDYDSEGLILMTNDGELSQHVMHPKYEVEKTYIA 60

Query: 148 RFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G++       L   G+ +        +  +      +  V V L  GKNR ++++F 
Sbjct: 61  TLEGRISGQVCRRLVTTGVKLDDGWIKLDRCAILDSSRESTLVKVVLHSGKNRIVRRIFG 120

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              + V RL+R   GP +LG L +G+ R +S+  +R  
Sbjct: 121 SIGFPVKRLVRTQIGPIKLGDLKSGTYRVLSQAEVRSL 158


>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 =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 53/193 (27%), Positives = 89/193 (46%), Gaps = 20/193 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             + ++ +KP  ++T     +G++++ D    + S V  VGRLD ++EGLL+LTND  L 
Sbjct: 2   PFKYYIIYKPFQVLTRFGKEEGKASLADYF-DVPSDVYPVGRLDYDSEGLLILTNDKSLN 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGD--MQVTLDTQKGS-- 185
             L  P     R Y V+  G V+ + +  LK+G+ I   G  Y     Q  +  ++    
Sbjct: 61  HRLLDPKFSHEREYWVQVDGAVNAEAIQQLKQGVKIAIDGKPYQTRRCQAAIFEEEPPVP 120

Query: 186 -------------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                          W+ + L EGKNR+++K+     +   RLIR       +  L  G 
Sbjct: 121 ERNPPIRFRKLIPAPWIRLTLGEGKNRQVRKMTAAVGFPTLRLIRYRIARITVEGLEPGQ 180

Query: 233 TREVSKKILREQL 245
            RE+ +K + + L
Sbjct: 181 MREMDRKEIFDLL 193


>gi|192361547|ref|YP_001983032.1| pseudouridylate synthase [Cellvibrio japonicus Ueda107]
 gi|190687712|gb|ACE85390.1| pseudouridylate synthase [Cellvibrio japonicus Ueda107]
          Length = 258

 Score =  169 bits (429), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 53/249 (21%), Positives = 101/249 (40%), Gaps = 20/249 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L++KP G+++  +  + R T+   +      V   GRLD ++EGLLLLT+DG L  ++
Sbjct: 9   LILFNKPYGVLSQFTAKEERPTLAQYI--RIPNVYPAGRLDHDSEGLLLLTDDGDLQHLI 66

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------D 180
             P+ +  + Y V+  G  +   L  L++G+ +        +V L              +
Sbjct: 67  SHPAHKQPKTYWVQVEGAPNSYALTKLRQGVELNDGMTQPAEVRLIPAPKLWERKPPIRE 126

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                  W+ + + EG+NR+++++         RL+R+  GP+ L  +  G  R  ++ +
Sbjct: 127 RANIPTQWLEIVITEGRNRQVRRMTAAVGHPTLRLVRVKIGPWTLEGIEPGKYR--TETV 184

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
              ++G         +  +   +        P    E      R K  + +       K 
Sbjct: 185 HAPKMGNTTNRRPSGSRPSGAKTGVPHKTPHPKATQERAHAGPRGKPAAPKSTAAKPAKT 244

Query: 301 --LATPVHR 307
             L  P  R
Sbjct: 245 LVLQKPKPR 253


>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 =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 80/187 (42%), Gaps = 19/187 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L   +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   HLIALNKPFGTICQFSPHETRGSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G  D   L  L++G+ +        +    T            
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAGALATLERGVDLGDYVTRPCRARFVTPPDTLWPRNPPV 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RLIR+  G   L    L  G TRE+
Sbjct: 120 RYRAAIPTTWIELEIAEGKNRQVRRMTAAVGFPTLRLIRVGIGALDLFALGLAPGETREL 179

Query: 237 SKKILRE 243
             +   E
Sbjct: 180 PPRAPWE 186


>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 =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 53/140 (37%), Positives = 81/140 (57%), Gaps = 1/140 (0%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ K IA +G  SRR+ E +I++ +VKVNG  +      V  +D IEV+G+ +   ++ 
Sbjct: 6   ERLQKRIANSGYTSRRKAETLISEGKVKVNGTTVTELGTKVKPSDTIEVEGIKIELEDKI 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
              L+HKP  ++T+ SD  GR+ V D    I +R+  VGRLD +T GLLLLTNDG    +
Sbjct: 66  -YILFHKPTQVITSVSDDRGRTVVTDYFKDIEARIYPVGRLDYDTSGLLLLTNDGEFTNL 124

Query: 134 LELPSTQWLRVYRVRFHGQV 153
           +  P  Q  + Y  +  G +
Sbjct: 125 MTHPRYQIKKKYVAKLKGYL 144


>gi|331004981|ref|ZP_08328391.1| pseudouridine synthase [gamma proteobacterium IMCC1989]
 gi|330421223|gb|EGG95479.1| pseudouridine synthase [gamma proteobacterium IMCC1989]
          Length = 237

 Score =  169 bits (428), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 92/251 (36%), Gaps = 45/251 (17%)

Query: 73  TRLWLYHKPIGLVTTHSDPD--------------GRSTVFDNLPSIFS--RVISVGRLDI 116
             L L +KP  +++  +                     + D L S      V   GRLD 
Sbjct: 2   PTLILLNKPFKVLSQFTPEKLQHAPTNITTPSNTAEKPLKDTLASYIKQKHVYPAGRLDY 61

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           ++EGLLLLT+DG L + +  P  +  + Y V+  G+ + + +  L+KG+ ++        
Sbjct: 62  DSEGLLLLTDDGALQQHISHPQYKLPKTYWVQVEGEQNLEAIIALRKGVELKDGLTKPAL 121

Query: 177 VTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
           V                  Q     W+++ + EGKNR+++++         RL+R S G 
Sbjct: 122 VEAIEEPDLWPRNPPVRFRQSIPTHWLSITISEGKNRQVRRMTAAVGLPTLRLVRASIGD 181

Query: 223 FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDF 282
           + L  L  G  R +                     + PI +     + + +   +  ++ 
Sbjct: 182 WTLEGLQPGEHRSI---------------AVPSPPNQPIKTKNKAGKPKAHRTRKSANNT 226

Query: 283 TRMKKNSSQKN 293
               K    K 
Sbjct: 227 NAKDKKGKHKR 237


>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 =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 52/192 (27%), Positives = 83/192 (43%), Gaps = 23/192 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +L +KP  +++  S      T+ D   +    +  VGRLD ++EGLLLLTND  L   
Sbjct: 3   QYFLIYKPFNMLSQFSREGDHQTLADLGFTFAKDIYPVGRLDADSEGLLLLTNDNFLKTK 62

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDMQVTLD----------- 180
           L  P  +  R Y V+  G+V  +    L  G+   I G  Y  +   +            
Sbjct: 63  LLEPRNRHTRTYYVQVEGEVTDEACRQLSAGVSISINGKQYKTLPAEIAKIAEPELPERN 122

Query: 181 -----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL-----A 230
                 +    +W++V LREGKNR+++++     +   RL+R S G   L          
Sbjct: 123 PPIRFRKNIPTSWLSVTLREGKNRQVRRMTAAVGFPTLRLVRWSIGKISLADKKINFPNP 182

Query: 231 GSTREVSKKILR 242
           G   EV+ K  +
Sbjct: 183 GDVWEVTPKEAK 194


>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 =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 79/177 (44%), Gaps = 16/177 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             ++ L++KP  ++   ++P  R T+ D +      V + GRLD ++EGLL+LT+ G + 
Sbjct: 12  HVQIILFNKPFNILCQFTEPGKRLTLADYI--SIPGVYAAGRLDYDSEGLLVLTDTGRIQ 69

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
           + +  P     + Y V+  G      +  L  G++++        V              
Sbjct: 70  QRIADPRADMAKSYWVQVEGVPTLAAIQQLTCGVLLEDGLTLPAIVEQIKPPSVWLRTPQ 129

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
             + ++    W+ + L E +NR I+++         RLIR + GP+QL  L  G  +
Sbjct: 130 IRERRQIPTTWLAITLTEDRNRLIRRMTAAVGLPTLRLIRQAVGPWQLNKLQPGDWK 186


>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 =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 102/242 (42%), Gaps = 15/242 (6%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           RV K++   G  SR E+ R+     + ++G+ L   +  +  T  +    +VDG PL   
Sbjct: 7   RVDKLLGSMGYGSRSEIARLGKVGGIVLDGVDLTDVSKRIAVTPDLPSRMQVDGRPLDPP 66

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
               + + +KP+G+  +H +      V+D LP  + R       +GRLD  T GLLLLT+
Sbjct: 67  AG-VVLILNKPLGMTCSHKEDGD--LVYDVLPDRWRRRDPAISTIGRLDKQTSGLLLLTD 123

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P     +VY       +   + ++   G +V++G         L+    +
Sbjct: 124 DGDLLHRVISPKRHVAKVYHATLARPLAGTEGDVFAAGGLVLEGEDKPLAPAELEVLSPT 183

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
            A +TV   EG+   ++++F      V  L R   G   L   L  G  R  +   +   
Sbjct: 184 EARLTVT--EGRYHMVRRMFAAVGNHVEALHRERVGGLVLPADLGPGDWRLATGAEVEAI 241

Query: 245 LG 246
             
Sbjct: 242 FA 243


>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 =  168 bits (427), Expect = 9e-40,   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   LIAFNKPCGVICQFSEHEKHPCLKDYVDR--PGFYPAGRLDTDSEGLLLLTDNGVLQAQI 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|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 =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 80/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L   +
Sbjct: 4   LIILNKPYGVICQFSAHEKHQCLKDFVEK--PGFYPAGRLDTDSEGLLLLTNNGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +               
Sbjct: 62  ADPKFKQVKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTHPAEVRVLEEGEADVLWPRVPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGST 233
               +   + WV + + EGKNR+++++     +   RL+R++ G   L    L  G  
Sbjct: 122 IRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQW 179


>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 =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 49/191 (25%), Positives = 80/191 (41%), Gaps = 28/191 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLA 131
              +++HKP G VT   D D   TV D        R+  VGRLD  T GLLL+T+DG   
Sbjct: 23  PHYYMFHKPFGCVTARRD-DRYPTVMDYFEELQNDRLSPVGRLDRETTGLLLITDDGIFN 81

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---------- 181
           + L  PS    + Y     G +  + ++ L+ G++++G         +            
Sbjct: 82  QKLTHPSYHKEKTYEFTLLGDLTPELVHKLETGVILKGADTLTAPAKITVTGHAVMSDIL 141

Query: 182 ------------QKGSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                       +   +  +T   + + EGK R+I+++ +  +  V  L RIS G   L 
Sbjct: 142 STLPEEIQKDIHKNRPDHPITYGIITISEGKKRQIRRMMKSVHCCVIELKRISIGDIVLD 201

Query: 227 T-LLAGSTREV 236
             L  G  +E+
Sbjct: 202 KALCPGEWKEI 212


>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 =  168 bits (427), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 56/295 (18%), Positives = 111/295 (37%), Gaps = 52/295 (17%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDD--PTLRIAGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        +    ++           
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G T+E+
Sbjct: 120 RYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGTIDLVQLGLQPGETKEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P   +                      + +E P       K      G  
Sbjct: 180 EP-----LLYPDFKD----------------------VPAEQPYRSRSYVKKPGGTGGKP 212

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
             +K      +++    +W          S+  +R+ N    P+  + R   R S
Sbjct: 213 MVRKNKDGSAKKSGTKRIWQ------MDESEKPRRKTNGTTRPNTKAPRGRSRNS 261


>gi|332968985|gb|EGK08027.1| ribosomal large subunit pseudouridine synthase E [Psychrobacter sp.
           1501(2011)]
          Length = 201

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 50/199 (25%), Positives = 89/199 (44%), Gaps = 26/199 (13%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + L++KP G+ +  SD         +       +   GRLD  +EGLLLLT+DG + +
Sbjct: 2   PSVILFNKPYGVQSQFSDDANNKFAPLSQFFTDKSLRVAGRLDATSEGLLLLTSDGRVNK 61

Query: 133 VLELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--------- 178
            +  P       +  + Y V+  G+   ++L  L +G+V++       +V          
Sbjct: 62  AITHPPKANAGRKQGKTYLVQVEGEPTAEQLEQLCQGVVLKDGKTLPAEVKHLTEKELPM 121

Query: 179 ---------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     + +   ++W+ + + EGKNR+++++         RLIR S   F+LG L 
Sbjct: 122 PLWQRDPPIRERKNIPDSWLMMTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFELGDLG 181

Query: 230 AGST-R-EVSKKILREQLG 246
            G   R  ++ K L +QLG
Sbjct: 182 VGEFVRVHLNAKHL-QQLG 199


>gi|326562796|gb|EGE13091.1| ribosomal large subunit pseudouridine synthase E [Moraxella
           catarrhalis 46P47B1]
          Length = 250

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/231 (25%), Positives = 100/231 (43%), Gaps = 33/231 (14%)

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           T+L L++KP G+ +    D DG  T+ D +     RV   GRLD ++EGLLLLT++G L 
Sbjct: 2   TKLVLFNKPYGVHSQFKKDHDGMITLADFIDDKTMRV--AGRLDKDSEGLLLLTDNGRLN 59

Query: 132 RVLELP---------STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             +  P          T+  + Y V+        ++  L++G++++       +V    +
Sbjct: 60  HAITTPPTAKNAKDKYTKCAKTYLVQVENIATNVQIQALEQGVMLKDGKTLPAKVQKLDE 119

Query: 183 K------------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                                  W+ + + EGKNR+I+++         RLIR   G +Q
Sbjct: 120 NELPIRLWQRNPPVRQRVNIPTTWLKITIVEGKNRQIRRMVAHVGLPCLRLIRSQIGIWQ 179

Query: 225 LGTLLAGSTR--EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
           L  L  G +R  ++ ++IL + LG       + N    + SS T     P 
Sbjct: 180 LNGLAVGESRVLQLDQQILLK-LGLSAQPTPKQNKPTNLISSNTKGAVNPK 229


>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 =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 80/178 (44%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + +KP G++   S  +    + D +          GRLD ++EGLLLLTN+G L   +
Sbjct: 4   LIILNKPYGVICQFSAHEKHQCLKDFVEK--PGFYPAGRLDTDSEGLLLLTNNGRLQAQI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D+ KL+LL++G+ +        +V +               
Sbjct: 62  ADPKFKQIKTYWAQVEGSPDEAKLDLLRRGVDLGDFVTHPAEVRVLEEGEADVLWPRVPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGST 233
               +   + WV + + EGKNR+++++     +   RL+R++ G   L    L  G  
Sbjct: 122 IRVRKSVPDFWVEIKISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLNLELGQW 179


>gi|196233257|ref|ZP_03132103.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196222728|gb|EDY17252.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 188

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 49/181 (27%), Positives = 80/181 (44%), Gaps = 16/181 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  +HKP G+++  +    R             V  +GRLD  +EGLLLL+++  L   L
Sbjct: 2   LLAFHKPYGVLSQFTPDGSRHRPLAEF-DFPKGVYPLGRLDAESEGLLLLSDEAALNARL 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P+    R Y  +      ++ L  L++G+VI G      +V L               
Sbjct: 61  LHPTRGHYRTYWAQVERVPTREALTQLERGVVIGGRQTLPCRVWLLDPQPAVSPRVPPIR 120

Query: 181 -TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 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|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 =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 81/188 (43%), Gaps = 27/188 (14%)

Query: 78  YHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +KP G+++  +   G     + D +P    RV + GRLD ++EGLL+LT  G L   L 
Sbjct: 1   MNKPYGVLSQFTPEPGSQWRCLADLIP--IPRVYAAGRLDADSEGLLVLTAHGRLQHRLT 58

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--------------- 180
            P     RVY V+  G   + +L  L  G++IQG       V+                 
Sbjct: 59  NPHLSHWRVYWVQVEGSPSESQLQKLASGVIIQGKRTRPALVSWLKGKAAPIVRERDPPI 118

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLAGS 232
              Q    +W+ + L+EG+NR+++++         RLIR          P  +  L  G 
Sbjct: 119 RVRQSIPTSWLELKLKEGRNRQVRRMTAAVGLPTLRLIRHRIELMDGEPPLSIEGLDPGQ 178

Query: 233 TREVSKKI 240
            R+VS + 
Sbjct: 179 WRQVSSRE 186


>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 =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 52/275 (18%), Positives = 100/275 (36%), Gaps = 31/275 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDD--PTLRIAGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        +    ++           
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G T+E+
Sbjct: 120 RYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGTIDLVQLGLQPGETKEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P          D P                       R  K+ S K   +
Sbjct: 180 EP-----LLYPDF-------KDVPAEQPYRSRSYVRKPGGTGGKPMVRKNKDGSAKKSGT 227

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQR 331
           K+        +    +N        +        R
Sbjct: 228 KRIWQMDESEKPRRKTNGTTRPNTKAPRGRSRNSR 262


>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 =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 50/262 (19%), Positives = 105/262 (40%), Gaps = 25/262 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFIDD--PTLRIAGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        +    ++           
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G T+E+
Sbjct: 120 RYRASIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLGLQPGETKEI 179

Query: 237 SKKILREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKN 293
              +L         E+   ++  +  P  +    +  +    S       R+ +    + 
Sbjct: 180 EP-LLYPDFKDVPAEQPYRSRSYVKKPGGTGGKPMVRKNKDGSVKKSGTKRIWQMDESEK 238

Query: 294 GLSKQKKLATPVHR--RNLASN 313
              K      P  +  R  + N
Sbjct: 239 PRRKTNGTTRPNTKAPRGRSRN 260


>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 =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 44/178 (24%), Positives = 78/178 (43%), Gaps = 21/178 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +  KP G++   S  +    + D +          GRLD ++EGLLLLTNDG L   +
Sbjct: 6   LIVLSKPYGVICQFSAHEKYGCLKDYV--SLPDFYPAGRLDTDSEGLLLLTNDGRLQARI 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ KL++L++G+ +        +V +               
Sbjct: 64  ADPKFKLEKTYWAQVEGSPDEAKLDMLRRGVDLGDFVTRPAKVRVLETGEADVLWQRVPP 123

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT--LLAGST 233
               +   + WV + + EGKNR+++++     +   RL+R++ G   L    L  G  
Sbjct: 124 IRVRKSVPDFWVEIRISEGKNRQVRRMTAKAGFPCLRLVRVAIGRLNLFDLGLALGQW 181


>gi|325136481|gb|EGC59087.1| ribosomal large subunit pseudouridine synthase B [Neisseria
           meningitidis M0579]
          Length = 200

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/172 (34%), Positives = 100/172 (58%), Gaps = 3/172 (1%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
            R+ LY+K  G + +  DP GR ++FD LP   S R +++GRLDINT GLL+LT  G L 
Sbjct: 9   PRIILYYKQEGEIVSRDDPQGRVSIFDRLPQAASSRWVAIGRLDINTSGLLILTTSGELV 68

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +    PS +  R Y VR  G +  +++ +L ++G++++       ++     +G+N W  
Sbjct: 69  QRFAHPSFEVEREYAVRVLGGLTGEQMRVLTEEGVMLEDGLAKVERIREQGGEGANKWYN 128

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           V ++EG+NRE++++FE     V+RL+R+ +GP  L   L  G   E++   +
Sbjct: 129 VVIKEGRNREVRRIFESQGLTVSRLVRVGFGPIGLPNRLKRGQFYELNPAEV 180


>gi|297537798|ref|YP_003673567.1| pseudouridine synthase [Methylotenera sp. 301]
 gi|297257145|gb|ADI28990.1| pseudouridine synthase [Methylotenera sp. 301]
          Length = 183

 Score =  168 bits (425), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 47/181 (25%), Positives = 81/181 (44%), Gaps = 23/181 (12%)

Query: 75  LWLYHKPIGLVTTHSDPD------GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + L++KP  +V   S  D      G  T+ D +      V + GRLD ++EGLL+LT+DG
Sbjct: 2   IILFNKPFNVVCQFSAHDPGNGKTGHPTLKDFI--QIPDVYAAGRLDTDSEGLLILTDDG 59

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------- 179
            L   L  P  +  + Y V+  G    + L  L +GI +        QV L         
Sbjct: 60  MLQHRLSDPKRKEFKTYWVQVEGTPSTEDLEPLIRGIDLSDFVAKPAQVRLIPEPESLWL 119

Query: 180 ------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 + +    +W+ + + EGKNR+++++     +   RLIR + G + +  +  G  
Sbjct: 120 RNPPIRERKAIPTSWLEIKISEGKNRQVRRMTAKIGFPTLRLIRYAIGQYTIDGIQNGQH 179

Query: 234 R 234
           +
Sbjct: 180 K 180


>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 =  168 bits (425), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/282 (19%), Positives = 108/282 (38%), Gaps = 29/282 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   +     T+   +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIIIFNKPYDVLSQFREDSKHLTLSHFIHD--PELRLAGRLDLDSEGLMFLTDHGGLNQF 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     
Sbjct: 120 RFRASIPTTWVELQICEGRNRQVRRMTAAVGFPTLRLIRTQIGTIDLVKLGLQPGE---- 175

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            +  +   L P       V  D P Y+  +  R       E  D  ++  K   +  G +
Sbjct: 176 -QVEIEPLLYPDF---KDVPADKP-YTGRSAPRSAAKKPFEQKDGKSKFNKEQPKDKGAN 230

Query: 297 KQ-KKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRR 337
           K  KKL +   +R   +    AK    +  +    +     R
Sbjct: 231 KAGKKLPSGGTKRVWQTEEGEAKPRRKTNGTTRPGKIRRSNR 272


>gi|206603683|gb|EDZ40163.1| Protein of unknown function [Leptospirillum sp. Group II '5-way
           CG']
          Length = 298

 Score =  168 bits (425), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 65/234 (27%), Positives = 117/234 (50%), Gaps = 13/234 (5%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNV---MSTDHIEVDGVPLRKAER 72
            + I++ G+ +R      +   R+ + +G L++     V     ++ +      +  A+ 
Sbjct: 23  DRWISKLGLGTRGMAREWVRDGRLSLGDGTLVQHVDQFVQGTPGSEPVFRLDQKILSADP 82

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--------IFSRVISVGRLDINTEGLLLL 124
             ++ ++KP G++ T +DP GR T+ +++            SR++ VGRLD  + GL+LL
Sbjct: 83  PAVFAFNKPRGVLVTRTDPGGRETICESIGRSSGQRTGMDMSRLMPVGRLDQASSGLILL 142

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDMQVTLDTQK 183
           TN       L  P+ ++ R YRV+    + +    + 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|323209958|gb|EFZ94867.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 150

 Score =  168 bits (425), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/149 (44%), Positives = 87/149 (58%), Gaps = 6/149 (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  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           DG LA  L  PS +  R Y VR  GQVD+
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFGQVDE 150


>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 =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 50/267 (18%), Positives = 106/267 (39%), Gaps = 30/267 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   + +   TV   +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPYDVLSQFREDEAHLTVSSFIKD--PELRIAGRLDLDSEGLMFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQK--------- 183
           +  PS +  + Y  +  G V ++ L  L+ G+ +        +   +D  +         
Sbjct: 60  ITHPSNKKYKTYLAQVDGDVTEEALEQLRNGVELADGMTLPAKAMKVDEPEWLWDRDPPV 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G   E+
Sbjct: 120 RYRASIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLIRTQIGSINLIRLGLQPGEQTEI 179

Query: 237 SK------KILRE---QLGPHLLEEAQVNLDAPIYSSET-LVRDRPNIISEVPDDFTRMK 286
                   K L E         +++       P++  +    +  PN          +M 
Sbjct: 180 EPLLFPDFKDLPEDKPYRSRSYVKKPGGTGGKPMHQKKKEGDKKDPNKKKSGTKRIWQMD 239

Query: 287 KNSSQKNGLSKQKKLATPVHR-RNLAS 312
           ++   +   +   +  T   R R+  S
Sbjct: 240 ESEKPRRKTNGTTRPNTKAPRGRSRNS 266


>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 =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 54/177 (30%), Positives = 85/177 (48%), 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  GDALTRPGNCI-KVYEIWVRGHVTDEHIAEAKRGVESKHGLLKALVVEKLGTGGAKTKLK 123

Query: 191 VGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           + + EGKNR I+++F            KV  L RIS G F+L  + +G  R ++ + 
Sbjct: 124 IVIDEGKNRHIRRLFGALKDPKFGTPLKVLELKRISIGSFEL-DIESGKWRYLTVEE 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 =  167 bits (424), Expect = 2e-39,   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   LIALNKPYGVICQFSPHEKYRTLKDFV--NVPNVYPAGRLDTDSEGLLLLTDDGKQQARI 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|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 =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 53/292 (18%), Positives = 108/292 (36%), Gaps = 49/292 (16%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRL--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ +             ++           
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPATAIKVSEPEWLWERNPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G  +E+
Sbjct: 120 RFRANIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLGLKPGDVKEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P   +                      + +E P       K      G  
Sbjct: 180 EP-----LLYPDFKD----------------------VPAEEPYRSRSYVKKPGGTGGKP 212

Query: 297 KQKKLATPVHRRNLASNVW-MAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             +K      +++    +W M +G      ++   R     ++P    +   
Sbjct: 213 MVRKNKDGSTKKSGTKRIWQMDEGEKPRRKTNGTTRPNA--KAPRGRGRNDR 262


>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 =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 47/195 (24%), Positives = 87/195 (44%), Gaps = 25/195 (12%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + L++KP G+ +  SD         +       +   GRLD  +EGLLLLT+DG + + +
Sbjct: 6   VILFNKPYGVQSQFSDDANNKFAPLSQFFTDKSLRVAGRLDATSEGLLLLTSDGQVNKAI 65

Query: 135 ELPST-----QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------- 178
             P       +  + Y V+  G    ++L  L++G++++       +V            
Sbjct: 66  THPPKANAGRKQGKTYLVQVEGIPSNEQLEQLRQGVLLKDGQTLPAEVKHISEEDLPMPL 125

Query: 179 -------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                   + +   ++W+ + + EGKNR+++++         RLIR S   F+LG L  G
Sbjct: 126 WQRDPPIRERKSVPDSWLMMTIYEGKNRQVRRMTAHVGLPCLRLIRWSAAGFELGNLAVG 185

Query: 232 ST-R-EVSKKILREQ 244
              R  ++ K L+E 
Sbjct: 186 EFVRVHLNDKRLKEL 200


>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 =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 42/190 (22%), Positives = 77/190 (40%), Gaps = 19/190 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KKILREQLGP 247
            +   +   P
Sbjct: 181 PRAPWDGFAP 190


>gi|170693552|ref|ZP_02884711.1| pseudouridine synthase [Burkholderia graminis C4D1M]
 gi|170141707|gb|EDT09876.1| pseudouridine synthase [Burkholderia graminis C4D1M]
          Length = 189

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 44/180 (24%), Positives = 77/180 (42%), Gaps = 19/180 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSAHETRASLADWVK--VPGVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  + ++ Y  +  G VD   L  L +G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGAVDSAALKKLARGVDLGDYVTKPCRAEYVEPGDTLWTRTPPI 119

Query: 181 --TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RL+R+  G   +    L  G + E+
Sbjct: 120 RYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGMGALDIFSLGLQPGESVEL 179


>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 =  167 bits (424), Expect = 2e-39,   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   LIVFNKPCGVVCQFGAHEKHRSLKDFIDA--PGFYPAGRLDTDSEGLLLLTCNGRMQARI 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|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 =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 60/264 (22%), Positives = 102/264 (38%), Gaps = 44/264 (16%)

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           T+L L++KP G+ +    D DG  T+ D +     RV   GRLD ++EGLLLLT++G L 
Sbjct: 2   TKLVLFNKPYGVHSQFKKDHDGMITLADFIDDKTMRV--AGRLDKDSEGLLLLTDNGRLN 59

Query: 132 RVLELP---------STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             +  P          T+  + Y V+        ++  L++G++++       +V    +
Sbjct: 60  HAITTPPTAKNAKDKYTKCAKTYLVQVENIATNVQIQALEQGVMLKDGKTLPAKVQKLDE 119

Query: 183 K------------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                                  W+ + + EGKNR+I+++         RLIR   G +Q
Sbjct: 120 NELPIRLWQRNPPVRQRVNIPTTWLKITIVEGKNRQIRRMVAHVGLPCLRLIRSQIGIWQ 179

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           L  L  G +R +      +     LL+        P  +  T +       +  P     
Sbjct: 180 LNGLAVGESRVL------QLDQQTLLKLGLSAQPTPKQNKPTNLISSNTKGAVNP----- 228

Query: 285 MKKNSSQKNGLSKQKKLATPVHRR 308
               S + + L K      P   R
Sbjct: 229 ---KSGKIHLLKKPSWRVRPPKFR 249


>gi|134296698|ref|YP_001120433.1| pseudouridine synthase [Burkholderia vietnamiensis G4]
 gi|134139855|gb|ABO55598.1| pseudouridine synthase [Burkholderia vietnamiensis G4]
          Length = 192

 Score =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 43/182 (23%), Positives = 77/182 (42%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G  D   L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPDAADLKALARGVDLGDYVTRPCRAEFIEPPAALWPRTPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T E+ 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGVLDIFALGIAPGETIELP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 49/267 (18%), Positives = 105/267 (39%), Gaps = 30/267 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   + +   TV   +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPYDVLSQFREDEAHLTVSSFIKD--PELRIAGRLDLDSEGLMFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQK--------- 183
           +  PS +  + Y  +  G V ++ L  L+ G+ +        +   +D  +         
Sbjct: 60  ITHPSNKKYKTYLAQVDGDVTEEALEQLRNGVELADGMTLPAKAMKVDEPEWLWDRDPPV 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G   E+
Sbjct: 120 RYRASIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLIRTQIGSINLIRLGLQPGEQTEI 179

Query: 237 SK------KILRE---QLGPHLLEEAQVNLDAPIYSSET-LVRDRPNIISEVPDDFTRMK 286
                   K L E         +++       P++  +    +  PN          +M 
Sbjct: 180 EPLLFPDFKDLPEDKPYRSRSYVKKPGGTGGKPMHQKKKEGDKKDPNKKKSGTKRIWQMD 239

Query: 287 KNSSQKNGLSKQKKLATPVHRRNLASN 313
           ++   +   +   +  T    R  + N
Sbjct: 240 ESEKPRRKTNGTTRPNTKAP-RGRSRN 265


>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 =  167 bits (423), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 82/179 (45%), Gaps = 18/179 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLA 131
           RL L +KP G+++  +   G+  V D L        V   GRLD ++EGLLLLT+DG L 
Sbjct: 3   RLILLNKPFGVLSQFT--GGKEGVEDTLAHLVDVPDVYPAGRLDKDSEGLLLLTDDGKLQ 60

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G+   D L  L +G+ ++       +               
Sbjct: 61  SRIAEPRYKIAKAYLVQVEGEPGDDALEKLSRGVELKDGMTRPARAKRIDPPPVWERDPP 120

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               +   ++W+ + + EG+NR+++++         RLIR   G + +  +  G+ R++
Sbjct: 121 VRYRKSVPDSWIALEITEGRNRQVRRMTAAVGLPTLRLIRWRIGEWSVDGIAPGTYRKI 179


>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 =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/292 (19%), Positives = 110/292 (37%), Gaps = 49/292 (16%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   T+ D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTMSDFVSDSTLRL--AGRLDMDSEGLVFLTDHGGLNQY 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ ++       + +   Q           
Sbjct: 60  ITNPANKKFKTYLVQVDGDVTEEALEQLRKGVELKDGMTLPAEASKVEQPEWLWERDPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL--GTLLAGSTREV 236
                   +WV + + EG+NR+++++     +   RLIR   G   L    L  G T+E+
Sbjct: 120 RFRASVPTSWVEISICEGRNRQVRRMTAAVGFPTLRLIRTKIGAIDLVQMGLQPGETKEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P                      D  NI +E P       K      G  
Sbjct: 180 EP-----LLYP----------------------DFQNIPAEEPYRSRSYVKKPGGTGGKP 212

Query: 297 KQKKLATPVHRRNLASNVW-MAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             +K      +++    +W M         ++   R     ++P    +   
Sbjct: 213 MVRKNKDGSVKKSGTKRIWQMDDSEKPKRKTNGTTRPNT--KAPRGRGRNGR 262


>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 =  166 bits (422), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 45/179 (25%), Positives = 73/179 (40%), Gaps = 15/179 (8%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
             HKP G+++  +   G          +   V  +GRLD ++EGLLLL+++ GL   L  
Sbjct: 4   ALHKPYGVLSQFTPEPGSRWRTLAEFGLPPAVYPLGRLDADSEGLLLLSDEPGLNTRLLN 63

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---------------T 181
           P     R Y V+         L  L++G+ I                             
Sbjct: 64  PDQAHRREYWVQVERVPTDAALAQLQRGVKIGDYATRPCAARRLDPAPTLPPRDPPIRAR 123

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           +   + W+ + L EGKNR+++++         RL+R+  G F LG L  G  RE++   
Sbjct: 124 KNVPDCWLALELIEGKNRQVRRMTAAIGHPTLRLVRVRIGDFALGKLAVGQWRELTADE 182


>gi|330895553|gb|EGH27863.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. japonica str.
           M301072PT]
          Length = 190

 Score =  166 bits (421), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 42/165 (25%), Positives = 80/165 (48%), Gaps = 16/165 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|303286639|ref|XP_003062609.1| pseudouridylate synthase [Micromonas pusilla CCMP1545]
 gi|226456126|gb|EEH53428.1| pseudouridylate synthase [Micromonas pusilla CCMP1545]
          Length = 386

 Score =  166 bits (421), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 110/276 (39%), Gaps = 41/276 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + D  +       QRVSK++++ G+ASRRE E +I +  V VNG  +    + V     I
Sbjct: 79  VDDGELPPHPIQTQRVSKLMSQRGMASRREAEALIDRGDVIVNGGEVATRGMKVAIDATI 138

Query: 61  EV----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR---------------------- 94
           ++    DG       +    + +KP G V+       R                      
Sbjct: 139 DIAGDSDGGANALLAKKVTVVLNKPPGYVSNLPSRGEREASELITPRNAIYHHSTGGGVV 198

Query: 95  ----------STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
                         +++      +   GRLD ++ GLL+LT DG LAR +     +  +V
Sbjct: 199 GGGADADAATRRKLEDVCRDARALNVCGRLDKDSRGLLVLTTDGVLARAIVG-GNEIPKV 257

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           Y V       +++L  L   + + G     M+V    +      +   LR+GK R+I+++
Sbjct: 258 YEVVVDAIATREQLAALNGPVALDGERLLPMRV----ETLEGTTLRFELRQGKKRQIRRL 313

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            E    +V  L R+  G   +G L  G  R +S+  
Sbjct: 314 CEGLALRVLDLRRVHVGTCDVGDLPEGRWRLMSEAE 349


>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 =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 56/185 (30%), Positives = 93/185 (50%), Gaps = 11/185 (5%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGL 130
            +L++ +KP G + T SD  GR TV+D LP        + +GRLD++++GLLL T +G +
Sbjct: 12  KKLFVLNKPKGYLVTRSDDLGRKTVYDLLPDWAFNEGWMPIGRLDLDSKGLLLFTTNGHI 71

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  L  P  +  +VY +   G V  + +    KG+         ++V      G+   ++
Sbjct: 72  SNALTTP-KKCTKVYEIWVRGHVMDEHIAEALKGVQTSQGLLKALEVKKIGMGGAKTKLS 130

Query: 191 VGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
           V + EGKNR I+++F            KV  L RIS G F+L  +  G+ R +S++  + 
Sbjct: 131 VVIDEGKNRHIRRLFGALKDPKFGTPLKVLELNRISIGDFKL-DIDIGTWRFLSEEEEKM 189

Query: 244 QLGPH 248
            L  H
Sbjct: 190 LLDKH 194


>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 =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 55/294 (18%), Positives = 110/294 (37%), Gaps = 52/294 (17%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRL--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ +        +    ++           
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPAKAIKVSEPEWLWERNPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G  +E+
Sbjct: 120 RYRANIPTSWIEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLGLRPGDVKEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P   +                      + +E P       K      G  
Sbjct: 180 EP-----LLYPDFKD----------------------VPAEQPYRSRSYVKKPGGTGGKP 212

Query: 297 KQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
             +K      +++    +W          S+  +R+ N    P+  + R   R 
Sbjct: 213 MVRKNKDGSAKKSGTKRIWQ------MDESEKPRRKTNGTTRPNTKAPRGRGRN 260


>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 =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 54/292 (18%), Positives = 108/292 (36%), Gaps = 49/292 (16%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   TV D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRKDEAHMTVSDFVDDPTLRL--AGRLDMDSEGLVFLTDHGGLNQF 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y V+  G V ++ L  L+KG+ +             ++           
Sbjct: 60  ITNPANKKYKTYLVQVDGDVTEEALEQLRKGVELNDGMTLPATAIKVSEPEWLWERNPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +WV + + EG+NR+++++     +   RLIR   G   L    L  G  +E+
Sbjct: 120 RYRANIPTSWVEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGSIDLVQLGLRPGDVKEI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P   +                      + +E P       K      G  
Sbjct: 180 EP-----LLYPDFKD----------------------VPAEEPYRSRSYVKKPGGTGGKP 212

Query: 297 KQKKLATPVHRRNLASNVW-MAKGIHSSFLSDSGQREENHRRSPSFPSKRSL 347
             +K      +++    +W M +       ++   R     ++P    + S 
Sbjct: 213 MVRKNKDGSAKKSGTKRIWQMDESEKPRRKTNGTTRPNT--KAPRGRGRNSR 262


>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 =  166 bits (420), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 42/182 (23%), Positives = 75/182 (41%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   + TL    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFTLGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 74/176 (42%), Gaps = 19/176 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLLALNKPFGTICQFSPHETRASLADWVK--VPNVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G VD   L  L +G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGAVDAATLKKLARGVDLGDYVTRPCRAEYVEPTDTLWVRTPPI 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGS 232
                    W+ + + EGKNR+++++     +   RL+R+  G   +    L  G 
Sbjct: 120 RYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFSLGLQPGE 175


>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 =  165 bits (419), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 54/212 (25%), Positives = 86/212 (40%), Gaps = 25/212 (11%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                ++  L +KP G+++  +   G              V + GRLD ++EGLLLLT++
Sbjct: 3   NPNRGSQTLLLNKPYGVLSQFTREQGSRWGCLADWVSVPEVYAAGRLDADSEGLLLLTSN 62

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G L + L  P     R Y  +  G+    +L  L++G+ IQG      +      +    
Sbjct: 63  GRLQQRLTDPRFGHWRTYWAQVEGEATASQLTQLEQGVPIQGKLTLPARAQPLASQLSDA 122

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQ 224
                           +W+T+ LREG+NR+++++         RLIR +        P  
Sbjct: 123 LPPRDPPIRTRATIPTSWITLSLREGRNRQVRRMTAAVGLPTLRLIRTTIDLMDGEAPLS 182

Query: 225 LGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
           L  L AG  R  S     EQ    LL   +V 
Sbjct: 183 LEGLSAGEWRPASTAE--EQRLMRLLSSRRVQ 212


>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 =  165 bits (419), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 58/231 (25%), Positives = 91/231 (39%), Gaps = 31/231 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G ++  S+   R T+   +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTMSQFSEHPTRPTLAACV--SVPGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  +  + Y  +  G  D   L  L+ G+ +        +V                 
Sbjct: 61  ADPRHKLEKTYLAQVEGIPDAAALARLRAGVDLGDFVTQPARVRAIDAPDWLWPRQPPVR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                  AW+ + +REGKNR+++++     +   RL+R+  GP  L    L  G+  EV 
Sbjct: 121 FRAAIPTAWLELKIREGKNRQVRRMTAAVGFPTLRLVRVGIGPLDLRALGLAPGACCEV- 179

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
              L  QLG        +   AP    E   R   +   +  D   R +  
Sbjct: 180 ---LPAQLG--------LAPAAPRMRQEPAPRSHVSKTRQANDTKRRSRYK 219


>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 =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 52/190 (27%), Positives = 89/190 (46%), Gaps = 20/190 (10%)

Query: 75  LWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +  ++KP G+++    +     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 KKILREQLGP 247
            +  R QL P
Sbjct: 180 SRE-RRQLMP 188


>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 =  165 bits (418), Expect = 1e-38,   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 + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKA--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  165 bits (418), Expect = 1e-38,   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 + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PSVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPHHKLVKRYWAQVDGAPGPADLKALTRGVDLGDYVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 49/267 (18%), Positives = 106/267 (39%), Gaps = 30/267 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   + +   T+   +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPFDVLSQFREDEAHLTLSHFIHD--PDLRLAGRLDLDSEGLMFLTDHGGLNQY 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P+ +  + Y  +  G V ++ L  L+KG+ +        +     Q           
Sbjct: 60  ITNPTNKKFKTYLAQVDGDVTEEALEQLRKGVELADGMTLPAKAIKVDQPEWLWDRDPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +W+ + + EG+NR+++++     +   RLIR   G   L    L  G  +E+
Sbjct: 120 RFRANIPTSWIELQICEGRNRQVRRMTAAVGFPTLRLIRTKIGAIDLVRLGLQPGEQKEI 179

Query: 237 SK------KILRE---QLGPHLLEEAQVNLDAPIYSSET-LVRDRPNIISEVPDDFTRMK 286
                   K L E         +++       P++  +    +  PN          +M 
Sbjct: 180 EPLLYPDFKDLPEDKPYRSRSYVKKPGGTGGKPMHQKKKEGDKKDPNKKKSGTKRIWQMD 239

Query: 287 KNSSQKNGLSKQKKLATPVHR-RNLAS 312
           ++   +   +   +  T   R R+  S
Sbjct: 240 ESEKPRRKTNGTTRPNTKAPRGRSRNS 266


>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 =  165 bits (418), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 46/198 (23%), Positives = 81/198 (40%), Gaps = 27/198 (13%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +        L +KP G+++  +  +G     + D +     +V + GRLD ++EGLL+LT
Sbjct: 11  KTQADLTTLLLNKPYGVLSQFTSEEGSRWRCLSDFVD--VPQVYAAGRLDADSEGLLILT 68

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-- 183
           ++G L + L  P     R Y  +  G  + ++L  L  G+V+QG      +      +  
Sbjct: 69  SNGRLQQRLTDPRFGHWRSYWAQVEGTPNTEQLQQLCDGVVVQGRRTLPAKARWLQGQDL 128

Query: 184 ---------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------P 222
                              W+ + L EG+NR+++++         RL+R          P
Sbjct: 129 PQLPERTPQIRFRAAIPTNWLQLSLSEGRNRQVRRMTAAVGLPTLRLVRCCIDLMDNGPP 188

Query: 223 FQLGTLLAGSTREVSKKI 240
             L  L  GS R V+   
Sbjct: 189 LDLTGLQPGSWRTVTAAE 206


>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 =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 74/176 (42%), Gaps = 19/176 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLLALNKPFGTICQFSPHETRASLADWVK--VPNVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G VD   L  L +G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGAVDAATLRKLARGVDLGDYVTRPCRAEYVEPTDTLWSRTPPI 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGS 232
                    W+ + + EGKNR+++++     +   RL+R+  G   +    L  G 
Sbjct: 120 RYRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFSLGLQPGE 175


>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 =  164 bits (417), Expect = 1e-38,   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   LIVFNKPYGVICQFSPHEKHRSLKEFI--GLPDVYPAGRLDTDSEGLLLLTANGRLQAKI 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  + ++ Y  +  G  D+ KL+LL+ G+ +        Q+ L               
Sbjct: 62  ADPRHKTVKTYWAQLEGSPDEAKLDLLRHGVDLGDFVTRPAQIRLPEKSETDRLWSRVPP 121

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGST 233
               +   + W+ + + EGKNR+++++     +   RL+R+  G   L    L  G  
Sbjct: 122 IRVRKSVPDFWLEIRISEGKNRQVRRMTAKAGYPCLRLVRVGIGRLDLWQLDLAPGQW 179


>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 =  164 bits (417), Expect = 1e-38,   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 + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  164 bits (417), Expect = 1e-38,   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 + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LLALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 55/279 (19%), Positives = 107/279 (38%), Gaps = 47/279 (16%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ + +KP  +++     +   T+ D +     R+   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVILNKPYDVLSQFRADEKHPTMADFVNDKDLRL--AGRLDMDSEGLVFLTDHGGLNQY 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P+ +  + Y V+  G V ++ L  L+KG+ ++       +    ++           
Sbjct: 60  ITNPANKKFKTYMVQVEGDVTEEALEQLRKGVELKDGITLPARAEKVSEPEWLWERNPPV 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL--GTLLAGSTREV 236
                   +WV + + EG+NR+++++     +   RLIR   G   L    L  G TRE+
Sbjct: 120 RFRASVPTSWVEISICEGRNRQVRRMTSAVGFPTLRLIRTKIGEIDLVRMGLQPGETREI 179

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
                   L P                      D  N+ +E P       K      G  
Sbjct: 180 EP-----LLYP----------------------DFQNVPAEEPYRSRSYVKKPGGTGGKP 212

Query: 297 KQKKLATPVHRRNLASNVW-MAKGIHSSFLSDSGQREEN 334
             +K      +++    +W M +       ++   R   
Sbjct: 213 MVRKNKDGSVKKSGTKRIWQMDESEKPRRKTNGTTRPNT 251


>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 =  164 bits (416), Expect = 2e-38,   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 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D ++L LL++ + +        ++ L               
Sbjct: 60  ANPRFKLTKTYWAQLEGSPDDERLALLQRPLDLGDFVAQPARIRLLDEHETARIWQRDPP 119

Query: 181 ---TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTRE 235
               +   + W+ + + EGKNR+++++     +   RLIR+  G   L  L    G  RE
Sbjct: 120 IRVRKSVPDFWLQIQICEGKNRQVRRMTAKAGYPCLRLIRVGIGRVNLFDLGIELGQWRE 179


>gi|159486060|ref|XP_001701062.1| pseudouridine synthase [Chlamydomonas reinhardtii]
 gi|158281561|gb|EDP07316.1| pseudouridine synthase [Chlamydomonas reinhardtii]
          Length = 241

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 97/246 (39%), Gaps = 25/246 (10%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER- 72
            RV +++A  G   RRE ++M+ +  V        +    +   D +    + L   E  
Sbjct: 1   MRVERLLANLGYGKRRECQQMVKKGHVM------RKDGGKLKVGDKVAWSDLELEGGEEL 54

Query: 73  ----TRLWLYHKPIGLVTTHSDPDG--RSTVFDNLP-----SIFSRVISVGRLDINTEGL 121
                 L   +KP G V T  D +      V+D LP          +  VGRLD +T GL
Sbjct: 55  DPPGPLLLAINKPTGYVVTAPDDEKVSDPVVYDLLPYSRFGRRRPFLSCVGRLDKDTSGL 114

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK----KG-IVIQGICYGDMQ 176
           LLLT+DG L   +  P     +VY       +              G + ++G     + 
Sbjct: 115 LLLTDDGTLLHRINSPKRGIWKVYEATLADPLSPKAAEAAAKKFASGTLTLEGDFSPLLP 174

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L+     +A   V + EG+  +++++F     KV  L R+S G   LG L     R +
Sbjct: 175 ARLERTGERSA--RVAICEGRYHQVRRMFAAVGNKVVGLRRVSVGGLALGDLPEAEWRFL 232

Query: 237 SKKILR 242
           + + L 
Sbjct: 233 TPQDLE 238


>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 =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 59/214 (27%), Positives = 92/214 (42%), Gaps = 29/214 (13%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
            A R    L+HKP G+++  +   G     + D +      V + GRLD ++EGLLLLT 
Sbjct: 9   PASRPTTLLFHKPYGVLSQFTPEPGSRWRCLADFI--AVPGVYAAGRLDADSEGLLLLTA 66

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGDMQVTL----- 179
           +G L + L  P+    R Y V+  G+  Q  + L  L++G+VIQG       V       
Sbjct: 67  NGRLQQRLTDPAFGHWRTYWVQVEGEAGQRPEALQQLRQGVVIQGRLTRPALVRCLSDPK 126

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY------GPFQ 224
                           +W+ + L+EG+NR+++++         RLIR++        P  
Sbjct: 127 LPERDPPIRQRATIPVSWLELQLQEGRNRQVRRMTARVGLPTLRLIRVAIDLMDGEAPLS 186

Query: 225 LGTLLAGSTREVSKKI---LREQLGPHLLEEAQV 255
           L  L  G  R VS +    L   L   +  EA  
Sbjct: 187 LSGLKPGDWRRVSHREEHRLARLLQRSVEAEAGP 220


>gi|145348269|ref|XP_001418577.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578806|gb|ABO96870.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 230

 Score =  164 bits (416), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/229 (26%), Positives = 105/229 (45%), Gaps = 19/229 (8%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK---- 69
           R+SK +A  G+ASRR  + +I   RVKVNG  +      V  + D + VDG  +      
Sbjct: 1   RLSKALASLGVASRRGADDLIFGGRVKVNGETVTAPQTKVNLNADVVMVDGKIVEGGVNF 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGR-STVFDNLPSI------------FSRVISVGRLDI 116
            +    ++ +KP G V +      +  TV+D                   R+ +VGRLD+
Sbjct: 61  VKEHAYFMLNKPKGFVCSTKSNSAQGKTVYDLFEQWRDEFKAAYPGKLPPRLFTVGRLDV 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
            T GLLLLT DG  ++ +  PS++ ++ Y V  + +  + ++  + KG  + G     ++
Sbjct: 121 ATTGLLLLTTDGDWSQRVAHPSSEVVKQYVVTANNKPTRAQIAAMAKGTEVDGARVVPVR 180

Query: 177 VT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           V  +    G    + V + +G+NRE++ +       V  L R   G  +
Sbjct: 181 VESMGADGGPANRILVEVVDGRNREVRVLCADAGVDVKNLKRTRVGGLR 229


>gi|289810570|ref|ZP_06541199.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 147

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 64/145 (44%), Positives = 83/145 (57%), Gaps = 6/145 (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  RT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTN 126
                 R+  Y+KP G + T +DP+GR TVFD LP    +R I+VGRLD+NT GLLL T 
Sbjct: 62  SAEQICRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGARWIAVGRLDVNTCGLLLFTT 121

Query: 127 DGGLARVLELPSTQWLRVYRVRFHG 151
           DG LA  L  PS +  R Y VR  G
Sbjct: 122 DGELANRLMHPSREVEREYAVRVFG 146


>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 =  164 bits (415), Expect = 2e-38,   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 + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDCVTRPCRAEFIEPPDALWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAIGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  164 bits (415), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 42/190 (22%), Positives = 77/190 (40%), Gaps = 19/190 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPTDLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFALGIAPGETIALP 180

Query: 238 KKILREQLGP 247
            +   +   P
Sbjct: 181 PRAPWDGFAP 190


>gi|148242785|ref|YP_001227942.1| pseudouridine synthase [Synechococcus sp. RCC307]
 gi|147851095|emb|CAK28589.1| Pseudouridine synthase [Synechococcus sp. RCC307]
          Length = 205

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 53/198 (26%), Positives = 82/198 (41%), Gaps = 29/198 (14%)

Query: 76  WLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L HKP G+++  +   G     +   +P     V + GRLD ++EGLLLLT+DG L   
Sbjct: 9   LLLHKPYGVLSQFTPEVGSRWDCLASLVP--IKGVYAAGRLDADSEGLLLLTSDGALQHQ 66

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           L  P     R YR +  G   +  L  L++GI ++       +  L              
Sbjct: 67  LTNPRFGHWRQYRAQVEGAPTEADLEPLRRGIQLKDGPSRPARAQLLDPSVAAGIAERNP 126

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------PFQLGTLLA 230
                      W+ + L EG+NR+++++     +   RLIR S        P  L  +  
Sbjct: 127 PIRHRLSVPTRWLELELTEGRNRQVRRMTAAIGFPTLRLIRWSLDLMDGQPPLNLDGMEP 186

Query: 231 GSTREVSKKILR--EQLG 246
           G  R VS    +  +QLG
Sbjct: 187 GQWRWVSAAEEKRLKQLG 204


>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 =  163 bits (413), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 47/188 (25%), Positives = 78/188 (41%), Gaps = 23/188 (12%)

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 TREVSKKI 240
           +R VSK+ 
Sbjct: 184 SRAVSKEE 191


>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 =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 42/182 (23%), Positives = 74/182 (40%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVSRPCRAEFIEPPETLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   WV + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWVELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>gi|289807291|ref|ZP_06537920.1| putative ribosomal large subunit pseudouridine synthase B
           [Salmonella enterica subsp. enterica serovar Typhi str.
           AG3]
          Length = 153

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 40/150 (26%), Positives = 68/150 (45%), Gaps = 15/150 (10%)

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
              V + GRLD ++EGLL+LTNDG L   L  P  +  ++Y V+  G  D   L  L+ G
Sbjct: 1   MQGVYAAGRLDRDSEGLLVLTNDGALQARLTQPGKRTGKIYYVQVEGIPDNAALQALRTG 60

Query: 165 IVIQGICYGDMQVTL---------------DTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           + +         + +               + +    +W+ V L EG+N +++++     
Sbjct: 61  VTLNDGPTLPAGIEIVAEPDWLWPRTPPIRERKNIPTSWLKVTLYEGRNHQVRRMTAHVG 120

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
               RLIR S G + L  L  G   E++++
Sbjct: 121 HPTLRLIRYSMGDYTLNGLDNGQWCEIAQE 150


>gi|311694975|gb|ADP97848.1| RNA pseudouridylate synthase [marine bacterium HP15]
          Length = 175

 Score =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 37/148 (25%), Positives = 66/148 (44%), Gaps = 14/148 (9%)

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
               +   GRLD ++EGLLLLT +G L   +  PS +  + Y V+  G + ++ L  L  
Sbjct: 2   HIPGIYPAGRLDYDSEGLLLLTAEGSLQHRIASPSLKMPKTYWVQVEGNISEEALRHLAS 61

Query: 164 GIVIQGICYGDMQV--------------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           G+ ++       +                        +W+ + + EGKNR+++++     
Sbjct: 62  GVQLKDGLTRPAKADRMPAPTVWPRVPPVRHRDNIPTSWIELTITEGKNRQVRRMTAAVG 121

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVS 237
           +   RLIR   G + L  L +G+ R V+
Sbjct: 122 FPTLRLIRYRIGDWTLDGLESGAHRTVT 149


>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 =  163 bits (412), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 39/169 (23%), Positives = 70/169 (41%), Gaps = 17/169 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFAL 169


>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 =  162 bits (411), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 43/182 (23%), Positives = 82/182 (45%), Gaps = 19/182 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++ +++KP  +++   +     TV   +      +   GRLD+++EGL+ LT+ GGL + 
Sbjct: 2   KIVVFNKPYDVLSQFREDSAHLTVSSFIAD--PELRIAGRLDLDSEGLMFLTDHGGLNQY 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  PS +  + Y V+  G + +D L  L+KG+ +        Q T   +           
Sbjct: 60  ITHPSNKKYKTYLVQVDGDITEDALEKLRKGVELADGLTLPAQATKVEEPEWLWERNPPV 119

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   +WV + + EG+NR+++++     +   RLIR   G   L    L  G  +E+
Sbjct: 120 RFRASIPTSWVEISICEGRNRQVRRMTATVGFPTLRLIRTQIGSINLVKLGLQPGEQKEI 179

Query: 237 SK 238
             
Sbjct: 180 EP 181


>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 =  162 bits (411), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 40/175 (22%), Positives = 82/175 (46%), Gaps = 16/175 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +L L++KP  +++  +D + R T+ + +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   KLLLFNKPFHVLSQFTDSEARKTLSEFIE--IKGVYPAGRLDYDSEGLLLLTDDGQLQAQ 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|307730777|ref|YP_003908001.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
 gi|307585312|gb|ADN58710.1| pseudouridine synthase [Burkholderia sp. CCGE1003]
          Length = 189

 Score =  162 bits (411), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 43/176 (24%), Positives = 75/176 (42%), Gaps = 19/176 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLLALNKPFGTICQFSAHETRASLADWV--SVPGVYPAGRLDSDSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------------T 178
           +  P  + ++ Y  +  G VD   L  L +G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQVEGAVDAAALKKLARGVDLGDYVTKPCRADYVDPADRLWPRTPPI 119

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGS 232
                    W+ + + EGKNR+++++     +   RL+R+  G   +    L+ G 
Sbjct: 120 RYRAAIPTTWIELSIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGLMPGE 175


>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 =  162 bits (410), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 46/173 (26%), Positives = 82/173 (47%), Gaps = 16/173 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP+ +++  S    +  +   L +   R+   GRLD ++EGLL+LT+ G L   L
Sbjct: 4   LILLNKPMNMLSQFSSEGEKQGISTLLSAPGYRI--AGRLDSDSEGLLVLTSYGRLQAYL 61

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P     + Y V+  GQ+D+  +  L+ G+ ++       +V +               
Sbjct: 62  TAPKHNTWKYYYVQVEGQIDEQAVCRLQAGVQLKDGPTLPARVKVIEPPSLWQRTPPVRY 121

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                 +W+ +GL+EG+NR+I+++     +   RL+R   GPF+L  L  G  
Sbjct: 122 RAHIPTSWLEIGLQEGRNRQIRRMTAHVGYPTLRLVRFRSGPFKLADLGPGEY 174


>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 =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 51/188 (27%), Positives = 95/188 (50%), Gaps = 22/188 (11%)

Query: 71  ERTRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +  R ++ HKP G ++    +    +  +   L       +++GRLD  +EGLLLLT DG
Sbjct: 2   KEHRHFILHKPYGYLSQFITNQTKRKKKMLGELYDFPEGTMAIGRLDFASEGLLLLTTDG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY--GDMQVTL----- 179
            +++ +   S+++ + Y V+  G + Q+ +N LKKG+ I  +G  Y     + ++     
Sbjct: 62  KVSQEI--RSSKYEKEYYVQVDGLITQEAINQLKKGVEIGFEGKKYITKPGKASIINNPE 119

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    D + 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|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 =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 39/169 (23%), Positives = 70/169 (41%), Gaps = 17/169 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 39  LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 96

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 97  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPETLWPRNPPIR 156

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L
Sbjct: 157 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFAL 205


>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 =  161 bits (408), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 37/182 (20%), Positives = 77/182 (42%), Gaps = 21/182 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  +    + + +     RV   GRLD ++EGLLLLT++G     +
Sbjct: 2   LIALNKPYGYICQFSPHEKHPNLKELV--NVPRVYPAGRLDTDSEGLLLLTDNGQQQARI 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|46205033|ref|ZP_00209673.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Magnetospirillum
           magnetotacticum MS-1]
          Length = 228

 Score =  161 bits (408), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/197 (27%), Positives = 92/197 (46%), Gaps = 14/197 (7%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----EVDGVPLRKA 70
           R+ +++A  G  SRREVE +     V+++G  L  AA  +     +     + G  L   
Sbjct: 6   RLDRLLANLGYGSRREVEGLAWAGLVRLDGETLTDAAQRIPLDPDLSARMTIQGQLLDPL 65

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTN 126
                 + HKP+G+  +H +      V+  LP  + R       VGRLD  T GLLLLT+
Sbjct: 66  PGL-CLMLHKPLGVTCSHKEAG--PLVYSLLPERWRRRDPALSTVGRLDKETSGLLLLTD 122

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQVTLDTQKGS 185
           DG L   +  P  +  + YRV     +  D+ ++L  G +++ G     + V ++    +
Sbjct: 123 DGALLHRIISPKAKVAKRYRVTLARPLQGDETSILASGELMLDGEDKPLLPVEMEADDAT 182

Query: 186 NAWVTVGLREGKNREIK 202
           +   TV L EG+  +++
Sbjct: 183 HC--TVTLHEGRYHKVR 197


>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 =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 58/184 (31%), Positives = 85/184 (46%), Gaps = 14/184 (7%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLL 124
           +       L + +KP G + T +D  GR TV+D LP        + +GRLD+ ++GLLL 
Sbjct: 3   ITANNSKILLVLNKPKGYLVTRTDDLGRKTVYDLLPDWAFHEGWMPIGRLDLESKGLLLF 62

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV-IQGICYGDMQVTLDTQK 183
           T +G +  +L  P     +VY V   G V  + +    KG+  I G      +V      
Sbjct: 63  TTNGKIGDILTKPGNCI-KVYEVWVRGFVTDEHIIQASKGVESIYG--LLKAKVVKVGIG 119

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFN-------WKVNRLIRISYGPFQLGTLLAGSTREV 236
           G+   + V L EGKNR I+++F            KV  L RIS G F+L  L  G  R +
Sbjct: 120 GAKTKLLVELEEGKNRHIRRLFGALKDPKFGTPLKVLTLNRISIGNFKL-DLEIGKWRYL 178

Query: 237 SKKI 240
           S + 
Sbjct: 179 SLEE 182


>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 =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 90/237 (37%), Gaps = 12/237 (5%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A A   SRRE E+ I    V V+G+++E     V     I +       A 
Sbjct: 3   DSIRLAKRVADAVPCSRREAEQYIEGGWVTVDGVVIEEPGHRVSPQQAIHLSPDATLVAI 62

Query: 72  RTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+        +T  +      +    L    S +  V  L+    GL++
Sbjct: 63  NPVTILLHKPAGIDADAALRLITPENLYAEDRSGIRFLKKHTSELKPVDVLETYASGLMV 122

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  +AR L   +    + Y     G +  + L LL  G+   G     ++V+   + 
Sbjct: 123 FTQDWHVARKLVDDAATVEQEYIAEVSGDLIPNGLALLNHGLNFNGKPLAPIKVSWQNE- 181

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   L+ G+  +I  + E    K+  L RI      + +L AG  R +    
Sbjct: 182 ---TRLRFALKAGRRGQIAHMCEMVGLKLLNLKRIRIARLPMASLPAGQWRYLKGYE 235


>gi|323447017|gb|EGB02989.1| hypothetical protein AURANDRAFT_34656 [Aureococcus anophagefferens]
          Length = 273

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 23/240 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---------LRKAERTRLWL 77
           SRR  +  +A  RV+VNG   +  ++ + S D + +DG           L        + 
Sbjct: 36  SRRAADAAVAAGRVRVNGETAK-PSLRLRSGDTLALDGKKRDWEALAAKLEGGGGLEYYA 94

Query: 78  YHKPIGLVTTHSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           YHKP G+  T    D RS         L +   R+   GRLD+++ GL++LTNDG  A  
Sbjct: 95  YHKPEGVACTTDANDRRSLRRAPALKKLFAGGKRIFPAGRLDVDSCGLVVLTNDGAAADA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVTLDTQKGS 185
              PS++  +VY V    +   D +  L  G+ I        +    G   +  D  +G 
Sbjct: 155 ALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIATPLQRGSKAEKTG-KTLPCDVARGD 213

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + + L EG+NR+++++ E   ++V  L R+++GP  LG L  G+ R ++   +   L
Sbjct: 214 GRGLVITLAEGRNRQLRRMAEALGYEVTGLRRVAFGPVSLGDLRPGTLRPLAAAEVDALL 273


>gi|167585691|ref|ZP_02378079.1| Pseudouridine synthase, Rsu [Burkholderia ubonensis Bu]
          Length = 192

 Score =  160 bits (406), Expect = 2e-37,   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 + +    V + GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVEGAPGPADLKALARGVDLGDYVTRACRAEFIEPPDALWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAKPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGSLDIFALGIAPGETITLP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 51/203 (25%), Positives = 85/203 (41%), Gaps = 22/203 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           R ++ +KP G+++  S   G      +L      V  VGRLD ++EGLLL+T+D  L   
Sbjct: 3   RYFIIYKPFGVLSQFS---GEGQTLASLFDFPKEVYPVGRLDKDSEGLLLITDDKWLNHH 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKG----- 184
           L  PS    R Y  +  G    + L  L  G+ I+              L ++       
Sbjct: 60  LLNPSFGHQRTYWAQVEGIPTPESLKALGNGVKIKVDGKEYLTKPSIAKLLSESPELPDR 119

Query: 185 ----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                      ++W+ + L EGKNR+++K+     +   RL R S     +     G  +
Sbjct: 120 DPPIRYRKNVPDSWIELTLIEGKNRQVRKMTAAVGFPTLRLARKSMEKINIIGFKVGEVQ 179

Query: 235 EVSKKILREQLGPHLLEEAQVNL 257
           E+ ++ +  QLG    +E+  N 
Sbjct: 180 ELDRETVYHQLGLTGFKESAKNF 202


>gi|323455461|gb|EGB11329.1| hypothetical protein AURANDRAFT_61729 [Aureococcus anophagefferens]
          Length = 294

 Score =  160 bits (406), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 110/241 (45%), Gaps = 23/241 (9%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---------LRKAERTRLWL 77
           SRR  +  +A  RV+VNG   +  ++ + S D + +DG           L        + 
Sbjct: 36  SRRAADAAVAAGRVRVNGETAK-PSLRLRSGDTLALDGKKRDWEALAAKLEGGGGLEYYA 94

Query: 78  YHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           YHKP G+  T    D RS         L +   R+   GRLD+++ GL++LTNDG  A  
Sbjct: 95  YHKPEGVACTTDANDRRSLRRAPALKKLFAGGKRIFPAGRLDVDSCGLVVLTNDGAAADA 154

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQVTLDTQKGS 185
              PS++  +VY V    +   D +  L  G+ I        +    G   +  D  +G 
Sbjct: 155 ALQPSSKLAKVYEVELDRRAADDDVAALAAGVEIATPLQRGSKAEKTG-KTLPCDVARGD 213

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
              + + L EG+NR+++++ E   ++V  L R+++GP  LG L  G+ R ++   +   L
Sbjct: 214 GRGLVITLAEGRNRQLRRMAEALGYEVTGLRRVAFGPVSLGDLRPGTLRPLAAAEVDALL 273

Query: 246 G 246
            
Sbjct: 274 A 274


>gi|297517087|ref|ZP_06935473.1| 23S rRNA pseudouridine synthase F [Escherichia coli OP50]
          Length = 147

 Score =  160 bits (406), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 45/148 (30%), Positives = 73/148 (49%), Gaps = 5/148 (3%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +  
Sbjct: 3   PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNGQLIEP 61

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             AE   L   +KP+G+V+T  D + R  + D + +   RV  +GRLD +++GL+ LTN 
Sbjct: 62  REAEDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRVFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           G L   +        + Y V     + +
Sbjct: 120 GDLVNKILRAGNDHEKEYLVTVDKPITE 147


>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 =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 48/201 (23%), Positives = 88/201 (43%), Gaps = 33/201 (16%)

Query: 75  LWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP G+ +   D   +  +T+ +       R+   GRLD  +EGLL+LT+DG + +
Sbjct: 6   LILFNKPYGVQSQFRDDSNNDHTTLSEYFTDKSLRI--AGRLDATSEGLLILTSDGRINK 63

Query: 133 VLELPST---------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
            +  P +         +  + Y V+  G V   +L  L  G++++         TL    
Sbjct: 64  AITQPPSAKNFAQNKQKQGKTYLVQVEGVVTAVQLKELASGVILKDGKTLPASATLLDEA 123

Query: 180 --------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                         + +    +W+ + + EGKNR+++++         RLIR S   F+L
Sbjct: 124 DLPITLWQRDPPIRERKNIPTSWLMLTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFEL 183

Query: 226 GTLLAGST-R-EVSKKILREQ 244
           G L  G   R  ++ +  R+ 
Sbjct: 184 GELGVGEFVRIHLNSEQCRKL 204


>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 =  159 bits (404), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 52/208 (25%), Positives = 104/208 (50%), Gaps = 19/208 (9%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--AE 71
            R+++ +A     SRRE E+++ + RVK+N    + A+V V   D + +D   ++    +
Sbjct: 1   MRINQFLAHYTKHSRREAEKLVLEGRVKINHEHAKLASV-VKENDKVFLDKRLIKPLKNK 59

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  + +YHKP G + + +DP  R  ++++L   ++    VGRLD  +EG+L+L++   + 
Sbjct: 60  KFSVLVYHKPKGELVSKADPLKRRVIYESLEKKYAHFAPVGRLDFASEGVLILSDSKAVV 119

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT------------- 178
             L   +    + Y V+  G V ++  N +++G+ ++    G  Q T             
Sbjct: 120 SALMHAN--LEKEYLVKIQGFVTREMENAMQEGLKLENATKGAHQKTPIKSMEFAPFIGY 177

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVF 205
            +       + + V + EGKNRE+++ F
Sbjct: 178 EIIKNHAKYSKLRVVINEGKNRELRRFF 205


>gi|146297843|ref|YP_001192434.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146152261|gb|ABQ03115.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
          Length = 190

 Score =  159 bits (404), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 47/186 (25%), Positives = 84/186 (45%), Gaps = 22/186 (11%)

Query: 73  TRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            R ++  KP G ++    +   +  +   L       +++GRLD ++EGLLLLT DG ++
Sbjct: 2   HRHFILFKPYGYLSQFIYELKRKKKLLGELHDFPEGTMAIGRLDEDSEGLLLLTTDGKVS 61

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL---------- 179
             +   S +  + Y V+  G +  + +  L+KG+ I  +G  Y     T           
Sbjct: 62  EQI--RSKKVDKEYYVQVDGIITPEAIEKLQKGVEIGFEGGKYKTKPCTAFIVTEIPDFG 119

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G  +W ++ + EGK R+++K+     +   RL+R+  G   L  L AG 
Sbjct: 120 PRAKKIRDERHGPTSWASITVNEGKFRQVRKMTAAVGFPTLRLVRVRIGNVYLQNLKAGE 179

Query: 233 TREVSK 238
             EV+ 
Sbjct: 180 VLEVND 185


>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 =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 45/183 (24%), Positives = 86/183 (46%), Gaps = 22/183 (12%)

Query: 76  WLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +   KP G ++    +      +   L      ++++GRLD ++EGLLLLT DG ++  +
Sbjct: 25  YKIFKPHGFLSQFVPETKKNKKLLGELAQFPVGIMAIGRLDHDSEGLLLLTTDGMVSHRV 84

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL------------- 179
              S +  + Y V+  G +D + +  L++G+ I  +G  Y  +   +             
Sbjct: 85  --RSKKVEKEYYVQVDGIIDDEAIIRLQQGVEIGIKGEKYLTLPCKVVKLDGEPNLPDNG 142

Query: 180 ----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               D + G  +WV++ + EGKNR+I+K+     +   RL+R+  G   L  +  G   E
Sbjct: 143 RRVRDPRHGPLSWVSITISEGKNRQIRKMTAAAGFPTMRLVRVRIGNIHLSDMQPGEVFE 202

Query: 236 VSK 238
           +++
Sbjct: 203 LTQ 205


>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 =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 47/187 (25%), Positives = 80/187 (42%), Gaps = 28/187 (14%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +++KP G VT   D     TV D        R+  VGRLD  T GLLL+T+DG   + L 
Sbjct: 1   MFNKPFGCVTARRDTLY-PTVMDYFSELHNDRLNPVGRLDRETTGLLLITDDGNWNQQLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWV---- 189
            P+    + Y     G + +D+   L+ GI+++G  +     ++TL  +      +    
Sbjct: 60  HPAYHKKKTYLFTVLGDLTEDRRQFLENGILLKGSPVPTSPAKITLFKKDTLANILDTLH 119

Query: 190 -------------------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLL 229
                               + + EG+ R+I+++ +  +  V  L RIS     L  +L 
Sbjct: 120 PEVRNAVRTNLPSHPVTYGEITISEGRKRQIRRMMKAVHCCVIELKRISIDDIHLDESLA 179

Query: 230 AGSTREV 236
            G  +E+
Sbjct: 180 PGKWKEI 186


>gi|289675786|ref|ZP_06496676.1| pseudouridine synthase, Rsu [Pseudomonas syringae pv. syringae FF5]
          Length = 179

 Score =  159 bits (403), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 38/155 (24%), Positives = 73/155 (47%), Gaps = 16/155 (10%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L L++KP  ++T  SD +GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLILFNKPFDVLTQFSDEEGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 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|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 =  159 bits (403), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 27/130 (20%), Positives = 50/130 (38%), Gaps = 3/130 (2%)

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           ++L+T+DG  +  +  P     + Y V     +  D       G+ +           LD
Sbjct: 1   MVLMTDDGQWSHRVTSPRHHCEKTYLVTLEHPLSDDTAQQFADGVQLYNEKSLTKPAQLD 60

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTLLAGSTREVSKK 239
             +     V + + EG+  ++K++F     +V  L R   G   L   L  G  R ++ +
Sbjct: 61  VIEP--QRVRLTISEGRYHQVKRMFAAVGNRVIELHRERIGDITLDDDLAPGEYRPLTTE 118

Query: 240 ILREQLGPHL 249
            +     PHL
Sbjct: 119 EIASVGAPHL 128


>gi|31747805|gb|AAO38400.1| Lfe193p2 [Leptospirillum ferrooxidans]
          Length = 164

 Score =  159 bits (402), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 51/133 (38%), Positives = 76/133 (57%), Gaps = 2/133 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAERT 73
           R+ K++A  GI SRR  E +IA   V VNG +       V    D + V+G  L + + T
Sbjct: 29  RLQKLLAHRGITSRRNAEELIAGGLVTVNGKVETTPGTKVDPQRDVVVVEGRMLPREKET 88

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L+L++KP G+++   DPDG+ T+ D  P+I   +  +GRLD  TEG+LLLTN+G L++ 
Sbjct: 89  FLFLFYKPKGVISAVFDPDGKPTLKDFFPNISPLLH-IGRLDFQTEGVLLLTNNGDLSQR 147

Query: 134 LELPSTQWLRVYR 146
           +  P     R Y 
Sbjct: 148 ILHPRFAIPRTYL 160


>gi|255069983|ref|XP_002507073.1| pseudouridylate synthase [Micromonas sp. RCC299]
 gi|226522348|gb|ACO68331.1| pseudouridylate synthase [Micromonas sp. RCC299]
          Length = 334

 Score =  158 bits (401), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 102/240 (42%), Gaps = 27/240 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---EVDGVPLRKA 70
           QR+SK+IA     SRRE ER+I++ +V VNG+L+            I   E+      ++
Sbjct: 90  QRISKIIALREFCSRREAERLISRSQVVVNGVLI-HQGSKAECDSEIQLAEIGDQVWFQS 148

Query: 71  ERTRLWLYHKPIGLV----------------TTHSDPDGRSTVFDNLPSIFSRVISVGRL 114
           + T     +KP G V                TT       S       +   ++   GRL
Sbjct: 149 KSTV--ALNKPRGYVSNLPSHGEVEACSLLITTTGSHIHSSKWSSRTENDNGQLNVCGRL 206

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
           D N+ GLL+L+ DG LAR +        + Y V     V Q+ L+ L             
Sbjct: 207 DKNSRGLLVLSQDGVLAREVIAGVF-VSKTYLVEVDKMVTQNDLDRLNGPCKFLTDVIRP 265

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           ++V L         +   LREGKNR+I+++ E     V  L R+  G  +LG+L  GS R
Sbjct: 266 IRVRLLAP----TLLEFVLREGKNRQIRRMCEQMGLIVVDLFRVRLGKSELGSLPEGSWR 321


>gi|223940798|ref|ZP_03632631.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890528|gb|EEF57056.1| pseudouridine synthase [bacterium Ellin514]
          Length = 192

 Score =  158 bits (401), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 51/196 (26%), Positives = 90/196 (45%), Gaps = 20/196 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP G+++  +  DG              V  +GRLD ++EGLLLL+++  L   L
Sbjct: 2   LIAFNKPYGVLSQFT-RDGSPNRPLAHFGFPKNVYPIGRLDADSEGLLLLSDEAALNERL 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  Q  R+Y  +       + L  L+KG+++Q       +  L               
Sbjct: 61  LHPRQQHGRIYWAQVEHVPSPEVLTRLEKGVIVQARRTLPCKAWLIDPQPAVPPRVPPIR 120

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           + +     WV + L EGKNR+++++         RL+R+  G FQL  L AG  + ++  
Sbjct: 121 ERKSIPAVWVGLELVEGKNRQVRRMTAAVGHPTLRLMRMQIGKFQLADLPAGKWKVLTPA 180

Query: 240 ILREQLGPHLLEEAQV 255
             R+ +   L+EE+++
Sbjct: 181 E-RDMV---LMEESKI 192


>gi|303285788|ref|XP_003062184.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226456595|gb|EEH53896.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 244

 Score =  158 bits (401), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 103/243 (42%), Gaps = 33/243 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLR----K 69
           R+ K +A+ G+ASRR  E +I   RV VNG+++     +V+  D +    G  ++    +
Sbjct: 1   RLGKALAQLGVASRRASEDLIFAGRVAVNGVVVTAPQHHVVLADDVVAVDGKVIQGGVEE 60

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRST-------------VFDNLPSI------------ 104
                 +L +KP G +  ++    +               V D                 
Sbjct: 61  TREHLYFLLNKPKGYICANAKSPNKPPGKGERGGGASGKLVMDLFDEWKAAWRKKHPKRL 120

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             R+ +VGRLD+NT G+LL+T DG   + +  P ++ ++ Y +    +  + ++  +  G
Sbjct: 121 PPRLFTVGRLDVNTTGMLLVTTDGQWCQRVAHPKSEVVKSYVLTASARPTKAQIRAMAAG 180

Query: 165 IVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
             + G     + V     D   G    V V + +G+NRE++++         +L R+  G
Sbjct: 181 AEVDGAFVKPVNVRSMDNDRDGGPPNRVLVEVVDGRNREVRQLASSAGVDCKKLKRVRVG 240

Query: 222 PFQ 224
             +
Sbjct: 241 GLR 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 =  158 bits (401), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 96/239 (40%), Gaps = 31/239 (12%)

Query: 73  TRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L L++KP G+++     D +  +T+ D        +   GRLD  +EGLLLLT DG +
Sbjct: 2   PTLILFNKPYGVLSQFRSDDNNNFATLSDYFTD--KSLRVAGRLDATSEGLLLLTADGQV 59

Query: 131 ARVLELP-----STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
            + L  P       Q  + Y ++  G     +L  L+ G+ ++       +V   ++   
Sbjct: 60  NKALTHPPKANAGKQQGKTYWIQVEGDASDAQLQQLQTGVPLKDGITLPAEVVRLSEAQI 119

Query: 183 -------------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                        +    W+ + + EGKNR+++++         RLIR++   F LG L 
Sbjct: 120 AEHIWQASDKIAKRKVTTWLAITIFEGKNRQVRRMAAHVGLPCLRLIRMASSGFSLGNLE 179

Query: 230 AGST--REVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            G++    +S   L+       ++        P    +  V    ++ S+ P    R  
Sbjct: 180 VGASTQIPLSPADLKRL----GVQPLSTATTTPQSRKKPRVLTPKSLQSKHPTSRRRQP 234


>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 =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 49/178 (27%), Positives = 87/178 (48%), Gaps = 16/178 (8%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL L++KP  +++  SD +G+ T+ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 3   RLILFNKPYQVISQFSDSEGKKTLADFIDT--KNVYPAGRLDFDSEGLLLLTDDGLLQHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P  +  + Y V+  G  D   +  L  G+ ++       +V +  +           
Sbjct: 61  ISDPKHKSYKTYWVQVEGIPDNLAIQHLVNGVDLKDGKTLPAKVNIIDEPNLWDRHPPIR 120

Query: 183 ---KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                  +W+ + + EGKNR+++++         RL+R+S G + L  L  G  +E+S
Sbjct: 121 QRSNDVTSWLEIQIMEGKNRQVRRMTAAVGHPTLRLVRVSIGQWHLEQLKPGEFKELS 178


>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 =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 49/192 (25%), Positives = 84/192 (43%), Gaps = 19/192 (9%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSPHEARASLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G  D   L  L++G+ +        +    T            
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFVTPPDTLWPRTPPI 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RLIR+  G   +    L  G TRE+
Sbjct: 120 RYRAAIPTTWIELEIAEGKNRQVRRMTAAIGFPTLRLIRVGIGALDVFALGLAPGETREL 179

Query: 237 SKKILREQLGPH 248
             +   E+   H
Sbjct: 180 PPRAPWERAVRH 191


>gi|330864071|emb|CBX74147.1| ribosomal large subunit pseudouridine synthase F [Yersinia
           enterocolitica W22703]
          Length = 162

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 41/149 (27%), Positives = 75/149 (50%), Gaps = 5/149 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           +  R++K I+ +GI SRR+ +R + Q  V +NG         V   D ++V+G  +   +
Sbjct: 5   SSIRLNKYISESGICSRRDADRYVEQGNVFINGKRAA-VGDQVYVGDVVKVNGQLIEPRD 63

Query: 72  RTRLWL--YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + L L   +KP+G+++T  D +  + V  +  +   RV  +GRLD +++GL+ LTN G 
Sbjct: 64  ESDLILIALNKPVGIISTTEDGESDNIV--DFVNHSKRVFPIGRLDKDSQGLIFLTNHGD 121

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKL 158
           L   +        + Y V  +  V  + +
Sbjct: 122 LVNKILRAGNDHEKEYVVTVNKPVTDEFI 150


>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 =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 84/187 (44%), Gaps = 19/187 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSAHETRASLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G         
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNPPI 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   AW+ + + EGKNR+++++     +   RL+R+  G   +    L  G TRE+
Sbjct: 120 RHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALGLAPGETREL 179

Query: 237 SKKILRE 243
             +   E
Sbjct: 180 PPRAPWE 186


>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 =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 48/201 (23%), Positives = 87/201 (43%), Gaps = 33/201 (16%)

Query: 75  LWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
           L L++KP G+ +   D   +  +T+ +       R+   GRLD  +EGLL+LT+DG + +
Sbjct: 6   LILFNKPYGVQSQFRDESNNDHTTLSEYFTDKSLRI--AGRLDATSEGLLILTSDGRINK 63

Query: 133 VLELPST---------QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---- 179
            +  P +         +  + Y V+  G V   +L  L  G+V++          L    
Sbjct: 64  AITQPPSAKGFAQNKQKQGKTYLVQVEGMVTSVQLKALASGVVLKDGKTLPASAVLVDEV 123

Query: 180 --------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                         + +    +W+ + + EGKNR+++++         RLIR S   F+L
Sbjct: 124 DLPITLWEREPPIRERKNIPTSWLMLTIYEGKNRQVRRMTAHVGLPCLRLIRWSVAGFEL 183

Query: 226 GTLLAGST-R-EVSKKILREQ 244
           G L  G   R  ++ +  R+ 
Sbjct: 184 GELGVGEFVRIHLNSEQCRKL 204


>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 =  158 bits (399), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 51/205 (24%), Positives = 92/205 (44%), Gaps = 15/205 (7%)

Query: 43  NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +GI ++     +   D + +DG      +  +  L HKP G  T+H  P    +VFD LP
Sbjct: 4   DGIQIDPEIDEISLGDTLLIDGKSFEITQ-YKYVLMHKPAGYETSHL-PSHNPSVFDLLP 61

Query: 103 SIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPS----TQWLRVYRVRFHGQVDQD 156
             +    + + GRLD++T GLLL ++DG     L         +  ++Y V         
Sbjct: 62  KHYIKRGLQAAGRLDVDTTGLLLFSDDGQFIHRLISGKVGTKQEIEKIYEVTGARPFSDL 121

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           +L  L +G+ +        ++   ++    ++  + +G+  GK  ++K++       V+ 
Sbjct: 122 QLQRLLEGVDLDDEP----EIIYASRATLLADGRLELGITTGKYHQVKRMVAAVGNHVDG 177

Query: 215 LIRISYGPFQLG-TLLAGSTREVSK 238
           L R S GP++L   L AGS  E+  
Sbjct: 178 LHRRSVGPYELPADLAAGSYIEIDP 202


>gi|323969847|gb|EGB65128.1| RNA pseudouridylate synthase [Escherichia coli TA007]
          Length = 191

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 37/193 (19%), Positives = 77/193 (39%), Gaps = 4/193 (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  LGTVTK----KCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSG 116

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKK 287
           +  G  R+++   L +         ++V   A        ++     + +  +   R   
Sbjct: 117 IPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPAS 176

Query: 288 NSSQKNGLSKQKK 300
           N  +     ++KK
Sbjct: 177 NGKRFTSPGRKKK 189


>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 =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 64/158 (40%), Positives = 85/158 (53%), Gaps = 6/158 (3%)

Query: 34  MIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTH 88
           MIA  RV V G +      ++V S   + +DG  +     + E  R+ +Y+KP G + T 
Sbjct: 1   MIAAGRVSVEGKIATLGDRIDVHSGVKVRIDGQIINLSHAQKEICRVLMYYKPEGELCTR 60

Query: 89  SDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
           SDP+GR+TVFD LP    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|205373780|ref|ZP_03226582.1| ribosomal large subunit pseudouridine synthaseB (pseudouridylate
           synthase) (uracil hydrolyase) [Bacillus coahuilensis
           m4-4]
          Length = 131

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 30/123 (24%), Positives = 62/123 (50%), Gaps = 2/123 (1%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-- 181
           +TNDG  + +L  P  +  + Y  +  G   + +L  L++GI ++       +V   +  
Sbjct: 1   MTNDGEFSNLLTHPKYEIDKTYIAKIKGIPTRQELTKLQRGIKLEDGMTAPAKVKFISAD 60

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +  +   V + + EG+NR+++++FE   + V +L R  +G   L  L AG  RE++   +
Sbjct: 61  RSKNTCIVELTIHEGRNRQVRRMFEALGFPVMKLRRERFGTLTLKGLNAGEARELTPHEV 120

Query: 242 REQ 244
           ++ 
Sbjct: 121 KQL 123


>gi|325526198|gb|EGD03833.1| pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 192

 Score =  157 bits (397), Expect = 3e-36,   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 + +    V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGAADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+ +++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQGRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KK 239
            +
Sbjct: 181 PR 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 =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 49/187 (26%), Positives = 84/187 (44%), Gaps = 19/187 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSVHETRASLGDWVKT--PGVYPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--------- 184
           +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G         
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALWPRNPPI 119

Query: 185 ------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                   AW+ + + EGKNR+++++     +   RL+R+  G   +    L  G TRE+
Sbjct: 120 RHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALGLAPGETREL 179

Query: 237 SKKILRE 243
             +   E
Sbjct: 180 PPRAPWE 186


>gi|330752330|emb|CBL87284.1| RNA pseudouridine synthase family protein [uncultured Flavobacteria
           bacterium]
          Length = 195

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 48/189 (25%), Positives = 86/189 (45%), Gaps = 15/189 (7%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +  + ++ +KP G ++  S   G+  + D +  + + V  VGRLD ++EGLLL++ND  +
Sbjct: 3   KGKKYYIIYKPKGCLSQFSKEHGKRALGD-VFDLPTDVYPVGRLDEDSEGLLLISNDKSI 61

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQKGS--- 185
              L  P     R Y V+  GQ+ +  +  L  G+ I  +G  +  +   +         
Sbjct: 62  NSKLLNPLNGHWRTYWVQVSGQIHKSAIKALVNGVDIVVKGKIHSTLPARVKKGNPPKNI 121

Query: 186 ---------NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     +WV + L EGK R+++K+     +   RL+R      +LG L     + +
Sbjct: 122 LPLNVSEKETSWVKISLCEGKYRQVRKMTAKVGFPTLRLVRTHIEELELGELKPSEFKSL 181

Query: 237 SKKILREQL 245
            KK L  +L
Sbjct: 182 DKKALFHKL 190


>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 =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 49/188 (26%), Positives = 86/188 (45%), Gaps = 22/188 (11%)

Query: 70  AERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             + + +L +KP G ++    +      +   L     + +++GRLD ++EGLLLLT DG
Sbjct: 9   EPKHQHFLIYKPYGFLSQFVPETRKSKPLLGQLYEFPEKTMAIGRLDHDSEGLLLLTTDG 68

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYG--DMQVTL----- 179
             + ++   S    + Y V+  G+V Q +L  L++G+ I   G  Y     +V L     
Sbjct: 69  MQSHLI--RSKTIEKEYYVQVDGEVSQAQLAKLRQGVEIGISGGKYLTLPCKVELLIHEP 126

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     D + G   W++V + EGKNR+++K+         RL+R+  G   L  + 
Sbjct: 127 NLPARGKKIRDPRHGPTNWLSVTIDEGKNRQVRKMTAAVGLPTLRLVRVRIGAIHLKQMQ 186

Query: 230 AGSTREVS 237
            G    V+
Sbjct: 187 PGEVIPVT 194


>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 =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 40/154 (25%), Positives = 70/154 (45%), Gaps = 17/154 (11%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTNDG L   L 
Sbjct: 2   VLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDRDSEGLLVLTNDGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL---------------D 180
            P  +  ++Y V+  G  D   L  L+ G+ +         + +               +
Sbjct: 60  QPGKRTGKIYYVQVEGIPDNAALQALRTGVTLNDGPTLPAGIEIVAEPDWLWPRTPPIRE 119

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            +    +W+ V L EG+N +++++         R
Sbjct: 120 RKNIPTSWLKVTLYEGRNHQVRRMTAHVGHPTLR 153


>gi|167835720|ref|ZP_02462603.1| pseudouridine synthase family protein [Burkholderia thailandensis
           MSMB43]
          Length = 192

 Score =  157 bits (397), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 48/187 (25%), Positives = 82/187 (43%), Gaps = 19/187 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++ D + +    V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPFGTICQFSPHETRASLGDWVKT--PDVYPAGRLDADSEGLLLLTDDGALQAK 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G  D   L  L++G+ +        +    T            
Sbjct: 60  IAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFVTPPETLWPRNPPV 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + + EGKNR+++++     +   RLIR+  G   +    L  G TRE+
Sbjct: 120 RYRAAIPTTWIELEIAEGKNRQVRRMTAAVGFPTLRLIRVGIGALDVFALGLSPGETREL 179

Query: 237 SKKILRE 243
             +   E
Sbjct: 180 PPRAPWE 186


>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 =  156 bits (395), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 47/184 (25%), Positives = 88/184 (47%), Gaps = 25/184 (13%)

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            + ++ HKP G ++    +   +  +   L      ++++GRLD ++EGLLLLT DG ++
Sbjct: 11  HQHFIIHKPYGYLSQFKYELKRKKKLLGELYDFPEGIMAIGRLDEDSEGLLLLTTDGKMS 70

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY--GDMQVTL-------- 179
            ++   S +  + Y V+  G + Q+ +  +K G+ I  +G  Y     +  +        
Sbjct: 71  EIV--RSKKVEKEYYVQVDGLITQEAIEKMKNGVEIGFEGTKYMTKPCKAFIVNEIPNFG 128

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G  +W ++ + EGK R+++K+     +   RL+R+  G   LG L A  
Sbjct: 129 ERGKKIRDERHGPTSWASIVVTEGKFRQVRKMTAAVGFPTLRLVRVRVGNIHLGNLQA-- 186

Query: 233 TREV 236
            REV
Sbjct: 187 -REV 189


>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 =  156 bits (395), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 48/188 (25%), Positives = 88/188 (46%), Gaps = 24/188 (12%)

Query: 73  TRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            R +  +KP G ++   T+  P  +  +   L +     ++VGRLD ++EGLLLLT +G 
Sbjct: 2   HRYFKIYKPYGYLSQFITNEKPRKKKKLLGELGNFPEETMAVGRLDQDSEGLLLLTTNGK 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYG-------------- 173
            +  +    +   + Y V+  G++ ++ + LLK G+ I   G  Y               
Sbjct: 62  ESARIT--GSSVEKEYYVQVDGEITEEAIALLKNGVEISINGTKYRSLPCKAFKLYTRPV 119

Query: 174 ---DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +   D + G  +W+++ L EGK R++KK+     +   RL+R+  G  +L  + +
Sbjct: 120 FPERAKKIRDERHGPTSWISITLTEGKFRQVKKMTAVVGFPTLRLVRVRIGNEKLEHMNS 179

Query: 231 GSTREVSK 238
           G   E+ K
Sbjct: 180 GEVIELEK 187


>gi|223992791|ref|XP_002286079.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220977394|gb|EED95720.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 370

 Score =  156 bits (395), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 58/278 (20%), Positives = 106/278 (38%), Gaps = 53/278 (19%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG------------ILLERAAVNVMSTDHIE 61
           QR+ KV+A  G+ +R +   +   +R+                  ++  +  V S   + 
Sbjct: 90  QRIDKVLADRGVGTRSQTFDLAKAKRIT---WSTSPDATHEERTRIKGPSEKVPSNASLF 146

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG-----RSTVFDNLPSIFSR--VISVGRL 114
           +DG     A    L +YHKP  +++   D        R  +   L   ++R  +  VGRL
Sbjct: 147 LDGNL-LPAPTPLLLVYHKPKFVLSVMEDDKKYQDQQRKHLGHILEPRYARSGMHPVGRL 205

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIVIQGICYG 173
           D +T GL+L ++DG L + L  P     + Y     G+V+  +L  +L  G+      + 
Sbjct: 206 DYDTTGLILFSSDGKLTQRLLHPRRGVEKEYVATVQGEVNASELREMLANGVETTDGTFA 265

Query: 174 DMQVTLDTQKGSN-----------------------------AWVTVGLREGKNREIKKV 204
              + + +  G +                             + V + + EGK R ++++
Sbjct: 266 ANLIAVTSSNGPSEVSEEDLNNVPEEDEGGDETTDEPYNGPYSDVRLVVSEGKYRMVRRI 325

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                  V  L R  +G   L  L  G  R+V+ + L 
Sbjct: 326 LANSGHPVVELRRERHGEILLDDLPVGKFRDVTPEELE 363


>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 =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 49/192 (25%), Positives = 88/192 (45%), Gaps = 22/192 (11%)

Query: 67  LRKAERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           ++     + +  +KP G ++    +   R  +   L S  S+ +++GRLD ++EGLLLLT
Sbjct: 12  IKDDISHQHFKIYKPYGFLSQFLPEARKRKKLLGELFSFPSKTMAIGRLDHDSEGLLLLT 71

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL---- 179
            DG ++  +   S    + Y V+  G +    +  L+ G+ I   G  Y  +   +    
Sbjct: 72  TDGMMSHQI--RSKGIEKEYYVQVDGDITASAITALQLGVEIGINGEKYQTLPCNVFRLT 129

Query: 180 -------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        D + G  +WV++ L EGKNR+I+K+     +   RL+R+  G   +G
Sbjct: 130 EEPQLPVRGRKIRDPRHGPTSWVSITLCEGKNRQIRKMTAAVGFATLRLVRVRIGNIFVG 189

Query: 227 TLLAGSTREVSK 238
            + AG    +S 
Sbjct: 190 GMQAGDVTPLSD 201


>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 =  155 bits (393), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 46/191 (24%), Positives = 90/191 (47%), Gaps = 22/191 (11%)

Query: 68  RKAERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
             +E  R +   KP G ++    +      +   L    + ++++GRLD ++EGLLLLT 
Sbjct: 17  DPSEPHRHFKIFKPHGFLSQFVPETRKSKKLLGELALFPTGIMAIGRLDHDSEGLLLLTT 76

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL----- 179
           DG ++  +   S +  + Y V+  G +D + +  L+ G+ I  +G  Y  +   +     
Sbjct: 77  DGMVSHRV--RSKKVEKEYYVQVDGDIDDEAIIRLRLGVEIGIKGEKYLTLPCKVFKLDG 134

Query: 180 ------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                       D + G  +W+++ + EGKNR+I+K+    ++   RL+R+  G   L  
Sbjct: 135 EPELPSNGRKIRDPRHGPMSWISITISEGKNRQIRKMTAAADFPTMRLVRVRIGNIMLDN 194

Query: 228 LLAGSTREVSK 238
           +  G   E+++
Sbjct: 195 MQPGKVIELTE 205


>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 =  155 bits (393), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 50/193 (25%), Positives = 86/193 (44%), Gaps = 19/193 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           R+    RL   +KP G +   S  + R+++ D + +    V   GRLD ++EGLLLLT+D
Sbjct: 39  REPCPMRLIALNKPFGTICQFSAHETRASLGDWVKT--PGVYPAGRLDADSEGLLLLTDD 96

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG--- 184
           G L   +  P  + ++ Y  +  G  D   L  L++G+ +        +    T  G   
Sbjct: 97  GALQAKIAEPRHKLVKRYWAQVEGAPDAAALAALERGVDLGDYVSRPCRARFITPPGALW 156

Query: 185 ------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLA 230
                         AW+ + + EGKNR+++++     +   RL+R+  G   +    L  
Sbjct: 157 PRNPPIRHRAAIPTAWIELEIAEGKNRQVRRMTAAVGFPTLRLVRVGIGALDVFALGLAP 216

Query: 231 GSTREVSKKILRE 243
           G TRE+  +   E
Sbjct: 217 GETRELPPRAPWE 229


>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 =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 51/218 (23%), Positives = 82/218 (37%), Gaps = 26/218 (11%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +  R    L++KP G+++  +                  V + GRLD ++EGLLLL++ 
Sbjct: 4   SRKRRLTTLLFNKPYGVLSQFTPETASRWRCLAEFINVPGVYAAGRLDADSEGLLLLSDQ 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
           G L + L  P     R Y V+  G  D  +L  L++GI IQ       +      +    
Sbjct: 64  GRLQQRLTDPRCGHWRSYWVQVEGHPDDPQLQKLREGIEIQHQRTLPARARWLQGEDIPL 123

Query: 184 -------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY----GP--FQ 224
                           +W+ + LREG+NR+++++         RL+R       G     
Sbjct: 124 LPERDPPIRVRATIPTSWLELSLREGRNRQVRRMTAAVGLPTLRLVRCRIDLMDGGKALD 183

Query: 225 LGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDA 259
           L  L AG  R V+      L   L   +         A
Sbjct: 184 LNDLPAGRWRSVTNAEQERLNRLLSSRVPRPRSAGRGA 221


>gi|291336757|gb|ADD96295.1| hypothetical protein [uncultured organism MedDCM-OCT-S08-C1656]
          Length = 169

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 45/162 (27%), Positives = 79/162 (48%), Gaps = 3/162 (1%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           N    ++ K +A AG+ SRR+ E  I    V +NG   +     +  +D ++V+G  ++ 
Sbjct: 5   NSQRPKLQKFLADAGLCSRRKGEEWIEDGLVTINGENAKLGERVIPDSDIVKVNGKRVQV 64

Query: 70  AE-RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTN 126
                   L +KP G   ++ D      +F+ L S +   R+   GRLD+++EG+++LTN
Sbjct: 65  KRIPNITLLVNKPKGYTCSNDDEYADRLIFELLESKYRSVRLFCAGRLDVDSEGMVILTN 124

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           +G LA  L  PS    + Y++      D   L  L  G +++
Sbjct: 125 NGTLAHRLTHPSQMVRKKYKIEIDTPFDTKDLPSLINGELVE 166


>gi|307102233|gb|EFN50580.1| hypothetical protein CHLNCDRAFT_14498 [Chlorella variabilis]
          Length = 183

 Score =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 48/183 (26%), Positives = 76/183 (41%), Gaps = 25/183 (13%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKA--ERTRLW 76
           IA AG+ASRR  + +I   +VKVNG ++      V    D + V G  +  A  +R   +
Sbjct: 1   IAAAGVASRRGADDLIFGGQVKVNGKVVTEPGTQVDLRKDRVAVSGREISAAAVQRKYYF 60

Query: 77  LYHKPIGLVTT----HSDPDGRSTVFDNLPSIFSRV------------------ISVGRL 114
             +KP G + +    H D      V        +R                    +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 MQV 177
           + +
Sbjct: 181 LAI 183


>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 =  155 bits (392), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 51/190 (26%), Positives = 87/190 (45%), Gaps = 24/190 (12%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPD--GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                 L  ++KP G++   +D     R T+      +   V + GRLD ++EGLLLLT+
Sbjct: 17  PRNTPMLIAFNKPYGVLCQFTDRSQPPRPTLAGF--GLPKDVYAAGRLDHDSEGLLLLTD 74

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------ 180
           DGGLA  L  P  +  + Y V+  G   +++L  L+ G+V+        +V         
Sbjct: 75  DGGLAHRLTDPLHKQPKTYWVQVEGDPREEQLQALRDGVVLNDGPTRPAKVRRLDPVPAL 134

Query: 181 ---------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT---- 227
                     +   ++W+ V + EG+NR+++++         RL+R++ GP +L      
Sbjct: 135 WPRDPPVRFRKTVPDSWLEVVIIEGRNRQVRRMTAAAGLPTLRLVRVAMGPHRLHDRDGT 194

Query: 228 -LLAGSTREV 236
            L  G  REV
Sbjct: 195 PLAPGEWREV 204


>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 =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 43/180 (23%), Positives = 74/180 (41%), Gaps = 19/180 (10%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL   +KP G +   S  + R+++   +      V   GRLD ++EGLLLLT+DG L   
Sbjct: 2   RLIALNKPYGTICQFSAHETRASLATWV--NVPDVYPAGRLDADSEGLLLLTDDGALQAR 59

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------- 183
           +  P  + ++ Y  +  G      L  L++G+ +        +                 
Sbjct: 60  IAEPRHKLVKRYWAQLDGAAPASALAALERGVDLGDYVSRPCRARFIEPPSGLWQRDPPV 119

Query: 184 -----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREV 236
                    W+ + L EG+NR+++++     +   RLIR+  G   L    L  G  R +
Sbjct: 120 RYRAAIPTTWIELALGEGRNRQVRRMTAAVGFPTLRLIRVGIGALDLFALGLAPGQWRAL 179


>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 =  154 bits (390), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 46/191 (24%), Positives = 91/191 (47%), Gaps = 22/191 (11%)

Query: 67  LRKAERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +  + +   KP G ++    +   + ++   L +    ++++GRLD ++EGLLLLT
Sbjct: 13  VATLQTHQHFKIFKPYGFLSQFVPEKRKKKSLLGELFNFPENIMAIGRLDHDSEGLLLLT 72

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL---- 179
            DG ++  +   S    + Y V+  G++    ++LL+KG+ I   G  Y  +        
Sbjct: 73  TDGMMSYKI--RSKGIEKEYYVQVDGEITAQAMSLLQKGVEIAINGATYLTLPCKAFKLD 130

Query: 180 -------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        D + G  +WV++ L EGKNR+I+K+     +   RL+R+  G   + 
Sbjct: 131 VEPKLPTRGRKIRDPRHGPTSWVSITLCEGKNRQIRKMTAAVGFATLRLVRVRIGDIHID 190

Query: 227 TLLAGSTREVS 237
           +++AG    ++
Sbjct: 191 SMIAGDVVTLT 201


>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 =  154 bits (389), Expect = 2e-35,   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 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD---- 180
           T+DGGL   +  P  +  + Y V+  G  D   L  L++G+ +        +        
Sbjct: 77  TDDGGLQARIADPRFKMEKTYWVQVEGVPDAAALQALERGVQLNDGPTLPARARRLDVPP 136

Query: 181 -----------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 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|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 =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 45/187 (24%), Positives = 80/187 (42%), Gaps = 45/187 (24%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           ++ +  R+ L++KP  ++   +D  GR T+ D +P     V + GRLD ++EGLL+LTND
Sbjct: 60  KENQPKRVVLFNKPYDVLPQFTDEAGRRTLKDFIP--VQGVYAAGRLDCDSEGLLVLTND 117

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------- 179
           G                             L  L+ G+ +         + +        
Sbjct: 118 G----------------------------VLQALRTGVTLNDGPTLPAGIEIVAEPDWLW 149

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  + +    +W+ V L EG+NR+++++         RLIR S G + L  L  G 
Sbjct: 150 PRTPPIRERKNIPTSWLKVTLYEGRNRQVRRMTAHVGHPTLRLIRYSMGDYTLNGLDNGQ 209

Query: 233 TREVSKK 239
            RE++++
Sbjct: 210 WREIAQE 216


>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 =  154 bits (389), Expect = 2e-35,   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|322490748|emb|CBZ26012.1| putative tRNA pseudouridine synthase A [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 694

 Score =  154 bits (389), Expect = 3e-35,   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  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 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|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 =  153 bits (388), Expect = 3e-35,   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 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----------- 180
             +  P  +  + Y V+  G  D   L  L++G+ +        +               
Sbjct: 64  ARIANPRFKMEKTYWVQVEGVPDAAALQALERGVQLNDGPTLPARARRLDAPPPVGEREP 123

Query: 181 ----TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                Q   + W+ + +REG+NR+++++         RL+R + GPF L  L  G+  EV
Sbjct: 124 PIRVRQHIPDTWIELVIREGRNRQVRRMTAAVGHPTLRLVRAAIGPFPLDGLAPGTWAEV 183


>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 =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 49/182 (26%), Positives = 82/182 (45%), Gaps = 22/182 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRST-VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +L HKP G ++       R   +   L       +++GRLD ++EGLLLLT DG ++ ++
Sbjct: 5   FLIHKPYGYLSQFIYELKRPKKLLGELYDFPGNTMAIGRLDEDSEGLLLLTTDGMMSEIV 64

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQV--------------- 177
              S +  + Y  +  G + ++ +  LK  + I   G  Y   +                
Sbjct: 65  --RSKKVEKEYYAQVDGLITEEAIEKLKNRVEIGFNGKKYLTKKCNAFILETIPNLGERG 122

Query: 178 --TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
               D + G  +WV++ L EGK R+++K+     +   RL+R+  G   L  L AG   E
Sbjct: 123 KKIRDERHGPTSWVSITLTEGKFRQVRKMTSAVGFPTLRLVRVRVGNIHLNDLKAGEVLE 182

Query: 236 VS 237
           VS
Sbjct: 183 VS 184


>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 =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 44/180 (24%), Positives = 86/180 (47%), Gaps = 22/180 (12%)

Query: 77  LYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +  KP G ++    +   R  +   L +  + ++++GRLD ++EGLLLLT DG  +  + 
Sbjct: 1   MIFKPYGYLSQFVGERRKRKPLLGELANFPTGIMAIGRLDHDSEGLLLLTTDGKTSHAVR 60

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL-------------- 179
             S    + Y ++  G++ +  ++ L +G+ I  +G  Y  +                  
Sbjct: 61  SKS--IEKEYYLQLDGEITEQAISSLCEGVEIGIKGEKYRTLPCRARRLDQAPDLPPRGR 118

Query: 180 ---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              D + G  +W+ + + EGKNR+++K+     +   RL+R+  G  +LGTL  G  + +
Sbjct: 119 KIRDARHGPTSWLAITITEGKNRQLRKMTAAVGFATLRLVRVRIGDIRLGTLQPGEVKSL 178


>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 =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 74/221 (33%), 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: 338 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAEDDVHVAGHQSRLRFAPPRLWMY 397

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           HKP  ++ + SD  GR+ +  +        ++ 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|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 =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 46/188 (24%), Positives = 84/188 (44%), Gaps = 22/188 (11%)

Query: 70  AERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E    +   KP G ++    +   R  +   L       +++GRLD ++EGLLLLT DG
Sbjct: 13  KEEHHHFKIFKPYGFLSQFVPETRKRKKLLAELADFPKGTMAIGRLDHDSEGLLLLTTDG 72

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL------- 179
            ++  +   S +  + Y V+  G +  D +  L+ G+ I  +G  Y  +   +       
Sbjct: 73  MVSHQV--RSKKVEKEYYVQLDGDITADAITQLQNGVEIGIKGDKYLTLPCRVFKLASEP 130

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     D + G  +W+++ + EGKNR+I+K+     +   RL+R+  G   +  + 
Sbjct: 131 NLPANGRKVRDLRHGPMSWISITISEGKNRQIRKMTAAAGFPTLRLVRVRIGNIDINEMQ 190

Query: 230 AGSTREVS 237
           AG    +S
Sbjct: 191 AGDVLPLS 198


>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 =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 36/159 (22%), Positives = 62/159 (38%), Gaps = 31/159 (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--------FQLGTLLAGSTREVSK 238
           R+           G           L  L  G  R ++ 
Sbjct: 121 RVQIQVTGRSPQQGKGKSAATWCLTLEGLSPGQWRPLTP 159


>gi|322503526|emb|CBZ38612.1| unnamed protein product [Leishmania donovani BPK282A1]
          Length = 877

 Score =  153 bits (387), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 71/228 (31%), Positives = 106/228 (46%), Gaps = 18/228 (7%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLY 78
           + RAG  SRRE   +IA  +V+VN +        V + D + V G   R      RLW+Y
Sbjct: 521 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHQSRLRFAPPRLWIY 580

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           HKP  ++ + +D  GR+ +  +        ++ 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     
Sbjct: 641 KSMVQRTYLLRVRPAFDPVLVHKLNTEGIQINGRLYRNAEFFVNPATKSRYSVKVK---- 696

Query: 197 KNREIK-------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               ++        + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 697 ----VRGESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 740


>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 =  152 bits (385), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 88/240 (36%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G +++     V  T  +E+D        
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKVT-TQKVELDPEAKATVP 61

Query: 72  RTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L H P G+        ++  +  +        L   F R+ +   L     GLL+
Sbjct: 62  EPVTILMHAPAGMDAETAMASISAETLSEEHRFSKRPLKGHFLRLTASADLQAKASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R L   + +  + Y V   G +    LN L  G+  +G     ++ +   + 
Sbjct: 122 FTQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKGKELPAVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I    E    KV  + RI  G   +G +  G  R +S K 
Sbjct: 182 ----RLRFAM---KNPQPGVIALFCEAVGLKVIAIRRIRIGGVSIGKVPVGQWRYLSGKE 234


>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 =  152 bits (385), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 71/228 (31%), Positives = 106/228 (46%), Gaps = 18/228 (7%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLY 78
           + RAG  SRRE   +IA  +V+VN +        V + D + V G   R      RLW+Y
Sbjct: 521 LPRAGFCSRREAAAIIASGQVRVNNVTERNPFRLVQAQDDVHVAGHQSRLRFAPPRLWIY 580

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           HKP  ++ + +D  GR+ +  +        ++ 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     
Sbjct: 641 KSMVQRTYLLRVRPAFDPVLVHKLNTEGIHINGRLYRNAEFFVNPATKSRYSVKVK---- 696

Query: 197 KNREIK-------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
               ++        + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 697 ----VRGESMPIAHLMQHLGRTVERGGRISFGPFALSNLAVGSVREVT 740


>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 =  152 bits (385), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 74/283 (26%), Positives = 114/283 (40%), Gaps = 72/283 (25%)

Query: 68  RKAERTRLWLYHKPIGLVTTH--SDPDGRSTVFDNL---------------------PSI 104
              ERT + LYHKPI +VTTH  +D  GR  V+D++                     P+ 
Sbjct: 26  SPPERTVVLLYHKPINVVTTHAANDVKGRMNVYDDVLSMKGFSGWNHVGKSADRERTPAS 85

Query: 105 F-------SRVISVGRLDINTEGLLLLTNDGGLARVLE--------LPSTQWLRVYRVRF 149
           F       S++ ++GRLD  T GLLLLTNDGGL   +                + Y    
Sbjct: 86  FAEATQIRSKLHAIGRLDAETTGLLLLTNDGGLVHHVTNKDSVSHQHHGNPVFKTYEALV 145

Query: 150 HGQVDQD--KLNLLK-KGIVIQ---GICYGDMQVTLDTQKG--SNAWVTVGLREGKNREI 201
            G  D     L  ++ +G+ I    G     +   +        +  V++ + EGKNR+I
Sbjct: 146 MGFYDNHSPLLEKMRTQGVNIGDKYGGTTRPVDELIVKTNPTLKSTLVSLTICEGKNRQI 205

Query: 202 KKVFEFFNWKVNRLIRISYG-PFQLGTLL-AGSTREVSKKILREQLGPHLLEEAQVNLDA 259
           +++F      V RL R   G    L ++  AG  R +++K +                  
Sbjct: 206 RRMFHALGSGVIRLCRTQIGRSLTLSSVPMAGQWRILTEKEV------------------ 247

Query: 260 PIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
                ET +  RP  I EV    +R  K +    G S+++K +
Sbjct: 248 -----ETALDWRPRYIGEV-SALSRAGKTTKAVTGTSRRRKRS 284


>gi|82523723|emb|CAI78504.1| S4 domain protein [uncultured beta proteobacterium]
          Length = 240

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 97/244 (39%), Gaps = 23/244 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+SK +A     SRRE E++I    V+V+G+++E     V ++  IE+D        
Sbjct: 3   DSIRLSKRVAELRACSRREAEQIITGGWVRVDGVVIEEPQFRV-ASQRIEIDPQADPSQI 61

Query: 72  RTRLWLYHKPIGLVTTHSDP------------DGRSTVFDNLPSIFSRVISVGRLDINTE 119
                L HKP G+  +  D             +   T    L + F+++ +   L+ +  
Sbjct: 62  EPVTLLLHKPAGVRISDDDKTALQLLRADSLWEHDGTGISPLKAHFTQLTACVPLEADAS 121

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL++ T D  + R L   +        V   G++  + L  L KGI   G     ++V+ 
Sbjct: 122 GLVVFTQDWRIVRKLTDDAATLEHEVIVEVSGELIPNGLKRLNKGIPYHGHTPAAIKVSW 181

Query: 180 DTQKGSNAWVTVGLR---EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +      + V L+    G   +I  + E    +V  + RI  G   L  +  G  R +
Sbjct: 182 QNE----TRLRVALKGCQIG---QIAHLCEAVGLQVVSMKRIRLGGIPLAKVPPGQWRYM 234

Query: 237 SKKI 240
            +  
Sbjct: 235 REDE 238


>gi|255654429|ref|ZP_05399838.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-23m63]
          Length = 141

 Score =  152 bits (384), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 43/136 (31%), Positives = 64/136 (47%), Gaps = 5/136 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
           QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5   QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE- 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G V+  +D     TV D +   +       VGRLD +TEGLL+LTNDG L
Sbjct: 64  YIYLMMNKPDGYVSATTD-KYDPTVLDLIDLSYLAFEPFPVGRLDKDTEGLLVLTNDGKL 122

Query: 131 ARVLELPSTQWLRVYR 146
           +  +  P     + Y 
Sbjct: 123 SHRVLSPKKHVPKTYY 138


>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 =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 43/186 (23%), Positives = 85/186 (45%), Gaps = 22/186 (11%)

Query: 68  RKAERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +  E  + +   KP G ++    +   +  +   L +   + +++GRLD ++EGLLLLT 
Sbjct: 14  KPTENHQHFKIFKPYGFLSQFVPESRKKKHLLGELFNFPDKTMAIGRLDHDSEGLLLLTT 73

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------------- 167
           DG ++  +       ++ Y V+  G++  D ++ L+ G+ I                   
Sbjct: 74  DGMMSYKV--RDKSIVKEYYVQVDGEITTDAISQLQNGVEIGINSTKYLTMPCKAFKLDC 131

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           +       +   D + G  +W+++ L EGKNR+I+K+     +   RL+R+  G   +  
Sbjct: 132 EPQLPARGRKIRDPKHGPTSWISITLCEGKNRQIRKMTAAVGFATLRLVRVRIGNIGIDN 191

Query: 228 LLAGST 233
           L+AG  
Sbjct: 192 LIAGDV 197


>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 =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 40/135 (29%), Positives = 65/135 (48%), Gaps = 1/135 (0%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQG 169
           +GRLD ++EGL+L+TNDG L++ +  P  +  + Y     G++       L   G+ +  
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 AGSTREVSKKILREQ 244
            GS R +S+  +R  
Sbjct: 121 PGSYRVLSQAEVRSL 135


>gi|56808585|ref|ZP_00366316.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 141

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 39/133 (29%), Positives = 66/133 (49%), Gaps = 2/133 (1%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           +D +T G+L+LTNDG     +  P  +  +VY  R  G   ++ L  L +GIVI G    
Sbjct: 1   MDWDTSGVLILTNDGDFTDTMIHPRNEIDKVYLARVKGIATKENLRPLTRGIVIDGKKTK 60

Query: 174 DMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             +  +       + + V + + EG+N ++KK+FE     V++L R  +G   L  L  G
Sbjct: 61  PARYNIVRVEADKNRSIVELTIHEGRNHQVKKMFESVGLLVDKLSRTRFGTVDLKGLRPG 120

Query: 232 STREVSKKILREQ 244
             R ++KK + + 
Sbjct: 121 EARRLNKKEISQL 133


>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 =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 93/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMAAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +    + +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNE----SRLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTAKE 234


>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 =  151 bits (382), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 42/179 (23%), Positives = 81/179 (45%), Gaps = 22/179 (12%)

Query: 72  RTRLWLYHKPIGLVTT---HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
               +  +KP G ++    H +      +   L +    V++VGRLD  +EGLLLLT DG
Sbjct: 2   DHHYYKIYKPYGYLSQFINHQNKRRNKKLLSELYTFSDNVMAVGRLDEKSEGLLLLTTDG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGD--MQVTL----- 179
             +  +    ++  + Y V   G + ++ +  L+ G+ I  +G  Y     +  +     
Sbjct: 62  KFSNYITS--SKIEKEYHVMVDGVITEEAVLKLQNGVEISVEGKPYKTKNCKAKILRDTS 119

Query: 180 --------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   D + G  +W+++ L EGK R+++K+     +   RL+R+  G ++L  +  
Sbjct: 120 HIVERFVRDERHGITSWLSITLAEGKFRQVRKMTAKVGFPTLRLVRVRIGDYKLEEMKP 178


>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 =  151 bits (382), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 54/273 (19%), Positives = 101/273 (36%), Gaps = 52/273 (19%)

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           TV D +      +   GRLD+++EGL+ LT+ GGL + +  P+ +  + Y V+  G V +
Sbjct: 2   TVSDFVDD--PTLRIAGRLDMDSEGLVFLTDHGGLNQFITNPANKKYKTYLVQVDGDVTE 59

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQ---------------KGSNAWVTVGLREGKNRE 200
           + L  L+KG+ +        +    ++                   +W+ + + EG+NR+
Sbjct: 60  EALEQLRKGVELNDGMTLPAKAIKVSEPEWLWDRDPPVRYRASIPTSWIEISICEGRNRQ 119

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVSKKILREQLGPHLLEEAQVNLD 258
           ++++     +   RLIR   G   L    L  G T+E+        L P   +       
Sbjct: 120 VRRMTSAVGFPTLRLIRTKIGTIDLVQLGLQPGETKEIEP-----LLYPDFKD------- 167

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAK 318
                          + +E P       K      G    +K      +++    +W   
Sbjct: 168 ---------------VPAEQPYRSRSYVKKPGGTGGKPMVRKNKDGSAKKSGTKRIWQ-- 210

Query: 319 GIHSSFLSDSGQREENHRRSPSFPSKRSLRRTS 351
                  S+  +R+ N    P+  + R   R S
Sbjct: 211 ----MDESEKPRRKTNGTTRPNTKAPRGRSRNS 239


>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 =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 45/177 (25%), Positives = 82/177 (46%), Gaps = 17/177 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L  ++KP+  ++  +   G   +      +   V + GRLD ++EGLLLLT+DGGL   +
Sbjct: 12  LIAFNKPMNTLSQFTSEGGWPALDGF--GLPKGVYAAGRLDRDSEGLLLLTDDGGLQARI 69

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL--------------- 179
             P  +  +VY     G  D   L+ L++G+ ++       +                  
Sbjct: 70  SSPKYRSPKVYFALVEGVPDDAALDHLRRGVTLKDGQTAPCEAEAVAAPDWIWDRDPPVR 129

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +  ++ W+ + L EG+NR+++++     + V RL+R S GP  +  L  G  RE+
Sbjct: 130 IRKSITDTWLKLTLTEGRNRQVRRMCAGVGFPVIRLVRFSIGPHDIRDLPPGMWREL 186


>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 =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 94/245 (38%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G++++     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIDEPHFKV-STQKIELSPEAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +   + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  ESVTIILHKPASASAESALQMITPGTLSAEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTTKE 234


>gi|120436300|ref|YP_861986.1| pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117578450|emb|CAL66919.1| pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 194

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 48/193 (24%), Positives = 87/193 (45%), Gaps = 24/193 (12%)

Query: 71  ERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +  R +  +KP G ++   T+  P G+  +  +L       +S+GRLD ++EGLLLLT +
Sbjct: 4   DYHRHFKIYKPYGYLSQFITNQKPGGKHKLLGDLYDFPEGTMSIGRLDKDSEGLLLLTTN 63

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYG------------ 173
           G L+  +        + Y  +  G +  + +  L+ G+ I   G  Y             
Sbjct: 64  GKLSTKINRG--GIEKEYYAQVDGDITDEAMIKLQNGVEISIFGKAYKSLKCKAEKLKNR 121

Query: 174 -----DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                  +   D + G  +W+++ L EGK R++KK+     +   RL+R+  G   +  +
Sbjct: 122 PSFPERAKKIRDERHGPTSWISISLTEGKFRQVKKMTSAVGFPTLRLVRVRIGNETIKNM 181

Query: 229 LAGSTREVSKKIL 241
            AG   E++K  L
Sbjct: 182 DAGEVIELNKVDL 194


>gi|302187180|ref|ZP_07263853.1| RNA-binding S4 [Pseudomonas syringae pv. syringae 642]
          Length = 236

 Score =  150 bits (380), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 94/240 (39%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI--------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                + HKP          ++T  +     S +   L   F R+ ++  L  N  GL++
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYIKRPLKGHFMRLEAISSLQANASGLMV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   + 
Sbjct: 122 FSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I  + E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 182 ----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTAKE 234


>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 =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 52/181 (28%), Positives = 90/181 (49%), Gaps = 21/181 (11%)

Query: 77  LYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           + HKP G+++   +P  R  T+  +L       +++GRLD+ +EGLLLLT DG ++  + 
Sbjct: 1   MVHKPWGMISQFVNPAKRKKTLLGDLYGFPEGTMAIGRLDVPSEGLLLLTTDGKVSAEI- 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY--GDMQVTL------------ 179
             S  + + Y V+  G +    L  LK G+ I  +G  Y     +  L            
Sbjct: 60  -RSNAYEKEYYVQVDGIMTAAALENLKTGVEIGFKGTKYVTKPGKAMLLKDPRFPLRSQK 118

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             D + G  +W+++ ++EGK R+++K+     +   RL+R+  G  +LG L  G+  EV 
Sbjct: 119 IRDERHGPTSWISIIIKEGKFRQVRKMTAAVGFPTLRLVRVRIGTMKLGELAIGAVVEVE 178

Query: 238 K 238
           K
Sbjct: 179 K 179


>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 =  149 bits (378), Expect = 4e-34,   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  HKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 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|330950630|gb|EGH50890.1| RNA-binding S4 [Pseudomonas syringae Cit 7]
          Length = 236

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 56/245 (22%), Positives = 92/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       A 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADAP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTAKE 234


>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 =  149 bits (377), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 92/240 (38%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G +++     V  T  +E+D      A 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKVT-TQKVELDPEAKATAP 61

Query: 72  RTRLWLYHKPIGL-VTTHSDPDGRSTVFDN-------LPSIFSRVISVGRLDINTEGLLL 123
                L + P G  V T     G  T+ +        L   F R+ +   L  N  GLL+
Sbjct: 62  EPVTLLLNVPAGTDVDTAMASLGPQTLSEEHRFGKRPLKGHFLRLTASADLQANASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R L   + +  + Y V   G++    LN L  G+  +G     ++ +   + 
Sbjct: 122 FTQDWKILRKLTADAAKIEQEYVVEVEGEMVAHGLNRLNHGLTYKGKELPAVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I    +    KV  + RI  G   +G +  G  R +S K 
Sbjct: 182 ----RLRFAM---KNPQPGVIALFCQAVGLKVVAIRRIRIGGVSIGKVPLGQWRYLSAKE 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 =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 96/240 (40%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI--------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                + HKP          ++T  +  +  S     L   F R+ ++  L  N  GL++
Sbjct: 62  EPVTIILHKPASASAESALQMITPGTLSEEHSYSKRPLKGHFMRLEAISSLQANASGLMV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +   + 
Sbjct: 122 FSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I ++ E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 182 ----RLRFAM---KNPQPGIIAQLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRYMTTKE 234


>gi|330959244|gb|EGH59504.1| S4 domain-containing protein [Pseudomonas syringae pv. maculicola
           str. ES4326]
          Length = 236

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 94/240 (39%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E     V ST  +E+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKVELSPDAKADSP 61

Query: 72  RTRLWLYHKPI--------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                + HKP          ++T  +  +  S     L   F R+  +  L  N  GL++
Sbjct: 62  EAVTIILHKPASASAESALQMITPGTLSEEHSYSKRPLKGHFMRLEPISSLQANASGLMV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            + D  + R L    ++  + Y V   G +    LN L  G+  +G     ++ +   + 
Sbjct: 122 FSQDWKILRKLTDDRSKIEQEYVVEITGDMVAHGLNRLNHGLTYKGKELPAVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I ++ E    K+  + RI  G   +G L  G  R ++ K 
Sbjct: 182 ----RLRFAM---KNPQPGIIAQLCEAVGLKIVSIRRIRIGGVSMGKLPEGQWRYMTSKE 234


>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 =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 47/192 (24%), Positives = 80/192 (41%), Gaps = 18/192 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
             R ++ +KP  +V+          + +          +VGRLD  +EGLL+LT +  + 
Sbjct: 9   PHRYFIINKPPNMVSQFVSSHDVRLLGELDFDFPEGTHAVGRLDSMSEGLLILTTNKKVT 68

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGI---CYGDMQVTLDTQKG-- 184
            +L L      R Y V     V  + + LL+ GI I  +G         +V +  +    
Sbjct: 69  NLLFLGEVPHTRTYWVNVGHIVPPETVQLLRTGIPIRVKGGGYYTTAPCEVEVIERPAIL 128

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                       N W+++ L EGK  +++K+    N +  RL+R S    +LG L  G  
Sbjct: 129 PWHQSEGQPGVPNTWLSITLTEGKYHQVRKMVREANHRCKRLVRASIEDLELGDLPPGGV 188

Query: 234 REVSKKILREQL 245
           RE+ ++     L
Sbjct: 189 REIGEEEFFRLL 200


>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 =  149 bits (376), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 92/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTAKE 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 =  149 bits (376), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 94/245 (38%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G++++     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIDEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
            +   + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  ESVTIILHKPASASAESALQMITPGTLSAEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTTKE 234


>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 =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 93/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELSPDAKANSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTTKE 234


>gi|289674640|ref|ZP_06495530.1| RNA-binding S4 [Pseudomonas syringae pv. syringae FF5]
          Length = 236

 Score =  148 bits (375), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 92/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVDHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTAKE 234


>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 =  148 bits (375), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 84/240 (35%), Gaps = 18/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R+SK +A A   SRRE E+ I    V V+G ++E     V     I +       A 
Sbjct: 3   DSIRLSKRVAEALACSRREAEQYIEGGWVSVDGKVIEEPGHRVDPQQAIVLSPDATLVAV 62

Query: 72  RTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+        +T  +      +    L      +     L+    GLL+
Sbjct: 63  DPVTILLHKPAGMDAAAALQCITPENLYAEDRSGIRFLKKHTVDLKPTDSLESLASGLLV 122

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  +AR L   +    + Y     G +  + L LL  G+ +       ++V+   + 
Sbjct: 123 FTQDWHVARKLVDDAAGIEQEYIAEVSGTLVANGLALLNHGLSMNRKPLAPVKVSWQNE- 181

Query: 184 GSNAWVTV---GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +     G++ G   +I  + E     +  L RI      +  L  G  R +    
Sbjct: 182 ---TRLRFAGKGIQRG---QIPYMCEQVGLTLVGLKRIRMARMPMAALPVGQWRYLKGYE 235


>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 =  148 bits (375), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 43/184 (23%), Positives = 75/184 (40%), Gaps = 25/184 (13%)

Query: 73  TRLWLYHKPIGLVTTHS----DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            + +L  KP G ++  S        +      L S    ++ +GRLD  +EGLLL+T DG
Sbjct: 4   HQHYLLFKPYGYLSQLSSNDLHQKRKKKFLAELYSWPDGIMPIGRLDEKSEGLLLMTTDG 63

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTL----- 179
            L+  +    +   + Y     G   + +L  L +GI I    +        V +     
Sbjct: 64  KLSDHI--NRSGIEKEYYALVDGIPTEAQLEQLSQGIEIGINGKKYRTKPCGVKILETSP 121

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     D + G   W+++ + EGK R+++K+    +    RL+RI  G  +L  + 
Sbjct: 122 ALPDRGKKIRDARHGPTTWLSITIIEGKFRQVRKMTSAIDCPTLRLVRIRIGSLKLKAIQ 181

Query: 230 AGST 233
            G  
Sbjct: 182 PGEV 185


>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 =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 90/238 (37%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYL 230


>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 =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 93/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPAVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTTKE 234


>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 =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 38/138 (27%), Positives = 69/138 (50%), Gaps = 3/138 (2%)

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICY 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 STREVSKKILREQLGPHL 249
           S R ++++ L+  L  H 
Sbjct: 121 SYRSLTQEELK-GLAAHF 137


>gi|251773013|gb|EES53569.1| pseudouridine synthase [Leptospirillum ferrodiazotrophum]
          Length = 237

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 57/182 (31%), Positives = 91/182 (50%), Gaps = 6/182 (3%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +KP G++ T SDP+GR  V D L         F R+  +GRLD  + GLLLLTN     
Sbjct: 53  LNKPRGVLVTLSDPEGRPVVGDFLRRTPWSDGSFGRIRPLGRLDAASAGLLLLTNYQEPW 112

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                P     R YRV+    +  +   L   G   +G  Y  ++V ++ +   ++W+ +
Sbjct: 113 SHFLSPEGGVRRRYRVKIRPGLRAEDRKLFLSGKAGEGAGYRRVEVEIEREGPKSSWLLI 172

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
            L EG+NREI+ V  +  ++V  LIR+++GPF LG L  G    V+++  +  +     E
Sbjct: 173 SLVEGRNREIRNVLTYHGYEVLHLIRLAFGPFLLGDLKPGEVSSVTEEAKKAGVVWERWE 232

Query: 252 EA 253
            +
Sbjct: 233 SS 234


>gi|255523816|ref|ZP_05390781.1| pseudouridine synthase [Clostridium carboxidivorans P7]
 gi|255512519|gb|EET88794.1| pseudouridine synthase [Clostridium carboxidivorans P7]
          Length = 180

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 41/173 (23%), Positives = 75/173 (43%), Gaps = 26/173 (15%)

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
           +       + V  VGRLD +TEGLLLLTNDG     L  P     + Y     G +D++ 
Sbjct: 2   YFFDDDKMNGVFHVGRLDKDTEGLLLLTNDGEFEHKLMHPQEHIEKTYFFWALGSLDEEN 61

Query: 158 LNLLKKGIVI-QGIC-YGDMQVT---------------------LDTQKGSNAWVT--VG 192
              L++GI I +G       ++                      +D+ + +   V+  + 
Sbjct: 62  RKQLEQGIYIGKGEILTKPAKIEVHRCGMYKDFKHEMPIDNLNNIDSNQYNQPVVSGYLT 121

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQ 244
           + EG+N ++K++ +     V  L R+S G   L  ++  G  R +++  +++ 
Sbjct: 122 ITEGRNHQVKRMLKAAGCYVVYLKRVSIGGLMLDESMEKGRYRLLTEVEIKKL 174


>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 =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 90/238 (37%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDLEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYL 230


>gi|296390524|ref|ZP_06879999.1| hypothetical protein PaerPAb_20321 [Pseudomonas aeruginosa PAb1]
          Length = 236

 Score =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 92/238 (38%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G++    L  L++G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVTGELAAGGLERLRQGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYL 230


>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 =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 93/259 (35%), Gaps = 26/259 (10%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K +       +R++K +A     SRRE E+ I    V VNG ++E     V S   +EVD
Sbjct: 6   KPVPPAPREGERLAKRVAEMVPCSRREAEQYIEGGWVSVNGQVVEEPMFRV-SDQRVEVD 64

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-------------------FDNLPSI 104
                        L HKP G     +       V                      L   
Sbjct: 65  PDASLLELSAVTLLLHKPPGFDAMAAPGQANRHVKSAQQLLSAATHATDDASGVRLLKRH 124

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           F+++ +   L+    GL++ T D  + R L   +    +   V   G+V    L  + +G
Sbjct: 125 FAKLTACVPLETAASGLVVFTQDWRVLRKLTEDAQLMEQEVIVEVAGEVPAQSLQRINQG 184

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGL---REGKNREIKKVFEFFNWKVNRLIRISYG 221
           + + G     ++V+L++   +++ +   L     G    I  + E    ++  + R+  G
Sbjct: 185 LAVDGQPLPAVKVSLNSTGETSSKLRFALKGSHPGL---IAYLCERLGLQIVSMKRLRIG 241

Query: 222 PFQLGTLLAGSTREVSKKI 240
              +  L  G  R +    
Sbjct: 242 RVSMTQLPLGQWRYLQAHE 260


>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 =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 90/238 (37%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVTGDLAAGGLERLRHGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCESEGLEVRSIRRLRIGALSLARLPLGEWRYL 230


>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 =  148 bits (373), Expect = 2e-33,   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|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 =  148 bits (373), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 44/183 (24%), Positives = 82/183 (44%), Gaps = 22/183 (12%)

Query: 71  ERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +    +   KP G ++    +      +   L    +  +++GRLD ++EGLLLLT DG 
Sbjct: 29  QPHHHYKIFKPYGYLSQFVPERRKSKKLLAELALFPAGTMAIGRLDHDSEGLLLLTTDGM 88

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL-------- 179
           ++  +   S +  + Y V+  G +D   +  L+ G+ I  +G  Y  +   +        
Sbjct: 89  VSHQV--RSKKVEKEYYVQVDGDIDDAAILKLQTGVEIGIKGEKYLTLPCKVFKLENEPE 146

Query: 180 ---------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    D + G  +WV++ + EGKNR+I+K+     +   RL+R+  G   L  + +
Sbjct: 147 LPSNGRKPRDPKHGPMSWVSITIGEGKNRQIRKMTAAAGFPTLRLVRVRIGNIHLDRMQS 206

Query: 231 GST 233
           G  
Sbjct: 207 GEV 209


>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 =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 55/245 (22%), Positives = 93/245 (37%), Gaps = 29/245 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+       + 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72  RTRLWLYHKPI-------------GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
                + HKP              G ++       R      L   F R+ ++  L  N 
Sbjct: 62  EPVTIILHKPASASAEEALQMITPGTLSVEHSYSKRP-----LKGHFMRLEAISSLQANA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++ + D  + R L    ++  + Y V   G++    LN L  G+  +G     ++ +
Sbjct: 117 SGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNRLNHGLTYKGKELPSVKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +      +   +   KN +   I  + E    K+  + RI  G   +G L  G  R 
Sbjct: 177 WQNEN----RLRFAM---KNPQPGIIALLCEAVGLKIVAIRRIRIGGVSMGKLPEGQWRY 229

Query: 236 VSKKI 240
           ++ K 
Sbjct: 230 MTTKE 234


>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 =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 89/237 (37%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A     SR E ++ I    V V+G+++E     +     + +    +    
Sbjct: 3   DPIRLDKHVAAVFGCSRGEAQQYIEGGWVSVDGVVVEEPQAPIT-GQQVSLAADAVLGQA 61

Query: 72  RTRLWLYHKPIGLVT----THSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLL 123
           +    L +KP G+        + P  RS    T    L   F R+ +   LD    GLL+
Sbjct: 62  KPATLLLNKPAGMSCEAAVALATPQSRSSLDQTEIRVLKRHFLRLSAPMPLDDEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   +    + Y V   G++    +  L  G++ Q       +V+   ++
Sbjct: 122 LSQDGRILRRLTADAATIEQEYLVEVRGELRPYGMARLASGLLYQQRSLPACKVSWQNEE 181

Query: 184 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +       V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCNEVGLDVVTIRRLRVGRISLGKLALGEWRYL 230


>gi|298710181|emb|CBJ26256.1| pseudouridine synthase [Ectocarpus siliculosus]
          Length = 387

 Score =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 74/320 (23%), Positives = 130/320 (40%), Gaps = 51/320 (15%)

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGL 130
           R ++ HKP G VT+  D    GR TV+D   +        VGRLD +T G+LL T+D  L
Sbjct: 2   RYFMLHKPRGCVTSTVDDTGRGRPTVYDVAKAAGVPNFGPVGRLDFDTSGVLLFTDDYKL 61

Query: 131 ARVLELPSTQ----------WLRVYRVRFHGQVDQDK--LNLLKKGI----VIQGI---C 171
            + +  P+ +            +VY +   G +  +   ++LL++ +     + G     
Sbjct: 62  KKAISSPTYKGKAAVGTVPSMEKVYHLLVAGTITPEDKGMDLLQEPLHFSRKLDGPGGSW 121

Query: 172 YGDMQVTLDTQKGSNA-----------------WVTVGLREGKNREIKKVFEFFNWKVNR 214
               +  +   K                     W+ V LREGKNR+I+++     +++ R
Sbjct: 122 TKPAEARVLLTKTFKTGQPVPWRFKPGTVATITWIEVVLREGKNRQIRRLCRRSEFELTR 181

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ-VNLDA---PIYSSETLVRD 270
           L RIS GP  LG +  GS RE++++ +       L E+     +DA    + S  +    
Sbjct: 182 LHRISVGPIVLGDVEEGSCRELTRQEVEALYKRCLPEDPLCPTIDAVQDILQSRLSQTAR 241

Query: 271 RPNIISEVPDDFTRMKKNSSQ---KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSD 327
           R    +EV     + +++SS          ++  A    +R  A+     +       + 
Sbjct: 242 RIRTTAEVGGHRFKAREHSSAMDVPQKDMPERPTAEDAEQR-RAAKARDGERGCPCRTTQ 300

Query: 328 SGQREENHRRSPSFPSKRSL 347
              R    RR  +F ++  L
Sbjct: 301 GPGR----RRVKAFATEEDL 316


>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 =  147 bits (371), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 90/238 (37%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCESEGLEVRSIRRLRIGALPLARLPLGEWRYL 230


>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 =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 88/237 (37%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A     SR E ++ I    V V+G+++E     +     + +    +    
Sbjct: 3   DPIRLDKHVAAVFGCSRGEAQQYIEGGWVSVDGVVVEEPQAPIT-GQQVSLAADAVLGQA 61

Query: 72  RTRLWLYHKPIGLVT----THSDPDGRS----TVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L +KP G+        + P  RS    T    L   F R+ +   LD    GLL+
Sbjct: 62  EPATLLLNKPAGMSCEAAVALATPQSRSSLDQTEIRVLKRHFLRLSAPMPLDDEASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L+ DG + R L   +    + Y V   G++    +  L  G+V Q       +V+   ++
Sbjct: 122 LSQDGRILRRLTADAATIEQEYLVEVRGELRPYGMARLASGLVYQQRSLPACKVSWQNEE 181

Query: 184 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +       V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCNEVGLDVVTIRRLRVGRISLGKLALGEWRYL 230


>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 =  146 bits (370), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 51/189 (26%), Positives = 86/189 (45%), Gaps = 22/189 (11%)

Query: 69  KAERTRLWLYHKPIGLVTTH-SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             +  + +L +KP G ++    +      +   L     + +++GRLD ++EGLLLLT D
Sbjct: 8   AEQAHQHFLIYKPYGFLSQFVPETRKSKPLLGQLYDFPDKTMAIGRLDHDSEGLLLLTTD 67

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ--GICYG--DMQVTL---- 179
           G  + ++   S    + Y V+  G V Q +L  L++G+ I   G  Y     QV L    
Sbjct: 68  GMQSHLIRSKS--IEKEYYVQVDGLVSQAQLLQLQQGVEIGISGGKYLTLPCQVELLTTE 125

Query: 180 -----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                      D + G  +W++V + EGKNR+++K+         RL+R+  G   L  +
Sbjct: 126 PNLPARGKKIRDPRHGPTSWLSVTIAEGKNRQVRKMTAAVGLPTLRLVRVRIGHICLKQM 185

Query: 229 LAGSTREVS 237
             G    VS
Sbjct: 186 QPGEVLPVS 194


>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 =  146 bits (370), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 47/164 (28%), Positives = 75/164 (45%), Gaps = 26/164 (15%)

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 QGICYGDMQVT-----------------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +G      + T                  + +    +W+++ LREG+NR+I+++      
Sbjct: 61  KGQRTRPARATSLDSSFWFDLPERTPPIRERRTIPTSWLSISLREGRNRQIRRMTAAVGL 120

Query: 211 KVNRLIRISYG------PFQLGTLLAGSTREVS---KKILREQL 245
              RLIR S        P  L  L  G  R V+   ++ L+  L
Sbjct: 121 PTLRLIRRSIDLMDGGPPLSLEGLAPGQWRPVNSAEEERLKALL 164


>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 =  146 bits (370), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 42/186 (22%), Positives = 81/186 (43%), Gaps = 25/186 (13%)

Query: 71  ERTRLWLYHKPIGLVTTH---SDPDGRSTVF-DNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++   +  +KP G+++      + + R   F   L      ++ VGRLD  +EGLLLLT 
Sbjct: 2   KKHLHFKIYKPFGMLSQFISNDEKEARKKHFLGELYDFPEGIMPVGRLDEKSEGLLLLTT 61

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQ 182
           DG L+  +    +   + Y  +  G++  + +  L++G++I    +       +V     
Sbjct: 62  DGKLSDTI--NQSGIEKEYYAQLDGEIPHEDILQLERGVLIGLSGKKYITKPCRVKALLD 119

Query: 183 KG---------------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                             N+W+++ + EGK R+++K+     +   RLIR+  G   L  
Sbjct: 120 PPLLTDPDKKLRIGTHRPNSWISITITEGKFRQVRKMTAAVGFPTLRLIRVRIGTQILED 179

Query: 228 LLAGST 233
           L  G+ 
Sbjct: 180 LQPGTV 185


>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 =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 58/254 (22%), Positives = 90/254 (35%), Gaps = 32/254 (12%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R++K +A     SRRE E+ I    V V+G+++E     V+    IE+       A
Sbjct: 1   MEPVRLAKRLAEMLSCSRREAEQYIEGGWVTVDGVVVEEPQFRVL-DQTIELSKDASLLA 59

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGR--STVFDNL------PSIFSRVIS----------VG 112
                 L HKP G       P GR   +  + L      P   S +            V 
Sbjct: 60  LAPVTLLLHKPAGHEAGLDAPAGRGVPSAAELLVAANQSPDDRSGIRPLKKHFSAAELVT 119

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQG 169
            L     GL++ T D  +AR L   +        V   G++    L  L     G    G
Sbjct: 120 PLATAASGLVVFTQDWRVARKLREDAGVLEHEVIVEVTGEIKPGGLERLNRIDHGFTFNG 179

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLR-E--GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           +     +V+      S A +   L+ E  G   +I  + E    +V  + R+  G   + 
Sbjct: 180 VLLPPAKVSWQ----SEARLRFALKGERPG---QIAYMCESVGLRVEAMKRLRIGRVPMS 232

Query: 227 TLLAGSTREVSKKI 240
            L +G  R +    
Sbjct: 233 NLQSGRWRYLLPHE 246


>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 =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 97/236 (41%), Gaps = 17/236 (7%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+++ +A     SR E E+ I    VKV+G ++E     V S   +E+D     +   
Sbjct: 34  PIRLARRVAELAQCSRSEAEQYIEGGWVKVDGQVVELPGHMVTSE-RVEIDPKARLQPVE 92

Query: 73  TRLWLYHKPIGL------------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
              +L HKP G+            +      +G ++    L   F R+ S+  L+    G
Sbjct: 93  PATFLLHKPAGVDLEAVADTLATLLPPQERWEGDTSNIRTLRKNFQRLASLVPLEPEASG 152

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L++L+ DG + R L        + + V   G ++   L+ L  G+  +G+     +V+  
Sbjct: 153 LVVLSQDGRVRRRLVEDFATIEQEFVVEVEGSLEPWGLSRLSHGLTFEGLELPPGKVSWQ 212

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +      +   L+  +  +++ +      +V  + R+  G   L  +  G+ R +
Sbjct: 213 NE----TRLRFALKGPRPGQLRAMCTQVGLEVVSIRRLRIGRIPLAKMPPGAWRYL 264


>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 =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 86/240 (35%), Gaps = 20/240 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G +++     V  T  +E+D        
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVSVDGEVIDEPQFKVT-TQKVELDPEAKATVP 61

Query: 72  RTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L H P G+        ++  +  +        L   F R+ +   L     GLL+
Sbjct: 62  EPVTILLHAPAGVDAETAMASISAETLSEEHRFSKRPLKGHFLRLTASADLQAKASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R L   + +  + Y V   G +    LN L  G+  +G      ++      
Sbjct: 122 FTQDWKILRKLTADAAKIEQEYVVEVEGDMVAHGLNRLNHGLTYKG-----KELXXXXXX 176

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I    E    KV  + RI  G   +G +  G  R +S K 
Sbjct: 177 XXXNRLRFAM---KNPQPGVIALFCEAVGLKVVAIRRIRIGGVSIGKVPVGQWRYLSGKE 233


>gi|218506664|ref|ZP_03504542.1| pseudouridylate synthase, subunit B protein [Rhizobium etli Brasil
           5]
          Length = 157

 Score =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 72/113 (63%), Positives = 88/113 (77%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            +     +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP
Sbjct: 45  TEGEAKAERISKVMARAGVASRRDIERMIMEGRVTLNGKVLETPVVNVTLADRIEVDGVP 104

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +R  ERTRLWLYHKP GLVTT++DP+GR TVFDNLP    RV+S+GRLDINTE
Sbjct: 105 IRGIERTRLWLYHKPAGLVTTNADPEGRPTVFDNLPEELPRVMSIGRLDINTE 157


>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 =  146 bits (369), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 90/238 (37%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELYIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCEREGLEVRSIRRLRIGALSLARLPLGEWRYL 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 =  146 bits (368), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 91/236 (38%), Gaps = 19/236 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+S+ +      SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   EPIRLSRRLVELIACSRREAELYIEGGWVSVDGTVVEEPQFKVL-DQRVELLPGARPEPL 61

Query: 72  RTRLWLYHKPIG--------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G        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 GSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   L+    G   +++ + E    +V  + R+  G   L  L +G  R +
Sbjct: 182 H----LRFALKGAQPG---QLRFMCESEGLEVRGIRRLRIGALSLARLPSGEWRYL 230


>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 =  145 bits (367), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 40/183 (21%), Positives = 81/183 (44%), Gaps = 24/183 (13%)

Query: 73  TRLWLYHKPIGLVTTH---SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            + +  +KP G ++     S       +   L +     +S+GRLD  +EGLLLLT DG 
Sbjct: 8   HKHFKLYKPDGYLSQFINNSKKRRNKKLLGELYNFPEGTMSIGRLDEMSEGLLLLTTDGK 67

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDM---------- 175
           ++  +    +++ + Y V+  G + +  +N ++ G+ I    +                 
Sbjct: 68  VSAAVTS--SKYEKEYIVQVSGDITEGAINEMRNGLTIPINGKQYDTKPCTAFKLNKTPQ 125

Query: 176 -----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                +    ++ G  +W+++ +REGK R+++K+     +   RL+RI  G + L  +  
Sbjct: 126 FPERQKAIRSSRHGETSWLSISIREGKFRQVRKMTAKVGFPTLRLVRIRIGNYHLEDMQP 185

Query: 231 GST 233
           G  
Sbjct: 186 GQV 188


>gi|268611607|ref|ZP_06145334.1| RNA pseudouridine synthase family protein [Ruminococcus
           flavefaciens FD-1]
          Length = 201

 Score =  145 bits (367), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 56/192 (29%), Positives = 82/192 (42%), Gaps = 25/192 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARV 133
            ++++KP   VT   D   R TV D  P+  S R+  VGRLD +T GLLLLT+DG L   
Sbjct: 6   YYMFNKPQNCVTAKRDAVHR-TVMDFFPADLSERLHPVGRLDKDTCGLLLLTDDGDLDFR 64

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ----------- 182
           +  P     + Y     G +D +K+  L+KGI + G         L  +           
Sbjct: 65  IMQPDRHVSKTYFFYAIGTMDDEKIRSLEKGISMVGFTSRPASFRLIRKYRISQLEEFFP 124

Query: 183 -----------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLA 230
                       G      + + EGK  E+K++ E  + K+  L RIS G   L   L  
Sbjct: 125 SERRERYLKNPDGPAFAAELTIHEGKKHEVKRMLEAVHCKIFYLKRISIGGLSLDDSLAE 184

Query: 231 GSTREVSKKILR 242
           G  R ++   L+
Sbjct: 185 GQYRPLNDYELQ 196


>gi|213423650|ref|ZP_03356630.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 165

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 35/137 (25%), Positives = 61/137 (44%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           + AA  ++    +  DG PL +    R ++ +KP G V +  DPD  + ++     +  +
Sbjct: 25  KNAAFKLLPEHAVAYDGNPLAQQHGPRYFMLNKPQGYVCSTDDPDHPTVLYFLDEPVAYK 84

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           + + GRLDI+T GL+L+T+DG  +  +  P     + Y V     V  D      KG+ +
Sbjct: 85  LHAAGRLDIDTTGLVLMTDDGQWSHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQL 144

Query: 168 QGICYGDMQVTLDTQKG 184
                     TL+    
Sbjct: 145 HNEKDLTKPATLEVITP 161


>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 =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 89/240 (37%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G +++     V +   + +D      A 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKVGA-QTVALDPEAKATAP 61

Query: 72  RTRLWLYHKPIG------LVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L + P G      + +  +D   +        L   F R+ +   L  N  GLL+
Sbjct: 62  EPVTILLNVPAGQDLDSAMQSIGADSLSEEHRYGKRPLRGHFLRLTASDDLQPNASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R L     +  + Y V   G++    LN L  G+  +G     ++ +   + 
Sbjct: 122 FTQDWKVLRKLTADVAKIEQEYVVEVEGEMIDHGLNRLNHGLTYKGRELPPVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I    +    KV  + RI  G   +G +  G  R +S K 
Sbjct: 182 ----RLRFAM---KNPQPGVIALFCQAVGLKVVAIRRIRVGGVSIGKVPLGQWRYLSAKE 234


>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 =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 31/133 (23%), Positives = 61/133 (45%), Gaps = 6/133 (4%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
            + +VGRLD +T G+LL+TNDG     +  P  +  ++YR       D+     LK G++
Sbjct: 5   DMQAVGRLDADTTGVLLITNDGQFNHRMTSPKYKAAKLYRAGLKHPADETFCQSLKNGVL 64

Query: 167 I--QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           +          +  L+    +   + + + EGK  ++K++      +V  L R+ +G + 
Sbjct: 65  LHDDDETVQAAEAVLE----NPHTLLLTITEGKYHQVKRMVAAAGNRVETLHRLKFGEWS 120

Query: 225 LGTLLAGSTREVS 237
              L  G  + ++
Sbjct: 121 AEHLAPGEWQFIT 133


>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 =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 40/187 (21%), Positives = 78/187 (41%), Gaps = 24/187 (12%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLT 125
              +   +  +KP G+++  +  D        L   +     ++ +GRLD  +EGLLLLT
Sbjct: 2   PNSQHIHYKMYKPYGVLSQLASNDNNQVKKKFLSEFYNFPQGIMPIGRLDEKSEGLLLLT 61

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV--IQGICYGDMQVTL---- 179
            DG L+  +        + Y  +  G +  + L+ ++KG+V  + G  Y      +    
Sbjct: 62  TDGKLSDTINRA--GIEKEYYAQLDGIITNEALHKIEKGVVIGLNGTTYTTKTCIVKHIE 119

Query: 180 -------------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                          +   N+W+++ + EGK R+++K+     +   RL+R+      L 
Sbjct: 120 TPKNIPEPSTKIRLGRHRPNSWISICITEGKFRQVRKMTAAVGFPTLRLVRVRIHNITLD 179

Query: 227 TLLAGST 233
            L  G+ 
Sbjct: 180 NLTLGAV 186


>gi|49081944|gb|AAT50372.1| PA1110 [synthetic construct]
          Length = 237

 Score =  144 bits (363), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 90/238 (37%), Gaps = 23/238 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +A     SRRE E  I    V V+G ++E     V+    +E+      +  
Sbjct: 3   DPIRLSKRLAELTACSRREAELHIEGGWVSVDGEVIEEPQFKVL-DQRVELLPGARAETI 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG----------RSTVFDNLPSIFSRVISVGRLDINTEGL 121
                L HKP G    H D +G            +    L   F+R      LD    GL
Sbjct: 62  EPATLLLHKPAGW--RHDDFEGLLAAGRRWSDDPSPLRALKKHFARQRPTLALDSEASGL 119

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ +   G+ R L     +  + Y V   G +    L  L+ G+  QG      +V+   
Sbjct: 120 VVFSQQHGVLRKLVDDGARLEQEYLVEVAGDLAAGGLERLRHGLAYQGRRLSPCKVSWQN 179

Query: 182 QKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           +    + +   L++   G   +++ + E    +V  + R+  G   L  L  G  R +
Sbjct: 180 E----SHLRFALKDVLPG---QLRFMCEREGLEVRSIRRLRIGALSLARLPLGEWRYL 230


>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 =  143 bits (361), Expect = 4e-32,   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|3402689|gb|AAC28992.1| unknown protein [Arabidopsis thaliana]
          Length = 303

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 54/156 (34%), Positives = 82/156 (52%), Gaps = 15/156 (9%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHI 60
           +    ENF   PQR+SKV+A AG+ASRR  E +I   +V VNGIL       V  + D I
Sbjct: 148 RRFYNENFKEQPQRLSKVLAAAGVASRRTSEELIFDGKVTVNGILCNTPQTRVDPSRDII 207

Query: 61  EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRS--TVFDNLPSIF---------SRV 108
            V+G  + K       +  +KP G + +  + + +S  ++FD   S +          R+
Sbjct: 208 YVNGNRIPKKLPPKVYFALNKPKGYICSSGEKEIKSAISLFDEYLSSWDKRNPGTPKPRL 267

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            +VGRLD+ T GL+++TNDG  A+ L  PS+   + 
Sbjct: 268 FTVGRLDVATTGLIVVTNDGDFAQKLSHPSSSLPKE 303


>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 =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 43/190 (22%), Positives = 78/190 (41%), Gaps = 19/190 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  + 
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALP 180

Query: 238 KKILREQLGP 247
            +   +   P
Sbjct: 181 PRAPWDGFAP 190


>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 =  143 bits (360), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 49/195 (25%), Positives = 82/195 (42%), Gaps = 23/195 (11%)

Query: 73  TRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            R +L +KP  +++   T+            L       ++VGRLD ++EGLLL+T DG 
Sbjct: 2   HRHFLIYKPYRMLSQFMTNDRHQKNKRFLGELYDFPENAMAVGRLDEHSEGLLLITTDGQ 61

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QG--ICYGDMQV-------- 177
           L+  +   S    + Y     G + +  +  L+ G+ I   G        QV        
Sbjct: 62  LSHHI-NKSGIVDKEYAALVDGLITEQAIEQLQNGVTISINGSTYDTKPCQVQKPNQIPD 120

Query: 178 -------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                    D + G  +WV V L EGK R+++K+     +   RL R+  GP+ + +L  
Sbjct: 121 LPETKQKIRDERHGPTSWVNVTLSEGKFRQVRKMTGVVGFPTLRLARVRIGPYNVLSLRN 180

Query: 231 GSTREVSKKILREQL 245
               E+S + +R   
Sbjct: 181 QQVIELSDQEIRSLF 195


>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 =  143 bits (360), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 59/211 (27%), Positives = 92/211 (43%), Gaps = 17/211 (8%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
            ++G  ++   + V   + + V G  L   E     + HKP G+VT  +D     T +  
Sbjct: 27  TLDGRAMKDPRMPVDVGERVRVRGEELVLREHAH-LMLHKPHGVVTARADGRH-PTAYAL 84

Query: 101 LP--SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV----- 153
           L    +F+ + +VGRLD++  GLLL T DG L   L  P     R Y V           
Sbjct: 85  LEGAPLFAELRAVGRLDLDAVGLLLWTTDGQLVHALTHPRRAVPRTYHVALAAPFEAPPR 144

Query: 154 -DQDKLNL-LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            D   + L L+ G     + +  +        L T  G+ A  TV L +G   E+K++F 
Sbjct: 145 DDDGAVALELRDGLRPRVVALGALDEAAAHPALLTPPGTEALATVTLLDGAYHEVKRIFA 204

Query: 207 FFNWKVNRLIRISYGPFQLG-TLLAGSTREV 236
                V  L R+ +GP +L  TL AG+ + +
Sbjct: 205 ALGSHVLCLARVRHGPVELPRTLEAGAWQLL 235


>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 =  143 bits (360), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 47/169 (27%), Positives = 78/169 (46%), Gaps = 21/169 (12%)

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYR 146
           ++S    R      L S     + +GRLD  +EGLLLLT DG L+  +   S+   + Y 
Sbjct: 7   SNSTQQKRKRFLGELGSFPQGTMPIGRLDEKSEGLLLLTTDGKLSDYV--NSSGIEKEYY 64

Query: 147 VRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL-----------------DTQKGSNA 187
               G + Q++++ LKKG+ I   G  Y      +                 D + G  +
Sbjct: 65  ALVDGDISQEEISSLKKGVEIGFDGKKYQTKPCKVFKLDNAPLLPERGKKIRDARHGPVS 124

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           W+++ L EGK R+++K+         RL+R+  G  QLG L +G+ + +
Sbjct: 125 WISITLTEGKFRQVRKMTSAVGCPTLRLVRVRVGNIQLGNLESGAVKPI 173


>gi|262365461|gb|ACY62018.1| putative RNA pseudouridylate synthase-family protein [Yersinia
           pestis D182038]
          Length = 194

 Score =  142 bits (359), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 56/207 (27%), Positives = 90/207 (43%), Gaps = 19/207 (9%)

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-GTLLAGSTREVSKK---ILREQL 245
            V L EG+NRE+++++E    +V+RLIR+ YG   L   L  G   E+  K    LRE  
Sbjct: 61  NVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDINLPKGLPRGGWTELDLKATNYLREL- 119

Query: 246 GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPV 305
                    V LD    S   + +DR  + +       R  K  ++ +G     +  +  
Sbjct: 120 ---------VELDVETVSKLPVEKDRRRVKAN---QIRRAVKRHTEVSGRQVAGRQGS-A 166

Query: 306 HRRNLASNVWM-AKGIHSSFLSDSGQR 331
            + +   NV   A    +S  S   +R
Sbjct: 167 RKGSTRQNVGNAAPAATASRRSGPKKR 193


>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 =  142 bits (358), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 82/232 (35%), Gaps = 15/232 (6%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +      SRRE E  IA   V V+G ++E     V     +E+         
Sbjct: 3   EPVRLAKRLVELVACSRREAELYIAGGWVMVDGQIVEEPQFMVSE-QLVELHPNADLTPI 61

Query: 72  RTRLWLYHKPIGL----VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
                L+H         +   +      +    L   F ++     L+ N  GL +LT D
Sbjct: 62  EPATLLFHHLNATNTTAICAGTRSADDLSGIHLLRQHFFKLTPCTPLERNASGLTVLTQD 121

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             + R L+  +    + Y V   G++  D L LL  G+   G      +V+   +     
Sbjct: 122 FRIIRKLKDEAATIEQEYIVEIAGEIMADGLKLLNHGLKFNGKPLPPAKVSWQNE----T 177

Query: 188 WVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +   L+    G   +I  + +     V  + RI  G   +  L     R +
Sbjct: 178 RLRFALKGVIPG---QIAAMCQKVGLDVISMRRIRIGRISMAKLQPDQWRYL 226


>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 =  142 bits (358), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 92/237 (38%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A     SR E ++ I    V VNG+++E       +   +E+    + +  
Sbjct: 3   DPIRLDKCVAAQFGCSRGEAQQYIEGGWVSVNGVVVEEPQALATAAQ-VELAADAVLEPA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGR---STVFDN-----LPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+    +    +    +  DN     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 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +       V  L R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCGEVGLDVVSLRRLRVGRVSLGKLAIGQWRYL 230


>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 =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 45/186 (24%), Positives = 85/186 (45%), Gaps = 18/186 (9%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           + R ++ +KP  +V+     D  + + +   +      +VGRLD  +EGLL+LT +  + 
Sbjct: 27  KNRYFIINKPFNMVSQFISSDAVNLLGNLDFTFPEGTHAVGRLDNESEGLLILTTNKKVT 86

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICY--GDMQVTLD------ 180
           R+L   + +  R Y V    +V ++ L  L+ GI I+   G  Y     + ++       
Sbjct: 87  RLLFQGTKKHTRTYLVLVKNKVSEETLKQLQTGISIRVKGGGNYISSPCEASIVTDAKAI 146

Query: 181 -------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                   +   + W+ + L EGK  +++K+    N +  RLIR+S     L  L  G+ 
Sbjct: 147 YSYAADTRENYPHTWLLLTLTEGKFHQVRKMVLAVNHRCLRLIRVSIENMLLHDLQPGAV 206

Query: 234 REVSKK 239
           +E  ++
Sbjct: 207 KEFEEE 212


>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 =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 39/125 (31%), Positives = 65/125 (52%), Gaps = 5/125 (4%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + Q+N    R++K I+  G  SRR  +++I + RV +NG         V+  D + VDG 
Sbjct: 1   MSQDNAK--RLNKFISETGFCSRRAADKLIEEGRVTINGKQP-EMGTKVLPGDDVCVDGK 57

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+   E+      +KP G+  T ++ D    + D +     R+  +GRLD  ++GL+ LT
Sbjct: 58  PVASKEKPIYIALNKPTGITCT-TERDIPGNIVDFI-GHKKRIFPIGRLDKPSDGLIFLT 115

Query: 126 NDGGL 130
           NDG +
Sbjct: 116 NDGDI 120


>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 =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 41/181 (22%), Positives = 74/181 (40%), Gaps = 25/181 (13%)

Query: 76  WLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +  +KP G+++  +  + R          L       + VGRLD  +EGLLL+T DG L+
Sbjct: 9   FKLYKPFGMLSQLASNEERQIRSKRFLSELHEFPEGTMPVGRLDEKSEGLLLMTTDGKLS 68

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLD--------- 180
             +        + Y  +  G +    + +L  G+ I  +GI Y     T+          
Sbjct: 69  DTI--NRKGIEKEYYAQLDGDISPKAIEILATGVEIGFEGIRYTTKPCTVQKINFKPSLP 126

Query: 181 --------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                    +   N+W+++ + EGK R+++K+     +   RL+R+  G   L  L    
Sbjct: 127 APDKRIRLARHRPNSWISIVITEGKFRQVRKMTAAVGFPTLRLVRVRIGALILDDLGPEE 186

Query: 233 T 233
            
Sbjct: 187 V 187


>gi|186475332|ref|YP_001856802.1| pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184191791|gb|ACC69756.1| pseudouridine synthase [Burkholderia phymatum STM815]
          Length = 189

 Score =  141 bits (356), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 43/182 (23%), Positives = 77/182 (42%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R+++ D +      V   GRLD ++EGLLLLT+DG L   +
Sbjct: 3   LLALNKPFGTICQFSPHETRASLADWVK--VPGVYPAGRLDSDSEGLLLLTDDGTLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------QVTLDTQK--- 183
             P  + ++ Y  +  G   +  L  L +G+ +                Q   D      
Sbjct: 61  AEPRHKLVKRYWAQVEGAPTEQHLEALARGVDLGDYVTRPCRAGFVEPGQALWDRTPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +    L  G +  +S
Sbjct: 121 YRAAIPTTWIELSITEGKNRQVRRMTAAVGFPTLRLVRVGVGALDIFSLGLQPGESIGLS 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 56/240 (23%), Positives = 92/240 (38%), Gaps = 22/240 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A     SR E E+ I    + V+G+L E A   V     I +    +    
Sbjct: 3   DTIRLAKRVAEELGCSRTEAEQFIEGGWITVDGVLTEEAGARVAPEQAIVLLPDAVPAPL 62

Query: 72  RTRLWLYHKPIGL--VTTHSDPDGRSTVFDNLPSIFSRVISVGR----------LDINTE 119
                L HKP G+  +          T     P   S +  + R          L+ +  
Sbjct: 63  DPVTILLHKPAGMRTIDAIDPEQSWITPATLGPDDRSGLRFLRRHTKALTLTNPLEDSAS 122

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GLL+LT D  + R L   +++  + + V   G +D   L LL+KG+   G     M+V+ 
Sbjct: 123 GLLVLTQDWRIERALVQEASRIEQEFVVEVTGTLDAAGLELLQKGLKWNGKPIASMKVSW 182

Query: 180 DTQKGSNAWVTVGLR--E-GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                S   +   ++  E G   +I  + E    +V  + RI  G   +  L  G  R +
Sbjct: 183 Q----SEHKLRFAIKAAERG---QIPYLCEKVGLQVVSIKRIRIGRMSMAALPVGQWRYL 235


>gi|218461411|ref|ZP_03501502.1| probable RNA-pseudouridine synthase protein, ribosomal large
           subunit B [Rhizobium etli Kim 5]
          Length = 153

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 68/109 (62%), Positives = 86/109 (78%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
            + +   +R+SKV+ARAG+ASRR++ERMI + RV +NG +LE   VNV   D IEVDGVP
Sbjct: 45  TESDAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRVLETPVVNVTLADRIEVDGVP 104

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
           +R  ERTRLWLYHKP GLVTT++DP+GR+TVFDNLP    RV+S+GRLD
Sbjct: 105 IRGIERTRLWLYHKPAGLVTTNADPEGRATVFDNLPEELPRVMSIGRLD 153


>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 =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 78/189 (41%), Gaps = 27/189 (14%)

Query: 76  WLYHKPIGLVT---THSDPDGRSTVF-DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           +   KP G ++   ++ +   R   F   L       +++GRLD  +EGLLL+T DG L+
Sbjct: 6   FKLFKPYGFISQLLSNDERQARKKKFLSELHDFPEGTMAIGRLDEKSEGLLLMTTDGKLS 65

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTL---------- 179
             +    +   + Y V+  G +  D ++ +  G+ I   G  Y      +          
Sbjct: 66  DTI--NRSGIEKEYYVQVDGMITDDAIDQMAAGVEIGFDGKKYQTKPCKVRRLIENPTLP 123

Query: 180 -------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                  D + G   W+ V + EGK R+++K+     +   RL+RI  G   L  L    
Sbjct: 124 ERSKKIRDARHGPTPWIAVTITEGKFRQVRKMTSAVGFPTLRLVRIRIGSQTLMGLEPRQ 183

Query: 233 TREVSKKIL 241
             EV  K L
Sbjct: 184 VIEV--KEL 190


>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 =  140 bits (354), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 42/182 (23%), Positives = 77/182 (42%), Gaps = 19/182 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  + ++ Y  +  G      L  L +G+ +        +                  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAEFIEPPDTLWPRNPPIR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL--LAGSTREVS 237
                   W+ + + EGKNR+++++     +   RL+R+  G   +  L    G T  ++
Sbjct: 121 YRAAIPTTWIELAITEGKNRQVRRMTAAVGFPTLRLVRVGIGALDIFALGIAPGETIALA 180

Query: 238 KK 239
            +
Sbjct: 181 PR 182


>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 =  140 bits (354), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 87/248 (35%), Gaps = 35/248 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKA 70
            P R+SK +      SRRE +  I    + V+G ++E     V     +E+  G  L   
Sbjct: 3   EPTRLSKRVIELLGCSRREADLYITGGWISVDGQVVEAPQFKV-GDQRVELLPGANLEPV 61

Query: 71  ERTRLWLYHKPIGLVTTH------------SDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           E     L H P G                  DP  R      L   F R      L    
Sbjct: 62  E-PVTLLVHCPTGTSAAQLQHLLVHERHWEEDPHARRV----LHGHFLRQEQSLPLQNGA 116

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL++L+ D    R L     +  + Y V   G++    L  LKKG+V +G  +   + +
Sbjct: 117 SGLVVLSQDWRAQRKLREDGAKLEQEYLVDVAGELPASALERLKKGLVHKGTQFPPCKAS 176

Query: 179 LDTQKGSNAWVTVGLREGKN------REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
             +++     +   L   KN      R+I         KV  + RI  G   +  L  G 
Sbjct: 177 WQSEQ----RLRFAL---KNPAPDLLRQI---CAALGLKVLGMKRIRIGGVPMAKLPVGQ 226

Query: 233 TREVSKKI 240
            R +  K 
Sbjct: 227 WRYLGDKE 234


>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 =  139 bits (352), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 87/237 (36%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K IA A   SR E ++ I    V V+G+++E       +   + +    +    
Sbjct: 3   DPIRLDKCIAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAAQ-VTLAENAVLAPA 61

Query: 72  RTRLWLYHKPIGLVT---THSDPDGRSTVFDN-----LPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+              +  D      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 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCGEVGPEVVSIRRLRVGRVSLGKLAIGEWRYL 230


>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 =  139 bits (351), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 87/237 (36%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E ++ I    V V+G+++E       +   + +    +    
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQTLATAAQ-VTLAENAVLAPA 61

Query: 72  RTRLWLYHKPIGLVT---THSDPDGRSTVFDN-----LPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+              +  D      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 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCGEVGLEVVSIRRLRVGRVSLGKLAIGEWRYL 230


>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 =  139 bits (351), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 90/245 (36%), Gaps = 24/245 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +A     SRRE E  I    V V+G L+E   + V     IE+      K  
Sbjct: 3   DPVRLAKRVAEQFGCSRREAELYIEGGWVTVDGELVEAPFLKVGPQQRIELQPGATAKEI 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL-------------DINT 118
                L HKP   +   SD DG                    L             D + 
Sbjct: 63  APVTLLLHKPA-ELPIDSDNDGPRRALQASEHWADDPSRTEPLQRHLLRHTLLLPLDADA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL +L+    + R+L     +  + Y V   G+ ++  L LL KGI  +G      +V+
Sbjct: 122 SGLSVLSQQREVIRLLGDTRNKLEQEYVVEVSGEAEEGGLALLAKGIGHRGRILPKAKVS 181

Query: 179 LDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             ++      + V ++E   G   E++ + E    +V    RI  G   +  L  G  R 
Sbjct: 182 WQSEN----RLRVVVKEPAPG---EVRMLCEAIGLRVVASKRIRIGRLSMAKLPVGHWRF 234

Query: 236 VSKKI 240
           + +  
Sbjct: 235 LGEHE 239


>gi|289811254|ref|ZP_06541883.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 114

 Score =  139 bits (351), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 22/112 (19%), Positives = 42/112 (37%), Gaps = 3/112 (2%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +  +  P     + Y V     V  D      KG+ +          TL+    +   V 
Sbjct: 1   SHRITSPRHHCEKTYLVTLESPVADDTAAQFAKGVQLHNEKDLTKPATLEV--ITPVQVR 58

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
           + + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 59  LTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 110


>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 =  139 bits (351), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 89/240 (37%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A     SR E ++ I    V V+GI++E    N+  T H+ +        +
Sbjct: 3   APVRLDKYLAAMLHCSRGEAQQYIEGGWVSVDGIVVEEPQANIT-TQHVTLAPDAQLGVD 61

Query: 72  RTRLWLYHKPIG--------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKPIG        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 GSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +++   G   ++  +      +V  L R+  G   LG L +G  R +    
Sbjct: 182 ----RLRFAIKQVQPG---QLHDMCAQVGLEVIGLRRLRIGRIALGKLASGEWRYLPNSE 234


>gi|289661981|ref|ZP_06483562.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 236

 Score =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 89/236 (37%), Gaps = 19/236 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E ++ I    V V+G+++E       +   + +    +    
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQALATAGQ-VTLAEDAVLAPA 61

Query: 72  RTRLWLYHKPIGLV--------TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+         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 GSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +   KN    +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI---KNVQPGQLRYMCGEVGLEVVNIRRLRVGRVSLGKLAIGQWRYL 230


>gi|260220876|emb|CBA28881.1| hypothetical protein Csp_A09350 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 201

 Score =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 49/177 (27%), Positives = 76/177 (42%), Gaps = 19/177 (10%)

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  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDI 116
               AER    + HKP G   +   P    +++  LPS             V +VGRLD 
Sbjct: 61  DWPYAERA-YLMLHKPAGTECSQK-PSTYPSIYTLLPSPLRLRPQKAAVQGVQAVGRLDQ 118

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           +T G+LLLT+DG     +  P     +VY V     +D  ++N L  G+V+      
Sbjct: 119 DTTGMLLLTDDGKFIHRMSSPKHHVPKVYEVTVKHPLDDKQVNKLLSGVVLDDDPKP 175


>gi|330752219|emb|CBL87177.1| ribosomal large subunit pseudouridine synthase B [uncultured
           Sphingobacteria bacterium]
          Length = 230

 Score =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 105/244 (43%), Gaps = 21/244 (8%)

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 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTV 191
           L   + +  RVY +  +  +++  +N L     ++      ++    +D  + +   + +
Sbjct: 121 LNQKNRKVRRVYLIELNKDIEKKDINKL-----LKDRKTIKIESASHVDGYQANYIGLEM 175

Query: 192 GL-RE----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
            +  E    G    I ++     +++ R+ R  Y       L  G  R +  + + E++ 
Sbjct: 176 TIGSENILKG---VINRM----GFEIERIDRSYYAGLTKKDLKRGWIRPL--QEMEERMM 226

Query: 247 PHLL 250
            H +
Sbjct: 227 KHFI 230


>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 =  138 bits (349), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/249 (22%), Positives = 85/249 (34%), Gaps = 30/249 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK +A     SRRE E +I    V+V+G + E     V     + V      +    
Sbjct: 17  IRLSKRVAEMRGCSRREAEWLIEGGWVQVDGRMTEAPGARVRPDQDVVVAQNAKAEEAPP 76

Query: 74  RLWLYHKPIGLVTT-----HSDPD----------------GRSTVFD-----NLPSIFSR 107
              L HKP G           DP                 GR  V D      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+  ++      +  G+R G   +I  + E    +V  L R+  G   L  
Sbjct: 197 NGRPLPPAKVSWQSETRLRFALK-GIRPG---QIPAMCEAVGLQVTALKRLRIGRVSLAR 252

Query: 228 LLAGSTREV 236
           +  G  R +
Sbjct: 253 VPEGQWRYL 261


>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 =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 40/185 (21%), Positives = 73/185 (39%), Gaps = 25/185 (13%)

Query: 75  LWLYHKPIGLVTTH---SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +   KP G+++             +   L      ++SVGRLD ++EGLL LT DG  +
Sbjct: 3   YYKIFKPYGMLSQFVYNQKRRKNKRLLGELSDFPEGIMSVGRLDQDSEGLLFLTTDGKFS 62

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------------------QGIC 171
             +    +   + Y V+  G   ++ +  L KG+ I                    Q + 
Sbjct: 63  HHITS--SGMEKEYWVQVDGIAKKEHVEKLSKGLKISIYGKPYQTLACQVKLMEPPQDLP 120

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                +  +   G  +W+++ L EGK R+++K+         RL+R   G   +  + A 
Sbjct: 121 KRAKDIRNENDHGVTSWLSITLTEGKFRQVRKMTAKIGLPTLRLVRYRIGEQTIEQMQAE 180

Query: 232 STREV 236
              E+
Sbjct: 181 EVIEM 185


>gi|289667011|ref|ZP_06488086.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 236

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 88/236 (37%), Gaps = 19/236 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E ++ I    V V+G+++E       +   + +    +    
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQQYIEGGWVSVDGVVVEEPQALATAGQ-VTLAEDAVLAPA 61

Query: 72  RTRLWLYHKPIGLV--------TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+         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 GSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +   KN    +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI---KNVQPGQLRYMCGEVGLEVVNIRRLRVGRVSLGKLAIGQWRYL 230


>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 =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 92/236 (38%), Gaps = 19/236 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E +  I    V V+G+++E       +      D   L  AE
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATAAQITLADDAVLSPAE 62

Query: 72  RTRLWLYHKPIGLVT----THSDPDGRSTV----FDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+        + P  RS +       L   F R+ +   L+    GLL+
Sbjct: 63  PA-TLLLHKPAGVSVEAALALATPTTRSALDQSDIRVLKRHFLRLTAPLPLENAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L++DG + R L   ++   + + V   G V    +  L  G+V Q       +V+   + 
Sbjct: 122 LSHDGRVLRRLSADASSIEQEFLVEVQGDVRPYGMARLAHGLVYQQRSLLPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +   KN    +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI---KNVQPGQLRYMCGEVGLEVVSIRRLRVGRVSLGKLAIGEWRYL 230


>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 =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 46/175 (26%), Positives = 78/175 (44%), Gaps = 19/175 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G ++  S+   R T+ + +      V   GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTMSQFSEHPSRPTLAEWI--ATPGVYPAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK----------- 183
             P  +  + Y  +  G  D+  L  L++GI +        +V    +            
Sbjct: 61  ADPRHKLAKTYFAQVEGIPDEAALARLRQGIDLGDFHTLPAKVRAVEEPSWLWPRNPPVR 120

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG--TLLAGS 232
                  +W+ + +REGKNR+++++     +   RL+R + G   L    L  G 
Sbjct: 121 FRAAIPTSWLELQIREGKNRQVRRMTAAVGFPTLRLLRATIGRLDLRELGLQPGQ 175


>gi|328463102|gb|EGF34868.1| 16S pseudouridylate synthase [Lactobacillus helveticus MTCC 5463]
          Length = 170

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 45/170 (26%), Positives = 79/170 (46%), Gaps = 5/170 (2%)

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            +KP G+++T  +   R+ +    P   +  ++ 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|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 =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 49/246 (19%), Positives = 91/246 (36%), Gaps = 34/246 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           QR++KV+A     SRRE E+ IAQ  V V+G  ++   V V ++  +++D     +A   
Sbjct: 13  QRLAKVVAALVPCSRREAEQYIAQGWVSVDGQCVDAPQVRVTTSQRVQIDPQARLQAVVP 72

Query: 74  RLWLYHKPIGLVT--------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
             +L HKP G+ T          +   G ++      +    + ++  L +   GL + +
Sbjct: 73  ATFLVHKPAGMETESAMDLLGESAHWSGDASGIRRSKAHQVGLKTLLPLPVQASGLCVFS 132

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
            D  + R L   +    +       G +  D L  L  G++  G      +V+  ++   
Sbjct: 133 QDFRVVRKLTEDAAFVEQELVAEVKGTIAPDGLARLGHGLLRDGRPLPPARVSWQSETRL 192

Query: 183 --------KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       AW               +      +++ L RI  G   +  L  G  R
Sbjct: 193 RFATKGIAPEWTAW---------------MCAQVGLELSALRRIRIGRIAMAGLPLGQWR 237

Query: 235 EVSKKI 240
            + +  
Sbjct: 238 YLPEGE 243


>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 =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 28/121 (23%), Positives = 50/121 (41%), Gaps = 15/121 (12%)

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            L  P  +  ++Y V+  G   QD L  L+ G+ +           L             
Sbjct: 7   RLTQPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVDEPAWLWPRNPP 66

Query: 180 --DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
             + +    +W+ + L EG+NR+++++     +   RLIR + G + L  L  G  REV+
Sbjct: 67  IRERKSIPTSWLKITLYEGRNRQVRRMTAHVGFPTLRLIRYAMGDYSLDNLANGEWREVT 126

Query: 238 K 238
            
Sbjct: 127 D 127


>gi|261332662|emb|CBH15657.1| tRNA pseudouridine synthase A, putative [Trypanosoma brucei
           gambiense DAL972]
          Length = 688

 Score =  136 bits (343), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 110/233 (47%), Gaps = 24/233 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKAERTR 74
           + + RAG  SRRE   +IA  +V+V+ ++       V + ++I V    G    +    R
Sbjct: 348 RCLPRAGFCSRREALAVIASGQVRVDNVVERNPFRLVRAENNIHVASHSGRL--RFAPPR 405

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           LW+YHKP  ++ + +D  GR+ +F     I     ++ VG L +   GLLLLTNDG L+R
Sbjct: 406 LWMYHKPAHVIVSRNDVAGRA-LFTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSR 464

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            LE P     + Y +R    VD    + L  +GI I G  Y +M+  ++    S   + V
Sbjct: 465 FLENPKCMIQQTYLLRVRPAVDPVLAHKLNFQGITINGKQYKNMEFFVNPAMKSRFSLKV 524

Query: 192 GLREGKNREIK-------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    ++        + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 525 K--------VRGEVMPVAHLMQHLGRTVERGGRISFGPFSLSGLPVGSLREVT 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 =  136 bits (343), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 72/233 (30%), Positives = 110/233 (47%), Gaps = 24/233 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKAERTR 74
           + + RAG  SRRE   +IA  +V+V+ ++       V + ++I V    G    +    R
Sbjct: 348 RCLPRAGFCSRREALAVIASGQVRVDNVVERNPFRLVRAENNIHVASHSGRL--RFAPPR 405

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLAR 132
           LW+YHKP  ++ + +D  GR+ +F     I     ++ VG L +   GLLLLTNDG L+R
Sbjct: 406 LWMYHKPAHVIVSRNDVAGRA-LFTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSR 464

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            LE P     + Y +R    VD    + L  +GI I G  Y +M+  ++    S   + V
Sbjct: 465 FLENPKCMIQQTYLLRVRPAVDPVLAHKLNFQGITINGKQYKNMEFFVNPAMKSRFSLKV 524

Query: 192 GLREGKNREIK-------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                    ++        + +     V R  RIS+GPF L  L  GS REV+
Sbjct: 525 K--------VRGEVMPVAHLMQHLGRTVERGGRISFGPFSLSGLPVGSLREVT 569


>gi|323435911|ref|ZP_01048953.2| pseudouridylate synthase [Dokdonia donghaensis MED134]
 gi|321496226|gb|EAQ40187.2| pseudouridylate synthase [Dokdonia donghaensis MED134]
          Length = 190

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 45/192 (23%), Positives = 77/192 (40%), Gaps = 27/192 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGR----STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            R +   KP G ++     D R                  ++VGRLD ++EGLL +T DG
Sbjct: 2   HRHFKLFKPYGYLSQLITNDARQARKKKFLKEFYDFPEGTMAVGRLDEHSEGLLFMTTDG 61

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICY--GDMQVTL----- 179
            L+  +   ++   + Y  +  G +  + +  L +G+ I  +G  Y     +        
Sbjct: 62  KLSHTI--NTSGVEKEYYAQVDGAITDEAILALTQGVEISVEGKKYITKPCKARRIDGDP 119

Query: 180 ----------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                     D + G   W+++ + EGK R+++K+     +   RL+RI  G   L  L 
Sbjct: 120 GFPERSKKIRDLRHGPAPWISITITEGKFRQVRKMTSAVGFATLRLVRIKIGSQTLKGLE 179

Query: 230 AGSTREVSKKIL 241
                EV  K L
Sbjct: 180 PSQVIEV--KEL 189


>gi|327480070|gb|AEA83380.1| S4 domain-containing protein [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 57/245 (23%), Positives = 89/245 (36%), Gaps = 24/245 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +A     SRRE E  I    V V+G L+E   + V     IE+      K  
Sbjct: 3   DPVRLAKRVAEQFGCSRREAELYIEGGWVTVDGELVEAPFLKVGPQQRIEMQPGATAKEI 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRL-------------DINT 118
                L HKP   +   SD DG                    L             D   
Sbjct: 63  APVTLLLHKPA-ELPIDSDNDGPRRALQASEHWADDPSRTEPLQRHLLRHTLLLPLDAGA 121

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
            GL +L+    + R+L     +  + Y V   G+ ++  L LL KGI  +G      +V+
Sbjct: 122 SGLSVLSQQREVIRLLGDTRNKLEQEYVVEVSGEAEEGGLALLAKGIGHRGRILPKAKVS 181

Query: 179 LDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
             ++      + V ++E   G   E++ + E    +V    RI  G   +  L  G  R 
Sbjct: 182 WQSEN----RLRVVVKEPAPG---EVRMLCEAIGLRVVASKRIRIGRLSMAKLPVGHWRF 234

Query: 236 VSKKI 240
           + +  
Sbjct: 235 LGEHE 239


>gi|166712972|ref|ZP_02244179.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 236

 Score =  135 bits (341), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 89/236 (37%), Gaps = 19/236 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E +R I    V V+G+++E       +      D   L   E
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQRYIEGGWVSVDGVVVEEPQAPATAAQITLADDAVLSPVE 62

Query: 72  RTRLWLYHKPIGLV--------TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+         T  +      +    L   F R+ +   L+    GLL+
Sbjct: 63  PA-TLLLHKPAGVSAEAALALATPTTRSALDQSDIRVLKRHFLRLTAPLPLEEAASGLLI 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L++DG + R L   ++   + + V   G V    +  L  G+V Q       +V+   + 
Sbjct: 122 LSHDGRVLRRLSADASSIEQEFLVEVQGDVRPYGMARLAHGLVYQQRSLSPCKVSWQNED 181

Query: 184 GSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +   KN    +++ +      +V  + R+  G   LG L  G    +
Sbjct: 182 ----RLRFAI---KNVQPGQLRYMCGEVGLEVVSIRRLRVGRVSLGKLAIGEWCYL 230


>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 =  135 bits (341), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 119/293 (40%), Gaps = 41/293 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           + +++ I+ +G  SR + E  I    V V+G ++    V V     +     P+      
Sbjct: 22  EWLARRISLSGQMSRSQAEVAIRNGEVVVDGQVVRH-NVQVSDHCDVICRDQPVEPPGDP 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------------------VISVGRLD 115
           ++WL +KP G+V + +   G +T+ D       R                   I +  + 
Sbjct: 81  KVWLINKPRGVVCSATRIRGLTTLPDLFEIWHKRRANELSHNINNVDLIPPHFIVINPIP 140

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL--KKGIVIQGICYG 173
           +   GL++LTNDG  A  +  P ++ L V+ VR  G++ +D+      ++G+ +  + YG
Sbjct: 141 VMCSGLVILTNDGEFAHNMAHPRSKVLSVFLVRVKGRLPEDRFKSWRRREGVKVGNVDYG 200

Query: 174 DMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
            + V +D +   +  W+ V L          +    N  V ++   S+GP++  T     
Sbjct: 201 QVFVGIDKRPSEDVTWLRVRLV---------MTNEKNL-VTKINSSSFGPYRSSTAYV-- 248

Query: 233 TREVSKKILREQLGPHL--LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
                  I  + + PH+  L   ++  DA + +  TLV         + D   
Sbjct: 249 -----DYICPQPVSPHVRHLAPRRIARDAIMAAKGTLVNPITGEFVSIFDQAR 296


>gi|145309058|gb|ABP57738.1| 16S rRNA pseudouridine synthase [Chromobacterium violaceum]
          Length = 150

 Score =  135 bits (341), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 37/148 (25%), Positives = 68/148 (45%), Gaps = 3/148 (2%)

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--TLDT 181
           +T  G LA  +  PS +  R Y VR  G++  + +  +  G+ ++       +V      
Sbjct: 1   ITTSGELANRMMHPSFEVEREYSVRVLGELTPEIMKQMVAGVELEDGEARFDRVFQKGGP 60

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKI 240
           ++ +N W  V ++EG+NRE++++FE F   V+RLIR+ +G   L   L  G   E++   
Sbjct: 61  EEAANQWFNVVIKEGRNREVRRMFEHFGLTVSRLIRVRFGNIGLPPRLKRGQFYELNSAE 120

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLV 268
           +   +    L        AP+  +    
Sbjct: 121 VAAVMKWSNLTVTGGKKAAPVKKASAKA 148


>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 =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 88/237 (37%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E +  I    V V+G+++E     + +   + +    +    
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEP-QALATVAQVTLAANAVLAPA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG--------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+    +              +    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 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCGEVGLEVRSIRRLRVGRVSLGKLAIGEWRYL 230


>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 =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 54/249 (21%), Positives = 84/249 (33%), Gaps = 30/249 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+SK +A     SRRE E +I    V+V+G + E     V     + V      +    
Sbjct: 17  IRLSKRVAGMRGCSRREAEWLIEGGWVQVDGRMTEAPGARVRPDQDVVVAQNAKAEEAPP 76

Query: 74  RLWLYHKPIGLVTT-----HSDPD----------------GRSTVFD-----NLPSIFSR 107
              L HKP G           DP                 G   V D      L   F +
Sbjct: 77  VTLLLHKPAGWEAGIGHGPAGDPRQARSGGAPDAGTLLEPGNRYVGDSPPVRVLQRHFRQ 136

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
                 L     GL++ T D  +AR L        +       G++ +  L  L +G+  
Sbjct: 137 QECFTPLADAASGLVVYTQDRRMARRLAEDIELLEQECIATVEGRIAEGGLERLCRGLEF 196

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            G      +V+  ++      +  G+R G   +I  + E    +V  L R+  G   L  
Sbjct: 197 NGRPLPPARVSWQSETRLRFALK-GIRPG---QIPAMCEAVGLQVTALKRLRIGRVSLAK 252

Query: 228 LLAGSTREV 236
           +  G  R +
Sbjct: 253 VPEGQWRYL 261


>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 =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/248 (21%), Positives = 85/248 (34%), Gaps = 34/248 (13%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A     SRRE E  I    V+V+G +++     V     + +      +A 
Sbjct: 5   ESVRLAKRLAEQEQCSRREAELHITAGNVQVDGKVVQLPETRVRPEQQVTLRSGAQPEAV 64

Query: 72  RTRLWLYHKPIGLVTTHSDPDGR------------------STVFDNLPSIFSRVISVGR 113
                L +KP G   T   P GR                        L   F  + S   
Sbjct: 65  PPVTLLMNKPAGY--TQGRPYGRVRSAHSLLGEASMAQVDTPMPLLVLAQHFKNLESFLP 122

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           L +   GL++ T D  +AR L        +   V   GQ+ +D L L+K G+ I      
Sbjct: 123 LPLPASGLIVYTQDKRVARKLGEEGMWLEQECIVGVEGQIHEDGLELMKAGLPIGKRQLP 182

Query: 174 DMQVTLDTQKGSNAWVTVGLR-----EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
             +V+   +      +   L+     E     I  +      +V  L R+  G   L  +
Sbjct: 183 PCRVSWQNENH----LRFALKGIAPDE-----IDAMCTEVGLRVVSLRRLRIGRLSLAKV 233

Query: 229 LAGSTREV 236
             G  R +
Sbjct: 234 PEGQWRYL 241


>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 =  133 bits (336), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 135/313 (43%), Gaps = 32/313 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERTRL 75
           + + RAG  SRRE   +IA  +V+V+ ++       V + + I V+     LR A   RL
Sbjct: 347 RCLPRAGFCSRREALSIIASGQVRVDNVVERNPFRLVRAENSIHVESHSGRLRFA-PPRL 405

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           W+YHKP  ++ + +D  GR+ +  +        ++ VG L +   GLLLLTNDG L+R+L
Sbjct: 406 WMYHKPAYVIVSRNDVAGRTLITKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRLL 465

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           E P T   + Y +R    +D    + L  +GI++ G  Y +++  ++    S   + V  
Sbjct: 466 ENPKTMIQQTYLLRVRPAIDPVLAHKLNTEGILVNGKRYNNVEFFVNPAMKSRHSLKVK- 524

Query: 194 REGKNREIK-------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS--------- 237
                  ++        + +     V R  RIS+GPF +  L  GS REV+         
Sbjct: 525 -------VRGETMPVAHLMQHLGRTVERGGRISFGPFSMSGLPVGSIREVTVPPYYMQHS 577

Query: 238 ---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
               K   E+  P    +    L       E   R+   + +   ++        SQ+  
Sbjct: 578 GAVWKEFIERDWPFFRRQRVSRLRRLSRYRELTPRELEELDNFTYEELKDALSFESQELK 637

Query: 295 LSKQKKLATPVHR 307
            + +++L     R
Sbjct: 638 ATSEEELRRMSVR 650


>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 =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 87/237 (36%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A A   SR E +  I    V V+G+++E       +   + +    +    
Sbjct: 3   DPIRLDKCVAAAFGCSRGEAQHYIEGGWVSVDGVVVEEPQALATAAQ-VTLAENAVLAPA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDG--------RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L HKP G+    +              +    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 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ +      +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRYMCGEVGLEVRSIRRLRVGRVSLGRLAIGEWRYL 230


>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 =  132 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 52/275 (18%), Positives = 92/275 (33%), Gaps = 55/275 (20%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           P R+++ +A     SRRE E  IA   V V+G ++E     V S   +E+          
Sbjct: 4   PVRLARRLAELVHCSRREAELYIAGGWVSVDGQVVEEPQFMV-SQQKVELHPDATLVPVE 62

Query: 73  TRLWLYHKP----------------------IGLVTTH-SDPDGRSTV------------ 97
           +   L+H+P                       G  +   SD +G+S +            
Sbjct: 63  SVTILFHQPSPQPSDGTTSHSTRPPKNGDQVAGYPSGRGSDREGQSLILADSIRQLPSAD 122

Query: 98  ---------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
                       L   F R+     L ++  GL + T D  + R L   +    + Y V 
Sbjct: 123 TRAADDRSGIRLLKQHFVRLTQCLPLQLHASGLTVFTQDYRVIRKLTEDAATIEQEYVVE 182

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVF 205
             G++  D   LL  G+   G     ++V+   +      +   L+    G   ++  + 
Sbjct: 183 VAGELVPDGFKLLNHGLSFNGKPLPPVKVSWQNE----THLRFALKGAQPG---QVAHMC 235

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +V  + R+  G   +  L  G  R +    
Sbjct: 236 LAVGLQVQAMKRLRIGRMSMCKLPLGQWRYLMPYE 270


>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 =  132 bits (333), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 82/258 (31%), Gaps = 45/258 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +A+    SR   E+ I    V V+G ++E     V S   + +            
Sbjct: 12  RLSKRVAQQFQCSRTTAEQYIEGGWVSVDGQVVELPGARVASAQSVVLAPDANPMELTPV 71

Query: 75  LWLYHKPIGLV--------TTHSDPDGRS-------------TVFDNLPS---------- 103
             L HKP G           TH  P                     +LP           
Sbjct: 72  TLLLHKPPGYEAGLGLVTGATHRAPGAHGSRSQGAPQAVALLNAQSHLPEDAAGTRVLLR 131

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            F ++     L     GL++ T D  +AR L+       +   V   GQ+    L  L  
Sbjct: 132 HFKQLECFTPLPTEASGLVVYTQDRRVARKLQEDIETLEQECIVEVAGQIADGGLQKLCH 191

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-----KVFEFFNWKVNRLIRI 218
           G+   G     ++V+      S   +   L+ G    I+      + E     V  + RI
Sbjct: 192 GLSFNGRPLPPIKVSWQ----SETRLRFALK-G----IRPGQIPAMCEAVGLSVRAIKRI 242

Query: 219 SYGPFQLGTLLAGSTREV 236
             G   L  +  G  R +
Sbjct: 243 RIGRVPLAKVPEGQWRYL 260


>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 =  132 bits (333), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 93/240 (38%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E+    V +   +E+      +  
Sbjct: 3   EPIRLSKRLIEQLGCSRREAELYIEGGWVTVDGVVVEQPQFKV-ADQRVELLPGARAETL 61

Query: 72  RTRLWLYHKPIGLVTTHSDP--------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L ++  G  T  +          +        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 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L   KN +   I+++ E    KV  + RI  G   +G L +G  R ++   
Sbjct: 182 H----LRMVL---KNPQPGLIEQLCETAGLKVLAMRRIRLGGVSMGKLPSGQWRYLAATE 234


>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 =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 88/237 (37%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+ K +A     SR E ++ I    V V+G+++E     + +   + +    +    
Sbjct: 3   EPIRLDKCVAALFGCSRGEAQQYIEGGWVSVDGVVVEEPQT-LATAPQVTLAADAVLAPA 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--------IFSRVISVGRLDINTEGLLL 123
                L HK  G+    +          +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 GSNAWVTVGLREGKNR----EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                +   +          +++ + +    +V  + R+  G   LG L  G  R +
Sbjct: 182 ----RLRFAI----KHVQPGQLRFMCKEVGLEVVSIRRLRVGRISLGKLAIGEWRYL 230


>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 =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/271 (18%), Positives = 83/271 (30%), Gaps = 47/271 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M DK+   ++    R++K +A     SR   E+ I    V V+G + E     V     +
Sbjct: 1   MTDKHPAPDHI---RLAKRVAEQLNCSRSTAEQFIEGGFVSVDGRVEEAPGARVRPDQAV 57

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLV--------------TTHSDPDGRSTVFDN------ 100
            V       A      L HKP G                +  S   G  +          
Sbjct: 58  VVAPDASLLALTPVTLLLHKPAGFEAGLGQPGQGGAPHSSQGSRSQGAPSAATLLSAASH 117

Query: 101 ----------LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
                     L   F ++     L     GL++ T D  +AR L        +   V   
Sbjct: 118 LPEDASGIRVLQRHFKQLECFTPLPTEASGLVVYTQDKRIARKLAEDIESLEQECIVEVA 177

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-----KVF 205
           G +  + L  L  G+   G     ++V+   +      +   L+ G    I+      + 
Sbjct: 178 GDIAPNGLQRLCHGLSFNGRPLPPIKVSWQNE----TRLRFALK-G----IRPGQIPAMC 228

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           E        + RI  G   L  +  G  R +
Sbjct: 229 EAVGLTAVGIKRIRIGRVPLAKVPEGQWRYL 259


>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 =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 86/243 (35%), Gaps = 25/243 (10%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE +  I    V V+G ++E     V     +E+      +  
Sbjct: 12  EPTRLSKRVIELFGCSRREADLYITGGWVTVDGQVVEAPQFKVK-DQRVELLPGASLEPV 70

Query: 72  RTRLWLYHKPIG--------LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L H P G        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 GSNAWVTVGLREGKN------REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
                +   L   KN      ++I    +    +VN + RI  G   +  L  G  R + 
Sbjct: 191 ----RLRFAL---KNPAPDLLQQI---CKALGLQVNAMKRIRVGGVPMAKLPVGQWRYLG 240

Query: 238 KKI 240
            K 
Sbjct: 241 DKE 243


>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 =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 80/258 (31%), Gaps = 45/258 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK +A+    SR   E+ I    V V+G ++E     V S   + +            
Sbjct: 12  RLSKRVAQQFQCSRTTAEQYIEGGWVSVDGQVVELPGARVASAQSVVLAPDANLMELTPV 71

Query: 75  LWLYHKPIGLVT---------------THSDPDGRSTVFDNLPS---------------- 103
             L HKP G                    S   G       L +                
Sbjct: 72  TLLLHKPPGYEAGLGLVTGATHGAPGAHGSRSQGAPQAVTLLNAQSHLPEDAAGTRVLLR 131

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            F ++     L     GL++ T D  +AR L+       +   V   GQ+    L  L  
Sbjct: 132 HFKQLECFTPLPTEASGLVVYTQDRRVARKLQEDIETLEQECIVEVAGQIADGGLQKLCH 191

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-----KVFEFFNWKVNRLIRI 218
           G+   G     ++V+      S   +   L+ G    I+      + E     V  + RI
Sbjct: 192 GLSFNGRPLPPIKVSWQ----SETRLRFALK-G----IRPGQIPAMCEAVGLSVRAIKRI 242

Query: 219 SYGPFQLGTLLAGSTREV 236
             G   L  +  G  R +
Sbjct: 243 RIGRVPLAKVPQGQWRYL 260


>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 =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 31/106 (29%), Positives = 54/106 (50%)

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            PS +  + Y     G   + KL  L++GI+++G      +V + +QK  +  V + + E
Sbjct: 17  HPSYETFKTYEADLSGTPSRAKLQRLEQGILLEGKPTAPARVKILSQKKHSTKVAITIHE 76

Query: 196 GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           G+  ++KK+F      VN L RI+YG  +L TL  G  + +S   +
Sbjct: 77  GRKHQVKKMFAAIGHPVNHLKRIAYGKLELQTLATGQFKRLSPTEI 122


>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 =  131 bits (330), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 87/247 (35%), Gaps = 38/247 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A     SR + ER I    V V+G  +E     V     + +      +  
Sbjct: 3   ESVRLAKRLAADLSCSRGDAERYIEGGWVAVDGKTVEEPGARVSPGQTVALLPGAKLEDI 62

Query: 72  RTRLWLYHKPIGLVTTHS----------------DPDGRSTVFDNLPSIFSRVISVGRLD 115
           +    L HKP G    +                 D  GR      L  +F+ +  V  L+
Sbjct: 63  KPVTILVHKPAGTYADNEPGSALDLIIPKNLMPGDRSGRR----YLKRMFNGLKLVTPLE 118

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
               GL++ T +  ++R L        + Y  +  G++ +  L  L++G+  +G     M
Sbjct: 119 RAASGLVVYTQEYAVSRKLMEEGRLVEQEYVAQVTGKLSEADLARLQRGMAFEGRAATPM 178

Query: 176 QVTLDTQKGSNAWVTVGLR-------EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
           +V+   +      +   L+       E        V +    ++ +L RI  G   L  +
Sbjct: 179 KVSWQNE----THLRFALKTPLPGFIE-------YVCDTAGLQLQQLRRIRIGRLPLAGM 227

Query: 229 LAGSTRE 235
             G  R 
Sbjct: 228 AVGQWRY 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 =  131 bits (330), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 42/97 (43%), Positives = 61/97 (62%), Gaps = 1/97 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA+AGIASRR+ E +I Q +VKVNG +++     V   D +EV+ +PL K E  
Sbjct: 2   ERLQKVIAQAGIASRRKAEELIQQGKVKVNGKIVKELGTKVTPQDKVEVNNIPLEKEE-P 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
             +L +KP G++++ SD  GRS V D  P I  R+  
Sbjct: 61  VYFLLYKPTGVISSVSDDKGRSVVTDFFPEITQRLFP 97


>gi|213028620|ref|ZP_03343067.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 122

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 42/123 (34%), Positives = 68/123 (55%), Gaps = 5/123 (4%)

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  AE--RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E     L   +KP+G+V+T  D + R  + D + +   R+  +GRLD +++GL+ LTN 
Sbjct: 62  READDLVLIALNKPVGIVSTTEDGE-RDNIVDFV-NHSKRIFPIGRLDKDSQGLIFLTNH 119

Query: 128 GGL 130
           G L
Sbjct: 120 GDL 122


>gi|25453489|gb|AAL25966.2| probable pseudouridylate synthase [Azotobacter vinelandii]
          Length = 152

 Score =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 42/153 (27%), Positives = 72/153 (47%), Gaps = 8/153 (5%)

Query: 94  RSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ 152
             TV D L     + +   GRLD+ T GLLLLTNDG  +R +  P  +  +VY V     
Sbjct: 2   HRTVLDLLDEPDRQGLHLAGRLDLGTTGLLLLTNDGHWSRRITHPRYKLAKVYYVETAEP 61

Query: 153 VDQDKLNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           + ++ +    +G+    + +      + L     +     + L EG+  ++K++F +F  
Sbjct: 62  IGEEYIETFARGLYFAFEDLVTQPAHLELLGSHSA----RLTLFEGRYHQVKRMFGYFRN 117

Query: 211 KVNRLIRISYGPFQL-GTLLAGSTREVSKKILR 242
            V RL R S GP +L   L  G  R ++ + ++
Sbjct: 118 PVLRLHRESMGPLRLESELPPGHYRPLTSEEIQ 150


>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 =  130 bits (328), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 135/313 (43%), Gaps = 32/313 (10%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--PLRKAERTRL 75
           + + RAG  SRRE   +IA  +V+V+ ++       V + + I V+     LR A   RL
Sbjct: 347 RCLPRAGFCSRREALSIIASGQVRVDNVVERNPFRLVRAENSIHVESHSGRLRFA-PPRL 405

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           W+YHKP  ++ + +D  GR+ +  +        ++ VG L +   GLLLLTNDG L+R+L
Sbjct: 406 WMYHKPAYVIVSRNDVAGRTLMTKHARILGMDHLVPVGSLPMRAHGLLLLTNDGELSRLL 465

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           E P T   + Y +R    +D    + L  +GI++ G  Y +++  ++    S   + V  
Sbjct: 466 ENPKTMIQQTYLLRVRPAIDPVLAHKLNTEGILVNGNRYNNVEFFVNPAMKSRYSLKVK- 524

Query: 194 REGKNREIK-------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS--------- 237
                  ++        + +     V R  RIS+GPF +  L  GS REV+         
Sbjct: 525 -------VRGETMPVAHLMQHLGRTVERGGRISFGPFSMSGLPVGSIREVTVPPYYMQHS 577

Query: 238 ---KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNG 294
               K   E+  P    +    L       E   R+   + +   ++        SQ+  
Sbjct: 578 GAVWKEFIERDWPFFRRQRVSRLRRLSRYRELTPRELEELDNFTYEELKDALSFESQELK 637

Query: 295 LSKQKKLATPVHR 307
            + +++L     R
Sbjct: 638 ATSEEELRRMSVR 650


>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 =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 39/163 (23%), Positives = 77/163 (47%), Gaps = 24/163 (14%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L    + ++++GRLD  +EGL+LLT +G  +  +   ++   + Y  +  G + + ++ +
Sbjct: 16  LADFPNGIMAIGRLDETSEGLILLTTNGAYSYHV--NNSNIEKEYYAQVDGIITEKEIKI 73

Query: 161 LKKG--IVIQG--ICYGDMQVTL--------------DTQKGSNAWVTVGLREGKNREIK 202
           L+KG  I I G        +                 D + G  +WV++ + EGK R+++
Sbjct: 74  LQKGLPISINGSIYHTKPCKAKRIDTPLLPPTRQRIRDDRHGPTSWVSITVTEGKFRQVR 133

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           K+     +   RL R+  G +++  +  G     S+KI+ E L
Sbjct: 134 KMTAAVGFPTLRLARVRIGEYKIEQMQPGD----SEKIVVEAL 172


>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 =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 89/244 (36%), Gaps = 27/244 (11%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G  +E     V   + + +    +    
Sbjct: 3   EPIRLSKRLIELYRCSRREAELYIEGGWVSVDGRAVEEPQFKV-GDEEVVLHPDAVATPV 61

Query: 72  RTRLWLYHKPIGLVT------------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
                L HKP G                 SD D R      L   F R+ ++  L+    
Sbjct: 62  EPVTLLLHKPAGETLEQALARLGPATRAESDRDPRRP----LSRHFHRLTALLPLEPAAS 117

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           GL + +   G+ R L   S    + + V   G+   D L  L  G+  +G      +V+ 
Sbjct: 118 GLQVFSQQRGVLRRLGEESDAPEQEFVVEIAGEPAADGLARLGHGLDQRGRPLPPCKVSR 177

Query: 180 DTQKGSNAWVTVGLR--E-GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
            +++     +   L+  + G   +I+ +      +V  L RI  G   +  L  G  R +
Sbjct: 178 QSERH----LRFALKAPQAG---QIEHMCRSLGLEVLALRRIRIGRLAMAGLPVGQWRYL 230

Query: 237 SKKI 240
            ++ 
Sbjct: 231 GERE 234


>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 =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 87/236 (36%), Gaps = 19/236 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E+ I    V V+G+++E+    V     +E+      +  
Sbjct: 3   EPVRLSKRLIEQLGCSRREAEQYIEGGWVTVDGVVVEQPQFKV-EQQRVELLPGARAETL 61

Query: 72  RTRLWLYHKPIGLVTTHSDP--------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L ++P G+ +  +          +        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 GSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                + + L   KN    +I ++  +   ++  + RI  G   +G L  G  R +
Sbjct: 181 ---THLRMVL---KNPQPGQISELCAYLRLELISMRRIRLGGVSMGKLPLGQWRYL 230


>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 =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 25/126 (19%), Positives = 55/126 (43%), Gaps = 14/126 (11%)

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-------------- 179
           +  P  +  + Y V+  G  ++  L  L+KG+ ++       +V L              
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 ILREQL 245
            ++   
Sbjct: 121 EIKALF 126


>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 =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 90/240 (37%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E+ I    V V+G+++E+    V     +E+      +  
Sbjct: 3   EPVRLSKRLIEQLGCSRREAEQYIEGGWVTVDGVVVEQPQFKV-EQQRVELLPGARAETL 61

Query: 72  RTRLWLYHKPIGLVTT--------HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L ++P G+ +          S  +        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 GSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                + + L   KN    +I ++  +   ++  + RI  G   +G L  G  R ++   
Sbjct: 181 ---THLRMVL---KNPQPGQISELCAYLRLELLGMRRIRLGGVSMGKLPLGQWRYLATSE 234


>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 =  129 bits (325), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 84/241 (34%), Gaps = 32/241 (13%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVDGVPLRKAERT 73
           R++K +A     SR + ER I      V+G  +E     V     +  + G  L    R 
Sbjct: 6   RLAKRLAEELSCSRGDAERYIEGGWAAVDGKPVEEPGFRVEPGQSVGLLPGARLEDV-RP 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF------------DNLPSIFSRVISVGRLDINTEGL 121
              L HKP G+         R  +               L  +F+ +  V  L+    GL
Sbjct: 65  VTILLHKPAGIYANDEPGSARDLILPENLMPGDRSGQRYLKRMFNGLKLVTPLERAASGL 124

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ T +  +AR L        + Y  +  GQ+    L  L++G+   G     M+V+   
Sbjct: 125 VVYTQEYPVARKLVEEGRYVEQEYVAQVSGQLSAADLARLQRGMAYDGRAATPMKVSWQN 184

Query: 182 QKGSNAWVTVGLR-------EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +      +   L+       E        V +    ++  L RI  G   +  L+ G  R
Sbjct: 185 E----THLRFALKTPAPGFIE-------YVCDAAGLRLQALRRIRIGRLPMAGLVPGQWR 233

Query: 235 E 235
            
Sbjct: 234 Y 234


>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 =  129 bits (325), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 38/113 (33%), Positives = 59/113 (52%), Gaps = 2/113 (1%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL--R 68
            + +R+ KVI+  G  SRR  E++I + RVKVN  ++    V +     I++D   +   
Sbjct: 1   MSLERLQKVISSRGYCSRRAAEKLILENRVKVNDQIINTLGVKIDPKAEIKIDNRLVLSD 60

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
              +   +L++KP  ++TT  DP  R TV D    +  RV  VGRLD +  GL
Sbjct: 61  SNNQKYYYLFYKPRLVLTTMYDPKKRKTVNDYFKDLNHRVYPVGRLDYDVSGL 113


>gi|317969165|ref|ZP_07970555.1| pseudouridine synthase [Synechococcus sp. CB0205]
          Length = 178

 Score =  129 bits (325), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 39/143 (27%), Positives = 60/143 (41%), Gaps = 20/143 (13%)

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD- 180
           +LLT++G L + L  PS    R Y  +  G   +D LN L+ G+VIQG      Q     
Sbjct: 1   MLLTSNGRLQQRLTDPSWGHWRRYWSQVEGVPSEDALNALRSGLVIQGQRTLPAQAQALQ 60

Query: 181 -------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG------ 221
                         Q    +W+ + LREG+NR+++++         RL+R++        
Sbjct: 61  DPGWPERDPPIRVRQSIPTSWLQLELREGRNRQVRRMTAAVGLPTLRLLRVAMDLMDGGP 120

Query: 222 PFQLGTLLAGSTREVSKKILREQ 244
           P  L  L  G  R V+    R  
Sbjct: 121 PLSLDGLAPGQWRSVNDDEDRRL 143


>gi|167947963|ref|ZP_02535037.1| hypothetical protein Epers_16024 [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 145

 Score =  129 bits (324), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 25/135 (18%), Positives = 55/135 (40%), Gaps = 3/135 (2%)

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L+T+DG  +  +  P+ +  + Y V     + +     L++GI++         V L   
Sbjct: 5   LITDDGAWSHRILAPARKCSKRYLVTLAESLSERDAERLRQGILLCSEARPTKPVQLQLV 64

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
             ++    + + E +  ++K++F     +V  L R   G  QL   L  G+ R +++  +
Sbjct: 65  SSNSC--RLTITEDRYHQVKRMFAALGNRVVVLHRERIGALQLDPDLSPGNYRALTEDEI 122

Query: 242 REQLGPHLLEEAQVN 256
                  L  +   +
Sbjct: 123 SGIFAEPLNRQRWPS 137


>gi|324112364|gb|EGC06342.1| ribosomal large subunit pseudouridine synthase F [Escherichia
           fergusonii B253]
          Length = 177

 Score =  128 bits (322), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 28/173 (16%), Positives = 62/173 (35%), Gaps = 4/173 (2%)

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           G L   +        + Y V     +  + +  +  G++I G            +K +  
Sbjct: 7   GDLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVLILGTVTK----KCKVKKEAPF 62

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
              + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +    
Sbjct: 63  VFRITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKL 122

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
                ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 123 IENSTSEVKPKAKAKPKTAGIKRPVVKMEKTSEKGGRPASNGKRFTSPGRKKK 175


>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 =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 89/242 (36%), Gaps = 23/242 (9%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E+ I    V V+G+++E+    V     +E+      +  
Sbjct: 14  EPVRLSKRLIEQLGCSRREAEQYIEGGWVTVDGVVVEQPQFKV-EQQRVELLPGARAETL 72

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------LPSIFSRVISVGRLDINTEGL 121
                L ++P G+ +   D      +             L   F+R   V  L+    GL
Sbjct: 73  EPVTLLLNQPAGMDS--EDARASMNMGSLSEAHREGVRALHGHFARQACVAPLERGASGL 130

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
            + T D  ++R +E    +  + + +   G+     L  L +G +         + +   
Sbjct: 131 QVFTQDWRVSRKIEADLRRLEQEFIIEVRGETTPQALERLARGAMRNDRELPKAKASWQN 190

Query: 182 QKGSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +      + + L   KN    +I ++  +   ++  + RI  G   +G L     R ++ 
Sbjct: 191 E----THLRMVL---KNPQPGQISELCAYLRLELLGMRRIRLGGVSMGKLPLAQWRYLAT 243

Query: 239 KI 240
             
Sbjct: 244 SE 245


>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 =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 88/237 (37%), Gaps = 21/237 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E+    V     +E+      +A 
Sbjct: 19  EPVRLSKRLIEQLGCSRREAELYIEGGWVTVDGVVVEQPQFKV-EHQAVELLPGANAEAL 77

Query: 72  RTRLWLYHKPIGLVTTHSD---------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                L ++P G+    +             R  V   L   F+R+     L+    GL 
Sbjct: 78  DPVTLLLNQPAGVDIDTARASMNMASLSEAHREGVRA-LHGHFTRLTCSAPLERGASGLQ 136

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R +E    +  + Y +   G+     L  L +G           + +   +
Sbjct: 137 VFTQDWRVTRKIEADLRRLEQEYIIEVRGETTPQALERLARGATRNDRELPKAKASWQNE 196

Query: 183 KGSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                 + + L   KN    +I ++  +   ++  + RI  G   +G L  G+ R +
Sbjct: 197 ----THLRLAL---KNPQPGQISEICAYLRLEILSMRRIRLGGVSMGKLPVGNWRYL 246


>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 =  127 bits (320), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 52/127 (40%), Gaps = 14/127 (11%)

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 AGSTREV 236
            G  R +
Sbjct: 121 PGDYRRI 127


>gi|56808584|ref|ZP_00366315.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and related
           pseudouridylate synthases [Streptococcus pyogenes M49
           591]
          Length = 109

 Score =  127 bits (320), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 38/90 (42%), Positives = 54/90 (60%), Gaps = 1/90 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R++K IA AGIASRR+ E +I Q  V +NG ++   A  V S D +E++G P+   E  
Sbjct: 1   MRINKYIAHAGIASRRKAEELIKQGLVTLNGQVIMDLATTVKSGDVVEIEGSPI-YNEEK 59

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
             +L +KP G +++ SD  GR TV D LP 
Sbjct: 60  VYYLLNKPRGAISSVSDDKGRKTVLDLLPQ 89


>gi|218184438|gb|EEC66865.1| hypothetical protein OsI_33363 [Oryza sativa Indica Group]
          Length = 513

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 37/141 (26%), Positives = 64/141 (45%), Gaps = 12/141 (8%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGLLLLT 125
             + +KP  +  +   P    +V+  LP    +         V ++GRLD +T GLLLL+
Sbjct: 9   YVMMNKPAAVECSQK-PSTYPSVYTLLPDPLRQRPGPGKILGVQTIGRLDQDTTGLLLLS 67

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +DG     +  P  Q  + YRV     + Q + + L KG+V+       +      Q+G 
Sbjct: 68  DDGSFIHRVSSPKKQIQKTYRVHAKYDLSQQQKDQLLKGVVLNDDPKPVIAADCVLQEG- 126

Query: 186 NAWVTVGLREGKNREIKKVFE 206
            +   + + EGK  +IK++F 
Sbjct: 127 -SIFDLTVTEGKYHQIKRMFA 146


>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 =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 88/249 (35%), Gaps = 32/249 (12%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A     SRRE E  I    V+V+G +++     V     + +      +A 
Sbjct: 9   ESIRLAKRLAEQEQCSRREAELHIVAGNVQVDGKVVQVPETRVRPDQVVILRKDAKPEAI 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------------LPSIFSRVISVGRLD 115
                L +KP G+    +    RS                     L   F  + S   + 
Sbjct: 69  PPVTILMNKPAGMTQGPAYGRVRSAHSLLSEDTKAKLDTPMPQLVLDHHFRNLESFLTIP 128

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----C 171
           +   GL++ T D  +AR L        +   V   GQ+ +D L +L +G+ I G      
Sbjct: 129 LPASGLIVYTQDKRVARKLAEEGIWLEQEIIVGVEGQIIEDGLEILYEGLPIPGGNGHRR 188

Query: 172 YGDMQVTLDTQKGSNAWVTVGLR----EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                V+      S + +   L+    E    EI+K+       V  + R+  G   L  
Sbjct: 189 MPPCHVSWQ----SESHLRFALKGIAPE----EIEKMCAAIGLTVVSMRRLRLGRVSLAK 240

Query: 228 LLAGSTREV 236
           +  G  R +
Sbjct: 241 VPEGQWRYL 249


>gi|317406580|gb|EFV86770.1| RNA pseudouridylate synthase [Achromobacter xylosoxidans C54]
          Length = 241

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 51/242 (21%), Positives = 87/242 (35%), Gaps = 34/242 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R++K +A     SR + ER I    V V+G ++E     V     + +      +  R  
Sbjct: 6   RLAKRLAAEQSCSRGDAERYIEGGWVAVDGKVVEEPGFRVSPGQVVVLLPGARLEEMRPV 65

Query: 75  LWLYHKPIGLVTTHSDP--------------DGRSTVFDNLPSIFSRVISVGRLDINTEG 120
             L HKP GL  + SDP               G  +    L  +F+ +     L+    G
Sbjct: 66  SILVHKPAGL--SASDPAHSALGLVVPENLMPGDRSGQRYLKRMFNGLKLATPLERAASG 123

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L++ T +  +AR L        + Y  +  G +D   L  L++G+  +G     M+V+  
Sbjct: 124 LVVYTQEYAVARKLVEEGRHVEQEYIAQVRGTLDAVGLARLQRGLAYEGRPATPMKVSWQ 183

Query: 181 TQKGSNAWVTVGLR-------EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
            +      +   L+       E          +    ++  L RI  G   +  L  G  
Sbjct: 184 NE----THLRFALKTPALGFIE-------YACDMAGLELQALRRIRIGRLPMAGLAVGQW 232

Query: 234 RE 235
           R 
Sbjct: 233 RY 234


>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 =  126 bits (316), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 81/245 (33%), Gaps = 37/245 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + T  R+SK +   G+ SRRE +  I Q  VKV+G ++      V     I + G P   
Sbjct: 2   DETSVRLSKRMVELGLCSRREADACIEQGLVKVDGKVVNTLGARVRPEQQITLAGKPQAM 61

Query: 70  AERTRLWLYHKPIGLVT---------THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           A      L ++P G            + +  DG   V   L      + +VG +D    G
Sbjct: 62  ATLPVTMLLNRPAGEEAPPAQLLGPDSRAPQDGAEQV--WLARHRQHLTAVGAVDERCHG 119

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           LL+LT D  L R L     +    + ++       D L      I + G      +++  
Sbjct: 120 LLVLTQDKKLPRHLA----ECEMEFLLQVEQAPAADALKARVAAIRLDGKPLRQCKISRQ 175

Query: 181 TQKGSNAWV---------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +       V          +       R+           +     I  G   L  L  G
Sbjct: 176 SDHQLRCAVYAPRAGFFAEIS------RQ-------LGVSLQSARCIRIGRLALAGLQPG 222

Query: 232 STREV 236
             R +
Sbjct: 223 QWRYL 227


>gi|262365460|gb|ACY62017.1| RNA pseudouridylate synthase-family protein [Yersinia pestis
           D182038]
          Length = 152

 Score =  126 bits (316), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 52/121 (42%), Positives = 72/121 (59%), Gaps = 6/121 (4%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDHIEVDGVPLR 68
               +++ K++ARAG  SRRE+E +I Q RV V+G + +    V V  +  I +DG  L 
Sbjct: 25  KIVGEKLQKILARAGHGSRREIEAIIQQGRVSVDGKVSKLGDRVEVTQSTKIRLDGHLLS 84

Query: 69  KAERT----RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLL 123
             E      R+  Y+KP G + T +DP+GR TVFD LP    SR ++VGRLD+NT GLLL
Sbjct: 85  IKESEENVCRVLAYYKPEGELCTRNDPEGRPTVFDRLPKLRGSRWVAVGRLDVNTSGLLL 144

Query: 124 L 124
            
Sbjct: 145 F 145


>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 =  126 bits (316), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 89/240 (37%), Gaps = 19/240 (7%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G +++     V     +E+D      A 
Sbjct: 3   DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIDEPQFKV-GDQKVELDKDAKATAP 61

Query: 72  RTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                L + P G+        +   +  +        L   F R+ +   L     GLL+
Sbjct: 62  EPVTILLNVPAGMDVDSAMQSLNAETLSEEHRYGKRPLRGHFLRLTASADLQPKASGLLV 121

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            T D  + R L   + +  + Y V   G +    LN L+ G+  +G     ++ +   + 
Sbjct: 122 FTQDWKVLRKLTADAAKIEQEYVVEVEGDMVAHGLNRLQHGLTHKGKELPPVKASWQNEN 181

Query: 184 GSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
                +   +   KN +   I +  E    KV  + RI  G   +G +  G  R +S K 
Sbjct: 182 ----RLRFAM---KNPQPGIIAQFCEAVGLKVIGIRRIRIGGVSIGKVPVGQWRYLSGKE 234


>gi|241767931|ref|ZP_04765482.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
 gi|241360905|gb|EER57713.1| pseudouridine synthase [Acidovorax delafieldii 2AN]
          Length = 142

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 38/142 (26%), Positives = 64/142 (45%), Gaps = 17/142 (11%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            RL  ++KP G+++  +       + D +      V   GRLD ++EGLLLLT+DG L  
Sbjct: 3   PRLIRFNKPYGVLSQFTAEGRWQGLKDYID--LPGVYVAGRLDADSEGLLLLTSDGKLQA 60

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------------- 179
            +  P  +  + Y V+  G  D+  L  L+ G+V+        +  L             
Sbjct: 61  RIADPRFKMEKTYWVQVEGIPDEAALAALRHGVVLNDGPTLPARARLLEPAPAVWPRNPP 120

Query: 180 --DTQKGSNAWVTVGLREGKNR 199
             + +    AW+ + +REG+NR
Sbjct: 121 IRERKAIPTAWIELAIREGRNR 142


>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 =  124 bits (313), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 46/169 (27%), Positives = 77/169 (45%), Gaps = 8/169 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +RV  +++R G  +R       ++  + V+G  +        ++  + VDG  L   +  
Sbjct: 40  ERVDALLSRLGYCTRSTARAFASRHEIVVDGTRVRGVDAKARAS-TLRVDGEALDHPDG- 97

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGG 129
            L   HKP G V +H + +G + V++ LP  + R       +GRLD +T GLLLLT+DG 
Sbjct: 98  VLVAMHKPRGTVCSHDEREG-ANVYELLPERWRRRKPSIETIGRLDKDTSGLLLLTDDGA 156

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVIQGICYGDMQV 177
           L   L  P     + YRVR  G + +  + +   G + + G        
Sbjct: 157 LNHALTSPKKDVGKWYRVRTDGPIPRACVEVFASGELTLSGEEKSCKPA 205


>gi|255018863|ref|ZP_05290989.1| hypothetical protein LmonF_16091 [Listeria monocytogenes FSL
           F2-515]
          Length = 128

 Score =  124 bits (313), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 32/117 (27%), Positives = 60/117 (51%), Gaps = 2/117 (1%)

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNA 187
            A +L  P  +  + Y  R  G  +++ +  L++G+VI G      +V + +  +    A
Sbjct: 1   FANLLMHPKNEVSKTYIARIKGIPEREVIRQLERGVVIDGRKTAPAKVKVRSSDKTKDKA 60

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V + + EG+NR+++K+FE   ++V +L R  Y    L  L AG  RE+S   +++ 
Sbjct: 61  IVEITIHEGRNRQVRKMFEAVGFEVQKLSREEYSFLNLRGLNAGERRELSHHEVKQL 117


>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 =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 50/207 (24%), Positives = 85/207 (41%), Gaps = 47/207 (22%)

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-----WLRVYRV---------RFH 150
            S++ ++GRLD +T GLLLLTNDGGL   +  P+++       + Y           +  
Sbjct: 2   HSKLHAIGRLDADTTGLLLLTNDGGLVHWITNPTSKQDSDPIPKTYEAVIMGHHYLPQCD 61

Query: 151 GQVDQDK------LNLLKKGIVIQ---GICYGDMQV--TLDTQKGSNAWVTVGLREGKNR 199
           G    +       + L++ G ++    G     +     L     S   V++ + EGKNR
Sbjct: 62  GPFTNNDNNTYPLMTLIQNGALLPQKYGGHTRPVDRLSVLSHPTRSTTRVSITISEGKNR 121

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL-------------------GTLLAGSTREVSKKI 240
           +I+++F      V +L R+S G   L                     L  G  R + ++ 
Sbjct: 122 QIRRMFHAIGSGVMKLHRVSVGDLNLSGLMPLEERIQRETSDVARDELKEGEWRVLHEEE 181

Query: 241 LREQLG---PHLLEEAQVNLDAPIYSS 264
           + + LG    HL++E   N +    SS
Sbjct: 182 VLKGLGWKCRHLVDEHDRNTNQRSQSS 208


>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 =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 26/170 (15%), Positives = 59/170 (34%), Gaps = 4/170 (2%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 1   MNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFR 56

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +       
Sbjct: 57  ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIEN 116

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
             ++V   A        ++     + +  +   R   N  +     ++KK
Sbjct: 117 SSSEVKPKAKAKPKTAGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKK 166


>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 =  124 bits (311), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 38/138 (27%), Positives = 68/138 (49%), Gaps = 6/138 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDGVPLRK-A 70
            ++ K +   GI SR++ + +I    V +NG  ++    ++ S+  + +++DG  +    
Sbjct: 1   MKLIKYLQYQGIGSRKQCQWLIRGGYVSINGTCMDDTDADIDSSSVETLDIDGKAVTVIP 60

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDG 128
           E     L +KP    T+H  P    ++F   P     +   +VGRLD +T G+LL+TNDG
Sbjct: 61  EPYFYILLNKPTDYETSHK-PKHYRSIFSLFPDNMRNIDMQAVGRLDADTTGVLLITNDG 119

Query: 129 GLARVLELPSTQWLRVYR 146
            L   L  P+ +  +  R
Sbjct: 120 HLNHKLTSPNHKNPQTVR 137


>gi|260219993|emb|CBA27086.1| hypothetical protein Csp_A00520 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 279

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 92/261 (35%), Gaps = 40/261 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           T +R+SK +      SR+E E+ I    V+VNG+++E     V   + I +D        
Sbjct: 17  TGERLSKRVMALKDCSRKEAEQYIEGGWVQVNGVVVEEPQHRVD-RETITLDPNASLMEL 75

Query: 72  RTRLWLYHKPIG---------------------------------LVTTHSDPDGRSTVF 98
                L +KP G                                 L+T  +  +G     
Sbjct: 76  TPVTLLLNKPAGHTDGLEELTPVRAGAPARTGAPGHKAPPANARALLTPANHWEGDPADT 135

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
             L   F+ + +   L+    GL++ T D    R L    +     + V   G+V+ D L
Sbjct: 136 RVLKRHFNHLEADVELETGATGLVVFTQDWRTTRKLTEDMSTMEHEFLVEVKGEVEPDAL 195

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL---REGKNREIKKVFEFFNWKVNRL 215
             +   +  + +    ++V++++    ++ +   +     G    I  + E     +  +
Sbjct: 196 KPIAYALKDERLDLPQVKVSVNSTTPESSRLRFAIKGSHPGL---IAFLCEKAGLHILGM 252

Query: 216 IRISYGPFQLGTLLAGSTREV 236
            RI  G   L  L  G  R +
Sbjct: 253 KRIRLGRVALSDLPVGQWRYL 273


>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 =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 88/241 (36%), Gaps = 21/241 (8%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R+SK +      SRRE E  I    V V+G+++E+    V     +E+      +  
Sbjct: 3   EPVRLSKRLIEQLGCSRREAELYIEGGWVTVDGVVVEQPQFKV-GQQRVELLPGARAEPL 61

Query: 72  RTRLWLYHKPIGLVTTHSD---------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                L ++P  + +  +             R  V   L   F+R   V  L+    GL 
Sbjct: 62  EPVTLLLNQPADMDSESARASINMGSLSETHREGVRA-LHGHFARQACVAPLERGASGLQ 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           + T D  + R +E    +  + + V   GQ     L  L +G +         + +   +
Sbjct: 121 VFTQDWRVTRKIEADLRRLEQEFIVEVRGQTTPQALERLARGAMRNDRELPKAKASWQNE 180

Query: 183 KGSNAWVTVGLREGKN---REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
                 + + L   KN    +I ++  +   ++  + RI  G   +G L  G  R V+  
Sbjct: 181 ----THLRMAL---KNPQPGQIAELCAYLRLELVGMRRIRLGGVSMGKLPLGQWRYVAAT 233

Query: 240 I 240
            
Sbjct: 234 E 234


>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 =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 92/265 (34%), Gaps = 35/265 (13%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++N  +E     ++++  +  GI S R V   +     KVN  ++       +  D IE+
Sbjct: 305 ERNTKKEKI---KLNQYCSYNGICSSRFVNNNVQNGLFKVNDKIVYENVEICLGVDKIEL 361

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSD---------------------PDGRSTVFDNL 101
                   +     + +KP   ++  +D                      + +   +   
Sbjct: 362 TNRGKDLLKNKITIILNKPKHYLSISNDNKSYKKLLVRNLIRNENKYIQEEHKCMSYFIY 421

Query: 102 PSIF----SRVISVGRLDINTEGLLLLTNDGGLARVLELP-STQWLRVYRVRFHGQVDQD 156
            ++       +   GRLD N+ GLL+ T +      L         + Y ++ +  + Q+
Sbjct: 422 KNVNIEKVPNLYVCGRLDANSSGLLIFTQNTLSNNYLLYRYKYNIEKEYVIKTYNSITQE 481

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR-EIKKVFEFFNWKVNRL 215
            + LLK+   + G     +      Q   N  +   + +G     I+K+    N K+  L
Sbjct: 482 NMKLLKEHFYVDG----KLIYKCHIQYVDNFTLIFKIYQG-FHKIIRKMCMLSNIKIKSL 536

Query: 216 IRISYGPFQLGTLLAGSTREVSKKI 240
            RI  G   L  L  G  R +    
Sbjct: 537 HRIRIGNIHLNDLPIGKWRFLMPNE 561


>gi|330955284|gb|EGH55544.1| pseudouridine synthase, Rsu [Pseudomonas syringae Cit 7]
          Length = 132

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 41/128 (32%), Positives = 60/128 (46%), Gaps = 5/128 (3%)

Query: 26  ASRREV--ERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
            +R     + + +A  RV+V+G         V     + +D   L+  +  R ++ HKP 
Sbjct: 6   GTRNHACVDSLALASGRVQVDGQATRDPHHEVREFSCVALDEEILQAGKAARYFMLHKPE 65

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
           G V+  SD     TV D L       +   GRLD NT GL+L+TNDG  +R L  P T+ 
Sbjct: 66  GCVSATSDAQH-PTVLDLLDEPDKHELHIAGRLDFNTTGLMLITNDGQWSRRLTQPQTKM 124

Query: 142 LRVYRVRF 149
            +VY V  
Sbjct: 125 PKVYYVET 132


>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 =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 59/173 (34%), Gaps = 6/173 (3%)

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
              +        + Y V     +  + +  +  G+ I G            +K +     
Sbjct: 1   MNKILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFR 56

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           + L +G NR+I+++ E F ++V +L R       L  +  G  R+++   L +     L+
Sbjct: 57  ITLVQGLNRQIRRMCEHFGYEVKKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF--KLI 114

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
           E +         +    V  +  ++          +  S+ K   S  +K   
Sbjct: 115 ENSSSEAKPKAKAKPKTVGIKRPVVKMEKTAEKGGRPASNGKRFTSPGRKKKG 167


>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 =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 45/180 (25%), Positives = 75/180 (41%), Gaps = 11/180 (6%)

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  EGRNREVRRMWEAVGVQVSRLIRVRYGDIDLPKGLPRGGWVEL-------GLAQINYLRQ 113

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASN 313
            V L+    +   + +D+  I +       R  K  ++ +  +          RR  A N
Sbjct: 114 LVELNDETVTKVAVEKDQRRIKAN---QIRRAVKRHTKISTRTSTSPAKRASSRRQSAGN 170


>gi|205373779|ref|ZP_03226581.1| ribosomal large subunit pseudouridine synthase B [Bacillus
           coahuilensis m4-4]
          Length = 125

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 38/100 (38%), Positives = 60/100 (60%), Gaps = 1/100 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KVIA +GIASRR+ E +I + +VKVNG++++     V   D +EV+GV + + E+ 
Sbjct: 2   ERLQKVIAHSGIASRRKSEELIVEGKVKVNGVIVKELGTKVGPNDTVEVEGVKVEREEK- 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
             +L +KP G+++   D   R  V D  P I  R+   GR
Sbjct: 61  VYFLLYKPRGVISAVRDDKDRKVVTDFFPHIQERIYPXGR 100


>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 =  123 bits (309), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 43/162 (26%), Positives = 71/162 (43%), Gaps = 25/162 (15%)

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--GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDA 259
            G   L    L AG  REV++    +Q    LL  +  +  A
Sbjct: 121 DGEIVLSIKDLSAGMWREVTRTE--DQRLQRLLSRSATHRSA 160


>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 =  123 bits (309), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 84/255 (32%), Gaps = 34/255 (13%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
            P R++K +A     SRRE E+ I    V V+G+++E     V     I +       A 
Sbjct: 3   EPVRLAKRLAEMLACSRREAEQYIEGGFVTVDGVVVEEPQFRV-QNQAIALSPDASLLAL 61

Query: 72  RTRLWLYHKPIGL--------------------VTTHSDPDGRSTVFDNLPSIFSRVISV 111
                L HKP G                     +T  +      +    L   FS    +
Sbjct: 62  TPVTILLHKPAGYEASDTPGANPASAGKTAAQLLTAANHASDDRSGIRPLKKHFSSSELL 121

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK---KGIVIQ 168
             L     GL++ + D  +AR L   +        V   G++    L  L     G   +
Sbjct: 122 TPLATAASGLVVFSGDWRVARKLREDARVLEHEVVVEVSGEIKPGGLERLNRIDHGFTYR 181

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLR-E--GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
           G      +V+      S   +   L+ E  G   +I  + +    K+  + R+  G   L
Sbjct: 182 GALLPPAKVSWQ----SETRLRFALKGEVPG---QIAYMCDSVGLKIEAMKRLRVGRMPL 234

Query: 226 GTLLAGSTREVSKKI 240
             L  G  R +    
Sbjct: 235 SQLQPGQWRYLMPYE 249


>gi|213023878|ref|ZP_03338325.1| 23S rRNA pseudouridine synthase F [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 165

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 63/169 (37%), Gaps = 7/169 (4%)

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            +        + Y V     +  + +  +  G+ I G            +K +     + 
Sbjct: 1   KILRAGNDHEKEYLVTVDKPITDEFIRGMGAGVPILGTVTK----KCKVKKEAPFVFRIT 56

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEE 252
           L +G NR+I+++ E+F ++V +L R       L  +  G  R+++   L +     L+E 
Sbjct: 57  LVQGLNRQIRRMCEYFGYEVTKLERTRIMNVSLSGIPLGEWRDLTDDELIDLF--KLIEG 114

Query: 253 AQVN-LDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKK 300
           +            +T    RP +  E  ++  R   +  +     ++KK
Sbjct: 115 SSSEAKPKAKAKPKTAGIKRPVVAIEKSNEKARPASSGKRFTSPGRKKK 163


>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 =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 86/239 (35%), Gaps = 17/239 (7%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
                R++K +A     SRRE E +I    V+V+G+        V +   +E++     +
Sbjct: 6   EEEGIRLAKRVAAIAGCSRREAELLIENGAVRVDGVPALLPQSRVHAHQKVEIEPGAKPE 65

Query: 70  AERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
                  L HKP G+        +   +  +        LP+       +  L+    GL
Sbjct: 66  PVVPVTLLLHKPAGMATDTAHRLLVAANHHEPERAGMRFLPAHAKAQRCMTPLETGASGL 125

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           ++ T +  + R L+  +        V   G++  ++L   ++            +V++  
Sbjct: 126 VVYTQEWRIERKLQEDAGVLEHEVMVDVSGKLSPEQLVRFER---------SPARVSIGR 176

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           Q      +   L+  +  +I  + +    ++  + RI  G   L  L  G  R +S   
Sbjct: 177 QADEQTGLRFALKGARPGQIAHLCDEAGLRILAMRRIRIGRVPLAGLEPGQWRYLSPHE 235


>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 =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 24/129 (18%), Positives = 47/129 (36%), Gaps = 15/129 (11%)

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 VSKKILREQ 244
           ++   + + 
Sbjct: 122 LTLAEVSQL 130


>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 =  121 bits (304), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 88/249 (35%), Gaps = 32/249 (12%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A     SRRE E  I    V+V+G +++     V     + +      +A 
Sbjct: 9   ESIRLAKRVAEQEQCSRREAELHIVAGNVQVDGKVVQVPETRVRPDQVVILRKDAKPEAI 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------------LPSIFSRVISVGRLD 115
                L +KP G+    +    RS                     L   F  + S   + 
Sbjct: 69  PPVTILMNKPSGMTQGKAYGRVRSAHSLLREDTKAKLDTPMPQLVLDHHFRNLESFLTIP 128

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----C 171
           +   GL++ T D  +AR L        +   V   GQ+ +D L +L +G+ I G      
Sbjct: 129 LPASGLIVYTQDKRVARKLAEEGMWLEQEIIVGVEGQIIEDGLEILYEGLPIPGGNGHRR 188

Query: 172 YGDMQVTLDTQKGSNAWVTVGLR----EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                V+  ++      +   L+    E    EI+K+       V  + R+  G   L  
Sbjct: 189 MPPCHVSWQSENH----LRFALKGIAPE----EIEKMCAAIGLTVVSMRRLRLGRVSLAK 240

Query: 228 LLAGSTREV 236
           +  G  R +
Sbjct: 241 VPEGQWRYL 249


>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 =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 37/134 (27%), Positives = 59/134 (44%), Gaps = 10/134 (7%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIV 166
           +  VGRLD +T GLLL ++ G L + L  P  +  + Y     G V +D+L   L  G+ 
Sbjct: 1   MHPVGRLDYDTSGLLLFSSSGALTQRLLHPKHEVEKEYVAVVTGIVVEDELRATLAAGV- 59

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
            +G         L       + V + + EGK+R ++++       V  L R   G   L 
Sbjct: 60  -RGYLNVFDAQAL-------STVRLTVSEGKHRMVRRILANCGHPVVSLHRDRLGAVALN 111

Query: 227 TLLAGSTREVSKKI 240
            L AG  R ++ + 
Sbjct: 112 DLPAGEYRPLTTEE 125


>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 =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 88/249 (35%), Gaps = 32/249 (12%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A     SRRE E  I    V+V+G +++     V     + +      +A 
Sbjct: 9   ESIRLAKRVAEQEQCSRREAELHIVAGNVQVDGKVVQVPETRVRPDQVVILRKDAKPEAI 68

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN----------------LPSIFSRVISVGRLD 115
                L +KP G+    +    RS                     L   F  + S   + 
Sbjct: 69  PPVTILMNKPAGMTQGPAYGRVRSAHSLLREDTKAKLDTPMPQLVLDHHFRNLESFLTIP 128

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI----C 171
           +   GL++ T D  +AR L        +   V   GQ+ +D L +L +G+ I G      
Sbjct: 129 LPASGLIVYTQDKRVARKLAEEGMWLEQEIIVGVEGQIIEDGLEILYEGLPIPGGNGHRR 188

Query: 172 YGDMQVTLDTQKGSNAWVTVGLR----EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                V+  ++      +   L+    E    EI+K+       V  + R+  G   L  
Sbjct: 189 MPPCHVSWQSENH----LRFALKGIAPE----EIEKMCAAIGLAVVSMRRLRLGRVSLAK 240

Query: 228 LLAGSTREV 236
           +  G  R +
Sbjct: 241 VPEGQWRYL 249


>gi|255066492|ref|ZP_05318347.1| ribosomal large subunit pseudouridine synthase E [Neisseria sicca
           ATCC 29256]
 gi|255049372|gb|EET44836.1| ribosomal large subunit pseudouridine synthase E [Neisseria sicca
           ATCC 29256]
          Length = 149

 Score =  119 bits (299), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 35/140 (25%), Positives = 61/140 (43%), Gaps = 19/140 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L + +KP G++   S  +    + D +          GRLD ++EGLLLLTNDG L   +
Sbjct: 6   LIVLNKPYGVICQFSAHEKYGCLKDYV--SLPDFYPAGRLDTDSEGLLLLTNDGRLQARI 63

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------- 180
             P  +  + Y  +  G  D+ KL++L++G+ +        +V +               
Sbjct: 64  ADPKFKLEKTYWAQVEGSPDEAKLDMLRRGVDLGDFVTRPAKVRVLEAGEADVLWPRVPP 123

Query: 181 ---TQKGSNAWVTVGLREGK 197
               +   + WV + + EGK
Sbjct: 124 IRVRKSVPDFWVEIRISEGK 143


>gi|323456406|gb|EGB12273.1| hypothetical protein AURANDRAFT_61319 [Aureococcus anophagefferens]
          Length = 221

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 39/196 (19%), Positives = 76/196 (38%), Gaps = 31/196 (15%)

Query: 67  LRKAERTRLWLYHKPIGLVTTH----SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           L + +    +L +KP G+++              + D   +  +  ++VGRLD  TEGLL
Sbjct: 6   LLQQQHHAHFLLYKPDGVLSQFVTRAKVKKRHRFLGDLGHAFPAGTMAVGRLDRATEGLL 65

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---- 178
           LLT DG L+  +     +  + Y     G +    L  L++G+ + G+     +      
Sbjct: 66  LLTTDGRLSYHVTTAG-RVEKEYWAELDGVISDGALAALERGVDV-GVRGAGGRARSAPY 123

Query: 179 ---------------------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
                                       ++WV + + +GK  +++K+     +   RL+R
Sbjct: 124 AARAVAATRLAAPPPLPPRRRRVPAHRPHSWVALTVLDGKYHQVRKMTAAVGFPTLRLVR 183

Query: 218 ISYGPFQLGTLLAGST 233
              G  ++G +  G  
Sbjct: 184 ARIGHLRVGAMRPGDV 199


>gi|307545654|ref|YP_003898133.1| pseudouridine synthase [Halomonas elongata DSM 2581]
 gi|307217678|emb|CBV42948.1| pseudouridine synthase [Halomonas elongata DSM 2581]
          Length = 343

 Score =  118 bits (297), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 34/135 (25%), Positives = 64/135 (47%), Gaps = 16/135 (11%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           RL+L+HKP   ++  +D +GR+T+ +++      +   GRLD ++EGLLLL++DG L   
Sbjct: 3   RLYLFHKPYRTLSQFTDSEGRATLAEHID--VPGIYPAGRLDHDSEGLLLLSDDGELIHR 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD------------- 180
           +  P  +  + Y V+  GQ + D L  L+ G+ ++       +V                
Sbjct: 61  ISHPKHKQPKTYWVQVEGQPNDDALAALRDGVELKDGRTRPARVRRLESVSLPDRQPPVD 120

Query: 181 -TQKGSNAWVTVGLR 194
             +     W+ + + 
Sbjct: 121 PRRHPVTQWLELIIT 135


>gi|224003727|ref|XP_002291535.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220973311|gb|EED91642.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 441

 Score =  118 bits (296), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 40/170 (23%), Positives = 73/170 (42%), Gaps = 24/170 (14%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV----------------- 153
            GRLDI++ G+++ T  G +AR L  P T+  + Y V+    V                 
Sbjct: 265 AGRLDIDSTGVIIFTRAGIMARRLIAPDTKIPKEYIVKVQPAVQPTTHEKEAGLLSLPSP 324

Query: 154 DQDKLNLLKKGIVI--QGICYGD-MQVTLDTQKGSNA---WVTVGLREGKNREIKKVF-E 206
            ++  +LL+ G  +          ++     +    +    + + L+EGK R+I+++  E
Sbjct: 325 TRNLTSLLRGGKRLWNDKKALKPVLEAEWLEENPVLSNGGTLRLVLQEGKKRQIRRMCRE 384

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVN 256
                V  L+R S GP QL TL  G  R + ++ +RE       ++ +  
Sbjct: 385 ILGMHVVSLVRKSIGPIQLDTLPEGKWRPLKEQEVREIFADTPHKKRKKA 434



 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/123 (21%), Positives = 43/123 (34%), Gaps = 33/123 (26%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQR------------VKVNGILLERA-AVNV 54
            +  T  R+SK ++  GI SRRE  R++ +              + V G  +     V V
Sbjct: 66  DDTTTQIRLSKRMSELGICSRREAARILKEANETTSDLKYLKEIIYVRGEPVTEGTGVKV 125

Query: 55  MSTD-HIEV-------------DGVPLRKAERT------RLWLYHKPIGLVTTHSDPDGR 94
              +  IE+              G  +  AER          + +KPIG V+   +    
Sbjct: 126 SPNEKRIEIKAGDSPIDEDSDGSGYFVPYAERPWDEIRGDTIVLNKPIGYVSGQEEHQHI 185

Query: 95  STV 97
             V
Sbjct: 186 PAV 188


>gi|330873630|gb|EGH07779.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 129

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 33/104 (31%), Positives = 55/104 (52%), Gaps = 2/104 (1%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
                +L+L++KP  ++T  SD  GR+T+ D +      +   GRLD ++EGLLLLTNDG
Sbjct: 27  PPAEPKLFLFNKPFDVLTQFSDEGGRATLKDFIK--IPGIYPAGRLDRDSEGLLLLTNDG 84

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            L   +  P  +  + Y V+  G+   ++L  L+ G+ +     
Sbjct: 85  QLQARIADPKHKLAKTYWVQVEGEPTDEQLQQLRDGVQLNDGPT 128


>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 =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 88/256 (34%), Gaps = 43/256 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+++ +AR    SR   E++I    V V G +++     V +  ++ V         R  
Sbjct: 12  RLTRRVARQLNCSRSTAEQLIENGCVSVQGQVVQAPGARVSAQQNVTVAQDAALPDPRPV 71

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN----------------LPSIFSRVISVGRLDINT 118
             L HKP G   + + P                         LP  F  +  +  L    
Sbjct: 72  TLLLHKPAGFAASSAAPPDGPQASALLHAASHLAEDASGMRVLPRHFLHLACLTPLPTEA 131

Query: 119 EGLLLLTNDGGLAR----------VLELPSTQW---LRVYRVRFHGQVDQDKLNLLKKGI 165
            GL++ T D  LAR           L  P+ Q     +   V+  G +  D L  L++G+
Sbjct: 132 SGLVVYTQDRRLARVFAQDFAQDMALRQPAQQTHSPEQECIVQVAGTIAPDGLQRLRQGL 191

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-----KVFEFFNWKVNRLIRISY 220
           ++ G+    ++ +   +      +   L+ G    ++      +       V  + RI  
Sbjct: 192 LLDGLRLPPIRASWQNE----TRLRFALK-G----VRPGQIPAICAAVGLTVEAIKRIRI 242

Query: 221 GPFQLGTLLAGSTREV 236
           G   L     G  R +
Sbjct: 243 GRVALARQPPGQWRYL 258


>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 =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 30/112 (26%), Positives = 50/112 (44%), Gaps = 1/112 (0%)

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGL 193
             P     + Y V   G V    L  +++G+ + +G     ++V    Q   +  + + L
Sbjct: 1   MHPRHHQPKTYDVLVRGIVPASALATMRRGMTLAEGEQLRPVEVESRLQANGHTRLRMVL 60

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +G NR+I+++       + RL RIS GP  LG L  GS R +S   +   L
Sbjct: 61  HQGVNRQIRRMCRDLGLTILRLKRISLGPIGLGDLPVGSCRFLSAAEITALL 112


>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 =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 22/95 (23%), Positives = 39/95 (41%), Gaps = 3/95 (3%)

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                +  D      +GI ++G     +   L+    S   V + + EGK  ++K++F  
Sbjct: 2   WLADPIQADYAEQFNRGIELRGEREMTLPAQLEV--ISETEVLLTIHEGKYHQVKRMFAA 59

Query: 208 FNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
              KV  L R   G   L  TL  G  R ++++ +
Sbjct: 60  LGNKVIGLHRERIGQITLDETLEPGEYRYLTEEEV 94


>gi|91229061|ref|ZP_01262887.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
 gi|91187454|gb|EAS73794.1| pseudouridine synthase family 1 protein [Vibrio alginolyticus
           12G01]
          Length = 177

 Score =  116 bits (292), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 34/119 (28%), Positives = 62/119 (52%), Gaps = 2/119 (1%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            P    +  ++ +++KP   ++  +D DGR T+ D +P     V + GRLD ++EGL++L
Sbjct: 48  KPKVPPKDRKVIIFNKPYDTLSQFTDGDGRKTLADYIP--IKNVYAAGRLDRDSEGLMVL 105

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           TNDG L   L  P ++  + Y V+  G   +  L  L+KG+ ++       +V +  + 
Sbjct: 106 TNDGILQAKLTQPKSKSPKTYWVQVDGAPQEQDLEKLRKGVELKDGMTLPAEVEVIPKP 164


>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 =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 85/247 (34%), Gaps = 19/247 (7%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           KN    +    R++K +A     SRRE E +I    V+V+G+        V +   +E+ 
Sbjct: 2   KNNNAPDDEGIRLAKRVAALAGVSRREAELLIENGAVRVDGVPAVLPQSRVQAHQQVEIA 61

Query: 64  GVPLRKAERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLD 115
                +       L +KP G+        +   +  +        LP+       +  L+
Sbjct: 62  AGAKPEPVVPVTMLLYKPAGMPTDNAHRLLVAANHHEPERAGQKFLPAHLKGQHCMTPLE 121

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
               GL+  T +  + R L+  +        V   G V  + L   ++            
Sbjct: 122 TGASGLVAYTQEFRIERKLQEDAGILEHEVMVDVAGTVSPEVLMRFER---------SPA 172

Query: 176 QVTL--DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
           +V++    + G    +   L+  +  +I  + +     +  + RI  G   L  L  G  
Sbjct: 173 RVSIGRQAEDGKQTGLRFALKGARPGQIAHLCDQMGLTIVAMRRIRIGRVPLAGLQPGQW 232

Query: 234 REVSKKI 240
           R ++   
Sbjct: 233 RYLAPHE 239


>gi|20451741|emb|CAD30266.1| ribosomal small chain pseudouridine synthase A [Listonella
           anguillarum]
          Length = 109

 Score =  116 bits (290), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 31/109 (28%), Positives = 48/109 (44%), Gaps = 3/109 (2%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDIN 117
            +E  G  L      R  + HKP G V +H D     T F  L       +   GRLD++
Sbjct: 3   EVEWQGRELIL-HGPRYIMLHKPTGYVCSHEDGFNH-TAFILLDEVNVQDLHFAGRLDVD 60

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           T GL+L+T+DG  +  +  P  +  + YRV     ++ + +     GI 
Sbjct: 61  TTGLVLITDDGQWSHRITSPKHKCDKTYRVWLADPIEANYVEQFLTGIE 109


>gi|255654430|ref|ZP_05399839.1| putative RNA pseudouridine synthase [Clostridium difficile
           QCD-23m63]
          Length = 103

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 48/96 (50%), Gaps = 3/96 (3%)

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEF 207
             G V ++ +    +G+V+    Y  M   L+  +    + + + + EGK  ++K++FE 
Sbjct: 4   IDGVVTEEDVEAFLEGVVLDDG-YKTMPSQLNILKSDDESEIELTIHEGKFHQVKRMFES 62

Query: 208 FNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              KV  L R+S G  +L  +L  G  RE++ + ++
Sbjct: 63  VGKKVVYLKRLSMGNLKLDESLELGEYRELTDEEIK 98


>gi|291519152|emb|CBK74373.1| pseudouridine synthase family [Butyrivibrio fibrisolvens 16/4]
          Length = 117

 Score =  115 bits (289), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 19/110 (17%), Positives = 47/110 (42%), Gaps = 2/110 (1%)

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
                   + Y V    ++  + +  +  G+ +  +     +  ++  K  +    + L 
Sbjct: 1   MRAVNAHEKEYIVTVDKEITAEFIKSMSSGVYLDELEVTTRKCQIE--KLGSNKFRIILT 58

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +G NR+I+++ +   ++V  L R+     QLG L   + R+V+ + L+  
Sbjct: 59  QGLNRQIRRMCQALGYRVRTLKRVRIMNIQLGNLKEDTYRDVTPEELKTL 108


>gi|218682180|ref|ZP_03529781.1| RNA-binding S4 domain protein [Rhizobium etli CIAT 894]
          Length = 130

 Score =  114 bits (285), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 55/87 (63%), Positives = 69/87 (79%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +   +R+SKV+ARAG+ASRR++ERMI + RV +NG  L+   VNV   D IEVDGVP+R 
Sbjct: 44  DAKAERISKVMARAGVASRRDIERMIMEGRVTLNGRALDTPVVNVTLADRIEVDGVPIRG 103

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRST 96
            ERTRLWLYHKP GLVTT++DP+GRST
Sbjct: 104 IERTRLWLYHKPAGLVTTNADPEGRST 130


>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 =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 74/239 (30%), Gaps = 25/239 (10%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A+    SR   E+ I    V V+G ++E  A  V  T  + +         
Sbjct: 8   EAVRLAKRVAQQLGCSRATAEQYIEGGWVSVDGRVVEEPAARVAPTQAVALAPDANLLDL 67

Query: 72  RTRLWLYHKPIGLVTT-HSDPDGRSTVFDN-----LPSIFSRVISVGRLDINTEGLLLLT 125
           R    L H+P           +  +   D      L      +     L     GL + T
Sbjct: 68  RPVTLLLHRPANANAQEFLRAERHAAELDRPGTRVLRRHLRALECAAPLPAGASGLTVYT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            +  +AR L        +   V   GQ+  D L  L + +   G         L     +
Sbjct: 128 QERRIARRLAEDMALLEQECTVHVEGQIAPDGLQALGRNLPHHGGPAAPH---LKASWQN 184

Query: 186 NAWVTVGLR--------EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + + L+        E        +      +V  + RI  G   L  L  G  R +
Sbjct: 185 ETHLRLALKGVDMARIPE--------LCAAVGLRVLGVRRIRMGRLPLARLPEGQWRYL 235


>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 =  113 bits (284), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 86/246 (34%), Gaps = 35/246 (14%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYHKP 81
           G+ S R     + +  ++VNG ++ +        D +E+   G  L +  +    + +KP
Sbjct: 240 GLCSSRFAFNNLRRGIIQVNGQVVFQNVSISPGKDRVELTKAGRELLRN-KNVTIILNKP 298

Query: 82  IGLVTTHSDPDGRSTVF-------------------------DNLPSIFSRVISVGRLDI 116
              ++  +D      +                          +      +++   GRLD 
Sbjct: 299 KYYLSILNDHKTNKKLLARNLIRNENKFIEEEHKCMSYFINRNLNIEKVNKLYVCGRLDA 358

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ-WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           N+ GLL+ T +  +   L         + Y V     +++  +  L++  ++ G      
Sbjct: 359 NSTGLLVFTQNTLICSYLLNRYKYLVEKEYIVEAADPIEEVHMKRLRENALVDGKLIYKC 418

Query: 176 QVTLDTQKGSNAWVTVGLREGKNR-EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           ++    Q      ++  L +G     I+K+    N K+  L R+  G   L  L  G  R
Sbjct: 419 RI----QYVDCFTLSFTLYQG-FHKIIRKLCLLSNIKIRALHRVRIGGIHLKGLPLGKWR 473

Query: 235 EVSKKI 240
            +    
Sbjct: 474 FLMPNE 479


>gi|325116556|emb|CBZ52110.1| putative 16S pseudouridylate synthase [Neospora caninum Liverpool]
          Length = 255

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 82/246 (33%), Gaps = 81/246 (32%)

Query: 76  WLYHKPIGLVTTHSDP---------------------------DGRSTVFDNL-PSIFSR 107
            L +KP+  ++   D                            + R  V  NL P+  ++
Sbjct: 7   VLLNKPMHYLSCQVDRQMGGGRGKPLCRQLLVPERRWEAPSQGERRREVKRNLSPAKCNK 66

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK----- 162
           ++  GRLD+++ GL + T DG LA  +  P  +  + Y V     V    L LL+     
Sbjct: 67  LVCAGRLDVDSTGLTVFTQDGRLASQIVGPGKRVSKEYYVEVDLPVSVGALTLLRHGLSL 126

Query: 163 KGIVIQGIC---------------------------------YGDMQVT---------LD 180
            G+ +                                     Y   +            +
Sbjct: 127 DGLELLPAKVRLLPPLRDAFFASLPPSGVSTSAPSSPTSLASYAFAEEKRVGSAEDTGAE 186

Query: 181 TQKGSNAWV------TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +  S  WV      ++ L EG++R+I+++ E    +V ++ R+  G   LG L  G  R
Sbjct: 187 GKDESEIWVGRTTRLSIELLEGRHRQIRRMCELVGLRVLKIHRVRIGKISLGALPQGRWR 246

Query: 235 EVSKKI 240
            +    
Sbjct: 247 LLLPHE 252


>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 =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 74/239 (30%), Gaps = 25/239 (10%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
              R++K +A+    SR   E+ I    V V+G ++E  A  V  T  + +         
Sbjct: 8   EAVRLAKRVAQQLGCSRATAEQYIEGGWVSVDGRVVEEPAARVAPTQAVALAPDANLLDL 67

Query: 72  RTRLWLYHKPIGLVTT-HSDPDGRSTVFDN-----LPSIFSRVISVGRLDINTEGLLLLT 125
           R    L H+P           +  +   D      L      +     L     GL + T
Sbjct: 68  RPVTLLLHRPANANAQEFLRAERHAAELDRPGTRVLRRHLRALECAAPLPAGASGLTVYT 127

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            +  +AR L        +   V   GQ+  D L  L + +   G         L     +
Sbjct: 128 QERRIARRLAEDMALLEQECTVHVEGQIAPDGLQALGRNLPHHGGLAAPH---LKASWQN 184

Query: 186 NAWVTVGLR--------EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
              + + L+        E        +      +V  + RI  G   L  L  G  R +
Sbjct: 185 ETHLRLALKGVDMARIPE--------LCAAVGLRVLGVRRIRMGRLPLARLPEGQWRYL 235


>gi|26247383|ref|NP_753423.1| hypothetical protein c1514 [Escherichia coli CFT073]
 gi|26107784|gb|AAN79983.1|AE016759_257 Hypothetical protein c1514 [Escherichia coli CFT073]
          Length = 118

 Score =  113 bits (283), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 35/114 (30%), Positives = 57/114 (50%), Gaps = 5/114 (4%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L   L 
Sbjct: 2   ILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGALQARLT 59

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            P  +  ++Y V+  G   QD L  L+ G+ +           L  +    AW+
Sbjct: 60  QPGKRTGKIYYVQVEGIPTQDALEALRNGVTLNDGPTLPAGAELVEEP---AWL 110


>gi|255024632|ref|ZP_05296618.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 105

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 31/107 (28%), Positives = 51/107 (47%), Gaps = 5/107 (4%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D + V G P+   E 
Sbjct: 1   MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQVTVHGTPVVYQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDIN 117
              ++ HKP  +V+   D +   TV D L      +    VGRLD +
Sbjct: 60  FVYFMLHKPQNVVSATED-NVSETVIDLLAQEDTLTNPFPVGRLDKD 105


>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 =  110 bits (276), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 45/265 (16%), Positives = 95/265 (35%), Gaps = 35/265 (13%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           N   E     ++++     G+ S R     +++  ++VN  ++    +     D +E+  
Sbjct: 207 NKKTEKCREMKITQYCWHEGLCSSRFAFNNLSRGIIQVNDQVVFENIIISPGRDKVELTK 266

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD---------NLPSIFS------- 106
            G  L +  +    + +KP   ++  +D      +            +            
Sbjct: 267 VGKELLRN-KNITIILNKPKYYLSILNDHKTNKKLLARNLIRNENKFIEEEHKCMSYFIN 325

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-WLRVYRVRFHGQVDQD 156
                    ++   GRLD N+ GLL+ T +  L   L         + Y ++    +++ 
Sbjct: 326 KNVNIEKVNKLYVCGRLDANSTGLLVFTQNTLLCSYLLNKHKHQVEKEYMIKTAEPIEEV 385

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR-EIKKVFEFFNWKVNRL 215
            + LL+K I++ G      ++    Q   +  ++  L +G     I+K+    N K+  L
Sbjct: 386 HMELLRKNILVDGKLIYKCRI----QYVDSFTLSFTLYQG-FHKIIRKLCLLSNIKIKAL 440

Query: 216 IRISYGPFQLGTLLAGSTREVSKKI 240
            R+  G   L  L  G  R +    
Sbjct: 441 HRVRIGGIHLKGLPLGKWRFLMPNE 465


>gi|11967881|emb|CAC19451.1| hypothetical pseudouridine synthase [Streptococcus pneumoniae]
          Length = 75

 Score =  109 bits (274), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 29/76 (38%), Positives = 47/76 (61%), Gaps = 1/76 (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 RLWLYHKPIGLVTTHS 89
            +L +KP G++++ +
Sbjct: 60 VYYLLNKPRGVISSVT 75


>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 =  109 bits (273), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 26/108 (24%), Positives = 47/108 (43%), Gaps = 5/108 (4%)

Query: 149 FHGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVF 205
             G + +D    +  G+ +  G       + L  + G    + + + + EGK  ++K++F
Sbjct: 1   IEGMLPEDAKERMAAGLTLSDGTETLPADLELVRRGGCGELSEIRLTIHEGKFHQVKRMF 60

Query: 206 EFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILREQLGPHLLEE 252
           E     V  L R+S G   L  TL  G  R ++++ L E L     E+
Sbjct: 61  ETLGCHVVYLKRLSMGTLTLDETLKPGEYRPLTREEL-ELLNKTDQEQ 107


>gi|291326167|ref|ZP_06573862.1| ribosomal large subunit pseudouridine synthase E [Providencia
           rettgeri DSM 1131]
 gi|291315271|gb|EFE55724.1| ribosomal large subunit pseudouridine synthase E [Providencia
           rettgeri DSM 1131]
          Length = 182

 Score =  109 bits (273), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 33/139 (23%), Positives = 62/139 (44%), Gaps = 17/139 (12%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           +     T++ L++KP  ++   +D  GR T+   +P   + V + GRLD ++EGLL+LTN
Sbjct: 33  VSSQTPTKIILFNKPFDVLPQFTDEQGRDTLKKYIP--ITDVYAAGRLDRDSEGLLILTN 90

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------- 179
           DG L   L  P  +  ++Y  +  G   +D L   ++G+ +         + L       
Sbjct: 91  DGKLQARLTQPQKKTGKIYYAQVEGIPSEDALLKFRRGLTLNDGPTLPAGIELVDEPEWL 150

Query: 180 --------DTQKGSNAWVT 190
                   + +    +W+ 
Sbjct: 151 WQRNPPIRERKNIPTSWLK 169


>gi|76665077|emb|CAJ17986.1| rRNA pseudouridylate synthase [Candidatus Phytoplasma solani]
          Length = 96

 Score =  109 bits (272), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 32/88 (36%), Positives = 48/88 (54%), Gaps = 1/88 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ KV+A A + SRR+ E +I Q+RVKVN  ++      V  +D I VD   + K    
Sbjct: 2   ERLQKVLAAANLVSRRKAETLILQKRVKVNNQIVYELGTKVSPSDVITVDNTLITKT-PL 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             +L +KP G ++T  D   R TV D +
Sbjct: 61  FYYLLNKPQGYLSTAKDNKTRQTVLDLI 88


>gi|258544931|ref|ZP_05705165.1| RNA pseudouridine synthase family protein [Cardiobacterium hominis
           ATCC 15826]
 gi|258519851|gb|EEV88710.1| RNA pseudouridine synthase family protein [Cardiobacterium hominis
           ATCC 15826]
          Length = 141

 Score =  109 bits (272), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 31/108 (28%), Positives = 55/108 (50%), Gaps = 2/108 (1%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L L +KP  ++   +D  GR+T+ D +      V   G LD ++EGL++LT+DG L   +
Sbjct: 30  LILLNKPFNVLCQFTDKSGRATLADYVD--VPNVYPAGLLDFDSEGLVVLTDDGRLQARI 87

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             P  +  + Y V+  G+ D+  L  L+ G+ ++       + TL  +
Sbjct: 88  ADPRFKLAKRYWVQVEGEADEAALVQLRAGVWLKDKKAQTARKTLPAE 135


>gi|262038667|ref|ZP_06012031.1| ribosomal large subunit pseudouridine synthase B [Leptotrichia
           goodfellowii F0264]
 gi|261747309|gb|EEY34784.1| ribosomal large subunit pseudouridine synthase B [Leptotrichia
           goodfellowii F0264]
          Length = 112

 Score =  108 bits (271), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 34/102 (33%), Positives = 54/102 (52%), Gaps = 3/102 (2%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           +     + +KP G++++  D + R TV D L + +    V  +GRLDI+TEGLL+LTNDG
Sbjct: 11  KPFIYIMMNKPDGVISSTEDDEHR-TVIDLLENKYRTYSVFPIGRLDIDTEGLLILTNDG 69

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            L   L  P+    + Y V     V +  +  L+ GI ++  
Sbjct: 70  ILTHKLLAPNKHVDKKYYVELKNPVLKSDIEKLENGIELENG 111


>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 =  108 bits (271), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 96/238 (40%), Gaps = 38/238 (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  EVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+    +++              E     + +K  G+V   +  + + T+ + L   F  
Sbjct: 59  EIKKQLIKETNAIAQNINLDIVFENEDFLIINKRSGMVVHPAPGNMQDTLVNALLFHFKN 118

Query: 107 ---------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG---- 151
                    R   V R+D +T GLLL+  TN+      L L   Q  R Y+    G    
Sbjct: 119 NLSNINGEIRPGIVHRIDKDTSGLLLVAKTNEAHNYFALLLKKHQIERKYQAIIVGKMDH 178

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + ++  + LK  +          ++T      +++ +   L+ G+  +I+
Sbjct: 179 TITNINLPIGRNTSSRLKMEVTAHNSKEAFTKITSLKASETHSLIQCELKTGRTHQIR 236


>gi|254521767|ref|ZP_05133822.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219719358|gb|EED37883.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 232

 Score =  107 bits (267), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 80/249 (32%), Gaps = 38/249 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K ++      R E  R I    V V+G ++E+    V     I V        
Sbjct: 1   MEPIRLDKRLSALLGIPRGEARRYIEGGWVTVDGEVVEQPQRPVDDNAVIVVAEQASDDK 60

Query: 71  ERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L HKP G+        V++ S  +  ++    L   F  +     L     GL+
Sbjct: 61  AERVSMLLHKPAGVAAETLCALVSSDSRSELDASGIRPLQRHFHGLQLAASLPAADSGLV 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRF-HGQVD--QDKLNLLKKGIVIQGICYGDMQVTL 179
           +++ D      L+    +  + Y +    G  +     L  L+          G  +V+ 
Sbjct: 121 VVSQDPATLAHLQRNLGRTEQEYLIEVAEGGPERGPWLLARLQH-------ESGGAKVSW 173

Query: 180 DTQ-------KGSNAW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            ++       KG  A  + V +                 +V  + R+  G   LG L  G
Sbjct: 174 QSEQRLRFAGKGLTAKGLRVAVT------------AAGLQVAAVRRLRIGRVALGPLPPG 221

Query: 232 STREVSKKI 240
             R +    
Sbjct: 222 QWRYLGSDE 230


>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 =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 91/255 (35%), Gaps = 33/255 (12%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            ++++  +  G+ S R     + +  +K+N  ++       ++ D +E+  V     +  
Sbjct: 287 IKLNQYCSYKGLCSSRFAYNNLKKGILKINDNIVYENVDVSINKDRVELTKVGKILLKDR 346

Query: 74  RLWLYHKPIGLVTTHSD----------------------PDGRSTVFDNLPSIF----SR 107
              + +KP   ++   D                       + +   +    +I     + 
Sbjct: 347 ITIIVNKPKHYLSISPDNKLNNKKLLVRNLIRNENKYIEEEHKCMSYFIYKNINIEKVNN 406

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP-STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           +   GRLD N+ GLL+ T D   +  L      Q  + Y +    ++++  L +LK  + 
Sbjct: 407 LYVCGRLDANSSGLLIYTQDSIASSYLLNKYKYQVEKEYIITTFNEINECHLKMLKDNLF 466

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR-EIKKVFEFFNWKVNRLIRISYGPFQL 225
           + G     +      Q   +  +   L +G     I+K+    N K+  L RI  G   L
Sbjct: 467 VDG----KLIYKCHIQYVDSFTLIFKLYQG-FHKIIRKICLLSNIKIRSLHRIRIGKIHL 521

Query: 226 GTLLAGSTREVSKKI 240
             L  G  R +    
Sbjct: 522 NNLPLGKWRFLMPNE 536


>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 =  106 bits (264), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 77/246 (31%), Gaps = 32/246 (13%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K ++      R E  R I    V VNG ++E+    V     I V      + 
Sbjct: 1   MEPIRLDKRLSALLGIPRGEARRYIEGGWVTVNGDVVEQPQRPVDDRAVIVVAEQASDEK 60

Query: 71  ERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L +KP G+        V++ S  +  ++    L   F  +     L  +  GL+
Sbjct: 61  AERVSMLLNKPAGVAAETLCALVSSDSRSELDASDIRPLQRHFHGLQLAASLPASDSGLV 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRF------HGQVDQDKLNLLKKG--IVIQGICYGD 174
           +++ D      L+    +  + Y +         G     +L     G  +  Q      
Sbjct: 121 VVSQDPATLAHLQRNLGRTEQEYLIEVAEGGPERGPWLMARLQQEAGGGKVSWQSEQRLR 180

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                 T KG  A VT                    +V  + R+  G   LG L  G  R
Sbjct: 181 FAGKGLTAKGLRAAVT----------------AAGLQVTGVRRLRIGRVALGPLPPGQWR 224

Query: 235 EVSKKI 240
            +    
Sbjct: 225 YLGSDE 230


>gi|300928307|ref|ZP_07143843.1| RNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|300463693|gb|EFK27186.1| RNA pseudouridine synthase [Escherichia coli MS 187-1]
          Length = 167

 Score =  106 bits (264), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 33/99 (33%), Positives = 56/99 (56%), Gaps = 2/99 (2%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
              L  P  +  ++Y V+  G   QD +  L+ G+ +  
Sbjct: 95  QARLTQPGKRTGKIYYVQVEGFPTQDAIEALRNGVTLND 133


>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 =  106 bits (264), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 28/194 (14%), Positives = 69/194 (35%), Gaps = 9/194 (4%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I        +VT +T+        + L +G NR+I+++ E   ++V +L R+  
Sbjct: 1   MSSGVRILDTVTLPCKVTKETKFS----FRIVLTQGLNRQIRRMCEALGYEVFKLRRVRI 56

Query: 221 GPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               L  +  G  R ++   + E L    + +  V  +    +       R    +++ D
Sbjct: 57  MNISLDGIPNGKWRYLTDDEVAEILA---MCDGSVGTEEASKTDSRGRNIRKATDAKLFD 113

Query: 281 DFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
                + +++++N  ++  +       R+ A N    +        D   R         
Sbjct: 114 SREENQGSTARRNQKTRTFRGNNADEFRH-APNSKKGQQKRRQR-DDESSRPAKEHYKAK 171

Query: 341 FPSKRSLRRTSAKK 354
              + +  +    +
Sbjct: 172 TQGEHAKPQGEHGR 185


>gi|313607203|gb|EFR83670.1| ribosomal small subunit pseudouridine synthase A, putative
           [Listeria monocytogenes FSL F2-208]
          Length = 99

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 4/96 (4%)

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
            +  G V  + +     GI +    Y      L+    +   + V ++EGK  ++K++F 
Sbjct: 1   AKIDGDVVAEDVTAFADGITLDDG-YTCKSARLEIINPNE--IKVTIQEGKFHQVKRMFA 57

Query: 207 FFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
                V+ L RIS G  QL  +L  G  R +++  L
Sbjct: 58  ARGKTVSYLKRISMGNLQLDESLELGEYRPLTETEL 93


>gi|229016829|ref|ZP_04173757.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|228744390|gb|EEL94464.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 96

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 21/87 (24%), Positives = 50/87 (57%), Gaps = 2/87 (2%)

Query: 160 LLKKGIVIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
           +L++G++++        V + +  ++   A V + + EG+NR+++++FE  + KV +L R
Sbjct: 1   MLERGVMLEDGKTAPANVKITSWDKRKETAIVQLTIHEGRNRQVRRMFEALDCKVVKLKR 60

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQ 244
             Y   ++G+L  G  RE++   +++ 
Sbjct: 61  ERYAFLEVGSLRPGDARELTPHEVKQL 87


>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 =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 90/237 (37%), Gaps = 43/237 (18%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            I   N   +R+ K +A+     R ++E++I Q  V++NG + ++A   + S D +EV  
Sbjct: 3   KITFTNREKERLDKALAKKLQKPRNQIEQLIKQGYVRINGKIEKKAGSKLKSGDLVEVTI 62

Query: 63  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                        D   + + E   + + +KP GLV   +      T+ D L +      
Sbjct: 63  PEPKVSQPKDVHFDVERIYEDED--ILVLNKPAGLVVHPAPSVKEPTLVDWLKANDISLS 120

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
                 R   V RLD  T GL+++  +    + L   L      R Y       + +D +
Sbjct: 121 TLSGEERHGIVHRLDKETSGLIVIAKNNETHQALSKQLQDKSMGRYYLAIVEPPLKEDLI 180

Query: 159 ----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIK 202
                     N LK G+V  G       V L T K  N    +    L  G+  +I+
Sbjct: 181 IEKPIARNPKNRLKMGVVEGGRYAKSAFVKLTTSK--NNKYELIGAKLFTGRTHQIR 235


>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 =  104 bits (259), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 25/100 (25%), Positives = 47/100 (47%), Gaps = 1/100 (1%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+ K +++    SR  V R +  +RV ++G +++  A+ +     +  DG PL++    
Sbjct: 1   MRLDKFLSQQLGVSRALVARELRAKRVTIDGEVVKSGAIKLTPEQDVRFDGNPLQQMVGP 60

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           R ++ +KP G V +  DPD   TV   L    +  +    
Sbjct: 61  RYFMLNKPQGYVCSTEDPDH-PTVLYFLDEPVAYKLPCRW 99


>gi|289806402|ref|ZP_06537031.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 100

 Score =  103 bits (257), Expect = 4e-20,   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|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 =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 60/168 (35%), Gaps = 25/168 (14%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L+ + KP G+ TT +   G     D       R+  VGRLD +T GLLLL++DG     +
Sbjct: 22  LFAFFKPRGMETTCTAGSGLRKFLDR-----GRLHPVGRLDRDTTGLLLLSSDGDCTNRI 76

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVI--------------QGICYGDMQVTL 179
               +   + Y     G + +  +   + +G+ +               G       V  
Sbjct: 77  LH--STINKTYAALVRGVLPEGLMKKVVSEGVDLPDGHVDVTRLETINDGDTVPFGLVAY 134

Query: 180 DTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                     + V +    G+NR +++        V  L R   G  +
Sbjct: 135 PLSSIPTNGCSMVRITTTCGRNRVVRRTLCALGHPVLLLHREEIGGIK 182


>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 =  103 bits (257), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 2/97 (2%)

Query: 150 HGQVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           + +V    +   +KGIV   G       + +       + V + ++EGK  ++KK+F   
Sbjct: 2   NERVTSADVAAFEKGIVFADGYQCQPANLKILKADKHQSTVLLTIQEGKFHQVKKMFLAQ 61

Query: 209 NWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQ 244
             KV  L R+S GP +L   L  G  R ++   +++ 
Sbjct: 62  GKKVIALKRLSMGPLELDERLAVGEYRSLTLAEMKKL 98


>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 =  102 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 82/249 (32%), Gaps = 38/249 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+ K ++      R E  R I    V VNG ++E+    V  +  I V        
Sbjct: 1   MEPTRLDKRLSALLGIPRGEARRYIEGGWVSVNGEVVEQPQRPVDESAVIVVAEQASDDK 60

Query: 71  ERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 L HKP G+        +++ S  +  ++    L   F  +     L  +  GL+
Sbjct: 61  AERVTMLLHKPAGVAAEALCALISSDSRSELDASGTRPLQRHFHGLQLAAALPASDSGLV 120

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRF-HGQVD--QDKLNLLKKGIVIQGICYGDMQVTL 179
           +++ D      L+    +  + Y +    G  +     +  L+          G  +V+ 
Sbjct: 121 VVSQDPATLAHLQRNLGRTEQEYLIEVAEGGPERGPWLMARLQH-------ESGGAKVSW 173

Query: 180 DTQ-------KGSNAW-VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
            ++       KG  A  + V +                 +V  + R+  G   LG L  G
Sbjct: 174 QSEQRLRFAGKGLTAKGLRVAV------------GAAGLQVAAVRRLRIGRVALGPLPPG 221

Query: 232 STREVSKKI 240
             R +    
Sbjct: 222 QWRYLGSDE 230


>gi|218674542|ref|ZP_03524211.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli GR56]
          Length = 110

 Score =  102 bits (256), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 27/102 (26%), Positives = 51/102 (50%)

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +D +++  +  GI   G            Q   N+W+ V L EG+NR+I+++ E    + 
Sbjct: 8   LDDEEIAAMTSGIRHDGEVLTATATRRLRQGDRNSWIEVELDEGRNRQIRRMLEALGAEC 67

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
            RL+R++ G  +LG L  G+ R +++  L+       +E A+
Sbjct: 68  LRLVRVAIGGLELGELPKGAVRALTEAELQALRRSAGMERAR 109


>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 =  102 bits (254), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 43/99 (43%), Gaps = 2/99 (2%)

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             ++YR       D+     L++G+++       +       +  ++ + + + +GK  +
Sbjct: 1   MAKLYRATLKHPADESLCAALRQGVLLHDDNE-TVSAAAAELENPHSLL-LTITQGKYHQ 58

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +K++      +V  L R+ +G ++   LL G  R +  +
Sbjct: 59  VKRMVAAAGNRVEALHRLRFGDWECEDLLPGQWRFIQPE 97


>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 =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 92/241 (38%), Gaps = 37/241 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     SR  ++++I +  V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNVK-PSYKVKEDDEVVVNIPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK------ 157
                V RLD +T G++++  +      L     +   L+ Y     G + +++      
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYVAIVEGVIKEEEGKIEAP 190

Query: 158 -----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                ++  +  +V  G     +   L+  K +N +V   ++ G+  +I+  F +    V
Sbjct: 191 IGRHPVDRKRMAVVQDGRYALTLYKVLERFK-NNTFVEATIKTGRTHQIRVHFSYIGHPV 249

Query: 213 N 213
            
Sbjct: 250 V 250


>gi|291336628|gb|ADD96174.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 109

 Score =  101 bits (253), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 47/94 (50%), Positives = 68/94 (72%)

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
             RV+SVGRLD+++EGL+LLTN+G LA +LE PST WLR Y+VR +G+      + L+ G
Sbjct: 1   MPRVVSVGRLDLDSEGLILLTNNGELANLLEAPSTNWLRQYKVRVYGRPQISGFDKLRLG 60

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
           + ++GI Y  +++ L+ Q GSNAW+ + LREGK 
Sbjct: 61  VTLEGIKYKPIRIELERQTGSNAWLNIALREGKK 94


>gi|303289291|ref|XP_003063933.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226454249|gb|EEH51555.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 126

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 36/126 (28%), Positives = 57/126 (45%), Gaps = 16/126 (12%)

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           V  VGRLD +++GL+LLT+DG +   L  P+ +  + Y V       +++L  L+ G+VI
Sbjct: 1   VFPVGRLDRDSDGLVLLTDDGRVPDALLDPTRKATKTYHVDVRPAPSEEELRRLRGGVVI 60

Query: 168 Q------GICYGDMQVTLDTQKG----------SNAWVTVGLREGKNREIKKVFEFFNWK 211
           +      G+      V                  N    +   EG+NR+I+K+ E     
Sbjct: 61  ETTQQRGGVSTTAPTVRARRGDSLSNPTRQRGLPNHIARIRDAEGRNRQIRKMCEAIGVD 120

Query: 212 VNRLIR 217
           V RL R
Sbjct: 121 VLRLRR 126


>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 =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 91/241 (37%), Gaps = 37/241 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++    +R+   +A     SR  ++++I +  V VNG  ++  +  V   D I V+    
Sbjct: 12  EKEDEGKRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNVK-PSYKVKEDDEIVVNIKEA 70

Query: 68  RK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
            K              E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAAGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK------ 157
                V RLD +T G++++  +      L     +   L+ Y     G + +++      
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYIAIVEGVIKEEEGKVEAP 190

Query: 158 -----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                ++  +  +V +G     +   L+  K +N +V   ++ G+  +I+  F +    V
Sbjct: 191 IGRHPVDRKRMAVVQEGRYALTLYKVLERFK-NNTFVEATIKTGRTHQIRVHFSYIGHPV 249

Query: 213 N 213
            
Sbjct: 250 V 250


>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 =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 87/240 (36%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I    V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTVK-PSYKVKENDEVVVNIPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV--DQDKLNLL 161
                V RLD +T G++++  +      L     +    + Y     G +  ++ K+  L
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKHEEGKIEAL 190

Query: 162 --------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   KK  VI+   Y      +  +   N  +   ++ G+  +I+    +    V 
Sbjct: 191 IGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLIEAVIKTGRTHQIRVHMAYIGHPVV 250


>gi|328462442|gb|EGF34470.1| ribosomal large subunit pseudouridine synthase B [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 102

 Score = 99.9 bits (248), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 32/100 (32%), Positives = 46/100 (46%)

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
            GR  V D    +  R+  VGRLD +T GLL++TNDG LA  L  P     + Y  +  G
Sbjct: 2   KGRKVVTDYFEDVQERLYPVGRLDYDTSGLLVMTNDGELANHLMHPRYALEKKYVAKVEG 61

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
             ++  L  LK G+ I G      +V + +   +     V
Sbjct: 62  IPNRPALAPLKTGVSIDGKMTAPAKVEILSTDKAKKTAIV 101


>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 = 99.9 bits (248), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 48/133 (36%), Positives = 72/133 (54%), Gaps = 6/133 (4%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGL 130
              +L +KP   VT  SDP+ ++TV D +     F  +  VGRLD +T GLLL+T++G L
Sbjct: 61  --YYLLNKPKKAVTAVSDPE-KTTVIDLIASADRFQPLYPVGRLDRDTTGLLLITSNGQL 117

Query: 131 ARVLELPSTQWLR 143
              + LP  +  R
Sbjct: 118 GYEMLLPEKRSQR 130


>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 = 99.5 bits (247), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 19/80 (23%), Positives = 39/80 (48%), Gaps = 2/80 (2%)

Query: 167 IQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
           ++       +V L +  +K   + V + + EG+NR+++++FE    +V +L R  Y    
Sbjct: 2   LEDGKTAPAKVKLLSLDKKKQTSIVQITIHEGRNRQVRRMFEAIGHEVLKLKREEYAFLN 61

Query: 225 LGTLLAGSTREVSKKILREQ 244
           L  L  G  RE++   ++  
Sbjct: 62  LAGLKTGEKRELTPHEVKRL 81


>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 = 98.7 bits (245), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 89/241 (36%), Gaps = 37/241 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           ++    +R+   +A     SR  ++++I +  V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLASELDYSRSYIKKLIEEGLVLVNGKNVK-PSYKVKEDDEVIVNIKEA 70

Query: 68  RK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
            K              E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIEVVPENIPLDILYEDEDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK------ 157
                V RLD +T G++++  +      L     +   L+ Y     G + +++      
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHMSLSNQIKERSVLKKYVAIVEGVIKEEEGKIEAP 190

Query: 158 -----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                ++  +  +V  G     +   L+  K +N +V   ++ G+  +I+    +    V
Sbjct: 191 IGRHPVDRKRMAVVQDGRYALTLYKVLERFK-NNTFVEATIKTGRTHQIRVHLSYIGHPV 249

Query: 213 N 213
            
Sbjct: 250 V 250


>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 = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 84/242 (34%), Gaps = 45/242 (18%)

Query: 5   NIVQENFTPQRVSKVIAR-------AGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           ++ +ENF   R+ K +         + I       ++I + +V VNG  +     ++   
Sbjct: 4   DVTRENFYR-RLDKFLRNTLKDFPLSTIY------KLIRKGKVYVNGKRVRDPGFDLEEG 56

Query: 58  DHIEV------------DGVPLRK--------AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           D +E+            D   L           E     + +KP G+          +T+
Sbjct: 57  DTVEIKYVNLENLPKRSDKKDLTPVPMKLDIIHENDNYLVLNKPAGIAIHPGKGVHVATL 116

Query: 98  FD--NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +               V RLD +T GLL++  +   ARVL          + Y     G
Sbjct: 117 IEGLLYYGQEQGFEPFLVHRLDKDTSGLLIVAKNREAARVLTEMFRGRNMEKEYIALVKG 176

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +    N LK  I + G       V++   K + + + V +  G+  +I++      + 
Sbjct: 177 VPE----NNLKITIPLDGQEAVSEIVSVKPLK-NVSLLRVKIHTGRKHQIRRHLSQIGFP 231

Query: 212 VN 213
           V 
Sbjct: 232 VV 233


>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 = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 38/243 (15%), Positives = 82/243 (33%), Gaps = 41/243 (16%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I    V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTVK-PSYKVKENDEVVVNIPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD------- 156
                V RLD +T G++++  +      L     +    + Y     G +  +       
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAP 190

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +    VI+   Y      +  +   N  V   ++ G+  +I+    F   
Sbjct: 191 IGRHPVDRKKMA---VIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAFIGH 247

Query: 211 KVN 213
            V 
Sbjct: 248 PVV 250


>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 = 97.9 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 37/81 (45%), Gaps = 4/81 (4%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +  G+ I+       +VT    +   +   + L +G NR+I+++   F + V +L R+  
Sbjct: 1   MSSGVKIKDGMTKPCKVT----RVDQSTFRIVLTQGMNRQIRRMSRAFGFTVTKLKRVRI 56

Query: 221 GPFQLGTLLAGSTREVSKKIL 241
              +L  L  G  R V+ + L
Sbjct: 57  LNIELDDLEVGKWRSVTFEEL 77


>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 = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 83/236 (35%), Gaps = 38/236 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M + N+     T  R+ KV+A     SR +VE+++    V VN  ++ + +  V+  D I
Sbjct: 1   MNNFNV----ETAGRIDKVLAHELDVSRNQVEKLVKDGLVSVNKKMVTKTSFKVVEGDEI 56

Query: 61  EVDGVPLRKAERT-------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--- 104
             +     K E                L + +KP GLV   +      T+ D L      
Sbjct: 57  TYEFKEAEKREPVEIDFDVEILYEDEYLMVVNKPSGLVVHPAPSVKEPTLVDWLVKKGIS 116

Query: 105 ------FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D  T G L++  D  +  +L   L      R Y       + +D
Sbjct: 117 LSTISGEERHGIVHRIDKETTGALVIAKDNKVHEMLSEQLQDKSMGRYYLALIDHFLKED 176

Query: 157 KL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +          N LK  +V  G         L T +     +   L  G+  +I+
Sbjct: 177 VVVDKPIGRNPHNRLKMDVVPHGKPAKTAFKKLLTSEYDVELIAAKLFTGRTHQIR 232


>gi|261883893|ref|ZP_06007932.1| pseudouridine synthase, Rsu:RNA-binding S4:pseudouridine synthase
           [Campylobacter fetus subsp. venerealis str. Azul-94]
          Length = 163

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 32/141 (22%), Positives = 63/141 (44%), Gaps = 19/141 (13%)

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG----DMQV 177
           +LLT+   +A  L    +   R Y ++  G++  + +  +++G   +    G      Q+
Sbjct: 1   MLLTDAPAIAEALM--GSDIEREYYLKIKGEITPNVIAAMQEGFFAKDATKGAHATPKQI 58

Query: 178 ----------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                     T+ +  G    +TV + EG+NRE+++   +++ +V  L R+S+G   L  
Sbjct: 59  SMAFKPFLAYTIISLSGGYTRLTVIINEGQNRELRRFLGYYDLEVMDLNRVSFGRVSLDQ 118

Query: 228 LLAGSTREVSKKI---LREQL 245
           L  G  R  +      LR+ L
Sbjct: 119 LGEGKWRYFTNSEYDDLRDFL 139


>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 = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 54/222 (24%), Positives = 82/222 (36%), Gaps = 34/222 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVP 66
           R+ KV++ A  ASR +V R+I    V V GI  E+A+  V   + I          D +P
Sbjct: 17  RLDKVLSAALGASRNQVARLIEAGAVSVEGIPAEKASRKVEPGERIAYRILEAPRRDSLP 76

Query: 67  LRK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVISVG 112
           +        E   L + +KP G+V   +      T+   L              R   V 
Sbjct: 77  VEFDVEVLYEDEYLMILNKPAGVVVHPAPSVREPTLVHWLVQRGISLSTLAGEERHGIVH 136

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK----------LNL 160
           RLD  T G L++  TN    A   EL S +  R Y       + +D            N 
Sbjct: 137 RLDKETSGALVIAKTNAVHQALSEELKSREMGRYYLALIDHPLKEDLTVDAPIARNPANR 196

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           LK  +V  G       + L   +  +  +   L  G+  +I+
Sbjct: 197 LKMAVVEGGREARTDFLKLAEGEEGSELIAARLHTGRTHQIR 238


>gi|229023034|ref|ZP_04179549.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228738257|gb|EEL88738.1| Pseudouridine synthase [Bacillus cereus AH1272]
          Length = 90

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 2/81 (2%)

Query: 166 VIQGICYGDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           +++        V + +  ++   A V + + EG+NR+++++FE  + KV +L R  Y   
Sbjct: 1   MLEDGKTAPANVKITSWDKRKETAIVQLTIHEGRNRQVRRMFEALDCKVVKLKRERYAFL 60

Query: 224 QLGTLLAGSTREVSKKILREQ 244
           ++G+L  G  RE++   +++ 
Sbjct: 61  EVGSLRPGDARELTPHEVKQL 81


>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 = 96.4 bits (239), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 88/240 (36%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV--DQDKLNLL 161
                V RLD +T G++++  +      L     +    + Y     G +  ++ K+  L
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKHEEGKIEAL 190

Query: 162 --------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   KK  VI+   Y      +  +   N  V   ++ G+  +I+    +    V 
Sbjct: 191 IGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGHPVV 250


>gi|297521852|ref|ZP_06940238.1| 23S rRNA pseudouridine synthase F [Escherichia coli OP50]
          Length = 142

 Score = 95.6 bits (237), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 24/144 (16%), Positives = 53/144 (36%), Gaps = 4/144 (2%)

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            +  +  G+ I G            +K +     + L +G NR+I+++ E F ++V +L 
Sbjct: 1   FIRGMSAGVPILGTVTK----KCKVKKEAPFVFRITLVQGLNRQIRRMCEHFGYEVKKLE 56

Query: 217 RISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIIS 276
           R       L  +  G  R+++   L +         ++V   A        ++     + 
Sbjct: 57  RTRIMNVSLSGIPLGEWRDLTDDELIDLFKLIENSSSEVKPKAKAKPKTAGIKRPVVKME 116

Query: 277 EVPDDFTRMKKNSSQKNGLSKQKK 300
           +  +   R   N  +     ++KK
Sbjct: 117 KTAEKGGRPASNGKRFTSPGRKKK 140


>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 = 95.6 bits (237), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 85/243 (34%), Gaps = 50/243 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKAE 71
           R+ K +A     SR +++ +I    V VN I + +    V   D I ++      ++   
Sbjct: 11  RIDKYVANNSEISRNDIKELIENGAVFVNSIKINKPKFVVKEGDEILIERLLDKQIKVEP 70

Query: 72  RTR----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
           +              + +KP GLV   +     +T+ + L   F           R+  V
Sbjct: 71  QNIHLDIVYECDDYLIINKPSGLVVHPAPGHHDNTLVNALMYHFKNNLSDVNGLLRMGVV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ- 168
            R+D +T GLLL+  +          L + +  R Y     G++  ++L+     I +  
Sbjct: 131 HRIDKDTSGLLLIAKNNKAHNYFASLLKTHEIKRSYYAIVEGKIANEELH-----IELPI 185

Query: 169 GICYGDMQVTLDTQKGSNAWVTVG-------------------LREGKNREIKKVFEFFN 209
           G    + Q    ++  S    T+                    L+ G+  +I+    +  
Sbjct: 186 GRDTKNRQKYAVSETNSKPAYTIVNVVKYFKMNNKDFSLVKCNLKTGRTHQIRVHLAYIK 245

Query: 210 WKV 212
             V
Sbjct: 246 HPV 248


>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 = 95.2 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 82/243 (33%), Gaps = 41/243 (16%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I    V VNG  ++  +  V   D + ++    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLVFVNGKTVK-PSYKVKENDEVVLNVPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPEDIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD------- 156
                V RLD +T G++++  +      L     +    + Y     G +  +       
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAP 190

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +    VI+   Y      +  +   N  V   ++ G+  +I+    +   
Sbjct: 191 IGRHPVDRKKMA---VIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PIV 250


>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 = 95.2 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 86/243 (35%), Gaps = 47/243 (19%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMS 56
            + +ENF   R+ K +       R +++        ++I + +V VNG  ++  + ++  
Sbjct: 4   EVTKENFYR-RLDKFL-------RNQLKDVPLSVIYKLIRKGKVYVNGKRVKDPSFDLEE 55

Query: 57  TDHIEVDGVPLRK--------------------AERTRLWLYHKPIGLVTTHSDPDGRST 96
            D +E   V L                       E     + +KP  +          +T
Sbjct: 56  GDVVEFRYVNLENLPKRSEKKDLTPVPMKLDVLYEGKHYLVLNKPPNIAIHPGKGVHVAT 115

Query: 97  VFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
           + + L             V RLD +T GLL++  D   AR+L          + Y     
Sbjct: 116 LIEGLLHYGQEKGFSPFLVHRLDKDTSGLLVVAKDREAARILTELFKDRNIEKEYVTLVR 175

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           G  +    N +K  I + G       V++ + +   + + V +  G+  +I++      +
Sbjct: 176 GTPE----NNMKITIPLDGQEAISEIVSVKSLR-DVSLLRVKIHTGRKHQIRRHLSQIGF 230

Query: 211 KVN 213
            V 
Sbjct: 231 PVV 233


>gi|330864072|emb|CBX74148.1| hypothetical protein YEW_ID35840 [Yersinia enterocolitica W22703]
          Length = 132

 Score = 95.2 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 24/133 (18%), Positives = 48/133 (36%), Gaps = 2/133 (1%)

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
             G +      +K +    ++ L +G NR+I+++ + F ++V +L R       L  L  
Sbjct: 1   MLGTVTKKCKVRKEAPFVFSITLVQGLNRQIRRMCKHFGYEVTKLERTRIMNVNLKGLPI 60

Query: 231 GSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
           G  R++    L E     L+E +  +           V  +   IS           ++ 
Sbjct: 61  GEWRDLRDDELIELF--KLIENSSSDEKPQKKPKAKPVVAKKPAISRSKPAEKSETNSAG 118

Query: 291 QKNGLSKQKKLAT 303
           +K      +K   
Sbjct: 119 RKRFTQPGRKKKG 131


>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 = 94.9 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 85/237 (35%), Gaps = 39/237 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E++++I  ++V VNG + ++    +   D I
Sbjct: 1   MIYEFLIDDSNQNARLDVFLANVVELSRSEIQKLIDDKKVLVNGKIQKK-NYKLNLNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
            +D       ++          E   L + +K   ++   ++     T+ + L   F   
Sbjct: 60  TLDYEKPDKTIKAQKQDLDIVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNL 119

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ-- 155
                  R   V RLD +T GL+++  D      L+         + Y    HG++D+  
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDECG 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +V         Q          + V V ++ G+  +I+
Sbjct: 180 TIEEYMSRNPKDRKKM---MVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIR 233


>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 = 94.9 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 36/103 (34%), Positives = 56/103 (54%), Gaps = 10/103 (9%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-VNVMSTDH 59
          M DK     +   +++ K++AR+G  SRRE+E  + + R+ ++G   +    ++V ST  
Sbjct: 1  MSDK-----SQRTEKLQKILARSGHGSRREIEGYLQEGRISIDGTKAKLGDRIDVTSTAK 55

Query: 60 IEVDGVPLRKAERT----RLWLYHKPIGLVTTHSDPDGRSTVF 98
          I +DG  L   E      R+  Y+KP G + T SDP GR TVF
Sbjct: 56 IRLDGRILNIREAQKDVCRVLAYYKPEGELCTRSDPQGRPTVF 98


>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 = 94.9 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 83/223 (37%), Gaps = 35/223 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R+ K ++     SR ++E++I ++ VKV+  ++ +    +     I V+   + +     
Sbjct: 12  RLDKFLSEKLGESRNQIEQLIKKEYVKVDDKIIAKTGYKLKENQEILVELPEVEESISFD 71

Query: 70  --------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVG 112
                    E   + + +KP  LV   +      T+ D L +            R   V 
Sbjct: 72  VDFDVEIIYEDEHILVINKPYNLVVHPAASVKEPTLVDWLKTKDISLSTISGEERHGIVH 131

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----------NL 160
           RLD  T G++++  TN+  +A   +L      R Y       +  + +          N 
Sbjct: 132 RLDKGTSGVMVVAKTNEAHVALSKQLEDKTMGRYYLAIIDLPLKDNIIIDKPIARNPNNR 191

Query: 161 LKKGIVIQGICYGDMQVTL-DTQKGSNAWVTVGLREGKNREIK 202
           LK GIV +G         +  ++      +   L  G+  +I+
Sbjct: 192 LKMGIVEKGKNAKTAFAKIALSEDEKYELICCKLFTGRTHQIR 234


>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 = 94.9 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 85/237 (35%), Gaps = 39/237 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E++++I  ++V VNG + ++    +   D I
Sbjct: 1   MIYEFLIDDSNQNARLDVFLANVVELSRSEIQKLIDDKKVLVNGKIQKK-NYKLNLNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
            +D       ++          E   L + +K   ++   ++     T+ + L   F   
Sbjct: 60  TLDYEKPDKTIKAQKQDLDIVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNL 119

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ-- 155
                  R   V RLD +T GL+++  D      L+         + Y    HG++D+  
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDECG 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +V         Q          + V V ++ G+  +I+
Sbjct: 180 TIEEYMSRNPKDRKKM---MVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIR 233


>gi|168703294|ref|ZP_02735571.1| RNA pseudouridylate synthase [Gemmata obscuriglobus UQM 2246]
          Length = 275

 Score = 94.9 bits (235), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 87/247 (35%), Gaps = 45/247 (18%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWL 77
           R  V++++   RV VNG  + R    V   D + V                  E   L +
Sbjct: 14  RTRVKQLLRSGRVVVNGASVTRHDHTVRPADKVGVAREAPPAPPSASGLEIVHEDAHLVV 73

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDGGLAR 132
             KP GL+T  ++ +   T F  L          R   V RLD +T GLLL      +  
Sbjct: 74  IDKPSGLLTVATESEKLDTAFVRLSDYLRARNAGRPFVVHRLDRDTSGLLLFARSAEVRD 133

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKL---NLLKKGIVIQ---------GICYGDMQVTLD 180
            L+    +  + Y     G+ +  +    N L +G  ++                + T+ 
Sbjct: 134 QLQGNWEELTKTYLAVVEGRPESSEGGVENYLTEGRDLRVRASPRPGPDGKRAASRYTVR 193

Query: 181 TQKGSNAWVTVGLREGKNREIK-------------KVFEFFNWKVNRLI----RISYG-P 222
             +G  + V V +  G+  +I+             K++      V RL     R+S+  P
Sbjct: 194 QTRGGYSLVEVEIETGRKHQIRVHLAGLGCPVAGDKMYGATTDPVRRLGLHAWRLSFDHP 253

Query: 223 FQLGTLL 229
           F L  L 
Sbjct: 254 FTLERLE 260


>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 = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTRE 235
             ++  + S   V + + EGK  ++K++F+  N KV  L R+  G  +L   L  G  RE
Sbjct: 1   AKVEVIENSEDKVYITITEGKYHQVKRMFKAVNNKVLYLKRVQMGNLKLDDKLKVGKYRE 60

Query: 236 VSKKIL 241
           +++K +
Sbjct: 61  LTEKEI 66


>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 = 94.1 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 30/137 (21%), Positives = 53/137 (38%), Gaps = 7/137 (5%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELP-STQWLRVYRVRFHGQVDQDKLNLLKKG 164
           + +   GRLD N+ GLL+ T D   +  L      +  + Y +    ++++  L +LK  
Sbjct: 46  NNLYVCGRLDANSTGLLIYTQDSMASSYLLNKYKYEVEKEYIITTFNEINECHLKMLKDN 105

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR-EIKKVFEFFNWKVNRLIRISYGPF 223
           + + G     +      Q   +  +   L +G     I+K+    N K+  L R   G  
Sbjct: 106 LFVDG----KLIYKCHIQYVDSFTLIFKLYQG-FHKIIRKICLLSNIKIRSLHRTRIGKI 160

Query: 224 QLGTLLAGSTREVSKKI 240
            L  L  G  R +    
Sbjct: 161 HLNNLPLGKWRFLMPNE 177


>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 = 94.1 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 82/236 (34%), Gaps = 41/236 (17%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DG 64
            R+   ++   I  SR    ++I +  V VN   ++  + NV   D I V        D 
Sbjct: 1   MRIDTYLSEV-IGKSRSFCSKIIKKGLVLVNNKTVK-PSYNVNLGDEILVKIPQEEKLDL 58

Query: 65  VPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVISVG 112
            P         E     + +KP GL    +  +  +T+ + L   F        R   V 
Sbjct: 59  KPANIPLNIIYENQYYLIINKPAGLCVHPAPGNFDNTLVNALLYHFQINDDNDVRPGIVH 118

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL------------ 158
           RLD +T GL+L+  +  +   +       +  + Y    +G    D++            
Sbjct: 119 RLDKDTSGLILVAKNRDVREKMSEMFKEREVDKKYLAICYGNPKWDEILVENSIGRHPVD 178

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +    V++   Y   ++T+  +  +     V +  G+  +I+    +    + 
Sbjct: 179 RKKMA---VVENGRYAKTKITVLKRYDNIFLADVKIYTGRTHQIRVHCSYLGCPII 231


>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 = 94.1 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 86/248 (34%), Gaps = 35/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RAA 51
           M +  +  E    +R+   +      SR  ++ +I    V VNG + +           +
Sbjct: 1   MNEYKVSLEQ-EGKRLDVFLTDVMEGSRSYIQSLIKSGHVLVNGKVGKANLRLNADSTIS 59

Query: 52  VNVMSTDHIEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V++   + +E+  + +P+    E   + + +KP G+V   +  +   T+ + L      +
Sbjct: 60  VDIPEPESVEILPEDIPVEYLYEDHDIIIVNKPRGMVVHPAIGNYSGTLVNALLYHCKDL 119

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK 157
                      V RLD +T G+++   +      L          R Y     G + ++K
Sbjct: 120 SGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLALVQGNIVEEK 179

Query: 158 -----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                       + +K  +V +          +  + G +  V   L  G+  +I+  F 
Sbjct: 180 GIIKAPIGRHPKDRMKMAVVFENSKEAVTHFKVLERYGYHTLVECVLETGRTHQIRVHFA 239

Query: 207 FFNWKVNR 214
                V  
Sbjct: 240 HIGHPVVN 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 = 94.1 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 86/248 (34%), Gaps = 35/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RAA 51
           M +  +  E    +R+   +      SR  ++ +I    V VNG + +           +
Sbjct: 1   MNEYKVSLEQ-EGKRLDVFLTDVMEGSRSYIQSLIKSGHVLVNGKVGKANLRLNADSTIS 59

Query: 52  VNVMSTDHIEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V++   + +E+  + +P+    E   + + +KP G+V   +  +   T+ + L      +
Sbjct: 60  VDIPEPESVEILPEDIPVEYLYEDHDIIIVNKPRGMVVHPAIGNYSGTLVNALLYHCKDL 119

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK 157
                      V RLD +T G+++   +      L          R Y     G + ++K
Sbjct: 120 SGINGEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKAHSAKRTYLALVQGNIVEEK 179

Query: 158 -----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                       + +K  +V +          +  + G +  V   L  G+  +I+  F 
Sbjct: 180 GIIKAPIGRHPKDRMKMAVVFENSKEAVTHFKVLERYGYHTLVECVLETGRTHQIRVHFA 239

Query: 207 FFNWKVNR 214
                V  
Sbjct: 240 HIGHPVVN 247


>gi|169837001|ref|ZP_02870189.1| pseudouridylate synthase [candidate division TM7 single-cell
           isolate TM7a]
          Length = 92

 Score = 94.1 bits (233), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 27/77 (35%), Positives = 39/77 (50%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +KPI  V +        T++  LP  F  +  VGRLD N+ GLLLLTNDG  A  +  
Sbjct: 1   MLNKPINYVCSRKQQGKTPTIYSLLPDKFHNLKPVGRLDANSSGLLLLTNDGDFAFRMTH 60

Query: 137 PSTQWLRVYRVRFHGQV 153
           P  +  + Y V    ++
Sbjct: 61  PKFKKNKQYNVTLDKEL 77


>gi|289807462|ref|ZP_06538091.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 74

 Score = 93.3 bits (231), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 26/73 (35%), Positives = 42/73 (57%)

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
             GQVD+ KL  L +G+ ++        +     +G N W  V L EG+NRE+++++E  
Sbjct: 2   VFGQVDESKLRDLSRGVQLEDGPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAV 61

Query: 209 NWKVNRLIRISYG 221
             +V+RLIR+ YG
Sbjct: 62  GVQVSRLIRVRYG 74


>gi|317052412|ref|YP_004113528.1| pseudouridine synthase, RluA family [Desulfurispirillum indicum S5]
 gi|316947496|gb|ADU66972.1| pseudouridine synthase, RluA family [Desulfurispirillum indicum S5]
          Length = 313

 Score = 92.9 bits (230), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 93/246 (37%), Gaps = 47/246 (19%)

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----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
             +           V RLD +T GL+L+       + L     + +  R Y    HG +D
Sbjct: 121 DGLPAIGGVLRPGIVHRLDKDTSGLMLVAKTEVAHQRLVSMFAAKEIDRCYLALCHGSLD 180

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---------------WVTVG---LREG 196
              +    +G + +          ++  KG  A               WV++    L  G
Sbjct: 181 DSGVI---EGNIGRDPKDRKRMAIVEADKGKTARTHYRLLEKFFCHQQWVSLIECRLDTG 237

Query: 197 KNREIK 202
           +  +I+
Sbjct: 238 RTHQIR 243


>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 = 92.9 bits (230), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 89/224 (39%), Gaps = 37/224 (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  -DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
            D       E   L + +KP G+V      +  +T+ + L   FS          R   V
Sbjct: 69  QDIDIEVVYEDEHLAVINKPCGMVVHPGTGNFENTLVNALLHKFSGRLSSINGVIRPGIV 128

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------L 158
            RLD +T GLL++  T++  +     L S Q  R+Y     G + +D            +
Sbjct: 129 HRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N LK  +V  G         L+       ++ + L+ G+  +I+
Sbjct: 189 NRLKMAVVPNGKEAVTYFEVLERFDKYT-FIKLRLKTGRTHQIR 231


>gi|330896109|gb|EGH28330.1| S4 domain-containing protein [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 161

 Score = 92.9 bits (230), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 31/143 (21%), Positives = 58/143 (40%), Gaps = 10/143 (6%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
           L   F R+ ++  L  N  GL++ + D  + R L    ++  + Y V   G++    LN 
Sbjct: 24  LKGHFMRLEAISSLQANASGLMVFSQDWKILRKLTDDRSKIEQEYVVEISGEMVAHGLNR 83

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE---IKKVFEFFNWKVNRLIR 217
           L  G+  +G     ++ +   +      +   +   KN +   I  + E    K+  + R
Sbjct: 84  LNHGLTYKGKELPAVKASWQNEN----RLRFAM---KNPQPSIIALLCEAVGLKIVAIRR 136

Query: 218 ISYGPFQLGTLLAGSTREVSKKI 240
           I  G   +G L  G  R ++ K 
Sbjct: 137 IRIGGVSMGKLPEGQWRYMTAKE 159


>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 = 92.6 bits (229), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKALADLTELSRSQANEAIKAGTVLVNGKSAK-AKYAVKEGDVITYVLPEEEVLEYKA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 92.6 bits (229), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKALADLTELSRSQANEAIKAGTVLVNGKSAK-AKYAVKEGDVITYELPEEEVLEYKA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 92.6 bits (229), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 92/238 (38%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             T  R+ K +A     SR +    I +  V VNG +++ A  +V S D I         
Sbjct: 6   KETGLRLDKALANVTDLSRSQANEQIKKGLVLVNGQVVK-AKYSVKSGDEITYQLPEEEI 64

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                + +P+    E + L + +K  G+V   S      T+ + L              R
Sbjct: 65  LDYKAENLPIDIIYEDSDLAIVNKAQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    +VL  EL + + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + + +  K+ + ++G      + T+  + G    + + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQSVTVKGKDAVT-RFTVLERFGDYTLLELSLETGRTHQIRVHMAYIGHPV 241


>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 = 92.6 bits (229), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 83/233 (35%), Gaps = 37/233 (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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGIVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 92.6 bits (229), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 88/239 (36%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR-- 68
           +R+ K I+     SR +++ +I Q+ V VN I++ +   +V     I +       ++  
Sbjct: 10  ERIDKYISNNSEISRNDIKSLIEQKAVLVNDIVVNKPKFSVNEGQVITILKLIDKEIKIE 69

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
                     E   L +  KP G+V   +     +T+ + L   F           R   
Sbjct: 70  AQNIDLDIAYEDEYLLVLKKPSGMVVHPAPGHHENTLVNALLYHFKNNLSNENGLLRPGI 129

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVI 167
           V R+D +T GLLL+  +  + ++L     +    R Y     G +   KL L L  G  I
Sbjct: 130 VHRIDKDTSGLLLIAKNNEVHKILAEGFATKTINRKYVAICDGILKSPKLKLDLPIGRDI 189

Query: 168 QG--------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +               + + ++  +   +    + V   L  G+  +I+    +    V
Sbjct: 190 KNRQLMAITNANSKSAVTHLELLKSFYYENQPKSLVKATLETGRTHQIRVHCAYIKNPV 248


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 87/250 (34%), Gaps = 43/250 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K + ++ E+   +R+ K IA+     SR  ++ +I    V+VNG   +  ++ + + D 
Sbjct: 3   VKTRRLIAESD-GERLDKYIAQKETDLSRSFIQALIDSGHVQVNGKTAK-PSLKLKNGDT 60

Query: 60  IEVDGVPLRKAE-------------RTRLWLYHKPIGLVTTHSDPDGRST----VFDNLP 102
           I ++  P    E                L L +KP GL    +      T    V    P
Sbjct: 61  ITIEISPETPPELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLALEP 120

Query: 103 SIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV-- 153
            +       R   V RLD +T GLLL+  +      L     +    + Y     G++  
Sbjct: 121 KMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRETLANLSAQFKERTVRKYYLTLVKGELHP 180

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      D      +   +V  G         L   +G  + + V L  G+  +I+
Sbjct: 181 AEGFIEAPLGRDPQNRQKIA--VVSNGRHARTGYKVLRYIQGY-SLLEVKLETGRTHQIR 237

Query: 203 KVFEFFNWKV 212
             F      V
Sbjct: 238 VHFAAIGHPV 247


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 83/243 (34%), Gaps = 41/243 (16%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I  + V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDELVFVNGKTVK-PSYKVKENDEVVVNIPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD------- 156
                V RLD +T G++++  +      L     +    + Y     G +  +       
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAP 190

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +    VI+   Y      +  +   N  V   ++ G+  +I+    +   
Sbjct: 191 IGRHPVDRKKMA---VIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PIV 250


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKALADLTELSRSQANEAIKAGTVLVNGKSAK-AKYAVKEGDVITYELPEEEVLEYKA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMVAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|328946167|gb|EGG40312.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1087]
          Length = 298

 Score = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 85/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVAGQRLDKAVAELTYLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDIIYYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTSFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 83/243 (34%), Gaps = 41/243 (16%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I  + V VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDELVFVNGKTVK-PSYKVKENDEVVVNIPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD------- 156
                V RLD +T G++++  +      L     +    + Y     G +  +       
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKDEEGKIEAP 190

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +    VI+   Y      +  +   N  V   ++ G+  +I+    +   
Sbjct: 191 IGRHPVDRKKMA---VIEDGRYALTLYKVLERFKENTLVEAVIKTGRTHQIRVHMAYIGH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PIV 250


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 87/235 (37%), Gaps = 38/235 (16%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           DK  +  +   +R+   ++     SR   + +I +  V +NG + +  +  V++ DHI V
Sbjct: 17  DKLDITSDSFSERIDIFLSEKLNRSRSYFKNLIDEGLVTLNGKICK-PSSKVVAGDHIIV 75

Query: 63  ----DGVPLRKAE--------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
               D + L   E             + +KP GLV   +  +   T+ + L + F  +  
Sbjct: 76  LIPDDSIDLTPKEIDFEVIYDSKWYAVINKPAGLVVHPAPGNTTDTLVNGLLAKFKNIDD 135

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---- 156
                   + RLD +T GLL++  +  + + +       +  +VY     G+   D    
Sbjct: 136 NDNVRPGIIHRLDKDTSGLLIIAKNRDVRQQMSELFQKREVKKVYLAVCMGEPKNDYYMI 195

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        +   ++  G      +V +  +       +V +  G+  +I+
Sbjct: 196 DNFIGRSLTDRKKMA--VLQNGGKRAVSEVKILKRSSGIFLASVAIHTGRTHQIR 248


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 87/232 (37%), Gaps = 34/232 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I+    +P+R+ K +      SR  +++M+ Q  V VN  ++ + +  +   D +E+  
Sbjct: 2   KILYSLTSPKRIDKFLVEVTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKN 61

Query: 65  V---------------PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
                           PL    E   L + +KP G++   +    ++T+ + L       
Sbjct: 62  EQCVIDSQKELLPFACPLEIVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKHYLKTD 121

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK- 163
                 RLD NT GL+++  +      L+         + Y    H + D   L+ +   
Sbjct: 122 DFYITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMHHLHFMINE 181

Query: 164 --GIVIQG---ICYGDMQ--------VTLDTQKGSNAWVTVGLREGKNREIK 202
             G   Q    +  GD +        V +  Q  + A V V +  G+  +I+
Sbjct: 182 PIGHSYQDKLRMKTGDAKNVKEAISIVKVIEQYQNTALVEVSIITGRTHQIR 233


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 87/232 (37%), Gaps = 34/232 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I+    +P+R+ K +      SR  +++M+ Q  V VN  ++ + +  +   D +E+  
Sbjct: 2   KILYSLTSPKRIDKFLVEVTDYSRTSIKKMLEQNLVLVNDNIITKQSYLLQKNDSVEIKN 61

Query: 65  V---------------PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
                           PL    E   L + +KP G++   +    ++T+ + L       
Sbjct: 62  EQCVIDSQKELLPFACPLEIVFEDQDLLVINKPSGMLVHPTSFQEQNTLANALKHYLKTD 121

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK- 163
                 RLD NT GL+++  +      L+         + Y    H + D   L+ +   
Sbjct: 122 DFYITHRLDKNTSGLIVICKNQKALCCLQQQFMQKTVKKSYYAIVHNRFDMHHLHFMINE 181

Query: 164 --GIVIQG---ICYGDMQ--------VTLDTQKGSNAWVTVGLREGKNREIK 202
             G   Q    +  GD +        V +  Q  + A V V +  G+  +I+
Sbjct: 182 PIGHSYQDKLRMKTGDAKNAKEAISIVKVIEQYQNTALVEVSIITGRTHQIR 233


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 83/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  ENLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+G+  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQGVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 84/238 (35%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I    V VNG   ++A   V   D I  +      
Sbjct: 6   KEAGVRLDKALADLTDLSRSQASEQIKAGLVLVNGKT-QKAKYAVKEGDIIHYERPQEEV 64

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                  +PL    E   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLVNALLFHIKDLSSINGVIR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    + L  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQTVTAKGKPAVTHFKVLE-RFGQYSLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 84/238 (35%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I +  V VNG  ++ A   V   D +         
Sbjct: 6   KEAGIRLDKALADLTELSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPKEEV 64

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                + +PL    E   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LEYTAENIPLDIIYEDADVAVVNKPQGMVVHPSVGHTSGTLVNALMYHIKDLSSINGVIR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--------- 156
              V R+D +T GLL++  +      L  EL   + LR Y    HG +  D         
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHGTIPNDRGVIEAPIG 184

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             + +  K+ +  +G         L+ + G+   V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQAVTAKGKPALTHFKVLE-RFGNYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 92.2 bits (228), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 89/237 (37%), Gaps = 37/237 (15%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ K +ARA    SR  +++++ +  V VNG  + + +  +   + + +          
Sbjct: 16  ERLDKFLARAYPDFSRSYIKKLVKEGLVYVNGEEVRKPSRKLREGERVILHVPEPEPLDV 75

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
             + +P+    E   + +  KP GLV   S      T+ + L      + S+G       
Sbjct: 76  KPENIPINIIYEDEDIAVVEKPCGLVVHPSPGYTSGTLVNALLYHIKDLSSIGGVERPGI 135

Query: 113 --RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK----------- 157
             RLD  T G++++  +    R L       +  + Y+V   G V +D            
Sbjct: 136 VHRLDKETAGVMVIAKNNTAHRNLVRQFQERKTEKFYKVLVKGLVKKDYGAIDTPIARHP 195

Query: 158 LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           ++  +  +  +G     +  V    +K     + V +  G+  +I+  F      V 
Sbjct: 196 VDRKRFWVRKEGKEALTEYWVLKRYEKYEITLLKVKIHTGRTHQIRVHFASIGHPVL 252


>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 = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 87/237 (36%), Gaps = 40/237 (16%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           QRV KV+A  G+   SR  +++++A   V +NG +L + +V V   D + V+  P ++  
Sbjct: 54  QRVDKVLA-LGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVEMRPTQQSM 112

Query: 70  ------------AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISV 111
                        E   L + +KP GLV   +  +   T+       D       R   V
Sbjct: 113 AFQPETMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLLARDEKARQVPRAGIV 172

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDK 157
            RLD +T GL+++  +      L   + + +  R Y                   + +D 
Sbjct: 173 HRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKHREVDAPIGRDP 232

Query: 158 LNLLKKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            N L+  +V   +           L     +++ V   L  G+  +I+         
Sbjct: 233 RNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMASLGHP 289


>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 = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 85/238 (35%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I +  V VNG  ++ A   V   D +         
Sbjct: 6   KEAGVRLDKALADLTELSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPKEEV 64

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                + +PL    E   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LEYTAENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHTSGTLVNALMYHIKDLSSINGVIR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--------- 156
              V R+D +T GLL++  +      L  EL   + LR Y    HG +  D         
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIG 184

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             + +  K+ +  +G         L+ + G+   V + L  G+  +I+    +  + V
Sbjct: 185 RSEKDRKKQAVTAKGKPAVTHFKVLE-RFGNYTLVELTLETGRTHQIRVHMAYIGYPV 241


>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 = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 100/249 (40%), Gaps = 39/249 (15%)

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  DHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           DH+ +   P++K              E   L + +KP G+V   S      T+ + L S 
Sbjct: 64  DHVVIKVPPVKKTELLPEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSH 123

Query: 105 FS--------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG--- 151
                     R   V R+D +T GLL++   N       L+L S +  R Y    HG   
Sbjct: 124 APLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFS 183

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    +D+D  N  K+ +V  G         L++   + + +   L  G+  +I+ 
Sbjct: 184 EKRGTIKAPIDRDPKNRQKQAVVANGREAITHFKVLESFS-NYSLIEAVLETGRTHQIRV 242

Query: 204 VFEFFNWKV 212
              +    V
Sbjct: 243 HMAYIGHPV 251


>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 = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 32/123 (26%), Positives = 59/123 (47%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG 
Sbjct: 11  EHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKVELLRKGC 70

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            I  I    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++ 
Sbjct: 71  TIDDIHIRPLELKIIKPNLLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKS 130

Query: 226 GTL 228
             L
Sbjct: 131 SDL 133


>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 = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 85/238 (35%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
                R+ K +A     SR +    I +  V VNG  ++ A   V   D +         
Sbjct: 6   KEAGVRLDKALADLTELSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPKEEV 64

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   + + +KP G+V   S      T+ + L      + S      
Sbjct: 65  LEYTAENIPLDIIYEDDDVAVVNKPQGMVVHPSVGHMSGTLVNALMYHIKDLSSINGVIR 124

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--------- 156
              V R+D +T GLL++  +      L  EL   + LR Y    HG +  D         
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIG 184

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             + +  K+ +  +G         L+ + G+   V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQAVTAKGKPAVTHFKVLE-RFGNYTLVELTLETGRTHQIRVHMAYIGHPV 241


>gi|213419764|ref|ZP_03352830.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 59

 Score = 91.8 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKIL 241
            V + + EG+  ++K++F     +V  L R   G   L   L  G  R ++++ +
Sbjct: 1   QVRLTISEGRYHQVKRMFAAVGNRVVELHRERIGAITLDENLAPGEYRPLTEEEI 55


>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 = 91.8 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 100/249 (40%), Gaps = 39/249 (15%)

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  DHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           DH+ +   P++K              E   L + +KP G+V   S      T+ + L S 
Sbjct: 60  DHVVIKVPPVKKTELLPEKIPLDIVYEDDDLIVVNKPQGMVVHPSAGHSEHTLVNALLSH 119

Query: 105 FS--------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG--- 151
                     R   V R+D +T GLL++   N       L+L S +  R Y    HG   
Sbjct: 120 APLSTINGEFRPGIVHRIDKDTSGLLMVAKNNFAHEHLSLDLKSHKTGRKYLAIVHGNFS 179

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    +D+D  N  K+ +V  G         L++   + + +   L  G+  +I+ 
Sbjct: 180 EKRGTIKAPIDRDPKNRQKQAVVANGREAITHFKVLESFS-NYSLIEAVLETGRTHQIRV 238

Query: 204 VFEFFNWKV 212
              +    V
Sbjct: 239 HMAYIGHPV 247


>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 = 91.8 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 87/237 (36%), Gaps = 40/237 (16%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           QRV KV+A  G+   SR  +++++A   V +NG +L + +V V   D + V+  P ++  
Sbjct: 54  QRVDKVLA-LGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVEMRPTQQSM 112

Query: 70  ------------AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISV 111
                        E   L + +KP GLV   +  +   T+       D       R   V
Sbjct: 113 AFQPEAMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLLARDEKARQVPRAGIV 172

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDK 157
            RLD +T GL+++  +      L   + + +  R Y                   + +D 
Sbjct: 173 HRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKRREVDAPIGRDP 232

Query: 158 LNLLKKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            N L+  +V   +           L     +++ V   L  G+  +I+         
Sbjct: 233 RNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMASLGHP 289


>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 = 91.8 bits (227), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 86/240 (35%), Gaps = 35/240 (14%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           ++    +R+   +A     +R  ++++I      VNG  ++  +  V   D + V+    
Sbjct: 12  EKEDEGKRIDVFLAAELDYTRSYIKKLIVDGLAFVNGKTVK-PSYKVKENDKVVVNIPEA 70

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +PL    E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 71  EKIDVLPENIPLDILYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGINGI 130

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV--DQDKLNL- 160
                V RLD +T G++++  +      L     +    + Y     G +  +++K+   
Sbjct: 131 LRPGIVHRLDKDTSGVMVVAKNDKAHISLSNQIKERSVFKKYVAIVEGVIKNEEEKIEAP 190

Query: 161 -------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   KK  VI+   Y      +  +   N  +   ++ G+  +I+    F    V 
Sbjct: 191 IGRHPVDRKKMAVIEDGRYALTLYKVLERFKENTLIEAVIKTGRTHQIRVHMAFIGHPVV 250


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 83/241 (34%), Gaps = 34/241 (14%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           K  V      QR+ + +A     SRR   R I +  V +NG     A   +   D+I V 
Sbjct: 11  KGRVTTALAGQRLDQGLAEVFTLSRRRSRRAIDEGGVYLNGKRCRTAGRKLSCHDNIRVV 70

Query: 63  --DGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------PSIFS 106
             +G  L          ++  L+L HK  G     +    R T+ D L       P+  S
Sbjct: 71  MLEGERLIPFTPAQLVWQQPPLYLIHKKSGQYAQEALHRSRGTLPDELARHLELTPAQAS 130

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL-ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            +  V RLD +T GL+L +    + + L         + Y        D D    ++  +
Sbjct: 131 ELRPVHRLDRDTSGLMLFSASAAMLQHLQAHWHDAVEKRYLAVVSPAPDWDD-QRIR--L 187

Query: 166 VIQ-------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            I                   D +  +  ++ + A V +    G++ +++         +
Sbjct: 188 AIDRNRDAHGRYHLSPDGRACDSEAHVVERRDNRALVELVPHTGRSHQLRVHLSALGCPI 247

Query: 213 N 213
            
Sbjct: 248 L 248


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 44/89 (49%), Gaps = 3/89 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ K +A + +  R+ V   I +  ++VNG ++   ++++    D I+  G  +    +
Sbjct: 1   MRLDKFLAESSVGRRKIVRIYIKEGLIEVNGEVITEPSMDINENSDVIKYLGKVVSYTGK 60

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
              ++++KP G +T   D D R TVF   
Sbjct: 61  -VYYMFNKPAGCITARKDKDHR-TVFVFF 87


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 87/237 (36%), Gaps = 40/237 (16%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           QRV KV+A  G+   SR  +++++A   V +NG +L + +V V   D + V+  P ++  
Sbjct: 54  QRVDKVLA-LGVSEFSRSYLQQLLADGAVTLNGKVLLKPSVKVAVGDRLRVEMRPTQQSM 112

Query: 70  ------------AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISV 111
                        E   L + +KP GLV   +  +   T+       D       R   V
Sbjct: 113 AFQPETMDLQVVYEDEDLLVINKPAGLVVHPAPGNWTGTLLNGLLARDEKARQVPRAGIV 172

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDK 157
            RLD +T GL+++  +      L   + + +  R Y                   + +D 
Sbjct: 173 HRLDKDTSGLMVVARNRSTMDALIKMIAAREVSRQYLALAHKQWGSRKRREVDAPIGRDP 232

Query: 158 LNLLKKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            N L+  +V   +           L     +++ V   L  G+  +I+         
Sbjct: 233 RNRLRMAVVDLNLHPGKQARTDFDLLDGDAAHSLVRCTLHTGRTHQIRVHMASLGHP 289


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/224 (22%), Positives = 88/224 (39%), Gaps = 37/224 (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  -DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
            D       E   L + +KP G+V      +  +T+ + L   F           R   V
Sbjct: 69  QDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFRGRLSSINGVIRPGIV 128

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------L 158
            RLD +T GLL++  T++  +     L S Q  R+Y     G + +D            +
Sbjct: 129 HRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N LK  +V  G         L+       ++ + L+ G+  +I+
Sbjct: 189 NRLKMAVVPNGKEAVTYFEVLERFDKYT-FIKLRLKTGRTHQIR 231


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 63/335 (18%), Positives = 114/335 (34%), Gaps = 64/335 (19%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGV 65
           R+   + AR+   SR +V+++I + RV VNG+ ++ A+  + S D I V        D +
Sbjct: 22  RLDVFLSARSPDCSRSQVQKLIREGRVTVNGLPVK-ASYEIRSGDCIAVWLPEAVGEDSL 80

Query: 66  PLRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
             R        E   + + +K  G++          T+   L +  SR+ S         
Sbjct: 81  QPRPMPLEILFEDDDVLVLNKAPGVIVHPGAGHEEGTLVHGLLAHCSRLASRGAPRRPGI 140

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG----------------Q 152
           V RLD  T G L++         L          + Y    +G                 
Sbjct: 141 VHRLDRGTSGALMVAKSERAYLELIRQFKHHEVGKEYLALVYGTMAGASGEIRTGMGRHP 200

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           VD+ ++ +L+KG           Q  +    G  + + V ++ G+  +I+         V
Sbjct: 201 VDRKRMAVLEKG-----GREAVSQWKVAVAWGEVSLLRVVIKTGRTHQIRVHLSHMQHPV 255

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP---HLLEEAQVNLDAPIYSSE---- 265
                   G    G       R V   +LRE L      +L    +    P+  ++    
Sbjct: 256 V-------GDETYGGGKR-KARAVKSDVLRELLMEVDRQMLHAVGLAFRHPVSGADLSFT 307

Query: 266 -TLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             L  D   ++  +     +     S  +G+   K
Sbjct: 308 APLPPDFAGLLERIRISLQKEGAGRSDPSGVGMDK 342


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 84/237 (35%), Gaps = 37/237 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I +  V VNG  +++A   V   D I  D      
Sbjct: 6   KVAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQ-VKKAKYTVQEGDRITFDIPKKEV 64

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                  +PL    +   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    +VL  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDQGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +   +  K+ +  +G      +  +  + G    V + L  G+  +I+    +    
Sbjct: 185 RSDKDRKKQAVTAKGKPAVT-RFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 91/239 (38%), Gaps = 36/239 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           I+ E    +R+  V+++     SR  ++ ++   R+ V+G   E+ +  V   + + VD 
Sbjct: 11  ILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDGTP-EKPSARVRGGEQVMVDW 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IF 105
                      G+PL    E   + + HKP G +T     H+D    + V  ++P     
Sbjct: 70  PQIEPSNWLAEGLPLHILHEDADILVLHKPAGQLTHPGAGHADGTLVNGVLAHVPENAYL 129

Query: 106 SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD +T GLL++  T     + + +L      R Y     G           +
Sbjct: 130 PRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHREYLALVTGAMTGGGRVDAPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
            +   + L+  +   G         L  +   ++++ + L  G+  +I+  +       
Sbjct: 190 GRHAQDRLRMTVRDDGRPAQT-DYRLVERFPRHSYLRLRLATGRTHQIRVHMT-HIGHP 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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 87/234 (37%), Gaps = 36/234 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RAAVNVMSTDHIEVDGV 65
           R+ KV+      SR +++ +I Q  V VNG + +            + V   + +E++  
Sbjct: 22  RLDKVLVEESELSRTQIQSLIKQGLVTVNGQVEKANYKLSGQELIEMQVPEEEVLEIEAQ 81

Query: 66  PLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----------VG 112
            +      E   L + +K  G+V   S    R T+ + L   F   ++          V 
Sbjct: 82  AIPLDIIYEDDDLLVINKEAGMVVHPSKGHPRDTLVNALVYHFGNHLAAGSDSYRPGLVH 141

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +    R L   L      R+Y     G            + +D  N
Sbjct: 142 RIDKDTSGLLVVAKNNESHRYLSQQLMDHTLGRIYYCLVEGQMEVKQGSIEIPLARDPKN 201

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            LK     QG         L++   S + +   L+ G+  +I+  FE     + 
Sbjct: 202 RLKYHADAQGKPAWTDFEVLES-YPSASLIQAELKTGRTHQIRAHFEHIGHPII 254


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 37/170 (21%), Positives = 70/170 (41%), Gaps = 24/170 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR 68
             QR+ + +A A   SR + + +I +  VKVNG  +++ A  V   + +E    +  P+ 
Sbjct: 7   QKQRLDQFVAEAAQISRSQAKEIIEKGLVKVNGKTVQKPAYKVKEGERVEFEVPEPEPIE 66

Query: 69  KA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------ 112
                       E   + + +KP G+V   +      T+ + L      +  +G      
Sbjct: 67  VKPEAIPLEVIYEDQDVIVINKPAGMVVHPAPGHYSGTLVNALLHHCKDLGGIGGALRPG 126

Query: 113 ---RLDINTEGLLLLT-NDGGLARVLEL-PSTQWLRVYRVRFHGQVDQDK 157
              RLD +T GL+++  ND     ++E   +    R YR   +G   ++ 
Sbjct: 127 IVHRLDKDTAGLIVVAKNDLAQQSLIEQFKNRSVGRFYRALIYGIPKREH 176


>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 = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/224 (22%), Positives = 85/224 (37%), Gaps = 37/224 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFVQKIIEEGNVLVNQTQVLKPAYKVKSGDIIKVVIPEPKQLSIVA 68

Query: 63  -DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
            D       E   L + +KP G+V      +  +T+ + L   F           R   V
Sbjct: 69  QDINIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFRGRLSSINGVIRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK-----------L 158
            RLD +T GLL++         L   L S Q  R+Y     G + +D            +
Sbjct: 129 HRLDKDTSGLLVVAKTDEAHVKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N LK  +V  G         L+       +V + L+ G+  +I+
Sbjct: 189 NRLKMAVVPNGKEAVTYFEVLERFDKYT-FVKLRLKTGRTHQIR 231


>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 = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKSLADLTELSRSQANEAIKAGTVLVNGKSAK-AKYVVKEGDVITYVLPEEEVLEYKA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 32/123 (26%), Positives = 59/123 (47%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG 
Sbjct: 214 EHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKVELLRKGC 273

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            I  I    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++ 
Sbjct: 274 TIDDIHIRPLELKIIKPNLLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKS 333

Query: 226 GTL 228
             L
Sbjct: 334 SDL 336



 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R+SK+++ + + SR + + +I    VKV+  ++++    +     IEV+G  +     T+
Sbjct: 14 RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQ-NTVIDVNSKIEVNGCEINVDITTK 72

Query: 75 LWLYHKPIGLVTTHS 89
          LW  +KP  +     
Sbjct: 73 LWGIYKPKNVFCNTD 87


>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 = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I    V VNG   + A   V   D I              
Sbjct: 11  RLDKSLADLTELSRSQANEAIKAGTVLVNGKSAK-AKYVVKEGDVITYVLPEEEVLEYKA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPLDIIYEDADVAVVNKPQGMVVHPSAGHTSGTLVNALMYHVKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMIAKNDKAHNALAAELKDKKSLRKYVAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      + T+  + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFTVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|319745315|gb|EFV97632.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae ATCC 13813]
          Length = 296

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 84/237 (35%), Gaps = 37/237 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I +  V VNG  +++A   V   D I  D      
Sbjct: 6   KIAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQ-VKKAKYTVQEGDRITFDIPKEEV 64

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                  +PL    +   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDYQAENIPLDIIYQDDDVAVVNKPQGMVVHSSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    +VL  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +   +  K+ +  +G      +  +  + G    V + L  G+  +I+    +    
Sbjct: 185 RSDKDRKKQAVTAKGKP-AITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>gi|284007320|emb|CBA72674.1| ribosomal large subunit pseudouridine synthase E [Arsenophonus
           nasoniae]
          Length = 90

 Score = 91.0 bits (225), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 35/87 (40%), Gaps = 15/87 (17%)

Query: 165 IVIQGICYGDMQVTL---------------DTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           ++++       +  L                 +    +W+ + L EG+NR+I+++     
Sbjct: 1   MLLKDGMTKPAKAELVAEPDWLWPRHPPIRIRKNIPTSWLKISLSEGRNRQIRRMTANIG 60

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREV 236
           +   RLI  S   FQL  L  G  +E+
Sbjct: 61  FPTLRLILYSIANFQLDNLQPGEWKEI 87


>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 = 91.0 bits (225), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 52/224 (23%), Positives = 89/224 (39%), Gaps = 37/224 (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  -DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
            D       E   L + +KP G+V      +  +T+ + L   FS          R   V
Sbjct: 69  QDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPGIV 128

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------L 158
            RLD +T GLL++  T++  +     L S Q  R+Y     G + +D            +
Sbjct: 129 HRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N LK  +V  G         L+       ++ + L+ G+  +I+
Sbjct: 189 NRLKMAVVPNGKEAVTYFEVLERFDKYT-FIKLRLKTGRTHQIR 231


>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 = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 91/239 (38%), Gaps = 36/239 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           I+ E    +R+  V+++     SR  ++ ++   R+ V+G   E+ +  V   + + VD 
Sbjct: 2   ILPEEQAGERLDTVLSQLLPETSRSRIQALLRDGRILVDGTP-EKPSARVRGGEQVMVDW 60

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IF 105
                      G+PL    E   + + HKP G +T     H+D    + V  ++P     
Sbjct: 61  PQIEPSNWLAEGLPLHILHEDADILVLHKPAGQLTHPGAGHADGTLVNGVLAHVPENAYL 120

Query: 106 SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD +T GLL++  T     + + +L      R Y     G           +
Sbjct: 121 PRGGIVHRLDKDTTGLLVVAKTEMARQSLIDQLGDHTMHREYLALVTGAMTGGGRVDAPI 180

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
            +   + L+  +   G         L  +   ++++ + L  G+  +I+  +       
Sbjct: 181 GRHAQDRLRMTVRDDGRPAQT-DYRLVERFPRHSYLRLRLATGRTHQIRVHMT-HIGHP 237


>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 = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 91/240 (37%), Gaps = 35/240 (14%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLE-----RAAVNV----MS 56
           ++E +  +R+ KVIA      SR +V++ I    V VNG  ++          V      
Sbjct: 8   IEEEYDGERIDKVIAALNDEWSRSQVQQWIKNGLVTVNGRTVKANYKSELGDTVAISPPE 67

Query: 57  TDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
            + + V+  P+      E   + + +KP G+V   +    R T+ + L +    +     
Sbjct: 68  PEPLHVEPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGING 127

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +    R L  +L +    R Y+   HG           
Sbjct: 128 VLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTIDA 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +DK +  K  +  +          +  +     +V   L  G+  +I+   ++  + 
Sbjct: 188 PIGRDKRDRKKMAVTDENGKEAVTHFRVLERFRQYTYVECQLETGRTHQIRVHMKYIGYP 247


>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 = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 84/237 (35%), Gaps = 37/237 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I +  V VNG  +++A   V   D I  D      
Sbjct: 6   KIAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQ-VKKAKYTVQEGDRITFDIPKEEV 64

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                  +PL    +   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    +VL  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +   +  K+ +  +G      +  +  + G    V + L  G+  +I+    +    
Sbjct: 185 RSDKDRKKQAVTAKGKP-AITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 86/234 (36%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
            R+ K ++     SR      I   +V VNG  +++A   V   D +             
Sbjct: 10  IRLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYQVPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 69  AEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ + ++G         L+ + G    + + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTVKGKPAVTRFQVLE-RFGDYTLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 90.6 bits (224), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 83/239 (34%), Gaps = 49/239 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I +  V VNG  ++ A   V   D I              
Sbjct: 11  RLDKALADLTDLSRSQANDEIKKGTVLVNGEPVK-AKYTVKEGDIISYQLPEEEILDYEA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +P+    E   L + +K  G+V   S      T+ + L              R   V 
Sbjct: 70  EDIPIEIVYEDEYLAIINKAQGMVVHPSAGHSSGTLVNALLYHIKDLSTINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-- 168
           R+D +T GLL++  +     +L     + + LR Y    HG +  D      +G+ I+  
Sbjct: 130 RIDKDTSGLLMIAKNDKAHHILADELKAKKSLRKYLAIVHGNLPND------RGM-IEAP 182

Query: 169 -GICYGDMQVTLDTQKGSN--------------AWVTVGLREGKNREIKKVFEFFNWKV 212
            G    D +    T KG +                V + L  G+  +I+    +    V
Sbjct: 183 IGRSEKDRKKQAVTAKGKDAITRFQVVERFGDFTLVELSLETGRTHQIRVHMAYIGHPV 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 = 90.6 bits (224), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 84/237 (35%), Gaps = 37/237 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I +  V VNG  +++A   V   D I  D      
Sbjct: 6   KIAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQ-VKKAKYTVQEGDRITFDIPKEEV 64

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                  +PL    +   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDYQAENIPLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    +VL  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +   +  K+ +  +G      +  +  + G    V + L  G+  +I+    +    
Sbjct: 185 RSDKDRKKQAVTAKGKP-AITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>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 = 90.2 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 90/251 (35%), Gaps = 41/251 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK  N   +    QR+   ++      SR +++R+IAQ  V++NG  +  A   +   D+
Sbjct: 1   MKTINHYADPEIGQRLDVYLSNCYPDISRSQLQRLIAQGLVEINGKKVA-AKYKIKPGDY 59

Query: 60  I----------EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I           V+   +      E   + + +KP G+V   ++ +   T+ + L     
Sbjct: 60  INLTIPDPVGVSVEAENIALDIYFEDEDVIVINKPRGMVVHPAEGNYTGTMVNALLYHCR 119

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
            +           V RLD +T GLL++  +      L     +    R Y    HG + Q
Sbjct: 120 DLSGINGVLRPGIVHRLDKDTSGLLMVAKNDLAHNNLAAQLEKRLVNRRYLALVHGNLKQ 179

Query: 156 DK-------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D                 +   +  +          +  + G    + + L  G+  +I+
Sbjct: 180 DAGTVDAPIGRDACSRQKMA--VTDRNSRSAVTHFKVLKRFGRYTLLELKLETGRTHQIR 237

Query: 203 KVFEFFNWKVN 213
              ++  ++V 
Sbjct: 238 VHMKYIGYQVV 248


>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 = 90.2 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 92/236 (38%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I+ +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVIQFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQDIPLNIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T++   A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|323127056|gb|ADX24353.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis ATCC 12394]
          Length = 297

 Score = 90.2 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 92/236 (38%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I+ +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVIQFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQDIPLNIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T++   A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 90.2 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 32/123 (26%), Positives = 59/123 (47%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG 
Sbjct: 234 EHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKIELLRKGC 293

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            I  I    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++ 
Sbjct: 294 TIGDIIIRPLELKIIKPNFLYKWLKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKS 353

Query: 226 GTL 228
             L
Sbjct: 354 SDL 356



 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+SK+++ + + SR + + +I    VKV+  ++++    +     IEV+G  +     T+
Sbjct: 29  RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQ-NTVIDVNSKIEVNGCEINVDITTK 87

Query: 75  LWLYHKPIGLVTTHS 89
           LW  +KP  +     
Sbjct: 88  LWGIYKPKHVFCNTD 102


>gi|25011477|ref|NP_735872.1| hypothetical protein gbs1435 [Streptococcus agalactiae NEM316]
 gi|24413015|emb|CAD47094.1| unknown [Streptococcus agalactiae NEM316]
          Length = 296

 Score = 90.2 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 81/237 (34%), Gaps = 37/237 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVP 66
                R+ K +A     SR +    I +  V VNG  +++A   V   D I  D      
Sbjct: 6   KIAGVRLDKALADNSELSRSQANEEIKKGIVLVNGQ-VKKAKYTVQEGDRITFDIPKEEV 64

Query: 67  LRKAERTR----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
           L                 + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDYQAENISLDIIYQDDDVAVVNKPQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    +VL  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMVAKNDRAHQVLAEELKDKKSLRKYLAIVHGNLPNDRGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +   +  K+ +  +G      +  +  + G    V + L  G+  +I+    +    
Sbjct: 185 RSDKDRKKQAVTAKGKP-AITRFHVLERFGDYTLVELSLETGRTHQIRVHMAYIGHP 240


>gi|124267192|ref|YP_001021196.1| ribosomal large subunit pseudouridine synthase D [Methylibium
           petroleiphilum PM1]
 gi|124259967|gb|ABM94961.1| ribosomal large subunit pseudouridine synthase D [Methylibium
           petroleiphilum PM1]
          Length = 334

 Score = 90.2 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 45/223 (20%), Positives = 84/223 (37%), Gaps = 35/223 (15%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ + +A  AG  SR  ++ +I   +V+++G  +   A  V +   IE+          
Sbjct: 33  ERLDRWLATLAGEFSRNHLQTLIEGGQVRIDGQTVTARARRVSAGQQIEITLLPTPESQA 92

Query: 63  -DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVG 112
               P+      E   L +  KP GLV   +  +   TV +         +   R   V 
Sbjct: 93  FRPEPVALPVVFEDAHLLVIDKPAGLVVHPAPGNWSGTVLNGLLAHHAGAAALPRAGIVH 152

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLN 159
           RLD +T GL+++         L     + +  R Y    HG            + +D ++
Sbjct: 153 RLDKDTSGLMVVAKTLPAMTSLVRAIAAREVHREYLALVHGVLRQAVFSVDAPIGRDPVS 212

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +K  + + G       V L   + + + V   L  G+  +I+
Sbjct: 213 RIKMAV-LAGGRTARTDVELIAARDAVSAVRCTLHTGRTHQIR 254


>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 = 89.9 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 82/238 (34%), Gaps = 37/238 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
                R+ K +A     SR +    I    V VNG   ++A   V   D I  +      
Sbjct: 6   KEAGVRLDKALADLTDLSRSQASEQIKAGLVWVNGKT-QKAKYAVKEGDIIHYERPQEEV 64

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                  +PL    E   + + +KP G+V   S      T+ + L              R
Sbjct: 65  LDCVAQNIPLEIVYEDEDVAVINKPQGMVVHPSVGHPSGTLVNALLFHIKDLSSINGVIR 124

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
              V R+D +T GLL++  +    + L  EL   + LR Y    HG            + 
Sbjct: 125 PGIVHRIDKDTSGLLMIAKNDQAHQALAKELKEKKSLRQYIALVHGNLPNDRGVIEAPIG 184

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + + +  K+ +  +G         L+      + V + L  G+  +I+    +    V
Sbjct: 185 RSEKDRKKQTVTAKGKPAVTHFKVLERFD-QYSLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 89.9 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 33/123 (26%), Positives = 60/123 (48%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             +I V  LD + EG++LLTNDG  A  L+  +   L  Y ++   ++  +K+ LL+KG 
Sbjct: 224 EHLIIVNSLDSDMEGIILLTNDGDFANKLKDINNNILTTYLIKTQEELTNEKIELLRKGC 283

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            I GI    +++ +        W+ +   E     +  +F  +N  + +  R S+GP++ 
Sbjct: 284 TIGGITIRPLELKIIKPNFLYKWIKLTYVEKSQTHLNLLFSKYNMTIRKCKRYSFGPYKS 343

Query: 226 GTL 228
             L
Sbjct: 344 SDL 346



 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 38/75 (50%), Gaps = 1/75 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R+SK+++ + + SR + + +I    VKV+  ++++    +     IEV+G  +     T+
Sbjct: 14 RLSKILSLSSVVSRNKAQELIRSGNVKVDNQIVKQ-NTVIDVNSKIEVNGCEINVDITTK 72

Query: 75 LWLYHKPIGLVTTHS 89
          LW  +KP  +     
Sbjct: 73 LWGIYKPKNVFCNTD 87


>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 = 89.9 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 91/233 (39%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I +  V VNG  ++ A  NV S D+I              
Sbjct: 11  RLDKALAETTDLSRSQANEQIKKGLVLVNGQAVK-AKYNVKSGDNITYQLPEEEVLDYQA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +P+    E + L + +K  G+V   S      T+ + L              R   V 
Sbjct: 70  ENLPIDIIYEDSDLAIINKAQGMVVHPSAGHSSGTLVNALMYHIKDLSSINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +    +VL  EL + + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMVAKNDKAHQVLAEELKAKKSLRNYLAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ + ++G      + T+  + G    + + L  G+  +I+    +    V
Sbjct: 190 RKKQSVTVKGKDAVT-RFTVLERFGDYTLLELSLETGRTHQIRVHMAYIGHPV 241


>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 = 89.9 bits (222), Expect = 5e-16,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 80/242 (33%), Gaps = 44/242 (18%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            +R+ K IA     +R +++ +I Q  V VN   + +    V   D IE+          
Sbjct: 9   SERIDKYIANNSEITRNDIQALIVQGAVFVNSTKINKNKYIVHENDEIEIIKLLDKQQNI 68

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
               +PL    E     + +KP GLV   +      T+ ++L   F           R+ 
Sbjct: 69  EAQNLPLEIVYECDDYLVINKPSGLVVHPAPGHSSGTLVNSLMYHFKNNLSDVNGLLRMG 128

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV-------------D 154
            V R+D +T GLLL+  +          L + +  R Y     G +             D
Sbjct: 129 IVHRIDKDTSGLLLVAKNNETHNYFAKLLKNHEIKRTYYAIVDGHIENRLINLDLPIGRD 188

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            +        +  Q        + +         +   V   L+ G+  +I+    +   
Sbjct: 189 PNNRQKFA--VTEQNSKEAFTALEVIKYLNLAGQNKTLVKCNLKTGRTHQIRVHLAYIKH 246

Query: 211 KV 212
            V
Sbjct: 247 PV 248


>gi|322411546|gb|EFY02454.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. dysgalactiae ATCC 27957]
          Length = 297

 Score = 89.9 bits (222), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 90/236 (38%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR 68
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I+    +   L 
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVIQFELPEEEVLE 66

Query: 69  KA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                       E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQVIPLDIIYEDEALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T++   A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDEAHQALAAELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 89.9 bits (222), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 92/241 (38%), 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---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                 V+  P+      E   + + +KP G+V   +    R T+ + L +    +    
Sbjct: 67  EPEPLHVEPEPIPLDIYYEDEDVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCRDLSGIN 126

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
                  V R+D +T GLL++  +    R L  +L +    R Y+   HG          
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDAAHRSLVEQLVNKTVTRRYKAIVHGVIPHDYGTID 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK +  K  +  +          +  +     +V   L  G+  +I+   ++  +
Sbjct: 187 APIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRHYTYVECQLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|213616320|ref|ZP_03372146.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 56

 Score = 89.5 bits (221), Expect = 6e-16,   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|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 = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 77/235 (32%), Gaps = 33/235 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
               +R+   +A+  + SR   +R+I    V V+G         V + + +EV   P+  
Sbjct: 12  EAAGERLDLFLAQ-PLGSRARAQRLIDAGLVTVDGA-ARPKRHKVSAGERVEVTPEPVVD 69

Query: 70  AER------------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISV 111
            E               L +  KP G+V   +  +   T+   L          SR   V
Sbjct: 70  VEPSGDAPFAVAWEDEHLLIVDKPAGVVVHPAPGNRTGTLSQALAGRAAGGEDPSRAGIV 129

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            RLD +T GLL++       R L   + +    R Y     G            + +D+ 
Sbjct: 130 HRLDRDTSGLLIVAKTEEAHRELKRMIEARDVTREYVALVEGTPPARSGTIDAPIGRDRR 189

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +                L+     +A + V L  G+  +I+   E     V 
Sbjct: 190 VRTRMSTETDDPRDARTHFRLERALPDSALLRVTLETGRTHQIRVHLEAIGHPVV 244


>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 = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 82/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K ++     SR      I   +V VNG   ++A   V   D +             
Sbjct: 10  QRLDKALSELTELSRSLANEQIKAGQVLVNGQ-AKKAKYTVQEGDIVTYHVPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 69  AEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G         L+ + G  + + + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTAKGKPAVTRFQVLE-RFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 83/236 (35%), Gaps = 39/236 (16%)

Query: 4   KNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLER-----AAVNVM-- 55
           K +  E    QR+ KV+    G+ SR  ++  +    + VNG +++      +   V   
Sbjct: 6   KKLKLELEKTQRLDKVLTGELGL-SRTTIQSWLKAGLISVNGEVVKSNYKAQSGDEVTIL 64

Query: 56  --STDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVF-----------D 99
               D I +    +      E   L + +KP G+V   S      T+            D
Sbjct: 65  QKEEDVITIQPENIPLDIVFEDDSLIVVNKPSGMVVHPSKGHYSGTLVNALLYHSNSLSD 124

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG------ 151
           +      R   V R+D +T GLL++  +  + + L       +  R Y     G      
Sbjct: 125 STSEEIYRPGLVHRIDKDTSGLLVIAKNNDVHQKLAEQIAENKMNREYIAIVDGHFAHET 184

Query: 152 -----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 + + + N LK+ +  +G         +       + V+  L  G+  +I+
Sbjct: 185 GVVDAPLSRHQTNRLKRVVE-KGGKNAITHFEVLDSFSDYSLVSCRLETGRTHQIR 239


>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 = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 84/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I +  V VNG  ++ A   V   D +              
Sbjct: 11  RLDKALADLTDLSRSQANDEIKKGTVLVNGKAVK-AKYAVKVGDVVTYEVPEEEVLEYKA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  ENIPLDIVYEDEDVAVVYKPQGMVVHPSAGHTSGTLVNALMYHIKDLSSINGVIRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG +  D           + +
Sbjct: 130 RIDKDTSGLLMIAKNDTAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTHFKVLE-RFGNYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 86/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVASQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G+ + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGNYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 89.5 bits (221), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 86/237 (36%), Gaps = 39/237 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E++++I +++V VN    ++    +   D I
Sbjct: 1   MMYEFLIDDSNQNTRLDVFLANEVELSRSEIQKLIDEKKVLVNEKTQKK-NYKLNLNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           + D       ++          E   L + +K   ++   ++     T+ + L S F   
Sbjct: 60  KFDYEKPDKTIKPQQHDLDIVYEDDYLAIINKDKNVIVHPTETIYSDTLVNYLMSNFENL 119

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-- 155
                  R   V RLD +T GL+++  D      L   + + +  + Y    HG++D+  
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNNTHLKLKEIIKNHEITKTYLCIVHGKIDECG 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   ++                    + V V ++ G+  +I+
Sbjct: 180 TIEEYMTRNPKDRKKM---MISDEGKLSISNYERLDYNDDYSLVKVQIKTGRTHQIR 233


>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 = 89.5 bits (221), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 90/239 (37%), Gaps = 38/239 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M     V++ F+  RV K ++      SR  ++++I    V  NG +++ A   + + D 
Sbjct: 1   MIQTVTVEKEFSGNRVDKFLSEQFPDLSRSYIQKLIKDGHVTANGKIVK-ANYKLNALDT 59

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + +D   L++              E   + + +KP G+V   S      T+ + L     
Sbjct: 60  LALDKPELQEPDIVPENIPIDILYEDEDILIVNKPKGMVVHPSAGHYSGTLVNALMYHCK 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G LL+  +  + + L   L      R+Y    HG + 
Sbjct: 120 DQLSGINGIMRPGIVHRIDMDTTGSLLVCKNDFVHQDLAEQLKEHSIQRIYHAIVHGVIK 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +D+           +   K  +  +   +      +  +  +  ++   L  G+  +I+
Sbjct: 180 EDEGTIDAPIGRHPIERKKMSVNYKNGKHAVTHYKVIERFKNYTYIKCRLETGRTHQIR 238


>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 = 89.5 bits (221), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 83/237 (35%), Gaps = 39/237 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  + ++ ++    R+   +A     SR E+++ I  ++V VN    ++    + S D I
Sbjct: 1   MIYEFLIDDSNQNTRLDVFLANEVELSRSEIQKFIEDKKVLVNYKPQKK-NYKLNSNDKI 59

Query: 61  EVD----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           + D       +R          E   L + +K   ++   ++     T+ + L   F   
Sbjct: 60  KFDYEKEDKTIRAQKHDLDVVYEDDYLAIINKDKDVIVHPTETIYSDTLVNYLMYNFKNL 119

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ-- 155
                  R   V RLD +T GL+++  D      L+         + Y    HG++D+  
Sbjct: 120 SDVDGDYRRGIVHRLDKDTTGLIIIAKDNDTHLKLKEIIKNHEIIKTYLCIVHGKIDESG 179

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +V         Q          + V V ++ G+  +I+
Sbjct: 180 TIKEYMTRNPKDRKKM---MVSDEGKLSISQYERLDYNDDYSLVKVQIKTGRTHQIR 233


>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 = 89.5 bits (221), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 79/243 (32%), Gaps = 34/243 (13%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAV----NVMS 56
           IV       R+   +      SR  ++ +I    V V G + +              +  
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEGSRSYIQSLIKGGHVTVGGKVGKANLRLTPDTIIRVEIPE 64

Query: 57  TDHIEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
            + IEV  + +PL    E   + + +KP G+V   +  +   T+ + L      +     
Sbjct: 65  PESIEVKPEDIPLDYLYEDHDIVIVNKPRGMVVHPAVGNYSGTLVNALLFHCKDLSGING 124

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK----- 157
                 V RLD +T G++++  +      L          R Y     G + ++K     
Sbjct: 125 EIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKTHSARRTYWALVQGNIVEEKGTIKA 184

Query: 158 ------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  + +K  +V +          +  + G    V   L  G+  +I+  F      
Sbjct: 185 PIGRHPKDRMKMAVVFENSKDAVTHFKVLERYGHQTLVECNLETGRTHQIRVHFAHIGHP 244

Query: 212 VNR 214
           V  
Sbjct: 245 VVN 247


>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 = 89.1 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 85/243 (34%), Gaps = 48/243 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR ++E++I +  VKVN  ++ ++   +   + +EV            
Sbjct: 11  RLDKFLANKLNVSRNQIEQLIKKGYVKVNEKVITKSGYKLKENEKVEVLPIKKEEKETKK 70

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVISV 111
               +P+   +   L + +KP G+V   +     +T+ D L              R   V
Sbjct: 71  ANFDIPILYEDED-LLVINKPPGIVVHPAPSYKEATLVDWLKQKGYSLSTIAGEERFGIV 129

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL----------N 159
            R+D  T G L++  +      L          R Y +  +  + + K           N
Sbjct: 130 HRIDKETSGALVIAKNNKTHEFLSNQLKDKSMGRYYLMLLNEPLKEAKCVEEKIGRNPKN 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            LK  IV  G     + V +     +    T     G+  +I+         + +L R  
Sbjct: 190 RLKMAIVKNGKEAKTLFVPIFDNLTAAKLYT-----GRTHQIR-------VHLTKLGRYI 237

Query: 220 YGP 222
            G 
Sbjct: 238 LGD 240


>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 = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 48/229 (20%), Positives = 84/229 (36%), Gaps = 39/229 (17%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DG 64
            +R+ K I+     SR +++ +I ++ V VNG ++++    +     IEV        D 
Sbjct: 9   SERIDKYISDNSAISRNDIKSLILEKAVFVNGKVIQKPNFILKPDAEIEVIKVIDKTIDL 68

Query: 65  VPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---------S 110
            P +       E   L + +KP GLV   +      T+ + L   F  +           
Sbjct: 69  KPEKMDLDIVYEDEHLIVINKPSGLVVHPAPGHYSQTLVNGLIYHFKNLSNENGLLRPGI 128

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL---------N 159
           V R+D +T GLL++  TN         L + +  R Y     G  +   +          
Sbjct: 129 VHRIDKDTSGLLIIAKTNQVHQLLAKMLKNHEIKRSYIAIVEGFFENKIVHLNLPIGRSQ 188

Query: 160 LLKKGIVIQGICYGDM--QVTLDTQ----KGSNAWVTVGLREGKNREIK 202
             +K + I      +    V L  Q    K   + V   L  G+  +I+
Sbjct: 189 KDRKKMEITNNNSKNAITHVYLIKQFYYEKQPLSLVECQLETGRTHQIR 237


>gi|146318440|ref|YP_001198152.1| YlyB [Streptococcus suis 05ZYH33]
 gi|145689246|gb|ABP89752.1| YlyB [Streptococcus suis 05ZYH33]
          Length = 309

 Score = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 82/233 (35%), Gaps = 35/233 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---------ILLERAAVNVMSTDHIEV-- 62
            R+ K ++     SR      I   +V VNG          + +     +   + I+   
Sbjct: 10  IRLDKALSDLTDLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTYQIPEVEEIDYVA 69

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G    V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKEAVTRFQVLE-RFGDYTLVELTLETGRTHQIRVHMAYIGHPV 241


>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 = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 94/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S      T+ + L     
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPNGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>gi|167944991|ref|ZP_02532065.1| ribosomal large subunit pseudouridine synthase B [Endoriftia
          persephone 'Hot96_1+Hot96_2']
          Length = 88

 Score = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 29/80 (36%), Positives = 47/80 (58%), Gaps = 5/80 (6%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
          +R+ KV+A AG+ SRRE+E  I++ R++VNG   +     V+ +D I +DG P  +    
Sbjct: 10 ERLQKVLANAGVGSRREIEGWISEGRIEVNGETAK-LGQRVVGSDRIRIDGRPFSQKRME 68

Query: 70 AERTRLWLYHKPIGLVTTHS 89
          A   R+ +Y+KP G + T  
Sbjct: 69 APERRVLVYNKPEGELVTRK 88


>gi|325696405|gb|EGD38295.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK160]
          Length = 298

 Score = 89.1 bits (220), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 86/242 (35%), Gaps = 37/242 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I     
Sbjct: 4   IIEASVVGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDIIYYELP 62

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                    + +PL    +   + + +KP G+V   S      T+ + L      +    
Sbjct: 63  EPEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGIN 122

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
                  V R+D +T GLL++  +      L       + LR Y    HG          
Sbjct: 123 GVLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIE 182

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +   
Sbjct: 183 APIGRSEKDRKKQAVTAKGKSALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGH 241

Query: 211 KV 212
            V
Sbjct: 242 PV 243


>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 = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 59  IVVTIPEPEALDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>gi|332360722|gb|EGJ38531.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK49]
          Length = 298

 Score = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 84/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K +A     SR      I   R+ VNG  +++A   V   D I             
Sbjct: 12  QRLDKAVAELTFLSRSLANEQIKDGRILVNGQ-VKKAKYVVKEGDVISYELPEPEVVEYV 70

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 71  PEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L     + + LR Y    HG            + + + 
Sbjct: 131 HRIDKDTSGLLMIAKNDQAHVALADELKNKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 190

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    V
Sbjct: 191 DRKKQAVTAKGKPALTRFQVLE-RFGDFSLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 85/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>gi|257090036|ref|ZP_05584397.1| pseudouridylate synthase [Enterococcus faecalis CH188]
 gi|256998848|gb|EEU85368.1| pseudouridylate synthase [Enterococcus faecalis CH188]
          Length = 301

 Score = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 59  IVVTIPEPEVLDMIAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>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 = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 52/226 (23%), Positives = 91/226 (40%), Gaps = 41/226 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  V+++I +  V VN I + + A  V S D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFVQKIIEEGNVWVNQIQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
              D   L + E   +   +KP G+V      +  +T+ + L   FS          R  
Sbjct: 69  QEIDIEVLYEDEHLAVI--NKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V RLD +T GLL++  T++  +     L S Q  R+Y     G + +D           
Sbjct: 127 IVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVINAPIGRH 186

Query: 158 -LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +N LK  +V  G         L+       ++ + L+ G+  +I+
Sbjct: 187 PVNRLKMAVVPNGKEAVTYFEVLERFDKYT-FIKLRLKTGRTHQIR 231


>gi|332361351|gb|EGJ39155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1056]
          Length = 298

 Score = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 86/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG  +++A   V   D I      
Sbjct: 5   IESSVAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-VKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVPEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 83/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K ++     SR      I   +V VNG  +++A   V   D +             
Sbjct: 10  QRLDKALSDLTELSRSLANEQIKAGQVLVNGQ-VKKAKYTVQEGDIVTYHVPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 69  AEDIPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>gi|332366655|gb|EGJ44398.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1059]
          Length = 298

 Score = 89.1 bits (220), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 87/241 (36%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG  +++A   V   D I      
Sbjct: 5   IEASVVGQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQ-VKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L     + + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKAKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>gi|257082401|ref|ZP_05576762.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
 gi|256990431|gb|EEU77733.1| pseudouridylate synthase [Enterococcus faecalis E1Sol]
          Length = 301

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINTPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>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 = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/254 (17%), Positives = 88/254 (34%), Gaps = 44/254 (17%)

Query: 1   MKDKN--IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+++     +E  T +R+ K + A+    SR  ++++I    V+VNG  ++     + S 
Sbjct: 1   MREERFFTAEETVTNERIDKFLSAQMPDRSRSYIQKLIKDGLVEVNGKQVKT-NYKLGSE 59

Query: 58  DHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D +++    L                E T L + +KP G+V   +      T+ + L   
Sbjct: 60  DEVKLQIPELEVPDILPEEIPLDILYEDTDLLVVNKPKGMVVHPAPGHYTGTLVNALMYH 119

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
                       R   V R+D++T G LL+  +    ++L   L      R Y    HG 
Sbjct: 120 CRENLSGINGVMRPGIVHRIDMDTTGSLLVCKNDRAHQILAEQLKDHSITRRYEAIVHGN 179

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           + +D                 +   +             +  + G+   +   L  G+  
Sbjct: 180 LKEDSGTVNAPIGRHPTDRKKMS--VHAPHGREAVTHYRVLERFGNYTHIECELETGRTH 237

Query: 200 EIKKVFEFFNWKVN 213
           +I+         + 
Sbjct: 238 QIRVHMASIGHPIL 251


>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 = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           ++G++++       ++     +G+N W  V ++EG+NRE++++FE     V+RL+R+ +G
Sbjct: 6   EEGVMLEDGLAKVERIYEQGGEGANKWYNVVIKEGRNREVRRIFESQGLTVSRLVRVGFG 65

Query: 222 PFQLGT-LLAGSTREVSKKIL 241
           P  L   L  G   E++   +
Sbjct: 66  PIGLPNRLKRGQFYELNPAEV 86


>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 = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 81/234 (34%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
            R+ K ++     SR      I   +V VNG  +++A   V   D I             
Sbjct: 10  IRLDKALSDLTELSRSLANEQIKSGQVLVNGH-VKKAKYTVQEGDVITYQIPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 69  AEDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDEAHMALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G         L+ + G    + + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTAKGKPAVTRFQVLE-RFGDYTLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 86/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 18/76 (23%), Positives = 36/76 (47%)

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
              +  +    + +    AW+ V + EG+NR+++++     +   RLIR     F L  L
Sbjct: 8   DFLWQRISPIRERKHIPTAWLEVKIDEGRNRQVRRMTAHIGFPTLRLIRYQLAGFNLQNL 67

Query: 229 LAGSTREVSKKILREQ 244
           +  + R +++  LRE 
Sbjct: 68  MPKTYRTLTQNELREL 83


>gi|325687371|gb|EGD29392.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK72]
          Length = 298

 Score = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 83/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K +A     SR      I   R+ VNG  +++A   V   D I             
Sbjct: 12  QRLDKAVAELTDLSRSLAHEQIKDGRILVNGQ-VKKAKYAVKEGDVISYELPEPEVVEYV 70

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 71  AEDIPLEIVYQDEDVAVINKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGINGVLRPGIV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 131 HRIDKDTSGLLMVAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 190

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    V
Sbjct: 191 DRKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHPV 243


>gi|255030766|ref|ZP_05302717.1| hypothetical protein LmonL_19661 [Listeria monocytogenes LO28]
          Length = 69

 Score = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           R+ K+++  G  SR+EV+ ++    V VNG + + +   V    D I V G P+   E 
Sbjct: 1  MRLDKLLSHTGFGSRKEVKPLLKSGAVVVNGTIQKDSKTQVNPDKDQITVHGTPVVYQE- 59

Query: 73 TRLWLYHKP 81
             ++ HKP
Sbjct: 60 FVYFMLHKP 68


>gi|257087008|ref|ZP_05581369.1| pseudouridylate synthase [Enterococcus faecalis D6]
 gi|256995038|gb|EEU82340.1| pseudouridylate synthase [Enterococcus faecalis D6]
          Length = 301

 Score = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 94/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S      T+ + L     
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSVGHPNGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 51/226 (22%), Positives = 89/226 (39%), Gaps = 41/226 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++ A   +R  V+++I +  V VN   + + A  V S D I+V            
Sbjct: 9   RLDRYLSEALSKTRSFVQKIIEEGNVWVNQRQVLKPAYKVKSGDIIKVVIPEPKQLSLVA 68

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
              D   + + E   +   +KP G+V      +  +T+ + L   F           R  
Sbjct: 69  QDIDIEVVYEDEHLSVI--NKPRGMVVHPGAGNFENTLVNALLHKFKGRLSSINGVIRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V RLD +T GLL++  T++  +     L S Q  R+Y     G + +D           
Sbjct: 127 IVHRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVVDAPIGRH 186

Query: 158 -LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +N LK  IV  G         L+       +V + L+ G+  +I+
Sbjct: 187 PVNRLKMAIVPNGKEAVTYFEVLERFDKYT-FVKLRLKTGRTHQIR 231


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D I              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVITYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|9971939|gb|AAG10501.1|AF279106_63 predicted ribosomal large subunit pseudouridine synthase D
           [uncultured marine gamma proteobacterium EBAC31A08]
          Length = 310

 Score = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 84/234 (35%), Gaps = 35/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  KN+  +  +  R+ K  A      SR ++++ I + RV +NG  + +    V   D 
Sbjct: 1   MIVKNVPND-LSSMRLDKATAEMFTDYSRTQIKKWIEEGRVLINGE-VSQPRDKVYENDQ 58

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLV----TTHSDPDGRSTVFDNLP 102
           IE+     +K              E     + +KP GL+    +   D    + +    P
Sbjct: 59  IELSPKEEQKVSWEAQDIDFEIHFENEDFIIINKPAGLIMHPGSGCYDGTLANGLIYKFP 118

Query: 103 S--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG------- 151
                 R   V RLD +T G+LL+  +              + ++ Y     G       
Sbjct: 119 ELINIPRSGIVHRLDKDTSGILLVARNESFRNFFINEMQERRVVKKYTSIVIGSTLGSFS 178

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +DK N  K  I   G       V L    G+ + + + +  G+  +I+
Sbjct: 179 IEEPIGRDKNNRTKMAIREDGKDALT-FVKLKENIGNYSVLDIRIETGRTHQIR 231


>gi|330883599|gb|EGH17748.1| ribosomal large subunit pseudouridine synthase E [Pseudomonas
           syringae pv. glycinea str. race 4]
          Length = 75

 Score = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 31/59 (52%)

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
            +    +W+ + ++EG NR+++++         RL+R+  G + L  L  G  REV+ K
Sbjct: 16  RKSVPTSWLELVIKEGCNRQVRRMTAAVGLPTLRLVRVRIGDWTLDGLDQGQYREVAAK 74


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 93/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S      T+ + L     
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPNGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++         L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKSDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDTFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 83/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K ++     SR      I   +V VNG  +++A   V   D +             
Sbjct: 10  QRLDKALSDLTELSRSLANEQIKAGQVLVNGQ-VKKAKYIVQEGDIVAYHVPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 69  AENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G         L+ + G  + + + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTAKGKPAVTRFQVLE-RFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 83/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K ++     SR      I   +V VNG   ++A   V   D +             
Sbjct: 10  QRLDKALSDLTELSRSLANEQIKAGQVLVNGQ-AKKAKYTVQEGDIVTYHVPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ ++L      +           V
Sbjct: 69  AENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNSLMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 85/234 (36%), Gaps = 40/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           IV+ +  P+R+ K ++     SR  +++++ + RV   G+ ++ A+  + + D I VD  
Sbjct: 28  IVEPDAVPERIDKYLSERLSGSRSFLQKLLKENRVSAGGVPVK-ASYRICAGDVIRVDIP 86

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                      +PL    E   L + +KP G+V          T+ + L           
Sbjct: 87  AQSEPDILAEDIPLDILYEDDDLLVVNKPKGMVVHPGAGHYSHTLVNALMYHCRDNLSGI 146

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD---- 156
               R   V R+D NT G LL+  +      +   L      R YR   HG++  D    
Sbjct: 147 NGVLRPGIVHRIDQNTTGSLLVCKNDFSHNFIAGQLKEHSITRRYRAIVHGKISSDGTVN 206

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   +   +   +  +          +  Q     ++   L  G+  +I+
Sbjct: 207 APIGRHPVERKKMA--VNEKNGKPAVTHYRVLEQFEKFTYIECVLETGRTHQIR 258


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 85/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVASQRLDKAVAELTDLSRSLAHEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L    + +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHINDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G    V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYTLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 88.3 bits (218), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKAGQVLVNGQ-VKKAKYTVQEGDIVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G  + + + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLE-RFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 93/249 (37%), Gaps = 40/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  ++    T  R+ KV++   IA SR ++++ +    V+VN  +++ A   V   D 
Sbjct: 1   MENIKLIITEKTIGRIDKVLSEELIAYSRSQIQQWLKDSLVRVNNKVVK-ANYKVQPADE 59

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + +            + +PL    E   + + +KP G+V   S    + T+   L     
Sbjct: 60  VIIQLPKPKMMVVSPENIPLDIVYEDQDVVVINKPQGMVVHPSAGHFKGTMVHALLYHIK 119

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D +T GLL++  +      L   L     LR Y    HG+V  
Sbjct: 120 DLSSINDVIRPGIVHRIDKDTSGLLIVAKNNQAHEALAKQLKDKTILRKYIALVHGEVPH 179

Query: 156 DKL------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           ++               ++   +I+          +  +      + + L  G+  +I+ 
Sbjct: 180 EQGTIDAPIGRSKTNRKMQA--IIKDGRSAVTHFKVLEKFTGYTLIELQLETGRTHQIRV 237

Query: 204 VFEFFNWKV 212
             ++    V
Sbjct: 238 HMKYIGHPV 246


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 88/242 (36%), Gaps = 47/242 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ K I+  +   +R+ K +       SR  ++ +I++  +KV+G  ++     +  ++ 
Sbjct: 1   METKEIIYASPKSERIDKFLQNELSDLSRTNIQNLISEGYIKVDGNTVKT-NYKLKESNV 59

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +D             +P+    E   L + +KP G+V   S      T+ + L     
Sbjct: 60  ITIDYKEPEELDVVKQDIPVDIVYEDNDLLIVNKPKGMVVHPSAGHKDGTLVNALLYHCE 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   + + +  R Y    HG +  D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKEVKRKYYALVHGSIKHD 179

Query: 157 KLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAWVTV-------GLRE-----GKNRE 200
                  G +   I     +      +D  K S     V        L E     G+  +
Sbjct: 180 Y------GTIDAPIARNPKERKEMAVIDEGKPSITHFKVIDRFEKYTLIECELETGRTHQ 233

Query: 201 IK 202
           I+
Sbjct: 234 IR 235


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 80/233 (34%), Gaps = 46/233 (19%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIE---VD 63
           R+ K +       R +++        ++I + +V VN   ++  +  +   D +E   V+
Sbjct: 13  RLDKFL-------RNQLKDVPLSVIYKLIRKGKVYVNKKRVKDPSFELEEGDVVELRYVN 65

Query: 64  GVPLRKA-----------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
              L K                  E     + +KP  +          +T+ + L     
Sbjct: 66  LENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLLHYGQ 125

Query: 107 RV----ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNL 160
                   V RLD +T GLL++  +   AR+L          + Y     G  +    N 
Sbjct: 126 EKGFSPFLVHRLDKDTSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPE----NN 181

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +K  I + G       V++   K   + + V +  G+  +I++      + V 
Sbjct: 182 MKLTIPLDGQEAVSEIVSVKPLK-DVSLLRVKIHTGRKHQIRRHLSQIGFPVV 233


>gi|91204218|emb|CAJ71871.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 274

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/209 (20%), Positives = 89/209 (42%), Gaps = 24/209 (11%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERTRLWL 77
            IA     S ++ ++++  + V VN   +  A+  +   D IEV  G   +  ++T   L
Sbjct: 18  FIANKLSLSNKKAKQLLDDRLVFVNRKRVWIASYQLKPGDSIEVLSGKTHQPEKKTYDIL 77

Query: 78  YH--------KPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTND 127
           ++        KP G+VT     +G++++  +L + F+  R+ +V RLD +T G L+   +
Sbjct: 78  FNDDCYVIVSKPPGIVT-----NGQNSIERDLRTQFNRDRIQAVHRLDKDTSGALIFAKN 132

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                 ++         ++YRV   G++ +     +   +   G       +TL  +  +
Sbjct: 133 ENAFEEMKKVFKKHDIQKIYRVIVTGKICEPAF-TINSPV---GGQTAVTHITLLKKGKN 188

Query: 186 NAWVTVGLRE-GKNREIKKVFEFFNWKVN 213
            +++ V   E G+  +I+         V 
Sbjct: 189 TSYLEVA-TETGRRHQIRIHLASIGHPVI 216


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 90/247 (36%), Gaps = 47/247 (19%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLER 49
           M++K +   + E  + +R+ K +       R E++        +++    V+VNG  + +
Sbjct: 1   MENKIVELSINEENSYRRLDKFL-------RNELKAVPLSEIYKLLRTGCVQVNGKTVRK 53

Query: 50  AAVNVMSTDHIEVD-------------GVPLRK---AERTRLWLYHKPIGLVTTHSDPDG 93
               +   D + +               +PL+     E   L + +K  G+    S+   
Sbjct: 54  PYTELYVGDKVTIKADLAVYRQKKDLPSIPLKLDILYEDDNLLILNKKAGITIHPSEKTR 113

Query: 94  RSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
            +T+   L    ++       V RLD +T G+L++  +   AR L     +    + Y  
Sbjct: 114 STTLIQGLHFYGAKKGFKPHLVHRLDRDTSGVLVIAKNVKTARTLSHMFRNRLVKKEYIT 173

Query: 148 RFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G++     ++       + G         L+  +   + + V L  G+  +I+K F 
Sbjct: 174 LVSGKIFGDGFIDK-----PLDGSEALTEYKVLENFR-DTSLLRVILHTGRTHQIRKHFA 227

Query: 207 FFNWKVN 213
                V 
Sbjct: 228 LIGNPVV 234


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 79/243 (32%), Gaps = 37/243 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I +E     R+ K ++      SR  ++ +I    + VN   ++     + + D I V 
Sbjct: 7   KITEEENIGIRIDKYLSNIIEGKSRSFIQGLIDSGAILVNNKEVKS-NYKLRNHDEIIVS 65

Query: 64  -GVPLR------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              P+               E   + + +KP G+V   +  +   T+ + L      +  
Sbjct: 66  MPEPIELDVEPEDIDLNIVYEDEDVIVLNKPQGVVVHPAPGNYSGTLVNGLLYHCKDLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-------- 151
                    V R+D +T G+L++  +      L     +    R Y     G        
Sbjct: 126 INGVIRPGIVHRIDKDTSGILVIAKNDDAHNHLAKQFKNHSIKREYYALVEGKFSKIEGT 185

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + ++K + LK  I+  G         L+      A V   L  G+  +I+      
Sbjct: 186 VDKPIGRNKKDRLKMAIMEDGKRAVTHYNVLEQYNNGTALVKCTLETGRTHQIRVHMASI 245

Query: 209 NWK 211
              
Sbjct: 246 GHP 248


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 82/234 (35%), Gaps = 37/234 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           QR+ K ++     SR      I   +V VNG   ++A   V   D +             
Sbjct: 10  QRLDKALSDLTELSRSLANEQIKAGQVLVNGQ-AKKAKYTVQDGDIVTYHVPEPEVLEYV 68

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP G+V   S      T+ + L      +           V
Sbjct: 69  AENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIV 128

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKL 158
            R+D +T GLL++  +      L       + LR Y    HG            + + + 
Sbjct: 129 HRIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEK 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           +  K+ +  +G         L+ + G  + + + L  G+  +I+    +    V
Sbjct: 189 DRKKQAVTAKGKPAVTRFQVLE-RFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 94/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S      T+ + L     
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPNGTLVNALLHHAD 127

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 188 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 245

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 246 HMKYIGYP 253


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 68  IVVTIPEPEALDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 127

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 188 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 245

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 246 HMKYIGYP 253


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 68  IVVTIPEPEVLDMIAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 127

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 188 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 245

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 246 HMKYIGYP 253


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 86/250 (34%), Gaps = 43/250 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + +V E+   +R+ K I +     SR  ++ ++    ++VNG   +  ++ + + D 
Sbjct: 1   MKTRKLVAESD-GERLDKYITQKETDLSRSFIQELVEAGHIQVNGKNAK-PSLKLKNGDT 58

Query: 60  IEVDGVPLRKAE-------------RTRLWLYHKPIGLVTTHSDPDGRST----VFDNLP 102
           I ++  P    E                L L +KP GL    +      T    V    P
Sbjct: 59  ITIEIPPETPPELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLINGVLALEP 118

Query: 103 SIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV-- 153
            +       R   V RLD +T GLLL+  +      L     +    + Y     G++  
Sbjct: 119 EMEDFDDPLRPGIVHRLDKDTSGLLLVAKNREALANLSAQFKERTVRKYYLTLVQGELHP 178

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      D      +   +V  G         L   +G  + + V L  G+  +I+
Sbjct: 179 AEGFIEAPLGRDPQNRQKIA--VVSNGRPARTGYKVLRYIQGY-SLLEVKLETGRTHQIR 235

Query: 203 KVFEFFNWKV 212
             F      V
Sbjct: 236 VHFAAIGHPV 245


>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 = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 95/248 (38%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S    + T+ + L     
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSAGHPKGTLVNALLHHAD 127

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 188 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 245

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 246 HMKYIGYP 253


>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 = 87.5 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 83/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  ENIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L   L   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQDLKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 80/225 (35%), Gaps = 34/225 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------G 64
           T QR+   +A     SR +V ++I    V VNG  + +    V   D + V+        
Sbjct: 9   TAQRLDTFLATLLNLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPEDRVHVNWSEELFEK 68

Query: 65  VPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVF--DNLPSIFSRVISVG 112
           VP+             E  ++ + +KP GL++  +  +   ++            V  V 
Sbjct: 69  VPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPTSFNESESLLGAALFHCNHQPVFLVH 128

Query: 113 RLDINTEGLLLLT-NDGGLARVLELPSTQWLRVYR-VRFHGQVD------QDKLNL---- 160
           RLD +T G+++L  N   L  + +    + ++ Y     H  +D         L      
Sbjct: 129 RLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKRYYLALVHFPLDSLSGTISAPLERVGNN 188

Query: 161 ---LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               K G           + T+  Q    A +   L  G+  +I+
Sbjct: 189 KVMWKVGNSSNKAKNAFTKFTVLNQNEKAALIKCELLTGRTHQIR 233


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG L ++A  +V   D I              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQL-KKAKYSVQEGDVITYQVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++  +      L       + LR Y    HG +  D           + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNIPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G    + + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFRVLE-RFGDYTLLELQLETGRTHQIRVHMAYIGHPV 241


>gi|325689795|gb|EGD31799.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK115]
          Length = 298

 Score = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 85/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVVGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDIIYYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKSALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 85/240 (35%), Gaps = 40/240 (16%)

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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVNVTIPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 NDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVIS 179

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
            D    +   I         M VT +  K +     V        L E     G+  +I+
Sbjct: 180 HDD-GTIDAPIGRDKKDRQSMTVTREGSKNAVTHFHVLERFQDFTLVECRLETGRTHQIR 238


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 86/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSFANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|154685962|ref|YP_001421123.1| YlyB [Bacillus amyloliquefaciens FZB42]
 gi|154351813|gb|ABS73892.1| YlyB [Bacillus amyloliquefaciens FZB42]
          Length = 304

 Score = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 86/240 (35%), Gaps = 40/240 (16%)

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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVNVTIPEPEELDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 NDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGVIS 179

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
            D    +   I         M VT ++ K +     V        L E     G+  +I+
Sbjct: 180 HDD-GTIDAPIGRDKKDRQSMTVTRESSKNAVTHFHVLERFQDFTLVECRLETGRTHQIR 238


>gi|301633483|gb|ADK87037.1| pseudouridine synthase, RluA family [Mycoplasma pneumoniae FH]
          Length = 309

 Score = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/225 (19%), Positives = 80/225 (35%), Gaps = 34/225 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------G 64
           T QR+   +A     SR +V ++I    V VNG  + +    V   D + V+        
Sbjct: 9   TAQRLDTFLATLLNLSRVKVAKLIVDGLVSVNGKKITKNGWLVQPEDRVHVNWSEELFEK 68

Query: 65  VPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVF--DNLPSIFSRVISVG 112
           VP+             E  ++ + +KP GL++  +  +   ++            V  V 
Sbjct: 69  VPVEVQPYDFPLDILYEDEQIMVVNKPNGLISHPTSFNESESLLGAALFHCNHQPVFLVH 128

Query: 113 RLDINTEGLLLLT-NDGGLARVLELPSTQWLRVYR-VRFHGQVD------QDKLNL---- 160
           RLD +T G+++L  N   L  + +    + ++ Y     H  +D         L      
Sbjct: 129 RLDRDTSGVIMLAKNQSSLLHLQKQLQQRVMKRYYLALVHFPLDSLSGTISAPLERVGNN 188

Query: 161 ---LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               K G           + T+  Q    A +   L  G+  +I+
Sbjct: 189 KVMWKVGNSSNKAKNAFTKFTVLNQNEKAALIKCELLTGRTHQIR 233


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 90/236 (38%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQNIPLDIIYEDDTLAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T+    A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|327489656|gb|EGF21448.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1058]
          Length = 298

 Score = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 84/241 (34%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASAAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDVISYEQPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G    V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYTLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 87/233 (37%), Gaps = 36/233 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            I+    + QR+ K +      SR  +++M+ Q  + VN   + +A+  +   D+I+++ 
Sbjct: 2   KILYSLMSSQRIDKFLVENTNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINN 61

Query: 65  V-PLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
             P+ + ++                 L + +KP G++   +    ++T+ + L       
Sbjct: 62  ELPIVQEQKKLLPFVYSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYYLKTD 121

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN----- 159
                 RLD NT GL+++  +      L+         + Y    H + D   L+     
Sbjct: 122 NFYITHRLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQHLHFMINE 181

Query: 160 ----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +K G   +        V +  Q  + A V V +  G+  +I+
Sbjct: 182 PIGHSYQDKLRMKTGNS-KNTKEAISIVKVLEQYKNTALVEVSIITGRTHQIR 233


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 90/249 (36%), Gaps = 38/249 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  +  +    T +R+ K ++     SR  V+++     + VNG + + ++  V++ D I
Sbjct: 1   MAKQTWIVSEDTKERLDKYLSSNTELSRTRVQQLADDGMIFVNGKVAKSSS-KVVTGDEI 59

Query: 61  EVD---GVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
             D     P+             E   + + +KP G+V   +  +  +T+ + L      
Sbjct: 60  SCDVPEDRPVDILPENIPLDILYEDHDIIVINKPKGMVVHPAPGNYSNTMVNALLYHCKD 119

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
           +           V R+D +T G ++   +      +   L +    RVY+    G +  D
Sbjct: 120 LSGINGVIRPGIVHRIDKDTTGCIVACKNDKAHEAIAKQLENKTCHRVYKTIVVGNITHD 179

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKV 204
              L+   I         M+VT +  + +     V             L  G+  +I+  
Sbjct: 180 D-GLIDAPIGRDPRDRQRMKVTEENSRDARTHFHVLERFNVATYLECRLETGRTHQIRAH 238

Query: 205 FEFFNWKVN 213
            ++ N  V 
Sbjct: 239 MKYINHPVM 247


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 86/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 80/236 (33%), Gaps = 40/236 (16%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP---- 66
           R+ K     +   GI SR +V+  I     ++NG + ++    +M  + + + G      
Sbjct: 28  RLDKFWGTALEEEGI-SRGKVKDWIKAGFAEINGKICKKPNQKLMGNEELTLKGEAELTS 86

Query: 67  LRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--------S 110
           L   E     +Y        +KP GL T  +      T+   +   F  +          
Sbjct: 87  LVPEELPLEIIYNDGKIAVINKPAGLTTHPAPSCPTGTLVHRMIHHFPEIRDMDEWRPGI 146

Query: 111 VGRLDINTEGLL--LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK----------- 157
           V RLD  T GL+   L     LA        +  + Y    HG   ++            
Sbjct: 147 VHRLDKFTSGLITVALNEHDRLAMSTAFADREVNKAYLAIVHGVPKREFGEIDQPMGRHP 206

Query: 158 LNLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  K  +V++G      + +V      G  + V V +  G+  +I+         
Sbjct: 207 VHKTKMAVVLKGGRDARSEYEVLWSDPAGRASLVKVKIYTGRTHQIRVHMAHIGHP 262


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 84/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +    I ++ V VNG  ++ A   V   D +              
Sbjct: 11  RLDKALADLTELSRSQANDEIKKETVLVNGKAVK-AKYAVKVGDVVTYEVPEEEVLEYTA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   + + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  ENIPLDIIYEDEDVAVVNKPQGMVVHPSVGHTSGTLVNALMYHIKDLSSINGVIRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG +  D             +
Sbjct: 130 RIDKDTSGLLMIAKNDAAHNALAAELKDKKSLRKYVAIVHGNIPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + GS   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTHFKVLE-RFGSYTLVELTLETGRTHQIRVHMAYIGHPV 241


>gi|332360785|gb|EGJ38592.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK355]
          Length = 298

 Score = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 84/241 (34%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   ++ VNG   ++A   V   D +      
Sbjct: 5   IEASIAGQRLDKAVAELTDLSRSLANEQIKDGQILVNGQ-AKKAKYAVKEGDVVSYELSE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHAALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G    V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYTLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 87.5 bits (216), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 90/236 (38%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T+    A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHLPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  ENLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 85/245 (34%), Gaps = 46/245 (18%)

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 NLP---------SIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVR 148
            L          S   R   V RLD  T G++++  TN+  L    +L      R Y   
Sbjct: 118 WLKLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAI 177

Query: 149 FHGQVDQDKL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGK 197
               + ++ +          N LK  I   G         +         +    L  G+
Sbjct: 178 LDLALKENVIIEKPIGRNPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACKLYTGR 237

Query: 198 NREIK 202
             +I+
Sbjct: 238 THQIR 242


>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 = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 88/236 (37%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSETMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++       + L   L + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDAAHQALTEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|324991250|gb|EGC23184.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK353]
          Length = 298

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 84/241 (34%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I    + VNG   ++A   V   D I      
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLANEQIKDGWILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKSALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 86/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|260221244|emb|CBA29613.1| Ribosomal large subunit pseudouridine synthase D [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 335

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 85/238 (35%), Gaps = 42/238 (17%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           +R+ + +A      SR  ++++I    V+VNG ++ + +  V   + + V+  P  +   
Sbjct: 34  ERLDRALAFSVQEFSRSYLQQLIESGFVQVNGKVVTKTSGKVKVGEELTVELKPTPQSQA 93

Query: 70  -----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVG 112
                       E   + + +KP GLV   +  +   T+ + L +         R   V 
Sbjct: 94  FKPEPMALDVVHEDEHVLVINKPAGLVVHPAPGNWSGTLLNGLLAYSPHAALVPRAGIVH 153

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVR------------FHGQVDQDKL 158
           RLD +T GL+++         L     + +  R Y                   + +D  
Sbjct: 154 RLDKDTSGLMVVARSRTAMDALVNAIAAREVSRQYFAIAHKTWPWTRLKEVDAPIGRDPR 213

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNA----WVTVGLREGKNREIK-KVFEFFNWK 211
           N L+  +V   +     +   D    SN+    WV   L  G+  +I+  +       
Sbjct: 214 NRLRMAVV-DLVHQSGKEARTDFSLISNSQVACWVRCILHTGRTHQIRVHM-AHIGHP 269


>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 = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 93/253 (36%), Gaps = 44/253 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M++ +I V E+   QR+ K ++   +    SR  +  +I +  + VNG ++  A   V  
Sbjct: 1   MREIDIWVAEDADSQRIDKYLSM--VVEDLSRSRIASLIEEGSILVNGEVIR-AKYKVKP 57

Query: 57  TDHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            DHI     D + L  A          E   + + +KP G+V   ++ +   T+ + L  
Sbjct: 58  ADHITAAFEDEMALEAAPEKMELDIRYEDHDVIVINKPKGIVVHPANGNQSGTLVNGLLY 117

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
               +           V R+D +T GLL++  +      L   L +    R+Y    HG 
Sbjct: 118 HCKDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHASLSKQLQNKSVNRLYYALVHGV 177

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNRE 200
           ++ +    +   I         M V     K +     V        L E     G+  +
Sbjct: 178 IEHEF-GTIDAPIGRDPKDRQKMAVIATNSKPARTHFRVVERFAKYTLVECRLETGRTHQ 236

Query: 201 IKKVFEFFNWKVN 213
           I+   ++    V 
Sbjct: 237 IRVHMQYIGHPVV 249


>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 = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 85/245 (34%), Gaps = 46/245 (18%)

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 NLP---------SIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVR 148
            L          S   R   V RLD  T G++++  TN+  L    +L      R Y   
Sbjct: 118 WLKLKNISLSTISGEERHGIVHRLDKGTSGVMVIAKTNEAHLNLSKQLEDKSMGRYYLAI 177

Query: 149 FHGQVDQDKL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGK 197
               + ++ +          N LK  I   G         +         +    L  G+
Sbjct: 178 LDLALKENVIIEKPIRRNPNNRLKMSIEENGRYAKSAFSKIALSDNEKFELIACKLYTGR 237

Query: 198 NREIK 202
             +I+
Sbjct: 238 THQIR 242


>gi|315027878|gb|EFT39810.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 310

 Score = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 94/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP G+V   S      T+ + L     
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQGMVVHPSVGHPNGTLVNALLHHAD 127

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 188 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 245

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 246 HMKYIGYP 253


>gi|291530266|emb|CBK95851.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           siraeum 70/3]
          Length = 304

 Score = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 81/241 (33%), Gaps = 47/241 (19%)

Query: 14  QRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           +R  K +A    GI +R     +I Q    VNG +  +    + + D + +D        
Sbjct: 13  ERTDKFLALQDTGI-TRSAAAALIEQGCCLVNGKIAAK-NQKLKTGDTVTLDVPEAQPAD 70

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RV 108
                +PL    E + L + +KP G+V   +      T+ + L               R 
Sbjct: 71  ILPENIPLDIVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCGDSLSGINGVIRP 130

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQD--------- 156
             V R+D +T GLL++  +   A  +     +     R Y     G + +D         
Sbjct: 131 GIVHRIDRDTSGLLIVAKN-DTAHNILAEQIKVHSFTREYMAVVQGVIKEDGTVDAPIGR 189

Query: 157 ---KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKV 212
                  +   +  +          ++    +N  V + L  G+  +I+  +  +    V
Sbjct: 190 HKTDRKKMC--VTTENSREAITHYFVEQTYRNNTLVRLRLETGRTHQIRVHM-AYIGHPV 246

Query: 213 N 213
            
Sbjct: 247 T 247


>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 = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 82/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDIVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  ENLPLDIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 85/227 (37%), Gaps = 36/227 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRK 69
            + QR+ K +      SR  +++M+ Q  + VN   + +A+  +   D+I+++   P+ +
Sbjct: 1   MSSQRIDKFLVENTNYSRTLIKKMLDQNLILVNDNFISKASYLLKKNDYIQINNELPIVQ 60

Query: 70  AERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVG 112
            ++                 L + +KP G++   +    ++T+ + L             
Sbjct: 61  EQKKLLPFVYSLEIIFEDQDLLIVNKPSGMLVHPTSFHEQNTLANALKYYLKTDNFYITH 120

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN----------- 159
           RLD NT GL+++  +      L+         + Y    H + D   L+           
Sbjct: 121 RLDKNTSGLIIICKNQIALNSLQQQFMQKTIRKSYYAIVHNRFDMQHLHFMINEPIGHSY 180

Query: 160 ----LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +K G   +        V +  Q  + A V V +  G+  +I+
Sbjct: 181 QDKLRMKTGNS-KNTKEAISIVKVLEQYKNTALVEVSIITGRTHQIR 226


>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 = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 39/183 (21%), Positives = 75/183 (40%), Gaps = 27/183 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K +    +  +  R+ + +A      SR  +++++   +V VNG L++ A+  V + DH
Sbjct: 12  LKQEFYPTDLESDVRIDRYLAETCPELSRSYIQKLLKSGQVLVNGRLIK-ASYVVTADDH 70

Query: 60  IEVD-GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IEVD    +               E   + L +KP G+V   +      T+ + L     
Sbjct: 71  IEVDVPEAVEPEIEAEPMDLDILYEDQDIILVNKPKGMVVHPAAGHYSHTLVNGLMYHCK 130

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G+L++  +      +   L      R Y+   HG + 
Sbjct: 131 NQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAAQLKEHSITRRYQAIVHGVIK 190

Query: 155 QDK 157
           +D+
Sbjct: 191 EDE 193


>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 = 87.2 bits (215), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 61/326 (18%), Positives = 119/326 (36%), Gaps = 58/326 (17%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           TP R+ + + R  +  A+R +V+  I + RV VN   ++     + S D I++       
Sbjct: 32  TPMRIDQYLTRQ-VENATRNKVQEAIEEGRVLVNEKRVKS-NYRIKSCDTIQITFLRPPA 89

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIF 105
                + +P+    E   L + +K  G+V   +  +   T+            + L    
Sbjct: 90  PELAPEDIPIDIIYEDEDLMVINKKPGMVVHPAFGNWTGTLANAILHHIGIGAEELDKSS 149

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD NT GL+++  +      L       Q +++Y+    G V  ++   +  
Sbjct: 150 LRPGIVHRLDKNTSGLIIVAKNPVALHRLARQFADRQVVKIYKAIVWG-VPAEQSGTITT 208

Query: 164 GIVIQGICYGDMQV----TLDTQKGSN--------------AWVTVGLREGKNREIKKVF 205
            I   G    D +V      + + G                + +++ L  G+  +I+   
Sbjct: 209 NI---GRSKKDRKVMANFPYEGKDGKTAITDYSVTENLHWFSLLSLTLHTGRTHQIRAHM 265

Query: 206 EFFNWKVNRLIRISYGPFQLGTLL----AGSTREVSKKILREQLGPHLLEEAQVNLDAPI 261
           +    ++  L   +YG   L TL      G  R + + + R+ L    L   Q     P+
Sbjct: 266 QHLGHQI--LGDETYGGAVLRTLPFSRSEGFVRNLLELLPRQALHAATLSFHQPTTREPL 323

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKK 287
             +  L  D  + I ++        +
Sbjct: 324 SFTAPLPEDMQSAIEKIRAVVEANSR 349


>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 = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 89/243 (36%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K+IA R    SR  V++++ +  + VNG   +  A  V   D +EV   
Sbjct: 15  ISEREHGERLDKLIASRVTGMSRSFVQQLMKRGAILVNGEPCK-PAQRVRYGDRLEVYLP 73

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
           P+                 E   + ++ KP G+VT  +      T+ + L +I   +   
Sbjct: 74  PVEPPTDLEPEFLPIPVIYEDDDIIVFDKPPGIVTHPAPGHEHGTLVNALKAIRPDLQVQ 133

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG---------- 151
                  V RLD +T GLL++         L     S   ++ Y    HG          
Sbjct: 134 PSHRPGIVHRLDKDTSGLLVVAKTEAARLALLEQWQSRSVVKKYTALVHGVVEPDSGTID 193

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D +   K  +V  G         L+  + +   + V +  G+  +I+    F   
Sbjct: 194 APISRDPVERTKMAVVSWGRPAITHFRVLERFRCAT-LLDVTIETGRTHQIRVHCAFIGH 252

Query: 211 KVN 213
            V 
Sbjct: 253 PVV 255


>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 = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 46/230 (20%), Positives = 80/230 (34%), Gaps = 42/230 (18%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV---------- 62
           +R+ K I+     +R + + +I Q+ V V+    + +    V     I V          
Sbjct: 10  ERIDKYISDNSEITRNDAKALIEQEAVYVDDKKFVRKPNYMVREGMVITVLRLLEKESNI 69

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
               +PL  + E   L + +KP GLV   +      T+ + L   F           R+ 
Sbjct: 70  EAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDTNGLLRLG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            V R+D +T GLL++  D      L   L + Q  R Y     G +  +K+  +   I  
Sbjct: 130 IVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILP-NKVTKINLPIQR 188

Query: 168 QGICYGDMQVTLDTQ---------------KGSNAWVTVGLREGKNREIK 202
                  M +  D +                   + V   L  G+  +I+
Sbjct: 189 DTKNRKLMSIHKDGKSSVTYVHMLKSFYIDNKPYSLVKCELETGRTHQIR 238


>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 = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 84/243 (34%), Gaps = 44/243 (18%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
           +   +R+ KV+A +    SR  ++ +I    VKVNG  +++    +   D + V+  P  
Sbjct: 33  DLDGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGDEVSVEIKPRL 92

Query: 68  -------------RKAERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRV 108
                           E   + + +KP  LV   +      T+      ++ +     R 
Sbjct: 93  EDMDFIATPMDIDVVYEDDDILVINKPARLVVHPAAGHWDDTLLNGLLAYNPIFRTLPRA 152

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLN------- 159
             V RLD +T GL+++  +      L  +L +    R Y     G+   DK+        
Sbjct: 153 GIVHRLDRDTTGLMVVAKNEKAMLDLVQQLQARTVKREYWALTRGKAPADKVIEAAIERD 212

Query: 160 -----LLKKGIVIQGICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                    G   +G         +      + +    +WV   L+ G+  +I+   E  
Sbjct: 213 PRNPLRFTIG---KGGRAKPATTHIRCIDQKEVKGKPFSWVACRLKTGRTHQIRVHMESI 269

Query: 209 NWK 211
              
Sbjct: 270 GLP 272


>gi|256959131|ref|ZP_05563302.1| pseudouridylate synthase [Enterococcus faecalis DS5]
 gi|256949627|gb|EEU66259.1| pseudouridylate synthase [Enterococcus faecalis DS5]
          Length = 301

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 94/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 1   MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP  +V   S    + T+ + L     
Sbjct: 59  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHPKGTLVNALLHHAD 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 119 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 178

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 179 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 237 HMKYIGYP 244


>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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 48/233 (20%), Positives = 84/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K IA     SR +    I    V VNG   + A  +V + D I              
Sbjct: 11  RLDKAIADLTELSRGQANDAIKAGIVLVNGQAAK-AKYSVKAGDIITYEIQEEEVLDYQA 69

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    E   L + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLDVVYEDEDLAIINKPQGMVVHPSAGHSSGTMVNALLYQIKDLSGINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +    R L     + + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMVAKNDAAHRALADELKAKKSLRKYLAIVHGNLPNDRGIIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ ++ +G      +  +  + G    V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVIARGKEAVT-RFQVIERFGDYTLVELTLETGRTHQIRVHMAYIGHPV 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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 82/233 (35%), Gaps = 35/233 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---------ILLERAAVNVMSTDHIEV-- 62
            R+ K ++     SR      I   +V VNG          + +     +   + I+   
Sbjct: 10  IRLDKALSDLTDLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTYQIPEVEEIDYVA 69

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G    V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKEAVTRFQVLE-RFGDYTLVELTLETGRTHQIRVHMAYIGHPV 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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 81/241 (33%), Gaps = 47/241 (19%)

Query: 14  QRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           +R  K +A    GI +R     +I Q    VNG +  +    + + D + +D        
Sbjct: 12  ERTDKFLALQDTGI-TRSAAAALIEQGCCLVNGKIAAK-NQKLKTGDTVTLDVPEAQPAD 69

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RV 108
                +PL    E + L + +KP G+V   +      T+ + L               R 
Sbjct: 70  ILPENIPLDIVYEDSDLLVVNKPKGMVVHPAPGHYSGTLVNALMYHCGDSLSGINGVIRP 129

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQD--------- 156
             V R+D +T GLL++  +   A  +     +     R Y     G + +D         
Sbjct: 130 GIVHRIDRDTSGLLIVAKN-DTAHNILAEQIKVHSFTREYMAVVQGVIKEDGTVDAPIGR 188

Query: 157 ---KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKV 212
                  +   +  +          ++    +N  V + L  G+  +I+  +  +    V
Sbjct: 189 HKTDRKKMC--VTTENSREAVTHYFVEQTYRNNTLVRLRLETGRTHQIRVHM-AYIGHPV 245

Query: 213 N 213
            
Sbjct: 246 T 246


>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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 50/224 (22%), Positives = 90/224 (40%), Gaps = 37/224 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR--- 68
           R+ + ++ A   +R  ++++I +  V VN   + + A  V + D I+V   +   L    
Sbjct: 9   RLDRYLSEALSKTRSFIQKIIEEGNVWVNQTQVFKPAYKVRNGDIIKVVIPEPKQLSLVA 68

Query: 69  -------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
                    E   L + +KP G+V      +  +T+ + L   FS          R   V
Sbjct: 69  QDIDIDVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFSGRLSSINGVIRPGIV 128

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------L 158
            RLD +T GLL++  T++  +     L S Q  R+Y     G + +D            +
Sbjct: 129 HRLDKDTSGLLVVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVVDAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N LK  +V  G         L+       +V + L+ G+  +I+
Sbjct: 189 NRLKMAVVPNGKEAVTYFEVLERFDKYT-FVKLRLKTGRTHQIR 231


>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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 84/248 (33%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A   G  SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINGEWSRSQVQQWIKDDVVTVNGKSVK-VNYKVKENDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREIKK 203
             KG  I      D +        +  K +     V        L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 35/252 (13%), Positives = 84/252 (33%), Gaps = 43/252 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+      +  + +R+ + ++      SR  +++++   ++ VN   ++     +   D 
Sbjct: 1   MEQIKFTADR-SGERIDRFLSENLENLSRSYIQKLLKDGKISVNQSSVK-PNYKISENDK 58

Query: 60  IEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IEV   D   L             E + + + +KP  +V   +      T+ + +     
Sbjct: 59  IEVFIPDPEVLDILPENIPLDILYEDSDILIVNKPKNMVVHPAPGHYEHTLVNAVMYHCK 118

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G LL+  +    +++   L      R Y    HG++ 
Sbjct: 119 DNLSGINGILRPGIVHRIDMDTTGSLLICKNDKAHQIIAEQLKEHSITRRYHAIVHGKIK 178

Query: 155 QD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +D                 +      +   +     T+  +     ++   L  G+  +I
Sbjct: 179 EDNGVVNAPIGRHPIDRKKMST--KAKNGKHAVTHYTVLRRFKDYTYIECELETGRTHQI 236

Query: 202 KKVFEFFNWKVN 213
           +         + 
Sbjct: 237 RVHMASIGHPIL 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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 49/224 (21%), Positives = 87/224 (38%), Gaps = 37/224 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ + ++     +R  V+++I +  V VN   + + A  V S D I +            
Sbjct: 9   RLDRYLSEVLSKTRSFVQKIIEEGNVWVNQTQVLKPAYKVRSGDIIRIVIPEPKQLSLVA 68

Query: 63  -DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
            D       E   L + +KP G+V      +  +T+ + L   FS          R   V
Sbjct: 69  QDIDIEVVYEDEHLAVINKPRGMVVHPGAGNFENTLVNALLHKFSGKLSSINGVIRPGIV 128

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------L 158
            RLD +T GLL++  T++  +     L S Q  R+Y     G + +D            +
Sbjct: 129 HRLDKDTSGLLIVAKTDEAHIKLSEALKSHQIKRIYYAICEGVLKEDSGVVDAPIGRHPV 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N LK  ++  G         L+       +V + L+ G+  +I+
Sbjct: 189 NRLKMAVIPNGKQAVTYFEVLERYDKYT-FVKLRLKTGRTHQIR 231


>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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 84/243 (34%), Gaps = 44/243 (18%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL- 67
           +   +R+ KV+A +    SR  ++ +I    VKVNG  +++    +   D + V+  P  
Sbjct: 48  DLDGERLDKVLASSLKDISRSRLKTLIEDGLVKVNGKTVDKPKEKMSFGDEVSVEIKPRL 107

Query: 68  -------------RKAERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRV 108
                           E   + + +KP  LV   +      T+      ++ +     R 
Sbjct: 108 EDMDFIATPMDIDVVYEDDDILVINKPARLVVHPAAGHWDDTLLNGLLAYNPIFRTLPRA 167

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLN------- 159
             V RLD +T GL+++  +      L  +L +    R Y     G+   DK+        
Sbjct: 168 GIVHRLDRDTTGLMVVAKNEKAMLDLVQQLQARTVKREYWALTRGKAPADKVIEAAIERD 227

Query: 160 -----LLKKGIVIQGICYGDMQVTL------DTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                    G   +G         +      + +    +WV   L+ G+  +I+   E  
Sbjct: 228 PRNPLRFTIG---KGGRAKPATTHIRCIDQKEVKGKPFSWVACRLKTGRTHQIRVHMESI 284

Query: 209 NWK 211
              
Sbjct: 285 GLP 287


>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 = 86.8 bits (214), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 93/237 (39%), Gaps = 37/237 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M++   +QE+    R+   +      SR +++ +I    + +NG   + A+V + + D +
Sbjct: 1   MEEIFTLQEDENLIRLDVYLGDKLELSRSKIQSLIESGNISLNGNKAK-ASVKLKTGDTV 59

Query: 61  EVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVF--------- 98
            V+     KA             E   + + +KP G+VT  ++ +   T+          
Sbjct: 60  YVNYQEENKAEIKAQDIALDIVYEDDDVLVVNKPRGMVTHVANGNHEGTLVNALLYYLKD 119

Query: 99  -DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
             +L +   R   V R+D +T GLL++  +   +  L          RVY +  +G +D+
Sbjct: 120 DISLQNGMYRAGIVHRIDKDTSGLLVVAKNDFSSTELTNQLKDHSMTRVYTLICNGVIDE 179

Query: 156 DKL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +          + +K   VI+   Y    +          +    L+ G+  +I+
Sbjct: 180 ETVIEQNIGRNPKDRMKY-CVIEDGKYAHTTIIPLEIFEKYTYAKAILKTGRTHQIR 235


>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 = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 86/253 (33%), Gaps = 45/253 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  +++ +    +R+ K +       SR  +++++    + VNG  ++ A   +   D 
Sbjct: 1   MEQMSLISKK-KGERIDKFLGENLDDLSRSYIQKLLKDGLILVNGKKVK-ANYKLNEGDQ 58

Query: 60  IEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIF 105
           I+V   D  PL  A          E   + + +KP G+V   S      T+ +  L    
Sbjct: 59  IDVEVPDPEPLDIAAENIPLDILYEDEDILIVNKPKGMVVHPSPGHPDHTLVNAILYHCG 118

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQV 153
             +           V R+D+NT G LL+  +   A  +    L      R Y    HG +
Sbjct: 119 EHLSGINGVIRPGIVHRIDMNTTGSLLICKN-DHAHQILAEQLKEHSITRRYHAIVHGSL 177

Query: 154 DQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             D                 +     + G         L+   G+  ++   L  G+  +
Sbjct: 178 KADTGTVNASIGRHPTDRKKMST-KALNGRHAVTHYRVLERL-GNYTYIECELETGRTHQ 235

Query: 201 IKKVFEFFNWKVN 213
           I+         + 
Sbjct: 236 IRVHMASIGHPIL 248


>gi|324995685|gb|EGC27597.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK678]
          Length = 298

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 85/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   ++ VNG   ++A   V   D I      
Sbjct: 5   IESSVAGQRLDKAVAELTDLSRSLANEQIKDGQILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVPEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIQDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHLALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 86.4 bits (213), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 85/248 (34%), Gaps = 42/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M D  ++       R+ K I+     SR  V+ ++    + VNG   E+ +  V + D I
Sbjct: 1   MADFELIVATKAG-RLDKYISEHSDLSRSRVQELLGSGDILVNGKQ-EKPSYKVANNDQI 58

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
            V            + +PL    E   + + +KP G+V   S      T+ + L +    
Sbjct: 59  TVHVPKLVPLNVEPEDIPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTKF 118

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      LE         RVY    HG   + 
Sbjct: 119 LAASPEGFRPGIVHRIDKDTSGLLMIAKNANARTSLESQLAHKTNKRVYLAIVHGNFKEA 178

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                            +    +++G         +  Q    A V+  L  G+  +I+ 
Sbjct: 179 TGTIDAPIARNPKDRKKMA---IVEGGKEAVTHFHVLEQYPGYALVSCQLETGRTHQIRV 235

Query: 204 VFEFFNWK 211
             ++    
Sbjct: 236 HMKYIGHP 243


>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 = 86.4 bits (213), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 86/248 (34%), Gaps = 37/248 (14%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D     V +    +R+   ++R    SR    ++I  ++V+VNG+++ + +  +   +
Sbjct: 1   MSDIRYLPVPDGLANERIDSALSRMLGLSRSAAGKLIDDEKVRVNGVVVAK-SHRLSINE 59

Query: 59  HIEVDGVP--LRKA---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP----- 102
            IE D  P  L+ A         E   L + +KP+G+           TV DNL      
Sbjct: 60  IIEADLEPPALKPAPIVGMDIVYEDEDLVVVNKPVGVAAHGGPGWDGPTVIDNLEAAGFR 119

Query: 103 ----SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R   V RLD+ T G + +         L+      +  + Y     G  D  
Sbjct: 120 ISTSGPPERKGIVHRLDVGTSGAMAVAKSELAYTKLKHAFKERRVHKTYHALVSGHPDPA 179

Query: 157 KL-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           K               +  +V  G        T +   G+ A + + L  G+  +I+  F
Sbjct: 180 KGTIDAPIARHPSKEWRMAVVAGGRPAITHYQTQELLPGA-ALLDITLETGRTHQIRVHF 238

Query: 206 EFFNWKVN 213
                   
Sbjct: 239 SAIGHPCV 246


>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 = 86.4 bits (213), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 87/250 (34%), Gaps = 54/250 (21%)

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----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              D   L             E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  AIPDPEELDILPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREI 201
               KG  I    G    D Q     + G +A      +       L E     G+  +I
Sbjct: 183 ----KG-TIDAPIGRDKKDRQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 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 = 86.4 bits (213), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 85/245 (34%), Gaps = 42/245 (17%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI++++   QR+ K+++      SR +++  I +  VKVNG +++     V   D I V 
Sbjct: 7   NIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKS-NYKVKLNDKIVVT 65

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              +                E   + + +KP G+V   S      T+ + L      +  
Sbjct: 66  EKEVVEADIKPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--- 156
                    V R+D +T GLL++  +    R L  +L S    R Y    HG +  D   
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDYGT 185

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                         +    V+           +         +   L  G+  +I+   +
Sbjct: 186 IDAPIGRNKNDRQAMA---VVDDGKEAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMK 242

Query: 207 FFNWK 211
           +  + 
Sbjct: 243 YIGYP 247


>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 = 86.4 bits (213), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 92/236 (38%), Gaps = 43/236 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           I++E    +R+   I+     SR +V+  +    VKVNG + ++ +  +   D IEVD  
Sbjct: 13  IIEEADAKKRLDVFISEKLNISRSQVKNYLNS--VKVNG-IEKKLSYALKINDKIEVDIK 69

Query: 64  --GVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTV----------F 98
                +                E   L + +KP G+    S  +   T+          F
Sbjct: 70  NSDKEIDIENPKAENISLDIIYEDKYLLVINKPAGMSVHCSASEITGTLVNALLYNIKDF 129

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           D +    SR   + RLD +T G++++  +  +   ++    + +  ++Y     G +  +
Sbjct: 130 DFI-GNKSRAGIIHRLDKDTSGIMIIGKNADIVSSIQEQFKNRKIKKIYHAIVIGVLKDN 188

Query: 157 KLNL---------LKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +          +K + + +        + +  +  ++  + + L+ G+  +I+
Sbjct: 189 YLEINLPIGRHQVYRKKMTVREDGKKALTHIKVLKRFKNHTLIEIDLKTGRTHQIR 244


>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 = 86.4 bits (213), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 97/236 (41%), Gaps = 35/236 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNG-------ILLERAAV 52
           M +K          R+ KV+++     SR ++++ + +  V++NG        ++    +
Sbjct: 1   MTEKKEFTITTETGRIDKVLSQLLPDYSRSQIQQWLKKDLVEINGQTSKGNHKVVADEKI 60

Query: 53  NVMSTDHIEVD----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           +V   D + +D     +PL    E  ++ + +KP G+V   S      T+ + L +    
Sbjct: 61  SVTIPDPVSLDLVPEDIPLDIVYEDDQVLVVNKPQGMVVHPSPGHPNGTLVNALLAHTPL 120

Query: 107 -------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD- 156
                  R   V R+D +T GLL++  TN+   +   +L +   LR Y    HG +++D 
Sbjct: 121 SEINGVFRPGIVHRIDKDTSGLLMVAKTNEAHESLSEQLKAKSNLREYLALVHGNIEEDE 180

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     KL+ +K+ IV  G         ++        +   L  G+  +I+
Sbjct: 181 GTIDAPIGRSKLDRMKQAIVPDGRPAVTHFEVVERFT-DYTLIRCRLETGRTHQIR 235


>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 = 86.4 bits (213), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 88/233 (37%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ ++ +G      +  +  + G  + V + L  G+  +I+    + +  V
Sbjct: 190 RKKQAVIAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIDHPV 241


>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 = 86.4 bits (213), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 89/236 (37%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++       +VL   L + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDAAHQVLTEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|326692704|ref|ZP_08229709.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           argentinum KCTC 3773]
          Length = 308

 Score = 86.4 bits (213), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 86/237 (36%), Gaps = 37/237 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M DK  +       R+  ++A   +  SR  +   +    V VNG  ++R +  V + D 
Sbjct: 1   MTDKITINITDQTGRIDAILANQNLPYSRTVLANWVQSGEVLVNGQRVKR-SYKVAAGDV 59

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +    ++               E   L + +KP G+V   +      T+ + L     
Sbjct: 60  ISIQPPAVQPTEIVAEAMPLDIVYEDADLLVVNKPQGMVVHPAAGHTSGTLVNGLLHHAP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L   L + +  R+Y     G+ +++
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQALSAQLKAHKNDRIYYALVRGEFEEN 179

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       ++  K+ +  +G         +  +      + V L  G+  +I+
Sbjct: 180 TGTINAPIARHAIDRKKQAVQ-EGGREAVTHFEVIARYVGYTLLKVRLETGRTHQIR 235


>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 = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 85/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+ K +A     SR      I + +V VNG  +++A   V   D I+ +   + +     
Sbjct: 11  RLDKALADLTPLSRAVANEQIKEGKVLVNG-TVKKAKYTVKEGDIIQYEVPEVEEVSYEA 69

Query: 71  ---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
                    E   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLVNALLYHIKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMVAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLE-RFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 87/246 (35%), 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--------DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I          D  P               + +KP G+V   +      T+ + L     
Sbjct: 59  ISFVVPEPVVLDIKPENLPLDIVYEDDDLLVVNKPQGMVVHPAAGHPNGTLVNALMYHTE 118

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   L   + LR Y    HG+  ++
Sbjct: 119 LSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEALSADLKDKKNLRQYYALVHGEFSEN 178

Query: 157 K---LNLL-------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           K      L       KK  VI G         +  +      + V L  G+  +I+    
Sbjct: 179 KGTIKAPLGRSKTDRKKQAVIAGGRDAVTHFEVVKRYVGYTLLRVTLETGRTHQIRVHMA 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>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 = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 88/254 (34%), Gaps = 44/254 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K+         R+ + +++     SR E+ + I   +VKVN  +++  +  +   D 
Sbjct: 1   MLKKSYEYHGDQSLRLDRYLSQRLDSYSRSEIAQWIKTGQVKVNKQVVK-PSYRLNPMDK 59

Query: 60  IE----------VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPD-------------- 92
           I           ++G  L      E   L + +K  G+V   S                 
Sbjct: 60  ISLAIEEEQKLPIEGESLDLDIVYEDKDLLVINKAKGMVVHPSKGHLSGTLVNALLAYAQ 119

Query: 93  -GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRF 149
               T+ D     + R   V RLD +T GL+++       + L   L + Q  R Y    
Sbjct: 120 KNHFTLSDL--GDYYRPGIVHRLDKDTSGLMVVAKSDPAYQALLEDLANHQLDRKYLALI 177

Query: 150 HGQVDQDK------LNLL-KKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNR 199
           +G +   +      L    K  +   G   G   VT      Q  + A + + L  G+  
Sbjct: 178 YGHLPDKQGTIDIPLRRHPKDRMRYVGDPLGKEAVTHFKQIAQVENYALLRLSLETGRTH 237

Query: 200 EIKKVFEFFNWKVN 213
           +I+    + +  V 
Sbjct: 238 QIRAHLAYLDHPVV 251


>gi|323210422|gb|EFZ95309.1| 23S rRNA pseudouridylate synthase B [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
          Length = 127

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 33/134 (24%), Positives = 50/134 (37%), Gaps = 11/134 (8%)

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL-GTL 228
                  +     +G N W  V L EG+NRE+++++E    +V+RLIR+ YG   L   L
Sbjct: 1   GPAAFKTIKFSGGEGINQWYNVTLTEGRNREVRRLWEAVGVQVSRLIRVRYGDIPLPKGL 60

Query: 229 LAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
             G   E+        L         V L     S   + +DR  + +       R  K 
Sbjct: 61  PRGGWTELD-------LAQTNYLRGLVELPPETSSKVAVEKDRRRMKAN---QIRRAVKR 110

Query: 289 SSQKNGLSKQKKLA 302
            SQ  G  +     
Sbjct: 111 HSQIAGGRRSGGRN 124


>gi|255024455|ref|ZP_05296441.1| RNA pseudouridine synthase family protein [Listeria monocytogenes
           FSL J1-208]
          Length = 73

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 5/71 (7%)

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLA 230
               ++ +     +   + V ++EGK  ++K++F      V+ L RIS G   L  +L  
Sbjct: 1   CKPARLEI----INPNEIKVTIQEGKFHQVKRMFAARGKTVSYLKRISMGNLPLDESLEL 56

Query: 231 GSTREVSKKIL 241
           G  R +++  L
Sbjct: 57  GEYRPLTETEL 67


>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 = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 84/245 (34%), Gaps = 55/245 (22%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-----------E 61
            R+ K ++     A+R +V++ I    V VNG    +A   +   D I           E
Sbjct: 31  IRIDKFLSEKLANATRNKVQQAIDAGSVLVNGKP-TKANYKIKPMDDIKVMMEKPPRDTE 89

Query: 62  VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
           V    +      E   L + +KP G+V   +  +   T+ + L   F  +          
Sbjct: 90  VYPEKIELDIIYEDKYLLIVNKPAGMVVHPAHGNWSGTLANALVYHFQDLPEMKGNEGRP 149

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++         L          R Y     G+  +D      +G  
Sbjct: 150 GLVHRIDKDTSGLLVIAKQEEAMTHLASQFFHHTIDRTYIALVWGEPKED------EG-T 202

Query: 167 IQGICYGDMQ------VTLDTQKGSNA--------WVT-VGLRE-----GKNREIKKVFE 206
           I+G      +      V  D ++G +A         +  V L +     G+  +I+   +
Sbjct: 203 IEGNVGRSAKNRKVMDVFPDGEQGKHAITHWKVLKRLRYVSLIQCNLETGRTHQIRAHMK 262

Query: 207 FFNWK 211
           +    
Sbjct: 263 YIGHP 267


>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 = 86.0 bits (212), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 86/239 (35%), Gaps = 38/239 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++    E     R+ K ++      SR  ++++I ++ V VNG  ++ A   +   DH
Sbjct: 1   MEERRYTAEKNDLMRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVK-ANYKLSLEDH 59

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V    L++              E   + + +KP G+V   S      T+ + L     
Sbjct: 60  ISVTIPELKEPDILPEQIPLDILYEDEDILVVNKPKGMVVHPSAGHYSGTLVNALMFHCK 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G L++  +    + L   L      R Y    HG + 
Sbjct: 120 DQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLAEQLKDHTITRKYHAIVHGVLK 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +D            +   K  +  +   +      +  +     +V   L  G+  +I+
Sbjct: 180 EDNGTIDAPIGRHPVERKKMSVNYKNGKHAVTHYRVLKRFEKFTYVECQLETGRTHQIR 238


>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 = 86.0 bits (212), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 85/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  L    EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 86.0 bits (212), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 85/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+ K +A     SR      I + +V VNG  +++A   V   D I+ +   + +     
Sbjct: 11  RLDKALADLTPLSRAVANEQIKEGKVLVNG-TVKKAKYTVKEGDIIQYEVPEVEEVSYEA 69

Query: 71  ---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
                    E   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLE-RFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 86/239 (35%), Gaps = 38/239 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++    E     R+ K ++      SR  ++++I ++ V VNG  ++ A   +   DH
Sbjct: 1   MEERRYTTEKNDLMRIDKFLSEKLPDLSRSYLQKLIKEKEVLVNGQPVK-ANYKLSLEDH 59

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V    L++              E   + + +KP G+V   S      T+ + L     
Sbjct: 60  ISVMIPELKEPDILPEQIPLDILYEDEDILVVNKPKGMVVHPSAGHYSGTLVNALMFHCK 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G L++  +    + L   L      R Y    HG + 
Sbjct: 120 DQLSGINGVMRPGIVHRIDMDTTGSLIVCKNDFAHQSLAEQLKDHTITRKYHAIVHGVLK 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +D            +   K  +  +   +      +  +     +V   L  G+  +I+
Sbjct: 180 EDNGTIDAPIGRHPVERKKMSVNYKNGKHAVTHYRVLKRFEKFTYVECQLETGRTHQIR 238


>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 = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 79/241 (32%), Gaps = 35/241 (14%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G +  +    V+    IEV
Sbjct: 8   KSEITATQTGQRLDQTLAELFPDYSRTRIKEWILDGSVTIDGNVSNKPREKVLEGQEIEV 67

Query: 63  DGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            G  L +               E   + + +K  GLV      +   T+ + L      +
Sbjct: 68  -GATLVEETTAKAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHCPGI 126

Query: 109 I------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--------- 151
                   V RLD +T GL+++         L     + +  R Y     G         
Sbjct: 127 ELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVMGSLISGGTVD 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +D+         +V+ G          +  + ++  + + L  G+  +I+        
Sbjct: 187 EPIDRHPTKRTHMAVVLSGKPAMTHFRVAEKFR-AHTRLRLRLESGRTHQIRVHMAHLGH 245

Query: 211 K 211
            
Sbjct: 246 T 246


>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 = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 84/244 (34%), Gaps = 46/244 (18%)

Query: 13  PQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           P R+ K + +  +  A+R +V+  I + RV VNG  ++     + S D I++        
Sbjct: 33  PMRIDKYLTQQ-VENATRNKVQEAITEGRVLVNGKPVKS-NYKIKSCDLIQITFLRPPAP 90

Query: 63  ----DGVPLRK-AERTRLWLYHKPIGLVT-----------THSDPDGRSTVFDNLPSIFS 106
               + +P+    E   L + +K  G+V             ++           L     
Sbjct: 91  EMAPENIPIDIIYEDADLMVVNKEAGMVVHPAFGNWTGTLANAILHHIGNDTGELDCSLQ 150

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL------ 158
           R   V RLD +T GL+++  +    + L       Q  ++Y     G  +          
Sbjct: 151 RPGIVHRLDKDTSGLIIIAKNPLALQRLARQFAQRQVEKIYHALVWGVPEPASGTIKTNI 210

Query: 159 ---NLLKKGIV------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                 +K +       I G         ++  +   + V++ L  G+  +I+   +   
Sbjct: 211 GRSKKNRKVMTTYPFEGIDGKHAITDYAVIEDLRYF-SLVSIKLHTGRTHQIRVHLQHLG 269

Query: 210 WKVN 213
             + 
Sbjct: 270 HPIL 273


>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 = 85.6 bits (211), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 40/231 (17%), Positives = 86/231 (37%), Gaps = 40/231 (17%)

Query: 11  FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---------- 59
           F  +R+ + +  A    SR    ++I +  V+VN  ++E+ +  V   D           
Sbjct: 20  FNKERLDQFLLNATKEESRSYYSKLIKEGLVRVNDKIVEKPSFIVKPYDKITLFLKPKEP 79

Query: 60  --IEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRV 108
             IE D + +    E   + + +K   +V      + R+T+ + L +           R 
Sbjct: 80  LYIEYDKLNITVLYEDDYIIVINKERNMVVHPGPGNFRNTILNALINSINKDEFTDQERP 139

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQ 155
             V RLD  T G+L++     + R L     + Q  + Y    +G            + +
Sbjct: 140 GIVHRLDKETTGVLIIAKSEKIMRKLSEQFKNRQVKKTYLALVYGDVNYKEGFISMPIKR 199

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREGKNREIK 202
            K++  K  + + G      + ++  +        + + V +  G+  +I+
Sbjct: 200 SKIHRQKMEVNLSG-KVAFTEYSVINKGIFEKQIVSLLKVNIFTGRTHQIR 249


>gi|315037134|gb|EFT49066.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
          Length = 310

 Score = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 94/248 (37%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N+  +     R+ KV++      SR ++++ + ++ V VNG  +  A   V + D 
Sbjct: 10  MEQINVTIQTEKG-RIDKVLSEHLPNHSRSQIQQWLKEKHVTVNGETVR-ANYKVTAGDE 67

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +KP  +V   S    + T+ + L     
Sbjct: 68  IVVTIPEPEVLDMVAEDIPLTIVYEDNDVIVVNKPQDMVVHPSAGHPKGTLVNALLHHAD 127

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            + +         V R+D +T GLL++  +      L     +   LR Y    HG +  
Sbjct: 128 HLSAINDVVRPGIVHRIDKDTSGLLMVAKNDQAHESLAKQLKEKTSLRKYVALVHGVIPH 187

Query: 156 DKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           DK               ++   VI+G        T+  +  +   V + L  G+  +I+ 
Sbjct: 188 DKGEINAPIGRSKVDRKMQA--VIEGGKEAVTHFTVLERFDAFTLVELQLETGRTHQIRV 245

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 246 HMKYIGYP 253


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 86/238 (36%), Gaps = 41/238 (17%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            +K I++E+   +R+ K +A     SR  ++ M+    + VNG + +     V   D I 
Sbjct: 3   NEKLIIEESHARERIDKAVAELTGKSRSAIQIMLKSGDITVNGEIAK-PNYKVQVGDEIY 61

Query: 62  V------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNL 101
           +            + +PL    E   + + +KP G+V   S      T+        D+L
Sbjct: 62  LEVREPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDL 121

Query: 102 PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV---- 153
             I  ++    V R+D +T GLL++  +      L   L      R Y    HG +    
Sbjct: 122 SGINGKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQK 181

Query: 154 ---------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     ++    +   +V  G         ++   G    +   L  G+  +I+
Sbjct: 182 GTIEAPIGRAKEDRQKMA--VVRDGKEARTHFEVIERLPGYT-LINCKLDTGRTHQIR 236


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 85/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+ K +A     SR      I + +V VNG  +++A   V   D I+ +   + +     
Sbjct: 11  RLDKALADLTPLSRAVANEQIKEGKVLVNG-TVKKAKYTVKEGDIIQYEVPEVEEVSYEA 69

Query: 71  ---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
                    E   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLDIVYEDQDVVVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L  EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMVAKNDQAHVALAEELKDKKSLRKYWAIVHGNLPNDRGMIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G+   V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLE-RFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>gi|268610335|ref|ZP_06144062.1| pseudouridine synthase rRNA-specific [Ruminococcus flavefaciens
          FD-1]
          Length = 108

 Score = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
           R+ K I+     +R +++ + A+  V VNG  ++R+   + +  D + V G  +  +ER
Sbjct: 4  IRLDKFISERTEYTRSQIKSLCAKGSVTVNGSPVKRSDTKIDTGADDVTVCGNAIS-SER 62

Query: 73 TRLWLYHKPIGLVTTHSDPDGRSTV 97
           R  L +KP G V++  D DG + +
Sbjct: 63 FRYILLNKPKGYVSSTDDKDGETVI 87


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 88/245 (35%), Gaps = 38/245 (15%)

Query: 5   NIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNG---------ILLERAAVNV 54
            + QEN    R+   ++ +    SR  ++R+I + +V VN           + +R AV V
Sbjct: 7   EVDQENAKS-RLDVFLSGQCHDLSRSYIQRLIEEGQVTVNDLPTKANYKLRVGDRVAVEV 65

Query: 55  MSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
              + ++V   P+      E   + + +KP G+V   ++ +   T+ + L      +   
Sbjct: 66  PPAEELQVVPEPIPLDIYYEDNDVIVVNKPRGMVVHPAEGNTSGTLVNALLYHCRDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNL 160
                   V RLD +T GL+++  +      L          R YR   H  + ++++  
Sbjct: 126 NGVLRPGIVHRLDKDTSGLIMVAKNDLAHNSLAQQLKDRTVTRRYRALVHNNI-REEVGT 184

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFF 208
           +   I         M V     K +     V        L E     G+  +I+    + 
Sbjct: 185 VNAPIGRDPRDRQRMAVVERNSKPAVTHYRVLERFGQYTLVECRLETGRTHQIRVHMAYI 244

Query: 209 NWKVN 213
              V 
Sbjct: 245 GHPVV 249


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 86/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 241


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 86/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++   +D  LA   EL   + LR Y    HG +  D           + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEASIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 241


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 81/235 (34%), Gaps = 39/235 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----------RAAV 52
           K  V+E     R+ K +A     SR  V++++   +V V+G +++               
Sbjct: 5   KVEVKETEKGMRIDKFLAEKASKSRSSVQQLLKDGQVTVDGEVVKPNYKCQLGDIVEMEE 64

Query: 53  NVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                  IE + +PL    E   L + +KP G+V   S      T+ + L      +   
Sbjct: 65  RAPEVIEIEAEDIPLDIYYEDEDLLVVNKPEGMVVHPSAGHYTGTLVNALLYHCKDLSGI 124

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQV------- 153
                   V R+D +T GLL++  +      L          R Y    HG +       
Sbjct: 125 NGKIRPGIVHRIDKDTSGLLMVAKNDAAHESLASQLKAKTSHREYVALVHGDIAHQKGTI 184

Query: 154 ------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  +D    +   +V  G         L+ + G    +T  L  G+  +I+
Sbjct: 185 EAPIGRAKDDRQKMA--VVGDGKEARTHFEVLE-RFGDFTLITCQLDTGRTHQIR 236


>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 = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 42/244 (17%), Positives = 93/244 (38%), Gaps = 39/244 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           IV + +   R+ K+I+      SR  ++++I  ++V  NG +++ A+ +V   D I ++ 
Sbjct: 11  IVTDEYDGMRIDKLISELIDSLSRTYIKKLIDDKKVSCNGKVVK-ASFHVSENDEIVMEI 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
            P+                E   + + +KP  +V   +    + T+ + +          
Sbjct: 70  PPIEIPQILPQDIPLDIIYEDNDVVVVNKPKDMVVHPAAGHYKDTLVNAIMYHCKDNLSG 129

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK-- 157
                R   V R+D +T G +++  +    + +   L      RVY    +G + +D+  
Sbjct: 130 INGVMRPGIVHRIDKDTTGSVIICKNDNAHQSIAEQLKEHSINRVYHAICYGVIKEDEGD 189

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEF 207
                   +N  KK  V+ G  Y      +  +   +   ++   L+ G+  +I+     
Sbjct: 190 VTAPIGRSVNDRKKMAVVPGGKYASTHYRVLKRFPEDGFTYIECKLQTGRTHQIRVHMSH 249

Query: 208 FNWK 211
               
Sbjct: 250 IGHP 253


>gi|327470139|gb|EGF15603.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK330]
          Length = 298

 Score = 85.6 bits (211), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 84/241 (34%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I    + VNG   ++A   V   D I      
Sbjct: 5   IESSVAGQRLDKAVAELTDLSRSLANEQIKDGLILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  SEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDFSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 81/233 (34%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VN   +++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKSGQVLVNDQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 86/250 (34%), Gaps = 54/250 (21%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V+E    +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V
Sbjct: 8   TVKEEQKSERIDKFLA--GINNEWSRSQVQQWIKDGVVTVNGNDIK-GNYKVKENDEIAV 64

Query: 63  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  AIPEPEELDIRAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L          R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREI 201
               KG  I    G    + Q     + G NA      +       L E     G+  +I
Sbjct: 183 ----KG-TIDAPIGRDKKERQSMAVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 83/236 (35%), Gaps = 40/236 (16%)

Query: 15  RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           R  KV+A   +A  SR  +++++AQ  V +NG +L + A  V + D + ++  P ++   
Sbjct: 59  RADKVLAEC-VAEFSRSYLQQLLAQGAVTLNGRVLVKPATKVAAGDRMVLEMRPTQQSMA 117

Query: 70  -----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVG 112
                       E   L + +KP GLV   +  +   T+ + L           R   V 
Sbjct: 118 FQPEDMALDVVYEDEHLLVVNKPAGLVVHPAPGNWTGTLLNGLLGRDPKAREVPRAGIVH 177

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDKL 158
           RLD +T GL+++         L   + +    R Y                   + +D  
Sbjct: 178 RLDKDTSGLMVVARSRAAMDALVAMIAARDVSRQYLALAHKAWGPRKHREVDAPIGRDPR 237

Query: 159 NLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           N L+  +V             + L       + V   L  G+  +I+         
Sbjct: 238 NRLRMAVVDLAQHAGKTARTDIDLLAGNEEVSLVRCTLHTGRTHQIRVHMASLGHP 293


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 80/243 (32%), Gaps = 34/243 (13%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAV----NVMS 56
           IV       R+   +      SR  ++ +I    V V G + +              +  
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEGSRSYIQSLIKGGHVTVGGKVGKANLRLTPDTVIRVEIPE 64

Query: 57  TDHIEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
            + IEV  + +PL    E   + + +KP G+V   +  +   T+ + L      +     
Sbjct: 65  PESIEVKPEDIPLDYLYEDHDIVIVNKPRGMVVHPAVGNYSGTLVNALLFHCKDLSGING 124

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK----- 157
                 V RLD +T G++++  +      L          R Y     G + ++K     
Sbjct: 125 EIRPGIVHRLDKDTSGVMMVAKNDAAHIGLAEQVKAHSARRTYWALVQGNIVEEKGTIKA 184

Query: 158 ------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  + +K  +V +          +  + G    V   L  G+  +I+  F +    
Sbjct: 185 PIGRHPKDRMKMAVVFENSKDAVTHFKVLARYGHQTLVECNLETGRTHQIRVHFVYIGHP 244

Query: 212 VNR 214
           V  
Sbjct: 245 VVN 247


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 83/234 (35%), Gaps = 38/234 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VKVN  ++ +    +   + IEV   
Sbjct: 17  VNSEYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIINKNGRKLKLGEKIEVLIP 76

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV- 111
                    + +PL    E     L +K  G+V   +  +   T+ + L    + + SV 
Sbjct: 77  EEENIDIEPENIPLNIVYENDDFILINKSYGMVVHPAYGNYTGTLVNALLYYTNNLSSVN 136

Query: 112 --------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL--- 158
                    RLD +T GL+L+  +      L          + Y     G   ++ L   
Sbjct: 137 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGR 196

Query: 159 -NLL-------KKGIVI--QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              L       +K + I  +          +  Q    + V V +  G+  +I+
Sbjct: 197 IENLIGRDSKDRKKMTIVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIR 250


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 82/233 (35%), Gaps = 42/233 (18%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            +   R+ K ++     A+R  +E++I    VKVN  ++++    + S + IEV      
Sbjct: 15  EYEGMRLDKYLSEQIEEATRSYLEKLIDNNFVKVNSKIIKKNGRKLKSGEKIEVLIPEEE 74

Query: 63  ------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---- 111
                 + +PL    E     + +K  G+V   +  +   T+ + L    + + SV    
Sbjct: 75  NIDIEAENIPLDVVYENDDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSVNGNI 134

Query: 112 -----GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL------ 158
                 RLD +T GL+L+  +      L          + Y     G   ++ L      
Sbjct: 135 RPGIIHRLDKDTSGLILIAKNNFAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGRIEN 194

Query: 159 ---------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +   +V +          +  Q    + V V +  G+  +I+
Sbjct: 195 LIGRDIKDRKKMA--VVKENGKIAISNYRVIEQVEGYSLVEVAIETGRTHQIR 245


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 89/245 (36%), Gaps = 48/245 (19%)

Query: 13  PQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           P R+ + ++R  +  A+R +V+  I   RV VN  +++     + S D IE+        
Sbjct: 33  PMRIDQYLSRQ-VENATRNKVQEAIEDGRVLVNDKVVKS-NYRIKSCDLIEMTFLRPPAP 90

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-----------NLPSIFS 106
               + +P+    E + L + +K  G+V   +  +   T+ +           +L     
Sbjct: 91  ELAPEDIPIAIVYEDSELMVINKEPGMVVHPAFGNWTGTLANAILHHIGENAGSLDESEL 150

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----------- 153
           R   V RLD +T GL+++  +      L       + ++ Y+    G             
Sbjct: 151 RPGIVHRLDKDTSGLIIIAKNPTALHRLAKQFADRKVVKTYKALVWGVPATPEGTIRTNI 210

Query: 154 --DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFF 208
              +    ++      +G       +T    +    W   +++ L  G+  +I+   +  
Sbjct: 211 GRSRKDRKVMAN-FPYEGEEGKTA-ITDYRLEEDLHWFSLLSLTLHTGRTHQIRAHMQHL 268

Query: 209 NWKVN 213
             ++ 
Sbjct: 269 GHQIL 273


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 87/243 (35%), Gaps = 46/243 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMST 57
           IV EN    R+ K +       R++++        ++I + +V VNG  ++  +  +   
Sbjct: 2   IVNENNYYSRLDKFL-------RKQLQNMPLSAIYKIIRKGKVLVNGKRVKEPSFRLEIG 54

Query: 58  DHIEVDGVPLRK------------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           D IE+     +                    E   L + +KP G+          +T+ +
Sbjct: 55  DEIEIKEETTKYNREKNNQIIPIKMDFEILYEDENLLIINKPAGIPIHPGKGTHIATLIE 114

Query: 100 NLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
            L             V RLD +T G+ ++  +   AR L   + S    +VY     G++
Sbjct: 115 GLMYYGKEHNFTPYLVHRLDKHTSGVFVVAKNVNTARELNEIISSRAVEKVYTTLCVGEM 174

Query: 154 DQDKLNLLKKGIVIQGICYGD---MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            + ++      I + G         Q    +  G  + + V ++ G+  +I+K       
Sbjct: 175 KKSEVIK----IPLDGKNAVTIYEKQKQFKSGLGYFSLLRVQIKTGRKHQIRKHLSLIGH 230

Query: 211 KVN 213
            V 
Sbjct: 231 PVI 233


>gi|45644651|gb|AAS73039.1| predicted pseudouridine synthase D, 23S rRNA-specific [uncultured
           marine gamma proteobacterium EBAC20E09]
          Length = 311

 Score = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 87/237 (36%), Gaps = 40/237 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M++K  V +  +  R+ KV   + I     SR ++++ I + RV +N  +       V  
Sbjct: 1   MENKKTVSKEHSKMRLDKV---STIIFEDFSRTQIKKWILEGRVFLNDDIA-SPRDLVHE 56

Query: 57  TDHIEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            D I++D +   K              E     + +K   L+          T+ + L  
Sbjct: 57  GDSIQIDPIAEEKISWVPEEIDIDVIYENDDYLIINKQPNLIMHPGAGCSSGTLANALLH 116

Query: 104 IFSRVI------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---- 151
            +  +        V RLD +T G++L+  +          L   +  ++Y     G    
Sbjct: 117 HYPELKNIARAGIVHRLDKDTSGVILVARNDKFRNYFVDLLQKREVTKLYSAIVVGTIIG 176

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  + +DK N +K  I   G    +  V L    G+ + + + +  G+  +I+
Sbjct: 177 SFKVTDPIGRDKKNRVKMSIRSDG-KESETFVKLKESLGNYSLLDISIMTGRTHQIR 232


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 76/243 (31%), Gaps = 43/243 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+   IA     SR   ER++  + VKVNG + +     V S D I +D       E T
Sbjct: 17  MRLDAYIADNTDISRSFAERLVTDEFVKVNG-VSKPKKYKVKSGDSIVIDVPREEVPELT 75

Query: 74  RLWL-------------YHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVISVGR 113
            + +              +KP G+    +      T+       FD       R   V R
Sbjct: 76  PVKMDIEIIYDCDEFAVINKPAGITVHPAPGHADDTIVNAMLAEFDITDDNDLRPGIVHR 135

Query: 114 LDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ-------------DKL 158
           LD +T GL+++  +     VL          + Y     G+  +                
Sbjct: 136 LDKDTSGLMIVAKNRKSREVLSKVFADRDIDKRYLAVCWGKPKELEFTIEQPIGRHYKDR 195

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK----VNR 214
             +    V +   Y    V +  Q  +     + +  G+  +I+       +     V  
Sbjct: 196 KRMC---VREDGRYSKSGVRVLKQNNNAFLAEIRIFTGRTHQIRVHMSHAGFPLAGDVVY 252

Query: 215 LIR 217
             R
Sbjct: 253 GHR 255


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 93/242 (38%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                     + +P+    E   + + +KP G+V   +      T+ + L    +     
Sbjct: 67  PEPEVLEVVPENIPIEIIYEDEDVAVVNKPRGMVVHPAPGHTTGTLVNALMYHCNDLSSI 126

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
               R   V R+D +T GLL++  +      L  +L +    RVY+   HG         
Sbjct: 127 NGVVRPGIVHRIDKDTSGLLMIAKNDRAHESLVNQLKAKTTERVYQAIVHGNIPHDHGTI 186

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +DK++     +  +         T+  + G   +V   L  G+  +I+  F++  
Sbjct: 187 DAPIGRDKVDRQSMTVTEENSRDAVTHFTVLERFGDFTFVECQLETGRTHQIRVHFKYIG 246

Query: 210 WK 211
           + 
Sbjct: 247 FP 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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 79/233 (33%), Gaps = 46/233 (19%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIE---VD 63
           R+ K +       R +++        ++I + +V VN   ++  + ++   D +E   V+
Sbjct: 13  RLDKFL-------RNQLKDVPLSVIYKLIRKGKVYVNRKRVKDPSFDLEEGDVVELRYVN 65

Query: 64  GVPLRKA-----------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD--NLPSI 104
              L K                  E     + +KP  +          +T+ +       
Sbjct: 66  LENLPKRSEKKDLTPVPMKLDVLYEDDHYLVLNKPPNIAIHPGKGVHVATLIEGLLYYGQ 125

Query: 105 FSRVIS--VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNL 160
                   V RLD  T GLL++  +   AR+L          + Y     G  +    N 
Sbjct: 126 EKGFSPFLVHRLDKETSGLLVVAKNREAARILTELFKGRNIEKEYVTLVRGVPE----NN 181

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +K  I + G       V++   K   + + V +  G+  +I++      + V 
Sbjct: 182 MKITIPLDGQEAVSEIVSVKPLK-DVSLLRVKIHTGRKHQIRRHLSQIGFPVV 233


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 88/246 (35%), Gaps = 41/246 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + DK I  + F  ++    I+     SR  ++++I  + V VNG  ++   V +   D I
Sbjct: 7   ISDKKIRCDVFLSEK----ISNL---SRTSIQKLIKGKLVFVNGKNIK-PNVILEIGDEI 58

Query: 61  EV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
            V   D   +             E   + + +KP  +V   +  + + T+ + L +    
Sbjct: 59  TVSIPDKKEITLVAEDIDLDIVYEDDYIIIINKPRNMVVHPAVGNEKHTLVNALLNHCKL 118

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
                 R   V RLD +T GL++   D      L     + +  + Y    +G       
Sbjct: 119 SMINSERPGIVHRLDKDTTGLIICAKDDETHLKLVEMFANREINKKYLAICNGSFSKENG 178

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +D+ +  K  +  +       +  +       + V V L  G+  +I+  F  
Sbjct: 179 LIDKPIGRDEKDRKKMSVKSKSGKAAITEYNVLISNLKYSLVDVTLHTGRTHQIRVHFSS 238

Query: 208 FNWKVN 213
            N  + 
Sbjct: 239 LNHPII 244


>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 = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 82/239 (34%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV---------- 62
           +R+ K I+     +R + + +I Q+ V V+    + +    V     I V          
Sbjct: 10  ERIDKYISDNSEITRNDAKALIEQEAVYVDDRKFVRKPNYMVREGMVITVLRLLEKESNI 69

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
               +PL  + E   L + +KP GLV   +      T+ + L   F           R+ 
Sbjct: 70  EAVDMPLDIRYEDEYLLILNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDANGLLRLG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  D      L   L + Q  R Y     G            + +D
Sbjct: 130 IVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYLAICEGILPNKTTKINLPIQRD 189

Query: 157 KLNLLKKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             N     I   G   + Y  M  +        + V   L  G+  +I+    +    V
Sbjct: 190 TKNRKLMSIHKDGKSSVTYVHMLKSFYIDNKPYSLVKCELETGRTHQIRVHLAYIKHPV 248


>gi|330685506|gb|EGG97159.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 305

 Score = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 79/236 (33%), Gaps = 44/236 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   N   QR+ KV+       SR +++  I +  VKVN  +++     V   D+I V  
Sbjct: 8   ITDSNHVGQRLDKVLPELNSGWSRSQIQDWIKEDLVKVNDKVVK-PNYKVKQNDNIVVTE 66

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
             + +A             E   + + +KP G+V   S      T+ + L      +   
Sbjct: 67  QEVVEADITPENLNLDIFYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD--- 156
                   V R+D++T GLL++  +  +A       L +    R Y    HG +  D   
Sbjct: 127 NGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMAKSVKRKYIALVHGNIPHDYGT 185

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +    V+           +         +   L  G+  +I+
Sbjct: 186 VDAPIGRNKKDRQAMA---VVDDGKEAVTHFNVLEHFKDYTLIECELETGRTHQIR 238


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 89/249 (35%), Gaps = 43/249 (17%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K +VQE+   +R+   ++  G+    SR  +++ I +  VKVN  +++     +   D I
Sbjct: 6   KILVQEDDAKKRLDVFLS--GVINDLSRSYIQKGIEEGWVKVNERIVK-PHYKLKKGDVI 62

Query: 61  EVD------------GVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
             D             +PL      R + + +KP G+V   +  +   T+ + L      
Sbjct: 63  VADIPSPKPLSLEPENIPLDIIHEDRDIIVVNKPRGMVVYPAPGNYSGTLVNALLYHTKD 122

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQ 155
           +           V RLD +T G++++  +  +A        +     + Y     G + +
Sbjct: 123 LSGINGVMRPGIVHRLDKDTSGVIVVAKN-DMAHRELAMQFKNKLVKKTYLAVVWGNIPE 181

Query: 156 DK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           D+              ++  +  +          +  +     ++ V +  G+  +I+  
Sbjct: 182 DRATIEAPIGRHPAKRVEMAVTAKNGKEAITHFKVLERFEDFTFIEVNIETGRTHQIRVH 241

Query: 205 FEFFNWKVN 213
             F    V 
Sbjct: 242 MSFIGHPVV 250


>gi|238810211|dbj|BAH70001.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 315

 Score = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 78/229 (34%), Gaps = 40/229 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHI--------EVDG 64
           +R+ K I +    SR +++ +I Q  V +N  + + +    V     I        E+  
Sbjct: 18  ERIDKYIGQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLNKEIKI 77

Query: 65  VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
            P+      +       + +KP  LV   S      T+ + L   F           R  
Sbjct: 78  EPVNIPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSNENGLLRPG 137

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----QVDQDKLNLLKK 163
            V R+D +T GLL++  +  +   L       +  R Y     G     + +  L + + 
Sbjct: 138 IVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKINLPIARN 197

Query: 164 GI------VIQGICYGDMQVTLDTQ----KGSNAWVTVGLREGKNREIK 202
            +      V +        V L       K   + V   L+ G+  +I+
Sbjct: 198 TVDRKMMSVHKEGKEAITFVHLLKHFYLDKEPMSLVRCELKTGRTHQIR 246


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 87/250 (34%), Gaps = 54/250 (21%)

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  ---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              D   L             E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  AIPDPEELDILPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREI 201
               KG  I    G    D Q     + G +A      +       L E     G+  +I
Sbjct: 183 ----KG-TIDAPIGRDKKDRQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>gi|325694604|gb|EGD36513.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK150]
          Length = 298

 Score = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 85/241 (35%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLANEQIKDGRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLSNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIEHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 90/265 (33%), Gaps = 56/265 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + I  EN   QR+ + +A+    + SR  ++ +I +  +KV+G L++     + S  
Sbjct: 1   MVTQRITDENALGQRLDQWLAKQYHNVLSRSRLQALIREGYLKVDGQLIKEPKTKLKSNQ 60

Query: 59  HIEV----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            IE+           G  +      E   + + +KP GLV    + +   T+ + L    
Sbjct: 61  IIELTMPALRDAEPSGEAIALDILFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIHHC 120

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS-------TQWLRVYRVR 148
                      R   V RLD NT G++++  +  LA              +   R Y   
Sbjct: 121 GKSLSGIGGVKRPGIVHRLDKNTSGVMVVAKN-DLAHKSLSAQFFDHGRTSALDRRYHAL 179

Query: 149 FHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV----------TLDTQKGSNA 187
             G  +++             N  K+ +V     +    V          T   +    +
Sbjct: 180 IWGSPNRNVWTIDAPVGRSPHNRTKQAVVYNQCLHARHAVTHFSLLEQYGTCADKTPFAS 239

Query: 188 WVTVGLREGKNREIK-KVFEFFNWK 211
            +   L  G+  +I+  +       
Sbjct: 240 LLECRLETGRTHQIRVHM-AHIGHP 263


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 78/240 (32%), Gaps = 35/240 (14%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G + ++    V+    + V
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWILAGSVFIDGEVSDKPRFKVLEGQVVTV 67

Query: 63  DGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            G  L +               E   + + +K  GLV      +   T+ + L      +
Sbjct: 68  -GATLEEETKAQAEAIDLDIIYEDDHILIINKQAGLVVHPGAGNQDGTLMNALLHHCPGI 126

Query: 109 I------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
                   V RLD +T GL+++         L   L + +  R Y     G         
Sbjct: 127 ELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVTGTIISGGTID 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +D+          V+           +  +  ++  + + L  G+  +I+        
Sbjct: 187 EPIDRHPTKR-THMAVVHNGKPAMTHYRVAEKFRAHTRLRLRLESGRTHQIRVHMAHIGH 245


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 88/251 (35%), Gaps = 45/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK   +V E    +R+ K I +  +G+ SR  ++ +++   + VN    +  ++ + + D
Sbjct: 1   MKTFKLVAET-AGERLDKYITQKESGL-SRSFIQELVSSGHILVNNQSAK-PSLRLKTGD 57

Query: 59  HIEVD------------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRST----VFDNL 101
            I ++             +PL    +   L L +KP GL    +      T    V    
Sbjct: 58  TITIEIPPETPSELKAEDIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALE 117

Query: 102 PSIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV- 153
           P +       R   V RLD +T GLLL+  +      L     +    + Y     G++ 
Sbjct: 118 PEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTIRKYYLALVKGELR 177

Query: 154 ------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                       D      +   +V  G         L   +G  + + V L  G+  +I
Sbjct: 178 PAEGFIEAPLGRDPQNRQKIA--VVSDGRHARTGYKVLRYIQGY-SLLEVKLETGRTHQI 234

Query: 202 KKVFEFFNWKV 212
           +  F      V
Sbjct: 235 RVHFAAIGHPV 245


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 83/245 (33%), Gaps = 51/245 (20%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M   +I   E    +R+ K +A      SR +V++ +   +V VNG  ++     +   D
Sbjct: 1   MNQIDITASEEQKSERIDKFLASTENDWSRTQVQQWVKDGQVVVNGSPVKS-NYKIQPGD 59

Query: 59  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 155 QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSN-----AWVT----VGLRE-----GK 197
            D          I    G    D Q    T+ G N       +       L E     G+
Sbjct: 180 HDDG-------TIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGR 232

Query: 198 NREIK 202
             +I+
Sbjct: 233 THQIR 237


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 83/237 (35%), Gaps = 41/237 (17%)

Query: 14  QRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
           QR+ K +   G+    SR  V+R I     +++G+ +  A++ + +   + +D       
Sbjct: 20  QRLDKAL--CGLLPELSRAAVQRAITAGACRIDGMPVATASLKLKAGQAVCLDLPDTANE 77

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--------S 110
                  +    +   L L +KP GL          +T+   L   F R+          
Sbjct: 78  LRAEDEAVDILWQDEHLLLCNKPAGLTVHPCPSCPENTLVQRLLHHFPRLREQEGLRPGV 137

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ-----DKL----- 158
           V RLD +T GLLL+  D      +       +  + Y     G   Q     + L     
Sbjct: 138 VHRLDKDTSGLLLVALDEPTRLRMSEAFARREVHKEYLALVGGVPPQTGTCREPLGRHPT 197

Query: 159 NLLKKGIVIQ--GICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +K  +V +  G      D +V   + +   + V V +  G+  +I+         
Sbjct: 198 AKVKMAVVPENRGGKTAHSDWRVLWSSPRKDFSLVAVRIHTGRTHQIRVHMAHVGHP 254


>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 = 84.8 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 89/236 (37%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VN    ++A   V + D I  +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNDQQ-KKAKYTVQAGDVICFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L + +KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQNIPLDIIYEDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T+    A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 79/239 (33%), Gaps = 36/239 (15%)

Query: 11  FTPQRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
              +R+ + +  A      SR +++R I   +  V+G +    +  + S   +E+     
Sbjct: 23  MRNERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVELAIAPA 82

Query: 63  -------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------R 107
                  +G          L +  KP GL           T+   L   F         R
Sbjct: 83  ATAVEPEEGDLTIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRLVHHFDALRAQEGFR 142

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQ 155
              V R+D +T GLLL+    G+   L          + Y    HG           + +
Sbjct: 143 PGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLALVHGVPPATGEVDAPIGR 202

Query: 156 DKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              + ++  +V  G     + +V     +G  A V V +  G+  +I+       + + 
Sbjct: 203 HPTHKVRMAVVKGGKPARSEWRVLHAAPEGHYALVAVRIHSGRTHQIRVHMAHAGFPLW 261


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEAR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGFT-LINCKLDTGRTHQIR 236


>gi|255022986|ref|ZP_05294972.1| hypothetical protein LmonocyFSL_05005 [Listeria monocytogenes FSL
           J1-208]
          Length = 302

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LIKCKLDTGRTHQIR 236


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 83/242 (34%), Gaps = 46/242 (19%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR-- 68
           +R+ K I+     SR +++ +I Q+ V VN +++ +    V     I V       +   
Sbjct: 10  ERIDKYISNNSEISRNDIKALIEQKAVFVNDVVVNQPKFIVREGQVISVTKLIDKEIHIE 69

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
                     E   L +  KP G+V   +     +T+ + L   F           R   
Sbjct: 70  AQDIDLDIAYEDEHLLVIKKPSGMVVHPAPGHHENTLVNALLFHFKNNLSNENGLLRPGI 129

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELP---STQWLRVYRVRFHGQVDQDKLNL-LKKG 164
           V R+D +T GLL++  TN+      L      +    R Y     G +   K+ L L  G
Sbjct: 130 VHRIDKDTSGLLIVAKTNE---VHQLLSEGFSNKSINRKYFAICDGVLKSKKMKLDLPIG 186

Query: 165 IVIQG--------------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             ++               I   +M  +          V   L  G+  +I+    + N 
Sbjct: 187 RDVKNRQQMSVTNSNSKHAITNLEMLKSFYFDNQPKCLVKATLETGRTHQIRVHCAYINN 246

Query: 211 KV 212
            +
Sbjct: 247 PI 248


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 46/221 (20%), Positives = 83/221 (37%), Gaps = 33/221 (14%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           +R+ +V+ + AG  SR  ++ +I    V+V+G     A+  V +   +EV+ VP  +   
Sbjct: 28  ERLDRVLVSIAGEFSRSHLQHLIELGHVRVDGQPASTASRRVKAGQRVEVELVPTDESRA 87

Query: 70  -----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVG 112
                       E   L +  KP GLV   +  +   T+ +         +   R   V 
Sbjct: 88  FRPQPMALAILYEDEHLLVLDKPAGLVVHPAPGNWSGTLLNGLLAHHAAAATLPRAGIVH 147

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG---------QVDQDKLNLL 161
           RLD +T G++++         L     +    R Y    HG          V +D ++ +
Sbjct: 148 RLDKDTSGVMMVGKSLPAVTALVRDIAARDVHRRYLALAHGAVATQRIDAPVGRDPVSRV 207

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  +V  G       V    Q    + V   L  G+  +I+
Sbjct: 208 RMAVVASGKPART-DVECLAQHDGVSAVRCTLHTGRTHQIR 247


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 46/227 (20%), Positives = 88/227 (38%), Gaps = 38/227 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QR+ K +A      SR  +++++ Q  V++NG  +++ A  V + D I V+  P ++++ 
Sbjct: 39  QRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKAGDRIAVEMRPTQQSQA 98

Query: 73  TR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVG 112
            R              + + HKP GLV   +  +   T+ + L           R   V 
Sbjct: 99  FRPEQWPLDVVYEDEHILVIHKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQVPRAGIVH 158

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDKL 158
           RLD +T GL+++         L   + + +  R Y                H  + +D  
Sbjct: 159 RLDKDTSGLMVVARSRSAMDALVRMIAAREVSRQYVALGWGGWTGAAHRSVHAPIGRDPR 218

Query: 159 NLLKKGIV-IQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
           N L+  +V +      + +   D    +     V   L  G+  +I+
Sbjct: 219 NRLRMAVVDLAQHPGKEARTDFDLIDANEEVCLVRCTLHTGRTHQIR 265


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 79/239 (33%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  I  E    QR+ K ++ +  A SR +++  I +  VKVN  +++     V   DHI 
Sbjct: 5   EFKITDERRVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKS-NYKVKLNDHII 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S      T+ + L      +
Sbjct: 64  VTEKEVVEADIQPEDLDLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D +T GLL++  +  +A       L +    R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKN-DIAHRGLVEQLMNKSVKRKYTALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         +   L  G+  +I+
Sbjct: 183 YGTVDAPIGRNKNDRQAMA---VVDDGKEAVTHFNVLEHFKDYTLIECELETGRTHQIR 238


>gi|294786018|ref|ZP_06751305.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
 gi|294486355|gb|EFG33718.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_27]
          Length = 316

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 86/235 (36%), Gaps = 40/235 (17%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVN----------V 54
           V   +   R+ K ++   I  A+R  +E++I    VK+N  ++ +              +
Sbjct: 12  VSSEYEGMRLDKYLSEQ-IEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEISI 70

Query: 55  MSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSI 104
              ++I+++   +      E     + +K  G+V   +  +   T+        +NL SI
Sbjct: 71  PEEENIDIEAENISLDIVYENDDFIVINKSYGMVVHPAYGNYSGTLVNALLYYTNNLSSI 130

Query: 105 FSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL-- 158
              +    + RLD +T GL+L+  +      L          + Y     G   ++ L  
Sbjct: 131 NGNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNG 190

Query: 159 ---NLLKKG--------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              NL+ +G        +V +          +  Q    + V + +  G+  +I+
Sbjct: 191 RIENLIGRGSKDRKKMAVVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIR 245


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 79/240 (32%), Gaps = 50/240 (20%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ K +A      SR +V++ I    + VNG  ++     V   D I V          
Sbjct: 16  ERIDKFVASVNHEWSRTQVQQWIKDGVITVNGKTVK-GNYKVKENDEITVTVPEPEELDI 74

Query: 63  ---DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
              D       E   + + +KP G+V   +      T+ + L    + +           
Sbjct: 75  RAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMYHCTDLSGINGVMRPGI 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           V R+D +T GLL++  +      L          R Y+   HG +  D      KG  I 
Sbjct: 135 VHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYQAIVHGVIPHD------KG-TID 187

Query: 169 GICYGDMQ-----VTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWK 211
                D +        +  K +     V        L E     G+  +I+   ++  + 
Sbjct: 188 APIARDKKDRQSMAVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIGYP 247


>gi|284007738|emb|CBA73551.1| 23S rRNA pseudouridine synthase D [Arsenophonus nasoniae]
          Length = 325

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 85/234 (36%), Gaps = 31/234 (13%)

Query: 9   ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           E+   QR+ + +A      SR  ++  I   RV VNG ++ R    V  ++ I +D    
Sbjct: 13  ESQLGQRLDQALAELFPDYSRSRIKEWILDNRVLVNGKIINRPKEKVFGSEQIAIDVLIE 72

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                    +PL    E   + + +KP  LV      +   TV + L   +  +I     
Sbjct: 73  EDMRWQPQNIPLNIVYEDDEILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIINVPRA 132

Query: 110 -SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKLNLL 161
             V RLD +T GL+++         L   L   +  R Y    +G++       + +   
Sbjct: 133 GIVHRLDKDTTGLMVIAKTIPAQTHLVEALQRREITREYEAVVNGRMTAGGTVDEPIARH 192

Query: 162 ---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  + I  +    +    +     ++  + + L  G+  +I+      N  
Sbjct: 193 PTKRTHMAIHPMGKPAITHYRVMEHFRAHTRLRLRLESGRTHQIRVHMAHINHP 246


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 82/236 (34%), Gaps = 42/236 (17%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K +++    A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKLKLGEKIEVSIP 71

Query: 63  --DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
             + + +           E     + +K  G+V   +  +   T+        +NL SI 
Sbjct: 72  KEENIDIEAENISLDIVYENDDFIVINKSYGMVVHPAYGNYSGTLVNALLYYTNNLSSIN 131

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL--- 158
             +    + RLD +T GL+L+  +      L          + Y     G   ++ L   
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGR 191

Query: 159 ------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +V +          +  Q    + V + +  G+  +I+
Sbjct: 192 IENLIGRDSKDRKKMA--VVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIR 245


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 85/245 (34%), Gaps = 42/245 (17%)

Query: 5   NIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           NI++++   QR+ K+++      SR +++  I +  VKVNG +++     V   D I V 
Sbjct: 7   NIIEQSQVGQRIDKLVSDLNKDWSRSQLQDWIKEGLVKVNGKVIKS-NYKVKLNDKIVVT 65

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              +                E   + + +KP G+V   S      T+ + L      +  
Sbjct: 66  EKEVVEADIKPENLNLDIYYEDEDVAVVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--- 156
                    V R+D +T GLL++  +    R L  +L S    R Y    HG +  D   
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDVAHRHLVEQLMSKTVKRKYTALVHGNIPHDYGT 185

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                         +    V+           +         +   L  G+  +I+   +
Sbjct: 186 IDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMK 242

Query: 207 FFNWK 211
           +  + 
Sbjct: 243 YIGYP 247


>gi|291484098|dbj|BAI85173.1| hypothetical protein BSNT_02552 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 303

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 86/245 (35%), Gaps = 51/245 (20%)

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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 155 QDKLNLLKKGIVIQ---GICYGDMQ---VTLDTQKGSNAW--VT----VGLRE-----GK 197
            D          I    G    D Q   VT D +     +  +       L E     G+
Sbjct: 180 HDDG-------TIDAPIGRDKKDRQSMTVTRDGKSAVTHFHVLERFQDFTLVECQLETGR 232

Query: 198 NREIK 202
             +I+
Sbjct: 233 THQIR 237


>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 = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 79/239 (33%), Gaps = 36/239 (15%)

Query: 11  FTPQRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
              +R+ + +  A      SR +++R I   +  V+G +    +  + S   +E+     
Sbjct: 23  MRNERLDRFLGEALSHTDLSREKIKRAIRDGQCTVDGTVCTTPSTRLRSGQRVELAIAPA 82

Query: 63  -------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------R 107
                  +G          L +  KP GL           T+   L   F         R
Sbjct: 83  ATAVEPEEGDLTIIHRDEHLLVIDKPAGLTVHPCPSCPEGTLVHRLVHHFDALRAQEGFR 142

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQ 155
              V R+D +T GLLL+    G+   L          + Y    HG           + +
Sbjct: 143 PGIVHRIDKDTSGLLLVALSEGVRLKLSEAFAERTVEKEYLALVHGVPPATGEVDAPIGR 202

Query: 156 DKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              + ++  +V  G     + +V     +G  A V V +  G+  +I+       + + 
Sbjct: 203 HPTHKVRMAVVKGGKPARSEWRVLHAAPEGHYALVAVRIHSGRTHQIRVHMAHAGFPLW 261


>gi|319777728|ref|YP_004137379.1| pseudouridine synthase [Mycoplasma fermentans M64]
 gi|318038803|gb|ADV35002.1| Pseudouridine synthase [Mycoplasma fermentans M64]
          Length = 307

 Score = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 78/229 (34%), Gaps = 40/229 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHI--------EVDG 64
           +R+ K I +    SR +++ +I Q  V +N  + + +    V     I        E+  
Sbjct: 10  ERIDKYIGQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLNKEIKI 69

Query: 65  VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
            P+      +       + +KP  LV   S      T+ + L   F           R  
Sbjct: 70  EPVNIPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSNENGLLRPG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----QVDQDKLNLLKK 163
            V R+D +T GLL++  +  +   L       +  R Y     G     + +  L + + 
Sbjct: 130 IVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKINLPIARN 189

Query: 164 GI------VIQGICYGDMQVTLDTQ----KGSNAWVTVGLREGKNREIK 202
            +      V +        V L       K   + V   L+ G+  +I+
Sbjct: 190 TVDRKMMSVHKEGKEAITFVHLLKHFYLDKEPMSLVRCELKTGRTHQIR 238


>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 = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 83/237 (35%), Gaps = 36/237 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++ I   N    R+ + +A+    SR +VE ++    V V+G    +  V +   + I
Sbjct: 1   MNERKIFH-NTEMARLDQALAKLLGESRNQVEALVRGGNVWVDGEKSSKGGVKLKGGERI 59

Query: 61  EVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--- 104
           EV+   LR+              E     + +KP G V   +     +T+ D L      
Sbjct: 60  EVEIPLLRENPAMEVEFEVEILHEEEHFIVLNKPSGAVVHGAPSVKEATLVDWLKKKGIS 119

Query: 105 ------FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V RLD  T G +++       R L   L      R Y       + +D
Sbjct: 120 LSTLNGEERHGIVHRLDKETSGAIVIAKSNEAHRRLSLQLQEKSMGRYYLAIIDHPLKED 179

Query: 157 KL----------NLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTVGLREGKNREIK 202
           +           + LK   V  G       V L ++  GS   +   L  G+  +I+
Sbjct: 180 QRVECYLGRHPHHRLKIAKVPVGRYAKSAFVKLEESIDGSKELIAAKLFTGRTHQIR 236


>gi|308190331|ref|YP_003923262.1| pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307625073|gb|ADN69378.1| pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 307

 Score = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 78/229 (34%), Gaps = 40/229 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHI--------EVDG 64
           +R+ K I +    SR +++ +I Q  V +N  + + +    V     I        E+  
Sbjct: 10  ERIDKYIGQNSELSRNDIKELIEQGAVYINDNVQVHKCNYIVREGQEITIVKLLDKEIKI 69

Query: 65  VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
            P+      +       + +KP  LV   S      T+ + L   F           R  
Sbjct: 70  EPVNIPLDIKYEDDDLVIINKPSNLVVHPSPGHYNDTLVNGLLYHFKNNLSNENGLLRPG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----QVDQDKLNLLKK 163
            V R+D +T GLL++  +  +   L       +  R Y     G     + +  L + + 
Sbjct: 130 IVHRIDKDTSGLLIIAKNNKMHNSLTDMLKRHEIERSYLAIVRGLIENPLTKINLPIARN 189

Query: 164 GI------VIQGICYGDMQVTLDTQ----KGSNAWVTVGLREGKNREIK 202
            +      V +        V L       K   + V   L+ G+  +I+
Sbjct: 190 TVDRKMMSVHKEGKEAITFVHLLKHFYLDKEPMSLVRCELKTGRTHQIR 238


>gi|321315311|ref|YP_004207598.1| pseudouridylate synthase [Bacillus subtilis BSn5]
 gi|320021585|gb|ADV96571.1| pseudouridylate synthase [Bacillus subtilis BSn5]
          Length = 303

 Score = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 84/245 (34%), Gaps = 51/245 (20%)

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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVTVTVPEPEALDVLAEPLDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 155 QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSN-----AWVT----VGLRE-----GK 197
            D          I    G    D Q    T+ G N       +       L E     G+
Sbjct: 180 HDDG-------TIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGR 232

Query: 198 NREIK 202
             +I+
Sbjct: 233 THQIR 237


>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 = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 84/248 (33%), Gaps = 39/248 (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-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I V   P+                E   + + +KP G+V   +      T+ + L    
Sbjct: 60  EISVTEKPVEEVDLVAQDLGLEIYYEDKDVAIVYKPKGMVVHPAPGHPDGTLVNGLMHAI 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQV 153
           + +           V R+D +T GLL++  +  +A       L      R Y    HG +
Sbjct: 120 TDLSGINGEIRPGIVHRIDKDTSGLLMIAKN-DIAHRGLVDQLVDKSVTRKYTALVHGVI 178

Query: 154 DQDK----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
             +               ++  ++    +      +         V   L  G+  +I+ 
Sbjct: 179 PHEFGTIDAPIGRNQKDRQEMAIVDNGKHAVTHFNVLETFDKYTLVECVLETGRTHQIRV 238

Query: 204 VFEFFNWK 211
             +   + 
Sbjct: 239 HMKHIGFP 246


>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 = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 84/245 (34%), Gaps = 51/245 (20%)

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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVTVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTAVVHGLIS 179

Query: 155 QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSN-----AWVT----VGLRE-----GK 197
            D          I    G    D Q    T+ G N       +       L E     G+
Sbjct: 180 HDDG-------TIDAPIGRDKKDRQSMTVTRDGKNAVTHFHVLERFQDFTLVECQLETGR 232

Query: 198 NREIK 202
             +I+
Sbjct: 233 THQIR 237


>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 = 84.5 bits (208), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 85/233 (36%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG  +++A   V   D +              
Sbjct: 11  RLDKALSDLSELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++   +D  L    EL   + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDDAHLVLAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 241


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 82/234 (35%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  +    V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDEITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L         LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKPAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 40/82 (48%), Gaps = 4/82 (4%)

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           +++G+ I G      ++     + +    ++ L +G NR+I+++ + F + V +L RI  
Sbjct: 1   MERGVEILGQVTKPCKLK----RINENTYSIILTQGLNRQIRRMSKVFGFNVVKLERIRI 56

Query: 221 GPFQLGTLLAGSTREVSKKILR 242
               L  +  G  R ++++ + 
Sbjct: 57  LNITLEDIEYGKWRYINREEIE 78


>gi|313623251|gb|EFR93499.1| ribosomal large subunit pseudouridine synthase D [Listeria innocua
           FSL J1-023]
          Length = 297

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 2   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIRYEAR 60

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 61  EPEELEILAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 120

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 121 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 180

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         ++   G    +   L  G+  +I+
Sbjct: 181 APIGRAKEDRQKMA--VVRDGKEARTHFEVIERLPGYT-LINCKLDTGRTHQIR 231


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/260 (19%), Positives = 91/260 (35%), Gaps = 46/260 (17%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           TP R+   +A+  +  A+R +V+  IA+ RV VNG  ++     + S D IEV       
Sbjct: 32  TPMRIDVYLAQQ-VENATRNKVQEAIAEHRVLVNGKTIKS-NYRIKSLDSIEVTFLRPPA 89

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-----------NLPSIF 105
                + +P+    E   L + +K   +V   +  +   T+ +           +L    
Sbjct: 90  PELAPEDIPIDIIYEDEDLMVVNKASDMVVHPAFGNWTGTLANAILHHIGKEAGDLDCSD 149

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK-LNLLK 162
            R   V RLD NT GL+++  +      L     + Q  + Y+    G  +    L    
Sbjct: 150 MRPGIVHRLDKNTSGLIIIAKNSTALHRLARQFANRQVEKKYQAIVWGVPEPATGLIKTN 209

Query: 163 KG-------------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            G                +       +  +       + V V L  G+  +I+   +   
Sbjct: 210 IGRSVRNRKVMTSYPFEGKDGKTAITEYRVQQSLCYFSLVEVTLHTGRTHQIRVHMQHLG 269

Query: 210 WKVNRLIRISYGPFQLGTLL 229
             +  L   +YG   +  L 
Sbjct: 270 HPI--LGDETYGGSSIRNLP 287


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 88/246 (35%), Gaps = 38/246 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K+  IV E    +R+ K +A   +  SR  ++ +I +  +KVN    +     + + D I
Sbjct: 3   KNVFIVDEKDRGERIDKYLAEIFVDKSRSFIQGLIEKDDIKVNNKTPKS-NYKLRALDEI 61

Query: 61  EV-----DGVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           EV     + + +   E     LY        +KP G+V   +  +   T+ + L      
Sbjct: 62  EVTFSEPEVLRVEAEEIPINILYEDKDVVVVNKPQGMVVHPAPGNYNGTLVNALLYHCKD 121

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----- 151
           + S         V R+D +T G+L++  +      L          R Y     G     
Sbjct: 122 LSSINGIIRPGIVHRIDKDTSGVLVVAKNDEAHNKLSDQLKDHSMKREYYALVEGRLKND 181

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  + ++K + LK GIV +G         +  +      +   L  G+  +I+   
Sbjct: 182 KGIIDKPLARNKRDRLKIGIV-EGGKRAVTHYEVLERFNGYTLIKCILETGRTHQIRVHM 240

Query: 206 EFFNWK 211
               + 
Sbjct: 241 ASIGFP 246


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 87/234 (37%), Gaps = 39/234 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V+E+    R+   +A   +  SR  ++++I  ++V VNG  +E+A   V   D I ++ 
Sbjct: 13  LVEEDEDGDRLDVYLADQFVDMSRSYIQKIIKDKKVTVNGK-VEKAKYLVKEEDKIVIEI 71

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +P+    E   + + +KP G+V   +  +   T+ + +          
Sbjct: 72  PKPKVLEVVPQDIPIEIVYEDDDIIIVNKPQGMVVHPAPGNYEGTLVNAILYHCKGNLSS 131

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYR-----------VR 148
                R   V R+D +T G+L++  +      L   L      R Y            V 
Sbjct: 132 INGVIRPGIVHRIDKDTSGILMIAKNNNAHNCLAEQLKDHSITREYEFICHSVFKEDNVT 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + ++  + LK  IV  G         ++   G    V   L  G+  +I+
Sbjct: 192 VDRPIGRNPKDRLKMAIVPNGKRAVTHFEVIERFNGYTH-VRARLETGRTHQIR 244


>gi|254994200|ref|ZP_05276390.1| hypothetical protein LmonocytoFSL_15395 [Listeria monocytogenes FSL
           J2-064]
          Length = 296

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 82/236 (34%), Gaps = 42/236 (17%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K +++    A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VSSEYEGMRLDKYLSKQIEEATRSYLEKLIDNNYVKINSKVINKNGRKLKLGEKIEVSIP 71

Query: 63  --DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
             + + +           E     + +K  G+V   +  +   T+        +NL SI 
Sbjct: 72  KEENIDIEAENISLDIVYENDDFIVINKSYGMVVHPAYGNYSGTLVNALLYYTNNLSSIN 131

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL--- 158
             +    + RLD +T GL+L+  +      L          + Y     G   ++ L   
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGR 191

Query: 159 ------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +V +          +  Q    + V + +  G+  +I+
Sbjct: 192 IENLIGRDSKDRKKMA--VVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIR 245


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 48/233 (20%), Positives = 91/233 (39%), Gaps = 37/233 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ K+I A     +R +V++ +    V VNG  ++ A   V + D + V   +  PL+  
Sbjct: 13  RIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVK-ANFKVTAGDVVTVTIPEVKPLKAV 71

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS--VG 112
                     E  ++ + +KP G+V   +      T+ +       LP I   +    V 
Sbjct: 72  AEPIPLEIVYEDDQVIVVNKPQGMVVHPAPGHPDGTLVNGLLYHTKLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  T    L+   +L +   +R Y    HG   +D+            +
Sbjct: 132 RIDKDTSGLLMVAKTEAAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++ +V  G         L+    +   V   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVADGRHAVTHFQVLERFT-NYTLVKCILDTGRTHQIRVHMAYIHHPV 243


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKSGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 38/243 (15%), Positives = 76/243 (31%), Gaps = 34/243 (13%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RAAVNVMS 56
           IV       R+   +      SR  ++ +I    V V G + +            V +  
Sbjct: 5   IVSAEQEGMRLDVFLTEQMEGSRSYIQSLIKGGHVIVGGKVGKANLRLTPNMVIQVEIPE 64

Query: 57  TDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
            + +EV    +      E   + + +K  G+V   +  +   T+ + L      +     
Sbjct: 65  PESVEVKPEDIPLDVLYEDHDIIIVNKARGMVVHPAVGNYSGTLVNALLFHCKDLSGING 124

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK----- 157
                 V RLD +T G+++   +      L     +    R Y     G + ++K     
Sbjct: 125 EIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAKRTYWALVQGNIVEEKGTIKA 184

Query: 158 ------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  + +K  +V +          +  + G    V   L  G+  +I+  F      
Sbjct: 185 PIGRHPKDRMKMAVVFENSKDAVTHFRVLERYGHQTLVECNLETGRTHQIRVHFAHIGHP 244

Query: 212 VNR 214
           V  
Sbjct: 245 VVN 247


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 91/263 (34%), Gaps = 60/263 (22%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           RV K +       R+ ++        + +   +VK+NG  ++  +  +   D IE+    
Sbjct: 29  RVDKFL-------RKMLKNVPLSAIYKFLRTGKVKINGKKVKDPSTKLNIGDVIELIEES 81

Query: 67  LRKAERTR------------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           L    R                    +   +KP G+         + ++ + L       
Sbjct: 82  LDNYSREYLELKPVKMDLDIIYEDELIIAINKPAGVSVHPGKNVNKPSIIEGLIHYGKEN 141

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                 V RLD  T G+L++  D  +AR L   + S    ++Y     G+V +  +N   
Sbjct: 142 GFEPFLVHRLDKETSGVLIVAKDRSVARELSEIISSRNVEKIYNALVFGKVQKVTINT-- 199

Query: 163 KGIVIQGICYGDM-------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
               I G             +V L+      +++ V +  G+  +I+K     N  +   
Sbjct: 200 ---PIDGQDAVSHIIPIEYFRVKLNGISVELSFLEVEIETGRKHQIRKHLSSINCPIVGD 256

Query: 216 IRISYGPFQLGTLLAGSTREVSK 238
               YG F+L        RE SK
Sbjct: 257 K--DYGNFRLN-------REFSK 270


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 82/234 (35%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  +    V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDDITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L         LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKPAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 87/233 (37%), Gaps = 38/233 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I+ EN    R+   I+ +    SR  ++++I +  VKVNG   +++   +   D + V+ 
Sbjct: 7   IIHENLVNCRLDVFISNSLEGKSRSYIQKLIQEGHVKVNGKD-KKSNYKLKLHDSVIVNN 65

Query: 65  -----VPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                  +           E   + + +KP G+V   +  +   T+ + L          
Sbjct: 66  IENEFQKINPENIDLDILYEDKDIIVINKPQGMVVHPATSNYSGTLVNGLLYHCDTLSTL 125

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--- 157
           +  +R   V R+D +T G+L++  +     VL     +    R Y     G + +D    
Sbjct: 126 NDDTRPGIVHRIDKDTSGVLVVAKNNKAHEVLAEQLKEHSMKREYIALVEGILKKDNGFI 185

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +K  +V +G         +  +   N  V   L  G+  +I+
Sbjct: 186 DKPLGRNPKDRIKMAVVQEGKNAITH-YEVLKRFKKNTLVKCILETGRTHQIR 237


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 86/243 (35%), Gaps = 33/243 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K    V E+   QR+ + +A      SR  ++  I  +RV VNG+++++    V+ ++ 
Sbjct: 5   VKLNATVSESQLGQRLDQALAELFPDYSRSRIKEWILDRRVTVNGVIIDKPKEKVLGSEQ 64

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +D             +PL    E   + + +KP GLV      +   TV + L   F 
Sbjct: 65  IAIDAEIEEEARWEAQDIPLDIVYEDEDILVINKPRGLVVHPGAGNPDGTVLNALLHHFP 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------R 148
                 R   V RLD +T GL+++         L   L   +  R Y             
Sbjct: 125 AIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVESLQLREITREYEAVAIGRMTAGGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +         +   G         ++  +  +  + + L  G+  +I+      
Sbjct: 185 VDEPISRHSTKRTHMAVHPTGKPATTHYRIMEHFRV-HTRLRLRLETGRTHQIRVHMAHI 243

Query: 209 NWK 211
           N  
Sbjct: 244 NHP 246


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 93/265 (35%), Gaps = 56/265 (21%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           K  + +    +RV K +++    SR ++E++I    V VN   +++  V + + D ++V+
Sbjct: 3   KRFISDKN--ERVDKFLSQKLNVSRNQIEQLIKNSLVSVNSKTIKKGGVKLQAGDTVDVE 60

Query: 64  ---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP------ 102
                           +P+   +   L + +KP G+V   +     +T+ D L       
Sbjct: 61  IKEAESSKEDYEVNFDIPVLYEDEDVLVI-NKPPGIVVHPAPSVKEATLVDWLKTKNYRL 119

Query: 103 ---SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYR----------V 147
              +   R   V R+D  T G L++  +      L   L      R Y           V
Sbjct: 120 STIAGEERFGIVHRIDKETSGALIIAKNNKAHEFLSAQLKDKTMGRYYIMLLNEPLKEAV 179

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + ++  N LK   V  G     + V +     +    T     G+  +I+     
Sbjct: 180 CVDKPIARNPKNRLKMAYVKNGREAKTLFVPVYENVAAAKLFT-----GRTHQIR----- 229

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGS 232
                  +   + G + LG  L G 
Sbjct: 230 -------VHLSTIGRYILGDTLYGK 247


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMEKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIRYEAR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEILAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         ++   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVIERLPGYT-LINCKLDTGRTHQIR 236


>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 = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 82/234 (35%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  +    V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDEITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALIYHIKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L         LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKPAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 86/248 (34%), Gaps = 50/248 (20%)

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  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                      D       E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKK 203
             KG  I    G    + Q     + G NA      +       L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEIR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 82/237 (34%), Gaps = 31/237 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV VNG  + +    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILEDRVTVNGKKVTKPKEKVLGGEAIAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
               +A             E T + + +KP  LV      +   TV + L   +      
Sbjct: 70  QIEEEARWLPQDIALDIVYEDTDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPAIIDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-----DKL 158
            R   V RLD +T GL+++         L   L + +  R Y     G +       + +
Sbjct: 130 PRCGIVHRLDKDTTGLMVVAKSVPAQTHLVTALQAREITREYEAVAIGTMTAGGTVNEPI 189

Query: 159 NLL---KKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  + +            +     ++  + + L  G+  +I+      N  
Sbjct: 190 ARHSTKRTHMAVHPTGKPATTHYRIMEHFRAHTRLRLRLESGRTHQIRVHMAHINHP 246


>gi|255522642|ref|ZP_05389879.1| hypothetical protein LmonocFSL_15771 [Listeria monocytogenes FSL
           J1-175]
          Length = 279

 Score = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 84/241 (34%), Gaps = 33/241 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L     + Q +R Y     G          
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247

Query: 212 V 212
           V
Sbjct: 248 V 248


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 83/235 (35%), Gaps = 38/235 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ + +       SR  ++++++Q  V +NG    +AA  V + D + V+  P  +++  
Sbjct: 59  RLDRALVDLVPEFSRSYLQQLLSQGLVALNGQQATKAAARVKAGDTLTVEMRPTLQSQAF 118

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGR 113
           R              L + +KP GLV   +  +   T+ + L        +  R   V R
Sbjct: 119 RPEALPIDVVYEDAHLLVVNKPAGLVVHPAPGNWGGTLLNGLLARDAKAQLVPRAGIVHR 178

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR------------FHGQVDQDKLN 159
           LD +T GL+++  D      L   + +    R Y                   + +D  N
Sbjct: 179 LDKDTSGLMVVARDRTTMDALVRMIAARTVHRQYLAIAHRPWTGVPNRAVQAPIGRDPRN 238

Query: 160 LLKKGIV-IQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            L+  +V +        +  +          WV   L  G+  +I+         
Sbjct: 239 RLRMAVVNLDTHAGKPARTDIRWLAGNDLGCWVECTLHTGRTHQIRVHMASLGHP 293


>gi|46191229|ref|ZP_00206720.1| COG1187: 16S rRNA uridine-516 pseudouridylate synthase and
          related pseudouridylate synthases [Bifidobacterium
          longum DJO10A]
          Length = 329

 Score = 83.7 bits (206), Expect = 4e-14,   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|126727906|ref|ZP_01743733.1| RNA pseudouridylate synthase [Rhodobacterales bacterium HTCC2150]
 gi|126702798|gb|EBA01904.1| RNA pseudouridylate synthase [Rhodobacterales bacterium HTCC2150]
          Length = 102

 Score = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 6/80 (7%)

Query: 74  RLWLYHKPIGLVTTHSDPD----GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           ++ L++KP G+++  +D       R+T+   +      V + GRLD ++EGLL+LT+DG 
Sbjct: 25  QVILFNKPFGVLSQFTDKGTQGSERATLSKFID--VPNVYAAGRLDRDSEGLLVLTDDGK 82

Query: 130 LARVLELPSTQWLRVYRVRF 149
           L   +  P  +  + Y V+ 
Sbjct: 83  LQAKIAHPKNKMPKTYWVQV 102


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 81/238 (34%), Gaps = 41/238 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A      SR  ++++I +  V VNG     A+  +   D I V           
Sbjct: 16  RIDRYLADHLDGQSRNSIQKLIEEGLVLVNGNACR-ASYKLQEKDQIFVSVPDAVLTELR 74

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
            + +PL    E  +L + +KP  +V   +      T+ + +               R   
Sbjct: 75  PERIPLDILYEDDQLLIVNKPKEMVVHPAPGHNTGTLVNAIMYHCGKELSGINGEIRPGI 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQV-------------DQ 155
           V R+D+NT G L++       R +     +    RVYR   +G +             D 
Sbjct: 135 VHRIDMNTTGSLIVCKTDAAHRFIASQIKEHSVHRVYRAIVYGHLNPTEGTIRTSIGRDP 194

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +  G+   G         L   + + ++V   L  G+  +I+         + 
Sbjct: 195 RDRKKMSVGVK-NGRQAITHYRELARLRNNFSYVEFELETGRTHQIRVHMASIGHPIL 251


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 47/234 (20%), Positives = 82/234 (35%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  +    V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFTDYSRSQIQLWLKNGAVSVNGQPVK-ANYKVKQGDEITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L         LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAQQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKSAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 88/251 (35%), Gaps = 45/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+   +V E    +R+ K I +  +G+ SR  ++ +++   + VN    +  ++ + + D
Sbjct: 1   MRTFKLVAET-AGERLDKYITQKESGL-SRSFIQELVSSGHILVNNQSAK-PSLRLKTGD 57

Query: 59  HIEVD------------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRST----VFDNL 101
            I ++             +PL    +   L L +KP GL    +      T    V    
Sbjct: 58  TITIEIPPETPSELKAENIPLEIIFQDKDLLLINKPPGLTVHPAPGHPDHTLVNGVLALE 117

Query: 102 PSIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV- 153
           P +       R   V RLD +T GLLL+  +      L     +    + Y     G++ 
Sbjct: 118 PEMEDFDDPLRPGIVHRLDKDTSGLLLVAKNRQALANLSAQFKERTVRKYYLALVKGELR 177

Query: 154 ------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                       D      +   +V  G         L   +G  + + V L  G+  +I
Sbjct: 178 PAEGFIEAPLGRDPQNRQKIA--VVSDGRHARTGYKVLRYIQGY-SLLEVKLETGRTHQI 234

Query: 202 KKVFEFFNWKV 212
           +  F      V
Sbjct: 235 RVHFAAIGHPV 245


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 41/224 (18%), Positives = 82/224 (36%), Gaps = 37/224 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           +R+   +++    +R  ++ +I    + VNG    +A+  V   D I +D +PL K    
Sbjct: 11  ERIDIYLSKKLDETRSRIQELIKSNNILVNGKK-TKASYKVNFGDEIFID-IPLLKEVDI 68

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
                      E   L + +K  G+V   S      T+ + +      +           
Sbjct: 69  IPQDIDIDIVYEDKYLAIINKYAGMVVHPSKGHEEDTLVNAIMYKIKDLSGINGDLRPGI 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--KLNLL----- 161
           V RLD NT GL+++  D      L     + +  ++Y     G+V++   ++  +     
Sbjct: 129 VHRLDKNTSGLIIIAKDDKTHFKLSEMFKNKEIKKIYYAIVKGKVNKKSGRIETMIGRNP 188

Query: 162 ---KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              KK  V+           +       + + V L  G+  +I+
Sbjct: 189 NDRKKMAVVDNGKLAITNFEVIDSNEKFSLLKVDLETGRTHQIR 232


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 88/236 (37%), Gaps = 42/236 (17%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V E     R+ K +A      SR   +++I   +V+ NG++ +   + + + D + V+  
Sbjct: 25  VAEGTLGVRLDKWLAEQLPELSRSRCQKLIESGQVQRNGLVCQDKNLILKTGDRLVVNIP 84

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                      +PL    E  +L + +KP GLV          TV + L +    +  +G
Sbjct: 85  ELIPLDVVAQNIPLDILYEDEQLIIINKPAGLVVHPGPGHPDGTVVNALLAHCPDLAGIG 144

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ------ 155
                    RLD +T G +++         L++   +    R+Y    +G   +      
Sbjct: 145 GVQRPGIVHRLDKDTTGAMVVAKTELALHNLQVQLKEKTARRLYWGIVYGSPKEIQGTVN 204

Query: 156 -------DKLNLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       +  GIV   +G         L  + G+++W+   L  G+  +I+
Sbjct: 205 LPVGRHPGDRQKM--GIVPVEKGGREAVTHWRLLERIGNHSWLEFQLETGRTHQIR 258


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 85/247 (34%), Gaps = 48/247 (19%)

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  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                      D       E   + + +KP G+V   +    + T+ + L    + +   
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L          R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ--GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKV 204
             KGI+    G    + Q     + G NA      +       L E     G+  +I+  
Sbjct: 183 --KGIIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVH 240

Query: 205 FEFFNWK 211
            ++  + 
Sbjct: 241 MKYIGYP 247


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 81/233 (34%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I   +V VNG   ++A   V   D +              
Sbjct: 11  RLDKALSDLTELSRSLANEQIKVGQVLVNGQ-AKKAKYTVQEGDIVTYHVPEPEVLEYVA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDLPLEIIYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDEAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G  + + + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPAVTRFQVLE-RFGDYSLLELQLETGRTHQIRVHMAYIGHPV 241


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 84/235 (35%), Gaps = 42/235 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           I+ EN    R+   I+ +    SR  ++++I +  VKVNG   +++   +   D + V+ 
Sbjct: 7   IIHENLVNCRLDLFISNSLEGKSRSYIQKLIQEGHVKVNGKD-KKSNYKLKLHDSVVVNN 65

Query: 64  ----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                  +           E   + + +K  G+V   +  +   T+ + L          
Sbjct: 66  IEKEDKKINPENIEMDILYEDNDIIVINKSQGMVVHPATSNYSGTLVNALLYHCDTLSTL 125

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQD---- 156
           +  +R   V R+D +T G+L++  +     +L     +    R Y     G V ++    
Sbjct: 126 NDDTRPGIVHRIDKDTSGVLVVAKNNKAHEILAEQLKEHSMKREYIAVVEGIVKEENGLV 185

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        +    V++G         +  +   N  V   L  G+  +I+
Sbjct: 186 DEPLGRNPKDRIKMA---VVEGGKNAVTHYEVLKRFKKNTLVKCILETGRTHQIR 237


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 82/226 (36%), Gaps = 38/226 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ K +A      SR  +++++AQ  V++NG    + A  V + D + V   P ++    
Sbjct: 40  RLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGDQVAVRMRPTQQSQAF 99

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGR 113
                      E   L +  KP GLV   +  +   T+ + L           R   V R
Sbjct: 100 KPESLPLDVVHEDEHLLVIDKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQVPRAGIVHR 159

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLN 159
           LD +T GL+++  +      L   + + +  R Y     G             + +D  N
Sbjct: 160 LDKDTSGLMVVARNRAAMDALVRMIAAREVSRQYLALAWGAWSGSEQRRIRAPIGRDPRN 219

Query: 160 LLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
            L+  +V  G   G    T   L         V   L  G+  +I+
Sbjct: 220 RLRMAVVDLGQHAGKEACTDFDLLASGEEVCLVRCTLHTGRTHQIR 265


>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 = 83.7 bits (206), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 93/238 (39%), Gaps = 38/238 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +++ I+ +     R+   +++     SR  ++++I ++ + VNG+ ++ A   V + D +
Sbjct: 3   EEQFIINQEENGMRIDVFLSKKMDNVSRSYIQKLIKEKEISVNGMAVK-ANYKVSANDIV 61

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           ++            + +PL    E   + + +KP G+V   S      T+ + L      
Sbjct: 62  QLTIPDLSEPDILPENIPLDILYEDADILIVNKPKGMVVHPSPSHYTGTLVNALMYYCKD 121

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D++T G LL+  +    + L   L      R+Y    HG + +
Sbjct: 122 DLSGINGVMRPGIVHRIDMDTTGSLLVCKNDFAHQKLAEDLKVHNIKRIYHAIVHGVIKE 181

Query: 156 DK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D+           ++  K  I  +          +  +  +  ++   L  G+  +I+
Sbjct: 182 DEGTVEGPIGRHPIDRKKMSINYKNGKPAVTHYRVLKRFSNYTYIECQLETGRTHQIR 239


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 87/243 (35%), Gaps = 40/243 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V +  +  R+ + ++      SR  +++++ +Q++ VNG  ++ A   V   D I V   
Sbjct: 8   VSDGQSGIRIDRYLSEMNEELSRSYIQKLLKEQKITVNGSAVK-ANYKVQEGDEISVAVP 66

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                    + +PL    E   + + +KP G+V   S      T+ + +           
Sbjct: 67  DIKEPDILPEDIPLDILYEDDDVLIVNKPKGMVVHPSAGHTSGTLVNAIMFHCKDNLSGI 126

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK--- 157
               R   V R+D +T G LL+  +    R L   L      R YR    G + +D+   
Sbjct: 127 NGVLRPGIVHRIDKDTTGALLVCKNDNAHRNLAEQLKEHSIRRRYRAIVAGVLKEDEGTI 186

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFF 208
                   ++  K  +  +          +  +  +  +V   L  G+  +I+  +    
Sbjct: 187 EGPIGRHPIDRKKMAVNYKNGKDAVTHYKVLERFKNATYVECRLETGRTHQIRVHMT-SI 245

Query: 209 NWK 211
              
Sbjct: 246 GHP 248


>gi|8575702|gb|AAF78056.1|AF263561_1 23S rRNA pseudouridine synthase [secondary endosymbiont of
           Glycaspis brimblecombei]
          Length = 314

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 86/234 (36%), Gaps = 31/234 (13%)

Query: 9   ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           E+   QR+ + +A      SR  ++  I   RV+VNG ++ R    V  ++ I +D    
Sbjct: 2   ESQLGQRLDQTLAELFPDYSRSRIKEWILDNRVQVNGKIINRPKEKVFGSEQIAIDVLIE 61

Query: 64  --------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                    +PL    E   + + +KP  LV      +   TV + L   +  +I     
Sbjct: 62  EDMRWQPQNIPLNIVYEDDEIIVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIINVPRA 121

Query: 110 -SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKLNLL 161
             V RLD +T GL+++         L   L   +  R Y    +G++       + +   
Sbjct: 122 GIVHRLDKDTTGLMVIAKTIPAQTHLVEALQLREITREYEAVVNGRMTAGGTVDEPIARH 181

Query: 162 ---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  + I  +    +    +     ++  + + L  G+  +I+      N  
Sbjct: 182 PTKRTHMAIHPLGKPAITHYRVMEHFRAHTRLRLRLESGRTHQIRVHMAHINHP 235


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 90/232 (38%), Gaps = 37/232 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           I +++   +R+   +A     +R  ++++I    VKVNG+L++     +   D ++V+  
Sbjct: 10  IAEKDDVDKRIDSFLASELDYTRSYLKKLILDGLVKVNGLLIK-PNYKLKEGDSVDVNIP 68

Query: 64  ----------GVPL-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                      +PL    E   + + +KP G+V   +  +   T+ + L      +    
Sbjct: 69  EAEEIDLSPENIPLDIIYEDDDIIVINKPQGMVVHPAPGNYSGTLVNALLYHCKNLSGIN 128

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG---------- 151
                  V RLD +T G++++  +      L     +   L+ Y     G          
Sbjct: 129 GELRPGIVHRLDKDTSGVMVVAKNDKAHLDLSNQIKERTILKKYIAIVEGVIKDDEGSIE 188

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             + +D +   KK  V +   Y      +  +  +N+ +   ++ G+  +I+
Sbjct: 189 APIGRDHVER-KKMAVTEDGRYALTLYKVLERYKNNSLIEATIKTGRTHQIR 239


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 46/227 (20%), Positives = 87/227 (38%), Gaps = 38/227 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QR+ K +A      SR  +++++ Q  V++NG  +++ A  V   D I V+  P ++++ 
Sbjct: 39  QRLDKALAELVPEFSRSYLQQLLLQGCVRLNGREVQKPASRVKVGDRIAVEMRPTQQSQA 98

Query: 73  TR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVG 112
            R              + + HKP GLV   +  +   T+ + L           R   V 
Sbjct: 99  FRPEQWPLDVVYEDEHILVIHKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQVPRAGIVH 158

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDKL 158
           RLD +T GL+++         L   + + +  R Y                H  + +D  
Sbjct: 159 RLDKDTSGLMVVARSRSAMDALVRMIAAREVSRQYVALGWGGWTGAAHRSVHAPIGRDPR 218

Query: 159 NLLKKGIV-IQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
           N L+  +V +      + +   D    +     V   L  G+  +I+
Sbjct: 219 NRLRMAVVDLAQHPGKEARTDFDLIDANEEVCLVRCTLHTGRTHQIR 265


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 82/226 (36%), Gaps = 38/226 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ K +A      SR  +++++AQ  V++NG    + A  V + D + V   P ++    
Sbjct: 44  RLDKALAELVPEFSRSYLQQLLAQGDVRLNGQPAAKPAHKVRAGDQVAVRMRPTQQSQAF 103

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGR 113
                      E   L +  KP GLV   +  +   T+ + L           R   V R
Sbjct: 104 KPESLPLDVVHEDEHLLVIDKPAGLVVHPAPGNWSGTLLNALLGRDAQAMQVPRAGIVHR 163

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLN 159
           LD +T GL+++  +      L   + + +  R Y     G             + +D  N
Sbjct: 164 LDKDTSGLMVVARNRAAMDALVRMIAAREVSRQYLALAWGAWSGSEQRRIRAPIGRDPRN 223

Query: 160 LLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
            L+  +V  G   G    T   L         V   L  G+  +I+
Sbjct: 224 RLRMAVVDLGQHAGKEACTDFDLLASGEEVCLVRCTLHTGRTHQIR 269


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/181 (20%), Positives = 68/181 (37%), Gaps = 25/181 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +  +  E    +R+ + IA     SR + + +I    V +NG ++++ +  V   + +
Sbjct: 1   MPEIVVDSEK-KGKRLDQFIASIADISRSQAKNLIEDGEVSINGRIVKKPSYKVKEGETV 59

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                         + +PL    E   + + +KP GLV   +      T+ + L      
Sbjct: 60  SFEIPEPIPLDLQPENIPLDIVYEDKDVIVINKPAGLVVHPAPGHYSGTLVNALLYYCKD 119

Query: 108 VIS---------VGRLDINTEGLLLLT-NDGGLARVLEL-PSTQWLRVYRVRFHGQVDQD 156
                       V RLD +T GLL++  ND     ++E        R YR    G  ++ 
Sbjct: 120 FQGINGTLRPGIVHRLDKDTAGLLVVAKNDLAQQSLIEQFKRRTVGRFYRALVLGIFEKQ 179

Query: 157 K 157
            
Sbjct: 180 H 180


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 88/241 (36%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I+ +    +R+ KV++      SR +V++ I    V VNG   +       + D IE+  
Sbjct: 4   IIPDEQAGERIDKVLSTLNADWSRTQVQQWIKDGNVLVNGQKPKT-NYKCTANDKIEISI 62

Query: 63  ------DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                 D VP +       E   + + +KP G+V   +   G  T+ + L +  + +   
Sbjct: 63  PEPEELDVVPEKMDLDIYYEDKDVLVVNKPKGMVVHPAAGHGTGTLVNGLMAHCTDLSGI 122

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---- 156
                   V R+D +T GLL++  +      L  +L +    R YR   HG +  D    
Sbjct: 123 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLMNKTVTRKYRAVVHGVIPHDYGTI 182

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+    +      +  +      V   L  G+  +I+   ++  +
Sbjct: 183 DAPIARDPKDRQSMTVVDNGKHAVTHFQVLERFRDFTLVECQLETGRTHQIRVHMKYIGY 242

Query: 211 K 211
            
Sbjct: 243 P 243


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/214 (17%), Positives = 83/214 (38%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRKA-ERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAALNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +  L           ++  + RLD +T G+++   + G+
Sbjct: 102 VINKREGLLSVSTDRVKERTAYRLLSDYVKQSDPRNKIFVLHRLDRDTSGIMMFAKNQGV 161

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQD-KL--------NLLKKGIVIQG-ICYGDMQVT 178
              L+   ++    R Y     G+ ++D  L          ++  + ++G       +  
Sbjct: 162 KEQLQSNWSEMITQRTYVAVIEGRPEKDTDLIVSNLVENKNMQVYVTLEGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L     S + + + L  G+  +I+   +     V
Sbjct: 222 LLQTNNSYSLLELELETGRKNQIRAQMQSIGHPV 255


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 84/228 (36%), Gaps = 38/228 (16%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
                R+ K++       SR  +++ I    +KVN I   +    ++  D I +      
Sbjct: 15  KEKSIRLDKILVKHLNSFSRSSIKKWILSGFIKVNNITANKPKKKILFKDRISLIINKKS 74

Query: 63  DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRV 108
           + + ++K         E + + + +KP   V      +   T+ + L   +       R 
Sbjct: 75  NFIKIKKENIFLNIIFEDSEILIINKPTNFVVHLGYGNTSGTLLNALIFHYPDNLLIPRA 134

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLN------ 159
             V RLD NT G+L++         L       + ++ Y V   G+++   K+       
Sbjct: 135 GIVHRLDRNTTGILVVAKTISTYYFLINLFKKRKIIKEYDVIVIGRIEVDGKIEKPIKRD 194

Query: 160 -----LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +  GI   G        ++ T   ++ ++ + L+ G+  +I+
Sbjct: 195 IYNRTKMTVGI---GGKQAITYYSVITIFKNHTYLRIQLKTGRMHQIR 239


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 84/248 (33%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I +  V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKEDVVTVNGKSVK-VNYKVKENDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREIKK 203
             KG  I      D +        +  K +     V        L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVIERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>gi|327460457|gb|EGF06794.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK1057]
          Length = 298

 Score = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 84/241 (34%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++ +   QR+ K +A     SR      I   R+ VNG   ++A   V   D I      
Sbjct: 5   IEASVAGQRLDKAVAELTDLSRSLAHEQIKDSRILVNGQ-AKKAKYAVKEGDVISYELPE 63

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                   + +PL    +   + + +KP G+V   S      T+ + L      +     
Sbjct: 64  PEVVEYVAEDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGING 123

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------- 151
                 V R+D +T GLL++  +      L       + LR Y    HG           
Sbjct: 124 VLRPGIVHRIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEA 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + + + +  K+ +  +G         L+ +    + V + L  G+  +I+    +    
Sbjct: 184 PIGRSEKDRKKQAVTAKGKPALTRFQVLE-RFADYSLVELQLETGRTHQIRVHMAYIGHP 242

Query: 212 V 212
           V
Sbjct: 243 V 243


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 38/225 (16%), Positives = 84/225 (37%), Gaps = 48/225 (21%)

Query: 15  RVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVNVMSTDHI------ 60
           R+ K +       R++        + ++I   ++KVNG  ++  +  +   D I      
Sbjct: 11  RLDKFL-------RKKLLNLPLSAIYKLIRTGKIKVNGKKVKNPSYKIEIGDEITIEEDI 63

Query: 61  -----EVDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                E++   +          E   + + +KP G+          +T+ + L       
Sbjct: 64  SKYNREINNKVVPIKMDLDIVYEDNDILIINKPAGIPIHPGKGTHIATLIEGLIYYGQEK 123

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-KLNLL 161
                 V RLD +T G+L++  +   AR L   +      + Y     G++ ++ K++  
Sbjct: 124 NFTPHLVHRLDKHTSGILIIAKNTQSARELGDIIAGRSIKKEYIALCKGKLSKEGKID-- 181

Query: 162 KKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKK 203
              I ++        +T     T  G  + + V ++ G+  +I+K
Sbjct: 182 ---IPLENKQALTTFITQKVYKTHLGEFSLLNVNIKTGRKHQIRK 223


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 65/165 (39%), Gaps = 25/165 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------D 63
           R+ K + A     SR +++ +I    V+V+G  +++    V +   +E+          +
Sbjct: 17  RLDKFLVAHFPELSRSQIQGLIRDGFVRVSGKTVQKTGFLVEAGKEVEIRIPPPQPTSLE 76

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLP-----SIFSRVISV 111
             P+      E   L L +KP G+V   S    R T+      ++P         R   V
Sbjct: 77  PEPIPLEVIFENQDLLLVNKPAGMVVHPSAGHDRGTLVHAALAHIPELEGIHGEERPGVV 136

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
            RLD +T GL+LL  +    R L+      +  + Y     G+  
Sbjct: 137 HRLDKDTSGLILLAKNDRAHRWLQDQFRLRKVQKTYLALVDGRPP 181


>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 = 83.3 bits (205), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 81/237 (34%), Gaps = 44/237 (18%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V   +   R+ K +A   I  A+R  +E++I    VK+N  ++ +    + S + IE+  
Sbjct: 12  VSPEYEGMRLDKYLAEQ-IEEATRSYLEKLIDNSYVKINSKVINKNGRKLKSGEKIEISI 70

Query: 63  ----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                     + +PL    E     L +K   +V   +  +   T+ + L    + + SV
Sbjct: 71  PEEENIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYNGTLVNALLYYTNNLSSV 130

Query: 112 ---------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN- 159
                     RLD +T GL+L+  +      L          + Y     G    + L  
Sbjct: 131 NGNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCIVKGNFSDENLEG 190

Query: 160 --------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +V +          +  Q    + V V +  G+  +I+
Sbjct: 191 RIENLIGRDTKDRKKMA--VVKENGKLAISNYRVVEQVKDYSLVEVLIETGRTHQIR 245


>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 = 83.3 bits (205), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 61/317 (19%), Positives = 115/317 (36%), Gaps = 58/317 (18%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           TP R+ + + +  +   +R +V+  I + RV VNG  ++     V S DHI +       
Sbjct: 10  TPMRIDRYLTQQ-VENMTRNKVQAAIEEGRVLVNGKPVKS-NYRVKSCDHIHLTFLRPPA 67

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIF 105
                + +P+    E   L +  K  G+V   +  +   T+            D L    
Sbjct: 68  PELAPEDIPITILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADELDKTE 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++  +      L     + Q  +VY+    G    +    +K 
Sbjct: 128 MRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAES-GTIKT 186

Query: 164 GIVIQGICYGDMQV----TLDTQKGSN--------------AWVTVGLREGKNREIKKVF 205
            I   G  + + +V      +  +G +              + + V L  G+  +I+   
Sbjct: 187 NI---GRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGYFSLMDVTLHTGRTHQIRVHL 243

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLGPHLLEEAQVNLDAPI 261
           +     +  L   +YG     TL    +   ++ +L    R+ L    L   Q     P+
Sbjct: 244 QHLGHSI--LGDETYGGATPRTLPFSKSEPFTRNLLELMSRQALHAQTLRFRQPTTGEPL 301

Query: 262 YSSETLVRDRPNIISEV 278
             S  L  D   ++ ++
Sbjct: 302 SFSAPLPEDMELVLEKI 318


>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 = 83.3 bits (205), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 82/247 (33%), Gaps = 46/247 (18%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V  N   +R+ K + R  +  A+R +V+  I + RV VNG  ++     V   D I V  
Sbjct: 28  VAPNQARERIDKFLTRQ-VENATRNKVQEAIEESRVLVNGKPIKS-NYKVCPNDEIFVIF 85

Query: 63  ----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                     + +PL    E   L + +KP G+V   +  +   T+   +          
Sbjct: 86  THPPAPDLEPENIPLDIVFEDEFLLVINKPAGMVVHPAYANWTGTLAGAVLYHTQNRLSE 145

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
                 R   V RLD +T GL+++  D      L          ++Y     G       
Sbjct: 146 TGKEALRPGIVHRLDKDTSGLIVVAKDDATHYALAKQFAERTTEKIYTALVWGCPKPPSG 205

Query: 154 --------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKK 203
                    +    ++      +           + ++  +  + + + L  G+  +I+ 
Sbjct: 206 TIQTNIWRSKRDRKIMAN-YPFESETGKPAITDYEVKEDFHWFSLLDLQLHTGRTHQIRA 264

Query: 204 VFEFFNW 210
             +    
Sbjct: 265 HLQHLGH 271


>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 = 83.3 bits (205), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 83/244 (34%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
            ++E    +R+ KVIA      SR +V++ + +  V VNG  ++         D +    
Sbjct: 7   TIEEQHDGERIDKVIAELNEQWSRSQVQQWLKEGHVLVNGKAVK-PNYKCHVDDEVVISI 65

Query: 61  ------EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                 +V   P+      E   + + +KP G+V   +      T+ + L +    +   
Sbjct: 66  PSPEPLDVAPEPIPLDIYYEDADVLVVNKPRGMVVHPAPGHMHGTLVNALLAHCQDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD---- 156
                   V R+D +T GLL++  +      L     +    R Y    HG +  D    
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDLAHESLVNQLVNKTVTRKYVAIVHGVIPHDYGTI 185

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                        +    V++          +  +     +V   L  G+  +I+   ++
Sbjct: 186 DAPIGRDPRDRQSMA---VVENGKEAVTHFRVLERFEHYTFVECQLETGRTHQIRVHMKY 242

Query: 208 FNWK 211
             + 
Sbjct: 243 IGYP 246


>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 = 83.3 bits (205), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 89/236 (37%), Gaps = 37/236 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           + QR+ K +A     SR +    I Q  V VNG   ++A   V + D I  +        
Sbjct: 8   SGQRLDKALADLSPLSRGQANDQIKQGLVLVNGQQ-KKAKYTVQAGDVICFELPKEEVLE 66

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
                +PL    E   L +  KP G+V   S      T+ + L              R  
Sbjct: 67  YQAQNIPLDIIYEDDTLAIITKPQGMVVHPSGGHPSGTMVNALMYHIKDLSSINGVVRPG 126

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  T+    A   EL + + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 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 = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 88/247 (35%), Gaps = 37/247 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK+ N   E     R+ KVIA   +A  +R +V+ +I + ++ VN +        V   D
Sbjct: 1   MKEINFTIEESAKGRLDKVIAEN-VADLTRSQVQSLIKKGQILVNDVPTTN-RYQVKPND 58

Query: 59  HIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            + +   D V +             E   + + +KP G+V   +      T+ + L +  
Sbjct: 59  QVIIKLPDPVAIDVQPEKMDLDIVYEDDDVIVVNKPQGMVVHPAPGHDHGTLVNGLLAHT 118

Query: 106 S--------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D +T GLL++  +      L   L      R Y    HG + +
Sbjct: 119 PLATINGELRPGIVHRIDKDTSGLLMVAKNDQALVSLSKQLKDKTNQRKYWAIVHGNIKE 178

Query: 156 DKL---------NLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVF 205
           D              +K + I       +    +  + G    +   L  G+  +I+   
Sbjct: 179 DTGTINAPIGRSKKDRKKMAINEEGRPAVTHFKVLERFGEYTLIECQLETGRTHQIRVHL 238

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 239 KYIGHPV 245


>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 = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 79/233 (33%), Gaps = 35/233 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A      SR  ++ +I +  V VNG      A  +   D + V           
Sbjct: 19  RLDRYLAEKLPDRSRASLQELIREGFVTVNGRPAR-PASPLKPGDRVTVELPPPAPTTAT 77

Query: 63  -DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
            + +PL    E   L +  KP GL T  +      T+ + L S F         R   V 
Sbjct: 78  AEDIPLTVIYEDEDLAVIDKPAGLTTHPAPGHPAGTLLNALLSRFPELRDSGLDRPGIVH 137

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD----------KLNL 160
           RLD +T GL+++         L     + +  +VY     G V+                
Sbjct: 138 RLDKDTSGLMVVARSRQAHARLSDQFRNREVTKVYLALVRGCVEPAEGIIEAAIGRHRTQ 197

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            KK  V +       +  +  +  ++  + V +  G+  +I+         V 
Sbjct: 198 RKKMTVSEQGREARSRFKVIRRFRNHTLLEVRIYTGRTHQIRVHLAAIGHPVI 250


>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 = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 42/231 (18%), Positives = 84/231 (36%), Gaps = 42/231 (18%)

Query: 11  FTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           +  +R+ K +A      SR  +++ +    V VN    + A++ V   D + +       
Sbjct: 12  YAGERIDKYLAEVMNDYSRSFLQKQLKDGNVSVNEKTAK-ASLKVAEDDEVRIFIPENKE 70

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------- 106
                + +PL    E  +L + +KP G+V   S      T+ + L               
Sbjct: 71  PDIVPEDIPLDILYEDQQLLVVNKPKGMVVHPSAGHYSQTLVNALMFHCKDQLSGINGVL 130

Query: 107 RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------- 156
           R   V R+D++T G L++  T+    +   +L      R+YR   HG++ +D        
Sbjct: 131 RPGIVHRIDMDTTGALVVCKTDLAHQSLAEQLKVHSITRLYRAIVHGRLKEDFGTIEGTI 190

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +   I ++          +  +     +V   L  G+  +I+
Sbjct: 191 GRHPTDRKKMA--INVRNGKPATTHYKVLERFDRFTYVECELETGRTHQIR 239


>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 = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 81/248 (32%), Gaps = 44/248 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  I  E    QR+ K ++ +  A SR +++  I +  VKVN  +++     V   DHI 
Sbjct: 5   EFKITDETQVGQRIDKFLSESNDAWSRSQLQDWIKEDLVKVNDKVIKS-NYKVKLNDHII 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S      T+ + L      +
Sbjct: 64  VTEKEVVEADIQPEDLDLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D +T GLL++  +  +A       L +    R Y    H  +  D
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKN-DIAHRGLVEQLMAKSVKRKYTALVHDNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                            +    V+           +         +   L  G+  +I+ 
Sbjct: 183 YGTVDAPIGRNKNDRQAMA---VVDDGKEAVTHFNVIEHFKDYTLIECELETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 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 = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 86/247 (34%), Gaps = 48/247 (19%)

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  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                      D       E   + + +KP G+V   +    + T+ + L    + +   
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ--GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKV 204
             KGI+    G    + Q     + G NA      +       L E     G+  +I+  
Sbjct: 183 --KGIIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVH 240

Query: 205 FEFFNWK 211
            ++  + 
Sbjct: 241 MKYIGYP 247


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 87/259 (33%), Gaps = 54/259 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK+  I  +N   QR+ K + +     G   +  + + I  +++KVN          +  
Sbjct: 1   MKEIKI-NQNDANQRLDKFLMKTFPKLG---KSMMYKAIRNKKIKVNRKRCT-FDQKIQE 55

Query: 57  TDHI-------EVDGVPLRK----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
            D I        ++   +             E   + + +KP GL++       +  + +
Sbjct: 56  NDSILLFLPPDVLEEKKVETNYISSKLDVIYEDENILIVNKPYGLLSQSDQSQNQDCLVN 115

Query: 100 NL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRV 144
            +           P+           RLD NT GL++   +    R +   + +    ++
Sbjct: 116 RVQAYLMEKNEYDPNKEHSFAPSICHRLDRNTTGLVIAAKNANALRKVNEAIANRTIQKM 175

Query: 145 YRVRFHGQVDQDK------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           YR    G  +Q              +  +     ++G     M V ++   G N+  T+ 
Sbjct: 176 YRAHVVGTFEQKDFTMCYYIRKENTIAKVSD-KKLEGYQKALMDVHVERDDGENSICTIT 234

Query: 193 LREGKNREIKKVFEFFNWK 211
           L  G+  +I+ +       
Sbjct: 235 LHTGRFHQIRALMGHIQHP 253


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 84/234 (35%), Gaps = 40/234 (17%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V+EN    R+ + +A      SR  ++++I Q +V+VNG +     +N+   D I +   
Sbjct: 9   VEENSA--RIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLEVP 66

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                    + +PL    E  +L + +KP GLV   +      T+ + L +    +  +G
Sbjct: 67  EAQPLELQAEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCPHLPGIG 126

Query: 113 ---------RLDINTEGLLLLT-NDGGLARVLELPSTQWL-RVYRVRFHGQVD------- 154
                    RLD +T G + +   D     +     T+   R Y    +G          
Sbjct: 127 GVQRPGIVHRLDKDTTGAIAIAKTDIAYKHIQAQLQTKTARREYLGVVYGAPKTSSGKVD 186

Query: 155 ------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       +    V +G         +  + G+   +   L  G+  +I+
Sbjct: 187 LPIGRHPQDRKKMAIVPVEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIR 240


>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 = 82.9 bits (204), Expect = 7e-14,   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



 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 32/134 (23%), Positives = 54/134 (40%), Gaps = 28/134 (20%)

Query: 76  WLYHKPIGLVTTHSDP---------------------------DGRSTVFDNL-PSIFSR 107
            L +KP+  ++   D                            + R  V  NL P+  ++
Sbjct: 7   VLLNKPMHYLSCQVDRQMGGGRGKPLCRQLLTPERRWEETGQGERRREVKSNLSPAKCNK 66

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           ++  GRLD+++ GL + T DG LA  L  P  +  + Y V     V    L LL+ G+ +
Sbjct: 67  LVCAGRLDVDSTGLTVFTQDGRLASQLVGPGKRVSKEYHVEVDLPVSAGALTLLRHGLSL 126

Query: 168 QGICYGDMQVTLDT 181
            G+     +V L +
Sbjct: 127 DGLELLPAKVRLLS 140


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 86/247 (34%), Gaps = 48/247 (19%)

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  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                      D       E   + + +KP G+V   +    + T+ + L    + +   
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ--GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKV 204
             KGI+    G    + Q     + G NA      +       L E     G+  +I+  
Sbjct: 183 --KGIIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVH 240

Query: 205 FEFFNWK 211
            ++  + 
Sbjct: 241 MKYIGYP 247


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 76/238 (31%), Gaps = 37/238 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D     E   P R+ +V+A + G   RR    +I   RV V+     + A+ +    H
Sbjct: 1   MTDSFFYPEGLPPIRLDRVLALQLGFGVRR-CRALIEAGRVLVDDRPCAKGAL-IRPGQH 58

Query: 60  IEV-----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSR 107
           I V           D   + + E        KP GL T        + +   LP      
Sbjct: 59  IRVSLPEDAAPDCHDVRLVDRNES--FAALAKPDGLHTVA--GQEAACLESCLPGLGLEG 114

Query: 108 VISVGRLDINTEGLLL--LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
              + RLD  T GL+L         A  +   + Q  + Y     G+V    L    +G 
Sbjct: 115 WELLNRLDCLTSGLVLAAAEKRDAAAYKVWQDAGQVSKWYLALARGEV--ATLE--CRGR 170

Query: 166 VIQ------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++                    +V    Q   N  + V + +G+  +I+         
Sbjct: 171 ILDDKRSVVRVTADEDEPLRWTRVRALRQIDGNTLLLVKIFKGRRHQIRAHLAHAGHP 228


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 49/282 (17%), Positives = 93/282 (32%), Gaps = 51/282 (18%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM--- 55
           M D    +V +    +R+   ++R    SR +   +I    V+V+G    ++A  V    
Sbjct: 1   MSDSRTLMVPDGLAGERLDAALSRLFGVSRTKAAELIEAGLVQVDGAPAAKSA-RVSAGV 59

Query: 56  --------STDHIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
                       + V    +       +   + +  KP+G+    S      TV  +L  
Sbjct: 60  LLDVELPAPPGEVTVVPETVENLRIVHDDDEIVVVDKPVGVAAHPSPGWTGPTVIGHLAG 119

Query: 102 -------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
                       R   V RLD+ T GL+++        VL+    +    ++Y     G 
Sbjct: 120 AGFSISTSGAAERKGIVHRLDVGTSGLMVVAKTEYSYTVLKRAFKERTVKKIYHALVQGH 179

Query: 153 VD------QDKLNL-----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D         ++       K G+V  G        TL+  + +   + + L  G+  +I
Sbjct: 180 PDPFTGTVDAPIDRHPNHDYKFGVVAGGKPSITHYETLEAFRYAT-LLEITLETGRTHQI 238

Query: 202 K-KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-EVSKKIL 241
           +  +                G    G     + R E+S++ L
Sbjct: 239 RVHM-SAIGHPCC-------GDLTYGADPVLAERLELSRQWL 272


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 94/253 (37%), Gaps = 42/253 (16%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M++ N+   E +T +R+ KV++    G  SR  ++++     + VN   ++  +  V + 
Sbjct: 1   MEEYNLESSEEWTDRRLDKVLSEYFDGY-SRSFIKKLFDDGLILVNSKAVK-PSYKVRAG 58

Query: 58  DHIEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I++            + +PL    E   + L +KP G+V   +      T+ + L   
Sbjct: 59  DMIDISVPDPVSIDIVPEDIPLDIIYEDDDVILVNKPKGMVVHPAPGHYSGTLVNGLMYH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
           F           R   V R+D++T G+L++  +    R L   L      R Y    +G 
Sbjct: 119 FGSSLSGINGEFRPGIVHRIDMDTTGVLVVCKNDNAHRALSEQLHEHSITRKYYAIVYGN 178

Query: 153 VDQDKLN---------LLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
           +  D+             +K + I    G         L+   G   ++   L  G+  +
Sbjct: 179 ISSDEGTVDAPIGRSPKDRKKMAINNRNGRRAVTHYRVLERFGGRYTYIECQLETGRTHQ 238

Query: 201 IKKVFEFFNWKVN 213
           I+         + 
Sbjct: 239 IRVHMASIGHPIL 251


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 85/244 (34%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V  + +  R+ K I  + +    SR +V+  I    VKVN   ++     V   DHI +
Sbjct: 26  TVDADSSKTRLDKYITES-LGEEVSRSQVQLWITDGHVKVNEEPVKS-NYKVSQGDHIVL 83

Query: 63  ------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                       + +PL  A E   + + +KP G+V   +      T+ + L      + 
Sbjct: 84  SVPQPSVVEIIPEDIPLEIAFEDRDVIVVNKPRGMVVHPAPGHSSGTLVNALMFHCKDLS 143

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG------- 151
                     V R+D +T GL++   +      L   L      R Y    HG       
Sbjct: 144 GINGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKDHSVNRRYLALVHGNISHDQG 203

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +D  +     +  +   +     T+  + G  + + + L  G+  +I+   ++
Sbjct: 204 TIDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKY 263

Query: 208 FNWK 211
               
Sbjct: 264 IGHP 267


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 48/260 (18%), Positives = 92/260 (35%), Gaps = 50/260 (19%)

Query: 13  PQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           P R+ + + R  +  A+R +V+  I   RV VNG  ++     V S D IE+        
Sbjct: 37  PMRIDQYLTRQ-VENATRNKVQEAIEDGRVLVNGKSVKS-NYRVKSCDSIEMTFLRPPAP 94

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVT-----------THSDPDGRSTVFDNLPSIFS 106
               + +P+    E + L + +K  G+V             ++      T  + L +   
Sbjct: 95  ELAPEDIPIDIVYEDSDLMVVNKAPGMVVHPAFGNWTGTLANAILHHFGTDAEELETDEL 154

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD-------- 156
           R   V RLD +T GL+++  +      L       +  ++Y     G  +          
Sbjct: 155 RPGIVHRLDKDTSGLIIVARNPTALHRLARQFADRKVSKLYTAILWGVPEPQEGTIHTNI 214

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV---TVGLREGKNREIKKVFEFF 208
                   ++      +G+      +T      +  W     + L  G+  +I+   +  
Sbjct: 215 GRSRRDRKVMAN-FPYEGLEGKTA-ITDYRVTENLHWFSLAELTLHTGRTHQIRAHMQHL 272

Query: 209 NWKVNRLIRISYGPFQLGTL 228
             ++  L   +YG   L TL
Sbjct: 273 GHQI--LGDTTYGGASLRTL 290


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 91/246 (36%), Gaps = 39/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D  ++ +     R+ KV+       +R ++++MI    +KVNG  +++A   V   D 
Sbjct: 1   MSDYKVLADKTG--RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGD-VKKANYKVNLGDE 57

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I  D   ++K              E   + + +KP G+V   S      T+ + L     
Sbjct: 58  ITFDKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 117

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L   L      R Y    HG + +D
Sbjct: 118 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYIALVHGNIKED 177

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      K++  K+ +V  G         +  + G    V   L  G+  +I+   
Sbjct: 178 SGTIDAPLGRSKVDRKKQAVVKDGRNAVTHF-EVLKRYGDYTLVKCVLETGRTHQIRVHM 236

Query: 206 EFFNWK 211
           ++    
Sbjct: 237 KYIGHP 242


>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 = 82.9 bits (204), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 83/248 (33%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVK-VNYKVKENDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREIKK 203
             KG  I      D +        +  K +     V        L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLDRFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 82.5 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 84/247 (34%), Gaps = 50/247 (20%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             + +R+ K ++ +    SR  ++ +I + +V+V G  ++  +  V    +I +   P++
Sbjct: 30  EDSGERIDKYLSGKLTEYSRSYLKGLIDEGKVRVEGKPVKS-SFKVTEGINISISIPPVK 88

Query: 69  KA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
           +A             E   + L +KP G+V   +      T+ + L              
Sbjct: 89  EAEIIPENIPLDILYEDEDVILINKPKGMVVHPAAGHYTGTLVNALMYHCRDNLSGINGE 148

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD------ 156
            R   V R+D++T G+++   +  ++  +    L      R Y+   +G    +      
Sbjct: 149 LRPGIVHRIDMDTTGVIIACKN-DVSHRIIAEQLKEHSIKRKYQAIVYGVFKDEEGRIEG 207

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREGKNREIK-KV 204
                      +   ++  G         +      N    A +   L  G+  +I+  +
Sbjct: 208 SIGRSKTDRKKMA--VIPDGKPAVTHYRVIRNYTSPNGNNFAHIECELETGRTHQIRVHM 265

Query: 205 FEFFNWK 211
                  
Sbjct: 266 T-SIGHP 271


>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 = 82.5 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 83/248 (33%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVK-VNYKVKENDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREIKK 203
             KG  I      D +        +  K +     V        L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 82.5 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 82/245 (33%), Gaps = 45/245 (18%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V V+G++  +    V+    IE+
Sbjct: 8   KSEITATQTGQRLDQTLAELFPDYSRTRIKEWIQAGAVYVDGMVQTKPREKVLEGQEIEI 67

Query: 63  D---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +      ++            E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  EATLKEEIKAEAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNSDGTLMNALLHHCPEIE 127

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                  V RLD +T GL+++         L   L + +  R Y     G +        
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVSGTMT------- 180

Query: 162 KKGIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVF 205
             G+V + I     + T                +  +  ++  + + L  G+  +I+   
Sbjct: 181 AGGVVDEPIARHPTKRTHMAVHHSGRPSVTHYRVAEKFRAHTRLRLRLETGRTHQIRVHM 240

Query: 206 EFFNW 210
                
Sbjct: 241 AHIGH 245


>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 = 82.5 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 83/248 (33%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVK-VNYKVKENDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQAEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREIKK 203
             KG  I      D +        +  K +     V        L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>gi|157376631|ref|YP_001475231.1| lysozyme [Shewanella sediminis HAW-EB3]
 gi|157319005|gb|ABV38103.1| Lysozyme [Shewanella sediminis HAW-EB3]
          Length = 323

 Score = 82.5 bits (203), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 78/231 (33%), Gaps = 33/231 (14%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G +  +    V+    I+V
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWIQAGWVYIDGTVSIKPREKVLEGQVIQV 67

Query: 63  DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +   + +              E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  EATLVEETKAKAQAIDLDIVYEDDHILVINKQAGLVVHPGAGNSDGTLMNALLHHCPNIE 127

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
                  V RLD +T GL+++         L   L + +  R Y     G          
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVQGSLISGGTVDE 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D+          V+           +  +  ++  + + L  G+  +I+
Sbjct: 188 PIDRHPTKR-THMAVVHNGKPAMTHYRVAEKFRAHTRLRLRLESGRTHQIR 237


>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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 43/220 (19%), Positives = 83/220 (37%), Gaps = 32/220 (14%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ K +A      SR  ++  I    VK++ + + R    V +   +EV+          
Sbjct: 19  RLDKALAALFPDYSRTRIKEWILDDLVKIDDVTVNRPREKVYTGQQVEVNATLEDEVVFH 78

Query: 64  --GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRL 114
              +PL    E   + + +KP GLV      +   TV + L   +  ++       V RL
Sbjct: 79  PQNIPLDIIFEDEHILVINKPAGLVVHPGAGNPDGTVLNALLHHYPEIVEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLK 162
           D +T GL+++         L   L + +  R Y            R    + +DK N +K
Sbjct: 139 DKDTTGLMVIAKTVPAQTHLVTSLQAREITREYDAIAMGCFTAGGRVEAPIGRDKANRVK 198

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   G  +      +  +  ++  + + L  G+  +I+
Sbjct: 199 MAVATVGGKHAVTHYRVAEKYRAHTRLRLRLETGRTHQIR 238


>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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 90/252 (35%), Gaps = 51/252 (20%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R+   +A+A    SR  V+ +I   +VKV+G + + A   +   + IE++G P  + 
Sbjct: 57  AGMRLDAYLAQALPDISRARVQILIEAGQVKVDGAVPK-AKAKLKGGETIEIEGQPQLEP 115

Query: 71  --------------ERTRLWLYHKPIGLVT-----THSDPDGRSTVF-----------DN 100
                         E   L + +KP G++      +  D   R T+            D+
Sbjct: 116 LHAIPEDIPLQIVYEDEYLAVVNKPAGMMVHAGAGSTDDERNRGTLVNAVLFHMGKTADS 175

Query: 101 LPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
           L  +   +    V RLD  T GL+++  D    R L       +  + Y    HG++ + 
Sbjct: 176 LSGVGGELRPGIVHRLDKQTSGLIVVAKDDVTHRRLGEMFSERRVSKTYLTLAHGELKKA 235

Query: 157 K-------LNLLKKGIVI-----QGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREI 201
                      L + I +      G            LDT  G   +V V +  G+  +I
Sbjct: 236 DTTVSLPIARDLVRRIRMTTRRGDGRSAVSHFHVLERLDTPYGKFTFVEVKIETGRTHQI 295

Query: 202 KKVFEFFNWKVN 213
           +   +     V 
Sbjct: 296 RVHLQSLGHPVV 307


>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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 88/237 (37%), Gaps = 39/237 (16%)

Query: 12  TPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP 66
           T +R+ K++A A +A  SR + +  I   ++ V+G  ++           I V   D  P
Sbjct: 10  TTERLDKLVADA-VATVSRSQAKLAIEAGQITVDGATVK-PKDKPKVGATIRVSLPDPEP 67

Query: 67  LR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RV 108
           L             E   + + +KP G+V   +      T+ + L             R 
Sbjct: 68  LDLTPEDIPLEIVYEDADVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSQINGTLRP 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK--------- 157
             V R+D +T GLL++  +    + L   L +   LR Y    HG + ++          
Sbjct: 128 GIVHRIDKDTSGLLMVAKNDHAHQSLSAQLQAKTNLREYVAIVHGNIKEEDGVIRAPLGR 187

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              +  K+ IV  G         L+ + G+   +   L  G+  +I+    + N  V
Sbjct: 188 SPKDRKKQAIVADGRPAVTHFRVLE-RYGTYTLIACRLETGRTHQIRVHMAYINHPV 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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 91/246 (36%), Gaps = 39/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D  ++ +     R+ KV+       +R ++++MI    +KVNG  +++A   V   D 
Sbjct: 1   MSDYKVLADKTG--RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGD-VKKANYKVNLGDE 57

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I  D   ++K              E   + + +KP G+V   S      T+ + L     
Sbjct: 58  ITFDKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 117

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L   L      R Y    HG + +D
Sbjct: 118 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKED 177

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      K++  K+ +V  G         +  + G    V   L  G+  +I+   
Sbjct: 178 SGTIDAPLGRSKVDRKKQAVVKDGRNAVTHF-EVLKRYGDYTLVKCVLETGRTHQIRVHM 236

Query: 206 EFFNWK 211
           ++    
Sbjct: 237 KYIGHP 242


>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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 81/237 (34%), Gaps = 44/237 (18%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V   +   R+ K +A   I  A+R  +E++I    VK+N  ++ +    + S + IE+  
Sbjct: 12  VSPEYEGMRLDKYLAEQ-IEEATRSYLEKLIDNSYVKINSKVINKNGRKLKSGEKIEISI 70

Query: 63  ----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                     + +PL    E     L +K   +V   +  +   T+ + L    + + SV
Sbjct: 71  PEEENIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYTGTLVNALLYYTNNLSSV 130

Query: 112 ---------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN- 159
                     RLD +T GL+L+  +      L          + Y     G    + L  
Sbjct: 131 NGNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCIVKGNFSDENLEG 190

Query: 160 --------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +V +          +  Q    + V V +  G+  +I+
Sbjct: 191 RIENLIGRDTKDRKKMA--VVKENGKLAISNYRVVEQVKDYSLVEVLIETGRTHQIR 245


>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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 59/313 (18%), Positives = 110/313 (35%), Gaps = 50/313 (15%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           TP R+ + + +  +   +R +V+  I + RV VNG  ++     V S DHI +       
Sbjct: 32  TPMRIDRYLTQQ-VENMTRNKVQAAIEEGRVLVNGKPVKS-NYRVKSCDHIHLTFLRPPA 89

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIF 105
                + +P+    E   L +  K  G+V   +  +   T+            D L    
Sbjct: 90  PELAPEDIPITILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADELDKTE 149

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD------- 156
            R   V RLD +T GL+++  +      L     + Q  +VY+    G    +       
Sbjct: 150 MRPGIVHRLDKDTSGLIIIAKNPTALHKLARQFANRQVEKVYKAIVWGVPKAESGTIKTN 209

Query: 157 -----KLNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                K   +      +G    +      +    G  + + V L  G+  +I+   +   
Sbjct: 210 IGRSHKNRKVMANFPYEGAEGKHAITDYQVVEDLGYFSLMDVTLHTGRTHQIRVHLQHLG 269

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLGPHLLEEAQVNLDAPIYSSE 265
             +  L   +YG     TL    +   ++ +L    R+ L    L   Q     P+  S 
Sbjct: 270 HSI--LGDETYGGATPRTLPFSKSEPFTRNLLELMSRQALHAQTLRFRQPTTGEPLSFSA 327

Query: 266 TLVRDRPNIISEV 278
            L  D   ++ ++
Sbjct: 328 PLPEDMELVLEKI 340


>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 = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 82/236 (34%), Gaps = 42/236 (17%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           R+ K +A        SR  +++++    V VN  +++ A       DH+ ++        
Sbjct: 16  RIDKYLAEC--CPDLSRSYLQKLLKDGAVSVNTRIVK-ANYKTQPGDHVILNIPDLQTPD 72

Query: 64  ----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFSRVIS 110
                +PL    E   L + +KP  +V   S      T+         DNL  I   +  
Sbjct: 73  IKPENIPLDILYEDQWLMVVNKPKDMVVHPSAGHMEGTLVNAVMAHCGDNLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK--------- 157
             V R+D +T G LL+  D  + R L   L      R YR    G + +D+         
Sbjct: 133 GIVHRIDKDTTGALLICKDDMVHRNLAEQLKEHSIKRRYRAIVQGNIKEDEGTVDAPIGR 192

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             ++  K  I  +          +  + G   ++   L  G+  +I+         
Sbjct: 193 HPIDRKKMAINHKNGKEAVTHYKVLERFGQTTYIECRLETGRTHQIRVHMASLGHP 248


>gi|255029306|ref|ZP_05301257.1| hypothetical protein LmonL_09598 [Listeria monocytogenes LO28]
          Length = 245

 Score = 82.5 bits (203), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 50/234 (21%), Positives = 84/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E+   +RV KVIA     SR  ++ M+    + VNG L +     V   D I     
Sbjct: 7   IIEESHARERVDKVIAEMMGKSRSAIQLMLKNGDITVNGELAK-PNYKVQVGDEIHYEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    + +PL    E   + + +KP G+V   S      T+        D+L  I 
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASGTLVNALLFHCDDLSGIN 125

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
            ++    V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         L+   G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVLERLPGYT-LINCKLDTGRTHQIR 236


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/182 (19%), Positives = 63/182 (34%), Gaps = 30/182 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V  +   QR+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D 
Sbjct: 12  VVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITIDV 71

Query: 64  ---------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  +      E   + + +KP GLV   +      T+ + L +        
Sbjct: 72  PPPVPAEPAGEAIALDIVYEDADIIVLNKPRGLVVHPAAGHETGTLVNALIAHCGASLSG 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQ 155
                R   V RLD +T GL++   +    + L        R       Y     G   +
Sbjct: 132 IGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHGRTGELRRGYLAFVWGVPGR 191

Query: 156 DK 157
             
Sbjct: 192 KY 193


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 47/223 (21%), Positives = 88/223 (39%), Gaps = 37/223 (16%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ K+I A     +R +V++ +    V VNG  ++ A   V + D + V   +  PL+  
Sbjct: 13  RIDKIITAHETTHTRSQVQKWLQDGLVTVNGNPVK-ANFKVTAGDVVTVTIPEVKPLKAV 71

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS--VG 112
                     E  ++ + +KP G+V   +      T+ +       LP I   +    V 
Sbjct: 72  AEPIPLEIVYEDDQVIVVNKPQGMVVHPAPGHPDGTLVNGLLYHTKLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  T    L+   +L +   +R Y    HG   +D+            +
Sbjct: 132 RIDKDTSGLLMVAKTEAAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             ++ +V  G         L+    +   V   L  G+  +I+
Sbjct: 192 RKRQAVVADGRHAVTHFQVLERFT-NYTLVKCILDTGRTHQIR 233


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 85/248 (34%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVK-VNYKVKENDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQAEDMGLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKK 203
             KG  I    G    + Q     + G NA      +       L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/227 (19%), Positives = 82/227 (36%), Gaps = 42/227 (18%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------E 61
           R+ K +A A      SR  +++++   +V VNG  ++ A+  V+  D I          E
Sbjct: 6   RIDKYLAEA--CPDLSRSYIQKLLKSGQVLVNGQGIK-ASYIVVEDDRIELEVPEAVEPE 62

Query: 62  VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RV 108
           +D  P+      E   L L +KP G+V   +      T+ + L               R 
Sbjct: 63  IDAEPMDLDILYEDQDLILINKPKGMVVHPAAGHYSHTLVNGLMYHCKDQLSGINGVMRP 122

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK--------- 157
             V R+D++T G+++   +      +   L      R Y+   HG + +D+         
Sbjct: 123 GIVHRIDMDTTGVIIACKNDMAHSSIAAQLKEHSITRRYQAIVHGVIAEDEGTVDAPIGR 182

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   K  I  Q          +  +      V   L  G+  +I+
Sbjct: 183 HPVERKKMSINYQNGKNAVTHYRVLNRFRQYTHVECRLETGRTHQIR 229


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 78/233 (33%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA- 70
           R+ K +A     SR      I   ++ VNG   ++A   V   D I     D   +    
Sbjct: 13  RLDKAVADLTELSRGLANEQIKNGQILVNGE-AKKAKYAVKEGDVISYEVPDPEVVEYVA 71

Query: 71  ---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
                    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 72  EDLPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 132 RIDKDTSGLLMIAKNDQAHLALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 191

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G    V + L  G+  +I+    +    V
Sbjct: 192 RKKQAVTAKGKPALTRFQVLE-RFGDYTLVELQLETGRTHQIRVHMAYIGHPV 243


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 83/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR      I   ++ VNG L+++A   V   D I              
Sbjct: 11  RLDKAVADLTDLSRSLANEQIKTGKILVNG-LVKKAKYTVKEGDVISYELPEIEEIEYVT 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  ENIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHPV 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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 33/168 (19%), Positives = 67/168 (39%), Gaps = 25/168 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           +R+ K +++    SR +++ +I +  +KVN   ++  +  V   D IEV           
Sbjct: 15  ERIDKYLSQKISLSRSQIQDLIDKGLIKVNEKEVKS-SYKVKVGDKIEVIVPPPEETEIK 73

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
              +P+    E   + + +KP G+V   +      T+ + L      +  +G        
Sbjct: 74  PQDIPIEIVYEDDDIVIINKPKGMVVHPAHGHYNDTLVNALLYRIKDLSGIGGEIRPGIV 133

Query: 113 -RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK 157
            RLD +T GLL++  +    + L          R Y     G++  ++
Sbjct: 134 HRLDKDTTGLLIIAKNDVSHQRLSEQLKNRILKRTYWAICEGEIPWEE 181


>gi|85711025|ref|ZP_01042085.1| Pseudouridylate synthase [Idiomarina baltica OS145]
 gi|85694938|gb|EAQ32876.1| Pseudouridylate synthase [Idiomarina baltica OS145]
          Length = 322

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 87/236 (36%), Gaps = 47/236 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           IV E+   +R+ +++A      SR  +++ I + +V V+  ++E+    +     + +D 
Sbjct: 10  IVPESLAGKRLDQILAELFPDYSRSRMKKWITEGKVSVDAQVIEKPREKLEFGALVAID- 68

Query: 65  VPLRKAERTR--------------LWLYHKPIGLVTTHSDPDGRSTV------FDNLPSI 104
             L + ER +              + + +KP GLV          T+      +D     
Sbjct: 69  AELEREERYQAQPIELDIVYEDEDILIINKPAGLVVHPGAGAPDGTLLNGLLHYDPDIDH 128

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   + RLD +T GL+++  +      L   +   +  R Y    +G +         
Sbjct: 129 VPRAGIIHRLDKDTTGLMVVARNIPAQTQLVDMMQKREITREYEAVCNGVMT-------A 181

Query: 163 KGIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
            G+V + I     + T                +  +  ++  + + L  G+  +I+
Sbjct: 182 GGMVDEPIGRHPTKRTHMAVVSSGKPAVTHYRVVERFRAHTLLRLRLESGRTHQIR 237


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 85/239 (35%), Gaps = 39/239 (16%)

Query: 1   MKDK--NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++K   +       +R+ K++ +    +R  +++ +    V VNG +++ A       D
Sbjct: 1   MENKIIELTLSLEKSERLDKILTKELSHTRSVIQQWLKSGFVSVNGEVVK-ANYKAKDGD 59

Query: 59  HIEV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV-------F 98
           H+ +            + +PL    E   L + +KP G+V   S      T+        
Sbjct: 60  HVTIQIEEEEELTVLAENIPLEIVFEDEHLLVINKPSGMVVHPSKGHSTGTLVNALLYHV 119

Query: 99  DNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--- 151
           D L           V R+D +T GLL++         L   L      R Y     G   
Sbjct: 120 DQLSKGSESYRPGIVHRIDKDTSGLLVVAKTPQAHVGLSNQLMDHSMTRSYVAIVEGSFE 179

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +D  N LK+ +  +G         +   K   + + + L  G+  +I+
Sbjct: 180 HITGTVDAPLARDPHNRLKRCVQKEGKQAITHFTVIQALKE-TSVLRLNLETGRTHQIR 237


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 78/239 (32%), Gaps = 40/239 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGIL-LERAAVNVMSTDHIEV--------DG 64
           +R+ K I+     +R + + +I Q+ V ++    + +    V     I +        + 
Sbjct: 10  ERIDKYISDNSEITRNDAKALIEQEAVYIDDKKFVRKPNYMVREGMVITILRLLEKETNI 69

Query: 65  VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
             +      R       + +KP GLV   +      T+ + L   F           R+ 
Sbjct: 70  EAVNMPLDIRYEDDNLLVLNKPSGLVVHPAPGHLNDTLVNALMYHFKNNLSDTNGLLRLG 129

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK------LNLL 161
            V R+D +T GLL++  D      L   L + Q  R Y     G +          +   
Sbjct: 130 IVHRIDKDTSGLLIIAKDNETHNELAKMLKNHQIKRTYIAICKGILPNKVTKINLPIQRD 189

Query: 162 KKGIVI-----QG---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            K   +      G   + Y  +  T        + V   L  G+  +I+    +    V
Sbjct: 190 AKNRKLMSIHKDGKSSVTYVHLLKTFYIDNKPYSLVKCELETGRTHQIRVHLAYIKHPV 248


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/175 (20%), Positives = 64/175 (36%), Gaps = 25/175 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           + E+    R+ KV+A     SR+ ++ ++ +  V VN   + +A+  V   D IEV    
Sbjct: 8   IDEDTKLDRLDKVLAEKLDFSRKRIKDLLDEGNVLVN-QKVMKASYKVCVNDEIEVSIPE 66

Query: 64  -------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                    P+      E   + + +KP G+V   +      T+ + L      +     
Sbjct: 67  LDSTQVLPEPIDLDIVYEDHDIIVINKPKGMVVHPAPGHYSGTLVNALLYHCKDLSGING 126

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
                 V R+D +T GLL++  +      L   L      R Y    H     + 
Sbjct: 127 VMRPGIVHRIDKDTSGLLVVAKNDKAHEALSQQLQDKTCHREYVAIVHKPFTHEY 181


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 91/246 (36%), Gaps = 39/246 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D  ++ +     R+ KV+       +R ++++MI    +KVNG  +++A   V   D 
Sbjct: 4   MSDYKVLADKTG--RLDKVVTNIFTDYTRSQLKKMIDDGNIKVNGD-VKKANYKVNLGDE 60

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I  D   ++K              E   + + +KP G+V   S      T+ + L     
Sbjct: 61  ITFDKPEVKKLSLEPENIPLDIVYEDDDVIVVNKPQGMVVHPSPGHFEHTLVNALLYHSP 120

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L   L      R Y    HG + +D
Sbjct: 121 LSTINGTYRPGIVHRIDKDTSGLLMVAKNDMAHQSLAKQLKDKTNTREYVALVHGNIKED 180

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      K++  K+ +V  G         +  + G    V   L  G+  +I+   
Sbjct: 181 SGTIDAPLGRSKVDRKKQAVVKDGRNAVTHF-EVLKRYGDYTLVKCVLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
           ++    
Sbjct: 240 KYIGHP 245


>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 = 82.2 bits (202), Expect = 1e-13,   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



 Score = 81.0 bits (199), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 32/134 (23%), Positives = 54/134 (40%), Gaps = 28/134 (20%)

Query: 76  WLYHKPIGLVTTHSDP---------------------------DGRSTVFDNL-PSIFSR 107
            L +KP+  ++   D                            + R  V  NL P+  ++
Sbjct: 7   VLLNKPMHYLSCQVDRQMGGGRGKPLCRQLLTPERRWEETGQGERRREVKSNLSPAKCNK 66

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           ++  GRLD+++ GL + T DG LA  L  P  +  + Y V     V    L LL+ G+ +
Sbjct: 67  LVCAGRLDVDSTGLTVFTQDGRLASQLVGPGKRVSKEYHVEVDLPVSAGALTLLRHGLSL 126

Query: 168 QGICYGDMQVTLDT 181
            G+     +V L +
Sbjct: 127 DGLELLPAKVRLLS 140


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 88/243 (36%), Gaps = 39/243 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            + E    +R+ K + A+ G  SR +V++ I   +V+VNG    ++   +   D + +  
Sbjct: 7   TILEENKNERIDKFLTAQNGEWSRSQVQQWIKDGQVQVNGK-ATKSNYKMQVEDQVTLSI 65

Query: 63  ----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                     + +PL    E   + + +KP G+V   +      T+ + L      +   
Sbjct: 66  PEPEELDVIAEDIPLDVVYEDADVIVVNKPRGMVVHPAPGHYTGTLVNALLYHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +       
Sbjct: 126 NGVIRPGIVHRIDKDTSGLLMVAKNDHAHESLVSQLKAKTTKRHYKAIVHGVIPHQH-GT 184

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKVFEFF 208
           ++  I         M VT D  + +    TV             L  G+  +I+   ++ 
Sbjct: 185 IEAPIGRDKKDRQSMTVTEDNSRDAVTHFTVLECFKDFTYVQCELETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 247


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 77/236 (32%), Gaps = 44/236 (18%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           I   N   QR+ KV+       SR +++  I +  VKVN  +++     V   D+I V  
Sbjct: 8   ITDSNHVGQRLDKVLPELNSDWSRSQIQDWIKEDLVKVNDKVVK-PNYKVKQNDNIVVTE 66

Query: 65  VPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
             +                E   + + +KP G+V   S      T+ + L      +   
Sbjct: 67  QEVVDADITPENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKNLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD--- 156
                   V R+D++T GLL++  +  +A       L +    R Y    HG +  D   
Sbjct: 127 NGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMAKSVKRKYVALVHGNIPHDYGT 185

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +    V+           +         +   L  G+  +I+
Sbjct: 186 VDAPIGRNKKDRQAMA---VVDDGKEAVTHFNVLEHFKDYTLIECELETGRTHQIR 238


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 79/237 (33%), Gaps = 44/237 (18%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V   +   R+ K ++   I  A+R  +E++I    VK+N  ++ +    +   + IEV  
Sbjct: 12  VNSEYEGMRLDKYLSEQ-IEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVSI 70

Query: 63  ------DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVF-------DNLPSI 104
                 D  P               + +K  G+V   +  +   T+        +NL SI
Sbjct: 71  PEEENIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSI 130

Query: 105 FSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL-- 158
              +    + RLD +T GL+L+         L          + Y     G   ++ L  
Sbjct: 131 NGNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSG 190

Query: 159 -------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +V +          +  Q    + V V +  G+  +I+
Sbjct: 191 RIENLIGRDSKDRKKMA--VVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIR 245


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 48/227 (21%), Positives = 84/227 (37%), Gaps = 38/227 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKA 70
           QR+ + +       SR  ++++I    V +NGI++ + +  V + D   IE+   P  +A
Sbjct: 39  QRLDRALVELVPEFSRSYLQQLIDLGGVTINGIVIHKPSTRVKAADVGTIELRPTPQSQA 98

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVG 112
                       E   L + +KP GLV   +  +   T+ + L           R   V 
Sbjct: 99  FKPETMALNVVFEDEHLMVINKPAGLVVHPAPGNWSGTLLNGLLARDAKAMNLPRAGIVH 158

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVY------------RVRFHGQVDQDKL 158
           RLD +T GL+++     +   L     + +  R Y            RV  +  + +D  
Sbjct: 159 RLDKDTSGLMVVARTRPVMDALIRSIAAREVSRQYVALAHGPWTGNRRVEINAPIGRDPR 218

Query: 159 NLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           N L+  +V             V L        WV   L  G+  +I+
Sbjct: 219 NRLRMAVVDLARNPGKLARTDVELLQNCDQGCWVLCTLHTGRTHQIR 265


>gi|124024488|ref|YP_001018795.1| pseudouridylate synthase specific to ribosomal large subunit
           [Prochlorococcus marinus str. MIT 9303]
 gi|123964774|gb|ABM79530.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9303]
          Length = 324

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 84/239 (35%), Gaps = 39/239 (16%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR 68
           P R+ + + ++    SR  +++ I    V+VNGI    A   +   D +++      PL 
Sbjct: 27  PMRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGR-AKTPLRQGDEVQLWMPPPEPLP 85

Query: 69  KA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS 110
                        E   L + +KP GL    +  +   T+ +       +LP I  ++  
Sbjct: 86  YLQPEAMHLDVLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLHHCSDLPGISGKLRP 145

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKK-G- 164
             V RLD +T G +++         L+    +    R Y    HG    D+  ++   G 
Sbjct: 146 GIVHRLDKDTTGCIVIAKSQEALVKLQQQIQKRIASRNYLAVVHGAPTGDQGTIVAAIGR 205

Query: 165 ----------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     +   G  +     TL  + G  + +   L  G+  +I+         + 
Sbjct: 206 HPVDRKKYAVVTEDGGRHACTHWTLVERLGDYSLLRFQLDTGRTHQIRVHCAHIGHPIV 264


>gi|119713310|gb|ABL97374.1| putative ribosomal large subunit pseudouridine synthase D
           [uncultured marine bacterium EB80_02D08]
          Length = 310

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 83/234 (35%), Gaps = 35/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  KN+   N   +R+ K  A      SR ++++ I   +V VNG +  +    V   D 
Sbjct: 1   MIIKNVPN-NLALKRLDKAAAEMFTDYSRTQIKKWIEDGKVLVNGEI-SQPREKVHENDE 58

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLV----TTHSDPDGRSTVFDNLP 102
           IE++    +K              E     + +KP GL+    +   D    + +    P
Sbjct: 59  IELNPAEEQKVSWEPEDIQFEVHFENEDFIIINKPAGLIMHPGSGCYDGTLANGLIFKFP 118

Query: 103 S--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY--RVR-------- 148
                 R   V RLD +T G+LL+                 + ++ Y   V         
Sbjct: 119 ELVNIPRSGIVHRLDKDTSGILLVARTESFRNFFINEMQERRVIKKYSSIVIGSTLGSFS 178

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +DK N  K  I   G       V L    G+ + + V +  G+  +I+
Sbjct: 179 IEDPIGRDKNNRTKMAIREDGKDALT-FVKLKENIGNYSVLDVRIETGRTHQIR 231


>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 = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 84/237 (35%), Gaps = 36/237 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  I+    + +R+ K +A      SR  ++ +I    V VNG   +   + +   D 
Sbjct: 1   MEEIIIIFNELSSKRIDKFLAEQLDGYSRSFIQNIIDGNNVLVNGKPCKS-NLKLKMQDE 59

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + + L    E   L + +KP G+V   +     +T+ + L     
Sbjct: 60  ITVIIPEPQEMNVVPENISLNILYEDEDLIVINKPQGMVVHPASGVYNNTLVNALLYHCK 119

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
            +           V R+D +T G++++  +      L   L      R Y     G + +
Sbjct: 120 DLSGINGKLRPGIVHRIDKDTSGVIVVAKNDKSHNFLAAQLKEHSMKREYIALVEGIIKE 179

Query: 156 DK-------LNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++           K+ I I   +G         +  +   N  V   L  G+  +I+
Sbjct: 180 EEGTINQPLARDPKERIKIAVVKGGREAITHYKVIERFKENTLVRCILETGRTHQIR 236


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 46/226 (20%), Positives = 85/226 (37%), Gaps = 38/226 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ + +       SR  +++++AQ  V +NG  + +AA  V + D + ++  P  +++  
Sbjct: 50  RIDRALVELVPEFSRSYLQQLLAQGGVSLNGRPVRKAASRVNAGDRVVLEMRPTVQSQAF 109

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
           R              L + +KP GLV   +     +T+ + L +         R   V R
Sbjct: 110 RPQPMDIDVVYEDAHLLVLNKPAGLVVHPAPGHWSATLLNGLLARDANALLLPRAGIVHR 169

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLN 159
           LD +T GL+++  D      L  ++   Q  R Y    HG             + +D  N
Sbjct: 170 LDKDTSGLMVVARDRATMDALVAQIARRQVQRQYLALAHGAWSGPRSRSVQAPIGRDPRN 229

Query: 160 LLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L+  +V             V          W+   L  G+  +I+
Sbjct: 230 RLRMAVVDLARHAGKCARTDVLCLDATPQGCWLQCRLHTGRTHQIR 275


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 82/239 (34%), Gaps = 42/239 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA 70
           R+ K IA     SR +++ +I  + V VN  L+ + +  V     I++    D  P  +A
Sbjct: 11  RIDKYIASNSSLSRADIQELIKSKAVFVNNGLVCKPSYIVHPPQEIKIIRLLDKTPKIEA 70

Query: 71  ---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVISV 111
                    E   L +  KP GL+   S     +T+ + L   F           R   V
Sbjct: 71  QNIKLDIIYEDDHLVIIDKPSGLIVHPSPTHYENTLANGLLYHFKNNLSDTNGLLRPGIV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            R+D +T GLL++T    +   L     +    R Y       +   KL  +   I +  
Sbjct: 131 HRIDKDTSGLLIVTKTNAVHIKLAEMFKNHSIKRSYIAICDNFLTDKKL-RINLPIGLDP 189

Query: 170 ICYGDMQVTLDTQKGSNAWVTVG---LRE-------------GKNREIKKVFEFFNWKV 212
                 +VT    K +   V +      E             G+  +I+      N  +
Sbjct: 190 KNPQKRKVTNIKAKEAITNVELIKTFYHEKQPKSLVKCNLETGRTHQIRVHLAHINNPI 248


>gi|84995704|ref|XP_952574.1| hypothetical protein [Theileria annulata]
 gi|65302735|emb|CAI74842.1| hypothetical protein TA11550 [Theileria annulata]
          Length = 238

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 67/183 (36%), Gaps = 29/183 (15%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNL--------------PSIFSRVISVGRLDINTEGL 121
            L HKP G ++T+S    + +    +              P   ++++ +  L++   GL
Sbjct: 67  VLLHKPYGYMSTYSKNSQKWSKNLLIKENRSDNDIQTGLEPCKLNKIVPISPLEVKCSGL 126

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           L+ + D  L        +     + V F  +V   KL  L   I + G   G + V   +
Sbjct: 127 LIYSQDKSLFNKF----SDCEEEFYVVFKDKVTDYKLRFLTGEIFLDGCSVGHVLVKDHS 182

Query: 182 QKGSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +K ++       V L        +K+      ++  L R      +LG+L  G  R +  
Sbjct: 183 EKSASISFKGSSVKL--------RKICLLAGLEIKTLKRTRISNIKLGSLSLGEWRLIRP 234

Query: 239 KIL 241
             L
Sbjct: 235 YEL 237


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 84/233 (36%), Gaps = 38/233 (16%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            ++E    +R+ K ++      SR ++   I+   +KVNG  ++ A   V + D I +D 
Sbjct: 7   TIEEQQQGERIDKALSSLQSEWSRTQIGNWISDGVIKVNGDAVK-AKYKVKAGDIIAIDV 65

Query: 65  VPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
             + +              E   + + +KP G+V   +      T+ + L      +   
Sbjct: 66  PEVEELDVVPENLDLDIVYEDADVLVVNKPKGMVVHPAPGHMGGTLVNGLMYHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--------- 151
                   V R+D +T GLL++  +      L     +    R Y    HG         
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDTAHESLVNQLVNKTVTRKYIALVHGHIAHDKGTI 185

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              + +D+ +  K+ +V     +      +  + G    V   L  G+  +I+
Sbjct: 186 DAPIGRDQKDRQKQAVV-DNGKHAVTHFQVVERFGDYTLVECRLETGRTHQIR 237


>gi|256028259|ref|ZP_05442093.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289766191|ref|ZP_06525569.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
 gi|289717746|gb|EFD81758.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D11]
          Length = 328

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 42/236 (17%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VNSKYEGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVLIP 71

Query: 63  -----DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                D  P               + +K  G+V   +  +   T+        +NL SI 
Sbjct: 72  EEENIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSIN 131

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL--- 158
             +    + RLD +T GL+L+         L          + Y     G   ++ L   
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENLSGR 191

Query: 159 ------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +V +          +  Q    + V V +  G+  +I+
Sbjct: 192 IENLIGRDSKDRKKMA--VVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIR 245


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 82/239 (34%), Gaps = 50/239 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            ++E    +R+ K ++      SR ++   I+   +KVNG  ++ A   V + D I +D 
Sbjct: 7   TIEEQQQGERIDKALSSLQSEWSRTQIGNWISDGNIKVNGDAVK-AKYKVKAGDVIAIDV 65

Query: 64  --GVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
               PL             E   + + +KP G+V   +      T+ + L      +   
Sbjct: 66  PEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAPGHMTGTLVNGLMYQCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y    HG +  D    
Sbjct: 126 NGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHD---- 181

Query: 161 LKKGIVIQ-----GICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
             KG  I             Q  +D  K +     V        L E     G+  +I+
Sbjct: 182 --KG-TIDAPIGRDQKDRQKQAIVDNGKHAVTHFHVVERFGDYTLVECRLETGRTHQIR 237


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V+E+   +R+ + +A A    SR  ++ ++    V V+G ++ + +  V   + +     
Sbjct: 14  VEEHQAGKRLDQFLAEAYPDFSRSYIKELVEGGYVLVDGQVVYKPSRKVKGGEVVVLCVP 73

Query: 61  EVDGVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           +V+ + L   +     LY         KP GLV   S      T+ + L   +  + +VG
Sbjct: 74  KVEPLSLPAEDIPLEILYEDDDLAVVVKPCGLVVHPSPGYTSGTLVNALLFRWRDLPTVG 133

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLL 161
                    RLD NT G++++       R L       + L+VYR    G V++D+   L
Sbjct: 134 EWYRPGIVHRLDRNTMGVMVVAKRELAHRRLAEQFEKRKVLKVYRALVKGLVERDE-GTL 192

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSN-------------AWVTVGLREGKNREIKKVFEFF 208
              +           V+   +                 + + + +  G+  +I+      
Sbjct: 193 SMPLARDPRHRKRFTVSEKGRDAITHYKVLKRYRSLSVSLLEIRIYTGRTHQIRVHMAGI 252

Query: 209 NWKVN 213
              V 
Sbjct: 253 GHPVL 257


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 84/240 (35%), Gaps = 33/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L   + + Q +R Y     G          
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKTMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 81/238 (34%), Gaps = 40/238 (16%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           R+       +A   I SR +V   I      V+G +  +  + +   + + +        
Sbjct: 27  RLDAFWSARLASEDI-SRAKVRAAIEAGLALVDGEICRKPGLKLRGGEALTLRLPETPSE 85

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
               DG          + + +KP GL    +      T+ + L   F  + +        
Sbjct: 86  AKAEDGELKLLYLDGDVLVLNKPAGLTIHPASSQPDGTLVNRLLHHFPDMRAMAGDRPGI 145

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-LNLLKKG--- 164
           V RLD +T GLLL+  T    LA   +    +  + Y    HG+ ++   +  L  G   
Sbjct: 146 VHRLDKDTSGLLLVAQTESARLALAADFAERRVAKTYLALVHGRPERSDGVIELPVGRDP 205

Query: 165 -------IVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +V +G        ++      G+ + + V +  G+  +I+         + 
Sbjct: 206 KHPTKMAVVAKGGREAKSSWKLAWTAPDGTASLLEVAIATGRTHQIRVHMAAMGHPIV 263


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 47/264 (17%), Positives = 90/264 (34%), Gaps = 49/264 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + + F  +R+    A  G      SR  +   I + +V V+G+++ + ++ V S   + 
Sbjct: 8   TITDEFHNKRLD---AALGGLIDTHSRSTLREYIDEGKVAVDGVVITKPSIKVSSGQIVS 64

Query: 62  V--------DGVPLRKAERTRL-----WLYHKPIGLVTT----HSDPDGRSTVFDNLPSI 104
           V        D  P               + +KPI  V        D    + V  + P  
Sbjct: 65  VTIPDPEDLDAKPQDLPLDIIYQDDDILIINKPINFVVHPGAGIKDGTVMNAVLYHFPQT 124

Query: 105 --FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVD------ 154
               R   V RLD +T GL+++       +VL     +    R Y     GQ+       
Sbjct: 125 SSLPRAGIVHRLDKDTSGLMVIALSQLAQQVLTKAIAKHDVVREYEAIAEGQITAGGTID 184

Query: 155 ---------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                    + K+ ++ +GI             +  +  ++  + + L  G+  +I+   
Sbjct: 185 APIGRDPYVRTKMAVMPEGI----GREAVTHYRVMERFRAHTRLRLRLETGRTHQIRVHM 240

Query: 206 EFFNWKVNRLIRISYGPFQLGTLL 229
              +  +  L    YG  +L  L 
Sbjct: 241 ASIHHPL--LGDNQYGGKRLKMLP 262


>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 = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 90/240 (37%), Gaps = 40/240 (16%)

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------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I V            + +PL    E + + + +KP G+V   +      T+ + L    
Sbjct: 60  EILVRIPEAVELEVLPEDIPLDVVYEDSDVIVINKPKGMVVHPAAGHVSGTLVNALLHHC 119

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D +T GLL++  +      L   L      R+Y    HG++ 
Sbjct: 120 QDLSGINGVKRPGIVHRIDKDTSGLLMVAKNDLAHESLAQQLKDKTTERLYIALVHGEIP 179

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
            + L  ++  +         M VT    K +     V        + E     G+  +I+
Sbjct: 180 HE-LGTIEAPVGRDKNDRQRMTVTDKNSKAAVTHFRVLERYEGFTVVECKLETGRTHQIR 238


>gi|258593870|emb|CBE70211.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [NC10 bacterium 'Dutch sediment']
          Length = 314

 Score = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/233 (16%), Positives = 80/233 (34%), Gaps = 34/233 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI-----LLERAAVN----VMSTDHIEVDGV 65
           R+ + ++ A    R +++R+I   RV V+G       +          +       +   
Sbjct: 19  RLDRYLSTATGLPRSQIQRLIKAGRVLVDGRCPKASAIAHPGQQISLSIPPPQPSTLTPE 78

Query: 66  PLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------R 113
           P+      E T + + +KP GLV   +      T+   +      +  +G         R
Sbjct: 79  PIPLDILYEDTDMLVLNKPAGLVVHPAPGHHSGTLVHAILYHCPDLPGIGEERRPGIVHR 138

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK-GIVIQGI 170
           LD  T G++++  T+    +   +    +  + Y    HG+V Q +  +    G   +  
Sbjct: 139 LDKETSGVMVVAKTDTAMASLATQFKGRRVQKTYIALVHGEVKQPQGQIAADIGRHERDR 198

Query: 171 CYGDMQVTLDTQKGSNAWV-----TVGLRE-----GKNREIKKVFEFFNWKVN 213
               ++     +  +N  V      + L E     G+  +I+         V 
Sbjct: 199 KRMAVRTRKGREAVTNYRVIKRLGGLTLLELQPQTGRTHQIRVHLSAIGHPVV 251


>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 = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 76/249 (30%), Gaps = 52/249 (20%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           I  E    +R+ K ++      SR ++++ I +  + VN   ++     +   D I+++ 
Sbjct: 15  IAGEEHAGERIDKFVSECLDGVSRTQIQQWIKEGHISVNEKQVK-PNYKLAEGDRIKLNI 73

Query: 64  ---------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                      P+      E   + + +KP G+V   +      T+ + L      +   
Sbjct: 74  PDPEQVDIRPEPIPLDIYYEDKDVIVVNKPRGMVVHPAPGHSSGTLVNALMYHCKDLSGI 133

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GL++          L          R Y     G +  ++   
Sbjct: 134 NGEMRPGIVHRIDKDTSGLIMAAKHDKAHASLADQLKEHSVTRKYLALVQGNLAHEQ--- 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
                       G ++  +          TV  +  K        E     V       +
Sbjct: 191 ------------GTVEAPIGRDPKDRKLYTVTEKNSK--------EAVTHFVVM---ERF 227

Query: 221 GPFQLGTLL 229
           G + L  L 
Sbjct: 228 GDYTLTELK 236


>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 = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 51/300 (17%), Positives = 102/300 (34%), Gaps = 54/300 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG---------ILLERAAVN--V 54
             Q +   +R+   +A     +R  V+++I    V+++G          +    A++  V
Sbjct: 24  TPQGDEEGKRIDAFLAEELGLTRSYVQKLIRLGNVEISGIRRALKPALKVTAEMAIHIVV 83

Query: 55  MSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
              + +E++  P++     E   + + +KP GLV   +  +   T+   L   +      
Sbjct: 84  PPAETLEIEPEPVKFGIIYEDPYIIVVNKPAGLVVHPAPGNWHGTLVHGLLYKYRDMRKF 143

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV-----------RF 149
               R   V RLD  T GLL++     + + L+    S    + Y               
Sbjct: 144 DEEVRPGIVHRLDSGTSGLLVVARTPKILQNLQNQFRSRSVEKKYLALSCGKLRKAAGFI 203

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + + + N L   +   G      +  +       +++   L  G+  +I+      +
Sbjct: 204 EEPIGRSQRNRLMMTVTDTGRPALT-EYRILWTHQKYSFIECTLHTGRTHQIR-----VH 257

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
            K     R    P     L        +K+ L+   G   L   ++  D PI  S    R
Sbjct: 258 LK----HRGC--PIVGDGL------YGTKQSLQRTPGRMFLHAWKLAFDHPINGSRMSFR 305


>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 = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 87/245 (35%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +P+    E   + L +K  G+V      +   T+ + L   FS++  
Sbjct: 81  PHPPRDTEVYPEDIPIDIIYEDNDVVLVNKVAGMVVHPGYGNWSGTLVNALTHHFSQLPQ 140

Query: 111 ----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL+++ +      L          R Y     G + +D +
Sbjct: 141 LPGNDGRPGLVHRIDKDTSGLLVISKNEKSMASLAKQFFDHSIKRKYLALVWGDLPEDGI 200

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------VGLRE-----GKNREIKKVFE 206
                G  I+     D+    +  K S            V L E     G+  +I+   +
Sbjct: 201 ISGYIGRSIKDRKVMDLYDDPEKGKWSVTHYKVVKRLNYVTLIECQLETGRTHQIRAHMK 260

Query: 207 FFNWK 211
                
Sbjct: 261 AIGHP 265


>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 = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>gi|254556664|ref|YP_003063081.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045591|gb|ACT62384.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 307

 Score = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 25/166 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ KV+A    + +R +V+++I   +V VNG L E +  +V   D I V    +++    
Sbjct: 18  RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQL-EASKYHVKPGDEIVVAAQTVQQTTIE 76

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                     E   + + +KP G+V   +      T+ + L             R   V 
Sbjct: 77  PENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
           R+D +T GLL++  +    + L   L +   LR Y    HG + +D
Sbjct: 137 RIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKED 182


>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 = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 82/243 (33%), Gaps = 42/243 (17%)

Query: 1   MKDKNIV----QENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M D   V    +E    QR+ K +AR     SR   ++++    V ++G + + A+  + 
Sbjct: 1   MSDSENVWLKAEEQDENQRIDKYLARVMPEISRSYFQKLLKDGGVFIDGKVAK-ASDRLQ 59

Query: 56  STDHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRST----VF 98
             D I       R+              E   L + +KP G+V          T    V 
Sbjct: 60  CGDEIYFQMPKSREPDIEPEDLSLDILYEDPYLLVINKPKGMVVHPCPGHYSGTLVNGVL 119

Query: 99  DNLPSIFSRVISV------GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFH 150
            +     S +  V       R+D +T G L++  D    R L   L      R YR    
Sbjct: 120 FHCKGQLSGINGVLRPGIVHRIDKDTTGALVVCKDDQTHRNLAVQLAEHTITRRYRAIVT 179

Query: 151 GQVDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G +  D+           ++  K  I  +          +  + G   ++   L  G+  
Sbjct: 180 GNLSADEGTVEGPIGRHPVDRKKMSINFKNGKDAVTHYRVLERFGKATYIECRLETGRTH 239

Query: 200 EIK 202
           +I+
Sbjct: 240 QIR 242


>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 = 81.8 bits (201), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 46/222 (20%), Positives = 85/222 (38%), Gaps = 35/222 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ KV+A    + +R +V+++I   +V VNG L E +  +V   D I V    +++    
Sbjct: 31  RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQL-EASKYHVKPGDEIVVAAQTVQQTTIE 89

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                     E   + + +KP G+V   +      T+ + L             R   V 
Sbjct: 90  PENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 149

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------NL 160
           R+D +T GLL++  +    + L   L +   LR Y    HG + +D              
Sbjct: 150 RIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKEDTGTINAPLGRSPKD 209

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            KK  +I+          +  +      ++  L  G+  +I+
Sbjct: 210 RKKQAIIKTGRPAVTHFKVLKRYQHYTLISCRLETGRTHQIR 251


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 82/227 (36%), Gaps = 40/227 (17%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A      SR  ++++I Q +V+VNG +     +N+   D I +           
Sbjct: 15  RIDRYLAEELPDLSRSRIQQLIEQGKVQVNGKVCTSKKINLKVGDRITLEVPEAQPLEIQ 74

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
            + +PL    E  +L + +KP GLV   +      T+ + L +    +  +G        
Sbjct: 75  AEDIPLDILYEDDQLLILNKPAGLVVHPAPGHSHGTLVNALLAHCPDLPGIGGVQRPGIV 134

Query: 113 -RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD-------------QD 156
            RLD +T G + +  T+        +L +    R Y    +G                  
Sbjct: 135 HRLDKDTTGAIAIAKTDIAYKHIQAQLQAKTARREYLGVVYGAPKTASGKVDLPIGRHPQ 194

Query: 157 KLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +   + I +G         +  + G+   +   L  G+  +I+
Sbjct: 195 DRKKMAV-VPIEEGGRSAITHWQIQERLGNFTLIHFQLETGRTHQIR 240


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 40/166 (24%), Positives = 70/166 (42%), Gaps = 25/166 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ KV+A    + +R +V+++I   +V VNG L E +  +V   D I V    +++    
Sbjct: 18  RLDKVLAALQSVWTRSQVDKLIKTDQVTVNGQL-EASKYHVKPGDEIVVAAQTVQQTTIE 76

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                     E   + + +KP G+V   +      T+ + L             R   V 
Sbjct: 77  PENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 136

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
           R+D +T GLL++  +    + L   L +   LR Y    HG + +D
Sbjct: 137 RIDKDTSGLLMVAKNDRAHQSLAAQLKAKTNLREYVALVHGVIKED 182


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 51/289 (17%), Positives = 109/289 (37%), Gaps = 48/289 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ + +A A    SR    ++I    V +NG  + R++  V     +EV          
Sbjct: 1   MRLDQYLASAIPDFSRSFARKIIDLGGVHLNGRRMRRSSFPVPGHAAVEVYLDHRDLDIF 60

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSR-----VISV 111
             D   +   +R  L + +KP G+ +  +    + T+++     L   +++     +  V
Sbjct: 61  ALDDEHILLRDR-YLVVVNKPPGINSQPTPARYKGTLYEALLRLLDDPYNKGRKPSLGMV 119

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ---VDQDKLNLLKKGI- 165
            RLD +T G+++ +      + L     + +  + Y     G       +  +LL +   
Sbjct: 120 QRLDRDTSGVMIFSIHARAHKSLSDIFAARRVQKHYLALVAGCMQAPQGEFRSLLARQHR 179

Query: 166 ------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
                 V +G      +  +  + G    + V +  G++ +I+  F      +  L  I 
Sbjct: 180 TNLMKSVARGGKEAVTRYRVIEKFGDAELLEVEIPTGRSHQIRVHFAEAGHPL--LGDIR 237

Query: 220 YGPFQLGTLLAGSTR--EVSKKIL--REQLGPHLLEEAQVNLDAPIYSS 264
           YG            R  +V +++L  R     H + +  +N++AP+   
Sbjct: 238 YGG-------PDRWRGVDVPRQMLHARRLELLHPISKEPLNIEAPLPQD 279


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 86/244 (35%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV+VNG ++ +    V+  + I VD 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKPKEKVLGGEQILVDA 69

Query: 64  -----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP GLV      +   T+ + L   +  ++  
Sbjct: 70  LIEEDNRWEPQDIPLDVVYEDEDILVINKPRGLVVHPGAGNPDGTILNALLHRYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAVGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIKKVFEF 207
           G+V + I     + T                      ++  + + L  G+  +I+     
Sbjct: 183 GMVEEPISRHPTKRTHMAVHPMGKPAITHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            N  
Sbjct: 243 INHP 246


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 85/237 (35%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           R+ + +A  GI    SR  ++++I    V++NG  + + +  V + D + ++  P  ++ 
Sbjct: 49  RLDRALA--GIVPEFSRSYLQQLIEAAVVQLNGRAVTKPSAKVKAGDELIIELRPTPQSQ 106

Query: 71  -------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISV 111
                        E   L +  KP GLV   +  +   T+ + L       S   R   V
Sbjct: 107 AFKPEAMALDIVFEDPYLLVIDKPAGLVVHPAPGNWSGTLLNGLLARDPQASFLPRAGIV 166

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDK 157
            RLD +T GL+++         L   + +    R Y    HG             + +D 
Sbjct: 167 HRLDKDTSGLMVVARQRQAMDQLVSMIAARSVSREYIALAHGAWQGARTREVSAAIGRDP 226

Query: 158 LNLLK-KGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            N L+   + ++          ++L      +  V   L  G+  +I+         
Sbjct: 227 RNRLRMAAVDLEKNAGKPALTVISLLQNGERHCLVKCKLHTGRTHQIRVHMALLGHP 283


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 83/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K ++     SR      I + ++ VNG  +++A   V   D I              
Sbjct: 11  RLDKAVSELTELSRGLANEQIKEGKILVNGQ-VKKAKYTVKEGDVISYEVPQMEEVTYEA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVYQDADVVVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGELRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L     + + LR Y    HG            + +   +
Sbjct: 130 RIDKDTSGLLMVAKNDAAHVALADELKAKKSLRKYWAIVHGNLPNDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G      +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKPALT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 93/249 (37%), Gaps = 40/249 (16%)

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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I+V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QIKVEIPEPEALDVEAEAMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGII- 178

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
           Q     +   I         M VT ++ K +     V        + E     G+  +I+
Sbjct: 179 QHDTGTIDAPIGRDKKDRQSMTVTKESSKQAVTHFDVIERFDDFTVVECRLETGRTHQIR 238

Query: 203 KVFEFFNWK 211
              ++  + 
Sbjct: 239 VHMKYIGYP 247


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 83/240 (34%), Gaps = 33/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 13  KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 72

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 73  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 132

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L     + Q +R Y     G          
Sbjct: 133 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 192

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 193 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 251


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 90/249 (36%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +V   ++  R+ K +A       SR  ++++I + +V VNG L  +A+  V   + I 
Sbjct: 6   KVVVNSEYSGLRLDKFLAEQEELELSRSFIKKLIEEGKVTVNG-LHRKASYKVRGGEIIA 64

Query: 62  V------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V            + +PL    E   L + +K  G+V   ++ +   T+ + L      +
Sbjct: 65  VLLPPPRELSVKPEEIPLDIVYEDEDLVVVNKKAGMVVHPAEGNWDGTLVNALLYHCQNL 124

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--- 154
             +G         RLD +T GLL++  +    + L       + +R Y    HG +    
Sbjct: 125 SGIGGVLRPGIVHRLDKDTSGLLVVAKNDLAHQSLAEQIKEKKAVREYWTIVHGYLKNKE 184

Query: 155 ----------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                           +   +V  G     +   L+        +   L  G+  +I+  
Sbjct: 185 GIIDLPIGRHPRDRQKMA--VVSNGKTAQTVYKVLEEFNKGFTLIQAKLLTGRTHQIRVH 242

Query: 205 FEFFNWKVN 213
           F +    V 
Sbjct: 243 FSYLGHPVL 251


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 83/240 (34%), Gaps = 33/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 13  KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 72

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 73  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 132

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L     + Q +R Y     G          
Sbjct: 133 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 192

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 193 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 251


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 87/240 (36%), Gaps = 39/240 (16%)

Query: 11  FTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            T QR+ + + A     SR  ++  I   RV+VNG  ++  +  + + D +EV       
Sbjct: 9   DTGQRIDQWLHAHLPDFSRSRIQEWIKSARVRVNGAAVKT-SYTLRAADAVEVEPADPPP 67

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
                + +PLR   E   +    KP G+V          T+ + L   F+ +  VG    
Sbjct: 68  LNATAEDIPLRILYEDADVVAIDKPAGMVVHAGAGVHSGTLVNALLHRFATLSGVGGPLR 127

Query: 113 -----RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
                RLD  T G+LL+  +    + L       +  +VY    HG V  +    +++ I
Sbjct: 128 PGIVHRLDRFTSGVLLVAKNDAAHQKLAAQFSGREIEKVYLALVHGTVKPET-GRIERPI 186

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVN 213
               +    M   L   + + +   V        L E     G+  +I+         V 
Sbjct: 187 ARDPVHRARMTARLAEGRAAWSEYRVLRRFPDFTLLEVRIGTGRTHQIRVHLASIRHPVV 246


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 86/243 (35%), Gaps = 48/243 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +Q      R+ K I+      SR  V+ ++ ++ + VN   +E+ +  + + D 
Sbjct: 1   MPKKYELQVENEYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHK-VEKVSYKIQAGDK 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE++   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEINVPAVKPLDVVPENIPLDIVYEDEVVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++  +          L   + +  R+Y    HG 
Sbjct: 120 DLAQSPEGF-RPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK--RIYWAIVHGD 176

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V++          +  Q    + +   L  G+  
Sbjct: 177 FGEENGVIDAPIGRNPYDRKKMA---VVENGKKAVTHFKVLKQFKGYSLIECQLETGRTH 233

Query: 200 EIK 202
           +I+
Sbjct: 234 QIR 236


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 82/249 (32%), Gaps = 42/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    V VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEVLVNGKK-SKVSYKVQKGDL 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------- 99
           I+V  +PL                E   + + +KP G+V   +      T+ +       
Sbjct: 60  IQVTVLPLEPLKLEAENIPLDIVYEDEDIIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
           +L           V R+D +T GLL++  +      LE  L +    R Y    HG   +
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +                 +    V++          +  Q    + V   L  G+  +I+
Sbjct: 180 EEGTIDAPIGRNPKDRKQMA---VVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIR 236

Query: 203 KVFEFFNWK 211
               +    
Sbjct: 237 VHMAYIGHP 245


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/206 (18%), Positives = 68/206 (33%), Gaps = 38/206 (18%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
            +R+   ++     SR ++  +I    V+VNG +  +    + + + + +D         
Sbjct: 9   SERLDVFLSSQLGISRNQISNLIKSAAVRVNGAVQTKPGYKLSAGELVRIDYPASAPQQT 68

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------R 107
                   V +   +   L + +KP GL    +      T+ D L S            R
Sbjct: 69  SAERLNFDVEILYEDDD-LLVVNKPAGLTVHPAASVKEPTLVDWLKSRGYLLSTLGGELR 127

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFH----------GQVDQ 155
              V RLD  T G LL+  +      L   L      R+Y                 + +
Sbjct: 128 AGIVHRLDKLTSGALLVAKNNAAHAALSAQLSDKSMGRIYLALIDLPLKEPCVIERPISR 187

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDT 181
           +  N LK GIV  G         + +
Sbjct: 188 NPANRLKMGIVPGGRSAKSAFYEILS 213


>gi|311068067|ref|YP_003972990.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
 gi|310868584|gb|ADP32059.1| pseudouridylate synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 48/226 (21%), Positives = 81/226 (35%), Gaps = 47/226 (20%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M    I        +R+ K +A A    SR +V++ +    ++VNG  ++ A   +   D
Sbjct: 1   MDQFEITALPEQKSERIDKFLASAEKDWSRTQVQQWVKDGHIEVNGSPVK-ANYKMQPGD 59

Query: 59  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            ++V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QVKVTVPEPEALDVLAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHVTGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLT-ND---GGLARVLELPSTQWLRVYRVRFHGQ 152
             +           V R+D +T GLL++  ND     L   L   +    R Y    HG 
Sbjct: 120 KDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVHKT--VTRKYMAVVHGI 177

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
           +  D                G +   +   K     +TV  REGKN
Sbjct: 178 ISHDD---------------GTIDAPIGRDKKDRQSMTVV-REGKN 207


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 90/258 (34%), Gaps = 58/258 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK K   Q +    R+   +  +   +R ++  +I    V VNG L  +A   + ++D I
Sbjct: 1   MKFKITEQTDS---RLDHFLVASTELNRSQITTLIKDGLVMVNG-LTTKAGYKLKNSDEI 56

Query: 61  EVDGV------PLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
            ++        PL+          E   + + +KP GLV   S+    +T+   L     
Sbjct: 57  TLNLEAKEETNPLKPKNIDLNIVYEDDDIMVINKPKGLVVHPSETFSETTLVSGLLHHTD 116

Query: 102 -----PSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLE---LPSTQWLRVYRVRFHG 151
                     R   + R+D +T GL+L+  TN+   A  +    L S    R Y     G
Sbjct: 117 TLSTHNDDPLRPGILHRIDKDTSGLILVAKTNE---AHKILAQDLKSHDIKREYIALVEG 173

Query: 152 QVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNAWVTV------------GLRE 195
            +D +      KG+    + +          + T K +     V             L  
Sbjct: 174 VLDHN------KGVIDAPIARHPKIRTKMAVVATGKPAITHFEVMRTFRDHTLLHCKLET 227

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+    +    V 
Sbjct: 228 GRTHQIRVHLAYIKHPVT 245


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 83/240 (34%), Gaps = 33/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L     + Q +R Y     G          
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247


>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 = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 83/240 (34%), Gaps = 33/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 9   KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVRENQFIEI 68

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 69  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 128

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L     + Q +R Y     G          
Sbjct: 129 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 189 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 247


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 42/226 (18%), Positives = 76/226 (33%), Gaps = 38/226 (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  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
                     E   L + +KP GLV   +      T+ + L +   ++  +G        
Sbjct: 86  PEVIPLDILYEDDVLIIINKPAGLVVHPAPGHESGTLVNALLAHCPKLTGIGGVQRPGIV 145

Query: 113 -RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--KLNLLKKGIVI 167
            RLD +T G + +  T+        +L +    R Y    +G    +   +N       +
Sbjct: 146 HRLDKDTTGAIAIAKTDQAHGHLQAQLQAKTAQRQYLGVVYGAPSAESGTINQPIGRHPV 205

Query: 168 QGICYGDMQVTLDTQKGSNAW-----------VTVGLREGKNREIK 202
                  + V    +     W           +   L  G+  +I+
Sbjct: 206 DRKKMAVVPVEKGGRPAITHWQVRERLGNYTLMHFQLETGRTHQIR 251


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 85/248 (34%), Gaps = 50/248 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+ K +A      SR +V++ I    V VNG  ++     V   D I V  
Sbjct: 8   TVAEEQKSERIDKFVAEINSEWSRSQVQQWIKDDVVTVNGKSVK-VNYKVKGNDEITVTI 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            D   L             E   + + +KP G+V   +      T+ + L    + +   
Sbjct: 67  PDPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKK 203
             KG  I    G    + Q     + G NA      +       L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + +D 
Sbjct: 10  TVSESQLGQRLDQTLAELFPDYSRSRIKEWILNQRVSVNGTVTDKPKEKVLGGERVTIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP   V      +   TV + L   +      
Sbjct: 70  EIEEEQRWEPQNIPLDIVYEDEDIIVINKPRDFVVHPGAGNPDGTVLNALLHHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGTMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMSVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 80/233 (34%), Gaps = 35/233 (15%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           T  R+ + +A  G+    SR  ++  I    + ++GI +++    V  +  +EV      
Sbjct: 16  TGLRLDQALA--GLFPDYSRTRIKEWILSGAITIDGITVDKPREKVFESQLVEVTATLEE 73

Query: 63  ------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVI 109
                   + L    E   + + +K  GLV      +   T+ + L           R  
Sbjct: 74  EVSAKAQNIDLNIVYEDDHILVINKQAGLVVHPGAGNADGTLMNALLYHCPDIEHVPRAG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKLNLLK 162
            V RLD +T GL+++         L   L +   +R Y     G +       + +    
Sbjct: 134 IVHRLDKDTTGLMVVAKTVEAQTHLVAALQARDIVREYEAIVLGTMTAGGTVDEPIERHA 193

Query: 163 ----KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  VI G         +  +  ++  + + L  G+  +I+        +
Sbjct: 194 TRRTQMAVIHGGRPSVTHYRVSEKFRAHTRLRLRLESGRTHQIRVHMAHIGHE 246


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 86/243 (35%), Gaps = 48/243 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +Q      R+ K I+      SR  V+ ++ ++ + VN   +E+ +  + + D 
Sbjct: 4   MPKKYELQVENEYGRLDKFISEQIPDLSRTRVKELVKEKEILVNHK-VEKVSYKIQAGDK 62

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE++   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 63  IEINVPAVKPLDVVPENIPLDIVYEDEVVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 122

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++  +          L   + +  R+Y    HG 
Sbjct: 123 DLAQSPEGF-RPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK--RIYWAIVHGN 179

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V++          +  Q    + +   L  G+  
Sbjct: 180 FGEENGVIDAPIGRNLYDRKKMA---VVENGKKAVTHFKVLKQFKGYSLIECQLETGRTH 236

Query: 200 EIK 202
           +I+
Sbjct: 237 QIR 239


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 82/249 (32%), Gaps = 42/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    V VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTNLSRSRIKELVQAGEVLVNGKK-SKVSYKVQKGDL 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------- 99
           I+V  +PL                E   + + +KP G+V   +      T+ +       
Sbjct: 60  IQVTVLPLEPLKLEAENIPLDIVYEDEDVIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
           +L           V R+D +T GLL++  +      LE  L +    R Y    HG   +
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +                 +    V++          +  Q    + V   L  G+  +I+
Sbjct: 180 EEGTIDAPIGRNPKDRKQMA---VVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIR 236

Query: 203 KVFEFFNWK 211
               +    
Sbjct: 237 VHMAYIGHP 245


>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 = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 81/234 (34%), Gaps = 38/234 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K +A     A+R  +E++I    VK+N  ++ +    + S + +E+   
Sbjct: 12  VNPEYEGMRLDKYLAEQIEEATRSYLEKLIDNSYVKINSKIINKNGRKLKSGEKVEISIP 71

Query: 63  ---------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV- 111
                    + +PL    E     L +K   +V   +  +   T+ + L    + + SV 
Sbjct: 72  EEENIDIEAENIPLDIVFENDDFILVNKKYNMVVHPAYGNYTGTLVNALLYYTNNLSSVN 131

Query: 112 --------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-- 159
                    RLD +T GL+L+  +      L          + Y     G    + L   
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKNNFAHAKLASMFTDKTIHKTYLCIVKGNFSDENLEGR 191

Query: 160 ---------LLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +K + I  +          +  Q    + V V +  G+  +I+
Sbjct: 192 IENLIGRDTKDRKKMAIVKENGKLAISNYRVVEQVKDYSLVEVLIETGRTHQIR 245


>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 = 81.0 bits (199), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 88/248 (35%), 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  HIEV---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I+V   +   L             E   + + +KP G+V   +      T+ + L +  
Sbjct: 60  QIKVEIPEPEVLDVEAEPMDLDIYYEDADVLVVNKPRGMVVHPAPGHVSGTLVNGLMAHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L     +    R Y    HG + 
Sbjct: 120 TDLSGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRKYTAVVHGIIQ 179

Query: 155 QDKL---------NLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKK 203
            D              ++ + +            D  +       V   L  G+  +I+ 
Sbjct: 180 HDTGTIDAPIGRDKKDRQSMTVTKESAKQAVTHFDVIERFQDFTVVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 81.0 bits (199), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 85/237 (35%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
                 + +P+    +   + + +K  G+V   S      T+ + L    + +       
Sbjct: 69  SLEVLAEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNALMHHITDLSGINGTI 128

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++  +      L   L     LR Y    HG +  +K       
Sbjct: 129 RPGIVHRIDKDTSGLLMVAKNDAAHEKLAAQLKDKTSLREYIALVHGVIPHEKGTIDAPL 188

Query: 158 ---LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  KK  +I G        T+  +      V++ L  G+  +I+   ++  + 
Sbjct: 189 GRSKQDRKKQDIIDGGRAAVTHFTVLERFKDFTLVSLKLETGRTHQIRVHMKYIGYP 245


>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 = 81.0 bits (199), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 80/236 (33%), Gaps = 40/236 (16%)

Query: 7   VQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++ N    R+ K +    A +   SR  ++ +I    V VNG +  +   N++    IE+
Sbjct: 3   IKANVEKVRLDKYLVDALAESTEYSRSYIQTLIKDGNVIVNGNVETKQNFNLIGDIEIEI 62

Query: 63  DGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPD----------GRSTVFD 99
           +   ++               E   + + +KP  +V      +          GR   F 
Sbjct: 63  NIPEVKTSTINPEKIDLDIVYEDDDILVVNKPNNMVVHPGAGNTEGTMVNALLGRDAEFL 122

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDK 157
           +      R   V R+D  T GLL++  +    +VL          + Y     G++ +DK
Sbjct: 123 STIGGVERPGIVHRIDKQTTGLLIVAKNDKSHQVLTEMLKNHEIYKEYVALVWGEIKEDK 182

Query: 158 L-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       +  K  +  +   Y      +  +      V   +  G+  +I+
Sbjct: 183 GIIDAPIGRHQNDRKKMMVTSKNSKYAVTNFEVIKRLDKTTLVKCAIETGRTHQIR 238


>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 = 81.0 bits (199), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 90/247 (36%), Gaps = 38/247 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M +  + +ENF  QR+   +A+    SR +++ +I  ++V VN   ++ A   +   D I
Sbjct: 1   MDNFKVDKENF-GQRLDVYLAKLVDLSRSQIKNLIDNEKVLVNKKNVK-AGYKLSEDDVI 58

Query: 61  EV----DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
            +    D  P  +        E   + +  KP  LV      +   T+ + L   F    
Sbjct: 59  SLEYPKDNKPFAEKIDFNVIYEDEYIAVISKPQDLVVHIGAGNSSGTLVNGLLYKFKNQL 118

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD NT GL+++  +      L     ++Q  + Y    HG+  +   
Sbjct: 119 SDLDPLRPGIVHRLDKNTSGLMIIAKNNQAHINLVDQFKNSQIKKYYLAIVHGKTPESGI 178

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                    +    +   +V +       +     +    + + + L  G+  +I+    
Sbjct: 179 IAEPIGRNPNDRKKMA--VVYKNSKQAITKYKKLKEFQEYSLLNINLLTGRTHQIRVHMA 236

Query: 207 FFNWKVN 213
           +  + V 
Sbjct: 237 YIGYPVL 243


>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 = 81.0 bits (199), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/211 (19%), Positives = 81/211 (38%), Gaps = 35/211 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------------DGVPLRKA- 70
           E+ + ++ + VN   ++     +   D + +                    D   L+K  
Sbjct: 36  EKNLRKKNITVNNKKVKNL-FKLEINDIVNIFTELKIENKINKKKQIFNINDYNELKKNF 94

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             E     + +KP G  +       + +V D L S       V RLD +T GL+LL  + 
Sbjct: 95  VFECEDYCVLNKPYGYASQ-DGSKVKLSVIDILNSTKKNYYIVHRLDKDTSGLMLLAKNR 153

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK----GIVIQGICYGDMQVTLDTQ 182
             A+       S +  + Y V  +G++ ++K  +  K    G  I+   Y      + ++
Sbjct: 154 FYAKKFSEMFKSREVKKKYLVIINGKIKKNKGEIHSKEKVNGKEIESKLY----FEVISK 209

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           K + +++ + L  G+  +I+K F      V 
Sbjct: 210 KNNFSYLEIDLITGRKHQIRKQFSDIGHPVV 240


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 88/237 (37%), Gaps = 52/237 (21%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R ++++   +  + VN  ++++    V + D ++V      
Sbjct: 38  EPLRVDKFLMN--FIENATRNKIQKAAKEGNIYVNDAVVKQ-NYKVKAGDEVKVLFEHPP 94

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSR 107
                  + +PL    E   + + +KP G+V      +   T+       FDNLP+  S 
Sbjct: 95  YEMLLTPEDIPLNIVHEDDDVLVVNKPAGMVVHPGHGNYSGTLINALVFHFDNLPNNSSN 154

Query: 108 VIS-VGRLDINTEGLLLLTNDGGLARVLELPSTQW-----LRVYRVRFHGQVDQDK---- 157
               V R+D +T GLL++         +   S Q+      R Y     G V+ D+    
Sbjct: 155 RPGLVHRIDKDTSGLLVVA---KTEHAMTHLSKQFFNKTSSREYIALVWGNVEDDQGTIE 211

Query: 158 -------LNLLKKGIVIQ---GICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                   N L+  + ++               +  + G    ++  L  G+  +I+
Sbjct: 212 GHIGRHPKNRLQNTVFLEDDADEKGKPAVTHYKVIERLGYVTLLSCKLETGRTHQIR 268


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 79/210 (37%), Gaps = 31/210 (14%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL-----WLYHKPI 82
           R + + ++  + V+VNG +    A  +   D +EV G                 + +KP 
Sbjct: 22  RNDCKNLLKYKSVQVNGEVQTYHAFELHPGDEVEV-GKKTNLPFELLYEDDDMIVINKPS 80

Query: 83  GLVTTHSDPDGRST----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           GLV+  +  +   T    V +       +   V RLD +T G+L+   +  L + L    
Sbjct: 81  GLVSEETRNNKYQTAFYMVMEYCRKKRQQCYLVHRLDQDTSGVLMFVKNKKLYQELTHNW 140

Query: 139 TQWLRV--YRVRFHGQ-----------VDQDKLNL--LKKGIVIQGICYGDMQVTLDTQK 183
            ++++   Y     GQ           V+  +L +   K+G  +    Y  ++V+ D   
Sbjct: 141 NKYVKTRGYVAILEGQCRKSGTIKNHLVEDKQLKMRIAKEG-QLAITHYKPLEVSKD--- 196

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                + V L  G+  +I+      N  + 
Sbjct: 197 --YTMMEVFLDTGRKNQIRVHMASLNHPII 224


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 83/240 (34%), Gaps = 33/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K I+       R+ +V+A+     SR +++  I    VKV+GI   +A   V     IE+
Sbjct: 13  KKIIPPELAGARLDQVLAKLFPDYSRSQLQNWIRGGHVKVDGIQKTKAREKVWENQFIEI 72

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +                    E   L + +KP+GL+          T+ + L      + 
Sbjct: 73  EAQLEPNERWVPQPIPLDVIYEDETLLVINKPVGLIVHPGAGVRDQTLINALLHYDPSLS 132

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
            V       RLD +T GLLL+         L     + Q +R Y     G          
Sbjct: 133 VVPRAGIIHRLDKDTSGLLLIARTLASHHALIKAMKARQIVREYEAIVKGVLISGRTIEA 192

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            V +  ++  +  +V +          +  +  ++  + V L  G+  +I+      +  
Sbjct: 193 PVGRHPIHRTRMAVV-EFGRPAITHFRIIKRYRAHTHIRVQLETGRTHQIRVHMAHIHHP 251


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 78/236 (33%), Gaps = 42/236 (17%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V   +   R+ K ++     A+R  +E++I    VK+N  ++ +    +   + IEV   
Sbjct: 12  VNSEYKGMRLDKYLSEQIEEATRSYLEKLIDNNYVKINSKIINKNGRKLKLGEKIEVSIP 71

Query: 63  -----DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                D  P               + +K  G+V   +  +   T+        +NL SI 
Sbjct: 72  EEENIDIEPENIPLDIVYENNDFIVINKNYGMVVHPAYGNYTGTLVNALLYYTNNLSSIN 131

Query: 106 SRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL--- 158
             +    + RLD +T GL+L+         L          + Y     G   ++ +   
Sbjct: 132 GNIRPGIIHRLDKDTSGLILVAKSNYAHAKLASMFIDKTIHKTYLCIVKGNFSEENISGR 191

Query: 159 ------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +V +          +  Q    + V V +  G+  +I+
Sbjct: 192 IENLIGRDSKDRKKMA--VVKENGKIAISNYKVVEQVEGYSLVEVAIETGRTHQIR 245


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 88/244 (36%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------- 57
            V E+   QR+ + +A      SR  ++  I +QRV++NG ++++    V+         
Sbjct: 10  TVDESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNVIDKPKEKVLGGESVSITA 69

Query: 58  ---DHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
              + +  D  P++     E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  IIEEDVRWDAQPIQLDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++  +      L   L + +  R Y    +G +          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQAREITREYEAVANGTMT-------AG 182

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G V + I     + T                +     ++  + + L  G+  +I+     
Sbjct: 183 GSVAEPIARHPTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            N  
Sbjct: 243 INHP 246


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 78/239 (32%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  I  E+   QR+ K+++      SR +++  I +  VKVN  +++     V   DHI 
Sbjct: 5   EFKITDESQVGQRIDKLLSEMNDEWSRSQLQDWIKEDLVKVNDKVIKS-NYKVKLNDHII 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S      T+ + L      +
Sbjct: 64  VTEKEVVEADIQPEDLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKDL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D +T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKN-DIAHRGLVEQLMDKTVKRKYTALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    ++           +         +   L  G+  +I+
Sbjct: 183 YGTVDAPIGRNKNDRQAMA---IVDDGKDAVTHFNVLEHFKDYTLIECELETGRTHQIR 238


>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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 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 = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>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 = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 78/238 (32%), Gaps = 31/238 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     I +
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVHVDGVVVNKPREKVYELQQILI 67

Query: 63  D---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           D      +  A          E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  DATLEEEVHAAAQAIDLDIVYEDDDIIVINKQAGLVVHPGAGNADGTLMNALLHHCPDIE 127

Query: 110 S------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD----- 156
                  V RLD +T GL+++         L   L + +  R Y     G +        
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVMGTMTGGGTVDE 187

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                L       V+           +  +  ++  + + L  G+  +I+   E+   
Sbjct: 188 PIGRHLTKRTHMAVLHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIRVHMEYIGH 245


>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 = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 90/241 (37%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + E +  +R+ KVIA      SR +V++ I +Q V VN   ++ A     + D + V   
Sbjct: 8   IDEEYDNERIDKVIAALNEDWSRSKVQQWIKKQLVTVNDQHVK-ANYKCSAGDIVVVRLP 66

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                    + +PL    E   + + +KP G+V   +    R T+ + L +    +    
Sbjct: 67  EPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCHDLSGIN 126

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
                  V R+D +T GLL++  +    + L          R Y+   HG          
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKKTVTRKYKAIVHGVIPHDYGTID 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK +  K  +  +          +  +     ++   L  G+  +I+   ++  +
Sbjct: 187 APIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRQYTFIECQLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|58337436|ref|YP_194021.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
 gi|58254753|gb|AAV42990.1| pseudouridine synthase [Lactobacillus acidophilus NCFM]
          Length = 302

 Score = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 87/243 (35%), Gaps = 48/243 (19%)

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------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE+            + +PL    E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEITVPAVKPLDIVAENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++    T    L + L   + +  R+Y    HG 
Sbjct: 120 DLAQSPEGF-RPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNK--RIYWAIVHGN 176

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V++          +  Q    + +   L  G+  
Sbjct: 177 FSEEQGSIDAPIGRNPYDRKKMA---VVENGKKAITHFKVLKQFKGYSLIECQLETGRTH 233

Query: 200 EIK 202
           +I+
Sbjct: 234 QIR 236


>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 = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/182 (19%), Positives = 63/182 (34%), Gaps = 30/182 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V  +   QR+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D 
Sbjct: 85  VVAGDEGSQRLDRVLAARCPELSRSRLKALILDGRVAIAGTPVRDPAYHASPGETITIDV 144

Query: 64  ---------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  +      E   + + +KP GLV   +      T+ + L +        
Sbjct: 145 PPPVPAEPAGEAIALDIVYEDADIIVLNKPRGLVVHPAAGHETGTLVNALIAHCGASLSG 204

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQ 155
                R   V RLD +T GL++   +    + L        R       Y     G   +
Sbjct: 205 IGGVRRPGIVHRLDKDTTGLMVAAKNDKAHQSLSAQFADHGRTGELRRGYLAFVWGVPGR 264

Query: 156 DK 157
             
Sbjct: 265 KY 266


>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 = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 87/243 (35%), Gaps = 48/243 (19%)

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------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE+            + +PL    E   + + +KP G+V   +      T+ + L     
Sbjct: 63  IEITVPAVKPLDIVAENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 122

Query: 102 -----PSIFSRVISVGRLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++    T    L + L   + +  R+Y    HG 
Sbjct: 123 DLAQSPEGF-RPGIVHRIDKDTSGLLMIAKNATARESLEQQLANKTNK--RIYWAIVHGN 179

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V++          +  Q    + +   L  G+  
Sbjct: 180 FSEEQGSIDAPIGRNPYDRKKMA---VVENGKKAITHFKVLKQFKGYSLIECQLETGRTH 236

Query: 200 EIK 202
           +I+
Sbjct: 237 QIR 239


>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 = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 84/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>gi|213858018|ref|ZP_03384989.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 82

 Score = 80.6 bits (198), Expect = 4e-13,   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|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 = 80.6 bits (198), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E   + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 85/250 (34%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +   +R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVIRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 76/238 (31%), Gaps = 44/238 (18%)

Query: 7   VQENFTPQRVSKVIARAG-----IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + +    +R+ K ++          SR  ++++I    V VN     +    +   D I+
Sbjct: 14  IDKTQEGERIDKFLSDMLSSDERTYSRSYIQKLIEAGNVCVNDK-NTKTGYKISYNDLIK 72

Query: 62  V------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           V            + +PL    E   + L +KP G+V   S      T+ + L    S  
Sbjct: 73  VMIPYLEDINIVAENIPLDIVYEDDDIILVNKPKGMVVHPSAGHYTGTLVNALMYHCSNN 132

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVR------- 148
                   R   V R+D +T G+++   +   A +            R Y          
Sbjct: 133 LSGINGVMRPGIVHRIDKDTTGIIVACKN-DAAHISLSEQLKEHNITRYYYAICHNCFKE 191

Query: 149 ----FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +  +   K  I  +          +     + A++   L  G+  +I+
Sbjct: 192 KEGTVDAPIGRHPVERKKMAINYKNGKKAVTHYEVLENFRNFAYIKCKLETGRTHQIR 249


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 85/240 (35%), Gaps = 47/240 (19%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +  R    +R +V++ I    V+VNG+ ++     V   D+I +           
Sbjct: 31  RIDKFLMDRLPNVTRNKVQKAIKDGFVQVNGVTIK-PNYKVHPDDNIRIALPEPPRDTEV 89

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
             + +PL    E + L + +K  G+V   +  +   T+ + L   F ++           
Sbjct: 90  KPENIPLDIVYEDSDLLIVNKEAGMVVHPAHQNWEGTLVNALAYHFQQLPEMQGNEGRPG 149

Query: 111 -VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD----KLNLLKK 163
            V R+D +T GLL++         L          R Y     G+++ +     +NL   
Sbjct: 150 LVHRIDKDTSGLLVIAKTEKSMTALAKQFFDHSIERTYYALVWGELEDEEGTIDVNL--- 206

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVT-------VGLRE-----GKNREIKKVFEFFNWK 211
           G   +     D     D  + +            V L +     G+  +I+   ++    
Sbjct: 207 GRSFKDRRITDAFPEGDFGRTAITHYKVLERLRYVTLIQCNLETGRTHQIRAHMKYIGHP 266


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 83/229 (36%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVTVDGKKINKPKEKVLGGELVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP GLV      +   TV + L   + +++  
Sbjct: 70  QIEEDARWAPQDIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPKIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>gi|219849171|ref|YP_002463604.1| pseudouridine synthase, RluA family [Chloroflexus aggregans DSM
           9485]
 gi|219543430|gb|ACL25168.1| pseudouridine synthase, RluA family [Chloroflexus aggregans DSM
           9485]
          Length = 310

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 57/283 (20%), Positives = 100/283 (35%), Gaps = 56/283 (19%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV    + QR+ + +A      SR +V+R+I Q  V   G    RA+  +     I V  
Sbjct: 18  IVPSEASGQRIDRFLAASMPDLSRTQVQRLIEQGMVLYAGRP-TRASQPLHPGTIIHVTI 76

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                     + +PL    E   + + +KP G+V   +    R T+ + L + +      
Sbjct: 77  PPPVPVELMPESIPLDIVYEDADVAVINKPAGMVVHPAPGHPRGTLVNALLARYPDLAIS 136

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD +T GLL++       R L  +  + +  ++Y+    G          
Sbjct: 137 GEVRPGIVHRLDRDTSGLLVIARHDAALRALVEQQQARRMRKIYQALVVGRPPVCGTIDA 196

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +D  + L+  +V  G         +    G  + + V L  G+  +I+       + 
Sbjct: 197 PIGRDPRDRLRMAVVADGRPARTH-YRVIATFGDYSLLEVQLETGRTHQIRVHLRHLGYP 255

Query: 212 V------------NRLIRISYGPFQLGTL-----LAGSTREVS 237
           +             RL R        G L       G  RE +
Sbjct: 256 IVGDPVYGPRRSHLRLTRQ---FLHAGQLGFFHPRDGQWREFT 295


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 9   TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 68

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 69  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 188

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 189 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 236


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 88/241 (36%), Gaps = 41/241 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M   N+  E  T +R+ + ++      SR  ++++I Q  V +N  +     + V + D 
Sbjct: 1   MTAFNLQVEE-TGERLDRYLSENLPNLSRSRIQQLIEQGNVHLNEQICTTKKITVKAGDR 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I ++   ++               E   L + +KP GLV   +      T+ + L +   
Sbjct: 60  ITLEIPEVQPLQVQAQDIPLDILYEDDHLLILNKPAGLVVHPAPGHPDGTLVNALLAHCP 119

Query: 107 RVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRF------ 149
            +  +G         RLD +T G + +  T+    +   +L +    R Y          
Sbjct: 120 NLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYHSLQAQLQAKTARREYLGVVYGAPKT 179

Query: 150 -HGQVDQ------DKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +G++D+           +   + I+ G         +  + G+   V   L  G+  +I
Sbjct: 180 ENGKIDEPIGRHPQDRKKMAV-VPIEKGGRNAVTHWQILERLGNQTLVLFQLETGRTHQI 238

Query: 202 K 202
           +
Sbjct: 239 R 239


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 47/266 (17%), Positives = 76/266 (28%), Gaps = 61/266 (22%)

Query: 2   KDKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K +   +    R+   +  A AG  SR  ++ +I Q  V +NG  +      V   D 
Sbjct: 11  NRKVLTAGDDAAGRLDAFLTEALAGEFSRNRIKSLIEQGAVSINGATVTEPKRKVHPGDS 70

Query: 60  IEV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
             +           G  +      E   L +  KP GLV      +   T+ + L     
Sbjct: 71  FRIALPEPEDPEPKGEAIPLDVLYEDADLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCG 130

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFH 150
                     R   V RLD +T G++++  +    R L              R YR    
Sbjct: 131 DSLSGIGGVKRPGIVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVW 190

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------------------------ 186
           G+        LK  I       GD       ++ S+                        
Sbjct: 191 GRP-----RQLKGKIDAPLGRAGDRTKRAVKREDSDDAREAITHYEVVERYHEKPDGTSL 245

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWK 211
            + V   L  G+  +I+         
Sbjct: 246 ASTVECHLETGRTHQIRVHMAHIGHP 271


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 89/241 (36%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + E +  +R+ KVIA      SR +V++ I  Q V VN   ++ A     + D + V   
Sbjct: 8   IDEEYDNERIDKVIAALNEDWSRSKVQQWIKNQLVTVNDQHVK-ANYKCSAGDIVVVRLP 66

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                    + +PL    E   + + +KP G+V   +    R T+ + L +    +    
Sbjct: 67  EPEPLYVEPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCHDLSGIN 126

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
                  V R+D +T GLL++  +    + L          R Y+   HG          
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDMAHQALVDQLVKKTVTRKYKAIVHGVIPHDYGTID 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +DK +  K  +  +          +  +     ++   L  G+  +I+   ++  +
Sbjct: 187 APIGRDKRDRKKMAVTEENGKEAVTHFRVLERFRQYTFIECQLETGRTHQIRVHMKYIGY 246

Query: 211 K 211
            
Sbjct: 247 P 247


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 90/245 (36%), Gaps = 41/245 (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  ------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
                       EV  V +  ++   + + +K  G+           T+  +L +++   
Sbjct: 75  LLAPSLQSGIKPEVGPVEVVYSDPDVVVV-NKAAGVTVHPGTGCESGTLVHHLAALYPEL 133

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG------- 151
                 R   V RLD +T GLL +  +      L       +  + Y    HG       
Sbjct: 134 ARFDGERPGVVHRLDKDTSGLLTVALNESARLALTRSFARREVDKEYLTLVHGRPEAEGT 193

Query: 152 ---QVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
               + +D  + ++  +V +G        +    +  G  + + V +  G+  +I+    
Sbjct: 194 VDHPLGRDPQSKIRMAVVPRGGKEALTRFKRVWTSPDGRVSLLRVRILTGRTHQIRVHMA 253

Query: 207 FFNWK 211
           +  + 
Sbjct: 254 YLGFP 258


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 35/231 (15%), Positives = 76/231 (32%), Gaps = 33/231 (14%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G++  +    V+    I +
Sbjct: 8   KSEITATQTGQRLDQTLAELYPDYSRTRIKEWIQAGWVYIDGVVSTKPREKVLEGQEIAI 67

Query: 63  DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +     +              E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  EATLKEETAAKAQAIDLDIVYEDDHIIVINKQAGLVVHPGAGNQDGTLMNALLHHCPGIE 127

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---------- 151
                  V RLD +T GL+++         L     + +  R Y     G          
Sbjct: 128 LVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAVVLGTLISGGTVDE 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D+          V+           +  +  ++  + + L  G+  +I+
Sbjct: 188 PIDRHPTKR-THMAVVHNGKPAMTHYRVAEKFRAHTRLRLRLESGRTHQIR 237


>gi|163846479|ref|YP_001634523.1| RluA family pseudouridine synthase [Chloroflexus aurantiacus
           J-10-fl]
 gi|222524258|ref|YP_002568729.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl]
 gi|172045876|sp|Q45826|Y901_CHLAA RecName: Full=Uncharacterized RNA pseudouridine synthase Caur_0901;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|163667768|gb|ABY34134.1| pseudouridine synthase, RluA family [Chloroflexus aurantiacus
           J-10-fl]
 gi|222448137|gb|ACM52403.1| pseudouridine synthase, RluA family [Chloroflexus sp. Y-400-fl]
          Length = 316

 Score = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 90/242 (37%), Gaps = 36/242 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V    T +R+ + +A      SR +V+R+I Q  V  +G     A+  V     I    
Sbjct: 18  VVPPTQTAERIDRFLAGAMPDLSRAQVQRLIEQGFVLYDGRSPR-ASQPVRPGAVIQLTI 76

Query: 61  ------EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                 E+   P+      E   + + +KP G+V   +    R T+ + L + +      
Sbjct: 77  PPPIPTELVAEPIPLDVVYEDADIAVINKPAGMVVHPAPGHPRGTLVNALLARYPDLAIG 136

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRFHGQVDQ------ 155
              R   V RLD +T GLL++       R L       +  ++Y+    G+  +      
Sbjct: 137 GELRPGIVHRLDRDTSGLLVIARHDQAMRSLVDQQQARRMRKIYQALVIGRPPETGTIDA 196

Query: 156 ----DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               D  + L+  +V  G         LDT  G  + + V L  G+  +I+       + 
Sbjct: 197 PIGRDPRDRLRMAVVPDGRPARTHYRLLDT-FGDYSLLEVQLETGRTHQIRVHLRHLGYP 255

Query: 212 VN 213
           + 
Sbjct: 256 IV 257


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 78/245 (31%), Gaps = 43/245 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILL---------ERAAVN 53
           IV       R+   +A        SR  ++++I    V V+G            E   + 
Sbjct: 7   IVDGENAKCRLDVFLANQ--CQDISRSYIQKLIEDGLVTVDGKPARANHKLRVEETIHMQ 64

Query: 54  VMSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
           +   + ++V+   +      E + + + +KP G+V   ++ +   T+ + L      +  
Sbjct: 65  IPPAEELKVEPENIPLDIYYEDSHVIVVNKPRGMVVHPAEGNIAGTLVNALLYHCHDLSG 124

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV------ 153
                    V RLD +T GL++        + L          R Y+   H  +      
Sbjct: 125 INGIMRPGIVHRLDKDTSGLIMAAKHDQAHQSLARQLKDRTVTRRYQALVHHNIKGDFGT 184

Query: 154 -------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                  D      +   +V +          +  + G    +   L  G+  +I+    
Sbjct: 185 INAPIGRDPRDRQKMA--VVERNSKNAVTHFQVLERFGDYTLIECRLETGRTHQIRVHMA 242

Query: 207 FFNWK 211
           +  + 
Sbjct: 243 YIGFP 247


>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 = 80.2 bits (197), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 85/234 (36%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  + ++ V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVK-ANYKVKQGDEITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHVKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L   L     LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKPAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 83/239 (34%), Gaps = 39/239 (16%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR 68
           P R+ + + ++    SR  +++ I    V+VNGI    A   +   D +E+      PL 
Sbjct: 27  PMRLDRWLVSQRSEQSRSHIQKFIEAGLVRVNGITGR-AKTPLRQGDEVELWMPPPEPLP 85

Query: 69  KA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS 110
                        E   L + +KP GL    +  +   T+ +       +LP I  ++  
Sbjct: 86  YLQPEEMPLDVLFEDRHLIVINKPAGLTVHPAPGNRNGTLVNGLLHHCSDLPGISGKLRP 145

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKK-G- 164
             V RLD +T G +++         L+    +    R Y    HG    D+  ++   G 
Sbjct: 146 GIVHRLDKDTTGCIVIAKSQEALVKLQEQIQKRIASRNYLAVVHGAPSGDQGTIVAAIGR 205

Query: 165 ----------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     +   G  +     TL  +    + +   L  G+  +I+         + 
Sbjct: 206 HPVDRKKYAVVTEDGGRHACTHWTLVERLADYSLLRFKLDTGRTHQIRVHCAHIGHPIV 264


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 87/246 (35%), 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  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E             + +PL    E + + + +KP G+V   +      T+ + +      
Sbjct: 59  EFEIPQAEVLDVAAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKD 118

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   L      R Y    HG++  D
Sbjct: 119 LSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELAND 178

Query: 157 K----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           K          L   KK  V+ G         +  +      + + L  G+  +I+    
Sbjct: 179 KGTIEAPIGRNLKDRKKQAVVSGGKPAVTHFEVLERFVGYTLIALRLETGRTHQIRVHMH 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 86/232 (37%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A     SR +  + I    V VNG   ++A  +V + D I              
Sbjct: 11  RLDKALADLSNLSRSQANQAIKDGSVLVNGRP-KKAKYSVKAGDVISFEEPEEEVLDYQA 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
           + +PL    E   L + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  ENLPLEIVYEDQDLAVVNKPQGMVVHPSVGHSSGTLVNALLYRIKDLSTINGVVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +    + L     + + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMVAKNDQAHQALADELKAKKSLRKYLAIVHGNLPNDRGKIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G         L+ + G+ + + + L  G+  +I+    +    
Sbjct: 190 RKKQAVTAKGRPAVTHFHVLE-RFGNYSLLELRLETGRTHQIRVHMAYIGHP 240


>gi|224418218|ref|ZP_03656224.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           canadensis MIT 98-5491]
          Length = 340

 Score = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 89/243 (36%), Gaps = 57/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           VQ+  T  R+ K + +    SR ++ ++I ++++ +NG+ +++   ++   D I +    
Sbjct: 15  VQQEETKMRLDKFLTQKLGLSRNQISKIIQEKQITLNGVFIQKNGTSLNFNDQIILTLPN 74

Query: 64  ----------GVPLRKAERTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIF------- 105
                      +P+   +   L + +KPI L+   +   D + T+ D L           
Sbjct: 75  KQEKSKPNHLNIPILYEDED-LLILNKPINLIVHQTHQDDSQYTLQDWLQENNFSLSNLG 133

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV---YRVRFHGQVDQDKLNL 160
              R   + RLD  T G +++  +   A  +     +  +    Y V             
Sbjct: 134 DSYRQGIIHRLDKTTSGAIVIAKN-NYAHEILSQQLK-SKEMGRYYVCVIDSP------- 184

Query: 161 LKKGIVIQG-------------ICYGDMQVTLDTQK-----GSNAWVTVG---LREGKNR 199
           LK+ I+I                   D  ++ + +       +N  + +    L  G+  
Sbjct: 185 LKQNILIDAPLIRHPKNRLKYIPTTKDTPLSKEAKTAFFKIINNDKIELIGAKLFSGRTH 244

Query: 200 EIK 202
           +I+
Sbjct: 245 QIR 247


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 51/242 (21%), Positives = 85/242 (35%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V   D   L
Sbjct: 16  ERIDKFVA--GINNEWSRSQVQQWIKDDVVTVNGKAVK-VNYKVKEEDEITVTIPDPEAL 72

Query: 68  R----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                        E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I    G    + Q     + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 82/248 (33%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    + VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKK-SKVSYKVQKDDL 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------- 99
           I+V  +PL                E   + + +KP G+V   +      T+ +       
Sbjct: 60  IQVIVLPLEPLKLEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
           +L           V R+D +T GLL++  +      LE  L +    R Y    HG   +
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 156 D------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +                +    V++          +  Q    + V   L  G+  +I+ 
Sbjct: 180 EGTIDAPIGRNPKDRKQMA---VVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
              +    
Sbjct: 237 HMAYIGHP 244


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFVA--GINNEWSRTQVQQWIKDNVVTVNGKAVK-GNYKVKEEDEITVTIPEPEEL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQGICYGDMQVTL---DTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I      D +        + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIARDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 86/233 (36%), Gaps = 38/233 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       +R  +++ I +  V VNG  L+ A   V  +D I +           
Sbjct: 15  RLDKVLTELLPSITRSHIQQWIKEGNVTVNGENLK-ANYKVQPSDEIVIIEPELVSLEVL 73

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +P+    +   + + +K  G+V   S      T+ + L      +           V
Sbjct: 74  AEDIPIEIVYQDEDVVVVNKAQGMVVHPSAGHQTGTLVNALMYHIKDLSGINGTIRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD-----------KL 158
            R+D +T GLL++  +      L   L     LR Y    HG +  +           K+
Sbjct: 134 HRIDKDTSGLLMVAKNDSAHEKLAAQLKDKTSLREYIALVHGVIPHEKGTIDAPLGRSKV 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  K+ I I G        T+  +      V++ L  G+  +I+   ++  + 
Sbjct: 194 DRKKQDI-IDGGREAVTHFTVLERFKDFTLVSLKLETGRTHQIRVHMKYIGYP 245


>gi|301632247|ref|XP_002945202.1| PREDICTED: ribosomal large subunit pseudouridine synthase D-like
           [Xenopus (Silurana) tropicalis]
          Length = 341

 Score = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 83/226 (36%), Gaps = 38/226 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ K +A      SR  +++++AQ  V ++G    + A  V + D + V+  P +++   
Sbjct: 39  RLDKALAELVPELSRSYLQQLLAQGLVCLDGAASRKPAHKVKAGDALVVEIRPTQQSQAF 98

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   L + +KP GLV   +      T+ + L           R   V R
Sbjct: 99  KPEPVPVPVVFEDAHLLVVNKPAGLVVHPAPGHWSGTLLNGLMGRDPKAMLLPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDKLN 159
           LD +T GL+++  +      L   +   Q  R Y                   + +D  N
Sbjct: 159 LDKDTSGLMVVARERTTMDALVRLIAQRQVRRQYLALGHCVWRGGGLRTVDAALGRDPRN 218

Query: 160 LLKKGIV-IQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
            L+  +V +        +   +   G++    V   L  G+  +I+
Sbjct: 219 RLRMAVVDLAQHAGKPARTDFEYLAGNDLGCLVRCTLHTGRTHQIR 264


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 82/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVTIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E + + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 86/231 (37%), Gaps = 43/231 (18%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R +V++   Q  + VNG  ++     V + D ++V      
Sbjct: 36  EPLRVDKFLMN--FVENATRNKVQQAAKQGNIFVNGEPVKS-NHRVKANDEVKVLFPHPP 92

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSR 107
                  + +PL    E   L + +KP G+V      +   T+       F+NLP+  S 
Sbjct: 93  HEDLLVPENIPLNIVYEDDSLLVVNKPAGIVVHPGHGNYSGTLINALVYHFENLPNNSSN 152

Query: 108 VIS-VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++         L     +    R Y     G +++D+       
Sbjct: 153 RPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYIALVWGNIEEDEGTVCGHI 212

Query: 158 ----LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                + L+  +   G    +      +  + G    ++  L  G+  +I+
Sbjct: 213 GRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLISCKLETGRTHQIR 263


>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 = 80.2 bits (197), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 84/248 (33%), Gaps = 50/248 (20%)

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  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                      D       E   + + +KP G+V   +    + T+ + L    + +   
Sbjct: 67  PEPEELDIQPEDMNLEVYYEDADVLVVNKPRGMVVHPAPGHTKGTLVNGLMHHCTDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y+   HG +  D    
Sbjct: 127 NGVMRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVAKTVTRRYKAIVHGVIPHD---- 182

Query: 161 LKKGIVIQ---GICYGDMQVTLDTQKGSNAWVT---------VGLRE-----GKNREIKK 203
             KG  I    G    + Q     + G NA              L E     G+  +I+ 
Sbjct: 183 --KG-TIDAPIGRDKKERQSMTVDENGKNAVTHFQVLDRFKDFTLVECRLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 89/247 (36%), Gaps = 38/247 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    + +ENF  QR+   +A+    SR +++ +I  ++V VN   ++ A   +   D I
Sbjct: 1   MDTFKVDKENF-GQRLDVYLAKLVDLSRSQIKNLIDNEKVLVNNKNVK-AGYKLSEDDVI 58

Query: 61  EV----DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
            +    D  P  +        E   + +  KP  LV      +   T+ + L   F    
Sbjct: 59  SLEYPKDSKPFAEKIDFNVIYEDDYIAVISKPQDLVVHIGAGNSSGTLVNGLLYKFKNQL 118

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD NT GL+++  +      L     ++Q  + Y    HG+  +   
Sbjct: 119 SNLDPLRPGIVHRLDKNTSGLMIIAKNNQAHINLVDQFKNSQIKKYYLAIVHGKTPESGI 178

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                    +    +   +V +       +     +    + + + L  G+  +I+    
Sbjct: 179 IEEPIGRNPNDRKKMA--VVYKNSKQAITKYKKLKEFQEYSLLNINLLTGRTHQIRVHMA 236

Query: 207 FFNWKVN 213
           +  + V 
Sbjct: 237 YIGYPVL 243


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 87/244 (35%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            + E+   QR+ + +A      SR  ++  I   RV+VNG ++ +A   V+  + I +D 
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDA 69

Query: 64  -----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                       +PL    E   + + +KP GLV      +   T+ + L   +  +   
Sbjct: 70  LIEEDTRWEPQDIPLDVVYEDEDILVINKPRGLVVHPGAGNPDGTILNALLYRYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAVGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G+V + I     + T                +     ++  + + L  G+  +I+     
Sbjct: 183 GMVEEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            N  
Sbjct: 243 INHP 246


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 55/313 (17%), Positives = 100/313 (31%), Gaps = 49/313 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           ++ ++   QR+ + +A      SR  ++  I  +RV +NG  + +    VM  + +    
Sbjct: 10  VISDSQLGQRLDQALAECFPDYSRSRIKEWILAERVSLNGKTVAKPREKVMGGEAVLIQA 69

Query: 61  ----EVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
               EV   P   A           + +KP  LV      +   TV + L          
Sbjct: 70  EFEEEVAAKPQDIALDIVYEDDDILVINKPADLVVHPGAGNHDGTVLNALLHHCPSIANV 129

Query: 106 SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++  T       V +L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVAQLQAREITREYEAIALGVMTAGGHVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +         +   G         +  +  ++  + + L  G+  +I+           
Sbjct: 190 GRHPQRRTHMAVTELGKPAVTH-YRIREKFRAHTRLRLRLETGRTHQIRVHMAHLGH--- 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVS--KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
                   P     L +G  R V    + LRE L        Q    A +     +  + 
Sbjct: 246 --------PLVGDPLYSGRPRPVKGWSEELREFLRRF---NRQALHAAMLRLEHPITGEM 294

Query: 272 PNIISEVPDDFTR 284
               + +PDD  R
Sbjct: 295 MQWTAPIPDDMVR 307


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 83/229 (36%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP GLV      +   T+ + L   +  ++  
Sbjct: 70  QIEEDARWAPQDIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTILNALLYYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E   + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFVA--GINNEWSRTQVQQWIKDNVVTVNGKAVK-GNYKVKEEDEITVTIPEPEEL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQGICYGDMQVTL---DTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I      D +        + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIARDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 87/242 (35%), Gaps = 39/242 (16%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +   +  +R+ KVIA      SR +V++ I    V VN   ++ A     + D + V   
Sbjct: 8   IDAEYDNERIDKVIAALNEEWSRSKVQQWIKDGLVTVNDQHVK-ANYKSSAGDVVVVRLP 66

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                    + +PL    E   + + +KP G+V   +    R T+ + L +  + +    
Sbjct: 67  EPEPLHVVPENIPLDIYYEDADVLVVNKPRGMVVHPAPGHMRGTLVNALLAHCTDLSGIN 126

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
                  V R+D +T GLL++  +    + L          R Y+   HG +  D    +
Sbjct: 127 GVLRPGIVHRIDKDTSGLLMVAKNDMAHQSLVDQLVKKTVTRKYKAIVHGVIPHDY-GTI 185

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFN 209
              I         M VT +  K +     V          E     G+  +I+   ++  
Sbjct: 186 DAPIGRDKRDRKKMTVTEENGKEAVTHFRVLERFRHYTFVECQLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 83/243 (34%), Gaps = 38/243 (15%)

Query: 6   IVQENFTPQRVSKVIA-RAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V+ +    R+ K I    G   SR +V+  IA   V VN   ++     V   D I + 
Sbjct: 25  TVEADAAKTRIDKYITENLGEDVSRSQVQLWIADGHVSVNDGPIKS-NYKVSQGDRIVLK 83

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL  A E   + + +KP G+V   +      T+ + L      +  
Sbjct: 84  VPEPSAVEIIPEDIPLEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNALMFHCKDLSG 143

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-------- 151
                    V R+D +T GL++   +      L   L      R Y    HG        
Sbjct: 144 INGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGNISHDQGT 203

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +     +  +   +     T+  + G  + + + L  G+  +I+   ++ 
Sbjct: 204 IDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYI 263

Query: 209 NWK 211
              
Sbjct: 264 GHP 266


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 86/231 (37%), Gaps = 43/231 (18%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R +V++   Q  + VNG  ++     V + D ++V      
Sbjct: 36  EPLRVDKFLMN--FVENATRNKVQQAAKQGNIFVNGEPVKS-NHRVKANDEVKVLFPHPP 92

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSR 107
                  + +PL    E   L + +KP G+V      +   T+       F+NLP+  S 
Sbjct: 93  HEDLLVPENIPLNIVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINALVYHFENLPNNSSN 152

Query: 108 VIS-VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++         L     +    R Y     G +++D+       
Sbjct: 153 RPGLVHRIDKDTSGLLVVAKTEEAMLHLTQQFFNKTTQREYIALVWGNIEEDEGTVCGHI 212

Query: 158 ----LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                + L+  +   G    +      +  + G    ++  L  G+  +I+
Sbjct: 213 GRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLISCKLETGRTHQIR 263


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 78/240 (32%), Gaps = 46/240 (19%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ + +A A    SR  ++ +I +  V +NG + + A+  + + D + +   P    E  
Sbjct: 16  RLDQFLASAAAGLSRARIQDLIKEGHVTLNGGVAK-ASARLRAGDAVTLHEPPPVPTETV 74

Query: 74  R-------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                         L + +KP GLV   +  +   TV + L              R   V
Sbjct: 75  AEEIALDVLFEDDDLIVINKPAGLVVHPAAGNWSGTVVNALLHHCQTLSGIGGEQRPGIV 134

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------------QV 153
            RLD +T G L++  +    + L       +  ++Y     G                 V
Sbjct: 135 HRLDKDTSGCLVVAKNDAAHQSLAKQFAGREVTKIYLALAAGKWARKSGVIEAPIGRHPV 194

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + K+ +L                 +  +      V   L  G+  +I+   +     + 
Sbjct: 195 QRKKMTVLPA----DKGRAAKTGYRVLLELPVGTLVECTLHTGRTHQIRVHLKHLGHPIL 250


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 88/246 (35%), 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  ---DGVPLR-KAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              D   +    E   + + +         K  G+V   S      T+ + +      + 
Sbjct: 61  IIPDEKEIDLVPENINIKILYEDSDIAVIDKEAGIVVHPSHGHESGTLVNAVMYHIKDLS 120

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-- 156
                     V RLD +T GLL++  +      L     S+   + Y     G+++++  
Sbjct: 121 GINGEIRPGIVHRLDKDTSGLLIIAKNDTAHLRLSEMFGSSGIRKTYIAILKGKINKESG 180

Query: 157 KLNLL---------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           KL  L         K  +V            +  +    + V V ++ G+  +I+   ++
Sbjct: 181 KLETLIGRDPKDRKKMAVVKTNGKTAITYFQVLDKNEKFSLVKVNIQTGRTHQIRVHMKY 240

Query: 208 FNWKVN 213
             + V 
Sbjct: 241 LGYPVL 246


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 84/246 (34%), Gaps = 43/246 (17%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH------ 59
           V+     QR+ + +       SR  V+++IA   V VNG  + +    +   D       
Sbjct: 17  VESEQVGQRLDRFLVSVLDGVSRSGVQQLIADALVLVNGK-VSKPGYVLRLKDRVTALRA 75

Query: 60  --------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                   +    +PL    E   L + +K  G+V   +  +   T+ + L + +  +  
Sbjct: 76  TPASQMKQVTPQNLPLEVVFEDDDLLIVNKAAGMVVHPAPGNYEGTLVNALVAHYPELQQ 135

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-- 157
                    + RLD +T GLL++  +      L       + ++ Y     G V+ D+  
Sbjct: 136 DEGDMRPGIIHRLDKDTSGLLMVAKNAQSQAALIEQMKQHKIIKRYLALVEGNVELDQGS 195

Query: 158 -----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                        ++   + +           +  +   +  V V +  G+  +I+  F+
Sbjct: 196 IDAPIGRDTRHRQMMA--VTLTEGRDAVTHFRVLQRFRKHTLVLVQIVTGRTHQIRVHFQ 253

Query: 207 FFNWKV 212
                V
Sbjct: 254 AIKHPV 259


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 84/244 (34%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            + E+   QR+ + +A      SR  ++  I   RV+VNG ++ +    V  ++ I +D 
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILADRVQVNGKVINKPKEKVFGSEQILIDA 69

Query: 64  -----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                       +PL    E   + + +KP  LV      +   T+ + L   +  +   
Sbjct: 70  LIEEDNRWEPQDIPLNVIYEDEDILIINKPRDLVVHPGAGNPDGTILNALLYRYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVAVGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIKKVFEF 207
           G+V + I     + T                      ++  + + L  G+  +I+     
Sbjct: 183 GMVEEPISRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            N  
Sbjct: 243 INHP 246


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 41/257 (15%), Positives = 89/257 (34%), Gaps = 49/257 (19%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M ++ I   V    T +RV   ++     +R  ++++I    V VN   ++  +  V   
Sbjct: 35  MSEEKISVTVSTEKTNKRVDSFLSEKTDLTRSRIQQLIKDGNVSVNNKSVKS-SYKVEEN 93

Query: 58  DHIEVDGVPLRKAERTRLWL----------------YHKPIGLVTTHSDPDGRSTVFDNL 101
           D IE+    + +AE+  +                   +K  G+V   +  +   T+ + +
Sbjct: 94  DRIEI---IIPEAEKVEIIAENIDINIIYEDKDIAVINKKAGMVVHPAHGNYSRTLVNAI 150

Query: 102 PSIFSRVIS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH 150
                 +           V RLD +T GL+++  +      L       +  + Y     
Sbjct: 151 LYHIKDLSGINGEIRPGIVHRLDKDTSGLIVVAKNDKAHIKLAEMFQKKEVKKTYLAILK 210

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--------------AWVTVGLREG 196
           G+++++    L+  I         M V  +  KG                  V V +  G
Sbjct: 211 GKLNRES-GRLETQIGRDADDRKKMSVLKENDKGKKAITNYNVILSNELFTLVKVYIETG 269

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+   ++  + + 
Sbjct: 270 RTHQIRVHMKYLGYPIL 286


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  MVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 82/243 (33%), Gaps = 38/243 (15%)

Query: 6   IVQENFTPQRVSKVIA-RAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V  +    R+ K +    G   SR +V+  IA   V VN   ++     V   D I + 
Sbjct: 27  TVDADAAKTRIDKYLTENLGEDVSRSQVQLWIADGHVSVNDGPIKS-NYKVSQGDRIVLK 85

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL  A E   + + +KP G+V   +      T+ + L      +  
Sbjct: 86  VPEPSAVEIIPEDIPLEIAFEDGDVIVVNKPRGMVVHPAPGHSSGTLVNALMFHCKDLSG 145

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-------- 151
                    V R+D +T GL++   +      L   L      R Y    HG        
Sbjct: 146 INGELRPGIVHRIDKDTTGLIMAAKNDKAHASLAAQLKEHSVNRRYLALVHGNISHDQGT 205

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +D  +     +  +   +     T+  + G  + + + L  G+  +I+   ++ 
Sbjct: 206 IDAPIGRDAQDRKLYTVTDRNSKHAVTHFTVVERFGDYSLLELKLETGRTHQIRVHMKYI 265

Query: 209 NWK 211
              
Sbjct: 266 GHP 268


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 83/230 (36%), Gaps = 31/230 (13%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+ +++    V+ +  IE+
Sbjct: 8   KSEITATQTGLRLDQALAELFPDYSRTRIKEWILSGAVYVDGVKVDKPREKVLESQQIEI 67

Query: 63  D---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PS 103
           +      ++            E   + + +K  GLV      +   T+ + L        
Sbjct: 68  EATFEEEVKAKAQAIDLNIVYEDDHIIIVNKQAGLVVHPGAGNADGTLMNALLHHCPAIE 127

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QD 156
           +  R   V RLD +T GL+++         L   L + + +R Y     G +       +
Sbjct: 128 MVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREIVREYEAIVLGTMTAGGTVDE 187

Query: 157 KLNLL----KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +        +  V  G         +  +  ++  + + L  G+  +I+
Sbjct: 188 PIERHPTKRTQMSVQHGGRPSVTHYRVSEKFRAHTRLRLRLESGRTHQIR 237


>gi|91200050|emb|CAJ73092.1| similar to ribosomal large subunit pseudouridine synthase D
           [Candidatus Kuenenia stuttgartiensis]
          Length = 335

 Score = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 84/240 (35%), Gaps = 41/240 (17%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----------RAAVNVMSTDH 59
             +R+ + I+      SR  +++++ +  + VNG +++            A V V     
Sbjct: 24  ESKRIDRFISSRFPDLSRTYIQKLVKEGAIVVNGNVVKSSYFIKKGDVISATVPVPEETK 83

Query: 60  IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--------- 109
           I  + +PL    E   L L +KP  +V   +      T+ + +      +          
Sbjct: 84  ITPEDIPLNIIYEDDYLMLINKPYDMVVHPAGGHPSGTLVNAVTFYCQNLSQINGPLKAG 143

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            V RLD +T G++L+     +   + +   +    + Y     G+V  D  N +   I  
Sbjct: 144 IVHRLDRDTSGVMLVIKSDAVHSHIAMQFEKRLVKKEYFAVVEGEVAFDS-NEINMPIGR 202

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIKKVFEFFNWKVN 213
             +    M V  DT K + +   V   E              G+  +I+   +     V 
Sbjct: 203 HRVDRQKMAVRRDTGKNATSVYEVI--ERFRGYTLVKIMPKTGRTHQIRVHMQAIGHPVV 260


>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 = 79.8 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 87/241 (36%), Gaps = 45/241 (18%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R +V++   Q  + VNG  ++     V + D ++V      
Sbjct: 40  EPLRVDKFLMN--FVENATRNKVQQAAKQGNIFVNGQPVKS-NHRVKANDEVKVYFAHPP 96

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSR 107
                  + +PL+   E   L + +KP G+V      +   T+       F+NLP+  S 
Sbjct: 97  HEDLLIPENIPLQIVYEDDSLLVVNKPAGMVVHPGHGNYSGTLINALVYHFENLPNNSSN 156

Query: 108 VIS-VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++         L          R Y     G V+ D+       
Sbjct: 157 RPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFHKTTEREYIALVWGNVEADEGTVRGHI 216

Query: 158 ----LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNW 210
                + L+  +   G    +      +  + G    V+  L  G+  +I+  + +    
Sbjct: 217 GRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLVSCRLETGRTHQIRVHM-KHIGH 275

Query: 211 K 211
            
Sbjct: 276 T 276


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 46/266 (17%), Positives = 78/266 (29%), Gaps = 61/266 (22%)

Query: 2   KDKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K +  +     R+   +  A +G  SR  ++ +I Q  V +NG+ +      V   D 
Sbjct: 21  NRKVLTADENAAGRLDAFLTEALSGEFSRNRIKALIEQGAVSINGVTVLEPKRKVHPGDR 80

Query: 60  IEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
            E+            + +P+    E   L +  KP GLV      +   T+ + L     
Sbjct: 81  FEITLPAPEDPEPKGEDIPIDVLYEDDDLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCG 140

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFH 150
                     R   V RLD  T G++++  +    R L        R       Y+    
Sbjct: 141 DSLSGIGGVRRPGIVHRLDKETSGVMVVAKNDAAHRHLSDQFADHGRTGPLERAYQAVVW 200

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------AWVTVG--LRE------- 195
           G+        LK  I       GD       ++ S+          V     E       
Sbjct: 201 GRP-----RQLKGTINAALGRAGDRTKRAVKREESDDAREAITHYEVVERYHEKPDGTCL 255

Query: 196 ----------GKNREIKKVFEFFNWK 211
                     G+  +I+         
Sbjct: 256 AATVECHLETGRTHQIRVHMAHIGNP 281


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +RV VNG++++     V+  + + +D 
Sbjct: 10  TVSESQLGQRLDQTLAELFPDYSRSRIKEWILDRRVTVNGVMVDTPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                              E   + + +KP   V      +   TV + L   +  ++  
Sbjct: 70  EIEEAQRWEPQNLPLDIVYEDEDIIVINKPRDFVVHPGAGNPDGTVLNALLHHYPAIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGNMTAGGTVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I  +RV VNG++++     V+  + + +D 
Sbjct: 10  TVSESQLGQRLDQTLAELFPDYSRSRIKEWILDRRVTVNGVMVDTPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                              E   + + +KP   V      +   TV + L   +  ++  
Sbjct: 70  EIEEAQRWEPQDLPLDIVYEDEDIIVINKPRDFVVHPGAGNPDGTVLNALLHHYPAIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGNMTAGGTVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 39/231 (16%), Positives = 75/231 (32%), Gaps = 35/231 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHG 151
                  V RLD +T GL+++         L   L      R Y                
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDK 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPMGKHAVTHYRVAEHFRE-HTRIRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 89/252 (35%), Gaps = 46/252 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V       R+ KV++      SR ++++ I   +V VN +++    V V   D I  
Sbjct: 3   KYSVPHELNGIRLDKVLSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+ A          E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+V   G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREI 201
                      D+ K+ +LK G    G        TL+   KGS + V   L  G+  +I
Sbjct: 183 IIKNNIGRSRSDRQKMTILKYG----GKEAVTHYKTLELFYKGSISMVECKLSTGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 239 RVQLSHLKHSVV 250


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 39/231 (16%), Positives = 75/231 (32%), Gaps = 35/231 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVFEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHG 151
                  V RLD +T GL+++         L   L      R Y                
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQ 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPMGKPAVTHYRVAERFRE-HTRIRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 37/240 (15%), Positives = 77/240 (32%), Gaps = 35/240 (14%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G   ++    V+    + +
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWILSGSVFIDGETSDKPRFKVLEGQVVTI 67

Query: 63  DGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            G  L +               E   + + +K  GLV      +   T+ + L      +
Sbjct: 68  -GATLEEETKAEAEAIDLDIIYEDDHILVINKQAGLVVHPGAGNQSGTLMNALLHHCPGI 126

Query: 109 I------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
                   V RLD +T GL+++         L   L + +  R Y     G         
Sbjct: 127 ELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIVTGTIIAGGTVD 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +D+          V+           +  +  ++  + + L  G+  +I+        
Sbjct: 187 EPIDRHPTKR-THMAVVHNGKPAMTHYRVAEKFRAHTRLRLRLESGRTHQIRVHMAHIGH 245


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 39/226 (17%), Positives = 79/226 (34%), Gaps = 38/226 (16%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +++     SR  ++++I Q  V++N  +     +NV   D I +           
Sbjct: 50  RIDRFLSQELPDLSRSRIQQLIEQGNVQLNDKVCTSKKINVKLGDRITLEIPEAQPLELL 109

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
            + +PL    E  +L + +KP GLV   +      T+ + L +    +  +G        
Sbjct: 110 AEDIPLDILYEDDQLLILNKPAGLVVHPAPGHPDGTLVNALLAHCPNLPGIGGVQRPGIV 169

Query: 113 -RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-------------QD 156
            RLD +T G + +         L  +L +    R Y    +G                  
Sbjct: 170 HRLDKDTTGAIAIAKTEVAHHHLQAQLKAKTARREYLGVVYGAPKVESGTIDLPIGRHPQ 229

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +    + QG         +  + G+   +   L  G+  +I+
Sbjct: 230 DRKKMAIMPIEQGGRSAVTHWQVLERLGNFTLIRFQLETGRTHQIR 275


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 87/239 (36%), Gaps = 46/239 (19%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V +   P R+   +A+  +  A+R +V+  I++ RV+VNG  ++ A   + S D IE+  
Sbjct: 27  VAQTQKPMRIDVYLAQQ-VENATRNKVQEAISEHRVRVNGKTVK-ANYKIKSLDSIEITF 84

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVT-----------THSDPDGRSTVFDN 100
                     + +P+    E   L + +K  G+V             ++      T  + 
Sbjct: 85  LRPPAPELAPEDIPVDIIYEDNDLMVINKAPGMVVHPAFGNWTGTLANAILHHLGTDAEK 144

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV-DQDK 157
           L +   R   V RLD NT GL+++         L       Q  + Y+    G     + 
Sbjct: 145 LDTTELRPGIVHRLDKNTSGLIIVAKHATALHRLAKQFAERQVEKKYQAIVWGVPEPPEG 204

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSN--------------AWVTVGLREGKNREIK 202
           +     G  I+           + ++G                + V + L  G+  +I+
Sbjct: 205 IVKTNIGRSIRDRKVMT-SYDFEGKEGKTAVTEYRVVENLRYFSLVEMILHTGRTHQIR 262


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 39/231 (16%), Positives = 74/231 (32%), Gaps = 35/231 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLAGKVQVNGEVVTKPRTRVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHG 151
                  V RLD +T GL+++         L   L      R Y                
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDK 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +         +   G         +      +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPMGKPAVTH-YRVAEHFREHTRIRLRLETGRTHQIR 237


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 81/236 (34%), Gaps = 43/236 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     SR      I   ++ VNG  +++A   V + D I  +   L + E   
Sbjct: 11  RLDKAVADLTSLSRSHANEQIKNGQILVNGQ-VKKAKYAVKAGDVITYE---LPEPEALE 66

Query: 75  LWL----------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
                               +K  G+V   S      T+ + L      +          
Sbjct: 67  YVAENLPLDIVYQDEDVAVVNKAQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPG 126

Query: 111 -VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  +      L  EL   + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      +  +  + G+   V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKPAVT-RFHVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 79.8 bits (196), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 44/230 (19%), Positives = 83/230 (36%), Gaps = 34/230 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  +   QR+   +A+     SR  +   I    V +NG +       ++  + +EV  
Sbjct: 33  TVPTDLAGQRLDAALAKLLPDYSRSRLSTWIKDGNVLLNGQVAR-PKERLIGGETLEVHI 91

Query: 65  VPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
               +               E   + + +KP GLV   +  +   T+ + L +       
Sbjct: 92  QHSHETAAFTPEPMPLDIVFEDDSVIVLNKPAGLVVHPAAGNWSGTLLNGLLAHCPALAE 151

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN-- 159
             R   V RLD +T GL+++         L  +L      R+YR    G V    K++  
Sbjct: 152 IPRAGIVHRLDKDTSGLMVVAKTPAAQNSLVQQLQERSVKRIYRAVADGIVPFDGKIDTL 211

Query: 160 -------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   LK  +V  G       + +  +  S++++   L  G+  +I+
Sbjct: 212 IGRDPHNRLKMAVVGFGGKKAVTHIKVLERYQSHSYIECTLETGRTHQIR 261


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+ +         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMAVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 82/249 (32%), Gaps = 42/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    + VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMTDLSRSRIKELVQAGEILVNGKK-SKVSYKVQKDDL 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------- 99
           I+V  +PL                E   + + +KP G+V   +      T+ +       
Sbjct: 60  IQVIVLPLEPLKLEAENIPLDIVYEDKDVIVVNKPQGMVVHPAAGHPSHTLVNALLYHTR 119

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
           +L           V R+D +T GLL++  +      LE  L +    R Y    HG   +
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +                 +    V++          +  Q    + V   L  G+  +I+
Sbjct: 180 EEGTIDAPIGRNPKDRKQMA---VVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIR 236

Query: 203 KVFEFFNWK 211
               +    
Sbjct: 237 VHMAYIGHP 245


>gi|254757932|ref|ZP_05209959.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
          Length = 249

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 81/243 (33%), Gaps = 40/243 (16%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-- 156
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHDKG 184

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                        +   V +   +      +  +      V   L  G+  +I+   ++ 
Sbjct: 185 TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 37/233 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK- 69
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 13  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 71

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS--VG 112
                     E  ++ +  KP G+V   +      T+ +      +LP I   +    V 
Sbjct: 72  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  T    L+   +L +   +R Y    HG   +D+            +
Sbjct: 132 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++ +V  G         L+  +    ++   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVADGRHAVTHFQVLERFEHYT-FIKCILETGRTHQIRVHMAYIHHPV 243


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 81/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E   + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 37/233 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK- 69
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 13  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 71

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS--VG 112
                     E  ++ +  KP G+V   +      T+ +      +LP I   +    V 
Sbjct: 72  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  T    L+   +L +   +R Y    HG   +D+            +
Sbjct: 132 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++ +V  G         L+  +    ++   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVADGRHAVTHFQVLERFEHYT-FIKCILETGRTHQIRVHMAYIHHPV 243


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 78/244 (31%), Gaps = 36/244 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           IV       R+   +      SR  ++ +I    + V G  + +A + +     + V   
Sbjct: 5   IVNAEQDGMRLDVFLTEHMEGSRSYIQSLIKGGHITV-GAKVGKANLRLTPNAVVRVEIP 63

Query: 63  ---------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                    + +PL    E   + + +K  G+V   +  +   T+ + L      +    
Sbjct: 64  EPESVEVKPEDIPLDVLYEDHDIIIVNKQRGMVVHPAVGNYSGTLVNALLYHCKDLSGIN 123

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK---- 157
                  V RLD +T G+++   +      L     +    R Y     G + ++K    
Sbjct: 124 GEIRPGIVHRLDKDTSGVMMAAKNDAAHIGLAEQVKEHSAKRTYLALVQGNIVEEKGTIK 183

Query: 158 -------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   + +K  +V +          +  + G    V   L  G+  +I+  F     
Sbjct: 184 APIGRHPKDRMKMAVVFENSKDAVTHFNVVERFGHQTLVECNLETGRTHQIRVHFAHIGH 243

Query: 211 KVNR 214
            V  
Sbjct: 244 PVVN 247


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 57/269 (21%), Positives = 99/269 (36%), Gaps = 55/269 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++  +       R+ KV+A   A   SR +++  + +  VK++G++++ A   V   D
Sbjct: 1   MTEELKISITEEKGRIDKVLAEKLANY-SRSQIQLWLKEACVKIDGVVVK-ANYKVQKGD 58

Query: 59  HIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I +            + +PL    E   + + +KP G+V   S      T+ + L    
Sbjct: 59  RITIQIPEPETLDLIAENLPLEIVYEDADVAVINKPQGMVVHPSAGHPNGTLVNALIYHL 118

Query: 106 S---------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
           +         R   V R+D +T GLL++  +      L   L     LR Y    HG + 
Sbjct: 119 NSLSSINGVIRPGIVHRIDKDTSGLLMVAKNDQAHEDLAKQLKDKTSLRKYVALVHGVIP 178

Query: 155 QDKLNLLKKGIVIQGICY----GDMQVTLDTQKGSNAWVTV-------GLRE-----GKN 198
            D      KG++   I        MQ  +D  K +     V        L E     G+ 
Sbjct: 179 HD------KGVIRAPIGRSTVDRKMQAVVDNGKDAVTHFQVLERYEDYTLVELQLETGRT 232

Query: 199 REIKKVFEFFNW-----KVNRLIRISYGP 222
            +I+   ++  +      V  L R   G 
Sbjct: 233 HQIRVHMQYIGYPLVGDPVYGLKRTIKGN 261


>gi|332999362|gb|EGK18947.1| ribosomal large subunit pseudouridine synthase D [Shigella flexneri
           VA-6]
          Length = 326

 Score = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINS 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
               +A             E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 53/285 (18%), Positives = 84/285 (29%), Gaps = 82/285 (28%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+   +AR    ASR +++R I + RV VNG+++++ A  V   D I +    LR     
Sbjct: 21  RLDAYLARFLAQASRTKIQRGIREGRVTVNGVVVQKPAYTVQPGDVITL--RILRPPPVE 78

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------- 105
                       E   L + +K  GLV   +  +   T+ + L                 
Sbjct: 79  IVPEPIPLDIVYEDPYLIVVNKQAGLVVHPARGNRSGTLVNALLYYIGSGPVRFDEEDDL 138

Query: 106 ----------------------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--W 141
                                  R   V RLD +T GL+++  D      L         
Sbjct: 139 PEDDEIGLSMVSTGPTEAKLEAPRPGIVHRLDKDTTGLIVVAKDDVTHTGLARQFEHRTI 198

Query: 142 LRVYRVRFHGQV-------------DQDKLNLLKKGIVIQGICYGDMQ-VTLDTQKGSNA 187
            R Y     G               D      +   +V        +    +     + A
Sbjct: 199 ARTYLAIVWGVPDPPRGRIEAAIGRDPRDRQRMA--VVPDDRGKRAVTHYEVVEALPAAA 256

Query: 188 WVTVGLREGKNREIK---KVFEFFNWKVN----RLIR-ISYGPFQ 224
            V   L  G+  +I+   +        V        R I YGP  
Sbjct: 257 LVRFKLETGRTHQIRVHAR---HIGHPVLGDPTYGGRTIRYGPHT 298


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 86/240 (35%), Gaps = 43/240 (17%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        ASR +V++      + VNG+ ++ A   V + D ++V      
Sbjct: 25  EPLRVDKFLMN--FVENASRNKVQQAAKDGNIFVNGVAVK-ANHRVKANDEVKVMFAHPP 81

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                  + +PL    E   L + +KP GLV      + + T+ + L   F  +      
Sbjct: 82  HEYLLVPEPIPLDIVYEDEELIIINKPAGLVVHPGHGNYQGTLINGLIYHFQHLPMNSSD 141

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++         L     +    R Y     G + QD+       
Sbjct: 142 RPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYVALVWGNLAQDEGTIIGHI 201

Query: 158 ----LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                N L+  +   G    +      +  + G    V+  L  G+  +I+  F +    
Sbjct: 202 GRHPKNRLQMTVFPDGSEGKEAITHYKVLERFGYVTIVSCRLETGRTHQIRAHFTYIGHP 261


>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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 80/238 (33%), Gaps = 42/238 (17%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           QR+   +A +    +R  ++ +I    + VNG  ++     +   D I+V+   LR    
Sbjct: 15  QRLDTFLAESFEQWTRSHIQNLIKNGNITVNGQHIKS-GYKLKDGDIIKVEVPELRPIDI 73

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
                      E   + + +KP G+V   +  +  +T+ + L +    +           
Sbjct: 74  QPEDIPLNILYEDEDIIVINKPQGMVVHPAAGNYSATLVNALLAHCKDLSGINGEIRPGI 133

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD------------ 156
           V R+D +T G+L++  +      L     +    R Y     G + +D            
Sbjct: 134 VHRIDKDTSGVLVVAKNDMAHVALAQQIKEKTAIRKYVALLEGDIKEDTGVINAPIARHP 193

Query: 157 -KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +    V+ G         +  + G    +   L  G+  +I+    +    V 
Sbjct: 194 TDRKKMA---VVSGGRSAVTHFKVLERFGRYTLIEARLETGRTHQIRVHMAYIGHPVV 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 = 79.5 bits (195), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 91/252 (36%), Gaps = 43/252 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  +V E  +  R+   I+ R    SR  +++++    V VNG L++     + S+D 
Sbjct: 5   MEEIKLVSEE-SGVRIDAWISSRLKEYSRSYIQKLLNDGHVLVNGSLVKS-NYKIKSSDE 62

Query: 60  IEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + + +    E   + + +KP G+V   +  +   T+ + L     
Sbjct: 63  ITVQIPEPEVLDIVPENIEIPVLYEDEHVLVVNKPKGMVVHPAAGNYSGTLVNALMDYCG 122

Query: 107 ----------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                     R   V R+D +T G+L++  +N+      L+L      RVY    HG + 
Sbjct: 123 DSLSSINGVIRPGIVHRIDKDTSGVLVVAKSNEAHEKLSLKLKDHDINRVYVALVHGIIR 182

Query: 155 QD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++                 +   +             +  +      V V L  G+  +I
Sbjct: 183 EESGKIDAPIGRHPVDRKKMA--VNTNNGRRAVTYFKVLERFKDATLVEVKLETGRTHQI 240

Query: 202 KKVFEFFNWKVN 213
           +    +  + + 
Sbjct: 241 RVHMSYIGYPII 252


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 83/233 (35%), Gaps = 37/233 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------EV 62
           R+ K +A     SR      I   ++ VNG L+++A   V   D I              
Sbjct: 11  RLDKAVADLTDLSRSLANEQIKTGKILVNG-LVKKAKYTVKEGDVISYELPEVEEVEYVP 69

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVYQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLN 159
           R+D +T GLL++  +      L       + LR Y    HG            + + + +
Sbjct: 130 RIDKDTSGLLMIAKNDQAHVALADELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             K+ +  +G         L+ + G  + V + L  G+  +I+    +    V
Sbjct: 190 RKKQAVTAKGKSALTRFQVLE-RFGDYSLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 82/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + +V VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E + + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 96/245 (39%), Gaps = 39/245 (15%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           + + +      +  ++ R++ Q RVKVN  L++     V ++D + VDG+ +    R + 
Sbjct: 3   IERYLTEHHQGTPGQIFRLLRQGRVKVNDRLIDSPRETVDTSDQVTVDGLAVTGR-RPQY 61

Query: 76  WLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +++KP+G+ T  +   P    ++ + L      +  +  L     GL L+T+D      
Sbjct: 62  LVFNKPVGVQTDLTPVVPHSLGSMLNALDQQ-QSLQILADLPRTIAGLTLVTDDNTFLTE 120

Query: 134 LELPSTQWLRVYRVRFHG--QVDQDKLNLLKKGIVIQGICYGDMQV------TLDTQKGS 185
           ++  +  W    RV+  G   +       L + I  + +     QV      TL T    
Sbjct: 121 VQGQT--WPSTLRVQLTGTTPLT------LPQNIAAEVVEQRPDQVHQWTMLTLQTTALD 172

Query: 186 --NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-TLLAGSTREVSKKILR 242
              AW+                E  +     + RI +GP +L   L  G+ R +  + + 
Sbjct: 173 SVTAWL----------------ESLSRVSGAINRIGWGPIKLSPDLAVGTYRGLFPQEID 216

Query: 243 EQLGP 247
             L P
Sbjct: 217 ALLTP 221


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 85/242 (35%), Gaps = 47/242 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  + I+  +   +R+ K + +     SR  ++ +I++  +KV+G  ++     +   + 
Sbjct: 1   MDTQKIIYTSPKSERIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKT-NYKLKEGNV 59

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +D             +P+    E   L + +K  G+V   S      T+ + L     
Sbjct: 60  ITIDYKEPEELDVVKQDIPVDIVYEDNDLIIVNKAKGMVVHPSVGHKDGTLVNALLFHSE 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   + +    R Y    HG +  D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGSIKHD 179

Query: 157 KLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAWVTV-------GLRE-----GKNRE 200
                  G +   I     +      +D  K S     V        L E     G+  +
Sbjct: 180 Y------GTIDAPIARNPKERKEMAIIDEGKPSITHFKVIDRFEKYTLIECELETGRTHQ 233

Query: 201 IK 202
           I+
Sbjct: 234 IR 235


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 88/240 (36%), Gaps = 42/240 (17%)

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------------VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +E             + +PL    E + + + +K  G+V   +      T+ + L     
Sbjct: 60  VETELPEARELEILPEDIPLDILYEDSDVIVINKARGMVVHPAAGAADGTLVNALLHHCE 119

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
            +           V RLD +T G+++   +      L     +    R+YR    G + +
Sbjct: 120 DLSGINGVIRPGIVHRLDKDTSGVMVAAKNDRAHVDLAEQIREKTAQRIYRAIVCGTIAE 179

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D             +   +    V+ G         +  +  ++  V   L+ G+  +I+
Sbjct: 180 DRGEIRAPIGRHPTERKKMA---VVPGGKEATTLFRVVERFPAHTLVECRLKTGRTHQIR 236


>gi|291545734|emb|CBL18842.1| 16S rRNA uridine-516 pseudouridylate synthase and related
          pseudouridylate synthases [Ruminococcus sp. SR1/5]
          Length = 68

 Score = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 18/62 (29%), Positives = 34/62 (54%), Gaps = 1/62 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
              R++K ++  G+ SRRE +R+    RV VNG L+    + ++    I +DG P++  
Sbjct: 2  DEKIRINKYLSDIGVCSRREADRLTEAGRVTVNGELVST-GMKILPDAEICIDGKPVKNR 60

Query: 71 ER 72
          ++
Sbjct: 61 KK 62


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>gi|324005834|gb|EGB75053.1| pseudouridine synthase, RluA family [Escherichia coli MS 57-2]
          Length = 326

 Score = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYSPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 85/244 (34%), Gaps = 49/244 (20%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+D  I + +    +RV K ++   G  SR ++   + +  VKVNG  ++     V   D
Sbjct: 1   MEDLTIEITKEMAGERVDKAVSSIDGDWSRSQISNWVKEGAVKVNGETVK-PNYKVRLQD 59

Query: 59  HIEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I V    L +              E   + + +KP G+V   +    + T+ + L    
Sbjct: 60  IIIVTPPELEELDVVPEDLNLEIVYEDEDVLVVNKPKGMVVHPAPGHAKGTLVNGLMHHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           + +           V R+D +T GLL++  +      L          R Y    HG + 
Sbjct: 120 TDLSGINGVVRPGIVHRIDKDTSGLLMVAKNDAAHTSLVDQLVKKTVTRKYVALVHGHIP 179

Query: 155 QDKLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAWVTV-------GLRE-----GKN 198
            D      KG +   I     +      +D  K +     V        L E     G+ 
Sbjct: 180 HD------KGTIQAPIARDPKERQNMAIVDKGKHAVTHFRVLERFGNFTLVECRLETGRT 233

Query: 199 REIK 202
            +I+
Sbjct: 234 HQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 84/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFVA--GINNEWSRSQVQQWIKDDVVTVNGKTVK-VNYKVKEEDEITVTIPEPEAL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I    G    + Q     + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>gi|126649705|ref|ZP_01721941.1| YlyB [Bacillus sp. B14905]
 gi|126593424|gb|EAZ87369.1| YlyB [Bacillus sp. B14905]
          Length = 303

 Score = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 81/239 (33%), Gaps = 50/239 (20%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            ++E    +R+ K ++      SR ++   ++   +KVNG  ++     V + D I +D 
Sbjct: 7   TIEEQQQGERIDKALSSLQSEWSRTQIGNWVSDGNIKVNGDAVK-PKYKVKAGDVIAIDV 65

Query: 64  --GVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
               PL             E   + + +KP G+V   +      T+ + L      +   
Sbjct: 66  PEAEPLDVIAENLALDIVYEDADVLVVNKPKGMVVHPAPGHLTGTLVNGLMYQCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL++  +      L     +    R Y    HG +  D    
Sbjct: 126 NGIMRPGIVHRIDKDTSGLLMVAKNDVAHESLVDQLVNKTVTRKYIALVHGHIAHD---- 181

Query: 161 LKKGIVIQ-----GICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
             KG  I             Q  +D  K +     V        L E     G+  +I+
Sbjct: 182 --KG-TIDAPIGRDQKDRQKQAIVDNGKHAVTHFHVVERFGDYTLVECRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 86/236 (36%), Gaps = 43/236 (18%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           I +E+   +R+   +A+     SR  ++ +I + +V +N  +++ A   +   + + +D 
Sbjct: 7   IAEESDVDKRIDLFLAKNLESFSRSYIQDLIKKGKVTINNKIIK-ANYRLKEGECVVLDI 65

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +P+    E   + L +KP G+V   +    + T+ + L          
Sbjct: 66  PKPEPLEIVPENIPIDILYEDEDVILVNKPKGMVVHPAAGHYKGTLVNALLYHCKSNLSG 125

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD--- 156
                R   V R+D++T G++++  +    + +   L +    R Y     G + +D   
Sbjct: 126 INGVLRPGIVHRIDMDTTGVIIICKNDIAHQHIAKQLANHSITRKYVAIVTGNIKEDEGV 185

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +   G         L+   G   ++   L  G+  +I+
Sbjct: 186 IDAAIARSKSDRKKMA--VDKDGKRAVTHYKVLERLNGYT-YIECVLETGRTHQIR 238


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRSGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 84/229 (36%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V E+   QR+ +V+A      SR  ++  I    V +NG ++ +A   +   D I    
Sbjct: 10  VVAEHQVGQRLDQVLAEMFPDYSRTRLKEWILAGFVNLNGNVVVKAREKMQYGDKIILNA 69

Query: 61  EVDGVP---------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
           EVD            +   E   + + +KP G V      +   TV + L   +  +I  
Sbjct: 70  EVDEEVRYEPQDLPLVIVYEDDDILVINKPAGFVVHPGAGNPDGTVLNALLFHYPDIIDV 129

Query: 110 ----SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------QV 153
                V RLD +T GL+++  T       V  L + +  R Y     G           +
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTIPAQTHLVTALQARRITREYEAVVSGTMTAGGFVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +      +  +   G         +  +  +++ + + L  G+  +I+
Sbjct: 190 GRHATKRTQMAVRPLGKPAKTH-YRVAEKYRAHSLLRLRLESGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.5 bits (195), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 77/241 (31%), Gaps = 35/241 (14%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T QR+ + +A      SR  ++  I    V ++G +  +    V+    + V
Sbjct: 8   KSEITATQTGQRLDQTLADLFPDYSRTRIKEWILDGSVTIDGDVSNKPREKVLEGQIVVV 67

Query: 63  DGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            G  L +               E   + + +K  GLV      +   T+ + L      +
Sbjct: 68  -GATLVEETTAKAQAIDLNIVYEDDHILVINKQAGLVVHPGAGNSDGTLLNALLHHCPGI 126

Query: 109 I------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--------- 151
                   V RLD +T GL+++         L     + +  R Y     G         
Sbjct: 127 ELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVSALQAREITREYEAIVLGSLISGGTVD 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +D+         +V  G          +  + ++  + + L  G+  +I+        
Sbjct: 187 EPIDRHPTKRTHMAVVYSGKPAMTHFRVAEKFR-AHTRLRLRLESGRTHQIRVHMAHLGH 245

Query: 211 K 211
            
Sbjct: 246 T 246


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 82/247 (33%), Gaps = 54/247 (21%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +  R   +SR  +++      + VNG  ++  +  V   D I +        
Sbjct: 40  EPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGAAVKS-SYKVRPEDVITLMLDRPKHD 98

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   L + +KP GLV      +   T+ + +      + +      
Sbjct: 99  NTIEAEDIPLDIVYEDDVLMVINKPAGLVVHPGAGNFHGTLINAVAWHLKDMPAFDPNDP 158

Query: 111 ----VGRLDINTEGLLLL-------TNDGG-LARVLELPSTQWLRVYRVRFHGQVDQDK- 157
               V R+D +T GLL++       T+ G               R Y     G   +++ 
Sbjct: 159 EVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTH------RSYNALVWGNFTEEEG 212

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + L+  +   G   G   VT   +  + G    +   L  G+  +I+  
Sbjct: 213 RIEGNIARDPRDRLRMAVFPPGSETGKPAVTHYRVIERFGYTTLIECVLETGRTHQIRAH 272

Query: 205 FEFFNWK 211
            +     
Sbjct: 273 MKHIGHP 279


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 90/243 (37%), Gaps = 37/243 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           I +++   +R+   +A     +R  ++++I  + VKVNG  ++     V   D I     
Sbjct: 10  IAEKDDVDKRIDSFLASEVDYTRSYLKKLILDELVKVNGKSVK-PNYKVREGDVINLNIP 68

Query: 61  ---EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
              E+D  P         E   + + +KP G+V   +  +   T+ + L    + +    
Sbjct: 69  EAEEIDLKPENIPLDIIYEDDDIIVVNKPQGMVVHPAPGNLSGTLVNALLYHCTNLSGIN 128

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG---------- 151
                  V RLD +T G++++  +      L         L+ Y     G          
Sbjct: 129 GELRPGIVHRLDKDTSGVMVVAKNDKAHLELSNQIKNRTILKKYLAIVEGVIKNDEGAVE 188

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +D +   KK  V++   Y      +  +  +N+ V   ++ G+  +I+    +   
Sbjct: 189 APIGRDHIER-KKMAVVKDGRYALTLYRVLERYKNNSLVEAIIKTGRTHQIRVHMAYIGH 247

Query: 211 KVN 213
            + 
Sbjct: 248 PIV 250


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 84/231 (36%), Gaps = 43/231 (18%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R +V++   Q  + VNG  ++ A   V + D ++V      
Sbjct: 35  EPLRVDKFLMN--FVENATRNKVQQAAKQGNIFVNGEPVK-ANHRVKANDVVKVLLSHPP 91

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                  + +PL    E   L + +KP G+V      +   T+ + L   F  + +    
Sbjct: 92  HEDLLVPENIPLNIVYEDDALLVVNKPAGMVVHPGHGNYSGTLINALVYHFEHLPNNSSN 151

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++         L          R Y     G +++D+       
Sbjct: 152 RPGLVHRIDKDTSGLLVIAKTEEAMLHLTQQFFYKTTQREYIALVWGNIEEDEGTVRGHI 211

Query: 158 ----LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                + L+  +   G    +      +  + G    V+  L  G+  +I+
Sbjct: 212 GRHLKDRLQMDVFPDGSHGKEAVTHYKVLERFGYVTLVSCRLETGRTHQIR 262


>gi|332638853|ref|ZP_08417716.1| pseudouridine synthase [Weissella cibaria KACC 11862]
          Length = 304

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 92/248 (37%), Gaps = 40/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M ++ +V  + T  R+ KV+A A    +R +V   I    + VNG  +++A  +V   D 
Sbjct: 1   MSEETLVITDQTG-RLDKVVADAFDDYTRTQVTGWINDGILTVNGA-VKKAKYSVKPNDE 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I+             + +PL    E   L + +KP G+V   +      T+ + L     
Sbjct: 59  IKFTVPEAVEIDLQPEDIPLDIVYEDDDLLVVNKPQGMVVHPALGHESGTLVNALMFHTP 118

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG----- 151
                   R   V R+D +T GLL++  +      L   L   + LR Y    HG     
Sbjct: 119 LSTINGVVRPGIVHRIDKDTSGLLMVAKNDKAHESLSAQLKDKKNLRQYYALVHGEFVEN 178

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KV 204
                  + +   +  K+ +V  G         +  +      + V L  G+  +I+  +
Sbjct: 179 EGTIKAPLGRSSADRKKQAVVAGGRDAVTHF-KVVKRFVGYTLLQVTLETGRTHQIRVHM 237

Query: 205 FEFFNWKV 212
             +    V
Sbjct: 238 -AYIGHPV 244


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKEEDEITVTIPEPEEL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGIMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQGICYGDMQVTL---DTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I      D +        + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIARDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 81/239 (33%), Gaps = 51/239 (21%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ K +A      SR ++++ I    V VNG  ++     ++  D + V     +K    
Sbjct: 16  RIDKELAHHLTDISRSQLQKWIEDGNVTVNGEKVK-PKYKLVVGDRVVVQPKKPQKIDLE 74

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
                     E   + + +KP G+V   +      T+ + L             R   V 
Sbjct: 75  PENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPGIVH 134

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQDKLNLLKKGIVIQ- 168
           R+D +T GLL++  +  LA        +     R Y    HG + ++      +G  I  
Sbjct: 135 RIDKDTSGLLMIAKN-DLAHRSLAAQLKAKTNEREYVALVHGVIKEE------RG-TIDA 186

Query: 169 --GICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIKKVFEFFNWK 211
             G    D +     + G +A     + E              G+  +I+   ++    
Sbjct: 187 PLGRSKKDRKKQAVVEDGRHAVTHFKVLELFQHYTLVSCRLETGRTHQIRVHMKYIGHP 245


>gi|325496332|gb|EGC94191.1| 23S rRNA pseudouridine synthase D [Escherichia fergusonii ECD227]
          Length = 326

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  MVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLYYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 36/240 (15%), Positives = 74/240 (30%), Gaps = 46/240 (19%)

Query: 14  QRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            R+ + +  A      SR +V+R I      V+G +    +  V +   IE+        
Sbjct: 1   MRLDRFLGEALREQDVSREKVKRAIRDGGCLVDGAVCTDVSAKVGAGQSIELRMEAEPTS 60

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
               +G      +   L + +KP G+    +      T+   L + F  + +        
Sbjct: 61  VQPEEGELEILYQDAWLAVLNKPAGMTVHPAPSCPDGTLVHRLVARFPSLRAQEGFRPGI 120

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD------------ 156
           V RLD +T GL+ +         L     + +  + Y     G                 
Sbjct: 121 VHRLDKDTSGLICVALTEEARMRLSEAFAAREIRKEYLALVQGVPAPAGTVDAPLGRHPT 180

Query: 157 ---KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              K+ + K G           +  +  +    + + V +  G+  +I+         + 
Sbjct: 181 VKVKVAVAKNG------KEARSEWRVLHKGQGYSLLEVRIFTGRTHQIRVHMAHIGHPLW 234


>gi|291514728|emb|CBK63938.1| ribosomal large subunit pseudouridine synthase D [Alistipes shahii
           WAL 8301]
          Length = 361

 Score = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 75/234 (32%), Gaps = 47/234 (20%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           TP R+ K +  R    SR  ++       + VNG   +  +  V   D I++        
Sbjct: 40  TPMRLDKFLTVRMEHCSRNRIQAAADSGNILVNGKAAKS-SYKVKPLDRIQIVMPYPRRE 98

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------- 106
                + +PL    E   L L  KP GLV      +   T+ + L    +          
Sbjct: 99  VELVAEDIPLDIPYEDQWLLLVDKPAGLVVHPGVGNYSGTLVNALMHHLNKQGIPAEEQN 158

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-------- 156
           R   V R+D NT GLL++  D      L          R Y     G  D+D        
Sbjct: 159 RAGLVHRIDKNTSGLLVIAKDEQTHARLAKQFFDHTIQRRYVALVWGNFDEDEGTITGNI 218

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   K+ +   G       +      +  + G    V   L  G+  +I+
Sbjct: 219 GRSPKDRQKMFVFADG---SDGKHAVTHWKVLKRYGYVTLVECRLETGRTHQIR 269


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 75/255 (29%), Gaps = 47/255 (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------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                + +            DG          + +  KP GL           T+   L 
Sbjct: 77  EPGQTVTLTLAVPAAKVTPEDGDLAVLYRDAAIAVLDKPAGLTVHPCPSCPEGTLVHRLV 136

Query: 103 SIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG- 151
             F  + +        V R+D +T GLLL+     +   L       Q  + Y    HG 
Sbjct: 137 RHFPELAAQEGFRPGIVHRIDKDTSGLLLVALTEAVRLELSRAFAERQVHKEYLALVHGV 196

Query: 152 ---------QVDQDKLNLLKKGIVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKN 198
                     + +  L+ +K  +V +           +V L    G  A V V +  G+ 
Sbjct: 197 PKAQGELEAPIGRHPLHKVKMAVVPENRGGKPARSAWRVLLADPDGRFALVAVRIFTGRT 256

Query: 199 REIKKVFEFFNWKVN 213
            +I+         + 
Sbjct: 257 HQIRVHMAHLGHPLW 271


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 87/240 (36%), Gaps = 43/240 (17%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R ++++      ++VNG ++++    V + D + V      
Sbjct: 29  EPLRVDKFLMN--FIEKATRNKIQQAAKNGNIQVNGAVVKQ-NHKVKANDVVRVLFEHPP 85

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFS- 106
                  + +PL    E   L + +KP G+V      +   T+       FDNLP   S 
Sbjct: 86  YEFLLTPEDIPLDIVFEDDTLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPENSSG 145

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
           R   V R+D +T GLL++         L          R Y     G V++D+       
Sbjct: 146 RPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSEREYIAIVWGNVEEDQGTVEGHI 205

Query: 158 ----LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                N ++  +   G    +      +  + G    ++  L  G+  +I+   +     
Sbjct: 206 GRHPKNRMQNTVYEDGDQGKEAVTHYKVLERLGYVTKISCKLETGRTHQIRVHMKHIGHT 265


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 84/233 (36%), Gaps = 39/233 (16%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V      +R+ ++IA R    SR   + ++    V VNG      A  +   D IE+   
Sbjct: 16  VAAEEDGERLDRLIAARVAEISRSYAQSLVKAGDVYVNGEPAR-PARRIHEGDTIEILLP 74

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
           P+ +               E   + ++ KP GLVT  +      T+ + + ++   V   
Sbjct: 75  PVPEPDDLTPEYIPVPVIYEDDDVIIFDKPAGLVTHPAPGHEHGTLVNVVKALRPDVPLL 134

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG--------- 151
                   V RLD +T GL+++  +    R L         ++ Y    HG         
Sbjct: 135 MGGKRPGIVHRLDKDTSGLIVVAKNEEARRYLVQQWQQRDVVKRYIALVHGVIRENEGTI 194

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              + +D  N  +  +V  G         L+  + +   + V +  G+  +I+
Sbjct: 195 DAPISRDPRNRKRMAVVPNGRPAVTHFRVLERFRDAT-LLNVQIETGRTHQIR 246


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKEEDEITVTIPEPEEL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQGICYGDMQVTL---DTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I      D +        + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIARDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 79.1 bits (194), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 93/246 (37%), Gaps = 43/246 (17%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V      +R+ K +++     SR  ++++I   +V VNG  ++R +  V   DHI +   
Sbjct: 10  VSSEEEGKRIDKYLSKLNKDLSRSYIQKLIDNDKVLVNGESVKR-SFKVNRGDHIRLIIP 68

Query: 63  ----DG-VPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                G  P+        E   + + +K  GLV   +  +  +T+ + L +         
Sbjct: 69  PPEDSGIKPVEMDLDIIYEDKDILVLNKNAGLVVHPAPGNHENTLVNALIAYCDNLSTIS 128

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV---YRVRFHGQV------- 153
             +R   V RLD +T G++++  +  ++    +   +  +    YR    G++       
Sbjct: 129 GVNRPGIVHRLDKDTSGVMVIAKN-DISHRKLVEQFKQRKTKKYYRTLLKGELPYKEGKI 187

Query: 154 ------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                 D      +   +  +          +      +++V V L+ G+  +I+  F +
Sbjct: 188 DAPIGRDPHDRKKMA--VTRKNSKKAVTYFKVLEFFRDHSYVEVELKTGRTHQIRVHFSY 245

Query: 208 FNWKVN 213
             + V 
Sbjct: 246 MGFPVV 251


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/230 (16%), Positives = 76/230 (33%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QD 156
                  V RLD +T GL+++         L   L      R Y     G++        
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQ 187

Query: 157 KLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
            +        +  +            +      +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 82/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + RV V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVTVDGKTINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E + + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E    QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSEKQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++  +      L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKNVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 81/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I + +V VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDKVTVNGKTINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E   + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 81/236 (34%), Gaps = 43/236 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+ K +A     SR      I   ++ VNG  +++A   V + D I  +   L + E   
Sbjct: 11  RLDKAVADLTPLSRSHANEQIKNGQILVNGQ-VKKAKYAVKAGDVITYE---LPEPEALE 66

Query: 75  LWL----------------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
                               +K  G+V   S      T+ + L      +          
Sbjct: 67  YVAENLPLDIVYQDEDVAVVNKAQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPG 126

Query: 111 -VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQD 156
            V R+D +T GLL++  +      L  EL   + LR Y    HG            + + 
Sbjct: 127 IVHRIDKDTSGLLMIAKNDDAHIKLAEELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRS 186

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  K+ +  +G      +  +  + G+   V + L  G+  +I+    +    V
Sbjct: 187 EKDRKKQAVTAKGKPAVT-RFHVLERFGNYTLVELQLETGRTHQIRVHMAYIGHPV 241


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFVA--GINNEWSRTQVQQWIKDDVVTVNGKAVK-GNYKVKEEDEITVTIPEPEEL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQGICYGDMQVTL---DTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I      D +        + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIARDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 63/327 (19%), Positives = 119/327 (36%), Gaps = 58/327 (17%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           TP R+ + + +  +  A+R +V++ I +QRV VNG  ++     + S DHI +       
Sbjct: 10  TPMRIDRYLTQQ-VENATRNKVQKAIEEQRVLVNGKPVKS-NYRIKSCDHIHITFLRPPA 67

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIF 105
                + +P+    E   L +  K  G+V   +  +   T+            D+L    
Sbjct: 68  PELAPEDIPISILYEDDDLMVIDKEAGMVVHPAFGNWTGTLANAILHHLGKDADDLDKTE 127

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++  +      L       Q  +VY+    G  +      +K 
Sbjct: 128 MRPGIVHRLDKDTSGLIIVAKNPVALHKLATQFARRQVEKVYKAIVWGVPNPPS-GTIKT 186

Query: 164 GIVIQGICYGDMQV----TLDTQKGSNAW-----VT---------VGLREGKNREIKKVF 205
            I   G  + + +V      +  +G +A      V          + L  G+  +I+   
Sbjct: 187 NI---GRSHKNRKVMANFPFEGAEGKHAITDYLVVEDLAYFALMDMTLHTGRTHQIRVHL 243

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL----REQLGPHLLEEAQVNLDAPI 261
           +     +  L   +YG     TL    +   +  +L    R+ L    L   Q     P+
Sbjct: 244 QHLGHPI--LGDQTYGGATPRTLPFSKSEPFTHNLLELMGRQALHAETLRFRQPTTGEPL 301

Query: 262 YSSETLVRDRPNIISEVPDDFTRMKKN 288
             +  L  D   ++ ++     R  + 
Sbjct: 302 AFTAPLPEDMKTVLEKIRSVMKRTTQT 328


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 80/240 (33%), Gaps = 45/240 (18%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVN----------VMSTDH 59
             +R+   +AR  I   SR  V+R+I    V+V+G  ++               V   + 
Sbjct: 9   AGERLDVFLARQ-IENCSRSYVQRLITDGNVRVDGAPVK-PNYKLRSGEEICCTVPPAEE 66

Query: 60  IEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
           + +  + +PL    E   + + +K  G+V   +  +   T+ + L      +        
Sbjct: 67  VVIAAEDIPLDVLYEDEDIIVINKARGMVVHPAAGNLTGTLVNALLFRCRDLSGINGELR 126

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD--------- 156
              V RLD +T G+++   +      L     S    R YR   HG + +          
Sbjct: 127 PGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKDARREYRALVHGNIAERAGVITGDIG 186

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
                   +   IV  G         +  + G    V+  L  G+  +I+  +       
Sbjct: 187 RHPTDRKRMA--IVRSGGKSATTHFEVLERFGDYTLVSCVLETGRTHQIRVHMT-SIGHP 243


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 85/234 (36%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  + ++ V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFSNYSRSQIQLWLKERAVSVNGEPVK-ANYKVKQGDEITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHVKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L   L     LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKPAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 54/295 (18%), Positives = 104/295 (35%), Gaps = 51/295 (17%)

Query: 9   ENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E   P+R+ + +A    A SR  V+++I Q  V VNG + +R    V + D+I +     
Sbjct: 8   EAGAPERLDRWLADNVEAFSRNRVQQLIEQGAVSVNGEVCDRKKELVTAGDYIILSVPEA 67

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFSRVISVG- 112
                  + +PL    E  +L + +KP G+V   +      T V   L     ++  VG 
Sbjct: 68  QPYELTPEDIPLDILYEDDQLLIVNKPAGMVVHPAPGHATGTLVHALLFYCGEQLTGVGG 127

Query: 113 --------RLDINTEGLLLLT-NDGGLARVLELPSTQWLR-VYRVRFHGQVDQDKLN--- 159
                   RLD NT G +++   +  L  + +    +  +  Y    +G    ++     
Sbjct: 128 VQRPGIVHRLDKNTTGAMVVAKTETALCNLQQQIQAKTAKREYLGIVNGAPKAEQGTIDQ 187

Query: 160 ------LLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                   +K + I     G            + G+   +   L  G+  +I+    +  
Sbjct: 188 PIGRHPKHRKKMSILPVESGGRTAITHWKTVERLGNYTLIHFQLETGRTHQIRVHSAYLG 247

Query: 210 WKVN---RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPI 261
             +          +   +L      + R             H + +A V+ +AP+
Sbjct: 248 LPIIGDPDYGSTRFPGVKLPGQALHAFR---------LTLSHPITQAVVSAEAPL 293


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 88/252 (34%), Gaps = 46/252 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V       R+ K ++     ASR ++++ I   +V VN +++    V V   D I  
Sbjct: 3   KYSVPHELNGIRLDKALSSLLENASRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+ A          E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+V   G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREI 201
                      D+ K+ +LK G    G         L+   KGS + V   L  G+  +I
Sbjct: 183 VIKNNIGRSRSDRQKMTILKYG----GKEAVTHYKILELFYKGSISMVECKLSTGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 239 RVQLSHLKHSVV 250


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 82/247 (33%), Gaps = 45/247 (18%)

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----------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V+            P+      E   + + +K  GLV   +      TV + L      +
Sbjct: 84  VEVPEPEPAEIIAEPIPLNIVYEDEDVIVINKQRGLVVHPAPGHHSGTVVNALMYHCQDL 143

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD- 156
                      V R+D +T GLL+   +      L   L      R Y    HG +  D 
Sbjct: 144 SGINGSIRPGIVHRIDKDTSGLLMAAKNDAAHASLSAQLKEHTVTRKYIALVHGNLPHDR 203

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                          +    +  +   +     ++  +      + + L  G+  +I+  
Sbjct: 204 GTVDAPIGRDSRDRKMFA--VTDKNSKHAVTHFSVIERLDDYTVLELQLETGRTHQIRVH 261

Query: 205 FEFFNWK 211
            ++    
Sbjct: 262 MKYIGHP 268


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPSKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 84/236 (35%), Gaps = 38/236 (16%)

Query: 15  RVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           R+   +A   +G  SR  ++R+I   RV ++G    RA+  + + D + ++  P      
Sbjct: 20  RLDLFLASHESGF-SRARLQRLIESGRVTISGKAAIRASQKLRTGDIVMLEEPPATPLEL 78

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
                      E   L +  KP GLV   +      T+ + L      +  +G       
Sbjct: 79  IPQDIPLSILYEDHDLLVLDKPAGLVVHPAAGHVSGTLVNALLFHCRDLAGIGGVMRPGI 138

Query: 113 --RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKG 164
             RLD +T GLL++  T+       L+    Q  + Y+   +G   +      L + +  
Sbjct: 139 VHRLDKDTSGLLVVAKTDAAHQGLALQFKKHQVGKTYQALVYGDPREKTGQIDLPVGRHP 198

Query: 165 IVIQGICYG-------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +  + +            +  +  + G    + V +  G+  +I+         V 
Sbjct: 199 VERKKMSTKSRRGKEAATRWRIAERFGVATLLNVDIVTGRTHQIRVHLAAIGHPVV 254


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 88/246 (35%), Gaps = 41/246 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV+E     R+ K ++ A    SR   +++I ++ V+++ + ++  +  V + D IEV  
Sbjct: 7   IVEEQDQGVRLDKYLSTAMDDCSRSRAQQLIDEEAVRIDDLPVKN-SYKVKAGDEIEVTL 65

Query: 63  -DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            +   L             E   + + +KP GLV      +   T+ + L      +   
Sbjct: 66  PEEEALEAQPQEMALNVVYEDHDVIVINKPKGLVVHPGPGNPDHTLVNGLLWHCHDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV------- 153
                   V R+D +T GL++   +    + L   L      R Y    HG +       
Sbjct: 126 NGVLRPGIVHRIDKDTSGLIVACKNDNAHQSLAKQLAEKTAGRQYYALVHGVINHEYGTI 185

Query: 154 ------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                 D+     +   +  +          +  +  +   V+  L  G+  +I+   ++
Sbjct: 186 DAPIGRDEKDRQKMA--VTEKNSRPAITHFKVVERFDNYTLVSCRLETGRTHQIRVHMQY 243

Query: 208 FNWKVN 213
             + + 
Sbjct: 244 IGFPIV 249


>gi|295109999|emb|CBL23952.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           obeum A2-162]
          Length = 304

 Score = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 84/237 (35%), Gaps = 42/237 (17%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ + +A +    SR  +++++ +++V VNG +++ A     S D+IE           
Sbjct: 15  IRIDRYLADQCPEHSRSYIQKLLKEEQVLVNGRVIK-ANYKTQSGDYIEFHIPDPEVPDI 73

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVI 109
             + +PL    E   + + +KP  +V   S      T+ + + +             R  
Sbjct: 74  LPENIPLDILYEDDYVLVVNKPKDMVVHPSAGHTSGTLVNAVMAHCGEHLSGINGVLRPG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----------- 156
            V R+D +T G LL+  D  + R L   L      R YR    G + +D           
Sbjct: 134 IVHRIDKDTTGALLICKDDVVHRDLAEQLKEHSIKRRYRAVVQGNLKEDEGTVNAPVGRH 193

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +   I  +          +  + G   ++   L  G+  +I+         
Sbjct: 194 PTDRKKMA--INHKNGKEAITHYKVLERFGQATYIECRLETGRTHQIRVHMASLGHP 248


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 84/243 (34%), Gaps = 46/243 (18%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           N+  EN    R+   ++      SR  ++R+I Q  + +N  +     + V   D ++++
Sbjct: 4   NLTVEN-KGNRLDLWLSNQLTDISRSHIQRLIEQGNIILNNEVCTNKKIKVKIGDRLQIN 62

Query: 64  ---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                PL             E  +L + +KP  LV   +      T+   L    S +  
Sbjct: 63  LPEPKPLELKPEPLPLDILYEDEQLIIINKPANLVVHPAPGHETGTLVHGLLYHCSNLAG 122

Query: 111 VG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD-QDKL 158
           +G         RLD +T G +++  T+        ++ +    R Y    +G +  Q+  
Sbjct: 123 IGGVQRPGIVHRLDKDTTGAMVVAKTDFAHQNLQAQIKNKTAKREYLGIIYGVLTNQEDK 182

Query: 159 NLLKKGIV--------IQGICYGDMQVTLDTQKGSNAW-----------VTVGLREGKNR 199
               +GI+        I       + +    ++    W           V   L  G+  
Sbjct: 183 ENSHQGIINLPIGRHPIDRKKMAVVPLEKRGREAITHWEILERLGNYSLVKFTLETGRTH 242

Query: 200 EIK 202
           +I+
Sbjct: 243 QIR 245


>gi|297180028|gb|ADI16253.1| pseudouridylate synthases, 23S RNA-specific [uncultured bacterium
           HF0010_16H03]
          Length = 309

 Score = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/222 (21%), Positives = 85/222 (38%), Gaps = 36/222 (16%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR--- 68
           QR+ K  A       SR ++++ I + R+ VNG L  +   +V   D IE++    R   
Sbjct: 12  QRLDKA-ATELFDEYSRTQIKKWILEGRILVNGDL-SKPRDSVHENDEIEINPTKERKVS 69

Query: 69  ----------KAERTRLWLYHKPIGLV----TTHSDPDGRSTVFDNLPS--IFSRVISVG 112
                       E     + +KP GL+    +   D    + + +  P      R   V 
Sbjct: 70  WEPQNINFETYHECEDFIIINKPPGLIMHPGSGCYDGTLANGLINKYPDLENLPRCGIVH 129

Query: 113 RLDINTEGLLLLT-NDGGLARVLELP-STQWLRVYRVRFHG----------QVDQDKLNL 160
           RLD +T G+LL+  N+G     ++L    +  + Y     G           + +DK N 
Sbjct: 130 RLDKDTSGVLLVARNEGFRNYFIQLMQERRVTKKYTAIVVGSTLGSFSIEDPIGRDKSNR 189

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            K  +   G        T +   G+ + + + +  G+  +I+
Sbjct: 190 TKMSVRPDGKEALTFVKTSERI-GNYSILDIAIETGRTHQIR 230


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 84/232 (36%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+ K +A     SR +    I Q+RV VNG   ++A   V   D I              
Sbjct: 11  RLDKALADLTPLSRSQANDQIKQKRVLVNGSP-KKAKYIVQVGDCISYHIPEESSLDYQA 69

Query: 64  -GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
             +PL    +   L + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  QDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHVKDLSSINGVIRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++       ++L     + + LR Y    HG + +D             +
Sbjct: 130 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 190 RKKQTVTAKGKEALTRFKVLE-RFGRYSLVELQLETGRTHQIRVHMAYIGHP 240


>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 = 79.1 bits (194), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 82/247 (33%), Gaps = 54/247 (21%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +  R   +SR  +++      + VNG  ++  +  V   D I +        
Sbjct: 40  EPVRIDKFLYERMQHSSRNRIQKAADAGFIHVNGTAVKS-SYKVRPEDVITLMLDRPKHD 98

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   L + +KP GLV      +   T+ + +      + +      
Sbjct: 99  NTIEAEDIPLDIVYEDDVLMVINKPAGLVVHPGAGNFHGTLINAVAWHLKDMPAFDPNDP 158

Query: 111 ----VGRLDINTEGLLLL-------TNDGG-LARVLELPSTQWLRVYRVRFHGQVDQDK- 157
               V R+D +T GLL++       T+ G               R Y     G   +++ 
Sbjct: 159 EVGLVHRIDKDTSGLLVVAKTPDAKTDLGRQFFNKTTH------RSYNALVWGNFTEEEG 212

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + L+  +   G   G   VT   +  + G    +   L  G+  +I+  
Sbjct: 213 RIEGNIARDPRDRLRMAVFPPGSETGKPAVTHYRVIERFGYTTLIECILETGRTHQIRAH 272

Query: 205 FEFFNWK 211
            +     
Sbjct: 273 MKHIGHP 279


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G  +
Sbjct: 3  PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDIVKVNGQLI 59


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 69/177 (38%), Gaps = 30/177 (16%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              +   P RV K +        A+R ++++ I    V+VN  +++     V + DHI V
Sbjct: 25  TASDGQEPLRVDKYLMN--FIENATRSKIQQSIKDGAVRVNDEVVKS-NYKVKAGDHIRV 81

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNL 101
                        + +PL    E   L + +KP G+V      +   T+       FDNL
Sbjct: 82  LFKHPPHENLLVPEDIPLDIVYEDDTLVVVNKPAGMVVHPGHGNYSGTLINALIHHFDNL 141

Query: 102 PSIFSRVIS-VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           P+  S     V R+D +T GLL++  T         +  +    R Y     G  D+
Sbjct: 142 PNNSSNRPGLVHRIDKDTSGLLVVAKTEHAMSYLSAQFAAKTSEREYVAIVWGNFDE 198


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 88/245 (35%), Gaps = 44/245 (17%)

Query: 9   ENFTPQRVSKVIARA-GIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
            N   +R+   +    G   SR  V+  I      VNG    + ++ +   +++ +    
Sbjct: 17  PNAAGKRLDVFLGEQVGDGFSRGRVQEWIKIGLASVNGKPWTKPSLRLRGGENVCLLGRA 76

Query: 63  DGVPLRKAERTR--------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
           +G  L   +           L + +KP GL T  +      T+   L   F  + +    
Sbjct: 77  EGNCLTPEQGDLAVLYRDDWLLVLNKPAGLTTHPAPSCPEGTLVHRLLHHFPELAALDSE 136

Query: 111 ----VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNL--- 160
               V RLD +T GLL++  T    LA   +    +  +VY    HG+  D+  ++L   
Sbjct: 137 RPGIVHRLDKDTSGLLVVALTERARLALAEDFAERRVDKVYLALVHGRPQDRGDIDLPMG 196

Query: 161 -----------LKKGIVIQGICYGDM-QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                      LKKG    G       ++   ++ G  + + V +  G+  +I+      
Sbjct: 197 RHPTHKTRMAVLKKG----GRPARSAYEMLWSSRDGRFSLLRVRIFTGRTHQIRVHLAAI 252

Query: 209 NWKVN 213
              + 
Sbjct: 253 GHPII 257


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 86/245 (35%), Gaps = 39/245 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV- 65
            ++    +R+   I+     SR + +  I ++ VKVN   ++  +  +   D IEV    
Sbjct: 7   TEKADEGKRLDIFISDKLNISRAKAQEAIEKKFVKVNNY-VKTKSYKIKFNDLIEVSDEF 65

Query: 66  --PLRKAERT--------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              L  +E+                L +  KP G+V          T+ + L     ++ 
Sbjct: 66  SLKLENSEKLIPQNIPIQVIYKDDYLIVLSKPAGMVVYPCAGHPDGTLMNALAYHVKKLA 125

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ------ 152
           +VG         RLD +T G++++  D      L       +  + Y    +GQ      
Sbjct: 126 NVGAPFRPGIVHRLDKDTSGVMVVALDDETYYKLVEAFKKREIKKEYLALVYGQLRGSGK 185

Query: 153 VDQDKLNLL--KKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFF 208
           +       +  +K + I+     +     +  K   +  ++ V +  G+  +I+  F   
Sbjct: 186 ITTPVGRAIYDRKKMSIKSKKAKEAITEWEVIKNFKNYTFLKVKILTGRTHQIRVHFSSI 245

Query: 209 NWKVN 213
              V 
Sbjct: 246 GHPVI 250


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 91/251 (36%), Gaps = 44/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +       R+ K +A      SR  V+ +I    + VN   +E+A+  V   D 
Sbjct: 1   MTKKYELTVENEKGRLDKYLADKIDDLSRTRVKELIDDGLILVN-QKVEKASYKVKDGDA 59

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IEV            + +PL    E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEVTVPAVKPLDVIPENIPLDIIYEDNDVIVVNKPQGMVVHPAAGHPDHTLVNALLYHTK 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++  +  +       L   + +  R+Y    HG 
Sbjct: 120 DLASSPEGF-RPGIVHRIDKDTSGLLMIAKNSQVRESLEDQLAHKTNK--RLYLAIVHGN 176

Query: 153 VDQDKL-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
             +++            +  K G+V  G  +      +  Q    + +   L  G+  +I
Sbjct: 177 FAEEEGTIDAPIARNPHDRKKMGVV-AGGKHAVTHFKVIEQFKGYSLIQCKLETGRTHQI 235

Query: 202 KKVFEFFNWKV 212
           +    +    V
Sbjct: 236 RVHLSYIGHPV 246


>gi|257898611|ref|ZP_05678264.1| pseudouridylate synthase [Enterococcus faecium Com15]
 gi|257836523|gb|EEV61597.1| pseudouridylate synthase [Enterococcus faecium Com15]
          Length = 303

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 85/234 (36%), Gaps = 40/234 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ KV+       SR +++  + ++ V VNG  ++ A   V   D I V           
Sbjct: 14  RIDKVLTNLFSDYSRSQIQLWLKERAVSVNGQPVK-ANYKVKQGDEITVLIPEPETLDVV 72

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
            + +PL    E   + + +KP G+V   S      T+ + L              R   V
Sbjct: 73  PENIPLTIVYEDEDVAVINKPQGMVVHPSAGHTHGTMVNALMYHIKDLSTINGVIRPGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L   L     LR Y    HG++  +K            
Sbjct: 133 HRIDKDTSGLLMVAKNDQAHESLAKQLKDKTSLRKYVALVHGEIPHEKGTINAPIGRSKE 192

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              ++  I   G         L+  +G    V + L  G+  +I+   ++  + 
Sbjct: 193 NRKMQA-IREDGKPAVTHFTVLERFEGFT-LVELKLETGRTHQIRVHMKYIGYP 244


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/231 (16%), Positives = 79/231 (34%), Gaps = 44/231 (19%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRK 69
           T +R+   +      SR ++ ++I ++ V+V+G ++ R+ V +     + V      ++ 
Sbjct: 11  TIERLDTFLTSILGQSRSQIAQLIKKELVQVDGKVVSRSGVKLKKNQVVLVKFPPAEIKP 70

Query: 70  A-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVI 109
           A           E   + + +KP GL    +     +T+ D L              R  
Sbjct: 71  ALDIDFDVEILYEDDDILVINKPTGLTVHPAPSVKEATLVDWLKHKGMRLSSLSGEERHG 130

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----------- 156
            V RLD  T G +++  +      L   L      R Y    +  +  +           
Sbjct: 131 IVHRLDKGTSGAMVIAKNNSTHEFLSDQLQDKSMGRYYLAVINPPLKDELTEVIFPIARS 190

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                K+  L+ G           +V   +   +N  +   L  G+  +I+
Sbjct: 191 SHNRLKMAPLEHG----KYAKSAFKVLAYSNDEANQLIACKLYTGRTHQIR 237


>gi|89055892|ref|YP_511343.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp.
           CCS1]
 gi|88865441|gb|ABD56318.1| ribosomal large subunit pseudouridine synthase D [Jannaschia sp.
           CCS1]
          Length = 310

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 75/236 (31%), Gaps = 53/236 (22%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLR-KAERT 73
           SR  + R+I    V +NG ++      V   D +E+            + +PL    E  
Sbjct: 8   SRTRLARLIPAGAVAINGRVVTDPKARVAEGDGVEITVEDAAEVETVAEDIPLDIVHEDD 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRLDINTEGLLL 123
            L + +KP G+V   +      T+ + L   F           R   V R+D +T GLL+
Sbjct: 68  DLIVVNKPAGMVVHPAPGSPSGTLVNALLHHFGGKLSGVGGEKRPGIVHRIDKDTSGLLV 127

Query: 124 LTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQ----------- 168
           +         L          R Y    HG  D      L+  KG+  +           
Sbjct: 128 VAKSDRAHHGLAAQFADHSMEREYLALCHGVPDGSD-PRLRGVKGVSFEGSTVKITTQLA 186

Query: 169 --------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                         G  +   +V +    G  A V+  L  G+  +I+        
Sbjct: 187 RHKTDRQRQAVLFSGGRHAVTRVRVLEAHGPVALVSCRLETGRTHQIRVHMSHVGH 242


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 87/232 (37%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+ K +A     SR +    I Q+RV VNG L ++A   V   D I              
Sbjct: 11  RLDKALADLTPLSRSQANDQIKQKRVLVNG-LPKKAKYIVQVGDCISYHIPEESSLDYQA 69

Query: 64  -GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
             +PL    +   L + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  QDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHIKDLSSINGVIRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++       ++L     + + LR Y    HG + +D           + +
Sbjct: 130 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSEKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G     +   L+ + G   +V + L  G+  +I+    +    
Sbjct: 190 RKKQTVTAKGKEALTLFKVLE-RFGHYTFVELQLETGRTHQIRVHMAYIGHP 240


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 93/247 (37%), Gaps = 45/247 (18%)

Query: 9   ENFTPQ------RVSKV-IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++ TP+      R+ KV +      SR E+++ I   +V VN   +E+A   V   D I+
Sbjct: 4   QSITPELEEKGLRLDKVILNHMPDRSRTEIQKWIKAGQVIVNDN-VEKANYKVEEEDVIQ 62

Query: 62  V------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------- 101
           V            + +PL    E   + + +KP G++   S      T+ + L       
Sbjct: 63  VTLPDPQSTEIRPEDIPLDIIYEDEDVIVVNKPTGMIVHPSAGIYSGTLVNALLYHCHDL 122

Query: 102 --PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
              +  +R   V R+D  T GLL++  +    R L   L     +R Y    HG ++ + 
Sbjct: 123 SAINGITRPGIVHRIDKETSGLLMVAKNDNAHRSLSKQLEEHSVVRRYVALVHGVINHN- 181

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVF 205
           +  ++  I         M VT    K +     V        L E     G+  +I+   
Sbjct: 182 VGRIEAPIGRDSKDRKKMAVTSKNAKDAITNFKVLERYDDMTLIECRLETGRTHQIRVHM 241

Query: 206 EFFNWKV 212
           ++    V
Sbjct: 242 QYIGHPV 248


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 78/234 (33%), Gaps = 33/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K K+ +    T QR+ + +A      SR  ++  I    V ++G + ++    V+    
Sbjct: 10  IKLKSEITSIQTGQRLDQTLADLFPDYSRTRIKEWILSGAVSIDGNVSDKPRTKVLEGQE 69

Query: 60  IEV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V              +      E   + + +K  GLV      +   T+ + L     
Sbjct: 70  IIVLATLEEETSAKAEAIDLDIVYEDDHILVINKQAGLVVHPGAGNQDGTLMNALLHHCP 129

Query: 107 RVI------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
            +        V RLD +T GL+++         L   L + +  R Y     G       
Sbjct: 130 GIELVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVTALQAREITREYEAIVQGGIIAGGT 189

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +D+          V+           +  +  ++  + + L  G+  +I+
Sbjct: 190 VDEPIDRHPTKR-THMAVVHNGKPAMTHYRVAEKFRAHTRLRLRLESGRTHQIR 242


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 84/232 (36%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+ K +A     SR +    I Q+RV VNG   ++A   V   D I              
Sbjct: 11  RLDKALADLTPLSRSQANDQIKQKRVLVNGSP-KKAKYIVQVGDCISYHIPEESSLDYQA 69

Query: 64  -GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
             +PL    +   L + +KP G+V   S      T+ + L              R   V 
Sbjct: 70  QDIPLDIVYQDDVLVIINKPQGMVVHPSAGHSTGTLVNALLYHVKDLSSINGVIRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++       ++L     + + LR Y    HG + +D             +
Sbjct: 130 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVHGNLPKDRGVIEAPIGRSDKD 189

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +  +G         L+ + G  + V + L  G+  +I+    +    
Sbjct: 190 RKKQTVTAKGKEALTRFKVLE-RFGRYSLVELQLETGRTHQIRVHMAYIGHP 240


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/231 (17%), Positives = 75/231 (32%), Gaps = 35/231 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V V+G ++ +    VM  + I V
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEVITV 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PS 103
                D V             E   + + +KP   V          TV + L       +
Sbjct: 68  LAELEDEVRWEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLFHCPEVA 127

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHG 151
              R   V RLD +T GL+++         L   L      R Y                
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRHITREYEAIAIGRMTAGGKVDK 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 188 PIGRHATKRTLMAVSPMGKPAVTHFRVAEHFRE-HTRIRLRLETGRTHQIR 237


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/227 (17%), Positives = 79/227 (34%), Gaps = 41/227 (18%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPL 67
           +R+ K I       SR +V+  + + RV VNG  ++     + + D + +       + +
Sbjct: 21  ERIDKFITLQNEDWSRSQVQAWVKEGRVTVNGEPIKN-NYKLQAEDEVTLRVPPPKEMAI 79

Query: 68  RKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
           +  E +   +Y        +KP GLV   +      T+ + L +    +           
Sbjct: 80  QPEEMSLDIVYEDSDVVVVNKPRGLVVHPAPGHYSGTLVNGLLAHCKDLSGINGVLRPGI 139

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK----------- 157
           V R+D +T GLL++  +      L   L +    R Y    HG +  +            
Sbjct: 140 VHRIDKDTSGLLMVAKNDKAHMGLAEQLKAHTVNRKYVALVHGVIPHEMGTIEAPIGRDP 199

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +   +V +          +  +      V + L  G+  +I+
Sbjct: 200 KNRQQMA--VVFENSKPAVTHFIVLERFKEYTMVELKLETGRTHQIR 244


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/168 (22%), Positives = 63/168 (37%), Gaps = 30/168 (17%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
           +R+ K +A  GI    SR +V++ I    V VNG  ++     V   D I V   D   L
Sbjct: 16  ERIDKFVA--GINNEWSRSQVQQWIKDDVVTVNGKAVK-VNYKVKEEDEITVTIPDPEAL 72

Query: 68  R----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                        E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
             V R+D +T GLL++  +      L     +    R Y+   HG + 
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLLNQLVAKTVTRRYKAIVHGVIP 180


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 88/251 (35%), Gaps = 45/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK+   V EN   +R+ + ++   +A  SR  ++++I +  V VN   ++ A   +   D
Sbjct: 1   MKEFFTV-ENQDGERIDRYLSEE-LADRSRSYIQKLIKENYVTVNQKPVK-ANYRLSLGD 57

Query: 59  HIEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            +E+D             +PL    E   + + +KP  +V   +      T+ + L    
Sbjct: 58  RVEIDLPEAKEPDIRPEDIPLDILYEDKDIIIVNKPKQMVVHPAPGHYSQTLVNALMYHC 117

Query: 106 S----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQV 153
                      R   V R+D++T G L+   +    + L     +    R+Y    HG +
Sbjct: 118 GSDLSGINGTMRPGIVHRIDMDTTGSLVACKNDMAHQSLSRQLKEHSIRRIYVAIVHGNI 177

Query: 154 DQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            ++             +   +   I  +          +  + G   ++   L  G+  +
Sbjct: 178 KEEYGTVNAPIGRHPTERKKMS--IHSRNGREAVTHYQVLERFGDYTYIRCELETGRTHQ 235

Query: 201 IKKVFEFFNWK 211
           I+         
Sbjct: 236 IRVHMASLGHP 246


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/180 (21%), Positives = 65/180 (36%), Gaps = 31/180 (17%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V E     R+   +A+ G   +R    + +A   V +NG+   ++A  V + D +E    
Sbjct: 10  VDETGDGMRLDAFLAKEGAYTTRSAAAKRVAAGEVSINGVAARKSAT-VKAGDVVEYQVF 68

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFS--- 106
                       +PL  + E  ++ +  K  GLVT  +D  P   + V   +        
Sbjct: 69  IDPRVFDLESADIPLDVRYEDDQVLVISKQAGLVTHPADGHPQQDTLVNALIHHCGRENL 128

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD 156
                   R+  V RLD +T GL+L        + L          R Y    HG +  +
Sbjct: 129 CNVQGEQDRLGIVHRLDRDTSGLMLAAKTNEAGQKLMEDIADRDVDRHYLALVHGWIPLE 188


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 34/128 (26%), Positives = 63/128 (49%), Gaps = 3/128 (2%)

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
            I   +I V  L  ++EGL+LLTNDG  AR L+      +  Y V+   ++  +K+ L++
Sbjct: 219 DIPEHLIVVNSLSASSEGLVLLTNDGDFARNLKGIENNIITSYIVKVKEELTNEKIKLIE 278

Query: 163 KGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNR-EIKKVFEFFNWKVNRLIRISY 220
           KG  +  +    + V +  Q  S+  W+ +   E K+   +  +F  +   + +  R S+
Sbjct: 279 KGCNVGDVHIRPLDVHVIKQHSSSPKWIKLTYVE-KSHTYLNLLFSKYGLTIRKCKRFSF 337

Query: 221 GPFQLGTL 228
           GP++   L
Sbjct: 338 GPYKASDL 345



 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 47/107 (43%), Gaps = 12/107 (11%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---IEVDGVPLRKAE 71
           R+SK+++ + + SR + + +I   +VK    +  +     +  D    IE+DG P+    
Sbjct: 14  RLSKILSLSAVTSRGKAQELIKNGKVK----VNNQVVRQNVVVDINSAIELDGKPILVDV 69

Query: 72  RTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLD 115
            T+LW  +KP  +  +     + + +       P     ++  GRL 
Sbjct: 70  TTKLWGIYKPKHVFCSSETNYEYEEKKQALKIAPPH--ELLPCGRLP 114


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 92/249 (36%), Gaps = 49/249 (19%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           I  +   P R+ K +        A+R ++++   +  + VN +++++    V + D I+V
Sbjct: 58  IASKGQEPLRIDKYLMN--FIENATRNKIQQAAKEGHIWVNDLVVKQ-NYKVKAGDQIKV 114

Query: 63  -------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRST--------VFDN 100
                        + +PL    E + L + +KP G+V      +   T        V D 
Sbjct: 115 MFTHPPYEFLLTPEDIPLDVVYEDSDLMVVNKPPGMVVHPGHGNYSGTLINALLFHVKDL 174

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-----LRVYRVRFHGQVDQ 155
             +   R   V R+D +T GLL++      A+ +   + Q+      R Y     G V++
Sbjct: 175 PLNADERPGLVHRIDKDTSGLLVVA---KTAKAMTHLAKQFFDKTSEREYVAIVWGNVEE 231

Query: 156 DK-----------LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
           ++            N L+  +   G    +      +  + G    V+  L  G+  +I+
Sbjct: 232 EQGTVRGHIGRHPKNRLQMAVFPDGDQGKEAVTHYKVMERLGYVTLVSCVLETGRTHQIR 291

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 292 AHMKHIGHT 300


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 84/228 (36%), Gaps = 42/228 (18%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           R+ K +A  G+    SR  ++++I    V V G+   + +  V + D + ++  P  +  
Sbjct: 49  RLDKALA--GLVPEFSRSYLQQLIEDGGVLVKGLKAIKTSAKVKAGDELTIELRPTPQSQ 106

Query: 70  ------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISV 111
                        E   L + +KP GLV   +  +   T+ + L       S   R   V
Sbjct: 107 AFKPEEMALDIVYEDRHLIVVNKPAGLVVHPAPGNWSGTLLNGLLAHDPQASFMPRAGIV 166

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDK 157
            RLD +T GL+++         L   + +    R Y    HG             + +D 
Sbjct: 167 HRLDKDTSGLMVVARQRQTMDQLVSMIAARTVSREYIALAHGTWEGAKTRQVEAPIGRDP 226

Query: 158 LNLLKKGIV-IQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            N L+  +V ++          ++L      +  V   L  G+  +I+
Sbjct: 227 RNRLRMAVVDLEKNSGKAASTVISLLDNAEKHCLVKCKLHTGRTHQIR 274


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 82/241 (34%), Gaps = 43/241 (17%)

Query: 10  NFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVN----------VMSTD 58
           + T +R+   +AR     SR  V+R+I    V+V+G  ++               V   +
Sbjct: 7   DSTGERLDVFLARQMENCSRSYVQRLITDGNVRVDGARVK-PNYKLRSGEEICCTVPPAE 65

Query: 59  HIEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
            + +  + +PL    E   + + +K  G+V   +  +   T+ + L      +       
Sbjct: 66  EVVIAAEDIPLDVLYEDEDIIVINKERGMVVHPAAGNLTGTLVNALLFRCRDLSGINGEL 125

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-------- 156
               V RLD +T G+++   +      L     S    R YR   HG + +         
Sbjct: 126 RPGIVHRLDKDTSGVMVAAKNDMAHHFLAQQIRSKAARREYRALVHGNIAERAGVITGDI 185

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNW 210
                    +   IV  G         +  + G   +V+  L  G+  +I+  +      
Sbjct: 186 GRHPTDRKRMA--IVRSGGKSATTHFEVLERFGDYTFVSCVLETGRTHQIRVHMT-SIGH 242

Query: 211 K 211
            
Sbjct: 243 P 243


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 77/235 (32%), Gaps = 39/235 (16%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-----------EV 62
           R+ K +      A+R ++++      + VN I ++     V   D +            V
Sbjct: 31  RIDKYLMHLLENATRNKIQQAATSGNIFVNNIPVKS-NYKVKPFDVVTIMLSHPPFENRV 89

Query: 63  DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP-SIFSRVISV 111
           D   +      E   L L +KP GLV      +   T+       F NLP +   R   V
Sbjct: 90  DPEDIPLDIVYEDDALLLINKPAGLVVHPGHGNYTGTLVNALAFHFQNLPLNSSERPGLV 149

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK-----------L 158
            R+D +T GLL++         L     +    R Y     G V +D+            
Sbjct: 150 HRIDKDTTGLLVIAKTEQAMTHLAKQFENKTSEREYIAIVWGNVQKDEGTIEGNLARHLK 209

Query: 159 NLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + ++  +               +  + G    ++  L  G+  +I+   +     
Sbjct: 210 DRMQMAVFADPEIGKPAITHYKVLERFGYITVISCKLETGRTHQIRAHLKHIGHP 264


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 83/234 (35%), Gaps = 33/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K    V E+   QR+ + +A      SR  ++  I  +R+ VNG  +++    V+  + 
Sbjct: 5   VKLNATVAESQLGQRLDQALAELFPDYSRSRIKEWILNRRITVNGTTIDKPKEKVLGGEQ 64

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +D             +PL    E   + + +KP  LV      +   TV + L   F 
Sbjct: 65  ISIDAEIEEEARWEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHFP 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------R 148
                 R   V RLD +T GL+++         L   L   +  R Y             
Sbjct: 125 AIADVPRAGIVHRLDKDTTGLMVVAKTVPSQTHLVDALQRREITREYEAVAIGRMTAGGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  + +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 185 VNEPISRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/230 (16%), Positives = 77/230 (33%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVHVNGEVVTKPRTRVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDCTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QD 156
                  V RLD +T GL+++         L   L      R Y     G++      + 
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVEQ 187

Query: 157 KLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
            +        +  +            +  +   +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPLGKPAVTHYRVAERFREHTRIRLRLETGRTHQIR 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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 81/260 (31%), Gaps = 58/260 (22%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
             EN   QR+ + +A+   G  SR  ++ +I +  +K++G L++     + S   IE+  
Sbjct: 8   TNENACGQRIDQWLAKQYKGEISRSRLQTLIREGHLKIDGQLIKEPKTKLKSNQIIELII 67

Query: 63  --------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------- 104
                    G  L      E   + + +KP GLV    + +   T+ + L          
Sbjct: 68  PAPNDARPQGEALALDIFFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIYHCSDSLSG 127

Query: 105 ---FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQ 155
                R   V RLD +T G++++  +    R L        R       Y     G  ++
Sbjct: 128 IGGIKRPGIVHRLDKDTSGVMVIAKNDIAHRNLNAQFADHGRTSALDRRYHAIIWGSPNR 187

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------------ 195
               ++                 V  +     +A     L E                  
Sbjct: 188 NIATIDTFLARSSHD--RTKRAVVHSEHANARHAITHFSLLEKYGTCNDTTPFASLLECR 245

Query: 196 ---GKNREIK-KVFEFFNWK 211
              G+  +I+  +       
Sbjct: 246 LETGRTHQIRVHM-AHIGHP 264


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHLGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y              +  +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 85/252 (33%), Gaps = 41/252 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+ N+  +  +  R+ + +A+     SR  ++++I +  V++N  L       +   D 
Sbjct: 1   MKEINLYNQENS-DRLDRYLAQQLPDLSRSRIQKLIEEGNVQLNHNLCTSKKATIQPGDS 59

Query: 60  IEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +   D  PL             E  ++ + +KP  LV   +      T+ + L +   
Sbjct: 60  IHLTIPDAKPLDLKPEAIPLDILYEDDQILIVNKPANLVVHPAPGHENGTLVNALLAHCP 119

Query: 107 RVISVG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
            +  +G         RLD +T G + +         L  +L +    R Y    +G    
Sbjct: 120 NLAGIGGVQRPGIVHRLDKDTTGAIAIAKTDHAHHHLQAQLKAKTARRDYLGVVYGSPAT 179

Query: 156 D-------------KLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +                 +   + ++ G         +  + G+   +   L  G+  +I
Sbjct: 180 ETGTINFPIGRHPSDRKKMAV-VPLEKGGRSAITHWQIKERLGNYTLIHFQLETGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         + 
Sbjct: 239 RVHTAHIGHPII 250


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 64/339 (18%), Positives = 105/339 (30%), Gaps = 75/339 (22%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           P R+ K ++R     A + SR  + R+IA+  V VNG  +      +   D I +     
Sbjct: 15  PPRLDKALSRDVPEDAAL-SRTRLARLIAEGAVSVNGTPVTDPKSRISEGDSIAITVPQA 73

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------- 104
                  + +PL    E   L +  KP G+V   +      T+ + L             
Sbjct: 74  QDTHIAAESIPLDIVFEDDDLIVIDKPAGMVVHPAPGSPGGTLVNALLHHCGDTLSGVGG 133

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK----- 157
             R   V R+D +T GLL++         L          R YR   +G  D        
Sbjct: 134 MKRPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFEDHSVERYYRAVVYGVPDAADPRLRG 193

Query: 158 ----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----------LRE-- 195
                     +  +  G+           VT +  + +     V           L E  
Sbjct: 194 LRGVSFETGNIIKITSGLARHRTDRQKQAVTFEGGRHAVTRARVVDTFGQPPVAALMECW 253

Query: 196 ---GKNREIK-KVFEF----FNWKVNRLIRISYGPFQLGTL-LAG--STREVSKKILREQ 244
              G+  +I+  +           V    R       L  L  AG  + R+  ++ L   
Sbjct: 254 LETGRTHQIRVHMAHAGHGLVGDPVYGGRR----KLPLRALSEAGLKAARDFPRQALHAA 309

Query: 245 -LG-PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
            LG  H +    +  +AP+    T + D         D 
Sbjct: 310 VLGFVHPVSGEALEFEAPLPDDMTALIDALRATPSRTDA 348


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 88/252 (34%), Gaps = 46/252 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V       R+ K ++      SR ++++ I   +V VN +++    V V   D I  
Sbjct: 3   KYSVPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+ A          E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+V   G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRKYKVLVWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREI 201
                      D+ K+ +LK G    G        TL+   KGS + V   L  G+  +I
Sbjct: 183 VIKNNIGRSRSDRQKMTILKYG----GKEAVTHYKTLELFYKGSISMVECKLSTGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 239 RVQLSHLKHSVV 250


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 86/240 (35%), Gaps = 43/240 (17%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        ASR +V++      + VNG+ ++     V + D ++V      
Sbjct: 30  EPLRVDKFLMN--FVENASRNKVQQAAKDGNIFVNGVAVKS-NHRVKANDEVKVMFAHPP 86

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                  + +PL    E   L + +KP GLV      + + T+ + L   F ++      
Sbjct: 87  HEYLLVPELIPLNIVYEDEELIIINKPAGLVVHPGHGNYQGTLINGLIYHFEQLPKNSSD 146

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++         L     +    R Y     G + +D+       
Sbjct: 147 RPGLVHRIDKDTSGLLVVAKTEEAMNHLAKQFFNKTSEREYIALVWGNIPEDEGTITGHI 206

Query: 158 ----LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                N L+  +   G    +      +  + G    V+  L  G+  +I+  F +    
Sbjct: 207 GRHPKNRLQMTVFPDGSEGKEAITHYKVLERFGYVTLVSCRLETGRTHQIRAHFTYIGHP 266


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 79/246 (32%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
              +     R+ + +A      SR  ++ +I    V VNG   +     V   D I V  
Sbjct: 4   TTDDADGKIRLDQYLAAHLPELSRSRIQSLIKSGDVLVNGSPAK-PKNPVSRGDSITVRI 62

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                       +PL    E   + + +K  G+V   +  +   T+ + L      +  +
Sbjct: 63  PEPEPAEAQPQDIPLDILYEDEDVVVINKESGMVVHPAAGNPDGTIVNALLHHCGDLSGI 122

Query: 112 G---------RLDINTEGLLLLT-NDGGLARVLEL-PSTQWLRVYRVRFHGQVDQDK--- 157
           G         RLD +T G L++  NDG    +     +    + Y     G   Q     
Sbjct: 123 GGVERPGIVHRLDKDTSGCLVIAKNDGAHQSLTAQFAARSTEKRYLAVVQGIPSQSSGTV 182

Query: 158 --------LNLLKKGIVIQGICYG---DMQVTLDTQKGSNAWVTVGLREGKNREIK-KVF 205
                   +N LK  +V  G       D  +        ++ V   L  G+  +I+  + 
Sbjct: 183 FTHIGRHPVNRLKMAVVNPGSGKAAITDYDLLCADPSTDSSLVLCTLHTGRTHQIRVHML 242

Query: 206 EFFNWK 211
            +    
Sbjct: 243 -YLGHP 247


>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 = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 87/229 (37%), Gaps = 34/229 (14%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRK 69
           R+ + +A      SR  ++  I    VK++G ++ R    V +   + V    +   + K
Sbjct: 19  RLDQAVASLFPDYSRTRIKEWILADMVKIDGEVINRPREKVYTGQTVGVQAVLEDEVVFK 78

Query: 70  AERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRL 114
           A++ +         + + +KP GLV      +   TV + L   F ++I       V RL
Sbjct: 79  AQKIKLEIVYEDDDILVINKPAGLVVHPGAGNPDGTVLNALLHHFPQIIEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLK 162
           D +T GL+++         L   L + +  R Y                 + +DK++ +K
Sbjct: 139 DKDTTGLMVVAKTVPAQTHLVTSLQAREITREYEAIAMGGFTAGGFVEAPIGRDKVHRVK 198

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNW 210
             +   G  +      +  +  ++  + + L  G+  +I+  +      
Sbjct: 199 MAVNSTGGKHALTHYRVSEKYRAHTRLRLRLETGRTHQIRVHMM-HIGH 246


>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 = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 93/245 (37%), Gaps = 38/245 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  +  +N    R+ KV +      SR ++++++    + VNG   E+A   V S D 
Sbjct: 1   MKETVVEMQNG---RLDKVCSEIFSDYSRSQIKQLLDGGNITVNGKT-EKAKYKVKSGDV 56

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +            + +PL    E   + + +KP G+V   +      T+ + L     
Sbjct: 57  IRLEEPETKTLELRPENIPLDIVYEDDDVIVINKPQGMVVHPAPGHDEHTLVNALLYHCP 116

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    R L   L     +R Y    HG++ +D
Sbjct: 117 LSTINGTFRPGIVHRIDKDTSGLLMVAKNDKAHRSLAKQLKDKTNIREYVALVHGRIAED 176

Query: 157 K----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           +          L   KK  V++          +  +     +V   L  G+  +I+   +
Sbjct: 177 EGTINAPIGRSLKDRKKQAVVKDGRNAVTHFEVLKKYRDYTFVKCILETGRTHQIRVHMK 236

Query: 207 FFNWK 211
           +    
Sbjct: 237 YIGHP 241


>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 = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 38/231 (16%), Positives = 75/231 (32%), Gaps = 35/231 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+V+G ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVQVDGEVVTKPRTKVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDEDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHG 151
                  V RLD +T GL+++         L   L      R Y                
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQ 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPMGKPAVTHYRVAERFRE-HTRIRLRLETGRTHQIR 237


>gi|312171425|emb|CBX79684.1| ribosomal large subunit pseudouridine synthase D [Erwinia amylovora
           ATCC BAA-2158]
          Length = 325

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 83/234 (35%), Gaps = 33/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K    V E+   QR+ + +A      SR  ++  I  +R+ VNG  +++    V+  + 
Sbjct: 5   VKLNATVAESQLGQRLDQALAELFPDYSRSRIKEWILNRRITVNGTTIDKPKEKVLGGEQ 64

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +D             +PL    E   + + +KP  LV      +   TV + L   F 
Sbjct: 65  ISIDAEIEEEARWEAQDIPLAIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHFP 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------R 148
                 R   V RLD +T GL+++         L   L   +  R Y             
Sbjct: 125 AIADVPRAGIVHRLDKDTTGLMVVAKTVPSQTHLVDALQRREITREYEAVAIGRMTAGGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  + +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 185 VNEPISRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/230 (19%), Positives = 72/230 (31%), Gaps = 41/230 (17%)

Query: 11  FTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-------- 61
               R+ K IA      SR +++  I   RV VNG  ++ A   +   D I         
Sbjct: 43  DAKIRIDKYIAEEMKEVSRSQIQMWIGNGRVLVNGTAIK-ANYKLAEGDRIVLSVPEPES 101

Query: 62  VDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
           VD VP               + +K  GLV   +      T+ + L      +        
Sbjct: 102 VDIVPENIPLDVVYEDSDVIVINKQRGLVVHPAPGHSSGTLVNALMYHCHDLSGINGELR 161

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD--------- 156
              V R+D +T GLL+   +      L   L      R Y    HG +  D         
Sbjct: 162 PGIVHRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIALVHGHLSHDQGTVDAPIG 221

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  L    +  +   +      +  + G    + + L  G+  +I+
Sbjct: 222 RDSGDRKLFT--VTERNSKHAVTHFLVIERLGDYTLLELQLETGRTHQIR 269


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 39/171 (22%), Positives = 65/171 (38%), Gaps = 22/171 (12%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
            R   V RLD +T GL+++         L   L   +  R Y     G + 
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMT 180


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 85/243 (34%), Gaps = 57/243 (23%)

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----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V   +  PL             E   + + +KP G+V   +      T+ + L +    +
Sbjct: 63  VQVPEPEPLDVTAEPMDLDIYYEDQDVLVVNKPRGMVVHPAPGHLTGTLVNGLMAHCDDL 122

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
                      V R+D +T GLL++  +      L     +    R Y    HG +  D 
Sbjct: 123 SGINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVNKTVTRKYTALVHGVIPHD- 181

Query: 158 LNLLKKGIVIQ---GICYGDMQ---VTLDTQKGSNAWVTV-------GLRE-----GKNR 199
                 G  I    G    D Q   VT +  K +     V        + E     G+  
Sbjct: 182 -----HG-TIDAPIGRDKKDRQSMTVTRENGKHAVTHFEVIERFDDFTVVECQLETGRTH 235

Query: 200 EIK 202
           +I+
Sbjct: 236 QIR 238


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 55/294 (18%), Positives = 101/294 (34%), Gaps = 48/294 (16%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V E +  +R+ + ++      SR   +++I    V  +G  +++ +  V     I +  
Sbjct: 11  MVDEEYDRKRLDQFLSSVYPEYSRSYFQKLIKDGYVFEDGKDIKKPSYKVRKGQEITLVI 70

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                     + +P+    E   + + +KP G+V   S      T+ + L   F  +   
Sbjct: 71  PPPETLEIKPENIPVDILFEDEDIAVVYKPAGMVVHPSPGHTSGTLVNALLYHFRNISEY 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDK-L 158
                   V RLD +T GL+++      A        Q     + Y     G V  D   
Sbjct: 131 GGKERAGIVHRLDKDTAGLMIIAKS-EFAHKELQKQFQERTVDKRYIAVVTGIVQNDHGF 189

Query: 159 NLLKKGIVI--------QGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
             L  G  I        +     D      V   ++K +   V + L  G+  +I+  F 
Sbjct: 190 IDLPIGRSIYNRKKMGTEATNLRDALTEYWVKNRSEKENLTVVDIKLHTGRTHQIRVHFS 249

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAP 260
                +       YG F+   L +   R +S + L      H L   ++  D P
Sbjct: 250 AIGHPLFNDK--VYG-FKKSQLRSEKMRSISDQTL-----YHALLAYRIAFDHP 295


>gi|159029548|emb|CAO87700.1| rluD [Microcystis aeruginosa PCC 7806]
          Length = 308

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/227 (16%), Positives = 79/227 (34%), Gaps = 38/227 (16%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR- 68
           +R+   + ++    SR  ++++I Q  +++NG +       V   D +++   D  PL+ 
Sbjct: 13  ERLDAWMGSQLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITIPDSQPLQL 72

Query: 69  ---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
                      E   L + +KP  LV   +      T+ + L      +  +G       
Sbjct: 73  SAEAIDLDILYEDEYLIIINKPADLVVHPAPGHESGTLVNALLHHCPNLAGIGGIQRPGI 132

Query: 113 --RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
             RLD +T G +++  T+        +L +    R Y    HG    +            
Sbjct: 133 VHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYMALVHGVPKSETGTIDLPISRHR 192

Query: 157 -KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +    V +G         +  + G+   +   L  G+  +I+
Sbjct: 193 SDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIR 239


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/171 (21%), Positives = 64/171 (37%), Gaps = 22/171 (12%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDSRVTVNGKKINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E   + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
                V RLD +T GL+++         L   L + +  R Y     G + 
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMT 180


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNLDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 88/253 (34%), Gaps = 45/253 (17%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +++V E +   +R+ + +A   +   SR +V+ +I +  V V G   ++    +   
Sbjct: 1   METRDVVIEGSHEGERLDRFLAE-TLCDVSRSQVKNLIDEGLVLVGGRP-QKPGYRIRKG 58

Query: 58  DHIEV------------DGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I+V              +PL      R L +  KP GLV   +      T+ + L   
Sbjct: 59  DIIQVRIPAARETGLVAQEMPLNIVYEDRDLVVIDKPQGLVVHPAHGHWEGTLVNALLYR 118

Query: 105 FSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRFHGQV 153
              +           V RLD +T GL+++  +    R L       +  R Y    HG +
Sbjct: 119 VKDLSGINGELRPGIVHRLDKDTSGLMVVAKNDQAHRDLADQIKARKIRREYVAVVHGVI 178

Query: 154 -------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
                               +   +V +G        T+  +      V   L  G+  +
Sbjct: 179 RENSGTIDAPIGRSPSDRKKMA--VVREGRPAVTH-YTVLRRYRDYTLVRARLETGRTHQ 235

Query: 201 IKKVFEFFNWKVN 213
           I+  F +    V 
Sbjct: 236 IRVHFAYIRHPVV 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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 87/246 (35%), 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  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             + +PL    E + + + +KP G+V   +      T+ + +      
Sbjct: 59  QFEIPQAEVLDVVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKD 118

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
           + S         V R+D +T GLL++  +      L   L      R Y    HG++  D
Sbjct: 119 LSSINGVIRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGELAND 178

Query: 157 K----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           K          L   KK  V+ G         +         + + L  G+  +I+    
Sbjct: 179 KGTIEAPIGRNLKDRKKQAVVSGGKPAVTHFEVLEGFVGYTLIALRLETGRTHQIRVHMH 238

Query: 207 FFNWKV 212
           +    V
Sbjct: 239 YIGHPV 244


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 81/234 (34%), Gaps = 41/234 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K I+     SR  V+ ++    + VN    E+ +  V   D I V            
Sbjct: 14  RLDKYISEHSDLSRSRVQELLTSGDILVNSKQ-EKPSYKVAIGDKISVHVPKLVPLNVEP 72

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    E   + + +KP G+V   S      T+ + L +    + +         V 
Sbjct: 73  EDIPLDIVYEDNDVIVVNKPQGMVVHPSAGHPNHTLVNALMNHTKELAASPEGFRPGIVH 132

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQD-------------K 157
           R+D +T GLL++  +      LE         RVY    HG   +              +
Sbjct: 133 RIDKDTSGLLMIAKNTQARESLESQLAHKTNKRVYLAIVHGNFKEASGTIDAPIARNPKE 192

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +    V++          +  Q  + A V+  L  G+  +I+   ++    
Sbjct: 193 RKKMA---VVESGKAAVTHFKVLEQYPNYALVSCQLETGRTHQIRVHMKYIGHP 243


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 88/252 (34%), Gaps = 46/252 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V       R+ K ++      SR ++++ I   +V VN +++    V V   D I  
Sbjct: 3   KYSVPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+ A          E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+V   G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQKQVIRKYKVLVWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREI 201
                      D+ K+ +LK G    G        T++   KGS + V   L  G+  +I
Sbjct: 183 VIKNNIGRSRSDRQKMTILKYG----GKEAVTHYKTIELFYKGSISMVECKLSTGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 239 RVQLSHLKHSVV 250


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 78/244 (31%), Gaps = 48/244 (19%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D          
Sbjct: 11  RLDRVLATRCPALSRSRLKVLILDGRVAIAGSAVRDPAYHASPGETITIDVPPPVAPEPE 70

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
           G  +      E   + + +KP GLV   +      T+ + L +             R   
Sbjct: 71  GEAIALEIVHEDDDIIVINKPRGLVVHPAAGHETGTLVNALIAHCGESLSGIGGVRRPGI 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQDKLNLLKKG 164
           V RLD +T GL++   +    + L        R       Y     G  ++ +   ++  
Sbjct: 131 VHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRTGELRRGYYAFVWGVPNRAR-GTIEAP 189

Query: 165 IVIQGICYGDMQVTLDTQKGSNAW--------------VTVGLRE---GKNREIKKVFEF 207
           I         M V    ++    W              V++   +   G+  +I+     
Sbjct: 190 IDRHPYAREKMAVRDGGREAITHWEVLETFTGRSGGEIVSLIACQLETGRTHQIRVHLAH 249

Query: 208 FNWK 211
               
Sbjct: 250 LGHP 253


>gi|306520956|ref|ZP_07407303.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 453

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 83/225 (36%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN   +E+A   V   D+I ++          
Sbjct: 167 RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNK-VEKAKYLVKEEDNIVIEIPEPKVLEVL 225

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
              +P+    E   + + +KP  +V   +  +  +T+ + +               R   
Sbjct: 226 PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 285

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL---------- 158
           V R+D +T GLL++  +      L     +    R Y    +G V +DK+          
Sbjct: 286 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 345

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  +V  G         ++            L  G+  +I+
Sbjct: 346 KDRLKMAVVKDGKNAITHFEVVERFDKFTHM-RARLETGRTHQIR 389


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 89/250 (35%), Gaps = 37/250 (14%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGI---------LLE 48
           M ++   I+ +N   QR+ K +A      SR  ++++I    V VN           + +
Sbjct: 1   MSEEREYIIDDNDVDQRLDKFLAYQNEELSRSYIQKLIDNGEVTVNKEEKKNSYRLQVGD 60

Query: 49  RAAVNVMSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVF------- 98
              + +   + +E+    +     AE   + + +K   LV   +    + T+        
Sbjct: 61  EVKLIIPQPEEVEIKPESIPLEVIAEDEDIVVINKQADLVVHPAPGHKQGTLVNALLYHC 120

Query: 99  DNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           DNL  I   +    V RLD +T G ++   +    R L       +  ++Y     G + 
Sbjct: 121 DNLSGINGEIRPGIVHRLDKDTSGAIVAAKNDQAHRNLVKQFKERRTEKIYLALVEGNIK 180

Query: 155 QDKLN-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
            +K               +  +  +       +  +  + G+  WV + L  G+  +I+ 
Sbjct: 181 HNKAKIDAAIGRDPYNRKRMAVTKRNSKQAVTRFEVLERFGNYTWVKLKLETGRTHQIRV 240

Query: 204 VFEFFNWKVN 213
              + +  V 
Sbjct: 241 HMSYIDNPVV 250


>gi|298530973|ref|ZP_07018374.1| pseudouridine synthase, RluA family [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298508996|gb|EFI32901.1| pseudouridine synthase, RluA family [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 535

 Score = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 86/256 (33%), Gaps = 42/256 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            VQE+    R+ + +    I     SR  V+  I +  + ++G +  + A  + +   ++
Sbjct: 8   TVQESQAGSRLDR-LVMQNIPRPAPSRSRVQDWIRKGNILLDGTVCLKPAHKLSAGQTVQ 66

Query: 62  V-------DGVPLRKAERTRLW-----LYHKPIGLVTTHSDPDGRSTVFDN--------- 100
           V       D  P+              + +KP GL    S  D   T+            
Sbjct: 67  VLAREENEDLEPVAGKLDIVYMDREMVVLNKPAGLSVHPSSSDPAPTLVHYLLYACPGLR 126

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL 158
           L +   R   V RLD +T GL++   +      L       +  + Y     G + QD+ 
Sbjct: 127 LMTDRQRPGIVHRLDKDTTGLMVAALNQEAKEDLAGQFAGRRVHKTYLALVCGALKQDEG 186

Query: 159 ---------NLLKKGIVI--QGICYGDM-QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                       +  +    +G       +V      G  + V V +  G+  +I+  F 
Sbjct: 187 IINVPLARDQQSRARVAPSREGRSARTAYKVLKRDPSGLWSLVQVQIFTGRTHQIRVHFS 246

Query: 207 FFNWKVNRLIRISYGP 222
             N  V    RI YG 
Sbjct: 247 HLNHPVLG-DRI-YGG 260


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y              +  +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/250 (14%), Positives = 84/250 (33%), Gaps = 39/250 (15%)

Query: 2   KDKNIVQENFTPQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            ++NIV      + R+ K ++     +R  ++++I  + + VN     + A  +   D I
Sbjct: 22  NEENIVVLKEEAESRIDKFLSERLELTRTRIQQLIKDENILVN-EKKTKPAYKIEENDTI 80

Query: 61  EV-----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +V     + V ++          E   L + +K  G+V   ++     T+ + +      
Sbjct: 81  KVVIPELETVEIKPENIDIEIIYEDNDLAVINKKAGIVVHPANGHYSGTLVNAILYYIKD 140

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ- 155
           +           V RLD +T GLL++  +      L          + Y     G++ Q 
Sbjct: 141 LSGINGEIRPGIVHRLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKKTYLAILKGKLSQK 200

Query: 156 ------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                       +    +     +           + +Q      V V +  G+  +I+ 
Sbjct: 201 SGRIVTQIGRDKNDRKKMTVTNDLNSGKTAITNYEVISQTEKFTLVKVHIETGRTHQIRV 260

Query: 204 VFEFFNWKVN 213
             +   + + 
Sbjct: 261 HMKHLGYPIL 270


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 62/303 (20%), Positives = 106/303 (34%), Gaps = 67/303 (22%)

Query: 1   MKDK-NIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MKDK  ++      QR+ K +A   I    SR  +E +I + R+ VN   +++ +  +  
Sbjct: 8   MKDKLKVIYTLQEMQRLDKFLAELKIQELYSRTFIEHLIEEDRILVNLTPVKK-SYLLKE 66

Query: 57  TDHIEVD------------GVPLRKA-ERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNL 101
            D + ++             +PL    E   L + +K  G++      +P+G        
Sbjct: 67  GDEVIINLPEPEPMNVLPQDIPLDVVYEDEYLAIINKKAGMIVHPGFGNPEGTLVNAILY 126

Query: 102 P--------SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
                      F+R   V RLD  T GL+++  +      L       +  + Y     G
Sbjct: 127 RFGENLSSGKEFNRPGIVHRLDRGTSGLIIIAKNDLTHAKLSDMFARREIKKTYFAITTG 186

Query: 152 QVDQDKLNL---LKKGIVIQGICYGDMQVTLDTQ------KGSNAWVTVGLRE-----GK 197
             + +K  +   L +           + VT + +      K    W    L E     G+
Sbjct: 187 IPEPEKGEIETYLAR----SNKNPRTICVTNEGRYALTHYKTIKTWHYFALVEINPATGR 242

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS-------KKILREQLGPHLL 250
             +I+  F    + +            LG LL  S R V        KK + E L  HL 
Sbjct: 243 MHQIRVHFAHIRYPI------------LGDLLYNSRRYVQSLVPQNMKKKVTELLVNHLR 290

Query: 251 EEA 253
            +A
Sbjct: 291 RQA 293


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/227 (16%), Positives = 77/227 (33%), Gaps = 38/227 (16%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
           +R+   + +     SR  ++++I Q  +++NG +       V   D +++   D  PL  
Sbjct: 13  ERLDAWMGSHLPDLSRSRLQKLIEQGYIQLNGQICTNKNTKVGQGDRLKITIPDSQPLEL 72

Query: 70  A----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
                      E   L + +KP  LV   +      T+ + L      +  +G       
Sbjct: 73  TAEAIELDILYEDDYLIIINKPADLVVHPAPGHESGTLVNALLHHCPNLAGIGGIQRPGI 132

Query: 113 --RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------------ 156
             RLD +T G +++  T+        +L +    R Y    HG    +            
Sbjct: 133 VHRLDKDTTGAIVIAKTDQAHQHLQAQLKTKTARREYIALVHGVPKSETGTIDLPIGRHR 192

Query: 157 -KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +    V +G         +  + G+   +   L  G+  +I+
Sbjct: 193 SDRQKMAIIAVEKGGRNAVTHWQVKERLGNYTLMEFRLETGRTHQIR 239


>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 = 78.3 bits (192), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 78/248 (31%), Gaps = 51/248 (20%)

Query: 9   ENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
                QR+   +A  G+     SR +V+R++    V V+G   + AA  +     I V  
Sbjct: 10  PEAAAQRLD--VALLGLLGDDFSRAQVQRLLRDGLVLVDGQAAK-AAQKLRPGQAIAVRL 66

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
            D  P              E   L + +KP GLV   S      T+   L      +  V
Sbjct: 67  PDPEPSELIPMAMDLAILHEDEDLIIINKPPGLVVHPSPGHAEGTLVHGLLHHCGGLAEV 126

Query: 112 G---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD------ 154
           G         RLD +T G L+   +    R L     + +  + Y    HG+        
Sbjct: 127 GGKLRPGIVHRLDKDTSGALVAAKNDRAHRGLVARFAAGRVQKEYLALVHGRPAKRGRVD 186

Query: 155 ------QDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIK-KVF 205
                       +      QG             +  G  + + V +  G+  +I+  + 
Sbjct: 187 SGIGRHPGDRKRMSS----QGSRTKPALSQWRVCRSFGEASLLRVNIHTGRTHQIRVHLS 242

Query: 206 EFFNWKVN 213
           E     V 
Sbjct: 243 EA-GHPVL 249


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 85/244 (34%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            + E+   QR+ + +A      SR  ++  I   RV+VNG ++ +A   V+  + I +D 
Sbjct: 10  TIAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKVINKAKEKVLGGEQISIDA 69

Query: 64  -----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                       +PL    E   + + +KP  LV      +   T+ + L   +  +   
Sbjct: 70  LIEEDTRWEPQDIPLDVVYEDEDILIINKPRDLVVHPGAGNPDGTILNALLYRYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVAVGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIKKVFEF 207
           G+V + I     + T                      ++  + + L  G+  +I+     
Sbjct: 183 GMVEEPISRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            N  
Sbjct: 243 INHP 246


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 71/241 (29%), Gaps = 52/241 (21%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
              +R+   +       SR    +++    V VNG         V   D I V+      
Sbjct: 13  DAGERLDSYLGAQSACPSRSACAKLVEAGSVAVNGETCLSKKQAVAEGDRICVELPEIRE 72

Query: 64  -GVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
            G  + +A       E   L +  K  GLV   +      T+ + L              
Sbjct: 73  PGAIVPQAIPLDIRYEDDYLIVLSKQRGLVCHPAHGHEDGTLANALVHHCGIEHLGTVQG 132

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNL 160
             R   V RLD +T GL+L   D    R L   + +    R Y    HG++  D+  +N 
Sbjct: 133 EDRPGIVHRLDRDTSGLMLAAKDDETQRELQNLIRTRTLDRRYITLVHGEIVMDEGTINT 192

Query: 161 LKKGI-----------VIQGICYGDM--------QVTLDTQKGSNAWVTVGLREGKNREI 201
              GI           V                 +            V   L  G+  +I
Sbjct: 193 ---GIARSTRDRVKMAVSDDPFARQAITTFQVLERFEPARGDEGYTLVECHLYTGRTHQI 249

Query: 202 K 202
           +
Sbjct: 250 R 250


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 85/244 (34%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV VNGI++ +    V+  +HI +D 
Sbjct: 10  TVTESQLGQRLDQALAELFPDYSRSRIKEWILEDRVSVNGIIINKPKEKVLGGEHIAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                       + L    E   + + +KP  LV      +   TV + L   + ++   
Sbjct: 70  LIEEENRWEAQDIALDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPQIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G +          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGTMT-------AG 182

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G V + I     + T                +     ++  + + L  G+  +I+     
Sbjct: 183 GTVREPIARHPTKRTHMSVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            N  
Sbjct: 243 INHP 246


>gi|293365515|ref|ZP_06612224.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|307703473|ref|ZP_07640415.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|291315883|gb|EFE56327.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|307622880|gb|EFO01875.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 298

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 72/210 (34%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
               + VNG   + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNGQ-AQNATYLLDIGDRVTIDIPAEEGFESLEAINRPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + + +       V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDVDSIITRRVAKGGKYAHTSYKVVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|218506712|ref|ZP_03504590.1| RNA-pseudouridine synthase protein, ribosomal large subunit B
           [Rhizobium etli Brasil 5]
          Length = 102

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 28/93 (30%), Positives = 49/93 (52%), Gaps = 4/93 (4%)

Query: 2   KDKNIVQENFTPQR--VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TD 58
           +++  +  +   +R  + + +++ G  SR + ER+IA+ RV ++G  +   +  V   T 
Sbjct: 11  RERPKLTADAAGKRVTLPRALSKLGYCSRTQAERLIAESRVSIDGRTVNDPSAWVDLVTA 70

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDP 91
            I VDG  +  AE     + +KP GLVTT  DP
Sbjct: 71  KIRVDGHVI-AAEAKIYLILNKPRGLVTTRHDP 102


>gi|24212923|ref|NP_710404.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|45656097|ref|YP_000183.1| hypothetical protein LIC10192 [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24193592|gb|AAN47422.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|45599330|gb|AAS68820.1| conserved hypothetical protein [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 312

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 90/244 (36%), Gaps = 42/244 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAG-IASRREVERMIAQQRVKV-NGILLERAAVNV--- 54
           ++ K  V E F+  R+ + +    G   SR  +++ I    V+  +G +L++++  V   
Sbjct: 3   LELKADVSEEFSGNRLDRFLKYSLGDEISRATIQKWIEAGYVQGQDGKILDKSSWKVKTG 62

Query: 55  -------MSTDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
                       + ++ +P+      ER    + HKP G+ +     D   ++ + L   
Sbjct: 63  EKYLLSIPPKPPLNLEPIPMELPVILERENFLIIHKPSGIASHSGPGDRSPSLVNGLIYH 122

Query: 105 FS---------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           F          R   V RLD  TEGL+L+  +      L       +  + Y     G  
Sbjct: 123 FKELSKMGGEARPGIVHRLDKPTEGLILIAKNDRAHGKLSELFRKREIEKKYYAWVQGHP 182

Query: 154 DQDK-----------LNLLKKGIVIQGIC----YGDMQVTLDTQKGSNAWVTVGLREGKN 198
            ++            +  LK  +  +G      Y  ++          +++ VGL  G+ 
Sbjct: 183 PEESGTIDLPIARHPVERLKMTVSPKGRRSITHYKVLKYINSRSGRKFSFIEVGLETGRT 242

Query: 199 REIK 202
            +I+
Sbjct: 243 HQIR 246


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 77/238 (32%), Gaps = 42/238 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD- 156
                      V R+D++T GLL++  +    R L  +L      R Y    HG +  D 
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKNDIAHRELVEQLMDKSVKRKYIALVHGNIPHDY 183

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                           +    V+           +         V   L  G+  +I+
Sbjct: 184 GTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 72/184 (39%), Gaps = 31/184 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + I  E+   QR+ + +A+      SR  ++ +I +  +K++G L+      + S   IE
Sbjct: 3   QQITDEDALGQRIDQWLAKHYQNELSRSRLQTLIREGYLKIDGKLVTEPKTKIKSNQTIE 62

Query: 62  V----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
           +          +G  +      E   + + +KP GLV      +   T+ + L       
Sbjct: 63  LTIPTLNNAYPEGEAIPLHILFEDDHIIVVNKPAGLVVHPGHGNWTGTLVNALIYHCGDS 122

Query: 106 -------SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQW-LRVYRVRFHGQ 152
                   R   V RLD NT G++++  ND    G  A+  +   T    R Y     G 
Sbjct: 123 LSGIGGVRRPGIVHRLDKNTSGVIVVAKNDLAHKGLSAQFSDHGRTGVLDRRYHALIWGS 182

Query: 153 VDQD 156
            +++
Sbjct: 183 PNRN 186


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV +NG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLINGKVCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/171 (23%), Positives = 64/171 (37%), Gaps = 22/171 (12%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
            R   V RLD +T GL+++         L   L   +  R Y     G + 
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMT 180


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 90/251 (35%), Gaps = 43/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  N++ EN    R+ K+IA      SR +++ MI +  V VNG  +E+A+      D 
Sbjct: 1   MEKINLLVENNNNYRLDKIIALNMEELSRTQIQEMIGRGLVLVNGK-VEKASYKTKLNDQ 59

Query: 60  IEV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE+            + +PL    E   + +  KP G++   S      T+ + L     
Sbjct: 60  IEITIEDNSDLEIEAEDIPLNVVYEDKDVIVIDKPTGMIVHPSPGITSGTLVNALLFHCK 119

Query: 102 ----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVD 154
                +  +R   V R+D  T GLL++  +  +A              R Y    HG + 
Sbjct: 120 DLSGINGVNRPGIVHRIDKETSGLLMVAKN-DIAHRFLSEQLKDHSVTRRYVALVHGLIP 178

Query: 155 -------------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                         +    +   +            T+  +  + + +   L  G+  +I
Sbjct: 179 HVQGKIDAPIGRNPNDRQSMC--VTKNNSKNAITNFTVLKRYKNMSLIECRLETGRTHQI 236

Query: 202 KKVFEFFNWKV 212
           +    +  + V
Sbjct: 237 RVHMSYIGYPV 247


>gi|291546177|emb|CBL19285.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           SR1/5]
          Length = 304

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 86/246 (34%), Gaps = 44/246 (17%)

Query: 6   IVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            V++  +  R+ + +A   +G+ SR  +++++ + ++ V G    ++   V   D I ++
Sbjct: 7   TVEKEESGIRIDRYLAEKDSGL-SRSFLQKLLKEGQITV-GEKAAKSNYKVRENDRIHLE 64

Query: 64  ------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                        +PL    E   + + +KP G+V   +    + T+ + + +       
Sbjct: 65  IPDSSEPDIVPEDIPLDILYEDEDVLIVNKPKGMVVHPAAGHYQGTLVNAVMAHCGDSLS 124

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD-- 156
                 R   V R+D +T G LL+  +    R L   L      R YR    G + +D  
Sbjct: 125 GINGVMRPGIVHRIDKDTTGALLVCKNDIAHRDLAEQLKCHSIRRRYRAVVQGNLKEDEG 184

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +   I  +          +  + G   +V   L  G+  +I+   
Sbjct: 185 TIEGPIGRHPTDRKKMA--INHKNGKDAITHYKVLERFGEATYVECRLETGRTHQIRVHM 242

Query: 206 EFFNWK 211
                 
Sbjct: 243 ASIGHP 248


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 65/174 (37%), Gaps = 25/174 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEIIL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP G V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDDDILVINKPRGFVVHPGAGTPDGTVLNALLHHYPNIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVD 154
                  V RLD +T GL+++         L         ++R Y     G++ 
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIGRMT 181


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y              +  +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 91/249 (36%), Gaps = 56/249 (22%)

Query: 13  PQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           P R+ K + +  +  A+R +V+  I ++RV VNG  ++     + S D I +        
Sbjct: 37  PMRIDKYLTQQ-VENATRNKVQEAIEEERVLVNGRPVKS-NYRIKSCDTILITFLRPPAP 94

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDNLPSIFS 106
               + +P+    E + L + +K  G+V   +  +   T+            ++L +   
Sbjct: 95  ELAPEDIPIDIVYEDSDLMVVNKEPGMVVHPAFGNWTGTLANAILHHIGRDAESLDASEL 154

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           R   V RLD +T GL+++  +      L       Q  ++Y+    G  D       + G
Sbjct: 155 RPGIVHRLDKDTSGLIIIAKNPTALHRLARQFAMRQVQKIYKAIVWGVPDP------RSG 208

Query: 165 IVIQGICYGDMQVTL------DTQKGSN--------------AWVTVGLREGKNREIKKV 204
            ++  I        +      +   G +              + V++ L  G+  +I+  
Sbjct: 209 TILTNIGRSKKNRKIMANYPYEGLDGKHAITDYLVEENLHWFSVVSLTLHTGRTHQIRAH 268

Query: 205 FEFFNWKVN 213
            +     + 
Sbjct: 269 MQHTGNPIL 277


>gi|291542663|emb|CBL15773.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           bromii L2-63]
          Length = 306

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 84/252 (33%), Gaps = 43/252 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +  +  E  +  R+ K I+ A I  SR     +I    V VN  ++ +    +   D 
Sbjct: 1   MNEFKLNCET-SGVRLDKFISDANIDLSRSAAVNLIENGAVLVNDSVVSK-KYKLSQGDI 58

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + V+             +PL    E   L + +KP G+V   +  +   T+ + L     
Sbjct: 59  VVVNVPDPTPYEAKAENIPLDIVYEDECLLVVNKPKGMVVHPAAGNYDGTLVNALLYHCG 118

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQV- 153
                     R   V R+D +T GLL++  +    R L     +    R Y     G + 
Sbjct: 119 DSLSGINGVLRPGIVHRIDKDTSGLLIVAKNDFSHRSLAEQIKEHSFTREYESIVFGNLK 178

Query: 154 ------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                       +      +   ++ +         ++ T+      +   L  G+  +I
Sbjct: 179 NDEGTVDAPIGRNPKDRKKMC--VIEKNSKNAVTHYSVITRYKGYTHIKCKLETGRTHQI 236

Query: 202 KKVFEFFNWKVN 213
           +    +    V+
Sbjct: 237 RVHMAYIGHPVS 248


>gi|225620833|ref|YP_002722091.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
 gi|225215653|gb|ACN84387.1| Pseudouridylate synthase [Brachyspira hyodysenteriae WA1]
          Length = 329

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 88/243 (36%), Gaps = 48/243 (19%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K   I+ E+   +R+   I+     +R +V+  +    + VN    ++ + ++   D+I 
Sbjct: 30  KKSFIITEDDIGKRLDTFISEKLNITRSQVKNYLTS--IIVNDA-EKKLSYSLKLNDNII 86

Query: 62  VDGVPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVF----- 98
           +D   + K                   E   L + +KP G+    S  +   T+      
Sbjct: 87  IDSDNIFKEKTDTANPIPENIDLDILYEDKYLLVINKPAGMSVHCSPSEMSGTLVNALLY 146

Query: 99  ----DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-----WLRVYRVRF 149
                +      R   + RLD +T GL+++   G  A ++     Q       ++Y    
Sbjct: 147 KIKDFDFVGNKERAGIIHRLDKDTSGLMII---GKNANIVSSIQEQFKNRTIKKIYHAIV 203

Query: 150 HGQVDQDKLNL---------LKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
            G +  + + +          +K + + +        + +  +  S+  + + L+ G+  
Sbjct: 204 VGVLKDNYIEINLPIGRHHVYRKKMTVREDGKEALTHIKVLKRFNSHTLIEINLKTGRTH 263

Query: 200 EIK 202
           +I+
Sbjct: 264 QIR 266


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 47/264 (17%), Positives = 93/264 (35%), Gaps = 54/264 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + I  E    QR+ + +A+    + SR  ++ +I +  +K++G  ++     +    
Sbjct: 1   MVIQKITDEGALGQRLDQWLAKQYHNVFSRSRLQTLIREGYLKIDGQFIKEPKTKLRPKQ 60

Query: 59  HIEV------DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            IE+      D  P  +A       E   + + +KP GLV    + +   T+ + L    
Sbjct: 61  IIELAMPDLRDAEPSAEAIALDILFEDDHIIVINKPAGLVVHPGNGNWTGTLVNALIYHC 120

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRF 149
                      R   V RLD NT G++++  +    + L    +   R       Y    
Sbjct: 121 GNSLSGIGGVKRPGIVHRLDKNTSGVMIVAKNDLAHKSLSAQFSDHGRTCALDRRYHALI 180

Query: 150 HGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT---LDTQKGSN-------AW 188
            G   ++             N  K+ ++ +   Y    VT   L  + GS+       + 
Sbjct: 181 WGTPHRNVWTIDASLGRSPHNRTKQAVIHKQNPYARHAVTHFSLLEKYGSHADSTSFASL 240

Query: 189 VTVGLREGKNREIK-KVFEFFNWK 211
           +   L  G+  +I+  +       
Sbjct: 241 LECRLETGRTHQIRVHM-AHIGHP 263


>gi|293415867|ref|ZP_06658507.1| rluD [Escherichia coli B185]
 gi|291432056|gb|EFF05038.1| rluD [Escherichia coli B185]
          Length = 326

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 86/244 (35%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      + R T+ +          +
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYRGTLVNAIAWHMKDIPD 151

Query: 101 LPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
             +    V  V R+D +T GLL++  T D      L+  +    R YR    G V QD+ 
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVGQDEG 211

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 78/233 (33%), Gaps = 36/233 (15%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I  E    QR+ K+++      SR +++  I    V VNG +++     V   D I+V 
Sbjct: 7   KIEDEALVGQRIDKLLSDFNSEWSRSQLQDWIKNDLVTVNGKIIKS-NYKVKLNDEIQVT 65

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              +                E   + + +KP G+V   S      T+ + L      +  
Sbjct: 66  EKEVVEADILPENLNLDIYYEDKDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKDLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL- 158
                    V R+D +T GLL++  +    R L  +L      R Y    HG +  D   
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKNDVAHRGLVEQLMDKTVKRKYTALVHGNIPHDYGT 185

Query: 159 --------NLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      ++ + V+           +         +   L  G+  +I+
Sbjct: 186 IDAPIGRNKKDRQSMDVVDDGKEAVTHFNVLEHFNDYTLIECQLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 76/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 83/234 (35%), Gaps = 39/234 (16%)

Query: 6   IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++ E    +R+ KV++   A   SR +V++ I +   KVN   ++       + D I ++
Sbjct: 7   VINEEQAGERIDKVLSTVNA-EWSRSQVQQWIKEGHAKVNDKTVK-GNYKCKTGDAIIIE 64

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              L                E   + + +KP G+V   +      T+ + L +    +  
Sbjct: 65  VPELEELDVVAEEMDLDIYYEDQDVLVVNKPRGMVVHPAPGHHSGTLVNGLMAHCKDLSG 124

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL- 158
                    V R+D +T GLL++  +      L     +    R Y+   HG +  D   
Sbjct: 125 INGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAKTVTRRYKAIVHGIIAHDHGT 184

Query: 159 --------NLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                      ++ + +      D     T+  +    + V   L  G+  +I+
Sbjct: 185 IDAPIGRDKQDRQSMTVTDENSRDAVTHFTVLQRFKDFSLVECKLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 76/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 76/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 45/226 (19%), Positives = 77/226 (34%), Gaps = 41/226 (18%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------VD-- 63
           R+ K IA      SR +++  I   RV VNG  ++ A   +   DHI         VD  
Sbjct: 36  RIDKYIAEEMKEVSRSQIQLWIGNGRVLVNGTAVK-ANYKLAEGDHIVLSVPEPESVDIM 94

Query: 64  --GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
              +PL    E + + + +K  GLV   +      T+ + L      +           V
Sbjct: 95  PENIPLDVVYEDSDVIVINKQRGLVVHPAPGHSSGTLVNALMYHCHDLSGINGELRPGIV 154

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD------------- 156
            R+D +T GLL+   +      L   L      R Y    HG +  D             
Sbjct: 155 HRIDKDTSGLLMAAKNDQAHASLAAQLKDHSVTRKYIALVHGHLSHDQGTVDAPIGRDSG 214

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              +    +  +   +      +  + G    + + L  G+  +I+
Sbjct: 215 DRKMFT--VTERNSKHAVTHFLVIERLGDYTLLELQLETGRTHQIR 258


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + +     V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVMVNGKVWDTPKEKVLGGEVVAINA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                +R            E   + + +KP GLV      +   TV + L   +  +   
Sbjct: 70  EIDEEVRFEAQDIPLTIVYEDDDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPPITDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRI-HTRLRLRLETGRTHQIR 237


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 76/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNNDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 63/341 (18%), Positives = 110/341 (32%), Gaps = 81/341 (23%)

Query: 13  PQRVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           P R+ K ++R      +   SR  + R+I +  V V+G L+  A   V     + +    
Sbjct: 15  PPRLDKALSRDVPADES--LSRTRLARLIEEGAVAVDGKLVTDAKAKVAEGAAVCITVSE 72

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                   + +PL    E   L + +KP GLV   +      T+ + L            
Sbjct: 73  ADESHIGPEDIPLDIVHEDADLIVINKPAGLVVHPAPGSPSGTLVNALLHHCGDDLSGVG 132

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLL 161
              R   V R+D +T GLL++       + L     +    R YR   +G  D +    L
Sbjct: 133 GVKRPGIVHRIDKDTSGLLVVAKSDAAHQGLAAQFEAHSVERYYRALCYGVPDAND-PRL 191

Query: 162 K--KGIVIQGI-----------------------------CYGDMQVTLDTQKGSNAWVT 190
           +  KG+  +                                     V +  Q G+ + + 
Sbjct: 192 RGIKGVSFEPGNVMRITTQLARHKHDRQKQAVLFHGGRHAVTRARVVEVFGQPGAVSLIE 251

Query: 191 VGLREGKNREIK-KVFEF----FNWKVNRLIR----ISYGPFQLGTLLAGSTREVSKKIL 241
             L  G+  +I+  +           V    R     S+G        A + R   ++ L
Sbjct: 252 CWLETGRTHQIRVHMAHAGHGLVGDPVYGGKRKLSARSFG-----ADAAEAVRSFPRQAL 306

Query: 242 REQ-LG-PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
               LG  H +  A +  +API      +       ++  D
Sbjct: 307 HAAVLGFEHPVTGAGMRFEAPIPQDMQALISALKQPAKSRD 347


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 67/328 (20%), Positives = 112/328 (34%), Gaps = 62/328 (18%)

Query: 1   MKDKNIVQENFT-PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           M  + I+  +   P R+ K +A A   SR  V+ +IA+  V++ G  +  A+V V     
Sbjct: 1   MAAEEIITGSIQVPARLDKALADATELSRARVQALIAEGAVEIAGKAVTSASVKVTENTP 60

Query: 59  -HIEV----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             I V            + L  A E   L + +KP G+V   +  +   T+ + L     
Sbjct: 61  FRITVPAVVEAEAQAQDIALDVAFEDEDLIVVNKPAGMVVHPAAGNPDGTLVNALLHHCR 120

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD 154
                     R   V R+D +T GLL++         L          R Y     G   
Sbjct: 121 GQLSGIGGVARPGIVHRIDKDTSGLLVVAKSDAAHEGLAAQFAEHSVHRRYLAVCGGHPS 180

Query: 155 QD-----------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNRE 200
                          N  K  ++ +    G   +T   +    G+ A +   L  G+  +
Sbjct: 181 PAEGTINERLGRSDANRKKMAVLPKNSSRGKHAITHYKVLKPIGAAALIECRLETGRTHQ 240

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL-----GPHLLEEAQV 255
           ++            +   S G   LG  + G     + K+L+  L         L  A++
Sbjct: 241 VR------------VHCASIGHALLGDPIYGR----TPKVLKPLLSQLKFARQALHAAEL 284

Query: 256 NLDAPIYSSE-TLVRDRPNIISEVPDDF 282
               PI  SE     D P  + E+ D+ 
Sbjct: 285 GFIHPILGSELRFSADLPADMQELIDEL 312


>gi|163755786|ref|ZP_02162904.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
 gi|161324307|gb|EDP95638.1| ribosomal large subunit pseudouridine synthase D [Kordia algicida
           OT-1]
          Length = 346

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 89/247 (36%), Gaps = 43/247 (17%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             ++   P RV K +     G A+R ++++      + VNG  ++     V   D I+V 
Sbjct: 23  TAEKGQQPLRVDKYLMNFIEG-ATRNKIQQAAKDGNIFVNGKPVKS-NYKVKGNDVIKVL 80

Query: 63  ------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP 102
                       + +P+    E   L + +KP G+V      +   T+       FDNLP
Sbjct: 81  FAHPPYENLLVGEDIPIDIVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLP 140

Query: 103 SI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-- 157
                R   V R+D +T GLL++         L          R+Y     G V++D+  
Sbjct: 141 KNSNERPGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTSERIYYALVWGNVEEDEGT 200

Query: 158 ---------LNLLKKGIVI-QGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                     N L+  +   +    G   VT   +  + G    V+  L  G+  +I+  
Sbjct: 201 VEGNIGRHPKNRLQNTVFFGEDADKGKPAVTHYKVLERLGYVTLVSCQLETGRTHQIRVH 260

Query: 205 FEFFNWK 211
            +     
Sbjct: 261 MKHIGHT 267


>gi|33866856|ref|NP_898415.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Synechococcus sp. WH 8102]
 gi|33639457|emb|CAE08841.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Synechococcus sp. WH 8102]
          Length = 331

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 81/247 (32%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           +V     P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +    
Sbjct: 29  LVYPKPLPMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGK-AKTPLRQGDEVQMWM 87

Query: 61  -------EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
                   +   P+      E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 88  PPPEPLPYLKPEPMALDVLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 147

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L+    +    R Y    HG    D   
Sbjct: 148 ISGKLRPGIVHRLDKDTTGCIVIAKSQQALVRLQGQIQKRIASREYLAVVHGVPGGDSGT 207

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +      Y     TL  + G  + +   L  G+  +I+    
Sbjct: 208 IVGAIGRHPADRKKYAV-VNDDSGRYACTHWTLQERLGDYSLLRFKLDTGRTHQIRVHCA 266

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 267 HINHPVV 273


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 81/226 (35%), Gaps = 33/226 (14%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPL 67
                R+ + +A A   SR   +  IAQ RV+V   ++E+ +  +   + + V  +  P 
Sbjct: 8   RMEGVRLDQAVAEACGVSRSRAQEWIAQGRVQVGEKVVEKPSYRLKGEEVLVVPPEEKPF 67

Query: 68  RKA---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS----------R 107
                       E   L + +KP GL+T  +      TV +  L   F           R
Sbjct: 68  VAPQDLAIPVLYEDEDLLVLNKPAGLLTHPAPGVYTGTVVNALLGRYFPLQEAERPEEVR 127

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL----- 160
              V RLD +T G+L++   GG    L         ++ Y     G   +  L       
Sbjct: 128 PGIVHRLDKDTSGVLVVAKHGGALEALARAFRDRLVMKRYLAITEGHPKEGTLIAPIGRH 187

Query: 161 --LKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              +  + + GI   Y + +  +    G  A V      G+  +I+
Sbjct: 188 PVERHKMHVGGIAPRYAETEFRILATAGPYALVEARPHTGRTHQIR 233


>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 = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 78/236 (33%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   F     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGTVLNALLFHFPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G++ + I     + TL +                    +  + + L  G+  +I+
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIR 237


>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 = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/231 (17%), Positives = 75/231 (32%), Gaps = 35/231 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V V+G ++ +    VM  + I V
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVTVDGNVVTKPRTKVMGGEVITV 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PS 103
                D V             E   + + +KP   V          TV + L       +
Sbjct: 68  LAELEDEVRWEAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLFHCPEVA 127

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHG 151
              R   V RLD +T GL+++         L   L      R Y                
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDK 187

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 188 PIGRHATKRTLMAVSPMGKPAVTHFRVAEHFRE-HTRIRLRLETGRTHQIR 237


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 76/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 88/252 (34%), Gaps = 46/252 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V       R+ K ++      SR ++++ I   +V VN +++    V V   D I  
Sbjct: 3   KYSVPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+ A          E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIAAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+V   G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREI 201
                      D+ K+ +LK G    G        TL+   KGS + V   L  G+  +I
Sbjct: 183 VIKNNIGRSRSDRQKMTILKYG----GKEAVTHYKTLELFYKGSISMVECKLSTGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 239 RVQLSHLKHSVV 250


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 62/325 (19%), Positives = 115/325 (35%), Gaps = 58/325 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +       +R+ KV+A        SR  ++ +I +  V +N   +++ A  V + D I+V
Sbjct: 10  MTTAEEAGKRLDKVLAER-YPDAYSRSYLQWLIEENHVLLNHKPVKKRA-KVAAGDRIDV 67

Query: 63  D-----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFS-- 106
                  + L+          E   + + +KP GLV      +   T V   L       
Sbjct: 68  CFVLAPEIELKPEKIFLDIIHEDEAIIVVNKPAGLVVHPGAGNWTGTFVNGLLYHCKKLP 127

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLN 159
                R   V RLD  T GLL+          L     S +  + Y     G   +  ++
Sbjct: 128 EGETLRPGIVHRLDKETTGLLVAAKTAEAQHKLVELFSSRRVYKEYIAVCVGNPGKGTVD 187

Query: 160 L--LKKGI------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +      +++G               S + V + L  G+  +I+      + K
Sbjct: 188 APIARHPVHRQKMAIVEGGRRSVTHYETLKYDVSLSLVKLVLETGRTHQIR-----VHMK 242

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
                    G   LG  + GS+  +++K    QLG  +L  A++    P+   E ++   
Sbjct: 243 -------QIGFPVLGDPVYGSS-AMNQKF---QLGRQMLHAAKLIFPHPVTGKEMVLE-- 289

Query: 272 PNIISEVPDDFTRMKKNSSQKNGLS 296
               + VPD+  ++    S  +G  
Sbjct: 290 ----APVPDEMAKVMARLSCLSGFQ 310


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 88/240 (36%), Gaps = 42/240 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K +++      R+ K ++      SR  V+ +I  + + VN    E+ +  V + D 
Sbjct: 1   MPKKYLLEVKDEHGRLDKFVSEQVPDLSRTRVKELIQDKNILVNNK-SEKVSYKVQAGDC 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           + V+   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 60  VLVNVPAVKPLDVVPENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTK 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++  +          L   + +  R+Y    HG 
Sbjct: 120 DLAQSPEGF-RPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK--RIYWAIVHGN 176

Query: 153 VDQD--KLNLL--------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             ++   ++ L        KK  V++          +  Q    + +   L  G+  +I+
Sbjct: 177 FGEEGGTIDALIGRNPYDRKKMAVVENGKKAVTHFKVLEQFKGFSLIECQLETGRTHQIR 236


>gi|329728841|gb|EGG65262.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 305

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 77/239 (32%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +     +   V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKNYTLVECQLETGRTHQIR 238


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 87/241 (36%), Gaps = 46/241 (19%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V       R+ K ++      SR ++++ I   +V VN +++    V V   D I  
Sbjct: 3   KYSVPHELNGIRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+ A          E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIATANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+V   G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREI 201
                      D+ K+ +LK G    G        TL+   KGS + V   L  G+  +I
Sbjct: 183 VIKNNIGRSRSDRQKMTILKYG----GKEAVTHYKTLELFYKGSISMVECKLSTGRTHQI 238

Query: 202 K 202
           +
Sbjct: 239 R 239


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 48/195 (24%), Positives = 72/195 (36%), Gaps = 30/195 (15%)

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------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            D +E+              +PL    E   L + +KP G+V   +      T+ + L  
Sbjct: 61  GDVLEIAVPEAEDYDVVAQDIPLEIVFEDADLLVVNKPAGMVVHPAPGTPDGTLVNALLH 120

Query: 104 IF----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHG 151
            F           R   V R+D +T GLL++         L     +    R Y    HG
Sbjct: 121 HFGGELSGVGGEKRPGIVHRIDKDTSGLLVVAKSDRAHHGLARQFEKHTARRAYLAVVHG 180

Query: 152 QVDQDKLNLL-KKGI 165
             D     L+  +G+
Sbjct: 181 VPDVADPRLMGTRGV 195


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 82/236 (34%), Gaps = 40/236 (16%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +  R   ASR  ++  I    V VNG  ++  +  V   D I +           
Sbjct: 31  RVDKFLMGRMENASRNRIQNAIDAGNVLVNGKTVKS-SYKVKPADEISIVFPHPPRDTEV 89

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP G+V      +   T+ +           LP    R  
Sbjct: 90  YPEDIPLDIVYEDNDLLVVNKPAGMVVHPGYNNYTGTLVNALAFHFEQLPQLPGNEGRPG 149

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD------KLNLL 161
            V R+D +T GLLL++ +      L          R Y     G + ++          L
Sbjct: 150 LVHRIDKDTSGLLLISKNEITMTKLAKQFFDHSITRKYIALAWGDIAENGTVTGFIGRSL 209

Query: 162 KKGIVI---QGICYGDMQV---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  IV+        G   V   T+  + G    ++  L  G+  +I+   +     
Sbjct: 210 KNRIVMDVYDDEEKGKWSVTHYTVLERLGYVTLISCQLETGRTHQIRAHMQHIGHP 265


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 79/239 (33%), Gaps = 47/239 (19%)

Query: 9   ENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------ 61
           E F  +R+ KV+A      SR  + ++I    VK+NG +  +        D IE      
Sbjct: 41  EGFWGERLDKVLAAHLPDVSRARLAKLIENGSVKLNGAVTTKIRAKATEGDEIELLEPPK 100

Query: 62  ------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                       V+   +   E   + + +KP GLV      +   T+ + L   F  + 
Sbjct: 101 LDEALAFEPQSFVEFEVI--YEDPSIIVVNKPAGLVVHPGAGNPDGTLLNGLLYHFPELK 158

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKL--- 158
                  V RLD +T GL+++         L     +    R Y     G   +D +   
Sbjct: 159 DVPRAGIVHRLDRDTTGLMVVARTLAAQTNLVRQLQERTVKREYWALTMGTAAEDFVVDV 218

Query: 159 ---------NLLK-----KGIVIQGICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIK 202
                       K      G+  +        V   +  G   +WV   L  G+  +I+
Sbjct: 219 PIGRDPKSRIRFKGFPGSTGVRAKPARTRARAVGWSSVDGIPASWVACRLDTGRTHQIR 277


>gi|227115223|ref|ZP_03828879.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
          Length = 325

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 83/238 (34%), Gaps = 33/238 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV++NG ++ +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       + L    E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +         +   G         ++  + ++  + + L  G+  +I+      N  
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIRVHMAHINHP 246


>gi|261378502|ref|ZP_05983075.1| tRNA pseudouridine synthase C [Neisseria cinerea ATCC 14685]
 gi|269145046|gb|EEZ71464.1| tRNA pseudouridine synthase C [Neisseria cinerea ATCC 14685]
          Length = 234

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 38/182 (20%), Positives = 56/182 (30%), Gaps = 35/182 (19%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRL 114
           D I  DG  +           +KP G++   S  D R TVF        I   V  V RL
Sbjct: 3   DIIYRDGRTV---------AVNKPAGILVHRSWLDSRETVFAMQTLRDQIGQHVYPVHRL 53

Query: 115 DINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNL 160
           D  T G+LL   D   AR+L          + Y     G +              DK+  
Sbjct: 54  DRPTSGVLLFALDTEAARLLTQQFEQKNIRKTYWAIVRGHLPSDGIIDYPLKYCPDKIAE 113

Query: 161 LKKGIVIQGICYG---------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                VIQ                Q  L       +W  +    G+  ++++  +     
Sbjct: 114 AHTESVIQDAQTACRCIARTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHP 173

Query: 212 VN 213
           + 
Sbjct: 174 IV 175


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 88/252 (34%), Gaps = 46/252 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  ++      R+ K ++      SR  V+ ++  Q + VNG  +E+ +  + + D 
Sbjct: 1   MTKEYSLEVKNEKGRLDKFVSEQIPDLSRTRVKELVKDQNILVNGK-VEKVSYKIQAGDK 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IEV+   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEVNIPAVKPLDVIPENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSK 119

Query: 107 ---------RVISVGRLDINTEGLLLL--TNDGGLA--RVLELPSTQWLRVYRVRFHGQV 153
                    R   V R+D +T GLL++  T     +    L   + +  R+Y    HG  
Sbjct: 120 ALAQSPEGFRPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHKTNK--RLYWAIVHGNF 177

Query: 154 DQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            ++                 +    V++          +  Q    + +   L  G+  +
Sbjct: 178 AEENGVIDAPIGRNPYDRKKMA---VVETGKKAITHFKVLEQFKDYSLIECQLETGRTHQ 234

Query: 201 IKKVFEFFNWKV 212
           I+   ++    V
Sbjct: 235 IRVHLDYIGHPV 246


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 76/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKPKGMVVHPSPGHYTNTLVNGLMYQIKDL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>gi|147678153|ref|YP_001212368.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
 gi|146274250|dbj|BAF59999.1| pseudouridylate synthase [Pelotomaculum thermopropionicum SI]
          Length = 312

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 88/241 (36%), Gaps = 37/241 (15%)

Query: 9   ENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    +R+   +A      +R  V+++IA+    VNG     A+  V   D + +     
Sbjct: 11  EEDAGKRLDLFLAGEMEGLTRTYVQKLIAEGMASVNGQRGR-ASYRVKPGDVVVLQVPEP 69

Query: 63  DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
           +G+ ++K         E   + + +KP G+V   +D +   T+ + L    S +      
Sbjct: 70  EGLEIKKEPIPLEVYYEDADVIVINKPRGMVVHPADGNYSGTLVNALLYHCSDLSGINGV 129

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------Q 152
                V RLD +T GL+++  +      L       Q  R Y    HG            
Sbjct: 130 MRPGIVHRLDKDTSGLIMVAKNDTAHLSLARQLKERQITRRYLALVHGLLKEQSGMVDAP 189

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +D  +  K  ++ +       +  +  +     ++ + L  G+  +I+    +    V
Sbjct: 190 IGRDPRDRKKMAVLQKNAKQAVTRYRVLERFKGYTYIELMLETGRTHQIRVHMSYIGHPV 249

Query: 213 N 213
            
Sbjct: 250 V 250


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 83/234 (35%), Gaps = 39/234 (16%)

Query: 6   IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++ E    +R+ KV++   A   SR +V++ I +   KVN   ++       + D I ++
Sbjct: 7   VINEEQAGERIDKVLSTVNA-EWSRSQVQQWIKEGHAKVNDKTVK-GNYKCKTGDAIIIE 64

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              L                E   + + +KP G+V   +      T+ + L +    +  
Sbjct: 65  VPELEELDVVAEEMDLDIYYEDQDVLVVNKPRGMVVHPAPGHHSGTLVNGLMAHCKDLSG 124

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL- 158
                    V R+D +T GLL++  +      L     +    R Y+   HG +  D   
Sbjct: 125 INGVMRPGIVHRIDKDTSGLLMVAKNDLAHESLVSQLVAKTVTRRYKAIVHGVIAHDHGT 184

Query: 159 --------NLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                      ++ + +      D     T+  +    + V   L  G+  +I+
Sbjct: 185 IDAPIGRDKQDRQSMTVTDENSRDAVTHFTVLQRFKDFSLVECKLETGRTHQIR 238


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 61/177 (34%), Gaps = 35/177 (19%)

Query: 13  PQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           P R+ K +       A     SR  + ++IA+  V V+G ++      +     +EV   
Sbjct: 15  PPRLDKALGRDVPDDASL---SRSRLAKLIAEGAVSVDGAVVTDPRHRIAEGSVVEVTVA 71

Query: 63  ---------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-------- 104
                    + +PL    E   L + +KP G+V   +      T+ + L           
Sbjct: 72  MAEESHIVGEDIPLDVVFEDDDLIVVNKPAGMVVHPAPGTPNGTLVNALIHHCGETLSGV 131

Query: 105 --FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
               R   V R+D  T GLL+          L     +    R Y    +G  DQ+ 
Sbjct: 132 GGMKRPGIVHRIDKETTGLLVAAKSDRAHHHLADQFAAHTVERRYLAVCYGLPDQND 188


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 83/250 (33%), Gaps = 54/250 (21%)

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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP  +V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRSMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V R+D +T GLL++  +      L     +    R Y+   HG +  D  
Sbjct: 125 GINGVMRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD-- 182

Query: 159 NLLKKGIVIQGICYGDMQVT-----LDTQKGSNAWVTV-------GLRE-----GKNREI 201
               KG  I      D +        +  K +     V        L E     G+  +I
Sbjct: 183 ----KG-TIDAPIARDKKERQSMTVDENGKHAVTHFQVLERFKDFTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWK 211
           +   ++  + 
Sbjct: 238 RVHMKYIGYP 247


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 92/289 (31%), Gaps = 70/289 (24%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           I+      +R+  ++A      SR +V+R I Q  + VN     + +  +   D I    
Sbjct: 15  IISPEDVGERLDTLLAHKLESVSRSQVQRAIEQGTILVNDHP-SKPSYKLREGDRILILT 73

Query: 61  --------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------- 98
                          VD   +   E  ++ +  KP G+V   S     +T+         
Sbjct: 74  IPRVPQGEVALIPSYVDLRVV--YEDDKIIVIDKPAGMVVHPSPGHYDNTLVNALIARYP 131

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ- 155
           D L     R   V RLD +T GL+++  D      L+    + +  + Y +   G +D  
Sbjct: 132 DLLKQPTDRPGIVHRLDKDTSGLIIVARDLDTLNYLQGQMKARKIFKEYTLLCCGALDPP 191

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG--LREGKNREIKKV 204
                      L    K  VI G      + +   Q      + +   +  G+  +I+  
Sbjct: 192 EGRIEAPIGRDLRDRTKMSVIAGGKEAVTEYS-TIQSLGKYTLAIARPIT-GRTHQIRVH 249

Query: 205 FEFFNWKVNRLIRIS----YGPFQLGTL--------------LAGSTRE 235
           F            I+    YG  +L  L                G  +E
Sbjct: 250 FAAIGHP------IAGDPIYGNCRLEGLNRQFLHASRLGVVMPNGEYKE 292


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 79/249 (31%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V     P R+ K +      +SR  ++       + VNG  ++     V  +D + +
Sbjct: 27  RTVVDSGQMPVRIDKYLFEKMQHSSRNRIQNAADAGFIHVNGKPVKS-NYKVRPSDVVTL 85

Query: 63  ------DGVPLRKAERTR--------LWLYHKPIGLVTTHSDPDGRSTV----------F 98
                     +   E           L + +KP GLV      +   T+           
Sbjct: 86  MLDRPQHDTTIEPEEMPLEVVYEDNDLMVINKPAGLVVHPGAGNFHGTLVNALAWYLKDL 145

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           D        V  V R+D +T GLLL+         L +   +    R Y     G    +
Sbjct: 146 DTYDPNDPEVGLVHRIDKDTSGLLLIAKTPEAKSKLGVQFLNKTTHRSYVALVWGNFTDE 205

Query: 157 K-----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           +            + L+  ++      G   VT   +  + G   W+   L  G+  +I+
Sbjct: 206 EGRIEGNIARDPKDRLRMTVLPSDSEMGKPAVTHYKVLERFGYTTWIECVLETGRTHQIR 265

Query: 203 KVFEFFNWK 211
              ++    
Sbjct: 266 AHMKYIGHP 274


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/255 (16%), Positives = 80/255 (31%), Gaps = 51/255 (20%)

Query: 10  NFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +   QR+ + +A +     SR  V+ +I Q  V +NG  ++     ++  + + V     
Sbjct: 12  DAAGQRLDQWLAASLGPDMSRSRVQMLIRQGAVSINGKPVDETKRKMLPGESVSVAMPEP 71

Query: 63  -----DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                 G  +      E   L + +KP GLV      +   T+ + L             
Sbjct: 72  EPAEPQGENIALDVLYEDDALIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGG 131

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHGQVDQ--- 155
             R   V RLD  T G++++       + L              R Y     G   +   
Sbjct: 132 VRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGLTGDLERAYLALVWGIPQRPTG 191

Query: 156 -------DKLNLLKKGIVIQGICYGDMQVT----------LDTQKGSNAWVTVGLREGKN 198
                     + +++ +V +G       VT             +  + + V   L  G+ 
Sbjct: 192 TVDAPLGRAADRVRRAVVPEGRDDARHAVTHFAVQERFGEKQQEFATASLVECRLETGRT 251

Query: 199 REIKKVFEFFNWKVN 213
            +I+         V 
Sbjct: 252 HQIRVHMAHIGHPVI 266


>gi|329297086|ref|ZP_08254422.1| RluA family pseudouridine synthase [Plautia stali symbiont]
          Length = 326

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/220 (17%), Positives = 80/220 (36%), Gaps = 31/220 (14%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QR+ + +A      SR  ++  I ++RV VNG ++++    V+  + + +D         
Sbjct: 18  QRLDQTLAELFPDYSRSRIKEWILERRVSVNGTIIDKPKEKVLGGERVAIDAEIEEEQRW 77

Query: 64  ---GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
               +PL    E   + + +KP  LV      +   TV + L   +       R   V R
Sbjct: 78  EAQNIPLDIVYEDDHILVINKPRDLVVHPGAGNPDGTVLNVLLYHYPAIADVPRAGIVHR 137

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-----DKLNLL---KK 163
           LD +T GL+++         L   L   +  R Y     G +       + +      + 
Sbjct: 138 LDKDTTGLMVVAKTVPAQTHLVETLQLREITREYEAVAIGTMTAGGTVNEPMARHSTKRT 197

Query: 164 GIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +            +     ++  + + L  G+  +I+
Sbjct: 198 HMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIR 237


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 82/234 (35%), Gaps = 41/234 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I++E    +R+ K +A     SR  ++ M+    + V+G + +     V   D I +   
Sbjct: 7   IIEEKNARERIDKAVAELTGKSRSAIQIMLKNGDITVSGEIAK-PNYKVQVGDEIHLEVR 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                    + +PL    E   + + +KP G+V   S     ST+ + L      +    
Sbjct: 66  EPEELEVLAEDIPLDIYFEDKDMLVVNKPEGMVVHPSAGHASSTLVNALLFHCKDLSGIN 125

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
                  V R+D +T GLL++  +      L   L      R Y    HG +        
Sbjct: 126 GKIRPGIVHRIDKDTSGLLMVAKNDHAHESLAKQLKDKTSDREYIALVHGDIVHQKGTIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 ++    +   +V  G         ++  +G    +   L  G+  +I+
Sbjct: 186 APIGRAKEDRQKMA--VVRDGKEARTHFEVIERLEGYT-LINCKLDTGRTHQIR 236


>gi|318040686|ref|ZP_07972642.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp.
           CB0101]
          Length = 404

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 86/246 (34%), Gaps = 39/246 (15%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +      P R+ + + A+    SR  +++ I    V+VNG+    A   +  +D +E+  
Sbjct: 14  LTYPKPLPMRLDRWLVAQRPEQSRARIQKFIESGYVRVNGVTGR-AKTPLRQSDTVELWM 72

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
                        +PL    E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 73  PPPEPLPYLMPQEIPLDVLFEDEHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 132

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK-- 157
           I  ++    V RLD +T G +++         L++   +    R Y    HG    +   
Sbjct: 133 ISGKLRPGIVHRLDKDTTGCIVVAKSQEALVKLQVQIQKRIASREYLAVVHGVPAAEHGT 192

Query: 158 ---------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                     +  K  +V      +     TL  + G  + +   L  G+  +I+     
Sbjct: 193 IVGAIGRHPADRKKYAVVHDDSGRHACTHWTLVERLGDYSLMRFKLDTGRTHQIRVHCAH 252

Query: 208 FNWKVN 213
               + 
Sbjct: 253 IGHPIV 258


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 37/233 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK- 69
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 14  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 72

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS--VG 112
                     E  ++ +  KP G+V   +      T+ +      +LP I   +    V 
Sbjct: 73  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 132

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  T    L+   +L +   +R Y    HG   +D+            +
Sbjct: 133 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 192

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++ +V  G         L+  +    ++   L  G+  +I+    + +  V
Sbjct: 193 RKRQAVVAAGRHAVTHFQVLERFEHYT-FIKCILETGRTHQIRVHMAYIHHPV 244


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/174 (21%), Positives = 65/174 (37%), Gaps = 25/174 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLAGKVQVNGEVVTKPRTKVMGGEEIIL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                D               E   + + +KP G V          TV + L   +    
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDDDILVINKPRGFVVHPGAGTPDGTVLNALLHHYPSIA 127

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVD 154
              R   V RLD +T GL+++         L         ++R Y     G++ 
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIGRMT 181


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 80/222 (36%), Gaps = 33/222 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----------IEVD 63
            R+ + +A A   SR + +  I   RV+V   ++ + A  +   +           +  +
Sbjct: 1   MRLDQAVAEALSVSRAKAQAWIQAGRVRVGDRVVLKPAYRLKGEEVAVEPVEEAPMVLPE 60

Query: 64  GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----------PSIFSRVISV 111
            +P+    E   +   +KP GL+T  +      TV + L           P    R   V
Sbjct: 61  DLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPGIV 120

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL-------NLLK 162
            RLD +T G+L++   GG+   L         ++ Y     G   +  L          +
Sbjct: 121 HRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGHPREGVLIAPIGRHPRER 180

Query: 163 KGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             + + G+   Y + +  +    G  A V      G+  +I+
Sbjct: 181 HKMHVGGLAARYAETEFQVLATAGPYALVEARPHTGRTHQIR 222


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/225 (17%), Positives = 74/225 (32%), Gaps = 40/225 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+ +++A     SR ++  +I    V VN  L+ + +  V+  D I              
Sbjct: 11  RLDQILASYLSISRNQISELIKSGNVYVNDNLMLKPSFKVLLNDKIGFNLPKAKFENCEF 70

Query: 61  --EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVI 109
             + D   L + +   + + +KP  L    +     +T+ + L              R  
Sbjct: 71  KADFDVEILYEDDD--ILVLNKPSNLTVHPAPSVKEATLVEWLKQNGYMLSTLNGDIRAG 128

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--------- 158
            V RLD  T G++++  +      L   L      RVY       +    +         
Sbjct: 129 IVHRLDKGTSGVIVVAKNNASHSALAAQLSDKSMGRVYLALIDFNLKDKLIIDRPIGRNP 188

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            N LK  +   G         +  +   N  +   L  G+  +I+
Sbjct: 189 QNRLKNSVAANGRAAKSAFTNIICEDDLN-LIAAKLFTGRTHQIR 232


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 84/233 (36%), Gaps = 39/233 (16%)

Query: 6   IVQENFTPQRVSKVIA---RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           I+ E+   +R+ KV+A    A   SR   + +I +  + VNGI +++    +   D +EV
Sbjct: 13  IISEDEVGERLDKVLARRFNAKY-SRTYFQFLIDKHLILVNGIAVKK-RTLLQEGDEVEV 70

Query: 63  ------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD---------- 99
                       + +PL    E   L + +KP G+V   +  +   T  +          
Sbjct: 71  QFLASPESNLMPENIPLSILYEDEHLLVINKPAGMVVHPAPGNWSGTFVNALLYYCQKLP 130

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
            LP    R   V RLD  T GLL+        + L     S +  + Y     G+    +
Sbjct: 131 LLPDTI-RPGIVHRLDKGTSGLLVAAKTLETQQKLIELFASRKVYKAYLAICIGRPADGE 189

Query: 158 LNL--------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +           K+  VI                   ++V + +  G+  +I+
Sbjct: 190 IQAPIGRHPIHRKQMAVIPTGKPAISFCKTLGWSDKLSFVQIEIATGRTHQIR 242


>gi|315613225|ref|ZP_07888135.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sanguinis
           ATCC 49296]
 gi|315314787|gb|EFU62829.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sanguinis
           ATCC 49296]
          Length = 298

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 72/210 (34%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRK-AERTRLWLYHKP 81
               + VNG   + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNGQP-QNATYLLDIGDRVTIDIPAEEGFESLEAIDRPLDVLYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + + +       V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDVDSIITRRVAKGGKYAHTSYKVVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 62/177 (35%), Gaps = 32/177 (18%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             QR+ +V+A   +   SR  ++ +I    V + G  ++  A  V + + I V       
Sbjct: 31  QSQRLDRVLAEQ-VEDLSRTRLKALIVAGHVSIGGAPVQDPAYQVKADETIIVEVPPAVA 89

Query: 63  ---DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------S 106
              +G  +      E   L + +KP GLV   +      T+ + L +             
Sbjct: 90  PEPEGENIPLNIVYEDDDLLVLNKPKGLVVHPAAGHETGTLVNALIAHCGTSLSGIGGVK 149

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQDK 157
           R   V RLD +T GL+++  +    + L        R       Y     G   +  
Sbjct: 150 RPGIVHRLDKDTTGLMVVAKNDRAHQSLTAQFADHGRTGALRRGYMAFVWGAPSRSH 206


>gi|229175258|ref|ZP_04302773.1| RNA pseudouridine synthase [Bacillus cereus MM3]
 gi|228608090|gb|EEK65397.1| RNA pseudouridine synthase [Bacillus cereus MM3]
          Length = 79

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 6/81 (7%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAER-TRLWLYHKPIGLVTTHSDP-DGRSTVFD 99
           +NG +   +A+ V   D + +DG  + K E+      +HKP+G+  T ++  +G    + 
Sbjct: 3   INGEICTHSAL-VSDGDVVTIDGQVIVKEEKEKVYIAFHKPVGITCTAAEHIEGNIIDYI 61

Query: 100 NLPSIFSRVISVGRLDINTEG 120
           N P    R+  VGRLD  +EG
Sbjct: 62  NYPE---RIFPVGRLDKASEG 79


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 82/246 (33%), Gaps = 54/246 (21%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ K +  R   +SR  +++      + VNG  ++     V   D I +         
Sbjct: 44  PVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGSPVKS-NYKVRPEDVITLMLDRPKHDN 102

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
               + +PL    E T L + +KP GLV      +   T+ + +      + +       
Sbjct: 103 TIEAEDIPLDIVYEDTVLMVINKPAGLVVHPGAGNFHGTLINAVAWHLRDMPAFDPNDPE 162

Query: 111 ---VGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVRFHGQVDQDK-- 157
              V R+D +T GLL++  T D   A                 R Y     G   +D+  
Sbjct: 163 VGLVHRIDKDTSGLLVVAKTPDAKTALGKQFFNKTTH------RSYNALVWGNFTEDEGR 216

Query: 158 ---------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVF 205
                     + L+  +   G   G   VT   +  + G    +   L  G+  +I+   
Sbjct: 217 IEGNIARDPRDRLRMTVFPPGSETGKHAVTHYRVLERFGYTTLIECILETGRTHQIRAHM 276

Query: 206 EFFNWK 211
           +     
Sbjct: 277 KHIGHP 282


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 90/253 (35%), Gaps = 48/253 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  ++      R+ K ++      SR  V+ ++  Q + VNG  +E+ +  + + D 
Sbjct: 1   MTKEYSLEVKNEKGRLDKFVSEQIPDLSRTRVKELVKDQNILVNGK-VEKVSYKIQAGDK 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IEV+   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEVNIPAVKPLDVIPENIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTK 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLL--TNDGGLA--RVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++  T     +    L   + +  R+Y    HG 
Sbjct: 120 ALAQSPEGF-RPGIVHRIDKDTSGLLMIAKTAKARESLEDQLAHKTNK--RLYWAIVHGN 176

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V++          +  Q    + +   L  G+  
Sbjct: 177 FAEENGVIDAPIGRNPYDRKKMA---VVETGKKAITHFKVLEQFKDYSLIECQLETGRTH 233

Query: 200 EIKKVFEFFNWKV 212
           +I+   ++    V
Sbjct: 234 QIRVHLDYIGHPV 246


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 83/249 (33%), Gaps = 43/249 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            K +  +   P RV K +        A+R +V++      V VN I ++     V   D 
Sbjct: 18  YKFVAADGQEPLRVDKFLMN--FIENATRNKVQQAAKAGNVLVNDIAVKS-NHKVKPKDV 74

Query: 60  IEV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V             + +PL    E   + + +KP G+V      +   T+ + L    
Sbjct: 75  VRVVLAYPPAENLLVAEDIPLDIIYEDDAVIVVNKPAGMVVHPGHGNYSGTLVNGLIHHI 134

Query: 106 SRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
             + +        V R+D +T GLL++         L          R+Y     G +++
Sbjct: 135 ENLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMAHLSKQFFDRTTERLYYALVWGNIEE 194

Query: 156 DK-----------LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D+            N L+  +   G    +      +  +      V   L  G+  +I+
Sbjct: 195 DEGRIEGNIGRSLKNRLQMAVFPDGDFGKHAVTHFKVLERLTYVTLVQCKLETGRTHQIR 254

Query: 203 KVFEFFNWK 211
             F+     
Sbjct: 255 AHFKHIGHT 263


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 92/253 (36%), Gaps = 50/253 (19%)

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  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I+VD V                  E   + + +KP G+V   S      T+ + L     
Sbjct: 57  IQVDSVQPTPISLEPENMPLDIVYEDDDVIVVNKPQGMVVHPSPGHPDHTLVNALLYHSP 116

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L   L + + LR Y    HG++ +D
Sbjct: 117 LSTINGEFRPGIVHRIDKDTSGLLMVAKNDKAHQFLSQQLQAQKNLRKYVALVHGRIKED 176

Query: 157 KLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNRE 200
                  G+V    G    D +       G +A     + E              G+  +
Sbjct: 177 ------SGVVNAPIGRSPKDRKKQAVVSDGRSAVTHFEVLERFADYTLVACRLETGRTHQ 230

Query: 201 IKKVFEFFNWKVN 213
           I+   ++    + 
Sbjct: 231 IRVHMKYIGHPIV 243


>gi|327385684|gb|AEA57158.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Lactobacillus casei BD-II]
          Length = 306

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 37/233 (15%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK- 69
           R+ KVI A     +R +V++ +    V VNG    +A   V S D I +   +  PL   
Sbjct: 13  RIDKVITAHETTHTRSQVQKWLQDGLVTVNGQP-TKANYKVASGDVIAISIPEAKPLEAI 71

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS--VG 112
                     E  ++ +  KP G+V   +      T+ +      +LP I   +    V 
Sbjct: 72  PEPIPLDIVYEDDQVIVVDKPQGMVVHPAPGHPDGTLVNGLLYHTDLPGINGVIRPGIVH 131

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  T    L+   +L +   +R Y    HG   +D+            +
Sbjct: 132 RIDKDTSGLLMVAKTEKAQLSLSAQLKAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRD 191

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++ +V  G         L+  +    ++   L  G+  +I+    + +  V
Sbjct: 192 RKRQAVVAAGRHAVTHFQVLERFEHYT-FIKCILETGRTHQIRVHMAYIHHPV 243


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/239 (16%), Positives = 81/239 (33%), Gaps = 38/239 (15%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ K +A A    +R  ++++I+   V V G    +A       D I V        
Sbjct: 13  AGIRIDKFLAEAIPDVTRSHIQKLISTGLVTV-GQKAVKANYKTALNDEIAVRIPEPEIP 71

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
               + +PL    E   + + +KP G+V   +     +T+ + +               R
Sbjct: 72  DIQPEDIPLDILYEDNDILIVNKPKGMVVHPAPGHYSNTLVNAVMYHCRDNLSGINGVAR 131

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----KLNLL 161
              V R+D++T G L++  +    + L   L      R Y    HG + +D       + 
Sbjct: 132 PGIVHRIDMDTTGSLIICKNDTAHQALAEQLKEHHITRKYHAVVHGNLKEDSQTVDAPIG 191

Query: 162 KKGIVIQGICYGD-------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +  +  + +               +  + G   ++   L  G+  +I+         + 
Sbjct: 192 RHPVDRKKMSTRAPHGRQAVTHYKVLERFGEYTYIECELETGRTHQIRVHMASIGHPIV 250


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 78/236 (33%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G++ + I     + TL +                    +  + + L  G+  +I+
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIR 237


>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 = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 74/236 (31%), Gaps = 39/236 (16%)

Query: 14  QRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           QR+       +   G+  R  V+  I   R ++NG +  +AA  +M    + +       
Sbjct: 15  QRLDVFWQTCLEEEGVG-RSRVQAWIKDGRARINGQVCSKAATRLMPGQTLTLAPEYTDS 73

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVI 109
                DG          L + +K   +    +      T+   +   F         R  
Sbjct: 74  SVVPDDGPLNVFFADEDLVVVNKTPAMTVHPAPSVAEPTLVHRVAHHFPALLSQSGERPG 133

Query: 110 SVGRLDINTEGLLL--LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG--- 164
            V RLD +T GL++  L+    L+      S +  + Y     G  D      L  G   
Sbjct: 134 IVHRLDKDTSGLIVLALSESARLSLTQAFASREVYKEYLALVAGVPDSSGTVSLALGRHP 193

Query: 165 -------IVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWK 211
                  +V +G    + +  L         + V V +  G+  +I+         
Sbjct: 194 SIKTRMAVVERGGRAAETRFELLWSAADRSASLVRVRIMTGRTHQIRVHMAALGHP 249


>gi|168334458|ref|ZP_02692629.1| putative pseudouridylate synthase [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 304

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 50/276 (18%), Positives = 96/276 (34%), Gaps = 56/276 (20%)

Query: 1   MKDKNIVQ-ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M DK ++   N    RV K +       +R  +++ I    + +NG +   A   + + D
Sbjct: 1   MNDKLLLTINNIADIRVDKFLTEQLPQYTRSYIQKQIELGLLLINGKVA-PARTRIKTGD 59

Query: 59  HIE--------VDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVF------- 98
            IE        VD  P         E + + + +KP  +V   S      T+        
Sbjct: 60  TIEFTIAPPREVDITPSEIKLDIIYEDSDILIVNKPKNMVVHPSAGHYNDTLVNALLFYA 119

Query: 99  -DNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
            D+L  I   +    V R+D +T GLL++  +      L   L      R Y    +G +
Sbjct: 120 KDSLSGINGEIRPGIVHRIDKDTTGLLMVAKNDHSHVFLSDLLKDHNIERKYNALVYGNI 179

Query: 154 DQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            +D                 +    +++       +  +  + G+   + + L+ G+  +
Sbjct: 180 KEDFFTIDRPIARNPKDRKKMA---IVENGRRAVTECRVLERFGNATHIELSLQTGRTHQ 236

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
           I+            +   S G   LG  L G ++ +
Sbjct: 237 IR------------VHLTSIGHPLLGDPLYGRSKHL 260


>gi|86153072|ref|ZP_01071277.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612140|ref|YP_001000956.1| ribosomal large subunit pseudouridine synthase A [Campylobacter
           jejuni subsp. jejuni 81-176]
 gi|157415544|ref|YP_001482800.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|167005866|ref|ZP_02271624.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|85843957|gb|EAQ61167.1| ribosomal pseudouridine synthase [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249616|gb|EAQ72575.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 81-176]
 gi|157386508|gb|ABV52823.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307748184|gb|ADN91454.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315932431|gb|EFV11374.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 322

 Score = 77.5 bits (190), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D I              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDVLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ +   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDKENKFSKNAKSAFINIVKTENLTLMAAKLFTGRTHQIR 238


>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 = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/179 (21%), Positives = 67/179 (37%), Gaps = 23/179 (12%)

Query: 1   MKDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ + I+     P+R+   +  R    SR  ++RMI    V+VN  + +  +  + + D 
Sbjct: 1   MQTEFIISAGEQPKRLDVFLVQREPKLSRAALQRMITAGWVRVNSHIAKS-SQRIRAGDV 59

Query: 60  IEVD----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I  D          G   +     E     + +KP G+VT  S     +T+ + L    +
Sbjct: 60  IVFDTPQPAPLRIAGETQQLEVLFEDHACLVLNKPAGIVTHPSPGHWSNTLLNALLDHCA 119

Query: 107 R------VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
           R         V RLD +T G++++       R L          R Y     G   Q +
Sbjct: 120 RGGGAATPGVVHRLDKDTSGVMVVAKTEEAHRKLSEQFERHSITRQYEALVVGVPAQSE 178


>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 = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVSINA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L   L   +  R Y     G +          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKGS----------------NAWVTVGLREGKNREIK 202
           G V + I     + T  +                    +  + + L  G+  +I+
Sbjct: 183 GTVDEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIR 237


>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 = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 78/236 (33%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVVTKPRTKVMGGEVIVVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADGTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G++ + I     + TL +                    +  + + L  G+  +I+
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIR 237


>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 = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 88/242 (36%), Gaps = 48/242 (19%)

Query: 2   KDKNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           K ++IV E     RV K++    A     SR +++  I +  V+VNG+ ++ A    +  
Sbjct: 3   KSQHIVTEQQGKTRVDKLLTQLLADQ---SRSQIQGWIDEGLVEVNGVSVK-ANYKCVEG 58

Query: 58  D------------HIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
           D             +E + +PL    E + + + +KP G+V   S      T+   L   
Sbjct: 59  DALTWEIPETKPLILEPENIPLDVVYEDSDVIVINKPKGMVVHPSAGHQTGTLVHALLYH 118

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                  +   R   V R+D +T GLL++  +    + L   L   Q  R Y    HG++
Sbjct: 119 CDDLSGINGIERPGIVHRIDKDTSGLLVVAKNDVAHQKLSDQLQQKQLKRKYVAIVHGEI 178

Query: 154 -------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
                        D      +    V+           +  +     +V   L  G+  +
Sbjct: 179 GHDTGLIDAPIGRDPKDRQKMA---VVDNGKSAITHFRVIERFPDYTFVECQLETGRTHQ 235

Query: 201 IK 202
           I+
Sbjct: 236 IR 237


>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 = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 77/229 (33%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  +RV VN  + ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDRRVLVNDKICDKPKEKVLGGEVVAIDA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEPQDIPLDIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>gi|325686216|gb|EGD28262.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 304

 Score = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 82/249 (32%), Gaps = 42/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +    + QR+ K +A      SR  ++ ++    V VNG    + +  V   D 
Sbjct: 1   MNREYELTAEESGQRLDKYLAGEMIDLSRSRIKELVQAGEVLVNGKK-SKVSYKVQKGDL 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------- 99
           I+V  +PL                E   + + +KP G+V   +      T+ +       
Sbjct: 60  IQVTVLPLEPLKLEAENIPLDIVYEDEDIIVVNKPQGMVVHPAVGHPSHTLVNALLYHTR 119

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
           +L           V R+D +T GLL++  +      LE  L +    R Y    HG   +
Sbjct: 120 DLADSPEGFRPGIVHRIDKDTSGLLMVAKNAAARESLEKQLAAKSNKRQYLAIVHGNFAE 179

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +                 +    V++          +  Q    + V   L  G+  +I+
Sbjct: 180 EEGTIDAPIGRNPKDRKQMA---VVEKGKSAVTHFKVLEQYQGYSLVECQLETGRTHQIR 236

Query: 203 KVFEFFNWK 211
               +    
Sbjct: 237 VHMAYIGHP 245


>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 = 77.1 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+   +A+     SR  +   I    V  NG         ++  + + V+  P ++    
Sbjct: 38  RLDAALAKMLPDYSRSRIAGWIKDGEVLCNGQPA-SPKTKLIGGEQLAVNIQPSQETQAY 96

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 97  TPEAMPLDIVYEDDSVLVLNKPAGLVVHPAAGNWTGTLLNGLLAHASELSQVPRAGIVHR 156

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN---------LL 161
           LD +T GL+++         L  +L S    R+YR    G V    K+           L
Sbjct: 157 LDKDTSGLMVVAKTLPAQNHLVQQLQSRSVKRIYRAIADGIVPFDGKIETQIGRDPHNRL 216

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 217 KMAVVKFGGKEAITHVKVLERYQAHSYIECSLETGRTHQIR 257


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 75/239 (31%), Gaps = 40/239 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK  +         R    +A     +R  V+  I + RV  NG   + A   V   D  
Sbjct: 1   MKTLDPAAPEEKGLRADVFLAARLDCTRSAVQHDIQEGRVTRNGKPAK-ANTKVKEGDVF 59

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +V            + +PL    E   + + +KP G+V   +  +   T+ + L      
Sbjct: 60  QVQVLPPVDLEARPENIPLDILYEDQDVIVVNKPRGMVVHPAAGNPDGTLVNALLYHCRD 119

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD 156
           +           V RLD +T G+++   +      L     +    R Y     G +  D
Sbjct: 120 LSGINGVIRPGIVHRLDKDTSGVMICAKNDRAHLSLAEQIQKKEAKRTYLAIVRGNIKDD 179

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +   +V  G  +      +  + G    V   L  G+  +I+
Sbjct: 180 RGHIETQLDRDPRDRKKMA--VVPSGGRWAATDYEVLERYGKFTVVRCRLLTGRTHQIR 236


>gi|213420845|ref|ZP_03353911.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 278

 Score = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 40/171 (23%), Positives = 64/171 (37%), Gaps = 22/171 (12%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + +D 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
            R   V RLD +T GL+++         L   L   +  R Y     G + 
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMT 180


>gi|239617850|ref|YP_002941172.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
 gi|239506681|gb|ACR80168.1| pseudouridine synthase, RluA family [Kosmotoga olearia TBF 19.5.1]
          Length = 299

 Score = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 80/230 (34%), Gaps = 38/230 (16%)

Query: 15  RVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
           R+ K +        ++S   + +++ +  V+VNG  ++  +  +   D + V+       
Sbjct: 18  RLDKFLRHVLPDLKLSS---IYKLLRKGNVRVNGKRIKAPSYELSLGDVVAVNYRGNIEY 74

Query: 64  -------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                         +P++   E        KP GL           T+ + L +   R  
Sbjct: 75  LKRLKESRELIPHNLPIKILYEDESFLAVDKPAGLAVHPGKGVQIVTLIEGLLAYGKRNG 134

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T G+LL+      AR L       +  + Y     G + +     LK 
Sbjct: 135 FKPFLVHRLDKHTSGVLLVAKSPQAARELTAMFREKRIDKRYVTLVKG-LPEKSRAYLKD 193

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             VI G+      +      G  +++ V L  GK  +I++        V 
Sbjct: 194 --VIDGLREESEYIVKKAYSG-CSFLEVRLFTGKKHQIRRQMAKIGHPVV 240


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 71/189 (37%), Gaps = 33/189 (17%)

Query: 1   MKDKNI--VQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVN 53
           M  + I  +  +  P R+ K +AR     A + SR  + R+IA   V+V+GI++      
Sbjct: 1   MSHRRISFIIADTPPPRLDKALARDVPEDANL-SRTRLGRLIADGSVQVDGIVVTDPRAR 59

Query: 54  VMSTDHIEVDGV------------PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +     I VD              PL    E + L + +KP G+V   +      T+ + 
Sbjct: 60  IFEGQEITVDVEEAEDSHILAESIPLEVVFEDSDLIVINKPAGMVVHPAPGSPSGTLVNA 119

Query: 101 LPSI----------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVR 148
           L +             R   V R+D +T GLL++         L          R Y+  
Sbjct: 120 LLAHCGDDLSGVGGMKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAKQFEKHTVERYYQAL 179

Query: 149 FHGQVDQDK 157
            +G  D + 
Sbjct: 180 VYGVPDAND 188


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 73/236 (30%), Gaps = 52/236 (22%)

Query: 15  RVSKVI-ARAGIASRR--EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           R+ K + A      R   EV+++I    + VN   ++     +   D +       ++A 
Sbjct: 26  RIDKFLIADLN---RSWNEVQKLIRNGEINVNNKKIKDHQFLLKEGDVVTYWDKLKKQAD 82

Query: 71  ---------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                                E  ++ + +K  G  +     +    + + L   F    
Sbjct: 83  TQLRPVPNTQAYEELKKMILYENDQIIILNKKHGYASQGG-ANPNYNIPEILNLYFKNFY 141

Query: 110 SVGRLDINTEGLLLLTNDGGLA---RVLELPSTQWLRVYRVRFHGQV------------- 153
            + RLD  T GLL++  +  +A     +        + Y     GQ+             
Sbjct: 142 IIHRLDQLTSGLLIIAKNKDIATEISTIIQEKAFITKKYIAVVQGQIKVQKGLIDRPLLF 201

Query: 154 -DQDKLNLLKKGIVIQGICYGDMQVTLDT------QKGSNAWVTVGLREGKNREIK 202
              ++         +    Y   + + +       Q    + + + + EG+  +I+
Sbjct: 202 NTNNQKQTCYNEEQLLEGKYLPARTSYEVIEEYQYQDEMYSILDLQIFEGRKHQIR 257


>gi|328952411|ref|YP_004369745.1| pseudouridine synthase, RluA family [Desulfobacca acetoxidans DSM
           11109]
 gi|328452735|gb|AEB08564.1| pseudouridine synthase, RluA family [Desulfobacca acetoxidans DSM
           11109]
          Length = 331

 Score = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 79/244 (32%), Gaps = 38/244 (15%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V+      R+   + R     SR  ++R I    V+VN     +   ++   D + V   
Sbjct: 20  VEAEEEGLRLDHFLVRKMPSFSRARLQRWIKAGLVQVN-QEERQPHYHMRKGDRVAVSPP 78

Query: 66  PLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
            +++              E   L   +KP GL           T+ + L      +  +G
Sbjct: 79  EVQRWHLAPEPIPLKILYEDEDLLALNKPPGLTVHPGAGQSSGTLVNALLHHCPDLGGIG 138

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
                    RLD +T G++++       + L     + +  + Y     G+  +++  + 
Sbjct: 139 DVQRPGLVHRLDKDTSGVMVVAKTDRAHQALIKQFKNRRVDKRYLALVWGRFSENQGEIE 198

Query: 162 ---------KKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    +  + +   +G         L    G  +W+ + L  G+  +I+       
Sbjct: 199 EEIGRHPTQRHKMAVTSRRGRPAATSWRRLQEYPGPFSWLELKLHTGRTHQIRVHLSSLG 258

Query: 210 WKVN 213
             V 
Sbjct: 259 HPVV 262


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 85/240 (35%), Gaps = 39/240 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++D     E+   QR+   ++      SR  ++ +I Q  V VN ++ +    NV + D 
Sbjct: 11  VEDIGKPTESKLSQRLDLWLSNELPDLSRSRIQNLILQGNVTVNDLICKSKKENVKNGDR 70

Query: 60  IEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +   D  PL             E   L + +KP GLV   +      T+ + L +   
Sbjct: 71  IHIAIPDAEPLDLKPEAIPLDILYEDESLIIINKPAGLVVHPAAGHPGGTLVNALLAHCP 130

Query: 107 --------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                   R   V RLD +T G +++  T+        +L +    R Y    +G +  +
Sbjct: 131 LAEIGGVLRPGIVHRLDKDTSGAIVVAKTDFAHQHLQAQLKAKTARREYLGVVYGTLKTE 190

Query: 157 -------------KLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +   + I+ G         +  + G+   +   L  G+  +I+
Sbjct: 191 NGTIDLPIGRHSVDRKKMAV-VTIEKGGRSAVTHWQIQERLGNYTLIHFQLETGRTHQIR 249


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 48/271 (17%), Positives = 80/271 (29%), Gaps = 62/271 (22%)

Query: 1   MKDKNIVQENFTPQ-------RVSKVIARA---GIASRREVERMIAQQRVKVNGILLERA 50
           M D+   Q + T         R+   +A A   G+ SR  V+ +I    V VNG    +A
Sbjct: 1   MPDREAQQGHETLVVGEDAAGRLDAWLAEALAPGL-SRSRVKALIEAGAVSVNGTPARQA 59

Query: 51  AVNVMSTDHIEV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
              +   D I +          +G  +      E   L + +K  GLV      +   T+
Sbjct: 60  KHKIKPGDEISLVVPDPEDPEPEGEDIPLSILYEDADLIVINKQAGLVVHPGAGNWTGTL 119

Query: 98  FDNLPSIF----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------ 141
            + L               R   V RLD +T G++++       R L             
Sbjct: 120 VNALIHHCGDSLSGIGGVRRPGIVHRLDRDTTGVMVVAKHDQAHRHLADQFADHGLTGPL 179

Query: 142 LRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQ----------VTLDTQKGS 185
            R Y+    G+           L   +  I  + +   D            V     +  
Sbjct: 180 ERAYQAVVWGKPAGLKGTIDAGLGRARDRIR-RAVRTDDAPDVRHAVTHYLVRERYGEKP 238

Query: 186 NAWVTVGLRE-----GKNREIKKVFEFFNWK 211
           +      L E     G+  +I+         
Sbjct: 239 DGTCAATLVECRLETGRTHQIRVHMAHIGHP 269


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 86/242 (35%), Gaps = 46/242 (19%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
            R+ K ++      SR ++++ I   +V VN +++    V V   D I     +   L+ 
Sbjct: 13  IRLDKALSSLLENVSRNQIQKAIKDSQVLVNDVIISDPDVLVKENDIILFSFKEPEELKI 72

Query: 70  A----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
           A          E   L + +K  G+           T+ + L      +  +G       
Sbjct: 73  AAANVALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTKNLSDIGSSERPGI 132

Query: 113 --RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV--------------- 153
             RLD +T GL+++  +     +L       Q +R Y+V   G +               
Sbjct: 133 VHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKVLVWGVINPLEGVIKNNIGRSR 192

Query: 154 -DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            D+ K+ +LK G    G        TL+   KGS + V   L  G+  +I+         
Sbjct: 193 SDRQKMTILKYG----GKEAVTHYKTLELFYKGSISMVECKLSTGRTHQIRVQLSHLKHS 248

Query: 212 VN 213
           V 
Sbjct: 249 VV 250


>gi|257462225|ref|ZP_05626642.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|317059894|ref|ZP_07924379.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|313685570|gb|EFS22405.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
          Length = 318

 Score = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 85/238 (35%), Gaps = 47/238 (19%)

Query: 8   QENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           QE    +R+   +      A+R  +E++IA+  VK +  ++ +    +   + I+V    
Sbjct: 13  QEKDQGKRLDLFLKEQLPEATRSYLEKLIAEGYVKCDEKVITKNGKKLKGKEAIQVSIPE 72

Query: 64  ---------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------- 106
                     +PL    E   L + +K   +V   +  +   T+ + L            
Sbjct: 73  EEEMKMEAEKLPLDIVYEDEYLLVINKAANMVVHPALGNYTGTLVNALLYYCKESLSDVN 132

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD +T GL+++  +  +   L L        + Y     G+  ++K    
Sbjct: 133 GTLRPGIVHRLDKDTTGLIVVAKNNQIHHRLALMFQEKTIQKTYLAIVKGRFSEEK---- 188

Query: 162 KKG--IVIQGICYGDMQV---------------TLDTQKGSNAWVTVGLREGKNREIK 202
           K+G  + +      D +                 +      ++ V V ++ G+  +I+
Sbjct: 189 KEGDLVTLIARDRKDRKKMAVSQSHGKKAVSHYKVLWNGEKHSLVEVNIKTGRTHQIR 246


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   +V V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDKVSVDGKTINKPKEKVLGGEIVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E + + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEAARWEPQEIPLDIVYEDSDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGKMTAGGLVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 82/234 (35%), Gaps = 33/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K    V E+   QR+ + +A      SR  ++  I  +R+ VN  ++++    V+  + 
Sbjct: 5   VKLNATVSESQLGQRLDQALAELFPDYSRSRIKEWILDRRITVNDTIIDKPKEKVLGGEQ 64

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +D             +PL    E   + + +KP  LV      +   TV + L   F 
Sbjct: 65  ISIDAEIEEEARWEAQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYHFP 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------R 148
                 R   V RLD +T GL+++         L   L   +  R Y             
Sbjct: 125 AIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRMTAGGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 185 VDQPISRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 85/244 (34%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      +   T+ +          +
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDIPD 151

Query: 101 LPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
             +    V  V R+D +T GLL++  T D      L+  +    R YR    G V+QD+ 
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TIIGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>gi|254780610|ref|YP_003065023.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter asiaticus str. psy62]
 gi|254040287|gb|ACT57083.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 340

 Score = 77.1 bits (189), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 83/238 (34%), Gaps = 50/238 (21%)

Query: 15  RVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEV-------- 62
           R+ + +A +     SR  V+ +I    + +NG++ +     V+  D   I V        
Sbjct: 24  RIDRWLATSLKEQFSRSYVKILILNGFISINGMVSKNPNRKVVPGDSFLITVPAAQKLNI 83

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVI 109
             + +PL    E   + + +KP GLV   +  +   T+ + L           +   R  
Sbjct: 84  AQENIPLDILYEDDDIIVINKPAGLVVHPAPGNWTGTLVNALLYHCHNNLSSINGVKRPG 143

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG-QVDQDKL---- 158
            V RLD +T G++++  +    + L        +       Y     G  +    +    
Sbjct: 144 IVHRLDKDTTGVMVVAKNDLAHQKLSEQFVDHGKSTRLKRAYYAMVWGIPLPDSGIINAP 203

Query: 159 ------NLLKKGIV-IQGIC-------YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 N L++ +  I           Y  +++       + + +   L  G+  +I+
Sbjct: 204 LGRCKSNRLRRAVKGIDDKTADSAITHYQTIEIYNKNSNFAVSLLKCHLETGRTHQIR 261


>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 = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 81/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV++NG ++ +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDNRVQINGNVINKPKEKVLGGESVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       + L    E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 42/261 (16%), Positives = 89/261 (34%), Gaps = 64/261 (24%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK + IV E  +  R+ K +    I    +R  +++++  + V+VNG  ++  +    + 
Sbjct: 1   MKQEYIVPEKSSGLRIDKFLTE--ICPDYTRSFLQKLLKSELVEVNGKPVKS-SYKTAAG 57

Query: 58  DHIEVD-GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D +  +    +               E   + L +KP G+V   +      T+ + L   
Sbjct: 58  DTVTFEVPEAVEAEITAQEMPLDILYEDEDVILINKPKGMVVHPAAGHYEGTLVNGLMHH 117

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
                       R   V R+D++T G+L++  +      +   L      R Y     G 
Sbjct: 118 CREQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLKVHSITRKYYAVVFGS 177

Query: 153 VDQDKLNLLKKGIVIQGICYGD--------MQVTLDTQKGSNAW--VTV-------GLRE 195
           +  D           +G  +           +++++++ G +A     V        L E
Sbjct: 178 LKDD-----------EGTIHAPIGRHPNDRKKMSINSKNGKDAVTHYKVLERFHGYTLVE 226

Query: 196 -----GKNREIKKVFEFFNWK 211
                G+  +I+         
Sbjct: 227 CRLETGRTHQIRVHMASIGHP 247


>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 = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 74/183 (40%), Gaps = 27/183 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + +V+E     R+ K ++ R    SR  +++++  + V V G  ++       + D 
Sbjct: 1   MKQQFVVEEEDKAIRIDKYLSERCPELSRSYLQKLLKAEAVFVGGKPVKS-NYKTAAGDL 59

Query: 60  IE------VDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IE      V+   + +        E + + L +KP G+V   +      T+ + L +   
Sbjct: 60  IELEVPEAVEPKIVPEEMDLDILYEDSDIILINKPKGMVVHPAAGHYSGTLVNGLMAHCR 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G+L++  +      +   L      R Y    HG + 
Sbjct: 120 ADLSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHNSIAEQLKVHSITRKYYAVVHGVMK 179

Query: 155 QDK 157
           +D+
Sbjct: 180 EDE 182


>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 = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 37/170 (21%), Positives = 63/170 (37%), Gaps = 28/170 (16%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
             TP R+  V+A    +SR +V   I   RV+VNG +  ++++ +   + + VD      
Sbjct: 10  TATPGRLDAVLAGLADSSRSQVSAWIDAGRVRVNGQVTTKSSLKLRGGETLIVDVPPPVL 69

Query: 64  ------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------- 106
                  VPL    E   L   +KP G+ T  +      T+ + L               
Sbjct: 70  AHVEPENVPLDVLYEDDALIAINKPPGMTTHPAPGVTTGTLVNALLGRMPLPEQDGARGP 129

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
              R   V RLD +T G++++         L     + +  + Y     G
Sbjct: 130 DGYRPGIVHRLDKDTSGVIVVAKTVEAHAKLADAFKARETRKTYLALAGG 179


>gi|13473214|ref|NP_104781.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
 gi|14023962|dbj|BAB50567.1| pseudouridine synthase [Mesorhizobium loti MAFF303099]
          Length = 329

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 83/259 (32%), 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---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                     G  +      E   L + +KP GLV      +   T+ + L         
Sbjct: 63  MPEPEPAAPQGEAIALDVLYEDDALIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDSLS 122

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVD 154
                 R   V RLD  T G++++       + L        R       Y     G   
Sbjct: 123 GIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKALSEAFADHGRTGDLERAYLALVWGIPQ 182

Query: 155 Q----------DKLNLLKKGIVIQGICYGDMQVT---LDTQKGSN-------AWVTVGLR 194
           +             + +++ +V +G       VT   +  + G N       + V   L 
Sbjct: 183 RPTGTVDAPLGRAADRVRRAVVPEGRDDARHAVTHFAVQERFGENQQEFATASLVECRLE 242

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+         V 
Sbjct: 243 TGRTHQIRVHMAHIGHPVI 261


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 82/244 (33%), Gaps = 49/244 (20%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGIL---------LERAAVNVMSTDH 59
           +   +R+   + R     SR   +R++A+  V V+G            E  A  +   + 
Sbjct: 7   DQAGERLDVFLVRQLPTLSRSYAQRLVAEGHVTVDGERRKANFKLSGGESVACTIPPAEA 66

Query: 60  IEV--DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
           +E+  + +PL    E   + + +KP G+V   +      T+ + L    S +        
Sbjct: 67  VEIRAENIPLNVLYEDADIIVINKPRGMVVHPAAGVYTGTLVNALLHHCSDLSGINGDLR 126

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGI 165
              V RLD +T G+++   +      L          R YR   +G + +      + G+
Sbjct: 127 PGIVHRLDKDTSGVMVAAKNDMAHHFLARQIRDKEARREYRAIVYGNIVE------RAGV 180

Query: 166 VIQGI-----CYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIK-KVFEF 207
           +   I         M +  +  K +     V             L  G+  +I+  +   
Sbjct: 181 ITGDIGRHPTDRKKMAIVRENGKPATTHFEVLERFGDYTFVACRLETGRTHQIRVHMT-S 239

Query: 208 FNWK 211
               
Sbjct: 240 IGHP 243


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 77/229 (33%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV+VNG  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDNRVQVNGKTINKPKEKVLGGETVAIDA 69

Query: 64  ----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                              E + + + +KP  LV      +   TV + L   +  +   
Sbjct: 70  QIEEDARWEPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L +    R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQARDITREYEAVAIGTMTAGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 81/241 (33%), Gaps = 33/241 (13%)

Query: 3   DKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  I  +     R+  V+A      SR  ++  I    V ++G+  ++    V   + + 
Sbjct: 7   EARIPTDKM-GHRLDAVLAELFSDYSRNRIQDWIRAGLVTLDGVEHKKPNFKVFGDESVV 65

Query: 62  V------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
           +              +P+    E   + + +KP GLV      +   T+ + L   +   
Sbjct: 66  LLAEIEDEVSYQAQDIPIEVVYEDEDILVLNKPAGLVVHPGAGNPDGTLLNALLFHYETI 125

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
               R   V RLD  T GL+++  +      L  +L      RVY     G         
Sbjct: 126 REVPRAGIVHRLDKETSGLMVVAKNVPAQTHLVEQLQQHDVERVYDAIVVGKMISGGTIS 185

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +   +  +  ++  G         +  +   +  V V L  G+  +I+    +  +
Sbjct: 186 KPIGRHPTDRKRMAVLTVGGKPATSHYRVLERFREHTHVRVKLETGRTHQIRVHMAYLGF 245

Query: 211 K 211
            
Sbjct: 246 P 246


>gi|330956144|gb|EGH56404.1| ribosomal large subunit pseudouridine synthase B [Pseudomonas
          syringae Cit 7]
          Length = 75

 Score = 76.8 bits (188), Expect = 5e-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|40889481|pdb|1QYU|A Chain A, Structure Of The Catalytic Domain Of 23s Rrna
           Pseudouridine Synthase Rlud
          Length = 349

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 76/229 (33%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 33  TVSENQLGQRLDQALAEXFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINA 92

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 93  EIEEEARFEPQDIPLDIVYEDEDIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 152

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL ++         L   L   +  R Y                 +
Sbjct: 153 PRAGIVHRLDKDTTGLXVVAKTVPAQTRLVESLQRREITREYEAVAIGHXTAGGTVDEPI 212

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         +      +  + + L  G+  +I+
Sbjct: 213 SRHPTKRTHXAVHPMGKPAVTH-YRIXEHFRVHTRLRLRLETGRTHQIR 260


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 55/255 (21%), Positives = 89/255 (34%), Gaps = 52/255 (20%)

Query: 1   MKDKN--IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M + N  I +     QR+ K++       SR +++  I +  V VNG  ++ A   V   
Sbjct: 1   MTEFNYEITEAEQAGQRIDKLLPEFNSDWSRSQIQDWIKEDLVTVNGKKVK-ANHKVKLN 59

Query: 58  DHIEV--------DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D IEV        D  P         E + + + +KP G+V   S      T+ + L   
Sbjct: 60  DKIEVTEKETVEADIKPENLNLDIYYEDSDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQ 119

Query: 105 FSRVIS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
              +           V R+D +T GLL++  +    R L  +L +    R Y    HG +
Sbjct: 120 IKDLSGINGEIRPGIVHRIDKDTSGLLMVAKNDIAHRNLVEQLMAKTVTRKYTALVHGNI 179

Query: 154 DQDKLNLLKKGIVIQ---GICYGDMQ--VTLDTQKGSNAWVTV-------GLRE-----G 196
             D          I    G    D Q    +D  K +     V        L E     G
Sbjct: 180 PHDYG-------TIDAPIGRDKKDRQSMAVVDDGKDAVTHFNVLEHFKDYTLVECELETG 232

Query: 197 KNREIKKVFEFFNWK 211
           +  +I+   ++    
Sbjct: 233 RTHQIRVHMKYIGHP 247


>gi|158522832|ref|YP_001530702.1| RluA family pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158511658|gb|ABW68625.1| pseudouridine synthase, RluA family [Desulfococcus oleovorans Hxd3]
          Length = 329

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 81/247 (32%), Gaps = 51/247 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRKAERT 73
           R+  ++A     SR     +I    + V+G   ++ +  V     I   G  P +K E+ 
Sbjct: 19  RLDTLVAGQWDCSRHSAALLIKNGTILVDGRP-QKPSYKVGVNQSIT--GRIPSQKPEKP 75

Query: 74  --------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
                          L + +KP GLV   +      T+ + L   F  + +VG       
Sbjct: 76  GPEPAPLPLLFEDAFLLVVNKPPGLVVHPAPGHEGGTLVNRLLHHFPAIGTVGEPDRPGI 135

Query: 113 --RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDK 157
             RLD NT G L++       + L     S Q  + Y    +G            + +  
Sbjct: 136 VHRLDRNTSGALVVAKTAAAHQALSDMFKSRQVRKTYLALVYGQMKSTGGVVTLPIGRHS 195

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
           L   +K + +        +     +K     + + + +  G+  +I+            L
Sbjct: 196 LE--RKKMSVSSPQARPAETRWKVRKAFVDASLLELEIHTGRTHQIR-------VHCTAL 246

Query: 216 IRISYGP 222
            R   G 
Sbjct: 247 QRPVVGD 253


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 81/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           IV E+   +R+ + +A      SR  ++  I   +V ++  ++E+    V++   + VD 
Sbjct: 10  IVTESLAGKRLDQALAELFPDYSRSRLKSWITDGKVTIDTKVIEKPREKVVAGALVAVDA 69

Query: 64  ---GVPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
              G     A+            + + +KP GLV          T+ + L     ++   
Sbjct: 70  EIEGEERHAAQPVELDIVYEDDDILVINKPAGLVVHPGAGAPDRTLLNGLLHYDPQLDLV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL----- 158
                + RLD +T GL+++  +      L          R Y    +G +    +     
Sbjct: 130 PRAGIIHRLDKDTTGLMVVARNVPAQTQLVSMMQDRDITREYEAVCNGVMTAGGMVDQPI 189

Query: 159 -----NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +V  G         LD  + ++  + + L  G+  +I+
Sbjct: 190 GRHPTKRTHMAVVQSGKPAVTHYRVLDRYR-AHTLLRLRLESGRTHQIR 237


>gi|283956675|ref|ZP_06374154.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283791924|gb|EFC30714.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 322

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D I              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLYDEIKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDVLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGAILIAKNNFTHQRLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ V   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIR 238


>gi|160902202|ref|YP_001567783.1| RluA family pseudouridine synthase [Petrotoga mobilis SJ95]
 gi|160359846|gb|ABX31460.1| pseudouridine synthase, RluA family [Petrotoga mobilis SJ95]
          Length = 319

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 88/248 (35%), Gaps = 45/248 (18%)

Query: 7   VQENFTPQRVSKVIAR-AGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           V+     +R+   IA+   I  SR  ++  I + ++ VNG   ++    V   D I++D 
Sbjct: 8   VEREDEQKRLDIYIAQKMPIEISRNLIQNAITKGQITVNGSQ-KKPHYKVKQGDEIQIDF 66

Query: 64  ---------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--- 104
                           +PL    E   L + +KP GL+   +      T+ + L      
Sbjct: 67  HELVEETKEENILPENIPLNILYEDEELIVINKPAGLIVHPTPSIKTGTLVNALMHHVKD 126

Query: 105 -------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV---YRVRFHGQVD 154
                   +R+  V RLD  T G+L++  +   +  L     +  +    Y     G + 
Sbjct: 127 LDKTMQDPNRLGIVHRLDKETSGVLVVAKN-AFSHHLLSKEFKERKTMKYYLAIVEGTLK 185

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           + +           +   K+ +V  G        TL         V + LR G+  +I+ 
Sbjct: 186 EKEGEINLPLGRHPILRHKRAVVYNGKEAITEYKTLKEFGDLATLVWIRLRTGRTHQIRV 245

Query: 204 VFEFFNWK 211
            F++    
Sbjct: 246 HFKYIGNP 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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 79/242 (32%), Gaps = 47/242 (19%)

Query: 13  PQ-RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P+ R+   +      SR  +  MI + RV VNG   ++A   + + D I   G+ L K  
Sbjct: 21  PEVRLDVCLTEKTGTSRSFIRNMIEEGRVLVNGET-KKANYRIRAEDKI---GINLPKPR 76

Query: 72  RTRL----------------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
             ++                 + +KP G+V   +      T+ + L      +       
Sbjct: 77  ELKVVPQQIPLEIIYEDDDLLVVNKPQGMVVHPAPGVWEGTLVNALLYHCRDLSGINGII 136

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV----------- 153
               V R+D +T GLL++  +      L   L   +  R Y    HG +           
Sbjct: 137 RPGIVHRIDKDTSGLLVVAKNDESHNQLAGQLKEHKMQRKYLAVVHGVLSEPSGTIDAPI 196

Query: 154 --DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             D      +   +V +          ++ +      +   L  G+  +I+    +    
Sbjct: 197 GRDPKDRKKMA--VVFKHSRPAVTHYEVEERFIGYTKIKAVLETGRTHQIRVHMAYIRNP 254

Query: 212 VN 213
           V 
Sbjct: 255 VL 256


>gi|86149976|ref|ZP_01068204.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88596472|ref|ZP_01099709.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 84-25]
 gi|218562892|ref|YP_002344671.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85839422|gb|EAQ56683.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni CF93-6]
 gi|88191313|gb|EAQ95285.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Campylobacter jejuni subsp. jejuni 84-25]
 gi|112360598|emb|CAL35395.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284926505|gb|ADC28857.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315927093|gb|EFV06444.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315928797|gb|EFV08067.1| pseudouridine synthase, RluA family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 322

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D I              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDVLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ V   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIR 238


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 85/228 (37%), Gaps = 31/228 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV+VNG    +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILEDRVQVNGKTTNKPKEKVLGGETVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E + + + +KP  LV      +   TV + L   +  +I  
Sbjct: 70  QIEEEARWEPQDIPLDIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIIDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKL 158
                V RLD +T GL+++         L   L   +  R Y     G +      ++ +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGTMTAGGTVEEPI 189

Query: 159 NLL---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIK 202
                 +  + +  +    +    +     ++  + + L  G+  +I+
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIR 237


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 84/227 (37%), Gaps = 40/227 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A      SR  +++++ +  V VNG    + +  V + D + V+  P  +++  
Sbjct: 45  RLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGDVLSVELRPTPQSQAF 104

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGR 113
           R              L + +KP GLV   +  +   T+ + L           R   V R
Sbjct: 105 RPEAMALDTVYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGLLSLDPRAGNVPRAGIVHR 164

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDKLN 159
           LD +T GL+++  +  +   L   + + +  R Y                   + +D  N
Sbjct: 165 LDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLALGHRAWQGSQTRVVEEAIGRDPRN 224

Query: 160 LLK-KGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L+   + +    G         LDT +     V   L  G+  +I+
Sbjct: 225 RLRMAAVDLAVHAGKPARTDLAVLDTCEDG-CLVHCTLHTGRTHQIR 270


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + I +D 
Sbjct: 10  TVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGTIGDKPKEKVLGGERIAIDV 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFQPQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRI-HTRLRLRLETGRTHQIR 237


>gi|145589104|ref|YP_001155701.1| RluA family pseudouridine synthase [Polynucleobacter necessarius
           subsp. asymbioticus QLW-P1DMWA-1]
 gi|145047510|gb|ABP34137.1| ribosomal large subunit pseudouridine synthase D [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 318

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 84/239 (35%), Gaps = 40/239 (16%)

Query: 11  FTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
              +R+ KV+A      SR  ++  +    V V+G  + +A   +   + ++V       
Sbjct: 1   MAGERLDKVLAGSLPDYSRNRLKAWVEAGAVMVDGK-VTKARYLLRGGESVKVFPQEMPE 59

Query: 63  ------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
                 + +PL    E   + + +KP GLV   +  +   T+ + L   F  + S     
Sbjct: 60  QFAFSPENIPLEVVYEDDSIIVINKPPGLVVHPAAGNWSGTLLNGLLHRFPELKSLPRAG 119

Query: 111 -VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV------------DQ 155
            V RLD +T GL+++  T     A V +L      R Y     G              DQ
Sbjct: 120 IVHRLDKDTSGLMVVARTAHAQTALVRQLQERTVGRRYLAWVWGDAPSQGKVLASVGRDQ 179

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWK 211
                +  G   QG     +   +      N   A +   L  G+  +I+   E   + 
Sbjct: 180 RDRLKMAAGSP-QGKPAATLFRRIAKGNVENAPVALLECRLETGRTHQIRVHLESLGFP 237


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 82/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+    R+ + +A      SR  ++  I   RVKVNG ++ +    V+  + I +D 
Sbjct: 10  TVTESQLGHRLDQALAELFPDYSRSRIKEWILDDRVKVNGKIINKPKEKVLGGEEIAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E + + + +KP  LV      +   T+ + L   +  ++  
Sbjct: 70  LIEEEARWEPQNIPLDIVYEDSDILVINKPRDLVVHPGAGNPDGTILNALLYYYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGTMTAGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 81/234 (34%), Gaps = 39/234 (16%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
           I+QE     R+ KV+A       SR   + +I +  V +NG  +++        D +   
Sbjct: 13  IIQEMEAGIRLDKVLADRYKSNGSRTYFQMLIEKGLVLLNGEPVKK-RFKPNVGDDVELF 71

Query: 61  -----EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFS--- 106
                E+D +P +       E   L + +KP+G+V   +  +   T V   L        
Sbjct: 72  FAAAPEIDLIPEQIPLNILYEDEHLLIINKPVGMVVHPAPGNWTGTFVNALLYHCGYSLS 131

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVR--------- 148
                  R   V RLD  T G+L+      + + L     + Q  + Y            
Sbjct: 132 DASVDSIRPGIVHRLDKETSGVLVAAKTLSVQQKLMELFAARQVYKEYWAICLGNPGNCE 191

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  + +  ++  +  +   G        TL+          + L  G+  +I+
Sbjct: 192 LNWPIGRHPIHRKQMTVREDGKEALTFCETLEVGNEI-CLAKLILSTGRTHQIR 244


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 71/180 (39%), Gaps = 25/180 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K +  +      +R+ K +++    SR +++ +I ++ +KVN   ++  +  V   D IE
Sbjct: 3   KQRYEIYVEGESERIDKYLSKKVPLSRSQIQDLIEKELIKVNEKPIKN-SYKVKLGDRIE 61

Query: 62  V------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V              +P+    E   + + +KP G+V   +      T+ + L      +
Sbjct: 62  VIIPPPVETEVKPQDIPIEIVYEDEDMVIINKPKGMVVHPAHGHYNDTLVNALLYRVKDL 121

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK 157
             +G         RLD +T GLL++  +    + L          R Y     G++  ++
Sbjct: 122 SGIGGELRPGIIHRLDKDTTGLLIIAKNDLSHQKLSEQLKNRTLRRTYWALCEGEIPWEE 181


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   RV+VNG    +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILDDRVQVNGKTTNKPKEKVLGGETVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
               +A             E + + + +KP  LV      +   TV + L   +  +   
Sbjct: 70  QIEEEARWEPQDIALNIVYEDSDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGTMTAGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>gi|332970080|gb|EGK09077.1| ribosomal large subunit pseudouridine synthase D [Kingella kingae
           ATCC 23330]
          Length = 371

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 81/233 (34%), Gaps = 40/233 (17%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILL---------ERAAVNVM 55
           IV  +    R+   +A+     SR  +   I    V+ NG            E  +V + 
Sbjct: 31  IVPNDLAGMRLDAALAKLLPDYSRSRITTWIKDGFVQCNGKTASPKEKLIGGEELSVQIQ 90

Query: 56  STDHIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +D                    E   + + +KP GLV   +  +   T+ + L +    
Sbjct: 91  QSDE----NQAYEPEHMDLNIVFEDDTVIVLNKPAGLVVHPAAGNWTGTLLNGLLAHCPE 146

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKL 158
                R   V RLD +T GL+++         L  +L +    R+YR    G V    K+
Sbjct: 147 LSQVPRAGIVHRLDKDTSGLMVVAKTLPAQNSLVQQLQNRTVKRIYRAVADGIVPFDGKI 206

Query: 159 N---------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      LK  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 207 ETLIGRDPHNRLKMAVVKFGGKEAVTHVKVLERYHAHSYIECSLETGRTHQIR 259


>gi|227554161|ref|ZP_03984208.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|227176703|gb|EEI57675.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis HH22]
          Length = 297

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPTQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 82/247 (33%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V +    +R+   +  A G  SR  V+++I    V V+   +++ +  + +   I    
Sbjct: 7   VVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFYI 66

Query: 65  VPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             +                E   + +  KP GLV   S      T+ + L      +  +
Sbjct: 67  PQVEPLEVLPEDIPFDVVYEDEDILVLIKPCGLVVHPSPGYSSGTLVNALLFRIKELSGI 126

Query: 112 G---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---- 156
           G         RLD NT GL+++       R L  E    + L+ Y     G + +D    
Sbjct: 127 GGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKRYHALVSGLLREDSGTV 186

Query: 157 ---------KLNLLKKGIVIQGICYGDM-QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                            +V  G       +V    +K    ++ V +  G+  +I+    
Sbjct: 187 EKSIGRHPVDRKKFS--VVEDGKPAKTEYEVIKRFEKHRITFLDVRIHTGRTHQIRVHLS 244

Query: 207 FFNWKVN 213
           F    V 
Sbjct: 245 FIGHPVL 251


>gi|78185708|ref|YP_378142.1| pseudouridine synthase, RluD [Synechococcus sp. CC9902]
 gi|78170002|gb|ABB27099.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp.
           CC9902]
          Length = 339

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 84/247 (34%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +      P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 32  LTYPKPLPMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKQGK-AKTPLREGDQVQLWM 90

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   + + +K  GL    +  +   T+ +       +LP 
Sbjct: 91  PPPEPLPYLKPQPMDLDVLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 150

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L++   + +  R Y    HG  D D   
Sbjct: 151 ISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGVPDGDSGT 210

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y     TL  + G  + +   L  G+  +I+    
Sbjct: 211 IIGAVGRHPVDRKKYAV-VSDESGRYARTHWTLIERFGDYSLLRFKLDTGRTHQIRVHCA 269

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 270 HINHPVV 276


>gi|291519437|emb|CBK74658.1| ribosomal large subunit pseudouridine synthase D [Butyrivibrio
           fibrisolvens 16/4]
          Length = 305

 Score = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 60/321 (18%), Positives = 107/321 (33%), Gaps = 62/321 (19%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M +  I+ E  + +  R+ K +A A    SR   ++ I    V VNG  ++         
Sbjct: 1   MDEFTIIIEEPSDEGIRIDKYLAAALPEKSRSYYQKAIDNGFVLVNGKQIKS-KYQTKLG 59

Query: 58  DHIEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I V   P+++              E + + + +KP G+V   +      T+ + L   
Sbjct: 60  DEIIVSIEPVKEIDILPEDIPIDILYEDSDVIVVNKPKGMVVHPAPGHYSGTLVNALMYH 119

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
                       R   V R+D+NT G LL+  +      +   +      R+Y+    G 
Sbjct: 120 CKDSLSGINGEIRPGIVHRIDMNTTGSLLVCKNDKAHNDIAAQIKVHSVNRIYKGIVVGN 179

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V+          T+  Q    ++V   L  G+  
Sbjct: 180 FKEEEGTINANIGRNPKDRKKMA---VVSDGREAITHYTVLEQYKGFSYVQFKLETGRTH 236

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS-TREVSKKILREQ----LGPHLLEEAQ 254
           +I+         +            LG  + G   + +  + L  Q    + P   E  +
Sbjct: 237 QIRVHMAHIGHPL------------LGDDVYGKPVKGLEGQTLHAQTLGFVQPTTGEYVE 284

Query: 255 VNLDAPIYSSETLVRDRPNII 275
           VN   P Y  E L + R  II
Sbjct: 285 VNAPLPAYFEELLTKYRKTII 305


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 35/174 (20%), Positives = 64/174 (36%), Gaps = 25/174 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVQVNGEVVTKPRTKVMGGEEIIL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP G +          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDDDILVINKPRGFIVHPGAGTPDGTVLNALLHHYPNIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVD 154
                  V RLD +T GL+++         L         + R Y     G++ 
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFTREYEAIAIGRMT 181


>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 = 76.8 bits (188), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/231 (17%), Positives = 79/231 (34%), Gaps = 34/231 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++  +   +VKVNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLLDGKVKVNGEVISKPRTKVMGGEEIIL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   L + +KP G V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDDDLLVINKPRGFVVHPGAGTPDGTVLNALLHHYPNIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVD-----Q 155
                  V RLD +T GL+++         L         ++R Y     G++      +
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKKRNFVREYEAIAIGRMTAGGRVE 187

Query: 156 DKLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
             +        +  +            +      +  + + L  G+  +I+
Sbjct: 188 QPIGRHSTKRTLMAVTPTGKPAITHYRVAEHFREHTRIRLRLETGRTHQIR 238


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 85/244 (34%), Gaps = 48/244 (19%)

Query: 10  NFTPQRVSKVIARAGIA-----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
               +R+ KV+    +      SR  ++  +    V V+G  + +A   +   + I+V  
Sbjct: 28  KMAGERLDKVL----VGTLPDYSRNRLKTWVEAGAVMVDGK-VTKARYLLRGGESIKVFP 82

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPS--I 104
                      + +PL    E   + + +KP GLV   +  +   T+        P   +
Sbjct: 83  QEMPEQFAFNPEDIPLDVVYEDGDIIVINKPPGLVVHPAAGNWSGTLLNGLLFRYPELKM 142

Query: 105 FSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV--------- 153
           F R   V RLD +T GL+++  T+    + V +L      R Y     G           
Sbjct: 143 FPRAGIVHRLDKDTSGLMVVARTSQAQTSLVRQLQDRTVGRRYLAWVWGDAPSQGKVLAS 202

Query: 154 ---DQDKLNLLKKGIVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEF 207
              DQ     +  G   QG     +   L     Q+     +   L  G+  +I+  FE 
Sbjct: 203 VGRDQRDRLKMAAGSP-QGKPAATLFRRLSKGLVQETPVTLLECRLETGRTHQIRVHFES 261

Query: 208 FNWK 211
             + 
Sbjct: 262 LGFP 265


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 82/236 (34%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVP 66
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V       D   
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYDNEI 100

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
           + +        E   L + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPEDIPLHIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDNPDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      ++  +    R YR    G VDQD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRRYRALVWGIVDQDEGTIVGSIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMADPTQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>gi|323466424|gb|ADX70111.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 310

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 86/243 (35%), Gaps = 48/243 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +Q      R+ K ++      SR  V+ ++ ++ + VN   +E+ +  + + D 
Sbjct: 8   MPKKYELQVENEYGRLDKFVSEQIPDLSRTRVKELVKEKEILVNHK-VEKVSYKIQAGDK 66

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE++   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 67  IEINVPAVKPLDVVPENIPLDIVYEDEDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHTQ 126

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQ 152
                P  F R   V R+D +T GLL++  +          L   + +  R+Y    HG 
Sbjct: 127 DLAQSPEGF-RPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK--RIYWAIVHGN 183

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
             ++                 +    V++          +  Q    + +   L  G+  
Sbjct: 184 FGEENGVIDAPIGRNPYDRKKMA---VVENGKKAVTHFKVLRQFKGYSLIECQLETGRTH 240

Query: 200 EIK 202
           +I+
Sbjct: 241 QIR 243


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 88/259 (33%), Gaps = 60/259 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + IV E  +  R+ K +       +R  +++++  + V+VNG  ++  +    + D 
Sbjct: 1   MKQEYIVPEKSSGLRIDKFLTESCPDYTRSFLQKLLKSELVEVNGKPVKS-SYKTAAGDT 59

Query: 60  IEVD-GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +  +    +               E   + L +KP G+V   +      T+ + L     
Sbjct: 60  VTFEVPEAVEAEITAQEMPLDILYEDEDVILINKPKGMVVHPAAGHYEGTLVNGLMHHCR 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G+L++  +      +   L      R Y     G + 
Sbjct: 120 EQLSGINGVMRPGIVHRIDMDTTGVLIVCKNDLAHNSIAEQLKVHSITRKYYAVVFGSLK 179

Query: 155 QDKLNLLKKGIVIQGICYGD--------MQVTLDTQKGSNAW--VTV-------GLRE-- 195
            D           +G  +           +++++++ G +A     V        L E  
Sbjct: 180 DD-----------EGTIHAPIGRHPNDRKKMSINSKNGKDAVTHYKVLERFHGYTLVECR 228

Query: 196 ---GKNREIKKVFEFFNWK 211
              G+  +I+         
Sbjct: 229 LETGRTHQIRVHMASIGHP 247


>gi|323464710|gb|ADX76863.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Staphylococcus pseudintermedius ED99]
          Length = 305

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 82/248 (33%), Gaps = 48/248 (19%)

Query: 5   NIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           NI       QR+ K++    +     SR +++  I +  ++VNG  ++     +   D I
Sbjct: 7   NIEDATHHLQRIDKILPEFNSEW---SRSQLQEWIKEGLIEVNGKAVKS-NYKLKLGDRI 62

Query: 61  EVDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           E+    +                E   + + +KP G+V   S      T+ + L      
Sbjct: 63  EITEKEVVEADIQAENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKN 122

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
           +           V R+D +T GLL++  +    R L  +L +    R Y    HG +  +
Sbjct: 123 LSGINSEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAKTVKRKYIALVHGHIPHE 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                            +    V+           +     +   V   L  G+  +I+ 
Sbjct: 183 FGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVIETFKNYTLVECELETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 92/249 (36%), Gaps = 39/249 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  +       R+  ++A+  +  SR  +   +    + VNG+ ++R A  V + D 
Sbjct: 1   MTKKITINIIDQIGRIDAILAKENLPYSRTTLAEWLQTGHILVNGVQVKR-AYKVTTGDT 59

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +            + +PL    E   + + +KP G+V   +      T+ + L     
Sbjct: 60  ITILQPEVITTEIIAEDIPLDIIYEDDDILVVNKPQGMVVHPAAGHSSGTLVNALLFHAP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG----- 151
                   R   V R+D +T GLL++  +    + L   L + +  R+Y     G     
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDQAHQGLSAQLKAHKNDRIYYALVRGEFVEN 179

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KV 204
                  +++ K++  K+ +  +G         +  +      + V L  G+  +I+  +
Sbjct: 180 SGTINAPINRHKVDRKKQAVQ-EGGREAITHFEVIERYVGYTLLKVRLETGRTHQIRVHM 238

Query: 205 FEFFNWKVN 213
             +    V 
Sbjct: 239 T-YIGHPVV 246


>gi|227329204|ref|ZP_03833228.1| 23S rRNA pseudouridine synthase D [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 325

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 82/238 (34%), Gaps = 33/238 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV++NG +  +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVTNKPKEKVLGGESVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       + L    E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +         +   G         ++  + ++  + + L  G+  +I+      N  
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIRVHMAHINHP 246


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 76/245 (31%), Gaps = 41/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
            V+      RV   +A      SR  +++++ Q  V VNG  ++     V   D      
Sbjct: 7   TVETEDEDTRVDAYLASQIDRMSRSYIQKILKQGGVLVNGKAVK-PNYKVCEDDRIEIEI 65

Query: 60  -------IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVIS 110
                  IE + +PL    E   + + +KP  +V   +      T+ +  L     R+  
Sbjct: 66  PENEELDIEAEDIPLDILYEDDDVLIVNKPKDMVVHPAAGHYEHTLVNALLFHCRDRLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD--- 156
                    V R+D +T G L++  +    + L   L      R YR    G    +   
Sbjct: 126 INGVMRPGIVHRIDKDTTGALVICKNDAAHQSLAAQLAVHSITRRYRAIVAGNFKDETFT 185

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                         +   +      +    V +       A+V   L  G+  +I+    
Sbjct: 186 VEGNIGRSANDRKKMAV-VSPDKGKHAVTHVKVLQNLKGYAYVECELETGRTHQIRVHMA 244

Query: 207 FFNWK 211
                
Sbjct: 245 HIGHP 249


>gi|308751621|gb|ADO45104.1| pseudouridine synthase, RluA family [Hydrogenobacter thermophilus
           TK-6]
          Length = 326

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 82/247 (33%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V +    +R+   +  A G  SR  V+++I    V V+   +++ +  + +   I    
Sbjct: 15  VVDQEAQGKRLDLFLTEAYGEFSRSYVQKLIEDGFVLVDDKEIKKPSRRLKAGQKITFYI 74

Query: 65  VPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             +                E   + +  KP GLV   S      T+ + L      +  +
Sbjct: 75  PQVEPLEVLPEDIPFDVVYEDEDILVLIKPCGLVVHPSPGYSSGTLVNALLFRIKELSGI 134

Query: 112 G---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---- 156
           G         RLD NT GL+++       R L  E    + L+ Y     G + +D    
Sbjct: 135 GGKERPGIVHRLDKNTAGLMVVAKSDKAHRSLVEEFMQRRVLKRYHALVSGLLREDSGTV 194

Query: 157 ---------KLNLLKKGIVIQGICYGDM-QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                            +V  G       +V    +K    ++ V +  G+  +I+    
Sbjct: 195 EKSIGRHPVDRKKFS--VVEDGKPAKTEYEVIKRFEKHRITFLDVRIHTGRTHQIRVHLS 252

Query: 207 FFNWKVN 213
           F    V 
Sbjct: 253 FIGHPVL 259


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 84/227 (37%), Gaps = 40/227 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ K +A      SR  +++++ +  V VNG    + +  V + D + V+  P  +++  
Sbjct: 45  RLDKALAELVPEFSRSYLQQLLGEGGVLVNGRAAAKPSARVQAGDVLSVELRPTPQSQAF 104

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGR 113
           R              L + +KP GLV   +  +   T+ + L           R   V R
Sbjct: 105 RPEAMALDTVYEDEHLRIVNKPAGLVVHPAPGNWSGTLLNGLLALDPRAGNVPRAGIVHR 164

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFHGQVDQDKLN 159
           LD +T GL+++  +  +   L   + + +  R Y                   + +D  N
Sbjct: 165 LDKDTSGLMVVARERSVMDALVRMIAAREVSRQYLALGHRAWQGAQTRVVEEAIGRDPRN 224

Query: 160 LLK-KGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L+   + +    G         LDT +     V   L  G+  +I+
Sbjct: 225 RLRMAAVDLAVHAGKPARTDIAVLDTCENG-CLVHCTLHTGRTHQIR 270


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 85/243 (34%), Gaps = 42/243 (17%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           V E     R+ K ++   I    SR  ++ +I ++ VKVN   L+     +   D IE+ 
Sbjct: 8   VDEQDEGLRIDKYLSN--IFKDKSRSFIQGLIEKENVKVNSKTLKS-NYKLKKADEIEIM 64

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +P+    E   + + +K  G+V   +  +   T+ + L      + S
Sbjct: 65  IPEPEILSVEAENIPIDIVYEDEDVIVVNKAQGMVVHPAPGNYNGTLVNALLYHCKDLSS 124

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK-- 157
                    V R+D +T G+L++  +      L   L      R Y     G++  +   
Sbjct: 125 INGVIRPGIVHRIDKDTSGILVIAKNDDAHNKLSEQLKDHSMKREYYALIEGRLKNNDGT 184

Query: 158 ---------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                     + LK GI+  G         ++   G    V   L  G+  +I+      
Sbjct: 185 IDKPLGRCKKDRLKIGIIEDGKRAVTHYEVVERYNGYT-LVKCVLETGRTHQIRVHMASI 243

Query: 209 NWK 211
            + 
Sbjct: 244 GFP 246


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +   GI    SR +V++ I  + V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFV--TGINNEWSRTQVQQWIKDEVVTVNGKAVK-GNYKVKEEDEITVTIPEPEEL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQGICYGDMQVTL---DTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I      D +        + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIARDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 81/242 (33%), Gaps = 45/242 (18%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P R+ K +        A+R +++       + +N   ++     V   D + V      
Sbjct: 27  QPLRIDKYLMN--FVENATRNKIQSAAKDGCIFINNSPVKS-NYKVKPNDFVTVKFKHPP 83

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFS- 106
                  + +P+    E   L + +KP G+V      +   T+       F+NLP+  S 
Sbjct: 84  HENLLIAEDIPIDVVYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIFHFENLPNNSSD 143

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------- 157
           R   V R+D +T GLL++         L     +    R Y     G + +D+       
Sbjct: 144 RPGLVHRIDKDTSGLLVVAKTEQAMAHLSNQFAKKTSEREYVALVWGNMTEDEGIIEGNI 203

Query: 158 ----LNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                N L+  + +               +  + G    V+  L  G+  +I+   +   
Sbjct: 204 GRHPKNRLQNTVYLDDEADKGKPAITHYKVIERLGYVTLVSCKLETGRTHQIRVHMKHIG 263

Query: 210 WK 211
             
Sbjct: 264 HT 265


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 37/214 (17%), Positives = 80/214 (37%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRKA-ERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +    D L     R  +  + RLD +T G+++   +  +
Sbjct: 102 VINKREGLLSVSTDRIKERTAYRILSDYLKECDPRNKIFVLHRLDRDTSGIMMFAKNQKV 161

Query: 131 ARVLELPSTQ--WLRVYRVRFHGQVDQD-KL--------NLLKKGIVIQG-ICYGDMQVT 178
              L+   ++    R Y     G+ ++D  L          ++  +   G       +  
Sbjct: 162 KEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVTQDGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L       + V + L  G+  +I+   +     +
Sbjct: 222 LLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPI 255


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/180 (22%), Positives = 62/180 (34%), Gaps = 30/180 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +   +   QR+  ++A  G+  SR    R +    V VNG  + +    V   D I    
Sbjct: 8   VAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAK-KHPVAPGDTIVYQV 66

Query: 64  ----------GVPLR---KAERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFS--- 106
                     G P+    + E   L +  K +GLV   S D D  + V   +    +   
Sbjct: 67  EEPVEPGPLRGQPIDLDIRFEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGAENL 126

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R+  V RLD +T GL+L   +      L          R Y    HG +  D
Sbjct: 127 CNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAHD 186


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 82/248 (33%), Gaps = 48/248 (19%)

Query: 5   NIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           NI       QR+ K++    +     SR +++  I +  ++VNG  ++     +   D I
Sbjct: 7   NIEDATHHLQRIDKILPEFNSEW---SRSQLQEWIKEGLIEVNGKAVKS-NYKLKLGDRI 62

Query: 61  EVDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           E+    +                E   + + +KP G+V   S      T+ + L      
Sbjct: 63  EITEKEVVEADIQAENLNLDIYYEDDDVAIVYKPKGMVVHPSPGHYTGTLVNGLMYQIKN 122

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
           +           V R+D +T GLL++  +    R L  +L +    R Y    HG +  +
Sbjct: 123 LSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVEQLMAKTVKRKYIALVHGHIPHE 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                            +    V+           +     +   V   L  G+  +I+ 
Sbjct: 183 FGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVIETFKNYTLVECELETGRTHQIRV 239

Query: 204 VFEFFNWK 211
             ++  + 
Sbjct: 240 HMKYIGYP 247


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 82/237 (34%), Gaps = 31/237 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    QR+ + +A      SR  ++  I ++RV VNG ++++    V+  + + +  
Sbjct: 10  TVSEAQLGQRLDQTLAELFPDYSRSRIKEWILERRVSVNGTVIDKPKEKVLGGEQVSISA 69

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEQRWEAQNIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLYHYPPIVDV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-----DKL 158
            R   V RLD +T GL+++         L   L   +  R Y     G +       + +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVETLQLREITREYEAVAIGTMTAGGTVNEPM 189

Query: 159 NLL---KKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  + +            +     ++  + + L  G+  +I+      N  
Sbjct: 190 ARHSTKRTHMAVHPMGKPATTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHP 246


>gi|255974981|ref|ZP_05425567.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T2]
 gi|307285489|ref|ZP_07565628.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|255967853|gb|EET98475.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T2]
 gi|306502713|gb|EFM71978.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
          Length = 297

 Score = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLNEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAKAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/180 (22%), Positives = 62/180 (34%), Gaps = 30/180 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +   +   QR+  ++A  G+  SR    R +    V VNG  + +    V   D I    
Sbjct: 8   VAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAK-KHPVAPGDTIVYQV 66

Query: 64  ----------GVPLR---KAERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFS--- 106
                     G P+    + E   L +  K +GLV   S D D  + V   +    +   
Sbjct: 67  EEPVEPGPLRGQPIDLDIRFEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGAENL 126

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R+  V RLD +T GL+L   +      L          R Y    HG +  D
Sbjct: 127 CNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAHD 186


>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 = 76.4 bits (187), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 42/244 (17%), Positives = 79/244 (32%), Gaps = 50/244 (20%)

Query: 12  TPQRVSKVIARAG---IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             +R+ K +  +      SR +V+  I    V VN   ++     + S DH+   G+ + 
Sbjct: 22  AGERIDKFVTDSLNEDSISRTQVQEWIKSGAVLVNQNTVK-PNYKLSSGDHV---GIRVP 77

Query: 69  KAERTR----------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
           + E                   + + +KP G+V   +      TV + L      +    
Sbjct: 78  EPEDAAIVAEDIPLDIVYEDADVIVINKPRGMVVHPAPGHSSGTVVNALMYHCKDLSGIN 137

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV-------- 153
                  V R+D +T GLL+   +      L   L      R Y    HG +        
Sbjct: 138 GVLRPGIVHRIDKDTSGLLMAAKNDLAHVSLAEQLKDHSVSRKYIALVHGNLPHDQGTID 197

Query: 154 -----DQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                DQ+   L    +  +   +       L+        V + L  G+  +I+   ++
Sbjct: 198 APIGRDQNDRKLFT--VTDRNSKHAVTHFAVLERIADDYTIVELQLETGRTHQIRVHMKY 255

Query: 208 FNWK 211
             + 
Sbjct: 256 IGYP 259


>gi|317154041|ref|YP_004122089.1| RluA family pseudouridine synthase [Desulfovibrio aespoeensis
           Aspo-2]
 gi|316944292|gb|ADU63343.1| pseudouridine synthase, RluA family [Desulfovibrio aespoeensis
           Aspo-2]
          Length = 596

 Score = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 79/243 (32%), Gaps = 47/243 (19%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVN-------------VMST 57
           R+ K     +A  G+ SR  V+  I      V+G ++ R                 V  +
Sbjct: 30  RLDKFWARELADEGV-SRGRVQEWIESGLALVDGEVVTRGKHKLAGRETLRIGDAGVAPS 88

Query: 58  DH--IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
           D     V G      E   + +  K  GL T  +  +   T+ ++L   +          
Sbjct: 89  DDAAQAVPGELEVVFEDAHVAVIDKRAGLTTHPAPGEPGPTLVNHLLHRWPDVASDISGM 148

Query: 107 ---RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL--- 158
              R   V RLD +T GL+++  T    L    +    +  +VY     G+  Q      
Sbjct: 149 DRQRPGIVHRLDKDTSGLMVVALTEGDRLRLAADFAGRRVRKVYLAVVLGRPAQPAGTID 208

Query: 159 --------NLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                      +  +V +G      D +V     +G  + V V +  G+  +I+      
Sbjct: 209 APMGRHPSQKTRMAVVARGGREAVSDYRVLWTGPRGLASLVAVRIHTGRTHQIRVHMAHI 268

Query: 209 NWK 211
              
Sbjct: 269 GHP 271


>gi|47779342|gb|AAT38571.1| predicted ribosomal large subunit pseudouridine synthase D
           [uncultured gamma proteobacterium eBACHOT4E07]
          Length = 311

 Score = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 86/236 (36%), Gaps = 38/236 (16%)

Query: 1   MKDKNIVQENFTPQRVSK---VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+    + E+ + +R  K   +I      SR ++++ I + RV +N  +       V + 
Sbjct: 1   MEVTKKITEDLSMERFDKACALIFN--DYSRSQLKKWIIEGRVLLNNEIA-SPKEIVTTD 57

Query: 58  DHIEVD---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRST----VFDN 100
           D I ++      ++            E     + +KP  LV          T    +   
Sbjct: 58  DEISLNPIFKKIIQWEPENIDFEVVHEDENFLIINKPSKLVIHPGSGCDSGTLANGLLFK 117

Query: 101 LP--SIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----- 151
            P  +   R   V RLD +T G+LL+  T       V  L   +  ++Y+    G     
Sbjct: 118 YPELNKMPRAGIVHRLDKDTSGILLVARTEKFRNYFVSLLQERKVKKIYKAVVVGKIIGS 177

Query: 152 -----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 + +DK N +K  I   G       V L    G+ + V V +  G+  +I+
Sbjct: 178 FQINEPIGRDKTNRIKMSIRSDG-KEAISFVKLHESLGNYSVVDVSIETGRTHQIR 232


>gi|310766696|gb|ADP11646.1| 23S rRNA pseudouridine synthase D [Erwinia sp. Ejp617]
          Length = 325

 Score = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 82/234 (35%), Gaps = 33/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K    V E+    R+ + +A      SR  ++  I  + + VNG+++++    V+  + 
Sbjct: 5   VKLNATVAESQLGHRLDQALAELFPDYSRSRIKEWILNRHITVNGVIIDKPKEKVLGGEQ 64

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +D             +PL    E   + + +KP  LV      +   TV + L   F 
Sbjct: 65  ISIDAEIEEEARWEAQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHFP 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------R 148
                 R   V RLD +T GL+++         L   L   +  R Y             
Sbjct: 125 AIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDSLQRREITREYEAVAIGRMTAGGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 185 VDQPISRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>gi|187250787|ref|YP_001875269.1| pseudouridine synthase [Elusimicrobium minutum Pei191]
 gi|186970947|gb|ACC97932.1| Pseudouridine synthase [Elusimicrobium minutum Pei191]
          Length = 299

 Score = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 72/187 (38%), Gaps = 31/187 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K  +  + T  R+   ++      SR  ++ +I Q +V VNG    + A  +   D+
Sbjct: 1   MSNKETLTFSGTSARLDLFLSENKPDYSRGLIQNLIKQGKVTVNGK-ERKPAWPLAEGDN 59

Query: 60  IEVD--------G-VPLRKAERTRLWLYHKPIGLVTTHSDPD----------GRSTVFDN 100
           +E++        G   L   E   +++ +KP G++     P           G  T+   
Sbjct: 60  VEIEWPSVENKTGLKDLIIFEDKNMFVINKPSGMLVHPQSPVWEENPAAAFIGEETLVSL 119

Query: 101 L----PSIFS----RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH 150
           +    P  F     R   V RLD +T G++++  +      +     + +  + Y     
Sbjct: 120 ILANPPKNFEKGITRAGLVHRLDKDTSGVMIIAKNSKTQDAMVEMFANREMHKTYEAIVC 179

Query: 151 GQVDQDK 157
           G V  DK
Sbjct: 180 GVVPDDK 186


>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 = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 3/68 (4%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAER 72
          QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E 
Sbjct: 5  QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE- 63

Query: 73 TRLWLYHK 80
            ++L  K
Sbjct: 64 -YIYLIKK 70


>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 = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 86/248 (34%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++  + V +     R+ K ++      SR  ++ +I ++ +KVN  L++     + + D
Sbjct: 1   MEENILKVSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKN-NYKLKACD 59

Query: 59  HI----------EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I          +V+   +      E   + + +K  G+V   +  +   T+ + L    
Sbjct: 60  EIVITMPEAETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--- 151
           + + S         V R+D +T G+L++  +      L   L      R Y     G   
Sbjct: 120 TDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFK 179

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK N LK  I   G         L+        +   L  G+  +I+ 
Sbjct: 180 NDSGIIDKPLGRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
                   
Sbjct: 240 HMASLGHP 247


>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 = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 47/270 (17%), Positives = 87/270 (32%), Gaps = 51/270 (18%)

Query: 3   DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE-----------RA 50
           ++  V+E     R+   +A +    SR  ++++I+ + V VNG                 
Sbjct: 5   NRYTVEEEDEQTRLDVFLAGQNPELSRARIQKLISLELVTVNGRPARASHRVRGGDCVEL 64

Query: 51  AVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
            V    T  IE + +PL    E   + + +KP GLV   +      T+ + L      + 
Sbjct: 65  KVPDPETPRIEPEAIPLEVCFEDPDVLVVNKPRGLVVHPAVGHYSGTLVNALLHHCRDLS 124

Query: 110 S---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD-- 156
                     V RLD +T GLL++  +      L   L     LR Y    HG+  ++  
Sbjct: 125 GINGILRPGIVHRLDRDTSGLLMVAKNDAAHLALAGQLKDRAVLRRYTALVHGRPRRETG 184

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +   +  +          +  +    + + + L  G+  +I+   
Sbjct: 185 TVDAPIGRHPRDRQRMA--VTPRSGRAARTHYRVVRRFDKFSLLELTLDTGRTHQIRVHM 242

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
                 +             G L  G  R 
Sbjct: 243 AHVGHPLV------------GDLKYGHARP 260


>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 = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/180 (22%), Positives = 62/180 (34%), Gaps = 30/180 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +   +   QR+  ++A  G+  SR    R +    V VNG  + +    V   D I    
Sbjct: 8   VAAPDDAGQRLDALLAARGLYPSRSAAARAVDDGLVFVNGAEVAK-KHPVAPGDTIVYQV 66

Query: 64  ----------GVPLR---KAERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFS--- 106
                     G P+    + E   L +  K +GLV   S D D  + V   +    +   
Sbjct: 67  EEPVEPGPLRGQPIDLDIRFEDEDLIVLSKQVGLVCHPSVDHDDGTLVNALIYHCGAENL 126

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R+  V RLD +T GL+L   +      L          R Y    HG +  D
Sbjct: 127 CNVQGEDDRLGIVHRLDRDTSGLMLAAKNDETGYALMSDIRDRAVDRRYLALVHGVIAHD 186


>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 = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 82/236 (34%), Gaps = 35/236 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  + I+  +   +R+ K + +     SR  ++ +I++  +KV+G  ++     +   + 
Sbjct: 1   MDTQKIIYTSPKSERIDKFLQQELTDVSRTNIQNLISEGYIKVDGNNIKT-NYKLKDGNV 59

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I ++             +P+    E   L + +K  G+V   S      T+ + L     
Sbjct: 60  ITIEYKEPEELDVVKQDIPIDIVYEDDDLIIVNKAKGMVVHPSVGHKDGTLVNALLFHSE 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   + +    R Y    HG +  D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLIVAKNDKAHVKLSEMIANKDVKRKYYALVHGSIKHD 179

Query: 157 KL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          K+  VI           +  +      +   L  G+  +I+
Sbjct: 180 YGTIDAPIARNPKERKEMAVIDEGKLSITHFKVVDRFEKYTLIECELETGRTHQIR 235


>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 = 76.4 bits (187), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 77/238 (32%), Gaps = 41/238 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +V      +R  + IA A      SR +++R I+  ++ ++  +       + S  HI  
Sbjct: 44  MVSPQAAGERADRFIAAALAGDAISRGKIQRAISDGQLLIDNTVCTSPKTKLKSGQHIVF 103

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       +G          + + +KP GL    +      T+   L   F  + +
Sbjct: 104 SMEAPAACVSPEEGELEVLYRDAHMLVINKPAGLTVHPAPSCPEGTLVHRLLHHFPELEA 163

Query: 111 --------VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN- 159
                   V R+D +T GLLL+  T    LA        +  + Y     G  + D    
Sbjct: 164 QEGFRPGIVHRIDKDTSGLLLIALTEKARLALSDAFAGRRIHKEYLALVKGIPEGDSGEI 223

Query: 160 ----------LLKKGIVIQG-ICYGDMQVTLDTQKGSN----AWVTVGLREGKNREIK 202
                       +  +V  G       +V L    G        V V +  G+  +I+
Sbjct: 224 DAPVGRHPTHKTRMAVVRGGREALSTWRVLLADPHGGGGTGWTLVAVRIHTGRTHQIR 281


>gi|302335822|ref|YP_003801029.1| pseudouridine synthase, RluA family [Olsenella uli DSM 7084]
 gi|301319662|gb|ADK68149.1| pseudouridine synthase, RluA family [Olsenella uli DSM 7084]
          Length = 342

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 78/257 (30%), Gaps = 50/257 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V  +    R+   +A      SR    R+I +  V +N       +  V   D I+   
Sbjct: 9   LVGPDADGMRLDAFLATVDGCPSRSACARLIGEGAVTINSTPATSKSECVCLGDRIQACV 68

Query: 62  -------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---- 104
                         D     + E   L +  K  GLV   S      T+ + L +     
Sbjct: 69  PVAQGGPGALSPNPDIELDVRFEDEHLLVLSKQAGLVCHPSPGHVDDTLANALVAHCGYG 128

Query: 105 -------FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
                    R   V RLD++T GL++      + R L   +      R Y V   G V  
Sbjct: 129 HLGMLQGDDRPGIVHRLDMDTSGLMVAAKSDEVQRALQDLIRLRALDRRYVVLVQGYVAP 188

Query: 156 DK-----------LNLLKKGIVIQGICYGDM---QVTLDTQKGSN-----AWVTVGLREG 196
           D             + L+  +        +      TL+  + S      + +   L  G
Sbjct: 189 DAGTVTTGIARSTRDRLRMAVS-DDPMAREAITTFATLERFEASRSDEGYSLLECHLYTG 247

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+        +V 
Sbjct: 248 RTHQIRVHMRHIGHQVV 264


>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 = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 86/254 (33%), Gaps = 54/254 (21%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMST 57
             K +V       R+   +++        SR  ++ +I  + V+VNG   +++   + S 
Sbjct: 3   SKKFLVCSEEENMRLDVFLSK---CFQDKSRSYIQNVIEYKLVEVNGK-AKKSNYKIKSG 58

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D+IE+            + +PL    E   + + +KP G++   +      T+ + L + 
Sbjct: 59  DNIEITIPDPVNLNIQSEDIPLDILYEDKDVIVVNKPQGMIVHPAPGVYEGTLVNALLNH 118

Query: 105 FSRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
              +           V R+D +T G+L++  +      L   L      R Y     G V
Sbjct: 119 CRDLSGINGVTRPGIVHRIDKDTSGILVVAKNDNSHNKLAKQLKDHSMTREYIALVEGVV 178

Query: 154 DQDKLNLLKKGIVIQGICYGDMQV----------------TLDTQKGSNAWVTVGLREGK 197
                  L +G V + I                        +  +  +N  +   L  G+
Sbjct: 179 ------KLDEGTVDEPIARHPKDKIKMAVCVNGKRAITHYKVIKRFKNNTLIKCILETGR 232

Query: 198 NREIKKVFEFFNWK 211
             +I+    +    
Sbjct: 233 THQIRVHMAYIGHP 246


>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 = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 85/232 (36%), Gaps = 37/232 (15%)

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 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                 V RLD +T GL+++         L   L   +  R Y     G++    +  ++
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMTAGGM--VE 186

Query: 163 KGIVIQGICYGDMQVTLDTQKGS------------NAWVTVGLREGKNREIK 202
           KGI  +      +    +T K +            +  + + L  G+  +I+
Sbjct: 187 KGIS-RHATKRTLMAVNETGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>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 = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 46/263 (17%), Positives = 88/263 (33%), Gaps = 42/263 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V  +   +R+   +A   G+  +R  ++R+I   RV VNG      +  +   + + ++
Sbjct: 18  VVPGSAAGERLDVFLAEQDGLDLTRSAIQRLIRSHRVWVNGRTAR-PSRRLEPGEEVVIE 76

Query: 64  -------GVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                  GV           E   + + +KP G V   +    + T+ + L + +  +  
Sbjct: 77  LPEPAPSGVVPEALPLDVVYEDPDVVVLNKPRGWVVHPAPGHPQGTLANALLARYPEMEG 136

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG-------- 151
           VG         RLD +T GLL++       R L     +    R Y     G        
Sbjct: 137 VGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQIKERRVHREYLALVRGWPEVREGT 196

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +   +  +  ++  G         +  Q G    +   L  G+  +I+    F 
Sbjct: 197 VEAPIGRHPADRTRMTVLTTGGRPARTHFAVVEQVGRYTLLRCWLDTGRTHQIRVHLAFI 256

Query: 209 NWKV----NRLIRISYGPFQLGT 227
              V        R + G   L  
Sbjct: 257 GLPVAGDPVYGGRRAQGELGLEG 279


>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 = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 86/248 (34%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++  + V +     R+ K ++      SR  ++ +I ++ +KVN  L++     + + D
Sbjct: 1   MEENILKVSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNDKLIKS-NYKLKACD 59

Query: 59  HI----------EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I          +V+   +      E   + + +K  G+V   +  +   T+ + L    
Sbjct: 60  EIVITMPEVETLKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--- 151
           + + S         V R+D +T G+L++  +      L   L      R Y     G   
Sbjct: 120 TDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFK 179

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK N LK  I   G         L+        +   L  G+  +I+ 
Sbjct: 180 NDSGVIDKPLGRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
                   
Sbjct: 240 HMASLGHP 247


>gi|319403704|emb|CBI77289.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           rochalimae ATCC BAA-1498]
          Length = 333

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 38/184 (20%), Positives = 71/184 (38%), Gaps = 31/184 (16%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++I  EN   QR+ + +A+   G  SR  ++ +I +  +K++G L++     + S   IE
Sbjct: 3   QHITNENACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKIDGQLIKEPKTKLKSNQIIE 62

Query: 62  V----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           +           G  L      E   + + +KP GLV    + +   T+ + L       
Sbjct: 63  LTIPTPNEAQPQGEALVLDILFEDNHIIVINKPAGLVVHPGNGNWTGTLVNGLIYHCRDS 122

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQ 152
                   R   V RLD +T G++++  +    R L        R       Y     G 
Sbjct: 123 LSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADHGRTSALDRRYHAVIWGS 182

Query: 153 VDQD 156
            +++
Sbjct: 183 PNRN 186


>gi|315149952|gb|EFT93968.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0012]
          Length = 297

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAKAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 91/236 (38%), Gaps = 36/236 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K   I++E +  QR+   +A+     SR  ++ +I +++V VNG  ++     + S D++
Sbjct: 3   KYNFIIEEEYENQRIDVYLAQEFENISRSHIQDLIGKKKVFVNGKAVKS-NYKLKSRDNV 61

Query: 61  EV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           E    D   L+            E   + + +K  G+V   +  +   T+ + L      
Sbjct: 62  EFEIPDNEELKIEAENIPLDIVYEDRDIVVVNKAQGMVVHPAPGNYNGTLVNALLYHCKD 121

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD 156
           +           V R+D +T G+L++  +    + L     +    RVYR    G + +D
Sbjct: 122 LSGINGVLRPGIVHRIDKDTSGILVVAKNDAAHKNLANQLKEHSMNRVYRAVVEGIIKED 181

Query: 157 ----KLNLLKKGIV------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  L +  +       ++G         +  +  ++  +   L  G+  +I+
Sbjct: 182 EGTVDKPLARHPVERVKIAVVKGGRNAVTHYKVLERYRNSTLIECKLETGRTHQIR 237


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 81/244 (33%), 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  -----------DGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL      R  +  +KP GLV      +   T+ +          +
Sbjct: 92  DRPRYENEVIPEDIPLNIVYEDRCLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 151

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK- 157
             +    V  V R+D +T GLL++         L     +    R YR    G V+QD+ 
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTHLGNQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TVVGNIGRNPKDRMQMAVLSDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>gi|312900037|ref|ZP_07759354.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|311292794|gb|EFQ71350.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
          Length = 297

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAKAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 44/258 (17%), Positives = 81/258 (31%), Gaps = 52/258 (20%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
               + T +R+ + +A A     SR  V+ +IA+  V ++G     A   +     I + 
Sbjct: 5   TTDSDATGKRLDQWLAAALGPELSRSRVQSLIAEGHVTIDGAPAREAKQKLREGMTIAIV 64

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                      + +PL    E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LPEPEPAEPIAENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG--- 151
                 R   V RLD +T G++++  +    R L        R       Y     G   
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRSHRHLSEQFADHGRTGDLERAYLALVWGMTE 184

Query: 152 --------QVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQKGSNAWVTVGL 193
                    + +   +  K+ +V          I      +    L+      + V   L
Sbjct: 185 RPQGFIDAHLGRSHRDRTKQAVVNEEREDARHAITHYVTVEKFAPLEDATALASLVECRL 244

Query: 194 REGKNREIKKVFEFFNWK 211
             G+  +I+         
Sbjct: 245 ETGRTHQIRVHMAHIGHP 262


>gi|327441137|dbj|BAK17502.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 300

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 83/244 (34%), Gaps = 50/244 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M    +  E F  +R+ K +++     SR ++   + ++R+ VNG  ++ A   V   D 
Sbjct: 1   MTVVTLTIEEFAGERIDKALSQMEESWSRSQISNWLDEERILVNGAAVK-AKYKVKQGDV 59

Query: 60  IEV------DGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IEV      D   + +        E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEVTVPEVEDLEIIPEDLNLEIVYEDADVLVVNKPRGMVVHPAPGHATGTLVNGLMHHCK 119

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
            +           V R+D +T GLL++  +      L          R Y    HG +  
Sbjct: 120 DLSGINGVARPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEKSVTRKYTALVHGHIAH 179

Query: 156 DKLNLLKKGIVIQ-----GICYGDMQVTLDTQKGSNAWV-------TVGLRE-----GKN 198
           +      KG  I             Q  +D  K +              L E     G+ 
Sbjct: 180 E------KG-TIDAPIGRDQKDRQKQAVVDKGKHAVTHFQVIERFGEFTLVECRLETGRT 232

Query: 199 REIK 202
            +I+
Sbjct: 233 HQIR 236


>gi|85057870|ref|YP_456786.1| ribosomal large subunit pseudouridine synthase D [Aster yellows
           witches'-broom phytoplasma AYWB]
 gi|84789975|gb|ABC65707.1| ribosomal large subunit pseudouridine synthase D [Aster yellows
           witches'-broom phytoplasma AYWB]
          Length = 306

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 87/244 (35%), Gaps = 49/244 (20%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M +K   ++  +   QR+   ++     ++ + +++I  Q+V VN     + +  +   D
Sbjct: 1   MNEKKEFLISASEAFQRLDHFLSAHINLNKSQCQKLILAQQVLVN-TKSSKKSYLLKPQD 59

Query: 59  HIEV------DGVPLRKA---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            I V      + + L+           E   L + +KP  LV   S    ++T+ + L  
Sbjct: 60  LITVIIPQTHESINLQTPQNLNLDIIYEDPYLAVINKPANLVVHPSLSFQKTTLVNGLLH 119

Query: 104 IF--------SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            F         R   V RLD NT GLL++  TND      +     +  ++Y     G +
Sbjct: 120 QFNTLSHIDTQRPGIVHRLDKNTTGLLIVAKTNDVSDKLQIAFQQRKITKIYWALIEGFL 179

Query: 154 DQDKLNLLKKG----------IVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKN 198
           +   +  L  G          ++  G        TL             L E     G+ 
Sbjct: 180 EDKGIIKLPIGRNNHNRLKMQVMPDGKTAVTHFKTLQRFS------HFSLMECNLETGRT 233

Query: 199 REIK 202
            +++
Sbjct: 234 HQLR 237


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 80/241 (33%), Gaps = 36/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I+ E    +R+ K ++      SR + ++MI    + VNG    +        D IE+  
Sbjct: 7   IINEEVAGERLDKAVSLLNEELSRSQAQQMIKDGHILVNGQ-GTKTNYKCSIDDKIEISF 65

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            +   L             E   + + +KP G+V   +      T+ + L +    +   
Sbjct: 66  PEPEELDVLPEEMDLDIYYEDGDVLVVNKPKGMVVHPAPGHASGTLVNGLMAHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD---- 156
                   V R+D +T GLL++  +      L          R Y+   HG +  D    
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDMAHESLVNQLVEKTVTRKYQAIVHGTIPHDYGTV 185

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +   V+ G  +      +  +      V   L  G+  +I+   ++  +
Sbjct: 186 DAPLGRDPKDRQSMTVVDGGKHAVTHFHVIHRYKDFTHVECQLETGRTHQIRVHMKYIGY 245

Query: 211 K 211
            
Sbjct: 246 P 246


>gi|319406711|emb|CBI80344.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp.
           1-1C]
          Length = 333

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 70/184 (38%), Gaps = 31/184 (16%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++I  EN   QR+ + +A+   G  SR  ++ +I +  +K++G L++     + S   IE
Sbjct: 3   QHITSENACGQRIDQWLAKQYKGELSRSRLQTLIREGYLKIDGQLIKEPKTKLKSNQIIE 62

Query: 62  V----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           +           G  +      E   + + +KP GLV    + +   T+ + L       
Sbjct: 63  LTIPTPNDAQPQGEAIALDILFEDNHIIVINKPAGLVVHPGNGNWTGTLVNGLIYHCRDS 122

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQ 152
                   R   V RLD +T G++++       R L        R       Y     G 
Sbjct: 123 LSGIGGIKRPGIVHRLDKDTSGVMVIAKSDFAHRNLNAQFADHGRTSPLDRRYHAVIWGS 182

Query: 153 VDQD 156
            +++
Sbjct: 183 PNRN 186


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 51/313 (16%), Positives = 105/313 (33%), Gaps = 51/313 (16%)

Query: 6   IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V  +   +R+   +A   +   +R  ++R+I  Q+++VNG      +  +   + + V+
Sbjct: 18  VVPASAAGERLDVFLAGQDSLELTRSAIQRLIRSQQIRVNGRPAR-PSRRLEPGEEVVVE 76

Query: 64  -------GVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                  GV           E   + + +KP G V   +    + T+ + L + +  +  
Sbjct: 77  LPAPAPSGVVAEPLPLDVVYEDADVVVLNKPRGWVVHPAPGHPQGTLANALLARYPEMEG 136

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-------- 151
           VG         RLD +T GLL++       R L  +L      R Y     G        
Sbjct: 137 VGGPGRPGIVHRLDRDTTGLLVVARSPLAYRELVRQLKERGVHREYLALVRGSPEVREGT 196

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + +  ++  +  ++  G         +  + G    +   L  G+  +I+    F 
Sbjct: 197 VDAPIGRHPVDRKRMAVLPGGGRPARTHFEVVERAGRYTLLRCWLDTGRTHQIRVHLAFI 256

Query: 209 NWKV----NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
              V        R + G   L      +TR            PH  +   ++   P  + 
Sbjct: 257 GLPVAGDPVYGGRRAEGELGLEGQALHATR---------LAFPHPRDGRPMDFTVPPPAD 307

Query: 265 ETLVRDRPNIISE 277
                +R    ++
Sbjct: 308 FQRALERARQGAQ 320


>gi|227872363|ref|ZP_03990714.1| pseudouridylate synthase [Oribacterium sinus F0268]
 gi|227841792|gb|EEJ52071.1| pseudouridylate synthase [Oribacterium sinus F0268]
          Length = 303

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 85/243 (34%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V +    QR+ K ++       SR  + + I +  V VNG   + A++ V + D I+   
Sbjct: 5   VAKEEEGQRLDKYLSEQKDHDFSRSYLGKCIQEGCVSVNGEKAK-ASLKVKAGDRIDFDI 63

Query: 63  ----DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------- 101
               D   L +A       E   L + +K  G+V   +      T+ + +          
Sbjct: 64  PEQKDPEVLPEAIPLDIVYEDDDLLVVNKERGMVVHPAAGHYSGTLVNAVLAHAGSSLSS 123

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK-- 157
            +  +R   V R+D +T GLLL+  +    + L   L      R Y     G++ ++   
Sbjct: 124 INGVNRPGIVHRIDKDTTGLLLICKNDLSHQSLAKQLEEHSITRRYHALVFGKIKEEDGI 183

Query: 158 ---------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                     +  K+ I  +          +  +   +  V   L  G+  +I+   +  
Sbjct: 184 ISAPIGRDEKDRKKQAISYKHGKEALTHYKVLERFSDSTLVECRLETGRTHQIRVHMKSI 243

Query: 209 NWK 211
              
Sbjct: 244 GHP 246


>gi|328724994|ref|XP_001952731.2| PREDICTED: hypothetical protein LOC100168337, partial
           [Acyrthosiphon pisum]
          Length = 1131

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 37/181 (20%), Positives = 72/181 (39%), Gaps = 28/181 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILL-----ERAAVNVMS 56
           +  I  EN    R+ K++       SR +++  I    V+VNG ++      +    +++
Sbjct: 477 EFKIETENEIGVRIDKLLPDLNPDWSRNQIQDWIKLGLVEVNGKVIKANYKTKLNDVIVA 536

Query: 57  TDHI--EVD------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           T+ +  EVD      G+ +   ++    +Y KP G+V   +      T+ + L  +   +
Sbjct: 537 TEKVIEEVDIVAEDLGIEVYYEDKDVAVVY-KPKGMVVHPAPGHYTGTLVNGLMYVIKDL 595

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D +T GLL++  +  +A       L      R Y    HG +  +
Sbjct: 596 SGINGEIRPGIVHRIDKDTSGLLMIAKN-DIAHRGLVEQLVDKTVTREYTALVHGNIPHE 654

Query: 157 K 157
            
Sbjct: 655 F 655


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 89/237 (37%), Gaps = 31/237 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I +QRV++NG ++++    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGKMVDKPKEKVLGGESVAIDA 69

Query: 64  ---------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                      P+      E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  LIEEDARWEAQPISLDIVYEDEDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKL 158
                V RLD +T GL+++         L   L + +  R Y     G +      ++ +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVEEPI 189

Query: 159 NLL---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  + +  +    +    +     ++  + + L  G+  +I+      N  
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHP 246


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 91/251 (36%), Gaps = 40/251 (15%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++ + IV E    QR+ K I+      SR  V++++ +  V VNG   + A   +   D
Sbjct: 1   MREIDVIVTEEEAFQRIDKYISEKEDDLSRSRVQQLLQEGIVCVNGNACK-ANYKIKPKD 59

Query: 59  HIE---VDGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           HI     D + +           + E   + + +KP G+V   +  +   T+ + L    
Sbjct: 60  HITAVFCDEIEMEAKPEQMDLDIRYEDHDVIVINKPKGMVVHPAVGNQTGTLVNGLLYHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
             +           V R+D +T GLL++  +      L   L +    R+Y    HG + 
Sbjct: 120 KDLSGINGVLRPGIVHRIDKDTTGLLIVAKNDKAHTALSKQLQNKTVNRLYYALVHGVI- 178

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
           +     +   I         M VT    K +     V        L E     G+  +I+
Sbjct: 179 EHDFGTIDAPIGRDVKDRQKMAVTATNAKDARTHFKVIERFAHYTLVECRLETGRTHQIR 238

Query: 203 KVFEFFNWKVN 213
              ++    V 
Sbjct: 239 VHMQYIKHPVV 249


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 86/248 (34%), Gaps = 38/248 (15%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++  + V +     R+ K ++      SR  ++ +I ++ +KVN  L++     + + D
Sbjct: 1   MEENILKVSKENEGIRIDKYLSEMLNGKSRSFIQGLIEKESIKVNNKLIKS-NYKLKACD 59

Query: 59  HI----------EVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I          +V+   +      E   + + +K  G+V   +  +   T+ + L    
Sbjct: 60  EIVITMPEAEILKVESEDIDLDILYEDKDVIVVNKEQGMVVHPAPGNYNGTLVNALLFHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--- 151
           + + S         V R+D +T G+L++  +      L   L      R Y     G   
Sbjct: 120 TDLSSINGVIRPGIVHRIDKDTSGVLVIAKNDESHNKLAAQLKDHSMNREYYALVEGRFK 179

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + +DK N LK  I   G         L+        +   L  G+  +I+ 
Sbjct: 180 NDSGVIDKPLGRDKKNRLKIAITEDGRRAITHYEVLERYDTGCTLIKCKLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
                   
Sbjct: 240 HMASLGHP 247


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQMAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 37/214 (17%), Positives = 80/214 (37%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRKA-ERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +    D L     R  +  + RLD +T G+++   +  +
Sbjct: 102 VINKREGLLSVSTDRIKERTAYRILSDYLKECDPRNKIFVLHRLDRDTSGIMMFAKNQKV 161

Query: 131 ARVLELPSTQ--WLRVYRVRFHGQVDQD-KL--------NLLKKGIVIQG-ICYGDMQVT 178
              L+   ++    R Y     G+ ++D  L          ++  +   G       +  
Sbjct: 162 KEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVTQDGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L       + V + L  G+  +I+   +     +
Sbjct: 222 LLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPI 255


>gi|153951567|ref|YP_001397630.1| ribosomal large subunit pseudouridine synthase A [Campylobacter
           jejuni subsp. doylei 269.97]
 gi|152939013|gb|ABS43754.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. doylei 269.97]
          Length = 322

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D I              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISITSLKLYDEIKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDILYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ V   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIR 238


>gi|323969764|gb|EGB65046.1| S4 domain-containing protein [Escherichia coli TA007]
          Length = 56

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +  R++K I+ +GI SRRE +R I Q  V +NG         V   D ++V+G
Sbjct: 3  PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGKRAT-IGDQVKPGDVVKVNG 56


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 83/242 (34%), Gaps = 54/242 (22%)

Query: 14  QRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +R+ K +   GI    SR +V++ I    V VNG  ++     V   D I V        
Sbjct: 16  ERIDKFV--TGINNEWSRSQVQQWIKDDVVTVNGKAVK-VNYKVKEEDEITVTIPEPEAL 72

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
                D       E   + + +KP G+V   +      T+ + L    + +         
Sbjct: 73  DIQPEDLNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLSGINGVMRP 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D +T GLL++  +      L     +    R Y+   HG +  D      KG  
Sbjct: 133 GIVHRIDKDTSGLLMVAKNDMAHESLVNQLVAKTVTRRYKAIVHGVIPHD------KG-T 185

Query: 167 IQ---GICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFN 209
           I    G    + Q     + G NA      +       L E     G+  +I+   ++  
Sbjct: 186 IDAPIGRDKKERQSMTVDENGKNAVTHFQVLERFKDFTLVECRLETGRTHQIRVHMKYIG 245

Query: 210 WK 211
           + 
Sbjct: 246 YP 247


>gi|311029948|ref|ZP_07708038.1| pseudouridylate synthase [Bacillus sp. m3-13]
          Length = 204

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 35/204 (17%), Positives = 74/204 (36%), Gaps = 35/204 (17%)

Query: 7   VQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + E+    R+ KV++      SR +V++ I + ++ VNG    +        D+I V   
Sbjct: 9   IDESQKNDRIDKVLSTQNEEWSRSQVQQWIKEGQILVNGEK-TKPNYKCSVGDNITVTIP 67

Query: 63  -----DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                D VP         E   + + +KP G+V   +      T+ + L +  + +    
Sbjct: 68  EPEALDVVPEEMDLDIYYEDADVIVVNKPRGMVVHPAVGHVTGTLVNGLMAHCNDLSGIN 127

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                  V R+D +T GLL++  +               ++        V +     +  
Sbjct: 128 GVLRPGIVHRIDKDTSGLLMVAKN----------DFAHEKLVNQLVAKTVTRKY-QAIVH 176

Query: 164 GIVIQGICYGDMQVTLDTQKGSNA 187
           G++   +   D  +  D ++  + 
Sbjct: 177 GVIAHDVGTVDAPIGRDKKESPSH 200


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  +HI +D 
Sbjct: 10  TVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGNIGDKPKEKVLGGEHIAIDV 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFQPQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRI-HTRLRLRLETGRTHQIR 237


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 78/246 (31%), Gaps = 41/246 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRV-KVNGILLERAAVNVMSTDH----- 59
            V    + +R+  V+A A   SR  ++ ++ +  V    G ++ +A+  V   +      
Sbjct: 14  TVSTEASGKRLDAVLAAACELSRSRIQTLLREGHVRTAGGSVISQASARVWEGERYLLTL 73

Query: 60  -------IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                  +E + +PL    E   L + +KP G+V   S      T+   L          
Sbjct: 74  PPVKPLILEPEDLPLDILFEDEHLIVLNKPAGIVVHPSHGHDHGTLVHALLHHCKTLPGI 133

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD------ 154
               R   V RLD +T G L++     + + L          R Y     G         
Sbjct: 134 NGVERPGIVHRLDKDTSGSLVIAKSEVVHQRLSEMFAEHNLNRQYIAWCRGVPSWRVKCI 193

Query: 155 -------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                    +   +    V            ++   G  + + + L  G+  +I+     
Sbjct: 194 ELPIGRHPHQRQKMA---VTDSGRESITDAAVEHIFGPFSQMRLTLHTGRTHQIRVHMAH 250

Query: 208 FNWKVN 213
            N  V 
Sbjct: 251 ENLPVL 256


>gi|257081816|ref|ZP_05576177.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis E1Sol]
 gi|256989846|gb|EEU77148.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis E1Sol]
          Length = 297

 Score = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 84/244 (34%), 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  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      +   T+ +          +
Sbjct: 93  DRPRYENEVIPEDIPLNIVYEDKYLMIVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 152

Query: 101 LPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
             +    V  V R+D +T GLL++  T D      ++  +    R YR    G V+QD+ 
Sbjct: 153 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGIVEQDEG 212

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 213 TIIGNIGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMK 272

Query: 207 FFNW 210
               
Sbjct: 273 HIGH 276


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 66/170 (38%), Gaps = 26/170 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
           +P+R+ + +       SR +++++I   RV ++G   +     +   + + VD       
Sbjct: 14  SPERLDRFLVEQLPELSRSQLKKLIDDGRVLLDGAAAK-PGSKLKGGETLTVDVPDPSPA 72

Query: 64  -----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
                 +PL    E   L +  KP G+V   +    + T+ + L      +  +G     
Sbjct: 73  EAVSEDIPLVILYEDRHLIVIDKPPGMVVHPAPGHYQGTLVNALLHHCQDLSGIGGELRP 132

Query: 113 ----RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
               RLD +T G+++   T+    +   +  +    R Y    HG +  D
Sbjct: 133 GIVHRLDKDTSGVMVATKTDSAHQSLAAQFKAHSITRRYIALIHGVLTGD 182


>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 = 76.0 bits (186), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 92/249 (36%), Gaps = 39/249 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K  ++      R+  V+A+  +  SR  +   +    + VN   ++R +  V S D 
Sbjct: 1   MTEKITLEITNETGRIDAVLAKKSLPYSRTVLAEWLQDGHIVVNQTQVKR-SYKVNSGDL 59

Query: 60  IEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +            + +PL    E   L + +KP G+V   +      T+ + L     
Sbjct: 60  ITILPPAVQNTEIIAENMPLDIIYEDNDLLVVNKPQGMVVHPAAGHTSGTLVNALLYHAP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    + L   L + +  R+Y     G+  +D
Sbjct: 120 LSTINGSFRPGIVHRIDRDTSGLLMVAKNDKAHQALSEQLKAHKNERIYYALVRGEFSED 179

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KV 204
                      K++  K+ +   G         + T+      + + L  G+  +I+  +
Sbjct: 180 SGTINAPLARHKVDRKKQAVQ-AGGREAITHFEVVTRYVGYTLLKIRLETGRTHQIRVHM 238

Query: 205 FEFFNWKVN 213
             +    + 
Sbjct: 239 T-YIGHPII 246


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 80/236 (33%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A      SR  ++  + + ++ VNG ++ +  + VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGEVITKPRMKVMGGEVIVVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V         STV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADSTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G++ + I     + TL +                    +  + + L  G+  +I+
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIR 237


>gi|57238152|ref|YP_179402.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni RM1221]
 gi|57166956|gb|AAW35735.1| ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Campylobacter jejuni RM1221]
 gi|315058713|gb|ADT73042.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni subsp. jejuni S3]
          Length = 322

 Score = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D I              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDVLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ V   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIR 238


>gi|86150741|ref|ZP_01068957.1| RluA [Campylobacter jejuni subsp. jejuni 260.94]
 gi|205356297|ref|ZP_03223063.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315124736|ref|YP_004066740.1| RluA [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
 gi|85841911|gb|EAQ59157.1| RluA [Campylobacter jejuni subsp. jejuni 260.94]
 gi|205345902|gb|EDZ32539.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8421]
 gi|315018458|gb|ADT66551.1| RluA [Campylobacter jejuni subsp. jejuni ICDCCJ07001]
          Length = 322

 Score = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D I              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDIISIASLKLCNEIKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDVLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGSILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ V   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDKENKFSKNAKSAFINVVKTENLTLMAAKLFTGRTHQIR 238


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 34/169 (20%), Positives = 58/169 (34%), Gaps = 30/169 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R+ +V+A R    SR  ++ +I   RV + G  +   A +    + I +D  P       
Sbjct: 21  RLDRVLAARCPELSRSRLKALILDGRVAIAGNPVRDPAYHASPGETITIDVPPPAPAEPA 80

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
                     E   + + +KP GLV   +      T+ + L +             R   
Sbjct: 81  GEAIALDIAHEDADIIVLNKPRGLVVHPAAGHETGTLVNALIAHCGASLSGIGGVRRPGI 140

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQV 153
           V RLD +T GL+++  +    + L        R       Y     G  
Sbjct: 141 VHRLDKDTTGLMVVAKNDRAHQSLSAQFADHGRTGELRRGYFAFVWGVP 189


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 56/302 (18%), Positives = 104/302 (34%), Gaps = 65/302 (21%)

Query: 13  PQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           P R+ + + +  +  A+R +V+  I + RV VN   ++     + S D IE+        
Sbjct: 33  PMRIDQYLTQQ-VENATRNKVQEAIEEGRVLVNENRVKS-NYRIKSCDVIEMTFLRPPAP 90

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVT-----------THSDPDGRSTVFDNLPSIFS 106
               + +P+    E   L + +K  G+V             ++         + L     
Sbjct: 91  ELTAENIPIEIIYEDCDLMVVNKKAGMVVHPAFGNWTGTLANAILHHIGMDAEELDQAEL 150

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           R   V RLD NT GL+++  +      L       + ++VY+    G  D     +    
Sbjct: 151 RPGIVHRLDKNTSGLIIVAKNPIALHRLARQFAERKVIKVYKAIVWGVPDPAAGTITTN- 209

Query: 165 IVIQGICYGDMQV----TLDTQKGSN--------------AWVTVGLREGKNREIKKVFE 206
               G    D +V      + + G                + +++ L  G+  +I+   +
Sbjct: 210 ---IGRSKKDRKVMANFPFEGEYGKTAITDYSVMENLQWFSLLSLRLHTGRTHQIRAHLQ 266

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI-----LREQLGPHLLEEAQVNLDAPI 261
               ++  L  ++YG   L TL        SK       L E L    L    ++   PI
Sbjct: 267 HLGHQI--LGDVTYGGTILRTLP------FSKSESFVKNLLELLPRQALHAETLSFHQPI 318

Query: 262 YS 263
             
Sbjct: 319 SH 320


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 82/246 (33%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           I +E     R+   ++   I   SR + + +I    V VN   ++ A+ ++ S D ++VD
Sbjct: 17  IPKEKDEGLRLDLYLSEQ-IEDLSRSKAKMLINNNSVMVNDNWVK-ASYSITSGDVVKVD 74

Query: 64  GVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRST-VFDNLPSI---- 104
              ++                E   L + +KP  +V      + R T V   L       
Sbjct: 75  TQLIQSEITLIPQSIPLDIVYEDEYLLVVNKPRNMVVHPGAGNYRDTMVNALLYHCQNLS 134

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKL 158
               + R   V RLD +T GLL++        +L          R Y     G   + K 
Sbjct: 135 DGTSYERPGIVHRLDKDTSGLLVVAKQNETHDILSEEIKNRRVARTYLALVIGDFSKKKA 194

Query: 159 ----------NLLKKGIVIQGICYGDMQVTLDTQ---KGSNAWVTVGLREGKNREIKKVF 205
                        KK  V+ G      +V +          +++   L  G+  +I+   
Sbjct: 195 TIDLPIGRDPRNRKKMAVVHGGKRAITKVEMLRSFQNPEKISYLKCSLETGRTHQIRVHL 254

Query: 206 EFFNWK 211
               + 
Sbjct: 255 SHLGYP 260


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 35/139 (25%), Positives = 64/139 (46%), Gaps = 15/139 (10%)

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG 151
           + ++ V + +P     +I +  L+  +EGLLLLTNDG  A+ L+      L  Y ++   
Sbjct: 213 EKKNHVTNYIPE---HLIIINSLNSGSEGLLLLTNDGDFAKNLKDIQNNILTTYLIKVQE 269

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK------KVF 205
            +  DK+ LL+KG  I       + + +   K ++ W+     E      K       +F
Sbjct: 270 DLCIDKIKLLRKGCFINNQHIYPVNIEIIKSKHTSKWIKFTYVE------KSHNYLLYLF 323

Query: 206 EFFNWKVNRLIRISYGPFQ 224
             +N  + +  R S+GP++
Sbjct: 324 SKYNITIRKCKRFSFGPYK 342



 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/77 (25%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R+SK+++ + + SR + + +I    +KVN   +    V +     I+V   P++    T+
Sbjct: 14 RLSKILSLSSVTSRNKAQELIKNGDIKVN-NQVVNQNVFIDVNSKIQVKDKPIQVDICTK 72

Query: 75 LWLYHKPIGLVT-THSD 90
          LW  +KP  +   T  D
Sbjct: 73 LWGIYKPKHIFCNTEKD 89


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 82/238 (34%), Gaps = 33/238 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV++NG +  +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVTNKPKEKVLGGESVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       + L    E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVDQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +         +   G         ++  + ++  + + L  G+  +I+      N  
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIRVHMAHINHP 246


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 85/244 (34%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      +   T+ +          +
Sbjct: 93  DRPRYENEVIPEDIPLNIVYEDKFLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDIPD 152

Query: 101 LPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
             +    V  V R+D +T GLL++  T D      L+  +    R YR    G V+QD+ 
Sbjct: 153 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVEQDEG 212

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 213 TIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMK 272

Query: 207 FFNW 210
               
Sbjct: 273 HIGH 276


>gi|308274565|emb|CBX31164.1| Uncharacterized RNA pseudouridine synthase ylyB [uncultured
           Desulfobacterium sp.]
          Length = 335

 Score = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 83/245 (33%), Gaps = 43/245 (17%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIE---V 62
            E+ +  R+  V++    + SR     +I + ++ V N   +++    V   D I     
Sbjct: 28  DESVSGIRLDIVVSSYIPLCSRSIAASLINKGKITVCN--QIKKQGYKVKFGDKITGTIP 85

Query: 63  DGVPLRK----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
           D  P+             E + + + +KP G+V   +      T+ + L      +  +G
Sbjct: 86  DPEPVSFLPEPIELNILYEDSDIIVINKPPGIVAHPAPGHYSGTLVNALLFHCPDLTGIG 145

Query: 113 ---------RLDINTEGLLLLT-NDGGLARV-LELPSTQWLRVYRVRFHGQVDQDK---- 157
                    RLD +T G L++  ND     + L+    +  + Y     G  + D     
Sbjct: 146 GEIRPGIVHRLDKDTSGALVVAKNDISHTNLCLQFKERRIRKKYLALVWGNPEHDSGSIT 205

Query: 158 ---------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +   ++ +     +    +  +  S +   + L+ G+  +I+      
Sbjct: 206 LPIGRHPSNRKKMS--VLTRKPKTAETLWKVIERYKSVSLWEIDLKTGRTHQIRVHCAAI 263

Query: 209 NWKVN 213
              V 
Sbjct: 264 KHPVI 268


>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 = 76.0 bits (186), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 80/237 (33%), Gaps = 45/237 (18%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     IE+
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQRIEI 67

Query: 63  D---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +      +  A          E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  NATLEEEVHAAAQAIELDIVYEDDDILVINKQAGLVVHPGAGNADGTLMNALLHHCPNIE 127

Query: 110 S------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                  V RLD +T GL+++         L   L + +  R Y     G +        
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVLGTMT------- 180

Query: 162 KKGIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
             G V + I     + T                +  +  ++  + + L  G+  +I+
Sbjct: 181 AGGTVDEPIGRHPTKRTHMAVHHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIR 237


>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 = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 34/236 (14%), Positives = 80/236 (33%), Gaps = 38/236 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+ K ++     +R  ++++I  + + VN     + A  +   D I+V     + V ++ 
Sbjct: 36  RIDKFLSERLELTRTRIQQLIKDENILVN-EKKTKPAYKIEENDTIKVVIPELETVEIKP 94

Query: 70  A--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
                    E   L + +K  G+V   ++     T+ + +      +           V 
Sbjct: 95  ENIDIEIIYEDNDLAVINKKAGIVVHPANGHYSGTLVNAILYHIKDLSGINGEIRPGIVH 154

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV-------------DQDK 157
           RLD +T GLL++  +      L          ++Y     G++             D++ 
Sbjct: 155 RLDKDTSGLLIIAKNDKAHLKLSQMFHDKTVKKIYLAILKGKLNQKSGRIVTQIGRDKND 214

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +     +           + +Q      V V +  G+  +I+   +   + + 
Sbjct: 215 RKKMTVINDLNSGKTAITNYEVISQTEKFTLVKVHIETGRTHQIRVHMKHLGYPIL 270


>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 = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 33/130 (25%), Positives = 62/130 (47%), Gaps = 3/130 (2%)

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
            I   +I V  L  ++EGL+LLTNDG  AR L+      +  Y ++   ++  +K+ L++
Sbjct: 218 DIPEHLIVVNSLSASSEGLVLLTNDGDFARNLKDAHNNIITTYIIKVKEELTNEKIKLIE 277

Query: 163 KGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKNR-EIKKVFEFFNWKVNRLIRISY 220
           +G  +  +    + V +      S  W+     E K+   +  +F  +N  + +  R S+
Sbjct: 278 RGCHVGDLHIRPLTVHVIKPNCASPKWIKFTYVE-KSHTHLDLLFSKYNLTIRKCKRFSF 336

Query: 221 GPFQLGTLLA 230
           GP++   L A
Sbjct: 337 GPYKASDLSA 346



 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 41/75 (54%), Gaps = 1/75 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R+SK+++ + + SR + + +I   +VKVN  ++ +  V V     IE++G P+     T+
Sbjct: 14 RLSKILSLSAVTSRGKAQELIKNGKVKVNNQVVRQ-NVAVDINSAIELEGKPILVDVTTK 72

Query: 75 LWLYHKPIGLVTTHS 89
          LW  +KP  +  +  
Sbjct: 73 LWGIYKPKHVFCSSE 87


>gi|283954844|ref|ZP_06372360.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. jejuni 414]
 gi|283793684|gb|EFC32437.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Campylobacter jejuni subsp. jejuni 414]
          Length = 322

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 83/232 (35%), Gaps = 48/232 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+   +A+    SR +V  +I +  V+VN  + ++ +  + + D +              
Sbjct: 11  RLDVFLAKKLNQSRNQVALLIEKDCVQVNDKIQDKNSFKLKNGDVVFIASLNLCNEVKPQ 70

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVIS 110
            EVD       E   L + +KP  LV   +     +T+ D L              R   
Sbjct: 71  FEVDFDIDVLYEDEDLLVLNKPSNLVVHGASSVKNATLVDWLIEKKYTLSNLGGEIRAGL 130

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV 166
           V RLD +T G +L+  +    + L   L      R+Y       + +DK+         +
Sbjct: 131 VHRLDKDTSGAILIAKNNFTHQKLSEQLADKSMGRIYLALIDLPLKEDKIIVEKF----L 186

Query: 167 IQGICYGDMQVTLDTQKG-----SNAWVTVGLRE-----------GKNREIK 202
           ++       ++ +D +        +A++ V   E           G+  +I+
Sbjct: 187 MRSPSNAIKKIAIDEENKFSKNAKSAFINVIKTENLTLMAAKLFTGRTHQIR 238


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 82/242 (33%), Gaps = 46/242 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K +++      R+ K ++      SR  V+ +I    + VN    E+ +  V + D 
Sbjct: 1   MPKKYLLEVKDEHGRLDKFVSEQIPDLSRTRVKELIQDDNILVNQKK-EKVSYKVQAGDQ 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IEV+   ++               E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IEVNVPAVKPLDVVPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHSDHTLVNALLYHTK 119

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLA----RVLELPSTQWLRVYRVRFHGQV 153
                    R   V R+D +T GLL++  +          L   + +  R+Y    HG  
Sbjct: 120 DLAKSPEGFRPGIVHRIDKDTSGLLMIAKNAKARESLEDQLAHKTNK--RIYWAIVHGNF 177

Query: 154 DQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            ++                 +    V++          +  Q    + +   L  G+  +
Sbjct: 178 SEENGTIDAPIGRNPYDRKKMA---VVERGKKAITHFKVLKQFKGYSLIECQLETGRTHQ 234

Query: 201 IK 202
           I+
Sbjct: 235 IR 236


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  +HI +D 
Sbjct: 10  TVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGSIGDKPKEKVLGGEHIAIDV 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFQPQDIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTSGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRI-HTRLRLRLETGRTHQIR 237


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 82/234 (35%), Gaps = 33/234 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K    V E+    R+ + +A      SR  ++  I  + + VNG+++++    V+  + 
Sbjct: 5   VKLNATVAESQLGHRLDQALAELFPDYSRSRIKEWILNRHITVNGVIIDKPKEKVLGGEQ 64

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +D             +PL    E   + + +KP  LV      +   TV + L   F 
Sbjct: 65  ISIDAEIEEEARWEAQDIPLDIVYEDEDILVVNKPRDLVVHPGAGNPDGTVLNALLHHFP 124

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------R 148
                 R   V RLD +T GL+++         L   L   +  R Y             
Sbjct: 125 AIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVDALQRREITREYEAVAIGRMTAGGT 184

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 185 VDQPISRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V   + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKIWDKPKEKVFGGEAVAINV 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP GLV      +   TV + L   +  +I  
Sbjct: 70  EIEEDVRFEPQDIPLDIVYEDDDILVINKPRGLVVHPGAGNPDGTVLNALLHYYPPIIDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVESLQLREITREYEAVAIGHMTSGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRI-HTRLRLRLETGRTHQIR 237


>gi|256616825|ref|ZP_05473671.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ATCC 4200]
 gi|256963780|ref|ZP_05567951.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis HIP11704]
 gi|257084358|ref|ZP_05578719.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Fly1]
 gi|257087643|ref|ZP_05582004.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis D6]
 gi|307271727|ref|ZP_07552998.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|307276911|ref|ZP_07558021.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|256596352|gb|EEU15528.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ATCC 4200]
 gi|256954276|gb|EEU70908.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis HIP11704]
 gi|256992388|gb|EEU79690.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Fly1]
 gi|256995673|gb|EEU82975.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis D6]
 gi|295113627|emb|CBL32264.1| pseudouridine synthase, RluA family [Enterococcus sp. 7L76]
 gi|306506334|gb|EFM75494.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|306511605|gb|EFM80604.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|315025558|gb|EFT37490.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
 gi|315032794|gb|EFT44726.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315143807|gb|EFT87823.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
 gi|315162164|gb|EFU06181.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
          Length = 297

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 82/236 (34%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVP 66
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V       D   
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYDNEI 100

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
           + +        E   L + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPEDIPLNIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDNSDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      ++  +    R YR    G VDQ++          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGIVDQNEGTVVGSIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMPDPAQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>gi|257421756|ref|ZP_05598746.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis X98]
 gi|257163580|gb|EEU93540.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis X98]
 gi|315155543|gb|EFT99559.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
          Length = 297

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 86/242 (35%), Gaps = 47/242 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ K I   + T +R+ K +       SR  ++ +I++  +KV+G  ++     +   + 
Sbjct: 1   MEAKIIKYTSQTVERIDKFLQKELSELSRTNIQNLISEGYIKVDGKEIKT-NFKLKDGNE 59

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I ++             +P+    E + L + +K  G+V   S      T+ + L     
Sbjct: 60  ITIEYKEPEELDVVKQDIPVDIVYEDSDLIVVNKAKGMVVHPSAGHRDGTLVNALLFHSE 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   + +    R Y    HG +  D
Sbjct: 120 LSSINGTIRPGIVHRIDKDTSGLLVVAKNDKAHVKLSEMIANKDVKRKYYALVHGSIKHD 179

Query: 157 KLNLLKKGIVIQGICYGDMQ----VTLDTQKGSNAWVTV-------GLRE-----GKNRE 200
                  G +   I     +      +D  K S     V        L E     G+  +
Sbjct: 180 Y------GTIDAPIARNPKERKEMAIIDEGKPSITHFKVVERFEKYTLIECELETGRTHQ 233

Query: 201 IK 202
           I+
Sbjct: 234 IR 235


>gi|229549211|ref|ZP_04437936.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis ATCC
           29200]
 gi|255971927|ref|ZP_05422513.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T1]
 gi|256957901|ref|ZP_05562072.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis DS5]
 gi|257416850|ref|ZP_05593844.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis AR01/DG]
 gi|257420067|ref|ZP_05597061.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|300861004|ref|ZP_07107091.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|229305448|gb|EEN71444.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis ATCC
           29200]
 gi|255962945|gb|EET95421.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T1]
 gi|256948397|gb|EEU65029.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis DS5]
 gi|257158678|gb|EEU88638.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis ARO1/DG]
 gi|257161895|gb|EEU91855.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T11]
 gi|300850043|gb|EFK77793.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|315035177|gb|EFT47109.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
 gi|315148637|gb|EFT92653.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|315159322|gb|EFU03339.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315168785|gb|EFU12802.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
 gi|315573843|gb|EFU86034.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315580414|gb|EFU92605.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
 gi|323481597|gb|ADX81036.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
 gi|327535892|gb|AEA94726.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           OG1RF]
          Length = 297

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLS 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/223 (19%), Positives = 78/223 (34%), Gaps = 36/223 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           R+  V+A+    SR +   +I    V VN   + + +  +   D I V+  P ++ +   
Sbjct: 11  RLDVVVAKELQISRNQALNLIKDSLVSVNLKPVSKPSFLLSENDEICVNFAPKKEVQNEY 70

Query: 75  --------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVISV 111
                         L + +KP  +V   +     +T+ + L              R   V
Sbjct: 71  EVNFDIPIIYEDDDLIVLNKPPQIVVHQAPSVKEATLVEWLNKKGFMLSNLNGDVRAGIV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------N 159
            RLD  T G +++  +      L   L      R+Y       + +D +          N
Sbjct: 131 HRLDKGTSGAIVVAKNNFAHAKLSEQLSDKSMGRIYLALTDLPLKEDIIIDKPIGRNPNN 190

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            LKK IV          V L ++ G N  +   L  G+  +I+
Sbjct: 191 RLKKAIVADAKFAKSAFVNLLSEGGVN-LIAAKLFTGRTHQIR 232


>gi|323700732|ref|ZP_08112644.1| pseudouridine synthase, RluA family [Desulfovibrio sp. ND132]
 gi|323460664|gb|EGB16529.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           ND132]
          Length = 562

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/253 (16%), Positives = 79/253 (31%), Gaps = 63/253 (24%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE------- 61
           R+ K     +A  G+ SR  V+  I      V+G +  +  + +       I        
Sbjct: 22  RLDKFWGRELAGEGV-SRGRVKGWIESGLALVDGEVTTKGNLKLARGQVAVIRAAAPEAD 80

Query: 62  ----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                     V G      E   + +  KP GL    +  +   T+ + L   +  + + 
Sbjct: 81  PLGPASPPEPVSGDIEAVYEDEHMLVIVKPAGLTVHPAPSEPGPTLVNLLIHQWPDIAAE 140

Query: 111 -----------VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                      V RLD +T GL+ +  T    LA        +  +VY    HG+ +   
Sbjct: 141 NSGMDPQRPGIVHRLDKDTSGLMAVARTESARLALSASFAGHETFKVYLALVHGRPE--- 197

Query: 158 LNLLKKGIVI-----------------QGICYG--DMQVTLDTQKGSNAWVTVGLREGKN 198
              L +G++                  +G      D +V     +G  +   V +  G+ 
Sbjct: 198 ---LAEGVIDAPMGRHPTHKTLMAVLPKGGREARSDYRVLWTGPRGLASLAAVRIHTGRT 254

Query: 199 REIKKVFEFFNWK 211
            +I+         
Sbjct: 255 HQIRVHMAHIGHP 267


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 78/236 (33%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G++ + I     + TL +                    +  + + L  G+  +I+
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIR 237


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/188 (23%), Positives = 71/188 (37%), Gaps = 34/188 (18%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           P+R+ K IAR     A + SR  + +++A   V +NG +L      V   D I V     
Sbjct: 15  PKRLDKAIARDVPADASL-SRSRIAKLLASGDVALNGAVLTDPRAKVAEDDEITVTLPDA 73

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                  + +PL    E   L + +KP G+V   +      T+ + L             
Sbjct: 74  AESHMGPEDIPLDLVFEDDDLIVINKPSGMVVHPAPGSPSGTLVNALMHHCGDSLSGVGG 133

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V R+D  T GLL++         L     +    R YR   +G  D +    L+
Sbjct: 134 EKRPGIVHRIDKETSGLLVVAKSDKAHHGLAAQFEAHTVERYYRAVVYGVPDSND-PRLR 192

Query: 163 --KGIVIQ 168
             +G+  +
Sbjct: 193 GIRGVNFE 200


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/272 (18%), Positives = 84/272 (30%), Gaps = 70/272 (25%)

Query: 13  PQRVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           P R+ K +AR      +   SR  + R+I +  V V+G +++     V     I +    
Sbjct: 15  PPRLDKALARDVPAEES--LSRTRLARLIGEGAVTVDGAVVDDPKAKVAEDAQIAITVAE 72

Query: 63  --------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                   + +PL    E   L + +KP G+V   +      T+ + L            
Sbjct: 73  AEDSHIGPEDIPLDVVYEDDDLIVINKPAGMVVHPAPGSPNGTLVNALLHHCGDDLSGVG 132

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLL 161
              R   V R+D  T GLL++         L     +    R YR   +G  D +    L
Sbjct: 133 GVKRPGIVHRIDKETSGLLVVAKSDAAHHGLAAQFEAHSVERYYRAVCYGVPDAND-PRL 191

Query: 162 K--KGIVIQGI-----------------------------CYGDMQVTLDTQKGSNAWVT 190
           +  KG+  +                                     V +    G+ + V 
Sbjct: 192 RGIKGVSFEPGNIMRLTTQLARHKTDRQKQAVLFHGGRHAVTRSRIVEVFGNPGAISLVE 251

Query: 191 VGLREGKNREIK-KVFEF----FNWKVNRLIR 217
             L  G+  +I+  +           V    R
Sbjct: 252 CWLETGRTHQIRVHMAHAGHGLVGDPVYGGKR 283


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 77/231 (33%), Gaps = 33/231 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA- 70
           R+ K +      +R ++++ I    + +N   ++ A  N+   D I V   D   L    
Sbjct: 16  RLDKFLEEILEINRSQIKKNIVDGNILLNNNKVK-AGYNLKLDDEITVEYEDDFSLSPEK 74

Query: 71  -------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVGRL 114
                  E   L +  KP  LV      +   T+ + L         P    R   V RL
Sbjct: 75  IDFDVLYEDDYLAVISKPQELVVHPGAGNKSGTLVNGLLYKFKELSNPIDNDRPGIVHRL 134

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLK 162
           D +T GL+L+         L     + Q  + Y    HG + +D            N +K
Sbjct: 135 DKDTSGLMLIAKKDEAYYKLVEMFKNRQIDKHYLAICHGNIYEDFDVKAPIGRDPNNRIK 194

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             ++ +          +         + V L  G+  +I+    + N  V 
Sbjct: 195 MRVIDENSKEAYTSFKVLKNFDKYTLLDVHLHTGRTHQIRVHLAYVNHPVV 245


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 81/236 (34%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVP 66
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V       D   
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYDNEI 100

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVI 109
           + +        E   L + +KP GLV      +   T+ + +                V 
Sbjct: 101 IPEDIPLHIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHLKDDPVYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      ++  +    R YR    G VDQD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGVQFFNKTTKRRYRALVWGIVDQDEGTIVGSIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMADPTQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 77/231 (33%), Gaps = 41/231 (17%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +P R+ K +       SR  ++       + VNG   +  +  V   D I +        
Sbjct: 37  SPLRLDKFLTIHMERCSRNRIQTAADAGNILVNGKPAKS-SYKVKPGDRISLVMPYPKRE 95

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------- 109
                + +PL    E   L L +KP G+V      +  +T+ + L      +        
Sbjct: 96  IEIIPENIPLEIPYEDDDLLLVNKPAGMVVHPGHGNYSATLVNALTYYLQNLPLFQEGDM 155

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL------ 158
               V R+D NT GLL++  +      L          R Y     G  ++D+       
Sbjct: 156 RAGLVHRIDKNTSGLLVIAKNERAHARLAKQFFDHTITRRYVALVWGNFEEDEGTITGNI 215

Query: 159 ----NLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
                  +K  V +    G   VT   +  + G    +   L  G+  +I+
Sbjct: 216 GRSPKDRQKMWVFEDGSDGKHAVTHYRVLKRYGYVTLIECRLETGRTHQIR 266


>gi|227519595|ref|ZP_03949644.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX0104]
 gi|229544944|ref|ZP_04433669.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX1322]
 gi|256763299|ref|ZP_05503879.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T3]
 gi|256853972|ref|ZP_05559337.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T8]
 gi|257079838|ref|ZP_05574199.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis JH1]
 gi|257090805|ref|ZP_05585166.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis CH188]
 gi|294779490|ref|ZP_06744886.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|307270621|ref|ZP_07551912.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|307287513|ref|ZP_07567556.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|307290324|ref|ZP_07570239.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|312902437|ref|ZP_07761643.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|227072945|gb|EEI10908.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX0104]
 gi|229309836|gb|EEN75823.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecalis
           TX1322]
 gi|256684550|gb|EEU24245.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T3]
 gi|256710915|gb|EEU25958.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis T8]
 gi|256987868|gb|EEU75170.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis JH1]
 gi|256999617|gb|EEU86137.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis CH188]
 gi|294453447|gb|EFG21853.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|306498517|gb|EFM68019.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306501251|gb|EFM70554.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306512931|gb|EFM81572.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|310634107|gb|EFQ17390.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0635]
 gi|315030281|gb|EFT42213.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315164911|gb|EFU08928.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
 gi|315170401|gb|EFU14418.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
 gi|315579152|gb|EFU91343.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 297

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 82/241 (34%), Gaps = 50/241 (20%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            RV K +  R   ASR  +++      V  NG  ++  +  V   D I V          
Sbjct: 40  MRVDKYLFDRLTNASRNRIQKAADAGFVMANGKPVKS-SYKVKPQDVITVMMDRPRYENE 98

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRV 108
              + +PL    E   L + +KP GLV      +   T+ +          +  +    V
Sbjct: 99  VIPEDIPLNIVYEDKHLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPDYDANDPHV 158

Query: 109 ISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---- 157
             V R+D +T GLL++       TN G         +    R YR    G V+QD+    
Sbjct: 159 GLVHRIDKDTSGLLVIAKTPDAKTNLGNQFF-----NKTTKRRYRALVWGNVEQDEGTVV 213

Query: 158 -------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                   + ++  ++      +      +  + G    V   L  G+  +I+   +   
Sbjct: 214 GNIGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIG 273

Query: 210 W 210
            
Sbjct: 274 H 274


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGKLCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   T  + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDGTXLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 80/249 (32%), Gaps = 59/249 (23%)

Query: 13  PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           P R+ K ++R        SR  + R++ +  V VNG         V   D + +      
Sbjct: 15  PPRLDKALSRDVPEEAHLSRTRLARLVEEGAVSVNGAEARDVKSRVAEGDEVVITVPVAE 74

Query: 63  ------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
                 + +PL    E   L + +KP G+V   +    R T+ + L              
Sbjct: 75  ESDILPENIPLDIVYEDADLLVVNKPAGMVVHPAPGTPRGTLVNALLHHCGGDLSGVGGV 134

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNL--- 160
            R   V R+D +T GLL++         L          RVY+   +G  D     L   
Sbjct: 135 RRPGIVHRIDKDTSGLLVVAKSDQAHHGLAAQFEAHSAERVYQAIVYGVPDAADPRLGGL 194

Query: 161 ----LKKG--------------------IVIQGICYGDMQVTLDTQKGSN---AWVTVGL 193
                + G                    ++  G  +   +  +  + G     A +   L
Sbjct: 195 RGVGFEPGNVLRITTQLARHRTDRQKQAVLFDGGKHAVTRAQVTERLGDPASVALIECRL 254

Query: 194 REGKNREIK 202
             G+  +I+
Sbjct: 255 ETGRTHQIR 263


>gi|315173724|gb|EFU17741.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
          Length = 297

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFEGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 73/238 (30%), Gaps = 36/238 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  ++         R+   + +    +R ++ ++I Q  V V+G    ++ + +  +  +
Sbjct: 1   MTQEDSTFTTDEAVRLDVFLTQQLGQTRNQITQLIEQNCVSVDGKETAKSGLKLKPSQTV 60

Query: 61  -------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--- 104
                        E+D       E   + + +KP  L    +      T+ D L      
Sbjct: 61  IIRFPEQKSTPAQEIDFDVDILFEDDDILVINKPSSLTVHPAPSVKEPTLVDWLKHKGIA 120

Query: 105 ------FSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVR-------- 148
                   R   V RLD  T G +++   N+   A  L+L      R Y           
Sbjct: 121 LSTLSGEERHGIVHRLDRGTSGAMVIAKNNEAHEALSLQLQDKTMGRYYLAIITPAMKET 180

Query: 149 ---FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGKNREIK 202
                  + +   N LK  I   G         L         +    L  G+  +I+
Sbjct: 181 ITVIDRPIGRSANNRLKMAISESGKNAKTAFAKLLPSHDETEELIACKLYTGRTHQIR 238


>gi|256961078|ref|ZP_05565249.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Merz96]
 gi|293384024|ref|ZP_06629918.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|293386837|ref|ZP_06631407.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|312908026|ref|ZP_07767009.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312978446|ref|ZP_07790184.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|256951574|gb|EEU68206.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis Merz96]
 gi|291078504|gb|EFE15868.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|291083671|gb|EFE20634.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|310626117|gb|EFQ09400.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|311288595|gb|EFQ67151.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
          Length = 297

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGGAIEQLN 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 84/232 (36%), Gaps = 37/232 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +A      SR ++++ I    V VN   ++    ++ + D ++V           
Sbjct: 17  RIDKQLATLLSDVSRSQIKKWIEDGNVTVNKQSVK-PKYHLQAGDIVQVIPEQPQKIDLE 75

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVG 112
            + +PL    E   + + +KP G+V   S      T+ + L             R   V 
Sbjct: 76  PENIPLEIVYEDDDVLVVNKPQGMVVHPSAGHPNHTLVNALLYHCPLSHINGEYRPGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK-----------LN 159
           R+D +T GLL++  +    R L   L +    R Y    HG + +D+            +
Sbjct: 136 RIDKDTSGLLMVAKNDRAHRSLAAQLKAKTNQREYVALVHGVIKEDQGTIDAPLGRSPKD 195

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ +V  G         +  +      V   L  G+  +I+   ++    
Sbjct: 196 RKKQAVVADGRPAVTHF-RVLKRYLHYTLVACKLETGRTHQIRVHMKYIGHP 246


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 85/236 (36%), Gaps = 57/236 (24%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
            R+ K + +    SR ++ ++I ++++ +NG+ +++   ++   D I +           
Sbjct: 1   MRLDKFLTQKLGLSRNQISKIIQEKQITLNGVFIQKNGTSLNFNDQIILTLPNKQEKSKP 60

Query: 64  ---GVPLRKAERTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIF---------SRVIS 110
               +P+   +   L + +KPI L+   +   D + T+ D L              R   
Sbjct: 61  NHLNIPILYEDED-LLILNKPINLIVHQTHQDDSQYTLQDWLQENNFSLSNLGDSYRQGI 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV---YRVRFHGQVDQDKLNLLKKGIVI 167
           + RLD  T G +++  +   A  +     +  +    Y V             LK+ I+I
Sbjct: 120 IHRLDKTTSGAIVIAKN-NYAHEILSQQLK-SKEMGRYYVCVIDSP-------LKQNILI 170

Query: 168 QG-------------ICYGDMQVTLDTQK-----GSNAWVTVG---LREGKNREIK 202
                              D  ++ + +       +N  + +    L  G+  +I+
Sbjct: 171 DAPLIRHPKNRLKYIPTTKDTPLSKEAKTAFFKIINNDKIELIGAKLFSGRTHQIR 226


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 89/249 (35%), Gaps = 47/249 (18%)

Query: 1   MKDKNIVQENFT---------PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERA 50
           +  K+ +Q   T          QR+   ++      SR  ++++I Q  V +N  +    
Sbjct: 11  VTQKSKIQNRMTVINLLVSQNTQRLDLYLSSELQNLSRSRLQQLIEQGHVLLNDQVCTSK 70

Query: 51  AVNVMSTDHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            VNV   D I V            + +PL    E  +L + +KP GLV   +      T+
Sbjct: 71  KVNVKVGDRICVEIPSLQPLKLVAEDIPLDILYEDEQLLILNKPAGLVVHPAPGHLDGTL 130

Query: 98  FDNLPSIFSRVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYR 146
            + L +  + +  +G         RLD +T G + +  T+        +L +    R Y 
Sbjct: 131 VNALLAHCANLPGIGGVQRPGIVHRLDKDTTGAIAIAKTDIAYQHLQAQLQAKTARREYL 190

Query: 147 VRFHGQV-DQDKLNLL--------KKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGL 193
              +G    +  +  L        +K + I    QG         +  +  +   +   L
Sbjct: 191 GVVYGVPKTESGIINLPISRHPQDRKKMAIVPTEQGGRTAITHWQIRERLSNYTLIHFQL 250

Query: 194 REGKNREIK 202
             G+  +I+
Sbjct: 251 ETGRTHQIR 259


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 61/183 (33%), Gaps = 31/183 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K ++       R+   +A +  G  SR  V+ +I Q  V VNG  +      +   D 
Sbjct: 11  PRKELIAGEDAEGRLDAWLAASLGGDLSRNRVKALIEQGAVFVNGTAVTEPKRKIKPGDQ 70

Query: 60  IEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           + +            + +PL    E   L +  KP GLV      +   T+ + L     
Sbjct: 71  LVIAMPEPEDPEPKGEDIPLTVLYEDKDLIVLSKPAGLVVHPGAGNWTGTLVNALIHHCG 130

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFH 150
                     R   V RLD  T G++++  +    R L              R Y+    
Sbjct: 131 DSLSGIGGVKRPGIVHRLDKETSGVMVVAKNDIAHRHLADQFADHGRSGPLERAYQALVW 190

Query: 151 GQV 153
           G+ 
Sbjct: 191 GRP 193


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/211 (21%), Positives = 75/211 (35%), Gaps = 39/211 (18%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE- 71
            R+S+  AR GI SR   +R+I +  V +NG  ++   + V S  D   V    LR    
Sbjct: 3   IRISQFCARVGICSRGAAKRLIKKGHVLLNGTAVKS-DIPVKSGLDPGCVS--LLRAPGL 59

Query: 72  RTRLWLYHKPIGLVTT---------------HSDPDGRSTVF-----------DNLPSIF 105
                + HKP   ++T                +D   +S +               PS  
Sbjct: 60  GGISVMLHKPECYLSTYTQRVCSTSRDYIYLQTDLWAKSLLIPSNRSEEDLRGHLDPSRL 119

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
            R++ +  LD +  GL L + D  L              Y + F   + + KL +L+  I
Sbjct: 120 RRLLCINPLDYSASGLSLFSEDISLFNRF----NDCEECYDISFRDTLTESKLCVLRGEI 175

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            + G     + V +     +     + L  G
Sbjct: 176 YLDGELIPPLTVEVLGDYSA----RIRLHGG 202


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 73/246 (29%), Gaps = 52/246 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V      +R+   +       SR    +++    V VNG         V   D I ++ 
Sbjct: 8   LVPSEAAGERLDAYLGAQDACPSRSACAKLVEAGAVAVNGETCLSKKQVVCEGDRISIEL 67

Query: 64  ------GVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                 G  + +A       E   L +  K  GLV   +      T+ + L         
Sbjct: 68  PEVREPGAIVPQAIPLDIRYEDDHLLVLSKQRGLVCHPAHGHEDGTLANALVYHCGIEHL 127

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQ 155
                  R   V RLD +T GL+L   D    R L   + +    R Y    HG++  D+
Sbjct: 128 GTVQGEDRPGIVHRLDRDTSGLMLAAKDDETQRALQNLIRTRTLDRRYITLVHGEIVMDE 187

Query: 156 DKLNLLKKGI-----------VIQGICYGDM--------QVTLDTQKGSNAWVTVGLREG 196
             +N    GI           V                 +            V   L  G
Sbjct: 188 GTINT---GIARSTRDRVKMAVSDDPFARQAITTFQVLERFEPARGDEGYTLVECHLYTG 244

Query: 197 KNREIK 202
           +  +I+
Sbjct: 245 RTHQIR 250


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 76/229 (33%), Gaps = 31/229 (13%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           N V++    QR+ + IA      SR  ++  +   +V+V+G ++ +    VM  + I + 
Sbjct: 9   NTVKDAQLGQRLDQAIAELFSDFSRSRLKDWLLDGKVQVDGEVVTKPRTKVMGGEVIVLH 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
               D               E   + + +KP G V          TV + L   F  +  
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDIIVINKPRGFVVHPGAGTPDGTVLNALLHHFPDIAE 128

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDK 157
                 V RLD +T GL+++         L   L      R Y     G++      +  
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGRVEQP 188

Query: 158 LNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
           +        +  +            +      +  + + L  G+  +I+
Sbjct: 189 IGRHSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>gi|260435696|ref|ZP_05789666.1| pseudouridylate synthase, 23S rRNA-specific [Synechococcus sp. WH
           8109]
 gi|260413570|gb|EEX06866.1| pseudouridylate synthase, 23S rRNA-specific [Synechococcus sp. WH
           8109]
          Length = 333

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 83/247 (33%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +      P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 29  LAYPKPLPMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGK-AKTPLRQGDEVQLWM 87

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 88  PPPEPLSYLKPEPMDLDVLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 147

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L++   +    R Y    HG    D   
Sbjct: 148 ISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGVPAGDSGT 207

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y     TL  + G  + +   L  G+  +I+    
Sbjct: 208 IVGPIGRHPADRKKYAV-VSSENGRYACTHWTLVERLGDYSLLRFKLDTGRTHQIRVHCA 266

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 267 HMNHPVV 273


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 96/248 (38%), Gaps = 39/248 (15%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +  I+ EN    R+   ++ R    SR  ++ +I + +VKVNG +L+++   +   D
Sbjct: 1   METREFIIDENSVNTRLDLFLSERMEDKSRSYIQGLIEKSQVKVNG-ILKKSNYKLKIKD 59

Query: 59  HIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            I +            + +PL    E + + + +KP G+V   +      T+ + L +  
Sbjct: 60  KILITIPDPVGLDIEPEDIPLDIVYEDSDVIVVNKPQGMVVHPASGVYTGTLVNALLNHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
           S +           V R+D +T G+L++  +      L   L      R Y     G + 
Sbjct: 120 SDLSGINGVTRPGIVHRIDKDTSGILVVAKNDKSHNKLAEQLKDHSMTRAYTALVEGILK 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +D+           +  +K  ++  G         L+  K SN  V   L  G+  +I+ 
Sbjct: 180 EDEGTIDKPLGRHPVERIKISVIKDGKRAVTHYRVLERFK-SNTLVECVLETGRTHQIRV 238

Query: 204 VFEFFNWK 211
              +    
Sbjct: 239 HMAYIGHP 246


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 86/237 (36%), Gaps = 31/237 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I +QRV++NG  ++R    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNTVDRPKEKVLGGESVAIDA 69

Query: 64  ---------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                      P+      E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  LIEEEARWEAQPISLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKL 158
            R   V RLD +T GL+++         L   L + +  R Y     G +       + +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVDEPI 189

Query: 159 NLL---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  + +  +    +    +     ++  + + L  G+  +I+      N  
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHP 246


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 90/236 (38%), Gaps = 36/236 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K    V  +   +R+   +A     SR  +++ I +  +KVNG +++     +   D I 
Sbjct: 4   KYAFTVTRDDEKKRLDIFLADKLQDSRSFLKKGIVEGWIKVNGSIVK-PNYRLRQEDQII 62

Query: 62  V------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V            + +PL    E   + + +KP G+V   +  +   T+ + L +    +
Sbjct: 63  VTVPQALQPLIDPEDIPLDIIFEDRDIVVINKPRGMVVYPAPGNYSGTLINALLNHTKDL 122

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
            +         V RLD +T G++++  +      L   L S +  +VY+    G+V +DK
Sbjct: 123 SARGGTMRPGIVHRLDKDTSGVIVVAKNDTAHINLSKQLKSREVKKVYQTLVWGKVQEDK 182

Query: 158 -----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +   +  +  +          +  +     ++ V +  G+  +I+
Sbjct: 183 ATINAPIGRHPIKRKEMAVTTKNSKEAITHFKVLERFDEFTFLEVAIETGRTHQIR 238


>gi|294085882|ref|YP_003552642.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292665457|gb|ADE40558.1| pseudouridine synthase, RluA family [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 341

 Score = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 80/241 (33%), Gaps = 41/241 (17%)

Query: 14  QRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------V 62
           QR+ K +A          SR  ++ +I  +R+  +G  L   +  V    H        V
Sbjct: 23  QRIDKFLAEHLDDDGQSLSRSRIKALILDKRLLEDGRTLADPSSTVKPLCHYALELPPPV 82

Query: 63  D------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
           D       +PL    E   + + +KP G+V   +      T+ + L +            
Sbjct: 83  DATPKAENIPLDVLYEDAHIIVLNKPAGMVVHPAPGSLTGTLVNALIAHCGDSLTGIGGV 142

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ-VDQDKL---- 158
            R   V RLD +T G+++          L     +    R Y     G  VD+D +    
Sbjct: 143 MRPGIVHRLDKDTSGVMMAAKTDAAHHTLTSMFAAHDLDRRYHALVWGTGVDRDGMVDAP 202

Query: 159 ------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 +  K+ +  +G         + T     + V   L  G+  +I+       + V
Sbjct: 203 LGRSTHDRKKQAVNPRGRHAITHWRVMRTLPPFGSLVECTLETGRTHQIRVHMAHIGYPV 262

Query: 213 N 213
            
Sbjct: 263 I 263


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 85/244 (34%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPS 103
                      + +PL    E   L + +KP GLV      +   T+         ++P 
Sbjct: 92  DRPRYENEVIPEDIPLNIVYEDKFLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDIPD 151

Query: 104 I---FSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
                  V  V R+D +T GLL++  T D      L+  +    R YR    G V+QD+ 
Sbjct: 152 YNANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGNVEQDEG 211

Query: 158 ----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                      + ++  ++      +      +  + G    V   L  G+  +I+   +
Sbjct: 212 TIVGNVGRNPKDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMK 271

Query: 207 FFNW 210
               
Sbjct: 272 HIGH 275


>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 = 75.6 bits (185), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 50/303 (16%), Positives = 98/303 (32%), Gaps = 59/303 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIKKVFE 206
            G++ + I     + TL +                    +  + + L  G+  +I+    
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMA 241

Query: 207 FFNWKVN----RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
           +    +        R             G+T E++ +++R+      L    +  D P+ 
Sbjct: 242 YLQHPLLGDTAYGGRARI--------PKGATEELT-EMIRD-FDRQALHAVMLKFDHPVT 291

Query: 263 SSE 265
             E
Sbjct: 292 GEE 294


>gi|78213965|ref|YP_382744.1| ribosomal large subunit pseudouridine synthase D [Synechococcus sp.
           CC9605]
 gi|78198424|gb|ABB36189.1| Pseudouridine synthase, RluD [Synechococcus sp. CC9605]
          Length = 333

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 83/247 (33%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +      P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 29  LAYPKPLPMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKTGK-AKTPLRQGDEVQLWM 87

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 88  PPPEPLPYLKPEPMDLDVLFEDDHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 147

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L++   +    R Y    HG    D   
Sbjct: 148 ISGKLRPGIVHRLDKDTTGCIVIAKSQEALVRLQVQIQKRIASREYFAVVHGVPGGDSGT 207

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y     TL  + G  + +   L  G+  +I+    
Sbjct: 208 IVGAIGRHPADRKKYAV-VSSENGRYACTHWTLVERLGDYSLLRFKLDTGRTHQIRVHCA 266

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 267 HMNHPVV 273


>gi|294660309|ref|NP_852991.2| pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284811965|gb|AAP56559.2| Pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284930466|gb|ADC30405.1| Pseudouridine synthase [Mycoplasma gallisepticum str. R(high)]
          Length = 311

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 81/235 (34%), Gaps = 33/235 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     V  +    R+   +      SR +   +I    VKVN  L+ +    +   D +
Sbjct: 1   MPKHTFVNNDSEKIRLDIFLTYNLNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVV 60

Query: 61  E----------VDGVPLRKAERTRL-------WLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           E          V    L   ++  +        + +KP  +++  +  +   T+ + L  
Sbjct: 61  ELEYEESIFNKVSNEILPFNKKLDIVYEDDDLIIVNKPTNMLSHPTTHNEPDTLLNCLMY 120

Query: 104 IFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DK 157
              +  V    RLD +T GL++ T +      ++   T+    R Y    H   ++    
Sbjct: 121 HNKKQKVYLAHRLDKDTTGLIVATKNFKALEKIQEQITKRIMKRYYLAIVHYPFNELRAV 180

Query: 158 LNL---------LKKGIV-IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++          LK G+   +       ++ +  Q    A +   L  G+  +I+
Sbjct: 181 IDAPIGYLKDHDLKFGVENTKNPKNAITKIYVLDQNKKYALIKCELLTGRTHQIR 235


>gi|254796544|ref|YP_003081380.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Neorickettsia risticii str. Illinois]
 gi|254589781|gb|ACT69143.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Neorickettsia risticii str. Illinois]
          Length = 315

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 49/253 (19%), Positives = 80/253 (31%), Gaps = 41/253 (16%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           IV E     R+   + R     SR  ++  I   RVK +G +    +  V+  +   +  
Sbjct: 16  IVAECDVGNRLDVFLHRYLPFFSRTFIKHCIKGGRVKADGKIRLEPSKQVLLGEEYHLLD 75

Query: 65  VPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
           +PL +  R               L + HKP GLV      +   T+ + L   +      
Sbjct: 76  LPLEQKPRHAFVQPLDVRYEDDSLLVIHKPAGLVVHPGIGNKEQTLVNILEHHYPTEQLS 135

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD---QD 156
                R   V RLD +T G L++         L     +    R Y    H        +
Sbjct: 136 NLDSSRPGIVHRLDKDTAGFLIVAKTNPSHVRLSEMIKEGVIRREYLALVHSVPASLRGE 195

Query: 157 KLNLLKKG---IVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
               +K+G   ++I             V   T     + V   L  G+  +I+   +   
Sbjct: 196 IKKSIKRGQRKMMIGKCSGKPALTYYNVLARTVDRKYSLVHCKLGSGRTHQIRLHMKSIG 255

Query: 210 WKVN-----RLIR 217
             V       L R
Sbjct: 256 CPVVGDKLYGLKR 268


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 85/244 (34%), Gaps = 40/244 (16%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V +  T  R+ KV+A      SR  +++ I    V+VNG  ++     +   D + +
Sbjct: 6   KLTVDDTLTG-RIDKVLAHQFNQFSRSHLQKWIVDGNVRVNGQPVK-PKYKLAVGDQVVI 63

Query: 63  DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
           +    +K              E   + + +KP G+V   +      T+ + L        
Sbjct: 64  EPEAPQKVDLTPEKIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLST 123

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQD-- 156
                R   V R+D +T GLL++  +  LA        +     R Y    HG + QD  
Sbjct: 124 INGEFRPGIVHRIDKDTSGLLMVAKN-DLAHRSLAAQLKAKTNQREYVALVHGVIKQDAG 182

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                    K +  K+ +V  G         +  +      V+  L  G+  +I+   + 
Sbjct: 183 TIDAPIGRSKKDRKKQAVVSDGRHAVTHF-KVLRRFRHYTLVSCRLETGRTHQIRVHMKS 241

Query: 208 FNWK 211
               
Sbjct: 242 IGHP 245


>gi|297571262|ref|YP_003697036.1| pseudouridine synthase [Arcanobacterium haemolyticum DSM 20595]
 gi|296931609|gb|ADH92417.1| pseudouridine synthase, RluA family [Arcanobacterium haemolyticum
           DSM 20595]
          Length = 306

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/287 (15%), Positives = 93/287 (32%), Gaps = 61/287 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA---------VNVMS 56
            + + F   R+   +A+    SR  +  +IA   V ++G++  ++          +N+ +
Sbjct: 5   FIPDGFAGDRLDAALAKMTGLSRSRIADLIASGDVYLDGVIPGKSDRVNAGAMVMINIPA 64

Query: 57  TDHIE-----VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
              +E     V+G+ +   +   + +  KP+G+    S       V   L          
Sbjct: 65  PASVEPELTPVEGMGVLYEDDD-IIVVDKPVGVAAHASQNFEGPNVLGALLAAGVRLTTS 123

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ----- 155
               R+  V RLD+ T G +++        +L+         ++Y     G  D      
Sbjct: 124 GPQERMGIVHRLDVGTTGAMVVAKSELAYTMLKRAFRDRTVTKIYHALVQGHPDPMNGTV 183

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK------- 202
                 D  +  K G+   G        T++   G+ + + V L  G+  +I+       
Sbjct: 184 EAPIGRDHRHQWKMGVRADGKHSVTHYDTIEAMAGA-SLLEVHLETGRTHQIRVHMSALR 242

Query: 203 -------------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                        ++      +   L  +  G         G   EV
Sbjct: 243 HPCVGDDMYGADPRLSAKLGLERQWLHAVRLGF---DHPRTGHYIEV 286


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 77/251 (30%), Gaps = 46/251 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            +  V      QR+ K +A   +    SR  ++++I ++RV VNG  +   +  V     
Sbjct: 25  YERAVDAEAAGQRLDKWLA--TVIPTLSRARLQQLIGEKRVSVNGQTIGEGSRRVKPGQT 82

Query: 60  IEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           + V+  P   A             E   L +  K  G+V      +   T+ + L +   
Sbjct: 83  VRVEEPPPIAATPQPEAIALTVVYEDDDLIVIDKAAGMVVHPGPGNPDHTLVNALLAHCG 142

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD 154
                     R   V RLD +T GL++          L          R Y     G+  
Sbjct: 143 PSLSGIGGERRPGIVHRLDKDTSGLMIAAKTDLAHHGLAEQFACHSLTREYLCLVWGRPR 202

Query: 155 QD-------------KLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNRE 200
                          +   +   +V +G          +   +G  + V   L  G+  +
Sbjct: 203 PAAGSIDAPLGRHPTQRKKMA--VVSRGGKRALTHYRVVGDVEGIASIVKCTLSTGRTHQ 260

Query: 201 IKKVFEFFNWK 211
           ++         
Sbjct: 261 VRVHMAHIGHP 271


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/222 (20%), Positives = 84/222 (37%), Gaps = 34/222 (15%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+   +A+     SR  + + +    VKV+G ++      ++  + +EV          
Sbjct: 34  ERLDAALAKLLPDYSRSRLTQWVKDGLVKVDGQVVA-PKTKMLGGEKLEVTLQLTNEEMA 92

Query: 63  -DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVG 112
               P+      E   + + +KP GLV   +  +   T+ + L           R   V 
Sbjct: 93  FQPEPMDLPIVFEDEHILVINKPAGLVVHPAAGNWSGTLLNGLLHHCPALASVPRAGIVH 152

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD----------QDKLNL 160
           RLD +T GL+++         L  +L +    RVYR    G V           +D  N 
Sbjct: 153 RLDKDTSGLMVVAKTLPAQTELVRQLQARTVKRVYRAIADGVVPFDGTIDANIGRDANNR 212

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           LK  ++  G       + +  +  S++ V   L  G+  +I+
Sbjct: 213 LKMAVLKFGGKPAITHIRVLERFASHSHVECKLETGRTHQIR 254


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 79/239 (33%), Gaps = 38/239 (15%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMST---------- 57
           P R+ K + R     A + SR  + R+IA   V V+G ++      +             
Sbjct: 21  PPRLDKALGRDVPNDAAL-SRSRLARLIADGAVAVDGQVVTDPRFRIAEGAQVAVTVAVA 79

Query: 58  --DHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------- 104
              HIE   + L    E   L + +KP G+V   +      T+ + L             
Sbjct: 80  VESHIEAQDITLDVVFEDDDLIVINKPAGMVVHPAPGTADGTLVNALIHHCGDSLSGVGG 139

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V R+D +T GLL++         L          R Y    +G  + +    L+
Sbjct: 140 LKRPGIVHRIDKDTSGLLVVAKSDRAHHHLADQFADHTVERRYIAVCYGVPEAND-PRLR 198

Query: 163 --KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI-K-KVFEFFN-WKVNRLI 216
             KG   +      +Q  L   +       V    G+   + + ++        V  L+
Sbjct: 199 GIKGTSFEPGNILKIQTQLGRHRTDRQRQAVSFTAGR-HAVTRVRILAALGAMPVAALV 256


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VN  L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNSKLCDKPKEKVLGGEQVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +  STV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDEDIIVINKPRDLVVHPGAGNPDSTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++       R L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQRRLVESLQRREITREYEAVAIGHMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>gi|254247414|ref|ZP_04940735.1| Pseudouridine synthase, Rsu [Burkholderia cenocepacia PC184]
 gi|124872190|gb|EAY63906.1| Pseudouridine synthase, Rsu [Burkholderia cenocepacia PC184]
          Length = 193

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 29/104 (27%), Positives = 49/104 (47%), Gaps = 2/104 (1%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L   +KP G +   S  + R ++ D + +    V + GRLD ++EGLLLLT+DGGL   +
Sbjct: 3   LIALNKPFGTICQFSAHETRPSLGDWVKT--PGVYAAGRLDADSEGLLLLTDDGGLQARI 60

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
             P  + ++ Y  +  G      L  L +G+ +        +  
Sbjct: 61  AEPRHKLVKRYWAQVDGAPGPADLKALARGVDLGDYVTRPCRAE 104


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 47/224 (20%), Positives = 78/224 (34%), Gaps = 36/224 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KVIA      SR  ++  + ++RV VNG+   +    V   D IE+    L   +  
Sbjct: 30  RLDKVIAELFPQYSRSRLQGWLKEERVLVNGVAAAKGNQKVQGMDRIELSPGVLAHMQAL 89

Query: 74  --------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPS------IFSRVISVGR 113
                            + +K  GLV   +      T+ + L           R   V R
Sbjct: 90  IPEDMNLDIVARTNEYTVVNKQAGLVVHPAPGHWTGTLMNGLYHLDPELIHVPRAGIVHR 149

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD----------QDKLNLL 161
           LD +T GL+++         L   L +    RVY     G++           +D  N L
Sbjct: 150 LDADTTGLMVVARTQETQVKLVQMLQARIVKRVYLAMVWGRISSPLTVNNPLGRDPRNRL 209

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTV---GLREGKNREIK 202
           +  +V  G         +   +     VT+    L  G+  +I+
Sbjct: 210 RMAVVDHGKPAVTHFTPVAFGELLEVPVTLMVCRLETGRTHQIR 253


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/276 (16%), Positives = 88/276 (31%), Gaps = 57/276 (20%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYSPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIKKVFE 206
            G++ + I     + TL +                    +  + + L  G+  +I+    
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIRVHMA 241

Query: 207 FFNWKVN----RLIRISYGPFQLGTLLAGSTREVSK 238
           +    +        R             G+T E+++
Sbjct: 242 YLQHPLLGDTAYGGRARI--------PKGATEELTE 269


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/264 (17%), Positives = 94/264 (35%), Gaps = 54/264 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + +  E    QR+ + +A+    + SR  ++ +I +  +K++G  ++     +    
Sbjct: 1   MVIQKVTDEGALDQRLDQWLAKQYHDVLSRSRLQTLIREGCLKIDGQFIKEPKTKLKPNQ 60

Query: 59  HIEVDGVPLRKAERT-------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            IE++   LR AE +              + + +KP GLV    + +   T+ + L    
Sbjct: 61  IIELEMPNLRDAEPSAEAIALDILYEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIYHC 120

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRF 149
                      R   V RLD NT G++++  +    + L    +   R       Y    
Sbjct: 121 GNSLSGIGGVKRPGVVHRLDKNTSGVMVVAKNDLAHKSLSAQFSDHGRTCALDRRYHALI 180

Query: 150 HGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT---LDTQKGSN-------AW 188
            G   ++             N  K+ +V +   +    VT   L  + G++       + 
Sbjct: 181 WGTPHRNVWTIDASLGRSPHNRTKQAVVHKQTPHARHAVTHFSLLEKYGTHADSTSFASL 240

Query: 189 VTVGLREGKNREIK-KVFEFFNWK 211
           +   L  G+  +I+  +       
Sbjct: 241 LECRLETGRTHQIRVHM-AHIGHP 263


>gi|313496998|gb|ADR58364.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 352

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 85/242 (35%), Gaps = 36/242 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVP 66
           QR+ +V A    A  SR  +   I + R+ V+G ++           +      E  G  
Sbjct: 50  QRLDQV-AAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSLLTLEAEQEAQGEW 108

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGR 113
           + +        E   + + +KP GLV   +      T+ + L      ++       V R
Sbjct: 109 IAEDIELDIVYEDDHILVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAGIVHR 168

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-DKLNL-------LKK 163
           LD +T GL+++         L  ++ + +  R+Y     G V    K++        +++
Sbjct: 169 LDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHGGMRQ 228

Query: 164 GIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIRI 218
            + +  G         +  +  S+  V V L  G+  +I+       + +        R 
Sbjct: 229 RMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRF 288

Query: 219 SY 220
             
Sbjct: 289 RI 290


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 80/224 (35%), Gaps = 33/224 (14%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----------IE 61
              R+ + +A A   SR + +  I   RV+V   ++ + A  +   +           + 
Sbjct: 7   EGVRLDQAVAEALSVSRAKAQAWIQAGRVRVGDRVVLKPAYRLKGEEVAVEPVEEAPMVL 66

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----------PSIFSRVI 109
            + +P+    E   +   +KP GL+T  +      TV + L           P    R  
Sbjct: 67  PEDLPIPILYEDEDVLALNKPPGLLTHPAPGVYSGTVVNLLLARYYGPVEKGPPELVRPG 126

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL-------NL 160
            V RLD +T G+L++   GG+   L         ++ Y     G   +  L         
Sbjct: 127 IVHRLDKDTSGVLVVAKHGGVLEGLARAFRDRLVMKRYLAITEGHPREGVLIAPIGRHPR 186

Query: 161 LKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  + + G+   Y + +  +    G  A V      G+  +I+
Sbjct: 187 ERHKMHVGGLAARYAETEFQVLATAGPYALVEARPHTGRTHQIR 230


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 78/236 (33%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+++   QR+ + +A      SR  ++  + + ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKDSQLGQRLDQAVAELFTDFSRSRLKEWLLEGKIAVNGDVITKPRTKVMGGEVITVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDLPLNIVYEDDDIIVINKPRDFVVHPGAGQADKTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V RLD +T GL+++         L   L      R Y     G +         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRDVTREYEAIVIGTMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G++ + I     + TL +                    +  + + L  G+  +I+
Sbjct: 182 GGMIDKPIGRHSTKRTLMSVSPMGKHAVTHYRVAEHFREHTRLRLRLETGRTHQIR 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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 85/242 (35%), Gaps = 36/242 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVP 66
           QR+ +V A    A  SR  +   I + R+ V+G ++           +      E  G  
Sbjct: 18  QRLDQV-AAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSQLALQAEQEAQGEW 76

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGR 113
           + +        E   + + +KP GLV   +      T+ + L      ++       V R
Sbjct: 77  VAEDIELDIVYEDDHIMVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAGIVHR 136

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-DKLNL-------LKK 163
           LD +T GL+++         L  ++ + +  R+Y     G V    K++        +++
Sbjct: 137 LDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHGGMRQ 196

Query: 164 GIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIRI 218
            + +  G         +  +  S+  V V L  G+  +I+       + +        R 
Sbjct: 197 RMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRF 256

Query: 219 SY 220
             
Sbjct: 257 RI 258


>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 = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 80/241 (33%), Gaps = 49/241 (20%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           + +  R+ + +A     SR + +  I    V V G ++ + +  +   + +EV       
Sbjct: 5   SASGVRLDQALAFEANTSRAKAQEWIEAGLVTVGGKVVTKPSYKLR-GETVEVEPPPPQP 63

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------- 106
                + +PL    E   L + +KP G++T  +      T+ + +   F           
Sbjct: 64  ASVAAEDIPLHILYEDPDLIVINKPAGMITHPAPGVYSGTLVNAILGRFGLDLSLGESEE 123

Query: 107 --------------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
                         R   V RLD  T G++++       R L          + Y     
Sbjct: 124 EGGLLLQAQKPELIRPGIVHRLDKGTSGVIVVARHEAAHRRLAEAFAGRSVYKRYIALTV 183

Query: 151 GQVDQDKLNLL-------KKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREI 201
           G   +  L+         +  + + G+     Q    +      +A V+  L  G+  +I
Sbjct: 184 GIPREGLLSAPIGRHPVDRTRMHVGGVAARHAQTEFEVLAVAEPHALVSAILHTGRTHQI 243

Query: 202 K 202
           +
Sbjct: 244 R 244


>gi|49066398|gb|AAT49291.1| putative bacteriocin [Prevotella nigrescens]
 gi|242332477|tpg|DAA06525.1| TPA_exp: NigA [Prevotella nigrescens]
          Length = 363

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 77/247 (31%), Gaps = 54/247 (21%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------D 63
              R+ K +  R   +SR  +++      + VNG  ++     V   D I +       D
Sbjct: 43  EAVRIDKFLFERMQHSSRNRIQKAADAGSIYVNGTPVKS-NYKVRPNDVITLMLDRPKHD 101

Query: 64  GVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFS 106
              + +        E   + + +KP GLV      + R T+ +          N      
Sbjct: 102 NTIVAEDMPLNVVYEDNEIMVINKPAGLVVHPGAGNFRGTLINAIAWHLRDLKNFDPNDP 161

Query: 107 RVISVGRLDINTEGLLLL--TNDGG------LARVLELPSTQWLRVYRVRFHGQVDQDK- 157
            V  V R+D +T GLLL+  T D                     R Y     G   +D+ 
Sbjct: 162 AVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTH------RSYVALVWGNFTEDEG 215

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + L+  +       G   VT   +  + G    +   L  G+  +I+  
Sbjct: 216 RIEGNIGRDSKDRLRMKVFDTDSGIGKPAVTHYKVLERFGYTTLIECILETGRTHQIRAH 275

Query: 205 FEFFNWK 211
            +     
Sbjct: 276 MKHIGHP 282


>gi|284931618|gb|ADC31556.1| Pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 311

 Score = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 82/235 (34%), Gaps = 33/235 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M     V  +    R+   +      SR +   +I    VKVN  L+ +    +   D +
Sbjct: 1   MPKHTFVNNDSEKIRLDIFLTYNLNLSRNKTSFLILNDLVKVNKKLVNKNNFVLKVGDVV 60

Query: 61  E----------VDGVPLRKAERTRL-------WLYHKPIGLVTTHSDPDGRSTVFDNLP- 102
           E          V    L   ++  +        + +KP  +++  +  +   T+ + L  
Sbjct: 61  ELEYEESIFNKVSNEILPFNKKLDIVYEDDDLIIVNKPTNMLSHPTTHNEPDTLLNCLMY 120

Query: 103 -SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DK 157
            +   +V    RLD +T GL++ T +      ++   T+    R Y    H   ++    
Sbjct: 121 YNKKQKVYLAHRLDKDTTGLIVATKNFKSLEKIQEQITKRIMKRYYLAIVHYPFNELRAV 180

Query: 158 LNL---------LKKGIV-IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++          LK G+   +       ++ +  Q    A +   L  G+  +I+
Sbjct: 181 IDAPIGYLKDHDLKFGVENTKNPKNAITKIYVLDQNKKYALIKCELLTGRTHQIR 235


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 75/229 (32%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E+   QR+ + +A      SR  ++  I   RV+VNG    +    V+  + + +  
Sbjct: 10  TVAESQLGQRLDQAMAELFPDYSRSRIKEWILDDRVQVNGKTANKPKEKVLGGEIVAIAA 69

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
              +               E   + + +KP   V      +   TV + L   + ++   
Sbjct: 70  QIEEDPRWEPQDIALDVVYEDCDILVINKPRDRVVHPGAGNPDGTVLNALLHYYPKIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQEREITREYEAVAIGTMTAGGTVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         L+  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVYPMGKPAVTHYRILEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 80/237 (33%), Gaps = 44/237 (18%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           + +    QR+ K ++ AG+   SR  V+ ++ Q  V+ +G  +   +  V      E+  
Sbjct: 46  IPDTAAGQRLDKALS-AGLPDLSRSRVQALLEQGCVRGDGRTITDPSQRVKYGQIFELRM 104

Query: 63  ----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + +  KP GLV   +  +   T+ + L +        
Sbjct: 105 PGSAAAEPLPQDIPLDVVYEDADVLVVDKPAGLVVHPAAGNPDGTLVNALLAHCGDSLSG 164

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ---- 155
                R   V RLD +T GL+++  +      L    +     R Y     G  +     
Sbjct: 165 IGGVRRPGIVHRLDKDTSGLMVVAKNDRAHHGLSDQFSDRTLSRTYLALVWGVPNPTQGR 224

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIK 202
                         +   +V  G      +  +    G + + V   L  G+  +I+
Sbjct: 225 IEGNIGRSSADRKKMA--VVTGGGKPAGTKYRVVKSFGMAASLVECVLETGRTHQIR 279


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 36/214 (16%), Positives = 80/214 (37%), Gaps = 28/214 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRKA-ERTRLW 76
           SR  V+ ++++ ++ VNG +  +    +   D          +E +   LR   E   L 
Sbjct: 42  SRSSVKGLLSRGQISVNGKVTRQFDAPLNPNDTVGINYGRGKVEFNNPLLRIVWEDDDLI 101

Query: 77  LYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSR--VISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  +D     T +    D +     R  +  + RLD +T G+++   +  +
Sbjct: 102 VINKREGLLSVSTDRIKERTAYRILSDYVKECDPRNKIFVLHRLDRDTSGIMMFAKNQKV 161

Query: 131 ARVLELPSTQ--WLRVYRVRFHGQVDQD-KL--------NLLKKGIVIQG-ICYGDMQVT 178
              L+   ++    R Y     G+ ++D  L          ++  +   G       +  
Sbjct: 162 KEQLQSNWSEAITQRTYVAVIEGRPEKDTDLIVSNLVENKHMQVYVTQDGDGKEAITRYR 221

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           L       + V + L  G+  +I+   +     +
Sbjct: 222 LLQTNNRYSLVELDLETGRKNQIRAQMQSIGHPI 255


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/258 (18%), Positives = 94/258 (36%), Gaps = 26/258 (10%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKAER 72
            IA +   S+ + + +I  + V VN   +  A+ N+   D +E+      + + +   E 
Sbjct: 16  FIAESLKISKNQAKDIIDSRNVIVNNKRVWIASHNLKPGDVVEIVQSEPKNDLKILY-ED 74

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
             +    KP  +V+        S+  D L       ++ ++ RLD  T G+LL   D  +
Sbjct: 75  DYIIAIDKPPTIVS----DKESSSAEDLLRKKLKNDKIKAIHRLDKETSGVLLFAKDYKI 130

Query: 131 ARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
               +        L++Y    H   ++           I+G         L    G   +
Sbjct: 131 FEKFKEIWEDKNVLKIYLAISH---NEANFKDFTINHDIEGKQAITHLKVLSKGNGFT-Y 186

Query: 189 VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL--REQLG 246
             V +  G+  +I+K        +          F+   L     + V++++L   + + 
Sbjct: 187 FQVRIETGRKHQIRKHLASIRHPIVGDKIYGIKKFE-NNL----VKRVTRQMLHSHKLVL 241

Query: 247 PHLLEEAQVNLDAPIYSS 264
           PH     ++ + API S 
Sbjct: 242 PHPYLNKKIEITAPIPSD 259


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 94/261 (36%), Gaps = 45/261 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVNV 54
           D+ +V  +   +R+ KVI       R++        + +   +++V+++G         +
Sbjct: 2   DRFVVSRHDDGRRLDKVI-------RKKWPSLPLGAMMKAFRKKQVRIDGARA-SFDQRL 53

Query: 55  MSTDHIEV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV-FD 99
           +    I V               G  +       LW+  KP GL++      G S V   
Sbjct: 54  VEGQEILVPWESAPTDVGAKRTGGHLVTVYRDESLWVVSKPAGLLSQPDKKGGDSVVTRA 113

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD- 156
            LP    +  +V RLD NT G+++L   G   R L       +  +VY     G + ++ 
Sbjct: 114 FLPGSSFQPQAVNRLDRNTSGIMVLALTGESLRDLSSRWRDGEMEKVYLALVVGDLPEEG 173

Query: 157 --KLNLLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                L K G      +  +G     +   L +  G  +   V L  G++ +I+      
Sbjct: 174 SIDAPLSKDGSSNKVFVDSKGQSSLTLYRRLASGGGL-SLCLVTLITGRSHQIRVHMSHI 232

Query: 209 NWKVNRLIRISYGPFQLGTLL 229
              V  L  + YG   L  + 
Sbjct: 233 GHPV--LGDVKYGDRALNGVK 251


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 82/236 (34%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V           
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYENEI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVI 109
             + +PL    E   + + +KP GLV      +   T+ + L                V 
Sbjct: 101 IPENIPLNIVYEDPYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPEYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      ++  +    R YR    G V+QD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRRYRALVWGNVEQDEGTIVGSIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMSDPSMGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 85/246 (34%), Gaps = 45/246 (18%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+++G ++      +   D IEV   
Sbjct: 55  IPEAMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLHGEVVR-PRAAISGGDRIEVVPQ 113

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPDAVEL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD------- 156
            R   V RLD +T GL+++         L  +L +    R Y     G+  ++       
Sbjct: 174 PRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEEATIDAPI 233

Query: 157 -----KLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVF 205
                    +    +I+   G        TLD      A V++    L  G+  +I+  F
Sbjct: 234 GRDPRDRTRMA---IIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRTHQIRVHF 290

Query: 206 EFFNWK 211
           E     
Sbjct: 291 ESEGHP 296


>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 = 75.2 bits (184), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 51/275 (18%), Positives = 91/275 (33%), Gaps = 70/275 (25%)

Query: 10  NFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +  PQR+ K ++R     A + SR  + R++ +  V+VNG ++  A   V + D IE   
Sbjct: 12  DDPPQRLDKALSRDVPEEATL-SRTRLARLLEEGAVQVNGAVMRDAKARVTAGDLIEILV 70

Query: 62  -------VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                  +    +      E   L + +KP G+V   +      T+ + L          
Sbjct: 71  PEARESHISAEAIALTVVYEDDDLIVINKPAGMVVHPAPGSPEGTLVNALLHHCGDSLSG 130

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN 159
                R   V R+D +T GLL++       + L     +    R YR   +G  D     
Sbjct: 131 VGGSKRPGIVHRIDKDTSGLLVVAKSDAAHQGLAAQFEAHSVERSYRAVVNGVPDAGDPR 190

Query: 160 L-------LKKG--------------------IVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           L        + G                    ++ +G  +   +  +    G+     V 
Sbjct: 191 LRGLPGISFEAGNILRIATRLARHKTDRQKQAVLFEGGRHAVTRARVIESFGTPGV--VS 248

Query: 193 LRE-----GKNREIK-KVFEF----FNWKVNRLIR 217
           L E     G+  +I+  +           V    R
Sbjct: 249 LMECWLETGRTHQIRVHMAHAGHGLIGDPVYGGRR 283


>gi|319943653|ref|ZP_08017934.1| ribosomal large subunit pseudouridine synthase D [Lautropia
           mirabilis ATCC 51599]
 gi|319742886|gb|EFV95292.1| ribosomal large subunit pseudouridine synthase D [Lautropia
           mirabilis ATCC 51599]
          Length = 332

 Score = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 88/242 (36%), Gaps = 45/242 (18%)

Query: 12  TPQRVSKVIARA------GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
             QR+ + + R       GI SR  ++R IA   V+V+   +   ++ +   + IEV+  
Sbjct: 25  QGQRLDQFLTRYLQERLDGI-SRTRIQRWIALGAVRVD-QQVRLPSLRLKGVESIEVEPQ 82

Query: 66  PLR-----KAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNL------PSIF 105
           PL        +   L + H         KP GLVT  +  + R+T+ + L       +  
Sbjct: 83  PLESDTAFAPDPVPLAIVHQDADITVIDKPAGLVTHPAPGNWRNTLMNGLLHADPKAARL 142

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVR----------FHGQV 153
            R   V RLD +T GLL+          L   L S Q  R Y               G +
Sbjct: 143 PRAGIVHRLDRDTSGLLVCARSERAFASLTAQLASRQMGRRYLAIACGQTPAQGTVEGNI 202

Query: 154 DQDKLNLLKKGIVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +D+ N L+  +V Q           ++   +     A +   L  G+  +I+       
Sbjct: 203 GRDERNRLRMAVV-QPPAGKPARTHYRLLAASPDAEAAAILCKLESGRTHQIRVHMAHIG 261

Query: 210 WK 211
             
Sbjct: 262 HP 263


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/230 (16%), Positives = 72/230 (31%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A   +  SR  ++  +   ++ VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFVDFSRSRLKEWLLDGKITVNGTVVTKPRTKVMGGECITVL 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP   V          TV + L   +     
Sbjct: 69  AELEDEQRWEAQDIPLNIVYEDDDILVINKPRDFVVHPGAGTPDRTVLNALLFHYPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQ 152
             R   V RLD +T GL+++         L          R Y                 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRDLQKRNITREYEAIAIGKMTAGGMIDKP 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 189 IGRHSTKRTLMAVNQMGKPAVTHYRVAEHFRE-HTRIRLRLETGRTHQIR 237


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 78/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGHLCDKPKEKVLGGEQVSINA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEVRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 84/246 (34%), Gaps = 45/246 (18%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V++ G ++      +   D IEV   
Sbjct: 55  IPETMHGERLDKALAKLLPDYSRSRLQQWIDAGAVRLRGEVVR-PRAAISGGDRIEVVPQ 113

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPDAVEL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD------- 156
            R   V RLD +T GL+++         L  +L +    R Y     G+  ++       
Sbjct: 174 PRAGIVHRLDKDTSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEEATIDAPI 233

Query: 157 -----KLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVF 205
                    +    +I+   G        TLD      A V++    L  G+  +I+  F
Sbjct: 234 GRDPRDRTRMA---IIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRTHQIRVHF 290

Query: 206 EFFNWK 211
           E     
Sbjct: 291 ESEGHP 296


>gi|317968170|ref|ZP_07969560.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp.
           CB0205]
          Length = 325

 Score = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 84/246 (34%), Gaps = 39/246 (15%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +      P R+ + + A+    SR  +++ I    V+VNG+    A   +   D +E+  
Sbjct: 14  LTYPKPLPMRLDRWLVAQRPEQSRARIQKFIDAGYVRVNGVTGR-AKTPLRLNDTVELWM 72

Query: 63  -----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                        +PL    E   L + +KP GL    +  +   T+ + L      +  
Sbjct: 73  PPPEPLPYLIPQDIPLDVLYEDEHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 132

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDK-- 157
           +G         RLD +T G +++         L++   + +  R Y    HG    D   
Sbjct: 133 IGGEMRPGIVHRLDKDTTGCIVVAKSQEALVKLQVQIQKRVASREYLAVVHGAPAGDNGT 192

Query: 158 ---------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                     +  K  +V  G   +     TL  + G  A +   L  G+  +I+     
Sbjct: 193 IVGAIGRHPADRKKYAVVHDGSGRHACTHWTLLERLGDYALMRFKLDTGRTHQIRVHCAH 252

Query: 208 FNWKVN 213
               + 
Sbjct: 253 IGHPIV 258


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 83/236 (35%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V           
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYENEI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPENIPLTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      L+  +    R YR    G V+QD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGVVEQDEGTIVGNIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 86/239 (35%), Gaps = 43/239 (17%)

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--GVPLR----------KAERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFS- 106
            +     +             E   + + +KP GL+   + S  +  + V   L      
Sbjct: 67  YEITEEQISIVPVPMDLDIVYEDDAILVVNKPKGLIVHPSPSTLNQPTLVHGLLAHTTQL 126

Query: 107 -------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQ---WLRVYRVRFHG--- 151
                  R   V R+D +T GLL++  TN+   A  + +   +     R Y    H    
Sbjct: 127 SDLNGELRPGIVHRIDKDTTGLLVVAKTNE---AHEILVEDLKQRLISREYVAIVHHQFK 183

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +D  N  +  +  Q          L  +    + +   L  G+  +I+
Sbjct: 184 HQSATVDAPIGRDPKNRQRMAVTDQNSKQAVTHFYLAERFNDFSVLRCKLDTGRTHQIR 242


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I   +V V+G  + +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDDKVTVDGKKINKPKEKVLGGELVAIDA 69

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                A             E   + + +KP GLV      +   TV + L   +  ++  
Sbjct: 70  QIEEDARWAPQEIPLDIVYEDNDILVINKPRGLVVHPGAGNPDGTVLNALLYYYPEIMDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y            R    +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGNMTAGGRVDEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 SRHSTKRTHMAVHPMGKPATTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 75/230 (32%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             V+E+   QR+ + +A      SR  ++  + + +V VNG ++ +    VM  + I V 
Sbjct: 9   QTVKESQLGQRLDQAVAELFTDFSRSRLKEWLLEGKVMVNGNVVTKPRTKVMGGEAITVQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D               E   + + +KP  LV          TV + L   F     
Sbjct: 69  AELEDEQRWEAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGTPDGTVLNALLFHFPPIAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQ 152
             R   V RLD +T GL+++         L  EL      R Y                 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRELQKRNITREYEAIAIGKMTAGGMIDKP 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 189 IGRHSTKRTLMAVSPLGKPAVTHYRVAEHFRE-HTRIRLRLETGRTHQIR 237


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV+VNG L+ +    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAEMFPDYSRSRIKEWILGDRVQVNGKLINKPKEKVLGGEEISIDA 69

Query: 64  ----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                              E   + + +KP  LV      +   TV + L   +  +   
Sbjct: 70  IIEEDARWEPQNIELNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
           GIV + I     + T                      ++  + + L  G+  +I+
Sbjct: 183 GIVEEPISRHPTKRTHMAVHPMGKPAITRYRVMEHFRAHTRLRLRLETGRTHQIR 237


>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 = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 82/259 (31%), Gaps = 51/259 (19%)

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---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                     G  +      E   L + +KP GLV      +   T+ + L         
Sbjct: 80  MPEPEPAEPQGENIALDVLYEDDELIVINKPAGLVVHPGAGNWTGTLVNALIHHCGDSLS 139

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHGQVD 154
                 R   V RLD  T G++++       + L              R Y     G   
Sbjct: 140 GIGGVRRPGIVHRLDKETSGVMVVAKTDRAHKSLSEAFADHGLTGDLERAYLALVWGIPQ 199

Query: 155 Q----------DKLNLLKKGIVIQGICYGDMQVT----------LDTQKGSNAWVTVGLR 194
           +             + +++ +V +G       VT             +  + + V   L 
Sbjct: 200 RPTGRVDAPLGRAADRVRRAVVPEGRDDARHAVTHFAVQERFGESQQEFATASMVECRLE 259

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+         V 
Sbjct: 260 TGRTHQIRVHMAHIGHPVI 278


>gi|319408111|emb|CBI81764.1| ribosomal large subunit pseudouridine synthase D [Bartonella
           schoenbuchensis R1]
          Length = 340

 Score = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 85/262 (32%), Gaps = 56/262 (21%)

Query: 4   KNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + I  E+   QR+ + +A+      SR  ++ +I +  +KV+G L++     +     IE
Sbjct: 3   QQITDESALGQRIDQWLAKKYHNELSRSRLQTLIREGYLKVDGQLIKEPKTKLQPNQTIE 62

Query: 62  ----------VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
                     ++G  +      E   + + +KP GLV    + +   T+ + L       
Sbjct: 63  LIIPPLKNVHLEGEAIVLDILFEDDHVIVINKPAGLVVHPGNGNWTGTLVNALIHHCGDS 122

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-------WLRVYRV---- 147
                   R   V RLD NT G++++  +   A                  R Y      
Sbjct: 123 LSGIGGVKRPGIVHRLDKNTSGVMVVAKN-DFAHKSLSAQFSDHGRTCALDRRYHALIWN 181

Query: 148 -------RFHGQVDQDKLNLLKKGIV----------IQGICYGDMQVTLDTQKGSNAWVT 190
                       + +   N +K+ +V          I      +   T    +   + + 
Sbjct: 182 APRRNIGTIDVPLGRSPHNRIKQTVVRHQNVHARHAITHFSLLEKYKTCADAEPFASLLE 241

Query: 191 VGLREGKNREIK-KVFEFFNWK 211
             L  G+  +I+  +       
Sbjct: 242 CRLETGRTHQIRVHM-AHIGHP 262


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 80/238 (33%), Gaps = 43/238 (18%)

Query: 15  RVSKVIARAGI---ASRREVERMIAQQRVKVNGILLE-----RAA----VNVMSTDHIEV 62
           R+   +A  GI    SR  ++++I    + VNG  ++     +A     V +  T+ +EV
Sbjct: 34  RIDVYLA--GIFDHLSRSFIQKLIGDGYITVNGTRVKANYKLKAGELVRVEIPYTEELEV 91

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
              P+      E   + + +KP G+V   +  +   T+ + L      +           
Sbjct: 92  SAEPIPLEILYEDRDVIVINKPQGMVVHPAPGNYSGTLVNALLWHCKDLSGINGVMRPGI 151

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ------------- 155
           V RLD +T G+++   +      L          R Y    HG + +             
Sbjct: 152 VHRLDKDTSGVIMAAKNDETHASLAKQIKDRTVTRRYLALIHGVIPEPAGIIEAPIGRDP 211

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +   +  +          +  +     +V   L  G+  +I+    +  + V 
Sbjct: 212 KDRKKMA--VTTKNSKPAVTHYKVLERFNKYTFVECKLETGRTHQIRVHMAYLKYPVV 267


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 84/228 (36%), Gaps = 38/228 (16%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
            QR+ + ++      SR  ++ +I Q  V+VNG +     + +   +++EV+  P++ A 
Sbjct: 32  TQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEVEIPPVQAAQ 91

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------ 112
                       E  +L + +KP GLV   +      T+   L +    +  +G      
Sbjct: 92  LVAQDIPLDILYEDEQLLILNKPAGLVVHPAPGHLEGTLVHALLAHCPNLPGIGGVQRPG 151

Query: 113 ---RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----------- 156
              RLD +T G + +  T+       L+L S    R Y    +G    +           
Sbjct: 152 IVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKIARREYLGVVYGAPKSESGTIDLPIGRH 211

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   +    V QG         +  + G+   +   L  G+  +I+
Sbjct: 212 PQQRKKMAIVPVEQGGRNAITNWHIKERLGNYTLIHFQLETGRTHQIR 259


>gi|257869733|ref|ZP_05649386.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           gallinarum EG2]
 gi|257803897|gb|EEV32719.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           gallinarum EG2]
          Length = 299

 Score = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 90/244 (36%), Gaps = 46/244 (18%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGI--------LLERAAVNV 54
            E   PQ++   +   GI      + ++A+      ++ VN          +       V
Sbjct: 7   YERQEPQQLKYFLKEQGI-----SKGLLAKIKFQGGKIFVNDQRQNVLYSLVQNDTVTIV 61

Query: 55  MSTD----HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-- 107
           +  +     + +D  P+    E   L + +KP G+ +  +      T+ + + + + +  
Sbjct: 62  IPDEGEHETVLLDETPIEIVYEDQHLLIVNKPAGIASIPAQYHPNGTMANRVKAYYKQQG 121

Query: 108 -----VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
                +  V RLD +T GL+L    G     L  +L   Q ++ Y+    G         
Sbjct: 122 YQDQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDVQLRQKQLIKKYQAIVAGQIQELASHG 181

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +D  +LLK+   ++G      +  L  +    A VT+ L  G+  +I+  F  
Sbjct: 182 EITYPIARDLSSLLKRKTSLEGKSART-EYWLTKKDQQVAVVTILLHTGRTHQIRVHFAA 240

Query: 208 FNWK 211
            +  
Sbjct: 241 IHCP 244


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 86/248 (34%), Gaps = 43/248 (17%)

Query: 4   KNIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + IV +  +  R+ K +    I  ASR +V++      VKVNG  ++     V   + I 
Sbjct: 30  RIIVDKGQSLVRIDKFLCDR-IENASRNQVQKAAEAGFVKVNGNPVKS-NYKVKPLEEIT 87

Query: 62  V-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------- 99
           +             + +PL    E   L + +KP GLV      + R T+ +        
Sbjct: 88  IYMDTPPHEIEIIPEDIPLNIVYEDDYLMVVNKPAGLVVHPGHGNYRGTLVNAIAWHMKN 147

Query: 100 --NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
                +   RV  V R+D +T GLL++         L +   +    R YR    G    
Sbjct: 148 NSCYDANDPRVGLVHRIDKDTSGLLVIAKTPEAKSKLGIQFFNKTTKREYRALVWGNIEE 207

Query: 152 -------QVDQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + ++  + L+  +        +      +  + G    V   L  G+  +I+
Sbjct: 208 EEGRIEGNIARNPKDRLQMAVFADPEIGKHAVTHYKVLERLGYVTLVACRLETGRTHQIR 267

Query: 203 KVFEFFNW 210
              +    
Sbjct: 268 VHMKHIGH 275


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 87/238 (36%), Gaps = 43/238 (18%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ K++AR     SR  +++ I    V+V+G  + R    V   + IEV          
Sbjct: 75  ERLDKLLARHFSEFSRSRLQQWIESGAVRVDGQ-VRRPRDAVQMGNRIEVQPQAAPEASA 133

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVG 112
              + VPL    E   L + +KP GLV   +  +   TV + L           R   V 
Sbjct: 134 FAPEDVPLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRDPGAASLPRAGIVH 193

Query: 113 RLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
           RLD  T GL+++    T    L R L   +    R Y     G           + +D  
Sbjct: 194 RLDKETSGLMVVARTLTAQTDLVRQL--QARTVKRTYIALVWGRTYDEGTIDAPIGRDPR 251

Query: 159 NLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLR--E-GKNREIKKVFEFFNWK 211
              +  IV    G        TL T      +V++ +   E G+  +I+  FE     
Sbjct: 252 ERTRMAIVQTASGKPSRTHFRTLATVPLGRGFVSMVMCKLETGRTHQIRVHFESIGHP 309


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 83/236 (35%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V           
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVVMDRPRYENEI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   + + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPEDIPLNIVYEDKYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDVPDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      L+  +    R YR    G V+QD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRKYRALVWGTVEQDEGTIVGNIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMSDPAVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>gi|146320632|ref|YP_001200343.1| YlyB [Streptococcus suis 98HAH33]
 gi|145691438|gb|ABP91943.1| YlyB [Streptococcus suis 98HAH33]
          Length = 243

 Score = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/200 (21%), Positives = 73/200 (36%), Gaps = 33/200 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNG---------ILLERAAVNVMSTDHIEV-- 62
            R+ K ++     SR      I   +V VNG          + +     +   + I+   
Sbjct: 10  IRLDKALSDLTDLSRSVANEQIKAGQVLVNGQPKKAKYSVQVGDVLTYQIPEVEEIDYVA 69

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VG 112
           + +PL    +   + + +KP G+V   S      T+ + L      +           V 
Sbjct: 70  EDIPLEIVFQDEDVAVVNKPQGMVVHPSAGHTSGTLVNALLYHVKDLSGINGVLRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-- 168
           R+D +T GLL++  +      L  EL   + LR Y    HG +  D      +G+ I+  
Sbjct: 130 RIDKDTSGLLMIAKNDDAHTKLAAELKDKKSLRKYWAIVHGNLPND------RGV-IEAP 182

Query: 169 -GICYGDMQVTLDTQKGSNA 187
            G    D +    T KG  A
Sbjct: 183 IGRSEKDRKKQAVTAKGKEA 202


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/176 (22%), Positives = 68/176 (38%), Gaps = 26/176 (14%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----- 60
           V+E     R+   +A      SR  ++R+I +  V+V G  ++  +  V   + I     
Sbjct: 9   VEEEEAGVRLDVYLARNLPENSRSYLQRLINEGYVQVGGRKVK-PSYKVKPGEEILVFLP 67

Query: 61  -----EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                EV+  P+      E   L + +KP G+V        R T+ + L           
Sbjct: 68  PAETLEVEPEPIPLEIIYEDEDLLVVNKPRGMVVHPGAGHKRGTLVNALLYHCRSLSGIN 127

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
              R   V RLD +T GLL++  +      L   L   + L+ Y    +G+V   +
Sbjct: 128 GVLRPGIVHRLDKDTSGLLMVAKNDAAHLSLSAQLKERRVLKEYWALVYGEVKPAQ 183


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 80/229 (34%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VNG + ++    V+  +++ ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGKMCDKPKEKVLGGENVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEDVRFEAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMSVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 81/229 (35%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I + RV++NG ++ +    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKEWILENRVQINGNVINKPKEKVLGGESVAIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       + L    E   + + +K   LV      +   TV + L   +  ++  
Sbjct: 70  LIEEEARWEAQDIKLDIVYEDQDILVINKSRDLVVHPGAGNPDGTVLNALLHHYPEIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
                V RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQAREITREYEAVAIGSMTAGGMVEQPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 190 ARHATKRTHMAVHPMGKPAVTHYRIMEHFR-AHTRLRLRLETGRTHQIR 237


>gi|88809823|ref|ZP_01125329.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805]
 gi|88786207|gb|EAR17368.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 7805]
          Length = 327

 Score = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 82/251 (32%), Gaps = 49/251 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE-----VERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +      P R+ + +       RRE     +++ I    V+VNG   + A   +   D +
Sbjct: 26  LTYPKPLPMRLDRWLVSQ----RREQSRARIQKFIDAGLVRVNGRTGK-AKTPLRQGDEV 80

Query: 61  EVD---GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------- 99
           ++      PL              E   L + +KP GL    +  +   T+ +       
Sbjct: 81  QLWMPPPEPLPYLKPEAMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCP 140

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
           +LP I  ++    V RLD +T G +++         L++   +    R Y    HG    
Sbjct: 141 DLPGISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGVPSG 200

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D                     +  +   +     +L  + G  + +   L  G+  +I+
Sbjct: 201 DSGTIVGAIGRHPVDRKKYAV-VSTESGRFACTHWSLQERLGDYSLLRFKLDTGRTHQIR 259

Query: 203 KVFEFFNWKVN 213
                 N  V 
Sbjct: 260 VHCAHMNHPVV 270


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/245 (16%), Positives = 81/245 (33%), Gaps = 45/245 (18%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     IE+
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVIVNKPREKVFELQQIEI 67

Query: 63  D---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                  +  A          E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  AATLEEEVHAAAQAIELNIVYEDDHILVINKQAGLVVHPGAGNADGTLMNALLHHCPDIE 127

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
            V       RLD +T GL+++         L   L + +  R Y     G +        
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVMGTMTGG----- 182

Query: 162 KKGIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVF 205
             G V + I     + T                +  +  ++  + + L  G+  +I+   
Sbjct: 183 --GTVDEPIGRHPTKRTHMAVHHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIRVHM 240

Query: 206 EFFNW 210
           E+   
Sbjct: 241 EYIGH 245


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 92/252 (36%), Gaps = 47/252 (18%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVM 55
           MK +N ++ E+    R+   I++        SR   +++I  + V VNG + +++   + 
Sbjct: 1   MKTENFLINEDEANSRLDVFISK---CFEEKSRSYAQKLIEDKNVLVNGSI-KKSNYKLK 56

Query: 56  STDHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NL 101
           + D++EV   +   +             E   + +  KP G+V    + +   T+ +  L
Sbjct: 57  TGDNVEVTIKEDETINIEPEDIKLNILYEDEDVIVIDKPQGMVVHPGNGNYSGTLVNGLL 116

Query: 102 PSIFS--------RVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFH 150
               S        R   V R+D +T G+L++  +   A ++           R Y     
Sbjct: 117 YHCDSLSSINGDVRPGIVHRIDKDTSGVLVVAKN-DNAHIILSEQLKEHSMKREYVALVE 175

Query: 151 GQVDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G +  D+            + +K+ +V +          +  +   N  V   L  G+  
Sbjct: 176 GIIKDDEGTIDEPLGRNPKDRIKRAVV-RNGKNAITHYEVIRRFNKNTLVKCILETGRTH 234

Query: 200 EIKKVFEFFNWK 211
           +I+      N  
Sbjct: 235 QIRVHMAHINHP 246


>gi|225077010|ref|ZP_03720209.1| hypothetical protein NEIFLAOT_02062 [Neisseria flavescens
           NRL30031/H210]
 gi|224951567|gb|EEG32776.1| hypothetical protein NEIFLAOT_02062 [Neisseria flavescens
           NRL30031/H210]
          Length = 238

 Score = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 52/168 (30%), Gaps = 26/168 (15%)

Query: 72  RTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +R    +KP G++   S     + R  V      I   V  V RLD  T G+LL   D 
Sbjct: 8   DSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLFALDT 67

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYG- 173
             AR+L     +    + Y     G +              DK+   +    +Q      
Sbjct: 68  EAARLLTQQFENKTIEKTYWAIVRGHLPSDGLIDYALKYMPDKIAEAQTEATLQEAQTAY 127

Query: 174 --------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     Q  L       +W  +    G+  ++++  +     + 
Sbjct: 128 RCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIV 175


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 76/198 (38%), Gaps = 24/198 (12%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK------AERTRLWLYHKPI 82
           + V+ ++  ++V VNG ++ +   ++   D I VD  P          E   L + +KP 
Sbjct: 23  KNVKNLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSLDIIYEDRELIVINKPA 82

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           GL++     +   T +  +           RV  V RLD  T G+LL   +  +   L+ 
Sbjct: 83  GLLSMAGGNEKEKTAYHLVGEYLKSKNKNARVFIVHRLDKETSGVLLFAKNEIIKNKLQN 142

Query: 137 PSTQWL--RVYRVRFHGQVDQDKL-------NLLKKGIVIQGICYGDMQVT---LDTQKG 184
                +  R Y     G++ +              + + I     G + +T   +  +  
Sbjct: 143 NWNDIVYKRGYLAIIEGKLKKKHGTIKNHLDESKTQMVYIANNGKGKLAITNYKVLKESR 202

Query: 185 SNAWVTVGLREGKNREIK 202
            N+ + V L  G+  +I+
Sbjct: 203 YNSLIEVFLETGRKNQIR 220


>gi|312953695|ref|ZP_07772531.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|310628369|gb|EFQ11652.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|315151826|gb|EFT95842.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
          Length = 297

 Score = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 90/245 (36%), Gaps = 48/245 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ-- 155
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G ++Q  
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKLTKIYYALVGGAIEQLS 178

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                       L+ L K  VI+   +   +  L  +    A V + L  G+  +I+  F
Sbjct: 179 EHQLIEKPIGRDLSSLLKRQVIETGQFASTEYWLAKRGAQAAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNW 210
           E    
Sbjct: 239 EAIGC 243


>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 = 74.4 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/252 (16%), Positives = 87/252 (34%), Gaps = 42/252 (16%)

Query: 1   MKDKNIVQENFT-PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           MK+ N+  +     +RV K +A      SR  ++++I   ++KVN   ++  +  +   D
Sbjct: 1   MKEYNLKVDKSEAGKRVDKFLASQFDDFSRNYIQKLIEDSKIKVNSNPVQN-SYLIKEAD 59

Query: 59  HIEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---- 101
            I+V             D       E   + + +K   +V   +      T+ + L    
Sbjct: 60  EIKVIIDKAKKSSIKAVDIELDIIYEDQDIIIINKDADMVVHPAPGHYDDTIVNALLAYT 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
                 +   R   V RLD +T GLLL+  +    + L       +  + Y     G + 
Sbjct: 120 NDLSAINGVKRPGIVHRLDKDTSGLLLVAKNDKSHKELSRQFKKREVDKYYLALLKGILP 179

Query: 155 -------------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                         ++   +   +  +       +  +     ++  V V +  G+  +I
Sbjct: 180 YKTGKIDAPIGRHPNQRKKMA--VRKRKSKKAVSRFKILESFKNHTLVEVKIETGRTHQI 237

Query: 202 KKVFEFFNWKVN 213
           +  F +  + V 
Sbjct: 238 RVHFAYLGYPVV 249


>gi|319638811|ref|ZP_07993569.1| pseudouridine synthase [Neisseria mucosa C102]
 gi|317399715|gb|EFV80378.1| pseudouridine synthase [Neisseria mucosa C102]
          Length = 238

 Score = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 52/168 (30%), Gaps = 26/168 (15%)

Query: 72  RTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +R    +KP G++   S     + R  V      I   V  V RLD  T G+LL   D 
Sbjct: 8   DSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLFALDT 67

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYG- 173
             AR+L     +    + Y     G +              DK+   +    +Q      
Sbjct: 68  EAARLLTQQFENKTIEKTYWAIVRGHLPSDGLIDYALKYMPDKIAEAQTEATLQEAQTAY 127

Query: 174 --------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     Q  L       +W  +    G+  ++++  +     + 
Sbjct: 128 RCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIV 175


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 85/242 (35%), Gaps = 36/242 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVP 66
           QR+ +V A    A  SR  +   I + R+ V+G ++           +      E  G  
Sbjct: 50  QRLDQV-AAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVHGGSLLALEAEQEAQGEW 108

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGR 113
           + +        E   + + +KP GLV   +      T+ + L      ++       V R
Sbjct: 109 IAEDIELDIVYEDDHILVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAGIVHR 168

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-DKLNL-------LKK 163
           LD +T GL+++         L  ++ + +  R+Y     G V    K++        +++
Sbjct: 169 LDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHGGMRQ 228

Query: 164 GIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIRI 218
            + +  G         +  +  S+  V V L  G+  +I+       + +        R 
Sbjct: 229 RMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRF 288

Query: 219 SY 220
             
Sbjct: 289 RI 290


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 63/318 (19%), Positives = 114/318 (35%), Gaps = 48/318 (15%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V+E F+ +R+ + +A      SR   + +I    V ++   +++ +  V +         
Sbjct: 9   VEEEFSNKRLDQFLALVYPEYSRSFYQNLIENGFVLLDNSPVKKPSTKVKTGQEFTIIIP 68

Query: 62  --------VDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   L + +KP G+V   S      T+ + L   F  V    
Sbjct: 69  PPEPLEIEPENIPLEICYEDEDLAVVYKPPGMVVHPSVGHTSGTLVNALLYHFKNVSQYQ 128

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK-LNL 160
                  V RLD +T GLL++       + L       +  + Y+    G V +D  L  
Sbjct: 129 GKERAGIVHRLDKDTAGLLIVAKTEFAHKELQKMFQDREIDKKYKAIVSGIVKKDHGLID 188

Query: 161 LKKGIVIQGIC--------YGDM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           L  G  I              D      V    +K +   V + L  G+  +I+  F   
Sbjct: 189 LPIGRSIYNRQKMGTVSTNLKDALTEYWVEKRFEKHNLTLVDIKLHTGRTHQIRVHFSAI 248

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS--ET 266
              +       YG F+   L +    E++K  L ++L  H L   ++    P  S     
Sbjct: 249 GHPL--FNDFVYG-FKKSNLSS----ELAKN-LSDKLNYHALVAYKLTFRHPRTSQILNV 300

Query: 267 LVRDRPNIISEVPDDFTR 284
            ++  P  I E+  + ++
Sbjct: 301 ELKSLPKEIEEILQELSK 318


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/223 (18%), Positives = 72/223 (32%), Gaps = 36/223 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+   +A     SR +   +I    V VN     + ++ +   D I V            
Sbjct: 11  RLDVALASELKISRNQATNLIKNALVSVNSKPALKPSMQLNQNDEICVKFALPKEKTNDY 70

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
             +       E   + + +KP  +V   +     +T+ + L          +   R   V
Sbjct: 71  EANFEIPVIYEDEDILVLNKPPQIVVHQAPSVKEATLVEWLNQKGFMLSNLNGDLRAGIV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------N 159
            RLD  T G +++  +      L   L      R+Y       + Q+ +          N
Sbjct: 131 HRLDKGTSGAIVVAKNNAAHAALSAQLNDKSMGRIYLALTDLPLKQECIIDKPIGRSPSN 190

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            LK GIV  G       + L  Q      +   L  G+  +I+
Sbjct: 191 RLKMGIVTNGRHAKSAFLNL-VQTDEVNLIAAKLFTGRTHQIR 232


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 38/171 (22%), Positives = 62/171 (36%), Gaps = 30/171 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ +V+A RA   SR  ++ +I   RV +    L   A +V + D I +D          
Sbjct: 14  RLDRVLALRAPELSRSRLKALILAGRVAIGETPLCDPAYHVGAGDTITIDVPPAIAAEPA 73

Query: 64  GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
           G P+      E   + +  KP GLV   +      T+ + L +             R   
Sbjct: 74  GEPIALDIVHEDDDIIVIDKPRGLVVHPAAGHETGTLVNALIAHCGASLSGIGGVRRPGI 133

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQ 155
           V RLD +T GL++   +    + L        R       Y     G  ++
Sbjct: 134 VHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRTGALRRGYYAFVWGVPNR 184


>gi|226943324|ref|YP_002798397.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
 gi|226718251|gb|ACO77422.1| Pseudouridine synthase [Azotobacter vinelandii DJ]
          Length = 336

 Score = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 99/289 (34%), Gaps = 41/289 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------GV 65
           QR+ +V A    A  SR  +   I   R+ V+G    R    V     +E+D      G 
Sbjct: 35  QRLDQV-AAQLFAEHSRSRLAAWIKDGRLTVDGA-ALRPRDIVHGGALLELDAEQQAQGE 92

Query: 66  PLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVG 112
            + +A       E  ++ + +KP GLV   +      T+ + L           R   V 
Sbjct: 93  WIAQAIELDIVHEDEQILVLNKPAGLVVHPAAGHADGTLLNALLHHVPGLVNVPRAGIVH 152

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---------LNLL 161
           RLD +T GL+++         L  +L      R+Y     G +                 
Sbjct: 153 RLDKDTTGLMVVAKTLQAQTRLVEQLQKRSVSRIYEAIVVGVITAGATIDAPIGRHGQQR 212

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIR 217
           ++  V++G         +  +  ++    + L  G+  +I+       + +        R
Sbjct: 213 QRMAVVEGGKPAVSHYRVLERFRAHTHARIKLETGRTHQIRVHMAHVGYSLVGDPVYGGR 272

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQLGP--HLLEEAQVNLDAPIYSS 264
               P    TL+  + RE  ++ L  +     H     ++  +AP+   
Sbjct: 273 FRIPPAASPTLVQ-ALREFPRQALHARFLELDHPASGERLKWEAPLPDD 320


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 46/225 (20%), Positives = 79/225 (35%), Gaps = 31/225 (13%)

Query: 9   ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E+   QR+ + +A      SR  ++  I   +V VNGI        V+  +HIE+     
Sbjct: 13  ESQLGQRLDRALAELFPTYSRSRIKEWILAHQVTVNGITKSIPKEKVLGGEHIEIHTYIE 72

Query: 63  DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTV----FDNLPS--IFSRV 108
           +               E T + + +KP GLV      +   T+     D  P      R 
Sbjct: 73  ENKRWMPQKIPLNIIYEDTDILVINKPSGLVVHPGAGNPDHTILNALLDYYPDITHVPRA 132

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-----DKLNLL 161
             V RLD +T GL+++         L   L +    R Y     G +       + +   
Sbjct: 133 GIVHRLDKDTTGLMVIAKTLRAQTSLVDALQARLVTREYEAIAVGHITAGGSINEPIARH 192

Query: 162 KKGIVIQGI-CYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           K       +   G   VT   +     ++  + + L  G+  +I+
Sbjct: 193 KSKRTHMAVHPLGKSAVTHYRILQHFRAHTRLRLRLETGRTHQIR 237


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 85/245 (34%), 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  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                     + +PL    E + L L +KP G+V   +      T+ + L          
Sbjct: 68  PEEKPTEIRAEEIPLDIVYEDSELLLVNKPKGMVVHPAPGHSGGTLVNALLGRPGPELSS 127

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK-- 157
                R   V R+D +T GLLL+       R L     +    R Y     G++ +D+  
Sbjct: 128 INGVLRPGIVHRIDRDTTGLLLVCKKDRAHRALAEQLKEHTITRRYHAILCGRMREDEGK 187

Query: 158 ---------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                     +  K+ I  +          +  +      V   L  G+  +I+      
Sbjct: 188 VDAPIGRSRRDRKKQAIDWERGREAVTHYRVLERFSEYTLVECRLETGRTHQIRVHMASI 247

Query: 209 NWKVN 213
              V 
Sbjct: 248 GHPVL 252


>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 = 74.4 bits (182), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 76/250 (30%), Gaps = 45/250 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++  +   QR+ K +       +R  ++R I ++RV V+  + +  +  V    HI +  
Sbjct: 13  LLHADDAGQRLDKALCCHFPDLTRSTLQRWIKEERVIVDHEVAKLPSQKVRVGQHIIIYP 72

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIF 105
                +             E   L + +KP G+V          T+ + L      P   
Sbjct: 73  SEPEPSTALPEEIALEILFEDEHLIVLNKPAGMVVHPGAGVNHGTLVNALLYHCGTPDNP 132

Query: 106 S----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
                      R   V RLD  T G+++          L          R Y     G  
Sbjct: 133 HGGLSGIGGVIRPGIVHRLDKETSGIMVAAKQDHAHIHLSRQFEQRTIGRRYLALTRGIP 192

Query: 154 DQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              +           ++  K  +V QG      +  +    G  A +   L  G+  +I+
Sbjct: 193 QPAQGRIEGAIGRHPIHRTKMAVVEQGGRAAATRYKVLEPLGQFALIRCRLESGRTHQIR 252

Query: 203 -KVFEFFNWK 211
             +       
Sbjct: 253 VHMT-HIGHP 261


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/231 (17%), Positives = 80/231 (34%), Gaps = 42/231 (18%)

Query: 11  FTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
              +R+ K  A+  +    SR +++  I    + VNG  ++ A   +   D I +     
Sbjct: 23  DAKERIDKY-AKTQLGEEFSRSQIQLWIEAGNLVVNGAPVK-ANYKLAEGDRIVLVIPEA 80

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                  + +PL    E + + + +KP G+V   +      T+ + L      +      
Sbjct: 81  EPTEIVPEDIPLEIYYEDSDVIVVNKPRGMVVHPAPGHTSGTLVNALMFHCKDLSGINGE 140

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----- 158
                V R+D +T GL++   +      L   L +    R Y    HG V  D+      
Sbjct: 141 LRPGIVHRIDKDTSGLIMAAKNDKAHASLAAQLKAHTVTRKYYALVHGNVSHDQGTVDAP 200

Query: 159 -------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +   I  +   +      +  + G    + + L  G+  +I+
Sbjct: 201 IGRDPHDRKMYTVIE-RNSKHAVTHFQVVERFGDYTLLELKLETGRTHQIR 250


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 48/235 (20%), Positives = 88/235 (37%), Gaps = 43/235 (18%)

Query: 15  RVSKVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           R+ K   + G      SR +++  I    V VNG  ++     ++  DH+++        
Sbjct: 16  RIDK---QLGHHFDQFSRSQIQHWIEDGHVLVNGKQVK-PKYKLLVGDHVQIIPEEPQKI 71

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVI 109
               + +PL    E   + + +KP G+V   +      T+ + L             R  
Sbjct: 72  DLAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPG 131

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  +    R L   L +    R Y    HG + +DK          
Sbjct: 132 IVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRS 191

Query: 158 -LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  K+G+V+ G         L+  K +   V   L  G+  +I+   ++    
Sbjct: 192 LKDRKKQGVVVDGRHAVTHFNVLERFK-NYTLVACQLETGRTHQIRVHMKYIGHP 245


>gi|254468337|ref|ZP_05081743.1| ribosomal large subunit pseudouridine synthase D [beta
           proteobacterium KB13]
 gi|207087147|gb|EDZ64430.1| ribosomal large subunit pseudouridine synthase D [beta
           proteobacterium KB13]
          Length = 346

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 82/233 (35%), Gaps = 33/233 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             K I+   F   R+  V++      SR +++ MI    + +NG  + +    V+  + I
Sbjct: 7   NKKLIIPATFFGSRLDAVLSNLVPEFSRSKIQSMIKNDLIFLNGSHVSQ-NYKVVGGEEI 65

Query: 61  EVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP----- 102
            ++GV   +              E   + + +KP  LV      +   T+ + L      
Sbjct: 66  VINGVIEDEIDVIAENISLDIVYEDDDILVLNKPYNLVVHPGSGNANGTLLNGLLYYNKD 125

Query: 103 -SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-------- 151
                R   V RLD +T GL+++  +      L     S    R YR    G        
Sbjct: 126 LEKLPRGGIVHRLDKDTTGLMVVAKNEESQNNLISQLQSKSVYREYRAIVWGQIWQNKVI 185

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              + +      K  +        + ++ +  +   + +V   L+ G+  +I+
Sbjct: 186 QKPIGRHPRQRTKMAVTKVNGKDAETKLEILERFNYHTYVRCLLKTGRTHQIR 238


>gi|255659830|ref|ZP_05405239.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260847905|gb|EEX67912.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 302

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 62/202 (30%), Gaps = 27/202 (13%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA-----ERTRLWLYHKPIGLV 85
              V VNG     A + V + D + +        VP+        E     + +KP  ++
Sbjct: 37  NGTVLVNGKKNGDARLRVHTGDELTLLWQEVSSVVPVDLPLDILYEDETFLVVNKPADMI 96

Query: 86  TTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
              +    R T+   +   F R      +  + RLD +T G+++L     +   +     
Sbjct: 97  VHPTHRAARDTLVHAVAGYFERRGEAAGIHPLYRLDRDTTGIVILAKSARIQHAMTKHHG 156

Query: 140 QWLRVYRVRFHGQVD----------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           Q  R Y     G +D             +       V         +        + + +
Sbjct: 157 QIYREYLALAQGHLDCLSGRIDMPIGRDITRANHWQVRADGRRALTEYETIASWPAYSLL 216

Query: 190 TVGLREGKNREIKKVFEFFNWK 211
            + L  G+  +I+  F      
Sbjct: 217 KIHLLTGRTHQIRVHFAALGHP 238


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 84/228 (36%), Gaps = 38/228 (16%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
            QR+ + ++      SR  ++ +I Q  V+VNG +     + +   +++EV+  P++ A 
Sbjct: 29  TQRLDRYLSSVIPDLSRSRIQDLIEQGYVQVNGKVCYSKNITLDGGEYLEVEVPPVQAAQ 88

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------ 112
                       E  +L + +KP GLV   +      T+   L +    +  +G      
Sbjct: 89  LVAQDIPLDILYEDEQLLILNKPAGLVVHPAPGHLEGTLVHALLAHCPNLPGIGGVQRPG 148

Query: 113 ---RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----------- 156
              RLD +T G + +  T+       L+L S    R Y    +G    +           
Sbjct: 149 IVHRLDKDTTGAIAIAKTDIAYKQLQLQLQSKTARREYLGVVYGAPKSESGTMDLPIGRH 208

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   +    V QG         +  + G+   +   L  G+  +I+
Sbjct: 209 PQQRKKMAIVPVEQGGRNAITNWYIKERLGNYTLIHFQLETGRTHQIR 256


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 86/248 (34%), Gaps = 57/248 (22%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ +N++  E     R+ KV+  +    SR  ++++I + RV +NG + + A       D
Sbjct: 1   MEQENMIVTEELVGVRLDKVLNESFEDYSRSYLQQLIKEGRVLINGQVAK-ANYKCRLND 59

Query: 59  HIEVDGVPLRKAE----------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            IE++   + + E                   + + +KP  +V   +      T+ + L 
Sbjct: 60  QIEIN---IPEPEVLDVIPEEMDLDIVYQDDYVIVVNKPENMVVHPAPGSMSGTLVNGLM 116

Query: 103 SIFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
           +  + +           V R+D +T GLL++  +      L          R Y    HG
Sbjct: 117 AQVTDLSGINGVLRPGIVHRIDKDTSGLLMVAKNDVAHESLVNQLVEKTVTRRYVALVHG 176

Query: 152 QVDQDKLNLLKKGIVIQ-----GICYGDMQVTLDTQKGSNAWVTV-------GLRE---- 195
            +  D       G  I                +++ K +     V        L E    
Sbjct: 177 VIPHD------NG-TIDAPIGRDPKDRKKMAVVESGKHAVTHFKVLQRFKEFTLIECRLE 229

Query: 196 -GKNREIK 202
            G+  +I+
Sbjct: 230 TGRTHQIR 237


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 80/248 (32%), Gaps = 49/248 (19%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLE-----RAAVNV----M 55
           I   +   +R+   + R     SR   +R+I ++RV V+G   +     R    V     
Sbjct: 4   IFSADCAGERLDVFLVRKMPDLSRSYAQRLIEEKRVTVDGTPRKANYKLRGGECVACDLP 63

Query: 56  STDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
             + + V    +      E   + + +KP G+V   +      T+ + L      +    
Sbjct: 64  PVEEVSVRAENIPLDILYEDADIIVVNKPRGMVVHPAAGISGGTLVNALLYHCRDLSGIN 123

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLL 161
                  V RLD +T G++    +    R L     +    R YR   +G + +      
Sbjct: 124 GALRPGIVHRLDKDTSGVMAAAKNDAAHRSLAEQIQKKEARREYRAIVYGNIAE------ 177

Query: 162 KKGIVIQGI-----CYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIK-K 203
           + GI+   I         M +  +  K +     V             L  G+  +I+  
Sbjct: 178 RAGIITGDIGRHPTDRKRMAIVRENGKHATTHFEVLERFGGYTFVACRLETGRTHQIRVH 237

Query: 204 VFEFFNWK 211
           +       
Sbjct: 238 MT-SIGHP 244


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 34/166 (20%), Positives = 60/166 (36%), Gaps = 35/166 (21%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-- 74
            K+    G  S R+++R I    V VNG +    +  +   D +E D   L K+E  +  
Sbjct: 19  QKL---QGKHSLRKIKRAIENNHVCVNGAVERFYSFQLSKGDLVEFDDSVLEKSESEKPV 75

Query: 75  ------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                       L +Y+KP G+   +SD  G       L   F     + RLD  T G +
Sbjct: 76  PERDAILFEDDHLLIYNKPSGM---NSDEFG-------LGKFFPSFPLIHRLDKETTGCI 125

Query: 123 LLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           +      +   +       +  + Y     G  ++      ++G+ 
Sbjct: 126 MFAKYPKVKNRMIELFKGKKISKHYLAVVDGVPNK------REGVE 165


>gi|291536189|emb|CBL09301.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 310

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/258 (15%), Positives = 85/258 (32%), Gaps = 50/258 (19%)

Query: 1   MKDKNI-VQENFTPQRVSKVIA--------RAGIASRREVERMIAQQRVKVNGILLERAA 51
           MK +   ++  +  +R+ K ++         +   SR   +++I    VKVN  + + A 
Sbjct: 1   MKQETFEIEAEYEGERLDKYLSVIFEQSKTSSNAPSRSFFQKLIRDGHVKVNDSIAK-AN 59

Query: 52  VNVMSTDHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
             +   D + V            + +PL    E   L + +KP G+V   S      T+ 
Sbjct: 60  YRLRMDDLVCVEIPDAVETPILPEDIPLDILYEDDDLLVVNKPKGMVVHPSAGHYSGTLV 119

Query: 99  DNLPSIFS----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYR 146
           + +               R   V R+D++T G L++  +      +     +    R YR
Sbjct: 120 NAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHVKIAEQIKEHSVNRRYR 179

Query: 147 VRFHGQVDQDK-------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              +G V  D+                +   I  +          +  +  +  ++   L
Sbjct: 180 GIVYGVVKDDEGTINAPIGRHPTNRKKMA--INKKNGKPAITHYKVLERFSNYTYMEFKL 237

Query: 194 REGKNREIKKVFEFFNWK 211
             G+  +I+         
Sbjct: 238 ETGRTHQIRVHMASIGHP 255


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 87/237 (36%), Gaps = 31/237 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I +QRV++NG +++R    V+  + + +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKTWILEQRVQINGNMVDRPKEKVLGGESVAIDA 69

Query: 64  ---------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                      P+      E   + + +KP  LV      +   TV + L   +  +   
Sbjct: 70  LIEEDARWEAQPISLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHHYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKL 158
                V RLD +T GL+++         L   L + +  R Y     G +       + +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGGTVDEPI 189

Query: 159 NLL---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  + +  +    +    +     ++  + + L  G+  +I+      N  
Sbjct: 190 ARHSTKRTHMAVHPMGKPAVTHYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHP 246


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 86/236 (36%), Gaps = 39/236 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ K++AR     SR  +++ I    V+V+G    RA  +V     IEV          
Sbjct: 69  ERLDKLLARHFSEFSRSRIQQWIEDGAVRVDGEP-SRAKASVQMGQKIEVQPQAAPESMA 127

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVG 112
              + VPL    E   + + +KP GLV   +  +   TV + L       +   R   V 
Sbjct: 128 FTAEDVPLDVVYEDDAMLVINKPAGLVVHPAAGNWSGTVLNGLLHRDPSAARLPRAGIVH 187

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNL 160
           RLD  T GL+++         L  +L +    R Y     G           + +D    
Sbjct: 188 RLDKETSGLMVVARTLVAQTDLVRQLAARTVKRTYLALVWGETPDDGTIDAPIGRDPRER 247

Query: 161 LKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWK 211
            +  IV    G        TL T       V++ + +   G+  +I+  FE     
Sbjct: 248 TRMAIVHTNSGKPSRTHFETLGTVPLGRGKVSMVMCQLETGRTHQIRVHFESIGHP 303


>gi|148240684|ref|YP_001226071.1| pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           7803]
 gi|147849223|emb|CAK24774.1| Pseudouridylate synthase, 23S RNA-specific [Synechococcus sp. WH
           7803]
          Length = 333

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 84/247 (34%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           ++     P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 29  LIYPKPLPMRLDRWLVSQRSEQSRARIQKFIDAGYVRVNGNTGK-AKTPLRQGDEVQLWM 87

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 88  PPPEPLPYLKPEAMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 147

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L++   +    R Y    HG    D   
Sbjct: 148 ISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYLAVVHGVPAGDSGT 207

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y     +L  + G  + +   L  G+  +I+    
Sbjct: 208 IVGAIGRHPADRKKYAV-VSGENGRYACTHWSLQERLGDYSLLRFKLDTGRTHQIRVHCA 266

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 267 HMNHPVV 273


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 49/270 (18%), Positives = 85/270 (31%), Gaps = 66/270 (24%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------ 61
           P R+ K +AR     A + SR  + R++    V++NG+++      +   D +E      
Sbjct: 15  PPRLDKALARDVPEDAAL-SRSRLARLVPDGAVRINGVVVTDVKARLGEGDAVEIALDIP 73

Query: 62  VD----GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------- 104
           VD    G P+      E   L + +KP G+V   +      T+ + L             
Sbjct: 74  VDSDMGGEPIPLDVVYEDDELIVINKPAGMVVHPAPGSPDGTLVNALIHHCGESLSGVGG 133

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNL-- 160
             R   V R+D +T GLL+          L     +    R Y+    G  D     L  
Sbjct: 134 LRRPGIVHRIDKDTSGLLVAAKTDRAHHGLAAQFEAHDVERHYQALCFGLPDAADPRLRG 193

Query: 161 -----LKKGIVIQ---------------------GICYGDMQVTLDTQKGSNAWVTVG-- 192
                 + G +++                     G         ++T  G      +   
Sbjct: 194 IRGTSFEPGNILKIQTQLARHKTDRQRQAVVWSNGRHAVTRARRVETFGGPPVVARIECW 253

Query: 193 LREGKNREIK-KVFEF----FNWKVNRLIR 217
           L  G+  +I+  +           V    R
Sbjct: 254 LETGRTHQIRVHMAHAGHGLVGDPVYGGKR 283


>gi|295099509|emb|CBK88598.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           cylindroides T2-87]
          Length = 305

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 81/239 (33%), Gaps = 39/239 (16%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE---------RA 50
           M+ +  I+ +     RV K +A     SR+ V+ ++ +  + VNG   +           
Sbjct: 1   METREFIIDDENAKIRVDKAVASLLDFSRKRVKDILDEGNILVNGSPCKASYILQEGDHL 60

Query: 51  AVNVMSTDHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            VN+     +EV  + +PL    E   + + +KP G+V   +      T+ + L      
Sbjct: 61  LVNIPEVQSLEVLPENIPLNIVYEDDDVIVINKPKGMVVHPAFGHVSGTLVNALMYHCKD 120

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV--- 153
           +           V R+D +T GLL++  +      L   L +    R Y    H      
Sbjct: 121 LSGINGVMRPGIVHRIDKDTSGLLVVCKNDKAHLALSEQLSNKTCHREYLAIVHHPFSHE 180

Query: 154 ----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     D+     +   +            T+       A V   L  G+  +I+
Sbjct: 181 HGTINAPIGRDEKDRQKMA--VTANNSKEAITHFTVLENFKDYALVRCRLETGRTHQIR 237


>gi|220933994|ref|YP_002512893.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995304|gb|ACL71906.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. HL-EbGR7]
          Length = 315

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 86/238 (36%), Gaps = 32/238 (13%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLER-----AAVNVMSTDHI 60
           V E  + QR+   +AR     SR  +++ +    V+V+G    R         V+    +
Sbjct: 14  VPEALSGQRLDAALARMFPSYSRSRIQQWMEAGWVRVDGETPRRRDTALGGARVVIEARV 73

Query: 61  E------VDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSR 107
           E       + +PL    E   L + +KP GLVT  +  +   T+ + L           R
Sbjct: 74  EAASEDRAEDIPLEVIYEDDSLLVINKPPGLVTHPAAGNREGTLVNALLHHAPDLAALPR 133

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GLL++         L  +L +    R Y     G           + +
Sbjct: 134 AGIVHRLDKETSGLLVVARTLEAHTDLVRQLQARTVGREYLALVQGVIVAGGTVDAPIGR 193

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             ++  K+  V+ G         ++ +   +  + V L  G+  +I+      +  + 
Sbjct: 194 HPVDR-KRMAVVAGGKEAITHYRVEARLPHHTLLRVRLETGRTHQIRVHMAHVHHPIV 250


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 80/244 (32%), Gaps = 41/244 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL----------------ERA 50
           V E     RV   +++    SR     +     V V+G ++                   
Sbjct: 11  VPEGLAGMRVDAALSKLLGISRTVAAELATAGDVSVDGAVVGKSERLVADSMLDVLLPEP 70

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
           A  +M  + I V G+ +  ++   +   +KP+G+    +      TV   L +   R+ +
Sbjct: 71  AAPLMPKEEI-VPGLDILYSDDD-VIAVNKPVGVAAHPTVGWEGPTVVGGLAAAGFRIST 128

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DK 157
            G         RLD+ T G++++        VL+         + Y     G  D     
Sbjct: 129 SGPPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAFRDRTVDKTYHALVQGHPDPLTGT 188

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +            +  +  +G        TL+  + +   + + L  G+  +I+  F   
Sbjct: 189 IEAPIGRHPSAGWRFAVTTEGKHAVTHYETLEAFQEAT-LLKIHLETGRTHQIRVHFSAL 247

Query: 209 NWKV 212
           +   
Sbjct: 248 HHPC 251


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 38/230 (16%), Positives = 77/230 (33%), Gaps = 43/230 (18%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           P+R+   + ++ G  +R ++  +I  + V V+G  + R  V + +   ++V+        
Sbjct: 12  PERLDTFLTSQIGQ-TRSQIAGLIKHECVFVDGKKVPRPGVKLKAGQVVKVEFPEAKQEK 70

Query: 64  ------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRV 108
                  V +   +   L + +KP G+    +     +T+ D L              R 
Sbjct: 71  ALDVNFDVEILYEDDDVLVI-NKPSGVTVHPAPSVKEATLVDWLKHKGIRLSTISGEERH 129

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK--------- 157
             V RLD  T G +++  +      L   L      R Y       + +D          
Sbjct: 130 GIVHRLDKGTSGTMVVAKNNEAHEFLSKQLQDKSMGRYYIAVIVPPLKEDITVVESNIGR 189

Query: 158 ----LNLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTVGLREGKNREIK 202
                  +  G+   G     M   L  ++      +   L  G+  +I+
Sbjct: 190 SSHNRLKMACGLE-HGKYAKTMFKQLALSEDEHTQLIACKLFTGRTHQIR 238


>gi|39938617|ref|NP_950383.1| pseudouridylate synthase [Onion yellows phytoplasma OY-M]
 gi|39721726|dbj|BAD04216.1| pseudouridylate synthases [Onion yellows phytoplasma OY-M]
          Length = 303

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 58/305 (19%), Positives = 112/305 (36%), Gaps = 55/305 (18%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M +K   ++  +   QR+   +      ++ + +++I  Q+V VN    ++ +  + + D
Sbjct: 1   MNEKKEFLISASEAFQRLDHFLLTHINLNKSQCQKLILAQQVLVNSKPAKK-SYLLKAQD 59

Query: 59  HIEV------DGVPLRKA---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            I V      + V L+           E   L + +KP  LV   S     +T+ + L  
Sbjct: 60  LITVIIPQTQESVNLQTPQNLNLDIIYEDPYLAVINKPANLVAHPSLSFQETTLVNGLLY 119

Query: 104 IF--------SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            F         R   V RLD NT GLL++   ND      +     +  ++Y     G +
Sbjct: 120 QFATLSHVDTQRPGIVHRLDKNTTGLLIIAKNNDVSDKLQIAFQQRKITKIYWALIEGFL 179

Query: 154 DQDKLNLLKKG----------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +      L  G          ++  G        TL       + +   L  G+  +++ 
Sbjct: 180 EDKGTIKLPIGRNPHNRLKMQVIPDGKTAVTHFKTLQRFSHF-SLMEFNLETGRTHQLR- 237

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK--KILREQLGP--HLLEEAQVNLDA 259
               F    + L R   G      LL GS+  ++   + L  ++    H +    + L+A
Sbjct: 238 --AHF----SFLKRPIIG-----DLLYGSSHHITPLGQFLHAKMLKFNHPITNQNLILEA 286

Query: 260 PIYSS 264
           P+ ++
Sbjct: 287 PLPAN 291


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 83/244 (34%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V E    +RV   +AR    SR     +IA   V V+G  + ++   V+    + V    
Sbjct: 12  VPEGLAGERVDAALARMFGLSRTRGAELIAAGNVLVDGAPVGKSD-RVLPGSTVAVTIPV 70

Query: 63  --DGVPLRKAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             D + +       + + H         KP+G+    S      TV  +L     R+ + 
Sbjct: 71  EADPLAVVPEVVEGIKILHDDDDIVVIDKPVGVAVHPSPGWSGPTVVGHLAGAGFRISTS 130

Query: 112 G---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--QDKL 158
           G         RLD+ T G++++        VL+         +VY     G  D  +  +
Sbjct: 131 GAPERQGIVQRLDVGTSGVMVICKSEHAYSVLKNAFRRRTVDKVYHALVQGHPDPLEGTI 190

Query: 159 NL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +           K  ++  G        TL+  + + + + + L  G+  +I+       
Sbjct: 191 DAPIGRHPKADYKFAVMADGRHSVTHYETLEAHRFA-SLLEIHLETGRTHQIRVHMAALK 249

Query: 210 WKVN 213
               
Sbjct: 250 HPCV 253


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 31/71 (43%), Gaps = 1/71 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P R+SK +      SRRE E  I    V V+G+++E     V ST  IE+       + 
Sbjct: 15 DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGVVIEEPHFKV-STQKIELSPDAKADSP 73

Query: 72 RTRLWLYHKPI 82
               + HKP 
Sbjct: 74 EPVTIILHKPA 84


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 79/236 (33%), Gaps = 38/236 (16%)

Query: 5   NIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH---- 59
            +  E    QR+   +++     SR  ++++I+Q  VKVN  L       V   D     
Sbjct: 10  EVNSEYEITQRLDIWLSQQMLELSRSHIQKLISQGNVKVNDQLCTSKKAIVHQGDKIILV 69

Query: 60  --------IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                   IE + +PL    E   L + +KP GLV   +      T+ + L +       
Sbjct: 70  IPPPIPLAIEANDIPLDILYEDDALLIINKPAGLVVHPAPGHSEGTLVNALLAHCDSLAG 129

Query: 106 ----SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKL 158
                R   V RLD +T G +++  T+        +L +    R Y    +G       +
Sbjct: 130 IGGVQRPGIVHRLDKDTTGAIMVAKTDHAYQHLQAQLQAKTARREYLGVVYGSPKTDSGI 189

Query: 159 NLLKKG-IVIQGICYGDMQVTLDTQKGSNAW-----------VTVGLREGKNREIK 202
             L  G   +         V    +     W           +   L  G+  +I+
Sbjct: 190 INLPIGRHRVDRKKMAVTPVERGGKIAVTHWEVKERLGNFSMILFRLETGRTHQIR 245


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 81/244 (33%), Gaps = 42/244 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            + E+   +R+ K+++      SR +V++ I    + VNG   E+A   + + D +E+  
Sbjct: 7   TILEHEANERLDKMVSSIREEWSRSQVQQWIKDGDITVNGKK-EKANYRLQTGDLVEIEV 65

Query: 63  ------DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                 D  P               + +KP G+V   S+     T+ + L      +   
Sbjct: 66  PEPELPDIEPEDLHLDIYYEDADVLVVNKPKGMVVHPSNGHFTGTLVNGLMYHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV------- 153
                   V R+D +T GLL++  +      L   L      R Y    HG +       
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDYAHEKLAAQLSEKTVTRKYFALVHGNIPHEAGTI 185

Query: 154 ------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                 D      +    V+           +  +     ++   L  G+  +I+   ++
Sbjct: 186 DAPIGRDPADRQRMA---VVDNGKDAVTHFHVLERFDRYTFIECRLETGRTHQIRVHMKY 242

Query: 208 FNWK 211
               
Sbjct: 243 IGHP 246


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 75/222 (33%), Gaps = 44/222 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I + RV VNG+++ +    V+  +HI +D             + L    E  
Sbjct: 6   SRSRIKEWILEGRVSVNGVIINKPKEKVLGGEHIAIDALIEEENRWEAQDIALDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   + ++        V RLD +T GL+++   
Sbjct: 66  DILVINKPRDLVVHPGAGNPDGTVLNALLHHYPQIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                 L   L   +  R Y     G +          G V + I     + T  +    
Sbjct: 126 VPAQTRLVESLQLREITREYEAVAIGTMT-------AGGTVREPIARHPTKRTHMSVHPM 178

Query: 186 ----------------NAWVTVGLREGKNREIKKVFEFFNWK 211
                           +  + + L  G+  +I+      N  
Sbjct: 179 GKPAVTHYRIMEHFRVHTRLRLRLETGRTHQIRVHMAHINHP 220


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/230 (17%), Positives = 77/230 (33%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + +A    A  SR  ++  +   ++ VNG ++ +    VM  + I V
Sbjct: 9   NTVKDSQLGQRLDQAVAEL-FADFSRSRLKEWLLDGKIAVNGEVITKPRTKVMGGELITV 67

Query: 63  ------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                         +PL    E   + + +KP   V          TV + L   F    
Sbjct: 68  QAELEDEERFEAQDIPLNIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHFPAIA 127

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QD 156
              R   V RLD +T GL+++         L   L      R Y     G++        
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGKMTAGGMVDK 187

Query: 157 KLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
            +        +  +            +      +  + + L  G+  +I+
Sbjct: 188 AIGRHSTKRTLMAVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>gi|329577387|gb|EGG58842.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 297

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 87/250 (34%), Gaps = 58/250 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE 61
             +  T Q+V   +   G+      + ++A+      +++VNG  ++ A   + + D ++
Sbjct: 6   TYDKETTQQVKYFLKEQGV-----SKGLLAKVKFQGGKIQVNG-TVQNAIYPLQTGDVVK 59

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             D  P+    E     + +KP G+ +  +      T+ + +   + R
Sbjct: 60  MTIPDEAEHETLLTDDEPIEIVFEDDHFLVVNKPAGIASIPAQYHPSGTMANRVKGYYKR 119

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK 157
                  +  V RLD +T GL+L    G  A  L        +  ++Y     G      
Sbjct: 120 QNYVNQVIHVVTRLDRDTSGLMLFAKHG-FAHALIDQELREKKVTKIYYALVGG-----A 173

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNA-------W----------VTVGLREGKNRE 200
           +  L +  +I+     D+   L  Q    A       W          V + L  G+  +
Sbjct: 174 IEQLNEHQLIEKPIGRDLSSLLKRQVIETANCFSTEYWLAKRGAQAAAVRIQLHTGRTHQ 233

Query: 201 IKKVFEFFNW 210
           I+  FE    
Sbjct: 234 IRVHFEAIGC 243


>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 = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 85/249 (34%), Gaps = 50/249 (20%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   +SR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQEMMRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKS-SYKVKPMDVITVMM 91

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      +   T+ +          +
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 151

Query: 101 LPSIFSRVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
             +    V  V R+D +T GLL++       TN G         +    R YR    G V
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFF-----NKTTKRRYRALVWGNV 206

Query: 154 DQDK-----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +QD+            + ++  ++      +      +  + G    V   L  G+  +I
Sbjct: 207 EQDEGTVVGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLKRLGYVTLVECILETGRTHQI 266

Query: 202 KKVFEFFNW 210
           +   +    
Sbjct: 267 RVHMKHIGH 275


>gi|260775124|ref|ZP_05884022.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260608825|gb|EEX34987.1| ribosomal large subunit pseudouridine synthase D [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 325

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/230 (16%), Positives = 75/230 (32%), Gaps = 35/230 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V+++   QR+ + IA    A  SR  ++  +   +V+VNG ++ +    VM  + I + 
Sbjct: 10  TVKDSQLGQRLDQAIAEL-FADFSRSRLKEWLVDGKVQVNGEVITKPRTKVMGGEIITLQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
               D               E   + + +KP   V          TV + L   +  +  
Sbjct: 69  AELEDEERWEAQDIPLDIVYEDDDIMVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIAE 128

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQ 152
                 V RLD +T GL+++         L   L      R Y            R    
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGRVEQP 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +         +   G          +  +  +  + + L  G+  +I+
Sbjct: 189 IGRHSTKRTLMAVSPMGKPAVTHYRVAEHFRE-HTRIRLRLETGRTHQIR 237


>gi|167031685|ref|YP_001666916.1| RluA family pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858173|gb|ABY96580.1| pseudouridine synthase, RluA family [Pseudomonas putida GB-1]
          Length = 352

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 85/242 (35%), Gaps = 36/242 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLER-----AAVNVMSTDHIEVDGVP 66
           QR+ +V A    A  SR  +   I + R+ V+G ++           +      E  G  
Sbjct: 50  QRLDQV-AAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDLVYGGSLLALEAEQEAQGEW 108

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGR 113
           + +        E   + + +KP GLV   +      T+ + L      ++       V R
Sbjct: 109 IAEDIELDIVYEDDHIMVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAGIVHR 168

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ-DKLNL-------LKK 163
           LD +T GL+++         L  ++ + +  R+Y     G V    K++        +++
Sbjct: 169 LDKDTTGLMVVAKTLQAQTKLVEQMQARKVSRIYECIVIGVVTAGGKIDAPIGRHGGMRQ 228

Query: 164 GIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIRI 218
            + +  G         +  +  S+  V V L  G+  +I+       + +        R 
Sbjct: 229 RMAVTDGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYGGRF 288

Query: 219 SY 220
             
Sbjct: 289 RI 290


>gi|153002938|ref|YP_001377263.1| RluA family pseudouridine synthase [Anaeromyxobacter sp. Fw109-5]
 gi|152026511|gb|ABS24279.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. Fw109-5]
          Length = 339

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 55/345 (15%), Positives = 108/345 (31%), Gaps = 73/345 (21%)

Query: 6   IVQENFTPQRVSKV---------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            + E+   QR+ K+         ++         V +M   ++++VNG   + A   V +
Sbjct: 5   TISEDAAGQRLDKLVRKALRDVPLSH--------VYKMFRTRKIRVNGGRGK-AEQLVAA 55

Query: 57  TDHIEVDG--VPLRKAERTR------------------LWLYHKPIGLVTTHSDPDGRST 96
            D + + G    L   +                     +    KP GL          +T
Sbjct: 56  GDVVVIRGDEERLLARQEPEPGARAGAVTFGVLHEDADVLAVDKPAGLAAHPGTGISGAT 115

Query: 97  VFD----------NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLR 143
           + +          +LP    +     RLD +T G++L+  +      L           +
Sbjct: 116 LVEMARAHLGTPADLPPTEFKPSPAHRLDRDTSGVVLVAKNRKTMVRLTELFTDGADVKK 175

Query: 144 VYRVRFHGQVDQDK--------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            Y     G++ ++                +   +G+ +Q        V+   +    + +
Sbjct: 176 TYLALVKGKMPREAGTIDLPLAEHEQTARSKAARGVNLQEALTRWKVVSAMKEA---SLL 232

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST--REVSKKILREQLGP 247
            V +  G+  +I++  E     V    R  YG F            R +     R +L P
Sbjct: 233 AVTIETGRTHQIRRHLEAVGHPVLG-DR-RYGDFPTNRAARQRWGLRRMFLHAWRLEL-P 289

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           H    A + L+AP+         R N+ S       R     + +
Sbjct: 290 HPTTGAPLRLEAPLPGELLEALSRANLSSPAGTASGRAAPRGAAR 334


>gi|313159132|gb|EFR58507.1| pseudouridine synthase, RluA family [Alistipes sp. HGB5]
          Length = 362

 Score = 74.1 bits (181), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 46/231 (19%), Positives = 77/231 (33%), Gaps = 41/231 (17%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +  R    SR  ++       + VNG   +  +  V   D I++        
Sbjct: 41  APLRLDKFLTVRMEKCSRNRIQAAADSGSILVNGKAAKS-SYKVKPLDRIQIVMPYPRRE 99

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   L + +KP GLV      +   T+ + L      +        
Sbjct: 100 VEIIPENIPLEIPYEDDDLLIVNKPAGLVVHPGHGNYSGTLVNALTYHLRNLPLFQEGDM 159

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL------ 158
               V R+D NT GLL++  +      L          R Y     G  ++D+       
Sbjct: 160 RAGLVHRIDKNTSGLLVVAKNEQSHARLAKQFFDHTIGRRYVALVWGNFEEDEGTITGNI 219

Query: 159 ----NLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
                  +K  V +    G   VT   +  + G    V   L  G+  +I+
Sbjct: 220 GRSPRDRQKMFVFEDGSDGKHAVTHWRVLKRYGYVTLVECRLETGRTHQIR 270


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 87/254 (34%), Gaps = 38/254 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQ-QRVKVNGI------LLERAAVNV---- 54
           + +EN    R+    A     SR+   ++I Q   + VNG       +L      V    
Sbjct: 8   VTKENHQL-RIDDF-AYQHHISRK-ALKVIKQCGDILVNGEHQTVRYVLNEGDYVVFIYP 64

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
              + I  + VPL    E   L +  KP G+    +      T+ + L   +  +     
Sbjct: 65  PEDNQIIPENVPLYIVYEDDFLLIVDKPKGMACFPTRSHPCQTLANALSYYYHSIELDST 124

Query: 109 -ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL------- 160
              V RLD +T GL+++     +  ++        R Y+    GQV+Q  ++L       
Sbjct: 125 VHFVNRLDKDTAGLMMIAKYREIHDMMCQNIQHIYRRYQAHVEGQVEQGVIDLPIHKDGQ 184

Query: 161 -LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
            +++ I   G         L+   G  + V   L  G+  +I+         +       
Sbjct: 185 NMRRIIDENGKDSRTYYRCLEYSDGI-SRVECILETGRTHQIRVHMAAIGHPL------- 236

Query: 220 YGPFQLGTLLAGST 233
            G   L     G+ 
Sbjct: 237 IGDL-LYGGKPGTF 249


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 39/198 (19%), Positives = 76/198 (38%), Gaps = 24/198 (12%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK------AERTRLWLYHKPI 82
           + V+ ++  ++V VNG ++ +   ++   D I VD  P          E   L + +KP 
Sbjct: 38  KNVKNLLKFKQVSVNGQVISQFDYSLKRDDEIVVDRNPNNNSSLDIIYEDRELIVINKPA 97

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           GL++     +   T +  +           RV  V RLD  T G+LL   +  +   L+ 
Sbjct: 98  GLLSMAGGNEKEKTAYHLVGEYLKSKNKNARVFIVHRLDKETSGVLLFAKNEIIKNKLQN 157

Query: 137 PSTQWL--RVYRVRFHGQVDQDKL-------NLLKKGIVIQGICYGDMQVT---LDTQKG 184
                +  R Y     G++ +              + + I     G + +T   +  +  
Sbjct: 158 NWNDIVYKRGYLAIIEGKLKKKHGTIKNHLDESKTQMVYIANNGKGKLAITNYKVLKESR 217

Query: 185 SNAWVTVGLREGKNREIK 202
            N+ + V L  G+  +I+
Sbjct: 218 YNSLIEVFLETGRKNQIR 235


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 92/243 (37%), Gaps = 47/243 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +  E   P+R+ +V+ARA    SR  ++ ++    V+ +G ++   A  V +   I++  
Sbjct: 27  VRDEGSVPERLDRVLARAFDDLSRARLQALVRDGLVQCDGAVVRDPARKVGAGSRIDLTV 86

Query: 64  ---------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  L  A   E   L +  KP GLV   +      T+ + L +        
Sbjct: 87  PAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAGHEDGTLVNRLIAHCGASLSG 146

Query: 106 ----SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQVDQ 155
                R   V RLD +T GLL++  ND    G  A+  +   +    R Y     G  + 
Sbjct: 147 IGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSGALERAYLALVWGVPEP 206

Query: 156 ----------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                           +K+ +++ G   + I +  ++  L    G  A +   L  G+  
Sbjct: 207 RAGTIRANLARSRHNREKIAVVRDGEGREAITHYRVEA-LPAADGVTALLRCRLETGRTH 265

Query: 200 EIK 202
           +I+
Sbjct: 266 QIR 268


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 84/243 (34%), Gaps = 39/243 (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  --DG------VPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
             D        P+      E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 97  RADDENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 156

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD  T GL+++         L  +L +    R Y     G           +
Sbjct: 157 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 216

Query: 154 DQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFF 208
            +D  +  +  I     G        TLD      A V++   +   G+  +I+  FE  
Sbjct: 217 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVQCQLETGRTHQIRVHFESE 276

Query: 209 NWK 211
              
Sbjct: 277 GHP 279


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 92/251 (36%), Gaps = 43/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+ + +V E  +  R+ K ++     SR  ++ +I +Q+V VNG  ++  +  V   D I
Sbjct: 1   MEKRRLVVEK-SGLRLDKYVSDHCELSRSFLQDLIKEQQVLVNGKAVKS-SYKVNLEDII 58

Query: 61  EV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           E               +PL    E   + + +K  G+V   S      T+ + L      
Sbjct: 59  EFAVPDLEEIEVIPQDIPLNVLYEDEDVIVVNKEKGMVVHPSLGHQDGTLVNALLFHCQD 118

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQV-- 153
           +           V R+D +T G L++  +  +A +       + +  R YR+  HG +  
Sbjct: 119 LSGINGKIRPGIVHRIDKDTSGCLVIAKN-DVAHIALSKQIETKEAYREYRLIVHGNIQH 177

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      D      +   +V +          +  + G   +++  L  G+  +I+
Sbjct: 178 EDGLIDAPIGRDPKDRQRMA--VVAENSRPAKTHFHVLKRFGQYTYLSCLLETGRTHQIR 235

Query: 203 KVFEFFNWKVN 213
              ++    V 
Sbjct: 236 VHMKYIQHPVL 246


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 83/225 (36%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN   +E+A   V   D+I ++          
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNK-VEKAKYLVKEEDNIVIEIPEPKVLEVL 87

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
              +P+    E   + + +KP  +V   +  +  +T+ + +               R   
Sbjct: 88  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 147

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL---------- 158
           V R+D +T GLL++  +      L     +    R Y    +G V +DK+          
Sbjct: 148 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 207

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  +V  G         ++            L  G+  +I+
Sbjct: 208 KDRLKMAVVKDGKNAITHFEVVERFDKFTHM-RARLETGRTHQIR 251


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 83/236 (35%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V           
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYENEI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   + + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPEDIPLTIVYEDPYVMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      L+  +    R YR    G V+QD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGLQFFNKTTKRRYRALVWGVVEQDEGTIVGNIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PKDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I  QRV VNG + +     V+  + + ++ 
Sbjct: 10  TVSESQLGQRLDQALAEMFPDYSRSRIKEWILDQRVLVNGQMCDTPKEKVLGGERVAINA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L   L   +  R Y     G +          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMT-------AG 182

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
           G V + I     + T                +      +  + + L  G+  +I+
Sbjct: 183 GTVSEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIR 237


>gi|241760654|ref|ZP_04758746.1| tRNA pseudouridine synthase C [Neisseria flavescens SK114]
 gi|241318835|gb|EER55361.1| tRNA pseudouridine synthase C [Neisseria flavescens SK114]
          Length = 264

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 52/168 (30%), Gaps = 26/168 (15%)

Query: 72  RTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +R    +KP G++   S     + R  V      I   V  V RLD  T G+LL   D 
Sbjct: 34  DSRTIAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLFALDT 93

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYG- 173
             AR+L     +    + Y     G +              DK+   +    +Q      
Sbjct: 94  EAARLLTQQFENKTIEKTYWAIVRGYLPSDGLIDYALKYMPDKIAEAQTEATLQEAQTAY 153

Query: 174 --------DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     Q  L       +W  +    G+  ++++  +     + 
Sbjct: 154 RCLAQTELPFQSALRYPTSRYSWAELTPYTGRKHQLRRHMKHIFHPIV 201


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 80/237 (33%), Gaps = 45/237 (18%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + +A      SR  ++  I    V V+G+++ +    V     IE+
Sbjct: 8   KSEISATQTGLRLDQALAELFPDYSRTRIKEWILSDAVYVDGVMVNKPREKVFELQRIEI 67

Query: 63  D---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +      +  A          E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  NATLEEEVHAAAQAIELDIVYEDDDILVINKQAGLVVHPGAGNADGTLMNALLHHCPNIE 127

Query: 110 S------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                  V RLD +T GL+++         L   L + +  R Y     G +        
Sbjct: 128 HVPRAGIVHRLDKDTTGLMVVAKTVEAQTHLVAALQAREITREYEAIVLGTMT------- 180

Query: 162 KKGIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
             G V + I     + T                +  +  ++  + + L  G+  +I+
Sbjct: 181 AGGTVDEPIGRHPTKRTHMAVHHSGKPAVTHYRVAEKFRNHTRLRLRLESGRTHQIR 237


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 75/239 (31%), Gaps = 44/239 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + NI  +  T  RV K++       SR +++  I    V  N  +++     V   DHI 
Sbjct: 5   EFNITDKEQTGMRVDKLLPELNSDWSRNQIQDWIKAGLVVANDKVVKS-NYKVKLNDHIV 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +K  G+V   S     +T+ + L      +
Sbjct: 64  VTEKEVVEADILPENLNLDIYYEDDDVAVVYKTKGMVVHPSPGHYTNTLVNGLMYQIKNL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D++T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDMDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYIALVHGNIPHD 182

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                            +    V+           +         V   L  G+  +I+
Sbjct: 183 YGTIDAPIGRNKNDRQSMA---VVDDGKEAVTHFNVLEHFKDYTLVECQLETGRTHQIR 238


>gi|325115730|emb|CBZ51285.1| pseudouridine synthase, related [Neospora caninum Liverpool]
          Length = 567

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 60/136 (44%), Gaps = 13/136 (9%)

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-N 159
           L  +   +I V  L +  +G +LLTNDG  A  ++ P  +   V+ VR  G +   ++  
Sbjct: 246 LAELPRHLIVVRPLPVEADGFVLLTNDGDFAHAVQKPENRVQSVFDVRVSGTLPSYRVWE 305

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-----KV-FEFFNWKVN 213
             + G+   G  +G + V L     + AW+ + L E      +     ++       K+ 
Sbjct: 306 SWRCGVASGGFDFGPVWVELLRAWHNAAWLRLHLVE------RPGMDLRMLLSSIGLKLR 359

Query: 214 RLIRISYGPFQLGTLL 229
           RL R + GP++  ++ 
Sbjct: 360 RLRRYAIGPYRASSIP 375



 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-R 72
           + +++ ++ AG+ SRRE E+ IA  +V VNG  + +  V V S   +   G  +      
Sbjct: 17  EWLARRLSLAGVLSRREAEKAIAAGQVTVNGETICQ-NVEVCSEAIVCYKGAFVPPPVMT 75

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            +L+   KP  ++    + +   T+   +  ++
Sbjct: 76  PQLFGLVKPRRVLCVMEEREDMPTLHTLMRHLY 108


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 81/243 (33%), Gaps = 38/243 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +     T QR+ K+++      SR +++  I  + V VNG  ++ A   V   D I + 
Sbjct: 7   EVTDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIK-ANYKVKLHDSIVIT 65

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              +                E   + + +KP G+V   S      T+ + L      +  
Sbjct: 66  EKEVVDADIQPENLNLDIYYEDKDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQDKL 158
                    V R+D +T GLL++  +  +A       L +    R Y    HG +  D  
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKN-DIAHRSLVDQLVAKSVKRKYTALVHGNIPHDYG 184

Query: 159 ---------NLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       ++ + V+           +         +   L  G+  +I+   ++ 
Sbjct: 185 TVDAPIGRNKKDRQSMDVVDDGKDAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 247


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 79/248 (31%), Gaps = 48/248 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K I        R    +A    +A R +   +I    V +NG  L + +  +   D 
Sbjct: 17  MTEKEIKICESAQARADAFLAAELNVA-RNQALNLIKSGLVSLNGKPLTKPSAKLNLGDV 75

Query: 60  IEVD---------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           + +                 VP+   +   L + +KP  LV   +      T+ D L + 
Sbjct: 76  LRIKFEQSEQNAAKFEAEFEVPIIYEDED-LLVLNKPANLVVHPAPSVKEPTLVDWLGAK 134

Query: 105 ---------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
                     SR   V RLD  T G +++  +      L          R+Y       +
Sbjct: 135 GFLLSNLSGQSRAGIVHRLDKGTSGAIVVAKNNAAHAALSSQLSDKSMGRIYLALTDLPL 194

Query: 154 DQDK----------LNLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVG---LR 194
            Q+            N LKK IV  G         L         +  NA V +    L 
Sbjct: 195 KQNCTVWRAIGRNPANRLKKAIVPDGRAAKSAFANLLFSEFDGPAQSKNAGVNLIAAKLF 254

Query: 195 EGKNREIK 202
            G+  +I+
Sbjct: 255 TGRTHQIR 262


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 43/236 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGV 65
           RV K +A      +R  +++ I +  + VN  ++      V + DHI        EVD +
Sbjct: 16  RVDKYLAEVFPEYTRSFIQKQIEKGGILVNQKVINS-KYQVKADDHIIMTIPDPIEVDII 74

Query: 66  PLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFSRVIS-- 110
           P               + +KP  +V   +  +   T+         D L  I   +    
Sbjct: 75  PEPIDIEIVYEDDDLMIVNKPQDMVVHPAPGNYSGTLVNGLLYHCKDKLSGINGEIRPGI 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD------------ 156
           V R+D +T GLL++  +      L   L      R Y    +G   +D            
Sbjct: 135 VHRIDKDTSGLLMIAKNDKAHLGLSELLKDHHITRKYHAIVYGGFKEDEGTIEEPIGRST 194

Query: 157 -KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +    +++   Y      +  +     ++ + L  G+  +I+   +     
Sbjct: 195 QDRKKMA---IVRDGRYAKTDYKVLERFKQFTYIELTLHTGRTHQIRVHMKHIGHP 247


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 80/242 (33%), Gaps = 47/242 (19%)

Query: 14  QRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            R+ K +    A A   SR +++  I  + V+VNG    +A+  V   D + +       
Sbjct: 30  MRLDKYLNLHVANA---SRTKIQNGIEAEAVRVNGQP-TKASYKVKPFDVVTLSLPQPPR 85

Query: 63  DGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
           D   + +        E   L + +K  G+V   +  +   T+ + L   F ++ +     
Sbjct: 86  DTEIIPENLPLDIIYEDDVLLIVNKAAGMVVHPAFGNWTGTLINGLVYHFQQLPTGRNGE 145

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK------ 157
                V R+D +T GLL++         L          R Y     G+   +K      
Sbjct: 146 GRPGLVHRIDKDTSGLLVIAKTEFAMTFLASQFADHSIERTYHALIWGEPKAEKGTITGH 205

Query: 158 -----LNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNW 210
                 +     + + G          +  K     + +   L  G+  +I+   +    
Sbjct: 206 VGRSARDRRVMDVYVDGSQGKHAVTHYEVIKPLRYVSLIKCNLETGRTHQIRAHMKHIGH 265

Query: 211 KV 212
            +
Sbjct: 266 PI 267


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 83/236 (35%), Gaps = 41/236 (17%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V           
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEDGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYENEI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPENIPLTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDIPDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  T D      ++  +    R YR    G ++QD+          
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGIQFFNKTTKRKYRALVWGVMEQDEGTIVGNIARN 220

Query: 158 -LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  ++       +      +  + G    V   L  G+  +I+   +    
Sbjct: 221 PRDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRVHMKHIGH 276


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 91/255 (35%), Gaps = 46/255 (18%)

Query: 1   MKDKNIVQENFT-PQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  + E  T  QR+ + ++    G+ SR  ++ ++A+  V+ NG  + + ++ + + 
Sbjct: 1   MEQREFIVEQETAGQRIDRFLSGEDTGL-SRSALQALVAEGHVQCNGKAVAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D + +   D  P+             E   L + +KP G+V   +  +   T+ + L   
Sbjct: 59  DTVLLEIPDAKPIEAVPQDIPLEIVYEDAHLLVVNKPKGMVVHPAPGNPDGTLVNALLWH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
                       R   V R+D +T GLL++  D      L          R Y+   +G 
Sbjct: 119 CKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYGG 178

Query: 153 V--DQDKLNLLKKGIVIQGICYGDMQVT------------LDTQKGSNAWVTVGLREGKN 198
              D+  +        I          T            +  + G    +   L+ G+ 
Sbjct: 179 FAQDEGFVEANLGRSKIDRKKMAVYPATEPHTKYAYTGYKVLERLGEFTLLECRLKTGRT 238

Query: 199 REIK-KVFEFFNWKV 212
            +I+  +    +  V
Sbjct: 239 HQIRVHM-ASIHHPV 252


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 83/236 (35%), Gaps = 42/236 (17%)

Query: 8   QENFTPQ--RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           Q    PQ  R+ + ++ +    SR  ++ +I+Q  V VN  +     + +   DHIEV  
Sbjct: 16  QTTLEPQNYRLDRWLSESLETLSRSRIQTLISQGHVTVNQKVCVSKKLTLKRGDHIEVKI 75

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
               PL             E   L + +K  GLV   S      T+ + L +        
Sbjct: 76  PPNEPLELEAVDIPLDILYEDEHLIIINKQAGLVVHPSAGHVNDTLVNALLAHCDTLAGI 135

Query: 106 ---SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---- 156
               R   V RLD +T G +++  T+    +   ++ +    R Y    +G    D    
Sbjct: 136 GGVERPGIVHRLDKDTTGAIVVAKTDFSLQSLQQQIKNKTAQRQYLGVVYGSHKADFGTI 195

Query: 157 ---------KLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        +   + I+ G         +  + G+ + +   L  G+  +I+
Sbjct: 196 EQPIGRHLADRKKMAV-VTIERGGRNAITHWQIQERLGNYSLILFTLETGRTHQIR 250


>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 = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 86/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V E    +R+   +       SR  V+ +I    ++V+    ++ +  + + + I V+ 
Sbjct: 8   LVDEEMEGERLDAFVTEQLDELSRSLVKTLIENGEIRVDSKQ-QKPSYRLKAGEEIIVEI 66

Query: 64  -----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                       +PL    +   + +  KP G+V   +  +  +T+ + L      +   
Sbjct: 67  PAVRELKLKAQDIPLSFIYQDKDIAVIDKPKGMVAHPAHGNWENTLVNALLFHLKDLSGI 126

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD---- 156
                   V RLD +T G++++  +    R L   +      R Y    HG + ++    
Sbjct: 127 NGELRPGIVHRLDKDTSGVMVIAKNDMAHRQLAAQIKDHSINREYITLVHGIIKENLGSI 186

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                        +    VI G         +  + G+   + V L  G+  +I+  F +
Sbjct: 187 EAPIGRSKQDRKKMA---VIAGGRPAVSNYQVLERLGNYTLLKVKLLTGRTHQIRVHFAY 243

Query: 208 FNWKVN 213
               V 
Sbjct: 244 IKHPVV 249


>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 = 73.7 bits (180), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 81/236 (34%), Gaps = 40/236 (16%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +      ASR  ++  I    V VN   ++ A+  V   D I +           
Sbjct: 31  RIDKFLMHRMENASRNRIQNAIEAGNVLVNQKTVK-ASYKVKPADEISIVFPHPPRDTEV 89

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP G+V      +   T+ +           LP    R  
Sbjct: 90  YPEDIPLDIVYEDNDLLVVNKPAGMVVHPGYNNYTGTLVNALAFHFEQLPQLPGNEGRPG 149

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD------KLNLL 161
            V R+D +T GLLL++ +      L          R Y     G +++D           
Sbjct: 150 LVHRIDKDTSGLLLISKNEITMTRLAKQFFDHTITRKYVALAWGDIEKDGTVTGYIGRSA 209

Query: 162 KKGIVI---QGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  IV+        G   VT   +  + G    ++  L  G+  +I+   +     
Sbjct: 210 KNRIVMDVYDDEEKGKWSVTHYAVLERLGYVTLISCQLETGRTHQIRAHMQHIGHP 265


>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 = 73.7 bits (180), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 72/237 (30%), Gaps = 43/237 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+ K +A A   SR  V+ +IA   V++ G     A+  V   +   +            
Sbjct: 16  RLDKALADATGLSRERVKGLIADGVVEIAGKAARSASAKVAEGERYFIALPPPEPLETVA 75

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVIS---------V 111
             +PL    E   L + +KP G+V   +  +   T+ +  L     R+           V
Sbjct: 76  QDIPLDVVFEDAYLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCAGRLSGINGVARPGIV 135

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV-------------DQD 156
            R+D +T GLL++         L          R Y     G                  
Sbjct: 136 HRIDKDTSGLLVVAKSDAAHEGLAKQFADHSITRRYLAACAGHPNPPSGTVSGRIGRSDR 195

Query: 157 KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
               +   ++      G   VT      +    A +   L  G+  +++        
Sbjct: 196 DRKKMA--VLPDDSTRGKHAVTHYETVRRLNHAALIECRLETGRTHQVRVHCASIGH 250


>gi|297184482|gb|ADI20596.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EBAC_27G05]
          Length = 311

 Score = 73.7 bits (180), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 44/230 (19%), Positives = 80/230 (34%), Gaps = 34/230 (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  D------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
           D             +PL    E     + +KP GLV          T+ + L   +    
Sbjct: 64  DPILENRVSWEAEDIPLNIHHEEDEFLIINKPYGLVMHPGAGCNNGTLANALAFHYPQLI 123

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ------VDQ 155
              R   V RLD +T GLL++            +L + +  + Y     GQ      ++Q
Sbjct: 124 QLPRCGIVHRLDKDTSGLLVIAKTEKFRNFFVEKLQNREIFKEYEALVVGQVIGSFSIEQ 183

Query: 156 DKLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +  I +            ++L       + V + +  G+  +I+
Sbjct: 184 AIERDPRNRIKMRTTDFGREAISHISLIKFYNGYSHVAIEIETGRTHQIR 233


>gi|295105659|emb|CBL03203.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii SL3/3]
          Length = 310

 Score = 73.7 bits (180), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 93/257 (36%), Gaps = 50/257 (19%)

Query: 1   MKDKNIVQENFT-PQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  + E  T  QR+ + ++    G+ SR  ++ ++A+  V+ NG  + + ++ + + 
Sbjct: 1   MEQREFIVEQETAGQRIDRFLSGEDTGL-SRSALQALVAEGHVQCNGKTVAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D + +   D  P+             E + L + +KP G+V   +  +   T+ + L   
Sbjct: 59  DTVLLEIPDAKPIEAVPQDIPLEIVYEDSHLLVVNKPKGMVVHPAPGNQDGTLVNALLWH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
                       R   V R+D +T GLL++  D      L          R Y+   +G 
Sbjct: 119 CKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYGG 178

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREG 196
             QD                 +   +      +     T   +  + G    +   L+ G
Sbjct: 179 FAQDEGFVEANLGRSKTDRKKMA--VYPANEPHTKYAYTGYKVLERLGEFTLLECRLKTG 236

Query: 197 KNREIK-KVFEFFNWKV 212
           +  +I+  +    +  V
Sbjct: 237 RTHQIRVHM-ASIHHPV 252


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 71/182 (39%), Gaps = 27/182 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+   I  E     R+ K I+      SR  +++ I    ++VNG  ++     V + DH
Sbjct: 1   MELYEITSEE-NGVRIDKFISDHFPQWSRTIIQQWIVDNHIQVNGTPIKS-KYKVKAGDH 58

Query: 60  IEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           IE+   D +PL             E   + + +KP G+V   +      T+ + L     
Sbjct: 59  IEIREPDPIPLEIPAENLNLDIIYEDGDVLVVNKPRGMVVHPAPGHYTGTLVNGLMYHCH 118

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
            +           V R+D +T GLL++  +      L  +L + +  R Y     G +  
Sbjct: 119 DLSGINGVMRPGIVHRIDKDTSGLLMVAKNDRAHESLVNQLKNKETKRRYYAIVSGIIPH 178

Query: 156 DK 157
           DK
Sbjct: 179 DK 180


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 83/249 (33%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +     T  R+ K +  R   A+R  +++      + VNG  ++     +   D + +
Sbjct: 34  RTVADPGQTLIRIDKFLVDRMNNATRSRIQQAAEAGAIFVNGRPVKS-NYRIKPGDVVTL 92

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------- 101
                        + +PL    E   L + +KP GLV      +   T+ + L       
Sbjct: 93  ELLRPRRELEIIPEDIPLDIVYEDDVLLVINKPAGLVVHPGHGNYTGTLVNALAYYLRED 152

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD-- 154
                +   +  V R+D +T GLL++         L          R YR    G+ D  
Sbjct: 153 PEYDPMDPSLGLVHRIDKDTSGLLVVAKRAEAKSDLCKQFYYKTTHRSYRALVWGRFDYP 212

Query: 155 ---------QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
                    +D  + L+  +       G   VT   +  +    +W+   L  G+  +I+
Sbjct: 213 IGTITGNIGRDLKDRLQMAVFPPDGDIGKPAVTHYQVLEELAYVSWIECRLETGRTHQIR 272

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 273 AHMKHIGHT 281


>gi|322375304|ref|ZP_08049817.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
 gi|321279567|gb|EFX56607.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
          Length = 298

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 70/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
               + VN    + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVTIDIPAEEGFETLEAIDRPLDILFEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + + +       V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGNGDLEPEGEIIAPIARDVNSIITRRVAKGGKYAHTSYKVVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G    + + L  G+  +I+  F    + 
Sbjct: 211 SYGDIHLIDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/214 (17%), Positives = 85/214 (39%), Gaps = 30/214 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRKA---- 70
           ++++ G  SR  V+ ++A ++V VN  +  +  + +   D + ++     + L       
Sbjct: 27  LLSKMGGMSRNSVKSLLAHRQVMVNNKITTQFNLALQPEDLVVINNGRGNIELNHPKLKI 86

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLL 122
             E   L +  K  GL+T  +     +T F  L +        +R+  V RLD  T G++
Sbjct: 87  IFEDEYLIVVEKKEGLLTVSTGNPDETTAFSILKNHVKKSSPDNRIYVVHRLDRETSGVI 146

Query: 123 LLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLN----LLKKGIVIQ-------- 168
           +   +  +  +L+    +    R+Y     G+V++++      LL+    ++        
Sbjct: 147 MFAKNKEVQTILQENWHRIITRRIYVALVEGKVEKEQDTIVSWLLENEKSLKIHSSATDN 206

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           G               + + + + L  G+  +I+
Sbjct: 207 GGQQAVTHYRCVRSNDNYSLLEIELETGRKNQIR 240


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 75/236 (31%), Gaps = 45/236 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN------------GILLE----RA 50
           + E     R    +A+    SR    ++ A+  V V+            G ++       
Sbjct: 10  IPEGLEGMRADAALAKLLGLSRSATAQLCAEGGVTVDSQELGKSERLASGQVVSVLLPEP 69

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-------- 102
              ++  + + V+G+ +  ++   +   HKP+G+    S      TV   L         
Sbjct: 70  EKPLLPREEL-VEGMDVLYSDAD-IICVHKPVGVAAHPSVGWDGPTVIGGLRAAGYNVAS 127

Query: 103 -SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD--QDK 157
                R   V RLD+ T G++++ + G     L+         + Y     G  D  +  
Sbjct: 128 LGPTERQGIVHRLDVGTSGVMVVASSGRAYSALKHAFKHRTVKKTYHAVVQGLPDPIEGT 187

Query: 158 LN-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++                 V+           L       + + V L  G+  +I+
Sbjct: 188 IDAPIGRHPKSGWKFA---VLDDGKAAVTHYRLIEAFREASLIEVHLETGRTHQIR 240


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/258 (15%), Positives = 85/258 (32%), Gaps = 50/258 (19%)

Query: 1   MKDKNI-VQENFTPQRVSKVIA--------RAGIASRREVERMIAQQRVKVNGILLERAA 51
           MK +   ++  +  +R+ K ++         +   SR   +++I    VKVN  + + A 
Sbjct: 1   MKQETFEIEAEYEGERLDKYLSVIFEQSKTSSNAPSRSFFQKLIRDGHVKVNDSIAK-AN 59

Query: 52  VNVMSTDHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
             +   D + V            + +PL    E   L + +KP G+V   S      T+ 
Sbjct: 60  YRLRMDDLVCVEIPDAVETPILPEDIPLDILYEDDDLLVVNKPKGMVVHPSAGHYSGTLV 119

Query: 99  DNLPSIFS----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYR 146
           + +               R   V R+D++T G L++  +      +     +    R YR
Sbjct: 120 NAIMFHCKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKIAEQIKEHSVNRRYR 179

Query: 147 VRFHGQVDQDK-------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
              +G V  D+                +   I  +          +  +  +  ++   L
Sbjct: 180 GIVYGVVKDDEGTINAPIGRHPTNRKKMA--INEKNGKPAITHYKVLERFSNYTYMEFKL 237

Query: 194 REGKNREIKKVFEFFNWK 211
             G+  +I+         
Sbjct: 238 ETGRTHQIRVHMASIGHP 255


>gi|322387849|ref|ZP_08061457.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
 gi|321141351|gb|EFX36848.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
          Length = 299

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 74/211 (35%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               ++VNG   + A   +   D + +D     G      +        E     + +KP
Sbjct: 33  RGGDIRVNGHP-QNATYLLDIGDEVVIDIPPEEGFETLEAIDYPLDILFEDDHFLIINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  FGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKKAIEKRYYALVKGDGHLEPQGEIIAPIARDEDSIITRRVA-KGGKYAHTSYQIV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G+   V + L  G+  +I+  F    + 
Sbjct: 210 ASYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 77/229 (33%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V EN   QR+ + +A      SR  ++  I  QRV VN  L ++    V+  + + ++ 
Sbjct: 10  TVSENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNDQLCDKPKEKVLGGERVSINA 69

Query: 64  --GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                +R            E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  EIDEEVRFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQV 153
            R   V RLD +T GL+++         L   L   +  R Y                 +
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +  +  + + L  G+  +I+
Sbjct: 190 SRHPTKRTHMAVHPMGKPAVTHYRIMEHFRV-HTRLRLRLETGRTHQIR 237


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 91/259 (35%), Gaps = 40/259 (15%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----R 49
           M DK  ++     +    R+ +V A    A  SR  +   I   R+ V+G ++       
Sbjct: 34  MSDKIELRAEVPSELGGQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 92

Query: 50  AAVNVMSTDHIEVDGVPLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
               +  T   E  G  + +        E   + + +KP GLV      H+D    + + 
Sbjct: 93  GGSILELTAEQEAQGEWIAQDIELDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALL 152

Query: 99  DNLPSIF--SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
            ++P I    R   V RLD +T GL+++  T       V +L S    R+Y     G V 
Sbjct: 153 HHIPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVAQLQSRSVSRIYECIVIGVVT 212

Query: 155 QD---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           ++  V++G         +  +  S+  V V L  G+  +I+   
Sbjct: 213 AGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHM 272

Query: 206 EFFNWKVN----RLIRISY 220
              N+ +        R   
Sbjct: 273 AHINFPLVGDPAYGGRFRI 291


>gi|306825158|ref|ZP_07458500.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
 gi|304432594|gb|EFM35568.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus sp. oral
           taxon 071 str. 73H25AP]
          Length = 298

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 70/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
               + VN    + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNDRP-QNATYLLDIGDRVTIDIPAEEGFESLEAIDRPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + + +       V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGNGDLEPEGEIIAPIARDVDSIITRRVAKGGKYAHTSYKVVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G    + + L  G+  +I+  F    + 
Sbjct: 211 SYGDIHLIDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 80/245 (32%), Gaps = 40/245 (16%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+   +       SR    R+I Q  V V+   +++ +  +   + + V   
Sbjct: 11  VQNKEQGQRLDAFVPVHCKNLSRNACARLIRQGLVTVD-KSVKKPSYVLKPGEMVSVTVP 69

Query: 63  ----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                     D       E   +   +KP G+V   +     +T+ + L +    +  +G
Sbjct: 70  EPETADIVAQDMDLAILYEDRDIVAVNKPPGMVVHPAPGHSSNTLVNALLAHCKDLSGIG 129

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----- 156
                    RLD  T G++L   +      L   L   +  + Y    HG + +D     
Sbjct: 130 GVQRPGIVHRLDKETSGVILAAKNDAAHAGLSEQLAQRRVEKFYLALAHGVIKEDTGVID 189

Query: 157 --------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +      +G     +  T+  +     +V V ++ G+  +I+      
Sbjct: 190 LPLARHPSDRKRMHVSTPAKGREALSLW-TVKERFLDATYVKVQIKTGRTHQIRVHLAAL 248

Query: 209 NWKVN 213
           +  V 
Sbjct: 249 HHPVI 253


>gi|25028588|ref|NP_738642.1| putative ribosomal large subunit pseudouridine synthase
           [Corynebacterium efficiens YS-314]
 gi|259507644|ref|ZP_05750544.1| RluA family RNA pseudouridine synthase [Corynebacterium efficiens
           YS-314]
 gi|23493873|dbj|BAC18842.1| putative ribosomal large subunit pseudouridine synthase
           [Corynebacterium efficiens YS-314]
 gi|259164823|gb|EEW49377.1| RluA family RNA pseudouridine synthase [Corynebacterium efficiens
           YS-314]
          Length = 309

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 77/242 (31%), Gaps = 37/242 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDG 64
           V E     RV   +++    SR     +     V V+G  + ++   V  +  D +  + 
Sbjct: 10  VPEGLAGMRVDAALSKLLGISRTTAAELAEAGDVSVDGSAVRKSDRLVADSMLDVLLPEP 69

Query: 65  -VPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             PL   E              L   +KP+G+    +      TV   L +   R+ + G
Sbjct: 70  AQPLVPREEIVPGLDILYADDDLIAVNKPVGVAAHPTVGWEGPTVVGGLAAAGFRISTSG 129

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--QVDQDKLN 159
                    RLD+ T G++++        VL+         + Y     G     +  + 
Sbjct: 130 PPERKGIVQRLDVGTSGVMVVAASERGYTVLKRAFRDRTVQKTYHALVQGHPDPTEGTIE 189

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      +  +   G        T++  + +   V V L  G+  +I+  F   + 
Sbjct: 190 APIGRHPSSGWRFAVTTDGKHAVTHYETIEAFQEAT-LVKVHLETGRTHQIRVHFSALHH 248

Query: 211 KV 212
             
Sbjct: 249 PC 250


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 86/238 (36%), Gaps = 53/238 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           +K+ +IV +     R+ +  A     I +R  V++ I +Q++ V+G + +     ++   
Sbjct: 3   IKEIHIVPQLSEKIRLQEYAASIFTSITTRSAVKKAIKKQQILVDGEIGQT-GDWILEGQ 61

Query: 59  HIEVDGVPLRKAERTRLW--------------LYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            IE+    L+  ++ +++              + +KP G  T+    +   T+ + LP  
Sbjct: 62  QIEL----LQPQKQQKVFELRLEVIYEDDHIAVINKPAGYPTSG---NYHKTIKNALPFN 114

Query: 105 FSR---------VISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                            RLD  T G+LL   TN   +    +    +  + Y     G  
Sbjct: 115 LQASKEIDKLEIPQPAHRLDNPTSGILLCAKTNKALIELNRQFQDKEIQKTYIAIVEGCF 174

Query: 154 DQDKL--------NLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +++               + + G I +   +++L   K            G+  +I+
Sbjct: 175 PEEQQIFNDEIEEKQATTAVKLLGTIMFKSAKLSLLEAKPLT---------GRTHQIR 223


>gi|221135103|ref|ZP_03561406.1| RluA family pseudouridine synthase [Glaciecola sp. HTCC2999]
          Length = 330

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 38/220 (17%), Positives = 75/220 (34%), Gaps = 33/220 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ +V+A      SR +++  I    VKV+  ++  A   +   + I++  V   +    
Sbjct: 25  RLDQVLADLFPEYSRSKLKEWILAGFVKVDDEVVTVARQKMQGDEQIDIHAVIAVQVLNT 84

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRL 114
                     E   + + +KP GLV      +   TV + L           R   V RL
Sbjct: 85  PQNIELDIVFEDEHVLVINKPAGLVVHPGAGNADGTVLNALLAHHPEIENIPRAGIVHRL 144

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLK 162
           D +T GL+++         L  +L +    R Y     G           + +       
Sbjct: 145 DKDTTGLMVVAKTLIAQTYLVEQLQTRVMSREYEALVMGTMVAGGFVDEPIGRHPTKRTS 204

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   G         +  +  ++  + + L  G+  +I+
Sbjct: 205 MAVRATG-KEATTHYRIKEKFRAHTHLRLKLESGRTHQIR 243


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 30  EVERMIAQQRVKVNGILL---------ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHK 80
           +V+R +A   V++NG  +         +R  +++      +VD       E   L   +K
Sbjct: 33  QVDRWLAAGMVRLNGQPIIEDCVCGKGDRLELDIPDHQEAQVDDNWQLVWESDELMAINK 92

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           P  L  + +  +   T+   +     +     + RLD  T GL+LL  +    R  +   
Sbjct: 93  PPLLPVSRTTRNLYMTLISLVRRQTPYPDAQLLHRLDTETSGLILLAKNREADRKWKPQL 152

Query: 139 TQW--LRVYRVRFHGQVDQDKL-----------NLLKKGIVI-----QGICYGDMQVT-- 178
            +    +VY+   HG  + D L           + ++  + +                  
Sbjct: 153 AKLIRRKVYQAWVHGSPNWDHLLMECELSEKAGSDIRSQVYVVEPQSDSQYLKPRPSKTE 212

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  + GS + +   L  G+  +I+         + 
Sbjct: 213 FLVLQRAGSKSLIQCELFTGRKHQIRAQLAHLGHPII 249


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 72/239 (30%), Gaps = 46/239 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+ K++A+    SRR     +   R+ + G L +     V     +  +    ++     
Sbjct: 27  RLDKLVAQRFGLSRRAAGDAVLNGRIDLEGQLCDEPGRLVPPESVLRFNPNRPKERKVVT 86

Query: 71  -------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-------FSRVISVGRLDI 116
                  E   L + +KP GL+T  ++     T+   +             V  V RLD 
Sbjct: 87  AKLDILFEDRHLLIVNKPAGLLTLETEARETDTLRGRVLKHQSLRRRGRPFVGIVHRLDR 146

Query: 117 NTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
            T G + L       + L     S    R Y     G V +D       G+V   I    
Sbjct: 147 ETSGAIALALTPEAMKPLQALFRSHAVERRYLAIVAGAVAED------HGVVEAAIVSRP 200

Query: 175 MQVTLDTQKGSN--------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
            +V     +  +                    + +   L  G+  +I+         V 
Sbjct: 201 GEVRRRLARPGDPDARDALTRFRVLERFGCDASLLACELETGRGHQIRVHLASIGHPVL 259


>gi|113954535|ref|YP_731894.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp.
           CC9311]
 gi|113881886|gb|ABI46844.1| 23S RNA-specific pseudouridylate synthase [Synechococcus sp.
           CC9311]
          Length = 295

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 56/293 (19%), Positives = 103/293 (35%), Gaps = 55/293 (18%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK 69
            R+ + + ++    SR  +++ I    V+VNG   + A   + + D +++      PL  
Sbjct: 1   MRLDRWLVSQRSEQSRSRIQKFIDAGYVRVNGKTGK-AKTPLRNGDQVQLWMPPPEPLPY 59

Query: 70  A-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS- 110
                       E   L + +KP GL    +  +   T+ +       +LP I  ++   
Sbjct: 60  LKPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCQDLPGISGKLRPG 119

Query: 111 -VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK---------- 157
            V RLD +T G +++         L+    Q    R Y    HG    +           
Sbjct: 120 VVHRLDKDTTGCIVVAKSQEALVRLQAQIQQRIASREYLAVVHGVPQGESGTIIGAIGRH 179

Query: 158 -LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
            ++  K  +V      Y     TL  + G  + +   L  G+  +I+      N  V   
Sbjct: 180 PVDRKKYAVVSDDSGRYARTHWTLQERLGDYSLLRFKLDTGRTHQIRVHCAHINHAVV-- 237

Query: 216 IRISYGPFQLG---TLLAGSTREVSKKILRE-QLG-PHLLEEAQVNLDAPIYS 263
                G         L      E+  + L   QLG  H + + ++  +AP+ S
Sbjct: 238 -----GDITYSRCRKLPV----ELPGQALHAFQLGLDHPITKERMLFEAPVPS 281


>gi|306829567|ref|ZP_07462757.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus mitis ATCC
           6249]
 gi|304428653|gb|EFM31743.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus mitis ATCC
           6249]
          Length = 298

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 70/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
               + VN    + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVTIDIPAEEGFETLEAIDRPLDILFEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + + +       V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGNGDLEPEGEIIAPIARDVDSIITRRVAKGGKYAHTSYKVVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G    + + L  G+  +I+  F    + 
Sbjct: 211 SYGDIHLIDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 87/242 (35%), Gaps = 42/242 (17%)

Query: 9   ENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           EN    R+ + +A      SR  ++++I +Q +KVN   ++ A   ++  D +EV     
Sbjct: 8   ENEEGDRIDRYLAEEMPERSRSYLQKLIKEQYIKVNNKPVK-ANYRLVLGDRVEVCIPEA 66

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                  + +PL    E   + + +KP  +V   +      T+ + L             
Sbjct: 67  KEPDIEPENIPLDILYEDEDVIVVNKPKQMVVHPAPGHYSGTLVNALMYHCGNELSGING 126

Query: 106 -SRVISVGRLDINTEGLLLLT-ND-GGLARVLELPSTQWLRVYRVRFHGQVDQD------ 156
            SR   V R+D++T G L++  ND    +  ++L      R+Y    HG + ++      
Sbjct: 127 TSRPGIVHRIDMDTTGSLIICKNDMAHQSLAVQLEEHSINRIYEAIVHGNIKEEEGTVNA 186

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                      +   I  +          +  + G   ++   L  G+  +I+       
Sbjct: 187 PIGRHPTDRKKMS--IHAKNARNAITHYKVLKRFGDYTYIQCKLETGRTHQIRVHMASIG 244

Query: 210 WK 211
             
Sbjct: 245 HP 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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 38/253 (15%), Positives = 84/253 (33%), Gaps = 42/253 (16%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFVVKPNSQ 61

Query: 60  IEV-------DGVPLRKAE--------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
           I +       D   ++  E           L + +K   +    S  +  +T+ + L   
Sbjct: 62  ITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLSNTNNTIVNALLAS 121

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHG- 151
                  +   R   V R+D  T GLL++  +      L      + Q  + Y     G 
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKT-HKLLSEMFKNHQIYKEYLAIVSGV 180

Query: 152 ----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                      + + +++  K  +  +          +  +   N  V   ++ G+  +I
Sbjct: 181 IKPNKGLIDAPIGRSQIDRKKMSVTAKNSKQAITTFEVVERFLKNTLVKCQIQTGRTHQI 240

Query: 202 KKVFEFFNWKVNR 214
           +  F + N  V  
Sbjct: 241 RVHFNYINHPVLN 253


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 81/247 (32%), Gaps = 39/247 (15%)

Query: 3   DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + +V +   P R+ K +  R    +R + +  I +  VKVN   ++     V   D I 
Sbjct: 38  YRIVVDKGQEPVRIDKFLMDRVPNITRNKTQNAIREGFVKVNDQEVK-PNYKVRPEDIII 96

Query: 62  V-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +             + +P+    E   L + HK  G+V   +  +   T+ + L   F  
Sbjct: 97  ISLPEPPRESEVVPEDIPINIVYEDDDLLVVHKEAGMVVHPAYNNWTGTLVNALAYHFKN 156

Query: 108 VIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
           +          V R+D +T GLL++       + L          R Y     G+  Q+ 
Sbjct: 157 LPENRDGRPGLVHRIDKDTSGLLVVAKSEHALQHLAKQFFDHTIERTYYALVWGEPKQEA 216

Query: 158 LNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVT-------VGLRE-----GKNREIKKV 204
             +    G  ++           D  + +            V L +     G+  +I+  
Sbjct: 217 GTIDVNLGRSLKDRRVTAAFPEGDFGRHAVTHYKVLKNLRYVSLVQCNLETGRTHQIRAH 276

Query: 205 FEFFNWK 211
            +     
Sbjct: 277 MKHLGHP 283


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 47/232 (20%), Positives = 81/232 (34%), Gaps = 48/232 (20%)

Query: 10  NFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
                R+ +V+A    A  SR +++  +   RV+VNG+ L+     ++  + I +D    
Sbjct: 11  EMAGMRLDQVLAEL-FADYSRSKLQSWVKSGRVQVNGLTLK-PRDKLVGGETIALDAEAE 68

Query: 64  ------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRV 108
                   P+      E   L + +KP GLV   +  +   T+ + L +         R 
Sbjct: 69  IVITAEPEPIPLEIIFEDESLLIVNKPAGLVVHPAIGNWNGTLLNALLNHDSSLETLPRA 128

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V R+D  T GLL++         L   L      R Y     G++          G V
Sbjct: 129 GIVHRIDKETSGLLMVAKTLQAHNSLTQQLQDRDITREYLAITRGRMT-------AGGTV 181

Query: 167 IQ--GICYGDMQVTLDTQKGS--------------NAWVTVGLREGKNREIK 202
            +  G    D +     + G               +  V V L  G+  +I+
Sbjct: 182 DEPIGRHPTDRKRYAVRENGKHAVTHYRVGQRFTRHTLVQVKLETGRTHQIR 233


>gi|188996912|ref|YP_001931163.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931979|gb|ACD66609.1| pseudouridine synthase [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 270

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 92/255 (36%), Gaps = 20/255 (7%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-----AERT 73
            IA +   S+ + + +I  + V VN   +  A+ N+   D +E+    L+       E  
Sbjct: 16  FIAESLKISKNQAKDIIDSRNVIVNNKRVWIASHNLKPGDVVEIVQSELKNDLKILYEDD 75

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +    KP  +V+          +   L +   ++ ++ RLD  T G+LL   D  +   
Sbjct: 76  YIIAIDKPPTIVSDKESSSAEDILRKKLKND--KIKAIHRLDKETSGVLLFAKDYKIFEK 133

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            +        L++Y    H   ++           I G         L+   G   +  V
Sbjct: 134 FKEIWEDKNVLKIYLAISH---NEANFKDFTINQDIDGKQAITHLKVLNKGNGFT-YFQV 189

Query: 192 GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--EQLGPHL 249
            +  G+  +I+K        +      S   F+   L     + V++++L   + +  H 
Sbjct: 190 RIETGRKHQIRKHLASIRHPIVGDKIYSIKKFE-NNL----VKRVTRQMLHSYKLVLTHP 244

Query: 250 LEEAQVNLDAPIYSS 264
               ++ + AP+ S 
Sbjct: 245 YLNKKIEITAPLPSD 259


>gi|148243331|ref|YP_001228488.1| pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
 gi|147851641|emb|CAK29135.1| Pseudouridylate synthases, 23S RNA-specific [Synechococcus sp.
           RCC307]
          Length = 316

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 85/243 (34%), Gaps = 47/243 (19%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR 68
           P R+ + + ++    SR  +++ I    V+VNG     A   +   D I++      PL 
Sbjct: 21  PMRLDRWLVSQRPEQSRARIQKFIEAGYVRVNGTTGR-AKTPLRHGDEIKLWMPPPEPLP 79

Query: 69  KA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS 110
                        E   L + +KP GL    +  +   T+ +       +LP I  ++  
Sbjct: 80  YLQPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPGISGKLRP 139

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG--------------- 151
             V RLD +T G +++         L++   + +  R Y    HG               
Sbjct: 140 GIVHRLDKDTTGCIVIAKSQQALVKLQVQIQKRVASREYLAVVHGVPAGESGTIVGAIGR 199

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             VD+ K  +    +      Y     +L  + G  + +   L  G+  +I+      N 
Sbjct: 200 HPVDRKKYAV----VSSDNGRYACTHWSLQERLGDYSLLRFKLDTGRTHQIRVHCAHRNH 255

Query: 211 KVN 213
            V 
Sbjct: 256 PVV 258


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 81/246 (32%), Gaps = 41/246 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I ++    +R+   +  R    SR  ++R+IA   V VNG    +A   +   D++ +  
Sbjct: 12  IAEDVDKGKRLDLFLVERLPELSRTHIQRIIAAGEVTVNGK-AGKANYKLAPADYVTIRL 70

Query: 63  -DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            +  P              E   + + +KP G+V   +  +   T+ + L     R+   
Sbjct: 71  PEPKPAEIKAEAISLDILYEDEDIIVINKPRGMVVHPAAGNYEGTLVNALLRHCDRLSGI 130

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD---- 156
                   V RLD +T G++++         L     +    R Y    HG + ++    
Sbjct: 131 NGVSRPGIVHRLDKDTSGVMMVAKTDRAHLDLARQIKERTAGRKYVAIVHGNIKENQGII 190

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                        +   +V            +  + G    V   L  G+  +I+    +
Sbjct: 191 NAPIGRHPTDRKKMA--VVFTNSKEAITTFQVLERFGDYTLVECRLFTGRTHQIRVHMAY 248

Query: 208 FNWKVN 213
               V 
Sbjct: 249 IGHPVV 254


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 79/245 (32%), Gaps = 45/245 (18%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ +    T  R+ + IA      SR  ++  I    V V+G+++ +    V+ +  IE+
Sbjct: 8   KSEISATQTGLRLDQAIAELFPDYSRTRLKEWILGGNVYVDGVVVTKPREKVLESQVIEI 67

Query: 63  DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +     +              E   + + +K  GLV      +   T+ + L      + 
Sbjct: 68  EATLEEEVAAEAQEIDLDIVYEDDHILVINKQAGLVVHPGAGNADGTLMNALLHHCPEIE 127

Query: 110 SV------GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
            V       RLD +T GL+++         L   L +    R Y     G +        
Sbjct: 128 HVPRAGIIHRLDKDTTGLMVVAKTVEAQTHLVAALQARDITREYEAIVLGTMT------- 180

Query: 162 KKGIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVF 205
             G V   I     + T                +  +  ++  + + L  G+  +I+   
Sbjct: 181 AGGTVDAPIGRHPTKRTHMAVHHSGRPSVTHYRVAEKFRAHTRLRLRLETGRTHQIRVHM 240

Query: 206 EFFNW 210
                
Sbjct: 241 AHIGH 245


>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 = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 52/280 (18%), Positives = 95/280 (33%), Gaps = 58/280 (20%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V ++   QR+ + +A      SR  ++  I   RV+VN  ++ +    ++  + IE+D 
Sbjct: 10  TVADSQLGQRLDQALAEMFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKIEIDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                       +PL    E   + + +KP  LV      +   TV + L   +  +   
Sbjct: 70  LIEEDVRWEPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIANV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIKKVFEF 207
           G+V + I     + T                      ++  + + L  G+  +I+     
Sbjct: 183 GLVNEPISRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWKVNRLIRISYGPFQLGTLLAGSTREVS--KKILREQL 245
            +  +        G      L AG  R +      LRE L
Sbjct: 243 IHHAL-------IG----DQLYAGRPRPLKGASDELRETL 271


>gi|195953891|ref|YP_002122181.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1]
 gi|195933503|gb|ACG58203.1| pseudouridine synthase, RluA family [Hydrogenobaculum sp. Y04AAS1]
          Length = 308

 Score = 73.3 bits (179), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 90/237 (37%), Gaps = 36/237 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M    I  +    +R+  +I+      SR  ++R+I +  V +NG  + +++  V   D 
Sbjct: 1   MPQIKITPD-IAGERIDVLISNIYKDISREYIKRIIKENGVLINGEKVFKSSKKVFENDV 59

Query: 60  IEVDGVP-----LRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +E +  P     ++  +     LY         KP G+ +        +T+ + L + F 
Sbjct: 60  LEFEIPPPKKLDVKAQDIHIDILYEDNDLAVVVKPSGMPSHTGPGHDENTLVNALLAKFG 119

Query: 107 RVISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--QV 153
            +  +G         RLD  T GL+++  +    + L L   + +  + Y+   +G  + 
Sbjct: 120 DLSVIGGVERPGIVHRLDRYTHGLMVIAKNDVSHQKLSLMFKNKEVDKHYKAIVYGISRF 179

Query: 154 DQDKLNLL-----KKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  +           +  +          + +L+    + + + + +  G+  +I+
Sbjct: 180 KEQTIETFIRRHPTNRLKFEVANEGKLAITKYSLEKPLKNASLLDIKIYTGRTHQIR 236


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 86/242 (35%), Gaps = 46/242 (19%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
            R+ K +++     SR ++++ I   +V VN +++    V V   D I     +   L+ 
Sbjct: 13  IRLDKALSQLLEKISRNQIQKAIKNSQVLVNDVIISDPDVLVKENDVILFAFKEPEELKI 72

Query: 70  A----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
           A          E   L + +K  G+           T+ + L      +  +G       
Sbjct: 73  AAVNIALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLYHTKNLSDIGSAARPGI 132

Query: 113 --RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------------Q 152
             RLD +T GL+++  +     +L       Q +R Y+    G                +
Sbjct: 133 VHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALVWGVINPLAGVIKNNIGRSR 192

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
           V++ K+++LK G    G        TL+   G   + V   L  G+  +I+         
Sbjct: 193 VERQKMSILKYG----GKEAVTHYKTLELFYGGTISMVECRLNTGRTHQIRVQLSHVKHS 248

Query: 212 VN 213
           V 
Sbjct: 249 VV 250


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 44/231 (19%), Positives = 82/231 (35%), Gaps = 47/231 (20%)

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  LRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
           L +        E  +L + +KP GLV   +      T+ + L +    +  +G       
Sbjct: 70  LPEHIPLDILYEDDQLLIVNKPAGLVVHPAPGHSGGTLVNALLAHCGDLPGIGGVQRPGI 129

Query: 113 --RLDINTEGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHG---------------- 151
             RLD +T G + +     LA        +     R Y    +G                
Sbjct: 130 VHRLDKDTSGAIAIA-KTELAHRHLQAQIKAKTARREYLGVVYGVPKTSSGRIDLPIGRH 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            VD+ K+ +    +             +  + G+   +   L  G+  +I+
Sbjct: 189 PVDRKKMAV----VASDKGRSAVTHWQIQERLGNFTLLQFQLETGRTHQIR 235


>gi|163801775|ref|ZP_02195672.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
 gi|159174283|gb|EDP59087.1| pseudouridine synthase Rlu family protein [Vibrio sp. AND4]
          Length = 255

 Score = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 29/193 (15%), Positives = 58/193 (30%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ L      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGLLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
            A+     V V             L E     G+  ++++        +           
Sbjct: 140 TAYKPLAKVEVPYSTGKFPTTRYCLMEMNPKTGRKHQLRRHMAHLRHPIVGDTTHGDGKH 199

Query: 214 -RLIRISYGPFQL 225
            +L R  +   +L
Sbjct: 200 NKLYRTEFDSHRL 212


>gi|170723708|ref|YP_001751396.1| RluA family pseudouridine synthase [Pseudomonas putida W619]
 gi|169761711|gb|ACA75027.1| pseudouridine synthase, RluA family [Pseudomonas putida W619]
          Length = 352

 Score = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 80/245 (32%), Gaps = 42/245 (17%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEVDGVP 66
           QR+ +V A    A  SR  +   I + R+ V+G ++           +      E  G  
Sbjct: 50  QRLDQV-AAQLFAEYSRSRLTSWIKEGRLTVDGAVVRPRDTVHGGSMLALEAEQEAQGEW 108

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGR 113
           + +        E  ++ + +KP GLV   +      T+ + L      ++       V R
Sbjct: 109 IAEDIELDIVYEDDQIMVINKPAGLVVHPAAGHASGTLLNALLHHVPDIVNVPRAGIVHR 168

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ------------DKLN 159
           LD +T GL+++         L  +L S    R+Y     G V                  
Sbjct: 169 LDKDTTGLMVVAKTLQAQTKLVEQLQSRTVSRIYECIVIGVVTAGGKINAPIGRHGGARQ 228

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRL 215
            +    V +G         +  +  S+  V V L  G+  +I+       + +       
Sbjct: 229 RMA---VTEGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGFPLVGDQTYG 285

Query: 216 IRISY 220
            R   
Sbjct: 286 GRFRI 290


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 79/251 (31%), Gaps = 50/251 (19%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
              R+   +A      SR    +++ + +V +NG  +   +  V+  D + V    G P 
Sbjct: 15  DGIRIDAFLAAQDELPSRSACAKLVEEGKVFINGTPVSSKSEKVLLGDRLMVVLPKGEPE 74

Query: 68  R-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                         + E   L +  K  GLV   S      T+ + L +           
Sbjct: 75  AGLLVPNPDIPLDIRFEDQYLIVLSKQAGLVCHPSPGHIDDTLANALVAHCGYEHLGLLQ 134

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD++T GL++      + + L   +      R Y V   G V  D+   +
Sbjct: 135 GEDRPGIVHRLDMDTSGLMVAAKSDEVQKALQDLIRLRVLDRRYVVLVQGYVAPDE-GTI 193

Query: 162 KKGI--VIQGICYGDM-----------------QVTLDTQKGSNAWVTVGLREGKNREIK 202
           + GI   I+      +                 +     +    + +   L  G+  +I+
Sbjct: 194 ETGIARSIRDRLKMTVTDAPGAREAITTFRTLERFEAGRRGEGYSLLECHLYTGRTHQIR 253

Query: 203 KVFEFFNWKVN 213
                    V 
Sbjct: 254 VHMRHVGHPVV 264


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 77/241 (31%), Gaps = 46/241 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----- 69
           R+ +++A+    SR +V   I    V ++G + ++  V V    ++ V   P  +     
Sbjct: 11  RLDQLLAQELNISRSQVLGCIKAGLVSMDGKICQKGGVEVKPGSYVCVQEPPTAEITPLP 70

Query: 70  --------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISVG 112
                    E   L + +KP  L    +      ++ D L          +  SR   V 
Sbjct: 71  TTLNIECLYEDEDLLVINKPPHLAVHPAPSLKEESLVDYLVAKGYQLSNLNGTSRCGIVH 130

Query: 113 RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG------------------Q 152
           RLD  T G L++  +      L   L S Q  R Y     G                  +
Sbjct: 131 RLDKETSGALVIAKNNACHAHLSAQLQSRQMGRYYVALIQGHLREPLFVECHLGRHPKNR 190

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           + +  L+ LK    ++G                   V   L  G+  +++   E     +
Sbjct: 191 LKRANLDALK----VKGGKPSKTFFVPLFDGLKCQLVGARLYSGRTHQVRAHLESLGRPI 246

Query: 213 N 213
            
Sbjct: 247 L 247


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 83/225 (36%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN   +E+A   V   D+I ++          
Sbjct: 17  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNK-VEKAKYLVKEEDNIVIEIPEPKVLEVL 75

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
              +P+    E   + + +KP  +V   +  +  +T+ + +               R   
Sbjct: 76  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 135

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL---------- 158
           V R+D +T GLL++  +      L     +    R Y    +G V +DK+          
Sbjct: 136 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 195

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  +V  G         ++            L  G+  +I+
Sbjct: 196 KDRLKMAVVKDGKNAITHFEVVERFDKFTHM-RARLETGRTHQIR 239


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 85/244 (34%), Gaps = 49/244 (20%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            P R+ K +    +  A+R +++    +  + VN   ++     V   D I+V       
Sbjct: 28  APLRIDKWLMNK-VENATRNKIQAAAKEGNIYVNDQPVKS-NYKVKPLDVIKVLFEHPPF 85

Query: 63  ------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFS-R 107
                 + +PL    E   L + +KP G+V      +   T+       FDNLP   S R
Sbjct: 86  ENLLVGEDLPLDIVYEDDTLLVVNKPAGMVVHPGHGNYSGTLINALIYHFDNLPKNSSDR 145

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-----LRVYRVRFHGQVDQDK----- 157
              V R+D +T GLL++         +   S Q+      R Y     G +++D+     
Sbjct: 146 PGLVHRIDKDTSGLLVVA---KTEHAMAHLSKQFKDKTSEREYVAIVWGNMEEDEGTIEG 202

Query: 158 ------LNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                  N L+  + +               +  +      V+  L  G+  +I+   + 
Sbjct: 203 NIGRHPKNRLQNTVYMDDDADKGKPAVTHYKVLERLTYVTLVSCKLETGRTHQIRVHMKH 262

Query: 208 FNWK 211
               
Sbjct: 263 IGHT 266


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 81/243 (33%), Gaps = 38/243 (15%)

Query: 5   NIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I     T QR+ K+++      SR +++  I  + V VNG  ++ A   V   D I + 
Sbjct: 7   EITDTRHTGQRIDKLLSDYNHDWSRSQIQDWIKHELVIVNGKAIK-ANHKVKLHDSIVIT 65

Query: 64  GVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
              +                E   + + +KP G+V   S      T+ + L      +  
Sbjct: 66  EKEVVDADIQPENLNLDIYYEDKDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDLSG 125

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQDKL 158
                    V R+D +T GLL++  +  +A       L +    R Y    HG +  D  
Sbjct: 126 INGEIRPGIVHRIDKDTSGLLMVAKN-DIAHRSLVDQLVAKSVKRKYTALVHGNIPHDYG 184

Query: 159 ---------NLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       ++ + V+           +         +   L  G+  +I+   ++ 
Sbjct: 185 TVDAPIGRNKKDRQSMDVVDDGKDAVTHFNVLEHFKDYTLIECQLETGRTHQIRVHMKYI 244

Query: 209 NWK 211
            + 
Sbjct: 245 GYP 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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 78/235 (33%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E    QR+ + +A      SR  ++  I   +V+VNG L+ +    V+  + I +D 
Sbjct: 10  TVAETQLGQRLDQALAELFSDYSRSRIKEWILDNKVQVNGKLINKPKEKVLGGEVISIDA 69

Query: 64  ----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   + + +KP  LV      +   TV + L   +      
Sbjct: 70  IIEEDARWEPQDIELNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPAIADV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L   L   +  R Y     G +          
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAIALGCMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
           G+V + I     + T                      ++  + + L  G+  +I+
Sbjct: 183 GMVEEPISRHPTKRTHMAVHPMGKSAVTHYRVMEHFRAHTRLRLRLETGRTHQIR 237


>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 = 73.3 bits (179), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
          QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E
Sbjct: 5  QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE 63


>gi|168700598|ref|ZP_02732875.1| ribosomal large subunit pseudouridine synthase [Gemmata
           obscuriglobus UQM 2246]
          Length = 354

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 37/175 (21%), Positives = 68/175 (38%), Gaps = 29/175 (16%)

Query: 10  NFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
                R+ + + +  +    SR  V+R I    V +NG  + + +  V   D + V    
Sbjct: 38  KSEGMRLDQYV-QLHLGADWSRSVVQRAIESGGVLLNGRPVLKPSYKVRKNDRLHVTMPE 96

Query: 63  --------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------- 106
                   + +PL    +   L L +KP  +V   +  +   T+ + L   F        
Sbjct: 97  PTHEIPVPEDIPLDILYQDEWLALVNKPADMVVHPAKGNWSGTLVNALQWHFREHLSTGA 156

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD 156
              R   V RLD +T G++L+  D    R L +   S +  + Y     G++++D
Sbjct: 157 GHLRAGIVHRLDKDTSGVILVAKDDLTHRDLAMQFESRKVFKEYVAIAAGELERD 211


>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 = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 65/175 (37%), Gaps = 31/175 (17%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           P R+ K +AR     A + SR  + R++ Q  V+V+G ++        +   I VD    
Sbjct: 15  PPRLDKALARDVPEDANL-SRTRLGRLLEQGAVQVDGTVVTDPRSRAEAGQQITVDVEEA 73

Query: 64  --------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------- 104
                    +PL    E   L + +KP G+V   +      T+ + L +           
Sbjct: 74  EDSHILAEEIPLEVVFEDADLIVINKPAGMVVHPAPGSPSGTLVNALLAHCGDDLSGVGG 133

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
             R   V R+D +T GLL++         L          R Y+   +G  D + 
Sbjct: 134 MKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAKQFEKHTVERYYQALVYGVPDAND 188


>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 = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 85/251 (33%), Gaps = 41/251 (16%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++ +I+        R+ K I+     SR  V+ ++ +  + VN    + A   V + DH
Sbjct: 1   MREIDIIAAAEEAGVRIDKYISEQEELSRSRVQSLLQEGLILVNEKPAK-ANYKVKAQDH 59

Query: 60  IE--VDGVPL-----------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I    D                + E   + + +KP  +V   +  +   T+ + L     
Sbjct: 60  ITACFDDEMELEARPEAMELDVRYEDEDVIVINKPKNIVVHPAAGNQTGTLVNGLLYHCK 119

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVD 154
            +           + R+D +T GLL++  +  LA         S    R+Y    HG + 
Sbjct: 120 DLSGINGTLRPGIIHRIDKDTTGLLIVAKN-DLAHASLSKQLQSKTVNRLYYALVHGVI- 177

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
           Q     +   I         M VT    K +     V        L E     G+  +I+
Sbjct: 178 QHDFGTIDAPIGRDVKDRQKMAVTSTNSKDARTHFQVIERFENYTLVECRLETGRTHQIR 237

Query: 203 KVFEFFNWKVN 213
              ++    V 
Sbjct: 238 VHMQYIGHPVV 248


>gi|167945138|ref|ZP_02532212.1| pseudouridine synthase [Endoriftia persephone 'Hot96_1+Hot96_2']
          Length = 55

 Score = 72.9 bits (178), Expect = 6e-11,   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|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 = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 82/232 (35%), Gaps = 45/232 (19%)

Query: 15  RVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK 69
           R+ + +A   +   SR  ++++I Q  V++N  +       +   D +EV      PL  
Sbjct: 14  RIDRWLANQ-VDSLSRSHIQKLIEQGHVQINHKICTSKKYALQIGDQVEVHIPAPQPLAL 72

Query: 70  A----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------------- 106
                      E   L + +KP GLV   +      T+   L +                
Sbjct: 73  EPEPMDLEILFEDDHLLIVNKPAGLVVHPAPGHATGTLVHGLLAHCQDGQGSTLSGIGGV 132

Query: 107 -RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------Q 152
            R   V RLD +T G +++  TN        ++ +   LR Y    +G            
Sbjct: 133 ERPGIVHRLDKDTTGAIMVAKTNQAHQHLQAQIAAKTALREYVGLVYGRPSALTGRMEFP 192

Query: 153 VDQDKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + + + + +K  +V +  G         +    G+ A V   L  G+  +I+
Sbjct: 193 IGRHRSDRIKMAVVPEEQGGKVAVTHWQILQPLGNYALVKFRLETGRTHQIR 244


>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 = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 75/227 (33%), Gaps = 33/227 (14%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           Q++   QR+ + +A      SR  ++  I Q RV ++G +       V++   + VD   
Sbjct: 12  QDHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKVLAGQQVHVDVEL 71

Query: 67  LR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
                            E   + +  KP GLV          T+ + L   +  +     
Sbjct: 72  EDDTRWDAQDIALNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPDIAEVPR 131

Query: 109 -ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQVDQ 155
              V RLD +T GL+++         L   L + Q  R Y                 + +
Sbjct: 132 AGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGR 191

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +V  G          +  +G +  + + L  G+  +I+
Sbjct: 192 HPTQRTHMAVVPNGRPSVTHYRVHEKFRG-HTRLRLRLETGRTHQIR 237


>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 = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 42/230 (18%), Positives = 74/230 (32%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------ 57
           N V ++    R+ +VIA      SR  V+  I +  V VNG ++ +  + +M        
Sbjct: 9   NTVNDSQLGMRLDQVIAELYPDYSRSRVKEWILKNMVSVNGEIVNKPRLKMMGGEELFIK 68

Query: 58  ----DHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIF---- 105
               D +      +PL    E   + + +KP   V          TV +  L        
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDEHILVINKPRDFVVHPGAGTPDRTVLNALLFHCPALAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQ 152
             R   V RLD +T GL+++         L   L   +  R Y                 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEAIAMGKMTGGGTVEKP 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +     +   +   G          +  +     V + L  G+  +I+
Sbjct: 189 IGRHATKRICMAVHELGKPAITHYRVAEHFREHTRLV-LRLETGRTHQIR 237


>gi|284799501|ref|ZP_05984156.2| tRNA pseudouridine synthase [Neisseria subflava NJ9703]
 gi|284798057|gb|EFC53404.1| tRNA pseudouridine synthase [Neisseria subflava NJ9703]
          Length = 238

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 52/168 (30%), Gaps = 26/168 (15%)

Query: 72  RTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +R    +KP G++   S     + R  V      I   V  V RLD  T G+LL   D 
Sbjct: 8   DSRTVAVNKPAGMLVHRSWLDKHETRFAVQTLRDQIGQHVYPVHRLDRPTSGVLLFALDT 67

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICY-- 172
             AR+L     +    + Y     G +              DK+   +    +Q      
Sbjct: 68  EAARLLTQQFENKTIEKTYWAIVRGHLPSDGLIDYALKYMPDKIAEAQTEATLQEAQTTY 127

Query: 173 -------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     Q  L       +W  +    G+  ++++  +     + 
Sbjct: 128 RCLAQTELPFQSALRYPTSRYSWAELTPHTGRKHQLRRHMKHIFHPIV 175


>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 = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 65/175 (37%), Gaps = 31/175 (17%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           P R+ K +AR     A + SR  + R++ Q  V+V+G ++        +   I VD    
Sbjct: 15  PPRLDKALARDVPEDANL-SRTRLGRLLEQGAVQVDGTVVTDPRSRAEAGQQITVDVEEA 73

Query: 64  --------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------- 104
                    +PL    E   L + +KP G+V   +      T+ + L +           
Sbjct: 74  EDSHILAEEIPLEVVFEDADLIVINKPAGMVVHPAPGSPSGTLVNALLAHCGDDLSGVGG 133

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
             R   V R+D +T GLL++         L          R Y+   +G  D + 
Sbjct: 134 MKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAKQFEKHTVERYYQALVYGVPDAND 188


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 35/200 (17%), Positives = 65/200 (32%), Gaps = 22/200 (11%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------DGVPLRKAERTRLW 76
            S++  +R+I +  V VNG     A   +   + +             V L   ER  +W
Sbjct: 28  GSKKRAKRLIDEGLVSVNGQKELLARRRLKGGEVVRFPLTEAPFKPPNVKLLFRERG-VW 86

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           ++ KP  + T   +     TV          +  V RLD  T G ++      L    + 
Sbjct: 87  VFEKPPFITTNEGEKSLEETVRKLF---NPNLKVVHRLDKQTTGPVIAVESEKLFEAFKK 143

Query: 137 P--STQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
                +  + Y     G++  +  +        I G     + VT            V +
Sbjct: 144 QFKRREVKKEYLCLVKGKLRSRQTVRR-----PIDGKSAVSL-VTPLEHFKRATLCRVEI 197

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I++      + V 
Sbjct: 198 ETGRKHQIRRHLASVGYPVV 217


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 83/241 (34%), Gaps = 43/241 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+   +  E+    R+ K +    +    SR  +++++   +V V G  ++ A+  V   
Sbjct: 1   MERFRVTDED-GGVRIDKYLTS--VCEGLSRSYLQKLLKSGQVLVGGQGVK-ASYAVQEG 56

Query: 58  DHIE------VDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D IE      V+   L +        E   + L +KP G+V   +      T+ + L   
Sbjct: 57  DLIELEVPEAVEPEILAEPMDLDVLYEDEDIILINKPKGMVVHPAAGHYTHTLVNGLLDH 116

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
                       R   V R+D++T G+++   +      L   L      R Y+   HG 
Sbjct: 117 CRGQLSGINGVMRPGIVHRIDMDTTGVIIACKNDLAHSCLAEQLKEHSITRRYQAIVHGV 176

Query: 153 VDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           V +D+           +   K  I             +  +      V   L  G+  +I
Sbjct: 177 VKEDEGTVDAPIGRHPVERKKMSINYNNGREAVTHYKVLRRFRQYTHVECRLETGRTHQI 236

Query: 202 K 202
           +
Sbjct: 237 R 237


>gi|11967875|emb|CAC19446.1| putative pseudouridine synthase [Streptococcus mitis]
          Length = 46

 Score = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 19/45 (42%), Positives = 27/45 (60%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           R++K IA AG+ASRR+ E +I Q  V VN  ++   A  + S D
Sbjct: 1  MRINKYIAHAGVASRRKAEELIKQGLVTVNSQVVRELATTIKSGD 45


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/236 (13%), Positives = 86/236 (36%), Gaps = 40/236 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           K  ++E    +R+   ++     SR +V+  ++   + VNG + ++ + ++   D +E+ 
Sbjct: 3   KFSIEEKDLNKRLDIFVSEKLNISRSQVKNYLSS--ILVNGNI-KKLSYSLKLNDIVEIN 59

Query: 63  ----DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
               D                  E   L + +KP  +    S  +   T+ + L      
Sbjct: 60  IKTDDNEEEEDILAENIDLDILYEDEYLLVVNKPCNMSVHCSPSERHGTLVNALLYHIKD 119

Query: 108 VISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD 156
              VG         RLD +T G++++  +  +   ++         ++Y     G + ++
Sbjct: 120 FNFVGDKSRAGIIHRLDKDTSGIMIVGKNADIVSAIQEQFKNRTIKKIYHAIVIGVLREN 179

Query: 157 KLNL---------LKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              +          +K + + +        + +  +   +  + V ++ G+  +I+
Sbjct: 180 FYEINLPIGRHSVYRKKMTVREDGKKALSYIKVLNRFKKHTLIEVNIKTGRTHQIR 235


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 78/249 (31%), Gaps = 46/249 (18%)

Query: 3   DKNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLER-------AA 51
              I     T QR+ K++    +     SR +++  I    VKVN  +++          
Sbjct: 5   QFKIENPEDTGQRIDKLLPEYHSEW---SRTQIQDWIKASLVKVNDQVIKSNYKTKMNDH 61

Query: 52  VNVMSTDHIEVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + V   + +E D  P               + +KP G+V   S      T+ + L     
Sbjct: 62  IVVTEKETVEADIQPENLNLDIYYEDDDVAIVYKPKGMVVHPSAGHYTGTLVNGLMYQMK 121

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
            +           V R+D +T GLL++  +    R L     +    R Y    HG++  
Sbjct: 122 NLSGINGEIRPGIVHRIDKDTSGLLMVAKNDVAHRSLVDQLVNKTVTRKYVALVHGKIPH 181

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D                 +    V+           +         +   L  G+  +I+
Sbjct: 182 DYGTVDAPIGRNKNDRQSMD---VVDDGKEAVTHFNVLEHFNKYTLIECQLETGRTHQIR 238

Query: 203 KVFEFFNWK 211
              ++  + 
Sbjct: 239 VHMKYIGYP 247


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 81/243 (33%), Gaps = 39/243 (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  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD  T GL+++         L  +L +    R Y     G           +
Sbjct: 174 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 233

Query: 154 DQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFF 208
            +D  +  +  I     G        TLD      A V++   +   G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRTHQIRVHFESE 293

Query: 209 NWK 211
              
Sbjct: 294 GHP 296


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 87/260 (33%), Gaps = 38/260 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            ++ +   +R+ +V+A      SR  ++  I   +V+++G +       VM    +E+  
Sbjct: 10  TIEPHHEGKRLDQVLADLFTDYSRTRLKEWILGGKVQLDGKVCLLPKEKVMGGQQVEIAT 69

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
              D    +          E   L +  KP GLV          TV + L   +  +   
Sbjct: 70  ELEDDTRWQAQDLPLNIVYEDEHLLVIDKPAGLVVHPGAGTPDGTVLNALLHRYPDIAEV 129

Query: 109 ---ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD-----QDKL 158
                V RLD  T GL+++  T    +  V  L   +  R Y     G +       + +
Sbjct: 130 PRAGIVHRLDKETTGLMVVAKTIPAQIRLVYALQKRRITREYEAIVVGHMTAGGTVDEPI 189

Query: 159 NLL--KKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIK-KVF----EFFN 209
           +    ++ ++              +  +  ++  +   L  G+  +I+  +         
Sbjct: 190 SRHSTQRTMMAVNPMGKPAITHYRVAERFRAHTRLRCRLETGRTHQIRVHMAHINHALVG 249

Query: 210 WKVN--RLIRISYGPFQLGT 227
             V   RL  I     +L  
Sbjct: 250 DPVYGGRLRPIRNASVELSD 269


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 81/243 (33%), Gaps = 39/243 (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  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD  T GL+++         L  +L +    R Y     G           +
Sbjct: 174 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 233

Query: 154 DQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFF 208
            +D  +  +  I     G        TLD      A V++   +   G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRTHQIRVHFESE 293

Query: 209 NWK 211
              
Sbjct: 294 GHP 296


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 86/241 (35%), Gaps = 51/241 (21%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E    +R+   +A+A    SR  ++R+I +    V G  + + +  V   D + +  
Sbjct: 11  TVSEEQAGERLDTFLAKAYPELSRSYIKRLIEEGFALVEGK-VRKPSYRVKEGDRVTLSV 69

Query: 63  ----------DGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                     + +P+      R + +  KP GLV   S      T+ + L      + S+
Sbjct: 70  PEPEPLEVKPEDIPIEVVYEDRDVVVIVKPCGLVVHPSPGYTSGTLVNALLYHIKDLSSI 129

Query: 112 G---------RLDINTEGLLLLT-NDGGLARVLEL-PSTQWLRVYRVRFHGQVDQDKLNL 160
           G         RLD  T GL+++  ND     ++E   S +  ++YR    G V ++    
Sbjct: 130 GGVERPGIVHRLDKETAGLMVVAKNDTSHRNLVEQFASRRTEKLYRALVKGTVKEE---- 185

Query: 161 LKKGI-VIQGICYGDMQVTLDTQKGSN------------------AWVTVGLREGKNREI 201
              GI  +    +   +    T    +                    + V +  G+  +I
Sbjct: 186 --HGILELPIGRHPFHRKKFSTSSPRSKPAKSEFWVLERFPGLELTLLKVKIYTGRTHQI 243

Query: 202 K 202
           +
Sbjct: 244 R 244


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 45/194 (23%), Positives = 73/194 (37%), Gaps = 42/194 (21%)

Query: 1   MKDKNIVQENFT--------------PQRVSKVIARA-GIASRREVERMIAQQRVKVNGI 45
           M D +I +E+                P+R+ KVIAR     SR  ++  I    V VNG 
Sbjct: 1   MTDTDITKESLAAPEPLEFLVPYTALPERLDKVIARLIPEHSRSRLQGWIEAGHVLVNGQ 60

Query: 46  L--LERAAVNVMSTDHIEV-------------DGVPLRKAERTRLWL-YHKPIGLVTTHS 89
              +++ A      D + V             + V  +  +++  W+  +KP GLVT   
Sbjct: 61  PGRVKQMA---NPGDKLVVWEQAPPEALAFTPEDVDFQVVDQSSDWIVVNKPAGLVTHPG 117

Query: 90  DPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
             +   T+ + L   +       R   V RLD +T GLL++         L     +   
Sbjct: 118 AGNWSGTLLNGLLYRYPELATVARAGIVHRLDKDTSGLLVVARHEKAQTHLIRQLQARSV 177

Query: 142 LRVYRVRFHGQVDQ 155
            R Y    HG + +
Sbjct: 178 SREYVALVHGLLTR 191


>gi|169335579|ref|ZP_02862772.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258317|gb|EDS72283.1| hypothetical protein ANASTE_01994 [Anaerofustis stercorihominis DSM
           17244]
          Length = 307

 Score = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 91/241 (37%), Gaps = 35/241 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           I+ E F   R+ + I++    S+ E+++++ ++ +KVNG   +  +      D ++    
Sbjct: 5   IITEEFMDMRLDRFISKVTTLSKGEIQKLLRKKYIKVNGKK-QEGSYRTEKLDKVQFFLS 63

Query: 63  ---------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                          + + +   ++  + L  KP G+++          V + +  + S+
Sbjct: 64  DEVFKQDNLHSKLNTNNLNIIYEDKN-IILIDKPSGILSQADGSSKEDIVSNLISYLNSK 122

Query: 108 VIS-VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-------- 156
               V RLD+NT G++L   +     +L     +    + Y     G  D++        
Sbjct: 123 STGIVTRLDLNTSGIVLAGKNRRALMLLNEMSKNKLIDKRYLTLVRGDFDREGKVTHYGI 182

Query: 157 ---KLNLLKKG-IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              K N L  G   + G      +  +  +   +  + V L  GK  +I+   +   + V
Sbjct: 183 KDNKENKLILGNKKVDGSFEVSAEFIIKKRYKYHTLLEVRLITGKTHQIRSQLDKMGFPV 242

Query: 213 N 213
            
Sbjct: 243 V 243


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 48/218 (22%), Positives = 82/218 (37%), Gaps = 33/218 (15%)

Query: 10  NFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +  PQR+ K + R    A + SR  + R++ +  V+VNG ++  A   V + D IE+   
Sbjct: 12  DDPPQRLDKALVRDVPEAAVLSRTRLARLLEEGAVRVNGAVVSEAKARVQAGDLIEIVVP 71

Query: 63  ---------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                    + + L    E   L + +KP G+V   +      T+ + L           
Sbjct: 72  EARESHMAPEAIALEVVYEDDDLIVVNKPAGMVVHPAPGSPEGTLVNALLHHCGDSLSGV 131

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK--L 158
               R   V R+D  T GLL++       + L     +    R YR   +G  +     L
Sbjct: 132 GGAKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFEAHSVERQYRAVVYGVPEASDPRL 191

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
             L+ GI  +      +  T   +  ++      L EG
Sbjct: 192 RGLR-GISFEPGNILRI-ATRLARHKTDRQRQAVLFEG 227


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 68/209 (32%), Gaps = 26/209 (12%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWL--------- 77
           SR+ V++ I +  V++NG+  E     V   D I +  +     ++    L         
Sbjct: 31  SRKGVKKAIKKGAVRLNGMPAET-GRWVQPGDIITLVDLEETPPKQYEFTLEVVYEDDHF 89

Query: 78  --YHKPIGLVTTHSDPDGRSTVFDN--------LPSIFSRVISVGRLDINTEGLLLLTND 127
              +KP G+  + +    R+ V           LP        V RLD+ T GLL++   
Sbjct: 90  AVINKPAGVKVSGN--QYRTIVNMLPGNLKASPLPDALKWAKPVHRLDVPTSGLLMVAKT 147

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQV-DQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                 L  +L      + Y     G    +  +     G          +Q     +  
Sbjct: 148 TQAHIHLGQQLEQKTIKKAYHAIVKGTPAARGHIRTPINGQSAHSEFEV-LQTVPSLRNE 206

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           + + V +    G+  +++         + 
Sbjct: 207 TLSLVRLSPHTGRTHQLRVHLASLGHPIT 235


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 81/237 (34%), Gaps = 46/237 (19%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I +  
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 63  --------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   D   L      E   + + +KP G+V   S      T+ + L          
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAEC 128

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLR-VYRVRFH-------G 151
               R   V R+D +T GLL++  +      + L      +  +  Y    H       G
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKN--ATARISLEKQLANKINKREYIAIVHANFKHSSG 186

Query: 152 QVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D        +   +    V+          T+  Q    + V   L  G+  +I+
Sbjct: 187 VIDAPIGRNPYQRQQMA---VVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIR 240


>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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 85/244 (34%), 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  -----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      + + T+ +          +
Sbjct: 93  DRPRYENEVIPEDIPLNIIYEDKYLMVVNKPAGLVVHPGHGNYQGTLVNAIAWHMKDNPD 152

Query: 101 LPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
             +    V  V R+D +T GLL++  T D      ++  +    R YR    G V+QD+ 
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|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 = 72.9 bits (178), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 88/244 (36%), Gaps = 47/244 (19%)

Query: 1   MKD-KNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D K+ V +N  P+R+   +A   I  +R ++  +I  + V V+  L+ R  V + S  
Sbjct: 1   MSDIKSYVCDN--PERLDIFLASE-IGQTRSQIASLIKHKCVFVDEKLVTRPGVKLKSGQ 57

Query: 59  HIEVD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +I+V+               V +   +   L + +KP G+    +     +T+ D L   
Sbjct: 58  NIKVEFPEAKESPALDIDFNVEILYEDDDVLVI-NKPSGVTVHPAPSVKEATLVDWLKHK 116

Query: 105 ---------FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                      R   V RLD  T G +++  +      L   L      R Y    +  +
Sbjct: 117 GIRLSNISGEERHGIVHRLDKGTSGTMVVAKNNEAHEFLSEQLQDKSMGRYYLAVLNPPL 176

Query: 154 DQDKLNLLKKGI------VIQGICYGDM---------QVTLDTQKGSNAWVTVGLREGKN 198
             + +  +++ I       ++  C             +V   +      +V   L  G+ 
Sbjct: 177 KDE-ITTIEQNIGRSAHNRLKMTCTDAGKSKYAKTMFKVLSLSNDEKQQFVACKLFTGRT 235

Query: 199 REIK 202
            +I+
Sbjct: 236 HQIR 239


>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 = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 42/225 (18%), Positives = 83/225 (36%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN  + E+A   V   D+I ++          
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNKI-EKAKYLVKEEDNIVIEIPEPKVLEVV 87

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
              +P+    E   + + +KP  +V   +  +  +T+ + +               R   
Sbjct: 88  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 147

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL---------- 158
           V R+D +T GLL++  +      L     +    R Y    +G V ++K+          
Sbjct: 148 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKENKITVDKPIGRNP 207

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  +V  G         ++            L  G+  +I+
Sbjct: 208 KDRLKMAVVKDGKNAITHFEVVERFDKFTHM-RAKLETGRTHQIR 251


>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 = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 89/247 (36%), Gaps = 48/247 (19%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVN 53
           K+  + +ENF  +R+ +V+       R+E        + +++ +  V+VNG  +   +  
Sbjct: 21  KEFKVTKENFY-ERLDRVL-------RKELSDLKLSSIYKLLRRGNVRVNGNKIRDGSWK 72

Query: 54  VMSTDHIEV----DGVPLRKAERTR-----------------LWLYHKPIGLVTTHSDPD 92
           +   D ++V    D   L++ E +R                 +    KP G+        
Sbjct: 73  MEIGDKVQVVFSGDPSKLKRLEESRELTPKHIPLDILFEDDLIVAVDKPSGISVHPGKGI 132

Query: 93  GRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR 146
              T+ + L +  +        V RLD +T G++L       AR L          + Y 
Sbjct: 133 QIITLVEGLMAYGNSKGFVPRPVHRLDKHTSGVILFAKSPEAARELSKLFRERGVEKGYF 192

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
               G    +K   L   +  +      +  T++    + + + + L  GK  +I++   
Sbjct: 193 TLVKGFP--EKRGKL---VSQREKFVESLAFTVEKSYATTSLLWIDLFTGKKHQIRRQLS 247

Query: 207 FFNWKVN 213
              + V 
Sbjct: 248 EAGYPVV 254


>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 = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 90/249 (36%), Gaps = 42/249 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +VQ  ++ +R+  V++      SR +++R I  ++V +N  +       V+S + IE++ 
Sbjct: 15  VVQIAYSGKRLDWVLSELLPQFSRSQIKRWIINKKVVINNQISVLPKKKVISGEIIEIND 74

Query: 65  VPLRKA-------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           +                        E   + + +KP  +V      + + TV + L   +
Sbjct: 75  INNDSTSDCNNNILIPQNISLNIVYEDNDILVINKPSNMVVHPGVKNNKDTVLNALLYRY 134

Query: 106 SRVI-------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----- 151
             ++        V RLD +T GL+++         L       Q ++ Y     G     
Sbjct: 135 PSIMQISKQAGIVQRLDKDTTGLMIIAKTYLAYTNLLQSFKMKQVIKEYDAVVCGTFSYN 194

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KV 204
                  + +  +N     +   G         +++   + + + V L  G+  +I+  +
Sbjct: 195 AGIISQPIRRHSINRTCMTVHPHGKPAVTRYSVVESFGRTYSRIRVYLETGRTHQIRVHM 254

Query: 205 FEFFNWKVN 213
             + N  V 
Sbjct: 255 -AYINHPVV 262


>gi|116072001|ref|ZP_01469269.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107]
 gi|116065624|gb|EAU71382.1| Pseudouridine synthase, RluD [Synechococcus sp. BL107]
          Length = 339

 Score = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 83/247 (33%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +      P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 32  LTYPKPLPMRLDRWLVSQRTEQSRARIQKFIDAGYVRVNGKQGK-AKTPLREGDQVQLWM 90

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   + + +K  GL    +  +   T+ +       +LP 
Sbjct: 91  PPPEPLPYLRPQPMDLDVLFEDEHIIVLNKSAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 150

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L++   + +  R Y    HG  + D   
Sbjct: 151 ISGKLRPGIVHRLDKDTSGCIVVAKSQEALVKLQVQIQKRVASREYFAVVHGVPNGDSGT 210

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y      L  + G  + +   L  G+  +I+    
Sbjct: 211 IIGAVGRHPVDRKKYAV-VSDESGRYARTHWFLVERFGDYSLLRFKLDTGRTHQIRVHCA 269

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 270 HINHPVV 276


>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 = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 87/248 (35%), Gaps = 38/248 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK + +V       R+ + ++ R    SR  +++++ +Q V V    ++     V + D 
Sbjct: 1   MKQEYVVAPEEAGVRIDRYLSDRCQDISRSYLQKLLKEQSVLVEEKPVKS-NYKVNAGDR 59

Query: 60  IEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + L +KP G+V   +      T+ + L S   
Sbjct: 60  ISVFFPESKEPEIQPEDIPLNIIYEDKDIILINKPKGMVVHPAAGHYSGTLVNGLMSHCR 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D++T G+L++  +      +   L      R Y    HG + 
Sbjct: 120 SELSGINGVMRPGIVHRIDMDTTGVLIVCKNDMAHSSISEQLKEHSITRKYAAIVHGVLK 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +D+           ++  K  I  +          +  +     ++   L  G+  +I+ 
Sbjct: 180 EDEGTVNAPIGRHPVDRKKMSINEKNGREAVTHYRVLERFKQFTYIECQLETGRTHQIRV 239

Query: 204 VFEFFNWK 211
                   
Sbjct: 240 HMASIGHP 247


>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 = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 81/237 (34%), Gaps = 46/237 (19%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I +  
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 63  --------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   D   L      E   + + +KP G+V   S      T+ + L          
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAKC 128

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLR-VYRVRFH-------G 151
               R   V R+D +T GLL++  +      + L      +  +  Y    H       G
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKN--ATARISLEKQLANKINKREYIAIVHANFKHSSG 186

Query: 152 QVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D        +   +    V+          T+  Q    + V   L  G+  +I+
Sbjct: 187 VIDAPIGRNPYQRQQMA---VVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIR 240


>gi|294788953|ref|ZP_06754193.1| ribosomal large subunit pseudouridine synthase D [Simonsiella
           muelleri ATCC 29453]
 gi|294483055|gb|EFG30742.1| ribosomal large subunit pseudouridine synthase D [Simonsiella
           muelleri ATCC 29453]
          Length = 391

 Score = 72.9 bits (178), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 77/232 (33%), Gaps = 40/232 (17%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILL---------ERAAVNVMS 56
           V       R+   +A+     SR  +   I    V  N             E   + +  
Sbjct: 51  VPNELAGMRLDAALAKMLPDYSRSRITTWIKDGLVLCNNQEASPKDKLIGGEELHIQIQQ 110

Query: 57  TDHIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           +D                    E   + + +KP GLV   +  +   T+ + L +     
Sbjct: 111 SDE----NQAFEPELMDLDIVFEDDAVIVLNKPAGLVVHPAAGNWTGTLLNGLLAHCPEL 166

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN 159
               R   V RLD +T GL+++     +   L  +L +    R+YR    G V    K+ 
Sbjct: 167 SQVPRAGIVHRLDKDTSGLMVVAKTLPVQNHLVQQLQNRSVKRIYRAVADGVVPFDGKIE 226

Query: 160 ---------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     LK  +V  G       V +  +  S++++   L  G+  +I+
Sbjct: 227 TLIGRDPHNRLKMAVVKFGGKEAITHVKVLERYQSHSYIECSLETGRTHQIR 278


>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 = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 87/247 (35%), Gaps = 39/247 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M    +  ++    RV K +A      SR ++++ IA   V+VNG  ++ A   +   D 
Sbjct: 1   MDTFKLTVDDTLTGRVDKALAHHFRQFSRSQLQKWIADGNVQVNGEAVK-AKAKLAVGDQ 59

Query: 60  IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + +     +K              E   + + +KP G+V   +      T+ + L     
Sbjct: 60  VVIKPEAPQKIDLVPEKIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHCP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQ 155
                   R   V R+D +T GLL++  +  LA        +     R Y    HG + Q
Sbjct: 120 LSTINGEFRPGIVHRIDKDTSGLLMVAKN-DLAHRSLAAQLKAKTNQREYVALVHGVIKQ 178

Query: 156 D-----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           D           K +  K+ IV  G         L+  +     V+  L  G+  +I+  
Sbjct: 179 DAGTVDAPIGRSKKDRKKQAIVSDGRHAVTHFKVLERFRHYT-LVSCRLETGRTHQIRVH 237

Query: 205 FEFFNWK 211
            +     
Sbjct: 238 MKSIGHP 244


>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 = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 42/221 (19%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+   +A+     SR  +   I    V+ NG         ++  + + V   P  +    
Sbjct: 35  RLDAALAKLLPDYSRSRITSWIKDGLVQCNGQTA-SPKHKLIGGELLRVQIQPSDENQAF 93

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 94  EPEAMDLDIVYEDDSVIVLNKPAGLVVHPAAGNWTGTLLNGLLAHCPELGQVPRAGIVHR 153

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN---------LL 161
           LD +T GL+++         L  +L +    R+YR    G V    K+           L
Sbjct: 154 LDKDTSGLMVVAKTLPAQNHLVQQLQNRSVKRIYRAVADGIVPFDGKIETLIGRDPHNRL 213

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V++  +  +++++   L  G+  +I+
Sbjct: 214 KMAVVKFGGKEAVTHVSVLERYQAHSYIECRLETGRTHQIR 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 = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 19/59 (32%), Positives = 35/59 (59%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R++K+I+ +G+ SRRE ++ I + RV VNG L +     V   D + +D + ++  + T
Sbjct: 4  RLNKLISDSGLCSRREADKFIEEGRVTVNGSLPQ-VGQKVTEGDIVMLDDIQVKIGKHT 61


>gi|256371990|ref|YP_003109814.1| pseudouridine synthase, RluA family [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008574|gb|ACU54141.1| pseudouridine synthase, RluA family [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 309

 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 85/237 (35%), Gaps = 33/237 (13%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-------- 61
           +   +R+ + +A AG   R   ++++    V V+G + +R +  + + + +E        
Sbjct: 11  SLAGERLDRAVAIAGGIERAFAQQLVDDGGVLVDGRVEQRRSRRLRAGELLEATWPDPAA 70

Query: 62  ---VDGVPLRKAERTRLWLYHKPIGLVTTHSD-PDGRSTVFDN----------LPSIFSR 107
               +G P+   E   + +  KP GL+   +   D R +V D           LP    R
Sbjct: 71  PPAPEGAPVVCYEDDDVAVIDKPAGLIVHRTHLRDVRPSVADWALERWPSLRALPGDPLR 130

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD--------- 156
              V RLD  T GL+++    G    L       +  R YR    G   Q          
Sbjct: 131 RGLVHRLDRGTSGLMVIALSAGAYESLRRAVHDHEVERRYRALVVGVPPQAARIEAPLGR 190

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            L  L +  V+ G      Q+ +       + V + L  G+  +I+         + 
Sbjct: 191 DLRDLSRVAVVSGGRDARTQLRVVWHGPDTSLVELTLETGRTHQIRVHLSAIGHPIV 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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 81/237 (34%), Gaps = 46/237 (19%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I +  
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 63  --------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   D   L      E   + + +KP G+V   S      T+ + L          
Sbjct: 69  PYPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAKC 128

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLR-VYRVRFH-------G 151
               R   V R+D +T GLL++  +      + L      +  +  Y    H       G
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKN--ATARISLEKQLANKINKREYIAIVHDNFKHSSG 186

Query: 152 QVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D        +   +    V+          T+  Q    + V   L  G+  +I+
Sbjct: 187 VIDAPIGRNPYQRQQMA---VVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIR 240


>gi|223939777|ref|ZP_03631648.1| pseudouridine synthase, RluA family [bacterium Ellin514]
 gi|223891553|gb|EEF58043.1| pseudouridine synthase, RluA family [bacterium Ellin514]
          Length = 318

 Score = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 89/249 (35%), Gaps = 38/249 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            +   V+ +   +R+   +     A SR  ++R+I Q  +KVNG  ++    +  + + I
Sbjct: 6   SESFTVEVSLPSERLDTFLRERFPAVSRGTIQRLIEQGHIKVNGQTIK-PTHHPRAGELI 64

Query: 61  EV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           EV            + +PL    E + L + +K  GLV   +      T+ + L      
Sbjct: 65  EVYWPEARPAEARPEDIPLDIIFEDSDLLVLNKAPGLVVHPAAGHEEHTLVNALLHHCEG 124

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
                    R   V RLD  T G L++  +      L    +     + Y     G+V +
Sbjct: 125 QLSGIGGVARPGIVHRLDKETSGCLVVAKNDAAHMALAEQFSGRTLEKTYLAIVCGEVVR 184

Query: 156 DKLN---------LLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKV 204
           +              +K + +      +   +   ++  +   W+   L  G+  +I+  
Sbjct: 185 NSGEIRASIARHPTHRKRMTVTDGSGREAWTSYKVRERFSGATWLEALLHTGRTHQIRVH 244

Query: 205 FEFFNWKVN 213
           F+   + + 
Sbjct: 245 FQHLGYPIV 253


>gi|303233294|ref|ZP_07319965.1| pseudouridine synthase, RluA family [Atopobium vaginae PB189-T1-4]
 gi|302480594|gb|EFL43683.1| pseudouridine synthase, RluA family [Atopobium vaginae PB189-T1-4]
          Length = 338

 Score = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 76/253 (30%), Gaps = 52/253 (20%)

Query: 1   MKDKN---IVQENFTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMS 56
           M  +    +V   F   R+   +A       R    + I +  V++N       A +V  
Sbjct: 1   MSQERQTFLVSPQFDRMRLDSFLAAQTDMPARSACAKYIERGCVEINNTEALSKAEHVRL 60

Query: 57  TDHIEVDGVPLRKA---------------ERTRLWLYHKPIGLVTTHSDPDGRSTV---- 97
            D + +     +K                E   L +  K  GLV   S      T+    
Sbjct: 61  GDRVSIVVETQQKPTVIMPNPQIPLDVRYEDEYLLVISKQKGLVCHPSSGHIDDTLANAL 120

Query: 98  -----FDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR 148
                FD+L  +        V RLD++T GL++   D      L   +    + R Y   
Sbjct: 121 VAHCGFDHLGKLQGDDRPGIVHRLDMDTTGLMVAAKDNETQEQLQDLIRLRDFDRRYLAL 180

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD-------------------TQKGSNAWV 189
             G V  D+   +  GI         M V+ D                         + +
Sbjct: 181 VQGYVSPDE-GTITTGIARSKKNRLKMCVSKDPLSRQAITTFKTLDRFEASAHDDGYSLL 239

Query: 190 TVGLREGKNREIK 202
              L  G+  +I+
Sbjct: 240 ECHLYTGRTHQIR 252


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 69/224 (30%), Gaps = 41/224 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLE----------------RAAVNVM-S 56
           R+ +V+A      SR +++  I    V VNG ++                    V V   
Sbjct: 22  RLDQVLADLFPEYSRSKLKTWIQDGNVSVNGEVITVPRHKMQMDELVTVQAEMDVQVTSE 81

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVIS 110
              I +D       E   + + +KP  LV      +   TV + L           R   
Sbjct: 82  AQDIALD----IVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNHVPEIDKVPRAGI 137

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKL 158
           V RLD +T GL+++         L  +L   +  R Y                 + +   
Sbjct: 138 VHRLDKDTTGLMVVAKTIPAQTHLVDQLQRREVSREYEAIALGTMVAGGIVDEPIGRHAT 197

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +   G         ++  +     + + L  G+  +I+
Sbjct: 198 KRTHMAVREMGKPAITHFRVIEKFRAYTH-LRLKLETGRTHQIR 240


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 44/254 (17%), Positives = 89/254 (35%), Gaps = 46/254 (18%)

Query: 1   MKDKN-IVQENFTPQRVS----KVIARAGIASRREVERMIAQQRVKVNG-------ILLE 48
           MK +N +V ++    R+     K I      SR  ++ +I    V+VN            
Sbjct: 1   MKIRNFLVNDDEENLRLDLFICKHIQDK---SRSYIQNLIEDNLVEVNHRMKKSNYKTKT 57

Query: 49  RAAVNVMSTDHIEVD--GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
              + V   D +E++  G  ++     E + + + +KP G++   +      T+ + L +
Sbjct: 58  GDNIKVSLPDAVELNIKGEDIKLDILYEDSDVIVVNKPQGMIVHPASGVYTGTLVNALLN 117

Query: 104 IFS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG 151
                        R   V R+D +T G+L++  +      L   L      R Y     G
Sbjct: 118 HCREDLSGINGIARPGIVHRIDKDTSGILVIAKNDMSHNKLSEQLKDHSMTREYIALVEG 177

Query: 152 QVDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            + ++           K + +K  +V +G         +  +      V   L  G+  +
Sbjct: 178 IIKEEKGSLDKPIGRHKKDKIKMAVV-EGGKRAVTHYEVIKRFKEYTLVKCILETGRTHQ 236

Query: 201 IK-KVFEFFNWKVN 213
           I+  +  +    V 
Sbjct: 237 IRVHMC-YLGHPVV 249


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 80/224 (35%), Gaps = 36/224 (16%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++ V       
Sbjct: 55  IRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAVHESHSED 113

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
                      E   + + +KP G+V      +   T+ + L   F +         V R
Sbjct: 114 LPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLPRAGLVHR 173

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKL 158
           +D +T GLL++  T    L+ + +L      R Y               +    + +   
Sbjct: 174 IDKDTTGLLVIARTKSAQLSLINQLKDKSVYRHYQCIALGAVHEVLRHAQIDAPIGRHST 233

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  K  +   G       V         + + + L+ G+  +I+
Sbjct: 234 HRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIR 277


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 84/243 (34%), Gaps = 39/243 (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  --DG------VPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
             D        P+      E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 102 RADDENAFVAEPVDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 161

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD  T GL+++         L  +L +    R Y     G           +
Sbjct: 162 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 221

Query: 154 DQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFF 208
            +D  +  +  I     G        TLD      A V++   +   G+  +I+  FE  
Sbjct: 222 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVQCQLETGRTHQIRVHFESE 281

Query: 209 NWK 211
              
Sbjct: 282 GHP 284


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 82/242 (33%), Gaps = 43/242 (17%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D   +   +     R+   IAR    SR     +IA+  V V+G    ++   V +  
Sbjct: 1   MSDHRSMPVPDGLEGDRLDTAIARLFGLSRTRAAELIAEGNVLVDGAPAAKSD-RVNAGA 59

Query: 59  HIEV----------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL- 101
            +++                 G+ +   E   + +  KP G+V   +      TV D L 
Sbjct: 60  WLDITLPPPPNPPAPRPEPVPGMRIVY-EDADIVVVDKPAGVVAHPTIGWSGPTVVDGLL 118

Query: 102 --------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG 151
                        R   V RLD NT GL+++         L+    +    +VY     G
Sbjct: 119 AAGVAVATSGAAERQGIVHRLDANTTGLMVVAKSEIAYSSLKRAFKERTVEKVYHALVQG 178

Query: 152 QVD------QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             D         ++    G     +V  G        TL+  + + + + + L  G+  +
Sbjct: 179 HPDPLRGTIDAPIDRHPSGDGRFAVVAGGRPSVTHYTTLEAFRAA-SLLEIDLETGRTHQ 237

Query: 201 IK 202
           I+
Sbjct: 238 IR 239


>gi|270292781|ref|ZP_06198992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
 gi|270278760|gb|EFA24606.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
          Length = 298

 Score = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
               + VN    + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNDRP-QNATYLLDIGDRVTIDIPAEEGFESLKAIDRPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGIASIPS-VNHSNTIANFIKGYYVKRGYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + + +       V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDVDSIITRRVAKGGKYAHTSYKVVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 38/233 (16%), Positives = 82/233 (35%), Gaps = 39/233 (16%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    +R+   +      A+R  +E++I +  V  N  ++ +    +   + I++     
Sbjct: 14  EEDQGKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGRKLKGKEVIQLAIPEE 73

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFS 106
                  + +PL    E   L + +K   +V   +  +   T+         +NL  +  
Sbjct: 74  EKMEIVAENIPLDIVYEDKYLLVVNKQANMVVHPALGNYSGTLVNALLYYCKENLSDMNG 133

Query: 107 RVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-LL 161
            +    V RLD +T GL+++  +  +   L L        + Y     G+  ++K    L
Sbjct: 134 VIRPGIVHRLDKDTTGLIIVAKNNQVHSKLALMFQEKTIRKTYVAIVKGRFSEEKKEGRL 193

Query: 162 KKGIVIQGICYGDMQV------------TLDTQKGSNAWVTVGLREGKNREIK 202
           +  I         M V             +      ++ V V +  G+  +I+
Sbjct: 194 ETLITRDSKDRKKMTVSQIQGKKAISNYRVLLDGDKHSLVEVKIETGRTHQIR 246


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 78/235 (33%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V+E+   QR+ +  A      SR  ++  +    + VNG ++ +A + VM  + I V  
Sbjct: 10  TVKESQLGQRLDQAAAELFSDFSRSRIKEWLLAGNMTVNGEVVTKARLKVMGGEEITVKA 69

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
              D               E   L + +KP   V          TV + L   +  +   
Sbjct: 70  ELEDEERWLAQDISLDIVYEDDDLLVINKPRDFVVHPGAGTPDGTVLNALLFHYPNIAEV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAVVVGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
           G++ + I     + TL                      +  + + L  G+  +I+
Sbjct: 183 GMIEKPIGRHPNKRTLMAVHELGKDAVTHYRVAEHFRIHTRIRLRLETGRTHQIR 237


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 60/165 (36%), Gaps = 28/165 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+  V+A    ASR +V   IA   VKV G  + + ++ +   + I+V            
Sbjct: 13  RLDAVLAALSGASRSQVAAWIAGGHVKVEGQPVTKVSLKLRGGERIDVSPPALPDARVEA 72

Query: 63  DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF-------------DNLPSIFSRV 108
           + +PL    E   L   +KP G+VT  +      T+              D       R 
Sbjct: 73  EDLPLDVIYEDDYLIAVNKPPGMVTHPAPGVLSGTLVNALLGRMPLPEQPDYDSEAGYRP 132

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
             V RLD +T G++++    G    L       +  + Y     G
Sbjct: 133 GIVHRLDKDTSGVIVVAKTVGAHARLAAAFKDRETRKTYLAIAAG 177


>gi|310828937|ref|YP_003961294.1| pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308740671|gb|ADO38331.1| pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 321

 Score = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 96/252 (38%), Gaps = 53/252 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK    + EN   QR+ + +++   +A R  +++M+ ++R+K+NG+        + S D 
Sbjct: 1   MKQ-YTIDENSGNQRLDRYLSKLMPLADRNFLQKMLRKKRIKLNGVRA-EPKDMIHSGDT 58

Query: 60  IEV----------DGVPLRKA----------------ERTRLWLYHKPIGLVTTHSDPDG 93
           ++V              +++                 E   L + +KP GL++  +D  G
Sbjct: 59  VQVYFSEETIAGFQEKKVQRHFDLKPEIKKIFEPPVYEDDHLLVVNKPAGLLSQ-ADSSG 117

Query: 94  RSTVFDNLPSIFSR---------VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
             ++ D   +   +         V+   RLD NT G++L+  D    + +   +   Q L
Sbjct: 118 NISLIDAARTYLKKNATDTKAFEVVISNRLDRNTSGIILMPKDYPTLQTVNAAIRERQAL 177

Query: 143 RVYRVRFHGQVD-QDKLNLLKKGIVIQGI-------CYGDMQVTLDTQKGSN----AWVT 190
           + Y     G +     L        I+           G  +V LD     N      + 
Sbjct: 178 KEYHTIVLGVLKKPGTLTGFLTKDTIENKSAIQSQSEKGAKEVRLDYCPLMNNGKFTLLE 237

Query: 191 VGLREGKNREIK 202
           + L  G++ +I+
Sbjct: 238 ITLHTGRSHQIR 249


>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 = 72.5 bits (177), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V+E+   QR+ +  A      SR  ++  +    + VNG ++ +A + VM  + I V  
Sbjct: 10  TVKESQLGQRLDQAAAELFSDFSRSRIKEWLLAGNMTVNGEVVTKARLKVMGGEEITVKA 69

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                       +PL    E   L + +KP   V          TV + L   +  +   
Sbjct: 70  ELEDEERWLAQDIPLDIVYEDDDLLVINKPRDFVVHPGAGTPDGTVLNALLFHYPNIAEV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAVVVGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
           G++ + I     + TL                      +  + + L  G+  +I+
Sbjct: 183 GMIEKPIGRHPNKRTLMAVHELGKDAVTHYRVAEHFRIHTRIRLRLETGRTHQIR 237


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 85/249 (34%), Gaps = 44/249 (17%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K +  +   P R+ K +        A+R ++++      + VN +L+++    V + D I
Sbjct: 19  KVVAAKGQEPLRIDKFL--MNFIENATRSQIQKAAKDGHIWVNNVLVKQ-NYKVKAGDDI 75

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------- 98
            V             + +PL    E   L + +KP G+V      +   T+         
Sbjct: 76  RVMFSHPPYEFLLQPEDIPLDIVYEDDVLLVVNKPAGMVVHPGHGNYSGTLINALLHHCK 135

Query: 99  -DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
            D   +   R   V R+D +T GLL++         L          R Y     G V+ 
Sbjct: 136 VDLPNNSSDRPGLVHRIDKDTSGLLVVAKTEAAMTFLSKQFFDKTSEREYVAIVWGNVEA 195

Query: 156 DK-----------LNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIK 202
           D+            N L+  +  +G    +      +  + G    ++  L  G+  +I+
Sbjct: 196 DEGTIEGHLGRHPKNRLQMHVFPEGDQGKEAITHYKVLERLGYVTVISCKLETGRTHQIR 255

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 256 VHMKHIGHT 264


>gi|296122834|ref|YP_003630612.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296015174|gb|ADG68413.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 325

 Score = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 55/301 (18%), Positives = 94/301 (31%), Gaps = 69/301 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLR-KAERTRLWLYH 79
           RM+A   V ++G +       V     + +            +  PL    E   L + +
Sbjct: 37  RMVAAGLVTIDGQVAAT-TQRVHPGQQVTIQLTEPPDLFVPPEPTPLEILFEDDSLLVIN 95

Query: 80  KPIGLVT--THSDPDGRST--VFDNLPSI-----FSRVISVGRLDINTEGLLLLTNDGGL 130
           KP GL+   T   PDG     V   L          R   V RLD +T G + +  +  L
Sbjct: 96  KPAGLIAHPTGEIPDGTLINAVQHYLDKQSTHPGLERPGIVHRLDRDTSGAMAICKE-HL 154

Query: 131 ARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--------MQVTL 179
           +  L     Q     + Y     G +  D+L      ++   I             +   
Sbjct: 155 SHRLLSIQFQLGRISKSYLALVEGVLTDDQL------VIDLPIGRAPGCSSALMSCRADA 208

Query: 180 DTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
              + S   + V        L E     G+  +I+            +   + G   +G 
Sbjct: 209 LEAQASKTSLRVVERFPQHTLVEAKPRTGRMHQIR------------IHLATIGFPIVGD 256

Query: 228 ---LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
              L  G  R +      E++   LL   Q    A +  +  L  +  +  + +PDD  +
Sbjct: 257 EFYLKGGEIRPLVWPE-SERVQVSLLINRQALHAACLSFAHPLTNEWQDFQAPLPDDLRQ 315

Query: 285 M 285
            
Sbjct: 316 A 316


>gi|156975510|ref|YP_001446417.1| tRNA pseudouridine synthase C [Vibrio harveyi ATCC BAA-1116]
 gi|156527104|gb|ABU72190.1| hypothetical protein VIBHAR_03241 [Vibrio harveyi ATCC BAA-1116]
          Length = 255

 Score = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 32/203 (15%), Positives = 63/203 (31%), Gaps = 39/203 (19%)

Query: 62  VDGVPLRKAERTRLW-LYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           VD V L    +   +   +KP G++   S  D      V   L       V  + RLD  
Sbjct: 10  VDPVVLEIVYQDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRP 69

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           T G+L+      +A  +       +  + Y     G ++++ +      + +  I     
Sbjct: 70  TSGVLVFALSSEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFA 129

Query: 176 QVTLDTQKGSNAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
               + Q+   A+     V V             L E     G+  ++++        + 
Sbjct: 130 SQEKEAQEAVTAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIV 189

Query: 214 -----------RLIRISYGPFQL 225
                      +L R  +   +L
Sbjct: 190 GDTTHGDGKHNKLYRTEFDSHRL 212


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 80/224 (35%), Gaps = 36/224 (16%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++ V       
Sbjct: 55  IRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAVHESHSED 113

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
                      E   + + +KP G+V      +   T+ + L   F +         V R
Sbjct: 114 LPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLPRAGLVHR 173

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKL 158
           +D +T GLL++  T    L+ + +L      R Y               +    + +   
Sbjct: 174 IDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDAPIGRHST 233

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  K  +   G       V         + + + L+ G+  +I+
Sbjct: 234 HRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIR 277


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 68/344 (19%), Positives = 126/344 (36%), Gaps = 73/344 (21%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+     +R+   + +R    SR  ++++I    V VNG     A+  V   D + +  
Sbjct: 99  VVKSKLEGRRLDTYLTSRFPDYSRSVIQKVIDANAVMVNGKPAR-ASQKVREGDFVSLRL 157

Query: 63  ----DG-VPLRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
               DG +P +    T ++      +  KP G+VT     +   TV + L   +      
Sbjct: 158 PELWDGTIPAQDIPLTVIYEDQWLSIIDKPAGMVTHPGKGNWSGTVVNALQHRYDTLSQL 217

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV--DQDKL 158
              +R   V RLD +T GLL++  D  +   L     +    + Y     G    D+D +
Sbjct: 218 AGSTRPGVVHRLDRDTTGLLIVARDDTIHGKLAQLFETRTIEKEYLAICSGIPERDRDWI 277

Query: 159 NL-------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-------------LREGKN 198
           +        +++ + I+G          D  + +  +  V              L  G+ 
Sbjct: 278 DQPLGPHPTVREKMAIRGEA--------DGGRPARTFYEVVERFDRFALVRCQPLT-GRT 328

Query: 199 REIKKVFEFFNWKVN--RL----IRISYGPFQLGTLLAG---STREVSKKILR----EQL 245
            +I+         +   +L     RI+ G   LG    G       ++++ L     + L
Sbjct: 329 HQIRVHLTHVGLPILADKLYSGRDRITRGDL-LGWQARGDDHDHVLLTRQALHAHRLKFL 387

Query: 246 GPHLLEEAQVNLDAPIYSSETL--VRDRPNIISEVPDDFTRMKK 287
            P   E  ++    P   +ETL  +R RP   S  P  F+  ++
Sbjct: 388 HPATGEPLEIRSPLPPDMAETLETLRQRPAASSTNPTRFSITRR 431


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 83/238 (34%), Gaps = 40/238 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIEGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------D 99
                       +E + +PL    E   + + +KP G+V   +  +   T+        D
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCD 122

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
           +L  I   +    V R+D +T G+L++  +    + L          R Y     G    
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +   + LK  +V  G         L     S + V   L  G+  +I+
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFN-SCSLVKCTLETGRTHQIR 239


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 63/162 (38%), Gaps = 24/162 (14%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ K++AR     SR  ++R I Q  V V+G   +     V   + + +          
Sbjct: 40  ERLDKIVARHLPDYSRSRIQRWIEQGYVTVDGKAAQGKQTVVGDEEIVVLPQLAEEDLAF 99

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVG 112
                G P+   +R  + + +KP GLV   +  +   T+ + L           R   V 
Sbjct: 100 VPEPVGFPVLFEDRD-ILVVNKPAGLVVHPAAGNWSGTLLNGLLHHLPKSAAIPRAGIVH 158

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
           RLD +T GL+++         L  +L +    R Y     G+
Sbjct: 159 RLDKDTSGLMVVAKTLEAQTHLVRQLQARTVRREYLALVWGE 200


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 81/237 (34%), Gaps = 46/237 (19%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I +  
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 63  --------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                   D   L      E   + + +KP G+V   S      T+ + L          
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAKC 128

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLR-VYRVRFH-------G 151
               R   V R+D +T GLL++  +      + L      +  +  Y    H       G
Sbjct: 129 DEILRPGIVHRIDKDTSGLLMIAKN--ATARISLEKQLANKINKREYIAIVHANFKHSSG 186

Query: 152 QVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D        +   +    V+          T+  Q    + V   L  G+  +I+
Sbjct: 187 VIDAPIGRNPYQRQQMA---VVASGKKAITHFTVLEQFPGYSLVKCVLETGRTHQIR 240


>gi|326575838|gb|EGE25761.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis CO72]
          Length = 355

 Score = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 80/224 (35%), Gaps = 36/224 (16%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++ V       
Sbjct: 55  IRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAVHESHSED 113

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
                      E   + + +KP G+V      +   T+ + L   F +         V R
Sbjct: 114 LPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLPRAGLVHR 173

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKL 158
           +D +T GLL++  T    L+ + +L      R Y               +    + +   
Sbjct: 174 IDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDAPIGRHST 233

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  K  +   G       V         + + + L+ G+  +I+
Sbjct: 234 HRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIR 277


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 88/241 (36%), Gaps = 46/241 (19%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ + +A+     SR  ++ +I Q  +++NG +       V S D + +   P++     
Sbjct: 13  RLDRWLAQKLPDLSRSRLQTLIEQGNLQLNGTICTDKKTLVKSGDRLHLLIPPVKPLDLQ 72

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
                     E  +L + +KP GLV   S    + T+ + L S  S +  +G        
Sbjct: 73  PQDIPLDILYEDDQLIIINKPAGLVVHPSPGHEQGTLVNALLSHCSNLAGIGGVQRPGIV 132

Query: 113 -RLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHG----------------QV 153
            RLD +T G L++         L+         R Y    +G                 +
Sbjct: 133 HRLDKDTTGALVVAKTDYAHHHLQQQLKAKTARREYLGIVYGVPKTTSGKINLSIGRHPI 192

Query: 154 DQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           ++ K+ +    + ++ G         +  + G+ + +   L  G+  +I+   +  N  +
Sbjct: 193 ERKKMAV----VPLEKGGREAITHWEILERLGNYSLIYFRLETGRTHQIRVHCQAMNHPI 248

Query: 213 N 213
            
Sbjct: 249 V 249


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          R++K+I+ +G+ SRRE ++ I + RV VNG L +     V   D + +D + ++
Sbjct: 7  RLNKLISDSGLCSRREADKFIEEGRVTVNGSLPQ-VGQKVTEADIVMLDDIQIK 59


>gi|330811803|ref|YP_004356265.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379911|gb|AEA71261.1| Ribosomal large subunit pseudouridine synthase D [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 320

 Score = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 89/246 (36%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----R 49
           M DK  ++     +    R+ +V A    A  SR  +   I   R+ V+G ++       
Sbjct: 1   MSDKIELRAEVPSELGGQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 59

Query: 50  AAVNVMSTDHIEVDGVPLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
               +  T   E  G  + +        E   + + +KP GLV      H+D    + + 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIALDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALL 119

Query: 99  DNLPSIF--SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
            ++P I    R   V RLD +T GL+++  T       V +L S    R+Y     G V 
Sbjct: 120 HHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVT 179

Query: 155 QD---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           ++  V++G         +  +  S+  V V L  G+  +I+   
Sbjct: 180 AGGKINAPIGRHGQQRQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
              N+ 
Sbjct: 240 AHINFP 245


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 64/175 (36%), Gaps = 24/175 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNV--MST 57
            V +  T  R+ K +       SR +++R I    V VNG  ++     +A   V     
Sbjct: 9   TVTDGMTG-RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEPE 67

Query: 58  DHIEVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
             +E+D  P               + +KP G+V   +      T+ + L           
Sbjct: 68  TPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYHAPLSSING 127

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
             R   V R+D +T GLL++       R L   L     LR Y    HG + +++
Sbjct: 128 ELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENE 182


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 83/238 (34%), Gaps = 40/238 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------D 99
                       +E + +PL    E   + + +KP G+V   +  +   T+        D
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCD 122

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
           +L  I   +    V R+D +T G+L++  +    + L          R Y     G    
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +   + LK  +V  G         L     S + V   L  G+  +I+
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFN-SCSLVKCTLETGRTHQIR 239


>gi|326576921|gb|EGE26827.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis O35E]
          Length = 355

 Score = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 80/224 (35%), Gaps = 36/224 (16%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            R+ K+ A   G  SR  +++ I + ++ VNG +++     V   D + ++ V       
Sbjct: 55  IRLDKLCADIFGGFSRANLKKFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAVHESHSED 113

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
                      E   + + +KP G+V      +   T+ + L   F +         V R
Sbjct: 114 LPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLPRAGLVHR 173

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKL 158
           +D +T GLL++  T    L+ + +L      R Y               +    + +   
Sbjct: 174 IDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCVALGAVHEVLRHAQIDAPIGRHST 233

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  K  +   G       V         + + + L+ G+  +I+
Sbjct: 234 HRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIR 277


>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 = 72.5 bits (177), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/175 (22%), Positives = 64/175 (36%), Gaps = 24/175 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNV--MST 57
            V +  T  R+ K +       SR +++R I    V VNG  ++     +A   V     
Sbjct: 9   TVTDGMTG-RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIEPE 67

Query: 58  DHIEVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
             +E+D  P               + +KP G+V   +      T+ + L           
Sbjct: 68  TPVEIDLEPENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYHAPLSSING 127

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
             R   V R+D +T GLL++       R L   L     LR Y    HG + +++
Sbjct: 128 ELRPGIVHRIDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENE 182


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 88/246 (35%), Gaps = 43/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  +P R+ K +    + ASR  ++       V  NG  ++  +  V   D + V  
Sbjct: 32  VVDKGQSPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKS-SYKVKPQDVLTVMM 90

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP GLV      +   T+ + +      V +
Sbjct: 91  DRPRYENDIIPEDIPLDVVYEDEDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLRDVPT 150

Query: 111 ----------VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
                     V R+D +T GLL++  T D      L+  +    R Y     G V++D+ 
Sbjct: 151 YNPNDPQVGLVHRIDKDTSGLLVIAKTPDAKTNLGLQFYNKTTKREYNALVWGIVEEDEG 210

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + ++  + I     G   VT   +  + G    V   L  G+  +I+  
Sbjct: 211 TITGNIGRNPRDRMQMAV-ISDPTQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRVH 269

Query: 205 FEFFNW 210
            +    
Sbjct: 270 MKHIGH 275


>gi|306519054|ref|ZP_07405401.1| putative RNA pseudouridine synthase [Clostridium difficile
          QCD-32g58]
          Length = 63

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAE 71
          QR+ K+++  G  SR E+++   Q  V VNG  +      V    D I  +G  +   E
Sbjct: 5  QRIDKILSNLGYGSRSEIKKYCKQGSVVVNGSEVSNPGTQVDTENDEILFNGEEVIYRE 63


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 83/238 (34%), Gaps = 40/238 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF-------D 99
                       +E + +PL    E   + + +KP G+V   +  +   T+        D
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIIYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLYHCD 122

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
           +L  I   +    V R+D +T G+L++  +    + L          R Y     G    
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +   + LK  +V  G         L     S + V   L  G+  +I+
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFN-SCSLVKCTLETGRTHQIR 239


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 86/235 (36%), Gaps = 41/235 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-------- 57
           +V +    +RV   +AR    SR     +IA   V V+G  + ++   V +         
Sbjct: 12  LVPDGLEGERVDAAMARLFGLSRTRAAELIADGLVTVDGSAVAKSD-RVSAGSMLDATIP 70

Query: 58  ---DHIE-----VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              D +E     V+G+ +   +   + +  KP+G+    S      TV  +L +   R+ 
Sbjct: 71  SQADPLEIKPEIVEGIKIIYDDDAFVVI-DKPVGVAVHPSPGWQGQTVVGHLAAAGFRIS 129

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--QD 156
           + G         RLD+ T G++++        VL+         + Y     G  D  + 
Sbjct: 130 TSGAKEREGIVQRLDVGTSGVMVIAKSEHAYSVLKNAFRQRTVDKTYHALVQGHPDPLEG 189

Query: 157 KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            ++           K  +   G        TL+  + + + + + L  G+  +I+
Sbjct: 190 TIDAPIGRNPKYDYKFAVRADGRHSVTHYETLEAHRFA-SLLKIHLETGRTHQIR 243


>gi|322391936|ref|ZP_08065400.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
 gi|321145162|gb|EFX40559.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
          Length = 299

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 75/211 (35%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               ++VNG   + A   +   D + +D     G      +        E     + +KP
Sbjct: 33  RGGDIRVNGRP-QNATYLLDVGDEVVIDIPPEEGFETLEAIDYPLDILFEDDHFLIINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  FGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y   F G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKKAIEKHYYALFKGDGHLEPQGEIIAPIARDEDSIITRRVA-KGGKYAHTSYQIV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G+   V + L  G+  +I+  F    + 
Sbjct: 210 ASYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 83/225 (36%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN   +E+A   V   D+I ++          
Sbjct: 29  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNK-VEKARYLVKEEDNIVIEIPEPKVLEVL 87

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
              +P+    E   + + +KP  +V   +  +  +T+ + +               R   
Sbjct: 88  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 147

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL---------- 158
           V R+D +T GLL++  +      L     +    R Y    +G V +DK+          
Sbjct: 148 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 207

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  +V  G         ++            L  G+  +I+
Sbjct: 208 KDRLKMAVVKDGKNAITHFEVVERFDKFTHM-RARLETGRTHQIR 251


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 90/250 (36%), Gaps = 46/250 (18%)

Query: 7   VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           V    +P R+   + +  +  A+R +V+  I + RV VNG  ++ A   + S D IEV  
Sbjct: 41  VSRTQSPMRIDVYLTQQ-VENATRNKVQEAIEEGRVVVNGKCVK-ANYRLKSCDVIEVTF 98

Query: 63  ----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTV-----------FDN 100
                     + +P+    E   L + +K  G+V   +  +   T+            + 
Sbjct: 99  LRPPAPELAPEAIPIAIMYEDDDLMVINKEPGMVVHPAFGNWTGTLANAILHHLGNSAEA 158

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD-- 156
           L +   R   V RLD +T GL+++  +      L       +  ++Y+    G   Q   
Sbjct: 159 LDASEMRPGIVHRLDKDTSGLIIIAKNPIALHKLARQFAERKVGKIYKALTWGVPKQASG 218

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV---GLREGKNREIKK 203
                     K   +      +G+      +T    + +  W +V    L  G+  +I+ 
Sbjct: 219 TITTNIGRSHKNRKVMANFPFEGLEGKTA-ITDYCVEENLEWFSVMSLRLHTGRTHQIRV 277

Query: 204 VFEFFNWKVN 213
             +     + 
Sbjct: 278 HLQHLGLPIV 287


>gi|297170431|gb|ADI21463.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0070_10G19]
          Length = 312

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 78/241 (32%), Gaps = 47/241 (19%)

Query: 1   MKDKNIVQENFTPQRVS----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           +KDK  V E     R+     K + R    SR +++  I    V++N    +     ++S
Sbjct: 2   IKDKFFVDETMHGTRLDIAITKYLGRK--YSRNQIKNFILGGCVQINDENCK-PKDKLVS 58

Query: 57  TDHIEVD----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTV----FD 99
            D IE +             +      E     +  K   L+      + + T+      
Sbjct: 59  GDEIEFNFNDYHDSSWMPEKIDFNVIDETNDYIIVEKSPNLIMHPGAGNEQGTLANGLLF 118

Query: 100 NLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
             P      R   V RLD +T GLL++         +     +    + Y     G    
Sbjct: 119 RFPELAKLPRCGIVHRLDKDTSGLLVVAKTNEFRNHIVSEFQNRNVKKYYYALIKGNILG 178

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREGKNREI 201
                  + +DK N ++  +   G      + T   +        + V V +  G+  +I
Sbjct: 179 QIIINEPILRDKSNRIRMTVDQAG-----REATSIVKNIETFDFYSLVEVEILTGRTHQI 233

Query: 202 K 202
           +
Sbjct: 234 R 234


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 83/238 (34%), Gaps = 40/238 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------D 99
                       +E + +PL    E   + + +KP G+V   +  +   T+        D
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCD 122

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
           +L  I   +    V R+D +T G+L++  +    + L          R Y     G    
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +   + LK  +V  G         L     S + V   L  G+  +I+
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFN-SCSLVKCTLETGRTHQIR 239


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/224 (20%), Positives = 80/224 (35%), Gaps = 38/224 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+ K ++  G  SR +V+  I    + VNG  ++ A   +   D +EV+           
Sbjct: 13  RIDKWVSDRGEWSRSQVQEWIKTGALLVNGSAVK-ANYKLQVGDEVEVNVPEAVELEVLP 71

Query: 64  -GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVG 112
             +PL    E   + + +K  G+V   +      T+ + L          +   R   V 
Sbjct: 72  EDIPLEIVFEDEDVIVVNKARGMVVHPAAGHTSGTLVNALLYHCDDLSGINGVKRPGIVH 131

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           R+D +T GLL++  +      L          R Y    HG++  + L  ++  I     
Sbjct: 132 RIDKDTTGLLMVAKNDLAHESLASQLKDKTIKREYIALVHGELVHE-LGTIEAPIGRDTN 190

Query: 171 CYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
               M VT    K +     +        L E     G+  +I+
Sbjct: 191 DRQRMTVTDRNAKEAVTHFRLLERYKDFTLVECKLETGRTHQIR 234


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/266 (17%), Positives = 75/266 (28%), Gaps = 61/266 (22%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K +   +    R+   +  A  G  SR  ++ +I Q  V VN + +  +   V   D 
Sbjct: 11  NRKVLTAGDDASGRLDAFLTEALGGEFSRNRIKGLIEQGAVSVNALTVTESKRKVHPGDT 70

Query: 60  IEV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
            ++           G  +      E   L +  KP GLV      +   T+ + L     
Sbjct: 71  FQIALPEPEDPEPKGEAITLDVLYEDQDLIVLVKPAGLVVHPGAGNWTGTLVNALIHHCG 130

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFH 150
                     R   V RLD +T G++++  +    R L              R YR    
Sbjct: 131 DSLSGIGGVKRPGIVHRLDKDTSGVMVVAKNDAAHRHLSDQFADHGRNGPLERAYRAVVW 190

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------AWVTVG--LRE------- 195
           G+        LK  I       GD       +  S+          V     E       
Sbjct: 191 GRP-----RQLKGTIDAPLGRAGDRTKRAVKRDDSDDAREAITHYEVVDRYHEKPDGTSL 245

Query: 196 ----------GKNREIKKVFEFFNWK 211
                     G+  +I+         
Sbjct: 246 ASAVECHLETGRTHQIRVHMAHIGHP 271


>gi|296269399|ref|YP_003652031.1| pseudouridine synthase, RluA family [Thermobispora bispora DSM
           43833]
 gi|296092186|gb|ADG88138.1| pseudouridine synthase, RluA family [Thermobispora bispora DSM
           43833]
          Length = 310

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 78/244 (31%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDG 64
           V E    +R+   ++R    SR     +IA   V V+G +  ++   + +     + +  
Sbjct: 9   VPEGLEGERLDAALSRLFGFSRTRAADLIAAGDVLVDGAVPSKSD-RLRAGQWLDVTIPP 67

Query: 65  ---------VPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                     P+       E   + + +KP G+    +      TV   L     RV   
Sbjct: 68  PPAPPAPRLEPIPGMSILYEDEDIIVINKPAGVAAHPTVGWTGPTVLGGLLGAGHRVSTS 127

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------ 154
                   V RLD NT G +++         L+      +  + Y     G +D      
Sbjct: 128 GAAERQGIVHRLDANTTGAMVVAKSELAYARLKRAFKERKVEKRYHAMVQGHMDPLRGTI 187

Query: 155 QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              ++    G     +V  G        T++  + + + + V +  G+  +I+       
Sbjct: 188 DAPIDRHPSGDGRFAVVAGGKEAITHYDTIEAFRAA-SLLDVKIETGRTHQIRVHLSALG 246

Query: 210 WKVN 213
               
Sbjct: 247 HPCV 250


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 87/238 (36%), Gaps = 43/238 (18%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           +R+ K++AR     SR  +++ I    V+V+G  + R    V   + IE+          
Sbjct: 56  ERLDKLLARHFSEFSRSRLQQWIESGAVRVDGH-VRRPRDAVQMGNRIEIQPQAAPESSA 114

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVG 112
              + VPL    E   L + +KP GLV   +  +   TV + L           R   V 
Sbjct: 115 FSPEDVPLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRDPGAALLPRAGIVH 174

Query: 113 RLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
           RLD  T GL+++    T    L R L   +    R Y     G           + +D  
Sbjct: 175 RLDKETSGLMVVARSLTAQTDLVRQL--QARTVKRTYIALVWGRTYDEGTIDAPIGRDPR 232

Query: 159 NLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLR--E-GKNREIKKVFEFFNWK 211
              +  +V    G        TL T      +V++ +   E G+  +I+  FE     
Sbjct: 233 ERTRMAVVHTASGKPSRTHFRTLATVPLGRGFVSMVMCKLETGRTHQIRVHFESIGHP 290


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 81/243 (33%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D +EV   
Sbjct: 43  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PRAAVCGGDRVEVVPQ 101

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 102 RAADESAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPEAAEL 161

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD  T GL+++         L  +L +    R Y     G           +
Sbjct: 162 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 221

Query: 154 DQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFF 208
            +D  +  +  I     G        TLD      A V++    L  G+  +I+  FE  
Sbjct: 222 GRDPRDRTRMAIIETASGKPARTHFKTLDVVDLGRAQVSLVRCQLETGRTHQIRVHFESE 281

Query: 209 NWK 211
              
Sbjct: 282 GHP 284


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 81/237 (34%), Gaps = 46/237 (19%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V+   +  R+ K IA      SR  V+ +I Q+ +  NG L  + +  V + D I +  
Sbjct: 10  VVKSEESGVRLDKYIATHISTISRTRVQELIKQKLITTNG-LQTKLSYKVNTNDKINIEI 68

Query: 63  --------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   D   L      E   + + +KP G+V   S      T+ + L          
Sbjct: 69  PSPQPLSLDPENLNLDIIYEDDDVIVVNKPQGMVVHPSAGHPDHTLVNGLIYHTKNLAEC 128

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLR-VYRVRFH-------G 151
               R   V R+D +T GLL++  +      + L      +  +  Y    H       G
Sbjct: 129 DEIFRPGIVHRIDKDTSGLLMIAKN--ATARISLEKQLANKINKREYIAIVHANFKHSSG 186

Query: 152 QVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D        +   +    V+          T+  Q    + V   L  G+  +I+
Sbjct: 187 VIDAPIGRNPYQRQQMA---VVASGKKAITHFTVLEQFPGYSLVKCILETGRTHQIR 240


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 88/251 (35%), Gaps = 43/251 (17%)

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---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE+   D V L             E   + +  KP G++   S      T+ + L     
Sbjct: 70  IEITILDNVDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGTLVNALLFHCK 129

Query: 102 ----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVD 154
                +  +R   V R+D  T GLL++  +   A  L          +R Y    HG + 
Sbjct: 130 DLSGINGVNRPGIVHRIDKETSGLLMVAKN-DNAHRLLSKQLKDHTVVRRYVALVHGLIP 188

Query: 155 QD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +                 +   +            T+  +  + + +   L  G+  +I
Sbjct: 189 HEHGKVDAPIGRNPKDRQSMA--VTRTNSKEAVTNFTVLKRYNAMSLIECRLETGRTHQI 246

Query: 202 KKVFEFFNWKV 212
           +    +  + V
Sbjct: 247 RVHMSYIGYPV 257


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 86/244 (35%), Gaps = 45/244 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V ++   QR+ + +A      SR  ++  I   RV+VN  ++ +    ++  + IEVD 
Sbjct: 10  TVADSQLGQRLDQALAELFPDYSRSRIKEWILDNRVQVNDKIINKPKEKMLGGEKIEVDA 69

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP  LV      +   TV + L   +  ++  
Sbjct: 70  LIEEDVRWEPQNIPLNIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPEIVNV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQRREITREYEAVATGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G+V + I     + T                +     ++  + + L  G+  +I+     
Sbjct: 183 GLVNEPISRHPTKRTHMAVHPMGKPAVTHYRVMEHFRAHTRLRLRLETGRTHQIRVHMAH 242

Query: 208 FNWK 211
            +  
Sbjct: 243 IHHP 246


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 42/231 (18%), Positives = 72/231 (31%), Gaps = 45/231 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERTR----------- 74
           SR +   MI    V +NG   +     V   D + V      R  E+ R           
Sbjct: 29  SRSQARGMIDHGCVMINGSPCKSVGTTVKPGDLVAVRYDKHQRYREKKRQWDDRTFEIVF 88

Query: 75  ----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL 124
               + + +K  G +T  +D    +++ D +               V RLD  T GLL+ 
Sbjct: 89  EDEHIIVVNKSAGTLTVPTDRGEPNSLVDRVSIYLSYSKSKKEAFVVHRLDRETSGLLVF 148

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL---LKKGIVIQGICYGDMQ--- 176
                +A +L       +  RV+     G V +D+      L  G  +        +   
Sbjct: 149 GKHEPIADLLIEQFKDRRPTRVFHAIVAGNVSEDEGTFESHLATGSNLDRYETRPGKDTD 208

Query: 177 --------VTLDTQKGSNAWVTVGLRE------GKNREIKKVFEFFNWKVN 213
                   V    ++ S+      L E       +N +++  F      V 
Sbjct: 209 QAITHYKVVRRLAERESSHGEETTLIEAQLETSKRN-QVRVQFANAGHPVL 258


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 72/243 (29%), Gaps = 46/243 (18%)

Query: 15  RVSKVIARA-----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           R+ + +A          SR  ++ +I   RV + G  +   A  + + D + +D  P   
Sbjct: 28  RLDRFLAERPEIVDAHLSRSRIKALIESGRVSLRGAAIRDPAKKLAAGDAVSLDVPPPEP 87

Query: 70  A-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------S 106
           A             E   L +  KP GLV   +      T+ + L +             
Sbjct: 88  AEPQAEEIALDIVYEDAHLIVIDKPAGLVVHPASGHESGTLVNALIAHCGESLSGVGGVK 147

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHGQVDQDK--L 158
           +   V R+D +T GLL++         L              R Y     G  D+    +
Sbjct: 148 KPGIVHRIDKDTTGLLVVAKTDAAHHGLSRLFADHGRTLSLTREYLAFVWGVPDRAHGTI 207

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSN----------AWVTVGLREGKNREIKKVFEFF 208
                   IQ      +      +  ++          + V   L  G+  +I+      
Sbjct: 208 ETSLGRHSIQREKMAVVPEARGREAITHWEKVADYGVASLVRCQLETGRTHQIRVHMAHI 267

Query: 209 NWK 211
              
Sbjct: 268 GHP 270


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/227 (16%), Positives = 84/227 (37%), Gaps = 41/227 (18%)

Query: 13  PQRVS----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           PQR+     K++A     SR +++  I + +VKVN  +       ++  + I++  V + 
Sbjct: 18  PQRLDQAIAKLLAD---YSRSQIKGWILEGKVKVNDQVTILPNKKILGGEIIKIS-VMIE 73

Query: 69  KAERTR----------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
           +                     + + +KP  +V      +   T+ + L   +       
Sbjct: 74  REHEQYWKAQNIALNIVYEDDDIIVINKPRDMVVHSGAGNLDGTILNALLYYYPAIANVP 133

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK-----LN 159
           R   V RLD NT GL+++         L   L +   +R Y     G ++ D      + 
Sbjct: 134 RAGIVHRLDKNTTGLMIVGKTLSAQTKLVELLRTRSIIREYEAITIGIINNDGTVEQPIA 193

Query: 160 LL---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIK 202
                +  + +  +    +   ++  +  ++  + + L  G+  +I+
Sbjct: 194 RHATKRTHMTVNPLGKPAITHYSIIERFRAHTRLRLRLETGRTHQIR 240


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 75/232 (32%), Gaps = 37/232 (15%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------ 57
           N V EN    R+ +VIA+     SR  ++  I    V VNG ++++    +M        
Sbjct: 9   NTVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQ 68

Query: 58  ----DHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D +      +PL    E   + + +KP   V          TV + L         
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLHHCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQ 152
             R   V RLD +T GL+++         L   L   +  R Y                 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQMTGGGTIEKP 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR-E-GKNREIK 202
           + +     +   +   G          +  +       + LR E G+  +I+
Sbjct: 189 IGRHSTKRICMAVHEMGKDAITHYRVAERFREHT---RIVLRLETGRTHQIR 237


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 79/235 (33%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I   RV+VNG L+ +    V+  + I +D 
Sbjct: 10  TVAESQLGQRLDQALAELFPDYSRSRIKDWILDDRVQVNGKLINKPKEKVLGGEEIAIDA 69

Query: 64  ----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                              E   + + +K   LV      +   TV + L   +  +   
Sbjct: 70  IIEEDARWEPQNIALNIVYEDDDILVINKSRDLVVHPGAGNPDGTVLNALLYHYPEIADV 129

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVIAKTVPAQTRLVESLQLREITREYEAVATGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
           G+V + I     + T                      ++  + + L  G+  +I+
Sbjct: 183 GMVEEPISRHPTKRTHMAVHPMGKPAITHYRVMEHFRAHTRLRLRLETGRTHQIR 237


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 95/254 (37%), Gaps = 53/254 (20%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K I ++   P RV K +        A+R ++++      + VN + +++    V + D +
Sbjct: 24  KFIAEKGQNPLRVDKYLMN--YIEKATRNKIQKAAKDGNIYVNDVPVKQ-NYKVKAGDVV 80

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FD 99
           +V             + +PL    E   L + +KP G+V      +   T+       F+
Sbjct: 81  QVMFEHPPYEFLLTPENIPLDIVYEDDTLLVVNKPAGMVVHPGHGNYSGTLINALVYHFE 140

Query: 100 NLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-----LRVYRVRFHGQV 153
           NLP+  S R   V R+D +T GLL++         +   S Q+      R Y     G V
Sbjct: 141 NLPNNSSDRPGLVHRIDKDTSGLLVIA---KTEHAMAHLSKQFFDKTSEREYIAIVWGNV 197

Query: 154 DQDK-----------LNLLKKGIVIQGICYGDMQ-----VTLDTQKGSNAWVTVGLREGK 197
           ++D+            N L+  +  +G      +     + +  + G    V   L  G+
Sbjct: 198 EEDEGTVEGNIGRHPKNRLQNTVY-EGEDAEKGKPAVTHLKVLERFGYVTLVACKLETGR 256

Query: 198 NREIKKVFEFFNWK 211
             +I+   +     
Sbjct: 257 THQIRVHMKHIGHT 270


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/221 (18%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+   +A+     SR  +   I +  V VNG   +     ++  + + V      +    
Sbjct: 40  RLDAALAKLLPDYSRSRLADWIKEGAVSVNGKPAK-PKDKLIGGEKLAVQIRESNETLAF 98

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  TPEAMDLDIIYEDDSVIVLNKPAGLVVHPAAGNWSGTLLNGLLAHCPALQNIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN---------LL 161
           LD +T GL+++         L  +L +    R+YR    G V    K+           +
Sbjct: 159 LDKDTSGLMVVAKTLPAQNHLVQQLQTRTVKRIYRAVADGIVPFDGKIETQIGRDPHNRV 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKEAVTHVKVLERYQAHSYIECALETGRTHQIR 259


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 37/233 (15%), Positives = 82/233 (35%), Gaps = 39/233 (16%)

Query: 9   ENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    +R+   +      A+R  +E++I +  V  N  ++ +    +   + I++     
Sbjct: 14  EEDQGKRLDLFLKEQLPEATRSYLEKLITEGYVLCNEKVITKNGKKLKGKEVIQLAIPEE 73

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFS 106
                  + +PL    E   L + +K   +V   +  +   T+         +NL  +  
Sbjct: 74  EEMEIVAENIPLDIVYEDKYLLVVNKQANMVVHPALGNYSGTLVNALLYYCKENLSDMNG 133

Query: 107 RVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-LL 161
            +    V RLD +T GL+++  +  +   L L        + Y     G+  +++    L
Sbjct: 134 VIRPGIVHRLDKDTTGLIIVAKNNQVHSKLALMFQEKTIRKTYVAIVKGRFSEERKEGRL 193

Query: 162 KKGIVIQGICYGDMQV------------TLDTQKGSNAWVTVGLREGKNREIK 202
           +  I         M V             +      ++ V V +  G+  +I+
Sbjct: 194 ETLITRDPKDRKKMTVSQIQGKKAISNYRVLLDGDKHSLVEVKIETGRTHQIR 246


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 61/160 (38%), Gaps = 25/160 (15%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ + +    +A SR +V+R+I +  V+V+G  + +    +   + +EV      PL   
Sbjct: 24  RLDQFLTACELALSRSQVKRLIDEGAVQVDGAEVRKPGFKLQGGEAVEVALPAPQPLAAE 83

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
                     E   + +  KP GLV   +      T+ + L +    +  +G        
Sbjct: 84  PQAIPLDICYEDEHIIVVDKPAGLVVHPAPGHPDGTLVNALLAHCHDLSGIGGALRPGIV 143

Query: 113 -RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRF 149
            RLD +T G+++ T        +     + +  R Y    
Sbjct: 144 HRLDKDTSGVMVATKTEIAHHAMVETFQAHRLERAYLAVV 183


>gi|154498381|ref|ZP_02036759.1| hypothetical protein BACCAP_02370 [Bacteroides capillosus ATCC
           29799]
 gi|150272449|gb|EDM99634.1| hypothetical protein BACCAP_02370 [Bacteroides capillosus ATCC
           29799]
          Length = 299

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 80/215 (37%), Gaps = 30/215 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGV--------PLRKAERTRLW 76
           SR  V+ +++ ++V V+G ++ R    +   + + +   G         P+   +R  L 
Sbjct: 31  SRNAVKHLLSGRQVAVDGKIVTRFDWPLEPGEVVTILPQGREEQTKAPFPILYQDRD-LI 89

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
              KP GL+T   + + + T +  L           ++  V RLD +T G +L   +  +
Sbjct: 90  AIDKPAGLLTVGHEGERQRTAYRLLADTLRDGSREKKLFVVHRLDRDTSGAVLFARNEEM 149

Query: 131 ARVLELPSTQWLRV--YRVRFHGQVDQDK------LNLLKKGIVIQGI-----CYGDMQV 177
            R L+      ++   Y     G  ++++      L      +V  G           + 
Sbjct: 150 KRALQEDWDSLVKERIYLAVTVGAPEREEGVVRSWLRETSTRVVYSGGPGSGAKEAVTRY 209

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            +  + G  A V V L  G+  +I+         V
Sbjct: 210 KVLARSGEYALVRVALDTGRKNQIRVHMADLGCPV 244


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 72/218 (33%), Gaps = 39/218 (17%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKA-----------E 71
            I SR+  ++ I Q  V +N          V   D I +     + K            E
Sbjct: 34  TITSRKAFKKAIKQGCVTLNNKQAYTGDY-VNENDLITIYKDKSISKKPSIQIPLKVLFE 92

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISVGRLDINTEGLL 122
              L + HKP G+  +    + + T+ + LP             R +   RLD  T G L
Sbjct: 93  DNHLAIIHKPAGVEVSG---NKKYTIENALPSLLKKSNQKDALDRPLPAHRLDYPTSGCL 149

Query: 123 LL--TNDGGLARVLELPSTQWLRVYR-VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L+  T++   A        +  + Y  V    Q+ + K++       I          TL
Sbjct: 150 LIGKTSETLQALHRMFEKREISKKYIAVTLGNQITEGKIDK-----PIDDKASLTTFKTL 204

Query: 180 DTQKGSN----AWVTVGLREGKNREIKK-VFEFFNWKV 212
            T           V +    G+  +++K + +     +
Sbjct: 205 QTITSKKYNALNLVLLTPHTGRRHQLRKHMMQ-LGNPI 241


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 83/245 (33%), Gaps = 37/245 (15%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +V +  T  RV   +ARA   SR     +I   +V +   +L+ A   V   D I +   
Sbjct: 7   VVTDKDTGIRVDIYVARALDISRSYAGNLIKNGKVSMRNRILK-ANYRVAEGDEIVIEKD 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                    + +PL    E   + + +K  G+V   +  +   T+ + L           
Sbjct: 66  EAEDLTVEAENIPLDIVYEDKDIIIVNKARGMVVHPAAGNPNGTLVNALLWHCGGELSGI 125

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--- 157
               R   V RLD +T GL++        + L          R Y    HG + + K   
Sbjct: 126 NGVIRPGIVHRLDKDTSGLMVAAKTDAAHKSLAEQIKSHTARRTYVALVHGNIVEAKGRI 185

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    + +K  + ++         T+  + G+   V   L  G+  +I+    +  
Sbjct: 186 DAPLGRHPKDRVKMAVNMKDGKDAITHFTVLERFGNYTLVQCRLETGRTHQIRVHMAYIG 245

Query: 210 WKVNR 214
             V  
Sbjct: 246 HPVVN 250


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 81/243 (33%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E    +R+ K +A+     SR  +++ I    V+V G  +      V   D IEV   
Sbjct: 55  IPETLHGERLDKALAKLLPDYSRSRLQQWIDAGAVRVGGAAVR-PREAVCGGDRIEVVPQ 113

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                              E   L + +KP GLV   +  +   TV + L   +      
Sbjct: 114 RAADENAFVAEPIDLDVVYEDDTLLVINKPAGLVVHPAAGNWSGTVLNGLLHRYPQAAGL 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD  T GL+++         L  +L +    R Y     G           +
Sbjct: 174 PRAGIVHRLDKETSGLMVVARTLPAQTDLVRQLQARTVKRTYLALVWGETPEAGTIDAPI 233

Query: 154 DQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFF 208
            +D  +  +  I     G        TLD      A V++   +   G+  +I+  FE  
Sbjct: 234 GRDPRDRTRMAIIETASGKPARTHFKTLDVIDLGRAQVSLVQCQLETGRTHQIRVHFESE 293

Query: 209 NWK 211
              
Sbjct: 294 GHP 296


>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 = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/280 (17%), Positives = 94/280 (33%), 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---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
              + +    +      E   + +  KP G+V   +      T+ + L + +  +     
Sbjct: 61  AQPVALVPEAIPLHVVYEDADVVVVEKPAGMVVHPAPGHPNGTLVNALLARYPDMQVGGD 120

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----- 158
                V RLD  T GLL++       R L     + Q  ++Y     G+  Q +      
Sbjct: 121 LRPGIVHRLDAGTSGLLVVARHDQALRHLTALQHARQMRKIYLAVAEGRFKQAEGLIDAP 180

Query: 159 ------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 + L+  +   G          + + G+   + + L  G+  +I+   +     +
Sbjct: 181 VGRHPHDRLRMAVTPTGREARTHYRVCE-ELGNYTLLELRLETGRTHQIRVHLQHLGRPI 239

Query: 213 N--------------RLIRISYGPFQLG-TLLAGSTREVS 237
                           L R       LG  LL GS RE +
Sbjct: 240 LGDPLYGVRKGRPTFGLERQFLHAHCLGFQLLDGSWREFT 279


>gi|225449104|ref|XP_002276664.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 348

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/225 (15%), Positives = 76/225 (33%), Gaps = 57/225 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I + ++ V+G ++      + +   +    +P ++ +             +   +KP GL
Sbjct: 52  INKGQITVDGTVVTEPKTILRAGSKLVYHRLPWQEPDAPYLLEILYEDDDVIALNKPSGL 111

Query: 85  VTTHSDPDGRSTVFDNLPS-----------IFSRVISVGRLDINTEGLLLLT-------- 125
                    + TV   L               S  + V RL   T G+LL          
Sbjct: 112 QVLPGGLFQQRTVLTQLQWRANKQNSLPACQESHSVPVHRLGRGTSGILLCAKTKLAKTR 171

Query: 126 -----NDGGLA---RVL-----ELPSTQWLRVYRVRFHGQVDQDKLNL-----------L 161
                 DG        L          +  ++YR   +G +D+D++ +           +
Sbjct: 172 LAAYFADGTSVVGGNRLDADMKSRTMRKISKIYRALVNGILDKDEIVIEQPIGMVQYPGV 231

Query: 162 KKGIVIQGICYGDM--QVTLDTQ--KGSNAWVTVGLREGKNREIK 202
            KG+ +          +V++  +  +G +  V V ++ G+  +I+
Sbjct: 232 AKGLYVASPSGKPALSKVSILERDVQGDHMIVQVEIQSGRPHQIR 276


>gi|325954148|ref|YP_004237808.1| pseudouridine synthase [Weeksella virosa DSM 16922]
 gi|323436766|gb|ADX67230.1| pseudouridine synthase, RluA family [Weeksella virosa DSM 16922]
          Length = 362

 Score = 72.1 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 51/239 (21%), Positives = 90/239 (37%), Gaps = 45/239 (18%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +  R   A+R ++++      + VN + ++     V   D I++           
Sbjct: 32  RIDKFLMIRIENATRNKIQQAAENGNILVNNLPVKS-NYKVKPGDFIQIMLENPPREHKI 90

Query: 63  --DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSI---FSRVI 109
             + +PL    E  ++ +  KP G+V      +   T+       FDNLPS+     R  
Sbjct: 91  IAEDLPLNIVFEDDQVLVIDKPAGMVVHPGHGNYSGTLVNALKFHFDNLPSMSAELERPG 150

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKK-GIV 166
            V R+D +T GLL++         L L        R Y     G V +D+  +    G  
Sbjct: 151 LVHRIDKDTSGLLVIAKTEQAMNHLALQFANHTTTRKYNALVWGNVTEDEGTITGHIGRH 210

Query: 167 IQGICYGDMQVTLDTQKGSNA-----WVT----VGLRE-----GKNREIKKVFEFFNWK 211
           ++      M V  D  +G +A      +     V L E     G+  +I+  F++    
Sbjct: 211 LKDRMQ--MAVFEDGSQGKHAVTHYKVLERLSYVTLVECQLETGRTHQIRTHFKYIGHP 267


>gi|269960587|ref|ZP_06174959.1| tRNA pseudouridine synthase C [Vibrio harveyi 1DA3]
 gi|269834664|gb|EEZ88751.1| tRNA pseudouridine synthase C [Vibrio harveyi 1DA3]
          Length = 255

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 58/193 (30%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
            A+     V V             L E     G+  ++++        +           
Sbjct: 140 TAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIVGDTTHGDGKH 199

Query: 214 -RLIRISYGPFQL 225
            +L R  +   +L
Sbjct: 200 NKLYRTEFDSHRL 212


>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 = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 89/246 (36%), Gaps = 43/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +  TP R+ K +    + ASR  ++       V  NG  ++  +  V   D + V  
Sbjct: 32  VVDKGQTPVRIDKYLFERIVNASRNRIQTAADAGFVMANGKPVKS-SYKVKPLDVLTVMM 90

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP GLV      +   T+ + +      V S
Sbjct: 91  DRPRYENDIIPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLRDVPS 150

Query: 111 ----------VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
                     V R+D +T GLL++  T D   +  ++  +    R Y     G V++D+ 
Sbjct: 151 YDPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGMQFYNKTTKREYNALVWGIVEEDEG 210

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + ++  ++      G   VT   +  + G    V   L  G+  +I+  
Sbjct: 211 TITGNIGRNPKDRMQMAVM-SDPTQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRVH 269

Query: 205 FEFFNW 210
            +    
Sbjct: 270 MKHIGH 275


>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 = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 32/206 (15%), Positives = 71/206 (34%), Gaps = 26/206 (12%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----------------AERTRLW 76
           R+  Q+ +KVN   +  +   V + D I + G+                     E   + 
Sbjct: 33  RLFRQKSIKVNNKRITDSNYVVKTGDEIIIYGIKDEPSFVIYDNSWKLDSEIVYEDDNIL 92

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLARV 133
           L +K  G +         + VF       +   R   VGRLD  T GL++   +      
Sbjct: 93  LINKKAGTIVHGDSNCLDNQVFSYFKFRQNSAFRPSHVGRLDKWTSGLIMYAKNYQTLTE 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-------NLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           L   +    ++Y ++       + +        L +K +  + + + + ++        +
Sbjct: 153 LNHKTEFLDKIYVLKSDYNPHDEIVSVYIHHDELQQKMVATKNMQHPNDKIAKTRFFKKD 212

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKV 212
             +   L  G+  +I+   E+  + +
Sbjct: 213 NKLYAQLFTGRKHQIRATLEYLGYPI 238


>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 = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 45/226 (19%), Positives = 78/226 (34%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A+     SR  ++  I    VKVNG ++ +A   V   + IEV           
Sbjct: 19  RLDQALAQLFPYYSRSRLKVWIESDLVKVNGNIVNKAREKVFGGELIEVQAEIEEEVRFE 78

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   V RL
Sbjct: 79  PQDIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVTSGVMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|255322530|ref|ZP_05363675.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           showae RM3277]
 gi|255300438|gb|EET79710.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           showae RM3277]
          Length = 354

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 80/247 (32%), Gaps = 46/247 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K I   +    R    +A    +A R +   +I    V +NG  L + +V +   D 
Sbjct: 17  MTEKEIKILDGAQARADAFLATELNVA-RNQALNLIKSGLVSLNGKPLNKPSVKLNLGDI 75

Query: 60  IEVDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI- 104
           + +                      E   L + +KP  LV   +      T+ D L +  
Sbjct: 76  LRIKFEQSDPETTKFEAEFEVPIIYEDDDLLVLNKPANLVVHPAPSVKEPTLVDWLGAKG 135

Query: 105 --------FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                    SR   V RLD  T G +++  +      L   L      R+Y       + 
Sbjct: 136 FLLSNLSGQSRAGIVHRLDKGTSGAIVVAKNNAAHAALSNQLSDKSMGRIYLALTDLPLK 195

Query: 155 QDKL----------NLLKKGIVIQGICYGDMQVTLD------TQKGSNAWVTVG---LRE 195
           Q+ +          N LKK IV  G         L         +  NA V +    L  
Sbjct: 196 QNCIVERAIGRNPANRLKKAIVSSGRAAKSAFANLLFSEFDGPVQSKNAGVNLIAAKLFT 255

Query: 196 GKNREIK 202
           G+  +I+
Sbjct: 256 GRTHQIR 262


>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 = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 53/238 (22%), Positives = 83/238 (34%), Gaps = 43/238 (18%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           +R+ K++AR     SR  +++ I    V+V+G  + R    V   + IEV      +   
Sbjct: 69  ERLDKLLARHFSEFSRSRLQQWIESGAVRVDGE-VRRPRDAVQMGNRIEVQPQAAPESQA 127

Query: 70  -----------AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVG 112
                       E   L +  KP GLV   +  +   TV       D   +   R   V 
Sbjct: 128 FAPEDVALDVVYEDDALLVIDKPAGLVVHPAAGNWSGTVLNGLLHRDPTAAALPRAGIVH 187

Query: 113 RLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
           RLD  T GL+++    T    L R L   +    R Y     G           + +D  
Sbjct: 188 RLDKETSGLMVVARTLTAQTDLVRQL--QARTVKRTYLALVWGRIYEEGTIDAPIGRDPR 245

Query: 159 NLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIKKVFEFFNWK 211
              +  IV    G        TL T     ++V++    L  G+  +I+  FE     
Sbjct: 246 ERTRMAIVHTNSGKPSRTHFRTLATVPLGRSFVSMVRCQLETGRTHQIRVHFESIGHP 303


>gi|239996651|ref|ZP_04717175.1| ribosomal large subunit pseudouridine synthase D [Alteromonas
           macleodii ATCC 27126]
          Length = 327

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/220 (15%), Positives = 71/220 (32%), Gaps = 33/220 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKA 70
           R+ +V+A      SR +++  I    V VNG ++      +   + + V     V +   
Sbjct: 22  RLDQVLADLFPEYSRSKLKTWIQDGNVAVNGEVITVPRHKMQMDELVTVQAEMDVQVTSE 81

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRL 114
                     E   + + +KP  LV      +   TV + L +    +        V RL
Sbjct: 82  AQDIALNIVYEDEHILVINKPADLVVHPGAGNPSGTVLNALLNHCPEIDKVPRAGIVHRL 141

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLK 162
           D +T GL+++         L  +L   +  R Y                 + +       
Sbjct: 142 DKDTTGLMVVAKTIPAQTHLVDQLQRREMSREYEAVALGTMVAGGIVDAPIGRHATKRTH 201

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   G         ++  +     + + L  G+  +I+
Sbjct: 202 MAVREMGKPAVTHFRVIEKFRAYTH-LRLKLETGRTHQIR 240


>gi|77461057|ref|YP_350564.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf0-1]
 gi|77385060|gb|ABA76573.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           fluorescens Pf0-1]
          Length = 320

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 89/246 (36%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----R 49
           M DK  ++     +    R+ +V A    A  SR  +   I + R+ V+G ++       
Sbjct: 1   MSDKIELRAEVPSELGGQRLDQV-AAQLFAEHSRSRLSAWIKEGRLTVDGAVIRPRDIVH 59

Query: 50  AAVNVMSTDHIEVDGVPLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
               +  T   E  G  + +        E   + + +KP GLV      H+D    + + 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIELDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALL 119

Query: 99  DNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
            ++P I    R   V RLD +T GL+++         L  +L S    R+Y     G V 
Sbjct: 120 HHVPDIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTKLVAQLQSRSVSRIYECIVIGVVT 179

Query: 155 QD---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                           ++  V++G         +  +  S+  V V L  G+  +I+   
Sbjct: 180 AGGKINAPIGRHGQQRQRMAVMEGGKPAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
              N+ 
Sbjct: 240 AHINFP 245


>gi|167957398|ref|ZP_02544472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [candidate division TM7 single-cell isolate
           TM7c]
          Length = 379

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 92/236 (38%), Gaps = 40/236 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           KD  +++     +R+  ++    G  SR   ++MI   +V V+G + + A   V    ++
Sbjct: 101 KDCYLLESKSDKKRLDILLVEKVGKESRSTYQKMITAGQVLVDGKIAKNAKQLVGIESNV 160

Query: 61  EVDGV-----PLRKA---ERTRLWLYHKPIGLVT----------THSDPDGRSTVFDNLP 102
           +++       P++     E   + + +KP G++T          T +D     T   N  
Sbjct: 161 KIESKQQKFTPIKYETIYEDNDIIVINKPAGMLTHAKGAIAEEFTAADIVKPIT---NYK 217

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKL-- 158
           +  +R   + RLD NT G+LL+  +   A  ++   +Q    + Y     G   Q K   
Sbjct: 218 ADTNRPGIIHRLDRNTSGVLLMVKNSDAASKIQKQFSQRTVKKTYYAIVCGIPYQHKALI 277

Query: 159 -----------NLLKKGIVIQGICYGDM-QVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +  + G+   G       +V     K + + + +  + G+  +++
Sbjct: 278 DLPIERNPSRPSTFRVGV--NGKSAQTSYEVERSIIKKNISLIKLQPKTGRTHQLR 331


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 88/251 (35%), Gaps = 43/251 (17%)

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---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           IE+   D V L             E   + +  KP G++   S      T+ + L     
Sbjct: 60  IEITILDNVDLDIEPEDISLKIVYEDEDVIVVDKPTGMIVHPSAGIMHGTLVNALLFHCK 119

Query: 102 ----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVD 154
                +  +R   V R+D  T GLL++  +   A  L          +R Y    HG + 
Sbjct: 120 DLSGINGVNRPGIVHRIDKETSGLLMVAKN-DNAHRLLSKQLKDHTVVRRYVALVHGLIP 178

Query: 155 QD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +                 +   +            T+  +  + + +   L  G+  +I
Sbjct: 179 HEHGKVDAPIGRNPKDRQSMA--VTRTNSKEAVTNFTVLKRYNAMSLIECRLETGRTHQI 236

Query: 202 KKVFEFFNWKV 212
           +    +  + V
Sbjct: 237 RVHMSYIGYPV 247


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 70/177 (39%), Gaps = 26/177 (14%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           IV+E     R+ KV+ +     SR +V++ I    VKVNG  ++         D I    
Sbjct: 7   IVREEEKSVRLDKVLTQLEEKWSRSQVQQWIKDGNVKVNGSQVKT-NYKCAIEDKIIISI 65

Query: 61  ----EVDGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
               E+D VP         E   + + +KP G+V   +      T+ + L +    +   
Sbjct: 66  PEPEELDVVPENMDLDIYFEDADVIVVNKPRGMVVHPAPGHPSGTLVNGLMAHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
                   V R+D +T GLL++  +      L  +L +    R Y+   HG +  D 
Sbjct: 126 NGVLRPGIVHRIDKDTSGLLMVAKNDLAHEKLVEQLVNKTVTRKYKAIVHGIIPHDH 182


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 84/241 (34%), Gaps = 52/241 (21%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + N+  + F  QR+ K I      SR  V+R I + +V VN  ++ +    V   D ++
Sbjct: 6   SEVNLRLDLFLLQRIPKAI------SRSFVQRAIKEGKVTVND-VIRKPNYRVKFGDVVK 58

Query: 62  -----------VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                      ++  P++     E   + + +KP G++          T+ + L      
Sbjct: 59  ISIPSNAQSISIEPEPIQIGVIYEDEDIIVVNKPAGMIVHPIPSHNSGTLVNALLYHCKD 118

Query: 108 VISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           +  +G         RLD +T G++++  +      L       +  ++Y     G+V   
Sbjct: 119 LKGIGGELRPGIVHRLDKDTSGVMVVAKNDFAHHNLSNQFKDRKVFKMYLALVSGKV--- 175

Query: 157 KLNLLKKGIVI---QGICYGDMQVTLDTQKGSNAWVTV-------GL-----REGKNREI 201
               L+  I I   +           +  + +     V        L     + G+  +I
Sbjct: 176 --EHLEGDIQISIARHPVLRTKMAASEIGRIAVTHYKVIKYFEHATLLMAFPKTGRTHQI 233

Query: 202 K 202
           +
Sbjct: 234 R 234


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 85/249 (34%), Gaps = 50/249 (20%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +     RV K +  R   +SR  +++      V  NG  ++  +  V   D I V  
Sbjct: 33  VVDKGQEMVRVDKYLFDRLTNSSRNRIQKAADAGFVMANGKAVKS-SYKVKPMDVITVMM 91

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   L + +KP GLV      +   T+ +          +
Sbjct: 92  DRPRYENEVIPEDIPLDIVYEDKYLMVVNKPAGLVVHPGHGNYHGTLVNAIAWHMKDNPD 151

Query: 101 LPSIFSRVISVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
             +    V  V R+D +T GLL++       TN G         +    R YR    G V
Sbjct: 152 YDANDPHVGLVHRIDKDTSGLLVIAKTPDAKTNLGNQFF-----NKTTKRRYRALVWGNV 206

Query: 154 DQDK-----------LNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +QD+            + ++  ++      +      +  + G    V   L  G+  +I
Sbjct: 207 EQDEGTVVGNIGRNPRDRMQMTVLPDDQGKHAVTHYRVLERLGYVTLVECILETGRTHQI 266

Query: 202 KKVFEFFNW 210
           +   +    
Sbjct: 267 RVHMKHIGH 275


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 82/233 (35%), Gaps = 44/233 (18%)

Query: 12  TPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            P RV K +    +  A+R ++++   +  + VN ++++     V + D + V       
Sbjct: 30  QPLRVDKYLMNR-VENATRSKIQKAAKEGNIFVNNVIVKS-NYKVKANDVVTVLFAHPPY 87

Query: 63  ------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRV 108
                 + + +    E   L + +K  G+V      +   T+        DNLP+  S  
Sbjct: 88  ELLLTPEDIDIDIVYEDDDLLVVNKQPGMVVHPGHGNYSGTLINALIHHIDNLPNNSSNR 147

Query: 109 IS-VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-------- 157
              V R+D +T GLL++         L          R Y     G ++ D+        
Sbjct: 148 PGLVHRIDKDTSGLLVVAKTEEAMTHLAKQFFDKTTEREYVALVWGNIEDDEGTIEGHIG 207

Query: 158 ---LNLLKKGIVIQGICYGDMQV-----TLDTQKGSNAWVTVGLREGKNREIK 202
               N L+  + +        +       +  + G    V+  L  G+  +I+
Sbjct: 208 RHPKNRLQNTVFLDEDAEEKGKAAVTHFKVLERFGYVTLVSCKLETGRTHQIR 260


>gi|116074038|ref|ZP_01471300.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916]
 gi|116069343|gb|EAU75095.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9916]
          Length = 343

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 83/247 (33%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +      P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 32  LTYPKPLPMRLDRWLVSQRSEQSRARIQKFIDAGFVRVNGKTGK-AKTPLRDGDEVQLWM 90

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 91  PPPEPLPYLKPEPMDLDVLFEDDHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 150

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--- 156
           I  ++    V RLD +T G +++         L++   +    R Y    HG    D   
Sbjct: 151 ISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQVQIQKRIASREYMAVVHGLPQGDSGS 210

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y     TL  + G  + +   L  G+  +I+    
Sbjct: 211 IVGAIGRHPADRKKYAV-VSGESGRYACTHWTLVERLGDYSLLRFKLDTGRTHQIRVHCA 269

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 270 HMNHPVV 276


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 83/225 (36%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   +A   G  SR  ++++I   +VKVN   +E+A   V   D+I ++          
Sbjct: 17  RLDIYLAEQLGDMSRSYIQKIIKDGKVKVNNK-VEKARYLVKEEDNIVIEIPEPKVLEVL 75

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
              +P+    E   + + +KP  +V   +  +  +T+ + +               R   
Sbjct: 76  PQDIPIDIVYEDDDVLIINKPQDMVVHPAPGNYENTLVNGILYHCKDKLSSINGVIRPGI 135

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL---------- 158
           V R+D +T GLL++  +      L     +    R Y    +G V +DK+          
Sbjct: 136 VHRIDKDTSGLLMIAKNNYAHNFLAEQLKEHTITREYEFICYGVVKEDKITVDKPIGRNP 195

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  +V  G         ++            L  G+  +I+
Sbjct: 196 KDRLKMAVVKDGKNAITHFEVVERFDKFTHM-RARLETGRTHQIR 239


>gi|87123536|ref|ZP_01079387.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917]
 gi|86169256|gb|EAQ70512.1| Pseudouridine synthase, RluD [Synechococcus sp. RS9917]
          Length = 329

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 81/247 (32%), Gaps = 41/247 (16%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +      P R+ + + ++    SR  +++ I    V+VNG   + A   +   D +++  
Sbjct: 29  LTYPKPLPMRLDRWLVSQRSEQSRARIQKFIDAGFVRVNGKTGK-AKTPLRQGDAVQLWM 87

Query: 64  --GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
               PL              E   L + +KP GL    +  +   T+ +       +LP 
Sbjct: 88  PPPEPLPYLKPEPMDLDVLFEDEHLIVINKPAGLTVHPAPGNKDGTLVNGLLHHCPDLPG 147

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV------ 153
           I  ++    V RLD +T G +++         L+L   +    R Y    HG        
Sbjct: 148 ISGKLRPGIVHRLDKDTTGCIVIAKSQEALVKLQLQIQKRIASREYLAVVHGVPRGDSGT 207

Query: 154 -------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +  +   Y     +L  +    + +   L  G+  +I+    
Sbjct: 208 IVGAIGRHPADRKKYAV-VSGENGRYACTHWSLQERLADYSLLRFKLDTGRTHQIRVHCA 266

Query: 207 FFNWKVN 213
             N  V 
Sbjct: 267 HMNHPVV 273


>gi|159486376|ref|XP_001701217.1| hypothetical protein CHLREDRAFT_179001 [Chlamydomonas
          reinhardtii]
 gi|158271917|gb|EDO97727.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 235

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEV 62
          R++KV+A  G+ASRR  E +IA  RV+VNG L++     V    D +EV
Sbjct: 48 RLAKVLAACGVASRRACEGLIADGRVRVNGNLVKEQGTTVDPARDKVEV 96



 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 20/133 (15%), Positives = 48/133 (36%), Gaps = 10/133 (7%)

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG-T 227
           G     ++V +    G    + + + EGK  E++++ +     +  L R+  G F+L   
Sbjct: 106 GTFVSPLEVEVL---GDPRRLRIVVAEGKKHEVRELVKAAGMNLLSLRRVRIGGFRLPRD 162

Query: 228 LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR------PNIISEVPDD 281
           L  G  + ++   L+        E A V+      + +            P  + ++P++
Sbjct: 163 LGLGGFKALTPADLKLITDARAQELASVSGATRAAAQQAAQTAATRRASVPRALRDMPEE 222

Query: 282 FTRMKKNSSQKNG 294
                + +     
Sbjct: 223 VLEKFRKARGDKS 235


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 87/245 (35%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILL---------ERAAVNVM 55
           ++ E     R+ KV+A R    +R  ++R++ +++V +NG            +  A+ + 
Sbjct: 8   VLSEREEGIRLDKVLAERLPDLTRTAIQRLLEEEQVLINGKPAAKNRKGRAGDSVALRIP 67

Query: 56  STDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
             + + +    +      E   L + +KP G+V   +  + + T+ + L +         
Sbjct: 68  DPEPLCLQAENVPLDIVYEDDDLLVVNKPQGMVVHPAPGNYQGTLVNALLAHCGNSLSGI 127

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQD---- 156
               R   V R+D +T GLL++  +    + L     +    R Y     G++ Q+    
Sbjct: 128 NGVIRPGIVHRIDKDTSGLLMVAKNDFAHQGLARQIKEHSFRREYEAVVAGRMKQESGVV 187

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                        +   +  +          +  +      + + L  G+  +I+    +
Sbjct: 188 NAPIGRHPIDRKKMA--VTEKNSKEAVTYFRVIAEYPGYTHIRLRLETGRTHQIRVHMAY 245

Query: 208 FNWKV 212
               V
Sbjct: 246 LGHPV 250


>gi|116329455|ref|YP_799175.1| pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
 gi|116122199|gb|ABJ80242.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis L550]
          Length = 312

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 94/256 (36%), Gaps = 44/256 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKV-NGILLERAAVNVMS 56
           ++ K  V E F+  R+ + + +       SR  +++ I    V+  +  + ++++  V +
Sbjct: 3   LELKAEVLEEFSGNRLDRFL-KFSFGDEMSRATIQKWIECGYVRNQDRKICDKSSWKVKT 61

Query: 57  TDH----------IEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            +           + ++ +P+      ER    + HKP G+ +     D   ++ + L  
Sbjct: 62  GEQYFLSIPPRPPLSLEPIPMTLPVVLEREDYLIIHKPPGIASHSGPGDRSPSLVNGLLH 121

Query: 104 IFSRVISVG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
            F  +  VG         RLD  TEGL+L+  +      L       +  + Y     G 
Sbjct: 122 HFKELSKVGGEARPGIVHRLDKPTEGLMLIAKNDRAHGKLSELFRKREIEKKYYAWIQGH 181

Query: 153 VDQDK-----------LNLLKKGIVIQGIC----YGDMQVTLDTQKGSNAWVTVGLREGK 197
           +  +            +  LK  +  +G      Y  ++          ++V VGL  G+
Sbjct: 182 LPAETGTIDLPIARHPIERLKMTVSPKGRKSVTHYKVLKYVNSRSGRKFSFVEVGLETGR 241

Query: 198 NREIKKVFEFFNWKVN 213
             +I+  F+     V 
Sbjct: 242 THQIRIHFQSQRCPVV 257


>gi|291533845|emb|CBL06958.1| ribosomal large subunit pseudouridine synthase D [Megamonas
           hypermegale ART12/1]
          Length = 304

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 83/238 (34%), Gaps = 46/238 (19%)

Query: 15  RVSKVIARAGIA-----SRREVERMIAQQRVKVNGILLERAAVNVMSTD----------H 59
           R+   +A          SR  +++MI    + VN   ++RA   + + D           
Sbjct: 14  RLDVFLA----GQEDNPSRASIQKMITDGAITVNNQ-VKRANYKLKANDQITMVFEPPTE 68

Query: 60  IEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFSRV 108
           IEV    +      E   + + +K  G+V   +      T+         D L  I  ++
Sbjct: 69  IEVKPENIPLDILYEDNDIIVINKARGMVVHPAAGVYSGTLVNALLYHCHDELSGINGKI 128

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK------- 157
               V RLD +T G++++  +      L L   S   ++ Y    HG + ++K       
Sbjct: 129 RPGIVHRLDKDTSGVMVVAKNDFAHNDLALQIGSKTAIKEYVALVHGNITEEKGIINGNI 188

Query: 158 ----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               ++  K  +V  G         +  +  +  +V   L  G+  +I+    +    
Sbjct: 189 GRHPIDRKKMAVVTNGGKPATTVFHVLERYKNCTFVQCRLLTGRTHQIRVHMAYIGHP 246


>gi|296086047|emb|CBI31488.3| unnamed protein product [Vitis vinifera]
          Length = 347

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 33/227 (14%), Positives = 75/227 (33%), Gaps = 62/227 (27%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I + ++ V+G ++      + +   +    +P ++ +             +   +KP GL
Sbjct: 52  INKGQITVDGTVVTEPKTILRAGSKLVYHRLPWQEPDAPYLLEILYEDDDVIALNKPSGL 111

Query: 85  VTTHSDPDGRSTVFDNLPS-----------IFSRVISVGRLDINTEGLLLL--------- 124
                    + TV   L               S  + V RL   T G+LL          
Sbjct: 112 QVLPGGLFQQRTVLTQLQWRANKQNSLPACQESHSVPVHRLGRGTSGILLCAKTKLAKTR 171

Query: 125 --------------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---------- 160
                           D  +         +  ++YR   +G +D+D++ +          
Sbjct: 172 LAAYFADGTSVVGGNRDADMKSRTMR---KISKIYRALVNGILDKDEIVIEQPIGMVQYP 228

Query: 161 -LKKGIVIQGICYGDM--QVTLDTQ--KGSNAWVTVGLREGKNREIK 202
            + KG+ +          +V++  +  +G +  V V ++ G+  +I+
Sbjct: 229 GVAKGLYVASPSGKPALSKVSILERDVQGDHMIVQVEIQSGRPHQIR 275


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 91/247 (36%), 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  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
                      + +PL    E T + + +KP G+V      +   T+ +       +LP+
Sbjct: 85  DAPQHDSTIEAEEIPLNIVYEDTEVMVVNKPAGMVVHPGAGNFHGTLINAVAWHLKDLPT 144

Query: 104 IFSRVISVG---RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK- 157
             +   +VG   R+D +T GLL++  T D      L+  +    R Y     G  ++++ 
Sbjct: 145 FDANDPAVGLVHRIDKDTSGLLVIAKTPDAKTKLGLQFFNKTTHRSYHALVWGNFNEEEG 204

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + L+  +       G   +T   +  + G    +   L  G+  +I+  
Sbjct: 205 RIEGNIARDPKDRLRMCVFPPDSAVGKTAITHYRVLERFGYVTLIECILETGRTHQIRAH 264

Query: 205 FEFFNWK 211
            +     
Sbjct: 265 MKHIGHP 271


>gi|297819936|ref|XP_002877851.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
 gi|297323689|gb|EFH54110.1| pseudouridine synthase family protein [Arabidopsis lyrata subsp.
           lyrata]
          Length = 387

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/224 (16%), Positives = 71/224 (31%), Gaps = 56/224 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I   +++++G +++     + S   +    +P ++ +             L   +KP GL
Sbjct: 59  IQNGQIQIDGEVVKDPNTLLRSGSKLVYHRLPWKEPDTPYSLQVLYEDDDLIALNKPSGL 118

Query: 85  VTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTEGLLLLTNDGGLAR 132
                    + TV   L   F               + V RL   T G+LL         
Sbjct: 119 QVLPGGLFQQRTVLTQLQWCFRKNDSYTGSRESPHPVPVHRLGRGTSGILLCAKTKLAKT 178

Query: 133 VLE-------------------LPSTQWLRVYRVRFHGQVDQDKL---NLL--------K 162
            L                        +  ++YR    G V++D++     L         
Sbjct: 179 KLAAYFAEGTSLVGSGNLEQECGKGRKLSKIYRALADGIVEEDEVVIKQPLGVVRYPGVA 238

Query: 163 KGIVI---QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
           KG+ +   +G         L+  K  N   V V ++ G+  +I+
Sbjct: 239 KGLYVASPEGKPAFSKVAVLERDKQKNCTLVKVEIQSGRPHQIR 282


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 82/235 (34%), Gaps = 34/235 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++  + V EN   QR+ + +A      SR  ++  I   +V V+G ++ +  + +M  + 
Sbjct: 5   LELNSTVNENQLGQRLDQALAELFPDYSRSRIKEWILADKVSVDGEIVNKPRLKMMGGEV 64

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V              +PL    E   + + +KP  LV          TV + L   + 
Sbjct: 65  IVVQAEIEDEQRFEAQDIPLNIVYEDDDIIVINKPRDLVVHPGAGCPDGTVLNGLLYHYP 124

Query: 107 RV------ISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRV---------- 147
            +        V RLD +T GL+++  +      L        ++ R Y            
Sbjct: 125 DIAEVPRAGIVHRLDKDTTGLMVVAKNIPTQTRLVRALQKRKKFTREYEAIALGNMTGGG 184

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                + +         +   G         ++  + ++  + + L  G+  +I+
Sbjct: 185 MIEKPIGRHSTKRTHMAVQELGKPAITHYRVVEHFR-AHTRLRLRLETGRTHQIR 238


>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 = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 86/229 (37%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V +    +R+ + +A      SR  ++  I   +V ++G ++ +    ++  + IE+D 
Sbjct: 13  VVPQTLLGKRLDQALAEMFPDYSRSRIKDWILADQVSIDGQIVNKPREKLLGEELIEIDA 72

Query: 64  GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            + +++             E   + + +KP  LV      +   T+ + L S    + S 
Sbjct: 73  SIEIQERHSAQEIDLNIVYEDEHILVINKPTNLVVHPGAGNANGTILNALLSHVPDIASV 132

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
                V RLD +T GL+++         L  +L + +  R Y    +G           +
Sbjct: 133 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAVVYGNLIAGGSVDEPI 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +V  G         +  +  ++  + + L  G+  +I+
Sbjct: 193 GRHPTKRTNMAVVQSGKPALTH-YRVKHKYRAHTHLRLKLESGRTHQIR 240


>gi|167630173|ref|YP_001680672.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
 gi|167592913|gb|ABZ84661.1| pseudouridine synthase, rlua family [Heliobacterium modesticaldum
           Ice1]
          Length = 369

 Score = 71.8 bits (175), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 78/238 (32%), Gaps = 44/238 (18%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV   + + G+  SR   +  I +  V ++G  L+ A   +   D IEV           
Sbjct: 48  RVDVWLVQKGLVPSRSHGQNWIKEGLVTLDGGPLK-ANYRLRPGDVIEVAPPAPEAVEIL 106

Query: 63  -DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------V 111
            + +PL    +   + + +KP GLV   ++     T+ + L      +           V
Sbjct: 107 PEDIPLEIIFQDADIAVINKPAGLVVHPAEGHWSGTLVNALLYHIKDLSGINGELRPGIV 166

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV-------------DQD 156
            R+D +T GLL++  +      L       +  R Y    HG +             D  
Sbjct: 167 HRIDKDTSGLLVVAKNDRAHIHLTEQVKDHRVRREYLAVVHGVIGAETGRVEAPIGRDPK 226

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKV 212
               +    VI G         +  +      + +   L  G+  +I+         V
Sbjct: 227 DRQRMA---VIAGGKSAITHFRVLARYPEQGFSLLHCRLETGRTHQIRVHLAHIGHPV 281


>gi|257869391|ref|ZP_05649044.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
 gi|257803555|gb|EEV32377.1| pseudouridylate synthase [Enterococcus gallinarum EG2]
          Length = 301

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 86/238 (36%), Gaps = 39/238 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++  V  +    RV KV+A    ASR ++++ + +  V   G  +  A   V + D +
Sbjct: 1   MNNQIEVVIHEEKGRVDKVLADRLEASRSQIQQWLKEGAVTCQGDPIR-ANYKVKAGDQL 59

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
            +            + +PL    +   + + +KP G+V   S      T+ + L    + 
Sbjct: 60  VIQVPEPESLDLEPEDIPLTIVYQDQDVAVINKPQGMVVHPSAGHPNGTLVNALLYHMTD 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   L     LR Y    HG +  +
Sbjct: 120 LSSINDVVRPGIVHRIDKDTSGLLMIAKNDHAHEALAKQLKDKTSLRKYVALVHGNISHE 179

Query: 157 KL------------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K               ++   V +         T+  +      V + L  G+  +I+
Sbjct: 180 KGTINAPIGRSKVNRKMQA--VQEDGKPAVTHFTVLERFDQFTLVELQLETGRTHQIR 235


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 81/237 (34%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ K +    +  ASR  ++  I    V VN   ++  +  V   D I V          
Sbjct: 31  RIDKFLMHR-VENASRNRIQNAIELGNVLVNDKAIKS-SYKVKPLDVISVVLPHPPRDTE 88

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
              + +PL    E   + + +KP GLV      +   T+ + L   F ++ +        
Sbjct: 89  VYPENIPLDIVYEDDDVLVVNKPAGLVVHPGYNNYTGTLVNGLVYHFQQLPTLPGNDGRP 148

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQD---------K 157
             V R+D +T GLLL++ +      L     +    R Y     G ++ D          
Sbjct: 149 GLVHRIDKDTSGLLLISKNERSMTWLARQFYEHTIARKYLALVWGDLEIDGTVTGYIGRS 208

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWK 211
           +   +   +      G   VT         +VT+   E   G+  +I+   +     
Sbjct: 209 IKDRRVMSIYDDPEKGKWSVTHYRVLQRMTYVTLIECELETGRTHQIRAHMKHIGHP 265


>gi|329667353|gb|AEB93301.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           johnsonii DPC 6026]
          Length = 304

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 84/235 (35%), Gaps = 42/235 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVIA      SR +++ ++  + + VN    E+ +  V S D I+V   P++     
Sbjct: 15  RLDKVIAEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVIDVTIPPVKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS--V 111
                     E + + + +KP G+V   S      T+ +       +L           V
Sbjct: 74  AENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTRDLADSPEGFRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD-------------QD 156
            R+D +T GLL++  +      LE  L      R Y    HG  +              +
Sbjct: 134 HRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAIVHGNFEVKNGVINAPIGRNPN 193

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   +  +G        T+  Q  + + V   L  G+  +I+   ++    
Sbjct: 194 NRKQMA--VNPKGKAAVTHF-TVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHP 245


>gi|295397129|ref|ZP_06807237.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
 gi|294974627|gb|EFG50346.1| ribosomal large subunit pseudouridine synthase D [Aerococcus
           viridans ATCC 11563]
          Length = 294

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 70/226 (30%), Gaps = 51/226 (22%)

Query: 19  VIARAGIASRREVERMIA--QQRVKVNGILLERAAVNVMSTDHIEV----DGV-----PL 67
            +   GI SRR + R I     ++ VNG   E     +   D + V    +G       +
Sbjct: 17  FLKHKGI-SRRLLSR-IKFHGGQILVNGQ-EENVRHQLTVGDKVTVILPNEGKQEIIEAI 73

Query: 68  RKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLD 115
                   E       +KP G  +  S  + + ++ + L + + R       +  V RLD
Sbjct: 74  HLPIDILFEDDHYIAVNKPAGYTSIPSQYNPQGSMANILKAYYQRQDYDNQVIHVVTRLD 133

Query: 116 INTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
            +T G++L       A  L           + Y      +V          G +   I  
Sbjct: 134 RDTSGVMLFAKH-AFAHGLIDQQMQQKGIEKTYLAISDKRVSD-----FNHGFIDDPIAR 187

Query: 173 GDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
               +                 L  Q G+     V L  G+  +I+
Sbjct: 188 SPRSIIERRVHESGQSALTEYWLAEQVGALKVYKVQLHTGRTHQIR 233


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 82/259 (31%), Gaps = 54/259 (20%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
               + T +R+ + +A A     SR  V+ +IA+  V ++G+        +     I V 
Sbjct: 73  TTDSDATGKRLDQWLAAALGPDLSRSRVQSLIAEGHVTIDGVPARETKQKLREGMTIAVV 132

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                      + +PL    E   L + +KP GLV    + +   T+ + L         
Sbjct: 133 LPEPEPAEPIAENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 192

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG--Q 152
                 R   V RLD +T G++++  +    R L        R       Y     G  +
Sbjct: 193 GIGGIRRPGIVHRLDKDTSGVMVVAKNDLSHRHLSEQFADHGRTGDLERAYLALVWGMTE 252

Query: 153 VDQDKLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVG-------------LRE-- 195
             Q  ++    G   +      +  +   D +     + TV              L E  
Sbjct: 253 RPQGYIDAHL-GRSHRDRTKQAVVNEERDDARHAITHYATVEKFGPREDATALASLVECR 311

Query: 196 ---GKNREIKKVFEFFNWK 211
              G+  +I+         
Sbjct: 312 LETGRTHQIRVHMAHIGHP 330


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 37/166 (22%), Positives = 61/166 (36%), Gaps = 23/166 (13%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNV--MSTDHIEVDGVP 66
           R+ K +       SR +++R I    V VNG  ++     +A   V       +E+D  P
Sbjct: 4   RIDKELGHHFPQFSRSQLKRWIDDGTVTVNGQTVKAKYQLQAGDRVVIKPETPVEIDLEP 63

Query: 67  LRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGR 113
                          + +KP G+V   +      T+ + L             R   V R
Sbjct: 64  ENIPLDIVYEDDDVLVVNKPQGMVVHPAPGHPNHTLVNALMYYAPLSSINGELRPGIVHR 123

Query: 114 LDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
           +D +T GLL++       R L   L     LR Y    HG + +++
Sbjct: 124 IDKDTSGLLMVAKTDRAHRSLTAQLKEKSNLREYVALVHGVIKENE 169


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 74/238 (31%), Gaps = 47/238 (19%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           N +P R+ K +    G  SR  V+  I    V VN   ++     +     I +      
Sbjct: 34  NQSPLRIDKFLMDRIGEVSRNRVQNAIKTGSVLVNDQEIK-PNFKIKPGQKITLILPKST 92

Query: 63  -DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------- 106
            D + +           E   L + +KP GLV        + T+ + L            
Sbjct: 93  TDKLRIVPQNIPLNVVYEDEDLLVVNKPPGLVVHPGVGHFKGTLVNALAYHLRLDPNQIS 152

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                 RV  V R+D NT GLL++  +      L          R Y     G+  ++  
Sbjct: 153 TGNFQERVGLVHRIDKNTSGLLVVAKNEFALSHLAKQFFYHTIERTYNALVWGEP-EEDR 211

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGS--------------NAWVTVGLREGKNREIK 202
             +   +        D  V  +  +G                + +   L  G+  +I+
Sbjct: 212 GTINAHVGRHPRFRKDFTVFPEGDQGKWAVTHYQVLERLYYVSLIKCTLETGRTHQIR 269


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 85/234 (36%), Gaps = 39/234 (16%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           ++     +R+ + + R     +R ++++++    V+VN   ++ A   +   + + V   
Sbjct: 9   IEPGQAAERLDRFLTRQLPELTRSQLKKLVDDGLVRVNDQTVK-AGAKLRGGETVCVTLP 67

Query: 63  ---------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                    + +PL    E + L + +K  G+V   +      T+ + L      +  VG
Sbjct: 68  QAQSVETLPEDLPLTVLYEDSDLIVINKAAGMVVHPAAGHSSGTLVNALLYHCHDLSGVG 127

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--QDKLN 159
                    RLD +T G+++ T +      L          R Y    HGQV   +  ++
Sbjct: 128 GELRPGIVHRLDKDTSGVMVATKNDVTHNHLAAQFKDHSIQRRYVALVHGQVQNARGTID 187

Query: 160 L-------LKKGIVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +K +  +G          +V         + + + L  G+  +I+
Sbjct: 188 APIGRHPTHRKKMTSKGRGGRRAVTHWKVLRRYDADRLSLLEMRLETGRTHQIR 241


>gi|224100817|ref|XP_002312025.1| predicted protein [Populus trichocarpa]
 gi|222851845|gb|EEE89392.1| predicted protein [Populus trichocarpa]
          Length = 377

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/224 (15%), Positives = 71/224 (31%), Gaps = 56/224 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW----------LYHKPIGL 84
           I   ++ ++G +++     +     +    +P R+ +   L             +KP GL
Sbjct: 62  IHNGQITIDGEVVKEPKAILRDGMELVYHRLPWREPDAPYLLQVLYEDDDMVALNKPPGL 121

Query: 85  VTTHSDPDGRSTVFDNLPS-----------IFSRVISVGRLDINTEGLLLLT-------- 125
                    + TV   L               S  + V RL   T G+LL          
Sbjct: 122 QVLPGGLFQQRTVLMQLQWRASKGSSSLAIQGSHPVPVHRLGRGTSGILLCAKTKVAKTS 181

Query: 126 ------------NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-----------LK 162
                        D   A + +    +  ++YR   +G ++QDK+ +           + 
Sbjct: 182 LAAYFADGTSLIGDSSNANMEQSKRRKISKIYRALVNGILNQDKIIIKQPIGTMRYPGVA 241

Query: 163 KGIVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIK 202
           KG+ +            +V     + +   V V +  G+  +I+
Sbjct: 242 KGLYVASPSGKPALSKVEVLERDSQLNQTLVQVEIESGRPHQIR 285


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 74/233 (31%), Gaps = 38/233 (16%)

Query: 8   QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
            E    +R+ + +A R    SR  ++ +I    V  +G ++   +  V       V    
Sbjct: 17  TEADGGERLDRFLASRLSEMSRSRLKALIEAGTVTCDGAVIRLPSAAVRPGAIYTVALPP 76

Query: 63  ------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                  G  L      E + L +  KP GLV   +  +   T+ + L +          
Sbjct: 77  AIPAAPQGQALDLTVLYEDSDLIVIDKPAGLVVHPAPGNPDGTLVNALIAHCGDSLAGIG 136

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV-----------RFH 150
              R   V RLD +T G+++          L     +    R Y                
Sbjct: 137 GERRPGIVHRLDKDTSGVMVAAKTELALNALSAAFAARDLDREYLALCWGAPQPAEGEIE 196

Query: 151 GQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           G + +D  +  +  +V +G         TL         +   L  G+  +I+
Sbjct: 197 GPIGRDPRDRKRMAVVARGGKPALTHYRTLRRFGLGATLLACRLATGRTHQIR 249


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/194 (23%), Positives = 74/194 (38%), Gaps = 30/194 (15%)

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------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +            + +PL    E   L + +KP G+V   +      T+ + L   F  
Sbjct: 66  VIAVPQAEESHIGPEDIPLDIVWEDDDLVVVNKPAGMVVHPAPGTPTGTLVNALLHHFGG 125

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQ 155
                   +R   V R+D +T GLL++         L          R YR   +G  +Q
Sbjct: 126 KLSGVGGVARPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFEAHSADRAYRAICYGVPNQ 185

Query: 156 DKLNLL-KKGIVIQ 168
               LL  +G+ ++
Sbjct: 186 GDPRLLGTRGVSVE 199


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 93/247 (37%), Gaps = 55/247 (22%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++ E   P+R+ +V+AR  +    SR  ++ ++ +  V+ +GI++   A  V +   I++
Sbjct: 25  VLDEGTVPERLDRVLAR--VFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCRIDL 82

Query: 63  D----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                      G  L  A   E   L +  KP GLV   +      T+ + L +      
Sbjct: 83  SVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAGHEDGTLVNRLIAHCGASL 142

Query: 106 ------SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQV 153
                  R   V RLD +T GLL++  ND    G  A+  +   +    R Y        
Sbjct: 143 SGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSGALERAYLALVWNVP 202

Query: 154 DQ----------------DKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLRE 195
           +                 +K+ ++++G   +G          D   + G  A +   L  
Sbjct: 203 EPRAGTIRANLARSRHNREKIAVVREG---EGREAITHYRVEDVHGEGGVTALLRCHLET 259

Query: 196 GKNREIK 202
           G+  +I+
Sbjct: 260 GRTHQIR 266


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 79/244 (32%), Gaps = 39/244 (15%)

Query: 6   IVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++  +   +R+ +V+  A  G+ SR  +++ +   R  V+G+ + R          + ++
Sbjct: 7   LITADTAGRRLDRVLRDAAPGL-SRAALQKAVLAGRCLVDGLPVSRPDAKTRPGQRVLLE 65

Query: 64  ----GVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                  L   E     L+        +KP GL           T+   L   F ++   
Sbjct: 66  LPPTENALSPEEGHLELLWQDESLVVCNKPAGLTVHPCPSCPEHTLVQRLLGRFPQLGRL 125

Query: 109 -----ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL--- 158
                  V RLD +T GLLL+  T    LA        +  + Y     G   +      
Sbjct: 126 EGLRPGIVHRLDKDTSGLLLVALTEPARLALSAAFARREVHKEYLALVSGLPPEQGECRE 185

Query: 159 -------NLLKKGIVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                    +K  ++ +           +   +T     + + V +  G+  +I+     
Sbjct: 186 PLGRHPTAKIKMAVLPETRGGKPAHTTWKRLWNTPDQRVSLLAVRIHTGRTHQIRVHLAH 245

Query: 208 FNWK 211
               
Sbjct: 246 LGHP 249


>gi|198277498|ref|ZP_03210029.1| hypothetical protein BACPLE_03720 [Bacteroides plebeius DSM 17135]
 gi|198269996|gb|EDY94266.1| hypothetical protein BACPLE_03720 [Bacteroides plebeius DSM 17135]
          Length = 356

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 86/248 (34%), Gaps = 41/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +   P R+ K +    + ASR  ++       V  NG  ++  +  V   D + V
Sbjct: 32  RTVVDKGQAPVRIDKYLFERIVNASRNRIQMAADNGFVMANGKPVKS-SYKVKPLDVLTV 90

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L + +KP GLV      +   T+ + +      V
Sbjct: 91  MMDRPRYENDIIPEDIPLNIVYEDDDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLRDV 150

Query: 109 IS----------VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
            +          V R+D +T GLL++  T D   +  L+  +    R Y     G V+QD
Sbjct: 151 PTYNPNDPQVGLVHRIDKDTSGLLVVAKTPDAKTSLGLQFYNKTTKREYNALVWGIVEQD 210

Query: 157 K-----------LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKK 203
           +            + ++  ++              +  + G    V   L  G+  +I+ 
Sbjct: 211 EGTITGNIGRNPRDRMQMAVMSDPEQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRV 270

Query: 204 VFEFFNWK 211
             +     
Sbjct: 271 HMKHIGHT 278


>gi|117928240|ref|YP_872791.1| ribosomal large subunit pseudouridine synthase D [Acidothermus
           cellulolyticus 11B]
 gi|117648703|gb|ABK52805.1| ribosomal large subunit pseudouridine synthase D [Acidothermus
           cellulolyticus 11B]
          Length = 314

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/260 (17%), Positives = 79/260 (30%), Gaps = 70/260 (26%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL-------------------- 46
           V E    +RV   IAR    SR  V  +IA  +V+V+G++                    
Sbjct: 13  VPEGLDGERVDVAIARLLGLSRTRVADLIAAGQVRVDGVVPAKSARLAAGSWLEVRVPRP 72

Query: 47  -----------LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
                      +   AV     D + VD                KP G+    S     +
Sbjct: 73  GPPRPPVIPTPVADMAVVYDDPDIVVVD----------------KPAGVAAHPSPGWEGA 116

Query: 96  TVFDNL---------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
           TV   L              R   V RLD+ T GL+++         L+      +  ++
Sbjct: 117 TVLGALLAAGYRVATSGAAERQGIVHRLDVGTSGLMVVAKSERAYSTLKRAFREREVHKI 176

Query: 145 YRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
           Y     G            +D+  ++  +  +V  G        TL+    + + + + L
Sbjct: 177 YHALVQGHPDPVRGTIDAPIDRHPVHEFRFAVVAGGKPSVTHYTTLEALPAA-SLLEIEL 235

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+           
Sbjct: 236 ETGRTHQIRVHMAAIRHPCV 255


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/232 (18%), Positives = 75/232 (32%), Gaps = 37/232 (15%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------ 57
           N V EN    R+ +VIA+     SR  ++  I    V VNG ++++    +M        
Sbjct: 9   NTVGENQLGMRLDQVIAQLYPDYSRSRIKDWILNGMVSVNGDVVKKPREKMMGGEELFIQ 68

Query: 58  ----DHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D +      +PL    E   + + +KP   V          T+ + L         
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTILNALLHYCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQ 152
             R   V RLD +T GL+++         L   L   +  R Y                 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQMTGGGTIEKP 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR-E-GKNREIK 202
           + +     +   +   G          +  +       + LR E G+  +I+
Sbjct: 189 IGRHSTKRICMAVHEMGKDAITHYRVAERFREHT---RIVLRLETGRTHQIR 237


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 83/239 (34%), Gaps = 43/239 (17%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K I  +   P RV K +        A+R ++++      + VN  ++++    V + D +
Sbjct: 19  KFIASKGQEPLRVDKFL--MNFIENATRNKIQQAAKDGHIWVNEKIVKQ-NYKVKAGDEV 75

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------- 98
           +V             + +PL    E   L + +KP G+V      +   T+         
Sbjct: 76  KVLFEHPPYELLLTPENIPLDIVYEDDVLLVVNKPAGMVVHPGHGNYTGTLINALLYHSK 135

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           D   +   R   V R+D +T GLL++         L          R Y     G V+ +
Sbjct: 136 DLPVNSNDRPGLVHRIDKDTSGLLVVAKTEAAMTHLAKQFFDKTSEREYVALVWGNVEDE 195

Query: 157 K-----------LNLLKKGIVIQGICYGDMQVT--LDTQKGSNAWVTVGLREGKNREIK 202
                        N L+  +  +G    +      +  + G    V+  L  G+  +I+
Sbjct: 196 SGTIEGNIARNPKNRLQMQVFPEGEQGKEAVTHYGVLERLGYVTLVSCKLETGRTHQIR 254


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 83/229 (36%), Gaps = 42/229 (18%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K + +R   ASR +++       + VNG  ++  +  V   D + V           
Sbjct: 38  RVDKFLMSRLPNASRTKIQEAADAGNILVNGKAVKS-SYKVKPKDIVSVVMAYPRREIEI 96

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----------PSIFSRV 108
             + +PL    E   L + +KP G+V   S      T+ + L            +   R 
Sbjct: 97  IPENIPLNIVYEDDDLMVVNKPAGMVVHPSYGHYTGTLVNALAWHLKGNPLFKDNNDPRP 156

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--------L 158
             V R+D +T GLL++  T        L+  +    R Y     G ++ +          
Sbjct: 157 GLVHRIDKDTSGLLVIAKTEKAKTHLGLQFFNKTSDRKYVAVCWGNLEDETGTITGHIGR 216

Query: 159 NLLKKGIV--IQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           NL  + ++       +G   VT   +  + G    V   L  G+  +I+
Sbjct: 217 NLTNRKVMACFPDGSHGKHAVTHYRVLERLGYVNVVECILETGRTHQIR 265


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 83/247 (33%), Gaps = 63/247 (25%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + ASR  +++      V  NG  ++  +  V   D I V           
Sbjct: 42  RVDKYLFERIVNASRNRIQKAAEGGFVMANGKPVKS-SYKVKPLDVITVMMDRPRYENEI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ +          +  +    V 
Sbjct: 101 IPEDIPLTIVYEDPYLMVVNKPAGLVVHPGHGNYHGTLVNALAWHMKDNPDYDANDPHVG 160

Query: 110 SVGRLDINTEGLLLL-------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
            V R+D +T GLL++       TN G         +    R YR    G V+QD      
Sbjct: 161 LVHRIDKDTSGLLVIAKTPDAKTNLGNQFF-----NKTTKRKYRALVWGIVEQD------ 209

Query: 163 KGIVIQGICYGDM---------QVTLDTQKGSNAWV-----TVGLRE-----GKNREIKK 203
           +G +I  I                T+     ++  V      V L E     G+  +I+ 
Sbjct: 210 EGTIIGNIARNPKDRMQMAVMSDPTVGKHAVTHYRVLERLGYVTLVECILETGRTHQIRV 269

Query: 204 VFEFFNW 210
             +    
Sbjct: 270 HMKHIGH 276


>gi|23015589|ref|ZP_00055361.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 327

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 78/259 (30%), Gaps = 59/259 (22%)

Query: 4   KNIVQENFTPQ----RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           + +      P+    R+ + +A R    SR  ++ +I   RV ++   +  A++ V    
Sbjct: 7   QRLTPPAVEPEEAATRLDRWLAARLPELSRTRIKALIEDGRVSLDATTISDASLRVKPGQ 66

Query: 59  HIEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
              V             D       E   L +  KP G+V   +  +   T+ + L +  
Sbjct: 67  CFTVEVPPDAPAEPEAQDIALSVVYEDEDLIVIDKPAGMVVHPAPGNPDETLVNALLAHC 126

Query: 106 ----------SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                      R   V R+D +T GLL+   T+        +       R Y     G  
Sbjct: 127 GESLAGIGGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGLAAQFAEHSLERAYWALVWGTP 186

Query: 154 DQDKLNLLKKGIVIQGIC------YGDMQVTLDTQKGSNAWVT---------VGLRE--- 195
                   ++G  I+G           M V     K +              V L E   
Sbjct: 187 SP------RQG-EIEGNIGRNPNDRKKMAVVKSGGKPALTRYRVLKSFAGGAVSLVECRL 239

Query: 196 --GKNREIK-KVFEFFNWK 211
             G+  +I+  +       
Sbjct: 240 ATGRTHQIRVHMT-AQGHP 257


>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 = 71.4 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  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQP-HVGQKVTAEDVVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 75/227 (33%), Gaps = 33/227 (14%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           Q++   QR+ + +A      SR  ++  I Q RV ++G +       V++   + VD   
Sbjct: 12  QDHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKVLAGQKVHVDVEL 71

Query: 67  LR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SR 107
                            E   + +  KP GLV          T+ + L   +       R
Sbjct: 72  ADDTRWDAQNIELNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPAIAEVPR 131

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQVDQ 155
              V RLD +T GL+++         L   L + Q  R Y                 + +
Sbjct: 132 AGIVHRLDKDTTGLMVVAKTIPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGR 191

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +V  G          +  +G +  + + L  G+  +I+
Sbjct: 192 HPTQRTHMAVVPNGRESVTHYRVHEKFRG-HTRLRLRLETGRTHQIR 237


>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 = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/91 (30%), Positives = 46/91 (50%), Gaps = 3/91 (3%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAER 72
            R+ KVI +    SR+E++R+  Q +V V+  +  R   NV S+   I V G  L   E 
Sbjct: 1   MRLDKVIEQQLNTSRKEMKRLFQQGKVFVDHRIERRPERNVDSSLHQIMVAGRQLETQE- 59

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            R ++ +KP G+VT + D   ++ +    P 
Sbjct: 60  -RYYIVNKPKGVVTANLDQQHQTVIALIAPE 89


>gi|296284607|ref|ZP_06862605.1| pseudouridine synthase D large subunit [Citromicrobium
           bathyomarinum JL354]
          Length = 314

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 70/242 (28%), Gaps = 45/242 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
            P R+ K +A A   SR  ++ +IA  +V V G      +  V +     +         
Sbjct: 13  APARLDKALADATDLSRERIKGLIADGQVSVGGKRATSPSAKVAAGTPFTIALPAPTPLE 72

Query: 63  ----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRV 108
               D   +   E   L +  KP G+V   +  +   T+ + L           +   R 
Sbjct: 73  AEPQDIPLVVAYEDAHLIVVDKPAGMVVHPAAGNRDGTLVNALLYHCRGQLSGINGVERP 132

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV------------- 153
             V R+D +T GLL++  T+        +       R Y     GQ              
Sbjct: 133 GIVHRIDKDTSGLLVVAKTDAAHEGLARQFADHSISRRYVAVCAGQPRPAEGTIDARLGR 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREGKNREIKKVFEFFN 209
                  +    V+              +        + +   L  G+  +++       
Sbjct: 193 SDRDRKKMA---VLDPQSTRGKHAVTHYRTTKTFGVASILECRLETGRTHQVRVHCASIG 249

Query: 210 WK 211
             
Sbjct: 250 HP 251


>gi|330896110|gb|EGH28331.1| RNA-binding S4 [Pseudomonas syringae pv. japonica str. M301072PT]
          Length = 74

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 30/71 (42%), Gaps = 1/71 (1%)

Query: 12 TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P R+SK +      SRRE E  I    V V+G ++E     V ST  IE+       + 
Sbjct: 3  DPIRLSKRLIELVGCSRREAELFIEGGWVTVDGEVIEEPHFKV-STQKIELSPDAKADSP 61

Query: 72 RTRLWLYHKPI 82
               + HKP 
Sbjct: 62 EPVTIILHKPA 72


>gi|226941139|ref|YP_002796213.1| RluD [Laribacter hongkongensis HLHK9]
 gi|226716066|gb|ACO75204.1| RluD [Laribacter hongkongensis HLHK9]
          Length = 349

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 78/240 (32%), Gaps = 35/240 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + +     R+   +A      SR  + + I    V+V+G  +       +    +EVD 
Sbjct: 21  TIPDTLAGDRLDAALAALMPDQSRSRLTQWIKDGHVRVDGSTVTVPRSKTVLGQQVEVDE 80

Query: 65  V---------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPS-- 103
                           P+   +R ++ + +KP GLVT   + +   T+ +     +P   
Sbjct: 81  QLSLDEMAFAPEDIEIPVIYEDR-QILVVNKPAGLVTHPGNGNWSGTLLNGLLYRVPELA 139

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----RFHGQVDQDK 157
              R   V RLD +T GL+++         L     +    R YR        G +  DK
Sbjct: 140 HVPRAGIVHRLDKDTSGLMVVAKTVAAQLDLIRQLQARTVKRHYRAIACGNVAGDITIDK 199

Query: 158 L------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                    +K  +V  G       V        +  V   L  G+  +I+         
Sbjct: 200 AIGRDPKTRVKMAVVAFGGKPAITHVRPLEMFEHHTLVECRLETGRTHQIRVHMASIGCP 259


>gi|308233940|ref|ZP_07664677.1| pseudouridine synthase, RluA family [Atopobium vaginae DSM 15829]
 gi|328943952|ref|ZP_08241417.1| ribosomal large subunit pseudouridine synthase D [Atopobium vaginae
           DSM 15829]
 gi|327491921|gb|EGF23695.1| ribosomal large subunit pseudouridine synthase D [Atopobium vaginae
           DSM 15829]
          Length = 338

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 85/257 (33%), Gaps = 50/257 (19%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V       R+   ++    + +R     +I Q++V++N  L    +  V   D I V  
Sbjct: 9   LVTPQHDRMRLDAFLSTCSELGARNACAHLIEQRKVEINDTLALSKSERVRMGDRICVAQ 68

Query: 63  --DG-----------VPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---- 104
             D            +PL  + E   L +  K  GLV   S      T+ + L +     
Sbjct: 69  QIDNTSSSHIMPNASIPLDIRYEDDYLLVISKQTGLVCHPSPGHVDDTLSNALVAHCGYE 128

Query: 105 -------FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
                    R   V RLD++T GL++   D    + L   +    + R Y V   G V  
Sbjct: 129 HLGLLQGDDRPGIVHRLDMDTTGLMVAAKDNTTQQALQDLIRLRVFDRRYIVLVQGYVTP 188

Query: 156 DKLNLLKKGI-----------VIQGICYGDM--------QVTLDTQKGSNAWVTVGLREG 196
           D+   +  GI           + +     +         +    ++    + +   L  G
Sbjct: 189 DE-GTITTGIARSKKNRLKMCISKDPASREAITTFKTLERFEAGSKDDGYSLLECHLYTG 247

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+    +    V 
Sbjct: 248 RTHQIRVHMRYVGHSVV 264


>gi|291530201|emb|CBK95786.1| pseudouridine synthase, RluA family [Eubacterium siraeum 70/3]
          Length = 322

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/262 (16%), Positives = 95/262 (36%), Gaps = 57/262 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+  + + N + QR+ + ++++   G     ++ ++  +  +K+NG   +    ++   
Sbjct: 1   MKEIKVTK-NDSGQRIDRFLSKSFPLGQG---QICKLARKNCIKLNGKKCK-PDTHIAEN 55

Query: 58  DHIEV---DGVPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           D I++   D + + KA                  E   + L  KP+G+V    +     T
Sbjct: 56  DIIKLFIPDEMLIPKAKSDPDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGDSDT 115

Query: 97  VFDNLPSIFSRVIS-------------VGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
           + + + S   R                  R+D NT G+++   +    R+L       + 
Sbjct: 116 LINRIKSYLYRKGEYHPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRDREL 175

Query: 142 LRVYRVRFHGQVDQDKLNL---LKKG-----IVIQGICYG-----DMQVTLDTQKGSNAW 188
            ++Y     G+V  D   L   L+K      + I             +  +    G N+ 
Sbjct: 176 TKLYLCIACGKVTPDSATLTAYLEKNSDTNTVKISDKKTKSNLTIKTKYKVIAYNGENSL 235

Query: 189 VTVGLREGKNREIKKVFEFFNW 210
           + V L  G+  +I+    +   
Sbjct: 236 LKVDLLTGRTHQIRAHLAYIGH 257


>gi|254785221|ref|YP_003072649.1| ribosomal large subunit pseudouridine synthase D [Teredinibacter
           turnerae T7901]
 gi|237685566|gb|ACR12830.1| ribosomal large subunit pseudouridine synthase D [Teredinibacter
           turnerae T7901]
          Length = 333

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 53/278 (19%), Positives = 95/278 (34%), Gaps = 52/278 (18%)

Query: 2   KDKNIVQE--NFTPQ--RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            + NIV+    FT    R+ +V A      SR  +++ I Q R+ VNG   +   + +  
Sbjct: 19  PESNIVEAQVPFTAMDSRLDQVAAELFPEFSRARLQQWIKQGRLTVNGEPAK-PKLKLAG 77

Query: 57  TDHIEV------DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            + + +       G  L +        E   + + +KP GLV   +  +   T+ + L  
Sbjct: 78  GECLRLSVLEEPQGEWLPEPIPLDVVYEDEAILVLNKPAGLVVHPAAGNYTGTLLNGLIH 137

Query: 104 I------FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV-------- 147
                    R   V RLD +T GL+++         L  +L +    R Y          
Sbjct: 138 HRQAQSLLPRAGIVHRLDKDTSGLMVVAKTTAAQNNLVAQLQARTVKREYEALAIGEVRS 197

Query: 148 --RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  + +   N  +  +V  G         L    G    + + L  G+  +I+   
Sbjct: 198 SGFVDAPIGRHPTNRTRMAVVSSGKPAVTHYTALARFDGFTH-LRLQLETGRTHQIRVHM 256

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
               + +             G  + G  R +  K+LRE
Sbjct: 257 AHLGYPLV------------GDPVYG--RRLPAKLLRE 280


>gi|331266315|ref|YP_004325945.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326682987|emb|CBZ00604.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 298

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 70/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
               + VNG   + A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGAILVNGQP-QNATYLLDIGDRVTIDIPAEEGFESLEAIDRPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQEYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQRKSIEKRYFALVKGAGVLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKVVV 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +   V + L  G+  +I+  F    + 
Sbjct: 211 SYRNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 84/235 (35%), Gaps = 42/235 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVIA      SR +++ ++  + + VN    E+ +  V S D I+V   P++     
Sbjct: 15  RLDKVIAEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVIDVTIPPVKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS--V 111
                     E + + + +KP G+V   S      T+ +       +L           V
Sbjct: 74  AENLHLDIVYEDSDVIVVNKPQGIVVHPSAGHPDHTLVNGLLYHTRDLADSPEGFRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD-------------QD 156
            R+D +T GLL++  +      LE  L      R Y    HG  +              +
Sbjct: 134 HRIDKDTSGLLMIAKNDRARESLEKQLAEKINKREYLAIVHGNFEVKNGVINAPIGRNPN 193

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   +  +G        T+  Q  + + V   L  G+  +I+   ++    
Sbjct: 194 NRKQMA--VNPKGKAAVTHF-TVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHP 245


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 82/249 (32%), Gaps = 43/249 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            K +      P RV K +        A+R ++++      V VN I ++     V   D 
Sbjct: 18  YKFVASAGQEPLRVDKFLMN--FIENATRSKLQQAAKAGNVLVNEISVKS-NHKVKPNDV 74

Query: 60  IEV-------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + +             + +PL    E   + + +KP G+V      +   T+ + L    
Sbjct: 75  VRIVLAYPPAESLLVAEDIPLDIIYEDDTVIVVNKPAGMVVHPGHGNYSGTLVNGLIHHI 134

Query: 106 SRVIS--------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
             + +        V R+D +T GLL++         L     +    R+Y     G V +
Sbjct: 135 ENLPTNSNERPGLVHRIDKDTSGLLVVAKTEFAMANLSRQFFERTTERLYYALVWGNVAE 194

Query: 156 DK-----------LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D+            N L+  +   G    +      +  +      V   L  G+  +I+
Sbjct: 195 DEGRIEGNIGRSLKNRLQMAVFPDGDFGKHAVSHYKVLERLTYVTLVECKLETGRTHQIR 254

Query: 203 KVFEFFNWK 211
             F+     
Sbjct: 255 AHFKHIGHT 263


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 87/237 (36%), Gaps = 47/237 (19%)

Query: 15  RVSKVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           R+ K   + G      SR +++  I    V VNG  ++     ++  DH+++        
Sbjct: 16  RIDK---QLGHHFDQFSRSQIQHWIEDGHVLVNGEQVK-PKYKLLVGDHVQIIPEEPQKI 71

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVI 109
               + +PL    E   + + +KP G+V   +      T+ + L             R  
Sbjct: 72  DLTPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPNHTLVNALLYHSPLSTINGEFRPG 131

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK--LNLLKKGI 165
            V R+D +T GLL++  +    R L   L +    R Y    HG + +DK  ++    G 
Sbjct: 132 IVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPL-GR 190

Query: 166 VIQGICYGDMQVTLDTQKGSNAW--------VTVGLRE---GKNREIKKVFEFFNWK 211
            ++        V +D +     +         T+   +   G+  +I+   ++    
Sbjct: 191 SLKDRKKQA--VVVDGRHAITHFNVLERFKNYTLVACQLETGRTHQIRVHMKYIGHP 245


>gi|307709450|ref|ZP_07645907.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307619764|gb|EFN98883.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 298

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D + +D     G      + +      E     + +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVTIDIPAEEGFETLEAIERPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKIVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 85/252 (33%), Gaps = 43/252 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +   V EN   +R+ + +A      SR  ++++I    + VN   ++ A   +   D 
Sbjct: 1   MSEFFTV-ENEEGERIDRYLAEMLSDRSRSYIQKLIKDSHILVNNKPVK-ANYRLSCGDM 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---- 102
           +EV            + +PL    E   + + +KP  +V   +      T+ + L     
Sbjct: 59  LEVTIPSAKEPDILPEDIPLHILYEDADIIIVNKPKQMVVHPAPGHYSGTLVNALMFHCG 118

Query: 103 ------SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVD 154
                 +   R   V R+D++T G L++  +    + L     +    R+Y    HG   
Sbjct: 119 RELSGINGMMRPGIVHRIDMDTTGSLIVCKNDMAHQALSEQLKKHSIRRIYEAVVHGGFK 178

Query: 155 QD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++                 +      +          +  + G  +++   L  G+  +I
Sbjct: 179 EEEGTVSAPIGRHPTDRKRMST--HAKNAREAVTHYKVLERFGEYSYIQCELETGRTHQI 236

Query: 202 KKVFEFFNWKVN 213
           +         + 
Sbjct: 237 RVHMSSIGHPIV 248


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 81/241 (33%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +    +RV   +AR    SR     +  +  V VNG+   ++   + + D IEV    
Sbjct: 4   VPDALVGERVDAALARMLGLSRSRCAELAGEGHVLVNGVAAGKSD-RLGALDIIEVTIPE 62

Query: 63  -DGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
            +  P    +   L+      +  KP+G+           TV  NL +   R+ S     
Sbjct: 63  PESKPTPVTDMAILYDDEDIVVVDKPVGVAAHTGPGWEGPTVLGNLEAAGYRITSYGPPE 122

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL----- 158
               V RLD+ T G +++     LA  +   + +     +VY     G +D         
Sbjct: 123 RQGIVHRLDVGTSGAMMVAKS-ELAYTVMKRAFKERTIEKVYHAVVAGHLDPASGTIDAP 181

Query: 159 ------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                    +  ++  G        TL+   G+     V L  G+  +I+          
Sbjct: 182 IGRHPSREWRMAVIDGGKRAVTHYDTLELMAGAQLT-EVHLETGRTHQIRVHMAAVGHPC 240

Query: 213 N 213
            
Sbjct: 241 V 241


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 78/226 (34%), Gaps = 36/226 (15%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-----------D 58
               +R+ + +ARA   SR   +  I+   V+V G ++ + A  +               
Sbjct: 8   EAEGERLDQALARALGVSRARAQAWISAGHVRVAGEVVTKPARRLAGERVEVEVPPEPPA 67

Query: 59  HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVIS 110
            +E + + +    E   + + +KP G+VT  +    R T+ + L   +        R   
Sbjct: 68  RVEAEDLTVEILYEDEDMVVVNKPAGMVTHPAPGVTRGTLVNALLGRWVEPGGEPVRPGI 127

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG---------QVDQDKLN 159
           V RLD  T G++++       R L     Q    + Y     G          + +  ++
Sbjct: 128 VHRLDKETSGVIVVARHEAALRRLADAFKQRFVFKRYVALTEGVPANTTVIAPIGRHPVH 187

Query: 160 LLK---KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             K    GI      Y +    +       A V      G+  +I+
Sbjct: 188 RFKMHTGGIK---ARYAETDFEVVATAEGRALVEARPHTGRTHQIR 230


>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 = 71.0 bits (173), 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  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQP-HVGQKVTAEDVVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 84/235 (35%), Gaps = 42/235 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVIA      SR +++ ++  + + VN    E+ +  V S D I+V   P++     
Sbjct: 15  RLDKVIAEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVIDVTIPPVKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS--V 111
                     E + + + +KP G+V   S      T+ +       +L           V
Sbjct: 74  AENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTRDLADSPEGFRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD-------------QD 156
            R+D +T GLL++  +      LE  L      R Y    HG  +              +
Sbjct: 134 HRIDKDTSGLLMIAKNDKARESLEKQLAEKINKREYLAIVHGNFEVKNGVINAPIGRNPN 193

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   +  +G        T+  Q  + + V   L  G+  +I+   ++    
Sbjct: 194 NRKQMA--VNPKGKAAVTHF-TVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHP 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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 80/243 (32%), Gaps = 52/243 (21%)

Query: 3   DKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  I  +    QR+ K++       SR +++ +I +  V VN  +++     V   D I 
Sbjct: 5   EFKIENQELVGQRIDKLLPEFNNEWSRSQIQDLIKEDLVTVNEKVIKS-NYKVKLNDLII 63

Query: 62  VDGVPLR-------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V    +                E   + + +KP G+V   S      T+ + L      +
Sbjct: 64  VTEKEVVEADIQPENLNLDIYYEDEDVAIVYKPKGMVVHPSPGHYSGTLVNGLMYQIKDL 123

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD 156
                      V R+D +T GLL++  +  +A       L      R Y    HG +  D
Sbjct: 124 SGINGEIRPGIVHRIDKDTSGLLMVAKN-DIAHRGLVEQLMDKSVKRKYTALVHGNIPHD 182

Query: 157 KLNLLKKGIVIQ---GICYGDMQV--TLDTQKGSNAWVTV-------GLRE-----GKNR 199
                     I    G    D Q    +D  K +     V        L E     G+  
Sbjct: 183 YG-------TIDAPIGRNEKDRQSMDVVDNGKEAVTHFNVLEHFNDYTLIECQLETGRTH 235

Query: 200 EIK 202
           +I+
Sbjct: 236 QIR 238


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/214 (18%), Positives = 73/214 (34%), Gaps = 31/214 (14%)

Query: 18  KVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           K++ A+ GI S ++ +++I   RV + G  L  A          EV     +   +   W
Sbjct: 6   KLLSAQMGI-SHKQAQKLIDLGRVCLGGRKLTLARQLCPLQSKFEVQNSKAQILYQETDW 64

Query: 77  LY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           L+ +KP G+ +              L         + RLD+ T G+L L  +   A+ LE
Sbjct: 65  LFLNKPAGVNSYA------------LEKQHPPYKLLHRLDLPTTGVLALAQNHAHAQGLE 112

Query: 136 L-PSTQWLRVYRVRFHGQVDQDKLNLL-----------KKGIV--IQGICYGDM--QVTL 179
                   + Y     G + + +   +            KG V  +          ++T 
Sbjct: 113 AFKKRAVYKEYIALVQGVIKKPQTLRMPLRVQKSHIEDAKGFVKTLLDPAGRPACTKITP 172

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             Q  +   + V +  G   +I+         + 
Sbjct: 173 LKQYKNKTLLKVVITTGITHQIRAHLSALGCPIV 206


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 82/228 (35%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +Q     QR+ + +A      SR  ++  I    VKVNG ++  A   V   + +E+   
Sbjct: 7   IQPQHMGQRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVELCVE 66

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   + + +KP   V      + R TV + L   + +++   
Sbjct: 67  IEEESRFEPENLPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHYPKIVEVP 126

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV----------RFHGQVD 154
               V RLD +T GL+++         L   L   + +R Y            +    + 
Sbjct: 127 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFGVMTQGGKVDQPMS 186

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +      +  +   G         ++  + +   + + L  G+  +I+
Sbjct: 187 RHPTKRTQMAVHPLGKPAVTHYRIMERFR-NYTRLRLRLETGRTHQIR 233


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 74/233 (31%), Gaps = 38/233 (16%)

Query: 8   QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
            E    +R+ + +A R    SR  ++ +I    V  +G ++   +  V       V    
Sbjct: 17  TEADGGERLDRFLASRLSEMSRSRLKALIEAGTVTCDGAVIRLPSAAVRPGAIYTVALPP 76

Query: 63  ------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                  G  L      E + L +  KP GLV   +  +   T+ + L +          
Sbjct: 77  AIPAAPQGQALDLTVLYEDSDLIVIDKPAGLVVHPAPGNPDGTLVNALIAHCGDSLAGIG 136

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV-----------RFH 150
              R   V RLD +T G+++          L     +    R Y                
Sbjct: 137 GERRPGIVHRLDKDTSGVMVAAKTELALNALSAAFAARDLDREYLALCWGAPQPAEGEIE 196

Query: 151 GQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           G + +D  +  +  +V +G         TL         +   L  G+  +I+
Sbjct: 197 GPIGRDPRDRKRMAVVARGGKPALTYYRTLRRFGLGATLLACRLATGRTHQIR 249


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIIINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y                 + +         +   G      
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 79/242 (32%), Gaps = 39/242 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV   ++R    SR +   + AQ  V +NG    ++   + + D I +D   
Sbjct: 9   VPDALVGERVDAALSRMLGMSRSKCADLAAQGAVTLNGRTAGKSD-RLGAADIIGIDMPD 67

Query: 64  ---------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIF 105
                    G+ +   +   + +  KP+G+           TV  NL             
Sbjct: 68  PAVKAVPVTGMDILYDDEDIVVV-DKPVGVAAHTGPGWEGPTVLGNLAAAGYRITTHGPP 126

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---- 158
            R   V RLD+ T G +++     LA  +   + +     +VY     G +D        
Sbjct: 127 ERQGIVHRLDVGTSGAMMVAKS-ELAYSVMKRAFKERTVTKVYHAVVAGHLDPASGTIDA 185

Query: 159 -------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                     +  ++  G        TL+   G+     + L  G+  +I+         
Sbjct: 186 PIGRHPSREWRMAVIDGGKRAITHYDTLEMMAGA-CLAEIHLETGRTHQIRVHMAAVGHP 244

Query: 212 VN 213
             
Sbjct: 245 CV 246


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/227 (17%), Positives = 75/227 (33%), Gaps = 33/227 (14%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           Q++   QR+ + +A      SR  ++  I Q RV ++G +       +++   + V    
Sbjct: 12  QDHQFGQRLDQALAELFPDYSRTRIKEWILQDRVTLDGQVANTPREKILAGQQVHVNVEL 71

Query: 63  -DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
            D               E   + +  KP GLV          T+ + L   +  +     
Sbjct: 72  EDDTRWDAQDIELNIVYEDEHILVIDKPAGLVVHPGAGTPDGTILNALLHRYPGIAEVPR 131

Query: 109 -ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQVDQ 155
              V RLD +T GL+++         L   L + Q  R Y                 + +
Sbjct: 132 AGIVHRLDKDTTGLMVVAKTVPAQTHLVEALQARQITREYEAIAIGHMTAGGTVDAPIGR 191

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +V  G          +  +G +  + + L  G+  +I+
Sbjct: 192 HPTQRTHMAVVPNGRPSVTHYRVHEKFRG-HTRLRLRLETGRTHQIR 237


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 49/230 (21%), Positives = 85/230 (36%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IFSRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P      R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIVNVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHVNYP 245


>gi|258511340|ref|YP_003184774.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478066|gb|ACV58385.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 303

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/216 (15%), Positives = 73/216 (33%), Gaps = 40/216 (18%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRK-----------AERT 73
           I   RVKVNG   ++    +   D +           +   P+ K            E  
Sbjct: 35  IRTGRVKVNGKRAKQ-DTRLHEGDIVHLYFSDEDYASLHAHPVAKYQGVSRAIDILYEDD 93

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLL 124
            +   +KP+G++T  +D + ++++   + +            R   V RLD NT G+++ 
Sbjct: 94  EIVAVNKPVGVLTHPADGEYKTSLAAQVEAYVYDRGAREGAFRAAPVHRLDRNTSGVVVF 153

Query: 125 --TNDGGLARVLELPSTQWLRVYRVRFHGQVD---QDKLNLLKKG----IVIQGICYGDM 175
             T     A        +  + Y     G+     +  +++ ++G    +V       + 
Sbjct: 154 AKTARAAKAWADAFHRGEVEKEYLAIVEGEWSGRGRVAVDVRREGNVTRVVDDSGKPSET 213

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +       + V + L  G+  +I+         
Sbjct: 214 AYEVVASSRGTSLVRLHLLTGRTHQIRVHMAHLGHP 249


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/230 (15%), Positives = 73/230 (31%), Gaps = 41/230 (17%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
            QR+  ++  +    SR   +  I    V VNG ++ +    V     I +    + +  
Sbjct: 4   TQRLD-ILVSSKFSLSRSIAKHKIENNLVTVNGKIISKPNTKVDEESEIILKEEKIVEET 62

Query: 71  --------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------- 106
                         E   + + +KP  ++   +  D  +T+ + +  IF           
Sbjct: 63  KVLTPWKKDIEIVYEDKYILIVNKPNDIIVHPTSYDLSNTLANIIKYIFDSKKIKYNGDP 122

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN---- 159
            R+  V RLD  TEGL+++                 +  + Y    H  +    +     
Sbjct: 123 LRMGIVHRLDKCTEGLVIVAKSLDSFNAFTKLFLDQKIEKKYLALLHNHLQTRTVEVDAP 182

Query: 160 ------LLKKGIVIQGICYGDMQVTLDTQKGSNAWV-TVGLREGKNREIK 202
                   ++ +           +  +  K  N  +  V L  G+  +I+
Sbjct: 183 IKRVETSTRREVSRDIDAKEARTIFKEINKYKNFTLAEVELFTGRTHQIR 232


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 83/242 (34%), Gaps = 46/242 (19%)

Query: 12  TPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
             +R+ + +AR  +    +R  +++++    V +NG    +    + + D I V   D V
Sbjct: 13  AGERLDRALAR--LCPDQTRSGLQKLLECGLVTLNGKPAGKHD-RMRAGDEIVVEFPDPV 69

Query: 66  PLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVG-- 112
           PL             E   L + +KP G+V      +   T+ +  L      +  +G  
Sbjct: 70  PLEAKAQDIPIEVVYEDDDLLVVNKPQGMVVHPGAGNPDGTLVNALLFHCGDSLSGIGGV 129

Query: 113 -------RLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------ 157
                  R+D +T GLL++  +    + L         LR Y     G + +D       
Sbjct: 130 LRPGIVHRIDKDTSGLLMVAKNDRAHQSLAAQIKAHSFLREYEAVVCGVIKEDSGTVDAP 189

Query: 158 -------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +   +  +   +     T+  +      + + L  G+  +I+    +   
Sbjct: 190 VGRHPTNRKRMA--VTQKNSRHAVTHYTVLRRYTHYTHLRLRLETGRTHQIRLHMAYIGH 247

Query: 211 KV 212
            V
Sbjct: 248 PV 249


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/172 (19%), Positives = 62/172 (36%), Gaps = 22/172 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------ 57
           N V ++   +R+ +VIA      SR  ++  I   +V V+G ++++  + +M        
Sbjct: 9   NTVNDSQLGKRLDQVIAELYPDYSRTRIKDWILAGKVAVDGEIIDKPRIKMMGGEQLVIN 68

Query: 58  ----DHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIF---- 105
               D +  +   +      E   + + +KP   V          TV +  L        
Sbjct: 69  AEIEDEVRWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLWHCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
             R   V RLD +T GL+++         L   L      R Y     G++ 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVQAQTRLVRALQKRNITREYEAIAMGKMT 180


>gi|327538476|gb|EGF25140.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 321

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 42/231 (18%), Positives = 72/231 (31%), Gaps = 45/231 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-DGVPLRKAERTR----------- 74
           SR +   MI    V +NG   +     V   D + V      R  E+ R           
Sbjct: 29  SRSQARGMIDHGCVMINGSPCKSVGTTVKPGDLVAVRYDKHQRYREKKRQWDDRTFEIVF 88

Query: 75  ----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL 124
               + + +K  G +T  +D    +++ D +               V RLD  T GLL+ 
Sbjct: 89  EDEHIIVVNKSAGTLTVPTDRGEPNSLVDRVSIYLSYSKSKKEAFVVHRLDRETSGLLVF 148

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL---LKKGIVIQGICYGDMQ--- 176
                +A +L       +  RV+     G V +D+      L  G  +        +   
Sbjct: 149 GKHEPIADLLIEQFKDRRPTRVFHAIVAGNVAEDEGTFESHLATGSNLDRYETRPGKDTD 208

Query: 177 --------VTLDTQKGSNAWVTVGLRE------GKNREIKKVFEFFNWKVN 213
                   V    ++ S+      L E       +N +++  F      V 
Sbjct: 209 QAITHYKVVRRLAERESSHGEETTLIEAQLETSKRN-QVRVQFANAGHPVL 258


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 37/174 (21%), Positives = 63/174 (36%), Gaps = 29/174 (16%)

Query: 13  PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           P R+ K +AR    A   SR  + R+I +  V V+G ++      V     +++      
Sbjct: 15  PARLDKALARDVPEAANLSRTRLGRLIEEGAVTVDGAVVHDPRAKVAEGQVVQIKVEEAA 74

Query: 63  ------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----------F 105
                 + +PL    E   L +  KP G+V   +      T+ + L +            
Sbjct: 75  ESHILPEDIPLSVVFEDDDLIVIDKPAGMVVHPAPGSPSGTLVNALLAHCGDDLSGVGGM 134

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
            R   V R+D +T GLL++         L          R Y+   +G  D + 
Sbjct: 135 KRPGIVHRIDKDTTGLLVVAKSDAAHHGLAAQFEKHTVERYYQTLVYGVPDAND 188


>gi|197120482|ref|YP_002132433.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196170331|gb|ACG71304.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 339

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 58/349 (16%), Positives = 115/349 (32%), Gaps = 69/349 (19%)

Query: 6   IVQENFTPQRVSKV---------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            V  +   QR+ K+         ++         V +M   ++V+VNG   + A   V  
Sbjct: 5   TVTADAAGQRLDKLVRKALRDVPLSH--------VYKMFRTRKVRVNGQRGK-ADQLVAE 55

Query: 57  TDHIEVDGVPLRK--------------------AERTRLWLYHKPIGLVTTHSDPDGRST 96
            D + + G   R                      E   L    KP GL          +T
Sbjct: 56  GDVVVIRGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGAT 115

Query: 97  VF----------DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLR 143
           +           D+LP    +     RLD +T G++L+         L           +
Sbjct: 116 LVEMARGYLRTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEGVHK 175

Query: 144 VYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVG 192
            Y     G++ ++               +   ++G+ + +          +   + + V 
Sbjct: 176 TYLALVKGKMPREAGTIDLPLSEHEQTSRSKALRGVNFQEALTRWKVVSAAKEISLLAVT 235

Query: 193 LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST--REVSKKILREQLGPHLL 250
           +  G+  +I++  E     V    R  YG F            R +     + ++ PH L
Sbjct: 236 IETGRTHQIRRHLEAVGHPVAG-DR-RYGDFAFNRTARTRWGLRRMGLHAWKLEV-PHPL 292

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
             A + L+AP  +    V  R N+  ++P   T     +++++G  +++
Sbjct: 293 TGAPLRLEAPFPAELAEVLSRANL--KLPGSPTGAHAPAARRDGPHRER 339


>gi|255016577|ref|ZP_05288703.1| pseudouridine synthase family 1 protein [Bacteroides sp. 2_1_7]
          Length = 189

 Score = 71.0 bits (173), 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  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQP-HVGQKVTAEDVVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 86/248 (34%), Gaps = 40/248 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLER-----AAVNV 54
           M+   I +E+   QR+ KV+    G ASR  V+R I +  V VN   ++          V
Sbjct: 1   MEQWIITKEHHE-QRIDKVVVDLHGQASRTAVQRWINEGAVLVNEKEVKTNSKVQQGDKV 59

Query: 55  ----MSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                +   +E+ G  +      E + + + +KP GLV   +      T+ + L      
Sbjct: 60  TLTEPAAQEVELLGEDIPLDVVYEDSDVIVVNKPRGLVVHPAPGHESGTLVNALLFHCKD 119

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV--- 153
           +           V R+D +T GL++          L   L +    R Y+   HG +   
Sbjct: 120 LSGINGEIRPGIVHRIDKDTSGLIMAAKHDAAHEHLAAQLKAKTTERRYKAIVHGVIPHA 179

Query: 154 ----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                     D      +   +            +L+      ++++  L  G+  +I+ 
Sbjct: 180 KGTIDAPIGRDPKDRQKMA--VTHVNSRPAVTHFSLEETFKQYSYISCELETGRTHQIRV 237

Query: 204 VFEFFNWK 211
            F +    
Sbjct: 238 HFNYIGHP 245


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 79/235 (33%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E+   QR+ + +A      SR  ++  I  QRV VN  + +     V+  + + ++ 
Sbjct: 12  TVSESQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNDQMCDTPKEKVLGGERVAINA 71

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 72  EIEEEARFEPQDIPLDIVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIVDV 131

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L   L   +  R Y     G +          
Sbjct: 132 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVEALQLREITREYEAVAIGHMT-------AG 184

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
           G V + I     + T                +      +  + + L  G+  +I+
Sbjct: 185 GTVSEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIR 239


>gi|218263542|ref|ZP_03477623.1| hypothetical protein PRABACTJOHN_03310 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222665|gb|EEC95315.1| hypothetical protein PRABACTJOHN_03310 [Parabacteroides johnsonii
           DSM 18315]
          Length = 306

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 79/212 (37%), Gaps = 28/212 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDH---------IEVDGVPLRKA-ERTRLW 76
           S+  V+ ++A  ++ VNG +  +    ++  D          +E +   L    E   L 
Sbjct: 41  SKSSVKALLAHGQISVNGTVTSQFNTPLIPGDEVLISYERGKVEFNNPLLTIVWEDDDLI 100

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  S      T F  L          +++  + RLD +T GL++   +  +
Sbjct: 101 VVNKKEGLLSVSSTRVKERTAFHLLSGYVKKTDPRNKIFVLHRLDRDTSGLMMFAKNLQV 160

Query: 131 ARVLELPSTQ--WLRVYRVRFHGQVDQD---KLNLLKKGIVIQ-------GICYGDMQVT 178
            + L+         R Y     G+ ++D    ++ L +   +Q              +  
Sbjct: 161 QKALQSNWNSAITARTYVAVVEGRPEKDSDLIISNLTENTKMQVYVTTEGDGKEAITRYR 220

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           L    G+ + + + L  G+  +I+   +    
Sbjct: 221 LLHSNGAYSLLELDLETGRKNQIRAQMQSIGH 252


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 84/242 (34%), Gaps = 46/242 (19%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
            R+ K +++     SR ++++ I    V+VN +++    V V   D I     +   L+ 
Sbjct: 13  IRLDKALSQLLENVSRNQIQKSIKSSCVQVNDVIISDPDVLVKENDVILFSFKEPEELKI 72

Query: 70  A----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVIS 110
           A          E   L + +K  G+           T+ + L              R   
Sbjct: 73  AAANIALDIIYEDDDLIVINKAAGMTVHPGAGHHDDTLVNALLYHTKNLSDIGSSERPGI 132

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV--------------- 153
           V RLD NT GL+++  +     +L       Q +R Y+    G +               
Sbjct: 133 VHRLDKNTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALVWGVINPLEGVIKNNIGRSR 192

Query: 154 -DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            D+ K+ +LK G    G        TL+    G+ + V   L  G+  +I+         
Sbjct: 193 SDRQKMTILKYG----GKEAVTHYKTLELFYSGTISMVECKLSTGRTHQIRVQLSHLKHS 248

Query: 212 VN 213
           V 
Sbjct: 249 VV 250


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 92/247 (37%), Gaps = 55/247 (22%)

Query: 6   IVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           ++ E   P+R+ +V+AR  +    SR  ++ ++ +  V+ +GI++   A  V +   I++
Sbjct: 25  VLDEGTVPERLDRVLAR--VFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCRIDL 82

Query: 63  D----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                      G  L  A   E   L +  KP GLV   +      T+ + L +      
Sbjct: 83  SVPAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAGHEDGTLVNRLIAHCGASL 142

Query: 106 ------SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQV 153
                  R   V RLD +T GLL++  ND    G  A+  +   +    R Y        
Sbjct: 143 SGIGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSGALERAYLALVWNVP 202

Query: 154 DQ----------------DKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLRE 195
           +                 +K+ +++ G   +G          D   + G  A +   L  
Sbjct: 203 EPRAGTIRANLARSRHNREKIAVVRDG---EGREAITHYRVEDVHGEGGVTALLRCHLET 259

Query: 196 GKNREIK 202
           G+  +I+
Sbjct: 260 GRTHQIR 266


>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 (173), 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  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQP-HVGQKVTAEDIVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 91/262 (34%), Gaps = 46/262 (17%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----R 49
           M DK  ++     +    R+ +V A    A  SR  +   I   R+ V+G ++       
Sbjct: 1   MSDKIELRAEVPSELGGQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 59

Query: 50  AAVNVMSTDHIEVDGVPLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
               +  T   E  G  + +        E   + + +KP GLV      H+D    + + 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIELDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALL 119

Query: 99  DNLPSIF--SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV- 153
            ++P I    R   V RLD +T GL+++  T       V +L S    R+Y     G V 
Sbjct: 120 HHIPDIINVPRCGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVV 179

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +    V++G         +  +  S+  V V L  G+  +I+
Sbjct: 180 AGGKINAPIGRHGQQRQRMA---VMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIR 236

Query: 203 KVFEFFNWKVN----RLIRISY 220
                 N+ +        R   
Sbjct: 237 VHMAHINFPLVGDPAYGGRFRI 258


>gi|290968210|ref|ZP_06559753.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
 gi|290781692|gb|EFD94277.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
          Length = 305

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 82/251 (32%), Gaps = 38/251 (15%)

Query: 1   MKDKNIVQEN-FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+ K           R+   +AR    SR   + +I +  V+V   + + A   +     
Sbjct: 1   MEQKTWQSTPADEGVRLDVYVARMLSVSRTYAQDLIKKGLVRVQDNMGK-ANCRLEDGQC 59

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I V            + +PL    E   + + +K  G+V   +  +   T+ + L     
Sbjct: 60  ITVSFSPSAVLSAEPENIPLHILYEDAHIIVVNKARGMVVHPAPGNPSGTLVNALLYHCG 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVD 154
                     R   V RLD +T G++++       R L          R Y    HG + 
Sbjct: 120 GELSGINGVIRPGIVHRLDKDTSGVMVVAKTDPAHRGLAAQIKAHTAHRTYWALVHGNIA 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +++            + +K  +  +G         +  + G   W+   L  G+  +I+ 
Sbjct: 180 EERGTIEAPIGRHPKDRIKMAVTFKGGREATTHFHVLQRYGEYTWLACRLETGRTHQIRV 239

Query: 204 VFEFFNWKVNR 214
              +    V  
Sbjct: 240 HLAYIRHPVVN 250


>gi|109897660|ref|YP_660915.1| RluA family pseudouridine synthase [Pseudoalteromonas atlantica
           T6c]
 gi|109699941|gb|ABG39861.1| ribosomal large subunit pseudouridine synthase D [Pseudoalteromonas
           atlantica T6c]
          Length = 327

 Score = 71.0 bits (173), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 86/229 (37%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V +    +R+ + +A      SR  ++  I   +V V+G ++ +    ++  + IE+D 
Sbjct: 13  VVPQTLLGKRLDQALAEMFPDYSRSRIKDWILADQVAVDGQIVNKPREKLLGEELIEIDA 72

Query: 64  GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
            + +++             E   + + +KP  LV      +   T+ + L S    + S 
Sbjct: 73  SIEIQERHSAQEIELNIVYEDEHILVINKPTNLVVHPGAGNASGTILNALLSHVPEIASV 132

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
                V RLD +T GL+++         L  +L + +  R Y    +G           +
Sbjct: 133 PRAGIVHRLDKDTTGLMVVAKTIPAQTHLVEKLQAREISREYEAVVYGNLIAGGSVDEPI 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +V  G         +  +  ++  + + L  G+  +I+
Sbjct: 193 GRHPTKRTSMAVVQSGKPALTH-YRVKHKYRAHTHLRLKLESGRTHQIR 240


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 66/178 (37%), Gaps = 27/178 (15%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E     R+ + +A      SR  ++++I + RV V G   E+    +   D++ +  
Sbjct: 23  TVMEEQEGMRLDQFLAGELKEHSRSYIQKLIKEGRVTV-GDKKEKPGCRLKVEDNVVICV 81

Query: 65  VPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPS 103
            PL++              E   + L +KP  +V          T+         DNL  
Sbjct: 82  PPLKELEVLPEKMDLDIIYEDEDVILINKPKDMVVHPCPGRYTGTLVNGLLYHCRDNLSG 141

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK 157
           I   +    V R+D +T G+L++  +    + L   L      R Y    +    Q++
Sbjct: 142 INGVLRPGIVHRIDKDTTGVLVVCKNDMAHKSLAEQLKEHSITRKYEAIVYNNFTQEE 199


>gi|328955606|ref|YP_004372939.1| pseudouridine synthase, RluA family [Coriobacterium glomerans PW2]
 gi|328455930|gb|AEB07124.1| pseudouridine synthase, RluA family [Coriobacterium glomerans PW2]
          Length = 350

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 76/243 (31%), Gaps = 46/243 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V      QR+   +       +R    R+I +  V V+G +    +  V+S   ++   
Sbjct: 20  VVDATEAGQRLDAYLGGRRACPTRSACARLIERGAVSVDGAMQCSKSFIVLSGQRVDLAY 79

Query: 62  --------VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                   V G P+    + E   L +  K  GLV          T+ + L         
Sbjct: 80  SEQVEAAVVAGEPIPLDIRFEDEYLIVLSKQRGLVCHPGHGHDSGTLANALVHHCGIDHL 139

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
                  R   V RLD +T GL+L   D    R L   +      R Y    HG + +D 
Sbjct: 140 GTLQGEDRPGIVHRLDRDTSGLMLAAKDDATQRALQDLIRLRTLDRRYIALVHGVIARDA 199

Query: 158 -----------LNLLKKGIVIQGICYGDMQ-----VTLDTQKGSN--AWVTVGLREGKNR 199
                       + LK  +         +         D  +G      +   L  G+  
Sbjct: 200 GTIDTGLARSSRDRLKMAVSDDPAARQAITTFRVLERFDAARGDEGYTLIECHLYTGRTH 259

Query: 200 EIK 202
           +I+
Sbjct: 260 QIR 262


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 82/249 (32%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V E  TP R+ K +A      SR  ++       ++VNG  ++     V   D I +
Sbjct: 21  KVQVDEGQTPVRIDKYLAEKNPYQSRNRIQNAADAGFIQVNGTPVKS-NYKVRPNDVITL 79

Query: 63  -------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF---------- 98
                        + +P+    E   L + +K  G+V      +   T+           
Sbjct: 80  MLDYPKHDTSIVAENIPIDVVYEDDDLMVINKAAGMVVHPGAGNFTGTLINAIAYYLRDL 139

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           ++  +    V  V R+D +T GLL++         L     +    R Y     G + +D
Sbjct: 140 ESFDANNPEVGLVHRIDKDTSGLLVVAKTPEAKSALGKQFFNKTTHRSYNALVWGNIVED 199

Query: 157 K-----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           +            N L+  +       G   VT   +  + G    +   L  G+  +I+
Sbjct: 200 EGRIEGNIGRDPKNRLRMKVFEPDSGIGKSAVTHYRVLERFGYTTLIECILETGRTHQIR 259

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 260 AHMKHIGHP 268


>gi|315121810|ref|YP_004062299.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter solanacearum CLso-ZC1]
 gi|313495212|gb|ADR51811.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Candidatus Liberibacter solanacearum CLso-ZC1]
          Length = 340

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 83/259 (32%), Gaps = 52/259 (20%)

Query: 6   IVQENFTPQRVSKVIA-RAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           ++  N    R+ + +A       SR  V+ +I    + +NG++    +  V+  +   +D
Sbjct: 15  LLANNEAEGRIDRWLAINLKEKFSRSYVKTLILNGAISINGVVSINPSRKVVPGESFFID 74

Query: 64  ------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                        +PL    E   + + +K  GLV   +  +   T+ + L         
Sbjct: 75  VPQLQQLNIAAENIPLDILYEDDDIIVINKQAGLVVHPAPGNWTGTLVNALLHHCNNNLS 134

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELP------STQWLRVYRVRFHGQVD 154
                 R   V RLD +T G +++  +    + L              R Y     G   
Sbjct: 135 GINGIKRPGIVHRLDKDTTGTMVVAKNDIAHQRLSEQFADHGLHMGLKRSYYAMVWGVPS 194

Query: 155 QD-----------KLNLLKKGIV-IQGICYGDMQVTLDTQKGSN-------AWVTVGLRE 195
            D           K N L++ +  I+            T +  N       + +   L  
Sbjct: 195 PDSGTINAPLGRCKSNRLRRAVKRIEDKTGDRAVTRYQTVEIYNKNSNFAASLLRCDLET 254

Query: 196 GKNREIK-KVFEFFNWKVN 213
           G+  +I+  +     + + 
Sbjct: 255 GRTHQIRVHM-AHKGYPII 272


>gi|325197923|gb|ADY93379.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis G2136]
          Length = 374

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  + R T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +   ++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLPHSYIECSLETGRTHQIR 259


>gi|225870507|ref|YP_002746454.1| RNA pseudouridylate synthase [Streptococcus equi subsp. equi 4047]
 gi|225699911|emb|CAW93829.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           equi 4047]
          Length = 300

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 32/212 (15%), Positives = 70/212 (33%), Gaps = 39/212 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHK 80
               + VNG + + A   +   D + +D                + +   E     + +K
Sbjct: 33  KGGNIWVNG-VAQNAIYLLDIGDVVAIDIPNEESFEQLTAISHDLDIVY-EDEHFLILNK 90

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           P G  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     
Sbjct: 91  PAGYASIPS-AIHSNTIANFIKAYYIKQDYPNKQVHIVTRLDRDTSGLMLFAKHGYAHAR 149

Query: 134 L--ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L  +L      + Y     G             + +   +++ + +  +G         +
Sbjct: 150 LDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGRTDDSIITRTVTPKGKYAKTSYKVI 209

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                + + V + L  G+  +I+  F    + 
Sbjct: 210 ARYPENVSLVDITLHTGRTHQIRVHFAHLGFP 241


>gi|167750591|ref|ZP_02422718.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702]
 gi|167656517|gb|EDS00647.1| hypothetical protein EUBSIR_01567 [Eubacterium siraeum DSM 15702]
          Length = 322

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 94/262 (35%), Gaps = 57/262 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+  + + N + QR+ + ++++   G     ++ ++  +  +K+NG   +    ++   
Sbjct: 1   MKEIKVTK-NDSGQRIDRFLSKSFPLGQG---QICKLARKNCIKLNGKKCK-PDTHIAEN 55

Query: 58  DHIEV---DGVPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           D I++   D + + KA                  E   + L  KP+G+V    +     T
Sbjct: 56  DIIKLFIPDEMLIPKAKSDPDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGDSDT 115

Query: 97  VFDNLPSIFSRVIS-------------VGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
           + + + S                      R+D NT G+++   +    R+L       + 
Sbjct: 116 LINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRDREL 175

Query: 142 LRVYRVRFHGQVDQDKLNL---LKKG-----IVIQGICYG-----DMQVTLDTQKGSNAW 188
            ++Y     G+V  D   L   L+K      + I             +  +    G N+ 
Sbjct: 176 TKLYLCIACGKVTPDSATLTAYLEKNSDTNTVKISDKKTKSNLTIKTKYKVIAYNGENSL 235

Query: 189 VTVGLREGKNREIKKVFEFFNW 210
           + V L  G+  +I+    +   
Sbjct: 236 LKVDLLTGRTHQIRAHLAYIGH 257


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 90/239 (37%), Gaps = 38/239 (15%)

Query: 1   MKDKNIV-QENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M +  I+ +E+   +R+   +++     SR  ++ +I + +  + G  ++ A   +   D
Sbjct: 1   MDNFEIIAEESDINKRIDVFLSKNLESFSRSYIQDLIKKGKATIGGKTIK-ANYRLREGD 59

Query: 59  HIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF------- 98
            + +            + +PL    E   + L +KP G+V   +      T+        
Sbjct: 60  IVALAIPKPEPLEILPENIPLDIVYEDNDVILVNKPKGMVVHPAAGHYSGTLVNALLYHC 119

Query: 99  -DNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
            DNL  I   +    V R+D++T G++++  +    + +   L      R Y     G +
Sbjct: 120 KDNLSGINGVLRPGIVHRIDMDTTGIIIVCKNDNAHQHIAKQLAEHSITRKYVAIVSGNI 179

Query: 154 DQDK----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D+           N  KK  V +          +  +  +  ++   L  G+  +I+
Sbjct: 180 KEDEGVVDAAIARSKNDRKKMTVDKDGKRAVTHFKVLERLNNYTYIECVLETGRTHQIR 238


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 79/224 (35%), Gaps = 36/224 (16%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            R+ K+ A   G  SR  ++  I + ++ VNG +++     V   D + ++ V       
Sbjct: 55  IRLDKLCADIFGGFSRANLKNFIDEGQLTVNGKVVK-PKYAVKVGDILTLEAVHESHSED 113

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
                      E   + + +KP G+V      +   T+ + L   F +         V R
Sbjct: 114 LPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLPRAGLVHR 173

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKL 158
           +D +T GLL++  T    L+ + +L      R Y               +    + +   
Sbjct: 174 IDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDAPIGRHST 233

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  K  +   G       V         + + + L+ G+  +I+
Sbjct: 234 HRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIR 277


>gi|72080790|ref|YP_287848.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 289

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 87/238 (36%), Gaps = 39/238 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA- 70
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I++  D    +   
Sbjct: 1   MRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 60

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISV 111
                      +   + L +KP  LV      + ++T+ + L S F         R   V
Sbjct: 61  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 120

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            RLD +T GLLL+  +         EL + Q  R Y+    G            + +D  
Sbjct: 121 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 180

Query: 159 NLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I           V L      Q    + V   L  G+  +I+       + +
Sbjct: 181 NPLKKTISFFNSKPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 238


>gi|169349798|ref|ZP_02866736.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552]
 gi|169293366|gb|EDS75499.1| hypothetical protein CLOSPI_00536 [Clostridium spiroforme DSM 1552]
          Length = 278

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 79/198 (39%), Gaps = 24/198 (12%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA------ERTRLWLYHKPI 82
           + V+ ++  + V VN  ++ +    +   D + V+     K       E   L + +KP 
Sbjct: 23  KNVKNLLKYKLVMVNENVISQFDFPLKIGDVVIVNKKEDNKHNLEIIYEDKELIVINKPS 82

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           GL++     +   T +  +           +V  + RLD +T G+L+   +  +   L+ 
Sbjct: 83  GLLSISGGNEKEKTAYHLVGEYLKNKNKKAKVFVIHRLDKDTSGVLMFAKNEEIKNKLQN 142

Query: 137 PSTQWL--RVYRVRFHGQVDQ------DKLNLLK-KGIVIQGICYGDMQVT---LDTQKG 184
              + +  R Y     G++ +      + L+  K + + I     G + +T   +  +  
Sbjct: 143 NWNKIVYKRGYLAIIEGRLKEKSGTIKNYLDESKTQMVYITNNKKGKLAITNYRVLKETK 202

Query: 185 SNAWVTVGLREGKNREIK 202
            N+ V + L  G+  +I+
Sbjct: 203 YNSLVEIFLDTGRKNQIR 220


>gi|291557011|emb|CBL34128.1| pseudouridine synthase, RluA family [Eubacterium siraeum V10Sc8a]
          Length = 322

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 94/262 (35%), Gaps = 57/262 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA---GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+  + + N + QR+ + ++++   G     ++ ++  +  +K+NG   +    ++   
Sbjct: 1   MKEIKVTK-NDSGQRIDRFLSKSFPLGQG---QICKLARKNCIKLNGKKCK-PDTHIAEN 55

Query: 58  DHIEV---DGVPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           D I++   D + + KA                  E   + L  KP+G+V    +     T
Sbjct: 56  DIIKLFIPDEMLIPKAKSDPDDFTAVSDKIDIVYEDENILLVDKPVGMVVHEDESGDSDT 115

Query: 97  VFDNLPSIFSRVIS-------------VGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
           + + + S                      R+D NT G+++   +    R+L       + 
Sbjct: 116 LINRIKSYLYHKGEYRPENELSFAPALCNRIDRNTCGIVIAAKNAESLRILNQKIRDREL 175

Query: 142 LRVYRVRFHGQVDQDKLNL---LKKG-----IVIQGICYG-----DMQVTLDTQKGSNAW 188
            ++Y     G+V  D   L   L+K      + I             +  +    G N+ 
Sbjct: 176 TKLYLCIACGKVTPDSATLTAYLEKNSDTNTVKISDKKTKSNLTIKTKYKVIAYNGENSL 235

Query: 189 VTVGLREGKNREIKKVFEFFNW 210
           + V L  G+  +I+    +   
Sbjct: 236 LKVDLLTGRTHQIRAHLAYIGH 257


>gi|149003786|ref|ZP_01828618.1| phosphotransacetylase [Streptococcus pneumoniae SP14-BS69]
 gi|237650771|ref|ZP_04525023.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974]
 gi|237822358|ref|ZP_04598203.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974M2]
 gi|147758232|gb|EDK65234.1| phosphotransacetylase [Streptococcus pneumoniae SP14-BS69]
 gi|301794215|emb|CBW36634.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV104]
 gi|332075432|gb|EGI85901.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41301]
 gi|332202956|gb|EGJ17024.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47901]
          Length = 298

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D++ +D     G      +        E     + +KP
Sbjct: 33  RGGAILVNNQP-QNATYLLDVGDYVTIDIPAEEGFETLEAIEHPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKIVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVYIHLHTGRTHQIRVHFSHIGFP 240


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 79/246 (32%), Gaps = 54/246 (21%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ K +  R   +SR  +++      + VNG  ++     V   D I +         
Sbjct: 45  PVRIDKFLFERMQHSSRNRIQKAADAGFIHVNGAPVKS-NYKVRPEDTITLMLDRPKHDN 103

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
               + +PL    E   L + +KP GLV      +   T+ + +      + S       
Sbjct: 104 TIEAEDIPLDIVYEDNALMVVNKPAGLVVHPGAGNFHGTLINAIAWHLKDLPSFDPNDPE 163

Query: 111 ---VGRLDINTEGLLLL--TNDGG------LARVLELPSTQWLRVYRVRFHGQVDQDK-- 157
              V R+D +T GLL++  T D                     R Y     G +  D+  
Sbjct: 164 VGLVHRIDKDTSGLLVIAKTPDAKTILGKQFFNKTTH------RSYNALVWGNLTADEGR 217

Query: 158 ---------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVF 205
                     + L+  +       G   VT   +  + G    +   L  G+  +I+   
Sbjct: 218 IEGNIARDPKDRLRMTVFPPDSEIGKPAVTHYRVLERFGYTTLIECVLETGRTHQIRAHM 277

Query: 206 EFFNWK 211
           +     
Sbjct: 278 KHIGHP 283


>gi|1143378|dbj|BAA09443.1| ORFX [Zymomonas mobilis]
          Length = 317

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 86/240 (35%), Gaps = 42/240 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDH 59
           ++  + E     R+ + +A      SR  ++ +I+   V  N  G L+   A  + S D 
Sbjct: 4   EQVTLTEEMIGWRLDRALASLITRLSRERLKNLISSGCVS-NSQGALVRDPAFKIKSLDC 62

Query: 60  IEVDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSI 104
             VD +PL +               E   L + +KP G+V   +  +  +T+ +  L   
Sbjct: 63  FTVD-IPLPRPAHNEPQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLYHC 121

Query: 105 FSRVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-- 151
             ++  +G         R+D +T GLL++  T+        +       R YR    G  
Sbjct: 122 AGKLSGIGGVARPGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHSINRRYRAIVDGNP 181

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
                    + +  +N  K  IV  G     +          N + +   L  G+  +++
Sbjct: 182 SLQGHVDAPLARSSVNRQKMAIVSDGRGKRAVTHYCMITPLKNASLIECRLETGRTHQVR 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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 76/229 (33%), Gaps = 33/229 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+ + +A      SR  ++  I    V VNG  +      V+ ++ + ++ 
Sbjct: 10  TVAESQIGQRLDQALAELFPDYSRSRIKEWILADCVLVNGKKINTPKGRVLGSESVTINA 69

Query: 65  V------------PLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                        PL    E   + + +KP GLV      +   T+ + L   +      
Sbjct: 70  EIKENVRSIPQQIPLNIVYEDNDILVINKPRGLVVHPGAGNADGTILNALLHYYPAISNV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQV 153
            R   + RLD +T GL+++         L   L + +  R Y                 +
Sbjct: 130 PRAGIIHRLDKDTTGLMVVAKTVPAQTHLVEALQARKITREYEAIAIGNMIAGGAVEEPI 189

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +         +   G         ++  +     + + L  G+  +I+
Sbjct: 190 ARHASKRTHMAVHPMGKPAVTHYRIMEHFRAHTH-LRLRLETGRTHQIR 237


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 40/81 (49%), Gaps = 2/81 (2%)

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--NAWVTVGLREGKNREIKKVFE 206
             G V++  L  +  G +IQG+      V L  +K       + + + EG+N E++++ +
Sbjct: 205 IDGAVNKRHLIAISGGTIIQGVHCTPDSVELLPRKPDLLRPRLRIVVHEGRNHEVRELVK 264

Query: 207 FFNWKVNRLIRISYGPFQLGT 227
               +V+ L R+  G ++L +
Sbjct: 265 NAGLEVHSLKRVRIGGYRLPS 285



 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 30/49 (61%), Gaps = 2/49 (4%)

Query: 4   KNIVQENF--TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA 50
           +    ENF   PQR+SKV+A +G+ASRR  E +I Q +V VNG +    
Sbjct: 139 RRFYNENFREPPQRLSKVLAASGVASRRNSEELIFQGKVTVNGSVCNTP 187


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 83/237 (35%), Gaps = 40/237 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M     V E+   +R+ KVI        +     + R I +  V+V+G      +V +  
Sbjct: 1   MSYTFKVSEHHAGRRLDKVIRTLWPNLPLG---AMMRGIRKGLVRVDGRK-TSCSVRLED 56

Query: 57  TDHIEV----------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
              + V                 G      +   + + +K  GL+    D  G  ++ + 
Sbjct: 57  GQSVYVPWEEPELIEKSVKTKRTGALSIVYKDHYIMVLNKEAGLIIQP-DQSGEESLIER 115

Query: 101 L-----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-- 151
           +     P    R  +V RLD NT GL+++   G   R L+         + Y V   G  
Sbjct: 116 VWLEVEPEGDFRACAVHRLDRNTTGLVVVALHGQSLRELQRAFRDNDVDKTYLVAVRGQT 175

Query: 152 QVDQDKLNLLKK----GIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
            ++ D    L+K     IV             +   G +  + + V L  G++ +I+
Sbjct: 176 PLEGDITAPLQKDRDHNIVTASPDGLPAHTHYEKIAGDDECSLLKVSLLTGRSHQIR 232


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 84/244 (34%), Gaps = 40/244 (16%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
            EN   +R+ K +      A+R  V+++I    V++ G  + ++   +  T+ I V+   
Sbjct: 12  NENDKGKRIDKFLNELIDDATRSYVQKIIDNGLVEIQGKKITKSGNKLKGTEIIVVNIPE 71

Query: 64  ---------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------- 106
                     +PL    E + + + +K   LV   +  +   T+ + L            
Sbjct: 72  DEVLDLTPEDIPLDIIYEDSDIVVINKAPNLVVHPAHGNYSGTLVNALLYHIKDLSTING 131

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD------ 156
             R   V RLD +T G++++  +      L          ++Y     G   +       
Sbjct: 132 VIRPGIVHRLDKDTSGVIVVAKNDEAHGKLSEMFKEKTLEKIYVCIAKGIFKEKSGRIKT 191

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                      +   +V +          +  +  +++ V V +  G+  +I+   +  N
Sbjct: 192 LIGRDSRDRKKMA--VVNENGKIAISNYEVIDEGKNHSLVKVRIETGRTHQIRVHMKHLN 249

Query: 210 WKVN 213
             + 
Sbjct: 250 HPIM 253


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 86/257 (33%), Gaps = 51/257 (19%)

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------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+              +PL    E   L +  KP GLV   +    + T+ + L +    
Sbjct: 79  ELAVPPAKEAVPVAQDLPLNIVYEDAGLVVLDKPAGLVVHPAAGHAQGTLVNALMAHCGE 138

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRVRFHG 151
                    R   V RLD +T GLL+      + + L         +   +R Y     G
Sbjct: 139 SLSGIGGVKRPGIVHRLDKDTSGLLVAAKTDAVHQGLARLFADHGQNLHLVREYLAFVWG 198

Query: 152 QVDQD-----------KLNLLKKGIVIQGI------CYGDMQVTLDTQKGSNAWVTVGLR 194
              +              +  ++ +V + +       +  ++V     K   + +   L 
Sbjct: 199 VPARQSGRIEAALGRHAQDRERQAVVSEDVGRHAVTHWEVLEVFQRKGKPVASLIACQLE 258

Query: 195 EGKNREIKKVFEFFNWK 211
            G+  +I+         
Sbjct: 259 TGRTHQIRVHMAHIGHP 275


>gi|260887212|ref|ZP_05898475.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
 gi|260863274|gb|EEX77774.1| ribosomal large subunit pseudouridine synthase D [Selenomonas
           sputigena ATCC 35185]
          Length = 287

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/266 (17%), Positives = 94/266 (35%), Gaps = 43/266 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----------HIEVDGVPLR-KAERTRLWLYHK 80
           +++       +NG+    A + + S D           I  + +PL    E   L + +K
Sbjct: 19  KKLRRSGTFSLNGLPANAARIRIKSGDELCWHLAEESRIAPEDIPLEILYEDAALLIVNK 78

Query: 81  PIGLVTTHSDPDGRST----VFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134
           P G++   +  + R T    V  +  +   +     V RLD  T GL+L+  +  +   L
Sbjct: 79  PAGMLVHPTGGEYRHTLANAVLFHYEAHGEKHAFHPVHRLDRQTSGLVLIAKEAHVQH-L 137

Query: 135 ELPSTQWLRVYRVRFHGQVDQ-----DKLNLLKKGIVIQ------GICYGDMQVTLDTQK 183
                   R+Y     G++ +     D     + G +I+      G C      TL  ++
Sbjct: 138 LSAHNAIERIYLAVIEGKLPEPCGTIDAPIARRPGSIIERMVSPAGKCAVTHYATL-AER 196

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL-- 241
           G  + + + L  G+  +I+         +               L  G T  ++++ L  
Sbjct: 197 GGLSLLALRLATGRTHQIRVHLAHLAHPLLG-----------DDLYGGRTDRIARQALHA 245

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETL 267
                 H +   ++ + AP  +  + 
Sbjct: 246 HRLRFRHPISGKEITVHAPFPADMSA 271


>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 = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 92/245 (37%), Gaps = 51/245 (20%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           ++ E   P+R+ +V+AR     SR  ++ ++ +  V+ +GI++   A  V +   I++  
Sbjct: 12  VLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGSRIDLSV 71

Query: 64  ---------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  L  A   E   L +  KP GLV   +      T+ + L +        
Sbjct: 72  PAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAGHEDGTLVNRLIAHCGVSLSG 131

Query: 106 ----SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQVDQ 155
                R   V RLD +T GLL++  ND    G  A+  +   +    R Y        + 
Sbjct: 132 IGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSGALERAYLALVWNVPEP 191

Query: 156 ----------------DKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGK 197
                           +K+ ++++G   +G          D   + G  A +   L  G+
Sbjct: 192 RAGTIRANLARSRHNREKIAVVREG---EGREAITHYRVEDVHGEGGVTALLRCHLETGR 248

Query: 198 NREIK 202
             +I+
Sbjct: 249 THQIR 253


>gi|255657995|ref|ZP_05403404.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
 gi|260850197|gb|EEX70204.1| ribosomal large subunit pseudouridine synthase D [Mitsuokella
           multacida DSM 20544]
          Length = 296

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 88/259 (33%), Gaps = 49/259 (18%)

Query: 41  KVNGILLERAAVNVMSTDHIEVD----------GVPLR-KAERTRLWLYHKPIGLVTTHS 89
           +V GIL   A   V + D I  D           +PL  + E   L + +KP G +   +
Sbjct: 42  RVGGILCNAARTEVRTGDIITFDIVRPSDIEPEDLPLDIRYEDDYLLIVNKPAGQLVHPT 101

Query: 90  DPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
             +   T+ + +   +           V RLD NT GL+L+     +   L  P     +
Sbjct: 102 TKEAHGTLGNAVLYWYKAHGEHHAYHPVHRLDRNTSGLVLIAKVPQVQYKLT-PRHGEGK 160

Query: 144 ----VYRVRFHGQVD--QDKLNL----------LKKGIVIQGICYGDMQVTLDTQKGSNA 187
                Y     G++   +  ++           L+K +   G        T+ T  G  +
Sbjct: 161 LFHREYLALIEGELTPPEGLIDAPIARALPSIILRK-VSPDGQTARTHYDTVQT-DGKLS 218

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--EQL 245
            + + L  G+  +I+         +               L  G+   + ++ L      
Sbjct: 219 LIHLVLDTGRTHQIRVHLAHLGHPLLG-----------DDLYGGNLARIKRQALHAARLH 267

Query: 246 GPHLLEEAQVNLDAPIYSS 264
             H +  A++++  P+ S 
Sbjct: 268 FRHPMTGAEIDVQVPLPSD 286


>gi|71893806|ref|YP_279252.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 289

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 87/238 (36%), Gaps = 39/238 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA- 70
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I++  D    +   
Sbjct: 1   MRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 60

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISV 111
                      +   + L +KP  LV      + ++T+ + L S F         R   V
Sbjct: 61  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 120

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            RLD +T GLLL+  +         EL + Q  R Y+    G            + +D  
Sbjct: 121 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 180

Query: 159 NLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I           V L      Q    + V   L  G+  +I+       + +
Sbjct: 181 NPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 238


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 72/247 (29%), Gaps = 46/247 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A A G  SR  V+ +I    V  +G      +  + +     V           
Sbjct: 37  RLDRFLAAAIGTLSRSRVKALIEAGHVTRDGQPAGDPSEAIRTGATYVVAPPAAQPATPQ 96

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----------FSRVIS 110
              +PL    E   L +  KP GLV   +  +   T+ + L +             R   
Sbjct: 97  AQDIPLTILFEDRHLIVLDKPAGLVVHPAPGNQDGTLVNALLAHAGEELTGIGGEKRPGI 156

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQD----------- 156
           V RLD +T G++++     +A         S    R Y     G                
Sbjct: 157 VHRLDKDTSGVMVVAKS-EVAHTALSAAFASRDLERAYLALAWGVPAPASGEVDAPVGRH 215

Query: 157 --KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV-- 212
                 +   +   G        T      S A +   L  G+  +I+         +  
Sbjct: 216 PTDRKRMAV-VARNGKHALTRYATERAWGTSCALLRCRLATGRTHQIRVHMAHIGHPLVG 274

Query: 213 --NRLIR 217
               L R
Sbjct: 275 DPVYLRR 281


>gi|153840388|ref|ZP_01993055.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|260361363|ref|ZP_05774428.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus K5030]
 gi|260876822|ref|ZP_05889177.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|260895884|ref|ZP_05904380.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|260900382|ref|ZP_05908777.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|149745949|gb|EDM57079.1| RNA pseudouridine synthase family protein [Vibrio parahaemolyticus
           AQ3810]
 gi|308089361|gb|EFO39056.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus Peru-466]
 gi|308091361|gb|EFO41056.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AN-5034]
 gi|308108565|gb|EFO46105.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus AQ4037]
 gi|308113659|gb|EFO51199.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus K5030]
          Length = 255

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 52/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
            A+     V V             L E     G+  ++++        + 
Sbjct: 140 TAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIV 189


>gi|33519652|ref|NP_878484.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Candidatus Blochmannia floridanus]
 gi|34395754|sp|P59838|RLUD_BLOFL RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|33517315|emb|CAD83700.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Candidatus Blochmannia floridanus]
          Length = 321

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 37/225 (16%), Positives = 81/225 (36%), Gaps = 37/225 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---VDGVPLRKA 70
           R+  ++++     SR +++  I  ++V VN  +       V+  + IE   ++   + K+
Sbjct: 17  RLDYILSKLLPQYSRSQIKHWILNKKVVVNNQVSTLPRKKVVYGELIEIKYINNNDICKS 76

Query: 71  ERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------I 109
           E                 + + +K   +V        + TV + L   +  +        
Sbjct: 77  EDIVPQNIPLNIIYEDNDILVINKASNMVVHPGIGHYQGTVLNALLYRYPSILKISKQAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRF-------HGQVDQDKLNL 160
            V RLD +T GL+++         L       + ++ Y            G V+Q     
Sbjct: 137 IVQRLDKDTTGLMIIAKTVSAYDNLLRSFKLRKVVKEYDAIVYGKFTSNAGVVNQPMRRH 196

Query: 161 LKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
             K   +     G   VT   +  +  +++ V + L+ G+  +I+
Sbjct: 197 FAKRTFMSVHYTGKSAVTYYSVVEEFKAHSRVRINLKTGRTHQIR 241


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 80/241 (33%), Gaps = 37/241 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +    +RV   +AR    SR     +     V VNG+   ++   + + D IEV    
Sbjct: 4   VPDALVGERVDAALARMLGLSRSRCAELAGDGHVLVNGVAAGKSD-RLGALDIIEVTIPE 62

Query: 63  -DGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
            +  P    +   L+      +  KP+G+           TV  NL +   R+ S     
Sbjct: 63  PESKPTPVTDMAILYDDEDIVVVDKPVGVAAHTGPGWEGPTVLGNLEAAGYRITSYGPPE 122

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL----- 158
               V RLD+ T G +++     LA  +   + +     +VY     G +D         
Sbjct: 123 RQGIVHRLDVGTSGAMMVAKS-ELAYTVMKRAFKERTIEKVYHAVVAGHLDPASGTIDAP 181

Query: 159 ------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                    +  ++  G        TL+   G+     V L  G+  +I+          
Sbjct: 182 IGRHPSREWRMAVIDGGKRAVTHYDTLELMAGAQLT-EVHLETGRTHQIRVHMAAVGHPC 240

Query: 213 N 213
            
Sbjct: 241 V 241


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 81/236 (34%), Gaps = 36/236 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLE---------RAA 51
           +++ +V  +    R+   ++     SR  ++R+I    VKV  G  ++            
Sbjct: 32  EEEILVPPDMDGVRLDAFLSDFLGVSRTFIQRVIRDGYVKVFQGKRVKPSRSVLAGESLR 91

Query: 52  VNVMSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
             +     +++   P+      E   + +  KP G+V   +    R T+   L   +  +
Sbjct: 92  FKLPPPQRMDLVPEPVDFSVVYEDEDIIVVDKPAGVVVHPAPGHWRGTLVHGLLYRYPDI 151

Query: 109 ---------ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
                      V RLD  T GLL +  +      L+      +  + Y     G+V  ++
Sbjct: 152 GTINDVVRPGIVHRLDSTTSGLLAVARNTESLNELQSSFRDRKVGKFYLALSDGRVVGEE 211

Query: 158 L-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +           N  +  +   G       V     +G  +++   L  G+  +I+
Sbjct: 212 ISLDAPIGRDRNNRYRMTVTDDGKNART-DVYPLWNRGRYSFLICELHSGRTHQIR 266


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 82/244 (33%), Gaps = 49/244 (20%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  + I+    T      R+ + +A+     SR  ++  I    VKVNG ++ +A   V 
Sbjct: 1   MTQQKILTAEITADLLGARLDQALAQLFPDYSRSRIKVWIESDLVKVNGNIVNKAREKVF 60

Query: 56  STDHI------------EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + +            E   +PL    E   + + +KP  LV      +   TV + L 
Sbjct: 61  GGETVEITAEIEEEIRFEPQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALL 120

Query: 103 SIF------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
             +       R   V RLD +T GL+++  +      L   L   +  R Y     G + 
Sbjct: 121 HYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMT 180

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKN 198
           Q        G V + +     + T                      +   + + L  G+ 
Sbjct: 181 QG-------GKVDEPMARHPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRT 233

Query: 199 REIK 202
            +I+
Sbjct: 234 HQIR 237


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 88/244 (36%), Gaps = 40/244 (16%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +V       R+ K ++ A  G+ SR  +++++  + V+V+   ++  +  + + + IE +
Sbjct: 1   MVPAEAQGVRIDKFLSEACDGL-SRSYLQKLLKSELVEVDKRTVKN-SYKLSAGEKIEFE 58

Query: 64  ------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                        +PL    E + + L +KP G+V   +      T+ + L         
Sbjct: 59  VPEAAEPEIKAEDIPLDIIYEDSDIILVNKPKGMVVHPAAGHYSQTLVNGLMYHCRDGLS 118

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK- 157
                 R   V R+D++T G+L++  +      +   L      R Y    HG + +D+ 
Sbjct: 119 GINGVLRPGIVHRIDMDTTGVLIVCKNDFAHNAIAEQLKVHSITRKYFAIVHGVIQEDEG 178

Query: 158 ----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                     ++  K  I  +          +  +     +V   L  G+  +I+     
Sbjct: 179 TVDAPIGRHPVDRKKMSINRKNGKEAVTHYRVLERFRQFTYVECQLETGRTHQIRVHMAS 238

Query: 208 FNWK 211
               
Sbjct: 239 IGHP 242


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 58/332 (17%), Positives = 107/332 (32%), Gaps = 72/332 (21%)

Query: 13  PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           P R+ K ++R        SR  + R+I +  V V+G ++      V+    + +      
Sbjct: 15  PPRLDKALSRDVPETAALSRTRLARLITEGAVSVDGQVVTDPKARVVEGAQVAIALTEAE 74

Query: 63  ------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
                 + +PL    E   L +  KP G+V   +      T+ + L +            
Sbjct: 75  ESHIAPEAIPLVVVYEDDDLIVIDKPAGMVVHPAPGTPSGTLVNALLAHCGDNLSGVGGV 134

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------ 157
            R   V R+D +T GLL++         L          R Y    +G  D         
Sbjct: 135 KRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQFAAHSAERHYTALCYGVPDGSDPRLRGV 194

Query: 158 ---------LNLL------------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---L 193
                    +  L            ++ +V  G  +   +  +    G  A V++    L
Sbjct: 195 KGASFEPGNILRLTTQLTRHPTDRQRQAVVFHGGRHAVTRARVVESFGQPAAVSLIDCWL 254

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-EQLGPHLLEE 252
             G+  +I+         +            LG  + G  R++S + L  E +       
Sbjct: 255 ETGRTHQIRVHMAHAGHGL------------LGDPVYGGRRKLSPRALSPEAVDAIGAFP 302

Query: 253 AQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
            Q    A +     L  ++ +  + +PDD  R
Sbjct: 303 RQALHAAVLGFEHPLSGEKLSFSAPLPDDLER 334


>gi|294141810|ref|YP_003557788.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
 gi|293328279|dbj|BAJ03010.1| ribosomal large subunit pseudouridine synthase family protein
           [Shewanella violacea DSS12]
          Length = 287

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 66/177 (37%), Gaps = 21/177 (11%)

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
            A  V + + I  DG         +  +++KP G++   S     +T+     +  S   
Sbjct: 79  LAHKVDAAELI-FDG--------GQYSIWYKPYGMLCQGSKWGDHTTINRYAETHLSPDR 129

Query: 110 S---VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
               + RLD    GL+L+ +       L          + Y+V   GQ +  +   +  G
Sbjct: 130 PAFIIHRLDRAATGLVLIGHSKKTTAALAKLFELRLLDKYYQVIVEGQFNLGQQESVTIG 189

Query: 165 IVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN--RLI 216
             + G   C     +  D ++G  + V V +  G+  +I+  + E   + V   RL 
Sbjct: 190 TDVDGKAACSHAKLLQYDAERG-RSLVQVKIESGRKHQIRIHM-ESIGYPVVGDRLH 244


>gi|254229488|ref|ZP_04922902.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262393515|ref|YP_003285369.1| tRNA pseudouridine synthase C [Vibrio sp. Ex25]
 gi|151937953|gb|EDN56797.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262337109|gb|ACY50904.1| tRNA pseudouridine synthase C [Vibrio sp. Ex25]
          Length = 256

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 57/193 (29%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
                 A V V             L E     G+  ++++        +           
Sbjct: 140 TEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLRRHMAHLRHPIVGDTTHGDGKH 199

Query: 214 -RLIRISYGPFQL 225
            +L R  +   +L
Sbjct: 200 NKLYRTEFDSHRL 212


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 37/247 (14%), Positives = 87/247 (35%), Gaps = 36/247 (14%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M ++  +Q +   +    R+ +V+A+     SR  ++  I   ++ V+G +       ++
Sbjct: 1   MSEQISLQADVPTELGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPREKLL 60

Query: 56  STDHIEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + + V             D       E   + + +KP+GLV      +   TV + L 
Sbjct: 61  GGEVVSVETTIEAPREYEAQDIKLNIVYEDDDILVINKPMGLVVHPGAGNPNGTVLNALL 120

Query: 103 SIFSRVI------SVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQV 153
             +  +I       V RLD +T GL+++         L         + R Y    +G +
Sbjct: 121 HYYPEIINVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEALCNGTM 180

Query: 154 D-----QDKLNLL---KKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKV 204
                 +  +      +  + +  +    +    +  +  ++  + + L  G+  +I+  
Sbjct: 181 TAGGMVEKAIGRHPTQRTHMAVHELGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIRVH 240

Query: 205 FEFFNWK 211
               N  
Sbjct: 241 MAHLNHP 247


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 90/248 (36%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K ++       RV  V+++  +  SR  +   +    + VN   ++R +  V+S D 
Sbjct: 1   MANKILIHITDQAGRVDAVLSKENLSYSRTTLSNWLVDGTILVNNHKVKR-SYKVVSGDT 59

Query: 60  IEV------------DGVPLRKAERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +            + +PL          + +KP G+V   +      T+ + L     
Sbjct: 60  ISITPPETQETKIEAENIPLDIIYEDDDIIVVNKPQGMVVHPAAGHSSGTLVNALLHHSP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   L S +  RVY     G+  +D
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDKAHHSLSEQLKSHKNQRVYYALVRGEFTED 179

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      K++  K+ + I+G         +  +      + V L  G+  +I+   
Sbjct: 180 SGTIEAPIGRHKIDRKKQAV-IEGGREAVTHFRVLKRYVGYTLLKVNLETGRTHQIRVHM 238

Query: 206 EFFNWKVN 213
            +    V 
Sbjct: 239 SYIGHPVV 246


>gi|28899096|ref|NP_798701.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus RIMD
           2210633]
 gi|34582398|sp|Q87MD4|TRUC_VIBPA RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|28807320|dbj|BAC60585.1| pseudouridine synthase Rlu family protein [Vibrio parahaemolyticus
           RIMD 2210633]
          Length = 246

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 52/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 11  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 70

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 71  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 130

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
            A+     V V             L E     G+  ++++        + 
Sbjct: 131 TAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIV 180


>gi|330839025|ref|YP_004413605.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
 gi|329746789|gb|AEC00146.1| pseudouridine synthase, RluA family [Selenomonas sputigena ATCC
           35185]
          Length = 301

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/266 (17%), Positives = 94/266 (35%), Gaps = 43/266 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----------HIEVDGVPLR-KAERTRLWLYHK 80
           +++       +NG+    A + + S D           I  + +PL    E   L + +K
Sbjct: 33  KKLRRSGTFSLNGLPANAARIRIKSGDELCWHLAEESRIAPEDIPLEILYEDAALLIVNK 92

Query: 81  PIGLVTTHSDPDGRST----VFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL 134
           P G++   +  + R T    V  +  +   +     V RLD  T GL+L+  +  +   L
Sbjct: 93  PAGMLVHPTGGEYRHTLANAVLFHYEAHGEKHAFHPVHRLDRQTSGLVLIAKEAHVQH-L 151

Query: 135 ELPSTQWLRVYRVRFHGQVDQ-----DKLNLLKKGIVIQ------GICYGDMQVTLDTQK 183
                   R+Y     G++ +     D     + G +I+      G C      TL  ++
Sbjct: 152 LSAHNAIERIYLAVIEGKLPEPCGTIDAPIARRPGSIIERMVSPAGKCAVTHYATL-AER 210

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL-- 241
           G  + + + L  G+  +I+         +               L  G T  ++++ L  
Sbjct: 211 GGLSLLALRLATGRTHQIRVHLAHLAHPLLG-----------DDLYGGRTDRIARQALHA 259

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETL 267
                 H +   ++ + AP  +  + 
Sbjct: 260 HRLRFRHPISGKEITVHAPFPADMSA 285


>gi|328774056|gb|EGF84093.1| hypothetical protein BATDEDRAFT_8379 [Batrachochytrium
           dendrobatidis JAM81]
          Length = 379

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/196 (18%), Positives = 72/196 (36%), Gaps = 27/196 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAERT-RLWLYHKP 81
            + I + R+K+NG  +      + ++D +E         +   P+    ++  + + +KP
Sbjct: 45  RQAILKGRIKINGKAV-PLDYVIRNSDLVENTVHRHEPVITDTPIEIVHQSDSVLVVNKP 103

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +    +     +TV   L   +  + +  V R+D  T GL+L+  D   A  +     
Sbjct: 104 SSIPVHPTGRYRYNTVIHLLEYENKMNDLFLVNRIDRLTSGLVLIARDKNKAAYMMQEMR 163

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +  + Y  R  G+   D +           K G+ I          TL  +   N   
Sbjct: 164 ERRIHKTYLARVKGEFPADAIECHEPIETVEFKVGVNIVSPTGKPCS-TLFKRLSYNGLT 222

Query: 190 TVGLRE---GKNREIK 202
           +V   E   G+  +I+
Sbjct: 223 SVVQCEPLTGRTHQIR 238


>gi|258653360|ref|YP_003202516.1| pseudouridine synthase [Nakamurella multipartita DSM 44233]
 gi|258556585|gb|ACV79527.1| pseudouridine synthase, RluA family [Nakamurella multipartita DSM
           44233]
          Length = 308

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 82/252 (32%), Gaps = 41/252 (16%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV------ 52
           M D     V +     R+   +AR    SR  V  MI    V V+G+ + R++       
Sbjct: 1   MPDVRRLPVPDGLAGMRLDAGVARLLGLSRTTVAEMIDAGDVLVDGVPVARSSRMALDTW 60

Query: 53  ---------NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
                       +     VDG+ +   +   + +  KP+G+    S      TV   L  
Sbjct: 61  LEITLPEPDRPPAVQAQVVDGLSVLYRDADIVVV-DKPVGVAAHPSPGWTGPTVLGALAG 119

Query: 102 -------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
                       R   V RLD+ T G++++         L+    +    ++Y     G 
Sbjct: 120 LGIAVSTSGSAERQGIVHRLDVGTTGVMVVALSERAYTTLKAAFKERTVDKIYHALVQGH 179

Query: 153 VDQDK--LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D     ++           K  +V  G        TL+  + + + + V L  G+  +I
Sbjct: 180 PDPSAGTIDAPIGRHPSSDWKFAVVAGGKDSVTHYETLEAFRAA-SLLQVHLETGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +  F        
Sbjct: 239 RVHFAAVRHPCV 250


>gi|167765516|ref|ZP_02437580.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1]
 gi|167712701|gb|EDS23280.1| hypothetical protein CLOSS21_00010 [Clostridium sp. SS2/1]
 gi|291558984|emb|CBL37784.1| ribosomal large subunit pseudouridine synthase D
           [butyrate-producing bacterium SSC/2]
          Length = 305

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 78/235 (33%), Gaps = 42/235 (17%)

Query: 7   VQENFTPQRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V      +R+  V++     S   R  + ++  ++R  +NG    +        D I + 
Sbjct: 9   VTSEMAGKRLDVVLSEQ--CSDLTRSYINKLCKEERAALNGKT-SKGNKKCKEGDVITLQ 65

Query: 64  -GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
              P                E   + L +KP G+V   +      T+ + L +       
Sbjct: 66  VPEPTELEILPEEMNLDIVYEDQDVILINKPKGMVVHPAAGHYSGTLVNGLMAHCKDDLS 125

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK- 157
                 R   V R+D +T G+L++  +    + +          R Y    +G + +++ 
Sbjct: 126 GINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYDHSITRKYHAIVYGNIKEEEG 185

Query: 158 ----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +  K GIV+ G         L   K    ++   L  G+  +I+
Sbjct: 186 TVNAPIGRSLKDRKKMGIVMDGKHAVTHYKVLKRLKKGFTYIECQLETGRTHQIR 240


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 37/193 (19%), Positives = 78/193 (40%), Gaps = 20/193 (10%)

Query: 29  REVERMIAQQRVKVNGILLERAAVN---VMSTDHIEVDGVPLRKA-ERTRLWLYHKPIGL 84
           RE +R I + RV +NG  + + +     ++     E +G  L+   E     ++ KP G+
Sbjct: 28  REAKRAIDRGRVSINGKRVTQKSFKASGILKCIVFEPNGYGLKPIFETDHFAIFDKPSGV 87

Query: 85  VTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                      ++ D++  ++ +    V RLD  T GL++ + +     +L+    + + 
Sbjct: 88  AIHPKKLANTKSLLDDVRLLYGNDANLVHRLDKETSGLVIASKNKFAESILKQAFQNKEI 147

Query: 142 LRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVT 190
            + Y     G +D++          K   +K  ++I       +  V    + G N  V 
Sbjct: 148 QKKYLALIKGHLDKEITIKKPIAVNKDENIKVKVIISDEGKESITLVKPIKKIGKNTLVE 207

Query: 191 -VGLREGKNREIK 202
            + L  G+  +I+
Sbjct: 208 CIPLT-GRQHQIR 219


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 84/237 (35%), Gaps = 45/237 (18%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E     R+ + +A      SR  ++++I Q +V +NG         + + D +EV   
Sbjct: 16  VTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCRDKDRPLQAGDEVEVRIP 75

Query: 63  -------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                     P+      E   L + +KP GLV   +      T+   L +   R+    
Sbjct: 76  PATPTALQPEPIPLDILYEDDDLLVINKPRGLVVHPAPGHASGTLVHALLAHCPRLSGIN 135

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
                  V RLD +T G L++       + L  ++ +    R+Y     G          
Sbjct: 136 GEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQAKTARRLYLGVVFGRPAQSQGTVS 195

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  VD+ K+ +L  G   QG         L+   G+   +   L  G+  +I+
Sbjct: 196 APIGRHPVDRQKMAVLTPG---QGRVAVTHWQVLERL-GNYTLMQFELETGRTHQIR 248


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/226 (17%), Positives = 78/226 (34%), Gaps = 34/226 (15%)

Query: 10  NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+   +A+     SR  + + +    V ++G         ++  +HIEV      
Sbjct: 30  SLAGERLDAALAKLLPDYSRSRLTQWVKDGHVLLDGKPAA-PKTKLLGGEHIEVAVQQTE 88

Query: 63  -----DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                    +      E   + + +KP GLV   +  +   T+ + L      +      
Sbjct: 89  EQLAYHPEAIELPIVYEDDHIIIINKPAGLVVHPAAGNWTGTLLNGLLHHCPALTHVPRA 148

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLN------ 159
             V RLD  T GL+++         L     +    R+YR    G V    K+       
Sbjct: 149 GIVHRLDKETSGLMVVAKTIPAQTELVRQMQARSVKRIYRAIADGVVPFDGKIETLIGRD 208

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               ++  +V  G       V +     S++++   L  G+  +I+
Sbjct: 209 PHNRMRMAVVKFGGKQAITHVRVLATFPSHSYIECRLETGRTHQIR 254


>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 = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 86/230 (37%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYP 245


>gi|269966247|ref|ZP_06180336.1| tRNA pseudouridine synthase C [Vibrio alginolyticus 40B]
 gi|269829162|gb|EEZ83407.1| tRNA pseudouridine synthase C [Vibrio alginolyticus 40B]
          Length = 256

 Score = 70.6 bits (172), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 57/193 (29%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
                 A V V             L E     G+  ++++        +           
Sbjct: 140 TEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLRRHMAHLRHPIVGDTTHGDGKH 199

Query: 214 -RLIRISYGPFQL 225
            +L R  +   +L
Sbjct: 200 NKLYRTEFDSHRL 212


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 94/288 (32%), Gaps = 51/288 (17%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           +++   QR+ + ++      SR  ++ +I+   V VN          V   D I+V+   
Sbjct: 9   EQDGENQRLDRWLSERVQQLSRSRLQALISSGHVWVNNSPCTSKKATVQIGDRIQVEIPP 68

Query: 64  ---------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                     +PL    E   L + +KP GLV   +      T+ + L +          
Sbjct: 69  AIPLELKATNIPLDILYEDEELLIINKPAGLVVHPAPGHANDTLVNALLAHCETLAGIGG 128

Query: 106 -SRVISVGRLDINTEGLLLLT-NDGGLARVLELPSTQWLR------VYRVR--FHGQVDQ 155
             R   V RLD +T G + +   D     +      +  R      +Y V     G +DQ
Sbjct: 129 VQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQIQAKTARRQYLGIIYGVPKTTSGVIDQ 188

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                      +      QG      +  +  + G+   +   L  G+  +I+       
Sbjct: 189 PIGRHHSDRKKMAIVPEHQGGRSAITRWQVQERLGNYTLIEFELETGRTHQIRVHSASIG 248

Query: 210 WKVNRLIRISYG-----PFQLGTLLAGSTREVSKK-----ILREQLGP 247
             +    R+ YG        L      + + ++ +      L E + P
Sbjct: 249 HPIVG-DRV-YGKGRSVGVNLPGQALHAWK-LTLQHPTSGELIEAIAP 293


>gi|330977498|gb|EGH77444.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 320

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 86/230 (37%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYP 245


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 44/233 (18%), Positives = 81/233 (34%), Gaps = 40/233 (17%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------GVP 66
           QR+ +V A+  G  SR  +   I + R+ V+G +       V +   + +D      G  
Sbjct: 25  QRLDQVAAQLFGEYSRSRLSTWIKEGRLTVDGAVAR-PRDTVHAGSTLVLDAEQEAQGEW 83

Query: 67  LRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVGR 113
           + +        E   + +  KP GLV      H+D    + +  ++P I    R   V R
Sbjct: 84  IAQDIELNIVYEDEHMLVIDKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHR 143

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ------------DKLN 159
           LD +T GL+++         L     +    R+Y     G +               +  
Sbjct: 144 LDKDTTGLMVVAKTLQAQTNLVEQLQKRTVSRIYECICIGVITAGGTIDAPIGRSSSQRQ 203

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
            +    V  G         +  +  S+  V V L  G+  +I+  +     + 
Sbjct: 204 RMA---VTDGGKPAISHYRVLERYRSHTHVRVKLETGRTHQIRVHMT-HVGYP 252


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 78/243 (32%), Gaps = 50/243 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    +VQ  +   R+   +      SR ++ + I  + V VNG+ ++     +   D I
Sbjct: 9   MNKTLVVQSQYEGMRLDIFLKEVLDYSRSKINKEIKNKSVLVNGVSVKS-GYIIKKNDII 67

Query: 61  EV----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNL 101
            +    D V L           E   + +  KP  LV          T+         N+
Sbjct: 68  TLEILEDQVNLEPQKIDFKILFEDEYIMVISKPENLVVHPGAGVFSETLVNGLLDYNINI 127

Query: 102 PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
             I        V RLD +T GL+++  D    + L       +  + Y     G ++ + 
Sbjct: 128 KDIGEEDRPGIVHRLDKDTSGLMIIAKDALAYKKLVNMFKYGEIHKEYIAILTGHLENE- 186

Query: 158 LNLLKKGIVIQ---GICYGDMQ---VTLDTQKGSNAWV------------TVGLREGKNR 199
                  I +    G    D +   V     K + +               V +  G+  
Sbjct: 187 -------IRVDEPIGRNPKDRKSFTVIYSNSKNAISTFVPIKYMNGFTLCRVIIETGRTH 239

Query: 200 EIK 202
           +I+
Sbjct: 240 QIR 242


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 86/230 (37%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYP 245


>gi|297170255|gb|ADI21292.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_09F21]
          Length = 305

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 85/243 (34%), Gaps = 35/243 (14%)

Query: 2   KDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K  NI + N    R+   ++      SR  V+++I Q  V VN + +++    +   D I
Sbjct: 4   KTFNIDEANINK-RLDSFLSDILDDISRGLVQQLIEQGNVLVNDLEVKK-NYKLRLNDQI 61

Query: 61  EV--------DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------ 101
           +V        +  P         E    ++ +K  GL          +T+ + L      
Sbjct: 62  QVILQFPEVIEDEPQNIPLDIVFENEDFYIINKQAGLTVHPGAGQKDNTLLNGLLHLNKK 121

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-------- 151
               SR   V RLD  T GL+++  +     +L          R Y    HG        
Sbjct: 122 ACELSRCGIVHRLDKETSGLMVVAKNHSSQTILTNLIKDRAIERKYYALVHGNVISGGTI 181

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              +++   N L   +  +G       +  +  +   + + V L  G+  +I+   +   
Sbjct: 182 DEPIERHPKNRLIFIVDQEGKESKTHYLVKERYENF-SLLDVKLETGRTHQIRVHLKHIG 240

Query: 210 WKV 212
           + +
Sbjct: 241 FPI 243


>gi|302185255|ref|ZP_07261928.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           syringae 642]
          Length = 320

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 86/230 (37%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELVAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYP 245


>gi|291166433|gb|EFE28479.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Filifactor alocis ATCC 35896]
          Length = 293

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 88/227 (38%), Gaps = 41/227 (18%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ + I+      SR  ++++I ++RV VNG   ++ +  + S D+IE+          
Sbjct: 1   MRLDQFISSNLPSISRSYIQKLIDEKRVLVNGKYEKK-SFLLKSFDNIEIYIPEPKSIEI 59

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVI 109
             + +PL    E   + + +K  G+V   +  +   T+ + +           + + R  
Sbjct: 60  SPENIPLNILFEDKDILIVNKEKGMVVHPAPGNYSHTLVNAILYHCKGNLSEINGYIRPG 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL-------- 158
            V R+D +T G+L++  +   A        +     R Y++   G +    L        
Sbjct: 120 IVHRIDKDTSGILVIAKNND-AHQFLSEQFKEHSIQREYQLITFGNIKTTHLSIEQPIGR 178

Query: 159 ---NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              N L+  +V  G       +T+        ++   L  G+  +I+
Sbjct: 179 NPKNRLQMAVVPNGKPAITH-LTVIENFKDKTYLKARLETGRTHQIR 224


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 37/180 (20%), Positives = 64/180 (35%), Gaps = 25/180 (13%)

Query: 1   MKDKNIVQE---NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M+ K +  E   +   QR+ + +A      SR  ++  I    V+V+  ++      V  
Sbjct: 1   MEHKKLTAEVQPHQLGQRLDQTLAELFPEYSRSRIKTWIEAGLVQVDDKIVTVPKEKVFG 60

Query: 57  TDHI------------EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           T+ I                +PL    E   + + +K   LV      +  +TV + L  
Sbjct: 61  TEQIIMQAEIEEDTRFTPQNIPLDIVYEDEHILVINKSKDLVVHPGAGNPDNTVLNALLY 120

Query: 104 IF------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
            +       R   V RLD +T GL+++         L   L   Q  R Y     G + +
Sbjct: 121 HYPPIAEVPRAGIVHRLDKDTTGLMVVAKTIEAQTKLVRALQKRQITREYEAIASGIMTK 180


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 38/255 (14%), Positives = 81/255 (31%), Gaps = 46/255 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQ 61

Query: 60  IEV-------DGVPLRKAE--------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
           I +       D   ++  E           L + +K   +    S  +  +T+ + L   
Sbjct: 62  ITITIKDPILDPNLVKNDEIDLDIIYQDDDLLVINKQNNITVHPSLNNTNNTIVNALLAS 121

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQ 152
                  +   R   V R+D  T GLL++  +      L      + Q  + Y     G 
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIVAKNDKT-HKLLSEMFKNHQIYKEYLAIVTGV 180

Query: 153 V-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +              Q     +   +  +          +  +   N  V   ++ G+  
Sbjct: 181 IKPNKGLIDAPIGRSQTDRKKMS--VTAKNSKQAITTFEVVERFFKNTLVKCQIQTGRTH 238

Query: 200 EIKKVFEFFNWKVNR 214
           +I+  F + N  V  
Sbjct: 239 QIRVHFNYINHPVLN 253


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 59/314 (18%), Positives = 98/314 (31%), Gaps = 70/314 (22%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ K++A      SR  ++  I    V+VNG   +     V   D + V   P  +    
Sbjct: 34  RLDKILAALLDGHSRSRLQGWIEAGWVQVNGAPAK-VRQVVGPGDVLAVWEQPAPESLAF 92

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGR 113
                     AE     +  KP GLVT     +   T+ + L   +       R   V R
Sbjct: 93  TPEPIAFAVVAESPDWIVVDKPAGLVTHPGAGNWSGTLLNGLLHRYPELARVARAGIVHR 152

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLL 161
           LD +T GL+++  +      L  +L +    R Y            +    + +D    +
Sbjct: 153 LDKDTSGLMVVARNELAQTHLVRQLQARSMGREYIALAHGWLPVAGKVDRPIGRDARVPV 212

Query: 162 KKGIVIQGICYGDMQVTL--------DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +  +                          G    V   L  G+  +I+         + 
Sbjct: 213 RMSVE---RPIAPKPAITHYAPLRRGRAPDGPVTEVACRLETGRTHQIRVHLASLGHPL- 268

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L    YG    G L AG+TR              +L    ++ D P        R  P 
Sbjct: 269 -LADTLYG----GRLTAGATR-------------QMLHARALHFDDPGGGGPAAFRADP- 309

Query: 274 IISEVPDDFTRMKK 287
                PDD  ++++
Sbjct: 310 -----PDDMRQVQE 318


>gi|120437019|ref|YP_862705.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii
           KT0803]
 gi|117579169|emb|CAL67638.1| ribosomal large subunit pseudouridine synthase D [Gramella forsetii
           KT0803]
          Length = 354

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 86/241 (35%), Gaps = 45/241 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K + +    P RV K +        A+R ++++      + VNG  +++    V   D +
Sbjct: 25  KFVAEVGQNPLRVDKYLMN--FIENATRNKIQKAAKSGNIYVNGDTVKQ-NYKVKGGDTV 81

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FD 99
           +V             + +PL    E   L + +K  G+V      +   T+       FD
Sbjct: 82  QVMFEHPPYEYLLVPEDIPLDIVYEDDTLLVVNKQAGMVVHPGHGNYSGTLINALVHHFD 141

Query: 100 NLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           NLP+  S R   V R+D +T GLL++         L          R Y     G + ++
Sbjct: 142 NLPNNSSDRPGLVHRIDKDTSGLLVVAKTEEAMAHLSKQFFDKSSEREYVAIVWGNLAEE 201

Query: 157 K-----------LNLLK----KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +            N L+    +G  ++          +  + G    V   L  G+  +I
Sbjct: 202 EGTIEGNIGRNPRNRLQNIVFEGDDVENGKAAVTHYKVLERLGYVTLVACKLETGRTHQI 261

Query: 202 K 202
           +
Sbjct: 262 R 262


>gi|195621906|gb|ACG32783.1| RNA binding protein [Zea mays]
          Length = 379

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 33/236 (13%), Positives = 66/236 (27%), Gaps = 59/236 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW----------LYHKPIGL 84
           I   ++ V+G ++    + ++    +     P ++     L             +KP GL
Sbjct: 63  IRNGQITVDGEVVTDPDMTLVDGSKLVYHRFPWQEPFAPYLLEVLYEDDDMVALNKPSGL 122

Query: 85  VTTHSDPDGRSTVFDNL---------------PSIFSRVISVGRLDINTEGLLLLTNDGG 129
                    + TV   L                 + S  + V RL   T GLLL      
Sbjct: 123 QVLPKGLFQQRTVLAQLQLKDWKMASSCRFKRKDVQSHPVPVHRLGRGTSGLLLCAKTKV 182

Query: 130 LARVLE-------------------LPSTQWLRVYRVRFHGQVDQDKL-----------N 159
               L                        +  + YR    G +D D++            
Sbjct: 183 AKVRLASYFAEGAINAAKKRDKSEFSEERKISKFYRALVTGILDDDEVVVTQPIGLVHYP 242

Query: 160 LLKKGIVIQGICYGDM--QVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +G+            +V +  +    ++  V V +  G+  +I+    +    
Sbjct: 243 GVAEGLYAACSSGKPAMSKVCVLERLAHQNHTLVQVEIHSGRPHQIRIHLAYIGHP 298


>gi|42522844|ref|NP_968224.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39574040|emb|CAE79217.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 228

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 33/157 (21%), Positives = 61/157 (38%), Gaps = 19/157 (12%)

Query: 65  VPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNL-PSIFSRVISVGRLDINTEGLL 122
           + +   E+++ WL  +KP G+   +  PD R+ +   L P  +  +  V RLD  T GLL
Sbjct: 8   IQIPIVEKSKHWLVINKPSGVSVHNDPPDVRTLLKKQLTPGTYQDIHPVHRLDKETSGLL 67

Query: 123 LLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV--------------DQDKLNLLKKGIV 166
           L+  D   A  L       +  + Y     G++              D+ +     +G+ 
Sbjct: 68  LVGLDAETAANLSGQFQEHKVEKTYYALLRGELPVSTDWQEWNTPISDKAEGRKNPQGL- 126

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           ++          +       + V V L  G+  +I+K
Sbjct: 127 LKDRVEARTLYKVLEANKYFSLVEVRLITGRQHQIRK 163


>gi|317498467|ref|ZP_07956761.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894160|gb|EFV16348.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 305

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 78/235 (33%), Gaps = 42/235 (17%)

Query: 7   VQENFTPQRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V      +R+  V++     S   R  + ++  ++R  +NG    +        D I + 
Sbjct: 9   VTNEMAGKRLDVVLSEQ--CSDLTRSYINKLCKEERAALNGKT-SKGNKKCKEGDVITLQ 65

Query: 64  -GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
              P                E   + L +KP G+V   +      T+ + L +       
Sbjct: 66  VPEPTELEILPEEMNLDIVYEDQDVILINKPKGMVVHPAAGHYSGTLVNGLMAHCKDDLS 125

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK- 157
                 R   V R+D +T G+L++  +    + +          R Y    +G + +++ 
Sbjct: 126 GINGVLRPGIVHRIDKDTTGILIVCKNDMAHQSIAKQLYDHSITRKYHAIVYGNIKEEEG 185

Query: 158 ----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +  K GIV+ G         L   K    ++   L  G+  +I+
Sbjct: 186 TVNAPIGRSLKDRKKMGIVMDGKHAVTHYKVLKRLKKGFTYIECQLETGRTHQIR 240


>gi|330988806|gb|EGH86909.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 320

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 86/230 (37%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYP 245


>gi|289168022|ref|YP_003446291.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288907589|emb|CBJ22426.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 298

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 73/211 (34%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D + +D     G      + +      E     + +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVAIDIPAEEGFETLEAIERPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLESEGEIIAPIARDEDSIITRRVA-KGGKYAHTSYKIV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              GS   V + L  G+  +I+  F    + 
Sbjct: 210 ASYGSIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 87/243 (35%), 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  -DGVPL----------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
            +  P+             E   + +  KP G+V   +    R T+ + L + +      
Sbjct: 69  PEPQPVGLVAEALPLQIVYEDDDVVVIDKPAGIVVHPAPGHNRGTLVNALIARYPEMAIS 128

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD +T GLL+   +      L  +  + + L++Y V   G          
Sbjct: 129 GDLRPGIVHRLDRDTSGLLVAARNDRALHSLQAQQQARRMLKIYLVVVEGRMNESGGVID 188

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + +   + ++  ++  G         L+ + G  A +   L  G+  +I+  F   N 
Sbjct: 189 APIARHPTDRVRMAVMAGGRPARTHWRVLE-ELGEYALIEARLETGRTHQIRVHFASRNR 247

Query: 211 KVN 213
            V 
Sbjct: 248 PVL 250


>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 = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/171 (20%), Positives = 60/171 (35%), Gaps = 30/171 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ +V+A R    SR  ++ +I   RV + G  +   A +  S + I +D          
Sbjct: 113 RLDRVLATRCPALSRSRLKALILDGRVAIRGAPVRDPAYHAASGETITIDVPPPVAPEPA 172

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
           G  +      E   + +  KP GLV   +      T+ + L +             R   
Sbjct: 173 GEAIALEIVHEDDDIIVIDKPRGLVVHPAAGHETGTLVNALIAHCGESLSGIGGVRRPGI 232

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVDQ 155
           V RLD +T GL++   +    + L        R       Y     G  ++
Sbjct: 233 VHRLDKDTTGLMVAAKNDRAHQSLSAQFADHGRTGELRRGYYAFVWGAPNR 283


>gi|116329941|ref|YP_799659.1| pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
 gi|116123630|gb|ABJ74901.1| Pseudouridylate synthase, 23S RNA-specific [Leptospira
           borgpetersenii serovar Hardjo-bovis JB197]
          Length = 312

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 94/256 (36%), Gaps = 44/256 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKV-NGILLERAAVNVMS 56
           ++ K  V E F+  R+ + + +       SR  +++ I    V+  +  + ++++  V +
Sbjct: 3   LELKAEVLEEFSGNRLDRFL-KFSFGDEMSRATIQKWIECGYVRNQDRKICDKSSWKVKT 61

Query: 57  TDH----------IEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            +           + ++ +P+      ER    + HKP G+ +     D   ++ + L  
Sbjct: 62  GEQYFLSIPPRPPLNLEPIPMTLPVVLEREDYLIIHKPPGIASHSGPGDRSPSLVNGLLH 121

Query: 104 IFSRVISVG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
            F  +  VG         RLD  TEGL+L+  +      L       +  + Y     G 
Sbjct: 122 HFKELSKVGGEARPGIVHRLDKPTEGLMLIPKNDRAHGKLSELFRKREIEKKYYAWIQGH 181

Query: 153 VDQDK-----------LNLLKKGIVIQGIC----YGDMQVTLDTQKGSNAWVTVGLREGK 197
           +  +            +  LK  +  +G      Y  ++          ++V VGL  G+
Sbjct: 182 LPAETGTIDLPIARHPIERLKMTVSPKGRKSVTHYKVLKYVNSRSGRKFSFVEVGLETGR 241

Query: 198 NREIKKVFEFFNWKVN 213
             +I+  F+     V 
Sbjct: 242 THQIRIHFQSQRCPVV 257


>gi|87300810|ref|ZP_01083652.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 5701]
 gi|87284681|gb|EAQ76633.1| Pseudouridine synthase, RluD [Synechococcus sp. WH 5701]
          Length = 315

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 77/240 (32%), Gaps = 41/240 (17%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           P R+ + + A+    SR  +++ I    V+VNG+    A   +   D +++   P     
Sbjct: 21  PMRLDRWLVAQRPEQSRARIQKFIDAGYVRVNGVTGR-AKTPLRLHDEVQLWMPPPEPLP 79

Query: 71  -------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
                        E   L + +KP GL    +  +   T+ + L      +  +G     
Sbjct: 80  YLLPQPIPLDVLFEDAHLIVLNKPAGLTVHPAPGNRDGTLVNGLLHHCPDLPGIGGEMRP 139

Query: 113 ----RLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVD------------ 154
               RLD +T G +++         L++   + +  R Y    HG               
Sbjct: 140 GIVHRLDKDTTGCIVVAKSQEALVRLQVQIQKRVASREYLAVVHGAPAASSGTIVGAIGR 199

Query: 155 -QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      +  +   +     TL  + G  + +   L  G+  +I+         + 
Sbjct: 200 HPADRKKYAV-VAEEKGRFACTHWTLIERLGDYSLLRFRLDTGRTHQIRVHCAHIGHPIV 258


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 74/210 (35%), Gaps = 26/210 (12%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRL 75
           KV+A+    S ++ + +I +  V V+   +   RA +N  +T  IE         E   +
Sbjct: 8   KVLAQQQGISNKKAKELIDRGLVFVDDRKVRIARAEINTETTFRIEYPEDIEILYEDEDI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +              +         + RLD +T G+LLL  +        
Sbjct: 68  IAVNKPAQVDSYE------------IQDAIEGAELLHRLDRDTSGVLLLGRNREFIERAI 115

Query: 136 LP--STQWLRVYRVRFHGQVDQ-----DKLNLLKKGI---VIQGICYGDM--QVTLDTQK 183
               + +  + Y     G + +     + +  +KKG    +I  +        V  +  +
Sbjct: 116 KEFKNRRVEKHYVAWVDGVIYETVEIDEPIFTVKKGKAFSMIDPVRGKKAHTVVHPEEVQ 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G  + V + +  G+  +I+         + 
Sbjct: 176 GKKSKVKIDITTGRTHQIRVHLAHIGHPIV 205


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 83/249 (33%), Gaps = 41/249 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  + V  +    R+ KV+       +R +++ +I Q+++ VN          V   D 
Sbjct: 1   MEQFSFVVSDQESGRLDKVVTNHYPDLTRSKIQNLIKQEQILVN-QAPTTNRYKVSENDV 59

Query: 60  IEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I+V   D V +             E   + + +KP G+V   +      T+ + L     
Sbjct: 60  IDVTLPDPVEVSVKPEKMNLDIVFEDDDVIVVNKPQGMVVHPAPGHENGTLVNGLLDHAP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +      L   L +    R Y    HG   ++
Sbjct: 120 LATVNGELRPGIVHRIDKDTSGLLMVAKNDQAMLSLSAQLKAKTNQRKYLAIVHGNFKEE 179

Query: 157 -------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                            +    +++          +  +      +   L  G+  +I+ 
Sbjct: 180 AGTINAPIGRSKKDRKKMA---IVEDGRPAVTHFKVLERFTDYTLIECELETGRTHQIRV 236

Query: 204 VFEFFNWKV 212
             ++    V
Sbjct: 237 HLKYIGHPV 245


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 58/171 (33%), Gaps = 30/171 (17%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------VDGV 65
            QR+ +++A      SR  ++ +I    V +   ++   A  V + + I       VD  
Sbjct: 51  SQRLDRLLAEQIDDLSRTRLKALILAGHVSLGDTVVRDPAYQVKAGEAITIEVPPAVDPE 110

Query: 66  PLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRV 108
           P+ +        E   + +  K  GLV   +      T+ + L +             R 
Sbjct: 111 PVGENIPLDIVYEDDDIIVLDKQRGLVVHPAAGHENGTLVNALIAHCGASLSGIGGVKRP 170

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQV 153
             V RLD +T GL+++  +    + L        R       Y     G  
Sbjct: 171 GIVHRLDKDTTGLMVIAKNDHAHQSLTAQFADHGRTGELRRGYLAFVWGVP 221


>gi|56551646|ref|YP_162485.1| RluA family pseudouridine synthase [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241761227|ref|ZP_04759315.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752766|ref|YP_003225659.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|59803028|sp|P50513|RLUD_ZYMMO RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|56543220|gb|AAV89374.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374134|gb|EER63631.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552129|gb|ACV75075.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 317

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 88/240 (36%), Gaps = 42/240 (17%)

Query: 3   DKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDH 59
           ++  + E     R+ + +A      SR  ++ +I+   V  N  G L+   A  + S D 
Sbjct: 4   EQVTLTEEMIGWRLDRALASLITRLSRERLKNLISSGCVS-NSQGALVRDPAFKIKSLDC 62

Query: 60  IEVDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSI 104
             VD +PL +               E   L + +KP G+V   +  +  +T+ +  L   
Sbjct: 63  FTVD-IPLPRPAHNEPQDIPLEIVFEDEHLLVVNKPAGMVVHPAAGNYDNTLVNALLYHC 121

Query: 105 FSRVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-- 151
             ++  +G         R+D +T GLL++  T+        +       R YR    G  
Sbjct: 122 AGKLSGIGGVARPGIVHRIDKDTSGLLVVAKTDPAHAGLAAQFADHSINRRYRAIVDGHP 181

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +  +N  K  IV  G     +    + T   + + +   L  G+  +++
Sbjct: 182 SLQGHVDAPLARSSVNRQKMAIVSDGRGKRAVTHYRMITPLKNASLIECRLETGRTHQVR 241


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 81/236 (34%), Gaps = 51/236 (21%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------- 61
            P RV K +        A+R ++++      ++VN  ++++    V + D +        
Sbjct: 29  EPLRVDKFLMN--FVENATRNKIQKAAKNGSIQVNNKVVKQ-NYKVKAGDVVRAMFEHPP 85

Query: 62  ------VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFS- 106
                  + +PL    E   L + +KP G+V      +   T+        DNLP+  S 
Sbjct: 86  HEFLLTPEDIPLDIIYEDDDLLVVNKPAGMVVHPGHGNYSGTLINALIHHIDNLPNNSSE 145

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-----WLRVYRVRFHGQVDQDK---- 157
           R   V R+D +T GLL++         +   S Q       R Y     G V  D+    
Sbjct: 146 RPGLVHRIDKDTSGLLVVA---KTEHAMTHLSKQFFNKTTEREYVAIVWGNVVDDEGTIE 202

Query: 158 -------LNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
                   N L+  +                 +  + G    V   L  G+  +I+
Sbjct: 203 GNIGRHPKNRLQNTVFKDDEEEQGKPAVTHYKVLERLGYVTQVACKLETGRTHQIR 258


>gi|15900967|ref|NP_345571.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|15903050|ref|NP_358600.1| 23S rRNA pseudouridine synthase [Streptococcus pneumoniae R6]
 gi|111657593|ref|ZP_01408329.1| hypothetical protein SpneT_02001203 [Streptococcus pneumoniae
           TIGR4]
 gi|116516162|ref|YP_816460.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|149006229|ref|ZP_01829941.1| phosphotransacetylase [Streptococcus pneumoniae SP18-BS74]
 gi|149012907|ref|ZP_01833820.1| phosphotransacetylase [Streptococcus pneumoniae SP19-BS75]
 gi|168483173|ref|ZP_02708125.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|168491992|ref|ZP_02716135.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|168494532|ref|ZP_02718675.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|169832712|ref|YP_001694523.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|182684150|ref|YP_001835897.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|221231840|ref|YP_002510992.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225854594|ref|YP_002736106.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|303254191|ref|ZP_07340303.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           BS455]
 gi|303259761|ref|ZP_07345736.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|303262936|ref|ZP_07348871.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|303264899|ref|ZP_07350815.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|303266879|ref|ZP_07352757.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|303268916|ref|ZP_07354701.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|307127370|ref|YP_003879401.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|14972575|gb|AAK75211.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae TIGR4]
 gi|15458622|gb|AAK99810.1| 23S rRNA pseudouridine synthase [Streptococcus pneumoniae R6]
 gi|116076738|gb|ABJ54458.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|147762006|gb|EDK68968.1| phosphotransacetylase [Streptococcus pneumoniae SP18-BS74]
 gi|147763196|gb|EDK70136.1| phosphotransacetylase [Streptococcus pneumoniae SP19-BS75]
 gi|168995214|gb|ACA35826.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043330|gb|EDT51376.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629484|gb|ACB90432.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CGSP14]
 gi|183573763|gb|EDT94291.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|183575559|gb|EDT96087.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|220674300|emb|CAR68842.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           ATCC 700669]
 gi|225722385|gb|ACO18238.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|301802010|emb|CBW34739.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           INV200]
 gi|302598862|gb|EFL65896.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           BS455]
 gi|302635913|gb|EFL66413.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|302638966|gb|EFL69426.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|302641534|gb|EFL71896.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|302643577|gb|EFL73846.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|302645587|gb|EFL75818.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|306484432|gb|ADM91301.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|332075053|gb|EGI85524.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17545]
 gi|332201583|gb|EGJ15653.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA47368]
          Length = 298

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D++ +D     G      +        E     + +KP
Sbjct: 33  RGGAILVNNQP-QNATYLLDVGDYVTIDIPAEKGFETLEAIELPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKIVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVYIHLHTGRTHQIRVHFSHIGFP 240


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 37/198 (18%), Positives = 77/198 (38%), Gaps = 25/198 (12%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-----ERTRLWLYHKP 81
           S+ + ++MI  +++  NG LL   +  V     + V   P+ K      E     LY KP
Sbjct: 27  SQSQAQKMIDTKKIYQNGKLLTDKSAVVEGEIEVIVF-EPITKGLKPIFETKDFVLYDKP 85

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
            G++    + +   T+ D +   +  +   V R+D  T GL+L + +    + L      
Sbjct: 86  SGIMVHPRNRNTHYTLIDEIRYRYGPQANIVHRIDKETSGLVLASTNKEAEKALKQMFEH 145

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWV-------- 189
            Q  + Y     G +++  +  +++ I +        ++V +D        +        
Sbjct: 146 KQIQKRYLALVRGNIEKQLV--IEEPIALNRDYSKIKLKVKIDPSGKYAKTIINPLKQFG 203

Query: 190 TVGLRE-----GKNREIK 202
           +  L E     G+  +I+
Sbjct: 204 SFTLVEAIPITGRQHQIR 221


>gi|10045559|emb|CAC07917.1| putative protein [Arabidopsis thaliana]
          Length = 376

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 34/231 (14%), Positives = 70/231 (30%), Gaps = 63/231 (27%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I   +++++G +++     + S   +    +P ++ +             L   +KP GL
Sbjct: 56  IQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPSGL 115

Query: 85  VTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTEGLLLLTNDGGLAR 132
                    + TV   L   F               + V RL   T G+LL         
Sbjct: 116 QVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLAKT 175

Query: 133 VLE-------------------LPSTQWLRVYRVRFHGQVDQDKLNLL------------ 161
            L                        +  ++YR    G V++D+                
Sbjct: 176 KLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEARPFLLFVVIKQPIGV 235

Query: 162 ------KKGIVI---QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
                  +G+ +   +G         L+  +  N + V V ++ G+  +I+
Sbjct: 236 VRYPGVAQGLYVASPEGKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIR 286


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 42/185 (22%), Positives = 74/185 (40%), Gaps = 30/185 (16%)

Query: 1   MKDKNIVQENFT-PQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  V E  T  QR+ + ++    G+ SR  ++ ++A   V  NG L+ + ++ + + 
Sbjct: 1   MEQREFVVEQETAGQRIDRFLSGEDTGL-SRSALQALVADGHVLCNGRLVAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I +   D  P+             E   L + +KP G+V   +  +   T+ + L   
Sbjct: 59  DTIVLEIPDAKPIEAVPQDIPLEIVYEDEHLLVVNKPKGMVVHPAPGNPDGTLVNALLWH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
                       R   V R+D +T GLL++  D      L          R YR   +G 
Sbjct: 119 CKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYRTIVYGG 178

Query: 153 VDQDK 157
             QD+
Sbjct: 179 FAQDE 183


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 89/249 (35%), Gaps = 42/249 (16%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE-----R 49
           M DK  ++     +    R+ +V A    A  SR  +   I   R+ V+G ++       
Sbjct: 1   MSDKIELRAEVPSELGGQRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGAVIRPRDIVH 59

Query: 50  AAVNVMSTDHIEVDGVPLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
               +  T   E  G  + +        E   + + +KP GLV      H+D    + + 
Sbjct: 60  GGAILELTAEQEAQGEWVAQDIELDIVYEDDDILVINKPAGLVVHPAAGHADGTLLNALL 119

Query: 99  DNLPSIF--SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV- 153
            ++P I    R   V RLD +T GL+++  T       V +L S    R+Y     G V 
Sbjct: 120 HHVPDIINVPRCGIVHRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVV 179

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +    V++G         +  +  S+  V V L  G+  +I+
Sbjct: 180 AGGKINAPIGRHGQQRQRMA---VMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIR 236

Query: 203 KVFEFFNWK 211
                 N+ 
Sbjct: 237 VHMAHINFP 245


>gi|222624713|gb|EEE58845.1| hypothetical protein OsJ_10432 [Oryza sativa Japonica Group]
          Length = 458

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 69/236 (29%), Gaps = 59/236 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           I   ++ V+G +     + +     +    +P ++           E   +   +KP GL
Sbjct: 73  IRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFAPHLLDVLYEDDDMIALNKPSGL 132

Query: 85  VTTHSDPDGRSTVFDNL---------------PSIFSRVISVGRLDINTEGLLLL----- 124
                    + TV   L                   S  + V RL   T GLLL      
Sbjct: 133 QVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPVPVHRLGRGTSGLLLCAKTKL 192

Query: 125 -------------TNDGGLARVLELPS-TQWLRVYRVRFHGQVDQDKLNL---------- 160
                        TN G      ++    +  + YR    G ++ D++ +          
Sbjct: 193 AKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVTGILENDEVMITQPIGLVRYP 252

Query: 161 -LKKGIVIQ---GICYGDMQVTLDTQKGSNAWV-TVGLREGKNREIKKVFEFFNWK 211
            + +G+      G         L+  K  N  +  V +  G+  +I+    +    
Sbjct: 253 GVAEGLYAACSSGKPAMSKVRVLERLKIHNHTLIQVEIHSGRPHQIRIHLAYIGHP 308


>gi|168486485|ref|ZP_02710993.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
 gi|183570531|gb|EDT91059.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
          Length = 298

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D++ +D     G      +        E     + +KP
Sbjct: 33  RGGAILVNNQP-QNATYLLDVGDYVTIDIPAEEGFETLEAIEHPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHTRL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKIVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVYIHLHTGRTHQIRVHFSHIGFP 240


>gi|226724701|sp|Q0DST9|PUS5_ORYSJ RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA
           pseudouridylate synthase 5; AltName: Full=RNA-uridine
           isomerase 5
          Length = 397

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 69/236 (29%), Gaps = 59/236 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           I   ++ V+G +     + +     +    +P ++           E   +   +KP GL
Sbjct: 73  IRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFAPHLLDVLYEDDDMIALNKPSGL 132

Query: 85  VTTHSDPDGRSTVFDNL---------------PSIFSRVISVGRLDINTEGLLLL----- 124
                    + TV   L                   S  + V RL   T GLLL      
Sbjct: 133 QVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPVPVHRLGRGTSGLLLCAKTKL 192

Query: 125 -------------TNDGGLARVLELPS-TQWLRVYRVRFHGQVDQDKLNL---------- 160
                        TN G      ++    +  + YR    G ++ D++ +          
Sbjct: 193 AKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVTGILENDEVMITQPIGLVRYP 252

Query: 161 -LKKGIVIQ---GICYGDMQVTLDTQKGSNAWV-TVGLREGKNREIKKVFEFFNWK 211
            + +G+      G         L+  K  N  +  V +  G+  +I+    +    
Sbjct: 253 GVAEGLYAACSSGKPAMSKVRVLERLKIHNHTLIQVEIHSGRPHQIRIHLAYIGHP 308


>gi|91223469|ref|ZP_01258734.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
 gi|91191555|gb|EAS77819.1| pseudouridine synthase Rlu family protein [Vibrio alginolyticus
           12G01]
          Length = 256

 Score = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 28/193 (14%), Positives = 57/193 (29%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
                 A V V             L E     G+  ++++        +           
Sbjct: 140 TEYKPLAKVEVPYSTGKFPTTRYCLVEMKPKTGRKHQLRRHMAHLRHPIVGDTTHGDGKH 199

Query: 214 -RLIRISYGPFQL 225
            +L R  +   +L
Sbjct: 200 NKLYRTEFESHRL 212


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 91/248 (36%), Gaps = 37/248 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K ++       RV  V+++  +  SR  +   +    + VN   ++R +  V+S D 
Sbjct: 1   MANKILIHITDQAGRVDAVLSKENLSYSRTTLSNWLVDGTILVNNHKVKR-SYKVVSGDT 59

Query: 60  IEV------------DGVPLRKAERTRLW-LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +            + +PL          + +KP G+V   +      T+ + L     
Sbjct: 60  ISITPPETQETKIEAENIPLDIIYEDDDIIVVNKPQGMVVHPAAGHSSGTLVNALLHHSP 119

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
                   R   V R+D +T GLL++  +    R L   L S +  RVY     G+  +D
Sbjct: 120 LSTINGEFRPGIVHRIDRDTSGLLMVAKNDKAHRSLSEQLKSHKNQRVYYALVRGEFTED 179

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                      K++  K+ + I+G         +  +      + V L  G+  +I+   
Sbjct: 180 SGTIEAPIGRHKIDRKKQAV-IEGGREAVTHFRVLKRYVGYTLLKVSLETGRTHQIRVHM 238

Query: 206 EFFNWKVN 213
            +    V 
Sbjct: 239 SYIGHPVV 246


>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 = 70.2 bits (171), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLQAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 42/227 (18%), Positives = 74/227 (32%), Gaps = 45/227 (19%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPL 67
           QR+ + +A      SR  ++  I Q  V VNG ++      V   + IE+     D    
Sbjct: 17  QRLDQALAELFPDYSRSRLKTWIEQNLVHVNGDVVNVPRAKVYGGEQIEIVVEIDDDTRF 76

Query: 68  RKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP   V      +   TV + L   +       R   V R
Sbjct: 77  EPENLPLNIVYEDDDILVINKPKDFVVHPGAGNASGTVLNALLYHYPAIAEVPRAGIVHR 136

Query: 114 LDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD +T GL+++         L       +  R Y     G +        K G+V Q + 
Sbjct: 137 LDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIACGIMT-------KGGMVDQPMA 189

Query: 172 YGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
               + T                +  +  +   + + L  G+  +I+
Sbjct: 190 RHPTKRTHMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 236


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 87/235 (37%), Gaps = 43/235 (18%)

Query: 15  RVSKVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           R+ K   + G      SR +++  I    V VNG  ++     ++  DH+++        
Sbjct: 16  RIDK---QLGHHFDQFSRSQIQHWIEDGHVLVNGKQVK-PKYKLLVGDHVQIIPEEPQKI 71

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVI 109
               + +PL    E   + + +KP G+V   +      T+ + L             R  
Sbjct: 72  DLAPEDIPLDIVYEDDDVIVVNKPQGMVVHPAPGHPDHTLVNALLYHSPLSTINGEFRPG 131

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++  +    R L   L +    R Y    HG + +DK          
Sbjct: 132 IVHRIDKDTSGLLMVAKNDMAHRSLTAQLKAKTNKREYVALVHGVIKEDKGTIDAPLGRS 191

Query: 158 -LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  K+ +V+ G         L+  K +   V   L  G+  +I+   ++    
Sbjct: 192 LKDRKKQAVVVDGRHAVTHFNVLERFK-NYTLVACQLETGRTHQIRVHMKYIGHP 245


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 92/250 (36%), Gaps = 40/250 (16%)

Query: 1   MKD-KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+D K  + E    QR+ K++A      SR +++ +I    V ++   ++ A+  V + +
Sbjct: 1   MEDIKIRIVEEQKGQRIDKILAKELADFSRTQIQSLIQNGYVVIDEKPIK-ASYKVETGE 59

Query: 59  HIEV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---- 101
            + V            + +PL    E   + + +KP G++   S      T+ + L    
Sbjct: 60  DVIVYIPKPESTDILPEDIPLDVVYEDQDVIVINKPTGMIVHPSIGIYSGTLVNALLYHC 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                 +  +R   V R+D  T GLL++  +    + L   L      R Y    HG + 
Sbjct: 120 HDLSGINGVTRPGIVHRIDKETSGLLMVAKNDKAHQSLSKQLQEHTVTRRYLALVHGLIP 179

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
            +    ++  I         M  T    K +     V        L E     G+  +I+
Sbjct: 180 HEF-GRIEAPIGRDKNDRQKMTCTDKNAKDAITNFKVIERFRDMSLVECRLETGRTHQIR 238

Query: 203 KVFEFFNWKV 212
              ++  + V
Sbjct: 239 VHMQYIGYPV 248


>gi|57167607|ref|ZP_00366747.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter coli RM2228]
 gi|305433113|ref|ZP_07402269.1| RluA family pseudouridine synthase [Campylobacter coli JV20]
 gi|57020729|gb|EAL57393.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter coli RM2228]
 gi|304443814|gb|EFM36471.1| RluA family pseudouridine synthase [Campylobacter coli JV20]
          Length = 321

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 82/232 (35%), Gaps = 41/232 (17%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             P R+   +A+    SR ++  MI +  V VN  +  + +  +   D + ++ +PL + 
Sbjct: 7   DEPSRLDIFLAKNLQQSRNQIASMIEKNCVWVNDKIQNKNSFKLKVGDKLVLN-LPLVEE 65

Query: 71  ERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
            + +               L + +KP  LV   +     +T+ D L              
Sbjct: 66  AKPKFDIDFDIEILYEDEDLLVLNKPSNLVVHGAKSVRSATLVDWLIEKQYTLSTLGGEV 125

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL------ 158
           R   V RLD  T G +L+  +    + L   L      R+Y       + +DK+      
Sbjct: 126 RAGLVHRLDKETSGAILIAKNNFTHQKLSEQLSDKTMGRIYLALIDLPLKEDKIIIDKAL 185

Query: 159 -----NLLKKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                N +KK +    ++G            +    + +   L  G+  +I+
Sbjct: 186 IRSSANAIKKIVTNSFVKGSKEAKSAFVNLAKSEEVSLIGAKLFTGRTHQIR 237


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 86/243 (35%), Gaps = 44/243 (18%)

Query: 27  SRREVERMIAQQRVKV-NGILL---------ERAAVNVMSTDHIEVDGVPLRKA-ERTRL 75
           SRR+    I    + + NG+           +   V +   D IE + +PL  A E   L
Sbjct: 28  SRRK----IKNNGICLQNGVPASMKDLVHQGDSLEVILQPKDTIEAEDIPLSVAYEDDYL 83

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
            + +KP G++   +  +   T+ + +   +           V RLD NT GL L+  +  
Sbjct: 84  IVVNKPPGMLMHQTSSERFGTLANAIMYYYKVHGYDHDYHPVHRLDRNTSGLCLIAKESY 143

Query: 130 LARVLELPSTQWLRVY-----------RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +  + +     + R Y               H  + +D  +++K+    +         T
Sbjct: 144 VQHLFDKNRLFYARTYTALAQGRFPAMLATVHTPIGRDPDSIIKRNTR-EDGKEAHSDFT 202

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
                   + + + L  G+  +I+    +    +        G      L  GS R +++
Sbjct: 203 RLAVCDDFSLIRITLHTGRTHQIRVHSAYLGHPL-------IG----DDLYGGSRRFLNR 251

Query: 239 KIL 241
           + L
Sbjct: 252 QAL 254


>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 = 69.8 bits (170), Expect = 5e-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  IRLNKLISEAGVCSRREADNFIEMERVTVNGKQP-HVGQKVTAEDLVLVDGERLNVEKYI 61

Query: 74 RL 75
          RL
Sbjct: 62 RL 63


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 85/244 (34%), Gaps = 55/244 (22%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ K + +R   A+R  ++  I    VKVN     +A+  V   D I +          
Sbjct: 34  MRIDKFLMSRIQYATRSRIQYGIEIDSVKVNDKS-TKASYKVRPGDVITISLPHPPREDV 92

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFS---RV 108
              + +PL    E  ++ + +K  G+V   +  +   T+       F+NLP+  +   R 
Sbjct: 93  LIPEDIPLDIVYEDDQILIVNKKPGMVVHPAHGNWTGTLVNALAYHFENLPTHVNGKIRP 152

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             + R+D +T GLL++  T+        +       R Y     G  D       K G  
Sbjct: 153 GLIHRIDKDTSGLLVIAKTDYAMTFMAKQFADHSIERTYYAICWGVPDP------KSG-T 205

Query: 167 IQ---GICYGDMQVTLDTQKGSNAWVTVG-----------------LREGKNREIKKVFE 206
           I+   G    D ++    +   +  + +                  L  G+  +I+   +
Sbjct: 206 IKNYLGRSTKDRKLVTTYENEEDGKLAITHYKTLAAYHYVALIQCNLETGRTHQIRAHMK 265

Query: 207 FFNW 210
               
Sbjct: 266 SIGH 269


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 83/253 (32%), Gaps = 54/253 (21%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV +   P R+ K +  R   +SR  +++      + VN   ++     V   D I +  
Sbjct: 37  IVDKGQEPVRIDKFLFERMQHSSRNRIQKAADAGYIHVNNAPVKS-NYKVRPEDVITLML 95

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP GLV      +   T+ + +      + S
Sbjct: 96  DRPKHDNTIEAEDIPLDVVYEDDILMVVNKPAGLVVHPGAGNFHGTLINAIAWHLKDMPS 155

Query: 111 ----------VGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVRFHGQ 152
                     V R+D +T GLL++  T D   A                 R Y     G 
Sbjct: 156 FDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTH------RSYNAIVWGN 209

Query: 153 VDQDK-----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKN 198
           + +D+            + L+  +       G   VT   +  + G    +   L  G+ 
Sbjct: 210 MTEDEGRIEGNIARDPKDRLRMTVFPPDSEVGKPAVTHYRVIERFGYTTLIECILETGRT 269

Query: 199 REIKKVFEFFNWK 211
            +I+   +     
Sbjct: 270 HQIRAHMKHIGHP 282


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 78/226 (34%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------E 61
           R+ + +A+     SR  ++  I    VKVNGI++ +A   V   + +            E
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVFGGEQVEIQAEIEEEIRFE 78

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   V RL
Sbjct: 79  PQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|229824104|ref|ZP_04450173.1| hypothetical protein GCWU000282_01408 [Catonella morbi ATCC 51271]
 gi|229786458|gb|EEP22572.1| hypothetical protein GCWU000282_01408 [Catonella morbi ATCC 51271]
          Length = 309

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 86/241 (35%), Gaps = 46/241 (19%)

Query: 6   IVQENFTPQ----RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +E F  +    R+ KV+       SR  ++++I    V VNG   ++A   +   + +
Sbjct: 1   MTKEKFQLEGQAGRLDKVLTDLLPGESRSTIQKIIKDGLVSVNGQ-EQKANFKLKGDETL 59

Query: 61  EVDGVPLRKAERTR----------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            V    L   E +                 + + +KP GLV   S    + T+ + L   
Sbjct: 60  LVARRNLAVEEDSLPEPEAMDLDIIYEDEDILVINKPAGLVVHPSKGHLKGTLVNGLLHY 119

Query: 105 ----------FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG- 151
                     F R   V R+D +T GLL++       + L     +    R Y    HG 
Sbjct: 120 LNGNLSTGSDFYRPGIVHRIDKDTSGLLVVAKHNAAHQALADQLLNHDMRRSYIALVHGQ 179

Query: 152 ----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                      + +D  N L+  +  +G         ++  + +   + + L  G+  +I
Sbjct: 180 VKAPQGTIEAPLQRDPANRLRWTVAKEGKYALTRFQVMENFENAT-LLDLELETGRTHQI 238

Query: 202 K 202
           +
Sbjct: 239 R 239


>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 = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y                 + +         +   G      
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>gi|37524666|ref|NP_928010.1| tRNA pseudouridine synthase C [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784091|emb|CAE12960.1| unnamed protein product [Photorhabdus luminescens subsp. laumondii
           TTO1]
          Length = 256

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 56/186 (30%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S      TVF        I   V  V RLD  T G+LL+   
Sbjct: 7   QDDHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLELPSTQW--LRVYRVRFHGQVDQDKL-------------NLLKKG-------- 164
             +AR L          + Y     G V +  +             +   +G        
Sbjct: 67  SDVARQLSQQFEHHQLQKTYHAVVRGYVLESAIIDYALVEELDKIADKFAEGDKEAQSCV 126

Query: 165 IVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              + +   +  V +     S  + + +  + G+  ++++        +        G  
Sbjct: 127 TYYRPLATVECPVEIGRYPTSRFSLLELTPKTGRKHQLRRHMAHIRHPI-------IGDT 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y                 + +         +   G      
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 78/226 (34%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------E 61
           R+ + +A+     SR  ++  I    VKVNGI++ +A   V   + +            E
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVFGGEQVEIQAEIEEEIRFE 78

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   V RL
Sbjct: 79  PQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 237


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 79/233 (33%), Gaps = 40/233 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V  +   +R+S V++     SRR + R+I      VNG  +   +V V   D +  +  
Sbjct: 1   MVPSDLAGRRLSAVLSGRLGMSRRMLRRIIQAGGFYVNGEPVY-LSVTVQDGDRVTWERP 59

Query: 64  ---------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVI 109
                     +PL    E   + + +KP G++T  S  + R ++       L        
Sbjct: 60  EEEVAVEPENIPLEICYEDDDVIVVNKPAGMLTHPSPHERRGSLLAAAAHYLRDRGGVPH 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +V RLD  T G +L+         L+    Q    R Y    +     +    L     +
Sbjct: 120 AVHRLDKYTSGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAPEGCETGRWLT---FV 176

Query: 168 QGICYGDMQ------------------VTLDTQKGSNAWVTVGLREGKNREIK 202
            G+     +                       Q G  A V + L  G+  +I+
Sbjct: 177 DGLAPNPHRPSRRIVVPPDRGDRAVTHALPLVQAGPLALVALVLETGRTHQIR 229


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 39/196 (19%), Positives = 75/196 (38%), Gaps = 19/196 (9%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------- 70
            IA +   S+ + + +I  + V VN   +  A+  +   D +E+   P + A        
Sbjct: 16  FIAASLNISKNQAKDIIDSRNVLVNNKRVWIASHTLKEGDVVEIL-QPQQPATKELKIIY 74

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP    T  SD +  S  F     S   ++ ++ RLD  T G+LLL  D  
Sbjct: 75  EDEYIVAVNKPP---TLLSDREKDSVEFILREKSKNPKIKAIHRLDKETSGILLLAKDYK 131

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           +    +         ++Y    H   ++   N L   + +         + L  +    +
Sbjct: 132 VFERFKELWEDKIVFKLYLAISH---NEANFNHLTVNLPVDDKPAVSH-IKLVKKGNGFS 187

Query: 188 WVTVGLREGKNREIKK 203
           +  V +  G+  +I+K
Sbjct: 188 YFQVRIETGRKHQIRK 203


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 44/221 (19%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  + R T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWRGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIR 259


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 36/239 (15%), Positives = 77/239 (32%), Gaps = 38/239 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +  IV E     R+ + ++      SR  +++++    + +N   ++ A   V  +D 
Sbjct: 1   MNNLFIVDEELFDIRIDRYLSELLPDVSRSFIQKLLKDNEILLNDKPVK-ANYKVQPSDK 59

Query: 60  IEVD-GVPLRK------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I ++   P+               E     + +KP  +V   +      T+ + L     
Sbjct: 60  ININIPKPVEANIVAENIPLDIIYEDDDFLIVNKPKDMVVHPAPGHYTGTLVNGLMYHCK 119

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
                     R   V R+D +T G L++  +      +   L      R Y     G V 
Sbjct: 120 NHLSNINGVLRPGIVHRIDKDTTGALIICKNDYSHNFIAEQLKVHSITRKYVGIVQGVVK 179

Query: 155 QDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +            +N  +  I  +          +  +     ++   L  G+  +I+
Sbjct: 180 DESGTINAPIGRHPVNRKEMAINHKNGKEAVTHYKVLKRFDKYTFMEFQLETGRTHQIR 238


>gi|17978940|gb|AAL47436.1| AT3g52260/T25B15_30 [Arabidopsis thaliana]
          Length = 294

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 32/224 (14%), Positives = 71/224 (31%), Gaps = 56/224 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I   +++++G +++     + S   +    +P ++ +             L   +KP GL
Sbjct: 56  IQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPSGL 115

Query: 85  VTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTEGLLLLTNDGGLAR 132
                    + TV   L   F               + V RL   T G+LL         
Sbjct: 116 QVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLAKT 175

Query: 133 VLE-------------------LPSTQWLRVYRVRFHGQVDQDK--LNL---------LK 162
            L                        +  ++YR    G V++D+  +           + 
Sbjct: 176 KLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVIKQPIGVVRYPGVA 235

Query: 163 KGIVIQGICYGDM----QVTLDTQKGSNAWVTVGLREGKNREIK 202
           +G+ +    +        V    ++ + + V V ++ G+  +I+
Sbjct: 236 QGLYVASPEWKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIR 279


>gi|254670508|emb|CBA06264.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha153]
          Length = 373

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 116

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 117 VPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 237 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 277


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 76/238 (31%), Gaps = 45/238 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +      A+R +++       + VN I ++     V   D I +           
Sbjct: 31  RIDKYLMYLIPNATRNKIQNAATDGNIFVNDIPVKS-NYKVKPFDVITIMLSHPPFENHI 89

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP-SIFSRVISV 111
             + +PL    E   L L +K  G+V      +   T+       FDNLP +   R   V
Sbjct: 90  LPEDIPLNIVYEDDALLLINKEPGMVVHPGHGNYTGTLVNALAHHFDNLPMNSSERPGLV 149

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL-----PSTQWLRVYRVRFHGQVDQD---------- 156
            R+D +T GLL++         +        +    R Y     G V  +          
Sbjct: 150 HRIDKDTSGLLVVA---KTEAAMTHLAKQFEAKTTEREYIALVWGNVAAESGTIEGNLAR 206

Query: 157 -KLNLLKKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              + ++  +               +  + G    ++  L  G+  +I+   +     
Sbjct: 207 HLKDRMQMAVFADPEIGKPAITHYKVLERFGYVTLISCKLETGRTHQIRAHMKHIGHP 264


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 71/212 (33%), Gaps = 30/212 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKAERT 73
           K++A     S ++ + +I +  V V    +  A   +       +    D   + + E+ 
Sbjct: 6   KLLAAQEGISNKKAKELIDRGLVYVGDQKVRIARAEMPEETKFRIEEPADVKIIYQDEQ- 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            +   +KP  + +              +         + RLD +T G+LLL  D   A+ 
Sbjct: 65  -VVAVNKPAFIDSYE------------IEEAIEGAQLLHRLDRDTSGVLLLARDEAFAKK 111

Query: 134 LELP--STQWLRVYRVRFHGQVDQDK-----LNLLKKGI---VIQGICYGDM--QVTLDT 181
                   +  + Y     G V +       ++ +KKG     I          +V  D 
Sbjct: 112 AIEAFRQRKVHKEYVAWVEGVVVEPFEIDLPIHTIKKGKAFSKIDKKLGKPALTKVWPDE 171

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +G  + V + +  G+  +I+         + 
Sbjct: 172 VQGKKSKVRIEIETGRTHQIRVHLAHVGHPIV 203


>gi|225849242|ref|YP_002729406.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644151|gb|ACN99201.1| ribosomal large subunit pseudouridine synthase D
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 318

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 85/246 (34%), Gaps = 38/246 (15%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNV----------M 55
           V E +   R+ + +A+     SR   + +I +  +      +++ ++ V           
Sbjct: 9   VNEEYAGLRLDQFLAKVYPEYSRSYYQDLIEKGFILKEDKPIKKPSLKVKVGESYTVIIP 68

Query: 56  STDHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
               +EV  + +PL+   E   L + +KP G+V   S      T+ + L   F  V    
Sbjct: 69  PPQPLEVVPENIPLKVYYEDEDLAVVYKPPGMVVHPSVGHTSGTLVNALLYHFKNVSTYQ 128

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK-LNL 160
                  V RLD +T GL+++       + L     + +  + Y+    G V +D  +  
Sbjct: 129 GKERAGIVHRLDKDTAGLIIVAKSEFTHKELQKMFQNREIDKRYKAIVVGIVKKDHGIID 188

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVT------------VGLREGKNREIKKVFEFF 208
           L  G  I          T      +  WV             + L  G+  +I+  F   
Sbjct: 189 LPIGRSIYDRQKMGTVATNLRDALTEYWVEKRWEKHNLTMVDIKLHTGRTHQIRVHFSAI 248

Query: 209 NWKVNR 214
              +  
Sbjct: 249 GHPLLN 254


>gi|312601410|gb|ADQ90665.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 168]
          Length = 304

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 87/240 (36%), Gaps = 43/240 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------- 60
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I             
Sbjct: 16  IRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 75

Query: 61  ---EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVI 109
              EVD   + + +     L +KP  LV      + ++T+ + L S F         R  
Sbjct: 76  EPAEVDFEIIFQDQNM--ILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQD 156
            V RLD +T GLLL+  +         EL + Q  R Y+    G            + +D
Sbjct: 134 IVHRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRD 193

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             N LKK I           V L      Q    + V   L  G+  +I+       + +
Sbjct: 194 LKNPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 253


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 90/245 (36%), Gaps = 51/245 (20%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           ++ E   P+R+ +V+AR     SR  ++ ++ +  V+ +GI++   A  V +   I +  
Sbjct: 12  VLDEGTVPERLDRVLARVFDDLSRARLQGLVREGLVRCDGIVVRDPARKVGAGCRINLSV 71

Query: 64  ---------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  L  A   E   L +  KP GLV   +      T+ + L +        
Sbjct: 72  PAPLPAEPLGEALPLAVVHEDEDLIVIDKPAGLVVHPAAGHEDGTLVNRLIAHCGVSLSG 131

Query: 106 ----SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQVDQ 155
                R   V RLD +T GLL++  ND    G  A+  +   +    R Y        + 
Sbjct: 132 IGGVRRPGIVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRSGALERAYLALVWNVPEP 191

Query: 156 ----------------DKLNLLKKGIVIQGICYGDMQVTLD--TQKGSNAWVTVGLREGK 197
                           +K+ +++ G   +G          D   + G  A +   L  G+
Sbjct: 192 RAGTIRANLARSRHNREKIAVVRDG---EGREAITHYRVEDVHGEGGVTALLRCHLETGR 248

Query: 198 NREIK 202
             +I+
Sbjct: 249 THQIR 253


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 49/248 (19%), Positives = 83/248 (33%), Gaps = 42/248 (16%)

Query: 4   KNIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + +V +  T  R+ K +    +  ASR  V+  I  + V VN   ++  +  V   D I 
Sbjct: 23  RIVVDKGQTLLRIDKFLMHR-VENASRNRVQNAIEAENVLVNNRPVKS-SYKVKPGDLIT 80

Query: 62  V-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRST-----VFDN-- 100
           V             + +PL  + E   L + +KP G+V      +   T     V+    
Sbjct: 81  VVLPHPPRDTEIYPENIPLDIRYEDDDLLIVNKPAGMVVHPGYNNYTGTLVNALVYHFNQ 140

Query: 101 ---LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
              LP    R   V R+D +T GLL++  +      L          R Y     G + +
Sbjct: 141 LPQLPGNDGRPGLVHRIDKDTSGLLVIAKNEWTITNLAKQFFDHTIQRKYLALVWGDLQE 200

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------VGLRE-----GKNREIKK 203
           +       G  ++      +    D  K S            V L E     G+  +I+ 
Sbjct: 201 NGTVSGYIGRSLKDRRVMSVYENEDKGKWSVTHYRVLERLGYVTLIECQLETGRTHQIRA 260

Query: 204 VFEFFNWK 211
             +     
Sbjct: 261 HMQSIGHP 268


>gi|323188383|gb|EFZ73674.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           RN587/1]
          Length = 300

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y                 + +         +   G      
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 40/230 (17%), Positives = 84/230 (36%), Gaps = 46/230 (20%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+   +A+     SR  ++ +I Q  +++NG +       V   D + +   P+      
Sbjct: 13  RLDVWLAQKIPDLSRSRLQNLIEQGNLRLNGKICTDKKTKVQQGDLLYLFIPPVEPLNLQ 72

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
                     E  +L + +KP GLV   +    + T+ + L S  S +  +G        
Sbjct: 73  PEEIPLDVLYEDEQLIIINKPAGLVVHPAPGHEKGTLVNALLSHCSNLAGIGGVQRPGIV 132

Query: 113 -RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------------QV 153
            RLD +T G L++  T+        +L +    R Y    +G                 +
Sbjct: 133 HRLDKDTTGALVIAKTDYAHQHLQAQLKAKTARREYLGVVYGVPKTGSGTINLPIGRHPI 192

Query: 154 DQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++ K+ +    + ++ G         +  + G+   +   L  G+  +I+
Sbjct: 193 ERKKMAV----VPLEKGGRVAITHWEIRERLGNYTLIHFRLETGRTHQIR 238


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/216 (19%), Positives = 77/216 (35%), Gaps = 35/216 (16%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           P R+ K +AR     A + SR  + +++ +  ++++G +++ A   V     +E+     
Sbjct: 15  PPRLDKALARDVPEEASL-SRSRLAKLLDEGAIRIDGTVVQDAKARVTEGALVEITIAEA 73

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------- 104
                    +PL    E   L +  KP G+V   +      T+ + L             
Sbjct: 74  NESHIVGQDIPLNVVYEDDDLIVIDKPAGMVVHPAPGSPDGTLVNALIHHCGESLSGVGG 133

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK--LNL 160
             R   V R+D +T GLL+          L     +    R Y    +G +      +  
Sbjct: 134 MKRPGIVHRIDKDTSGLLVAAKTDRAHHGLAALFEAHDIERRYLALCYGVLSAADPRVRG 193

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           L KG+  +      +Q  LD  +         + EG
Sbjct: 194 L-KGVNFELGNILKIQTRLDRHRTDRQR-QAVIWEG 227


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 85/251 (33%), Gaps = 41/251 (16%)

Query: 1   MKD-KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++ K I        R+ K I+     SR  V+ ++A+  + VN   ++ A   V + D 
Sbjct: 1   MREIKIIAAAEDAGARIDKYISEQEDLSRSRVQALLAEGSILVNQNAVK-ANYKVKADDC 59

Query: 60  IE--VDGVPL-----------RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I    +                + E   + + +KP  +V   +  +   T+ + L     
Sbjct: 60  ITAVFNDEMEMEARPEKMELDVRYEDEDVIVINKPKNIVVHPAAGNQSGTLVNGLLYHCK 119

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVD 154
            +           V R+D +T GLL++  +  LA         S    R+Y    HG + 
Sbjct: 120 DLSGINGTLRPGIVHRIDKDTTGLLIIAKN-DLAHASLSKQLQSKTVNRLYYALVHGVI- 177

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
           Q     +   I         M VT    K +     V        L E     G+  +I+
Sbjct: 178 QHDFGTIDAPIGRDVKDRQKMAVTATNSKDARTHFQVIERFENYTLVECRLETGRTHQIR 237

Query: 203 KVFEFFNWKVN 213
              ++    V 
Sbjct: 238 VHMQYIGHPVV 248


>gi|317014156|gb|ADU81592.1| hypothetical protein HPGAM_03855 [Helicobacter pylori Gambia94/24]
          Length = 327

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 58/309 (18%), Positives = 108/309 (34%), Gaps = 55/309 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RLDEFLAKELRISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSQNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICY------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LK  I ++              ++L T +     +   L  G+  +I+          
Sbjct: 193 NRLKM-IALKAAKKEKSRYSKSEFISLLTSQNGMDLIGAKLFTGRTHQIR---AHL---- 244

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L R   G   L  L  G+   +SK+ +R  L  +L+E      +  +     L++D  
Sbjct: 245 EYLNRHIIGD-NLYGLN-GA---LSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDML 299

Query: 273 NIISEVPDD 281
             + +V D 
Sbjct: 300 EYLKKVFDK 308


>gi|220915194|ref|YP_002490498.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219953048|gb|ACL63432.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 339

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 60/352 (17%), Positives = 115/352 (32%), Gaps = 75/352 (21%)

Query: 6   IVQENFTPQRVSKV---------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            V  +   QR+ K+         ++         V +M   ++V+VNG   + A   V  
Sbjct: 5   TVTADAAGQRLDKLVRKALRDVPLSH--------VYKMFRTRKVRVNGQRGK-ADQLVAE 55

Query: 57  TDHIEVDGVPLRK--------------------AERTRLWLYHKPIGLVTTHSDPDGRST 96
            D + + G   R                      E   L    KP GL          +T
Sbjct: 56  GDVVVIRGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGAT 115

Query: 97  VF----------DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLR 143
           +           D+LP    +     RLD +T G++L+         L           +
Sbjct: 116 LVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLTETFTSGEGVHK 175

Query: 144 VYRVRFHGQVDQDK--------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            Y     G++ ++                +   +G+  Q        V+   +    + +
Sbjct: 176 TYLALVKGKMPREAGTIDLPLSEHEQTSKSKAMRGVNFQEALTRWKVVSAAKEI---SLL 232

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST--REVSKKILREQLGP 247
            V +  G+  +I++  E     V    R  YG F            R +     + ++ P
Sbjct: 233 AVTIETGRTHQIRRHLEAVGHPVAG-DR-RYGDFAFNRTARTRWGLRRMGLHAWKLEV-P 289

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           H L  A + L+AP  +    V  R N+  ++P   T     +++++G  +++
Sbjct: 290 HPLTGAPLRLEAPFPAELAEVLSRANL--KLPGSPTGAHAPAARRDGPHRER 339


>gi|282890613|ref|ZP_06299136.1| hypothetical protein pah_c022o218 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281499610|gb|EFB41906.1| hypothetical protein pah_c022o218 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 295

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 54/146 (36%), Gaps = 23/146 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---------------AERT 73
           ++++  I +   ++N  +   A+  V + D IE D   L+                 E  
Sbjct: 30  KQLKHAIERNLCRINQRVERFASTRVANGDQIEWDNDKLQFLFASSQLKFEAKRIIYEDA 89

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            L +Y KP G+    S       +   +      +  V RLD +T G+LL      +   
Sbjct: 90  DLLVYDKPAGINCDTS------GIVRLIHQKDPSLKLVHRLDRDTTGILLFAKTDAVLHK 143

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDK 157
           +     + +  + Y V   G + ++K
Sbjct: 144 MIRLFKTFKVKKTYYVIVDGAISKEK 169


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 42/217 (19%), Positives = 82/217 (37%), Gaps = 27/217 (12%)

Query: 19  VIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKA 70
           ++A + G  SRRE+ R      + +N +        V + D + V       +  P+   
Sbjct: 21  ILAKQMGF-SRREISRSHVSGSIYLNDVKCR-LTQEVHTNDIVTVRTEEPILESKPIILY 78

Query: 71  ERTRLWLYHKPIGLVTTHS----DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           E T + + +KP G+ +  S    D D  S +          V +VGRLD    G+++   
Sbjct: 79  EDTDIVVVNKPAGIPSHASAEHFDDDMGSILKRYYQDDAFTVRTVGRLDKGVSGIVVYAK 138

Query: 127 DGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLL-----KKG-----IVIQGICYGD 174
              +A +L     + L  + Y     G+ ++    L+     +KG     +   G     
Sbjct: 139 TKQMAALLASACEEQLLHKEYLAIVKGKFEEKWGKLIYTLGKEKGIRGRSVTADGQKCIT 198

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               + T+    + + V +  G+  +I+    +F   
Sbjct: 199 -NYEVITEGNFFSLIKVHIETGRLHQIRAGMAYFGHP 234


>gi|301167669|emb|CBW27252.1| putative pseudouridine synthase [Bacteriovorax marinus SJ]
          Length = 276

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 75/179 (41%), Gaps = 16/179 (8%)

Query: 47  LERAAVNVMSTDHIE---------VDGVPLRKAERTRLW-LYHKPIGLVTTHSDPDGRST 96
           + R   N+ S DHIE         VD   +++  +T+ W +++KP G+++  +    +++
Sbjct: 58  IRRVKTNLTSEDHIECHYDPNLPEVDMSLVQEIYKTKGWGVWYKPAGVLSQGTKFGDQAS 117

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD 154
           +  ++         + RLD  T GL+++     +AR+           + Y+    G + 
Sbjct: 118 ILRHVEKNVPNAYLIQRLDRETSGLMIIAYTDKVARIFTNAMKNRLIRKFYQAEVLGTLR 177

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           Q++  +      + G     +   +  +   +  + + +  G+  +I+K FE     V 
Sbjct: 178 QEQGEIA---FDLDGKSAKTL-YQVHEEFEQSTLLEIEIITGRFHQIRKHFEKIKHPVI 232


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 31/65 (47%), Gaps = 1/65 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS-TDHIEVDGVPLRKAER 72
           R+ K +   G  +R +++ M  + R+ VN +  +++   +   +D + VDG  +  AE 
Sbjct: 10 MRLDKYLTEMGQGTRSQIKEMARKGRITVNSVTEKKSDRKISPSSDAVAVDGRIVAYAEY 69

Query: 73 TRLWL 77
              L
Sbjct: 70 EYYML 74


>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 = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 43/294 (14%), Positives = 89/294 (30%), Gaps = 71/294 (24%)

Query: 9   ENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +   P R+ K ++R    +   SR  + +++    + +NG +       + +   +++  
Sbjct: 11  QEDPPARLDKALSRDVPESASLSRTRIAKLLDAGAITINGAVQTDPKAKITAGAQVDITV 70

Query: 63  ----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                     + +PL    E   L + +KP G+V   +      T+ + L   F      
Sbjct: 71  EEAVDSHIEPEDIPLDVMYEDDDLIVVNKPAGMVVHPAPGTPSGTLVNALLHHFAGKLSG 130

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLN 159
                R   V R+D  T GLL++         L          R Y     G  +     
Sbjct: 131 VGGSKRPGVVHRIDKETTGLLVVAKSDAAHHGLAAQFAAHTAERAYLAVTQGAPEASDPR 190

Query: 160 L-------LKKG--------------------IVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +        + G                    ++ +   +   +     + G+   + + 
Sbjct: 191 IRGVRGVSFETGGVLKVTTQLARHKHDRQRQAVLFENGRHAVTRARTIERFGNPHCLALV 250

Query: 193 ---LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
              L  G+  +I+         +            LG    G  R++  K L E
Sbjct: 251 ECRLETGRTHQIRVHMAHVGHGL------------LGDPTYGGRRKLPAKALSE 292


>gi|307708761|ref|ZP_07645223.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
 gi|307615127|gb|EFN94338.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
          Length = 298

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 73/211 (34%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D + +D     G      + +      E     + +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVAIDIPAEEGFETLEAIERPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEQEGEIIAPIARDEDSIITRRVA-KGGKYAHTSYKIV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G+   V + L  G+  +I+  F    + 
Sbjct: 210 ASYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|297180551|gb|ADI16763.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0010_11B23]
          Length = 307

 Score = 69.8 bits (170), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 89/244 (36%), Gaps = 34/244 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +  +  + E  +  RV   +A    A SR  V+++I++ +V +NG   +R    +  +D 
Sbjct: 2   ISKRFQIDEENSNNRVDIFLANNLDAISRGIVQQLISEGKVTINGKETKR-NYLLKPSDI 60

Query: 60  IEV------DGV------PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           +E+      +G       P+    E    ++ +K  GL          +T+ + +     
Sbjct: 61  VEITFELESNGEDEAQDIPVDITFENDDFFVINKHSGLTVHPGAGQKDNTLINGILHIRK 120

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-QVDQDK 157
                 R   V RLD +T GL++L  +     VL     +    R Y    HG  +    
Sbjct: 121 EQRDIPRYGLVHRLDKDTSGLMVLAKNLKAHTVLTELIQAKSIQRKYYALVHGTPISGKT 180

Query: 158 LN---------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           ++          L   +   G         ++ +  + + + V L  G+  +I+   +  
Sbjct: 181 IDLPIGRHPKNRLLFCVK-DGGREAITHFKIEKRFKNFSLLNVELETGRTHQIRVHLKHI 239

Query: 209 NWKV 212
              +
Sbjct: 240 GHPI 243


>gi|319405172|emb|CBI78777.1| ribosomal large subunit pseudouridine synthase D [Bartonella sp. AR
           15-3]
          Length = 333

 Score = 69.8 bits (170), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 37/187 (19%), Positives = 72/187 (38%), Gaps = 33/187 (17%)

Query: 4   KNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++I  EN   QR+ + +A+       SR  ++ +I +  +K++G L++   + + S   I
Sbjct: 3   QHITNENACGQRIDQWLAKQ-YKEELSRSRLQTLIREGYLKIDGQLIKEPKIKLKSNQII 61

Query: 61  EV----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--- 104
           E+           G  L      E   + + +KP GLV    + +   T+ + L      
Sbjct: 62  ELTIPTPNDARPQGEALALDILFEDNHVIVINKPAGLVVHPGNGNWTGTLVNALIYHCSD 121

Query: 105 -------FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                    R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 122 SLSGIGGIKRPGIVHRLDKDTSGVMVIAKNDLAHRNLNAQFADHGRTSALDRRYHAVIWG 181

Query: 152 QVDQDKL 158
             +++ +
Sbjct: 182 SPNRNIV 188


>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 = 69.8 bits (170), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 86/238 (36%), Gaps = 39/238 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA- 70
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I +  D    +   
Sbjct: 16  IRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIRIFNDYKRPKPQL 75

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISV 111
                      +   + L +KP  LV      + ++T+ + L S F         R   V
Sbjct: 76  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 135

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            RLD +T GLLL+  +         EL + Q  R Y+    G            + +D  
Sbjct: 136 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 195

Query: 159 NLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I           V L      Q    + V   L  G+  +I+       + +
Sbjct: 196 NPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 253


>gi|148989142|ref|ZP_01820532.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP6-BS73]
 gi|147925365|gb|EDK76443.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP6-BS73]
          Length = 298

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRK-----AERTRLWLYHKP 81
               + VN    + A   +   D++ +D     G      +        E     + +KP
Sbjct: 33  RGGAILVNNQP-QNATYLLDVGDYVTIDIPAEEGFETLEAIEHLLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKIVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVYIHLHTGRTHQIRVHFSHIGFP 240


>gi|237750038|ref|ZP_04580518.1| pseudouridine synthase D [Helicobacter bilis ATCC 43879]
 gi|229374449|gb|EEO24840.1| pseudouridine synthase D [Helicobacter bilis ATCC 43879]
          Length = 326

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 87/256 (33%), Gaps = 58/256 (22%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVN------GILLERAA----------VNVMST 57
            R+   +      SR +  + I    VK+N        +L++ A            V++T
Sbjct: 12  MRLDNALQEILKISRSQASQWIESNLVKMNEKNTKKSQILKKGACIEIYTIKNTSKVINT 71

Query: 58  DHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSR 107
           D + + G+ +    E +   + +KP  LV  H+      T+ D L          +   R
Sbjct: 72  DEL-IQGLDIEVIHENSDYLILNKPRNLVVHHAPSVKEVTLTDYLSAKNYELSTINGEMR 130

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV------------ 153
              V RLD +T G +L+  +          L +    R+Y    +  +            
Sbjct: 131 FGIVHRLDKDTSGAILVAKNNASHLRFAEMLQNRTMGRIYICVINKALQHNTFVECYMGR 190

Query: 154 DQDKLNLLKKGIVIQGICYGDM-------QVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
           + +    + K   +    Y          +  ++++ G    + V L  G+  +I+    
Sbjct: 191 NPNNRLKMAK---LDKEKYPFARDSKSEFRKIMESKNGVFELIGVRLFSGRTHQIR---- 243

Query: 207 FFNWKVNRLIRISYGP 222
                ++ L R  YG 
Sbjct: 244 ---VHLSTLQRYIYGD 256


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 82/256 (32%), Gaps = 56/256 (21%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V +  TP R+ K +A      SR  +++      ++VN   ++     V   D I +
Sbjct: 24  KIEVDKGQTPVRIDKFLAEKNPYQSRNRIQQAADSGCIRVNNQPVKS-NYKVRPGDVITL 82

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L + +KP G+V      +   T+ + +      +
Sbjct: 83  MLDRPKHDTSIIAEDIPLDIVYEDDVLMVVNKPAGMVVHPGAGNFTGTLINAVAWHLKDL 142

Query: 109 IS----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                       V R+D +T GLL++        VL     +    R Y     G + +D
Sbjct: 143 KGFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKTVLGKQFFNKTTHRSYNALVWGNLVED 202

Query: 157 KLNLLKKGIVIQGICYGDMQ---------------------VTLDTQKGSNAWVTVGLRE 195
                 +G  I+G    D +                       +  + G    V   L  
Sbjct: 203 ------EG-TIEGNVARDPKNRLRMKVFSPESGIGKNAVTHYRVIERYGYTTLVECILET 255

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+   +     
Sbjct: 256 GRTHQIRVHMKHIGHP 271


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 79/234 (33%), Gaps = 45/234 (19%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ +   QR+ + +A      SR  ++  I    V+VNG +       V+  + IE+   
Sbjct: 10  VQSHQMGQRLDQTLAELFPDYSRSRLKTWIEGNLVRVNGNIQNIPRTKVLGGEQIEIRAE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
                    + +PL    E   + + +KP   V      + R TV + L   + ++    
Sbjct: 70  VEEETHYEPENLPLDIVYEDDHILVLNKPKNFVVHPGAGNPRGTVLNALLYHYPQIAEVP 129

Query: 109 --ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
               V RLD +T GL+++         L       +  R Y     G +        K G
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVAFGVMT-------KGG 182

Query: 165 IVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            V + +     + T                      +   + + L  G+  +I+
Sbjct: 183 KVDEPMARHPTKRTAMAVHPMGKPAVTHYRIMEHFRNYTRLRLRLETGRTHQIR 236


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 83/254 (32%), 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--------DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+        D  P               + +KPIG+V      +   T+ + L      
Sbjct: 65  ELSVPEPVPTDLKPQNIPLDVVYEDDDLLVINKPIGMVVHPGAGNPDGTLVNALLHHCKE 124

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D +T GLL++  +     VL          R Y     G    
Sbjct: 125 NLSGINGELRPGIVHRIDKDTSGLLVVAKNDIAHNVLAKQFEDHSIQRTYLAFVWGMPKP 184

Query: 156 --DKLNLL-------KKGIVIQGICYGDM---QVTLDTQKGSN----AWVTVGLREGKNR 199
              ++  L       ++ +  +     D      TL+  KG      + +   L  G+  
Sbjct: 185 IHGRIETLIGRSKYNRQKMSAEVGSGKDAITNYKTLEVFKGKTIPDISLIECRLETGRTH 244

Query: 200 EIKKVFEFFNWKVN 213
           +I+         + 
Sbjct: 245 QIRVHLAHQGNPIL 258


>gi|307704763|ref|ZP_07641659.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307621672|gb|EFO00713.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 298

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 73/211 (34%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D + +D     G      + +      E     + +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVIIDIPAEGGFETLEAIERPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLETEGEIIAPIARDEDSIITRRVA-KGGKYAHTSYKIV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G+   V + L  G+  +I+  F    + 
Sbjct: 210 ASYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 52/246 (21%), Positives = 95/246 (38%), Gaps = 45/246 (18%)

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---VPLRKAERTR----------LWLYHKPIGLVTTHSDPDGRST-VFDNLPSI 104
            IE +      +    +            + +  KPIG+V      +   T V   L   
Sbjct: 61  QIEFENLIEETINLIPKKMDLNIIFEDQDIIIIDKPIGMVVHPGAGNYEDTMVNGLLYHC 120

Query: 105 FSRVIS---------VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
            + +           V R+D +T GLL++  +      +          R Y V  +G +
Sbjct: 121 KNNLSGMNGEDRPGIVHRIDKDTSGLLVVAKNDQAHAFIAKQFEEHSIKRSYLVFVYGIL 180

Query: 154 DQ-----DKL--------NLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREG 196
                  + L          +   + I+G        TL+  KG+     + V   L  G
Sbjct: 181 RPLHGKIETLIGRNKTNRQKMSADV-IRGKDAITNYETLEVFKGNKIPDISLVKCILETG 239

Query: 197 KNREIK 202
           +  +I+
Sbjct: 240 RTHQIR 245


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 36/217 (16%), Positives = 77/217 (35%), Gaps = 42/217 (19%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------GVPLR 68
            +   G +SR  + R+    ++ +NG+        +   D IEVD           VP+ 
Sbjct: 17  FLKANGFSSRT-IRRLKLGGKILINGVPAYT-NTRISCNDVIEVDLTEKSGIVPSPVPIN 74

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGL 121
              E   + + +K  G+V   +      T+ + +    ++         V RLD +T G+
Sbjct: 75  ILYEDDHIIVLNKQPGVVVHPTAFHYNDTIANGVIYYLNQKGKKGGFHPVNRLDRDTTGV 134

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-- 179
           L++         L     +  + Y     G V ++      +G++++ I   +  +    
Sbjct: 135 LIIA-LSQHMHNLIQTHGRMKKRYIAVVEGVVKEN------EGVIVEPIARREGSLIERC 187

Query: 180 --DTQKGSNAWVTVG-----LR----E---GKNREIK 202
             +  + +     V      L     E   G+  +I+
Sbjct: 188 VSEKGQKAITRFKVVKRLKDLTVLDIEPVTGRTHQIR 224


>gi|238917079|ref|YP_002930596.1| lysozyme [Eubacterium eligens ATCC 27750]
 gi|238872439|gb|ACR72149.1| lysozyme [Eubacterium eligens ATCC 27750]
          Length = 310

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 37/255 (14%), Positives = 85/255 (33%), Gaps = 45/255 (17%)

Query: 1   MKD--KNIVQE-NFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M D  +N++ E      R+ K +++     SR  +++++    + V+   ++     +  
Sbjct: 1   MSDSVQNLIAEPEDKGTRIDKYLSQELEDVSRSRIQKLLDDGDITVDDKCVKS-NYKLNG 59

Query: 57  TDHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           T+HI +            + +PL    E   + L  KP G+V   +      TV + L  
Sbjct: 60  TEHITITIPELIVPQILPENIPLNIIYEDDDVILIDKPKGMVVHPAAGHYTGTVVNALMY 119

Query: 104 IFS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG 151
                        R   V R+D+NT G+++   +      +   L      R Y    H 
Sbjct: 120 HCRDNLSGINGVMRPGIVHRIDMNTTGVIVACKNDKAHNDIAAQLAVHSITRKYYCIVHN 179

Query: 152 QVDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
           +  ++                ++   +  +   +      +       +++   L  G+ 
Sbjct: 180 RFKEEEGTVDAPIGRNPKDRKMMA--VDRKNGKHAVTHYRVLENFDKYSFIECQLETGRT 237

Query: 199 REIKKVFEFFNWKVN 213
            +I+         + 
Sbjct: 238 HQIRVHMASIGHPIL 252


>gi|227552604|ref|ZP_03982653.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecium
           TX1330]
 gi|227178230|gb|EEI59202.1| 23S rRNA pseudouridylate synthase RluD [Enterococcus faecium
           TX1330]
          Length = 307

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 45  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 104

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 105 SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQ 164

Query: 136 LPSTQWLRVYRVRFHG-------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G              + +D  +LLK+ +  +G      +  ++ +
Sbjct: 165 LREKKFVKKYQALVSGMLSNLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYRIEKR 223

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 224 LTEIALVDIQLHTGRTHQIRVHFSAIGC 251


>gi|257896942|ref|ZP_05676595.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com12]
 gi|293379115|ref|ZP_06625266.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|257833507|gb|EEV59928.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com12]
 gi|292642256|gb|EFF60415.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 299

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQ 156

Query: 136 LPSTQWLRVYRVRFHG-------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G              + +D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGMLSNLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYRIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 216 LTEIALVDIQLHTGRTHQIRVHFSAIGC 243


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 62/179 (34%), Gaps = 32/179 (17%)

Query: 8   QENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
            E    QR+ + +A + +   SR  ++ +I   +V V+G+ +   +  V++     V G+
Sbjct: 13  TEEDAGQRLDRWLAAS-VESLSRSRLKALIEAGQVAVDGVAVTDPSAKVLAGSEYTV-GI 70

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
           P  +A              E   L + +KP GL    +  +   T+   L          
Sbjct: 71  PEPRADTPTPEPMDLDVLHEDDHLIVINKPAGLSVHPAAGNWTGTLVHGLLHHCAGSLSG 130

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARV---LELPSTQWLRVYRVRFHGQVDQDK 157
                R   V RLD  T G++++     +A     ++       R Y            
Sbjct: 131 IGGVERPGIVHRLDKETSGVMVVAKS-DVAHKGLSIQFARHTVERAYIAFTRNAPSPKA 188


>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 = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 77/233 (33%), Gaps = 38/233 (16%)

Query: 8   QENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
            ++   QR+ K ++      SR  ++ +I+   V +N          V   D I+V+   
Sbjct: 9   DKDGENQRLDKWLSERVHQLSRSRLQALISSGHVWINNSPCTSKKATVQIGDRIQVEIPP 68

Query: 64  ---------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------- 105
                     +PL    E   L + +KP GLV   +      T+ + L +          
Sbjct: 69  AIPLELKATNIPLDILYEDEELLIINKPAGLVVHPAPGHENDTLVNALLAHCETLAGIGG 128

Query: 106 -SRVISVGRLDINTEGLLLLT-NDGGLARVLELPSTQWLR------VYRVR--FHGQVDQ 155
             R   V RLD +T G + +   D     +      +  R      +Y V     G +DQ
Sbjct: 129 VQRPGIVHRLDKDTTGAIAIAKTDHAHQHLQAQIQAKTARRQYLGIIYGVPKTTSGVIDQ 188

Query: 156 ------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +      QG         +  + G+   +   L  G+  +I+
Sbjct: 189 PIGRHPSDRQKMAIVPQHQGGRSAITHWKVKERLGNYTLIEFELETGRTHQIR 241


>gi|197294534|ref|YP_001799075.1| Pseudouridine synthase [Candidatus Phytoplasma australiense]
 gi|171853861|emb|CAM11823.1| Pseudouridine synthase [Candidatus Phytoplasma australiense]
          Length = 302

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 58/295 (19%), Positives = 108/295 (36%), Gaps = 53/295 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----E 61
           ++ E    QR+   +      ++ + +++IA ++V VN    ++    + + D I     
Sbjct: 8   LISEKNKMQRLDHFLVSQTTWNKSQCQKLIAAKKVLVNQKPTKK-NYLLKNQDLITIPTT 66

Query: 62  VDGVPLRKAERTRLWL-----------YHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
           V   PL   +   L L            +KP  L+   S      T+ + L   F     
Sbjct: 67  VFKTPLNIQKPYNLNLEVVYEDSDLAVINKPSNLIVHPSLSFEGITLVNALLHQFSSLSN 126

Query: 106 ---SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG--------- 151
               R   V RLD NT GL+L+  +   ++ L+   +Q    +VY     G         
Sbjct: 127 IDTPRPGIVHRLDKNTTGLMLIAKNDNTSQKLQTAFSQRTIKKVYWGLIEGFLENEGTIN 186

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + ++  + LK  ++  G        TL       + +   L  G+  +I+        
Sbjct: 187 LPIARNPNDRLKMTVLPNGKEAVTHFKTLKRLNNF-SLMQFVLETGRTHQIR---AHL-- 240

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVSKK----ILREQLGPHLLEEAQVNLDAPI 261
             + L +    P  LG  L GS    + +      +E +  H +   ++NL AP+
Sbjct: 241 --SYLKK----PL-LGDKLYGSKHYNTDEGQFLHAKELIFKHPISFQEINLQAPL 288


>gi|50365380|ref|YP_053805.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
 gi|50363936|gb|AAT75921.1| 23S rRNA pseudouridine synthase [Mesoplasma florum L1]
          Length = 323

 Score = 69.4 bits (169), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 32/220 (14%), Positives = 75/220 (34%), Gaps = 43/220 (19%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRL--------------W 76
           + + +  +K+NG  ++     + + D I V  +  P+ + +  ++               
Sbjct: 54  KWLRKGDIKINGKRIKDKDYLIKANDEIIVYDNNKPVLRDDFKKITNYDIDVIYEDSNLL 113

Query: 77  LYHKPIGL-----VTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTN 126
           +  KP  +     V T  D   ++ +FD      S      +  + RLD  T GL++   
Sbjct: 114 IVKKPYNVEVHSPVKTSMDDIVKNYLFDTNQYNPSEENSYVISHIHRLDKLTSGLIMYAK 173

Query: 127 DGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKLNL--------LKKGIVIQGIC--YG 173
           +     ++        +  + YR R    V +  +          ++K +  +     Y 
Sbjct: 174 NKQTHDIMVEAIQDKEKIEKYYRCRIDVPVTESLIAKGWIKYDPIIQKSVFSEEFRSDYK 233

Query: 174 DMQ----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +      V           + V +  G+  +I+   E++ 
Sbjct: 234 EATTIFNVVSLDVTNEQTELEVQILTGRKHQIRATLEYYG 273


>gi|328474367|gb|EGF45172.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 10329]
          Length = 255

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 52/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 20  QDEYFVAVNKPAGMLVHRSWLDKYETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 79

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +       +  + Y     G ++++ +      + +  I         + Q+  
Sbjct: 80  SEVASQVMPMFAEHKMEKTYHAIVRGWIEEEGVLDYALKVELDKIADKFASQEKEAQEAV 139

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
            A+     V V             L E     G+  ++++        + 
Sbjct: 140 TAYKPLAKVEVPYSTGKFPTTRYCLMEMKPKTGRKHQLRRHMAHLRHPIV 189


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 86/244 (35%), Gaps = 46/244 (18%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+  NI   EN+T +RV K +A       SR  +++++    + VN    +  ++ + S 
Sbjct: 1   METYNIEADENWTDKRVDKGLADYFDNY-SRSFLKKLLDDGNILVNDKKAK-PSLKIASG 58

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I++            + +PL    E   + + +KP G+V   +      T+ + L   
Sbjct: 59  DRIDITIPSIASVEIEPENIPLDIVYEDEDIIIVNKPKGMVVHPAPGHYSGTLVNGLMYH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
           F           R   V R+D++T GLL++  +      L   L      R Y       
Sbjct: 119 FKDSLSGINGELRPGIVHRIDMDTTGLLVVCKNDAAHNFLSEQLAVHSITRKYYAICFNY 178

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKN 198
             +D                 +   +  +          +  +  +N   +   L  G+ 
Sbjct: 179 FTEDEGIVDLPIGRHPTDRKKMA--VNYKNGRNAVTHYKVLKKLKNNFCLIECQLETGRT 236

Query: 199 REIK 202
            +I+
Sbjct: 237 HQIR 240


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 95/239 (39%), Gaps = 39/239 (16%)

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-----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            ++V     +G+ L K         E   + + +KP G+V      + + T+ + L +  
Sbjct: 62  IVKVLLPKEEGIYLEKENMDLNILYEDEDIIVINKPQGMVVHPGVGNTKGTLVNGLLAHC 121

Query: 106 S---------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
                     R   V R+D +T G+L++  TN        +L     LRVY     G + 
Sbjct: 122 KSLSNINGEERPGIVHRIDKDTSGILVIAKTNRAHEHLANQLKDHSMLRVYMALTEGVIK 181

Query: 155 QDKL-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +D             + +K  +V +G         +  +  +N+ +   L  G+  +I+
Sbjct: 182 EDMGTIDKDLGRNPSDRIKFAVVDEGKRAVTH-YKVINRYNNNSLIECRLETGRTHQIR 239


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 46/232 (19%), Positives = 80/232 (34%), Gaps = 38/232 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------GVP 66
           QR+ +V A+  G  SR  +   I   R+ V+G +       V +   + +D      G  
Sbjct: 22  QRLDQVAAQLFGEFSRSRLSTWIKDGRLTVDGAVAR-PRDTVHAGSTLVLDAEQEAQGEW 80

Query: 67  LRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVGR 113
           + +        E   L +  KP GLV      H+D    + +  ++P I    R   V R
Sbjct: 81  VAQDIELNIVYEDEHLLVIDKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ------------DKLN 159
           LD +T GL+++         L  +L      R+Y     G +               +  
Sbjct: 141 LDKDTTGLMVVAKTLQAQTNLVEQLQKRSVSRIYECICIGVITAGGTIDAPIGRSSSQRQ 200

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +    V  G         +  +  S+  V V L  G+  +I+       + 
Sbjct: 201 RMA---VTDGGKPAISHYRVLERYRSHTHVRVKLETGRTHQIRVHMSHVGYP 249


>gi|315222714|ref|ZP_07864603.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315188400|gb|EFU22126.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 296

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 48/279 (17%), Positives = 99/279 (35%), Gaps = 52/279 (18%)

Query: 38  QRVKVNGI---------LLERAAVNVMST------DHIEVDGVPLRKAERTRLWLYHKPI 82
             ++VNG          + ++ AV++ +         +E D   +   E     + +KP 
Sbjct: 35  GDIQVNGKKQNAIYLLDIGDKVAVDIPAEEGFGSLQAVEKDLEIV--YEDEHFLILNKPA 92

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           G+ +  S  +  +T+ + + + +        ++  V RLD +T GL+L    G     L 
Sbjct: 93  GVASIPS-VNHSNTMANFVKAYYIANHYENQQIHIVTRLDRDTSGLMLFAKHGYAHARLD 151

Query: 135 -ELPSTQWLRVYRVRFHG----QVDQDKLNLL-KKGIVI------QGICYGDMQVTLDTQ 182
            +L      + Y     G    + + D +  + ++G  I      +   Y      +  Q
Sbjct: 152 KQLQKKVIEKHYYALVKGSAPLKPEGDIIAPIAREGSSIITRCVAKNGKYAHTSYKVLAQ 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V + L  G+  +I+  F +  + +               L  GS   ++  I R
Sbjct: 212 YDDIYLVDIHLHTGRTHQIRVHFSYIGFPLLG-----------DDLYGGS---MTDGITR 257

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           + L  H L       +  +  S  L  D   +I ++ + 
Sbjct: 258 QALHCHSLRFYNPFHEEVVNKSSPLPEDFQTVIQKLSNK 296


>gi|194476821|ref|YP_002049000.1| Pseudouridine synthase, RluD [Paulinella chromatophora]
 gi|171191828|gb|ACB42790.1| Pseudouridine synthase, RluD [Paulinella chromatophora]
          Length = 315

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 87/254 (34%), Gaps = 53/254 (20%)

Query: 5   NIVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            +   +  P R+ + +A         SR  +++ I    V+VNGI        +   D +
Sbjct: 13  KLCYSDLVPMRLDRWLALKRPEQ---SRSRIQKFIYAGLVRVNGIK-SSTKTPLRQGDQV 68

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           ++               +PL    E   L + +KP  L    +  +   T+ + L    S
Sbjct: 69  QIWMPPPDLLPYLIPQHIPLDILFEDQYLIVVNKPADLTVHPAPGNKYGTLVNGLLFHCS 128

Query: 107 RVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG---- 151
            ++ +G         RLD +T G +++  T +   A  L++ +    R Y    HG    
Sbjct: 129 DLMGIGGEMRPGVVHRLDKSTTGCIVIAKTKEILAALQLQIQNRVVSREYIGIVHGVPAT 188

Query: 152 ------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                        V++ +  +L      +   Y      L  + G  + +   L  G+  
Sbjct: 189 NKGTIIGKLGRHPVNRKRYAVLVN----EKGRYACTHWCLIERWGDYSLLRFKLDTGRTH 244

Query: 200 EIKKVFEFFNWKVN 213
           +I+       + + 
Sbjct: 245 QIRIHCSHIGYPII 258


>gi|144575467|gb|AAZ53825.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae 7448]
          Length = 304

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 87/238 (36%), Gaps = 39/238 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA- 70
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I++  D    +   
Sbjct: 16  IRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 75

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISV 111
                      +   + L +KP  LV      + ++T+ + L S F         R   V
Sbjct: 76  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 135

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            RLD +T GLLL+  +         EL + Q  R Y+    G            + +D  
Sbjct: 136 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 195

Query: 159 NLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I           V L      Q    + V   L  G+  +I+       + +
Sbjct: 196 NPLKKTISFFNSKPAITNVELIKHFNYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 253


>gi|299142141|ref|ZP_07035274.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
 gi|298576230|gb|EFI48103.1| ribosomal large subunit pseudouridine synthase D [Prevotella oris
           C735]
          Length = 360

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 78/245 (31%), Gaps = 50/245 (20%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           TP R+ K +A      SR  +++      + VN   ++     V   D I +        
Sbjct: 37  TPVRIDKFLAEKNPYQSRNRIQQAADSGFIHVNDKPVKS-NYKVRPGDVITLMLDRPKHD 95

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   L + +K  G+V      +   T+ + +      + S      
Sbjct: 96  TSIVAEDIPLDIVYEDDALMVINKQAGMVVHPGAGNFTGTLINAVAWHLKDLESFDANDP 155

Query: 111 ----VGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVR---------F 149
               V R+D +T GLL++  T D   A            S        V           
Sbjct: 156 EVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNKTTHRSYNA----LVWGNLIDDEGTI 211

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +D  N L+  +       G   VT   +  + G    V   L  G+  +I+   +
Sbjct: 212 EGNIARDPKNRLRMKVFSPDSGIGKNAVTHYRVIERFGYTTLVECILETGRTHQIRAHMK 271

Query: 207 FFNWK 211
                
Sbjct: 272 HIGHP 276


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 92/239 (38%), Gaps = 39/239 (16%)

Query: 1   MKDKNIV-----QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M++KN +     Q +    R++  +      S R + +   + R+KVN   +   +  + 
Sbjct: 1   MEEKNNILKIKVQIDEEEIRLNHYLKNHANCSSRFIRKAAREGRIKVNNENVR-LSYMLK 59

Query: 56  STDHIEV-----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           + D IE+     +   +           E   + + +KP G+V   +      T+ + + 
Sbjct: 60  NDDVIELQINREENQDIVPEKMHLDVIYEDKDIVVINKPKGIVVHPTKRHQNGTLSNGVL 119

Query: 103 SIFSR------VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD 154
             F        V  V RLD++T GL+L+  +      L        +++ Y    HG + 
Sbjct: 120 YYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKSYLAIVHGNLK 179

Query: 155 QD--KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +    +N          L++ I  +G         +++ + ++  V + L  G+  +I+
Sbjct: 180 EKSGVINKPIYRVGEGTLRRVIDERGQRSVTRFKVVESYEDAD-LVELTLETGRTHQIR 237


>gi|15806790|ref|NP_295512.1| ribosomal large subunit pseudouridine synthase D [Deinococcus
           radiodurans R1]
 gi|6459564|gb|AAF11343.1|AE002020_2 ribosomal large subunit pseudouridine synthase D [Deinococcus
           radiodurans R1]
          Length = 338

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 85/261 (32%), Gaps = 50/261 (19%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----- 54
           M +  +  E    P R+  V++     SR +V   I    V+++G    +A+  +     
Sbjct: 17  MPESPVPLEFTADPGRLDAVVSLLSGVSRSQVAGWIEAGLVEIDGRAASKASQKLRGGEA 76

Query: 55  -------MSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------- 98
                  + +  +E + VPL    E   L   +KP G+VT  +      T+         
Sbjct: 77  LRVSPPPLPSAQVEPEDVPLDVIFEDEHLIAINKPPGMVTHPAPGVISGTLVNALLGRMS 136

Query: 99  -----DNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYR----- 146
                D       R   V RLD +T G++++  T              +  + Y      
Sbjct: 137 LPEQQDFDGPDGYRPGIVHRLDKDTSGVIVVAKTVAAHARLAAAFKDRETKKTYLAIAAG 196

Query: 147 -------VRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-------VTLDTQKGSNAWVTVG 192
                  V+    + + ++   ++ + + G    + Q          D    + A V   
Sbjct: 197 AWKAERPVQVDAPIGRHQIQ--RQRMTVGGAGAREAQTLFTPLDAHPDGHGRTLALVRAQ 254

Query: 193 LREGKNREIKKVFEFFNWKVN 213
            R G+  +I+         + 
Sbjct: 255 PRTGRTHQIRVHLAHLGSPIL 275


>gi|25011211|ref|NP_735606.1| hypothetical protein gbs1160 [Streptococcus agalactiae NEM316]
 gi|76787983|ref|YP_329799.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|77405506|ref|ZP_00782598.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77408702|ref|ZP_00785434.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77410529|ref|ZP_00786890.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77413047|ref|ZP_00789249.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|23095635|emb|CAD46819.1| unknown [Streptococcus agalactiae NEM316]
 gi|76563040|gb|ABA45624.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
 gi|77160945|gb|EAO72054.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|77163477|gb|EAO74427.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77172677|gb|EAO75814.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77175903|gb|EAO78680.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|319745122|gb|EFV97447.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus agalactiae
           ATCC 13813]
          Length = 294

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 74/212 (34%), Gaps = 40/212 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMS-TDHIEVD--GVPLRKA------------ERTRLWLYHK 80
              ++ VNG   E+ A+ ++   D + +D    P  +             E     + +K
Sbjct: 33  RGGKIFVNGE--EQNAIFLLEIGDVVTIDIPDEPSHETLEPVPHDLDIVYEDDHFLILNK 90

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           P G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     
Sbjct: 91  PFGFASIPS-SIHSNTIANFIKHYYVSNNYANQQVHIVTRLDRDTSGLMLFAKHGYAHAR 149

Query: 134 L--ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L  +L +    + Y     G             + +D  +++ + +  +   Y      +
Sbjct: 150 LDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSIITRRVH-ESGKYAHTSYQV 208

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             + G    V + L  G+  +I+  F    + 
Sbjct: 209 VARYGDVRLVDIKLHTGRTHQIRVHFAHIGFP 240


>gi|309389006|gb|ADO76886.1| ribosomal large subunit pseudouridine synthase D [Halanaerobium
           praevalens DSM 2228]
          Length = 303

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 38/245 (15%), Positives = 87/245 (35%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V++    QR+ K +A+     SR  ++++I ++ +KVN  ++++ +  +++ D IE+  
Sbjct: 7   TVKKKDQGQRIDKYLAKYFKDLSRSFIQKLIKEKEIKVNNRVIDK-SYKIINNDFIELKL 65

Query: 65  VPLRKAERTR------------LWLYHKPIGLVTTHSDPDGRSTV-------FDNL--PS 103
                  +              + + +K    V   +      T+        DNL   +
Sbjct: 66  KEQESKVKAVAMKLDIVYEDQDIIVINKDADRVVHPAPGHYNDTIVNGLLACVDNLSAIN 125

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV-------- 153
              R   V RLD +T GLL++  +    + L     +    + Y     G +        
Sbjct: 126 GIKRPGIVHRLDKDTSGLLIVAKNDKSHKSLAKQFKARTVDKYYFALIEGNLAYKKGKIE 185

Query: 154 -----DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                D +    +   +  +       +  +  +      V V +  G+  +I+  F + 
Sbjct: 186 APIGRDPNHRKKMA--VRKRHSKNAISRFKIIEEFNHYTLVEVKIETGRTHQIRVHFSYL 243

Query: 209 NWKVN 213
              + 
Sbjct: 244 GHPIV 248


>gi|254491724|ref|ZP_05104903.1| pseudouridine synthase, RluA family [Methylophaga thiooxidans
           DMS010]
 gi|224463202|gb|EEF79472.1| pseudouridine synthase, RluA family [Methylophaga thiooxydans
           DMS010]
          Length = 320

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 37/239 (15%), Positives = 83/239 (34%), Gaps = 39/239 (16%)

Query: 1   MKDK----NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M +K     I+ +     R+ + +A+     SR ++ + I    V V+   + R   +V+
Sbjct: 1   MSEKIQLQEIIPDELGGMRLDQALAKLFPDFSRGQLTKWIKAGDVTVD-EAILRPRDSVI 59

Query: 56  STDHIEVDGVPLRK--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             +++ +D     +               E   + + +KP G+V      + + T+ + L
Sbjct: 60  GGENVIIDTELQSQDESWSAEPIALDIVHEDDDVIIINKPAGMVVHPGAGNHQGTLVNAL 119

Query: 102 PSI------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVR----- 148
            +         R   V RLD  T GLL++         L     +    R Y+       
Sbjct: 120 LAHAPQLANIPRAGIVHRLDKATTGLLMVAKTLQAHNSLVSQLQARTVQREYQAIAIGVM 179

Query: 149 -----FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +  ++  +  I   G         ++ +  ++  +   L  G+  +I+
Sbjct: 180 TAGGTVDEPIGRHHIDRKRMAISQTGKPAITH-YRVEQRFRAHTHIRCKLETGRTHQIR 237


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 77/243 (31%), Gaps = 46/243 (18%)

Query: 15  RVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DG 64
           R+ K++         SR  ++++I ++ + VN  ++      V     I +       D 
Sbjct: 14  RLDKLLVELLTSYDYSRSYIQKLIKEECISVNNQIITNNNFLVKPNSQITITIKDPILDP 73

Query: 65  VPLRKAE--------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSR 107
             ++  +           L + +K   +    S  +  +T+ + L          +   R
Sbjct: 74  NLVKNEDIDLDIVYQDDDLLVINKQNNITVHPSLNNTNNTIVNALLASDVELSSINGELR 133

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQV----------- 153
              V R+D  T GLL++  +      L      + Q  + Y     G +           
Sbjct: 134 PGIVHRIDKQTTGLLIVAKNDKT-HKLLSEMFKNHQIYKEYLAIVTGVIKPNKGLIDAPI 192

Query: 154 --DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              Q     +   +  +          +  +   N  V   ++ G+  +I+  F + N  
Sbjct: 193 GRSQTDRKKMS--VTAKNSKQAITTFEVVERFLKNTLVKCQIQTGRTHQIRVHFNYINHP 250

Query: 212 VNR 214
           V  
Sbjct: 251 VLN 253


>gi|144227643|gb|AAZ44541.2| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyopneumoniae J]
          Length = 304

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 87/238 (36%), Gaps = 39/238 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA- 70
            R+  ++A+    SR+  + +I +++V +N  L+ +    V +   I++  D    +   
Sbjct: 16  IRIDILVAKLANLSRKVAQDLILEKKVLINNNLVLKKNQIVKTGQKIKIFNDYKRPKPQL 75

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISV 111
                      +   + L +KP  LV      + ++T+ + L S F         R   V
Sbjct: 76  EPAEIDFEIIFQDQNMILINKPKNLVVHPGVGNWKNTLVNGLISHFDSLEQLDHIRPGIV 135

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKL 158
            RLD +T GLLL+  +         EL + Q  R Y+    G            + +D  
Sbjct: 136 HRLDKDTTGLLLVAKNAKAHSFFVNELANRQIKRFYKAIVIGKVLHKFMKINLPIGRDLK 195

Query: 159 NLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LKK I           V L      Q    + V   L  G+  +I+       + +
Sbjct: 196 NPLKKTISFFNSKPAITNVELIKHFSYQNQDFSLVKCQLETGRTHQIRLHLAHIGYPI 253


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 83/253 (32%), Gaps = 54/253 (21%)

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
                      + +PL    E   L + +KP GLV      +   T+ + +      + S
Sbjct: 96  DRPKHDNTIEAEDIPLDVVYEDDVLMVVNKPAGLVVHPGAGNFHGTLINAIAWHLKDMPS 155

Query: 111 ----------VGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVRFHGQ 152
                     V R+D +T GLL++  T D   A                 R Y     G 
Sbjct: 156 FDPNDPEVGLVHRIDKDTSGLLVIAKTPDAKTALGKQFFNKTTH------RSYNAIVWGN 209

Query: 153 VDQDK-----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKN 198
           + +D+            + L+  +       G   VT   +  + G    +   L  G+ 
Sbjct: 210 MTEDEGRIEGNIARDPKDRLRMTVFPPDSEVGKPAVTHYRVIERFGYTTLIECILETGRT 269

Query: 199 REIKKVFEFFNWK 211
            +I+   +     
Sbjct: 270 HQIRAHMKHIGHP 282


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 42/202 (20%), Positives = 71/202 (35%), Gaps = 31/202 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------GVPLR-KAERTRLWL 77
           R+++R   Q +V +NG  ++     V S D I +D           +PL    E   L +
Sbjct: 30  RKIKR---QGQVLINGHPVKSFQTPVSSGDEISIDYGDDSCLTPMKMPLHIVYEDDFLLI 86

Query: 78  YHKPIGLVTT-HSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLA 131
            +KP GL+    SDP   +     L  + S+        + RLD NT GL+ +     + 
Sbjct: 87  VNKPAGLLVHPTSDPTEPTLAHGILYYLHSKGALGAFHPIHRLDRNTSGLVAIAKHPHIQ 146

Query: 132 RVLELPS-TQWLRVYRVRFHGQVD----------QDKLNLLKKGIVIQGICYGDMQVTLD 180
             L         R+Y     G                 N + K +V            + 
Sbjct: 147 HALSGGGAKGLKRLYLAVVTGIPSSLMGRIDAPIGRHPNSIIKRVVRSDGQPAITLYRVL 206

Query: 181 TQKGSNAWVTVGLREGKNREIK 202
           +     + V + L  G+  +I+
Sbjct: 207 STFSMASLVELELLTGRTHQIR 228


>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 = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 81/246 (32%), Gaps = 47/246 (19%)

Query: 12  TPQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
             +R+ K +        +    +R +++  IA   + VNG   +  +  +   D I VD 
Sbjct: 13  AAERLDKYLISCESVQQQCAGLNRSKLKA-IATG-ITVNGRDAK-LSTKIRPGDSIVVDW 69

Query: 64  -----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +K  G+VT  +  +   T+ + L   +      
Sbjct: 70  ADNIPDHIDPEDIPLDIIYEDGNVAVVNKKQGMVTHPALGNWSGTLVNALLFHWNRESVA 129

Query: 106 ---SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV------- 153
               R   V RLD +T GL++     +       +    +  + Y     G+        
Sbjct: 130 QTARRPGIVHRLDKDTSGLIITGKNRESEEWLQAQFRDRRVKKEYIAIVAGRPPHASGTI 189

Query: 154 ------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                 D       K     +   +   Q       GS + + + L+ G+  +I+   ++
Sbjct: 190 KTQIIRDPRNRKRFKAETGTENGKFAHTQYRCIACYGSFSLMRLQLKTGRTHQIRVHMKY 249

Query: 208 FNWKVN 213
               + 
Sbjct: 250 LGCPIL 255


>gi|331007320|ref|ZP_08330519.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
 gi|330418882|gb|EGG93349.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
          Length = 308

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 61/149 (40%), Gaps = 7/149 (4%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTN 126
            +  +  +++KP G+++  S      ++   +            V RLD  T G++L+ +
Sbjct: 93  HDHGQYSIWYKPHGMLSHGSKWGDHCSITRWVEQYHQPQRPSFLVHRLDRATSGIMLIAH 152

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           +  +A  L  +  + Q  + Y     G++   K + L   I  +        +  D +  
Sbjct: 153 NKKVAANLCAQFENRQTDKRYHAVVEGELPSGK-HTLTDPIDNKAAHSEIHTIAYDAENK 211

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           S + V + ++ G+  +I++    F + + 
Sbjct: 212 S-SLVDITIKTGRKHQIRRHLSQFGYPIL 239


>gi|27904851|ref|NP_777977.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34395768|sp|Q89AD9|RLUD_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|27904249|gb|AAO27082.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 317

 Score = 69.4 bits (169), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 85/230 (36%), Gaps = 53/230 (23%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ +V+A      SR  ++R I  + V VNG +L++    V+  D I ++     K    
Sbjct: 20  RLDQVLASLFKKHSRTILKRHILSKDVCVNGRILDQPDAKVLYKDIISINLKFKAKNDYQ 79

Query: 70  ---------AERTRLWLYHKPIGLV----------TTHSDPDGRSTVFDNLPSIFSRVIS 110
                     E   + + +K    V          T  +    R + F N+P    R   
Sbjct: 80  AENIFLNVIYEDDDILVINKQDNFVVHPGAGNTSGTLLNALLHRDSTFFNIP----RAGI 135

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           V RLD +T GL+++  +      L       + +R Y+   +G+V       +  G +++
Sbjct: 136 VHRLDKDTTGLMVIAKNNLSYMALIDQIKCKKVIREYQAIVYGKV-------ISGGTIVK 188

Query: 169 GICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
            I    ++ T                +  +   +  + + L  G+  +I+
Sbjct: 189 SIIRNPIKRTTMIVNKCGKRAITHYRILKRFTHHTHLKIILETGRTHQIR 238


>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 = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 39/230 (16%), Positives = 75/230 (32%), Gaps = 33/230 (14%)

Query: 5   NIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           N V+++   QR+ + IA    A  SR  ++      +V+VNG ++ +    VM  + I +
Sbjct: 9   NTVKDSQLGQRLDQAIAEL-FADFSRSRLKDGCWTGKVQVNGEVVTKPRTKVMGGEEITL 67

Query: 63  -----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV- 108
                D               E   + + +KP   V          TV + L   +  + 
Sbjct: 68  QAELEDEERWEAQDIPLDIVYEDDDIIVINKPRDFVVHPGAGTPDGTVLNALLHHYPDIA 127

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QD 156
                  V RLD +T GL+++         L   L      R Y     G++        
Sbjct: 128 EVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRNITREYEAIAIGRMTAGGKVDQ 187

Query: 157 KLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
            +        +  +            +      +  + + L  G+  +I+
Sbjct: 188 PIGRHSTKRTLMAVAPLGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>gi|303245339|ref|ZP_07331623.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
 gi|302493188|gb|EFL53050.1| pseudouridine synthase, RluA family [Desulfovibrio fructosovorans
           JJ]
          Length = 551

 Score = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 77/227 (33%), Gaps = 45/227 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL------RKAERTRLWLYH- 79
           +R  V   I + R  V+G +  +    +   + +   G+ L       +AE   L L H 
Sbjct: 38  TRARVRAAIEEGRATVDGAVCRKPGTKLRGGEAL---GLRLPALSSETEAEAGALKLLHA 94

Query: 80  --------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--------SVGRLDINTEGLLL 123
                   KP GL    +      T+ + L   F ++          V RLD +T GLLL
Sbjct: 95  DTDVIVLDKPAGLTVHPAPGLPEGTLVNRLLYRFPQLRDMAGERPGIVHRLDKDTSGLLL 154

Query: 124 L--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------------KLNLLKKGIVIQ 168
           +  T     A   +  + +  + Y    HG+ ++D                 +   +V +
Sbjct: 155 VALTESARQALAADFAARRVRKTYLALVHGRPERDGGDIRLPIGRDPKHRAKMA--VVAK 212

Query: 169 GICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G        ++       + + + V +  G+  +I+         + 
Sbjct: 213 GGREARSRWRLVWSAPDAAASLLEVDIFTGRTHQIRVHLAAIGHPIV 259


>gi|269468780|gb|EEZ80384.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 277

 Score = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 30/142 (21%), Positives = 55/142 (38%), Gaps = 7/142 (4%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLL 123
            P    ++    ++ KP G+ +  S       +   +     R    V RLD  T GL+L
Sbjct: 84  QPQLLLDKNDYSVWFKPAGVFSQGSKWGDHCALTRLVEKKLDRPTFLVHRLDRATSGLML 143

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           + +   +AR L          + Y     G+  ++K+  L+K I           VTL  
Sbjct: 144 IAHTKNMARDLSKMFADRNIDKTYLAIVEGKFTKEKI-TLEKPI---DGKNAVSHVTLLE 199

Query: 182 QKGSNAWVTVGLREGKNREIKK 203
            +   + + V +  G+  +I+K
Sbjct: 200 SEKFKSLLKVKIETGRKHQIRK 221


>gi|269219521|ref|ZP_06163375.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211100|gb|EEZ77440.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 309

 Score = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 77/240 (32%), Gaps = 41/240 (17%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++    V +  +  R+  V++R    SR      + +    ++G +  ++   V S  
Sbjct: 1   MPERRFYPVPDGLSGDRIDSVLSRMTGLSRSVCAAAVQKGEAWIDGAVASKSD-RVPSGA 59

Query: 59  HIEV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
            +E+              +G+ +R  E   + +  KP G+    S       V   L   
Sbjct: 60  VLEILVPDPPSLEPRPSAEGI-VRLYEDEDVVVVDKPAGMAAHPSLNFEGPDVLGTLMAE 118

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
                      R   V RLD+ T G +++         L+         +VY     G  
Sbjct: 119 GVKLTTHGPQERKGIVHRLDVGTTGCMVVAKSEAAYSALKRAFRDRAVEKVYHALVQGHP 178

Query: 154 DQ-----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D            D     K  +   G         L+   G+ + + V L  G+  +I+
Sbjct: 179 DPMSGTIEAPIGRDNRRQWKMAVRADGRPSVTHYEALEAMAGA-SLLEVRLETGRTHQIR 237


>gi|88657737|ref|YP_507302.1| ribosomal large subunit pseudouridine synthase A [Ehrlichia
           chaffeensis str. Arkansas]
 gi|88599194|gb|ABD44663.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Ehrlichia chaffeensis str. Arkansas]
          Length = 337

 Score = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 85/244 (34%), Gaps = 43/244 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMS-- 56
           ++ K  ++      R+ K IA     SR +V+++I   ++ +   ++        V    
Sbjct: 16  LEKKIFIKSGDENNRLDKFIASKLNISRNQVQQLIKDSKILLFDTIIRDNNHITKVNDIY 75

Query: 57  ---------TDHIEVDG-VPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                    +D I  +  +P+    E   + + +K  G+          +T+ + L + +
Sbjct: 76  NISIPIKTISDTITPNHYIPISVVYEDHDIIIINKAPGITVHPGAGTNNNTLVNALVAHY 135

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                     +R   + RLD +T GL+++  +      L   L   Q  + Y     G  
Sbjct: 136 GNSLSHVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSDLLLKKQIKKEYLAVVWGLP 195

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLREGKN 198
           +    N +K  I ++      M VT    KG                 + +   +  G+ 
Sbjct: 196 NPKS-NTIKNYICVKPNNKQMMTVTHLPHKGKLAITEYQTQKSFSNIASLIKCRIHTGRT 254

Query: 199 REIK 202
            +I+
Sbjct: 255 HQIR 258


>gi|23098677|ref|NP_692143.1| pseudouridine synthase [Oceanobacillus iheyensis HTE831]
 gi|22776904|dbj|BAC13178.1| pseudouridine synthase [Oceanobacillus iheyensis HTE831]
          Length = 322

 Score = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 81/231 (35%), Gaps = 45/231 (19%)

Query: 19  VIARAGIASRREVERMIAQQRV----KVNGI--------------LLERAAVNVMSTDHI 60
            + +    SRR    +I+ ++V    +VNG                +         +D I
Sbjct: 42  YLQQIHHFSRR---LLISLKKVPSSIQVNGTSQWVTYKLKREDILTVALPDEK--PSDAI 96

Query: 61  EVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGR 113
             + +PL    E     + +KP G     S     +T+ + L   + +      V  V R
Sbjct: 97  TPEKLPLDIIYEDAYCLVVNKPAGQACLPSMNHRHNTLANGLTYYYQKNSIPSTVHIVTR 156

Query: 114 LDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQ-----DKLNLLKKGI 165
           LD+NT GL+L+  +      L           RVY    HG+V       D     K+G 
Sbjct: 157 LDVNTSGLVLVAKN-QYVHSLFSRMQQEGNINRVYEAIVHGEVSPTSGIVDAPIARKEGS 215

Query: 166 VIQ------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +I+         Y      +       +WV + L  G+  +I+  F++   
Sbjct: 216 IIERTVDMRNGKYAKTNYRVLYADSIASWVEIKLETGRTHQIRVHFQYLGH 266


>gi|68171180|ref|ZP_00544587.1| Pseudouridine synthase, RluD [Ehrlichia chaffeensis str. Sapulpa]
 gi|67999411|gb|EAM86053.1| Pseudouridine synthase, RluD [Ehrlichia chaffeensis str. Sapulpa]
          Length = 323

 Score = 69.4 bits (169), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 85/244 (34%), Gaps = 43/244 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA--VNVMS-- 56
           ++ K  ++      R+ K IA     SR +V+++I   ++ +   ++        V    
Sbjct: 2   LEKKIFIKSGDENNRLDKFIASKLNISRNQVQQLIKDSKILLFDTIIRDNNHITKVNDIY 61

Query: 57  ---------TDHIEVDG-VPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                    +D I  +  +P+    E   + + +K  G+          +T+ + L + +
Sbjct: 62  NISIPTKTISDTITPNHYIPISVVYEDHDIIIINKAPGITVHPGAGTNNNTLVNALVAHY 121

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                     +R   + RLD +T GL+++  +      L   L   Q  + Y     G  
Sbjct: 122 GNSLSHVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSDLLLKKQIKKEYLAVVWGLP 181

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLREGKN 198
           +    N +K  I ++      M VT    KG                 + +   +  G+ 
Sbjct: 182 NPKS-NTIKNYICVKPNNKQMMTVTHLPHKGKLAITEYQTQKSFSNIASLIKCRIHTGRT 240

Query: 199 REIK 202
            +I+
Sbjct: 241 HQIR 244


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 78/231 (33%), Gaps = 41/231 (17%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              R+ K +  R    SR +++       V VNG  ++     +   D + +        
Sbjct: 28  ESVRIDKYLLDRMPNTSRNKIQSAAKSGSVVVNGSSVKS-NYKIKPKDEVTIVLPYPVRE 86

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP----SIF 105
                  +P+    E   + + +KP  +V      +   T+       FDNLP      F
Sbjct: 87  LELIAQDIPIDIVYEDDEVIVVNKPPNMVVHPGYGNYTGTLVNALVYHFDNLPERKLDYF 146

Query: 106 SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T G++++  T D       +       R Y+    G V++D       
Sbjct: 147 GRPGLVHRLDKHTTGVMVVAKTEDALTNLAKQFYDRTTERRYQALVWGDVEEDMRIEGNL 206

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVT-------VGLRE-----GKNREIK 202
           G  +       +    D  K +   V        V L E     G+  +I+
Sbjct: 207 GRSLNNRKVMTVFPEGDYGKHAVTHVKVLKRYGLVTLIECKLETGRTHQIR 257


>gi|296117562|ref|ZP_06836146.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969293|gb|EFG82534.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 308

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 75/233 (32%), Gaps = 39/233 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V E     R+   +A+    SR     + A+  V VNG  + ++   + +   +EV    
Sbjct: 10  VPEGNDGLRIDAALAKMLGLSRTVAAELCAEGAVLVNGTTVSKSD-RLTAGQWVEVTLPE 68

Query: 64  -GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
              PL   E              +   +KP+G+    S      TV   L          
Sbjct: 69  PAAPLVPKEELVEGMDVVYSDDDIIAVNKPVGVAAHPSVGWDGPTVIGGLAAAGFRISNS 128

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKL 158
               R   V RLD+ T G++++ +       L+    +    + Y     G  D     +
Sbjct: 129 GPPERKGIVHRLDVGTSGVMVVASSERAYTALKNAFKERTVHKTYHALVQGLPDPIVGTI 188

Query: 159 NL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +           K  +  +   +     +L       + + V L  G+  +I+
Sbjct: 189 DAPIGRHPSSGWKFAVT-EDGKHAITHYSLIEAFREASLLDVHLETGRTHQIR 240


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 36/229 (15%), Positives = 79/229 (34%), Gaps = 34/229 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V  +   +R+ +V+A+     SR  ++  I   ++ V+G +L      ++  + + V+  
Sbjct: 11  VPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEILNTPRTKLLGGEVLNVE-T 69

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
            +                 E   + + +KP+GLV      +   TV + L   +  +I  
Sbjct: 70  TIEAPREYLAQNIDLNIVYEDDHILVINKPMGLVVHPGAGNPDGTVLNALLHHYPDIINV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQD------ 156
                V RLD +T GL+++         L         + R Y    +G +         
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEALCNGTMTAGGMVEKP 189

Query: 157 ---KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       V +          +  +  ++  + + L  G+  +I+
Sbjct: 190 IGRHATQRTHMAVHEMGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIR 238


>gi|42572641|ref|NP_974416.1| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|229891781|sp|Q5M721|PUS5_ARATH RecName: Full=RNA pseudourine synthase 5; AltName: Full=RNA
           pseudouridylate synthase 5; AltName: Full=RNA-uridine
           isomerase 5
 gi|332645400|gb|AEE78921.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 369

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 34/224 (15%), Positives = 72/224 (32%), Gaps = 56/224 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I   +++++G +++     + S   +    +P ++ +             L   +KP GL
Sbjct: 56  IQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPSGL 115

Query: 85  VTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTEGLLLLTNDGGLAR 132
                    + TV   L   F               + V RL   T G+LL         
Sbjct: 116 QVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLAKT 175

Query: 133 VLE-------------------LPSTQWLRVYRVRFHGQVDQDK--LNL---------LK 162
            L                        +  ++YR    G V++D+  +           + 
Sbjct: 176 KLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVIKQPIGVVRYPGVA 235

Query: 163 KGIVI---QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
           +G+ +   +G         L+  +  N + V V ++ G+  +I+
Sbjct: 236 QGLYVASPEGKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIR 279


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 78/245 (31%), Gaps = 50/245 (20%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           TP R+ K +A      SR  +++      + VN   ++     V   D I +        
Sbjct: 54  TPVRIDKFLAEKNPYQSRNRIQQAADSGFIYVNDKPVKS-NYKVRPGDVITLMLDRPKHD 112

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   L + +K  G+V      +   T+ + +      + S      
Sbjct: 113 TSIVAEDIPLDIVYEDDALMVINKQAGMVVHPGAGNFTGTLINAVAWHLKDLESFDANDP 172

Query: 111 ----VGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVR---------F 149
               V R+D +T GLL++  T D   A            S        V           
Sbjct: 173 EVGLVHRIDKDTSGLLVVAKTADAKSALGKQFFNKSTHRSYNA----LVWGNLIDDEGTI 228

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +D  N L+  +       G   VT   +  + G    V   L  G+  +I+   +
Sbjct: 229 EGNIARDPKNRLRMKVFSPDSGIGKNAVTHYRVIERFGYTTLVECILETGRTHQIRAHMK 288

Query: 207 FFNWK 211
                
Sbjct: 289 HIGHP 293


>gi|22537251|ref|NP_688102.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|22534119|gb|AAM99974.1|AE014242_3 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
          Length = 294

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 74/212 (34%), Gaps = 40/212 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMS-TDHIEVD--GVPLRKA------------ERTRLWLYHK 80
              ++ VNG   E+ A+ ++   D + +D    P  +             E     + +K
Sbjct: 33  RGGKIFVNGE--EQNAIFLLEIGDVVTIDIPDEPSHETLEPVPHDLDIIYEDDHFLILNK 90

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           P G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     
Sbjct: 91  PFGFASIPS-SIHSNTIANFIKHYYVSNNYANQQVHIVTRLDRDTSGLMLFAKHGYAHAR 149

Query: 134 L--ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L  +L +    + Y     G             + +D  +++ + +  +   Y      +
Sbjct: 150 LDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSIITRRVH-ESGKYAHTSYQV 208

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             + G    V + L  G+  +I+  F    + 
Sbjct: 209 VARYGDVRLVDIKLHTGRTHQIRVHFAHIGFP 240


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 78/236 (33%), Gaps = 44/236 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-- 61
            VQ + +  R+ + +A   +A  SR  ++ +I Q  V +N          V S D +   
Sbjct: 12  TVQPDQSAMRLDRWLAEQ-VADLSRARIQALIDQGLVLLNNRPCR-PRDLVHSGDAVALT 69

Query: 62  --------VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                   ++  P+      E   L +  KP GLV   +      T+ + L +    +  
Sbjct: 70  IPAPEPLAIEARPIALDIVYEDEELIVIDKPRGLVVHPAPGHSDDTLVNALLAHCRNLSG 129

Query: 111 ---------VGRLDINTEGLLLLT-NDGGLARVLELPSTQWLRV-YRVRFHGQVDQD--- 156
                    V RLD +T GLL++   D     +      +  R  Y     G   +    
Sbjct: 130 INGVLRPGIVHRLDKDTTGLLVVAKTDRAHQHLQTQIQAKTARRDYLAIIAGAPAETTGT 189

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +  +G         L+   G+   V   L+ G+  +I+
Sbjct: 190 IDAPIGRHPVHRQKMA--VHPKGRPARTHWRVLERL-GNFTLVEFSLQTGRTHQIR 242


>gi|291336627|gb|ADD96173.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 59

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
          +K K +     T +R+SK +ARAG+ SRRE ER I   RV ++  ++  AA+NV + 
Sbjct: 2  VKFKTLFNNIDTEERISKRLARAGLCSRREAERWINAGRVSIDNEVINTAAINVSNK 58


>gi|225873450|ref|YP_002754909.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
 gi|225793546|gb|ACO33636.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
          Length = 355

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 90/255 (35%), Gaps = 48/255 (18%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V      QR+   +  +    SR  V+ ++   +V V+  L ERA++ +   + +EV G
Sbjct: 30  TVPAEAAGQRLDAWLTTQLPDVSRSRVKLLLDDGQVTVD-SLKERASLKLRGGESVEVRG 88

Query: 65  VPLRKA--------------ERTRLWLYHKPIGLVT-----THSDPDGRSTVFDNLPSIF 105
            P                  E   L + +KP G++             R T+ + L    
Sbjct: 89  EPAPPPLRAMAEDIPLDIIYEDKDLIVVNKPAGMMVHAGSGATDSARNRGTLVNALLGRQ 148

Query: 106 SRVI---------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
            ++           V RLD  T GL+++  +    + L       +  + Y    HG + 
Sbjct: 149 EKLSKTGGDLRPGIVHRLDKETSGLIIVARNDAAHQRLAEMFSQREIHKTYLALVHGHIA 208

Query: 155 QDKL---NLLKKGIV---------IQGICYG----DMQVTLDTQKGSNAWVTVGLREGKN 198
           +D+      + + ++          +G         +Q  ++T+ G    V+V +  G+ 
Sbjct: 209 EDRGTINAAIARDVIRRTRMTTRRTEGARTAISHYRVQRRIETRWGKFTLVSVRIETGRT 268

Query: 199 REIKKVFEFFNWKVN 213
            +I+         V 
Sbjct: 269 HQIRVHLSSIGHPVV 283


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            VQ     QR+ + +A      SR  ++  I    V VNG++       V   +HIE+  
Sbjct: 9   TVQPQQMGQRLDQTLAELFPDYSRSRLKTWIEDDLVLVNGVVQNVPRTKVYGDEHIEITV 68

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                     + +PL    E   + + +KP  LV      + + TV + L   + ++   
Sbjct: 69  EIEDETRFEPENIPLNIVYEDDDILVINKPKDLVVHPGAGNPKGTVLNALLYHYPQIAEV 128

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L       +  R Y     G +        K 
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMT-------KG 181

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
           G V + +     + T                +  +      + + L  G+  +I+
Sbjct: 182 GTVDEPMARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIR 236


>gi|149187993|ref|ZP_01866288.1| tRNA pseudouridine synthase C [Vibrio shilonii AK1]
 gi|148837981|gb|EDL54923.1| tRNA pseudouridine synthase C [Vibrio shilonii AK1]
          Length = 258

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 32/193 (16%), Positives = 56/193 (29%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D +    V   L       V  + RLD  T G+LL    
Sbjct: 18  QDQYLVAVNKPAGMLVHRSWLDKNETRFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFALS 77

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A             + Y     G + +  +      + +  I         + Q   
Sbjct: 78  SEIASQAMPMFAEHNIEKTYHAIVRGWITEGDVLDYPLKVELDKIADKFASQDKEAQPAV 137

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
            A+     V V             L E     G+  ++++     +  +           
Sbjct: 138 TAYQPLASVEVPYTTGRFPTSRYCLVEMKPKTGRKHQLRRHMHHLSHPIIGDTSHGDGKH 197

Query: 214 -RLIRISYGPFQL 225
            RL R  Y   +L
Sbjct: 198 NRLFREHYDSHRL 210


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 84/240 (35%), Gaps = 43/240 (17%)

Query: 12  TPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +    + ASR  ++       V  NG  ++  +  V   D + V        
Sbjct: 42  APVRIDKYLFERIVNASRNRIQTAADNGYVMANGKPVKS-SYKVKPLDVLTVMMDRPRYE 100

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------ 110
                + +PL    E   L + +KP GLV      +   T+ + +      V +      
Sbjct: 101 NDIIPEDIPLDIVYEDDDLMVVNKPAGLVVHPGCGNYHGTLVNAIAWHLRNVPTYDPNDP 160

Query: 111 ----VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------- 157
               V R+D +T GLL++  T D      ++  +    R Y     G +D+D+       
Sbjct: 161 QVGLVHRIDKDTSGLLVIAKTPDAKTHLGMQFYNKTTKREYNALVWGIIDEDEGTIEGNI 220

Query: 158 ----LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                + ++  ++      G   VT   +  + G    V   L  G+  +I+   +    
Sbjct: 221 GRNPKDRMQMAVM-SDPTQGKHAVTHYQVLERLGYVTLVKCVLETGRTHQIRVHMKHIGH 279


>gi|332088103|gb|EGI93228.1| ribosomal large subunit pseudouridine synthase D [Shigella boydii
           5216-82]
          Length = 300

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 33/149 (22%), Positives = 56/149 (37%), Gaps = 21/149 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD 154
                 L   L   +  R Y     G + 
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMT 154


>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 = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 52/277 (18%), Positives = 95/277 (34%), Gaps = 67/277 (24%)

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------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+            + +PL    E   L + +KP G+V   +      T+ + L      
Sbjct: 67  EITIEEAEDSHIGPEDIPLEVIYEDDDLIVINKPTGMVVHPAPGTPSGTLVNALLHHCGD 126

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D  T GLL++       + L          R YR   +G  D 
Sbjct: 127 NLSGVGGVKRPGIVHRIDKETSGLLVVAKSDVAHQGLAAQFEKHTVERYYRAICYGVPDA 186

Query: 156 DK---------------LNLL------------KKGIVIQGICYGDMQVTLDTQKGSN-- 186
           +                +  L            ++ ++ QG  +   +  +    G+   
Sbjct: 187 NDPRLRGVKGTSFEPGNILKLTTQLARHKTDRQRQAVLFQGGRHAITRARIVDSFGTPPV 246

Query: 187 -AWVTVGLREGKNREIK-KVFEF----FNWKVNRLIR 217
            A +   L  G+  +I+  +           V    R
Sbjct: 247 VALIECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKR 283


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 80/240 (33%), Gaps = 41/240 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+   +V E    +RV   ++R    SR     M     V+V+G+ + + ++ V +   I
Sbjct: 1   MERSILVPEGLEGERVDTALSRLLGLSRSVAAGMAESGDVEVDGVKVPK-SMRVTTGARI 59

Query: 61  EVD----GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNL---- 101
           +V       PL                    +  KP+G+    +      TV   L    
Sbjct: 60  DVTMPKPKEPLSIVAEPVPGMNVIYDDDAFVVVDKPVGVAAHAAAGWSGPTVIGGLAAAG 119

Query: 102 -----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQV 153
                     R   V RLD+ T G++++   G  A  +   + +     + Y     G  
Sbjct: 120 YQIATSGAAERQGIVHRLDVGTSGVMVVA-KGEHAYSVLKRAFKNRTVDKTYHALVQGLP 178

Query: 154 DQ--DKLNL------LKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     +         K G   +   G         L+  + + + V V L  G+  +I+
Sbjct: 179 DPVVGTIEAPIGRHPRKDGLYAVRTDGKHAVTHYEVLEAYRSA-SLVEVKLETGRTHQIR 237


>gi|254431057|ref|ZP_05044760.1| pseudouridylate synthase, 23S rRNA-specific [Cyanobium sp. PCC
           7001]
 gi|197625510|gb|EDY38069.1| pseudouridylate synthase, 23S rRNA-specific [Cyanobium sp. PCC
           7001]
          Length = 320

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 77/245 (31%), Gaps = 57/245 (23%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +      P R+ + + A+    SR  +++ I    V+VNG+    A   +   D +EV 
Sbjct: 13  QLTYPKPLPMRLDRWLVAQRPEQSRARIQKFIEAGYVRVNGVTGR-AKTPLRHGDRVEVW 71

Query: 64  ---GVPLRK-----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                PL              E   L + +KP GL    +  +   T+ + L      + 
Sbjct: 72  MPPPEPLPYLVAQAMPLDVLYEDAHLIVLNKPAGLTVHPAPGNKDGTLVNGLLHHCPDLP 131

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLELPSTQWLRV-----YRVRFHGQVDQ 155
            +G         RLD +T G +++         L     Q  +      Y    HGQ   
Sbjct: 132 GIGGELRPGIVHRLDKDTTGCIVVA---KSQEALVNLQVQIQKRIASRDYLGVVHGQPAA 188

Query: 156 DKLNLLKKGIVIQGICYGDMQVT------------------LDTQKGSNAWVTVGLREGK 197
           D       G VI  I                          +  + G  A +   L  G+
Sbjct: 189 D------HGTVIGAIGRHPADRKKYAVVSDASGRHACTHWQVQERLGDYALLRFKLDTGR 242

Query: 198 NREIK 202
             +I+
Sbjct: 243 THQIR 247


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 79/230 (34%), Gaps = 38/230 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E    QR+ +V+A      SR  +++ I    + V+G  + R    V + + I VD  
Sbjct: 10  VPEGLAGQRLDRVLAALFPDYSRSRLQQWIRAGWITVDGA-VRRPRDPVHAGEQISVDAE 68

Query: 66  PLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
           P  +              E   L +  KP GLV      +   T+ + L      + +  
Sbjct: 69  PEPETPLAPEPIPLRLLYEDDHLLVVDKPAGLVVHPGAGNPGGTLVNALLHYDPGLEALP 128

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD---------- 154
               V RLD  T G+L++         L  +L +    R Y+    G+            
Sbjct: 129 RAGIVHRLDKETSGVLVVARTYAAHHALVAQLQARTVGRGYQAVVVGRPTAGGRVDAPIA 188

Query: 155 --QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   +    V++          +  +  ++  + V L  G+  +I+
Sbjct: 189 RHPRDRKRMA---VVETGRPAVTHYRVAERFTAHTLLDVELETGRTHQIR 235


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 61/172 (35%), Gaps = 22/172 (12%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------ 57
           N V E+    R+ +V+A      SR  ++  I    V VNG ++++    +M        
Sbjct: 9   NTVGESQLGMRLDQVVAELYPDYSRSRIKDWILNGMVSVNGKVVKKPREKMMGGEELFIQ 68

Query: 58  ----DHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               D +      +PL    E   + + +KP   V          TV + L         
Sbjct: 69  AEIEDEVRWVAQDIPLDIVYEDDDILVINKPRDFVVHPGAGTPDGTVLNALLHHCPSLAE 128

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
             R   V RLD +T GL+++         L   L   +  R Y     GQ+ 
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTIQAQTRLVRALQKRKITREYEALAIGQMT 180


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/255 (14%), Positives = 79/255 (30%), Gaps = 46/255 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +K  +    T  R+ K++         SR  ++++I ++ + VN  ++      V     
Sbjct: 2   NKITLNSLNTTLRLDKLLVELLTSYDYSRSYIQKLIKEKCISVNDQIIINNNFLVKPNSE 61

Query: 60  IE------------VDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
           I             V    +      +   L + +K   +    S  +  +T+ + L   
Sbjct: 62  IVITIKDPILDTNLVKNKDIDLDIIYQDDDLLVINKQNNITVHPSLNNTNNTIVNALLAS 121

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQ 152
                  +   R   V R+D  T GLL++  +      L      S +  + Y     G 
Sbjct: 122 DVELSSINGELRPGIVHRIDKQTTGLLIIAKNDKT-HKLLSEMFKSHRIYKEYLAIVTGV 180

Query: 153 V-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +              Q     +   +  +          L  +   N  V   ++ G+  
Sbjct: 181 IKPNKGLIDAPIGRSQTDRKKMS--VTAKNSKQAITTFELVERFLKNTLVKCQIQTGRTH 238

Query: 200 EIKKVFEFFNWKVNR 214
           +I+  F + N  V  
Sbjct: 239 QIRVHFNYINHPVLN 253


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 81/221 (36%), Gaps = 33/221 (14%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----------IEVDG 64
           R+ + +A A   SR   +  I + RV+V   ++++ A  +   +           +  + 
Sbjct: 10  RLDQAVAEALGVSRARAQAWILEGRVRVGEKVVDKPAYRLKGEEVVVEPKEERPLVVPED 69

Query: 65  VPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----------RVISVG 112
           +PL    E   L + +KP GL+T  +      TV + L   +            R   V 
Sbjct: 70  LPLPILYEDEDLLVLNKPPGLLTHPAPGVYTGTVVNALLGRYYEPKAVERPEMVRPGIVH 129

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL-------LKK 163
           RLD +T G+L++   GG    L         ++ Y     G   +  L          + 
Sbjct: 130 RLDKDTSGVLVVAKHGGALEALSQAFRDRLVMKRYLALTEGHPKEGTLIAPIGRHPVERH 189

Query: 164 GIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + + G+   Y +    +    G +A V      G+  +I+
Sbjct: 190 KMHVGGVAPRYAETHFQVLATAGPHALVEARPHTGRTHQIR 230


>gi|22331748|ref|NP_190794.2| pseudouridine synthase family protein [Arabidopsis thaliana]
 gi|56744228|gb|AAW28554.1| At3g52260 [Arabidopsis thaliana]
 gi|332645401|gb|AEE78922.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 294

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/224 (15%), Positives = 72/224 (32%), Gaps = 56/224 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           I   +++++G +++     + S   +    +P ++ +             L   +KP GL
Sbjct: 56  IQNGQIQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPSGL 115

Query: 85  VTTHSDPDGRSTVFDNLPSIF------------SRVISVGRLDINTEGLLLLTNDGGLAR 132
                    + TV   L   F               + V RL   T G+LL         
Sbjct: 116 QVLPGGLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLAKT 175

Query: 133 VLE-------------------LPSTQWLRVYRVRFHGQVDQDK--LNL---------LK 162
            L                        +  ++YR    G V++D+  +           + 
Sbjct: 176 KLAAYFAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVIKQPIGVVRYPGVA 235

Query: 163 KGIVI---QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
           +G+ +   +G         L+  +  N + V V ++ G+  +I+
Sbjct: 236 QGLYVASPEGKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIR 279


>gi|322376764|ref|ZP_08051257.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
 gi|321282571|gb|EFX59578.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
          Length = 298

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 74/211 (35%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G-VPLRKAERTRLWLY--------HKP 81
               + VN    + A   +   D + ++     G   L   ER    LY        +KP
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDRVIINIPAEEGFETLEAIERPLNILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQDYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGYLESEGEIIAPIARDEDSIITRRVA-KGGKYAHTSYKIV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G+   V + L  G+  +I+  F    + 
Sbjct: 210 ASYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|15645364|ref|NP_207538.1| hypothetical protein HP0745 [Helicobacter pylori 26695]
 gi|3915378|sp|O25441|Y745_HELPY RecName: Full=Uncharacterized RNA pseudouridine synthase HP_0745;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|2313872|gb|AAD07795.1| conserved hypothetical protein [Helicobacter pylori 26695]
          Length = 327

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 56/309 (18%), Positives = 109/309 (35%), Gaps = 55/309 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RLDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKITPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L           +  R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKALSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICY------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LK  I ++ +            ++L T + +   +   L  G+  +I+          
Sbjct: 193 NRLKM-IALKAVKKEKSRYSKSEFISLLTSQNNLNLIGAKLFTGRTHQIR---AHL---- 244

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L R   G   L  L  G+   + K+ +R  L  +L+E      +  +     L++D  
Sbjct: 245 EYLNRHIIGD-NLYGLN-GA---LPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDML 299

Query: 273 NIISEVPDD 281
             + +V D 
Sbjct: 300 EYLKKVFDK 308


>gi|254361951|ref|ZP_04978082.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|153093498|gb|EDN74478.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
          Length = 266

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 82/244 (33%), Gaps = 49/244 (20%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  + I+    T      R+ + +A+     SR  ++  I    VKVNG ++ +A   V 
Sbjct: 1   MTQQKILTAEITADLLGARLDQALAQLFPDYSRSRIKVWIESDLVKVNGNIVNKAREKVF 60

Query: 56  STDHI------------EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + +            E   +PL    E   + + +KP  LV      +   TV + L 
Sbjct: 61  GGETVEITAEIEEEIRFEPQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALL 120

Query: 103 SIF------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
             +       R   V RLD +T GL+++  +      L   L   +  R Y     G + 
Sbjct: 121 HYYPPIAEVPRAGIVHRLDKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMT 180

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKN 198
           Q        G V + +     + T                      +   + + L  G+ 
Sbjct: 181 QG-------GKVDEPMARHPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRT 233

Query: 199 REIK 202
            +I+
Sbjct: 234 HQIR 237


>gi|291550385|emb|CBL26647.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus
           torques L2-14]
          Length = 304

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 88/243 (36%), Gaps = 42/243 (17%)

Query: 10  NFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV 65
           + T +R+ K +  R    SR  ++++I ++++ VN + ++ A   + + D I +   D  
Sbjct: 9   DITGERIDKFLDGRIESLSRSYIQKLIKEKKILVNQLPVK-ANYKLTTGDTIILQIPDPE 67

Query: 66  PLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFSR 107
           PL             E   + + +KP G+V   +      T+         +NL  I   
Sbjct: 68  PLDIQPENIPLDILYEDDDILVVNKPKGMVVHPAPGHYSHTLVNAVLYHCGENLSGINGV 127

Query: 108 VIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD------- 156
           +    V R+D+NT G LL+  +    ++L   L      R Y    HG + +D       
Sbjct: 128 IRPGIVHRIDMNTTGSLLICKNDKAHQILAEQLKEHSITRKYHSIVHGNLKEDTGTVNAP 187

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +          +      +  + G+  ++   L  G+  +I+        
Sbjct: 188 IGRHPTDRKKMST--KAPNGRHAVTHYRVLERFGNFTYIECQLETGRTHQIRVHMSSIGH 245

Query: 211 KVN 213
            + 
Sbjct: 246 PIL 248


>gi|225011533|ref|ZP_03701971.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-2A]
 gi|225004036|gb|EEG42008.1| pseudouridine synthase, RluA family [Flavobacteria bacterium
           MS024-2A]
          Length = 346

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 81/229 (35%), Gaps = 39/229 (17%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           +P RV K + AR    +R ++++      + V+G  ++     V   D ++V        
Sbjct: 31  SPLRVDKFLMARVENVTRSKIQQAAKAGSIFVDGNEVKS-NYKVKGGDKVKVLFSHPPYE 89

Query: 63  -----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSI-FSRV 108
                + +PL    E   L + +KP G+V      +   T+       FD LP     R 
Sbjct: 90  NLLVPEDMPLDIVFEDDILVVVNKPPGMVVHPGHGNYSGTLLNGLLYHFDQLPKNSNERP 149

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK--------- 157
             V R+D +T GLL++         L          R Y     G V +++         
Sbjct: 150 GLVHRIDKDTSGLLVIAKTEQAMTHLAKQFFDKTSERKYSALVWGDVKEEEGTIEGAIGR 209

Query: 158 --LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
              N L+  +        + +    +  + G    +   L  G+  +I+
Sbjct: 210 HPKNRLQMAVFEDNSQGKEAKTHFKVIERFGYVTLIECQLETGRTHQIR 258


>gi|76800233|ref|ZP_00781992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
 gi|76584552|gb|EAO61413.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 18RS21]
          Length = 267

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 74/212 (34%), Gaps = 40/212 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMS-TDHIEVD--GVPLRKA------------ERTRLWLYHK 80
              ++ VNG   E+ A+ ++   D + +D    P  +             E     + +K
Sbjct: 24  RGGKIFVNGE--EQNAIFLLEIGDVVTIDIPDEPSHETLEPVPHDLDIVYEDDHFLILNK 81

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           P G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     
Sbjct: 82  PFGFASIPS-SIHSNTIANFIKHYYVSNNYANQQVHIVTRLDRDTSGLMLFAKHGYAHAR 140

Query: 134 L--ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L  +L +    + Y     G             + +D  +++ + +  +   Y      +
Sbjct: 141 LDKQLQAKAIEKRYYALVSGSGDLADSGDIIAPIARDVDSIITRRVH-ESGKYAHTSYQV 199

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             + G    V + L  G+  +I+  F    + 
Sbjct: 200 VARYGDVRLVDIKLHTGRTHQIRVHFAHIGFP 231


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 181


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 181


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 82/236 (34%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V+ +   QR+ + +A      SR  ++  +   +++V+G ++ +    V+  + I + 
Sbjct: 9   DTVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
               D               E   L + +KP  LV          T+ + L   + ++  
Sbjct: 69  AELADEERWEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNALLFHYPQIAE 128

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                 V RLD +T GL+++         L   L   +  R Y     G++         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G+V +GI     + TL                      +  + + L  G+  +I+
Sbjct: 182 GGVVEKGISRHATKRTLMDVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/247 (18%), Positives = 83/247 (33%), 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 ----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK- 157
                     V R+D +T GLL++         L L   +    R Y     G   +D+ 
Sbjct: 145 FDPNDPEVGLVHRIDKDTSGLLVIAKTPMAKTKLGLQFFNKTTHRSYNALVWGNFTEDEG 204

Query: 158 ----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKV 204
                      + L+  +       G   VT   +  + G    V   L  G+  +I+  
Sbjct: 205 RIEGNIARDPKDRLRMTVFAPDSEIGKSAVTHYRVIERFGYVTLVECILETGRTHQIRAH 264

Query: 205 FEFFNWK 211
            +     
Sbjct: 265 MKHIGHP 271


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 81/237 (34%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ K +    +  ASR +++  I    V VN  +++  +  V   D I V          
Sbjct: 32  RIDKFLMNR-VENASRNKIQNAIDAGSVLVNDSVIKS-SYKVKPFDIISVVLPDPPRDTE 89

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
              + +PL    E   + + +K  G+V      +   T+ + L   F+++ +        
Sbjct: 90  VYPEDIPLDIMFEDDEVMVVNKVAGMVVHPGFNNYTGTLVNALTHHFNQLPTMPGNAGRP 149

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD---------K 157
             V R+D +T GLL++         L         +R Y     G + +D          
Sbjct: 150 GLVHRIDKDTSGLLVIAKSEWAMTYLAKQFFDHSIVRKYVAMVWGDIAEDGTITGYIGRN 209

Query: 158 LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           L   +   +      G   VT   +  + G    +   L  G+  +I+   +     
Sbjct: 210 LKDRRVMTMYDDPEKGKWSVTHYRVLERLGYVTLIECQLETGRTHQIRAHMQSIGHP 266


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 82/236 (34%), Gaps = 45/236 (19%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V+ +   QR+ + +A      SR  ++  +   +++V+G ++ +    V+  + I + 
Sbjct: 9   DTVKSSQLGQRLDQAVAELFTDFSRSRIKEWLLDGKIQVDGEVITKPRTIVLGGEAIILQ 68

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
               D               E   L + +KP  LV          T+ + L   + ++  
Sbjct: 69  AELADEERWEAQDIPLDIVYEDDDLLVINKPRDLVVHPGAGTPDGTILNALLFHYPQIAE 128

Query: 109 ----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                 V RLD +T GL+++         L   L   +  R Y     G++         
Sbjct: 129 VPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALAKRRITREYEAIAIGKMT-------A 181

Query: 163 KGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            G+V +GI     + TL                      +  + + L  G+  +I+
Sbjct: 182 GGVVEKGISRHATKRTLMDVNELGKPAVTHYRVAEHFREHTRIRLRLETGRTHQIR 237


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 81/240 (33%), Gaps = 44/240 (18%)

Query: 3   DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI- 60
           ++ I+  N +  R+   +  +    SR  ++++I    + VNG  ++     +   D I 
Sbjct: 2   EEIILVSNESGIRIDAWLCGKVKDYSRSYIQKLINDGMILVNGKPVKS-NYKIKQNDEIL 60

Query: 61  -------EVD------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                   +D       VP+   E   + +  KP G+V   +  +   T+ + L      
Sbjct: 61  ARIPEPQVLDVVAEDIDVPILY-EDEHIIVVDKPKGMVVHPAAGNYSGTLVNALLKHCGT 119

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D +T G+L++         L   L      RVY    HG + +
Sbjct: 120 NLSNINGIIRPGIVHRIDKDTSGVLVVAKSNAAHEGLSEKLKDHDIERVYIAVVHGIIRE 179

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D                 +   +  +       +  +  +     ++   L  G+  +I+
Sbjct: 180 DYGKIDAPIGRHPVDRKKMA--VNTKNGRRAVTRFKVLERFKDATYIEATLETGRTHQIR 237


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 80/228 (35%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------- 58
           +Q     QR+ + +A      SR  ++  I    VKVNG ++  A   V   +       
Sbjct: 10  IQPQHMGQRLDQTLAELFPDYSRSRLKTWIEGDLVKVNGEIINVARTKVYGGELVEICVE 69

Query: 59  -----HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                  E + +PL    E   + + +KP   V      + R TV + L   + +++   
Sbjct: 70  IEEESRFEPENLPLNIVYEDEHILVINKPKDFVVHPGAGNQRGTVLNALLYHYPKIVEVP 129

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV----------RFHGQVD 154
               V RLD +T GL+++         L   L   + +R Y            +    + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVQDLQKRKIIREYEAVAFGVMTQGGKVDQPMS 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +      +  +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHPTKRTQMAVHPLGKPAVTHYRIMERFR-NYTRLRLRLETGRTHQIR 236


>gi|225861064|ref|YP_002742573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298230857|ref|ZP_06964538.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae str. Canada MDR_19F]
 gi|298255783|ref|ZP_06979369.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae str. Canada MDR_19A]
 gi|298502886|ref|YP_003724826.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pneumoniae
           TCH8431/19A]
 gi|225728340|gb|ACO24191.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238481|gb|ADI69612.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pneumoniae
           TCH8431/19A]
 gi|327389344|gb|EGE87689.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA04375]
          Length = 298

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 71/210 (33%), Gaps = 36/210 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D++ +D     G      +        E     + +KP
Sbjct: 33  RGGAILVNNQP-QNATYLLDVGDYVTIDIPAEKGFETLEAIELPLDILYEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDT 181
             +L      + Y     G    + + + +  + +         V +G  Y      +  
Sbjct: 151 DKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGGKYAHTSYKIVA 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G+   V + L  G+  +I+  F    + 
Sbjct: 211 SYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/229 (19%), Positives = 86/229 (37%), Gaps = 37/229 (16%)

Query: 9   ENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           E    QR+ +++ A     SR  V+++I    ++VNG   + A++ V   D IE+     
Sbjct: 14  EAEAGQRLDRLVSANMPDLSRTYVQQLITDLHIRVNGRGAK-ASLPVQIGDQIEIFLPLA 72

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----- 109
                  + +PL    E   + L +K  G+V   +      T+ + L   +  +      
Sbjct: 73  KPTDIVAEDLPLDVIYEDADVLLVNKAAGMVVHPAPGHTTGTLVNALLYRYPHLTTSGDL 132

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QV 153
               V RLD  T GLL++        +L     + +  + Y     G            +
Sbjct: 133 RPGIVHRLDKETSGLLVIAKHDQARMMLTEQQMARRMHKKYLALVEGHWREPTGTIDAPI 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            ++  N L+  ++ +G         L+   G  + V   L  G+  +I+
Sbjct: 193 GRNPNNRLRMMVMPEGRYAVTHYQVLEVL-GPYSLVRATLETGRTHQIR 240


>gi|309378792|emb|CBX22618.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 374

 Score = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/221 (19%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  +HI V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEHIRVSIRPSAEYSAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  APEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  MPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/226 (19%), Positives = 80/226 (35%), Gaps = 34/226 (15%)

Query: 10  NFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                R+  V+A+     SR  +   I +  V VN    +     ++  + I V   P  
Sbjct: 35  EMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQ-PKDKMIGGELIAVTVRPSE 93

Query: 69  K--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRV 108
           +               E   + + +KP GLV   +  +   T+ + L +         R 
Sbjct: 94  ENLAFTPEPMDLDIIYEDDAVIVINKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRA 153

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN------ 159
             V RLD  T GL+++         L  +L      R+YR   +G V    K+       
Sbjct: 154 GIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRD 213

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               LK  +V  G       V +  +  S++++   L  G+  +I+
Sbjct: 214 PHNRLKMAVVKFGGKPAITHVKVLERYLSHSYIECSLETGRTHQIR 259


>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 = 69.1 bits (168), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 88/245 (35%), Gaps = 50/245 (20%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILL----------ERAAVN 53
           N+  EN    R+   ++      SR  ++++I Q  + +N  +           +R  VN
Sbjct: 4   NLTVEN-QGDRLDIWLSNQLTDISRSRIQKLIEQGNITLNNEVCPNKKIKLKIGDRLQVN 62

Query: 54  VMSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
           +     +E+   P+      E  +L + +K   LV   +      T+   L    S +  
Sbjct: 63  IPEPQPLELQPEPIPLDILYEDEQLIIINKSANLVVHPAPGHETGTLVHALLYHCSNLAG 122

Query: 111 VG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKL 158
           +G         RLD +T G +++  T+        ++ +    R Y    +G + +++  
Sbjct: 123 IGGVQRPGIVHRLDKDTTGAIVVAKTDFAHQNLQFQIKNRTAKREYLGIIYGVLNNEEDE 182

Query: 159 NLLKKGIVIQGICYGDMQV---------------------TLDTQKGSNAWVTVGLREGK 197
           N   KG++   +  G   V                      +  + G+ + V   L  G+
Sbjct: 183 NNRDKGMI--NLPIGRHPVDRKRMAVVPREKPGREAVTYWEIIERLGNYSLVKFILETGR 240

Query: 198 NREIK 202
             +I+
Sbjct: 241 THQIR 245


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGEQVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNLDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y                 + +         +   G      
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 83/249 (33%), Gaps = 40/249 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             + +V      +R+ KV+A+     SR  ++  I  QRV+V+G   +     V     I
Sbjct: 67  PRRVVVPNELAGERLDKVLAKVFPEFSRSRLQSWIEAQRVRVDGKPAK-IRQPVPLGATI 125

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           E+             + VPL    E   L + +KP G+V   +  +   TV + L   + 
Sbjct: 126 ELVPDLLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLHRYG 185

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD- 156
                  R   V RLD  T GL+++         L  +L +    R Y     G +  + 
Sbjct: 186 ETAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPDEG 245

Query: 157 --------KLNLLKKGIVIQGICYGDMQ------VTLDTQKGSNAWVTVGLREGKNREIK 202
                         +  V+ G      +       +   Q+     +   L  G+  +I+
Sbjct: 246 TIDAPIGRDPRERTRMAVVTGAAGKPARTHFRRVASAIWQRQPVTAIHCDLETGRTHQIR 305

Query: 203 KVFEFFNWK 211
                    
Sbjct: 306 VHCAHIGHP 314


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/226 (19%), Positives = 79/226 (34%), Gaps = 34/226 (15%)

Query: 10  NFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                R+  V+A+     SR  +   I +  V VN    +     ++  + I V   P  
Sbjct: 35  EMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQ-PKDKMIGGELIAVTVRPSE 93

Query: 69  K--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRV 108
           +               E   + + +KP GLV   +  +   T+ + L +         R 
Sbjct: 94  ENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRA 153

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN------ 159
             V RLD  T GL+++         L     +    R+YR   +G V    K+       
Sbjct: 154 GIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAIANGIVPFDGKIETQIGRD 213

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               LK  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 214 PHNRLKMAVVKFGGKPAITHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 86/250 (34%), Gaps = 44/250 (17%)

Query: 2   KDKNIVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           K+   V+  +  +R+ K ++         SR   +++I    V VN   +++A   + + 
Sbjct: 3   KETFEVEYEYEGERLDKYVSILFPEQ---SRSFFQKLIKDGNVSVNDK-VQKANYRLKTE 58

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D + V            + +PL    E   L + +KP G+V   S      T+ + +   
Sbjct: 59  DLVTVEIPDAVETQILPEDIPLDILYEDDDLLVVNKPKGMVVHPSAGHYSGTLVNAIMYH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQ 152
                       R   V R+D++T G L++  +      +     +    R YR   +G 
Sbjct: 119 CKDSLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHVFIAEQIKEHSVNRRYRGIVYGV 178

Query: 153 VDQDKLNLL---------KKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREI 201
           V  D+  +          +K + I      D      +  +     ++   L  G+  +I
Sbjct: 179 VRDDEGTIHAPIGRHPVDRKKMAINEKNGKDAITHYKVLERFDKYTYMEFKLETGRTHQI 238

Query: 202 KKVFEFFNWK 211
           +         
Sbjct: 239 RVHMASIGHP 248


>gi|34556846|ref|NP_906661.1| putative ribosomal pseudouridine synthase [Wolinella succinogenes
           DSM 1740]
 gi|34482561|emb|CAE09561.1| PUTATIVE RIBOSOMAL PSEUDOURIDINE SYNTHASE [Wolinella succinogenes]
          Length = 308

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 87/244 (35%), Gaps = 41/244 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA-ERTRLWLYHKPI 82
           S++E ++ I + RV++ G      +  V     +     D   L          L+ KP 
Sbjct: 27  SQKEAQKWIDKGRVRIQGEPFLDKSARVSGELEVLFFRPDSRGLEPLFIAPFFALFDKPA 86

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLELP--ST 139
            L+          ++ D +   F        R+D  T G++L+T       +L++   + 
Sbjct: 87  DLLVHPKGTFEHYSLMDEVRLRFGQEADLAHRIDKETSGIVLITRSKKEGAILKINFFNR 146

Query: 140 QWLRVYRVRFHGQVDQDKL---------NLLKKGIVI----QGICYGDMQVTLDTQKGSN 186
           +  + Y     G+++ +++           L  G+ +    +G         LD +  S+
Sbjct: 147 EVKKCYWALVRGKMEGERILDFPLKAQSKRLDLGVRMRVDEKGKSSLTQIKALDYEALSD 206

Query: 187 AWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
                 L E     G+  +I+       + +            LG  L G++ E+S+  L
Sbjct: 207 T----TLVEASPLTGRTHQIRLHLAHAGYPI------------LGDPLYGTSDELSRAYL 250

Query: 242 REQL 245
            + +
Sbjct: 251 EQAM 254


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIIYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQHLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 83/241 (34%), Gaps = 46/241 (19%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +++     SR ++++ I    V++N +++  + + V   D I             
Sbjct: 14  RLDKALSQLLENVSRNQIQKAIKSSCVQINNVIILDSDILVKENDIILFSFKEPEELTIE 73

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
             D       E   L + +K  G+           T+ + L      +  +G        
Sbjct: 74  AADIKLDIVYEDEDLIVINKAAGMTVHPGAGHHDDTLVNALLHHTRNLSDIGSSERPGIV 133

Query: 113 -RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV---------------- 153
            RLD +T GL+++  +     +L       Q +R Y+    G +                
Sbjct: 134 HRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVVRKYKALVWGVINPLEGTIKNNIGRSRS 193

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           D+ K+ +LK G    G        TL+    GS + V   L  G+  +I+         V
Sbjct: 194 DRQKMTILKYG----GKEAVTYYKTLELFYGGSISMVECKLATGRTHQIRVQLSHLKHSV 249

Query: 213 N 213
            
Sbjct: 250 V 250


>gi|326565266|gb|EGE15451.1| ribosomal large subunit pseudouridine synthase D [Moraxella
           catarrhalis 12P80B1]
          Length = 355

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/224 (17%), Positives = 79/224 (35%), Gaps = 36/224 (16%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
            R+ K+ A   G  SR  ++  I + ++ VNG +++     V   D + ++ V       
Sbjct: 55  IRLDKLCADIFGGFSRANLKNFIDEGQLMVNGKVVK-PKYAVKVGDILTLEAVHESHSED 113

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
                      E   + + +KP G+V      +   T+ + L   F +         V R
Sbjct: 114 LPENIDIDIIYEDEAVIIINKPAGMVVHPGAGNRTGTLVNALLYHFPKQAHLPRAGLVHR 173

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-------------RVRFHGQVDQDKL 158
           +D +T GLL++  T    L+ + +L      R Y               +    + +   
Sbjct: 174 IDKDTTGLLVIARTKSAQLSLIDQLKDKSVYRHYQCIALGAVHEVLRHAQIDAPIGRHST 233

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  K  +   G       V         + + + L+ G+  +I+
Sbjct: 234 HRTKMAVKQTGKPALTHIVNAKYLHERYSLLDIHLKTGRTHQIR 277


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 90/238 (37%), Gaps = 40/238 (16%)

Query: 3   DKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           D  IV ++    R+   IA      SR  ++++I + R++VN  + E+A+  V + D IE
Sbjct: 20  DVYIVSDDDADSRLDFYIASQYRDISRSYIQKLIKEDRIRVNSKI-EKASYKVKTGDKIE 78

Query: 62  VD--------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------D 99
           V+              G+ +   E   L + +K  G+V   +  +   T+         D
Sbjct: 79  VNMPEPQALEIEPQDIGIDIVY-EDDYLMVVNKQQGMVVHPAPGNPDRTLVNAVLFHCGD 137

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR------- 148
            L SI   +    V R+D NT GLL++  D    + L          R Y +        
Sbjct: 138 RLSSINGVIRPGIVHRIDKNTSGLLVIAKDNQTHQGLSDQFKVHSITREYEMICIGNVEW 197

Query: 149 ----FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G + ++  + +K  IV            L       + ++  L  G+  +I+
Sbjct: 198 QEKTIDGPIGRNPKDRMKMAIVKTNGKRAVTHFRLVENYDGYSHLSARLETGRTHQIR 255


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 181


>gi|195978164|ref|YP_002123408.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
 gi|195974869|gb|ACG62395.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equi subsp. zooepidemicus MGCS10565]
          Length = 298

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 81/238 (34%), Gaps = 53/238 (22%)

Query: 25  IASRR-EVERMIAQ---------------QRVKVNGILLERAAVNVMSTDHIEVD---GV 65
           +A+R+ +V+ ++ +                 + VNG + + A   +   D + +D     
Sbjct: 6   VATRKTKVKTLLKEHDVSKGLLAKIKYKGGNIWVNG-VAQNAIYLLDIGDVVAIDIPNEE 64

Query: 66  PLRK-----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
           P  +            E     + +KP G  +  S     +T+ + + + +        +
Sbjct: 65  PFEQLTAISHDLDIVYEDEHFLILNKPAGYASIPS-AIHSNTIANFIKAYYIKQDYPNKQ 123

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QV 153
           V  V RLD +T GL+L    G     L  +L      + Y     G             +
Sbjct: 124 VHIVTRLDRDTSGLMLFAKHGYAHARLDKQLQQRAINKRYYALVCGQERLPDQGEIIAPI 183

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +   +++ + +  +G         +     + + V + L  G+  +I+  F    + 
Sbjct: 184 GRTDDSIITRTVTPKGKYAKTSYKVIARYPENVSLVDIRLHTGRTHQIRVHFAHLGFP 241


>gi|268608720|ref|ZP_06142447.1| hypothetical protein RflaF_04377 [Ruminococcus flavefaciens FD-1]
          Length = 446

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 56/324 (17%), Positives = 111/324 (34%), Gaps = 58/324 (17%)

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---DGVPLRK---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           D I +   D   L            E   + +++KP G+    S      T+ +   ++F
Sbjct: 58  DVIVLRFGDDSFLEPNPDLDVPAVYESDGVIVFNKPSGMPVHPSIKHQGDTLGNKFAAMF 117

Query: 106 SRV--ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ-----DKL 158
             +   +V RLD +T GL ++      A        +  +VY     G++ +       +
Sbjct: 118 PDLTFRAVNRLDRDTSGLCVV---AKNALAANALQGRCEKVYYAAVTGEIPETGTIDAPI 174

Query: 159 NLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
              ++ I+I    +               G  +   + L  G+  +I+  F +       
Sbjct: 175 ARERESIIIRCVREDGQRAVTHYRRIAYNGRYSLAEIHLETGRTHQIRVHFSYIGH---- 230

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNI 274
                  P     L  G+         R  +G   L   Q++   P+   E  VR     
Sbjct: 231 -------PLAGDDLYGGT---------RCDIGRQALHCGQMSFTDPVTGEEVTVR----- 269

Query: 275 ISEVPDDFTRMKKNSSQKNGLSKQ 298
            +E+PDD   + K+  Q+    ++
Sbjct: 270 -AELPDDIKAIIKSDKQEEKKMER 292


>gi|285808641|gb|ADC36159.1| RluA family pseudouridine synthase [uncultured bacterium 162]
          Length = 326

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 63/201 (31%), Gaps = 25/201 (12%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE----------RTRLWLYHKPIGL 84
           +    V V+G+     + ++ S   +  +  P  + +             L   +KP GL
Sbjct: 69  LDNGEVTVDGVTA-NGSESLASGQTLVWNRPPWVEPDAPQHFEMLFDDPYLLAVNKPSGL 127

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST--QWL 142
            T        +T+   + +       V RL   T G++L       A  L       +  
Sbjct: 128 PTLPGGGFMENTLLRLVQNQCPSANPVHRLGRGTSGIVLFAKTPKAAAELCANWNTPRIQ 187

Query: 143 RVYRVRFHGQVDQDKLNLLKK-GIVIQ-----------GICYGDMQVTLDTQKGSNAWVT 190
           +VYR    G  + D   +L   G+V                       + ++  S     
Sbjct: 188 KVYRAVAQGVAEHDAYEILTPIGLVPHPLIGSVWGASPDGKPSKSVAKVISRAESTTTFE 247

Query: 191 VGLREGKNREIKKVFEFFNWK 211
           V L+ G+  +I+       + 
Sbjct: 248 VSLQSGRPHQIRIHLASIGYP 268


>gi|325203791|gb|ADY99244.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240355]
          Length = 374

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>gi|323156250|gb|EFZ42409.1| ribosomal large subunit pseudouridine synthase D [Escherichia coli
           EPECa14]
          Length = 300

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I  QRV VNG + ++    V+  + + ++             +PL    E  
Sbjct: 6   SRSRIKEWILDQRVLVNGKVCDKPKEKVLGGELVAINAEIEEEARFEPQDIPLDIVYEDE 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y                 + +         +   G      
Sbjct: 126 VPAQTRLVESLQRREITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMAVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>gi|304385442|ref|ZP_07367787.1| RluA family pseudouridine synthase [Pediococcus acidilactici DSM
           20284]
 gi|304328649|gb|EFL95870.1| RluA family pseudouridine synthase [Pediococcus acidilactici DSM
           20284]
          Length = 292

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 78/234 (33%), Gaps = 47/234 (20%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------------- 61
            KV+ R G AS+R +++ I Q     +G L++     V   D +                
Sbjct: 16  QKVLQRLG-ASQRLMQK-IRQ-----DGRLVDENERTVALKDKVMPFEPFWVELPDEDSD 68

Query: 62  ----VDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
               V   PL        WL  +KP GL       +   T+ + +   +    +V     
Sbjct: 69  PAVPVSDQPLDVIYEDDNWLVVNKPAGLTAVPGPSNRTDTLVNRIKGHWQANGAVNLVPH 128

Query: 113 ---RLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK------LNL 160
              RLD  T G+ L+     +A  L        +  + Y     G V  +K      L L
Sbjct: 129 LITRLDRFTSGITLVARH-QVANSLLSEQVRHRKIKKTYLALVDGVVSAEKGTFNQPLGL 187

Query: 161 LKKGI---VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              GI   V +G         +  +  +   V V L+ G+  +I+  F      
Sbjct: 188 AADGIHREVQEGGQSATTSFKVVQRFANQTLVQVHLKTGRTHQIRVHFANAGHP 241


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 84/237 (35%), Gaps = 45/237 (18%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           + +    QR+ KV++  G+    SR  +++ I    V VNG   + A + ++  + +EV 
Sbjct: 46  LDDEVIGQRLDKVLS--GLLPEFSRSRIQQWIEDGHVTVNGAPAK-AKMTMLGDELVEVA 102

Query: 64  GVPLRK--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
              +                 E   L + +KP GLV   +  +   T+ + L        
Sbjct: 103 PQSVPSDQPYGPEPMALDILHEDKALIVLNKPAGLVVHPAAGNWSGTLLNGLLHHCPALA 162

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD +T G++++         L  +L +    R Y     G          
Sbjct: 163 KVPRAGIVHRLDKDTSGIMVVAKTLAAQTDLVRQLQARSMKRQYLALVWGLPQLSGTINA 222

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQ------VTLDTQKGSNAWVTVGLREGKNREIK 202
            + +   + +K  +  Q +             T +  +   + +   L  G+  +I+
Sbjct: 223 PMARHPRDRIKMAVS-QSMRAKPAVTHYRRLATGEIDRKPVSLIHCRLETGRTHQIR 278


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 70/207 (33%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKA----------ERT 73
           SR  ++  I  QRV VNG L ++    V+  + + +D      +R            E  
Sbjct: 6   SRSRIKEWILNQRVLVNGQLCDKPKEKVLGGERVAIDAEIDEEIRFEAQDIPLDIVYEDD 65

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + + +KP  LV      +   TV + L   +       R   V RLD +T GL+++   
Sbjct: 66  DILVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKT 125

Query: 128 GGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDM 175
                 L   L   +  R Y              +  + +         +   G      
Sbjct: 126 VPAQTRLVESLQLREITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMSVHPMGKPAVTH 185

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++  +  +  + + L  G+  +I+
Sbjct: 186 YRIMEHFRV-HTRLRLRLETGRTHQIR 211


>gi|316971885|gb|EFV55608.1| pseudouridylate synthase 6 [Trichinella spiralis]
          Length = 404

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/210 (15%), Positives = 68/210 (32%), Gaps = 31/210 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRKAERTRLWLYHKP 81
           E  I   RV VNG         V + D I           +D       +   + + +KP
Sbjct: 88  EEAILAGRVTVNGQP-TSVDYVVENGDLIRHMCHRHELPVLDSAVDIVTDTEDILVVNKP 146

Query: 82  IG--LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
               +            ++         + +  RLD  T GL++   +  + + L     
Sbjct: 147 CSIPVHPCGRYHFNSLVLYLKHIGGMDNLKTFHRLDRLTSGLVIFLKNEKIEKKLRQQMI 206

Query: 138 STQWLRVYRVRFHGQVDQDK------LNLLKK--GIVIQGICYGDMQVTLDT-----QKG 184
             Q  + Y     G+  +++      L++L +  GI+       D + +L         G
Sbjct: 207 ENQIKKEYLCLVDGEFPEEEVVCDKPLDVLSQSMGIM---YITADGKPSLTKFYKLFSDG 263

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
             + +      G+  +I+   ++  + +  
Sbjct: 264 KTSILKCCPETGRTHQIRVHLQYLGYPIVN 293


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>gi|261209248|ref|ZP_05923640.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium TC 6]
 gi|289565997|ref|ZP_06446435.1| pseudouridylate synthase, 23S RNA-specific [Enterococcus faecium
           D344SRF]
 gi|294616199|ref|ZP_06695996.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|260076794|gb|EEW64529.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium TC 6]
 gi|289162195|gb|EFD10057.1| pseudouridylate synthase, 23S RNA-specific [Enterococcus faecium
           D344SRF]
 gi|291590954|gb|EFF22666.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
          Length = 299

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQ 156

Query: 136 LPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G++               D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGRLSDLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 216 LTEIALVDIQLHTGRTHQIRVHFSAIGC 243


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 39/234 (16%), Positives = 78/234 (33%), Gaps = 41/234 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +R+   ++R    SR     +I    V V+G    ++   V +   ++V    
Sbjct: 9   VPDGLEGERLDAALSRLFGFSRTRAAELIVSGDVLVDGSPAAKSD-RVHAGAWLDVTLPP 67

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                        G+ +   +   + + +KPIG+    +      TV   L     RV  
Sbjct: 68  PPTAPMPVAEPVPGMKIVYEDDDIVVV-NKPIGVAAHPTTGWTGPTVIGGLLGTGHRVAT 126

Query: 109 -------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD----- 154
                    V RLD NT G +++         L+    +    + Y     G  D     
Sbjct: 127 SGAAERQGIVHRLDANTTGAMVVAKSEHAYSHLKRAFKERTVDKRYHALVQGHPDPLRGT 186

Query: 155 -QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               ++    G     +V  G        T++  + + + + + L  G+  +I+
Sbjct: 187 VDAPIDRHPSGDGRFAVVAGGKESVTHYDTIEAFRAA-SLLDIKLETGRTHQIR 239


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 78/235 (33%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            VQ     QR+ + +A      SR  ++  I +  V VNG++       V   +HIE+  
Sbjct: 9   TVQPQQMGQRLDQTLAELFPDYSRSRLKTWIEEDLVLVNGVVQNVPRTKVYGDEHIEITV 68

Query: 63  ---DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
              D               E   + + +KP  LV      + + TV + L   + ++   
Sbjct: 69  EIEDETRFEPEAIPLNIVYEDEDILVINKPKDLVVHPGAGNPKGTVLNALLYHYPQIAEV 128

Query: 109 ---ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L       +  R Y     G +        K 
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMT-------KG 181

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
           G V + +     + T                +  +      + + L  G+  +I+
Sbjct: 182 GTVDEPMARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIR 236


>gi|307637434|gb|ADN79884.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 908]
 gi|325996024|gb|ADZ51429.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori 2018]
 gi|325997619|gb|ADZ49827.1| Ribosomal large subunit pseudouridylate synthase D [Helicobacter
           pylori 2017]
          Length = 327

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 57/310 (18%), Positives = 107/310 (34%), Gaps = 57/310 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSQNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVCLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICY------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            N LK  I ++              ++L T +     +   L  G+  +I+         
Sbjct: 192 NNRLKM-IALKAAQKEKSRYSKSEFISLLTSQNGMDLIGAKLFTGRTHQIR---AHL--- 244

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
              L R   G   L  L  G+   +SK+ +R  L  +L+E      +  +     L++D 
Sbjct: 245 -EYLNRHIIGD-NLYGLN-GA---LSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDM 298

Query: 272 PNIISEVPDD 281
              + +V D 
Sbjct: 299 LEYLKKVFDK 308


>gi|257888167|ref|ZP_05667820.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,141,733]
 gi|257824221|gb|EEV51153.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,141,733]
          Length = 299

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQ 156

Query: 136 LPSTQWLRVYRVRFHG-------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G              + +D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGMLSNLSAHSHIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 216 LTEIALVDIQLHTGRTHQIRVHFSAIGC 243


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 84/262 (32%), Gaps = 53/262 (20%)

Query: 3   DKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++ ++  + T + R+   + A+ G   SR  ++ +I   +V + G  +      V + D 
Sbjct: 11  NRKVLTADETAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVSLRGEPVTDPQRKVRNGDS 70

Query: 60  IEV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
            E+           G  +      E   L +  KP GLV      +   T+ + L     
Sbjct: 71  FEITLPEPEDPTPQGEDIPLDILHEDEDLIVISKPSGLVVHPGSGNWTGTLVNALIHHCG 130

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFH 150
                     R   V RLD +T G++++  +    R L L      R       Y+    
Sbjct: 131 DTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAVVW 190

Query: 151 G-----------QVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSNAWVTVGLR 194
           G            + +   +  ++ +        D      +V    Q+  +A     L 
Sbjct: 191 GRPRSLTGTVDAPLGRATGDRTRRAVKRPDSHDADEAITHYEVIERFQENPDATALASLV 250

Query: 195 E-----GKNREIKKVFEFFNWK 211
           E     G+  +I+         
Sbjct: 251 ECHLETGRTHQIRVHMAHIGHP 272


>gi|325206453|gb|ADZ01906.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M04-240196]
          Length = 374

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 181


>gi|119476986|ref|ZP_01617267.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119449793|gb|EAW31030.1| RNA pseudouridine synthase family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 280

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 34/215 (15%), Positives = 80/215 (37%), Gaps = 23/215 (10%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNG----ILLERAAVNVMSTDHIEVD----------G 64
           ++A     S+ ++++ + +  V ++G      L R+   +   D + +            
Sbjct: 17  LLAEDTGLSKTKIKQAMQKGAVWISGGRKAERLRRSKKRLKPGDQLHLYYNEDILTKNVP 76

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLL 122
           +P   ++     +++KP G++   S      T+ D +  I+   R   V RLD  T GL+
Sbjct: 77  MPTLISDHNDYSIWYKPYGVLCQGSKWGDHCTI-DRMIEIYTQKRSYLVHRLDRATTGLM 135

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTL 179
           ++ +   +A  L          + Y     G     +K   +     + G         L
Sbjct: 136 IIAHSKDMAAKLSKLFRDRAIDKRYLAIVDGDFPYCEKKQTITS--TLDGKKAISHMRRL 193

Query: 180 D-TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +Q+   + + V +  G+  +I++      + + 
Sbjct: 194 RYSQRHHQSLIDVNIETGRKHQIRRQLSDQGYPIV 228


>gi|329114084|ref|ZP_08242848.1| Ribosomal large subunit pseudouridine synthase D [Acetobacter
           pomorum DM001]
 gi|326696623|gb|EGE48300.1| Ribosomal large subunit pseudouridine synthase D [Acetobacter
           pomorum DM001]
          Length = 337

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 84/256 (32%), Gaps = 44/256 (17%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V      +R+ + +A      SR  ++ +I +  +K +G+ +   A    +   +E+  
Sbjct: 22  TVTPEQAGERIDRFLAAIMETLSRSRIKSLIEEGHLKCDGVCIREPAAIARAGMKVELTI 81

Query: 63  --------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  +      E   L +  KP GLV   +  +   T+ + L +        
Sbjct: 82  PPAAPAVPQGEDISFTVLYEDDDLIVLDKPAGLVVHPAPGNETGTLVNGLIAHCGESLKG 141

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRF--------- 149
                R   V RLD +T G+++      +A           +  R Y             
Sbjct: 142 IGGERRPGIVHRLDKDTSGVMVAA-KTEMAHQALSEDFAARRIDRTYLAFCWGLPNPAEG 200

Query: 150 --HGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G + +DK +  +  +  +G  +      TL       A V   L  G+  +I+  F 
Sbjct: 201 DFEGAIGRDKRDRKRMALTPKGGKWALTHYRTLQAFGTGAALVACKLATGRTHQIRVHFS 260

Query: 207 FFNWKV----NRLIRI 218
                +      L RI
Sbjct: 261 ANGHPLIGDPLYLRRI 276


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 83/238 (34%), Gaps = 40/238 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
           K+   + E     R  K +A    G+ SR  ++ +    ++ +NG   E+    +   D 
Sbjct: 5   KEVIKITEEEKGIRADKFLALKIDGV-SRNFIQGLFDDGKILINGK-AEKGKYKLSVGDC 62

Query: 59  -----------HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------D 99
                       +E + +PL    E   + + +KP G+V   +  +   T+        D
Sbjct: 63  VEVEIPEPEELKVEAEDIPLNIVYEDEDVIVVNKPKGMVVHPAPGNYTGTLVNALLHHCD 122

Query: 100 NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---- 151
           +L  I   +    V R+D +T G+L++  +    + L          R Y     G    
Sbjct: 123 DLSGINGVIRPGIVHRIDKDTSGILVVAKNDNAHQKLAEQFKDHSIKREYYAIVEGRFKK 182

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +   + LK  +V  G         L     S + V   L  G+  +I+
Sbjct: 183 EGGTIDAPLGRHHRDRLKYAVVKDGKRAVTHYEVLKVFN-SCSLVKCNLETGRTHQIR 239


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 84/239 (35%), Gaps = 39/239 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  I++ +    R+   +A      SR  ++++     + VN  +  ++   V   D+
Sbjct: 1   MKEF-ILECDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNIWVN-EVQAKSNYKVKPGDN 58

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I+V            + +PL    E   + + +KP G+V   +  +   T+ + L     
Sbjct: 59  IKVSVPDAEILDVEPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYSGTLVNALMKHCG 118

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--- 151
                     R   V R+D +T GLL++         L   L +    R Y     G   
Sbjct: 119 DSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALVDGIIY 178

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +  +   K  +  Q          +  +  S  +V + L  G+  +I+
Sbjct: 179 ENSGKIDAPIGRHPVERKKMSVNTQNGRNAITHFKVLERFPSATYVQLKLETGRTHQIR 237


>gi|148994152|ref|ZP_01823467.1| phosphotransacetylase [Streptococcus pneumoniae SP9-BS68]
 gi|168488941|ref|ZP_02713140.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|147927395|gb|EDK78425.1| phosphotransacetylase [Streptococcus pneumoniae SP9-BS68]
 gi|183572419|gb|EDT92947.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|332073458|gb|EGI83937.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA17570]
          Length = 298

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 58/161 (36%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLL 123
           E     + +KP G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L
Sbjct: 81  EDDHFLVLNKPYGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLML 139

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGI 170
               G     L  +L      + Y     G    + + + +  + +         V +G 
Sbjct: 140 FAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGG 199

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            Y      +    G+   V + L  G+  +I+  F    + 
Sbjct: 200 KYAHTSYKIVASYGNIHLVYIHLHTGRTHQIRVHFSHIGFP 240


>gi|148985070|ref|ZP_01818313.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP3-BS71]
 gi|148998365|ref|ZP_01825807.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP11-BS70]
 gi|149024900|ref|ZP_01836301.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP23-BS72]
 gi|225856742|ref|YP_002738253.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|225858911|ref|YP_002740421.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|307067719|ref|YP_003876685.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147755762|gb|EDK62807.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP11-BS70]
 gi|147922768|gb|EDK73885.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP3-BS71]
 gi|147929523|gb|EDK80517.1| inorganic polyphosphate/ATP-NAD kinase [Streptococcus pneumoniae
           SP23-BS72]
 gi|225721947|gb|ACO17801.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|225724376|gb|ACO20228.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|301800069|emb|CBW32664.1| putative RNA pseudouridylate synthase [Streptococcus pneumoniae
           OXC141]
 gi|306409256|gb|ADM84683.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
 gi|332200523|gb|EGJ14595.1| pseudouridine synthase, RluA family protein [Streptococcus
           pneumoniae GA41317]
          Length = 298

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 58/161 (36%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLL 123
           E     + +KP G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L
Sbjct: 81  EDDHFLVLNKPYGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLML 139

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGI 170
               G     L  +L      + Y     G    + + + +  + +         V +G 
Sbjct: 140 FAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGG 199

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            Y      +    G+   V + L  G+  +I+  F    + 
Sbjct: 200 KYAHTSYKIVASYGNIHLVYIHLHTGRTHQIRVHFSHIGFP 240


>gi|66043991|ref|YP_233832.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63254698|gb|AAY35794.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
          Length = 320

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 85/230 (36%), Gaps = 34/230 (14%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G    R    V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGG-ALRPRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNLL 161
           RLD +T GL+++  T       V +L S    R+Y     G V                 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++  V++G         +  +  S+  V V L  G+  +I+      N+ 
Sbjct: 196 QRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYP 245


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 79/244 (32%), Gaps = 49/244 (20%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  +  +Q   T      R+ + +A+     SR  ++  I    V VNG ++ +A   V 
Sbjct: 1   MTQQITLQTEVTSDLLGARLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKVF 60

Query: 56  ST------------DHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                            E   +PL    E   + + +KP  LV      +   TV + L 
Sbjct: 61  GGELIEIQAEIEEEIRFEPQNIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTVLNALL 120

Query: 103 SIFSRV------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
             + ++        V RLD +T GL+++         L   L   +  R Y     G + 
Sbjct: 121 HHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTALQKREITREYEAVASGIMT 180

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKN 198
           Q        G V + +     + T                      +   + + L  G+ 
Sbjct: 181 QG-------GKVDEPMARHPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRT 233

Query: 199 REIK 202
            +I+
Sbjct: 234 HQIR 237


>gi|3402691|gb|AAC28994.1| unknown protein [Arabidopsis thaliana]
          Length = 86

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 18/82 (21%), Positives = 40/82 (48%), Gaps = 3/82 (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-GTLLAGSTREVSKKILREQ 244
           +L   L  G   E+ +  L+  
Sbjct: 61  RLPSDLGLGKHVELKQSELKAL 82


>gi|330721752|gb|EGG99744.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC2047]
          Length = 287

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 24/161 (14%), Positives = 48/161 (29%), Gaps = 15/161 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGL 121
            P   A+     +++KP G+ +  S       ++  +            V RLD    GL
Sbjct: 85  EPQMIADEGAYSVWYKPYGMRSQGSKWGDHCALYRWVEVNHKPEKPAFLVHRLDRAATGL 144

Query: 122 LLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ-----DKLNLLKKGIVIQGICYGD 174
           +L+ +    A  L          + Y+V   GQ  +      K       +         
Sbjct: 145 ILVAHSKKAAVALTKLFEERNVDKRYQVIVVGQFSEQSGVWAKKQTFTAEV---DGKAAT 201

Query: 175 MQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     +   + + V +  G+  +I+       + V 
Sbjct: 202 SHARCLAYDAEKDRSLLEVTIETGRKHQIRYHLAAAGFPVV 242


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 80/226 (35%), Gaps = 34/226 (15%)

Query: 10  NFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                R+  V+A+     SR  +   I +  V VN    +     ++  + I V   P  
Sbjct: 35  EMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQ-PKDKMIGGELIAVTVRPSE 93

Query: 69  K--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRV 108
           +               E   + + +KP GLV   +  +   T+ + L +         R 
Sbjct: 94  ENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPASGNWSGTLLNGLLAHCPELSQVPRA 153

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN------ 159
             V RLD  T GL+++         L  +L      R+YR   +G V    K+       
Sbjct: 154 GIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAIANGIVPFDGKIETQIGRD 213

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               LK  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 214 PHNRLKMAVVKFGGKPAITHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 80/244 (32%), Gaps = 49/244 (20%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  +  +Q   T      R+ + +A+     SR  ++  I    V VNG ++ +A   V 
Sbjct: 1   MTQQITLQTEVTSDLLGARLDQALAQLFPDYSRSRIKVWIESDLVSVNGKIVNKAREKVF 60

Query: 56  ST------------DHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                            E   +PL    E   + + +KP  LV      +   TV + L 
Sbjct: 61  GGELIEIQAEIEEEIRFEPQNIPLNIVYEDDDILVINKPKDLVVHPGAGNPDGTVLNALL 120

Query: 103 SIFSRV------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
             + ++        V RLD +T GL+++         L   L   +  R Y     G + 
Sbjct: 121 HHYPQIAEVPRAGIVHRLDKDTTGLMVVAKTVPAQTHLVTALQRREITREYEAVASGIMT 180

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKN 198
           Q        G V + +     + T                      + + + + L  G+ 
Sbjct: 181 QG-------GKVDEPMARHPTKRTAMAVHPMGKPAVTHYRIMERFRNYSRLRLRLETGRT 233

Query: 199 REIK 202
            +I+
Sbjct: 234 HQIR 237


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 81/243 (33%), Gaps = 38/243 (15%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------GVP 66
           QR+ +V A+     SR  +   I   R+ V+G +L      V S   + ++      G  
Sbjct: 18  QRLDQVAAQLFSEYSRSRLSSWIKDGRLTVDGAVLR-PRDTVHSGSILALEAEQEAQGEW 76

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGR 113
           + +        E  ++ + +KP GLV   +      T+ + L      +I       V R
Sbjct: 77  VAQDIELDIVYEDDQILVINKPAGLVVHPAAGHPDGTLLNALLHHVPDIINVPRAGIVHR 136

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG----------QVDQDKLNLL 161
           LD +T GL+++         L     +    R+Y     G           + +      
Sbjct: 137 LDKDTTGLMVVAKTLQAQTNLVDQLQKRSVSRIYECIVVGVVIAGGKIDAPIGRHGGERQ 196

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIR 217
           +  +   G         +  +  S+  V V L  G+  +I+       + +       +R
Sbjct: 197 RMAVT-DGGKPAVSHYRVLKRFRSHTHVRVKLETGRTHQIRVHMAHVGYPLVGDQTYGVR 255

Query: 218 ISY 220
              
Sbjct: 256 FRI 258


>gi|325133782|gb|EGC56438.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M13399]
          Length = 356

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 22  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 80

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 81  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 141 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 201 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIR 241


>gi|205373291|ref|ZP_03226095.1| YlyB [Bacillus coahuilensis m4-4]
          Length = 301

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 77/242 (31%), Gaps = 56/242 (23%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVN---------GILLERAAVNVM 55
            V +    +R+ KV++      SR +V++ I    V VN             +   + V 
Sbjct: 7   TVTQEQVGERIDKVVSTINSDWSRSQVQQWIKDGHVLVNMEQKRTNYKSQASDVITIEVP 66

Query: 56  STDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
             + ++V+   L      E   + + +KP G+V   +      T+ + L      +    
Sbjct: 67  EAEVLDVEAEDLNLDVYYEDQDVIVVNKPKGMVVHPAPGHYSGTLVNGLMHHCKDLSGIN 126

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                  V R+D +T GLL++  +      L                  V +  +  L  
Sbjct: 127 GVMRPGIVHRIDKDTSGLLMVAKNDVAHEHLVNQ----------LVEKSVTRKYM-ALVH 175

Query: 164 GIVIQGICYGDMQV-----------TLDTQKGSNAWVTV-------GLRE-----GKNRE 200
           G++       D  +            +D  K +     V        L E     G+  +
Sbjct: 176 GVIQHDYGTIDAPIGRDSKDRQSMTIVDQGKHAVTHFEVKDRFEQYTLVECQLETGRTHQ 235

Query: 201 IK 202
           I+
Sbjct: 236 IR 237


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 28/216 (12%), Positives = 74/216 (34%), Gaps = 43/216 (19%)

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 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-------------NLLKKGIVIQGI 170
              DG             L+ Y     G   +D +              +L++ I ++ +
Sbjct: 143 AIKDG-------YKPENVLKKYLAVVIGNFPEDTIVFNKIVYKKRKKVKVLEE-IDLEHL 194

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKN----REIK 202
                 + +     + + + + +          +I+
Sbjct: 195 S----NIKVINSDKNYSLLEITI----FKATRHQIR 222


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 80/248 (32%), Gaps = 46/248 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +  +    R+ KV+A  G+    SR  ++  I    V VNG   +     V   D + V
Sbjct: 20  FIPPDVPADRLDKVLA--GLMPGHSRSRLQGWIEAGHVLVNGQAAK-VRQPVGPGDVLTV 76

Query: 63  DGVP----LRKAERTR----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
              P    L  +                + +KP GLVT     +   T+ + L   F   
Sbjct: 77  WEQPAPESLAFSPEPVDFDVIDSSSDWIVVNKPAGLVTHPGAGNWTGTLLNGLLHRFPEL 136

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFH 150
               R   V RLD +T GL+++  +      L  +L +    R Y               
Sbjct: 137 SRVARAGIVHRLDKDTSGLMVVARNELAQTHLVRQLQARSMGREYLALAHGWLAGAGTVD 196

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDM------QVTLDTQKGSN-AWVTVGLREGKNREIKK 203
             + +D    ++  +  + I           Q   + Q+G     V   L  G+  +I+ 
Sbjct: 197 RPIGRDARVPVRMSVE-RPIAAKPAITHYLPQRRGEAQEGERVTEVICRLETGRTHQIRV 255

Query: 204 VFEFFNWK 211
                   
Sbjct: 256 HLASLGHP 263


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 37/233 (15%), Positives = 75/233 (32%), Gaps = 48/233 (20%)

Query: 22  RAGIASRREV-------ERM---IA-QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            AG   R+         E++   I     + VNG  +   +  + + D +       R  
Sbjct: 11  HAGCCVRQAARGPMHLSEKLWRKIKWNGTITVNGSPVSSPSHRLEAGDRLVF-----RWE 65

Query: 71  ERTRLWLYH----------------KPIGLVTTHSDPDGRSTVFDNLPSIFSR------V 108
           E+  +   H                KP G++   +    R T+   +   F R      +
Sbjct: 66  EKAAVIPVHLPLSLLYEDEDLLVVDKPAGMLIHPTWSGARDTLVQAVGGYFRRTGQHCGI 125

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ--VDQDKLN----LLK 162
             + RLD +T G+L++         L    +Q  R Y     G+  + Q ++      + 
Sbjct: 126 HPLYRLDRDTTGVLMVAKSAFAKHALTRDHSQIYREYLAVCEGRWGIPQGRIEHPIGRVA 185

Query: 163 KGI----VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +G+    V         +  +  +      + + L  G+  +I+  F      
Sbjct: 186 EGVDRWTVRPDGRPAVTEYRILEENQEWTVLKIHLLTGRTHQIRVHFAHEGHP 238


>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 = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 116

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 117 VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 237 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 277


>gi|251772724|gb|EES53286.1| Ribosomal large subunit pseudouridine synthase, RluA family
           [Leptospirillum ferrodiazotrophum]
          Length = 313

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/245 (16%), Positives = 76/245 (31%), Gaps = 43/245 (17%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V    + +R+   +A+     SR  +++++ +  + VNG + E A+  +   D I V   
Sbjct: 4   VDPGESKKRLDHFLAQTCLPFSRSRIQKILDEGLITVNGRI-EPASYKIRGADIITVHIP 62

Query: 66  PLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
           P                 E   L + +KP  LV   +      T+ + L    SR  +  
Sbjct: 63  PPAPSEDAPEEMDLDILYEDEFLLVINKPPSLVVHPAPGHPNGTLLNGLLGHLSREEAGE 122

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD----- 154
                    V RLD NT GLL++     +   L          + Y     G        
Sbjct: 123 GEGPARAGLVHRLDQNTSGLLVVGKKSEVVDHLMEQFRGRTVSKSYIALAIGIPPSRRGL 182

Query: 155 --------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                             +   G         +   +   + + + L  G+  +I+   +
Sbjct: 183 IDAPIGRSNGDRKKFA--VTSGGKPSQTRYRVMTAYREGYSLLDITLLTGRTHQIRVHMQ 240

Query: 207 FFNWK 211
              + 
Sbjct: 241 HLGYP 245


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/226 (19%), Positives = 79/226 (34%), Gaps = 34/226 (15%)

Query: 10  NFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
                R+  V+A+     SR  +   I +  V VN    +     ++  + I V   P  
Sbjct: 35  EMAGGRLDAVLAKLMPDYSRSRLSSWIKEGAVIVNDKPAQ-PKDKMIGGELIAVTVRPSE 93

Query: 69  K--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRV 108
           +               E   + + +KP GLV   +  +   T+ + L +         R 
Sbjct: 94  ENLAFTPEPMDLDIIYEDDTVIVINKPAGLVVHPAAGNWSGTLLNGLLAHCSELSQVPRA 153

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN------ 159
             V RLD  T GL+++         L     +    R+YR   +G V    K+       
Sbjct: 154 GIVHRLDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRD 213

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               LK  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 214 PHNRLKMAVVKFGGKPAITHVKVLERYLAHSYIECSLETGRTHQIR 259


>gi|149921425|ref|ZP_01909878.1| pseudouridine synthase, RluA family protein [Plesiocystis pacifica
           SIR-1]
 gi|149817745|gb|EDM77210.1| pseudouridine synthase, RluA family protein [Plesiocystis pacifica
           SIR-1]
          Length = 311

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 69/222 (31%), Gaps = 37/222 (16%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------DGVPLRKAERTR-LW 76
           R++   +I    V VN + +    V V   + I V          D   +R   R     
Sbjct: 36  RKQAAAVIQAGGVYVNRLRVRLPQVLVAHGERITVYLEALDAKPLDPERVRFVHRGEDFV 95

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGG 129
           +  KP G+  +        ++ + L             V  V RLD    GL+L T    
Sbjct: 96  VLDKPAGVPVSAVRETCVGSLSEALIHQLESEGLERPYVGVVHRLDQGASGLVLFTIR-D 154

Query: 130 LARVLELP---STQWLRVYRVRFHGQVD-----QDKLNLLKK-GIVI---QGICYGDMQ- 176
           +A           +  R YRVR  G+          L  L+  G+ +             
Sbjct: 155 VANKSLHKQFRDHEIRRGYRVRVTGEPPAQLRCDAPLIKLRSGGVKVGSPGDGRSKPATT 214

Query: 177 -----VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +D + G    + V +  G+  +I+       + + 
Sbjct: 215 HFRHVARVDGEAGPEHLLDVEIETGRTHQIRAHAAHLGFPIV 256


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 84/261 (32%), Gaps = 53/261 (20%)

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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+            + +PL    E   L +  KP GLV      +   T+ + L      
Sbjct: 85  EITLPEPEDPTPKGEDIPLEILHEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGD 144

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                    R   V RLD +T G++++  +    R L L      R       YR    G
Sbjct: 145 TLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYRAVVWG 204

Query: 152 -----------QVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSNAWVTVGLRE 195
                       + +   +  ++ +        D      +V    Q+  +A     L E
Sbjct: 205 RPRTLSGTIDAPLGRATGDRTRRAVKRPDSQDADAAITHYEVIERFQENPDATALASLVE 264

Query: 196 -----GKNREIKKVFEFFNWK 211
                G+  +I+         
Sbjct: 265 CHLETGRTHQIRVHMAHIGHP 285


>gi|297622146|ref|YP_003710283.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
 gi|297377447|gb|ADI39277.1| RNA pseudouridylate synthase family protein [Waddlia chondrophila
           WSU 86-1044]
          Length = 284

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 75/192 (39%), Gaps = 24/192 (12%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVPLRKAERTRLWLYHKPIGLV 85
           ++ ++R+KV+G   +   +++     +EV        +GV +   +     ++ KP GL+
Sbjct: 30  LLKEERIKVDGQTCKLGTLSLKKGQILEVVKKQNVIAEGVKILYQDPHLAVVF-KPSGLL 88

Query: 86  TTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           +  +D +   T+   L   F    V  V RLD +T G+++   D      L       + 
Sbjct: 89  SVATDFEKNLTLHKILKEHFQPKTVEVVHRLDQDTSGVIVFALDKQTCLKLKILFEKHEI 148

Query: 142 LRVYRVRFHGQVDQ------DKLNLLKKGIV--IQGICYGDMQVT---LDTQKGSNAWVT 190
            R Y     G++          L+  +  +V        G + +T   ++        + 
Sbjct: 149 ERCYTAIVEGKLTPRSGSWRSYLHEDENYVVHSTDNARKGKLAITHYVVEGYSKKFTRLR 208

Query: 191 VGLREGKNREIK 202
           + L  GK  +I+
Sbjct: 209 LKLETGKKNQIR 220


>gi|257784642|ref|YP_003179859.1| pseudouridine synthase, RluA family [Atopobium parvulum DSM 20469]
 gi|257473149|gb|ACV51268.1| pseudouridine synthase, RluA family [Atopobium parvulum DSM 20469]
          Length = 336

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 84/251 (33%), Gaps = 56/251 (22%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   ++   +  SR    +++ + RV +N  L    +  +M  D + V           
Sbjct: 18  RLDAFLSAQDMLPSRSACVKLVEEGRVTINATLATSKSEKLMLGDRLLVSLPNAESQTGL 77

Query: 64  -----GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----------S 106
                 +PL  + E   L +  K IGLV   S      T+ + L +              
Sbjct: 78  LRPNPDIPLDIRFEDQYLIVLSKQIGLVCHPSPGHVDDTLANALVAHCGYEHLGMLQGED 137

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV----------- 153
           R   V RLD++T GL+L        + L   +      R Y V  HG V           
Sbjct: 138 RPGIVHRLDMDTSGLMLAVKSDEAQKALQDLIRLRVLDRRYIVLVHGYVAHDSGTIETGI 197

Query: 154 ---DQDKLNL-------LKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIK 202
               +D+L +        ++ I      +  ++     +KG   + +   L  G+  +I+
Sbjct: 198 ARSTRDRLKMTVSDAPGAREAIT----TFRTLERFEAGRKGDGYSLLECHLYTGRTHQIR 253

Query: 203 KVFEFFNWKVN 213
                    V 
Sbjct: 254 VHMRHIGHPVV 264


>gi|225572187|ref|ZP_03781051.1| hypothetical protein RUMHYD_00481 [Blautia hydrogenotrophica DSM
           10507]
 gi|225040359|gb|EEG50605.1| hypothetical protein RUMHYD_00481 [Blautia hydrogenotrophica DSM
           10507]
          Length = 343

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/263 (14%), Positives = 83/263 (31%), Gaps = 67/263 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           ++EN   QR+ K +++       +       +M+ ++ + +N          +   D ++
Sbjct: 6   IKENDAGQRLDKYLSKLLF----KAPKSFLYKMLRKKNITLNKKKA-SGNEKLKPGDQVQ 60

Query: 62  V------------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +                  D + L    E +++ + +KP G+++  S P+  S V   L 
Sbjct: 61  LFFSQETFEKFSRDDFYPTDDLQLEILYEDSQVMILNKPAGILSQKSRPEDVSLVEYMLS 120

Query: 103 SIFS------------RVISVGRLDINTEGLLLLTNDGGLARVLEL-----PSTQWLRVY 145
            +              R     RLD NT G++     G     L+            + Y
Sbjct: 121 YLLESGQFTQTDFRTFRPGICNRLDRNTTGIVAA---GKTLASLQSLSQMFHDRTLEKYY 177

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------AWVT 190
                G++         KG + +      + V+    KG+                  + 
Sbjct: 178 LCLVKGKI---IKKNFIKGYLHKDTKCNKVIVSSVPIKGAQPIETSYEPLTSNAKLTLLR 234

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
           V L  G+  +I+         + 
Sbjct: 235 VHLITGRTHQIRSHLASIGHPIL 257


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYQCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 181


>gi|314951376|ref|ZP_07854428.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313596434|gb|EFR75279.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
          Length = 307

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 45  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 104

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 105 SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQ 164

Query: 136 LPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G++               D  +LLK+ +  +G      +  ++ +
Sbjct: 165 LREKKFVKKYQALVSGRLSDLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 223

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 224 LTEIALVDIQLHTGRTHQIRVHFSAIGC 251


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 79/229 (34%), Gaps = 43/229 (18%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-LWLY 78
           ++  G   R  V+ ++A+ +V VNG         +     + V    + +A     L + 
Sbjct: 61  LSSTG---RNAVKSILARGQVSVNGQATTAYNYPLKPGFTVTVSKEKIEEAPPLIGLVIL 117

Query: 79  H---------KPIGLVTTHSDPDGRS---------TVFDNLPSIFSRVISVGRLDINTEG 120
           H         K  GL++  SD + +          T    + +  +R+  V RLD +T G
Sbjct: 118 HEDDDIVVVQKDAGLLSISSDKENKENELTAYRQLTAHVRVHNPRNRIFVVHRLDRDTSG 177

Query: 121 LLLLTNDGGLARVLELPSTQWLRV--YRVRFHGQV---------------DQDKLNLLKK 163
           +++        + L+    + ++   Y     G+V                    +  ++
Sbjct: 178 VMMFAKTEAAQQQLQNNWQEVVKERSYIALVDGKVRKAEGTITSWLRESSTLKMYSSFRE 237

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           G    G        TL T +   + + V L  G+  +I+   E     +
Sbjct: 238 G---DGQHAVTHYKTLQTNQHY-SLLEVHLETGRKNQIRVHMEDIGHPI 282


>gi|94987255|ref|YP_595188.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
 gi|94731504|emb|CAJ54867.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 541

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 81/240 (33%), Gaps = 40/240 (16%)

Query: 10  NFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
             T  R+ + +       G+ SR  ++++I     K++  +    +  +    HI +   
Sbjct: 12  EVTLVRLDQFLYNNLCTHGV-SRERLKKVIVSGGCKIDDKVCFSPSTRLKVGMHIFIQLP 70

Query: 63  ---------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---- 109
                    +G          L + +KP GL    +     ST+   L   F ++I    
Sbjct: 71  EVVSALLPEEGFLEILFSDEHLAIINKPPGLTVHPAPSCQESTLVHRLLKYFPKLIEQGG 130

Query: 110 ----SVGRLDINTEGLL--LLTNDGGLARVLELPSTQWLRVYRVRFHG----------QV 153
                V R+D +T GLL   LT D  L         +  + Y    HG           +
Sbjct: 131 LRPGIVHRIDKDTSGLLCIALTEDTRLKLSKIFLDRKINKEYLALVHGVPSMEGYIAVPL 190

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIK-KVFEFFNWK 211
            +D    +K  +  +G         L   K    + + + ++ G+  +I+  + +     
Sbjct: 191 GRDPKTKVKVAVNPKGKPAHTEWRVLHRGKNDVYSILALTIQTGRTHQIRVHM-KHIGHP 249


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIREGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSAEYSAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  APEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWSGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 87/251 (34%), Gaps = 45/251 (17%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNG---------IL 46
           MK K+ ++ E+    R+   I++        SR   +++I ++ V VN           +
Sbjct: 1   MKIKDFLINESEVNSRLDVFISK---CFEEKSRSYAQKLIEEKNVFVNNSSKKSNYKLKI 57

Query: 47  LERAAVNVMSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLP 102
            +   + +   + I +    ++     E   + +  KP G+V      +   T+ +  L 
Sbjct: 58  GDYVEIKIKEDEKINIKPEDIKLNIIYEDEDVIVIDKPQGMVVHPGAGNYSGTLVNGLLY 117

Query: 103 SIFS--------RVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHG 151
              S        R   V R+D +T G+L++  +   A ++           R Y     G
Sbjct: 118 HCDSLSSINGDVRPGIVHRIDKDTSGVLVVAKN-DSAHIILSEQLKEHSMKREYIALVEG 176

Query: 152 QVDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            +  D+            + +K+ +V  G         +  +   N  V   L  G+  +
Sbjct: 177 IIKNDEGIIDAPLGRNPKDRIKRAVVRNGKSAVTH-YNVLRRFNKNTLVKCILETGRTHQ 235

Query: 201 IKKVFEFFNWK 211
           I+      N  
Sbjct: 236 IRVHMAHINHP 246


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 49/191 (25%), Positives = 68/191 (35%), Gaps = 37/191 (19%)

Query: 7   VQENFTPQRVSKV----IARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           V +     R+ K+    + RAG A SR  V+R IA  RV V+G     A+V V ++  +E
Sbjct: 14  VDDGDPRDRLDKLVVHLLERAGHAASRAAVQRWIAAGRVLVDGEPAR-ASVAVRASALVE 72

Query: 62  V--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------ 101
           V              D V     E   L +  KP GLV   +      T+ + L      
Sbjct: 73  VRPEEPSPSPTAAEPDVVIPVVYEDEHLLVIDKPAGLVVHPARGHASGTLVNGLLALPGF 132

Query: 102 ---------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
                    P    R   V RLD  T GLL++  D      L+         R Y     
Sbjct: 133 ALAPADPRDPMGHVRPGIVHRLDRGTSGLLVVAKDEPTREALKDRFARHAIEREYAAIVA 192

Query: 151 GQVDQDKLNLL 161
           G+      + L
Sbjct: 193 GEARDATYDTL 203


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIR 259


>gi|323700246|ref|ZP_08112158.1| pseudouridine synthase, RluA family [Desulfovibrio sp. ND132]
 gi|323460178|gb|EGB16043.1| pseudouridine synthase, RluA family [Desulfovibrio desulfuricans
           ND132]
          Length = 305

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 75/238 (31%), Gaps = 30/238 (12%)

Query: 6   IVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVN------------GILLERAA 51
           +V +  + Q++ + + R  +G   R  +++ I   +V+V+            G  +    
Sbjct: 8   VVSQAESGQKLLQFLERRLSGEVPRSAIQKWIRTGQVRVDKGRKKPFDRLEAGQTVRIPP 67

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRV 108
                   +   G      E   L    KP GL     D    S V        +     
Sbjct: 68  YAPGQDKQVSEAGGLAVAYEDAELLAVAKPAGLAAHGGDGVDDSVVARLRAMYRNADFMP 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
               RLD +T GLLL      + R L     S    +VY     G+ D+    LL+  + 
Sbjct: 128 TLAHRLDRDTSGLLLAAKSYAVLRELNDLFASNGVAKVYLAWVDGRWDEPDGTLLEDVME 187

Query: 167 IQG-----------ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +G                 +VT        + V V L  G+  +I+         V 
Sbjct: 188 KRGAPGAERVRTGSGKTALARVTGLVSSRDRSLVAVRLLTGRTHQIRVQLASRGHAVI 245


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIR 259


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 160 LLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR 217
            + +G +++GI      V L  ++     AW+ + + EG+N E++++ +    +V+ L R
Sbjct: 2   AISEGTMVEGIHCVPDLVELMPKQHDIPRAWLRIVVHEGRNHEVRELVKNVGLEVDSLKR 61

Query: 218 ISYGPFQLGT 227
           +  G  +L +
Sbjct: 62  VRIGGVRLPS 71


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIR 259


>gi|126664287|ref|ZP_01735278.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BAL38]
 gi|126623707|gb|EAZ94404.1| ribosomal large subunit pseudouridine synthase D [Flavobacteria
           bacterium BAL38]
          Length = 346

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 82/237 (34%), Gaps = 43/237 (18%)

Query: 15  RVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           RV K +    I   +R ++++      + VN + ++     V + D + +          
Sbjct: 30  RVDKFLMNM-IENTTRNKIQQAAENGSILVNDVAVKS-NYKVKAGDVVRLVLAHPTYEQL 87

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP-SIFSRVIS 110
              + +PL    E  +L + +KP G+V      +   T+       F+NLP +   R   
Sbjct: 88  LTPENIPLDIVYEDDQLLVINKPAGMVVHPGHGNYSGTLVNALAYHFENLPMNSSERPGL 147

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQD----------- 156
           V R+D +T GLL++     LA              R Y     G +++D           
Sbjct: 148 VHRIDKDTTGLLVVA-KTELAMAYLSKQFAEKTSEREYVALVWGNIEEDEGTVEGNIGRH 206

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             N ++  +               +  + G    V+  L  G+  +I+   +     
Sbjct: 207 DTNRMRMAVHESDEKGKPAVTHYKVLERFGYVTLVSCQLETGRTHQIRVHMKHIGHT 263


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 78/227 (34%), Gaps = 45/227 (19%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPL 67
           QR+ + +A      SR  ++  I   +V+VNG L+ +    ++  + I +D         
Sbjct: 18  QRLDQALAELFPDYSRSRIKEWILDNKVQVNGKLINKPKEKMLGGEDISIDAIIEEDARW 77

Query: 68  RKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGR 113
                      E   + + +KP  LV      +   TV + L   + ++        V R
Sbjct: 78  EPQDIELNVVYEDDDILVINKPRDLVVHPGAGNPDGTVLNALLYRYPKIADVPRAGIVHR 137

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD +T GL+++         L   L   +  R Y     G +          G+V + I 
Sbjct: 138 LDKDTTGLMVVAKTVPAQTRLVESLQLREITREYEAIALGCMT-------AGGMVEEPIS 190

Query: 172 YGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
               + T                +     ++  + + L  G+  +I+
Sbjct: 191 RHPTKRTHMAVHPMGKPAITHYRVLEHFRAHTRLRLRLETGRTHQIR 237


>gi|94970372|ref|YP_592420.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Koribacter versatilis Ellin345]
 gi|94552422|gb|ABF42346.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Koribacter versatilis Ellin345]
          Length = 333

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 87/255 (34%), Gaps = 51/255 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V  +    R+ + + +     SR  V+ +I  +++ V+G    + +  +  ++ I+V G 
Sbjct: 9   VSADDANIRLDQYLVSHLPDVSRARVQALIDDEKILVDGKS-SKPSYKLRGSEVIDVVGE 67

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVT-----THSDPDGRSTVFDNLPSIFS 106
                              E   L + +KP G++         +   R T+ + L   F 
Sbjct: 68  YQPPPLRAIPEDIPLDVVYEDDDLAVINKPAGMMVHVGAGATEEERNRGTLVNALLYRFR 127

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG---- 151
                    R   V RLD  T GL+++  +    R L     S +  + Y    HG    
Sbjct: 128 ALSEVGGDMRPGIVHRLDKETSGLIVVAKNDVAHRKLAEQFSSRRVHKKYVALVHGWPKK 187

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDM------QVTLDTQKGSNAWVTVGLREGKN 198
                   + +D     +  +  +G    D       +  +++  G  A V V +  G+ 
Sbjct: 188 LKGTINLPIARDMSRRTR--MTTRGSGGRDALSHYEVKEKIESPYGKFALVEVKIETGRT 245

Query: 199 REIKKVFEFFNWKVN 213
            +I+         V 
Sbjct: 246 HQIRVHMASLGHPVV 260


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 82/230 (35%), Gaps = 46/230 (20%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ K ++      SR +V++ I    V++N +++  + V V   D I     +   L+  
Sbjct: 14  RLDKALSSLLEKVSRNQVQKAIKNSCVQINDVIISDSDVLVKENDTILFSFKEPEELKIT 73

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
                     E   L + +K  G+          +T+ + L      +  +G        
Sbjct: 74  SANITLDIIYEDDDLIVINKAAGITVHPGAKHHDNTLVNALLHHTKNLSDIGSAERPGIV 133

Query: 113 -RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ-------------- 155
            RLD  T GL+++  +     +L   +   Q +R Y+    G ++               
Sbjct: 134 HRLDKETTGLMVVAKNNKAHMLLAKQIEQRQVIRKYKALVWGVINPLEGIINNNIGRNRN 193

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
              K+ +LK G    G        TL+   G   + V   L  G+  +I+
Sbjct: 194 NRKKMTILKYG----GKKAVTHYKTLELFYGGTLSMVECKLSTGRTHQIR 239


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/225 (18%), Positives = 75/225 (33%), Gaps = 49/225 (21%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------ 63
           + +++      SR  ++  I    V V+G     A   V   + + VD            
Sbjct: 30  LQRLLPEH---SRSRLQSWIKSGLVTVDGK-ASTAKTKVWGGEKVSVDVQVKPESRAFIA 85

Query: 64  -GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRLD 115
             +PL    E   + + +KP G+V   +  +   T+ + L     ++        V RLD
Sbjct: 86  QDIPLDIVYEDDHILVVNKPAGMVVHPAAGNWDGTLLNALLFHAPQLHDVPRAGIVHRLD 145

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
             T GLL++         L  +L +    R YR    G        L + G+V Q +   
Sbjct: 146 KETSGLLVVAKTLNAQTHLVRQLQARTVKREYRAIVWG-------QLWRNGVVDQPLGRD 198

Query: 174 DMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
               T                +  +     ++   L  G+  +I+
Sbjct: 199 PRSRTKMAINRMGKPAITRYEILERFSVQTYLRCNLETGRTHQIR 243


>gi|301154795|emb|CBW14258.1| 23S rRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 324

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/177 (20%), Positives = 64/177 (36%), Gaps = 22/177 (12%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M     +Q     QR+ + +A      SR  ++  I  ++VK+NG + +     V   + 
Sbjct: 4   MTLTAEIQPEQMGQRLDQTLAELFPEYSRSRLKTWIEAKQVKMNGEIADIPRAKVYGGEQ 63

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           IE+              +PL    E   + + +KP  LV      +   TV + L   + 
Sbjct: 64  IEISVEVEDENRFEPQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYP 123

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                 R   V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 124 PIAEVPRAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 78/227 (34%), Gaps = 45/227 (19%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           QR+ + +A      SR  ++  I  + V VNG ++      V   + IE+          
Sbjct: 17  QRLDQTLAELFPDYSRSRLKTWIEDELVLVNGEVVILPRAKVYGGEQIEITVEIEEDSRF 76

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGR 113
             + +PL    E   + + +KP   V      +   TV + L   + ++        V R
Sbjct: 77  MPENLPLNIVYEDDDILVINKPKDFVVHPGAGNPTGTVLNALLYHYPQIAEVPRAGIVHR 136

Query: 114 LDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD +T GL+++         L       +  R Y     G +        K G+V Q + 
Sbjct: 137 LDKDTTGLMVIAKTIPAQTKLVRDLQKRKITREYEAIASGIMT-------KGGMVDQPMA 189

Query: 172 YGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
               + T                +  +  +   + + L  G+  +I+
Sbjct: 190 RHPTKRTQMAVHPMGKPAITHYRIMERFRNYTRLRLRLETGRTHQIR 236


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 54/296 (18%), Positives = 101/296 (34%), Gaps = 74/296 (25%)

Query: 6   IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ +N  P+R+ K IAR     A + SR  + R+I    V+V+G +   A   V+    I
Sbjct: 9   VIADNP-PKRLDKAIARDVPEEANL-SRTRLARLIESGGVEVDGAVASDAKARVLEGAQI 66

Query: 61  EV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS 106
            +            + + L    E   L + +KP G+V   +      T+ +  L    +
Sbjct: 67  VITVEDAEESHIGPEDIALDVIYEDADLIVINKPAGMVVHPAPGSPSGTLVNALLHHCGA 126

Query: 107 RVISVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            +  VG         R+D  T GLL++       + L          R Y+   +G  D 
Sbjct: 127 DLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFERHSVERYYQAVCYGVPDA 186

Query: 156 DK---------------LNLL------------KKGIVIQGICYGDMQVTLDTQKGSN-- 186
           +                +  L            ++ ++ +G  +   +  +    G+   
Sbjct: 187 NDPRLRGVRGASFEPGNILKLTTQLARHKTDRQRQAVLFEGGRHAVTRARIIEAFGAPAA 246

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            + V   L  G+  +I+         +            LG    G  R++S K L
Sbjct: 247 ASLVECWLETGRTHQIRVHMAHAGHGL------------LGDPTYGGKRKISPKAL 290


>gi|144897894|emb|CAM74758.1| ribosomal large subunit pseudouridine synthase D [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 327

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 62/323 (19%), Positives = 98/323 (30%), Gaps = 58/323 (17%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + V  +    R+ K + AR    SR  ++ +I   RV   G  +  A+  V       V 
Sbjct: 12  DAVTTDEAGSRLDKWLSARLPDLSRTRIKGLIDDSRVSAAGQTITDASARVKPGQCFVVA 71

Query: 63  -------DGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                  D +P         E   L +  KP GLV   +      T+ + L +       
Sbjct: 72  IPPERPADPLPQAMDLSVAYEDDDLIVIDKPPGLVVHPAPGSPDHTLVNALLAHCGESLS 131

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQV----- 153
                 R   V R+D +T GLL++  +      L    +     R YR    G       
Sbjct: 132 GIGGVKRPGIVHRIDKDTSGLLVVAKNDRAHHGLAEQFSVHSLERAYRALVWGVPMPAQG 191

Query: 154 --------DQDKLNLLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIK- 202
                          +   IV  G      +  +      G+ + V   L  G+  +I+ 
Sbjct: 192 EIHGNIGRSPQDRKKMA--IVSHGGKPALTRYRVLRSFAGGAVSLVECRLATGRTHQIRV 249

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
            +       +             G    G  R    K L +Q    LLE  +  L A + 
Sbjct: 250 HMT-SIGHPLV------------GDQTYGRARSTKVKHLPDQARLALLEFPRQALHASVL 296

Query: 263 S-SETLVRDRPNIISEVPDDFTR 284
                         S++PDDF  
Sbjct: 297 GFIHPNSGVMLKFESQIPDDFNE 319


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 77/247 (31%), Gaps = 61/247 (24%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN--------------VMST--- 57
           R+ K +A A   SR  V+ ++    V V+G      +                V      
Sbjct: 24  RLDKALAEASGLSRERVKALMQGGAVLVDGDPATNPSAKGSEGTPYTITLPPTVDPEAQP 83

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
             I++D       E   L + +KP G+V   +  +   T+ + L               R
Sbjct: 84  QDIKLD----VVFEDEHLLVVNKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGINGVAR 139

Query: 108 VISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
              V R+D +T GLL++  T++       +       R Y     G  +        +G 
Sbjct: 140 PGIVHRIDKDTSGLLVVAKTDNAHEGLAAQFAEHTINRRYLALCAGHPNP------AEG- 192

Query: 166 VIQGI-------CYGDMQVTLDTQKGSN--------------AWVTVGLREGKNREIKKV 204
            I+G              +  D+ +G +              A +   L  G+  +++  
Sbjct: 193 TIEGRIGRSERDRKKMAPLPEDSSRGKHAVTHYKTLRRLRDCALIECRLETGRTHQVRVH 252

Query: 205 FEFFNWK 211
            +     
Sbjct: 253 CQSIGHP 259


>gi|319410076|emb|CBY90410.1| K06180 ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis WUE 2594]
          Length = 392

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 58  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 116

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 117 VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 237 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 277


>gi|283850426|ref|ZP_06367715.1| pseudouridine synthase, RluA family [Desulfovibrio sp. FW1012B]
 gi|283574452|gb|EFC22423.1| pseudouridine synthase, RluA family [Desulfovibrio sp. FW1012B]
          Length = 558

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 73/240 (30%), Gaps = 44/240 (18%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
           R+       +A   + SR  V   I      V+G    +  + +   + + ++       
Sbjct: 25  RLDVFWSARLADLEV-SRARVRAAIEGGLATVDGADCRKPGLKLRGGETLTLNLPQVASE 83

Query: 64  -----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVIS 110
                G          L +  KP GL    +      T+ + L   F         R   
Sbjct: 84  TVAEAGSLRVLYADKELAVLDKPPGLTVHPAPGLPEGTLVNRLLHHFPGLREMAGERPGI 143

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV-------------DQ 155
           V RLD +T GLL++  T    LA   +  + Q  + Y    HG+              D 
Sbjct: 144 VHRLDKDTSGLLMVALTEPVRLALAADFAARQVHKTYLALVHGRPDGKGGDIRLPIGRDP 203

Query: 156 DKLNLLKKGIVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +   +  +G        +       G+ + + V +  G+  +I+         + 
Sbjct: 204 KYRTKMA--VPHKGGRPAHSRWRPVWTAPDGTASLLEVTIFTGRTHQIRVHMAAIGHPII 261


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/258 (17%), Positives = 87/258 (33%), Gaps = 61/258 (23%)

Query: 13  PQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           P+R+ K +AR     A + SR  + ++IA+  V++ G+ +      V+     E+     
Sbjct: 20  PERLDKALAREAPEEAAL-SRSRLMKLIAEGAVRLKGVPVTDPKARVLEGQVYEIVTGAA 78

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                  + +PL    E   L +  KP+G+V   +      T+ + L             
Sbjct: 79  AEVEALPEAIPLSVVWEDADLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGASLSGIGG 138

Query: 106 -SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK----- 157
             R   V R+D +T GLL++  T+        +  +    R Y    HG  +        
Sbjct: 139 EKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEPSDPRLRG 198

Query: 158 ----------LNLLKKG------------IVIQGICYGDMQVTLDTQKGSN---AWVTVG 192
                     +  +  G            +  +G  +   +  L  + G+    A V   
Sbjct: 199 IRGVSFEPGGVLRIATGIARHRTDRQRQAVTFEGGRHAVTRARLLERFGTPPAAALVECR 258

Query: 193 LREGKNREIKKVFEFFNW 210
           L  G+  +I+        
Sbjct: 259 LETGRTHQIRVHMSHVGH 276


>gi|325127790|gb|EGC50698.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis N1568]
          Length = 374

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLTHSYIECSLETGRTHQIR 259


>gi|257453790|ref|ZP_05619068.1| ribosomal large subunit pseudouridine synthase D [Enhydrobacter
           aerosaccus SK60]
 gi|257448717|gb|EEV23682.1| ribosomal large subunit pseudouridine synthase D [Enhydrobacter
           aerosaccus SK60]
          Length = 380

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 77/225 (34%), Gaps = 38/225 (16%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           +R+ K IA       SR +++  +    + VNG   ++    +   D + +         
Sbjct: 78  ERIDK-IAALVFSDYSREQIKNWLESGELTVNGA-AQKPKYRLKPNDMLVLKASLTAQQQ 135

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV----FDNLPS--IFSRVISVG 112
              + +PL    E   + + +KP+GLV      +G  T+      + P      R   V 
Sbjct: 136 DLPENIPLDILYEDEAVLVINKPVGLVVHPGAGNGSGTLVNALLFHYPDSRTLPRAGLVH 195

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF-------------HGQVDQDK 157
           R+D  T GL+++  D      L          R+Y+                   + +  
Sbjct: 196 RIDKETSGLMVIAKDSQSQLHLINQLKDKSVYRLYQAIVLASAAELARHRTIDAPIGRHP 255

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               K  +V  G         +     + + V+V L  G+  +I+
Sbjct: 256 TQRTKMAVVSSGKPAVTHLEKITAISDAVSLVSVRLETGRTHQIR 300


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 40/180 (22%), Positives = 66/180 (36%), Gaps = 31/180 (17%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V+ +F   R+   +A  A   +R    R +    V+VNG+++ + +  V  +D +E    
Sbjct: 6   VEGSFDGMRIDAFLAAVAAFPTRSAAARRVDAGEVRVNGVVVRK-SFTVRISDVVEYVVA 64

Query: 63  -DGVPLR----------KAERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFS--- 106
            D   L           + E   + +  K  GLVT  +D  P+  + V   +        
Sbjct: 65  MDARVLELMPADIPLDIRYEDDDVLVLSKQAGLVTHPADGHPEQDTLVNALIAHCGREKL 124

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD 156
                   R+  V RLD +T GL+L          L     +    R Y    HG +  D
Sbjct: 125 CNVQGEQDRLGIVHRLDRDTSGLMLAAKTDAAGLRLMEDIAARDVDRHYLALVHGWIPLD 184


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 86/236 (36%), Gaps = 42/236 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNG-------ILLERAAVNV- 54
           IV+E    +R+ K +   G+    SR +V+++I    VKV G        +    AV V 
Sbjct: 4   IVEEKHNGERIDKFL--VGVMENVSRTDVQKLIEAGEVKVGGGKVSKNFRVETGMAVVVE 61

Query: 55  ----MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
                 +  +E + +PL    E   + + +KP  LV    +   + T+   L   F    
Sbjct: 62  KMIEKESSTLEPEDIPLNIVYEDDDIVVINKPRNLVVHPGNGVSKGTLAAALLYHFKENL 121

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG------ 151
                  R   V RLD +T GL+++  +    R L     +    R Y     G      
Sbjct: 122 STVNGPLRPGIVHRLDKDTPGLMVVAKNDAAHRHLAHQLETRTLHRTYNALVWGCPRDLE 181

Query: 152 -----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 + ++  N LK  +V  G       V       +   + + L  G+  +I+
Sbjct: 182 GTIDAPIGRNPKNRLKMAVVKGGKESRTHYVAKQFFAIAT-LLELQLESGRTHQIR 236


>gi|257880319|ref|ZP_05659972.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,230,933]
 gi|257882173|ref|ZP_05661826.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,502]
 gi|257890978|ref|ZP_05670631.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,410]
 gi|257894233|ref|ZP_05673886.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,408]
 gi|258614733|ref|ZP_05712503.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Enterococcus faecium DO]
 gi|260562377|ref|ZP_05832891.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium C68]
 gi|293553066|ref|ZP_06673708.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|293559437|ref|ZP_06675975.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
 gi|293568340|ref|ZP_06679663.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|294621976|ref|ZP_06701121.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|257814547|gb|EEV43305.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,230,933]
 gi|257817831|gb|EEV45159.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,502]
 gi|257827338|gb|EEV53964.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,410]
 gi|257830612|gb|EEV57219.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,408]
 gi|260073301|gb|EEW61642.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium C68]
 gi|291588949|gb|EFF20774.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|291598455|gb|EFF29527.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|291602775|gb|EFF32985.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|291606592|gb|EFF35988.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
          Length = 299

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQ 156

Query: 136 LPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G++               D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGRLSDLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 216 LTEIALVDIQLHTGRTHQIRVHFSAIGC 243


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 82/237 (34%), Gaps = 49/237 (20%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ + + +     SR  ++  + Q  V VNG         V   +HI V    +  +E+ 
Sbjct: 33  RLDQALVKLFPEYSRSRLQDWVEQGLVTVNGK-AGSVKQKVWGGEHISVSPQ-IHPSEQP 90

Query: 74  R---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVG 112
                           + + +KP+GLV      + + T+ + L     ++        V 
Sbjct: 91  YHAEDIPLDIVYEDDAMLIINKPVGLVVHPGSGNWQGTLLNALLHHAPQLADVPRAGIVH 150

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           RLD +T GL+++         L     +    R Y     G++D+D        + I   
Sbjct: 151 RLDKDTSGLMVVAKSLVAQTALVRQMQARSVKREYLALVWGELDRDYTIN----VPI--G 204

Query: 171 CYGDMQVTLD-TQKGSNAWVTVGLRE--------------GKNREIK-KVFEFFNWK 211
            +   +V +  T+ G  A   VG+ E              G+  +I+  +       
Sbjct: 205 RHPSQRVKMATTESGKEAITHVGIEERFPYCTLVRCRLETGRTHQIRVHMT-HIGHP 260


>gi|73667158|ref|YP_303174.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia canis
           str. Jake]
 gi|72394299|gb|AAZ68576.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia canis
           str. Jake]
          Length = 323

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 87/244 (35%), Gaps = 43/244 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRV--------------KVNGIL 46
           ++ K  ++      R+ K+IA     SR +V+++I   +V              KVN I 
Sbjct: 2   LEKKIFIKIEEANNRLDKLIANKLNTSRNQVQQLIKDSKVSLFNNIITDNNHTTKVNDIY 61

Query: 47  LERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           +       +S   I    +P+    E   + + +K  G+          +T+ + L + +
Sbjct: 62  IINIPTKEISNTIIPNHSIPISVLYEDHDIIIINKTSGITVHPGAGTKNNTLVNALVAHY 121

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                     +R   + RLD +T GL+++  +      L   L   Q  + Y     G  
Sbjct: 122 GNALSTVGKATRPGIIHRLDKDTSGLMVIAKNEKSYYFLSELLLKKQIKKEYLAVVWGSP 181

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLREGKN 198
           +    N ++  I ++      M VT  + KG                 + +   +  G+ 
Sbjct: 182 NPKN-NTIQNYICVKPNNKQMMAVTHLSHKGKLAITEYKTKQNFSNIASLIKCRIHTGRT 240

Query: 199 REIK 202
            +I+
Sbjct: 241 HQIR 244


>gi|313896082|ref|ZP_07829636.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312975507|gb|EFR40968.1| pseudouridine synthase, RluA family [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 297

 Score = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 67/198 (33%), Gaps = 31/198 (15%)

Query: 43  NGILLERAAVNVMSTD----------HIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDP 91
           NG+    A   V   D           +  + +PL  A E   L +  KP G++   +  
Sbjct: 43  NGVPAIAARTAVRDGDMLSYALPIVSSVVPEDLPLAIAYEDDDLLIIDKPAGMLVHPTTQ 102

Query: 92  DGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           + R T+ + +  +++            RLD NT GLLL+     +            R Y
Sbjct: 103 ETRGTIANAVRGLYASRGDTLDFHPCHRLDRNTTGLLLIAKCPEVQYYFTKHRDAVRREY 162

Query: 146 RVRFHGQVDQ--DKLNL----------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
                G++    D ++           L++ +  +G        T+    G  + + + L
Sbjct: 163 LALIEGRLTPASDIIDAPIARALPSIILRR-VAPEGKPARTHYETV-ASDGRYSLLRLTL 220

Query: 194 REGKNREIKKVFEFFNWK 211
             G+  +I+         
Sbjct: 221 ETGRTHQIRVHLAHLGHP 238


>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 = 68.3 bits (166), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 87/240 (36%), Gaps = 43/240 (17%)

Query: 1   MKDKNIVQENFTPQ--RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M +K I+  N T Q  R+  ++A+     SR  +   +    + VN   ++R +  V   
Sbjct: 1   MMEKTII--NITTQVGRIDAILAKEDLQYSRTTLAEWLQNGHILVNNNKVKR-SYKVSVG 57

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I +            + +PL    E   + + +KP G+V   +      T+ + L   
Sbjct: 58  DTISIFPPEVASTEIIAEDIPLDIVYEDNDILVVNKPQGMVVHPAAGHSSGTLVNALLHH 117

Query: 105 FS--------RVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQV 153
                     R   V R+D +T GLL++  +  +A           +  R+Y     G+ 
Sbjct: 118 APLSTINGTFRPGIVHRIDRDTSGLLMVAKN-DVAHKALSAQLKAHKNDRIYYALVRGEF 176

Query: 154 DQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D            ++  ++ + + G         +    G    + V L  G+  +I+
Sbjct: 177 SEDSGTINAPIGRHPVDRKRQAVQVGGREAITHFEVVHRYVGFT-LLKVRLETGRTHQIR 235


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 81/238 (34%), Gaps = 36/238 (15%)

Query: 1   MKDKNIVQ----ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M ++  +Q     +   +R+ +V+A+     SR  ++  I   ++ V+G +       ++
Sbjct: 1   MSEQISLQAEVPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPREKLL 60

Query: 56  STDHIEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + + V             D       E   + + +KP+GLV      +   TV + L 
Sbjct: 61  GGEVVAVETTIEAPREYEAQDIKLNIVYEDDDILVINKPMGLVVHPGAGNPDGTVLNALL 120

Query: 103 SIFSRVI------SVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQV 153
             +  +I       V RLD +T GL+++         L         + R Y    +G +
Sbjct: 121 HYYPEIINVPRAGIVHRLDKDTTGLMVVAKTIQAQTHLVKALQKRENFTREYEALCNGTM 180

Query: 154 DQD---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                                V +          +  +  ++  + + L  G+  +I+
Sbjct: 181 TAGGMVEKPIGRHATQRTHMAVHEMGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIR 238


>gi|227542354|ref|ZP_03972403.1| conserved hypothetical protein [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227181868|gb|EEI62840.1| conserved hypothetical protein [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 80

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 21/80 (26%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGICYGDM 175
           LLL T DG LA  +  PS +  R Y VR         V    ++ L +G+ ++       
Sbjct: 1   LLLATTDGELANAMMHPSFEVEREYVVRVRAPEGEEKVSDAIVDRLARGVALEDGPAKFD 60

Query: 176 QVTLDTQKGSNAWVTVGLRE 195
           ++       S+ W  V ++E
Sbjct: 61  EIERIGGTDSHDWFRVVVKE 80


>gi|284929127|ref|YP_003421649.1| ribosomal large subunit pseudouridine synthase D [cyanobacterium
           UCYN-A]
 gi|284809586|gb|ADB95291.1| ribosomal large subunit pseudouridine synthase D [cyanobacterium
           UCYN-A]
          Length = 316

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 90/248 (36%), Gaps = 48/248 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K IV++     R+ + +++     SR  ++++I    + +N  + +     +++ D 
Sbjct: 1   MNLKLIVEDKGD--RIDRWLSKHILNISRARIQKLIQAGNIILNNKICKTKKEQLIAGDC 58

Query: 60  IEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +EV            + +PL    E   L + +K  G+V   S      T+   L     
Sbjct: 59  LEVFVPSPKKLELIPEAIPLDVLYEDKYLIIINKVAGMVVHPSPGHENGTLVHALLHHCR 118

Query: 107 RVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD- 154
            +  +G         RLD +T G +++  T+        ++      R Y    HG +  
Sbjct: 119 DLSGIGEVQRPGIVHRLDKDTTGTIVIAKTDFVHQHLQKQIRDRVVEREYLAIIHGVLKN 178

Query: 155 -QDKLNLLKKGIV--------IQGICYGDMQVTLDTQKGSNAW-----------VTVGLR 194
            ++  N++ KG++        I       M    + +K    W           V   L 
Sbjct: 179 RENNDNVVNKGVIDLPIGRHLIDRKKMAVMPSEKNGRKAVTYWKILERLGNYSMVNFKLG 238

Query: 195 EGKNREIK 202
            G+  +I+
Sbjct: 239 TGRTHQIR 246


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 65/229 (28%), Gaps = 35/229 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           +R+ + IA  G  SR    R I    V V+G   + A   +     + V+          
Sbjct: 15  ERIDRFIAARGGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVVNLEEGGRAAPA 74

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
               G          L    KP G+    +    R  + + + ++  + V  V RLD  T
Sbjct: 75  LAALGRERLLYADADLCAVDKPAGVPAQPTLTTDRGALPELVSALLGAPVTLVHRLDRET 134

Query: 119 EGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDM 175
            G+ +   T D   A      +    + Y           +    L  G   +      +
Sbjct: 135 SGVTVFARTRDAAAALAEAFRTGTPEKTYLALCARAPSPAEGRVALALG---KDPARPGL 191

Query: 176 QVTLDTQKGSNAWVTVGLRE-------------GKNREIKKVFEFFNWK 211
           +        +       LRE             G+  +I+         
Sbjct: 192 RRVDPAGDPAATRYR-TLREAPGGALVEARPETGRTHQIRVHLAALGAP 239


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 44/221 (19%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTLWIKEGAVIVNDKP-SQPKDKMIGGEQIRVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L  +L      R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVWQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>gi|327441282|dbj|BAK17647.1| pseudouridylate synthase, 23S RNA-specific [Solibacillus silvestris
           StLB046]
          Length = 294

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 76/228 (33%), Gaps = 41/228 (17%)

Query: 20  IARAGIASRREVERMIA--QQRVKVNGILLERAAVNVMSTDHIE--------------VD 63
           IA+ GI S+R     I      + VNG         +   D +               V 
Sbjct: 22  IAQWGI-SKR-ALTAIKFDGGAILVNGE-ERNVRHRLAEGDDVTIIFPVEEASEGLIPVQ 78

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDIN 117
           G      E   + L  KP  + +  S     +T+ + +   F +      V  V RLD +
Sbjct: 79  GELAVVYEDEAVLLVDKPAFMSSIPSREHPNNTLANLVYGYFEQQQHASTVHIVTRLDRD 138

Query: 118 TEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHG-----------QVDQDKLNLLKK 163
           T GL+L+         L     +     R Y     G            + +   +++++
Sbjct: 139 TSGLMLIAKH-RHIHHLMSEQQKKGQIHREYEAVAEGIIVQDQQSIIAPIGRKDTSIIER 197

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +   G  +    VT+ T+K +   + + L  G+  +I+    +    
Sbjct: 198 EVRPDG-QFAHTDVTVLTRKNNMTHIRLKLHTGRTHQIRVHMAYIGHP 244


>gi|325143909|gb|EGC66219.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis M01-240013]
          Length = 356

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 22  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 80

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 81  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 141 LDKETSGLMVVAKTLSAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 201 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 241


>gi|314937995|ref|ZP_07845306.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314941579|ref|ZP_07848463.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314948435|ref|ZP_07851823.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314991305|ref|ZP_07856784.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995356|ref|ZP_07860462.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313590449|gb|EFR69294.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313594078|gb|EFR72923.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313599599|gb|EFR78442.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313642670|gb|EFS07250.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313645160|gb|EFS09740.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 307

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 45  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 104

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 105 SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQ 164

Query: 136 LPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G++               D  +LLK+ +  +G      +  ++ +
Sbjct: 165 LREKKFVKKYQALVSGRLSDLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 223

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 224 LTEIALVDIQLHTGRTHQIRVHFSAIGC 251


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 83/243 (34%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V+E F+ +R+ + +A      SR   + +I  + V ++   + +++  V +         
Sbjct: 9   VEEEFSNKRLDQFLALVYPEYSRSFYQNLIENRFVLLDNNPVRKSSTKVKTGQEFTIIIP 68

Query: 62  --------VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   L + +KP G+V   S      T+ + L   F  V    
Sbjct: 69  PPEPLEIEPENIPLEIYYEDEDLAVVYKPPGMVVHPSVGHTSGTLVNALLYHFKNVSQYQ 128

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK-LNL 160
                  V RLD +T GLL++       + L       +  + Y+    G V +D  L  
Sbjct: 129 GKERAGIVHRLDKDTAGLLIVAKSEFAHKELQKMFQDREIDKKYKAIVSGIVKKDHGLID 188

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVT------------VGLREGKNREIKKVFEFF 208
           L  G  I          T      +  WV             + L  G+  +I+  F   
Sbjct: 189 LPIGRSIYNRQKMGTVATNPKDALTEYWVEKRFEKHNLTLVDIKLHTGRTHQIRVHFSAI 248

Query: 209 NWK 211
              
Sbjct: 249 GHP 251


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 52/310 (16%), Positives = 104/310 (33%), Gaps = 53/310 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPQITPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L           +  R   V
Sbjct: 73  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL---LKK--G 164
            RLD +T G +++  +      L   L +    R Y       + ++K+++   L +   
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLARNPN 192

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVG-----------LREGKNREIKKVFEFFNWKVN 213
             ++ I     +        S     +            L  G+  +I+           
Sbjct: 193 NRLKMIALKAAKKEKIRYSKSEFTSLLTSQNGMDLIGAKLFTGRTHQIR---AHL----E 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L R   G   L  L       + K+ +R  L  +L+E      +  +     L++D   
Sbjct: 246 YLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300

Query: 274 IISEVPDDFT 283
            + +V D  +
Sbjct: 301 YLKKVFDKES 310


>gi|148262258|ref|YP_001228964.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146395758|gb|ABQ24391.1| pseudouridine synthase, RluA family [Geobacter uraniireducens Rf4]
          Length = 296

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 27/154 (17%), Positives = 52/154 (33%), Gaps = 28/154 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLL 124
           E       +K  G+ +  +    + TV   + +    +        + RLD  T G++  
Sbjct: 84  EDANYLAVNKAAGINSQRTPYQLKGTVEYAVETYMKSLGSKEPARVIHRLDRGTSGVMFF 143

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYG 173
             D   A  +   L   +  +VY     G  D+++         LN  + G+ + G    
Sbjct: 144 PKDKRAATHISFLLKEGKVEKVYWAMVAGVPDEEQWTVDAPIAKLNKFRYGVALPGREAR 203

Query: 174 DMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
                +   KG+       L E     G+  +I+
Sbjct: 204 TAFRVIAVGKGA------TLLEALPFTGRTHQIR 231


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 49/213 (23%), Positives = 76/213 (35%), Gaps = 39/213 (18%)

Query: 13  PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           P R+ K +AR    A   SR  + ++IA+  V   G +L  A   V   + IE+  VP+ 
Sbjct: 15  PNRLDKALARDVPEAANLSRSRLAKLIAEGAVMRAGEVLTDAKAKVTEGEVIEIT-VPVA 73

Query: 69  KAERTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
           +    R              L + +KP G+V   +      T+ + L             
Sbjct: 74  EESHMRPEAIALDVVWEDHDLIVVNKPAGMVVHPAPGTPSGTLVNALLHHCGDDLSGVGG 133

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V R+D +T GLL++         L          R YR   +G  D      LK
Sbjct: 134 EKRPGIVHRIDKDTSGLLVVAKTDAAHHGLAAQFEKHTVERHYRALVYGMPDLAD-PRLK 192

Query: 163 --KGIVIQ-----GICYGDMQVTLDTQKGSNAW 188
             +G+  +      I     +   D QK +  W
Sbjct: 193 GVRGVSFEQGGIVKITTQLARHKTDRQKQAVTW 225


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 63/171 (36%), Gaps = 22/171 (12%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           +Q     QR+ + +A      SR  ++  I  ++VK+NG + +     V   + IE+   
Sbjct: 10  IQPEQMGQRLDQTLAELFPEYSRSRLKTWIEAKQVKMNGEIADIPRAKVYGGEQIEISVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                      +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDENRFEPQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
           R   V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>gi|210134948|ref|YP_002301387.1| pseudouridine synthase D [Helicobacter pylori P12]
 gi|210132916|gb|ACJ07907.1| pseudouridine synthase D [Helicobacter pylori P12]
          Length = 327

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 52/310 (16%), Positives = 105/310 (33%), Gaps = 57/310 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +++    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLSKELQISKNQVLHLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPQITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L           +  R   V
Sbjct: 73  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G + +  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIAIAKN-NFTHVCLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICY------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            N LK  I ++              ++L T + +   +   L  G+  +I+         
Sbjct: 192 NNRLKM-IALKAAKKEKSRYSKSEFISLLTSQNNLNLIGAKLFTGRTHQIR---AHL--- 244

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
              L R   G   L  L       + K+ +R  L  +L+E      +  ++    L++D 
Sbjct: 245 -EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLHFKVPLLKDM 298

Query: 272 PNIISEVPDD 281
              + +V D 
Sbjct: 299 LEYLKKVFDK 308


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 82/239 (34%), Gaps = 45/239 (18%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +  R   A+R +++  I  + V+VN     +A+  +  +D I V           
Sbjct: 30  RIDRFLMDRLQNATRTKIQAGIDAESVRVNDKP-TKASYKIKPSDIITVSLPHPPRETDL 88

Query: 63  --DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
             + +P+    E   L + +KP G+V   +  +   T+ + L   F  + +         
Sbjct: 89  KPENIPINIVFEDDDLLVINKPAGMVVHPAHGNWDGTLVNALVYHFQNLPTSRHGEVRPG 148

Query: 111 -VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            V R+D +T GL+++         L          R Y     G  +     +   G + 
Sbjct: 149 LVHRIDKDTSGLMVIAKTEFAMTYLARQFFEHTIERTYNALTWGVPNPQIGTI--TGFIG 206

Query: 168 QGICYGDMQVTLDTQKGSN---------------AWVTVGLREGKNREIKKVFEFFNWK 211
           + I    +Q   D +                   A V   L  G+  +I+  F+     
Sbjct: 207 RSIKDRKVQAIYDDESKGKWAVTHYTTLEDLGYVALVECKLETGRTHQIRAHFKHIGNP 265


>gi|222054177|ref|YP_002536539.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221563466|gb|ACM19438.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 298

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 74/238 (31%), Gaps = 43/238 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  K  V       R+    AR      S+ ++ R+I      ++  L+  A+  +   D
Sbjct: 1   MILKASVSAELAGMRLDDG-ARQLFPELSKTQIRRIIDWGGCTISDALVRVASRQLREGD 59

Query: 59  HIEV------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            I +             G      E       +K  GL +  +    + TV   +     
Sbjct: 60  LISLGVMEPERCVEITYGKGDLLYEDGGYLAINKAAGLNSQRTPYQLKGTVEYAVDCYLK 119

Query: 107 RV------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK- 157
            +        + RLD  T G++        A  +   L   +  +VY        +QD+ 
Sbjct: 120 SLGSKEPARVIHRLDRGTSGVMFFPKHKKAATHISFLLKEGKVEKVYWALVADVPEQDQW 179

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
                   LN  + G+ + G         +   KG+       L E     G+  +I+
Sbjct: 180 TVDAPIAKLNKFRYGVALPGREARTAFRVITAGKGA------TLIEAHPFTGRTHQIR 231


>gi|296135788|ref|YP_003643030.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
 gi|295795910|gb|ADG30700.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
          Length = 342

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 81/235 (34%), Gaps = 41/235 (17%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVK----VNGILLERAAVNVMSTDHI 60
           +V E    QR+ KV+A      SR  +++      V+    V G+   R       T  I
Sbjct: 35  VVPEADAGQRLDKVLAAQFSQYSRSRLQQWCEAGLVRMGAQVAGV---RDKARAGETLRI 91

Query: 61  EV-----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
            V           + +PL    E   L + +KP GLV   +  +   T+ + L + +   
Sbjct: 92  AVPALPEDTAFAPEDLPLNVVFEDADLAVLNKPAGLVVHPAAGNWSGTLLNGLLARYPET 151

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK--- 157
               R   V RLD +T GL++          L     +    R Y     G V +     
Sbjct: 152 AGLPRAGIVHRLDKDTSGLMVTARTLEAQTELVRRLQARTIHRQYLALAWGSVSRAFNVE 211

Query: 158 -------LNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREIK 202
                   + L+  +V  G            LDT+ G    +   L  G+  +I+
Sbjct: 212 APIGRHPRDRLRMAVVHGGKPARTDFTPLAELDTRWGPLTALRCKLHSGRTHQIR 266


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 73/207 (35%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR  ++  I Q  ++VNG  ++     V+  D +E+D     +              E  
Sbjct: 32  SRSRIQNWIKQGALRVNGKQVK-PKEKVIEGDQVELDVELEAQGDWEAQPIALDVVFEDE 90

Query: 74  RLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTND 127
            L + +K    V      HSD    + V  + P+     R   V RLD +T GL+++   
Sbjct: 91  HLLVINKQADFVVHPAAGHSDGTVVNAVLHHCPALSELPRAGIVHRLDKDTTGLMVIAKT 150

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----------IVIQGICYGDM 175
                 L  +L + +  R Y    +G++    +     G          +   G      
Sbjct: 151 LIAHNSLVEQLQAREMGREYECVVYGELTGGGVVEAAIGRHPQNRQKMAVTRGGKDAVTH 210

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              +   +G    + + L  G+  +I+
Sbjct: 211 YRLIRRWRGFTH-LRLKLETGRTHQIR 236


>gi|114771661|ref|ZP_01449065.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium
           HTCC2255]
 gi|114547733|gb|EAU50623.1| putative Pseudouridine synthase, Rlu [alpha proteobacterium
           HTCC2255]
          Length = 341

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 83/263 (31%), Gaps = 60/263 (22%)

Query: 6   IVQENFTPQRVSKVIAR---AGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            + EN  P R+ K +A    A +  SR  + ++IA+  V + G  + +      +     
Sbjct: 10  TLGENPAP-RLDKALASVVPAEVTLSRSRITKLIAEGAVTLAGEPITKLKYKAPAGSIFR 68

Query: 62  V-------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           +             + +PL    E   L + +KP G+V   +      T+ + L   F  
Sbjct: 69  IVMPPVQDYENAQPENIPLDIVFEDDHLIIVNKPAGMVVHPAPGSENGTLVNALLYYFDG 128

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D +T GLL++         L          R Y     G   +
Sbjct: 129 NLSGVGGEKRPGIVHRIDKDTSGLLVVAKSDSAHAGLAKQFADHSISRRYLAVSKGVPQK 188

Query: 156 DK--LNLLKKGIVIQGI--------------CYGDMQVTLDTQKGSNAWVTV-------G 192
               L  L+ G+  +                    M V  D  + +    TV        
Sbjct: 189 SDPRLAGLR-GVNFEDGGVIRVATNIARHKTDRKRMAVVQDAGRHAITRATVLENFAHSA 247

Query: 193 LRE-----GKNREIKKVFEFFNW 210
           L E     G+  +I+  F     
Sbjct: 248 LMECWLETGRTHQIRVHFSHIGH 270


>gi|294339951|emb|CAZ88314.1| Ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Thiomonas sp. 3As]
          Length = 342

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 81/235 (34%), Gaps = 41/235 (17%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVK----VNGILLERAAVNVMSTDHI 60
           +V E    QR+ KV+A      SR  +++      V+    V G+   R       T  I
Sbjct: 35  VVPEADAGQRLDKVLAAQFSQYSRSRLQQWCEAGLVRMGAQVAGV---RDKARAGETLRI 91

Query: 61  EV-----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
            V           + +PL    E   L + +KP GLV   +  +   T+ + L + +   
Sbjct: 92  AVPALPEDTAFAPEDLPLNVVFEDADLAVLNKPAGLVVHPAAGNWSGTLLNGLLARYPET 151

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK--- 157
               R   V RLD +T GL++          L     +    R Y     G V +     
Sbjct: 152 AGLPRAGIVHRLDKDTSGLMVTARTLEAQTELVRRLQARTIHRQYLALAWGSVSRAFNVE 211

Query: 158 -------LNLLKKGIVIQGICYGDMQ---VTLDTQKGSNAWVTVGLREGKNREIK 202
                   + L+  +V  G            LDT+ G    +   L  G+  +I+
Sbjct: 212 APIGRHPRDRLRMAVVHGGKPARTDFTPLAELDTRWGPLTALRCKLHSGRTHQIR 266


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/226 (17%), Positives = 81/226 (35%), Gaps = 44/226 (19%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
            R++  +      S R + +   + R+KVNG      +  + + D +E+      +    
Sbjct: 19  IRLNHYLKEVAQCSSRFIRKAAREGRIKVNGNNAR-LSYMLTNNDIVELQINRKEEQDII 77

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRL 114
                     E   + + +KP G+V   +      T+      + N  +  S V  V RL
Sbjct: 78  PEKMDLDIIYEDNDIIVVNKPKGIVVHPTKRHLNGTLSNGVLYYFNDKNENSIVRLVNRL 137

Query: 115 DINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---- 168
           D++T GL+L+  +      L        +++ Y    HG  ++D       G++ +    
Sbjct: 138 DMDTSGLVLIAKNAYSHMALSRDMQKDDFVKKYLAIVHGNFNED------SGVIDKPIYR 191

Query: 169 -GICYGDMQV-----------TLDTQKGSNAWVTVGLREGKNREIK 202
            G       +            +  Q  + + V + L  G+  +I+
Sbjct: 192 VGEGTLKRIIDERGQRSITLFKVIEQYKNASLVELTLETGRTHQIR 237


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 86/257 (33%), Gaps = 56/257 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           I+QE+   QRV K + +   A  +  + + I  +++KVN       A  ++  DH+    
Sbjct: 5   IIQEDDANQRVDKFLQKTLPALPKSLMYKYIRNKKIKVNRKRC-EIAQRLLPGDHVLCFI 63

Query: 61  --------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
                         +V        E   + L  KP GL+T     + +  + D       
Sbjct: 64  AEEFFETGEDCSFLKVSSELDVLYEDANVILMKKPSGLLTHKDSNEIQDNLADRFLHYLY 123

Query: 102 ------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG 151
                 P            RLD NTEG+++        R +   +   +  + Y     G
Sbjct: 124 KKGQYDPQTRQSFTPALCHRLDRNTEGIVIGAKTAEALRRMNAYIREHKVEKHYVCIVEG 183

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-----------------VTVGLR 194
            ++Q   ++    ++         +V L   +  N+                  V V L 
Sbjct: 184 VMEQKTGHV----VLWHKKDAKSNKVHLYAHEQKNSQRIETSYRTLHQGKRYAYVEVQLH 239

Query: 195 EGKNREIKKVFEFFNWK 211
            GK+ +I+ V  + +  
Sbjct: 240 TGKSHQIRAVMAYLHHP 256


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           R+ K +A  G +ASR    ++I    V VNG ++ +A+  V   D + V   PL 
Sbjct: 1  MRLDKFLAEHGLVASRTLAAKLIDAGCVSVNGKIVYKASQPVHRDDDVLVQESPLT 56


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 82/244 (33%), Gaps = 52/244 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVER--------MIAQQRVKVNGILLERAAV 52
           M +K +V ++    R+ K +       R+  +         +I +  VKVNG   +    
Sbjct: 1   MINKYLVDKDHVNIRLDKFM-------RKYSKEESLSIIFSLIRKGFVKVNGKKSKE-NY 52

Query: 53  NVMSTDHI-------EVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPD 92
            ++  D I        V    + K              E   +++ +KP  +     D  
Sbjct: 53  RLLLNDEIFFPDAAKIVMDKKIEKEIIDIDLFKNMIVFEDEDVFIINKPNNMPMHKGDKH 112

Query: 93  G---RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV 147
                 T      +    V    RLD+ TEGL++   +  + R +  E+ + + ++ Y  
Sbjct: 113 KFGLSETAKAYYNN--PNVNFANRLDLETEGLVIGCKNLQILRKVNEEIRNKKIIKRYIA 170

Query: 148 RFHGQ--------VDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
           +   +            K+ + +  + + +          +   K     + + L  G+ 
Sbjct: 171 KVEQKKLQLDEEFFSDKKIKIFEDRVRVSKDGLEAKTYFKVIEVKDFKVLLDIELITGRK 230

Query: 199 REIK 202
            +I+
Sbjct: 231 HQIR 234


>gi|116670141|ref|YP_831074.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter sp.
           FB24]
 gi|116610250|gb|ABK02974.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter sp.
           FB24]
          Length = 308

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 80/251 (31%), Gaps = 43/251 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---------ERAA 51
           M +K  V E     RV   +AR    SR +   +IA+  V   G  +             
Sbjct: 1   MPEKLTVPEELAGTRVDAGLARLMGISRSQAATLIAEGNVSSGGKAVGKSLKLASGTVLE 60

Query: 52  VNVM----STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           V V       + +E  V+G+ +   +   + +  KP+G+    S      TV   L  + 
Sbjct: 61  VVVPERRDPLEIVEEVVEGLKILLDDEDFVVI-DKPVGVAAHPSPGWVGPTVVGGLAGLG 119

Query: 106 SRVI---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD 154
            R+           V RLD+ T G +++         L+    +    +VY     G  D
Sbjct: 120 YRISTSGAPERAGIVHRLDVGTSGAMVVAKSERAYTALKRAFKERTVDKVYHAVVQGLPD 179

Query: 155 Q--DKLN-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                ++                 VI+          +    G  + V V L  G+  +I
Sbjct: 180 PLAGTIDAPIGRHPGHDWRFA---VIEDGRESVTHYEVLEAFGKASLVEVHLETGRTHQI 236

Query: 202 KKVFEFFNWKV 212
           +  F       
Sbjct: 237 RVHFSALRHPC 247


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/220 (17%), Positives = 79/220 (35%), Gaps = 38/220 (17%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----------- 75
           SR+ + +M  + R+++N   ++   V + S D IE +   L   E+T             
Sbjct: 41  SRKFIRKMGREYRIRLNCRYVKFTEVKLNSGDLIEFN---LNFKEKTYYDPAPLDLDIIY 97

Query: 76  -----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
                 + +KP  ++   +  +  +T+ + +            V  + RLD NT GLLL+
Sbjct: 98  EDRHLLVINKPANMLVHPTPVEKSNTIVNGVLYHMRNQGNYNLVRPIHRLDRNTTGLLLI 157

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVD--QDKLNL---------LKKGIVIQGIC 171
             +      +     +    R Y    HG V+  ++ +N          +K+ +      
Sbjct: 158 AKNQYAHNYITHQFQNNNIHREYLAFVHGNVEFKKESINAPIGKTRDSLIKRKVDHTLGK 217

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                + +    G  + + V L  G+  +I+         
Sbjct: 218 RAVTHIKVVKPGGLISLIRVKLETGRTHQIRVHLSHLGHP 257


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 77/236 (32%), Gaps = 45/236 (19%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P+R+ + +AR     SR  ++ +I +  V+++G  +  AAV V     + V        
Sbjct: 15  APERLDRALARTWPDLSRSRLQGLIREGGVRLDGAEIRDAAVRVAGGQTVAVTVPPARPA 74

Query: 63  -----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SR 107
                +   +   E   L +  KP GLV   +      T+ + L +             R
Sbjct: 75  TPEAEERALIIPYEDDDLIVIDKPPGLVVHPAPGHDSGTLVNALIAHCGASLSGIGGVRR 134

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHGQVDQDKLNLL 161
              V RLD +T GLL++  +      L L            R Y     G  +     + 
Sbjct: 135 PGIVHRLDKDTSGLLVVAKNDMAHAALSLQFADHGRSGQLERAYLALVWGVPEPRAGRID 194

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVT----VGLRE-----------GKNREIK 202
                          V  +  + +         +G+RE           G+  +I+
Sbjct: 195 AALARSDSNREKIAVVRPEKGRHAITHYRTEAVLGVREPVGLVRCRLETGRTHQIR 250


>gi|282892129|ref|ZP_06300604.1| hypothetical protein pah_c207o069 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498024|gb|EFB40368.1| hypothetical protein pah_c207o069 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 283

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 31/137 (22%), Positives = 56/137 (40%), Gaps = 12/137 (8%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-------RLWLYHKPIGL 84
              +  +RV V+  +++ A+  + +   I + GV   + E+         L +  KP GL
Sbjct: 28  REWLKHERVFVDDQIVKIASTPLEAGQTISL-GVRKARKEKVPILYEDAHLVVIEKPAGL 86

Query: 85  VTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           ++  ++ D   T    L   +   +V  V RLD +T G++L    G     L        
Sbjct: 87  LSVATNFDKAKTAHAFLKERYRPRKVYVVHRLDQDTSGVMLFALTGEAFFGLKALFADHD 146

Query: 141 WLRVYRVRFHGQVDQDK 157
             R Y    HG++ Q +
Sbjct: 147 IDREYTAVVHGKMTQQE 163


>gi|94264419|ref|ZP_01288209.1| Pseudouridine synthase, RluD [delta proteobacterium MLMS-1]
 gi|93455176|gb|EAT05394.1| Pseudouridine synthase, RluD [delta proteobacterium MLMS-1]
          Length = 310

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 39/253 (15%), Positives = 77/253 (30%), Gaps = 53/253 (20%)

Query: 11  FTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLE-----------RAAVNVMS 56
              +R+   +A        +R  +  +I Q  V V  +              +A + + +
Sbjct: 1   MAGRRLDHFLAEQLQDQELTRSRLRGLIRQGLVTV--VPATAAPEQAATPSRKAGLALKA 58

Query: 57  TDHIEVD-----GVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPS 103
            D + V+      V L   E   + LY         KP G+V   +    R T+ + L  
Sbjct: 59  GDRVAVEVPAAEPVALAAQEIPFVVLYEDGDLLVISKPPGVVVHPAAGHHRGTLVNGLLH 118

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
               +           V RLD +T G L++  +    R L     + +  ++Y     G+
Sbjct: 119 HCRDLSGISGELRPGIVHRLDKDTSGCLVVAKNDRAHRDLLAQFKNREVEKIYLALLSGK 178

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +  +             +   +      +G                   V++ L  G+  
Sbjct: 179 LAGEQGRVEGAIGRHPKQRQKMAVRPAGEGRAALTHWRLRQRFTAGYTLVSLRLDSGRTH 238

Query: 200 EIKKVFEFFNWKV 212
           +I+         V
Sbjct: 239 QIRVHMASLGHPV 251


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 84/259 (32%), Gaps = 49/259 (18%)

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     + HK  G+       D   ++ + L
Sbjct: 60  LGEEFVVDVIARPPSRLEPIAMDIPVLYDEDE-FMVIHKKAGIACHSGPGDDSPSLVNGL 118

Query: 102 PSIFSRVIS---------VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRF- 149
              F  +           V RLD  TEG+L++  T+    A           + Y     
Sbjct: 119 LYQFKNLSGTGGERRPGIVHRLDKPTEGVLIIAKTDRAHAALSKLFQDRLVEKTYYAWVL 178

Query: 150 ----------HGQVDQDKLNLLKKGIVIQGIC----YGDMQVTLDTQKGSN-AWVTVGLR 194
                     +  + +  +  +K  +   G      Y   ++ + TQ G   + + +GL 
Sbjct: 179 QAPVEAEGTINMPIGRHPVERVKMCVREDGRMAITHYKTEKI-VQTQTGRKFSLMKLGLE 237

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+         V 
Sbjct: 238 TGRTHQIRVHMAKVGCPVV 256


>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 = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 86/235 (36%), Gaps = 37/235 (15%)

Query: 11  FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGV- 65
           F+ +R+ +++++  +  SR  +++ I    V +NG +  +    ++  + I +   D   
Sbjct: 15  FSGKRLDQILSKLFMQYSRSCLKKWIIMNNVYINGKIENQPDKKILGGEKITIYSTDEKL 74

Query: 66  PLRKA---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
           P+            E + + + +KP GLV      +   T+ + L   +       R   
Sbjct: 75  PINLPQNIALNTIYEDSNILIINKPPGLVVHPGAGNQDGTILNALLYRYTNISSIPRCGI 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKL 158
           + RLD +T GL+++         L   L   + +R Y+    G           + +   
Sbjct: 135 IHRLDKDTSGLMVIAKTIFSYNKLVTLLKKRKIIRKYQGIIKGNMISGGIVNYPIMRHPF 194

Query: 159 NLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
             +   +    +    +    +  +   +  V+  L  G+  +I+  +     + 
Sbjct: 195 KRIC--MTTDSLGKKSITHYKIINRFKFHTHVSFRLETGRTHQIRVHML-HIGYP 246


>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 = 67.9 bits (165), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 79/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN    +     ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQ-PKDKMIGGESISVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  KPEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 67.9 bits (165), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 46/230 (20%), Positives = 82/230 (35%), Gaps = 46/230 (20%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
           R+ K ++      SR +V++ I    V+VNG+++  + V V   D I     +   L+  
Sbjct: 14  RLDKALSLLLKKVSRNQVQKAIKNYCVQVNGVIISDSDVLVKENDTILFSFKEPEELKIT 73

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISV 111
                     E   L + +K  G+          +T+ + L              R   V
Sbjct: 74  AANITLDIIYEDDDLIVINKAAGMTVHPGIRHHDNTLVNALLHHTKYLSDIGSAERPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ-------------- 155
            RLD +T GL+++  +     +L       Q +R Y+    G ++               
Sbjct: 134 HRLDKDTTGLMVVAKNNKTHILLANQIKQRQVIRKYKALVWGVINPLEGIIKNNVGRNRN 193

Query: 156 --DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
              K+ +LK G    G        TL+   G   + V   L  G+  +I+
Sbjct: 194 NRKKMTILKYG----GKKAVTYYKTLELFYGGTLSMVECKLSTGRTHQIR 239


>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 = 67.9 bits (165), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/182 (23%), Positives = 71/182 (39%), Gaps = 32/182 (17%)

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------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+            + +PL    E   L + +KP G+V   +      T+ + L      
Sbjct: 67  EITIEEAEDSHIGPEDIPLEVIYEDDDLIVINKPTGMVVHPAPGTPSGTLVNALLHHCGD 126

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D  T GLL++       + L          R YR   +G  D 
Sbjct: 127 NLSGVGGVKRPGIVHRIDKETSGLLVVAKSDVAHQGLAAQFEKHTVERYYRAICYGVPDA 186

Query: 156 DK 157
           + 
Sbjct: 187 ND 188


>gi|88658198|ref|YP_507572.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           chaffeensis str. Arkansas]
 gi|88599655|gb|ABD45124.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           chaffeensis str. Arkansas]
          Length = 307

 Score = 67.9 bits (165), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 93/252 (36%), Gaps = 61/252 (24%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE-------VERMIAQQRVKVNGILLERAAVN 53
           M    IV+E+    R+ K I       RR        VE+ + +  V ++   ++   V 
Sbjct: 2   MSKYYIVEEDDHNIRIDKFI-------RRILKIPQSLVEKFLRKGVVLLDNTKVKS-DVR 53

Query: 54  VMST-------DHIEVDGVPLRK------------------AERTRLWLYHKPIGLVTTH 88
           + +        D +  +   +RK                   E   + + +KP G ++  
Sbjct: 54  IKAGNVICVRYDRVIYERKQIRKICKADSDFLVHLIRNSVVYEDDDVLIINKPAG-ISVQ 112

Query: 89  SDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
                + ++ D +  I     +  V RLD +T G+L+L  +  ++R++     + +  + 
Sbjct: 113 GGTKVKISISDIVDKIRDGESMKIVHRLDKDTSGILMLARNARISRLIMHEFKNRRVEKK 172

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QKGSNAW-------VTVGLRE 195
           Y     G + ++ +  +   I I+      +    D+  Q+   ++         +GL E
Sbjct: 173 YLALTQG-IPKNDIGQINHSI-IKNKRSLSLDKVNDSYLQEAVTSFSVLKKLPYGIGLLE 230

Query: 196 -----GKNREIK 202
                G+  +I+
Sbjct: 231 LKPITGRKHQIR 242


>gi|67459733|ref|YP_247357.1| ribosomal large subunit pseudouridine synthase D [Rickettsia felis
           URRWXCal2]
 gi|67005266|gb|AAY62192.1| Ribosomal large subunit pseudouridine synthases, RluD subfamily
           [Rickettsia felis URRWXCal2]
          Length = 385

 Score = 67.9 bits (165), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 47/228 (20%), Positives = 80/228 (35%), Gaps = 45/228 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA----------ERT 73
           SR ++++ I   +V VN +++    V V   D I     +   L+ A          E  
Sbjct: 69  SRNQIQKAIKNSQVLVNDVIISDPDVLVKENDVILFSFKEPEELKIAAANIALDIIYEDD 128

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVGRLDINTEGLLLL 124
            L + +K  G+           T+ + L              R   V RLD +T GL+++
Sbjct: 129 DLIVINKAAGMTVHPGAGHHDDTLVNALLYHTKNLSDIGSAERPGIVHRLDKDTTGLMVV 188

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHG----------------QVDQDKLNLLKKGIV 166
             +     +L       Q +R Y+    G                +VD+ K+ +LK G  
Sbjct: 189 AKNNKAHMLLANQIEQRQVIRKYKALVWGVINPLEGVIKNNIGRSRVDRQKMTILKYG-- 246

Query: 167 IQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             G        TL+   KG+ + V   L  G+  +I+         V 
Sbjct: 247 --GKEAVTHYKTLELFHKGTISMVECKLSTGRTHQIRVQLSHLKHSVV 292


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 78/249 (31%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  V  N  P R+ K +A      SR  +++      + VNG  ++     V   D + +
Sbjct: 55  KVQVDANQDPVRIDKYLADKMAYQSRNRIQQAADAGFIHVNGKPVKS-NYKVRPNDLVTL 113

Query: 63  ------DGVPLRKAE--------RTRLWLYHKPIGLVTTHSDPDGRSTVFD--------- 99
                     ++  E          +L + +K  G+V      +   T+           
Sbjct: 114 MLDRPRHETSIKPEEIAINVVYEDDQLMVVNKEAGMVVHPGAGNFHGTLIQAVAWHLRDM 173

Query: 100 -NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
               +    V  V R+D +T GLL++         L     +    R Y     G + +D
Sbjct: 174 PEFDANDPEVGLVHRIDKDTSGLLVVAKTPTAKNALGKQFFNKTTHRSYNALVWGNIVED 233

Query: 157 K-----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           +            N L+  +       G   VT   +  + G    V   L  G+  +I+
Sbjct: 234 EGRIEGNIGRDPKNRLRMKVFDPDSGIGKTAVTHYKVLERFGYTTLVQCVLETGRTHQIR 293

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 294 AHMKHIGHP 302


>gi|260773303|ref|ZP_05882219.1| tRNA pseudouridine synthase C [Vibrio metschnikovii CIP 69.14]
 gi|260612442|gb|EEX37645.1| tRNA pseudouridine synthase C [Vibrio metschnikovii CIP 69.14]
          Length = 246

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/190 (19%), Positives = 60/190 (31%), Gaps = 42/190 (22%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDPYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGICYGDMQVTLDTQK 183
             +A +L     S Q  + Y     G ++Q  +    LK+   +  I     Q   + Q 
Sbjct: 67  SEVASILMPMFASQQMEKTYHAVVRGWIEQAGVLDYPLKQ--ELDKIADKFAQQDKEPQS 124

Query: 184 GSNAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN-------- 213
              A+     V V             L E     G+  ++++        +         
Sbjct: 125 AITAYQPLANVEVPFSTGKFATTRYSLMELKPKTGRKHQLRRHMAHLRHPIVGDTTHGDG 184

Query: 214 ---RLIRISY 220
              RL R  Y
Sbjct: 185 KHNRLYREQY 194


>gi|315180900|gb|ADT87814.1| pseudouridine synthase Rlu family protein [Vibrio furnissii NCTC
           11218]
          Length = 243

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/214 (16%), Positives = 67/214 (31%), Gaps = 46/214 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDAYIVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVD---------QDKLNLLKKGIVIQGICYGDM- 175
             +A  +     + +  + Y     G ++         +++L+ +      Q     D  
Sbjct: 67  SEIAANMMPMFANHEMEKTYHAIVRGWIEAGDVLDYPLKEELDKIADKFAKQDKAPQDAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN-------- 213
                    +V   T K         L E     G+  ++++        +         
Sbjct: 127 TAYQPLAQVEVPHSTGKFPTTRY--CLMEMKPKTGRKHQLRRHMAHLRHPIVGDTTHGDG 184

Query: 214 ---RLIRISYGPFQLGTLLAGSTREV---SKKIL 241
              RL R  Y   +L  L A   R V   +++ L
Sbjct: 185 KHNRLYREVYDAHRL-MLHASELRFVHPYTEQEL 217


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 1/63 (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 LWL 77
            L
Sbjct: 63 EAL 65


>gi|315604414|ref|ZP_07879480.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315314120|gb|EFU62171.1| ribosomal large subunit pseudouridine synthase D [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 310

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 83/249 (33%), Gaps = 39/249 (15%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M    +  V +    +RV   +AR    SR     + A   V +N  +    +  + + D
Sbjct: 1   MSSSRMLPVPDALVGERVDAALARMLGLSRSRCAELCAAGLVLIN-AVSADKSARLGADD 59

Query: 59  HIEV-----DGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            IEV     +  P    +   L+      +  KP+G+           TV  NL +   R
Sbjct: 60  IIEVTIPEPENKPAPVTDMEILYDDDDIVVVDKPVGVAAHTGPGWEGPTVLGNLEAAGYR 119

Query: 108 VIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQ 155
           + S         V RLD+ T G +++     LA  +   + +     ++Y     G +D 
Sbjct: 120 ITSHGPPERQGIVHRLDVGTSGAMMVAKS-ELAYSVMKRAFKERRIDKIYHAVVAGHLDP 178

Query: 156 --DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
               ++           +  ++  G        TL+   G+     V L  G+  +I+  
Sbjct: 179 PSGTIDAPIGRHPSREWRMAVIDGGKRAVTHYDTLELMAGAQLT-EVHLETGRTHQIRVH 237

Query: 205 FEFFNWKVN 213
                    
Sbjct: 238 MAAVGHPCV 246


>gi|154491501|ref|ZP_02031127.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC
           43184]
 gi|154088302|gb|EDN87347.1| hypothetical protein PARMER_01111 [Parabacteroides merdae ATCC
           43184]
          Length = 303

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 76/212 (35%), Gaps = 28/212 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDH---------IEVDGVPLRKA-ERTRLW 76
           S+  V+ ++A  ++ VNG +  +    +   +          +E +   L    E   L 
Sbjct: 41  SKSSVKALLAHGQISVNGTVTSQFNTPLTPGNEVLISYERGKVEFNNPLLTIVWEDDDLI 100

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
           + +K  GL++  S      T    L           ++  + RLD +T GL++   +  +
Sbjct: 101 VVNKKEGLLSVSSTRVKERTALHLLSEYVKKTDPRNKIFVLHRLDRDTSGLMMFAKNLQV 160

Query: 131 ARVLELPSTQ--WLRVYRVRFHGQVDQD-KL--------NLLKKGIVIQG-ICYGDMQVT 178
            + L+         R Y     G+ ++D  L          ++  +  +G       +  
Sbjct: 161 QKALQSNWNSAITARTYVAVVEGRPEKDSDLIVSNLTENAKMQVYVTAEGDGKEAITRYR 220

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           L    G+ + + + L  G+  +I+   +    
Sbjct: 221 LLHSNGAYSLLELDLETGRKNQIRAQMQSIGH 252


>gi|57239260|ref|YP_180396.1| pseudouridylate synthase [Ehrlichia ruminantium str. Welgevonden]
 gi|58579223|ref|YP_197435.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Welgevonden]
 gi|57161339|emb|CAH58262.1| ribosomal large subunit pseudouridine synthase D [Ehrlichia
           ruminantium str. Welgevonden]
 gi|58417849|emb|CAI27053.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Welgevonden]
          Length = 324

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 85/245 (34%), Gaps = 44/245 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K I +Q     +R+ K IA     SR +V+++I   ++ +   +++         D 
Sbjct: 1   MFEKKIFIQNGEENKRLDKFIALKLNISRNKVQQLIQNNKIYLFNKIVKDNNHITKVNDI 60

Query: 60  IEVD--------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
             ++               +P+    E   + + +K  G+           T+ + L + 
Sbjct: 61  YYINMPTQEHNCSITPNINIPITILYEDQDIIIINKEPGITVHPGAGTKDDTLVNGLIAH 120

Query: 105 F----------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
           +          SR   V RLD +T GL+++  +      L   L   Q  + Y     G 
Sbjct: 121 YGSTLSYIGKASRPGIVHRLDKDTSGLMVIARNEHSYYFLSDLLSKKQIKKEYLAVVWGI 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLREGK 197
            +  K N++K  I  +      M VT    KG                   V   +  G+
Sbjct: 181 PNP-KCNIIKNHIDTKSNNKQMMTVTHSRNKGKLAITEYNTIQTFASIATLVKCRIYTGR 239

Query: 198 NREIK 202
             +I+
Sbjct: 240 THQIR 244


>gi|31544701|ref|NP_853279.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|31541547|gb|AAP56847.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(low)]
 gi|284930765|gb|ADC30704.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. R(high)]
 gi|284931330|gb|ADC31268.1| RNA pseudouridine synthase [Mycoplasma gallisepticum str. F]
          Length = 330

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/263 (15%), Positives = 87/263 (33%), Gaps = 51/263 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK   +++      R+ K + +     +R  + +MI ++ + VN   +      +   D 
Sbjct: 1   MKKTIVIKSVDDCIRIDKFLFKYLKNYTRTNIYKMIRKKDITVNNQRI-DFDYILKVNDK 59

Query: 60  IEVDGVPLRKAERTR------------------LWLYHKPIGLVTTHSDPDG-------- 93
           I          ++                    L ++ KP+G+    +D           
Sbjct: 60  ITYYDFLRTDHKKKVPEFFKAKPELDLIYEDENLVIFEKPLGIPAQQTDEPSQYDHMQNR 119

Query: 94  ------RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVY 145
                 +S  +D L +       V RLD  T G++L   +    + L   + +    + Y
Sbjct: 120 LVHYLVKSNQYDYLNNQAYLPSIVNRLDTYTTGIMLGAKNLKAQQALNQIIKNRDLKKFY 179

Query: 146 RVRFHGQVDQDKLNLL--------KKGIVIQGICYGDMQVTLDT-------QKGSNAWVT 190
               HG+++  K  L         +  + IQ     D ++ +         +K +   + 
Sbjct: 180 HCLVHGEINPKKATLTAYLTKDPNRSLVSIQKEKTNDNKIIITRYQTLYYFKKQNYTLLD 239

Query: 191 VGLREGKNREIKKVFEFFNWKVN 213
           V L  G+  +I+      N  V 
Sbjct: 240 VELITGRTHQIRAHLASINHPVV 262


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 83/243 (34%), Gaps = 32/243 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERA-AVNVMSTD 58
           +  +  + E     R+   ++R     SR  V+ +I + +V VNG  ++R     V    
Sbjct: 2   ISKRFQIDEENANNRIDIFLSRKFDSLSRGIVQGLIDEGKVLVNGKTVDRDYKTKVDDQI 61

Query: 59  HIEVD----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            IE D           + L    E   L +  K  GL          ST+ + L  ++  
Sbjct: 62  EIEFDLETNNADLPQDINLNIVFENNDLLIIDKHAGLTVHPGAGQKDSTLINGLLYMYPD 121

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-------- 151
                R   V RLD +T GL+++         L     + +  R Y    HG        
Sbjct: 122 QKKIPRYGVVHRLDKDTSGLMIIARTLESHTNLTDLIQTRKIKRNYYALVHGQPIAGNTI 181

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              + +   N L   +  +G         +  +  + + + V L  G+  +I+   +   
Sbjct: 182 DKPIGRHPKNRLLFCVK-EGGREAITHFKVHKKFKNFSLLDVSLETGRTHQIRVHMQHIG 240

Query: 210 WKV 212
             +
Sbjct: 241 HPI 243


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 18  IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 77

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 78  LSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 137

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 138 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 194


>gi|300724802|ref|YP_003714127.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
 gi|297631344|emb|CBJ92039.1| pseudouridine synthase [Xenorhabdus nematophila ATCC 19061]
          Length = 250

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/186 (17%), Positives = 53/186 (28%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S      TVF        I   V  V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----------- 174
             +AR L          + Y     G V+ D +        +  I               
Sbjct: 67  SEVARTLSQQFEFHDIQKTYHAVVRGYVEGDDIIDYALMEQLDKIADKFADTDREAQSAI 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  +V    + G  +     L E     G+  ++++        +        G  
Sbjct: 127 THYRPLAKVECPVEIGRYSTSRFSLLELMPKTGRKHQLRRHMAHIRHPI-------IGDT 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|291528977|emb|CBK94563.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale M104/1]
          Length = 312

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 84/238 (35%), Gaps = 38/238 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D   VQ     +R+ K ++      SR   +R++ + ++ VN    ++A   + + D +
Sbjct: 3   RDTFEVQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKP-QKANYRLKTDDIV 61

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           +V              +PL    E   + + +KP G+V   S      T+ + +      
Sbjct: 62  DVTIPDAVQTPILPQDIPLDILYEDDDVLVVNKPKGMVVHPSAGHYSDTLVNAIMYHCKD 121

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQV-- 153
                    R   V R+D++T G L++  +      +          R+Y     G V  
Sbjct: 122 SLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKHHSCNRIYVGIVCGNVKN 181

Query: 154 DQDKLNLL-------KKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
           D+  +          +K + I             +  + G   ++   L  G+  +I+
Sbjct: 182 DEGTIEGAIGRNPNDRKKMAINEKNGKPAVTHYKVLERFGDYTYMQFKLETGRTHQIR 239


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 62/179 (34%), Gaps = 31/179 (17%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----- 63
             T  R+ K +A      SR   ++ I    V +NG +  + +  +   D + +      
Sbjct: 19  EPTLMRLDKYLAMMYPEYSRAFYQKHIVNHNVFINGEVQTKVSSRLSEGDVVTIHIQEKE 78

Query: 64  --------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------P 102
                    +PL K  E + + + +KP  +V   S      T+   L            P
Sbjct: 79  ELSELLPEEIPLHKVYEDSMIIVVNKPRDMVVHPSPGHHAGTIVHALLHEIGERLKQEFP 138

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKL 158
               R   V RLD +T G LL+T     A+ +           + Y     G+  Q ++
Sbjct: 139 EEPWRPGIVHRLDKDTSG-LLITAKTLKAKKIYGELFAKKLLQKRYLAVCVGKPLQTQI 196


>gi|52307928|gb|AAU38428.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 327

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 78/234 (33%), Gaps = 45/234 (19%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ +   QR+ + +A      SR  ++  I  + V +NG +       V   + +E+   
Sbjct: 13  VQPHQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE 72

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                      +PL    E   + + +KP   V      +   TV + L   + ++    
Sbjct: 73  IEDENRFEPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQITEVP 132

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
               V RLD +T GL+++         L   L   +  R Y     G +        K G
Sbjct: 133 RAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFGIMT-------KGG 185

Query: 165 IVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            V + +     + TL                     +   + + L  G+  +I+
Sbjct: 186 TVDEPMSRHPTKRTLMAVHPMGKPAVTHYRVMEHFRNYTRLRLRLETGRTHQIR 239


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 18  IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 77

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 78  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 137

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 138 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 194


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 81/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V+++   QR+ +  A      SR  ++  +    + VNG ++ +A V +M  + I V  
Sbjct: 10  TVKDSQLGQRLDQAAAELFSDFSRSRIKEWVLAGSISVNGEVITKARVKMMGGEEIVVKA 69

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                       +PL    E   + + +KP  LV          T+ + L   +      
Sbjct: 70  ELEDEERWLAQDIPLEIVYEDDDILVINKPRDLVVHPGAGTPDGTILNALLFHYPSIAEV 129

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L   L   +  R Y     G++          
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVRALQKRKITREYEAIVLGRMT-------AG 182

Query: 164 GIVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
           G++ + I     + TL                      +  + + L  G+  +I+
Sbjct: 183 GMIEKPIGRHPQKRTLMAVHELGKDAVTHYRVAEHFRIHTRLRLRLETGRTHQIR 237


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 63/172 (36%), Gaps = 32/172 (18%)

Query: 12  TPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVP 66
           + +R+   +A       SR  ++R+I + R+ +NG  +   +  +   D I ++     P
Sbjct: 18  SSKRIDVFLANRDPTF-SRSALQRLIGEGRILINGQTIR-PSQKIKPGDRIRLEVPRPEP 75

Query: 67  LRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------- 105
           L             E   L + HKP GLV   +  +   T+ + L   F           
Sbjct: 76  LDLKPEAIPFDILHEDAELLVLHKPAGLVVHPAPGNWSGTLVNALLHHFATSGVTPSHIG 135

Query: 106 --SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
              R   V RLD  T G++++  T+    A   +       RVY     G  
Sbjct: 136 GKERPGLVHRLDKETSGVMVIAKTDQAHRALAAQFKLHTITRVYEALIWGVP 187


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 38/187 (20%), Positives = 64/187 (34%), Gaps = 32/187 (17%)

Query: 13  PQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--------I 60
           P R+ K +AR        SR  + +MIA   V + G+ +      V             +
Sbjct: 29  PDRLDKALARQVPEDAALSRSRLMKMIADGDVTLEGVAVTNPKARVAEGQEYLLRLAPAV 88

Query: 61  EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
           ++D  P         E   L +  KP+G+V   +      T+ + L              
Sbjct: 89  DIDAQPEDIPLTVVWEDADLIVVDKPVGMVVHPAPGSYTGTLVNALLHHCGDTLSGVGGA 148

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLK- 162
            R   V R+D +T GLL++         L     +    R Y    HG  +      L+ 
Sbjct: 149 KRPGIVHRIDKDTSGLLVVAKTDRAHHGLAAQFEAHSVTRHYIALVHGAPNAAD-PRLRG 207

Query: 163 -KGIVIQ 168
            +G+  +
Sbjct: 208 IRGVSFE 214


>gi|217032147|ref|ZP_03437646.1| hypothetical protein HPB128_186g13 [Helicobacter pylori B128]
 gi|298736447|ref|YP_003728973.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
 gi|216946137|gb|EEC24746.1| hypothetical protein HPB128_186g13 [Helicobacter pylori B128]
 gi|298355637|emb|CBI66509.1| ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori B8]
          Length = 327

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 55/309 (17%), Positives = 104/309 (33%), Gaps = 55/309 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RLDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDAITLLTPQITPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICY------GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LK  I ++              ++L   +     +   L  G+  +I+          
Sbjct: 193 NRLKM-IALKAAKKEKSRYSKSEFISLLASQNGMDLIGAKLFTGRTHQIR---AHL---- 244

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L R   G   L  L       + K+ +R  L  +L+E      +  +     L++D  
Sbjct: 245 EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDML 299

Query: 273 NIISEVPDD 281
             + +V D 
Sbjct: 300 EYLKKVFDK 308


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/178 (18%), Positives = 64/178 (35%), Gaps = 28/178 (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  HIEV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            +               + +PL    E   + + +KP  ++          T+ + L + 
Sbjct: 60  IVTYTFPEKVEPGTVEPENIPLNIIYEDHDIIVVNKPPDMIVHPVHNKTSGTLVNALLNY 119

Query: 105 FSRVISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            + +  +G         RLD  T G++++  +      L     +    + Y     G
Sbjct: 120 CNDLQGIGGIMRPGIVHRLDKETSGVIVVAKNDRAHNSLVQQFKARTTEKYYLAIARG 177


>gi|86156486|ref|YP_463271.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85772997|gb|ABC79834.1| ribosomal large subunit pseudouridine synthase C [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 339

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 61/352 (17%), Positives = 113/352 (32%), Gaps = 75/352 (21%)

Query: 6   IVQENFTPQRVSKV---------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            V  +   QR+ K+         ++         V +M   ++V+VNG   + A   V  
Sbjct: 5   TVSADAAGQRLDKLVRKALRDVPLSH--------VYKMFRTRKVRVNGARGK-ADQVVAE 55

Query: 57  TDHIEVDGVPLRK--------------------AERTRLWLYHKPIGLVTTHSDPDGRST 96
            D + + G   R                      E   L    KP GL          +T
Sbjct: 56  GDVVVIRGDEERLLAKAAPAAPGGAPRVTFGVLHEDADLLAVDKPAGLAAHPGTGIEGAT 115

Query: 97  VF----------DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLR 143
           +           D+LP    +     RLD +T G++L+         L           +
Sbjct: 116 LVEMARGYLKTPDDLPPTEFKPSPAHRLDRDTSGVVLVAKHRKAMVRLGETFTTGEGVHK 175

Query: 144 VYRVRFHGQVDQDK--------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            Y     G++ ++                +   +G+  Q        V+   +    + +
Sbjct: 176 TYLALVKGKMPREAGTIDLPLSEHEQTSKSKAMRGVNFQEALTRWKVVSAAKEI---SLL 232

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST--REVSKKILREQLGP 247
            V +  G+  +I++  E     V    R  YG F            R +     R ++ P
Sbjct: 233 AVTIETGRTHQIRRHLEAVGHPVAG-DR-RYGDFAFNRTARTRWGLRRMGLHAWRLEV-P 289

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQK 299
           H L  A + L+AP  +    V  R N+  ++P   T      +++ G  +++
Sbjct: 290 HPLTGAPLRLEAPFPAELAEVLSRANL--KLPASPTGAHAPGARREGPHRER 339


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 76/228 (33%), Gaps = 42/228 (18%)

Query: 14  QRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG------- 64
            R+ K I+     IA R +++  I  + +KVN   ++  +  +   D I +D        
Sbjct: 9   IRIDKFISDELEEIA-REKIKDFIKDKLIKVNNKAVK-PSFKLSEGDEIFIDDSLFAIAE 66

Query: 65  --------VPLRKAERTRLW-----LYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVI 109
                     + + E   +      L   P G + T +  +       +D L  I     
Sbjct: 67  IKAENIDLKVVYENEDYAVIDKDSDLIVHPAGKIVTGTLVNALLYKYGYDGLSHIGGEDR 126

Query: 110 S--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--KLNLL-- 161
              V RLD +T GL+L+T +    +       + +  + Y     G  D+    +     
Sbjct: 127 PGIVHRLDKDTTGLILITKNNASYKYFKKMFETRKVDKYYYAIVFGNFDKKTGTIETFMD 186

Query: 162 -------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  K  +   G         L    G  + + + +  G+  +I+
Sbjct: 187 RDPNNRRKMAVRPAGRRAVSHYEVLREVDGF-SLLRIKIETGRTHQIR 233


>gi|33239671|ref|NP_874613.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. marinus str.
           CCMP1375]
 gi|33237196|gb|AAP99265.1| 23S RNA-specific pseudouridylate synthase [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 318

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 88/253 (34%), Gaps = 51/253 (20%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            ++     P R+ + + ++    SR  +++ I    V VNGI  +     + + D I++ 
Sbjct: 18  KLIYPKPLPMRLDRWLVSQRSEQSRARIQKFIEDGLVLVNGIQGKS-KTPLRTGDEIQLW 76

Query: 64  ---GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLP 102
                PL              E + + + +KP GL    +  +   T+ +       +LP
Sbjct: 77  VPPPEPLPYLKPQKMHLDIIFEDSHIIVINKPAGLTVHPAPGNKDRTLVNGLLHHCTDLP 136

Query: 103 SIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKL 158
            I  ++    V RLD +T G +++         L++   +    R Y    HG    D  
Sbjct: 137 GINGKLRPGIVHRLDKDTTGCIVIAKSQEALVNLQVQIQKRIASRRYIALVHGVPHGD-- 194

Query: 159 NLLKKGI----------------VIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNRE 200
               KGI                V+      D     + ++  G  + ++  L  G+  +
Sbjct: 195 ----KGIISAPIGRHPIDRKKYAVVNDGSGRDACTHWELKERLGDYSLLSFKLETGRTHQ 250

Query: 201 IKKVFEFFNWKVN 213
           I+         + 
Sbjct: 251 IRVHSAHIGHPIL 263


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 65/229 (28%), Gaps = 35/229 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           +R+ + IA  G  SR    R I    V V+G   + A   +     + V+          
Sbjct: 15  ERIDRFIAARGGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVVNLEEGGRAAPA 74

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
               G          L    KP G+    +    R  + + + ++  + V  V RLD  T
Sbjct: 75  LAALGRERLLYADADLCAVDKPAGVPAQPTLTTDRGALPELVSALLGAPVTLVHRLDRET 134

Query: 119 EGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDM 175
            G+ +   T D   A      +    + Y           +    L  G   +      +
Sbjct: 135 SGVTVFARTRDAAAALAEAFRTGTPEKTYLALCARAPSPAEGRVALALG---KDPARPGL 191

Query: 176 QVTLDTQKGSNAWVTVGLRE-------------GKNREIKKVFEFFNWK 211
           +        +       LRE             G+  +I+         
Sbjct: 192 RRVDPAGDPAATRYR-TLREAPGGARVEARPETGRTHQIRVHLAALGAP 239


>gi|167951161|ref|ZP_02538235.1| RNA-binding S4 domain protein [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 106

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 42/96 (43%), Gaps = 1/96 (1%)

Query: 195 EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKILREQLGPHLLEEA 253
           EG+ RE+++++E    +V+RL R+ YG   L + L  G  R ++   + + L    L   
Sbjct: 2   EGRQREVRRLWEAIGVQVSRLKRVRYGSVILESALKVGRWRALTHTEVNQLLEISGLPPE 61

Query: 254 QVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
           +    A      +  +  P    +      ++++ S
Sbjct: 62  KRQPPARAKHYRSDRQQAPRKQGQRAKSVGQLREQS 97


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 81/237 (34%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ K +    +  ASR +++  I    V VN  +++  +  V   D I V          
Sbjct: 32  RIDKFLMNR-VENASRNKIQNAIDAGSVLVNDSVIKS-SYKVKPFDIISVVLPDPPRDTE 89

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------- 110
              + +PL    E   + + +K  G+V      +   T+ + L   F+++ +        
Sbjct: 90  VYPEDIPLDIIFEDDEVMVVNKVAGMVVHPGFNNYTGTLVNALTHHFNQLPTMPGNAGRP 149

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD---------K 157
             V R+D +T GLL++         L         +R Y     G + +D          
Sbjct: 150 GLVHRIDKDTSGLLVIAKSEWAMTYLAKQFFDHSIMRKYVAMVWGDIAEDGTVTGYIGRN 209

Query: 158 LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           L   +   +      G   VT   +  + G    +   L  G+  +I+   +     
Sbjct: 210 LKDRRVMTMYDDSEKGKWSVTHYRVLERLGYVTLIECQLETGRTHQIRAHMQSIGHP 266


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 91/239 (38%), Gaps = 42/239 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV E+    R+   I  R  + SR  ++ +I ++++K+N  ++   +  V+S D I +  
Sbjct: 8   IVGEDENNLRLDVFINKRENLISRSRIKNLILKEKLKINDQIINSPSKKVLSGDEINLQI 67

Query: 63  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                      +       E   L + +KP G++      +   T+ + L          
Sbjct: 68  PEPKEASLKPYNFKLQIVYEDDDLLIINKPAGIIMHPGAGNYDETIVNALMHYNKDSLST 127

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHG--QVDQDK 157
                R   V R+D +T GL+++  +      L    ++    RVY++   G  +    K
Sbjct: 128 IGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRVYQLLIWGKLRPSSGK 187

Query: 158 LNLL-------KKGIVIQGIC-------YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++         ++ + +           Y  +++  + +  + + V   L  G+  +I+
Sbjct: 188 IDTFITRSSKNRQMMEVSNSKGKRAITNYKTIEIFENDKTPTLSLVECRLETGRTHQIR 246


>gi|332678564|gb|AEE87693.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida Fx1]
          Length = 332

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 80/233 (34%), Gaps = 36/233 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
              I+      +R+  VI       SR ++++ + +  + VNG    +    V+  + +E
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVE 70

Query: 62  VDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------P 102
           ++   L                E   + +  KP+ ++      +   TV + L       
Sbjct: 71  INIELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQ 130

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL 160
               R   V RLD +T GL++          L  +L   +  R Y     G++ Q+    
Sbjct: 131 DKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQEG--T 188

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV----GLRE-----GKNREIK 202
           + + I         M +    ++    +  + V     L E     G+  +I+
Sbjct: 189 INQPIGRDPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIR 241


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 85/233 (36%), Gaps = 45/233 (19%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            P RV K +        A+R +V++      + VNGI +++    V + D ++V      
Sbjct: 26  EPLRVDKFLMN--FIENATRNKVQQAAKDGNIYVNGIPVKQ-NYKVKAGDEVKVLLAYPP 82

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFS- 106
                  + +PL    E   L + +K  G+V      +   T+       F+NLP+  S 
Sbjct: 83  YENLLTPEDIPLDIVYEDDALLVVNKAAGMVVHPGHGNYSGTLINALVYHFENLPNNSSD 142

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------- 157
           R   V R+D +T GLL++         L          R Y     G +++++       
Sbjct: 143 RPGLVHRIDKDTSGLLVVAKTEAAMAYLSRQFFHKTSKREYVAIAWGNLNEEEGTIEGNI 202

Query: 158 ----LNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
                N L+  + +               +  + G    ++  L  G+  +I+
Sbjct: 203 GRNPKNRLQNIVYLGDDADQGKPAVTHYKVIERLGYVTLISCQLETGRTHQIR 255


>gi|254673628|emb|CBA09173.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           meningitidis alpha275]
          Length = 374

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 78/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMALDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQVPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +   ++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLIHSYIECSLETGRTHQIR 259


>gi|78221490|ref|YP_383237.1| tRNA pseudouridine synthase C [Geobacter metallireducens GS-15]
 gi|78192745|gb|ABB30512.1| tRNA pseudouridine synthase C [Geobacter metallireducens GS-15]
          Length = 270

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 50/273 (18%), Positives = 94/273 (34%), Gaps = 57/273 (20%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRST------VFDNLPSIFSRVISVGRLDINTEGLLLLT 125
              L   HKP+GL+   S  D   T      V D L     RV  V RLD  T G+LL  
Sbjct: 7   DEHLVAVHKPLGLLVHRSPIDRHETRFALQEVRDLL---GRRVYPVHRLDKPTSGVLLFA 63

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGI---- 170
            D   AR L     S    + Y     G + ++ +         +  ++G    G     
Sbjct: 64  LDPAFARGLVGAFASGSVTKTYLAVVRGTMPEEGVIDHPLAEEPDRFEQGRGNAGERAPQ 123

Query: 171 -------CYGDMQVTLDTQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVNRLIRISY 220
                     D+++ +   +   +  ++  L  R G+  ++++  +     +        
Sbjct: 124 SAVTGYRRLADVELPVAVGRYPTSRYSLVSLSPRTGRRHQLRRHLKHLFHPIV------- 176

Query: 221 GPFQLGTLLAGSTRE--------VSKKILR---EQLGPHLLEEAQVNLDAPIYSSETLVR 269
                G    G  R         ++ ++L    E   PH    A + + AP+  +   + 
Sbjct: 177 -----GDTKYGEGRHNRFFREELLTVRMLLHAVELTVPHPATGAPLTVCAPVEGAFAALL 231

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLA 302
            R   +S VP  +   +  S     +  +++++
Sbjct: 232 ARFGWLSAVPSRWLGPQGKSMAGEEMQTRQRIS 264


>gi|332292606|ref|YP_004431215.1| pseudouridine synthase, RluA family [Krokinobacter diaphorus
           4H-3-7-5]
 gi|332170692|gb|AEE19947.1| pseudouridine synthase, RluA family [Krokinobacter diaphorus
           4H-3-7-5]
          Length = 347

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 87/244 (35%), Gaps = 49/244 (20%)

Query: 12  TPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------- 61
            P RV K +        A+R ++++      ++VN I++++    V + D +        
Sbjct: 29  EPLRVDKFLMN--FVENATRNKIQKAAKNGSIQVNNIVVKQ-NYKVKAGDVVRAMFEHPP 85

Query: 62  ---------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIF 105
                    +D   +   E  +L + +KP G+V      +   T+        DNLP+  
Sbjct: 86  HEFLLTPEDIDIDVV--YEDDQLMVVNKPAGMVVHPGHGNYSGTLINALIHHVDNLPNNS 143

Query: 106 S-RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK----- 157
           S R   V R+D +T GLL++         L     +    R Y     G V  D+     
Sbjct: 144 SDRPGLVHRIDKDTSGLLVVAKTEQAMTHLSKQFFNKTTEREYVAIVWGNVVDDEGTIEG 203

Query: 158 ------LNLLKKGIVI-QGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                  N L+  +   +    G   VT   +  + G    V+  L  G+  +I+   + 
Sbjct: 204 NIGRHPKNRLQNTVFYGEDEDQGKPAVTHYKVIERLGYVTLVSCKLETGRTHQIRVHMKH 263

Query: 208 FNWK 211
               
Sbjct: 264 IGHT 267


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 87/232 (37%), Gaps = 37/232 (15%)

Query: 6   IVQENFTPQRVSKVIA---RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +V      +R+ + +A   R+   SR  + ++I    V VNG  + + +  +   D IE+
Sbjct: 1   MVDSPLVEKRLDQWLATTDRS--LSRTVIRKVIDLGGVHVNGRRVRKCSQALKRGDKIEL 58

Query: 63  --DGVPLRK---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
             D  PL                L + +KP G+ +  +    + T+++ L         P
Sbjct: 59  YRDQQPLTPFRLSEEDVLFRDDFLLVVNKPSGVESQPTPSRYKGTLYEALLVFLKDPYRP 118

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ-VDQ--DK 157
                +  V RLD  T G ++ +      + L     S +  +VY        +D   + 
Sbjct: 119 LDKPELGMVQRLDRETSGAMIFSIHSRCHKPLTEAWQSHRVRKVYHALVRDPGLDDEGEF 178

Query: 158 LNLLKKGI-------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++LL +         V +G      +  +  +    A V + L  G+  +I+
Sbjct: 179 ISLLARNRRTNRMKSVARGGKSAHTRYRVLKRLSGFALVEIQLLTGRMHQIR 230


>gi|225868502|ref|YP_002744450.1| RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701778|emb|CAW99179.1| putative RNA pseudouridylate synthase [Streptococcus equi subsp.
           zooepidemicus]
          Length = 298

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/212 (15%), Positives = 70/212 (33%), Gaps = 39/212 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---------------GVPLRKAERTRLWLYHK 80
               + VNG + + A   +   D + +D                + +   E     + +K
Sbjct: 33  KGGNIWVNG-VAQNAIYLLDIGDVVAIDIPNEESFEQLTAISHDLDIVY-EDEHFLILNK 90

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           P G  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     
Sbjct: 91  PAGYASIPS-AIHSNTIANFIKAYYIKQDYPNKQVHIVTRLDRDTSGLMLFAKHGYAHAR 149

Query: 134 L--ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L  +L      + Y     G             + +   +++ + +  +G         +
Sbjct: 150 LDKQLQQRAINKRYYALVCGQERLPDQGEIIAPIGRTDDSIITRTVTPKGKYAKTSYKVI 209

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                + + V + L  G+  +I+  F    + 
Sbjct: 210 ARYPENVSLVDIRLHTGRTHQIRVHFAHLGFP 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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 83/248 (33%), 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-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           V               +P+    E   L +  K  G+V      +   T+ + L   F  
Sbjct: 88  VLLTHPPRENVIVPQDIPINIVYEDDDLLVVDKEAGMVVHPGFGNWDGTLVNALAYHFEK 147

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD 156
                   RV  V R+D +T GLL++  +      L     +    R+Y     G + +D
Sbjct: 148 NGLKTDLDRVGLVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTTKRLYWAFVWGNLAED 207

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKK 203
                      L    +  V +    G   VT   +  +     WV   L  G+  +I+ 
Sbjct: 208 TGTIKGHIGRDLKNRMQMAVYEDGSLGKHAVTHYKVLERFRYMTWVECKLETGRTHQIRA 267

Query: 204 VFEFFNWK 211
            F      
Sbjct: 268 HFRHIGHT 275


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 53/316 (16%), Positives = 104/316 (32%), Gaps = 51/316 (16%)

Query: 4   KNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVN------VMS 56
           ++I  E    +R+   +++     SR  ++  I    VKVN  ++            +  
Sbjct: 9   RHIFDEKVYGKRLDAALSQQFSEYSRSRIQEWIQNGFVKVNDEVITSNKYKMAGFEDIEI 68

Query: 57  TDHIEVDGVPLRKA-------ERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS-- 103
              IEV G    +A       E   L + +KP GLV      + D    + +  + P   
Sbjct: 69  NAEIEVAGEWKPEAIDLDIVYEDDALLVINKPAGLVVHPGAGNQDGTMVNALLHHCPDLA 128

Query: 104 IFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVY-----RVRF-----HG 151
              R   + R+D  T GLL++  T     + V +L +  + R Y     RV         
Sbjct: 129 NLPRAGIIHRIDKETTGLLVVAKTIAAHTSLVEQLQNRAFTREYDAVVNRVMVSGGTIDK 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +         +V  G         ++ +   +  + + L  G+  +I+      +  
Sbjct: 189 PIGRHPTKRTSMAVVADGKRAITHYRVVE-KFLDHTHLKLRLETGRTHQIR-----VHMA 242

Query: 212 VNRLIRISYGPFQLGTLLAGSTR---EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
             +       P     L +G  R    ++   LR  +      + Q    + +       
Sbjct: 243 YLKF------PLIGDPLYSGRYRVPTRITP-ELRNTVDNF---KRQALHASLLGLQHPET 292

Query: 269 RDRPNIISEVPDDFTR 284
            +     + +P D  R
Sbjct: 293 DEYIEWRAPMPQDMAR 308


>gi|325335513|gb|ADZ11787.1| Pseudouridylate synthase, 23S RNA-specific [Riemerella
           anatipestifer RA-GD]
          Length = 354

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 83/248 (33%), 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-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           V               +P+    E   L +  K  G+V      +   T+ + L   F  
Sbjct: 90  VLLTHPPRENVIVPQDIPINIVYEDDDLLVVDKEAGMVVHPGFGNWDGTLVNALAYHFEK 149

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD 156
                   RV  V R+D +T GLL++  +      L     +    R+Y     G + +D
Sbjct: 150 NGLKTDLDRVGLVHRIDKDTSGLLVIAKNEYAMSFLAKQFFERTTKRLYWAFVWGNLAED 209

Query: 157 ----------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKK 203
                      L    +  V +    G   VT   +  +     WV   L  G+  +I+ 
Sbjct: 210 TGTIKGHIGRDLKNRMQMAVYEDGSLGKHAVTHYKVLERFRYMTWVECKLETGRTHQIRA 269

Query: 204 VFEFFNWK 211
            F      
Sbjct: 270 HFRHIGHT 277


>gi|317009246|gb|ADU79826.1| pseudouridine synthase D [Helicobacter pylori India7]
          Length = 327

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 53/308 (17%), Positives = 103/308 (33%), Gaps = 53/308 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RLDEFLAKELQISKNQVLNLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPQITPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLESKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN---------- 159
            RLD  T G +++  +      L   L +    R Y       + ++K++          
Sbjct: 133 HRLDKETSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 160 ------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  LK     +        ++L T + +   +   L  G+  +I+           
Sbjct: 193 NRLKMMALKAAKKEKSRYSKSAFISLLTSQNNLNLIGAKLFTGRTHQIR---AHL----E 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L R   G   L  L       + K+ +R  L  +L+E      +  ++    L++D   
Sbjct: 246 YLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLHFKVPLLKDMLE 300

Query: 274 IISEVPDD 281
            + +  D 
Sbjct: 301 YLKKNFDK 308


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 44/233 (18%), Positives = 79/233 (33%), Gaps = 40/233 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V  +   +R+S V++     SRR + R+I      +NG  +   +V V   D +  +  
Sbjct: 1   MVPSDLAGRRLSAVLSGRLGMSRRMLRRIIQAGGFYLNGEPVY-LSVTVQDGDRVTWERP 59

Query: 64  ---------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFSRVI 109
                     +PL    E   + + +KP G++T  S  + R ++       L        
Sbjct: 60  EEEVAVEPEDIPLEICYEDDDVIVVNKPAGMLTHPSPHERRGSLLAAAAHYLRDRGGVPH 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVI 167
           +V RLD  T G +L+         L+    Q    R Y    +     +    L     +
Sbjct: 120 AVHRLDKYTSGAVLIAKHAHAHHQLDRALRQGLVDRRYVAIVYAPEGCETGRWLT---FV 176

Query: 168 QGICYGDMQ------------------VTLDTQKGSNAWVTVGLREGKNREIK 202
            G+     +                       Q G  A V + L  G+  +I+
Sbjct: 177 DGLAPNPHRPSRRIVVPPDRGDRAVTHALPLVQAGPLALVALVLETGRTHQIR 229


>gi|161510965|ref|YP_089013.2| 23S rRNA pseudouridine synthase D [Mannheimia succiniciproducens
           MBEL55E]
          Length = 324

 Score = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 78/234 (33%), Gaps = 45/234 (19%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ +   QR+ + +A      SR  ++  I  + V +NG +       V   + +E+   
Sbjct: 10  VQPHQMGQRLDQTLAELFPDYSRSRLKTWIEDELVLLNGKVANIPREKVYGGEQVEITVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                      +PL    E   + + +KP   V      +   TV + L   + ++    
Sbjct: 70  IEDENRFEPQNIPLNIVYEDDDILVINKPKDFVVHPGAGNPNGTVLNALLYHYPQITEVP 129

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
               V RLD +T GL+++         L   L   +  R Y     G +        K G
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTQLVRALQKRKITREYEAIAFGIMT-------KGG 182

Query: 165 IVIQGICYGDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
            V + +     + TL                     +   + + L  G+  +I+
Sbjct: 183 TVDEPMSRHPTKRTLMAVHPMGKPAVTHYRVMEHFRNYTRLRLRLETGRTHQIR 236


>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 = 67.5 bits (164), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 83/235 (35%), Gaps = 42/235 (17%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVI       SR +++ ++  + + VN    E+ +  V S D I+V   P++     
Sbjct: 15  RLDKVITEKITDLSRTKIKELVNDKNILVNNK-AEKVSYKVQSGDVIDVTIPPVKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPSIFSRVIS--V 111
                     E + + + +KP G+V   S      T+ +       +L           V
Sbjct: 74  AENLHLDIVYEDSDVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTRDLADSPEGFRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVD-------------QD 156
            R+D +T GLL++  +      LE    +    R Y    HG  +              +
Sbjct: 134 HRIDKDTSGLLMIAKNDRARESLEKQLAKKINKREYLAIVHGNFEVKNGVINAPIGRNPN 193

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   +  +G        T+  Q  + + V   L  G+  +I+   ++    
Sbjct: 194 SRKQMA--VNPKGKAAVTHF-TVLEQFKNYSLVKCVLETGRTHQIRVHMKYIGHP 245


>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 = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/211 (15%), Positives = 75/211 (35%), Gaps = 36/211 (17%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------------ERTRLW 76
           +++ Q+ VK+NG  +  +   +   D + + G+  +                  E   + 
Sbjct: 33  KLLRQKCVKINGKRITDSNHIINEGDEVVIYGIKEQATIYIYDVGLQLDSKIIYEDDNIL 92

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +K  G V         + V   L    +   +   VGRLD  T GL++   +    R 
Sbjct: 93  IINKKAGKVVHGELLCLDNQVLSYLKFKQNSSFKPSHVGRLDKWTSGLIVYAKNYKALRE 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-------NLLKKGIVIQGI-----CYGDMQVTLDT 181
           L      + ++Y ++       + +         ++K IV +            ++ +D+
Sbjct: 153 LNDKIGFFDKIYTLKSDYNGGDNVVSAYIHHDEKMQKMIVTKNPAGLNNQIVKTKIYVDS 212

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            K     +T     G+  +I+   E+  + +
Sbjct: 213 NKLYAQLLT-----GRKHQIRATMEYLGYPI 238


>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 = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 37/171 (21%), Positives = 65/171 (38%), Gaps = 33/171 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+   +A+A    SR  V+ +I Q +V+V+G   +   + ++  + IE++G P       
Sbjct: 88  RLDAYLAKAMPDISRGRVQLLIEQGQVRVDGKTAKN-KLKLLGGERIEIEGEPRPAPLKA 146

Query: 71  -----------ERTRLWLYHKPIGLVTT-----HSDPDGRSTVFDNLPSIFS-------- 106
                      E   + +  KP G++         D     T+ + L   F+        
Sbjct: 147 MAEDIPLKIVYEDEHMAVIDKPAGMMVHAGSGLTDDARSGGTLVNALLHHFNVNLSSVGG 206

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
             R   V RLD  T GL+++  +    R L          + Y    HG+V
Sbjct: 207 ELRPGIVHRLDKQTSGLIMVAKNDRTHRALGEMFSDRSLEKRYLALVHGEV 257


>gi|88857987|ref|ZP_01132629.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
 gi|88819604|gb|EAR29417.1| pseudouridine synthase [Pseudoalteromonas tunicata D2]
          Length = 325

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 36/221 (16%), Positives = 71/221 (32%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAE 71
           R+ +++A      SR  ++  I    V++NG +       +   + + +     P R+ E
Sbjct: 19  RLDQILADLFPEYSRSRIKTWILDDMVQINGEIKNIPKEKLFGEEQVVISATIEPQREYE 78

Query: 72  RTRLWL-----------YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRL 114
              + L            +KP GLV      +   TV + L      +        V RL
Sbjct: 79  AQNIALNIVYEDDDILVINKPAGLVVHPGAGNADGTVLNALLHHCPEIANVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRV----------RFHGQVDQDKLNLL 161
           D +T GL+++         L         + R Y                 + +      
Sbjct: 139 DKDTTGLMVVAKTIPAQTRLVANLQARYNFTREYEAICTGTMTAGGMIDKPIGRHATKRT 198

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              + I G          +  + S+  + + L  G+  +I+
Sbjct: 199 HMDVTITGKPAVTHFRVAEKFR-SHTRLRLRLETGRTHQIR 238


>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 = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 76/243 (31%), Gaps = 47/243 (19%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           IV +     R+  ++A +G   SR    + I   +V VNG L       V   D I  + 
Sbjct: 8   IVTQADAGMRLDSLLAVSGAYPSRSAAVKQIEAGKVLVNG-LARSKRSIVAPGDTIVYEE 66

Query: 64  ----------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                     G P+    + E   +    K  GL    +      T+ + L   +     
Sbjct: 67  IPLATHIPLRGEPIPLDVRFEDRWMMAISKQAGLCVHPAPGHEGGTLVNALIYAYGRDSL 126

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
                  R   V RLD++T GL++   D      L   +   +  R Y    HG +  D 
Sbjct: 127 AHVQGDDRPGIVHRLDMDTSGLMMCAKDDTCGMALQDLVRDHKVDRRYLTLVHGNIAFDT 186

Query: 158 LN-----------LLKKGIVIQGICYGDMQ-----VTLDTQKGSN--AWVTVGLREGKNR 199
                         L+  I  +      +         +  +  N    +   L  G+  
Sbjct: 187 GQIDEPIGRVGDDRLRMKISYRPTARNALTTFTVLERFEAGRADNGYTLLECRLYTGRTH 246

Query: 200 EIK 202
           +I+
Sbjct: 247 QIR 249


>gi|89894036|ref|YP_517523.1| hypothetical protein DSY1290 [Desulfitobacterium hafniense Y51]
 gi|219668420|ref|YP_002458855.1| pseudouridine synthase [Desulfitobacterium hafniense DCB-2]
 gi|89333484|dbj|BAE83079.1| hypothetical protein [Desulfitobacterium hafniense Y51]
 gi|219538680|gb|ACL20419.1| pseudouridine synthase, RluA family [Desulfitobacterium hafniense
           DCB-2]
          Length = 302

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 80/228 (35%), Gaps = 36/228 (15%)

Query: 17  SKVIARAGIASRREVERMIAQQ-RVKVNG---------ILLERAAVNVMSTDHIEVDGVP 66
             ++ R    SR+ ++ +  Q  RV VNG            E  +V +   +   + G  
Sbjct: 22  QDILYRRFHFSRKLIQHL-KQGERVWVNGAFTFLTTRGKAGETLSVQLQPPEINSIPGEN 80

Query: 67  LRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDIN 117
           L      E       +KP G V   +    R T+ + +   +           + R+D N
Sbjct: 81  LPLEILYEDDYFIAINKPAGQVVHPTPRYPRGTIGNAVVGYWLAKGEARPFRPIHRIDRN 140

Query: 118 TEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQDK--LNL---------LKK 163
           T G++++  +   A           +  + YR    GQV +D+  +           +++
Sbjct: 141 TSGVVVIGKN-QFAHQQMAWQHAHGRIHKCYRGIVEGQVMEDQGTIKAPIALAPDSFIQR 199

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            I  +G     +   L+  + + + +   L  G+  +I+   +     
Sbjct: 200 QISPEGSPAVTLYKVLERYQDA-SLLEFILETGRTHQIRVHCQHLGHP 246


>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 = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 51/277 (18%), Positives = 94/277 (33%), Gaps = 67/277 (24%)

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------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +            + +PL    E   L + +KP G+V   +      T+ + L      
Sbjct: 67  SITVEEAEDSHIGPEDIPLEVIFEDDDLIVINKPAGMVVHPAPGTPSGTLVNALLHHCGD 126

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D  T GLL++       + L          R YR   +G  D 
Sbjct: 127 NLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFEKHTVERYYRAVCYGVPDG 186

Query: 156 DK---------------LNLL------------KKGIVIQGICYGDMQVTLDTQKGSN-- 186
           +                +  L            K+ ++ QG  +   +  +    G+   
Sbjct: 187 NDPRLRGVKGASFEPGNILKLTTQLARHKTDRQKQAVLFQGGRHAITRARIVDSFGTPPV 246

Query: 187 -AWVTVGLREGKNREIK-KVFEF----FNWKVNRLIR 217
            A +   L  G+  +I+  +           V    R
Sbjct: 247 VALIECWLETGRTHQIRVHMAHAGHGLVGDPVYGGKR 283


>gi|332992387|gb|AEF02442.1| ribosomal large subunit pseudouridine synthase D [Alteromonas sp.
           SN2]
          Length = 327

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/220 (15%), Positives = 70/220 (31%), Gaps = 33/220 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ +V+A      SR +++  I    V V+G ++      +   + + V           
Sbjct: 22  RLDQVLADLFPEYSRSKLKTWIQGGNVSVDGQVITVPRHKMQMDEVVTVSAEIEIQVTSQ 81

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRL 114
              + L    E   + + +K   LV      +   TV + L +    +        V RL
Sbjct: 82  AQDIALDIVYEDEHILVINKSADLVVHPGAGNPSGTVLNALLNHVPDIDKVPRAGIVHRL 141

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLK 162
           D +T GL+++         L  +L +    R Y                 + +       
Sbjct: 142 DKDTTGLMVVAKTLPAQTHLVDQLQTRVMSREYEAVAMGTMVAGGVVDEPIGRHATKRTH 201

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +   G         ++  +     + + L  G+  +I+
Sbjct: 202 MAVRENGKPAVTHFRVIEKFRAYTH-LRLKLETGRTHQIR 240


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 44/233 (18%), Positives = 86/233 (36%), Gaps = 38/233 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V ++   +R+   IA      SR  V+++I    V VN   +++A+  +   D +E+   
Sbjct: 13  VDQDSAGKRLDVFIADQYQDISRSYVQKLIKDGLVLVN-EEVKKASYKLEEGDRMEIAMP 71

Query: 63  DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
           +   L             E   L + +KP G+V   +  +   T+ + +           
Sbjct: 72  EPEVLEVLAQDIDLDIVYEDDDLLIVNKPQGMVVHPAPGNPDGTLVNAIMYHCKDKLSSI 131

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL-- 158
               R   V R+D NT GLL++  +    + L          R Y +   G V+ D++  
Sbjct: 132 NGVIRPGIVHRIDKNTSGLLVVAKNNASHQGLADQFKLHSITREYEMVCIGGVNWDQMTI 191

Query: 159 ---------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + LK  ++  G  +     T+        ++   L  G+  +I+
Sbjct: 192 DKNIGRNPKDRLKMAVLDTGGRHAVTHFTVIEHLEGYTYMKAKLETGRTHQIR 244


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/257 (17%), Positives = 86/257 (33%), Gaps = 58/257 (22%)

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 + E   + +  KP GLV   +D   + T+   L 
Sbjct: 72  DRVDLQVPPPEATELVAEEVEFTPLYEDEDILVLV--KPPGLVVHPADGHRQGTLVHGLL 129

Query: 103 SIFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
                +           V RLD +T G L++  +      L       +  + Y+    G
Sbjct: 130 HHCRNLSGISGQLRPGIVHRLDKDTSGCLVVAKNDLAHHNLVQQFKGREVEKTYQALLRG 189

Query: 152 QVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTV--------GLRE---- 195
            + +D        +V+      +    M V  +  + +     V         L E    
Sbjct: 190 ILAEDTGQ-----VVLPIGRHPVHRKKMAVRREGGREAVTHWRVRQRFSAGYTLVELLLE 244

Query: 196 -GKNREIKKVFEFFNWK 211
            G+  +I+         
Sbjct: 245 TGRTHQIRVHMAALGHP 261


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/226 (19%), Positives = 78/226 (34%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ + +A+     SR  ++  I   +V VNG ++ +A   V   + IE+           
Sbjct: 19  RLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVFGGELIEIQAEVEEEVRFE 78

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   V RL
Sbjct: 79  PQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|47230110|emb|CAG10524.1| unnamed protein product [Tetraodon nigroviridis]
          Length = 516

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 58/342 (16%), Positives = 118/342 (34%), Gaps = 52/342 (15%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKPIGLV 85
            + R+++N   ++  ++ + + DH++         V G PL    +   + +  KP  + 
Sbjct: 138 KEGRIRLNEQAVDDLSLVLRNNDHMKNTVHRHEPPVVGKPLEVLVDDGEVLVVDKPASIP 197

Query: 86  TTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
                    +TV   L      S + +V RLD  T G+LL       ++ L   +   + 
Sbjct: 198 VHPCGRFRHNTVIFILGKELGISELHTVHRLDRLTSGVLLFARTLETSKKLDQLVRDRKL 257

Query: 142 LRVYRVRFHGQVDQDKLN--------LLKKG---IVIQGICYGDMQVTLDTQKGSNAWVT 190
            + Y  R  G+  ++++           K G   +  +G     +   L +  G  + V 
Sbjct: 258 EKEYVCRVEGEFPEEEVICEQPILVVSFKVGLCRVDPKGKECRTVFQRL-SFNGKTSVVR 316

Query: 191 ---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQ-LGTLLAGSTREVSKKILRE 243
              V    G+  +I+   ++  + +         ++GP +  G LL  S     +++L+ 
Sbjct: 317 CLPVT---GRTHQIRVHLQYLGFPILNDPIYGSSAWGPHRGKGGLLDKS----DEELLKA 369

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLAT 303
            +  H  +E    LD P    E         +             S    G       A 
Sbjct: 370 LVEEHRSQENLHLLDLPDDVCEQEPEQHTASV---------TAGKSDGAEGQQPHIDPAP 420

Query: 304 PVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKR 345
           P    +  + V  + G+++              RSP+  + R
Sbjct: 421 PAGFSSTWTTVTESSGVNADVSERPPAE---TNRSPAEAADR 459


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           R+ K +A  G+A SR    ++I    V VNG ++ +A+  V   D + V   PL 
Sbjct: 1  MRLDKFLAEHGLAASRTLAAKLIDAGCVSVNGKIVYKASQPVHRDDDVLVQESPLT 56


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 86/247 (34%), Gaps = 59/247 (23%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +   +  +R+   +A    GI SR  ++++I    VK+NG +++ A   +   D +    
Sbjct: 9   IDSEYEDERIDSFLAEFEEGI-SRSYIQKLIKDSLVKINGNVIK-ANYRLKEGDILTYEV 66

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVIS 110
                     + +PL    E   + + +KP GLV   +      T+ +  L     R+  
Sbjct: 67  PQPVSLEIAAENIPLDILYEDEDIIVINKPKGLVVHPAAGHYSGTLVNALLYHCKDRLSG 126

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRF---------- 149
                    V R+D+NT G+L++  +    + +   L      R Y              
Sbjct: 127 INGVMRPGIVHRIDMNTTGVLVVCKNDKSHQSIAEQLKVHSITRKYEALVYNSFKQTEGT 186

Query: 150 ------HGQVDQDKLN-LLKKGI-------VIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
                    VD+ K+    K G        V++    G             A +   L+ 
Sbjct: 187 VDAPIGRHPVDRKKMAINHKNGKNAVTNYRVLENFNLG------YVHNQGYAHIECTLKT 240

Query: 196 GKNREIK 202
           G+  +I+
Sbjct: 241 GRTHQIR 247


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 78/226 (34%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------E 61
           R+ + +A+     SR  ++  I    VKVNGI++ +A   V   + +            E
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIESDLVKVNGIVVNKAREKVFGGEQVEIQAEIEEEIRFE 78

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   V RL
Sbjct: 79  PQDIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLHYYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAVASGVMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|320538536|ref|ZP_08038397.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320144643|gb|EFW36398.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 228

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 77/217 (35%), Gaps = 19/217 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDG 128
           E   L++ +KP G+            +        +++  V RLD  T G+LL+  T+  
Sbjct: 14  ENDSLFIINKPAGISVQGGAGISNCIIDILERQCAAKLFPVHRLDKETSGVLLIAKTSQA 73

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNA 187
                  L +   ++ YR        + +   ++  +   G          +  +  +++
Sbjct: 74  AAEYSKILQAKTIVKEYRAVCFYAPPK-QRGSIRTPLRENGTEKTAVTDYRVLKKTENHS 132

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
           ++++ L  G+  +I+                   P  L     G  ++   K L++  G 
Sbjct: 133 YLSLALHTGRKHQIRIHLASLGC-----------PIILDD-KYGDFKQ--NKALQKAFGI 178

Query: 248 HLLEEAQVNLDAPI-YSSETLVRDRPNIISEVPDDFT 283
             ++ +  +L  P+   S  ++   P  ++E  +   
Sbjct: 179 KKMQLSAYSLTLPLDGKSRQIIAPLPAHMTEALEKLE 215


>gi|261879908|ref|ZP_06006335.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
 gi|270333420|gb|EFA44206.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
          Length = 367

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 76/245 (31%), Gaps = 50/245 (20%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +A R   +SR  ++       + VN   ++     V   D I +        
Sbjct: 44  APLRIDKFLAERMQHSSRNRIQTAADAGCIFVNDRPVKS-NYKVRPLDVITLMLGRPKHD 102

Query: 63  -----DGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVF----------DNLPSIFS 106
                + +PL      R L + +K  G+V      +   T+           D       
Sbjct: 103 STIHAEDIPLDIVYEDRDLMVVNKKAGMVVHPGAGNFNGTLINAVAWHLRDLDTFDPNDP 162

Query: 107 RVISVGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVR---------F 149
            V  V R+D +T GLL++  T D   A            S        V           
Sbjct: 163 NVGLVHRIDKDTSGLLVVAKTADAKTALGKQFYNKTTHRSYHA----LVWGNPVADEGRI 218

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +D  + L+  +       G   VT   +  + G    V   L  G+  +I+   +
Sbjct: 219 EGNIGRDPKDRLRMKVFPPDSGIGKAAVTHYRVLERFGYVTLVQCVLETGRTHQIRAHMK 278

Query: 207 FFNWK 211
                
Sbjct: 279 HMGHP 283


>gi|168576177|ref|ZP_02722071.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|194398218|ref|YP_002037729.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Streptococcus pneumoniae G54]
 gi|183577907|gb|EDT98435.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|194357885|gb|ACF56333.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae G54]
          Length = 298

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 59/161 (36%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLL 123
           E     + +KP G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L
Sbjct: 81  EDDHFLVLNKPYGVASIPS-VNHSNTIANFIKGYYVKQNYENQQVHIVTRLDRDTSGLML 139

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGI 170
               G     L  +L      + Y     G    + + + +  + +         V +G 
Sbjct: 140 FAKHGYAHARLDKQLQKKSIEKRYFALVKGDGHLEPEGEIIAPIARDEDSIITRRVAKGG 199

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            Y      +    G+   V + L  G+  +I+  F +  + 
Sbjct: 200 KYAHTSYKIVASYGNIHLVYIHLHTGRTHQIRVHFSYIGFP 240


>gi|260767269|ref|ZP_05876210.1| tRNA pseudouridine synthase C [Vibrio furnissii CIP 102972]
 gi|260617777|gb|EEX42955.1| tRNA pseudouridine synthase C [Vibrio furnissii CIP 102972]
          Length = 243

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/214 (16%), Positives = 67/214 (31%), Gaps = 46/214 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDAYIVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVD---------QDKLNLLKKGIVIQGICYGDM- 175
             +A  +     + +  + Y     G ++         +++L+ +      Q     D  
Sbjct: 67  SEIAANMMPMFANHEMEKTYHAIVRGWIEVGDVLDYPLKEELDKIADKFAKQDKAPQDAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN-------- 213
                    +V   T K         L E     G+  ++++        +         
Sbjct: 127 TAYQPLAKVEVPHSTGKFPTTRY--CLMEMKPKTGRKHQLRRHMAHLRHPIVGDTTHGDG 184

Query: 214 ---RLIRISYGPFQLGTLLAGSTREV---SKKIL 241
              RL R  Y   +L  L A   R V   +++ L
Sbjct: 185 KHNRLYREVYDAHRL-MLHASELRFVHPYTEQEL 217


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 1/63 (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 LWL 77
            L
Sbjct: 63 EAL 65


>gi|257899597|ref|ZP_05679250.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com15]
 gi|293571564|ref|ZP_06682586.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
 gi|257837509|gb|EEV62583.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium Com15]
 gi|291608370|gb|EFF37670.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
          Length = 299

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 77/208 (37%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDTQ 156

Query: 136 LPSTQWLRVYRVRFHG-------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G              + +D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGMLSNLSAHGHIDLPIARDYSSLLKRMVSNEGRSAQT-EYWIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 216 LTEIALVDIQLHTGRTHQIRVHFSAIGC 243


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 84/243 (34%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVD 63
           +V      +R+ + +A R    SR +++  I + RV+V G    +A+  V    D +   
Sbjct: 14  VVDPEEAGERLDRFLAERLADTSRSQIQGWIDEGRVRV-GERPVKASHRVRPGEDVLVEP 72

Query: 64  GVPLRKAERTRLWLYH------------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
             P                         KP GLV   +    R T+   L +   R+   
Sbjct: 73  PEPEPLELVPEPIPLKIVFEDEDVVVVDKPRGLVVHPAPGHSRGTLVHGLLAHCGRLSRL 132

Query: 110 -------SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                   V R+D +T GLL+   T+   +    +       R Y    HG V  D   +
Sbjct: 133 GGSLRPGIVHRIDRDTSGLLVAAKTDLAYMGLAKQFHDHTVDREYLALVHGVVPHDHGTV 192

Query: 161 ---------LKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                    L++ + V++G         +  +      + + L  G+  +I+   EF  +
Sbjct: 193 DAPVGRHPHLRQQMAVVRGGRPAVTHFIVIERFARATLLRLRLETGRTHQIRVHMEFIGF 252

Query: 211 KVN 213
            V 
Sbjct: 253 PVI 255


>gi|255691622|ref|ZP_05415297.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
 gi|260622691|gb|EEX45562.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           finegoldii DSM 17565]
          Length = 306

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLER------AAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++  +        + V         E
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLQPGMKVQISKEKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVYIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L          R Y     G +++D   +        +   
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYGTVESFLTDRTLYVS 203

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 204 SSQQDDGGALSITHYRTIKRANGYSLIELDLETGRKNQIR 243


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/170 (17%), Positives = 64/170 (37%), Gaps = 28/170 (16%)

Query: 15  RVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ K I        SR  ++R I    V VN    ++ +  + + D +            
Sbjct: 14  RLDKFIQEKAPDWISRTYIQRAIKSGMVTVNNE-EKKPSYKLKNGDVVSFELPEEPKKVE 72

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------ 112
              + +PL+   E   + + +K  G+VT  +      T+ + L    +    +G      
Sbjct: 73  ILPENLPLKIIYEDKDIIVVNKDPGVVTHPTPTFLSGTLVNALMYHCNDFQGIGGELRPG 132

Query: 113 ---RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
              RLD +T G++++  +    + L +     +  + Y     G+V ++ 
Sbjct: 133 IVHRLDKDTSGVIVVAKNDKAHQSLSMQFKERKTEKTYIAIVSGEVKKNY 182


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 81/240 (33%), Gaps = 42/240 (17%)

Query: 2   KDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D   VQ     +R+ K ++      SR   +R++ + ++ VN    ++A   + + D +
Sbjct: 3   RDTFEVQSEQEGERLDKYLSSIYPDISRSFFQRILKENQILVNDKP-QKANYRLKTDDIV 61

Query: 61  EV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           +V              +PL    E   + + +KP G+V   S      T+ + +      
Sbjct: 62  DVTIPDAVQTPILPQDIPLDILYEDDDVLVVNKPKGMVVHPSAGHYSDTLVNAIMYHCKD 121

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ 155
                    R   V R+D++T G L++  +      +          R+Y     G V  
Sbjct: 122 SLSGINGEIRPGIVHRIDMDTTGSLIVCKNDESHIKISEQIKDHSCNRIYVGIVCGNVKD 181

Query: 156 D-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D                 +   I  +          +  + G   ++   L  G+  +I+
Sbjct: 182 DEGTIEGAIGRNPNDRKKMA--INEKNGKPAVTHYKVLERFGDYTYMQFKLETGRTHQIR 239


>gi|212639937|ref|YP_002316457.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
 gi|212561417|gb|ACJ34472.1| Pseudouridylate synthase, 23S RNA-specific [Anoxybacillus
           flavithermus WK1]
          Length = 292

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 46/264 (17%), Positives = 87/264 (32%), Gaps = 52/264 (19%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVD-----------GVPLRKA---ERTRLWLYHKPIG 83
            R++VN + +      + + D + V              P+  A   E   + + +KP  
Sbjct: 39  GRIEVNDVPVT-VRYVLKAGDEVCVSFPPEQKGANMVAEPIPLAIVYEDDYVIVINKPPH 97

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELP 137
           + T  S      T+ + L   + +      V  V RLD +T GL+L+         L   
Sbjct: 98  MSTIPSREHPHGTLANALLHHYEQQQLQTTVHVVTRLDRDTSGLVLVAKH-RHVHHLLSE 156

Query: 138 STQ---WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
             +     R Y    HG            + +   +++++ + + G         L  + 
Sbjct: 157 QQKQGRVKRRYEAVCHGYVIQLVGTIDAPIGRKGDSIIEREVRLDGQRAVTHYEVLQQKN 216

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE-VSKKILR 242
                V++ L  G+  +I+  F      +             G  L G  RE + ++ L 
Sbjct: 217 EMTH-VSIQLETGRTHQIRVHFSHIGHPLV------------GDDLYGGLREHIDRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
             E    H   E  +   AP+   
Sbjct: 264 SCELTFFHPFFEKTMTFHAPLPDD 287


>gi|254496550|ref|ZP_05109419.1| hypothetical protein LDG_0200 [Legionella drancourtii LLAP12]
 gi|254354229|gb|EET12895.1| hypothetical protein LDG_0200 [Legionella drancourtii LLAP12]
          Length = 321

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 74/228 (32%), Gaps = 44/228 (19%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DG- 64
           QR+  V+A      SR ++   I    V +N    +      +  D I +       D  
Sbjct: 18  QRIDSVLAHLLPDYSRSQISNWIKSGAVILNQKPCK-PKDKALDGDQITISVDLNLTDNN 76

Query: 65  --------VPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
                   +PL    E   L + +KP  +V      +   T+ + L      +       
Sbjct: 77  FDHCAPEAIPLNVVFEDDELLVLNKPANMVVHPGAGNREHTLVNALLHHAPSLHHLPRAG 136

Query: 111 -VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV-------------D 154
            + RLD +T GLL++         L     + +  R Y     G V              
Sbjct: 137 IIHRLDKDTTGLLVVAKTLTAHTSLIRQMQAREIQRHYVTLVQGHVISGGTIETGFGRHP 196

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +++L +     V++         T+  Q      + V L  G+  +I+
Sbjct: 197 RNRLKMA----VLEQGREAITHYTVKKQYQDYTLLDVKLMTGRTHQIR 240


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 49/225 (21%), Positives = 86/225 (38%), Gaps = 40/225 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV KV+A R    SR +V++ + +  V + G  +  A   V + DH+ +           
Sbjct: 15  RVDKVLAERLPDHSRSQVQQWLKEDAVTLEGETVR-ANYKVKAGDHLVIQVPEPEVVGLE 73

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVIS--V 111
            + +PL    +   + + +KP G+V   S      T+        D+L +I   V    V
Sbjct: 74  PENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNALLYHMDDLSTINDVVRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L   L     LR Y    HG +  +K            
Sbjct: 134 HRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYVALVHGNISHEKGTINAPIGRSKV 193

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++   VI+         T+  +      V + L  G+  +I+
Sbjct: 194 NRKMQA--VIENGKPAVTHFTVLERFDQFTLVELQLETGRTHQIR 236


>gi|253988118|ref|YP_003039474.1| tRNA pseudouridine synthase C [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779568|emb|CAQ82729.1| tRNA pseudouridine synthase C [Photorhabdus asymbiotica]
          Length = 256

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 30/186 (16%), Positives = 55/186 (29%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S      TVF        I   V  V RLD  T G+LL+   
Sbjct: 7   QDDHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLELPSTQW--LRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L          + Y     G V +         ++L+ +               
Sbjct: 67  SDIARQLSQQFEHHQLQKTYHAVVRGYVLESDVIDYALVEELDKIADKFADSDKGAQPSI 126

Query: 175 ------MQVTLDTQKGSN-----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  +V    + G       + + +  + G+  ++++        +        G  
Sbjct: 127 TYYRPLAKVECPVEIGRYPTSRFSLLELTPKTGRKHQLRRHMAHIRHPI-------IGDT 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|289209195|ref|YP_003461261.1| pseudouridine synthase [Thioalkalivibrio sp. K90mix]
 gi|288944826|gb|ADC72525.1| pseudouridine synthase, RluA family [Thioalkalivibrio sp. K90mix]
          Length = 319

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 80/238 (33%), Gaps = 32/238 (13%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----ILLERAAVNV----MS 56
           + E    QR+   +AR     SR ++ + + +  + VNG         +   +V      
Sbjct: 9   LPEEEAGQRLDAALARLFPEYSRSQLTQWLKEGALTVNGGQPKPRTPVQGGEHVVLEPPE 68

Query: 57  TDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSR 107
              +E +  P+      E   + + +KP GLV   +      T+ + L           R
Sbjct: 69  APVLEAEPEPIALDIVHEDPAVLVINKPAGLVVHPAAGHRAGTLVNALLHHDPNLSQLPR 128

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG----------QVDQ 155
              V RLD +T GL+++         L     Q    R YR    G           + +
Sbjct: 129 AGVVHRLDKDTTGLMVVARTPQAQTALVRQLQQRTVHREYRALVQGRVISGATIEEPIGR 188

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             ++  ++ +   G         +  +  ++  + V L  G+  +I+         + 
Sbjct: 189 HPVDRKRQAVT-GGGKPAVTHYRVAERFPAHTLLNVRLETGRTHQIRVHMAHIRHPIV 245


>gi|307610038|emb|CBW99572.1| ribosomal large subunit pseudouridine synthase D [Legionella
           pneumophila 130b]
          Length = 321

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/225 (19%), Positives = 78/225 (34%), Gaps = 38/225 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV +VIAR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDRVIARLLPEYSRSLISNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDHTMVNTD 76

Query: 64  -------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVI 109
                   +P++   E + + + +KP GLV      +   T+ + L           R  
Sbjct: 77  FNFCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-QVDQDKLN------- 159
            + RLD +T GLL++  +      L     + +  R Y    HG  +    ++       
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              LK  +   G         ++        + V L  G+  +I+
Sbjct: 197 KNRLKMAVTDFGRQAVTH-YNINKHYKDFTLLNVSLMTGRTHQIR 240


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 33/207 (15%), Positives = 61/207 (29%), Gaps = 27/207 (13%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRLWLYH 79
           R+I   +V+VN    ++    V + D + +              G      E     +  
Sbjct: 42  RLIRTGQVRVNSKR-KKPYDRVYAGDTVRIPPHFPETGDDPQRAGELQIVFENPDFTVLD 100

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGLARVLE 135
           KP G+         R  +   L   ++        V RLD  T GLLL   +    R ++
Sbjct: 101 KPAGVPVHSGTSARRDNMVLRLRKHYAGADFSPALVHRLDKETSGLLLAAKNYAWLRRIQ 160

Query: 136 LPSTQ--WLRVYRVRFHG-------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
               +    + Y    HG        ++   +   +K            +V         
Sbjct: 161 AMWNKNLVEKTYLAWVHGSWPSRWVNLEHRLIKTFEKMQPSPEGRPALSRVRSIASSRDK 220

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
             V + +  G+  +I+         V 
Sbjct: 221 TLVQIRIITGRTHQIRTQLSLSGHPVI 247


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 85/252 (33%), Gaps = 46/252 (18%)

Query: 4   KNIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K+ V       R+ K ++      SR ++++ +   +V VN I++    V V   D I  
Sbjct: 3   KHSVPHELNGIRLDKALSLLLKNVSRNQIQKAVKDSQVLVNDIIISDPDVLVKENDIILF 62

Query: 63  ---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
              +   L+            E   L + +K  G+           T+ + L      + 
Sbjct: 63  SFKEPEELKIEAANIALDIIYENDDLIVINKAAGMTVHPGLGHHNDTLVNALLHYTKNLS 122

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV----- 153
            +G         RLD +T GL+++  +     +L       Q +R Y+    G +     
Sbjct: 123 DIGSSERPGIVHRLDKDTTGLMVVAKNNKAHMLLANQIEQRQVIRKYKALIWGVINPLEG 182

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREI 201
                      D+ K+ +LK G    G        TL+   G   + V   L  G+  +I
Sbjct: 183 VIQNNIGRSRSDRQKMTILKYG----GKEAVTHYKTLELFYGGTISMVECKLNTGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 239 RVQLSHLKHSVV 250


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 46/244 (18%), Positives = 74/244 (30%), Gaps = 54/244 (22%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           R+ KV++ A      SR  +  +I Q  V   G  ++ A+  V     +EV         
Sbjct: 58  RLDKVLSDALGGAGLSRSRLRSLIDQGCVSSGGETIDDASRRVKPGQIVEVLVPAAEPAV 117

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVG----- 112
                +PL    E   L +  K   +V   +  +   T+ +  L     R+  +G     
Sbjct: 118 PLPQAIPLAIVHEDEDLLVIDKAAEMVVHPAAGNPDGTLVNALLAHCGDRLSGIGGVRRP 177

Query: 113 ----RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
               RLD  T GLL+        + L          R Y     G          ++G+ 
Sbjct: 178 GIVHRLDKGTSGLLVAAKTDRAHQGLTAQFADRSLSRTYLAVVWGVP------AAREGV- 230

Query: 167 IQG------ICYGDMQVTLDTQKGSNAWVTVG--------LRE-----GKNREIKKVFEF 207
           I+G           M V     K +     V         L E     G+  +I+     
Sbjct: 231 IEGNIGRHPGDRKRMAVLSRGGKPAVTRYRVVRSFGLLASLVECKLLTGRTHQIRVHMAH 290

Query: 208 FNWK 211
               
Sbjct: 291 VGHP 294


>gi|146328697|ref|YP_001210177.1| ribosomal large subunit pseudouridine synthase, RluD [Dichelobacter
           nodosus VCS1703A]
 gi|146232167|gb|ABQ13145.1| ribosomal large subunit pseudouridine synthase, RluD [Dichelobacter
           nodosus VCS1703A]
          Length = 322

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 44/228 (19%), Positives = 83/228 (36%), Gaps = 32/228 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VD 63
           IV  N    R+ +V+AR     SR   +  I    V +NG   +  ++ V + D I  V 
Sbjct: 13  IVDHNNHALRLDQVLARNYPEFSRNRWQDAINAGTVLLNGAAAKSKSL-VCAGDQITGVL 71

Query: 64  GVPLRKAERTR------------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIF 105
              ++  +  +            + + +KP GLV   +  +  +T+ + L          
Sbjct: 72  TQEIQTEDSAQNLPLNILYADDDIIVINKPAGLVVHPAVGNHDNTLLNALLYHFPQTKHL 131

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T G +++ +       L  +L +    R+Y    +G +       L  
Sbjct: 132 PRSGIVHRLDKDTSGAMVIAHSARAHTDLVRQLQNRSMGRIYLALVYGYITAGDTIDLPI 191

Query: 164 GIVIQGICY----GDMQVTLDTQKGSNAW-----VTVGLREGKNREIK 202
           G   +         D +  +   +    W     + V L  G+  +I+
Sbjct: 192 GRHAKDRLKMAVRPDGKPAITHYRIEERWQTLTLLRVQLETGRTHQIR 239


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 80/221 (36%), Gaps = 34/221 (15%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN    +     ++  + I V  +P  +    
Sbjct: 40  RLDAVLAKLMPDYSRSRLTSWIKEGAVIVNDKPAQ-PKDKMIGGESISVTVLPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  KPEAMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVQQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAVVKFGGKPAVTHVKVLERYLAHSYIECSLETGRTHQIR 259


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 18  IADSDAAGKRLDQWLAAALGPELSRSRVQSLIADGHVTIDGAPARETKQKLREGMNIAIV 77

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 78  LPEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYQCGDSLS 137

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 138 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 194


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/254 (17%), Positives = 88/254 (34%), Gaps = 47/254 (18%)

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---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPS 103
               +   D  P+             E   L + +KP G+V   +  +   T+ +  L  
Sbjct: 58  AVYLLQLPDPKPIEAVPQDIPLSIVYEDNDLIVVNKPKGMVVHPAPGNPDGTLVNALLYH 117

Query: 104 IFSRVISVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
              ++  +G         R+D +T GLL++  +    + L          RVY    +G 
Sbjct: 118 CAGQLSGIGGAIRPGIVHRIDKDTSGLLVVAKNDVAHQALSSQMSVHSIHRVYHAIVYGN 177

Query: 153 VDQD--KLNLL--------KKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKN 198
           + +D   +           KK  V+     G         +  + G+  ++   L+ G+ 
Sbjct: 178 LKEDEGFVEAWLGRDPRDRKKMAVLSENTTGARYAYTGWRVLERFGNFTYIACKLKTGRT 237

Query: 199 REIK-KVFEFFNWK 211
            +I+  +       
Sbjct: 238 HQIRVHM-ASIGHP 250


>gi|118581597|ref|YP_902847.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118504307|gb|ABL00790.1| ribosomal large subunit pseudouridine synthase D [Pelobacter
           propionicus DSM 2379]
          Length = 315

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 88/237 (37%), Gaps = 42/237 (17%)

Query: 10  NFTPQRVSKVIARAGIAS--RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVP 66
           +  P R+   ++   +AS  R  ++R+I    + V+G  +   ++ +   + I +    P
Sbjct: 8   DSEPVRLDLFLSSQ-LASETRSTIQRLIESGNIMVDGREVR-PSLKLKGGESISIQLPEP 65

Query: 67  LRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-- 112
           +               E   L + +KP G+V      +   T+ + L +  + +  +G  
Sbjct: 66  VAARPLPESIPLEVLYEDGDLIVINKPAGMVVHPGPGNSSGTLVNALLAHCTDLSGIGGE 125

Query: 113 -------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL----- 158
                  RLD  T G++++  +    + L          R+Y+   +G   QD       
Sbjct: 126 LRPGIVHRLDKGTSGVMVVAKNDRSHQALSAQFSVHSIKRIYQALVYGSPQQDSGRLEGQ 185

Query: 159 ------NLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF 207
                 + L++ G+  QG         +  + G    + + L  G+  +I+  + E 
Sbjct: 186 IGRHPTDRLRRSGLARQGKHAVTRW-RVRGRYGRICLMELRLETGRTHQIRVHMSEA 241


>gi|307706671|ref|ZP_07643477.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
 gi|307617915|gb|EFN97076.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK321]
          Length = 298

 Score = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 74/212 (34%), Gaps = 40/212 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---------------AERTRLWLYHK 80
               + VN    + A   +   D + +D +P+ +                E     + +K
Sbjct: 33  RGGAILVNDQP-QNATYLLDIGDLVIID-IPVEEGFETLEAIERPLDILYEDDHFLVLNK 90

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           P G+ +  S  +  +T+ + +   +        +V  V RLD +T GL+L    G     
Sbjct: 91  PYGVASIPS-VNHSNTIANFIKGYYVKQDYENQQVHIVTRLDRDTSGLMLFAKHGYAHAR 149

Query: 134 L--ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L  +L      + Y     G             + +D+ +++ + +  +G  Y      +
Sbjct: 150 LDKQLQKKSIQKRYFALVKGDGYLESEGEIIAPIARDEDSIITRRVA-KGGKYAHTSYKI 208

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               G+   V + L  G+  +I+  F    + 
Sbjct: 209 VASYGNIHLVDIRLHTGRTHQIRVHFSHIGFP 240


>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 = 67.1 bits (163), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 70/211 (33%), Gaps = 43/211 (20%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRL 75
           ++V   +  Q V VNG ++ +    +   D + +             D + +   E   L
Sbjct: 27  KQVRTWLKHQAVVVNGRVVTQFNHPLKPGDIVAIRSDRFAVPGTVVGDDIRICF-EDAAL 85

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTND 127
            +  KP  L+T  S+ +   TV+  L             RV  V RLD  T G+++    
Sbjct: 86  LVIDKPPDLLTIASEAEQEKTVYFQLTEYLRGNDVHSRERVWIVHRLDRETSGIMVFAKT 145

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------- 177
                +L+    +  + Y+    G +  DK    +    +        +V          
Sbjct: 146 PQAKGLLQTGWDKAEKRYQAVIEGSLPNDK-GTFRS--YLD--ETDPFRVISVPRTPTTR 200

Query: 178 ------TLDTQKGSNAWVTVGLREGKNREIK 202
                  +  +      V + L  G+  +I+
Sbjct: 201 HAVTHYRVLKRGKGRTLVELTLETGRRHQIR 231


>gi|148982218|ref|ZP_01816647.1| tRNA pseudouridine synthase C [Vibrionales bacterium SWAT-3]
 gi|145960609|gb|EDK25961.1| tRNA pseudouridine synthase C [Vibrionales bacterium SWAT-3]
          Length = 249

 Score = 66.7 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 66/212 (31%), Gaps = 42/212 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +     + +  + Y     G +++         + +  I     +   + Q+  
Sbjct: 67  SEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEAQEAV 126

Query: 186 NAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
            A+     V V             L E     G+  ++++        +           
Sbjct: 127 TAYEPLAKVEVPYSTGRFPTSRYCLVEMLPKTGRKHQLRRHMAHLRHPIVGDTSHGDGKH 186

Query: 214 -RLIRISYGPFQLGTLLAGSTREV---SKKIL 241
            RL R +    +L  L A   R +   +K+ L
Sbjct: 187 NRLFRENLDSHRL-LLHASELRFIHPFTKEEL 217


>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 = 66.7 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 91/239 (38%), Gaps = 42/239 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV E+    R+   I  R  + SR  ++ +I ++++K+N  ++   +  V+S D I +  
Sbjct: 8   IVGEDENNLRLDVFINKRENLISRTRIKNLILKEKLKINDQIINSPSKKVLSGDEINLQI 67

Query: 63  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                      +       E   L + +KP G++      +   T+ + L          
Sbjct: 68  PEPKEASLKPYNFKLQIVYEDDDLLIINKPAGIIMHPGAGNYDETIVNALMHYNKDSLST 127

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHG--QVDQDK 157
                R   V R+D +T GL+++  +      L    ++    RVY++   G  +    K
Sbjct: 128 IGDELRPGIVHRIDKDTSGLIVIAKNNETHENLSHQFSEHTITRVYQLLIWGKLRPSSGK 187

Query: 158 LNLL-------KKGIVIQGIC-------YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++         ++ + +           Y  +++  + +  + + V   L  G+  +I+
Sbjct: 188 IDTFITRSSKNRQMMEVSNSKGKRAITNYKTIEIFENDKTPTLSLVECRLETGRTHQIR 246


>gi|118594976|ref|ZP_01552323.1| pseudouridine synthase D [Methylophilales bacterium HTCC2181]
 gi|118440754|gb|EAV47381.1| pseudouridine synthase D [Methylophilales bacterium HTCC2181]
          Length = 349

 Score = 66.7 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 45/215 (20%), Positives = 80/215 (37%), Gaps = 47/215 (21%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--------------LRKAER 72
           SR  ++  I    +KV+G  L      ++  ++I +D  P                  E 
Sbjct: 31  SRGRIQAWIRDGHIKVDGQSLA-PKKKIIGGENISIDFQPDDELKQFEAEDMIIEAVYED 89

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTN 126
             + + +KP GLV      +   T+ + L   F       R   V RLD +T GL++++ 
Sbjct: 90  DHILVINKPAGLVVHPGAGNWSGTLLNGLLHHFPENKVLARAGIVHRLDKDTSGLMVVSK 149

Query: 127 DGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-CYGDMQVTLDTQK 183
                + L   L +    R YR    GQV        K G+V + I  +  ++V +   K
Sbjct: 150 TEVAQQHLIKQLQNKTVKREYRCIVWGQV-------WKNGVVKEPIGRHPTVRVKMAVNK 202

Query: 184 ----------------GSNAWVTVGLREGKNREIK 202
                           G ++++   L  G+  +I+
Sbjct: 203 IHGKESVTHYEVLERFGHHSYLRCNLETGRTHQIR 237


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 84/252 (33%), Gaps = 51/252 (20%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V     P R+ K +  R    SR +++  I  Q + VNG +  +A   +   D I++  
Sbjct: 20  TVDPGQKPYRIDKFLIDRLPNTSRNKIQLAIDNQFILVNG-IPTKANYKIRPYDKIQIVL 78

Query: 63  -----DGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP- 102
                +   + +        E   L + HKP G+V      +   T+       FDNLP 
Sbjct: 79  PNPPRNNELIPENIPLDIVYEDEALMVVHKPAGMVVHPGYNNWTGTLVNALIYYFDNLPT 138

Query: 103 --SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
             +   R   V R+D +T GLL++         L          R Y     G+ + +  
Sbjct: 139 APNNIGRPGLVHRIDKDTSGLLVVAKTEASLIALAKQFYDHSIARTYYALIWGEPETETG 198

Query: 159 NLLKKGIVIQ-GICYGDMQVTLD---TQKGSN--------------AWVTVGLREGKNRE 200
                 I I       D ++       +KG                + V   L  G+  +
Sbjct: 199 T-----IDINLDRSLQDRRIVAPYTNPEKGKRAVTHYQVVERLRYVSLVKCTLETGRTHQ 253

Query: 201 IKKVFEFFNWKV 212
           I+   +     +
Sbjct: 254 IRAHMKHMGHPI 265


>gi|319947093|ref|ZP_08021327.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747141|gb|EFV99400.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 296

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 88/249 (35%), Gaps = 52/249 (20%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVD-----G-VPLRKAERTRLWLY--------HKPIG 83
            ++ VNG + + A   +   D + +D     G   L   +R    LY        +KP G
Sbjct: 35  GQILVNG-IEQNAIYLLDIGDKVTIDIPSEEGYEALEAIDRDLEILYEDDHFLVLNKPAG 93

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL-- 134
           + +  S     +T+ + +   + R       V  V RLD +T G++L    G     L  
Sbjct: 94  VASIPS-SLHSNTIANFVKGYYVRNQYENQLVHIVTRLDKDTSGIMLFAKHGYAHARLDK 152

Query: 135 ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L +    + Y     G             + +D+ +++ + +  +G  Y      +   
Sbjct: 153 QLQAKTIQKHYFALVKGKGELASKGDIIAPIARDEDSIITRKVA-KGGKYAHTSYQVVQS 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            G    V + L  G+  +I+  F    + +               L  GS   +   ILR
Sbjct: 212 FGDIHLVDIQLHTGRTHQIRVHFSHIGFPLLG-----------DDLYGGS---LEDGILR 257

Query: 243 EQLGPHLLE 251
           + L  H L 
Sbjct: 258 QALHCHSLA 266


>gi|188994274|ref|YP_001928526.1| probable RNA pseudouridylate synthase [Porphyromonas gingivalis
           ATCC 33277]
 gi|188593954|dbj|BAG32929.1| probable RNA pseudouridylate synthase [Porphyromonas gingivalis
           ATCC 33277]
          Length = 324

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 33/218 (15%), Positives = 81/218 (37%), Gaps = 32/218 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLW 76
           SR  V++++ +++V +NG+   R    + + D + V    L +           +     
Sbjct: 39  SRTSVKQILTRRQVSINGVPTTRHDAELKAGDRVIVHRTQLPEELRHPLVRIIWQDDYFV 98

Query: 77  LYHKPIGLVT----THSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGL 130
           L  K  G+ T     + D      V D+L       ++  + RLD ++ G++L   +  +
Sbjct: 99  LIEKKAGVSTVASGVNKDRTALRIVSDHLKQYDPEVKIFMLNRLDKDSAGMVLFAKNKEV 158

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVIQGIC------------YGD 174
              +    ++    + + +   G++   +  L+  +    I+G               G 
Sbjct: 159 QGFVVDKWSKVVLEQRFVMAIEGEMPDAEGTLDPPRYQTSIKGKQSRIVAETPSVHSVGT 218

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            +  +  +    + V V L  G+N ++++        +
Sbjct: 219 ARYKVIRRGAVCSLVEVTLLSGRNNQLRRQMGQLGIPI 256


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/234 (15%), Positives = 74/234 (31%), Gaps = 49/234 (20%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             +R+ + +A+     SR  ++R+I Q +V++N    +     +   D + +    +   
Sbjct: 13  AGERLDQWLAQQLPELSRSRLQRLIEQGQVQLNEAPCQSKKTKLKVGDRLIL---KIPAP 69

Query: 71  ----------------ERTRLWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFSRVISVG- 112
                           E     + +KP G+V   +  +   T V   L      +  +G 
Sbjct: 70  ATMALAPEAMDLDILFEDEHFLIVNKPAGMVVHPAPGNYTGTLVHGLLAHCGENLAGIGG 129

Query: 113 --------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                   RLD +T G + +  T+        ++ +    R Y    +G    D    ++
Sbjct: 130 VQRPGIVHRLDKDTTGAIAIAKTDQAHQHLQAQIKAKTARREYMGIVYGCPRNDAAGTIE 189

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
             I         M V    +     W    + E              G+  +I+
Sbjct: 190 APIARHKGDRKKMAVDETGRPAVTHW---EIMERLGNYSLLYYKLETGRTHQIR 240


>gi|315638897|ref|ZP_07894069.1| RluA family pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315481115|gb|EFU71747.1| RluA family pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 325

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 89/248 (35%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M+   + +E     +++K++ +    SR +V  +I    V +N  +  + +  + + D I
Sbjct: 1   MQTFLVDEEARLDVKLAKILNQ----SRSQVSLLIENNAVLINDKIQNKNSFKLKNGDII 56

Query: 61  --------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIF 105
                         EV+       E   + + +KP  LV   +     +T+ D  L   +
Sbjct: 57  TLKTLPQKELKTQYEVNFEVDVLFEDEDVLVLNKPQNLVVHGASSVKEATLIDWLLAKKY 116

Query: 106 S--------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
           +        R   V RLD  T G +++  +    + L   L      R+Y       + +
Sbjct: 117 ALSNLAGELRAGLVHRLDKETSGAIIIAKNNFSHQRLSEQLQDKSLGRIYLALIDLPLKE 176

Query: 156 DKL---NLLK-------KGIVIQGICYGDMQVTLDTQKGSNAWVTV-----------GLR 194
           DK+     L        K I I+   Y      +  ++  +A++ +            L 
Sbjct: 177 DKIIINKALTRSTQNRIKKIAIERENYSP---KIKAKEAKSAFINLALAKDVNLIAAKLF 233

Query: 195 EGKNREIK 202
            G+  +I+
Sbjct: 234 SGRTHQIR 241


>gi|295100789|emb|CBK98334.1| ribosomal large subunit pseudouridine synthase D [Faecalibacterium
           prausnitzii L2-6]
          Length = 310

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 89/257 (34%), Gaps = 50/257 (19%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  + E     QR+ + ++    G+ SR  ++ ++A+  V  NG  + + ++ + + 
Sbjct: 1   MEQREFIVEAEAAGQRIDRFLSGEDTGL-SRSALQGLVAEGHVLCNGKSIAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I +   D  P+             E   L + +KP G+V   +  +   T+ + L   
Sbjct: 59  DTILLEIPDAKPIEAVPQDIPLDIVYEDDHLLVVNKPKGMVVHPAPGNPDGTLVNALLWH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
                       R   V R+D +T GLL++  D      L          R Y+   +G 
Sbjct: 119 CKGSLSGIGGEIRPGIVHRIDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYQTVVYGG 178

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREG 196
             QD                 +   +      +     T   +  + G    +   L+ G
Sbjct: 179 FAQDEGFVEANLGRSKTDRKKMA--VYPASEPHTKYAYTGYKVLERFGGFTLLECRLKTG 236

Query: 197 KNREIK-KVFEFFNWKV 212
           +  +I+  +       V
Sbjct: 237 RTHQIRVHM-ASIQHPV 252


>gi|225628223|ref|ZP_03786257.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|260167874|ref|ZP_05754685.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Brucella sp. F5/99]
 gi|261757311|ref|ZP_06001020.1| ribosomal large subunit pseudouridine synthase [Brucella sp. F5/99]
 gi|225616069|gb|EEH13117.1| pseudouridine synthase, RluA family protein [Brucella ceti str.
           Cudo]
 gi|261737295|gb|EEY25291.1| ribosomal large subunit pseudouridine synthase [Brucella sp. F5/99]
          Length = 334

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 59/177 (33%), Gaps = 31/177 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I   +   +R+ + +A A     SR  V+ +IA   V ++G         +    +I + 
Sbjct: 5   IADSDAAGKRLDQWLAAALGPELSRSRVQSLIAYGHVTIDGAPARETKQKLREGMNIAIV 64

Query: 63  ---------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                     G  +      E   L + +KP GLV    + +   T+ + L         
Sbjct: 65  LSEPEPAEPQGENIPLDILYEDDDLIVINKPAGLVVHPGNGNWTGTLVNALIYHCGDSLS 124

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                 R   V RLD +T G++++  +    R L        R       Y     G
Sbjct: 125 GIGGIRRPGIVHRLDKDTSGVMVVAKNDRAHRHLSEQFADHGRTGDLERAYLALVWG 181


>gi|257885366|ref|ZP_05665019.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,501]
 gi|257821222|gb|EEV48352.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecium 1,231,501]
          Length = 299

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/200 (17%), Positives = 76/200 (38%), Gaps = 36/200 (18%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D  P+    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETPIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKQGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQ 156

Query: 136 LPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G++               D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGRLSDLSAHGRIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIK 202
               A V + L  G+  +I+
Sbjct: 216 LTEIALVDIQLHTGRTHQIR 235


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 39/177 (22%), Positives = 67/177 (37%), Gaps = 25/177 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V E     R+ + +A      SR  ++++I Q +V +NG         + + D IEV  
Sbjct: 8   TVTEKQQGLRLDRGLAEQLPELSRSRLQQLIRQGQVWLNGQPCLDKDRPLQAGDQIEVRI 67

Query: 64  ----GVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                 PL+          E   L + +KP GLV   +      T+   L +   R+   
Sbjct: 68  PPATPTPLQPERIPLDILYEDEDLLVINKPRGLVVHPAPGHASGTLVHALLAHCPRLSGI 127

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
                   V RLD +T G L++       + L  ++ +    R+Y     G+  Q +
Sbjct: 128 NGEQRPGIVHRLDKDTTGALVIAKHDQAHQHLQAQIQAKTARRIYLGVVFGRPAQSQ 184


>gi|315639721|ref|ZP_07894860.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
 gi|315484498|gb|EFU74955.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           italicus DSM 15952]
          Length = 298

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 81/234 (34%), Gaps = 48/234 (20%)

Query: 19  VIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIE------------ 61
            +   GI SR     ++A+       + VN   +E     +   D +             
Sbjct: 18  FLKEQGI-SR----GLLAKIKFQGGAILVN-QRVENVLYFLQEGDIVTIVTPDEKEHETL 71

Query: 62  -VDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVG 112
            VD  P+    E   L + +KP  + +  +      T+ + +   + R       V  V 
Sbjct: 72  LVDNAPIEVVFEDDHLLIVNKPANVPSIPAQYHPNQTMANRVKGYYKRKNYPNQVVHIVT 131

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-------------QVDQDK 157
           RLD +T GL++    G     L  +L    + + Y+                   + ++ 
Sbjct: 132 RLDRDTTGLMVFAKHGFAHAKLDVQLRDKSFTKKYQALVFDEANALENHAEIIAPIGRND 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +L+++ +V  G  Y   +  L+ +    A V + L  G+  +I+  F      
Sbjct: 192 ASLIQRQVVTDG-RYAKTEYWLEKKYQQIALVDIQLHTGRTHQIRVHFASIGCP 244


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 45/254 (17%), Positives = 86/254 (33%), Gaps = 51/254 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  + +     R+ K++++     SR   ++MI    V VN    ++       +D 
Sbjct: 1   MPKKFKITDELG--RLDKIVSKLDPEISRSRAKKMIEDGDVIVNDSK-KKPKYETKVSDT 57

Query: 60  IEVDGVP-----LRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I +  V      ++          E   + + +KP G+V   S      T+ + L     
Sbjct: 58  ILIKDVKPETVSIKPENMPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALLFHSP 117

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQ 155
                   R   V R+D +T GLL++  +  +A           + LR Y    HG++ +
Sbjct: 118 LSSINGEYRPGIVHRIDKDTSGLLMVAKN-DMAHKALSKQLKAKKNLRKYVALVHGRIKE 176

Query: 156 DKLNLLKKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNR 199
           D       G++    G    D +       G  A     + E              G+  
Sbjct: 177 D------SGVIKAPIGRSPKDRKKQAIVADGRPAITHFEVMERFEDYTLIDCRLETGRTH 230

Query: 200 EIKKVFEFFNWKVN 213
           +I+   ++    + 
Sbjct: 231 QIRVHMQYIGHPIV 244


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 43/226 (19%), Positives = 76/226 (33%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------E 61
           R+ + +A+     SR  ++  I   +V VNG ++ +A   V   + I            E
Sbjct: 19  RLDQALAQLFPDYSRSRLKVWIENDQVWVNGKIVNKAREKVFGGELIEVQAEVEEEVRFE 78

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   V RL
Sbjct: 79  PQNIPLNIVYEDDDIIVINKPKDLVVHPGAGNPDGTVLNALLYHYPPIAEVPRAGIVHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L      R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRHITREYEAIASGIMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAVTHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|320536263|ref|ZP_08036307.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320146881|gb|EFW38453.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 312

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 32/247 (12%), Positives = 87/247 (35%), Gaps = 52/247 (21%)

Query: 1   MKDKNIVQENFTPQR-VSK----VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  K+ V +N    R + +     + +  +     + + +   +++VNG   +       
Sbjct: 1   MNKKDFVLDNNDSDRRLDRVVRLFLPKMPL---SVIYKALRSGKIRVNGQK-KHPDYKTK 56

Query: 56  STDHIEVD--------------GVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRS 95
             D + ++                P+R+ E   ++      + +KP+ +        GR 
Sbjct: 57  ENDVLSIEELLFSSFLQEHKTRNNPIRQIESLYIYKGKDLLVLNKPVDIAV-----HGRG 111

Query: 96  TVFDNLPSIFSRVI------SVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVYRV 147
           ++ +++ S + +         + RLD  TEG++  +    G       L      + Y  
Sbjct: 112 SLAESIASSYKKDSLSFKPGPLHRLDKGTEGIICFSQSLKGAQLFSACLKEGTCAKFYLG 171

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV---GLREGKNREIKKV 204
              G + ++        + I+     ++   +   + +   +++    L  GK  +I++ 
Sbjct: 172 IIEGALKKET-------VHIEQNTSEEITAIIPIAQNTEQTLSLAVFHLITGKKHQIRRH 224

Query: 205 FEFFNWK 211
                ++
Sbjct: 225 CHAIGYQ 231


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 88/250 (35%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  I+  +    R+   +A      SR  ++++     V  NGI ++     V + D+
Sbjct: 1   MKEF-ILNCDTDGVRIDSWLAGNLEDYSRSYIQKLCLDGNVWANGIQVKS-NYRVKTDDN 58

Query: 60  IEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I+V+             +PL    E   + + +KP G+V   +  +   T+ + L     
Sbjct: 59  IKVNVPEAEILDVEPEDIPLDIVYEDKHIIVINKPKGMVVHPAVGNYTGTLVNALMKHCG 118

Query: 107 ----------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--- 151
                     R   V R+D +T GLL++         L   L +    R Y     G   
Sbjct: 119 DSLSDINGVIRPGIVHRIDKDTSGLLVVAKSNIAHERLSEKLKTHDIKREYIALVDGIIY 178

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                    + ++ +   K  +  +          +  +  +  ++ + L  G+  +I+ 
Sbjct: 179 ENSGKIDAPIGRNPVERKKMCVNTENGRNAITHFKVLERFQNATYLELKLETGRTHQIRV 238

Query: 204 VFEFFNWKVN 213
              + N  + 
Sbjct: 239 HMAYINHPII 248


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 84/238 (35%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVP 66
             +R+ +++ A     SR  +++++      V+G+  +R A  +     + +D       
Sbjct: 13  AGKRLDRILGATVPELSRAALQKVVQAGCCTVDGLPEKRPAAKMRMGQTVTLDLPEHPDR 72

Query: 67  LRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--------S 110
           L+  E     L+        +KP GL           T+   L   F ++          
Sbjct: 73  LQPEEGHLELLWQDDHLVVCNKPAGLTVHPCPSCPEQTLVQRLLGRFPQLSRLEGQRPGI 132

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD +T GLL++  T    LA        Q  + Y     G           + +   
Sbjct: 133 VHRLDKDTSGLLVVALTEADCLALAAAFAERQVHKEYLALVSGLPPLEGQCREPLGRHPT 192

Query: 159 NLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
             +K  +V +       + + +   +T  GS + + V +  G+  +I+  +     + 
Sbjct: 193 AKIKMAVVPEDQGGRNAFTEWRRLWNTDDGSVSLLAVRIHTGRTHQIRVHMT-HLGYP 249


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 81/231 (35%), Gaps = 35/231 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVN------VMSTD 58
           IVQE+ + +R+  +++      SR +++  I  ++V VN   +            +   D
Sbjct: 31  IVQESQSGKRLDCILSELLPNYSRSKIKCWILSKKVNVNNQTVIIPKKKMMGGEFIEIKD 90

Query: 59  HIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
            + +D   +           E   + + +K   +V      +   T+ + L   +     
Sbjct: 91  IVNIDNNNIVPQDIPLDIVYEDDDIVVINKAKNMVVHPGAGNHSGTILNALLYKYPAITE 150

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------- 151
             R   V RLD +T GL+++  +      L       + +R Y     G           
Sbjct: 151 VFRSGIVQRLDKDTTGLMVVAKNMIAYHSLLRLFKKRKIIREYEAVVLGNFLHNEGTINQ 210

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +  ++  +  +   G         +++  G    + V L  G+  +I+
Sbjct: 211 PIRRHAVHRTRMTVNPMGKSAITHYSIIES-FGMYTRIRVRLETGRTHQIR 260


>gi|224373761|ref|YP_002608133.1| ribosomal large subunit pseudouridine synthase C [Nautilia
           profundicola AmH]
 gi|223589203|gb|ACM92939.1| ribosomal large subunit pseudouridine synthase C [Nautilia
           profundicola AmH]
          Length = 294

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 40/193 (20%), Positives = 75/193 (38%), Gaps = 20/193 (10%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA-ERTRLWLYHKPIGL 84
           RE +R I + RV VN   + + +          V   +G  L+   E T   ++ KP G+
Sbjct: 28  REAKRAIDRGRVSVNDKRITKKSQRATGRLKCIVFEPNGYGLKPIFETTHFAVFDKPSGV 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                      ++ D++ S   +    V RLD  T GL++ + +     VL+      + 
Sbjct: 88  AIHPKKLANTKSLLDDVRSLWGNDANLVHRLDKETSGLVMASKNKFSESVLKKAFQDKEI 147

Query: 142 LRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQK-GSNAWVT 190
            + Y     G +++D          K   +K  ++I       + +    +K G N  V 
Sbjct: 148 QKKYLALVKGHLEKDLTIKKPIAVNKDENIKVKVMIHPEGKESVTIIKPIKKIGENTLVE 207

Query: 191 -VGLREGKNREIK 202
            + L  G+  +I+
Sbjct: 208 CIPLT-GRQHQIR 219


>gi|296114958|ref|ZP_06833603.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
 gi|295978476|gb|EFG85209.1| pseudouridine synthase, RluA family protein [Gluconacetobacter
           hansenii ATCC 23769]
          Length = 323

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 83/251 (33%), Gaps = 43/251 (17%)

Query: 11  FTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
              QR  + +A   G  SR  ++ ++    +  +G++L   A  V +    E+       
Sbjct: 16  DAGQRTDRFMADTIGTLSRSRIKALMEAGHLLRDGVVLRDPADPVRAGMRYELRVPAAAP 75

Query: 63  ---DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------S 106
               G  +      E   L +  KP GLV   +  +   T+ + L               
Sbjct: 76  ATPQGQDIALDVLFEDRDLIVLDKPAGLVVHPAPGNEDGTLVNALLGHCGDSLTGIGGER 135

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRF-----------HGQV 153
           R   V RLD +T G+++          L     S    R Y+               G +
Sbjct: 136 RPGIVHRLDKDTSGVMVAAKTELAHHALSAAFASRDIERAYQAVCWGVLAPTTGSFDGAI 195

Query: 154 DQDKLNLLKKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +D+    +  ++  G          TLDT  GS + V   L  G+  +I+  F      
Sbjct: 196 GRDRRERKRMAVISNGGGKHALTHYRTLDTFHGSLSHVECKLATGRTHQIRVHFAHAGHA 255

Query: 212 V----NRLIRI 218
           +      L RI
Sbjct: 256 LVGDPTYLRRI 266


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 76/241 (31%), Gaps = 51/241 (21%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVM------------STDHI 60
           +R+   +  +    SR   +R+IA   V V+G    +A   +                 I
Sbjct: 10  ERLDVFLVRQMPALSRSYAQRLIAGGNVAVDGER-RKANFKLSGAEMVVCTLPPAEETEI 68

Query: 61  EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------- 110
             + +PL    E   + + +K  G+V   +      T+ + L    S +           
Sbjct: 69  CAEDIPLDILYEDADIIVINKRRGMVVHPAAGVHTGTLVNALLHHCSDLSGINGALRPGI 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           V RLD +T G+++   +      L          R YR   +G + +      + G++  
Sbjct: 129 VHRLDKDTSGVMVAAKNDMAHHYLARQIRDKEARREYRAIVYGNIVE------RAGVITG 182

Query: 169 GI-----CYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIK-KVFEFFNW 210
            I         M +  +  + +     V             L  G+  +I+  +      
Sbjct: 183 DIGRHPTDRKKMAIVRENGRPATTHFEVLERFGDYTFVACRLETGRTHQIRVHMT-SIGH 241

Query: 211 K 211
            
Sbjct: 242 P 242


>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 = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 34/174 (19%), Positives = 65/174 (37%), Gaps = 31/174 (17%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K + ++    SR   ++ I  +RV +N  +  + +  +   D + +           
Sbjct: 18  RLDKFLVSQNPKYSRAFYQQHILDKRVTINEQIQTKVSTQLAPGDIVSITIEEKEELSEL 77

Query: 63  --DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSR 107
             + +PL K  E   + + +KP  +V   +    R TV   L            P    R
Sbjct: 78  LPEAIPLEKIYEDEMILVINKPRDMVVHPAPGHTRGTVVHALLHEIGERLKQEFPEEPWR 137

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDKL 158
              + RLD +T G LL+T     A+++      + Q  + Y     G+     +
Sbjct: 138 PGIIHRLDKDTSG-LLITAKTRQAKMIYSELFATKQLKKSYLAICVGKPSASII 190


>gi|27382447|ref|NP_773976.1| pseudouridine synthase-like protein [Bradyrhizobium japonicum USDA
           110]
 gi|27355618|dbj|BAC52601.1| blr7336 [Bradyrhizobium japonicum USDA 110]
          Length = 335

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 75/243 (30%), Gaps = 46/243 (18%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ +V+A R    SR  ++ +I    V +    +   A +V   D I +D          
Sbjct: 22  RLDRVLAARLPDLSRSRLKALILAGAVSLKASAVRDPAYHVSHGDTIIIDVPEAAPAEPK 81

Query: 64  GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
           G  +      E   + + +KP GLV   +      T+ + L +             R   
Sbjct: 82  GEEIALDIVFEDDDIIVINKPRGLVVHPAAGHETGTLVNALIAHCGSTLSGIGGVRRPGI 141

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVR-----------FHGQV 153
           V RLD +T GL+++  +      L        R       Y                  +
Sbjct: 142 VHRLDKDTTGLMVVAKNDLAHASLSAQFADHGRTGAMRRGYMAFAWGVPGRHRGTVDAPI 201

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----AWVTVGLREGKNREIKKVFEFF 208
           D+      K  +   G         L++  G +     A +   L  G+  +I+      
Sbjct: 202 DRHPYAREKMAVRQGGREAVTHWEILESFPGRDGKPIAALLACELETGRTHQIRVHLAHI 261

Query: 209 NWK 211
              
Sbjct: 262 GHP 264


>gi|114321699|ref|YP_743382.1| ribosomal large subunit pseudouridine synthase D [Alkalilimnicola
           ehrlichii MLHE-1]
 gi|114228093|gb|ABI57892.1| ribosomal large subunit pseudouridine synthase D [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 313

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 79/240 (32%), Gaps = 38/240 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           ++ E  T QR+ + +A      SR  +++ I +  V++ G    R    V +   +    
Sbjct: 10  LIDEQQTGQRLDQALAALLPDYSRSRIQQWIREGAVRLEG-TAPRPRDKVAAGQQVTIRA 68

Query: 61  ------EVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------F 105
                  V   P+    + E   L +  KP GLV      +   T+ + L          
Sbjct: 69  ELEEEQRVSAEPIPLRIQYEDRHLLVIDKPAGLVVHPGAGNREGTLQNALLHHDPQLAEL 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV---------- 153
            R   V RLD +T GL+++         L  +L +    R Y    +G            
Sbjct: 129 PRSGIVHRLDKDTSGLMVVARSLAAHTALVAQLQARSVRREYLALVNGCPVAGGTVEAPI 188

Query: 154 --DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                    +    V++          ++ +  ++  +   L  G+  +I+       + 
Sbjct: 189 GRHPRDRKRMA---VVERGRPATTHYRVEERLAAHTLLRCFLETGRTHQIRVHMAHAGYP 245


>gi|126032015|gb|ABN71573.1| putative pseudouridylate synthase [uncultured bacterium]
          Length = 353

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 81/243 (33%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E +  +R+ K +A      SR  +++ +    V VNG  +  A   +   D ++V   
Sbjct: 37  IDERYAGERLDKALAFLIPDVSRSRLQQWVVAGAVTVNGGAVR-ARHTLTFGDVVKVTPQ 95

Query: 66  PLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
           P   A              E   + + +KP  LV   +      T+ + L +        
Sbjct: 96  PAPDAAAYKPEPMPLEVIFEDDAILVLNKPPKLVVHPAAGHWSGTLLNGLLAYAPTLIDV 155

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L  +L S    R Y     G   Q  +     
Sbjct: 156 PRAGIVHRLDADTSGLMVVAKTLAAQTDLVRQLQSRTVTREYWALVLGVPSQRGVIDAAI 215

Query: 164 GIVIQG---------ICYGDMQ---VTLDTQK---GSNAWVTVGLREGKNREIKKVFEFF 208
           G   +                +    TLD+ K      +W+   L  G+  +I+   E  
Sbjct: 216 GRDPRNPLRFKVSTTEAAKPARTHYATLDSTKNAGADISWLACRLETGRTHQIRVHLEHV 275

Query: 209 NWK 211
              
Sbjct: 276 GHP 278


>gi|261838022|gb|ACX97788.1| pseudouridine synthase D [Helicobacter pylori 51]
          Length = 327

 Score = 66.7 bits (162), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 106/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L           +  R   V
Sbjct: 73  ELDLEIEVIFEDKDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D    + +  D 
Sbjct: 297 DMLEYLKKFFDK 308


>gi|206603460|gb|EDZ39940.1| pseudouridylate synthase, 23S RNA-specific [Leptospirillum sp.
           Group II '5-way CG']
          Length = 340

 Score = 66.7 bits (162), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 79/256 (30%), Gaps = 53/256 (20%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V     P+R+   ++R  +  +R  V+R++ ++ V +N I     +  +   D I V  
Sbjct: 22  LVPRGEQPKRLDIYLSRNCLGFTRSRVQRLLEEKLVTINDIYPAS-SHKIRGGDRIRVLI 80

Query: 63  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                      D       E   L +  KP GLV   +      T+ + L   F      
Sbjct: 81  PPPRSQAAQPEDIHLEILYEDDDLIVISKPPGLVVHPAPGHASGTLVNGLLFHFQSQGDE 140

Query: 107 ----------------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
                           R   V RLD +T G++++     +   L          + Y   
Sbjct: 141 QKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKSETVVLDLMNQFKDRSVSKKYLAL 200

Query: 149 FHGQVDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
             G + +                      +   G         L+T   + + + V L  
Sbjct: 201 VKGILPKKRGEINAPIGRSTHDRKKFA--VRQDGKPSLTRYRVLETYHENYSLLEVTLLT 258

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+  F    + 
Sbjct: 259 GRTHQIRVHFRHLGFP 274


>gi|57505439|ref|ZP_00371367.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter upsaliensis RM3195]
 gi|57016264|gb|EAL53050.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter upsaliensis RM3195]
          Length = 325

 Score = 66.7 bits (162), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/234 (16%), Positives = 87/234 (37%), Gaps = 53/234 (22%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +++K++ +    SR +V  +I    V +N  +  + +  + + D I +  +P ++ +   
Sbjct: 15  KLAKILNQ----SRSQVSLLIENNAVLINDKIQNKNSFKLKNGDIITLKTLPQKELKAQY 70

Query: 75  --------------LWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS--------RVISV 111
                         + + +KP  LV   +     +T+ D  L   ++        R   V
Sbjct: 71  EVNFEVDVLFEDEDVLVLNKPQNLVVHGASSVKEATLIDWLLAKKYALSNLAGDLRAGLV 130

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL---NLLK---- 162
            RLD  T G +++  +    + L   L +    R+Y       + +DK+     L     
Sbjct: 131 HRLDKETSGAIIIAKNNFSHQRLSEQLQNKSLGRIYLALIDLPLKEDKIIINKALTRSTQ 190

Query: 163 ---KGIVIQGICYGDMQVTLDTQKGSNAWVTV-----------GLREGKNREIK 202
              K I I+   Y      +  ++  +A++ +            L  G+  +I+
Sbjct: 191 NRIKKIAIERENYNP---KIKAKEAKSAFINLALAKDVNLIAAKLFSGRTHQIR 241


>gi|299137599|ref|ZP_07030780.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
 gi|298600240|gb|EFI56397.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
          Length = 298

 Score = 66.7 bits (162), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 67/201 (33%), Gaps = 25/201 (12%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGL 84
           +    V +NGI+    + +V     +  +  P  + +  +          L   +KP GL
Sbjct: 41  LDSGEVTLNGIIAT-GSESVTLGQTLVWERPPWIEPDSPQHFEVLLDDSHLLAVNKPSGL 99

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWL 142
            T        +T+   +         V RL   T G++L       A  L     +++  
Sbjct: 100 PTLPGGGFMENTLLRLVQKQNPNANPVHRLGRATTGIVLFAKTPQAASQLSANWNTSRIQ 159

Query: 143 RVYRVRFHGQVDQDKLNLLKK-GIV---IQGICYGDMQ--------VTLDTQKGSNAWVT 190
           ++YR    G   QD   +L   G+V   + G  +              + ++  S     
Sbjct: 160 KIYRALAQGVAQQDAYEILTPIGLVPHPLIGSVWAASPSGKPSKSLAKVISRTTSTTTFE 219

Query: 191 VGLREGKNREIKKVFEFFNWK 211
           V L  G+ ++I+         
Sbjct: 220 VSLHSGRPQQIRIHLASIGHP 240


>gi|268607871|ref|ZP_06141602.1| pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 315

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 83/256 (32%), Gaps = 49/256 (19%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K ++ +N + QRV K I++A     +  + R+I ++ +KVNG      +  +M+ D + V
Sbjct: 3   KFVINDNDSGQRVDKFISKALPDLPKSMMYRLIRKKDIKVNGKRC-EISTKLMTDDVVTV 61

Query: 63  -------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
                              D       E   + + +KP+GL +  +      T+ + +  
Sbjct: 62  YVKQELSGTKQHDMSFLKADTALDTVYEDENVIIVNKPLGLDSHSNGEHNDDTLINRIKL 121

Query: 102 ---------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR-V 147
                    P   S        RLD NT GL+    +    R +          ++Y  +
Sbjct: 122 YLYNKNEYQPDEESSFAPALCSRLDRNTSGLVTAVKNAAALREINSAIRDGMVHKIYLCI 181

Query: 148 RFHGQVDQDKL-------NLLKKGIVIQGIC---YGDMQ--VTLDTQKGSNAWVTVGLRE 195
                     +          +  + I       Y  ++    +       + V V L  
Sbjct: 182 TIAQPPKSADIITAYHKKEDSRNIVRISDHPLDGYKPIKTGYEVLKSHKGLSLVKVTLFT 241

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+         
Sbjct: 242 GRTHQIRAHLSHVGAP 257


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 86/252 (34%), Gaps = 40/252 (15%)

Query: 1   MKD--KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M D     V E     R+ KV+++     SR  +++++    V VNG ++ +    + ++
Sbjct: 1   MSDHYNFTVSEENIGDRIDKVLSKQLPEMSRSSLQKLVNDGCVLVNGNIVSK-NYKIKNS 59

Query: 58  DHIEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPS 103
           D I V+             +P+    E   L + +KP G+V   +  +   T+ +  L  
Sbjct: 60  DTISVEIPEAEELKAEPQDIPIDIVYEDDSLLVVNKPQGMVVHPAAGNPDGTLVNALLFH 119

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVR---- 148
              R+ S         V R+D  T GLL++         L          R Y       
Sbjct: 120 CKGRLSSINGVIRPGIVHRIDKFTSGLLMVAKTDKAHNFLAQQIKDHNFTREYNAICIGR 179

Query: 149 -------FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                   +  + + K +  K  +  Q          +    G  + V   L  G+  +I
Sbjct: 180 FKEPTGTVNEPIGRSKFDRKKMCVTYQNCKEAVTHYEVLEDLGQYSLVKFRLETGRTHQI 239

Query: 202 KKVFEFFNWKVN 213
           +    F    V 
Sbjct: 240 RVHSAFIGHPVL 251


>gi|254285561|ref|ZP_04960525.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
 gi|150424423|gb|EDN16360.1| pseudouridine synthase Rlu family protein [Vibrio cholerae
           AM-19226]
          Length = 245

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|323341916|ref|ZP_08082149.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464341|gb|EFY09534.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 298

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 40/221 (18%), Positives = 73/221 (33%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+   +      SR ++  MI    +  N +   +A       D I         +D  P
Sbjct: 14  RIDHFLNEHLDLSRSKIASMIKDGTILCNDMP-TKANYKTKLNDCITASTYQIKTLDIEP 72

Query: 67  LR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------PSIFSRVISVGRL 114
           ++       E   L + +KP GLV    +     T+   L          + R   V R+
Sbjct: 73  VKMDIDVVYEDEYLLVVNKPRGLVVHPGNGVKSDTLLHGLLYYLNSNCDHYIRPGLVHRI 132

Query: 115 DINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL---------NLLKK 163
           D NT GLL++  D    + L          R Y    HG + Q  +             K
Sbjct: 133 DRNTSGLLVIAKDDKTHQFLAEQLLDKTMNRTYYALVHGVLPQAHVLIDAPIGPDKSNTK 192

Query: 164 GIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIK 202
            + +        +   +  +   +++ +   L  G+  +I+
Sbjct: 193 IMTVNQARSKPARTHFEKIETYINSSLICCKLETGRTHQIR 233


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/160 (24%), Positives = 60/160 (37%), Gaps = 25/160 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------- 63
           R+ K +A     SR +    I Q+RV VNG   ++A   V   D I              
Sbjct: 7   RLDKALADLTPLSRSQANDQIKQKRVLVNGSP-KKAKYIVQVGDCISYHIPEESSLDYQA 65

Query: 64  -GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
             +PL    +   L + +KP G+V   S      T+ + L              R   V 
Sbjct: 66  QDIPLDIVYQDDVLAIINKPQGMVVHPSAGHSTGTLVNALLYHVKDLSSINGVIRPGIVH 125

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
           R+D +T GLL++       ++L     + + LR Y    H
Sbjct: 126 RIDKDTSGLLMVAKTDKAHQLLADELKAKKSLRKYVAIVH 165


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 83/239 (34%), Gaps = 33/239 (13%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST 57
           + E     R+ K +A     SR  +  +I   +V VN             +R    V   
Sbjct: 6   INEENKGLRLDKALANQTEYSRSLLTELIKNDKVFVNSEAKKAKYKVKVGDRIEFEVPEA 65

Query: 58  DHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------- 106
           + +++  + +PL    E + + + +KP G+V   +      T+ + +             
Sbjct: 66  EVLDIVAEDLPLEIIYEDSDVAVVNKPQGMVVHPAAGHASGTLVNAIMYHIKDLSSINGV 125

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK------ 157
            R   V R+D +T GLL++  +      L   L      R Y    HG++  DK      
Sbjct: 126 IRPGIVHRIDKDTSGLLMIAKNDKAHESLAAQLKDKTSKRRYLAIVHGEIANDKGTIEAP 185

Query: 158 ----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               L   KK  V+ G         +  +      + + L  G+  +I+    +    V
Sbjct: 186 IGRNLKDRKKQAVVSGGKPAVTHFEVLERFYGYTLIALRLETGRTHQIRVHMNYIGHPV 244


>gi|254225113|ref|ZP_04918727.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V51]
 gi|125622500|gb|EAZ50820.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V51]
          Length = 245

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 27/170 (15%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASDVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAM 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G        L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFTTTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/256 (15%), Positives = 88/256 (34%), Gaps = 51/256 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           IV       R+ + + +      S  ++ + + +  VK+NG   +     +   D I V 
Sbjct: 7   IVDSESEGMRLDRYL-KKTFKNESLSKIFQALRKGDVKINGKKSKE-NYRLCLGDKITVK 64

Query: 64  GVPLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            +   K E+T+                     ++ +KP G V  H     +  + +    
Sbjct: 65  YLYSEKEEKTKKTFDFDEKKYKNMIIFENNDFFIINKP-GNVPMHKGTGHKHGLSEIFKK 123

Query: 104 IFSR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-- 157
           I+    +    RLD  T GL++   +    R +     + +  + Y     G++++DK  
Sbjct: 124 IYENDNINFANRLDYETSGLVIGCKNLKFLRYISEKIRNNEVQKKYVAAVDGEIEKDKFI 183

Query: 158 ----LNLLKKGIVIQGICYGDMQVTL----------------DTQKGSNAWVTVGLREGK 197
               L + + G++   +   D + ++                + +K     + + L  G+
Sbjct: 184 IENYLKITENGVIQSYVSDKDAKRSITKYKKINNRFFDKILNNIKKEKVTLLDIDLVTGR 243

Query: 198 NREIKKVFEFFNWKVN 213
             +I+         V 
Sbjct: 244 KHQIRVQLSSIGNPVI 259


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/229 (17%), Positives = 80/229 (34%), Gaps = 41/229 (17%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+   +++     SR  ++++I Q  + +N  +       V S D ++V           
Sbjct: 21  RIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKTKVNSGDRLQVFLPPPEPLELQ 80

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
            + +PL    E   L + +K  GLV   +      T+   L      ++ +G        
Sbjct: 81  PEPIPLDILYEDDSLIIINKSAGLVVHPAPGHTTGTLVHGLLYHCPNLVGIGGIQRPGIV 140

Query: 113 -RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-- 167
            RLD +T G +++  T+        +L +    R Y    +G    +  +     + I  
Sbjct: 141 HRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYGVPRHEDTHQGTINVPIGR 200

Query: 168 -QGICYGDMQVTLD--TQKGSNAW-----------VTVGLREGKNREIK 202
            +G       V ++   ++    W           V   L  G+  +I+
Sbjct: 201 HRGDRKKMAVVPVENGGREAITHWQIVERLGNYTLVEFRLETGRTHQIR 249


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 45/254 (17%), Positives = 88/254 (34%), Gaps = 51/254 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  + +     R+ K+++      SR   ++MI    + VN    ++      ++D 
Sbjct: 1   MPKKFKITDELG--RLDKIVSMLDPEISRSRAKKMIEDGDIIVNDSK-KKPKYETKASDT 57

Query: 60  ------------IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                       I+ + +PL    E   + + +KP G+V   S      T+ + L     
Sbjct: 58  LLIKDVKPETVSIKPENMPLDIVYEDEDVIVVNKPQGMVVHPSAGHPNHTLVNALLFHSP 117

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQ 155
                   R   V R+D +T GLL++  +  +A           + LR Y    HG++ +
Sbjct: 118 LSSINGEYRPGIVHRIDKDTSGLLMVAKN-DMAHKALSKQLKAKKNLRKYVALVHGRIKE 176

Query: 156 DKLNLLKKGIVIQGICYGD----MQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
           D       G++   I         Q  +   + +     V        L E     G+  
Sbjct: 177 D------SGVIKAPIARSPKDRKKQAIVADGRPAITHFEVMERFQDYTLIECRLETGRTH 230

Query: 200 EIKKVFEFFNWKVN 213
           +I+   ++    + 
Sbjct: 231 QIRVHMQYIGHPIV 244


>gi|88608012|ref|YP_506045.1| ribosomal large subunit pseudouridine synthase A [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600181|gb|ABD45649.1| ribosomal large subunit pseudouridine synthases, RluA family
           [Neorickettsia sennetsu str. Miyayama]
          Length = 330

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 81/247 (32%), Gaps = 36/247 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            K IV E     R+   + R     SR  ++  I   R++  G +    +  V+  +   
Sbjct: 2   YKCIVAECDAGNRLDVFLHRCLPFFSRSFIKHCIKGSRIESEGKIQLEPSRRVVVGEEYH 61

Query: 62  VDGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           +  +PL +  R               L + +KP GLV      +   T+ + L   +   
Sbjct: 62  LFDLPLERKPRHAFVQPLDVRYEDDCLLVIYKPAGLVVHPGIGNREQTLVNILEHHYPTE 121

Query: 107 --------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV--- 153
                   R   V RLD +T G L++  TN   L+    +      R Y    H      
Sbjct: 122 KLSSLDSSRPGIVHRLDKDTAGFLIVAKTNPAHLSLSQMIKEGVIRREYLALVHSVPASL 181

Query: 154 DQDKLNLLKKG---IVIQGICYGDMQ----VTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
             +    +K+G   ++I             V   T     + V   L  G+  +I+   +
Sbjct: 182 SGEIKKPIKRGQRKMMIGRCSGKPALTYYGVIARTVDRKCSLVHCRLGSGRTHQIRLHMK 241

Query: 207 FFNWKVN 213
                V 
Sbjct: 242 SIGCPVV 248


>gi|153216000|ref|ZP_01950222.1| tRNA pseudouridine synthase C [Vibrio cholerae 1587]
 gi|124114513|gb|EAY33333.1| tRNA pseudouridine synthase C [Vibrio cholerae 1587]
          Length = 244

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 48/231 (20%), Positives = 87/231 (37%), Gaps = 49/231 (21%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+   +A+     SR   +++I Q  V++NG + +R    +   + +EV           
Sbjct: 15  RLDTFLAQQHPEFSRSRWQQLIQQGHVRLNGQVCDRKNQPLSGGEVLEVVLPTPEPLDLV 74

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
            + +PL    E   L + +KP+ LV   +      T+   L +    +  +G        
Sbjct: 75  PEPLPLSILYEDEELLILNKPVDLVVHPAPGHSHGTLVHGLLAHCPDLTGIGGVQRPGIV 134

Query: 113 -RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ- 168
            RLD +T G++++         L  +L + Q  R Y    +GQ  +D      +G VI  
Sbjct: 135 HRLDKDTSGVMVVAKTEFALHHLQQQLKTRQMQRHYLGVVYGQPRED------RGTVITP 188

Query: 169 -GICYGDMQ--VTLDTQKGSN--------------AWVTVGLREGKNREIK 202
            G    D +    +  +KG                A V   L  G+  +I+
Sbjct: 189 LGRHPVDRKKMAVVPPEKGRTAITHWYVKERFRHCALVEFRLETGRTHQIR 239


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 34/202 (16%), Positives = 70/202 (34%), Gaps = 33/202 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKAERTRL 75
           K++A+    S  E + +I    V   G  +  A   +       IE    P    E   L
Sbjct: 8   KILAKQKNISNNEAKELIDSGLVYAKGQKVMIARALMSENTKFSIEEMPKPSVIFEDENL 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +                S   +   + RLD +T G+LLL  +   A +  
Sbjct: 68  IAINKPAAITSEK-------------ISQIYKFPLLHRLDKDTSGVLLLVKNDEFASLAI 114

Query: 136 LP--STQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQK-------- 183
                 +  ++Y     G + ++ +    +   + I+       +++ D ++        
Sbjct: 115 NEFKKMKVEKIYVAAVRGIMSEEVVVNEPI---LTIKNKNGAFSKISKDGKEAISEISPL 171

Query: 184 ---GSNAWVTVGLREGKNREIK 202
              G    V V ++ G+  +I+
Sbjct: 172 MVVGKKTLVKVVIKTGRTHQIR 193


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 39/223 (17%), Positives = 85/223 (38%), Gaps = 38/223 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
            R+S  +      S R   +   + R+KVNG  +   +  + + D +E+    + + E  
Sbjct: 19  IRLSHYLKNVAQCSSRFTRKAAREGRIKVNGENVR-LSYMLKNDDIVEL---QINRKEEQ 74

Query: 74  RLW----------------LYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISV 111
            +                 + +KP G+V   +      T+      + N  +  S V  V
Sbjct: 75  DIIPEKMDLDIIYEDDDIIVVNKPKGIVVHPTKRHLNGTLSNGVLYYFNDKNENSIVRLV 134

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK------LNLLKK 163
            RLD++T GL+L+  +      L        +++ Y    HG +++D       +  + +
Sbjct: 135 NRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFVKKYLAIVHGNLNEDSGVIDKPIYRVGE 194

Query: 164 G----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           G    ++ +       +  +  Q  + + V + L  G+  +I+
Sbjct: 195 GTLKRVIDERGQRSITRFKVVEQYKNASLVELTLETGRTHQIR 237


>gi|320546661|ref|ZP_08040973.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
 gi|320448716|gb|EFW89447.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           equinus ATCC 9812]
          Length = 296

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 75/211 (35%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGV------PLRK-----AERTRLWLYHKP 81
               + VNG + + A   +   D + +   D        P++       E     + +KP
Sbjct: 33  KGGNIWVNG-VEQNAIYLLDEGDVVTIEIPDEQEHETLIPVKHDLNIAYEDEHFLILNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + + + +        +V  V RLD NT GL+L    G     L
Sbjct: 92  YGYASIPS-ILHSNTIANFVKNYYLEQNYPNKQVHIVTRLDKNTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G             + +D+ +++ + +   G  Y      + 
Sbjct: 151 DKQLQNKTIEKRYYALVSGQGDLADEGEIIAPIARDEDSIITRRVHPSG-KYAHTSYKVV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + G  A V + L  G+  +I+  F    + 
Sbjct: 210 EKFGDVALVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|255068551|ref|ZP_05320406.1| tRNA pseudouridine synthase C [Neisseria sicca ATCC 29256]
 gi|255047187|gb|EET42651.1| tRNA pseudouridine synthase C [Neisseria sicca ATCC 29256]
          Length = 261

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 53/176 (30%), Gaps = 42/176 (23%)

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
            +R    +KP G++   S  D      V   L       V    RLD  T G+LL   D 
Sbjct: 34  DSRTIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPAHRLDRPTSGVLLFALDP 93

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
             AR+L          + Y     G +  D       G++   + Y   ++  ++Q  + 
Sbjct: 94  EAARLLTQQFEQKTTRKTYWAIVRGYLPDD-------GLIDYPLKYQPDKI-AESQTEAT 145

Query: 187 -----------------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                                        +W  +    G+  ++++  +     + 
Sbjct: 146 LQEAQTRYRRLARTELPFQSAARYPTSRYSWAELIPHTGRKHQLRRHMKHIFHPIV 201


>gi|110679108|ref|YP_682115.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           denitrificans OCh 114]
 gi|109455224|gb|ABG31429.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           denitrificans OCh 114]
          Length = 342

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 49/272 (18%), Positives = 89/272 (32%), Gaps = 65/272 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++    V +   P R+ K +AR     A + SR  + R+I +  V V+G++   A   V 
Sbjct: 3   VRQIQFVIDEAPPPRLDKALARDVPVEAAL-SRTRLARLIDEGGVLVDGVVQSNAKARVA 61

Query: 56  STDHIEV------DGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +   I +      D   L +        E + L + +KP G+V   +      T+ + L 
Sbjct: 62  AGAQITIQVQQAQDSHILPEDIALDVIHEDSDLIVVNKPAGMVVHPAPGTPSGTLVNALL 121

Query: 103 SI----------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
           S             R   V R+D +T GLL++         L     +    R Y    +
Sbjct: 122 SHCGADLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQFQAHTVERYYNCLVY 181

Query: 151 GQVDQDK-------LNLLKKG--------------------IVIQGICYGDMQVTLDTQK 183
           G  D +            + G                    ++ QG  +   +     + 
Sbjct: 182 GAPDANDPRLRGVKGARFEAGNILKLTTQLARHKTDRQRQAVLFQGGRHAVTRARSLERF 241

Query: 184 GSNAWVTVGLRE-----GKNREIKKVFEFFNW 210
           G+   +   L E     G+  +I+        
Sbjct: 242 GTPPVL--TLMECWLETGRTHQIRVHMAHAGH 271


>gi|291543962|emb|CBL17071.1| ribosomal large subunit pseudouridine synthase D [Ruminococcus sp.
           18P13]
          Length = 304

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 77/237 (32%), Gaps = 43/237 (18%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           ++  + +  R+ K +       SR  V+ +I Q  V  NG    +  + +   D + V  
Sbjct: 5   MLTADGSGMRLDKWLTEQLPELSRSGVQHLIEQGAVLCNGKPAAK-NLKLREGDGLLVQI 63

Query: 63  -DGVPLR-----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVI 109
            D  PL              E   L + +KP G+V   +      T+ +  L     R+ 
Sbjct: 64  PDPAPLEDVQPQNLPLEIVYEDEALLVVNKPKGMVVHPAAGHPDGTLVNALLYHCQGRLS 123

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ--- 155
                     V R+D NT GLL++       + L          R Y     G+  +   
Sbjct: 124 TINGVIRPGIVHRIDKNTSGLLMVAKTDFAHQHLAEQIKGHSFTREYEAIACGRFREPSG 183

Query: 156 ----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                          +   +  +   +      + TQ   +A +   L  G+  +I+
Sbjct: 184 TVDAPIGRSTADRQKMC--VTEKNARHAVTHYAVLTQFAKHAHIRCRLETGRTHQIR 238


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 85/235 (36%), Gaps = 41/235 (17%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV E     R+   I+ A    SR  ++ +I  ++V VN  + E+++  V   D+I +  
Sbjct: 9   IVDEEEEDLRLDVFISSALSDLSRTYIQSLIKDKKVTVNDKI-EKSSYKVAQLDNICILI 67

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                     + +P+    E   L + +K  G+V      +   T+ + L   F      
Sbjct: 68  PPAKELVIEAEDIPIEILYEDEDLAVVYKERGMVVHPGAGNANHTLVNALMYHFKGQLSS 127

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDKL 158
                R   V R+D +T GLL++     +A              R Y    HG +  D+ 
Sbjct: 128 INGIIRPGIVHRIDKDTSGLLMIAKS-DIAHRGLSEQLKEHTVQRTYTFICHGNIKADEF 186

Query: 159 -----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      + +K  +V  G       +T      + ++    L  G+  +I+
Sbjct: 187 TIDAPIGRNPRDRMKMAVVSDGKHAVTH-ITKIKSNENYSYAMANLETGRTHQIR 240


>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 = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 83/236 (35%), Gaps = 47/236 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-VPLRKAERTRL---------- 75
           SR  +E++  ++ +KVNGI   +    +   D IE+ G + ++K E   +          
Sbjct: 29  SR--IEKLFRKKDIKVNGIRTNQKDYTIAFNDQIEIYGLIDIKKEEAPLISSFSFKKIYE 86

Query: 76  ----WLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDG 128
                +  KP G+    S     + V   L        +   VGRLD  T G++L   + 
Sbjct: 87  DNNILIIDKPNGIEVHSSPNCLDNQVLAYLKFKQVDSFKPSHVGRLDKETSGIMLYAKNY 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQV---TLDTQ 182
              + L       ++ Y   F    +++      K + +   +      M      +   
Sbjct: 147 QALKYLNDNMENIIKTY--TFKSDFNEE-----SKDVELYLYKDEDKKRMAASFTKVPYS 199

Query: 183 KGSNAWVTV-------GLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           K S     +        L  G+  +I+         + +L +  YG F+ G   AG
Sbjct: 200 KLSKTHFYLESNKKYATLSSGRKHQIR-------VSLMKLGKPIYGDFKYGGKKAG 248


>gi|261252272|ref|ZP_05944845.1| tRNA pseudouridine synthase C [Vibrio orientalis CIP 102891]
 gi|260935663|gb|EEX91652.1| tRNA pseudouridine synthase C [Vibrio orientalis CIP 102891]
          Length = 240

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 29/193 (15%), Positives = 56/193 (29%), Gaps = 38/193 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +     + +  + Y     G +++         + +  I         + Q+  
Sbjct: 67  SEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQEKEAQEAI 126

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN---------- 213
                 A V V             L E     G+  ++++        +           
Sbjct: 127 TDYWPLAKVEVPHSTGKFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIVGDTTHGDGKH 186

Query: 214 -RLIRISYGPFQL 225
            +L R  Y   +L
Sbjct: 187 NKLYREVYDSHRL 199


>gi|258624386|ref|ZP_05719334.1| tRNA pseudouridine synthase C [Vibrio mimicus VM603]
 gi|258583348|gb|EEW08149.1| tRNA pseudouridine synthase C [Vibrio mimicus VM603]
          Length = 244

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQDKEAQSAI 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 31/206 (15%), Positives = 67/206 (32%), Gaps = 39/206 (18%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVN--------GILLERAAVNVMSTDHIEVDGVPLRK 69
           K++A     S  + + +I +  VKV         G +       +   + ++V       
Sbjct: 10  KLLALQEKISNSKAKELIDKGVVKVGDKKVLIARGEIRTDTKFTIKEINKVKV------I 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   + +  KP  L              D +   F   I + RLD  T G+++   +  
Sbjct: 64  FEDKDILVVDKPAFLTA------------DEVCKKFENAILLNRLDKETSGVMMFAKNEE 111

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQD-----------KLNLLKKGIVIQGICYGDMQ 176
             +       + +  + Y     G+V  +              + K  I ++        
Sbjct: 112 FQKKAIKEFQANRVYKEYVAIVEGKVVDEIEIDKPILTTKDRGMAKSKIDVKRGKPAKST 171

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK 202
           V     +G+ + + V +  G+  +I+
Sbjct: 172 VYPLLVEGNKSKIKVVIESGRTHQIR 197


>gi|332970317|gb|EGK09309.1| tRNA pseudouridine synthase C [Kingella kingae ATCC 23330]
          Length = 252

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 26/171 (15%), Positives = 52/171 (30%), Gaps = 28/171 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +     + +KP G++   S  D + TVF        +   V  V RLD  T G +L   +
Sbjct: 7   QTEHYVVVNKPAGMLVHRSRLDSQETVFLMQTLRDQLGQLVYPVHRLDKPTSGAMLWALN 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQ---------VDQDKLNLLKKGIVIQGICYGDMQ 176
              AR         Q  + Y     G            +++L+ +               
Sbjct: 67  SEAARWFTQQFEQKQIRKHYLAIVRGWTENVGCIDYPLKEQLDKIADMHAQSDKTAQAAC 126

Query: 177 VTLDTQKGSN--------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
               T + S               + + +  + G+  +I++  +     + 
Sbjct: 127 TEYQTLQRSECPFASSARYATSRYSLLHITPKTGRKHQIRRHMKHIFHPIV 177


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 38/233 (16%), Positives = 74/233 (31%), Gaps = 39/233 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN------------GILLE----RA 50
           + E     R    +A+    SR    ++ A+  V ++            G ++       
Sbjct: 10  IPEGLEGMRADAALAKLLGLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVVSVLLPEP 69

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-------- 102
              ++  + + V+G+ +   +   +   HKP+G+    S      TV   L         
Sbjct: 70  EKPLLPREEL-VEGMDVLYNDAD-IICVHKPVGVAAHPSVGWDGPTVIGGLRAAGYTVAS 127

Query: 103 -SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF-------HGQ 152
                R   V RLD+ T G++++ +       L+         + Y            G 
Sbjct: 128 SGPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSVKKTYHAVVQGLPDPIEGT 187

Query: 153 VDQDKLNLLKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           VD       K G    V+          +L       + + V L  G+  +I+
Sbjct: 188 VDAPIGRHPKSGWKFAVLDDGKAAITHYSLIEAFREASLIEVHLETGRTHQIR 240


>gi|84394418|ref|ZP_00993135.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
 gi|84374951|gb|EAP91881.1| pseudouridine synthase Rlu family protein [Vibrio splendidus 12B01]
          Length = 249

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 51/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +     + +  + Y     G +++         + +  I     +   + Q+  
Sbjct: 67  SEVASQVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEPQEAV 126

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
                 A V V             L E     G+  ++++        + 
Sbjct: 127 TVYEPLAKVEVPYSTGRFPTSRYCLVEMMPKTGRKHQLRRHMAHLRHPIV 176


>gi|258621635|ref|ZP_05716667.1| tRNA pseudouridine synthase C [Vibrio mimicus VM573]
 gi|258586107|gb|EEW10824.1| tRNA pseudouridine synthase C [Vibrio mimicus VM573]
          Length = 244

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHKMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQDKEAQSAI 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|262172099|ref|ZP_06039777.1| tRNA pseudouridine synthase C [Vibrio mimicus MB-451]
 gi|261893175|gb|EEY39161.1| tRNA pseudouridine synthase C [Vibrio mimicus MB-451]
          Length = 244

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQDKEAQSAI 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 35/222 (15%), Positives = 66/222 (29%), Gaps = 31/222 (13%)

Query: 12  TPQRVSKVIARA--GIASRREVERMIAQQRVKVN------------GILLERAAVNVMST 57
             Q++ + + R   G   R  + R I +  V+V+            G  +         T
Sbjct: 13  AGQKLVRFLERRVDGAVPRSAIMRWIRKGNVRVDKGRCKPFDLVKEGQTVRIPPYKAEET 72

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRL 114
              +         E        KP GL T   T  D      +         +     RL
Sbjct: 73  AQHKKLPELPIIYEDDNYLAVCKPAGLPTQGGTGHDDSVADRLLSMFADAHYKPAPAHRL 132

Query: 115 DINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDKLNLL---------- 161
           D +T G++L        + L        +  + Y     G+  ++    L          
Sbjct: 133 DRDTSGVILAGKSHQGQKDLSDFFAEHGEGGKFYLAEVEGRWPEEDWVELHDKMEKSGSK 192

Query: 162 -KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            ++ +V+         V   T    ++ + V L  G+  +I+
Sbjct: 193 GREKVVVGSGKDASSSVCPVTIGEKSSLLIVKLHTGRTHQIR 234


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 43/178 (24%), Positives = 68/178 (38%), Gaps = 30/178 (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---DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTV------- 97
           D I V   D  P+             E   + + +K  GLV   +      T+       
Sbjct: 58  DVIVVRVPDPEPMELVPEDIPLDIVYEDEDILVVNKQRGLVVHPAAGHWTGTLVHALLDK 117

Query: 98  FDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            D+L  I   +    V RLD +T GLL++         L+         RVY    HG
Sbjct: 118 VDDLEGIGGELRPGIVHRLDKDTTGLLVVAKSERAMASLQEQIRDHMVQRVYWALVHG 175


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 29/205 (14%), Positives = 69/205 (33%), Gaps = 36/205 (17%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE------RAAVNVMSTDHIEVDGVPLRKAE 71
           K+++     S RE + +I +  V V G+ ++                 I+    P    +
Sbjct: 6   KLLSHQQRISHREAKILIDRGMVSVGGMKVKIARGLFPLGTKFS----IQEAPKPKILMQ 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L    KP  + +     + +                + RLD  T G++LL  +G   
Sbjct: 62  DENLLAIDKPPFIASEELLKEHKE----------KGWTLLHRLDKETSGVILLVQEGSEF 111

Query: 132 RVLELPST---QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ------ 182
           +          +  + Y     G + ++    + K I+     +   +++ + +      
Sbjct: 112 QKSAKAEFKAQKVYKEYVAIVEGMIPEE--REITKPILTTKGHFAKSKISKEGESAYTKI 169

Query: 183 -----KGSNAWVTVGLREGKNREIK 202
                +G    + V ++ G+  +I+
Sbjct: 170 EPLAYEGKQTQLKVIIKTGRTHQIR 194


>gi|15640904|ref|NP_230535.1| tRNA pseudouridine synthase C [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121588124|ref|ZP_01677871.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|147674217|ref|YP_001216366.1| tRNA pseudouridine synthase C [Vibrio cholerae O395]
 gi|227081064|ref|YP_002809615.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|229505507|ref|ZP_04395017.1| tRNA pseudouridine synthase C [Vibrio cholerae BX 330286]
 gi|229510823|ref|ZP_04400302.1| tRNA pseudouridine synthase C [Vibrio cholerae B33]
 gi|229517944|ref|ZP_04407388.1| tRNA pseudouridine synthase C [Vibrio cholerae RC9]
 gi|229608526|ref|YP_002879174.1| tRNA pseudouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254848023|ref|ZP_05237373.1| tRNA pseudouridine synthase C [Vibrio cholerae MO10]
 gi|298498990|ref|ZP_07008797.1| tRNA pseudouridine synthase C [Vibrio cholerae MAK 757]
 gi|34582485|sp|Q9KTL4|TRUC_VIBCH RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|9655343|gb|AAF94050.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O1
           biovar El Tor str. N16961]
 gi|121547615|gb|EAX57714.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 2740-80]
 gi|146316100|gb|ABQ20639.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|227008952|gb|ACP05164.1| pseudouridine synthase Rlu family protein [Vibrio cholerae M66-2]
 gi|227012708|gb|ACP08918.1| pseudouridine synthase Rlu family protein [Vibrio cholerae O395]
 gi|229344659|gb|EEO09633.1| tRNA pseudouridine synthase C [Vibrio cholerae RC9]
 gi|229350788|gb|EEO15729.1| tRNA pseudouridine synthase C [Vibrio cholerae B33]
 gi|229357730|gb|EEO22647.1| tRNA pseudouridine synthase C [Vibrio cholerae BX 330286]
 gi|229371181|gb|ACQ61604.1| tRNA pseudouridine synthase C [Vibrio cholerae MJ-1236]
 gi|254843728|gb|EET22142.1| tRNA pseudouridine synthase C [Vibrio cholerae MO10]
 gi|297543323|gb|EFH79373.1| tRNA pseudouridine synthase C [Vibrio cholerae MAK 757]
          Length = 244

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|262195124|ref|YP_003266333.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262078471|gb|ACY14440.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 345

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 42/226 (18%), Positives = 78/226 (34%), Gaps = 50/226 (22%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKAERTRLW-LY 78
           ASRR V  + A  RV+VNG  +++ A+ V +   I +      D   + +A    +  L 
Sbjct: 38  ASRRRVTALFADGRVRVNGRKVKKGAI-VPAGAEIALTRLPVADEELVPQANHELVLDLL 96

Query: 79  H---------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----------RLDINTE 119
           +         KP GL +       R T+ + L + +    ++G          RLDI+T 
Sbjct: 97  YEDDAIAVVSKPAGLPSHPLRAGERDTLANALVAHYPECAAIGADPREAGLAHRLDIDTS 156

Query: 120 GLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDM 175
           G+L+          L     S    + Y     G     +  + L+++G     +   D 
Sbjct: 157 GVLVAARTQKAWHALRAAFGSGAVEKHYLALTFGAPSSGEMDVALVQRGRRAHPVFRDDA 216

Query: 176 QV-------------------TLDTQKGSNAWVTVGLREGKNREIK 202
                                 ++ + G    +      G+  +I+
Sbjct: 217 GFGGFGGRGERGDALPARTTWRIERRFGPACLLLCRAHTGRMHQIR 262


>gi|218675156|ref|ZP_03524825.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli GR56]
          Length = 199

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 37/185 (20%), Positives = 67/185 (36%), Gaps = 32/185 (17%)

Query: 1   MKDKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M  + ++  + T + R+   + A+ G   SR  ++ +I   +V + G  +      V   
Sbjct: 1   MGIRKVLTADETAEGRLDAWLTAQVGEDFSRSRIKALIKDGQVSMRGEPVTDPQRKVRVG 60

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D  E+            + +PL    E   L +  KP GLV   +  +   T+ + L   
Sbjct: 61  DSFEITLPEPEDPTPRGEDIPLDILYEDDDLIVISKPAGLVVHPASGNWTGTLVNALIHH 120

Query: 105 F----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVR 148
                       R   V RLD +T G++++  +    R L L      R       Y+  
Sbjct: 121 CGATLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAI 180

Query: 149 FHGQV 153
             G+ 
Sbjct: 181 VWGRP 185


>gi|153802299|ref|ZP_01956885.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
 gi|124122181|gb|EAY40924.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-3]
          Length = 245

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G ++          ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEDTNVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPRTGRKHQLRRHMAHLRHPIV 176


>gi|261364336|ref|ZP_05977219.1| tRNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288567596|gb|EFC89156.1| tRNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 235

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 53/176 (30%), Gaps = 42/176 (23%)

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
            +R    +KP G++   S  D      V   L       V    RLD  T G+LL   D 
Sbjct: 8   DSRTIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPAHRLDRPTSGVLLFALDP 67

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
             AR+L          + Y     G +  D       G++   + Y   ++  ++Q  + 
Sbjct: 68  EAARLLTQQFEQKTTRKTYWAIVRGYLPDD-------GLIDYPLKYQPDKI-AESQTEAT 119

Query: 187 -----------------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                                        +W  +    G+  ++++  +     + 
Sbjct: 120 LQEAQTQYRCLARTELPFQSAARYPTSRYSWAELIPHTGRKHQLRRHMKHIFHPIV 175


>gi|311895525|dbj|BAJ27933.1| putative ribosomal large subunit pseudouridine synthase D
           [Kitasatospora setae KM-6054]
          Length = 312

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 77/243 (31%), Gaps = 59/243 (24%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---------AAVNVM-- 55
           V +    +R+   +AR    SR +   + A+ +V ++G +  +           V +   
Sbjct: 12  VPDGLEGERLDAALARMFGFSRTKAAELAAEGKVTLDGAVAGKSDRVTAGSWLEVEIPAP 71

Query: 56  --STDHI--EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S      TV   L +   R+   
Sbjct: 72  AAPVQIVAEAVEGMRIIHDDDHVVVI-DKPVGVAAHPSPGWTGPTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNL 160
                   V RLD+ T G++++         L+         + Y     G  D      
Sbjct: 131 GAAERQGVVHRLDVGTSGIMVVAKSERAYTDLKRQFHDRVTEKKYNALVQGHPDP----- 185

Query: 161 LKKGIVIQGICYGDM----------QVTLDTQKGSN-----------AWVTVGLREGKNR 199
                 + G     +           VT D +               + + + L  G+  
Sbjct: 186 ------LSGTVDAPIGRHPSSDWKWAVTRDGKPSVTHYDLIEAYRAASLLDIKLETGRTH 239

Query: 200 EIK 202
           +I+
Sbjct: 240 QIR 242


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 81/245 (33%), Gaps = 52/245 (21%)

Query: 12  TPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
            P R+ K +      +   +R ++ +      V VNG  +++    V   D I V    L
Sbjct: 39  QPLRIDKFLHIFRQNS---TRNKISQSCRAGNVVVNGTAVKQ-NYRVKPGDRISV---LL 91

Query: 68  RKAERTRLWL-----YH------------KPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
            +  R  + +      +            K  G+V      +   T+ + L   F     
Sbjct: 92  SRPPRENVIIPQDIPLNIVYEDDDLVVVDKDPGMVVHPGHGNWDGTLINALAFHFEKNGV 151

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD--- 156
                RV  V R+D +T GLL++  +      L       +  R+Y     G +DQ+   
Sbjct: 152 KSDLDRVGLVHRIDKDTSGLLVIAKNEYALSYLAKQFFDRKTKRLYWAFVWGNLDQENGT 211

Query: 157 -------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFE 206
                   L    +  V +    G   VT   +  +     WV   L  G+  +I+  F+
Sbjct: 212 ITGNIGRHLKNRMQMAVFEDGSLGKHAVTHYKVVERFKYMTWVECKLETGRTHQIRAHFK 271

Query: 207 FFNWK 211
                
Sbjct: 272 HIGHT 276


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 38/233 (16%), Positives = 74/233 (31%), Gaps = 39/233 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN------------GILLE----RA 50
           + E     R    +A+    SR    ++ A+  V ++            G ++       
Sbjct: 10  IPEGLEGMRADAALAKLLGLSRSATAQLCAEGSVTIDSQELGKSERLTSGNVVSVLLPEP 69

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP-------- 102
              ++  + + V+G+ +   +   +   HKP+G+    S      TV   L         
Sbjct: 70  EKPLLPREEL-VEGMDVLYNDAD-IICVHKPVGVAAHPSVGWDGPTVIGGLRAAGYTVAS 127

Query: 103 -SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF-------HGQ 152
                R   V RLD+ T G++++ +       L+         + Y            G 
Sbjct: 128 SGPTERKGIVHRLDVGTSGVMVVASSERAYSALKHAFKYRSVKKTYHAVVQGLPDPIEGT 187

Query: 153 VDQDKLNLLKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           VD       K G    V+          +L       + + V L  G+  +I+
Sbjct: 188 VDAPIGRHPKSGWKFAVLDDGKAAVTHYSLIEAFREASLIEVHLETGRTHQIR 240


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 81/239 (33%), Gaps = 35/239 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V E+   QR+ + +A      SR  ++  I    V+VN  +       ++  + +E+  
Sbjct: 10  TVSESQLGQRLDQALAELFPDYSRSRIKAWILDGLVRVNRRVTAVPKEKMLGGESVEIQA 69

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                       +PL    E   + + +KP  LV      +   TV + L   F  ++  
Sbjct: 70  FIEEAPRWEAQAIPLNIVYEDDDILVINKPRDLVVHPGAGNADGTVLNALLHYFPPIVDV 129

Query: 110 ----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                V RLD +T GL+++         L   L + +  R Y     G +       L++
Sbjct: 130 PRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQAREITREYEAVAIGTMTAGG--TLEQ 187

Query: 164 GIVIQGICYGDMQVTLDTQKG-----------SNAWVTVGLREGKNREIKKVFEFFNWK 211
            I         M V    +             ++  + + L  G+  +I+      N  
Sbjct: 188 PIARHATKRTHMAVHPMGKPAVTNYRIMEHFRAHTRLRLRLETGRTHQIRVHMAHINHP 246


>gi|317401792|gb|EFV82407.1| pseudouridine synthase [Achromobacter xylosoxidans C54]
          Length = 336

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 40/164 (24%), Positives = 62/164 (37%), Gaps = 28/164 (17%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           R+ KV+A  G+    SR  ++  I    V+VNG   +     V   D I V   P  +A 
Sbjct: 45  RLDKVLA--GLLPDHSRSRLQGWIEAGNVQVNGAPGK-VRQTVGPGDEIAVWAQPAPEAL 101

Query: 71  -------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISV 111
                        E     + +KP GLV      +   T+ + L   +       R   V
Sbjct: 102 AFAPEAIDFPVVDESPDWIVVNKPAGLVVHPGAGNWSGTLLNGLLHRYPELAQVARAGIV 161

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
            RLD +T GL+++  +      L  +L +    R Y    HG +
Sbjct: 162 HRLDKDTSGLMVVARNEIAQTHLVRQLQARSMGREYVALAHGWL 205


>gi|266624507|ref|ZP_06117442.1| pseudouridylate synthase [Clostridium hathewayi DSM 13479]
 gi|288863645|gb|EFC95943.1| pseudouridylate synthase [Clostridium hathewayi DSM 13479]
          Length = 320

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 48/260 (18%), Positives = 87/260 (33%), Gaps = 59/260 (22%)

Query: 6   IVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           IV EN + QR+ K++A+    AG      + +M+ ++ + +NG      +  +++ D + 
Sbjct: 5   IVTENESGQRLDKLLAKYLNLAGKG---FLYKMMRKKNITLNGKKC-DGSEKLVTGDEVR 60

Query: 62  --VDGVPLRK-----------------AERTRLWLYHKPIGLVTTH---SDPDGRSTVFD 99
                  + K                  E   + L +KP G+++     SD      + D
Sbjct: 61  LFFSDETIGKFSVHTLQEVKKVNLQIIYEDDHILLVNKPSGMLSQKAKDSDESLVEYIID 120

Query: 100 NLPSIFS---------RVISVGRLDINTEGLLLLTNDGG--LARVLELPSTQ---WLRVY 145
            L S            R     RLD NT GL++    G       +     +     + Y
Sbjct: 121 YLVSSGQLSTEQLKSFRPSVCNRLDRNTSGLVVA---GKSLPGLQIMSAVFKDRSLHKYY 177

Query: 146 RVRFHGQVDQDKLNL--LKKGIVIQGICYGDMQV----------TLDTQKGSNAWVTVGL 193
           R    G V   ++    LKK  V   +     +V              Q      ++V L
Sbjct: 178 RCVVKGSVTDKQVITGFLKKDSVTNQVTITAAEVEGSVPVMTEYEPLGQAEGCTLLSVKL 237

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 238 ITGRTHQIRAHLASIGHPIL 257


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 60/163 (36%), Gaps = 24/163 (14%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV++      SR  +++ I    V V+G +   A + V   + + +   P  + E  
Sbjct: 26  RLDKVLSTLVPQYSRSRLQQWIDAGHVSVDGEIAR-AKMTVYGDEKVVIYPQPAPEDEAF 84

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
           +              + +  KP GLV   +  +   T+ + L           R   V R
Sbjct: 85  KPEAMDLNIAYEDAAILVIDKPAGLVVHPAAGNWSGTLLNGLLHYLPAIAGVPRAGIVHR 144

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
           LD +T GL+++         L  +L +    R Y     G  +
Sbjct: 145 LDKDTSGLMVVAKTLVAHTDLVRQLQARTVKREYLALVWGTPN 187


>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 = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+ K++   GI  SR   + +I   +V VNG ++++A   V +   +EV G  +  
Sbjct: 1  MKKERLDKLLVERGIVKSRERAKALIMAGKVLVNGQVVDKAGTAVPADARVEVKGEDIPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|15611749|ref|NP_223400.1| hypothetical protein jhp0682 [Helicobacter pylori J99]
 gi|11136015|sp|Q9ZL98|Y745_HELPJ RecName: Full=Uncharacterized RNA pseudouridine synthase jhp_0682;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|4155249|gb|AAD06270.1| putative [Helicobacter pylori J99]
          Length = 327

 Score = 66.4 bits (161), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 55/313 (17%), Positives = 107/313 (34%), Gaps = 63/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDAITLLTPKIVPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSQNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVCLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFF 208
            N LK  I ++       + +  ++    + +T       +   L  G+  +I+      
Sbjct: 192 NNRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNGMDLIGAKLFTGRTHQIR---AHL 244

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
                 L R   G   L  L       +SK+ +R  L  +L+E      +  +     L+
Sbjct: 245 ----EYLNRHIIGD-NLYGLNG----VLSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLL 295

Query: 269 RDRPNIISEVPDD 281
           +D    + +V D 
Sbjct: 296 KDMLEYLKKVFDK 308


>gi|315607390|ref|ZP_07882389.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|315250947|gb|EFU30937.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 367

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 77/245 (31%), Gaps = 50/245 (20%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +       SR  ++       ++VNG  ++     V   D + +        
Sbjct: 44  APVRIDKFLTEKNPHQSRNRIQSAADAGFIRVNGRPVKS-NYKVRPGDVVTLMLDRPKHD 102

Query: 63  -----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DN--LPSIFS 106
                + +PL    E   L + +KP G+V      +   T+         D     +   
Sbjct: 103 TSIVPEDIPLAVVYEDDGLMVINKPAGMVVHPGAGNFTGTLINAVAYYLKDLPTFDANSP 162

Query: 107 RVISVGRLDINTEGLLLL-------TNDGG-LARVLELPSTQWLRVYRVR---------F 149
            V  V R+D +T GLL++       T  G          S        V           
Sbjct: 163 EVGLVHRIDKDTSGLLVVAKTPEAKTCLGKQFFNKTTHRSYNA----LVWGNIVDDEGRI 218

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +D  N L+  +   G   G   VT   +  + G    V   L  G+  +I+   +
Sbjct: 219 EGNIARDPRNRLRMKVFAPGSGIGKSAVTHYRVLERFGYTTLVECRLETGRTHQIRAHMK 278

Query: 207 FFNWK 211
                
Sbjct: 279 HIGHP 283


>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 = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 90/255 (35%), Gaps = 59/255 (23%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD 
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVD- 63

Query: 65  VPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +P +  E T                + +  KP  ++          T+ + L +    + 
Sbjct: 64  LPEKPQEATVQPEEIELKVLYEDRDIVVIDKPRDMIVHPVPSKLSGTLVNALLNHCKDLQ 123

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDK 157
            VG         RLD  T G++++  +   A           +  + Y +   G+V +D 
Sbjct: 124 GVGGKLRPGIVHRLDKETSGVIVVAKN-DFAHQSLSKQFKDRKVKKTYILLVKGRVKKD- 181

Query: 158 LNLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTV--------GL-----REGKN 198
                +G+V   +      V       ++T K +     V         L     + G+ 
Sbjct: 182 -----EGVV--DLPLARHPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRT 234

Query: 199 REIKKVFEFFNWKVN 213
            +I+   +     + 
Sbjct: 235 HQIRVHMKSLGHPIM 249


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 33/165 (20%), Positives = 61/165 (36%), Gaps = 28/165 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ KV++      SR  +++ I    V V+G +   A + V   + + +   P  + E  
Sbjct: 50  RLDKVLSTLVPQYSRSRLQQWIDGGHVSVDGEVAR-AKMTVYGDEKVVIYPQPAPEDEAF 108

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGR 113
           +              + + +KP GLV   +  +   T+ + L      +        V R
Sbjct: 109 KPEAMDLAIVHEDAEMLVINKPAGLVVHPAAGNWSGTLLNGLLHYLPSISGVPRAGIVHR 168

Query: 114 LDINTEGLLLLT----NDGGLARVLELPSTQWLRVYRVRFHGQVD 154
           LD +T GL+++         L R L   +    R Y     G  +
Sbjct: 169 LDKDTSGLMVVAKTLIAHTDLVRQL--QARTVKREYLALVWGTPN 211


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 88/264 (33%), Gaps = 62/264 (23%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           +V    +  R+   +A     SR ++ +M+  +++ +N I   +  + +   D I +   
Sbjct: 1   MVTSQESGMRLDIFLATKLNLSRNKINKMLHNKQITLNQIQASKNGIILKEQDQIHIFPS 60

Query: 66  PLRKA------------ERTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIF------- 105
            L  A            E   L + +KPI LV   ++  D + T+ + L           
Sbjct: 61  LLETAKPTPKIHIPILYEDEDLLVLNKPINLVVHKTNQEDTQYTLHEWLKEQNFKLSNLG 120

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQDKLNL 160
              R   + RLD  T G +++  +   +  +        +  R Y    +  + QD    
Sbjct: 121 DSYREGIIHRLDKTTSGAIVIAKN-NHSHQILSQQLKTKEMGRYYLCVINQPLKQD---- 175

Query: 161 LKKGIVIQGICYG----------DMQVTLDTQKGSNAWVTVG-----------LREGKNR 199
               I+I                  + T D++    A+  +            L  G+  
Sbjct: 176 ----IIIDSPLIRHPKNRLKYITTSKQTPDSKDAKTAFFKIIDNGKTELIGAKLFSGRTH 231

Query: 200 EIKKVFEFFNWKVNRLIRISYGPF 223
           +I+          +++ R   G F
Sbjct: 232 QIR---AHL----SKINRHILGDF 248


>gi|218710322|ref|YP_002417943.1| tRNA pseudouridine synthase C [Vibrio splendidus LGP32]
 gi|218323341|emb|CAV19518.1| tRNA pseudouridine synthase C [Vibrio splendidus LGP32]
          Length = 252

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 51/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 10  QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 69

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +     + +  + Y     G +++         + +  I     +   + Q+  
Sbjct: 70  SEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEPQEAV 129

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
                 A V V             L E     G+  ++++        + 
Sbjct: 130 TVYEPLAKVEVPYSTGRFPTSRYCLVEMMPKTGRKHQLRRHMAHLRHPIV 179


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 79/234 (33%), Gaps = 39/234 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V      QR+   + R     SR  + ++I    V VNG  ++ A   +   + I V  
Sbjct: 1   MVTSGDQGQRLDHYLIRQLPEQSRSAIGKLIGAAHVLVNGQQVK-AGYRLHQDEIITVSF 59

Query: 64  ---------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                       +  +   E   L +  KP GLV   +   G  T+   L      + + 
Sbjct: 60  PPTPSLDLAPEKIDFSILFEDEHLLVIGKPPGLVVHPACGHGGGTLVHGLLYHCQDLPAL 119

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
                  V RLD +T G++L+       R L     + +  + Y         +++   L
Sbjct: 120 DAGRPGIVHRLDKDTSGVMLVAKSERSLRSLMADFKNRKIHKTYHALLLRSP-REREGRL 178

Query: 162 KKGIVIQGICYGDMQVTLDTQK-GSNAW------------VTVGLREGKNREIK 202
              I    +    M +  D  K  +  W            V +G+  G+  +I+
Sbjct: 179 VAPIGRHPVDRKKMAIRPDQGKYAATHWRVLESFINGWCLVEIGIETGRTHQIR 232


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 79/233 (33%), Gaps = 36/233 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
              I+      +R+  VI       SR ++++ + +  + VNG    +    V+  + +E
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVE 70

Query: 62  VDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------P 102
           ++   L                E   + +  KP+ ++      +   TV + L       
Sbjct: 71  INIELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQ 130

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL 160
               R   V RLD +T GL++          L  +L   +  R Y     G++ Q     
Sbjct: 131 DKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQG--T 188

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV----GLRE-----GKNREIK 202
           + + I         M +    ++    +  + V     L E     G+  +I+
Sbjct: 189 INQPIGRDPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIR 241


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 79/233 (33%), Gaps = 36/233 (15%)

Query: 3   DKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
              I+      +R+  VI       SR ++++ + +  + VNG    +    V+  + +E
Sbjct: 12  QNIIMHPKDAGKRIDVVINEQFEQFSRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVE 70

Query: 62  VDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------P 102
           ++   L                E   + +  KP+ ++      +   TV + L       
Sbjct: 71  INIELLPTNEWIAEDINLKIIFEDDDIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQ 130

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL 160
               R   V RLD +T GL++          L  +L   +  R Y     G++ Q     
Sbjct: 131 DKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLAERKVSRKYLAIVEGEIYQQG--T 188

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAW--VTV----GLRE-----GKNREIK 202
           + + I         M +    ++    +  + V     L E     G+  +I+
Sbjct: 189 INQPIGRDPTNRTKMAINYRGKEAITHYTPIEVYDGFTLIECQLETGRTHQIR 241


>gi|86146894|ref|ZP_01065213.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
 gi|85835346|gb|EAQ53485.1| pseudouridine synthase Rlu family protein [Vibrio sp. MED222]
          Length = 249

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 51/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  +     + +  + Y     G +++         + +  I     +   + Q+  
Sbjct: 67  SEVASEVMPMFANHEMQKTYHAIVRGWIEEGDTLDYALKVELDKIADKFAKEDKEPQEAV 126

Query: 186 N-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
                 A V V             L E     G+  ++++        + 
Sbjct: 127 TVYEPLAKVEVPYSTGRFPTSRYCLVEMMPKTGRKHQLRRHMAHLRHPIV 176


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 88/236 (37%), Gaps = 42/236 (17%)

Query: 5   NIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            +++E+    R+   I+       SR  ++++I    +KVNG + E+A   +   D IE+
Sbjct: 7   RVLEEDVDN-RLDLYISEQ-YEELSRSYIQKLIKDHHIKVNGKI-EKAKYMIKLGDEIEI 63

Query: 63  D------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
           +             +PL    E   + +  KP G+V   +  +   T+ + L        
Sbjct: 64  NLPQVEEVTIEPENIPLTIVYEDEDVIVVDKPQGMVVHPAPGNYSGTLVNALLFHCKNQL 123

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK 157
                  R   V R+D +T GLL++  +     +L          R Y     G + + +
Sbjct: 124 SDVNGPMRPGIVHRIDKDTSGLLVVAKNNAAHEILAEQFRAHTNTRKYHAIVVGNIREKE 183

Query: 158 -----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      ++ LK+ ++  G         L+  +    ++   L  G+  +I+
Sbjct: 184 AAVDAPIGRHPVDRLKRAVMNDGKHAVTHFKVLEVFRDFT-YIEAKLETGRTHQIR 238


>gi|118579004|ref|YP_900254.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118501714|gb|ABK98196.1| pseudouridine synthase, RluA family [Pelobacter propionicus DSM
           2379]
          Length = 306

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 83/237 (35%), Gaps = 41/237 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M  K  + +  + +R+ + ++   +    S+ E  R+I +    +NG ++  A+  V S 
Sbjct: 1   MIIKKTINDEVSGRRLDEALS--LLCDQVSKSEARRIIDRGGCNLNGSMVRVASRMVRSG 58

Query: 58  DHIEV--------DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           D I+V          + L +     E   L   +KP G+ T  +    + T+       F
Sbjct: 59  DTIDVGVMEPGRFRDLVLPQEALLHEDDDLIALNKPAGVNTQRTPYQLKGTLEYWASEYF 118

Query: 106 SRV------ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ-- 155
            R         + RLD  T G++L       A  L       Q  + Y     G   Q  
Sbjct: 119 RRQGNPEPARVIHRLDRGTSGVMLFPKHKRAAAWLSKRFHDGQVEKRYLALVSGTPGQIE 178

Query: 156 -------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
                   K+   + GIV  G      +  L  +    A V    +    G+  +I+
Sbjct: 179 WRVDGPIGKIASARYGIVAGGRSALT-EFRLLAESCGYALVEAKPLT---GRTHQIR 231


>gi|75676616|ref|YP_319037.1| pseudouridine synthase, RluD [Nitrobacter winogradskyi Nb-255]
 gi|74421486|gb|ABA05685.1| ribosomal large subunit pseudouridine synthase D [Nitrobacter
           winogradskyi Nb-255]
          Length = 351

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 76/260 (29%), Gaps = 69/260 (26%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKV----------NG-ILLERAAVNVMSTDHIEV 62
           R+ +V+A  +   SR  ++ +I    V +           G + +   A +V   D I +
Sbjct: 27  RLDRVLAVHSPDLSRSRLKSLILAGHVSIVKKASVAERTEGPVPVRDPAYHVAPGDTITI 86

Query: 63  D----------GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
                      G  +      E   L + +KP GLV   +      T+ + L +      
Sbjct: 87  HVPPAISAKPQGEAIALDIIYEDDDLIVINKPKGLVVHPAAGHHTGTLVNALIAHCGETL 146

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQV 153
                  R   V RLD +T GL++   +    + L        R       Y     G  
Sbjct: 147 SGIGGVCRPGIVHRLDKDTTGLMVAAKNDAAHKSLGAQFADHGRTGAMRRGYLAFVWGLP 206

Query: 154 DQDKLNLLKKGIV---IQGICYGDMQ--VTLDTQKGSNAW-----------------VTV 191
           ++        G V   I    Y   +  V    ++    W                 +  
Sbjct: 207 NR------SHGTVDAPIDRHPYAREKMAVRAGGREAITHWEVRQAFNGRDGKPVAALLAC 260

Query: 192 GLREGKNREIKKVFEFFNWK 211
            L  G+  +I+         
Sbjct: 261 QLATGRTHQIRVHLAHVGHP 280


>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 = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 87/240 (36%), Gaps = 32/240 (13%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K  + +N   +R+ K IA      SR ++++ I   +VKVN I +     N+   + I++
Sbjct: 10  KTCISQN--GKRLDKSIAEIFPEYSRNKIKKFIINNQVKVNDICIINPKKNIKGGECIKI 67

Query: 63  ----DGVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                   + K  +T   +Y        +K   ++         +T+  ++   +     
Sbjct: 68  KISKKNNLISKKRKTYKLIYEDDDILVINKYKDVIVHPGCDKHENTLLHDILFNYPDSKN 127

Query: 107 --RVISVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVYRVRF------HGQVDQD 156
             R   V RLD +T GL+L+  +       +  L      R YR          G V   
Sbjct: 128 LYRAGIVHRLDKDTTGLMLIARNSFSQKKLIKLLKLRLINREYRAVLLGKIICDGTVSAP 187

Query: 157 KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   K    ++    G   +T   +       ++V + L  G+  +I+    + N  V 
Sbjct: 188 IIRNSKNRTRMKVHISGKESITHYKIIKNFNDFSYVKINLESGRTHQIRLHMSYINHPVL 247


>gi|317012555|gb|ADU83163.1| hypothetical protein HPLT_03755 [Helicobacter pylori Lithuania75]
          Length = 327

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 55/309 (17%), Positives = 106/309 (34%), Gaps = 55/309 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKGVKKGGLALKEGDEITLLTPQITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLESKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHAHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           N LK  I ++       +       +L T + +   +   L  G+  +I+          
Sbjct: 193 NRLKM-IALKATKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL---- 244

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L R   G   L  L       + K+ +R  L  +L+E      +  +     L++D  
Sbjct: 245 EYLNRHIIGD-NLYGLNQ----ALFKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDML 299

Query: 273 NIISEVPDD 281
             + +V D 
Sbjct: 300 EYLKKVFDK 308


>gi|229530008|ref|ZP_04419398.1| tRNA pseudouridine synthase C [Vibrio cholerae 12129(1)]
 gi|229333782|gb|EEN99268.1| tRNA pseudouridine synthase C [Vibrio cholerae 12129(1)]
          Length = 244

 Score = 66.0 bits (160), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASDVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|288925171|ref|ZP_06419106.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|288337936|gb|EFC76287.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
          Length = 358

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 77/245 (31%), Gaps = 50/245 (20%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            P R+ K +       SR  ++       ++VNG  ++     V   D + +        
Sbjct: 35  APVRIDKFLTEKNPHQSRNRIQSAADAGFIRVNGRPVKS-NYKVRPGDVVTLMLDRPKHD 93

Query: 63  -----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DN--LPSIFS 106
                + +PL    E   L + +KP G+V      +   T+         D     +   
Sbjct: 94  TSIVPEDIPLAVVYEDDGLMVINKPAGMVVHPGAGNFTGTLINAVAYYLKDLPTFDANSP 153

Query: 107 RVISVGRLDINTEGLLLL-------TNDGG-LARVLELPSTQWLRVYRVR---------F 149
            V  V R+D +T GLL++       T  G          S        V           
Sbjct: 154 EVGLVHRIDKDTSGLLVVAKTPEAKTCLGKQFFNKTTHRSYNA----LVWGNIVDDEGRI 209

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFE 206
            G + +D  N L+  +   G   G   VT   +  + G    V   L  G+  +I+   +
Sbjct: 210 EGNIARDPRNRLRMKVFAPGSGIGKSAVTHYRVLERFGYTTLVECRLETGRTHQIRAHMK 269

Query: 207 FFNWK 211
                
Sbjct: 270 HIGHP 274


>gi|260776531|ref|ZP_05885426.1| tRNA pseudouridine synthase C [Vibrio coralliilyticus ATCC BAA-450]
 gi|260607754|gb|EEX34019.1| tRNA pseudouridine synthase C [Vibrio coralliilyticus ATCC BAA-450]
          Length = 241

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 27/195 (13%), Positives = 55/195 (28%), Gaps = 42/195 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 8   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIFALS 67

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------------- 170
             +A  +     + + ++ Y     G +++         + +  I               
Sbjct: 68  SDVASQVMPMFANHEMVKTYHAIVRGWIEEAGRLDYALKVELDKIADKHASQEKEAQEAI 127

Query: 171 ----CYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN-------- 213
                    ++   T K         L E     G+  ++++        +         
Sbjct: 128 TDYHTLAKAEIPYSTGKFPTTRY--CLMELKPLTGRKHQLRRHMAHLRHPIVGDTTHGDG 185

Query: 214 ---RLIRISYGPFQL 225
              +L R  Y   +L
Sbjct: 186 KHNKLFREVYDSHRL 200


>gi|255311484|ref|ZP_05354054.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 6276]
          Length = 335

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 43/183 (23%), Positives = 72/183 (39%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           ++ E  T  R+ K +++  G  SR   ++ I   RV+VNG +  R +  +   D +EV  
Sbjct: 15  VIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEVEL 73

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                      + +PL K  E   + + +KP  +V   +    + TV   L         
Sbjct: 74  IEEKEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLK 133

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ 155
              P    R   V RLD +T G LL+T     A+ L      + Q  ++Y         Q
Sbjct: 134 QEFPEEPWRPGIVHRLDKDTSG-LLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQ 192

Query: 156 DKL 158
           + +
Sbjct: 193 ELI 195


>gi|121728338|ref|ZP_01681368.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
 gi|121629393|gb|EAX61823.1| pseudouridine synthase Rlu family protein [Vibrio cholerae V52]
          Length = 244

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPIATGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|238763986|ref|ZP_04624942.1| tRNA pseudouridine synthase C [Yersinia kristensenii ATCC 33638]
 gi|238697803|gb|EEP90564.1| tRNA pseudouridine synthase C [Yersinia kristensenii ATCC 33638]
          Length = 257

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 57/186 (30%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L L     Q  + Y     G V +         ++L+ +               
Sbjct: 67  SDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDKIADKFSRPDKAPQPSV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  QV +    G        L E     G+  ++++        +        G  
Sbjct: 127 THYHALAQVEVPIAIGRYDTARFSLMELKPETGRKHQLRRHMAHIRHPI-------IGDS 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|188495145|ref|ZP_03002415.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           53638]
 gi|188490344|gb|EDU65447.1| ribosomal large subunit pseudouridine synthase E [Escherichia coli
           53638]
          Length = 104

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 40/64 (62%), Gaps = 2/64 (3%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + TR+ L++KP  ++   +D  GR T+ + +P     V + GRLD ++EGLL+LTN+G L
Sbjct: 37  QPTRVILFNKPYDVLPQFTDEAGRKTLKEFIP--VQGVYAAGRLDRDSEGLLVLTNNGAL 94

Query: 131 ARVL 134
              L
Sbjct: 95  QARL 98


>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 = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 86/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I +  V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRIGNLIEEGGVFLDGQQVSRASVRVTAGQMLDVDLS 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVSTPSITPQIVEGMRIVHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
              +  R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGLLERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRAVDKVYLALVQGHPDPFAG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AVKHPC 247


>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 = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 36/223 (16%), Positives = 76/223 (34%), Gaps = 32/223 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRK---------AERTRL 75
           SR  V+ ++ + +V V+  +  +    +     + +  +   +++          E   +
Sbjct: 38  SRNSVKSILTRGQVSVDDHIETKHNFMLNKGSTVRILKNKAAIQQDVFVGMSIMYEDDDI 97

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
            +  K  GL++  ++ + + T    L           RV  V RLD +T G+++   +  
Sbjct: 98  IVIEKESGLLSIATEKERKHTALHQLMHYVKQQHPANRVYVVHRLDKDTSGVMMFAKNER 157

Query: 130 LARVLELPSTQW--LRVYRVRFHGQVDQDK------------LNLLKKGIVIQGICYGDM 175
           + R L+         R Y     GQV ++K              +    +   G      
Sbjct: 158 VKRKLQNNWKDIVKERTYVALVEGQVAKEKGYIVSWLKESATRKMYSSRVKNDGQRAATR 217

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
              L T     + + + L  G+  +I+   E     V    R 
Sbjct: 218 YRVLQT-NNRYSLLELQLETGRKNQIRVHMEELGHPVVGDKRY 259


>gi|256831089|ref|YP_003159817.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580265|gb|ACU91401.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 245

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 44/201 (21%), Positives = 68/201 (33%), Gaps = 29/201 (14%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGR-STVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGG 129
              L   HKP GL+   +   GR   +   L      R+  V RLD  T GL+++     
Sbjct: 15  DEHLIAVHKPAGLLVHRNAHAGREPFLLQILRDQLGQRLYPVHRLDRPTSGLMIMALSPQ 74

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKL--NLLK------KGIVIQGICYGDMQVTL 179
            A  L L   S +  + Y     G V    L  + LK      +    +       ++  
Sbjct: 75  AAHALALQFASQEVHKTYLAVTRGFVPPQGLIDDALKSESGSLQEARTEFTRLATAEIPH 134

Query: 180 DTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                     + V V  R G+  +I++ F      +             G +L G  R+ 
Sbjct: 135 PVGPNPTARYSMVRVRPRTGRTHQIRRHFAHIRHPLI------------GDVLRGDGRQ- 181

Query: 237 SKKILREQLGPHLLEEAQVNL 257
             +  R+  G H L  A V L
Sbjct: 182 -NRFFRDHFGLHRLLLASVEL 201


>gi|227833472|ref|YP_002835179.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
 gi|227454488|gb|ACP33241.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
          Length = 307

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 80/241 (33%), Gaps = 41/241 (17%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++     V E     RV   +A+    SR  V ++ A   V+++G  + + +  + +  
Sbjct: 1   MRESRRLPVPEGLDGMRVDAALAKLLGISRARVSQLCAAGDVEIDGAAVGK-SERLNAGG 59

Query: 59  HIEVD----GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLP- 102
            I+V       PL   E              +    KP+G+    +      TV   L  
Sbjct: 60  WIDVMMPAPEEPLIPKEELVEGMDVLYADEDIICVCKPVGVAAHPTLGWDGPTVIGGLRA 119

Query: 103 --------SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
                       R   V RLD+ T G++++         L+         + Y     G 
Sbjct: 120 AGYALADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKNAFRERTVQKTYHAVVQGL 179

Query: 153 VDQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D     ++           K G+V  G         L+  + + + + V L  G+  +I
Sbjct: 180 PDPIVGTIDAPIGRHPSAGWKFGVVDDGKPAVTHYKLLEAFREA-SLLEVHLETGRTHQI 238

Query: 202 K 202
           +
Sbjct: 239 R 239


>gi|148656758|ref|YP_001276963.1| pseudouridine synthase [Roseiflexus sp. RS-1]
 gi|148568868|gb|ABQ91013.1| pseudouridine synthase [Roseiflexus sp. RS-1]
          Length = 299

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 69/213 (32%), Gaps = 40/213 (18%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DG---VPLRKAERT 73
           A  G A+  E   +IA+  V V+G+ +    + + +   I V    DG    P+   E  
Sbjct: 20  AALGDAT--EALWLIARGGVWVDGVRVRDPGMRLPADATIVVQRPPDGIYREPVVTPEMI 77

Query: 74  RL-----WLYHKPIG--LVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGL 121
                     +KPI   +  T  D +G                   +    RLD +T G+
Sbjct: 78  LYEDDDLIALNKPIDTYVEATPWDAEGHLRAALARFLALRNGTAPPLHLAHRLDRDTSGV 137

Query: 122 LLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           LL++    +   L+         + Y     G    D++ +       +G  +       
Sbjct: 138 LLISKTPDVNAALQRVFRDGAAHKTYLAICAGLPSFDEIEIETGHGRGRGGMFRVFPPEA 197

Query: 180 DTQKGSNAWVTVGLREG--------KNREIKKV 204
             +          L +G        + R ++++
Sbjct: 198 IGR---------TLPQGGTVKSMRTRFRVVRRL 221


>gi|331701048|ref|YP_004398007.1| RluA family pseudouridine synthase [Lactobacillus buchneri NRRL
           B-30929]
 gi|329128391|gb|AEB72944.1| pseudouridine synthase, RluA family [Lactobacillus buchneri NRRL
           B-30929]
          Length = 296

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 33/207 (15%), Positives = 65/207 (31%), Gaps = 35/207 (16%)

Query: 38  QRVKVNGI--LLERA-----AVNV-----MSTDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            +  VNG   L+ R       V V        DH+ V  VP+    E     + +KP G+
Sbjct: 38  GKTLVNGEASLVNRMLQTGDTVKVVLPPEPENDHVGVSNVPIEIVHEDPNFLVVNKPYGV 97

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVLELP 137
            +  +  +   ++ + +   + R       +  V RLD +T GL++       A  +   
Sbjct: 98  ASVPA-HNHVDSLVNRVKGYYQRQGYANQKIHIVTRLDKDTSGLVIFAKH-HFAHSVLDK 155

Query: 138 STQ---WLRVYRVRFHGQVDQDKLNL----------LKKGIVIQGICYGDMQVTLDTQKG 184
             +     + Y     G++      +            K  V+        +     +  
Sbjct: 156 QLKDRTIQKTYLAIVAGRISMPHFEIYLPIGRADDSFVKRQVVDSGKMSVTEAWTVRRLA 215

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWK 211
               + V L  G+  +I+         
Sbjct: 216 KQTLLKVRLHTGRTHQIRVHMAAIGHP 242


>gi|323498626|ref|ZP_08103618.1| tRNA pseudouridine synthase C [Vibrio sinaloensis DSM 21326]
 gi|323316324|gb|EGA69343.1| tRNA pseudouridine synthase C [Vibrio sinaloensis DSM 21326]
          Length = 241

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 48/172 (27%), Gaps = 31/172 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------------- 170
             +A  +     + +  + Y     G +++         + +  I               
Sbjct: 67  SEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQDKEAQEAV 126

Query: 171 ----CYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                    +V   T K         L E     G+  ++++        + 
Sbjct: 127 TDYRPLAKAEVPHSTGKFPTTRY--CLMEMKPLTGRKHQLRRHMAHLRHPIV 176


>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 = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 78/236 (33%), Gaps = 56/236 (23%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--------------- 58
           QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D               
Sbjct: 16  QRIDKLISCALEISRNRAQGLIAGGQVTISGRVINDNSYLTKTGDVYTIVTAVQKPSTLS 75

Query: 59  -------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                   +  +   +   ++      H   G+       +  +     L    + + SV
Sbjct: 76  PNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGI-------EHHTITNALLARFGAGLQSV 128

Query: 112 G---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
           G         RLD +T GL++          L  EL +  + + Y     G         
Sbjct: 129 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 188

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIK 202
               +V +  + +++      G      +  ++ + G   + +   L  G+  +I+
Sbjct: 189 HTNIRVKRSDITMMEAANS--GGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIR 242


>gi|262165137|ref|ZP_06032874.1| tRNA pseudouridine synthase C [Vibrio mimicus VM223]
 gi|262024853|gb|EEY43521.1| tRNA pseudouridine synthase C [Vibrio mimicus VM223]
          Length = 244

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G ++          ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEDADVLDYPLKEELDKIADKFAKQDKEAQSAI 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|308062067|gb|ADO03955.1| hypothetical protein HPCU_03975 [Helicobacter pylori Cuz20]
          Length = 327

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 105/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHAHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D      +V D 
Sbjct: 297 DMLEYFKKVFDK 308


>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 = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 79/250 (31%), Gaps = 53/250 (21%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRKAERTR 74
           +ASR E E  I   ++ VNG  +      +   D I+           +   L+  E   
Sbjct: 63  VASREEYEEKIRNGKIIVNGRKI-PVDYRIGPLDSIKHICTRIEAPVFNKPLLKLGETDN 121

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
              Y KP  +          +++   LP     +  V RLD  T G+++   +   A   
Sbjct: 122 YVAYLKPASVTVNTVGGYFYNSMVKRLP---PHLHVVHRLDRVTSGIIVFAKNKAAATNF 178

Query: 135 E--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQKGSNA 187
              L   +  + Y  R  G           KG +I     G        V   T K S  
Sbjct: 179 NQYLVGEKVSKTYIARVIG--------RFPKGEIICDQPLGTDFNLHRTVVTPTGKPSKT 230

Query: 188 WVTV-------GLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +        + E     G+  +I+   ++  +           P     +  G  RE
Sbjct: 231 IFKLLKTNGKESIVEAHPITGRTHQIRCHLQYLGY-----------PITNDEMYGGK-RE 278

Query: 236 VSKKILREQL 245
           V  K +++ L
Sbjct: 279 VYTKEMKDAL 288


>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 = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 1/60 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+++  G+ SRREVE +I + RV +NG      +  V   D +E+DG  L   +  R
Sbjct: 4  RINKLLSDTGLGSRREVEALIEEGRVWINGDRA-ELSDVVSEDDVVELDGEELPVRDLLR 62


>gi|229525503|ref|ZP_04414908.1| tRNA pseudouridine synthase C [Vibrio cholerae bv. albensis VL426]
 gi|229339084|gb|EEO04101.1| tRNA pseudouridine synthase C [Vibrio cholerae bv. albensis VL426]
          Length = 245

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASDVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|238796600|ref|ZP_04640107.1| tRNA pseudouridine synthase C [Yersinia mollaretii ATCC 43969]
 gi|238719578|gb|EEQ11387.1| tRNA pseudouridine synthase C [Yersinia mollaretii ATCC 43969]
          Length = 257

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 59/186 (31%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLL--T 125
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+  +
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
           +D   A  L+L   Q  + Y     G V +         ++L+ +               
Sbjct: 67  SDVARALSLQLEQHQMQKTYHAVVRGYVLEGGTVDYEMTEELDKIADKFSRPDKAPQPSV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  QV +    G        L E     G+  ++++        +        G  
Sbjct: 127 THYLPLAQVEVPVAIGRYETARFSLVELKPETGRKHQLRRHMAHIRHPI-------IGDS 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|86137869|ref|ZP_01056445.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           MED193]
 gi|85825461|gb|EAQ45660.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           MED193]
          Length = 346

 Score = 66.0 bits (160), Expect = 9e-09,   Method: Composition-based stats.
 Identities = 48/277 (17%), Positives = 92/277 (33%), Gaps = 67/277 (24%)

Query: 6   IVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           I+ E+  P+R+ K +     A A + SR  + R+I    + V+G++++ A   V     I
Sbjct: 9   IIAEDP-PKRLDKAVSRDVPAEATL-SRTRLARLIEAGSLTVDGVVVQDAKARVAEGAVI 66

Query: 61  EV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS 106
            +            + + L    E   L + +KP G+V   +      T+ +  L     
Sbjct: 67  TITVEEAEDSHIGPEDIALDVIFEDDDLIVINKPSGMVVHPAPGTPSGTLVNALLHHCGE 126

Query: 107 RVISVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            +  VG         R+D  T GLL++       + L          R YR   +G  D 
Sbjct: 127 NLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFEKHTVERYYRAICYGVPDA 186

Query: 156 DK---------------LNLL------------KKGIVIQGICYGDMQVTLDTQKGSN-- 186
           +                +  L            ++ ++ QG  +   +  +    G+   
Sbjct: 187 NDPRLRGVKGTSFEPGNILKLTTQLARHKHDRQRQAVLFQGGRHAVTRARIVEPFGAPPV 246

Query: 187 -AWVTVGLREGKNREIK-KVFEF----FNWKVNRLIR 217
            A +   L  G+  +I+  +                R
Sbjct: 247 VALIECWLETGRTHQIRVHMTHAGHGLVGDPTYGGKR 283


>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 = 66.0 bits (160), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 83/236 (35%), Gaps = 44/236 (18%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVIA      SR +++ ++  + + VN    E+ +  V + D I++   P +     
Sbjct: 15  RLDKVIAEKLKDLSRTKIKELVNDKNILVNHK-AEKVSYKVQAGDSIDITVPPAKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVIS 110
                     E   + + +KP G+V   S      T+ + L          P  F R   
Sbjct: 74  AQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTHELADSPEGF-RPGI 132

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD-------------Q 155
           V R+D +T GLL++  +      LE  L      R Y    HG  +              
Sbjct: 133 VHRIDKDTSGLLMVAKNDKARESLEKQLAEKINKREYLAIVHGNFETKNGVIDAPIGRNP 192

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +    +   +  +G        T+  Q    + V   L  G+  +I+   ++    
Sbjct: 193 NNRKQMA--VNPKGKAAVTHF-TVLEQFKDYSLVKCILETGRTHQIRVHMKYIGHP 245


>gi|317178897|dbj|BAJ56685.1| hypothetical protein HPF30_0588 [Helicobacter pylori F30]
          Length = 327

 Score = 66.0 bits (160), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 52/313 (16%), Positives = 106/313 (33%), Gaps = 63/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKIAPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GFDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFF 208
            N LK  I ++       + +  ++    + +T       +   L  G+  +I+      
Sbjct: 192 NNRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL 244

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
                 L R   G   L  L       + K+ +R  L  +L+E      +  ++    L+
Sbjct: 245 ----EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLHFKVPLL 295

Query: 269 RDRPNIISEVPDD 281
           +D    + +V D 
Sbjct: 296 KDMLEYLKKVFDK 308


>gi|157374654|ref|YP_001473254.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317028|gb|ABV36126.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 282

 Score = 66.0 bits (160), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 57/156 (36%), Gaps = 17/156 (10%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTN 126
           A+  +  L++KP G++   S     +T+     +  +       + RLD    GL+L+ +
Sbjct: 87  ADEGQYSLWYKPYGMLCQGSKWGDHTTINRYAETHLAPDRPAFIIHRLDRAATGLVLIGH 146

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD------MQVT 178
                  L          + Y+V   G      ++ L   + I     G        Q+ 
Sbjct: 147 SKKTTAALAKLFELRLLDKYYQVIVEGHFSNHGVDEL---VTIDSEVDGKPARSHAKQLK 203

Query: 179 LDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
            D ++ + + V V +  G+  +I+  +     + V 
Sbjct: 204 YDPEQ-NRSLVQVKIESGRKHQIRIHM-ASIGYPVV 237


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 58/170 (34%), Gaps = 31/170 (18%)

Query: 15  RVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+   +A    G  SR  ++ +I Q  V +NG  +      V   D +E+          
Sbjct: 24  RIDVWLAGEVGGDLSRSRLKALIEQGAVLLNGTPVTEPKKKVHPHDRVEIVMPEPEDPEP 83

Query: 63  --DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVI 109
             + +PL    E   L +  KP GLV      +   T+ + L               R  
Sbjct: 84  KGEDIPLDVEYEDDDLIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIGGVKRPG 143

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQV 153
            V RLD  T G++++  +    R L        R       Y+    G+ 
Sbjct: 144 IVHRLDKETSGVMVVAKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRP 193


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 79/240 (32%), Gaps = 36/240 (15%)

Query: 11  FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
              +R+ + +      +R EV++ I    V +    +  +  +V   D I          
Sbjct: 12  DEGKRLDQFLKERTGLTRSEVQKWIKAGNVSLLPKKMIHSNYHVSEGDRISFFWEEKKKQ 71

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVG---- 112
                 +PL    E   + + +K  G+V      +   T+ +  L     ++ SVG    
Sbjct: 72  ELIGQNIPLDILYEDNDMIVINKRRGVVVHPGAGNTEGTLVNALLFHCGEQLRSVGDPER 131

Query: 113 -----RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVD 154
                RLD +T G+++         +L  E+ S +  R Y    HG            + 
Sbjct: 132 PGIVHRLDKDTSGVMVAAKSERAYGILQKEIASHKAQRCYIALVHGQMEGDTGVIRLPLG 191

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           +   + +K  ++ +          +       +W+   L  G+  +I+         V  
Sbjct: 192 RSTKDRMKWDVLHETGRPAVTHFHVIEYLPHYSWIECKLETGRTHQIRVHMAHIRHAVVN 251


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            VQ +   QR+ + +A      SR  ++  I +  V VNG++       V   + IE+  
Sbjct: 9   TVQSHQMGQRLDQTLAELFPDYSRSCLKTWIEEDLVLVNGVVQNVPRSKVYGDEQIEITV 68

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                     + +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 69  EIEDETRFEPENIPLNIVYEDDDILVINKPKDLVVHPGAGNPSGTVLNALLYHYPPIAEV 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L       +  R Y     G +        K 
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKITREYEAVACGIMT-------KG 181

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
           G+V + +     + T                +  +      + + L  G+  +I+
Sbjct: 182 GMVDEPMARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIR 236


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 80/235 (34%), Gaps = 45/235 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            VQ +   QR+ + +A      SR  ++  I +  V VNG++       V   + IE+  
Sbjct: 9   TVQSHQMGQRLDQTLAELFPDYSRSRLKTWIEEDLVLVNGVVQNVPRSKVYGDEQIEITV 68

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                     + +PL    E   + + +KP  LV      +   TV + L   +      
Sbjct: 69  EIEDETRFEPENIPLNIVYEDDDILVINKPKDLVVHPGAGNPSGTVLNALLYHYPPIAEV 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GL+++         L       + +R Y     G +        K 
Sbjct: 129 PRAGIVHRLDKDTTGLMVVAKTIPAQTQLVRDLQKRKIIREYEAVACGIMT-------KG 181

Query: 164 GIVIQGICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
           G V + +     + T                +  +      + + L  G+  +I+
Sbjct: 182 GTVDEPMARHPTKRTHMAVHPMGKPAVTHYRIMERFRDYTRLRLRLETGRTHQIR 236


>gi|145631295|ref|ZP_01787067.1| SfhB [Haemophilus influenzae R3021]
 gi|144983080|gb|EDJ90580.1| SfhB [Haemophilus influenzae R3021]
          Length = 324

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/228 (16%), Positives = 76/228 (33%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     +R+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGERLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   + + +KP  LV      +   TV + L   +  ++   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
               V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +     +   +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRILMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 48/313 (15%), Positives = 102/313 (32%), Gaps = 64/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-----EVDGVPLRK 69
           R+ + +A+    S+ +   +I +  V      +++  + +   D I     ++   PL++
Sbjct: 13  RIDEFLAKELQISKNQALSLIKEGLVFCQKKEVKKGGLALKEGDEIALLTPKIAPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L +            R   V
Sbjct: 73  ELDLEIEVIFEDDDLLVLNKPPNLVVHKAPSVKEPTLVDWLEAKNYQLSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
            RLD +T G +++  +     V      +     R Y       + +      ++ I ++
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVYLSEQLKTKTMGRYYIALLSTPLSRK-----EEKISVE 186

Query: 169 -------GICYGDMQVTLDTQKGSNAWVT--VG-----------LREGKNREIKKVFEFF 208
                        M +  +  + S +  T  +            L  G+  +I+      
Sbjct: 187 CYLTRNPNNRLKMMAIKKEKSRYSKSEFTSLLTSQNNLNLIGAKLYTGRTHQIR------ 240

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
              +  L R   G   L  L       + K+ +R  L  +L+E      +  +     L+
Sbjct: 241 -VHLEYLNRHIIGD-NLYGLNE----ALPKEEIRIMLHAYLIEFKHPKSEQKLCFKVPLL 294

Query: 269 RDRPNIISEVPDD 281
           +D    + +  D 
Sbjct: 295 KDMLEYLKKFFDK 307


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 69/199 (34%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S  E + +I    V   G  +   RA +NV +   ++    P    E   L
Sbjct: 8   KILAMQLNISNNEAKDLIDSGLVFAKGQKVAIARALMNVNTKFSVQETSKPSVIFEDENL 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   +T+               S   +   + RLD  T G+LLL  +   A+   
Sbjct: 68  LAINKPA-FITSEK------------ISQMYKFPLLHRLDKETSGVLLLVKNEEFAKRAI 114

Query: 136 LPSTQ--WLRVYRVRFHGQVDQDK------LNLLKKGIVI----QGICYGDMQVTLDTQK 183
                    ++Y     G + ++       L +  KG  I    +        VT     
Sbjct: 115 EEFKHMRVEKIYIAAVRGILSEETRVSEPILTIKSKGAAISKISKDGKEAVSDVTPLMVV 174

Query: 184 GSNAWVTVGLREGKNREIK 202
           G    V V ++ G+  +I+
Sbjct: 175 GKKTLVKVAIKTGRTHQIR 193


>gi|294905868|ref|XP_002777696.1| Ribosomal large subunit pseudouridine synthase E, putative
           [Perkinsus marinus ATCC 50983]
 gi|239885587|gb|EER09512.1| Ribosomal large subunit pseudouridine synthase E, putative
           [Perkinsus marinus ATCC 50983]
          Length = 85

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 32/67 (47%)

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
            GRLD +  GLL+ T DG +A+ +    +     Y V        D++++L +G++I G 
Sbjct: 10  AGRLDSDCSGLLVYTQDGRIAKAISDRYSSIPMEYEVALKAPCTDDQMSMLSQGMLIDGK 69

Query: 171 CYGDMQV 177
                + 
Sbjct: 70  QVEGCEA 76


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/229 (19%), Positives = 78/229 (34%), Gaps = 43/229 (18%)

Query: 15  RVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           RV K +     G A+R  ++       + VN   ++     V   D + V          
Sbjct: 45  RVDKFLVDRMMG-ATRNRIQLAAEAGCILVNDKPVKS-NYRVKPLDVVSVVMDRPRRELE 102

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRV 108
              + +PL    E   L + +KP GLV      +   T+ +                 R+
Sbjct: 103 IIPEDIPLNIVYEDDDLLVVNKPAGLVVHPGHGNYTGTLVNALAYYLKDDPYYDPSDPRL 162

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK--------- 157
             V R+D +T GLL++         L L   +    R YR    G V +D+         
Sbjct: 163 GLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKRKYRALVWGIVQEDEGRIEGNIGR 222

Query: 158 --LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
              + ++  +  +G          T+  + G  + V   L  G+  +I+
Sbjct: 223 DPRDRMQMTVFPEGDQGKTAVTHYTVLERLGYVSLVECRLETGRTHQIR 271


>gi|191637795|ref|YP_001986961.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|301065920|ref|YP_003787943.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|190712097|emb|CAQ66103.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|300438327|gb|ADK18093.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
 gi|327381861|gb|AEA53337.1| Uncharacterized RNA pseudouridine synthase yhcT [Lactobacillus
           casei LC2W]
 gi|327385023|gb|AEA56497.1| Uncharacterized RNA pseudouridine synthase yhcT [Lactobacillus
           casei BD-II]
          Length = 300

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 84/235 (35%), Gaps = 41/235 (17%)

Query: 13  PQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P +++  + + G  SR +++++      V VN       A  V S D I V   P   A+
Sbjct: 11  PLKLAAFLKQQGF-SRAQLKKLRYQGGFVFVN-KRQRHTAYPVRSGDRILVQTAPEHAAD 68

Query: 72  RTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVIS 110
                              + +KP G+ +  +     +++ + + +           V  
Sbjct: 69  SVVPYSHDLAISYEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIKTKAESQAVHV 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRF--------HG----QVDQ 155
           V RLD +T GL++    G LA  L    L S  +++ Y            HG     +  
Sbjct: 129 VTRLDRDTSGLMVFAKHG-LAHSLLDQQLHSQDFVKQYVAIVTAQTPLATHGWIVLPIGV 187

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                +++ +   G        TLD Q  + A + V L  G+  +I+  F     
Sbjct: 188 SDGFYMRRVVTDTGKASVTEYRTLD-QNKAGAMMLVTLHTGRTHQIRVHFAAIGH 241


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 81/245 (33%), 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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVIS 110
                       +P+    E   L + +KP G+V   +  +   T+ +  L     R+ S
Sbjct: 67  PEPQELKAEPQDIPIDIVYEDDALLVVNKPKGMVVHPAAGNPDGTLVNALLYHCKGRLSS 126

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG-------- 151
                    V R+D  T GLL++         L     +    R Y     G        
Sbjct: 127 INGVIRPGIVHRIDKFTSGLLMVAKTDKAHNSLAAQIKEHSFTREYNAVCVGRFKEPTGT 186

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               + + K +  K  +  Q          +  + G  + V   L  G+  +I+    F 
Sbjct: 187 INEPIGRSKFDRKKMCVTYQNSKEAVTHYEVIEELGQYSLVRFRLETGRTHQIRVHSAFI 246

Query: 209 NWKVN 213
              V 
Sbjct: 247 GHPVL 251


>gi|94987157|ref|YP_595090.1| pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
 gi|94731406|emb|CAJ54769.1| Pseudouridylate synthases, 23S RNA-specific [Lawsonia
           intracellularis PHE/MN1-00]
          Length = 321

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 64/234 (27%), Gaps = 72/234 (30%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV---------------------DGVPLRK-- 69
           R I   + ++NG  +      V   D I +                     D  P+    
Sbjct: 38  RWIRTGQTRINGKRVT-PFTIVNFKDKIRIPPFAYEYKKKDLTTSLIHNQYDISPISSHT 96

Query: 70  --------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR----VISVGRLDIN 117
                   A      +++KP GL           ++   L   ++        V RLD +
Sbjct: 97  TSPLPPVIAHSPEFIIFYKPAGLAVHGGTGQ-TDSLAHRLSQHYAHSTFMPTPVHRLDKD 155

Query: 118 TEGLLLLT---NDGGLARVL-ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
           T GLLL+    N       L    STQ  + Y     G           + I ++ I   
Sbjct: 156 TSGLLLVAKTYNSLRYFSELFASHSTQLTKEYLAWVVGICP------WTQPICLEDILTK 209

Query: 174 DMQ-------------------------VTLDTQKGSNAWVTVGLREGKNREIK 202
             +                         V    Q    + + + L  G+  +I+
Sbjct: 210 KQKQDNYSRLNSYQNKLQQTSAQKASLTVRCIKQYKDKSLLLIKLHTGRTHQIR 263


>gi|71280552|ref|YP_270573.1| 23S rRNA pseudouridine synthase D [Colwellia psychrerythraea 34H]
 gi|71146292|gb|AAZ26765.1| ribosomal large subunit pseudouridine synthase D [Colwellia
           psychrerythraea 34H]
          Length = 324

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/153 (21%), Positives = 55/153 (35%), Gaps = 21/153 (13%)

Query: 27  SRREVERMIAQQRVKVNGILL----------ERAAVNVMSTDHIEVDGVPLR---KAERT 73
           SR  ++  I   +VKVNG +L          E   +N      I  +   +      E  
Sbjct: 32  SRSRIKDWILAGQVKVNGDVLLIPREKMYGGEEIDINAKVEAEIRFEAQNIPLNIVYEDD 91

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGRLDINTEGLLLLTND 127
            + + +KP GLV      +   T+ + L   +  +        V RLD +T GL+++   
Sbjct: 92  YILVINKPAGLVVHPGAGNPDGTLLNALLHHYPALNVVPRAGIVHRLDKDTTGLMVVAKT 151

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL 158
                 L   L   +  R Y    +G +    L
Sbjct: 152 IAAQTNLVDALQLREITREYEAVANGVMTAGGL 184


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 89/247 (36%), Gaps = 50/247 (20%)

Query: 1   MKDKNI---VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK KN    +       R+ K + ++    SR   ++ I  +RV VN  +  + A  ++ 
Sbjct: 1   MKSKNTLLFIVNETNRDRLDKFLVSQNPEYSRAFYQQHILDERVTVNEQVQTKVATQLVP 60

Query: 57  TDHI-------------EVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL- 101
            D +               + +PL K  E   + + +KP  +V   +    R TV   L 
Sbjct: 61  GDSVSIIIEEKEELLELLPEAIPLDKVYEDEMILVINKPRDMVVHPAPGHIRGTVVHALL 120

Query: 102 -----------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRV 147
                      P    R   + RLD +T G LL+T     A+ +      + Q  + Y  
Sbjct: 121 HEIGERLKQEFPEEPWRPGIIHRLDKDTSG-LLITAKTRQAKTIYSELFATKQLKKSYLA 179

Query: 148 RFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGSNA--------WVTVGLR--E- 195
              G+     ++  L +          +M V+L  ++             +++ L   E 
Sbjct: 180 ICVGKPTATLIHTKLAR----HHSKRKEMAVSLTGKEAITHCEVLAYNGKLSLVLLRPET 235

Query: 196 GKNREIK 202
           G+  +++
Sbjct: 236 GRTHQLR 242


>gi|229513013|ref|ZP_04402479.1| tRNA pseudouridine synthase C [Vibrio cholerae TMA 21]
 gi|229349906|gb|EEO14860.1| tRNA pseudouridine synthase C [Vibrio cholerae TMA 21]
          Length = 245

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/170 (15%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +  L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKAELPISTGKFATTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/211 (14%), Positives = 74/211 (35%), Gaps = 27/211 (12%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ERTRL 75
           K+++     S  E + +I +  V + G  L+ A   +    H ++  +P  K   +   +
Sbjct: 29  KLLSAQEGISHNEAKNLIDRGLVTIQGKKLKIARALLSPNTHFKIQQLPPIKIIFQDENI 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  L +            + +  ++ +   + RLD  T G+LLL  +     +  
Sbjct: 89  LALSKPAFLTS------------EEIVKLYPQWALLHRLDKETSGVLLLIKENSPFHLKA 136

Query: 136 LPSTQWL---RVYRVRFHGQVDQDK-------LNL--LKKGIVI-QGICYGDMQVTLDTQ 182
               +     + Y     G +D+++       +      K IV  +       ++T    
Sbjct: 137 KEEFKKEQIFKQYVAIVEGIIDEEQEITEPLIIQKGHFAKVIVAKKNGIKAYTKITPIEI 196

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +     + + ++ G+  +I+         + 
Sbjct: 197 ESKKTKLEILIKTGRTHQIRAHLAHIKHPII 227


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 86/244 (35%), Gaps = 49/244 (20%)

Query: 1   MKDKNIV-----QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M++KN V     Q N    R++  +      S R + +   + R+KVN   +   +  + 
Sbjct: 1   MEEKNNVLKLKVQINDEEIRLNHYLKNYAKCSSRFIRKAAREGRIKVNNENVR-LSYMLK 59

Query: 56  STDHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           + D IE+      +              E   + + +KP  +V   +      T+ + + 
Sbjct: 60  NNDLIEIQINRKEEQDIVPEKMKLDIIYEDEDIIVINKPKAIVVHPTKRHLNGTLSNGVL 119

Query: 103 SIFSR------VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD 154
             F        V  V RLD++T GL+L+  +      L        +++ Y    HG ++
Sbjct: 120 YYFKEKNENSIVRLVNRLDMDTSGLVLIAKNAYSHMALSRDMQKDDFIKRYLAIVHGNLE 179

Query: 155 QDKLNLLKKGIVIQ-----GICYGDMQVTLDTQKGSNA-----------WVTVGLREGKN 198
           +      K G++ +     G       +    QK                + + L  G+ 
Sbjct: 180 E------KSGVIDKPIYRVGEGTLKRVIDERGQKSITRFKVIESYENADLIELTLETGRT 233

Query: 199 REIK 202
            +I+
Sbjct: 234 HQIR 237


>gi|311693193|gb|ADP96066.1| protein containing pseudouridine synthase domain [marine bacterium
           HP15]
          Length = 273

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/153 (18%), Positives = 56/153 (36%), Gaps = 7/153 (4%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-VGRLDINTEGLLL 123
            P+      R  ++ KP GL+   S      ++         +    + RLD +  GL+L
Sbjct: 79  KPILLENAGRYTVWFKPHGLLAQGSQWGDHCSLLRLAEIQLEQPCHLIHRLDADAAGLML 138

Query: 124 LTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD- 180
           + +D   A  L    +     + Y+ R  G +  D    L     ++G        TL+ 
Sbjct: 139 IAHDSKAAGALSQCFSGRTMTKHYKARVAGLI--DAREQLVD-APVEGKAAVSRVSTLEL 195

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + G  + V V +  G+  +I++        + 
Sbjct: 196 DETGETSLVEVSIETGRKHQIRRHLAGLGHPII 228


>gi|294618813|ref|ZP_06698339.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|291594936|gb|EFF26287.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
          Length = 299

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/208 (16%), Positives = 76/208 (36%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERA-----AVNVM-------STDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
            ++KVN  +            V          + + +D   +    E   + + +KP G+
Sbjct: 37  GQIKVNDQVENVLFSLAKDDKVTIVIPAEGEHETVLLDETSIDIVYEDEHVLVVNKPAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--E 135
            +  +      T+ + + + + +       +  V RLD +T GL+L    G     L  +
Sbjct: 97  SSIPAQYHPNGTMANRVKAYYKKKGYENQVIHVVTRLDRDTSGLMLFAKHGFAHAKLDMQ 156

Query: 136 LPSTQWLRVYRVRFHGQVDQ-------------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           L   ++++ Y+    G++               D  +LLK+ +  +G      +  ++ +
Sbjct: 157 LREKKFVKKYQALVSGRLSDLSAHGHIDLPIARDYSSLLKRMVSDEGRSAQT-EYWIEKR 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNW 210
               A V + L  G+  +I+  F     
Sbjct: 216 LTEIALVDIQLHTGRTHQIRVHFSAIGC 243


>gi|283780614|ref|YP_003371369.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283439067|gb|ADB17509.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 355

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/177 (20%), Positives = 69/177 (38%), Gaps = 26/177 (14%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV- 62
           +V+E     R+ + +A R    SR ++ R+I    V +NG   + + A  V + D + + 
Sbjct: 40  VVEEREADGRLDQFLALRLHRYSRMQLRRVIDAGGVLLNGSRAKVKVAYRVSTGDRVSIV 99

Query: 63  ---------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                    +   +      E   L   +KP G+V   +      T+   L   F ++ +
Sbjct: 100 LPEMPSAGPNPEKIPLDILFEDEHLIAVNKPPGMVVHPARGHWSGTLTSALAFHFQQLST 159

Query: 111 VG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
           VG         RLD +T G++++  T+    +   +       + Y     G  D+D
Sbjct: 160 VGGQHRPGIVHRLDRDTSGVIIVAKTDPVHFSLAAQFADRTTAKEYFAITAGVPDRD 216


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 81/238 (34%), Gaps = 36/238 (15%)

Query: 1   MKDKNIVQ----ENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M ++  +Q     +   +R+ +V+A+     SR  ++  I   ++ V+G +       ++
Sbjct: 1   MSEQISLQADVPTDLGGKRLDQVLAQLFPDYSRSRIKTWILDDKITVDGEIFNTPRTKLL 60

Query: 56  STDHIEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + + V             D       E   + + +KP+GLV      +   TV + L 
Sbjct: 61  GGEVLNVETTIEAPREYIAQDIKLDIVYEDDDILVINKPMGLVVHPGAGNPDGTVLNALL 120

Query: 103 SIFSRVI------SVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQV 153
                +I       V RLD +T GL+++         L         + R Y    +G +
Sbjct: 121 HYHPEIINVPRAGIVHRLDKDTTGLMVVAKTIPAQTHLVTALQKRENFTREYEALCNGTM 180

Query: 154 D-----QDKLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIK 202
                 +  +           +            +  +  ++  + + L  G+  +I+
Sbjct: 181 TAGGMVEKPIGRHATQRTHMDVHEQGKPAITHYRVAEKFRAHTRLRLRLETGRTHQIR 238


>gi|227357259|ref|ZP_03841616.1| TruC protein [Proteus mirabilis ATCC 29906]
 gi|227162522|gb|EEI47511.1| TruC protein [Proteus mirabilis ATCC 29906]
          Length = 260

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/170 (19%), Positives = 61/170 (35%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   TVF        I   V  V RLD  T G+LL+   
Sbjct: 8   QDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLMALS 67

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKL---NLLKKGIVIQG------------- 169
             +AR L +     Q  +VY     G V++  +    L+++   I               
Sbjct: 68  SEVARTLSVCFEQHQMEKVYHAVVRGYVEEPMIIDSPLVEEHDKIADKFASQPPKIQHCI 127

Query: 170 ---ICYGDMQVTLDTQKGSNAWVTV-GLR-E-GKNREIKKVFEFFNWKVN 213
              +    ++  +   +   +  ++  LR E G+  ++++        + 
Sbjct: 128 THCVPLAKVEKEVAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPII 177


>gi|213403308|ref|XP_002172426.1| DRAP deaminase [Schizosaccharomyces japonicus yFS275]
 gi|212000473|gb|EEB06133.1| DRAP deaminase [Schizosaccharomyces japonicus yFS275]
          Length = 401

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/201 (20%), Positives = 63/201 (31%), Gaps = 36/201 (17%)

Query: 32  ERMIAQQRVKV------------NGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLY 78
           ER I   +VKV            NG ++  AA          V   P+R   E     + 
Sbjct: 62  ERAIRNGQVKVNNEPGNVDTVIQNGYVISHAAHRHEPP----VTDEPVRIVHEDEEYVVI 117

Query: 79  HKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLL--TNDGGLARVL 134
            KP G+    +     +TV   L   +    +    RLD  T GL+    T  G     +
Sbjct: 118 DKPAGIPVHPTGRYNHNTVLHILMHENKCPLLYPCNRLDRLTSGLMFFSKTPKGAERMRV 177

Query: 135 ELPSTQWLRVYRVRFHGQVDQD-----KLNLLK-------KGIVIQGICYGDMQVTLDTQ 182
            + S    + Y  R  G+   +        LL          +   G     +   L   
Sbjct: 178 HMISKDLQKEYVARVVGEFPAEKTITCDAKLLTVAPTLGLNRVHPDGKDAVTIFKRL-AF 236

Query: 183 KGSNAWVTVG-LREGKNREIK 202
            G  + V    L  G+  +I+
Sbjct: 237 DGHTSLVHCKPLT-GRTHQIR 256


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 83/262 (31%), Gaps = 53/262 (20%)

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  +      E   + +  KP GLV      +   T+ + L     
Sbjct: 71  FELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGNWTGTLVNALIHHCS 130

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFH 150
                     R   V RLD +T G++++  +    R L L      R       Y+    
Sbjct: 131 DTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAIVW 190

Query: 151 G-----------QVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSN-----AWV 189
           G            + +   +  ++ +        D      QV     +  +     + V
Sbjct: 191 GRPRTLSGTVDAPLGRATGDRTRRAVKRPDSQDADEAITHYQVIERFHEKPDATAFASLV 250

Query: 190 TVGLREGKNREIKKVFEFFNWK 211
              L  G+  +I+         
Sbjct: 251 ECRLETGRTHQIRVHMAHIGHP 272


>gi|317010964|gb|ADU84711.1| pseudouridine synthase [Helicobacter pylori SouthAfrica7]
          Length = 326

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 52/309 (16%), Positives = 106/309 (34%), Gaps = 56/309 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-----EVDGVPLRK 69
           R+ + +A+    S+ +   +I +  V      +++  + +   D I     ++   PL+K
Sbjct: 13  RIDEFLAKELQISKNQALSLIKEGLVLCQKKEVKKGGLALKEGDAIALLTLKITPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  L+   +      T+ D L S            R   V
Sbjct: 73  ELDLEIGVIFEDDDLLVLNKPPNLIVHKAPSVKEPTLVDWLESKNYQLSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ-------------- 155
            RLD +T G +++  +      L   L +    R Y       + +              
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLSRKGEKVSVECYLTRN 192

Query: 156 --DKLNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             ++L ++   I  +   Y   + T L T + +   +   L  G+  +I+         +
Sbjct: 193 PNNRLKMMA--IKNEKGRYSKSEFTSLLTSQNNLNLIGAKLYTGRTHQIR-------THL 243

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L R   G   L  L       + K+ +R  L  +L+E      +  +     L++D  
Sbjct: 244 EYLNRHIIGD-NLYGLNE----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDML 298

Query: 273 NIISEVPDD 281
             + ++ D 
Sbjct: 299 EYLKKIFDK 307


>gi|311693418|gb|ADP96291.1| pseudouridine synthase, RluA family [marine bacterium HP15]
          Length = 325

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 79/254 (31%), Gaps = 50/254 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR  ++  I    + VNG  + +    VM  D + +D  P  +              E  
Sbjct: 34  SRSRLQSWIKSGALTVNGE-VRKPRDKVMLDDRLALDAEPEAQVSWQAEEISLDIVYEDE 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            L + +KP GLV   +      T+ + L           R   V RLD +T G++++   
Sbjct: 93  HLLVINKPAGLVVHPAAGHADGTLVNALLNYAPEVENLPRAGIVHRLDKDTSGIMVVARS 152

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYG 173
                 L  +L +    R Y     G +               +   +   +V  G    
Sbjct: 153 LIAHTSLVDQLQTRTMGREYEAVVVGTLTGGATVDAPIGRHPRERKKMA--VVASGKPAV 210

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                L  +  ++  V   L  G+  +I+                   P     L  G  
Sbjct: 211 TH-YRLVERFAAHTHVRCKLESGRTHQIRVHMAHVKH-----------PLVGDPLYGGRL 258

Query: 234 R--EVSKKILREQL 245
           R  + +   LRE L
Sbjct: 259 RLPKGTTDELREAL 272


>gi|261344742|ref|ZP_05972386.1| hypothetical protein PROVRUST_06000 [Providencia rustigianii DSM
           4541]
 gi|282567184|gb|EFB72719.1| tRNA pseudouridine synthase C [Providencia rustigianii DSM 4541]
          Length = 252

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 27/172 (15%), Positives = 56/172 (32%), Gaps = 31/172 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D + TVF        I   V  + RLD  T G+LL    
Sbjct: 7   QDEFVVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQHVYPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR+L       +  + Y     G V           ++L+ +      +     D  
Sbjct: 67  SEVARLLAEQFEQHKMEKTYHAVVRGYVTDAQRLDYPLLEELDKIADKHASKEPKLQDCV 126

Query: 175 --------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                    +  +   +   +  ++   E     G+  ++++        + 
Sbjct: 127 THYRPLVTAECPVAIGRYETSRFSLV--ELKPETGRKHQLRRHMSHLRHPIL 176


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 76/197 (38%), Gaps = 22/197 (11%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKAERTRL 75
            I+     ++ + + +I  + V VN   +  A+  +   D +E+   D     K E++ +
Sbjct: 15  FISEVLGLTKNKAKEIIDSKNVFVNSKRVWIASHTLKKGDIVEIADIDNSFSWKPEKSVI 74

Query: 76  W------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +         KP  L    S+    S  +     +  R+ ++ RLD  T G+LL   +  
Sbjct: 75  YEDQFILAVQKPPFL---ESEGRKGSVEYQLRKVLDRRLKAIHRLDRETSGVLLFAKNEK 131

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           +    +      + ++VY    +G+         KK +V   +     +    T+K S  
Sbjct: 132 IFHRFKDLWHRKEVVKVYLSISYGE------AKFKKKVVNMPVDKKYAKSIFFTKKISKG 185

Query: 187 -AWVTVGLREGKNREIK 202
                V ++ G+  +I+
Sbjct: 186 FTLFEVEIKTGRKHQIR 202


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/156 (20%), Positives = 52/156 (33%), Gaps = 29/156 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------DGVPLR---KAERT 73
           SR  ++ +I Q  V +NG  +      V   D +E+           G  +    + E  
Sbjct: 38  SRSRLKALIEQGAVLLNGQPVTEPKKKVHPGDRVEIVMPEPEDPVPQGEDIPLDVEYEDE 97

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRLDINTEGLLL 123
            L +  KP GLV      +   T+ + L               R   V RLD  T G+++
Sbjct: 98  DLIVLVKPAGLVVHPGAGNWTGTLVNALIYHCGDSLSGIGGVKRPGIVHRLDKETSGVMV 157

Query: 124 LTNDGGLARVLELPSTQWLRV------YRVRFHGQV 153
           +  +    R L        R       Y+    G+ 
Sbjct: 158 VAKNDNAHRHLAAQFADHGRTGPLERAYKAVVWGRP 193


>gi|114797120|ref|YP_759725.1| RluA family pseudouridine synthase [Hyphomonas neptunium ATCC
           15444]
 gi|114737294|gb|ABI75419.1| pseudouridine synthase, RluA family [Hyphomonas neptunium ATCC
           15444]
          Length = 349

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/193 (20%), Positives = 71/193 (36%), Gaps = 33/193 (17%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
             V +  T  R+ + I R   A++ +VE+++   +++VNG   + A   +++ D +    
Sbjct: 8   ETVSDKETGARLDRWIKRRMNATQGQVEKLLRTGQIRVNGSRAK-ANTRLVTADEVRFPI 66

Query: 63  ------------DGVPLRKAERTRL-----------WLYHKPIGLVTTHSDPDGRST--V 97
                       +   + + +R  L              +KP GL        GR    +
Sbjct: 67  FAAEDAGARKAANAKQISEEDREFLRSIIIHEDDDMLAINKPAGLAVQGGSGQGRHVDGL 126

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
              +     R + V RLD +T G+LLL      A  L     S +  +VY     G    
Sbjct: 127 IAGMDVDGHRPVLVHRLDKDTSGVLLLAKHPAAAARLTELFRSREMDKVYWAVTVGVPSP 186

Query: 156 DKLNL---LKKGI 165
               +   + KG+
Sbjct: 187 QAGQIRCWMVKGV 199


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/220 (13%), Positives = 75/220 (34%), Gaps = 31/220 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERA-AVNVMSTDHIEVDGVPLRKAER 72
            R+ + +      +R ++++ I    + +N  +++      +     +  +   L   E 
Sbjct: 21  IRIDRYLVEKLNINRSQIKKYIDFGNILINNSVVKAGYMTKIGDIIDVSYEDEILLLPEE 80

Query: 73  TRLWLYH---------KPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVIS--VGRL 114
               + +         KP  LV      +   T+       F NL +   ++    V RL
Sbjct: 81  IDFKIIYEDEHIAVISKPQNLVVHPGSGNYNHTLVNGLLFKFKNLSNCGDKLRPGIVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------QVDQDKLNLLK 162
           D +T GL+++         L      ++  + Y     G           + +D  N  K
Sbjct: 141 DKDTSGLMIIAKTNLAYLKLVKDFKESKIRKTYIAVVEGKTDEFGIINEPIGRDPKNRKK 200

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             ++ +       +     +  + + +++ +  G+  +I+
Sbjct: 201 MAVIYENSKNAITEYKKIREFNNFSLISINILTGRTHQIR 240


>gi|270587172|ref|ZP_06221422.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae HK1212]
 gi|270318484|gb|EFA29582.1| ribosomal large subunit pseudouridine synthase E [Haemophilus
           influenzae HK1212]
          Length = 91

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 23/58 (39%), Positives = 39/58 (67%), Gaps = 2/58 (3%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           + T++ L++KP  ++T  +D  GR+T+ D +      V + GRLD ++EGLL+LTN+G
Sbjct: 36  DETKVVLFNKPFDVLTQFTDEQGRATLKDFI--SIPNVYAAGRLDRDSEGLLILTNNG 91


>gi|256847721|ref|ZP_05553166.1| pseudouridylate synthase [Lactobacillus coleohominis 101-4-CHN]
 gi|256715410|gb|EEU30386.1| pseudouridylate synthase [Lactobacillus coleohominis 101-4-CHN]
          Length = 297

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/234 (14%), Positives = 79/234 (33%), Gaps = 55/234 (23%)

Query: 12  TPQRVSKVIARAGIASRREVERM---IA--QQRVKVNGILLERAAVNVMSTDH--IEVD- 63
           +P ++ + +++ G+  R     +   I     +  V+   +      V+      I+VD 
Sbjct: 11  SPIKIKRYLSQLGMGHR-----LFNDIKNGDGQFLVDHRHVR-PTTQVLPNQTLTIQVDA 64

Query: 64  ----------GVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                       PL        WL  +KP G+ +     +   T+ + +           
Sbjct: 65  ETPDPTVQSSSQPLTIVYEDANWLVINKPTGIASIPGPTEDNGTILNRVKGYLEKNEDPN 124

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKK 163
            R   + RLD  T GLLL+      + ++     +    + Y     G++ +      + 
Sbjct: 125 QRPHLITRLDKYTSGLLLVAKHRVASSMISQQVEKHTMQKRYLAVVAGKLTK------QH 178

Query: 164 GIV---IQGICYGDMQVTLDTQKGSN------------AWVTVGLREGKNREIK 202
           G++   I+ +     ++     + +             + V + L  G+  +I+
Sbjct: 179 GVIDQPIKRVAGQTARIIDPAGQPARTEYWCQQTNEDYSLVQLQLHSGRTHQIR 232


>gi|238784871|ref|ZP_04628871.1| tRNA pseudouridine synthase C [Yersinia bercovieri ATCC 43970]
 gi|238714188|gb|EEQ06200.1| tRNA pseudouridine synthase C [Yersinia bercovieri ATCC 43970]
          Length = 257

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 57/186 (30%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L L     Q  + Y     G V +         ++L+ +               
Sbjct: 67  SDVARALSLQFEQHQIQKTYHAVVRGYVLEGGTVDYEMTEELDKIADKFSRPDKAPQPSV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  QV +    G        L E     G+  ++++        +        G  
Sbjct: 127 THHQPLAQVEMPVAIGRYDTARFSLMELKPETGRKHQLRRHMAHIRHPI-------IGDS 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|197286139|ref|YP_002152011.1| tRNA pseudouridine synthase C [Proteus mirabilis HI4320]
 gi|194683626|emb|CAR44534.1| tRNA pseudouridine synthase C [Proteus mirabilis HI4320]
          Length = 259

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/170 (19%), Positives = 61/170 (35%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   TVF        I   V  V RLD  T G+LL+   
Sbjct: 7   QDEYLVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKL---NLLKKGIVIQG------------- 169
             +AR L +     Q  +VY     G V++  +    L+++   I               
Sbjct: 67  SEVARTLSVCFEQHQMEKVYHAVVRGYVEEPMIIDSPLVEEHDKIADKFASQPPKIQHCI 126

Query: 170 ---ICYGDMQVTLDTQKGSNAWVTV-GLR-E-GKNREIKKVFEFFNWKVN 213
              +    ++  +   +   +  ++  LR E G+  ++++        + 
Sbjct: 127 THCVPLAKVEKEVAIGRYPTSRFSLLELRPETGRKHQLRRHMSHIRHPII 176


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 83/261 (31%), Gaps = 53/261 (20%)

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---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+           G  +      E   L +  KP GLV      +   T+ + L      
Sbjct: 85  EITLPEPEDPTPQGEDIPLDILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGA 144

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG 151
                    R   V RLD +T G++++  +    R L L      R       YR    G
Sbjct: 145 TLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYRAIVWG 204

Query: 152 -----------QVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSNAWVTVGLRE 195
                       + +   +  ++ +        D      +V     +  +A     L E
Sbjct: 205 RPRSLTGTVDAPLGRATGDRTRRAVKRPDSQDADEAITHYEVIERFHETPDATALASLVE 264

Query: 196 -----GKNREIKKVFEFFNWK 211
                G+  +I+         
Sbjct: 265 CRLETGRTHQIRVHMAHIGHP 285


>gi|46445765|ref|YP_007130.1| putative ribosomal large subunit pseudouridine synthase
           (pseudouridylate synthase), rluA [Candidatus
           Protochlamydia amoebophila UWE25]
 gi|46399406|emb|CAF22855.1| putative ribosomal large subunit pseudouridine synthase
           (pseudouridylate synthase), rluA [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 243

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 71/197 (36%), Gaps = 30/197 (15%)

Query: 43  NGILLERAAVNVMSTDHIEVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
           +GI+++     V+    I ++        G+ +   E   L + +KP GL++  +  +  
Sbjct: 2   DGIVVKNNHFEVLEGQVISLNQRKKIVGSGIQILY-EDADLAIIYKPSGLLSVATAFEKG 60

Query: 95  STVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
            T    L + +   +V  V RLD +T G+++   +      L+         R Y     
Sbjct: 61  ETTHALLKAHYKPRKVFVVHRLDQDTSGVMVFAFNEKTCNGLKDLFEVHDISRSYTAIVE 120

Query: 151 GQVDQ----------DKLNLLKKGIVIQGICYGDMQV----TLDTQKGSNAWVTVGLREG 196
           GQ+            +           +   YG + +    TL T K   + V + L  G
Sbjct: 121 GQLLSPSGTWKSYLYEDSQYFVH--ETEDETYGRLAITHYRTLKTLK-KYSLVELTLETG 177

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+   +     V 
Sbjct: 178 RKNQIRVHCQSAGHPVV 194


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 86/260 (33%), Gaps = 56/260 (21%)

Query: 4   KNIVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K I  +N    R+ K +      I SR ++++     ++ VN  ++++    +   D +E
Sbjct: 11  KIITNKNQKEIRIDKFLKNYIQNI-SRNQIQKWTTSGKILVNKNIVKK-NYKIKPLDFVE 68

Query: 62  VD----------------GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           ++                   +      E   + + +KP G+V      +   T+   + 
Sbjct: 69  IEISIPSVLDHLEYKNITAEKINLDILYEDEDVLVVNKPAGMVVHPGFGNETGTLIHGIK 128

Query: 103 SIFS----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
              +          R   V RLD +T GLL+   +    + L     S    R Y     
Sbjct: 129 YHLTNSNLNNFNLYRCGLVHRLDKDTSGLLVFAKNEYSQKHLFQQFYSRTIQRKYIALIW 188

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTL--DTQKGSNAWVTVG---------------- 192
           G + ++K  +   G + +          L  + Q+ +    +V                 
Sbjct: 189 GNLIEEKGTI--TGFIGRDPKNRKKMTILKQENQEFNKGKFSVTHYKVLERFKYLTYVSC 246

Query: 193 -LREGKNREIKKVFEFFNWK 211
            ++ GK  +I+  F+     
Sbjct: 247 NIKTGKTHQIRAHFKHLGHP 266


>gi|256828761|ref|YP_003157489.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256577937|gb|ACU89073.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 281

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/182 (15%), Positives = 64/182 (35%), Gaps = 19/182 (10%)

Query: 48  ERAAVNVMSTDHIEVD----------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            RA+  V   + +E++            P   A+     +++KP  +++  +      T+
Sbjct: 57  RRASAEVKPGERLEINYDPALLALVPAQPELIAKAKHYSVWNKPAAVLSQGTRFADHCTL 116

Query: 98  FDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
                +     + +  V RLD    G++LL +DG  A  L         ++ Y     G 
Sbjct: 117 PRLAQAKLGSRNELHPVHRLDREARGIMLLAHDGKAAAKLGELFRQGAVVKEYAAIVRGI 176

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWK 211
            D   + + +    + G         + +   S+  + +  +  G+  +I++        
Sbjct: 177 PDWTDIEVNE---PLDGKEARSRFHVVQSDPASDMTLLLARIDTGRKHQIRRHLNGLGHP 233

Query: 212 VN 213
           V 
Sbjct: 234 VM 235


>gi|153830556|ref|ZP_01983223.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
 gi|148873954|gb|EDL72089.1| pseudouridine synthase Rlu family protein [Vibrio cholerae 623-39]
          Length = 244

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G ++          ++L+ +      Q        
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEDTNVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLIEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|42523026|ref|NP_968406.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39575232|emb|CAE79400.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 290

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 25/156 (16%), Positives = 45/156 (28%), Gaps = 25/156 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISVGRLDINTEGLLLL 124
           +       +KP G      +        D +        +   V  V RLD  T G+LL 
Sbjct: 56  KDEYFIAVNKPSGFHVHPHENVQHRVSRDKICLYHARRMMKQHVYPVHRLDAGTSGVLLF 115

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI-----------C 171
                 A  L          + Y+    G V ++    L   + +               
Sbjct: 116 ALSSESASKLCRLFTERATHKTYQAVVRGFVKEEGEVQLP--LELDSTGDLVDAHTSFKR 173

Query: 172 YGDMQVTLDTQKGSN----AWVTVGLREGKNREIKK 203
              ++  +   K       +WV V    G+  +I++
Sbjct: 174 LATVEFPVAVGKKFPTARYSWVEVTPHTGRYHQIRR 209


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/169 (19%), Positives = 59/169 (34%), Gaps = 31/169 (18%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ K +       SR   +  I    V++NG +  R A  +   D + +D          
Sbjct: 16  RLDKYLTEVHPKYSRAFYQEHILSGLVQINGQINTRVATRLNCGDIVTIDIQEKEELLEL 75

Query: 64  ---GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVF------------DNLPSIFSR 107
               +PL K  E   + + +KP  +V   +      T+             +  P    R
Sbjct: 76  LPEAIPLDKVYEDGMILVINKPRDMVVHPAPGHFHGTLVHALLHEIGERLKEEFPEEPWR 135

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQV 153
              V RLD +T G L++T     A+ +      + +  + Y     G+ 
Sbjct: 136 PGIVHRLDKDTSG-LIITAKTRQAKKVFSELFSTKRLKKSYLAVCIGKP 183


>gi|163858109|ref|YP_001632407.1| hypothetical protein Bpetpseudo_11 [Bordetella petrii DSM 12804]
 gi|163261837|emb|CAP44139.1| pseudogene [Bordetella petrii]
          Length = 217

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L + +KP   +   SD  GR+T+ D +    S     GRLD ++EGLLLLTNDG  
Sbjct: 124 DTPSLLMLNKPFDALAQLSDDQGRATLKDFVD--VSDFYPAGRLDRDSEGLLLLTNDGRC 181

Query: 131 ARVL 134
            R L
Sbjct: 182 NREL 185


>gi|290473651|ref|YP_003466523.1| pseudouridine synthase [Xenorhabdus bovienii SS-2004]
 gi|289172956|emb|CBJ79727.1| pseudouridine synthase [Xenorhabdus bovienii SS-2004]
          Length = 250

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/186 (17%), Positives = 53/186 (28%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S      TVF        I   V  V RLD  T G+LL+   
Sbjct: 7   QDDHIVAVNKPAGWLVHRSWLARHETVFVMQTLRDQIGQHVFPVHRLDKPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +AR L          + Y     G V+ D +        +  I         + Q   
Sbjct: 67  SEVARTLSQQFECHHIQKTYHAIVRGYVEGDGIIDYALMEELDKIADKFADTDREAQSAI 126

Query: 186 NAW---------VTV--------GLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPF 223
             +         V +         L E     G+  ++++        +        G  
Sbjct: 127 THYRSLAKVECPVEIGRYPTSRFSLLELMPKTGRKHQLRRHMSHLRHPI-------IGDT 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|222086840|ref|YP_002545374.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
 gi|221724288|gb|ACM27444.1| pseudouridylate synthase [Agrobacterium radiobacter K84]
          Length = 343

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 37/185 (20%), Positives = 65/185 (35%), Gaps = 32/185 (17%)

Query: 3   DKNIVQENFTPQ-RVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           ++ ++  + T + R+   + A+     SR  V+ +I    V +NG  +  A   V   D 
Sbjct: 13  NRKVLTADETAEGRLDAWLTAQMDEELSRSRVQALIKANAVLLNGTPVTDAKRKVRPGDI 72

Query: 60  IEV----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
            E+           G  +      E   + +  KP GLV      +   T+ + L     
Sbjct: 73  YEISMPEPEDPTPQGEDIPLDVLFEDDDVIVISKPAGLVVHPGAGNWTGTLVNALIHHCG 132

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFH 150
                     R   V RLD +T G++++  +    R L L      R       Y+    
Sbjct: 133 DSLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTTPLERAYQAIVW 192

Query: 151 GQVDQ 155
           G+  Q
Sbjct: 193 GRPRQ 197


>gi|187931810|ref|YP_001891795.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. mediasiatica FSC147]
 gi|187712719|gb|ACD31016.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. mediasiatica FSC147]
          Length = 332

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 72/208 (34%), Gaps = 35/208 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 37  SRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINIELLPTNEWIAEDINLKIIFEDD 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ ++      +   TV + L           R   V RLD +T GL++    
Sbjct: 96  DIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 155

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                 L  +L   +  R Y     G++ Q     + + I         M +    ++  
Sbjct: 156 SIAYHNLVQQLAERKVSRKYLAIVEGEIYQQG--TINQPIGRDPTNRTKMAINYRGKEAI 213

Query: 186 NAW--VTV----GLRE-----GKNREIK 202
             +  + V     L E     G+  +I+
Sbjct: 214 THYTPIEVYDGFTLIECQLETGRTHQIR 241


>gi|170727493|ref|YP_001761519.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812840|gb|ACA87424.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 283

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/208 (19%), Positives = 84/208 (40%), Gaps = 26/208 (12%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINT 118
           +D   L  A+  +  L++KP G++   S     +T+     +  +       V RLD   
Sbjct: 82  IDDAEL-IADMGQYSLWYKPYGMLCQGSKWGDHTTINRYSETHLTPDRPAFIVHRLDRAA 140

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGD 174
            GL+L+ +   +   L       +  + Y+V   G+ +  ++++  +   +  +  C   
Sbjct: 141 TGLVLIGHSKSITAALAKLFELRELDKYYQVIVEGRFNSGREEVVTVDSDVDNKSACSHA 200

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN--RLIRISYG---PFQLGT- 227
             +  D ++ + + V V +  G+  +I+  +       V   RL  I+ G     QL + 
Sbjct: 201 KLLEYDAKQ-NRSLVQVKIDSGRKHQIRIHM-ASLGHPVVGDRLHGIASGSDINLQLTSC 258

Query: 228 -LL-----AGSTREVSKKILREQLGPHL 249
            L       G   E+++  L E+L P L
Sbjct: 259 YLKFPCPVTG---EINEFELPERLRPKL 283


>gi|323495104|ref|ZP_08100191.1| tRNA pseudouridine synthase C [Vibrio brasiliensis LMG 20546]
 gi|323310655|gb|EGA63832.1| tRNA pseudouridine synthase C [Vibrio brasiliensis LMG 20546]
          Length = 240

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/177 (14%), Positives = 51/177 (28%), Gaps = 41/177 (23%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKG-------IVIQGICYGDMQVT 178
             +A  +     + +  + Y     G +       L+ G       + +  I        
Sbjct: 67  SEVASQVMPMFANHEMEKTYHAIVRGWI-------LESGRLDYPLKVELDKIADKHASQE 119

Query: 179 LDTQKGSN-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
            + Q+        A V +             L E     G+  ++++        + 
Sbjct: 120 KEAQEAITDYQPLAQVEIPHSTGRFPTTRYCLMEMKPLTGRKHQLRRHMAHLRHPIV 176


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/228 (17%), Positives = 75/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 +D
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMD 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|258647021|ref|ZP_05734490.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
 gi|260404462|gb|EEW98009.1| ribosomal large subunit pseudouridine synthase D [Dialister invisus
           DSM 15470]
          Length = 562

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 32/194 (16%), Positives = 66/194 (34%), Gaps = 29/194 (14%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA-----ERTRLWLYHKPIGLV 85
              V +NG  +  A   +   D + +      D VP         E   L + +K  G++
Sbjct: 37  NGEVWLNGTRIHNAKTVLHEGDRVRLVWDESSDIVPADIPLDILYEDDTLLVVNKGTGMI 96

Query: 86  TTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
              ++     T+ + +   F +      +  V RLD NT G++++         L     
Sbjct: 97  IHPTNAGIHDTLVNAVAGYFQKKGEKSGIHPVYRLDRNTTGVVVVAKSAKAQYALTRSHD 156

Query: 140 QWLRVYRVRFHGQVDQDK------LNLLKKGIVIQ-----GICYGDMQVTLDTQKGSNAW 188
              R Y     G +  +       +   K+G +I+            + T+     +   
Sbjct: 157 LIHREYIAVAGGYIPGEFGIVDAPIGR-KEGSIIEWTVRKDGRPARTEYTVLRHGDNYTV 215

Query: 189 VTVGLREGKNREIK 202
           + + L  G+  +I+
Sbjct: 216 LKLHLLTGRTHQIR 229


>gi|62184670|ref|YP_219455.1| putative pseudouridine synthase [Chlamydophila abortus S26/3]
 gi|62147737|emb|CAH63481.1| putative pseudouridine synthase [Chlamydophila abortus S26/3]
          Length = 325

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/174 (20%), Positives = 66/174 (37%), Gaps = 31/174 (17%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K + ++    SR   ++ I  QRV +N  +  + +  ++  D + +           
Sbjct: 18  RLDKFLVSQNPKYSRAFYQQHIVDQRVTINEQIQTKVSTQLVPGDTVSITIEEKEEPSEL 77

Query: 63  --DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSR 107
             + +PL K  E   + + +KP  +V   +    R TV   L            P    R
Sbjct: 78  LPEAIPLEKIYEDEMILVINKPRDMVVHPAPGHTRGTVVHALLHEIGERLKQEFPEEPWR 137

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDKL 158
              + RLD +T G LL+T     A+++      + Q  + Y     G+     +
Sbjct: 138 PGIIHRLDKDTSG-LLITAKTRQAKMIYSELFATKQLKKSYLAICVGKPSASVI 190


>gi|30248520|ref|NP_840590.1| rluD; ribosomal large subunit pseudouridine synthase D
           [Nitrosomonas europaea ATCC 19718]
 gi|34395760|sp|Q82WZ5|RLUD_NITEU RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|30138406|emb|CAD84416.1| rluD; ribosomal large subunit pseudouridine synthase D
           [Nitrosomonas europaea ATCC 19718]
          Length = 344

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/230 (19%), Positives = 82/230 (35%), Gaps = 35/230 (15%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V +N    R+ + +A+     SR  ++  I Q+ V V+          V   + I V  
Sbjct: 35  TVPDNLAGLRLDQALAQLLPQWSRSRLQGWIEQKCVSVDSAAAT-CKQKVWGGESIRVIA 93

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                      + +PL+   E   L +  KP GLV    + +   T+ + L +   ++  
Sbjct: 94  GQTENDQSHQAEAIPLKILFEDDHLIIIDKPAGLVVHPGNGNWHGTLLNALLNHAPQLSQ 153

Query: 110 -----SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK----- 157
                 V RLD +T GLL++         L     Q    R Y     G++++D      
Sbjct: 154 VPRAGIVHRLDKDTTGLLVVAKTIEAQFDLARQLQQRTVKRHYLALVLGKLEKDGVVDAP 213

Query: 158 -----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                ++  +  +V  G         L+    S   +   L  G+  +I+
Sbjct: 214 IGRHPIHRTRMAVVQNGKPARTHYRVLEKFTAST-LLHCSLETGRTHQIR 262


>gi|15602344|ref|NP_245416.1| tRNA pseudouridine synthase C [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|34582475|sp|Q9CNF3|TRUC_PASMU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|12720737|gb|AAK02563.1| unknown [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 243

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 58/181 (32%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+LL    
Sbjct: 8   QDPYLIAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVYPIHRLDRPTSGVLLFALS 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGD-- 174
             +A +L L   + Q  + Y     G +  +         +L+ +            +  
Sbjct: 68  SEVANLLCLQFENKQVQKSYLAIVRGYLVGEGRIDYPLKVQLDKIADKFAQDDKAPQEAV 127

Query: 175 ------MQVTLD--TQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  +V +    +K      + V +    G+  ++++  +     +  L    YG  
Sbjct: 128 TDYLGLAKVEMPYCVKKYPTTRYSLVRLIPHTGRKHQLRRHMKHLFHPI--LGDTQYGDL 185

Query: 224 Q 224
            
Sbjct: 186 H 186


>gi|262202888|ref|YP_003274096.1| pseudouridine synthase [Gordonia bronchialis DSM 43247]
 gi|262086235|gb|ACY22203.1| pseudouridine synthase, RluA family [Gordonia bronchialis DSM
           43247]
          Length = 308

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 87/250 (34%), Gaps = 39/250 (15%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--------- 49
           M++  +  V +     R+   +AR    SR  V  +     V V+G+ + +         
Sbjct: 1   MRESRMLPVPDGLDGMRLDAALARMLGLSRTVVAGLADDGDVTVDGVAVGKSHRLAAGAL 60

Query: 50  AAVNVMSTDH-IEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
             V +   +  ++V+  P+   +       + +  KP+G+    S      TV   L + 
Sbjct: 61  LHVTLPEPERPLQVEPTPVEDLDVIYHDSDIIVVDKPVGVAAHPSLGWSGPTVLGALDAA 120

Query: 105 FSRVISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
             R+ + G         RLD+ T G++++        VL+    Q    + Y     G +
Sbjct: 121 GYRISTSGAPERQGIVSRLDVGTSGVMVVAVSERAYSVLKRAFKQRTVDKGYHALVQGHL 180

Query: 154 DQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           +  +   G        TL+    + + + + L  G+  +I+
Sbjct: 181 DPPTGTIDAPIGRHPGSDWRFAVTANGKPSITHYETLEMFAAA-SLLDIHLETGRTHQIR 239

Query: 203 KVFEFFNWKV 212
             F   +   
Sbjct: 240 VHFAALHHPC 249


>gi|163733966|ref|ZP_02141407.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           litoralis Och 149]
 gi|161392502|gb|EDQ16830.1| ribosomal large subunit pseudouridine synthase D [Roseobacter
           litoralis Och 149]
          Length = 342

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/272 (16%), Positives = 88/272 (32%), Gaps = 65/272 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++    V +   P R+ K +AR     A + SR  + R+I +  V V+G++       + 
Sbjct: 3   VRQIQFVIDEAPPLRLDKALARDVPVEAAL-SRTRLARLIDEGGVWVDGVVQHNPKARIE 61

Query: 56  STDHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +   + +            + +PL    E   L + +KP G+V   +      T+ + L 
Sbjct: 62  AGAQVTIHVQEAQDSHILPEDIPLDIIHEDADLIVVNKPAGMVVHPAPGTPSGTLVNALL 121

Query: 103 SI----------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
           +             R   V R+D +T GLL++         L     +    R Y    +
Sbjct: 122 AHCGDDLSGVGGLKRPGIVHRIDKDTSGLLVVAKSDAAHHGLAAQFQAHTVERYYNCLVY 181

Query: 151 GQVDQDK-------LNLLKKG--------------------IVIQGICYGDMQVTLDTQK 183
           G  D +            + G                    ++ QG  +   +     + 
Sbjct: 182 GAPDANDPRLRGVKGARFEAGNILKMTTQLARHKTDRQRQAVLFQGGRHAVTRARSVERY 241

Query: 184 GSNAWVTVGLRE-----GKNREIKKVFEFFNW 210
           G+   +   L E     G+  +I+        
Sbjct: 242 GTPPVL--TLMECWLETGRTHQIRVHMAHAGH 271


>gi|254995115|ref|ZP_05277305.1| sfhb-like protein [Anaplasma marginale str. Mississippi]
          Length = 328

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 82/244 (33%), Gaps = 57/244 (23%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------- 58
           + +E+   QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D       
Sbjct: 9   VTKEDDQ-QRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTA 67

Query: 59  ---------------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
                           +  +   +   ++      H   G+       +  +     L  
Sbjct: 68  VQKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGI-------EHHTITNALLAR 120

Query: 104 IFSRVISVG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG- 151
             + + SVG         RLD +T GL++          L  EL +  + + Y     G 
Sbjct: 121 FGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGI 180

Query: 152 ------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKN 198
                       +V +  + +++      G      +  ++ + G   + +   L  G+ 
Sbjct: 181 PCPKRGVIHTNIRVKRSDITMMEAANS--GGKPAKTEYEVEQELGEVASLIRCTLHTGRT 238

Query: 199 REIK 202
            +I+
Sbjct: 239 HQIR 242


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 81/256 (31%), Gaps = 56/256 (21%)

Query: 4   KNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +  E   P RV K +      +SR  +++      V VN   ++     +   D + +
Sbjct: 27  RIVADEGQKPLRVDKFMFEKLQHSSRNRIQKAAEAGFVHVNDQPVKS-NYKIRPNDVVTL 85

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD--------- 99
                        + +PL    E   L + +KP GLV      +   T+ +         
Sbjct: 86  MLDRPRHDNTIEAENIPLDIVYEDAELLVVNKPAGLVVHPGVGNFHGTLINAVAWHMKDD 145

Query: 100 -NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
            N  +    V  V R+D +T GLL++         L +   +    R Y+    G + +D
Sbjct: 146 KNFDANSPEVGLVHRIDKDTSGLLVVAKTPNAKTKLGVQFFNKTTTRSYKALVWGHIAED 205

Query: 157 KLNLLKKGIVIQGICYGDMQ---------------------VTLDTQKGSNAWVTVGLRE 195
           +         I+G    D +                       +  + G    +   L  
Sbjct: 206 EGR-------IEGNIGRDPKDRQRMTVFSPDSGIGKPAVTHYKVIERFGYTTLIECILET 258

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+   +     
Sbjct: 259 GRTHQIRAHMKHIGHP 274


>gi|254467318|ref|ZP_05080729.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium Y4I]
 gi|206688226|gb|EDZ48708.1| ribosomal large subunit pseudouridine synthase D [Rhodobacterales
           bacterium Y4I]
          Length = 341

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 65/330 (19%), Positives = 114/330 (34%), Gaps = 55/330 (16%)

Query: 6   IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ EN  P+R+ K ++R     A + SR  + R+I +  + V+G +++    NV +   I
Sbjct: 9   VIAENP-PKRLDKAVSRDVPEEAAL-SRTRLARLIGEGALTVDGAVVQDPKANVAAGAVI 66

Query: 61  EV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +            + +PL    E   L + +KP G+V   +      T+ + L   F  
Sbjct: 67  AIEVEEAEDSHIGPEDIPLEIVFEDDDLIVINKPAGMVVHPAPGSPSGTLVNALLHHFGG 126

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D  T GLL++       + L          R Y+   +G  D 
Sbjct: 127 NLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFEKHTVERYYQAICYGVPDG 186

Query: 156 DKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI-K-KVFEFFNW- 210
           +    L+  KG   +      +   L   K         L +G    + + ++ E F   
Sbjct: 187 ND-PRLRGVKGASFEPGNILKLTTHLARHKTDRQR-QAVLFQGGRHAVTRARICESFGNP 244

Query: 211 KVNRL------------IRISY--GPFQL-GTLLAGSTREVSKKILREQLGPHLLEEAQV 255
               L            IR+        L G    G  R++  K L E+    +    + 
Sbjct: 245 PCAALIECWLETGRTHQIRVHMAHAGHSLVGDPTYGGRRKLPAKALSEEAQEAVRAFPRQ 304

Query: 256 NLDAPIYSSETLVRDRP-NIISEVPDDFTR 284
            L A +      V   P    + +P D   
Sbjct: 305 ALHAAVLGFGHPVSGEPLRFEAPLPQDMAE 334


>gi|167627646|ref|YP_001678146.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
 gi|167597647|gb|ABZ87645.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
          Length = 328

 Score = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/181 (17%), Positives = 65/181 (35%), Gaps = 33/181 (18%)

Query: 3   DKNIVQENFTPQRVSKVIARAGI------ASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            K ++  +   +R+      + I       SR ++++ I    + VNG    ++   ++ 
Sbjct: 12  QKIMMHPDHAGKRID-----STINELFEQFSRSQIQKWIKDGLITVNGKT-TKSKHILLG 65

Query: 57  TDHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
            + +E++   L                E   + +  KPI +V      +   T+ + L  
Sbjct: 66  DEEVEINIELLPTNEWLAEDIDLNIVFEDNDIIVIDKPIDMVVHPGAGNMTGTISNALLH 125

Query: 102 ----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
                    R   V RLD +T GL++          L  +L   +  R Y     G++ +
Sbjct: 126 KYPNQDKLPRAGIVHRLDKDTSGLMVAAKSSIAYHNLVQQLSERKVSRKYLAIVEGEIYE 185

Query: 156 D 156
           +
Sbjct: 186 E 186


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 82/249 (32%), 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  -------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L +  KP GLV      +   T+ + +      +
Sbjct: 92  MLDRPKHDNTIEPEDIPLDVIYEDDDLMVIMKPAGLVVHPGAGNFHGTLINAIAWHLKDL 151

Query: 109 IS----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF------- 149
            S          V R+D +T GLLL+         L     +    R Y           
Sbjct: 152 ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKTKLGKQFFNKTTHRSYIALVWGNFVED 211

Query: 150 ----HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
                G + +D  + L+  +       G   VT   +  + G    +   L  G+  +I+
Sbjct: 212 EGRIEGNIARDPKDRLRMTVFPPDSEIGKHAVTHYKVIERFGYTTLIECILETGRTHQIR 271

Query: 203 KVFEFFNWK 211
              ++    
Sbjct: 272 AHMKYIGHP 280


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 84/245 (34%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE+  
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      + VPL    E   L + +KP G+V   +  +   TV + L   +     
Sbjct: 128 DLLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD----- 156
              R   V RLD  T GL+++         L  +L +    R Y     G + ++     
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFE 206
                  +   +       G         +D+   Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTSASGKPARTHFRRVDSAIWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWK 211
                
Sbjct: 308 HIGHP 312


>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 = 65.6 bits (159), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 29/202 (14%), Positives = 67/202 (33%), Gaps = 26/202 (12%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKA-------ERTRLW 76
           SR  +++++    ++ N   +   +  + + D +E++   G+  +         E   + 
Sbjct: 58  SRTRIKKLLRHGNIRCNNKPVTLHSHKLSAGDVVEINTYGGIAAKAGLPFPVLFEDQHVI 117

Query: 77  LYHKPIGLVTTHSDPDG--RSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLA 131
              KP+G+ T  +D     +  V   L           +V RLD    G+LL        
Sbjct: 118 AVEKPVGIATFSADGSASVQWIVAQALKEHSRGKIHAFAVHRLDKEVSGVLLFAKSKMAM 177

Query: 132 RVLELPSTQWLRVYRVRFHGQVD-----------QDKLNLLKKGIVIQGICYGDMQVTLD 180
             ++    +  + Y     G+ +           +D    +          +      + 
Sbjct: 178 DHIKEKWKEAEKRYYALVEGKPESPDGTIESWLVEDHAQKVHSTRESSKAKFSVTHYRII 237

Query: 181 TQKGSNAWVTVGLREGKNREIK 202
            Q      + V L+ G+  +I+
Sbjct: 238 KQVNQYTLLDVKLQTGRKNQIR 259


>gi|297626700|ref|YP_003688463.1| Pseudouridylate synthase, Uncharacterized RNA pseudouridine
           synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
 gi|296922465|emb|CBL57038.1| Pseudouridylate synthase, Uncharacterized RNA pseudouridine
           synthase [Propionibacterium freudenreichii subsp.
           shermanii CIRM-BIA1]
          Length = 306

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 82/246 (33%), Gaps = 40/246 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
            V +    QR+    AR    SR  V  +I + +V ++G  + +A+  V     I++D  
Sbjct: 5   FVPDGLEGQRIDAAAARMTGLSRSRVVDLIGEGKVLLDGSTVVKASERVRGGQTIDIDLS 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                         G+ +   +   + +  KP G+    S       V   L     R+ 
Sbjct: 65  EPTRVARVTPAVVEGMRIVHDDADIVVV-DKPAGVAAHPSVGWDGPDVVSGLAGAGFRIS 123

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V RLD+ T GL+++        +L+         + Y     G +D  + 
Sbjct: 124 TSGAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKRAFRDRTVDKYYLTLVQGHLDASEG 183

Query: 159 N-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                         K  +   G        T++  +G+ + + V L  G+  +I+  F  
Sbjct: 184 TIGAPIGRHPGSEWKFAVTADGRPSVTHYETVEMMRGA-SLLRVHLETGRTHQIRVHFAA 242

Query: 208 FNWKVN 213
            +    
Sbjct: 243 LHHPCV 248


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 49/225 (21%), Positives = 82/225 (36%), Gaps = 40/225 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGV 65
           RV KV+A R    SR ++++ + +  V + G  +  A   V + DH+         VD  
Sbjct: 15  RVDKVLAERLPNHSRSQIQQWLKEDAVTLKGETVR-ANYKVKAGDHLIIQVPEPEVVDLQ 73

Query: 66  PLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVIS--V 111
           P               + +KP G+V   S      T+        D+L +I   V    V
Sbjct: 74  PENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNALLYHMDDLSTINDVVRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L   L     LR Y    HG +  +K            
Sbjct: 134 HRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYVALVHGTISHEKGTINAPIGRSKV 193

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++   VI+         T+  +      V + L  G+  +I+
Sbjct: 194 NRKMQA--VIENGKPAVTHFTVLERFEQFTLVELQLETGRTHQIR 236


>gi|332974183|gb|EGK11117.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter sp.
           1501(2011)]
          Length = 456

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 82/249 (32%), Gaps = 48/249 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            V ++   QR+ K +A    A  SR +++  +    + VNG  +E+    V   D + + 
Sbjct: 149 TVTDDKAGQRIDK-LAAELFADHSRSQLQEWLKSGNLTVNGE-VEKPKYRVRVGDKLLLQ 206

Query: 64  GVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSI 104
               +               E   + + +KP+G+V      +   T+ + L       + 
Sbjct: 207 AKLEQHGTDEPEDIALDIMYEDDSVLVINKPVGMVVHPGAGNWTGTLVNGLLYHYPNQAH 266

Query: 105 FSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
             R   V R+D NT GLL++  T    +    +L      R Y+    G      +  LK
Sbjct: 267 LPRAGLVHRIDKNTSGLLVIGKTKAAQMELQDQLRDKTVYRHYQCIVAG-----DVASLK 321

Query: 163 KGIVIQG------ICYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKV 204
           +   I             M V+   +      + +             L  G+  +I+  
Sbjct: 322 RQRTIDAPIGRHRTQRTKMTVSSVGKPAVTHIMNITALNDNYSLLDVQLETGRTHQIRVH 381

Query: 205 FEFFNWKVN 213
                  + 
Sbjct: 382 LSHIGHPII 390


>gi|254509017|ref|ZP_05121122.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 16]
 gi|219548052|gb|EED25072.1| tRNA pseudouridine synthase C [Vibrio parahaemolyticus 16]
          Length = 240

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 49/172 (28%), Gaps = 31/172 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDDYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLIFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI--------------- 170
             +A  +     + +  + Y     G +++         + +  I               
Sbjct: 67  SEVASQVMPMFANHEMEKTYHAIVRGWIEESGRLDYALKVELDKIADKHASQDKEAQEAI 126

Query: 171 ----CYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                   ++V   T K         L E     G+  ++++        + 
Sbjct: 127 TDYWPLAKVEVPHSTGKFPTTRY--CLMEMKPLTGRKHQLRRHMAHLRHPIV 176


>gi|120554606|ref|YP_958957.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324455|gb|ABM18770.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
          Length = 267

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 63/177 (35%), Gaps = 19/177 (10%)

Query: 49  RAAVNVMSTDHIEVDGVPLRKAE--------RTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +    +     +  D   L +          + R  ++ KP GL++  S      ++   
Sbjct: 58  KPGTRI----QLFYDDQVLARKPETPTLLENKGRYSVWFKPHGLLSQGSQWGDHCSLLRL 113

Query: 101 LP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
               + +    V RLD +  GL+L+ +DG  A  L          ++YR R  G +  D 
Sbjct: 114 AEIELNTPCFLVHRLDADAAGLMLIAHDGKAAAALSELFAGRAMTKIYRARVAGNLMADD 173

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-VTVGLREGKNREIKKVFEFFNWKVN 213
           L L      + G        TL   + S+   V V +  G+  +I++        + 
Sbjct: 174 LRL---DTPLDGKDSISRVTTLSRDEDSDTTDVQVRIETGRKHQIRRHLAGIGHPIV 227


>gi|71279408|ref|YP_270347.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
 gi|71145148|gb|AAZ25621.1| RNA pseudouridine synthase family protein [Colwellia
           psychrerythraea 34H]
          Length = 318

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 26/153 (16%), Positives = 51/153 (33%), Gaps = 15/153 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTNDGGLA 131
             +++KP G+++  S      T+                V RLD    GL+++ +    A
Sbjct: 117 YSVWYKPYGMLSQGSKWSDHCTIARFAQQNLPNERPAFIVHRLDRAATGLIIVAHSKSAA 176

Query: 132 RVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD----TQKGS 185
           R L          + Y++  HG    D     +  I+   +     + T       +   
Sbjct: 177 RALSHMFEHHQLEKHYQIIVHG----DHRKRAQPDIIDSDVDGKKARSTFTCLAYDEMTD 232

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN--RLI 216
            + + V +  G+  +I+         V   RL 
Sbjct: 233 QSLIKVKIDSGRKHQIRLHAASIAMPVVGDRLH 265


>gi|315634350|ref|ZP_07889637.1| tRNA pseudouridine synthase C [Aggregatibacter segnis ATCC 33393]
 gi|315476940|gb|EFU67685.1| tRNA pseudouridine synthase C [Aggregatibacter segnis ATCC 33393]
          Length = 237

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 62/196 (31%), Gaps = 38/196 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D      V   L     + V  + RLD  T G+LL   +
Sbjct: 8   QDEHIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQLVYPIHRLDRPTSGVLLFALN 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              A +L       Q  + Y     G V  Q K++   K + +  I     Q   + Q  
Sbjct: 68  SETANLLCHQFEQKQTEKEYLAVVRGYVTGQGKIDYPLK-VQLDKIADKFAQQDKEPQSA 126

Query: 185 SN----------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                                   + V +  + G+  ++++  +     +  L    YG 
Sbjct: 127 VTFYDGLKTVEMPYGVGRYATSRYSLVRLIPKTGRKHQLRRHMKHIFHPI--LGDTQYGD 184

Query: 223 FQLGTLLAGSTREVSK 238
                      R +++
Sbjct: 185 LH-------QNRALTE 193


>gi|315586586|gb|ADU40967.1| RluA family ribosomal large subunit pseudouridine synthase
           [Helicobacter pylori 35A]
          Length = 327

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 53/313 (16%), Positives = 106/313 (33%), Gaps = 63/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKIAPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFF 208
            N LK  IV++       + +  ++    + +T       +   L  G+  +I+      
Sbjct: 192 NNRLKM-IVLK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL 244

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
                 L R   G   L  L       + K+ +R  L  +L+E      +  +     L+
Sbjct: 245 ----EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLL 295

Query: 269 RDRPNIISEVPDD 281
           +D    + +V D 
Sbjct: 296 KDMLEYLKKVFDK 308


>gi|207092511|ref|ZP_03240298.1| hypothetical protein HpylHP_06295 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 327

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 54/309 (17%), Positives = 108/309 (34%), Gaps = 61/309 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKIAPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  DLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L  G+   + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLN-GA---LPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEV 278
           D    + +V
Sbjct: 297 DMLEYLKKV 305


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 45/254 (17%), Positives = 80/254 (31%), Gaps = 61/254 (24%)

Query: 12  TPQRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVNV------------ 54
             +R+ + +A          SR  ++ +I    V VNG+++  A+  V            
Sbjct: 25  AGERLDRFLAAETAAAGADLSRTRLKTLIEGGHVSVNGVIVTEASFAVRAGQALAVAVPP 84

Query: 55  -----MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---- 105
                 + + I +D     + E   L +  KP GLV          T+ + L +      
Sbjct: 85  AAEPIPAGEAIALD----IRFEDEHLLVLDKPAGLVVHPGAGHESGTLVNALIAHCGDSL 140

Query: 106 ------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHG-- 151
                  R   V RLD +T GL+++       + L             LR Y     G  
Sbjct: 141 SGIGGVKRPGIVHRLDKDTSGLMVVAKTDRAHQGLARLFADHGRTLPLLREYLAFVWGAP 200

Query: 152 --------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                          VD++K+ ++      +G         L+      A +   L  G+
Sbjct: 201 DRASGLVDAPLGRHPVDREKIAIVAA---ARGRRAVTHWRLLEQLGPEVAALACRLETGR 257

Query: 198 NREIKKVFEFFNWK 211
             +I+       W 
Sbjct: 258 THQIRVHMASLGWP 271


>gi|326499976|dbj|BAJ90823.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326504092|dbj|BAK02832.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 389

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 31/236 (13%), Positives = 64/236 (27%), Gaps = 59/236 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----------WLYHKPIGL 84
           I   ++ V+G ++    + +     +    +  ++     L             +KP GL
Sbjct: 67  IRNGQITVDGQVVTDPDIILSEGSKLVYHRLSWKEPFAPYLLQVLYEDDDMLALNKPSGL 126

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVI---------------SVGRLDINTEGLLLLTNDGG 129
                    + TV   L     ++                 V RL   T GLLL      
Sbjct: 127 QVLPKGLFQQRTVLAQLQWKEWKMPPSSCSKKKNVQLHPVPVHRLGRGTSGLLLCAKTKL 186

Query: 130 LARVLEL-------------------PSTQWLRVYRVRFHGQV--DQDKLNL-------- 160
               L                        +  + YR    G +  D+D +          
Sbjct: 187 AKVQLASYFAEGAANAEKKRDGTEVGKEWKISKFYRALVTGILEHDEDVITQPIGLVHYP 246

Query: 161 -LKKGIVIQGICYGDM--QVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +G+ +          +V +  +    +   V V +  G+  +I+    +    
Sbjct: 247 GVAEGLYVACSSGKPAMSKVCVLERLAHQNQTLVQVEIHSGRPHQIRIHLAYIGHP 302


>gi|325283365|ref|YP_004255906.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
 gi|324315174|gb|ADY26289.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
          Length = 319

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 75/250 (30%), Gaps = 47/250 (18%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----------MSTDH 59
             T  R+  V A     SR +V   IA  RV+V G    +A+  +               
Sbjct: 11  TATAGRLDAVAAELTGESRSQVALWIAAGRVEVEGKAATKASHKLRGGEALHISPPPPAD 70

Query: 60  IEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVIS 110
           + V    +      E   L   +KP G+VT  +      T+ +       LP        
Sbjct: 71  LSVQPEQVPLDVLYEDDALIAVNKPPGMVTHPAPGVVSGTLVNALLGRLELPQQSDHDSP 130

Query: 111 -------VGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKLNL 160
                  V RLD +T G++++      A      S +     +VY     G+        
Sbjct: 131 AGYRPGIVHRLDKDTSGVIVVA-KTVQAHAALSASFKARETQKVYLAIAAGEWKAQTPAK 189

Query: 161 L----------KKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLRE---GKNREIKK 203
           +          ++ + + G    D Q           G    + +   E   G+  +I+ 
Sbjct: 190 VDAPIGRHPVQRQKMTVGGANPRDAQTRFVPLSHHPDGHGRTLALVRCEPRTGRTHQIRV 249

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 250 HLAHLGSPIV 259


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 44/255 (17%), Positives = 79/255 (30%), Gaps = 66/255 (25%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             QR+   +AR      R  + R++    V+VNG     A   + S+D + +  V + + 
Sbjct: 19  EGQRLDNFLARHLKGVPRSHIHRIVRSGEVRVNGGRA-SADQKLQSSDQVRIPPVRVAQP 77

Query: 71  ERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
           +  R               L   +KP G+        G S V   +              
Sbjct: 78  DAPRAAPALQFPVVFEDDFLLAINKPEGVAV-----HGGSGVSFGVIEALRAARPTAKFL 132

Query: 111 --VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             V RLD +T GLLL+         L   L      + Y     G   +         ++
Sbjct: 133 ELVHRLDRDTSGLLLIAKKRSALTTLHAALRERHADKRYLALVAGLWTRGA-------VM 185

Query: 167 IQGICYG------DMQVTLDTQKGSNA-----------------WVTVGLRE-----GKN 198
           I+   +       + +V +D Q+G  +                 W  + L +     G+ 
Sbjct: 186 IEAPLHKYLLANGERRVRVDVQQGQESRTQFRSQEQFALPGLGPWGGLSLMQARLLTGRT 245

Query: 199 REIKKVFEFFNWKVN 213
            +I+         + 
Sbjct: 246 HQIRVHLAHCGHPIV 260


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 83/236 (35%), Gaps = 44/236 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVIA      SR +++ ++  + + VN    E+ +  V + D I++   P +     
Sbjct: 15  RLDKVIAEKIKDLSRTKIKELVNDKNILVNNK-AEKVSYKVQAGDLIDITVPPAKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVIS 110
                     E   + + +KP G+V   S      T+ + L          P  F R   
Sbjct: 74  AQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTHKLADSPEGF-RPGI 132

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD-------------Q 155
           V R+D +T GLL++  +      LE  L      R Y    HG  +              
Sbjct: 133 VHRIDKDTSGLLMVAKNDKARESLEKQLAEKINKREYLAIVHGNFETKNGVIDAPIGRNP 192

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +    +   +  +G        T+  Q    + V   L  G+  +I+   ++    
Sbjct: 193 NNRKQMA--VNPKGKAAVTHF-TVLEQFKDYSLVKCVLETGRTHQIRVHMKYIGHP 245


>gi|18310186|ref|NP_562120.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           perfringens str. 13]
 gi|110800940|ref|YP_695859.1| RluA family pseudouridine synthase [Clostridium perfringens ATCC
           13124]
 gi|169344395|ref|ZP_02865365.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|182626167|ref|ZP_02953926.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
 gi|18144865|dbj|BAB80910.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           perfringens str. 13]
 gi|110675587|gb|ABG84574.1| pseudouridine synthase, RluA family [Clostridium perfringens ATCC
           13124]
 gi|169297468|gb|EDS79576.1| pseudouridine synthase, RluA family [Clostridium perfringens C str.
           JGS1495]
 gi|177908523|gb|EDT71051.1| pseudouridine synthase, RluA family [Clostridium perfringens D str.
           JGS1721]
          Length = 324

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 86/264 (32%), Gaps = 62/264 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + +  ++VNG   +    +++
Sbjct: 2   KIEIGTNEAGQRLDKFL-------RKYLKDVPLSAIFKALRKGDIRVNGKKQKE-KYSLL 53

Query: 56  STDHIEV--------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
             D IE+                     G      E   + L  K  G++      +G  
Sbjct: 54  EGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAP 113

Query: 96  TVFDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           T+ D + S   R               S  RLD NT G++    +    ++L   +   +
Sbjct: 114 TLTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERK 173

Query: 141 WLRVYRVRFHGQVDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
             + Y     G++   K          L K  V         ++ +D +     G+ + +
Sbjct: 174 VKKYYCALVKGKIQPGKYEAYISKDDELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 234 EIELITGRSHQLRAHLAHLGNPIV 257


>gi|322385565|ref|ZP_08059209.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
 gi|321270303|gb|EFX53219.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
          Length = 297

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 72/210 (34%), Gaps = 40/210 (19%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---------------AERTRLWLYHKPI 82
             + VNG   + A   +   D + VD +P  K                E     +  KP 
Sbjct: 35  GNILVNGQS-QNAIYLLDIGDKVTVD-IPSEKGFESLEAVDRDLSIVYEDEHFLVLDKPA 92

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           G+ +  S  +  +T+ + + + +        +V  V RLD +T GL+L    G     L 
Sbjct: 93  GVASIPS-VNHSNTMANFVKAYYIRQDYENQQVHIVTRLDRDTSGLMLFAKHGYAHARLD 151

Query: 135 -ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
            +L      + Y     G             + +D  +++ + +  +   Y      +  
Sbjct: 152 KQLQKKMIEKRYYALVQGSGELKLEGDIIAPIGRDPDSIITRCVT-KDGKYAHTSYKVVG 210

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           Q G    V + L  G+  +I+  F    + 
Sbjct: 211 QFGDIYLVDIRLHTGRTHQIRVHFAHLGFP 240


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 85/245 (34%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE+  
Sbjct: 69  VVPDELAGERLDKVLARLFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------PS 103
                      + VPL    E   L + +KP G+V   +  +   TV + L        +
Sbjct: 128 DLLPEQLAFTPEPVPLEIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD  T GL+++         L  +L +    R Y     G          
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 152 QVDQDKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFE 206
            + +D     +  +V    G         +DT   Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTGASGKPARTHFRRVDTAIWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWK 211
                
Sbjct: 308 HIGHP 312


>gi|331091184|ref|ZP_08340025.1| hypothetical protein HMPREF9477_00668 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404631|gb|EGG84170.1| hypothetical protein HMPREF9477_00668 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 320

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 56/336 (16%), Positives = 116/336 (34%), Gaps = 79/336 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVER-----MIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +  N   QR+ K++A+    S  E  +     M+ ++ + +NG         +++ D ++
Sbjct: 6   IAANEAGQRLDKLLAK--YLS--EAPKSFLYKMLRKKNIVLNGKKA-SGNEKLVAGDSVK 60

Query: 62  V--DGVPLRK-----------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +      ++K                  E   + L +KP G+++  ++    S V   + 
Sbjct: 61  LFLSDETIQKFSKEITVCKSNTKLDILYEDDDILLVNKPAGMLSQKAEAKDISLVEHLIS 120

Query: 103 SIFS------------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVR 148
            +              +     RLD NT GL++   +  G           +  + YR  
Sbjct: 121 YLLESGQLTRENLKSFKPSICNRLDRNTSGLVVCGKSLKGLQTMGQLFKERKLKKYYRCI 180

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVT----LDTQKGSN-----------AWVTVGL 193
             G V +       KG +I+      + V+     ++Q+                + V L
Sbjct: 181 VAGNVTE---KQYVKGYLIKDEKKNQVTVSDTYFPESQEIETEYRPIQQLKQGTLLEVHL 237

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE-QLGPHLLEE 252
             GK  +I+         V        G ++ G+      RE++ +  +E QL   LL  
Sbjct: 238 ITGKTHQIRAHLASQGHAV-------IGDYKYGS------REINDRYKKEYQLSHQLLHA 284

Query: 253 AQVNLDA----PIYSSETLVRDRPNIISEVPDDFTR 284
            ++ +      P  S +  V   P    ++ +  +R
Sbjct: 285 YRLEVPKTKELPQLSEKMFVAPLPKQFQKIIEGESR 320


>gi|257867857|ref|ZP_05647510.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC30]
 gi|257874186|ref|ZP_05653839.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC10]
 gi|257801940|gb|EEV30843.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC30]
 gi|257808350|gb|EEV37172.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC10]
          Length = 299

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 81/234 (34%), Gaps = 48/234 (20%)

Query: 19  VIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV----------- 62
            +   G+      + ++A+      ++ VN         ++   D + +           
Sbjct: 17  FLKEQGV-----SKGLLAKIKFQGGKIFVNDHEQNVL-FSLAQNDRVTIVIPPEGEHETM 70

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVG 112
             D  P+    E   L + +KP G+ +  +      T+ + + + +         +  V 
Sbjct: 71  LADPTPIEIVYEDAHLLVVNKPAGISSIPAQYHPTGTMANRVKAYYQAQHYEDQVIHVVT 130

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD-------------QDK 157
           RLD +T GL+L    G     L+      Q ++ Y+    G++              +D 
Sbjct: 131 RLDRDTSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAGELPALSAHGEIELPIARDL 190

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +LLK+ +  +G      +  L  +    A V + L  G+  +I+  F      
Sbjct: 191 TSLLKRKVSDEGKEART-EYWLKQRNSDCALVDIQLHTGRTHQIRVHFSAIGCP 243


>gi|168217835|ref|ZP_02643460.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
 gi|182380127|gb|EDT77606.1| pseudouridine synthase, RluA family [Clostridium perfringens NCTC
           8239]
          Length = 324

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 86/264 (32%), Gaps = 62/264 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + +  ++VNG   +    +++
Sbjct: 2   KIEIGTNEAGQRLDKFL-------RKYLKDVPLSAIFKALRKGDIRVNGKKQKE-KYSLL 53

Query: 56  STDHIEV--------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
             D IE+                     G      E   + L  K  G++      +G  
Sbjct: 54  EGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAP 113

Query: 96  TVFDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           T+ D + S   R               S  RLD NT G++    +    ++L   +   +
Sbjct: 114 TLTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERK 173

Query: 141 WLRVYRVRFHGQVDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
             + Y     G++   K          L K  V         ++ +D +     G+ + +
Sbjct: 174 VKKYYCALVKGKIQPGKYEAYISKDDELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 234 EIELITGRSHQLRAHLAHLGNPIV 257


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 39/176 (22%), Positives = 64/176 (36%), Gaps = 26/176 (14%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
            V+     QRV   +  A   SR +++R+  +  V+VNG  +++  + V +  HI V+  
Sbjct: 10  TVEPTKAGQRVDLFVGEALGLSRAKLKRLFEEGAVRVNGRAVKK-GLLVSAGQHILVEWE 68

Query: 64  ----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-- 110
                     G PL    E   L +  KP G  +    P    TV + L + +       
Sbjct: 69  EETREAVPDTGFPLVVLHEDAALVVVDKPAGRPSHPLKPGETGTVANALIARYPECAQAS 128

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                     RLDI T G+LL        + L       +  + Y     G +  +
Sbjct: 129 EDAREGGLCHRLDIETSGVLLAARTREAWQRLRTAFSGREVDKHYVALVTGPLADE 184


>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 = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 77/242 (31%), Gaps = 41/242 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGI-----------------LL 47
           I+ ++    R+ + +A+     SR  ++  I ++RV V+G                    
Sbjct: 4   IIPDHCAGLRLDQALAQLLAEWSRSRLQSWILEKRVSVDGACSLPRQKVWGGEKIVLSPA 63

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
              A      + I +D       E   + +  KP GLV      + + T+ + L     +
Sbjct: 64  RDPAETAHEPEAIALD----IVHEDHAIIIIDKPAGLVVHPGSGNWQGTLLNALLHHSPQ 119

Query: 108 VIS------VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG-------- 151
           +        V RLD  T GLL++         L     +    R Y     G        
Sbjct: 120 LSGIPRSGIVHRLDKETSGLLVVAKTLEAQTSLVRQLQKRTVKREYLALVWGSVSSHGRV 179

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              V +  +   +  +V  G      +  +  Q      +  GL  G+  +I+   +   
Sbjct: 180 DAPVGRHPVQRTRMAVVASGKEART-RYEVLEQFTDCTLLRCGLETGRTHQIRVHMQSLG 238

Query: 210 WK 211
             
Sbjct: 239 HP 240


>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 = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/258 (17%), Positives = 78/258 (30%), Gaps = 52/258 (20%)

Query: 6   IVQENFTPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNV--------- 54
           +  E     R+ + +A   A   SR  ++ +I +  V +NG  +      V         
Sbjct: 16  LADEKAEGNRLDQWLAARLAPDFSRSRIQALIREGAVTLNGRTVAEPKRKVAAGEFYCIT 75

Query: 55  -MSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
               +  E  G  +      E   L +  KP GLV      +   T+ + L         
Sbjct: 76  LPEPEAPEPQGEDIPLDILYEDEALIVIDKPAGLVVHPGPGNWTGTLVNALIHHCGDTLS 135

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHG--- 151
                 R   V RLD +T G++++       RVL              R Y     G   
Sbjct: 136 GIGGVRRPGIVHRLDRDTSGVMVVAKTDQAHRVLAEAFADHGQDGDLERAYVALVWGVPR 195

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVT----LDT------QKGSNAWVTVGL 193
                    + +   +   + +V QG       VT    L+       ++   A V   L
Sbjct: 196 RISGLVDAPLGRSASDRTLRAVVPQGRADARHAVTHYTVLERYGTGTPEEQIAALVECRL 255

Query: 194 REGKNREIKKVFEFFNWK 211
             G+  +I+         
Sbjct: 256 ETGRTHQIRVHMAHIGHP 273


>gi|327483626|gb|AEA78033.1| tRNA pseudouridine synthase C tRNA Psi65 [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/170 (15%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASDVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G        L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPIATGKFNTTRYCLMEMQPKTGRKHQLRRHMAHLRHPIV 176


>gi|319938961|ref|ZP_08013325.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319812011|gb|EFW08277.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 296

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/279 (16%), Positives = 94/279 (33%), Gaps = 52/279 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKPIG 83
             ++VNG   + A   +   D + +D                L    E     + +KP G
Sbjct: 35  GDIQVNGKK-QNAIYLLDIGDKVVIDIPAEEGFSSLCAVEKELDIVYEDKHFLILNKPSG 93

Query: 84  LVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL-- 134
           + +  S  +  +T+ + + + +        ++  V RLD +T GL+L    G     L  
Sbjct: 94  VASIPS-VNHSNTMANFVKAYYIANHYENQQIHIVTRLDRDTSGLMLFAKHGYAHARLDK 152

Query: 135 ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L      + Y     G             + ++  +++ +  V +   Y      +  Q
Sbjct: 153 QLQKKVIEKHYYALVKGSAPLKPEGDIIAPIAREDSSIITR-CVAKNGKYAHTSYKVLAQ 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
                 V + L  G+  +I+  F +  + +               L  GS   ++  I R
Sbjct: 212 YDDIYLVDIHLHTGRTHQIRVHFSYIGFPLLG-----------DDLYGGS---MTDGITR 257

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
           + L  H L       +  +  S  L  D   +I ++ + 
Sbjct: 258 QALHCHSLRFYNPFHEEVVNKSSPLPEDFQTVIQKLSNK 296


>gi|229523315|ref|ZP_04412722.1| tRNA pseudouridine synthase C [Vibrio cholerae TM 11079-80]
 gi|229339678|gb|EEO04693.1| tRNA pseudouridine synthase C [Vibrio cholerae TM 11079-80]
          Length = 244

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG------- 169
             +A  +     + +  + Y     G +++         ++L+ +      Q        
Sbjct: 67  SQIASDVMPMFANHEMEKTYHAIVRGWIEEADVLDYPLKEELDKIADKFAKQDKEAQSAV 126

Query: 170 ICYGD-MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             Y    +V L    G  A     L E     G+  ++++        + 
Sbjct: 127 TAYRPLAKVELPISTGKFATTRYCLIEMQPKTGRKHQLRRHMAHLRHPIV 176


>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 = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/264 (14%), Positives = 84/264 (31%), Gaps = 54/264 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + I  E    QR+ + + +      SR  ++ +I +  +K++G L+      +    
Sbjct: 1   MVTQQITDEGALGQRLDQWLTKQYHSALSRSRLQALIREGYLKIDGQLIHEPKTKLKPNQ 60

Query: 59  HIEV----------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            IE+           G  ++     E   + + +K  GLV    + +   T+ + L    
Sbjct: 61  MIELTIPILRDAKPSGEAIKLDILFEDDHVIVINKQAGLVVHPGNGNLTGTLVNALIYHC 120

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRF 149
                      R   V RLD NT G++++  +    + L    +   R       Y    
Sbjct: 121 GDSLSGIGGVKRPGIVHRLDKNTSGIMVVAKNDLAHKNLSAQFSDHGRTSALDRRYHALI 180

Query: 150 HGQVDQDKLN-----------LLKKGIVIQGICYGDMQVT----------LDTQKGSNAW 188
            G  +++                K+ ++     +    VT             +    + 
Sbjct: 181 WGSPNRNVWKIDAPLGRSPHNRTKQAVIYSQNPHARHAVTHFSLLEKYGICSDKTSFASL 240

Query: 189 VTVGLREGKNREIK-KVFEFFNWK 211
           +   L  G+  +I+  +       
Sbjct: 241 LECRLETGRTHQIRVHM-AHIGHP 263


>gi|332365269|gb|EGJ43032.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1059]
          Length = 291

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 72/205 (35%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D + +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVNPGDDVCLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAILFAKNPFVL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+    KL           +  K+ +  Q   Y +  V
Sbjct: 147 PILNRLL-EKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVEPQKGLYAETHV 205

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T   Q G  A V   L+ G+  +I+
Sbjct: 206 TRLKQFGQAALVKCQLKTGRTHQIR 230


>gi|308184530|ref|YP_003928663.1| hypothetical protein HPSJM_03780 [Helicobacter pylori SJM180]
 gi|308060450|gb|ADO02346.1| hypothetical protein HPSJM_03780 [Helicobacter pylori SJM180]
          Length = 327

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 56/311 (18%), Positives = 106/311 (34%), Gaps = 59/311 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLVLKEGDEITLLTPKITPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISV 111
                     E   L + +KP  LV   +      T+ D L S            R   V
Sbjct: 73  ELDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLKSQNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVCLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVT-------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            N LK  I ++       + +       L +Q G +  +   L  G+  +I+        
Sbjct: 192 NNRLKM-IALKVAQKEKSRYSKSEFTSLLASQNGMD-LIGAKLFTGRTHQIR---AHL-- 244

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRD 270
               L R   G   L  L       + K+ +R  L  +L+E      +  +     L++D
Sbjct: 245 --EYLNRHIIGD-NLYGLNE----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKD 297

Query: 271 RPNIISEVPDD 281
               + +V D 
Sbjct: 298 MLEYLKKVFDK 308


>gi|302382390|ref|YP_003818213.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193018|gb|ADL00590.1| pseudouridine synthase, RluA family [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 336

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 76/237 (32%), Gaps = 45/237 (18%)

Query: 11  FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTD-HIEV------ 62
               R+ K +ARA    SR  ++ ++AQ  V  +G ++   +   +  D  I V      
Sbjct: 25  MVGDRLDKALARALPTLSRGRLQALLAQGAVSHDGAVVTDGSSRAIPGDYDITVPPVMAA 84

Query: 63  ----DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SR 107
                 +PL    E   L +  KP G+    +      T+ + L              +R
Sbjct: 85  EPRAQAIPLTVLYEDADLIVIDKPAGMAAHPAPGTPDGTLVNALLHHCGATLSGIGGVAR 144

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV------------ 153
              V RLD +T G+++          L     +    R Y     G              
Sbjct: 145 PGIVHRLDKDTSGVMVAAKSDRAHAGLSALFATHDIERTYIALTRGAPSPTLGRIETLIG 204

Query: 154 ----DQDKLNLLKKG--IVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
               D+ K+ +LK G    I                 +   A V   L+ G+  +I+
Sbjct: 205 RSSSDRKKMAVLKSGGRNAITDYVVQARYAVPAKPGAAPLAARVACTLQTGRTHQIR 261


>gi|124516586|gb|EAY58094.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Leptospirillum rubarum]
          Length = 339

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 80/256 (31%), Gaps = 53/256 (20%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V     P+R+   ++      +R  V+R++ ++ V +N I     +  V   D I V  
Sbjct: 22  LVPRGEQPKRLDIYLSKNCLGFTRSRVQRLLEEKLVTINDIYPAS-SHKVRGGDRIRVLI 80

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                     + + L    E   L +  KP GLV   +      T+ + L   F      
Sbjct: 81  PPPRSQTAQPENIRLEILYEDEDLIVISKPPGLVVHPAPGHSSGTLVNGLLFHFQSQGDE 140

Query: 107 ----------------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
                           R   V RLD +T G++++     +   L          + Y   
Sbjct: 141 QKKGEPEEEEEAERPLRAGLVHRLDQDTSGVMVVGKTESVVLDLMNQFKDRSVSKKYLAL 200

Query: 149 FHGQVDQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
             G + +                      +   G         L+T   + + + V L  
Sbjct: 201 VKGILPKKRGEINAPIGRSTHDRKKFT--VRQDGKPSVTRYRVLETYHENYSLLEVTLLT 258

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+  F +  + 
Sbjct: 259 GRTHQIRVHFRYLGFP 274


>gi|322420987|ref|YP_004200210.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320127374|gb|ADW14934.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 303

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 74/232 (31%), Gaps = 59/232 (25%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------VPLRKA-----ERTRLWLY 78
           +++I    +K+NG  +      +   D + +            L        E T +   
Sbjct: 32  KKLINSGHLKINGSAV-EPGQILRFADQVTIKESSKTAALLARLTPEMDILFEDTWIVCL 90

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLAR 132
           +KP GL    ++     T+ D   ++        ++  V RLD  T G ++L      A 
Sbjct: 91  NKPAGLAVHRTEDPDEITLVDLAEALLKKRDGAGKLRPVNRLDKGTSGAIILAKSAVAAG 150

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +    +      ++Y     G++ +                 G +   LD ++   +++ 
Sbjct: 151 MFGKMVQEEGLGKLYLAMVEGKLQKQ----------------GTIDAPLDGKESQTSYLR 194

Query: 191 VG------------LREGKNREIK---KVFEFFNWKVNRLIRISYGPFQLGT 227
           +             L  G+  +I+   ++       V    R  YG   L  
Sbjct: 195 LFQGGGVALLAVYPLT-GRMHQIRQHFRM---IGHPVLGDKR--YGGRGLSG 240


>gi|167768022|ref|ZP_02440075.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1]
 gi|167710351|gb|EDS20930.1| hypothetical protein CLOSS21_02565 [Clostridium sp. SS2/1]
 gi|291561022|emb|CBL39822.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SSC/2]
          Length = 323

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/262 (16%), Positives = 87/262 (33%), Gaps = 58/262 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++ NI       QR+ K++++    A +  V +M+ ++ +K+NG         +   D 
Sbjct: 1   MRELNITT-REEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKAT-GNEKLSQGDQ 58

Query: 60  IEVD---------------GVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           + +                G    K     E   + + +KP G+++  S P+  S     
Sbjct: 59  VCIYLAEDTINKFREEVKAGKQKIKLDVLYEDENVIMVNKPWGILSQKSKPEDISINDQI 118

Query: 101 LPSIFS------------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYR 146
           +P   +            +     RLD NT G+++   + +G       L      + Y 
Sbjct: 119 IPYAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHRDMEKYYL 178

Query: 147 VRFHGQV--DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---------------WV 189
               G++   Q     LKK           ++V+     G++                 +
Sbjct: 179 CIVKGKIEGSQKVSAYLKK-----DEKTNKVKVSKQEIAGASHIETAYEPVISNDEFTLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWK 211
            V L  GK  +I+         
Sbjct: 234 KVELITGKTHQIRAHLASIGHP 255


>gi|312870084|ref|ZP_07730220.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094387|gb|EFQ52695.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 289

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 78/240 (32%), Gaps = 49/240 (20%)

Query: 12  TPQRVSKVIARAGIASR--REVERMIAQQRVKVNGILLERAAVNVMSTD----------- 58
            P ++ K +   G+  R   E+++   Q +  V+  ++      ++              
Sbjct: 11  EPVKIKKFLQSLGMGHRLFNEIKK--GQGQFLVDHRVVR-PTTQILPNQPLTIQVAPETA 67

Query: 59  --HIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RV 108
              + V   PL+ A     WL   KP G+ +         T+ + +            R 
Sbjct: 68  DPTVAVSHEPLKVAYEDDNWLVVDKPAGVSSIPGPTTSNGTILNRVKGYLEEQGSEDLRP 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
             + RLD  T GLLL+      + ++       + L+ Y     G+   D       G++
Sbjct: 128 HLITRLDRFTSGLLLVAKHHVASSMISQQVQQHRMLKEYTAVVSGRFADD------HGVI 181

Query: 167 IQGICYGDMQVT---------------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            Q I   + QV                ++ Q    A + + L  G+  +I+         
Sbjct: 182 DQPIARREGQVARVIAPDGQRAVTEYWVEDQGVDWARLRLQLHTGRTHQIRVHMASAGHP 241


>gi|308063469|gb|ADO05356.1| hypothetical protein HPSAT_03065 [Helicobacter pylori Sat464]
          Length = 327

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 105/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLYLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---TAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D      +V D 
Sbjct: 297 DMLEYFKKVFDK 308


>gi|227548930|ref|ZP_03978979.1| pseudouridine synthase [Corynebacterium lipophiloflavum DSM 44291]
 gi|227078955|gb|EEI16918.1| pseudouridine synthase [Corynebacterium lipophiloflavum DSM 44291]
          Length = 308

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 80/251 (31%), Gaps = 53/251 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----- 61
           V E     RV + +++    SR     ++A+  V ++       A  V  +D +      
Sbjct: 10  VPEGLEGMRVDQAVSKLFGLSRSVAAELVAEGSVLID-------ASRVAKSDRVRSGALL 62

Query: 62  -----------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF------ 98
                            VDG+ +  ++   +    KP+G+    +      TV       
Sbjct: 63  EVTLPEPRQAPAPKAELVDGLSIIYSDDD-VIAVDKPVGVAAHPTLGWEGPTVVGGLTAM 121

Query: 99  -DNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
              LP      R   V RLD+ T G++++ N      VL+    +    ++Y     G  
Sbjct: 122 GFTLPDAGPPERKGIVQRLDVGTSGVMVVANSVQGYSVLKRAFKERTVSKLYHAVVQGLP 181

Query: 154 DQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +   G         ++  + + + + + L  G+  +I+
Sbjct: 182 DPIAGTIDAPIGRHPSSGWKFAVTSDGRHAVTHYELVEAFREA-SLLEIRLETGRTHQIR 240

Query: 203 KVFEFFNWKVN 213
                      
Sbjct: 241 VHMSAVGHPCV 251


>gi|27365203|ref|NP_760731.1| tRNA pseudouridine synthase C [Vibrio vulnificus CMCP6]
 gi|34582413|sp|Q8DBG5|TRUC_VIBVU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|27361350|gb|AAO10258.1| tRNA pseudouridine synthase C [Vibrio vulnificus CMCP6]
          Length = 245

 Score = 65.2 bits (158), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 54/171 (31%), Gaps = 29/171 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A  +       +  + Y     G ++++ +L+   K + +  I         + Q  
Sbjct: 67  SEVASQVMPMFAGQEMSKTYHAIVRGWIEEEGELDYALK-VELDKIADKFASQEKEAQDA 125

Query: 185 SN-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
                  A V V            GL E     G+  ++++        + 
Sbjct: 126 ITLYKPLAKVEVPYSTSKFPTTRYGLMELKPKTGRKHQLRRHMAHLRHPIV 176


>gi|227535627|ref|ZP_03965676.1| pseudouridine synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|239631158|ref|ZP_04674189.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|227186757|gb|EEI66824.1| pseudouridine synthase [Lactobacillus paracasei subsp. paracasei
           ATCC 25302]
 gi|239525623|gb|EEQ64624.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
          Length = 300

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 84/235 (35%), Gaps = 41/235 (17%)

Query: 13  PQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P +++  + + G  SR +++++      V VN       A  V S D I V   P   A+
Sbjct: 11  PLKLAAFLKQQGF-SRAQLKKLRYQGGFVFVN-KRQRHTAYPVRSGDRILVQTAPEHAAD 68

Query: 72  RTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVIS 110
                              + +KP G+ +  +     +++ + + +           V  
Sbjct: 69  SVVPYSHDLAISYEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIKTKAESQAVHV 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRF--------HG----QVDQ 155
           V RLD +T GL++    G LA  L    L S  +++ Y            HG     +  
Sbjct: 129 VTRLDRDTSGLMVFAKHG-LAHSLLDQQLHSQDFVKQYVAIVTAQTPLATHGWIVLPIGV 187

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                +++ +   G        TLD Q  + A + V L  G+  +I+  F     
Sbjct: 188 SDGFYMRRVVTDTGKASVTEYRTLD-QNTAGAMMLVTLHTGRTHQIRVHFAAIGH 241


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 78/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 58  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 116

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 117 VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 176

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 177 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 236

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K   V  G       V +  +  +++++   L  G+  +I+
Sbjct: 237 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIR 277


>gi|268611664|ref|ZP_06145391.1| RluA family pseudouridine synthase [Ruminococcus flavefaciens FD-1]
          Length = 304

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 82/238 (34%), Gaps = 42/238 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K I+      +R  V+ ++ + ++ V+G  + +    +   D +EV           
Sbjct: 17  RIDKFISDNVEELTRSAVQGLMEKGKILVSGKSVSK-NYKLRDGDTVEVEIPEPEPMDAL 75

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
            + +PL    E + L + +KP G+V   +  +   T+ + L               R   
Sbjct: 76  PEDIPLDIVYEDSDLLVVNKPKGMVVHPAHGNHSGTLVNALLHHCGDSLSGINGVIRPGI 135

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRV-------RFHGQVD------Q 155
           V R+D NT GLL++  +      L          R Y            G +D      +
Sbjct: 136 VHRIDKNTSGLLIVAKNDAAHLHLAEQIKVHSFTREYEAVASGYFKETEGTIDAPIGRHK 195

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +   +  +         ++  Q G  A V + L  G+  +I+    +    V 
Sbjct: 196 TDRKKMC--VTTENSRNAVTHYSVIRQYGGYAHVRLRLETGRTHQIRVHLAYIGHPVL 251


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 77/240 (32%), Gaps = 47/240 (19%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVP 66
           RV K +    + +SR  +++      +  NG  ++  +  V   D + V       D   
Sbjct: 42  RVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMMDRPRYDNAI 100

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
           + +        E   L + +KP GLV      +   T+ +                 +V 
Sbjct: 101 IPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPRYDPNDPQVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------------- 154
            V R+D +T GLL++  T D      L+  +    R Y     G V+             
Sbjct: 161 LVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEGTIEGNIGRN 220

Query: 155 QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +    V+     G   VT   +  + G    V   L  G+  +I+   +     
Sbjct: 221 PKDRMQMA---VLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHT 277


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 78/238 (32%), Gaps = 45/238 (18%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-----------D 58
                R+ + +A     SR + +  I    V+V+G  + +A+  +               
Sbjct: 5   TAQGVRLDQALAYEAKTSRVKAQEWIEMGIVRVDGKPVTKASYRLKGEWVEVEPPPERPP 64

Query: 59  HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------------- 101
            +E + VPL    E   L + +KP G++T  +      T+ + +                
Sbjct: 65  SVEPENVPLEILYEDQDLVVVNKPAGMITHPAPGVTSGTLVNAILGRYAELRGVLATQLE 124

Query: 102 ----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
               P     +    V RLD +T G++L+       R L          + Y     G  
Sbjct: 125 DEEAPPRPELIRPGIVHRLDKDTSGVILVARHEAAHRRLSEAFRGRSVYKRYLAITVGHP 184

Query: 154 DQDKLNLL-------KKGIVIQGI--CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +             +  + + GI   Y +    +    G  A V+  L  G+  +I+
Sbjct: 185 KEGTFAAPIGRHPVDRTRMHVGGIAPRYAETDFEILAIAGEYALVSAILHTGRTHQIR 242


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 76/233 (32%), Gaps = 45/233 (19%)

Query: 15  RVSKVIARAGI-------ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
           R+ + +AR           SR  ++ +I   R+ VNG  +   +  V       +D    
Sbjct: 37  RIDRWLARCLEDRETDPPLSRNRLKTLILDGRLFVNGATITDPSSPVKPGATYRIDVPEA 96

Query: 64  --------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                    +PL    E   L +  KP G+    +    + T+ + L +           
Sbjct: 97  TPAIPEAQDLPLTVVYEDAALIVIDKPAGMTVHPAPGAPKDTLVNALIAHCGDSLSGIGG 156

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV-----------RFHG 151
             R   V R+D +T GLL++         L          R YR            R  G
Sbjct: 157 VKRPGIVHRIDKDTSGLLVVAKTDAAHHALAARFADHSIDRAYRALCWGRPIPPAGRIEG 216

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
            + +   + ++  +  +G     +    T+     +   +   L  G+  +I+
Sbjct: 217 AIGRHPRDRIRMAVRPEGSGKAAVTHFRTVRAFNEAATLLECRLETGRTHQIR 269


>gi|326795397|ref|YP_004313217.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546161|gb|ADZ91381.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
          Length = 250

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 61/164 (37%), Gaps = 27/164 (16%)

Query: 75  LWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP GL+   ++    +  + V      I  RV  V RLD  T G+LL+T D   A
Sbjct: 11  LVAVNKPSGLLVHRTELARGEMEAAVQLLRDQIGQRVYPVHRLDRGTSGVLLMTLDSESA 70

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDK-----LNLL--KKG---IVIQG---------I 170
             L  +  + +  + Y     G +         L  L  +KG     I+G          
Sbjct: 71  SQLGEQFMNREVKKEYSTLVRGHIHDSGSIDYPLAKLNEEKGRSRFKIEGTEQECVSHYE 130

Query: 171 CYGDMQVTLDTQKGSNAWV-TVGLR--EGKNREIKKVFEFFNWK 211
                 V +   K  +  +  + +R  +G+  +I++ F+     
Sbjct: 131 LIEKYTVPIPVSKYPSTRLSHIKVRPEQGRKHQIRRHFKHVFHP 174


>gi|194323822|ref|ZP_03057598.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|208779913|ref|ZP_03247257.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
 gi|194322186|gb|EDX19668.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|208744368|gb|EDZ90668.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
          Length = 317

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 72/208 (34%), Gaps = 35/208 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 22  SRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINIELLPTNEWIAEDINLKIIFEDD 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ ++      +   TV + L           R   V RLD +T GL++    
Sbjct: 81  DIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 140

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                 L  +L   +  R Y     G++ Q     + + I         M +    ++  
Sbjct: 141 SIAYHNLVQQLAERKVSRKYLAIVEGEIYQQG--TINQPIGRDPTNRTKMAINYRGKEAI 198

Query: 186 NAW--VTV----GLRE-----GKNREIK 202
             +  + V     L E     G+  +I+
Sbjct: 199 THYTPIEVYDGFTLIECQLETGRTHQIR 226


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 87/247 (35%), Gaps = 40/247 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           + + I+ E    QR    +A     +R  +++++ + R  V G  + ++   +   D I+
Sbjct: 11  QQRLIITEQEAGQRADVGLAAMLELTRSNMQKLLEEGR-AVRGSKVLKSNYKLRLGDEID 69

Query: 62  V------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           V            + +PL    E   + + +K  G+V   +  +   T+ + L      +
Sbjct: 70  VTLPEPQPLDVQPENIPLDIIYEDEDVVVVNKARGMVVHPAAGNLNGTLVNALLYHCKNL 129

Query: 109 IS---------VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV---- 153
                      V RLD +T G+++   +      L     +    R Y     G +    
Sbjct: 130 SGINGVIRPGIVHRLDKDTSGIMICAKNDAAHLSLSQQIQAKTAQRTYLAVVRGNIKTDS 189

Query: 154 ---------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                    D++    +   +V +G      +  +  + G    V   LR G+  +I+  
Sbjct: 190 GVIETLIARDKNDRKKMA--VVKEGGRDAVTEYEVLERFGKYTIVRCRLRTGRTHQIRVH 247

Query: 205 FEFFNWK 211
            E+  + 
Sbjct: 248 MEYLGYP 254


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/257 (17%), Positives = 89/257 (34%), Gaps = 50/257 (19%)

Query: 1   MKDKN-IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M+ +  IV+     QR+ + ++    G+ SR  ++ ++A+  V  NG    + ++ + + 
Sbjct: 1   MEQREYIVEAEGAGQRIDRFLSGEDTGL-SRSALQGLVAEGHVLCNGKAPAK-SLKLKAG 58

Query: 58  DHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           D I +   D  P+             E   L + +KP G+V   +  +   T+ + L   
Sbjct: 59  DIILLEIPDAKPIEAVPQEIPLDIIYEDAHLLVVNKPKGMVVHPAPGNPDGTLVNALLWH 118

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
                       R   V R+D +T GLL++  D      L          R Y    +G 
Sbjct: 119 CKGSLSGIGGEIRPGIVHRVDKDTSGLLVVAKDDATHIGLSQQMAVHSVERAYNTIVYGG 178

Query: 153 VDQD-------------KLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREG 196
             QD                 +   +      +     T   +  + G    +   L+ G
Sbjct: 179 FAQDEGFVESNLGRSKTDRKKMA--VYPASEPHTKYAYTGYKVLERLGEFTMLECRLKTG 236

Query: 197 KNREIK-KVFEFFNWKV 212
           +  +I+  +    +  V
Sbjct: 237 RTHQIRVHM-ASIHHPV 252


>gi|241668214|ref|ZP_04755792.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25015]
 gi|254876749|ref|ZP_05249459.1| ribosomal large subunit pseudouridine synthase D [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254842770|gb|EET21184.1| ribosomal large subunit pseudouridine synthase D [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 328

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 56/151 (37%), Gaps = 22/151 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ I    + VNG    ++   ++  + +E++   L                E  
Sbjct: 37  SRSQIQKWIKDGLITVNGKT-TKSKHILLGDEEVEINIELLPTNEWLAEDIDLNIVFEDN 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KPI +V      +   T+ + L           R   V RLD +T GL++    
Sbjct: 96  DIIVIDKPIDMVVHPGAGNMTGTISNALLHKYPNQDKLPRAGIVHRLDKDTSGLMVAAKS 155

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                 L  +L   +  R Y     G++ ++
Sbjct: 156 SIAYHNLVQQLSERKVSRKYLAIVEGEIYEE 186


>gi|254294738|ref|YP_003060761.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254043269|gb|ACT60064.1| pseudouridine synthase, RluA family [Hirschia baltica ATCC 49814]
          Length = 369

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/171 (18%), Positives = 56/171 (32%), Gaps = 28/171 (16%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
            F  +R+ K +   A   SR   + +I +  V ++   +      V++     +      
Sbjct: 28  EFAGERLDKWLPIAAPELSRSRAKAIIEKGDVLLDDTAITSPKHKVIADGRYVILMPPPL 87

Query: 63  DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
           D  PL +        E   L + +KP GLV   +      T+ + L    +  +      
Sbjct: 88  DAEPLPEDIPLDVLFEDEHLIILNKPAGLVVHPAPGSTSGTLVNALLHHCAGQLPGIGGV 147

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQV 153
                V RLD +T G+++       A         +    R Y     G  
Sbjct: 148 ARPGIVHRLDKDTSGVMVAA-KTEFAHTGLSSLFQAHFMERAYLAVTRGAP 197


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 77/262 (29%), Gaps = 52/262 (19%)

Query: 2   KDKNIVQENFTPQRVSKVI-ARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
             K +  +     R+   + A+ G   SR  ++ +I   +V + G  +      V + D 
Sbjct: 11  NRKVLTADESAEGRLDAWLTAQVGEEFSRSRIKALIKDGQVFLRGEPVTDPQRKVRTGDS 70

Query: 60  IEV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
            E+           G  +      E   + +  KP GLV      +   T+ + L     
Sbjct: 71  FELTLPEPEDPTPQGEDIPLDILHEDDDVIVISKPSGLVVHPGAGNWTGTLVNALIHHCS 130

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFH 150
                     R   V RLD +T G++++  +    R L L      R       Y+    
Sbjct: 131 NTLSGIGGVRRPGIVHRLDKDTTGVMVVAKNDIAHRHLSLQFADHGRTMPLERAYQAVVW 190

Query: 151 G-----------QVDQDKLNLLKKGIVIQGICYGDMQVT----------LDTQKGSNAWV 189
           G            + +   +  ++ +        D  +T                  + V
Sbjct: 191 GRPRSLSGMVDAPLGRATGDRTRRAVKRPDSQDADEAITHYQVVERFHEKPDATAFASLV 250

Query: 190 TVGLREGKNREIKKVFEFFNWK 211
              L  G+  +I+         
Sbjct: 251 ECRLETGRTHQIRVHMAHIGHP 272


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 69/200 (34%), Gaps = 28/200 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S  E + +I    V   G   +L R  +N  ++  +     P+   E   +
Sbjct: 8   KLLALQEGISNNEAKELIDSGLVSAGGKRLVLARGLLNENTSFKVTKLAKPVMIYEDDNI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   +T+         V +           + RLD  T G++LL  +    +   
Sbjct: 68  VAVNKPP-FITSEK-------VAEIFKFPL-----LNRLDKETSGVILLYKNEEFQKAAI 114

Query: 136 LP--STQWLRVYRVRFHGQVDQDKLNLL-------KKG----IVIQGICYGDMQVTLDTQ 182
               + +  + Y     G V  +    L       K G    I +         V+    
Sbjct: 115 KEFANNKVKKTYLAIVRGIVVDEFSVELPISTVKTKSGAFSKIDLSRGKTAITHVSPLMV 174

Query: 183 KGSNAWVTVGLREGKNREIK 202
           +G  + + VG+  G+  +I+
Sbjct: 175 EGKKSLIKVGIETGRTHQIR 194


>gi|37680745|ref|NP_935354.1| tRNA pseudouridine synthase C [Vibrio vulnificus YJ016]
 gi|320155588|ref|YP_004187967.1| tRNA pseudouridine synthase C/tRNA Psi65 [Vibrio vulnificus
           MO6-24/O]
 gi|37199494|dbj|BAC95325.1| pseudouridylate synthase, 23S RNA-specific [Vibrio vulnificus
           YJ016]
 gi|319930900|gb|ADV85764.1| tRNA pseudouridine synthase C tRNA Psi65 [Vibrio vulnificus
           MO6-24/O]
          Length = 245

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 54/171 (31%), Gaps = 29/171 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A  +       +  + Y     G ++++ +L+   K + +  I         + Q  
Sbjct: 67  SEVASQVMPMFAGQEMSKTYHAIVRGWIEEEGELDYALK-VELDKIADKFASQEKEAQDA 125

Query: 185 SN-----AWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
                  A V V            GL E     G+  ++++        + 
Sbjct: 126 ITLYKPLAKVEVPYSTGKFPTTRYGLMELKPKTGRKHQLRRHMAHLRHPIV 176


>gi|152996227|ref|YP_001341062.1| pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837151|gb|ABR71127.1| pseudouridine synthase [Marinomonas sp. MWYL1]
          Length = 242

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 29/164 (17%), Positives = 57/164 (34%), Gaps = 27/164 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP GL+   +     +  + V          V  V RLD  T G+L++   
Sbjct: 8   QDEHLVAVNKPAGLLVHRTNLAKDEEDAVVQRLRDQTGKWVFPVHRLDRGTSGVLVMAFS 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK-----LNLL-----KKGIVIQGICYGD- 174
             +AR L      ++  + Y     G  ++       L  L     +    I+G      
Sbjct: 68  PEVARRLSTQFAESKTQKTYHCLVRGYCNESGVINYPLAKLNEQKGRSRFKIEGTEREAE 127

Query: 175 ----------MQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEF 207
                     + V +        +W+ V  ++G+  +I++ F+ 
Sbjct: 128 TGFTRLIQYQLPVPVSRYDSMRLSWLEVTPKQGRKHQIRRHFKH 171


>gi|62260278|gb|AAX77894.1| unknown protein [synthetic construct]
          Length = 367

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 71/207 (34%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 63  SRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINIELLPTNEWIAEDINLKIIFEDD 121

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ ++      +   TV + L           R   V RLD +T GL++    
Sbjct: 122 DIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 181

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
                 L  +L   +  R Y     G           + +D  N  K  I  +G      
Sbjct: 182 SIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPIGRDPTNRTKMAINYRGKEAITH 241

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
             +++   G    +   L  G+  +I+
Sbjct: 242 YTSIEVYDGFT-LIECQLETGRTHQIR 267


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 71/207 (34%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 37  SRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINIELLPTNEWIAEDINLKIIFEDD 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ ++      +   TV + L           R   V RLD +T GL++    
Sbjct: 96  DIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 155

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
                 L  +L   +  R Y     G           + +D  N  K  I  +G      
Sbjct: 156 SIAYHNLVQQLAERKVSRKYLAIVEGEIYKQGTINQPIGRDPTNRTKMAINYRGKEAITH 215

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
             +++   G    +   L  G+  +I+
Sbjct: 216 YTSIEVYDGFT-LIECQLETGRTHQIR 241


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 82/244 (33%), Gaps = 57/244 (23%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------- 58
           + +E+   QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D       
Sbjct: 3   VTKEDDQ-QRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTA 61

Query: 59  ---------------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
                           +  +   +   ++      H   G+       +  +     L  
Sbjct: 62  VQKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGI-------EHHTITNALLAR 114

Query: 104 IFSRVISVG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG- 151
             + + SVG         RLD +T GL++          L  EL +  + + Y     G 
Sbjct: 115 FGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGI 174

Query: 152 ------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKN 198
                       +V +  + +++      G      +  ++ + G   + +   L  G+ 
Sbjct: 175 PCPKRGVIHTNIRVKRSDITMMEAANS--GGKPAKTEYEVEQELGEVASLIRCTLHTGRT 232

Query: 199 REIK 202
            +I+
Sbjct: 233 HQIR 236


>gi|27262446|gb|AAN87504.1| Ribosomal large subunit pseudouridine synthase D [Heliobacillus
           mobilis]
          Length = 327

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 82/261 (31%), Gaps = 53/261 (20%)

Query: 2   KDKNIVQENFTPQ-----------RVSKVIARA-GIASRREVERMIAQQRVKVNGILLER 49
             KN+  +   P            R+   +     + SR   +  I +  +KV G+ ++ 
Sbjct: 13  NAKNVETDEDFPMVFATLPEEVDSRLDVWLVNRELVPSRTHGQNWIKEGLIKVEGMTVK- 71

Query: 50  AAVNVMSTDHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRST 96
           A   +   D IEV            + +P+    +   + + +K  GLV   ++     T
Sbjct: 72  ANYRLRPGDRIEVVPAEPVSTEIIPENIPIDIVYQDAHVAVINKSAGLVVHPAEGHTSGT 131

Query: 97  VFDNLPSIFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVY 145
           + + L      +           V R+D +T GLL++         L       L  R Y
Sbjct: 132 LVNALLYHIKDLSGINGELRPGIVHRIDKDTSGLLVVAKHDEAHIHLAEQVKDHLVRREY 191

Query: 146 RVRFHGQV-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTV 191
               HG +             D      +   +V  G         L+    S  + V  
Sbjct: 192 LAIVHGIIGAETGRIDAPIGRDPKDRQKMA--VVSSGKASVTHLRVLERFPESGFSLVRC 249

Query: 192 GLREGKNREIKKVFEFFNWKV 212
            L  G+  +I+    +    V
Sbjct: 250 NLETGRTHQIRVHMAYIGHPV 270


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 76/226 (33%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------------DHIE 61
           R+ + +A+     SR  ++  I    VKVNGI++ RA   V                  E
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIENDLVKVNGIIVNRARGKVFGGEQIEIQAEIEEEIRFE 78

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   + RL
Sbjct: 79  PQNIPLNIVHEDDDIIIINKPKNLVVHPGAGNPDGTVLNALLYYYPPIAEVPRAGIIHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAITHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|332160586|ref|YP_004297163.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|318606936|emb|CBY28434.1| tRNA pseudouridine synthase C; tRNA Psi65 [Yersinia enterocolitica
           subsp. palearctica Y11]
 gi|325664816|gb|ADZ41460.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859592|emb|CBX69932.1| tRNA pseudouridine synthase C [Yersinia enterocolitica W22703]
          Length = 257

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 53/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRF------HGQVDQDKLNLLKKGIVIQGICYGD----- 174
             +AR L L     Q  + Y           G +D +    L K   I            
Sbjct: 67  SDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDK---IADKFARPDKAPQ 123

Query: 175 ---------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                     QV +    G        L E     G+  ++++        + 
Sbjct: 124 PSVTHYQALAQVEVPIAIGRYDTSRFSLMELKPETGRKHQLRRHMAHIRHPII 176


>gi|289449856|ref|YP_003475266.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridiales genomosp. BVAB3 str. UPII9-5]
 gi|289184403|gb|ADC90828.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridiales genomosp. BVAB3 str. UPII9-5]
          Length = 319

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 86/242 (35%), Gaps = 43/242 (17%)

Query: 14  QRVS----KVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +R+     + +   G   +R ++ + + ++RV +      +A + +    H++++   + 
Sbjct: 12  ERLDVTLTECLQELGHKLTRSDITKALNEKRVLLADGTFPKAGLKLTCPCHVKIELSEVA 71

Query: 69  KA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
                          E   L + +KP GLV   +      T+ + L +            
Sbjct: 72  VPRHEAEDLPLDIVFEDEYLLVVNKPRGLVVHPAPGHANGTLVNALLNYCGGNNLSDING 131

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------- 151
             R   V R+D +T GLL++  D  +   L   L      RVY+    G           
Sbjct: 132 EFRPGIVHRIDKDTSGLLVVAKDNSIHNKLAELLSVHAINRVYQAIVFGNFAETAGKIDA 191

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +D  N  K  + ++G        T+   +   + + + L  G+  +I+    +    
Sbjct: 192 PIGRDPRNRQKMAVTLKGKPALTHF-TVLASRPGYSLLRLNLETGRTHQIRVHLSYIGHP 250

Query: 212 VN 213
           V 
Sbjct: 251 VV 252


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 78/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K   V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIR 259


>gi|89256088|ref|YP_513450.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica LVS]
 gi|115314564|ref|YP_763287.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|167010773|ref|ZP_02275704.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC200]
 gi|169656565|ref|YP_001428170.2| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica FTNF002-00]
 gi|254367416|ref|ZP_04983442.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica 257]
 gi|254369095|ref|ZP_04985107.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|290954527|ref|ZP_06559148.1| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295312043|ref|ZP_06802858.1| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica URFT1]
 gi|89143919|emb|CAJ79138.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica LVS]
 gi|115129463|gb|ABI82650.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134253232|gb|EBA52326.1| ribosomal large subunit pseudouridine synthase D [Francisella
           tularensis subsp. holarctica 257]
 gi|157122045|gb|EDO66185.1| hypothetical protein FTAG_00024 [Francisella tularensis subsp.
           holarctica FSC022]
 gi|164551633|gb|ABU61214.2| RNA pseudouridine synthase, RluA family protein [Francisella
           tularensis subsp. holarctica FTNF002-00]
          Length = 332

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 54/148 (36%), Gaps = 22/148 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 37  SRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINIELLPTNEWIAEDINLKIIFEDD 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ ++      +   TV + L           R   V RLD +T GL++    
Sbjct: 96  DIIVIDKPVNMIVHPGAGNPTGTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 155

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQV 153
                 L  +L   +  R Y     G++
Sbjct: 156 SIAYHNLVQQLAERKVSRKYLAIVEGEI 183


>gi|317498384|ref|ZP_07956679.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316894278|gb|EFV16465.1| RluA family pseudouridine synthase [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 323

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/262 (16%), Positives = 87/262 (33%), Gaps = 58/262 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++ NI       QR+ K++++    A +  V +M+ ++ +K+NG         +   D 
Sbjct: 1   MRELNITT-REEGQRLDKILSKYLNKAPKSFVYKMLRKKNIKLNGKKAT-GNEKLSQGDQ 58

Query: 60  IEVD---------------GVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           + +                G    K     E   + + +KP G+++  S P+  S     
Sbjct: 59  VCIYLAEDTINKFREEVKAGKQKIKLDVLYEDENVIMVNKPWGILSQKSKPEDISINDQI 118

Query: 101 LPSIFS------------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYR 146
           +P   +            +     RLD NT G+++   + +G       L      + Y 
Sbjct: 119 IPYAVNQGLISEKELQVVKPSICNRLDRNTTGIIICGISIEGLQTMAEMLKHRDMEKYYL 178

Query: 147 VRFHGQV--DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA---------------WV 189
               G++   Q     LKK           ++V+     G++                 +
Sbjct: 179 CIVKGKLERTQKVSAYLKK-----DEKTNKVKVSKQEIAGASHIETAYEPMISNEEFTLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWK 211
            V L  GK  +I+         
Sbjct: 234 KVELITGKTHQIRAHLASIGHP 255


>gi|268679279|ref|YP_003303710.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268617310|gb|ACZ11675.1| pseudouridine synthase, RluA family [Sulfurospirillum deleyianum
           DSM 6946]
          Length = 326

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/228 (14%), Positives = 73/228 (32%), Gaps = 38/228 (16%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
             +R+   ++      R +VE++I +  V V+ +L  + ++ +  +  +  D        
Sbjct: 7   EAKRLDVAMSEILALPRNQVEKLIKKSGVYVDDVLTHKCSLKLQESSVVRYDFIEAEASK 66

Query: 64  -------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSR 107
                   VP+   +   + + +KP  L    +      T+ D L              R
Sbjct: 67  SAYEIDFDVPVLYEDED-ILVINKPPFLTVHGAPSVKEPTLVDWLQHRGISLSTISGEER 125

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL------- 158
              V R+D  T G L++  +      L          R Y       + ++ +       
Sbjct: 126 HGIVHRIDKETSGALVIAKNNEAHVKLASQLEDKSMGRYYLAIIDLPLKENVVVDLPIGR 185

Query: 159 ---NLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTVGLREGKNREIK 202
              + LK  +  +G            +  G    +   L  G+  +I+
Sbjct: 186 NPNHRLKMAVQREGRSAKSAFCKCSLSHDGKKELIAAKLFTGRTHQIR 233


>gi|317486117|ref|ZP_07944964.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
 gi|316922640|gb|EFV43879.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
          Length = 308

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 73/239 (30%), Gaps = 58/239 (24%)

Query: 17  SKVIARAGIASRREVE------RMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
            K++      SRR  E      R I   +V++NG   +     V   D I V        
Sbjct: 14  QKLLQ---FLSRRFEEPQSVLHRWIRTGQVRINGGRAK-PFDRVKLNDEIRVPPFAGAGT 69

Query: 63  ---------DGVPLRK--AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                     G  L    AE   + ++ KP G +  H       ++   L + F+     
Sbjct: 70  KAERVPASSGGKELPPIVAETADVIVFCKPSG-LPVHPGTGHTDSLTTRLEAAFAGSPFI 128

Query: 110 --SVGRLDINTEGLLL----LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
              V RLD +T GLLL          L+  L        + Y     G+    +   L+ 
Sbjct: 129 PAPVHRLDRDTSGLLLVGKTYAAVRRLSDALAAHDGSVAKDYLAWVQGECPWSRPKRLED 188

Query: 164 GIVIQ--------------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  +                          + V   T +   + V + L  G+  +I+
Sbjct: 189 HLAKRTVGAQGREKVVAGKSRTGGPDEKPASLTVRSLTVREGRSLVLIRLHTGRTHQIR 247


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 78/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K   V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIR 259


>gi|153806600|ref|ZP_01959268.1| hypothetical protein BACCAC_00870 [Bacteroides caccae ATCC 43185]
 gi|149131277|gb|EDM22483.1| hypothetical protein BACCAC_00870 [Bacteroides caccae ATCC 43185]
          Length = 306

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/221 (17%), Positives = 76/221 (34%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + + A+   ASR +++ +++++ V V+ ++        +  + V         E
Sbjct: 24  EPMELMEFLTAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLKPGMKVQISKDKGRKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHG-----------QVDQDKLNLL 161
           D +T GL++   D    R L          R Y     G            +    L + 
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 203

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             G    G            +    + V + L  G+  +I+
Sbjct: 204 SSG-YDDGGSKSITHYRTIKRANGYSLVELDLETGRKNQIR 243


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/244 (14%), Positives = 82/244 (33%), Gaps = 57/244 (23%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------- 58
           + +E+   QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D       
Sbjct: 9   VTKEDDQ-QRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTA 67

Query: 59  ---------------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
                           +  +   +   ++      H   G+       +  +     L  
Sbjct: 68  VQKPSTLSPNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGI-------EHHTITNALLAR 120

Query: 104 IFSRVISVG---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG- 151
             + + SVG         RLD +T GL++          L  EL +  + + Y     G 
Sbjct: 121 FGAGLQSVGSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGI 180

Query: 152 ------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKN 198
                       +V +  + +++      G      +  ++ + G   + +   L  G+ 
Sbjct: 181 PCPKRGVIHTNIRVKRSDITMMEAANS--GGKPAKTEYEVEQELGEVASLIRCTLHTGRT 238

Query: 199 REIK 202
            +I+
Sbjct: 239 HQIR 242


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 49/257 (19%), Positives = 91/257 (35%), Gaps = 45/257 (17%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   QR+ +V A+     SR  +   I    + V+G +L      V +   +E+      
Sbjct: 18  DLGGQRLDQVAAQLFSEHSRSRLAAWIKDGLLTVDGAVLR-PRDTVHAGAVLELSAEQQA 76

Query: 63  DGVPLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IFSRVI 109
            G  + +        E  ++ +  KP GLV      H+D    + +  ++P      R  
Sbjct: 77  QGEWVAQDIPLDIVYEDDQILVIDKPAGLVVHPAAGHADGTLLNALLHHVPDLINVPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-QVDQDKLNLL--KKG 164
            V RLD +T GL+++         L  +L +    R+Y     G  +    ++    + G
Sbjct: 137 IVHRLDKDTTGLMVVAKTLQAQTRLVEQLQARSVSRIYEAIVIGVIITGGTVDAPIGRHG 196

Query: 165 ------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVNRLIR 217
                  V++G         +  +  S+  V V L  G+  +I+  +     +       
Sbjct: 197 QQRQRMAVVEGGKPAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMT-HLGY------- 248

Query: 218 ISYGPFQLGTLLAGSTR 234
               P     L AG  R
Sbjct: 249 ----PLVGDPLYAGRFR 261


>gi|119476781|ref|ZP_01617091.1| tRNA pseudouridine synthase C [marine gamma proteobacterium
           HTCC2143]
 gi|119450037|gb|EAW31273.1| tRNA pseudouridine synthase C [marine gamma proteobacterium
           HTCC2143]
          Length = 243

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/169 (18%), Positives = 57/169 (33%), Gaps = 31/169 (18%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF--DNLPSIF-SRVISVGRLDINTEGLLLL--TNDG 128
            L   +KP GL+   S+ D   T F    L       V  V RLD  T GLLL   ++D 
Sbjct: 13  YLVAINKPSGLLVHRSNIDRHETQFALQLLRDQLGQHVYPVHRLDKPTSGLLLFALSSDV 72

Query: 129 GLARVLELPSTQWLRVYRVRF------HGQVDQDKLNLL--------KKGIVIQG----- 169
                LE  +    + Y           G +D               K+ I  +      
Sbjct: 73  AKTVSLEFSNQTIKKKYLALVRGWCAEQGTIDHALKEQFDKMSGKPKKQAIQAKDAVTHF 132

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                +++     +  ++  ++   E     G+  +I++ F+  +  + 
Sbjct: 133 TRLAKVELPFAVDRYPSSRYSLV--EARPVTGRKHQIRRHFKHISHPII 179


>gi|99081958|ref|YP_614112.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp.
           TM1040]
 gi|99038238|gb|ABF64850.1| ribosomal large subunit pseudouridine synthase D [Ruegeria sp.
           TM1040]
          Length = 337

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 85/240 (35%), Gaps = 38/240 (15%)

Query: 6   IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ +N  P+R+ K IAR     A + SR  + R+I    V V+G     A   V     I
Sbjct: 1   MIADNP-PKRLDKAIARDVPEEANL-SRTRLARLIESGGVFVDGARANDAKSRVAEGALI 58

Query: 61  EV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS 106
            +            + +PL    E   L + +KP G+V   +      T+ +  L    +
Sbjct: 59  VITVEEAEDSHIGPEDIPLDVIHEDADLIVINKPAGMVVHPAPGSPSGTLVNALLHHCGA 118

Query: 107 RVISVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            +  VG         R+D  T GLL++       + L          R Y+   +G  D 
Sbjct: 119 DLSGVGGVKRPGIVHRIDKETSGLLVVAKSDAAHQGLAAQFERHTVERYYQAVCYGVPDG 178

Query: 156 DKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI-K-KVFEFFNWK 211
           +    L+  +G   +      +   L   K         L EG    + + ++ E F   
Sbjct: 179 ND-PRLRGVRGTSFEPGNILKITTQLARHKTDRQR-QAVLFEGGRHAVTRARIIEAFGAP 236


>gi|254779279|ref|YP_003057384.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254001190|emb|CAX29153.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 327

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 50/305 (16%), Positives = 105/305 (34%), Gaps = 53/305 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL+K
Sbjct: 13  RIDEFLAKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKKGDAITLLTPKIVPKPLKK 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L           +  R   V
Sbjct: 73  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL-------NLLK 162
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFNWKVN 213
             + +  +     + +  ++   ++ +T       +   L  G+  +I+           
Sbjct: 193 NRLKMMALKAAKKEKSRYSKSEFSSLLTSPNNLNLIGAKLFTGRTHQIR---AHL----E 245

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L R   G   L  L       +SK+ +R  L  +L+E      +  +     L++D   
Sbjct: 246 YLNRHIIGD-NLYGLNQ----ALSKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 300

Query: 274 IISEV 278
            + +V
Sbjct: 301 YLKKV 305


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 78/221 (35%), Gaps = 34/221 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+  V+A+     SR  +   I +  V VN     +    ++  + I V   P  +    
Sbjct: 40  RLDAVLAKLLPDYSRSRLTSWIKEGAVIVNDKP-SQPKDKMIGGEQICVTVRPSEENLAF 98

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
                      E   + + +KP GLV   +  +   T+ + L +         R   V R
Sbjct: 99  VPEPMDLDIVYEDDTVIVVNKPAGLVVHPAAGNWTGTLLNGLLAHCPELSQIPRAGIVHR 158

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN---------LL 161
           LD  T GL+++         L     +    R+YR   +G V    K+           L
Sbjct: 159 LDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETQIGRDPHNRL 218

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K   V  G       V +  +  +++++   L  G+  +I+
Sbjct: 219 KMAAVKFGGKPAVTHVKVLERYLAHSYIECSLGTGRTHQIR 259


>gi|261856619|ref|YP_003263902.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261837088|gb|ACX96855.1| pseudouridine synthase, RluA family [Halothiobacillus neapolitanus
           c2]
          Length = 340

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 82/246 (33%), Gaps = 36/246 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +++  ++      QR+ + +A+     SR  ++  I    + ++G +       V+  + 
Sbjct: 3   LEETLLIPPECAGQRLDQALAKCWPDYSRSRIQDWIKSGEILLDGEVAR-PRATVLGGES 61

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           +E+              +PL    E   + + +K   +V   +  +   T+ + L     
Sbjct: 62  VELLAEIEEAVAAVPQDIPLDIIYEDDAIIVLNKSPDIVVHPAAGNPDGTLVNALLFHDP 121

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVY------RV---- 147
                 R   V RLD  T G++++      A  + + +    +  R Y       V    
Sbjct: 122 SLVSVPRAGVVHRLDKQTSGVMVVA-KTLAAHKILVENLAARKIRREYDTVVMGHVVAGG 180

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +   +  ++ +   G         L    G   W+ V L  G+  +I+     
Sbjct: 181 TVDAPIGRHPRDRQRQAVTATGKRAVTHYRVLQ-HYGEQTWLRVQLETGRTHQIRVHMAH 239

Query: 208 FNWKVN 213
               V 
Sbjct: 240 IRHPVI 245


>gi|251795307|ref|YP_003010038.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247542933|gb|ACS99951.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 322

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 76/213 (35%), Gaps = 30/213 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------- 70
           ++A      R  V+ ++A  +V VN  +  +    +   + + +     ++         
Sbjct: 39  LLAHLNQG-RNSVKSLLAHGQVYVNDRVETKYNYPLQPGETVVIRKEREKEKFPLIGLTI 97

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISVGRLDINTEGLL 122
             E   + +  K  GL+T  SD +   T +  L          +R+  V RLD +T G+L
Sbjct: 98  LHEDEHVIVASKEAGLLTIASDKETDMTAYRQLMAYVRESDPKNRIFIVHRLDRDTSGVL 157

Query: 123 LLTNDGGLARVLELPSTQWLRV--YRVRFHGQVDQDKLNL---LKKGIVI--------QG 169
           +      + + L+      ++   Y     G+V + +  +   LK+   +          
Sbjct: 158 MFAKSEAVQQKLQEEWQTIVKERSYVALVEGEVKRQEGTISSWLKETKTLRMYSSPHPND 217

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +      L       + V V L  G+  +I+
Sbjct: 218 GQHAVTHYKLLQAGKVFSLVEVHLETGRKNQIR 250


>gi|262184460|ref|ZP_06043881.1| pseudouridylate synthase [Corynebacterium aurimucosum ATCC 700975]
          Length = 292

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 75/226 (33%), Gaps = 39/226 (17%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRK 69
            RV   +A+    SR  V ++ A   V+++G  + + +  + +   I+V       PL  
Sbjct: 1   MRVDAALAKLLGISRARVSQLCAAGDVEIDGAAVGK-SERLNAGGWIDVMMPAPEEPLIP 59

Query: 70  AERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVI 109
            E              +    KP+G+    +      TV   L              R  
Sbjct: 60  KEELVEGMDVLYADEDIICVCKPVGVAAHPTLGWDGPTVIGGLRAAGYALADAGPTERKG 119

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DKLNL----- 160
            V RLD+ T G++++         L+         + Y     G  D     ++      
Sbjct: 120 IVHRLDVGTSGVMVVAASERAYSQLKNAFRERTVQKTYHAVVQGLPDPIVGTIDAPIGRH 179

Query: 161 ----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                K G+V  G         L+  + + + + V L  G+  +I+
Sbjct: 180 PSAGWKFGVVDDGKPAVTHYKLLEAFREA-SLLEVHLETGRTHQIR 224


>gi|94992422|ref|YP_600521.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94545930|gb|ABF35977.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 275

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 69/211 (32%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-----------AERTRLWLYHKP 81
               + VNG + + A   +   D + +D     P  K            E     + +KP
Sbjct: 7   KGGNILVNG-IEQNAIYLLQVGDVVTIDIPNEEPFEKLEAIPFDLDIVHEDDHFLVINKP 65

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           IG  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 66  IGFASIPS-AIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGLMLFAKHGYAHARL 124

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G     D+  +           + + +   G         + 
Sbjct: 125 DKQLQTRSIEKRYFALVSGNGTLPDEGDIIAPIGRSKDSIITRAVDPMGKYAKTSYKVVA 184

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 185 RYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 215


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 78/240 (32%), Gaps = 47/240 (19%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + +SR  +++      +  NG  ++  +  V   D + V           
Sbjct: 43  RVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMMDRPRYDNDI 101

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ +                 +V 
Sbjct: 102 IPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPRYDPNDPQVG 161

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------------- 154
            V R+D +T GLL++  T D      L+  +    R Y     G V+             
Sbjct: 162 LVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEGTIEGNIGRN 221

Query: 155 QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +    V+     G   VT   +  + G    V   L  G+  +I+   +     
Sbjct: 222 PKDRMQMA---VLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHT 278


>gi|320109289|ref|YP_004184879.1| RluA family pseudouridine synthase [Terriglobus saanensis SP1PR4]
 gi|319927810|gb|ADV84885.1| pseudouridine synthase, RluA family [Terriglobus saanensis SP1PR4]
          Length = 298

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 62/199 (31%), Gaps = 25/199 (12%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE----------RTRLWLYHKPIGLVT 86
              V VNG++    +  + S   +  +  P  + +             L   +KP GL T
Sbjct: 43  NGEVTVNGVIAT-GSEALTSGQMLVWNRPPWIEPDAPQHFEVLLDDPHLLAVNKPGGLPT 101

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRV 144
                   +T+   +         V RL   T G++L       A  L     +++  ++
Sbjct: 102 LPGGGFMENTLLRLVQKQSPDANPVHRLGRATTGIVLFAKTPQAASNLTADWNTSRIEKI 161

Query: 145 YRVRFHGQVDQDKLNLL---------KKG-IVIQGICYGDMQ--VTLDTQKGSNAWVTVG 192
           YR    G  D+D   +L         + G +          +    + ++        V 
Sbjct: 162 YRALAQGIADRDAYEILTPIGLVPHPRIGSVWAANPDGKPSKSLAKVISRTTDATTFEVS 221

Query: 193 LREGKNREIKKVFEFFNWK 211
           L  G+  +I+         
Sbjct: 222 LGSGRPHQIRIHLASIGHP 240


>gi|297379941|gb|ADI34828.1| pseudouridine synthase, RluA family [Helicobacter pylori v225d]
          Length = 327

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 105/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLELKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D      +V D 
Sbjct: 297 DMLEYFKKVFDK 308


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 78/240 (32%), Gaps = 47/240 (19%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + +SR  +++      +  NG  ++  +  V   D + V           
Sbjct: 42  RVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMMDRPRYDNDI 100

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ +                 +V 
Sbjct: 101 IPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPRYDPNDPQVG 160

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------------- 154
            V R+D +T GLL++  T D      L+  +    R Y     G V+             
Sbjct: 161 LVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEGTIEGNIGRN 220

Query: 155 QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +    V+     G   VT   +  + G    V   L  G+  +I+   +     
Sbjct: 221 PKDRMQMA---VLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHT 277


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 78/240 (32%), Gaps = 47/240 (19%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + +SR  +++      +  NG  ++  +  V   D + V           
Sbjct: 43  RVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMMDRPRYDNDI 101

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ +                 +V 
Sbjct: 102 IPEDIPLDIVYEDNDLMVINKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPRYDPNDPQVG 161

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------------- 154
            V R+D +T GLL++  T D      L+  +    R Y     G V+             
Sbjct: 162 LVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGIVENNEGTIEGNIGRN 221

Query: 155 QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +    V+     G   VT   +  + G    V   L  G+  +I+   +     
Sbjct: 222 PKDRMQMA---VLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHT 278


>gi|168209672|ref|ZP_02635297.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|168213116|ref|ZP_02638741.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
 gi|170712270|gb|EDT24452.1| pseudouridine synthase, RluA family [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715381|gb|EDT27563.1| pseudouridine synthase, RluA family [Clostridium perfringens CPE
           str. F4969]
          Length = 324

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 86/264 (32%), Gaps = 62/264 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + +  ++VNG   +    +++
Sbjct: 2   KIEIGTNEAGQRLDKFL-------RKYLKDVPLSAIFKALRKGDIRVNGKKQKE-KYSLL 53

Query: 56  STDHIEV--------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
             D IE+                     G      E   + L  K  G++      +G  
Sbjct: 54  DGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAP 113

Query: 96  TVFDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           T+ D + S   R               S  RLD NT G++    +    ++L   +   +
Sbjct: 114 TLTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERK 173

Query: 141 WLRVYRVRFHGQVDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
             + Y     G++   K          L K  V         ++ +D +     G+ + +
Sbjct: 174 VKKYYCALVKGKIQPGKYEAYISKDDELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 234 EIELITGRSHQLRAHLAHLGNPIV 257


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 83/256 (32%), Gaps = 54/256 (21%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             + +V +    +R+ KV+A+     SR  ++  I  +RV+V+G   +     V     I
Sbjct: 67  PRRVVVPDELAGERLDKVVAKVFPEFSRSRLQSWIEAERVRVDGKPAK-IRQPVPLGATI 125

Query: 61  EVDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
           E++   L +               E   L + +KP G+V   +  +   TV + L     
Sbjct: 126 ELEPDLLPEQLAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYG 185

Query: 102 --PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
              +   R   V RLD  T GL+++         L  +L +    R Y     G +  + 
Sbjct: 186 EAAAGLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPDE- 244

Query: 158 LNLLKKGIVIQGICYGDMQVT-------LDTQKGSNAWVTVG-----------LR---E- 195
                 G +   I     + T          +     +  V            +    E 
Sbjct: 245 ------GTIDAPIGRDPRERTRMAVVTGAAGKPARTHFRRVTSAIWQRQPVTAIHCDLET 298

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+         
Sbjct: 299 GRTHQIRVHCAHIGHP 314


>gi|188527412|ref|YP_001910099.1| hypothetical protein HPSH_03105 [Helicobacter pylori Shi470]
 gi|188143652|gb|ACD48069.1| hypothetical protein HPSH_03105 [Helicobacter pylori Shi470]
          Length = 327

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 106/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D    + +V D 
Sbjct: 297 DMLEYLKKVFDK 308


>gi|127513475|ref|YP_001094672.1| pseudouridine synthase [Shewanella loihica PV-4]
 gi|126638770|gb|ABO24413.1| pseudouridine synthase [Shewanella loihica PV-4]
          Length = 287

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/217 (17%), Positives = 84/217 (38%), Gaps = 27/217 (12%)

Query: 19  VIARAGIASRREVERMIAQQRVKV-NGI---LLERAAVNVMSTD--HIEVDGVPLRKA-- 70
           ++A A   S++E+++ +A+  V +  G     L RA   +   D  H+  +   L +   
Sbjct: 26  LLAEASQLSKQEIKQAMAKGAVWLTRGKYTQRLRRAKKPLKLGDQLHLYYNPKVLAQQVE 85

Query: 71  ------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGL 121
                 ++    +++KP  ++   S     +T+   + +  +       + RLD    GL
Sbjct: 86  DAQLILDKGEYSIWYKPYAMLCQGSKWSDHTTINRFVETHLTPQRPAFIIHRLDRAATGL 145

Query: 122 LLL----TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV 177
           +++    T    LA   E    +  + YRV   G+  +     +   +  +  C     V
Sbjct: 146 VIIGHSKTITAALAAQFEH--RELDKQYRVIVKGEFPKAT-RTITTEVDGKPACSHASLV 202

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
             D++    + V V +  G+  +I+  +     + V 
Sbjct: 203 EYDSE-LDMSLVQVKIETGRKHQIRIHM-ASIGFPVV 237


>gi|296876557|ref|ZP_06900608.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus parasanguinis
           ATCC 15912]
 gi|296432550|gb|EFH18346.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus parasanguinis
           ATCC 15912]
          Length = 297

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 73/211 (34%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
              ++ VNG   E A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGQILVNGRP-ENAIYLLDIGDRLVIDIPAEEGFETLKPMDRPLDILFEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S     +T+ + +   +        +V  V RLD +T G++L    G     L
Sbjct: 92  FGIASIPS-AIHSNTLANFVKGYYVKQGYENQQVHIVTRLDKDTSGVMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L S    + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQSKSIQKRYYALVKGSGKLDPVGEIIAPIARDEESIITRKVA-KGGKYAHTSYQVV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G    V + L  G+  +I+  F    + 
Sbjct: 210 QSFGDIYLVDIQLHTGRTHQIRVHFSHIGFP 240


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/225 (18%), Positives = 77/225 (34%), Gaps = 38/225 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDHTIVNTD 76

Query: 64  -------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVI 109
                   +P++   E + + + +KP GLV      +   T+ + L           R  
Sbjct: 77  FNYCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-QVDQDKLN------- 159
            + RLD +T GLL++  +      L     + +  R Y    HG  +    ++       
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              LK  +   G         ++        + V L  G+  +I+
Sbjct: 197 KNRLKMAVTDFGRQAVTH-YNINKHYKDFTLLNVSLMTGRTHQIR 240


>gi|189426227|ref|YP_001953404.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189422486|gb|ACD96884.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 295

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 77/234 (32%), Gaps = 40/234 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  +  V +    QR+ + +A+    S+ E  R+I +    VN  ++  A+  + + D +
Sbjct: 1   MIKQFSVAKEMAGQRLDETLAQLAGISKGEARRIIDRGGCAVNQAMVRVASRGMKAEDQL 60

Query: 61  EV----DG---VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
            V     G     L   E            +KP G+ +  +    + T+   +   F R 
Sbjct: 61  TVGFMEQGRFLELLLPPEAIVYQDKELLAINKPSGIASQRTPYQLKGTLEYWVAEEFVRQ 120

Query: 108 -----VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---- 156
                V  V RLD  T GL+L       A  L          + Y     G+  ++    
Sbjct: 121 GIKEPVRVVHRLDRGTSGLMLFPKHRQAAAWLSELFKQGGIQKRYLALVTGKPVEERWSC 180

Query: 157 -----KLNLLKKGIVIQGICYGD-----------MQVTLDTQKGSNAWVTVGLR 194
                KL   + GI+ +G                  V    + G    + V L 
Sbjct: 181 DGPIGKLGSARWGIMSEGRAALTDFRLLAAAEGLALVEAFPRTGRTHQIRVHLS 234


>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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/225 (18%), Positives = 77/225 (34%), Gaps = 38/225 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVNHTIVNTD 76

Query: 64  -------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVI 109
                   +P++   E + + + +KP GLV      +   T+ + L           R  
Sbjct: 77  FNLCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-QVDQDKLN------- 159
            + RLD +T GLL++  +      L     + +  R Y    HG  +    ++       
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              LK  +   G         ++        + V L  G+  +I+
Sbjct: 197 KNRLKMAVTDFGRQAVTH-YNINKHYKDFTLLNVSLMTGRTHQIR 240


>gi|78486049|ref|YP_391974.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78364335|gb|ABB42300.1| Pseudouridine synthase Rlu family protein [Thiomicrospira crunogena
           XCL-2]
          Length = 300

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 28/152 (18%), Positives = 57/152 (37%), Gaps = 18/152 (11%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------PSIFSRVISVGRL 114
           D V +  A+   +W  +KP G+++  S     +T+   +        P        V RL
Sbjct: 97  DPVLIEDADDFSVW--YKPKGVLSQGSKWGDHTTLNRWIETHYLFKEPPEKRPCWIVHRL 154

Query: 115 DINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV--DQDKLNLLKKGIVIQGI 170
           D  T+GL+L+ ++   A++L     + Q  + Y+    G+    +   +    G      
Sbjct: 155 DKATDGLILIAHNKKSAQMLARRFEAHQIGKSYQAWVKGKFGETERVFDQDVNGKT---- 210

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   +       + V V +  G+  +I+
Sbjct: 211 ALSKAHQLVYNSDNDCSLVQVTIATGRKHQIR 242


>gi|254491987|ref|ZP_05105165.1| RNA pseudouridine synthase family [Methylophaga thiooxidans DMS010]
 gi|224462802|gb|EEF79073.1| RNA pseudouridine synthase family [Methylophaga thiooxydans DMS010]
          Length = 279

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 31/168 (18%), Positives = 64/168 (38%), Gaps = 12/168 (7%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 121
            P   A+  +  +++KP G+++  S      T+                V RLD    GL
Sbjct: 84  EPELIADMGQYSIWNKPYGMLSQGSKWGDHCTITRWAEQHLTPQRNAFVVHRLDRAANGL 143

Query: 122 LLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYG--DM 175
           +++ ++   A +L     S Q  + Y++   G+  +     N +K  + + G        
Sbjct: 144 IIVAHEKKAAALLSGLFQSRQIEKRYQIWVEGEFSEQATVDNPVKVDLDLDGRHAVSFFT 203

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
           ++  D  K   + + V +  G+  +I++        V    R+ YG  
Sbjct: 204 RLKFDASK-QQSLLDVRIETGRKHQIRQHAASLGHPVVG-DRL-YGNI 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 = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 1/58 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          R+   +   G+A SRRE +R++   RV+VNG L+ +    V   D IEVDGV +R  +
Sbjct: 6  RLDAFLRDVGLAESRREAKRLVESGRVRVNGKLVRKPWWLVSPGDEIEVDGVTVRVED 63


>gi|329923371|ref|ZP_08278854.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
 gi|328941362|gb|EGG37655.1| pseudouridine synthase, RluA family [Paenibacillus sp. HGF5]
          Length = 353

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 86/233 (36%), Gaps = 45/233 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I+Q+     R  K+++R          ++  Q  + +NG  +   +V V + D +
Sbjct: 19  MLLKTILQKRMGVSR--KLLSRL---------KLTEQG-IMLNGTRVY-ISVKVQAGDLV 65

Query: 61  EVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+     R               E   L + +KP G++   +      T+ + +   +  
Sbjct: 66  EIRMEQERSNDMLPQPMELHILYEDEHLLVLNKPAGVIVHPTHGHYTDTLANGVVHYWQE 125

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF---------- 149
                R  +V RLD  T G+L++  +  + + +     +    + Y              
Sbjct: 126 KGWNYRFRAVHRLDQETSGVLVIAKNAYIHQHVSEQMIAGTVDKRYVAFVHGRPSPTGDI 185

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            G +D+D L   ++ +  +G          +T   S + V + L  G+  +I+
Sbjct: 186 DGPIDRDPLEPHRRIVTPEGYPSLTRYRVCET-YPSASLVELKLETGRTHQIR 237


>gi|289524245|ref|ZP_06441099.1| ribosomal large subunit pseudouridine synthase [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289502901|gb|EFD24065.1| ribosomal large subunit pseudouridine synthase [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 307

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 84/249 (33%), Gaps = 53/249 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVNVMSTD 58
           + E++   R+ + +       R++        + R I + RV VNG      +  +   D
Sbjct: 7   IDEDYDCVRLDRFL-------RKKYSEVPLGAIMRAIRKGRVTVNGEK-TDPSYRLYRGD 58

Query: 59  HIEV---DGVPLRKA------------ERTRLWLYHKPIGLVT---THSDPDGRSTVFDN 100
            + V   D   L+ +                + + +KP GL++   ++ D    +   + 
Sbjct: 59  EVSVPFEDPAKLKPSLNVADKPLEVIFMDENVLIINKPAGLLSQPASNEDDSVVNRALNL 118

Query: 101 LPSIFSRVI--SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           +       I     RLD N  G++ L  +    R L     + +  + Y     G++  +
Sbjct: 119 INKTKGGFIPTPAHRLDRNISGVMALALNFRSLRALTAMFRNRRVAKKYLAVVRGRLTGE 178

Query: 157 KL--------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT----VGLREGKNREIKKV 204
            +            K +V +G         +    G++A +     +    G++ +++  
Sbjct: 179 GVIEAPLERDERFLKTVVNKGAGKRSATRYMSLSAGNHASLVALEPIT---GRSHQLRVH 235

Query: 205 FEFFNWKVN 213
                  + 
Sbjct: 236 LSHIGHPIV 244


>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 = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 79/236 (33%), Gaps = 40/236 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--------IEVDG 64
           +RV + ++R     SR   ++++ +  V + G+ +++        D         +EVD 
Sbjct: 13  ERVDQFLSRQLPQLSRSAAQKLLEEGAVTLKGLPVKK-NYKTAEGDELVLSLPDPVEVDV 71

Query: 65  VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS---------RVI 109
           VP               + +KP+G+V   +      T+ +  L              R  
Sbjct: 72  VPQDIPLDVVYEDGDVIVINKPVGMVVHPAAGHPDGTLVNALLYHCGKSLSGINGELRPG 131

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            V R+D +T GL++   ++   LA   +L      R Y     G   +D+   ++  I  
Sbjct: 132 IVHRIDRDTSGLIIAAKSDFAHLALAEQLQDHSLYREYEAVAVGGFKEDE-GTVRAPIAR 190

Query: 168 QGICYGDMQVTLDTQKGSNAWVTV------------GLREGKNREIKKVFEFFNWK 211
                  M V     + +    TV             L  G+  +I+         
Sbjct: 191 HPTDRKKMAVNFLQGREAVTHYTVLERFSGCTHLQCRLETGRTHQIRVHMAHIGHP 246


>gi|227504711|ref|ZP_03934760.1| possible pseudouridylate synthase [Corynebacterium striatum ATCC
           6940]
 gi|227198721|gb|EEI78769.1| possible pseudouridylate synthase [Corynebacterium striatum ATCC
           6940]
          Length = 307

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 77/243 (31%), Gaps = 45/243 (18%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M++     V E     R    +A+    SR +   + A   V+V+G ++ ++   + +  
Sbjct: 1   MRESRRLPVPEGLEGMRADAALAKLIGISRGKAADLCAAGDVEVDGTIVGKSD-RLEAGG 59

Query: 59  HIEVD----GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLP- 102
            I+V       PL   E              +   HKP+G+    +      TV   L  
Sbjct: 60  WIDVMMPAPEEPLVPKEELVEGMDVLYADDDVICVHKPVGVAAHPTLGWEGPTVIGGLRA 119

Query: 103 --------SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
                       R   V RLD+ T G++++         L+    +    + Y     G 
Sbjct: 120 AGYQLADAGPTERKGIVHRLDVGTSGVMVVAASERAYSQLKAAFKERTVTKTYHAVVQGL 179

Query: 153 VDQ--DKLN-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
            D     ++                 V+ G  +      L       + + V L  G+  
Sbjct: 180 PDPIVGTIDAPIGRHPSSGWKFA---VVDGGKHAVTHYKLLEAFREASLLEVHLETGRTH 236

Query: 200 EIK 202
           +I+
Sbjct: 237 QIR 239


>gi|197334594|ref|YP_002155370.1| tRNA pseudouridine synthase C [Vibrio fischeri MJ11]
 gi|197316084|gb|ACH65531.1| tRNA pseudouridine synthase C [Vibrio fischeri MJ11]
          Length = 259

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/201 (17%), Positives = 65/201 (32%), Gaps = 41/201 (20%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-- 99
           VN  LLE     V     IE+    + + E   L   +KP G++   S  D   TVF   
Sbjct: 9   VNDELLEE---QVEP---IEL--EIVYRDEH--LIAINKPAGMLVHRSWLDKHETVFAMQ 58

Query: 100 -NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                I   V  + RLD  T G+L       +A  +     S +  + Y     G +++ 
Sbjct: 59  TLRDQIGQHVFPLHRLDRPTSGILFFALSSEIAAQVSPLFASREIKKTYHAIVRGWIEEA 118

Query: 157 K-LN-LLKKGIVIQGICYGDMQVTLDTQKGSN----------------------AWVTVG 192
             L+  LKK   +  I        ++ ++                           + + 
Sbjct: 119 DTLDYPLKK--ELDKIADKKASQEVEAKEAITEYKPLAKVELPYSTGKFPTTRYCLMELK 176

Query: 193 LREGKNREIKKVFEFFNWKVN 213
              G+  ++++        + 
Sbjct: 177 PHTGRKHQLRRHMAHLRHPIV 197


>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 = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 78/229 (34%), Gaps = 43/229 (18%)

Query: 15  RVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           RV K +     G A+R  ++       + VN   ++     V   D + +          
Sbjct: 45  RVDKFLVDRMMG-ATRNRIQLAAEAGCILVNDKPVKS-NYRVKPLDVVSIVMDRPRRELE 102

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRV 108
              + +PL    E   L + +KP GLV      +   T+ +                 R+
Sbjct: 103 IIPEDIPLNIVYEDDDLLVVNKPAGLVVHPGHGNYTGTLVNALAYYLKDDPYYDPSDPRL 162

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK--------- 157
             V R+D +T GLL++         L L   +    R YR    G V +D+         
Sbjct: 163 GLVHRIDKDTSGLLVVAKRPEAKSNLSLQFFNKTTKRKYRALVWGIVQEDEGRIEGNIGR 222

Query: 158 --LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
              + ++  +  +G          T+  + G  + V   L  G+  +I+
Sbjct: 223 DPRDRMQMTVFPEGDQGKTAVTHYTVLERLGYVSLVECRLETGRTHQIR 271


>gi|58617275|ref|YP_196474.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Gardel]
 gi|58416887|emb|CAI28000.1| SfhB protein homolog (peudouridylate synthase) [Ehrlichia
           ruminantium str. Gardel]
          Length = 324

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 84/245 (34%), Gaps = 44/245 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +K I +Q     +R+ K IA     SR  V+++I   ++ +   +++         D 
Sbjct: 1   MFEKKIFIQNGEENKRLDKFIALKLNISRNRVQQLIQNNKIYLFNKIVKDNNHITKVNDI 60

Query: 60  IEVD--------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
             ++               +P+    E   + + +K  G+           T+ + L + 
Sbjct: 61  YYINMPTQEHNCSITPNINIPITILYEDQDIIIINKEPGITVHPGAGTKDDTLVNGLIAH 120

Query: 105 F----------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
           +          SR   V RLD +T GL+++  +      L   L   Q  + Y     G 
Sbjct: 121 YGSTLSYIGKASRPGIVHRLDKDTSGLMVIARNEHSYYFLSDLLSKKQIKKEYLAVVWGI 180

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLREGK 197
            +  K N++K  I  +      M VT    KG                   V   +  G+
Sbjct: 181 PNP-KCNIIKNHIDTKSNNKQMMTVTHSQNKGKLAITEYNTIQTFASIATLVKCRIYTGR 239

Query: 198 NREIK 202
             +I+
Sbjct: 240 THQIR 244


>gi|325570826|ref|ZP_08146509.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
 gi|325156336|gb|EGC68518.1| ribosomal large subunit pseudouridine synthase D [Enterococcus
           casseliflavus ATCC 12755]
          Length = 305

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 39/234 (16%), Positives = 80/234 (34%), Gaps = 48/234 (20%)

Query: 19  VIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV----------- 62
            +   G+      + ++A+      ++ VN         ++   D + +           
Sbjct: 23  FLKEQGV-----SKGLLAKIKFQGGKIFVNDHEQNVL-FSLAQNDRVTIVIPPEGEHETM 76

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVG 112
             D  P+    E   L + +KP G+ +  +      T+ + + + +         +  V 
Sbjct: 77  LADPTPIEIVYEDAHLLIVNKPAGISSIPAQYHPTGTMANRVKAYYQAQHYEDQVIHVVT 136

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-------------QVDQDK 157
           RLD +T GL+L    G     L+      Q ++ Y+    G              + +D 
Sbjct: 137 RLDRDTSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAGDLSALSAHSEIDLPIARDL 196

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +LLK+ +  +G      +  L  +    A V V L  G+  +I+  F      
Sbjct: 197 TSLLKRKVSEEGKEART-EYWLKQRNSDCALVDVQLHTGRTHQIRVHFSAIGCP 249


>gi|322389492|ref|ZP_08063043.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
 gi|321143767|gb|EFX39194.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           parasanguinis ATCC 903]
          Length = 297

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 73/211 (34%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR-KAERTRLWLYHKP 81
              ++ VNG   E A   +   D + +D               PL    E     + +KP
Sbjct: 33  RGGQILVNGRP-ENAIYLLDIGDRLVIDIPAEEGFETLKPMDRPLDILFEDDHFLVLNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S     +T+ + +   +        +V  V RLD +T G++L    G     L
Sbjct: 92  FGIASIPS-AIHSNTLANFVKGYYVKQGYENQQVHIVTRLDKDTSGVMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L S    + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQSKTIQKRYYALVKGSGKLDPVGEIIAPIARDEDSIITRKVA-KGGKYAHTSYQVV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G    V + L  G+  +I+  F    + 
Sbjct: 210 QSFGDIHLVDIQLHTGRTHQIRVHFSHIGFP 240


>gi|94499372|ref|ZP_01305910.1| hypothetical protein RED65_11299 [Oceanobacter sp. RED65]
 gi|94429004|gb|EAT13976.1| hypothetical protein RED65_11299 [Oceanobacter sp. RED65]
          Length = 236

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 84/219 (38%), Gaps = 39/219 (17%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP GL+   S    D +      +  +    V  V RLD  T G+LL    G +A
Sbjct: 16  LIAINKPSGLLVHKSWVAKDAKEFALQIVRDMSGKHVFPVHRLDRPTSGVLLFGFSGEIA 75

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQDKL-NLLKKGIV---------------IQGICYGDM 175
           + ++    Q  + Y     G + +  L +   KG+                 + I Y ++
Sbjct: 76  QQVQAQWEQANKTYWAVVRGWLKEQTLVDHALKGMADYGQDVEIVQEAQTHFKPIDYVEI 135

Query: 176 QVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST- 233
              +D    S  +WV    ++G+  +I++  +  +  +        G  + G    G   
Sbjct: 136 DAEIDRYPKSRFSWVEAKPKQGRTHQIRRHLKHLSHPI-------IGDARYG---KGKYN 185

Query: 234 REVSK-----KIL---REQLGPHLLEEAQVNLDAPIYSS 264
           R +++     ++L   ++    H +  +++ + AP+  +
Sbjct: 186 RYITEHYDCPRLLLHHQQLEMTHPVSGSKLMITAPLEGA 224


>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 = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/225 (18%), Positives = 77/225 (34%), Gaps = 38/225 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDHTIVNTD 76

Query: 64  -------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVI 109
                   +P++   E + + + +KP GLV      +   T+ + L           R  
Sbjct: 77  FNLCKPENIPIQIIYEDSEVIVVNKPAGLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-QVDQDKLN------- 159
            + RLD +T GLL++  +      L     + +  R Y    HG  +    ++       
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTSLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              LK  +   G         ++        + V L  G+  +I+
Sbjct: 197 KNRLKMAVTDFGRQAVTH-YNINKHYKDFTLLNVSLMTGRTHQIR 240


>gi|270291159|ref|ZP_06197382.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|270280555|gb|EFA26390.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
          Length = 292

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 76/234 (32%), Gaps = 47/234 (20%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----------------- 59
            KV+ R G AS+R ++++    R      L++     V   D                  
Sbjct: 16  QKVLQRLG-ASQRLMQKIRQAGR------LVDENERTVALKDKLMPFEPFWIELPDEDSD 68

Query: 60  --IEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
             + V   PL        WL  +KP GL       +   T+ + +   +    +V     
Sbjct: 69  PAVPVSDQPLDVIYEDDNWLVVNKPAGLTAVPGPSNRTDTLVNRVKGHWQANGAVNLVPH 128

Query: 113 ---RLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK------LNL 160
              RLD  T G+ L+     +A  L        +  + Y     G V  +K      L L
Sbjct: 129 LITRLDRFTSGITLVARH-QVANSLLSEQVRHRKIKKTYLALVDGVVSAEKGTFNQPLGL 187

Query: 161 LKKGI---VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              GI   V +G         +  +  +   V V L+ G+  +I+  F      
Sbjct: 188 AADGIHREVQEGGQSATTSFKVVQRFANQTLVQVHLKTGRTHQIRVHFANAGHP 241


>gi|261408890|ref|YP_003245131.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261285353|gb|ACX67324.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 354

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 86/234 (36%), Gaps = 46/234 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I+Q+     R  K+++R          ++  Q  + +NG  +   +V V + D +
Sbjct: 19  MLLKTILQKRMGVSR--KLLSRL---------KLTEQG-IMLNGTRVY-ISVKVQAGDLV 65

Query: 61  EVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+     R               E   L + +KP G++   +      T+ + +   +  
Sbjct: 66  EIRMEQERSNDMLPQPMELHILYEDEHLLVLNKPAGVIVHPTHGHYTDTLANGVVHYWQE 125

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF---------- 149
                R  +V RLD  T G+L++  +  + + +     +    + Y              
Sbjct: 126 KGWNYRFRAVHRLDQETSGVLVIAKNAYIHQHVSEQMIAGTVDKRYVAFVHGRPSSQTGD 185

Query: 150 -HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             G +D+D L   ++ +  +G          +T   S + V + L  G+  +I+
Sbjct: 186 IDGPIDRDPLEPHRRIVTPEGYPSLTRYRVCET-YPSASLVELKLETGRTHQIR 238


>gi|324989625|gb|EGC21569.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK353]
          Length = 291

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/204 (20%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILIGNGKLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPRELALLNHVSAYVGETCYVVHRLDKETSGAILFAKNSFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  Q   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVEPQKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RVKQFGQAALVKCQLKTGRTHQIR 230


>gi|260682684|ref|YP_003213969.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260686282|ref|YP_003217415.1| putative pseudouridylate synthase [Clostridium difficile R20291]
 gi|260208847|emb|CBA61782.1| putative pseudouridylate synthase [Clostridium difficile CD196]
 gi|260212298|emb|CBE03063.1| putative pseudouridylate synthase [Clostridium difficile R20291]
          Length = 281

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 74/212 (34%), Gaps = 45/212 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTR----------LWLYHKPIG 83
            ++ V VNG + ++ ++ V S D IEV  D        +            + + +KP  
Sbjct: 23  KEKSVLVNG-VYKKPSLKVYSGDLIEVKIDEEKANFEPQDLNLQIIYDDFDIIMVNKPPF 81

Query: 84  LVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           +V   +      T+      + +      ++  V RLD+NT GL+++  +      L   
Sbjct: 82  MVVHPTKSHYDKTIANGISYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTA 141

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----MQVTLDTQKGSN----- 186
           +   +  + Y     G + ++      +G  I    Y      ++  +D +  S+     
Sbjct: 142 MSENKVEKKYITVVDGIIKEN------EG-TIDEPIYRPTEDSIKRIIDERGQSSVTHYK 194

Query: 187 --------AWVTVGLREGKNREIKKVFEFFNW 210
                     + V L  G+  +I+        
Sbjct: 195 VIERLENATVLEVSLETGRTHQIRVHMAHIGH 226


>gi|307722069|ref|YP_003893209.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
 gi|306980162|gb|ADN10197.1| pseudouridine synthase [Sulfurimonas autotrophica DSM 16294]
          Length = 302

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 40/212 (18%), Positives = 84/212 (39%), Gaps = 35/212 (16%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRK-----AER 72
           +I   G  +++E +R+IA+ R+ V+G  + + A  +    + I     P+ K      E 
Sbjct: 20  LIQELGY-TQKEAQRLIAKGRLFVSGKPMTKTAGEIEGEFEFIYF--EPITKGLEPTYEE 76

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLA 131
               ++ KP G++    +     ++ D L   + R  ++  R+D  T GL+L   +    
Sbjct: 77  EEFVIFDKPSGVLIHPQNRYTPYSLIDELKYQYGRDANITHRIDQETSGLVLCAKNKQSE 136

Query: 132 R--VLELPSTQWLRVYRVRFHGQVDQD---KLNLLKKGIVIQGI-CYGDMQVTLDTQKGS 185
           R   +        + Y    HG  +++   +  LL+     +       M V +D +  +
Sbjct: 137 RDIKMMFEQRDMKKKYLAFVHGHFEKELTVEAPLLRA----EDESAIVRMVVKVDEKGKA 192

Query: 186 N----------AWVTVGLRE-----GKNREIK 202
           +          + V + L E     G+  +I+
Sbjct: 193 SKTDFKPLQYFSEVDMTLVECSPYTGRQHQIR 224


>gi|83815887|ref|YP_445314.1| ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber DSM 13855]
 gi|83757281|gb|ABC45394.1| ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber DSM 13855]
          Length = 349

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 64/356 (17%), Positives = 109/356 (30%), Gaps = 94/356 (26%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ K + R    ASR +++R I +  +KVNG  +++ +  V   D I      +RK    
Sbjct: 10  RIDKYLTRFYPEASRTKIQRAIKKGHLKVNGTDVKK-SYGVEPGDEIVF--RLIRKPPMQ 66

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------------- 101
                       E   L + +KP G+V   +      T+   L                 
Sbjct: 67  AEPEAIPLDVVHEGDDLLVVNKPAGMVVHPAPGHRSGTLVHALLHHVDGGEVAADDERDE 126

Query: 102 ------------------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                                  R   V RLD  T GLL++   G   + L     +   
Sbjct: 127 VSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTSGLLVVAKRGRAHQPLAEQFKAHTV 186

Query: 142 LRVYRVRFHGQV-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            R YR    G+              D      +      +G        T++T     + 
Sbjct: 187 DRRYRAIVWGRFAPSDGTIEGAIGRDPHHRQRMAVVPEDEGKWARTHYETVET-HAHTSV 245

Query: 189 VTVGLREGKNREIK---KVFEFFNWKVN-----RLIRISYGPFQLGTLLAGSTREVSKKI 240
           V   L  G+  +I+   +        +         R+ YG        +G+ R    + 
Sbjct: 246 VEFELETGRTHQIRVHAR---AQGHPLLGDPKYGGQRVRYGT------QSGTRRTFYDQ- 295

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           L E L    L   ++  D P         +R    ++ P  + R+ +   Q+ G  
Sbjct: 296 LFETLPHPALHAYRLGFDHP------TTEERLRFEADPPPAWRRVLRELRQEEGAG 345


>gi|254974610|ref|ZP_05271082.1| putative pseudouridylate synthase [Clostridium difficile QCD-66c26]
 gi|255092002|ref|ZP_05321480.1| putative pseudouridylate synthase [Clostridium difficile CIP
           107932]
 gi|255313736|ref|ZP_05355319.1| putative pseudouridylate synthase [Clostridium difficile QCD-76w55]
 gi|255516418|ref|ZP_05384094.1| putative pseudouridylate synthase [Clostridium difficile QCD-97b34]
 gi|255649516|ref|ZP_05396418.1| putative pseudouridylate synthase [Clostridium difficile QCD-37x79]
 gi|306519647|ref|ZP_07405994.1| putative pseudouridylate synthase [Clostridium difficile QCD-32g58]
          Length = 300

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 74/212 (34%), Gaps = 45/212 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTR----------LWLYHKPIG 83
            ++ V VNG + ++ ++ V S D IEV  D        +            + + +KP  
Sbjct: 42  KEKSVLVNG-VYKKPSLKVYSGDLIEVKIDEEKANFEPQDLNLQIIYDDFDIIMVNKPPF 100

Query: 84  LVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           +V   +      T+      + +      ++  V RLD+NT GL+++  +      L   
Sbjct: 101 MVVHPTKSHYDKTIANGISYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTA 160

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----MQVTLDTQKGSN----- 186
           +   +  + Y     G + ++      +G  I    Y      ++  +D +  S+     
Sbjct: 161 MSENKVEKKYITVVDGIIKEN------EG-TIDEPIYRPTEDSIKRIIDERGQSSVTHYK 213

Query: 187 --------AWVTVGLREGKNREIKKVFEFFNW 210
                     + V L  G+  +I+        
Sbjct: 214 VIERLENATVLEVSLETGRTHQIRVHMAHIGH 245


>gi|319794365|ref|YP_004156005.1| pseudouridine synthase, rlua family [Variovorax paradoxus EPS]
 gi|315596828|gb|ADU37894.1| pseudouridine synthase, RluA family [Variovorax paradoxus EPS]
          Length = 322

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 85/245 (34%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEV 62
           +V E    QR+ + +A      SR  ++++I    V+  G  L +A+  V +     IE+
Sbjct: 19  VVSEALHGQRLDRALAALVPEFSRSYLQQLIEAGAVEFQGRTLTKASATVRAGQAGRIEL 78

Query: 63  DGVP------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----PSI-- 104
              P            +   E   L +  KP GLV   +      T+ + L    P    
Sbjct: 79  RPTPQSQAFRPEPMDLVTVFEDEHLRIVDKPAGLVVHPAPGHWSGTLLNGLLALDPKAVL 138

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV------------RFH 150
             R   V RLD +T GL+++         L   + + +  R Y              +  
Sbjct: 139 LPRAGIVHRLDRDTSGLMVVARTRAAMDALVALIAAREVKRQYLAIGHKPWVGAAARQVD 198

Query: 151 GQVDQDKLNLLKKGIV-IQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
             + +D  N L+  +V ++   G     +   LD+       V   L  G+  +I+    
Sbjct: 199 APIGRDPRNRLRMAVVDLERHSGKTARTLIERLDSHSEG-CVVRCTLETGRTHQIRVHMA 257

Query: 207 FFNWK 211
                
Sbjct: 258 SIGHP 262


>gi|253581824|ref|ZP_04859048.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           varium ATCC 27725]
 gi|251836173|gb|EES64710.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           varium ATCC 27725]
          Length = 313

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 79/237 (33%), Gaps = 48/237 (20%)

Query: 8   QENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            EN   +R+   +    I   A+R  ++++I    V++ G  + ++   +  T+ I V+ 
Sbjct: 13  NENDKGKRIDSFLNE--IIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTEIIVVNI 70

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +PL    E   + + +K   +V   +  +   T+ + L          
Sbjct: 71  PEDEILNVVPENIPLNIIYEDKDIVIINKTANMVVHPAHGNYNGTLVNALLYQIKDLSTI 130

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD--KL 158
               R   V RLD +T G++++  +      L          + Y     G       K+
Sbjct: 131 NGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFKEKTLEKTYICITKGIFKDKSGKI 190

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN-------------REIK 202
             L   I         M V     K + +   V L EGKN              +I+
Sbjct: 191 ETL---IGRDPKDRKKMTVVDINGKNAISNYEV-LDEGKNFSLVKVRIETGRTHQIR 243


>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 = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 72/206 (34%), Gaps = 26/206 (12%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----------------AERTRLW 76
           R+  Q+ +KVN   +  +   V + D I + G+                     E   + 
Sbjct: 33  RLFRQKSIKVNNKRIADSNYVVKTGDEIIIYGIKDEPSFVIYDNSWKLDSDIVYEDDNIL 92

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLP---SIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +K  G +         + VF  L    +   R   VGRLD  T GL++   +      
Sbjct: 93  LINKKAGTIVHGDSNCLDNQVFSYLKFKQNSAFRPSHVGRLDKWTSGLIMYAKNYPALAE 152

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKL-------NLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           L   +    ++Y ++       + +        L +K +  + + + D ++        +
Sbjct: 153 LNRKTEFLDKIYVLKSDYNPHDEIVSVYVHHDELQQKMVATKNMQHPDDKMAKTRFFKKD 212

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKV 212
             +   L  G+  +I+   E+  + +
Sbjct: 213 NKLYAQLFTGRKHQIRATLEYLEYPI 238


>gi|257876751|ref|ZP_05656404.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC20]
 gi|257810917|gb|EEV39737.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus EC20]
          Length = 299

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 81/234 (34%), Gaps = 48/234 (20%)

Query: 19  VIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV----------- 62
            +   G+      + ++A+      ++ VN         ++   D + +           
Sbjct: 17  FLKEQGV-----SKGLLAKIKFQGGKIFVNDHEQNVL-FSLAQNDRVTIVIPPEGEHETM 70

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVG 112
             D  P+    E   L + +KP G+ +  +      T+ + + + +         +  V 
Sbjct: 71  LADPTPIEIVYEDAHLLVVNKPAGISSIPAQYHPTGTMANRVKAYYQAQHYEDQVIHVVT 130

Query: 113 RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD-------------QDK 157
           RLD +T GL+L    G     L+      Q ++ Y+    G++              +D 
Sbjct: 131 RLDRDTSGLMLFAKHGFAHAKLDSQLRKKQVVKKYQALVAGELPALSAHGEIELPIARDL 190

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +LLK+ +  +G      +  L  +    A V + L  G+  +I+  F      
Sbjct: 191 TSLLKRKVSDEGKEART-EYWLKQRNSDFALVDIQLHTGRTHQIRVHFSAIGCP 243


>gi|255305986|ref|ZP_05350158.1| putative pseudouridylate synthase [Clostridium difficile ATCC
           43255]
          Length = 300

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 33/212 (15%), Positives = 71/212 (33%), Gaps = 45/212 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRKAERTRLWLYHKPIG 83
            ++ V VNG + ++ ++ V S D IEV            D       +   + + +KP  
Sbjct: 42  REKSVLVNG-VYKKPSLKVYSGDLIEVKIYEEKANFEPQDLNLQIIYDDFDIIMVNKPPF 100

Query: 84  LVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           +V   +      T+      + +      ++  V RLD+NT GL+++  +      L   
Sbjct: 101 MVVHPTKSHYDKTIANGISYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTA 160

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----------------VT 178
           +   +  + Y     G + ++      +G  I    Y   +                   
Sbjct: 161 MSENKVEKKYITVVDGIIKEN------EG-TIDEPIYRPTEDSIKRIIDEIGQSSVTHYK 213

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +  +  +   + V L  G+  +I+        
Sbjct: 214 VIERLENATVLEVSLETGRTHQIRVHMAHIGH 245


>gi|239815171|ref|YP_002944081.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
 gi|239801748|gb|ACS18815.1| pseudouridine synthase, RluA family [Variovorax paradoxus S110]
          Length = 327

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 87/236 (36%), Gaps = 38/236 (16%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGVP---- 66
           QR+ + +A      SR  ++++I    V++ G  L +A+  V +    HIE+   P    
Sbjct: 32  QRLDRALAALVPEFSRNYLQQLIEAGAVELQGRTLLKASATVRAGQTGHIELRPTPQSQA 91

Query: 67  --------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVG 112
                   +   E   L +  KP GLV   +      T+ + L       ++  R   V 
Sbjct: 92  FRPEPMDIVTVHEDEHLRIIDKPAGLVVHPAPGHWSGTLLNGLLALDPKAALLPRAGIVH 151

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRV------------RFHGQVDQDKL 158
           RLD +T GL+++  T     A V  + + +  R Y              +    + +D  
Sbjct: 152 RLDRDTSGLMVVARTRAAMDAMVALIAAREVKRQYLALGHKPWAGAAARQVDAPIGRDPR 211

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFFNWK 211
           N L+  +V      G    TL  +  SNA    V   L  G+  +I+         
Sbjct: 212 NRLRMAVVDLERHAGKTARTLIERLDSNAQACAVRCTLETGRTHQIRVHMASIGHP 267


>gi|220904744|ref|YP_002480056.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
 gi|219869043|gb|ACL49378.1| pseudouridine synthase [Desulfovibrio desulfuricans subsp.
           desulfuricans str. ATCC 27774]
          Length = 360

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 46/295 (15%), Positives = 88/295 (29%), Gaps = 82/295 (27%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRR----EV--ERMIAQQRVKVNGILLERAAVNV 54
           + +  +VQE  + Q++ + +       RR    +    R +   +V++NG   +     V
Sbjct: 18  VTEIPVVQEPESGQKLLQFLQ------RRLNLPQAMLHRWVRTGQVRINGSRCK-PFSRV 70

Query: 55  MSTDHIEV------------------------------DGVPLRK--AERTRLWLYHKPI 82
            + D + +                              DG PL     +   LW + KP 
Sbjct: 71  QTGDTVRLPPFAMKMAAQCDSASPTPASKGKSKDDAPEDGPPLPPLVGKSGYLWAFDKPA 130

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDG---GLARVLE 135
           G +  H       ++   L   F+ V      V RLD  T G++L+          +   
Sbjct: 131 G-LPVHPGTGHEDSLTTRLSCHFAGVSFMPTPVHRLDRGTSGIILVAASYAALDETQRAL 189

Query: 136 LPSTQWLRVYRVRFHGQVD------------QDKLNLLK--KGIVIQ--GICYGDMQVTL 179
             +    + Y     G+              ++ ++  +  + +             V  
Sbjct: 190 RANAMH-KEYVAWVAGRWPHTQTCLVRHFLRKEAVDGFERVRPVKADAPDAKEALCLVRA 248

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +     + V V L  G+  +I+         V            LG    G TR
Sbjct: 249 LSIADRASLVQVRLLTGRTHQIRVQLSSLGHPV------------LGDTKYGQTR 291


>gi|71910662|ref|YP_282212.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|71853444|gb|AAZ51467.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
          Length = 301

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 69/211 (32%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-----------AERTRLWLYHKP 81
               + VNG + + A   +   D + +D     P  K            E     + +KP
Sbjct: 33  KGGNILVNG-IEQNAIYLLQVGDVVTIDIPNEEPFEKLEAIPFDLDIVHEDDHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           IG  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  IGFASIPS-AIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G     D+  +           + + +   G         + 
Sbjct: 151 DKQLQTRSIEKRYFALVSGNGMLPDEGDIIAPIGRSKDSIITRAVDPMGKYAKTSYKVVA 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 241


>gi|257875741|ref|ZP_05655394.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
 gi|257809907|gb|EEV38727.1| pseudouridylate synthase [Enterococcus casseliflavus EC20]
          Length = 302

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 49/225 (21%), Positives = 82/225 (36%), Gaps = 40/225 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGV 65
           RV KV+A R    SR ++++ + +  V + G  +  A   V + DH+         VD  
Sbjct: 15  RVDKVLAERLPNHSRSQIQQWLKEDAVTLMGETVR-ANYKVKAGDHLIIQVPEPEVVDLQ 73

Query: 66  PLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVIS--V 111
           P               + +KP G+V   S      T+        D+L +I   V    V
Sbjct: 74  PENIPLTIVYQDADVAVINKPQGMVVHPSAGHPNGTLVNALLYHMDDLSTINDVVRPGIV 133

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T GLL++  +      L   L     LR Y    HG +  +K            
Sbjct: 134 HRIDKDTSGLLMIAKNDQAHESLAKQLKDKTSLRKYVALVHGTISHEKGTINAPIGRSKV 193

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++   VI+         T+  +      V + L  G+  +I+
Sbjct: 194 NRKMQA--VIENGKPAVTHFTVLERFEQFTLVELQLETGRTHQIR 236


>gi|332184383|gb|AEE26637.1| Ribosomal large subunit pseudouridine synthase D [Francisella cf.
           novicida 3523]
          Length = 331

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 70/207 (33%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-------------AERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 37  SRAQIQKWLKEGSIIVNGQ-ATKPKYIVLGDEEVEINVELLPTNEWIAEDIKLNIIYEDD 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ +V      +   TV + L           R   V RLD +T GL++    
Sbjct: 96  DIIVIDKPVNMVVHPGAGNPTGTVSNALLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 155

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
                 L  +L   +  R Y     G           + +D  N  K  I  +G      
Sbjct: 156 SIAYHNLVQQLAERKVSRKYLAIVEGEIYQQGTINQPIGRDSTNRTKMAINHRGKEAITH 215

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++   G    +   L  G+  +I+
Sbjct: 216 YTPIEVYDGFT-LLECQLETGRTHQIR 241


>gi|281490911|ref|YP_003352891.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|281374669|gb|ADA64189.1| Ribosomal large subunit pseudouridine synthase D, RluA family
           [Lactococcus lactis subsp. lactis KF147]
          Length = 293

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 49/286 (17%), Positives = 95/286 (33%), Gaps = 63/286 (22%)

Query: 20  IARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV------DGVPLR 68
           ++R GI SRR    ++ +      ++ VNG   + A   +   D + V      D   L 
Sbjct: 18  LSRHGI-SRR----LLTKVKFDGGKITVNGQ-EKNAIYRLEKDDLVTVTVPDEPDNEKLI 71

Query: 69  KA--------ERTRLWLYHKPIGL--VTTHSDPDGRST--VFDNLPSIF---SRVISVGR 113
                     E     +  KP G   +T    P G  +  V   +         V  + R
Sbjct: 72  PDDFPLNVLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQKNYANQTVHIITR 131

Query: 114 LDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRFHG-----------QVDQDKLN 159
           LD +T G++ L      A  L           + Y    +             + +   +
Sbjct: 132 LDRDTSGIMFLAKH-RYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGRRDDS 190

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           ++++ +         +   +  ++ ++ A + + L  G+  +I+  F    + +      
Sbjct: 191 IIQRQVRFDEKAKDALTSYVVAERKNDLALLDIILHTGRTHQIRVHFSHLGYPL------ 244

Query: 219 SYGPFQLGTLLAGSTREVSKKILR----EQLGPHLLEEAQVNLDAP 260
             G      L  G+   +S++ L     + L P   E   V LD P
Sbjct: 245 -IG----DDLYGGNHDLISRQALHCHHLQFLNPFTDEMVHVELDMP 285


>gi|218288262|ref|ZP_03492561.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218241621|gb|EED08794.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 303

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 71/207 (34%), Gaps = 40/207 (19%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRK-----------AERT 73
           I   RVKVNG   ++    +   D +           +   P+ K            E  
Sbjct: 35  IRTGRVKVNGKRAKQ-DTRLHEGDIVHLYFSDEDYASLHAHPVAKYQGVSRAIDILYEDD 93

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLL 124
            +   +KP G++T  +D + ++++   + +            R   V RLD NT G+++ 
Sbjct: 94  EIVAVNKPAGVLTHPADGEYKTSLAAQVEAYVYDRGAREGAFRAAPVHRLDRNTSGVVIF 153

Query: 125 --TNDGGLARVLELPSTQWLRVYRVRFHGQVD---QDKLNLLKKG----IVIQGICYGDM 175
             T     A        +  + Y     G      +  +++ ++G    +V       + 
Sbjct: 154 AKTARAAKAWADAFQRGEVEKEYLAIVEGAWSGRGRVAVDVQREGNVTRVVEDSGKPSET 213

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              +       + V + L  G+  +I+
Sbjct: 214 AYEVVASSRGTSLVRLRLLTGRTHQIR 240


>gi|303272139|ref|XP_003055431.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226463405|gb|EEH60683.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 126

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 2/63 (3%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRK 69
            P+R  KV+A  G   R E +  I   RV   G +++   A V V   D + VDG P+  
Sbjct: 48  EPERADKVLASHGYCKRSEAKAWIRHGRVTFEGDVVKTCDAKVVVRLYDGVCVDGKPVPL 107

Query: 70  AER 72
            ++
Sbjct: 108 TKK 110


>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 = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 90/255 (35%), Gaps = 59/255 (23%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD 
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVD- 63

Query: 65  VPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +P +  E T                + +  KP  ++          T+ + L +    + 
Sbjct: 64  LPEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNALLNHCKDLQ 123

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDK 157
            VG         RLD  T G++++  +   A           +  + Y +   G+V +D 
Sbjct: 124 GVGGKLRPGIVHRLDKETSGVIVVAKN-DFAHQSLSKQFKDRKVKKTYILLVKGRVKKD- 181

Query: 158 LNLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTV--------GL-----REGKN 198
                +G+V   +      V       ++T K +     V         L     + G+ 
Sbjct: 182 -----EGVV--DLPLARHPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRT 234

Query: 199 REIKKVFEFFNWKVN 213
            +I+   +     + 
Sbjct: 235 HQIRVHMKSLGHPIM 249


>gi|167950611|ref|ZP_02537685.1| 16S rRNA pseudouridylate synthase A [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 94

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 8/92 (8%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
                V+G   ++ ++NVM    + +DG  + + E  R ++ HKP G V        RS 
Sbjct: 2   AGGCAVDGEPQKQPSLNVMEAAAVSLDGGLVARHE-PRYFMLHKPEGYVCFQ---PSRSF 57

Query: 97  VFDNLPSIFSRV----ISVGRLDINTEGLLLL 124
           +         R+     S+GRLDI+T GLLL+
Sbjct: 58  ILACSICWMRRLLWVSTSLGRLDIDTTGLLLI 89


>gi|110803565|ref|YP_698546.1| pseudouridylate synthase [Clostridium perfringens SM101]
 gi|110684066|gb|ABG87436.1| pseudouridine synthase, RluA family [Clostridium perfringens SM101]
          Length = 324

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 86/264 (32%), Gaps = 62/264 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + +  ++VNG   +    +++
Sbjct: 2   KIEIGTNEAGQRLDKFL-------RKYLKDVPLSAIFKALRKGDIRVNGKKQKE-KYSLL 53

Query: 56  STDHIEV--------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
             D IE+                     G      E   + L  K  G++      +G  
Sbjct: 54  DGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAP 113

Query: 96  TVFDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           T+ D + S   R               S  RLD NT G++    +    ++L   +   +
Sbjct: 114 TLTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERK 173

Query: 141 WLRVYRVRFHGQVDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
             + Y     G++   K          L K  V         ++ +D +     G+ + +
Sbjct: 174 VNKYYCALVKGKIQPGKYEAYISKDDELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 234 EIELITGRSHQLRAHLAHLGNPIV 257


>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 = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 74/233 (31%), Gaps = 39/233 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-------------- 52
           V E    +RV   +AR    SR     +IA   V V+G  + ++                
Sbjct: 9   VPEGLDGERVDAALARLFGLSRSRAAELIAAGDVLVDGRTVVKSDRLHGGGWLEVTLPPP 68

Query: 53  -NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                     V G+ +   E   + +  KP+G+    +      TV   L          
Sbjct: 69  PAPPRPVAEPVPGMTILY-EDEHIVVVSKPVGVAAHPTIGWNGPTVLGGLLGAGHTVATS 127

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------ 154
               R   V RLD NT G +++         L+      +  + Y     G  D      
Sbjct: 128 GAAERQGIVHRLDANTTGAMVVAKSEIAYSRLKRAFKERRVDKRYHALVQGHPDPLRGTI 187

Query: 155 QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++    G     +V  G        TL+  + + + + + L  G+  +I+
Sbjct: 188 DAPIDRHPSGDGRFAVVAGGRPSITHYDTLEAFRAA-SLLEIDLETGRTHQIR 239


>gi|15672346|ref|NP_266520.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12723234|gb|AAK04462.1|AE006273_8 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 293

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 50/286 (17%), Positives = 95/286 (33%), Gaps = 63/286 (22%)

Query: 20  IARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV------DGVPLR 68
           ++R GI SRR    ++ +      ++ VNG   + A   +   D + V      D   L 
Sbjct: 18  LSRHGI-SRR----LLTKVKFDGGKITVNGQ-EKNAIYRLEKDDLVTVTVPDEPDNEKLI 71

Query: 69  KA--------ERTRLWLYHKPIGL--VTTHSDPDGRST--VFDNLPSIF---SRVISVGR 113
                     E     +  KP G   +T    P G  +  V   +         V  + R
Sbjct: 72  PDDFPLNVLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQKNYANQTVHIITR 131

Query: 114 LDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRFHG-----------QVDQDKLN 159
           LD +T GL+ L      A  L           + Y    +             + +   +
Sbjct: 132 LDRDTSGLMFLAKH-RYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGRRDDS 190

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           ++++ +         +   +  ++ ++ A + + L  G+  +I+  F    + +      
Sbjct: 191 IIQRQVRFDEKAKDALTSYVVAERKNDLALLDIILHTGRTHQIRVHFSHLGYPL------ 244

Query: 219 SYGPFQLGTLLAGSTREVSKKILR----EQLGPHLLEEAQVNLDAP 260
             G      L  G+   +S++ L     + L P   E   V LD P
Sbjct: 245 -IG----DDLYGGNHDLISRQALHCHHLQFLNPFTDEMVHVELDMP 285


>gi|303236145|ref|ZP_07322746.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302483651|gb|EFL46645.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 360

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 79/251 (31%), Gaps = 50/251 (19%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV +   P RV K I      +SR  +++      + VN   ++     V   D I +  
Sbjct: 36  IVDKGQEPVRVDKYIFEKMQHSSRNRIQKAADAGCIYVNDKPVKS-NYKVRPDDIITLML 94

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------N 100
                      + +PL    E   + + +KP GLV      +   T+ +          +
Sbjct: 95  DRPKHDNTIEAEEIPLDIVYEDDEIMVINKPAGLVVHPGAGNFHGTLINAIAWHLKDLKD 154

Query: 101 LPSIFSRVISVGRLDINTEGLLLL--TNDGG------LARVLELPSTQWLRVYRVR---- 148
                  V  V R+D +T GLLL+  T D                S        V     
Sbjct: 155 FDPNDPAVGLVHRIDKDTSGLLLIAKTPDAKTFLGKQFFNKTTHRSYNA----LVWGNLV 210

Query: 149 -----FHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNRE 200
                  G + +D  + L+  +       G   VT   +  + G    V   L  G+  +
Sbjct: 211 EDEGRIEGNIGRDPKDRLRMAVFPPESGIGKNAVTHYRVLERFGYTTLVECRLETGRTHQ 270

Query: 201 IKKVFEFFNWK 211
           I+   +     
Sbjct: 271 IRAHMKHIGHP 281


>gi|58584466|ref|YP_198039.1| pseudouridylate synthase, 23S RNA-specific [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
 gi|58418782|gb|AAW70797.1| Pseudouridylate synthases, 23S RNA-specific [Wolbachia endosymbiont
           strain TRS of Brugia malayi]
          Length = 389

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 34/230 (14%), Positives = 74/230 (32%), Gaps = 52/230 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAV 52
           M +   +       R+ + I       RR         +E+ + +  +KVN    + +  
Sbjct: 1   MGNIKTISVKDNNVRLDRYI-------RRIFPNLKQSVIEKSLRRGLIKVNDCKAKSSD- 52

Query: 53  NVMSTDHIEV---------------DGVPLRK------AERTRLWLYHKPIGLVTTHSDP 91
            V S   I +               +   +         E   +   +KP G++      
Sbjct: 53  RVNSGQIITIKYLDYIENANSDCKHNEKLVELLRSNILYEDEYILAINKPAGVIVQGG-I 111

Query: 92  DGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
             + ++ D L  +        V RLD +T G ++   +  +AR L       +  + Y  
Sbjct: 112 KVKISISDLLDQVREGETFKIVHRLDRDTSGAIIFARNANVARYLMEEFKGRRVKKTYLA 171

Query: 148 RFHGQVDQDKLNLLKKGIV----IQGICYGDMQVTLDTQKGSNAWVTVGL 193
              G   ++      +G++    ++    G  +V +D     +A     +
Sbjct: 172 LTSGIPSKN------RGVIDYPLVKKYVSGQEKVVIDKNSPQDATTRFSI 215


>gi|317153563|ref|YP_004121611.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
 gi|316943814|gb|ADU62865.1| pseudouridine synthase [Desulfovibrio aespoeensis Aspo-2]
          Length = 289

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/181 (24%), Positives = 65/181 (35%), Gaps = 33/181 (18%)

Query: 1   MKDKN--IVQENFTPQRVSKVIARAGI--AS----RREVERMIAQQRVKVNGILLERAAV 52
           M  +   IV       R+ +  A  G+   S    RR   R+    +V V+G        
Sbjct: 1   MPQRETCIVAPGLAGVRLDR--AMTGLIPGSGLRLRR---RLCEAGQVTVDGR-ARGPGY 54

Query: 53  NVMSTDHIEV--------------DGVPLRKAERTRLW-LYHKPIGLVTTHSDPDGRSTV 97
            V S   + +              D   LR  ERT L+   +KP G+ +         +V
Sbjct: 55  KVRSGQVLALLAPPTDRMADLMPQDIPELRVVERTDLFAAVYKPGGVHSAAIAGKDGLSV 114

Query: 98  FDNLPSIFSRVISV--GRLDINTEGLLLLT--NDGGLARVLELPSTQWLRVYRVRFHGQV 153
              LP++F     V   RLD  T GLLL+    DG         +    + Y    HG++
Sbjct: 115 EAALPALFPDAAPVLLNRLDFPTSGLLLVALGPDGAETYRASEEAGGVRKFYLAVVHGRL 174

Query: 154 D 154
           D
Sbjct: 175 D 175


>gi|261839435|gb|ACX99200.1| hypothetical protein HPKB_0602 [Helicobacter pylori 52]
          Length = 327

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 106/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  ELDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLCFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D    + +V D 
Sbjct: 297 DMLEYLKKVFDK 308


>gi|227497602|ref|ZP_03927823.1| possible pseudouridylate synthase [Actinomyces urogenitalis DSM
           15434]
 gi|226832928|gb|EEH65311.1| possible pseudouridylate synthase [Actinomyces urogenitalis DSM
           15434]
          Length = 304

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 78/245 (31%), Gaps = 42/245 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---D 63
           V +    +RV   +AR    SR +V  + AQ  V+++G +L ++   V +   IEV   D
Sbjct: 6   VPDGLVGERVDAALARMTGLSRSKVSELCAQGGVRMDGAVLGKSDRLV-AGSLIEVDLPD 64

Query: 64  GVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
             PL  A               + +  KP G+    S       V   L ++        
Sbjct: 65  PRPLGPAPTPVDGMSLVYEDEDIVVVDKPAGIAAHPSMGWDGPDVLGALKAMHVQVATSG 124

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-- 159
              R   V RLD+ T G +++        VL+      +  ++Y     G +D       
Sbjct: 125 AAERQGIVSRLDVGTSGAMIVAKGERAYSVLKRAFREHEVDKIYHALVQGHLDPSSGTID 184

Query: 160 -----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +    +I G         +     +     + L  G+  +I+      
Sbjct: 185 APIGRHPSREWKMA---IIDGGRESVTHYDVIESMPAADLAEIHLETGRTHQIRVHMSAV 241

Query: 209 NWKVN 213
                
Sbjct: 242 GHPCV 246


>gi|294674059|ref|YP_003574675.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
 gi|294471803|gb|ADE81192.1| RNA pseudouridine synthase family protein [Prevotella ruminicola
           23]
          Length = 277

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 37/206 (17%), Positives = 69/206 (33%), Gaps = 31/206 (15%)

Query: 27  SRREVERMIAQQR-VKVNGILLERAAVNVMSTDHIEVDGVPLRKA-----------ERTR 74
           SR +++  + Q R +KVNG  + +    +     + V      +            E   
Sbjct: 14  SRSKIKATL-QGRGIKVNGKTVSQFDFQLEPGMKVAVSKTKRNQQSFKSRYVKIVYEDKW 72

Query: 75  LWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGG 129
           L +  K  G+++           TV D+      +      V RLD +T GL++   D  
Sbjct: 73  LIVIEKAEGILSMAAGHSSLNVKTVLDDYFKKSRQKCTAHVVHRLDRDTSGLMVYAKDME 132

Query: 130 LARVLELPSTQW--LRVYRVRFHGQV--DQDKLNLLKKGI---------VIQGICYGDMQ 176
             ++LE         R Y     G++  D+  +    K              G  Y    
Sbjct: 133 TEQILEHNWHDIVYDRRYVAVCSGEMENDEGTIANWLKDNKAYVTYSSPTDNGGKYAVTH 192

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK 202
             +  +   ++ V   L  G+  +I+
Sbjct: 193 YHVLDRTTDHSLVEFKLETGRKNQIR 218


>gi|238751458|ref|ZP_04612950.1| tRNA pseudouridine synthase C [Yersinia rohdei ATCC 43380]
 gi|238710325|gb|EEQ02551.1| tRNA pseudouridine synthase C [Yersinia rohdei ATCC 43380]
          Length = 257

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L L     Q  + Y     G V +         ++L+ +               
Sbjct: 67  SEVARALSLQFEQHQIQKTYHAVVRGYVLEADTIDYEMTEELDKIADKFARPDKAPQPSV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  +V +    G        L E     G+  ++++        + 
Sbjct: 127 THYKPLAKVEVPVAIGRYDTARFSLLELKPETGRKHQLRRHMAHIRHPII 176


>gi|134301739|ref|YP_001121707.1| pseudouridine synthase, RluA family protein [Francisella tularensis
           subsp. tularensis WY96-3418]
 gi|134049516|gb|ABO46587.1| pseudouridine synthase, RluA family protein [Francisella tularensis
           subsp. tularensis WY96-3418]
          Length = 317

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 54/148 (36%), Gaps = 22/148 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR ++++ + +  + VNG    +    V+  + +E++   L                E  
Sbjct: 22  SRAQIQKWLKEGSITVNGR-ATKPKHIVLGDEEVEINIELLPTNEWIAEDINLKIIFEDD 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + +  KP+ ++      +   TV + L           R   V RLD +T GL++    
Sbjct: 81  DIIVIDKPVNMIVHPGAGNPTGTVSNTLLHRYKDQDKLPRAGIVHRLDKDTSGLMVAAKS 140

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQV 153
                 L  +L   +  R Y     G++
Sbjct: 141 SIAYHNLVQQLAERKVSRKYLAIVEGEI 168


>gi|227486639|ref|ZP_03916955.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
 gi|227235351|gb|EEI85366.1| pseudouridylate synthase [Anaerococcus lactolyticus ATCC 51172]
          Length = 297

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/227 (17%), Positives = 79/227 (34%), Gaps = 40/227 (17%)

Query: 14  QRVSKVIARAGIAS--RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VP 66
            RV K I+   + S  R +++  I    +KVN   ++  +  +   D I +D        
Sbjct: 9   IRVDKYISDE-LDSIPREKIKDFIKASLIKVNDKKIK-PSFKLQMGDEIFIDDSLFEVQE 66

Query: 67  LRKA--------ERTRLWLYHK-------PIGLVTTHSDPDG--RSTVFDNLPSIFSRVI 109
           ++          E     + +K       P G + T +  +       +D L  I     
Sbjct: 67  IKAEDIPLDIVYENNDYAIINKQKNLIVHPAGAIVTGTLVNALLYKYGYDGLSHIGGDDR 126

Query: 110 S--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--KLNLL-- 161
              V RLD +T GL+++  +    R L     + Q  + Y     G  D+   ++     
Sbjct: 127 PGIVHRLDKDTTGLMVIAKNNESYRYLKTLFETRQVRKEYLAIVFGNFDEKCGRIENFMD 186

Query: 162 ------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +K  V         +  + ++    + V V +  G+  +I+
Sbjct: 187 RDPHNRRKMAVRPSGRRAISEYEVLSETDGFSLVKVHIITGRTHQIR 233


>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 = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 39/255 (15%), Positives = 88/255 (34%), Gaps = 59/255 (23%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD 
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSMIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVD- 63

Query: 65  VPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +P +  E T                + +  KP  ++          T+ + L      + 
Sbjct: 64  LPEKPQEATVQPEEIELKVLYEDRDIIVIDKPGDMIVHPVPSKLSGTLVNALLHHCKDLQ 123

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDK 157
            VG         RLD  T G++++  +   A           +  + Y +   G++  D 
Sbjct: 124 GVGGKLRPGIVHRLDKETSGVIVVAKN-DFAHQSLSKQFKDRKVKKTYILLVKGKMKND- 181

Query: 158 LNLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTV--------GL-----REGKN 198
                +G++   +      V       ++T K +     V         L     + G+ 
Sbjct: 182 -----EGVI--DLPLARHPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRT 234

Query: 199 REIKKVFEFFNWKVN 213
            +I+   +     + 
Sbjct: 235 HQIRVHMKSLGHPIM 249


>gi|149377766|ref|ZP_01895499.1| Pseudouridylate synthase, 23S RNA-specific [Marinobacter algicola
           DG893]
 gi|149357938|gb|EDM46427.1| Pseudouridylate synthase, 23S RNA-specific [Marinobacter algicola
           DG893]
          Length = 325

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 79/257 (30%), Gaps = 54/257 (21%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR  ++  I    + VNG   +     VM  D +E+D  P  +              E  
Sbjct: 34  SRSRLQGWIKSGALTVNGKSCK-PRDKVMLGDRLELDAEPEAQVSWEAESIDLDIVYEDE 92

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            L + +KP GLV   +      T+ + L           R   V RLD +T G++++   
Sbjct: 93  HLLVINKPAGLVVHPAAGHADGTLVNALLNHAPEVENLPRAGIVHRLDKDTSGIMVVARS 152

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYG 173
                 L  +L +    R Y     G +               +   +   +V  G    
Sbjct: 153 LIAHTSLVDQLQTRTMGREYEAIVVGTLTGGSTVDAPIGRHPRERKKMA--VVPTGKPAV 210

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN----RLIRISYGPFQLGTLL 229
                L  +  ++  V   L  G+  +I+         +        R+         L 
Sbjct: 211 TH-YRLVERFAAHTHVRCKLESGRTHQIRVHMAHVKHPLVGDPQYGGRLR--------LP 261

Query: 230 AGSTREVSKKILREQLG 246
            G     +   LRE L 
Sbjct: 262 KG-----TTDELREVLA 273


>gi|15675107|ref|NP_269281.1| hypothetical protein SPy_1127 [Streptococcus pyogenes M1 GAS]
 gi|13622265|gb|AAK34002.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 301

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 69/211 (32%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-----------AERTRLWLYHKP 81
               + VNG + + A   +   D + +D     P  K            E     + +KP
Sbjct: 33  KGGNILVNG-IEQNAIYLLQVGDVVTIDIPNEEPFEKLEAIPFDLDIVHEDDHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           IG  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  IGFASIPS-AIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G     D+  +           + + +   G         + 
Sbjct: 151 DKQLQTRSIEKRYFALVSGNGMLPDEGDIIAPIGRSKDSIITRAVDPMGKYAKTSYKVVA 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 241


>gi|328461874|gb|EGF34095.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus MTCC 5462]
          Length = 260

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 42/207 (20%), Positives = 78/207 (37%), Gaps = 36/207 (17%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVT 86
           V VNG  ++ A   V + D + V   +  PL+            E  ++ + +KP G+V 
Sbjct: 2   VTVNGKPVK-ANFKVTAGDVVTVTIPEVKPLKAVAEPIPLEIVYEDDQVIVVNKPQGMVV 60

Query: 87  THSDPDGRSTVFD------NLPSIFSRVIS--VGRLDINTEGLLLL--TNDGGLARVLEL 136
             +      T+ +       LP I   +    V R+D +T GLL++  T    L+   +L
Sbjct: 61  HPAPGHPDGTLVNGLLYHTKLPGINGVIRPGIVHRIDKDTSGLLMVAKTETAQLSLSAQL 120

Query: 137 PSTQWLRVYRVRFHGQVDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            +   +R Y    HG   +D+            +  ++ +V  G         L+    +
Sbjct: 121 KAKTSIREYLALVHGTFKEDEGTIDAPLGRDPRDRKRQAVVADGRHAVTHFQVLERFT-N 179

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKV 212
              V   L  G+  +I+    + +  V
Sbjct: 180 YTLVKCILDTGRTHQIRVHMAYIHHPV 206


>gi|319953859|ref|YP_004165126.1| ribosomal large subunit pseudouridine synthase d [Cellulophaga
           algicola DSM 14237]
 gi|319422519|gb|ADV49628.1| ribosomal large subunit pseudouridine synthase D [Cellulophaga
           algicola DSM 14237]
          Length = 363

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 81/239 (33%), Gaps = 43/239 (17%)

Query: 4   KNIVQENFTPQRVSKVIAR---AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           K +  +   P RV K +       +  R ++++      + VN I +++    V + D +
Sbjct: 36  KVVASKGQEPLRVDKFLMNFIENAV--RNKIQQAARAGHIWVNDIQVKQ-NYRVKAGDEV 92

Query: 61  EV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF-------- 98
            V             + +P+    E   L + +K  G+V      +   T+         
Sbjct: 93  RVLFEHPPHEFLLVPEDIPINIVYEDDVLMVVNKEPGMVVHPGHGNYSGTLINALLHHTK 152

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           D   +   R   V R+D +T GLL++         L          R Y     G +++D
Sbjct: 153 DLAVNSNERPGLVHRIDKDTSGLLVIAKTDEAMTFLSKQFFDKTSEREYVALVWGNMEED 212

Query: 157 KL-----------NLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
           +            N L+  +   G    D      +  + G    ++  L  G+  +I+
Sbjct: 213 EGTIEGHVGRHPSNRLQMTVFPDGEQGKDAVTHFKVLERLGYLTLISCKLETGRTHQIR 271


>gi|116494411|ref|YP_806145.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|116104561|gb|ABJ69703.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
          Length = 300

 Score = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 84/235 (35%), Gaps = 41/235 (17%)

Query: 13  PQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P +++  + + G  SR +++++      V VN       A  V S D I V   P   A+
Sbjct: 11  PLKLAAFLKQQGF-SRAQLKKLRYQGGFVFVN-KRQRHTAYLVRSGDRILVQTAPEHAAD 68

Query: 72  RTR--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVIS 110
                              + +KP G+ +  +     +++ + + +           V  
Sbjct: 69  SVVPYSHDLAISYEDDDYLIVNKPAGVASIPAVGRQNNSMANMVKAYLIKTKAESQAVHV 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRF--------HG----QVDQ 155
           V RLD +T GL++    G LA  L    L S  +++ Y            HG     +  
Sbjct: 129 VTRLDRDTSGLMVFAKHG-LAHSLLDQQLHSQDFVKQYVAIVTAQTPLATHGWIVLPIGV 187

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                +++ +   G        TLD +  + A + V L  G+  +I+  F     
Sbjct: 188 SDGFYMRRVVTDTGKASVTEYRTLD-ENTAGAMMLVTLHTGRTHQIRVHFAAIGH 241


>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 = 64.4 bits (156), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/225 (18%), Positives = 72/225 (32%), Gaps = 42/225 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRK-AERT 73
           SR  ++ +I +  + VNG    +A   V + D I V            + +PL    E  
Sbjct: 22  SRSFIQGLIEEGHILVNGA-ARKANYKVRAMDQITVVIPPPRELKVEAENIPLEVLYEDE 80

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLL 124
            + + +KP G+V   +      T+ + L      +           V R+D +T GLL++
Sbjct: 81  DVLVVNKPQGMVVHPAPGAWTKTMVNALLYHCRNLSGINGVLRPGIVHRIDKDTSGLLVV 140

Query: 125 TNDGGLARVLELPS---TQWLRVYRVRFHGQV-------------DQDKLNLLKKGIVIQ 168
             +  LA              R Y    HG V             D      +   +V Q
Sbjct: 141 AKN-DLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVDAPVGRDPADRKKMA--VVFQ 197

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     +  +      +   L  G+  +I+    +    V 
Sbjct: 198 NAKEAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVL 242


>gi|315103148|gb|EFT75124.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA2]
          Length = 306

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 85/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G L+ RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQLVSRASVRVATGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVATPSITPQIVEGMRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AIKHPC 247


>gi|294635111|ref|ZP_06713622.1| tRNA pseudouridine synthase [Edwardsiella tarda ATCC 23685]
 gi|291091488|gb|EFE24049.1| tRNA pseudouridine synthase [Edwardsiella tarda ATCC 23685]
          Length = 264

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 29/177 (16%), Positives = 56/177 (31%), Gaps = 41/177 (23%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LL+   
Sbjct: 6   QDEHLVAINKPAGWLVHRSWLDRKEKVVVMQTVRDQLGRHVYTVHRLDRPTSGVLLMGLS 65

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL-------------NLLK---------- 162
             +AR L       Q  +VY     G +  + L             +  +          
Sbjct: 66  SEVARALAQQFEQHQIHKVYHAVVRGYLQGEALLDYPLTPELDKIADRFRSAERGPQPAQ 125

Query: 163 ---KGIVIQGICYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVN 213
              +G+          +V L   +      + V +  + G+  ++++        + 
Sbjct: 126 THYRGV-------ATAEVPLAIGRYPTARFSLVELTPQTGRKHQLRRHMAHLRHPII 175


>gi|258405801|ref|YP_003198543.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257798028|gb|ACV68965.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 285

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 83/244 (34%), Gaps = 42/244 (17%)

Query: 3   DKNIVQENFTPQRVS---KVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++  V E +   R+    +++A  +G+   R+ ++  A  RV+ NG    +    + +  
Sbjct: 8   ERIAVPEEWHGVRIDQGLRLLAPESGL---RQRQQWCASGRVRQNGRTERKGG-RLEAGA 63

Query: 59  HIEVDGVPLRKAERT-----------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            +E+   PL    +             L    KP  +       +   +V   LP++F R
Sbjct: 64  TLELLPEPLPSKPQPASGVRVVSVVNALAAVFKPGNVHCEAQSHNPEPSVESVLPNLFPR 123

Query: 108 VIS--VGRLDINTEGLLLLT-NDGGL-ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                + RLD  T GL+L+  + G      +     +  + Y    HG+    +L   + 
Sbjct: 124 QRPRLLNRLDYPTSGLVLVALSQGAFDQYQIWQDEGRVRKTYWAEIHGEWTGPELLKWR- 182

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAW---------------VTVGLREGKNREIKKVFEFF 208
              I+      + V  +       W               V V + +G+   I+      
Sbjct: 183 ---IETAKRKRVAVVFEPDPDPLRWTHVRALYRIAPGRTRVEVVIAKGRRHHIRAHLAAA 239

Query: 209 NWKV 212
              +
Sbjct: 240 GTPI 243


>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 = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 96/247 (38%), Gaps = 39/247 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I+ E   P R+ + + ++    SR  ++ +I    V +N    + A   + + D+I++ 
Sbjct: 18  EIIYELPLPMRLDRWLVSKRPEQSRARIQNLINAGLVLINYKTAK-AKTPLKTGDNIQIW 76

Query: 64  ---GVPLRK-----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLP 102
                PL              E   + + +K  GL+   +      T+ +       +LP
Sbjct: 77  MPPPEPLVYLKPEKMHLNILYEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLP 136

Query: 103 SIFSRVIS--VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD---- 154
            I  ++    V RLD +T G +++  + +  +   +++      R Y    HG  +    
Sbjct: 137 GINGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIRDKIASRNYIAVIHGVPNTSEG 196

Query: 155 -------QDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                  +DK+N LK  +V +    Y      L  + G+ + ++  L  G+  +I+    
Sbjct: 197 KIVGHIGRDKINRLKYAVVDENSGRYACTYWKLLERFGNYSLMSFKLDTGRTHQIRVHCA 256

Query: 207 FFNWKVN 213
           + N  + 
Sbjct: 257 YINHPIL 263


>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 = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 85/245 (34%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE+  
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------PS 103
                      + VPL    E   L + +KP G+V   +  +   TV + L        +
Sbjct: 128 DLLPEQLAFTPEPVPLDIVYEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD  T GL+++         L  +L +    R Y     G          
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 152 QVDQDKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFE 206
            + +D     +  +V    G         +DT   Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTGASGKPARTHFRRVDTALWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWK 211
                
Sbjct: 308 HIGHP 312


>gi|225389034|ref|ZP_03758758.1| hypothetical protein CLOSTASPAR_02779 [Clostridium asparagiforme
           DSM 15981]
 gi|225044909|gb|EEG55155.1| hypothetical protein CLOSTASPAR_02779 [Clostridium asparagiforme
           DSM 15981]
          Length = 342

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 58/356 (16%), Positives = 112/356 (31%), Gaps = 88/356 (24%)

Query: 6   IVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           IV  N   QR+ K++A    +AG      + +M+ ++ + +NG      +  +   D I 
Sbjct: 5   IVTPNEAGQRLDKLLAKYMNQAGKG---FLYKMMRKKNITLNGKKC-DGSERLGEGDEIR 60

Query: 62  -------------------VDG---VPLRKAERTRLWLYHKPIGLVTT---HSDPDGRST 96
                              + G    P    E + + + +KP GL++      D      
Sbjct: 61  LFLADETIAKFTGGGAAKPISGYYPKPDIIYEDSHILVVNKPAGLLSQKAREDDTSLNEA 120

Query: 97  VFDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARVLELP-----STQWL 142
           + + L              R     RLD NT GL++    G     L++           
Sbjct: 121 ILNYLIDSGRMPVEQLRTFRPSICNRLDRNTSGLVVA---GRSLAGLQVMNAVFKDRSIH 177

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------QVTLDTQKGSNAW----- 188
           + Y+    G + +     L  G + +      +          V + T+    AW     
Sbjct: 178 KYYQCIVKGSLKE---KQLIAGFLRKDEASNTVDIYPLEVENSVPIMTEYLPLAWGGGFT 234

Query: 189 -VTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI-----LR 242
            + V L  G++ +I+         +            LG    G  R V++++     LR
Sbjct: 235 LLQVTLITGRSHQIRAHLASIGHPI------------LGDFKYGD-RSVNEEMKKRYGLR 281

Query: 243 EQL--GPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            QL     L+    + +     +        P   + V +    + +       +S
Sbjct: 282 AQLLHSWKLVMPEDLAVPLDYLAGREFFAPLPEKFNRVLEGERMLPRQPFSAKNMS 337


>gi|6942292|gb|AAF32394.1|AF224466_1 putative pseudouridylate synthase [Haemophilus ducreyi]
          Length = 250

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/226 (19%), Positives = 76/226 (33%), Gaps = 45/226 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST------------DHIE 61
           R+ + +A+     SR  ++  I    VKVNGI++ RA   V                  E
Sbjct: 19  RLDQALAQLFPDYSRSRIKVWIENDLVKVNGIIVNRARGKVFGGEQIEIQAEIEEEIRFE 78

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
              +PL    E   + + +KP  LV      +   TV + L   +       R   + RL
Sbjct: 79  PQNIPLNIVHEDDDIIIINKPKNLVVHPGAGNPDGTVLNALLYYYPPIAEVPRAGIIHRL 138

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL+++  +      L   L   +  R Y     G + Q        G V + +  
Sbjct: 139 DKDTTGLMVVAKNIPAQTHLVTALQKRRITREYEAIASGIMTQG-------GKVDEPMAR 191

Query: 173 GDMQVTLDTQKG----------------SNAWVTVGLREGKNREIK 202
              + T                      +   + + L  G+  +I+
Sbjct: 192 HPTKRTAMAVHPMGKPAITHYRIMERFRNYTRLRLRLETGRTHQIR 237


>gi|257095460|ref|YP_003169101.1| RluA family pseudouridine synthase [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257047984|gb|ACV37172.1| pseudouridine synthase, RluA family [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 375

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 78/224 (34%), Gaps = 38/224 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           QR+ +V+AR     SR  ++  I + RV V G +       +   + I +          
Sbjct: 40  QRLDQVLARLLSQHSRSRLQDWIREGRVAVGGAVTVEPRFRLWGGETIALTESTDERAEA 99

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVG 112
              + +PLR   E   L +  K  GLV      + R T+ + L     ++        V 
Sbjct: 100 SAPEEIPLRIVFEDDTLIVLDKQAGLVVHPGSGNWRGTLLNGLLHHAPQLARVPRAGIVH 159

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           RLD +T GL+++         L  +L +    R Y+    G V+   +     G   +  
Sbjct: 160 RLDKDTTGLMVVAKTLEAQTDLVRQLQARSVKRCYQALVRGIVEGAGIVDAPIG---RHP 216

Query: 171 CYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
                   +   + +     V        L E     G+  +I+
Sbjct: 217 TVRTRMAVVSGGRPARTHYRVLERFVACTLIECALETGRTHQIR 260


>gi|329964802|ref|ZP_08301825.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
 gi|328524653|gb|EGF51716.1| pseudouridine synthase, RluA family [Bacteroides fluxus YIT 12057]
          Length = 303

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 73/211 (34%), Gaps = 30/211 (14%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIEVDGVPLR-KA 70
           A+   ASR +++ +++++ V V+ ++        +  + V         E +   ++   
Sbjct: 31  AKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQISREKGRKEFNHKLIKIVY 90

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + +  K  GL++ +++     T +  L     R      V  V RLD +T GL++ 
Sbjct: 91  EDAYIIVIEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYIVHRLDRDTSGLMMF 150

Query: 125 TNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLLKKGIVIQGIC 171
             D      L          R Y     G+           +   KL +    I   G  
Sbjct: 151 AKDEKTQNTLRDHWHDIVFDRRYVAVVAGEMEKNVGSVSSWLTDRKLYVYSSPID-DGGK 209

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     +    + V + L  G+  +I+
Sbjct: 210 EAITHYRTIKRANGYSLVELNLETGRKNQIR 240


>gi|317476220|ref|ZP_07935471.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
 gi|316907631|gb|EFV29334.1| RluA family pseudouridine synthase [Bacteroides eggerthii
           1_2_48FAA]
          Length = 303

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 39/221 (17%), Positives = 77/221 (34%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++        +  + V         E
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQISREKGRKE 80

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 81  FSNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYIVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D      L          R Y     G+           +   KL + 
Sbjct: 141 DRDTSGLMMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEMENNAGMVRSWLTDRKLYVY 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 201 SSPTDDGGKEAVTHYRTIKRANGF-SLVELVLETGRKNQIR 240


>gi|269138083|ref|YP_003294783.1| tRNA pseudouridine synthase C [Edwardsiella tarda EIB202]
 gi|267983743|gb|ACY83572.1| tRNA pseudouridine synthase C [Edwardsiella tarda EIB202]
 gi|304558127|gb|ADM40791.1| tRNA pseudouridine synthase C [Edwardsiella tarda FL6-60]
          Length = 276

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/180 (16%), Positives = 57/180 (31%), Gaps = 34/180 (18%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
           G+ +   +   L   +KP G +   S  D   +  V   +  +    V +V RLD  T G
Sbjct: 11  GMEIIYQDEH-LVAINKPAGWLVHRSWLDRKEKVVVMQTVRDMLGRHVYTVHRLDRPTSG 69

Query: 121 LLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQ 168
           +LLL     +AR L       Q  +VY     G           +  + L+ +       
Sbjct: 70  VLLLGLSSEVARALAQQFEQHQIHKVYHAVVRGYLQGEALLDYPLTPE-LDKIADRFRSP 128

Query: 169 GIC----------YGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                            +V L   +   +  ++   E     G+  ++++        + 
Sbjct: 129 DRAPQPAQTHYRGLATAEVPLAIGRYPTSRFSLV--ELMPQTGRKHQLRRHMAHLRHPII 186


>gi|325956350|ref|YP_004291762.1| Pseudouridine synthase [Lactobacillus acidophilus 30SC]
 gi|325332915|gb|ADZ06823.1| Pseudouridine synthase [Lactobacillus acidophilus 30SC]
          Length = 301

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 70/209 (33%), Gaps = 36/209 (17%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKA-ERTRLWLYHKPI 82
              + VN       +  + + D +                  P+    E     + +KP+
Sbjct: 38  NGLILVNHKR-RYTSFRLKTNDEVIFVTGEEKKNDFLKPSNNPVEPVLETKNYIILNKPV 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLE 135
           G+++  S  +    + + L   F+R          + RLD +T GL+L+  +        
Sbjct: 97  GVLSIPSRYEDNDAIVNRLMGYFTRKGAKDLKPHVITRLDRDTSGLVLVGKNAVAHARFS 156

Query: 136 LPSTQ-WLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLDTQ 182
               + +++ Y    HG  +  +L  L            K+G++  G      +  +  Q
Sbjct: 157 KMGKERFIKKYHAIVHGNFESTELTGLIDEPIGKIDSGVKRGVIPDGKSAQT-EYKVLKQ 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               + V + L  G+  +I+    +    
Sbjct: 216 VPGASLVELRLLTGRTHQIRVHMAYLGHP 244


>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 = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 76/210 (36%), Gaps = 26/210 (12%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A+A   S    + +I +  V  NG  +  A + +  + + EV     P    E  ++
Sbjct: 8   KLLAKAKCISHNLAKSLIDKGLVSSNGKKITIARLELPLSANFEVAEIKKPKVIFEDKQI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +           +D L  +F     + RLD  T G++LL  +     +  
Sbjct: 68  LALDKPPFIES-----------YD-LSDMFEGWSLLHRLDKQTSGVILLIQENSPFHLKA 115

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDK-----LNLLKKGI----VIQGICYGDMQVTLDTQK 183
             + +     + Y    HG +         ++ +KKG     + +       Q+T  +  
Sbjct: 116 KEAFKKQAVYKEYICLLHGILADSITINKPISTIKKGFAKSRIDKNGLSAHTQLTPLSIV 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G        +  G+  +I+   +  N  + 
Sbjct: 176 GKKTQAQAIITTGRTHQIRVHCQSINHPIV 205


>gi|322831582|ref|YP_004211609.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321166783|gb|ADW72482.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 259

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/170 (21%), Positives = 57/170 (33%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D   TVF        I   V +V RLD  T G+LLL   
Sbjct: 7   QDEHLIAVNKPAGMLVHRSWLDRHETVFVMQTLRDQIGQHVFTVHRLDKPTSGVLLLALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR+L     + Q  +VY     G V Q         ++L+ +               
Sbjct: 67  SDVARLLSQQFENNQMSKVYHAVVRGYVPQDGTLDYALTEELDKIADKFASPDKAPQPAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  QV +    G        L E     G+  ++++        + 
Sbjct: 127 THYRVVAQVEMPVAVGRYDTARYSLVELKPETGRKHQLRRHMSHLRHPII 176


>gi|306827367|ref|ZP_07460654.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pyogenes ATCC
           10782]
 gi|304430514|gb|EFM33536.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus pyogenes ATCC
           10782]
          Length = 301

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 69/211 (32%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-----------AERTRLWLYHKP 81
               + VNG + + A   +   D + +D     P  K            E     + +KP
Sbjct: 33  KGGNILVNG-IEQNAIYLLQVGDVVTIDIPNEEPFEKLEAIPFDLDIVHEDDHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           IG  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  IGFASIPS-AIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G     D+  +           + + +   G         + 
Sbjct: 151 DKQLQTRSVEKRYFALVSGNGTLPDEGDIIAPIGRSKDSIITRAVDPMGKYAKTSYKVVA 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 241


>gi|159902752|ref|YP_001550096.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9211]
 gi|159887928|gb|ABX08142.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9211]
          Length = 327

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 83/248 (33%), Gaps = 57/248 (22%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA- 70
           P R+ + + ++    SR  +++ I +  VKVN   + +A   +   D I++   P     
Sbjct: 26  PMRLDRWLVSQRSEQSRARIQKFINEGLVKVN-EKIGKAKTPLRQGDEIKLWLPPPEPLP 84

Query: 71  -------------ERTRLWLYHKPIGLVTTHSDPDGRSTVF-------DNLPSIFSRVIS 110
                        E   L + +K  G+    +  +   T+        ++LP I  ++  
Sbjct: 85  YLKPEKISLDILYEDKYLIVINKQAGIAVHPAPGNKFGTLVNGLLHHCNDLPGISGKLRP 144

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWL-----RVYRVRFHGQVDQDKLNLLKK 163
             V RLD +T G +++         L     Q       R+Y    HG    D      K
Sbjct: 145 GIVHRLDKDTTGCIVVA---KTQEALVNLQKQIQTRVASRIYLAIVHGVPKGD------K 195

Query: 164 GIVIQGICYGDMQVT------------------LDTQKGSNAWVTVGLREGKNREIKKVF 205
           G +I  I    +                     L  + G  + ++  L  G+  +I+   
Sbjct: 196 GTIIGAIGRHPVDRKKYAVVTNEMARYACTHWELKERLGDYSLLSFKLDTGRTHQIRVHC 255

Query: 206 EFFNWKVN 213
             F   + 
Sbjct: 256 AHFGHPIL 263


>gi|319938146|ref|ZP_08012544.1| pseudouridine synthase [Coprobacillus sp. 29_1]
 gi|319806667|gb|EFW03316.1| pseudouridine synthase [Coprobacillus sp. 29_1]
          Length = 279

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 75/196 (38%), Gaps = 21/196 (10%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-----LRKAERTRLWLYHKPI 82
           R +++ ++  Q V V+G +    A ++     +E+         +   E   + +  KP 
Sbjct: 23  RNDIKNLLKYQNVWVDGHIETHYAYDLQVGQTVEIQAKKNDMPFVILYEDKEIIVIDKPC 82

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           GL++  +  +   T +  +          +  V RLD  T G+L+   +  L  +L    
Sbjct: 83  GLLSEQTAKENEKTAYQYVKQYLYKKKENIFLVHRLDQYTSGILMFVKNKKLYDILTQNW 142

Query: 139 TQWLRV--YRVRFHGQV--DQDKLNLL-----KKGIVIQGICYGDMQVTLDTQKGSN--- 186
            ++++   Y     GQ+   +  +         + + I     G   +T   Q  SN   
Sbjct: 143 NKYVKTRGYIAIVEGQMKKTKGTIENYLAESKTQNVYITTKEQGKKAITHYKQIQSNKRY 202

Query: 187 AWVTVGLREGKNREIK 202
           + + V L  G+  +I+
Sbjct: 203 SMLEVYLDTGRKNQIR 218


>gi|222153007|ref|YP_002562184.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222113820|emb|CAR41903.1| putative RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 301

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 76/234 (32%), Gaps = 52/234 (22%)

Query: 28  RREVERMIAQ---------------QRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
           R +V+ ++                   + VNG   + A   V   D + +   D +P  K
Sbjct: 10  RSKVKTLLKSHDVSKGLLAKVKYKGGNILVNGQ-EQNAIYLVDVGDVVTIHIPDELPFEK 68

Query: 70  -----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISV 111
                       E     + +KP+G  +  S     +T+ + + + +        +V  V
Sbjct: 69  LEAVPHPLDIVYEDDHFLVLNKPVGYASIPS-AIHSNTIANFIKAYYFEQNYPNKQVHIV 127

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDK 157
            RLD +T GL+L    G     L  +L      + Y     G             + + K
Sbjct: 128 TRLDRDTSGLMLFAKHGYAHARLDKQLQKRSIEKRYFALVSGNGQLPDFGEIVEPIGRSK 187

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +++ + +   G         +     +   V + L  G+  +I+  F    + 
Sbjct: 188 DSIITRTVDPMGKYAKTTYEVVARFAENVHLVDIKLHTGRTHQIRVHFSHIGFP 241


>gi|217033764|ref|ZP_03439190.1| hypothetical protein HP9810_7g45 [Helicobacter pylori 98-10]
 gi|216943813|gb|EEC23253.1| hypothetical protein HP9810_7g45 [Helicobacter pylori 98-10]
          Length = 327

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 52/313 (16%), Positives = 105/313 (33%), Gaps = 63/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFF 208
            N LK  I ++       + +  ++    + +T       +   L  G+  +I+      
Sbjct: 192 NNRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL 244

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
                 L R   G   L  L       + K+ +R  L  +L+E      +  +     L+
Sbjct: 245 ----EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLL 295

Query: 269 RDRPNIISEVPDD 281
           +D    + +V D 
Sbjct: 296 KDMLEYLKKVFDK 308


>gi|153875465|ref|ZP_02003256.1| ribosomal large subunit pseudouridine synthase D [Beggiatoa sp. PS]
 gi|152068071|gb|EDN66744.1| ribosomal large subunit pseudouridine synthase D [Beggiatoa sp. PS]
          Length = 321

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 85/238 (35%), Gaps = 38/238 (15%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M           P+    R+ K +A      SR  +++ I    V VN  +  RA   V 
Sbjct: 1   MTQIQTFNAQIPPEMAGYRLDKALADLFPDYSRARLQQWIRGGYVLVN-SISWRAKDKVK 59

Query: 56  STDHI--------EVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + I        EV   P         E   + + +KP GL+        ++T+ + L 
Sbjct: 60  GGEDIQITAQLEEEVSWQPQTLPLTLLYEDKDILVVNKPAGLIVHPGAGHQQNTLVNALL 119

Query: 103 SI------FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--- 151
           +         R   V RLD +T G+L++       + L  +L + ++LR Y+    G   
Sbjct: 120 NYAPELAQLPRAGIVHRLDKDTSGVLVVARSLPAHKHLVEQLQNREFLREYKAIVIGALI 179

Query: 152 -------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   + +      +  +V +G         L   +  + ++ V L  G+  +I+
Sbjct: 180 SGSTVDAPIGRHPTQRTRMAVVKKGKPAITHYRVLQRYRV-HTFIRVQLETGRTHQIR 236


>gi|19746076|ref|NP_607212.1| hypothetical protein spyM18_1088 [Streptococcus pyogenes MGAS8232]
 gi|21910322|ref|NP_664590.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28895899|ref|NP_802249.1| hypothetical protein SPs0987 [Streptococcus pyogenes SSI-1]
 gi|50914193|ref|YP_060165.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71903490|ref|YP_280293.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94988598|ref|YP_596699.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94990474|ref|YP_598574.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94994396|ref|YP_602494.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|139473780|ref|YP_001128496.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|209559410|ref|YP_002285882.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pyogenes NZ131]
 gi|251782299|ref|YP_002996601.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|19748247|gb|AAL97711.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|21904518|gb|AAM79393.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|28811149|dbj|BAC64082.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
 gi|50903267|gb|AAT86982.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|71802585|gb|AAX71938.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94542106|gb|ABF32155.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94543982|gb|ABF34030.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94547904|gb|ABF37950.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|134272027|emb|CAM30266.1| putative RNA pseudouridylate synthase [Streptococcus pyogenes str.
           Manfredo]
 gi|209540611|gb|ACI61187.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pyogenes NZ131]
 gi|242390928|dbj|BAH81387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 301

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 69/211 (32%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-----------AERTRLWLYHKP 81
               + VNG + + A   +   D + +D     P  K            E     + +KP
Sbjct: 33  KGGNILVNG-IEQNAIYLLQVGDVVTIDIPNEEPFEKLEAIPFDLDIVHEDDHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           IG  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  IGFASIPS-AIHSNTIANFIKAYYVDNHYLDQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G     D+  +           + + +   G         + 
Sbjct: 151 DKQLQTRSIEKRYFALVSGNGTLPDEGDIIAPIGRSKDSIITRAVDPMGKYAKTSYKVVA 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RYSENVHLVDIKLHTGRTHQIRVHFAHIGFP 241


>gi|323350661|ref|ZP_08086322.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
 gi|322123081|gb|EFX94772.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
          Length = 291

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 42/204 (20%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAILFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  Q   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVEPQKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RVKQFGQAALVKCQLKTGRTHQIR 230


>gi|255100096|ref|ZP_05329073.1| putative pseudouridylate synthase [Clostridium difficile QCD-63q42]
          Length = 300

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 74/212 (34%), Gaps = 45/212 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTR----------LWLYHKPIG 83
            ++ V VNG + ++ ++ V S D IEV  D        +            + + +KP  
Sbjct: 42  REKSVLVNG-VYKKPSLKVYSGDLIEVKIDEEKANFEPQDLNLQIIYDDFDIIMVNKPPF 100

Query: 84  LVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           +V   +      T+      + +      ++  V RLD+NT GL+++  +      L   
Sbjct: 101 MVVHPTKSHYDKTIANGISYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTA 160

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----MQVTLDTQKGSN----- 186
           +   +  + Y     G + ++      +G  I    Y      ++  +D +  S+     
Sbjct: 161 MSENKVEKKYITVVDGIIKEN------EG-TIDEPIYRPTEDSIKRIIDERGQSSVTHYK 213

Query: 187 --------AWVTVGLREGKNREIKKVFEFFNW 210
                     + V L  G+  +I+        
Sbjct: 214 VIERLENATVLEVSLETGRTHQIRVHMAHIGH 245


>gi|126698644|ref|YP_001087541.1| putative pseudouridylate synthase [Clostridium difficile 630]
 gi|115250081|emb|CAJ67901.1| putative pseudouridylate synthase [Clostridium difficile]
          Length = 300

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 74/212 (34%), Gaps = 45/212 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRKAERTRLWLYHKPIG 83
            ++ V VNG + ++ ++ V S D IEV            D       +   + + +KP  
Sbjct: 42  REKSVLVNG-VYKKPSLKVYSGDLIEVKIYEEKANFEPQDLNLQIIYDDFDIIMVNKPPF 100

Query: 84  LVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           +V   +      T+      + +      ++  V RLD+NT GL+++  +      L   
Sbjct: 101 MVVHPTKSHYDKTIANGISYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTA 160

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----MQVTLDTQKGSN----- 186
           +   +  + Y     G + ++      +G  I    Y      ++  +D +  S+     
Sbjct: 161 MSENKVEKKYITVVDGIIKEN------EG-TIDEPIYRPTEDSIKRIIDERGQSSVTHYK 213

Query: 187 --------AWVTVGLREGKNREIKKVFEFFNW 210
                     + V L  G+  +I+        
Sbjct: 214 VIERLENATVLEVSLETGRTHQIRVHMAHIGH 245


>gi|332884260|gb|EGK04528.1| hypothetical protein HMPREF9456_00855 [Dysgonomonas mossii DSM
           22836]
          Length = 355

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 81/248 (32%), Gaps = 42/248 (16%)

Query: 5   NIVQENFTPQ-RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             V +      RV K +A   +  SR  +++      + VN   ++     +   D I V
Sbjct: 30  RFVADKGQGMIRVDKYLAMHIVGVSRNRIQQAAEADCILVNNTPVKS-NYRIKPLDVISV 88

Query: 63  -------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFD--------- 99
                        + +PL    E   L + +KP GLV      + + T+ +         
Sbjct: 89  VMNRPPRELEIIPEDIPLDVVYEDEDLMVINKPPGLVVHPGFGNYQGTMVNAIAYRLKDT 148

Query: 100 -NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
               S   R+  V R+D +T GL+L+  +      L     +    R Y     G +  D
Sbjct: 149 PEYDSKDPRLGIVHRIDKDTSGLILVAKNAYAKTHLSAQFFNKTTKRQYIALVWGNISDD 208

Query: 157 KLNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVT-------VGLRE-----GKNREIKK 203
           +  +    G  ++      +    D  K +            V L +     G+  +I+ 
Sbjct: 209 EGRIEANIGRSLKNRMLMTVFPEADYGKHAVTHYKVLERLGYVTLIQCRLETGRTHQIRV 268

Query: 204 VFEFFNWK 211
             +   + 
Sbjct: 269 HMKHIGYT 276


>gi|323140403|ref|ZP_08075332.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
 gi|322415088|gb|EFY05878.1| pseudouridine synthase, RluA family [Phascolarctobacterium sp. YIT
           12067]
          Length = 217

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 59/162 (36%), Gaps = 21/162 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L +  KP G++   +  +  +T++D + + +        +  V RLD NT GL++ 
Sbjct: 13  EDDFLLIIDKPAGMLVHPTVSERGTTLYDYVKAYYEATGINAVIHPVSRLDRNTSGLVIF 72

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQ------GICY 172
             +  +   L     Q  + Y     G+ +      +  +   K+G +I+         Y
Sbjct: 73  AKEPIVQHWLS--QQQVEKEYLALACGRFETSEGIIEAPIAR-KEGSIIERCVDYTRGKY 129

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                 +     ++  + V L  G+  +I+         +  
Sbjct: 130 AKTAYEVLASYSNHTLLKVRLFTGRTHQIRVHLASIGHPLVN 171


>gi|167762842|ref|ZP_02434969.1| hypothetical protein BACSTE_01200 [Bacteroides stercoris ATCC
           43183]
 gi|167699182|gb|EDS15761.1| hypothetical protein BACSTE_01200 [Bacteroides stercoris ATCC
           43183]
          Length = 302

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/221 (18%), Positives = 78/221 (35%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++        +  + V         E
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKALLSKRVVYVDSVITTQYNFPLKPGMKVQISREKGRKE 80

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   L +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 81  FNNKLLKIVYEDAYLIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYIVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GLL+   D      L          R Y     G+           +   KL + 
Sbjct: 141 DRDTSGLLMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEMENNAGMVRSWLTDRKLYVY 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 201 SSPTDDGGKEAITHYRTIKRANGF-SLVELMLETGRKNQIR 240


>gi|291545928|emb|CBL19036.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 322

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 51/264 (19%), Positives = 88/264 (33%), Gaps = 80/264 (30%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMI-----AQQRVKVNGILLERAAVNVM 55
           MK+  I+ EN   QR  K +A+      RE  +        ++ + +NG         + 
Sbjct: 1   MKEF-IINENEAGQRFDKYLAKLL----REAPKSFFLQNDEEKNITLNGKKAT-GNEKLF 54

Query: 56  STDHIEV-------------DGVPLRKA------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           S DH+++             D  P          E   + L +KP G+++  +D DG  +
Sbjct: 55  SGDHVKLFLSDETFEKFSGNDSAPRAHYALDIIYEDENILLINKPAGMLSQPAD-DGTPS 113

Query: 97  VFDNLPSIF-------------SRVISVGRLDINTEGLLLLTNDGGLARVL-----ELPS 138
           + + L                  R     RLD NT GL+     G     L        S
Sbjct: 114 LVEYLTGYLLKNGSLTENDLRTFRPSVCNRLDRNTSGLIAA---GKSLSGLQELSGMFKS 170

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSN--------- 186
            +  + Y     G + +++         I+G    D    +VT+  Q+  N         
Sbjct: 171 RELHKYYLCLVEGVLKEER--------YIKGYLAKDKKSNKVTIYKQEKENALPVETKYY 222

Query: 187 --------AWVTVGLREGKNREIK 202
                     + V L  G+  +I+
Sbjct: 223 PLGTNGTRTLLKVELITGRAHQIR 246


>gi|282862147|ref|ZP_06271210.1| pseudouridine synthase, RluA family [Streptomyces sp. ACTE]
 gi|282563172|gb|EFB68711.1| pseudouridine synthase, RluA family [Streptomyces sp. ACTE]
          Length = 313

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 87/248 (35%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV  VI+R    SR +   + A  +V+V+G +  +       A + V     
Sbjct: 12  VPDGLEGERVDAVISRLFGFSRTKAAELAAAGKVQVDGAVAGKSERVHGGAWLEVEMPQA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  PAPVQIVAEPVEGMEIVHDDDDIVVIM-KPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVD----- 154
                   V RLD+ T GL+++      A  L     +     + Y     G  D     
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKS-ERAYTLLKAQFRDRVVEKKYHALVQGHPDPMSGT 189

Query: 155 -QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF 207
               +    +      +  +G         ++  + + + + + L  G+  +I+  +   
Sbjct: 190 IDAPIGRHPQHDYKWAVTAEGKPSVTHYDLIEAYRAA-SLLDIKLETGRTHQIRVHMSAH 248

Query: 208 FNWKVNRL 215
            +  V  L
Sbjct: 249 RHPCVGDL 256


>gi|124024982|ref|YP_001014098.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL1A]
 gi|123960050|gb|ABM74833.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL1A]
          Length = 326

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 80/241 (33%), Gaps = 43/241 (17%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR 68
           P R+ + + ++    SR  V++ I     +VNG   + A   V   D I++      PL 
Sbjct: 26  PMRLDRWLVSQRAEQSRAHVQKFIEAGFARVNGKTGK-AKTPVRPGDIIQLWVPPPEPLP 84

Query: 69  K-----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
                        E   L + +K  G+    +  +   T+ + L      +  +G     
Sbjct: 85  YLKPEEIDLDILYEDDHLIVINKTAGMAVHPAPGNKSGTLVNGLIHHCPDLPGIGGKLRP 144

Query: 113 ----RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
               RLD +T G +++  T +  +   +++      R Y    HG +  +    +  G +
Sbjct: 145 GIVHRLDKDTTGCIVVAKTQEALVKLQIQIQKRVASRNYIAVVHGAIKDN--EGMIVGSI 202

Query: 167 IQGICYGDMQVTLDTQKGS---NAW-----------VTVGLREGKNREIKKVFEFFNWKV 212
            +          +D + G      W           +   L  G+  +I+         +
Sbjct: 203 GRHPKDRKKYAVVDEESGRYACTHWKLIENLGNFSLLKFKLDTGRTHQIRVHSAHIGHPI 262

Query: 213 N 213
            
Sbjct: 263 I 263


>gi|317182056|dbj|BAJ59840.1| hypothetical protein HPF57_0766 [Helicobacter pylori F57]
          Length = 327

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 106/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKIVPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHLE 245

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 246 H----LNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D    + +V D 
Sbjct: 297 DMLEYLKKVFDK 308


>gi|317177424|dbj|BAJ55213.1| hypothetical protein HPF16_0616 [Helicobacter pylori F16]
          Length = 327

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 52/313 (16%), Positives = 105/313 (33%), Gaps = 63/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFF 208
            N LK  I ++       + +  ++    + +T       +   L  G+  +I+      
Sbjct: 192 NNRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNHLNLIGAKLFTGRTHQIR---AHL 244

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
                 L R   G   L  L       + K+ +R  L  +L+E      +  +     L+
Sbjct: 245 ----EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLL 295

Query: 269 RDRPNIISEVPDD 281
           +D    + +V D 
Sbjct: 296 KDMLEYLKKVFDK 308


>gi|218132473|ref|ZP_03461277.1| hypothetical protein BACPEC_00332 [Bacteroides pectinophilus ATCC
           43243]
 gi|217992583|gb|EEC58585.1| hypothetical protein BACPEC_00332 [Bacteroides pectinophilus ATCC
           43243]
          Length = 229

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 65/171 (38%), Gaps = 30/171 (17%)

Query: 15  RVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           R+ + +A+        SR  ++++I    V VNG  ++ A   +   D I++        
Sbjct: 16  RIDRYMAQEREELSDLSRSYLQKLIQDGNVLVNGCNIK-ANYKLKKADIIDITLPDIKEP 74

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
               + +PL    E   + + +KP G+V   +      T+ + L               R
Sbjct: 75  QIEAENIPLDILYEDEDIIVINKPKGMVVHPAAGHYSGTLVNALMYHCRDNLSGINGVMR 134

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD 156
              V R+D+NT G+L+   +      +   L      R Y    + + +++
Sbjct: 135 PGIVHRIDMNTTGVLVACKNDFAHNAISAQLSVHSITRKYEAIVYNRFNEE 185


>gi|78778581|ref|YP_396693.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9312]
 gi|78712080|gb|ABB49257.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus
           marinus str. MIT 9312]
          Length = 319

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 88/246 (35%), Gaps = 37/246 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNV---- 54
            I+ E   P R+ + + ++    SR  ++  I    V VN    +     +   NV    
Sbjct: 18  EIIYELPLPMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAKAKTPLKNGDNVQIWM 77

Query: 55  -MSTDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
                 I +    +      E   + + +K  GL+   +      T+ +       +LP 
Sbjct: 78  PPPEPLIYLKPEKMDLNILFEDKHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLPG 137

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFH--------- 150
           I  ++    V RLD +T G +++         L+    +    R Y    H         
Sbjct: 138 INGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEGQ 197

Query: 151 --GQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
             G + +DKLN LK  +V +    Y      L+ + G+ + ++  L  G+  +I+     
Sbjct: 198 IVGHIGRDKLNRLKYKVVEETTGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCAH 257

Query: 208 FNWKVN 213
            N  + 
Sbjct: 258 INHPIV 263


>gi|294507190|ref|YP_003571248.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
 gi|294343518|emb|CBH24296.1| Ribosomal large subunit pseudouridine synthase D [Salinibacter
           ruber M8]
          Length = 379

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 63/357 (17%), Positives = 109/357 (30%), Gaps = 96/357 (26%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ K + R    ASR +++R I +  +KVNG  +++ +  V   D I      +RK    
Sbjct: 40  RIDKYLTRFYPEASRTKIQRAIKKGHLKVNGADVKK-SYGVEPGDEIVF--RLIRKPPMQ 96

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------------- 101
                       E   L + +KP G+V   +      T+   L                 
Sbjct: 97  AEPEAIPLDVVHEDDDLLVVNKPAGMVVHPAPGHRSGTLVHALLHHVDGGEVAADDERDE 156

Query: 102 ------------------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                                  R   V RLD  T GLL++   G   + L     +   
Sbjct: 157 VSEDEVGLSLVNALPQSPDHPVVRPGIVHRLDKGTSGLLVVAKRGRAHQPLAEQFKAHTV 216

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS--------------NA 187
            R YR    G        +  +G + +   +      +   +G                +
Sbjct: 217 DRRYRAIVWGHFAPSDGTI--EGAIGRDPHHRQRMAVVPGDEGKWARTHYETVETYAHTS 274

Query: 188 WVTVGLREGKNREIK---KVFEFFNWKVN-----RLIRISYGPFQLGTLLAGSTREVSKK 239
            V   L  G+  +I+   +        +         R+ YG        +G  R    +
Sbjct: 275 VVEFELETGRTHQIRVHAR---AQGHPLLGDPKYGGQRVRYGT------QSGKRRAFYDQ 325

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
            L   L    L   ++  D PI      + DR    ++ P  + R+ +   Q+ G  
Sbjct: 326 -LFGTLPHPALHAYRIGFDHPI------MEDRLRFEADPPPAWRRVLRELRQEEGAG 375


>gi|300858799|ref|YP_003783782.1| hypothetical protein cpfrc_01382 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|300686253|gb|ADK29175.1| hypothetical protein cpfrc_01382 [Corynebacterium
           pseudotuberculosis FRC41]
 gi|302331059|gb|ADL21253.1| Putative pseudouridine synthase [Corynebacterium pseudotuberculosis
           1002]
          Length = 307

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 36/232 (15%), Positives = 77/232 (33%), Gaps = 38/232 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN----GIL----------LERAAV 52
           V E     RV   +++    SR     +     V V+    G            +     
Sbjct: 9   VPEGLAGMRVDAALSKLLGISRTVAADLATAGDVLVDALPVGKSDRIAEGQWLDVTLPET 68

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             ++     V+G+ +  ++   L   +KP+G+    +      TV   L +   R+ + G
Sbjct: 69  KDLTPREELVEGMDILYSDDD-LIAVNKPVGVAAHPTLGWEGPTVIGGLAAAGFRISTSG 127

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKLN 159
                    RLD+ T G++++        VL+    +    + Y     G +D     ++
Sbjct: 128 PPERKGIVQRLDVGTSGVMVIAASERGYSVLKRAFKERTVSKTYHALVQGHMDPFTGTID 187

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +  +   G        TL+    + + + + L  G+  +I+
Sbjct: 188 APIGRHPSAGWRFAVTSDGKHAVTHYETLEAFAEA-SLLKIHLETGRTHQIR 238


>gi|254441292|ref|ZP_05054785.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
 gi|198251370|gb|EDY75685.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
          Length = 344

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/182 (22%), Positives = 68/182 (37%), Gaps = 32/182 (17%)

Query: 6   IVQENFTPQRVSKVIA-----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            + EN  P R+ K +A      A + SR  + R++A   V+VNG ++       +  D +
Sbjct: 9   TLAENP-PARMDKALALNVPLDASL-SRSRLMRLLADGAVQVNGAVVTDPRAKPVEGDAV 66

Query: 61  EV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+            + +PL    E   L + +KP G+V   +      T+ + L      
Sbjct: 67  EILVEIADDYHVLPEDIPLDVVFEDDDLIVINKPTGMVVHPAPGTPGGTLVNALLHHCGD 126

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
                    R   V R+D  T GLL++         L     +    R YR   +G  D 
Sbjct: 127 ALSGVGGEKRPGIVHRIDKETSGLLVVAKTDRAHHGLAAQFEAHTVERHYRAICYGVPDS 186

Query: 156 DK 157
           + 
Sbjct: 187 ND 188


>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 = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 31/207 (14%), Positives = 65/207 (31%), Gaps = 40/207 (19%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRK 69
           KV+A+    S  + + +I +  VKV    +        E     V     I+V       
Sbjct: 8   KVLAKQENISNSKAKDLIDKGLVKVGDKKVLIARGDISENTKFIVKEVAPIKV------I 61

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   +    KP  L              D +   F   + + RLD  T G++L   +  
Sbjct: 62  FQDDDILAVDKPAFLTA------------DEVSRKFPNYLLLNRLDKETSGVMLFAKNEE 109

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQDKL------------NLLKKGIVIQGICYGDM 175
                     +    + Y     G+V  + +             + +  + ++       
Sbjct: 110 FQTKAIREFKNNNVYKEYVAVVEGKVIDEIVVDKPILTIKNNKGVARSKVDMKKGKSAKT 169

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
            V     +G+ + + V +  G+  +I+
Sbjct: 170 TVYPMLVEGNKSKIKVVIDTGRTHQIR 196


>gi|302868912|ref|YP_003837549.1| RluA family pseudouridine synthase [Micromonospora aurantiaca ATCC
           27029]
 gi|302571771|gb|ADL47973.1| pseudouridine synthase, RluA family [Micromonospora aurantiaca ATCC
           27029]
          Length = 314

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 58/176 (32%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +     R+ + ++R    SR     +I      V+G +    +  V +   +EV    
Sbjct: 16  VPDGLDGMRLDQAVSRLLGLSRTAAAGLIDAGDALVDG-VARPNSYKVKAGSWLEVTLPA 74

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                        G+ +  A+   + +  KP+G+    S      TV   L  I  R+  
Sbjct: 75  PAAPPAVVPQAVPGLTVVYADDDIVVV-DKPVGVAAHPSPGWTGPTVIGGLAGIGHRIST 133

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                    V RLD+ T G++ +         L+      +  + Y     G  D 
Sbjct: 134 SGAAERQGVVHRLDVGTTGIMAVAKSERAYTALKRAFKYREVEKRYHAVVQGHPDP 189


>gi|260583056|ref|ZP_05850838.1| tRNA pseudouridine synthase C [Haemophilus influenzae NT127]
 gi|260093907|gb|EEW77813.1| tRNA pseudouridine synthase C [Haemophilus influenzae NT127]
          Length = 222

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 57/165 (34%), Gaps = 14/165 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A ++          + Y     G +  +++++   K I +  I     Q   + Q+ 
Sbjct: 67  SEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEA 125

Query: 185 SN-----AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                    V +    G+  ++++  +     +  L    YG   
Sbjct: 126 VTDYEGLKIVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDLH 168


>gi|255004408|ref|ZP_05279209.1| sfhb-like protein [Anaplasma marginale str. Virginia]
          Length = 340

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 78/236 (33%), Gaps = 56/236 (23%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--------------- 58
           QR+ K+I+ A   SR   + +IA  +V ++G ++   +    + D               
Sbjct: 16  QRIDKLISCALEISRNRAQGLIAGGQVTISGRVINNNSYLTKTGDVYTIVTAVQKPSTLS 75

Query: 59  -------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
                   +  +   +   ++      H   G+       +  +     L    + + SV
Sbjct: 76  PNYDIDLKVVYEDHDVIVIDKDPYIAVHPGNGI-------EHHTITNALLARFGAGLQSV 128

Query: 112 G---------RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--------- 151
           G         RLD +T GL++          L  EL +  + + Y     G         
Sbjct: 129 GSSSRPGIVHRLDKDTSGLMVAAKTENAYYRLSEELANQGFKKEYLAVAWGIPCPKRGVI 188

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIK 202
               +V +  + +++      G      +  ++ + G   + +   L  G+  +I+
Sbjct: 189 HTNIRVKRSDITMMEAANS--GGKPAKTEYEVEQELGEVASLIRCTLHTGRTHQIR 242


>gi|322418067|ref|YP_004197290.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320124454|gb|ADW12014.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 300

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 39/225 (17%), Positives = 73/225 (32%), Gaps = 45/225 (20%)

Query: 15  RVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------- 61
           R+    K +      S+ E+ R+I      +N +L+  A+  V   D +           
Sbjct: 15  RLDDAAKALFSQ--LSKGEIRRVIDWGGCNINQVLVRVASRQVKEGDEVALGVMEAERCI 72

Query: 62  --VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGR 113
             V        E       +K  G+ +  +    + TV   +      +        V R
Sbjct: 73  DLVYQKNELLYEDKDFLAVYKAAGVNSQRTPYQLKGTVEYAVECYMKSIGLRDPSRVVHR 132

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ---------DKLNLLK 162
           LD  T G++        A ++   L   +  + Y     G  DQ         D++   +
Sbjct: 133 LDRGTSGVMFFPKHKQAATLISNLLKEGKVQKTYWALVSGSPDQQGWKVDAPLDRVGKFR 192

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
            G+ ++G     +   L   KG      V + E     G+  +I+
Sbjct: 193 YGVSLRGKPARTVFSVLGEGKG------VTVIEAKPLTGRTHQIR 231


>gi|148552990|ref|YP_001260572.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas
           wittichii RW1]
 gi|148498180|gb|ABQ66434.1| ribosomal large subunit pseudouridine synthase D [Sphingomonas
           wittichii RW1]
          Length = 321

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 82/249 (32%), Gaps = 47/249 (18%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHIEV- 62
           +V ++    R+ + +A A    SR  ++ +I+  +V   +G L    A+ V       V 
Sbjct: 11  VVPQDAEGWRLDRALAAALPTLSRERLKALISSGQVSHADGALARDPAMKVAPGARFAVI 70

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                       D   +   E   L +  KP GLV   +  +   T+ + L         
Sbjct: 71  VPDPAPAHNAAQDIPLVVAYEDEHLIVIDKPAGLVVHPAAGNPDGTLVNALLHHCRGSLS 130

Query: 107 ------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV----- 153
                 R   V R+D +T GL++   T+   +    +       R YR    G       
Sbjct: 131 GIGGVERPGIVHRIDKDTSGLMVAAKTDPAHVGLAAQFARHSIDRRYRAIVAGTPRLAAG 190

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      D+ K+ ++  G   +G         ++  + + A V   L  G+  +++
Sbjct: 191 TVDAPLARSTADRKKIAIVADG---RGKRAVTHYSVIEPLRRA-ALVECRLETGRTHQVR 246

Query: 203 KVFEFFNWK 211
                    
Sbjct: 247 VHMASLGHP 255


>gi|118581355|ref|YP_902605.1| RluA family pseudouridine synthase [Pelobacter propionicus DSM
           2379]
 gi|118504065|gb|ABL00548.1| pseudouridine synthase, RluA family [Pelobacter propionicus DSM
           2379]
          Length = 310

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 50/294 (17%), Positives = 96/294 (32%), Gaps = 62/294 (21%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------------GVPLRKAERTRLWL 77
            ++I    VKVN      A   +   D + +               G+ +   E  ++ +
Sbjct: 32  RKLIRSGAVKVNAAPAT-ADSLLTIDDRVTLKESTSLTALISTERPGLDILY-EDDQIAI 89

Query: 78  YHKPIGLVTTHSDPDGRS-----TVFDNLPSIFSRVISVGRLDINTEGLLLL----TNDG 128
            +KP GL    +     +     T F        ++  V RLD  T G ++L    T  G
Sbjct: 90  VNKPSGLAMHRTAEQETNLVEQGTAFMAWRGTPCKLYPVNRLDRGTSGAVILAKSSTAAG 149

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV---IQGICYGDMQVTLDTQKGS 185
              R ++   T   ++Y     G+ D         G++   + G         L  Q   
Sbjct: 150 IFGRQVK--ETGLDKLYLALVAGRPDGA-------GVIDAPLDGKECRT-DYRLLAQGCG 199

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS------YGPFQLGTLLAG----STRE 235
            + + +    G+  +I++  E     +    R S         F L +   G      R 
Sbjct: 200 FSLLELLPFSGRMHQIRRHLEMIGHPILGDQRYSGRVVEELAGFALHSFRTGLTMPDGRR 259

Query: 236 ------VSKKILREQLGPHLLEEAQVNLDA--PIYSSETLVRDRPNIISEVPDD 281
                 ++ ++L       L ++  +  D+  P+     L RD   +   +P+ 
Sbjct: 260 LVVCAPLTDELL------ALCQQGGIESDSLLPLLKRVALSRDEAGVAGNLPEA 307


>gi|291532509|emb|CBL05622.1| pseudouridine synthase, RluA family [Megamonas hypermegale ART12/1]
          Length = 288

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 66/188 (35%), Gaps = 27/188 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVD------GVPLRKA-----ERTRLWLYHKPIGLVTTHSD 90
           VNG  +      V   D IE +         ++       E     +  K  G++T    
Sbjct: 41  VNGQKVRATQAIVKPNDIIEYNLPVTSKVEAIQIPLNIVFEDDYFLIVDKIAGMLTHPLT 100

Query: 91  PDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            +   T+ + +   F++         + RLD NT GL++      L   L     ++ R 
Sbjct: 101 FENTQTLANGVMYHFAKTNQNVGCHPLYRLDRNTSGLVVFAKMPQLQHQLANNHQKFQRY 160

Query: 145 YRVRFHGQVDQDK------LNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLR 194
           Y    HG++ Q +      +   K  I++        +      +  +  + + + + L 
Sbjct: 161 YYALVHGKLSQKQGQINAPIGRKKDSIILHEVNDEGKHAITNYHVIKEFENYSLIELWLE 220

Query: 195 EGKNREIK 202
            G+  +I+
Sbjct: 221 TGRTHQIR 228


>gi|308235716|ref|ZP_07666453.1| pseudouridylate synthase [Gardnerella vaginalis ATCC 14018]
          Length = 50

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           +++F    + V RL+R   GP +LG L AGS R +S+  +R  
Sbjct: 2   RRIFGAVGYPVKRLVRTQIGPIKLGDLKAGSYRVLSQTEVRSL 44


>gi|315504618|ref|YP_004083505.1| pseudouridine synthase, rlua family [Micromonospora sp. L5]
 gi|315411237|gb|ADU09354.1| pseudouridine synthase, RluA family [Micromonospora sp. L5]
          Length = 314

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 58/176 (32%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +     R+ + ++R    SR     +I      V+G +    +  V +   +EV    
Sbjct: 16  VPDGLDGMRLDQAVSRLLGLSRTAAAGLIDAGDALVDG-VARPNSYKVKAGSWLEVTLPA 74

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                        G+ +  A+   + +  KP+G+    S      TV   L  I  R+  
Sbjct: 75  PAAPPAVVPQAVPGLTVVYADDDIVVV-DKPVGVAAHPSPGWTGPTVIGGLAGIGHRIST 133

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                    V RLD+ T G++ +         L+      +  + Y     G  D 
Sbjct: 134 SGAAERQGVVHRLDVGTTGIMAVAKSERAYTALKRAFKYREVEKRYHAVVQGHPDP 189


>gi|157412550|ref|YP_001483416.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9215]
 gi|157387125|gb|ABV49830.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9215]
          Length = 319

 Score = 64.0 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 92/247 (37%), Gaps = 39/247 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I+ E   P R+ + + ++    SR  ++  I    V VN    + A   + + D+I++ 
Sbjct: 18  EIIYELPLPMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAK-AKTPLKNGDNIQIW 76

Query: 64  ---GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLP 102
                PL              E   + + +K  GL+   +      T+ +       +LP
Sbjct: 77  MPPPEPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLP 136

Query: 103 SIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFH-------- 150
            I  ++    V RLD +T G +++         L+    +    R Y    H        
Sbjct: 137 GINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEG 196

Query: 151 ---GQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G + +DKLN LK  +V +    Y      L+ + G+ + ++  L  G+  +I+    
Sbjct: 197 QIVGNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCA 256

Query: 207 FFNWKVN 213
             N  + 
Sbjct: 257 HINHPIV 263


>gi|328907882|gb|EGG27645.1| ribosomal RNA large subunit methyltransferase J
          [Propionibacterium sp. P08]
          Length = 245

 Score = 64.0 bits (155), Expect = 4e-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|320161265|ref|YP_004174489.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
 gi|319995118|dbj|BAJ63889.1| pseudouridine synthase [Anaerolinea thermophila UNI-1]
          Length = 231

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 58/160 (36%), Gaps = 16/160 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + +  KP GL++     +    T+   L     ++  + RLD +T G+++L       + 
Sbjct: 20  ILVISKPAGLLSIRDGYNPNLPTIQGVLEPKLGKLWMIHRLDKDTSGIMVLARTSEAHKN 79

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTLD 180
           L+      +  ++Y     G  + D++              +  +  +     +  V + 
Sbjct: 80  LDRQFAERKVRKIYYAICVGVPEWDEILIQSPLRVNGDRKHRTVVDFEHGKPAETHVRVI 139

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN--RLIRI 218
           ++ G   WV V    G   +I+       + +    L RI
Sbjct: 140 SRYGFYTWVEVHPHSGYTHQIRAHLSSIGYPLLGDSLYRI 179


>gi|330751985|emb|CBL80498.1| protein with similarity to pseudouridine synthase [uncultured
           Polaribacter sp.]
          Length = 105

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 39/85 (45%), Gaps = 2/85 (2%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYS 263
           + E+ +++V +L R      +LG L +G  RE+++  ++E    +++  +    +A +  
Sbjct: 1   MCEYLDYEVTKLKRTRIMNVELGYLQSGDWRELTEDEMKEI--NNMISSSSKTEEASVVE 58

Query: 264 SETLVRDRPNIISEVPDDFTRMKKN 288
            ++         +   +DF +   +
Sbjct: 59  EKSKQAKPKRSKAPTKNDFNKKSAS 83


>gi|324992609|gb|EGC24530.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK405]
 gi|327460012|gb|EGF06351.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1]
 gi|327472158|gb|EGF17595.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK408]
 gi|327488602|gb|EGF20402.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1058]
          Length = 291

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/205 (19%), Positives = 72/205 (35%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+     L           +  K+ +  +   Y +  V
Sbjct: 147 PILNRLL-EKREISREYWALVQGKFPAKNLIYKDKIGRDRHDRRKRLVDPRKGLYAETHV 205

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T   Q G +A V   L+ G+  +I+
Sbjct: 206 TRLKQFGQSALVKCQLKTGRTHQIR 230


>gi|320530955|ref|ZP_08031988.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
 gi|320136820|gb|EFW28769.1| pseudouridine synthase, RluA family [Selenomonas artemidis F0399]
          Length = 297

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 33/196 (16%), Positives = 63/196 (32%), Gaps = 27/196 (13%)

Query: 43  NGILLERAAVNVMSTDH----------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDP 91
           NG+    A   V   D           +  + +PL  A E   L +  KP G++   +  
Sbjct: 43  NGVPAIAARTAVRDGDVLSYALPIVSSVVPEDLPLAIAYEDDDLLIIDKPAGMLVHPTTQ 102

Query: 92  DGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVY 145
           + R T+ + +  +++            RLD NT GLLL+     +            R Y
Sbjct: 103 ETRGTIANAVRGLYASRGDTLDFHPCHRLDRNTTGLLLIAKRPEVQYYFTKHLDAVRRAY 162

Query: 146 RVRFHGQVDQDK------LNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLRE 195
                G++          +      I+++             T +   G  + + + L  
Sbjct: 163 LALIEGRLTPASDIIDAPIARALPSIILRRVAPDGKPARTHYTTERTTGRYSLLRLTLET 222

Query: 196 GKNREIKKVFEFFNWK 211
           G+  +I+         
Sbjct: 223 GRTHQIRVHLAHLGHP 238


>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 = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 33/179 (18%), Positives = 54/179 (30%), Gaps = 30/179 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            V      +R+  V+A      SR  ++ +I    V + G  +      V   D I +  
Sbjct: 19  TVDPEDAGKRIDAVLASHLETLSRNRIQSLIKAGDVSIGGAKIGEPKYRVNEGDEITLHL 78

Query: 64  ---------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                    G  +  +   E   + +  KP GLV      +   T+ + L          
Sbjct: 79  PEPEDPDPKGEDIPLSVVFEDAHVIVIDKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSG 138

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVD 154
                R   V R+D +T GLL++       + L        R       Y     G   
Sbjct: 139 IGGVKRPGIVHRIDKDTSGLLVVAKTDQAHQGLAAQFADHGRTGPLERAYSALVWGAPS 197


>gi|123967748|ref|YP_001008606.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. AS9601]
 gi|123197858|gb|ABM69499.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. AS9601]
          Length = 319

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 92/247 (37%), Gaps = 39/247 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I+ E   P R+ + + ++    SR  ++  I    V VN    + A   + + D+I++ 
Sbjct: 18  EIIYELPLPMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAK-AKTPLKNGDNIQIW 76

Query: 64  ---GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLP 102
                PL              E   + + +K  GL+   +      T+ +       +LP
Sbjct: 77  MPPPEPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLP 136

Query: 103 SIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFH-------- 150
            I  ++    V RLD +T G +++         L+    +    R Y    H        
Sbjct: 137 GINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEG 196

Query: 151 ---GQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G + +DKLN LK  +V +    Y      L+ + G+ + ++  L  G+  +I+    
Sbjct: 197 QIVGNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCA 256

Query: 207 FFNWKVN 213
             N  + 
Sbjct: 257 HINHPIV 263


>gi|254442724|ref|ZP_05056200.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
 gi|198257032|gb|EDY81340.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
          Length = 307

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 49/300 (16%), Positives = 92/300 (30%), Gaps = 59/300 (19%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGV 65
           R+ K+++ A    SR + +R      V ++G  + +    V   + +          D  
Sbjct: 17  RIDKLLSEAFPDHSRSDFQRAFDSDLVTLDGAPIAK-KQKVSEGEIVTFAMPTVQKLDMS 75

Query: 66  PLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
           P+        E   + + +KP GLV          T+   L               R   
Sbjct: 76  PIDMDLEVIFEDEHMVVVNKPAGLVVHPGAGPDEPTLAHGLLHHCQGQLSGIGGVERPGI 135

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVD------------- 154
           V RLD  T GL++      +A         S   ++ Y     G  +             
Sbjct: 136 VHRLDRETSGLIMAA-KTDVAHRALSELFQSRSLVKEYSALCCGIPELMSGTVERPIERH 194

Query: 155 QDKLNLLKKGIVIQGIC--YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             + + ++ G   +G           +         +   +  G+  +I+          
Sbjct: 195 PTQRHKMRVGFEGRGRAREAKTDWTLVKAYDAGYCHLRCRIHTGRTHQIR---------- 244

Query: 213 NRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
             L  I      LG  + G  R +    L +Q    +L    +  D P+  SE ++  +P
Sbjct: 245 VHLKSIR--HIILGDAVYG-YRPLPN--LPKQPERVMLHSCYLKFDHPLTGSELVLEAKP 299


>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 = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 46/272 (16%), Positives = 84/272 (30%), Gaps = 69/272 (25%)

Query: 7   VQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           +      +R+ +V+AR     A   SR  ++R++ + RV V+G ++  AA  V + D   
Sbjct: 35  IAAEDAGERLDRVLARRLALEAPELSRTRIQRLVTEGRVSVSGRVVGDAAGRVNAADVYT 94

Query: 62  V------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
           +            + +PL    E   L +  KP GLV   +      T+ + L       
Sbjct: 95  LFLPPPEAAEPVAENLPLTIVFEDAHLVVIDKPAGLVVHPAPGHASGTLVNALLYHCGDS 154

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQ 152
                   R   V R+D +T GLL++       + L        R       Y     G 
Sbjct: 155 LSGIGGVRRPGIVHRIDKDTSGLLVVAKSDLAHKGLAAQFADHGRTGPLERAYLAFVWGV 214

Query: 153 VD------------QDKLNLLKKGIVIQGICY-------------------GDMQVT--L 179
            +                  +   + + G                         QV   +
Sbjct: 215 PEAHGSVDAPIDRHPSHRQKMA--VRLSGRNAITHWEVQEAFVGHGRTHLRNKGQVKGEV 272

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             ++G  + +   L  G+  +I+         
Sbjct: 273 KMEEGVASLIECRLETGRTHQIRVHMAHVGHP 304


>gi|288553393|ref|YP_003425328.1| hypothetical protein BpOF4_01845 [Bacillus pseudofirmus OF4]
 gi|288544553|gb|ADC48436.1| hypothetical protein BpOF4_01845 [Bacillus pseudofirmus OF4]
          Length = 322

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 47/276 (17%), Positives = 85/276 (30%), Gaps = 58/276 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD------GVPLRKA--------ERTRLWLYHKP 81
              ++ VN   +      + S D +EV          LR          E   L + +KP
Sbjct: 62  KGGKILVNQKEVT-VRTTIFSGDRVEVYVPPEPKNESLRPECIPLDIHYEDDHLLVINKP 120

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ T  S      T+ + +   +          +V RLD +T GLL++   G     L 
Sbjct: 121 QGMPTIPSREHPSRTLANAVMGYYESHHIPFTFHAVNRLDRDTSGLLVVAKHGLAHDQLS 180

Query: 136 LPST--QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV---------------- 177
                 +  R Y     G V        ++G +   I      +                
Sbjct: 181 KGQRAGKLKRYYLALAEGFVQP------REGTIHAPIKRRPSSIIERMVAADGQEAITHY 234

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS 237
            +     + + V + L  G+  +I+  F      +               L  GS   ++
Sbjct: 235 KVINDNQAYSEVEINLETGRTHQIRVHFAHLGHPLLG-----------DDLYGGSIELLA 283

Query: 238 KKILREQLGP--HLLEEAQVNLDAPIYSSETLVRDR 271
           ++ L  Q     H      ++  AP+      V+D+
Sbjct: 284 RQALHCQRVELIHPFTGKHLHFSAPLPKDLIEVKDK 319


>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 = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+I+ AG+ SRRE E+ I + RVK+NG +     + V   D + +D + +   +  R
Sbjct: 4  RINKLISDAGLGSRREAEKYITEGRVKINGRIARLTDL-VCEKDIVLLDDIDIPIKDLIR 62


>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 = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 57/312 (18%), Positives = 96/312 (30%), Gaps = 97/312 (31%)

Query: 1   MKDKNIVQENFTPQRVSKVI--------ARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           MK K I+ EN   QR+ K +        ++          +M+ ++ VKVNG+ ++    
Sbjct: 1   MK-KLIIDENHANQRIDKYLKKLLCQAPSQLIY-------KMLRKKDVKVNGVKVKE-NY 51

Query: 53  NVMSTDHIE----------------VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDG 93
            + + D +E                +  + +      E  ++ +  KP GL+      + 
Sbjct: 52  ILQNHDVVELFLYEDKFQEYTRAQTIFDLKIEFQVIYEDDKILVVGKPAGLLVHEDINED 111

Query: 94  RST----VFDNLPSIFSRVI---------SVGRLDINTEGLLLLTNDGGLARVL------ 134
            +T    V   L                  V RLD NT G+++    G   R L      
Sbjct: 112 MNTLSNQVITYLYQKGEYDPQISLGFTPGPVHRLDRNTSGIVIF---GKTMRALQDLNEM 168

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---VTLDTQKGSN----- 186
                   + Y     G +    L          G    D     V + TQ         
Sbjct: 169 MKKRHCIEKTYLTICKGHMSSADLV---------GYMKKDGDQSLVKVVTQNTPGALMMH 219

Query: 187 ------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                       + + V L  G+  +I+         +       YG F+L        R
Sbjct: 220 TLVENIEYHQGFSLLKVQLVTGRTHQIRVHLASVGHPIIG--DSKYGDFELN-------R 270

Query: 235 EVSKKI-LREQL 245
           E+ KK  L+ Q 
Sbjct: 271 EMKKKYHLQHQF 282


>gi|294674881|ref|YP_003575497.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella ruminicola 23]
 gi|294472042|gb|ADE81431.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Prevotella ruminicola 23]
          Length = 347

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 42/244 (17%), Positives = 78/244 (31%), Gaps = 50/244 (20%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ K +      +SR  +++      + VN   ++     V   D I +         
Sbjct: 31  PIRIDKYLVEHQPHSSRNRIQQAADAGFIHVNEKPVKS-NYKVRPGDIITLMLDRPHYDT 89

Query: 63  ----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
               + +PL    E   L + +KP G+V      +   T+ + +      + S       
Sbjct: 90  TIEPEDIPLEVVYEDADLMVINKPAGMVVHPGCGNFNGTLVNAIAWHLKDLASYDPNDPE 149

Query: 111 ---VGRLDINTEGLLLL--TNDGGLA------RVLELPSTQWLRVYRVR---------FH 150
              V R+D +T GLL++  T D   +            S        V            
Sbjct: 150 VGLVHRIDKDTSGLLVVAKTPDAKTSLGKQFFNKTTHRSYNA----LVWGNFVEDEGRIE 205

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           G + +D  + L+  +       G   VT   +  + G    V   L  G+  +I+   + 
Sbjct: 206 GNIGRDPKDRLRMEVFPPDSEIGKPAVTHYKVMERYGYVTLVECILETGRTHQIRAHMKH 265

Query: 208 FNWK 211
               
Sbjct: 266 IGHP 269


>gi|254526037|ref|ZP_05138089.1| pseudouridylate synthase, 23S rRNA-specific [Prochlorococcus
           marinus str. MIT 9202]
 gi|221537461|gb|EEE39914.1| pseudouridylate synthase, 23S rRNA-specific [Prochlorococcus
           marinus str. MIT 9202]
          Length = 319

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 92/247 (37%), Gaps = 39/247 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I+ E   P R+ + + ++    SR  ++  I    V VN    + A   + + D+I++ 
Sbjct: 18  EIIYELPLPMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAK-AKTPLKNGDNIQIW 76

Query: 64  ---GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLP 102
                PL              E   + + +K  GL+   +      T+ +       +LP
Sbjct: 77  MPPPEPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLP 136

Query: 103 SIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFH-------- 150
            I  ++    V RLD +T G +++         L+    +    R Y    H        
Sbjct: 137 GINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEG 196

Query: 151 ---GQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G + +DKLN LK  +V +    Y      L+ + G+ + ++  L  G+  +I+    
Sbjct: 197 QIVGNIGRDKLNRLKYKVVEETSGRYACTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCA 256

Query: 207 FFNWKVN 213
             N  + 
Sbjct: 257 HINHPIV 263


>gi|238792761|ref|ZP_04636392.1| tRNA pseudouridine synthase C [Yersinia intermedia ATCC 29909]
 gi|238727869|gb|EEQ19392.1| tRNA pseudouridine synthase C [Yersinia intermedia ATCC 29909]
          Length = 257

 Score = 64.0 bits (155), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 33/170 (19%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L       Q  + Y     G V +         ++L+ +      Q        
Sbjct: 67  SDVARALSAQFEQHQIQKTYHAVVRGYVLEGGTVDYAMSEELDKIADKHSKQDKAPQPSV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  QV +    G        L E     G+  ++++        + 
Sbjct: 127 THYQPLAQVEVPIAIGRYDTARFSLLELKPETGRKHQLRRHMAHIRHPII 176


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 57/322 (17%), Positives = 101/322 (31%), Gaps = 56/322 (17%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           +    R+ + +A    ASR + +  IA   V+V+G+ + +    +       V       
Sbjct: 9   SAEGVRLDQAVAERTGASRAKAQAWIAAGYVRVDGVPVTKPGKRLKGETVEVVAPPDPPP 68

Query: 63  -------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------- 106
                  D   L + E   +   +KP G+ T  +      T+ + L   ++         
Sbjct: 69  RVAPEQRDLEILYEDEDMVVV--NKPPGMATHPAPGLTSGTLVNALMGRYAQAAVEGEPP 126

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKL--- 158
              R   V RLD +T G++++       R L          + Y     GQ  +  L   
Sbjct: 127 EQVRPGIVHRLDRDTSGVIVVGRHDAAVRRLADAFKNRFVFKRYVAITVGQPPEMTLVAP 186

Query: 159 ------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                    K  +      Y +   +L      +A V      G+  +I+      + K 
Sbjct: 187 IGRHPVERHKMHVSGVNARYAETDFSLLATVDGHALVDARPHTGRTHQIR-----VHLK- 240

Query: 213 NRLIRISYGPFQLGTLLAGS-TREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLVR 269
                  Y P  LG  L G  +  +S++ L   E   PH      +   AP+        
Sbjct: 241 -----HLYAPI-LGDELYGKPSPYISRQALHAYELRIPHPRSGRIMTFVAPVPRDMVAAW 294

Query: 270 DRPNIISEVPDDFTRMKKNSSQ 291
           +   +    PD   R       
Sbjct: 295 EA--LGGRWPDGLERADVAPPA 314


>gi|332828459|gb|EGK01164.1| hypothetical protein HMPREF9455_00204 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 316

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 28/152 (18%), Positives = 61/152 (40%), Gaps = 21/152 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-----------RL 75
           SR  ++ ++A +++KVNG L+ +    + + D + V      + E+             +
Sbjct: 34  SRNAIKSLLAHKQIKVNGKLVTQFDHELKAGDKVSVMKFDQSRKEKKLKGLKIVFEDDEI 93

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTND 127
            +  K  G ++  +D +   TV+  L             RV  + RLD    GL++   +
Sbjct: 94  IVIDKEAGFLSVSTDKEKLRTVYGALNEYVKKKSRNKTDRVFVLHRLDREASGLMVFARN 153

Query: 128 GGLARVLELPSTQWLRVYR--VRFHGQVDQDK 157
             L  + +      ++ Y       G+ +Q++
Sbjct: 154 AELQEIFQKNWNNLVKEYIYTAVVDGRPEQEE 185


>gi|332702347|ref|ZP_08422435.1| pseudouridine synthase, RluA family [Desulfovibrio africanus str.
           Walvis Bay]
 gi|332552496|gb|EGJ49540.1| pseudouridine synthase, RluA family [Desulfovibrio africanus str.
           Walvis Bay]
          Length = 297

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/216 (18%), Positives = 68/216 (31%), Gaps = 35/216 (16%)

Query: 33  RMIAQQRVKVNGILLE-----RAA--VNVMS-TDHIEVDGVPLRKA------ERTRLWLY 78
           + +   +++V+G   +      A   V V      +E +G PLR        E   L + 
Sbjct: 37  KWLRTGQLRVDGRRAKPFDRLEAGQTVRVPPYEAVVEPEGQPLRARPLTIIHEDDELLVI 96

Query: 79  HKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL- 134
            KP GL +   +      ++ +               RLD++T GLL+        R L 
Sbjct: 97  AKPAGLASQPGSGLTDSVQTRLKALYAGADFMPSCAHRLDMDTSGLLVAGKTYQSVRRLG 156

Query: 135 -ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG----------------ICYGDMQV 177
               S    + Y     GQ  +    LL+  I+  G                      +V
Sbjct: 157 DLFASGGVDKTYLAWVQGQWPEQGQILLRDHIIKDGRAHVRIGADNAPDGEQGKLALARV 216

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               ++     + V L  G+  +I+         V 
Sbjct: 217 RPMARRPDATLLAVELLTGRTHQIRIQLASRGHPVL 252


>gi|172060753|ref|YP_001808405.1| RluA family pseudouridine synthase [Burkholderia ambifaria MC40-6]
 gi|171993270|gb|ACB64189.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MC40-6]
          Length = 407

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 83/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV ++G   +     V     IE+      
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAK-IRQPVPLGARIELVPDLLP 123

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP G+V   +  +   T+ + L   +        R
Sbjct: 124 EQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 183

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 184 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGTIDAPIGR 243

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 244 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGH 303

Query: 211 K 211
            
Sbjct: 304 P 304


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/225 (12%), Positives = 78/225 (34%), Gaps = 32/225 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVP 66
           +++     SR  V+ ++ + +V V+G ++++    ++    + +             G+ 
Sbjct: 30  LLSIMSHTSRNSVKSILTRGQVTVDGKVIKKHNHPLLPNQVVAIQSNKAAIKETALVGMT 89

Query: 67  LRKAERTRLWLYHKPIGLVTTHS----DPDGRSTVFDNLP--SIFSRVISVGRLDINTEG 120
           +   +   + +  K  GL++  +    +      + + +   +  +R+  V RLD +T G
Sbjct: 90  ILYEDDA-IIVIDKEAGLLSIAAKFAQELTAHRQLINYVKQENHNNRIYVVHRLDRDTSG 148

Query: 121 LLLLTNDGGLARVLELPSTQWLRV--YRVRFHGQVDQDKL---------NLLK--KGIVI 167
           +++      + + ++      ++   Y V   G V +D+            +K       
Sbjct: 149 VMVFAKTEQVKQEMQENWKDIVKERIYSVLVEGIVSEDEGSIKTWLTESKAMKVHSATYD 208

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            G                   +   L  G+  +I+   E     V
Sbjct: 209 NGGKLAITHYKKIRNNDEFTLLEARLETGRKNQIRVHMETLGHPV 253


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 46/256 (17%), Positives = 87/256 (33%), Gaps = 48/256 (18%)

Query: 1   MKDKNIVQENFTP----QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           + D   ++ + TP     R+ KV+AR     SR  +++ I    V V+G +     + V 
Sbjct: 32  LPDMPPIELDLTPGDCGDRLDKVVARLVPQFSRSRMQQWIDDGFVTVDGKVGRT-RMTVY 90

Query: 56  STDHIEVDGVPLRK--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             +HI V      +               E   + + +KP GLV      +   T+ + L
Sbjct: 91  GDEHIVVLPQAAPEDTAFAPEEMALNIVYEDEAIIVVNKPAGLVVHPGSGNWSGTLLNGL 150

Query: 102 PSIF------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH--- 150
              +       R   V RLD +T GL+++     +   L  +L +    R Y        
Sbjct: 151 LHYWPALIGVPRAGIVHRLDKDTSGLMVVAKTLEVHTDLVRQLAARTVKREYFALVWGTP 210

Query: 151 ---GQVDQDKLNLLKKGI---VIQGICYGDMQVTLDTQKG------SNAWVTVGLREGKN 198
              G +D       +  I   V++ +         +  +         + +   L  G+ 
Sbjct: 211 NLSGTIDASMGRHPRDRIRMAVLESMSAKPAITHFERIESGLLDRRPVSLMRCRLETGRT 270

Query: 199 REIK-KV----FEFFN 209
            +I+  +    F    
Sbjct: 271 HQIRVHMQSIGFALVG 286


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 77/234 (32%), Gaps = 30/234 (12%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-G 64
           V +    +R+ +++A R    SRR    ++    V V+   ++ A+  +     +EV  G
Sbjct: 12  VADEDVGKRLDQLLAARVPELSRRMARTLLDIGGVFVDRTRVKVASRKLRPGQSVEVHLG 71

Query: 65  VPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             L +A +                         L +  KP GL++  +       +   L
Sbjct: 72  GALERATKEVGKEARKRDSRALPRFKIVFEDRDLVVVDKPAGLLSAPTPESDLGNLAALL 131

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN 159
                RV  V R+D+ T GLL+        + L       Q  R Y     G   +D   
Sbjct: 132 RERRERVYVVHRIDLQTSGLLVFAKTRRANQHLSERFREHQIERAYTAVVAGAPVED--- 188

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                + ++G         L       A +   L  G+  +I+       + V 
Sbjct: 189 TFTIDLPLRGRRATTHLQVLQRIGERAAVLDARLETGRTHQIRLHCLQRGYPVL 242


>gi|227824343|ref|ZP_03989175.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904842|gb|EEH90760.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 311

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 77/240 (32%), Gaps = 38/240 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
            E     R    +A     SR  ++  + +  V   G  ++ A+  V   D   V     
Sbjct: 14  AEKDQGLRADCYLADVLDLSRSSLQHDMEKGLVTKEGKPVK-ASYKVKLGDVFTVVIPPA 72

Query: 63  -----DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
                +  P+  A   E   + + +KP G+V   +  +   T+ + L      +      
Sbjct: 73  VSLEAEPEPIPLAILYEDEDVIVVNKPRGMVVHPAAGNYTGTLVNALLYHCKDLSGINGV 132

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQ----------- 152
                V RLD +T G+++   +      L          R Y     G            
Sbjct: 133 VRPGIVHRLDKDTSGVMVCAKNDRAHLSLSQQIKDKEAKRTYIAVVRGNIKDDRGHIETL 192

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
           +D+D  + ++  +V  G         +  + G    V   L+ G+  +I+  +  +    
Sbjct: 193 IDRDPKDRMRMAVVPSGGRLAVTDYEVLERYGRFTVVRCRLQTGRTHQIRVHMT-YLGHP 251


>gi|317180509|dbj|BAJ58295.1| hypothetical protein HPF32_0713 [Helicobacter pylori F32]
          Length = 327

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 52/313 (16%), Positives = 105/313 (33%), Gaps = 63/313 (20%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL---------- 158
            RLD +T G +++  +     V      +     R Y       + ++K+          
Sbjct: 133 HRLDKDTSGGIVIAKN-NFTHVYLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNP 191

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFF 208
            N LK  I ++       + +  ++    + +T       +   L  G+  +I+      
Sbjct: 192 NNRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL 244

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
                 L R   G   L  L       + K+ +R  L  +L+E      +  +     L+
Sbjct: 245 ----EYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLCFKVPLL 295

Query: 269 RDRPNIISEVPDD 281
           +D    + +V D 
Sbjct: 296 KDMLEYLKKVFDK 308


>gi|308182904|ref|YP_003927031.1| hypothetical protein HPPC_03775 [Helicobacter pylori PeCan4]
 gi|308065089|gb|ADO06981.1| hypothetical protein HPPC_03775 [Helicobacter pylori PeCan4]
          Length = 327

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 106/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLHLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR------- 241

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
             +  L R   G   L  L       + K+ +R  L  +L+E      +  +     L++
Sbjct: 242 VHLEYLNRHIIGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLCFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D      +V D 
Sbjct: 297 DMLEYFKKVFDK 308


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 77/249 (30%), 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  -------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L +  KP GLV      +   T+ + +      +
Sbjct: 89  MLDRPKHDNTIEAEDIPLDVVYEDDSLMVVMKPAGLVVHPGAGNFHGTLINAIAWHLRGL 148

Query: 109 IS----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF------- 149
            S          V R+D +T GLLL+         L          R Y           
Sbjct: 149 ASFDANDPEVGLVHRIDKDTSGLLLIAKTPEAKSSLGKQFFYKTTHRSYIALVWGNIVDE 208

Query: 150 ----HGQVDQDKLNLLKKGI---VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                G + +D  + L+  +                +  + G    +   L  G+  +I+
Sbjct: 209 QGRIEGNISRDPKDRLRMTVFPPESDIGKPAVTHYKVIERFGYTTLIECVLETGRTHQIR 268

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 269 AHMKHIGHP 277


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 81/240 (33%), Gaps = 42/240 (17%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ + +  R   +SR  +++      V VN   ++     V   D I +         
Sbjct: 32  PVRIDRFMTERLQHSSRNRIQKAADAGFVHVNERPVKS-NYKVRPGDVITLMLDRPHHDT 90

Query: 63  ----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------- 110
               + +PL    E   L + +KP G+V      +   T+ + +      + S       
Sbjct: 91  TIEAEDIPLDVVYEDDALMVINKPAGMVVHPGAGNFHGTLINAVAWHLRNMPSFDANDPE 150

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF-----------HGQVD 154
              V R+D +T GLL++       R L L   +    R Y                G + 
Sbjct: 151 VGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTTHRSYNALVWANFAEDEGRIEGNIG 210

Query: 155 QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +D  + L+  +       G   VT   +  + G   +V   L  G+  +I+   +     
Sbjct: 211 RDPRDRLRMAVFPPDSETGKPAVTHYRVLERFGYVTFVECILETGRTHQIRAHMKHIGHP 270


>gi|171320446|ref|ZP_02909479.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
 gi|171094306|gb|EDT39380.1| pseudouridine synthase, RluA family [Burkholderia ambifaria MEX-5]
          Length = 369

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 83/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV ++G   +     V     IE+      
Sbjct: 23  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAK-IRQPVPLGARIELVPDLLP 81

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP G+V   +  +   T+ + L   +        R
Sbjct: 82  EQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 141

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 142 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGTIDAPIGR 201

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 202 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGH 261

Query: 211 K 211
            
Sbjct: 262 P 262


>gi|87121619|ref|ZP_01077507.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
 gi|86163151|gb|EAQ64428.1| RNA pseudouridine synthase family protein [Marinomonas sp. MED121]
          Length = 289

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 80/210 (38%), Gaps = 25/210 (11%)

Query: 30  EVERMIAQQRVKVN-GILLERA-----AVNVMSTDHIEVDGVPLRK--------AERTRL 75
           E++  IA+  + +  G  ++R      A+ V    H   +   L +        A+    
Sbjct: 31  EIKNAIAKGALWIGRGKKVQRLRRVKKALKVGEELHFYYNPKVLDQIVPEAKLVADLVSY 90

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGGLAR 132
            +++KP G+++  S     +T+     +       V  V RLD    GL+++ +    AR
Sbjct: 91  SVWYKPYGMLSQGSKWSDHTTISRWAQTHLTPERPVFIVHRLDRAATGLIIIAHTKAAAR 150

Query: 133 VLELPSTQW--LRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AW 188
            L     Q    + Y++  HG   + D+  ++ +   I G         L+    SN + 
Sbjct: 151 ALSGMFEQHALEKHYQIIVHGNHSEHDQPEVITQ--EIDGKSAQSTFNCLEHAPSSNLSL 208

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN--RLI 216
           + V +  G+  +I+         V   RL 
Sbjct: 209 IDVKIDSGRKHQIRLHAAGIGLPVVADRLH 238


>gi|115351782|ref|YP_773621.1| RluA family pseudouridine synthase [Burkholderia ambifaria AMMD]
 gi|115281770|gb|ABI87287.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           ambifaria AMMD]
          Length = 405

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 83/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV ++G   +     V     IE+      
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAK-IRQPVPLGARIELVPDLLP 123

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP G+V   +  +   T+ + L   +        R
Sbjct: 124 EQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 183

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 184 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGTIDAPIGR 243

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 244 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGH 303

Query: 211 K 211
            
Sbjct: 304 P 304


>gi|315924025|ref|ZP_07920252.1| RluA protein [Pseudoramibacter alactolyticus ATCC 23263]
 gi|315622651|gb|EFV02605.1| RluA protein [Pseudoramibacter alactolyticus ATCC 23263]
          Length = 314

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 84/264 (31%), Gaps = 71/264 (26%)

Query: 6   IVQENFTPQRVSKVI------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            + +N   QR+ + +      A  G        +M+ ++R+K++G         +     
Sbjct: 5   TISDNAAEQRMDRFLIKWLPQASKGFL-----MKMLRKKRIKLDGHRA-SPRDYLQKGQV 58

Query: 60  IEVD----------GVPLRKAERT-----------------RLWLYHKPIGLVTTHSDPD 92
           +             G P    E +                  L   +KP+GL+T   D  
Sbjct: 59  LTFYFSEETYRQFRGQPAAPGEPSLPDSLKALMQPPLYEDDHLIAVNKPVGLLTQP-DHT 117

Query: 93  GRSTVFDN---LPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR 146
           G  ++ D    LP   +       RLD NT G++L+  D    + +   + S    + Y 
Sbjct: 118 GTPSLADLAGTLPHSGTFHPAPANRLDRNTSGIVLIPKDYPTQKQIAAAIRSHLIRKSYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---NAWVT------------- 190
               G++         +G  +      + +  +  ++      AW+              
Sbjct: 178 AIVAGKIT--------RGAKLHSRLTKNPRANIVQEETDGQREAWLRYQPLCSGDAASLI 229

Query: 191 -VGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +I+         + 
Sbjct: 230 AIELGSGRSHQIRVQLAGIGHPII 253


>gi|322411665|gb|EFY02573.1| Ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus dysgalactiae subsp. dysgalactiae
           ATCC 27957]
          Length = 300

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 70/211 (33%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRK-----------AERTRLWLYHKP 81
               + VNG + + A   +   D + +D     P  K            E     + +KP
Sbjct: 33  KGGNILVNG-IEQNAIYLLDIGDVVTIDIPKEEPFEKLEAIPFDLDIVYEDDHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +G  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  VGFASIPS-AIHSNTIANFIKAYYVEKSYPNQQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     GQ    D+  +           + + +   G         + 
Sbjct: 151 DKQLQTRAIEKRYFALVSGQGALPDEGDIVAPIGRSKDSIITRAVDSMGKYAKTSYKVVA 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RYPENVHLVDIKLHTGRTHQIRVHFAHLGFP 241


>gi|268590539|ref|ZP_06124760.1| tRNA pseudouridine synthase [Providencia rettgeri DSM 1131]
 gi|291313926|gb|EFE54379.1| tRNA pseudouridine synthase [Providencia rettgeri DSM 1131]
          Length = 252

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 63/172 (36%), Gaps = 31/172 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
               +   +KP G++   S  D + TVF        I   V  + RLD  T G+LL    
Sbjct: 7   HDEYMVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQYVYPIHRLDRPTSGILLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK------LNLL---------KKGIVIQGI 170
             +AR+L     + Q  +VY     G + +++      L  L         ++ ++ + +
Sbjct: 67  SDVARLLSAQFENHQLEKVYHAVVRGYLTEEQTIDYPLLEELDKIADKHASREPVLQECV 126

Query: 171 CY----GDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
            +      ++  +   +   +  ++   E     G+  ++++        + 
Sbjct: 127 THCKPIATVECAIAIGRYETSRFSLV--ELKPETGRKHQLRRHMSHLRHPII 176


>gi|325688842|gb|EGD30850.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK115]
          Length = 291

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 42/204 (20%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  Q   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVEPQKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RIKQFGQAALVKCQLKTGRTHQIR 230


>gi|308177850|ref|YP_003917256.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307745313|emb|CBT76285.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 314

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 78/246 (31%), Gaps = 41/246 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL-ERAAVNV---------M 55
           +V  +    R+   IAR     R     +    +V+VNG  + +   + V          
Sbjct: 12  LVDPDDAGARLDAYIARVLQIPRTLASSLCKDSQVQVNGRTISKSLRIKVGDQLVVTIPP 71

Query: 56  STDHIEVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------- 104
             D +E+    + +    A+     +  KP+G+    S      TV   L +        
Sbjct: 72  QADPLEIKVEKVEELKIIADDDDYVVIDKPVGVAAHPSPGWVGPTVVGALMAEGYNITTS 131

Query: 105 --FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVD--QDKL 158
               R   V RLD+ T GL+++         L+    +    ++Y     G  D  Q  +
Sbjct: 132 GAAERQGIVHRLDVGTSGLMVVAKTERAYTELKRAFKERTPKKIYHAVVQGLPDPLQGTI 191

Query: 159 N-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +                 V+ G         +    G  + V V L  G+  +I+  F  
Sbjct: 192 DAPIGRHPGHDWKFA---VLDGGRDSVTHYKVIEAFGRASLVEVHLETGRTHQIRVHFSA 248

Query: 208 FNWKVN 213
           F     
Sbjct: 249 FGHPCV 254


>gi|218192587|gb|EEC75014.1| hypothetical protein OsI_11092 [Oryza sativa Indica Group]
          Length = 461

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 68/236 (28%), Gaps = 59/236 (25%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           I   ++ V G +     + +     +    +P ++           E   +   +KP GL
Sbjct: 76  IRDGQITVCGEVATDPDIILREGSKLVYHRLPWQEPCAPHLLDVLYEDDDMIALNKPSGL 135

Query: 85  VTTHSDPDGRSTVFDNL---------------PSIFSRVISVGRLDINTEGLLLL----- 124
                    + TV   L                   S  + V RL   T GLLL      
Sbjct: 136 QVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPVPVHRLGRGTSGLLLCAKTKL 195

Query: 125 -------------TNDGGLARVLELPS-TQWLRVYRVRFHGQVDQDKLNL---------- 160
                        TN G      ++    +  + YR    G ++ D++ +          
Sbjct: 196 AKAQLAAYFAEGATNAGKSRDETDICKARKISKFYRALVTGILENDEVMITQPIGLVRYP 255

Query: 161 -LKKGIVIQ---GICYGDMQVTLDTQKGSNAWV-TVGLREGKNREIKKVFEFFNWK 211
            + +G+      G         L+  K  N  +  V +  G+  +I+    +    
Sbjct: 256 GVAEGLYAACSSGKPAMSKVRVLERLKIHNHTLIQVEIHSGRPHQIRIHLAYIGHP 311


>gi|209542655|ref|YP_002274884.1| RluA family pseudouridine synthase [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|209530332|gb|ACI50269.1| pseudouridine synthase, RluA family [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 322

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 76/237 (32%), Gaps = 42/237 (17%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +     QR  + +A   G  SR  V+ ++    V  +G +L   A  V +    E+  
Sbjct: 11  TPETEHAGQRTDRFLADMVGTLSRSRVKALMEGGHVLRDGHVLREPADPVRAGLCYEIRM 70

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
            P   A             E + L +  KP GLV   +  +   T+ + L +        
Sbjct: 71  PPAIPATPRAQAIPFAILYEDSDLIVLDKPAGLVVHPAPGNEDGTLVNALLAHCGDSLTG 130

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD--- 156
                R   V RLD +T G++++         L     +    R Y     G +      
Sbjct: 131 IGGERRPGIVHRLDKDTSGVMVVAKTEQAHTALSDAFAARDIDRTYLALAWGILSPASGT 190

Query: 157 ----------KLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                         +   +V  G  +      TL +  G  + V   L  G+  +I+
Sbjct: 191 FEGAIGRDRRDRKRMA--VVTHGGKHAMTHYRTLHSFHGGISSVECRLATGRTHQIR 245


>gi|171779340|ref|ZP_02920304.1| hypothetical protein STRINF_01185 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281957|gb|EDT47388.1| hypothetical protein STRINF_01185 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 296

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 75/211 (35%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGV------PLRK-----AERTRLWLYHKP 81
               + VNG + + A   +   D + +   D        P++       E     +++KP
Sbjct: 33  KGGNIWVNG-VEQNAIYLLDVGDVVTIEIPDEQEHETLIPVKHDLDIAYEDDHFLIFNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  HGYASIPS-VLHSNTIANFVKYYYMEQNYPNKQVHIVTRLDKDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L S    + Y     G             + +D+ +++ + +   G  Y      + 
Sbjct: 151 DKQLQSKTIEKRYYALVSGQGELEDEGEIIAPIARDEDSIITRRVHPSG-KYAHTSYRVV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + G  A V + L  G+  +I+  F    + 
Sbjct: 210 ERFGDVALVDIRLHTGRTHQIRVHFAHIGFP 240


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 65/322 (20%), Positives = 108/322 (33%), Gaps = 66/322 (20%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR----- 68
           R  + +A R    SR  +++++A  RV V G ++   A  V + D   V           
Sbjct: 43  RADRFLAARLPDLSRTRLQKLVADGRVSVGGRVVGDPAERVNAGDEWTVRVPAPEPAAPV 102

Query: 69  --------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
                     E   L +  KP GLV   +  +   T+ + L +             R   
Sbjct: 103 PEKMDLSIAYEDDFLIVVDKPAGLVVHPAPGNWSGTLVNGLLAHCGASLSGIGGVKRPGI 162

Query: 111 VGRLDINTEGLLLL--TN---DGGLARVLELPSTQ-WLRVYRVRFHGQVDQD-------- 156
           V RLD +T GLL++  T+    G  A+  +   T    R Y     G  DQ         
Sbjct: 163 VHRLDKDTSGLLVVAKTDAAHAGLAAQFADHGRTGPLERAYYAFVWGVPDQRGTVDAPID 222

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----AWVTVGLREGKNREIKKVFEF 207
                   +   +   G         L+   G++     + +   L  G+  +I+     
Sbjct: 223 RHPTHRQKMA--VRQSGREAITHWERLEVFAGADGAPLASLIECQLETGRTHQIRVHLAH 280

Query: 208 FNWKVNRLIRISYG-PFQLGT--LLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
               +  L    YG  F+     L  G+      + L   LG   L  A++    P+   
Sbjct: 281 VGHPL--LGDEVYGQGFRTKASRLPEGA------RALLAALGRQALHAARLGFAHPVTDE 332

Query: 265 ETLVRDRPNIISEVPDDFTRMK 286
           E L        S +P+D  R++
Sbjct: 333 ELL------FESPLPEDLARLR 348


>gi|116624899|ref|YP_827055.1| RluA family pseudouridine synthase [Candidatus Solibacter usitatus
           Ellin6076]
 gi|116228061|gb|ABJ86770.1| pseudouridine synthase, RluA family [Candidatus Solibacter usitatus
           Ellin6076]
          Length = 304

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 58/199 (29%), Gaps = 25/199 (12%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGLVT 86
              V +NG +    + +V S   +  +  P  +           E   L   +KP GL T
Sbjct: 43  NGEVTLNG-VAATGSESVRSGQILIWNRPPWIEPDVPKHFEVLFEDPHLLAVNKPSGLPT 101

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST--QWLRV 144
                   +T+   +         V RL   T G++L       A  L       +  ++
Sbjct: 102 LPGGGFLENTLLRLVQKHTPNANPVHRLGRATSGIVLFARTPQAASNLFANWNTPKIRKI 161

Query: 145 YRVRFHGQVDQDKLNLL---------KKG-IVIQGICYGDMQ--VTLDTQKGSNAWVTVG 192
           YR         D   +L         + G +          +    + ++  S     V 
Sbjct: 162 YRALAQNIAQHDAYEILTPIGLVPHPRIGSVWAANPSGKPSKSLAKVISRSTSTTTFEVS 221

Query: 193 LREGKNREIKKVFEFFNWK 211
           L  G+  +I+         
Sbjct: 222 LNSGRPHQIRIHLASIGHP 240


>gi|209694302|ref|YP_002262230.1| tRNA pseudouridine synthase C [Aliivibrio salmonicida LFI1238]
 gi|208008253|emb|CAQ78398.1| tRNA pseudouridine synthase C [Aliivibrio salmonicida LFI1238]
          Length = 263

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 53/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V  + RLD  T G+L       +A
Sbjct: 34  LIAINKPAGMLVHRSWLDKHETVFAMQTLRDQIGQHVFPLHRLDRPTSGILFFALSSAVA 93

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
                   S +  + Y     G +++         ++L+ +      + +   +      
Sbjct: 94  AQFSPLFASREIKKTYHAIVRGWIEEGDILDYPLKEQLDKIADKKASKDVEAKEAITEYK 153

Query: 176 -----QVTLDTQKGSNAWV---TVGLREGKNREIKKVFEFFNWKVN 213
                ++   T K   +      +    G+  ++++        + 
Sbjct: 154 PLANVELPYSTGKFPTSRYCLMELKPHTGRKHQLRRHMAHLRHPIV 199


>gi|212636284|ref|YP_002312809.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212557768|gb|ACJ30222.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 278

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 32/204 (15%), Positives = 56/204 (27%), Gaps = 41/204 (20%)

Query: 41  KVNGILLER--AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
            V+            V     I          E   +   HKP GL+   S    R   F
Sbjct: 8   TVDSETAAEQLLTEEVAPHIEILF--------EDDDVVAIHKPAGLLVHRSYLARRERFF 59

Query: 99  DN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
                   +   V  V RLD  T G+LL      +A  L     +    + Y     G +
Sbjct: 60  AMQLTRDKVGCHVFPVHRLDRPTSGILLFAKSSEMANALCEQFAAHSIDKEYLAIVRGNM 119

Query: 154 DQDK-LN-LLKKGIVIQGICYGDMQVTLDTQKGSNAW----------------------V 189
            +   L+  LK+   +  +   D+      Q    ++                      V
Sbjct: 120 HEAATLDYALKE--ELDDVADKDVDPNKAAQDAITSYKPLLNSEIPYASGRYATSRYALV 177

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            +    G+  ++++        + 
Sbjct: 178 HLSPHTGRKHQLRRHMAHLRHPIL 201


>gi|116749359|ref|YP_846046.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116698423|gb|ABK17611.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
          Length = 304

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 77/236 (32%), Gaps = 45/236 (19%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------EV 62
           ++++IAR  + S    E +I    V ++G +    A  +   + I             E+
Sbjct: 25  LARLIARYLLISEDRAEDLIDFGSVYIDGRVERNPARTLRGGEEIVVNWPRHGTQRHYEI 84

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRL 114
           D   +   +   L  Y K  G+ +  +  D  + ++  L              V    RL
Sbjct: 85  DPARILYRD-AHLLAYDKEAGVPSQQTPADAYNNLYAALIRFLAGEARASAPYVALHHRL 143

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D  T G+++   D  + R L       + ++ Y     G        +L +   ++ IC 
Sbjct: 144 DRETSGVMVFALDRAVNRRLGESFQEKRVVKDYLAWVDGVP------VLDRWTAVEDICR 197

Query: 173 GDMQVT---LDTQKGSNAWVTVGLR------------EGKNREIKKVFEFFNWKVN 213
            D +         K +   + V LR             G+  +I+         V 
Sbjct: 198 KDGRYRTCPQGRGKAARTLLRVLLRAGDRALIAARPVTGRTHQIRLHLAACGHPVI 253


>gi|168205450|ref|ZP_02631455.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
 gi|170662972|gb|EDT15655.1| pseudouridine synthase, RluA family [Clostridium perfringens E str.
           JGS1987]
          Length = 324

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 87/264 (32%), Gaps = 62/264 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + +  ++VNG   +    +++
Sbjct: 2   KIEIGTNEAGQRLDKFL-------RKYLKDVPLSAIFKALRKGDIRVNGKKQKE-KYSLL 53

Query: 56  STDHIEV--------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
             D IE+                     G      E   + L  K  G++      +G +
Sbjct: 54  EGDVIEIRYLQSVVTKEKKKPNFQMVDSGSLQVVYEDENMLLVEKWPGVLVHSDKKNGAA 113

Query: 96  TVFDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           T+ D + S   R               S  RLD NT G++    +    ++L   +   +
Sbjct: 114 TLTDYVLSYLFRKGDYVPENELTFTPASCNRLDRNTSGIVFFGKNFEGLKLLNEMIRERK 173

Query: 141 WLRVYRVRFHGQVDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ----KGSNAWV 189
             + Y     G++   K          L K  V         ++ +D +     G+ + +
Sbjct: 174 VKKYYCALVKGKIQPGKYEAYISKDDELNKSTVYDTERPDTKKIKMDVKVLQTNGAFSLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 234 EIELITGRSHQLRAHLAHLGNPIV 257


>gi|253584151|ref|ZP_04861349.1| pseudouridine synthase [Fusobacterium varium ATCC 27725]
 gi|251834723|gb|EES63286.1| pseudouridine synthase [Fusobacterium varium ATCC 27725]
          Length = 294

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 29/206 (14%), Positives = 75/206 (36%), Gaps = 31/206 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----------GVPLRKAERTRL 75
           SR  ++ ++ +++V V   ++ +    ++    + VD           GV +   +   +
Sbjct: 31  SRTSIKSLLTKRKVFVGNDVVSQYNHPLLPGQTVTVDWGKVTIETVMKGVSVIYEDDD-I 89

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
            +  K  G+++  ++ +   T ++ L           ++  V RLD +T G+++      
Sbjct: 90  LVVEKENGILSIATNNEREKTAYNILKDYLKNKDPKNKIFVVHRLDRDTSGIMIFAKTEK 149

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI-----QGICYGDMQ 176
              +L      +   R Y     G V ++K      L   +  I       +        
Sbjct: 150 AQDILQTTWNDSVKERTYIALVEGTVQKEKDTIISYLQENRAFITYSSQNPKDGKKAISH 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK 202
             +  +  + + + V +  G+  +I+
Sbjct: 210 YKVLKKNKNYSLLEVNIETGRKNQIR 235


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 51/334 (15%), Positives = 103/334 (30%), Gaps = 73/334 (21%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----------RAAVNVMSTDHIEV 62
           R+   ++R     SR   +R I + +V VNG+ ++             ++       ++ 
Sbjct: 27  RIDHYLSRLYPNFSRVAFQRTIEEGKVLVNGLPVKISRRLRVNDVIEFSLPAEPDQRVQP 86

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVIS--VG 112
           + +PL    +   L + +K   ++      + R T+       FD+L  +  +  +  V 
Sbjct: 87  EDIPLDILYDDEYLCVINKTANMIVHPGRGNYRGTLAGALQFHFDSLSDVAGQYRAGIVH 146

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ------------------ 152
           RLD +T G+L++  D  + + L          + Y     G+                  
Sbjct: 147 RLDRDTSGVLVVAKDNTVHQHLSRQFEERSVEKEYHAIVWGEMQFDADYVETYVRVSFRN 206

Query: 153 -------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                     D          +Q    G   V L  Q G    + V +            
Sbjct: 207 RERMMVCPPGDNARQAATFYEVQQRFRGFTYVKLQPQTGRTHQLRVHMH----------- 255

Query: 206 EFFNWKVNRLIRISYGP--FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYS 263
                 +    R+  G    +L  +L     E  ++     +    L   ++  + P+  
Sbjct: 256 -HLGHPIIA-DRLYEGKTCVKLSDILP----ETPEEADETLIDRQALHARRLAFNHPVTK 309

Query: 264 SE-----TLVRDRPNIISEVPDDFTRMKKNSSQK 292
                   L  D    +  +     + KK+ S K
Sbjct: 310 KRMVFEAPLPADFQKTLDTLKTHAIKPKKSPSSK 343


>gi|299143164|ref|ZP_07036244.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Peptoniphilus sp. oral taxon 386 str. F0131]
 gi|298517649|gb|EFI41388.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Peptoniphilus sp. oral taxon 386 str. F0131]
          Length = 293

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 37/213 (17%), Positives = 79/213 (37%), Gaps = 32/213 (15%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVP 66
            + + G++SR  +   I ++ + +NG  + R  + +   D + V             G  
Sbjct: 25  FLVQNGLSSR-FIRGSIEEENIYLNGEKIYRNEL-LRENDELFVKFSDESLNAKVQHGKL 82

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEG 120
               E   + + +KP  +VT  +  D  +T+ + +   F       +V  V RLD +T G
Sbjct: 83  DIIYEDDDIVVVNKPPYMVTHTAKDDVENTLLNFVAGYFEDNKIRRKVRIVNRLDRDTSG 142

Query: 121 LLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK------LNLLKKG---IVIQG 169
           ++++  +   +             + Y    +G +  D       +++ K G   IV   
Sbjct: 143 IVIVAKN-SFSHSSIQEQFGDSVKKEYVAIVNGIIKNDSGIIEKPIDIAKDGIRRIVSPD 201

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             Y      +  +      V + L  G+  +I+
Sbjct: 202 GKYSKTSYEVIKRNDFFTLVKLRLYTGRTHQIR 234


>gi|257469932|ref|ZP_05634024.1| pseudouridine synthase, RluA family protein [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064162|ref|ZP_07928647.1| RNA pseudouridylate synthase [Fusobacterium ulcerans ATCC 49185]
 gi|313689838|gb|EFS26673.1| RNA pseudouridylate synthase [Fusobacterium ulcerans ATCC 49185]
          Length = 294

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/206 (14%), Positives = 77/206 (37%), Gaps = 31/206 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----------GVPLRKAERTRL 75
           SR  ++ ++ +++V V   ++ +    ++    + VD           GV +   +   L
Sbjct: 31  SRTSIKSLLTKRKVFVGNDVVSQYNHPLLPGQTVTVDWGKVTIDTTMKGVSIIYEDDDVL 90

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
            +  K  G+++  +D +   T ++ L           ++  V RLD +T G+++      
Sbjct: 91  VV-EKESGILSIATDNEREKTAYNMLKEYLKNKDPKNKIFVVHRLDRDTSGIMIFAKTEK 149

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDK---LNLLKKGIVI--------QGICYGDMQ 176
              +L      +   R Y     G V ++K   ++ L++            +        
Sbjct: 150 AQDILQTTWNDSVKERTYVALVEGVVYKEKDTIISYLQENKAFITYSSQNPKEGKKAISH 209

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK 202
             +  +  + + + V +  G+  +I+
Sbjct: 210 YKVLKKNKNYSLLEVNIETGRKNQIR 235


>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 = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 86/247 (34%), Gaps = 44/247 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVAAGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVATPSITPQIVEGMRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQ-- 155
                 R   V RLD+ T GL+++      A +L   + +     +VY     G  D   
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKS-EHAYILLKQAFRDRTVDKVYLALVQGHPDPFT 182

Query: 156 ---------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVF 205
                    D  +  K  IV  G        T++  + +   + V L  G+  +I+  + 
Sbjct: 183 GTIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM- 240

Query: 206 EFFNWKV 212
                  
Sbjct: 241 AAIKHPC 247


>gi|170703044|ref|ZP_02893871.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
 gi|170132052|gb|EDT00553.1| pseudouridine synthase, RluA family [Burkholderia ambifaria
           IOP40-10]
          Length = 365

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 83/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV ++G   +     V     IE+      
Sbjct: 23  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAK-IRQPVPLGARIELVPDLLP 81

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP G+V   +  +   T+ + L   +        R
Sbjct: 82  EQLAFTPEPVPLDVIYEDDALLVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 141

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 142 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEDGTIDAPIGR 201

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 202 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHVGH 261

Query: 211 K 211
            
Sbjct: 262 P 262


>gi|33152257|ref|NP_873610.1| tRNA pseudouridine synthase C [Haemophilus ducreyi 35000HP]
 gi|34582379|sp|P59840|TRUC_HAEDU RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|33148479|gb|AAP95999.1| probable pseudouridine synthase Rlu family protein [Haemophilus
           ducreyi 35000HP]
          Length = 243

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 33/193 (17%), Positives = 66/193 (34%), Gaps = 39/193 (20%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T+F        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKAETLFAMQTLRDQINQHVFPIHRLDRPTSGVLLFALNSEMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQ----- 182
             L        +  + Y     G + +  +++   K +++  I     Q     Q     
Sbjct: 72  -RLMSEQFEQHKVEKEYLAIVRGYIAEKGEIDYPLK-VILDKIADKFSQPKAAQQAVTFY 129

Query: 183 -------------KGSNAWVTVG-L--REGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                        K +    ++  L  + G+  ++++  +     +        G  + G
Sbjct: 130 QNLAKVEMPYSTGKYATTRYSLVALSPKTGRKHQLRRHMKHLFHPI-------MGDTKYG 182

Query: 227 TLLAGSTREVSKK 239
            L     R +++K
Sbjct: 183 DLH--QNRRLTEK 193


>gi|294085986|ref|YP_003552746.1| pseudouridine synthase [Candidatus Puniceispirillum marinum
           IMCC1322]
 gi|292665561|gb|ADE40662.1| pseudouridine synthase, RluA family [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 335

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 35/199 (17%), Positives = 63/199 (31%), Gaps = 55/199 (27%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMS 56
             + E+    R+ +V+       RR        ++E+M+    ++++G   + A+  V  
Sbjct: 13  ETISEDEDGSRLDRVL-------RRLIPGLAQGQIEKMLRNGLIRIDGAKAKSAS-RVAV 64

Query: 57  TDHIE---------------------------VDGVPLRKA-------ERTRLWLYHKPI 82
              I                            + G PL+K        E       +KP 
Sbjct: 65  GQQIRLPISIDALATVKPAANKMSAKALGAPSIGGAPLQKTFDDMVIGEGKGWLALNKPS 124

Query: 83  GLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           GL     T +       +         R+  V R+D +T G+LLL      AR L     
Sbjct: 125 GLAVQGGTGTKQHVDGMLAALAARGGDRLRLVHRIDKDTSGVLLLAKTLQSARSLTDAFH 184

Query: 140 QW--LRVYRVRFHGQVDQD 156
           +    + Y     G   ++
Sbjct: 185 KHAIEKTYLALCMGLPPEE 203


>gi|322435857|ref|YP_004218069.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
 gi|321163584|gb|ADW69289.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX9]
          Length = 297

 Score = 63.7 bits (154), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 76/249 (30%), Gaps = 41/249 (16%)

Query: 19  VIAR-AGIASRREVERM---IAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKA-- 70
           +++  AG+      E     +    V ++GI    A   ++S+  I V   P  +     
Sbjct: 21  LLSHLAGLYPHSSAEAWQENLDNGEVTLDGITA--AGSELLSSGQILVWKRPAWIEPDAP 78

Query: 71  -------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                  +   L   +KP GL T        +T+   +         V RL   T G+++
Sbjct: 79  QHFEVLFDDLHLLAVNKPSGLPTLPGGGFLENTLLRLVHRHSPSANPVHRLGRATTGIVM 138

Query: 124 LTNDGGLARVLELPST--QWLRVYRVRFHGQVDQDKLNLLKK-GIVIQ-----------G 169
                  A  L       +  ++YR    G   Q+   +L   G+V             G
Sbjct: 139 FAKTAQAAAGLTADWNTPRVQKIYRALAQGVARQEAYEILTPIGLVPHPRLGSVWAASAG 198

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR--LIRISYG--PFQL 225
                    + ++  +     V L  G+  +I+         +    L    YG     L
Sbjct: 199 GKASKSSAKVISRTAATTTFEVRLGSGRPHQIRIHLASIGHPLVGDPL----YGSTGLPL 254

Query: 226 GTLL--AGS 232
             L    G 
Sbjct: 255 DDLPGLPGD 263


>gi|291543834|emb|CBL16943.1| pseudouridine synthase, RluA family [Ruminococcus sp. 18P13]
          Length = 326

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 57/342 (16%), Positives = 110/342 (32%), Gaps = 91/342 (26%)

Query: 3   DKNIVQENFTPQRVSKVIARA------GIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
            +  +Q+N   QR+ K +A++      G+     + + I  + +K NG      +  +  
Sbjct: 2   RQITIQQNDAGQRLDKFLAKSMPALPKGL-----MCKFIRTKHIKRNGKRCA-ISDRLEP 55

Query: 57  TDHIEV---DG------------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
            D +     D                         E T++ + +KP+GLV    +     
Sbjct: 56  GDVLTFFISDDFFPEHAPQQTPDFLKAPAKLDVVYEDTQVLILNKPVGLVVHADNGGTED 115

Query: 96  TVFDNL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL-----ELP 137
           T+   +           P+           RLD NT GL++       A  L      + 
Sbjct: 116 TLIHRVLHHLYQAGTYDPAGEQSFTPALCNRLDRNTGGLVIAA---KTAAALRDVNELIR 172

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLK-------KG--IVI-----QGICYGDMQVTLDTQK 183
           S Q  + Y       +   + + ++        G  + I     +G    D +  +  Q+
Sbjct: 173 SRQLCKQYL-CVTAALPPRQQDRVQAYHRKQPAGNLVEIRDAPAEGFAPIDTEYRVLAQE 231

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS------TREVS 237
              + V V L  G+  +I+         +            LG    GS       R  +
Sbjct: 232 QGLSLVLVTLHTGRTHQIRAHLAHLGAPL------------LGDNKYGSVRANRRYRVFT 279

Query: 238 KKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVP 279
           +++   +LG   L+ A     AP+        + P + +  P
Sbjct: 280 QQLWAWRLGFPELDGAL----APLSGRIVTAPEVPFVSAFFP 317


>gi|303287646|ref|XP_003063112.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226455748|gb|EEH53051.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 417

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 42/191 (21%), Positives = 64/191 (33%), Gaps = 40/191 (20%)

Query: 5   NIVQENFTPQRVSKVIARA-------GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
            I     TP R+   IA         G  +R  V   I    V VNG++  +A+  V   
Sbjct: 77  PIDVPKPTPARLDAYIATHAPPSEGGGGITRARVVASIKAGLVDVNGVVARKASERVSPG 136

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----- 99
           D I V            + +PL  K E   + + +KP G+V   +      T+ +     
Sbjct: 137 DVIRVALKPTPPTEAAPEDIPLDVKYEDEHVLVVNKPAGMVVHPAPGHSSGTLVNAVLFR 196

Query: 100 -------------NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRV 144
                        N     +R   V RLD  T GL+++  +      L     +    R 
Sbjct: 197 CGCPAMRVASGNANTADGVARPGIVHRLDKGTSGLIVVAKNEAAHASLCEQFATRVVRRR 256

Query: 145 YRVRFHGQVDQ 155
           Y     G  +Q
Sbjct: 257 YLAICLGSPEQ 267


>gi|229918468|ref|YP_002887114.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
 gi|229469897|gb|ACQ71669.1| pseudouridine synthase, RluA family [Exiguobacterium sp. AT1b]
          Length = 287

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 79/218 (36%), Gaps = 40/218 (18%)

Query: 19  VIARAGIASRREVERMIA-QQRVKVNG--ILLERAAVNVMSTDHIEV------------- 62
           ++   GI SR+ +  ++  +  ++VNG    +      +   D + V             
Sbjct: 20  LMQDMGI-SRK-MLTLVKHEGDIEVNGMHRTVRH---ELEPGDEVSVRFPPESPSLDMVA 74

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLD 115
              P+R   E   L    KP G+ T  S      T+ + +   + R+        + RLD
Sbjct: 75  SERPIRILYEDDTLLAVDKPAGIATIPSRLHPTDTLANAVLGYYQRIGLSSAIHVINRLD 134

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL---------LKKG 164
            +T G++L    G +         +   +R Y+     +V    ++          +++ 
Sbjct: 135 RDTSGVVLFAKYGFIHHRFSELQKANGLMRTYKALVEEEVTPQTIDAPIGRAENSIMERV 194

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  +G       +      GS + +T+ L  G+  +I+
Sbjct: 195 VTTEGQRAITHILACQP-FGSGSLLTIRLETGRTHQIR 231


>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 = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 74/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|297182616|gb|ADI18775.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF4000_36I10]
          Length = 319

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 59/325 (18%), Positives = 109/325 (33%), Gaps = 53/325 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++ +     R+ + +A+     SR  ++  I    + VNG    R    +M  + I V G
Sbjct: 10  VIPDELAGSRLDQAVAQLFPDYSRSRLQSWIKSGELTVNGSQ-YRPRDKIMGGEEIRV-G 67

Query: 65  VPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
             L+                E   L + +KP+GLV   +      T+ + L         
Sbjct: 68  AELQDEGDWQPQQIDFGLFYEDEHLLVLNKPVGLVVHPAAGHYDGTLVNALIEHCPGLAQ 127

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-------- 154
             R   V RLD +T GL+++         L  +L +    R Y    +G +         
Sbjct: 128 LPRAGIVHRLDKDTSGLMVVAKTLEAHTSLVKQLQARNVHREYEALVYGVMTGGGKVDEP 187

Query: 155 ----QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                 +   +   +V  G         +  +    + V   L  G+  +I+        
Sbjct: 188 MGRHPQQRKKMA--VVRAGGKEAITHYRIIERFTHFSHVRCLLETGRTHQIRVHMAHIKH 245

Query: 211 KVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDA-PIYSSETLVR 269
            +        G      L AG  R+   K   E L   L    +  L A  +        
Sbjct: 246 PL-------IG----DALYAGRLRQ--PKGASELLIETLRTFRRQALHARKLELIHPATD 292

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNG 294
           +  +  +++PDDF R++   + ++G
Sbjct: 293 ELVSWETDLPDDFQRLRTVLASEDG 317


>gi|325969898|ref|YP_004246089.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324025136|gb|ADY11895.1| pseudouridine synthase [Spirochaeta sp. Buddy]
          Length = 229

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/188 (14%), Positives = 53/188 (28%), Gaps = 37/188 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGL 121
           E   L + +K  G +    D  G  T+ D +               +    RLD  T G+
Sbjct: 10  EDNHLIIINKLCGELVQG-DVTGDETLADLVKEYLRVNYNKQGNVFLGIPHRLDRPTSGI 68

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKL-------NLLKKGIVI--- 167
           ++          L      +   + Y           +  L           K + +   
Sbjct: 69  VVYAKTEKALIRLNELFKGSAMKKTYWAIVDHMPNQTEGTLVHYIVRDTKTNKSVALSVE 128

Query: 168 -QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
            +G     +   L +   +   + V L  G++ +I+  F      +             G
Sbjct: 129 KKGGKLAKLDYKLISASKNYFLLEVNLHTGRHHQIRAQFAAIGLHIK------------G 176

Query: 227 TLLAGSTR 234
            L  G+ R
Sbjct: 177 DLKYGAAR 184


>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 = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 78/229 (34%), Gaps = 41/229 (17%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+   +++     SR  ++++I Q  + +N  +       V   D ++V           
Sbjct: 21  RIDLWLSQNLDQISRSHLQKLIEQGNIYLNNQVCLNKKTKVNLGDRLQVFLPPPEPLELQ 80

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
            + +PL    E   L + +K  GLV   +      T+   L      ++ +G        
Sbjct: 81  PEPIPLDILYEDDSLIIINKSAGLVVHPAPGHTSGTLVHGLLYHCPNLVGIGGVQRPGIV 140

Query: 113 -RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI-- 167
            RLD +T G +++  T+        +L +    R Y    +G       +     + I  
Sbjct: 141 HRLDKDTTGAIVVAKTDYAHQHLQAQLKAKTARREYLGVVYGVPRHKDTHQGTINVPIGR 200

Query: 168 -QGICYGDMQVTLD--TQKGSNAW-----------VTVGLREGKNREIK 202
            +G       V ++   ++    W           V   L  G+  +I+
Sbjct: 201 HRGDRKKMAVVPVENGGREAITHWQIVERLGNYTLVEFRLETGRTHQIR 249


>gi|319425744|gb|ADV53818.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 280

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 29/200 (14%), Positives = 57/200 (28%), Gaps = 39/200 (19%)

Query: 50  AAVNVMSTDHIEVDGVPLRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVF----- 98
             +     DH+ +D    +        E   +   HKP GL+   S    R   F     
Sbjct: 8   LDMPDDELDHVVLDNTDEQAPDIRILFEDEHIVAIHKPAGLLVHRSYLARRERFFAMQLT 67

Query: 99  -DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            D +      V  V RLD  T G+LL      +A  L          + Y     G + +
Sbjct: 68  RDLVGC---HVFPVHRLDRPTSGVLLFAKSSEVANALCEQFAEHSIEKQYLALVRGNMHE 124

Query: 156 DKLNLLKKGIVIQ---------GICYGDM----------QVTLDTQKGSNA---WVTVGL 193
             +      + +               D           ++   + +   +    V +  
Sbjct: 125 SGILDYPLKVELDELGDKHARQDKTAQDAVTAFKPLLNTEIPYPSGRYPTSRFALVQLTP 184

Query: 194 REGKNREIKKVFEFFNWKVN 213
           + G+  ++++        + 
Sbjct: 185 KTGRKHQLRRHMAHLRHPIL 204


>gi|254507454|ref|ZP_05119589.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
 gi|219549710|gb|EED26700.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 16]
          Length = 254

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 58/165 (35%), Gaps = 30/165 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   + + +KP GL++      +   +++  L +I+  +  V RLD++T GL+LL     
Sbjct: 28  EDEHILVANKPSGLLSVPGRLEEHYDSLWSRLVAIYPDIQVVHRLDMDTSGLMLLAKHKE 87

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKG-------IVIQGI 170
                       L        +VY  R  G    D     L L+          +     
Sbjct: 88  AERSLKKQFQYRLTH------KVYYARVWGHPTNDNGEIDLPLICDWPNRPRQIVCFDDG 141

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                   +  ++   + V +  +  G++ +++  + +     + 
Sbjct: 142 KPSKTLYQVVKREERTSIVRLLPIT-GRSHQLRVHM-QALGHPIV 184


>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 = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 84/245 (34%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE+  
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      + VPL    E   L + +KP G+V   +  +   T+ + L   +     
Sbjct: 128 DLLPEQLAFTPEPVPLEIIYEDDTLVVINKPAGMVVHPAAGNWSGTLLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD----- 156
              R   V RLD  T GL+++         L  +L +    R Y     G + ++     
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFE 206
                  +   +       G         +D+   ++     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTSAAGKPARTHFRRVDSAIWERQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWK 211
                
Sbjct: 308 HIGHP 312


>gi|297183890|gb|ADI20012.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium EB000_65A11]
          Length = 318

 Score = 63.7 bits (154), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 84/233 (36%), Gaps = 33/233 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           +  + IV E+    R+  V A A     SR  ++  I    + V+G    ++   V   +
Sbjct: 5   INHQEIVPEDLAFNRLDHV-ASALFPQYSRSRLQTWIKNGELVVDGQK-RKSKDKVTGGE 62

Query: 59  HIEVDGVPLR------------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-- 104
            + +    +               E   L + +KP GLV      +   T+ + L     
Sbjct: 63  LVAIQSSAIETTYEAQAIPLNVAYEDEHLLVVNKPSGLVVHPGAGNFDGTLLNGLLHHAE 122

Query: 105 ----FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-K 157
                 R   V RLD +T GLL++         L  +L +    R+Y    +G + +  K
Sbjct: 123 QLNGIPRAGIVHRLDKDTTGLLVVAKTLTTQHHLVQQLQARSVSRIYDAVVYGSLTRSGK 182

Query: 158 LNLL-------KKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++         +  + I+ G         +    G ++ + + L  G+  +I+
Sbjct: 183 VDQPIGRHTTQRTKMAIRPGGKPAITHYKVVRNFGEHSHIELALETGRTHQIR 235


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/247 (15%), Positives = 82/247 (33%), Gaps = 44/247 (17%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +V+     +R+ K +     G  +R  ++++I  ++V+  G  L +    + + + I V 
Sbjct: 8   LVEPEQAGERLDKFLPTVLPGY-TRSALQKLIEGEQVRCEGEPLNK-KHKLRAGETISVT 65

Query: 63  --DGVPLRK----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
             D  PL             E + L + +KP  +V   +  +   T+ + L         
Sbjct: 66  IPDPEPLDVLPEEIPLDILYEDSDLLVVNKPKHMVVHPAAGNYTGTLVNALLHHCRGSLS 125

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQV----- 153
                 R   V R+D +T GLL++  +      L     +    R Y    +G+      
Sbjct: 126 GINGVIRPGIVHRIDKDTSGLLIVAKNDQAHVGLAAQIKEHSFDRTYEAVVYGKFVESTG 185

Query: 154 --------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                    +     +   +  +          +  + G    + + L  G+  +I+   
Sbjct: 186 TVDKPIGRSEKDRKKMC--VTTKNSKPAVTHYEVLGEYGQFTHLRLRLETGRTHQIRVHM 243

Query: 206 EFFNWKV 212
                 V
Sbjct: 244 ASIGHPV 250


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 74/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 82/237 (34%), Gaps = 47/237 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +V+      R+ + +A      SR   +R+I   +V +N       +  V + D + V  
Sbjct: 9   VVEAANEGDRLDRYVADHVPDLSRTYAQRLIEAAQVLLNNRQAR-PSTPVHAGDTVTVHL 67

Query: 64  ---------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                      PL      E   + +  KP  +V   +    R T+ + L + +      
Sbjct: 68  PAPQPVGLVAEPLPLQIVYEDRDVVVIDKPASMVVHPAPGHDRGTLVNALIARYPEMAIN 127

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD +T GLL+   +    R L  +  +   L++Y     G++ +      
Sbjct: 128 GDMRPGIVHRLDRDTSGLLVAARNERALRSLQAQQQARTMLKIYLAVVEGRMPE------ 181

Query: 162 KKGIVIQGICYGD-----MQVTLDTQKGSNAWVTV------GLRE-----GKNREIK 202
            +G++   I         M V    +     W  +       L E     G+  +I+
Sbjct: 182 LEGVIDAPIARHPTDRVRMAVVAGGRPARTHWRVLEDLGEYTLIEARLETGRTHQIR 238


>gi|226226809|ref|YP_002760915.1| ribosomal large subunit pseudouridine synthase D [Gemmatimonas
           aurantiaca T-27]
 gi|226090000|dbj|BAH38445.1| ribosomal large subunit pseudouridine synthase D [Gemmatimonas
           aurantiaca T-27]
          Length = 329

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 45/235 (19%), Positives = 79/235 (33%), Gaps = 39/235 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRK 69
           R+  ++A     SR +   +IA   V VNG   E+A+    + D + V      G  +  
Sbjct: 20  RLDLLVADHASVSRTQAATLIANGNVLVNGAR-EKASYKGETGDVVRVTIPPPPGRDIVA 78

Query: 70  A--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVG 112
                    E   L +  K  G+V   +  +   T+ + L              R   V 
Sbjct: 79  EQIPLDVVYEDEHLLVVDKAAGMVVHPAPGNWTGTLVNALLGRGEPLAEGGGEDRAGLVH 138

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           RLD +T GLL++       R L     + Q  R Y     G + ++++  ++K I  +  
Sbjct: 139 RLDKDTSGLLVVAKSDAAHRTLSSALAARQVTRRYAAVCWGHLAEERI-TVEKPIA-RDP 196

Query: 171 CYGDMQVTLDTQKGSNA------------WVTVGLREGKNREIKKVFEFFNWKVN 213
                   + + K S               +   L  G+  +I+         V 
Sbjct: 197 RDRTRMAIVQSGKASRTDFTRLARFDSVDLLRAHLHTGRTHQIRVHLASTGHPVV 251


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 88/255 (34%), Gaps = 59/255 (23%)

Query: 7   VQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           V++     R+ + +        SR  +++ I + +VKVNG + ++ +  +   + +EVD 
Sbjct: 6   VEKREEGWRLDQFLKEKTPSWISRSLIQKAIKEGKVKVNGQI-KKPSYKLKEGEIVEVD- 63

Query: 65  VPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           +P +  E T                + +  KP  ++          T+ + L      + 
Sbjct: 64  LPEKPQEATVQPEEIELKVLYEDRDIVVIDKPGDMIVHPVPSKLSGTLVNALLHHCKDLQ 123

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDK 157
            VG         RLD  T G++++  +   A           +  + Y +   G+V  D 
Sbjct: 124 GVGGKLRPGIVHRLDKETSGVIVVAKN-DFAHQSLSKQFKDRKVKKTYILLVKGRVKSD- 181

Query: 158 LNLLKKGIVIQGICYGDMQV------TLDTQKGSNAWVTV--------GL-----REGKN 198
                +G++   +      V       ++T K +     V         L     + G+ 
Sbjct: 182 -----EGVI--DLPLARHPVLRIKMAVVETGKEAITEYRVLKRFDDVATLVLAFPKTGRT 234

Query: 199 REIKKVFEFFNWKVN 213
            +I+   +     + 
Sbjct: 235 HQIRVHMKSLGHPIM 249


>gi|120599561|ref|YP_964135.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120559654|gb|ABM25581.1| tRNA pseudouridine synthase C [Shewanella sp. W3-18-1]
          Length = 280

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/200 (14%), Positives = 58/200 (29%), Gaps = 39/200 (19%)

Query: 50  AAVNVMSTDHIEVDGVPLRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVF----- 98
             +     DH+ +D    +        E   +   HKP GL+   S    R   F     
Sbjct: 8   LDMPDDELDHVVLDNTDEQAPDIRILFEDEHIVAIHKPAGLLVHRSYLARRERFFAMQLT 67

Query: 99  -DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            D +      V  V RLD  T G+LL      +A  L          + Y     G + +
Sbjct: 68  RDLVGC---HVFPVHRLDRPTSGVLLFAKSSEVANALCEQFAEHSIEKQYLALVRGNMHE 124

Query: 156 DKLNLLKKGIVIQGI-------------------CYGDMQVTLDTQKGSNA---WVTVGL 193
             +      + +  +                      + ++   + +   +    V +  
Sbjct: 125 SGILDYPLKVELDELGDKHARQDKAAQDAVTAFKPLLNAEIPYPSGRYPTSRFALVQLTP 184

Query: 194 REGKNREIKKVFEFFNWKVN 213
           + G+  ++++        + 
Sbjct: 185 KTGRKHQLRRHMAHLRHPIL 204


>gi|218130909|ref|ZP_03459713.1| hypothetical protein BACEGG_02504 [Bacteroides eggerthii DSM 20697]
 gi|217987253|gb|EEC53584.1| hypothetical protein BACEGG_02504 [Bacteroides eggerthii DSM 20697]
          Length = 303

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 39/221 (17%), Positives = 77/221 (34%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++        +  + V         E
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQISREKGRKE 80

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 81  FSNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYIVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D      L          R Y     G+           +   KL + 
Sbjct: 141 DRDTSGLMMFAKDEKTQNTLRDNWHNIVTDRRYVAVVAGEMENNAGMVRSWLTDRKLYVY 200

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 201 SSPTDDGGKESVTHYRTIKRANGF-SLVELVLETGRKNQIR 240


>gi|239908035|ref|YP_002954776.1| putative pseudouridine synthase [Desulfovibrio magneticus RS-1]
 gi|239797901|dbj|BAH76890.1| putative pseudouridine synthase [Desulfovibrio magneticus RS-1]
          Length = 290

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 47/222 (21%), Positives = 76/222 (34%), Gaps = 43/222 (19%)

Query: 15  RVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+ K +       G+  RR   R+I    + VNG LL  A   V +   +      +   
Sbjct: 19  RLDKALELMLPEVGLRGRR---RLIESGGLTVNGRLL-PAGYRVRAGQTV-----AMVPQ 69

Query: 71  ERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGR 113
           +R R                 L +KP GL +      G  +V   LP IF    S  + R
Sbjct: 70  DRERRFGPADVPVVLTAGDYVLLNKPSGLHSAALAQGGGESVEALLPDIFPGRPSFLLSR 129

Query: 114 LDINTEGLL--LLTNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLL-KKG 164
           LD  T GLL    + +          S +  + Y    HG+ D        +L+   +K 
Sbjct: 130 LDSLTTGLLPAAFSPEAAATYRDMEESGEVDKTYLAVGHGEPDVTYFRCDGELDAADRKK 189

Query: 165 IVIQGICYGD----MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +      D     +V     +G        +++G   +I+
Sbjct: 190 TRVLDRATIDSLRMTEVEALETRGGVTLFRCTIKKGARHQIR 231


>gi|293390024|ref|ZP_06634358.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290950558|gb|EFE00677.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 237

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 61/195 (31%), Gaps = 36/195 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L     + V  + RLD  T G+LL   +
Sbjct: 8   QDDVLVAVNKPAGMLVHRSWLDRHETQFVMQILRDQIGQLVYPIHRLDRPTSGVLLFALN 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-------------QDKLNLLKK-------GI 165
              A ++       Q  + Y     G V                  +   +        +
Sbjct: 68  SETANLVCHQFEQKQTEKQYLAVVRGYVTGQGEIDYPLKVQLDKIADKFAQQDKAPQSAV 127

Query: 166 VI-QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
               G+   +M   +     S  + V +  + G+  ++++  +     +        G  
Sbjct: 128 TFYDGLKTVEMPYGVGRYAASRYSLVRLTPKTGRKHQLRRHMKHIFHPIL-------GDM 180

Query: 224 QLGTLLAGSTREVSK 238
           Q G L     R +++
Sbjct: 181 QYGDLH--QNRALTE 193


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 35/60 (58%), Gaps = 1/60 (1%)

Query: 15 RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
          R++K+I+ AG+ SRRE E+ I + RVK+NG +     + V   D + +D + +   +  R
Sbjct: 4  RINKLISDAGLGSRREAEKYITEGRVKINGRIARLTDL-VCEKDIVLLDDIDIPIKDLIR 62


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 90/248 (36%), Gaps = 45/248 (18%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAA---------VNV 54
             +E+    R  + +A A  G+ +R  ++++   + V+V    + +           ++V
Sbjct: 7   TSEESDAGVRADRWLASAAEGLLTRSAIQKLCDCKAVRVGEKPVSKNDRLRGGETFIIDV 66

Query: 55  MSTD--HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVIS 110
                  I    +P+    E   L + +KP G+V   +      T+ +  L     R+ S
Sbjct: 67  PDAQPLDIVPQDIPIEIVYEDGDLLVVNKPKGMVVHPAPGHPNGTLVNALLYHCQGRLSS 126

Query: 111 ---------VGRLDINTEGLLLLT-ND---GGLARVLELPSTQWLRVYRVRF-------H 150
                    V R+D +T GLL++  ND   G LA  ++  S    R+Y            
Sbjct: 127 INGVIRPGIVHRIDKDTSGLLIVAKNDAAHGTLAEQIKNHSF--TRIYNAVVYGGFSTDE 184

Query: 151 GQVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           G VD      Q+    +   +  +          +  + G   W+ + L  G+  +I+  
Sbjct: 185 GTVDAPIGRSQNDRKKMC--VTDRNARGAVTHYRVLERLGRFTWLKLCLETGRTHQIRVH 242

Query: 205 FEFFNWKV 212
             +    V
Sbjct: 243 MAYIGHPV 250


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 62/172 (36%), Gaps = 30/172 (17%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPL 67
            P+R+ + +AR     SR  ++ +I +  V+++G  +   AV V     + V     +P 
Sbjct: 15  APERLDRALARLWPDLSRNRLQGLIREGGVRLDGAEIRDGAVKVAGGQRVAVAVPQALPA 74

Query: 68  RKAERTR----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SR 107
             A + R          L +  KP GLV   +      T+ + L +             R
Sbjct: 75  TPAAQARDLAIVYEDDDLIVIDKPAGLVVHPAPGHPDGTLVNALIAHCGASLSGIGGVRR 134

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHGQV 153
              V RLD +T GLL++  +      L L            R Y     G  
Sbjct: 135 PGIVHRLDKDTSGLLVVAKNDLAHAGLSLQFADHGRSGMLERAYLALVWGVP 186


>gi|59711220|ref|YP_203996.1| tRNA pseudouridine synthase C [Vibrio fischeri ES114]
 gi|59479321|gb|AAW85108.1| tRNA pseudouridine synthase [Vibrio fischeri ES114]
          Length = 259

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 63/201 (31%), Gaps = 41/201 (20%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-- 99
           VN  LLE  A  +   + +  D           L   +KP G++   S  D   TVF   
Sbjct: 9   VNDELLEEQAEPI-ELEIVYRD---------EHLIAINKPAGMLVHRSWLDKHETVFAMQ 58

Query: 100 -NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
                I   V  + RLD  T G+L       +A  +     S +  + Y     G +++ 
Sbjct: 59  TLRDQIGQHVFPLHRLDRPTSGILFFALSSEIAAQVSPLFASREIKKTYHAIVRGWIEEA 118

Query: 157 -KLN-LLKKGIVIQGICYGDMQVTLDTQKGSN----------------------AWVTVG 192
             L+  LKK   +  I        ++ ++                           + + 
Sbjct: 119 NTLDYPLKK--ELDKIADKKASQEVEAKEAITEYKPLAKVELPYSTGKFPTTRYCLMELK 176

Query: 193 LREGKNREIKKVFEFFNWKVN 213
              G+  ++++        + 
Sbjct: 177 PHTGRKHQLRRHMAHLRHPIV 197


>gi|126724897|ref|ZP_01740740.1| Pseudouridine synthase, RluD [Rhodobacterales bacterium HTCC2150]
 gi|126706061|gb|EBA05151.1| Pseudouridine synthase, RluD [Rhodobacterales bacterium HTCC2150]
          Length = 347

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 58/185 (31%), Gaps = 44/185 (23%)

Query: 9   ENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           EN   QR+ + +       RR        +VE+M  +  ++V+G  ++ A   V     I
Sbjct: 11  ENEAEQRLDRWM-------RRHFPDLSQGQVEKMCRKGEIRVDGGRVK-ANTRVTQGQLI 62

Query: 61  EV----DG-VPLRKAERT------------------RLWLYHKPIGLVTTHSDPDGRSTV 97
            +    DG   +   E                     +   +KP G+         R   
Sbjct: 63  RIPPLKDGPKKVYYDEPKISDADRKLMMDMVIYKDDYIIALNKPPGIPVQGGSGQKRHID 122

Query: 98  F---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
                       +   V RLD +T G+LLL  +   A  L     S +  ++Y     G 
Sbjct: 123 GLSEALRFDSDEKPRLVHRLDKDTSGVLLLARNQRSASELTAVFRSRESRKIYWAAVGGV 182

Query: 153 VDQDK 157
                
Sbjct: 183 PHPKM 187


>gi|311029802|ref|ZP_07707892.1| pseudouridine synthase, RluA family protein [Bacillus sp. m3-13]
          Length = 302

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 44/208 (21%), Positives = 70/208 (33%), Gaps = 41/208 (19%)

Query: 42  VNGILLERAAVNVMSTDHIEV-------------DGVPLRKA-ERTRLWLYHKPIGLVTT 87
           VNG  +      +   D IEV             + +PL    E   + + +KP G+ + 
Sbjct: 45  VNGSAVT-VRYILHEGDTIEVLFPKEEPSEDLVAEEIPLDIVFEDEYVLVVNKPAGMASI 103

Query: 88  HSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--VLELPST 139
            S      T+      + +L  I + +  V RLD +T GL+L+           L+    
Sbjct: 104 PSREHRHGTLANAVLGYYHLKGICATIHIVTRLDRDTSGLMLIAKHRHAHHLFSLQQKEF 163

Query: 140 QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQKGSNA------- 187
              R Y    HG++  D  +    G V   I   D      +V  D Q+           
Sbjct: 164 GVKRRYEALVHGEMTGDAGS--ACGKVDAPIGRKDSSIIEREVRSDGQRAVTHYEVLRVG 221

Query: 188 --WVTVGLR-E-GKNREIKKVFEFFNWK 211
             W  V L  E G+  +I+         
Sbjct: 222 AGWSHVTLHLETGRTHQIRVHMAHLGHP 249


>gi|126738738|ref|ZP_01754434.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           SK209-2-6]
 gi|126719919|gb|EBA16626.1| ribosomal large subunit pseudouridine synthase D [Roseobacter sp.
           SK209-2-6]
          Length = 344

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 47/263 (17%), Positives = 92/263 (34%), Gaps = 63/263 (23%)

Query: 6   IVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           ++ EN  P+R+ K ++R     A + SR  + R+I    + V+G+++      +     I
Sbjct: 9   VITENP-PKRLDKAVSRDVPEEAAL-SRTRLARLIEAGSLLVDGVVVLDPKARIAEGAQI 66

Query: 61  EV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFS 106
            +            + +PL    E   L + +KP G+V   +      T+ +  L     
Sbjct: 67  SITVEEAEDSHIGPEDIPLEVIYEDDDLIVINKPAGMVVHPAPGTPSGTLVNALLHHCGE 126

Query: 107 RVISVG---------RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           ++  VG         R+D  T GLL++  T+        +       R YR   +G  D 
Sbjct: 127 KLSGVGGVKRPGIVHRIDKETSGLLVVAKTDAAHQGLAAQFEKHTVERYYRAVCYGVPDG 186

Query: 156 DKLNL-------LKKG--------------------IVIQGICYGDMQVTLDTQ---KGS 185
           +   L        + G                    ++ QG  +   +  +       G+
Sbjct: 187 NDPRLRGVKGASFESGNILKLTTQLARHKHDRQRQAVLFQGGRHAVTRARIVEPFGNPGT 246

Query: 186 NAWVTVGLREGKNREIK-KVFEF 207
            A +   L  G+  +I+  +   
Sbjct: 247 AALIECWLETGRTHQIRVHMTHA 269


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 41/252 (16%), Positives = 90/252 (35%), Gaps = 53/252 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRR---EVE-----RMIAQQRVKVNGILLERAAV 52
           M+ +  V E     R+   I       R+   E++      +I +  VKVN   +++   
Sbjct: 1   MEKETTVNEKNYYSRLDTFI-------RKNYPEIKLGAIYGLIRKGFVKVNEKRVKKNNY 53

Query: 53  NVMSTDHIEV--DGVPLRK-------------------AERTRLWLYHKPIGLVTTHSDP 91
            +   D++++  D   L +                    E   L + +KP  +       
Sbjct: 54  ILEIGDNVKIILDENKLEELSRPTQPSLKARPVSFDIIYEDKDLLVINKPAKVSVHPGSK 113

Query: 92  DGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYR 146
           +  +T+ + +            V RLD  T G++++  +   AR L     S +  + Y 
Sbjct: 114 EEMATIIEGVMHYSRGEFEPHLVHRLDKLTSGVMVVAKNKQTARELTQLIKSRETRKYYL 173

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------AWVTVGLREGKNRE 200
               G +++      K G ++  +     Q+  + +K  +      + V + L  G+  +
Sbjct: 174 TLLVGNLNK------KSGELVSTVYGKTAQLKFNLKKKFDLFGELYSLVEIELYTGRKHQ 227

Query: 201 IKKVFEFFNWKV 212
           I+  F    + +
Sbjct: 228 IRVQFADLGFPI 239


>gi|146292442|ref|YP_001182866.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145564132|gb|ABP75067.1| tRNA pseudouridine synthase C [Shewanella putrefaciens CN-32]
          Length = 275

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/200 (14%), Positives = 58/200 (29%), Gaps = 39/200 (19%)

Query: 50  AAVNVMSTDHIEVDGVPLRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVF----- 98
             +     DH+ +D    +        E   +   HKP GL+   S    R   F     
Sbjct: 3   LDMPDDELDHVVLDNTDEQAPDIRILFEDEHIVAIHKPAGLLVHRSYLARRERFFAMQLT 62

Query: 99  -DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            D +      V  V RLD  T G+LL      +A  L          + Y     G + +
Sbjct: 63  RDLVGC---HVFPVHRLDRPTSGVLLFAKSSEVANALCEQFAEHSIEKQYLALVRGNMHE 119

Query: 156 DKLNLLKKGIVIQGI-------------------CYGDMQVTLDTQKGSNA---WVTVGL 193
             +      + +  +                      + ++   + +   +    V +  
Sbjct: 120 SGILDYPLKVELDELGDKHARQDKAAQDAVTAFKPLLNAEIPYPSGRYPTSRFALVQLTP 179

Query: 194 REGKNREIKKVFEFFNWKVN 213
           + G+  ++++        + 
Sbjct: 180 KTGRKHQLRRHMAHLRHPIL 199


>gi|308179960|ref|YP_003924088.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|308045451|gb|ADN97994.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 293

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 66/190 (34%), Gaps = 28/190 (14%)

Query: 38  QRVKV-NGILLERAAVNVM---STDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPD 92
             + + +G +     + +        + V   P++       WL  +KP GL +     +
Sbjct: 47  GVITIHDGDIA---GIQLPDEAPDTAVAVSEQPIQIEYEDANWLVLNKPAGLTSVPGPSN 103

Query: 93  GRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS--TQWLR 143
              T+ + +            R   + RLD +T GL+L+        +L  P    Q ++
Sbjct: 104 RTDTLVNRIKGYLIASHASNQRPHLITRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVK 163

Query: 144 VYRVRFHGQVDQD----------KLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTVG 192
            Y+    G +               +  ++ +   G       QV  D  + + + + + 
Sbjct: 164 TYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAGQRAITTYQVEADQLQHNVSRLRLE 223

Query: 193 LREGKNREIK 202
           L  G+  +I+
Sbjct: 224 LVTGRTHQIR 233


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/230 (14%), Positives = 77/230 (33%), Gaps = 35/230 (15%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++E+    R+ K +       SR + + +I +  V VNG  ++     +   D I     
Sbjct: 26  IEEDIESMRLDKYMGNRFSYYSRNKWQDLIGEGLVLVNGEKIKYTRT-ISKGDEISYYFK 84

Query: 66  PLRKAERTR----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRL 114
            +++ E  +          L + +KP  L    S     +T+   +       +  + R+
Sbjct: 85  DMKEPEVNKDIEIIYDDGDLIIVNKPANLPVIPSGKYYYNTLHTIMQERLGCHLNMINRI 144

Query: 115 DINTEGLLLLTNDGGLARVL-----ELPSTQWLRVYRVRFH--GQVDQ---------DKL 158
           D  T G ++L+    +A           +    + Y         ++          +  
Sbjct: 145 DRETSGCVILSRGSLVASKFCAMLANKNNNNIKKTYIAIVENAKDIEDSFTVEGYMQEVG 204

Query: 159 NLLKKGIVI------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + L +   I      +   Y   +     + G  A + + L  G+  +I+
Sbjct: 205 DKLYRRYQILHKENVEDSKYSKTKFKTVKKIGDYAILKIRLYTGRMHQIR 254


>gi|212636064|ref|YP_002312589.1| pseudouridine synthase [Shewanella piezotolerans WP3]
 gi|212557548|gb|ACJ30002.1| Pseudouridine synthase [Shewanella piezotolerans WP3]
          Length = 281

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 24/158 (15%), Positives = 51/158 (32%), Gaps = 19/158 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTND 127
           +  +  +++KP G+    S     +T+     +          + RLD+   GL++L + 
Sbjct: 88  DEGQYSVWYKPFGMRCQGSKWSDHTTINRFAETHLEPARSAYIIHRLDLAATGLIVLGHS 147

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDT- 181
                 +     +    + Y+V   G+    K       + I              L   
Sbjct: 148 KKTTAAIAKLFETRALDKYYQVIVEGEFPDSK-------VTIDTDVDGKSALSHAHLLEY 200

Query: 182 -QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN--RLI 216
             + + + V V +  G+  +I+         V   RL 
Sbjct: 201 NAELNQSKVQVKIESGRKHQIRLHMASVGHPVIGDRLH 238


>gi|312867737|ref|ZP_07727943.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311096800|gb|EFQ55038.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 297

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 38/211 (18%), Positives = 76/211 (36%), Gaps = 38/211 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G-VPLRKAERT--------RLWLYHKP 81
              ++ VNG   E A   +   D + +D     G   L+  +R+           + +KP
Sbjct: 33  RGGQILVNGRP-ENAIYLLDIGDRLVIDIPAEEGFETLKPMDRSLDILFEDDHFLILNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S     +T+ + +   +        +V  V RLD +T G++L    G     L
Sbjct: 92  FGIASIPS-AIHSNTLANFVKGYYVKQGYENQQVHIVTRLDKDTSGVMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L S    + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQSKTIQKRYYALVKGSGKLDPVGEIIAPIARDEDSIITRKVA-KGGKYAHTSYQVV 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G    V + L  G+  +I+  F    + 
Sbjct: 210 QSFGDIYLVDIQLHTGRTHQIRVHFSHIGFP 240


>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 = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 79/240 (32%), Gaps = 47/240 (19%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +    + +SR  +++      +  NG  ++  +  V   D + V           
Sbjct: 43  RVDKYLFERLVNSSRNRIQKAADAGLIMANGKPVKS-SYKVKPCDVLTVMMDRPRYDNDI 101

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVI 109
             + +PL    E   L + +KP GLV      +   T+ + +               +V 
Sbjct: 102 IPEDIPLDIVYEDNDLMVVNKPAGLVVHPGCGNYHGTLVNAIAWHLKDNPKYDPNDPQVG 161

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------------- 154
            V R+D +T GLL++  T D      L+  +    R Y     G V+             
Sbjct: 162 LVHRIDKDTSGLLVVAKTPDAKTHLGLQFYNKTTKRKYNALVWGVVENNEGTIEGNIGRN 221

Query: 155 QDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +    V+     G   VT   +  + G    V   L  G+  +I+   +     
Sbjct: 222 PKDRMQMA---VLSDPAQGKHAVTHYRVLERLGYVTLVECVLETGRTHQIRVHMKHIGHT 278


>gi|317493195|ref|ZP_07951618.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918855|gb|EFV40191.1| RNA pseudouridylate synthase [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 256

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/170 (17%), Positives = 51/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   TVF        I   V  V RLD  T G+LL+   
Sbjct: 7   QDEHLVALNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFPVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----------- 174
             +AR+L       +  + Y     G ++ + +        +  I               
Sbjct: 67  SEVARMLSEQFEQREMNKTYHAVVRGYLEGEAVIDYALTPELDKIADKFSSPDKAPQTAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                   V +    G        L E     G+  ++++        + 
Sbjct: 127 THYRSLATVEMPVAVGKYQTARYSLIELKPETGRKHQLRRHMAHLRHPII 176


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 84/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVATPSITPQIVEGMRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AIKHPC 247


>gi|213965290|ref|ZP_03393487.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           amycolatum SK46]
 gi|213952142|gb|EEB63527.1| ribosomal large subunit pseudouridine synthase D [Corynebacterium
           amycolatum SK46]
          Length = 327

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 76/243 (31%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V       RV   +A+    SR  V  + A   + V+G+ + ++   +     + V    
Sbjct: 27  VPPGLAGMRVDAGVAKLLGLSRTAVADLAAAGDITVDGVSVGKSD-RLEENAFLSVLLPP 85

Query: 63  DGVPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
              PL   E              L   HKP+G+    S      TV   L          
Sbjct: 86  VEKPLVPKEELVEGMDVLYHDSDLVAVHKPVGVAAHPSVGWEGPTVIGGLAAAGFRISTS 145

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DKL 158
               R   V RLD+ T G++++        VL+    + +  + Y     G  D     +
Sbjct: 146 GPPERKGIVHRLDVGTSGVMVVACSERGYSVLKRAFKNREVSKTYHALVQGHPDPLSGTI 205

Query: 159 NL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +           +  +   G        TL+    +   + V L  G+  +I+  F   N
Sbjct: 206 DAPIGRHPSAGWRFAVRQDGKHAVTHYETLEAFAPAT-LLKVNLETGRTHQIRVHFSALN 264

Query: 210 WKV 212
              
Sbjct: 265 HPC 267


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 87/242 (35%), Gaps = 41/242 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           IV E+   +R+ +++++     SR  +++ I  +RV V+    +R    +     I +  
Sbjct: 13  IVPEDLAEKRLDQILSQLFPAYSRTRLQQWIHDKRVLVDNEF-KRPRDKIKPGAKITIVA 71

Query: 63  ----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV----FDNLP--SIF 105
                     + +PL    E   L + +KP GLV      +   T+      +LP     
Sbjct: 72  NLHEAIDWEAENLPLDIIFEDDALVVINKPAGLVVHPGAGNRHKTLVNALLHHLPALKKL 131

Query: 106 SRVISVGRLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHG---------- 151
            R   + RLD +T GLL++         L + L+  + +  R Y     G          
Sbjct: 132 PRAGIIQRLDKDTSGLLIIPKILNAHTQLVKQLQARTMK--REYTAIIQGLLIAGGSINA 189

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            + +     L+K + +             +  +   +  + V L  G+  +I+      +
Sbjct: 190 PIGRH--PKLRKKMAVTENHGKPAVSHYRVIERFNHHTLINVQLETGRTHQIRVHMAHIH 247

Query: 210 WK 211
             
Sbjct: 248 HP 249


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 74/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRIANIPREKVLGGEKIEITVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|293394695|ref|ZP_06638987.1| tRNA pseudouridine synthase C [Serratia odorifera DSM 4582]
 gi|291422821|gb|EFE96058.1| tRNA pseudouridine synthase C [Serratia odorifera DSM 4582]
          Length = 257

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 35/173 (20%), Positives = 55/173 (31%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D R TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDQYLVAVNKPAGWLVHRSWLDSRETVFVMQTVRDQIGQHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A +L       Q  + Y     G V Q     L   +  +     D     D +   
Sbjct: 67  SEVAHLLSQQFEQHQVQKTYHAVVRGFVTQG--ARLDYPLTQERDKIADKFAEQDKEPQP 124

Query: 186 N-------AWVTV------------GLRE-----GKNREIKK-VFEFFNWKVN 213
                   A V +             L E     G+  ++++ +       + 
Sbjct: 125 AVTHYRPLAQVEMPVAIGRYDSARYSLMELQPETGRKHQLRRHMT-HLRHPII 176


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 85/245 (34%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE+  
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGASIELVP 127

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------PS 103
                      + VPL    E   L + +KP G+V   +  +   TV + L        +
Sbjct: 128 DLLPEQLAFTPEPVPLEIVFEDDTLVVINKPAGMVVHPAAGNWSGTVLNGLLYRYGDAAA 187

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD  T GL+++         L  +L +    R Y     G          
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 152 QVDQDKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFE 206
            + +D     +  +V    G         +DT   Q+     +   L  G+  +I+    
Sbjct: 248 PIGRDPRERTRMAVVTGASGKPARTHFRRVDTAIWQRQPVTAIHCDLETGRTHQIRVHCA 307

Query: 207 FFNWK 211
                
Sbjct: 308 HIGHP 312


>gi|254555966|ref|YP_003062383.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254044893|gb|ACT61686.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 293

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 66/190 (34%), Gaps = 28/190 (14%)

Query: 38  QRVKV-NGILLERAAVNVM---STDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPD 92
             + + +G +     + +        + V   P++       WL  +KP GL +     +
Sbjct: 47  GVITIHDGDIA---GIQLPDEAPDTAVVVSEQPIQIEYEDANWLVLNKPAGLTSVPGPSN 103

Query: 93  GRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS--TQWLR 143
              T+ + +            R   + RLD +T GL+L+        +L  P    Q ++
Sbjct: 104 RTDTLVNRIKGYLIASHASNQRPHLITRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVK 163

Query: 144 VYRVRFHGQVDQD----------KLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTVG 192
            Y+    G +               +  ++ +   G       QV  D  + + + + + 
Sbjct: 164 TYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAGQRAITTYQVEADQLQHNVSRLRLE 223

Query: 193 LREGKNREIK 202
           L  G+  +I+
Sbjct: 224 LVTGRTHQIR 233


>gi|254294409|ref|YP_003060432.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254042940|gb|ACT59735.1| pseudouridine synthase, RluA family [Hirschia baltica ATCC 49814]
          Length = 343

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 79/247 (31%), Gaps = 68/247 (27%)

Query: 15  RVSKVIARAGIASRR-------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           R+ + +       RR       +VE+++ +  V+V+G   +  +  +     + V     
Sbjct: 21  RLDRWLK------RRFPGLTQGQVEKLLRKGEVRVDGSRAKS-STRLEPGQVVRVPPMPS 73

Query: 63  --DGVPLRKAERTRL--------------------WLYHKPIGLVT-----THSDPDGRS 95
              G    + E                        ++ +KP GL       T    DG +
Sbjct: 74  TDQGKKHPQKEEEVYVSPRDAELIQSLILYEDEDVYVLNKPSGLAVQGGTKTLRHVDGMA 133

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
                      R+  V RLD +T GLL+L      A  +     S +  ++Y     G  
Sbjct: 134 NALTRPGQDKPRL--VHRLDKDTSGLLVLAKTAQSAAEMSKHFRSRELDKIYWAVVKGVP 191

Query: 154 DQD----------------KLNLLKKGIV-IQGICYGDMQVTLDTQKGSN-AWVTVGLRE 195
           + +                   L+  G+   +G  +      + +  G   +WV +    
Sbjct: 192 NPNEGELRGWMMKAHGPGQDKELMTAGVHGQKGAVFAITDFKVVSTAGQRASWVALKPST 251

Query: 196 GKNREIK 202
           G+  +++
Sbjct: 252 GRKHQLR 258


>gi|71275230|ref|ZP_00651517.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71899549|ref|ZP_00681705.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|170731225|ref|YP_001776658.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71164039|gb|EAO13754.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71730678|gb|EAO32753.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|167966018|gb|ACA13028.1| pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 330

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/289 (15%), Positives = 97/289 (33%), Gaps = 59/289 (20%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V    + QR+   + ++     R  + +++   +V+VNG  ++ A   +   D +    
Sbjct: 22  VVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVK-AERKLDGGDEVRLPP 80

Query: 62  ---VDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPS 103
              +    +                 E  RL   +KP G+ +          +    +  
Sbjct: 81  LRLIQDRAIVAPSAAFLARMEAAIVFEDARLLALNKPSGMASHGGSGVSYGVIEAMRILR 140

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPST-------QWLRVYRVRFHGQV 153
               +  V RLD +T GLL++          + L   ++          + Y     G++
Sbjct: 141 PKQELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRGIAKRYLTLLSGRM 200

Query: 154 DQDKLN-------LLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
               ++        L+ G      V         +  L  ++G  ++  V +  G+  +I
Sbjct: 201 PNGVMSVDAPLHINLRHGGERHVRVHHDGKPSKSRFRLLERRGGQSYCEVLIETGRTHQI 260

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +   +     V             G    G  +EV++K LR+Q+G   L
Sbjct: 261 RVHAQHLGHPVT------------GDDKYGD-QEVNRK-LRDQIGLQRL 295


>gi|327467897|gb|EGF13387.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK330]
          Length = 291

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G++    L           +  K+ +  +   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKLPAKNLIYKDKIGRDRHDRRKRLVDPRKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RLKQFGQAALVKCQLKTGRTHQIR 230


>gi|190570815|ref|YP_001975173.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|213019659|ref|ZP_03335464.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
 gi|190357087|emb|CAQ54492.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus Pel]
 gi|212994700|gb|EEB55343.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Culex quinquefasciatus JHB]
          Length = 307

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 59/175 (33%), Gaps = 42/175 (24%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHI------ 60
           R+ + I       RR         +E+ + +  +KV+    + +   V S   I      
Sbjct: 16  RLDRYI-------RRIFPNLKQSAIEKSLRKGLIKVDNCTAKSSD-RVSSGQTIMIRYLD 67

Query: 61  ---------EVDGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                    + +   +         E   +   +KP G++        + ++ D L  I 
Sbjct: 68  YIENTNSDCKYNEKLVNLLRENILYEDEYILAINKPAGVIVQGG-IKVKISISDLLDQIR 126

Query: 106 SR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
            R     V RLD +T G+++   +  +A+ L       +  + Y     G   +D
Sbjct: 127 EREIFKIVHRLDRDTSGVIIFARNASVAKYLMEEFKGRRIKKTYLALTFGIPSKD 181


>gi|126695551|ref|YP_001090437.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9301]
 gi|126542594|gb|ABO16836.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. MIT 9301]
          Length = 319

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 93/247 (37%), Gaps = 39/247 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            I+ E   P R+ + + ++    SR  ++  I    V VN    + A   + + D+I++ 
Sbjct: 18  EIIYELPLPMRLDRWLVSKRPEQSRARIQHFINSGLVLVNYKTAK-AKTPLKNGDNIQIW 76

Query: 64  ---GVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLP 102
                PL              E   + + +K  GL+   +  +   T+ +       +LP
Sbjct: 77  MPPPEPLIYLKPEKMDLNILFEDEHIIVINKQSGLIVHPAPGNKSGTLVNGLLFHCKDLP 136

Query: 103 SIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFH-------- 150
            I  ++    V RLD +T G +++         L+    +    R Y    H        
Sbjct: 137 GINGKLRPGIVHRLDKDTSGCMVVAKSQEALVNLQKQIKEKIASREYIAVIHGAPNSEEG 196

Query: 151 ---GQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
              G + +DKLN LK  +V +    Y      L+ + G+ + ++  L  G+  +I+    
Sbjct: 197 QIVGHIGRDKLNRLKYKVVEETSGRYARTYWKLEERFGNYSLMSFKLDTGRTHQIRVHCA 256

Query: 207 FFNWKVN 213
             N  + 
Sbjct: 257 HINHPIV 263


>gi|315924134|ref|ZP_07920360.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622536|gb|EFV02491.1| ribosomal large subunit pseudouridine synthase D [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 287

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 42/221 (19%), Positives = 86/221 (38%), Gaps = 42/221 (19%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGI---LLERAAVNVMSTDHIEV-------DGV 65
           + K+    G +SR  + R+I   R+ +NG    L++     V   D IEV       D  
Sbjct: 7   LQKI---QGYSSR-ILRRIIRDGRLMINGKDRWLVDD----VHRGDTIEVMLPRESVDVR 58

Query: 66  PLRK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRL 114
           P+R       E   +   +K  GLVT  +      T+ + +   F       +V  V RL
Sbjct: 59  PVRGIVDIIYEDDEILAVNKDAGLVTHPTKSHQLDTLGNLVAGYFESTGQYAKVRFVTRL 118

Query: 115 DINTEGLLLLTNDGGLARVLELPS--TQWLRVYRVRFHGQVDQDK------LNLLKKG-- 164
           D +T G++++  +  +   L+      +  + Y    +G  ++        +   + G  
Sbjct: 119 DSDTSGVIVIAKNKYIHHYLQSHQLIPKPEKRYLAFVNGCPEEMVGTIDLPIGRAEDGIH 178

Query: 165 --IVIQGICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIK 202
             ++ +G         ++T  +   + + + L  G+  +I+
Sbjct: 179 RCVMPEGKPSITHYRVVETFPEQKASAIALRLETGRTHQIR 219


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 83/246 (33%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G  +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVATPSITPQIVEGTRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AIKHPC 247


>gi|58336973|ref|YP_193558.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227903532|ref|ZP_04021337.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus ATCC 4796]
 gi|58254290|gb|AAV42527.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus NCFM]
 gi|227868419|gb|EEJ75840.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           acidophilus ATCC 4796]
          Length = 300

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 61/162 (37%), Gaps = 23/162 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVISVGRLDINTEGLLL 123
           E     L +KP  +++  S  +    + + L   F        +   + RLD +T GL+L
Sbjct: 85  ETKNYILVNKPANVLSIPSRYEDDDAIVNRLMGYFMEKKEKDLKPHVITRLDRDTSGLVL 144

Query: 124 LTNDGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGI 170
           +  +             ++++ Y    HG   +DKL  L            K+G+V+ G 
Sbjct: 145 VGKNSIAHARFSKIGKEKFIKKYHAIVHGNFAEDKLEGLIDQPIGKIDAGVKRGVVLNGK 204

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
                   LD   G+ + V + L  G+  +I+  +  +    
Sbjct: 205 SAQTEYRVLDQVSGA-SLVELRLLTGRTHQIRVHMM-YLGHP 244


>gi|28199848|ref|NP_780162.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182682599|ref|YP_001830759.1| RluA family pseudouridine synthase [Xylella fastidiosa M23]
 gi|28057969|gb|AAO29811.1| pseudouridylate synthase [Xylella fastidiosa Temecula1]
 gi|182632709|gb|ACB93485.1| pseudouridine synthase, RluA family [Xylella fastidiosa M23]
 gi|307578881|gb|ADN62850.1| pseudouridylate synthase [Xylella fastidiosa subsp. fastidiosa
           GB514]
          Length = 330

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/289 (15%), Positives = 98/289 (33%), Gaps = 59/289 (20%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V    + QR+   + ++     R  + +++   +V+VNG  ++ A   +   D +    
Sbjct: 22  VVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVK-AERKLDGGDEVRLPP 80

Query: 62  ---VDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPS 103
              +    +                 E  RL   +KP G+ +          +    +  
Sbjct: 81  LRLIQDRAIVAPSAAFLARMEAAIVFEDARLLALNKPSGMASHGGSGISYGVIEAMRILR 140

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGL---ARVLELPST-------QWLRVYRVRFHGQV 153
               +  V RLD +T GLL++     +    + L   ++          + Y     G++
Sbjct: 141 PKQELELVHRLDRDTSGLLIMAKKRAVLIELQALMREASVNGKEGRGIAKRYLTLLSGRM 200

Query: 154 DQDKLN-------LLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
               ++        L+ G      V         +  L  ++G  ++  V +  G+  +I
Sbjct: 201 PNGVMSVDAPLHINLRHGGERHVRVHHDGKPSKSRFRLLERRGGQSYCEVLIETGRTHQI 260

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +   +     V             G    G  +EV++K LR+Q+G   L
Sbjct: 261 RVHAQHLGHPVT------------GDDKYGD-QEVNRK-LRDQIGLQRL 295


>gi|238787243|ref|ZP_04631042.1| tRNA pseudouridine synthase C [Yersinia frederiksenii ATCC 33641]
 gi|238724505|gb|EEQ16146.1| tRNA pseudouridine synthase C [Yersinia frederiksenii ATCC 33641]
          Length = 257

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 53/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHG------QVDQDKLNLLKKGIVIQGICYGD----- 174
             +AR L L     Q  + Y     G       +D +    L K   I            
Sbjct: 67  SDVARALSLQFEQHQIQKTYHAVVRGYVLAGDTIDYEMTEELDK---IADKFSRPDKAPQ 123

Query: 175 ---------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                     +V +    G        L E     G+  ++++        + 
Sbjct: 124 PSVTHYQPLAKVEVPVAIGRYDTARFSLLELLPETGRKHQLRRHMAHIRHPII 176


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 84/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVVTPSITPQIVEGMRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AIKHPC 247


>gi|323697656|ref|ZP_08109568.1| pseudouridine synthase [Desulfovibrio sp. ND132]
 gi|323457588|gb|EGB13453.1| pseudouridine synthase [Desulfovibrio desulfuricans ND132]
          Length = 275

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 41/232 (17%), Positives = 75/232 (32%), Gaps = 40/232 (17%)

Query: 15  RVSKVIARAGIAS----RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------- 63
           R+ + +      S    RR   R+  + R+ V+G    +    V +   +EV        
Sbjct: 17  RLDRALEAVMPGSGLRLRR---RLCDEGRILVDGR-ARKPGYRVRTGQLVEVKEGREMTT 72

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--GRLDIN 117
               GV + K E       +KP G+ +          V   LP++F  +  V   RLD  
Sbjct: 73  PGELGVRIVKWEDG-FAAVNKPGGVHSAIISGRDEPCVEAVLPALFPGMEPVLLNRLDRL 131

Query: 118 TEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
           T GLLL+  T +   A +         + Y  R  G++D   +  ++  +         +
Sbjct: 132 TSGLLLVALTPEARDAYLEYEDQGAIKKFYLARVRGRLDG--IVSVRNRLDTDDRKTTRV 189

Query: 176 QVTLD--------------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               D                    + V   + +G   +I+         + 
Sbjct: 190 LAEPDEDARRWTGVTALSHDNAADTSLVRCLITKGARHQIRAHLASIGHPIV 241


>gi|212710403|ref|ZP_03318531.1| hypothetical protein PROVALCAL_01464 [Providencia alcalifaciens DSM
           30120]
 gi|212686985|gb|EEB46513.1| hypothetical protein PROVALCAL_01464 [Providencia alcalifaciens DSM
           30120]
          Length = 252

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 33/171 (19%), Positives = 52/171 (30%), Gaps = 29/171 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D + TVF        I   V  + RLD  T G+LL    
Sbjct: 7   QDEYVVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGD----- 174
             +AR+L       +  +VY     G V          L  L K I  +           
Sbjct: 67  SDVARLLAEQFEQHRMEKVYHAIVRGYVMDGDRLDYPLLEELDK-IADKNATKEPRLQEC 125

Query: 175 -------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                    V      G        L E     G+  ++++        + 
Sbjct: 126 VTHYKPLATVECSVAIGRYDTARFSLVELKPETGRKHQLRRHMSHLRHPII 176


>gi|261493572|ref|ZP_05990092.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261310754|gb|EEY11937.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 242

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 30/165 (18%), Positives = 51/165 (30%), Gaps = 26/165 (15%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL   +   A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETVFAMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSETA 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGD------ 174
           RV+       Q  + Y     G +             L+ +      +            
Sbjct: 72  RVMSEQFEQHQVQKTYLAVVRGYLQGSAQIDYPLTVILDKIADKFSQEKEAQAAITDYKG 131

Query: 175 -MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
              V +    G +      L E     G+  ++++  +     + 
Sbjct: 132 LATVEMPYAVGKHQTARYSLVELSPKTGRKHQLRRHLKHLFHPIM 176


>gi|189466071|ref|ZP_03014856.1| hypothetical protein BACINT_02441 [Bacteroides intestinalis DSM
           17393]
 gi|189434335|gb|EDV03320.1| hypothetical protein BACINT_02441 [Bacteroides intestinalis DSM
           17393]
          Length = 303

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 41/227 (18%), Positives = 81/227 (35%), Gaps = 42/227 (18%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNVM-STDHI--E 61
            P  + + +A +   ASR +++ +++++ V V+ ++        +  + V  S D    E
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDSVITTQYNFPLKPGMKVQISRDKGKKE 80

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGR 113
                L+   E   + +  K  GL++  S+     T +  L     R       V  V R
Sbjct: 81  FHNKLLKIVYEDAYIIVVEKMQGLLSVSSERQKERTAYHILNEYVQRSNGRGSNVYIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVI---- 167
           LD +T GL++   D    R L     +    R Y     G+++++       G +I    
Sbjct: 141 LDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVAGEMEKNA------GCIISWLT 194

Query: 168 ------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        G            +    + V + L  G+  +I+
Sbjct: 195 DRTLYVYSSPTDDGGQKSITHYRTIKRANGYSLVELNLETGRKNQIR 241


>gi|123443491|ref|YP_001007464.1| tRNA pseudouridine synthase C [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090452|emb|CAL13320.1| Conserved hypothetical protein [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 257

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/173 (19%), Positives = 53/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRF------HGQVDQDKLNLLKKGIVIQGICYGD----- 174
             +AR L L     Q  + Y           G +D +    L K   I            
Sbjct: 67  SDVARALSLQFEQHQIQKTYHAVVRGYVLEDGTIDYEMTEELDK---IADKFARPDKAPQ 123

Query: 175 ---------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                     QV +    G        L +     G+  ++++        + 
Sbjct: 124 PSVTHYQALAQVEVPIAIGRYDTSRFSLMQLKPETGRKHQLRRHMAHIRHPII 176


>gi|71899934|ref|ZP_00682081.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|71730297|gb|EAO32381.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
          Length = 330

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/289 (15%), Positives = 97/289 (33%), Gaps = 59/289 (20%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V    + QR+   + ++     R  + +++   +V+VNG  ++ A   +   D +    
Sbjct: 22  VVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVK-AERKLDGGDEVRLPP 80

Query: 62  ---VDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPS 103
              +    +                 E  RL   +KP G+ +          +    +  
Sbjct: 81  LRLIQDRAIVAPSAAFLARMEAAIVFEDARLLALNKPSGMASHGGSGISYGVIEAMRILR 140

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPST-------QWLRVYRVRFHGQV 153
               +  V RLD +T GLL++          + L   ++          + Y     G++
Sbjct: 141 PKQELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRGIAKRYLTLLSGRM 200

Query: 154 DQDKLN-------LLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
               ++        L+ G      V         +  L  ++G  ++  V +  G+  +I
Sbjct: 201 PNGVMSVDAPLHINLRHGGERHVRVHHDGKPSKSRFRLLERRGGQSYCEVLIETGRTHQI 260

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +   +     V             G    G  +EV++K LR+Q+G   L
Sbjct: 261 RVHAQHLGHPVT------------GDDKYGD-QEVNRK-LRDQIGLQRL 295


>gi|258543199|ref|YP_003188632.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256634277|dbj|BAI00253.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637337|dbj|BAI03306.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640389|dbj|BAI06351.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643446|dbj|BAI09401.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646501|dbj|BAI12449.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649554|dbj|BAI15495.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652540|dbj|BAI18474.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655598|dbj|BAI21525.1| ribosomal RNA large subunit 23S rRNA pseudouridine synthase D
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 337

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 84/257 (32%), Gaps = 46/257 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V      +R+ + +A A +   SR  ++ +I +  +  +G+ +   A    +   + + 
Sbjct: 22  TVTPEQAGERIDRFLA-ATMETLSRSRIKSLIEEGHLACDGVCIREPAAIARAGMEVVLT 80

Query: 63  ---------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                     G  +      E   L +  KP GLV   +  +   T+ + L +       
Sbjct: 81  IPPAAPAVPQGEDISFTVLYEDDDLIVLDKPAGLVVHPAPGNETGTLVNGLIAHCGESLK 140

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRF-------- 149
                 R   V RLD +T G+++      +A           +  R Y            
Sbjct: 141 GIGGERRPGIVHRLDKDTSGVMVAA-KTEMAHQALSEDFAARRIDRAYLAFCWGLPNPAE 199

Query: 150 ---HGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
               G + +DK +  +  +  +G  +      TL       A V   L  G+  +I+  F
Sbjct: 200 GDFEGAIGRDKRDRKRMALTPKGGKWALTHYRTLQAFGTGAALVACKLATGRTHQIRVHF 259

Query: 206 EFFNWKV----NRLIRI 218
                 +      L RI
Sbjct: 260 SANGHPLIGDPLYLRRI 276


>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 (153), Expect = 6e-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|208434657|ref|YP_002266323.1| pseudo uridine synthase D [Helicobacter pylori G27]
 gi|208432586|gb|ACI27457.1| pseudo uridine synthase D [Helicobacter pylori G27]
          Length = 333

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 51/308 (16%), Positives = 102/308 (33%), Gaps = 53/308 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + + +    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 19  RIDEFLTKELQISKNQVLNLIKEGLVFCQKKEVKKGGLALKEGDEITLLTPKITQKPLKR 78

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L           +  R   V
Sbjct: 79  GLDLEIEVIFEDEDLLVLNKPPNLVVHKAPSVKEPTLVDWLEFKNYELSNLGLKERYGIV 138

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDK------------ 157
            RLD +T G +++  +      L   L +    R Y       + ++K            
Sbjct: 139 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKTMGRYYIALLSTPLKEEKMSVECYLTRNPN 198

Query: 158 ----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +  LK     +        ++L T + +   +   L  G+  +I+           
Sbjct: 199 NRLKIIALKAAKKEKSRYSKSEFISLLTSQNNLNLIGAKLFTGRTHQIR---AHL----E 251

Query: 214 RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
            L R   G   L  L       + K+ +R  L  +L+E      +  +     L++D   
Sbjct: 252 YLNRHIMGD-NLYGLNQ----ALPKEEIRIMLHAYLIEFKHPRSEQKLRFKVPLLKDMLE 306

Query: 274 IISEVPDD 281
            + +V D 
Sbjct: 307 YLKKVFDK 314


>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 = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 79/243 (32%), Gaps = 48/243 (19%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DG 64
           P R+ K +       SR  ++R   Q+ + VNG  ++  +  V   D I +       D 
Sbjct: 44  PMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKS-SYKVKPLDEIVILLDRPKYDN 102

Query: 65  VPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSR 107
             + +        E   L +  KP GLV      +   T+ +          +       
Sbjct: 103 EIIAEDIPLDIVYEDEDLMVVDKPAGLVVHPGCGNYTGTLVNAIAWHLKDNPDYDPNDPT 162

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-------- 157
           V  V R+D +T GLL++  +      L     +    R+Y     G   +++        
Sbjct: 163 VGLVHRIDKDTSGLLVVAKNADAKTHLGKQFFNKTTKRLYNALVWGNFQEEEGRIEGNIA 222

Query: 158 ---LNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLRE-----GKNREIKKVFEFF 208
               + ++  +       G   VT     +  N    V L E     G+  +I+   +  
Sbjct: 223 RHPKDRMQMAVFPPDSEIGKHAVTHYRVLENFNY---VTLVECRLETGRTHQIRAHMKHI 279

Query: 209 NWK 211
              
Sbjct: 280 GHP 282


>gi|330993274|ref|ZP_08317210.1| Ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           sp. SXCC-1]
 gi|329759676|gb|EGG76184.1| Ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           sp. SXCC-1]
          Length = 323

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 85/261 (32%), Gaps = 53/261 (20%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNV---------- 54
           I   +   QR  + IA A G  SR  V+ ++    +  NG  L   A  V          
Sbjct: 11  IATADDAGQRTDRFIATATGALSRSRVKALMESGHLLRNGSPLRDPAEPVRAGMCYEIHL 70

Query: 55  -------MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
                       I +D       E   L +  KP G+V   +  +   T+ + L +    
Sbjct: 71  PPAIPATPQGQDIALD----ILYEDRDLIVLDKPAGMVVHPAPGNEDGTLVNALLAHCGE 126

Query: 106 --------SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRF------ 149
                    R   V RLD +T G+++   T     A  L     +  R Y+         
Sbjct: 127 SLTGIGGEKRPGIVHRLDKDTSGIMVAAKTELAHQALSLAFAERRIDRAYQAICWGLPVP 186

Query: 150 -----HGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
                 G + +D+ +  +  ++  G     +     ++T  G  A V   L  G+  +I+
Sbjct: 187 AQGSFDGAIGRDRRDRKRMAVIANGGGKQALTHYRVIETFHGGLAHVECRLATGRTHQIR 246

Query: 203 KVFEF-----FNWKVNRLIRI 218
             F           V  L RI
Sbjct: 247 VHFAHAGHALVGDPV-YLRRI 266


>gi|327183169|gb|AEA31616.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1118]
          Length = 301

 Score = 63.3 bits (153), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 70/209 (33%), Gaps = 36/209 (17%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKA-ERTRLWLYHKPI 82
              + VN       + ++ + D +                  P+    E     + +KP 
Sbjct: 38  NGLILVNHKR-RYTSFHLKTNDEVIFVTGEEKKNDFLKPSNNPVEPVLETKNYIILNKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLE 135
           G+++  S  +    + + L   F+R          + RLD +T GL+L+  +        
Sbjct: 97  GVLSIPSRYEDNDAIVNRLMGYFTRKGAKDLKPHVITRLDRDTSGLVLVGKNAVAHARFS 156

Query: 136 LPSTQ-WLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLDTQ 182
               + +++ Y    HG  +  +L  L            K+G++  G      +  +  Q
Sbjct: 157 KIGKERFIKKYHAIVHGNFESTELTGLIDEPIGKIDSGVKRGVIPDGKSAQT-EYKVLKQ 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               + V + L  G+  +I+    +    
Sbjct: 216 VPGASLVELRLLTGRTHQIRVHMAYLGHP 244


>gi|303251277|ref|ZP_07337455.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307252489|ref|ZP_07534385.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649819|gb|EFL79997.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306860081|gb|EFM92098.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 247

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 39/203 (19%), Positives = 69/203 (33%), Gaps = 41/203 (20%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  V RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSGVLLFALNSKMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLN-LLKKGIVIQGICYGD------------ 174
             L        Q  + Y     G  +D+ +++  LK  +++  I                
Sbjct: 72  -RLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYQLK--VILDKIADKFSQPKEAQQAVTF 128

Query: 175 ----MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 V +    G +      L E     G+  ++++  +     +        G  + 
Sbjct: 129 YQNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------MGDTKY 181

Query: 226 GTLLAGSTREVSKKILREQLGPH 248
           G L     R +++K   ++L  H
Sbjct: 182 GDLH--QNRTLTEKTGCDRLMLH 202


>gi|42526895|ref|NP_971993.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41817210|gb|AAS11904.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 305

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 85/238 (35%), Gaps = 49/238 (20%)

Query: 1   MKDKN---IVQENFTPQRVS----KVIARA---GIASRREVERMIAQQRVKVNGILLERA 50
           M  +N    + E+ + +R+     K + +    G+ S       I + +++VNG   E  
Sbjct: 1   MSKENKIFYIGEDDSGRRLDRVIRKFLGKMPLSGVYS------AIRRGKIRVNGKK-ENG 53

Query: 51  AVNVMSTDHIEVD----GVPLRKAERTRLWLYHKPIGLVTTHSD-----------PDGRS 95
           A      D I +D    G+    +E    +   KP  ++    D             G  
Sbjct: 54  AYLTQKGDEISMDLSLFGLTAPASEDQTNYSISKP-DVLLKTDDLLFINKRSGELVHGEK 112

Query: 96  TVFDNLPSIFS--------RVISVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVY 145
           ++ + +   F         +V ++ RLD +T G+L  +    G       L   +  + Y
Sbjct: 113 SLCEAVLKYFPSKEKSLSFKVGALHRLDKDTSGILAFSQSLKGAQGFSRALQEGKIGKFY 172

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
                G+     L+  K   +I G     +   LD  K  N + V   L  G+  +I+
Sbjct: 173 IGITEGRPS---LSEFKS--IIDGKECLCLIRILDFSKEENLSLVLFNLITGRKHQIR 225


>gi|325473944|gb|EGC77132.1| RNA pseudouridylate synthase [Treponema denticola F0402]
          Length = 264

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 85/238 (35%), Gaps = 49/238 (20%)

Query: 1   MKDKN---IVQENFTPQRVS----KVIARA---GIASRREVERMIAQQRVKVNGILLERA 50
           M  +N    + E+ + +R+     K + +    G+ S       I + +++VNG   E  
Sbjct: 1   MSKENKIFYIGEDDSGRRLDRVIRKFLGKMPLSGVYS------AIRRGKIRVNGKK-ENG 53

Query: 51  AVNVMSTDHIEVD----GVPLRKAERTRLWLYHKPIGLVTTHSD-----------PDGRS 95
           A      D I +D    G+    +E    +   KP  ++    D             G  
Sbjct: 54  AYLTQKGDEISMDLSLFGLTAPASEDQTNYSISKP-DVLLKTDDLLFINKRSGELVHGEK 112

Query: 96  TVFDNLPSIFS--------RVISVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVY 145
           ++ + +   F         +V ++ RLD +T G+L  +    G       L   +  + Y
Sbjct: 113 SLCEAVLKYFPSKEKSLSFKVGALHRLDKDTSGILAFSQSLKGAQGFSRALQEGKIGKFY 172

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
                G+     L+  K   +I G     +   LD  K  N + V   L  G+  +I+
Sbjct: 173 IGITEGRPS---LSEFKS--IIDGKECLCLIRILDFSKEENLSLVLFNLITGRKHQIR 225


>gi|315639323|ref|ZP_07894485.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315480649|gb|EFU71291.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 308

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 56/139 (40%), Gaps = 15/139 (10%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  NG L+++    +     + V      GV +   E     +  KP G+
Sbjct: 32  EAQKLIDKKRLFCNGNLVKKKNEILQGVVELIVYENAPKGVKIVY-ENEEFAVLEKPSGV 90

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLL--TNDGGLARVLELPS 138
           ++    P+GR   +     I+         V RLD  T GL+L+  T +  +        
Sbjct: 91  LS---HPNGRHCAYSLCDEIWELWGMEACVVHRLDKETSGLILVAKTKNSQVEFKTMFEK 147

Query: 139 TQWLRVYRVRFHGQVDQDK 157
            +  + Y     G + ++ 
Sbjct: 148 REIQKEYLALTQGLIKEEF 166


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 92/246 (37%), Gaps = 55/246 (22%)

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-------LRKAERTR-----------LWLYHKPIGLVTTHSDP 91
            +   D ++V    G         L   E              + L++K   +V  H   
Sbjct: 51  RLQDGDIVKVFYMGGETAVKKFIDLSPKETEYIKKGIVYEDEDVLLFNKSPNMV-MHKGS 109

Query: 92  DGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
                + + L S + R     + R+D  T GL++   +  + R L          + Y +
Sbjct: 110 GHDYGLSEMLKSYYQREDFTFINRIDKATSGLIIGAKNLPMTRKLSEDMRDGNINKRYYI 169

Query: 148 RFHGQVDQDKLNL---LKK----GIVIQGICYGDMQ----VTLDTQKGSNAWVTVGLREG 196
              G+VD+++  +   LKK     + ++    G  +      +  +  +   +   L  G
Sbjct: 170 LVEGRVDREEFQIKSYLKKTDTHVVELEKYEKGAKESISYFKVVQRGKNRTILEGTLGTG 229

Query: 197 KNREIK 202
           +  +++
Sbjct: 230 RTHQLR 235


>gi|257468836|ref|ZP_05632930.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           ulcerans ATCC 49185]
          Length = 342

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 78/235 (33%), Gaps = 44/235 (18%)

Query: 8   QENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            EN   +R+   +    +   A+R  ++++I    V++ G  + ++   +  T+ I V+ 
Sbjct: 42  DENDKGKRIDSFLNE--VIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTETITVNI 99

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +PL    E   + + +K   +V   +  +   T+ + L          
Sbjct: 100 PEDEILDVIPENIPLNIIYEDKDIVVINKAPDMVVHPAHGNYNGTLVNALLYHIKDLSTI 159

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD---- 156
               R   V RLD +T G++++  +      L          + Y     G         
Sbjct: 160 NGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFKEKTLEKTYICIAKGIFKDKSGRI 219

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        +   + I G         LD +K   + V V +  G+  +I+
Sbjct: 220 ETLIGRDSRDRKKMAV-VDINGKNAISNYEILDEEKNF-SLVKVRIETGRTHQIR 272


>gi|91792903|ref|YP_562554.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91714905|gb|ABE54831.1| tRNA pseudouridine synthase C [Shewanella denitrificans OS217]
          Length = 298

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 48/166 (28%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
           +   HKP GL+   S      R         +    V  V RLD  T G+LL      +A
Sbjct: 61  IVAIHKPAGLLVHRSYLARKERFFAMQLTRDLIGCHVFPVHRLDRPTSGVLLFAKSSEVA 120

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW- 188
           R L       +  + Y     G + +  L      + +  +     +     Q+   ++ 
Sbjct: 121 RNLCEQFAEHKIKKDYLALVRGNMHEAGLLDYPLRVELDDVADKHAKADKPAQEAQTSYQ 180

Query: 189 ---------------------VTVGLREGKNREIKKVFEFFNWKVN 213
                                + +    G+  ++++        + 
Sbjct: 181 PLLNSEIPFSSGRYPTSRFALIKLSPHTGRKHQLRRHMAHLRHPIL 226


>gi|91775965|ref|YP_545721.1| ribosomal large subunit pseudouridine synthase D [Methylobacillus
           flagellatus KT]
 gi|91709952|gb|ABE49880.1| ribosomal large subunit pseudouridine synthase D [Methylobacillus
           flagellatus KT]
          Length = 356

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 33/171 (19%), Positives = 63/171 (36%), Gaps = 24/171 (14%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            + +     R+ + + R     SR  ++  I    V ++      A   V   + +++  
Sbjct: 11  TITQELGGMRLDQALQRLMPEHSRSRIQGWIKDGLVTIDDETPT-AKFKVWGGEQVQIKP 69

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                      + +PL    E   + + +KP G+V   +  +   T+ + L     ++  
Sbjct: 70  QATPEALAFEPENIPLEVVFEDEHILVINKPAGMVVHPAAGNWSGTLLNALLYHAPQLKD 129

Query: 110 -----SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                 V RLD +T GLL++         L  +L +    R YR    GQV
Sbjct: 130 VPRAGIVHRLDKDTSGLLVVAKTLAAQTNLVRQLQARTVKREYRTIVWGQV 180


>gi|326803815|ref|YP_004321633.1| pseudouridine synthase, RluA family [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651014|gb|AEA01197.1| pseudouridine synthase, RluA family [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 300

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 75/228 (32%), Gaps = 37/228 (16%)

Query: 19  VIARAGIASRREVERMIA--QQRVKVNGILL-----ERAAVNVM-------STDHIEVDG 64
            + + G+ SRR++ + I      + VN   +           V        S D I    
Sbjct: 17  FLRQKGV-SRRQLAK-IKYHGGTIIVNNKRVGSKYFLSLGDQVTIIYPAEGSQDQIMAVD 74

Query: 65  VPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDI 116
            PL    E     + +KP G  +  S      ++ + + + F R       +  V RLD 
Sbjct: 75  FPLDILYEDRDYLIVNKPAGYTSIPSQFKDEYSMANFVKAYFVRKNYENQVIHVVTRLDR 134

Query: 117 NTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---LNL---LKKGIVIQ 168
            T G ++          +   + S    + Y    H  +  D+   +      K+G +I+
Sbjct: 135 FTSGAMIFAKHKYAHSQIDQLMQSGGINKQYLAFTHSAIGSDQHGLIEAPIGRKEGSIIE 194

Query: 169 -----GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   +   +  L+  +       V L  G+  +I+  F +    
Sbjct: 195 RCIRADGQHAKTEYWLEDSQAGLYRYRVQLHTGRTHQIRVHFAYLGAP 242


>gi|297194901|ref|ZP_06912299.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|297152522|gb|EFH31815.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           pristinaespiralis ATCC 25486]
          Length = 313

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 87/251 (34%), Gaps = 48/251 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   I+R    SR +   + A  +V+V+G ++ +       A + V     
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVQVDGSVVGKSERVHGGAWLEVEMPQA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  PAPVQIVAEPVEGMEIVHDDDDIVVIV-KPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKL 158
                   V RLD+ T GL+++        +L+    +    + Y     G  D     +
Sbjct: 131 GASERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQFRERVVDKRYHALVQGHPDPLSGTI 190

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSN-------------AWVTVGLREGKNREIK-KV 204
           +       I      D +  +  +   +             + + + L  G+  +I+  +
Sbjct: 191 DA-----PIGRHPTADYKWAVTAEGKPSVTHYDLIEAFRAASLLDIKLETGRTHQIRVHM 245

Query: 205 FEFFNWKVNRL 215
               +  V  L
Sbjct: 246 AAHRHPCVGDL 256


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 82/246 (33%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V +    +R+ KV+AR     SR  ++  I  +RV+++G   +     V     IE+  
Sbjct: 69  VVPDELAGERLDKVLARVFPEFSRNRLQSWIEAERVRIDGKPAK-IRQPVPLGATIELVP 127

Query: 65  VPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
             L +               E   L + +KP G+V   +  +   T+ + L   +     
Sbjct: 128 DLLPEQLAFTPEPVPLAIVYEDDTLVVINKPAGMVVHPAAGNWSGTLLNGLLYRYGDAAA 187

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD  T GL+++         L  +L +    R Y     G + ++     
Sbjct: 188 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPEEGTIDA 247

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVT-----------VG-LR---E-GKNREIKKVF 205
             G   +        VT  + K +                V  +    E G+  +I+   
Sbjct: 248 PIGRDPR-ERTRMAVVTSASGKPARTHFRRVDSAIWERQPVTAIHCDLETGRTHQIRVHC 306

Query: 206 EFFNWK 211
                 
Sbjct: 307 AHIGHP 312


>gi|294678331|ref|YP_003578946.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           capsulatus SB 1003]
 gi|294477151|gb|ADE86539.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           capsulatus SB 1003]
          Length = 347

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 38/186 (20%), Positives = 64/186 (34%), Gaps = 32/186 (17%)

Query: 14  QRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVD---- 63
           +R+ K +A         SR  + R+IA+  V  +G+ +      V   +   I V+    
Sbjct: 19  ERLDKALAALVPEEAALSRSRLARLIAEGAVTRDGVAITDQKAKVAPGEVYMIAVEPPRA 78

Query: 64  ------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------S 106
                  +PL    E   L +  KP G+V   +      T+ + L   F          +
Sbjct: 79  VETLAQDIPLTVLWEDEDLIVIDKPAGMVVHPAPGSEDGTLVNALLHHFGGRLSGIGGEA 138

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLK-- 162
           R   V R+D  T GLL++         L     +    R Y     G         L+  
Sbjct: 139 RPGIVHRIDKETSGLLVVAKSDRAHHGLAAQFEKHTVHRHYTALVQGVPSAAD-PRLRGI 197

Query: 163 KGIVIQ 168
           +G+  +
Sbjct: 198 RGVNFE 203


>gi|332645402|gb|AEE78923.1| RNA pseudourine synthase 5 [Arabidopsis thaliana]
          Length = 416

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 33/219 (15%), Positives = 70/219 (31%), Gaps = 56/219 (25%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIGLVTTHS 89
           ++++G +++     + S   +    +P ++ +             L   +KP GL     
Sbjct: 91  IQIDGEVVKDPNTLLRSGSKLVYSRLPWKEPDTPYSLEVLYEDDDLIALNKPSGLQVLPG 150

Query: 90  DPDGRSTVFDNLPSIF------------SRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
               + TV   L   F               + V RL   T G+LL          L   
Sbjct: 151 GLFQQRTVLTQLQWCFGKNDSYIGSRESPHPVPVHRLGRGTSGILLCAKTKLAKTKLAAY 210

Query: 136 -----------------LPSTQWLRVYRVRFHGQVDQDK--LNL---------LKKGIVI 167
                                +  ++YR    G V++D+  +           + +G+ +
Sbjct: 211 FAEGTSLVGSGNLDQECGTGRKLSKIYRALADGIVEEDEVVIKQPIGVVRYPGVAQGLYV 270

Query: 168 ---QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
              +G         L+  +  N + V V ++ G+  +I+
Sbjct: 271 ASPEGKPAFSKVFVLERDREKNCSLVKVEIQSGRPHQIR 309


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 33/215 (15%), Positives = 74/215 (34%), Gaps = 29/215 (13%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----------AERTRLWL 77
           R  ++  +A+ +V VNGI        +     + +    +             E   + +
Sbjct: 30  RNSIKSALARGQVSVNGIPRTVHNFPLEQGQTVALSKEKVAPVVPLTGLRILHEDEAIIV 89

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            HK  GL++  S  +   T +  L         ++R+  + RLD +T G+++      + 
Sbjct: 90  IHKDAGLLSVASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSGVMMFAKSEAIQ 149

Query: 132 RVLELPSTQW--LRVYRVRFHGQVDQDKLNL---LKKGIVIQ--------GICYGDMQVT 178
           + ++    +    R Y     GQV ++   +   LK+   ++           +      
Sbjct: 150 QEMQQAWKEVVYERTYIALVEGQVKKETGTITSWLKESKTLKMYSSPYPNDGQHAVTHYK 209

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   + + V L  G+  +I+   E     + 
Sbjct: 210 RLQANRHFSLLEVRLETGRKNQIRVHMEDIGHPIV 244


>gi|311693912|gb|ADP96785.1| tRNA pseudouridine synthase C [marine bacterium HP15]
          Length = 247

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 31/172 (18%), Positives = 58/172 (33%), Gaps = 34/172 (19%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLLLLTND 127
              L   HKP GL+   S  D   T F        +    V  V RLD  T G+L+   D
Sbjct: 11  DEHLLAVHKPAGLLVHRSPIDKHETEFALQYARALNGGQHVYPVHRLDRPTSGVLVFARD 70

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYG---------- 173
              AR L   L + +  + Y     G   +  +  + L++    +               
Sbjct: 71  SDTARTLGMALMAGEVTKTYLAMVRGWPPEHGEIDHPLRE--EPEDRRLKGEEQPVRDAL 128

Query: 174 -------DMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                    ++ ++ +K  ++   V   E     G+  ++++  +  N  + 
Sbjct: 129 TYYRTLTTTEIPVEIEKYPSSRYAVV--ELNPKTGRKHQLRRHMKHINHPII 178


>gi|259502474|ref|ZP_05745376.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
 gi|259169617|gb|EEW54112.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           antri DSM 16041]
          Length = 289

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 38/226 (16%), Positives = 79/226 (34%), Gaps = 41/226 (18%)

Query: 13  PQRVSKVIARAGIASR--REVERMIAQQRVKVNGILLERAAVNVMSTD------------ 58
           P ++ K +   G+  R   E+++   Q +  V+  ++      ++               
Sbjct: 12  PVKIKKFLQSLGMGHRLFNEIKK--GQGQFLVDHRVVR-PTTQILPNQPLTIKVAPEPAD 68

Query: 59  -HIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVI 109
             + V   PL+   E     +  KP G+ +         TV + +            R  
Sbjct: 69  PTVAVSHEPLKVVYEDDSWLVIDKPAGVTSVPGPSITNGTVLNRVKGHLEKQGSEDLRPH 128

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRF-------HGQVDQDKLNL 160
            + RLD  T GLLL+      + ++       + L+ Y           HG +DQ  +  
Sbjct: 129 LITRLDRFTSGLLLVAKHHVASSMISQQVQQHRMLKEYTAVVSGRFADGHGIIDQPIVR- 187

Query: 161 LKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            ++G    I+         +  ++ Q+   A + + L  G+  +I+
Sbjct: 188 -REGQAARIIAPDGQQAVTEYWVEDQEPDWARLRLQLHTGRTHQIR 232


>gi|224539550|ref|ZP_03680089.1| hypothetical protein BACCELL_04455 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224518831|gb|EEF87936.1| hypothetical protein BACCELL_04455 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 303

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 42/227 (18%), Positives = 81/227 (35%), Gaps = 42/227 (18%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNVM-STDHI--E 61
            P  + + +A +   ASR +++ +++++ V V+ ++        +  + V  S D    E
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDSVITTQYNFPLKPGMKVQISRDKGKKE 80

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGR 113
                L+   E   + +  K  GL++  S+     T +  L     R       V  V R
Sbjct: 81  FHNNLLKIVYEDAYIIVVEKMQGLLSVSSERQKERTAYHILNEYVQRSNGRGSNVYIVHR 140

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVI---- 167
           LD +T GL++   D    R L     +    R Y     G+++++       G VI    
Sbjct: 141 LDRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVTGEMEKNA------GCVISWLT 194

Query: 168 ------------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        G            +    + V + L  G+  +I+
Sbjct: 195 DRTLYVYSSPTDDGGQKAITHYRTIKRANGYSLVELDLETGRKNQIR 241


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 36/229 (15%), Positives = 64/229 (27%), Gaps = 35/229 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           +R+ + IA  G  SR    R I    V V+G   + A   +     + V+          
Sbjct: 15  ERIDRFIAARGGISRGLARRAIEAGGVFVDGRRCKVAGRTLTPGQQVVVNLEEGGRAASA 74

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
               G          L    KP G+    +    R  + + + ++  + V  V RLD  T
Sbjct: 75  PAALGRERLLYADADLCAVDKPAGVPAQPTLTTDRGALPELVSALLGAPVTLVHRLDRET 134

Query: 119 EGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDM 175
            G+ +       A  L     +    + Y           +    L  G   +      +
Sbjct: 135 SGVTVFARTREAAAALAEAFRTGAPEKTYLALCARAPSPAEGRVALALG---KDPARPGL 191

Query: 176 QVTLDTQKGSNAWVTVGLRE-------------GKNREIKKVFEFFNWK 211
           +        +       LRE             G+  +I+         
Sbjct: 192 RRVDPAGDPAATRYR-TLREAPGGAQVEARPETGRTHQIRVHLAALGAP 239


>gi|302546161|ref|ZP_07298503.1| RluA family RNA pseudouridine synthase [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463779|gb|EFL26872.1| RluA family RNA pseudouridine synthase [Streptomyces himastatinicus
           ATCC 53653]
          Length = 313

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 42/257 (16%), Positives = 82/257 (31%), Gaps = 60/257 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVN------------- 53
           V +    +RV   IAR    SR +   + A  +V+V+G +  ++                
Sbjct: 12  VPDGLEGERVDAAIARMFGFSRTKAAELAAAGKVQVDGSVAGKSDRVSGGAWLEVEMPQA 71

Query: 54  VMSTDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                 +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  AAPVQIVAEPVEGMEIVHDDDDIVVIA-KPVGVAAHPSPGWSGTTVIGGLAAAGFRIATS 130

Query: 109 ------ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V RLD+ T GL+++        +L+         + Y     G  D      
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQFRERTVEKRYHALVQGHPDP----- 185

Query: 161 LKKGIVIQGICYGDM----------QVTLDTQKGSN-----------AWVTVGLREGKNR 199
                 + G     +           VT D +               + + + L  G+  
Sbjct: 186 ------LSGTIDAPIGRHPQHDYKWAVTADGKPSVTHYDLIEAFRAASLLDIKLETGRTH 239

Query: 200 EIK-KVFEFFNWKVNRL 215
           +I+  +    +  V  L
Sbjct: 240 QIRVHMSAHRHPCVGDL 256


>gi|302206504|gb|ADL10846.1| Ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudotuberculosis C231]
 gi|308276746|gb|ADO26645.1| Ribosomal large subunit pseudouridine synthase D [Corynebacterium
           pseudotuberculosis I19]
          Length = 307

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 75/232 (32%), Gaps = 38/232 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVN----GIL----------LERAAV 52
           V E     RV   +++    SR     +     V V+    G            +     
Sbjct: 9   VPEGLAGMRVDAALSKLLGISRTVAADLATAGDVLVDALPVGKSDRIAEGQWLDVTLPET 68

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             ++     V+G+ +  ++   L   +KP+G+    +      TV   L +   R+ + G
Sbjct: 69  KDLTPREELVEGMDILYSDDD-LIAVNKPVGVAAHPTLGWEGPTVIGGLAAAGFRISTSG 127

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG---------- 151
                    RLD+ T G++++        VL+    +    + Y     G          
Sbjct: 128 PPERKGIVQRLDVGTSGVMVIAASERGYSVLKRAFKERTVSKTYHALVQGHTDPFTGTID 187

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             + +      +  +   G        TL+    + + + + L  G+  +I+
Sbjct: 188 APIGRHPSAGWRFAVTSDGKHAVTHYETLEAFAEA-SLLKIHLETGRTHQIR 238


>gi|320011298|gb|ADW06148.1| pseudouridine synthase, RluA family [Streptomyces flavogriseus ATCC
           33331]
          Length = 313

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 86/248 (34%), Gaps = 42/248 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   I+R    SR +   + A  +V+V+G +  +       A + V     
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVQVDGAVAGKSERVHGGAWMEVEMPQA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  PAPVQIVAEPVEGMEIVHDDDDIVVIM-KPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVD----- 154
                   V RLD+ T GL+++      A  L     +     + Y     G  D     
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKS-ERAYTLLKAQFRDRVVEKKYHALVQGHPDPMSGT 189

Query: 155 -QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF 207
               +    +      +  +G         ++  + + + + + L  G+  +I+  +   
Sbjct: 190 IDAPIGRHPQHDYKWAVTAEGKPSVTHYDLIEAYRAA-SLLDIKLETGRTHQIRVHMSAH 248

Query: 208 FNWKVNRL 215
            +  V  L
Sbjct: 249 RHPCVGDL 256


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 84/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVATPSITPRIVEGMRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AIKHPC 247


>gi|171913853|ref|ZP_02929323.1| pseudouridine synthase, RluA family protein [Verrucomicrobium
           spinosum DSM 4136]
          Length = 303

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 74/252 (29%), Gaps = 45/252 (17%)

Query: 3   DKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           D  + +     QR+   +       SR  ++ +I    + +NG   +     +   D I 
Sbjct: 2   DFTVNESAPAKQRLDHYLQGELPDMSRTRLQGLIKDGHILLNGKAAK-PNTPLKQGDRIT 60

Query: 62  VD------------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           ++             +PL    E   + + +KP GLV   +  +   T+ + L      +
Sbjct: 61  MEVPDPVPTEVVPQDIPLNVLFEDEHIIVINKPDGLVVHPAAGNPDGTLVNALLFHCKNL 120

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--- 154
             +G         RLD  T G ++          L          ++Y    +G      
Sbjct: 121 SGIGGELRPGIVHRLDKETSGCMVAAKHDLAHTRLTEAFSQRDLTKIYLAAVNGTPSSSS 180

Query: 155 ----------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
                           +    ++ G    +     D        A +   L  G+  +I+
Sbjct: 181 GRIENRIGRHPVDRKRMA---LVTGEAGKEALTEWDRVAVHQGCALIRCRLLTGRTHQIR 237

Query: 203 -KVFEFFNWKVN 213
             + E     + 
Sbjct: 238 VHMKEALGCPIL 249


>gi|240047580|ref|YP_002960968.1| Pseudouridine synthase [Mycoplasma conjunctivae HRC/581]
 gi|239985152|emb|CAT05162.1| Pseudouridine synthase [Mycoplasma conjunctivae]
          Length = 306

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 81/241 (33%), Gaps = 45/241 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------------- 60
           R+  V+A+    SR+    +I    VKV+  ++ +    +     I              
Sbjct: 17  RIDLVVAKHLNVSRKISRYLIEANSVKVDNKVVNKVNFLLREGQFISILNNYQEPQLKVE 76

Query: 61  --EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RV 108
             +VD   + +     + + +KP  LV    + +   T+ + L   F+          R 
Sbjct: 77  AQKVDFEIVYQDND--IIVINKPKNLVVHPGNGNWDKTLVNGLLHEFATNLSDVNGEIRP 134

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QVDQ 155
             V RLD +T GLLL+  +    + L   L + +  R Y     G            + +
Sbjct: 135 GIVHRLDKDTSGLLLVAKNNQAHKYLAKQLENHEIERKYIAIVVGKIPHTKMRINLPIGR 194

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDT----QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           D  N  KK +           V L      +    + V   L  G+  +I+       + 
Sbjct: 195 DNQNRTKKVVSSFNSKNAITNVELINTFVYKNEHFSIVKCILETGRTHQIRVHLSHIGYP 254

Query: 212 V 212
           +
Sbjct: 255 I 255


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 37/86 (43%), Gaps = 6/86 (6%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ + +   G+A SR      I   +V VNG  + +A+  V   D +EV+       +  
Sbjct: 4  RLDRALTDRGLARSRTVAAGWIRDGKVSVNGAPVTKASTPVSEQDRVEVE---TSPEDEY 60

Query: 74 RLWLYHKPIGLVTTHS--DPDGRSTV 97
               HK +G +   S  DP GR  +
Sbjct: 61 ASRAAHKLVGALECFSDVDPAGRRCL 86


>gi|167645622|ref|YP_001683285.1| RluA family pseudouridine synthase [Caulobacter sp. K31]
 gi|167348052|gb|ABZ70787.1| pseudouridine synthase, RluA family [Caulobacter sp. K31]
          Length = 329

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 34/222 (15%), Positives = 65/222 (29%), Gaps = 42/222 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------------------VPLRKAE 71
           ++    +V+V+G   + A   + +   I V                         L   E
Sbjct: 36  KLFRSGQVRVDGSRAK-ADTKLAAGSQIRVPPLPDAPDPDEKQKLSPRDIAFAKSLVLYE 94

Query: 72  RTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +   +KP GL              +        +R   V RLD +T G+LLL     
Sbjct: 95  DEEVLALNKPAGLAVQGGTKTTHHIDKLLSAWGEGVNRPKLVHRLDRDTSGVLLLGKTPA 154

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQD----KLNLLKKGI---VI---------QGIC 171
            A  L       +  + Y     G         +L+L K+G+    +          G  
Sbjct: 155 AAARLSGSFAKRKAQKTYWAIVAGNPHPTEGVIELHLAKRGVGDRELVVPAEPKDPDGQP 214

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                V++        W+ +    G+  +++   +     + 
Sbjct: 215 AETEFVSISRAGPRVTWMALRPHTGRTHQLRAHMKAIGHPIL 256


>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 = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 79/248 (31%), 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------DGVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           V          +   +     +Y         K  G+V      +   T+ + L   F  
Sbjct: 94  VLLAHPPRENVIIPQDIPVNIIYEDDDLVVVDKEAGMVVHPGFGNWDGTLVNALAYHFEK 153

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   RV  V R+D +T GLL++  +      L     +    R+Y     G + +D
Sbjct: 154 NGEKSDLDRVGLVHRIDKDTSGLLVIAKNEYALSFLAKQFFNRTTKRLYWAFVWGNLQED 213

Query: 157 K-----------LNLLKKGIVIQG--ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
           +            N ++  +   G    +      +  +     WV   L  G+  +I+ 
Sbjct: 214 EGTIRGHIGRHPKNRMQMSVYEDGSQGKHAVTHYKVLERFKYMTWVECKLETGRTHQIRA 273

Query: 204 VFEFFNWK 211
            F      
Sbjct: 274 HFRHIGHT 281


>gi|284048346|ref|YP_003398685.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
 gi|283952567|gb|ADB47370.1| pseudouridine synthase, RluA family [Acidaminococcus fermentans DSM
           20731]
          Length = 285

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 43/218 (19%), Positives = 82/218 (37%), Gaps = 32/218 (14%)

Query: 13  PQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-----AAVNV-----MSTDHIEV 62
           PQR+   +   G+ S    +++ A   ++VNG +++R         V          +E 
Sbjct: 11  PQRLKSFLRDQGL-SGTYWKKLKAAGALQVNGEIIQRDLLLQPGDRVAWTFLPEPCTLEP 69

Query: 63  DGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLD 115
           +  PL   E T L+L   KP GLVT ++  +    +   +   F      S V  V RLD
Sbjct: 70  EEAPLSILEETELYLAVDKPAGLVTHNAGKERTPALSRRVAWYFQTHHISSAVHPVSRLD 129

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRV-----------RFHGQVDQDKLNLLKKG 164
             T G++L   +  L     L   +  + Y                  + +   +++++ 
Sbjct: 130 RETSGVVLFAKNACLHH--MLSRNRLEKTYLALTLGHWEQPAGILDWPIGRRPGSIVERQ 187

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +   G      +  +  +K   + V   L  G+  +I+
Sbjct: 188 VDPDGQPART-RYQVLGEKEGLSLVRFQLETGRTHQIR 224


>gi|254881959|ref|ZP_05254669.1| RNA pseudouridylate synthase [Bacteroides sp. 4_3_47FAA]
 gi|294775568|ref|ZP_06741078.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|319641038|ref|ZP_07995742.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_40A]
 gi|254834752|gb|EET15061.1| RNA pseudouridylate synthase [Bacteroides sp. 4_3_47FAA]
 gi|294450618|gb|EFG19108.1| pseudouridine synthase, RluA family [Bacteroides vulgatus PC510]
 gi|317387282|gb|EFV68157.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_40A]
          Length = 308

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 38/222 (17%), Positives = 77/222 (34%), Gaps = 34/222 (15%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA------ER 72
           AGI SR +V+ ++A + + V+ ++  +    +     +++    +    +        E 
Sbjct: 40  AGI-SRSKVKALLANRVILVDNVITTQYNFALKPGMKVQISKVKNNREFKHPMLKLVYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             + +  K  GL++  ++     T    L         F+RV  V RLD  T GL++   
Sbjct: 99  AYILVVEKKEGLLSVSTEHQKERTAQHILNEYVKRSHRFNRVFVVHRLDRETSGLMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI----------QGICY 172
           D      L          R Y     G +++D   +        +          +G   
Sbjct: 159 DEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWLTDRKLYVYSSPVDNGEGKFA 218

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
                T+    G  + V + L  G+  +I+  + +     V 
Sbjct: 219 VTHYKTIKRANGY-SLVELDLETGRKNQIRVHMLD-LGHPVV 258


>gi|154148379|ref|YP_001406840.1| RluA family pseudouridine synthase [Campylobacter hominis ATCC
           BAA-381]
 gi|153804388|gb|ABS51395.1| pseudouridine synthase, RluA family [Campylobacter hominis ATCC
           BAA-381]
          Length = 357

 Score = 62.9 bits (152), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 64/171 (37%), Gaps = 26/171 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------GV 65
           +  R+   + +    SR ++  +I +  + VN  +  +A+  + + D + ++        
Sbjct: 21  SSIRLDIFLTKILKISRNKILNLIEENHIFVNNSVQNKASFKLKNDDIVGINFPLKKENE 80

Query: 66  PLRK---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSR 107
            L++          E   L + +KP G+V   +      T+ + L          +   R
Sbjct: 81  NLKQNANFDIEILYEDDDLLVLNKPSGVVVHPAKSVKEPTLAEWLKQKKYMLSSINGDER 140

Query: 108 VISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
              V RLD  T G +L+  T+   +    +L      R+Y       + ++
Sbjct: 141 AGIVHRLDKQTSGAILVAKTDFAHVKLAAQLKDKSMGRIYLAFLDLALKEN 191


>gi|311104863|ref|YP_003977716.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           xylosoxidans A8]
 gi|310759552|gb|ADP15001.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           xylosoxidans A8]
          Length = 332

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/164 (23%), Positives = 61/164 (37%), Gaps = 28/164 (17%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-- 69
           R+ KV+A  G+    SR  ++  I    V VNG   +     V   D + V   P  +  
Sbjct: 41  RLDKVLA--GLLPEHSRGRLQGWIEAGNVHVNGRPGK-VRQTVGPGDELTVWPQPAPESL 97

Query: 70  ------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SV 111
                        E     + +KP GLVT     +   T+ + L   +  +        V
Sbjct: 98  AFAPEPVDFAVVDESPDWIVVNKPAGLVTHPGAGNWSGTLLNGLLYRYPELTQVARAGIV 157

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
            RLD +T GL+++  +      L  +L +    R Y    HG +
Sbjct: 158 HRLDKDTSGLMVVARNETAQTHLVRQLQARSMGREYVALAHGWL 201


>gi|294806510|ref|ZP_06765351.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
 gi|294446373|gb|EFG14999.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens SD
           CC 1b]
          Length = 281

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 36/210 (17%), Positives = 75/210 (35%), Gaps = 28/210 (13%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLE------RAAVNVM---STDHIEVDGVPLR-KA 70
           A+   ASR +++ +++++ V V+ ++         A + V         E +   L+   
Sbjct: 9   AKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVKISKQKGKKEFNNRLLKIVY 68

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + +  K  GL++ +++     T +  L     R      V  V RLD +T GL++ 
Sbjct: 69  EDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRLDRDTSGLMMF 128

Query: 125 TNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--------QGICY 172
             D    R L     +    R Y     G +++D   +        +         G   
Sbjct: 129 AKDEKTQRTLRDNWHEIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVSSSEYDDGGSK 188

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +    + + + L  G+  +I+
Sbjct: 189 SITHYKTIKRANGYSLLELDLETGRKNQIR 218


>gi|89093551|ref|ZP_01166499.1| pseudouridine synthase [Oceanospirillum sp. MED92]
 gi|89082241|gb|EAR61465.1| pseudouridine synthase [Oceanospirillum sp. MED92]
          Length = 322

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/227 (16%), Positives = 87/227 (38%), Gaps = 32/227 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V ++   +R+ + +A+     SR  ++  I    + VNG  +++    ++  + I +D  
Sbjct: 11  VTDDLVGKRLDQAVAQLFPDYSRSRLQGWIKDGSLTVNGE-VKKPREKLLGGEAIAIDAN 69

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
                      +PL    E   + + +KP GLV   +      T+ + L      +    
Sbjct: 70  LEVIEDHKPQNIPLDIVYEDEHILVINKPAGLVVHPAVGHRDGTLLNALLYHCPDIAQVP 129

Query: 109 --ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL------ 158
               V RLD++T GL+++         L  +L      R Y    +G +    +      
Sbjct: 130 RAGIVHRLDMDTTGLMVVAKTIAAQTELVEQLQERSMGREYEAVVNGVMTGGGVVDEPMG 189

Query: 159 --NLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIK 202
             +  ++ + + G+    +    +  +  S+  + + L  G+  +I+
Sbjct: 190 RHSKNRQKMAVVGVGKEAVTHYRVLKKLRSHTHIRLKLETGRTHQIR 236


>gi|312884948|ref|ZP_07744638.1| tRNA pseudouridine synthase C [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367425|gb|EFP94987.1| tRNA pseudouridine synthase C [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 241

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 25/172 (14%), Positives = 49/172 (28%), Gaps = 31/172 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +       +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDDYFVAVNKPAGMLVHRSWLDKHETQFVMQTLRDQIGQHVFPLHRLDKPTSGVLIFALS 66

Query: 128 GGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT---- 181
             +A  +          + Y     G ++Q  +      + +      D   TLD     
Sbjct: 67  SEIASSVMPMFANHEMNKTYHAIVRGWIEQAGVLDYPLKVELD--KIADKHATLDKEAQD 124

Query: 182 -----QKGSNAWV---------------TVGLREGKNREIKKVFEFFNWKVN 213
                Q  +   +                +  R G+  ++++        + 
Sbjct: 125 AITDYQPIAKTELPIAMGKFPTTRYCMMELKPRTGRKHQLRRHMAHLRHPII 176


>gi|150005860|ref|YP_001300604.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC
           8482]
 gi|149934284|gb|ABR40982.1| putative RNA pseudouridylate synthase [Bacteroides vulgatus ATCC
           8482]
          Length = 308

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/222 (17%), Positives = 77/222 (34%), Gaps = 34/222 (15%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA------ER 72
           AGI SR +V+ ++A + + V+ ++  +    +     +++    +    +        E 
Sbjct: 40  AGI-SRSKVKALLANRVILVDNVITTQYNFALKPGMKVQISKVKNNREFKHPMLKLVYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             + +  K  GL++  ++     T    L         F+RV  V RLD  T GL++   
Sbjct: 99  AYILVVEKKEGLLSVSTEHQKERTAQHILNEYVKRSHRFNRVFVVHRLDRETSGLMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI----------QGICY 172
           D      L          R Y     G +++D   +        +          +G   
Sbjct: 159 DEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWLTDRKLYVSSSPVDNGEGKFA 218

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
                T+    G  + V + L  G+  +I+  + +     V 
Sbjct: 219 VTHYKTIKRANGY-SLVELDLETGRKNQIRVHMLD-LGHPVV 258


>gi|116740184|gb|ABK20858.1| 23S rRNA pseudouridine synthase [Escherichia coli]
          Length = 38

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 10 NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI 45
            +  R++K I+ +GI SRRE +R I Q  V +NG 
Sbjct: 3  PDSSVRLNKYISESGICSRREADRYIEQGNVFLNGK 38


>gi|95931222|ref|ZP_01313943.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
 gi|95132741|gb|EAT14419.1| pseudouridine synthase [Desulfuromonas acetoxidans DSM 684]
          Length = 295

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 29/229 (12%), Positives = 68/229 (29%), Gaps = 45/229 (19%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK------ 69
           + + I+ A   S+  + +++ + +V       +     V   D +++  V +        
Sbjct: 19  LQRHISAA---SKSYLRQLLKKGKV-------KGPRGVVSEQDQLKLGDVLILPDSGRLS 68

Query: 70  ------------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                              E   + +  KP GL    S+      +   +  +       
Sbjct: 69  ELLAATAQPSLEQQLFILYESREILIVDKPSGLAIHSSEGHQDRNLAALVDELIRSRGDA 128

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            +V  + RLD+ T G +L          L       +  + Y     G+     L  ++ 
Sbjct: 129 YQVAPIHRLDLETSGPVLFGKGKKACSELGKLFMCHEVEKSYLALVAGKTPGRGL--IQS 186

Query: 164 GIVIQGICYGDMQV-TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +  +G             +    + + V L  G+  +I++        
Sbjct: 187 EVPSKGKTKEAQTAFQALDRNEQASLLKVTLYTGRQHQIRRQLAELGHP 235


>gi|325067131|ref|ZP_08125804.1| pseudouridine synthase, RluA family protein [Actinomyces oris K20]
          Length = 306

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 78/242 (32%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V + F  +RV   +AR    SR  VE +     V+  G  L +++  + + + +EVD   
Sbjct: 8   VPDGFDGERVDAALARMTGLSRSRVEDLCEAGEVRRGGETLAKSS-RLRAGELLEVDLPD 66

Query: 64  ---GVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                P+         LY         KP G+    S       V   L ++  RV + G
Sbjct: 67  PRPVEPVATPVEGMELLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVRVATSG 126

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
                    RLD+ T G++++        VL+         +VY     G +D     + 
Sbjct: 127 AAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTID 186

Query: 162 K----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                      K  +I+G         +           + L  G+  +I+         
Sbjct: 187 APIGRHPSREWKMAIIEGGRESITHYDVIEAMPGACLAEIHLETGRTHQIRVHMAAVGHP 246

Query: 212 VN 213
             
Sbjct: 247 CV 248


>gi|190575132|ref|YP_001972977.1| putative ribosomal large subunit pseudouridine synthase C
           [Stenotrophomonas maltophilia K279a]
 gi|190013054|emb|CAQ46686.1| putative ribosomal large subunit pseudouridine synthase C
           [Stenotrophomonas maltophilia K279a]
          Length = 324

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 83/248 (33%), Gaps = 44/248 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V  +   QR+   +  +   A R  V +++   +V+VNG   + A   + + D + V  
Sbjct: 20  TVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAK-AERKLEAGDEVRVPP 78

Query: 63  -----DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNL 101
                +G  +                E  RL   +KP G+ +            T+    
Sbjct: 79  VRLTEEGDKVGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALR 138

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL-----ELPSTQWLRVYRVRFHGQVDQD 156
           P     +  V RLD +T GLL++         L     E       + Y     G++   
Sbjct: 139 PG--QTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRYLTLLAGRMPDG 196

Query: 157 KL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIKKV 204
            +     L  G+   G  +  +            +  ++G +++  V +  G+  +I+  
Sbjct: 197 VMTVDAPLHVGLRQGGERHVQVNAIGKESISHFRVLERRGGHSYCEVRIETGRTHQIRVH 256

Query: 205 FEFFNWKV 212
            +     V
Sbjct: 257 AQHLGHPV 264


>gi|295694723|ref|YP_003587961.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
 gi|295410325|gb|ADG04817.1| pseudouridine synthase, RluA family [Bacillus tusciae DSM 2912]
          Length = 322

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 41/232 (17%), Positives = 72/232 (31%), Gaps = 57/232 (24%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHI-----------------EVDGVPLRKA---ER 72
           + I   RVKVN    +   + +   D +                 +  GVP       E 
Sbjct: 33  KWIRVGRVKVNRKKGK-PDLVLHEGDTVQLFVSDEEYAALRRRGPKFQGVPRTFEILYED 91

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI----------SVGRLDINTEGLL 122
             L + +KP GL+T     + R T+ + + +                +  RLD NT G++
Sbjct: 92  GDLLVVNKPAGLLTHPDRQEHRDTLINRVLAYLYDKGEWDGRAFAPAAANRLDRNTSGIV 151

Query: 123 LLTNDGGLARVL-----ELPSTQWLRVYRVRFHGQV-DQDKLNLL------KKGIVIQGI 170
           L+   G  A+ L      L   +  + Y    HG++     L              + G 
Sbjct: 152 LI---GKHAQALRELADALRGRRVDKRYLALVHGRIETPGTLKQALIRDHENNRTRLAGE 208

Query: 171 CYGDMQVTLDTQKGSN-----------AWVTVGLREGKNREIKKVFEFFNWK 211
             G   V  +T +                + + L  G+  +I+         
Sbjct: 209 KRGRHGVAPETLEAETRYRPLAVAERLTLLDITLVSGRTHQIRAHLAAAGHP 260


>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 = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 82/250 (32%), Gaps = 53/250 (21%)

Query: 6   IVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           IV      +RV K I+       SR  V+ ++ Q  V +NG L    +  + + D +   
Sbjct: 39  IVSHVDDGKRVDKFISANAPDDLSRARVQALVRQGNVTINGELPRGTSTKISNGDVVRFL 98

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      + +PL    E   L +  KP G+V   +  +   T+ + L         
Sbjct: 99  MPPPEDAIPQPENIPLDILHEDDDLIVLIKPAGMVVHPAPGNWSGTLVNALLHHCDGNLS 158

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVD 154
                 R   V RLD +T G++++         L+       R       Y     G   
Sbjct: 159 GIGGVKRPGIVHRLDKDTSGVMVVAKSYRAHIDLQEQFADHGRTGPLERAYWALAWGAPP 218

Query: 155 Q-----DKL------NLLKKGIVIQGICYGDMQVT-----------LDTQKGSNAWVTVG 192
           +     D L        +++ +V +G       +T             + +   + +   
Sbjct: 219 RMKGKVDTLIGRHPTRRVQRAVVEEGAPDAKHAITHYEVVKRFEDAERSGEAMASLIECK 278

Query: 193 LREGKNREIK 202
           L  G+  +I+
Sbjct: 279 LETGRTHQIR 288


>gi|223935079|ref|ZP_03626997.1| pseudouridine synthase [bacterium Ellin514]
 gi|223895963|gb|EEF62406.1| pseudouridine synthase [bacterium Ellin514]
          Length = 260

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 31/155 (20%), Positives = 58/155 (37%), Gaps = 23/155 (14%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTN 126
            E   L + +KP GLV   +  D  S++   +       S    V RLD  T G++++  
Sbjct: 30  HEDAELLVINKPAGLVCHPTKGDEYSSLISRVRLHLGPESHPHLVNRLDRETSGIVIVAK 89

Query: 127 DGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK-------------LNLLKKGIVIQGIC 171
           D   AR L       +  + Y    HG V +++             +  +K  +V +G  
Sbjct: 90  DDTTARGLRRIWEGREVQKEYLAIVHGHVREEQGTIQAALGKDTSSIIAIKDTVV-EGGA 148

Query: 172 YG----DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  ++     ++G    + V    G+  +I+
Sbjct: 149 ASQTDFTVKKRFSREEGDFTLLRVLPHTGRKHQIR 183


>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 = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 42/231 (18%), Positives = 83/231 (35%), Gaps = 39/231 (16%)

Query: 9   ENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGI------LLERAAVNV---MST 57
           E     R+   IA       SR  ++++I    V V+G       +++   V V      
Sbjct: 10  EEDEGVRLDIYIAEQ-YDDLSRSYIQKVIKDNGVTVDGRPEKNRYIVKVGQVIVVSLPEA 68

Query: 58  DHIEV--DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------- 106
             +EV    +PL    E   L + +KP  +V   +  +  +T+ + L             
Sbjct: 69  KELEVTAQNIPLDIVYEDDDLLVVNKPQDMVVHPAPGNYENTMVNALLYHCKGKLSSING 128

Query: 107 --RVISVGRLDINTEGLLLLT-------------NDGGLARVLELPSTQWLRVYRVRFHG 151
             R   V R+D +T GLL++               D    R     S   ++  R   + 
Sbjct: 129 IIRPGIVHRIDKDTSGLLMVAKNNHAHQFLSEQLKDHSTTRKYHGISVGTIKEERATINA 188

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + + + + LK  + + G       + +  + G + ++   L  G+  +I+
Sbjct: 189 PIARHQTDRLKMAV-LAGGRNAVTHIQVLNRFGDHTYMEAQLETGRTHQIR 238


>gi|46446340|ref|YP_007705.1| hypothetical protein pc0706 [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399981|emb|CAF23430.1| conserved hypothetical protein [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 298

 Score = 62.9 bits (152), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 31/140 (22%), Positives = 54/140 (38%), Gaps = 20/140 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------GVPLRK----AERTRLW 76
           R+++RMI Q   +VNG +   A+  + + D + ++           L +     E   L+
Sbjct: 33  RQLKRMIEQNDCQVNGRIERFASTFLGTGDRVSLNLKNPQQTFNRQLEQSRILYEDEDLF 92

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +Y KP  +     D  G   +   L   F  +  + RLD  T G+L L  +      L  
Sbjct: 93  IYDKPAEMNC---DEQG---IIALLRPSFPSIQLIHRLDRQTTGVLALAKNKTTFEALVN 146

Query: 137 P--STQWLRVYRVRFHGQVD 154
                +  + YR    G + 
Sbjct: 147 QFKQLKVSKSYRAIVDGILT 166


>gi|312866863|ref|ZP_07727076.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
 gi|311097646|gb|EFQ55877.1| pseudouridine synthase, RluA family [Streptococcus parasanguinis
           F0405]
          Length = 287

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 77/204 (37%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRK------------AE 71
           R++   +  ++ V VNG  +      V   D I++    D  P ++             +
Sbjct: 28  RKIRHFLRTKKHVLVNGETI-NWQSPVQKGDQIQLIFDADDYPEKELPAGDPSLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + + +KP G+ T  ++P   S +      + S    V RLD  T G +L   +  + 
Sbjct: 87  DEHVIIVNKPEGMKTHANEPTEISLLNHVSSYVGSTCYVVHRLDKETSGAILFAKNPFIL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L      R Y     G + Q  +           +  K+ +  +   Y + QVT
Sbjct: 147 PILNRILEDKNIQREYWALIQGSLAQKTIVYKDKIGRDRHDRRKRLVDPRKGQYAETQVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              + G N+ V   L+ G+  +I+
Sbjct: 207 QLKKIGRNSLVKCQLKTGRTHQIR 230


>gi|290967748|ref|ZP_06559303.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
 gi|290782264|gb|EFD94837.1| pseudouridine synthase, RluA family [Megasphaera genomosp. type_1
           str. 28L]
          Length = 301

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 85/243 (34%), Gaps = 45/243 (18%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------GVPL---RKAERTRLW 76
           RR ++          NG ++      V + D I +           PL   R  E   L 
Sbjct: 29  RRRIK---HSGTCTCNGQVI-GLQNFVHTGDTICISLPVRQAFAPEPLAFTRVYEDRHLL 84

Query: 77  LYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           + +KP GL+   +      T+      +    +       V RLD NT GL ++  +  +
Sbjct: 85  VINKPAGLLMHPTAGQRSGTLANAVSYYYITSNQHCAYHPVHRLDKNTSGLCMIAKNPYV 144

Query: 131 ARVLEL-PSTQWLRVYR-----------VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
             + +  P+  + R+Y               H  V + + +++K+ + + G       V 
Sbjct: 145 QSLFDHAPNRYYKRLYLALSTGYFPTPTATVHSPVGRAENSIIKRCVCLDGQKAHTDFVR 204

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           L     + + + V L  G+  +I+    +  + +               L  G+   +S+
Sbjct: 205 LAAAD-TYSLLQVSLHTGRTHQIRVHCSYLGFPLLG-----------DDLYGGTHELLSR 252

Query: 239 KIL 241
           + L
Sbjct: 253 QAL 255


>gi|303252861|ref|ZP_07339020.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307247850|ref|ZP_07529886.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|302648291|gb|EFL78488.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306855652|gb|EFM87819.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
          Length = 247

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 38/202 (18%), Positives = 68/202 (33%), Gaps = 39/202 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  V RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSGVLLFALNSKMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD------------- 174
             L        Q  + Y     G  +D+ +++   K +++  I                 
Sbjct: 72  -RLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLK-VILDKIADKFSQPKEAQQAVTFY 129

Query: 175 ---MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                V +    G +      L E     G+  ++++  +     +        G  + G
Sbjct: 130 QNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------IGDTKYG 182

Query: 227 TLLAGSTREVSKKILREQLGPH 248
            L     R +++K   ++L  H
Sbjct: 183 DLH--QNRTLTEKTGCDRLMLH 202


>gi|298385355|ref|ZP_06994913.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_14]
 gi|298261496|gb|EFI04362.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_14]
          Length = 306

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLER------AAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++  +        + V         E
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMKVQISKEKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FHNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVFIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L     +    R Y     G +++D   +        +   
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGTMEKDYDTVVSWLTDKTLYVS 203

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 204 SSDYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 243


>gi|187779918|ref|ZP_02996391.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC
           15579]
 gi|187773543|gb|EDU37345.1| hypothetical protein CLOSPO_03514 [Clostridium sporogenes ATCC
           15579]
          Length = 317

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 34/264 (12%), Positives = 77/264 (29%), Gaps = 67/264 (25%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA- 50
           K ++  N   QR+ K              +             I +  +KVNG   +   
Sbjct: 2   KIVIGANEAGQRLDKF-----------CRKWLKDVPLSAIYKAIRKGEIKVNGKKSKEKN 50

Query: 51  ---------AVNVMSTDH----IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                    + NV S       + +D       E   + L  K  G++      +G  T+
Sbjct: 51  FLEEGDIVESFNVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTL 110

Query: 98  FDNLPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                      RLD NT G+++   +    + L   +   +  
Sbjct: 111 TDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYESLKTLNEMIRDRKIE 170

Query: 143 RVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSN----AWV 189
           + Y     G++                + K  +         ++ ++ +        +++
Sbjct: 171 KYYSSLVKGRIKDGIYEAYISKNQDTNMSK--IYNEPKPNTKKIAMEVKTIQTCGSFSFI 228

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 229 EIELLTGRSHQLRAHLSHLGNPII 252


>gi|254361102|ref|ZP_04977247.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261495410|ref|ZP_05991858.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153092588|gb|EDN73643.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261308915|gb|EEY10170.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 242

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 53/166 (31%), Gaps = 28/166 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL   +   A
Sbjct: 12  LIAINKPAGVLVHRSWLDKHETVFAMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSETA 71

Query: 132 RVLELPSTQ---WLRVYRVRFHGQVD-------------QDKLNLLKKGIVI-------Q 168
             +     +     + Y     G +                  +   +           +
Sbjct: 72  -RIMSEQFEQHLVQKTYLAVVRGYLQGSAQIDYPLKVILDKIADKFSQEKEAQAAITDYK 130

Query: 169 GICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVN 213
           G+   +M   +   + S  + V +  + G+  ++++  +     + 
Sbjct: 131 GLATVEMPYPVGKHQTSRYSLVELSPKTGRKHQLRRHLKHLFHPIM 176


>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 = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 77/244 (31%), Gaps = 48/244 (19%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------------ 61
           R+ +V+A      SR  ++ +IA+ RV   G  +   +  V   +               
Sbjct: 29  RLDRVLANHLPELSRTRLQALIAEGRVLRAGRPVAGGSAKVAPGEVFTVEVPPPEPAEPE 88

Query: 62  VDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVIS 110
              +PL    E   L +  KP GLV   +  +   T+ + L               R   
Sbjct: 89  PQDIPLDIVFEDDDLIVIDKPAGLVVHPAPGNPDGTLVNALLFHCGASLSGIGGVRRPGI 148

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG------------- 151
           V RLD +T GL+++  +    + L        R       Y     G             
Sbjct: 149 VHRLDKDTSGLMVVAKNDRAHQKLAAQFADHGRTGPLERAYLAFVWGVPELPSGTVDAPL 208

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS-NAWVTVGLREGKNREIKKVFEF 207
               V ++++ +   G       +  ++   DTQ     + V   L  G+  +I+     
Sbjct: 209 ARHPVSRERIAVRANG-RFAITHWQRVEAYEDTQGRPVASLVECQLETGRTHQIRVHMAH 267

Query: 208 FNWK 211
               
Sbjct: 268 IGHP 271


>gi|269795564|ref|YP_003315019.1| ribosomal large subunit pseudouridine synthase D [Sanguibacter
           keddieii DSM 10542]
 gi|269097749|gb|ACZ22185.1| ribosomal large subunit pseudouridine synthase D [Sanguibacter
           keddieii DSM 10542]
          Length = 311

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 81/246 (32%), Gaps = 41/246 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV   +AR    SR    ++ +   V+++G  L ++   +     IEVD   
Sbjct: 8   VPDGLAGERVDAALARMLGLSRTVAAQIASDGGVRLDGRALGKSD-RLAPDSWIEVDVPD 66

Query: 64  -----GVPLRKAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNLP------- 102
                G  +       + + +         KP+G+    S      TV   L        
Sbjct: 67  PSAPRGPVVVAEPVPGMKIMYDDDDVVVIDKPVGVAAHPSVGWTGPTVVGALIAAGYTIA 126

Query: 103 --SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG--QVDQD 156
                 R   V RLD+ T GL+++        V++    +    +VY     G  +    
Sbjct: 127 TSGAAERQGIVHRLDVGTSGLMVVAKSEHAYSVMKRAFKERTVEKVYHALVQGHPEPTTG 186

Query: 157 KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            ++           K G+V  G         L+    + + V V L  G+  +I+  F  
Sbjct: 187 TIDAPIGRHPNHDYKFGVVADGKPSVTHYEVLEMLSAA-SLVEVHLETGRTHQIRVHFSA 245

Query: 208 FNWKVN 213
                 
Sbjct: 246 LRHPCV 251


>gi|298368341|ref|ZP_06979659.1| ribosomal large subunit pseudouridine synthase D [Neisseria sp.
           oral taxon 014 str. F0314]
 gi|298282344|gb|EFI23831.1| ribosomal large subunit pseudouridine synthase D [Neisseria sp.
           oral taxon 014 str. F0314]
          Length = 373

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 77/226 (34%), Gaps = 34/226 (15%)

Query: 10  NFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +    R+   +A+     SR  +   I +  V VNG         ++  + I V      
Sbjct: 35  DMAGLRLDSALAKLMPDYSRSRLATWIKEDLVIVNGKPAR-PKEKLIGGEFITVTVRSSE 93

Query: 69  K--------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRV 108
           +               E   + + +K  GLV   +  +   T+ + L +         R 
Sbjct: 94  ESLAFLPEKMDLDIVYEDDTVIVVNKSAGLVVHPAAGNWSGTLLNGLLAHCPELGQIPRA 153

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD-QDKLN------ 159
             V RLD  T GL+++         L     +    R+YR   +G V    K+       
Sbjct: 154 GIVHRLDKETSGLMVVAKTLPAQNSLVRQLQERTVKRIYRAVANGIVPFDGKIETLIGRD 213

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               LK  +V  G       V +  +  +++++   L  G+  +I+
Sbjct: 214 PHNRLKMAVVKYGGKPAITHVKVLERYPAHSYIECSLETGRTHQIR 259


>gi|297538120|ref|YP_003673889.1| RluA family pseudouridine synthase [Methylotenera sp. 301]
 gi|297257467|gb|ADI29312.1| pseudouridine synthase, RluA family [Methylotenera sp. 301]
          Length = 363

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 76/225 (33%), Gaps = 49/225 (21%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------- 62
           + +++      SR  ++  I +  V V+  L   +   V   + + V             
Sbjct: 30  LQRMLPEH---SRSRLQTWIKEGLVTVD-KLPSTSKTKVWGGEQVVVQVQAKPENYAYVA 85

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISVGRLD 115
           + +PL    E   + + +KP G+V   +  +   T+ + L           R   V RLD
Sbjct: 86  EDIPLDIVFEDDHIIIINKPAGMVVHPAAGNWSGTLLNALLFHAPELKDVPRAGIVHRLD 145

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
            +T G+L++         L  +L +    R YR    G        L + G+V Q I   
Sbjct: 146 KDTSGILVVAKTLAAQTNLVRQLQARTVKREYRAIVWG-------QLWRNGVVDQAIGRD 198

Query: 174 DMQVT----------------LDTQKGSNAWVTVGLREGKNREIK 202
               T                +  +     ++   L  G+  +I+
Sbjct: 199 PRSRTKMALNRMGKPAITRYEILERFSVQTYLRCNLETGRTHQIR 243


>gi|157150847|ref|YP_001450507.1| 23S rRNA pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157075641|gb|ABV10324.1| 23S rRNA pseudouridine synthase [Streptococcus gordonii str.
           Challis substr. CH1]
          Length = 295

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 88/251 (35%), Gaps = 52/251 (20%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D + +D     G      + K      E     +  KP
Sbjct: 33  RGGGILVNDEP-QNAIYLLDIGDKVTIDIPKEEGFESLEAISKKLEVVFEDDHFLILDKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  AGVASIPS-VNHSNTMANYVKAYYIDSGYENHQVHIVTRLDKDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKRAIEKRYLALVKGDGLLEKEGEIILPIARDEDSIITRRVA-KGGKYAHTSYKVI 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            Q G+   V + L  G+  +I+  F    + +               L  GS   +++ I
Sbjct: 210 EQFGNIYLVDIHLHTGRTHQIRVHFSHIGFPLLG-----------DDLYGGS---LTEGI 255

Query: 241 LREQLGPHLLE 251
            R+ L  H L+
Sbjct: 256 SRQALHCHTLK 266


>gi|170727628|ref|YP_001761654.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169812975|gb|ACA87559.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 285

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/210 (14%), Positives = 59/210 (28%), Gaps = 41/210 (19%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD 90
             + I           +  A ++  +   IE+        E   + + HKP GL+   S 
Sbjct: 16  ANKEIEAG--------VNEAELHDETAPEIEI------LFEDDDIVVIHKPAGLLVHRSY 61

Query: 91  PDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVY 145
              R   F    +       V  V RLD  T G+LL      +A  L     +    + Y
Sbjct: 62  LARRERFFAMQMTRDKVGCHVFPVHRLDRPTSGILLFAKSSEMANNLCEQFSAKTVEKQY 121

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW----------------- 188
                G + +         + +      D+      Q+   ++                 
Sbjct: 122 LAIVRGNMHEADTLDYALKVELDDHGDKDVDPNKAAQEAVTSYQPLLNTEIPFPSGRYAT 181

Query: 189 -----VTVGLREGKNREIKKVFEFFNWKVN 213
                V +    G+  ++++        + 
Sbjct: 182 SRYAMVKLIPHTGRKHQLRRHMAHLRHPIV 211


>gi|262282807|ref|ZP_06060574.1| 23S rRNA pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
 gi|262261059|gb|EEY79758.1| 23S rRNA pseudouridine synthase [Streptococcus sp. 2_1_36FAA]
          Length = 295

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 88/251 (35%), Gaps = 52/251 (20%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKP 81
               + VN    + A   +   D + +D     G      + K      E     +  KP
Sbjct: 33  RGGGILVNDEP-QNAIYLLDIGDKVTIDIPKEEGFESLEAISKKLEVVFEDDHFLILDKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G+ +  S  +  +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  AGVASIPS-VNHSNTMANYVKAYYIDSGYENHQVHIVTRLDKDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L      + Y     G             + +D+ +++ + +  +G  Y      + 
Sbjct: 151 DKQLQKRAIEKRYLALVKGDGLLEKEGEIIAPIARDEDSIITRRVA-KGGKYAHTSYKVI 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            Q G+   V + L  G+  +I+  F    + +               L  GS   +++ I
Sbjct: 210 EQFGNIYLVDIHLHTGRTHQIRVHFSHIGFPLLG-----------DDLYGGS---LTEGI 255

Query: 241 LREQLGPHLLE 251
            R+ L  H L+
Sbjct: 256 SRQALHCHTLK 266


>gi|189463385|ref|ZP_03012170.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136]
 gi|189429814|gb|EDU98798.1| hypothetical protein BACCOP_04104 [Bacteroides coprocola DSM 17136]
          Length = 307

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 37/219 (16%), Positives = 68/219 (31%), Gaps = 29/219 (13%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ER 72
           AGI SR  V+ ++  + V V+  +       +     +++     +            E 
Sbjct: 40  AGI-SRTRVKALLTNRVVLVDNNIQTLYNYPLKPGMKVQISREKNKHEFRHPMLKILYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTN 126
             L +  K  GL++  +D     T    L     R      V  V RLD  T G+++   
Sbjct: 99  AYLIVVEKKEGLLSVATDHQKEKTAQHILNEYVKRQHRNNRVFVVHRLDRETSGIMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--------QGICYGD 174
           D      L          R Y     G +++D+  +        +         G  Y  
Sbjct: 159 DEKTQHTLRDNWHDIVRDRRYVSIVMGDMEKDQGTVESWLTDRKLYVSSSPVDDGGKYSV 218

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +    + V + L  G+  +I+   +     V 
Sbjct: 219 THYRTIKRANGYSLVELQLETGRKNQIRVHMQSLGHPVV 257


>gi|325918635|ref|ZP_08180739.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535142|gb|EGD07034.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 328

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 55/325 (16%), Positives = 113/325 (34%), Gaps = 61/325 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RVTEEGDKAAPPSSFLARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
              +     V             G    G   EV+K+ LR+QLG   L     +L+  + 
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-EVNKR-LRDQLGLKRLFLHAASLEFALD 303

Query: 263 SSETLVRDRPNIISEVPDDFTRMKK 287
           + +T       +  E+ +   R+ +
Sbjct: 304 AGKTPYVLSAPLAPELAEALDRLGR 328


>gi|302533940|ref|ZP_07286282.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp. C]
 gi|302442835|gb|EFL14651.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp. C]
          Length = 313

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 35/176 (19%), Positives = 64/176 (36%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV   IAR    SR +   + A+ +V V+G ++ + +  V     +EV+   
Sbjct: 12  VPDGLEGERVDAAIARMFGFSRTKAAELAAEGKVSVDGSVVGK-SERVHGGAWLEVEMPA 70

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                        G+ +   +   + +  KP+G+    S     +TV   L +   R+  
Sbjct: 71  PPRPVELVAEPVPGMEIIHDDDDVVVIM-KPVGVAAHPSPGWTGTTVIGGLAAAGYRIST 129

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
                    V RLD+ T GL+ +         L+    +    + Y     G  D 
Sbjct: 130 SGASERQGIVHRLDVGTSGLMAVAKSERAYTSLKNQFRERVVDKRYHALVQGHPDP 185


>gi|189184769|ref|YP_001938554.1| ribosomal large subunit pseudouridine synthase C [Orientia
           tsutsugamushi str. Ikeda]
 gi|189181540|dbj|BAG41320.1| ribosomal large subunit pseudouridine synthase C [Orientia
           tsutsugamushi str. Ikeda]
          Length = 312

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 77/240 (32%), Gaps = 60/240 (25%)

Query: 4   KNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           K  + +     R+ K +    +         +ER I +  +KVN     +A + V   D 
Sbjct: 2   KITINDCLVTTRLDKFLKRKYSHLTQG---VIERGIRKGHIKVNDAK-SKAKLQVKDNDV 57

Query: 60  IEV--------------------DGVPLRK-----------AERTRLWLYHKPIGLVTTH 88
           + +                    D V ++            AE +   + +KP  L+ T 
Sbjct: 58  LTIADYLTTCSNQKHIKLKKKVKDNVGVKALAHKIVNDYKIAETSDYIIINKPA-LLPTQ 116

Query: 89  SDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
                  ++ D +     S +     V RLD  T GLL++  +   A  L          
Sbjct: 117 GGSKISLSLDDAIKYLNKSFYYDFKLVHRLDRETSGLLIIAKNHKTAIKLSQAFLHHSIE 176

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + Y     G   Q        G +I  I        L+TQ G    V++     K  ++K
Sbjct: 177 KEYTAILQGVPSQ------LSGEIITNI-TKTGDRMLETQNGGK--VSIT----KY-QVK 222


>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 = 62.5 bits (151), Expect = 9e-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|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 = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 29/201 (14%), Positives = 69/201 (34%), Gaps = 31/201 (15%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----ERT 73
           K++A     S RE + +I +  V  +G  +       + +D ++ + +  +      E  
Sbjct: 7   KILALQEKISNREAKDLIDKGCVFSHGKKV--VVARALMSDKVKFNVIKTKNPQIIFEDD 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++   +KP        D + +                  RLD  T G++LL  D    ++
Sbjct: 65  KIIAINKP--YSCVSEDLEKKINAKLL-----------NRLDKETSGVILLCKDEDFRKL 111

Query: 134 LELPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDT 181
                 +    + Y     G + ++ ++N     I  +G     +          +T   
Sbjct: 112 CIEEFKKHRVYKSYIAVLDGVLAEEIEVNEPIFTIKAKGGALSKVSKDGLNASSIITPIM 171

Query: 182 QKGSNAWVTVGLREGKNREIK 202
            +       + ++ G+  +I+
Sbjct: 172 MQSKKTLAKIVIQTGRTHQIR 192


>gi|114331227|ref|YP_747449.1| pseudouridine synthase, RluA family protein [Nitrosomonas eutropha
           C91]
 gi|114308241|gb|ABI59484.1| ribosomal large subunit pseudouridine synthase D [Nitrosomonas
           eutropha C91]
          Length = 342

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 87/232 (37%), Gaps = 39/232 (16%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I  +N    R+ +V+A+     SR  ++R I + RV V+G         +   + I V  
Sbjct: 34  IAPDNLAGLRLDQVLAQLLPQWSRSRLQRWIGEDRVSVDGS-AGSTRQKIWGGEIIHVTA 92

Query: 63  -----------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                      + +PL    E   L +  KP GLV    + +   T+ + L +   ++  
Sbjct: 93  GLVESDQSHQAEAIPLSIIYEDDHLIVIDKPAGLVVHPGNGNWHGTLLNALLNHAPQLSQ 152

Query: 110 -----SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLK 162
                 V RLD +T GLL++  T +  L  V +L      R Y     G +++D L    
Sbjct: 153 VPRAGIVHRLDKDTTGLLVVAKTIEAQLDLVRQLQQRTVKRHYFALALGGIEKDGLVDAP 212

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIK 202
            G   +   +      +   K +  +  +        L +     G+  +I+
Sbjct: 213 IG---RHPVHRTRMAVVKNGKPARTYYRILEKFVACTLLQCSLETGRTHQIR 261


>gi|157376301|ref|YP_001474901.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
 gi|157318675|gb|ABV37773.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
          Length = 278

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 26/170 (15%), Positives = 47/170 (27%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           E   +   HKP GL+   S    R   F        +   V  V RLD  T G+LL    
Sbjct: 35  EDDDVVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLFAKS 94

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  L     +    + Y     G + +         + +      D+      Q   
Sbjct: 95  SEMANKLCEQFEAKTVDKHYLAIVRGNMHEADTLDYALKVELDDHGDKDVDPNKAAQDAV 154

Query: 186 NAW----------------------VTVGLREGKNREIKKVFEFFNWKVN 213
            ++                      V +    G+  ++++        + 
Sbjct: 155 TSYQPLLNTEIPFPSGRYATSRYALVKLTPHTGRKHQLRRHMAHLRHPIV 204


>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 = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/170 (17%), Positives = 61/170 (35%), Gaps = 28/170 (16%)

Query: 15  RVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           R+ K +        SR  ++R I    V VNG   ++ +  V S D I ++         
Sbjct: 13  RLDKFVMEKTPEWISRTFIQRAIKNGEVLVNG-TSKKPSYKVKSGDIITLNAPEAPEIPE 71

Query: 64  ----GVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------ 112
                +PL      R + + +K  G++T         T+ + +      +  +G      
Sbjct: 72  ILPEDIPLDIIYEDRDILVINKQPGIITHPIPSHTSGTIVNGVLYHCKDLQGIGGVLRPG 131

Query: 113 ---RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK 157
              RLD +T G++++  +    + L          ++Y     G   + +
Sbjct: 132 IVHRLDKDTSGVMVIAKNDLAHQSLTKQFKDRLTEKLYICLVKGVPKRKE 181


>gi|57505358|ref|ZP_00371287.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           upsaliensis RM3195]
 gi|57016494|gb|EAL53279.1| ribosomal large subunit pseudouridine synthase C [Campylobacter
           upsaliensis RM3195]
          Length = 308

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 55/139 (39%), Gaps = 15/139 (10%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  NG L+++    +     + V      GV +   E     +  KP G+
Sbjct: 32  EAQKLIDKKRLFCNGNLVKKKNEILQGVVELIVYENAPKGVKIVY-ENEEFAVLEKPSGV 90

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLL--TNDGGLARVLELPS 138
           ++    P+GR   +     I+         V RLD  T GL+L   T +  +        
Sbjct: 91  LS---HPNGRHCAYSLCDEIWELWGMEACVVHRLDKETSGLILAAKTKNSQVEFKTMFEK 147

Query: 139 TQWLRVYRVRFHGQVDQDK 157
            +  + Y     G + ++ 
Sbjct: 148 REIQKEYLALTQGLIKEEF 166


>gi|46447425|ref|YP_008790.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia
           amoebophila UWE25]
 gi|46401066|emb|CAF24515.1| putative 23S rRNA pseudouridine synthase [Candidatus Protochlamydia
           amoebophila UWE25]
          Length = 219

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/178 (16%), Positives = 60/178 (33%), Gaps = 35/178 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG---RSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   L++ +KP GL+T  S        S     L  ++ +     + +V RLD    G++
Sbjct: 10  EDNHLFVLNKPAGLLTQPSGTAHDSLESQAKAYLKIVYQKPGNVFLEAVHRLDKPVSGIV 69

Query: 123 LLTNDGGLARVLEL-----PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------- 170
           +    G  ++ L        + Q  ++Y          ++   L+  ++           
Sbjct: 70  VF---GKTSKALTRLNASVRAKQTKKIYYAWVDSVPVDEQ-KTLENFLIHNDFQAQVVSS 125

Query: 171 -----CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIR--ISYG 221
                    +   +  +K   A + + L  G+  +I+             IR  I YG
Sbjct: 126 KHPQAKLAKLTYRVIERKSVGALLEIKLETGRYHQIRAQLAHLGCP----IRGDIRYG 179


>gi|332638678|ref|ZP_08417541.1| ribosomal large subunit pseudouridine synthase D [Weissella cibaria
           KACC 11862]
          Length = 303

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 81/247 (32%), Gaps = 40/247 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASR--REVERMIAQQRVKVNGILLE-----RAAVN 53
           M   + + +     ++   +A+ G++ R    V+R      V + G  +      +    
Sbjct: 1   MAQFSWINQGDETLKIKTFLAQRGVSHRMFSIVKR--GGGAVLLAGKQVRTVDEVKPGDK 58

Query: 54  VM-------STDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           V        S D + +  +P+        WL   K  G+ +     D  +T+ + +    
Sbjct: 59  VTIVMPPEESNDVVAMSDLPITVLYEDENWLVVEKEAGVTSVPGKADRETTMVNRVKGYL 118

Query: 106 SR-------VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQ 155
           +R          V RLD  T G+ LL      A  L           + Y     G +  
Sbjct: 119 ARSGAEDLVPHVVTRLDRFTSGVALLAKH-RFAHGLLDKQLQTHSVDKRYYAIVDGDLPD 177

Query: 156 D-----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
           D             + +++ +   G      +  +  + G+   V V L  G+  +I+  
Sbjct: 178 DYGFIDAPIGRMDDDFIRREVREDGRPSQT-EYWVVKRFGNQTLVRVQLHTGRTHQIRVH 236

Query: 205 FEFFNWK 211
           F++    
Sbjct: 237 FKYLGHP 243


>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 = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 76/242 (31%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V + F  +RV   +AR    SR  VE +     V+  G  L +++  + + + +EVD   
Sbjct: 8   VPDGFDGERVDAALARMTGLSRSRVEDLCEAGEVRRGGETLAKSS-RLRAGELLEVDLPD 66

Query: 64  ---GVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                P+         LY         KP G+    S       V   L ++        
Sbjct: 67  PRPVEPVATPVEGMELLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVQVATSG 126

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD+ T G++++        VL+         +VY     G +D     + 
Sbjct: 127 AAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTID 186

Query: 162 K----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                      K  +I+G         +           + L  G+  +I+         
Sbjct: 187 APIGRHPSREWKMAIIEGGRESITHYDVIEAMPGACLAEIHLETGRTHQIRVHMAAVGHP 246

Query: 212 VN 213
             
Sbjct: 247 CV 248


>gi|38234158|ref|NP_939925.1| putative pseudouridine synthase [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200420|emb|CAE50108.1| Putative pseudouridine synthase [Corynebacterium diphtheriae]
          Length = 308

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 78/232 (33%), Gaps = 38/232 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL--------------LERAAV 52
           V E     RV   +++    SR     +     V V+G                +    V
Sbjct: 10  VPEGLAGMRVDAALSKLLGISRTAAADLAIAGDVVVDGHCVGKSDRLSEGQWLDVTLPEV 69

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
             ++     ++G+ +  ++   +   +KP+G+    +      TV   L +   R+ + G
Sbjct: 70  RDLTPREELIEGMDILYSDDD-VIAVNKPVGVAAHPTLGWEGPTVIGGLAAAGFRISTSG 128

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKLN 159
                    RLD+ T G++++        VL+    +    + Y     G +D     ++
Sbjct: 129 PPERKGIVQRLDVGTSGVMVVAASERGYSVLKRAFKERTVTKTYHSLVQGHMDPLSGTID 188

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +  +   G        T++    + + + + L  G+  +I+
Sbjct: 189 APIGRHPSAGWRFAVTTDGKHAVTHYETIEAFAEA-SLLRIHLETGRTHQIR 239


>gi|29346052|ref|NP_809555.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253568538|ref|ZP_04845949.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_6]
 gi|29337946|gb|AAO75749.1| RNA pseudouridylate synthase [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251842611|gb|EES70691.1| RNA pseudouridylate synthase [Bacteroides sp. 1_1_6]
          Length = 306

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLER------AAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++  +        + V         E
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVLVDNVITTQFNFPLQPGMKVQISKEKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FHNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVFIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L     +    R Y     G +++D   +        +   
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGTMEKDYDTVVSWLTDKTLYVS 203

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 204 SSDYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 243


>gi|238918767|ref|YP_002932281.1| tRNA pseudouridine synthase C [Edwardsiella ictaluri 93-146]
 gi|238868335|gb|ACR68046.1| tRNA pseudouridine synthase C [Edwardsiella ictaluri 93-146]
          Length = 263

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 54/173 (31%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +  +    V +V RLD  T G+LLL   
Sbjct: 6   QDDHLVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDMIGRHVYTVHRLDRPTSGVLLLGLS 65

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGIC---- 171
             +AR L       Q  +VY     G           +  + L+ +              
Sbjct: 66  SEIARALAQQFEQHQIHKVYHAVVRGYLQGEALLDYPLTPE-LDKIADRFRSPDRAPQPA 124

Query: 172 ------YGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                     +V L   +   +  ++   E     G+  ++++        + 
Sbjct: 125 QTYYRGLATAEVPLAIGRYPTSRFSLV--ELRPQTGRKHQLRRHMAHLRHPII 175


>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 = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 80/234 (34%), Gaps = 39/234 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNV-----M 55
           +V +    +RV   I+R    SR     ++    V V+G            V V      
Sbjct: 8   MVPDGLAGERVDVGISRMLGLSRTRAADLVTAGHVLVDGRAPARSTRLEPGVMVHVELPD 67

Query: 56  STDHIEV-----DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
               +EV     +G+ L   +   + +  KP+G+    S      TV  +L         
Sbjct: 68  EKPAVEVRPQIAEGMSLIHQDDDIVVI-DKPVGVAAHPSAGWSGPTVLGHLAAAGVEIRT 126

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DK 157
                R   V RLD+ T GL+++         L+    + +  +VY     G  DQ    
Sbjct: 127 SGDPERQGIVSRLDVGTSGLMVVARTERAYTTLKDAFRAREVGKVYHAICQGTPDQPRGT 186

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +            K  +   G        TL+  +G+   + +GL  G+  +I+
Sbjct: 187 IEAPIGRSPQHDYKFAVREDGKHSVTHYETLEELQGAT-LLRIGLETGRTHQIR 239


>gi|194366450|ref|YP_002029060.1| RluA family pseudouridine synthase [Stenotrophomonas maltophilia
           R551-3]
 gi|194349254|gb|ACF52377.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia
           R551-3]
          Length = 324

 Score = 62.5 bits (151), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 83/248 (33%), Gaps = 44/248 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  +   QR+   +  +   A R  V +++   +V+VNG   + A   + + D + V  
Sbjct: 20  TVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAK-AERKLEAGDEVRVPP 78

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNL 101
           V L +                     E  RL   +KP G+ +            T+    
Sbjct: 79  VRLSEEGDKAGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALR 138

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL-----ELPSTQWLRVYRVRFHGQVDQD 156
           P     +  V RLD +T GLL++         L     E       + Y     G++   
Sbjct: 139 PG--QTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRYLTLLAGRMPDG 196

Query: 157 KL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIKKV 204
            +     L  G+   G  +  +            +  ++G +++  V +  G+  +I+  
Sbjct: 197 VMTVDAPLHVGLRQGGERHVQVNAIGKESISHFRVLERRGGHSYCEVRIETGRTHQIRVH 256

Query: 205 FEFFNWKV 212
            +     V
Sbjct: 257 AQHLGHPV 264


>gi|260582391|ref|ZP_05850183.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|260094542|gb|EEW78438.1| pseudouridylate synthase [Haemophilus influenzae NT127]
          Length = 324

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 74/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>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 = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 73/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V   + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVFGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|295884073|gb|ADG57579.1| RluD [Streptococcus sanguinis]
 gi|332363746|gb|EGJ41526.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK49]
          Length = 291

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D + +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVNPGDDVCLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSTYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  +   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RLKQFGQAALVKCQLKTGRTHQIR 230


>gi|291301467|ref|YP_003512745.1| pseudouridine synthase RluA family [Stackebrandtia nassauensis DSM
           44728]
 gi|290570687|gb|ADD43652.1| pseudouridine synthase, RluA family [Stackebrandtia nassauensis DSM
           44728]
          Length = 312

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 83/256 (32%), Gaps = 46/256 (17%)

Query: 1   MKDKN----IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M ++     +V +     R+ +VI+R    SR     +++   V V+G    + +  V +
Sbjct: 1   MSNRESREVLVPDGLDGLRIDQVISRLFGLSRTVAAELVSAGEVTVDGQECMK-STRVAA 59

Query: 57  TDHIE-----------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF- 98
              +                  V+G+ +  ++   + +  KP+G+    S      TV  
Sbjct: 60  GGQLSVLLPEPPKPASAPEPELVEGLAVIYSDDD-IAVVDKPVGVAAHSSPGWNGPTVVA 118

Query: 99  --------DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
                    ++     R   V RLD+ T GL+ +         L+      +  + YR  
Sbjct: 119 GLAAAGHRISVHGPPERQGIVHRLDVGTSGLMAVAKSERAYSALKRAFKQREVDKRYRTV 178

Query: 149 FHGQVD------QDKLNL-----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
             G  D         +        K  +   G        TL+    + + + V L  G+
Sbjct: 179 IQGHPDPLRGTIDAPIARHPGHDFKFAVRAGGRASITHYDTLEAFPAA-SLLDVQLETGR 237

Query: 198 NREIKKVFEFFNWKVN 213
             +I+  F        
Sbjct: 238 THQIRVHFSALRHPCV 253


>gi|116493188|ref|YP_804923.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116103338|gb|ABJ68481.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 294

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 58/175 (33%), Gaps = 21/175 (12%)

Query: 57  TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------- 108
             ++ +   PL      + WL  +KP GL       D   T+ + +   +  +       
Sbjct: 68  DQNVAISDGPLDIIFEDKNWLLVNKPAGLTAVPGPSDREDTLVNRIKGHWQAIESKNMMP 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK------LN 159
             V RLD  T G+ L+     ++  L        +  ++Y     G V  +K      L 
Sbjct: 128 HLVTRLDRFTSGITLVARH-QVSNSLLSEQVAHHKIKKIYLAMVDGVVQAEKGTFNQSLG 186

Query: 160 LLKKGI---VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           L   GI   V            +  +  +   V + L+ G+  +I+  F      
Sbjct: 187 LAADGIHREVRDDGQQATTSFKVLKRFENQTLVQIHLKTGRTHQIRVHFANAGHP 241


>gi|295091829|emb|CBK77936.1| pseudouridine synthase, RluA family [Clostridium cf.
           saccharolyticum K10]
          Length = 345

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 91/258 (35%), Gaps = 55/258 (21%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
            V +N   QR+ K++ +   +A +  V +M+ ++ + +NG      +  ++  D I    
Sbjct: 5   TVTKNEAGQRLDKLLFKYMNLAGKSFVYKMLRKKNITLNGKKC-DGSERLLEGDEIRLFL 63

Query: 62  -------VDGVPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                     V ++K  R +         +   +KP G+++  +  DG  ++ + L +  
Sbjct: 64  SEETIEKFSEVKVQKVSRVKLEIVYEDEDVIFINKPAGMLSQKA-RDGDESLVEYLIAYL 122

Query: 106 S-------------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
                         R     RLD NT GL+         + L          + Y     
Sbjct: 123 MESGQLTKEELKSFRPSVCNRLDRNTSGLVAAGKSLPGLQELSRIIKDRSIGKYYLCLVK 182

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLRE 195
           GQV Q       +G +++      ++VT + + GS               +  + V L  
Sbjct: 183 GQVKQPSRI---EGWLLKDERTNRVEVTKEERGGSLPICTEYTPLLRSGAHTLLKVKLIT 239

Query: 196 GKNREIKKVFEFFNWKVN 213
           G++ +I+         V 
Sbjct: 240 GRSHQIRAHLASIGCPVV 257


>gi|329122013|ref|ZP_08250622.1| RluA family pseudouridine synthase [Dialister micraerophilus DSM
           19965]
 gi|327467065|gb|EGF12577.1| RluA family pseudouridine synthase [Dialister micraerophilus DSM
           19965]
          Length = 290

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/193 (16%), Positives = 67/193 (34%), Gaps = 27/193 (13%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHI------EVDGVPLRKAERTRL-----WLYHKPIGLV 85
              V +NG+ +  A + V   D +      E D +P     +         +  K   ++
Sbjct: 37  NGSVILNGVQIYNANIVVHVNDKVVCEWSEETDIIPSCIPLKIIYEDNTLLIIDKDADMI 96

Query: 86  TTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
              +     +T+ + +   + +      +  + RLD NT GL+++     L   L     
Sbjct: 97  IHPTSKTETNTLVNAISGYYKKNNQMSGIHPIYRLDRNTTGLIVVAKSAKLQYELSKEHG 156

Query: 140 QWLRVYRVRFHGQVDQDKLNLL-----KKGIVI-----QGICYGDMQVTLDTQKGSNAWV 189
              R Y     G+    + +++     K+G +I                +  +K S   +
Sbjct: 157 TIKREYLAVVEGRFKNKEGSIIYPIGRKEGSIIEWKVRDDGKEARTDYKVIEEKPSCTLL 216

Query: 190 TVGLREGKNREIK 202
            + L  G+  +I+
Sbjct: 217 KLRLYTGRTHQIR 229


>gi|260662712|ref|ZP_05863606.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
 gi|260552793|gb|EEX25792.1| pseudouridylate synthase [Lactobacillus fermentum 28-3-CHN]
          Length = 294

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 72/237 (30%), Gaps = 43/237 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERM---IA--QQRVKVNGILLERAAVNVMSTD--HIEVDG 64
            P ++   +   G+  R     +   I       +V+   +      ++      + V  
Sbjct: 11  EPIKIKTFLHSLGMGHR-----LFNDIKNGAGEFQVDHRRVR-PTTKILPNQPLTLTVQP 64

Query: 65  VP----LRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
            P    +  +E     +Y        +KP+G+ +         T+ + +           
Sbjct: 65  EPGDATVATSEEPLTIVYEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPD 124

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------ 157
            R   + RLD +T GLLL+      + ++          + YR    G   ++       
Sbjct: 125 LRPHLITRLDRDTAGLLLVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDAP 184

Query: 158 LNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +K  I  +          +   +  +G    V + L  G+  +I+         
Sbjct: 185 IARIKGQIEREVNPAGQPAKTEYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHP 241


>gi|283798031|ref|ZP_06347184.1| pseudouridine synthase, RluA family [Clostridium sp. M62/1]
 gi|291074333|gb|EFE11697.1| pseudouridine synthase, RluA family [Clostridium sp. M62/1]
          Length = 345

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 91/258 (35%), Gaps = 55/258 (21%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
            V +N   QR+ K++ +   +A +  V +M+ ++ + +NG      +  ++  D I    
Sbjct: 5   TVTKNEAGQRLDKLLFKYMNLAGKSFVYKMLRKKNITLNGKKC-DGSERLLEGDEIRLFL 63

Query: 62  -------VDGVPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                     V ++K  R +         +   +KP G+++  +  DG  ++ + L +  
Sbjct: 64  SEETIEKFSEVRVQKVSRVKLEIVYEDEDVIFINKPAGMLSQKA-RDGDESLVEYLITYL 122

Query: 106 S-------------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
                         R     RLD NT GL+         + L          + Y     
Sbjct: 123 MESGQLTKEELKSFRPSVCNRLDRNTSGLVAAGKSLPGLQELSRIIKDRSIGKYYLCLVK 182

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS---------------NAWVTVGLRE 195
           GQV Q       +G +++      ++VT + + GS               +  + V L  
Sbjct: 183 GQVKQPSRI---EGWLLKDERTNRVEVTKEERGGSLPICTEYTPLLRSGAHTLLKVKLIT 239

Query: 196 GKNREIKKVFEFFNWKVN 213
           G++ +I+         V 
Sbjct: 240 GRSHQIRAHLASIGCPVV 257


>gi|29832675|ref|NP_827309.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           avermitilis MA-4680]
 gi|29609795|dbj|BAC73844.1| putative pseudouridylate synthase [Streptomyces avermitilis
           MA-4680]
          Length = 314

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 64/175 (36%), Gaps = 27/175 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   I+R    SR +   + A  +V V+G ++ +       A + V     
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVLVDGTVVGKSERVHGGAWLEVEMPQA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   L +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  PAPVQIVAEPVEGMEIVHDDDDVLVIV-KPVGVAAHPSPGWSGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
                   V RLD+ T GL+++         L+    +    + Y     G  D 
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTVDKRYHALVQGHPDP 185


>gi|229490347|ref|ZP_04384188.1| pseudouridine synthase, RluA family [Rhodococcus erythropolis
           SK121]
 gi|229322637|gb|EEN88417.1| pseudouridine synthase, RluA family [Rhodococcus erythropolis
           SK121]
          Length = 308

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 53/310 (17%), Positives = 99/310 (31%), Gaps = 66/310 (21%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV------ 52
           M++   +   +     RV   +AR    SR  V  +  +  V V+G+ + ++        
Sbjct: 1   MRESRSMPVPDGLDAMRVDAGLARLLGLSRTVVAALAEEGSVLVDGVAVGKSDRLTAGSW 60

Query: 53  --NVMSTD----HIE---VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
              V+        IE   V+G+ +  A+   +    KP+G+    S      TV   L  
Sbjct: 61  LEVVLPEPPRPLTIEATPVEGMEILYADDDVV-AVDKPVGVAAHASVGWTGPTVIGGLAA 119

Query: 102 -------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
                       R   V RLD+ T G++++        +L+    Q    + Y     G 
Sbjct: 120 AGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQRTIDKRYHALVQGH 179

Query: 153 VDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D               N  +  +   G        T++  + + + + V L  G+  +I
Sbjct: 180 PDPSSGTIDAPIGRHHGNDWRFTVTADGKPSVTHYDTIEAFQAA-SLLDVHLETGRTHQI 238

Query: 202 K--------------------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +                    ++ E    +   L  +S G         G   E+  K  
Sbjct: 239 RVHFSALRHPCCGDLTYGADPRLAERLGLERQWLHAVSLGFAHPAD---GRWVEIKSKYP 295

Query: 242 REQLGPHLLE 251
           ++    H LE
Sbjct: 296 KDL--EHALE 303


>gi|125718992|ref|YP_001036125.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           sanguinis SK36]
 gi|125498909|gb|ABN45575.1| Ribosomal large subunit pseudouridine synthase D, putative
           [Streptococcus sanguinis SK36]
          Length = 299

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 41/205 (20%), Positives = 73/205 (35%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V S D I +               +G  + +  +
Sbjct: 36  RKIRHFLRTKKHVSVNG-LAINWQTVVKSGDDICLIFDEEDYPQKTILFGNGELVEELYQ 94

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 95  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 154

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+    KL           +  K+ +  +   Y +  V
Sbjct: 155 PILNRLL-EKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHV 213

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T   Q G  A V   L+ G+  +I+
Sbjct: 214 TRVKQFGQAALVKCQLKTGRTHQIR 238


>gi|85714567|ref|ZP_01045554.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
 gi|85698452|gb|EAQ36322.1| pseudouridine synthase, RluD [Nitrobacter sp. Nb-311A]
          Length = 351

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 57/182 (31%), Gaps = 41/182 (22%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGIL-----------LERAAVNVMSTDHIEV 62
           R+ +V+A  +   SR  ++ +I    V V               +   A +V   D I +
Sbjct: 27  RLDRVLAVHSPDLSRSRLKSLILAGHVSVVKKASAAERTSGPPSVSDPAYHVAPGDTITI 86

Query: 63  ----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
                      G  +      E   L + +KP GLV          T+ + L +      
Sbjct: 87  RVPPPISAKPQGEAIALDIVYEDNDLIVINKPKGLVVHPGAGHQAGTLVNALIAHCGGSL 146

Query: 107 -------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQV 153
                  R   V RLD +T GL++   +    + L        R       Y     G  
Sbjct: 147 SGIGGVCRPGIVHRLDKDTTGLMVAAKNDAAHKSLSTQFADHGRTGAMRRGYLAFVWGLP 206

Query: 154 DQ 155
           ++
Sbjct: 207 NR 208


>gi|309972703|gb|ADO95904.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 324

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 74/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|293604136|ref|ZP_06686544.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           piechaudii ATCC 43553]
 gi|292817361|gb|EFF76434.1| ribosomal large subunit pseudouridine synthase D [Achromobacter
           piechaudii ATCC 43553]
          Length = 343

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/164 (23%), Positives = 63/164 (38%), Gaps = 28/164 (17%)

Query: 15  RVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---- 67
           R+ KV+A  G+    SR  ++  I    V VNG   +     V   D + V   P     
Sbjct: 52  RLDKVLA--GLLPDHSRSRLQGWIESGNVHVNGAPGK-IRQTVGPGDQLLVWAQPAPDAR 108

Query: 68  ----RKAERTRL------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------V 111
                  E T +       + +KP GLVT     +   T+ + L   +  + +      V
Sbjct: 109 AFTPEPVEFTVVDESADWIVVNKPAGLVTHPGAGNWSGTLLNGLLYRYPELAAVARAGIV 168

Query: 112 GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
            RLD +T GL+++  +      L  +L +    R Y    HG +
Sbjct: 169 HRLDKDTSGLMVVARNEKAQTHLVRQLQARSMGREYIALAHGWL 212


>gi|83312285|ref|YP_422549.1| pseudouridylate synthase, 23S RNA-specific [Magnetospirillum
           magneticum AMB-1]
 gi|82947126|dbj|BAE51990.1| Pseudouridylate synthase, 23S RNA-specific [Magnetospirillum
           magneticum AMB-1]
          Length = 505

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 79/249 (31%), Gaps = 57/249 (22%)

Query: 4   KNIVQENFTPQ----RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           + +      P+    R+ + +A R    SR  ++ ++   RV +    +  A++ V    
Sbjct: 185 QRLTPPAVEPEEAGTRLDRWLALRLPELSRTRIKGLMEDGRVSLEETTISDASLRVKPGQ 244

Query: 59  HIEVD---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
              VD     P +            E   L +  KP G+V   +  +   T+ + L +  
Sbjct: 245 CFVVDVPPDAPAQPEPQDIALTVVYEDEDLIVIDKPAGMVVHPAPGNPDETLVNALLAHC 304

Query: 106 ----------SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                      R   V R+D +T GLL+   T+        +  +    R Y     G  
Sbjct: 305 GESLAGIGGVKRPGIVHRIDKDTSGLLVAAKTDAAHRGLATQFAAHTLERAYWALVWGTP 364

Query: 154 DQDKLNLLKKGIVIQGIC------YGDMQVTLDTQKGSNAWVT---------VGLRE--- 195
                   ++G  I+G           M V     K +              V L E   
Sbjct: 365 SP------RQG-EIEGNIGRNPNDRKKMAVVKSGGKPALTRYRVLKSFAGGAVSLVECRL 417

Query: 196 --GKNREIK 202
             G+  +I+
Sbjct: 418 ATGRTHQIR 426


>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 = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 41/225 (18%), Positives = 71/225 (31%), Gaps = 42/225 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLR-KAERT 73
           SR  ++ +I +  V VNG    +A   V + D I V            + +PL    E  
Sbjct: 56  SRSFIQGLIEEGHVLVNGA-ARKANYKVRAMDQIAVVIPPPRELKVEAENIPLEILYEDE 114

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLL 124
            + + +K  G+V   +      T+ + L      +           V R+D +T GLL++
Sbjct: 115 DVLVVNKSQGMVVHPAPGAWTKTLVNALLYHCRNLSGINGVLRPGIVHRIDKDTSGLLVV 174

Query: 125 TNDGGLARVLELPS---TQWLRVYRVRFHGQV-------------DQDKLNLLKKGIVIQ 168
             +  LA              R Y    HG V             D      +   +V Q
Sbjct: 175 AKN-DLAHQGLAEQIKAHSMARRYLAIVHGVVFEPSGTVEAPIGRDPADRKKMA--VVFQ 231

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     +  +      +   L  G+  +I+    +    V 
Sbjct: 232 NAKEAVTHYEVLERFRDFTLLEARLETGRTHQIRVHMAYLKHPVL 276


>gi|116330669|ref|YP_800387.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116124358|gb|ABJ75629.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 377

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 63/171 (36%), Gaps = 20/171 (11%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + ++    R+   +++     SR   ++ I + R+ V G  ++   + +   D +    
Sbjct: 15  FISKDDVGIRLDHFLSKKFTYHSRNVWQKEINEGRISVLGKKVKS-GILLREGDTVVY-- 71

Query: 65  VPLRKAERTR---LWLYH---------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVIS 110
            P+ + E        + +         KP  L    +    +  +   L     F  + +
Sbjct: 72  QPIERKEPPVRKDYKILYEDEFFVAVDKPGDLPVHPAGKYRKGNLLTLLKESGKFENLFT 131

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN 159
           V RLD  T G++L   D   A +L     S +  + Y  + +G   + K+ 
Sbjct: 132 VHRLDRETSGVVLFAKDSKAASLLSGLFSSRKIQKYYITKVYGDFPRRKIA 182


>gi|154496245|ref|ZP_02034941.1| hypothetical protein BACCAP_00530 [Bacteroides capillosus ATCC
           29799]
 gi|150274328|gb|EDN01405.1| hypothetical protein BACCAP_00530 [Bacteroides capillosus ATCC
           29799]
          Length = 300

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/219 (17%), Positives = 70/219 (31%), Gaps = 42/219 (19%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLRKA-------ERT 73
           RR   + +    + ++G+ +      V +   +       EV G  +          +  
Sbjct: 36  RRV--KWLEDG-ILLDGVRVT-VGDRVRAGQILSVVVGDTEVSGAIVPAPGPLDIVYQDQ 91

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+           T+ + L   + +         V RLD  T GLLL+   
Sbjct: 92  DVLVLNKAPGVAVHPGPGHYSDTIGNFLMDYYRKQGILADFHPVHRLDRGTSGLLLVALH 151

Query: 128 GGLA----RVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICY 172
           G         L  PS +  RVY     G            + + + ++L + +   G   
Sbjct: 152 GHAQEVLKEQLHSPSFR--RVYLAVCEGAPNPPSGVIDAPIGRLEGSVLARTVRPDGQRA 209

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                TL T     A V + L  G+  +I+         
Sbjct: 210 VTHYRTLRTVN-DRALVRLELETGRTHQIRVHMAHLGHP 247


>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 = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 74/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|116328674|ref|YP_798394.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116121418|gb|ABJ79461.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 377

 Score = 62.5 bits (151), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 63/171 (36%), Gaps = 20/171 (11%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + ++    R+   +++     SR   ++ I + R+ V G  ++   + +   D +    
Sbjct: 15  FISKDDVGIRLDHFLSKKFTYHSRNVWQKEINEGRISVLGKKVKS-GILLREGDTVVY-- 71

Query: 65  VPLRKAERTR---LWLYH---------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVIS 110
            P+ + E        + +         KP  L    +    +  +   L     F  + +
Sbjct: 72  QPIERKEPPVRKDYKILYEDEFFVAVDKPGDLPVHPAGKYRKGNLLTLLKESGKFENLFT 131

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN 159
           V RLD  T G++L   D   A +L     S +  + Y  + +G   + K+ 
Sbjct: 132 VHRLDRETSGVVLFAKDSKAASLLSGLFSSGKIQKYYITKVYGDFPRRKIA 182


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 79/243 (32%), Gaps = 48/243 (19%)

Query: 13  PQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P R+ K +       SR  ++R   Q+ + VNG  ++  +  V   D I +         
Sbjct: 45  PMRIDKFLMEHLYNTSRNRLQRAAEQEFILVNGRPVKS-SYKVKPLDEIVILLDRPKYEN 103

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSR 107
               + +PL    E   L +  KP GLV      +   T+ +          +       
Sbjct: 104 EIIPEDIPLDIVYEDEDLMVVDKPAGLVVHPGCGNYTGTLVNAIAWHLKDNPDYDPNDPT 163

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-------- 157
           V  V R+D +T GLL++  +      L     +    R+Y     G    ++        
Sbjct: 164 VGLVHRIDKDTSGLLVVAKNADAKTHLGRQFFNKTTQRLYNALVWGSFQDEEGRIEGNIA 223

Query: 158 ---LNLLKKGIVIQGICYGDMQVT-LDTQKGSNAWVTVGLRE-----GKNREIKKVFEFF 208
               + ++  +       G   VT     +  N    V L E     G+  +I+   +  
Sbjct: 224 RHPKDRMQMAVFPPDSGIGKHAVTHYRVLENFNY---VTLVECRLETGRTHQIRAHMKHI 280

Query: 209 NWK 211
              
Sbjct: 281 GHP 283


>gi|15839195|ref|NP_299883.1| pseudouridylate synthase [Xylella fastidiosa 9a5c]
 gi|9107828|gb|AAF85403.1|AE004067_10 pseudouridylate synthase [Xylella fastidiosa 9a5c]
          Length = 330

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 46/289 (15%), Positives = 98/289 (33%), Gaps = 59/289 (20%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           +V    + QR+   + ++     R  + +++   +V+VNG  ++ A   +   D I    
Sbjct: 22  VVPAEHSGQRLDNFLLSKLKGVPRSLIYKLVRSGQVRVNGGRVK-AERKLDGGDEIRLPP 80

Query: 62  ---VDGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPS 103
              +    +                 E  RL   +KP G+ +          +    +  
Sbjct: 81  LRLIQDRAIVAPSAAFLARMEAAIVFEDARLLALNKPSGMASHGGSGISYGVIEAMRILR 140

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPST-------QWLRVYRVRFHGQV 153
               +  V RLD +T GLL++          + L   ++          + Y     G++
Sbjct: 141 PKQELELVHRLDRDTSGLLIMAKKRAALIELQALMREASVNGKEGRGIAKRYLTLLSGRM 200

Query: 154 DQDKLN-------LLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
               ++        L++G      V         +  L  ++G  ++  V +  G+  +I
Sbjct: 201 PNGVMSVDAPLHINLRQGGERHVRVHHDGKPSKSRFRLLERRGGQSYCEVLIETGRTHQI 260

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           +   +     V             G    G  +EV+++ LR+Q+G   L
Sbjct: 261 RVHAQHLGHPVT------------GDDKYGD-QEVNRR-LRDQIGLQRL 295


>gi|158520422|ref|YP_001528292.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
 gi|158509248|gb|ABW66215.1| pseudouridine synthase [Desulfococcus oleovorans Hxd3]
          Length = 258

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 53/165 (32%), Gaps = 23/165 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGL 121
           E   L   +KP GL+    D  G  T+ +                 +  V RLD    G+
Sbjct: 18  EDNHLLALYKPAGLLVQG-DSTGDPTLLELGRCWLKIRYNKPGKVFLGMVHRLDRPVAGV 76

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL----LKKG---IVIQGICY 172
           +L       A  +          + Y     G + +++  L     ++G    +I     
Sbjct: 77  VLFCRTSKAAGRISAQFRDGVTAKQYVAVVEGVIPENEGRLANHIFRRGPTSHIIDVPTP 136

Query: 173 GDMQVTL----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  L      +  S   V + L  G++ +I+  F    + V 
Sbjct: 137 KSREARLAFHVIDRTDSRTLVKIDLETGRHHQIRVQFAHLGFPVV 181


>gi|301060346|ref|ZP_07201209.1| pseudouridine synthase, RluA family [delta proteobacterium NaphS2]
 gi|300445542|gb|EFK09444.1| pseudouridine synthase, RluA family [delta proteobacterium NaphS2]
          Length = 265

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 57/164 (34%), Gaps = 23/164 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTEGL 121
           E T + + +KP G+V          T+   L    + +  +G         RLD +T GL
Sbjct: 24  EDTWIIVLYKPPGIVVHPGPGHSSGTLVHGLLKHCTDLSGIGGTLRPGIVHRLDKDTSGL 83

Query: 122 LLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD----KLNLLKKGIVIQ------- 168
           +L+  +    + L          + Y    HG +  +     L + +  +  +       
Sbjct: 84  MLVAKNDMAHQALARQFKDGTVHKEYVALVHGLLPSESGTIDLPICRHPVRRKEMSIAKS 143

Query: 169 -GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            G     +   +   +   + +++ ++ G+  +I+  F      
Sbjct: 144 GGRNALTLWKKIAECEEGFSLLSITIKTGRTHQIRVHFAHLGHP 187


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/171 (20%), Positives = 62/171 (36%), Gaps = 22/171 (12%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   + + +KP  LV      +   TV + L   +  ++   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
               V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>gi|227515440|ref|ZP_03945489.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|227086199|gb|EEI21511.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
          Length = 294

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 72/237 (30%), Gaps = 43/237 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERM---IA--QQRVKVNGILLERAAVNVMSTD--HIEVDG 64
            P ++   +   G+  R     +   I       +V+   +      ++      + V  
Sbjct: 11  EPIKIKTFLHSLGMGHR-----LFNDIKNGAGEFQVDHRRVR-PTTKILPNQPLTLTVQP 64

Query: 65  VP----LRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
            P    +  +E     +Y        +KP+G+ +         T+ + +           
Sbjct: 65  EPGDATVATSEEPLTIVYEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPD 124

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------ 157
            R   + RLD +T GLLL+      + ++          + YR    G   ++       
Sbjct: 125 LRPHLITRLDRDTAGLLLVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDTP 184

Query: 158 LNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +K  I  +          +   +  +G    V + L  G+  +I+         
Sbjct: 185 IARIKGQIEREVNPAGQPAKTEYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHP 241


>gi|218509234|ref|ZP_03507112.1| RNA-pseudouridylate synthase protein, ribosomal large subunit D
           [Rhizobium etli Brasil 5]
          Length = 274

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 78/249 (31%), Gaps = 52/249 (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-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVI 109
             + +PL    E   L +  KP GLV      +   T+ + L               R  
Sbjct: 65  RGEDIPLDILYEDDDLIVISKPAGLVVHPGSGNWTGTLVNALIHHCGATLSGIGGVRRPG 124

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG-----------Q 152
            V RLD +T G++++  +    R L L      R       Y+    G            
Sbjct: 125 IVHRLDKDTTGVMVVAKNDVAHRHLSLQFADHGRTMPLERAYQAIVWGRPRSLTGTVDAP 184

Query: 153 VDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
           + +   +  ++ +        D      +V     +  +A     L E     G+  +I+
Sbjct: 185 LGRATGDRTRRAVKRPDSQDADQAITHYEVIERFHETPDATALASLVECRLETGRTHQIR 244

Query: 203 KVFEFFNWK 211
                    
Sbjct: 245 VHMAHIGHP 253


>gi|88800777|ref|ZP_01116334.1| pseudouridine synthase [Reinekea sp. MED297]
 gi|88776483|gb|EAR07701.1| pseudouridine synthase [Reinekea sp. MED297]
          Length = 328

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 85/244 (34%), Gaps = 34/244 (13%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLE---------R 49
           +K+  IV      +R  + IA    A  SR  +++ I + R+ VNG  L+          
Sbjct: 8   IKESQIVPNELGQKRFDQ-IAAQLFADYSRSRIQQWIKEGRLTVNGKTLKPRDKLIGGET 66

Query: 50  AAVNVMSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             ++V        +  P+      E  ++ +  KP GLV          TV + L   + 
Sbjct: 67  LTLDVTLESDERWEAEPVELNVVYEDEQIIVIDKPAGLVVHPGAGTPSGTVLNGLLYRYP 126

Query: 107 RVIS------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV----------R 148
            + +      V RLD +T GL+++         L   L      R Y             
Sbjct: 127 ELAAVPRAGIVHRLDKDTTGLMVVARTLTAQTHLAGQLQDRSMGREYYALCMGVMTGGGV 186

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            +  +D+   +  K  +   G+    +    ++ +  ++  V   L  G+  +I+     
Sbjct: 187 VNEPIDRHPKHRTKMAVAPTGMGKDAITHYRVEQRFRNHTLVRCKLETGRTHQIRVHLSH 246

Query: 208 FNWK 211
             + 
Sbjct: 247 IGYP 250


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/171 (20%), Positives = 62/171 (36%), Gaps = 22/171 (12%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   + + +KP  LV      +   TV + L   +  ++   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
               V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 72/209 (34%), Gaps = 36/209 (17%)

Query: 27  SRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEVDGVPLRKAERT-----RLWLYHK 80
           S+RE++R IA  RV VNG  +++ +       ++I     P+ K         R  ++ K
Sbjct: 27  SQREIQRYIAIGRVLVNGAPIVKPSDYLQGEVEYIYF--EPISKGLAPHFIEERFVVFDK 84

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLAR--VLELP 137
           P G++    +     ++ D L + F        R+D  T GL+L   D        +   
Sbjct: 85  PSGMLIHPQNRFTEYSLIDELKAQFGMNANIAHRIDQETSGLVLCAKDKKSEVDIKMMFQ 144

Query: 138 STQWLRVYRVRFHGQVDQD---KLNLLKKGIVIQGIC--YGDMQVTLDTQKG-------- 184
                + Y    HG++ ++      LL+              M V +D            
Sbjct: 145 ERDMKKKYLAMVHGELKEELRIDAPLLR----YDDEKSALVRMVVKVDPTGKESLTFVRP 200

Query: 185 -------SNAWVTVGLREGKNREIK-KVF 205
                      V      G+  +I+  +F
Sbjct: 201 LKYFPITDTTLVECSPHTGRQHQIRVHMF 229


>gi|145641509|ref|ZP_01797087.1| SfhB [Haemophilus influenzae R3021]
 gi|145273800|gb|EDK13668.1| SfhB [Haemophilus influenzae 22.4-21]
          Length = 324

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 61/171 (35%), Gaps = 22/171 (12%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
           R   V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/171 (20%), Positives = 62/171 (36%), Gaps = 22/171 (12%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   + + +KP  LV      +   TV + L   +  ++   
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 110 ---SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
               V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>gi|254521304|ref|ZP_05133359.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219718895|gb|EED37420.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 307

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 53/286 (18%), Positives = 94/286 (32%), Gaps = 58/286 (20%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  +   QR+   +  +   A R  V +++   +V+VNG   + A   + + D + V  
Sbjct: 3   TVPADRAGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAK-AERKLEAGDEVRVPP 61

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNL 101
           V L +                     E  RL   +KP G+ +            T+    
Sbjct: 62  VRLTEEGDKAGPPEAFMRRLEQAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALR 121

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL-----ELPSTQWLRVYRVRFHGQVDQD 156
           P     +  V RLD +T GLL++         L     E       + Y     G++   
Sbjct: 122 PG--QTLELVHRLDRDTSGLLIVAKKRSALSELQALLREDHGAGIRKRYLTLLTGRMPDG 179

Query: 157 KL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIKKV 204
            +     L  G+   G  +  +            +  ++G +++  V +  G+  +I+  
Sbjct: 180 VMTVDAPLHVGLRQGGERHVQVNAIGKESISHFRVLERRGGHSYCEVRIETGRTHQIRVH 239

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
            +     V             G    G    V  K LREQ+G   L
Sbjct: 240 AQHLGHPVA------------GDDKYGD--PVVNKRLREQIGLKRL 271


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 79/241 (32%), Gaps = 34/241 (14%)

Query: 3   DKNIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLER-----AAVN 53
           D+ I  ++    R+ K +      +G+   RE  R+I    V VNG              
Sbjct: 31  DRIIAGDSDDGLRLDKFLLKLLPDSGL---RERRRLIENGLVMVNGRSCRSGLKMFPGAE 87

Query: 54  V---MSTDH---IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           V    + D    +E+        +       +KP GL +        S+V + L  IF  
Sbjct: 88  VVLLEAEDRSCAVEILSQVKVVKQGEGFGTVYKPEGLHSAAIAGSAESSVEECLSGIFPG 147

Query: 108 VISV--GRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNL--- 160
              +   RLD  T G+LL+                    +VY  + HG  +   +     
Sbjct: 148 KEPILANRLDFLTSGMLLIAFGVERENEFRECEDSGTVDKVYHAKVHGIPEGPFVVKNSL 207

Query: 161 ----LKKGIVIQG----ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                K+  V+        +   +V ++      + + V + +G   +I+       + +
Sbjct: 208 DTADRKRTKVLDDQAPEERWSSAEV-VERYDDGTSLLEVRIAKGARHQIRAHLAHAGFPI 266

Query: 213 N 213
            
Sbjct: 267 V 267


>gi|328881776|emb|CCA55015.1| Ribosomal large subunit pseudouridine synthase D [Streptomyces
           venezuelae ATCC 10712]
          Length = 313

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 85/247 (34%), Gaps = 40/247 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   IAR    SR +   + A  +V+V+G ++ +       A + V     
Sbjct: 12  VPDGLEGERVDAAIARMFGFSRTKAAELAAAGKVQVDGSVVGKSERVSGGAWLEVEMPGA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KPIG+    S     +TV   L +   R+   
Sbjct: 72  AAPVQIVAEPVEGMEIVHDDDDIVVIM-KPIGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD------ 154
                   V RLD+ T GL+++         L+    +    + Y     G  D      
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTVDKRYHALVQGHPDPMSGTI 190

Query: 155 QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFF 208
              +           +   G         ++  + + + + + L  G+  +I+  +    
Sbjct: 191 DAPIGRHPNHDYKWAVTADGKPSVTHYDLIEAYRSA-SLLDIKLETGRTHQIRVHMSAHR 249

Query: 209 NWKVNRL 215
           +  V  L
Sbjct: 250 HPCVGDL 256


>gi|186475732|ref|YP_001857202.1| RluA family pseudouridine synthase [Burkholderia phymatum STM815]
 gi|184192191|gb|ACC70156.1| pseudouridine synthase, RluA family [Burkholderia phymatum STM815]
          Length = 436

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 83/245 (33%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            V      +R+ KV+A+     SR  ++  I  QRV V+G   +     V     IE+  
Sbjct: 84  TVPPGLAGERLDKVLAKVFPEFSRSRLQSWIEAQRVHVDGQPAK-IRQPVPLGASIELVP 142

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      + VPL    E   L + +KP GLV   +  +   TV + L   +     
Sbjct: 143 DLLPEQLAFTAEPVPLDVVYEDDTLVVINKPAGLVVHPAAGNWSGTVLNGLLHRYGDAAA 202

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---------- 151
              R   V RLD  T GL+++         L  +L +    R Y     G          
Sbjct: 203 GLPRAGIVHRLDKETSGLMVVARTLEAQTDLVRQLQARTVKRRYLALVWGNMPDDGTIDA 262

Query: 152 QVDQDKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFE 206
            + +D     +  +V    G         +D+   ++   + +   L  G+  +I+    
Sbjct: 263 PIGRDPRERTRMAVVTGAAGKPARTHFRRIDSTVWERQPVSAIHCDLETGRTHQIRVHCA 322

Query: 207 FFNWK 211
                
Sbjct: 323 HIGHP 327


>gi|114561967|ref|YP_749480.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333260|gb|ABI70642.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 281

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 26/159 (16%), Positives = 52/159 (32%), Gaps = 21/159 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +     +++KP G+    S     +T+    +           + RLD    GLL+L + 
Sbjct: 88  DEAEYSIWYKPYGMRCQGSKWSDHTTINRYAELNMQPQRNAFIIHRLDRAATGLLVLGHS 147

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDMQVTLDT- 181
                 +     + +  + Y+V   G+            + I             TL T 
Sbjct: 148 KKATAAIAKLFETRELEKYYQVIVEGEFP-------SNPVTINTPVDNKPALSHATLLTY 200

Query: 182 -QKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN--RLI 216
             + + + V V +  G+  +I+  +       V   RL 
Sbjct: 201 NSELNQSKVQVKIDTGRKHQIRIHM-ASLGHPVVGDRLH 238


>gi|332686243|ref|YP_004456017.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370252|dbj|BAK21208.1| similar to ribosomal large subunit pseudouridine synthase D
           [Melissococcus plutonius ATCC 35311]
          Length = 298

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 92/246 (37%), Gaps = 48/246 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILL---------ERAAV 52
           + +   P+++   +   GI      +R++A+      ++KVN  +          ++  V
Sbjct: 6   IYDENEPKQIKYFLRELGI-----SKRLLAKIKFQGGKIKVNHQIQNVLFYLTKNDQLQV 60

Query: 53  NVMSTDHIE---VDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
            + +    E   +D  P+    E     + +KP+ + +  +      T+ + + + +   
Sbjct: 61  VIPNEAEHETMLLDTTPIDIIFEDEHYLVVNKPVNIPSIPAQYHPNGTMANRVKAYYKEK 120

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHG------- 151
                 V  V RLD +T GL+L    G  A  L        + +++Y+    G       
Sbjct: 121 NYANQVVHIVTRLDRDTTGLMLFAKHG-FAHALLDQELRNKRVVKIYQALVGGNIANLDS 179

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                  + +D  +L+K+ ++  G      +  ++ +    A V + L  G+  +I+  F
Sbjct: 180 HGRIDLPIGRDHSSLMKRQVISTGQQ-AITEYWIEEKYTDFAAVRIQLHTGRTHQIRVHF 238

Query: 206 EFFNWK 211
                 
Sbjct: 239 SAIGCP 244


>gi|313813196|gb|EFS50910.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL025PA1]
          Length = 306

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 83/245 (33%), Gaps = 40/245 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V ++G  + RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLC 64

Query: 64  ----GVPLRKAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNL--------- 101
                  +       +W+ H         KP G+    S      +V ++L         
Sbjct: 65  DPVATPSITPQIVEGMWIIHDDSDIVVVDKPAGVAAHPSLGWEGPSVVEHLAAAGFAIST 124

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ---- 155
                R   V RLD+ T GL+++        +L+         +VY     G  D     
Sbjct: 125 SGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGT 184

Query: 156 -------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF 207
                  D  +  K  IV  G        T++  + +   + V L  G+  +I+  +   
Sbjct: 185 IDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-AA 242

Query: 208 FNWKV 212
                
Sbjct: 243 IKHPC 247


>gi|192360779|ref|YP_001983659.1| pseudouridine synthase Rlu family protein [Cellvibrio japonicus
           Ueda107]
 gi|190686944|gb|ACE84622.1| pseudouridine synthase, RluA family subfamily [Cellvibrio japonicus
           Ueda107]
          Length = 320

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/215 (15%), Positives = 67/215 (31%), Gaps = 30/215 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLE---------RAAVNVMSTDHIEVDGVPLRK---AERTR 74
           SR  ++  I    + V+G + +           A++       + +   +      E   
Sbjct: 32  SRSRLQGWIKDGLLTVDGRVAKPKDKLIGGETLALHAELEAQGDWEPEAIELDIIHEDDD 91

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTNDG 128
           L + +K  GLV   +  +   T+ + L +         R   V RLD +T GL+++    
Sbjct: 92  LLIINKQAGLVVHPAAGNYTGTLVNALLNHAPSLVNIPRAGIVHRLDKDTTGLMVVAKTL 151

Query: 129 GLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
                L  +L      R Y                 + +  L      ++ QG       
Sbjct: 152 EAHTDLVAQLADRSVSREYEAVAVGAMTGGGTVDAPIGRHPLQRKLMAVLSQGGKRAVTH 211

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  +   +  + V L  G+  +I+         
Sbjct: 212 YRVAKRYPHHTHIRVKLETGRTHQIRVHMAHVGHP 246


>gi|198274965|ref|ZP_03207497.1| hypothetical protein BACPLE_01124 [Bacteroides plebeius DSM 17135]
 gi|198272412|gb|EDY96681.1| hypothetical protein BACPLE_01124 [Bacteroides plebeius DSM 17135]
          Length = 308

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 33/215 (15%), Positives = 66/215 (30%), Gaps = 28/215 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLW 76
           SR  V+ ++A + V V+  +  +    +     ++V     +            E   L 
Sbjct: 44  SRTRVKALLANRVVLVDNNIQTQYNFPLKPGMKVQVSREKNKHEFRHPMLKILYEDAYLI 103

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGL 130
           +  K  GL++  +D     T    L     R      +  V RLD  T G+++   D   
Sbjct: 104 VVEKKEGLLSVATDHQKERTAQHILNEYVKRTHRNNRIFVVHRLDRETSGIMMYAKDEKT 163

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--------QGICYGDMQVT 178
              L          R Y     G +++D+  +        +         G         
Sbjct: 164 QHTLRDNWHDIVYDRRYVSIVMGDMEKDQGTVRSWLTDRKLYVSSSPVDDGGKLSITHYR 223

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +    + + + L  G+  +I+   +     V 
Sbjct: 224 TIKRANGYSLMELQLETGRKNQIRVHMQSLGHPVV 258


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 69/215 (32%), Gaps = 47/215 (21%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------EVDGVP 66
           R+   ++R    SR    ++I   +V V+     + ++ V+    +        E+D VP
Sbjct: 48  RLDYFLSRELGTSRAFSTKLIRDGQVSVSWCPRVKPSMKVLPGGSVTAVVPPPEELDLVP 107

Query: 67  LRKAERTRL-----WLYHKPIGLVTTHSDPDGRST----VFDNLPSIF-----SRVISVG 112
                R         +  KP GLV   +    R T    +    P +       R   V 
Sbjct: 108 EDVPFRVVYEDADLIVVDKPAGLVVHPAPGHWRGTLVHGLLFRYPDMEALNGVRRPGIVH 167

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           RLD  T GLL++  +G     L     Q    + Y    HG+                  
Sbjct: 168 RLDATTSGLLVVARNGLAMEELVRCFKQRTLRKEYLALAHGRP----------------- 210

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREG------KNR 199
              + ++ L   +       + + EG      + R
Sbjct: 211 QLPEGEIRLPIGRDPKNRKRMTILEGGRDSLTRYR 245


>gi|241895991|ref|ZP_04783287.1| 23S rRNA pseudouridylate synthase RluD [Weissella paramesenteroides
           ATCC 33313]
 gi|241870722|gb|EER74473.1| 23S rRNA pseudouridylate synthase RluD [Weissella paramesenteroides
           ATCC 33313]
          Length = 305

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 80/241 (33%), Gaps = 42/241 (17%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQ--RVKVNGILLERAAVNVMSTDHIEV--- 62
            ++ +  R+   +A+ G++ R  +  +I +   +V +N   +     +V   D +EV   
Sbjct: 8   NQSDSTLRIKTFLAQRGVSHR--MFAIIKRGGGQVLLNHRPVRTLD-DVEPGDLVEVKMP 64

Query: 63  ----------DGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR---- 107
                       +P++       WL   K  G+ +     D  +T+ + +          
Sbjct: 65  AEKSNAIVAASDLPIKILYEDENWLVVDKVAGVTSVPGKADRETTMVNRVKGYLISEGAE 124

Query: 108 ---VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQD----- 156
                 V RLD  T G+ LL      A  L           + Y     G V  D     
Sbjct: 125 DLVPHVVTRLDRFTSGVALLAKH-RFAHGLLDKQLQTHTVDKRYYAIVDGIVPDDHGFID 183

Query: 157 ------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                   + +++ +   G      +  +  +  +   V V L  G+  +I+  F++   
Sbjct: 184 APIGRMDNDFIRREVRADGRPSQT-EYWVVNRMPNQTLVKVQLHTGRTHQIRVHFKYIGH 242

Query: 211 K 211
            
Sbjct: 243 P 243


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 89/252 (35%), Gaps = 42/252 (16%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D   V   +   +R+ + + R     SR  V+++IA+ +  V+G  + +A   + + +
Sbjct: 1   MSDSTKVYTADQDGERLDRFLTRMEPTLSRAHVQKVIAEGQALVSGR-VRKANYKLQAGE 59

Query: 59  HIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            +              + +PL    E + + + +K  G+V   +      T+ + L    
Sbjct: 60  KVTFHLPEAKPVEILPEDIPLDILYEDSDIIVINKARGMVVHPATGIYTGTLVNALLYHC 119

Query: 106 SRVIS---------VGRLDINTEGLLLLT-NDGGLARVLELPSTQWL-RVYRVRFHGQVD 154
             +           V RLD +T G+++   ND     + E   T+   R+YR    G + 
Sbjct: 120 KDLSGINGEIRPGIVHRLDKDTSGVMVAAKNDAAHLDLAEQIRTKAAHRIYRAIVCGNIR 179

Query: 155 QD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++                 +   IV +          +  + G+   V   L  G+  +I
Sbjct: 180 EEAGVIKGDIGRHPTDRKKMA--IVHEHGKPAVTHFRVLERFGAYTLVECRLETGRTHQI 237

Query: 202 KKVFEFFNWKVN 213
           +         V 
Sbjct: 238 RVHMASIGHPVL 249


>gi|192361858|ref|YP_001982092.1| putative pseudouridylate synthase [Cellvibrio japonicus Ueda107]
 gi|190688023|gb|ACE85701.1| putative pseudouridylate synthase [Cellvibrio japonicus Ueda107]
          Length = 291

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/151 (19%), Positives = 59/151 (39%), Gaps = 5/151 (3%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLL 124
           P R  +  R  +++KP GL+   S      ++   +  +  R    V RLD +  GL+L+
Sbjct: 100 PQRLEDVGRYSVWYKPHGLLAQGSQWGDHCSLLRWVEVVRQRECFLVHRLDADAAGLILI 159

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            +D   A  L          + Y+    G++    L  L++ +  +          +D Q
Sbjct: 160 AHDAQAAAALSQLFQGRSLRKHYQAWVSGELQATGL-RLEQPLDGKDALTWVNTAVID-Q 217

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             + + V V +  G+  +I++        + 
Sbjct: 218 PNNRSLVDVRIETGRKHQIRRHLAAIGHPIM 248


>gi|52425127|ref|YP_088264.1| tRNA pseudouridine synthase C [Mannheimia succiniciproducens
           MBEL55E]
 gi|52307179|gb|AAU37679.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 236

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 52/181 (28%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D      V   L     R V  + RLD  T G+LL    
Sbjct: 7   QDEHIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGRLVYPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
              A +L     + Q  + Y     G +            +L+ +      +        
Sbjct: 67  SETANLLCQQFETKQVEKSYLAVVRGYLTGSERIDYPLKIQLDKIADKFAQEDKAPQPAV 126

Query: 177 -------------VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                         T        A V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKTVEKPYATPRYATSRYALVRLVPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|332524051|ref|ZP_08400303.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
 gi|332315315|gb|EGJ28300.1| pseudouridine synthase, RluA family [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 284

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 72/211 (34%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK-----------AERTRLWLYHKP 81
              R++VNG +   A   +   D + +   D +P  K            E     + +KP
Sbjct: 21  KGGRIEVNG-IERNAIYLLDIGDEVSITIPDELPFEKLEAISHPLDIVYEDDHFLVINKP 79

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 80  VGYASIPS-AIHSNTIANFIKGYYVDQDYPNKQVHIVTRLDRDTSGLMLFAKHGYAHARL 138

Query: 135 --ELPSTQWLRVYRVRFHGQ---VDQDKLNL---------LKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G+    DQ ++           + + +   G         + 
Sbjct: 139 DKQLQARAIEKRYFALVCGEGQLPDQGEIVAPIGRSKDSIITRTVDPMGKYARTTYQVVG 198

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 199 RYAENVHLVDIKLHTGRTHQIRVHFSHIGFP 229


>gi|297171550|gb|ADI22548.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           Oceanospirillales bacterium HF0500_09M11]
          Length = 519

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 78/229 (34%), Gaps = 35/229 (15%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           V   +   R+ +  A    G  SR  ++  I +  + V+G    R    ++  + +    
Sbjct: 211 VDAQYAGIRLDQAAAELFDGF-SRSRLQNWIKEGVLTVDGR-AARPKDKLLGGEALTLAV 268

Query: 61  ----EVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVF------DNLPSIF 105
               E+D  P               + +KP GLV   +      T+       D+  S  
Sbjct: 269 ELAPEIDDQPEAIELPVIYQDQDLIVINKPAGLVVHPAAGHADGTLLNGLLHLDDRLSSL 328

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQV 153
            R   V RLD +T GL+++         L  +L      R Y+                +
Sbjct: 329 PRAGIVHRLDRDTTGLMVVARSVEAHTGLVAQLQDKSLYREYQAIAMGVMTGGGTVDAPM 388

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  ++  ++ +V  G         +  +  ++  V V L  G+  +I+
Sbjct: 389 GRHPVDRKRQAVVTHGGKPAVTHYRVLDRYRAHTRVQVRLETGRTHQIR 437


>gi|120555026|ref|YP_959377.1| pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120324875|gb|ABM19190.1| tRNA pseudouridine synthase C [Marinobacter aquaeolei VT8]
          Length = 245

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 58/167 (34%), Gaps = 30/167 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           L   HKP GL+   S  D   T F        +    V  V RLD  T G+LL   D   
Sbjct: 14  LLAVHKPAGLLVHRSPIDKHETEFALQYARAMNGGEHVYPVHRLDRPTSGVLLFARDPET 73

Query: 131 ARV--LELPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIV---IQG------------IC 171
           AR   L + +    + Y     G   +  +  + L++      ++G              
Sbjct: 74  ARALGLAMMAGAVSKTYLAMVRGWAPEQGVIDHPLREEPEDRRLKGQEQPVREALTRYRR 133

Query: 172 YGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
               ++ +  ++   +  ++   E     G+  ++++  +  N  + 
Sbjct: 134 LATTELPVAIERYPTSRYSLV--ELKPETGRKHQLRRHMKHINHPII 178


>gi|227528997|ref|ZP_03959046.1| RluA family pseudouridine synthase [Lactobacillus vaginalis ATCC
           49540]
 gi|227351009|gb|EEJ41300.1| RluA family pseudouridine synthase [Lactobacillus vaginalis ATCC
           49540]
          Length = 294

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 57/182 (31%), Gaps = 29/182 (15%)

Query: 55  MSTDHIEVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------ 107
              D++    +P++     R   + +KP G+ T    P    TV D+L +          
Sbjct: 66  KPNDNVIPINLPIQIIYEDRDFLILNKPAGVATV---PAHHVTVADSLVNRVRNYYERQG 122

Query: 108 -----VISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVD----- 154
                +    RLD +T GL++       A  +        Q  + Y     GQ+      
Sbjct: 123 YENLVIHVATRLDKDTSGLVVFPKH-RFAHAVMDQQLKKHQVKKNYYAVVGGQIKAPHGY 181

Query: 155 -----QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                           VI        +  L+      + + + L  G+  +I+  F++  
Sbjct: 182 IDAPIDRDPEKFVSRTVISTGKPSVTEYWLEKSSVQMSLLRIRLHTGRTHQIRVHFQYLG 241

Query: 210 WK 211
             
Sbjct: 242 HP 243


>gi|325686709|gb|EGD28735.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK72]
          Length = 291

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 73/204 (35%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVNPGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  +   Y +  V 
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPAKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHVN 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  + V   L+ G+  +I+
Sbjct: 207 RIKQFGQASLVKCQLKTGRTHQIR 230


>gi|119897309|ref|YP_932522.1| pseudouridylate synthase [Azoarcus sp. BH72]
 gi|119669722|emb|CAL93635.1| pseudouridylate synthase [Azoarcus sp. BH72]
          Length = 324

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/231 (18%), Positives = 75/231 (32%), Gaps = 36/231 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ +V+AR     SR  ++  +    ++++G +  +A   V   + + V G+P       
Sbjct: 32  RLDQVLARLFPEHSRSRLQAWLKDGLIRLDG-MERQAKHKVHGGEELVVAGLPPLPEQLA 90

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVG 112
                       E   + +  KP GLV      +   T+ + L           R   V 
Sbjct: 91  FEPEAIPLDVVYEDASILVIDKPAGLVVHPGSGNWSGTLLNALLHHAPALAGLPRAGIVH 150

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRF------HGQVDQDK----LNL 160
           RLD +T GL+++         L     Q    R Y           G++D D     +  
Sbjct: 151 RLDKDTTGLMVVAKTLEAQTDLVRQLQQRTVARHYYALVYGDIASDGEIDADIDRHPVQR 210

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +  +V  G              G    V   L+ G+  +I+         
Sbjct: 211 TRMAVVPGGRPALTRYAVRQRLHGLT-LVECRLQTGRTHQIRVHMAHLGHP 260


>gi|325479239|gb|EGC82335.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 303

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 65/209 (31%), Gaps = 39/209 (18%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERTRLWLYHK-------P 81
           VN  +++  +  +   D IE+D                    E     +  K       P
Sbjct: 36  VNDKIVK-PSFKLSEGDEIEIDDSLFHVPTIDPEAMDLKIVYENDDYAIIDKDSNVIVHP 94

Query: 82  IGLVTTHSDPDG--RSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLT--NDGGLARVLE 135
            G + T +  +G      +D L  I        V RLD +T GL+ +T  N         
Sbjct: 95  AGKIVTGTLVNGLLDRYGYDGLSHIGGDDRPGIVHRLDKDTTGLIAITKNNTSYKYFKKM 154

Query: 136 LPSTQWLRVYRVRFHGQVDQ--DKLNLL--------KKGIVIQGICYGDMQVTLDTQKGS 185
             + +  ++Y     G  D+  D +           +K  V            +  +   
Sbjct: 155 FETRKVDKIYYAIVFGTFDKKSDTIETFMDRDPHNRRKMAVTSSGRKAISHYEVVAETND 214

Query: 186 NAWVTVGLREGKNREIK-KVFEFFNWKVN 213
            + V V +  G+  +I+  +    N  + 
Sbjct: 215 YSLVKVKIVTGRTHQIRVHMT-HLNHPIL 242


>gi|157827593|ref|YP_001496657.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
 gi|157802897|gb|ABV79620.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           OSU 85-389]
          Length = 310

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/181 (18%), Positives = 61/181 (33%), Gaps = 46/181 (25%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV- 65
           R+ K +       RR         +E+ + Q+++ VN      A++ V+  D I +    
Sbjct: 21  RLDKYL-------RRLYPLLTQGVIEKALRQKQIIVNSKKA-EASLRVVEGDEIFIHDKF 72

Query: 66  --PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VF 98
             P+ +  +                         +   +KP GL T        S     
Sbjct: 73  NLPIAQPTKLVFTDAEITLAKKITTEYLIYEDDNIIAINKPAGLATQGGSKINLSVDSAL 132

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD 156
             L S  +    V RLD  T GLLL+  +   +  L     +    + Y    +G+  +D
Sbjct: 133 KYLNSQGADFKLVHRLDKETSGLLLIAKNYVSSVKLHDAFKEKLVEKTYLAVTYGKPIKD 192

Query: 157 K 157
           +
Sbjct: 193 Q 193


>gi|291276623|ref|YP_003516395.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963817|emb|CBG39653.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 322

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 79/249 (31%), Gaps = 54/249 (21%)

Query: 1   MKDKNIVQENFTP-QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+++ I+    TP +R+   +       + ++ ++I    V +NG    +    +   D 
Sbjct: 1   MQEQEIITT--TPHKRIDTFLCSFLHLPKNQILQLIKNSLVLLNGSPCAKGGKELKIGDR 58

Query: 60  I------------------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           I                  E+D       E   L + +KP  LV   +      T+ D L
Sbjct: 59  INILAPTSRPKILESKTSLEID----TIYEDDHLLILNKPSDLVIHPAPSQKAETLLDWL 114

Query: 102 PSI---------FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFH 150
            +            R   V RLD +T G + +  +      L   L +    R Y     
Sbjct: 115 KAKGYTLSTISGEERCGIVHRLDKDTTGAIAIAKNNLAHNSLANQLQTRTMGRYYLAIID 174

Query: 151 GQVDQDK----------LNLLKKGIVIQGICYGDMQVT-------LDTQKGSNAWVTVGL 193
             + +             N LK    +  + +   + +         +   S   V + L
Sbjct: 175 QPIKEALSIHCHMGRNPKNRLKM-CKLDPLVFPQARESKSLFLPLFLSHNHSYQLVAIKL 233

Query: 194 REGKNREIK 202
             G+  +I+
Sbjct: 234 FTGRTHQIR 242


>gi|237714573|ref|ZP_04545054.1| RNA pseudouridylate synthase [Bacteroides sp. D1]
 gi|262406439|ref|ZP_06082988.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_22]
 gi|293373837|ref|ZP_06620181.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|298481084|ref|ZP_06999278.1| RNA pseudouridylate synthase [Bacteroides sp. D22]
 gi|229445342|gb|EEO51133.1| RNA pseudouridylate synthase [Bacteroides sp. D1]
 gi|262355142|gb|EEZ04233.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_22]
 gi|292631236|gb|EFF49870.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|295083972|emb|CBK65495.1| pseudouridine synthase, RluA family [Bacteroides xylanisolvens
           XB1A]
 gi|298272658|gb|EFI14225.1| RNA pseudouridylate synthase [Bacteroides sp. D22]
          Length = 306

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 79/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNVM---STDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVKISKQKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L     +    R Y     G +++D   +        +   
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 203

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 204 SSEYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 243


>gi|251795436|ref|YP_003010167.1| pseudouridine synthase [Paenibacillus sp. JDR-2]
 gi|247543062|gb|ACT00081.1| pseudouridine synthase, RluA family [Paenibacillus sp. JDR-2]
          Length = 316

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 69/208 (33%), Gaps = 40/208 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV------------DGVPLRKA-ERTRLWLYHKPIGLVT 86
           + VNG+     A  V   D + +              +PL    E   L + +KP G++ 
Sbjct: 51  ITVNGVRAYTTA-KVTEGDSVAIRMEEEISEDILPQDLPLSIVFEDDYLLVVNKPAGIIV 109

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPS 138
             +     +T+ + +   +       R   V RLD +T GL+++  +  + + L   L +
Sbjct: 110 HPTKGHYTNTLANGIVHHWQVRGERVRFRPVHRLDEDTSGLVVIAKNPYIHQQLSEQLQA 169

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------------ 186
              +++Y    +G        +   G  I           +  +   +            
Sbjct: 170 GTIMKIYCAYVYGTPSPADGTV---GAPIDRNPEDPHVRIVTPEGYPSVTHYKTAAVFGG 226

Query: 187 ---AWVTVGLREGKNREIKKVFEFFNWK 211
              + V + L  G+  +I+   +     
Sbjct: 227 GQASKVRLKLETGRTHQIRVHMKHIGCP 254


>gi|261868111|ref|YP_003256033.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413443|gb|ACX82814.1| tRNA pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 237

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 59/195 (30%), Gaps = 36/195 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L     + V    RLD  T G+LL   +
Sbjct: 8   QDDVLVAVNKPAGMLVHRSWLDRHETQFVMQILRDQIGQLVYPFHRLDRPTSGVLLFALN 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-------------QDKLNLLKK-------GI 165
              A ++       Q  + Y     G V                  +   +        +
Sbjct: 68  SETANLVCHQFEQKQTEKQYLAVVRGYVTGQGEIDYPLKVQLDKIADKFAQQDKAPQSAV 127

Query: 166 VI-QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
               G+   +M   +     S  + V +  + G+  ++++  +     +  L    YG  
Sbjct: 128 TFYDGLKTVEMPYGVGRYAASRYSLVRLTPKTGRKHQLRRHMKHIFHPI--LGDTQYGDL 185

Query: 224 QLGTLLAGSTREVSK 238
                     R +++
Sbjct: 186 H-------QNRALTE 193


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 83/249 (33%), Gaps = 44/249 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL--------------LERAAV 52
           V +    +RV   I+R    SR +   + A  +V+V+G +              +E    
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVQVDGSVAGKSERVHGGAWLEVEMPGA 71

Query: 53  NVMSTDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                  +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+  
Sbjct: 72  P-APVQIVAEPVEGMEIVHDDDDIVVIM-KPVGVAAHPSPGWTGTTVIGGLAAAGYRIST 129

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVD---- 154
                    V RLD+ T GL+++      A  L     +     + Y     G  D    
Sbjct: 130 SGAAERQGIVHRLDVGTSGLMVVAKS-ERAYTLLKAQFRDRVVDKRYHALVQGHPDPMSG 188

Query: 155 --QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                +           +  +G         ++  + + + + + L  G+  +I+  +  
Sbjct: 189 TIDAPIGRHPNHDYKWAVTAEGKPSVTHYDLIEAYRAA-SLLDIKLETGRTHQIRVHMSA 247

Query: 207 FFNWKVNRL 215
             +  V  L
Sbjct: 248 HRHPCVGDL 256


>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 = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/215 (15%), Positives = 75/215 (34%), Gaps = 29/215 (13%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK----------AERTRLWL 77
           R  ++  +A+ +V VNGI        +     + +    +             E   + +
Sbjct: 74  RNSIKSALARGQVSVNGIPRTVHNFPLEQGQTVALSKEKVTPVVPLTGLRILHEDEAIIV 133

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            HK  GL++  S  +   T +  L         ++R+  + RLD +T G+++      + 
Sbjct: 134 IHKDAGLLSVASAQEQEVTAYRQLTAHVRREHPYNRIFVLHRLDRDTSGVMMFAKSEAIQ 193

Query: 132 RVLELPSTQW--LRVYRVRFHGQVDQDKLNL---LKKGIVIQ--------GICYGDMQVT 178
           + ++    +    R Y     GQV + +  +   LK+   ++           +      
Sbjct: 194 QEMQKAWKEVVYERTYIALVEGQVKKAEGTITSWLKESKTLKMYSSPYPNDGQHAVTHYK 253

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           L       + + V L  G+  +I+   E     + 
Sbjct: 254 LLQANRHFSLLEVRLETGRKNQIRVHMEDIGHPIV 288


>gi|125973321|ref|YP_001037231.1| RluA family pseudouridine synthase [Clostridium thermocellum ATCC
           27405]
 gi|256005428|ref|ZP_05430391.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281417524|ref|ZP_06248544.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|125713546|gb|ABN52038.1| pseudouridine synthase, RluA family [Clostridium thermocellum ATCC
           27405]
 gi|255990568|gb|EEU00687.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           2360]
 gi|281408926|gb|EFB39184.1| pseudouridine synthase, RluA family [Clostridium thermocellum JW20]
 gi|316940446|gb|ADU74480.1| pseudouridine synthase, RluA family [Clostridium thermocellum DSM
           1313]
          Length = 318

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 45/217 (20%), Positives = 76/217 (35%), Gaps = 39/217 (17%)

Query: 32  ERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD------GVPLRKA--------ERT 73
           ER+I     Q ++  N   +   AV V   D IEVD      G+ ++          E  
Sbjct: 28  ERLIKKLKRQGKILCNNRPVYVNAV-VCENDIIEVDLDFDDSGIFIQPEDIPIDIIYEDE 86

Query: 74  RLWLYHKPIGLVT--THSDPDGR--STVFDNL--PSIFSRVISVGRLDINTEGLLLLTND 127
            L   +K  G+V   T S P G   + V  +L    I  ++  V RLD +T G+++   +
Sbjct: 87  FLIALNKQPGIVVHPTCSHPGGTLANAVAFHLQKKGIVKKIRPVIRLDRDTSGIIIFAKN 146

Query: 128 GGLARVLELPSTQWL--RVYRVRFHGQVDQD--KLNL---------LKKGIVIQGICYGD 174
                 L          + Y    H  ++ D   ++L         + + I   G     
Sbjct: 147 PYCQEFLIRQMNDKTFIKEYIGIVHKVLENDNGTIDLPIARKPGSIMLRHISPDGDPAVT 206

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               L+   G+   V   L  G+  +I+   +     
Sbjct: 207 HYTVLERLNGAT-LVKFRLETGRTHQIRVHCQAIGHP 242


>gi|297183636|gb|ADI19762.1| hypothetical protein [uncultured gamma proteobacterium EB000_37F04]
          Length = 322

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 41/207 (19%), Positives = 72/207 (34%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNV----------MSTDHIEVDGVPLRK---AERT 73
           SR  +   I   R++ N     R    V           + D +E    PL      E  
Sbjct: 37  SRSRLAEWIKAGRLQRNHQ-ASRPKDKVAVDDQLLLWPETEDRVEWAPEPLPLDILYEDE 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + + +KP GLV   +      T+ + L       S   R   V RLD +T G++L    
Sbjct: 96  HVIVLNKPAGLVVHPATGHQTGTLVNGLLAHAPEMSALPRGGIVHRLDKDTSGVMLAARS 155

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
               + L  +L      R+Y     G           + +   + LK  +V  G      
Sbjct: 156 AIAHKSLVAQLADRSVSRLYSAVCRGTFTGGGTIDAPIGRHPTSRLKMAVVEDGKPSRTH 215

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++ +  ++  ++V L  G+  +I+
Sbjct: 216 -YRIEKRFSAHTHLSVSLETGRTHQIR 241


>gi|257870826|ref|ZP_05650479.1| pseudouridine synthase [Enterococcus gallinarum EG2]
 gi|257804990|gb|EEV33812.1| pseudouridine synthase [Enterococcus gallinarum EG2]
          Length = 283

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 43/217 (19%), Positives = 79/217 (36%), Gaps = 33/217 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRKA-E 71
           R+V  ++  ++ V+VNG         V   D + +               +   +    E
Sbjct: 28  RKVRHLLRTRKNVRVNGETA-LFHQEVAGGDQLTLLLEEADYTYQPVISGNKEKITVLFE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG 128
              L + +KP G+ T  + P+   T+ ++L +  S   R   V RLD  T G++L   + 
Sbjct: 87  DEHLIVVNKPAGIKTHPNQPNETDTLMNDLAAYLSPETRPYVVHRLDKETSGVILFAKNP 146

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----------IVIQGICYGDMQ 176
            +  +L   L S Q  R Y+    GQ+DQ++    K G          I  +        
Sbjct: 147 LVLPILGRMLESKQIYRRYQATVWGQLDQNQTIRKKIGRDRHDRRKRVIDPRNGLSAVTH 206

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           V +  +      +   L  G+  +I+         + 
Sbjct: 207 VEIAARNAQTTSIYCVLDTGRTHQIRVHLASIGHPIV 243


>gi|332673452|gb|AEE70269.1| RluA family ribosomal large subunit pseudouridine synthase
           [Helicobacter pylori 83]
          Length = 327

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 53/312 (16%), Positives = 104/312 (33%), Gaps = 61/312 (19%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRK 69
           R+ + +A+    S+ +V  +I +  V      +++  + +   D I      +   PL++
Sbjct: 13  RLDEFLAKELQISKNQVLYLIKEGLVFCQKKGVKKGGLALKKGDEITLLTPKITPKPLKR 72

Query: 70  A---------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISV 111
                     E   L + +KP  LV   +      T+ D L              R   V
Sbjct: 73  GLDLEIGVIFEDEDLLVLNKPPNLVIHKAPSVKEPTLVDWLEFKNYELSNLGSKERYGIV 132

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL----------- 158
            RLD +T G +++  +      L   L +    R Y       + ++K+           
Sbjct: 133 HRLDKDTSGGIVIAKNNFTHVHLSEQLKTKMMGRYYIALLSTPLKEEKMSVECYLTRNPN 192

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-------V--GLREGKNREIKKVFEFFN 209
           N LK  I ++       + +  ++    + +T       +   L  G+  +I+       
Sbjct: 193 NRLKM-IALK---AAKKEKSRYSKSEFTSLLTSQNNLNLIGAKLFTGRTHQIR---AHL- 244

Query: 210 WKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L R   G   L  L       + K+  R  L  +L+E      +  +     L++
Sbjct: 245 ---EYLNRHIIGD-NLYGLNQ----ALPKEETRIMLHAYLIEFKHPRSEQKLRFKVPLLK 296

Query: 270 DRPNIISEVPDD 281
           D      +V D 
Sbjct: 297 DMLEYFKKVFDK 308


>gi|260174510|ref|ZP_05760922.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
          Length = 306

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQISKQKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L          R Y     G +++D   +        +   
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 203

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 204 SSEYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 243


>gi|322514573|ref|ZP_08067606.1| tRNA pseudouridine synthase C [Actinobacillus ureae ATCC 25976]
 gi|322119512|gb|EFX91599.1| tRNA pseudouridine synthase C [Actinobacillus ureae ATCC 25976]
          Length = 250

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 68/202 (33%), Gaps = 39/202 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSEMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD------------- 174
             L        Q  + Y     G  +D+ +++   K +++  I                 
Sbjct: 72  -RLMSEQFEQHQMEKGYLAVVRGYLLDKGEIDYPLK-VILDKIADKFSQPKEAQQAVTFS 129

Query: 175 ---MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                V +    G +      L E     G+  ++++  +     +        G  + G
Sbjct: 130 QNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------MGDTKYG 182

Query: 227 TLLAGSTREVSKKILREQLGPH 248
            L     R +++K   ++L  H
Sbjct: 183 DLH--QNRTLTEKTGCDRLMLH 202


>gi|194366931|ref|YP_002029541.1| RluA family pseudouridine synthase [Stenotrophomonas maltophilia
           R551-3]
 gi|194349735|gb|ACF52858.1| pseudouridine synthase, RluA family [Stenotrophomonas maltophilia
           R551-3]
          Length = 329

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/217 (18%), Positives = 74/217 (34%), Gaps = 31/217 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIE------VDGVPLRKA-ERTR 74
           SR  +   I    V ++G         R    V  T  +E       + +PL    E   
Sbjct: 35  SRSRLTEWIKNGDVLLDGAQARPRDPLRGGEVVTLTVVLETQTDAQPEDIPLDVLFEDEY 94

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDG 128
           L + +KP+GLV      +   T+ + L       ++  R   V RLD +T G++++    
Sbjct: 95  LLVINKPVGLVVHPGAGNHSGTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTL 154

Query: 129 GLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDMQ 176
                L  +L +    R Y     G           +D+   + LK G+  +        
Sbjct: 155 EAQTALVEQLAARDVHRQYLAIVMGALVAGGTADAPIDRHPRDRLKMGVR-EDGKEAVTH 213

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             L  +  ++  +   L  G+  +I+         + 
Sbjct: 214 YRLRERFRAHTALECRLETGRTHQIRVHMAHIRHPIV 250


>gi|49083826|gb|AAT51150.1| PA4544 [synthetic construct]
          Length = 321

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 91/264 (34%), Gaps = 39/264 (14%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGV 65
           QR+ + IA       SR  +   I   R+ V+G +      +   A  V+  +  E  G 
Sbjct: 18  QRLDQ-IAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQLVLEAEQ-EAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPS--IFSRVISVG 112
            L +        E   + +  KP GLV   +      T+ +    ++P      R   V 
Sbjct: 76  WLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVPRAGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---KLNLLKKGI-- 165
           RLD +T GL+++         L  +L +    R+Y     G +         + + G+  
Sbjct: 136 RLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHGVQR 195

Query: 166 ----VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIR 217
               V+           +  +  ++    V L  G+  +I+       + +        R
Sbjct: 196 QKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGR 255

Query: 218 ISYGPFQLGTLLAGSTREVSKKIL 241
               P    TL+  + RE  ++ L
Sbjct: 256 FRIPPVASQTLVQ-TLREFPRQAL 278


>gi|329955144|ref|ZP_08296101.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
 gi|328526143|gb|EGF53162.1| pseudouridine synthase, RluA family [Bacteroides clarus YIT 12056]
          Length = 297

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/221 (17%), Positives = 77/221 (34%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++        +  + V         E
Sbjct: 15  EPMELMEFLAAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQISREKGRKE 74

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 75  FSNKLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYIVHRL 134

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D      L          R Y     G+           +   KL + 
Sbjct: 135 DRDTSGLMMFAKDEKTQNTLRDNWHDIVTDRRYVAVVAGEMENNAGMVRSWLTDRKLYVY 194

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 195 SNPTDDGGKEAITHYRTIKRANGF-SLVELNLETGRKNQIR 234


>gi|313891609|ref|ZP_07825216.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313119887|gb|EFR43072.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 290

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 31/193 (16%), Positives = 67/193 (34%), Gaps = 27/193 (13%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHI------EVDGVPLRKAERTRL-----WLYHKPIGLV 85
              V +NG+ +  A + V   D +      E D +P     +         +  K   ++
Sbjct: 37  NGSVILNGVQIYNANIVVHVNDKVVCEWSEETDIIPSCIPLKIIYEDNTLLIIDKDEDMI 96

Query: 86  TTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
              +     +T+ + +   + +      +  + RLD NT GL+++     L   L     
Sbjct: 97  IHPTSKTETNTLVNAISGYYKKNNQMSGIHPIYRLDRNTTGLIVVAKSAKLQYELSKEHG 156

Query: 140 QWLRVYRVRFHGQVDQDKLNLL-----KKGIVI-----QGICYGDMQVTLDTQKGSNAWV 189
              R Y     G+    + +++     K+G +I                +  +K S   +
Sbjct: 157 TIKREYLAVVEGRFKNKEGSIIYPIGRKEGSIIEWKVRDDGKEARTDYKVIEEKPSCTLL 216

Query: 190 TVGLREGKNREIK 202
            + L  G+  +I+
Sbjct: 217 KLRLYTGRTHQIR 229


>gi|237719529|ref|ZP_04550010.1| RNA pseudouridylate synthase [Bacteroides sp. 2_2_4]
 gi|229451389|gb|EEO57180.1| RNA pseudouridylate synthase [Bacteroides sp. 2_2_4]
          Length = 306

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 24  EPMELMEFLATKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQISKQKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L          R Y     G +++D   +        +   
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 203

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 204 SSEYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 243


>gi|111018085|ref|YP_701057.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
 gi|110817615|gb|ABG92899.1| pseudouridylate synthase [Rhodococcus jostii RHA1]
          Length = 302

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 77/242 (31%), Gaps = 37/242 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---------AAVNVMST 57
           V +     RV   +AR    SR  V ++  +  V V+G  + +           V +   
Sbjct: 3   VPDGLEAMRVDAGLARLLGLSRTAVAQLTEEGSVLVDGAPVGKSDRLSAGAWLEVELPEP 62

Query: 58  DH-IEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL---------PS 103
              + ++  P+   E       +    KP+G+    S      TV   L           
Sbjct: 63  PRPLTIEAEPVEGMEILYADDDVVAVDKPVGVAAHASVGWTGPTVIGGLAAAGFRISTSG 122

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--KLN 159
              R   V RLD+ T G++++        +L+    Q    + Y     G  D     ++
Sbjct: 123 AHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQRTIDKRYHALVQGHPDPSSGTID 182

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      K  +   G        T++  + + + + + L  G+  +I+  F     
Sbjct: 183 APIGRHRSNDWKFAVTADGKPSITHYDTVEAFQAA-SLLDIHLETGRTHQIRVHFAALRH 241

Query: 211 KV 212
             
Sbjct: 242 PC 243


>gi|15599740|ref|NP_253234.1| pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|116052689|ref|YP_793005.1| pseudouridine synthase [Pseudomonas aeruginosa UCBPP-PA14]
 gi|218893639|ref|YP_002442508.1| pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|254238708|ref|ZP_04932031.1| pseudouridine synthase [Pseudomonas aeruginosa C3719]
 gi|254244558|ref|ZP_04937880.1| pseudouridine synthase [Pseudomonas aeruginosa 2192]
 gi|296391365|ref|ZP_06880840.1| pseudouridine synthase [Pseudomonas aeruginosa PAb1]
 gi|313107189|ref|ZP_07793388.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa 39016]
 gi|12231021|sp|P33640|RLUD_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9950788|gb|AAG07932.1|AE004868_3 pseudouridine synthase [Pseudomonas aeruginosa PAO1]
 gi|115587910|gb|ABJ13925.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126170639|gb|EAZ56150.1| pseudouridine synthase [Pseudomonas aeruginosa C3719]
 gi|126197936|gb|EAZ61999.1| pseudouridine synthase [Pseudomonas aeruginosa 2192]
 gi|218773867|emb|CAW29681.1| pseudouridine synthase [Pseudomonas aeruginosa LESB58]
 gi|310879890|gb|EFQ38484.1| ribosomal large subunit pseudouridine synthase D [Pseudomonas
           aeruginosa 39016]
          Length = 320

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 91/264 (34%), Gaps = 39/264 (14%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGV 65
           QR+ + IA       SR  +   I   R+ V+G +      +   A  V+  +  E  G 
Sbjct: 18  QRLDQ-IAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQLVLEAEQ-EAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPS--IFSRVISVG 112
            L +        E   + +  KP GLV   +      T+ +    ++P      R   V 
Sbjct: 76  WLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVPRAGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---KLNLLKKGI-- 165
           RLD +T GL+++         L  +L +    R+Y     G +         + + G+  
Sbjct: 136 RLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHGVQR 195

Query: 166 ----VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIR 217
               V+           +  +  ++    V L  G+  +I+       + +        R
Sbjct: 196 QKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGR 255

Query: 218 ISYGPFQLGTLLAGSTREVSKKIL 241
               P    TL+  + RE  ++ L
Sbjct: 256 FRIPPVASQTLVQ-TLREFPRQAL 278


>gi|226360214|ref|YP_002777992.1| pseudouridine synthase RluD [Rhodococcus opacus B4]
 gi|226238699|dbj|BAH49047.1| pseudouridine synthase RluD [Rhodococcus opacus B4]
          Length = 308

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 79/250 (31%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---------ER 49
           M++   +   +     RV   +AR    SR  V ++  +  V V+G  +           
Sbjct: 1   MRETRSMPVPDGLEAMRVDAGLARLLGLSRTAVAQLTEEGSVLVDGAPVGKSDRLSAGTW 60

Query: 50  AAVNVMSTDH-IEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
             V +      + ++  P+   E       +    KP+G+    S      TV   L   
Sbjct: 61  LEVELPEPPRPLTIEAEPVEGMEILYADDDVVAVDKPVGVAAHASVGWTGPTVIGGLAAA 120

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                      R   V RLD+ T G++++        +L+    Q    + Y     G  
Sbjct: 121 GFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQRTIDKRYHALVQGHP 180

Query: 154 DQD--KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +   G        T++  + + + + + L  G+  +I+
Sbjct: 181 DPSSGTIDAPIGRHRSNDWKFAVTADGKPSITHYDTVEAFQAA-SLLDIHLETGRTHQIR 239

Query: 203 KVFEFFNWKV 212
             F       
Sbjct: 240 VHFAALRHPC 249


>gi|22127019|ref|NP_670442.1| tRNA pseudouridine synthase C [Yersinia pestis KIM 10]
 gi|45442581|ref|NP_994120.1| tRNA pseudouridine synthase C [Yersinia pestis biovar Microtus str.
           91001]
 gi|51597324|ref|YP_071515.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis IP
           32953]
 gi|108806509|ref|YP_650425.1| tRNA pseudouridine synthase C [Yersinia pestis Antiqua]
 gi|108813124|ref|YP_648891.1| tRNA pseudouridine synthase C [Yersinia pestis Nepal516]
 gi|145598957|ref|YP_001163033.1| tRNA pseudouridine synthase C [Yersinia pestis Pestoides F]
 gi|149366961|ref|ZP_01888994.1| tRNA pseudouridine synthase C [Yersinia pestis CA88-4125]
 gi|153949809|ref|YP_001399991.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis IP
           31758]
 gi|162421605|ref|YP_001607777.1| tRNA pseudouridine synthase C [Yersinia pestis Angola]
 gi|165927134|ref|ZP_02222966.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165939825|ref|ZP_02228365.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|166011912|ref|ZP_02232810.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166211483|ref|ZP_02237518.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167399889|ref|ZP_02305407.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167419839|ref|ZP_02311592.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167425312|ref|ZP_02317065.1| tRNA pseudouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|167468860|ref|ZP_02333564.1| tRNA pseudouridine synthase [Yersinia pestis FV-1]
 gi|170023309|ref|YP_001719814.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis YPIII]
 gi|186896429|ref|YP_001873541.1| tRNA pseudouridine synthase C [Yersinia pseudotuberculosis PB1/+]
 gi|218928206|ref|YP_002346081.1| tRNA pseudouridine synthase C [Yersinia pestis CO92]
 gi|229837745|ref|ZP_04457905.1| tRNA U65 pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|229840967|ref|ZP_04461126.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229843068|ref|ZP_04463218.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229903567|ref|ZP_04518680.1| tRNA U65 pseudouridine synthase [Yersinia pestis Nepal516]
 gi|270487346|ref|ZP_06204420.1| tRNA pseudouridine synthase C [Yersinia pestis KIM D27]
 gi|294503055|ref|YP_003567117.1| hypothetical protein YPZ3_0945 [Yersinia pestis Z176003]
 gi|34582458|sp|Q8ZH72|TRUC_YERPE RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|21960067|gb|AAM86693.1|AE013915_2 hypothetical protein y3143 [Yersinia pestis KIM 10]
 gi|45437446|gb|AAS62997.1| Pseudouridylate synthases, 23S RNA-specific [Yersinia pestis biovar
           Microtus str. 91001]
 gi|51590606|emb|CAH22247.1| conserved hypothetical protein [Yersinia pseudotuberculosis IP
           32953]
 gi|108776772|gb|ABG19291.1| tRNA pseudouridine synthase C [Yersinia pestis Nepal516]
 gi|108778422|gb|ABG12480.1| tRNA pseudouridine synthase C [Yersinia pestis Antiqua]
 gi|115346817|emb|CAL19703.1| Conserved hypothetical protein [Yersinia pestis CO92]
 gi|145210653|gb|ABP40060.1| tRNA pseudouridine synthase C [Yersinia pestis Pestoides F]
 gi|149290575|gb|EDM40651.1| tRNA pseudouridine synthase C [Yersinia pestis CA88-4125]
 gi|152961304|gb|ABS48765.1| tRNA pseudouridine synthase [Yersinia pseudotuberculosis IP 31758]
 gi|162354420|gb|ABX88368.1| tRNA pseudouridine synthase [Yersinia pestis Angola]
 gi|165912228|gb|EDR30865.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           IP275]
 gi|165921030|gb|EDR38254.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           F1991016]
 gi|165989178|gb|EDR41479.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166207254|gb|EDR51734.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166962580|gb|EDR58601.1| tRNA pseudouridine synthase [Yersinia pestis biovar Orientalis str.
           MG05-1020]
 gi|167050597|gb|EDR62005.1| tRNA pseudouridine synthase [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167055712|gb|EDR65496.1| tRNA pseudouridine synthase [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169749843|gb|ACA67361.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186699455|gb|ACC90084.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229679337|gb|EEO75440.1| tRNA U65 pseudouridine synthase [Yersinia pestis Nepal516]
 gi|229689944|gb|EEO82003.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. India 195]
 gi|229697333|gb|EEO87380.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Orientalis
           str. PEXU2]
 gi|229704122|gb|EEO91134.1| tRNA U65 pseudouridine synthase [Yersinia pestis Pestoides A]
 gi|262361091|gb|ACY57812.1| hypothetical protein YPD4_0903 [Yersinia pestis D106004]
 gi|262365333|gb|ACY61890.1| hypothetical protein YPD8_1205 [Yersinia pestis D182038]
 gi|270335850|gb|EFA46627.1| tRNA pseudouridine synthase C [Yersinia pestis KIM D27]
 gi|294353514|gb|ADE63855.1| hypothetical protein YPZ3_0945 [Yersinia pestis Z176003]
 gi|320014170|gb|ADV97741.1| tRNA U65 pseudouridine synthase [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 257

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 63/186 (33%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDRNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR+L L     Q  + Y     G V +         ++L+ +               
Sbjct: 67  SDVARMLSLQFEQHQIQKTYHAVVRGYVLEGGTVDYAMAEELDKIADKFAKSDKAPQPSV 126

Query: 175 --------MQVTLDTQKGSNAWVTVG-LR-E-GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                   ++V L   +   A  ++  L+ E G+  ++++        +        G  
Sbjct: 127 SHYEALAQVEVPLAIGRYETARYSLVALKPETGRKHQLRRHMAHIRHPI-------IGDS 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>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 = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 83/249 (33%), Gaps = 44/249 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL--------------LERAAV 52
           V +    +RV   I+R    SR +   + A  +V+V+G +              +E    
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVQVDGSVAGKSERVHGGAWLEVEMPGA 71

Query: 53  NVMSTDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                  +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+  
Sbjct: 72  P-APVQIVAEPVEGMEIVHDDDDIVVIM-KPVGVAAHPSPGWTGTTVIGGLAAAGYRIST 129

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVD---- 154
                    V RLD+ T GL+++      A  L     +     + Y     G  D    
Sbjct: 130 SGAAERQGIVHRLDVGTSGLMVVAKS-ERAYTLLKAQFRDRVVDKKYHALVQGHPDPMSG 188

Query: 155 --QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                +           +  +G         ++  + + + + + L  G+  +I+  +  
Sbjct: 189 TIDAPIGRHPNHDYKWAVTAEGKPSVTHYDLIEAYRAA-SLLDIKLETGRTHQIRVHMSA 247

Query: 207 FFNWKVNRL 215
             +  V  L
Sbjct: 248 HRHPCVGDL 256


>gi|145637336|ref|ZP_01792996.1| SfhB [Haemophilus influenzae PittHH]
 gi|145269428|gb|EDK09371.1| SfhB [Haemophilus influenzae PittHH]
          Length = 324

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 61/171 (35%), Gaps = 22/171 (12%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPISEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
           R   V RLD +T GL+++         L       +  R Y     G + +
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTK 180


>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 = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 83/238 (34%), Gaps = 39/238 (16%)

Query: 13  PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
           P RV K +  R   A+R ++++      ++ N  ++++    V   D I V         
Sbjct: 29  PLRVDKFLMTRIRNATRNKIQQAARDGNIRANEQVIKQ-NYRVKPGDTIRVLFEHPPYEN 87

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLP-SIFSRVI 109
               + +PL    E   L + +KP G+V      +   T+        D LP +  +R  
Sbjct: 88  LLLPEDIPLDIVYEDEVLLVVNKPAGMVVHPGHGNYTGTLVNALVHHLDQLPLNSDNRPG 147

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV-----------RFHGQVDQD 156
            V R+D  T GLL++         L          R Y                G + ++
Sbjct: 148 LVHRIDKETSGLLVIAKTEAAMANLARQFFDKTTRREYLALVWGNVADDSGTVEGPIGRN 207

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             N L+  +   G    +      ++ + G    V+  L  G+  +I+   +     +
Sbjct: 208 PKNRLQMQVFPDGSQGKEAVTHYRVEERLGYVTLVSCRLETGRTHQIRVHMQHIGHTI 265


>gi|120553810|ref|YP_958161.1| RluA family pseudouridine synthase [Marinobacter aquaeolei VT8]
 gi|120323659|gb|ABM17974.1| ribosomal large subunit pseudouridine synthase D [Marinobacter
           aquaeolei VT8]
          Length = 325

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 46/257 (17%), Positives = 80/257 (31%), Gaps = 54/257 (21%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-------------ERT 73
           SR  ++  I    + VNG    +    VM  D + +D  P  +              E  
Sbjct: 34  SRSRLQSWIKSGALTVNGKS-RKPRDKVMMGDSLALDAEPEVQVTWEAEPISLDIVYEDE 92

Query: 74  RLWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTND 127
            L + +KP GLV      H+D    + + +  P      R   V RLD +T G++++   
Sbjct: 93  HLLVINKPAGLVVHPAAGHTDGTLVNALLNYAPEVENLPRAGIVHRLDKDTSGIMVVARS 152

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYG 173
                 L  +L +    R Y     G +                   +   +V  G    
Sbjct: 153 LIAHTSLVDQLQTRTMGREYEAVVVGALTGGATVDAPIGRHPQDRKRMA--VVSSGKPAV 210

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN----RLIRISYGPFQLGTLL 229
                L  +  ++  V   L  G+  +I+         +        R+         L 
Sbjct: 211 TH-YRLLERFAAHTLVRCKLESGRTHQIRVHMAHVRHPLVGDPAYGGRLR--------LP 261

Query: 230 AGSTREVSKKILREQLG 246
            G     + + LR+ L 
Sbjct: 262 KG-----TTEELRDVLA 273


>gi|107099793|ref|ZP_01363711.1| hypothetical protein PaerPA_01000811 [Pseudomonas aeruginosa PACS2]
          Length = 317

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 91/264 (34%), Gaps = 39/264 (14%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGV 65
           QR+ + IA       SR  +   I   R+ V+G +      +   A  V+  +  E  G 
Sbjct: 15  QRLDQ-IAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQLVLEAEQ-EAQGE 72

Query: 66  PLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPS--IFSRVISVG 112
            L +        E   + +  KP GLV   +      T+ +    ++P      R   V 
Sbjct: 73  WLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVPRAGIVH 132

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---KLNLLKKGI-- 165
           RLD +T GL+++         L  +L +    R+Y     G +         + + G+  
Sbjct: 133 RLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHGVQR 192

Query: 166 ----VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIR 217
               V+           +  +  ++    V L  G+  +I+       + +        R
Sbjct: 193 QKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGR 252

Query: 218 ISYGPFQLGTLLAGSTREVSKKIL 241
               P    TL+  + RE  ++ L
Sbjct: 253 FRIPPVASQTLVQ-TLREFPRQAL 275


>gi|32423742|gb|AAP81266.1| pseudouridine synthase [Pseudomonas aeruginosa PA14]
          Length = 320

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 49/264 (18%), Positives = 91/264 (34%), Gaps = 39/264 (14%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGIL------LERAAVNVMSTDHIEVDGV 65
           QR+ + IA       SR  +   I   R+ V+G +      +   A  V+  +  E  G 
Sbjct: 18  QRLDQ-IAAQLFPEHSRSRLAGWIKDGRLTVDGAVLRPRDIVHSGAQLVLEAEQ-EAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPS--IFSRVISVG 112
            L +        E   + +  KP GLV   +      T+ +    ++P      R   V 
Sbjct: 76  WLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVPRAGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---KLNLLKKGI-- 165
           RLD +T GL+++         L  +L +    R+Y     G +         + + G+  
Sbjct: 136 RLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHGVQR 195

Query: 166 ----VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV----NRLIR 217
               V+           +  +  ++    V L  G+  +I+       + +        R
Sbjct: 196 QKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYPLVGDPVYGGR 255

Query: 218 ISYGPFQLGTLLAGSTREVSKKIL 241
               P    TL+  + RE  ++ L
Sbjct: 256 FRIPPVASQTLVQ-TLREFPRQAL 278


>gi|57239048|ref|YP_180184.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
 gi|58578991|ref|YP_197203.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
 gi|57161127|emb|CAH58040.1| putative ribosomal large subunit pseudouridine synthase C
           [Ehrlichia ruminantium str. Welgevonden]
 gi|58417617|emb|CAI26821.1| Ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Welgevonden]
          Length = 305

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 85/250 (34%), Gaps = 58/250 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE-------VERMIAQQRVKVNGILLERAAVN 53
           M     +QE+    R+ + I       R+E       +E+ +  + + ++G+ ++     
Sbjct: 1   MGKYYTIQEDNLGVRIDRFI-------RKELRIPQSLIEKFLRNRIILLDGLKVKS-NTK 52

Query: 54  VMSTDHIEVDGVPLRK-------------------------AERTRLWLYHKPIGLVTTH 88
           +   + I V    +                            E   + + +KP G+    
Sbjct: 53  LNVGNVIYVQNECIISKEKKDKKVCKFASESLVKLICDNIVYEDDNVLVINKPSGVSVQG 112

Query: 89  SDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
                + ++ D L SI     +  V RLD +T G+L+L  +  ++R++       +  + 
Sbjct: 113 G-SKVKISISDVLDSIRIGESMKIVHRLDKSTSGILMLARNARVSRLIMNEFKDRKVKKK 171

Query: 145 YRVRFHGQVDQDK------LNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWVTVG- 192
           Y     G  D D       +   K GI ++           M  TL         + +  
Sbjct: 172 YLALTCGIPDDDFGQIDYPIVKKKHGITLEKNMSFMQQAVTMFSTLRKLPNDIGLLDLQP 231

Query: 193 LREGKNREIK 202
           +  G+  +I+
Sbjct: 232 IT-GRKHQIR 240


>gi|299783552|gb|ADJ41550.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 329

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 72/237 (30%), Gaps = 43/237 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERM---IA--QQRVKVNGILLERAAVNVMSTD--HIEVDG 64
            P ++   +   G+  R     +   I       +V+   +      ++      + V  
Sbjct: 46  EPIKIKTFLHSLGMGHR-----LFNDIKNGAGEFQVDHRRVR-PTTKILPNQPLTLTVQP 99

Query: 65  VP----LRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
            P    +  +E     +Y        +KP+G+ +         T+ + +           
Sbjct: 100 EPGDATVATSEEPLTIVYEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPD 159

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------ 157
            R   + RLD +T GLLL+      + ++          + YR    G   ++       
Sbjct: 160 LRPHLITRLDRDTAGLLLVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFAKEHGIIDAP 219

Query: 158 LNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +K  I  +          +   +  +G    V + L  G+  +I+         
Sbjct: 220 IARIKGQIEREVNPAGQPAKTEYWAEESRGDWTLVRLRLHSGRTHQIRVHMASVGHP 276


>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 = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 38/216 (17%), Positives = 80/216 (37%), Gaps = 33/216 (15%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVM----------STDH---IEVDGVPLRK-AERTR 74
           R+++ M  ++RVKVN  +    +  V+            D    ++V+  P+    E   
Sbjct: 29  RDIQMMFRKKRVKVNSRVA--HSQRVLKKGDVLTLELPQDKDYGVDVEQGPITVLYEDAH 86

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TN 126
             + +K   ++   +      T+ + +   +       +V  V RLD +T G +L   T 
Sbjct: 87  TLVVNKAPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTK 146

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---------IVIQGICYGDMQV 177
           +       EL + +  R+Y     G++D D +     G         ++ +       + 
Sbjct: 147 EAQQYYTDELQAGRIDRIYTGLVEGRIDADGMVDAPIGVDPVFDNRRVIDEFGQPAQTEY 206

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           T+   +G N  +   L  G+  +I+   E     + 
Sbjct: 207 TVLGYEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIV 242


>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 = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 65/197 (32%), Gaps = 33/197 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL-------------WLYHKP 81
           I +  +K+N  ++   +  +   D IE     + + E                     KP
Sbjct: 106 IEKGLIKINNKII-EPSTIIHHHDEIE---HQVHRHEPPVYCDKLTIVKETNDFIAIDKP 161

Query: 82  IGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
             + V         + +F      ++ +  V RLD  T G+LLL      AR  +   T 
Sbjct: 162 SSIPVHPCGRYRHNTVIFILAHEGYTNLRPVHRLDRMTSGILLLAKTIQAAREFQSYMTI 221

Query: 141 WLRVYRVRFHG--------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
             + Y  R  G              ++D  K+++    I   G         L   + +N
Sbjct: 222 KKKEYLCRVRGRLEKTTVTSKIGRKRIDDKKIHVSVNEIEEDGKECHSEFNPLFYDEKTN 281

Query: 187 AWVTVGLR-EGKNREIK 202
             V V L   G+  +I+
Sbjct: 282 TTVAVALLGSGRTHQIR 298


>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 = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 75/241 (31%), Gaps = 39/241 (16%)

Query: 10  NFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           +   +R+ K +       SR   +  I +  V VN     +A   +   D + V    + 
Sbjct: 9   DEQGKRLDKWLTDQSDDWSRSLTQSWIQEGYVTVNDET-SKANYKLKIGDVVRVKVPEVE 67

Query: 69  K-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----- 110
           +              E   + + +KP G+V   +      T+ + L      +       
Sbjct: 68  ELEITAEDLDLDIVYEDQDVIVVNKPAGMVVHPAPGHPSGTLVNGLMYHCQDLSGINGVA 127

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKG 164
               V R+D +T GLL++         L          R Y     G +  +K   +   
Sbjct: 128 RPGIVHRIDKDTSGLLMVAKHDKAHESLVDQLKNKTTIRQYEALVVGTIPHEK-GTVDAP 186

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTV---------GLRE---GKNREIKKVFEFFNWKV 212
           I         M VT +  + +     V          L E   G+  +I+   ++  + +
Sbjct: 187 IGRDPQDRQKMTVTEENARDAVTHFQVIERMNGYTHVLCELETGRTHQIRVHMKYIGYPI 246

Query: 213 N 213
            
Sbjct: 247 V 247


>gi|327463496|gb|EGF09815.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1057]
          Length = 299

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 40/205 (19%), Positives = 72/205 (35%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 36  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILIGNGKLVEELYQ 94

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 95  DQHLIIVNKPEGMKTHANEPIELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 154

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+    KL           +  K+ +  +   Y +  V
Sbjct: 155 PILNRLL-EKREISREYWALIQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHV 213

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T   Q G  A V   L+ G+  +I+
Sbjct: 214 TRLKQLGQAALVKCQLKTGRTHQIR 238


>gi|190150190|ref|YP_001968715.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|307250101|ref|ZP_07532064.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|307261347|ref|ZP_07543022.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307263527|ref|ZP_07545142.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|189915321|gb|ACE61573.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|306857898|gb|EFM89991.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306869078|gb|EFN00880.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306871170|gb|EFN02899.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 247

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 68/202 (33%), Gaps = 39/202 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSEMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD------------- 174
             L        Q  + Y     G  +D+ +++   K +++  I                 
Sbjct: 72  -RLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLK-VILDKIADKFSQPKEAQQAVTFY 129

Query: 175 ---MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                V +    G +      L E     G+  ++++  +     +        G  + G
Sbjct: 130 QNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------MGDTKYG 182

Query: 227 TLLAGSTREVSKKILREQLGPH 248
            L     R +++K   ++L  H
Sbjct: 183 DLH--QNRTLTEKTGCDRLMLH 202


>gi|118474442|ref|YP_892925.1| RNA pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
 gi|118413668|gb|ABK82088.1| RNA pseudouridine synthase [Campylobacter fetus subsp. fetus 82-40]
          Length = 319

 Score = 61.7 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 81/229 (35%), Gaps = 52/229 (22%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKA-ERTRLWLY 78
             G  S +E +++  + R+ VN  +  +          I+ +  P  L+   E     ++
Sbjct: 22  NLGY-SMKEAQKLCDKGRLLVNDAVCGKNDPVFGEAYFIDYECEPKGLKPIFECDEFGVF 80

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVL 134
            KP G+++    P+GR+  +     I+S          RLD  T G++++  +   A  L
Sbjct: 81  DKPSGVLS---HPNGRNCEYSLCDEIWSLWGKKACVAHRLDRETSGVIVVAKNANSALNL 137

Query: 135 EL--PSTQWLRVYRVRFHGQVDQDKLNLL-----------------KKGIVIQG-----I 170
           +    +    + Y     G+ D + L+                    +G VI        
Sbjct: 138 KKSFENRAVAKTYLAFVRGKFDGNGLDKFHINDFEDFKDKLEFFDNIQGFVIDKNMDITK 197

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LRE----------------GKNREIK 202
            Y D+++ ++        VTV  L E                G+  +I+
Sbjct: 198 DYDDIKIRMEICPEGKRAVTVVKLVEYYPKFDISLVECYPLTGRQHQIR 246


>gi|322378406|ref|ZP_08052860.1| RNA pseudouridine synthase [Helicobacter suis HS1]
 gi|322380087|ref|ZP_08054343.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321147494|gb|EFX42138.1| pseudouridine synthase [Helicobacter suis HS5]
 gi|321149162|gb|EFX43608.1| RNA pseudouridine synthase [Helicobacter suis HS1]
          Length = 342

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 81/257 (31%), Gaps = 47/257 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M            +R+   + ++ G+A + ++ + I   RV+VN   + +  + +   D 
Sbjct: 9   MVQIERTFTAMQEERLDTFLTKSLGVA-KNQILQCIKSSRVQVNDKTILKGGLKLKIGDE 67

Query: 60  IEV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-- 104
           + +             D       E   + + +KP  L    +      T+ D L +   
Sbjct: 68  VVLKPSQAPLEVYKPTDLKIEILYEDEDILVLNKPPYLAMHPAISLHEPTLVDYLQAKGV 127

Query: 105 -------FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
                   SR   V RLD NT G +++  +      L   L   +  R Y       + +
Sbjct: 128 TLSTLSGESRCGIVHRLDKNTSGAVVIAKNNATHANLATQLQIREMGRYYLALITEPLKK 187

Query: 156 DK------------------LNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTVGLREG 196
                               L+ L++   I G  Y     + L +       +   L  G
Sbjct: 188 PMRVECHLGRHPKNRLKMTNLDTLRQ--NINGGRYSKTDFIPLLSNARGIQLIAAKLYSG 245

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +++   E     + 
Sbjct: 246 RTHQVRAHLESLGRHIL 262


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 78/235 (33%), Gaps = 44/235 (18%)

Query: 8   QENFTPQRVSKVIARAGI---ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
            EN   +R+   +    +   A+R  ++++I    V++ G  + ++   +  T+ I V+ 
Sbjct: 13  DENDKGKRIDSFLNE--VIDDATRSYIQKIIDGGYVEITGKKVTKSGNKLKGTETITVNI 70

Query: 64  -----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +PL    E   + + +K   +V   +  +   T+ + L          
Sbjct: 71  PEDEILDVIPENIPLNIIYEDKDIVVINKAPDMVVHPAHGNYNGTLVNALLYHIKDLSTI 130

Query: 107 ----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD---- 156
               R   V RLD +T G++++  +      L          + Y     G         
Sbjct: 131 NGVIRPGIVHRLDKDTSGVIVVAKNDEAHSTLSDMFKEKTLEKTYICIAKGIFKDKSGRI 190

Query: 157 ---------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        +   + I G         LD +K   + V V +  G+  +I+
Sbjct: 191 ETLIGRDSRDRKKMAV-VDINGKNAISNYEILDEEKNF-SLVKVRIETGRTHQIR 243


>gi|226307021|ref|YP_002766981.1| pseudouridine synthase RluD [Rhodococcus erythropolis PR4]
 gi|226186138|dbj|BAH34242.1| putative pseudouridine synthase RluD [Rhodococcus erythropolis PR4]
          Length = 308

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 53/310 (17%), Positives = 99/310 (31%), Gaps = 66/310 (21%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV------ 52
           M++   +   +     RV   +AR    SR  V  +  +  V V+G+ + ++        
Sbjct: 1   MRESRSMPVPDGLDAMRVDAGLARLLGLSRTVVATLAEEGSVLVDGVAVGKSDRLTAGSW 60

Query: 53  --NVMSTD----HIE---VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
              V+        IE   V+G+ +  A+   +    KP+G+    S      TV   L  
Sbjct: 61  LEVVLPEPPRPLTIEATPVEGMEILYADDDVV-AVDKPVGVAAHASVGWTGPTVIGGLAA 119

Query: 102 -------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
                       R   V RLD+ T G++++        +L+    Q    + Y     G 
Sbjct: 120 AGFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTLLKRAFKQRTIDKRYHALVQGH 179

Query: 153 VDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D               N  +  +   G        T++  + + + + V L  G+  +I
Sbjct: 180 PDPSSGTIDAPIGRHHGNDWRFTVTADGKPSVTHYDTIEAFQAA-SLLDVHLETGRTHQI 238

Query: 202 K--------------------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +                    ++ E    +   L  +S G         G   E+  K  
Sbjct: 239 RVHFSALRHPCCGDLTYGADPRLAERLGLERQWLHAVSLGFAHPAD---GRWVEIKSKYP 295

Query: 242 REQLGPHLLE 251
           ++    H LE
Sbjct: 296 KDL--EHALE 303


>gi|254486362|ref|ZP_05099567.1| 23S rRNA pseudouridylate synthase [Roseobacter sp. GAI101]
 gi|214043231|gb|EEB83869.1| 23S rRNA pseudouridylate synthase [Roseobacter sp. GAI101]
          Length = 349

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/267 (15%), Positives = 80/267 (29%), Gaps = 65/267 (24%)

Query: 6   IVQENFTPQRVSKV------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           I+++    QR+ +       +   G   R  +E+M  +  ++VNG  ++ A+  +     
Sbjct: 8   IIEQGDGDQRLDRWFKRMFPLISQG---R--IEKMCRKGDIRVNGGRVK-ASTRLEVGQE 61

Query: 60  IEV----DGVPLRKAERTRL-------------------WLYHKPIGL----VTTHSDPD 92
           I +    D       +RTR+                      +KP GL     +  SD  
Sbjct: 62  IRIPPLPDTEAPPPPKRTRISDADAKFIRSCVIYRDDYIIALNKPPGLPVQGGSGQSDRH 121

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
             +     +  +  +   V RLD +T G+L++     +A  L       Q  ++Y     
Sbjct: 122 VDALADALMFDLDEKPRLVHRLDKDTSGVLIMARTRSIAADLTSSFRHRQTRKIYWAAVA 181

Query: 151 GQVDQD-------KLNLLKKGIVIQGIC-----------------YGDMQVTLDTQKGSN 186
           G             +     G   +G                         TL       
Sbjct: 182 GVPHPKNGTIKFGLVKAFGHGARGEGEKMYCVHPKDMDTTEGAKRATTDYATLAQAGTRT 241

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
            WV +    G+  +++         + 
Sbjct: 242 CWVALIPVTGRTHQLRAHMAEIGHPIV 268


>gi|160884288|ref|ZP_02065291.1| hypothetical protein BACOVA_02266 [Bacteroides ovatus ATCC 8483]
 gi|156110027|gb|EDO11772.1| hypothetical protein BACOVA_02266 [Bacteroides ovatus ATCC 8483]
          Length = 317

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 35  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQISKQKGKKE 94

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 95  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 154

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L          R Y     G +++D   +        +   
Sbjct: 155 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 214

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 215 SSEYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 254


>gi|91205071|ref|YP_537426.1| ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
 gi|122425980|sp|Q1RJX7|RLUC_RICBR RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|91068615|gb|ABE04337.1| Ribosomal large subunit pseudouridine synthase [Rickettsia bellii
           RML369-C]
          Length = 301

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/181 (18%), Positives = 61/181 (33%), Gaps = 46/181 (25%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV- 65
           R+ K +       RR         +E+ + Q+++ VN      A++ V+  D I +    
Sbjct: 12  RLDKYL-------RRLYPLLTQGVIEKALRQKQIIVNSKKA-EASLRVVEGDEIFIHDKF 63

Query: 66  --PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VF 98
             P+ +  +                         +   +KP GL T        S     
Sbjct: 64  NLPIAQPTKLVFTDAEITLAKKITTEYLIYEDDNIIAINKPAGLATQGGSKINLSVDSAL 123

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD 156
             L S  +    V RLD  T GLLL+  +   +  L     +    + Y    +G+  +D
Sbjct: 124 KYLNSQGADFKLVHRLDKETSGLLLIAKNYVSSVKLHDAFKEKLVEKTYLAVTYGKPIKD 183

Query: 157 K 157
           +
Sbjct: 184 Q 184


>gi|325695366|gb|EGD37266.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK150]
          Length = 291

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 75/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG+ +      V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNGLSI-NWQTVVKPGDDIRLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  +   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RVKQFGQAALVKCQLKTGRTHQIR 230


>gi|165976282|ref|YP_001651875.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|165876383|gb|ABY69431.1| probable pseudouridine synthase Rlu family protein [Actinobacillus
           pleuropneumoniae serovar 3 str. JL03]
          Length = 247

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 68/202 (33%), Gaps = 39/202 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSEMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD------------- 174
             L        Q  + Y     G  +D+ +++   K +++  I                 
Sbjct: 72  -RLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLK-VILDKIADKFSQPKEAQQAVTFY 129

Query: 175 ---MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                V +    G +      L E     G+  ++++  +     +        G  + G
Sbjct: 130 QNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------MGDTKYG 182

Query: 227 TLLAGSTREVSKKILREQLGPH 248
            L     R +++K   ++L  H
Sbjct: 183 DLH--QNRTLTEKTGCDRLMLH 202


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/225 (18%), Positives = 76/225 (33%), Gaps = 38/225 (16%)

Query: 14  QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           QRV  V+AR     SR  +   I    V +N +  +      +  D I ++         
Sbjct: 18  QRVDSVLARLLPEYSRSLICNWIKTGAVTLNNLPCK-PKDKALGGDLITINVDYTIDNTD 76

Query: 64  -------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVI 109
                   +P++   E + + + +KP  LV      +   T+ + L           R  
Sbjct: 77  FNLCKPENIPIQIVYEDSEVIVVNKPASLVVHPGAGNKEHTLVNALLHHCPELQLLPRAG 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-QVDQDKLN------- 159
            + RLD +T GLL++  +      L     + +  R Y    HG  +    ++       
Sbjct: 137 IIHRLDKDTTGLLIVAKNLISHTYLIRQMQNREIKRHYLTLVHGYVISGGTIDTGFGRHP 196

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              LK  +   G         ++        + V L  G+  +I+
Sbjct: 197 KNRLKMAVTDFGRQAVTH-YNINKHYKDFTLLNVSLMTGRTHQIR 240


>gi|33592279|ref|NP_879923.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis Tohama I]
 gi|33571924|emb|CAE41444.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis Tohama I]
 gi|332381696|gb|AEE66543.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           pertussis CS]
          Length = 320

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 75/237 (31%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KV+A      SR  ++  I    V VNG   +     V   D + V   P  +    
Sbjct: 29  RLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAK-VRQAVGPGDVLSVWEQPAPESRAF 87

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGR 113
                     AE     +  KP GLVT     +   T+ + L   +       R   V R
Sbjct: 88  APEPVAFDVVAESPDWIVVDKPAGLVTHPGAGNWSGTLLNGLLHRYPELARVARAGIVHR 147

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLL 161
           LD +T GL+++  +      L  +L +    R Y                 + +D    +
Sbjct: 148 LDKDTSGLMVVARNERAQTHLVRQLQARTMGRQYIALAHGWLGAAGTVDRPIGRDARVPV 207

Query: 162 KKGIVIQGICYGDMQVTLDTQK-------GSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +  + I         D ++          + V   L  G+  +I+         
Sbjct: 208 RMSVE-RPIAPKPAVTHFDPRRRGCAEGGARVSEVLCRLETGRTHQIRVHLASLGHP 263


>gi|332360116|gb|EGJ37930.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1056]
          Length = 290

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNG-LAINWQTVVNPGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+    KL           +  K+ +  +   Y +  V
Sbjct: 147 PILNRLL-EKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHV 205

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
               Q G  + V   L+ G+  +I+
Sbjct: 206 NRLKQFGQASLVKCQLKTGRTHQIR 230


>gi|307245726|ref|ZP_07527812.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307254697|ref|ZP_07536525.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307256915|ref|ZP_07538693.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307259139|ref|ZP_07540869.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306853428|gb|EFM85647.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306862370|gb|EFM94336.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306864649|gb|EFM96554.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306866806|gb|EFM98664.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 244

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/202 (18%), Positives = 68/202 (33%), Gaps = 39/202 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  V RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPVHRLDRPTSGVLLFALNSKMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD------------- 174
             L        Q  + Y     G  +D+ +++   K +++  I                 
Sbjct: 72  -RLMSEQFEQHQLEKGYLAVVRGYLLDKGEIDYPLK-VILDKIADKFSQPKEAQQAVTFY 129

Query: 175 ---MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                V +    G +      L E     G+  ++++  +     +        G  + G
Sbjct: 130 QNLASVEMPYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------MGDTKYG 182

Query: 227 TLLAGSTREVSKKILREQLGPH 248
            L     R +++K   ++L  H
Sbjct: 183 DLH--QNRTLTEKTGCDRLMLH 202


>gi|288560866|ref|YP_003424352.1| rRNA methylase [Methanobrevibacter ruminantium M1]
 gi|288543576|gb|ADC47460.1| rRNA methylase [Methanobrevibacter ruminantium M1]
          Length = 264

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 23/88 (26%), Positives = 41/88 (46%), Gaps = 6/88 (6%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-VDGVPLRKAE 71
          +R+ K +     IASR + + MI  + VKVN  ++ +A+  V   D +E ++   LR   
Sbjct: 3  ERLDKYLVNNNLIASRTKSKEMIKSKNVKVNDKIITKASYTVRDGDKVEIINDESLRYVS 62

Query: 72 RTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
          R  L    K  G + + +      ++ D
Sbjct: 63 RGGL----KLEGAIDSFNLNFNEKSIMD 86


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/180 (20%), Positives = 53/180 (29%), Gaps = 27/180 (15%)

Query: 1   MKDKNIVQEN-FTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M    I  E     QR+   + ARA   SR   + +I +  V V G +       V    
Sbjct: 1   MNQIVITSEAADAGQRLDAFLGARAEGISRSRAKTLIEEGAVTVGGAVETNPRAPVKKGL 60

Query: 59  HIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
              V+  P   A             E   L + +K  G+    +      T+ + L    
Sbjct: 61  VYAVNMPPPVPAMPEAEAIPLEILFEDAHLVILNKAAGMAVHPAPGSQTGTLVNALLHHC 120

Query: 106 S----------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
                      R   V RLD  T G+++   T                 RVYR    G  
Sbjct: 121 QGQLSGIGGVERPGIVHRLDKLTSGVMVAAKTESAHTGLAALFERHDIDRVYRAVTRGAP 180


>gi|328957083|ref|YP_004374469.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
 gi|328673407|gb|AEB29453.1| pseudouridylate synthase [Carnobacterium sp. 17-4]
          Length = 303

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 81/266 (30%), Gaps = 65/266 (24%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA-----------ERTRLWLYHKPIG 83
            +++VN   +      +   D ++V   D  P               E     + +KP G
Sbjct: 37  GKIEVNETEVT-VRYLLKDKDIVQVTIPDEAPHETTVPINIPIDIVYEDDHYLVVNKPYG 95

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVLEL 136
           + +  S      T+ + +   + R       +  V RLD +T GL+L    G  A  L  
Sbjct: 96  VASVPSQVHPEGTMANRVKGYYVRQNYADQVIHIVTRLDRDTTGLMLFAKHG-YAHALMD 154

Query: 137 PS---TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS------NA 187
                 +  + Y     G     +L+  + G +   I      +       S        
Sbjct: 155 AKLRAKEITKKYTALISG-----QLDKAEHGFIDAPIARTTDSIITRRAHESGKEALTEY 209

Query: 188 WVT----------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGS---TR 234
           W+           + L  G+  +I+  F                P     L  G      
Sbjct: 210 WIKGSFPQATLVDIQLHTGRTHQIRVHFTHIGH-----------PLMGDDLYGGEKNNW- 257

Query: 235 EVSKKIL--REQLGPHLLEEAQVNLD 258
            ++++ L  RE    H     Q+NL+
Sbjct: 258 -ITRQALHCRELNFSHPFTNEQINLE 282


>gi|303228397|ref|ZP_07315230.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516899|gb|EFL58808.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 306

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/272 (15%), Positives = 82/272 (30%), Gaps = 56/272 (20%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHI--------EVDGVPLRKA---ERTRLWLYHKPIGLV 85
              + +NG         V   DH+        E    P+      E   +   +K  G++
Sbjct: 40  DGIITINGQPAT-WDTLVHGGDHLLMKLAPEQEFSRTPMNLEIVYEDDYILAVNKAAGVL 98

Query: 86  ----TTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
               +T  D    + V               V RLD +T G++++     +    +   T
Sbjct: 99  MHPTSTVRDGTLANGVLYYYDETEQAHDFHPVHRLDKDTSGIVIIAKTSIVQHAFDKQRT 158

Query: 140 QWLRVYRVRFHGQVDQDKLNL-----LKKGIVIQGICY---GDMQ--VTLDTQKGSN--- 186
           ++ +VY     G +    L +      K G +I+  C       +  VT+  +   +   
Sbjct: 159 KFKKVYDAIVEGTMPSQSLTIKWPIGRKAGSIIERCCTSIGKPARTDVTVLARHIVSQPV 218

Query: 187 ------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
                         V   L  G+  +I+       +           P     L  G   
Sbjct: 219 QMNKNLSTQQVLTHVQCVLHTGRTHQIRVHLSHLGY-----------PLAGDDLYGGHLD 267

Query: 235 EVSKKILRE--QLGPHLLEEAQVNLDAPIYSS 264
            + ++ L        H + +  + L AP+ + 
Sbjct: 268 HIRRQALHAGYLAFTHPMTQEYIELRAPMPTD 299


>gi|299146120|ref|ZP_07039188.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_23]
 gi|298516611|gb|EFI40492.1| RNA pseudouridylate synthase [Bacteroides sp. 3_1_23]
          Length = 317

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 35  EPMELMEFLATKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQISKQKGKKE 94

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 95  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 154

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L          R Y     G +++D   +        +   
Sbjct: 155 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 214

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 215 SSEYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 254


>gi|90411938|ref|ZP_01219946.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
 gi|90327196|gb|EAS43568.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum 3TCK]
          Length = 239

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/155 (18%), Positives = 62/155 (40%), Gaps = 18/155 (11%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++    +P+   +V+  +   +     V RLD++T GL++L  +    R 
Sbjct: 26  IIMLNKPSGLLSNPGRNPEHYDSVYSRVLRDYPEAHIVHRLDMSTSGLIMLAVNKDAERH 85

Query: 134 LELP--STQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
           L          +VY  R  G  DQD     L L+       K+ +  +          + 
Sbjct: 86  LHAQFRERATQKVYYARIWGHPDQDTGTVDLPLICDWPNRPKQKVCYEDGKPSVTHYEVV 145

Query: 181 TQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
            ++     V +  +  G++ +++  + +     + 
Sbjct: 146 AREAQTTLVRLHPIT-GRSHQLRVHM-QALGHPII 178


>gi|315922777|ref|ZP_07919017.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
 gi|313696652|gb|EFS33487.1| RNA pseudouridylate synthase [Bacteroides sp. D2]
          Length = 317

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 78/220 (35%), Gaps = 29/220 (13%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 35  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVQISKQKGKKE 94

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 95  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 154

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--- 167
           D +T GL++   D    R L          R Y     G +++D   +        +   
Sbjct: 155 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVEGSMEKDYDTVVSWLTDKTLYVS 214

Query: 168 -----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 G            +    + + + L  G+  +I+
Sbjct: 215 SSEYDDGGSKSITHYKTIKRANGYSLLELDLETGRKNQIR 254


>gi|261886282|ref|ZP_06010321.1| RNA pseudouridine synthase [Campylobacter fetus subsp. venerealis
           str. Azul-94]
          Length = 319

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/229 (17%), Positives = 81/229 (35%), Gaps = 52/229 (22%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP--LRKA-ERTRLWLY 78
             G  S +E +++  + R+ VN  +  +          I+ +  P  L+   E     ++
Sbjct: 22  NLGY-SMKEAQKLCDKGRLLVNDAVCGKNDPVFGEAYFIDYECEPKGLKPIFECDEFGVF 80

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVL 134
            KP G+++    P+GR+  +     I+S          RLD  T G++++  +   A  L
Sbjct: 81  DKPSGVLS---HPNGRNCEYSLCDEIWSLWGKKACVAHRLDRETSGVIVVAKNANSALNL 137

Query: 135 EL--PSTQWLRVYRVRFHGQVDQDKLNLL-----------------KKGIVIQG-----I 170
           +    +    + Y     G+ D + L+                    +G VI        
Sbjct: 138 KKSFENRAVAKTYLAFVRGKFDGNGLDKFHINDFEDFKDKLEFFDNIQGFVIDKNMDITK 197

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LRE----------------GKNREIK 202
            Y D+++ ++        VTV  L E                G+  +I+
Sbjct: 198 DYDDIKIRMEICPEGKRAVTVVKLVEYYPKFDISLVECYPLTGRQHQIR 246


>gi|167771608|ref|ZP_02443661.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM
           17241]
 gi|167666248|gb|EDS10378.1| hypothetical protein ANACOL_02980 [Anaerotruncus colihominis DSM
           17241]
          Length = 338

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/270 (15%), Positives = 82/270 (30%), Gaps = 72/270 (26%)

Query: 1   MKDKNIVQENFTPQRVSKVI--------ARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           M++  I   N   QRV K +                    + I  +R+K+NG      + 
Sbjct: 18  MREFQI-NGNDAGQRVDKFLTKAVPLLPQSMLY-------KAIRTKRIKLNGKRC-EIST 68

Query: 53  NVMSTDHIEV----------DGVP--LRKA-------ERTRLWLYHKPIGLVTTHSDPDG 93
            + + D + +          DG    LR         E   + L +KP GLV    +   
Sbjct: 69  RLCTGDQLTLYLNDSFFDSRDGAFSFLRSPAAIDIIYEDENILLVNKPAGLVVHEDEHQS 128

Query: 94  RSTVFDNLPSIFSRVIS-------------VGRLDINTEGLLLLTNDGGLARVLELPST- 139
             T+ + +                        R+D NT G+++   +    R+L      
Sbjct: 129 SDTLINRIQHHLYNCGVYNPAEENSFAPALCNRIDRNTAGIVIAAKNAAALRILNEKIKA 188

Query: 140 -QWLRVYRVRFHGQVDQD--KLNLLKKGIVIQGICYGDMQV---------------TLDT 181
            +  ++Y    HG + ++   L    +    +      + V                +  
Sbjct: 189 RELQKLYLCIVHGTMPKESDTLKAFLR----KDARTNTVAVYDHPIPDGRTILTHYRVVA 244

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           QK   + + + L  G+  +I+         
Sbjct: 245 QKDRLSLLEIDLLTGRTHQIRAHLAHIGHP 274


>gi|314927283|gb|EFS91114.1| ribosomal RNA large subunit methyltransferase J
          [Propionibacterium acnes HL044PA1]
          Length = 257

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 1/63 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ + +  AG+A SR    R++ + RV VNGI++ + A+ V ++D++  D          
Sbjct: 14 RLDQALVEAGLARSRTLATRLVREGRVTVNGIVVTKPAMKVSASDNLVADEEVWVSRAAY 73

Query: 74 RLW 76
          +L 
Sbjct: 74 KLL 76


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 86/235 (36%), Gaps = 41/235 (17%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I  EN   +R+   IAR+  G+ +R   +R+I   ++ V+G   ++ ++ +   + + V 
Sbjct: 7   IFPENSEIERLDSFIARSVNGM-TRATAQRLIEAGQITVDGHP-QKPSLKLKGGERLMVT 64

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +K  G+V      +   T+ + L    + +  
Sbjct: 65  IPPPVAAEPAAETIPLEILFEDRNLVVVNKAAGMVVHPGAGNSGGTLVNALLGHCTDLSG 124

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLN 159
           +G         R+D +T G+L++       + L     +    RVY    +G    DK  
Sbjct: 125 IGGELRPGIVHRIDKDTSGVLVVAKSDAAHQSLAEQFKEHTIKRVYLALVYGAPKDDKGR 184

Query: 160 LLKK------------GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           L               G    G         +   +G    + + L  G+  +I+
Sbjct: 185 LESHIGRHPVDRKRMSGKAKHGKHAVTHWRVVGRYRGIT-LLRLRLETGRTHQIR 238


>gi|72383396|ref|YP_292751.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus str. NATL2A]
 gi|72003246|gb|AAZ59048.1| ribosomal large subunit pseudouridine synthase D [Prochlorococcus
           marinus str. NATL2A]
          Length = 326

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 80/241 (33%), Gaps = 43/241 (17%)

Query: 13  PQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLR 68
           P R+ + + ++    SR  +++ I     +VNG   + A   V   D I++      PL 
Sbjct: 26  PMRLDRWLVSQRAEQSRAHIQKFIEAGFARVNGKTGK-AKTPVRPGDIIQLWVPPPEPLP 84

Query: 69  K-----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG----- 112
                        E   L + +K  G+    +  +   T+ + L      +  +G     
Sbjct: 85  YLKPEEIDLDILYEDDHLIVINKTAGIAVHPAPGNKSGTLVNGLIHHCPDLPGIGGKLRP 144

Query: 113 ----RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
               RLD +T G +++  T +  +   +++      R Y    HG +  +    +  G +
Sbjct: 145 GIVHRLDKDTTGCIVVAKTQEALVKLQIQIQKRVASRNYIAVVHGAIKNN--EGMIVGSI 202

Query: 167 IQGICYGDMQVTLDTQKGS---NAW-----------VTVGLREGKNREIKKVFEFFNWKV 212
            +          +D + G      W           +   L  G+  +I+         +
Sbjct: 203 GRHPKDRKKYAVVDEESGRYACTHWKLIKNLGNFSLLKFKLDTGRTHQIRVHSAHIGHPI 262

Query: 213 N 213
            
Sbjct: 263 I 263


>gi|327489667|gb|EGF21458.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1058]
          Length = 295

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLYVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRQGYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVQGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  Q G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKIIEQFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 80/237 (33%), Gaps = 43/237 (18%)

Query: 13  PQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           P R+ K +       G+  R  + + + + ++K+NG   +  +  V + D I +      
Sbjct: 11  PVRLDKYLMEQYPSLGLG-R--LNKALRENKIKLNGKK-QPLSTRVQNGDVIRLFLKDEQ 66

Query: 63  -DGVPLRKA----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISV 111
            +  PL  A    E   + + +KP G+     D     T+   + +  +        +  
Sbjct: 67  LEDRPLPSAVFVYEDEDILVVNKPAGIEV---DGPAADTLLKRVQTTLAAAGKAGHAVLC 123

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK-------LNLLK 162
            RLD  T GL+LL  +      L          + Y     G+            L   +
Sbjct: 124 HRLDTGTSGLVLLAKNQATELFLTQAIKARTIEKRYLCVTFGRPQPPAALMHDYLLKDAE 183

Query: 163 KGIV--IQGICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +G+V  I     G  +V          G  A + V L  G+  +I+         + 
Sbjct: 184 RGVVKIITSPASGAKEVITGYETLAVSGRLALLEVELVTGRTHQIRAHLAHIGCPIL 240


>gi|116334072|ref|YP_795599.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116099419|gb|ABJ64568.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 299

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/199 (15%), Positives = 64/199 (32%), Gaps = 36/199 (18%)

Query: 38  QRVKVNGILLE-----RAAVNV-------MSTDHIEVDGVPLR-KAERTRLWLYHKPIGL 84
             V ++G  +           V           H+     PL    E     + +KP G+
Sbjct: 38  GVVTLDGQPVRVIAMATPGQVVGLQLPPEPDNPHVTPSFAPLDILYEDEHFLVVNKPAGM 97

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELP 137
            +  S      T+ + +      +         V RLD +T G++L       A  +   
Sbjct: 98  ASVPSHLYSEDTLANRVKGHLLTIQAPSTVTHIVTRLDRDTSGVVLFAKH-HFAHSVLDK 156

Query: 138 S---TQWLRVYRV-----------RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                Q  + Y             +  G + ++  + +K+ +   G    + +V +    
Sbjct: 157 QLKLKQIDKRYVAVASGRMMPAHQQLTGPIGREAGSFIKRTVRPDG-RAAETEVWVRATS 215

Query: 184 GSNAWVTVGLREGKNREIK 202
            + + + V L  G+  +I+
Sbjct: 216 ATASLLAVKLHTGRTHQIR 234


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/254 (17%), Positives = 79/254 (31%), Gaps = 53/254 (20%)

Query: 5   NIVQEN-FTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           NI+ +    P RV K +     G A+R ++++      V VN   ++     V + D I 
Sbjct: 26  NIIADKGQEPLRVDKFLMNRVEG-ATRNKIQQACDNGMVIVNDKPVKS-NYKVKAHDRIV 83

Query: 62  V------DGVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           V      +   +   E     +Y        +K  G+V      +   T+ + L      
Sbjct: 84  VYSNKNPENTQVIPEELPLNIIYEDEDLMIINKLPGMVVHPGCGNYTGTLVNGLAWYLGD 143

Query: 106 -----------SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
                       R   V R+D NT GLL++         L          R Y     G 
Sbjct: 144 HTTTPAPEPSIPRFGLVHRIDKNTSGLLVVAKSEKAMNDLAKQFFDHTVQRRYLALVWGD 203

Query: 153 VDQDKL---------NLLKKGIVI--QGICYGDMQVTLDTQKGSNAWVTVGLRE-----G 196
            ++D+             +K +    +G    +        +  N    V L E     G
Sbjct: 204 FEEDEGTIEAHVGRHQRFRKIMDAYPEGEYGKEAITHYKVLERFNY---VTLIECRLETG 260

Query: 197 KNREIKKVFEFFNW 210
           +  +I+   +    
Sbjct: 261 RTHQIRVHMQHIGH 274


>gi|58582695|ref|YP_201711.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84624582|ref|YP_451954.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|58427289|gb|AAW76326.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae KACC10331]
 gi|84368522|dbj|BAE69680.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 328

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 53/305 (17%), Positives = 107/305 (35%), Gaps = 61/305 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RVNEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLIGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +           TL  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMSVDAPLHIGLRQGGERHVQVNAIGKPSLSHFTLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
              +     V             G    G   +V+K+ LR+QLG   L     +L+  + 
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRLFLHAASLEFALD 303

Query: 263 SSETL 267
           + +T 
Sbjct: 304 AGQTP 308


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 76/241 (31%), Gaps = 34/241 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEV-DG 64
           V + F  +RV   +AR    SR  V  +     V+ NG  L + A ++      +++ D 
Sbjct: 8   VPDGFDGERVDAALARMTGLSRSRVGDLCEAGGVRRNGEDLAKSARLHAGELLEVDLPDP 67

Query: 65  VPLRKAERTR-----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG- 112
            P+                  + +  KP G+    S       V   L ++  RV + G 
Sbjct: 68  RPVEPVATPVEGMELLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMRVRVATSGA 127

Query: 113 --------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLK 162
                   RLD+ T G++++        VL+         +VY     G +D     +  
Sbjct: 128 AERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHTVDKVYHALVQGHLDPSSGTIEA 187

Query: 163 ----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                     K  +I+G         +           + L  G+  +I+          
Sbjct: 188 PIGRHPSREWKMAIIEGGRESITHYDVIEAMPGACLAEIHLETGRTHQIRVHMAAVGHPC 247

Query: 213 N 213
            
Sbjct: 248 V 248


>gi|184156035|ref|YP_001844375.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
 gi|183227379|dbj|BAG27895.1| pseudouridylate synthase [Lactobacillus fermentum IFO 3956]
          Length = 294

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/238 (13%), Positives = 72/238 (30%), Gaps = 45/238 (18%)

Query: 12  TPQRVSKVIARAGIASRREVERM---IA--QQRVKVNGILLERAAVNVMSTD--HIEVDG 64
            P ++   +   G+  R     +   I       +V+   +      ++      + V  
Sbjct: 11  EPIKIKTFLHSLGMGHR-----LFNDIKNGAGEFQVDHRRVR-PTTKILPNQPLTLTVQP 64

Query: 65  VP----LRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
            P    +  +E     +Y        +KP+G+ +         T+ + +           
Sbjct: 65  EPGDATVATSEEPLTIVYEDDNWLVVNKPVGVASVPGPHVVNGTILNRVKGYLVAKDAPD 124

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------ 157
            R   + RLD +T GLLL+      + ++          + YR    G    D       
Sbjct: 125 LRPHLITRLDRDTAGLLLVAKHNVASSMISPQVEGHTMQKEYRAIVAGTFATDHGFIDAP 184

Query: 158 LNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
           +  +K  I  +          +   +  +G    V + L  G+  +I+  +       
Sbjct: 185 IARIKGQIEREVNPAGQPAKTEYWAEESRGDWTLVRLRLHSGRTHQIRVHM-ASVGHP 241


>gi|238760461|ref|ZP_04621598.1| tRNA pseudouridine synthase C [Yersinia aldovae ATCC 35236]
 gi|238701303|gb|EEP93883.1| tRNA pseudouridine synthase C [Yersinia aldovae ATCC 35236]
          Length = 257

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/170 (20%), Positives = 60/170 (35%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHIVAVNKPAGWLVHRSWLDSNETVFVMQTVRDQIGQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L L     Q  + Y     G V +         ++L+ +      Q        
Sbjct: 67  SEVARTLSLQFEQHQIQKTYHAVVRGYVLESGTVDYAMAEELDKIADKRARQDKAPQPSV 126

Query: 175 --------MQVTLDTQKGSNAWVTVG-LR-E-GKNREIKKVFEFFNWKVN 213
                   ++V L   +   A  ++  L+ E G+  ++++        + 
Sbjct: 127 THYQPVAQVEVPLAIGRYETARYSLVALKPETGRKHQLRRHMAHIRHPII 176


>gi|54307622|ref|YP_128642.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
 gi|46912045|emb|CAG18840.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium profundum SS9]
          Length = 239

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 61/154 (39%), Gaps = 16/154 (10%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++    +P+   +V+  +   +     V RLD++T GL++L  +    R 
Sbjct: 26  IIMLNKPSGLLSNPGRNPEHYDSVYSRVLRDYPEAHIVHRLDMSTSGLIMLAVNKDAERH 85

Query: 134 LELP--STQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
           L          +VY  R  G  DQD     L L+       K+ +  +          + 
Sbjct: 86  LHAQFRERATQKVYYARIWGHPDQDTGTVDLPLICDWPNRPKQKVCYEDGKPSVTHYEVV 145

Query: 181 TQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
            ++     V +  +  G++ +++   +     + 
Sbjct: 146 AREAQTTLVRLHPIT-GRSHQLRVHMQALGHPII 178


>gi|188577474|ref|YP_001914403.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|188521926|gb|ACD59871.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 313

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 53/305 (17%), Positives = 107/305 (35%), Gaps = 61/305 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 6   VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 64

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 65  RVNEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 124

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 125 N--QNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLSLLIGRMP 182

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +           TL  ++G +++  V +  G+  +I+
Sbjct: 183 DGVMSVDAPLHIGLRQGGERHVQVNAIGKPSLSHFTLLERRGGHSYCEVRIETGRTHQIR 242

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
              +     V             G    G   +V+K+ LR+QLG   L     +L+  + 
Sbjct: 243 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRLFLHAASLEFALD 288

Query: 263 SSETL 267
           + +T 
Sbjct: 289 AGQTP 293


>gi|260102907|ref|ZP_05753144.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|260083278|gb|EEW67398.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
          Length = 275

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 75/218 (34%), Gaps = 40/218 (18%)

Query: 32  ERMIAQ----QRVKVNGILLERAAVNVMSTDHIE-VDGV------------PLRKA-ERT 73
           + +I        + VN       + ++ + D +  V G             P+    E  
Sbjct: 29  QALIKARHHHGMILVNHKR-RYLSFHLSAGDEVIFVSGEEKKNQFLKPSNNPVDPGFETK 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTN 126
              + +KP G+++  S  +    V + L   F +          + RLD +T GL+L+  
Sbjct: 88  NYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQNKKDLKPHVITRLDRDTSGLVLVGK 147

Query: 127 DGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGICYG 173
           +              +++ Y    HG   +D+L  +      K+G      +V  G    
Sbjct: 148 NAIAHARFSKIGKDNFVKKYHAIVHGNFAEDELTGIIDEPIGKEGDGVKRAVVANGKKAQ 207

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                L   +G+ + V + L  G+  +I+    +    
Sbjct: 208 TRYRVLKQVEGA-SLVELRLLTGRTHQIRVHMAYLGHP 244


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 82/234 (35%), Gaps = 45/234 (19%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             + QR+ K +A     SR  V+ +I +  V V G  L + +   ++     +       
Sbjct: 13  EESGQRLDKALAEGSGLSRERVKALIEEGAVTVAGTPLRQPSAKSVAGTEWTIAVPVPAA 72

Query: 63  -----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------- 106
                  +PL    E   L +  KP G+V   +  +   T+ + L               
Sbjct: 73  AEAVAQDIPLTVVYEDADLIVVDKPAGMVVHPAAGNPDGTLVNALLHHCRGQLSGIGGVA 132

Query: 107 RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ--------- 155
           R   V R+D +T GLL++  T+        +      +R YR    G             
Sbjct: 133 RPGIVHRIDKDTSGLLVVAKTDVAHEGLARQFADHSIVRAYRAVTGGAPTPPAGTIRGAI 192

Query: 156 -------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   K+ L+++G   +G        TL+    S+A V   L  G+  +++
Sbjct: 193 ARSSHDRKKMALVEEG---RGKHAVTHYRTLERLD-SSALVECRLETGRTHQVR 242


>gi|228474393|ref|ZP_04059128.1| pseudouridine synthase YjbO [Staphylococcus hominis SK119]
 gi|228271752|gb|EEK13099.1| pseudouridine synthase YjbO [Staphylococcus hominis SK119]
          Length = 288

 Score = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 58/160 (36%), Gaps = 22/160 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E T L +  KP+ L    S      ++ + +    +             V RLD NT G+
Sbjct: 80  EDTYLIIVSKPVHLNCAPSREHPHDSLIERVMYYLNHSTNKVQYVVPHIVTRLDRNTTGI 139

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGIC 171
           ++ T  G +   L   + +  + Y    +G           + ++K +++ + I   G  
Sbjct: 140 VIFTKHGHI-HHLMS-TFEIDKRYICVCYGKTKEQSMIEAPIGRNKDSIITRCITPSG-K 196

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           Y   +    +   S +   V L  G+  +I+  F+     
Sbjct: 197 YAKTEYKTLSSHHSASLCEVKLHTGRTHQIRVHFKHIGHP 236


>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 = 61.7 bits (149), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+ K +  AG ++SR    ++IA   V+VNG +  +A++ V   D + V
Sbjct: 1  MRLDKYLVEAGFVSSRTLAAKLIAAGDVQVNGKVARKASMLVGPEDTLYV 50


>gi|47459310|ref|YP_016172.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma mobile
           163K]
 gi|47458640|gb|AAT27961.1| ribosomal large subunit pseudouridine synthase C [Mycoplasma mobile
           163K]
          Length = 314

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 89/265 (33%), Gaps = 43/265 (16%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  KN IVQEN T + + K + R      + ++E++   + +K+NG  +      +   D
Sbjct: 18  MNKKNFIVQENDTKRTIYKYLLRMLNTIPKSKLEKLFRNKDIKINGKRISSKTYVLQFND 77

Query: 59  HIEV-------------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            IEV                         D       E   + + +KP  L+   S    
Sbjct: 78  EIEVFGIFDEDSIENFTRSKQKKQTTKTFDKKLEIIFENLDILIINKPNNLIMHSSKNSL 137

Query: 94  RSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
              V + L  +         +GRLD  T GL++   +      L    + + ++Y     
Sbjct: 138 DEQVLNYLNYVKIDSFVPTHIGRLDKETSGLVVYAKNYKTLIELLDKQSDFEKIYTFIPF 197

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---------GSNAWVTVGLREGKNREI 201
             + +  +  L    + +      MQ++ + +K          S  +    L  G+  +I
Sbjct: 198 CNLSEKDV--LVTVNISEDEINKKMQISNEGKKSITRIFYDGNSQRYYAQILT-GRKHQI 254

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLG 226
           + V   F  K   L    Y      
Sbjct: 255 RLVLADF-LKCPILGERKYANLTKD 278


>gi|282879373|ref|ZP_06288116.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281298486|gb|EFA90912.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 355

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 84/249 (33%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +   P RV K +  R   +SR  +++      V VN   ++     V   D I +
Sbjct: 24  RIVVDKGQEPLRVDKYMFERLKHSSRNRIQKAADAGFVHVNDQPVKS-NYKVRPLDVITL 82

Query: 63  -------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E + L + +K  G+V      +   T+ + +      +
Sbjct: 83  MLDAPQHDHTIEAEDIPLDIVYEDSDLMVVNKAPGMVVHPGAGNFHGTLINAVAWHLKDL 142

Query: 109 IS----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
            S          V R+D +T GLL++         L L   +    R Y     G  +++
Sbjct: 143 TSFDANDPAVGLVHRIDKDTSGLLVIAKTPVAKTKLGLQFFNKTTHRSYNALVWGNFNEE 202

Query: 157 K-----------LNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           +            + L+  +       G   VT   +  + G    V   L  G+  +I+
Sbjct: 203 EGRIEGNIGRDPRDRLRMNVFPPDSEIGKSAVTHYRILERFGYVTLVECILETGRTHQIR 262

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 263 AHMKHIGHP 271


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 71/199 (35%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-PLRKA-ERTRL 75
           K++A     S R  + +I +  V   G  +  A   +  +   +++ + P++   E   +
Sbjct: 6   KLLALQEGISNRAAKELIDRGVVYAAGKKVSVARGELSPSTKFKIEKIAPIKVLFEDEYI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +                +   ++  + RLD  T G+LLLT D    +   
Sbjct: 66  MAVDKPAFITSEE-------------VAEIKKLPLLHRLDRETSGVLLLTKDDEFRQKAV 112

Query: 136 LP--STQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDMQ-----VTLDTQK 183
                 +  + Y     G+V +       +  +KKG         D +     +     +
Sbjct: 113 NAFKKREVHKEYIAIVEGKVVEATEVNAPILTIKKGNTAYSKISPDGKEAISYIEPLMIE 172

Query: 184 GSNAWVTVGLREGKNREIK 202
           G  + + V +  G+  +I+
Sbjct: 173 GKRSKIKVTIETGRTHQIR 191


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 49/318 (15%), Positives = 104/318 (32%), Gaps = 49/318 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + +V E+    R+   + ++  G  SR ++   +     +V+G ++   +  V +  
Sbjct: 1   MMREFVVPESANGFRIDLFLTQSCDGY-SRSQIRDAVQNDGAEVDGRIIR-PSYKVKAGQ 58

Query: 59  HIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            +              + +PL    E   L + +KP G+V   +  +   T+   L   F
Sbjct: 59  KVRFRVPPPASDDTVPENIPLDILYEDDGLVVINKPAGMVVHPARGNWTGTLTSALAFRF 118

Query: 106 SRVISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD 154
             +  VG         RLD +T G++++  +  +   L          + Y     G++D
Sbjct: 119 QSLSDVGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDRLVQKEYTAITFGRLD 178

Query: 155 QD---------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +D                   +++G              +  + G    V V  + G+  
Sbjct: 179 RDRDWIHASIGRHPYQRDKQAIREGHAT--SKTASTFYEVVERHGRVTRVDVRPKTGRTH 236

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDA 259
           +I+         +    R+ YG      L     R ++   +         E  ++ L  
Sbjct: 237 QIRVHLAHIGCPIL-CDRL-YGGHS--ELSRSQIRRLAGTEVATPGVKPTPEGEEILLSR 292

Query: 260 PIYSSETLVRDRPNIISE 277
               ++ L    P    E
Sbjct: 293 QALHAKALTFTNPQTGKE 310


>gi|238650483|ref|YP_002916335.1| hypothetical protein RPR_02200 [Rickettsia peacockii str. Rustic]
 gi|238624581|gb|ACR47287.1| hypothetical protein RPR_02200 [Rickettsia peacockii str. Rustic]
          Length = 303

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 61/175 (34%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A++ V   D I ++     
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNSQKA-EASLRVKGGDKIFINDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P+++ E+                         L   +KP GL T        S       
Sbjct: 66  PVKQPEKLVFTDAEIKLATKITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGTDFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKP 180


>gi|255019802|ref|ZP_05291878.1| Ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970731|gb|EET28217.1| Ribosomal large subunit pseudouridine synthase D [Acidithiobacillus
           caldus ATCC 51756]
          Length = 320

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 80/233 (34%), Gaps = 36/233 (15%)

Query: 12  TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             QR+  V+       SR  ++ ++ Q  V V+G    R +  +   + + +  +P   A
Sbjct: 17  AGQRLDAVLKELLPELSRSRLQTLLQQGSVLVDGS-AHRPSYRIRGGEGVVLH-LPQTPA 74

Query: 71  ER--------------TRLWLYHKPIGLVTTHSDPDGRST----VFDNLP--SIFSRVIS 110
           E               ++L +  KP GL T       R T    V  + P      R   
Sbjct: 75  EHWQAEAMDLTIVHEDSQLLVIDKPAGLATHPGAGRPRGTLANAVLAHCPANERLPRAGI 134

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD++T GLL++  T     + + +L      R Y     G           + +   
Sbjct: 135 VHRLDMDTSGLLVVAKTELARQSLIAQLADRSMHREYLALVQGALTGGGHVEAPIGRHPQ 194

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + L+  +   G         L  +   ++ + + L  G+  +I+         
Sbjct: 195 DRLRMTVRRDGRPART-DYRLVERFPRHSLLRLRLATGRTHQIRVHMRHLGHP 246


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 69/201 (34%), Gaps = 31/201 (15%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A+    S  E + +I    V   G +L+ A   +       V     P    E   +
Sbjct: 6   KLLAKQENISNNEAKDLIDAGLVSAKGQILKVARAEMSENTKFSVQKVAKPAIVFENDDI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            + +KP   V+            + L  IF     + RLD  T G++LL  +        
Sbjct: 66  LVVNKPPFFVS------------EKLEKIFK-FKLLNRLDKETSGIVLLYKNEEFKERAI 112

Query: 136 LP--STQWLRVYRVRFHGQVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQ---------- 182
               + +  + Y     G V ++      + I  I+G      +++   +          
Sbjct: 113 KEFKNMRVKKTYIAIVQGIVSEEM--EFDEPILTIKGKTGAFSRISPHGKSAITRIFPLM 170

Query: 183 -KGSNAWVTVGLREGKNREIK 202
             G  + V + +  G+  +I+
Sbjct: 171 ISGKKSLVKIEIDTGRTHQIR 191


>gi|332535815|ref|ZP_08411548.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332034793|gb|EGI71331.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 254

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 50/177 (28%), Gaps = 27/177 (15%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
           G      +       +KP GL+   S  D          L       V  V RLD  T G
Sbjct: 11  GELTILYQDENYVAINKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSG 70

Query: 121 LLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG 169
           +LL       AR +          + Y     G   +         ++L+ +      Q 
Sbjct: 71  VLLFALSSEAARDMNQLFIEGTIAKRYLALVRGFAPESVFLDKPLKEELDKIADKFADQD 130

Query: 170 ICYGDM--------QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
               +         Q  L    G    V   L E     G+  +I++  +  +  + 
Sbjct: 131 KAPQEAQTQFNCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRHLKHLSLPII 187


>gi|116748594|ref|YP_845281.1| pseudouridine synthase [Syntrophobacter fumaroxidans MPOB]
 gi|116697658|gb|ABK16846.1| ribosomal large subunit pseudouridine synthase D [Syntrophobacter
           fumaroxidans MPOB]
          Length = 255

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 32/184 (17%), Positives = 58/184 (31%), Gaps = 36/184 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGL 121
           E   L   +KP GL+    D  G +++ D                    V RLD    G+
Sbjct: 16  EDNHLLGLYKPAGLLVQG-DRTGEASLLDLGKKWLKECCGKPGKVFLAMVHRLDRPVAGV 74

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK---LNLLKKG-----IVIQGIC 171
           +L       A  +     S +  + Y     G V       +N L++      +++    
Sbjct: 75  VLFCRTSKAAARISAQFRSGRIRKHYLAVAEGDVTPSAGRLVNQLERHDERSSVIVAEAT 134

Query: 172 YGDMQVTL----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
               +  L        GS + + + L  G++ +I+       + +            LG 
Sbjct: 135 PRSREARLSYRVLDVAGSRSLLEIELETGRHHQIRLQLAHLGFPI------------LGD 182

Query: 228 LLAG 231
           L  G
Sbjct: 183 LRYG 186


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 80/225 (35%), Gaps = 39/225 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-------- 65
           R+ + +AR+    +R  V+R+I + RV V+G  +E+ ++ +   + I V           
Sbjct: 17  RLDQFVARSVEGMTRSTVQRLIDEGRVTVDGK-VEKPSLKLRGGERIVVAVPPPAPAVPE 75

Query: 66  -----PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------- 112
                 +   E + L + +K  G+V          T+ + L +  + +  +G        
Sbjct: 76  AEEIPLVILHEDSDLVVVNKSAGMVVHPGAGTPGGTLVNALLAHCTDLSGIGGEIRPGIV 135

Query: 113 -RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL----------- 158
            R+D +T G+L++  +      L          R+Y     G    D             
Sbjct: 136 HRIDKDTTGVLVVAKNDRSHEGLARQFREHTIKRIYLALVFGSPKTDTGRIEGAIGRHPT 195

Query: 159 NLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + L+  G    G         L    G    + + L  G+  +I+
Sbjct: 196 DRLRMSGKAKHGKHAVTHWKVLARYPGMT-LLRLRLETGRTHQIR 239


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/228 (16%), Positives = 69/228 (30%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    V +N  +       V   + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVNLNDRIANIPREKVFGGERIEIIVE 69

Query: 63  --DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
             D               E   + + +KP  LV      +   TV + L   +       
Sbjct: 70  VEDDTRFEPENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIAEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>gi|325921639|ref|ZP_08183476.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           gardneri ATCC 19865]
 gi|325547873|gb|EGD18890.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           gardneri ATCC 19865]
          Length = 328

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 54/325 (16%), Positives = 112/325 (34%), Gaps = 61/325 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V ++   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPQDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RVNEEGDKAAPPSAFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QTLELVHRLDRDTSGLLIVAKKRSALTEMQALMREDDRVQGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
              +     V             G    G   EV+K+ LR+QLG   L     +L+  + 
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-EVNKR-LRDQLGLKRLFLHAASLEFALD 303

Query: 263 SSETLVRDRPNIISEVPDDFTRMKK 287
           + +        +  E+ D   R+ +
Sbjct: 304 AGKAPYVLNAPLAPELADALDRLGR 328


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 79/239 (33%), Gaps = 40/239 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             +R+ K +A+     SR  ++  I  QRV+V+G   +     V     IE+    L + 
Sbjct: 66  AGERLDKALAQLFPEFSRSRLQSWIEAQRVRVDGEPAK-VRQPVPLGATIELVPDLLPEQ 124

Query: 71  --------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVI 109
                         E   L +  KP GLV   +  +   T+ + L   +        R  
Sbjct: 125 LAFTPEPVPLAIVYEDEALVVIDKPAGLVVHPAAGNWNGTLLNGLLHRYGEAAAGLPRAG 184

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDK 157
            V RLD  T GL+++         L  +L +    R Y     G           + +D 
Sbjct: 185 IVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGRTPASGTIDAPIGRDP 244

Query: 158 LNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +V    G        T+D+   Q    + +   L  G+  +I+         
Sbjct: 245 RERTRMAVVTGASGKPARTHFRTVDSVLWQNQPVSAIQCDLETGRTHQIRVHCAHLGHP 303


>gi|83645042|ref|YP_433477.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83633085|gb|ABC29052.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 297

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/153 (18%), Positives = 58/153 (37%), Gaps = 9/153 (5%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGL 121
            P   A+     ++ KP GL+T  S+     ++    +       +V  + RLD    GL
Sbjct: 97  QPTLVADHDAYSIWCKPAGLLTQGSEWGDHCSLLRMAELHFQSKRQVFLLHRLDREAMGL 156

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-QVT 178
           +++ ++   A      L      + Y  R  G++ Q++  +      + G       QV 
Sbjct: 157 VIIAHNKAAAGRFGALLQDNALDKFYLARVKGRLAQEQGEI---DFPVDGKSALSYYQVQ 213

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  ++ V V L  G+  +I++ F    + 
Sbjct: 214 HYDDATDSSLVRVKLITGRKHQIRRHFADLGYP 246


>gi|325981783|ref|YP_004294185.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
 gi|325531302|gb|ADZ26023.1| pseudouridine synthase, RluA family [Nitrosomonas sp. AL212]
          Length = 285

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/208 (21%), Positives = 76/208 (36%), Gaps = 34/208 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--------------AER 72
           SR  ++  I ++R+ VNG +   A   V   +H+E+  + +                 E 
Sbjct: 5   SRSRLQTWIVEKRILVNGQIAT-AKQLVWGNEHVEIFPLKIAAESPFVAEAIHLNTIEED 63

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             L + +KP GLVT   + + + T+ + L           R   V RLD NT GLL++  
Sbjct: 64  ETLIIINKPAGLVTHPGNGNWQGTLLNALLHHAPELKNIPRAGIVHRLDKNTTGLLVIAK 123

Query: 127 DGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK----------LNLLKKGIVIQGICYGD 174
                  L     Q    R Y     G++ Q            ++  K  I  +G     
Sbjct: 124 TLAAQTSLVRQLQQRTVKRDYLALVLGEIKQAGNIDAPIGRHPIHRTKMTITSKGKPART 183

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
               ++  +G    +   L  G+  +I+
Sbjct: 184 NYQVIENFEG-CTLLQCSLETGRTHQIR 210


>gi|296875626|ref|ZP_06899697.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 15912]
 gi|296433423|gb|EFH19199.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 15912]
          Length = 274

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 76/204 (37%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG  +      V   D I++               D   + +  +
Sbjct: 15  RKIRHFLRTKKHVLVNGETI-NWQSPVQKGDQIQLIFDADDYPEKELPAGDPNLVEELYQ 73

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + + +KP G+ T  ++P   + +      + S    V RLD  T G +L   +  + 
Sbjct: 74  DEHVIIVNKPEGMKTHANEPTEIALLNHVSSYVGSTCYVVHRLDKETSGAILFAKNPFIL 133

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L      R Y     G + Q  +           +  K+ +  +   Y + QVT
Sbjct: 134 PILNRILEDKNIQREYWALIQGSLAQKTIVYKDKIGRDRHDRRKRLVDPRKGQYAETQVT 193

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              + G N+ V   L+ G+  +I+
Sbjct: 194 QLKKIGRNSLVKCQLKTGRTHQIR 217


>gi|302386355|ref|YP_003822177.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
 gi|302196983|gb|ADL04554.1| pseudouridine synthase, RluA family [Clostridium saccharolyticum
           WM1]
          Length = 320

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/269 (15%), Positives = 86/269 (31%), Gaps = 77/269 (28%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVER-----MIAQQRVKVNGILLERAAVNVMSTDHI 60
           IV +N   QR+ K++++         E+     M+ ++ + +NG      +  ++  D +
Sbjct: 5   IVSQNEAGQRLDKLLSKYLNL----AEKSFLYKMMRKKNITLNGKKC-DGSEKLVQGDEV 59

Query: 61  EV--DGVPLRK-----------------AERTRLWLYHKPIGLVTTHSDPDGRSTV---F 98
           ++      + K                  E   + L +KP G+++  +     S V    
Sbjct: 60  KLFLSDETIGKFSQIKLPEVRKVSLNILYEDEHILLINKPAGMLSQKARESDESLVEYMI 119

Query: 99  DNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLAR--VLELPSTQ---WLRV 144
           + L S            R     RLD NT GL++    G       L   + +     + 
Sbjct: 120 NYLVSNGRLSTEQLRSFRPSVCNRLDRNTSGLVVG---GKSLAGLQLMSAAFKDRSIHKY 176

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQK-----------------G 184
           Y+    G +   ++        I G         QVT+  Q                  G
Sbjct: 177 YQCVVKGHISDRQV--------ITGYLTKSEASNQVTVHKQPVTGSVPIVTEYEPVQYHG 228

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               + + L  G+  +I+       + + 
Sbjct: 229 EYTLLRITLITGRTHQIRAHLSSIGYPIV 257


>gi|315185268|gb|EFU19047.1| pseudouridine synthase [Spirochaeta thermophila DSM 6578]
          Length = 300

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 36/222 (16%), Positives = 72/222 (32%), Gaps = 41/222 (18%)

Query: 15  RVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
           R+ ++    ++   + SR  V R +    + + G  +   +  V     I +D   L + 
Sbjct: 17  RLDRIVRTLLSHLPL-SR--VFRALRTGEILLEGKRV-PPSTRVSRGARIHIDRSLLPER 72

Query: 71  ---------------ERTRLWLYHKPIGLVT----THSDPDGRSTVFDNLPSIFSRVI-S 110
                          E   L + +KP G V     + +D   RS + D +P   +     
Sbjct: 73  KPQQKGKASSLPILLETDHLLILNKPPGAVVHGPGSLTD-QVRSYLKDRIPPSLAFTPSP 131

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + RLD  T G+L+   +  G       L   +  + Y     G + +      +  +  +
Sbjct: 132 LHRLDRLTSGILVFSRSIHGARWFTQALREGRIEKTYLALLEGTLAEP--ARWEDLLTRE 189

Query: 169 GICYGDMQ--------VTLDTQKGSNAWVTVGLREGKNREIK 202
           G               V       +   V   +  G+  +I+
Sbjct: 190 GRRSRPSPHGRPALTDVRPLLAAPTATLVLCTIHTGRMHQIR 231


>gi|255994448|ref|ZP_05427583.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Eubacterium saphenum ATCC 49989]
 gi|255993161|gb|EEU03250.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Eubacterium saphenum ATCC 49989]
          Length = 318

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/212 (15%), Positives = 70/212 (33%), Gaps = 45/212 (21%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV------------DGVPLRKA-ERTRLWLYHKPIGLVT 86
           +++NG   +       + D IE+             G+ +    E   L +  KP G+V 
Sbjct: 58  IRLNGKPAKNWFTP-KAGDVIELVMPKESSYFTPYSGIEINAVYEDEHLLVIDKPAGIVV 116

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPST- 139
             +     +T+   L           ++  + RLD++T GLL++  +  +   +      
Sbjct: 117 HPTHGYEENTIAHALIHYMDTVGEEFKIRFINRLDMDTTGLLMIAKNQFIQNAVVSEMKR 176

Query: 140 -QWLRVYRVRFHGQVDQDKLNLLKKGIV---IQGICYGDMQVTLDTQKGSNAWVTVG--- 192
               + Y    HG          ++GI+   I+ +     +  ++  K S     V    
Sbjct: 177 GNVEKRYLAVVHGLPCN------REGIIDAPIKAVEGEPRRQVMEGGKPSITEYKVVGVS 230

Query: 193 -----------LREGKNREIKKVFEFFNWKVN 213
                      L  G+  +I+   +     + 
Sbjct: 231 DELNVSFLDVRLHTGRTHQIRVHLKHIGCPIL 262


>gi|225021946|ref|ZP_03711138.1| hypothetical protein CORMATOL_01978 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305681500|ref|ZP_07404307.1| pseudouridine synthase, RluA family [Corynebacterium matruchotii
           ATCC 14266]
 gi|224945232|gb|EEG26441.1| hypothetical protein CORMATOL_01978 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305659705|gb|EFM49205.1| pseudouridine synthase, RluA family [Corynebacterium matruchotii
           ATCC 14266]
          Length = 310

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/234 (17%), Positives = 78/234 (33%), Gaps = 41/234 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----- 61
           V E     RV   +++    SR     +  +  V ++G    ++   +     +E     
Sbjct: 10  VPEGLADMRVDVALSKLFGLSRTVSADLATKGDVLIDGKPATKSD-KITDGAWLEVLLPE 68

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      VDG+ +  A+   L    KP+G+    +      TV   L +   R+ +
Sbjct: 69  PQKPLVPTEELVDGLEILYADED-LIAVDKPVGVAAHPTVGWDGPTVVGGLAAAGYRIST 127

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DK 157
            G         RLD+ T G++++        VL+    +    + Y     G +D     
Sbjct: 128 SGPPERNGIVQRLDVGTSGVMVVAASERGYSVLKRAFKERTVSKTYHALVQGHMDPLAGT 187

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +            K  +   G        TL+    + + + V L  G+  +I+
Sbjct: 188 IEANIGRHPSSGWKFAVTSDGKHAVTHYETLEAFVAA-SLLEVHLETGRTHQIR 240


>gi|322390416|ref|ZP_08063937.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 903]
 gi|321142874|gb|EFX38331.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           parasanguinis ATCC 903]
          Length = 287

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 77/204 (37%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRK------------AE 71
           R++   +  ++ V VNG  +      V   D I++    D  P ++             +
Sbjct: 28  RKIRHFLRTKKHVLVNGETI-NWQSPVQKGDQIQLIFDADDYPEKELPAGDPSLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + + +KP G+ T  ++P   + +      + S    V RLD  T G +L   +  + 
Sbjct: 87  DEHVIIVNKPEGMKTHANEPTEIALLNHVSSYVGSTCYVVHRLDKETSGAILFAKNPFIL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L      R Y     G + Q  +           +  K+ +  +   Y + QVT
Sbjct: 147 PILNRILEDKNIQREYWALIQGSLAQRTIVYKDKIGRDRHDRRKRLVDPRKGQYAETQVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              + G N+ V   L+ G+  +I+
Sbjct: 207 QLKKIGRNSLVKCQLKTGRTHQIR 230


>gi|282883125|ref|ZP_06291724.1| pseudouridine synthase, RluA family [Peptoniphilus lacrimalis
           315-B]
 gi|281296937|gb|EFA89434.1| pseudouridine synthase, RluA family [Peptoniphilus lacrimalis
           315-B]
          Length = 300

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 38/226 (16%), Positives = 77/226 (34%), Gaps = 32/226 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRK------ 69
           K + +  I+SR  + R   +  + VNG       V V   D + +      L        
Sbjct: 23  KFLEKMDISSR-HIRRACRENSIYVNGKRTFE-NVEVKKGDSVAIRFPDESLNALCQYKD 80

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTE 119
                E   L + +K    VT  +  D + T+ + L   F       +V  V RLD +T 
Sbjct: 81  IDICYEDYDLLIVNKEYNCVTHTAKDDSKDTLLNYLAGYFEKNNIKRKVRFVNRLDRDTS 140

Query: 120 GLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL----------LKKGIVI 167
           GL+++  +      +     + Q  ++Y     G   + +  +          +++ +  
Sbjct: 141 GLIIVAKNSYAHAKIMDEFSNNQVDKIYLAICRGDFKEKQGEIVKKISLCQDGIRREVDD 200

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               Y   +  +       A V + L  G+  +I+   +     + 
Sbjct: 201 DNGKYAKTKYQVLKDNKKLALVKLKLFTGRTHQIRVHLKSIGHPII 246


>gi|302879313|ref|YP_003847877.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
 gi|302582102|gb|ADL56113.1| pseudouridine synthase, RluA family [Gallionella capsiferriformans
           ES-2]
          Length = 326

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 45/220 (20%), Positives = 80/220 (36%), Gaps = 33/220 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ +V+A      SR  ++  +   +V ++G         V   + + V           
Sbjct: 26  RLDQVLATLLPEYSRSRLQEWVTLNQVLLDGKPAIS-KQKVWGGEKLAVLPQVTQSEQPY 84

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGR 113
             + +PL    E   L + +KP+GLV      + + T+ + L   +       R   V R
Sbjct: 85  QAEDIPLDIVYEDDDLLVINKPVGLVVHPGSGNWQGTLLNALLHHWPELALVPRAGIVHR 144

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ------VDQDKLNLLKKGI 165
           LD +T GLL++         L  +L      R Y    HG+      VDQ         +
Sbjct: 145 LDKDTSGLLVVAKTLISQTNLVRQLQERSVKREYLALVHGELSHGGYVDQPIGRHPSNRV 204

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
            +  +  G   VT   ++    S   +   L  G+  +I+
Sbjct: 205 KMAVVETGKDAVTHYKVERTFPSCTLLRCTLETGRTHQIR 244


>gi|227509368|ref|ZP_03939417.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
 gi|227191080|gb|EEI71147.1| pseudouridylate synthase [Lactobacillus brevis subsp. gravesensis
           ATCC 27305]
          Length = 297

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 30/197 (15%), Positives = 67/197 (34%), Gaps = 29/197 (14%)

Query: 42  VNGILLERAAVNV-----MSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRS 95
           VN  L+    V V        D++    +P++   E     + +K  G+ +  +      
Sbjct: 49  VNRKLITNDVVTVVLPPEPENDNVPASDLPIQIVFEDEHFLVVNKSAGVASVPAHNRAND 108

Query: 96  TVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR 146
           ++ + +   + R       +  V RLD +T GL++         VL  +L   Q  + Y 
Sbjct: 109 SLVNRVKGYYQRNHYANQKIHIVTRLDKDTSGLVIFAKHHFAHSVLDKQLKDHQIKKTYL 168

Query: 147 VRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
               G            + +   +L+K+ +   G        T    +  +  + + +  
Sbjct: 169 AIVEGVFSTTHFEIYLPIKRAAGSLVKRQVGFPGKMSVTEAWTKQRLR-QHTLLKLQIHT 227

Query: 196 GKNREIK-KVFEFFNWK 211
           G+  +I+  +       
Sbjct: 228 GRTHQIRVHMT-AIGHP 243


>gi|81429051|ref|YP_396051.1| pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610693|emb|CAI55744.1| Pseudouridine synthase, 23S-rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 306

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/284 (16%), Positives = 91/284 (32%), Gaps = 57/284 (20%)

Query: 27  SRREVERMIA--QQRVKVNGI------------LLER-AAVNVMSTDHIEVDGVPLRKAE 71
           SR ++ + I     ++ VNG             ++    A  V     I V G      E
Sbjct: 25  SRSQLSK-IKFSGGQILVNGQEAHTNIRLVQNDVVTVYLAPEVAVEHVIPVKGDLKIAYE 83

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLL 124
                +  KP  + +  +     +T+ + +             V  V RLD +T GL++ 
Sbjct: 84  DDHFLIVDKPAFVASLPAPNHPNNTMANFVKQYLIDEQAESLAVHVVTRLDRDTSGLMMF 143

Query: 125 TNDGGLARVLE---LPSTQWLRVY--------------RVRFHGQVDQDKLNLLKKGIVI 167
           T  G  A  L    L S +  + Y                     + + +   +++ +V 
Sbjct: 144 TKHG-FAHSLLDRQLQSKELQKTYIAIASGDMREDLPQHAWIDRPIKRSEEFYMRR-VVG 201

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           +G      +            V + L  G+  +I+  F      +        G      
Sbjct: 202 EGGKRSLTEYWQAAHGDGATLVKLKLLTGRTHQIRVHFASLGHSL-------IG----DN 250

Query: 228 LLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLV 268
           L  G + ++  +     R+    H  EE  + + +P+ +  + V
Sbjct: 251 LY-GESNDLLPRQALHCRQLTFYHPFEERTITVKSPVPADFSAV 293


>gi|289665912|ref|ZP_06487493.1| pseudouridylate synthase [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 328

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 99/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RVNEEGDKAAPPPSFMARLEAAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRL 291


>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 = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 37/199 (18%), Positives = 63/199 (31%), Gaps = 26/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ERTRL 75
           K++A     S  E + +I +  V V    +  A   +       V  V   +   E   L
Sbjct: 8   KLLAEQEGISNSEAKSLIDRGLVYVGNSKVMIARGEISPKTVFIVQKVEKVRPIFENDDL 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +  KP  + +            D +   F     + RLD  T G+L+L  +        
Sbjct: 68  IVVDKPAFVNS------------DEIERQFKGSQLLHRLDRETSGVLMLVKNEEFRLKAI 115

Query: 136 LPSTQ--WLRVYRVRFHGQVDQDK-----LNLLKKG-----IVIQGICYGDMQVTLDTQK 183
               +    + Y     G V +       L   KKG      V +       +VT     
Sbjct: 116 QEFKKDNVYKEYVAWVEGLVSEPFVVDQPLITEKKGNKAYTKVAKKGKPAITEVTPLEVS 175

Query: 184 GSNAWVTVGLREGKNREIK 202
           G    V + +  G+  +I+
Sbjct: 176 GKKTKVQLIIHHGRTHQIR 194


>gi|329296365|ref|ZP_08253701.1| tRNA pseudouridine synthase C [Plautia stali symbiont]
          Length = 259

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/166 (16%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D   +  V   +       V +   LD  T G+LL+     + 
Sbjct: 11  LVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTAHCLDRPTSGVLLMGLSSEIG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +D          ++L+ +    V +            
Sbjct: 71  RLLAQQFEQHQIQKTYHAVVRGWLDGSATLDYPLVEELDKIADKFVTEPRAPQPAVTDYR 130

Query: 176 ---QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
              Q  L    G  +     L E     G+  ++++        + 
Sbjct: 131 ALAQAELPVAIGKYSSARYTLVELSPHTGRKHQLRRHMAHLRHPII 176


>gi|329120441|ref|ZP_08249106.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327461899|gb|EGF08229.1| ribosomal large subunit pseudouridine synthase D [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 373

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/207 (20%), Positives = 73/207 (35%), Gaps = 31/207 (14%)

Query: 27  SRREVERMIAQQRVKVNGILL---------ERAAVNVMS-TDHIEVDGVPLR---KAERT 73
           SR  +   I +  V V+G            E  AV V    + +     P+      E  
Sbjct: 53  SRSRLAGWIKEGAVAVDGKAARPKDKLIGGETLAVRVRERNETLAFTPEPMDLDIVYEDD 112

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            + +  KP GLV   +  +   T+ + L +         R   V RLD +T GL+++   
Sbjct: 113 SVMVLDKPAGLVVHPAAGNWSGTLLNGLLAYCPALQNVPRAGIVHRLDKDTSGLMVVAKT 172

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLL---------KKGIVIQGICYGDM 175
                 L     +    R+YR    G V    K+  L         K  +V  G      
Sbjct: 173 LAAQTDLVRQMQARSVKRIYRAVADGIVPFDGKIETLIGRDPHNRTKMAVVGFGGKEAVT 232

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
            V +  +  +++++   L  G+  +I+
Sbjct: 233 HVKVLERYLAHSYIECALETGRTHQIR 259


>gi|23006096|ref|ZP_00048580.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 279

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 86/235 (36%), Gaps = 47/235 (20%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           +R+ + +ARA    SR  ++ ++    V+ +G +L   A  V +   +++          
Sbjct: 10  ERLDRALARAFEDLSRARLQALVRDGLVRCDGAVLRDPARKVGAGCRLDLSVPAPLPAEP 69

Query: 64  -GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVI 109
            G  L      E   L +  KP GLV   +      T+ + L +             R  
Sbjct: 70  MGEALPLTVVHEDEDLIVIDKPAGLVVHPAAGHEDGTLVNRLIAHCGASLSGIGGVRRPG 129

Query: 110 SVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQVDQ-------- 155
            V RLD +T GLL++  ND    G  A+  +        R Y        +         
Sbjct: 130 IVHRLDKDTSGLLVVAKNDLAHQGLSAQFADHGRNGALERAYLALVWNVPEPRHGTIRAN 189

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   +K+ ++++G   + I +  ++  L    G  A +   L  G+  +I+
Sbjct: 190 LARSRHNREKIAVVREGEGREAITHYRVEA-LPGADGVTALLRCRLETGRTHQIR 243


>gi|120434465|ref|YP_860167.1| RNA pseudouridylate synthase [Gramella forsetii KT0803]
 gi|117576615|emb|CAL65084.1| RNA pseudouridylate synthase [Gramella forsetii KT0803]
          Length = 289

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/204 (16%), Positives = 73/204 (35%), Gaps = 39/204 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLE-----RAAVNVM------STDHI-EVDGVPLRKAERTR 74
           +R  +++ I ++ V +NG   +     +    +        T  + +++   L   E   
Sbjct: 31  TRSSLKKAIKKRLVLINGEKAQTSDWIKPGQKIDLLKPFAETKKVFKLNFEVL--FEDEH 88

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISVGRLDINTEGLLLL- 124
           + + HKP G  T+    +   T+ + LP               +   RLD  T G+LL  
Sbjct: 89  IAVVHKPPGFPTSG---NYFKTIENALPHNLSSSSEIDTLPYPLPAHRLDNPTSGILLCA 145

Query: 125 -TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQ 182
            TN   +         Q  + Y     G++ +  +++       I       + + ++  
Sbjct: 146 KTNSSLIKLQEAFAQKQIQKTYYAIVSGEIKEKIEIDS-----PIDQKISKTILIPIEFY 200

Query: 183 KGSNAWVTVG----LREGKNREIK 202
           +  N   T+     L  G+  +++
Sbjct: 201 QIENKNYTLVELNPLT-GRTHQLR 223


>gi|67459415|ref|YP_247039.1| ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
 gi|75536169|sp|Q4UKQ3|RLUC_RICFE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|67004948|gb|AAY61874.1| Ribosomal large subunit pseudouridine synthase [Rickettsia felis
           URRWXCal2]
          Length = 305

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 60/175 (34%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A++ V   D I ++     
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNSQKA-EASLRVKGGDKIFINDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P+++ E+                         L   +KP GL T        S       
Sbjct: 66  PVKQPEKLVFTDAEIKLAKKITTDYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +      L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGADFKLVHRLDKETSGLLLIAKNYLSNVKLHDAFKEKLVVKTYFAVTYGKP 180


>gi|282854248|ref|ZP_06263585.1| pseudouridine synthase, RluA family [Propionibacterium acnes J139]
 gi|282583701|gb|EFB89081.1| pseudouridine synthase, RluA family [Propionibacterium acnes J139]
 gi|314923234|gb|EFS87065.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL001PA1]
 gi|314967001|gb|EFT11100.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL082PA2]
 gi|314980957|gb|EFT25051.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA3]
 gi|315091688|gb|EFT63664.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL110PA4]
 gi|315093078|gb|EFT65054.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL060PA1]
 gi|327327821|gb|EGE69597.1| RNA pseudouridine synthase, RluA family [Propionibacterium acnes
           HL103PA1]
          Length = 306

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 84/246 (34%), Gaps = 42/246 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           +V +    +RV    AR    SR  +  +I    V + G L+ RA+V V +   ++VD  
Sbjct: 5   LVPDGLDGERVDVAAARMSGVSRSRISSLIEDGGVFLGGQLVSRASVRVATGQMLDVDLC 64

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------- 101
                         G+ +   +   + +  KP G+    S      +V ++L        
Sbjct: 65  DPVATPSITPQIVEGMRIIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAIS 123

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--- 155
                 R   V RLD+ T GL+++        +L+         +VY     G  D    
Sbjct: 124 TSGAPERQGIVQRLDVGTSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTG 183

Query: 156 --------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFE 206
                   D  +  K  IV  G        T++  + +   + V L  G+  +I+  +  
Sbjct: 184 TIDAPIGRDHRHDWKMAIVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-A 241

Query: 207 FFNWKV 212
                 
Sbjct: 242 AIKHPC 247


>gi|251790751|ref|YP_003005472.1| tRNA pseudouridine synthase C [Dickeya zeae Ech1591]
 gi|247539372|gb|ACT07993.1| pseudouridine synthase [Dickeya zeae Ech1591]
          Length = 260

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 28/186 (15%), Positives = 57/186 (30%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LL+   
Sbjct: 7   QDEHLIAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM- 175
             +AR+L       +  + Y     G V +         ++L+ +               
Sbjct: 67  ADVARLLAQQFEQHRMEKTYHAVVRGYVMEDGVIDYALTEELDRIADKFADPDKAPQPAV 126

Query: 176 -----------QVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                       V +     +  + + +  + G+  ++++        +        G  
Sbjct: 127 SHYRVLARAEMPVAIGRYDTARYSLLELSPKTGRKHQLRRHMAHLRHPI-------IGDT 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>gi|32266282|ref|NP_860314.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
 gi|32262332|gb|AAP77380.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
          Length = 351

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 83/243 (34%), Gaps = 58/243 (23%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRK 69
           R+   ++    +S+ ++  +I  ++V +NGIL  +    + + D I+V     +  PL  
Sbjct: 17  RLDSYLSIQLQSSKNQIHHIIKNKQVWLNGILCLKNGTLLKAKDCIQVQSPCANNTPLSS 76

Query: 70  ----------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SI 104
                            +   + + +KP  LV  H+      T+ D L          S 
Sbjct: 77  SYTISADDERFSIDIVYQDEDVLIINKPPHLVIHHAPSVKEPTLVDWLKLNAHILYTLSG 136

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL---- 158
             R   + RLD  T G L +         L   L S Q  R Y       +  ++     
Sbjct: 137 EERYGIIHRLDKQTSGALAIAKSNLAYTTLTKELKSRQMGRYYLAIIDTPLKDNQQVQCF 196

Query: 159 ------NLLK-------------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                 N LK             KG+  +      +++   +  G+   + + L  G+  
Sbjct: 197 MGRNPHNRLKMSKIHIRSNSPIPKGV--RDSKSSFIKI-ATSDNGAFELIAIKLHTGRTH 253

Query: 200 EIK 202
           +I+
Sbjct: 254 QIR 256


>gi|314936786|ref|ZP_07844133.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
 gi|313655405|gb|EFS19150.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
          Length = 288

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 58/160 (36%), Gaps = 22/160 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E T L +  KP+ L    S      ++ + +    +             V RLD NT G+
Sbjct: 80  EDTYLIIVSKPVHLNCAPSREHPHDSLIERVMYYLNHSTNKVQYIVPHIVTRLDRNTTGI 139

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGIC 171
           ++ T  G +   L   + +  + Y    +G           + ++K +++ + I   G  
Sbjct: 140 VIFTKHGHI-HHLMS-TFEIDKRYICVCYGKTKEQSMIEAPIGRNKDSIITRCITPSG-K 196

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           Y   +    +   S +   V L  G+  +I+  F+     
Sbjct: 197 YAKTEYKTLSSHHSASLCEVKLHTGRTHQIRVHFKHIGHP 236


>gi|304312830|ref|YP_003812428.1| Putative pseudouridine synthase A [gamma proteobacterium HdN1]
 gi|301798563|emb|CBL46793.1| Putative pseudouridine synthase A [gamma proteobacterium HdN1]
          Length = 301

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/176 (14%), Positives = 58/176 (32%), Gaps = 24/176 (13%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLL 122
           P+  ++  +  +++KP GL++  S+     ++    +   +       V R+D  T GL+
Sbjct: 85  PICISDEGQYSVWYKPAGLLSQGSEYGDHYSLLRQVELHSNPRREAFLVHRIDRETTGLI 144

Query: 123 LLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-------- 172
           L+ ++   A  L          + Y     G++  +          I G           
Sbjct: 145 LVAHNERAAAKLSQLFSGRDVEKHYLACVSGEI-AEVGAKFTIDQAIDGKNAVSHITVLD 203

Query: 173 --GDMQVTLDTQKGSN--------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
                 V  +    +           + V +  G+  +I+K  +   + V    R 
Sbjct: 204 SRAPASVQSEPSDRAQDLRKIDHGCLLDVRIETGRKHQIRKHLQGAGFPVIGDHRF 259


>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 = 61.0 bits (147), Expect = 2e-07,   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|328759180|gb|EGF72796.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL025PA2]
          Length = 285

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 43/229 (18%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------------GVP 66
           +G+ SR  +  +I    V +NG  + RA+V V +   ++VD                G+ 
Sbjct: 2   SGV-SRSRISSLIEDGGVFLNGQQVSRASVRVATGQMLDVDLCDPVATPSITPQIVEGMR 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVGRLDIN 117
           +   +   + +  KP G+    S      +V ++L              R   V RLD+ 
Sbjct: 61  IIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVG 119

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ-----------DKLNLLKKG 164
           T GL+++        +L+         +VY     G  D            D  +  K  
Sbjct: 120 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMA 179

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKV 212
           IV  G        T++  + +   + V L  G+  +I+  +        
Sbjct: 180 IVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-AAIKHPC 226


>gi|119477573|ref|ZP_01617723.1| putative 23S rRNA pseudouridylate 746 synthase [marine gamma
           proteobacterium HTCC2143]
 gi|119449076|gb|EAW30316.1| putative 23S rRNA pseudouridylate 746 synthase [marine gamma
           proteobacterium HTCC2143]
          Length = 223

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 31/161 (19%), Positives = 59/161 (36%), Gaps = 21/161 (13%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D I V        +     L +KP GL++ +   P  + +V   L   F     V RLD
Sbjct: 15  HDEITV------IYQDDSFLLINKPTGLLSLSGKHPRNKDSVHYRLVQDFPTATLVHRLD 68

Query: 116 INTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI 167
             T G++L+     +   L     +    + Y+   +G++  +       +   K    +
Sbjct: 69  FGTSGIMLVALSKEVNGNLTRQFQARSVKKTYKALLYGEMADNSGVIDFPIAKDKDNFPL 128

Query: 168 QGICYGDMQ------VTLDTQKGSNAWVTVGLREGKNREIK 202
           Q ICY D +        ++   G+   V      G+  +++
Sbjct: 129 QKICYRDGKEAVTRYRVIEKIAGNCTKVEFTPSSGRTHQLR 169


>gi|294643719|ref|ZP_06721519.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
 gi|292640957|gb|EFF59175.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CC 2a]
          Length = 279

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 33/165 (20%), Positives = 66/165 (40%), Gaps = 19/165 (11%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLE------RAAVNVM---STDHIE 61
            P  + + +A +   ASR +++ +++++ V V+ ++         A + V         E
Sbjct: 24  EPMELMEFLAAKMPDASRTKLKSLLSKRVVFVDNVITTQFNFPLEAGMKVKISKQKGKKE 83

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   L+   E   + +  K  GL++ +++     T +  L     R      V  V RL
Sbjct: 84  FNNRLLKIVYEDAYIIVVEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQFRVFIVHRL 143

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK 157
           D +T GL++   D    R L     +    R Y     G +++D 
Sbjct: 144 DRDTSGLMMFAKDEKTQRTLRDNWHEIVTDRRYVAVVEGSMEKDY 188


>gi|90580793|ref|ZP_01236596.1| putative ribosomal large subunit pseudouridine synthase A [Vibrio
           angustum S14]
 gi|90438061|gb|EAS63249.1| putative ribosomal large subunit pseudouridine synthase A [Vibrio
           angustum S14]
          Length = 233

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/154 (15%), Positives = 58/154 (37%), Gaps = 16/154 (10%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT-NDGGLAR 132
           +   +KP G+++     P+   ++F  +   +     V RLD+ T GL++L  N      
Sbjct: 26  IIAVNKPAGILSNPGRAPEHHDSIFARVLEKYPNSQIVHRLDMGTSGLIVLALNKKAECH 85

Query: 133 -VLELPSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
              +    +  +VY  R  G ++QD     L L+       ++ +             + 
Sbjct: 86  LKAQFRERETQKVYYARVWGHIEQDTGTVDLPLICDWPNRPRQKVCFDDGKPSITHYEVL 145

Query: 181 TQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
           ++      V +    G++ +++  + +     + 
Sbjct: 146 SRDEKTTLVRLLPVTGRSHQLRVHM-QALGHPIL 178


>gi|300814457|ref|ZP_07094719.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300511427|gb|EFK38665.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 300

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/226 (16%), Positives = 78/226 (34%), Gaps = 32/226 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRK------ 69
           K + +  I+SR  + R   +  + VNG       V V   D + +      L        
Sbjct: 23  KFLEKMDISSR-HIRRACRENSIYVNGKRTFE-NVEVKKGDSVAIKFPDESLNALCQYKD 80

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTE 119
                E   L + +K    VT  +  D + T+ + L + F       +V  V RLD +T 
Sbjct: 81  IDICYEDYDLLIVNKEYNCVTHTAKDDSQDTLLNYLAAYFEKNNIKRKVRFVNRLDRDTS 140

Query: 120 GLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL----------LKKGIVI 167
           GL+++  +      +     + Q  ++Y     G   + +  +          +++ +  
Sbjct: 141 GLIIVAKNSYAHAKIMDEFSNNQVDKIYLAICRGDFKEKQGEIVKKISLCQDGIRREVDD 200

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               Y   +  +       A V + L  G+  +I+   +     + 
Sbjct: 201 DNGKYAKTKYQVLKDNKKLALVKLKLFTGRTHQIRVHLKSIGHPII 246


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 81/244 (33%), Gaps = 36/244 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQ--------RVKVNGILLERAAVNV--MS 56
           V E     R+ + +      +R EV++ I +          V+ N  + ++  +      
Sbjct: 8   VDEKQDGMRLDQFLKEVSGLTRSEVQKWIKEGYAISLPNRMVRSNYHISDKEKIQFSWEE 67

Query: 57  TDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PS 103
              IE+    ++     E   + + +K  G+V      +  +T+ + L            
Sbjct: 68  KKEIELIPQKIKLDILYEDEHIIVINKSRGMVVHPGAGNIDNTLVNALLYHCGESLLKVG 127

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNL- 160
             +R   V RLD +T G+++          ++         R Y    HGQ++     + 
Sbjct: 128 EKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATHEAKRTYLTLVHGQMEGPDGKID 187

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSN----------AWVTVGLREGKNREIKKVFEFFNW 210
           L  G  ++     D+Q        ++          + +   L  G+  +I+    +   
Sbjct: 188 LPLGRSLKDRMKWDVQPKTGKNAITHFHVLEFMTKYSLLECKLETGRTHQIRVHMSYIGH 247

Query: 211 KVNR 214
            V  
Sbjct: 248 PVIN 251


>gi|163751074|ref|ZP_02158305.1| tRNA pseudouridine synthase C [Shewanella benthica KT99]
 gi|161329235|gb|EDQ00234.1| tRNA pseudouridine synthase C [Shewanella benthica KT99]
          Length = 284

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 47/170 (27%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           E   +   HKP GL+   S    R   F        +   V  V RLD  T G+LL    
Sbjct: 41  EDDDIVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLFAKS 100

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +A  L          + Y     G + +         + +  +   ++      Q   
Sbjct: 101 SEMANTLCEQFADKTIEKHYLAIVRGNMHEAATLDYPLKVELDDLGDKNVAADKPAQDAM 160

Query: 186 NAW----------------------VTVGLREGKNREIKKVFEFFNWKVN 213
            ++                      V +    G+  ++++        + 
Sbjct: 161 TSYQPLLNTEIPFSSGRYASSRYALVKLTPHTGRKHQLRRHMAHLRHPIL 210


>gi|33860753|ref|NP_892314.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
 gi|33633695|emb|CAE18652.1| putative pseudouridylate synthase specific to ribosomal large
           subunit [Prochlorococcus marinus subsp. pastoris str.
           CCMP1986]
          Length = 322

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 89/246 (36%), Gaps = 37/246 (15%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE-----RAAVNV---- 54
            I  E   P R+ + + ++    SR  ++  I    V VN    +     +   N+    
Sbjct: 18  EITYEMSLPMRLDRWLVSKRPEQSRARIQYFINAGLVLVNYKTAKAKTPLKTGDNIQIWM 77

Query: 55  -MSTDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-------NLPS 103
                 I +    +      E   + + +K  GL+   +      T+ +       +LP 
Sbjct: 78  PPPEPLIYLKPEKMNLNILFEDEHIIVINKQSGLIVHPAPGHKSGTLVNGLLFHCKDLPG 137

Query: 104 IFSRVIS--VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD----- 154
           I  ++    V RLD +T G +++  + +  +   +++      R Y    HG  +     
Sbjct: 138 INGKLRPGIVHRLDKDTSGCMVVAKSQESLVNLQIQIKEKIASRNYIAVIHGVPNTSEGK 197

Query: 155 ------QDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                 +DKLN LK  +V +    Y      L  + G+ + ++  L  G+  +I+     
Sbjct: 198 IVGHIGRDKLNRLKYAVVDEKSGRYACTYWKLLERLGNYSLMSFKLDTGRTHQIRVHCAH 257

Query: 208 FNWKVN 213
            N  + 
Sbjct: 258 INHPIL 263


>gi|315281680|ref|ZP_07870254.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria marthii FSL S4-120]
 gi|313614674|gb|EFR88244.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria marthii FSL S4-120]
          Length = 296

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/264 (16%), Positives = 90/264 (34%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V S D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKSGDQVRLTFPTEQQNERLLAEHTELEIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +      S +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPHGSVANFVKGHYETQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L+  
Sbjct: 156 TFLQQGLLKRRYQAFTGGVLAEQEGSIEAPIGRKEVSIMERFVTPEGKYAKTNYAVLERY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTTLLQRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEEYMAFDLPLPAD 287


>gi|304437126|ref|ZP_07397088.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369885|gb|EFM23548.1| ribosomal large subunit pseudouridine synthase D [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 294

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 66/200 (33%), Gaps = 32/200 (16%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRK------------AERTRLWLYHKPIGLVTTH 88
            +NGI    A   +   D I  D +P+               E   L +  KP G +   
Sbjct: 41  TLNGIPAVAARTMLKDGDWIAYD-LPIVSSVIPESLPLSIIYEDDDLLVLDKPAGQLVHP 99

Query: 89  SDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           +  +   T+ + +   ++            RLD NT GLLL+     +   +   +T   
Sbjct: 100 TTKETHGTIANAVRGYYAACGVHLDFHPCHRLDRNTSGLLLIAKHPEVQYQIAQQNT-LK 158

Query: 143 RVYRVRFHGQVDQDK------LNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTV 191
           R Y     G +   +      +      I++     +G       VT+ T  G  + + +
Sbjct: 159 REYLALIAGSLTPPEGCIDVPIARALPSIILRCVSTEGKSACTHYVTVQT-DGRYSLLRL 217

Query: 192 GLREGKNREIKKVFEFFNWK 211
            L  G+  +I+         
Sbjct: 218 QLDTGRTHQIRVHLAHLGHP 237


>gi|297624276|ref|YP_003705710.1| pseudouridine synthase [Truepera radiovictrix DSM 17093]
 gi|297165456|gb|ADI15167.1| pseudouridine synthase, RluA family [Truepera radiovictrix DSM
           17093]
          Length = 312

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 60/177 (33%), Gaps = 29/177 (16%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           E    +R+   IA A   SR   + ++    V+++G  + +A+  +   + + V      
Sbjct: 7   EAPAGERLDVAIAVALELSRTYAKDLVLGGYVQLDGQPVAKASTKLSGRELVSVVLPPPR 66

Query: 63  ------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------------- 101
                 +  PL    E   L    KP G+    +      TV + L              
Sbjct: 67  PLRVEPENTPLDIIYEDDDLAAIDKPPGMTAHPTATVREGTVVNALLGRMALAKEKLFDP 126

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD 156
                R   V RLD  T G++++  +    R L     +    + Y     G ++ D
Sbjct: 127 EDEDYRPGIVHRLDKETSGVMVVAKNDAAHRELASAFKKRLTEKEYIAIAVGTLEDD 183


>gi|254721426|ref|ZP_05183215.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
          Length = 139

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 27/123 (21%), Positives = 45/123 (36%), Gaps = 19/123 (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  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                        D       E   + + +KP G+V   +      T+ + L    + + 
Sbjct: 65  TIPEPEELDIQPEDMNLEIYYEDADVLVVNKPRGMVVHPAPGHTSGTLVNGLMHHCTDLS 124

Query: 110 SVG 112
            + 
Sbjct: 125 GIN 127


>gi|254448982|ref|ZP_05062436.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HTCC5015]
 gi|198261376|gb|EDY85667.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HTCC5015]
          Length = 353

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 79/241 (32%), Gaps = 39/241 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------- 58
           + +    QR+ KV++      SR  +++ +    + ++G +L      V   +       
Sbjct: 13  IPDEHAGQRLDKVLSALFPDFSRSRLQQWLKDGCITLDGQVL-PGKHKVDGGELLRADFP 71

Query: 59  -------HIEVDGVPLRK-AERTRLWLYHKPIGLVTTHS----DPDGRSTVFDNLPS--I 104
                   +E   +PL    E   + +  KP G+V   +    D   ++ +    P    
Sbjct: 72  EQEDLSGAVEAQDIPLVVLYEDDDILVVDKPAGMVVHPAAGNPDGTLQNALLFYAPELAG 131

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--------- 153
             R   V RLD +T GLL++  +    + L  +L      R+Y     G           
Sbjct: 132 VPRSGIVHRLDKDTSGLLVVARNHSAHQSLVAQLQERSVSRIYEAIVFGVPVSGGRVEGN 191

Query: 154 ---DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                     +   +   G         ++ +   ++ V   L  G+  +I+       +
Sbjct: 192 IGRHPGDRKKMA--VRQVGGKEAVTHYRVEAKYRHHSHVRCQLETGRTHQIRVHMSHIGF 249

Query: 211 K 211
            
Sbjct: 250 P 250


>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 (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
             R+   +A  G+  SR + + +I   RV+V+G +  + +  V     IEV G      
Sbjct: 3  ERVRLDVALAARGLVESRAKAQELIRAGRVRVDGAVATKPSRKVGPEARIEVVG-----P 57

Query: 71 ERTRLWLYHKPIGLVTTH 88
          E       HK +G +   
Sbjct: 58 EPYVGRAAHKLLGALAAF 75


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 80/247 (32%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V    +  R+ K ++      SR  ++  I    VKVNG  ++  +  V   D I +  
Sbjct: 25  VVDSGQSMMRLDKYLSHHLKNISRNRIQNAIDTDSVKVNGSSVKS-SYKVKPFDDISISI 83

Query: 65  VPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           V   +  +                 + L +K   +V      +   T+ + L   F  + 
Sbjct: 84  VRSSRIPKEVIPQNIPLDIVYEDDDVLLVNKAQEMVVHPGHGNPDGTLVNALVYHFGNLP 143

Query: 110 S----------VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
           S          V R+D  T GLL++  +    + L          R Y     G+  + K
Sbjct: 144 SARDGEIRPGLVHRIDKGTSGLLVIAKNEYALQFLAKQFADHTTERTYYALIWGEPKEPK 203

Query: 158 LNLLKK-GIVIQGICYGDMQVTLDTQKGSNAWVTV--GLR---------E-GKNREIKKV 204
             +    G   +     D+    +  K +     V   LR         E G+  +I+  
Sbjct: 204 GTINAHIGRGFKDRRISDVFPEGEYGKEAITHYEVLKSLRYVSLIKCNLETGRTHQIRAH 263

Query: 205 FEFFNWK 211
            ++    
Sbjct: 264 MKYLGHP 270


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 32/154 (20%), Positives = 55/154 (35%), Gaps = 24/154 (15%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+ +V+A R    SR  ++ +I   +V ++   +   A +V S D I +D       E  
Sbjct: 13  RLDRVLAARLPELSRSRLKALILAGQVSLSTGAVRDPAYHVASGDTITIDVPEAAPPEPK 72

Query: 74  R-------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
                         + +  KP GLV   +      T+ + L +             R   
Sbjct: 73  AEAIPLHVVYEDDDIVVLDKPAGLVVHPAAGHETGTLVNALIAHCGASLSGIGGVKRPGI 132

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
           V RLD +T GL+++  +      L        R 
Sbjct: 133 VHRLDKDTTGLMVVAKNDHAHASLSAQFADHGRT 166


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 39/219 (17%), Positives = 77/219 (35%), Gaps = 46/219 (21%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--------PLRK 69
           K      IA+   +E++  ++ +KVN   +      V   D +EV G+         ++K
Sbjct: 21  KYFPNLTIAT---IEKLFRKKEIKVNSKRITDKKFVVSENDLVEVYGISESNLNLPQIKK 77

Query: 70  A--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINT 118
                    E   + +  K   LV    D    + V   L        +   VGRLD  T
Sbjct: 78  VSFDFQIIYEDANILIIDKKENLVIHGEDNSLDNQVLSYLKHKQIDSFKPSHVGRLDKET 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--Q 176
            GL++   +    + L   S  + +VY+         D L+     + ++   Y D   +
Sbjct: 138 SGLIVYAKNYLTLKQLNEKSFNFKKVYQ------FKSDFLS--SSPLELKLYFYKDENNK 189

Query: 177 VTLDTQKGSNAWV--TV-----------GLREGKNREIK 202
             +   +  N+ +  ++            +  G+  +I+
Sbjct: 190 TKISKTQKENSKLAHSIFYCENNKKFAQIIT-GRKHQIR 227


>gi|116628160|ref|YP_820779.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMD-9]
 gi|116101437|gb|ABJ66583.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           thermophilus LMD-9]
          Length = 298

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 66/201 (32%), Gaps = 36/201 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRL-----WLYHKP 81
               + VNG   + A   V   D + ++           P+              + +KP
Sbjct: 33  EGGHIWVNGE-EQFATYPVHEGDVVAIEIPDEAPHETLKPIPFDLDIVYEDDNFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S  +  +T+ + +   F        RV  V RLD +T GL+L    G     +
Sbjct: 92  YGYASIPS-VNHDNTMANFVKHHFVSNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARM 150

Query: 135 --ELPSTQWLRVYRVRFHGQV----DQDKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G+     + + +  + + +       V +   Y      L  
Sbjct: 151 DKQLQQKSIKKHYYALVEGETKLEQEGEIIAPIARDVDSIITRRVHKSGKYAHTSYRLVG 210

Query: 182 QKGSNAWVTVGLREGKNREIK 202
             G    V + L  G+  +I+
Sbjct: 211 DYGRVKLVDINLHTGRTHQIR 231


>gi|158316843|ref|YP_001509351.1| RluA family pseudouridine synthase [Frankia sp. EAN1pec]
 gi|158112248|gb|ABW14445.1| pseudouridine synthase, RluA family [Frankia sp. EAN1pec]
          Length = 313

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 79/246 (32%), Gaps = 43/246 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +     R+   IAR    SR     ++   +V V+G +  R+   V     ++V    
Sbjct: 13  VPDGLDGIRLDAAIARMFGLSRTAAATLVDDGQVSVDGQVRGRSD-RVSGGAWLDVALPA 71

Query: 64  -GVPLRKAERTR--LWLYH---------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
              PL         L + H         KP+G+    +      TV   L +   RV   
Sbjct: 72  PPRPLTVEPTPVGGLRILHDDDDIVVVDKPVGVAAHPAPGFTGPTVIGALAAAGYRVSTS 131

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------ 154
                   V RLD+ T G + +        +L+      +  + YR    G  D      
Sbjct: 132 GSAERQGVVHRLDVGTTGAMAVAKSERAYTLLKRAFREREVEKEYRAVVQGHPDPLRGTV 191

Query: 155 QDKLNLL--KKG---IVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEF 207
              ++    + G   +V  G          DT++     + ++V L  G+  +I+     
Sbjct: 192 DAPIDRHPRRPGLFAVVADG---KPSVTHYDTEEAFRAASLLSVRLETGRTHQIRVHMAA 248

Query: 208 FNWKVN 213
                 
Sbjct: 249 LRHPCV 254


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 81/244 (33%), Gaps = 36/244 (14%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQ--------RVKVNGILLERAAVNV--MS 56
           V E     R+ + +      +R EV++ I +          V+ N  + ++  +      
Sbjct: 8   VDEKQDGMRLDQFLKEVSGLTRSEVQKWIKEGYAISLPNRMVRSNYHISDKEKIQFSWEE 67

Query: 57  TDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PS 103
              IE+    ++     E   + + +K  G+V      +  +T+ + L            
Sbjct: 68  KKEIELIPQKIKLDILYEDEHIIVINKSRGMVVHPGAGNIDNTLVNALLYHCGESLLKVG 127

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNL- 160
             +R   V RLD +T G+++          ++         R Y    HGQ++     + 
Sbjct: 128 EKTRPGIVHRLDKDTSGVMVAVKSDIAYEKVKNEIATHEAKRTYLTLVHGQMEGPDGKID 187

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSN----------AWVTVGLREGKNREIKKVFEFFNW 210
           L  G  ++     D+Q        ++          + +   L  G+  +I+    +   
Sbjct: 188 LPLGRSLKDRMKWDVQPKTGKNAITHFHVLEFMPKYSLLECKLETGRTHQIRVHMSYIGH 247

Query: 211 KVNR 214
            V  
Sbjct: 248 PVIN 251


>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 = 61.0 bits (147), Expect = 3e-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|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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 75/249 (30%), Gaps = 49/249 (19%)

Query: 11  FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
              +R+  V+A    A SR  ++ +I    V V G  +      V   D + +       
Sbjct: 24  DAGKRLDAVLATHLEALSRNRIQSLIKSGDVTVGGAKIVEPKYRVNEGDALTLTLPQAED 83

Query: 63  -----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------S 106
                + +P+    E   L +  KP GLV      +   T+ + L               
Sbjct: 84  PEPKGEDIPVTVVFEDEHLIVVDKPAGLVVHPGAGNWTGTLVNALIHHCGDSLSGIGGVK 143

Query: 107 RVISVGRLDINTEGLLLL--TND---GGLARVLELPSTQ-WLRVYRVRFHGQVDQDKLNL 160
           R   V R+D +T GLL++  T+    G  A+  +   T    R Y     G     K  +
Sbjct: 144 RPGIVHRIDKDTSGLLVVAKTDQAHKGLAAQFADHGRTGPLERAYSALVWGAPSGLKGTI 203

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAW-----------------VTVGLREGKNREIK- 202
                  Q        V    ++    W                 +   L  G+  +I+ 
Sbjct: 204 NANLARSQANRQKIAVVKTSGRQAITHWQVKERFGNAEQPALASLLECRLETGRTHQIRV 263

Query: 203 KVFEFFNWK 211
            +       
Sbjct: 264 HM-AHIGHP 271


>gi|90422129|ref|YP_530499.1| pseudouridine synthase RluD [Rhodopseudomonas palustris BisB18]
 gi|90104143|gb|ABD86180.1| ribosomal large subunit pseudouridine synthase D [Rhodopseudomonas
           palustris BisB18]
          Length = 391

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 78/253 (30%), Gaps = 58/253 (22%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILL----------ERAAVNVMSTDHIEVD 63
           R+ +V+A RA   SR  ++ +I   +V++                  A +V + D I +D
Sbjct: 70  RLDRVLALRAPELSRSRLKALILAGQVRL--RPADASAALPTPLRDPAYHVEAGDTITID 127

Query: 64  ----------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                     G  +      E   + +  KP GLV   +      T+ + L +       
Sbjct: 128 VPPAVAAEPAGEAIALDIVYEDDDIIVIDKPKGLVVHPAAGHETGTLVNALIAHCGNSLS 187

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG--- 151
                 R   V RLD +T GL+++  +    + L        R       Y+    G   
Sbjct: 188 GIGGVRRPGIVHRLDKDTTGLMVVAKNDKAHKSLSEQFADHGRTNEMRRGYKAFIWGAPN 247

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----QKGSNAWVTVGLREGKN 198
                    +D+      K  +   G          DT      K   + +   L  G+ 
Sbjct: 248 RPHGTVDAPIDRHPFAREKMAVRDGGREAVTHWEVEDTFLGRGGKPVVSLLACQLETGRT 307

Query: 199 REIKKVFEFFNWK 211
            +I+         
Sbjct: 308 HQIRVHLAHIGHP 320


>gi|206896098|ref|YP_002247034.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206738715|gb|ACI17793.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 315

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/211 (19%), Positives = 75/211 (35%), Gaps = 38/211 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVDGV--PLRKAERTRLWLYH--- 79
           SR  ++  I    V+ NG ++ + ++ V   D   I +      L+ A+     +Y+   
Sbjct: 33  SRTWIQNNIKAGLVRCNGDVVTKPSLRVKKGDLLEIRLRSRISELQPADVEYSVVYYDEH 92

Query: 80  -----KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTEGLLLLT 125
                KP  LV   +      T+   L   F +V +VG         RLD +T GL+L+ 
Sbjct: 93  LAVIDKPPNLVVHPAPSVKGLTLCHGLLKDFPQVKNVGSAERPGIVHRLDKDTSGLMLVA 152

Query: 126 NDGGLARVLELPSTQ--WLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGI--C 171
                   L    ++    R Y V  +G           + +D  N  +  +V  G    
Sbjct: 153 LSEKGYAGLTKMISEKSVSRKYLVAVYGVANRPFEVDAPIGRDPRNPTRMAVVPHGKNAY 212

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                V    +    + +   L  G+  +I+
Sbjct: 213 TRFRPVQCLEKV---SLLEAELFTGRTHQIR 240


>gi|167624728|ref|YP_001675022.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354750|gb|ABZ77363.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 281

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 21/154 (13%), Positives = 55/154 (35%), Gaps = 19/154 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTND 127
           ++ +  +++KP G+    S     +T+   + +          + RLD+   GL++L ++
Sbjct: 88  DQEQYSIWYKPFGMRCQGSKWSDHTTINRYIETHLNPARNAYLIHRLDLAATGLIVLGHN 147

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDT--- 181
             +   +     +    + Y+V   G+    K       + I   +         +    
Sbjct: 148 KKVTAAIAKLFETRALDKFYQVIVEGKFPDGK-------VTIDTDVDNKSALSHAERLEY 200

Query: 182 -QKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
             + + + V V +  G+  +I+  +       V 
Sbjct: 201 NSELNQSKVQVKIESGRKHQIRIHM-ASLGHPVV 233


>gi|55821440|ref|YP_139882.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus LMG 18311]
 gi|55823366|ref|YP_141807.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           thermophilus CNRZ1066]
 gi|55737425|gb|AAV61067.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus LMG 18311]
 gi|55739351|gb|AAV62992.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus thermophilus CNRZ1066]
 gi|312278771|gb|ADQ63428.1| Pseudouridine synthase [Streptococcus thermophilus ND03]
          Length = 298

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 66/201 (32%), Gaps = 36/201 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRL-----WLYHKP 81
               + VNG   + A   V   D + ++           P+              + +KP
Sbjct: 33  EGGHIWVNGE-EQFATYPVHEGDVVAIEIPDEAPHETLKPIPFDLDIVYEDDNFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S  +  +T+ + +   F        RV  V RLD +T GL+L    G     +
Sbjct: 92  YGYASIPS-VNHDNTMANFVKHHFVSNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARM 150

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G+   ++    +  + + +       V +   Y      L  
Sbjct: 151 DKQLQQKSIKKHYYALVEGETKLEQQGEIIAPIARDVDSIITRRVHKSGKYAHTSYRLVG 210

Query: 182 QKGSNAWVTVGLREGKNREIK 202
             G    V + L  G+  +I+
Sbjct: 211 DYGRVKLVDINLHTGRTHQIR 231


>gi|323466963|gb|ADX70650.1| Pseudouridine synthase [Lactobacillus helveticus H10]
          Length = 321

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 76/218 (34%), Gaps = 40/218 (18%)

Query: 32  ERMIAQ----QRVKVNGILLERAAVNVMSTDHIE-VDGV------------PLRKA-ERT 73
           + +I        + VN       + ++ + D +  V G             P+    E  
Sbjct: 52  QALIKARHHHGMILVNHKR-RYLSFHLSAGDEVIFVSGEEKKNQFLKPSNNPVDPGFETK 110

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTN 126
              + +KP G+++  S  +    V + L   F +          + RLD +T GL+L+  
Sbjct: 111 NYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQNKKDLKPHVITRLDRDTSGLVLVGK 170

Query: 127 DGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGICYG 173
           +              +++ Y    HG   +D+L  +      K+G      +V  G    
Sbjct: 171 NAIAHARFSKIGKDNFVKKYHAIVHGNFAEDELTGIIDEPIGKEGDGVKRAVVANGKKAQ 230

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                L   +G+ + V + L  G+  +I+    +  + 
Sbjct: 231 TRYRVLKQVEGA-SLVELRLLTGRTHQIRVHMAYLGYP 267


>gi|167619842|ref|ZP_02388473.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis Bt4]
          Length = 385

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 81/238 (34%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             +R+ K +A+     SR  +++ I  +RV+V+G   +     V     IE+        
Sbjct: 56  AGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAK-IRQAVPLGATIELLPDLLPEQ 114

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 115 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 174

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD  T GL+++         L     +    R Y     G           + +D  
Sbjct: 175 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGTIDAPIGRDPR 234

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 235 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 292


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/208 (17%), Positives = 78/208 (37%), Gaps = 33/208 (15%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----------------DGVPLRKA 70
           R +V ++I   ++KVN  L  + ++ V   D I+V                 +       
Sbjct: 25  RVKVVKLIMNGQIKVNEKLTFKNSLIVAKDDVIKVEIHDETTSDFITSVEPYNLKLEVLF 84

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF--DNLPSIFSRVISVGRLDINTEGLLLLT-ND 127
           E   L + +KP GL+T  +  + ++++       +  + V  V RLD +T G +++  N 
Sbjct: 85  EDKDLMVINKPSGLLTHPTTFNEKASLLAACIFHNNKNPVYLVHRLDRDTSGAIVVCKNQ 144

Query: 128 GGLARVLELPSTQWLRVYRVRFH--------GQVDQDKLNLLKKGIVIQGICYGDM---- 175
             L  +      + L+ Y V           G ++     +    ++ +           
Sbjct: 145 ASLLNLQNQLQNRTLKRYYVALVHFPFNALTGSINAPLARVNNNKVMFKIAQTAKAKQAI 204

Query: 176 -QVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  +  Q    A +++ L  G+  +I+
Sbjct: 205 TKFKVINQNEKAALISLELLTGRTHQIR 232


>gi|310640966|ref|YP_003945724.1| pseudouridine synthase, rlua family protein [Paenibacillus polymyxa
           SC2]
 gi|309245916|gb|ADO55483.1| pseudouridine synthase, RluA family protein [Paenibacillus polymyxa
           SC2]
          Length = 319

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 54/322 (16%), Positives = 117/322 (36%), Gaps = 65/322 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I+Q+     R  K+I++          ++  Q  + +NGI +   +V V S D +
Sbjct: 19  MLLKTILQKRMNISR--KLISKL---------KLTEQG-IMLNGIRVY-ISVKVKSGDRV 65

Query: 61  EV-------DG---VPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+       D     P+      E   L + +K  G+V   +      T+ + +   +  
Sbjct: 66  EIRMERERSDDILPEPIPFEILFEDEHLLVVNKAAGMVVHPTHGHYTGTLANGVVHYWQA 125

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV-----------R 148
                R   V RLD  T G+L++  +  + + +     +    + Y             R
Sbjct: 126 KGELFRFRPVHRLDQETTGVLVVAKNPYVHQHISEQMIAGTVDKRYTALVHGRPQQQEGR 185

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF 207
             G +D++  N   + +   G     +   L+      + + + L  G+  +I+  +  +
Sbjct: 186 VDGPIDRNPDNPHLRMVTPDGYPALTL-YKLEEVWSGGSRIGLKLESGRTHQIRVHMT-Y 243

Query: 208 FNWKVN--RLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
               +   ++ RI+                  ++ L +QL   +  +A    +  +    
Sbjct: 244 IGCPLIGDKMYRIT------PNDAV-------QRELYDQLDARMPRQALHASELSLV--H 288

Query: 266 TLVRDRPNIISEVPDDFTRMKK 287
            +  +R    + +PDD  RM++
Sbjct: 289 PVTGERMTFYAPLPDDMIRMQE 310


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  ++   G   SR      I   RV+V+G ++++A   V     IEV G P+    R 
Sbjct: 7  RLDVLLVERGWFDSRSRARAAILAGRVRVDGRVVDKAGATVDPGAQIEVAGDPIPYVSRG 66

Query: 74 RLWLYH 79
           L L H
Sbjct: 67 GLKLEH 72


>gi|296136842|ref|YP_003644084.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
 gi|295796964|gb|ADG31754.1| pseudouridine synthase, RluA family [Thiomonas intermedia K12]
          Length = 329

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 79/257 (30%), Gaps = 70/257 (27%)

Query: 12  TPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
             QR+   +AR       S   + R++    V+VNG     A   + S+D + +  V + 
Sbjct: 19  EGQRLDNFLARHLKGVPLS--HIHRIVRSGEVRVNGGRA-SADQKLQSSDQVRIPPVRVA 75

Query: 69  KAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
           + +  R               L   +KP G+        G S V   +            
Sbjct: 76  QPDTPRSAPALQFPIVFEDDFLLAINKPEGVAV-----HGGSGVSFGVIEALRAARPTAK 130

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
               V RLD +T GLLL+         L   L      + Y     G   +         
Sbjct: 131 FLELVHRLDRDTSGLLLIAKKRSALTTLHAALRERHADKRYLALVAGLWTRGA------- 183

Query: 165 IVIQGICYG------DMQVTLDTQKGSNA-----------------WVTVGLRE-----G 196
           ++I+   +       + +V +D Q+G  +                 W  + L +     G
Sbjct: 184 VMIEAPLHKYLLANGERRVRVDAQQGQESRTQFRSQEQFALPGLGPWGGLSLMQARLLTG 243

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+         + 
Sbjct: 244 RTHQIRVHLAHCGHPIV 260


>gi|300767769|ref|ZP_07077679.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300494754|gb|EFK29912.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 293

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/190 (15%), Positives = 65/190 (34%), Gaps = 28/190 (14%)

Query: 38  QRVKV-NGILLERAAVNVM---STDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPD 92
             + + +G +     + +        + V   P++       WL  +K  GL +     +
Sbjct: 47  GVITIHDGDIA---GIQLPDEAPDTAVVVSEQPIQIEYEDANWLVLNKSAGLTSVPGPSN 103

Query: 93  GRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS--TQWLR 143
              T+ + +            R   V RLD +T GL+L+        +L  P    Q ++
Sbjct: 104 RTDTLVNRIKGYLIASHASNQRPHLVTRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVK 163

Query: 144 VYRVRFHGQVDQD----------KLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTVG 192
            Y+    G +               +  ++ +   G       QV  D  + + + + + 
Sbjct: 164 TYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAGQRAITTYQVEADQLQHNVSRLRLE 223

Query: 193 LREGKNREIK 202
           L  G+  +I+
Sbjct: 224 LVTGRTHQIR 233


>gi|183597604|ref|ZP_02959097.1| hypothetical protein PROSTU_00890 [Providencia stuartii ATCC 25827]
 gi|188023103|gb|EDU61143.1| hypothetical protein PROSTU_00890 [Providencia stuartii ATCC 25827]
          Length = 252

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/170 (17%), Positives = 61/170 (35%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D + TVF        I   V  + RLD  T G+LL    
Sbjct: 7   QDEYMVAVNKPAGMLVHRSWLDSKETVFVMQTLRDQIGQFVYPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM- 175
             +AR L     S Q  ++Y     G V+          ++L+ +      +     +  
Sbjct: 67  SDVARQLAAQFESHQIEKIYHAVVRGYVEAPQTIDYPLLEQLDKIADKHATREPALQECV 126

Query: 176 ---------QVTLDTQKGSNAWVT-VGLR-E-GKNREIKKVFEFFNWKVN 213
                    + ++   +   +  + + L+ E G+  ++++        + 
Sbjct: 127 THCQPIAQVECSVAIGRYPTSRFSLLELKPETGRKHQLRRHMSHIRHPII 176


>gi|83719070|ref|YP_442774.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
 gi|83652895|gb|ABC36958.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
          Length = 391

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 81/238 (34%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             +R+ K +A+     SR  +++ I  +RV+V+G   +     V     IE+        
Sbjct: 62  AGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAK-IRQAVPLGATIELLPDLLPEQ 120

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 121 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 180

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD  T GL+++         L     +    R Y     G           + +D  
Sbjct: 181 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGTIDAPIGRDPR 240

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 241 ERTRMAVVTGAAGKPARTHFRTVDTTPWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 298


>gi|194466992|ref|ZP_03072979.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454028|gb|EDX42925.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 290

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/242 (15%), Positives = 73/242 (30%), Gaps = 43/242 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIA-----QQRVKVNGILLERAAVNVMS----- 56
           + +   P ++ K +   G+  R     +       +    V+   +      ++      
Sbjct: 6   IYKGTEPIKIKKYLQSLGMGHR-----LFNDLKNGEGEFLVDHRKVR-PTTQILPNQPLT 59

Query: 57  --------TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                    D +E+    L        WL   KP G+ +         TV + +      
Sbjct: 60  IRAQPELADDTVEISNESLNVVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA 119

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKL 158
                 R   + RLD  T GLLL+      + ++     Q    + Y     GQV  +  
Sbjct: 120 NNSADLRPHLITRLDRFTGGLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHG 179

Query: 159 NL-----LKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +      K G    ++ +       +  ++ +      V V L  G+  +I+  F    
Sbjct: 180 EINKPIGRKDGQAARVIDENGQRALTEYWVEERGAKWTRVRVRLHTGRTHQIRVHFAAIG 239

Query: 210 WK 211
             
Sbjct: 240 HP 241


>gi|116629980|ref|YP_815152.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238853582|ref|ZP_04643952.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           202-4]
 gi|282851411|ref|ZP_06260776.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 224-1]
 gi|311110388|ref|ZP_07711785.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri MV-22]
 gi|116095562|gb|ABJ60714.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           ATCC 33323]
 gi|238833800|gb|EEQ26067.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus gasseri
           202-4]
 gi|282557379|gb|EFB62976.1| pseudouridine synthase, RluA family [Lactobacillus gasseri 224-1]
 gi|311065542|gb|EFQ45882.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           gasseri MV-22]
          Length = 299

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 87/251 (34%), Gaps = 48/251 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVM 55
           M+   +  EN TPQ++ + + R G       +R +         + VN       +  + 
Sbjct: 1   MQYFKLKFENKTPQKLGRFLLRNGF-----SKRALTNSQHNGGMILVNHHR-RYTSYLLH 54

Query: 56  STDHIEV------DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             D +            L+ +        E+    + +K  G+++  S  +    V + L
Sbjct: 55  PGDEVIFILGEEKKNQWLKPSTNQLNIVFEQHDYLVVNKEAGVLSIPSRYEDNDAVVNRL 114

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQV 153
              F +          + RLD +T GL+L+  +               ++ Y    HG  
Sbjct: 115 IYYFQKNGQKDLKPHVITRLDRDTSGLVLVGKNAVAHARFSEMGKDCFIKKYHAIVHGNF 174

Query: 154 DQDK--------LNLL----KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +++        +  L    K+GIV  G         L+   G+ + V + L  G+  +I
Sbjct: 175 SKEQETGTIDAPIGKLDAGVKRGIVANGQRSITKYRVLEQVNGA-SLVELQLLTGRTHQI 233

Query: 202 K-KVFEFFNWK 211
           +  + ++    
Sbjct: 234 RVHM-QYLGHP 243


>gi|166712251|ref|ZP_02243458.1| pseudouridylate synthase [Xanthomonas oryzae pv. oryzicola BLS256]
          Length = 328

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 52/305 (17%), Positives = 106/305 (34%), Gaps = 61/305 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RVNEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QNLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLSLLIGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMSVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
              +     V             G    G   +V+K+ LR+QLG   L     +L+  + 
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRLFLHAASLEFALD 303

Query: 263 SSETL 267
           + +T 
Sbjct: 304 AGQTP 308


>gi|288926989|ref|ZP_06420884.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|315608748|ref|ZP_07883726.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
 gi|288336235|gb|EFC74621.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           D17]
 gi|315249598|gb|EFU29609.1| ribosomal large subunit pseudouridine synthase D [Prevotella buccae
           ATCC 33574]
          Length = 294

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 39/212 (18%), Positives = 74/212 (34%), Gaps = 28/212 (13%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW-- 76
           ++A     SR +++  +  + +KVNG    R    +     I V         R+R    
Sbjct: 24  LLANVKGESRSKIKATLKGRGIKVNGKQTTRFDYPLEPGMKISVSRNKRNDTFRSRYVRL 83

Query: 77  --------LYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLL 123
                   +  K +G+++    HS  + +  + D       +     V RLD +T GL++
Sbjct: 84  VYEDRHIVVLEKAVGILSMAAGHSSLNVKKVLDDYFKKTRQKCTAHVVHRLDRDTSGLMI 143

Query: 124 LTNDGGLARVLELPSTQW--LRVYRVRFHGQV--DQDKLNLLKKGI---------VIQGI 170
                 + ++LE         R Y     G+V  D+  +    K           V  G 
Sbjct: 144 YAKSKEIEQMLEHDWHHVVYDRRYVAVVSGEVYDDEGTIANWLKDNKAYVTYSSPVDNGG 203

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            Y      +  +   ++ V   L  G+  +I+
Sbjct: 204 KYAVTHFHVLRRTTDHSLVEYRLETGRKNQIR 235


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           T QR+  ++    + S R+E + +I    VKVN  ++++    V ST  IE+   P
Sbjct: 1  MTKQRLDTLLVERNLCSSRQEAQGLIRAGEVKVNQQVIDKPGTPVESTAEIELQAKP 57


>gi|159038967|ref|YP_001538220.1| RluA family pseudouridine synthase [Salinispora arenicola CNS-205]
 gi|157917802|gb|ABV99229.1| pseudouridine synthase, RluA family [Salinispora arenicola CNS-205]
          Length = 314

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 63/176 (35%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +     R+ + +AR    SR     ++ +    V+G  +   +  V +   +EV    
Sbjct: 16  VPDGLDGMRLDQAVARLFGLSRTSAAALVDEGAALVDG-TVRVNSYKVRAGAWLEVTLPA 74

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-- 108
                        G+ +  A+   + + +KP+G+    S      TV   L +I  R+  
Sbjct: 75  PAAPPAVVPQAVSGLRVVYADDDIVVV-NKPVGVAAHPSPGWSGPTVIGGLAAIGHRIAT 133

Query: 109 -------ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                    V RLD+ T G++++         L+      +  + Y     G +D 
Sbjct: 134 SGAAERQGVVHRLDVGTTGIMVVAKSEQAYTGLKRAFKYREVEKRYHAVVQGHLDP 189


>gi|257138984|ref|ZP_05587246.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis E264]
          Length = 385

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 81/238 (34%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             +R+ K +A+     SR  +++ I  +RV+V+G   +     V     IE+        
Sbjct: 56  AGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAK-IRQAVPLGATIELLPDLLPEQ 114

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 115 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 174

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD  T GL+++         L     +    R Y     G           + +D  
Sbjct: 175 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGTIDAPIGRDPR 234

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 235 ERTRMAVVTGAAGKPARTHFRTVDTTPWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 292


>gi|228477070|ref|ZP_04061708.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Streptococcus salivarius SK126]
 gi|228251089|gb|EEK10260.1| ribosomal large subunit pseudouridine synthase, RluD   family
           [Streptococcus salivarius SK126]
          Length = 298

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 67/201 (33%), Gaps = 36/201 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRL-----WLYHKP 81
               + VNG   + A   V   D + ++           P+              + +KP
Sbjct: 33  EGGHIWVNGE-EQFATYPVHEGDVVAIEIPDEAPHETLKPIPFDLDIVYEDDNFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S  +  +T+ + +   F        RV  V RLD +T GL+L    G     +
Sbjct: 92  YGYASIPS-VNHDNTMANFVKHHFVSNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARM 150

Query: 135 --ELPSTQWLRVYRVRFHGQ--VDQ--DKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G   +++  + +  + + +       V +   Y      L  
Sbjct: 151 DKQLQQKSIKKHYYALVEGDTKLEEQGEIIAPIARDVDSIITRRVHKSGKYAHTSYRLVA 210

Query: 182 QKGSNAWVTVGLREGKNREIK 202
             G    V + L  G+  +I+
Sbjct: 211 DYGRVKLVDINLHTGRTHQIR 231


>gi|89075424|ref|ZP_01161841.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
 gi|89048840|gb|EAR54410.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           sp. SKA34]
          Length = 245

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 52/167 (31%), Gaps = 27/167 (16%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL      +
Sbjct: 11  YLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFGLSSEI 70

Query: 131 ARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           A  +          + Y     G + +  +      + +  I   +     + Q    A+
Sbjct: 71  ASQMMPLFAGRDMHKTYHAVVRGWIKEAAVLDYPLKVELDKIADKNASEEKEAQPAVTAY 130

Query: 189 ---VTVG--------------LRE-----GKNREIKKVFEFFNWKVN 213
               TV               L E     G+  ++++     +  + 
Sbjct: 131 EPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHII 177


>gi|238927181|ref|ZP_04658941.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
 gi|238884963|gb|EEQ48601.1| pseudouridylate synthase [Selenomonas flueggei ATCC 43531]
          Length = 294

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 66/200 (33%), Gaps = 32/200 (16%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRK------------AERTRLWLYHKPIGLVTTH 88
            +NGI    A   +   D I  D +P+               E   L +  KP G +   
Sbjct: 41  TLNGIPAVAARTMLKDGDWIAYD-LPIVSSVIPESLPLSIIYEDDDLLVLDKPAGQLVHP 99

Query: 89  SDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           +  +   T+ + +   ++            RLD NT GLLL+     +   +   +T   
Sbjct: 100 TTKETHGTIANAVRGYYAACGVHLDFHPCHRLDRNTSGLLLIAKHPEVQYQIAQQNT-LR 158

Query: 143 RVYRVRFHGQVDQDK------LNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTV 191
           R Y     G +   +      +      I++     +G       VT+ T  G  + + +
Sbjct: 159 REYLALIAGSLTPPEGCIDVPIARALPSIILRCVSTEGKSACTHYVTVQT-DGRYSLLRL 217

Query: 192 GLREGKNREIKKVFEFFNWK 211
            L  G+  +I+         
Sbjct: 218 QLDTGRTHQIRVHLAHLGHP 237


>gi|56750446|ref|YP_171147.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81299921|ref|YP_400129.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
 gi|56685405|dbj|BAD78627.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 6301]
 gi|81168802|gb|ABB57142.1| ribosomal large subunit pseudouridine synthase D [Synechococcus
           elongatus PCC 7942]
          Length = 313

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 87/246 (35%), Gaps = 48/246 (19%)

Query: 1   MKDKNIVQENFTP-QRVSKVIARA-GIASRREVERMIAQQRVKVNGILL----------E 48
           M D+  ++    P +R+ + +A+     SR  ++++IA  +++VNG +           +
Sbjct: 1   MSDRLQLEITEVPSERLDRWLAQQWPHLSRARLQKLIAAGQLRVNGEVCDQKRWQPRLGD 60

Query: 49  RAAVNVMSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           R  + +  T+ I +    +      E   L + +K +G+V   +      T+   L +  
Sbjct: 61  RLELEMPPTEAIALAPEEIPLDILYEDADLLIVNKAVGMVVHPAAGHDTGTLVHALLAHC 120

Query: 106 ----------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-----LRVYRVRFH 150
                      R   V RLD +T G +++         L     Q       R Y     
Sbjct: 121 GDSLTGIGGEQRPGIVHRLDKDTTGAMVVA---KTEAALLSLQDQIRQKTAQREYLGVVF 177

Query: 151 GQVDQD-------------KLNLLKKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREG 196
           G   QD                 +   + I+ G  +      +  + G+ A +   L  G
Sbjct: 178 GSPRQDSGQVEEPIGRHLRDRKRMAV-VPIERGGRWALTHWQVRERLGNYALLHYRLATG 236

Query: 197 KNREIK 202
           +  +I+
Sbjct: 237 RTHQIR 242


>gi|168182364|ref|ZP_02617028.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|237794773|ref|YP_002862325.1| RluA family pseudouridine synthase [Clostridium botulinum Ba4 str.
           657]
 gi|182674479|gb|EDT86440.1| pseudouridine synthase, RluA family [Clostridium botulinum Bf]
 gi|229262158|gb|ACQ53191.1| pseudouridine synthase, RluA family [Clostridium botulinum Ba4 str.
           657]
          Length = 317

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/264 (12%), Positives = 77/264 (29%), Gaps = 67/264 (25%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA- 50
           K ++  N   QR+ K              +             I +  +KVNG   +   
Sbjct: 2   KIVIGANEAGQRLDKF-----------CRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKN 50

Query: 51  ---------AVNVMSTDH----IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                    + NV S       + +D       E   + L  K  G++      +G  T+
Sbjct: 51  FLEEGDIVESFNVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTL 110

Query: 98  FDNLPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                      RLD NT G+++   +    + L   +   +  
Sbjct: 111 TDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIE 170

Query: 143 RVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSN----AWV 189
           + Y     G++                + K  +         ++ ++ +        +++
Sbjct: 171 KYYSSLVKGRIKDGVYEAYISKNEDTNMSK--IYNEPKPNTKKIAMNVKTIQTCGSFSFI 228

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 229 EIELLTGRSHQLRAHLSHLGNPII 252


>gi|71907236|ref|YP_284823.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas
           aromatica RCB]
 gi|71846857|gb|AAZ46353.1| ribosomal large subunit pseudouridine synthase D [Dechloromonas
           aromatica RCB]
          Length = 318

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/232 (17%), Positives = 78/232 (33%), Gaps = 35/232 (15%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ +V+A      SR  ++  + +  V+V+G         +M  + + V           
Sbjct: 29  RLDQVLAELLPQHSRNRLQGWVREACVQVDGKPETEPKRKMMGGEKLLVSEPEDVRNQPE 88

Query: 63  --DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------GR 113
             + +PL    E   L + +KP GLV      +   T+ + L      +  V       R
Sbjct: 89  LPEDIPLDVVFEDETLLVINKPAGLVVHPGSGNWSGTLMNALLHHVPGIEVVPRAGIVHR 148

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLL 161
           LD +T GLL++         L  +L +    R+Y              +  + +     +
Sbjct: 149 LDKDTSGLLVVAKTLEAQTDLVRQLQARTVRRIYLALAAGAMKHEGTVNEPIGRHPSQRI 208

Query: 162 KKGIVIQGICYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K  IV +          + +        +V   L  G+  +I+      +  
Sbjct: 209 KMAIVPENRGGKPAITNIRILEAFTYTTFVECSLETGRTHQIRVHMAAIHHP 260


>gi|317012766|gb|ADU83374.1| hypothetical protein HPLT_04870 [Helicobacter pylori Lithuania75]
          Length = 242

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 75/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENVSHKKAKALIDLGLVSIGGKKLMVARKELPKNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVEKEYLALVQGIIEEE--REINAPILTFKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|170759830|ref|YP_001786858.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406819|gb|ACA55230.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 317

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/264 (12%), Positives = 77/264 (29%), Gaps = 67/264 (25%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA- 50
           K ++  N   QR+ K              +             I +  +KVNG   +   
Sbjct: 2   KIVIGANEAGQRLDKF-----------CRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKN 50

Query: 51  ---------AVNVMSTDH----IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                    + NV S       + +D       E   + L  K  G++      +G  T+
Sbjct: 51  FLEEGDIVESFNVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTL 110

Query: 98  FDNLPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                      RLD NT G+++   +    + L   +   +  
Sbjct: 111 TDYVLSYLYDKGDYTPELEVTFTPAPCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIE 170

Query: 143 RVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSN----AWV 189
           + Y     G++                + K  +         ++ ++ +        +++
Sbjct: 171 KYYSSLVKGRIKDGVYEAYISKNEDTNMSK--IYNEPKPNTKKIAMNVKTIQTCGSFSFI 228

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 229 EIELLTGRSHQLRAHLSHLGNPII 252


>gi|189424176|ref|YP_001951353.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189420435|gb|ACD94833.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 300

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 74/234 (31%), Gaps = 44/234 (18%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERT-----------RLWL 77
             ++I      +NG         + +   I +   G  L    R            RL  
Sbjct: 31  CRKLIKSGACTLNGTK-SSPDTLLSAGAIISLKESGQVLELLNRPLPPIDLLWQDDRLLA 89

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVISVGRLDINTEGLLLL----TN 126
            +KP G +  H   +    + D   +          R   V RLD  T G++LL    +N
Sbjct: 90  INKPAG-LAMHPAAEVDENLADIASAWLEKKANYPVRAYPVNRLDRGTSGVVLLATSSSN 148

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-----VIQGICYGDMQVTLDT 181
            G L R ++       ++Y     G         + +GI      + G        +L  
Sbjct: 149 AGILGRQVK--EEGLDKIYLTVVEG---------MLEGIGEISQPLDGKESISRYRSLSV 197

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF-QLGTLLAGSTR 234
            + S +++ V    G+  +I++        V    R    P   L  +   S R
Sbjct: 198 GE-SCSFLLVEPVTGRTHQIRRHLSAIGHPVLGDKRYDAQPLATLPGIALHSFR 250


>gi|28378819|ref|NP_785711.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|300768863|ref|ZP_07078757.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308181018|ref|YP_003925146.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28271656|emb|CAD64562.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|300493596|gb|EFK28770.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|308046509|gb|ADN99052.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 300

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 84/243 (34%), Gaps = 44/243 (18%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVN------------GILLER 49
           +    TP +V  ++A+ G+ +R     ++ +       + V+            G  +  
Sbjct: 6   INHETTPMKVKTLLAQHGV-TRS----LLKKVKFHGGAILVDERPVLAIHMLTGGETVTM 60

Query: 50  AAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
                +  DH+ V  +P+    E     + +KP G+ +  +     +T+ + +   +   
Sbjct: 61  VTPAEIGNDHLGVSTLPIDILYEDRDYLIVNKPAGVASVPAHALPDNTLANRVKGYYQAA 120

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLN 159
                 V    RLD +T G++L         +++         ++Y     G++  D   
Sbjct: 121 HYDNEVVHITTRLDRDTSGIVLFAKHHFAHSIIDHQLKAHAMRKMYLAVVSGELTTDH-G 179

Query: 160 LLKKGI------VIQGICYGDMQVTL----DTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
            L   I       I+     D + +L      ++  N   V V L  G+  +I+  F   
Sbjct: 180 WLDAPIGRAADSFIKRTTRPDGKPSLTEYWVVKRLRNMTVVRVRLHTGRTHQIRVHFAAS 239

Query: 209 NWK 211
              
Sbjct: 240 GHP 242


>gi|324995861|gb|EGC27772.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK678]
          Length = 291

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/204 (20%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  +  V VNG L       V S D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKNHVSVNG-LAINWQTVVKSGDDICLIFDEEDYPQKTILFGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  +   Y +  VT
Sbjct: 147 PILNRLLEKREISREYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  A V   L+ G+  +I+
Sbjct: 207 RLKQLGQAALVKCQLKTGRTHQIR 230


>gi|229586508|ref|YP_002845009.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
 gi|228021558|gb|ACP53266.1| Ribosomal large subunit pseudouridine synthase [Rickettsia africae
           ESF-5]
          Length = 303

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 61/175 (34%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A++ V   D I ++     
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNAQKA-EASLRVKGGDKIFINDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P+++ E+                         L   +KP GL T        S       
Sbjct: 66  PVKQPEKLVFTDAEIKLAKKITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGADFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKP 180


>gi|157962549|ref|YP_001502583.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847549|gb|ABV88048.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 305

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/162 (15%), Positives = 57/162 (35%), Gaps = 11/162 (6%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRL 114
           D    D   L   E+  +W  +KP G+    S     +T+   + +          + RL
Sbjct: 101 DETVTDAELLFDEEQYSVW--YKPFGMRCQGSKWSDHTTINRFIETQLTPPRNAYIIHRL 158

Query: 115 DINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D+   GL++L +   +   +     +    + Y+V   G+  + ++ +     V      
Sbjct: 159 DLAATGLIVLGHTKKVTAAIAQLFETRALDKFYQVIVEGKFPEGQVTINTD--VDNKKAL 216

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
               +     + + + V V +  G+  +I+  +       V 
Sbjct: 217 SHAHILEYNSELNQSKVQVKIESGRKHQIRIHM-ASLGHPVI 257


>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 = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 89/247 (36%), Gaps = 52/247 (21%)

Query: 12  TPQRVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV---- 65
             +R+ + +AR   GI +R   +R+I + RV V+  L E+ ++ +   + + V       
Sbjct: 17  EAERLDQFVARSVQGI-TRSAAQRLIEEGRVTVDDRL-EKPSLKLRGGERVVVTVPPPAP 74

Query: 66  ---------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---- 112
                     +   E   + +  KP G+V   +  +   T+ + L +  + +  +G    
Sbjct: 75  AVPEAEEIPLVVLHEDGDVVVVDKPAGMVVHPAAGNPGGTLVNALLAHCTDLSGIGGEIR 134

Query: 113 -----RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
                R+D +T G+L++         L          RVY    +G   +DK  +  +G 
Sbjct: 135 PGIVHRIDKDTSGVLVVAKSDRAHESLSRQFHDHTVKRVYLALVYGSPREDKGRI--EGA 192

Query: 166 VIQGICYGDMQ----VTLDTQKGSNAW-----------VTVGLREGKNREIK-KVFEF-- 207
           +  G    D +         +     W           + + L  G+  +I+  + E   
Sbjct: 193 I--GRHPTDRKKMSGAARHGKHAVTHWRVAARFTGVTLLRLRLETGRTHQIRVHMAEAGF 250

Query: 208 --FNWKV 212
                +V
Sbjct: 251 PLVGDEV 257


>gi|21242847|ref|NP_642429.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
 gi|21108337|gb|AAM36965.1| pseudouridylate synthase [Xanthomonas axonopodis pv. citri str.
           306]
          Length = 328

 Score = 61.0 bits (147), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 98/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            +                       E  RL   +KP G+ +            T+    P
Sbjct: 80  RINDEDDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRL 291


>gi|325270275|ref|ZP_08136882.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
 gi|324987576|gb|EGC19552.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           multiformis DSM 16608]
          Length = 296

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/212 (19%), Positives = 80/212 (37%), Gaps = 29/212 (13%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL--W 76
           ++A     SR +V+  +  + +KVNG  + +    + + D + V         R+R    
Sbjct: 27  LLANLKE-SRSKVKATLQNRGIKVNGKCVTQFDHPLQAGDKVSVSKSKKNDQFRSRYVKI 85

Query: 77  LY--------HKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLL 123
           +Y         K  G+++           TV D+   +  +      V RLD +T GL++
Sbjct: 86  IYEDRFLVVVEKNTGILSMAAGHASLNVKTVLDDYFRMTRQKCTAHVVHRLDRDTSGLMI 145

Query: 124 LTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK---LNLLKKGI--------VIQGI 170
              D    ++LE         R Y     G+++Q++    N LK           V  G 
Sbjct: 146 YAKDMQTEQLLERDWHNIVYDRRYIAVVSGEMEQEEGTVANWLKDNKAYVTYSSPVDNGG 205

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            Y      +  +  +++ V   L  G+  +I+
Sbjct: 206 KYAVTHFRVLDRTVAHSLVEYRLETGRKNQIR 237


>gi|319902371|ref|YP_004162099.1| pseudouridine synthase, RluA family [Bacteroides helcogenes P
           36-108]
 gi|319417402|gb|ADV44513.1| pseudouridine synthase, RluA family [Bacteroides helcogenes P
           36-108]
          Length = 309

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/226 (15%), Positives = 80/226 (35%), Gaps = 41/226 (18%)

Query: 12  TPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIE 61
            P  + + + A+   ASR +++ +++++ V V+ ++        +  + V         E
Sbjct: 21  EPMELMEFLTAKMPDASRTKLKSLLSKRIVYVDSVITTQYNFPLKPGMKVQISREKGRKE 80

Query: 62  VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
            +   ++   E   + +  K  GL++ +++     T +  L     R      V +V RL
Sbjct: 81  FNHKLIKIVYEDAYIIVIEKMQGLLSVNTERQKERTAYTILNEYVQRSGRQHRVYTVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVI----- 167
           D +T GL++   D      L          R Y     G+++++       G+V      
Sbjct: 141 DRDTSGLMMFAKDEKTQNTLRDNWHDIVFDRRYVAVVSGEMEKNA------GVVSSWLTD 194

Query: 168 -----------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       G            +    + + + L  G+  +I+
Sbjct: 195 RTLYVYSSPTNDGGKEAITHYRTIKRANGYSLMELNLETGRKNQIR 240


>gi|283956117|ref|ZP_06373604.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792437|gb|EFC31219.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 250

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 74/201 (36%), Gaps = 31/201 (15%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA +N  +  ++     P    E  ++
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSHGKKVVVARALMNDKARFNVIKTKNPQIIFEDDKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 67  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 113

Query: 136 LPSTQW--LRVYRVRFHGQVDQD------------KLNLLKKGIVIQGICYGDMQVTLDT 181
               +    + Y     G + ++            K   L K +   G+    + +T   
Sbjct: 114 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKCGALSK-VSKDGLSALSI-ITPIM 171

Query: 182 QKGSNAWVTVGLREGKNREIK 202
            +       + ++ G+  +I+
Sbjct: 172 LQSKKTLAKIVIQTGRTHQIR 192


>gi|323691883|ref|ZP_08106137.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323504090|gb|EGB19898.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 333

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 45/302 (14%), Positives = 100/302 (33%), Gaps = 66/302 (21%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           + +N   QR+ K++A+   +A +  + +M+ ++ + +NG      +  +   D ++    
Sbjct: 6   ITKNEAGQRLDKLLAKYLNLAGKSFIYKMLRKKNITLNGKKC-DGSEKLSEGDEVKLFLS 64

Query: 62  ------VDGVPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
                    V ++K  + +         + L +KP G+++  +     S V   +     
Sbjct: 65  DETIEKFSEVKIQKVRKRKLDVVYEDDDIILINKPSGMLSQKAKETDESLVEYLIQYLLD 124

Query: 102 -----PSIFSRVIS--VGRLDINTEGLLLLTNDGG--LARVLELPSTQ---WLRVYRVRF 149
                     +       RLD NT G+++    G       L   + +     + Y    
Sbjct: 125 GGKLTKEDMRQFKPSVCNRLDRNTSGIVIA---GKSLPGLQLMSEAIKERTIGKYYLCIV 181

Query: 150 HGQVD-----QDKLNLLKKGIVI----------QGICYGDM--QVTLDTQKGSNAWVTVG 192
            G V         L   +K   +          +      +  Q       G +  + V 
Sbjct: 182 KGSVAGPKEIDGYLKKNEKTNQVTVLKANELCREDKDALPIRTQYRPLCSDGRHTLLEVK 241

Query: 193 LREGKNREIKKVFEFFNWKVN--------RLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L  G++ +I+         +          + R +   + + + +  + R V  K LRE 
Sbjct: 242 LITGRSHQIRAHLASIGHPIAGDYKYGDPAVNREARDKYAVQSQMLHAWRLVMPKELREP 301

Query: 245 LG 246
           L 
Sbjct: 302 LA 303


>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 = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 74/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KLLSVQENISHKKAKALIDSGLVSIGGQKLMVARKELPKNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F     + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKDWALLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLAIVQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAITIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>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 = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/212 (19%), Positives = 79/212 (37%), Gaps = 29/212 (13%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA-- 70
           ++A  G  ++ +V+  +  + +KVNG ++ +    +   D I +      D    R    
Sbjct: 28  LLANVGE-TKSKVKATLKNRGIKVNGKIVTQFDHQLKIGDKIAISKSKKNDQFKSRYVKL 86

Query: 71  --ERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLL 123
             E   L +  K +G+++    H+  + +  + D             V RLD +T GL++
Sbjct: 87  VYEDKYLVVVEKNVGILSMGAGHASLNVKKVLDDYFHKTKQNCTAHVVHRLDRDTSGLMI 146

Query: 124 LTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK---LNLLKKGI--------VIQGI 170
              D    ++LE         R Y     G++  D+    N LK           V  G 
Sbjct: 147 YAKDMQTEQLLEHDWHNIVYDRRYIAVLSGEMADDEGTIANWLKDNKSYITYSSPVDNGG 206

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            Y         +  +++ V   L  G+  +I+
Sbjct: 207 KYAVTHFFTIDRTVNHSLVEFKLETGRKNQIR 238


>gi|260425298|ref|ZP_05779278.1| ribosomal large subunit pseudouridine synthase D [Citreicella sp.
           SE45]
 gi|260423238|gb|EEX16488.1| ribosomal large subunit pseudouridine synthase D [Citreicella sp.
           SE45]
          Length = 345

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 44/195 (22%), Positives = 70/195 (35%), Gaps = 32/195 (16%)

Query: 5   NIVQENFTPQRVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            I+     P R+ K +AR     A + SR  + R+IA+  V   G  L      V   D 
Sbjct: 6   RIIIGEAPPPRLDKALARDVPEEAAL-SRTRLARLIAEGAVTRAGEALTDPKARVAEGDE 64

Query: 60  IEV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           I +            + +PL    E   L +  KP G+V   +      T+ + L   F 
Sbjct: 65  ILITVPQAEDSHIGPEDIPLSIVWEDEDLVVVDKPAGMVVHPAPGTPSGTLVNALLHHFG 124

Query: 106 ---------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVD 154
                    +R   V R+D +T GLL++         L          R Y    +G  D
Sbjct: 125 GRLSGVGGVARPGIVHRIDKDTSGLLVVAKSDRAHHGLAAQFEAHSADRAYLAVVYGVPD 184

Query: 155 QDKLNLL-KKGIVIQ 168
                L+  +G+ ++
Sbjct: 185 AGDPRLVGTRGVSME 199


>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 = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 85/234 (36%), Gaps = 48/234 (20%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVD-GVPLRK------------AERTRLWLYHKPIGLV 85
           R+ VNG  +   +  V+  D IEVD   P  +             E + + + +KP  ++
Sbjct: 42  RLFVNGKTVR-LSYRVLEGDKIEVDVNKPESQNVDPEKMDLNIVYEDSDIIVLNKPANMI 100

Query: 86  TTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPST 139
              +      T+ + L   F        V  V RLD++T GL+L+  +   + +      
Sbjct: 101 VHPTKNYQHGTLSNGLLYYFREKGENCIVRLVNRLDMDTSGLVLVAKN-QFSHMALARDM 159

Query: 140 QWL---RVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +     + Y     G            + +++   +++ I  +G         ++  K +
Sbjct: 160 KLDTFKKEYIAVVRGNLSSLKGTIDKPIYKEEEEPIRRTIDDRGQESITHFEVVERYKNA 219

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +  V + L  G+  +I+            +   S G   +G  L G   E+ K+
Sbjct: 220 DK-VKLVLETGRTHQIR------------VHLSSIGNPIIGDSLYGEESELIKR 260


>gi|227893162|ref|ZP_04010967.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus ultunensis
           DSM 16047]
 gi|227865028|gb|EEJ72449.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus ultunensis
           DSM 16047]
          Length = 310

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/217 (15%), Positives = 75/217 (34%), Gaps = 38/217 (17%)

Query: 32  ERMIAQ----QRVKVNGILLERAAVNVMSTDHIE-VDGV------------PLRKA-ERT 73
           + +I        + VN       +  + + D +  + G             P++   E  
Sbjct: 38  QALIKARYHHGMILVNHKR-RYLSFRLRTGDEVIFISGEEKKNEFLKPSSNPVKPVLETK 96

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTN 126
              +  KP G+++  S  +    + + L   F++          + RLD +T GL+L+  
Sbjct: 97  NYIVLDKPAGVLSIPSRYEDNDAIVNRLMGYFAKKNMSNLKPHVITRLDRDTSGLVLVGK 156

Query: 127 DGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLLKK--------GI---VIQGICYGD 174
           +             ++++ Y    HG   +DKL  +          G+   V++G     
Sbjct: 157 NAIAHARFSKIGKEKFVKKYHAIVHGNFSEDKLTGVIDAPIGKKGSGVKRAVVEGGKKAQ 216

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +  +  Q    + V + L  G+  +I+    +    
Sbjct: 217 TKYRVLKQVSGASLVELRLLTGRTHQIRVHMAYLGHP 253


>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 = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           T QR+  ++    + S R+E + +I    VKVN  ++++    V ST  IE+   P
Sbjct: 1  MTKQRLDTLLVERNLCSSRQEAQGLIRAGEVKVNQQVIDKPGTPVESTAEIELQAKP 57


>gi|87201058|ref|YP_498315.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           aromaticivorans DSM 12444]
 gi|87136739|gb|ABD27481.1| ribosomal large subunit pseudouridine synthase D [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 332

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 83/239 (34%), Gaps = 45/239 (18%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP------- 66
           QR+ K +A A   SR  V+ ++ + RV++ G ++ +A++        E+           
Sbjct: 24  QRLDKALADASGLSRERVKALLGEGRVRLGGAVVSQASLKPAEGTPFEIHVPEAAPAEAI 83

Query: 67  ------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------RVIS 110
                 +   E   L +  KP GLV   +  +   T+ + L               R   
Sbjct: 84  AQAIPLVVVHEDDALIVVDKPAGLVVHPAAGNPDGTLVNALLHHCRGQLSGIGGVARPGI 143

Query: 111 VGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV--------------- 153
           V R+D +T GLL++  T+        +       R Y+    G                 
Sbjct: 144 VHRIDKDTSGLLVVAKTDAAHEGLARQFADHSITRAYKCVTAGVPMPPSGTVRGAIARSS 203

Query: 154 -DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            D+ K+ L+  G   +G        TL   +G+ A V   L  G+  +++         
Sbjct: 204 HDRKKMALVDDG---RGKHAVTHFRTLAALQGA-ALVECRLETGRTHQVRVHLASIGHP 258


>gi|331004934|ref|ZP_08328347.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
 gi|330421258|gb|EGG95511.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC1989]
          Length = 333

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/180 (20%), Positives = 65/180 (36%), Gaps = 31/180 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLER--------- 49
           ++++ IV +    +RV +V A +     SR  ++  I Q  + V+G              
Sbjct: 5   IQEQCIVPDTDAGKRVDQV-AASLFQQYSRSRIQEWIKQGTILVDGQKCRSKDKLLSGEM 63

Query: 50  --AAVNVMSTDH-----IEVDGVPLRKAERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
              AV ++  D      I +D           + + +KP GLV        D    + + 
Sbjct: 64  ITLAVELIEDDRWLPQDIAID----EVYSDEHIIIINKPAGLVVHPGAGMPDGTLLNGLL 119

Query: 99  DNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
            + P      R   V RLD +T GL+++         L  +L      R Y     G++ 
Sbjct: 120 FHYPELSTLPRAGIVHRLDKDTTGLMVVARSLLAHTSLVQQLQDRSLGREYEAVVMGELT 179


>gi|323484810|ref|ZP_08090167.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323401916|gb|EGA94257.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 333

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 45/302 (14%), Positives = 100/302 (33%), Gaps = 66/302 (21%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           + +N   QR+ K++A+   +A +  + +M+ ++ + +NG      +  +   D ++    
Sbjct: 6   ITKNEAGQRLDKLLAKYLNLAGKSFIYKMLRKKNITLNGKKC-DGSEKLSEGDEVKLFLS 64

Query: 62  ------VDGVPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
                    V ++K  + +         + L +KP G+++  +     S V   +     
Sbjct: 65  DETIEKFSEVKIQKVRKRKLDVVYEDDDIILINKPSGMLSQKAKETDESLVEYLIQYLLD 124

Query: 102 -----PSIFSRVIS--VGRLDINTEGLLLLTNDGG--LARVLELPSTQ---WLRVYRVRF 149
                     +       RLD NT G+++    G       L   + +     + Y    
Sbjct: 125 GGKLTKEDMRQFKPSVCNRLDRNTSGIVIA---GKSLPGLQLMSEAIKERTIGKYYLCIV 181

Query: 150 HGQVD-----QDKLNLLKKGIVI----------QGICYGDM--QVTLDTQKGSNAWVTVG 192
            G V         L   +K   +          +      +  Q       G +  + V 
Sbjct: 182 KGSVAGPKEIDGYLKKNEKTNQVTVLKANELCREDKDALPIRTQYRPLCSDGRHTLLEVK 241

Query: 193 LREGKNREIKKVFEFFNWKVN--------RLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           L  G++ +I+         +          + R +   + + + +  + R V  K LRE 
Sbjct: 242 LITGRSHQIRAHLASIGHPIAGDYKYGDPAVNREARDKYAVQSQMLHAWRLVMPKELREP 301

Query: 245 LG 246
           L 
Sbjct: 302 LA 303


>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 = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/214 (16%), Positives = 79/214 (36%), Gaps = 29/214 (13%)

Query: 29  REVERMIAQQRVKVNGILL------ERAA--VNVMSTDH---IEVDGVPLRK-AERTRLW 76
           R+++ M  ++RVKVN  +       ++       +  D    ++V+  P+    E     
Sbjct: 41  RDIQMMFRKKRVKVNSRVAHSQRALKKGDVLTLELPQDKDYGVDVEKGPITVLYEDAHTL 100

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TNDG 128
           + +K   ++   +      T+ + +   +       +V  V RLD +T G +L   T + 
Sbjct: 101 VVNKDPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTKEA 160

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---------IVIQGICYGDMQVTL 179
                 EL + +  R+Y     G++D D +     G         ++ +       +  +
Sbjct: 161 QQYYTDELQAGRIDRIYTGLVEGRIDADGMVDAPIGVDPVFDNRRVIDEFGQPAQTEYIV 220

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +G N  +   L  G+  +I+   E     + 
Sbjct: 221 LNHEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIV 254


>gi|260779409|ref|ZP_05888300.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260604499|gb|EEX30799.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 245

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 60/171 (35%), Gaps = 36/171 (21%)

Query: 68  RKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           R  E   + + +KP GL++      +   +++  L  I+  +  V RLD++T GL+L   
Sbjct: 16  RVFEDEGILVVNKPSGLLSVPGRAEEHYDSMWSRLKDIYPDIQPVHRLDMSTSGLMLFAK 75

Query: 127 D--------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGD 174
           +              L        +VY  R  G+V+Q +       + +           
Sbjct: 76  NKPTESALKKQFQFRLTH------KVYYARVWGRVEQQEGE-----VDLPLICDWPNRPK 124

Query: 175 MQVTLDTQKGSNAWVTVGLRE------------GKNREIKKVFEFFNWKVN 213
            +V  +  K S     V  RE            G++ +++   +     + 
Sbjct: 125 QKVCFEQGKPSKTLFEVAKREEQTTIVRLLPITGRSHQLRVHMQALGHPIV 175


>gi|15892267|ref|NP_359981.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           conorii str. Malish 7]
 gi|20139551|sp|Q92IS6|RLUC_RICCN RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|15619407|gb|AAL02882.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           conorii str. Malish 7]
          Length = 303

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 61/175 (34%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A++ V   D I ++     
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNAQKA-EASLRVKGGDKIFINDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P+++ E+                         L   +KP GL T        S       
Sbjct: 66  PVKQPEKLVFTDAEIKLAKKITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGADFKLVHRLDKKTSGLLLIAKNYLSSVKLHNAFKEKLVVKTYFAVTYGKP 180


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

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 89/251 (35%), Gaps = 56/251 (22%)

Query: 3   DKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++  V+      R+ +         G      +++++   +++V+G  ++ A   V    
Sbjct: 5   EQITVEAGEAGMRLDRWFKTHFPGLGFG---HLQKLLRSGQIRVDGGRVK-ADSRVEPGQ 60

Query: 59  HI-----EVD--------GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDG 93
            +     EVD        G  +R              E  ++++++KP GL         
Sbjct: 61  VVRIPPLEVDKKGESALTGHSIRNQGDADVLAKMLIHEDPKVFVFNKPAGLAVQGGSGVT 120

Query: 94  RSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
           R  V D L +  ++       V RLD +T G+L++      A  L     + +  + Y  
Sbjct: 121 R-NVDDMLEAWRNQKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKKTYWA 179

Query: 148 RFHGQVD--QDKLNLL------KKG----IVIQGICYGDMQVT----LDTQKGSNAWVTV 191
              G     +DK++        + G    +   G    D  V+    ++    +  W+ +
Sbjct: 180 LVKGVPPKREDKISTWLIKEPTEDGDRVRVAAHGEKGADHAVSYYRIIEQAAQTMTWLEM 239

Query: 192 GLREGKNREIK 202
               G+  +++
Sbjct: 240 EPYTGRTHQLR 250


>gi|260914145|ref|ZP_05920618.1| tRNA pseudouridine synthase C [Pasteurella dagmatis ATCC 43325]
 gi|260631778|gb|EEX49956.1| tRNA pseudouridine synthase C [Pasteurella dagmatis ATCC 43325]
          Length = 241

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 61/181 (33%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+LL    
Sbjct: 8   QDDYLVAVNKPAGMLVHRSWLDMHETQFVMQTLRDQIGQHVYPIHRLDRPTSGVLLFALS 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A +L L     Q  + Y     G +            KL+ +    V +     D  
Sbjct: 68  SEVANLLCLQFEDKQVEKSYLAIVRGYLTGKERIDYPLKVKLDKVADKFVQEDKAPQDAV 127

Query: 177 ------VTLD----TQKGSNAWVTVG--LRE-GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                 +T++     +K +    ++   L + G+  ++++  +     +  L    YG  
Sbjct: 128 TDYQGLLTVEMPYSVKKYNTTRYSLVRLLPQTGRKHQLRRHMKHIFHPI--LGDTQYGDL 185

Query: 224 Q 224
            
Sbjct: 186 H 186


>gi|197117385|ref|YP_002137812.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197086745|gb|ACH38016.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 302

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 77/231 (33%), Gaps = 57/231 (24%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------VPLRKA-----ERTRLWLY 78
           +++I+   VKVNG  +  AA  +   D + +            L        E + +   
Sbjct: 32  KKLISSGHVKVNGSPV-EAAQLLRFADQVTLKESSKTAAFLARLTPELDILFEDSWIISL 90

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLAR 132
           +K  GL    ++      + D   ++        R+  V RLD  T G ++L      A 
Sbjct: 91  NKAPGLSVHRTEDPDEVNLVDLAEALLQKRDGVGRLRPVNRLDKGTSGAIILAKSAVAAG 150

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +    +      ++Y     G++        K+G++            LD ++   +++ 
Sbjct: 151 MFGKMVQEEGLGKLYLALVEGKLQ-------KQGVI---------DAPLDGKESQTSYLR 194

Query: 191 --------------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                         +    G+  +I++ F+     +    R  YG   L  
Sbjct: 195 LFHGGGVSLLAVYPIT---GRMHQIRQHFKMIGHPILGDKR--YGGRALTG 240


>gi|126736635|ref|ZP_01752375.1| Pseudouridine synthase, RluD [Roseobacter sp. CCS2]
 gi|126713948|gb|EBA10819.1| Pseudouridine synthase, RluD [Roseobacter sp. CCS2]
          Length = 351

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 31/190 (16%), Positives = 59/190 (31%), Gaps = 47/190 (24%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNV 54
              ++  +   QR+ + +       RR         +E+M  +  V+V+G  ++  +  V
Sbjct: 5   QTRVIGPDDGDQRLDRYL-------RRLFPHLTQGRIEKMCRKGEVRVDGGRVKSNS-RV 56

Query: 55  MSTDHIEV-----------------------DGVPLRK---AERTRLWLYHKPIGLVTTH 88
                I +                       D   ++     +   +   +KP GL T  
Sbjct: 57  EVGQKIRIPPLPTEEEAAAAASLAKHGVTKADAKLIQSCVIYKDDHIIAINKPHGLATQG 116

Query: 89  SDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--R 143
                R         +     +   V RLD +T G+LLL     +A+ L          +
Sbjct: 117 GTNTTRHVDGLSEALMFDYDEKPRLVHRLDKDTSGVLLLARTRMMAKQLTENLKHRETRK 176

Query: 144 VYRVRFHGQV 153
           +Y     G  
Sbjct: 177 IYWAAVAGVP 186


>gi|288905218|ref|YP_003430440.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus UCN34]
 gi|306831289|ref|ZP_07464449.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|325978193|ref|YP_004287909.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|288731944|emb|CBI13509.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus gallolyticus UCN34]
 gi|304426525|gb|EFM29637.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus gallolyticus
           subsp. gallolyticus TX20005]
 gi|325178121|emb|CBZ48165.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 296

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 72/215 (33%), Gaps = 46/215 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGV------PLRK-----AERTRLWLYHKP 81
               + VNG + + A   +   D + +   D        P++       E     + +KP
Sbjct: 33  KGGNIWVNG-VEQNAIYLLNVGDVVTIEIPDEEEHETLVPVKHDLNIAYEDEHFLIINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  HGYASIPS-VLHSNTIANFVKHYYLEQNYPNKQVHIVTRLDKDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--------------- 177
             +L +    + Y     G     K  L  KG +I  I   D  +               
Sbjct: 151 DKQLQNKTIEKRYYALVSG-----KGELADKGEIIAPIARSDDSIITRCVHPSGKYAHTS 205

Query: 178 -TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  + G  A V + L  G+  +I+  F    + 
Sbjct: 206 YEVVARFGEVALVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|304438735|ref|ZP_07398663.1| RluA family pseudouridine synthase [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372737|gb|EFM26315.1| RluA family pseudouridine synthase [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 292

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/213 (15%), Positives = 76/213 (35%), Gaps = 29/213 (13%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKAERTRLWLY------- 78
           R + R I ++ + +N  L +R  V++   D + +   D  P    E  ++ +        
Sbjct: 31  RYIRRSIREEMIYINEKLNKR-NVDLQPGDVVSIKIPDEEPNAIPEDYKVEILYEDGDIL 89

Query: 79  --HKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             +K   ++    D     T+      +     I  +V  + RLD +T G++L+  +   
Sbjct: 90  AVNKEPFMIVHAVDFKQTGTISNYVQCYFLKHDIHRKVRLINRLDRDTSGVILIAKNSNA 149

Query: 131 ARVLELP--STQWLRVYRVRFHGQVD-----QDKLNLLKKGIVIQ---GICYGDMQVTLD 180
              +         L+ Y     G V+     ++ ++    GI+ +      Y        
Sbjct: 150 HSTVARELQDRNILKKYYAIVEGVVEGSGIIEEPIDRGPDGILREVNPNGKYAKTSYEAI 209

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             K +   + V L  G+  +I+   ++    + 
Sbjct: 210 LSKNNMTLLRVVLHTGRTHQIRVHLKYIGHPIV 242


>gi|157964329|ref|YP_001499153.1| ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
 gi|157844105|gb|ABV84606.1| Ribosomal large subunit pseudouridine synthase [Rickettsia
           massiliae MTU5]
          Length = 306

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 37/188 (19%), Positives = 67/188 (35%), Gaps = 44/188 (23%)

Query: 4   KNIVQENFTPQ--RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           KN++ +  TP   R+ K + R       G+     +E+ + Q+++ VN      A++ V 
Sbjct: 2   KNMIIDVNTPISSRLDKYLKRLYPLLTQGV-----IEKALRQKQITVNSQK-TEASLRVK 55

Query: 56  STDHIEVDGV---PLRKAERTR-----------------------LWLYHKPIGLVTTHS 89
             D I ++     P+++ E+                         L   +K  GL T   
Sbjct: 56  GGDKIFINDKFNLPVKQPEKLVFTDAEIKLAKKITTDYLIYADDNLIAINKLAGLATQGG 115

Query: 90  DPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVY 145
                S       L    +    V RLD  T GLLL+  +   +  L     +   ++ Y
Sbjct: 116 SKINLSIDSALKYLNYKGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLVVKTY 175

Query: 146 RVRFHGQV 153
               +G+ 
Sbjct: 176 FAVTYGKP 183


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

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 38/215 (17%), Positives = 74/215 (34%), Gaps = 45/215 (20%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRKA--------- 70
           E+++   +++V+G  ++     + +   + V             G  + +          
Sbjct: 34  EKLLRTGQIRVDGKRVKS-GERLEAGQQVRVPPLGDEAPSPSSSGHAVPRPAAEGEIRAL 92

Query: 71  ------ERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
                 E   L + +K  GL        P     + ++L         V RLD +T G+L
Sbjct: 93  RRAILHEDAHLIVINKEAGLAVQGGTGTPHHLDGMLESLADGGETPRLVHRLDKDTSGVL 152

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------QDKLNLLKKG----IVI--- 167
           +L      AR L     S + L+VY     G+        +  L  +  G    + I   
Sbjct: 153 VLARTQAAARALTSAFRSREALKVYWAIVVGRPPMLQGTIKGALAKVAGGRGERMEINEE 212

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +G         +D    + AWV +  R G+  +++
Sbjct: 213 EGKRAVTDFRVVDQAAKACAWVELHPRTGRTHQLR 247


>gi|325263985|ref|ZP_08130718.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           D5]
 gi|324031023|gb|EGB92305.1| ribosomal large subunit pseudouridine synthase C [Clostridium sp.
           D5]
          Length = 331

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 48/292 (16%), Positives = 88/292 (30%), Gaps = 82/292 (28%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVMST 57
            +  V +N   QR+ K++A+      RE       +M+ ++ + +NG         ++  
Sbjct: 2   QQITVGDNEAGQRLDKLLAKYL----REAPKSFLYKMLRKKNITLNGKKA-SGNEKLLRG 56

Query: 58  DHIEV---------------------------DGVPLR-KAERTRLWLYHKPIGLVTTHS 89
           D I++                            G  L    E + + L +KP G+++  +
Sbjct: 57  DEIKLFLADETIAKFAGDAKPHAENGMLNRLSYGESLNIIYEDSHIILINKPAGMLSQKA 116

Query: 90  DPDGRSTVFDNLPSIFS------------RVISVGRLDINTEGLLLLTNDGGLARVLEL- 136
                S V      +              R     RLD NT G++         + L   
Sbjct: 117 ADTDVSLVEHLTAYLLRSGALTEDEMRTFRPSVCNRLDRNTSGMVAAGKSLQGLQELSRL 176

Query: 137 -PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----VTLDTQKGSN---- 186
                  + Y     G+V++           I G    D +     +T   ++GS     
Sbjct: 177 FKDRTLGKYYHCLVKGEVNETS--------HIHGFLKKDAENNQVHITAGQEEGSTAIET 228

Query: 187 -----------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                        + V L  GK  +I+         +  L    YG  +L  
Sbjct: 229 EFRPLKSGNDVTLLEVHLITGKTHQIRAHLASVGHPI--LGDYKYGDRRLND 278


>gi|313677455|ref|YP_004055451.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312944153|gb|ADR23343.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 237

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/136 (21%), Positives = 49/136 (36%), Gaps = 20/136 (14%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            PL   E       +KP   V+T +D +   T+   +           RLD  T G+LL+
Sbjct: 7   KPLIIEESEDYIFINKPP-FVSTLADRNDTVTILSLVKKYNDDYQICHRLDKETSGVLLV 65

Query: 125 TNDGGLARV--LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             +    R   ++    Q  ++Y     G      L+              D +V L   
Sbjct: 66  AKNPEAYRNASMQFEHRQVEKIYTAIVDG------LHQF-----------KDEEVNLPLH 108

Query: 183 KGSNAWVTVGLREGKN 198
             ++ +V +  R+GKN
Sbjct: 109 TTASGYVKISHRQGKN 124


>gi|161507179|ref|YP_001577133.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DPC 4571]
 gi|160348168|gb|ABX26842.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DPC 4571]
          Length = 298

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 75/218 (34%), Gaps = 40/218 (18%)

Query: 32  ERMIAQ----QRVKVNGILLERAAVNVMSTDHIE-VDGV------------PLRKA-ERT 73
           + +I        + VN       + ++ + D +  V G             P+    E  
Sbjct: 29  QALIKARHHHGMILVNHKR-RYLSFHLSAGDEVIFVSGEEKKNQFLKPSNNPVDPVFETK 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTN 126
              + +KP G+++  S  +    V + L   F +          + RLD +T GL+L+  
Sbjct: 88  NYIVLNKPAGVLSIPSRYEDNDAVVNRLMGYFLQQNKKDLKPHVITRLDRDTSGLVLVGK 147

Query: 127 DGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGICYG 173
           +              +++ Y    HG   +D+L  +      K+G      +V  G    
Sbjct: 148 NAIAHARFSKIGKDNFVKKYHAIVHGNFAEDELTGIIDEPIGKEGDGVKRAVVANGKKAQ 207

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                L   +G+ + V + L  G+  +I+    +    
Sbjct: 208 TRYRVLKQVEGA-SLVELRLLTGRTHQIRVHMAYLGHP 244


>gi|167581726|ref|ZP_02374600.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis TXDOH]
          Length = 389

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 81/238 (34%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             +R+ K +A+     SR  +++ I  +RV+V+G   +     V     IE+        
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESERVRVDGAPAK-IRQAVPLGATIELLPDLLPEQ 118

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD  T GL+++         L     +    R Y     G           + +D  
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


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

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 88/251 (35%), Gaps = 56/251 (22%)

Query: 3   DKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++  V+      R+ +         G      +++++   +++V+G  ++ A   V    
Sbjct: 5   EQITVEAGEAGMRLDRWFKTHFPGLGFG---HLQKLLRSGQIRVDGGRVK-ADTRVEPGQ 60

Query: 59  HI-----EVD--------GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDG 93
            +     EVD        G  +R              E  ++++++KP GL         
Sbjct: 61  MVRVPPLEVDKKGESALTGHSIRNQGDADVLSKMLIHEDPKVFVFNKPAGLAVQGGSGVT 120

Query: 94  RSTVFDNLPSIFS----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
           R  V D L +  S    +   V RLD +T G+L++      A  L     + +  + Y  
Sbjct: 121 R-NVDDMLEAWRSPKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKKTYWA 179

Query: 148 RFHGQVD--QDKLNLL----------KKGIVIQGICYGDMQVT----LDTQKGSNAWVTV 191
              G     +DK++            +  +   G    D  V+    ++    +  W+ +
Sbjct: 180 LVKGVPPKREDKISTWLIKEPTPDGDRVRVAAHGEKGADHAVSYYRVIEQAAQTMTWLEM 239

Query: 192 GLREGKNREIK 202
               G+  +++
Sbjct: 240 EPYTGRTHQLR 250


>gi|161524654|ref|YP_001579666.1| RluA family pseudouridine synthase [Burkholderia multivorans ATCC
           17616]
 gi|189350589|ref|YP_001946217.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans ATCC 17616]
 gi|160342083|gb|ABX15169.1| pseudouridine synthase, RluA family [Burkholderia multivorans ATCC
           17616]
 gi|189334611|dbj|BAG43681.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans ATCC 17616]
          Length = 400

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 84/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV+V+G   +     V     IE+      
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAK-IRQPVPLGATIELVPDLLP 123

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP GLV   +  +   T+ + L   +        R
Sbjct: 124 EQLAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 183

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 184 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGAMPDEGTIDAPIGR 243

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 244 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCSHVGH 303

Query: 211 K 211
            
Sbjct: 304 P 304


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+   ++  G+  SR   +  I + RV VNG + +++++ V  +  I+++      A R
Sbjct: 1  MRLDVYLSTQGLCDSRARAQDAIQEGRVTVNGRIAKKSSMPVDDSMDIKLEEAETAFASR 60

Query: 73 TRLWLYH--KP 81
              LY   KP
Sbjct: 61 AGYKLYDVLKP 71


>gi|221198059|ref|ZP_03571105.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2M]
 gi|221204383|ref|ZP_03577400.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2]
 gi|221175240|gb|EEE07670.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2]
 gi|221181991|gb|EEE14392.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           multivorans CGD2M]
          Length = 399

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 84/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV+V+G   +     V     IE+      
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAK-IRQPVPLGATIELVPDLLP 123

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP GLV   +  +   T+ + L   +        R
Sbjct: 124 EQLAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 183

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 184 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGAMPDEGTIDAPIGR 243

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 244 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCSHVGH 303

Query: 211 K 211
            
Sbjct: 304 P 304


>gi|221212790|ref|ZP_03585766.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Burkholderia multivorans CGD1]
 gi|221167003|gb|EED99473.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) (rRNA pseudouridylate synthase D)
           [Burkholderia multivorans CGD1]
          Length = 400

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 84/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV+V+G   +     V     IE+      
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAK-IRQPVPLGATIELVPDLLP 123

Query: 63  -------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP GLV   +  +   T+ + L   +        R
Sbjct: 124 EQLAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 183

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 184 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGAMPDEGTIDAPIGR 243

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 244 DPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCSHVGH 303

Query: 211 K 211
            
Sbjct: 304 P 304


>gi|58617049|ref|YP_196248.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Gardel]
 gi|58416661|emb|CAI27774.1| Ribosomal large subunit pseudouridine synthase C [Ehrlichia
           ruminantium str. Gardel]
          Length = 305

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 85/250 (34%), Gaps = 58/250 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE-------VERMIAQQRVKVNGILLERAAVN 53
           M     +QE+    R+ + I       R+E       +E+ +  + + ++G+ ++     
Sbjct: 1   MGKYYTIQEDNLGVRIDRFI-------RKELRIPQSLIEKFLRNRIILLDGLKVKS-NTK 52

Query: 54  VMSTDHIEVDGVPLRK-------------------------AERTRLWLYHKPIGLVTTH 88
           +   + I V    +                            E   + + +KP G+    
Sbjct: 53  LNVGNVIYVQNECIISKEKKDKKVCKLASESLVRLICDNIVYEDDNVLVINKPSGVSVQG 112

Query: 89  SDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
                + ++ D L SI     +  V RLD +T G+L+L  +  ++R++       +  + 
Sbjct: 113 G-SKVKISISDVLDSIRIGESMKIVHRLDKSTSGILMLARNSRVSRLIMNEFKDRKVKKK 171

Query: 145 YRVRFHGQVDQDK------LNLLKKGIVIQG-----ICYGDMQVTLDTQKGSNAWVTVG- 192
           Y     G  D D       +   K GI ++           M  TL         + +  
Sbjct: 172 YLALTCGIPDDDCGQIDYPIVKKKHGITLEKNMSFVQQAVTMFSTLRKLPNDIGLLDLQP 231

Query: 193 LREGKNREIK 202
           +  G+  +I+
Sbjct: 232 IT-GRKHQIR 240


>gi|332366862|gb|EGJ44603.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1059]
          Length = 295

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLYVVYEDEHFLVLDKPAGVASIPS-VNHTNTMANFVKAYYIGQGYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  Q G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIEQFGDVYLVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|323342987|ref|ZP_08083218.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322463051|gb|EFY08246.1| ribosomal large subunit pseudouridine synthase D [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 291

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/211 (16%), Positives = 80/211 (37%), Gaps = 25/211 (11%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLR- 68
           ++ ++++    SR +++ ++  + + ++  +  +    + +   I +         PL+ 
Sbjct: 14  LNYLLSQDLPYSRSKIKSLLKHECISIDNEVTTQFDDLITAGQTITIVSHNQQRDTPLQI 73

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVF----DNLPSIFS--RVISVGRLDINTEGLL 122
             E   + +  KP  L+T  +  +   T F    D +    S  R+  V RLD +T G+L
Sbjct: 74  LYEDKDILVVDKPYKLLTVSNRKEEELTAFRLASDYVKKQDSKNRIFVVHRLDQDTSGVL 133

Query: 123 LLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQDK---LNLLKKGIVIQGICYGDMQ 176
           +        + L           R+Y     G V +DK    + L++            Q
Sbjct: 134 MFAKS-EYVKRLYQDKWSELVDERLYVAIVEGVVPKDKDVIRSFLRQNKTTHMYSTSSGQ 192

Query: 177 -----VTLDTQKGSNAWVTVGLREGKNREIK 202
                  +  +  +N  + + +  G+  +I+
Sbjct: 193 EAITNYEVIKRTENNTILKIQIDTGRKNQIR 223


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/223 (15%), Positives = 69/223 (30%), Gaps = 35/223 (15%)

Query: 19  VIARAGIASRREVERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV---------DGVPLR 68
            + + G  S ++    I Q   + VN   +      +   D + +         +     
Sbjct: 16  FLQQQGF-S-KKTTSAIKQNGALLVNHEPVT-VRYQLQPGDKLTIILPTEIPSANLQAFH 72

Query: 69  KA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDIN 117
                  E   L +  KP       S      ++ + + +             V RLD N
Sbjct: 73  HPLDIVYEDDYLLIVCKPSIQNCAPSREHPHESLIEQVIAYCHENDNDFTPHIVTRLDRN 132

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGI-- 170
           T GL+LL   G +  +L     +  + Y    HG      + +  +      I+ + +  
Sbjct: 133 TTGLVLLAKHGHIHHLLSHI--KINKRYIALCHGATQPEGIIEAPIARANDSIITRQVSS 190

Query: 171 --CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              Y          K + +   V L  G+  +I+  F++    
Sbjct: 191 TGKYAKSTYRTLNSKQNVSLCEVTLHTGRTHQIRVHFQYIGHP 233


>gi|260912047|ref|ZP_05918609.1| RluA family ribosomal large subunit pseudouridine synthase
           [Prevotella sp. oral taxon 472 str. F0295]
 gi|260633852|gb|EEX51980.1| RluA family ribosomal large subunit pseudouridine synthase
           [Prevotella sp. oral taxon 472 str. F0295]
          Length = 298

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/215 (16%), Positives = 69/215 (32%), Gaps = 30/215 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLW 76
           SR +++ ++    V V+G  + +    +     + V                  E   L 
Sbjct: 37  SRNKLKDILRGHGVFVDGKCVTQFDYRLQPGMKVTVSRAKKAAPFKSRYIKIVYEDRYLI 96

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
           +  K  G+++  +       V   L + F       R   V RLD  T GL++   D   
Sbjct: 97  VVDKSAGVLS-MAAGHSSLNVKAILDTYFEKSGQKCRAHVVHRLDRETSGLMVYAKDMDT 155

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQD--KLNLLKKGI---------VIQGICYGDMQV 177
            ++LE         R Y     G++  +   ++   K           V  G  Y     
Sbjct: 156 EQILEHNWHDIVYDRRYVAVVSGEIVDEGGTISSWLKDNNSYITYSSPVDNGGKYAVTHF 215

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            +  +  +++ V   L  G+  +I+         V
Sbjct: 216 HVLNRTTTHSLVEYKLETGRKNQIRVHTADIGHPV 250


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 39/239 (16%), Positives = 88/239 (36%), Gaps = 38/239 (15%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M+ K  IV E     R  K ++      SR  ++++  +  V +N   ++  +  +++ +
Sbjct: 1   MEIKEFIVTEEKQNIRCDKFLSDKLEDFSRESLKKLFKEGEVFLNDEKVK-PSRKLIAGE 59

Query: 59  HIEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            ++V+             +P+    E   + +  KP G+V   ++ +   T+ + L    
Sbjct: 60  RVKVNLPEPEVLDVIAENIPINIVYEDEDVVIVDKPQGMVVHPANGNHSGTLVNALMYHV 119

Query: 106 SRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--- 151
             + S         V R+D +T GLL++  +      L +        R Y+   HG   
Sbjct: 120 KDLSSINGVIRPGIVHRIDKDTSGLLIIAKNDNAHNHLAVQFKEHSINRRYKTICHGIIH 179

Query: 152 --------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    + +DK+   +  +             +  +     ++ V L  G+  +I+
Sbjct: 180 ENSGTIDAPIGRDKIKRKEMCVTQSNSKRAVTHFDVIKRYDKYTFLDVHLETGRTHQIR 238


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 37/165 (22%), Positives = 62/165 (37%), Gaps = 24/165 (14%)

Query: 14  QRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-- 70
           QR+ K++A R    SR  ++R I    + VNG   + A   V+  + I V      +   
Sbjct: 40  QRLDKLVAGRLSQYSRSRLQRWIEDGHITVNGEKAQ-AKQTVIGDEEICVIPQLAEEDLA 98

Query: 71  ------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVG 112
                       E   + + +KP  LV   +  +   T+ + L       +   R   V 
Sbjct: 99  FTPEAVDFPVVFEDNAILVVNKPASLVVHPAAGNWSGTLLNGLLYRDPKSATVPRAGIVH 158

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           RLD  T G++++  T +     V +L +    R Y     G   Q
Sbjct: 159 RLDKETSGVMVVAKTIEAQTDLVRQLQARTVKREYLALVWGDTPQ 203


>gi|218439930|ref|YP_002378259.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
 gi|218172658|gb|ACK71391.1| pseudouridine synthase [Cyanothece sp. PCC 7424]
          Length = 548

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 34/154 (22%), Positives = 57/154 (37%), Gaps = 27/154 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTN 126
           E   L + +KP GL++      D   +V   L  +      + SV RLD++T GLLLL  
Sbjct: 346 EDDYLIIINKPEGLLSVPGRSSDRYDSVISRLNHLLPDGHLLRSVHRLDLDTSGLLLLAR 405

Query: 127 DGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQ-VTLD 180
           +  +   L       +  ++Y+    G+V Q +       I +       +  +Q V   
Sbjct: 406 NDQIYNHLAQQFRDRKIEKIYQALVQGRVSQPQGT-----IKLPLWGDPRFRPLQTVDFI 460

Query: 181 TQKGSNAWVTVGLRE------------GKNREIK 202
             K S     V   E            G+  +I+
Sbjct: 461 RGKESITQFRVIAFEDNFTRVEFMPITGRTHQIR 494


>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 = 60.6 bits (146), Expect = 4e-07,   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|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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 65/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KLLSVQENISHKKAKALIDSGLVSIGGQKLMVARKELPQNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F     + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWALLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLAIVQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>gi|325927798|ref|ZP_08189023.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           perforans 91-118]
 gi|325541788|gb|EGD13305.1| ribosomal large subunit pseudouridine synthase C [Xanthomonas
           perforans 91-118]
          Length = 328

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 99/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RINEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDEKYGEA-DVNKR-LRDQLGLKRL 291


>gi|313889046|ref|ZP_07822704.1| pseudouridine synthase, RluA family [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844919|gb|EFR32322.1| pseudouridine synthase, RluA family [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 298

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/229 (15%), Positives = 79/229 (34%), Gaps = 31/229 (13%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
            +V+  +   G++SR  + + +    + +N  +  +    +   D + +   D  P    
Sbjct: 22  IKVNDFLKERGVSSR-LIRKSVKSGNIYLNSRVNRKNKF-LKKGDLVSLRFEDEEPNGGV 79

Query: 71  ERTRL---------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLD 115
           E+  L          + +K   +VT  +  D   T+ + L   F       +V  V RLD
Sbjct: 80  EQKDLDIIYEDDDLVIVNKEPFMVTHTAKDDADGTLLNYLLGYFEEEGLKRKVRFVNRLD 139

Query: 116 INTEGLLLLTNDGGLARVLELP-STQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQ 168
            +T GL++   +      +         + Y     G  ++ +      +   + GI  +
Sbjct: 140 RDTSGLVVAAKNSFAQDKISSDFKEDVKKKYLAVVEGVFEEKEGLIDGPIATSEDGIRRE 199

Query: 169 -GICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                G   +T   +  +    + V + L  G+  +I+         + 
Sbjct: 200 VNYVIGKRSLTSYEVLDEYKDMSLVLLTLHTGRTHQIRVHMAHIGHPIL 248


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 42/232 (18%), Positives = 74/232 (31%), Gaps = 38/232 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEVDGV 65
           V E  +  R+   +A     SR     +I    V  +G + + R A  +       V+  
Sbjct: 44  VPEEDSGARLDLFLAGELSLSRSRARSLIDGGAVS-SGQVKKIRPAFKIQPGQIYRVEIP 102

Query: 66  PLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
               A             E   + + +KP G+V          T+ + L   +       
Sbjct: 103 EAAPAEIAAQDMPFDVVYEDDDVIVVNKPAGVVVHPGAGRPDGTLVNGLMFRYPEIGRIG 162

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR---V--------RFH 150
              R   V RLD+ T GL+++       R L     + + L+ Y    V           
Sbjct: 163 DSVRPGIVHRLDVGTSGLMVVARSDAAFRGLTEAFQAHEVLKEYLGLGVGALKAPEGTVD 222

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             + +D  N LK  +   G         +   +     + V L  G+  +I+
Sbjct: 223 APIGRDPRNRLKMCVSWDGRDAVT-DYKVLWTRARCNLIRVRLHTGRTHQIR 273


>gi|300023530|ref|YP_003756141.1| pseudouridine synthase [Hyphomicrobium denitrificans ATCC 51888]
 gi|299525351|gb|ADJ23820.1| pseudouridine synthase, RluA family [Hyphomicrobium denitrificans
           ATCC 51888]
          Length = 344

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 76/254 (29%), Gaps = 53/254 (20%)

Query: 10  NFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---- 63
               QR+ + +A+  I   SR  ++ +I    V  +G  +  A   V       V+    
Sbjct: 18  EDAGQRLDRWLAQK-IEDLSRARIQALIRDGYVS-DGGTIREARTPVKPGITYRVELPPA 75

Query: 64  ------GVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
                 G  L      E   L +  KP GLV   +      T+ + L +           
Sbjct: 76  SEPDVAGETLPLSIVYEDADLIVIDKPTGLVVHPAAGHASGTLVNALIAHCGDSLSGIGG 135

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHG--QVDQD 156
             R   V RLD +T GLL++       + L        R       Y     G   + + 
Sbjct: 136 VKRPGIVHRLDKDTSGLLVVAKTDAAHQGLADQFKSHGRDGRLFRSYLAFVWGRLPLPKG 195

Query: 157 KLNLLKKG-----------IVIQGICYGDMQVTL------DTQKGSNAWVTVGLREGKNR 199
            ++  + G           +  +          +      +   G  + V + L  G+  
Sbjct: 196 TISA-RLGRSQANRTKIAVVRGEAGRSATTHYEVLQVFPGERSTGDVSLVRLVLETGRTH 254

Query: 200 EIKKVFEFFNWKVN 213
           +I+         V 
Sbjct: 255 QIRVHLAHIGHPVL 268


>gi|256832316|ref|YP_003161043.1| pseudouridine synthase, RluA family [Jonesia denitrificans DSM
           20603]
 gi|256685847|gb|ACV08740.1| pseudouridine synthase, RluA family [Jonesia denitrificans DSM
           20603]
          Length = 313

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 74/234 (31%), Gaps = 39/234 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DHIEVDG 64
           V +    QRV   +AR    SR  +        V V+G    +    V     D +  D 
Sbjct: 10  VPDGLVGQRVDAALARMLGLSRSAILAAFDAGDVYVDGRPAAKGDRIVQGAVIDVVLPDP 69

Query: 65  VPLRKAE--------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
             +   E                 + +  KP+G+    +      TV   L +   R+  
Sbjct: 70  REVDATEDEPQPVPGMRIVHDDEHIVVVDKPVGVAAHSAVGWSGPTVVGALAAAGYRIST 129

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--QVDQDK 157
                    V RLD+ T GL+++         L+         +VY     G  +  +  
Sbjct: 130 SGAAERQGIVHRLDVGTSGLMVVAKSELAYTRLKRAFRERTVDKVYHTVVQGHPEPTKGT 189

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++           K  ++  G         ++    S + VTV L  G+  +I+
Sbjct: 190 IDAPIGRHPKAEFKFAVMADGKRSITHYEVMEML-PSASLVTVHLETGRTHQIR 242


>gi|72058953|ref|XP_781802.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
 gi|115955042|ref|XP_001182766.1| PREDICTED: hypothetical protein [Strongylocentrotus purpuratus]
          Length = 613

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/321 (15%), Positives = 107/321 (33%), Gaps = 52/321 (16%)

Query: 32  ERMIAQQRVKVN-GILLERAAVNVMSTD----HIE-----VDGVPLRKAERTR-LWLYHK 80
           E  I +  ++VN G       + + + D     +      V G P++    T+   + +K
Sbjct: 75  ETAIHEGLIRVNKGK--ASPDLILKNNDFMQSKVHRHEPPVSGEPIQIIADTQDYLVINK 132

Query: 81  PIGL-VTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLE--L 136
           P  + V         + VF       F  + ++ RLD  T GLLL      ++  L+  +
Sbjct: 133 PSSIPVHPCGKYRHNTIVFILGKDYGFKGLHTIHRLDRLTSGLLLFARTLQVSHRLDAYV 192

Query: 137 PSTQWLRVYRVRFHGQVD--------QDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSN 186
              +  + Y  + HG+             +   K G+  V +       +    +  G  
Sbjct: 193 RERKLEKTYVCKAHGEFPSTPVVCEEPIFIVSHKIGVCRVKEDGKPCKTRFERLSYDGET 252

Query: 187 AWVTVGLREGKNREIKKVFEFFNWK----------VNRLIRISYGPFQLGTLLAGSTREV 236
           + +      G+  +I+   ++  +           V    R   G  QL     G     
Sbjct: 253 SIIKCHPHTGRMHQIRVHLQYLGFPIINDPLYNNTVWGQHRGRGGNNQLTDEQVG----- 307

Query: 237 SKKILREQ-----LGPHLLEEAQVNLDAPIYSSE-TLVRDRPNIISEVPDDFTRMKKNSS 290
               +R+      L   L+++  +++D+ +  +    + ++P + S +          + 
Sbjct: 308 ----IRQLINYPFLLKDLIDQHDIDIDSALEKARLQALINKPKVTSHIDTAIPEDAPLTP 363

Query: 291 QKNGLSKQKKLATPVHRRNLA 311
                SK   + +   R +  
Sbjct: 364 GSQEPSKDAVINSKDVRTSGT 384


>gi|330881340|gb|EGH15489.1| ribosomal large subunit pseudouridine synthase D(pseudouridine
           synthase) (Uracil hydrolyase) [Pseudomonas syringae pv.
           glycinea str. race 4]
          Length = 190

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/164 (25%), Positives = 66/164 (40%), Gaps = 25/164 (15%)

Query: 14  QRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGV 65
           QR+ +V A    A  SR  +   I   R+ V+G +L      V     +E+       G 
Sbjct: 18  QRLDQV-AAQLFAEHSRSRLSAWIKDGRLTVDGGVLR-PRDIVHGGAVLELIAEQEAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISVG 112
            + +        E  ++ + +KP GLV      H+D    + +  ++P I    R   V 
Sbjct: 76  WVAQDIELDIIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIVH 135

Query: 113 RLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD 154
           RLD +T GL+++  T       V +L S    R+Y     G V 
Sbjct: 136 RLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVT 179


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 73/222 (32%), Gaps = 47/222 (21%)

Query: 14  QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + +   G   +R++ +  I +  V VNG+ + + +  V     IEV     R  ER
Sbjct: 1   MRLDQFLVSKGFFTTRQKAKEAIKRGFVFVNGVRVTKPSARVSGDAEIEV-----RCEER 55

Query: 73  TR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
            R  W            ++ D R  + D       +   V  L  +  G LL  ++    
Sbjct: 56  PRGYWKL----------AEIDARWKIID-------KNDIVLDLGSSAGGFLLYASERAKK 98

Query: 129 ----GLARVLELPSTQWL---RVYRVRFHGQVDQD--KLNLLKKGIVIQGICYGD----- 174
                 +R  E    +     +  RV        D   L  L   +++  +         
Sbjct: 99  VYGIEFSREFEEELRKIESDRKNVRVFIGDAFTFDTSMLEPLD--VILDDLTLEPSASLK 156

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
                         V   ++EGKN E    FE +  +V  +I
Sbjct: 157 ALSRFLPLLKDGGRVLFVMKEGKNPE----FEEYGLEVVDVI 194


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

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/232 (15%), Positives = 73/232 (31%), Gaps = 53/232 (22%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------------------DGVPL 67
           ++++   +V+V+G  ++     V     + V                        DG  L
Sbjct: 35  QKLMRSGQVRVDGGRVKT-DARVQPGQVVRVPPMDVDAKTPKSGPIASHDLKHAGDGELL 93

Query: 68  RK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGL 121
            +    E  ++++ +KP GL         R            +      V RLD +T G+
Sbjct: 94  ARMLLHEDEKVFVLNKPAGLAVQGGSGLNRHIDQMLEAWTSKKGEKPRLVHRLDRDTSGV 153

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--------------DKLNLLKKGI 165
           L++    G A+ L          + Y     G   +              +  + ++  I
Sbjct: 154 LVVARTRGAAQKLTAAFRERDTKKTYWALVKGVPRKHDDKISTWVVKEQTEDGDRMR--I 211

Query: 166 VIQGICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              G    D  V+    L+T   S AW+ +    G+  +++         + 
Sbjct: 212 ARHGEDGADHAVSYYRVLETAAQSLAWLEMEPYTGRTHQLRLHALHIGHPII 263


>gi|225872530|ref|YP_002753985.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
 gi|225792126|gb|ACO32216.1| pseudouridine synthase, RluA family [Acidobacterium capsulatum ATCC
           51196]
          Length = 301

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 32/198 (16%), Positives = 62/198 (31%), Gaps = 25/198 (12%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGLVTT 87
             + +NGI  +  + +V +   +  +  P  +           E   L   +KP GL T 
Sbjct: 44  GEITLNGITAQ-GSESVAAGQVLVWNCPPWTEPDAPLHFDVLFEDDELIAVNKPSGLPTL 102

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVY 145
                  +T+   +         V RL   T G++L   T  G         +++  +VY
Sbjct: 103 PGSGFLENTLLRLVRRYAPHASPVHRLGRATSGIVLFSKTAQGAALLEAIWNTSKVQKVY 162

Query: 146 R-VRFHGQVDQDK--------LNLLKKGIVIQGICYGD---MQVTLDTQKGSNAWVTVGL 193
           R V  +    ++         +   + G V      G        +  +  +     V L
Sbjct: 163 RAVAVNVAEHEEYEIHTPIGRVPHPRLGSVWAASSTGKPSWSSAKVLARGTTTTTFEVTL 222

Query: 194 REGKNREIKKVFEFFNWK 211
             G+  +I+         
Sbjct: 223 HSGRPHQIRIHLASVGHP 240


>gi|167587072|ref|ZP_02379460.1| pseudouridine synthase, RluA family protein [Burkholderia ubonensis
           Bu]
          Length = 401

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 50/244 (20%), Positives = 85/244 (34%), Gaps = 40/244 (16%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V  +   +R+ K +A+     SR  ++  I  QRV+V+G   +     V     IE+   
Sbjct: 62  VPPSLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRVDGAPAK-IRQPVPLGATIELAPD 120

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                     + VPL    E   L + +KP GLV   +  +   T+ + L   +      
Sbjct: 121 LLPEQLAFTPEPVPLDIVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAG 180

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------Q 152
             R   V RLD  T GL+++         L  +L +    R Y     G           
Sbjct: 181 LPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPDEGTIDAP 240

Query: 153 VDQDKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEF 207
           + +D     +  +V    G        T+DT   Q+   + +   L  G+  +I+     
Sbjct: 241 IGRDPRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAH 300

Query: 208 FNWK 211
               
Sbjct: 301 AGHP 304


>gi|225181681|ref|ZP_03735121.1| pseudouridine synthase, RluA family [Dethiobacter alkaliphilus AHT
           1]
 gi|225167662|gb|EEG76473.1| pseudouridine synthase, RluA family [Dethiobacter alkaliphilus AHT
           1]
          Length = 312

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 95/245 (38%), Gaps = 38/245 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E    +R+   ++R     +R  V+++IA+  V+V+G   ++A   + + + +EV  
Sbjct: 7   TVDEVLAGERLDVAVSRHVEELTRARVQKLIAEDYVQVDGKP-QKANYRLRAGETVEVTV 65

Query: 65  VPLRKAE-------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV 111
             ++ AE                + + +KP GLV   +      T+ + L      +  +
Sbjct: 66  PEVKPAEIAAEKIDLDILYEDQDVLVLNKPKGLVIHPAAGHAGGTLVNALLHHCDDLSGI 125

Query: 112 G---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ--VDQDKL 158
           G         RLD +T G++++  +      L     +    R Y    HG+  V+Q  +
Sbjct: 126 GGEARPGIVHRLDKDTSGVMVVAKNDRAHLSLSRQFKAHSVTREYVAIVHGEPAVEQGTI 185

Query: 159 NLL-------KKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           +         +K + +     G   VT   +  + G  +++ + L  G+  +I+      
Sbjct: 186 DAAIARHPKERKKMALTTAEKGRRAVTHFKVLDRFGEYSYLALRLETGRTHQIRVHLSSL 245

Query: 209 NWKVN 213
              V 
Sbjct: 246 GHPVV 250


>gi|224542885|ref|ZP_03683424.1| hypothetical protein CATMIT_02079 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524215|gb|EEF93320.1| hypothetical protein CATMIT_02079 [Catenibacterium mitsuokai DSM
           15897]
          Length = 322

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 46/267 (17%), Positives = 86/267 (32%), Gaps = 63/267 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVI--------ARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           MK K ++ +    QR+ K +        +           +M+ ++ VKVNG  ++    
Sbjct: 1   MK-KLVIDQYDDHQRIDKYLKKVLVQAPSSLIY-------KMLRKKDVKVNGKRVKE-NY 51

Query: 53  NVMSTDHIE----------------VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDG 93
            + S D +E                +  +P+      E   + +  KP GL+      + 
Sbjct: 52  ILHSGDEVELFLYEDKFKEYTKPLTIYELPITFKVVYEDAHILIVDKPAGLLVHEDINES 111

Query: 94  RSTV-------------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL---ARVLELP 137
            +T+             +D   +I      V RLD NT GL++   D         +   
Sbjct: 112 VNTLSNQVLTYLHQKGEYDPEKNISFTPGPVHRLDRNTSGLVIFGKDMRALQDLNTMMKT 171

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----------VTLDTQKGSN 186
                + Y     G +    L+   K    +G  Y   +           V +  +  + 
Sbjct: 172 RQGIEKKYLTIAMGHMKDATLSGYVKKNEDEGKMYLVKKDTPGALSMKTIVHVLKRCSTC 231

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + V V L  G+  +I+         V 
Sbjct: 232 SLVEVQLITGRTHQIRIHLSATGHPVM 258


>gi|88797409|ref|ZP_01112999.1| putative 23S rRNA pseudouridylate 746 synthase [Reinekea sp.
           MED297]
 gi|88780278|gb|EAR11463.1| putative 23S rRNA pseudouridylate 746 synthase [Reinekea sp.
           MED297]
          Length = 223

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 33/174 (18%), Positives = 64/174 (36%), Gaps = 22/174 (12%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            +D + +   +   L + +KP GL+  +  DP  R +V   L      +  + RLD  T 
Sbjct: 14  CLDDIEIVHEDDA-LLVINKPSGLLALSGKDPRNRDSVHARLVKRCPSIRMIHRLDFGTS 72

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV-------------DQDKLNLLKKG 164
           GL++L     +A  L       +  +VY+    GQ+             D +    ++ G
Sbjct: 73  GLMVLAKSKTMATTLNRQFQQREVTKVYQAILWGQLANASGRINAHIARDDENFPKMRIG 132

Query: 165 IVIQGICYG--DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
              +G      D QV +   + + + V    R G+  +++         +    
Sbjct: 133 ---EGGKPAQTDYQVLVTDMRANTSTVEFYPRTGRTHQLRIHSAHIGHPILGCD 183


>gi|289668996|ref|ZP_06490071.1| pseudouridylate synthase [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 328

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/288 (17%), Positives = 99/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RVNEEGDKAAPPPSFMARLEAAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GL+++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLVIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFKLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRL 291


>gi|192359752|ref|YP_001982432.1| RNA pseudouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
 gi|190685917|gb|ACE83595.1| RNA pseudouridine synthase family protein [Cellvibrio japonicus
           Ueda107]
          Length = 254

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/169 (18%), Positives = 55/169 (32%), Gaps = 27/169 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP GL+   S  D   T F        I  RV  V RLD  T G LL    
Sbjct: 10  QDEHLLAVNKPTGLLVHRSPIDRHETRFALQLVRDQIGRRVYPVHRLDKPTSGALLFALT 69

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHG---------QVDQDKLNLLKKGIVIQG------- 169
             +AR L       Q  + Y     G            +++++        +        
Sbjct: 70  PDIARQLGQQFEQHQVRKTYVAVVRGLCEGEGVIDHPLREEIDACADMRTDKSSQPAITH 129

Query: 170 -ICYGDMQVTLDTQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
                 +++     K  ++  ++     L  G+  +I++  +  N  + 
Sbjct: 130 YKHLASVELPYCVDKYPSSRYSLVRCHPLT-GRKHQIRRHLKHINHPII 177


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 46/281 (16%), Positives = 89/281 (31%), Gaps = 48/281 (17%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
             +R+  +I+ +   SR + + +I+   V +    +   +    + D   V         
Sbjct: 14  AKKRLDVLISASLNISRSKAQCIISDGGVTLLDTPVLNNSHLTNTGDVYTVTVPDTPQST 73

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISVG--- 112
                  +PL    E   + +  K   +           T+    L    + + +VG   
Sbjct: 74  SIDPNHDIPLHIIYEDEHIIVIDKAPNIAVHPGHGTKNDTLAHALLAHCGNALCAVGNSH 133

Query: 113 ------RLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
                 RLD +T GL+++        VL   L   ++ + Y     G         ++  
Sbjct: 134 RPGIIHRLDKDTSGLMVIAKTEKAYLVLSQALEEKKFRKEYLALIWGVPTTKHC-FIQTN 192

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTV-------------GLREGKNREIK-KVFEFFNW 210
           + ++      M+VTL   K +N    +              L  G+  +I+  +      
Sbjct: 193 LDVKRSDKTMMEVTLSRGKHANTEYIIEKTFGNVASLARCILHTGRTHQIRVHM-SHIGH 251

Query: 211 KVNRLIRISYGPFQLGTLLAG--STREVSKKILRE-QLGPH 248
            V       YG     +L  G    R   ++ L    LG H
Sbjct: 252 SVVGDQ--KYGKNNKKSLRCGIPEVRNFKRQALHACLLGFH 290


>gi|77462967|ref|YP_352471.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides 2.4.1]
 gi|77387385|gb|ABA78570.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides 2.4.1]
          Length = 349

 Score = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 50/291 (17%), Positives = 91/291 (31%), Gaps = 77/291 (26%)

Query: 13  PQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
           P R+ K +       A     SR  + ++I +  V++ G  +      V       I +D
Sbjct: 20  PDRLDKALVREAPEEAAL---SRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEIALD 76

Query: 64  ----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                      +PL    E   L +  KP+G+V   +      T+ + L           
Sbjct: 77  APAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGESLSGI 136

Query: 106 ---SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG--QVDQDKL 158
               R   V R+D +T GLL++  T+        +  +    R Y    HG  +V   +L
Sbjct: 137 GGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEVSDPRL 196

Query: 159 N-------------LLKKG------------IVIQGICYGDMQVTLDTQKGSNAWVTVG- 192
                          +  G            +  +G  +   +  L  + G  + + +  
Sbjct: 197 RGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLERFGMPSVLALVE 256

Query: 193 --LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             L  G+  +I+         +             G    G  R++S K L
Sbjct: 257 CRLETGRTHQIRVHMAHAGHGLI------------GDQTYGGRRKLSPKAL 295


>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 = 60.6 bits (146), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+   +   G   SR   +  IA   V+VNG ++ + A  V   D IEV G P+  
Sbjct: 1  MAGERLDVALVSRGHFPSRERAQEAIAAGMVRVNGRVITKPARKVDPGDAIEVTGDPIGY 60

Query: 70 AER 72
            R
Sbjct: 61 VGR 63


>gi|315058171|gb|ADT72500.1| Ribosomal large subunit pseudouridine synthase D [Campylobacter
           jejuni subsp. jejuni S3]
          Length = 250

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 71/201 (35%), Gaps = 31/201 (15%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----ERT 73
           K++A     S RE + +I +  V  +G  +       + +D    + +  +      E  
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSHGKKV--MVARALMSDKARFNVIKAKNPQIIFEDD 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++   +KP   V+            D      +++  + RLD  T G++LL  D    ++
Sbjct: 65  KIIAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKL 111

Query: 134 LELPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDT 181
                 +    + Y     G + ++ ++N     I  +G     +          +T   
Sbjct: 112 CIEEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGGALSKVSKDGLSALSIITPIM 171

Query: 182 QKGSNAWVTVGLREGKNREIK 202
            +       + ++ G+  +I+
Sbjct: 172 MQSKKTLAKIVIQTGRTHQIR 192


>gi|219682312|ref|YP_002468696.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|219622045|gb|ACL30201.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Tuc7 (Acyrthosiphon pisum)]
 gi|311086711|gb|ADP66792.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. TLW03 (Acyrthosiphon pisum)]
 gi|311087807|gb|ADP67886.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. JF98 (Acyrthosiphon pisum)]
          Length = 312

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/225 (15%), Positives = 81/225 (36%), Gaps = 33/225 (14%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----G 64
           + + QR+  V+++     SR  ++++I   +V VN  ++ +    ++  + + +      
Sbjct: 14  SLSGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKD 73

Query: 65  VPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVI 109
           + +   E            + + +KP GLV      +   T+ + L           R  
Sbjct: 74  LLVDIPENIFLDIVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHYKNSKDLPRAG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARV--LELPSTQWLRVYRVRFHG----------QVDQDK 157
            V RLD +T GL+++  +        L L   + +R Y    HG           + +  
Sbjct: 134 IVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMIAGGTINKPIMRHY 193

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  +   G         + ++   +  + + L  G+  +I+
Sbjct: 194 NRRTCMMVHHLGKPSVTH-YKVLSRFKFHTHIAIRLETGRTHQIR 237


>gi|297172749|gb|ADI23715.1| pseudouridylate synthases, 23S RNA-specific [uncultured
           Oceanospirillales bacterium HF4000_21D01]
          Length = 321

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 82/238 (34%), Gaps = 32/238 (13%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V ++ +  R+ ++ A+     SR  ++  I    + VN   L      + + D +EV+  
Sbjct: 11  VPQDLSGYRLDQIAAKLFPDYSRARLQIWIKDGSLLVNARRLR-PRDRLHAGDKLEVNAE 69

Query: 66  -PLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FS 106
            P+++             E   L + +KP  +V   +   G  T+ + L           
Sbjct: 70  LPVQENWLAEPMALDIVFEDDCLIIVNKPANMVVHPASGHGDGTLLNGLLHHHNALQQLP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD-----QDKLN 159
           R   V RLD +T GL+++         L     +    R Y     G +         L 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTLASHAALVNQMQARGIAREYEAVVQGVLTGGGTVDAALG 189

Query: 160 LL----KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 KK  V++          +  +  S+  + V L  G+  +I+      N  + 
Sbjct: 190 RHPVNRKKRAVLEIGQRAVTHYRVIKRYRSHTHLEVKLDTGRTHQIRVHMAHLNHPIV 247


>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 = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           + QR+   +    +  SR++ +R+I    VKVN  ++++    V  +  I +   P
Sbjct: 1  MSKQRLDNRLVELNLCDSRQQAQRLIRAGEVKVNQQIIDKPGTEVDPSAEIVLQAKP 57


>gi|326405945|gb|ADZ63016.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 293

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 49/284 (17%), Positives = 93/284 (32%), Gaps = 63/284 (22%)

Query: 22  RAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA 70
           R GI SRR    ++ +      ++ VNG   + A   +   D + V      D   L   
Sbjct: 20  RHGI-SRR----LLTKVKFDGGKITVNGQ-EKNAIYRLEKDDLVTVTVPDEPDNEKLIPD 73

Query: 71  --------ERTRLWLYHKPIGL--VTTHSDPDGRST--VFDNLPSIF---SRVISVGRLD 115
                   E     +  KP G   +T    P G  +  V   +         V  + RLD
Sbjct: 74  DFPLNVLFEDDHYLVVEKPAGKPSITGSLHPTGAMSNAVKGYISQKNYANQTVHIITRLD 133

Query: 116 INTEGLLLLTNDGGLARVLELPST---QWLRVYRVRFHG-----------QVDQDKLNLL 161
            +T G++ L      A  L           + Y    +             + +   +++
Sbjct: 134 RDTSGIMFLAKH-RYAHALMNQHKFRDTMEKRYFAIVNDQDLPDSGRIDLPIGRRDDSII 192

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
           ++ +         +   +  ++ ++ A + + L  G+  +I+  F    + +        
Sbjct: 193 QRQVRFDEKAKDALTSYVVAERKNDLALLDIILHTGRTHQIRVHFSHLGYPL-------I 245

Query: 221 GPFQLGTLLAGSTREVSKKILR----EQLGPHLLEEAQVNLDAP 260
           G      L  G+   +S++ L     + L P   E   V LD P
Sbjct: 246 G----DDLYGGNHDLISRQALHSHHLQFLNPFTDEMVHVELDMP 285


>gi|332361173|gb|EGJ38977.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1056]
          Length = 295

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDKHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|269303280|gb|ACZ33380.1| RNA pseudouridine synthase family protein [Chlamydophila pneumoniae
           LPCoLN]
          Length = 283

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 71/228 (31%), Gaps = 48/228 (21%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+S  + ++    S++E+   I Q R +VNG +    +  V   D + +  +P  K + +
Sbjct: 13  RLSSFLRSQLPNHSKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQPS 72

Query: 74  RLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            LW      +Y KP  L T                +  +R  +V RLD  T G LL+   
Sbjct: 73  ILWEDDYSIIYEKPPHLTTEQ-------------MAHMTRFFTVHRLDKGTSGCLLMGKS 119

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK--LNLLKKGIVIQGICYGDMQVTLDTQK 183
              A  L       +  + Y     G   +    +      +           V      
Sbjct: 120 KQAATELMKLFKQRKIHKQYMALVFGHPKKKFGTVKSYTAPVY-----RRCGAVIFGAAS 174

Query: 184 GSNAWVTVG------------------LREGKNREIKKVFEFFNWKVN 213
            S   +T+                   +  G+  +I+         + 
Sbjct: 175 PSQGKLTITEWSVLDSYKRYSLMLCKPIT-GRTHQIRLQMGLLGHPIV 221


>gi|300113280|ref|YP_003759855.1| RluA family pseudouridine synthase [Nitrosococcus watsonii C-113]
 gi|299539217|gb|ADJ27534.1| pseudouridine synthase, RluA family [Nitrosococcus watsonii C-113]
          Length = 319

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 82/240 (34%), Gaps = 38/240 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            +      +R+ + +A+     SR  +++ I   +VKVN  L       V   + I V  
Sbjct: 10  TLPSELAGKRLDQALAQVFPAYSRSRLQQWIKHGQVKVNDALAR-PRDTVQGGEWIVVIA 68

Query: 63  --------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------F 105
                      PL      E   + + +KP GLV   +  +   T+ + L          
Sbjct: 69  EAEAETGWKSQPLPLEIIYEDEAIIVVNKPAGLVVHPAAGNRDGTLVNALLHHAPELERI 128

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
            R   V RLD +T GLL++  +      L   L + +  R Y+    G +       ++ 
Sbjct: 129 PRAGIVHRLDKDTSGLLVVARNLVAHHGLIQQLQARRITREYQAITVGVMTSGG--RIEA 186

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVG----LR-------E-GKNREIKKVFEFFNWK 211
            I    +    M V + T K +     V     +        E G+  +I+       + 
Sbjct: 187 PIQRHPVNRKRMAV-ISTGKPALTHYRVVSRFRIHTHILCRLETGRTHQIRVHLAHIGYP 245


>gi|322516374|ref|ZP_08069299.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
 gi|322125107|gb|EFX96500.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           vestibularis ATCC 49124]
          Length = 298

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 65/201 (32%), Gaps = 36/201 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRL-----WLYHKP 81
               + VNG   + A   V   D + ++           P+              + +KP
Sbjct: 33  EGGHIWVNGE-EQFATYPVHEGDVVAIEIPDEAPHETLKPIPFNLDIVYEDDNFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S  +  +T+ + +   F        RV  V RLD +T GL+L    G     +
Sbjct: 92  YGYASIPS-VNHDNTMANFVKYHFVSNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARM 150

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    ++    +  + + +       V +   Y      L  
Sbjct: 151 DKQLQQKSIKKHYYALVEGDTKLEQQGEIIAPIARDVDSIITRRVHKSGKYAHTSYRLVG 210

Query: 182 QKGSNAWVTVGLREGKNREIK 202
             G    V + L  G+  +I+
Sbjct: 211 DYGRVKLVDINLHTGRTHQIR 231


>gi|110004584|emb|CAK98921.1| probable pseudouridine synthase d protein [Spiroplasma citri]
          Length = 306

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/230 (17%), Positives = 83/230 (36%), Gaps = 45/230 (19%)

Query: 15  RVSKVIA-----RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------ 63
           R+ K++           SR +++ +I Q++V+VNG ++  A       DH+ ++      
Sbjct: 13  RIDKILTDYFKTNTTPFSRTKIQELIKQEKVQVNGQVVR-ANYVSQIGDHVIIEFPSAKA 71

Query: 64  ------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSR 107
                  +PL    E + L +  KP  LV   +      T+ + L          S   R
Sbjct: 72  SELTPLAIPLTILYEDSYLMVIDKPNNLVVHPAPGHQNDTLVNALLARGVQWSTASGEQR 131

Query: 108 VISVGRLDINTEGLLLLTNDGGLAR--VLELPSTQWLRVYRVRFHGQV------------ 153
              V R+D  T G L++  +  +      ++ + Q  R Y    HGQ+            
Sbjct: 132 PGIVHRIDRQTTGTLIIAKNDVVHHQLQQQIQTKQLQRRYLALVHGQIIENRAKIDAPIG 191

Query: 154 -DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            D +    +   +  +        + +  +     ++   L  G+  +I+
Sbjct: 192 RDPNNRKKMV--VTAKNSKKALTNIVVIERFNDYTYIECELESGRTHQIR 239


>gi|153954106|ref|YP_001394871.1| RluD2 [Clostridium kluyveri DSM 555]
 gi|219854718|ref|YP_002471840.1| hypothetical protein CKR_1375 [Clostridium kluyveri NBRC 12016]
 gi|146346987|gb|EDK33523.1| RluD2 [Clostridium kluyveri DSM 555]
 gi|219568442|dbj|BAH06426.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 319

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 87/259 (33%), Gaps = 56/259 (21%)

Query: 4   KNIVQENFTPQRVSKVIAR-------AGIASRREVERMIAQQRVKVNGILLERAAVNVMS 56
           K  +  N + QR+ K + +       +GI       + I +  +KVNG   +     +M 
Sbjct: 2   KVEIGSNESGQRLDKFLRKWLRDVPISGIY------KAIRKGDIKVNGKKTKE-KYFLMD 54

Query: 57  TDHIE---------------VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
            D +E               V+   L+   E   + L  K  G++          T+ D 
Sbjct: 55  KDIVEAQYIISKGKSFEFNKVNSNFLKITYEDENMILVEKWPGVLVHSDKKTDDVTLTDY 114

Query: 101 LPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVY 145
           + S                      RLD NT G+++   +    ++L   +      + Y
Sbjct: 115 VLSYLYDKGDFKPETEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEIIRERNIRKYY 174

Query: 146 RVRFHGQVDQD-----KLNLLKKGI--VIQGICYGDMQVTLDTQK----GSNAWVTVGLR 194
           +    G++++       L   K  I  V         ++++D +     G+ +   + L 
Sbjct: 175 QALVKGRINEGIYEGYILKDRKNNISNVYDSPKKNTKKISMDVKVLHTCGTYSLAELELI 234

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G++ +++         + 
Sbjct: 235 TGRSHQLRTHLAHLGNPII 253


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

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 36/251 (14%), Positives = 84/251 (33%), Gaps = 63/251 (25%)

Query: 7   VQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           V+ +    R+ +        +   G     ++++++   +V+V+G  ++     V     
Sbjct: 9   VEADEAGMRLDRWFKIHYPGL---GFG---QLQKLLRSGQVRVDGGRVKT-DARVQPGQM 61

Query: 60  IEV-----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDG 93
           + V                       DG  L +    E  ++ +++KP G+         
Sbjct: 62  VRVPPVDSDMKTKTGPIGSKDLKHSADGELLARMLLHEDDKVLVFNKPAGIAVQGGSGVN 121

Query: 94  RSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
           R            +      V RLD +T G+L++    G A+ L          + Y   
Sbjct: 122 RHIDGLLEAWTSPKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTYWAL 181

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNA----------------WVTV 191
             G V +   + +   +V +    GD M++    ++G++                 W+ +
Sbjct: 182 VRG-VPRKHQDKISTWLVKEQTPDGDRMRIAKHGEEGADHAISYYRVIDTAAQNLAWLEM 240

Query: 192 GLREGKNREIK 202
               G+  +++
Sbjct: 241 EPYTGRTHQLR 251


>gi|184201118|ref|YP_001855325.1| pseudouridine synthase RluD [Kocuria rhizophila DC2201]
 gi|183581348|dbj|BAG29819.1| pseudouridine synthase RluD [Kocuria rhizophila DC2201]
          Length = 325

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 77/234 (32%), Gaps = 37/234 (15%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGI-LLERAAVNVMSTDHIEV----DGVPLRK 69
           R+   +A     SR    ++ A+QRV   G  + +   V V  T  +EV    D   +  
Sbjct: 30  RLDAAVAAWTGLSRSAAAQLCAEQRVSHRGSPVAKSHRVAVSETYTVEVPVPEDPHRIAP 89

Query: 70  AERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISV 111
                L L H         KP G+    S      TV   L              R   V
Sbjct: 90  QHVPDLRLVHVEPSYVVVDKPAGVAAHPSPGWKGPTVVGALAGAGISVATSGAPERQGIV 149

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKLNL------- 160
            RLD+ T GL+++  + G    L+    +    +VY     G  D     ++        
Sbjct: 150 HRLDVGTSGLMVVAREEGAYSQLKRAFKERTVTKVYHAVVQGIPDPLKGTIDAPIGRHPG 209

Query: 161 --LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              +  ++  G         L+   G  + V V L  G+  +I+  F    +  
Sbjct: 210 HEWRFAVMEDGRNSVTHYEVLEA-FGRASLVEVHLETGRTHQIRVHFSALQYPC 262


>gi|260580730|ref|ZP_05848556.1| tRNA pseudouridine synthase C [Haemophilus influenzae RdAW]
 gi|260092547|gb|EEW76484.1| tRNA pseudouridine synthase C [Haemophilus influenzae RdAW]
          Length = 239

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/178 (16%), Positives = 57/178 (32%), Gaps = 31/178 (17%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  DP     V   L       V  + RLD  T G+LL      +A
Sbjct: 11  LVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALSSEIA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-- 186
            ++          + Y     G +  +++++   K I +  I     Q   + Q+     
Sbjct: 71  NLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEAITDY 129

Query: 187 --------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                               + V +    G+  ++++  +     +  L    YG   
Sbjct: 130 EGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHVFHPI--LGDTQYGDLH 185


>gi|16126223|ref|NP_420787.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus CB15]
 gi|221234996|ref|YP_002517432.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
 gi|13423445|gb|AAK23955.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus CB15]
 gi|220964168|gb|ACL95524.1| ribosomal large subunit pseudouridine synthase C [Caulobacter
           crescentus NA1000]
          Length = 331

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 34/222 (15%), Positives = 64/222 (28%), Gaps = 42/222 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV---------------------DGVPLRKAE 71
           ++    +V+V+G   + A   + +   I V                         L   E
Sbjct: 38  KLFRSGQVRVDGSRAK-ADTKLAAGSQIRVPPLPDAPDPSDKNKLSARDVAYAKSLVLYE 96

Query: 72  RTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +   +KP GL              +         R   V RLD +T G+LLL     
Sbjct: 97  DEEVLALNKPAGLAVQGGTKTTKHIDKLLSAWGEGVDRPRLVHRLDRDTSGVLLLGKTPS 156

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQD----KLNLLKKGI---------VIQGICYGD 174
            A  L       +  + Y     G         +L+L K+G+           +      
Sbjct: 157 AAARLSGAFAKRKAQKTYWAIVAGNPHPTEGVMELHLAKRGVGDRELVVPAQPKDPDAQP 216

Query: 175 MQ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   VT+        W+ +    G+  +++   +     + 
Sbjct: 217 AETEFVTISRAGPRVTWMALRPHTGRTHQLRAHMKAMGHPIL 258


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

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 36/251 (14%), Positives = 84/251 (33%), Gaps = 63/251 (25%)

Query: 7   VQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           V+ +    R+ +        +   G     ++++++   +V+V+G  ++     V     
Sbjct: 9   VEADEAGMRLDRWFKIHYPGL---GFG---QLQKLLRSGQVRVDGGRVKT-DARVQPGQM 61

Query: 60  IEV-----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDG 93
           + V                       DG  L +    E  ++ +++KP G+         
Sbjct: 62  VRVPPVDSDLKVKSGPIGSRDLKHSADGELLARMLLHEDDKVLVFNKPAGIAVQGGSGVN 121

Query: 94  RSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
           R            +      V RLD +T G+L++    G A+ L          + Y   
Sbjct: 122 RHIDGLLEAWTSPKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTKKTYWAL 181

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGSNA----------------WVTV 191
             G V +   + +   +V +    GD M++    ++G++                 W+ +
Sbjct: 182 VRG-VPRKHQDKISTWLVKEQTPDGDRMRIAKHGEEGADHAISYYRVIDTAAQNLAWLEM 240

Query: 192 GLREGKNREIK 202
               G+  +++
Sbjct: 241 EPYTGRTHQLR 251


>gi|311087296|gb|ADP67376.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. JF99 (Acyrthosiphon pisum)]
          Length = 312

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/225 (15%), Positives = 82/225 (36%), Gaps = 33/225 (14%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----G 64
           + + QR+  V+++     SR  ++++I   +V VN  ++ +    ++  + + +      
Sbjct: 14  SLSGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKD 73

Query: 65  VPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVI 109
           + +   E            + + +KP GLV      +   T+ + L   +       R  
Sbjct: 74  LLVDIPENIFLDIVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHYKNSRDLPRAG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARV--LELPSTQWLRVYRVRFHG----------QVDQDK 157
            V RLD +T GL+++  +        L L   + +R Y    HG           + +  
Sbjct: 134 IVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMIAGGTINKPIMRHY 193

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  +   G         + ++   +  + + L  G+  +I+
Sbjct: 194 NRRTCMMVHHLGKPSVTH-YKVLSRFKFHTHIAIRLETGRTHQIR 237


>gi|152986388|ref|YP_001350515.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
 gi|150961546|gb|ABR83571.1| pseudouridine synthase [Pseudomonas aeruginosa PA7]
          Length = 320

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 42/233 (18%), Positives = 77/233 (33%), Gaps = 40/233 (17%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGI------LLERAAVNVMST-------- 57
           QR+ + IA       SR  +   I   R+ V+G       ++   A  V+          
Sbjct: 18  QRLDQ-IAAQLFPEHSRSRLAGWIKDGRLTVDGAAARPRDIVHSGAQLVLEAEQEAQGEW 76

Query: 58  --DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVI 109
               IE+D       E   + +  KP GLV   +      T+ + L       +   R  
Sbjct: 77  VAQDIELD----IVHEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPGIANVPRAG 132

Query: 110 SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---KLNLLKKG 164
            V RLD +T GL+++         L  +L +    R+Y     G +         + + G
Sbjct: 133 IVHRLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVITSGGTIDAPIGRHG 192

Query: 165 I------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +      V+           +  +  ++    V L  G+  +I+       + 
Sbjct: 193 VQRQKMAVVDAGKVAVSHYRVLERFRAHTHTRVKLETGRTHQIRVHMSHIGYP 245


>gi|148926673|ref|ZP_01810354.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145845192|gb|EDK22287.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 251

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 75/199 (37%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA ++  +  ++     P    E  ++
Sbjct: 8   KLLALQEKISNREAKDLIDKGCVFSHGKKVVVARALMSDKARFNVIKAKNPQIIFEDDKI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 68  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 114

Query: 136 LPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDTQK 183
               +    + Y     G + ++ ++N     I ++G     +          +T    +
Sbjct: 115 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKVKGGALSKVSKDGLSALSIITPIMMQ 174

Query: 184 GSNAWVTVGLREGKNREIK 202
                  + ++ G+  +I+
Sbjct: 175 SKKTLAKIVIQTGRTHQIR 193


>gi|90580967|ref|ZP_01236768.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
 gi|90437845|gb|EAS63035.1| putative pseudouridine synthase Rlu family protein [Vibrio angustum
           S14]
          Length = 245

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 52/167 (31%), Gaps = 27/167 (16%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL      +
Sbjct: 11  YLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFGLSSEI 70

Query: 131 ARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           A  +          + Y     G + +  +      + +  I   +     + Q    A+
Sbjct: 71  ASQMMPLFAGRDMHKTYHAVVRGWIKEAAVLDYPLKVELDKIADKNASEEKEAQPAVTAY 130

Query: 189 ---VTVG--------------LRE-----GKNREIKKVFEFFNWKVN 213
               TV               L E     G+  ++++     +  + 
Sbjct: 131 EPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHII 177


>gi|152997613|ref|YP_001342448.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150838537|gb|ABR72513.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1]
          Length = 327

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 36/208 (17%), Positives = 73/208 (35%), Gaps = 34/208 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------ 74
           SR  ++  I +  +KV+G +  +    +   + + +D + +   E               
Sbjct: 32  SRSRIQSWIKEGVLKVDGKI-TKPKEKLFGGEVVTLD-IVIEAQEEHEAQAMDLDVVYED 89

Query: 75  --LWLYHKPIGLVTT----HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLL-- 124
             + + +KP GLV      + D    + +  + P      R   V RLD  T GL+++  
Sbjct: 90  DDIMIINKPAGLVVHPAVGNRDGTLMNAILHHAPETAHIPRAGIVHRLDKETTGLMVVAK 149

Query: 125 TNDGGLARVLELPSTQWLRVYR-----VRFHGQVDQDKLNLL-----KKGIVIQGICYGD 174
           T       V++L      R Y      V   G V  + +        K+ +         
Sbjct: 150 TLAAQTDLVMQLQERSMGREYEAVSIGVMTGGGVVDEPIGRHPHNRQKQAVEPVNGKDAV 209

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
               L  +  ++  + + L  G+  +I+
Sbjct: 210 THYRLVERFKNHTHIRLKLETGRTHQIR 237


>gi|288923211|ref|ZP_06417353.1| pseudouridine synthase, RluA family [Frankia sp. EUN1f]
 gi|288345447|gb|EFC79834.1| pseudouridine synthase, RluA family [Frankia sp. EUN1f]
          Length = 313

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 76/240 (31%), Gaps = 53/240 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V +     R+   +AR    SR     ++   +V V+G +  R+   V     +EV    
Sbjct: 13  VPDGLDGMRLDAALARMFGLSRTAAVSVVDDGQVSVDGQVRGRSD-RVAGGAWLEV---A 68

Query: 67  LRKAERTRLW---------LYH---------KPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           L    R             + H         KP+G+    +      TV   L +   R+
Sbjct: 69  LPAPPRPVTVDATPVEGLGILHDDDDIVVVDKPVGVAAHPAPGFTGPTVIGALAAAGYRI 128

Query: 109 I---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
                      V RLD+ T G++++        +L+      +  +VYR    G  D   
Sbjct: 129 STSGAAERQGVVHRLDVGTTGIMVVAKSERAYTLLKRAFRDREVEKVYRAVVQGHPDP-- 186

Query: 158 LNLLKKGI--VIQGICYGDMQVTLDTQKGSN-------------AWVTVGLREGKNREIK 202
              L+  +   I           +      +             + ++V L  G+  +I+
Sbjct: 187 ---LRGTVDAPIDRHPRRPGLFAVVAGGKPSVTHYDTEEAFRSASLLSVRLETGRTHQIR 243


>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 = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 65/199 (32%), Gaps = 20/199 (10%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--------ERTRLWL 77
            S++  +++I +    VNGI       N+     +E     L           E     +
Sbjct: 24  GSKKRAKKVIDEGLCAVNGIKERFYRKNLKPNTIVEFSIPKLLFTKTKIEILYEDEYFLV 83

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
            +KP  + +          V   L   F  +    RLD  T G L++     +  + +L 
Sbjct: 84  VNKPPFINSN----KNFPDVESLLRKRFKSIYVAHRLDKQTSGALIIAKSKEVFELFKLK 139

Query: 138 STQWLRV--YRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR 194
             +      Y     G + ++           I G      +  +  + G   ++ V + 
Sbjct: 140 FKKKEVKKKYLALVAGNLKKNSGKIKFS----IDG-KEAISRYQVVERVGKTDFLEVEIL 194

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+K F   N  + 
Sbjct: 195 TGRKHQIRKHFVSVNHPII 213


>gi|289640971|ref|ZP_06473141.1| pseudouridine synthase, RluA family [Frankia symbiont of Datisca
           glomerata]
 gi|289509286|gb|EFD30215.1| pseudouridine synthase, RluA family [Frankia symbiont of Datisca
           glomerata]
          Length = 340

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 76/237 (32%), Gaps = 47/237 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL---------LERAAVNV-MS 56
           V +     R+  VIAR    SR    +++   +  V+G +          E   V +   
Sbjct: 40  VPDGLDGLRLDAVIARMFGLSRTAAAQLVDDGQASVDGTVRGRSDRVGAGEWLDVRLPPP 99

Query: 57  TDHIEVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
            + + V   P+       +   + +  KPIG+    +      TV   L +   RV    
Sbjct: 100 PNPVRVAAEPVPGLLVIHDDDDIVVVSKPIGVAAHPAPGFTGPTVIGGLAAAGYRVATSG 159

Query: 109 -----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
                  V RLD+ T G++++         L+      +  ++YR    G  D       
Sbjct: 160 AAERQGVVHRLDVGTTGIMVVAKSERAYTALKRAFRDREVEKIYRALVQGHPDP------ 213

Query: 162 KKGIV---IQGICYGDMQVTLDTQKGSN-------------AWVTVGLREGKNREIK 202
             G V   I           +      +             + ++V L  G+  +I+
Sbjct: 214 SSGTVDAPIDRHPRKPGLFAVVAGGKPSVTHYDTEEAFRAASLLSVRLETGRTHQIR 270


>gi|311086138|gb|ADP66220.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. LL01 (Acyrthosiphon pisum)]
          Length = 312

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/225 (15%), Positives = 81/225 (36%), Gaps = 33/225 (14%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----G 64
           + + QR+  V+++     SR  ++++I   +V VN  ++ +    ++  + + +      
Sbjct: 14  SLSGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGEILTIHPFSKD 73

Query: 65  VPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVI 109
           + +   E            + + +KP GLV      +   T+ + L           R  
Sbjct: 74  LLVDIPENIFLDIVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHYKNSKDLPRAG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARV--LELPSTQWLRVYRVRFHG----------QVDQDK 157
            V RLD +T GL+++  +        L L   + +R Y    HG           + +  
Sbjct: 134 IVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGVVHGKMIAGGTINKPIMRHY 193

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  +   G         + ++   +  + + L  G+  +I+
Sbjct: 194 NRRTCMMVHHLGKPSVTH-YKVLSRFKFHTHIAIRLETGRTHQIR 237


>gi|33597725|ref|NP_885368.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           parapertussis 12822]
 gi|33574153|emb|CAE38483.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           parapertussis]
          Length = 320

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 75/237 (31%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KV+A      SR  ++  I    V VNG   +     V   D + V   P  +    
Sbjct: 29  RLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAK-VRQAVGPGDVLSVWEQPAPESRAF 87

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGR 113
                     AE     +  KP GLVT     +   T+ + L   +       R   V R
Sbjct: 88  APEPVAFDVVAESPDWIVVDKPAGLVTHPGAGNWSGTLLNGLLHRYPELARVARAGIVHR 147

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLL 161
           LD +T GL+++  +      L  +L +    R Y                 + +D    +
Sbjct: 148 LDKDTSGLMVVARNELAQTHLVRQLQARTMGRQYIALAHGWLGAAGTVDRPIGRDARVPV 207

Query: 162 KKGIVIQGICYGDMQVTLDTQK-------GSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +  + I         D ++          + V   L  G+  +I+         
Sbjct: 208 RMSVE-RPIAPKPAVTHFDPRRRGCAEGGARVSEVLCRLETGRTHQIRVHLASLGHP 263


>gi|271499489|ref|YP_003332514.1| pseudouridine synthase [Dickeya dadantii Ech586]
 gi|270343044|gb|ACZ75809.1| pseudouridine synthase [Dickeya dadantii Ech586]
          Length = 261

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 28/188 (14%), Positives = 58/188 (30%), Gaps = 38/188 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LL+   
Sbjct: 7   QDEHLIAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR+L       Q  ++Y     G V           ++L+ +               
Sbjct: 67  SDVARLLAQQFEQHQMEKMYHAVVRGYVMDDGVIDYALTEELDRIAD--KYADPDKAPQP 124

Query: 175 ----------MQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
                      ++ +   +      + + +  + G+  ++++        +        G
Sbjct: 125 AVSHYRVLAHAELPVAIGRYDTARYSLLELTPKTGRKHQLRRHMAHLRHPI-------IG 177

Query: 222 PFQLGTLL 229
               G L 
Sbjct: 178 DTTHGDLR 185


>gi|15639223|ref|NP_218671.1| hypothetical protein TP0231 [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189025464|ref|YP_001933236.1| hypothetical protein TPASS_0231 [Treponema pallidum subsp. pallidum
           SS14]
 gi|3322502|gb|AAC65220.1| conserved hypothetical protein [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018039|gb|ACD70657.1| hypothetical protein TPASS_0231 [Treponema pallidum subsp. pallidum
           SS14]
 gi|291059635|gb|ADD72370.1| RNA pseudouridine synthase superfamily [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 216

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/148 (19%), Positives = 52/148 (35%), Gaps = 20/148 (13%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA--RVLEL 136
           KP GL         R  V D L      R+  + RLD +T G+LL       A      L
Sbjct: 17  KPAGLAVQPG-ARVRVCVVDVLQKQLGVRLFPLHRLDKDTAGVLLFAKHARAAALYQGIL 75

Query: 137 PSTQWLRVYRVRFHGQVDQD--KLNLLKKGIVIQ-GICYGDMQV--------TLDTQKGS 185
            S + ++ YR    G+  ++   +      + I+ G      QV         +     +
Sbjct: 76  GSMRVIKRYRALCFGRPPRECGDIR-----VPIRTGTAARRRQVVRAAHTAYRVLRATDT 130

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
           + ++ + L  G+  +I+         + 
Sbjct: 131 HTYLELTLHSGRTHQIRIHLAALGCPII 158


>gi|312865090|ref|ZP_07725318.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
 gi|311099201|gb|EFQ57417.1| pseudouridine synthase, RluA family [Streptococcus downei F0415]
          Length = 303

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/208 (16%), Positives = 69/208 (33%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVD-----G----VPLRKA-----ERTRLWLYHKPIG 83
             + VNGI +  A   +   D + ++     G    +P++       E     + +KP G
Sbjct: 35  GHIWVNGIEV-NAIYLLAPGDRVSIEIPAEVGSPSLLPIQHPLDIVAEDEHFLVINKPAG 93

Query: 84  LVTTHS---DPDGRSTVFDNLPSI---FSRVISVGRLDINTEGLLLLTNDGGLARVL--E 135
             +  S   D    + V            ++  V RLD +T GL+L    G     +   
Sbjct: 94  YPSIPSILHDESMANFVKAYYEEQTYENQQIHIVTRLDKDTSGLMLFAKHGYAHSRMDKA 153

Query: 136 LPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
           L +    + Y     G             + ++  +++ + +   G  Y      +  + 
Sbjct: 154 LQAKTIEKRYYALVSGHKDLLDAGEIIAPIAREAESIITRRVHPSG-KYAHTSYRVLKRF 212

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWK 211
           G    V + L  G+  +I+  F      
Sbjct: 213 GPVKLVDIRLHTGRTHQIRVHFSHIGQP 240


>gi|33602573|ref|NP_890133.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           bronchiseptica RB50]
 gi|33577012|emb|CAE34092.1| ribosomal large subunit pseudouridine synthase D [Bordetella
           bronchiseptica RB50]
          Length = 320

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 75/237 (31%), Gaps = 42/237 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KV+A      SR  ++  I    V VNG   +     V   D + V   P  +    
Sbjct: 29  RLDKVLAGLLPGHSRSRLQGWIEAGYVLVNGAQAK-VRQAVGPGDVLSVWEQPAPESRAF 87

Query: 70  ----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGR 113
                     AE     +  KP GLVT     +   T+ + L   +       R   V R
Sbjct: 88  APEPVAFDVVAESPDWIVVDKPAGLVTHPGAGNWSGTLLNGLLHRYPELARVARAGIVHR 147

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RFHGQVDQDKLNLL 161
           LD +T GL+++  +      L  +L +    R Y                 + +D    +
Sbjct: 148 LDKDTSGLMVVARNELAQTHLVRQLQARTMGRQYIALAHGWLGAAGTVDRPIGRDARVPV 207

Query: 162 KKGIVIQGICYGDMQVTLDTQK-------GSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +  + I         D ++          + V   L  G+  +I+         
Sbjct: 208 RMSVE-RPIAPKPAVTHFDPRRRGCAEGGARVSEVLCRLETGRTHQIRVHLASLGHP 263


>gi|308189690|ref|YP_003922621.1| Pseudouridylate synthase [Mycoplasma fermentans JER]
 gi|307624432|gb|ADN68737.1| predicted Pseudouridylate synthase [Mycoplasma fermentans JER]
          Length = 280

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 81/248 (32%), Gaps = 47/248 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-----------------L 75
           +++  + +K+NG+ +      +   D I++ G+     +  +                 +
Sbjct: 33  KILRNKDIKINGVRINDPQYIINEKDIIQIYGIEANDYQNKKFENSAKKDFKIIYEDDNI 92

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLAR 132
            +  KPI L     +      V   L        +   VGRLD  T GL++   +     
Sbjct: 93  LIVSKPINLSVHSENNCLDKQVLSYLKYNQKDSFKPSHVGRLDKATSGLMIYAKNYATLV 152

Query: 133 VLELPSTQWLRVYRVRFH-------GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
            L   ++ + ++Y+++          +++      L K +V        +  TL   K +
Sbjct: 153 ELNYKTSFFEKIYKLKSDFKEAKKLVEINIQHDEKLYKMVVTNNTK-DPLAKTLFYTKNN 211

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKV-------------NRLIRISYGPFQLGTLLAGS 232
             + ++ L  GK  +I+         +               L   S     L      S
Sbjct: 212 KIFASI-LT-GKKHQIRLSMAHLKTPIYGDIKYGGKKADRLYLHCYSITFKNLDN----S 265

Query: 233 TREVSKKI 240
            + ++ K 
Sbjct: 266 LKYLNNKE 273


>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 = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 38/213 (17%), Positives = 67/213 (31%), Gaps = 34/213 (15%)

Query: 29  REV-ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWL 77
           R+  +  I Q +++V+G  +      + +   +     P  + E             LW 
Sbjct: 14  RQAWQERIEQGQIEVDGKTV-DPTYPLQAGQTLTYWRSPWVEPEVPLQLSVLHRDEDLWA 72

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLL--TNDGGLARV 133
             KP GL           TV + L   + +  +  + RL   T GLLLL  +  G     
Sbjct: 73  IDKPSGLPVLPGGDFVYHTVLEQLKIQYPQESLFPLHRLGTGTSGLLLLGRSTLGRRELS 132

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY-------------GDMQV--T 178
            +       ++YR    G    D     +    I  I Y                Q    
Sbjct: 133 RQFREHICRKIYR-TVIGPC--DLPEKFECHQAIGKIPYPQLGYIYAASSHGKPAQSYGR 189

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +     W+ V +R G+  +I+       + 
Sbjct: 190 ILARSPEKTWLEVEIRTGRPHQIRIHLASLGYP 222


>gi|324991124|gb|EGC23058.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK353]
          Length = 295

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 33/209 (15%), Positives = 68/209 (32%), Gaps = 38/209 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIE--------------VDGVPLRKAERTRLWLYHKPIG 83
             + VN    + A   +   D +               VD       E     +  KP G
Sbjct: 35  GNILVNHQP-QNAVYLLDIGDRVTIDIPSEKGFESLKAVDKDLSVIYEDEHFLVLDKPAG 93

Query: 84  LVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL-- 134
           + +  S  +  +T+ + + + +        +V  V RLD +T GL+L    G     L  
Sbjct: 94  VASIPS-VNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDK 152

Query: 135 ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L      + Y     G             + ++  +++ + +  +   Y      +  +
Sbjct: 153 QLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESIITRRVT-EDGKYAHTSYKVIER 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            G    V + L  G+  +I+  F    + 
Sbjct: 212 FGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|238754814|ref|ZP_04616165.1| tRNA pseudouridine synthase C [Yersinia ruckeri ATCC 29473]
 gi|238706974|gb|EEP99340.1| tRNA pseudouridine synthase C [Yersinia ruckeri ATCC 29473]
          Length = 257

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 57/186 (30%), Gaps = 34/186 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   S  D   TVF        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHMVAVNKPAGWLVHRSWLDRNETVFVMQTVRDQIDQHVYTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGD-- 174
             +AR+L       +  +VY     G V +D          L+ +      Q        
Sbjct: 67  SDVARLLSQQFEQHEVRKVYHAVVRGYVLEDDTLDYALTEELDKIADKFSSQDKAPKSAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPF 223
                  Q  +    G        L E     G+  ++++        +        G  
Sbjct: 127 THYRAMAQAEMPVAIGRYETARYSLMELTPETGRKHQLRRHMAHIRHPI-------IGDS 179

Query: 224 QLGTLL 229
             G L 
Sbjct: 180 THGDLR 185


>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 = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/223 (15%), Positives = 69/223 (30%), Gaps = 35/223 (15%)

Query: 19  VIARAGIASRREVERMIAQ-QRVKVNGILLERAAVNVMSTDHIEV---------DGVPLR 68
            + + G  S ++    I Q   + VN   +      +   D + +         +     
Sbjct: 16  FLQQQGF-S-KKTTSAIKQNGALLVNHEPVT-VRYQLQPGDKLTIILPTEIPSANLQAFH 72

Query: 69  KA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDIN 117
                  E   L +  KP       S      ++ + + +             V RLD N
Sbjct: 73  HPLDIVYEDDYLLIVCKPSLQNCAPSREHPHESLIEQVLAYCHENDNDFTPHIVTRLDRN 132

Query: 118 TEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKKGIVIQGI-- 170
           T GL+LL   G +  +L     +  + Y    HG      + +  +      I+ + +  
Sbjct: 133 TTGLVLLAKHGHIHHLLSHI--KINKRYIALCHGATQPEGIIEAPIARANDSIITRQVSS 190

Query: 171 --CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              Y          K + +   V L  G+  +I+  F++    
Sbjct: 191 TGKYAKSTYRTLNSKQNVSLCEVTLHTGRTHQIRVHFQYIGHP 233


>gi|327462178|gb|EGF08505.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1]
          Length = 295

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 33/209 (15%), Positives = 68/209 (32%), Gaps = 38/209 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIE--------------VDGVPLRKAERTRLWLYHKPIG 83
             + VN    + A   +   D +               VD       E     +  KP G
Sbjct: 35  GNILVNHQP-QNAVYLLDIGDRVTIDIPSEKGFESLKAVDKDLSVIYEDEHFLVLDKPAG 93

Query: 84  LVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL-- 134
           + +  S  +  +T+ + + + +        +V  V RLD +T GL+L    G     L  
Sbjct: 94  VASIPS-VNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDK 152

Query: 135 ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +L      + Y     G             + ++  +++ + +  +   Y      +  +
Sbjct: 153 QLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESIITRRVT-EDGKYAHTSYKVIER 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            G    V + L  G+  +I+  F    + 
Sbjct: 212 IGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>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 = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 73/253 (28%), Gaps = 55/253 (21%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
               +R+  V+A      SR  V+ +I    V V+G  +      V     + +      
Sbjct: 28  EDAGKRLDAVLAAHLADLSRTRVQALIRSGEVTVDGGKIVEPKYRVNEGATLALGLPEPE 87

Query: 63  -------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
                  D   +   E   L +  KP GLV      +   T+ + L              
Sbjct: 88  EAEPKGEDIPLVVVYEDDDLIVIDKPAGLVVHPGAGNWTGTLVNALIRHCGDSLSGIGGV 147

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHGQV------ 153
            R   V RLD  T GLL++       + L              R Y     G        
Sbjct: 148 RRPGIVHRLDKETSGLLVVAKTDAAHKGLSEQFADHGRSGPLERAYAALVWGAPATLRGT 207

Query: 154 ----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----AWVTVGLREGKN 198
                     ++ K+++++ G    G         L+    ++     + +   L  G+ 
Sbjct: 208 VDANLARSDANRQKISVVRNG----GRHAVTHWQVLERFGPADQPAVASLLECRLETGRT 263

Query: 199 REIKKVFEFFNWK 211
            +I+         
Sbjct: 264 HQIRVHMAHIGHP 276


>gi|312863550|ref|ZP_07723788.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
 gi|311101086|gb|EFQ59291.1| pseudouridine synthase, RluA family [Streptococcus vestibularis
           F0396]
          Length = 298

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 65/201 (32%), Gaps = 36/201 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDG---------VPLRKAERTRL-----WLYHKP 81
               + VNG   + A   V   D + ++           P+              + +KP
Sbjct: 33  EGGHIWVNGE-EQFATYPVHEGDVVAIEIPDEVPHETLKPIPFDLDIVYEDDNFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S  +  +T+ + +   F        RV  V RLD +T GL+L    G     +
Sbjct: 92  YGYASIPS-VNHDNTMANFVKYHFVSNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARM 150

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK----LNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G    ++    +  + + +       V +   Y      L  
Sbjct: 151 DKQLQQKSIKKHYYALVEGDTKLEQQGEIIAPIARDVDSIITRRVHKSGKYAHTSYRLVG 210

Query: 182 QKGSNAWVTVGLREGKNREIK 202
             G    V + L  G+  +I+
Sbjct: 211 DYGRVKLVDINLHTGRTHQIR 231


>gi|156503277|ref|YP_001429342.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FTNF002-00]
 gi|290954356|ref|ZP_06558977.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica URFT1]
 gi|295312220|ref|ZP_06803020.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica URFT1]
 gi|156253880|gb|ABU62386.1| pseudouridine synthase, Rlu family protein [Francisella tularensis
           subsp. holarctica FTNF002-00]
          Length = 309

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMTVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|148825977|ref|YP_001290730.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittEE]
 gi|148716137|gb|ABQ98347.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittEE]
          Length = 239

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/185 (15%), Positives = 54/185 (29%), Gaps = 37/185 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLIAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-------------QDKLNLLKK--------- 163
             +A ++          + Y     G +                  +   +         
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQENKGSQEAI 126

Query: 164 ----GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
               G+ I  + Y   +     Q    + V +    G+  ++++  +     +  L    
Sbjct: 127 TDYGGLKIVEMPYPAGRY----QTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQ 180

Query: 220 YGPFQ 224
           YG   
Sbjct: 181 YGDLH 185


>gi|15617005|ref|NP_240218.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219681757|ref|YP_002468143.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
 gi|257471459|ref|ZP_05635458.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. LSR1 (Acyrthosiphon pisum)]
 gi|11387080|sp|P57481|RLUD_BUCAI RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|25322332|pir||H84976 pseudouridylate synthase (EC 4.2.1.70) [imported] - Buchnera sp.
           (strain APS)
 gi|10039070|dbj|BAB13104.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. APS (Acyrthosiphon pisum)]
 gi|219624600|gb|ACL30755.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. 5A (Acyrthosiphon pisum)]
          Length = 312

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 35/225 (15%), Positives = 81/225 (36%), Gaps = 33/225 (14%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----G 64
           + + QR+  V+++     SR  ++++I   +V VN  ++ +    ++  + + +      
Sbjct: 14  SLSGQRLDLVLSKLFREYSRSYLKKLIIMNQVLVNESIVNQPDKKILGGETLTIHPFSKD 73

Query: 65  VPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVI 109
           + +   E            + + +KP GLV      +   T+ + L           R  
Sbjct: 74  LLVDIPENIFLDIVYEDSDILIINKPAGLVVHPGSGNKSGTILNALLYHYKNSKDLPRAG 133

Query: 110 SVGRLDINTEGLLLLTNDGGLARV--LELPSTQWLRVYRVRFHG----------QVDQDK 157
            V RLD +T GL+++  +        L L   + +R Y    HG           + +  
Sbjct: 134 IVHRLDKDTSGLMVIAKNIFSYNHLLLLLKEKKIIREYEGIVHGKMIAGGTINKPIMRHY 193

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  +   G         + ++   +  + + L  G+  +I+
Sbjct: 194 NRRTCMMVHHLGKPSVTH-YKVLSRFKFHTHIAIRLETGRTHQIR 237


>gi|16800037|ref|NP_470305.1| hypothetical protein lin0968 [Listeria innocua Clip11262]
 gi|16413427|emb|CAC96199.1| lin0968 [Listeria innocua Clip11262]
          Length = 296

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 39/264 (14%), Positives = 88/264 (33%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKA-------ERTRLWLYHKP 81
           A  +++VN         +V + D + +       +   L +        E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKTDDKVRLTFPTEQQNDRLLAEHTDLEVVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPTGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNRYAHARLS 155

Query: 136 L--PSTQWLRVYRVRFHGQVDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                    R Y+    G ++++            ++++++ +  +G         L   
Sbjct: 156 SFLQQGLLKRRYQAFTSGTLEEEAGSIEAPIGRKDVSIMERFVTPEGKYAKTNYEVLMRY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
            G +  + + L  G+  +I+  F +    +        G      +  G    + ++ L 
Sbjct: 216 NGFDH-LAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDQELLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H + E  +  D P+   
Sbjct: 264 SCHLHLVHPVTEEYMAFDLPLPED 287


>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 = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 88/251 (35%), Gaps = 43/251 (17%)

Query: 1   MKDKN-IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M  K   V E     R+  V+    I    SR+ ++ +I    ++V+    ++ A  + +
Sbjct: 1   MNQKEHYVHEEEKNMRLD-VLCAQ-ICPNLSRQYLKELIVDGDIQVD-FANKKPAYRLKA 57

Query: 57  TDHIEV---DGVPLRK----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            + I +   D VP +            E   + + +KP G+V   +      T+ + L +
Sbjct: 58  DERIVIKIPDPVPCQVMPESIDLDIVYEDGDVIVVNKPSGMVVHPASGTQSGTLVNALMA 117

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG- 151
               +           V R+D +T G+L++  +    R L         +R Y     G 
Sbjct: 118 HTKDLSGINGVNRPGIVHRIDKDTSGILVVAKNDLAHRHLARQLAEHSMVRQYVALVKGN 177

Query: 152 ----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                      V +  ++ ++  +V  G         ++   G   +V   L  G+  +I
Sbjct: 178 IVENSGTVDMPVGRHPVDRVRMAVVENGKSAVTHFEVIERL-GDFTYVAFRLETGRTHQI 236

Query: 202 KKVFEFFNWKV 212
           +   +     +
Sbjct: 237 RVHMQAIGHPI 247


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

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 40/269 (14%), Positives = 88/269 (32%), Gaps = 68/269 (25%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++  V ++    R+ +        +A        ++++++   +++V+G   +     V 
Sbjct: 5   EQRRVDDDEAGLRLDRWFKLHYPGLA---FG---QLQKLLRSGQIRVDGGRAKS-DTRVA 57

Query: 56  STDHIEV------------------------DGVPLRK---AERTRLWLYHKPIGLVTTH 88
               + V                        DG  L +    E  ++ +++KP GL    
Sbjct: 58  PGQMVRVPPLATDSKTSTNHPLTANTIKGRPDGDVLSQMVIYEDEKVIVFNKPAGLAVQG 117

Query: 89  SDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
                R  V D L +  ++       V RLD +T G+L++    G A  L          
Sbjct: 118 GSGVARH-VDDMLEAWRNKKGEKPRLVHRLDRDTSGILVVARTRGAATALTKAFRERDTK 176

Query: 143 RVYRVRFHG-----------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           ++Y     G                   D D++ + + G   +G  +      +  Q   
Sbjct: 177 KLYWAVVKGVPAKKEGRISTYLKKEQTPDGDRMRIARHG--DEGADHALSHYRVIDQVAQ 234

Query: 186 N-AWVTVGLREGKNREIKKVFEFFNWKVN 213
           N AW+ +    G+  +++         + 
Sbjct: 235 NFAWLELEPHTGRTHQLRVHAAHIGHPIL 263


>gi|73666929|ref|YP_302945.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia canis
           str. Jake]
 gi|72394070|gb|AAZ68347.1| ribosomal large subunit pseudouridine synthase C [Ehrlichia canis
           str. Jake]
          Length = 308

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 39/253 (15%), Positives = 77/253 (30%), Gaps = 72/253 (28%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE-------VERMIAQQRVKVNGILLERAAVNVMSTD 58
            V+E+    RV K +       RR        VE+ + +  V ++   ++     + + +
Sbjct: 7   TVKEDDQDVRVDKFV-------RRVLKIPQSLVEKFLRKGIVLLDNAKVKS-NTRIKTGN 58

Query: 59  HIEVD-----GVPLRKA--------------------ERTRLWLYHKPIGLVTTHSDPDG 93
            I +      G  +                       E   + + +KP G+         
Sbjct: 59  VIYIKCNTIIGEEIHTKRICKTDSSYLINLISNSILYEDDDVLIINKPAGVSVQGG-TKV 117

Query: 94  RSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
           R ++ D L  I     +  V RLD +T G+L+L  +   +R++     + +  + Y    
Sbjct: 118 RISISDILDKIRDGESMRIVHRLDKDTSGILMLARNARASRLIMHEFKNRRVEKKYLALT 177

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---------------VGLR 194
            G    D          I            +     N+                  +GL 
Sbjct: 178 QGIPKNDVGE-------INHSITKKKHNFYENIGTGNSIFQEAITSFFVLKKLPYDIGLL 230

Query: 195 E-----GKNREIK 202
           E     G+  +I+
Sbjct: 231 ELKPKTGRKHQIR 243


>gi|254557025|ref|YP_003063442.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254045952|gb|ACT62745.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 300

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 34/242 (14%), Positives = 79/242 (32%), Gaps = 42/242 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVN------------GILLER 49
           +    TP +V  ++A+ G+ +R     ++ +       + V+            G  +  
Sbjct: 6   INHETTPMKVKTLLAQHGV-TRS----LLKKVKFHGGAILVDERPVLAIHMLTGGETVTM 60

Query: 50  AAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
                +  DH+ V  +P+    E     + +KP G+ +  +     +T+ + +   +   
Sbjct: 61  VTPAEIGNDHLGVSTLPIDILYEDRDYLIVNKPAGVASVPAHALPDNTLANRVKGYYQAA 120

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD--- 156
                 V    RLD +T G++L         +++         ++Y     G++  D   
Sbjct: 121 HYDNEVVHITTRLDRDTSGIVLFAKHHFAHSIIDHQLKAHAMRKMYLAVVSGELTTDHGW 180

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                    +   K            +  +  +  +   V V L  G+  +I+  F    
Sbjct: 181 LDAPIGRAADSFIKRTTRPDGKPSLTEYWVVKRLCNMTVVRVRLHTGRTHQIRVHFAASG 240

Query: 210 WK 211
             
Sbjct: 241 HP 242


>gi|253701860|ref|YP_003023049.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776710|gb|ACT19291.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 302

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 77/231 (33%), Gaps = 57/231 (24%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------VPLRKA-----ERTRLWLY 78
           +++I+   VKVNG  +  AA  +   D + +            L        E + +   
Sbjct: 32  KKLISSGHVKVNGSSV-EAAQLLKYADQVTLKESSKTAAFLARLTPELDILFEDSWIISL 90

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLAR 132
           +K  GL    ++      + D   ++        R+  V RLD  T G ++L      A 
Sbjct: 91  NKAPGLSVHRTEDPDEVNLVDLAETLLQKRDGVGRLRPVNRLDKGTSGAIILAKSAVAAG 150

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
           +    +      ++Y     G++        K+G++            LD ++   +++ 
Sbjct: 151 MFGKMVQEEGLGKLYLALVEGKLQ-------KQGVI---------DAPLDGKESQTSYLR 194

Query: 191 --------------VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                         +    G+  +I++ F+     +    R  YG   L  
Sbjct: 195 LFHGGGVSLLAVYPIT---GRMHQIRQHFKMIGHPILGDKR--YGGRALTG 240


>gi|167836421|ref|ZP_02463304.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           thailandensis MSMB43]
          Length = 344

 Score = 60.2 bits (145), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 79/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     IE+        
Sbjct: 15  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVDGAPAK-IRQPVPLGATIELLPDLLPEQ 73

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 74  LAFTPEPVPLSIVYEDEAIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 133

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD  T GL+++         L     +    R Y     G           + +D  
Sbjct: 134 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALVWGQMPDKGTIDAPIGRDPR 193

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G         +DT   ++   + +   L  G+  +I+         
Sbjct: 194 ERTRMAVVTGAAGKPARTHFRAVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 251


>gi|42520290|ref|NP_966205.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila melanogaster]
 gi|42410028|gb|AAS14139.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila melanogaster]
          Length = 307

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 58/175 (33%), Gaps = 42/175 (24%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           R+ + I       RR         +E+ + +  +KVN    + +   V S   I +    
Sbjct: 16  RLDRYI-------RRIFPDLKQSVIEKSLRKGLIKVNDCKAKSSD-RVNSGQTITLKHLN 67

Query: 63  -----------DGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                      +   +         E   +   +KP G++        + ++ D L  I 
Sbjct: 68  YIENANSDRKYNEKLVNLLRENILYEDEYILAINKPAGVIVQGG-VKVKISMSDLLDQIR 126

Query: 106 SR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                  V RLD +T G+++   +  +AR L       +  + Y     G   +D
Sbjct: 127 EGETFKIVHRLDRDTSGVIIFARNANVARYLMEEFKGRRVKKTYLALTSGIPSKD 181


>gi|34497801|ref|NP_902016.1| pseudouridylate synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103657|gb|AAQ60018.1| probable pseudouridylate synthases [Chromobacterium violaceum ATCC
           12472]
          Length = 249

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 30/166 (18%), Positives = 54/166 (32%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   HKP  L+   ++ D   T F        I  RV  V RLD  T G LL   D    
Sbjct: 11  LIAIHKPSNLLVHRTELDRHETRFAIQMLRDQIGRRVYPVHRLDKGTSGALLFALDKDAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ------------DKLNLLKKGIV-------IQGI 170
           R L L     Q  + Y     G  D             D L  + + +            
Sbjct: 71  RELSLQFERQQVYKRYLAVVRGHPDDAGHIDHPLSRRPDDLEWIGEKVETAPQPAVTDYR 130

Query: 171 CYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVN 213
               +++ +  ++      + + +  + G+  ++++  +     + 
Sbjct: 131 TLARVELPIMVERYPTSRYSLLELEPQTGRKHQLRRHLKHIAHPII 176


>gi|324992871|gb|EGC24791.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK405]
 gi|325696535|gb|EGD38425.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK160]
 gi|327460322|gb|EGF06659.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1057]
          Length = 295

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERIGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|295109974|emb|CBL23927.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 330

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 87/256 (33%), Gaps = 64/256 (25%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           MK+  I  +N   QR  K +A+  G A +    +M+ ++ + +NG         + + D 
Sbjct: 1   MKEFQIT-DNEAGQRFDKYLAKLLGNAPKSFFYKMLRKKNITLNGKKA-SGNEKLKNGDQ 58

Query: 60  IEV---DGVPLRKAERTR----------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
           I++   D    + +++ +                + L  KP+G+++   D    S V   
Sbjct: 59  IKLFLSDDTFAKFSQQEQTARAVTDLDILYEDSDILLISKPVGMLSQPDDTKEPSLVEYL 118

Query: 101 LPSIFS------------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYR 146
           +  + +                  RLD NT G++         + L          + Y 
Sbjct: 119 IGYLLNNGSITEEGLRTFHPSVCNRLDKNTSGIVAAGKSLAGLQELSSLFHDRTIHKDYL 178

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSNAW--------------- 188
               G +  +K         I+G  Y D    +VT+   K  +A                
Sbjct: 179 CIVKGILTDNK--------QIRGYLYKDTKLNKVTISKIKIKDAQPIETRYEPLGHTSHM 230

Query: 189 --VTVGLREGKNREIK 202
             + V L  G+  +I+
Sbjct: 231 TLLRVRLITGRTHQIR 246


>gi|156742179|ref|YP_001432308.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
 gi|156233507|gb|ABU58290.1| pseudouridine synthase [Roseiflexus castenholzii DSM 13941]
          Length = 309

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 78/252 (30%), Gaps = 52/252 (20%)

Query: 25  IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGV--------PLRKAER 72
           + S  E   +IA+  V VNG  +    V +     + V    DG+         +   E 
Sbjct: 22  LGSEGEAAWLIARGGVWVNGRRVRDPDVRLPVDATVVVQRPPDGIYRDPVVTSAMILYED 81

Query: 73  TRLWLYHKPIG--LVTTHSDPDG--RSTVFDNL---PSIFSRVISVGRLDINTEGLLLLT 125
             L    KPI   +  T  D +G  R+ +   L         +    RLD +T G+LLL+
Sbjct: 82  ADLIALDKPIDTYVEATPWDAEGHLRAALAHFLEVRDGSAPPLHLAHRLDRDTSGVLLLS 141

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL------KKGI--VIQGICYGDM 175
               +   L+         + Y     G    D++ +       + G+  V      G  
Sbjct: 142 KAPDVNAALQRAFREGAVRKTYLALCAGLPAFDEIEIETGHGRGRGGVFRVFPHEEIGRA 201

Query: 176 QVTLDTQKGSNAWVTVG-------------LREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                T K     + V              L  G+  +I+    F    +        G 
Sbjct: 202 LPQGGTVKAMRTRLRVVRRMDDAALACATPLT-GRTHQIRLHLAFLGHPL-------IGD 253

Query: 223 FQLGTLLAGSTR 234
            + G     + R
Sbjct: 254 VKYGG--PSTWR 263


>gi|332360478|gb|EGJ38289.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK355]
          Length = 295

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVIYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


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

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 40/251 (15%), Positives = 88/251 (35%), Gaps = 56/251 (22%)

Query: 3   DKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++  V+      R+ +         G      +++++   +++V+G  ++ A   V    
Sbjct: 5   EQITVEAGEAGMRLDRWFKTHFPGLGFG---HLQKLLRSGQIRVDGGRVK-ADSRVEPGQ 60

Query: 59  HI-----EVD--------GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDG 93
            +     EVD        G  +R              E  ++++++KP GL         
Sbjct: 61  VVRVPPLEVDKKGESPLTGHSIRNQGDADVLAKMLIHEDPKVFVFNKPAGLAVQGGSGVT 120

Query: 94  RSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
           R  V D L +  ++       V RLD +T G+L++      A  L     + +  + Y  
Sbjct: 121 R-NVDDMLEAWRNQKGEKPRLVHRLDRDTSGVLVVARTRLAAMKLSEAFRARETKKTYWA 179

Query: 148 RFHGQVD--QDKLNLL----------KKGIVIQGICYGDMQVT----LDTQKGSNAWVTV 191
              G     +DK++            +  I   G    D  V+    ++    +  W+ +
Sbjct: 180 LVKGVPPKREDKISTWLIKEPTPDGDRVRIAAHGEKGADHAVSYYRIIEQAAQTMTWLEM 239

Query: 192 GLREGKNREIK 202
               G+  +++
Sbjct: 240 EPYTGRTHQLR 250


>gi|257463597|ref|ZP_05627988.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|317061151|ref|ZP_07925636.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
 gi|313686827|gb|EFS23662.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           D12]
          Length = 289

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 95/265 (35%), Gaps = 63/265 (23%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLR------------KAERTRLWLYHKPIGLVTT 87
           + +NG  ++  A  V   + I +     +              E   L + +K   LVT 
Sbjct: 35  IYLNGKKIKNTAKKVRKLNRILIVEKEKKTGIRPMEIPLDIVYEDENLLVLNKQANLVTH 94

Query: 88  HSDPDGRST-----VFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
            +     +T     V   L +    ++     RLD+NT GL+++T +   ++      T+
Sbjct: 95  PTTKKVDATLANGVVAYFLKTTGKTMVPRFYNRLDMNTTGLIIVTKN-AYSQAYLQEKTE 153

Query: 141 WLRVYRVRFHGQVDQDKL----------NLLKKGIVI---QGICYGDMQVTLDTQ--KGS 185
             + Y+    G V+QD+             L++ + +   +G       V +  +  + +
Sbjct: 154 VRKSYQTIVKGMVEQDEFYITRPIGKVGEDLRR-VELPVEKGGQEAKTFVKVLKRFPQKN 212

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAGSTREVSKKILREQ 244
              + V L  G+  +I+      + +         G P     L  G     S++ ++ Q
Sbjct: 213 RTLLEVTLFTGRTHQIR---AHLSLE---------GYPIVGDDLYGG-----SEETIKRQ 255

Query: 245 L---------GPHLLEEAQVNLDAP 260
           L          P   EE ++ +D P
Sbjct: 256 LLHAYRLCFQNPKNAEEQEIVIDLP 280


>gi|239978958|ref|ZP_04701482.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces albus J1074]
 gi|291450838|ref|ZP_06590228.1| ribosomal large subunit pseudouridine synthase [Streptomyces albus
           J1074]
 gi|291353787|gb|EFE80689.1| ribosomal large subunit pseudouridine synthase [Streptomyces albus
           J1074]
          Length = 314

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 85/247 (34%), Gaps = 40/247 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   I+R    SR +   + A  +V V+G  + +       A + V     
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVLVDGAAVGKSERVHGGAWLEVEMPAA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  PAPVQIVAEPVEGMEIVHDDDDIVVIV-KPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------ 154
                   V RLD+ T GL+++        +L+         + Y     G  D      
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQFRERTVDKRYHALVQGHPDPMSGTI 190

Query: 155 QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFF 208
              +    +      +  +G         ++  + + + + + L  G+  +I+  +    
Sbjct: 191 DAPIGRHPQHDYKWAVTAEGKPSVTHYDLIEAYRAA-SLLDIKLETGRTHQIRVHMSAHR 249

Query: 209 NWKVNRL 215
           +  V  L
Sbjct: 250 HPCVGDL 256


>gi|327539710|gb|EGF26317.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 333

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 48/313 (15%), Positives = 102/313 (32%), Gaps = 49/313 (15%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           +V E+    R+   + ++  G  SR ++   +     +V+G ++   +  V +   +   
Sbjct: 5   VVPESANGFRIDLFLTQSCDGY-SRSQIRDAVQNDGAEVDGRIIR-PSYKVKAGQKVRFR 62

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + +PL    E   L + +KP G+V   +  +   T+   L   F  +  
Sbjct: 63  VPPPASDDTVPENIPLDILYEDDGLVVINKPAGMVVHPARGNWTGTLTSALAFRFQSLSD 122

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--- 156
           VG         RLD +T G++++  +  +   L          + Y     G++D+D   
Sbjct: 123 VGGPTRPGIVHRLDRDTSGVIVVAKNNAVHLNLAAQWHDRLVQKEYTAITFGRLDRDRDW 182

Query: 157 ------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                           +++G              +  + G    V V  + G+  +I+  
Sbjct: 183 IHASIGRHPYQRDKQAIREGHAT--SKTASTFYEVVERHGRVTRVDVRPKTGRTHQIRVH 240

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
                  +    R+ YG      L     R ++   +         E  ++ L      +
Sbjct: 241 LAHIGCPIL-CDRL-YGGHS--ELSRSQIRRLAGTEVATPGVKPTPEGEEILLSRQALHA 296

Query: 265 ETLVRDRPNIISE 277
           + L    P    E
Sbjct: 297 KALTFTNPQTGKE 309


>gi|169836316|ref|ZP_02869504.1| pseudouridine synthase [candidate division TM7 single-cell isolate
           TM7a]
          Length = 42

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGT-LLAGSTREVSKKIL 241
           +F+  N +V  L R+  G   L   L  G  RE++++ L
Sbjct: 1   MFKAVNNEVLYLKRVKMGNLSLDEKLKLGEYRELTEEEL 39


>gi|332360854|gb|EGJ38660.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK49]
          Length = 295

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|332557842|ref|ZP_08412164.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides WS8N]
 gi|332275554|gb|EGJ20869.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides WS8N]
          Length = 349

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 50/291 (17%), Positives = 91/291 (31%), Gaps = 77/291 (26%)

Query: 13  PQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
           P R+ K +       A     SR  + ++I +  V++ G  +      V       I +D
Sbjct: 20  PDRLDKALVREAPEEAAL---SRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEIALD 76

Query: 64  ----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                      +PL    E   L +  KP+G+V   +      T+ + L           
Sbjct: 77  APAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGESLSGI 136

Query: 106 ---SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG--QVDQDKL 158
               R   V R+D +T GLL++  T+        +  +    R Y    HG  +V   +L
Sbjct: 137 GGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEVSDPRL 196

Query: 159 N-------------LLKKG------------IVIQGICYGDMQVTLDTQKGSNAWVTVG- 192
                          +  G            +  +G  +   +  L  + G  + + +  
Sbjct: 197 RGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLERFGMPSVLALVE 256

Query: 193 --LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             L  G+  +I+         +             G    G  R++S K L
Sbjct: 257 CRLETGRTHQIRVHMAHAGHGLI------------GDQTYGGRRKLSPKAL 295


>gi|78066563|ref|YP_369332.1| ribosomal large subunit pseudouridine synthase D [Burkholderia sp.
           383]
 gi|77967308|gb|ABB08688.1| ribosomal large subunit pseudouridine synthase D [Burkholderia sp.
           383]
          Length = 402

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 80/240 (33%), Gaps = 38/240 (15%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNVMST-----D 58
           +   +R+ K +A+     SR  ++  I  QRV V+G   +          +        +
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIQLVPDLLPE 124

Query: 59  HIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRV 108
            +     P+      E   L + +KP GLV   +  +   T+ + L   +        R 
Sbjct: 125 QLAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPRA 184

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQD 156
             V RLD  T GL+++         L  +L +    R Y     G           + +D
Sbjct: 185 GIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEEGTIDAPIGRD 244

Query: 157 KLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +  +V    G        T+DT   Q+   + +   L  G+  +I+         
Sbjct: 245 PRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHAGHP 304


>gi|150399091|ref|YP_001322858.1| RluA family pseudouridine synthase [Methanococcus vannielii SB]
 gi|150011794|gb|ABR54246.1| pseudouridine synthase, RluA family [Methanococcus vannielii SB]
          Length = 297

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/264 (14%), Positives = 94/264 (35%), Gaps = 56/264 (21%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
             V++    +++S  ++     S + +++   ++++ VN   +      ++  + + V+ 
Sbjct: 9   RKVEKKNAGKKLSDFLSEDFELSNKMIKKYDKEKKIFVNSKNI-SLKSKLVENEVVYVNI 67

Query: 64  ----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                      +P+    E   + +  KP  +V   +      T+ + + +         
Sbjct: 68  DAGNNTIIAEEIPISVIYEDEYVMIIDKPKNMVVHETKNVVSGTLSNAISNRQKVNNQNY 127

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKK 163
           ++  V RLD++T G+L++  +   +  L         + + Y    +G +       LK 
Sbjct: 128 KIRFVNRLDMDTTGILIVAKNP-YSHYLISKQMDEGIFEKKYICVVNGHL------RLKS 180

Query: 164 GI--------------VIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           GI               ++        + T+  +  + + + + L  GK  +I+      
Sbjct: 181 GIISNPLDLGEDGIKRELKNTGKESKTKYTVIEELKNASLLEIELFTGKTHQIR------ 234

Query: 209 NWKVNRLIRISYGPFQLGTLLAGS 232
                 +   S G F +G  L G 
Sbjct: 235 ------VHLSSIGNFIIGDELYGE 252


>gi|298207134|ref|YP_003715313.1| hypothetical protein CA2559_02735 [Croceibacter atlanticus
           HTCC2559]
 gi|83849768|gb|EAP87636.1| hypothetical protein CA2559_02735 [Croceibacter atlanticus
           HTCC2559]
          Length = 283

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/230 (17%), Positives = 78/230 (33%), Gaps = 42/230 (18%)

Query: 3   DKNIVQENFTPQRVSKV--IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +K+ V+E     R+ +   +    + SR  V++ I +  + +NG   + A   +     +
Sbjct: 5   EKHTVKEVTAHIRIQEYGPLVFNTLPSRSSVKKAIKKGLIFINGKQADSAD-WIEEGQLL 63

Query: 61  EVDGVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-- 106
           EV    L+              E   + + +KP G  T+    +   T+   LP      
Sbjct: 64  EV--FQLKPTTKHFKLNLDVLFEDDYVAVINKPAGYPTSG---NFFKTIAKALPYNLKIS 118

Query: 107 -------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                      + RLD  T G+L++  T    +    +L      + Y    H   D + 
Sbjct: 119 TKNDALLIPQPIHRLDNPTSGVLVVAKTKSSQINLNKQLELKGIQKTYIAVVHNTPDSNM 178

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
           L        I G         + T K  +   ++   E     G+  +++
Sbjct: 179 L--FND--NIDGKESESKLEIIKTFKVKDDIYSLV--ELFPKTGRTHQLR 222


>gi|242240403|ref|YP_002988584.1| tRNA pseudouridine synthase C [Dickeya dadantii Ech703]
 gi|242132460|gb|ACS86762.1| pseudouridine synthase [Dickeya dadantii Ech703]
          Length = 261

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 56/188 (29%), Gaps = 38/188 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LL+   
Sbjct: 7   QDDYLVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGRHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDMQ 176
             +AR+L L     Q  + Y     G V           ++L+ +               
Sbjct: 67  PEVARMLALQFEQHQMEKTYHAVVRGYVADEGVIDYALTEELDRIAD--KYADPNKAPQP 124

Query: 177 V------------TLDTQKGSNAWVT-VGLR--EGKNREIKKVFEFFNWKVNRLIRISYG 221
                         +   +   +  + + L    G+  ++++        +        G
Sbjct: 125 AVSAYRALARAEMPVAIGRYETSRYSLLELHPKTGRKHQLRRHMAHIRHPI-------IG 177

Query: 222 PFQLGTLL 229
               G L 
Sbjct: 178 DTTHGDLR 185


>gi|160889892|ref|ZP_02070895.1| hypothetical protein BACUNI_02323 [Bacteroides uniformis ATCC 8492]
 gi|156860884|gb|EDO54315.1| hypothetical protein BACUNI_02323 [Bacteroides uniformis ATCC 8492]
          Length = 303

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 31/165 (18%), Positives = 66/165 (40%), Gaps = 19/165 (11%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            P  + + +A +   ASR +++ +++++ + V+ ++  +    +     +++     RK 
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIIYVDSVITTQYNFPLKPGMKVQISREKGRKE 80

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                     E   + +  K  GL++ ++D     T +  L     R      V  V RL
Sbjct: 81  FNHKLMKIVYEDAYIIVIEKMQGLLSVNTDRQKERTAYTILNEYVQRSGKQHRVHIVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK 157
           D +T GL++   D    R L          R Y     G++++D 
Sbjct: 141 DRDTSGLMMFAKDEKTQRTLRDNWHGIVTDRRYVAVVVGEMEKDA 185


>gi|39998250|ref|NP_954201.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|39985196|gb|AAR36551.1| RNA pseudouridine synthase family protein [Geobacter sulfurreducens
           PCA]
 gi|307635144|gb|ADI85911.2| tRNA pseudouridine-65 synthase [Geobacter sulfurreducens KN400]
          Length = 250

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 59/171 (34%), Gaps = 32/171 (18%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRST------VFDNLPSIFSRVISVGRLDINTEGLLLLT 125
              L   HKP GL+   S  D   T      V D L     RV  V RLD  T G+L+  
Sbjct: 7   DQYLVAVHKPAGLLVHRSPIDRHETRFALQEVRDLL---GRRVYPVHRLDKPTSGVLVFA 63

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---NLLKKGIVIQGIC--------- 171
            D   AR L       +  + Y     G V  + +   +L ++   + G           
Sbjct: 64  LDPATARSLGDAFAGGRVNKTYLAVTRGIVPPEGIIDHSLSEEPDRLDGAKSSPAAPQPA 123

Query: 172 ------YGDMQVTLDTQKGSNAWV---TVGLREGKNREIKKVFEFFNWKVN 213
                   + ++ + T + +++      +    G+  ++++  +     + 
Sbjct: 124 VTVFRRLAEAELPVVTGRYASSRYSLAELTPHTGRRHQLRRHMKHIFHPII 174


>gi|327470007|gb|EGF15471.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK330]
          Length = 295

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|310829101|ref|YP_003961458.1| RluA family pseudouridine synthase [Eubacterium limosum KIST612]
 gi|308740835|gb|ADO38495.1| RluA family pseudouridine synthase [Eubacterium limosum KIST612]
          Length = 304

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 32/213 (15%), Positives = 75/213 (35%), Gaps = 42/213 (19%)

Query: 25  IASR--REVERMIAQQRVKVNGI------LLERAAVNVMSTDHIEVDGVPLRKA-----E 71
            +SR  R+++R      + +NG        ++R    V++      D   +        E
Sbjct: 33  YSSRLLRQLKR---DGSITLNGRDCWLTDPVQRGDQVVITFPEERFDIEAVEGPLDIVYE 89

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLT 125
              + + +K    VT  +      T+ +++   +       ++  V RLD +T GL+++ 
Sbjct: 90  DDEVLVVNKDADCVTHPTKSHQLDTLANHVAWYWEERGTPGKIRFVNRLDRDTTGLVVIA 149

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFH--------------GQVDQDKLNLLKKGIVIQG 169
            +  +   ++    +    + Y    +              G+  +D L      IV++ 
Sbjct: 150 KNKYVHHYIQSRMKTDAVKKTYIAFVNNVPEEKEGCIRVPIGRPSEDSLER----IVMED 205

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    +     + A V + L  G+  +I+
Sbjct: 206 GKESVTHFRVLESYRNAAMVELVLETGRTHQIR 238


>gi|157828222|ref|YP_001494464.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|165932925|ref|YP_001649714.1| hypothetical protein RrIowa_0413 [Rickettsia rickettsii str. Iowa]
 gi|157800703|gb|ABV75956.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           rickettsii str. 'Sheila Smith']
 gi|165908012|gb|ABY72308.1| hypothetical protein RrIowa_0413 [Rickettsia rickettsii str. Iowa]
          Length = 303

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 62/175 (35%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A+++V   D I ++     
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNSQKA-EASLSVKGGDKIFINDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P+++ E+                         L   +KP GL T        S       
Sbjct: 66  PVKQPEKLVFTDAEIKLAKKITTDYLIYADDNLIAINKPAGLATQGGTKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGTDFKLVHRLDKKTSGLLLIAKNYLSSVKLHDAFKEKLVVKTYFAVTYGKP 180


>gi|325674393|ref|ZP_08154081.1| RluA family RNA pseudouridine synthase [Rhodococcus equi ATCC
           33707]
 gi|325554653|gb|EGD24327.1| RluA family RNA pseudouridine synthase [Rhodococcus equi ATCC
           33707]
          Length = 302

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 50/299 (16%), Positives = 89/299 (29%), Gaps = 63/299 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---------ERAAVNVMST 57
           V +     RV   +AR    SR  V  +  +  V V+G                V +   
Sbjct: 3   VPDGLDGMRVDAGLARLLGLSRTAVATLTEEGAVLVDGAAAGKSDRLSAGTWLEVELPEP 62

Query: 58  DH-IEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL---------PS 103
              + ++  P+   E       +    KP+G+    S      TV   L           
Sbjct: 63  PRPLTIEAEPVEGMEILYADDDIVAVDKPVGVAAHASVGWTGPTVIGGLAAAGFRISTSG 122

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--KLN 159
              R   V RLD+ T G++++        VL+    Q    + Y     G  D     ++
Sbjct: 123 AHERQGIVHRLDVGTSGVMVVATSERAYTVLKRAFKQRTIDKRYHALVQGHPDPSSGTID 182

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-------- 202
                      K  +   G        T++  + + + + + L  G+  +I+        
Sbjct: 183 APIGRHRSNDWKFAVTADGKPSVTHYDTVEAFQAA-SLLDIHLETGRTHQIRVHFSALRH 241

Query: 203 ------------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KKILREQLG 246
                       ++ E    +   L   S G         G   E++    K L+  LG
Sbjct: 242 PCCGDLTYGADPRLAERLGLERQWLHARSLGFAHPAD---GHWVEITSDYPKDLQHALG 297


>gi|320528517|ref|ZP_08029674.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
 gi|320131103|gb|EFW23676.1| pseudouridine synthase, RluA family [Solobacterium moorei F0204]
          Length = 287

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 39/226 (17%), Positives = 76/226 (33%), Gaps = 40/226 (17%)

Query: 19  VIARAGIASRREVER--------MIAQQRVKVNGILLERAAVNVMSTDHIE---VDGVPL 67
           V++  G  SR E+ R         + ++ VKVN  ++    V V+   +IE   +    +
Sbjct: 21  VLSSLGF-SRHEILRFKFSAYQMYLNEKPVKVN-RVVHTGDVLVIQELNIETYTLHPSTV 78

Query: 68  RK---AERTRLWLYHKPIGLVTTHSDP----DGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           R     E   + +  KP G+ +  S      D  + + D        +  +GRLD +  G
Sbjct: 79  RPDILYEDEDVVVVCKPAGMPSHPSHHHLTDDMGTLLRDYYQDEHFVIRPIGRLDKDVSG 138

Query: 121 LLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK-------------LNLLKKGI 165
           +++   +   A  L          + Y     GQ++                     +G 
Sbjct: 139 IMIYAKNQLSAARLAAQRKDGILQKHYYAIVEGQLEDKDTLIFSLIKEDGQMAQSFNQG- 197

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G      +  +     +   + V L+ G+  +I+  F      
Sbjct: 198 ---GKQCVT-EYEVIKHYQTECLIRVYLKTGRTHQIRAGFAGIGHP 239


>gi|307566026|ref|ZP_07628484.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
 gi|307345214|gb|EFN90593.1| pseudouridine synthase, RluA family [Prevotella amnii CRIS 21A-A]
          Length = 297

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/192 (22%), Positives = 72/192 (37%), Gaps = 30/192 (15%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV------DGVPLRKA----ERTRLWLYHKPIGLVT--- 86
           +KVNG ++ +    + + D I +      D    R      E   L +  K +G+++   
Sbjct: 48  IKVNGKIVTQYDYQLKAGDKISISKSKKNDQFKSRYVKLVYEDKYLVVIEKNVGILSMAA 107

Query: 87  THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--L 142
            HS  + +S + D             V RLD +T GL++   D    ++LE         
Sbjct: 108 GHSSLNVKSVLDDYFQKSKQHCRAHVVHRLDRDTSGLMVYAKDMQTEQLLEHDWHNIVYD 167

Query: 143 RVYRVRFHGQVDQDK---LNLLKKGI--------VIQGICYG-DMQVTLDTQKGSNAWVT 190
           R Y     G++ Q +    N LK           V  G  Y      T+DT   S + V 
Sbjct: 168 RRYVAVLSGELMQQQGTVANWLKDNKSYVTYSSAVDNGGKYAVTHFFTIDT-TASYSLVE 226

Query: 191 VGLREGKNREIK 202
             L  G+  +I+
Sbjct: 227 FKLETGRKNQIR 238


>gi|170733153|ref|YP_001765100.1| RluA family pseudouridine synthase [Burkholderia cenocepacia MC0-3]
 gi|169816395|gb|ACA90978.1| pseudouridine synthase, RluA family [Burkholderia cenocepacia
           MC0-3]
          Length = 360

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 80/240 (33%), Gaps = 38/240 (15%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNVMST-----D 58
           +   +R+ K +A+     SR  ++  I  QRV V+G   +          +        +
Sbjct: 23  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIALVPDLLPE 82

Query: 59  HIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRV 108
            +     P+      E   L + +KP GLV   +  +   T+ + L   +        R 
Sbjct: 83  QLAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPRA 142

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQD 156
             V RLD  T GL+++         L  +L +    R Y     G           + +D
Sbjct: 143 GIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEAGTIDAPIGRD 202

Query: 157 KLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +  +V    G        T+DT   Q+   + +   L  G+  +I+         
Sbjct: 203 PRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHAGHP 262


>gi|311748343|ref|ZP_07722128.1| ribosomal large subunit pseudouridine synthase C [Algoriphagus sp.
           PR1]
 gi|126576852|gb|EAZ81100.1| ribosomal large subunit pseudouridine synthase C [Algoriphagus sp.
           PR1]
          Length = 237

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 56/162 (34%), Gaps = 31/162 (19%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           ++D   L   E     + +KP   +++  D      + D   +         RLD  T G
Sbjct: 3   KIDFQKLILFENADYLVINKPP-YLSSLDDRHEAQNILDLAKAYTPDAQLCHRLDKETSG 61

Query: 121 LLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ-------VDQDKLNLLKKGIVIQGIC 171
            L++  +    R L +   + +  ++Y     G        VD++ +    KG+      
Sbjct: 62  CLVIAKNPEAYRHLAIQFENRKVDKIYHAVVEGIQDYQNELVDRNLIAT-NKGV------ 114

Query: 172 YGDMQVTLDTQKGSNAWVTV------GLRE-----GKNREIK 202
               +V+   +     + T+       L E     G+  +I+
Sbjct: 115 ---AKVSKGGKSAQTYFQTLKTYAAHTLVECKPVTGRLHQIR 153


>gi|56478105|ref|YP_159694.1| ribosomal large subunit pseudouridine synthase D [Aromatoleum
           aromaticum EbN1]
 gi|56314148|emb|CAI08793.1| ribosomal large subunit pseudouridine synthase D [Aromatoleum
           aromaticum EbN1]
          Length = 306

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 83/249 (33%), Gaps = 45/249 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  +  +  +    RV + +AR     SR  ++  +   RV ++G     A   V   + 
Sbjct: 1   MHHRLTIPADCAGLRVDQALARLFPSHSRSRLQGWLKSGRVSLDGDQP-DAKFKVWGGES 59

Query: 60  IEVDGVP--------------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           +EVD  P              +   E   + +  KP+GLV      +   T+ + L    
Sbjct: 60  LEVDAAPPPEAAAEAPEDIPLVVVHEDEEILVIDKPVGLVVHPGSGNWSGTLLNALLHHA 119

Query: 106 SRVISV------GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------ 151
            ++ +V       RLD +T GLL++         L  +L +    R Y    H       
Sbjct: 120 PQLAAVPRAGIVHRLDKDTSGLLVVAKTLESQTALVRQLQARTVRRHYLALVHRAVAGAG 179

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
                + +      +  +V  G      +  +   +    +  V L E     G+  +I+
Sbjct: 180 MVEAPIGRHPTQRTRMAVVQSG------RAAVTRYRPRERFARVTLVECQLETGRTHQIR 233

Query: 203 KVFEFFNWK 211
               +    
Sbjct: 234 VHMAYIGHP 242


>gi|107029027|ref|YP_626122.1| pseudouridine synthase, RluD [Burkholderia cenocepacia AU 1054]
 gi|116689814|ref|YP_835437.1| RluA family pseudouridine synthase [Burkholderia cenocepacia
           HI2424]
 gi|254248088|ref|ZP_04941409.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184]
 gi|105898191|gb|ABF81149.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia AU 1054]
 gi|116647903|gb|ABK08544.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia HI2424]
 gi|124872864|gb|EAY64580.1| Pseudouridine synthase, RluD [Burkholderia cenocepacia PC184]
          Length = 402

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 80/240 (33%), Gaps = 38/240 (15%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNVMST-----D 58
           +   +R+ K +A+     SR  ++  I  QRV V+G   +          +        +
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIALVPDLLPE 124

Query: 59  HIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRV 108
            +     P+      E   L + +KP GLV   +  +   T+ + L   +        R 
Sbjct: 125 QLAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPRA 184

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQD 156
             V RLD  T GL+++         L  +L +    R Y     G           + +D
Sbjct: 185 GIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEEGTIDAPIGRD 244

Query: 157 KLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +  +V    G        T+DT   Q+   + +   L  G+  +I+         
Sbjct: 245 PRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHAGHP 304


>gi|256848967|ref|ZP_05554401.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-1A-US]
 gi|295692522|ref|YP_003601132.1| pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|312977754|ref|ZP_07789501.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus CTV-05]
 gi|256714506|gb|EEU29493.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-1A-US]
 gi|295030628|emb|CBL50107.1| Pseudouridine synthase [Lactobacillus crispatus ST1]
 gi|310895493|gb|EFQ44560.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus CTV-05]
          Length = 301

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 32/161 (19%), Positives = 60/161 (37%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLL 123
           E     + +KP G+++  S  +    V + L   F++          + RLD +T GL+L
Sbjct: 85  ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRDTSGLVL 144

Query: 124 LTNDGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGI 170
           +  +             ++++ Y    HG    ++L  L      KKG      +V  G 
Sbjct: 145 VGKNAISHARFSKIGKEKFVKKYHAIVHGNFAPNELTGLIDQPIGKKGSGVKRAVVADGK 204

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   LD   G+ + V + L  G+  +I+    +    
Sbjct: 205 DAQTAYRVLDQVTGA-SLVELRLLTGRTHQIRVHMAYLGHP 244


>gi|307129814|ref|YP_003881830.1| tRNA pseudouridine synthase [Dickeya dadantii 3937]
 gi|306527343|gb|ADM97273.1| tRNA pseudouridine synthase [Dickeya dadantii 3937]
          Length = 261

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 57/188 (30%), Gaps = 38/188 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LL+   
Sbjct: 7   QDEHLIAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDMQ 176
             +AR+L       Q  + Y     G V +         ++L+ +               
Sbjct: 67  PEVARLLAQQFEQHQMEKTYHAVVRGYVMEDGVIDYALTEELDRIAD--KFADPDKAPQP 124

Query: 177 VTLDTQKGSNAWVTVGL---------------REGKNREIKKVFEFFNWKVNRLIRISYG 221
                +  + A + V +               + G+  ++++        +        G
Sbjct: 125 AVSHYRVLARAEMPVAIGRYDTARYSLLQLNPKTGRKHQLRRHMAHLRHPI-------IG 177

Query: 222 PFQLGTLL 229
               G L 
Sbjct: 178 DTTHGDLR 185


>gi|269101936|ref|ZP_06154633.1| tRNA pseudouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161834|gb|EEZ40330.1| tRNA pseudouridine synthase C [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 259

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 33/172 (19%), Positives = 55/172 (31%), Gaps = 31/172 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL    
Sbjct: 21  QDEYLVAVNKPSGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFALS 80

Query: 128 GGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGICYGDMQVTLDTQK 183
             +A  +          + Y     G V +  +    LKK   +  I   +     + Q 
Sbjct: 81  SEMAAEMMPKFAGRDVHKTYHAVVRGWVKEAAVLDYPLKK--ELDKIADKNASKEQEAQP 138

Query: 184 GSNAW-----VTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
              A+     V V             L E     G+  ++++     +  + 
Sbjct: 139 AVTAYAPIAKVEVPIAVGRYSCSRYSLVEMKPETGRKHQLRRHMHHLSHHII 190


>gi|295688947|ref|YP_003592640.1| pseudouridine synthase [Caulobacter segnis ATCC 21756]
 gi|295430850|gb|ADG10022.1| pseudouridine synthase, RluA family [Caulobacter segnis ATCC 21756]
          Length = 332

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/222 (15%), Positives = 64/222 (28%), Gaps = 42/222 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV---------------------DGVPLRKAE 71
           ++    +V+V+G   + A   + +   I V                         L   E
Sbjct: 39  KLFRSGQVRVDGSRAK-ADTKLAAGSQIRVPPLPDAPDPADKNKLSARDVAYAKSLVLYE 97

Query: 72  RTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              +   +KP GL              +         R   V RLD +T G+LLL     
Sbjct: 98  DEEVLALNKPAGLAVQGGTKTTKHIDKLLSAWGEGVDRPRLVHRLDRDTSGVLLLGKTPS 157

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQD----KLNLLKKGI---------VIQGICYGD 174
            A  L       +  + Y     G         +L+L K+G+           +      
Sbjct: 158 AAARLSGAFAKRKAQKTYWAIVAGNPHPTEGVMELHLAKRGVGDRELVVPAQPKDADAQP 217

Query: 175 MQ---VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   VT+        W+ +    G+  +++   +     + 
Sbjct: 218 AETEFVTISRAGPRVTWMALRPHTGRTHQLRAHMKAMGHPIL 259


>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 = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 87/248 (35%), Gaps = 41/248 (16%)

Query: 1   MKDKNIVQENF-TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  + +   +    +R    +A+    SR +   ++A    +V G  +++AAV ++  D 
Sbjct: 1   MSTRLLPAPDMLIGKRFDVALAKMTGLSRAKAAELVASGSARVLGRDVDKAAV-LLEGDM 59

Query: 60  IEVDG---VPLRKAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           IE+D     P+ +   T + + +         KP+G+    S      TV  +L      
Sbjct: 60  IEIDEHDPEPVAEPIATDMAIVYEDDDVVVVDKPVGVAAHASVGWTGPTVLGSLLDRGVH 119

Query: 108 VISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG----- 151
           + S G         RLD+ T GL+L+       + +    ++    + Y     G     
Sbjct: 120 ITSYGAAGRQGIVSRLDVGTSGLMLVCKSELAYKEMRRQFSEHEVVKTYEALVQGNLQED 179

Query: 152 ------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIKK 203
                  + + K++  +  I   G          D  +  G      + L  G+  +I+ 
Sbjct: 180 KATIDAPIGRAKVSDFRFCITPAG---KPAITHWDVLERFGEATLARINLETGRTHQIRV 236

Query: 204 VFEFFNWK 211
            F      
Sbjct: 237 HFSSIGHP 244


>gi|206560228|ref|YP_002230992.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia J2315]
 gi|198036269|emb|CAR52165.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           cenocepacia J2315]
          Length = 361

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 80/240 (33%), Gaps = 38/240 (15%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNVMST-----D 58
           +   +R+ K +A+     SR  ++  I  QRV V+G   +          +        +
Sbjct: 23  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLVDGAPAKIRQPVPLGAKIALVPDLLPE 82

Query: 59  HIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRV 108
            +     P+      E   L + +KP GLV   +  +   T+ + L   +        R 
Sbjct: 83  QLAFTPEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPRA 142

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQD 156
             V RLD  T GL+++         L  +L +    R Y     G           + +D
Sbjct: 143 GIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEAGTIDAPIGRD 202

Query: 157 KLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +  +V    G        T+DT   Q+   + +   L  G+  +I+         
Sbjct: 203 PRERTRMAVVTGASGKPARTHFRTVDTCLWQRQPVSAIQCDLETGRTHQIRVHCAHAGHP 262


>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 = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 32/60 (53%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+ K++   G+  SR   + +I   +V VNG ++++A  +V+    IE+ G  +    R
Sbjct: 5  ERLDKLLVEKGLVKSRERAKALIMAGKVLVNGQVVDKAGASVLPDAVIEIKGDDIPYVSR 64


>gi|318040274|ref|ZP_07972230.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           CB0101]
          Length = 234

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/213 (20%), Positives = 71/213 (33%), Gaps = 29/213 (13%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L + +KP GL+      P+   ++   +   + +   V RLD +T GL+L+     L R 
Sbjct: 32  LLVLNKPHGLLCQPGLGPELADSLISRVQQRWPQAQLVHRLDRDTSGLILVALASELHRE 91

Query: 134 LELP--STQWLRVYRVRFHGQVDQDK------LNLLKK-----GIVIQGICYGDMQVTLD 180
           L       Q  + Y    HG  DQ        +  L+      G+   G         L 
Sbjct: 92  LSRMFAERQVQKRYVADVHGVPDQPHGLIEWPIAKLQHRPPLYGVDPAGKACSTRWRLLQ 151

Query: 181 TQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVNR--LIRISYGPF--QLGTLLAGSTRE 235
              G  + + +  L  G++ +++   +     +    L    YGP    L     GS   
Sbjct: 152 A-HGRCSRLELQPLT-GRSHQLRVHLQAIGHPILGDPL----YGPLASALDD-PLGSRLH 204

Query: 236 VSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
           +    L      H      +  DAP   S    
Sbjct: 205 LHAAALH---WLHPGSSESLAFDAPPPFSLPSP 234


>gi|119961612|ref|YP_947480.1| RNA RluA family pseudouridine synthase [Arthrobacter aurescens TC1]
 gi|119948471|gb|ABM07382.1| putative RNA pseudouridine synthase, RluA family [Arthrobacter
           aurescens TC1]
          Length = 308

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 81/259 (31%), Gaps = 59/259 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-H 59
           M    +V E     RV   +AR    SR     +I++  V   G+ L ++A  V  T   
Sbjct: 1   MSRSVVVPEELAGARVDAGLARLLDISRSAAALLISEGNVTSGGVPLGKSAKLVAGTVLD 60

Query: 60  IEV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V              +G+ +   +   + +  KP+G+    S      TV   L    
Sbjct: 61  VTVPERPDPLEVVEEVVEGLKILLDDEDFVVI-DKPVGVAAHPSPGWVGPTVVGGLAGAG 119

Query: 106 SRVI---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD 154
            R+           V RLD+ T G++++        VL+    +    +VY     G  D
Sbjct: 120 YRISTSGAPERAGIVHRLDVGTSGVMVVAKTEHAYTVLKRAFKERTVEKVYHAVVQGLPD 179

Query: 155 QDKLNLLKKGIVIQGICYGDM---------QVTLDTQKGSNAWVTV-------GLRE--- 195
                       ++G     +            ++  + S     V        L E   
Sbjct: 180 P-----------LEGTIDAPIGRHPGHDWRFAVIEDGRPSVTHYEVLEAFGKATLVEVHL 228

Query: 196 --GKNREIKKVFEFFNWKV 212
             G+  +I+  F       
Sbjct: 229 ETGRTHQIRVHFSALRHPC 247


>gi|325694474|gb|EGD36383.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK150]
          Length = 295

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|32033504|ref|ZP_00133831.1| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Actinobacillus pleuropneumoniae serovar 1 str. 4074]
 gi|126208338|ref|YP_001053563.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae L20]
 gi|126097130|gb|ABN73958.1| tRNA pseudouridine synthase C [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 247

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/202 (18%), Positives = 68/202 (33%), Gaps = 39/202 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   T F        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKHETQFAMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSEMA 71

Query: 132 RVLEL---PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGD------------- 174
             L        Q  + Y     G  +D+ +++   K +++  I                 
Sbjct: 72  -RLMSEQFEQHQLKKGYLAVVRGYLLDKGEIDYPLK-VILDKIADKFSQPKEAQQAVTFY 129

Query: 175 ---MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                V +    G +      L E     G+  ++++  +     +        G  + G
Sbjct: 130 QNLASVEMLYPAGKHQTARYSLVELLPKTGRKHQLRRHMKHLFHPI-------MGDTKYG 182

Query: 227 TLLAGSTREVSKKILREQLGPH 248
            L     R +++K   ++L  H
Sbjct: 183 DLH--QNRTLTEKTGCDRLMLH 202


>gi|125718029|ref|YP_001035162.1| 23S rRNA pseudouridine synthase [Streptococcus sanguinis SK36]
 gi|125497946|gb|ABN44612.1| 23S rRNA pseudouridine synthase, putative [Streptococcus sanguinis
           SK36]
          Length = 295

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|328948648|ref|YP_004365985.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
 gi|328448972|gb|AEB14688.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
          Length = 317

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 70/226 (30%), Gaps = 47/226 (20%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA----------- 70
           G  S  ++ R+I    V +N       +  + S   I+V  D                  
Sbjct: 28  GEISNSKIRRLIVSGAVYINSRQCRIPSFKINSGTAIKVLIDKEKFFFEKQPEDADFELT 87

Query: 71  ------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRL 114
                 E   L   +KP  L T  +    R    D                  V  + RL
Sbjct: 88  ENDVLFEDEYLIAINKPPFLPTEQTITGQRKNAHDCTVKYLWQKNSSLRNPPYVGIMHRL 147

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---LNLL-------- 161
           D  T G+LL T    + + +     +    ++YR    G++ + K   +           
Sbjct: 148 DRETSGILLFTKSRSVNKDISEMFKTRGIKKIYRAVCTGKLPEQKEFTVENFIARISPKS 207

Query: 162 ---KKGIVIQ--GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              K GIV +  G  +      + ++K     +   L  G+  +I+
Sbjct: 208 SACKMGIVPESRGGLFTKTDFKIISEKNGFIQIDCQLHTGRTHQIR 253


>gi|299136326|ref|ZP_07029510.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
 gi|298602450|gb|EFI58604.1| pseudouridine synthase, RluA family [Acidobacterium sp. MP5ACTX8]
          Length = 446

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 44/258 (17%), Positives = 81/258 (31%), Gaps = 51/258 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V+      R+   +A+A    SR  V  +I + +V V+G   +         + IE++G
Sbjct: 122 TVEPAAKEMRLDAYLAKAIPDISRARVVLLIEKGQVTVDGNPGKGKQKL-KGGEMIEIEG 180

Query: 65  VPLRKA--------------ERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFS- 106
            P  +               E   L +  K  G++           R T+ + L      
Sbjct: 181 EPRPEPLHAQPEDIPLTIVYEDDDLAVVDKAAGMMVHAGAGDSERNRGTLVNALLFHMGK 240

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG---- 151
                    R   V RLD  T GL+++  +    R L       +  +VY    HG    
Sbjct: 241 SLSQVSGDLRPGIVHRLDKQTSGLIVVAKNDSTHRKLSEMFSERRLRKVYLALVHGWIAP 300

Query: 152 ------------QVDQDKLNLLKKGIVIQGICYG----DMQVTLDTQKGSNAWVTVGLRE 195
                        + +D +  ++      G         +   +    G  + V V +  
Sbjct: 301 ATGAQDSGTIQLPISRDLVRRIRMTTRRSGGRSAVSHWRVLEKISGPYGKFSLVEVRIET 360

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +I+   +     V 
Sbjct: 361 GRTHQIRVHMQAIGHPVV 378


>gi|146338456|ref|YP_001203504.1| pseudouridine synthase [Bradyrhizobium sp. ORS278]
 gi|146191262|emb|CAL75267.1| pseudouridine synthase (pseudouridines 1911, 1915, 1917 in 23S RNA)
           [Bradyrhizobium sp. ORS278]
          Length = 384

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 83/251 (33%), Gaps = 57/251 (22%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKV------NGILLERAAVNVMSTDHIEVD-GVP 66
           R+ +V+A R    SR  ++ +I   +V +      +G  +   A +V + D I +D    
Sbjct: 66  RLDRVLAARLPELSRSRLKALILAGQVSLTSDSFGSGA-VRDPAYHVTTGDTITIDVPEA 124

Query: 67  LRKAERTR------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------- 105
           +    +              + +  KP GLV   +      T+ + L +           
Sbjct: 125 VAPEPQAEAIPLQIIYEDDDIIVIDKPSGLVVHPAAGHETGTLVNALIAHCGASLSGIGG 184

Query: 106 -SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQV----- 153
             R   V RLD +T GL+++  +      L        R       Y     G       
Sbjct: 185 VKRPGIVHRLDKDTTGLMVVAKNDMAHASLSAQFADHGRTGAMERGYLAFAWGVPHRPHG 244

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNRE 200
                       +DK+ +  KG   + I + ++Q +   + G    + +   L  G+  +
Sbjct: 245 TINAAIDRHPHARDKMAVRAKGR--EAITHYEVQESFTGRDGKPVASLIACHLETGRTHQ 302

Query: 201 IKKVFEFFNWK 211
           I+         
Sbjct: 303 IRVHLAHLGHP 313


>gi|256394870|ref|YP_003116434.1| pseudouridine synthase [Catenulispora acidiphila DSM 44928]
 gi|256361096|gb|ACU74593.1| pseudouridine synthase, RluA family [Catenulispora acidiphila DSM
           44928]
          Length = 312

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 63/176 (35%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           + +    +R+   +AR    SR     + A+ RV+V+G    ++   V       IE   
Sbjct: 12  IPDGLEGERLDAALARMFGLSRTRAAELAAEGRVRVDGSEAGKSD-RVRGGAWLEIELPA 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                      V+G+ +   +   + +  KP+G+    S     +TV   L +   R+  
Sbjct: 71  AADPVAVKAEAVEGMRIVHDDEDIVVI-DKPVGVAAHPSPGWLGTTVVGGLAAAGYRIST 129

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                    V RLD+ T GL+++        +L+         + Y     G  D 
Sbjct: 130 SGASERQGVVHRLDVGTSGLMVVAKSERAYTLLKQAFRDRTVDKRYHTLVQGHPDP 185


>gi|125623253|ref|YP_001031736.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|124492061|emb|CAL96989.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070003|gb|ADJ59403.1| ribosomal large subunit pseudouridine synthase [Lactococcus lactis
           subsp. cremoris NZ9000]
          Length = 293

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 49/286 (17%), Positives = 97/286 (33%), Gaps = 63/286 (22%)

Query: 20  IARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV------------ 62
           + R GI SRR    ++ +      ++ VNG + + A   +   D + +            
Sbjct: 18  LGRHGI-SRR----LLTKVKFDGGQIMVNG-IEKTAIYRLEKGDLVTITVPDEPDNEKLI 71

Query: 63  -DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGR 113
            D VPL    E     +  KP G  +          + + +    SR       V  + R
Sbjct: 72  PDDVPLNVLFEDDHYLVVEKPAGKASITGSLHPTGAMSNAVKGYISRKNYPNQTVHIITR 131

Query: 114 LDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRFHG-----------QVDQDKLN 159
           LD +T G++ L      A  L +         + Y    +             + +   +
Sbjct: 132 LDRDTSGIMFLAKH-RYAHALMVQHKFRDTLEKRYYAIINDGDLPDSGQIDLPIGRRDDS 190

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           ++++ +         +   + T++ ++ A + + L  G+  +I+  F    +        
Sbjct: 191 IIERQVRFDEKSKNALTSYVVTERKNDLALLDIILHTGRTHQIRVHFSHLGY-------- 242

Query: 219 SYGPFQLGTLLAGSTREVSKKILR----EQLGPHLLEEAQVNLDAP 260
              P     L  G+   +S++ L     + L P   E   V LD P
Sbjct: 243 ---PLVGDDLYGGNHDLISRQALHCHHLQFLNPFTDEMVHVELDMP 285


>gi|18855035|gb|AAL79727.1|AC091774_18 putative ribosomal large subunit pseudouridine synthase [Oryza
           sativa Japonica Group]
          Length = 275

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 38/168 (22%), Positives = 59/168 (35%), Gaps = 26/168 (15%)

Query: 15  RVSKVI-ARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------- 60
           R+   I AR G    SR  ++  I    V VNG  + + +  V   D +           
Sbjct: 73  RIDAWISARLGGGGVSRARIQASIRAGLVVVNGRPVSKVSHMVKGGDIVSCTVLELQPLR 132

Query: 61  -EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVIS 110
            E + +PL    E   L + +KP  +V   +  +   T+ + +             R   
Sbjct: 133 AEPEDIPLDIVYEDDHLLVVNKPAHMVVHPAPGNANGTLVNAILHHCKISTFTSLVRPGI 192

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
           V RLD  T GLL++  D      L          RVY     G  + +
Sbjct: 193 VHRLDKGTSGLLVVAKDEHSHAQLAEQFKLHTIRRVYISLTCGAPNPN 240


>gi|81428927|ref|YP_395927.1| pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610569|emb|CAI55620.1| Pseudouridylate synthase, 23S rRNA-specific [Lactobacillus sakei
           subsp. sakei 23K]
          Length = 300

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 67/196 (34%), Gaps = 35/196 (17%)

Query: 40  VKVNGILLERAAVNVMSTDHI-------------EVDGVPLRKAERTRLWLY-HKPIGLV 85
           V++N  L    A  V + D +              V GVP++       WL  +KP GL 
Sbjct: 40  VRLNNRL-SSPADQVQNGDQVSLTLPAELADETVAVSGVPIKVLYEDDYWLVVNKPAGLA 98

Query: 86  TTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELP- 137
           T     +   T+ + +   + +          + RLD +T G++L      +A+ L  P 
Sbjct: 99  TIPGPTNTTDTLLNRIKGYWQQNGATDLVPHIITRLDFDTSGIVLAAKH-QVAQSLLQPQ 157

Query: 138 --STQWLRVYRVRFHGQ--VDQDKLNLL--KKGIVIQGICYGDMQVTL-----DTQKGSN 186
               Q  + Y     G    +   +     + G+  +     D Q          Q    
Sbjct: 158 IEQHQLQKFYLAVVAGTGLPEFGTIKAPIGRVGVEPRRRVIADGQSAWTDYWRLAQDERL 217

Query: 187 AWVTVGLREGKNREIK 202
             + V +  G+  +I+
Sbjct: 218 TVLKVQIHTGRTHQIR 233


>gi|323351544|ref|ZP_08087198.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
 gi|322122030|gb|EFX93756.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis VMC66]
          Length = 295

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 59/171 (34%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +          +  Q G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-KDGKCAHTSYKIIEQFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|313889381|ref|ZP_07823029.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
 gi|313122213|gb|EFR45304.1| pseudouridine synthase, RluA family [Streptococcus pseudoporcinus
           SPIN 20026]
          Length = 296

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 35/211 (16%), Positives = 70/211 (33%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK-----------AERTRLWLYHKP 81
              R+ VNG +   A   +   D + +   +  P  K            E     + +KP
Sbjct: 33  KGGRIAVNG-IERNAIYLLDIGDIVSITIPNERPFEKLEAISHPLDIVYEDDHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  VGYASIPS-AIHSNTIANFIKGYYVEQDYPNKQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G             + + K +++ + +   G         + 
Sbjct: 151 DKQLQARAIEKRYFALVSGDGQLPDQGEIIAPIGRSKDSIITRTVDPMGKYARTSYQVVG 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RYAENVHLVDIKLHTGRTHQIRVHFSHIGFP 241


>gi|308048661|ref|YP_003912227.1| tRNA pseudouridine synthase C [Ferrimonas balearica DSM 9799]
 gi|307630851|gb|ADN75153.1| tRNA pseudouridine synthase C [Ferrimonas balearica DSM 9799]
          Length = 247

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 54/173 (31%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTND 127
           +   L   HKP GL+   S  D   T F    +  +    V  V RLD  T G+LL T  
Sbjct: 7   QDDHLVAVHKPSGLLVHRSWLDRHETQFAMQMTRDAVGCHVFPVHRLDRPTSGVLLFTKS 66

Query: 128 GGLARVLELPS---TQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGI------------- 170
              A  +           + Y     G V +  +L+   K + +  I             
Sbjct: 67  AETA-RIMSEKMAAHDIDKHYLALVRGYVHEAGELDYALK-VELDDIADKMADKDKAPQE 124

Query: 171 ------CYGDMQVTLDTQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
                     +++     +   +  ++     L  G+  ++++        + 
Sbjct: 125 AVTRYRPLAQVELPFAVGRYPTSRYSLMALEPLT-GRKHQLRRHMAHLRHPIV 176


>gi|78047980|ref|YP_364155.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
 gi|78036410|emb|CAJ24101.1| pseudouridylate synthase [Xanthomonas campestris pv. vesicatoria
           str. 85-10]
          Length = 328

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 99/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            + +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RINEEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFRLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDEKYGEA-DVNKR-LRDQLGLKRL 291


>gi|332654861|ref|ZP_08420603.1| ribosomal large subunit pseudouridine synthase D [Ruminococcaceae
           bacterium D16]
 gi|332516204|gb|EGJ45812.1| ribosomal large subunit pseudouridine synthase D [Ruminococcaceae
           bacterium D16]
          Length = 301

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 78/246 (31%), Gaps = 45/246 (18%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           I+      +R+   +A   +   +R   +R++ Q  V   G  L++ A        +EV 
Sbjct: 5   ILTAQEGGERLDAFVASQ-VEDLTRSAAQRLLEQGAVTSGGKPLKKNA-KTTPGMVVEVL 62

Query: 63  --DGVPLR----------KAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLP 102
             D  P+             E   + + +KP+GLV   +      T+         D+L 
Sbjct: 63  LPDPQPVEIVPQNIPLDVVYEDDDVIVVNKPVGLVVHPAPGHPDGTLVNALLYHCGDSLS 122

Query: 103 SIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD-- 156
            I   +    V R+D +T GL++   +      L   L      RVY     G   +D  
Sbjct: 123 GINGELRPGIVHRIDRDTSGLIIAAKNDRAHLALAAQLQDHTLARVYEAVAVGGFKEDRG 182

Query: 157 -----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                          +   +  +G         L    G    +   L  G+  +I+   
Sbjct: 183 TVNAPIGRHPVDRKKMA--VDPKGRPAVTHWKVLGRYPGCTH-LECRLETGRTHQIRVHM 239

Query: 206 EFFNWK 211
            +    
Sbjct: 240 AYLGHP 245


>gi|257069409|ref|YP_003155664.1| pseudouridine synthase, RluA family [Brachybacterium faecium DSM
           4810]
 gi|256560227|gb|ACU86074.1| pseudouridine synthase, RluA family [Brachybacterium faecium DSM
           4810]
          Length = 318

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 41/231 (17%), Positives = 76/231 (32%), Gaps = 51/231 (22%)

Query: 15  RVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+ K +       R  V+        R++ Q +++VNG   ++    + + D I V  + 
Sbjct: 28  RLDKFL-------RSRVKGVPAGLLFRLLRQGKLRVNGRKAQQ-NYRLQAGDEITVPALR 79

Query: 67  LRK---------------------AERTRLWLYHKPIGLVTTH-SD-PDGRSTVFDNLPS 103
           +                        E   L +  KP G+     +D P G       L  
Sbjct: 80  IDADAAPPPAVPPALIQQLRGTALHEDEDLLIIDKPAGVAVHRGTDVPAGVIDALRQLRP 139

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL----PSTQWLRVYRVRFHGQVDQDK-- 157
               +  + RLD +T G+L L     + R L         +  R Y     G    +   
Sbjct: 140 ELPDLELIHRLDRSTSGVLALAKSPSMLRYLHDLLRDREDEIERRYLALVAGHWPAETTI 199

Query: 158 ----LNLLKKGIVIQ-GICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
               L   +  +V+       +  V +  + G+    + V L  G+  +I+
Sbjct: 200 LDAPLRREENRVVVDPDGQRAETHVAVAQRFGNRATLLEVRLLTGRKHQIR 250


>gi|254252275|ref|ZP_04945593.1| Pseudouridine synthase RluD [Burkholderia dolosa AUO158]
 gi|124894884|gb|EAY68764.1| Pseudouridine synthase RluD [Burkholderia dolosa AUO158]
          Length = 400

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 84/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV+++G   +     V     IE+      
Sbjct: 64  SLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRIDGAPAK-IRQPVPLGATIELVPDLLP 122

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP G+V   +  +   T+ + L   +        R
Sbjct: 123 EQLAFTPEPVPLDVVYEDDALVVINKPAGVVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 182

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 183 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEAGTIDAPIGR 242

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 243 DPRERTRMAVVTGASGKPARTHFRTVDTCVWQRQPVSAIQCDLETGRTHQIRVHCSHVGH 302

Query: 211 K 211
            
Sbjct: 303 P 303


>gi|52079396|ref|YP_078187.1| putative pseudouridine synthase YhcT [Bacillus licheniformis ATCC
           14580]
 gi|52784756|ref|YP_090585.1| YhcT [Bacillus licheniformis ATCC 14580]
 gi|319646823|ref|ZP_08001052.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
 gi|52002607|gb|AAU22549.1| putative Pseudouridine synthase YhcT [Bacillus licheniformis ATCC
           14580]
 gi|52347258|gb|AAU39892.1| YhcT [Bacillus licheniformis ATCC 14580]
 gi|317391411|gb|EFV72209.1| pseudouridine synthase [Bacillus sp. BT1B_CT2]
          Length = 305

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 59/305 (19%), Positives = 102/305 (33%), Gaps = 77/305 (25%)

Query: 29  REVER-------MIAQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLR 68
           RE +         IA ++VKVN   +    V + S D + +D             G    
Sbjct: 27  REAKASKPVIQYWIANEKVKVNHKSVNH-NVRLESGDSVMIDLREEEESGIVPEYGELPV 85

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLL 122
             E   + + +KP G+ T  ++     T+ + +   F       +V  V RLD +T G +
Sbjct: 86  LFEDDHMLIVNKPAGMATHPNEAGQTGTLSNLVAFYFQMNGEERKVRHVHRLDKDTSGAV 145

Query: 123 LLTNDGGLARVLELPS---TQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQ 168
           +      LA  L        +  R Y     G            + +DK + +++ +   
Sbjct: 146 VFAKH-RLAHALLDEQLQRKELARTYVAVAEGKFRKKTGTISAPIGRDKHHPVRRRVSHS 204

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLR----E-GKNREIKKVFEFFNWKVNRLIRISYGPF 223
           G       VT    KG ++   V L     E G+  +I+                   P 
Sbjct: 205 GQPA----VTHFESKGYDSRHDVTLCRLQLETGRTHQIRVHLASIGH-----------PL 249

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFT 283
              TL  GS      K L ++   H +E         I  +  + ++R  + + +PDD  
Sbjct: 250 SGDTLYGGS------KGLFQRQALHAIE---------INVTHPITKERVTVAAPLPDDLK 294

Query: 284 RMKKN 288
                
Sbjct: 295 DEIGR 299


>gi|301168046|emb|CBW27632.1| putative tRNA pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 254

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 54/147 (36%), Gaps = 22/147 (14%)

Query: 71  ERTRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +  ++ +  KP GL+      + + R  +   +      RV  + RLD    G+LL   +
Sbjct: 19  QDEQVVIVTKPSGLLVHPYWKETNERDNLMRRVRDQIGQRVYPIHRLDRPVSGVLLFGLN 78

Query: 128 GGLARVLE---LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           G + + ++      T+  + Y     G+++ +       G+        D ++  D    
Sbjct: 79  GEIVKRIQEHWHDKTKVHKEYLALVFGEIENE-------GV-FDFQLTNDKKIKQDALTK 130

Query: 185 SN--------AWVTVGLREGKNREIKK 203
                       + + +  G+  +I++
Sbjct: 131 YRPLQSSERATLMQITIETGRTHQIRR 157


>gi|126435691|ref|YP_001071382.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           JLS]
 gi|126235491|gb|ABN98891.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           JLS]
          Length = 304

 Score = 59.8 bits (144), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 78/243 (32%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---------AAVNVMS- 56
           V E     RV   ++R    SR     +    RV ++G    +           V +   
Sbjct: 3   VPEGLGGMRVDAGLSRLLGLSRTAAAAIAEDGRVDIDGAPAGKSDRLTAGAWLEVRLPEA 62

Query: 57  -----TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   +E++G+ +  ++   +    KP G+    +      TV   L          
Sbjct: 63  PPPVENTPVEIEGMAVLYSDDD-IVAVDKPPGVAAHATVGWHGPTVLGGLAAAGFRISTS 121

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--KL 158
            I  R   V RLD+ T G++++        VL+    Q    + Y     G  D     +
Sbjct: 122 GIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHPDPSSGTI 181

Query: 159 NL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +           K  +   G        TL+  + + + + + L  G+  +I+  F   +
Sbjct: 182 DAPIGRHRGHDWKFAVTEGGRHSVTHYDTLEAFQAA-SLLDIELETGRTHQIRVHFAALH 240

Query: 210 WKV 212
              
Sbjct: 241 HPC 243


>gi|313672604|ref|YP_004050715.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
 gi|312939360|gb|ADR18552.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
          Length = 254

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 72/191 (37%), Gaps = 31/191 (16%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----------IEVD 63
            +VS +I++    S+R  ++ + ++RV   G +++     V   D           I+ +
Sbjct: 1   MKVSDIISKQYNISKRLAKKYLKERRVSYQGKIVKD-DYIVDQFDDKFVLEVSCPDIDFN 59

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                  +   +  ++KP  + T    P     + D L + F     + RLD  T+G++ 
Sbjct: 60  LKDFLLDDLGDIIFFYKPPFMHTERHKPTDELCLSDILNNEFKDFRFISRLDFETDGVIA 119

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY---GDMQVTLD 180
               G           +  + YR    G +++         I+I           +V++ 
Sbjct: 120 AIKTGYQ-------PVKVHKRYRAWVKGILNE---------IIIFDKKIDANKRKKVSII 163

Query: 181 TQKGSNAWVTV 191
            +KG N ++ +
Sbjct: 164 DEKGDN-FLRI 173


>gi|284037752|ref|YP_003387682.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283817045|gb|ADB38883.1| pseudouridine synthase, RluA family [Spirosoma linguale DSM 74]
          Length = 308

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 30/230 (13%), Positives = 78/230 (33%), Gaps = 43/230 (18%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---- 74
           +IA+    +R  ++ +++ +++ V+G +  +    +     + V      +  + R    
Sbjct: 32  LIAQLPHKNRNNIKSLLSNKQILVDGKVFTQFNHPLKPGQSVTVAANRAPQTSQYRGLTI 91

Query: 75  ------LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLL 122
                 L + +K  GL++  ++ +   T +  L       +  +++  + RLD  T G++
Sbjct: 92  LYEDQFLIVINKQAGLLSMATNKERDRTAYGILSEYTKKENPKNKIFIIHRLDRETSGVM 151

Query: 123 LLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           +      +   L   S       R Y     G  +        +G +   +      +  
Sbjct: 152 MFAKSEKVQ-RLMQESWNATTKERTYVALVEGIPEPP------QGTITSYLRESKALIVY 204

Query: 180 DTQKGSNAWVTVG------------LRE-----GKNREIKKVFEFFNWKV 212
            +Q      +++             L E     G+  +I+   +     V
Sbjct: 205 SSQNPDTGQLSITNYTVTKTGNGYALLELELETGRKNQIRVHMQDIGHPV 254


>gi|255655078|ref|ZP_05400487.1| putative pseudouridylate synthase [Clostridium difficile QCD-23m63]
 gi|296451065|ref|ZP_06892807.1| RluA family pseudouridine synthase [Clostridium difficile NAP08]
 gi|296880582|ref|ZP_06904544.1| RluA family pseudouridine synthase [Clostridium difficile NAP07]
 gi|296260072|gb|EFH06925.1| RluA family pseudouridine synthase [Clostridium difficile NAP08]
 gi|296428536|gb|EFH14421.1| RluA family pseudouridine synthase [Clostridium difficile NAP07]
          Length = 300

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 73/212 (34%), Gaps = 45/212 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRKAERTRLWLYHKPIG 83
            ++ V VNG + ++ ++ V S D IEV            D       +   + + +K   
Sbjct: 42  REKSVLVNG-VYKKPSLKVYSGDLIEVKINEEKANFEPQDLNLQIIYDDFDIIMVNKLPF 100

Query: 84  LVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           +V   +      T+      + +      ++  V RLD+NT GL+++  +      L   
Sbjct: 101 MVVHPTKSHYDKTIANGISYYIDNQKENVKIRFVNRLDMNTSGLVIVAKNAYAHHTLSTA 160

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD----MQVTLDTQKGSN----- 186
           +   +  + Y     G + ++      +G  I    Y      ++  +D +  S+     
Sbjct: 161 MSENKVEKKYITVVDGIIKEN------EG-TIDEPIYRPTEDSIKRIIDERGQSSVTHYK 213

Query: 187 --------AWVTVGLREGKNREIKKVFEFFNW 210
                     + V L  G+  +I+        
Sbjct: 214 VIERLENATVLEVSLETGRTHQIRVHMAHIGH 245


>gi|313764724|gb|EFS36088.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL013PA1]
 gi|313815789|gb|EFS53503.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL059PA1]
 gi|314915215|gb|EFS79046.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL005PA4]
 gi|314918556|gb|EFS82387.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA1]
 gi|314919819|gb|EFS83650.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL050PA3]
 gi|314931834|gb|EFS95665.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL067PA1]
 gi|314955990|gb|EFT00388.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL027PA1]
 gi|314958385|gb|EFT02488.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL002PA1]
 gi|315098276|gb|EFT70252.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL059PA2]
 gi|315101033|gb|EFT73009.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL046PA1]
 gi|327451042|gb|EGE97696.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA3]
 gi|327453603|gb|EGF00258.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL083PA2]
 gi|328753075|gb|EGF66691.1| pseudouridine synthase, RluA family [Propionibacterium acnes
           HL087PA1]
          Length = 285

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 79/229 (34%), Gaps = 43/229 (18%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD----------------GVP 66
           +G+ SR  +  +I    V ++G  + RA+V V +   ++VD                G+ 
Sbjct: 2   SGV-SRSRISSLIEDGGVFLDGQQVSRASVRVATGQMLDVDLCDPVATPSITPQIVEGMR 60

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PSIFSRVISVGRLDIN 117
           +   +   + +  KP G+    S      +V ++L              R   V RLD+ 
Sbjct: 61  IIHDDSDIVVV-DKPAGVAAHPSLGWEGPSVVEHLAAAGFAISTSGAPERQGIVQRLDVG 119

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ-----------DKLNLLKKG 164
           T GL+++        +L+         +VY     G  D            D  +  K  
Sbjct: 120 TSGLMVVAKSEHAYTLLKQAFRDRTVDKVYLALVQGHPDPFTGTIDAPIGRDHRHDWKMA 179

Query: 165 IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKV 212
           IV  G        T++  + +   + V L  G+  +I+  +        
Sbjct: 180 IVDGGRHSVTHYETVEAFRHAT-LLKVHLETGRTHQIRVHM-AAIKHPC 226


>gi|284008525|emb|CBA75052.1| tRNA pseudouridine synthase C [Arsenophonus nasoniae]
          Length = 248

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/189 (15%), Positives = 55/189 (29%), Gaps = 40/189 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   HKP G +   S  D      V   +       V  V RLD  T G+LL+   
Sbjct: 4   QDQHLIAIHKPAGWLVHRSWLDRHETRFVMQTVRDQIGQYVFPVHRLDKPTSGVLLMALS 63

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN--LLKKGI-VIQGI------------ 170
             +A +L          + Y     G V++  +    LK+    I               
Sbjct: 64  SEVACLLAQQFEYHAVEKKYHAIVRGYVNEAGIIDYPLKEEKDKIADKYASKISQPQSCI 123

Query: 171 ----CYGDMQVTLDTQKGSNAWVTV------GLREGKNREIKKVFEFFNWKVNRLIRISY 220
                   ++  ++  +   +  ++          G+  ++++        +        
Sbjct: 124 THYSPLAKVECPIEIGRYPTSRFSLLALKPKT---GRKHQLRRHMAHVRHPI-------I 173

Query: 221 GPFQLGTLL 229
           G    G L 
Sbjct: 174 GDTTHGDLR 182


>gi|312196232|ref|YP_004016293.1| pseudouridine synthase, RluA family [Frankia sp. EuI1c]
 gi|311227568|gb|ADP80423.1| pseudouridine synthase, RluA family [Frankia sp. EuI1c]
          Length = 325

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 76/238 (31%), Gaps = 48/238 (20%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGIL--------------LERAAV 52
           V +     R+   IAR    SR     ++   +V V+G                +E    
Sbjct: 24  VPDGLDGLRLDAAIARMFGLSRTVAAALVDDGQVSVDGAAPGRSDRVRGGAWLEVELPPS 83

Query: 53  NVMSTDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
               T+ I   VDG+ +   +   L +  KP+G+    +      TV   L +   R+  
Sbjct: 84  PRPVTEVIATPVDGLTIVHEDDD-LVVVDKPVGVAAHPAPGYTGPTVIGALAAAGYRIST 142

Query: 110 --------SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                    V RLD+ T G++++  +  G  A        +  + YR    G  D     
Sbjct: 143 SGAAERQGVVHRLDVGTTGVMVVAKSELGYAALKRAFREREVDKRYRAVVQGHPDP---- 198

Query: 160 LLKKGI--VIQGICYGDMQVTLDTQKGSN-------------AWVTVGLREGKNREIK 202
            L+  +   I           +      +             + + V L  G+  +I+
Sbjct: 199 -LRGTVDAPIDRHPRKPGLFAVVADGKPSVTHYDLEEAFRAASLLEVRLETGRTHQIR 255


>gi|297161299|gb|ADI11011.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces bingchenggensis BCW-1]
          Length = 312

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 83/259 (32%), Gaps = 64/259 (24%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +RV   IAR    SR +   + A  +V+V+G +  ++   V       +E   
Sbjct: 12  VPDGLEGERVDAAIARMFGFSRTKAAELAAAGKVQVDGSVAGKSD-RVSGGAWLEVEMPQ 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                      V+G+ +   +   + +  KP+G+    S      TV   L         
Sbjct: 71  AAPPVRIVAEPVEGMEIVHDDEHIVVV-DKPVGVAAHPSPGWTGPTVIGGLAAAGFRVST 129

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL 158
                R   V RLD+ T GL+++     LA  L     +     + Y+    G  D    
Sbjct: 130 SGAAERQGIVHRLDVGTSGLMVVAKS-ELAYTLLKQQFRERTVDKRYQALVQGHPDP--- 185

Query: 159 NLLKKGIVIQGICYGDM----------QVTLDTQKGSN-----------AWVTVGLREGK 197
                   + G     +           VT + +               + + + L  G+
Sbjct: 186 --------LSGTIDAPIGRHPQHDYKWAVTAEGKPSVTHYDLIEAFRAASLLDIKLETGR 237

Query: 198 NREIK-KVFEFFNWKVNRL 215
             +I+  +    +  V  L
Sbjct: 238 THQIRVHMAAHRHPCVGDL 256


>gi|57242694|ref|ZP_00370631.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Campylobacter upsaliensis RM3195]
 gi|57016623|gb|EAL53407.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Campylobacter upsaliensis RM3195]
          Length = 250

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 30/202 (14%), Positives = 73/202 (36%), Gaps = 33/202 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G  +  A V +       +     P    E  ++
Sbjct: 7   KLLALQENISNREAKDLIDRGLVFSHGKKIVLARVLMKEGTKFNLLKMKKPQILFEDEKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   ++   + + ++ +               RLD  T GL+LL  +    ++  
Sbjct: 67  LAINKPYSYISEELESEFKAKLL-------------NRLDKETSGLILLCKNEDFKKLCI 113

Query: 136 LP--STQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQ--------- 182
                 +  + Y     G + ++ +    ++    ++G      ++T + Q         
Sbjct: 114 EEFRKQRVYKSYIAVLDGVLAEELVVDEPIR---TLKGKNGAFSKITKEGQSALSIINPL 170

Query: 183 --KGSNAWVTVGLREGKNREIK 202
             +G      + ++ G+  +I+
Sbjct: 171 MIQGKKTLAKICIQTGRTHQIR 192


>gi|327474483|gb|EGF19889.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK408]
          Length = 295

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 34/208 (16%), Positives = 68/208 (32%), Gaps = 36/208 (17%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIE--------------VDGVPLRKAERTRLWLYHKPIG 83
             + VN    + A   +   D +               VD       E     +  KP G
Sbjct: 35  GNILVNHQP-QNAVYLLDIGDRVTIDIPSEKGFESLKAVDKDLSVIYEDEHFLVLDKPAG 93

Query: 84  LVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL-- 134
           + +  S  +  +T+ + + + +        +V  V RLD +T GL+L    G     L  
Sbjct: 94  VASIPS-VNHSNTMANFVKAYYIRQGYENQQVHIVTRLDKDTSGLMLFAKHGYAHARLDK 152

Query: 135 ELPSTQWLRVYRVRFHGQ-VDQDKLNLLK----------KGIVIQGICYGDMQVTLDTQK 183
           +L      + Y     G  + +++  ++             +V +   Y      +  + 
Sbjct: 153 QLQKKLIEKRYYALVRGSGLLEEQGEIIAPIGRNPESIITRLVTKDGKYAHTSYKVIERF 212

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWK 211
           G    V + L  G+  +I+  F    + 
Sbjct: 213 GDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|261839742|gb|ACX99507.1| pseudouridine synthase, RluA family protein [Helicobacter pylori
           52]
          Length = 237

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 75/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KLLSIQESISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F     + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWALLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALIQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|85703848|ref|ZP_01034951.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           217]
 gi|85671168|gb|EAQ26026.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           217]
          Length = 347

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 40/273 (14%), Positives = 76/273 (27%), Gaps = 72/273 (26%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNV 54
              +V  +   QR+ + I       RR        ++E+M  +  V+V+G  ++  A  +
Sbjct: 5   QTRVVGPDDGDQRLDRWI-------RRLFPHVGQVQIEKMCRKGEVRVDGGRVK-PATRL 56

Query: 55  MSTDHIEV------DGVP------LRKAERT-----------RLWLYHKPIGLVTTHSDP 91
                + +      D  P      +  A+              +   +KP GL       
Sbjct: 57  EVGQSVRIPPLPDTDERPTGALARISPADAKMIQSCVIYRDDHVIALNKPPGLPVQGGSK 116

Query: 92  DGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
             R    D L          +   V RLD +T G+LLL      A+ L          ++
Sbjct: 117 QTRHV--DGLAEALRFGAEEKPRLVHRLDKDTSGVLLLARTREAAKGLTAAFRHRNTRKI 174

Query: 145 YRVRFHGQVDQDK-------LNLLKKGIVIQGIC--------------YGDMQ---VTLD 180
           Y     G             +     G   +G                          ++
Sbjct: 175 YWAAVAGVPTPRMGTVRYGLVKAPGHGAKGEGEKMICVHPREVESTPGAKPATTDYAVIE 234

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +W+ +    G+  +++         V 
Sbjct: 235 AAGARTSWMALIPVTGRTHQLRAHMAEIGHPVV 267


>gi|301168827|emb|CBW28418.1| 23S rRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 324

 Score = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 73/228 (32%), Gaps = 33/228 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 10  VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 69

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------S 106
                    + +PL    E   + + +K   LV      +   TV + L   +       
Sbjct: 70  VEDETRFEAENIPLNIVYEDDDIIVINKSKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RFHGQVD 154
           R   V RLD +T GL+++         L       +  R Y                 + 
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKTIPAQTKLVRDLQKRKITREYEAVASGIMTKGGTVDQPMA 189

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +         +   G         ++  + +   + + L  G+  +I+
Sbjct: 190 RHATKRTLMAVHPMGKPAVTHYRIMENYR-NYTRLRLRLETGRTHQIR 236


>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 = 59.8 bits (144), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 41/258 (15%), Positives = 81/258 (31%), Gaps = 57/258 (22%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--------VPL-------RKAE 71
           SR  VE++  ++ +K+NG    +    +   D IE+ G         PL       +  E
Sbjct: 29  SR--VEKLFRKKDIKINGQRTNQKDYIIAFNDVIEIYGLIDTKKEEAPLLTSFSFKKIYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRVISVGRLDINTEGLLLLTNDG 128
              + +  KP G+    +     + V   L        +   +GRLD  T G++L   + 
Sbjct: 87  DANVLIIDKPNGIEVHSAPNCLDNQVLAYLKYKQVDSFKPSHIGRLDKETSGIMLYAKNY 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI---QGICYGDMQVTLD----T 181
              + L        + Y   F    + +      K + +   +      M  +      +
Sbjct: 147 QALKYLNDYMENIKKTY--TFKSDFNDE-----SKEVELFLYKDEEKKRMAASFTKVPYS 199

Query: 182 QKGSNAWVT------VGLREGKNREIK--KV---------FEFFNWKVNR--LIRISYGP 222
           +       T        L  G+  +I+   +         F++   K  R  L  +    
Sbjct: 200 KLSKTHLYTESNKKYATLFSGRKHQIRVTLMKLGKPIYGDFKYGGKKAARLMLHCLQIKF 259

Query: 223 FQLGTLLAGSTREVSKKI 240
             L     G  + ++   
Sbjct: 260 VGL----EGEYKYLNDLE 273


>gi|312140126|ref|YP_004007462.1| tRNA-pseudouridine synthase i [Rhodococcus equi 103S]
 gi|311889465|emb|CBH48782.1| tRNA-pseudouridine synthase I [Rhodococcus equi 103S]
          Length = 308

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 50/307 (16%), Positives = 92/307 (29%), Gaps = 65/307 (21%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL---------ER 49
           M++   +   +     RV   +AR    SR  V  +  +  V V+G              
Sbjct: 1   MRETRSMPVPDGLDGMRVDAGLARLLGLSRTAVATLTEEGAVLVDGAAAGKSDRLSAGTW 60

Query: 50  AAVNVMSTDH-IEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
             V +      + ++  P+   E       +    KP+G+    S      TV   L   
Sbjct: 61  LEVELPEPPRPLTIEAEPVEGMEILYADDDIVAVDKPVGVAAHASVGWTGPTVIGGLAAA 120

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                      R   V RLD+ T G++++        VL+    Q    + Y     G  
Sbjct: 121 GFRISTSGAHERQGIVHRLDVGTSGVMVVATSERAYTVLKRAFKQRTIDKRYHALVQGHP 180

Query: 154 DQD--KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +   G        T++  + + + + + L  G+  +I+
Sbjct: 181 DPSSGTIDAPIGRHRSNDWKFAVTADGKPSVTHYDTVEAFQAA-SLLDIHLETGRTHQIR 239

Query: 203 --------------------KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVS---KK 239
                               ++ E    +   L   S G         G   E++    K
Sbjct: 240 VHFSALRHPCCGDLTYGADPRLAERLGLERQWLHARSLGFAHPAD---GHWVEITSDYPK 296

Query: 240 ILREQLG 246
            L+  LG
Sbjct: 297 DLQHALG 303


>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 = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 79/249 (31%), 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----------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           I+++                 +PL    E   + + +KP  +V      +   T+ + L 
Sbjct: 64  IDINVNFNKTDTNLEHCIPEEIPLNIIYEDDDVLVLNKPANMVVHPGAGNKEHTLVNALL 123

Query: 103 SI------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV- 153
                     R   V RLD +T GLL++         L     + +  R Y     G + 
Sbjct: 124 HHSPSLIHLPRAGIVHRLDKDTTGLLIIAKTLPAHTSLIRQMQAREIKRHYITLVQGHII 183

Query: 154 ---------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                     +   N LK  +   G         +  Q      + V L  G+  +I+  
Sbjct: 184 SGGTIDTGFGRHPRNRLKMAVQEHGRQAITHYA-VKKQYHDFTLLDVNLMTGRTHQIRVH 242

Query: 205 FEFFNWKVN 213
             + +  V 
Sbjct: 243 LAYIHHPVV 251


>gi|146318712|ref|YP_001198424.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|146320920|ref|YP_001200631.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|253751821|ref|YP_003024962.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253753644|ref|YP_003026785.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253755475|ref|YP_003028615.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|145689518|gb|ABP90024.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|145691726|gb|ABP92231.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|251816110|emb|CAZ51733.1| putative RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251817939|emb|CAZ55717.1| putative RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251819890|emb|CAR45926.1| putative RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292558391|gb|ADE31392.1| Pseudouridine synthase, RluD [Streptococcus suis GZ1]
 gi|319758173|gb|ADV70115.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           JS14]
          Length = 297

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 36/209 (17%), Positives = 67/209 (32%), Gaps = 37/209 (17%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVD--------G--VPLRKA-----ERTRLWLYHKPI 82
             + VN  + + A   +   D + +D        G   P+        E       +KP+
Sbjct: 35  GNIWVND-IEQNATYLLDIGDRVTIDIPAEEDLTGSLKPIFFPLDIVYEDDHFLAINKPV 93

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           G  +  S     ST+ + +            +V  V RLD +T G++L    G     L 
Sbjct: 94  GYASIPS-ALHSSTIANFVKGYLIEQNYENKQVHIVTRLDRDTSGVMLFAKHGYAHARLD 152

Query: 135 -ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDTQ 182
            +L +    + Y     G    +   D +  + +         V +   Y      +   
Sbjct: 153 KQLQAKLIHKRYYALVKGNGQLEETGDIIAPIGRPEDSIITRCVTKNGKYAHTSYRVVQS 212

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            G    V + L  G+  +I+  F    + 
Sbjct: 213 WGDIHLVDIQLHTGRTHQIRVHFSHIGFP 241


>gi|260909666|ref|ZP_05916361.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 472 str. F0295]
 gi|260636225|gb|EEX54220.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 472 str. F0295]
          Length = 349

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 85/249 (34%), Gaps = 42/249 (16%)

Query: 4   KNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +   P R+ + +  R   +SR  +++      V VN   ++     V   D I +
Sbjct: 23  RIVVDKGQVPVRIDRFMTERLQHSSRNRIQKAADSGFVHVNERPVKS-NYKVRPGDVITL 81

Query: 63  -------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        + +PL    E   L + +KP G+V      +   T+ + +      +
Sbjct: 82  MLDRPHHDTTIEAEEIPLDVVYEDEALMVINKPAGMVVHPGAGNFNGTLINAVAWHLRNM 141

Query: 109 IS----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF------- 149
            S          V R+D +T GLL++       R L L   +    R Y           
Sbjct: 142 PSFDANDPEVGLVHRIDKDTSGLLVVAKTPEAKRKLGLQFFNKTTHRSYNALVWANFAEN 201

Query: 150 ----HGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
                G + +D  + L+  +       G   VT   +  + G   +V   L  G+  +I+
Sbjct: 202 EGRIEGNIGRDPRDRLRMAVFPPDSEMGKPAVTHYRVLERFGYVTFVECILETGRTHQIR 261

Query: 203 KVFEFFNWK 211
              +     
Sbjct: 262 AHMKHIGHP 270


>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 = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 66/226 (29%), Gaps = 55/226 (24%)

Query: 34  MIAQQRVKV--NGILLERA-AVNVMSTDHI----------------EVDGVPLRKAERTR 74
            I    V V  NG  ++   +  + + D +                +VDG  +   +   
Sbjct: 47  WIRDGHVTVTNNGKTVKIGKSYKLSAGDEVVVDAPAPRDLADIRPEKVDGFRIVHLDDDI 106

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVISVGRLDINTEGLLLLT 125
           + +  KP G+    S      TV   L              R   V RLD+ T GL+++ 
Sbjct: 107 VVV-DKPAGVAAHPSPGWHGPTVISALMGEGISVATSGAAERQGIVHRLDVGTSGLMVVA 165

Query: 126 NDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQ 176
                   L+    +    +VY     G  D        +G  I        G  +    
Sbjct: 166 RSERAYTELKRAFKERTVDKVYHTLVQGLPDP------LRG-TIDAPIGRHPGNEWKFAV 218

Query: 177 VT----------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           V           +    G  + V V L  G+  +I+  F       
Sbjct: 219 VEDGRNSITHYDVLEAFGPASLVEVHLETGRTHQIRVHFSALRHPC 264


>gi|114771239|ref|ZP_01448659.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HTCC2255]
 gi|114548164|gb|EAU51051.1| ribosomal large subunit pseudouridine synthase C [alpha
           proteobacterium HTCC2255]
          Length = 348

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 46/278 (16%), Positives = 89/278 (32%), Gaps = 75/278 (26%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERA 50
           M    I++  ++   QR+ + +       RR         +E+M  +   +V+G  ++ A
Sbjct: 1   MSGVQIIEVDDDGQDQRLDRFL-------RRTFPELGQGRIEKMCRKGECRVDGSRVK-A 52

Query: 51  AVNVMSTDHIEV---------------------DGVPLRKA---ERTRLWLYHKPIGLVT 86
           +  +     + V                     D   +R A   +   +   +KP GL  
Sbjct: 53  STRLSVGQTVRVPPLPDTKDMPRDTATAKITKADAQMIRDAVLYKDDYIIAINKPAGLAV 112

Query: 87  THSDPDGRSTV---FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                  R            + ++   V RLD +T G+LLL   G  A  L     S + 
Sbjct: 113 QGGSGQMRHVDGLSAALKFDLENKPKLVHRLDKDTSGVLLLARTGLAASGLTKAFQSRET 172

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGI-----------CYGDMQVT------------ 178
            ++Y     G     K+  +K G++  G            C    +VT            
Sbjct: 173 RKIYWAAVAGCPHP-KIGTIKYGLIKAGGHGPNGSGEKMQCIHPSEVTDMPDAKHATTDY 231

Query: 179 --LDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
             L+      +WV +  +  G+  +++         + 
Sbjct: 232 TVLEDVGKRASWVALVPIT-GRTHQLRAHMAELGNPIV 268


>gi|15618318|ref|NP_224603.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           CWL029]
 gi|15835936|ref|NP_300460.1| pseudouridine synthetase family protein [Chlamydophila pneumoniae
           J138]
 gi|33241749|ref|NP_876690.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
 gi|4376683|gb|AAD18547.1| predicted pseudouridine synthetase family [Chlamydophila pneumoniae
           CWL029]
 gi|8978775|dbj|BAA98611.1| pseudouridine synthetase family [Chlamydophila pneumoniae J138]
 gi|33236258|gb|AAP98347.1| pseudouridine synthetase [Chlamydophila pneumoniae TW-183]
          Length = 232

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 34/152 (22%), Positives = 57/152 (37%), Gaps = 22/152 (14%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+S  + ++    S++E+   I Q R +VNG +    +  V   D + +  +P  K + +
Sbjct: 27  RLSSFLRSQLPNHSKQEILASIRQHRCRVNGFIERFESYKVQPGDRVSLSLIPSTKQQPS 86

Query: 74  RLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            LW      +Y KP  L T                +  +R  +V RLD  T G LL+   
Sbjct: 87  ILWEDDYSIIYEKPPHLTTEQ-------------MAHMTRFFTVHRLDKGTSGCLLMGKS 133

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
              A  L       +  + Y     G   +  
Sbjct: 134 KQAATELMKLFKQRKIHKQYIAFVFGHPKKKF 165


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

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 70/232 (30%), Gaps = 53/232 (22%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------------------DGVPL 67
           ++++   +++V+G   +     +     I +                        DG  L
Sbjct: 35  QKLLRSGQIRVDGARAKS-DTRIQPGQTIRIPPLGVDPKEAKSGPIGGRDLRQSPDGELL 93

Query: 68  RK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGL 121
            +    E  ++ + +KP GL         R            +      V RLD +T G+
Sbjct: 94  SRMVLHEDAKVIVLNKPAGLAVQGGSGVNRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGV 153

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------------QVDQDKLNLLK 162
           L++    G A+ L          + Y     G                   D D++ + K
Sbjct: 154 LVVARTRGAAQQLTAAFRERDTKKTYWALVRGVPRKREDKISTWLVKEPTPDGDRVRIAK 213

Query: 163 KGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVN 213
            G    G  +      +  Q G N AW+ +    G+  +++         + 
Sbjct: 214 HGE--DGADHAISYYRIVEQAGQNLAWLEMEPYTGRTHQLRVHAAHIGHPII 263


>gi|288940534|ref|YP_003442774.1| RluA family pseudouridine synthase [Allochromatium vinosum DSM 180]
 gi|288895906|gb|ADC61742.1| pseudouridine synthase, RluA family [Allochromatium vinosum DSM
           180]
          Length = 326

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 79/228 (34%), Gaps = 34/228 (14%)

Query: 7   VQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---- 61
           V+ +    R+ +V+A+     SR  +++ I   +V V+          V   + I     
Sbjct: 15  VEPDLAGGRLDRVLAQLLPEFSRGRLQQWIEAGQVLVDDRPCR-VRDKVWGGESIRIEAE 73

Query: 62  ---VDGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FS 106
              VD    +        E   L +  KP GLV   +  +   T+ + L           
Sbjct: 74  LAVVDEHRPQAIALDLVYEDEHLLVIDKPAGLVVHPAAGNPDGTLLNALLHHAPELATLP 133

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVD 154
           R   V RLD +T GL+++         L  +L      R YR    G           + 
Sbjct: 134 RAGIVHRLDKDTTGLMVVARTLQAHCALVEQLQRRIVHREYRALVLGTLVAGGRVEAPIG 193

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +     +K  +V  G         L++  G +  + V L  G+  +I+
Sbjct: 194 RHPTQRVKMAVVGNGREAITHYRVLESYPG-HTLLAVELETGRTHQIR 240


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

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 36/252 (14%), Positives = 84/252 (33%), Gaps = 59/252 (23%)

Query: 4   KNIVQENFTPQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +  V E+    R+ +         G     ++++++   +V+V+G  ++ A+  + +   
Sbjct: 8   QKTVDEDEGGMRLDRWFKLHYPGVGFG---KLQKLLRSGQVRVDGGRVKTAS-RLEAGQV 63

Query: 60  IEV-------DGVPLR-------------------KAERTRLWLYHKPIGLVTTHSDPDG 93
           + +          PL                      E  ++ +++KP GL         
Sbjct: 64  VRIPPLDSAASDKPLHMTSNTIRDRHDEDVLRDMILYEDKKVLVFNKPSGLAVQGGSGIS 123

Query: 94  RST---VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
           RS    +         +     RLD +T G+L++    G A  L          + Y   
Sbjct: 124 RSVDSMLESLRDKAGQKPRLCHRLDRDTSGVLVVAKTRGAAAALTKSFRQRTTQKTYWAL 183

Query: 149 FHGQVDQ--------------DKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAWVT 190
             G   Q              +  + ++  +   G  + D  V+    +D+   + +WV 
Sbjct: 184 VRGIPRQKEGRISTYLVKEQTEDGDRMR--VAKHGERHADHAVSFYRVIDSNPRTVSWVE 241

Query: 191 VGLREGKNREIK 202
           +    G+  +++
Sbjct: 242 LSPHTGRTHQLR 253


>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 = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 88/241 (36%), Gaps = 43/241 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M+  N+ V++ F   R+   +++  I    SR  ++ +I +  V VN    ++    +  
Sbjct: 1   MEKINLQVEKEFDNVRLDLYLSK--IFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKV 57

Query: 57  TDHIEVD---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            D+IEV+      L+            E   + + +KP  +V   +      T+ + L  
Sbjct: 58  GDNIEVNIPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLH 117

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
               +           V R+D +T G+L++  +      L          RVY     G 
Sbjct: 118 HCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGI 177

Query: 153 VDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +  ++           ++ +K  +V +   +      +  +  ++  V   L  G+  +I
Sbjct: 178 IKDEQGTIEAPIGRHPVDRIKMAVV-KDGRHAVTHYKVIERFKNHTLVECRLETGRTHQI 236

Query: 202 K 202
           +
Sbjct: 237 R 237


>gi|126727903|ref|ZP_01743731.1| putative Pseudouridine synthase, Rlu [Rhodobacterales bacterium
           HTCC2150]
 gi|126702844|gb|EBA01949.1| putative Pseudouridine synthase, Rlu [Rhodobacterales bacterium
           HTCC2150]
          Length = 308

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 51/295 (17%), Positives = 100/295 (33%), Gaps = 65/295 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDH--------IEVDGVPLRKA-----ERTRLWLYH 79
           +++A+  +   G ++      V   D         +EVD +P         E   L + +
Sbjct: 2   KLLAEGAITFKGEVISDPRAKVQEGDEFTITVEQSVEVDVLPEDIPLEILFEDDDLIVVN 61

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRLDINTEGLLLLTNDGG 129
           KP+G+V   +      T+ + L   F           R   V R+D +T G+L++     
Sbjct: 62  KPVGMVVHPAPGSPSGTLVNALLHHFGGNLSGIGGEKRPGIVHRIDKDTSGVLVVAKSDA 121

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGS 185
               L     +    R Y    +G  D      LK  +G+  +G     +   L   +  
Sbjct: 122 AHHGLAAQFEAHTVNRKYHAICYGVPDNAD-PRLKGVRGVSFEGSNVVKINTQLARHRTD 180

Query: 186 NAWVTVGLREGKNREI-K-KVFEFFNWKVNRL-------------IRISY---GPFQLGT 227
               +V   +G+   + + ++ + +                    IR+     G   +G 
Sbjct: 181 RQRQSVYFNQGR-HAVTRARLVQRYGKPSVACLVECWLETGRTHQIRVHMTHTGHSLIGD 239

Query: 228 LLAGSTREVSKKIL------------REQLGP------HLLEEAQVNLDAPIYSS 264
              G  R++S K L            R+ L        H + + +++ DAP+ + 
Sbjct: 240 QTYGGRRKLSPKALSAAAIDAVAAFPRQALHAATLGFVHPITKEELSFDAPLPND 294


>gi|225165838|ref|ZP_03727617.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
 gi|224799926|gb|EEG18376.1| pseudouridine synthase [Opitutaceae bacterium TAV2]
          Length = 244

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/153 (18%), Positives = 55/153 (35%), Gaps = 15/153 (9%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLL 122
                 E  RL + +KP  +V   S     S++   +       +   + RLD  T G++
Sbjct: 8   EAWVVHEDERLLVVNKPGDVVCHPSKAGPWSSLAGAVREAKGLEKAHLIFRLDRETSGVV 67

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQ------VDQDKLNLLKKGIVIQGICYGD 174
           +   D  +A  L+      +  + Y     G+      VDQ   + L   + ++     D
Sbjct: 68  VFAKDERMASRLQRAMQERRVRKEYLAVLEGELREAVTVDQPLGDDLASPVFVKTCVRAD 127

Query: 175 MQVTL-----DTQKGSNAWVTVGLREGKNREIK 202
            +  +         G  + V V L  G+  +I+
Sbjct: 128 GKAAVSHFYPVACAGGFSLVRVRLETGRKHQIR 160


>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 = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 74/228 (32%), Gaps = 41/228 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +       +R  ++       +  NG  ++     V   D + +           
Sbjct: 45  RVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKS-NYRVKPEDVVTIMMTRPPRTFEI 103

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVI 109
             + +P++   E   L +  KP GLV      +   T+ + L                + 
Sbjct: 104 LPENIPIKIVYEDDDLLVVDKPAGLVVHPGHGNYTGTLVNALAWYLKDDPTYDPNDPALG 163

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++         L +        R YR    G V +D+          
Sbjct: 164 LVHRIDKDTSGLLVVAKKPEAKAHLSMQFFHKTTKREYRALVWGIVREDEGRIEGNIGRN 223

Query: 158 -LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
             + ++  +  +G          ++  + G    V   L  G+  +I+
Sbjct: 224 PRDRMQMTVFPEGDQGKTAVTHYSVLERLGYVTLVKCRLETGRTHQIR 271


>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 = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           T QR+  ++   G+A +R + + +I   +V VNG +  +A   V +   IEV
Sbjct: 1  MTRQRLDTLLVERGLAETRAKAQALIMAGQVLVNGQVQTKAGTQVAADAQIEV 53


>gi|329849859|ref|ZP_08264705.1| ribosomal large subunit pseudouridine synthase D [Asticcacaulis
           biprosthecum C19]
 gi|328841770|gb|EGF91340.1| ribosomal large subunit pseudouridine synthase D [Asticcacaulis
           biprosthecum C19]
          Length = 335

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 78/250 (31%), Gaps = 44/250 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD------ 58
            V  +    R+ + +       SR  ++ +IA+ R+  NG ++          D      
Sbjct: 24  TVTADEAGDRLDRALTVHFPDLSRARLQALIAEGRLSHNGAVITDGKHKARPGDYSLSIP 83

Query: 59  -HIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISV 111
             I  +  P         E   L + +K  G+    +      T+ +  L      +  +
Sbjct: 84  ALISANPEPQDIPLDILFEDEHLIVINKAPGMAAHPAPGTRDGTLVNALLFHCGESLSGI 143

Query: 112 G---------RLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQV------ 153
           G         RLD +T G+++      +A              R Y+    G        
Sbjct: 144 GGVLRPGIVHRLDKDTSGVMVAAKS-DVAHRSLSELFGRHDIDREYKAVVRGAPRYVSGT 202

Query: 154 ----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                     D+ K+ +L+ G   + I +  ++    T K   A ++  L  G+  +I+ 
Sbjct: 203 VNTRIGRSHHDRKKMAVLRGGGR-EAITHYRLEEVFGTVKPLAALLSCRLETGRTHQIRV 261

Query: 204 VFEFFNWKVN 213
                     
Sbjct: 262 HMAHLGCPCL 271


>gi|227877169|ref|ZP_03995243.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus crispatus
           JV-V01]
 gi|227863223|gb|EEJ70668.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus crispatus
           JV-V01]
          Length = 304

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/161 (19%), Positives = 60/161 (37%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLL 123
           E     + +KP G+++  S  +    V + L   F++          + RLD +T GL+L
Sbjct: 88  ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRDTSGLVL 147

Query: 124 LTNDGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGI 170
           +  +             ++++ Y    HG    ++L  L      KKG      +V  G 
Sbjct: 148 VGKNAISHARFSKIGKEKFVKKYHAIVHGNFAPNELTGLIDQPIGKKGSGVKRAVVADGK 207

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   LD   G+ + V + L  G+  +I+    +    
Sbjct: 208 DAQTAYRVLDQVTGA-SLVELRLLTGRTHQIRVHMAYLGHP 247


>gi|54114079|gb|AAV29673.1| NT02FT1763 [synthetic construct]
          Length = 309

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|239947789|ref|ZP_04699542.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922065|gb|EER22089.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 303

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/175 (18%), Positives = 62/175 (35%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN   +  A++ V   D I ++     
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNSQKV-EASLRVKGGDKIFINDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTH--SDPDGRSTVFDN 100
           P+++ ++                         L   +KP GL T           +    
Sbjct: 66  PVKQPKKLVFTDAEIKLAKKITTDYLIYEDDNLIAINKPAGLATQGGSKIKLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDVFKEKLVVKTYFAVTYGKP 180


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 49/269 (18%), Positives = 85/269 (31%), Gaps = 50/269 (18%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---- 64
           E+    R+  V++R    SR    ++I +  V+V        +  V  +  + V G    
Sbjct: 26  EDGEGHRLDFVLSREIGVSRSYASKLIKEGMVQV------SWSPRVKPSLKVRVGGTVTA 79

Query: 65  ----------VPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                      P     R         +  KP GLV   +    R T+   L   +  ++
Sbjct: 80  QLPPSEELELEPQDVPFRVVYQDQDLVVVDKPAGLVVHPAPGHWRGTLVHGLLYRYPDLM 139

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
                     V RLD  T GL+++  +G     L       +  +VY     G +  +  
Sbjct: 140 ELNGVKRPGIVHRLDATTSGLMVVARNGLAMEGLVRAFKDRRVGKVYLAMAAGTLRGEGS 199

Query: 159 NLLKKGIVIQGICYGDM---------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
             L  G                    +  +   +G  + V   ++ G+  +I+       
Sbjct: 200 VSLPIGRDPDNRKRMACVPWGREALTRYRVIWSRGGYSLVACQIKTGRTHQIRVHMRSLG 259

Query: 210 WKVNRLIRISYGP----FQLGTLLAGSTR 234
             +    RI  GP    F LG +   S R
Sbjct: 260 HPLVG-DRIYGGPCPEGFPLGRVFLHSWR 287


>gi|319897067|ref|YP_004135262.1| tRNA pseudouridine synthase [Haemophilus influenzae F3031]
 gi|317432571|emb|CBY80931.1| tRNA pseudouridine synthase [Haemophilus influenzae F3031]
          Length = 239

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 58/182 (31%), Gaps = 31/182 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A ++          + Y     G +  +++++   K I +  I     Q   + Q+ 
Sbjct: 67  SEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEA 125

Query: 185 SN----------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                                   + V +    G+  ++++  +     +  L    YG 
Sbjct: 126 ITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGD 183

Query: 223 FQ 224
             
Sbjct: 184 LH 185


>gi|282857614|ref|ZP_06266832.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
 gi|282584552|gb|EFB89902.1| ribosomal large subunit pseudouridine synthase D [Pyramidobacter
           piscolens W5455]
          Length = 315

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 79/240 (32%), Gaps = 47/240 (19%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRKAERTRL--- 75
           +   +  V++ G   +     V+   H+ V              DG P R          
Sbjct: 34  KYFRKGAVRLEGKRCQ-PNDRVLEGQHVWVPWEEPGTVGRAEMPDGTPRRLPLDVIYSDR 92

Query: 76  --WLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRVISVGRLDINTEGLLLLTNDG 128
              + +KP GL++        S V   L     P    ++  V RLD NT G++ L  DG
Sbjct: 93  CVMVVNKPAGLLSQPDVKGEDSVVTRALGYAVDPEFPPQL--VHRLDRNTSGVMALALDG 150

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQ----------DKLNLLKKGIVIQGICYGDMQ 176
              R L     + +  + Y     G++ +          D    L + +  +G      +
Sbjct: 151 PTTRALMECFKARRADKRYWAIVIGELPERGRIDVPLLKDADKKLVR-VDPKGERAVT-E 208

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
               T  G+ +   V L  G+  +I+         +  L  + YG F       G  R +
Sbjct: 209 YKRLTSSGAFSLAEVHLLTGRTHQIRVHMNHVGHPL--LGDVKYGDFGSK----GQLRSL 262


>gi|46581593|ref|YP_012401.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|46451016|gb|AAS97661.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris str. Hildenborough]
 gi|311235236|gb|ADP88090.1| pseudouridine synthase [Desulfovibrio vulgaris RCH1]
          Length = 390

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 48/156 (30%), Gaps = 19/156 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           P   AE   L+++ KP GL     T       + +  +            RLD +T GLL
Sbjct: 130 PPVVAETPDLFIFDKPAGLAVHPGTGHTDSLTTRLAQHFAKAPFMPTPAHRLDRDTSGLL 189

Query: 123 LLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKL----NLLKKGIVIQG------ 169
           L+     + R L           + Y     G           + L KG    G      
Sbjct: 190 LVARSYAMLRTLHEAFASHDALVKEYLAWVAGCWQPAAPVTLHDRLSKGAEASGFERVAS 249

Query: 170 ---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     V    ++   + + V L  G+  +I+
Sbjct: 250 DDEGAEAACTVRCLLREQHRSLLLVTLHTGRTHQIR 285


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             QR+ K +   G A +R + + +I    V V+G+L+++    V     I+V   P+R 
Sbjct: 1  MPRQRLDKKLVELGFAPTREKAQALIMAGMVTVDGLLVDKPGFLVKEGQKIDVK-EPVRY 59

Query: 70 AERTRLWLYHKPIGL 84
            R    L H   G 
Sbjct: 60 VSRGGYKLEHALEGF 74


>gi|291279336|ref|YP_003496171.1| hemolysin A [Deferribacter desulfuricans SSM1]
 gi|290754038|dbj|BAI80415.1| hemolysin A [Deferribacter desulfuricans SSM1]
          Length = 268

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              R+ K++ + G+A SR + +R+I    V VN   +++    +    HI++
Sbjct: 1  MAKDRLDKILFQRGLAESREKAQRLIMAGLVIVNNEKIDKPGTKIDENAHIKL 53


>gi|309778338|ref|ZP_07673264.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308913904|gb|EFP59718.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 293

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 70/198 (35%), Gaps = 33/198 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKAERTRLWLY--------HKPIG 83
            ++RV +N   + R    +   D I +    +   ++   +    LY        +KP  
Sbjct: 39  QERRVFLNNRHISRNHT-LHEKDTIRISLQAEEDTVKPWYKHVEILYEDDLFCIVNKPAN 97

Query: 84  LVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVL--E 135
           L+      +   TV + + + +      + V  + RLD  T G+L+         +L   
Sbjct: 98  LLVHSDGVESEHTVCNMVKAHYLTEGSNACVRPLHRLDYETSGVLIFCKLPFFQPMLDEM 157

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--------- 186
           L S Q  R Y     G+  Q     + +GI         M+V+ + ++            
Sbjct: 158 LKSKQIYREYEAFAVGRFTQKH-YTITRGIARDRHDARRMRVSDNGKEARTDVFVKQSFS 216

Query: 187 --AWVTVGLREGKNREIK 202
              W+   L  G+  +I+
Sbjct: 217 DFTWIRCRLHTGRTHQIR 234


>gi|288928148|ref|ZP_06421995.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
 gi|288330982|gb|EFC69566.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 317 str. F0108]
          Length = 300

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 70/205 (34%), Gaps = 30/205 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLW 76
           SR +++ ++    V VNG  + +    ++    + V                  E   L 
Sbjct: 38  SRNKLKDILRGHGVCVNGKCVTQFDYQLVPGMKVTVSRTKKAVPFKSRYIKIVYEDRYLI 97

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
           +  K +G+++  +       V   L + F       R   V RLD  T GLL+   D   
Sbjct: 98  VVDKSVGVLS-MAAGHSSLNVKAILDTYFENSGQKCRAHVVHRLDRETSGLLVYAKDMET 156

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQD--KLNLLKKGI---------VIQGICYGDMQV 177
            ++LE         R Y     G++  +   ++   K           V  G  Y     
Sbjct: 157 EQILEHNWHDMVYDRRYVAVVSGEIVDEGGTISSWLKDNSSYITYSSPVDNGGKYAVTHF 216

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            +  +  +++ V   L  G+  +I+
Sbjct: 217 HVLKRTTTHSLVEYKLETGRKNQIR 241


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 8/82 (9%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +  AG ++SR    ++IA + V+VNG +  +A++ V   D + V     R++E 
Sbjct: 1  MRLDKYLVEAGFVSSRTLAAKLIAARDVQVNGKVARKASMLVGPEDTLYV-----RQSEL 55

Query: 73 TRLW--LYHKPIGLVTTHSDPD 92
          T       HK  G +    D +
Sbjct: 56 TEYVSRAGHKLAGALDAFPDIE 77


>gi|145641594|ref|ZP_01797171.1| tRNA pseudouridine synthase C [Haemophilus influenzae R3021]
 gi|145273641|gb|EDK13510.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.4-21]
          Length = 239

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDAFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|332530535|ref|ZP_08406474.1| pseudouridine synthase, RluA family protein [Hylemonella gracilis
           ATCC 19624]
 gi|332040010|gb|EGI76397.1| pseudouridine synthase, RluA family protein [Hylemonella gracilis
           ATCC 19624]
          Length = 361

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 48/283 (16%), Positives = 92/283 (32%), Gaps = 72/283 (25%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNG-----ILLERAAVNVMSTDH--IEVDGV 65
           QR+ + ++      SR  ++++I    V + G     +++ ++A  V + +   IE+   
Sbjct: 30  QRLDRALSELVPEFSRSYLQQLIEAGAVTL-GPQPSQLVVRKSAHKVRAGEVGTIELRPT 88

Query: 66  PLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PS 103
           P  +A            E   L + HKP GLV   +  +   T+ + L           +
Sbjct: 89  PQSQAFKPEVMDLDIVHEDAHLLVIHKPAGLVVHPAPGNWSGTLLNGLLGRDQGRGEVAA 148

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----RFHGQVDQDK 157
              R   V RLD +T GL+++         L   + + +  R Y       ++G V +D 
Sbjct: 149 QLPRAGIVHRLDKDTSGLMVVARTRVAMEALVRMIAAREVSRQYLALAHRAWNGPVLRDV 208

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSN------------------------AWVTVGL 193
               ++GI         M V    +                              +   L
Sbjct: 209 GGAAQEGIGRDPANRLRMAVVDLARHPGKPALTTFELLGNAAPRPDEGLAQGACLLRCTL 268

Query: 194 REGKNREIKKVFEFFNW-----------KVNRLIRISYGPFQL 225
             G+  +I+                    V  L R +   ++L
Sbjct: 269 HTGRTHQIRVHAASIGHPLLGDGVYGGAPVVGLRRQALHAWRL 311


>gi|270294141|ref|ZP_06200343.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|317478898|ref|ZP_07938046.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
 gi|270275608|gb|EFA21468.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|316904932|gb|EFV26738.1| RluA family pseudouridine synthase [Bacteroides sp. 4_1_36]
          Length = 303

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 31/165 (18%), Positives = 66/165 (40%), Gaps = 19/165 (11%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
            P  + + +A +   ASR +++ +++++ + V+ ++  +    +     +++     RK 
Sbjct: 21  EPMELMEFLAAKMPDASRTKLKSLLSKRIIYVDSVITTQYNFPLKPGMKVQISREKGRKE 80

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRL 114
                     E   + +  K  GL++ ++D     T +  L     R      V  V RL
Sbjct: 81  FNHKLMKIVYEDAYIIVIEKMQGLLSVNTDRQKERTAYTILNEYVQRSGKQHRVHIVHRL 140

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK 157
           D +T GL++   D    R L          R Y     G++++D 
Sbjct: 141 DRDTSGLMMFAKDEKTQRTLRDNWHDIVTDRRYVAVVVGEMEKDA 185


>gi|108757756|ref|YP_630767.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461636|gb|ABF86821.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 316

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 81/235 (34%), Gaps = 39/235 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
            V  +   QRV   I  A   SR  ++R+     VKVNG   ++  + + +  HI V+  
Sbjct: 10  TVDADKAGQRVDLFIGEALGLSRARLKRLFEAGAVKVNGRPAKK-GLTLTAGQHIAVEVE 68

Query: 64  ---GVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
                 +  A+     L+         KP G  +         TV + L + +       
Sbjct: 69  EESREAVPDADFPLTVLHEDDSLVFVDKPAGRPSHPLQSGETGTVANALVARYPECALAS 128

Query: 109 ------ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-KLN 159
                     RLD+ T G+++   T D   A      S    + Y     G +  +  ++
Sbjct: 129 LDAREGGLCHRLDVETSGVVVAARTRDAWNAVREAFGSRAVDKRYLALVTGPLTDEGDID 188

Query: 160 L-LKKG------IV-----IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           L L+        +       +       + T+ ++ G  + V V +  G   +++
Sbjct: 189 LPLRHHPRHPDRVEPAPYGAEDARDAVSKFTVLSRSGEFSVVEVKILTGVLHQVR 243


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

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 35/232 (15%), Positives = 70/232 (30%), Gaps = 53/232 (22%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------------------DGVPL 67
           ++++   +++V+G   +     +     I +                        DG  L
Sbjct: 35  QKLLRSGQIRVDGARAKS-DTRIQPGQTIRIPPLGVDPKEKKTGPIGGRDLRQSPDGELL 93

Query: 68  RK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGL 121
            +    E  ++ + +KP GL         R            +      V RLD +T G+
Sbjct: 94  SRMVLHEDAKVIVLNKPPGLAVQGGSGVNRHIDKMLEAWTSQKGEKPRLVHRLDRDTSGV 153

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------------QVDQDKLNLLK 162
           L++    G A+ L          + Y     G                   D D++ + K
Sbjct: 154 LVIARTRGAAQQLTAAFRERDTKKTYWALVRGVPRKREDKISTWVVKEQTPDGDRVRIAK 213

Query: 163 KGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVN 213
            G    G  +      +  Q G N AW+ +    G+  +++         + 
Sbjct: 214 HGE--DGADHAISFYRIVEQAGQNLAWLEMEPYTGRTHQLRVHAAHIGHPII 263


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 11/86 (12%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+A SR + + +I   RV+V G ++ +A+  V  TD IEV   PLR 
Sbjct: 1  MERKRLDVLLVERGMAASRAKAQALIRAGRVRVAGRIVTKASAKVSLTDPIEVL-EPLRY 59

Query: 70 AERTRLWL--------YHKPIGLVTT 87
            R    L         + P G V  
Sbjct: 60 VGRGGYKLEAALEAFGVN-PRGWVCA 84


>gi|296332341|ref|ZP_06874802.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673620|ref|YP_003865292.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150259|gb|EFG91147.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411864|gb|ADM36983.1| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 302

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 87/262 (33%), Gaps = 49/262 (18%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLV 85
           +VKVN   +    V V   D + +D             G      E   + + +KP G+ 
Sbjct: 44  QVKVNHESVLN-NVIVKKGDRVFIDLQESEESSVIPEYGELDILFEDNHMLIVNKPAGIA 102

Query: 86  TTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE---L 136
           T  ++     T+ + +   +       +V  V RLD +T G ++      L+  +    L
Sbjct: 103 THPNEDGQTGTLANLIAYHYQVNGEICKVRHVHRLDQDTSGAIVFAKH-RLSHAILDQQL 161

Query: 137 PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKG 184
                 R Y     G            + +D+ +  ++ +   G       +V     K 
Sbjct: 162 EKKTLKRTYTAITEGKLKTKKGTIDSPIGRDRSHPTRRRVSPSGQTAVTHFKVVASNAKE 221

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL--R 242
               V + L  G+  +I+         +        G      L  G ++ ++++ L  +
Sbjct: 222 RLTLVELELETGRTHQIRVHMASIGHPL-------IG----DALYGGGSKLLNRQALHAK 270

Query: 243 EQLGPHLLEEAQVNLDAPIYSS 264
           +    H +    +  +AP  + 
Sbjct: 271 KVQAVHPITGELIVAEAPFPAD 292


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 87/262 (33%), Gaps = 64/262 (24%)

Query: 7   VQENFTPQRVSKVIARA-------GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           + +N   QR+ K + +A        +       + I  +R+K+NG      +  +   D 
Sbjct: 6   INKNDAGQRMDKFLTKAVPALPKNLMY------KYIRLKRIKLNGKRC-EISTKLSEGDS 58

Query: 60  I--EVDGV--PLRKAERTR----------------LWLYHKPIGLVTTHSDPDGRSTVFD 99
           +   ++    P ++ E  R                + L  KP GLV    +     T+ D
Sbjct: 59  VQLYINDEFFPEKRDEAHRFLNSPKDIEIVYEDENIILCDKPCGLVVHEDESGEADTLID 118

Query: 100 NL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
            +           P   +        R+D NT G+++   +    RVL       +  ++
Sbjct: 119 RVLHYLYDKGEYDPDTENSFTPALCNRIDRNTSGIVICAKNAESLRVLNQKVKDRELEKL 178

Query: 145 YRVRFHGQVDQ--DKLNLL------KKGIVIQGICYG-------DMQVTLDTQKGSNAWV 189
           Y     G  ++   +L          K + ++   +          +V  + ++   A +
Sbjct: 179 YLCVTVGIPNKKSAELKAFHRRDEKTKVVRVEDKSFPGSKTMITRYKVLAENKQSGLALL 238

Query: 190 TVGLREGKNREIKKVFEFFNWK 211
            V L  G+  +I+       + 
Sbjct: 239 EVDLVTGRTHQIRAHLAHIGYP 260


>gi|254457748|ref|ZP_05071176.1| pseudouridine synthase D [Campylobacterales bacterium GD 1]
 gi|207086540|gb|EDZ63824.1| pseudouridine synthase D [Campylobacterales bacterium GD 1]
          Length = 308

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 36/199 (18%), Positives = 72/199 (36%), Gaps = 28/199 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVM-STDHIEVDGVPLRKAERTRL---WLYHKPIGL 84
           +E +R+IA+ R+ +NG  + R A  +    + I  + +              ++ KP G+
Sbjct: 29  KEAQRLIAKGRLFINGEPMTRTAGEIEGEFEFIYFEPITKGLEATAVYDEFVVFDKPSGV 88

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLAR--VLELPSTQW 141
           +    +     ++ D L   + R      R+D  T GL+L   +    R   +       
Sbjct: 89  LIHPQNRKTPYSLIDELKYQYGRDANIAHRIDQETSGLVLCAKNKESERDIKMMFEQRDM 148

Query: 142 LRVYRVRFHGQVDQDKL---NLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVT------- 190
            + Y    HG++ +       LL++           M V + +  K S   +        
Sbjct: 149 KKKYLALVHGELKESICIEEPLLRRE---DESAIVRMVVKVHEEGKASKTDIRPLKYFAE 205

Query: 191 --VGLRE-----GKNREIK 202
             + L E     G+  +I+
Sbjct: 206 TDMTLVECSPYTGRQHQIR 224


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

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 78/263 (29%), Gaps = 62/263 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVM 55
              V E+    R+ +         RR         ++++    +++V G  +  A+  + 
Sbjct: 5   NRTVSEDEAGIRLDRYF-------RRHYPHLTQGALQKLCRTGQIRVEGKRV-EASTRLE 56

Query: 56  STDHIEV-----------------DGVPLRKAERTRLW------LYHKPIGLVTTHSDPD 92
               + V                 D    R+  +  ++        +KP GL        
Sbjct: 57  PGQTVRVPPIPMAAKPARDVPRPLDEKLAREIRKMVVYQDKHVIALNKPAGLAVQGGPGI 116

Query: 93  GRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
            +               R   V R+D +T GLLLL    G+A  L          ++Y  
Sbjct: 117 TKHVDMMLDGLREEDDPRPRLVHRIDKDTSGLLLLARTPGVAAKLAASFRGRDVKKIYWA 176

Query: 148 RFHGQVD------QDKLNLLKKG----IVIQGICYGDMQ------VTLDTQKGSNAWVTV 191
              G+ D         L  L  G     V       D Q        LD+     +W+ +
Sbjct: 177 VVVGRPDPLSGEIDQPLARLGAGPGSITVAADRKDADAQSARSVYEVLDSAARKFSWLEL 236

Query: 192 G-LREGKNREIKKVFEFFNWKVN 213
             L  G+  +++   E     + 
Sbjct: 237 SPLT-GRTHQLRVHCESLGTPIL 258


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 82/245 (33%), Gaps = 43/245 (17%)

Query: 9   ENFTPQRVSKVIARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDG--- 64
           E    QR+   ++     SR ++++ I    +++ NG +L   +  +   + IE+ G   
Sbjct: 19  EKGVGQRLDLFLSSLLNVSRNKIKKKILSGDLRLKNGAVL-EPSHRIRGIEEIEIRGGLT 77

Query: 65  ---------VPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
                      +      E   + + +K  G+V   S      T+ ++L   +       
Sbjct: 78  EEIPSLPKAEEIALEILYEDEEILIVNKQRGMVVHPSCGHWSGTLVNSLLFHYGESLPGS 137

Query: 107 ---RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD------- 154
              R   V RLD +T G++++       + L L  +Q    +VY      +         
Sbjct: 138 SLLRPGIVHRLDKDTSGVMVIAKTERSLKSLLLQFSQRTVQKVYLCLCKNRFPYLRYSFE 197

Query: 155 ------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                       +     ++G    + + TL       +++      G+  +I+      
Sbjct: 198 ANIHRHASDRKKMAVH-RLKG-KTAETRFTLLFASSQASFLKCEPVSGRTHQIRVHLSHL 255

Query: 209 NWKVN 213
            + + 
Sbjct: 256 GFPII 260


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

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 36/260 (13%), Positives = 85/260 (32%), Gaps = 60/260 (23%)

Query: 7   VQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           V  + T  R+ +         G     ++++++   +++V+G  ++     +     + +
Sbjct: 9   VDPDETGMRLDRWFKTHFPGLGFG---QLQKLLRSGQIRVDGGRVKS-DARLQPGQTVRI 64

Query: 63  ----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                                 DG  L +    E +++ +++KP GL         R  V
Sbjct: 65  PPMGVDEKGSAPLTAKTIRNRDDGDVLSQMLLHEDSKVLVFNKPAGLAVQGGSGVTR-NV 123

Query: 98  FDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            D L +  ++       V RLD +T G+L++    G A+ L          + Y     G
Sbjct: 124 DDMLEAWRNKKGEKPRLVHRLDRDTAGVLVVARTRGAAQALTAAFRERTTKKTYWALVTG 183

Query: 152 QVDQ--------------DKLNLLKKGIVIQGICYGDMQVT----LDTQKGSNAWVTVGL 193
                             D  + ++  +   G    D  V+    ++    +  W+ +  
Sbjct: 184 VPRDREGKISTWLVKEATDDGDRMR--VAKHGEPGADHAVSYYRIIEKAAQNLCWLELEP 241

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +++         + 
Sbjct: 242 YTGRTHQLRVHCLHLGHPIL 261


>gi|120601247|ref|YP_965647.1| pseudouridine synthase [Desulfovibrio vulgaris DP4]
 gi|120561476|gb|ABM27220.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           vulgaris DP4]
          Length = 390

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 48/156 (30%), Gaps = 19/156 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           P   AE   L+++ KP GL     T       + +  +            RLD +T GLL
Sbjct: 130 PPVVAETPDLFIFDKPAGLAVHPGTGHTDSLTTRLAQHFAKAPFMPTPAHRLDRDTSGLL 189

Query: 123 LLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKL----NLLKKGIVIQG------ 169
           L+     + R L           + Y     G           + L KG    G      
Sbjct: 190 LVARSYAMLRTLHEAFASHDALVKEYLAWVAGCWQPAAPVTLHDRLSKGAEASGFERVAS 249

Query: 170 ---ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     V    ++   + + V L  G+  +I+
Sbjct: 250 DDEGAEAACTVRCLLREQHRSLLLVTLHTGRTHQIR 285


>gi|113460997|ref|YP_719064.1| tRNA pseudouridine synthase C [Haemophilus somnus 129PT]
 gi|112823040|gb|ABI25129.1| tRNA pseudouridine synthase C [Haemophilus somnus 129PT]
          Length = 234

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 29/180 (16%), Positives = 60/180 (33%), Gaps = 28/180 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L + +KP G++   S  D      V   L       V  + RLD  T G+LL   +
Sbjct: 6   QDEFLVVVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALN 65

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDK-------------LNLLKKGIVIQGICY 172
            G+A +L       Q  + Y     G +   +              +   +   +Q    
Sbjct: 66  AGIANLLCSQFELKQVKKSYLAIVRGYLSDAQRIDYPLKVQLDKIADKFSRKEELQDAIT 125

Query: 173 -----GDMQVTLDTQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                  +++     + S++  ++  L    G+  ++++  +     +  L    YG   
Sbjct: 126 DYYGLKTVEMPYGVGRYSSSRYSLVRLMPHTGRKHQLRRHLKHIFHPI--LGDTQYGDLH 183


>gi|57237010|ref|YP_178812.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165814|gb|AAW34593.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 250

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 74/199 (37%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA ++  +  ++     P    E  ++
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSHGKKVVVARALMSDKARFNVIKAKNPQIIFEDDKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 67  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 113

Query: 136 LPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDTQK 183
               +    + Y     G + ++ ++N     I  +G     +          +T    +
Sbjct: 114 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGGALSKVSKDGLSALSIITPIMMQ 173

Query: 184 GSNAWVTVGLREGKNREIK 202
                  + ++ G+  +I+
Sbjct: 174 SKKTLAKIVIQTGRTHQIR 192


>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 = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 91/250 (36%), Gaps = 46/250 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++K I+ E F  +R    +A      SR   +++  +QRV VN  ++   +  +   D 
Sbjct: 1   MQEK-IIYEKFERERADSYLASIYKDYSRSYFQKLTDRQRVFVNDKII-PVSHKLKRGDI 58

Query: 60  IEVDGVPLRKAE-------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           I ++     K +                + + +K  G+V   S      T+ + L    +
Sbjct: 59  ITIEFEKEEKFQIKPEKIKIDIIYEDDDIVVVNKRSGIVVHPSYGHLSGTLLNALMGYSA 118

Query: 107 ---RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---- 157
                  + RLD +T G+++   T    ++   +L      ++Y     G + +++    
Sbjct: 119 GKYNPYLIHRLDKDTSGVIVFAKTEKAKISISKQLQKRVVKKIYYAAVKGVIAENRGIIK 178

Query: 158 --------------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                         +N L K + I        +  +  +K     + V +  G+  +I+ 
Sbjct: 179 APLGRSPKNRKLVSVNPLAKKVAI-------TEFKVIERKDDYTLLKVRIITGRTHQIRS 231

Query: 204 VFEFFNWKVN 213
             ++ N  V 
Sbjct: 232 HMKYINHPVI 241


>gi|148826937|ref|YP_001291690.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittGG]
 gi|148718179|gb|ABQ99306.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittGG]
          Length = 239

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|167624902|ref|YP_001675196.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167354924|gb|ABZ77537.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 279

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 29/170 (17%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           E   +   HKP GL+   S    R   F        +   V  V RLD  T G+LL    
Sbjct: 30  EDDDVVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGILLFAKS 89

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD-KLN-LLKKGI-VIQGICYGDMQVTLDTQ 182
             +A  L          + Y     G + +   L+  LK+ +  +        +   D  
Sbjct: 90  SEMANALCGQFADHTVDKEYLAIVRGNMHEAGTLDYALKEELDELGDKDVDPNKAAQDAV 149

Query: 183 KGSN-------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                                  A V +    G+  ++++        + 
Sbjct: 150 TSYQPLLNSEIPFSSGRYATSRYALVQLSPHTGRKHQLRRHMAHLRHPIL 199


>gi|153952563|ref|YP_001398347.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152940009|gb|ABS44750.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 250

 Score = 59.4 bits (143), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 74/199 (37%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA ++  +  ++     P    E  ++
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSHGKKVVVARALMSDKARFNVIKTKNPQIIFEDDKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 67  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 113

Query: 136 LPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDTQK 183
               +    + Y     G + ++ ++N     I  +G     +          +T    +
Sbjct: 114 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGGALSKVSKDGLSALSIITPIMMQ 173

Query: 184 GSNAWVTVGLREGKNREIK 202
                  + ++ G+  +I+
Sbjct: 174 SKKTLAKIVIQTGRTHQIR 192


>gi|304382476|ref|ZP_07364973.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
 gi|304336388|gb|EFM02627.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           marshii DSM 16973]
          Length = 302

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/223 (18%), Positives = 78/223 (34%), Gaps = 30/223 (13%)

Query: 19  VIARAGIASRREVERMIAQQR-VKVNGILLERAAVNVMSTDHIEVDGVPLRKA------- 70
           ++   G  SR +++  +   R VKVNG ++ +    +     + V      +        
Sbjct: 28  LLTHIGDKSRNKIKATL-SGRGVKVNGKIITQYDFPLPVGTKVSVSRSKQSEPFKSKYVK 86

Query: 71  ---ERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLL 122
              E   L +  K +G+++            V D+   +  +      V RLD  T GL+
Sbjct: 87  IVYEDRYLVVIEKNVGILSMAAGRRALHVKAVLDDYFKMSRQRCKAHVVHRLDRETSGLM 146

Query: 123 LLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK---LNLLKKGI--------VIQG 169
           +   D    ++LE       + R Y     G++++D+    N LK           V  G
Sbjct: 147 IYAKDMQTEQLLEHDWHRNVYDRRYMAVVSGEMEEDEGTVANWLKDNKAYITYASPVDNG 206

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
             Y         +  +++ V   L  G+  +I+         V
Sbjct: 207 GKYAVTHFRTLARTTTHSLVEFRLETGRKNQIRVHTADMGHPV 249


>gi|301170223|emb|CBW29827.1| tRNA pseudouridine synthase [Haemophilus influenzae 10810]
          Length = 239

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 58/182 (31%), Gaps = 31/182 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A ++          + Y     G +  +++++   K I +  I     Q   + Q+ 
Sbjct: 67  SEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEA 125

Query: 185 SN----------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                                   + V +    G+  ++++  +     +  L    YG 
Sbjct: 126 ITDYEGLKIVEMPYPAGRYQTVRYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGD 183

Query: 223 FQ 224
             
Sbjct: 184 LH 185


>gi|237807273|ref|YP_002891713.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
 gi|237499534|gb|ACQ92127.1| pseudouridine synthase [Tolumonas auensis DSM 9187]
          Length = 242

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 26/172 (15%), Positives = 53/172 (30%), Gaps = 30/172 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP GL+   S  D                  V +V RLD  T G+LL   D
Sbjct: 8   QDEHLVAINKPAGLLVHRSWLDKGETQFAMQMTRDQIGQHVYTVHRLDRPTSGILLFALD 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD---------QDKLNLLKKGIVIQGICYGDMQ 176
              AR+L       +  + Y     G            +++L+ +      Q       +
Sbjct: 68  PDTARLLTDAFAGHRMQKEYLALVRGWAPLQKFLDYPLKEELDRIADKFADQDKPAQPAK 127

Query: 177 VTL-----------DTQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
             +            + +  ++  ++     L  G+  ++++        + 
Sbjct: 128 THIRCLGRVELPFAVSPRHPSSRYSLVKLLPLT-GRKHQLRRHLAHLRHPIV 178


>gi|89257067|ref|YP_514429.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica LVS]
 gi|115315423|ref|YP_764146.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica OSU18]
 gi|167009454|ref|ZP_02274385.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           FSC200]
 gi|254368306|ref|ZP_04984325.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica 257]
 gi|89144898|emb|CAJ80243.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica LVS]
 gi|115130322|gb|ABI83509.1| pseudouridylate synthase [Francisella tularensis subsp. holarctica
           OSU18]
 gi|134254115|gb|EBA53209.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica 257]
          Length = 309

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>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 = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 81/215 (37%), Gaps = 31/215 (14%)

Query: 29  REVERMIAQQRVKVNGILL------ERAA--VNVMSTDH---IEVDGVPLRK-AERTRLW 76
           R+++ M  ++RVKVN  +       ++       +  D    ++V+  P+    E     
Sbjct: 29  RDIQMMFRKKRVKVNSRVAHSQRALKKGDVLTLELPQDKDYGVDVEKGPITVLYEDAHTL 88

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TNDG 128
           + +K   ++   +      T+ + +   +       +V  V RLD +T G +L   T + 
Sbjct: 89  VVNKDPFMLVHPAGQTKSCTLSNYVAGYYAKKNVVHKVRPVHRLDRDTSGCILFGKTKEA 148

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------VIQ--GICYGDMQVT 178
                 EL + +  R+Y     G++D + +     G+        VI   G       + 
Sbjct: 149 QQYYTDELQAGRIDRIYTGLVEGRIDANGMVDAPIGVDPVFDNRRVIDELGQPAQTEYIV 208

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           LD  +G N  +   L  G+  +I+   E     + 
Sbjct: 209 LD-HEGDNTLLRFKLLTGRTHQIRVHMEHIGHPIV 242


>gi|323492963|ref|ZP_08098101.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
 gi|323312794|gb|EGA65920.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           brasiliensis LMG 20546]
          Length = 245

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 27/169 (15%), Positives = 57/169 (33%), Gaps = 38/169 (22%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           +  ++   +KP GL++      +   +++  L   +  +  V RLD++T GL++L     
Sbjct: 19  QDEQILAVNKPSGLLSVPGRLEEHYDSMWSRLVETYPDIQVVHRLDMDTSGLMVLAKSKQ 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQV 177
                       L        +VY  R  G   QD+       + +            +V
Sbjct: 79  AERSLKKQFQYRLTH------KVYYARVWGHPQQDEGE-----VDLPLICDWPNRPRQKV 127

Query: 178 TLDTQKGSNAWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
             +  K S     V  RE            G++ +++  + +     + 
Sbjct: 128 CFEHGKPSQTRYQVVKREEKTSIVRLLPITGRSHQLRVHM-QALGHPIV 175


>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 = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 6/75 (8%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ + + ++G   SR + +  I +  VKVNG ++ + +  V  ++ IEV     +   R
Sbjct: 1  MRLDEFLKKSGYFKSRSQAKEAIKRGFVKVNGKVITKPSFQVKGSEKIEV---AEKGKPR 57

Query: 73 TRLWL--YHKPIGLV 85
              L    K  G+V
Sbjct: 58 GYYKLKELDKKYGIV 72


>gi|302332618|gb|ADL22811.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus JKD6159]
          Length = 284

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 62/195 (31%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPQEIPSVNLIPYARKVEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +  +    + +  ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKGNLK--KIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|56707234|ref|YP_169130.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110669704|ref|YP_666261.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118498217|ref|YP_899267.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. novicida U112]
 gi|194324401|ref|ZP_03058174.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|224456294|ref|ZP_03664767.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|254369904|ref|ZP_04985913.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FSC022]
 gi|254369919|ref|ZP_04985927.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254375025|ref|ZP_04990505.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida GA99-3548]
 gi|254874072|ref|ZP_05246782.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|56603726|emb|CAG44688.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis SCHU S4]
 gi|110320037|emb|CAL08071.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC198]
 gi|118424123|gb|ABK90513.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida U112]
 gi|151568165|gb|EDN33819.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis FSC033]
 gi|151572743|gb|EDN38397.1| ribosomal large subunit pseudouridine synthase C [Francisella
           novicida GA99-3548]
 gi|157122874|gb|EDO66991.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. holarctica FSC022]
 gi|194321466|gb|EDX18951.1| pseudouridine synthase, RluA family [Francisella tularensis subsp.
           novicida FTE]
 gi|254840071|gb|EET18507.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis MA00-2987]
 gi|282158342|gb|ADA77733.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis NE061598]
          Length = 309

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|329123449|ref|ZP_08252013.1| tRNA pseudouridine synthase C [Haemophilus aegyptius ATCC 11116]
 gi|327471031|gb|EGF16486.1| tRNA pseudouridine synthase C [Haemophilus aegyptius ATCC 11116]
          Length = 239

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 58/182 (31%), Gaps = 31/182 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A ++          + Y     G +  +++++   K I +  I     Q   + Q+ 
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEA 125

Query: 185 SN----------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                                   + V +    G+  ++++  +     +  L    YG 
Sbjct: 126 ITDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGD 183

Query: 223 FQ 224
             
Sbjct: 184 LH 185


>gi|2501677|sp|Q47417|TRUC_PECCC RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|496598|emb|CAA55982.1| unnamed protein product [Pectobacterium carotovorum]
          Length = 376

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 52/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LLL   
Sbjct: 121 QDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLLALS 180

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L     S Q  + Y     G V           ++L+ +               
Sbjct: 181 SEVARALSQQFESHQMQKTYHAVVRGYVLDDGVIDYALTEELDKIADKFTNPDKAPQPAV 240

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  Q  +    G        L E     G+  ++++     +  + 
Sbjct: 241 THYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHIHHPII 290


>gi|330445141|ref|ZP_08308793.1| tRNA pseudouridine 65 synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328489332|dbj|GAA03290.1| tRNA pseudouridine 65 synthase [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 245

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 52/169 (30%), Gaps = 27/169 (15%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL     
Sbjct: 9   DEYLIAVNKPAGMLVHRSWLDSHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFGLSS 68

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            +A  +          + Y     G + +  +      + +  I   +     + Q    
Sbjct: 69  EIAAEMMPMFAGRDMHKTYHAVVRGWIKEAAVLDYPLKVELDKIADKNASEEKEAQPAVT 128

Query: 187 AW---VTVG--------------LRE-----GKNREIKKVFEFFNWKVN 213
           A+    TV               L E     G+  ++++     +  + 
Sbjct: 129 AYEPLATVETDIAVGRYSTSRYCLVEMKPETGRKHQLRRHMHHLSHHII 177


>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 = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/215 (14%), Positives = 62/215 (28%), Gaps = 32/215 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A+    S ++ ++ I    V + G  L  A        H  +          +   L
Sbjct: 6   KILAKNLNISHKQAKKYIDMGLVSLQGKRLTLARQKFPLDTHFHIKECLKTDVLYQDQEL 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            + +K   + +   +   +   +  L           RLD +T GLLLL       + L 
Sbjct: 66  LVLNKATHIDSYTLERQHKP--YKLL----------HRLDKSTSGLLLLAQATFYTKALL 113

Query: 136 L-PSTQWLRVYRVRFHGQVD-QDKLNL----------LKKG-----IVIQGICYGDMQVT 178
                +  + Y     G +     L              KG     + ++G         
Sbjct: 114 AFKKREVYKEYLALIEGILKRPKTLTQPLSVRTNHMHFNKGFVKTFVDLKGKPAITHLYP 173

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +         + V +  G   +I+         + 
Sbjct: 174 I-YHTKQQTLLKVVIETGITHQIRAHLSHIGHPIV 207


>gi|226229096|ref|YP_002763202.1| ribosomal large subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
 gi|226092287|dbj|BAH40732.1| ribosomal large subunit pseudouridine synthase A [Gemmatimonas
           aurantiaca T-27]
          Length = 476

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/156 (19%), Positives = 55/156 (35%), Gaps = 17/156 (10%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSR---VISVGRLDINTE 119
             P    E   L + +KP G++T     P  +  V   L + +      + V RLD++T 
Sbjct: 265 NEPAVVYEDDHLLVVNKPSGMLTVPGRGPTMQDCVMTRLRARYPDATGQMVVHRLDLDTS 324

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN---LLKKGIV-----IQG 169
           GLLL   D   A  L+      +  + Y     G V  D  +    L+  +      I  
Sbjct: 325 GLLLAAKDPITASALQRLFSLREIDKHYVAWLDGVVTDDHGHIHLPLRMDVDDRPRNIHD 384

Query: 170 ICYGD---MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +G     +  +  +      V      G+  +++
Sbjct: 385 PVFGKPAHTEWQVMARTDGRTRVRFTPHTGRTHQLR 420


>gi|145636146|ref|ZP_01791816.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittHH]
 gi|145270668|gb|EDK10601.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittHH]
          Length = 239

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|121534542|ref|ZP_01666364.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
 gi|121306794|gb|EAX47714.1| pseudouridine synthase, RluA family [Thermosinus carboxydivorans
           Nor1]
          Length = 300

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 33/219 (15%), Positives = 70/219 (31%), Gaps = 34/219 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R+++++   + + +NG  +      V + D + V              G      E  
Sbjct: 31  SGRQIQKLTRHKGILLNGKTVY-LQKKVKADDTLRVLISGDSAYGVQPEQGPVEILYEDD 89

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            L + +KP   +   +      T+ + L     +      + +V RLD  T G ++   D
Sbjct: 90  YLLVINKPAYQLVHPTGSTTSGTLANYLAYHLEQRGIICTIRAVHRLDRETSGCIIFAKD 149

Query: 128 GGLARVLE--LPSTQWLRVYRVRFHGQVDQ--DKLNLL---------KKGIVIQGICYGD 174
                +LE  L +    R Y     G V      ++           ++ +   G     
Sbjct: 150 AHSQFLLEQQLAARTLKRTYWALVKGSVSPPAGTIDAPIGPHPHFANRRAVTAHGDPAIT 209

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              T+         + + L  G+  +I+       + + 
Sbjct: 210 HYQTI-RSFPDATLLELILDTGRTHQIRVHLAHLGYPIV 247


>gi|109947567|ref|YP_664795.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
 gi|109714788|emb|CAJ99796.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
          Length = 242

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 67/201 (33%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 6   KLLSVQENISHKKAKALIDLGLVSIGGKKLSVARKELPQNMHFNVQKIEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +           +D + S F     + RLD  T G++LL  +     +  
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKDWTLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
             + +     + Y     G V ++    +   I+         +++   Q+         
Sbjct: 114 KKAFKERAVKKEYLALVQGIVGEE--KEINAPILTIKTTKAFSKISKKGQEAITIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + V ++ G+  +I+
Sbjct: 172 IINKKTLLKVEIKTGRTHQIR 192


>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 = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/269 (15%), Positives = 87/269 (32%), Gaps = 72/269 (26%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE---------RMIAQQRVKVNGILLERAAVNVMS 56
            + E+   +R+ KV+        RE           +   ++ +KVNG+ ++     V  
Sbjct: 5   TITEDKANKRIDKVL--------RETFPRLPNGALFKAFRKKDIKVNGVRVKE-DHIVKL 55

Query: 57  TDHIEV-------DGVP-----------LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
            D +++       DGVP               E + L + +K  G+          +T+ 
Sbjct: 56  NDRVDIYIIDEILDGVPKAGELNYETAFSVAYEDSNLLIVNKKQGIPVHPDRTQTENTLI 115

Query: 99  DNLPSIFSRVIS-----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY 145
           D +                      RLD NT GL+++  +     ++     S +  + Y
Sbjct: 116 DFVKEYLKLKGEFEENSGFTPSLCHRLDRNTGGLVMIAKNSSTLHMVLKKMKSGEISKYY 175

Query: 146 RVRFHGQVD--QDKLNLL------KKGIVIQGICYGDMQVTL-------------DTQKG 184
           +    G+++  +D L         K  + I+     +    +               +  
Sbjct: 176 QCLVKGKMEKKEDILKAYLEKDEKKSRVFIKDTKSKNAVEIITGYKVLSYKELPDIGEGI 235

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           SN  + V L  G+  +I+         V 
Sbjct: 236 SN--LEVTLYTGRTHQIRAHLAHIGHPVV 262


>gi|308184739|ref|YP_003928872.1| hypothetical protein HPSJM_04875 [Helicobacter pylori SJM180]
 gi|308060659|gb|ADO02555.1| hypothetical protein HPSJM_04875 [Helicobacter pylori SJM180]
          Length = 242

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 75/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPENTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIIAPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|109899489|ref|YP_662744.1| pseudouridylate synthase [Pseudoalteromonas atlantica T6c]
 gi|109701770|gb|ABG41690.1| tRNA pseudouridine synthase C [Pseudoalteromonas atlantica T6c]
          Length = 252

 Score = 59.4 bits (143), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 34/169 (20%), Positives = 55/169 (32%), Gaps = 33/169 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   HKP GL+   S  D   T F        I   V  V RLD  T G+L+      +A
Sbjct: 12  LVAIHKPAGLLVHRSMIDRHETQFAMQMLRDQIGQHVFPVHRLDRPTSGVLVFALSADIA 71

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGICYGDMQVTLDTQKGSN- 186
           R+L  +       + Y     G V +  L    LK+   +  I     +   D Q+    
Sbjct: 72  RLLGEQFAGNTIAKTYFAIVRGHVKEAGLIDYALKE--KLDKIADKRAKQDKDAQEAQTE 129

Query: 187 ---------------------AWVTVGLREGKNREIKK-VFEFFNWKVN 213
                                  V +  + G+  ++++ +    N  + 
Sbjct: 130 YVPLQQFELPFAVSRYPSARYTLVRLHPKTGRKHQLRRHMC-HINHPIV 177


>gi|332678953|gb|AEE88082.1| Ribosomal large subunit pseudouridine synthase C [Francisella cf.
           novicida Fx1]
          Length = 309

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|149912122|ref|ZP_01900709.1| pseudouridine synthase-like protein [Moritella sp. PE36]
 gi|149804799|gb|EDM64840.1| pseudouridine synthase-like protein [Moritella sp. PE36]
          Length = 238

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 31/190 (16%), Positives = 57/190 (30%), Gaps = 39/190 (20%)

Query: 57  TDHIEVD--GVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            D++EV   G   +   R    LY        +KP GL++  S  + +      L    S
Sbjct: 10  GDNVEVRAAGKNTQLGVRHLEILYSDNDLVVINKPAGLLSVASANENKQHALAILRKQLS 69

Query: 107 R------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL 160
                  +  V RLD +T G+L+      +   +    +   + Y     G         
Sbjct: 70  HAKNSVALWPVHRLDRDTSGVLMFATSREMRDAVNEGWSGAEKTYLAVVEGSPKP----- 124

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSN-----------------AWVTVGLREGKNREIKK 203
             +G + Q +     +  +     S                    + V L  G+  +I+ 
Sbjct: 125 -SQGRIDQPLRMDPEKYQMIVGPHSEAKNAVTHFKTLRTVKELTLLEVKLETGRQHQIRV 183

Query: 204 VFEFFNWKVN 213
              +    V 
Sbjct: 184 HMAWLGHSVI 193


>gi|295095907|emb|CBK84997.1| Pseudouridylate synthases, 23S RNA-specific [Enterobacter cloacae
           subsp. cloacae NCTC 9394]
          Length = 228

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 37/195 (18%), Positives = 66/195 (33%), Gaps = 39/195 (20%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE+        +   L L +KP GL++ +  +P    +V   L   F     V R
Sbjct: 12  PCHDDIEI------LWQDEHLLLINKPSGLLSLSGKNPQNLDSVHHRLVQTFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G V+QD      +G V   I 
Sbjct: 66  LDFGTSGLMVIARNKAINAALCHQFSQRAVNKVYTALLCGHVEQD------EGTVDAPIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG--LRE---------------GKNREIKKVFEFFN 209
                     +   T K + +   V   + +               G+  +++   +   
Sbjct: 120 KDPALFPLMTICARTGKPARSRYRVVERIYQDTTMPLTRVELTPETGRTHQLRIHCQQLG 179

Query: 210 WKVNRLIRISYGPFQ 224
             +       YG  +
Sbjct: 180 HPILGCD--LYGGLE 192


>gi|332883134|gb|EGK03417.1| hypothetical protein HMPREF9456_01484 [Dysgonomonas mossii DSM
           22836]
          Length = 313

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 30/150 (20%), Positives = 61/150 (40%), Gaps = 21/150 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRKAERTR 74
           SR  V+ ++A +++KVNG L+ +    + + D + V             G+ +   +   
Sbjct: 33  SRNAVKSLLAHKQIKVNGKLITQFDFELKAKDKVSVMKYDQSRKEKRLKGLKIVFEDDD- 91

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDG 128
           L +  K  G ++  +D +   TV+++L          +RV  + RLD    GL++   D 
Sbjct: 92  LLVIEKEAGFLSVATDKEKSRTVYNSLNEYVKKKDKKARVYVLHRLDREVSGLMIFAKDM 151

Query: 129 GLARVLELP-STQWLR-VYRVRFHGQVDQD 156
            L  + +        +  Y     G+ +  
Sbjct: 152 ELQDIFQKNWDNLVPKYSYMAIVEGRPNPK 181


>gi|253732507|ref|ZP_04866672.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
 gi|253723788|gb|EES92517.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH959]
          Length = 273

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D I V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDIFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKAHVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKEAVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


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

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 81/262 (30%), Gaps = 63/262 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V ++    R+ +         RR         ++++    +V+V+G     AA  +   
Sbjct: 4   TVSDDEADIRLDRWF-------RRHYPHLTQGALQKLCRTGQVRVDGRRAT-AATRLEPG 55

Query: 58  DHIEV-----------------DGVPLRKAERTRLW------LYHKPIGLVTTHSDP--D 92
             + V                 D   +R+  +  ++      + +KP G+          
Sbjct: 56  QAVRVPPIPNASRPPPLAVKPLDARQVREINQMVIYRDDHVIVLNKPAGIAVQGGPGITH 115

Query: 93  GRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
               + D L       R   V R+D +T GLLL+    G+A  L          +VY   
Sbjct: 116 HIDALLDGLRDSPDDPRPRLVHRIDRDTSGLLLVARTPGVAAKLAAAFRGRDVHKVYWAV 175

Query: 149 FHGQVDQDK------LNLLKKG-----IVIQGICYGDMQV-----TLDTQKGSNAWVTVG 192
             G+           L  L  G     +V +      +        LD      +W+ + 
Sbjct: 176 VVGRPSPATGIIDQPLTRLGAGAGAISVVAERGDADAVHALSEYEVLDAAARKMSWLALS 235

Query: 193 -LREGKNREIKKVFEFFNWKVN 213
            L  G+  +++   E     + 
Sbjct: 236 PLT-GRTHQLRVHCEALGNPIL 256


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

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 43/263 (16%), Positives = 79/263 (30%), Gaps = 62/263 (23%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVM 55
              V E+    R+ +         RR         ++++    +++V G  +  A+  + 
Sbjct: 5   NRTVSEDEDGIRLDRYF-------RRHYPHLTQGALQKLCRTGQIRVEGKRV-EASTRLE 56

Query: 56  STDHIEV-----------------DGVPLRKAERTRLW------LYHKPIGLVTTHSDPD 92
               + V                 D    R+  +  ++      + +KP GL        
Sbjct: 57  PGQTVRVPPIPMAAKPARDVPRPLDEKLAREIRKMVVYQDKHVIVLNKPAGLAVQGGPGI 116

Query: 93  GRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV 147
            +               R   V R+D +T GLLLL    G+A  L          ++Y  
Sbjct: 117 TKHIDMMLDGLREEDDPRPRLVHRIDKDTSGLLLLARTPGVAAKLAASFRGRDVKKIYWA 176

Query: 148 RFHGQVD------QDKLNLLKKG----IVIQGICYGDMQ------VTLDTQKGSNAWVTV 191
              G+ D         L  L  G     V       D Q        LD+     +W+ +
Sbjct: 177 VVVGRPDPLSGEIDQPLARLGAGPGSITVAADRKDADAQFARSVYEVLDSAARKFSWLEL 236

Query: 192 G-LREGKNREIKKVFEFFNWKVN 213
             L  G+  +++   E     + 
Sbjct: 237 SPLT-GRTHQLRVHCESLGTPIL 258


>gi|325528651|gb|EGD05737.1| RluA family pseudouridine synthase [Burkholderia sp. TJI49]
          Length = 359

 Score = 59.0 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 84/241 (34%), Gaps = 40/241 (16%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV+++G   +     V     IE+      
Sbjct: 23  SLAGERLDKALAQLFPEFSRSRLQSWIDAQRVRIDGAPAK-IRQPVPLGATIELVPDLLP 81

Query: 63  -------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP GLV   +  +   T+ + L   +        R
Sbjct: 82  EQLAFTPEPVPLDVVYEDDALVVINKPAGLVVHPAAGNWSGTILNGLLHRYGDAAAGLPR 141

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVDQ 155
              V RLD  T GL+++         L  +L +    R Y     G           + +
Sbjct: 142 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGMMPEDGTIDAPIGR 201

Query: 156 DKLNLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           D     +  +V    G        T+DT   Q+   + +   L  G+  +I+        
Sbjct: 202 DPRERTRMAVVTGASGKPARTHFRTVDTCVWQRQPVSAIQCDLETGRTHQIRVHCSHVGH 261

Query: 211 K 211
            
Sbjct: 262 P 262


>gi|315648999|ref|ZP_07902093.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
 gi|315275680|gb|EFU39034.1| pseudouridine synthase, RluA family protein [Paenibacillus vortex
           V453]
          Length = 358

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 88/234 (37%), Gaps = 46/234 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I+Q+     R  K+I+R          ++  Q  + +NG  +   +  V + D I
Sbjct: 19  MLLKTIMQKRMGVSR--KLISRL---------KLTEQG-IMLNGTRVY-ISAKVQTGDII 65

Query: 61  EV-------DGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           E+       D +  +        E   L + +KP G++   +      T+ + +   +  
Sbjct: 66  EIRMEQERSDDMLPQPMELDILYEDGHLLVLNKPAGIIVHPTKGHYTDTLANGVVHYWLE 125

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH--------- 150
                R  +V RLD  T G+L++  +  + + +     +    + Y    H         
Sbjct: 126 QGWNYRFRAVHRLDQETSGVLVVAKNPYVHQHVSEQMIAGTVDKRYIALVHGTPASRSGD 185

Query: 151 --GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             G +D+D L   ++ +   G          +T K + + V + L  G+  +I+
Sbjct: 186 IEGPIDRDPLEPHRRIVTPGGYPSLTRYKVCETFKSA-SMVELKLETGRTHQIR 238


>gi|306821486|ref|ZP_07455089.1| RluA family pseudouridine synthase [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
 gi|304550501|gb|EFM38489.1| RluA family pseudouridine synthase [Eubacterium yurii subsp.
           margaretiae ATCC 43715]
          Length = 300

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/264 (15%), Positives = 88/264 (33%), Gaps = 51/264 (19%)

Query: 35  IAQQR--VKVN-GILLERAAVNVMSTDHIEV--DGVPLRKAERTR----------LWLYH 79
           I + +  + +N G + +     +   D I+V           + +          + ++ 
Sbjct: 40  IKKGKYVISINDGKIPKN--HIISEKDVIKVVMHDEKSDYISQEKNLDILFEDEDIIIFD 97

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARV 133
           KP G+V+  +     +T+ +    IF      S+V  + RLD++T G++ +  +      
Sbjct: 98  KPAGIVSHPTKSHLENTMLNYAQWIFEKKNIESKVRFISRLDMDTSGIITIAKNAFSHYA 157

Query: 134 LELP--STQWLRVYRVRFHGQVD--------QDKLNLLKKG---IVIQGICYGDMQVTLD 180
           L     S +  + Y     G            +K+   + G   I+            + 
Sbjct: 158 LSQGFLSDKIQKRYTAIVSGDTSILSDSGTIAEKIEKSEDGIKRIITDEGQEAITHYKIV 217

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +    + + + L  G+  +I+         +        G      L  G    +S++ 
Sbjct: 218 KRGEKYSVLELLLETGRTHQIRVHLSHLGLPI-------IG----DELYGGDMSVMSRQA 266

Query: 241 LR----EQLGPHLLEEAQVNLDAP 260
           L     E + P  +E+  V    P
Sbjct: 267 LHCHSLEIISPRSMEKISVTSPYP 290


>gi|134301269|ref|YP_001121237.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis WY96-3418]
 gi|134049046|gb|ABO46117.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. tularensis WY96-3418]
          Length = 309

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VTEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|113970985|ref|YP_734778.1| tRNA pseudouridine synthase C [Shewanella sp. MR-4]
 gi|113885669|gb|ABI39721.1| tRNA pseudouridine synthase C [Shewanella sp. MR-4]
          Length = 284

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/173 (14%), Positives = 52/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           +   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  QDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------- 175
                +A  L     +    + Y     G + +  +      + +  +            
Sbjct: 92  AKSSEVANALCEQFANHSIEKQYLALVRGNMHESGILDYALKVELDEVADKFANQDKAAQ 151

Query: 176 ------------QVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFFNWKVN 213
                       ++   + + + +    V +  + G+  ++++        + 
Sbjct: 152 DAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKTGRKHQLRRHMAHLRHPII 204


>gi|160897919|ref|YP_001563501.1| pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160363503|gb|ABX35116.1| pseudouridine synthase [Delftia acidovorans SPH-1]
          Length = 319

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/173 (17%), Positives = 54/173 (31%), Gaps = 22/173 (12%)

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFS-RVISVGRLDINT 118
           D  PL        L   +KP G +   +  D   T F    L       V    RLD  T
Sbjct: 47  DDAPLHILWRDEHLVAVYKPAGWLVHRTGLDAHETRFVLQTLRDQLGCHVYPAHRLDKGT 106

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGD 174
            G+L++      A+ L       +  + Y     G +    +  + L+     +      
Sbjct: 107 CGVLVMALHAQAAQRLGQAFAGQEVRKQYLALVRGWLPDAVEVDHALRPDDAPEDAPAQP 166

Query: 175 MQVTL---------DTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
            Q +L         +     +A   + L E     G+  +I++  +     + 
Sbjct: 167 AQTSLRCLARLEWPEAFDPRHAATRISLVEALPATGRRHQIRRHLKHVAHPII 219


>gi|145629453|ref|ZP_01785251.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.1-21]
 gi|144978296|gb|EDJ88060.1| tRNA pseudouridine synthase C [Haemophilus influenzae 22.1-21]
 gi|309750918|gb|ADO80902.1| tRNA U65 pseudouridine synthase [Haemophilus influenzae R2866]
          Length = 239

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|319776302|ref|YP_004138790.1| tRNA pseudouridine synthase [Haemophilus influenzae F3047]
 gi|317450893|emb|CBY87118.1| tRNA pseudouridine synthase [Haemophilus influenzae F3047]
          Length = 239

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|313683665|ref|YP_004061403.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313156525|gb|ADR35203.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 305

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/207 (20%), Positives = 81/207 (39%), Gaps = 33/207 (15%)

Query: 6   IVQENFTPQRVSK----VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--DH 59
           I ++   P+R  K    ++   GI ++ E +R+IA+ R+  NGI++   A  +     D 
Sbjct: 4   ITKKLHAPER-QKAFRFLMQELGI-TQSEAQRLIAKGRLSQNGIVMSNNAGYIEEGDFDF 61

Query: 60  IEVDGVPLRKAERTR---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLD 115
           I  + V L            +Y KP GL+    +     ++ D +   F    ++  R+D
Sbjct: 62  ICFEPVTLGLVPTFVEEEFAVYDKPSGLLVHPQNRHTPYSLNDEIKHRFGHEANITHRID 121

Query: 116 INTEGLLLLTND--GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
             T GL+L   +        +     Q  + Y     G + +                  
Sbjct: 122 QETSGLVLAARNKLSERTLKMMFEERQITKKYIAMVKGHLKE----------------PL 165

Query: 174 DMQVTLDTQKGSNAWVTVGLR---EGK 197
           D+Q  L  ++ +++ V + +R   EGK
Sbjct: 166 DIQEPLLRREDASSIVRMIVRVHPEGK 192


>gi|309356679|emb|CAP36772.2| hypothetical protein CBG_19546 [Caenorhabditis briggsae AF16]
          Length = 438

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/196 (18%), Positives = 65/196 (33%), Gaps = 24/196 (12%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHK 80
            +      R+ VNG  +      + + D +E         V  +P+R  +E   L +  K
Sbjct: 109 AKVACKMGRIYVNGEQMTDVDYVMKNGDRVEHWVHRHEHPVRDLPIRIISETDDLLVIEK 168

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA--RVLEL 136
           P  L           TV   L     +  +  + RLD  T G+LL   +          L
Sbjct: 169 PPSLPVHTCGQYAIHTVLGQLRENEEKTGLRVLHRLDRATSGVLLFAKNYETDLEFKTTL 228

Query: 137 PSTQWLRVYRVRFHGQVDQDKLN--------LLKKGI--VIQGICYGDMQVTLDTQKGSN 186
              +W + Y  +  G    ++          ++  GI  V                 G++
Sbjct: 229 KQGEWSKEYVCKVDGVFPDEEQVCEQPIGPLVISMGIQCVRPDGKEAKSTFRKLWSDGTH 288

Query: 187 AWVTVGLREGKNREIK 202
           + V V +  G+  +I+
Sbjct: 289 SVVQVHIETGRTHQIR 304


>gi|126666670|ref|ZP_01737647.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
 gi|126628715|gb|EAZ99335.1| Pseudouridylate synthases, 23S RNA-specific [Marinobacter sp.
           ELB17]
          Length = 325

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 77/231 (33%), Gaps = 38/231 (16%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++    + +R+ +  A      SR  ++  +    + VNG   +     VM  D +E+D 
Sbjct: 12  VIPPKLSDKRLDQAAAELMPEHSRSRLQSWVKSGALTVNGGQCK-PRDKVMLGDKLELDA 70

Query: 65  VPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIF 105
            P  +              E   + + +KP GLV   +      T+ + +          
Sbjct: 71  EPEAQVTWQAEAITLDIVYEDEHILIINKPAGLVVHPAAGHADGTLVNAILNIAPEVENL 130

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD--------- 154
            R   V RLD +T G++++         L  +L +    R Y     G +          
Sbjct: 131 PRAGIVHRLDKDTSGVMVVARSLIAHTSLVNQLQTRTMGREYEAVVVGTLTGGATVDAPI 190

Query: 155 ---QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +   +    V++          +  +  ++  V   L  G+  +I+
Sbjct: 191 GRHPTERKRMA---VVKSGKPAVTHYRVIERFSAHTHVRCKLESGRTHQIR 238


>gi|224368793|ref|YP_002602954.1| RluD1 [Desulfobacterium autotrophicum HRM2]
 gi|223691509|gb|ACN14792.1| RluD1 [Desulfobacterium autotrophicum HRM2]
          Length = 313

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 86/251 (34%), Gaps = 41/251 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M  K  + E    +R+  V+A      +R  V R I +  + V+G   ++ A  V   + 
Sbjct: 1   MNLKIEISEALMGRRLDLVVADVVHDTTRGAVVRAIEKGLILVSGNR-KKPAYRVKPGEV 59

Query: 60  I--------EVDGVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +        E++  P  +        E   + + +KP G+V      +   T+ + L   
Sbjct: 60  VCGSLGSESEIESKPRAESISLDFLHEDQWIVVVNKPAGMVVHPGAGNSSGTLLNALLHH 119

Query: 105 FS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
           F            R   V RLD +T G +++         L+      +  + Y     G
Sbjct: 120 FPSLTDTHCDPPLRGGIVHRLDKDTSGTIVVAKSKKAYEFLQKEFRFRRVEKRYIALATG 179

Query: 152 QVDQDKLN---------LLKKGIVIQGICYGDMQV--TLDTQKGSNAWVTVGLREGKNRE 200
            + + +           + +K + +        +    +  Q   +  + VGL+ G+  +
Sbjct: 180 IITETQGRITLPIGRHPIHRKRMAVNTERARPAETLWRVLGQMAGHTLLDVGLKTGRTHQ 239

Query: 201 IKKVFEFFNWK 211
           I+  F      
Sbjct: 240 IRVHFRALGHP 250


>gi|317182255|dbj|BAJ60039.1| hypothetical protein HPF57_0965 [Helicobacter pylori F57]
          Length = 242

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 66/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALTQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>gi|325297415|ref|YP_004257332.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
 gi|324316968|gb|ADY34859.1| pseudouridine synthase, RluA family [Bacteroides salanitronis DSM
           18170]
          Length = 307

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/219 (15%), Positives = 68/219 (31%), Gaps = 29/219 (13%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ER 72
           AGI SR  V+ ++  + V V+  +       +     +++     +            E 
Sbjct: 40  AGI-SRTRVKALLTNRVVLVDNTIQTLYNYPLQPGMCVQISREKHKHEFHHPMLKILYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRLDINTEGLLLLTN 126
             + +  K  GL++  ++     T    L     R+        V RLD  T G+++   
Sbjct: 99  AYIIVVEKKEGLLSVATERQKERTAQHILNEYVKRIHKGNRIYVVHRLDRETSGIMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL--------NLL--KKGIVIQGICYGD 174
           D      L          R Y     G+++QD+           L         G  Y  
Sbjct: 159 DEKTQHTLRDNWHDLVRDRRYVTIVQGEMEQDEGTVCSWLTDRKLYVSSSPTDDGGKYSV 218

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +    + + + L  G+  +I+   +     V 
Sbjct: 219 THYHTIKRANGFSLLELQLETGRKNQIRVHMQSLGHPVV 257


>gi|260772177|ref|ZP_05881094.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
 gi|260613044|gb|EEX38246.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           metschnikovii CIP 69.14]
          Length = 245

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 57/164 (34%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E   +   +KP GL++      +   +++  L +  S +  V RLD++T GL+L   +  
Sbjct: 19  EDEYILAVNKPSGLLSVPGKHIEHYDSMWSRLVAEHSEIQVVHRLDMSTSGLMLFAKNKY 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGI 170
                       L        +VY  R  G+++Q +               ++ +  +  
Sbjct: 79  MEAALKKQFQYRLTH------KVYYARVWGKLEQQQGEVDLPLICDWPNRPRQKVCFEHG 132

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
                   +  Q+     V +    G++ +++  +       + 
Sbjct: 133 KASKTLYQVVKQEEQTTIVRLFPVTGRSHQLRVHML-AIGHPIV 175


>gi|172058049|ref|YP_001814509.1| RluA family pseudouridine synthase [Exiguobacterium sibiricum
           255-15]
 gi|171990570|gb|ACB61492.1| pseudouridine synthase, RluA family [Exiguobacterium sibiricum
           255-15]
          Length = 293

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 60/192 (31%), Gaps = 34/192 (17%)

Query: 54  VMSTDHIEV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           V + D I V               G      E   L + +KP G+ +  S      ++ +
Sbjct: 55  VHAGDRIHVRFPEEQPAQDMHATSGELDILFEDDWLLIVNKPPGMASIPSRLHPERSLSN 114

Query: 100 NLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG 151
            +   + +      +  V RLD +T GL++          L          R Y     G
Sbjct: 115 FVLGYYRQHQIPYAIHIVNRLDRDTSGLVVFAKHSLAHHQLSKMQQNGLLDRRYVALIEG 174

Query: 152 QVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSN---AWVTVGLREGKNR 199
            +    ++L         +++ +   G       +T +     +   + +T+ L  G+  
Sbjct: 175 TIPAQTIDLPIGQTDHSFMERMVREDGQQAITHILTSEPITAFSRELSRLTIKLETGRTH 234

Query: 200 EIKKVFEFFNWK 211
           +I+         
Sbjct: 235 QIRVHLAALGHP 246


>gi|332288146|ref|YP_004418998.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
 gi|330431042|gb|AEC16101.1| tRNA pseudouridine synthase C [Gallibacterium anatis UMN179]
          Length = 242

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/175 (15%), Positives = 57/175 (32%), Gaps = 28/175 (16%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLL 122
           P+   ++  L   +KP G++   S  D      V   L       V  + RLD  T G+L
Sbjct: 8   PILYQDQA-LIAVNKPAGMLVHRSWLDKHETEFVMQKLRDQIGQYVFPIHRLDRPTSGVL 66

Query: 123 LLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD-------------QDKLNLL------ 161
           L      +A  +       Q  + Y     G +                  +        
Sbjct: 67  LFALSSEIANAVCRQFEQKQVQKQYLAVVRGYLTGQERIDYPLKPKWDKIADKFSQQDKT 126

Query: 162 -KKGIV-IQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVN 213
            ++ +   QG+   ++ V +     S  + V +  + G+  ++++  +     + 
Sbjct: 127 PQEAVTDYQGLATLEIPVAVGRYATSRYSLVRLTPQTGRKHQLRRHLKHIFHPII 181


>gi|208780244|ref|ZP_03247586.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
 gi|208743893|gb|EDZ90195.1| pseudouridine synthase, RluA family [Francisella novicida FTG]
          Length = 309

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|54310089|ref|YP_131109.1| tRNA pseudouridine synthase C [Photobacterium profundum SS9]
 gi|46914528|emb|CAG21307.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum SS9]
          Length = 245

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/174 (16%), Positives = 54/174 (31%), Gaps = 35/174 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL    
Sbjct: 8   QDEYLVAVNKPSGMLVHRSWLDRHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFGLS 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGI------------- 170
             +A  +       +  + Y     G +    +    LKK   +  I             
Sbjct: 68  SEIASQMMPVFSGREIHKTYHAVVRGWIKDAAVLDYPLKK--ELDKIADKNAAEEQEAQE 125

Query: 171 ------CYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                     ++  +   + + +   +   E     G+  ++++     N  + 
Sbjct: 126 AVTAYSPLATVETNIPVGRYATSRYCLV--EMKPETGRKHQLRRHMHHLNHHII 177


>gi|303228679|ref|ZP_07315504.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-134-V-Col7a]
 gi|303230316|ref|ZP_07317081.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-049-V-Sch6]
 gi|302515027|gb|EFL57004.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-049-V-Sch6]
 gi|302516659|gb|EFL58576.1| putative Ribosomal large subunit pseudouridine synthase D
           [Veillonella atypica ACS-134-V-Col7a]
          Length = 295

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/215 (16%), Positives = 75/215 (34%), Gaps = 31/215 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRK------AERTRL 75
           R V+ +  ++RVKVN  +   +   +   D I ++       GV + K       E    
Sbjct: 29  RNVQMIFRKKRVKVNSRVA-HSKRMLRKGDVITIELPQDKDYGVEVEKGPIEVLYEDEHT 87

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TND 127
            + +K   ++   +      T+ + +   +       ++  V RLD +T G+++   T +
Sbjct: 88  LVVYKSPFMLVHPAGQTKYHTLSNLVAGYYAKRGEVHKIRPVHRLDRDTTGVIMFGKTRE 147

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--VIQGICYGDM-------QVT 178
                  +L   +  RVYR    G++  D +     G+  V       D        +  
Sbjct: 148 AEQYYTKQLQEGRIHRVYRGLVEGKITSDGVVNEPIGVDPVFDNRRCVDEFGQDAVTEYH 207

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +       + +   L  G+  +I+         + 
Sbjct: 208 VIEYDDVQSLLEFTLLTGRTHQIRVHMAHIGHPII 242


>gi|39995777|ref|NP_951728.1| ribosomal large subunit pseudouridine synthase C [Geobacter
           sulfurreducens PCA]
 gi|39982541|gb|AAR34001.1| ribosomal large subunit pseudouridine synthase C [Geobacter
           sulfurreducens PCA]
 gi|298504786|gb|ADI83509.1| RNA pseudouridine synthase, RluA family [Geobacter sulfurreducens
           KN400]
          Length = 296

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/225 (16%), Positives = 71/225 (31%), Gaps = 39/225 (17%)

Query: 31  VERMIAQQRVKVNGILL---ERAAVN----VMSTDHIEVDGVPLRKA--------ERTRL 75
           + ++I+   +K+NG  +      A      +  +D        L  A        E    
Sbjct: 31  IRKLISAGHLKINGGAVAPDTLLAAGNTATIKESDRTR---QLLAAAKPQLDILWEDDYC 87

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
            + +KP GL    +   G + + +      +      ++  V RLD  T G  +L     
Sbjct: 88  VIVNKPAGLPVHRTAEAGEANLVELAEHFMAGRGTAVKLRPVNRLDRGTSGATILAKSSS 147

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            A +L          ++Y     G +     ++       + G        TL      +
Sbjct: 148 SAGMLGRYVKEEGLDKLYLAVTDGSLPDAGTIDT-----PLDGKDAHTDFRTLARDTAVS 202

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
             + + +  G+  +I+K        V    R        GTLL G
Sbjct: 203 FALVIPIS-GRMHQIRKHLSAIGHPVRGDRRYR------GTLLTG 240


>gi|116617792|ref|YP_818163.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
 gi|116096639|gb|ABJ61790.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc
           mesenteroides subsp. mesenteroides ATCC 8293]
          Length = 299

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/194 (18%), Positives = 62/194 (31%), Gaps = 26/194 (13%)

Query: 43  NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNL 101
           NG ++        S D +  D  PL        WL   KP G+ T     D   T+ + +
Sbjct: 54  NGDIVTIVMPTEKSNDLVVPDYKPLDIIFENEHWLVVDKPYGITTVPGHADRLHTLVNQV 113

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHG 151
                 +         V RLD +T G++LL      A  +    L      + Y     G
Sbjct: 114 KGHLETIKADDLVPHVVTRLDRDTSGIVLLAKH-RFAHAVLDQQLQDHTVEKFYLAYPSG 172

Query: 152 QVDQD-----------KLNLLKKGIVIQGICYGD---MQVTLDTQKGSNAWVTVGLREGK 197
            +  D             + +K+ +   G        ++   +  + +   V V L  G+
Sbjct: 173 ILADDHGDINAPIGRMDGDFIKREVRDDGKPSRTEYWVERRYEDDEQNMTRVKVQLHTGR 232

Query: 198 NREIKKVFEFFNWK 211
             +I+  F      
Sbjct: 233 THQIRVHFANIGHP 246


>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 (142), Expect = 1e-06,   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|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 = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 88/253 (34%), Gaps = 60/253 (23%)

Query: 2   KDKNIVQENFTPQ---RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           ++K +    +T +   R+ + +       SR  +++ I  + V VNG + + A+ ++++ 
Sbjct: 8   EEKTVFNYTYTGEDGLRLDQFVTNQFTDESRTTIKKWIKDKLVTVNGKVAK-ASQSLVNG 66

Query: 58  DHIEVDG---------VPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           D I V+           P+ +        E   + + +KP  LV   S     +T+ + L
Sbjct: 67  DLIGVEKPAPAEAEEFKPVAEKMALDIVFEDDDILVVNKPANLVVHPSVNHPTNTLVNGL 126

Query: 102 PSIFS-------------RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYR 146
                             R   V RLD +T GLL++         L     + Q  R+Y 
Sbjct: 127 LYHVQENGSQLAVGRESFRPGIVHRLDKDTTGLLVVAKSQAALENLTKQVANHQMTRIYA 186

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYG--DMQVTLDTQKGSNA---------------WV 189
              +G++        + G  I          ++  +T +                    V
Sbjct: 187 GLVYGEI-------FEAGGTIDAPIRRHEKDRLKFETNEAGRHAVTHFTVKHRYVGYTLV 239

Query: 190 TVGLREGKNREIK 202
              L  G+  +I+
Sbjct: 240 NFQLETGRTHQIR 252


>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 = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/214 (17%), Positives = 78/214 (36%), Gaps = 29/214 (13%)

Query: 29  REVERMIAQQRVKVNGILL------ERAA--VNVMSTDH---IEVDGVPLRK-AERTRLW 76
           R+++ M  ++RVKVN  +       ++       +  D    ++V+  P+    E     
Sbjct: 41  RDIQMMFRKKRVKVNSRVAHSQRALKKGDVLTLELPQDKDYGVDVEKGPITVLYEDAHTL 100

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TNDG 128
           + +K   ++   +      T+ + +   +       +V  V RLD  T G +L   T + 
Sbjct: 101 VVNKAPFMLVHPAGQTKSCTLSNYIAGYYAKKGVVHKVRPVHRLDRETSGCILFGKTKEA 160

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---------IVIQGICYGDMQVTL 179
                 EL + +  R+Y     G +D D +     G         ++ +       + T+
Sbjct: 161 QQYYTDELQAGRIDRIYTGLVEGHIDADGMVDEPIGVDPVFDNRRVIDEFGQPAQTEYTV 220

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +G N  +   L  G+  +I+   E     + 
Sbjct: 221 LGYEGDNTLLRFKLLTGRTHQIRVHMEHIGHPII 254


>gi|291563387|emb|CBL42203.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SS3/4]
          Length = 332

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/271 (13%), Positives = 84/271 (30%), Gaps = 71/271 (26%)

Query: 6   IVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--- 61
           ++++N   QR+ K +A+    AS+    +M+ ++ + +NG         +   D ++   
Sbjct: 5   VIEKNEAGQRLDKFLAKYMNEASKSFFYKMMRKKNITLNGKKC-EGNEKLAEGDVVKLFL 63

Query: 62  ----------VDGVPLRKA------ERTRLWLYHKPIGLVTT---HSDPDGRSTVFDNLP 102
                     V    ++K       E   + L +KP G+++     +D      + D L 
Sbjct: 64  AEDTIEKFSSVQVQEVKKVDLDILYEDDEIILVNKPAGMLSQKAKETDESLVEYLIDYLL 123

Query: 103 SIFS---------RVISVGRLDINTEGLLLLTNDGGLARVLEL-----PSTQWLRVYRVR 148
                        R     RLD NT G++     G     L++           + Y+  
Sbjct: 124 GSGKLTESGLRAFRPSVCNRLDRNTSGIVAA---GKSLAGLQMLSGVFKDRSIHKYYQCL 180

Query: 149 FHGQV----------------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
             G++                       + +          +G      ++    +  + 
Sbjct: 181 VSGEIRDVKTVDGWLLKDEKKNQVRILTEAEAKRFGG----RGGDEEPKRIRTKYEPIAT 236

Query: 187 ----AWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + V L  G++ +I+         + 
Sbjct: 237 DGRFTLLKVTLLTGRSHQIRAHLASLGHPIV 267


>gi|229551713|ref|ZP_04440438.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|258539108|ref|YP_003173607.1| pseudouridine synthase [Lactobacillus rhamnosus Lc 705]
 gi|229314918|gb|EEN80891.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|257150784|emb|CAR89756.1| Pseudouridine synthase [Lactobacillus rhamnosus Lc 705]
          Length = 300

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 76/240 (31%), Gaps = 49/240 (20%)

Query: 13  PQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P +++  + + G  SR +++++      + VN       A  + + D I V   P + A 
Sbjct: 11  PLKLAAFLKQQGF-SRAQLKKLRYQGGFIFVN-KRQRHTAYPLRNGDRILVQTAPEQAAA 68

Query: 72  RTR--------------LWLYHKPIGLVT-----THSDPDGRSTVFDNLPSIFSR--VIS 110
                              + +KP G+ +       +D          + +      V  
Sbjct: 69  SVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTHAESQAVHV 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVI 167
           V RLD +T GL++      LA  L           + Y         +  L+    G +I
Sbjct: 129 VTRLDRDTSGLMVFAKH-SLAHSLLDRQLHSENFLKQYLALVT---SKSLLS--AHGWII 182

Query: 168 Q--GICYGDMQVTLDTQKGSNAW--------------VTVGLREGKNREIKKVFEFFNWK 211
              G+  G     + ++ G  +               V V L  G+  +I+  F      
Sbjct: 183 LPIGVSTGFYMRRVVSETGKPSVTEYQTLAQNSHAAAVLVTLHTGRTHQIRVHFAAIGHP 242


>gi|300361258|ref|ZP_07057435.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus gasseri
           JV-V03]
 gi|300353877|gb|EFJ69748.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus gasseri
           JV-V03]
          Length = 299

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 85/241 (35%), Gaps = 46/241 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVM 55
           M+   +  EN TPQ++ + + R G       +R +         + VN       +  + 
Sbjct: 1   MQYFKLKFENKTPQKLGRFLLRNGF-----SKRALTNSQHNGGMILVNHHR-RYTSYLLH 54

Query: 56  STDHIEV------DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           S D +            L+ +        E+    + +K  G+++  S  +    V + L
Sbjct: 55  SGDEVIFILGEEKKNQWLKPSTNQLNIVLEQHDYLVINKEAGVLSIPSRYEDNDAVVNRL 114

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQV 153
              F +          + RLD +T GL+L+  +               ++ Y    HG  
Sbjct: 115 LYYFQKNGQKDLKPHVITRLDRDTSGLVLVGKNAVAHARFSEMGKDCFIKKYHAIVHGNF 174

Query: 154 DQDK--------LNLL----KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +++        +  L    K+GIV  G         LD   G+ + V + L  G+  +I
Sbjct: 175 SKEQEIGIIDAPIGKLDASVKRGIVANGQRSITKYRVLDQVNGA-SLVELQLLTGRTHQI 233

Query: 202 K 202
           +
Sbjct: 234 R 234


>gi|159906031|ref|YP_001549693.1| RluA family pseudouridine synthase [Methanococcus maripaludis C6]
 gi|159887524|gb|ABX02461.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C6]
          Length = 297

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 53/289 (18%), Positives = 108/289 (37%), Gaps = 60/289 (20%)

Query: 33  RMIA----QQRVKVNGILLERAAVNVMSTDHIEV---------DGVPLRK---AERTRLW 76
           +MI     ++++ VN  ++      +   + + V         D   L      E   L 
Sbjct: 34  KMIKKFDKEKKIFVNSKII-SLKSKLKENETVSVEIDCGINNIDPEELPLNVIYEDDDLL 92

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLT-NDGG 129
           +  KP  +V   +      T+ + + +         ++  V RLD++T GLL++  N   
Sbjct: 93  IVDKPKNMVVHPTKNVLSKTLANAISNHQKINNQNYKIRFVSRLDMDTTGLLIIAKNSYS 152

Query: 130 LARVLELPSTQW-LRVYRVRFHGQVD------QDKLNLLKKGIVIQ---GICYGDMQVTL 179
              + +        ++Y    +G++D      +D ++L   GI  +          +  +
Sbjct: 153 HQHLAKQMDEGILEKIYVAVVNGRLDLKEGIIEDSIDLNDDGIKRELSNSGKISKTKYKV 212

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
             +  + + + + L  G+  +I+            +   S G + LG +L G T   SK 
Sbjct: 213 IEELKNASVLEINLLTGRTHQIR------------VHLSSLGNYILGDILYGKT---SKL 257

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
           I R+ L  H+L                + ++R    S++PDD   + KN
Sbjct: 258 IDRQALHSHIL-----------RFIHPITKERKEFTSKLPDDMENLIKN 295


>gi|301156232|emb|CBW15703.1| tRNA pseudouridine synthase [Haemophilus parainfluenzae T3T1]
          Length = 238

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/195 (13%), Positives = 59/195 (30%), Gaps = 36/195 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+LL   +
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDTHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALN 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +  +         +L+ +      +     +  
Sbjct: 67  SEIANLMCQQFEQKTVQKSYLAIVRGYLQGEGRIDYPLKIQLDKIADKFAQEDKAPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +  + G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLNIVEMPYAVGRYQTTRYSLVKLIPQTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 QLGTLLAGSTREVSK 238
                     R +++
Sbjct: 185 H-------QNRALTE 192


>gi|227114681|ref|ZP_03828337.1| tRNA pseudouridine synthase C [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 261

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 55/170 (32%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LLL   
Sbjct: 7   QDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLLALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQV-DQDKLN-LLKKGI-VIQGICYGDMQVTLDTQ 182
             +AR L     S Q  ++Y     G V D   ++  L + +  I        +      
Sbjct: 67  SEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFTNPDKAPQPAV 126

Query: 183 KGSNAWVTVG--------------LRE-----GKNREIKKVFEFFNWKVN 213
               +   V               L E     G+  ++++     +  + 
Sbjct: 127 THYRSLAQVEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHIHHPII 176


>gi|294664687|ref|ZP_06730020.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
 gi|292605540|gb|EFF48858.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 10535]
          Length = 328

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 98/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +   
Sbjct: 21  VPEDRAGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 63  ----DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
               +G                   E  RL   +KP G+ +            T+    P
Sbjct: 80  RTNDEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFRLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRL 291


>gi|227544440|ref|ZP_03974489.1| RluA family pseudouridine synthase [Lactobacillus reuteri CF48-3A]
 gi|227185580|gb|EEI65651.1| RluA family pseudouridine synthase [Lactobacillus reuteri CF48-3A]
          Length = 314

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 72/241 (29%), Gaps = 43/241 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIA-----QQRVKVNGILLERAAVNVMS----- 56
           +     P ++ K +   G+  R     +       +    V+   +      ++      
Sbjct: 35  IYRGTEPIKIKKYLQSLGMGHR-----LFNDLKNGEGEFLVDHRKVR-PTTQILPNQPLT 88

Query: 57  --------TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                    D +E    PL        WL   KP G+ +         TV + +      
Sbjct: 89  IKAQPELADDTVESSNEPLNVVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA 148

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKL 158
                 R   + RLD  T GLLL+      + ++     Q    + Y     GQV  +  
Sbjct: 149 NNSADLRPHLITRLDRFTGGLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHG 208

Query: 159 NL-----LKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +      K G    ++ +       +  ++ +      V V L  G+  +I+  F    
Sbjct: 209 EINKPIGRKDGQAARVIDENGQRALTEYWVEERGAKWTRVRVRLHTGRTHQIRVHFAAIG 268

Query: 210 W 210
            
Sbjct: 269 H 269


>gi|321314645|ref|YP_004206932.1| putative RNA pseudouridine synthase [Bacillus subtilis BSn5]
 gi|320020919|gb|ADV95905.1| putative RNA pseudouridine synthase [Bacillus subtilis BSn5]
          Length = 302

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/262 (15%), Positives = 88/262 (33%), Gaps = 49/262 (18%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVDGVPLRK-------------AERTRLWLYHKPIGLV 85
           ++KVN   +    + V   D + +D   +                E   + + +KP G+ 
Sbjct: 44  QIKVNHESVLN-NMIVKKGDRVFIDLQEIEASSVIPEYGELDILYEDNHMLIVNKPAGIA 102

Query: 86  TTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE---L 136
           T  ++     T+ + +   +       +V  V RLD +T G ++      LA  +    L
Sbjct: 103 THPNEDGQTGTLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKH-RLAHAILDQQL 161

Query: 137 PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKG 184
                 R Y     G            + +D+ +  ++ +   G       +V     K 
Sbjct: 162 EKKTLKRTYTAIAEGKLRTKKGTINSPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKE 221

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
             + V + L  G+  +I+                   P    +L  G ++ ++++ L   
Sbjct: 222 RLSLVELELETGRTHQIRVHMASIGH-----------PLTGDSLYGGGSKLLNRQALHAN 270

Query: 243 EQLGPHLLEEAQVNLDAPIYSS 264
           +    H + +  +  +AP  + 
Sbjct: 271 KVQAVHPITDELIVAEAPFPAD 292


>gi|157414995|ref|YP_001482251.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385959|gb|ABV52274.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|307747633|gb|ADN90903.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
 gi|315931909|gb|EFV10864.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 250

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 74/199 (37%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA ++  +  ++     P    E  ++
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSHGKKVVVARALMSDKARFNVIKTKNPQIIFEDDKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 67  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 113

Query: 136 LPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDTQK 183
               +    + Y     G + ++ ++N     I  +G     +          +T    +
Sbjct: 114 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGGALSKVSKDGLSALSIITPIMMQ 173

Query: 184 GSNAWVTVGLREGKNREIK 202
                  + ++ G+  +I+
Sbjct: 174 SKKTLAKIVIQTGRTHQIR 192


>gi|300908288|ref|ZP_07125753.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
 gi|300894535|gb|EFK87892.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri SD2112]
          Length = 325

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 72/241 (29%), Gaps = 43/241 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIA-----QQRVKVNGILLERAAVNVMS----- 56
           +     P ++ K +   G+  R     +       +    V+   +      ++      
Sbjct: 31  IYRGTEPIKIKKYLQSLGMGHR-----LFNDLKNGEGEFLVDHRKVR-PTTQILPNQPLT 84

Query: 57  --------TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                    D +E    PL        WL   KP G+ +         TV + +      
Sbjct: 85  IKAQPELADDTVESSNEPLNVVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA 144

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKL 158
                 R   + RLD  T GLLL+      + ++     Q    + Y     GQV  +  
Sbjct: 145 NNSADLRPHLITRLDRFTGGLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHG 204

Query: 159 NL-----LKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +      K G    ++ +       +  ++ +      V V L  G+  +I+  F    
Sbjct: 205 EINKPIGRKDGQAARVIDENGQRALTEYWVEERGAKWTRVRVRLHTGRTHQIRVHFAAIG 264

Query: 210 W 210
            
Sbjct: 265 H 265


>gi|126461841|ref|YP_001042955.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17029]
 gi|126103505|gb|ABN76183.1| ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 349

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 52/291 (17%), Positives = 91/291 (31%), Gaps = 77/291 (26%)

Query: 13  PQRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD 63
           P R+ K +       A     SR  + ++I +  V++ G  +      V       I +D
Sbjct: 20  PDRLDKALVREAPEEAAL---SRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEIALD 76

Query: 64  ----------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------- 105
                      +PL    E   L +  KP+G+V   +      T+ + L           
Sbjct: 77  APAEVEARPEAIPLSVVWEDEDLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGESLSGI 136

Query: 106 ---SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG--QVDQDKL 158
               R   V R+D +T GLL++  T+        +  +    R Y    HG  +V   +L
Sbjct: 137 GGEKRPGIVHRIDKDTSGLLVVAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEVSDPRL 196

Query: 159 N-------------LLKKG------------IVIQGICYGDMQVTLDTQKGSN---AWVT 190
                          +  G            +  +G  +   +  L  + G+    A V 
Sbjct: 197 RGVRGTSFEPGGVLRIATGLARHRTDRQRQAVTFEGGRHAVTRARLLERFGTPPVLALVE 256

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
             L  G+  +I+         +             G    G  R++S K L
Sbjct: 257 CRLETGRTHQIRVHMAHAGHGLI------------GDQTYGGRRKLSPKAL 295


>gi|313894254|ref|ZP_07827819.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313441078|gb|EFR59505.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 288

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/214 (16%), Positives = 79/214 (36%), Gaps = 29/214 (13%)

Query: 29  REVERMIAQQRVKVNGILL------ERAA--VNVMSTDH---IEVDGVPLRK-AERTRLW 76
           R+++ M  ++RVKVN  +       ++       +  D    ++V+  P+    E     
Sbjct: 29  RDIQMMFRKKRVKVNSRVAHSQRSLKKGDVLTLELPQDKDYGVDVEKGPITVLYEDAHTL 88

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TNDG 128
           + +K   ++   +      T+ + +   +       +V  V RLD +T G +L   T + 
Sbjct: 89  VINKDPFMLVHPAGQTKSCTLSNYVAGYYAKKGVVHKVRPVHRLDRDTSGCILFGKTKEA 148

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---------IVIQGICYGDMQVTL 179
                 EL + +  R+Y     G++D D +     G         ++ +       +  +
Sbjct: 149 QQYYTDELQAGRIDRIYTGLVEGRIDSDGVVDAPIGIDPVFDNRRVIDEFGQPAQTEYIV 208

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  G +  +   L  G+  +I+   E     + 
Sbjct: 209 LSHDGDHTLLRFRLLTGRTHQIRVHMEHIGHPIV 242


>gi|159045150|ref|YP_001533944.1| ribosomal large subunit pseudouridine synthase D [Dinoroseobacter
           shibae DFL 12]
 gi|157912910|gb|ABV94343.1| ribosomal large subunit pseudouridine synthase D [Dinoroseobacter
           shibae DFL 12]
          Length = 347

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/178 (19%), Positives = 63/178 (35%), Gaps = 29/178 (16%)

Query: 9   ENFTPQRVSKVIAR---AGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           +   P R+ + +AR    G+  SR  + ++I    V+    +L      V + D + +  
Sbjct: 16  QPDPPPRLDRALARDVPEGLGLSRSRLVKLIEAGDVRRGAEVLASPKARVAAGDVLTLRL 75

Query: 64  GVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
           G P                E   L + +KP G+V   +      T+ + L          
Sbjct: 76  GAPAEVPLVAEAIPLDVIFEDADLIVVNKPAGMVVHPAPGSPAGTLVNALMHHCGDSLSG 135

Query: 106 ----SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                R   V R+D +T GLL++  ++        +  +    R+Y    HG  +   
Sbjct: 136 IGGEKRPGIVHRIDKDTSGLLVVAKSDHAHQGLAAQFAAHSVERIYDALVHGVPEASD 193


>gi|152999968|ref|YP_001365649.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160874589|ref|YP_001553905.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|151364586|gb|ABS07586.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|160860111|gb|ABX48645.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315266830|gb|ADT93683.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 287

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 51/173 (29%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  EDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------- 169
                +A  L     S    + Y     G + +  +      + +               
Sbjct: 92  AKSSEVANALCEQFASHTIEKQYLALVRGNMHESGILDYALKVELDELGDKNADPNKAAQ 151

Query: 170 ------ICYGDMQVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFFNWKVN 213
                     + ++   + +   +    V +  + G+  ++++        + 
Sbjct: 152 EAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHLRHPIV 204


>gi|28377784|ref|NP_784676.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|28270617|emb|CAD63523.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
          Length = 293

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 65/190 (34%), Gaps = 28/190 (14%)

Query: 38  QRVKV-NGILLERAAVNVM---STDHIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPD 92
             + + +G +     + +        + V   P++       WL  +K  GL +     +
Sbjct: 47  GVITIHDGDIA---GIQLPDEAPDTAVAVSEQPIQIEYEDANWLVLNKTAGLTSVPGPSN 103

Query: 93  GRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS--TQWLR 143
              T+ + +            R   + RLD +T GL+L+        +L  P    Q ++
Sbjct: 104 RTDTLVNRIKGYLMASHASNQRPHLITRLDRDTSGLVLVAKHRVAQGMLTEPRIAAQLVK 163

Query: 144 VYRVRFHGQVDQD----------KLNLLKKGIVIQGICY-GDMQVTLDTQKGSNAWVTVG 192
            Y+    G +               +  ++ +   G       QV  D  + + + + + 
Sbjct: 164 TYQAWIEGTITPASGTIDRPIGRVADSPRRVVTTAGQRAITTYQVEADQLQHNVSRLRLE 223

Query: 193 LREGKNREIK 202
           L  G+  +I+
Sbjct: 224 LVTGRTHQIR 233


>gi|86149810|ref|ZP_01068039.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88597099|ref|ZP_01100335.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|218562347|ref|YP_002344126.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|85839628|gb|EAQ56888.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|88190788|gb|EAQ94761.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|112360053|emb|CAL34845.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|284925964|gb|ADC28316.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315926823|gb|EFV06197.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
 gi|315929636|gb|EFV08817.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 250

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 74/199 (37%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V   G   ++ RA ++  +  ++     P    E  ++
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSYGKKVVVARALMSDKARFNVIKAKNPQIIFEDDKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 67  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 113

Query: 136 LPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDTQK 183
               +    + Y     G + ++ ++N     I ++G     +          +T    +
Sbjct: 114 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKVKGGALSKVSKDGLSALSIITPIMMQ 173

Query: 184 GSNAWVTVGLREGKNREIK 202
                  + ++ G+  +I+
Sbjct: 174 SKKTLAKIVIQTGRTHQIR 192


>gi|313204538|ref|YP_004043195.1| ribosomal large subunit pseudouridine synthase d [Paludibacter
           propionicigenes WB4]
 gi|312443854|gb|ADQ80210.1| ribosomal large subunit pseudouridine synthase D [Paludibacter
           propionicigenes WB4]
          Length = 356

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 73/240 (30%), Gaps = 45/240 (18%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ K +       SR  ++       + VNG  ++     +   D I +           
Sbjct: 39  RIDKHLVNCMSNTSRNRIQEAADAGNILVNGKPVKS-NYRIKPYDIISIVLSYPPSQFEI 97

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRVI 109
               +P+    E   + L +K   LV      +   T+ +             +  SR+ 
Sbjct: 98  IPQDIPINIVYEDDDIILVNKQPNLVVHPGFGNFDGTLLNAIAWHLKDHPEFDANDSRIG 157

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK---------- 157
            V R+D +T GL+L+         L     +    R Y     G V +D+          
Sbjct: 158 LVHRIDKDTSGLILIAKTEEAKAHLGKQFFNKTTQRRYHALVWGNVKEDEGTIVGALARD 217

Query: 158 -LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWK 211
             + +   +  +G         +   K    +  V L E     G+  +I+   +     
Sbjct: 218 PRDRMLFTVFPEGENPLAKHA-VTHYKVLERFAYVTLVECRLETGRTHQIRVHMKHIGHT 276


>gi|254523997|ref|ZP_05136052.1| ribosomal large subunit pseudouridine synthase D [Stenotrophomonas
           sp. SKA14]
 gi|219721588|gb|EED40113.1| ribosomal large subunit pseudouridine synthase D [Stenotrophomonas
           sp. SKA14]
          Length = 329

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 54/301 (17%), Positives = 103/301 (34%), Gaps = 42/301 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDHIEV------DGVPLRKA-ERTR 74
           SR  +   I    V ++G  +      R    V  T  +E       + +PL    E   
Sbjct: 35  SRSRLTEWIKAGDVLLDGAQVRPRDPLRGGEVVTLTVVLETQTDAQPEDIPLDVLFEDEH 94

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDG 128
           L + +KP+GLV      +   T+ + L       ++  R   V RLD +T G++++    
Sbjct: 95  LLVINKPVGLVVHPGAGNHSGTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKTL 154

Query: 129 GLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDMQ 176
                L  +L +    R Y     G           +D+   + LK  +  +        
Sbjct: 155 EAQTALVEQLAARDVHRQYLAIVMGALVAGGTADAPIDRHPRDRLKMAVR-EDGKEAITH 213

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR 234
             L  +  ++  +   L  G+  +I+         +    L    YG   L  L  G++ 
Sbjct: 214 YRLRERFRAHTALECRLETGRTHQIRVHMAHVRHPIIGDPL----YGG-ALK-LPKGASD 267

Query: 235 EVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           E+   +    R+ L    LE        P+ ++  +  D  +++  + DD          
Sbjct: 268 ELVAALRGFKRQALHAETLEFTHPITGEPVRNTAPVPEDMLHLMKVLRDDSEAFAARERD 327

Query: 292 K 292
           +
Sbjct: 328 R 328


>gi|58038975|ref|YP_190939.1| ribosomal large subunit pseudouridine synthase D [Gluconobacter
           oxydans 621H]
 gi|58001389|gb|AAW60283.1| Ribosomal large subunit pseudouridine synthase D [Gluconobacter
           oxydans 621H]
          Length = 322

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 83/234 (35%), Gaps = 37/234 (15%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V  +   QR  + +A A G  SR  V+ +I    + VNG  +   A  +     + +  
Sbjct: 11  VVDASTAGQRADRALADAIGTVSRSRVKALIESGNLSVNGKTVCEPAETLRDGMEMVLTF 70

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------ 105
                     + +PL    E   L +  K  GLVT  +  +   T+ + L          
Sbjct: 71  PAPTPARPVAEQIPLNILYEDDDLIVLDKQAGLVTHPAPGNETGTLVNALLGHCGEGFEG 130

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRV----------RF 149
                R   V RLD +T GL+++     +   L     +    R Y             F
Sbjct: 131 IGGEKRPGIVHRLDKDTSGLMVVAKTAMVHNALSEAFAARDIDRAYLALAWGLLPAEGEF 190

Query: 150 HGQVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            G + +DK +  +  +V  G          ++  + + + +   L  G+  +I+
Sbjct: 191 DGSIGRDKRDRKRMAVVGSGGKVALTRFKLIEPYQAAVSLIECRLATGRTHQIR 244


>gi|114048209|ref|YP_738759.1| tRNA pseudouridine synthase C [Shewanella sp. MR-7]
 gi|113889651|gb|ABI43702.1| tRNA pseudouridine synthase C [Shewanella sp. MR-7]
          Length = 284

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/173 (14%), Positives = 52/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           +   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  QDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------- 175
                +A  L     +    + Y     G + +  +      + +  +            
Sbjct: 92  AKSSEVANALCEQFANHSIEKQYLALVRGNMHESGILDYALKVELDEVADKFANQDKAAQ 151

Query: 176 ------------QVTLDTQKGSNA---WVTVGLREGKNREIKKVFEFFNWKVN 213
                       ++   + + + +    V +  + G+  ++++        + 
Sbjct: 152 DAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKTGRKHQLRRHMAHLRHPII 204


>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 = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 88/241 (36%), Gaps = 43/241 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M+  N+ V++ F   R+   +++  I    SR  ++ +I +  V VN    ++    +  
Sbjct: 1   MEKINLQVEKEFDNVRLDLYLSK--IFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKV 57

Query: 57  TDHIEVD---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            D+IEV+      L+            E   + + +KP  +V   +      T+ + L  
Sbjct: 58  RDNIEVNIPEPKLLQIEPEDINLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLH 117

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
               +           V R+D +T G+L++  +      L          RVY     G 
Sbjct: 118 HCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGI 177

Query: 153 VDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +  ++           ++ +K  +V +   +      +  +  ++  V   L  G+  +I
Sbjct: 178 IKDEQGTIEAPIGRHPVDRIKMAVV-KDGRHAVTHYKVIERFKNHTLVECRLETGRTHQI 236

Query: 202 K 202
           +
Sbjct: 237 R 237


>gi|167747168|ref|ZP_02419295.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662]
 gi|317473628|ref|ZP_07932917.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|167654128|gb|EDR98257.1| hypothetical protein ANACAC_01882 [Anaerostipes caccae DSM 14662]
 gi|316898918|gb|EFV20943.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 329

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 48/260 (18%), Positives = 85/260 (32%), Gaps = 72/260 (27%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           MK+  I  +    QR+ K++A+       +       +M+ ++ +K+NG      +  + 
Sbjct: 1   MKEIRI-SDREEEQRLDKLLAKYL----NKAPKSFLYKMLRKKNIKLNGKKA-SGSEKLK 54

Query: 56  STDHIEV---DGVPLRKAERTR----------------LWLYHKPIGLVTTHSDPDGRST 96
           S D + V   D       E  R                + + +KP G+++  + P   S 
Sbjct: 55  SGDVVCVYMADATIASFREEPRAERRKADLSVIYQDSNVLIINKPYGMLSQKAKPSDISV 114

Query: 97  VFDNLPSIFS------------RVISVGRLDINTEGLLL--LTNDGGLARVLELPSTQWL 142
               +P                R     RLD NT GLL+  ++ +G       L      
Sbjct: 115 NELIVPYCLEHGILKESDLELVRPSVCNRLDRNTTGLLIAGISLEGLQTMAEVLRDRSVR 174

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSN------------- 186
           + Y     G V++           I G    D    +V+   +K S              
Sbjct: 175 KYYYCIVKGMVNKKT--------RISGYICKDHRENKVSFSERKISGGSRIETAYEPMAA 226

Query: 187 ----AWVTVGLREGKNREIK 202
                 + V L  GK  +I+
Sbjct: 227 GHGFTLLRVELITGKTHQIR 246


>gi|319940421|ref|ZP_08014771.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
 gi|319810477|gb|EFW06819.1| pseudouridine synthase [Streptococcus anginosus 1_2_62CV]
          Length = 286

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 74/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV--------------PLRKAE 71
           R+V   +  ++ V VN   +      +   D I    D                     +
Sbjct: 28  RKVRHFLRIKKHVLVNQQPI-NWQSRIHPADAIVLIFDEEDYPEKSILMGKANLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + + +KP G+ T  ++P   + +      + +    V RLD  T G +L   +  + 
Sbjct: 87  DEHIIIVNKPEGIKTHANEPTELALLNHVYAYVGNTCYVVHRLDKETSGAVLFAKNPFIL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQ------DKL-----NLLKKGIVIQGICYGDMQVT 178
            +L   L + +  R Y     G   +      DK+     +  K+ +  +   Y + QVT
Sbjct: 147 PILNRLLENKEISREYWALVQGVFPKKRQIYTDKIGRDRHDRRKRLVDNKNGQYAETQVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              + G+N  +   L+ G+  +I+
Sbjct: 207 KLKEIGNNTLIKCQLKTGRTHQIR 230


>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 = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/135 (22%), Positives = 50/135 (37%), Gaps = 24/135 (17%)

Query: 12  TPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE-------- 61
             +R+ KV+AR      SR  ++  I   RV ++G        +V     +         
Sbjct: 38  AGERLDKVLARLFPTF-SRSRLQTWIDAGRVTLDGAPAR-LRQSVPLGATVRLVPDLLPQ 95

Query: 62  ---VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVI 109
                  P+      E   L +  KP GLV   +  +   T+ + L   +       R  
Sbjct: 96  ALAFAPEPVPLPIVYEDETLVVIDKPAGLVVHPAAGNWSGTLLNGLLHRYPDAAGLPRAG 155

Query: 110 SVGRLDINTEGLLLL 124
            V RLD +T GL+++
Sbjct: 156 IVHRLDKDTSGLMVV 170


>gi|260771000|ref|ZP_05879929.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|260614237|gb|EEX39427.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           CIP 102972]
 gi|315179046|gb|ADT85960.1| ribosomal large subunit pseudouridine synthase A [Vibrio furnissii
           NCTC 11218]
          Length = 259

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/166 (19%), Positives = 60/166 (36%), Gaps = 32/166 (19%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E   +   +KP GL++      +   +++  L + +  +  V RLD++T GL+L   D  
Sbjct: 33  EDDYILAVNKPSGLLSVPGRLAEHHDSMWSRLQAQYPEIQVVHRLDMSTSGLMLFAKDKY 92

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDMQ-VTL 179
                       L        ++Y  R  G + QD+  + L    +I        Q V  
Sbjct: 93  MEAALKKQFQYRLTH------KIYYARVWGVMAQDEGEIDLP---LICDWPNRPKQMVCH 143

Query: 180 DTQKGSNAWVTVGLRE------------GKNREIKKVFEFFNWKVN 213
           +T K S     V  RE            G++ +++   +     + 
Sbjct: 144 ETGKPSQTLFQVVKREAHTTVVRLLPITGRSHQLRVHMQALGHPIV 189


>gi|251792621|ref|YP_003007347.1| tRNA pseudouridine synthase C [Aggregatibacter aphrophilus NJ8700]
 gi|247534014|gb|ACS97260.1| tRNA pseudouridine synthase C [Aggregatibacter aphrophilus NJ8700]
          Length = 236

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 62/195 (31%), Gaps = 36/195 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L     + V  + RLD  T G+LL   +
Sbjct: 7   QDDVLVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQLVYPIHRLDRPTSGVLLFALN 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-------------QDKLNLLKK-------GI 165
             +A +L       Q  + Y     G V                  +   +        +
Sbjct: 67  SEIANLLCQQFEQKQTEKQYLAVVRGYVTGHGEIDYPLKIQLDKIADKFSQQDKAPQSAV 126

Query: 166 VI-QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +G+   +M   +     S  + V +  + G+  ++++  +     +  L    YG  
Sbjct: 127 TFYEGLQTVEMPYGVGCYATSRYSLVRLVPKTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 QLGTLLAGSTREVSK 238
                     R +++
Sbjct: 185 H-------QNRALTE 192


>gi|261838329|gb|ACX98095.1| pseudouridine synthase C [Helicobacter pylori 51]
          Length = 242

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 67/201 (33%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D L S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLL-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>gi|212693126|ref|ZP_03301254.1| hypothetical protein BACDOR_02633 [Bacteroides dorei DSM 17855]
 gi|237725459|ref|ZP_04555940.1| RNA pseudouridylate synthase [Bacteroides sp. D4]
 gi|265753523|ref|ZP_06088878.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
 gi|212664231|gb|EEB24803.1| hypothetical protein BACDOR_02633 [Bacteroides dorei DSM 17855]
 gi|229436146|gb|EEO46223.1| RNA pseudouridylate synthase [Bacteroides dorei 5_1_36/D4]
 gi|263235237|gb|EEZ20761.1| conserved hypothetical protein [Bacteroides sp. 3_1_33FAA]
          Length = 308

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/220 (17%), Positives = 74/220 (33%), Gaps = 30/220 (13%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA------ER 72
           AGI SR +V+ ++A + + V+ ++  +    +     +++    +    +        E 
Sbjct: 40  AGI-SRSKVKALLANRVILVDNVITTQYNFALKPGMKVQMSKAKNNREFKHPMLKLVYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             + +  K  GL++  ++     T    L         F+RV  V RLD  T GL++   
Sbjct: 99  AYILVVEKKEGLLSVSTERQKERTAQHILNEYVKRSHRFNRVFVVHRLDRETSGLMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDM 175
           D      L          R Y     G +++D            L      +        
Sbjct: 159 DEKTQNTLRDNWHDIVTDRRYVSIVSGDMEKDYGTVESWLTDRKLYVSSSPVDDGEGKFA 218

Query: 176 QVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVN 213
                T K +N  + V + L  G+  +I+         V 
Sbjct: 219 VTHYKTIKRANGYSLVELDLETGRKNQIRVHMSDLGHPVI 258


>gi|332670137|ref|YP_004453145.1| RluA family pseudouridine synthase [Cellulomonas fimi ATCC 484]
 gi|332339175|gb|AEE45758.1| pseudouridine synthase, RluA family [Cellulomonas fimi ATCC 484]
          Length = 312

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 53/306 (17%), Positives = 98/306 (32%), Gaps = 68/306 (22%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M +     V +    +RV   +AR    SR     + A   V+V+G  + ++   +++  
Sbjct: 1   MPEVRALPVPDGLAGERVDAALARLLGLSRTRAAEIAADGGVRVDGREVGKSD-RLLAGG 59

Query: 59  HIEVD------------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
            +EV+                  G+ +   +   + +  KP+G+    S      TV   
Sbjct: 60  WLEVEIPDPQGPAAPVVVPEPVPGMRIVHDDDDVVVVD-KPVGVAAHPSPGWTGPTVVGA 118

Query: 101 LPSIFSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRF 149
           L +   R+           V RLD+ T GL+++        VL+    +    +VY    
Sbjct: 119 LAAAGYRISTSGAAERQGVVHRLDVGTSGLMVVAKSEHAYTVLKRAFKERTVEKVYHALV 178

Query: 150 HG--QVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
            G  +     ++           K  +V  G         L+    S + V V L  G+ 
Sbjct: 179 QGHPEPTTGTIDAPIGRHPSADWKFAVVADGKPSVTHYEVLEML-PSASLVEVHLETGRT 237

Query: 199 REIKKVFEFFNWKVN--------------------RLIRISYGPFQLGTLLAGSTREVSK 238
            +I+  F                             L  +  G    GT   G   EV+ 
Sbjct: 238 HQIRVHFAALRHPCVGDLTYGADPSLAARTHLSRQWLHAVRLGFEHPGT---GEWLEVTS 294

Query: 239 KILREQ 244
           +  ++ 
Sbjct: 295 EYPQDL 300


>gi|304373162|ref|YP_003856371.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis HUB-1]
 gi|304309353|gb|ADM21833.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis HUB-1]
          Length = 297

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 69/179 (38%), Gaps = 27/179 (15%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           MK   ++ +  T  R+   + +    SR  V+ +IA  +V V+  ++ +    +     I
Sbjct: 1   MKKMKLIADEQT--RLDIFLRKKLELSRVFVQEIIANNQVWVDNQIVNKKNFILKQGSQI 58

Query: 61  EV--------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           EV              D       E   + +  KP  +V   +  +  +T+ + L   F+
Sbjct: 59  EVHYQEKEQNINAKAQDIELKIVFEDENVIVVDKPTNMVVHPAPGNYENTLVNALVYKFA 118

Query: 107 RVI---------SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
           ++           V RLD +T GL+L+  +  +   L   L   +  R Y     GQ++
Sbjct: 119 QLSNVNGSLRPGIVHRLDKDTSGLMLVAKNDKMHNFLAQQLKERKIKRKYYAIIEGQLE 177


>gi|169350066|ref|ZP_02867004.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552]
 gi|169293279|gb|EDS75412.1| hypothetical protein CLOSPI_00806 [Clostridium spiroforme DSM 1552]
          Length = 322

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 50/281 (17%), Positives = 86/281 (30%), Gaps = 66/281 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           MK K  + EN   QR+ K I +  +            +M  ++ +KVNG  +      + 
Sbjct: 1   MK-KIQITENDANQRIDKYIKKLLV----NAPTNFIYKMFRKKDIKVNGKKVNE-KYILK 54

Query: 56  STDHIE-------------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           + D +E                   V        E   + + +KP GL+      +  +T
Sbjct: 55  NNDVVEMFLYEDKFKEFTATKDIYNVKKTFKVLYEDNHVLIVYKPAGLLVHEDKNESVNT 114

Query: 97  V-------------FDNLPSIFSRVISVGRLDINTEGLLLL-TNDGGLA--RVLELPSTQ 140
           +              D           V RLD NT G+++     G L     +      
Sbjct: 115 LTNQVLSYLANKNELDLSRENTFMPGPVHRLDRNTSGIVIFGKTLGALQVLNEMIKQRHC 174

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKG--IVIQGICYGDMQ-------------VTLDTQKGS 185
             + Y     G+V+Q       KG  + +       +              V        
Sbjct: 175 IEKSYLTICKGKVNQ---KRNLKGYIVKLDDQAQVKLVSKDYPGALTMETIVKPVKYNND 231

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
            + V V L  G+  +I+      +  +    R  YG F+L 
Sbjct: 232 YSKVEVTLVTGRMHQIRVHLSSIDHPIIG-DR-KYGDFELN 270


>gi|157825473|ref|YP_001493193.1| ribosomal large subunit pseudouridine synthase C [Rickettsia akari
           str. Hartford]
 gi|157799431|gb|ABV74685.1| ribosomal large subunit pseudouridine synthase C [Rickettsia akari
           str. Hartford]
          Length = 303

 Score = 59.0 bits (142), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 60/175 (34%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A++ V + D I +      
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQITVNAQKA-EASLRVNAGDKIFIKDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P++  E+                         L   +KP GL T        S       
Sbjct: 66  PVKSPEKLVFTDAEIKLAQKITIDYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 126 LNYKGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLIVKTYCAITYGKP 180


>gi|320168624|gb|EFW45523.1| RNA pseudouridylate synthase domain-containing protein 2
           [Capsaspora owczarzaki ATCC 30864]
          Length = 515

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 80/208 (38%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           ++ I   RV VNG ++   +  +  +D +          V   P+R  AE   L +  KP
Sbjct: 144 DQAIRDGRVTVNGKVVA-PSYIIQDSDVLVHTAHRHEPPVTAAPIRVIAETDDLVVIDKP 202

Query: 82  IGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--P 137
             +    +      TV   + S   +S ++   RLD  T G+L++  +   A  +     
Sbjct: 203 ASIPVHVAGRFNVHTVISIMKSEMGYSNLLGCHRLDRLTSGVLVMAKNRAAAAAVTRLIT 262

Query: 138 STQWLRVYRVRFHGQVDQDKL---NLL-----KKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +  + Y  R  G   Q+++     L     K G+          + T+  ++ +N  +
Sbjct: 263 EREVEKFYICRVTGVFPQEQVTCTEPLLSFCPKFGLNGVDPSGKPAE-TVFVREQTNGVI 321

Query: 190 TVGL---REGKNREIKKVFEFFNWKVNR 214
           ++     + G+  +I+   ++  + +  
Sbjct: 322 SIVKCFPKTGRAHQIRVHLQYLGYPIEN 349


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPQEIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/258 (14%), Positives = 87/258 (33%), Gaps = 55/258 (21%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG----------VPLRKA-----E 71
           SR  ++++  ++ +KVNG         V   D I++ G            + +      E
Sbjct: 29  SR--IQKLFREKDIKVNGKRNIDKNFIVSKDDLIQIYGLTNVKQKLVFKKIEQKFNVIFE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-----SVGRLDINTEGLLLLTN 126
              + + +K  G+     +      V   L   F +V      S+GRLD  T G+++   
Sbjct: 87  DQNILVINKQAGVSMHSDENSLDKQVLSYL--NFKQVDSFVPSSIGRLDKVTSGVVVYAK 144

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVI--QGICYGDM 175
           +  + + L+  +    + Y    +  ++ ++          N +KK   +  + +    +
Sbjct: 145 NYSILKTLKS-NEHLRKTYVFMSNITLEPNQKIEHVFYHKYNPIKKKAELFKENVEESKI 203

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV-------------NRLIRISYGP 222
             TL  +  +N +  + +  G+  +I+       + +               L       
Sbjct: 204 TKTLLYKVKNNNYAEL-IT-GRKHQIRATLSKLGFPIFGDVKYGGKKDKRVYLHSYKIKF 261

Query: 223 FQLGTLLAGSTREVSKKI 240
             L     G    ++ + 
Sbjct: 262 HSLK----GEFEYLNNQE 275


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/227 (14%), Positives = 80/227 (35%), Gaps = 40/227 (17%)

Query: 19  VIARAGIASRREVERMIAQ----QRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA 70
           ++   G +S      +I +     R+ VN  +       +   D IE+    D V ++  
Sbjct: 17  ILINRGFSS-----TLIRKYKHSGRILVNNEI-SIVNRIIKKGDIIELYLDDDNVSVKPE 70

Query: 71  --------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDI 116
                   E   + + +K  G+V   +      T+ + +   + +      +  V RLD 
Sbjct: 71  KMDLHICYEDDDILVVNKDAGVVVHPTAGHPDGTLANGVAWYYEKNNINAPIRPVNRLDR 130

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQV-DQDKLNL---------LKKGIV 166
           +T GL++   +  +   L++      + Y     G + D+  ++L         +++ + 
Sbjct: 131 DTSGLIIFAKNPFMQNYLQIVCP-MKKFYIAIVRGDLEDRGTIDLPIKRKPGSTIERMVD 189

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             G         L   +   + V + L+ G+  +I+         + 
Sbjct: 190 DDGDKAVTDFYVLKRGE-KLSLVKLELKTGRTHQIRVHLSHIGHPII 235


>gi|300771948|ref|ZP_07081819.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33861]
 gi|300761334|gb|EFK58159.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33861]
          Length = 247

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/150 (16%), Positives = 52/150 (34%), Gaps = 17/150 (11%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E   + + +KP  + +      G   +       ++      RLD  T G+LL+  
Sbjct: 17  LIIHEDENIIVINKPPFIASLDEREGGEINILRLAKKYYADAQICHRLDKETSGILLIAK 76

Query: 127 DGGLARVLEL--PSTQWLRVYRVRFHG-QVDQD---KLNLLKKG---IVIQGICYGDMQV 177
           +    R++ +     +  + Y     G  + QD    L +L +G   + I        + 
Sbjct: 77  NPETYRLISIEFEKRRVDKTYHAIIEGTHIFQDLKIDLPILNQGNKNVTIDRYNGKPAET 136

Query: 178 TLDTQKGSNAWVTVGLRE-----GKNREIK 202
             ++ +         L E     G+  +I+
Sbjct: 137 IFNSIQYFKH---FTLVECKPITGRMHQIR 163


>gi|254444369|ref|ZP_05057845.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198258677|gb|EDY82985.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 249

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/189 (19%), Positives = 59/189 (31%), Gaps = 35/189 (18%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDG 128
             RL   HKP GL+   S  D R T F        I   V    R+D  T G+LL   D 
Sbjct: 20  DERLVAIHKPSGLLVHRSPIDRRETRFAIQLLRDQIGQHVYPAHRIDRPTSGILLFGLDE 79

Query: 129 G--LARVLELPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQG--------------I 170
               A  L   + +  + Y     G + +  L  + L K     G               
Sbjct: 80  AAGTALSLLFQNREIQKNYLAVTRGHLPESGLIDSPLHKYEDADGHIKSSETQEAETAYR 139

Query: 171 CYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWKVN-----------RLI 216
                ++   T++      + V +    G+  +I++        +            +L 
Sbjct: 140 RLATTELPYPTERYDTTRYSLVELTPHTGRRHQIRRHLAHIRHPIIGDVRHGCNKANKLA 199

Query: 217 RISYGPFQL 225
           R  +   +L
Sbjct: 200 RSHFAIHRL 208


>gi|322373374|ref|ZP_08047910.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus sp. C150]
 gi|321278416|gb|EFX55485.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus sp. C150]
          Length = 298

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/201 (18%), Positives = 67/201 (33%), Gaps = 36/201 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR-----------KAERTRLWLYHKP 81
               + VNG   + A   V   D + +   D  P               E     + +KP
Sbjct: 33  EGGHIWVNGE-EQFATYPVHEGDVVAIEIPDEAPHDTLTPIPFDLDIVYEDDNFLVVNKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S  +  +T+ + +   F        RV  V RLD +T GL+L    G     +
Sbjct: 92  YGYASIPS-VNHDNTMANFVKYHFVSNNYPNQRVHIVTRLDKDTSGLMLFAKHGYAHARM 150

Query: 135 --ELPSTQWLRVYRVRFHGQ--VDQ--DKLNLLKKGI-------VIQGICYGDMQVTLDT 181
             +L      + Y     G   +++  + +  + + +       V +   Y      L  
Sbjct: 151 DKQLQQKSIKKHYYALVEGDTKLEEQGEIIAPIARDVDSIITRRVHKSGKYAHTSYRLVG 210

Query: 182 QKGSNAWVTVGLREGKNREIK 202
             G    V + L  G+  +I+
Sbjct: 211 DYGRVKLVDINLHTGRTHQIR 231


>gi|317180199|dbj|BAJ57985.1| hypothetical protein HPF32_0403 [Helicobacter pylori F32]
          Length = 242

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 76/235 (32%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--QEINAPILTFKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|156401575|ref|XP_001639366.1| predicted protein [Nematostella vectensis]
 gi|156226494|gb|EDO47303.1| predicted protein [Nematostella vectensis]
          Length = 418

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 70/199 (35%), Gaps = 33/199 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------LWLY 78
           E+ I   ++ VNG  +      +   D +      + + E                + + 
Sbjct: 45  EKAIESGKITVNGEKV-LPTTVLRGNDVLR---NRVHRHEPPVTDQPLEIICNTDDIVVL 100

Query: 79  HKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP  +          +TV   L        + ++ R+D  T G+L+       AR+LE 
Sbjct: 101 NKPSSIPVHPCGRYRHNTVVFLLGKEHNLRNLYTIHRIDRLTSGILMFAKTLTRARMLEA 160

Query: 137 P--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----------K 183
                Q  + Y  R  G+   + ++  ++ I++     G  +V+ D +            
Sbjct: 161 QVRDRQVEKEYLCRVQGEFPSEPVD-CEQPIIVVSHKVGICRVSPDGKSCRTVFTKLHSN 219

Query: 184 GSNAWVTVGLREGKNREIK 202
           G ++ V      G+  +I+
Sbjct: 220 GKSSVVKCIPYTGRMHQIR 238


>gi|222823615|ref|YP_002575189.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           lari RM2100]
 gi|222538837|gb|ACM63938.1| ribosomal large subunit pseudouridine synthase D [Campylobacter
           lari RM2100]
          Length = 320

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/170 (15%), Positives = 61/170 (35%), Gaps = 25/170 (14%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+   ++     SR +V ++I +  + +N  +  +++  +   D I +    +++A+ +
Sbjct: 10  ERLDIFLSDILKQSRSQVAKLIKENCIYINEKIENKSSKKIKQKDEISIFLPLIKEAKES 69

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVIS 110
                          + + +K   +V   +     +T+ D L              R   
Sbjct: 70  YTPEFDIEILYEDDDVLVLNKAPNIVVHGASSVKEATLVDWLLHKGYTLSNLNGEHRAGL 129

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
           V RLD  T G +++  +    + L          R Y       +  DK+
Sbjct: 130 VHRLDKGTSGAIIIAKNNQAHQFLANQLLDKSMGRFYLALSELPLKNDKM 179


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+ K++  R    SR + +R I    V V+G L+++A   V     IE+ G     
Sbjct: 1  MVKERLDKLVTQRELYPSRSKAKRAIMAGLVLVDGELVDKAGTQVDVEADIEIKGKVHPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|158334165|ref|YP_001515337.1| RluA family pseudouridine synthase [Acaryochloris marina MBIC11017]
 gi|158304406|gb|ABW26023.1| pseudouridine synthase, RluA family [Acaryochloris marina
           MBIC11017]
          Length = 306

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/201 (14%), Positives = 60/201 (29%), Gaps = 37/201 (18%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           I   +V ++G         +    ++     P ++           E   +   HKP GL
Sbjct: 40  IETGQVTIDGRQAT-PDTVLKQGQNLAYHRPPWQEPTVPLTFDVLYEDADVLAIHKPSGL 98

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
                      T+   +   F +     + RL   T G++L+         L     + Q
Sbjct: 99  QVLPGGGFLEHTLLHQVQQRFPQGTPFPIHRLGRGTSGVVLMARSQQARAALSQQMRNRQ 158

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----------GICYGDMQ--------VTLDT 181
             +VYR        +   + L++   I            G  Y             T+  
Sbjct: 159 IQKVYRALIG---PEQTTHPLEEQFEITQAIGKVPYPELGYIYAATPKGRPAHSACTILQ 215

Query: 182 QKGSNAWVTVGLREGKNREIK 202
           ++     + V +  G+  +I+
Sbjct: 216 RRPEATLLAVTITTGRPHQIR 236


>gi|24379482|ref|NP_721437.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24377420|gb|AAN58743.1|AE014943_6 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 296

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 67/213 (31%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR-----------KAERTRLWLYHKP 81
              ++ VN    E A   +   D + +   D   L              E     +  KP
Sbjct: 33  KGGQILVNDQ-EENAIYLLDIGDRVTIIIPDEEALETLQPIKHDLNIVYEDEHFLILDKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + +   +        ++  V RLD +T GL+LL   G     L
Sbjct: 92  AGYASIPS-ILHTNTIANFVKYYYLKKDYPNKQIHIVTRLDKDTSGLMLLAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRF--HGQVDQ--DKLNLLKKGIVIQG----------ICYGDMQVT 178
             +L      + Y       GQ+    + +  + +    +             Y      
Sbjct: 151 DKQLQKKTIKKRYYALVSGQGQLPDQGEIIAPIARP---EDSIITRCVHPSGKYAHTSYK 207

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  + G  A V + L  G+  +I+  F    + 
Sbjct: 208 VLARYGDIALVDIQLHTGRTHQIRVHFAHIGFP 240


>gi|315127084|ref|YP_004069087.1| tRNA pseudouridine synthase C [Pseudoalteromonas sp. SM9913]
 gi|315015598|gb|ADT68936.1| tRNA pseudouridine synthase C [Pseudoalteromonas sp. SM9913]
          Length = 254

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 51/177 (28%), Gaps = 27/177 (15%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEG 120
           G      +        KP GL+   S  D   T F        I   V  V RLD  T G
Sbjct: 11  GELSILYQDENYVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQIGQHVFPVHRLDRPTSG 70

Query: 121 LLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG 169
           +LL       AR +          + Y     G   +         ++L+ +      Q 
Sbjct: 71  VLLFALSSEAARDMNQLFIEGTITKRYLALVRGFAPESVFLDKPLKEELDKIADKFADQD 130

Query: 170 ICYGDM--------QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
               +         Q  L    G    V   L E     G+  +I++  +  +  + 
Sbjct: 131 KAAQEAQTQFNCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRHLKHLSLPII 187


>gi|227326531|ref|ZP_03830555.1| tRNA pseudouridine synthase C [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 262

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/171 (18%), Positives = 53/171 (30%), Gaps = 29/171 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LLL   
Sbjct: 7   QDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLLALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L     S Q  + Y     G V           ++L+ +               
Sbjct: 67  SEVARALSQQFESHQMQKTYHAVVRGYVLDDGVIDYALTEELDKIADKFTNPDKAPQPAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKK-VFEFFNWKVN 213
                  Q  +    G        L E     G+  ++++ +    +  + 
Sbjct: 127 THYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMT-HIHHPII 176


>gi|190575601|ref|YP_001973446.1| putative ribosomal large subunit pseudouridine synthase D
           [Stenotrophomonas maltophilia K279a]
 gi|190013523|emb|CAQ47158.1| putative ribosomal large subunit pseudouridine synthase D
           [Stenotrophomonas maltophilia K279a]
          Length = 329

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 73/218 (33%), Gaps = 33/218 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLRKA-ERT 73
           SR  +   I    V ++G  +      +   + + ++             +PL    E  
Sbjct: 35  SRSRLTEWIKAGEVLLDGAQVR-PRDPLRGGEVVTLNVVLETQTDAQPEDIPLDVLFEDE 93

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            L + +KP+GLV      +   T+ + L       ++  R   V RLD +T G++++   
Sbjct: 94  HLLVINKPVGLVVHPGAGNHSGTLVNALLFRDPSVAVLPRAGIVHRLDKDTSGVMVVAKT 153

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
                 L  +L +    R Y     G           +D+   + LK  +  +       
Sbjct: 154 LEAQTALVEQLAARDVHRQYLAIVMGALVAGGTADAPIDRHPRDRLKMAVR-EDGKEAIT 212

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              L  +  ++  +   L  G+  +I+         + 
Sbjct: 213 HYRLRERFRAHTALECRLETGRTHQIRVHMAHVRHPII 250


>gi|117921265|ref|YP_870457.1| tRNA pseudouridine synthase C [Shewanella sp. ANA-3]
 gi|117613597|gb|ABK49051.1| tRNA pseudouridine synthase C [Shewanella sp. ANA-3]
          Length = 284

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/173 (14%), Positives = 52/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           +   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  QDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM------- 175
                +A  L     +    + Y     G + +  +      + +  +            
Sbjct: 92  AKSSEVANALCEQFANHSIEKQYLALVRGNMHESGVLDYALKVELDEVADKFANQDKAAQ 151

Query: 176 ------------QVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFFNWKVN 213
                       ++   + + + +    V +  + G+  ++++        + 
Sbjct: 152 DAVTQYEPLLNTEIPYPSGRYATSRFALVKLSPKTGRKHQLRRHMAHLRHPII 204


>gi|313899587|ref|ZP_07833096.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312955694|gb|EFR37353.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 293

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 69/195 (35%), Gaps = 33/195 (16%)

Query: 39  RVKVNGILL-------ERAAVNV---MSTDHIE--VDGVPLRKAERTRLWLYHKPIGLVT 86
           RV +N  ++       E+  V +   M  D IE   + + +   +     + +KP  L+ 
Sbjct: 42  RVSINNRIIHGNHMLQEQDTVRIFLAMEEDTIEPWYEDLEILFEDEL-FCIVNKPANLLV 100

Query: 87  THSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
                +   TV + + + +      + V  + RLD  T G ++      L  +L   L +
Sbjct: 101 HSDGIEHAHTVCNLVKAHYLLEGHNTCVRPLHRLDYETSGAMIFCKVPFLQPLLDAMLKN 160

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----------A 187
            Q  R Y     G + Q     + +GI         M+++   +                
Sbjct: 161 KQIYREYEAFARGYIAQKHC-TITRGIARDRHDARKMRISEHGKSARTDVFVKQNFMDFT 219

Query: 188 WVTVGLREGKNREIK 202
           W+   L  G+  +I+
Sbjct: 220 WIRCRLYTGRTHQIR 234


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/200 (16%), Positives = 65/200 (32%), Gaps = 28/200 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           KV+A+    S ++ + +I +  V V     ++ R  ++  +   I+    P    E  ++
Sbjct: 7   KVLAQQLGISNKKAKELIDRGLVYVGDKKVVIARGLIDTDTKFRIKRIEKPEILFEDEKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP  + +     D             S    + RLD  T G+LLL  +    +   
Sbjct: 67  LAINKPAHITSEEIKED-------------SGYELLHRLDKETSGVLLLVKNEAFRKKAI 113

Query: 136 LP--STQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
                ++  + Y     G V +            K    K  +           V     
Sbjct: 114 EEFRKSRVYKEYVAWVEGIVAEPYEIDYPILTIKKDGKAKSRLSASKGKPAKTYVEPLEI 173

Query: 183 KGSNAWVTVGLREGKNREIK 202
            G  + V   +  G+  +I+
Sbjct: 174 HGKKSKVKAVIETGRTHQIR 193


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 18/67 (26%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+ K++   G + SR   E +I    V VNGI +E+    +     I +    L    R
Sbjct: 9  ERLDKILFDRGLVTSRTRGEELIKNGDVLVNGISIEKPGKKIPVDAKILLLNEELTWVSR 68

Query: 73 TRLWLYH 79
            L L  
Sbjct: 69 GALKLLK 75


>gi|290580515|ref|YP_003484907.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254997414|dbj|BAH88015.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 296

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/213 (16%), Positives = 67/213 (31%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLR-----------KAERTRLWLYHKP 81
              ++ VN    E A   +   D + +   D   L              E     +  KP
Sbjct: 33  KGGQILVNDQ-EENAIYLLDIGDRVTIIIPDEEALETLQPIKHDLNIVYEDEHFLILDKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + +   +        ++  V RLD +T GL+LL   G     L
Sbjct: 92  AGYASIPS-ILHTNTIANFVKYYYLKKDYPNKQIHIVTRLDKDTSGLMLLAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRF--HGQVDQ--DKLNLLKKGIVIQG----------ICYGDMQVT 178
             +L      + Y       GQ+    + +  + +    +             Y      
Sbjct: 151 DKQLQKKTIKKRYYALVSGQGQLPDQGEIIAPIARP---EDSIITRCVHPSGKYAHTSYK 207

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  + G  A V + L  G+  +I+  F    + 
Sbjct: 208 VLARYGDIALVDIQLHTGRTHQIRVHFAHIGFP 240


>gi|167375438|ref|XP_001733644.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165905188|gb|EDR30257.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 402

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 46/135 (34%), Gaps = 18/135 (13%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL-------------WLYHKP 81
           I +  +K+N  L+   +  +   D IE     + + E                     KP
Sbjct: 106 IEKGLIKINNKLI-DPSTIIHHHDEIE---HQVHRHEPPVYCDKLTIVKETNDFIAIDKP 161

Query: 82  IGL-VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
             + V         + +F      +  +  V RLD  T G+LLL      AR  +     
Sbjct: 162 SSVPVHPCGRYRHNTVIFILSHEGYPNLRPVHRLDRMTSGILLLAKTIQAAREFQNHMVI 221

Query: 141 WLRVYRVRFHGQVDQ 155
             + Y  R  G++++
Sbjct: 222 KKKEYICRVRGKLEK 236


>gi|315103776|gb|EFT75752.1| ribosomal RNA large subunit methyltransferase J
          [Propionibacterium acnes HL050PA2]
          Length = 263

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 1/65 (1%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
          P R+ + +  AG+A SR    R++ + RV VN  ++ + A+ V +TD +  D        
Sbjct: 18 PVRLDQALVEAGLARSRTLATRLVREGRVTVNRAVVTKPAMKVSTTDVLVADEEVWVSRA 77

Query: 72 RTRLW 76
            +L 
Sbjct: 78 AHKLL 82


>gi|257452370|ref|ZP_05617669.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|257465837|ref|ZP_05630148.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|315916994|ref|ZP_07913234.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
 gi|317058913|ref|ZP_07923398.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313684589|gb|EFS21424.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium sp.
           3_1_5R]
 gi|313690869|gb|EFS27704.1| ribosomal large subunit pseudouridine synthase D [Fusobacterium
           gonidiaformans ATCC 25563]
          Length = 289

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 76/197 (38%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV-----------DGVPLR-KAERTRLWLYHKPIGLVTT 87
           + +NG  ++  A  V   + + +             +PL    E   L + +K   LVT 
Sbjct: 35  IYLNGKKIKNTAKKVRKLNRVFIVEKEKETGIRPMDIPLEIVYEDENLLILNKQANLVTH 94

Query: 88  HSDPDGRST-----VFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
            +     +T     V   L +    ++     RLD+NT GL+++T +   ++      T+
Sbjct: 95  PTTKKVDATLANGVVAYFLKTTGKTMVPRFYNRLDMNTTGLIIVTKN-AYSQAYLQEKTE 153

Query: 141 WLRVYRVRFHGQVDQDKL----------NLLKKGIVI---QGICYGDMQVTLDTQ--KGS 185
             + Y+    G V+QD+             L++ I +   +G       V +  +  + +
Sbjct: 154 VRKSYQTIVKGIVEQDEFYITKPIGKVGEDLRR-IELAVSEGGQEAKTFVKVLKRFPERN 212

Query: 186 NAWVTVGLREGKNREIK 202
              + V L  G+  +I+
Sbjct: 213 RTLLDVTLFTGRTHQIR 229


>gi|323345230|ref|ZP_08085453.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
 gi|323093344|gb|EFZ35922.1| ribosomal large subunit pseudouridine synthase D [Prevotella oralis
           ATCC 33269]
          Length = 299

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/205 (20%), Positives = 76/205 (37%), Gaps = 28/205 (13%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKAERTRL----- 75
           AS+ +V+  +  + ++VNG  + +    ++    + V     +     K  R        
Sbjct: 36  ASKSKVKATLKGRGIRVNGKTVTQFDFPLLPGMKVSVSKSKRNNNLQSKYVRIVYEDRFL 95

Query: 76  WLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
            +  K IG+++    HS  + ++ + D             V RLD +T GL++ T D   
Sbjct: 96  VVVEKNIGILSMAGGHSTLNVKNILDDYFSKGRQHCTAHVVHRLDRDTSGLMVYTKDTQT 155

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQDK---LNLLKKGI--------VIQGICYGDMQV 177
           A++LE         R Y     G+++ D+    N LK           V  G  Y     
Sbjct: 156 AQLLESDWHDIVYDRRYVAVVSGEMEDDEGTIANWLKDNKSYISYSSPVDNGGKYAVTHF 215

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
               +    + V   L  G+  +I+
Sbjct: 216 HTLQRTADYSLVEYKLETGRKNQIR 240


>gi|254473085|ref|ZP_05086483.1| ribosomal large subunit pseudouridine synthase D [Pseudovibrio sp.
           JE062]
 gi|211957806|gb|EEA93008.1| ribosomal large subunit pseudouridine synthase D [Pseudovibrio sp.
           JE062]
          Length = 349

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 67/183 (36%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             +   T +R+  V+A A I   SR  ++ +I   +V++    +      V + D I + 
Sbjct: 27  TPEPEDTGRRLDAVLA-AHIDDFSRNRLQALIRAGQVQIGQRTVLEPKYRVCAGDTITLI 85

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      + +PL    E   L +  KP GLV      +   T+ + L         
Sbjct: 86  VPEPEAAEPQPEDIPLTIVYEDEDLIVIDKPAGLVVHPGAGNPTGTLVNALIHHCGSSLS 145

Query: 106 -----SRVISVGRLDINTEGLLLLT-ND----GGLARVLELPSTQ-WLRVYRVRFHGQVD 154
                 R   V R+D +T GLL++  ND    G  A+  +   T    R Y+    G   
Sbjct: 146 GIGGVKRPGIVHRIDKDTTGLLVIAKNDMAHQGLAAQFADHGRTGPLERAYKALVWGAPT 205

Query: 155 QDK 157
             K
Sbjct: 206 AAK 208


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/201 (15%), Positives = 66/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDSGLVSIGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D L S F     + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YD-LASFFKGWALLHRLDKETSGVVLLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALTQGIIEEE--REINAPILTFKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>gi|199599112|ref|ZP_03212517.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
 gi|199590005|gb|EDY98106.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus rhamnosus
           HN001]
          Length = 300

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 78/240 (32%), Gaps = 49/240 (20%)

Query: 13  PQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P +++  + + G  SR +++++      + VN    +  A  + + D I V   P + A 
Sbjct: 11  PLKLAAFLKQQGF-SRAQLKKLRYQGGFIFVN-KRQQHTAYPLRNGDRILVQTAPEQAAA 68

Query: 72  RTR--------------LWLYHKPIGLVT-----THSDPDGRSTVFDNLPSIFSR--VIS 110
                              + +KP G+ +       +D          + +      V  
Sbjct: 69  SVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTHAESQAVHV 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVI 167
           V RLD +T GL++      LA  L           + Y         +  L+    G +I
Sbjct: 129 VTRLDRDTSGLMVFAKH-SLAHSLLDRQLHSENFLKQYLALVT---SKSLLS--AHGWII 182

Query: 168 Q--GICYGD--MQVTLDTQKGSNAWVT------------VGLREGKNREIKKVFEFFNWK 211
              G+  G    +V ++T K S                 V L  G+  +I+  F      
Sbjct: 183 LPIGVSTGFYMRRVVIETGKPSVTEYQTLAQNSDAAAVLVTLHTGRTHQIRVHFAAIGHP 242


>gi|45402|emb|CAA78140.1| putative protein of unknown function [Pseudomonas aeruginosa PAO1]
          Length = 185

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/164 (21%), Positives = 61/164 (37%), Gaps = 25/164 (15%)

Query: 14  QRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLE------RAAVNVMSTDHIEVDGV 65
           QR+ + IA       SR  +   I   R+ V+G ++         A  V+  +  E  G 
Sbjct: 18  QRLDQ-IAAQLFPEHSRSRLAGWIKDGRLTVDGAVVRPRDIVHSGAQLVLEAEQ-EAQGE 75

Query: 66  PLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPS--IFSRVISVG 112
            L +        E   + +  KP GLV   +      T+ +    ++P      R   V 
Sbjct: 76  WLAQDIELEIVYEDEHILVIDKPAGLVVHPAAGHQDGTLLNALLYHVPDIANVPRAGIVH 135

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
           RLD +T GL+++         L  +L +    R+Y     G + 
Sbjct: 136 RLDKDTTGLMVVAKTLEAHTKLVAQLQARSVSRIYEAIVIGVIT 179


>gi|59710878|ref|YP_203654.1| pseudouridine synthase for 23S rRNA and tRNAphe [Vibrio fischeri
           ES114]
 gi|197334224|ref|YP_002155030.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
 gi|59478979|gb|AAW84766.1| pseudouridine synthase for 23S rRNA and tRNAphe [Vibrio fischeri
           ES114]
 gi|197315714|gb|ACH65161.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           MJ11]
          Length = 245

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 59/169 (34%), Gaps = 38/169 (22%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           +   + + +KP GL++     P+   +++  L   F  +  V RLD++T GL+L   +  
Sbjct: 19  QDESILVVNKPSGLLSVPGRAPEHYDSMWSRLKVEFPDIQVVHRLDMSTSGLMLFAMNKY 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQV 177
                       L        ++Y  R  G ++QD+       I +            +V
Sbjct: 79  SERHLKKQFQYRLTH------KIYYARVWGNIEQDEGE-----IDLPLICDWENRPKQKV 127

Query: 178 TLDTQKGSNAWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
             +  K S     V  RE            G++ +++  +       + 
Sbjct: 128 CFEHGKPSQTRYQVVRREEKTTIVRLLPITGRSHQLRVHML-SIGHPIV 175


>gi|148544733|ref|YP_001272103.1| RluA family pseudouridine synthase [Lactobacillus reuteri DSM
           20016]
 gi|184154085|ref|YP_001842426.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|148531767|gb|ABQ83766.1| pseudouridine synthase, RluA family [Lactobacillus reuteri DSM
           20016]
 gi|183225429|dbj|BAG25946.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
          Length = 290

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 72/241 (29%), Gaps = 43/241 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIA-----QQRVKVNGILLERAAVNVMS----- 56
           +     P ++ K +   G+  R     +       +    V+   +      ++      
Sbjct: 6   IYRGTEPIKIKKYLQSLGMGHR-----LFNDLKNGEGEFLVDHRKVR-PTTQILPNQPLT 59

Query: 57  --------TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                    D +E    PL        WL   KP G+ +         TV + +      
Sbjct: 60  IKAQPELADDTVESSNEPLNVVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA 119

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKL 158
                 R   + RLD  T GLLL+      + ++     Q    + Y     GQV  +  
Sbjct: 120 NNSADLRPHLITRLDRFTGGLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHG 179

Query: 159 NL-----LKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +      K G    ++ +       +  ++ +      V V L  G+  +I+  F    
Sbjct: 180 EINKPIGRKDGQAARVIDENGQRALTEYWVEERGAKWTRVRVRLHTGRTHQIRVHFAAIG 239

Query: 210 W 210
            
Sbjct: 240 H 240


>gi|237709871|ref|ZP_04540352.1| RNA pseudouridylate synthase [Bacteroides sp. 9_1_42FAA]
 gi|229455964|gb|EEO61685.1| RNA pseudouridylate synthase [Bacteroides sp. 9_1_42FAA]
          Length = 308

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 39/220 (17%), Positives = 74/220 (33%), Gaps = 30/220 (13%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA------ER 72
           AGI SR +V+ ++A + + V+ ++  +    +     +++    +    +        E 
Sbjct: 40  AGI-SRSKVKALLANRVILVDNVITTQYNFALKPGMKVQMSKAKNNREFKHPMLKLVYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTN 126
             + +  K  GL++  ++     T    L         F+RV  V RLD  T GL++   
Sbjct: 99  AYILVVEKKEGLLSVSTERQKERTAQHILNEYVKRSHRFNRVFVVHRLDRETSGLMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDM 175
           D      L          R Y     G +++D            L      +        
Sbjct: 159 DEKTQNTLRDNWHDIVTDRRYVSIVSGNMEKDYGTVESWLTDRKLYVSSSPVDDGEGKFA 218

Query: 176 QVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVN 213
                T K +N  + V + L  G+  +I+         V 
Sbjct: 219 VTHYKTIKRANGYSLVELDLETGRKNQIRVHMSDLGHPVI 258


>gi|254391608|ref|ZP_05006807.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
 gi|294812119|ref|ZP_06770762.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
 gi|326440725|ref|ZP_08215459.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces clavuligerus ATCC 27064]
 gi|197705294|gb|EDY51106.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           clavuligerus ATCC 27064]
 gi|294324718|gb|EFG06361.1| Pseudouridine synthase [Streptomyces clavuligerus ATCC 27064]
          Length = 313

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 63/175 (36%), Gaps = 27/175 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   I+R    SR +   + A  +V V+G  + +       A + V     
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAAGKVLVDGAAVGKSERVHGGAWLEVEMPQA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S     +TV   L +   R+   
Sbjct: 72  PAPVQIVAEPVEGMEIVHDDDDIVVIV-KPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                   V RLD+ T GL+++        +L+         + Y     G  D 
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTLLKQQFRDRTVDKRYHALVQGHPDP 185


>gi|261253959|ref|ZP_05946532.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
 gi|260937350|gb|EEX93339.1| ribosomal large subunit pseudouridine synthase A [Vibrio orientalis
           CIP 102891]
          Length = 245

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/169 (16%), Positives = 55/169 (32%), Gaps = 38/169 (22%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   + + +KP GL++      +   +++  L   +  +  V RLD++T GL+L      
Sbjct: 19  EDQHILVANKPSGLLSVPGRLAEHYDSMWSRLVESYPDIQVVHRLDMDTSGLMLFAKHKE 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQV 177
                       L        +VY  R  G  +Q      L L+              +V
Sbjct: 79  AERSLKKQFQYRLTH------KVYYARVWGHPEQQSGQVDLPLIA-----DWPNRPKQKV 127

Query: 178 TLDTQKGSNAWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
                K S     V  +E            G++ +++  + +     + 
Sbjct: 128 CYQDGKPSQTLYQVVKQEEKTAIVRLLPITGRSHQLRVHM-QALGHPIV 175


>gi|323339639|ref|ZP_08079911.1| RluA family pseudouridine synthase [Lactobacillus ruminis ATCC
           25644]
 gi|323092935|gb|EFZ35535.1| RluA family pseudouridine synthase [Lactobacillus ruminis ATCC
           25644]
          Length = 304

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 72/228 (31%), Gaps = 36/228 (15%)

Query: 18  KVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRK 69
           +++   G+ S R + ++   Q  V++N       +  V   D + +       D   L  
Sbjct: 20  RILTNHGV-SHRMLAKLKRGQGNVRLNEEK-TVLSALVGQNDKVTLVLPPEKDDERILVS 77

Query: 70  AERTRL-------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLD 115
            ER ++        L  KP G+ +     +   T+ + +               +V RLD
Sbjct: 78  HERIKVVYEDENWLLLDKPAGISSVPGPSNDHDTMMNRVKGYLIDQKSENLVPHAVTRLD 137

Query: 116 INTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------LNL----LKK 163
             T GL+L    G    ++     +    + Y     G V +D       L       ++
Sbjct: 138 RFTSGLMLCAKHGFAQGLISKQVQEHSMEKRYLAVCSGFVKKDHGIIDLPLKKEDNGFRR 197

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +   G          +        V   L  G+  +I+  F  F   
Sbjct: 198 IVSCDGQNAVTEYWVRERFGNEATLVECVLHTGRTHQIRAHFAHFAHP 245


>gi|58698525|ref|ZP_00373428.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila ananassae]
 gi|225630144|ref|YP_002726935.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia sp. wRi]
 gi|225677282|ref|ZP_03788264.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Muscidifurax uniraptor]
 gi|58534967|gb|EAL59063.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Drosophila ananassae]
 gi|225590674|gb|EEH11919.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia endosymbiont of Muscidifurax uniraptor]
 gi|225592125|gb|ACN95144.1| ribosomal large subunit pseudouridine synthase C, putative
           [Wolbachia sp. wRi]
          Length = 307

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 58/175 (33%), Gaps = 42/175 (24%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           R+ + I       RR         +E+ + +  +KV+    + +   V S   I +    
Sbjct: 16  RLDRYI-------RRIFPDLKQSVIEKSLRKGLIKVDDCKAKSSD-RVNSGQTITLKHLN 67

Query: 63  -----------DGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                      +   +         E   +   +KP G++        + ++ D L  I 
Sbjct: 68  YIENANSDRKYNEKLVNLLRENILYEDEYILAINKPAGVIVQGG-VKVKISMSDLLDQIR 126

Query: 106 SR--VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                  V RLD +T G+++   +  +AR L       +  + Y     G   +D
Sbjct: 127 EGETFKIVHRLDRDTSGVIIFARNANVARYLMEEFKGRRVKKTYLALTSGIPSKD 181


>gi|221308760|ref|ZP_03590607.1| hypothetical protein Bsubs1_05088 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313082|ref|ZP_03594887.1| hypothetical protein BsubsN3_05029 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318008|ref|ZP_03599302.1| hypothetical protein BsubsJ_04973 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322282|ref|ZP_03603576.1| hypothetical protein BsubsS_05074 [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|255767213|ref|NP_388802.2| RNA pseudouridine synthase [Bacillus subtilis subsp. subtilis str.
           168]
 gi|239938792|sp|P54604|YHCT_BACSU RecName: Full=Uncharacterized RNA pseudouridine synthase yhcT;
           AltName: Full=RNA pseudouridylate synthase; AltName:
           Full=RNA-uridine isomerase
 gi|225184840|emb|CAB12749.2| putative RNA pseudouridine synthase [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291483387|dbj|BAI84462.1| hypothetical protein BSNT_01587 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 302

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 88/262 (33%), Gaps = 49/262 (18%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLV 85
           ++KVN   +    + V   D + +D             G      E   + + +KP G+ 
Sbjct: 44  QIKVNHESVLN-NMIVKKGDRVFIDLQESEASSVIPEYGELDILFEDNHMLIINKPAGIA 102

Query: 86  TTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE---L 136
           T  ++     T+ + +   +       +V  V RLD +T G ++      LA  +    L
Sbjct: 103 THPNEDGQTGTLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKH-RLAHAILDQQL 161

Query: 137 PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKG 184
                 R Y     G            + +D+ +  ++ +   G       +V     K 
Sbjct: 162 EKKTLKRTYTAIAEGKLRTKKGTINSPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKE 221

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
             + V + L  G+  +I+                   P    +L  G ++ ++++ L   
Sbjct: 222 RLSLVELELETGRTHQIRVHLASLGH-----------PLTGDSLYGGGSKLLNRQALHAN 270

Query: 243 EQLGPHLLEEAQVNLDAPIYSS 264
           +    H + +  +  +AP  + 
Sbjct: 271 KVQAVHPITDELIVAEAPFPAD 292


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 79/243 (32%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V + F  +RV   +AR    SR  V  + A   V+ N   L ++   + + D +EVD   
Sbjct: 8   VPDGFDGERVDTALARMTGLSRSRVGDLCAHGDVRRNVEALTKSD-RLHAGDLLEVDLPD 66

Query: 64  ---GVPLRKAERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG 112
                P+    +    LY         KP G+    S       V   L ++  RV + G
Sbjct: 67  PRPVEPVATPVKGMALLYEDEDIVVVDKPAGVAAHPSMGWDGPDVLGALKAMHVRVATSG 126

Query: 113 ---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL--- 158
                    RLD+ T G++++        VL+         +VY     G +D       
Sbjct: 127 AAERQGIVSRLDVGTSGVMIVAKGERAYSVLKRAFREHMVDKVYHALVQGHLDPSHGTID 186

Query: 159 --------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      K  IV  G         ++   G+     V L  G+  +I+        
Sbjct: 187 APIGRHPSREWKMAIVEGGRESVTHYDVIEAMPGA-CLAEVHLETGRTHQIRVHMAAVGH 245

Query: 211 KVN 213
              
Sbjct: 246 PCV 248


>gi|294139995|ref|YP_003555973.1| tRNA pseudouridine synthase C [Shewanella violacea DSS12]
 gi|293326464|dbj|BAJ01195.1| tRNA pseudouridine synthase C [Shewanella violacea DSS12]
          Length = 292

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 51/170 (30%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           E   +   HKP GL+   S    R   F        +   V  V RLD  T G+LL    
Sbjct: 49  EDDDIVAIHKPAGLLVHRSYLARRERFFAMQLTRDKVGCHVFPVHRLDRPTSGVLLFAKS 108

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---------- 175
             +A  L +        + Y     G + +         + +  +   D+          
Sbjct: 109 CEMANALCVQFADKTIEKHYLAIVRGNMHEAATLDYPLKVELDDLGDKDVNQDKPAQDAV 168

Query: 176 ---QVTLDTQKGSNA---------WVTVGLREGKNREIKKVFEFFNWKVN 213
              Q  L+T+    +          V +    G+  ++++        + 
Sbjct: 169 TSYQPLLNTEIPFTSGRYASSRYALVKLSPHTGRKHQLRRHMAHLRHPIL 218


>gi|228920104|ref|ZP_04083453.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839560|gb|EEM84852.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 307

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 87/265 (32%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       RV  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETRVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   E  +V++  P   +  
Sbjct: 274 INFLHPITKEAIEVDVPFPAKLNNK 298


>gi|163790580|ref|ZP_02185009.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Carnobacterium sp. AT7]
 gi|159874183|gb|EDP68258.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Carnobacterium sp. AT7]
          Length = 310

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 52/167 (31%), Gaps = 32/167 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLL 123
           E     + +KP G+ +  S      T+ + +   + R       +  V RLD +T GL+L
Sbjct: 92  EDEHYLVVNKPFGVASVPSQVHPEGTMANRVKGYYVRQNYDDQVIHIVTRLDRDTTGLML 151

Query: 124 LTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
               G  A  L        +  + Y     GQ ++      + G +   I      +   
Sbjct: 152 FAKHG-YAHALMDEKLRAKEITKKYTALISGQFNES-----EHGFIDAPIARTTDSIITR 205

Query: 181 TQKGS------NAWVT----------VGLREGKNREIKKVFEFFNWK 211
               S        W+           + L  G+  +I+  F      
Sbjct: 206 RAHESGKEALTEYWIKEAFPQATLVDIQLHTGRTHQIRVHFAHIGHP 252


>gi|90417173|ref|ZP_01225100.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2207]
 gi|90330949|gb|EAS46210.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2207]
          Length = 324

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/219 (16%), Positives = 76/219 (34%), Gaps = 32/219 (14%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+ ++ A      SR  ++  I    + V+G   +     ++  + I V           
Sbjct: 29  RLDQIAAELFSDYSRSRLQLWIKSGELTVDGQQ-QPPKFKLLGGETIAVSAQLKAEGDWQ 87

Query: 63  -DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV------GRL 114
            + +PL    E   + + +KP   V   +  +   T+ + L     ++ SV       RL
Sbjct: 88  AEDIPLNIVFEDEHIIVINKPTNFVVHPAAGNREGTLLNALLFHCPQLKSVPRAGIVHRL 147

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL---------NLLKK 163
           D +T GL+++         L  +L +    R Y     G +    L             K
Sbjct: 148 DKDTTGLMVVAKTLAAHTDLVAQLQARTVSREYESVVSGVMTGGGLVDQPIGRHPKQRVK 207

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             V++          +  +   + ++ + L  G+  +I+
Sbjct: 208 MAVVRDGKEARTHYKVVKRFDGHTYIRLKLETGRTHQIR 246


>gi|304385186|ref|ZP_07367532.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
 gi|304329380|gb|EFL96600.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici DSM 20284]
          Length = 301

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/221 (16%), Positives = 78/221 (35%), Gaps = 44/221 (19%)

Query: 24  GIASRREVERMIAQ------QRVKVNGILLERAAVNVMSTDHIEVD-------------G 64
              +R+ + R + +       ++ VN    +R    V + D + V+              
Sbjct: 17  TFLTRKRISRALLKSIKFNGGKILVN-EQPKRTNEMVTAGDQVTVELPPEPGNPHVVRSR 75

Query: 65  VPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDI 116
            P+    E     + +KP  L T  S  +   T+ + + + ++        V  V RLD 
Sbjct: 76  QPIDVIYEDQDYLVVNKPPFLPTVQSARNQTDTLVNRVKNYYAERDYESQVVHVVTRLDQ 135

Query: 117 NTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHG-----------QVDQDKLNLLK 162
           +T GL+L       A  +        +  + Y     G            +++D  + +K
Sbjct: 136 DTSGLVLFAKH-RFAHTIMDQDLRQHRVQKYYLAMATGRFAQSHGLIDAPIERDPASFIK 194

Query: 163 KGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +   G       +  +  Q  +++ + V L  G+  +I+
Sbjct: 195 RRVASAGNGKPSKTEYWVLEQTATDSLLKVQLHTGRTHQIR 235


>gi|237803088|ref|YP_002888282.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/Jali20/OT]
 gi|231274322|emb|CAX11117.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/Jali20/OT]
          Length = 335

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 70/183 (38%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
           ++ E  T  R+ K +++  G  SR   ++ I   RV+VNG +  R +  +   D      
Sbjct: 15  VIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEVEL 73

Query: 60  --------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                   +  + +PL K  E   + + +KP  +V   +    + TV   L         
Sbjct: 74  IEEEEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLK 133

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ 155
              P    R   V RLD +T G LL+T     A+ L      + Q  ++Y         Q
Sbjct: 134 QEFPEEPWRPGIVHRLDKDTSG-LLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQ 192

Query: 156 DKL 158
           + +
Sbjct: 193 ELI 195


>gi|332673797|gb|AEE70614.1| RNA pseudouridine synthase [Helicobacter pylori 83]
          Length = 242

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 76/235 (32%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPGVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVRENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--QEINAPILTFKTTKAFSKISKKGQEAVTMITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|166154000|ref|YP_001654118.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 434/Bu]
 gi|166154875|ref|YP_001653130.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
 gi|301335199|ref|ZP_07223443.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2tet1]
 gi|165929988|emb|CAP03471.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 434/Bu]
 gi|165930863|emb|CAP06425.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis L2b/UCH-1/proctitis]
          Length = 335

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 70/183 (38%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
           ++ E  T  R+ K +++  G  SR   ++ I   RV+VNG +  R +  +   D      
Sbjct: 15  VIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEVEL 73

Query: 60  --------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                   +  + +PL K  E   + + +KP  +V   +    + TV   L         
Sbjct: 74  IEEEEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLK 133

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ 155
              P    R   V RLD +T G LL+T     A+ L      + Q  ++Y         Q
Sbjct: 134 QEFPEEPWRPGIVHRLDKDTSG-LLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQ 192

Query: 156 DKL 158
           + +
Sbjct: 193 ELI 195


>gi|76789398|ref|YP_328484.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis A/HAR-13]
 gi|237805009|ref|YP_002889163.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|255317785|ref|ZP_05359031.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 6276s]
 gi|76167928|gb|AAX50936.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis A/HAR-13]
 gi|231273309|emb|CAX10224.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis B/TZ1A828/OT]
 gi|296436198|gb|ADH18372.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/9768]
 gi|296437127|gb|ADH19297.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/11222]
 gi|296438058|gb|ADH20219.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/11074]
 gi|297140560|gb|ADH97318.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis G/9301]
          Length = 335

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 70/183 (38%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
           ++ E  T  R+ K +++  G  SR   ++ I   RV+VNG +  R +  +   D      
Sbjct: 15  VIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEVEL 73

Query: 60  --------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                   +  + +PL K  E   + + +KP  +V   +    + TV   L         
Sbjct: 74  IEEEEPSSLIPEDIPLDKVYEDDMILVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLK 133

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ 155
              P    R   V RLD +T G LL+T     A+ L      + Q  ++Y         Q
Sbjct: 134 QEFPEEPWRPGIVHRLDKDTSG-LLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQ 192

Query: 156 DKL 158
           + +
Sbjct: 193 ELI 195


>gi|126173680|ref|YP_001049829.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|125996885|gb|ABN60960.1| tRNA pseudouridine synthase C [Shewanella baltica OS155]
          Length = 287

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 51/173 (29%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  EDEHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------- 169
                +A  L     S    + Y     G + +  +      + +               
Sbjct: 92  AKSSEVANALCEQFASHTIEKQYLALVRGNMHESGILDYALKVELDELGDKNADPNKAAQ 151

Query: 170 ------ICYGDMQVTLDTQKGSNA---WVTVGLREGKNREIKKVFEFFNWKVN 213
                     + ++   + +   +    V +  + G+  ++++        + 
Sbjct: 152 EAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHLRHPIV 204


>gi|330837755|ref|YP_004412396.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           coccoides DSM 17374]
 gi|329749658|gb|AEC03014.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           coccoides DSM 17374]
          Length = 233

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/188 (13%), Positives = 51/188 (27%), Gaps = 37/188 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGL 121
           E   L   +K  G +    D  G  T+ D +               +    RLD  T G+
Sbjct: 16  EDNHLIAVNKLPGELVQG-DKTGDVTLADAVRDYLKVKYGKPGNVYLGIPHRLDRPTSGV 74

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKL-----------NLLKKGIV 166
           +L          +      +   +VY           +  L             + + + 
Sbjct: 75  VLYCRTEKALGRMNEMFRGSDVSKVYWAVVDALPQNTEGTLVHYIFRDTRTNKSVARPVE 134

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
             G  +  +   +     +   + + L  G++ +I+         +             G
Sbjct: 135 TVGSKFAKLDYRIIGASRNYHLLEIVLHTGRHHQIRAQLAAIGLHIK------------G 182

Query: 227 TLLAGSTR 234
            L  G+ R
Sbjct: 183 DLKYGAAR 190


>gi|312216765|emb|CBX96715.1| hypothetical protein [Leptosphaeria maculans]
          Length = 791

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 52/148 (35%), Gaps = 27/148 (18%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------LWLY 78
           E+ I   RV VNG  +   +  + + D I      L + E                L + 
Sbjct: 120 EQAIKDGRVVVNGKPVPSTSTMIKNGDVIS---HTLHRHEPPCTAQPIGIVHEDNDLIVI 176

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G+    +     +++ + + +            RLD  T G++ +   G   +  E
Sbjct: 177 NKPAGMPVHPAGRYNFNSIIEIMRADRGYNWNPLPCNRLDRLTSGIMFI---GKHRKAAE 233

Query: 136 LPSTQ-----WLRVYRVRFHGQVDQDKL 158
             S Q       + Y  R  G+  + ++
Sbjct: 234 HMSAQIRGRTVKKEYITRVVGEFPEGEV 261


>gi|317129591|ref|YP_004095873.1| pseudouridine synthase [Bacillus cellulosilyticus DSM 2522]
 gi|315474539|gb|ADU31142.1| pseudouridine synthase, RluA family [Bacillus cellulosilyticus DSM
           2522]
          Length = 298

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/273 (16%), Positives = 86/273 (31%), Gaps = 47/273 (17%)

Query: 27  SRRE-VERMIAQQRVKVNGI------LLERAAV--NVMSTDHIEVDGVPLRKA-----ER 72
           SR+   +      ++ VNG        L    V   +   + +     P +       E 
Sbjct: 30  SRKALADIKFNGGQITVNGKEENVRYTLRLGDVIEVIFPKEKVSRSIKPYKIKLHIIFED 89

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTN 126
             + + +KP  L T  +  +G  ++   + + +      S   +V RLD +T GL+++  
Sbjct: 90  EHVIIINKPPHLPTIPTRNEGEPSLAGAILAYYIENGIPSTFHAVSRLDRDTSGLVMVAK 149

Query: 127 DGGLARVL---ELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVI------QGICYG 173
                  L      S +  R Y     G +  D     L + +K   I      +     
Sbjct: 150 H-RYMHDLCVKLQKSYEIKRSYVALVEGILSDDYNTIDLPISRKTTSIIEREVNEFGKSA 208

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                +  +      + + L  G+  +I+         +              TL  G  
Sbjct: 209 ITHYEVLKRYSGATLLQLTLETGRTHQIRVHMSAIGHPLLG-----------DTLYGGDV 257

Query: 234 REVSKKILR-EQLG-PHLLEEAQVNLDAPIYSS 264
           R + ++ L   QL   H + + +     PI   
Sbjct: 258 RYIDRQALHSHQLSFFHPINKREYTFHCPIPDD 290


>gi|269958889|ref|YP_003328678.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           centrale str. Israel]
 gi|269848720|gb|ACZ49364.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           centrale str. Israel]
          Length = 299

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 82/242 (33%), Gaps = 46/242 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVN---- 53
           M+ + +V+E     RV + +   G+    ++  +ER++ +  + +N   +  +A      
Sbjct: 1   MRREYLVEEACFGVRVDRYL--RGLLPGVTQSFIERLLRRGEILLNNTKVRSSARVSNGD 58

Query: 54  ---VMSTDHIEVDGVPLRK---------------AERTRLWLYHKPIGLVTTHSDPDGRS 95
              +   D I +    +R+                E   +   +KP G+        G  
Sbjct: 59  VLSIKHADRIVMREKEIRRLQHVPLLDLISNNILYEDQNVIAINKPAGVSVQGGSKVG-V 117

Query: 96  TVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
           ++ D L  I        V RLD +T G+L+L  D  +AR L       +  + Y     G
Sbjct: 118 SIGDLLDKIRPGGCCRIVHRLDKDTSGVLVLARDLDVARCLAREFRERRVQKEYIAITKG 177

Query: 152 QVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGKNRE 200
                          K+       +++        VT      +   +  V    G+  +
Sbjct: 178 VPHSASGEVNTPIFYKVQSATGERMLEKDAKTFFSVTRVLGNFAVVLLRPVT---GRKHQ 234

Query: 201 IK 202
           ++
Sbjct: 235 LR 236


>gi|90413524|ref|ZP_01221515.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
 gi|90325456|gb|EAS41939.1| putative pseudouridine synthase Rlu family protein [Photobacterium
           profundum 3TCK]
          Length = 244

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 28/173 (16%), Positives = 53/173 (30%), Gaps = 34/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL    
Sbjct: 8   QDEYLVAVNKPSGMLVHRSWLDRHETVFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFGLS 67

Query: 128 GGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGI------------- 170
             +A  +          + Y     G +    +    LKK   +  I             
Sbjct: 68  SEIASQMMPVFSGRDIHKTYHAVVRGWIKDAAVLDYPLKK--ELDKIADKNAAEQEAQDA 125

Query: 171 -----CYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                    ++  +   + + +   +   E     G+  ++++     N  + 
Sbjct: 126 VTAYSPLATIETNIPVGRYATSRYCLV--EMKPETGRKHQLRRHMHHLNHHII 176


>gi|238789504|ref|ZP_04633289.1| Pseudouridine synthase [Yersinia frederiksenii ATCC 33641]
 gi|238722454|gb|EEQ14109.1| Pseudouridine synthase [Yersinia frederiksenii ATCC 33641]
          Length = 249

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 80/235 (34%), Gaps = 52/235 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 29  PCHDKIE------TLYQDDHLVLINKPTGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHR 82

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 83  LDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSAVLCGHLDDN------EGVIDAAIA 136

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG---LRE------------------GKNREIKKVF 205
                     +     K + +   V      E                  G+  +++   
Sbjct: 137 KDPALFPLMSICAIHGKPARSRYQVVERFYHELEDKTLQPLTRVQLTPETGRTHQLRIHC 196

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL---REQLGPHLLEEAQVNL 257
           +     +       YG    G LL G+  E++ +++    E    H + +  +N 
Sbjct: 197 QQLGHPIWGCD--LYG----GRLLPGT--ELTPRLMLHASELHFVHPISKEWINA 243


>gi|254373560|ref|ZP_04989047.1| hypothetical protein FTCG_01516 [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|151571285|gb|EDN36939.1| hypothetical protein FTCG_01516 [Francisella novicida GA99-3549]
          Length = 309

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQTS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYAIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIRI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/229 (14%), Positives = 64/229 (27%), Gaps = 45/229 (19%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ K + + G  S R +   +I +  V V+G ++ + +         EV         R
Sbjct: 1   MRLDKYLYQKGFTSSRNKAAELIREGLVSVDGKVVTKPSF---ELQKGEVSIKAKPYVSR 57

Query: 73  TRLWLYH-------------------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV-- 111
               L H                      G  T      G   V            ++  
Sbjct: 58  AAYKLKHFLDTIDASFIKDAEVLDVGASTGGFTQILCEYGAKKVIALDVGSGQLHPTIKS 117

Query: 112 --GRLDINTEGLL--------LLTNDGGLAR--VLELPSTQWLRVYRVRFHGQVDQ--DK 157
               +D++   +         ++T D        +     +  + Y +       +   +
Sbjct: 118 KQNVIDMSNTDIRTFEHDPFDIVTCDVSFISVLKIVHHIDRLSKKYIIILFKPQFEVGKE 177

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW----VTVGLREGK--NRE 200
           +   K+G+V             + +     W      + L EGK  NRE
Sbjct: 178 VKRDKRGVVQDQKAIEKAMRQFEKKTKELGWQLVQRKISLVEGKEGNRE 226


>gi|1239996|emb|CAA65704.1| hypothetical protein [Bacillus subtilis subsp. subtilis str. 168]
          Length = 302

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 88/262 (33%), Gaps = 49/262 (18%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLV 85
           ++KVN   +    + V   D + +D             G      E   + + +KP G+ 
Sbjct: 44  QIKVNHESVLN-NMIVKKGDRVFIDLQESEASSVIPEYGELDILFEDNHMLIINKPAGIA 102

Query: 86  TTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE---L 136
           T  ++     T+ + +   +       +V  V RLD +T G ++      LA  +    L
Sbjct: 103 THPNEDGQTGTLANLIAYHYQINGETCKVRHVHRLDQDTSGAIVFAKH-RLAHAILDQQL 161

Query: 137 PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKG 184
                 R Y     G            + +D+ +  ++ +   G       +V     K 
Sbjct: 162 EKKTLKRTYTAIAEGKLRTKKGTINPPIGRDRSHPTRRRVSPGGQTAVTHFKVMASNAKE 221

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
             + V + L  G+  +I+                   P    +L  G ++ ++++ L   
Sbjct: 222 RLSLVELELETGRTHQIRVHLASLGH-----------PLTGDSLYGGGSKLLNRQALHAN 270

Query: 243 EQLGPHLLEEAQVNLDAPIYSS 264
           +    H + +  +  +AP  + 
Sbjct: 271 KVQAVHPITDELIVAEAPFPAD 292


>gi|304409553|ref|ZP_07391173.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|307303911|ref|ZP_07583664.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|304352071|gb|EFM16469.1| pseudouridine synthase [Shewanella baltica OS183]
 gi|306912809|gb|EFN43232.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 287

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 51/173 (29%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  EDDHLVAIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------- 169
                +A  L     S    + Y     G + +  +      + +               
Sbjct: 92  AKSSEVANALCEQFASHTIEKQYLALVRGNMHESGILDYALKVELDELGDKNADPNKAAQ 151

Query: 170 ------ICYGDMQVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFFNWKVN 213
                     + ++   + +   +    V +  + G+  ++++        + 
Sbjct: 152 EAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHLRHPIV 204


>gi|332668407|ref|YP_004451195.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332337221|gb|AEE54322.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 243

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 30/174 (17%), Positives = 59/174 (33%), Gaps = 24/174 (13%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSD-PDGRSTVFDNLPSIFSRVIS 110
           +       I VD           + +  KP GL++        +  ++  L + + +V  
Sbjct: 1   MKAHPLKIIHVD---------EHIIVCEKPSGLLSIPDRFDQEKPNLYHLLEAQYGQVWI 51

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG---QVDQDKLNLLK--- 162
           V R+D  T G+L+   +    R L          ++Y     G       +    +    
Sbjct: 52  VHRIDRETSGILVFARNEDAHRALNQQFLDRSVEKIYLALVEGRPMPPTGEINKAIAPHP 111

Query: 163 --KGIVI---QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G +I   +G     +   +DT K + A V   ++ G+  +I+  F      
Sbjct: 112 SIAGKMITSGKGKSALTLYKVVDTYK-AYALVEADIKTGRTHQIRVHFASIGHP 164


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           + +F N +V  L RI  G  +LG L  G  R +S K ++
Sbjct: 1   MCDFINHQVLELKRIQIGDIKLGNLPLGKWRYLSNKEVK 39


>gi|71276441|ref|ZP_00652717.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71901554|ref|ZP_00683637.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|170730991|ref|YP_001776424.1| pseudouridylate synthase [Xylella fastidiosa M12]
 gi|71162757|gb|EAO12483.1| Pseudouridine synthase, RluD [Xylella fastidiosa Dixon]
 gi|71728678|gb|EAO30826.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|167965784|gb|ACA12794.1| Pseudouridylate synthase [Xylella fastidiosa M12]
          Length = 331

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 85/256 (33%), Gaps = 35/256 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  V +    +R   V+A      SR  +   I    V +NG+L+      V   + +
Sbjct: 13  SRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVR-PRDPVYGGEVV 71

Query: 61  EV--------DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +        D VP         E   +++ +KP GL+      +   T+ + L      
Sbjct: 72  RLQVVPDIRTDAVPQDIPLDILYEDEHVFVLNKPAGLIVHPGAGNPDGTLVNALLHRDPA 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RF 149
                R   V RLD +T G++++         L  +L S Q  R Y              
Sbjct: 132 LAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHRQYLAVVVSALVSGGTV 191

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +  +++   + L+  +   G          +  +   A +   L  G+  +I+       
Sbjct: 192 NAAIERHPRDRLRMAVSDTGKEAVTHYRLRERFRAHTA-LECRLDTGRTHQIRVHMAHLR 250

Query: 210 WKVNRLIRISYGPFQL 225
             +    R+  G  +L
Sbjct: 251 HPIVG-DRLYGGSLKL 265


>gi|329313677|gb|AEB88090.1| Pseudouridine synthase [Staphylococcus aureus subsp. aureus T0131]
          Length = 258

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 17  VTVRKQLMTNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 76

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 77  HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 134

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 135 LVYGKTHTSGIIEANIRRSKDRIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 194

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 195 HQIRVHFQHIGHPIV 209


>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 = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/233 (15%), Positives = 84/233 (36%), Gaps = 40/233 (17%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGI---------LLERAAVNV 54
           V++ F   R+   +++  I    SR  ++ +I +  V VN           + +   VN+
Sbjct: 8   VEKEFDNVRLDLYLSK--IFEDKSRSYLQGIIDEGNVLVNNKEKKRNYKLKVGDNIKVNI 65

Query: 55  MSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                ++++   ++     E   + + +KP  +V   +      T+ + L S    +   
Sbjct: 66  PEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLSHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK--- 157
                   V R+D +T G+L++  +      L          RVY     G +   +   
Sbjct: 126 NGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDGQGTI 185

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   ++ +K  +V +   Y      +  +  ++  V   L  G+  +I+
Sbjct: 186 EAPIGRHPVDRIKMAVV-KDGRYAVTHYKVIERFKNHTLVECKLETGRTHQIR 237


>gi|257784215|ref|YP_003179432.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
 gi|257472722|gb|ACV50841.1| pseudouridine synthase [Atopobium parvulum DSM 20469]
          Length = 246

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/162 (17%), Positives = 55/162 (33%), Gaps = 33/162 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----------IFSRVISVGRLDINTE 119
           +   L   +KP G++  HSD     ++ D +               S+V ++ RLD  T 
Sbjct: 15  QDDYLLAVNKPAGMIV-HSDGTNEPSLTDLVCEKLCALESSNKIDLSQVQALNRLDKETT 73

Query: 120 GLLLLT--NDGGLARVLELPSTQWLRVYRVRFHGQV-------------DQDKLNLLKKG 164
           G++L +   +        + S +  + Y     G               D+     ++  
Sbjct: 74  GIVLFSLKKETQPQFDQLIASKELSKEYLAVVKGDFGLNKLLIDKAIGKDRHDAQKMR-- 131

Query: 165 IVIQGICYGD----MQVTLDTQKGSNAWVTVGLREGKNREIK 202
           I   G         ++V    Q    + + V L  G+  +I+
Sbjct: 132 ISDTGKPSQTEVRLIKVASSAQGQIQSLLLVNLLTGRKHQIR 173


>gi|227363858|ref|ZP_03847963.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325683068|ref|ZP_08162584.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
 gi|227071085|gb|EEI09403.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324977418|gb|EGC14369.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           reuteri MM4-1A]
          Length = 297

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 72/241 (29%), Gaps = 43/241 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIA-----QQRVKVNGILLERAAVNVMS----- 56
           +     P ++ K +   G+  R     +       +    V+   +      ++      
Sbjct: 13  IYRGTEPIKIKKYLQSLGMGHR-----LFNDLKNGEGEFLVDHRKVR-PTTQILPNQPLT 66

Query: 57  --------TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                    D +E    PL        WL   KP G+ +         TV + +      
Sbjct: 67  IKAQPELADDTVESSNEPLNVVYEDDNWLVVDKPAGVTSIPGPTVQNDTVLNRVKGYLIA 126

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKL 158
                 R   + RLD  T GLLL+      + ++     Q    + Y     GQV  +  
Sbjct: 127 NNSADLRPHLITRLDRFTGGLLLIAKHHIASSMISQQVQQHQMLKEYTALVEGQVMDEHG 186

Query: 159 NL-----LKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +      K G    ++ +       +  ++ +      V V L  G+  +I+  F    
Sbjct: 187 EINKPIGRKDGQAARVIDENGQRALTEYWVEERGAKWTRVRVRLHTGRTHQIRVHFAAIG 246

Query: 210 W 210
            
Sbjct: 247 H 247


>gi|325697307|gb|EGD39193.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK160]
          Length = 298

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V   D I +               +G  + +  +
Sbjct: 36  RKIRHFLRTKKHVSVNG-LAINWQTVVKPGDDICLIFDEEDYPQKTILLGNGELVEELYQ 94

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 95  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 154

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+    KL           +  K+ +  +   + +  V
Sbjct: 155 PILNRLL-EKREISRQYWALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLFAETHV 213

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T   Q G    V   L+ G+  +I+
Sbjct: 214 TRLKQFGQAGLVKCQLKTGRTHQIR 238


>gi|282850437|ref|ZP_06259816.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282579930|gb|EFB85334.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 321

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/143 (14%), Positives = 48/143 (33%), Gaps = 19/143 (13%)

Query: 28  RREVERMIAQQRVKVNGILLE---------RAAVNVMSTDHIEVDGVPLRK-AERTRLWL 77
           RR   R+ +   + VNG                + +       +  + L    E   + +
Sbjct: 34  RR---RLRSDGIITVNGKPATWNTLVHGGDHLIMKLTPEQEFSLSPMELDIIYEDEYILV 90

Query: 78  YHKPIGLV----TTHSDPDGRSTVFDNLP--SIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            +K   ++    +T  D    + V       + +     V RLD +T G++++     + 
Sbjct: 91  INKAANILMHPTSTVRDHTLANGVLHYYQETNQYYDFHPVHRLDKDTSGIVIIAKTSVVQ 150

Query: 132 RVLELPSTQWLRVYRVRFHGQVD 154
              +   T + ++Y     G + 
Sbjct: 151 HAFDKKHTHFYKIYDAIVEGHLP 173


>gi|218265033|ref|ZP_03478645.1| hypothetical protein PRABACTJOHN_04355 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221638|gb|EEC94288.1| hypothetical protein PRABACTJOHN_04355 [Parabacteroides johnsonii
           DSM 18315]
          Length = 359

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 73/228 (32%), Gaps = 41/228 (17%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K +       +R  ++       +  NG  ++     V   D + +           
Sbjct: 45  RVDKFLVDRMFGATRNRIQSAADAGCIMANGKPVKS-NYRVKPEDVVTIMMTRPPRTFEI 103

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVI 109
             + +P++   E   L +  KP GLV      +   T+ + L                + 
Sbjct: 104 LPENIPIKIVYEDDDLLVVDKPAGLVVHPGHGNYTGTLVNALAWYLKDDPTYDPNDPALG 163

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK---------- 157
            V R+D +T GLL++         L +        R YR    G V  D+          
Sbjct: 164 LVHRIDKDTSGLLVVAKKPEAKANLSMQFFHKTTKREYRALVWGIVRDDEGRIEGNIGRN 223

Query: 158 -LNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIK 202
             + ++  +  +G          ++  + G    V   L  G+  +I+
Sbjct: 224 PRDRMQMTVFPEGDQGKTAVTHYSVLERLGYVTLVKCRLETGRTHQIR 271


>gi|303237284|ref|ZP_07323854.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
 gi|302482671|gb|EFL45696.1| pseudouridine synthase, RluA family [Prevotella disiens FB035-09AN]
          Length = 299

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 74/204 (36%), Gaps = 28/204 (13%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA----ERTRLW 76
           S+ +++  +  + + VN  ++ +    + + D I V      D    R      E   + 
Sbjct: 35  SKSKIKATLQNRGIMVNKKIVTQFNYELHAGDKISVSTSKKNDQFQSRYVKLLYEDRYIV 94

Query: 77  LYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
           +  K  G+++    H+  + +  + D       +     V RLD +T GL++   D    
Sbjct: 95  VIEKAQGILSMEAGHASLNVKKVLDDYFKKSKQKCTAHVVHRLDRDTSGLMIYAKDMQAE 154

Query: 132 RVLELPSTQW--LRVYRVRFHGQVDQDK------LNLLKKGIVI-----QGICYGDMQVT 178
           ++LE         R Y     G ++ D       L   K  +        G  Y     +
Sbjct: 155 QILEHEWHNIVYDRRYVAVLSGIMEDDSGTISNWLKDNKAYVTYSSPFDNGGKYAVTHFS 214

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
           +  +  S++ V   L  G+  +I+
Sbjct: 215 VLKRSNSHSLVEFKLDTGRKNQIR 238


>gi|169349788|ref|ZP_02866726.1| hypothetical protein CLOSPI_00526 [Clostridium spiroforme DSM 1552]
 gi|169293356|gb|EDS75489.1| hypothetical protein CLOSPI_00526 [Clostridium spiroforme DSM 1552]
          Length = 275

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 67/210 (31%), Gaps = 46/210 (21%)

Query: 29  REVERMIA-QQRVKVNG--ILLERAAVNVMSTDHIEV---DG----VPLRK-----AERT 73
           ++  + I     + VNG    +      +   D IE+   D      P         E  
Sbjct: 26  KKAIKAIKMNGDILVNGNHQTVR---YRLKKNDVIELIWPDEISTMEPYEYSLKIIYEDE 82

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
              +  KP G+    +      T+ + +   F        V  V RLD +T+GL+L+  +
Sbjct: 83  NYLIIDKPAGIPCMPTKRYPNKTIANAIIYYFQMCNLKATVHLVNRLDKDTQGLMLIAKN 142

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---- 183
                +L     Q  RVY     G +  +       GI+ + I      V          
Sbjct: 143 RQAHYLLSKDIKQVKRVYHCLVEGILKGE-------GIIDKPIIKDKNSVKRLIDASGKK 195

Query: 184 -----------GSNAWVTVGLREGKNREIK 202
                       + + +   L+ G+  +I+
Sbjct: 196 AITVYRSLKIFDNKSLIECDLKTGRTHQIR 225


>gi|118471435|ref|YP_887490.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           smegmatis str. MC2 155]
 gi|118172722|gb|ABK73618.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           smegmatis str. MC2 155]
          Length = 309

 Score = 58.7 bits (141), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/256 (16%), Positives = 81/256 (31%), Gaps = 52/256 (20%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---- 55
           M  +++ V E     RV   ++R    SR  V  +  +  V+++G    ++   V     
Sbjct: 1   MDTRSMPVPEGLAGMRVDAGLSRLLGLSRTVVATLAEEGAVELDGAPAAKSDKLVAGAWL 60

Query: 56  -----------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
                          ++++G+ +  ++   +    KP G+    +      TV   L   
Sbjct: 61  EVRLPEAPKPVENTPVDIEGMNILYSDAD-IVAVDKPPGVAAHATVGWHGPTVLGGLAAA 119

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                   I  R   V RLD+ T G++++        VL+    Q    + Y     G  
Sbjct: 120 GFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHP 179

Query: 154 DQDKLNLLKKGIVIQ-------GICYGDMQVTLDTQKGSN----------AWVTVGLREG 196
           D         G  I        G  +    V       ++          + + + L  G
Sbjct: 180 DP------SSG-TIDAPIGRHRGHDWKFAVVEGGRHSVTHYDTLEMFQAASLLDIELETG 232

Query: 197 KNREIKKVFEFFNWKV 212
           +  +I+  F   +   
Sbjct: 233 RTHQIRVHFSALHHPC 248


>gi|237752376|ref|ZP_04582856.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229375865|gb|EEO25956.1| ribosomal large subunit pseudouridine synthase A [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 353

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 69/176 (39%), Gaps = 30/176 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           + +     R    +++    SR +V+ +I++Q + +N   L++    + + D +++    
Sbjct: 17  ITDKNQGIRADIFLSKTLNLSRSKVQNLISKQAILLNSKPLKKYGTILNANDTLKLISQA 76

Query: 63  ----D---------GVPLRKAERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPS----- 103
               D          +P+   E + L + +KP  L+    D  D + T+ D L       
Sbjct: 77  KAKQDSNSQHLQDLNIPIIY-EDSDLLILNKPANLIVHRIDENDTQFTLVDYLKQKGFAL 135

Query: 104 ----IFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                  R+  V RLD NT G +++  +      L   + S Q  R Y    +  +
Sbjct: 136 SNLGDSYRLGIVHRLDKNTSGAIVIAKNNATHAHLSMQIKSKQMGRYYLCIINQPL 191


>gi|332652460|ref|ZP_08418205.1| pseudouridine synthase, RluA family [Ruminococcaceae bacterium D16]
 gi|332517606|gb|EGJ47209.1| pseudouridine synthase, RluA family [Ruminococcaceae bacterium D16]
          Length = 327

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 48/290 (16%), Positives = 94/290 (32%), Gaps = 75/290 (25%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR------AGIASRREVERMIAQQRVKVNGILLE-RAAVN 53
           MK+   + +N   QR+ + +A+      A +      ++ I  +RVKVNG   +    + 
Sbjct: 1   MKEF-TIAKNDAGQRLDRWLAKTLPLLPAPL-----AQKYIRLKRVKVNGKGSKRDVRLQ 54

Query: 54  VMSTDHIEVDGVPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRS 95
           V     + ++     +                   E   + L  K  GLV    + +  +
Sbjct: 55  VGDVLQLYINDEFFDRPTPENAFLSLYQPKLNILYEDEHILLLDKRPGLVVHPDETERVN 114

Query: 96  TVFDNLPSIF---SRVIS----------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL 142
           T+  ++ +                      R+D NT G+++        RV+        
Sbjct: 115 TLLTHIQAYLYQKKEWSPYKENSFAPALCNRIDRNTGGIVIAAKTAEALRVMNQKIKDRE 174

Query: 143 --RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---------- 190
             + Y     G+++  +  L  +G + +      + V    Q G+   +T          
Sbjct: 175 LSKFYLCAVLGRMEPREGKL--EGFIWKDEVKKQVYVRSRPQPGAKTAITLYKTLAVQNG 232

Query: 191 VGLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
           + L E     G+  +I+  F      +            LG    GS RE
Sbjct: 233 LSLVECDLITGRTHQIRAQFAAAGHPL------------LGDGKYGSERE 270


>gi|15924840|ref|NP_372374.1| hypothetical protein SAV1850 [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|15927424|ref|NP_374957.1| hypothetical protein SA1668 [Staphylococcus aureus subsp. aureus
           N315]
 gi|21283520|ref|NP_646608.1| hypothetical protein MW1791 [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49486667|ref|YP_043888.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57650639|ref|YP_186732.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus COL]
 gi|87160591|ref|YP_494483.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus USA300_FPR3757]
 gi|88195673|ref|YP_500479.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus NCTC 8325]
 gi|148268322|ref|YP_001247265.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|150394384|ref|YP_001317059.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|151221954|ref|YP_001332776.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156980166|ref|YP_001442425.1| hypothetical protein SAHV_1835 [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|161510067|ref|YP_001575726.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253315181|ref|ZP_04838394.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus str. CF-Marseille]
 gi|253735270|ref|ZP_04869435.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|255006638|ref|ZP_05145239.2| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Mu50-omega]
 gi|257793791|ref|ZP_05642770.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|258413728|ref|ZP_05682001.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|258420765|ref|ZP_05683704.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9719]
 gi|258438426|ref|ZP_05689710.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|258443871|ref|ZP_05692210.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|258447326|ref|ZP_05695473.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|258448191|ref|ZP_05696318.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A6224]
 gi|258452660|ref|ZP_05700659.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A5948]
 gi|258453376|ref|ZP_05701359.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|262050142|ref|ZP_06022996.1| hypothetical protein SAD30_1106 [Staphylococcus aureus D30]
 gi|262052669|ref|ZP_06024861.1| hypothetical protein SA930_0805 [Staphylococcus aureus 930918-3]
 gi|269203487|ref|YP_003282756.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282895148|ref|ZP_06303367.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|282924181|ref|ZP_06331856.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282928588|ref|ZP_06336187.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|284024896|ref|ZP_06379294.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus 132]
 gi|294850278|ref|ZP_06791013.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|295406157|ref|ZP_06815965.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296276018|ref|ZP_06858525.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus MR1]
 gi|297207434|ref|ZP_06923871.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297244920|ref|ZP_06928797.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|300911518|ref|ZP_07128963.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|13701643|dbj|BAB42936.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           N315]
 gi|14247622|dbj|BAB58012.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204961|dbj|BAB95656.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49245110|emb|CAG43576.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57284825|gb|AAW36919.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus COL]
 gi|87126565|gb|ABD21079.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus USA300_FPR3757]
 gi|87203231|gb|ABD31041.1| ribosomal large subunit pseudouridine synthase, RluD subfamily,
           putative [Staphylococcus aureus subsp. aureus NCTC 8325]
 gi|147741391|gb|ABQ49689.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH9]
 gi|149946836|gb|ABR52772.1| pseudouridine synthase [Staphylococcus aureus subsp. aureus JH1]
 gi|150374754|dbj|BAF68014.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722301|dbj|BAF78718.1| conserved hypothetical protein [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368876|gb|ABX29847.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           USA300_TCH1516]
 gi|253726677|gb|EES95406.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TCH130]
 gi|257787763|gb|EEV26103.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9781]
 gi|257839515|gb|EEV63986.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9763]
 gi|257843369|gb|EEV67779.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9719]
 gi|257848470|gb|EEV72461.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9299]
 gi|257851277|gb|EEV75220.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8115]
 gi|257853913|gb|EEV76869.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A6300]
 gi|257858430|gb|EEV81306.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A6224]
 gi|257859635|gb|EEV82484.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus A5948]
 gi|257864468|gb|EEV87213.1| pseudouridine synthase [Staphylococcus aureus A5937]
 gi|259159418|gb|EEW44470.1| hypothetical protein SA930_0805 [Staphylococcus aureus 930918-3]
 gi|259161767|gb|EEW46355.1| hypothetical protein SAD30_1106 [Staphylococcus aureus D30]
 gi|262075777|gb|ACY11750.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus ED98]
 gi|282589797|gb|EFB94882.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A10102]
 gi|282592976|gb|EFB97978.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9765]
 gi|282762492|gb|EFC02633.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8117]
 gi|285817530|gb|ADC38017.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus 04-02981]
 gi|294822894|gb|EFG39328.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A9754]
 gi|294969154|gb|EFG45175.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8819]
 gi|296887897|gb|EFH26793.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297178000|gb|EFH37248.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus A8796]
 gi|300887150|gb|EFK82350.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|312830222|emb|CBX35064.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
 gi|315130506|gb|EFT86492.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS03]
 gi|315196801|gb|EFU27145.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS01]
 gi|320141300|gb|EFW33145.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320143572|gb|EFW35352.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|329727339|gb|EGG63795.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329729507|gb|EGG65909.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21189]
 gi|329732958|gb|EGG69302.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 273

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKEAVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>gi|167562573|ref|ZP_02355489.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           oklahomensis EO147]
 gi|167569756|ref|ZP_02362630.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           oklahomensis C6786]
          Length = 395

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 81/238 (34%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
             +R+ K +A+     SR  +++ I  +RV+V+G L +     V     IE+        
Sbjct: 66  AGERLDKALAQLFPEFSRSRLQQWIESERVRVDGALAK-IRQPVPLGATIELLPDLLPEQ 124

Query: 63  -----DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   L +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 125 LAFAPEPVPLSVVYEDDTLVVIDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 184

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKL 158
           V RLD  T GL+++         L     +    R Y     G           + +D  
Sbjct: 185 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWGQMPAEGTIDAPIGRDPR 244

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 245 ERTRMAVVTGAAGKPARTHFRTVDTAMWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 302


>gi|149173826|ref|ZP_01852455.1| ribosomal large subunit pseudouridine synthase [Planctomyces maris
           DSM 8797]
 gi|148847356|gb|EDL61690.1| ribosomal large subunit pseudouridine synthase [Planctomyces maris
           DSM 8797]
          Length = 342

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 54/312 (17%), Positives = 112/312 (35%), Gaps = 49/312 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           R+   + R     +R   +  I Q+ V VNG+ ++ AA  +   D + V           
Sbjct: 29  RIDHYLCRLYPNYTRVLFQTAIKQEAVLVNGLPVK-AARRMRVNDRVSVRLPELPDNRLP 87

Query: 63  -DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV-------FDNLPSIFSRVIS--V 111
            + +P+    E   + + +KP  ++      +   T+       FD L  +  +     V
Sbjct: 88  PEDIPIDIVYEDDWIAIINKPSDMIVHPGKGNYAGTLAGALQYHFDQLSDVAGQYRPGIV 147

Query: 112 GRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG--QVDQDKLNLL------ 161
            RLD NT G++++  D  +   L          + YR    G  + D D ++        
Sbjct: 148 HRLDRNTSGIMVVAKDNQVHAKLSAQFEKRDVQKEYRAIVWGRMEFDTDYIDTFMCVHPR 207

Query: 162 -KKGIVI--QGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIKKVFEFFNWKVNRLI 216
            ++ +++  +G    +     +  +      +V +  R G+  +++   +     +    
Sbjct: 208 AREKMIVCDEGGNARNAFTYYEVIERYQAFTYVRLKPRTGRTHQLRVHMQHIGHSIVA-D 266

Query: 217 RISYGPFQ------LGTLLAGSTREVSKKIL--REQLGPHLLEEAQVNLDAPIYSSETLV 268
           R+ YG  +      LG        E+   +L  R+ L  + LE        P+     L 
Sbjct: 267 RV-YGGHKSLKMKSLGIQAEADAAELESDVLIERQALHAYCLEFFHPQSGKPMKFEAPLP 325

Query: 269 RDRPNIISEVPD 280
            D  N ++ +  
Sbjct: 326 EDMQNTLAALDQ 337


>gi|145638949|ref|ZP_01794557.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittII]
 gi|145271921|gb|EDK11830.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittII]
          Length = 232

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/173 (15%), Positives = 51/173 (29%), Gaps = 29/173 (16%)

Query: 79  HKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G++   S  DP     V   L       V  + RLD  T G+LL      +A ++ 
Sbjct: 8   NKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALSSEIANLMC 67

Query: 136 L--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQVTLDT--- 181
                    + Y     G +            +L+ +      +     +     +    
Sbjct: 68  EQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAVTDYEGLKI 127

Query: 182 ----------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
                     Q    + V +    G+  ++++  +     +  L    YG   
Sbjct: 128 VEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDLH 178


>gi|258507862|ref|YP_003170613.1| pseudouridine synthase [Lactobacillus rhamnosus GG]
 gi|257147789|emb|CAR86762.1| Pseudouridine synthase [Lactobacillus rhamnosus GG]
 gi|259649190|dbj|BAI41352.1| pseudouridylate synthase [Lactobacillus rhamnosus GG]
          Length = 300

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 74/239 (30%), Gaps = 47/239 (19%)

Query: 13  PQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           P +++  + + G  SR +++++      + VN       A  + + D I V   P + A 
Sbjct: 11  PLKLAAFLKQQGF-SRAQLKKLRYQGGFIFVN-KRQRHTAYPLRNGDRILVQTAPEQAAA 68

Query: 72  RTR--------------LWLYHKPIGLVT-----THSDPDGRSTVFDNLPSIFSR--VIS 110
                              + +KP G+ +       +D          + +      V  
Sbjct: 69  SVVPYEHEFPICYEDDDYLVVNKPAGVASIPAVGRRNDSMANMVKAYLIKTHAESQAVHV 128

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVI 167
           V RLD +T GL++      LA  L           + Y            L      IV+
Sbjct: 129 VTRLDRDTSGLMVFAKH-SLAHSLLDRQLHSENFLKQYLALV----TSKSLLSAHGWIVL 183

Query: 168 Q-GICYGDMQVTLDTQKGSNAW--------------VTVGLREGKNREIKKVFEFFNWK 211
             G+  G     + ++ G  +               V V L  G+  +I+  F      
Sbjct: 184 PIGVSTGFYMRRVVSETGKPSVTEYQTLAQNSHAAAVLVTLHTGRTHQIRVHFAAIGHP 242


>gi|253999417|ref|YP_003051480.1| RluA family pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253986096|gb|ACT50953.1| pseudouridine synthase, RluA family [Methylovorus sp. SIP3-4]
          Length = 353

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/160 (21%), Positives = 59/160 (36%), Gaps = 25/160 (15%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------- 68
           + K++      SR  +++ I    V +       A   V   + ++V   P         
Sbjct: 24  LQKLLPEH---SRSRLQQWIKDGLVTLEPAQAVTAKTKVWGGERLQVQVQPSPDEHAFEA 80

Query: 69  -------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLD 115
                  + E   + + +KP GLV   +  +   T+ + L           R   V RLD
Sbjct: 81  EDIPLDVQYEDEHILVINKPAGLVVHPAAGNWSGTLLNALLHHAPVVKDLPRAGIVHRLD 140

Query: 116 INTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            +T GLL++  T     + V +L +    R YR    GQV
Sbjct: 141 KDTSGLLVVAKTLTAQTSLVRQLQARTVKREYRAIVWGQV 180


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 47/244 (19%), Positives = 79/244 (32%), Gaps = 47/244 (19%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D     V +     R+   IAR    SR     +I    V V+G    ++   V +  
Sbjct: 1   MSDVRSLPVPDGLEGDRLDSAIARMFGLSRTRAAEIIGDGGVLVDGSEAAKSD-RVSAGA 59

Query: 59  HIEVD----------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL- 101
            +EV                 G+ +   E T + +  KP+G+V   +      +V + L 
Sbjct: 60  WLEVTLPPPPTAPVPRPEAVPGMRIVH-EDTDIIVVDKPVGVVAHPTVGWTGPSVLEGLL 118

Query: 102 --------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG 151
                        R   V RLD NT GL+++        VL+    +    + Y     G
Sbjct: 119 ASGVQVATSGAAERQGIVHRLDANTTGLMVVAKSETAYSVLKRAFKERTVDKHYHTLVQG 178

Query: 152 QVD------QDKLNLLKKGIVIQGICY-----GDMQVTLDTQKGSN--AWVTVGLREGKN 198
             D         ++    G    G               DTQ+     + + + L  G+ 
Sbjct: 179 HPDPLRGTVDAPIDRHPAG---DGRWAVVAGGRPSVTHYDTQEAFRAASLLEIKLETGRT 235

Query: 199 REIK 202
            +I+
Sbjct: 236 HQIR 239


>gi|42525117|ref|NP_970497.1| pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
 gi|39577328|emb|CAE81151.1| Pseudouridylate synthase [Bdellovibrio bacteriovorus HD100]
          Length = 319

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 77/244 (31%), Gaps = 55/244 (22%)

Query: 11  FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            +  R+ K +A    I +R     ++    V +NG   + A+V +   D IE+       
Sbjct: 1   MSGLRLDKAMALIPEIGTRSRASHLLESNSVLLNGKPAK-ASVAIKENDLIEIQLPEPEP 59

Query: 63  ------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSR 107
                 D       E   L + +KP GLV   +      T+ + L              R
Sbjct: 60  TELQPFDLKLDVLFEDEDLIVINKPAGLVVHPAAGHAHDTLVNALIHHTDDLSMKFGEER 119

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-------------- 151
              V RLD  T G++++  +      L          R+Y     G              
Sbjct: 120 PGIVHRLDKETSGIIVIAKNDKAHESLTSQFKERSTHRIYYAVCLGTARTLSGSVRSFLA 179

Query: 152 --QVDQ--------DKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKN 198
              VD+        D    L           G   VT   +  +K   +++ + L  G+ 
Sbjct: 180 RHPVDRKRYASVLGDDRKPLTD--PNDDPGLGKWAVTHFEVLQRKSGMSYLKLKLETGRT 237

Query: 199 REIK 202
            +I+
Sbjct: 238 HQIR 241


>gi|153827526|ref|ZP_01980193.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
 gi|149738545|gb|EDM52900.1| pseudouridine synthase Rlu family protein [Vibrio cholerae MZO-2]
          Length = 172

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/140 (18%), Positives = 49/140 (35%), Gaps = 14/140 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+L+    
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDKHETEFVMQTLRDQIGQHVYPLHRLDRPTSGVLVFALS 66

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGICYGDMQVTLDTQK 183
             +A  +     + +  + Y     G +++  +    LK+   +  I     +   + Q 
Sbjct: 67  SQIASEVMPMFANHEMEKTYHAIVRGWIEEANVLDYPLKE--ELDKIADKFAKQDKEAQS 124

Query: 184 GSNAW-----VTVGLREGKN 198
              A+     V + +  GK 
Sbjct: 125 AVTAYRPLAKVELPISTGKF 144


>gi|313201439|ref|YP_004040097.1| RluA family pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440755|gb|ADQ84861.1| pseudouridine synthase, RluA family [Methylovorus sp. MP688]
          Length = 354

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/160 (21%), Positives = 59/160 (36%), Gaps = 25/160 (15%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR------- 68
           + K++      SR  +++ I    V +       A   V   + ++V   P         
Sbjct: 24  LQKLLPEH---SRSRLQQWIKDGLVTLEPAQAVTAKTKVWGGERLQVQVQPSPDEHAFEA 80

Query: 69  -------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLD 115
                  + E   + + +KP GLV   +  +   T+ + L           R   V RLD
Sbjct: 81  EDIPLDVQYEDEHILVINKPAGLVVHPAAGNWSGTLLNALLHHAPVVKDLPRAGIVHRLD 140

Query: 116 INTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            +T GLL++  T     + V +L +    R YR    GQV
Sbjct: 141 KDTSGLLVVAKTLTAQTSLVRQLQARTVKREYRAIVWGQV 180


>gi|227512235|ref|ZP_03942284.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227524034|ref|ZP_03954083.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
 gi|227084629|gb|EEI19941.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227088773|gb|EEI24085.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
          Length = 297

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/197 (15%), Positives = 67/197 (34%), Gaps = 29/197 (14%)

Query: 42  VNGILLERAAVNV-----MSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRS 95
           VN  L+    V V        D++    +P++   E     + +K  G+ +  +      
Sbjct: 49  VNRKLITNDVVTVVLPPEPENDNVPASDLPIQIVFEDEHFLVVNKLSGIASVPAHNRAND 108

Query: 96  TVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR 146
           ++ + +   + R       +  V RLD +T GL++         VL  +L   Q  + Y 
Sbjct: 109 SLVNRVKGYYQRNHYANQKIHIVTRLDKDTSGLVIFAKHHFAHSVLDKQLKDHQIKKTYL 168

Query: 147 VRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
               G            + +   +L+K+ +   G        T    +  +  + + +  
Sbjct: 169 AIVEGTFSTTHFEIYLPIKRADGSLVKRQVGFPGKMSITEAWTKQRLR-QHTLLKLQIHT 227

Query: 196 GKNREIK-KVFEFFNWK 211
           G+  +I+  +       
Sbjct: 228 GRTHQIRVHMT-AIGHP 243


>gi|217974069|ref|YP_002358820.1| pseudouridine synthase [Shewanella baltica OS223]
 gi|217499204|gb|ACK47397.1| pseudouridine synthase [Shewanella baltica OS223]
          Length = 287

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 52/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   L + HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 35  EDDHLVVIHKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 91

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG------------- 169
                +A  L     S    + Y     G + +  +      + +               
Sbjct: 92  AKSSEVANALCEQFASHTIEKQYLALVRGNMHESGILDYALKVELDELGDKNADPNKAAQ 151

Query: 170 ------ICYGDMQVTLDTQKGSNAW---VTVGLREGKNREIKKVFEFFNWKVN 213
                     + ++   + +   +    V +  + G+  ++++        + 
Sbjct: 152 EAVTAYEPLLNTEIPYPSGRYPTSRFALVRLSPKTGRKHQLRRHMAHLRHPIV 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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMTNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDRIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|66358534|ref|XP_626445.1| Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
           [Cryptosporidium parvum Iowa II]
 gi|46227837|gb|EAK88757.1| Yd1036cp-like RluD, S4+type 1 pseudouridine synthase
           [Cryptosporidium parvum Iowa II]
          Length = 481

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/191 (20%), Positives = 75/191 (39%), Gaps = 32/191 (16%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIE-----------VDGVPLRKAERTRLWLYHKP 81
           R+I Q+R+ VN   +      V + D I+           +D V +     T L ++ KP
Sbjct: 82  RLIDQRRLSVNDTPVNSLDYIVRNGDKIKHRSLFIELPVAIDKVKILYDSSTLLAVF-KP 140

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTNDGGLARV 133
            G+         + ++   + S +        + +  + RLD  T GL+LL+ D    + 
Sbjct: 141 CGIPCHPQGRFNKLSLTKLIQSEYLSKLNTNSTYIHPINRLDRVTSGLVLLSKDSSTTKN 200

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV---T 190
           L        + Y    +     + ++ + +   I+G+     +++LD   G  + V    
Sbjct: 201 LSSKVQFAHKYYLAMINES-TSNFISHISQ-SSIEGVSIR--ELSLDESHGITSHVIKCE 256

Query: 191 VGL-----REG 196
           +GL     REG
Sbjct: 257 IGLKTLKDREG 267


>gi|315186195|gb|EFU19957.1| pseudouridine synthase, RluA family [Spirochaeta thermophila DSM
           6578]
          Length = 319

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 81/253 (32%), Gaps = 66/253 (26%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+ + +A     +R +V++ IA   + ++G   +  +  V +   I   G  L +A    
Sbjct: 19  RLDQALAELLGITRSQVKQRIAD--LALDGRPAK-PSQRVHAGARIA--GTLLPEAPPDL 73

Query: 71  -----------ERTRLWLYHKPIGLVTTHSDPDGRSTVF----------------DNLPS 103
                      E     +  KP GLV      +   T+                 D+L  
Sbjct: 74  TPEPVPFTVLYEDPHCLVIDKPQGLVVHPGAGNPTGTLVHGLLHYSHELATRASSDDLDD 133

Query: 104 IFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNL 160
               R+  V RLD +T G+L++  D      L     +    ++Y     G         
Sbjct: 134 EERLRIGIVHRLDKDTSGVLVVAKDPATHHFLATQFKEKETKKLYLAVLKGTPPA----- 188

Query: 161 LKKGIVIQGICYGD----MQVTL----DTQKGSNAWVT----------VGL--REGKNRE 200
            ++G  I+G    D     + TL    D  K S+              V L    G+  +
Sbjct: 189 -REG-EIEGHLARDPVHRKKFTLLSRPDRGKYSHTRYRLLAAFGTHSFVALYPTTGRTHQ 246

Query: 201 IKKVFEFFNWKVN 213
           ++         + 
Sbjct: 247 LRVHTAALGCPIL 259


>gi|313619655|gb|EFR91288.1| pseudouridine synthase YjbO [Listeria innocua FSL S4-378]
          Length = 296

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 71/209 (33%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V + D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKTDDKVRLTFPTEQQNERLLAEHTDLEVVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPTGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNRYAHARLS 155

Query: 136 L--PSTQWLRVYRVRFHGQVDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                    R Y+    G ++++            ++++++ +  +G         L   
Sbjct: 156 SFLQQGLLKRRYQAFTSGTLEEEAGSIEAPIGRKDVSIMERFVTPEGKYAKTNYEVLMRY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            G +  + + L  G+  +I+  F +    
Sbjct: 216 NGFDH-LAIQLETGRTHQIRVHFSYIGHP 243


>gi|281354950|ref|ZP_06241444.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
 gi|281317830|gb|EFB01850.1| pseudouridine synthase [Victivallis vadensis ATCC BAA-548]
          Length = 321

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/140 (22%), Positives = 49/140 (35%), Gaps = 14/140 (10%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE----------RTRL 75
           R ++     IA   + +NG L       +   D IE     + + E             L
Sbjct: 39  RAIDEWRDRIAAGEIMLNGEL-SDPERRLELHDRIEYFPADIAEPEADLDYRIAYEDDAL 97

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +  KP  L    S P  + T++  L S + ++  V RLD  T GLL+   +   A  L 
Sbjct: 98  LVVDKPGNLCVHPSGPFFKHTLWHLLSSKYGKIHLVNRLDRETSGLLVAAKNPKAAAKLG 157

Query: 136 LPSTQWLRVYRVRFHGQVDQ 155
            P     + Y     G    
Sbjct: 158 KPGWPMRKEYLALVFGNFAD 177


>gi|253577780|ref|ZP_04855052.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850098|gb|EES78056.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 341

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/262 (17%), Positives = 88/262 (33%), Gaps = 76/262 (29%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           MK+  I++EN   QR  K +A+      RE       +M+ ++ + +NG         ++
Sbjct: 1   MKEF-IIEENEAGQRFDKYLAKLL----REAPKSFFYKMLRKKNITLNGKKAT-GNEKLL 54

Query: 56  STDHIE--VDGVPLRK-----------------AERTRLWLYHKPIGLVTTHSDPDGRST 96
             D I+  +      K                  E   + + +KP G+++  +  DG  +
Sbjct: 55  KGDTIKLFLSDETFDKFAGSSQAARAYCELDIVYEDPDIIIINKPAGMLSQPA-YDGEPS 113

Query: 97  VFDNLPSIF-------------SRVISVGRLDINTEGLLLL--TNDG-GLARVLELPSTQ 140
           + + L                  R     RLD NT G++    +  G      +    T 
Sbjct: 114 LVEYLTGYLLKKGDLTEEQLKTFRPSVCNRLDRNTSGMVCAGKSLAGLQFLSRIFHDRTL 173

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQK-------------- 183
             + Y     G++++           I+G  + D    +V +  Q+              
Sbjct: 174 H-KYYICLTKGKIEKPD--------HIRGYLHKDKKTNKVIVSRQEFKDSLPIETKYCPL 224

Query: 184 ---GSNAWVTVGLREGKNREIK 202
              G    + V L  G+  +I+
Sbjct: 225 GSNGKITLLEVELITGRTHQIR 246


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 1/52 (1%)

Query: 11 FTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              R+ K +    I+SR + + MI + ++ VNG ++ +A+  V   D I V
Sbjct: 1  MDKIRLDKAL-LKTISSRAKAQDMIKEGKISVNGKVITKASYLVSDEDDIVV 51


>gi|253687331|ref|YP_003016521.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
 gi|251753909|gb|ACT11985.1| pseudouridine synthase [Pectobacterium carotovorum subsp.
           carotovorum PC1]
          Length = 266

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LLL   
Sbjct: 12  QDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLLALS 71

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQV-DQDKLN-LLKKGI-VIQGICYGDMQVTLDTQ 182
             +AR L     S Q  ++Y     G V D   ++  L + +  I        +      
Sbjct: 72  SEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFTNPDKAPQPAV 131

Query: 183 KGSNAWVTVG--------------LRE-----GKNREIKKVFEFFNWKVN 213
               +   V               L E     G+  ++++        + 
Sbjct: 132 THYRSLAQVEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHLRHPII 181


>gi|149190306|ref|ZP_01868580.1| ribosomal large subunit pseudouridine synthase A [Vibrio shilonii
           AK1]
 gi|148835913|gb|EDL52876.1| ribosomal large subunit pseudouridine synthase A [Vibrio shilonii
           AK1]
          Length = 245

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/158 (18%), Positives = 58/158 (36%), Gaps = 38/158 (24%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++      +   +++  L  ++  +  V RLD++T GL+LL  +  
Sbjct: 19  EDEHILAVNKPSGLLSVPGKALEHYDSMWSRLVEVYPEIQVVHRLDMSTSGLMLLAKNKE 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-Q 176
                       L        +VY  R  G  D+       +G++    I         +
Sbjct: 79  AERSLKKQFQYRLTH------KVYYARVWGTPDE------SEGLIDLPLICDWPNRPRQK 126

Query: 177 VTLDTQKGSNAWVTVGLRE------------GKNREIK 202
           V  +  K S  +  V  +E            G++ +++
Sbjct: 127 VCYEHGKPSQTYYQVVKQEQQTSIVRLFPITGRSHQLR 164


>gi|312130287|ref|YP_003997627.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311906833|gb|ADQ17274.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 206

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/158 (19%), Positives = 57/158 (36%), Gaps = 19/158 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E     +  KP G+ +   D  G++   D++ S F     + RLD    GL++L     +
Sbjct: 5   ENDNYIILDKPSGIASQ--DEPGKN---DSILSAFPGCHVLTRLDKRVSGLMVLAKSAEV 59

Query: 131 ARVLELPSTQWLRVYR--VRFHGQVDQDKLNLL--KKGIV-------IQGICYGDMQVTL 179
           A        ++ + Y   V   G   +  L     K+G+        ++G     ++  L
Sbjct: 60  AARWS--PEKYSKTYHCIVNLPGPGKEGVLKHWIKKQGLKAKVFDHAVEGAKQAILRYQL 117

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK-VNRLI 216
                  A   V +  G+  +I+  F    +  V  L 
Sbjct: 118 RGNSQRYALYAVKIETGRFHQIRAQFSKVGFPLVGDLK 155


>gi|161506492|ref|YP_001573604.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867839|gb|ABX24462.1| hypothetical protein SARI_04699 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 260

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/166 (16%), Positives = 50/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKL---NLLKKGIVIQGICYGDMQVT-------- 178
           R L          + Y     G +  D L    LL++   I      + +          
Sbjct: 71  RRLAQQFEQHHIRKRYHAIVRGWLMDDALLDYPLLEERDKIADKFAREDKAPQPAVTQYR 130

Query: 179 --------LDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                   + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|19113793|ref|NP_592881.1| tRNA pseudouridylate synthase (predicted) [Schizosaccharomyces
           pombe 972h-]
 gi|1175381|sp|Q09709|YA32_SCHPO RecName: Full=Uncharacterized protein C18B11.02c
 gi|929888|emb|CAA90587.1| tRNA pseudouridylate synthase (predicted) [Schizosaccharomyces
           pombe]
          Length = 394

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/136 (21%), Positives = 47/136 (34%), Gaps = 13/136 (9%)

Query: 32  ERMIAQQRVKVNGIL--LERA---AVNVMSTDHIE---VDGVPL-RKAERTRLWLYHKPI 82
           E+ I   +VKVN  +  ++        V    H     V   P+    E     +  KP 
Sbjct: 62  EKAIRNGQVKVNNQIGNVDTLIENGYIVSHHAHRHEPPVSDQPVGIVHEDESYVVIDKPA 121

Query: 83  GLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLA--RVLELPS 138
           G+    +     +TV   L   +  S +    RLD  T GL+  +     A    + + S
Sbjct: 122 GVPVHPTGRYNHNTVLHILMKENKCSLLYPCNRLDRLTSGLMFFSKSPKAAEEMRVHMIS 181

Query: 139 TQWLRVYRVRFHGQVD 154
               + Y  R  G+  
Sbjct: 182 KSLKKEYVARVIGEFP 197


>gi|239994623|ref|ZP_04715147.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           ATCC 27126]
          Length = 279

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/122 (22%), Positives = 47/122 (38%), Gaps = 6/122 (4%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           + ++ V+        V+V   D +    +P+   +   +    KP GL+   S  D   T
Sbjct: 14  KGQLTVHSDEQTIGKVDVGEEDSVNALHLPVLYQDEH-IIAIEKPPGLLVHRSPIDRHET 72

Query: 97  VFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG 151
           VF        I   V    RLD  T G+L+ +    +A  L  ++   Q ++ Y     G
Sbjct: 73  VFAVQTLRDQIGQHVYPAHRLDRPTSGVLVFSFSSEIAAKLGQQMMDKQVVKTYHAIVRG 132

Query: 152 QV 153
            V
Sbjct: 133 FV 134


>gi|224543721|ref|ZP_03684260.1| hypothetical protein CATMIT_02934 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523374|gb|EEF92479.1| hypothetical protein CATMIT_02934 [Catenibacterium mitsuokai DSM
           15897]
          Length = 289

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 57/162 (35%), Gaps = 19/162 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLL 124
           E   + + +KPIG+     DP    ++ + + + +        V  + RLD +T GL++ 
Sbjct: 88  EDDLILVVNKPIGIAVYPDDPHKTDSLSNRVSAYYMTQGYDIPVRYIHRLDNDTSGLVVF 147

Query: 125 TNDGGLARVLELPST--QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV----- 177
                +   L+   +  +  R Y     G + + K   +++ +         M+V     
Sbjct: 148 CKCHLIQAYLDHALSIKEIQREYLAYVEGHIKEGKEYKIEQNLGKDRHSPSKMRVHSKGI 207

Query: 178 ------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                      K  +A V   L  G+  +I+         + 
Sbjct: 208 SAVTYYQCLENKEDHALVRCRLETGRKHQIRVHMASIGHPIL 249


>gi|332828687|gb|EGK01379.1| hypothetical protein HMPREF9455_02212 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 242

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 63/171 (36%), Gaps = 28/171 (16%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ K +A   +  SR  +++      + VN   ++     +   D I V          
Sbjct: 41  IRIDKYLAMHIVGVSRNRIQQAAEANCILVNDNPVKS-NYKIKPLDVISVVMNRPPRELE 99

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFSRV 108
              + +PL    E   L + +KP GLV      + + T+ +             +   R+
Sbjct: 100 IIPEDIPLDVVYEDDDLMVINKPPGLVVHPGFGNYQGTLVNAVAYLLKDTPEYDAKDPRL 159

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
             V R+D +T GL+++  +      L     +    R Y     G +++D+
Sbjct: 160 GIVHRIDKDTSGLIVVAKNAYAKAHLSAQFFNKTTKRQYVALVWGAIEEDE 210


>gi|325578324|ref|ZP_08148459.1| tRNA pseudouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
 gi|325160060|gb|EGC72189.1| tRNA pseudouridine synthase C [Haemophilus parainfluenzae ATCC
           33392]
          Length = 238

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/196 (15%), Positives = 61/196 (31%), Gaps = 38/196 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D      V   L       V  + RLD  T G+LL   +
Sbjct: 7   QDEYLVAVNKPAGMLVHRSWLDTHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALN 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A ++          + Y     G +  + +++   K I +  I     Q     Q+ 
Sbjct: 67  SEIANLMCQQFEQKTVQKSYLAIVRGYLQGKGQIDYPLK-IQLDKIADKFAQEDKAPQEA 125

Query: 185 SNAWVTVGLRE----------------------GKNREIKKVFEFFNWKVNRLIRISYGP 222
              +  + + E                      G+  ++++  +     +  L    YG 
Sbjct: 126 VTDYEGLNIVEMPYAVGRYQTTRYSLVKLIPQTGRKHQLRRHMKHIFHPI--LGDTQYGD 183

Query: 223 FQLGTLLAGSTREVSK 238
                      R +++
Sbjct: 184 LH-------QNRALTE 192


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 62/195 (31%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +  +    + +  ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKGNLK--KIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|258423127|ref|ZP_05686021.1| pseudouridine synthase [Staphylococcus aureus A9635]
 gi|257846691|gb|EEV70711.1| pseudouridine synthase [Staphylococcus aureus A9635]
 gi|323438855|gb|EGA96592.1| RNA pseudouridylate synthase [Staphylococcus aureus O11]
 gi|323441699|gb|EGA99344.1| RNA pseudouridylate synthase [Staphylococcus aureus O46]
          Length = 273

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKETVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>gi|51246582|ref|YP_066466.1| ribosomal large subunit pseudouridine synthase D [Desulfotalea
           psychrophila LSv54]
 gi|50877619|emb|CAG37459.1| related to ribosomal large subunit pseudouridine synthase D
           [Desulfotalea psychrophila LSv54]
          Length = 327

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 79/234 (33%), Gaps = 53/234 (22%)

Query: 15  RVSKVIA-RAGIASRREVERMI----AQQRVKVNGILLERAAVNVMSTDHIE-------- 61
           R+ + +A      SR     +I     ++ V V+   +++++  +   + +         
Sbjct: 31  RLDQFLAFSLPDVSR----ALITLSNKKELVLVDDE-VKKSSYRLKEGETVTCALWQAPP 85

Query: 62  -------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-- 112
                  VD   +   E   L +  KP G+V    + +   T+   L      +  VG  
Sbjct: 86  LSLEPQQVDFESI--YEDDSLLVLSKPPGIVVHPGNGNTEGTLVHGLLYHCREIGGVGDA 143

Query: 113 -------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL-- 161
                  RLD +T G +++  D    R L       Q  +VY     G   + +  ++  
Sbjct: 144 IRPGIVHRLDKDTSGAMVVAKDERSLRTLVDSFKERQVYKVYHALVCGIPKKYEGRIVAP 203

Query: 162 -------KKGIVIQGICYGDM------QVTLDTQKGSNAWVTVGLREGKNREIK 202
                  ++ + I                  +T+ G  + + V +  G+  +I+
Sbjct: 204 IGRHSVHRQKMAISERTGKFAATNWQVVEVFETKDGPYSLLRVHIETGRTHQIR 257


>gi|315638653|ref|ZP_07893827.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
 gi|315481277|gb|EFU71907.1| RNA pseudouridine synthase [Campylobacter upsaliensis JV21]
          Length = 250

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/202 (14%), Positives = 75/202 (37%), Gaps = 33/202 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   +L RA +   +  ++     P    E  ++
Sbjct: 7   KLLALQENISNREAKDLIDRGLVFSHGKKIVLARALMKEGTKFNLLKMKKPQILFEDEKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   ++   + + ++ +               RLD  T GL+LL  +    ++  
Sbjct: 67  LAINKPYSYISEGLESEFKAKLL-------------NRLDKETSGLILLCKNEDFKKLCI 113

Query: 136 LP--STQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQ--------- 182
                 +  + Y     G + ++ +    ++    ++G      ++  + Q         
Sbjct: 114 EEFRKQRVYKSYIAVLDGVLAEELVVDEPIR---TLKGKNGAFSKIAKEGQSALSIINPL 170

Query: 183 --KGSNAWVTVGLREGKNREIK 202
             +G      + ++ G+  +I+
Sbjct: 171 MIQGKKTLAKICIQTGRTHQIR 192


>gi|328946274|gb|EGG40418.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1087]
          Length = 297

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 60/172 (34%), Gaps = 23/172 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKGLSVIYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRQGYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGSGLLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +   G   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVTEDGDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 242


>gi|325283148|ref|YP_004255689.1| pseudouridine synthase [Deinococcus proteolyticus MRP]
 gi|324314957|gb|ADY26072.1| pseudouridine synthase [Deinococcus proteolyticus MRP]
          Length = 253

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/167 (22%), Positives = 55/167 (32%), Gaps = 34/167 (20%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINT 118
           G P    E    +  HKP   +T      G S V D +    S      +    RLD  T
Sbjct: 11  GRPRLLLEHPDFYALHKPALWLTHPVRSHGSSRVPDVVSFWQSETGESSLGPPHRLDRET 70

Query: 119 EGLLLLTNDGGLARV--LELPSTQWLRVYRVRFHGQV--DQDKLNL-------------- 160
            GLLLL+ D   AR   +        + YR    G       +L+               
Sbjct: 71  SGLLLLSRDSESARRFFVLFGQRLVAKTYRAIVRGVPAWTDYELDAPLGELGLGGGNRVI 130

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
           +++G+V  G         L+ + G        L E     G+  +I+
Sbjct: 131 MRQGVVPDGRPAVTAFRVLERRAGH------TLIEARPRTGRLHQIR 171


>gi|256823775|ref|YP_003147738.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
 gi|256797314|gb|ACV27970.1| pseudouridine synthase [Kangiella koreensis DSM 16069]
          Length = 282

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/147 (17%), Positives = 55/147 (37%), Gaps = 15/147 (10%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGL 121
            P   A+     +++KP G+ +  S      ++   +   F    +   V RLD    GL
Sbjct: 91  KPELIADEGDYSVWNKPNGVWSQGSKWGDHCSISRLVEEHFDYNRQTYVVHRLDKAARGL 150

Query: 122 LLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L+L ++   A  L     +    + Y    +GQ   D +       + + I     +  +
Sbjct: 151 LILAHNKEAAAALSAMFAKRTVEKHYLAWVNGQFPHDSIT------IDKPIDNKPAKSIV 204

Query: 180 DTQK----GSNAWVTVGLREGKNREIK 202
             ++       + ++V +  G+  +I+
Sbjct: 205 TLKEYDADKDRSLLSVQILTGRKHQIR 231


>gi|160933803|ref|ZP_02081191.1| hypothetical protein CLOLEP_02664 [Clostridium leptum DSM 753]
 gi|156867680|gb|EDO61052.1| hypothetical protein CLOLEP_02664 [Clostridium leptum DSM 753]
          Length = 298

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/214 (19%), Positives = 66/214 (30%), Gaps = 40/214 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLL 124
           E   L + +KP  +         R TV + +           R   + RLD +T GL++ 
Sbjct: 84  EDDALLILNKPPLMPVHPCPGHDRGTVCNFVSYYQKRKGEDWRFRPLNRLDKDTSGLVIG 143

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQ---GICYGDMQV 177
             D   A  L        + Y     G +  + +      LK+G  IQ   G        
Sbjct: 144 AKDSYTASAL----NDVGKTYFAVCQGSLPGEGVIDTPIRLKEGHSIQREAGEGGKPAVT 199

Query: 178 TLD------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                        S   + + L  G+  +I+            +   S G    G    G
Sbjct: 200 HWKSLAQGAAAGKSYTLLALTLETGRTHQIR------------VHLSSIGHPLAGDDFYG 247

Query: 232 STREV-SKKILR----EQLGPHLLEEAQVNLDAP 260
            +RE+ S++ L     E   P  L    V    P
Sbjct: 248 GSRELISRQALHCGLVELTHPFFLSRICVKAPFP 281


>gi|330469278|ref|YP_004407021.1| RluA family pseudouridine synthase [Verrucosispora maris AB-18-032]
 gi|328812249|gb|AEB46421.1| RluA family pseudouridine synthase [Verrucosispora maris AB-18-032]
          Length = 314

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/176 (18%), Positives = 60/176 (34%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +     R+ + +AR    SR     ++      V+G  +   +  V +   +EV    
Sbjct: 16  VPDGLDGMRLDQAVARLFGLSRTAAAALVDAGEALVDGA-VRPNSHKVRAGAWLEVTLPA 74

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------ 104
                        G+ +  A+   + +  KP+G+    S      TV   L +I      
Sbjct: 75  PAAAPVVVPQAVPGLRVVYADDDIVVV-DKPVGVAAHPSPGWTGPTVIGGLAAIGHTIAT 133

Query: 105 ---FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                R   V RLD+ T G++++         L+      +  + Y     G +D 
Sbjct: 134 SGAAERQGVVHRLDVGTTGVMVVAKSEQAYSALKRAFKYREVEKRYHAVVQGHLDP 189


>gi|324994489|gb|EGC26402.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK678]
          Length = 295

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 60/171 (35%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDKHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   +      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-KDGKHAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>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 = 58.3 bits (140), Expect = 2e-06,   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|110004533|emb|CAK98870.1| hypothetical rna pseudouridylate synthase c protein [Spiroplasma
           citri]
          Length = 312

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 65/218 (29%), Gaps = 50/218 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH------------- 79
           ++   +++KVN  +++     +   D I +    L   ER +   Y+             
Sbjct: 38  KLFRNKKIKVNNKVMKERNYKLQLGDQIIIFDKNLVVTERNQAVTYNNVETLPLQVVYED 97

Query: 80  -------KPIGLVT-----THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
                  KP G+       T  D   +  +               +  V RLD  T GL+
Sbjct: 98  DNILVVDKPHGVEMYSKFHTSLDAMVQHYLIQKHEYHPEDEQSFVISHVHRLDKLTRGLV 157

Query: 123 LLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           L   +     +L           + Y  +  G + +    L   G + +      M  T 
Sbjct: 158 LYAKNKITLDLLLAKINQKESIEKKYLAKCEGIIKETDFTL--TGYLYKNEDKQKMVFTK 215

Query: 180 DTQKGSN---------------AWVTVGLREGKNREIK 202
             Q  +                 W+ V L  G+  +I+
Sbjct: 216 TVQPHAKVVKTHFRVQHQLTNATWLEVTLITGRKHQIR 253


>gi|221194862|ref|ZP_03567919.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
 gi|221185766|gb|EEE18156.1| ribosomal large subunit pseudouridine synthase D [Atopobium rimae
           ATCC 49626]
          Length = 248

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 55/178 (30%), Gaps = 36/178 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS---------DPDGRSTVFDN---------LPSIFSRVISVG 112
           + + +   +KP G++             D     T+ D                 V ++ 
Sbjct: 6   QDSYILAVNKPAGIIIHSDGTSHAGERADMCAAETLTDLARVYLENNGCVQQAQDVQALH 65

Query: 113 RLDINTEGLLLLTNDGGLA---RVLELPSTQWLRVYRVRFHGQVDQDKL----------- 158
           RLD +T G++L + D         L        + Y     G+  + +            
Sbjct: 66  RLDKDTTGIVLFSLDKETQPLFDELIRSRNVH-KTYLAVVKGEFPEGEQDITLPIGRDRH 124

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
           +  +  +   G         L+ Q+   +  ++ L E   G+  +I+  F    + + 
Sbjct: 125 DARRMHVSKTGKAALTHVRRLEVQRRGQSTRSLMLAELGTGRKHQIRVHFSALGFPIV 182


>gi|291518249|emb|CBK73470.1| pseudouridine synthase, RluA family [Butyrivibrio fibrisolvens
           16/4]
          Length = 295

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 84/243 (34%), Gaps = 42/243 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE-RMIAQ--QRVKVNGILL---------ERAAVN 53
           I+   +   ++ K +   G +S        I +    V ++G  +         E   VN
Sbjct: 8   IISTEYDGFQIDKFLKTQGYSS---ANITAIKKMPNNVVIDGEWVHMNRKLSAGELLTVN 64

Query: 54  VMSTDH------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
           +   D       +++D   + + E   + + +KP GL    S      ++ + L   + +
Sbjct: 65  ISEEDSSEKIPAVKMDLDIVYEDED--IIVINKPAGLPIHPSLNHYEDSLANGLAYYYEQ 122

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQV--DQDK 157
                      RLD NT GL +++     A +L          R Y     G +   +  
Sbjct: 123 QGKPFIFRCANRLDKNTSGLTVISKHLVSANILSTMVKNREFHREYYAIVRGTLEQPEGT 182

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           ++          + + +  +          +  +K  ++ V++ L  G+  +I+  F++ 
Sbjct: 183 IDAPIGRVDDSIITRQVDFENGERAVTHYKVMDEKNGHSLVSIHLETGRTHQIRVHFKYI 242

Query: 209 NWK 211
              
Sbjct: 243 GHP 245


>gi|258646966|ref|ZP_05734435.1| ribosomal large subunit pseudouridine synthase C [Dialister invisus
           DSM 15470]
 gi|260404405|gb|EEW97952.1| ribosomal large subunit pseudouridine synthase C [Dialister invisus
           DSM 15470]
          Length = 305

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 85/246 (34%), Gaps = 45/246 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAV 52
           MK+  I +     +R+ + +         E+E          +  +++KVNG   E    
Sbjct: 1   MKEFRI-EGRHAGKRLDRFME--------EIEHWPHGMVVKAVRTKKLKVNGKK-EDGTY 50

Query: 53  NVMSTDHIEVDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            +   D +    +P  K        E   + +  K  GL+   S      T+   +    
Sbjct: 51  RLCEGDRVVSYVLPKEKRRDFTIVYEDEHILIADKKAGLLCMDSTGKTTRTLIGEVNEYL 110

Query: 106 SRV-----ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL 158
           +         V R+D NT GL+++  D     +L   +   +  +VY     G   + + 
Sbjct: 111 ADKGEPSAYMVHRIDFNTSGLMVIAKDEESKGILDRMIKERELEKVYLCIVSGVPKKKEG 170

Query: 159 NLL-------KKG-IVIQGICYGDMQVTL----DTQKGSN-AWVTVGLREGKNREIKKVF 205
           +L+       K+G + +  +     +  +      + G N + +   L  G+  +I+   
Sbjct: 171 HLIHYLFKDSKQGKVFLSDVPQKGAKSAVTDYHIVKTGQNLSLLECTLLTGRTHQIRSQM 230

Query: 206 EFFNWK 211
            +    
Sbjct: 231 AYIGHP 236


>gi|156932726|ref|YP_001436642.1| tRNA pseudouridine synthase C [Cronobacter sakazakii ATCC BAA-894]
 gi|156530980|gb|ABU75806.1| hypothetical protein ESA_00515 [Cronobacter sakazakii ATCC BAA-894]
          Length = 265

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 50/167 (29%), Gaps = 29/167 (17%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 12  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDMQVTLD 180
           R L       Q  + Y     G +           ++L+ +      Q        VT  
Sbjct: 72  RRLAQQFEQHQIQKRYHAIVRGWLTDSAVLDYPLVEELDKIADKFSRQDKEPQPA-VTHY 130

Query: 181 TQKGSNAW---------VTVGLRE-----GKNREIKKVFEFFNWKVN 213
               + +          V   L E     G+  ++++        + 
Sbjct: 131 RGLATTSQPVAVGRYDSVRYSLVEMLPQTGRKHQLRRHMAHLRHPII 177


>gi|114563871|ref|YP_751385.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114335164|gb|ABI72546.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 217

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/164 (18%), Positives = 61/164 (37%), Gaps = 22/164 (13%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL- 124
           +R  +R  + + +KP GL++     PD   T    L   +   I + RLD +T G+++  
Sbjct: 16  IRYKDRD-IIVINKPSGLLSNPGRSPDTHDTAITRLQRCYPEAILIHRLDCDTSGIMIFA 74

Query: 125 -TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDMQVTLDTQ 182
            T        ++  + Q  +VY     G VD+ +       G           Q+  D+ 
Sbjct: 75  RTKKAESHLKIQFQNRQAKKVYIAEVIGHVDEQQGKVNFALG---ANPDSPPFQMLTDSG 131

Query: 183 KGSNAWVTV-------GLRE-----GKNREIK-KVFEFFNWKVN 213
           K +  + +V        L E     G+  +++  +       + 
Sbjct: 132 KAALTYFSVLEHRAYSTLMELKPHTGRTHQLRVHML-ALGHTIL 174


>gi|317014367|gb|ADU81803.1| hypothetical protein HPGAM_04945 [Helicobacter pylori Gambia94/24]
          Length = 242

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 65/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLSIARKELPQNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F     + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKDWALLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G V+++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVRKEYLALVQGIVEEE--REINAPILTIKTTKAFSKISKKGQEAITIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 52/170 (30%), Gaps = 30/170 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------D 63
           R+  V+A +    SR  ++ +I    V V+G  +      V     + +           
Sbjct: 28  RLDAVLAGQIASLSRNRIQTLIKGGEVTVDGRKIVEPKHRVNEGQTLTLTLPEPEDPDPK 87

Query: 64  GVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
           G  +      E   L +  KP GLV      +   T+ + L               R   
Sbjct: 88  GENIPLSIIYEDDHLIVVDKPAGLVVHPGAGNLTGTLVNALIHHCGDSLSGIGSVKRPGI 147

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV------YRVRFHGQVD 154
           V R+D +T GLL++       + L        +       Y     G   
Sbjct: 148 VHRIDKDTSGLLVVAKTDQAHQGLSEQFADHGKTGPLERAYSALVWGAPS 197


>gi|283770934|ref|ZP_06343826.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
 gi|283461081|gb|EFC08171.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus H19]
          Length = 273

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTVDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVNALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKETVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 66/226 (29%), Gaps = 55/226 (24%)

Query: 34  MIAQQRVKV--NGILLERA-AVNVMSTDHI----------------EVDGVPLRKAERTR 74
            I    V V  NG  ++   +  + + D +                +VDG  +   +   
Sbjct: 47  WILDGHVTVTNNGKAVKIGKSYKLSAGDEVVVDASAPRDLADIRPEKVDGFRIVHLDEDI 106

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI---------FSRVISVGRLDINTEGLLLLT 125
           + +  KP G+    S      TV   L              R   V RLD+ T GL+++ 
Sbjct: 107 VVV-DKPAGVAAHPSPGWHGPTVISALMGEGISVATSGAAERQGIVHRLDVGTSGLMVVA 165

Query: 126 NDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQ-------GICYGDMQ 176
                   L+    +    +VY     G  D        +G  I        G  +    
Sbjct: 166 RSERAYTELKRAFKERTVDKVYHTLVQGLPDP------LRG-TIDAPIGRHPGNEWKFAV 218

Query: 177 VT----------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           V           +    G  + V V L  G+  +I+  F       
Sbjct: 219 VEDGRNSITHYDVLEAFGPASLVEVHLETGRTHQIRVHFSALRHPC 264


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFVIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTFGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|68250034|ref|YP_249146.1| tRNA pseudouridine synthase C [Haemophilus influenzae 86-028NP]
 gi|145632796|ref|ZP_01788529.1| tRNA pseudouridine synthase C [Haemophilus influenzae 3655]
 gi|229846708|ref|ZP_04466815.1| tRNA pseudouridine synthase C [Haemophilus influenzae 7P49H1]
 gi|68058233|gb|AAX88486.1| tRNA pseudouridine synthase C [Haemophilus influenzae 86-028NP]
 gi|144986452|gb|EDJ93018.1| tRNA pseudouridine synthase C [Haemophilus influenzae 3655]
 gi|229810197|gb|EEP45916.1| tRNA pseudouridine synthase C [Haemophilus influenzae 7P49H1]
          Length = 239

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPDGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|77462289|ref|YP_351793.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides 2.4.1]
 gi|332560170|ref|ZP_08414492.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides WS8N]
 gi|77386707|gb|ABA77892.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides 2.4.1]
 gi|332277882|gb|EGJ23197.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides WS8N]
          Length = 346

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/157 (21%), Positives = 51/157 (32%), Gaps = 33/157 (21%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------- 74
           VE+M    +V+V+G   + A+  V     I V   PL   +  R                
Sbjct: 34  VEKMCRTGQVRVDGARAK-ASDRVAEGMEIRV--PPLPDPDAPRPQASRVTKSDEQMIQD 90

Query: 75  --------LWLYHKPIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLL 122
                   + + +KP GL +      G   V             R   V RLD +T G+L
Sbjct: 91  CVIYRDNDIIVLNKPAGLPSQGGSGQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVL 150

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
           +L     +AR L          ++Y     G     +
Sbjct: 151 VLARTDRVARALSESFRHRNTRKIYWALVAGVPSPKQ 187


>gi|325689674|gb|EGD31678.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK115]
          Length = 295

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/162 (17%), Positives = 58/162 (35%), Gaps = 23/162 (14%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVIYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIGQGYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L    G     L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHGYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + + +  +   Y      +  + G    V + L  G+  +I+
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIR 231


>gi|295839444|ref|ZP_06826377.1| RluA family RNA pseudouridine synthase [Streptomyces sp. SPB74]
 gi|197698743|gb|EDY45676.1| RluA family RNA pseudouridine synthase [Streptomyces sp. SPB74]
          Length = 313

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 63/176 (35%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIE--- 61
           V +    +RV   ++R    SR +   + A  +V+V+G ++ + +  V       +E   
Sbjct: 12  VPDGLEGERVDAALSRMFGFSRTKAAELAAGGKVQVDGSVVGK-SERVRGGAWLEVEMPA 70

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                      V+G+ +   +   + +  KP+G+    S      TV   L +   R+  
Sbjct: 71  AAAPVRIVAEPVEGMEIVHDDEDVVVIM-KPVGVAAHPSPGWTGPTVIGGLAAAGYRIST 129

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                    V RLD+ T GL+++         L+         + Y     G  D 
Sbjct: 130 SGAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQFRVRTVDKRYHTLVQGHPDP 185


>gi|115372593|ref|ZP_01459900.1| ribosomal large subunit pseudouridine synthase C [Stigmatella
           aurantiaca DW4/3-1]
 gi|115370314|gb|EAU69242.1| ribosomal large subunit pseudouridine synthase C [Stigmatella
           aurantiaca DW4/3-1]
          Length = 330

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/263 (13%), Positives = 78/263 (29%), Gaps = 68/263 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           ++E+    R+ K +       R+ +         +MI  ++V+VNG   +     + + D
Sbjct: 15  IEEDSVGMRLDKYL-------RKRLANMPTSHLFKMIRVKKVRVNGKRAQ-PEQLLAAGD 66

Query: 59  HIEVDG-------------------------VPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            I + G                           +   E   +    KP G+         
Sbjct: 67  VIAIRGDEQQLLGPAPGGERLPPPPPPVDPSELVILLEDDWMMAVDKPSGMAVHTGSGIT 126

Query: 94  RSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143
             T+ D + +                 RLD  T G++L+                ++  +
Sbjct: 127 GGTLVDYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRARK 186

Query: 144 VYRVRFHGQVDQD--------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            Y     G++ QD                +  ++G+ +Q          +  Q    A +
Sbjct: 187 RYVTLVKGKMPQDSGVIDLPLSEHQQTAESKARRGVNMQEALTR---WKVIRQSSEAALL 243

Query: 190 TVGLREGKNREIKKVFEFFNWKV 212
           +  +  G+  +I++        V
Sbjct: 244 SCAIETGRTHQIRRHLAAVGHPV 266


>gi|291520763|emb|CBK79056.1| pseudouridine synthase, RluA family [Coprococcus catus GD/7]
          Length = 310

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 67/204 (32%), Gaps = 46/204 (22%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDG-----VPLRKAERTR--------LWLYHKPIGLVT 86
           + +NG  +    V + + D +  +        +  AE           + L +KP  LV 
Sbjct: 42  ILINGQRVTTRGV-LHAGDSLVFNMPNDRTQKVVPAEGPVSIVFENEDIVLVNKPARLVI 100

Query: 87  THSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
                    T+   L   +        +  +GRLD +T GL+L+  +   A+ LE     
Sbjct: 101 HPCHGHYSDTLLSYLAWYYRLLPEQPLLCPIGRLDKDTSGLILIAKNKYAAQQLERQRAN 160

Query: 141 W--LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSN------- 186
               RVY     G       N  K G++ + I          QV    +           
Sbjct: 161 HTLSRVYLALAEGHWT----NQSKSGLIDRPIEKVPECFNRYQVADTGRPSRTEYEVLSE 216

Query: 187 --------AWVTVGLREGKNREIK 202
                   + V + L+ G+  +I+
Sbjct: 217 FTYEETPFSLVRLKLQTGRTHQIR 240


>gi|255527608|ref|ZP_05394471.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
 gi|255508709|gb|EET85086.1| pseudouridine synthase, RluA family [Clostridium carboxidivorans
           P7]
          Length = 319

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/260 (13%), Positives = 82/260 (31%), Gaps = 58/260 (22%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++ M        I +  VKVNG   +     +M
Sbjct: 2   KIEIGPNEAGQRLDKFL-------RKWLKDMPLSAIYKSIRKGDVKVNGKKAKE-KYALM 53

Query: 56  STDHIEVDGVPLRKAERTRLWLYH----------------KPIGLVTTHSDPDGRSTVFD 99
             D IE   +   + ++    + +                K  G++          T+ D
Sbjct: 54  EGDLIETRDITSNQTKKKFNRIENSFLKIAYEDENMVVIEKWPGVLVHSDGKKKEHTLTD 113

Query: 100 NL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRV 144
            +           P            RLD NT G+++   +    ++L   +   +  + 
Sbjct: 114 YVLSYLYDKGDYTPENEVTFTPASCNRLDRNTSGIVIFGKNYEALKLLNEMIREKKIHKY 173

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGI-------CYGDMQVTLDTQKGSN----AWVTVGL 193
           Y+    G++              + I            +++++ +   +    + V + L
Sbjct: 174 YQALIKGRIKDGLYKAYIHKNESENISQVYDEPRKDTKEISMNVKNIQSCGTFSLVELEL 233

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G++ +++         + 
Sbjct: 234 LTGRSHQLRAHLNHLGNPIL 253


>gi|291524781|emb|CBK90368.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           DSM 17629]
          Length = 324

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 50/313 (15%), Positives = 93/313 (29%), Gaps = 110/313 (35%)

Query: 1   MKDKNIVQENFTPQRVSKVI------ARAGIASRREVERMIAQQRVKVNGILLERAAVNV 54
           MK+    + N   QR+ K +      A  G      + +M+ ++ +K+N          V
Sbjct: 1   MKEFKAGK-NEAGQRLDKYLKKILPNASMGF-----IYKMLRKKNIKLNDKKA-SGTEIV 53

Query: 55  MSTDHIEV-----------------------------DGVPLRKAERTRLWLYHKPIGLV 85
              D I++                             DG+ +   +   +   +KP+ ++
Sbjct: 54  SVDDKIKIFLSDDTFAKFSVNEDSLMKDFKALGALKPDGLGVVYEDDD-ILAANKPVNML 112

Query: 86  TTHS---DPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARV 133
           +  S   D      +   L              +     RLD NT GL+L+   G     
Sbjct: 113 SQKSKETDISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILM---GKSLHG 169

Query: 134 LE-----LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGS 185
           L+     L      + Y     G+VD+         + I+G    D    +V +  +  S
Sbjct: 170 LQYLSQVLKDRTAEKYYMALVAGEVDEP--------MTIEGFLTKDEAVNKVQITKESIS 221

Query: 186 N------------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +                          + V L  G++ +I+                S G
Sbjct: 222 DESLPIKTAYRPLKTIEMSASCHKATLLEVHLITGRSHQIR---AHL---------SSIG 269

Query: 222 PFQLGTLLAGSTR 234
              +G +  G  R
Sbjct: 270 HPIIGDMKYGDRR 282


>gi|194761918|ref|XP_001963138.1| GF15796 [Drosophila ananassae]
 gi|190616835|gb|EDV32359.1| GF15796 [Drosophila ananassae]
          Length = 524

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 59/333 (17%), Positives = 111/333 (33%), Gaps = 56/333 (16%)

Query: 25  IASR--REV-----ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERT 73
           + SR  R       ER +   ++ VN   + +    +   D     +    VP+     T
Sbjct: 162 VFSREFRAAPPEVYERSLEAGKLTVNNEKVPK-DYKIKHNDLLANVVHRHEVPVTSQPIT 220

Query: 74  RLWL------YHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLT 125
            +++       +KP  +          +TV   L        + ++ RLD  T GLLL  
Sbjct: 221 IVYMDKDIVVVNKPASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFG 280

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                AR LE    + Q  + Y  R  G+     +    + I +     G  +V+   + 
Sbjct: 281 RTSDKARELEQQIRNRQVQKEYVCRVEGRFPDGIIE-CCEPIDVVSYKIGVCKVSPKGKD 339

Query: 184 GSNAWVTVG------------LREGKNREIKKVFEFFNWKVNR--L--IRISYGPFQLGT 227
               +  +G            L  G+  +I+   ++  + ++   L    + +GP +   
Sbjct: 340 CKTTFQRIGEVGDCSIVHCKPLT-GRMHQIRVHLQYLGYPISNDPLYNHEV-FGPLKGRG 397

Query: 228 LLAGSTREVSKKILREQLGPHLLE-------EAQVNLDAPIYSSETLVRDRPNIISEV-- 278
              G   +  ++++   +G H  E       E      AP    +  VR+ P        
Sbjct: 398 GDIGGISD--EQLINNLIGIHNAENWLGIQDENGPARAAPPKEVQETVRNEPTNTVSTQT 455

Query: 279 ----PDDFTRMKKNSSQKNGLSKQKKLATPVHR 307
               PD     KKN+S  +    +     P  +
Sbjct: 456 CLDEPDSSYDPKKNTSDPHCSECKINYRDPEEK 488


>gi|313886881|ref|ZP_07820585.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas asaccharolytica PR426713P-I]
 gi|312923678|gb|EFR34483.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas asaccharolytica PR426713P-I]
          Length = 374

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 78/239 (32%), Gaps = 56/239 (23%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           TP R+ + +  R    SR  ++       + V+G  ++     V   + I +        
Sbjct: 54  TPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKS-NYKVKPLETITMMLAHPKQD 112

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFS 106
                + +PL    E  +L + +KP G+V      +   T+                  +
Sbjct: 113 WSITPEDIPLDIVYEDDQLLVVNKPAGMVVHPGHGNYSGTLVHALAYYLRNDPLYDPNDA 172

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKG 164
            V  V R+D +T GLLL+         L          R Y+    G++DQ +       
Sbjct: 173 SVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTGRRYQALVWGKLDQPQG------ 226

Query: 165 IVIQGICYGD---------MQVTLDTQKGSNAWVT-------VGL--RE---GKNREIK 202
             I+G    D            T +  K +    T       V L   E   G+  +I+
Sbjct: 227 -TIEGNIARDPRDRTRMTVYPPTSEIGKPAVTHYTQLERLGFVTLIACELETGRTHQIR 284


>gi|167854653|ref|ZP_02477433.1| tRNA pseudouridine synthase C [Haemophilus parasuis 29755]
 gi|167854190|gb|EDS25424.1| tRNA pseudouridine synthase C [Haemophilus parasuis 29755]
          Length = 242

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/169 (16%), Positives = 55/169 (32%), Gaps = 26/169 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL   +
Sbjct: 8   QDDELIAINKPAGMLVHRSWLDKHETVFAMQTLRNQIRQHVFPIHRLDRPTSGVLLFALN 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGIC----- 171
             +AR +       Q  + Y     G +  +         +L+ +      +        
Sbjct: 68  SEMARTMSQLFEQHQIQKSYLAVVRGYLQGEGRIDYPLKVQLDKIADKFSQEKEAQEAIT 127

Query: 172 ----YGDMQVTLDTQKGSNAWVTVG-LR--EGKNREIKKVFEFFNWKVN 213
                   +      K + A  ++  L    G+  ++++  +     + 
Sbjct: 128 DYRNIATAERPYPAGKFATARYSLVQLYPKTGRKHQLRRHLKHLFHPIM 176


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

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/282 (15%), Positives = 89/282 (31%), Gaps = 78/282 (27%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++  ++++    R+ +        +   G      +++++   +V+V+G   +     V 
Sbjct: 5   EQRRIEDDEAGLRLDRWFKLHYPGL---GFG---HLQKLLRSGQVRVDGGRAKT-DTRVQ 57

Query: 56  STDHIEV------------------------DGVPLRK---AERTRLWLYHKPIGLVTTH 88
               + +                        D   L +    E  ++++++KP GL    
Sbjct: 58  PGQMVRIPPMSGDAGRPKIGPLTANTMRDKHDDEVLSQMLIYEDEKVFVFNKPAGLAVQG 117

Query: 89  SDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
                R  V   L +  SR       V RLD +T G+L++    G A  L          
Sbjct: 118 GSGLNRH-VDKMLEAWRSRKGEKPRLVHRLDRDTSGVLVVARTRGAATALTKAFRERDTK 176

Query: 143 RVYRVRFHG-----------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           + Y     G                   D D++   K G           +V ++    +
Sbjct: 177 KTYWAILKGVPVPHEGRISTFLVKEQTPDGDRMRTAKHGEEGADHALTHYRV-IENLAQN 235

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            +WV +    G+  +++         V+ L     G   LG 
Sbjct: 236 FSWVEMEPYTGRTHQLR---------VHALH---IGNPILGD 265


>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 = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|223932325|ref|ZP_03624328.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|302023845|ref|ZP_07249056.1| RNA pseudouridylate synthase [Streptococcus suis 05HAS68]
 gi|330832880|ref|YP_004401705.1| RluA family pseudouridine synthase [Streptococcus suis ST3]
 gi|223899006|gb|EEF65364.1| pseudouridine synthase, RluA family [Streptococcus suis 89/1591]
 gi|329307103|gb|AEB81519.1| pseudouridine synthase, RluA family [Streptococcus suis ST3]
          Length = 297

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/209 (17%), Positives = 67/209 (32%), Gaps = 37/209 (17%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVD--------G--VPLRKA-----ERTRLWLYHKPI 82
             + VN  + + A   +   D + +D        G   P+        E       +KP+
Sbjct: 35  GNIWVND-IEQNATYLLDIGDRVTIDIPAEEDLTGSLKPIFFPLDIVYEDDHFLSINKPV 93

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           G  +  S     ST+ + +            +V  V RLD +T G++L    G     L 
Sbjct: 94  GYASIPS-ALHSSTIANFVKGYLIEQNYENKQVHIVTRLDRDTSGVMLFAKHGYAHARLD 152

Query: 135 -ELPSTQWLRVYRVRFHG----QVDQDKLNLLKK-------GIVIQGICYGDMQVTLDTQ 182
            +L +    + Y     G    +   D +  + +         V +   Y      +   
Sbjct: 153 KQLQAKLIHKRYYALVKGNGQLEETGDIIAPIGRPEDSIITRCVTKNGKYAHTSYRVVQS 212

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            G    V + L  G+  +I+  F    + 
Sbjct: 213 WGDIHLVDIQLHTGRTHQIRVHFSHIGFP 241


>gi|310823803|ref|YP_003956161.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309396875|gb|ADO74334.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 321

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/263 (13%), Positives = 78/263 (29%), Gaps = 68/263 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           ++E+    R+ K +       R+ +         +MI  ++V+VNG   +     + + D
Sbjct: 6   IEEDSVGMRLDKYL-------RKRLANMPTSHLFKMIRVKKVRVNGKRAQ-PEQLLAAGD 57

Query: 59  HIEVDG-------------------------VPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            I + G                           +   E   +    KP G+         
Sbjct: 58  VIAIRGDEQQLLGPAPGGERLPPPPPPVDPSELVILLEDDWMMAVDKPSGMAVHTGSGIT 117

Query: 94  RSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLR 143
             T+ D + +                 RLD  T G++L+                ++  +
Sbjct: 118 GGTLVDYVRAYLGPKAVRNDFTASPAHRLDRETSGVILVAKRRPAMVHFTEVFTESRARK 177

Query: 144 VYRVRFHGQVDQD--------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            Y     G++ QD                +  ++G+ +Q          +  Q    A +
Sbjct: 178 RYVTLVKGKMPQDSGVIDLPLSEHQQTAESKARRGVNMQEALTR---WKVIRQSSEAALL 234

Query: 190 TVGLREGKNREIKKVFEFFNWKV 212
           +  +  G+  +I++        V
Sbjct: 235 SCAIETGRTHQIRRHLAAVGHPV 257


>gi|126139263|ref|XP_001386154.1| DRAP deaminase [Scheffersomyces stipitis CBS 6054]
 gi|126093436|gb|ABN68125.1| DRAP deaminase [Scheffersomyces stipitis CBS 6054]
          Length = 585

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 66/202 (32%), Gaps = 37/202 (18%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKP 81
           ++ I   +V +N          V + D I          V    ++   E   L    KP
Sbjct: 124 KKAIDAGQVTLNKKPA-NLDSIVRNGDLISHRTYRKEPPVSSREIKIVYEDDDLIAIDKP 182

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
            G+    +     +T+         +V     RLD  T GL+ L      A  L  ++  
Sbjct: 183 SGIPVHPTGRYRYNTITKIFQHEMGKVVHPCNRLDRLTSGLMFLGKTAKGADKLVKQIRE 242

Query: 139 TQWLRVYRVRFHGQVDQDKLNL-----------------LKKGIVIQGICYGDMQVTLDT 181
               + Y  R  G+   +++ +                 LK+G   +       +V+ D 
Sbjct: 243 RSVRKEYIARVKGEFPLEEVEVDQPMRTIAHKLGLNRIDLKEG---KDAKTAFKRVSYDP 299

Query: 182 QKGSNAWVT-VGLREGKNREIK 202
           +    + V  + L  G+  +I+
Sbjct: 300 EH-DTSIVKCIPLT-GRTHQIR 319


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 29/73 (39%), Gaps = 9/73 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M  K +        R+   +AR G   SR + +  I    V V+G    +  + V  +  
Sbjct: 1  MSQKKL--------RLDVRLARDGYCPSREKAQAAIMAGLVFVDGERACKPGMMVDPSSV 52

Query: 60 IEVDGVPLRKAER 72
          IEV G PL    R
Sbjct: 53 IEVRGCPLPYVSR 65


>gi|313893624|ref|ZP_07827192.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313441768|gb|EFR60192.1| pseudouridine synthase, RluA family [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 322

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 18/134 (13%), Positives = 42/134 (31%), Gaps = 16/134 (11%)

Query: 37  QQRVKVNGILLE---------RAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLV- 85
           +  + VN                 + +       +  + L    E   + + +K  G++ 
Sbjct: 40  EGIITVNDEPATWNTLVHGGDHLVMKLTPEQEFSLSPMDLDIVYEDEHILVINKAAGVLM 99

Query: 86  ---TTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              +T  D    + V               V RLD +T G++++     +    +   T 
Sbjct: 100 HPTSTVRDHTLANGVLYYYQETHQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKHTH 159

Query: 141 WLRVYRVRFHGQVD 154
           + + Y     G++ 
Sbjct: 160 FYKTYDAIVEGKLP 173


>gi|307331663|ref|ZP_07610770.1| pseudouridine synthase, RluA family [Streptomyces violaceusniger Tu
           4113]
 gi|306882689|gb|EFN13768.1| pseudouridine synthase, RluA family [Streptomyces violaceusniger Tu
           4113]
          Length = 322

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 78/257 (30%), Gaps = 60/257 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD-------- 58
           V +    +RV   IAR    SR +   + A  +V+++G +  ++   V            
Sbjct: 21  VPDGLEGERVDAAIARMFGFSRTKAAELAAAGKVQLDGTVAGKSD-RVSGGAWLEVELPQ 79

Query: 59  ---HIEVDGVPLRKAE----RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
               + V   P+   E       + +  KP+G+    S      TV   L          
Sbjct: 80  AAPPVRVVAEPVEGMEIVHDDEDIVVVSKPVGVAAHPSPGWTGPTVIGGLAAAGFRVSTS 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
               R   V RLD+ T GL+++        VL+         + Y     G  D      
Sbjct: 140 GAAERQGIVHRLDVGTSGLMVVAKSELAYSVLKQAFRERTVDKRYHALVQGHPDP----- 194

Query: 161 LKKGIVIQGICYGDM----------QVTLDTQKGSN-----------AWVTVGLREGKNR 199
                 + G     +           VT D +               + + + L  G+  
Sbjct: 195 ------LSGTIDAPIGRHPQHDYKWAVTADGKPSVTHYDLIEAFRAASLLDIKLETGRTH 248

Query: 200 EIK-KVFEFFNWKVNRL 215
           +I+  +    +  V  L
Sbjct: 249 QIRVHMAAHRHPCVGDL 265


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|315037877|ref|YP_004031445.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
 gi|312276010|gb|ADQ58650.1| Pseudouridine synthase [Lactobacillus amylovorus GRL 1112]
          Length = 301

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 68/209 (32%), Gaps = 36/209 (17%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKA-ERTRLWLYHKPI 82
              + VN       +  + + D +                  P+    E     +  KP 
Sbjct: 38  NGLILVNHKR-RYTSFRLKTNDEVIFVTGEEKKNDFLKPSNNPVEPVLETKNYIILSKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTNDGGLARVLE 135
           G+++  S  +    + + L   F +          + RLD +T GL+L+  +        
Sbjct: 97  GVLSIPSRYEDDDAIVNRLMCYFIKEGKKDLKPHVITRLDRDTSGLVLVGKNAVAHARFS 156

Query: 136 LPSTQ-WLRVYRVRFHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLDTQ 182
               + +++ Y    HG  + D+L  L            K+G++  G      +  +  Q
Sbjct: 157 KIGKERFIKKYHAIVHGNFENDELTGLVDEPIGKIDSGVKRGVIPDGKSAQT-EYKVLKQ 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               + V + L  G+  +I+    +    
Sbjct: 216 VSGASLVELRLLTGRTHQIRVHMAYLGHP 244


>gi|146278539|ref|YP_001168698.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17025]
 gi|145556780|gb|ABP71393.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 346

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/157 (21%), Positives = 51/157 (32%), Gaps = 33/157 (21%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------- 74
           VE+M    +V+V+G   + A+  V     I V   PL   +  R                
Sbjct: 34  VEKMCRTGQVRVDGARAK-ASDRVAEGMEIRV--PPLPDPDAPRPQASRVTKSDEQMIQD 90

Query: 75  --------LWLYHKPIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLL 122
                   + + +KP GL +      G   V             R   V RLD +T G+L
Sbjct: 91  CVIYKDNDIIVLNKPAGLPSQGGSGQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVL 150

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
           +L     +AR L          ++Y     G     +
Sbjct: 151 VLARTDRVARALSESFRHRNTRKIYWALVAGVPSPKQ 187


>gi|332299970|ref|YP_004441891.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           DSM 20707]
 gi|332177033|gb|AEE12723.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           DSM 20707]
          Length = 376

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 78/239 (32%), Gaps = 56/239 (23%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           TP R+ + +  R    SR  ++       + V+G  ++     V   + I +        
Sbjct: 56  TPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKS-NYKVKPLETITMMLAHPKQD 114

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFS 106
                + +PL    E  +L + +KP G+V      +   T+                  +
Sbjct: 115 WSITPEDIPLDIVYEDDQLLVVNKPAGMVVHPGHGNYSGTLVHALAYYLRNDPLYDPNDA 174

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKG 164
            V  V R+D +T GLLL+         L          R Y+    G++DQ +       
Sbjct: 175 SVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTGRRYQALVWGKLDQPQG------ 228

Query: 165 IVIQGICYGD---------MQVTLDTQKGSNAWVT-------VGL--RE---GKNREIK 202
             I+G    D            T +  K +    T       V L   E   G+  +I+
Sbjct: 229 -TIEGNIARDPRDRTRMTVYPPTSEIGKPAVTHYTQLERLGFVTLIACELETGRTHQIR 286


>gi|308068172|ref|YP_003869777.1| RNA pseudouridine synthase (RNA-uridine isomerase) [Paenibacillus
           polymyxa E681]
 gi|305857451|gb|ADM69239.1| Hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           [Paenibacillus polymyxa E681]
          Length = 319

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/234 (16%), Positives = 85/234 (36%), Gaps = 46/234 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K I+Q+     R  K+I++          ++  Q  + +NG  +   +V V S D +
Sbjct: 19  MLLKTILQKRMNISR--KLISKL---------KLTEQG-IMLNGTRVY-ISVKVKSGDQV 65

Query: 61  EV-------DG---VPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+       D     P+      E   L + +K  G++   +      T+ + +   +  
Sbjct: 66  EIRMERERSDDILPEPIPFEILFEDEHLLVVNKAAGMIVHPTHGHYTGTLANGVVHYWQA 125

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRV-----------R 148
                R   V RLD  T G+L++  +  + + +     +    + Y             +
Sbjct: 126 KGELFRFRPVHRLDQETTGVLVVAKNPYVHQHISEQMIAGTVDKRYTALVHGRPELQEGK 185

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             G +D++  N   + +   G     +   L+      + + + L  G+  +I+
Sbjct: 186 VDGPIDRNPDNPHLRMVTPDGYPALTL-YKLEEVWNGGSRIGLKLESGRTHQIR 238


>gi|303238360|ref|ZP_07324895.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302594064|gb|EFL63777.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 322

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/267 (14%), Positives = 90/267 (33%), Gaps = 68/267 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE---------VERMIAQQRVKVNGILLERAAVNVMS 56
           I+ E+ + +R+ KV+        +E         + +   ++ VKVNGI ++        
Sbjct: 5   IIAEDSSNKRIDKVL--------KEKYPNMPQNFMYKAFRKKDVKVNGIRVKE-DYIANL 55

Query: 57  TDHIEV-------DGVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
            D +EV       +G  + +            E   L + +K  G+          +T+ 
Sbjct: 56  GDKVEVYIIDEILEGKSISEPTDYFKAFTVIYEDKNLLIVNKKQGIPVHPDKDQAENTLI 115

Query: 99  DNLPSIFSRVIS-----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY 145
           D + +                    RLD NT GL+++  +    +V+     + +  + Y
Sbjct: 116 DLVTAYIREKEVTSKTSGFSPALCHRLDRNTGGLIIIAKNNEALKVMLEKIKNKEVKKYY 175

Query: 146 RVRFHGQVDQ------DKLNLLKK--GIVIQGICYGDMQVTL-----------DTQKGSN 186
           +    G++++        L   ++   + I      +    +            T   S 
Sbjct: 176 QCLVRGKMEKPQGILKAYLEKDERKSRVYINDYKTRNSLEIITKYKTLSIIDNITADDSA 235

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + + V L  G+  +I+    +    + 
Sbjct: 236 SLLEVELVTGRTHQIRAHMSYIGHPIV 262


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/252 (16%), Positives = 76/252 (30%), Gaps = 53/252 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLE----------------R 49
           +V E     RV   +A+A   SR     +I    V ++G  +                  
Sbjct: 8   VVPEGLDSMRVDAAVAKAFGLSRTVAAELIEAGEVLIDGSRVTKSDRVSTGHSLEVTLPE 67

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRL-------WLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                M  + I V+G+ +   +   +          H  +G        DG + V     
Sbjct: 68  PKQAPMPKEEI-VEGLTVLYDDDDVIVVDKPVGVAAHPTLGW-------DGPTVVGGLQA 119

Query: 101 ----LPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
               LP      R   V RLD+ T G++++ N      VL+    +    + Y     G 
Sbjct: 120 MGYQLPDAGPPERKGIVQRLDVGTSGVMVVANSIPGYSVLKRAFKERTVEKTYHAVVQGL 179

Query: 153 VDQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D     ++           K  +   G         L+  + + + + V L  G+  +I
Sbjct: 180 PDPIVGTIDAPIGRHPSSGWKFAVTADGRHSVTHYEVLEAFREA-SLLEVHLETGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +           
Sbjct: 239 RVHMSSVGHPCV 250


>gi|227540229|ref|ZP_03970278.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239953|gb|EEI89968.1| pseudouridylate synthase [Sphingobacterium spiritivorum ATCC 33300]
          Length = 247

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/150 (16%), Positives = 52/150 (34%), Gaps = 17/150 (11%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           L   E   + + +KP  + +      G   +       ++      RLD  T G+LL+  
Sbjct: 17  LIIHEDENIIVINKPPFIASLDEREGGEVNILRLAKKYYADAQICHRLDKETSGILLIAK 76

Query: 127 DGGLARVLEL--PSTQWLRVYRVRFHG-QVDQD---KLNLLKKG---IVIQGICYGDMQV 177
           +    R++ +     +  + Y     G  + QD    L +L +G   + I        + 
Sbjct: 77  NPETYRLISIEFEKRRVDKTYHAIIEGTHIFQDLKIDLPILNQGNKNVTIDRYNGKPAET 136

Query: 178 TLDTQKGSNAWVTVGLRE-----GKNREIK 202
             ++ +         L E     G+  +I+
Sbjct: 137 IFNSIQYFKH---FTLVECKPITGRMHQIR 163


>gi|254283218|ref|ZP_04958186.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR51-B]
 gi|219679421|gb|EED35770.1| ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium NOR51-B]
          Length = 319

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 69/207 (33%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNV----------MSTDHIEVDGVPLRK---AERT 73
           SR  ++  I + ++ V+G ++ R    V           +   +   G  L      E  
Sbjct: 32  SRSRLKTWIQEGKLTVDG-VVLRPKDKVALDNQLELIAEAEAEVAWSGESLPLDICYEDD 90

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRLDINTEGLLLLTND 127
            + + +KP GLV   +      T+ + L +    +        V RLD +T G++ +   
Sbjct: 91  DVIVVNKPAGLVVHPAAGHPTGTLVNALLAHAPELQQQPRGGIVHRLDKDTSGVMFVAKS 150

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
               R L  +L +    R Y     G           + +      K  +V  G      
Sbjct: 151 HRAHRSLVTQLSARSVTREYAALCSGQLVAGGTIDQPIGRHPTARTKMAVVSDGKPAITH 210

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
               +  +     + V L  G+  +I+
Sbjct: 211 FRVANRFEHFT-QLQVNLETGRTHQIR 236


>gi|229496692|ref|ZP_04390406.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
 gi|229316589|gb|EEN82508.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas endodontalis ATCC 35406]
          Length = 330

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/152 (23%), Positives = 59/152 (38%), Gaps = 24/152 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----PLRKAERTRLW------ 76
           SR   ++ +  + +KVNG ++      V   D + V  V     L   E   LW      
Sbjct: 39  SRTTHKQYLRDRCIKVNGQVVSEHNAPVAVGDEVVVYSVGFAPVLDNTEVKVLWQDDWFI 98

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
           L  K  G+ T  S P  R TV+  +   +       ++  + RLD +T GL+L   D  +
Sbjct: 99  LVQKEPGIPTIASKPGDRHTVYRIVADHYKSGDAREKIFLLNRLDRDTRGLILFARDREV 158

Query: 131 ARVLELPSTQWLR-----VYRVRFHGQVDQDK 157
            + +      W +      +     G V ++K
Sbjct: 159 QQEILD---NWEKYILSQTFSALVEGVVPEEK 187


>gi|228907022|ref|ZP_04070887.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
 gi|228852613|gb|EEM97402.1| Pseudouridine synthase [Bacillus thuringiensis IBL 200]
          Length = 307

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 88/261 (33%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVNPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGNGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V++ +            +  ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVNKKQGTIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|168061155|ref|XP_001782556.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162665963|gb|EDQ52631.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 365

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/254 (15%), Positives = 65/254 (25%), Gaps = 90/254 (35%)

Query: 35  IAQQR-VKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPIG 83
           I   + ++V+G ++      +     +    +P R+ E             L   +KP G
Sbjct: 56  IQNGQQIRVDGNVITDPGFLLRDGVTLVYQRLPWREPEVPYRLGVLYEDDHLVAINKPSG 115

Query: 84  LVTTHSDPDGRSTVFDNLPS----------------------IFSRVISVGRLDINTEGL 121
           L         + TV   L                           +   V RL   T G+
Sbjct: 116 LQVLPGGLFQQRTVLKQLEWDNEEKEKHLQACLASVSSSDETRLWKPAPVHRLGRGTSGI 175

Query: 122 LLLTNDGGLARVL---------------ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV 166
           LL          L                L   +  + YR              L  GI+
Sbjct: 176 LLCAKSPAAKSKLAADLAAGTSVSIDRSALIDRKITKTYRA-------------LASGII 222

Query: 167 IQGICYGDMQV---------------TLDTQKGSNAWVTV---------GLRE-----GK 197
           ++   + D+ +               T    K S + VTV          L E     G+
Sbjct: 223 MEDEVFADIPIGKVKYSGVAGGLNMATEIGGKPSQSKVTVLWRDIVENQTLVEVQIYTGR 282

Query: 198 NREIKKVFEFFNWK 211
             +I+         
Sbjct: 283 PHQIRIHLAALGHP 296


>gi|77360895|ref|YP_340470.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875806|emb|CAI87027.1| tRNA pseudouridine synthase C [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 254

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 49/177 (27%), Gaps = 27/177 (15%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEG 120
           G      +        KP GL+   S  D          L       V  V RLD  T G
Sbjct: 11  GELTILYQDENYVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSG 70

Query: 121 LLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQG 169
           +LL       AR +          + Y     G   +         ++L+ +      Q 
Sbjct: 71  VLLFALSSEAARDMNQLFIEGTISKRYLALVRGFAPESVFLDKPLKEELDKIADKFADQD 130

Query: 170 ICYGDM--------QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
               +         Q  L    G    V   L E     G+  +I++  +  +  + 
Sbjct: 131 KAPQEAQTQFNCLHQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRHLKHLSLPII 187


>gi|15837541|ref|NP_298229.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa 9a5c]
 gi|34395837|sp|Q9PET9|RLUD_XYLFA RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|9105864|gb|AAF83749.1|AE003933_1 ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa 9a5c]
          Length = 331

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 85/256 (33%), Gaps = 35/256 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  V +    +R   V+A      SR  +   I    V +NG+L+      V   + +
Sbjct: 13  SRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVR-PRDPVYGGEVV 71

Query: 61  EV--------DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +        D VP         E   +++ +KP GLV      +   T+ + L      
Sbjct: 72  RLQVVPDIRTDAVPQDIPLDILYEDEHVFVLNKPAGLVVHPGAGNPDGTLVNALLHRDPA 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RF 149
                R   V RLD +T G++++         L  +L S Q  R Y              
Sbjct: 132 LAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHRQYLAVVVSALVSGGTV 191

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +  +++   + L+  +   G          +  +   A +   L  G+  +I+       
Sbjct: 192 NAAIERHPRDRLRMAVSDTGKEAVTHYRLRERFRAHTA-LECRLDTGRTHQIRVHMAHLR 250

Query: 210 WKVNRLIRISYGPFQL 225
             +    R+  G  +L
Sbjct: 251 HPIVG-DRLYGGSLKL 265


>gi|291528898|emb|CBK94484.1| Pseudouridylate synthases, 23S RNA-specific [Eubacterium rectale
           M104/1]
          Length = 324

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 49/305 (16%), Positives = 97/305 (31%), Gaps = 94/305 (30%)

Query: 1   MKDKNIVQENFTPQRVSKVI------ARAGIASRREVERMIAQQRVKVNGILLERAAVNV 54
           MK+    + N   QR+ K +      A  G      + +M+ ++ +K+N          V
Sbjct: 1   MKEFKAGK-NEAGQRLDKYLKKILPNASMGF-----IYKMLRKKNIKLNDKKA-SGTEIV 53

Query: 55  MSTDHIEV-----------------------------DGVPLRKAERTRLWLYHKPIGLV 85
              D I++                             DG+ +   +   + + +KP+ ++
Sbjct: 54  SVDDKIKIFLSDDTFAKFSVNEDSLMKDFKALGALKPDGLGVVYEDDD-ILVANKPVNML 112

Query: 86  TTHS---DPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARV 133
           +  S   D      +   L              +     RLD NT GL+L+   G     
Sbjct: 113 SQKSKETDISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILM---GKSLHG 169

Query: 134 LE-----LPSTQWLRVYRVRFHGQVDQ--------------DKLNLLKKGIVIQGICYGD 174
           L+     L      + Y     G+VD+              +K+ + K+ I  + +    
Sbjct: 170 LQYLSQVLKDRTAEKYYMALVAGEVDEPMTIEGFLTKDEAVNKVQITKEPISDESLPIKT 229

Query: 175 MQVTLDTQKGSNA-----WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
               +   + S++      + V L  G++ +I+                S G   +G + 
Sbjct: 230 AYRPIKIIEMSDSCHKATLLEVHLITGRSHQIR---AHL---------SSIGHPIIGDMK 277

Query: 230 AGSTR 234
            G  R
Sbjct: 278 YGDKR 282


>gi|221638143|ref|YP_002524405.1| Ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides KD131]
 gi|221158924|gb|ACL99903.1| Ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides KD131]
          Length = 343

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/157 (21%), Positives = 51/157 (32%), Gaps = 33/157 (21%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------- 74
           VE+M    +V+V+G   + A+  V     I V   PL   +  R                
Sbjct: 31  VEKMCRTGQVRVDGARAK-ASDRVAEGMEIRV--PPLPDPDAPRPQASRVTKSDEQMIQD 87

Query: 75  --------LWLYHKPIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLL 122
                   + + +KP GL +      G   V             R   V RLD +T G+L
Sbjct: 88  CVIYRDNDIIVLNKPAGLPSQGGSGQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVL 147

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
           +L     +AR L          ++Y     G     +
Sbjct: 148 VLARTDRVARALSESFRHRNTRKIYWALVAGVPSPKQ 184


>gi|42518750|ref|NP_964680.1| hypothetical protein LJ0825 [Lactobacillus johnsonii NCC 533]
 gi|41583036|gb|AAS08646.1| hypothetical protein LJ_0825 [Lactobacillus johnsonii NCC 533]
          Length = 299

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 90/250 (36%), Gaps = 46/250 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVM 55
           M+   +  EN TPQ++ + + + G       +R +         V VN       +  + 
Sbjct: 1   MQYFKLKFENKTPQKLGRFLLKNGF-----SKRALTNSQHHGGMVLVNHHR-RYTSYLLH 54

Query: 56  STDHIEV------DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D +        +   L+ +        E+    + +K  G+++  S  +    V + L
Sbjct: 55  AGDEVIFILGEEKENKWLKPSSKKLNIVFEQKDYLVINKDAGILSIPSRYEDSDAVVNRL 114

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPS-TQWLRVYRVRFHGQV 153
              F +          + RLD +T GL+L+  +             ++++ Y    HG  
Sbjct: 115 LHYFQQQKQTDLKPHVITRLDRDTSGLVLVGKNAVAHARFSKMEKNEFIKKYHAIVHGNF 174

Query: 154 DQDKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++ +               +K+G+V  G         LD  KG+ + + + L  G+  +I
Sbjct: 175 EEAQRQGTIDAPIGKIDAGVKRGVVNNGQRSVTKYRVLDQVKGA-SLIELQLLTGRTHQI 233

Query: 202 KKVFEFFNWK 211
           +   ++    
Sbjct: 234 RVHMQYLGHP 243


>gi|83854943|ref|ZP_00948473.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           NAS-14.1]
 gi|83941466|ref|ZP_00953928.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           EE-36]
 gi|83842786|gb|EAP81953.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           NAS-14.1]
 gi|83847286|gb|EAP85161.1| ribosomal large subunit pseudouridine synthase C [Sulfitobacter sp.
           EE-36]
          Length = 349

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/267 (14%), Positives = 82/267 (30%), Gaps = 65/267 (24%)

Query: 6   IVQENFTPQRVSKV------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           +V+E    QR+ +       +   G+     +E+M  +  ++V+G  ++ A+  +     
Sbjct: 8   VVEEGDGDQRLDRWFKRTFPLIGQGL-----IEKMCRKGDIRVDGGRVK-ASTRLEVGQT 61

Query: 60  IEV----DGVPLRKAERTRL-------------------WLYHKPIGL----VTTHSDPD 92
           + +    D       +RTR+                      +KP GL     +  SD  
Sbjct: 62  VRIPPLPDEKAPPPPKRTRISEADTKFIRSCVIYRDDHIIALNKPPGLPVQGGSGQSDRH 121

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFH 150
             +     +  +  +   V RLD +T G+L++     +A  L          ++Y     
Sbjct: 122 VDALADALMFELDEKPRLVHRLDKDTSGVLIMARTRSIAAALTASFRHRETRKIYWAAVA 181

Query: 151 GQVDQ-------DKLNLLKKGIVIQGIC-----YGDMQ------------VTLDTQKGSN 186
           G             +     G   +G         DM+             TL       
Sbjct: 182 GVPHPRNGTIKFGLVKAFGHGARGEGEKMYCVHPKDMETTEGAKRATTDYATLAQAGKRT 241

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
            W+ +    G+  +++         + 
Sbjct: 242 CWMALIPVTGRTHQLRAHMAEIGHPIV 268


>gi|294461273|gb|ADE76199.1| unknown [Picea sitchensis]
          Length = 386

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 70/233 (30%), Gaps = 65/233 (27%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           I   ++ V+G  +      +     +    +  R+           E   L   +KP GL
Sbjct: 50  IHNGQITVDGKTVNEPDTVLRIGPKLVYHRLSWREPIAPCKLYVLFEDDHLLAVNKPSGL 109

Query: 85  VTTHSDPDGRSTVFDNLPS-------------------IFSRVISVGRLDINTEGLLLL- 124
                    + TV   L                       S+ + V RL   T G+LL  
Sbjct: 110 QVLPGGLFQQRTVLTQLKWKASQSSKYRSVAGKAVADFQESQPVPVHRLGRGTSGILLCA 169

Query: 125 ----------TNDGGLARVLELPST----------QWLRVYRVRFHGQVDQDKLNL---- 160
                      +       +   S+          +  + YR    G ++Q+K+ +    
Sbjct: 170 KSEIAKSQLAADFADGTSFISRNSSSDIDAGEIKRRIYKTYRALADGIIEQNKIAIKQPI 229

Query: 161 -------LKKGIVIQGICYGDMQ--VTLDTQKGSN--AWVTVGLREGKNREIK 202
                  ++ G+ +        +  +T+ ++  +     V V +  G+  +I+
Sbjct: 230 GKMRYPGVRSGLYVASPTGKQAESRITVLSRDKNRNCTLVEVEIYSGRPHQIR 282


>gi|292669466|ref|ZP_06602892.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
 gi|292648919|gb|EFF66891.1| ribosomal large subunit pseudouridine synthase D [Selenomonas noxia
           ATCC 43541]
          Length = 290

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/197 (15%), Positives = 67/197 (34%), Gaps = 28/197 (14%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKA-----------ERTRLWLYHKPIGLVTTHSD 90
           VNG+ +  A   + + D +  +   +              E   L +  K  G +   + 
Sbjct: 42  VNGMPVIAARTVLRAGDMVSYELPVISSVIPEQLPLTVVYEDADLLVIDKSAGQLVHPTT 101

Query: 91  PDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
            +   TV + +  +++            RLD NT GLLL+     +   +    T   R 
Sbjct: 102 KEAHGTVANAVLGLYAARRAPLGFHPCHRLDRNTTGLLLIAKHPEVQYQIARQDT-LTRE 160

Query: 145 YRVRFHGQVDQDK------LNLLKKGIVIQGICY--GDMQVTLDTQK--GSNAWVTVGLR 194
           Y     G +  +K      +      I+++ +       +    T++  G++  + + L 
Sbjct: 161 YLALIKGMLSPEKGCIDAPIARALPSIILRHVAPDGKPARTHYQTEQTDGTHTLLRLHLE 220

Query: 195 EGKNREIKKVFEFFNWK 211
            G+  +I+         
Sbjct: 221 TGRTHQIRVHLAHLGHP 237


>gi|268319849|ref|YP_003293505.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262398224|emb|CAX67238.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 299

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 90/250 (36%), Gaps = 46/250 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVM 55
           M+   +  EN TPQ++ + + + G       +R +         V VN       +  + 
Sbjct: 1   MQYFKLKFENKTPQKLGRFLLKNGF-----SKRALTNSQHHGGMVLVNHHR-RYTSYLLH 54

Query: 56  STDHIEV------DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D +        +   L+ +        E+    + +K  G+++  S  +    V + L
Sbjct: 55  AGDEVIFILGEEKENKWLKPSSKKLNIVFEQKDYLVINKDAGILSIPSRYEDNDAVVNRL 114

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPS-TQWLRVYRVRFHGQV 153
              F +          + RLD +T GL+L+  +             ++++ Y    HG  
Sbjct: 115 LHYFQQQKQTDLKPHVITRLDRDTSGLVLVGKNAVAHARFSKMEKNEFIKKYHAIVHGNF 174

Query: 154 DQDKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++ +               +K+G+V  G         LD  KG+ + + + L  G+  +I
Sbjct: 175 EEAQRQGTIDAPIGKIDTGVKRGVVNNGQRSVTKYRVLDQVKGA-SLIELQLLTGRTHQI 233

Query: 202 KKVFEFFNWK 211
           +   ++    
Sbjct: 234 RVHMQYLGHP 243


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|153938225|ref|YP_001390782.1| RluA family pseudouridine synthase [Clostridium botulinum F str.
           Langeland]
 gi|168180094|ref|ZP_02614758.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|170754896|ref|YP_001781073.1| RluA family pseudouridine synthase [Clostridium botulinum B1 str.
           Okra]
 gi|226948698|ref|YP_002803789.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|152934121|gb|ABS39619.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           Langeland]
 gi|169120108|gb|ACA43944.1| pseudouridine synthase, RluA family [Clostridium botulinum B1 str.
           Okra]
 gi|182668924|gb|EDT80900.1| pseudouridine synthase, RluA family [Clostridium botulinum NCTC
           2916]
 gi|226843753|gb|ACO86419.1| pseudouridine synthase, RluA family [Clostridium botulinum A2 str.
           Kyoto]
 gi|295318854|gb|ADF99231.1| pseudouridine synthase, RluA family [Clostridium botulinum F str.
           230613]
          Length = 317

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/264 (13%), Positives = 78/264 (29%), Gaps = 67/264 (25%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA- 50
           K ++  N   QR+ K              +             I +  +KVNG   +   
Sbjct: 2   KIVIGANEAGQRLDKF-----------CRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKN 50

Query: 51  ---------AVNVMSTDH----IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                    + NV S       + +D       E   + L  K  G++      +G  T+
Sbjct: 51  FLEEGDIVESFNVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGEPTL 110

Query: 98  FDNLPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                   S  RLD NT G+++   +    + L   +   +  
Sbjct: 111 TDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIE 170

Query: 143 RVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSN----AWV 189
           + Y     G++                + K  +         ++ ++ +        +++
Sbjct: 171 KYYSSLVKGRIKDGVYEAYISKNEDTNMSK--IYNEPKPNTKKIAMNVKTIQTCGSFSFI 228

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 229 EIELLTGRSHQLRAHLNHLGNPII 252


>gi|326692754|ref|ZP_08229759.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc argentinum
           KCTC 3773]
          Length = 300

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 77/266 (28%), Gaps = 54/266 (20%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRLWLY-HKPIG 83
             +  NG  +  +   +   D + +             D  PL        WL   KP G
Sbjct: 37  GAILKNGQPVYTSDY-LDDGDEVTIVMPTEKSNDLVVPDYKPLNIIFENEHWLVVDKPYG 95

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLE- 135
           + T     D   T+ + +                V RLD +T G++LL      A  +  
Sbjct: 96  VTTVPGHADRLHTLVNQVKGHLEETNAEDLVPHVVTRLDRDTSGIVLLAKH-RFAHAVLD 154

Query: 136 --LPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGDM----QVT 178
             L      + Y     G + +D  +            +K+ +   G          +  
Sbjct: 155 QQLQEHTVEKFYLAYTSGILPEDHGDINAPIGRVEGDFIKREVRDDGKPSRTEYWVERRY 214

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK-----------VNRLIRISYGPFQLG- 226
            +        V V L  G+  +I+  F+                 + L R +   + +  
Sbjct: 215 DEDGDNPMTRVRVQLHTGRTHQIRVHFQNIGHPLVGDDLYGGPLWHGLERQALHAYHMKF 274

Query: 227 -TLLAGSTREVSKKILREQLGPHLLE 251
                G  RE + K+  +  G   L 
Sbjct: 275 YDPFIGDYREFNTKLPEDLKGLRDLA 300


>gi|254779554|ref|YP_003057660.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
 gi|254001466|emb|CAX29466.1| Pseudouridine synthase (RNA-uridine isomerase) (RNA pseudouridylate
           synthase) [Helicobacter pylori B38]
          Length = 242

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 76/235 (32%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPKNTHFSVQKVEKPGVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G V+++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLAIVQGIVEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|228964349|ref|ZP_04125466.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
 gi|228795333|gb|EEM42823.1| Pseudouridine synthase [Bacillus thuringiensis serovar sotto str.
           T04001]
          Length = 307

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 87/261 (33%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGNRTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|281420178|ref|ZP_06251177.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
 gi|281405673|gb|EFB36353.1| ribosomal large subunit pseudouridine synthase D [Prevotella copri
           DSM 18205]
          Length = 315

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 39/206 (18%), Positives = 68/206 (33%), Gaps = 30/206 (14%)

Query: 37  QQR-VKVNGILLERAAVNVMSTDHIEVDGVPLRKA-----------ERTRLWLYHKPIGL 84
           Q R +KVNG  + +    +     + V      +            E   L +  K IG+
Sbjct: 58  QGRGIKVNGKTITQFDYALKPGMKVSVSKTKKNQEVFKSRYLKIVYEDRYLIVVEKNIGI 117

Query: 85  VT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           ++    HS  + ++ + D             V RLD +T GL++   D      LE    
Sbjct: 118 LSMAAGHSTLNVKTVLDDYFHKTRQNCQAHVVHRLDRDTSGLMIYAKDKQTELALEDDWH 177

Query: 140 Q--WLRVYRVRFHGQVDQDK---LNLLKKGI--------VIQGICYGDMQVTLDTQKGSN 186
              + R Y     G+++ D+    N LK              G  Y         +  ++
Sbjct: 178 HNVYDRRYVALVSGEMEDDEGTVANWLKDNKAYITYSSDTDNGGKYAVTYYHTLERTTAH 237

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKV 212
           + V   L  G+  +I+         V
Sbjct: 238 SLVEFKLETGRKNQIRVHTADMGHPV 263


>gi|308063784|gb|ADO05671.1| hypothetical protein HPSAT_04685 [Helicobacter pylori Sat464]
          Length = 242

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 76/235 (32%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRALKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIIAPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|295702688|ref|YP_003595763.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium DSM 319]
 gi|294800347|gb|ADF37413.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium DSM 319]
          Length = 303

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 55/161 (34%), Gaps = 20/161 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLL 124
           E   + + +KPI L T  S    + T+ + + + F ++        V RLD +T G +L 
Sbjct: 88  EDEHVLIVNKPINLDTHPSSEQDQKTLLNAVAAYFQKIGLKTKPRHVHRLDSDTSGAILF 147

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGIC 171
           T     + V    L   +  R Y     G + ++             +  ++ +   G  
Sbjct: 148 TKHFVASSVFDQLLAERKINRTYIAIVQGIIKKEDGIINEPIGRDRHHATRRRVSRTGQA 207

Query: 172 YGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
                  L      N   + + L  G+  +I+       + 
Sbjct: 208 AKTRYRVLKRNTAKNETLIELSLETGRTHQIRVHMSHIGYP 248


>gi|119476934|ref|ZP_01617215.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2143]
 gi|119449741|gb|EAW30978.1| Pseudouridine synthase, RluD [marine gamma proteobacterium
           HTCC2143]
          Length = 318

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/230 (17%), Positives = 80/230 (34%), Gaps = 35/230 (15%)

Query: 6   IVQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V E     R+ + IA       SR  ++  I    + V+G   +++   + S + +E+ 
Sbjct: 10  TVPEGLEGSRLDQ-IAAQLFPDYSRARLQIWIKSGELTVDGE-AKKSREKLQSGELLELR 67

Query: 63  ----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
               D               E   L + +KP GLV      +   T+ + L +    + S
Sbjct: 68  AVVEDEERWDAESMDLDIVYEDEALLVVNKPAGLVVHPGSGNASGTLLNALLAHLPDIAS 127

Query: 111 V------GRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDK 157
           V       RLD +T G++++         L  +L +    RVY     G +      +  
Sbjct: 128 VPRAGIVHRLDKDTSGIMVVAKTLAAQNSLVNQLQARTVSRVYEAVVFGSLTGGGVVRAD 187

Query: 158 L-----NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +        K  ++  G         L  +  ++  +   L  G+  +I+
Sbjct: 188 IGRHPRQRTKMAVLAIGGKEATTHYRLIKRFNNHCHIRCMLETGRTHQIR 237


>gi|261880461|ref|ZP_06006888.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
 gi|270332800|gb|EFA43586.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bergensis DSM 17361]
          Length = 306

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 79/229 (34%), Gaps = 33/229 (14%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           D  +VQE  T   +  ++A     SR +++  +  + +KVNG  + R    ++    I V
Sbjct: 23  DNYVVQEESTL--LDWLLANLNE-SRTKIKATLKGRGIKVNGKQITRHDFPLVPGMKIAV 79

Query: 63  D----GVPLRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
                   L+        E   + +  K +G+++          V   L   F +     
Sbjct: 80  SKTKRNNTLKSRYVKIVYEDAYIIVVEKNVGILS-MPAGHHSLNVKAVLDEYFHKTKQPC 138

Query: 109 --ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLK 162
               V RLD +T GL++   D      L+         R Y     G ++QD+  ++   
Sbjct: 139 QAHVVHRLDRDTSGLMIYAKDKKTEFSLQADWKGTVYDRRYVAVVSGVMEQDEGTIDSWL 198

Query: 163 KG---------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           K              G  Y         +   ++ V   L  G+  +I+
Sbjct: 199 KDNKSYFSYSSSTDNGGKYAVTHFYTLDRSPQHSLVEFKLDTGRKNQIR 247


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/201 (15%), Positives = 69/201 (34%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +       V     P    E   +
Sbjct: 6   KLLSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTRFSVQKVEKPGVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +           +D L S F   + + RLD  T G++LL  +     +  
Sbjct: 66  LALFKPPFIES-----------YDLL-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
             + +     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKNRAVKKEYLALAQGIIEEE--REINAPILTFKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>gi|254796911|ref|YP_003081748.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           risticii str. Illinois]
 gi|254590147|gb|ACT69509.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           risticii str. Illinois]
          Length = 305

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 84/249 (33%), Gaps = 56/249 (22%)

Query: 15  RVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------- 61
           R+ K + R        S   +++ + ++ VK+N ++++ A+  V+  D +          
Sbjct: 12  RLDKYL-RDTFGPFPQS--ALQKALRKKAVKLNNVVVK-ASAAVLKGDSLTLSANFLQIL 67

Query: 62  -------------VDGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-L 101
                        VD   ++        E   +    KP G         G +T  DN +
Sbjct: 68  SSPREIPSDSSKVVDSKFVKFIASLMLYEDENVLAIDKPFGFPVQS--GYGITTSIDNAM 125

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL- 158
            SI      V RLD +T G+L+       AR L     +    + Y     G++ + K  
Sbjct: 126 KSINPEYRVVHRLDKHTTGVLIFAKTLDAARELWRLFSNRLVKKRYLAIVIGELKEKKGA 185

Query: 159 ------NLLKKGIV------IQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVF 205
                  +L KG        I    +   Q  +  +  + + + +  L  G+  +I+   
Sbjct: 186 VDCYINKVLFKGEEVMQCNHIGNGEHAITQFHVIKKFKNASLIELFPLT-GRKHQIRSQM 244

Query: 206 EFFNWKVNR 214
                 V  
Sbjct: 245 ASIGHPVLN 253


>gi|207091718|ref|ZP_03239505.1| hypothetical protein HpylHP_00901 [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 242

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 75/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENVSHKKAKALIDLGLVSIGGKKLMVARKELPKNTRFSVQKVEKPSVIFEDENV 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D L S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLL-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALIQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|90022196|ref|YP_528023.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus
           degradans 2-40]
 gi|89951796|gb|ABD81811.1| ribosomal large subunit pseudouridine synthase D [Saccharophagus
           degradans 2-40]
          Length = 321

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 82/243 (33%), Gaps = 42/243 (17%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           V +     R+ +V A      SR  +++ I   ++ V+    + A   V   +++ ++  
Sbjct: 11  VPQEMAGNRLDQVCADLFPDYSRSRIQQWIKSGKLLVDDKTGK-AKQKVFGGENLVLEPE 69

Query: 64  ----GVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
               G  L +        E   + + +K  GLV   +  +   T+ + L           
Sbjct: 70  LQEEGEWLPEPINLNIVYEDEHILVINKQAGLVVHPAAGNWSGTLLNGLLHHVPSLVNVP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           R   V RLD +T GL+++         L  +L +    R Y+   HG         L   
Sbjct: 130 RAGIVHRLDKDTTGLMVVAKSLPTQTHLVAQLQARTVSRHYQAVVHGTFAAKD--KLGT- 186

Query: 165 IVIQGICYGDMQVTLDTQKGSN----------------AWVTVGLREGKNREIKKVFEFF 208
           + I    +   +V +   + S                 A V + L  G+  +I+      
Sbjct: 187 VDIAIGRHPTQRVKMAALENSGKPAVTHYRVVKDLQGFAHVHLQLETGRTHQIRVHMAHI 246

Query: 209 NWK 211
            + 
Sbjct: 247 GYP 249


>gi|329667702|gb|AEB93650.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus johnsonii
           DPC 6026]
          Length = 299

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 90/250 (36%), Gaps = 46/250 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVM 55
           M+   +  EN TPQ++ + + + G       +R +         V VN       +  + 
Sbjct: 1   MQYFKLKFENKTPQKLGRFLLKNGF-----SKRALTNSQHHGGMVLVNHHR-RYTSYLLH 54

Query: 56  STDHIEV------DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D +        +   L+ +        E+    + +K  G+++  S  +    V + L
Sbjct: 55  AGDEVIFILGEEKENKWLKPSSKKLNIVFEQKDYLVINKDAGILSIPSRYEDSDAVVNRL 114

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPS-TQWLRVYRVRFHGQV 153
              F +          + RLD +T GL+L+  +             ++++ Y    HG  
Sbjct: 115 LHYFQQQKQTDLKPHVITRLDRDTSGLVLVGKNAVAHARFSKMEKNEFIKKYHAIVHGNF 174

Query: 154 DQDKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++ +               +K+G+V  G         LD  KG+ + + + L  G+  +I
Sbjct: 175 EEAQRQGTIDAPIGKIDTGVKRGVVNNGQRSVTKYRVLDQVKGA-SLIELQLLTGRTHQI 233

Query: 202 KKVFEFFNWK 211
           +   ++    
Sbjct: 234 RVHMQYLGHP 243


>gi|302333515|gb|ADL23708.1| RluA, Pseudouridylate synthases, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus JKD6159]
          Length = 273

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTVDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKETVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>gi|28199626|ref|NP_779940.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa Temecula1]
 gi|34395764|sp|Q87AR7|RLUD_XYLFT RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|28057741|gb|AAO29589.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa Temecula1]
          Length = 331

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 87/256 (33%), Gaps = 35/256 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLER---------AA 51
             +  V +    +R   V+A      SR  +   I    V +NG+L+             
Sbjct: 13  SRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVW 72

Query: 52  VNVMSTDHIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           + VM    I  D VP         E   +++ +KP GLV      +   T+ + L     
Sbjct: 73  LQVMPD--IRTDAVPQDIPLDILYEDEHVFVINKPAGLVVHPGAGNPDGTLVNALLHRDP 130

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH------GQ 152
                 R   V RLD +T G++++         L  +L S Q  R Y           G 
Sbjct: 131 ALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHRQYLAVVVSALVSGGT 190

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           V+       +  + ++    G   VT   L  +  ++  +   L  G+  +I+       
Sbjct: 191 VNAAIERHPRDRLRMEVSDTGKEAVTHYRLRERFRAHTALECRLDTGRTHQIRVHMAHLR 250

Query: 210 WKVNRLIRISYGPFQL 225
             +    R+  G  +L
Sbjct: 251 HPIVG-DRLYGGSLKL 265


>gi|188527777|ref|YP_001910464.1| hypothetical protein HPSH_05040 [Helicobacter pylori Shi470]
 gi|188144017|gb|ACD48434.1| hypothetical protein HPSH_05040 [Helicobacter pylori Shi470]
 gi|308062271|gb|ADO04159.1| hypothetical protein HPCU_05030 [Helicobacter pylori Cuz20]
          Length = 242

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 76/235 (32%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRALKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/237 (14%), Positives = 80/237 (33%), Gaps = 36/237 (15%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +D    + +   +R+   +  +    +R  ++++I Q+ + + G    ++   +   + I
Sbjct: 7   QDTIYAENSDKGKRLDAFVNESFDYLTRSYIQKLIEQRDIIIEGKEKNKSGNKLKGNEKI 66

Query: 61  EV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
            V              +P+ K  E   L + +K   +V   +  +   T+ + L      
Sbjct: 67  LVRIPEDEMLDIEPQDIPIEKVYEDKDLVVINKAPDMVVHPAPGNYSGTLVNALMHNIKD 126

Query: 107 --------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R   V RLD NT GL+++  +      L     +    + Y     G   + 
Sbjct: 127 LSNINGVIRPGIVHRLDKNTSGLIVIAKNDFSHLKLSDMFKNKDISKTYICICKGIFSEK 186

Query: 157 K--LNLLKKG---------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              +  L            +V +          +  + G  + V V +  G+  +I+
Sbjct: 187 TGRIENLIGRNPKNRKTMTVVQKNGKNAISNYKILDEAGDFSLVEVKIETGRTHQIR 243


>gi|302765707|ref|XP_002966274.1| hypothetical protein SELMODRAFT_168290 [Selaginella moellendorffii]
 gi|300165694|gb|EFJ32301.1| hypothetical protein SELMODRAFT_168290 [Selaginella moellendorffii]
          Length = 359

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 68/241 (28%), Gaps = 68/241 (28%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWL 77
           RR     I + ++++NG ++      + +   +     P  +           E   L  
Sbjct: 51  RR-----ILKGQIEINGEVVTSPDALIRNNASLVYHRFPWEEPSAPFMLEILYEDEHLLA 105

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLL------- 124
            +KP GL         + TV   L          +    V RL   T G+ +        
Sbjct: 106 INKPSGLQVLPGGLFQQRTVLSQLQWRVTDQVERNHPTPVHRLGRGTSGVYVCGTSLTKT 165

Query: 125 -----------------TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL------- 160
                            ++       +        +VYR    G V  DK+ +       
Sbjct: 166 FVYFKYLHFSGVLLCAKSDQARYRFEMLS------KVYRALVCGIVQDDKVIISIDQAIG 219

Query: 161 ------LKKGIVI---QGICYGDMQVTLDTQKGSNAWV-TVGLREGKNREIKKVFEFFNW 210
                 ++ G+ +   +G        TL      N+ V  V +  G+  +I+        
Sbjct: 220 RAHYPGVRGGLYMAVAKGKPSHSKVTTLKRNTEENSTVVEVEIFSGRAHQIRIHLASIGH 279

Query: 211 K 211
            
Sbjct: 280 P 280


>gi|283470219|emb|CAQ49430.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
          Length = 284

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQVHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|237734494|ref|ZP_04564975.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229382314|gb|EEO32405.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 328

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 76/260 (29%), Gaps = 70/260 (26%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           MK K  + EN   QR+ K + +  +            +M  ++ +KVNG  ++     + 
Sbjct: 7   MK-KLKITENDANQRIDKYLKKLLV----NAPNNFIYKMFRKKDIKVNGKKVDE-KYILS 60

Query: 56  STDHIE-------------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
             D +E                   V+       E   + +  KP GL+      +  +T
Sbjct: 61  LDDEVEMFLYDDKFKEFTETKSIYEVNRTFSVLYEDKHVLIVFKPAGLLVHEDANESINT 120

Query: 97  V-------------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL------ELP 137
           +              D           V RLD NT G+++    G     L         
Sbjct: 121 LTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIF---GKTLAALQNLNEMIKQ 177

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKG--IVIQ-------------GICYGDMQVTLDTQ 182
                + Y     GQ+          G  + ++             G    +  V     
Sbjct: 178 RHCIEKKYLTICRGQLSH---QRNLHGYMVKLENQAQVKLVKKDYPGALTMETIVRPLKY 234

Query: 183 KGSNAWVTVGLREGKNREIK 202
               + V V L  G+  +I+
Sbjct: 235 NCDYSLVEVTLITGRMHQIR 254


>gi|49484092|ref|YP_041316.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257425962|ref|ZP_05602386.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257428627|ref|ZP_05605025.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257431264|ref|ZP_05607641.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257433944|ref|ZP_05610302.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257436860|ref|ZP_05612904.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282904425|ref|ZP_06312313.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|282906248|ref|ZP_06314103.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282909167|ref|ZP_06316985.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911473|ref|ZP_06319275.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914645|ref|ZP_06322431.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M899]
 gi|282919611|ref|ZP_06327346.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282924991|ref|ZP_06332657.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|283958603|ref|ZP_06376054.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|293503717|ref|ZP_06667564.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510738|ref|ZP_06669443.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|293537280|ref|ZP_06671960.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|295428428|ref|ZP_06821057.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297590605|ref|ZP_06949243.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|49242221|emb|CAG40928.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|257271656|gb|EEV03802.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           55/2053]
 gi|257275468|gb|EEV06955.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           65-1322]
 gi|257278212|gb|EEV08860.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           68-397]
 gi|257282037|gb|EEV12174.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           E1410]
 gi|257284211|gb|EEV14334.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M876]
 gi|282313357|gb|EFB43753.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus C101]
 gi|282317421|gb|EFB47795.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           C427]
 gi|282321826|gb|EFB52151.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M899]
 gi|282325168|gb|EFB55478.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282327431|gb|EFB57726.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282331540|gb|EFB61054.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus Btn1260]
 gi|282596043|gb|EFC01007.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus C160]
 gi|283471121|emb|CAQ50332.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790752|gb|EFC29569.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Staphylococcus aureus subsp. aureus A017934/97]
 gi|290920125|gb|EFD97193.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus aureus subsp. aureus M1015]
 gi|291095383|gb|EFE25648.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466629|gb|EFF09150.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127828|gb|EFG57465.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           aureus subsp. aureus EMRSA16]
 gi|297575491|gb|EFH94207.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus MN8]
 gi|312437685|gb|ADQ76756.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|315195761|gb|EFU26148.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           CGS00]
          Length = 273

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTVDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKETVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>gi|328944704|gb|EGG38865.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK1087]
          Length = 290

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 75/204 (36%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG+ +      +   D I +               +G  + +  +
Sbjct: 28  RKIRHFLRTKKHVSVNGLSI-NWQTVIQPGDDICLIFDEEDYPQKTILLGNGELVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y     G+    KL           +  K+ +  +   Y +  VT
Sbjct: 147 PILNRLLEKREISREYCALVQGKFPSKKLIYKDKIGRDRHDRRKRLVDPRKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              Q G  + V   L+ G+  +I+
Sbjct: 207 RVKQFGQASLVKCQLKTGRTHQIR 230


>gi|241896391|ref|ZP_04783687.1| pseudouridylate synthase, 23S RNA-specific [Weissella
           paramesenteroides ATCC 33313]
 gi|241870371|gb|EER74122.1| pseudouridylate synthase, 23S RNA-specific [Weissella
           paramesenteroides ATCC 33313]
          Length = 297

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 30/158 (18%), Positives = 45/158 (28%), Gaps = 17/158 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN----LPSIFSRVISVGRLDINTEGLLLLTN 126
           E   L + +K  G+ T  + P    T+ +     L     R   V RLD  T G L++  
Sbjct: 90  ENDELMVVNKRKGVKTHPNSPGENGTMMNFAQAYLMKQDKRAYMVHRLDGQTTGALIIAK 149

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLN-LLKKG--------IVIQGICYGDM 175
              +  +L   L      R Y     G +        L  G          I G      
Sbjct: 150 VPYVVPILNQMLHDKTIKRTYLAWVDGHLTDSTGAITLAIGDHPTNSRLRQIDGANAKPA 209

Query: 176 QVTLDTQKG--SNAWVTVGLREGKNREIKKVFEFFNWK 211
                  K       V + L  G+  +I+         
Sbjct: 210 ITHWTKIKSVYQQTLVRLQLETGRTHQIRLHMAAIGHP 247


>gi|50545681|ref|XP_500379.1| YALI0B01276p [Yarrowia lipolytica]
 gi|49646245|emb|CAG82596.1| YALI0B01276p [Yarrowia lipolytica]
          Length = 337

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/165 (16%), Positives = 56/165 (33%), Gaps = 14/165 (8%)

Query: 63  DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTE 119
           D  P+R   E   L +  KP G+    +     ++V + L        +    RLD NT 
Sbjct: 105 DEKPIRIVFENDALVVVDKPGGIPVHPTGKYLFNSVKEILKHETGLEELYPAHRLDKNTT 164

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQG 169
           G+L+          +     S    + Y  R  G+    ++          +K+ +  + 
Sbjct: 165 GVLVFAKTSESVNHVTQQIMSRSAKKEYLARVKGRFPPGRVETHHPVVENTIKRNVQPKD 224

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
                 +V  D  +   + V      G+N +I++      + +  
Sbjct: 225 AHTAFERVAYDEHR-DLSIVRCLPSTGRNHQIRQHLLHLGYPIEN 268


>gi|330817148|ref|YP_004360853.1| Pseudouridine synthase RluD [Burkholderia gladioli BSR3]
 gi|327369541|gb|AEA60897.1| Pseudouridine synthase RluD [Burkholderia gladioli BSR3]
          Length = 398

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/174 (22%), Positives = 69/174 (39%), Gaps = 25/174 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           +V ++   +R+ K +A+     SR  ++  I +QRV+V+G   +     V     IE+  
Sbjct: 60  VVPDSLAGERLDKALAQLFPEFSRSRLQGWIDEQRVRVDGAPAK-VRQPVPLGATIELVP 118

Query: 63  -----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----- 105
                      + VPL    E   L +  KP GLV   +  +   T+ + L   +     
Sbjct: 119 DLLPEQLAFAPEPVPLSIVYEDEALVVIDKPAGLVVHPAAGNWSGTLLNGLLHRYGEAAA 178

Query: 106 --SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
              R   V RLD  T GL+++         L  +L +    R Y     G++ +
Sbjct: 179 GLPRAGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGRMPE 232


>gi|318057566|ref|ZP_07976289.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SA3_actG]
 gi|318081471|ref|ZP_07988794.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SA3_actF]
          Length = 313

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/175 (18%), Positives = 63/175 (36%), Gaps = 27/175 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   ++R    SR +   + A  +V+V+G ++ +       A + V     
Sbjct: 12  VPDGLEGERVDAALSRMFGFSRTKAAELAAGGKVQVDGSVVGKSERVRGGAWLEVEMPLA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S      TV   L +   R+   
Sbjct: 72  AAPVQIVAEPVEGMEIVHDDEDVVVIM-KPVGVAAHPSPGWTGQTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                   V RLD+ T GL+++         L+         + Y     G  D 
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQFRVRTVDKRYHTLVQGHPDP 185


>gi|227432332|ref|ZP_03914325.1| 23S rRNA pseudouridylate synthase RluD [Leuconostoc mesenteroides
           subsp. cremoris ATCC 19254]
 gi|227351938|gb|EEJ42171.1| 23S rRNA pseudouridylate synthase RluD [Leuconostoc mesenteroides
           subsp. cremoris ATCC 19254]
          Length = 299

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 35/194 (18%), Positives = 62/194 (31%), Gaps = 26/194 (13%)

Query: 43  NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNL 101
           NG ++        S D +  D  PL        WL   KP G+ T     D   T+ + +
Sbjct: 54  NGDIVTIVMPTEKSNDLVVPDYKPLDIIFENEHWLVVDKPYGITTVPGHADRLHTLVNQV 113

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHG 151
                 +         V RLD +T G++LL      A  +    L      + Y     G
Sbjct: 114 KGHLETIKADDLVPHVVTRLDRDTSGIVLLAKH-RFAHAVLDQQLQDHTVEKFYLAYPSG 172

Query: 152 -----------QVDQDKLNLLKKGIVIQGICYGD---MQVTLDTQKGSNAWVTVGLREGK 197
                       + +   + +K+ +   G        ++   +  + +   V V L  G+
Sbjct: 173 ILAYDHGDINAPIGRMDGDFIKREVRDDGKPSRTEYWVERRYEDDEQNMTRVKVQLHTGR 232

Query: 198 NREIKKVFEFFNWK 211
             +I+  F      
Sbjct: 233 THQIRVHFANIGHP 246


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 81/243 (33%), Gaps = 36/243 (14%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V +    QR+ K+ A      SR +++  +    + VN    E+A   V   D + ++ 
Sbjct: 108 TVTQEQAGQRIDKLAADMFTEHSRAQLQDWLKSGNLTVNDH-NEKAKYRVKIGDIVRLEA 166

Query: 65  VPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIF 105
              +               E   + + +KP+G+V      +   T+ + L       +  
Sbjct: 167 KLEQHGSDQPEDIKLDIIYEDDSVIVINKPVGMVVHPGAGNWSGTLVNGLLYHYPNQAHL 226

Query: 106 SRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG------------ 151
            R   V R+D NT GLL++  T    L    +L      R Y+    G            
Sbjct: 227 PRAGLVHRIDKNTSGLLVIGKTKAAQLELQEQLKDKSVYRHYQCVVAGDAPSLARQRTID 286

Query: 152 -QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             + + +    K  +   G       + +     + + + V L  G+  +I+        
Sbjct: 287 APIGRHRTQRTKMTVTSTGKTAITHIMKITPLSDTYSLLDVRLETGRTHQIRVHLSHIGH 346

Query: 211 KVN 213
            + 
Sbjct: 347 PII 349


>gi|88704640|ref|ZP_01102353.1| tRNA pseudouridine synthase C [Congregibacter litoralis KT71]
 gi|88700961|gb|EAQ98067.1| tRNA pseudouridine synthase C [Congregibacter litoralis KT71]
          Length = 255

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/166 (17%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L + +KP GL+   S  D + T F        I   V  V RLD  T GLL+   +  +A
Sbjct: 17  LVVINKPPGLLVHRSKIDRQETRFALQLLRDQIGQHVFPVHRLDKPTSGLLVFALNPEMA 76

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVD-----QDKLNLLKKGIVIQGICYGDMQ-------- 176
           + L       +  + Y     G           L   +  I  +                
Sbjct: 77  KRLADQFARREVSKQYLAVVRGYAPGHGTIDHALTEKRDPIADKRANTSKAPQEALTHYR 136

Query: 177 --------VTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   V +D   +   + V +    G+  ++++  +     + 
Sbjct: 137 RLAQIEWPVAVDRYPQARYSLVELRPHTGRKHQLRRHMKHIGHPII 182


>gi|306833402|ref|ZP_07466529.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus bovis ATCC
           700338]
 gi|304424172|gb|EFM27311.1| 23S rRNA pseudouridylate synthase RluD [Streptococcus bovis ATCC
           700338]
          Length = 296

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 71/215 (33%), Gaps = 46/215 (21%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGV------PLRK-----AERTRLWLYHKP 81
               + VNG + + A   +   D + +   D        P++       E     + +K 
Sbjct: 33  KGGNIWVNG-VEQNAIYLLNVGDVVTIEIPDEEEHETLVPVKHDLNIAYEDEHFLIINKS 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + +   +        +V  V RLD +T GL+L    G     L
Sbjct: 92  YGYASIPS-VLHSNTIANFVKYYYLEQNYPNKQVHIVTRLDKDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV--------------- 177
             +L +    + Y     G     K  L  KG +I  I   D  +               
Sbjct: 151 DKQLQNKTIEKRYYALVSG-----KGELADKGEIIAPIARSDDSIITRCVHPSGKYAHTS 205

Query: 178 -TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +  + G  A V + L  G+  +I+  F    + 
Sbjct: 206 YEVVARFGEVALVDIRLHTGRTHQIRVHFSHIGFP 240


>gi|82751504|ref|YP_417245.1| RNA pseudouridylate synthase [Staphylococcus aureus RF122]
 gi|82657035|emb|CAI81472.1| probable RNA pseudouridylate synthase [Staphylococcus aureus RF122]
          Length = 273

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTDDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTVDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKETVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>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 = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ +++   G   +R      I   RV+V G ++++A   V     IEV G P+    R
Sbjct: 6  IRLDQLLVERGYFPTRNRARAAILAGRVRVEGQVVDKAGAAVSPDARIEVAGDPIPYVSR 65

Query: 73 TRLWLYH 79
            L L H
Sbjct: 66 GGLKLEH 72


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

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 83/262 (31%), Gaps = 63/262 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V ++    R+ +         RR         ++++    +++V+G  +   +  +   
Sbjct: 7   TVSDDEADIRLDRWF-------RRHYPHLTQGALQKLCRTGQIRVDGGRVTT-STRLAPG 58

Query: 58  DHIEV-----------------DGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
             + V                 D   +R+  +  ++      + +KP G+          
Sbjct: 59  QAVRVPPIPQASRPAPVTHRTLDDRQVREIRKMVIYSDDQVIVLNKPAGIAVQGGPGITH 118

Query: 95  ST--VFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
               + D L       R   V R+D +T GLLLL    G+A  L     S    +VY   
Sbjct: 119 HIDGLLDGLREQPDDPRPRLVHRIDRDTSGLLLLARTPGVAAKLAASFRSRDVRKVYWAV 178

Query: 149 FHGQVDQDK------LNLLKKG----IVIQGICYGDMQ------VTLDTQKGSNAWVTVG 192
             G+           L  L  G    +V+ G    D          LD      +W+ + 
Sbjct: 179 TVGRPTPASGIVDQPLTRLGAGAGAIMVVAGRRDKDAVHALSEYEVLDAAGRKLSWLALS 238

Query: 193 -LREGKNREIKKVFEFFNWKVN 213
            L  G+  +++   E     + 
Sbjct: 239 PLT-GRTHQLRVHCEALGTPIL 259


>gi|294625341|ref|ZP_06703977.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
 gi|292600359|gb|EFF44460.1| pseudouridylate synthase [Xanthomonas fuscans subsp. aurantifolii
           str. ICPB 11122]
          Length = 328

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 50/288 (17%), Positives = 98/288 (34%), Gaps = 61/288 (21%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E+   QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +   
Sbjct: 21  VPEDRAGQRLDNFLLGQLRGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 63  ----DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
               +G                   E  RL   +KP G+ +            T+    P
Sbjct: 80  RTNDEGDKAAPPSSFMARLEAAIVFEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QSLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVEGRGITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMTVDAPLHIGLRQGGERHVQVNAIGKPSLSHFRLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
              +     V             G    G   +V+K+ LR+QLG   L
Sbjct: 258 VHAQHLGHPVA------------GDDKYGEA-DVNKR-LRDQLGLKRL 291


>gi|184155038|ref|YP_001843378.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|227514836|ref|ZP_03944885.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|260663582|ref|ZP_05864471.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|183226382|dbj|BAG26898.1| pseudouridine synthase [Lactobacillus fermentum IFO 3956]
 gi|227086826|gb|EEI22138.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus fermentum
           ATCC 14931]
 gi|260551808|gb|EEX24923.1| pseudouridine synthase [Lactobacillus fermentum 28-3-CHN]
 gi|299783021|gb|ADJ41019.1| Pseudouridine synthase [Lactobacillus fermentum CECT 5716]
          Length = 296

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 29/202 (14%), Positives = 58/202 (28%), Gaps = 41/202 (20%)

Query: 38  QRVKVNGILLE-----RAAVNV-------MSTDHIEVDGVPLRKA-ERTRLWLYHKPIGL 84
            ++++N  +            V        +   I V       A E     + +K  G+
Sbjct: 37  GQMRINDRVAWAIDQVEPGDVVYLVVPNEPANPTITVSDQTFEIAYEDEDFLVINKEAGV 96

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV-----------ISVGRLDINTEGLLLLTNDGGLARV 133
            T    P     V D+L +                    RLD +T GL++       A  
Sbjct: 97  ATV---PAHHVAVQDSLVNRVKGYYQRQNYPNQVTHVATRLDKDTSGLVVFPKH-RFAHA 152

Query: 134 LELPSTQ---WLRVYRVRFHGQVD----------QDKLNLLKKGIVIQGICYGDMQVTLD 180
           +     +     + Y     G++           +   +   K +V         +   +
Sbjct: 153 VLDRQLKARQVKKEYLAMVQGRLTVSHGYIDAPIRRDPDSFVKRLVAPDGKASATEYWCE 212

Query: 181 TQKGSNAWVTVGLREGKNREIK 202
               + + V V L  G+  +I+
Sbjct: 213 RVTDTTSLVRVRLHTGRTHQIR 234


>gi|303327488|ref|ZP_07357929.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio sp.
           3_1_syn3]
 gi|302862428|gb|EFL85361.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio sp.
           3_1_syn3]
          Length = 241

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/173 (20%), Positives = 63/173 (36%), Gaps = 29/173 (16%)

Query: 75  LWLYHKPIGL----VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +W   KP GL     T HSD      + D+      +     RLD +T G+LL+      
Sbjct: 8   VWALFKPAGLPTHPGTGHSDSLATR-LADHYAQAAFKPTPAHRLDKDTSGILLVAATFSA 66

Query: 131 ARVL--ELPSTQWLRVYRVRFHG--QVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQK- 183
            R L   +     ++ Y V   G     + +L  + L+KG+  +G       +T   ++ 
Sbjct: 67  LRELQEAIRQRSLIKEYVVWVRGRWPWPEARLLRHQLRKGLE-RGFEKMRAVLTAAGEER 125

Query: 184 --------------GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
                          + + + + L  G+  +I+         V  L  + YGP
Sbjct: 126 ALEALCLARPLRICENESLLLIRLFTGRTHQIRVQLASLGHPV--LGDVKYGP 176


>gi|227499078|ref|ZP_03929215.1| hemolysin A [Acidaminococcus sp. D21]
 gi|226904527|gb|EEH90445.1| hemolysin A [Acidaminococcus sp. D21]
          Length = 266

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 27/71 (38%), Gaps = 2/71 (2%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+   +   G+  SR + + +I    V V+   +++    V     I + G  L  
Sbjct: 1  MKKERLDLFLVEQGLFESRSKAQAVIMAGEVLVDDQKIDKPGTMVKPDAKITLLGKKLPF 60

Query: 70 AERTRLWLYHK 80
            R    L +K
Sbjct: 61 VSRGGYKL-NK 70


>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 = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 82/233 (35%), Gaps = 38/233 (16%)

Query: 7   VQENFT-PQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           ++EN     R+ K +  R    SR + + +I Q  V +NG  ++     +   D IE   
Sbjct: 26  IEENIDDSIRLDKYMGDRFSYYSRNKWQDLIGQGLVLLNGKKVKYTRT-INKGDEIEYHI 84

Query: 64  -GVPLRKAERTRLWLY--------HKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGR 113
            G+   + ++    +Y        +KP  L    S     +T+   +  + +  +  + R
Sbjct: 85  IGMKEPEVDKNVTIIYDDGDLIIANKPANLPVIPSGKYYHNTLHTIVKQMLNCNINMLNR 144

Query: 114 LDINTEGLLLLTNDGGLARVL-------ELPSTQWLRVYRVRFH--GQVDQDKLN---LL 161
           +D  T G ++++     A          +    +  + Y         ++ + +    +L
Sbjct: 145 IDRETSGCVVMSRGHETASKFCAMIARRKNTKKKIKKTYIAVVENAKNIEDNFIVEGYML 204

Query: 162 KKGIV------------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + G              I+G  Y         + G  A V   L  G+  +I+
Sbjct: 205 ESGHEYYRRFQTLHKENIEGSKYSKTAFKTIKRLGDYAIVMARLYTGRMHQIR 257


>gi|169838827|ref|ZP_02872015.1| hemolysin A [candidate division TM7 single-cell isolate TM7a]
          Length = 81

 Score = 57.9 bits (139), Expect = 3e-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|332305526|ref|YP_004433377.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
 gi|332172855|gb|AEE22109.1| pseudouridine synthase [Glaciecola agarilytica 4H-3-7+YE-5]
          Length = 252

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 58/171 (33%), Gaps = 29/171 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   +   HKP GL+   S  D          L       V  V RLD  T G+L+    
Sbjct: 8   QDEFIVAIHKPAGLLVHRSMIDRHETQFAMQLLRDQIGQHVFPVHRLDRPTSGVLVFALS 67

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD---------QDKLNLLK----------KGIV 166
             +AR+L  +  +    + Y     G V          ++KL+ +           +   
Sbjct: 68  ADIARILGEQFAANTVSKTYFAIVRGHVKAPGFIDYALKEKLDKIADKRANQDKDPQEAQ 127

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVG-LR--EGKNREIKK-VFEFFNWKVN 213
            + +     ++     +  +A  T+  L    G+  ++++ +    N  + 
Sbjct: 128 TEFVPIKQFELPFAVSRYPSARYTLVKLHPKTGRKHQLRRHMC-HINHPIV 177


>gi|294011927|ref|YP_003545387.1| ribosomal large subunit pseudouridine synthase D [Sphingobium
           japonicum UT26S]
 gi|292675257|dbj|BAI96775.1| ribosomal large subunit pseudouridine synthase D [Sphingobium
           japonicum UT26S]
          Length = 320

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 78/250 (31%), Gaps = 47/250 (18%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDH 59
            + E     R+ K +A      SR  ++ +IA+ +V   G           ++ V +   
Sbjct: 11  TIGEAQDGMRLDKALAELVPDLSRERLKALIAEGQVT--GRPAHAGRSPNPSMKVAAGQA 68

Query: 60  IEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIF 105
             +              +PL    E   L +  KP GLV   +  +   T+ +  L    
Sbjct: 69  FAIVLPPPMEAEAVAQDIPLAIVHEDADLIVIDKPAGLVVHPAAGNLDGTLVNALLHHCQ 128

Query: 106 SRVISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV- 153
            R+  +G         R+D +T GLL++         L     +    R+Y    +G   
Sbjct: 129 GRLSGIGGVARPGIVHRIDKDTSGLLVVAKSDRAHEGLAQQFKAHSIDRLYAAIVYGVPQ 188

Query: 154 ------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                              +      +G        T++  +G+ A V   L  G+  ++
Sbjct: 189 PAAGTVDSWIGRSDADRKKMAVHREGRGKHAVTHYRTMERLRGA-AMVECRLETGRTHQV 247

Query: 202 KKVFEFFNWK 211
           +         
Sbjct: 248 RVHMAHLGHP 257


>gi|210135145|ref|YP_002301584.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori P12]
 gi|210133113|gb|ACJ08104.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori P12]
          Length = 242

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 79/235 (33%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENVSHKKAKALIDLGLVSIGGKKLMVARKELPKNTRFSVQKIEKPSVIFEDENV 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +           +D + S F   + + RLD  T G++LL  +     +  
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKDWVLLHRLDKETSGVVLLVKENSEFHLKA 113

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
             + +     + Y V   G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKNRAVKKEYLVLAQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>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 = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/200 (19%), Positives = 67/200 (33%), Gaps = 26/200 (13%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWL 77
           R   +      R+ VNG  +      + + D +E         +  +P+R  +E   L++
Sbjct: 100 RNYAKIACKMGRIYVNGEQMTDVDYVMRNGDRVEHWAHRHEHPIRDLPIRVISETDDLFV 159

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA--RV 133
             KP  L           TV   L     R  +  + RLD  T G+LL   +        
Sbjct: 160 VEKPPSLPVHTCGQYAIHTVLGQLRVNEGRTGLRVLHRLDRATSGVLLFAKNYETDLEFK 219

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKGIV---IQGICYGDMQVTLDTQ 182
             L   +W + Y  +  G    ++          ++  GI      G         L   
Sbjct: 220 TTLKQGEWSKEYICKVDGVFPDEEQVCEQPIGPLVISMGIQCVRPDGKDAKSRFRKL-WS 278

Query: 183 KGSNAWVTVGLREGKNREIK 202
            G+ + V V +  G+  +I+
Sbjct: 279 DGTQSVVQVHIETGRTHQIR 298


>gi|310766621|gb|ADP11571.1| tRNA pseudouridine synthase C [Erwinia sp. Ejp617]
          Length = 265

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 59/167 (35%), Gaps = 29/167 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V +V RLD  T G+LL+     +A
Sbjct: 11  LVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLMALSSEVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHG----------QVDQDK---LNLLKKG--------IVIQ 168
           R+L       Q  + Y     G           + +++    +   +            +
Sbjct: 71  RLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEEQDKIADKFSQPEKAPQPAVTHWR 130

Query: 169 GICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKK-VFEFFNWKVN 213
           G+   ++ V +   Q    + V +    G+  ++++ +       + 
Sbjct: 131 GVATAELPVPVGRYQTSRYSLVEMLPESGRKHQLRRHMT-HLRHPII 176


>gi|188589626|ref|YP_001921981.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251780373|ref|ZP_04823293.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188499907|gb|ACD53043.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243084688|gb|EES50578.1| pseudouridine synthase, RluA family [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 322

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/265 (13%), Positives = 83/265 (31%), Gaps = 67/265 (25%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + ++ ++VNG         + 
Sbjct: 2   KIEIGANEAGQRLDKFL-------RKLLKDVPLSAIFKALRKKDIRVNGKKQSE-KYFLE 53

Query: 56  STDHIEVDGVPLRKAERTRLWLYH-----------------KPIGLVTTHSDPDGRSTVF 98
             D +E+  +     ++ +    +                 K  G++      +   T+ 
Sbjct: 54  EGDIVEIKYIKSNPEKKEKFIQVNFSGMKTAYEDENLLVVEKWPGILVHPDKDEKDPTLT 113

Query: 99  DNLPSIFSRVI-------------SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLR 143
           D + S                      RLD NT GL++   T +G  +    +   +  +
Sbjct: 114 DYVLSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRVRK 173

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYG---------------DMQVTLDTQKGSNAW 188
            Y     G+V       L  G +++                     M+VT     G+ + 
Sbjct: 174 YYVALVKGKVQDG----LHTGYILKNQDTNISKVYEKEVPDSKKIAMEVTTTQTNGAYSL 229

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           + + L  G++ +I+         + 
Sbjct: 230 LEINLITGRSHQIRAHLAHLGSPII 254


>gi|329889168|ref|ZP_08267511.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
 gi|328844469|gb|EGF94033.1| pseudouridine synthase, RluA family protein [Brevundimonas diminuta
           ATCC 11568]
          Length = 331

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 56/296 (18%), Positives = 90/296 (30%), Gaps = 70/296 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRR-------EVERMIAQQRVKVNGILLER-------AAV 52
           V E+    R+ +         RR       +VE+M    +++V+G  ++        AAV
Sbjct: 10  VAEDEDDIRLDRWFK------RRWPHLTHIQVEKMARSGQIRVDGSRVKPQDRLTAGAAV 63

Query: 53  NVMS---------TDHIEVDGVPLRKA------ERTRLWLYHKPIGLVTT--HSDPDGRS 95
            V            D  E+    +  A      E   +   +KP GL             
Sbjct: 64  RVPPLPDANPRKPGDLHELSERDIAYAKSLVLYEDHMVIALNKPHGLAVQGGTKTTKHID 123

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
            +         R   V RLD +T G+LLL      A+ L       Q  + Y     G  
Sbjct: 124 RLLSAWGEGMDRPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWAIVIGNP 183

Query: 154 DQD----KLNLLKKGI------------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                   + L K GI              +G        T+       AW+ +    G+
Sbjct: 184 KPSAGQIDMALKKTGINDFEMMRPAEPKDPKGEPAETAFATISRAAHRAAWMALRPFTGR 243

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG--STREVSKKILREQLGPHLLE 251
             +++         +            LG    G   +RE+S   L+ QL    +E
Sbjct: 244 THQLRAHMAAIGHPI------------LGDPKYGDDKSRELSG-PLKLQLHARRIE 286


>gi|326575127|gb|EGE25055.1| tRNA pseudouridine synthase C [Moraxella catarrhalis CO72]
          Length = 258

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 48/166 (28%), Gaps = 29/166 (17%)

Query: 76  WLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP  ++   S  D      V   L +     V  V RLD  T G+L+   D   A 
Sbjct: 27  VIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVFALDSQTAG 86

Query: 133 VLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGDMQVT 178
           +L          + Y     G +                 +              D QV 
Sbjct: 87  LLAKQFEDHHIQKSYLAVVRGIIGAGRIDYALKPRLDKIADKFSNPNKASKSAITDYQVL 146

Query: 179 LDTQKG----------SNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
             TQ+             + V +  +  G+  ++++  +     + 
Sbjct: 147 ATTQQPFISCRRFDSSRYSLVRLTPIT-GRKHQLRRHMKHIFHPIV 191


>gi|110833337|ref|YP_692196.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
 gi|110646448|emb|CAL15924.1| pseudouridylate synthase [Alcanivorax borkumensis SK2]
          Length = 323

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 80/229 (34%), Gaps = 35/229 (15%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           V+     QRV +V A    G  SR  ++  I    + VNG    +    +   + +    
Sbjct: 15  VKPEHAGQRVDQVAAELFEGF-SRSRLQTWIKNGVLTVNGAQ-TKPKEKLTGNESLTLEV 72

Query: 61  ----EVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
               E+D  P               + +KP GLV   +      T+ + L  +  R+ S 
Sbjct: 73  EIEPELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAGHADGTLLNGLLHLDERLNSL 132

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQV 153
                V RLD +T GL+++       + L  +L      R Y                 +
Sbjct: 133 PRAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVGVMTGGGKVDAPM 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  ++  K+ +V  G         +  +  ++  + V L  G+  +I+
Sbjct: 193 GRHPVDRKKQAVVKTGGKNAVTHYRVLDRYRAHTRIQVQLETGRTHQIR 241


>gi|116511223|ref|YP_808439.1| pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
 gi|116106877|gb|ABJ72017.1| Pseudouridylate synthase, 23S RNA-specific [Lactococcus lactis
           subsp. cremoris SK11]
          Length = 293

 Score = 57.9 bits (139), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/233 (15%), Positives = 81/233 (34%), Gaps = 48/233 (20%)

Query: 20  IARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHIEV------------ 62
           + R GI SRR    ++ +      ++ VNG + + A  ++   D + +            
Sbjct: 18  LGRQGI-SRR----LLTKVKFDGGKIMVNG-IEKTAIYHLEKGDLVTITVPDEPDNEKLI 71

Query: 63  -DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGR 113
            D VPL    E     +  KP G  +          + + +    SR       V  + R
Sbjct: 72  PDDVPLNVLFEDDHYLVVEKPAGKASITGSLHPTGAMSNAVKGYISRKNYPNQTVHIITR 131

Query: 114 LDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRFHG-----------QVDQDKLN 159
           LD +T G++ L      A  L +         + Y    +             + +   +
Sbjct: 132 LDRDTSGIMFLAKH-RYAHALMVQHKFRETLEKRYYAIINDGDLPDSGQIDLPIGRRDDS 190

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
           ++++ +         +   + T++ ++ A + + L  G+  +I+  F    + 
Sbjct: 191 IIERQVRFDEKSKNALTSYVVTERKNDLALLDIILHTGRTHQIRVHFSHLGYP 243


>gi|160942600|ref|ZP_02089845.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446079|gb|EDP23082.1| hypothetical protein FAEPRAM212_00074 [Faecalibacterium prausnitzii
           M21/2]
          Length = 316

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 104/316 (32%), Gaps = 76/316 (24%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI----------- 60
           TP R++K +                + ++K+NG   +  +  VM+ D I           
Sbjct: 26  TPGRLNKAL---------------RENKIKLNGKK-QPLSTRVMAGDEIKLFILDDVLDA 69

Query: 61  --EVDGVPLRKAERT--------RLWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSR 107
              V+G   + A           ++ + +KP G+     + D    R+ ++ N    +  
Sbjct: 70  DRRVEGPAWKNARTPAQVVYDCPQILIVNKPAGVAVDGPEDDTLLNRALLYLNKQGEYKE 129

Query: 108 VI-----SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYR-VRFHGQVDQDK-- 157
                     RLD  T GL+++  T +     +  + + +  + Y  V F   +  D   
Sbjct: 130 NDLYTPALCHRLDTGTSGLVIIAKTPEAEELFLSAIKNREVQKTYLCVTFGRPMPPDATL 189

Query: 158 ----LNLLKKGIV--IQGICYGDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEF 207
               L    +GIV  ++    G  +V    +     G  A + V L  G+  +I+     
Sbjct: 190 GGYLLKDADRGIVKIVEDKQPGAKEVETRYETIAVSGRLALLKVQLITGRTHQIRAHMAS 249

Query: 208 FNWKVNRLIRISYGPFQLGTLLAG---STREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
               +            LG    G   + RE+  K  +      L        D    S 
Sbjct: 250 IGCPI------------LGDSKYGNNSANRELKLKY-QALCAWELTMPRFTQPDFAFLSG 296

Query: 265 ETLVRDRPNIISEVPD 280
           +T    +P    +V D
Sbjct: 297 KTFHAPKPWYYQQVLD 312


>gi|325108531|ref|YP_004269599.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324968799|gb|ADY59577.1| pseudouridine synthase, RluA family [Planctomyces brasiliensis DSM
           5305]
          Length = 336

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 54/320 (16%), Positives = 114/320 (35%), Gaps = 69/320 (21%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+   ++      SR + ++ I    ++VNG         V  +  + + G  +      
Sbjct: 26  RLDAWLSSHSAGHSRSQWQKAIQAGEIRVNGQ-------KVKPSYRLRI-GEKISGQLKV 77

Query: 71  -----------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---- 109
                            +   L + +KP  L+      +   T+ + L   F+++     
Sbjct: 78  VAAPVVAPAPIALDILYQDEHLVVVNKPAHLIVHPGKANYGGTLANALVHHFNQLSETGG 137

Query: 110 -----SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV--DQDKLN- 159
                 V RLD +T G++++  +  +   L          + YR    G+V  D D +  
Sbjct: 138 EHRPGIVHRLDRDTSGVIVIALNNRVHENLSAQFADRTVEKEYRAIVWGKVEFDADIIET 197

Query: 160 ------LLKKGIVIQGICYGDMQV-----TLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                   ++ +++ G      Q      TL+  +G  +++ +  + G+  +++   ++ 
Sbjct: 198 HVRTHSKHREKMIVCGPDPEARQATTFYETLERFRGF-SYLKLLPKTGRTHQLRVHLQYL 256

Query: 209 NWKVNRLIRISYGP---FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
              +    R+ YG      L  LL       SK+ + E     +L E Q      +  + 
Sbjct: 257 RHPIVA-DRL-YGGHPQLALSELLE------SKEHMTE---DRVLIERQALHAHRLQFTH 305

Query: 266 TLVRDRPNIISEVPDDFTRM 285
            +  +R   IS +PDD  R 
Sbjct: 306 PVTEERVEFISPIPDDMQRT 325


>gi|126461165|ref|YP_001042279.1| RluA family pseudouridine synthase [Rhodobacter sphaeroides ATCC
           17029]
 gi|126102829|gb|ABN75507.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 346

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/157 (21%), Positives = 51/157 (32%), Gaps = 33/157 (21%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------- 74
           VE+M    +V+V+G   + A+  V     I V   PL   +  R                
Sbjct: 34  VEKMCRTGQVRVDGARAK-ASDRVAEGMEIRV--PPLPDPDAPRPQASRVTKSDEQMIQD 90

Query: 75  --------LWLYHKPIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLL 122
                   + + +KP GL +      G   V             R   V RLD +T G+L
Sbjct: 91  CVIYRDNDIIVLNKPPGLPSQGGSGQGERHVDGLTEALKFGYKERPKLVHRLDKDTSGVL 150

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
           +L     +AR L          ++Y     G     +
Sbjct: 151 VLARTDRVARALSESFRHRNTRKIYWALVAGVPSPKQ 187


>gi|257458419|ref|ZP_05623561.1| ribosomal large subunit pseudouridine synthase C [Treponema
           vincentii ATCC 35580]
 gi|257444223|gb|EEV19324.1| ribosomal large subunit pseudouridine synthase C [Treponema
           vincentii ATCC 35580]
          Length = 240

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/145 (20%), Positives = 46/145 (31%), Gaps = 13/145 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   L + +KP G+                   + S +  V RLD  T GLL+       
Sbjct: 18  EDEALCIVNKPYGIPVQGGAHISVCLTEILSKQLGSEIFPVHRLDKETSGLLVTAKSADA 77

Query: 131 AR--VLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGI----VIQGICYGDMQ--V 177
           AR       S    + Y     G  +          LL +GI    V++           
Sbjct: 78  ARSCRALFESQAVEKEYLALCFGGFEPSAHKKPVKKLLPEGIIDTPVVENGSPKPASSAY 137

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            L     + +  +V L  G+  +I+
Sbjct: 138 KLLASTDAYSLFSVRLHTGRMHQIR 162


>gi|282600856|ref|ZP_05979923.2| pseudouridine synthase, RluA family [Subdoligranulum variabile DSM
           15176]
 gi|282571159|gb|EFB76694.1| pseudouridine synthase, RluA family [Subdoligranulum variabile DSM
           15176]
          Length = 320

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 74/242 (30%), Gaps = 51/242 (21%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKA--------------- 70
           R  + +    +R+KVNG         + + D IE  ++                      
Sbjct: 28  RSMMYKAFRNKRIKVNGKRA-EPDTRLCTGDVIEMYINDEFFPAHTGTSKPKPPRRQPPV 86

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----------PSIFSRVIS--VGR 113
               E     + +KP  L+  H D  G   + D             P    R       R
Sbjct: 87  TIVYEDENFAVLYKPAHLLC-HRDRTGDPNLVDAFAAYLEAKGEYNPHAEQRFAPALCNR 145

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR-VRFHGQVDQDKLNLLKK-----GI 165
           LD  TEGL+L        R L   + +    + Y  +          +  L+       +
Sbjct: 146 LDRGTEGLVLAAKTYQALRDLNEIIRTDLMKKEYLTITVGAPPAGRHIAWLQHSEKNNKV 205

Query: 166 VI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISY 220
            I     +G       VT+  Q G  A   +GL  G+  +I+    +    V  L  I Y
Sbjct: 206 RIHARQSEGYKQIITDVTVIRQSGPFALCRIGLITGRTHQIRAHLSYLGHPV--LGDIKY 263

Query: 221 GP 222
           G 
Sbjct: 264 GN 265


>gi|220912349|ref|YP_002487658.1| pseudouridine synthase [Arthrobacter chlorophenolicus A6]
 gi|219859227|gb|ACL39569.1| pseudouridine synthase, RluA family [Arthrobacter chlorophenolicus
           A6]
          Length = 308

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 88/254 (34%), Gaps = 49/254 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-----SRREVERMIAQQRVKVNGILLERAAVNVM 55
           M ++ IV E +   R     A AG+A     SR     +IA+  V   G  L ++A  + 
Sbjct: 1   MPEQIIVTEEYGGTR-----ADAGLAAIMGISRSAAAALIAEGHVISRGKALGKSA-KLA 54

Query: 56  STDHIEV------DGVPLRKA--ERTRLWL-------YHKPIGLVTTHSDPDGRSTVFDN 100
           + D +EV      D + + +   E  ++ L         KP+G+    S      TV   
Sbjct: 55  AGDTLEVTIPERRDPLEVVEEIVEGLKILLDDDDFVVVDKPVGVAAHPSPGWVGPTVVGG 114

Query: 101 LPSIFSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRF 149
           L     R+           V RLD+ T G++++         L+    +    +VY    
Sbjct: 115 LAGAGYRISTSGSPERAGIVHRLDVGTSGVMVVAKSERAYTALKRAFKERTVDKVYHAVV 174

Query: 150 HGQVDQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
            G  D     ++           +  +  +G         L+   G  + V V L  G+ 
Sbjct: 175 QGLPDPLTGTIDAPIGRHPGHDWRFAVTEEGRPSVTHYEVLEA-FGKASLVEVHLETGRT 233

Query: 199 REIKKVFEFFNWKV 212
            +I+  F       
Sbjct: 234 HQIRVHFSALRHPC 247


>gi|116334307|ref|YP_795834.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116099654|gb|ABJ64803.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 294

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/230 (16%), Positives = 73/230 (31%), Gaps = 38/230 (16%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRK 69
           + + +   GI S R    +  Q  ++VNG  +   AV +   DH+ V          +  
Sbjct: 14  LKRFLTNQGI-SHRVFSDLKQQGTIRVNGQ-VTTPAVTLAVGDHVAVTFPPETADEAVAV 71

Query: 70  AERTRLWLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------RL 114
           +      L+         KP GL       +   T+ + +   +    +         RL
Sbjct: 72  SHEPITVLFENRDWLVVDKPAGLNVVPGPANRTDTLVNRIKGYWEAEHAENLVPHILTRL 131

Query: 115 DINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDKL---NLLK------ 162
           D  T G++       LA  L      + Q  + Y     G+++ D       L       
Sbjct: 132 DRFTSGVV-WVARHRLANSLASQLQAAHQIDKRYLAVVSGRLEADHAVIDAPLASDPTGY 190

Query: 163 -KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            + +   G      +  +  +  +   V V L  G+  +I+  F      
Sbjct: 191 NQMVSPTGKPART-EYWVQQRFATATVVAVKLHTGRTHQIRAHFASLGHP 239


>gi|294497315|ref|YP_003561015.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium QM B1551]
 gi|294347252|gb|ADE67581.1| Ribosomal large subunit pseudouridine synthase D [Bacillus
           megaterium QM B1551]
          Length = 303

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 55/161 (34%), Gaps = 20/161 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLL 124
           E   + + +KPI L T  S    + T+ + + + F ++        V RLD +T G +L 
Sbjct: 88  EDEHVLIVNKPINLDTHPSSEQDQKTLLNAVAAYFQKIGLKTKPRHVHRLDSDTSGAILF 147

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGIC 171
           T     + V    L   +  R Y     G + ++             +  ++ +   G  
Sbjct: 148 TKHFVASSVFDQLLAERKINRTYIALVQGIIKKEDGIINEPIGRDRHHATRRRVSRTGQA 207

Query: 172 YGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
                  L      N   + + L  G+  +I+       + 
Sbjct: 208 AKTRYRVLKRNTAKNETLIELSLETGRTHQIRVHMSHIGYP 248


>gi|222823998|ref|YP_002575572.1| ribosomal large subunit pseudouridine synthase [Campylobacter lari
           RM2100]
 gi|222539220|gb|ACM64321.1| putative ribosomal large subunit pseudouridine synthase
           [Campylobacter lari RM2100]
          Length = 250

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 71/202 (35%), Gaps = 33/202 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----ERT 73
           K++A     S    + +I +  V   G  +  A   + S     V    ++KA    E  
Sbjct: 7   KLLAMQEKISNNAAKDLIDKGCVFAMGKKVVIARALMSSKTRFVV--QKIKKAKILFEDD 64

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           ++   +KP G ++            +NL  +++  + + RLD  T G+LLL+ D      
Sbjct: 65  KIIALNKPYGEIS------------ENLEDVYNAKL-INRLDKETSGVLLLSKDEEFRLK 111

Query: 134 LELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----------MQVTLD 180
                 +    + Y     G + ++ L + +K   I+                  QV   
Sbjct: 112 CIQEYKKQNVYKSYLAIVDGVIAEE-LEICEKITTIKNKSGAFSKIDKFGLEAHTQVVPL 170

Query: 181 TQKGSNAWVTVGLREGKNREIK 202
                   +   ++ G+  +I+
Sbjct: 171 MVNAKKTLIKAIIKTGRTHQIR 192


>gi|210615565|ref|ZP_03290663.1| hypothetical protein CLONEX_02881 [Clostridium nexile DSM 1787]
 gi|210150232|gb|EEA81241.1| hypothetical protein CLONEX_02881 [Clostridium nexile DSM 1787]
          Length = 323

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 57/343 (16%), Positives = 108/343 (31%), Gaps = 86/343 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVER-----MIAQQRVKVNGILLERAAVNVMSTDHI 60
           IV  N   QR+ K++A+       E  +     M+ ++ + +NG         +   D +
Sbjct: 5   IVAANEAGQRLDKMLAKYL----NEAPKSFLYKMLRKKNIVLNGKKAT-GNEKLAVGDSV 59

Query: 61  EV--DGVPLRK----------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           ++      + K                 E   + L +KP+G+++  +  D  S V   + 
Sbjct: 60  KLFLADETIAKFSNIHAVHTNVTLDIIYEDENVLLINKPVGMLSQKAAADDESLVEHIIS 119

Query: 103 SIFS------------RVISVGRLDINTEGLLLLTNDGGLARVLELPST-----QWLRVY 145
            +              R     RLD NT GL+     G     L+   T        + Y
Sbjct: 120 YMLETRQLTEEELRKFRPSVCNRLDRNTSGLVAA---GKSLAGLQEMGTLFKNRSLRKYY 176

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---------------KGSNAWVT 190
           R    G+V   +      G +++      + V+   +                G   ++ 
Sbjct: 177 RCLVAGEVKHSQS---VSGYLVKDEKTNKVTVSKAEKGDCLPIETEYEPLWSNGKYTYLE 233

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLGP 247
           V L  G+  +I+       + +                  G  +  SKK+   L+EQ G 
Sbjct: 234 VHLITGRTHQIRAHLASIGYPII-----------------GDYKYGSKKVNDRLKEQYGL 276

Query: 248 HLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSS 290
                    L+ P  + E         ++ +P  F  + K   
Sbjct: 277 KSQLLHAYRLEMPACTGELSNLSERKFVAPLPKLFQNILKAEK 319


>gi|119471760|ref|ZP_01614120.1| tRNA pseudouridine synthase C [Alteromonadales bacterium TW-7]
 gi|119445383|gb|EAW26671.1| tRNA pseudouridine synthase C [Alteromonadales bacterium TW-7]
          Length = 254

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/166 (18%), Positives = 47/166 (28%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
               +KP GL+   S  D          L       V  V RLD  T G+LL       A
Sbjct: 22  FVAINKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLFALSSEAA 81

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R +          + Y     G             ++L+ +      Q     +      
Sbjct: 82  RDMNQLFIEGTIAKRYLALVRGFAPDSVFLDKPLKEELDKIADKFADQNKAPQEAQTQFN 141

Query: 176 ---QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
              Q  L    G    V   L E     G+  +I++  +  +  + 
Sbjct: 142 CLYQAALPIPIGKYPTVRYSLVECFPKTGRKHQIRRHLKHLSLPII 187


>gi|294893081|ref|XP_002774329.1| hypothetical protein Pmar_PMAR007910 [Perkinsus marinus ATCC 50983]
 gi|239879651|gb|EER06145.1| hypothetical protein Pmar_PMAR007910 [Perkinsus marinus ATCC 50983]
          Length = 100

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 43/80 (53%), Gaps = 3/80 (3%)

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL--KKGIVIQGICYGD 174
              GL++LTNDG  A  +  P ++ L V+ VR  G++ +D+      ++G+ +  + YG 
Sbjct: 1   MCSGLVILTNDGEFAHNMAHPRSKVLSVFLVRVKGRLPEDRFKSWRRREGVKVGNVAYGQ 60

Query: 175 MQVTLDTQKGSN-AWVTVGL 193
           + V +D +   +  W+ V L
Sbjct: 61  VFVGIDKRPSEDVTWLRVRL 80


>gi|256420248|ref|YP_003120901.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
 gi|256035156|gb|ACU58700.1| pseudouridine synthase [Chitinophaga pinensis DSM 2588]
          Length = 247

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 25/160 (15%), Positives = 61/160 (38%), Gaps = 15/160 (9%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   E     + +KP G++T     D +  ++   L   +  + +V RLD +T G++L  
Sbjct: 6   IIIKETADFVILNKPAGMLTIPDRHDNQLDSLQGLLKKHYGEIFTVHRLDKDTSGVILFA 65

Query: 126 NDGGLARVL---ELPSTQWLRVYRVRFHGQVDQD----KLNLLK----KGIVIQGICYGD 174
            +  +A              + Y+   +GQ+  +       +++    KG ++      +
Sbjct: 66  KN-EVAHKYYSQLFEGRNVKKFYKGLVNGQLHPETGSVDEAIMEHPTIKGRMVTNRKGKN 124

Query: 175 MQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            Q    +    G  + V + +  G+  +I+   +     +
Sbjct: 125 AQTDYQVLEAFGLYSLVQLQIHTGRTHQIRVHMKHLGHPI 164


>gi|254382579|ref|ZP_04997937.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           Mg1]
 gi|194341482|gb|EDX22448.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           Mg1]
          Length = 313

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 60/175 (34%), Gaps = 27/175 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV   IAR    SR +   + A  +V V+G ++ + +  V     +EV+   
Sbjct: 12  VPDGLEGERVDAAIARMFGFSRTKAAELAAAGKVSVDGSVVGK-SERVHGGAWLEVEMPA 70

Query: 64  -GVPLRKAERTRLWLYH-----------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
              P+         +             KP+G+    S     +TV   L +   R+   
Sbjct: 71  PPRPVELVAEPVPGMEIVHDDDDIVVVMKPVGVAAHPSPGWTGTTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
                   V RLD+ T GL+ +         L+    +    + Y     G  D 
Sbjct: 131 GASERQGVVHRLDVGTSGLMAVAKSERAYTSLKNQFRERVVDKRYHALVQGHPDP 185


>gi|189423553|ref|YP_001950730.1| pseudouridine synthase [Geobacter lovleyi SZ]
 gi|189419812|gb|ACD94210.1| pseudouridine synthase, RluA family [Geobacter lovleyi SZ]
          Length = 326

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/231 (17%), Positives = 80/231 (34%), Gaps = 41/231 (17%)

Query: 10  NFTPQRVSKVIA-RAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEV----- 62
               QR+   +A R    SR  V+R+I   +V +  G    R+++ +   + I V     
Sbjct: 13  EAAGQRLDAFLATRLTDLSRAAVQRLIDDGQVLLTEGKP--RSSMKLAGGEQITVEIPPP 70

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-- 112
                  + +PL    E   L + +K  G+           T+ + L    + +  +G  
Sbjct: 71  APAVPLAEQIPLDVLYEDHDLIVINKSAGMTVHPGAGVDSGTLVNALLGHCTDLSGIGGE 130

Query: 113 -------RLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQDKLN--- 159
                  RLD  T G+L++  +  +A              R+Y    +G  ++D      
Sbjct: 131 IRPGIVHRLDKGTSGVLVVAKN-DIAHRGLAEQFAAHSIKRLYWALIYGSPNEDTGKVSN 189

Query: 160 --------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    L+     +          +  + G+ + V + L  G+  +I+
Sbjct: 190 SIGRHPTDRLRMSGKAKHGKEATTNWRVLERFGAASLVQLRLETGRTHQIR 240


>gi|332665601|ref|YP_004448389.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332334415|gb|AEE51516.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 224

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 52/164 (31%), Gaps = 20/164 (12%)

Query: 70  AERTRLWLYHKPIGLV---TTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLL 124
           AE       +KP G     T  +D      V   L        V  V RLD  T G+LLL
Sbjct: 11  AETGAWIAVNKPFGFSVEKTLGADDTIEDQVLAYLSRQTTMPFVGIVHRLDRVTSGILLL 70

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHG--QVDQDKLNLL-------KKGIVIQGICYG 173
                  R L    +Q    ++Y     G  QV +  L+         KK +V       
Sbjct: 71  AKKKSALRKLNEQFSQRSVKKMYWAMVEGIPQVPEATLSQWLYKDQKEKKAVVFDEPAEN 130

Query: 174 D----MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                +   +     + A + + L  GK  +I+         + 
Sbjct: 131 RDACQLHYRVVQHNQTKALLEIELFTGKFHQIRVQMAALGSPII 174


>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 = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             QR+  ++    +  SR++ +R+I    V VN  ++++    V     I++   P
Sbjct: 1  MAKQRLDALLVNLDLCASRQQAQRLIRAGEVTVNQQVIDKPGTEVDILAVIKIKERP 57


>gi|311113351|ref|YP_003984573.1| ribosomal large subunit pseudouridine synthase D [Rothia
           dentocariosa ATCC 17931]
 gi|310944845|gb|ADP41139.1| ribosomal large subunit pseudouridine synthase D [Rothia
           dentocariosa ATCC 17931]
          Length = 324

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 72/241 (29%), Gaps = 51/241 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKV----N------------GILL--- 47
           V E     R+   +A A    R      I    V+V    N            G  +   
Sbjct: 16  VSEALVGMRLDAALAGALEIPRTRASGWIRDGHVRVVQCGNELKIGKSHKLSAGETVFVN 75

Query: 48  ----ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
                  A         +VDG  +   +   + +  KP G+    S      TV   L  
Sbjct: 76  APAPRDLADIQPE----KVDGFGIVYCDDDIVVV-DKPAGVAAHPSHGWHGPTVLSALLG 130

Query: 102 -------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
                       R   V RLD+ T GL+++         L+         +VY     G 
Sbjct: 131 EGVTVATSGAAERQGIVHRLDVGTSGLMVVARSERAYTELKRAFKDRTVEKVYHTLVQGL 190

Query: 153 VDQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D     ++           K  ++  G        TL++  GS + V V L  G+  +I
Sbjct: 191 PDPLMGTIDAPIGRHPGHEWKFAVIEDGRSSITYYETLES-FGSASLVEVHLETGRTHQI 249

Query: 202 K 202
           +
Sbjct: 250 R 250


>gi|294791518|ref|ZP_06756675.1| cytotoxin/hemolysin [Scardovia inopinata F0304]
 gi|294457989|gb|EFG26343.1| cytotoxin/hemolysin [Scardovia inopinata F0304]
          Length = 276

 Score = 57.5 bits (138), Expect = 3e-06,   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|224373114|ref|YP_002607486.1| hemolysin A [Nautilia profundicola AmH]
 gi|223589777|gb|ACM93513.1| hemolysin A [Nautilia profundicola AmH]
          Length = 236

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 33/68 (48%), Gaps = 4/68 (5%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK 69
           R+ + +       SR + + +I    VKVN  ++++ +  +  TD +EV   DG   R 
Sbjct: 1  MRLDQYLVTNEYTFSRNKAQEIIKSGYVKVNDKIIKKPSFKIAETDSVEVLQNDGYVSRA 60

Query: 70 AERTRLWL 77
          A + + +L
Sbjct: 61 AYKLKNYL 68


>gi|308183108|ref|YP_003927235.1| hypothetical protein HPPC_04830 [Helicobacter pylori PeCan4]
 gi|308065293|gb|ADO07185.1| hypothetical protein HPPC_04830 [Helicobacter pylori PeCan4]
          Length = 242

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 66/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMIARKELPKNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALTQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


>gi|292493653|ref|YP_003529092.1| pseudouridine synthase [Nitrosococcus halophilus Nc4]
 gi|291582248|gb|ADE16705.1| pseudouridine synthase, RluA family [Nitrosococcus halophilus Nc4]
          Length = 321

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 85/251 (33%), Gaps = 46/251 (18%)

Query: 1   MKDKNIVQENFTPQ----RVSKVIARAGIA-----SRREVERMIAQQRVKVNGILLE--- 48
           M++   +     P+    R+ + +A          SR  +++ I Q +VKVN        
Sbjct: 1   MQETIELNTTLPPELAGKRLDQALA----CVFPAYSRSRLQQWIKQGQVKVNDAPARPRD 56

Query: 49  --RAAVNVMSTDH----IEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
             R    V+        +     PL      E   + + +KP GLV   +  +   T+ +
Sbjct: 57  TVRGGEWVVLMAEMETAVVWQAQPLPLEIVYEDEAIIVVNKPAGLVVHPAAGNRDGTLVN 116

Query: 100 NLPSI------FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG 151
            L +         R   V RLD +T GLL++         L  +L + +  R YR    G
Sbjct: 117 ALLNHAPELAEIPRAGIVHRLDKDTSGLLVVARTLTAHHGLVQQLHARRVTRQYRAIAVG 176

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-----------VTVGLREGKNRE 200
            +    +  ++  I    +    M V    +     +           V+  L  G+  +
Sbjct: 177 VMTGGGI--IEAPIHRHPVDRKRMAVVSTGKPAITHYRVRARFRAHTDVSCRLETGRTHQ 234

Query: 201 IKKVFEFFNWK 211
           I+       + 
Sbjct: 235 IRVHLAHIGYP 245


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

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 10  EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 62

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 63  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 118

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 119 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 177

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 178 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 235

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 236 GNNLAWLEMEPYTGRTHQLR 255


>gi|227499062|ref|ZP_03929199.1| pseudouridine synthase [Acidaminococcus sp. D21]
 gi|226904511|gb|EEH90429.1| pseudouridine synthase [Acidaminococcus sp. D21]
          Length = 296

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/197 (19%), Positives = 67/197 (34%), Gaps = 27/197 (13%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNV------MSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           ++   +     V V  I L  A   V        TD +  +G      E   L   HK  
Sbjct: 33  KKARALFVNGLVTVWDIPL-SANDRVSFPFLPEETDLVPEEGPLTILYEDEVLLAVHKEQ 91

Query: 83  GLVT-----THSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLEL 136
           GL+      T      R  +F          +  V RLD  T G++L   +  L  +L  
Sbjct: 92  GLLVHNSGLTQESSLSRRVLFYYREHGIKAALHPVSRLDRETSGIVLFAKNAALHHMLTK 151

Query: 137 PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
              +  ++Y    HG            + +   +L+++ +  QG      +  +  Q  +
Sbjct: 152 APMK--KLYLALSHGPWEKFSGVIAQPIARKDGSLIERCVAPQGKPART-RYRVLWQDAA 208

Query: 186 NAWVTVGLREGKNREIK 202
            + V   L  G+  +I+
Sbjct: 209 KSVVAFHLYTGRTHQIR 225


>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 = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 79/235 (33%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPKNTHFSVQKVEKPGVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +           +D L S F   + + RLD  T G++LL  +     +  
Sbjct: 66  LALFKPPFIES-----------YDLL-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
             + +     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKNRAVKKEYLALTQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|242817540|ref|XP_002486976.1| DRAP deaminase (Rib2), putative [Talaromyces stipitatus ATCC 10500]
 gi|218713441|gb|EED12865.1| DRAP deaminase (Rib2), putative [Talaromyces stipitatus ATCC 10500]
          Length = 514

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/204 (14%), Positives = 67/204 (32%), Gaps = 45/204 (22%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           ++ I + RV ++G +       V +   +          V   P+    E   + +  KP
Sbjct: 70  KQAIEEGRVLISGKVA-NLDTIVPNGAIVSHSTHRHEPPVSSQPIGIIHEDDDMIVIDKP 128

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVLE--LP 137
            G+    +     +++ + + +     +++   RLD  T G++ ++ +   A      L 
Sbjct: 129 AGIPVHGAGRYHYNSIIEIMKADRPGSKILPCNRLDRLTSGVMFISKNARAAEEFSAQLK 188

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                + Y  R  G+           G+V+       +   L                G 
Sbjct: 189 ERSVQKEYVARVSGRFPD--------GVVLCDQPIMAVSPKL----------------GL 224

Query: 198 NREIKKVFEFFNWKV-NRLIRISY 220
           NR ++        +   +  RI+Y
Sbjct: 225 NR-VR----AAGKEARTKFRRIAY 243


>gi|326560902|gb|EGE11267.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 7169]
 gi|326566534|gb|EGE16680.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 12P80B1]
 gi|326569801|gb|EGE19851.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC8]
          Length = 254

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 49/166 (29%), Gaps = 29/166 (17%)

Query: 76  WLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP  ++   S  D      V   L +     V  V RLD  T G+L+   D   A 
Sbjct: 23  VIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVFALDSQTAG 82

Query: 133 VLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGDMQVT 178
           +L     +    + Y     G +                 +              D QV 
Sbjct: 83  LLAKQFENHHIQKSYLAVVRGIIGTGRIDYALKPRLDKIADKFSNPNKASKSAITDYQVL 142

Query: 179 LDTQKG----------SNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
             TQ+             + V +  +  G+  ++++  +     + 
Sbjct: 143 ATTQQPFISCRCFDSSRYSLVRLTPIT-GRKHQLRRHMKHIFHPIV 187


>gi|167957172|ref|ZP_02544246.1| Hemolysin A [candidate division TM7 single-cell isolate TM7c]
          Length = 199

 Score = 57.5 bits (138), Expect = 3e-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|167756776|ref|ZP_02428903.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402]
 gi|167702951|gb|EDS17530.1| hypothetical protein CLORAM_02325 [Clostridium ramosum DSM 1402]
          Length = 328

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 78/257 (30%), Gaps = 64/257 (24%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           MK K  + EN   QR+ K + +  +            +M  ++ +KVNG  ++     + 
Sbjct: 7   MK-KLKITENDANQRIDKYLKKLLV----NAPNNFIYKMFRKKDIKVNGKKVDE-KYILS 60

Query: 56  STDHIE-------------------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
             D +E                   V+       E   + +  KP GL+      +  +T
Sbjct: 61  LDDEVEMFLYDDKFKEFTETKSIYEVNKTFSVLYEDKHVLIVFKPAGLLVHEDANESINT 120

Query: 97  V-------------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL------ELP 137
           +              D           V RLD NT G+++    G     L         
Sbjct: 121 LTNQVLSYLASKNELDLSRENTFMPGPVHRLDRNTSGIVIF---GKTLAALQNLNEMIKQ 177

Query: 138 STQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQ-------GICYGDMQVTLDTQKGS 185
                + Y     GQ++        +  L+    ++       G    +  V        
Sbjct: 178 RHCIEKKYLTICRGQLNHQRNLHGYMIKLENQAQVKLVKKDYPGALTMETIVRPLKYNCD 237

Query: 186 NAWVTVGLREGKNREIK 202
            + V V L  G+  +I+
Sbjct: 238 YSLVEVTLITGRMHQIR 254


>gi|134295824|ref|YP_001119559.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           vietnamiensis G4]
 gi|134138981|gb|ABO54724.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           vietnamiensis G4]
          Length = 401

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/171 (22%), Positives = 65/171 (38%), Gaps = 25/171 (14%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +   +R+ K +A+     SR  ++  I  QRV ++G   +     V     IE+      
Sbjct: 65  SLAGERLDKALAQLFPEFSRSRLQSWIEAQRVLIDGAPAK-IRQPVPLGAKIELVPDLLP 123

Query: 63  -------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SR 107
                  + VPL    E   L + +KP GLV   +  +   T+ + L   +        R
Sbjct: 124 EQLAFAAEPVPLDVIYEDDALVVINKPAGLVVHPAAGNWSGTLLNGLLHRYGDAAAGLPR 183

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
              V RLD  T GL+++         L  +L +    R Y     G + ++
Sbjct: 184 AGIVHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALVWGTMPEE 234


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

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 10  EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 62

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 63  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 118

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 119 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 177

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 178 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRILEKA 235

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 236 GNNLAWLEMEPYTGRTHQLR 255


>gi|256830138|ref|YP_003158866.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256579314|gb|ACU90450.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 243

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/159 (19%), Positives = 65/159 (40%), Gaps = 22/159 (13%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLD 115
           G+ +   +R  + + +KP G++T  ++ +   T +  L             R+  V RLD
Sbjct: 15  GLVIIYEDRD-IIVVNKPAGMLTMATETEKTRTAYYALTDYVRKGNAKSRYRIFIVHRLD 73

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----NLLKKGIVIQGIC 171
             T G++L        R L+       ++Y    HGQ+ +       +L++ G+  +   
Sbjct: 74  RETSGIVLFAKTEVAKRTLQDQWEDTTKIYAAVVHGQMGKASGMLSSHLVESGVH-KVYA 132

Query: 172 YGDMQV--------TLDTQKGSNAWVTVGLREGKNREIK 202
             D  +        T+  ++G  + + V L  G+  +I+
Sbjct: 133 TRDAALGKLARTAWTVLKERGGYSLLDVTLLTGRKHQIR 171


>gi|227889588|ref|ZP_04007393.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
 gi|227849890|gb|EEJ59976.1| pseudouridylate synthase [Lactobacillus johnsonii ATCC 33200]
          Length = 299

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 90/250 (36%), Gaps = 46/250 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVM 55
           M+   +  EN TPQ++ + + + G       +R +         V VN       +  + 
Sbjct: 1   MQYFKLKFENKTPQKLGRFLLKNGF-----SKRALTNSQHHGGMVLVNHHR-RYTSYLLH 54

Query: 56  STDHIEV------DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + D +        +   L+ +        E+    + +K  G+++  S  +    V + L
Sbjct: 55  AGDEVIFILGEEKENKWLKPSSKKLNIVFEQKDYLVINKDAGILSIPSRYEDNDAVVNRL 114

Query: 102 PSIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPS-TQWLRVYRVRFHGQV 153
              F +          + RLD +T GL+L+  +             ++++ Y    HG  
Sbjct: 115 LHYFQQQKQTDLKPHVITRLDRDTSGLVLVGRNAVAHARFSKMEKNEFIKKYHAIVHGNF 174

Query: 154 DQDKLN------------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           ++ +               +K+GIV  G         LD  KG+ + + + L  G+  +I
Sbjct: 175 EEAQRQGTIDAPIGKIDTGVKRGIVNNGQRSVTKYRVLDQVKGA-SLIELQLLTGRTHQI 233

Query: 202 KKVFEFFNWK 211
           +   ++    
Sbjct: 234 RVHMQYLGHP 243


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

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 10  EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 62

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 63  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 118

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 119 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 177

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 178 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 235

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 236 GNNLAWLEMEPYTGRTHQLR 255


>gi|167950143|ref|ZP_02537217.1| 23S rRNA pseudouridine synthase D [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 306

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/221 (20%), Positives = 83/221 (37%), Gaps = 36/221 (16%)

Query: 15  RVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ +V+A    A  SR  ++R I   R+ ++G   +     V   + +E+          
Sbjct: 27  RLDQVVAEQ-FAQFSRSRLQRWIKDGRLLLDGRPGK-PKQKVRGGERLELVPQLEQEVTS 84

Query: 63  DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
              P+      E   L + +KP GLV   +  +   T+ + L   F       R   V R
Sbjct: 85  RPQPIPLDILFEDESLLVVNKPAGLVVHPAVGNPDGTLVNALLHYFPAISQVPRGGIVHR 144

Query: 114 LDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLL 161
           LD  T GLL++  T     A V +L +    R YR    G           + +  ++  
Sbjct: 145 LDKETSGLLVVAKTLQAQTALVAQLQARSMKREYRAFAQGVMAAGGKVDAPIGRHPVHRT 204

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +  +V  G         ++  +  +  + + L  G+  +I+
Sbjct: 205 RMAVVANGKPAVTHYRVIERYR-FHTDLRIQLETGRTHQIR 244


>gi|326796213|ref|YP_004314033.1| pseudouridine synthase [Marinomonas mediterranea MMB-1]
 gi|326546977|gb|ADZ92197.1| pseudouridine synthase, RluA family [Marinomonas mediterranea
           MMB-1]
          Length = 327

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 75/207 (36%), Gaps = 32/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERT 73
           SR  ++  I +  + V+G   + A   ++  + + +D             +P+    E  
Sbjct: 32  SRSRIQAWIKEGALLVDGKACK-AKEKLLGGEVVSLDVALEEQEAHEAQDIPIDIVYEDE 90

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTND 127
            + + +KP GLV   +      T+ + +       +   R   V RLD  T GL+++   
Sbjct: 91  HILVINKPAGLVVHPAVGHREGTLLNAILHHAPETAHVPRAGIVHRLDKETTGLMVVAKT 150

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKLNLL---KKGIVIQGICYGDM-- 175
                 L  +L      R Y     G +       + +      ++ + ++ I   D   
Sbjct: 151 LQAQTDLVAQLQERSMGREYEAITIGVMTGGGMVDEPIGRHPTNRQRMAVEPIHGKDALT 210

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              L  +  ++  + + L  G+  +I+
Sbjct: 211 HYRLLKRFKNHTHIRLKLETGRTHQIR 237


>gi|224024089|ref|ZP_03642455.1| hypothetical protein BACCOPRO_00808 [Bacteroides coprophilus DSM
           18228]
 gi|224017311|gb|EEF75323.1| hypothetical protein BACCOPRO_00808 [Bacteroides coprophilus DSM
           18228]
          Length = 307

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/219 (15%), Positives = 70/219 (31%), Gaps = 29/219 (13%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ER 72
           AG+ SR  V+ +++ + V VN  +  +    +     +++     +            E 
Sbjct: 40  AGV-SRTRVKALLSNRVVLVNNNIQTQYNFPLTPGMKVQISKDRNKHEFRHPMLKILYED 98

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTN 126
             L +  K  GL++  ++     T    L     R      V  V RLD  T G+++   
Sbjct: 99  AYLIVVEKKEGLLSVATEKQKERTAQHILNEYVKRQHRNNRVFVVHRLDRETSGIMMYAK 158

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQVDQDK--LNLLKKGIVI--------QGICYGD 174
           D      L          R Y     G +++D+  +        +         G  +  
Sbjct: 159 DEKTQHTLRDNWHDIVYDRRYVTIVTGDMEKDQGKVESWLTDRKLYVSSSPVDDGGKFSV 218

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +    + V + L  G+  +I+   +     V 
Sbjct: 219 THYHTIKRANGFSLVELQLETGRKNQIRVHMQTLGHPVV 257


>gi|312171317|emb|CBX79576.1| tRNA pseudouridine synthase C [Erwinia amylovora ATCC BAA-2158]
          Length = 255

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 59/167 (35%), Gaps = 29/167 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V +V RLD  T G+LL+     +A
Sbjct: 11  LVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLMALSSEVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHG----------QVDQDK---LNLLKKG--------IVIQ 168
            +L       Q  + Y     G           + +++    +   +            +
Sbjct: 71  HLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEERDKIADKFSQPEKAPQPAVTHWR 130

Query: 169 GICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKK-VFEFFNWKVN 213
           G+   ++ V +   + S  + V +    G+  ++++ +       + 
Sbjct: 131 GVATAELAVPIGRYETSRYSLVEMQPESGRKHQLRRHMT-HLRHPII 176


>gi|303230703|ref|ZP_07317450.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514463|gb|EFL56458.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 306

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/272 (15%), Positives = 79/272 (29%), Gaps = 56/272 (20%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHI--------EVDGVPLRKA---ERTRLWLYHKPIGLV 85
              + +NG         V   DH+        E     +      E   +   +K   ++
Sbjct: 40  DGIITINGQPAT-WDTLVHGGDHLLMKLAPEQEFSRTQMDLEIVYEDEYILAINKAASVL 98

Query: 86  ----TTHSDPDGRSTVFDNLPS--IFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
               +T  D    + V               V RLD +T G++++     +    +   T
Sbjct: 99  MHPTSTVRDGTLANGVLYYYDETEQAHDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKQRT 158

Query: 140 QWLRVYRVRFHGQVDQDKLNL-----LKKGIVIQGICY---GDM--------------QV 177
           ++ +VY     G +    L +      K G +I+  C                      V
Sbjct: 159 KFQKVYDAIVEGTMPSQSLTIKWPIGRKAGSIIERCCTSIGKPARTDVTVLARHIVSQPV 218

Query: 178 TLDTQKGSNAWVT---VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
            +D    +   +T     L  G+  +I+       +           P     L  G   
Sbjct: 219 QMDKNLSTQQILTHVQCVLHTGRTHQIRVHLSHLGF-----------PLVGDDLYGGHLD 267

Query: 235 EVSKKILRE--QLGPHLLEEAQVNLDAPIYSS 264
            + ++ L        H + +  V L AP+ + 
Sbjct: 268 YIRRQALHAGYLAFTHPMTQEYVELRAPLPTD 299


>gi|295097354|emb|CBK86444.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           NCTC 9394]
          Length = 261

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 52/168 (30%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 12  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +           ++L+ +      +            
Sbjct: 72  RLLSQQFEQHQMQKRYHAIVRGWLTDSATLDYPLVEELDKIADKFAREDKGPQPAVTDYR 131

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ + T K      ++   E     G+  ++++        + 
Sbjct: 132 GMATTELPVATSKFPTTRYSLV--ELLPKTGRKHQLRRHLAHLRHPII 177


>gi|257465425|ref|ZP_05629796.1| tRNA pseudouridine synthase C [Actinobacillus minor 202]
 gi|257451085|gb|EEV25128.1| tRNA pseudouridine synthase C [Actinobacillus minor 202]
          Length = 242

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 69/200 (34%), Gaps = 35/200 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKAETVFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSDMA 71

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--- 186
           R +     + Q  + Y     G ++          +++  +     Q     +  ++   
Sbjct: 72  RTMCELFENHQVKKGYLAVVRGYLEGKARVDYPLKVILDKVADKFSQEKEPQEAITDYQG 131

Query: 187 -AWVTV------------GLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            A V +             L E     G+  ++++  +     +        G  + G L
Sbjct: 132 LATVEMPYPAGKFQTARYSLVELSPQTGRKHQLRRHLKHLFHPI-------MGDTKYGDL 184

Query: 229 LAGSTREVSKKILREQLGPH 248
                R ++++   E+L  H
Sbjct: 185 H--QNRTLAEQSGVERLMLH 202


>gi|256842723|ref|ZP_05548211.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus 125-2-CHN]
 gi|256614143|gb|EEU19344.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus 125-2-CHN]
          Length = 301

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/162 (19%), Positives = 60/162 (37%), Gaps = 23/162 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLL 123
           E     + +KP G+++  S  +    V + L   F++          + RLD  T GL+L
Sbjct: 85  ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRYTSGLVL 144

Query: 124 LTNDGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGI 170
           +  +             ++++ Y    HG    ++L  L      KKG      +V  G 
Sbjct: 145 VGKNAISHARFSKIGKEKFVKKYHAIVHGNFAPNELTGLIDQPIGKKGSGVKRAVVADGK 204

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
                   LD   G+ + V + L  G+  +I+  +  +    
Sbjct: 205 DAQTAYRVLDQVTGA-SLVELCLLTGRTHQIRVHM-AYLGHP 244


>gi|237653787|ref|YP_002890101.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237625034|gb|ACR01724.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T]
          Length = 327

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/231 (18%), Positives = 75/231 (32%), Gaps = 39/231 (16%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+ + +AR     SR  ++  + +  ++V+G     A   V   + +E+D          
Sbjct: 37  RLDQALARLLPQHSRSRLQGWLKEGWIRVDGASP-DARRKVCGGECVEIDAPPPPEVTAA 95

Query: 64  ---GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGR 113
               +PL    E   L +  KP+GLV      +   T+ + L           R   V R
Sbjct: 96  LPEDIPLAVVYEDEDLLVIDKPVGLVVHPGSGNWSGTLLNALLHRNPALAGVPRAGIVHR 155

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD +T GL+++         L  +L +    R YR    G +          G   +   
Sbjct: 156 LDKDTSGLMVVAKTLAAQTELVRQLQARTVGRHYRALVQGALTAGGTVDAPIG---RHPT 212

Query: 172 YGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNW 210
                  +   + +     V        L E     G+  +I+        
Sbjct: 213 QRTRMAVVGNGRPAVTHYRVTERFPRATLVECRLETGRTHQIRVHMAHIGH 263


>gi|171059556|ref|YP_001791905.1| RluA family pseudouridine synthase [Leptothrix cholodnii SP-6]
 gi|170777001|gb|ACB35140.1| pseudouridine synthase, RluA family [Leptothrix cholodnii SP-6]
          Length = 369

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 78/239 (32%), Gaps = 50/239 (20%)

Query: 14  QRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK--- 69
           +R+ K + R A   SR  ++ ++    V+    +L ++   VM+   IEV   P  +   
Sbjct: 52  ERLDKWLVRIAPEFSRAHLQGLVEGGHVRCGEQVLRQSHKKVMAGQQIEVALWPTAQSTA 111

Query: 70  -----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVG 112
                       E   L +  KP GLV   +      T+ +         +   R   V 
Sbjct: 112 FRAEAMTLAVVHEDAHLLVIDKPAGLVVHPAAGHWSGTLLNGLLAHHAAAAHLPRAGIVH 171

Query: 113 RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLN 159
           RLD +T GL+L+         L     +    R Y    HG            + +D ++
Sbjct: 172 RLDKDTSGLMLVAKSLQAHTALVRAIAARDVKREYLALVHGAVMDGLQVIDAPLGRDPVS 231

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSN----------------AWVTVGLREGKNREIK 202
            ++  IV  G         L   +                   + V   L  G+  +I+
Sbjct: 232 RVRMAIVASGKPARTDVRRLAVAELPGDGVRQLPGATRAPRQVSAVHCQLHTGRTHQIR 290


>gi|94499595|ref|ZP_01306132.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Oceanobacter sp. RED65]
 gi|94428349|gb|EAT13322.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase) [Oceanobacter sp. RED65]
          Length = 318

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 79/238 (33%), Gaps = 47/238 (19%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV-- 62
           V  ++  QR+   + +R   A +  V R+I +  V+VN G +  +    V   D + +  
Sbjct: 14  VTADYVGQRIDNFLMSRIKGAPKSLVYRIIRKGEVRVNKGRI--KPEYKVKLGDVVRIPP 71

Query: 63  -------DGVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPD--GRSTVFDNLP 102
                  D  P+ K            E       +KP G+          G   V  NL 
Sbjct: 72  VKVKAEGDAAPISKDMAEGIEQSILFEDDYFLAVNKPRGMAVHGGSGISLGLIEVLRNLR 131

Query: 103 SIFSRVISVGRLDINTEGLLLLT---NDGGLARVLELPSTQWLRVYRVRFHGQVDQD--- 156
               R+  V RLD +T G++L+            +        + Y    +G   +    
Sbjct: 132 PKAKRLELVHRLDRDTSGVILVAKRRTALVAFHKMLQRKQGMQKRYLALVYGNWPKHLKD 191

Query: 157 -----KLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
                K N LK G  +    Q       + +++ +      V    V    G+  +I+
Sbjct: 192 VEVPLKKNELKSGERLVKVAQDGKPSHTRYSIERKFKGYTLVNAEPVT---GRTHQIR 246


>gi|114562440|ref|YP_749953.1| pseudouridylate synthase [Shewanella frigidimarina NCIMB 400]
 gi|114333733|gb|ABI71115.1| tRNA pseudouridine synthase C [Shewanella frigidimarina NCIMB 400]
          Length = 293

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 29/173 (16%), Positives = 50/173 (28%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 50  EDEHLVAIHKPAGLLVHRSYLARRERFFAMQMTRDLVGC---HVFPVHRLDRPTSGVLLF 106

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD-------------------KLNLLKK 163
                +AR L          + Y     G + +                      N   +
Sbjct: 107 AKSSEVARALCEQFADHSIKKHYLAIVRGNMHESGTLDYALKQEFDDLGDKHVDQNKAAQ 166

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVN 213
             V       + ++   + +   +   +  L    G+  ++++        + 
Sbjct: 167 DAVTDYQPLLNTEIPFSSGRYPTSRYGLVKLSPHTGRKHQLRRHMAHLRHPIV 219


>gi|71898901|ref|ZP_00681068.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
 gi|71731313|gb|EAO33377.1| Pseudouridine synthase, RluD [Xylella fastidiosa Ann-1]
          Length = 328

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 85/256 (33%), Gaps = 35/256 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  V +    +R   V+A      SR  +   I    V +NG+L+      V   + +
Sbjct: 10  SRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVR-PRDPVYGGEVV 68

Query: 61  EV--------DGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
            +        D VP         E   +++ +KP GLV      +   T+ + L      
Sbjct: 69  RLQVVPDIRTDAVPQDIPLDILYEDEHVFVINKPAGLVVHPGAGNPDGTLVNALLHRDPA 128

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV----------RF 149
                R   V RLD +T G++++         L  +L S Q  R Y              
Sbjct: 129 LAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHRQYLAVVVSALVSGGTV 188

Query: 150 HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +  +++   + L+  +   G          +  +   A +   L  G+  +I+       
Sbjct: 189 NAAIERHPRDRLRMAVSDTGKEAVTHYRLRERFRAHTA-LECRLDTGRTHQIRVHMAHLR 247

Query: 210 WKVNRLIRISYGPFQL 225
             +    R+  G  +L
Sbjct: 248 HPIVG-DRLYGGSLKL 262


>gi|254427100|ref|ZP_05040807.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
 gi|196193269|gb|EDX88228.1| pseudouridine synthase, RluA family [Alcanivorax sp. DG881]
          Length = 324

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 80/229 (34%), Gaps = 35/229 (15%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---- 60
           V+     QRV +V A    G  SR  ++  I    + VNG    +    +   + +    
Sbjct: 15  VKPEHAGQRVDQVAAELFDGF-SRSRLQTWIKNGVLTVNGAK-TKPKEKLTGNESLTLEV 72

Query: 61  ----EVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
               E+D  P               + +KP GLV   +      T+ + L  +  R+ S 
Sbjct: 73  EIEPELDDQPQSIDLDVVYQDDDLIVINKPTGLVVHPAAGHADGTLLNGLLHLDERLNSL 132

Query: 111 -----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVR----------FHGQV 153
                V RLD +T GL+++       + L  +L      R Y                 +
Sbjct: 133 PRAGIVHRLDRDTTGLMVVARSLEAHQSLVAQLQDKSLFRQYEAIAVGVMTGGGKVDAPM 192

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +  ++  K+ +V  G         +  +  ++  + V L  G+  +I+
Sbjct: 193 GRHPVDRKKQAVVKTGGKNAVTHYRVLDRYRAHTRIQVQLETGRTHQIR 241


>gi|148379407|ref|YP_001253948.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 3502]
 gi|153932742|ref|YP_001383785.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           ATCC 19397]
 gi|153936684|ref|YP_001387335.1| RluA family pseudouridine synthase [Clostridium botulinum A str.
           Hall]
 gi|148288891|emb|CAL82977.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           botulinum A str. ATCC 3502]
 gi|152928786|gb|ABS34286.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152932598|gb|ABS38097.1| pseudouridine synthase, RluA family [Clostridium botulinum A str.
           Hall]
 gi|322805749|emb|CBZ03314.1| ribosomal large subunit pseudouridine synthase C [Clostridium
           botulinum H04402 065]
          Length = 317

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/264 (13%), Positives = 79/264 (29%), Gaps = 67/264 (25%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA- 50
           K ++  N   QR+ K              +             I +  +KVNG   +   
Sbjct: 2   KIVIGANEAGQRLDKF-----------CRKWLKDVPLSAIYKAIRKGEIKVNGRKSKEKN 50

Query: 51  ---------AVNVMSTDH----IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                    + NV S       + +D       E   + L  K  G++      +G ST+
Sbjct: 51  FLEEGDIVESFNVKSKGEKKKFVRIDNNLKITYEDENMVLVEKWPGVLVHSDKKEGESTL 110

Query: 98  FDNLPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                   S  RLD NT G+++   +    + L   +   +  
Sbjct: 111 TDYVLSYLYDKGDYTPELEVTFTPASCNRLDRNTSGIVIFGKNYEALKTLNEMIRDRKIE 170

Query: 143 RVYRVRFHGQVDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSN----AWV 189
           + Y     G++                + K  +         ++ ++ +        +++
Sbjct: 171 KYYSSLVKGRIKDGIYEAYISKNEDTNMSK--IYNEPKPNTKKIAMNVKTIQTCGSFSFI 228

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G++ +++         + 
Sbjct: 229 EIELLTGRSHQLRAHLSHLGNPII 252


>gi|150390922|ref|YP_001320971.1| RluA family pseudouridine synthase [Alkaliphilus metalliredigens
           QYMF]
 gi|149950784|gb|ABR49312.1| pseudouridine synthase, RluA family [Alkaliphilus metalliredigens
           QYMF]
          Length = 308

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 45/285 (15%), Positives = 93/285 (32%), Gaps = 57/285 (20%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD---------GVPLRK---AERTRLWLYHKPIG 83
             +R+ +NG   +   + +   D I++D            +      E   + + +K  G
Sbjct: 45  KSKRILINGQYAKYHEL-LSEGDWIKIDMTEEASQFEPQEIPFNVVYEDIDVIVINKEPG 103

Query: 84  LVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +V+  +    + T+ +   +         R+  V RLD++T GLL++  +      +   
Sbjct: 104 IVSHPTKSHPKDTIANAAQNYLEKKGVACRIRFVNRLDMDTSGLLVIAKNP-YTHHIMSQ 162

Query: 138 S---TQWLRVYRVRFHGQV--------------DQDKLNLLKKGIVIQGICYGDMQVTLD 180
                +  + Y     G V                + +      +V         + T+ 
Sbjct: 163 QMKANEITKKYVAFVKGVVVANEGEIDGAIYRSSDETIKR----VVDDRGQQSLTKFTVL 218

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +      + V L  G+  +I+   E                  LG  L G    V  ++
Sbjct: 219 ERYADATMLEVSLLTGRTHQIRVHMESIGHP------------MLGDHLYG---YVDTEL 263

Query: 241 LREQ-LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
           +R Q L    L   Q      I    +L +D   + +++ D+  R
Sbjct: 264 IRRQALHASYLSFLQPRYKEKIEVRASLPKDLNELRNKLKDELLR 308


>gi|302518516|ref|ZP_07270858.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SPB78]
 gi|333027806|ref|ZP_08455870.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces sp. Tu6071]
 gi|302427411|gb|EFK99226.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           SPB78]
 gi|332747658|gb|EGJ78099.1| putative ribosomal large subunit pseudouridine synthase
           [Streptomyces sp. Tu6071]
          Length = 313

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/175 (18%), Positives = 63/175 (36%), Gaps = 27/175 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   ++R    SR +   + A  +V+V+G ++ +       A + V     
Sbjct: 12  VPDGLEGERVDAALSRMFGFSRTKAAELAAGGKVQVDGSVVGKSERVRGGAWLEVEMPRA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S      TV   L +   R+   
Sbjct: 72  AAPVQIVAEPVEGMEIVHDDEDVVVIM-KPVGVAAHPSPGWTGQTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                   V RLD+ T GL+++         L+         + Y     G  D 
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSERAYTSLKNQFRVRTVDKRYHTLVQGHPDP 185


>gi|238019027|ref|ZP_04599453.1| hypothetical protein VEIDISOL_00889 [Veillonella dispar ATCC 17748]
 gi|237864511|gb|EEP65801.1| hypothetical protein VEIDISOL_00889 [Veillonella dispar ATCC 17748]
          Length = 322

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/200 (15%), Positives = 66/200 (33%), Gaps = 34/200 (17%)

Query: 37  QQRVKVNGILL---------ERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLV- 85
              + VN             +   + +       +  + L    E   + + +K  G++ 
Sbjct: 63  NGIITVNDEPASWNTLVHGGDHLVMKLTPEQEFSLSPMDLDIVYEDEYILVINKEAGILM 122

Query: 86  ---TTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              +T  D    + V               V RLD +T G++++     +    +   T 
Sbjct: 123 HPTSTVRDHTLANGVLHYYQQTNQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKRTH 182

Query: 141 WLRVYRVRFHGQVDQDKLNL-----LKKGIVIQGICYGDMQV--TLDTQKGSNAWV--TV 191
           + + Y     GQ+  + +++      K G +I+  C  + +   T  T   SN  V   +
Sbjct: 183 FHKNYDAIVEGQLPTNHISVQWPIGRKPGSIIERCCTNEGKPAHTDITVIESNTIVKNKI 242

Query: 192 G---------LREGKNREIK 202
                     L  G+  +I+
Sbjct: 243 EQCFTHVQCLLHTGRTHQIR 262


>gi|227530166|ref|ZP_03960215.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus vaginalis
           ATCC 49540]
 gi|227349919|gb|EEJ40210.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus vaginalis
           ATCC 49540]
          Length = 291

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/233 (14%), Positives = 72/233 (30%), Gaps = 45/233 (19%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIA-----QQRVKVNGILLERAAVNVMSTD---- 58
            +   P ++ K +   G+  R     +       Q +  V+   +      ++       
Sbjct: 7   YQGAQPIKIKKFLQSLGMGHR-----LFNDLKNGQGKFLVDHRKVR-PTTKILPNQPLTI 60

Query: 59  ---------HIEVDGVPLRKAERTRLWL-YHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
                     +++   PL        WL   KP G+ +         TV +         
Sbjct: 61  IAQPELRDLSVKLSDAPLNIVYEDDNWLVIDKPAGVTSIPGPTVDNGTVLNRAVHYLVEE 120

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDK-- 157
                R   + RLD  T GLLL+      + ++     Q    + Y     G  D++   
Sbjct: 121 KSADQRPHLITRLDRYTGGLLLIAKHHVASSMISQQVQQHQMLKEYTAFVSGIFDKEHDI 180

Query: 158 ----LNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +   ++G    ++ +       +  ++ +      + V L  G+  +I+
Sbjct: 181 IDKPIAR-REGQVQRVIAEDGQRAVTEYWVEEEGADWTKLRVRLHTGRTHQIR 232


>gi|259909472|ref|YP_002649828.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|224965094|emb|CAX56626.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae Ep1/96]
 gi|283479545|emb|CAY75461.1| tRNA pseudouridine synthase C [Erwinia pyrifoliae DSM 12163]
          Length = 265

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 59/167 (35%), Gaps = 29/167 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V +V RLD  T G+LL+     +A
Sbjct: 11  LVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLMALSSEVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHG----------QVDQDK---LNLLKKG--------IVIQ 168
           R+L       Q  + Y     G           + +++    +   +            +
Sbjct: 71  RLLSQQFEQHQLQKTYHAVVRGWLEGADTLDYPLTEEQDKIADKFSQPEKAPQPAVTHWR 130

Query: 169 GICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKK-VFEFFNWKVN 213
           G+   ++ V +   Q    + V +    G+  ++++ +       + 
Sbjct: 131 GVATAELPVPVGRYQTSRYSLVEMLPESGRKHQLRRHMT-HLRHPII 176


>gi|182682370|ref|YP_001830530.1| RluA family pseudouridine synthase [Xylella fastidiosa M23]
 gi|182632480|gb|ACB93256.1| pseudouridine synthase, RluA family [Xylella fastidiosa M23]
 gi|307578653|gb|ADN62622.1| ribosomal large subunit pseudouridine synthase D [Xylella
           fastidiosa subsp. fastidiosa GB514]
          Length = 327

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 87/256 (33%), Gaps = 35/256 (13%)

Query: 2   KDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLER---------AA 51
             +  V +    +R   V+A      SR  +   I    V +NG+L+             
Sbjct: 9   SRQTTVPDGAAGRRFDAVLAELFPEFSRSRLTEWIKSGDVLLNGVLVRPRDPVYGGEVVW 68

Query: 52  VNVMSTDHIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           + VM    I  D VP         E   +++ +KP GLV      +   T+ + L     
Sbjct: 69  LQVMPD--IRTDAVPQDIPLDILYEDEHVFVINKPAGLVVHPGAGNPDGTLVNALLHRDP 126

Query: 106 -----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH------GQ 152
                 R   V RLD +T G++++         L  +L S Q  R Y           G 
Sbjct: 127 ALAAVPRAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSSRQVHRQYLAVVVSALVSGGT 186

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           V+       +  + ++    G   VT   L  +  ++  +   L  G+  +I+       
Sbjct: 187 VNAAIERHPRDRLRMEVSDTGKEAVTHYRLRERFRAHTALECRLDTGRTHQIRVHMAHLR 246

Query: 210 WKVNRLIRISYGPFQL 225
             +    R+  G  +L
Sbjct: 247 HPIVG-DRLYGGSLKL 261


>gi|319892885|ref|YP_004149760.1| ribosomal large subunit pseudouridine synthase D, YhcT
           [Staphylococcus pseudintermedius HKU10-03]
 gi|317162581|gb|ADV06124.1| ribosomal large subunit pseudouridine synthase D, YhcT
           [Staphylococcus pseudintermedius HKU10-03]
          Length = 276

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 72/201 (35%), Gaps = 28/201 (13%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLW----------LYHKPIGLVTT 87
           + VN          V + D I +  +    +     R            + +KP G+ T 
Sbjct: 37  ITVNDE-AANLQTIVHTGDEIYIPDEDAKSQYLPSYRYAQIAYEDDFLAIVYKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++    +   V  + RLD  T GLL++     + ++L   L +    R
Sbjct: 96  PNDLKESNTLMNHVIYTLNHPYVEPIHRLDQETVGLLIVAKHPIIKKILDRMLENNDIHR 155

Query: 144 VYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+ +               + +DK +  K+ +   G       ++ +  +     V + 
Sbjct: 156 IYKAQVKSLLPIKPQTIDLPIGKDKFHPNKRRVSPTGQRAVTHILSSEMIEEGVCEVMLK 215

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           L  G+  +I+       + V 
Sbjct: 216 LDTGRTHQIRVHLAEIGYPVL 236


>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 = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 10 NFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
              +R+ +V+   G +ASR +  R+I    V+V+G+++++AA  ++S   +E+ G
Sbjct: 6  RPERERLDRVLVSRGLVASREDAARLILAGLVRVDGVVVDKAAKPILSGAKVELTG 61


>gi|21231531|ref|NP_637448.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66768413|ref|YP_243175.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21113212|gb|AAM41372.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573745|gb|AAY49155.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 327

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 86/250 (34%), Gaps = 47/250 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+ T QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRTGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            L +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RLTEEGDKAAPPSAFQARLEAAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVDGRSITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMSVDAPLHIGLRQGGERHVQVNAIGKPSLSHFRLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKV 212
              +     V
Sbjct: 258 VHAQHLGHAV 267


>gi|309973117|gb|ADO96318.1| tRNA U65 pseudouridine synthase [Haemophilus influenzae R2846]
          Length = 239

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/181 (14%), Positives = 53/181 (29%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDAFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLTVVRGYLQGKAQIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|261822605|ref|YP_003260711.1| tRNA pseudouridine synthase C [Pectobacterium wasabiae WPP163]
 gi|261606618|gb|ACX89104.1| pseudouridine synthase [Pectobacterium wasabiae WPP163]
          Length = 261

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 54/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LLL   
Sbjct: 7   QDEHLVAVNKPSGWLVHRSWLDRKEKVVVMQTVRDQIGQHVYTVHRLDRPTSGVLLLALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L     S Q  ++Y     G V           ++L+ +               
Sbjct: 67  SEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFANPDKAPQPAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  QV +    G        L E     G+  ++++     +  + 
Sbjct: 127 THYRALAQVEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHLHHPII 176


>gi|188991778|ref|YP_001903788.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167733538|emb|CAP51742.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 327

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 86/250 (34%), Gaps = 47/250 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+ T QR+   +  +   A R  + +++   +V+VNG   + A   +   + + +  V
Sbjct: 21  VPEDRTGQRLDNFLLGQLKGAPRSLIYKLVRSGQVRVNGGRAK-AERKLEGGEEVRIPPV 79

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            L +                     E  RL   +KP G+ +            T+    P
Sbjct: 80  RLTEEGDKAAPPSAFQARLEAAIVFEDARLLALNKPTGVASHGGSGISFGAIETLRALRP 139

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     +       + Y     G++ 
Sbjct: 140 N--QTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDRVDGRSITKRYLTLLVGRMP 197

Query: 155 QDKL---NLLKKGIVIQGICYGDMQV---------TLDTQKGSNAWVTVGLREGKNREIK 202
              +     L  G+   G  +  +            L  ++G +++  V +  G+  +I+
Sbjct: 198 DGVMSVDAPLHIGLRQGGERHVQVNAIGKPSLSHFRLLERRGGHSYCEVRIETGRTHQIR 257

Query: 203 KVFEFFNWKV 212
              +     V
Sbjct: 258 VHAQHLGHAV 267


>gi|320155234|ref|YP_004187613.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
 gi|319930546|gb|ADV85410.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           MO6-24/O]
          Length = 250

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 59/175 (33%), Gaps = 45/175 (25%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++     P+   +++  L   +  +  V RLD++T GL++   +  
Sbjct: 19  EDDHILAVNKPSGLLSVPGRLPEHHDSMWSRLQEQYPEIQVVHRLDMSTSGLMVFAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV 177
                       L        ++Y  R  G V+ D       G++    I       MQ 
Sbjct: 79  AEAALKKQFQYRLTH------KIYYARVWGHVEAD------SGMIDLPLICDWPNRPMQK 126

Query: 178 TL-DTQKGSNAWVTVGLRE-----------------GKNREIK-KVFEFFNWKVN 213
              +  K S     V  RE                 G++ +++  + +     + 
Sbjct: 127 VCHEHGKPSQTEFQVAKREVHANGAQTTIMRLLPVTGRSHQLRVHM-QALGHPIV 180


>gi|317050965|ref|YP_004112081.1| pseudouridine synthase [Desulfurispirillum indicum S5]
 gi|316946049|gb|ADU65525.1| pseudouridine synthase [Desulfurispirillum indicum S5]
          Length = 273

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/172 (20%), Positives = 56/172 (32%), Gaps = 27/172 (15%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLL 123
           +       L   HKP GL+   S  D   T F        I   V  V RLD  T G+LL
Sbjct: 12  VIVYRDDHLIAIHKPAGLLVHRSSIDRHETRFAMQLLRDQIGQPVYPVHRLDKPTSGVLL 71

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL--NLLKKGI-VIQGICYG--DMQ 176
              +  +AR+L     S    + Y     G   +  +  + L++                
Sbjct: 72  FALNPEVARLLGALFVSAAVAKTYLAVVRGVPPRSGIIDSPLREERNRYDDQRTALEKAP 131

Query: 177 VTLDTQKGSNAWVTV------------GLRE-----GKNREIKKVFEFFNWK 211
            +  T+  + A V +             L E     G+  +I++ F+     
Sbjct: 132 QSAVTRFQTRATVELPFAVGPYPTSRYALVEVQPQTGRRHQIRRHFKHLCHP 183


>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 = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 83/236 (35%), Gaps = 39/236 (16%)

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  IEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGR 113
           + +  +   + + + LW      +Y KP  L T     +   T+  NL         V R
Sbjct: 59  VAIS-IVHNQQQPSLLWEDAHSCIYDKPPYLTT----EEIAKTLGRNL---------VHR 104

Query: 114 LDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ--DKLNLL------KK 163
           LD +T G LL        + L          + Y     G   Q    L         + 
Sbjct: 105 LDRDTTGCLLFAKTQDAMQKLSDLFKQRNIHKQYITLVFGLPKQCSGTLTTFTAPKYKRC 164

Query: 164 GIVIQGICY---GDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
           G V+ G      G + +T  T        ++ L E   G+  +I+   +     + 
Sbjct: 165 GAVLFGTTTPSQGKLTITKWTVLQRYKHYSLLLCEPITGRTHQIRLHMKHLGHPIV 220


>gi|15615410|ref|NP_243713.1| hypothetical protein BH2847 [Bacillus halodurans C-125]
 gi|10175468|dbj|BAB06566.1| BH2847 [Bacillus halodurans C-125]
          Length = 302

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/223 (18%), Positives = 72/223 (32%), Gaps = 35/223 (15%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRST 96
           V VN  +         S   I     P+      E     + +KP G+ T  S    + T
Sbjct: 58  VHVNDQVTLELPHEYPSPSMIA---EPVPFDVIYENDHYLVVNKPAGVPTIPSRDHPQGT 114

Query: 97  VFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVR 148
           + + L + F R        +V RLD +T GLL++         L          R Y   
Sbjct: 115 LANGLLNYFQRQKMAATFHAVNRLDKDTSGLLIVAKHQLAHDQLSKQQRQGNIKRTYMAI 174

Query: 149 FHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             G+++Q           K   L    V +          +  +      V V L  G+ 
Sbjct: 175 VQGEIEQQEGTITAPIARKEESLITREVREDGQLAITHFKVIDRLNQGTIVQVQLETGRT 234

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
            +I+  F +  + +       +G      L  G  + + ++ L
Sbjct: 235 HQIRVHFSYLGYPL-------FG----DDLYGGERKGIERQAL 266


>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 = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 68/212 (32%), Gaps = 48/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----VPLRKA---------ERTRLWLY 78
           +MI ++ + +NG+ +      +   D +E  G      P++           E   L + 
Sbjct: 35  KMIRKKNITINGLKISDIRHRLKEGDVVEFYGCETPTKPIKWEGLKPLRVVFESENLIIV 94

Query: 79  HKPIGLVTTHSDPD-----GRSTVFDNLPSIFSRVISV--GRLDINTEGLLLLTNDGGLA 131
            K   +     D           +     S       V   RLD+NT GLL+   +    
Sbjct: 95  DKEAKMPVQEDDKHPFNHMNNRLLKHLNYSNREGWKPVFIHRLDLNTTGLLIGAKNYKTF 154

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------ 183
             L     S +  + Y+    G V        KK  +   +   D +V++  ++      
Sbjct: 155 LKLNKSQKSLKIKKSYKALVQGNVS------FKKREISCFLLKKDGRVSISREQVEGAKE 208

Query: 184 -------------GSNAWVTVGLREGKNREIK 202
                         ++  + + L  G+  +I+
Sbjct: 209 AKTIANFLHFFPSINSTLLELTLITGRTHQIR 240


>gi|270291471|ref|ZP_06197693.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus
           acidilactici 7_4]
 gi|270280317|gb|EFA26153.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus
           acidilactici 7_4]
          Length = 301

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/221 (16%), Positives = 78/221 (35%), Gaps = 44/221 (19%)

Query: 24  GIASRREVERMIAQ------QRVKVNGILLERAAVNVMSTDHIEVD-------------G 64
              +R+ + R + +       ++ VN    +R    V + D + V+              
Sbjct: 17  TFLTRKRISRALLKSIKFNGGKILVN-EQPKRTNEMVTAGDQVTVELPPEPGNPHVVRSR 75

Query: 65  VPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDI 116
            P+    E     + +KP  L T  S  +   T+ + + + ++        V  V RLD 
Sbjct: 76  QPIDVIYEDQDYLVVNKPPFLPTVQSARNQTDTLVNRVKNYYAERDYESQVVHVVTRLDQ 135

Query: 117 NTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHG-----------QVDQDKLNLLK 162
           +T GL+L       A  +        +  + Y     G            +++D  + +K
Sbjct: 136 DTSGLVLFA-KRRFAHTIMDQDLRQHRVQKYYLAMATGRFAQSHGLIDAPIERDPASFIK 194

Query: 163 KGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +   G       +  +  Q  +++ + V L  G+  +I+
Sbjct: 195 RRVASAGNGKPSKTEYWVLEQTDTDSLLKVQLHTGRTHQIR 235


>gi|189237270|ref|XP_973027.2| PREDICTED: similar to ribosomal pseudouridine synthase [Tribolium
           castaneum]
          Length = 487

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/207 (17%), Positives = 71/207 (34%), Gaps = 25/207 (12%)

Query: 32  ERMIAQQRVKVN-GILLERAAVN-------VMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +     +        V+    + V   P+        + + +KP 
Sbjct: 85  ERCIQAGTLTVNYDKVPIDYKLKHNDLLANVVHRHEVPVTSQPITIVHMDEDIVVVNKPA 144

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
            +          +TV   L   +    + ++ RLD  T GLLL       AR +E     
Sbjct: 145 SIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRN 204

Query: 141 --WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--------GSNAWVT 190
               + Y  R  G+   + +   K+ I +     G  +V+   +         G N   +
Sbjct: 205 RLVQKEYVCRVEGEFPDEIIE-CKEPIEVVSYKIGVCKVSPKGKDCNTIFQKLGFNGKTS 263

Query: 191 VGL---REGKNREIKKVFEFFNWKVNR 214
           + L   + G+  +I+   ++  + V  
Sbjct: 264 IVLCKPKTGRMHQIRVHLQYLGYPVVN 290


>gi|329769221|ref|ZP_08260640.1| hypothetical protein HMPREF0433_00404 [Gemella sanguinis M325]
 gi|328839352|gb|EGF88932.1| hypothetical protein HMPREF0433_00404 [Gemella sanguinis M325]
          Length = 294

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 65/196 (33%), Gaps = 33/196 (16%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRKAERTRLWLYHKPI 82
              +KVNG   E     +   D +E+              +       E   L + +KP 
Sbjct: 38  DGSIKVNGK-EENVRYILKKNDVVEITLPSEEFSEHVRFFEDKLDIIYEDEYLLIVNKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI------SVGRLDINTEGLLLLTNDGGLARVLEL 136
            L +  S  +  S++ + +   F +         V RLD NT GL+L+         L  
Sbjct: 97  DLPSIPSRNNEDSSLLEIVNGYFKKNHYSTIPHIVTRLDKNTTGLVLIAKH-RHIHALFS 155

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNL--------LKKGIVIQGICYGDMQVTLDTQKGSN-- 186
              +  + Y     G+V+   +          +    V     Y   QV  +     N  
Sbjct: 156 KE-EIDKFYLALVVGKVEDGIIEANIKRASDSIITRCVADDGDYAKTQVWSEKYNFKNNI 214

Query: 187 AWVTVGLREGKNREIK 202
           + V + L  G+  +I+
Sbjct: 215 SLVKLKLFTGRTHQIR 230


>gi|229068942|ref|ZP_04202236.1| Pseudouridine synthase [Bacillus cereus F65185]
 gi|228714226|gb|EEL66107.1| Pseudouridine synthase [Bacillus cereus F65185]
          Length = 307

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 88/265 (33%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   E  +V++  P   ++ 
Sbjct: 274 INFLHPITKEAIEVDVPFPTKLNKK 298


>gi|49477179|ref|YP_035519.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49328735|gb|AAT59381.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 307

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNERLKEGDKLQVHMFMEEEYDVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGGTKYMSRQALHAMT 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|262374097|ref|ZP_06067374.1| 23S rRNA pseudouridylate synthase [Acinetobacter junii SH205]
 gi|262311108|gb|EEY92195.1| 23S rRNA pseudouridylate synthase [Acinetobacter junii SH205]
          Length = 310

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 83/240 (34%), Gaps = 52/240 (21%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQEGQRIDNFLFTRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETRLSIGDQIRVA 71

Query: 63  ---------------DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                          DGV      R         + +KP G+        G    +  + 
Sbjct: 72  PIRYEQKDETDAPVSDGVAQSLLSRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGLIE 127

Query: 103 SIF-----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV-- 153
           ++        +  + R+D +T GL++++      ++L   L   +  + Y     GQV  
Sbjct: 128 AMRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIKKTYAAIVKGQVSL 187

Query: 154 DQDKLNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           DQ  ++       L  G     +  +G         ++  K +   V      G+  +I+
Sbjct: 188 DQQLIDAPLLRYELANGERRVRVTKEGKPSKTEWKVIERFKAAT-LVHASPLSGRTHQIR 246


>gi|221142167|ref|ZP_03566660.1| pseudouridylate synthase [Staphylococcus aureus subsp. aureus str.
           JKD6009]
 gi|304380548|ref|ZP_07363223.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|269941321|emb|CBI49718.1| RNA pseudouridylate synthase [Staphylococcus aureus subsp. aureus
           TW20]
 gi|302751659|gb|ADL65836.1| RluA, Pseudouridylate synthase, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus str. JKD6008]
 gi|304340877|gb|EFM06802.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|329314526|gb|AEB88939.1| RluA, Pseudouridylate synthase, 23S RNA-specific [Staphylococcus
           aureus subsp. aureus T0131]
          Length = 273

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMD-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRCVSPTGQRAITHILTSKMIKEAVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>gi|157962710|ref|YP_001502744.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157847710|gb|ABV88209.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 284

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/189 (16%), Positives = 55/189 (29%), Gaps = 35/189 (18%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRV 108
                I      L + +   +   HKP GL+   S    R   F      D +      V
Sbjct: 26  DEEQEIAPHIEVLFEDDDIVVI--HKPAGLLVHRSYLARRERFFAMQLTRDLVGC---HV 80

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD-KLN-LLKKG 164
             V RLD  T G+LL      +A VL     +    + Y     G + +   L+  LK+ 
Sbjct: 81  FPVHRLDRPTSGILLFAKSSEMANVLCEQFAAHTVDKEYLAIVRGNMHEAGTLDYALKEE 140

Query: 165 I-VIQGICYGDMQVTLDTQKGSN-------------------AWVTVGLREGKNREIKKV 204
           +  +        +   D                         A V +    G+  ++++ 
Sbjct: 141 LDELGDKDVDPNKAAQDAVTSYKPLLNSEIPFSSGRYATSRYALVQLSPHTGRKHQLRRH 200

Query: 205 FEFFNWKVN 213
                  + 
Sbjct: 201 MAHLRHPIL 209


>gi|86151843|ref|ZP_01070057.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|86153369|ref|ZP_01071573.1| hypothetical RNA pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|121612323|ref|YP_001000404.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|167005346|ref|ZP_02271104.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|315124210|ref|YP_004066214.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|85841472|gb|EAQ58720.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|85843095|gb|EAQ60306.1| hypothetical RNA pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni HB93-13]
 gi|87249488|gb|EAQ72448.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|315017932|gb|ADT66025.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
          Length = 250

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 74/199 (37%), Gaps = 27/199 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA ++  +  ++     P    E  ++
Sbjct: 7   KLLALQEKISNREAKDLIDKGCVFSHGKKVVVARALMSDKARFNVIKTKNPQIIFEDDKI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   V+            D      +++  + RLD  T G++LL  D    ++  
Sbjct: 67  IAINKPYAYVSE-----------DLEKKFNAKL--LNRLDKETSGVILLCKDEDFRKLCI 113

Query: 136 LPSTQW--LRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ---------VTLDTQK 183
               +    + Y     G + ++ ++N     I  +G     +          +T    +
Sbjct: 114 EEFKKHRVYKSYIAVLDGVLAEEVEVNEPIFTIKAKGGALSKVSKDGLSALSIITPIMMQ 173

Query: 184 GSNAWVTVGLREGKNREIK 202
                  + ++ G+  +I+
Sbjct: 174 SKKTLTKIVIQTGRTHQIR 192


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

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 76/237 (32%), Gaps = 63/237 (26%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------------------DGVPL 67
           ++++   +++V+G   +     V     I V                        DG  L
Sbjct: 35  QKLLRSGQIRVDGARAKS-DTRVQPGQTIRVPPLGVDAKDTKTGPIGGRDLRHSSDGDLL 93

Query: 68  RK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDI 116
            +    E  ++ + +KP GL        G S V  ++  +     S        V RLD 
Sbjct: 94  SRMVLHEDAKVIVLNKPAGLAV-----QGGSGVSRHIDKMLEAWTSQKGEKPRLVHRLDR 148

Query: 117 NTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------------QVDQDK 157
           +T G+L++    G A+ L          ++Y     G                   D D+
Sbjct: 149 DTSGVLVIARTRGAAQQLTAAFRERDTRKIYWSLVKGVPRKREDRISTWLVKEQTPDGDR 208

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + + K G    G  +      +  Q G N AW+ +    G+  +++         + 
Sbjct: 209 MRIAKHG--DDGADHAISYYRIVEQAGQNLAWLEMEPYTGRTHQLRVHAAHIGHPII 263


>gi|146306651|ref|YP_001187116.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina ymp]
 gi|145574852|gb|ABP84384.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina ymp]
          Length = 332

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 82/246 (33%), Gaps = 63/246 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMST 57
           V  +F  QR+   +       R +++        R++ +  V+VN G +  +    + + 
Sbjct: 31  VAPDFAGQRIDNFL-------RTQLKGVPKTLIYRILRKGEVRVNKGRI--KPEYKLQAG 81

Query: 58  DHIEV---------DGVPLRK-----------AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           D + V         +  P+ +            E   L + +KP G+            +
Sbjct: 82  DIVRVPPLRLAERDEPEPVAQGLLERLEAAIVYEDKALIVLNKPAGIAVHGGSGLNYGVI 141

Query: 98  --FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-- 151
             F  L      +  V RLD +T GLL++     + R L   L      + Y     G  
Sbjct: 142 EAFRQLRPDAKDLELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGDGVDKRYMALVRGHW 201

Query: 152 ---------QVDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVGLRE-----G 196
                     + +  L   ++ + + G     + +  +  + G  A     L E     G
Sbjct: 202 ATAKKQVNAPLQKSNLRSGERMVEVDGEGKEALTLFRVLRRFGDFA----TLVEAKPVTG 257

Query: 197 KNREIK 202
           +  +I+
Sbjct: 258 RTHQIR 263


>gi|329728300|gb|EGG64739.1| pseudouridine synthase, RluA family [Staphylococcus aureus subsp.
           aureus 21172]
          Length = 258

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 17  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHL 76

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 77  HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 134

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 135 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 194

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 195 HQIRVHFQHIGHPIV 209


>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 = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+  VI R G  S R E  ++++ + V VNG ++   +  V + D + V
Sbjct: 9  RLDNVIYRMGFGSTRAEARQLVSHKAVTVNGQVVNIPSYQVKAGDVVAV 57


>gi|325289223|ref|YP_004265404.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964624|gb|ADY55403.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 303

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/228 (16%), Positives = 79/228 (34%), Gaps = 36/228 (15%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVP 66
           ++A   + S   V R+  Q +++VNG L+      + + D + ++             +P
Sbjct: 22  LLASKLLLSHSLVVRLKHQNKIQVNGQLVHT-NYRLQAGDFVTINIDLSEENNIIPESIP 80

Query: 67  LR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTE 119
           L    E       +KP G+    S   G  T+ + +   +  +        + RLD +T 
Sbjct: 81  LDIVYEDEDFVAVNKPAGMSIHPSRLGGTGTLANAVTYHWQGLGRNILFRPINRLDKDTS 140

Query: 120 GLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD-----------KLNLLKKGI 165
           GL+L+      A       L   +  R Y       + +D             N  ++ I
Sbjct: 141 GLVLI-GKSQFAHQGIFNQLKQHKIDRRYIALVERALTRDHGHIDQPIARPDANK-RRRI 198

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           V            +  +   +  +++ L  G+  +I+    +    V+
Sbjct: 199 VHPAGQAATTHYQVLDRYPDHTLLSLKLETGRTHQIRVHLSYIGHPVS 246


>gi|304438848|ref|ZP_07398773.1| RluA family ribosomal large subunit pseudouridine synthase
           [Peptoniphilus duerdenii ATCC BAA-1640]
 gi|304372689|gb|EFM26270.1| RluA family ribosomal large subunit pseudouridine synthase
           [Peptoniphilus duerdenii ATCC BAA-1640]
          Length = 313

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/253 (16%), Positives = 81/253 (32%), Gaps = 60/253 (23%)

Query: 1   MKDKNIVQENFTPQRVS----KVIARAGIASRREVERMI----AQQRVKVNGILLERAAV 52
           MK+  I+  N   QR+     K +  A        + +I     ++ + VN         
Sbjct: 1   MKE-IIINSNDKDQRLDRFMGKYLQNAK-------KSLIMKSIRKKNITVNNKKSA-PEY 51

Query: 53  NVMSTDHIEVD--GVPLRK----------------AERTRLWLYHKPIGLVTTHSDPDGR 94
            +   D +E+      + K                 E   + L  KP GL+T +   D  
Sbjct: 52  ILKENDRVEIYFSDETIEKFTKIKNHVKRDFPDIIYEDENIALVKKPRGLLTHNDKKDYE 111

Query: 95  STVFD-----------NLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPST-- 139
               D            +P +          RLD NT G+L+   +    R +       
Sbjct: 112 KNALDMFVSYMIHKGEYVPRVEKSFRPSFCNRLDRNTSGILIGCKNAQALREINDAIKRR 171

Query: 140 QWLRVYRVRFHGQVDQD--KLNLLKKG-----IVIQ---GICYGDMQVTLDTQKGSNAWV 189
           +  + Y     G +D++   ++ L+K      + +         +  +    + G    V
Sbjct: 172 EIEKHYMALVDGSIDEEIHDISYLEKDREKNKVSLNERGDGKEIETIIRPMEKLGEYTLV 231

Query: 190 TVGLREGKNREIK 202
            + L  G+  +I+
Sbjct: 232 DINLITGRTHQIR 244


>gi|196248006|ref|ZP_03146708.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
 gi|196212790|gb|EDY07547.1| pseudouridine synthase, RluA family [Geobacillus sp. G11MC16]
          Length = 299

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 85/240 (35%), Gaps = 46/240 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP GL T  S      T+ + L   + +      V  + RLD +T GL+L+
Sbjct: 87  EDEYVLVVNKPAGLATIPSRHHPGGTLANGLLHHYRQQQLDSTVHIITRLDRDTSGLVLV 146

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK--LNL---------LKKGIVIQGIC 171
                +  +L       Q  R Y    HG +D+++  ++          + + +   G  
Sbjct: 147 AKHRHVHHLLSTLQQKGQVTRTYEAVCHGVIDEEEGTIDAPIGRQNDSIIAREVREDGKR 206

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  L+   G   +V++ L  G+  +I+    +              P     L  G
Sbjct: 207 AITHFRVLERLSGYT-YVSLRLETGRTHQIRVHLAYLGH-----------PLAGDELYGG 254

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           S         RE +G   L   Q++   P        R      + +PDD  R+ + + +
Sbjct: 255 S---------REIIGRQALHSRQLSFFHPF------ARQLYTFTAPLPDDMARLIEAARK 299


>gi|138894383|ref|YP_001124836.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
 gi|134265896|gb|ABO66091.1| ribosomal large subunit pseudouridine synthase D-like protein
           [Geobacillus thermodenitrificans NG80-2]
          Length = 299

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 85/240 (35%), Gaps = 46/240 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP GL T  S      T+ + L   + +      V  + RLD +T GL+L+
Sbjct: 87  EDEYVLVVNKPAGLATIPSRHHPGGTLANGLLHHYRQQQLDSTVHIITRLDRDTSGLVLV 146

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK--LNL---------LKKGIVIQGIC 171
                +  +L       Q  R Y    HG +D+++  ++          + + +   G  
Sbjct: 147 AKHRHVHHLLSTLQQKGQVTRTYEAVCHGVIDEEEGTIDAPISRQNDSIIAREVREDGKR 206

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  L+   G   +V++ L  G+  +I+    +              P     L  G
Sbjct: 207 AITHFRVLERLSGYT-YVSLRLETGRTHQIRVHLAYLGH-----------PLAGDELYGG 254

Query: 232 STREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           S         RE +G   L   Q++   P        R      + +PDD  R+ + + +
Sbjct: 255 S---------REMIGRQALHSRQLSFFHPF------ARQLYTFTAPLPDDMARLIEAARK 299


>gi|46907201|ref|YP_013590.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes serotype 4b str. F2365]
 gi|254852463|ref|ZP_05241811.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|254931351|ref|ZP_05264710.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300764179|ref|ZP_07074174.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|46880468|gb|AAT03767.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Listeria monocytogenes serotype 4b str. F2365]
 gi|258605772|gb|EEW18380.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL R2-503]
 gi|293582902|gb|EFF94934.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes HPB2262]
 gi|300515169|gb|EFK42221.1| RluA family ribosomal large subunit pseudouridine synthase
           [Listeria monocytogenes FSL N1-017]
 gi|332311376|gb|EGJ24471.1| Pseudouridylate synthase [Listeria monocytogenes str. Scott A]
          Length = 296

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 89/264 (33%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A+ +++VN         +V + D + +          L           E   L + +KP
Sbjct: 37  AEGKIEVNNEEQNVL-YHVKAGDKVRLTFPTEQQNERLLAEYTDLDIIFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEKYMAFDLPLPAD 287


>gi|304319748|ref|YP_003853391.1| Ribosomal large subunit pseudouridine synthase C [Parvularcula
           bermudensis HTCC2503]
 gi|303298651|gb|ADM08250.1| Ribosomal large subunit pseudouridine synthase C [Parvularcula
           bermudensis HTCC2503]
          Length = 324

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 35/176 (19%), Positives = 59/176 (33%), Gaps = 41/176 (23%)

Query: 12  TPQRVSKVIARAGIASRR-------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
             QR+ + +       RR       +V++ + + +V++NG  ++ A   V S + + V  
Sbjct: 18  AGQRLDRWMK------RRFPGVTQGQVQKWLRKGQVRLNGGRVK-ADHRVESGEVVRVPP 70

Query: 63  -DGVP--------------------LRKAERTRLWLYHKPIGLVTTH--SDPDGRSTVFD 99
            D                       L   E   +   +KP GL              + D
Sbjct: 71  IDPEAAAPPPSRPVVGPAEAEMMRGLVIYEDDDILALNKPAGLAVQGGAKTLIHIDGMLD 130

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
                 +R   V RLD +T G+LLL     +A  L L     +  + Y     G  
Sbjct: 131 VFGEGEARPRLVHRLDRDTGGVLLLAKSRAVAATLSLAFQQHRIGKTYWAITKGVP 186


>gi|242212896|ref|XP_002472279.1| predicted protein [Postia placenta Mad-698-R]
 gi|220728646|gb|EED82536.1| predicted protein [Postia placenta Mad-698-R]
          Length = 448

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 77/207 (37%), Gaps = 31/207 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAERTR---LWLYHKPI 82
           +      +NG + +     V + D IE         V   P+R     R     +  KP 
Sbjct: 46  LESGVTTINGKIAK-PDTIVQNGDRIENVVHRHEPPVTATPVRIIHHDREREFIIIDKPG 104

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +    S    R+++ + L + F   +V ++ RLD  T GL+++     +A  L     +
Sbjct: 105 SIPVHASGRFFRNSLVEILKNDFGFKKVYTINRLDRLTSGLMIIPLSSSMANTLTQEFAA 164

Query: 139 TQWLRVYRVRFHGQVDQDKLN----LL----KKGIVI---QGICYGDMQVTLD-TQKGSN 186
               + Y  R  GQ  +++L     LL    + G+ +   +G     +   +        
Sbjct: 165 GTIRKEYIARCRGQFPEEELACEVPLLTIDRQMGLNVVHPEGKPAKTIFKRMHYDANTDT 224

Query: 187 AWVTVG-LREGKNREIKKVFEFFNWKV 212
           + V    L  G++ +I+   ++    V
Sbjct: 225 SVVHCEPLT-GRSHQIRVHLQYLGHPV 250


>gi|150402179|ref|YP_001329473.1| RluA family pseudouridine synthase [Methanococcus maripaludis C7]
 gi|150033209|gb|ABR65322.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C7]
          Length = 298

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 51/280 (18%), Positives = 109/280 (38%), Gaps = 47/280 (16%)

Query: 33  RMIA----QQRVKVNGI-LLERAAVNVMSTDHIEVD-GVPLRKAERTRLWLYH------- 79
           +MI     ++++ VN   +  ++ +    T  +E+D G+     E   L + +       
Sbjct: 34  KMIKKFDKEKKIFVNSKNISLKSKLKENETVSVEIDCGINTIDPENLALNIIYEDDDLLI 93

Query: 80  --KPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLA 131
             KP  +V   +      T+ + + +         ++  V RLD++T GLL++  D    
Sbjct: 94  VDKPKNMVVHPTKNVLSKTLANAVSNHQKINNQNYKIRFVNRLDMDTTGLLIIAKDPYSH 153

Query: 132 RVLELPSTQ--WLRVYRVRFHGQVD------QDKLNLLKKGI--VIQGI-CYGDMQVTLD 180
           + L     +    ++Y    +G +D      +D ++L   GI   +  +      +  + 
Sbjct: 154 QHLAKQMDEGILEKIYIAVVNGHLDLKEGIIEDSIDLNDDGIKRELSNVGKISKTKYKVI 213

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
            +  + + + + L  G+  +I+            +   + G   +G +L G   E+S  I
Sbjct: 214 EELKNASILEINLLTGRTHQIR------------VHLSNIGNPIIGDVLYG---EISDLI 258

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
            R+ L  H+L          +  S  L +D  N+I  + D
Sbjct: 259 NRQALHSHILSIIHPITKEKMKFSSNLPKDIENLIENLKD 298


>gi|323702975|ref|ZP_08114632.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
 gi|323532106|gb|EGB21988.1| pseudouridine synthase, RluA family [Desulfotomaculum nigrificans
           DSM 574]
          Length = 293

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 40/225 (17%), Positives = 82/225 (36%), Gaps = 40/225 (17%)

Query: 22  RAGIA-SR---REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------GVPLR 68
           R G+  SR   R  ++   ++ V ++G  +    V V     +E+            P+ 
Sbjct: 21  RQGLGVSRSLLRRAKQ---RRAVLLDGQPVNS-NVRVAPGAILEISMQQEVSSIVPEPMD 76

Query: 69  K---AERTRLWLYHKPIGLVTT--HSDPDG---RSTVFDNLPSIFS-RVISVGRLDINTE 119
                E   +   HKP G++     ++P G      ++  L      R   V R+D +T 
Sbjct: 77  LSIIYEDQDIMAVHKPPGMLVHPLTTEPTGTLANGVLYYWLQQGSPARFRPVHRIDRDTS 136

Query: 120 GLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK------LNLLKKGIVIQGIC 171
           GL+L+  +  + + L+    Q    R Y     G++ + K      ++  + G +I+ + 
Sbjct: 137 GLVLVARNSYVHQQLQSQINQGLMCRRYLAMVTGKLAKQKGTITAPIDR-EAGSLIKRVV 195

Query: 172 YGDMQV-----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +       +  Q    + V V L  G+  +++         
Sbjct: 196 TPAGKPAITHYRVLRQLSWGSLVRVELVTGRTHQVRVHMSHIGHP 240


>gi|291545303|emb|CBL18411.1| pseudouridine synthase, RluA family [Ruminococcus sp. SR1/5]
          Length = 380

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/174 (20%), Positives = 64/174 (36%), Gaps = 34/174 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLL 124
           E   +   +KP G+VT  S      ++ + + S F       +V S+GRLD  T G+LL 
Sbjct: 135 EDQDILAINKPAGIVTHPSGSHYSDSLANQVASYFRSKGEPTKVRSIGRLDKETSGILLF 194

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHG--QVDQDKL-------------NLLKKGI-- 165
             +   A  L+    +    + Y     G   VD+D               N LK  +  
Sbjct: 195 ARNQTAAARLQNQREEGISEKTYLAAVSGFMPVDEDGAFHRISVPLAPDPDNRLKMVVST 254

Query: 166 --VIQGICYGDMQVTLDTQKGSN-----AWVTVGLREGKNREIK-KVFEFFNWK 211
              + G  + +   ++    G +     + V + L+ G+  +I+  +       
Sbjct: 255 DGTLPGSKHAETLYSVLKSTGPDAAAPASLVMLRLKTGRTHQIRVHM-ASLGHP 307


>gi|269798210|ref|YP_003312110.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269094839|gb|ACZ24830.1| pseudouridine synthase, RluA family [Veillonella parvula DSM 2008]
          Length = 324

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 19/131 (14%), Positives = 41/131 (31%), Gaps = 16/131 (12%)

Query: 40  VKVNGILLE---------RAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLV---- 85
           + VNG                + +       +  + L    E   + + +K  G++    
Sbjct: 43  ITVNGKPATWNTLVHGGDHLIMKLTPEQEFSLSPMELDIIYEDEYILVINKAAGILMHPT 102

Query: 86  TTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLR 143
           +T  D    + V               V RLD +T G++++     +    +   T + +
Sbjct: 103 STIRDHTLANGVLHYYQETNQHYDFHPVHRLDKDTSGIVIIAKTSVVQHAFDKKHTHFYK 162

Query: 144 VYRVRFHGQVD 154
            Y     G + 
Sbjct: 163 SYDAIVEGHLP 173


>gi|160880920|ref|YP_001559888.1| RluA family pseudouridine synthase [Clostridium phytofermentans
           ISDg]
 gi|160429586|gb|ABX43149.1| pseudouridine synthase, RluA family [Clostridium phytofermentans
           ISDg]
          Length = 346

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/274 (14%), Positives = 86/274 (31%), Gaps = 81/274 (29%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVMSTDHI 60
            + +N   QR+ K +A+       +       +M+ ++ + +NG      A  ++  D +
Sbjct: 22  TIVQNEAGQRLDKFLAKYL----NKAPKSFFYKMLRKKNITLNGKKA-EGAEKLIEGDIV 76

Query: 61  E--------------------VDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
                                V+   ++     E + + + +KPIG+++  +     S V
Sbjct: 77  RLFLAEETIESFKESYQLDAKVNQRAVKLDVLYEDSHVVIINKPIGMLSQRAKESDVSLV 136

Query: 98  FDNLPSIFS------------RVISVGRLDINTEGLLLLTND----GGLARVLELPSTQW 141
              +  +              +     RLD NT G+++          ++  L+  S   
Sbjct: 137 ELLIAYLLEMGSLTKEELSTFKPSVCNRLDRNTSGIVIAGKSLLGLQEMSAKLQDRSLH- 195

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSN------------ 186
            + YR    G +         KG  I G    D    +V + T   ++            
Sbjct: 196 -KYYRCIVKGTMT--------KGARINGYLAKDEKTNKVRITTNDPNDGESSYIETEYQP 246

Query: 187 -------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                    + V L  GK  +I+         + 
Sbjct: 247 ILSKNGYTLLEVLLITGKTHQIRAHLSSIGHPII 280


>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 = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/267 (13%), Positives = 87/267 (32%), Gaps = 70/267 (26%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVM 55
           K  +  N + QR+ K +       R+         + + I +  VK+NG  ++    ++ 
Sbjct: 2   KIEIGANESGQRMDKFL-------RKMLTDVPLGAIYKSIRKGDVKINGKKVKE-KYSLN 53

Query: 56  STDHIEV-------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
             D +E+                   + + +   ++  + +  KP G++      +   T
Sbjct: 54  LGDIVEIRDIKTNAEKHNDFKAIEGANELKVTYEDQNMIIVEKKP-GVLVHSDKKNSDPT 112

Query: 97  VFDNLPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           + D + S                   S  RLD NT G+++   +    + L   +     
Sbjct: 113 LTDYVLSYLYDKGDYVPEEEITFTPASCNRLDRNTAGIIIFGKNYESLKDLNQMIRERHV 172

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--------------- 186
            + Y+    G++       L K  +++        +  + +K S                
Sbjct: 173 DKYYQALVCGKIKDG----LYKAHIVKDEKSNKSYIHKEPKKNSKEIEMEVKTIQTCGTY 228

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + + + L  G++ +I+         + 
Sbjct: 229 SLLEIQLITGRSHQIRAHLSSLGNPIV 255


>gi|47566178|ref|ZP_00237206.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
 gi|47556731|gb|EAL15062.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 92/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHYQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +  +
Sbjct: 165 ERKIKRTYVALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKNQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|228957662|ref|ZP_04119409.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
 gi|228802004|gb|EEM48874.1| Pseudouridine synthase [Bacillus thuringiensis serovar pakistani
           str. T13001]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 86/261 (32%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|229189473|ref|ZP_04316490.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
 gi|228594064|gb|EEK51866.1| Pseudouridine synthase [Bacillus cereus ATCC 10876]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 86/261 (32%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|127513571|ref|YP_001094768.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126638866|gb|ABO24509.1| tRNA pseudouridine synthase C [Shewanella loihica PV-4]
          Length = 273

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/173 (18%), Positives = 52/173 (30%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   L   HKP GL+   S    R   F      D +      V  V RLD  T G+LL 
Sbjct: 28  EDDDLVAIHKPAGLLVHRSYLARREKYFAMQMTRDLVGC---HVFPVHRLDRPTSGVLLF 84

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN--LLKKGI-VIQGICYGDMQVTL 179
                +A  L     S    + Y     G + +  L    LK+ +  +        +   
Sbjct: 85  AKSSEMANQLCEQFASKSVQKHYVALVRGNMHEPGLLDYPLKQELDELGDKNVDPNKAAQ 144

Query: 180 DTQKGSN-------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + Q   +                   A V +    G+  ++++        + 
Sbjct: 145 EAQTSYHPLLNCEIPYPSGRYASSRYALVQLTPHTGRKHQLRRHMAHLRHPII 197


>gi|329117419|ref|ZP_08246136.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
 gi|326907824|gb|EGE54738.1| pseudouridine synthase, RluA family [Streptococcus parauberis NCFD
           2020]
          Length = 297

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/211 (16%), Positives = 70/211 (33%), Gaps = 37/211 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRK-----------AERTRLWLYHKP 81
              ++ VN    + A   +   D + +   D +P  K            E     + +KP
Sbjct: 33  RGGKILVN-EQEQNATYLLDINDIVTIHIPDELPFEKLEAVSHPLDIVYEDEHFLVINKP 91

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
            G  +  S     +T+ + + + +        +V  V RLD +T GL+L    G     L
Sbjct: 92  FGFASIPS-AIHSNTIANFIKAYYIEKDYPNKQVHIVTRLDRDTSGLMLFAKHGYAHARL 150

Query: 135 --ELPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             +L +    + Y     G             + + K +++ + +   G         + 
Sbjct: 151 DKQLQARSIDKHYYALVSGPGQLPDSGEIIAPIGRSKDSIITRAVDPMGKYAKTTYQVVG 210

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +   V + L  G+  +I+  F    + 
Sbjct: 211 RFAENVHLVDIKLHTGRTHQIRVHFSHIGFP 241


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

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 22  EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 74

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 75  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 130

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 131 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 189

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 190 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 247

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 248 GNNLAWLEMEPYTGRTHQLR 267


>gi|317178694|dbj|BAJ56482.1| hypothetical protein HPF30_0385 [Helicobacter pylori F30]
          Length = 245

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 67/201 (33%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 9   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 68

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 69  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVRENSEFHLKA 116

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 117 KKAFKDRAVKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 174

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 175 IINKKTLLKVGIKTGRTHQIR 195


>gi|305433225|ref|ZP_07402381.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304443926|gb|EFM36583.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 250

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/207 (14%), Positives = 70/207 (33%), Gaps = 43/207 (20%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S RE + +I +  V  +G   ++ RA ++  +   I     P    E   +
Sbjct: 7   KLLALQENISNREAKDLIDKGCVFSHGKKVVVARALMSDKTKFSIVKTSKPKVIFEDENI 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   ++   +    + +               RLD  T G++LL  +    ++  
Sbjct: 67  IAINKPYAYISEELEKKFNAKLL-------------NRLDKETSGVILLCKNEDFRKICI 113

Query: 136 LPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKG----- 184
               +    + Y     G + ++        I I      I   +  ++  +++G     
Sbjct: 114 EEFKKQRVYKSYIAVLDGILAEE--------IEIDEPILTIKTKNGALSKISKEGLSAVS 165

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                          + ++ G+  +I+
Sbjct: 166 IFTPIMMQAKKTLAKIIIKTGRTHQIR 192


>gi|291166075|gb|EFE28121.1| pseudouridine synthase, RluA family [Filifactor alocis ATCC 35896]
          Length = 298

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/268 (16%), Positives = 86/268 (32%), Gaps = 55/268 (20%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLRKAERTR 74
           SRR          V VNG L       V   + I VD            GV     E   
Sbjct: 42  SRRA---------VNVNGTL-RFNHEPVHVGEIITVDLGENRSEYGLEEGVVDVIYEDED 91

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDG 128
           +   +K   +V   +      T+ + + S F       +V  + RLD +T G+LL+  + 
Sbjct: 92  IVAVNKSPFIVVHPTGTHLTGTLLNYMESWFRQNGILEKVRFISRLDRDTSGILLIAKNR 151

Query: 129 GLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN-------LLKKGI---VIQGICYGDMQ 176
                +          + Y     G++ + +             GI   V++       +
Sbjct: 152 YAHHRMSQAHQDMMMQKTYVALIEGKMKRQEGEINAPIGRRENDGIKREVMEDGQTAITK 211

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             +  +    + V +    G+  +++    +  + +        G     +L  G+   +
Sbjct: 212 YKVLKEGEKFSLVELTPVTGRTHQLRCHMAYIGYPL-------IG----DSLYGGNMEYM 260

Query: 237 SKKILR----EQLGPHLLEEAQVNLDAP 260
           +++ L     E   P   E+  +  + P
Sbjct: 261 NRQALHSVTLEFFSPRKEEKIYLKAELP 288


>gi|210631097|ref|ZP_03296753.1| hypothetical protein COLSTE_00638 [Collinsella stercoris DSM 13279]
 gi|210160185|gb|EEA91156.1| hypothetical protein COLSTE_00638 [Collinsella stercoris DSM 13279]
          Length = 227

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 50/154 (32%), Gaps = 27/154 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLLLT 125
           L    KP G++  H D  G  T+ D + +           +   ++ RLD +T G++L +
Sbjct: 16  LMAVDKPAGIIV-HGDGTGAPTLTDAVRAHLVASGEASASAAAQALQRLDRDTTGIVLFS 74

Query: 126 NDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---------------LNLLKKGIVIQ 168
            D          +      + Y    HG+    K               + + + G    
Sbjct: 75  LDKEAQPAFDRMIAERSIQKRYLAIVHGRFPAAKTMCQPLGRDRHDSRRMRVSRTGKPAH 134

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      D +    + + + L  G+  +I+
Sbjct: 135 TDAKRIAYAKADARAPERSLLAIDLHTGRKHQIR 168


>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 = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQENGENINPHIVTRLDRNTTGIVIFAKYGYIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|321474676|gb|EFX85641.1| hypothetical protein DAPPUDRAFT_32502 [Daphnia pulex]
          Length = 250

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/170 (20%), Positives = 57/170 (33%), Gaps = 48/170 (28%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPS-----IFSRVISVGRLDINTEGLLLLTNDGG 129
           +    KP GLVTT +D + +  + + LP         ++ +V RLD +T G+LLL ++  
Sbjct: 1   IVAIDKPHGLVTTDADGNAKVVLTNLLPGLSQALRVEKLYTVHRLDRDTTGILLLASNQT 60

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQ--------------DKLNLL------------ 161
           +A  L       +  + Y V   G                       +            
Sbjct: 61  VANKLNKLFLDHEIQKKYMVITKGIPSPREGTIDIPMCEKSIGDRQRMALRPVLSHSPDS 120

Query: 162 -------KKGIVIQGICY--------GDMQVTLDTQKGSNAWVTVGLREG 196
                   KG   + I +        G   V L+ + G    + V L EG
Sbjct: 121 LKSAKYNAKGKSFKAITHFWVKTTNAGTAFVELEPETGVRHQLRVHLSEG 170


>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 = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 88/241 (36%), Gaps = 43/241 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           M+  N+ V++ F   R+   +++  I    SR  ++ +I +  V VN    ++    +  
Sbjct: 1   MEKINLQVEKEFDNVRLDLYLSK--IFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKV 57

Query: 57  TDHIEVD---GVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
            D+IEV+      L+            E   + + +KP  +V   +      T+ + L  
Sbjct: 58  GDNIEVNIPEPKLLQIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLH 117

Query: 104 IFSRVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
               +           V R+D +T G+L++  +      L          RVY     G 
Sbjct: 118 HCKDLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGI 177

Query: 153 VDQDK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +  ++           ++ +K  +V +   +      +  +  ++  V   L  G+  +I
Sbjct: 178 IKYEQGTIEAPIGRHPVDRIKMAVV-KDGRHAVTHYKVIERFKNHTLVECRLETGRTHQI 236

Query: 202 K 202
           +
Sbjct: 237 R 237


>gi|50119965|ref|YP_049132.1| tRNA pseudouridine synthase C [Pectobacterium atrosepticum
           SCRI1043]
 gi|49610491|emb|CAG73936.1| putative RNA pseudouridylate synthase [Pectobacterium atrosepticum
           SCRI1043]
          Length = 261

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 53/170 (31%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   +  V   +       V +V RLD  T G+LLL   
Sbjct: 7   QDEHLVAVNKPSGWLVHRSWLDRKEKIVVMQTVRDQIGQHVYTVHRLDRPTSGVLLLALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR L     S Q  ++Y     G V           ++L+ +               
Sbjct: 67  SEVARALSQQFESHQMQKMYHAVVRGYVLDDGVIDYALTEELDKIADKFANPDKAPQPAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  Q  +    G        L E     G+  ++++     +  + 
Sbjct: 127 THYRSLAQAEMPVAIGRYPTARYSLMELKPQTGRKHQLRRHMSHLHHPII 176


>gi|309776002|ref|ZP_07670994.1| ribosomal large subunit pseudouridine synthase C
           [Erysipelotrichaceae bacterium 3_1_53]
 gi|308916284|gb|EFP62032.1| ribosomal large subunit pseudouridine synthase C
           [Erysipelotrichaceae bacterium 3_1_53]
          Length = 323

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 52/275 (18%), Positives = 89/275 (32%), Gaps = 83/275 (30%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLE---- 48
           MK+   + EN   QRV K I +        ++        + I  +++KVN    E    
Sbjct: 1   MKEF-YIGENDADQRVDKFIQKT-------MKTMPKSLMYKYIRNKKIKVNRKRCEISQR 52

Query: 49  ---------------------RAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
                                R  + V ST  I          E   + L +KP GL   
Sbjct: 53  LALGDTMQCYIAEEFYETQSMRQFLQVPSTLDIVY--------EDEHILLINKPKGLRAH 104

Query: 88  HSDPDGRSTVFDNL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
               + +  + D L           P+           R+D NT+GL++       A  L
Sbjct: 105 SDTSEVQDNLADRLLHYLYESQEYDPAHEQSFTPALCHRIDRNTQGLVIAA---KTAAAL 161

Query: 135 ELPSTQ-----WLRVYRVRFHGQV--DQDKL---------NLLKKGIVIQGICYGDMQ-- 176
              + +       + Y     G +   QD +         + + + I  +   Y  M+  
Sbjct: 162 RCMNEKIAAREVEKKYLCIIQGGLRKQQDHIVLYHRKKEQDNIAEVIEHEQEGYARMETS 221

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +   KGS + V V L  GK+ +I+ +  +    
Sbjct: 222 YRVLQDKGSYSLVEVELHSGKSHQIRALMSWLGHP 256


>gi|229844088|ref|ZP_04464229.1| tRNA pseudouridine synthase C [Haemophilus influenzae 6P18H1]
 gi|229813082|gb|EEP48770.1| tRNA pseudouridine synthase C [Haemophilus influenzae 6P18H1]
          Length = 239

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 57/185 (30%), Gaps = 37/185 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLK-------------- 162
             +A ++          + Y     G +            +L+ +               
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLTVVRGYLQGKAQIDYPLKIQLDKIADKFSQENKGSQEAI 126

Query: 163 ---KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRIS 219
              +G+ I  + Y   +     Q    + V +    G+  ++++  +     +  L    
Sbjct: 127 TDYEGLKIVEMPYPAGRY----QTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQ 180

Query: 220 YGPFQ 224
           YG   
Sbjct: 181 YGDLH 185


>gi|228984465|ref|ZP_04144642.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
 gi|228775168|gb|EEM23557.1| Pseudouridine synthase [Bacillus thuringiensis serovar tochigiensis
           BGSC 4Y1]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 91/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +  +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKNQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              V + L  G+  +I+      +   N        P     L  G TR +S++ L    
Sbjct: 225 VTLVMLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTRYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|229043131|ref|ZP_04190856.1| Pseudouridine synthase [Bacillus cereus AH676]
 gi|228726190|gb|EEL77422.1| Pseudouridine synthase [Bacillus cereus AH676]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 85/261 (32%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTLVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 245 -LGPHLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 IHFLHPITKEAIEVDVPFPTK 294


>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 = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
             QR+  ++    + S R+  +R+I    V+VN  ++++    V     I++   PL
Sbjct: 1  MAKQRLDNLLVTLNLCSSRQLAQRLIRAGEVRVNQQIIDKPGTEVDPGAEIQLQAKPL 58


>gi|77166008|ref|YP_344533.1| pseudouridine synthase, RluD [Nitrosococcus oceani ATCC 19707]
 gi|254436382|ref|ZP_05049888.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
 gi|76884322|gb|ABA59003.1| ribosomal large subunit pseudouridine synthase D [Nitrosococcus
           oceani ATCC 19707]
 gi|207088072|gb|EDZ65345.1| pseudouridine synthase, RluA family [Nitrosococcus oceani AFC27]
          Length = 319

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/170 (20%), Positives = 64/170 (37%), Gaps = 21/170 (12%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNV----M 55
            +      +R+ + +A+     SR  +++ I   +VKVN          +    +     
Sbjct: 10  TLPSELAGKRLDQALAQVFPAYSRSRLQQWIKHGQVKVNDAPARPRDTVQGGEWIVVMAE 69

Query: 56  STDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FS 106
           +   +     PL    + E   + + +KP GLV   +  +   T+ + L           
Sbjct: 70  AEAEVIWKSQPLPLEIRYEDEAIIVVNKPAGLVVHPAAGNRDGTLVNALLHHAPELERIP 129

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
           R   V RLD +T GLL++  +      L  +L + Q  R Y+    G + 
Sbjct: 130 RAGIVHRLDKDTSGLLVVARNLVAHHGLVRQLQARQITREYQAITVGVMT 179


>gi|313634007|gb|EFS00696.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri FSL N1-067]
          Length = 296

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 86/260 (33%), Gaps = 48/260 (18%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKPI 82
             +++VNG         V + D + +          L           E   L + +KP 
Sbjct: 38  DGKIEVNGTEQNVL-YEVQTGDEVRLTFPTEQQNERLLAEHTDLEIVFEDEFLLIINKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLE- 135
           G+ +  S      +V + +   +      S +  V RLD  T GL+L+  +      L  
Sbjct: 97  GIASIPSQYHPSGSVANFVKGHYEAQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLST 156

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            L      R Y+    G            + +  ++++++ +  +G         L   +
Sbjct: 157 FLQQGLLKRSYQAFVSGELAEQVGSIEAPIGRKAVSIMERVVTPEGKYAKTNYQVLARYQ 216

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
             +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L  
Sbjct: 217 AFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTDLLKRQALHS 264

Query: 243 -EQLGPHLLEEAQVNLDAPI 261
                 H L E  +  D P+
Sbjct: 265 CHLHLIHPLTEEYLAFDLPL 284


>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 = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 81/240 (33%), Gaps = 45/240 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------- 70
           SR  +ER+  ++ +KVN I +      V   D I + G+                     
Sbjct: 29  SR--IERLFREKDIKVNNIRVSDKQYKVKEGDLISIYGLIETSKHIDNKANTNINFKVIY 86

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---PSIFSRVISVGRLDINTEGLLLLTND 127
           E   L +  K   +     +      V   L        R  S+GR+D  T GL++   +
Sbjct: 87  EDKNLLIIDKAPNIAMHSEENCLDDQVLKYLNFKKVSSFRPASIGRIDKKTSGLVVYAKN 146

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLN---LLKKGI----VIQGICYGDMQVTLD 180
                  E    ++ ++Y  +F    D+D L+    LKK I    +I    +G    T+ 
Sbjct: 147 YKTLVEFENKQNKFDKIY--QFVSDFDEDVLDITVRLKKDIKNEKMIVDNNFGVKAQTIF 204

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN-------------RLIRISYGPFQLGT 227
            ++G+  +  + +  GK  +I+    +    +               L   S     L  
Sbjct: 205 YKEGNRKFAKI-IT-GKKHQIRATLAYLKTPILGDIKYGGKFAKRMYLHSYSIKFHDLSD 262


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

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 22  EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 74

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 75  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 130

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 131 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 189

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 190 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 247

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 248 GNNLAWLEMEPYTGRTHQLR 267


>gi|114707402|ref|ZP_01440299.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Fulvimarina pelagi HTCC2506]
 gi|114537283|gb|EAU40410.1| Prenyl group binding site (CAAX box):RNA-binding S4:Pseudouridine
           synthase:Pseudouridine synthase, Rlu:Pseudouridine
           [Fulvimarina pelagi HTCC2506]
          Length = 339

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 46/265 (17%), Positives = 76/265 (28%), Gaps = 57/265 (21%)

Query: 1   MKDKNIVQE-NFTPQRVSKVIARAGIAS----RREVERMIAQQRVKVNGILLERAAVNVM 55
           M+ +    E      R+   +A  G  S    R  ++ +I    V V G+    A   V 
Sbjct: 1   METREYTVEAEEAGMRIDAFLA--GRCSPELSRARIQSLIRAGDVTVGGVDTAAAKRRVK 58

Query: 56  STDHIEVD------------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             + + +              +PL    E   L +  KP GLV      +   T+ + L 
Sbjct: 59  EGEAVALRVPAPAEPEPEPEDIPLTIVFEDADLVVVDKPAGLVVHPGPGNWSGTLVNALL 118

Query: 103 SIF----------SRVISVGRLDINTEGLLLLTNDGGLARVLE-------LPSTQWLRVY 145
                         R   V RLD +T GLL++     +A               + +R Y
Sbjct: 119 HYCGEELSGINGVKRPGIVHRLDKDTSGLLVIA-KTDMAHRSLAEQFAAHGSDGRMVRSY 177

Query: 146 RVRFHGQVDQDKL-----------NLLKKGIVIQGIC--------YGDMQVTLDTQKGSN 186
           R    G                  + LK+ +V             Y  +           
Sbjct: 178 RAIVWGTPVPAVGRIETMLGRSSSDRLKRDVVAATQPDARQAITDYRILAGAGRAAGAEA 237

Query: 187 AWVTVGLREGKNREIKKVFEFFNWK 211
           + V   L  G+  +I+         
Sbjct: 238 SLVECRLATGRTHQIRVHMAHIGHP 262


>gi|228951772|ref|ZP_04113871.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
 gi|228807894|gb|EEM54414.1| Pseudouridine synthase [Bacillus thuringiensis serovar kurstaki
           str. T03a001]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 88/265 (33%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAERGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   E  +V++  P   ++ 
Sbjct: 274 INFLHPITKEAIEVDVPFPTKLNKK 298


>gi|254823760|ref|ZP_05228761.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
 gi|255521997|ref|ZP_05389234.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes FSL J1-175]
 gi|293592981|gb|EFG00742.1| ribosomal large subunit pseudouridine synthase D [Listeria
           monocytogenes FSL J1-194]
          Length = 296

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 89/264 (33%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A+ +++VN         +V + D + +          L           E   L + +KP
Sbjct: 37  AEGKIEVNNKEQNVL-YHVKAGDKVRLTFPTEQQNERLLAEYTDLDIIFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEKYMAFDLPLPAD 287


>gi|56459957|ref|YP_155238.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56178967|gb|AAV81689.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 236

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/170 (17%), Positives = 56/170 (32%), Gaps = 28/170 (16%)

Query: 72  RTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
              L + +KP GL+   S      R      L +     V  V RLD  T GLL+   + 
Sbjct: 10  DEHLAVINKPSGLLVHRSRIASGAREFAMQMLRNQLGCHVYPVHRLDRPTSGLLIFGLNS 69

Query: 129 GLARVLE--LPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM-- 175
            +AR L   L + +  + Y     G V +         ++L+ L                
Sbjct: 70  DVARTLTEQLTAREVSKTYHAVVRGYVPENGTIDYALKEELDKLADKDADPDKDKQPAVT 129

Query: 176 ------QVTLD---TQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                 Q+ L    ++K      ++   +   G+  ++++        + 
Sbjct: 130 HYQCLKQIELPYKVSKKHDTTRYSLVQMQPETGRKHQLRRHMAHIRHPIV 179


>gi|229177799|ref|ZP_04305172.1| Pseudouridine synthase [Bacillus cereus 172560W]
 gi|228605590|gb|EEK63038.1| Pseudouridine synthase [Bacillus cereus 172560W]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
             +VT+ L  G+  +I+
Sbjct: 225 TTFVTLQLETGRTHQIR 241


>gi|51246876|ref|YP_066760.1| pseudouridine synthase [Desulfotalea psychrophila LSv54]
 gi|50877913|emb|CAG37753.1| related to pseudouridine synthase [Desulfotalea psychrophila LSv54]
          Length = 235

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/168 (18%), Positives = 61/168 (36%), Gaps = 20/168 (11%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------PSIFSRVISVGRLD 115
           G+P+   ++  + +  KP GL+T  +D +   T    L        P   +RV  V RLD
Sbjct: 18  GLPILHEDKDIIVVV-KPTGLLTIGTDREKSRTAHYLLNDYVRKGNPKSSNRVYVVHRLD 76

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---LKKGIVIQGICY 172
            +T GLL+        + L+       + Y     G++ + +  +   L +    +    
Sbjct: 77  QDTSGLLIFAKSEEAKKFLQKDWENTEKHYLAIVCGKLKEKEGTISSYLTENKAYKVYST 136

Query: 173 GDMQV--------TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            D            +  +    + + + L  G+  +I+  F      V
Sbjct: 137 PDSTKGKLSKTAYKVIKEGKEVSLIDIHLLTGRKHQIRVHFAENGHPV 184


>gi|170717564|ref|YP_001784651.1| tRNA pseudouridine synthase C [Haemophilus somnus 2336]
 gi|168825693|gb|ACA31064.1| pseudouridine synthase [Haemophilus somnus 2336]
          Length = 240

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/191 (17%), Positives = 65/191 (34%), Gaps = 32/191 (16%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDI 116
           IE+D   L + E   +   +KP G++   S  D      V   L       V  + RLD 
Sbjct: 5   IELD--ILYQDEFLVVV--NKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDR 60

Query: 117 NTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK-------------LNLL 161
            T G+LL   + G+A +L       Q  + Y     G +   +              +  
Sbjct: 61  PTSGVLLFALNAGIANLLCSQFELKQVKKSYLAIVRGYLSDAQRIDYPLKVQLDKIADKF 120

Query: 162 KKGIVIQGICY-----GDMQVTLDTQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVN 213
            +   +Q           +++     + S++  ++  L    G+  ++++  +     + 
Sbjct: 121 SRKEELQDAITDYYGLKTVEMPYGVGRYSSSRYSLVRLMPYTGRKHQLRRHLKHIFHPI- 179

Query: 214 RLIRISYGPFQ 224
            L    YG   
Sbjct: 180 -LGDTQYGDLH 189


>gi|322418237|ref|YP_004197460.1| RluA family pseudouridine synthase [Geobacter sp. M18]
 gi|320124624|gb|ADW12184.1| pseudouridine synthase, RluA family [Geobacter sp. M18]
          Length = 319

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 78/231 (33%), Gaps = 41/231 (17%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           +  P+R+   I+R+    +R    R+I      VNG   ++ A+ +   + + V      
Sbjct: 11  DADPERLDSFISRSVPELTRSAALRLIETGFATVNGQK-QKPALRLKGGEVVTVIVPPPT 69

Query: 63  ------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG--- 112
                 + +PL    E   + + +K  G+V      +   T+ + L +    +  +G   
Sbjct: 70  PAEPQPEEIPLEILYEDADVVVVNKGAGMVVHPGAGNAEGTLVNALLAHCKDLSGIGGEL 129

Query: 113 ------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-------- 156
                 R+D +T G L++         L          R+Y    +G   ++        
Sbjct: 130 RPGIVHRIDKDTSGTLVIAKSDRAHNGLAEQFKVHSIKRIYLALVYGSPKEERGHIESVI 189

Query: 157 -----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +   +  G    G         ++ +      V + L  G+  +I+
Sbjct: 190 GRHPVERKKM-SGKARHGKNAITHW-RVEARYPGITLVRLKLETGRTHQIR 238


>gi|228469450|ref|ZP_04054458.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
 gi|228309025|gb|EEK17668.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           uenonis 60-3]
          Length = 232

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/171 (19%), Positives = 60/171 (35%), Gaps = 28/171 (16%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           TP R+ + +  R    SR  ++       + V+G  ++     V   + I +        
Sbjct: 55  TPLRIDRFLVDRMPHTSRHRIQLAAKAGLIWVDGEPVKS-NYKVKPLETITMMLAHPKQD 113

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----------NLPSIFS 106
                + +PL    E  +L + +KP G+V      +   T+                  +
Sbjct: 114 WSITPEDIPLDIVYEDDQLLVVNKPAGMVVHPGHGNYSGTLVHALAYYLRNDPLYDPNDA 173

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
            V  V R+D +T GLLL+         L          R Y+    G++DQ
Sbjct: 174 SVGLVHRIDKDTSGLLLVAKRTEAKIRLARQFFLKTTGRRYQALVWGKLDQ 224


>gi|191638831|ref|YP_001987997.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|190713133|emb|CAQ67139.1| Pseudouridine synthase [Lactobacillus casei BL23]
 gi|327382880|gb|AEA54356.1| hypothetical protein LC2W_2024 [Lactobacillus casei LC2W]
 gi|327386064|gb|AEA57538.1| hypothetical protein LCBD_2042 [Lactobacillus casei BD-II]
          Length = 287

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 39/222 (17%), Positives = 72/222 (32%), Gaps = 32/222 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKA---- 70
           + +A  G+ S R  ++M+    + V+G   +     V +   I  +      L       
Sbjct: 17  RWLAEQGV-SHRLFKKMLVDHLIWVDGQASDNG--PVEAGQIIRFEIPTSKTLTPEFAPL 73

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTE 119
               E     +  KP GL +        S++ + +            +   + RLD +T 
Sbjct: 74  EVIYEDANWLIVSKPAGLTSVPGPHTPNSSLLNRIAGYLVEQKIDAPQPAIMTRLDRDTV 133

Query: 120 GLLLLTNDGGLARVLELPSTQWL-RVYRVRFHGQVD------QDKLNLLKKG---IVIQG 169
           GL+L           +    + L + Y     G++          L L   G   IV   
Sbjct: 134 GLVLAAKHPYAQGRFDQAHQRTLTKHYLAVVSGKLPSPKGEIDAPLKLAADGIHRIVAAD 193

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +  +K +N  V V L  G+  +I+  F      
Sbjct: 194 GQTAVTKYRVLKEK-TNTLVDVQLLTGRTHQIRVHFASLGHP 234


>gi|332970065|gb|EGK09063.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 300

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/216 (20%), Positives = 75/216 (34%), Gaps = 42/216 (19%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGV-----PLRK-AERTRL 75
           +E E       V+VNG  +      V + D I V       DGV     PLR   E   L
Sbjct: 39  KEAEA------VEVNGETVY-LTSRVKAGDRIAVFLPGDAGDGVKPQSLPLRVVHEDEDL 91

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGG 129
            +  K  G+V   +      T+ + L + +        V  V RLD +T GL++      
Sbjct: 92  IILDKQPGVVVHPTRNYSEGTLANGLAAYWQERGEFHLVRPVTRLDKDTSGLIVFAKHPH 151

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVD------QDKLNL------LKKGIVIQGICYGDM 175
              VL       ++LR Y    HG ++      ++ +        L+  +  +G      
Sbjct: 152 AHAVLSGQMERKRYLREYLAVVHGSLEMEEGRVEEPIARSSETPHLRT-VSPEGAPART- 209

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           Q  +  +      V + L  G+  +I+         
Sbjct: 210 QYRVVRRWPEATLVRLRLETGRTHQIRVHMAHLGHP 245


>gi|302340475|ref|YP_003805681.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
 gi|301637660|gb|ADK83087.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
          Length = 229

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/185 (15%), Positives = 47/185 (25%), Gaps = 37/185 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   L + +K  G +    D  G  T+ D +               +    RLD  T G+
Sbjct: 7   EDNHLIVVNKRCGDIVQG-DKSGDPTLADEVKEYLREKYNKPGNVFLGIPHRLDRPTSGV 65

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-------------KLNLLKKGIV 166
           +L        R L L        ++Y          +             K         
Sbjct: 66  VLYARTEKALRRLSLSFREQHVEKIYWAVVDKMPPAESGTLVHYLRRDRKKNKSFASDTP 125

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                   M+  L         + + L  G++ +I+              RI       G
Sbjct: 126 TADSQEAKMRYRLVGATNRYYLLEIELLTGRHHQIRAQLAAVGC------RIR------G 173

Query: 227 TLLAG 231
            L  G
Sbjct: 174 DLKYG 178


>gi|298695119|gb|ADI98341.1| probable RNA pseudouridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 273

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 78/236 (33%), Gaps = 39/236 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGLVTT 87
           + +N          V + D + V             R               KP G+ T 
Sbjct: 37  ITINDKPARLMN-KVHTGDDVFVPTIDEKSNYVPSYRYAQIKYEDDDMAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHVIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEDNDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +T    K +   + + 
Sbjct: 156 IYKANVKALLPLKPQTIDMPIGKDKFHSNKRRVSPTGQRAITHILTSKMIKETVCQLEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKKIL 241
           L  G+  +I+         V    L    YG   L  L   S +      ++K+++
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELESYKIEFVHPLTKEVI 267


>gi|296501973|ref|YP_003663673.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
 gi|296323025|gb|ADH05953.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis BMB171]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 86/261 (32%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 245 -LGPHLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 IHFLHPITKEAIEVDVPFPTK 294


>gi|262047145|ref|ZP_06020104.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-3A-US]
 gi|293380273|ref|ZP_06626351.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
 gi|260572722|gb|EEX29283.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           crispatus MV-3A-US]
 gi|290923182|gb|EFE00107.1| pseudouridine synthase, RluA family [Lactobacillus crispatus 214-1]
          Length = 301

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 32/161 (19%), Positives = 59/161 (36%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLL 123
           E     + +KP G+++  S  +    V + L   F++          + RLD  T GL+L
Sbjct: 85  ENKNYLVVNKPAGVLSIPSRYEDDDAVVNRLLGYFAQKGQKNLKPHVITRLDRYTSGLVL 144

Query: 124 LTNDGGLARVLELPST-QWLRVYRVRFHGQVDQDKLNLL------KKG------IVIQGI 170
           +  +             ++++ Y    HG    ++L  L      KKG      +V  G 
Sbjct: 145 VGKNAISHARFSKIGKEKFVKKYHAIVHGNFAPNELTGLIDQPIGKKGSGVKRAVVADGK 204

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   LD   G+ + V + L  G+  +I+    +    
Sbjct: 205 DAQTAYRVLDQVTGA-SLVELRLLTGRTHQIRVHMAYLGHP 244


>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 = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHL 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|30019444|ref|NP_831075.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|229126707|ref|ZP_04255719.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
 gi|229143996|ref|ZP_04272412.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|29894988|gb|AAP08276.1| Ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 14579]
 gi|228639393|gb|EEK95807.1| Pseudouridine synthase [Bacillus cereus BDRD-ST24]
 gi|228656647|gb|EEL12473.1| Pseudouridine synthase [Bacillus cereus BDRD-Cer4]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 86/261 (32%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 245 -LGPHLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 IHFLHPITKEAIEVDVPFPTK 294


>gi|289449819|ref|YP_003475504.1| RluA family pseudouridine synthase [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184366|gb|ADC90791.1| pseudouridine synthase, RluA family [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 354

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 30/137 (21%), Positives = 49/137 (35%), Gaps = 24/137 (17%)

Query: 34  MIAQ----QRVKVNGILLERAAVNVMSTDHIEV---D-----GVPLRKAERTRL------ 75
           +I +     R++++G   E       S   I V   D       P+       +      
Sbjct: 30  LIKRVKLHGRMEIDGKP-ELMKTPAQSGQKIVVFYMDPAGEVNRPIEAQPDIPILFQDEW 88

Query: 76  -WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
             + +KP  LVT  +     + +   L S    +  V RLD +T GL++L  +G     L
Sbjct: 89  FIICNKPANLVTHPTYLHHANNLTARLCSDL--LHPVNRLDRDTSGLVILAKNGYAHHAL 146

Query: 135 ELPSTQWLRVYRVRFHG 151
              S    + Y    HG
Sbjct: 147 TTVS--IAKRYLALVHG 161


>gi|303235055|ref|ZP_07321679.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302493910|gb|EFL53692.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 273

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 89/242 (36%), Gaps = 45/242 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           MK  +   +  T  R+ + +     +     S       I +  + +NG   +R +  + 
Sbjct: 1   MKQISFNVDKKT--RLDEFLKKNHISHNLFIS-------IYKDDIFINGKHAKRNS-KLE 50

Query: 56  STDHIEVDGVPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             D + ++   LR  E                  +++ +KP   +T + D +     F +
Sbjct: 51  KGDIVTIN---LRDEENKYEPINMDIEVLYEDDDIFVLNKP-DKLTMNKDGEKSLANFVS 106

Query: 101 L----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD 156
                 +I  +V  + RLD +T G++++  +       +  S +  + Y     G     
Sbjct: 107 YLFKQRNIKQKVRFINRLDQDTSGVVMVAKNKIAQAYYQKNSFK--KKYLAIVKGNPKDQ 164

Query: 157 KLNLL--KKGIVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           K+ L   + GI  +    G   VT+       G  + V++ L  G+  +I+   E+ N  
Sbjct: 165 KIELNLKRDGIKTEIDENGKKSVTILENLKNYGDYSLVSLELLTGRTHQIRVSMEYINCP 224

Query: 212 VN 213
           + 
Sbjct: 225 IV 226


>gi|307719385|ref|YP_003874917.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           thermophila DSM 6192]
 gi|306533110|gb|ADN02644.1| ribosomal large subunit pseudouridine synthase D [Spirochaeta
           thermophila DSM 6192]
          Length = 319

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 79/246 (32%), Gaps = 52/246 (21%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---- 70
           R+ + +A     +R +V++ IA   + ++G   +  +  V +   I   G  L +A    
Sbjct: 19  RLDQALAELLGITRSQVKQRIAD--LALDGRPAK-PSQRVHAGARIA--GTLLPEAPPDL 73

Query: 71  -----------ERTRLWLYHKPIGLVTT-----------------HSDPDGRSTVFDNLP 102
                      E     +  KP GLV                     +   R+T  +   
Sbjct: 74  TPEPVPFTILYEDPHCLVIDKPQGLVVHPGAGNPTGTLVHGLLHYSHELAARATSEELDD 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVD------ 154
               R+  V RLD +T G+L++  D      L     +    ++Y     G         
Sbjct: 134 EERMRIGIVHRLDKDTSGVLVVAKDPATHHFLAAQFKEKETKKLYLAVLKGTPPAREGDI 193

Query: 155 QDKLNL---LKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +  L      +K   +        Y   +  L    G++++V +    G+  +++     
Sbjct: 194 EGHLARHPVHRKKFTLLSTPDRGKYSHTRYRLLAAFGTHSFVALYPTTGRTHQLRVHTAA 253

Query: 208 FNWKVN 213
               + 
Sbjct: 254 LGCPIL 259


>gi|238924045|ref|YP_002937561.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale ATCC 33656]
 gi|238875720|gb|ACR75427.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           rectale ATCC 33656]
          Length = 324

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 47/306 (15%), Positives = 91/306 (29%), Gaps = 105/306 (34%)

Query: 1   MKDKNIVQENFTPQRVSKVI------ARAGIASRREVERMIAQQRVKVNGILLERAAVNV 54
           MK+    + N   QR+ K +      A  G      + +M+ ++ +K+N          V
Sbjct: 1   MKEFKAGK-NEAGQRLDKYLKKILPNASMGF-----IYKMLRKKNIKLNDKKA-SGTEIV 53

Query: 55  MSTDHIEV-----------------------------DGVPLRKAERTRLWLYHKPIGLV 85
              D I++                             DG+ +   +   +   +KP+ ++
Sbjct: 54  SVDDKIKIFLSDDTFAKFSVNEDRLMKDFKALSALKPDGLGVVYEDDD-ILAANKPVNML 112

Query: 86  TTHS---DPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARV 133
           +  S   D      +   L              +     RLD NT GL+L+   G     
Sbjct: 113 SQKSKETDISANERLIGYLIKEGKLDFDTYKSFKPSVCNRLDRNTSGLILM---GKSLHG 169

Query: 134 LE-----LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM---QVTLDTQKGS 185
           L+     L +    + Y     G+VD+         + I+G    D    +V +  +  S
Sbjct: 170 LQYLSQVLKARTAEKYYMALVAGEVDEP--------MTIEGFLTKDEAVNKVQITREPIS 221

Query: 186 N------------------------AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG 221
           +                          + V L  G++ +I+         +        G
Sbjct: 222 DESLPIKTAYRPLKTIDMSASCHKATLLEVHLITGRSHQIRAHLSSIGHPI-------IG 274

Query: 222 PFQLGT 227
             + G 
Sbjct: 275 DIKYGD 280


>gi|323464082|gb|ADX76235.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus pseudintermedius ED99]
          Length = 276

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 72/201 (35%), Gaps = 28/201 (13%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLW----------LYHKPIGLVTT 87
           + VN          V + D I +  +    +     R            + +KP G+ T 
Sbjct: 37  ITVNDE-AANLQTIVHTGDEIYIPDEDAKSQYLPSYRYAQIAYEDDFLAIVYKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++    +   V  + RLD  T GLL++     + ++L   L +    R
Sbjct: 96  PNDLKESNTLMNHVIYTLNHPYVEPIHRLDQETVGLLIVAKHPIIKKILDRMLENNDIHR 155

Query: 144 VYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+ +               + +DK +  K+ +   G       ++ +  +     V + 
Sbjct: 156 IYKAQVKSLLPIKPQTIDLPIGKDKFHPNKRRVSPTGQRAVTHILSSEMIEEGVCEVMLK 215

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           L  G+  +I+       + V 
Sbjct: 216 LDTGRTHQIRVHLAEIGYPVL 236


>gi|257877015|ref|ZP_05656668.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
 gi|257811181|gb|EEV40001.1| pseudouridine synthase [Enterococcus casseliflavus EC20]
          Length = 284

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 44/218 (20%), Positives = 74/218 (33%), Gaps = 34/218 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---DG----VPLRKA---------E 71
           R+V   +  ++ V VN          V   D I +   D      P++           E
Sbjct: 28  RKVRHFLRTRKNVTVNQQPAM-FHQEVRGGDQITLIIEDSDYSYQPIQLGQADKVDVLFE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +     L     +   V RLD  T G++L   +
Sbjct: 87  DEHLLVLNKPAGVKTHPNQPLEADTLLNDAAAYLAPKQQQPYVVHRLDKETSGVVLFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----------IVIQGICYGDM 175
             +  +L   L + Q  R Y+    G++ QD+    K G          I  +       
Sbjct: 147 PLVLPILGRMLENKQIFRRYQATVWGKLTQDQTIAKKIGRDRHDRRKRIIDPRNGQSAIT 206

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            VT+   +     V   L  G+  +I+         V 
Sbjct: 207 HVTIAHTQQKTTDVYCVLDTGRTHQIRVHLASIGHPVV 244


>gi|297588693|ref|ZP_06947336.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
 gi|297574066|gb|EFH92787.1| RluA family pseudouridine synthase [Finegoldia magna ATCC 53516]
          Length = 273

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 82/235 (34%), Gaps = 35/235 (14%)

Query: 4   KNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           K I  +     R+ + +     ++    S       I +  + +NG   +R +  +   D
Sbjct: 2   KQISFDIDKKIRLDEFLKVNHISKNLFLS-------IYKDDILINGKHAKRNS-KLKPGD 53

Query: 59  HIEVD-------GVPLRK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-- 104
            + +D         P+        E   +++ +KP  L       +  +     L     
Sbjct: 54  KVTIDLKDEENNYEPINLDIEVLYEDDDIFVLNKPDKLTMNTDGEESLANFVSYLFEQRN 113

Query: 105 -FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN--LL 161
              +V  + RLD +T G++++  +           T + + Y     G     K+   L+
Sbjct: 114 INQKVRFINRLDQDTSGVVMVAKNKIAQAYY--QKTSFEKKYLAIVEGNPKNQKIELNLI 171

Query: 162 KKGIVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +  I  +    G   VT+       G  + V++ L  G+  +I+   E+ N  + 
Sbjct: 172 RDCIKTEIDENGKKSVTILKNIKSYGDYSLVSLKLLTGRTHQIRVSMEYINCPIV 226


>gi|219870928|ref|YP_002475303.1| tRNA pseudouridine synthase C [Haemophilus parasuis SH0165]
 gi|219691132|gb|ACL32355.1| tRNA pseudouridine synthase C, pseudouridylate synthase, 23S
           RNA-specific [Haemophilus parasuis SH0165]
          Length = 242

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 54/169 (31%), Gaps = 26/169 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL   +
Sbjct: 8   QDDELIAINKPAGMLVHRSWLDKHETVFAMQTLRDQIGQHVFLIHRLDRPTSGVLLFALN 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGD-- 174
             +AR +       Q  + Y     G +  +         +L+ +      +        
Sbjct: 68  SEMARTISQLFKQHQIQKSYLAVVRGYLQGEGRIDYPLKVQLDKIADKFSQEKEAQEAIT 127

Query: 175 -----MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                  V +    G  A     L +     G+  ++++  +     + 
Sbjct: 128 DYRNIATVEMPYPAGKFATARYSLVQLYPKTGRKHQLRRHLKHLFHPIM 176


>gi|217033961|ref|ZP_03439384.1| hypothetical protein HP9810_883g31 [Helicobacter pylori 98-10]
 gi|216943594|gb|EEC23042.1| hypothetical protein HP9810_883g31 [Helicobacter pylori 98-10]
          Length = 242

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 79/235 (33%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
               KP  + +           +D + S F   + + RLD  T G++LL  +     +  
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVVLLVRENSEFHLKA 113

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
             + +     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKNRAVKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + VG++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVGIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|117924690|ref|YP_865307.1| pseudouridine synthase [Magnetococcus sp. MC-1]
 gi|117608446|gb|ABK43901.1| pseudouridine synthase [Magnetococcus sp. MC-1]
          Length = 255

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/247 (13%), Positives = 79/247 (31%), Gaps = 36/247 (14%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV----GRLDINTEGLLLLTNDGGL 130
           L + +KP G +  H+ P G + +      +   +        RLD +T G L+L      
Sbjct: 22  LLIINKPAG-IPVHAGPGGGANLEALFGGLRFGLPKAPALAHRLDRDTSGCLVLGRHAKA 80

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQDK---------LNLLKKG----IVIQGICYGDM 175
              L       +  + Y     G   Q +         ++  ++G    +  +       
Sbjct: 81  LSKLGKLFSQGKVQKTYWAVVQGGPPQAQGSMDFPLYKISTAQQGWRMVVDPEQGKSSLT 140

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +  +  +++W+ +  + G+  +I+         +             G L  G+   
Sbjct: 141 LYRVLGRSATHSWLELTPKTGRTHQIRVHCAHVGLPIE------------GDLQYGAAPS 188

Query: 236 VSKKIL----REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             +  L    R+ + P    +A +N+ AP   +   + ++    +E            + 
Sbjct: 189 EPQLTLHLHARQIILPISASKAPINVSAPPPRAMRGLLEQCGYRAEAWPSTRFEPHTRAD 248

Query: 292 KNGLSKQ 298
           + G    
Sbjct: 249 ETGHGAA 255


>gi|257866939|ref|ZP_05646592.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257873272|ref|ZP_05652925.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
 gi|257800995|gb|EEV29925.1| pseudouridine synthase [Enterococcus casseliflavus EC30]
 gi|257807436|gb|EEV36258.1| pseudouridine synthase [Enterococcus casseliflavus EC10]
          Length = 284

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 44/218 (20%), Positives = 74/218 (33%), Gaps = 34/218 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---DG----VPLRKA---------E 71
           R+V   +  ++ V VN          V   D I +   D      P++           E
Sbjct: 28  RKVRHFLRTRKNVTVNQQPAM-FHQEVRGGDQITLIIEDSDYSYQPIQLGQADKVDVLFE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +     L     +   V RLD  T G++L   +
Sbjct: 87  DEHLLVLNKPAGVKTHPNQPLEADTLLNDAAAYLAPKQQQPYVVHRLDKETSGVVLFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG----------IVIQGICYGDM 175
             +  +L   L + Q  R Y+    G++ QD+    K G          I  +       
Sbjct: 147 PLVLPILGRMLENKQIFRRYQATVWGKLTQDQTIAKKIGRDRHDRRKRIIDPRNGQSAVT 206

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            VT+   +     V   L  G+  +I+         V 
Sbjct: 207 HVTIAHTQQKTTDVYCVLDTGRTHQIRVHLASIGHPVV 244


>gi|254482837|ref|ZP_05096074.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
 gi|214036918|gb|EEB77588.1| pseudouridine synthase, RluA family [marine gamma proteobacterium
           HTCC2148]
          Length = 312

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/226 (15%), Positives = 75/226 (33%), Gaps = 37/226 (16%)

Query: 11  FTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              +R+ ++ A+     SR  ++  I +  + V+G  L      V     + +D  P + 
Sbjct: 1   MDNERLDQIAAKLFPDYSRSRLQTWIKKGDLLVDGKQLRTRD-KVFYGAQLSIDTEPEQA 59

Query: 70  A-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVIS 110
                         E   + + +KP GLV   +      T+ + L       +   R   
Sbjct: 60  VGWQPQNIDLDIIYEDAHILVVNKPAGLVVHPAAGHPDGTLVNALLAHSPEMAQLPRGGI 119

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD------------QD 156
           V RLD+ T G+++        + L     +    R Y     G +               
Sbjct: 120 VHRLDMETSGIMVAAKSLLAHQDLVSQLQERTVRREYVAVCIGVMTGGGTVDEPMGRHPK 179

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +   +   +++ G         +  + G +  + V L  G+  +I+
Sbjct: 180 QRKKMA--VLVVGGKPAITHYRVTKRYGHHTRIAVNLETGRTHQIR 223


>gi|73663086|ref|YP_301867.1| RNA pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72495601|dbj|BAE18922.1| putative RNA pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 284

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 33/202 (16%), Positives = 66/202 (32%), Gaps = 34/202 (16%)

Query: 42  VNGILLERAAVNVMSTDHIEVD-GVPLRKA-------------ERTRLWLYHKPIGLVTT 87
           VNG  +      +   D +EV  G  +                E   L +  KP      
Sbjct: 38  VNGQTVT-VRKQLAIGDILEVYLGKEIPSTNLKPYQQPLNILFEDDYLIVVSKPPYQNCA 96

Query: 88  HSDPDGRST----VFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQW 141
            S      +    V   L      +    V RLD NT G+++L   G     L       
Sbjct: 97  PSRDHLHYSIVEQVLGYLNEKQPGINPHIVTRLDRNTSGIVILAKHG-FIHHLMSNLN-I 154

Query: 142 LRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
            + Y    +G+ +++ +          +++++ +   G         ++ ++G  +   V
Sbjct: 155 DKKYLCICYGKTEKEGVIDAPIARHPESIIQRRVDAAGKTAQTRFKRVEYKEGF-SMCEV 213

Query: 192 GLREGKNREIKKVFEFFNWKVN 213
            L  G+  +I+  F+     + 
Sbjct: 214 TLLTGRTHQIRVHFQHIGHSIV 235


>gi|325124374|gb|ADY83897.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           PHEA-2]
          Length = 233

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 34/185 (18%), Positives = 67/185 (36%), Gaps = 42/185 (22%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLEVGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVINKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDKL 158
             D +
Sbjct: 186 SLDSV 190


>gi|221133320|ref|ZP_03559625.1| pseudouridylate synthase [Glaciecola sp. HTCC2999]
          Length = 245

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/181 (16%), Positives = 57/181 (31%), Gaps = 30/181 (16%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDIN 117
           EV        +   +   +KP GL+   S  D          + ++    V +V RLD  
Sbjct: 3   EVSSQLPIIYQDEHIIAINKPSGLLVHRSMIDRHETRFAMQMVRNMIDQHVYTVHRLDKP 62

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGD 174
           T G+L+      +AR++          + Y     G      ++  LK+   +  I   D
Sbjct: 63  TSGVLVFALSSDVARLMTEQFTEKTIHKTYHALTRGWTKSQFVDYALKE--KLDKIADKD 120

Query: 175 MQVTLDTQKGSN----------------------AWVTVGLREGKNREIKKVFEFFNWKV 212
            Q     Q+                         +WV +  + G+  ++++        +
Sbjct: 121 AQQDKAPQEAQTHIACLQRFTYPKAVGRYPQARLSWVELNPQTGRKHQLRRHLAHVRHPI 180

Query: 213 N 213
            
Sbjct: 181 M 181


>gi|332365407|gb|EGJ43168.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK355]
          Length = 277

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 72/205 (35%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRK-AE 71
           R++   +  ++ V VNG L       V + D I +               +G  + +  +
Sbjct: 15  RKIRHFLRTKKHVSVNG-LAINWQSLVKAGDEICLIFDEEDYPQKTILLGNGELVEELYQ 73

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G++L   +    
Sbjct: 74  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGVVLFAKNPFVL 133

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L     +  R Y     G+     L           +  K+ +  +   Y +  V
Sbjct: 134 PILNRLL-EKREISRQYWALVQGKFPAKNLIYKDKIGRDRHDRRKRLVDPRKGLYAETHV 192

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T   Q G    V   L+ G+  +I+
Sbjct: 193 TRLKQFGQATLVQCQLKTGRTHQIR 217


>gi|26553465|ref|NP_757399.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
 gi|26453471|dbj|BAC43803.1| pseudouridine synthase [Mycoplasma penetrans HF-2]
          Length = 301

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/219 (15%), Positives = 65/219 (29%), Gaps = 41/219 (18%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTD--HIEVDGVPLRKA----------------ERTRLW 76
           I    +KVN          +   D   I +   P++K                 E   + 
Sbjct: 35  IKNGDIKVNHKK-TTWNYKLQENDSLQIFLRLKPIKKELKLNFLEAKPILNVIYEDKNII 93

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTNDG 128
           + +KP GL+      +   T+ + +                   RLD  T GL +   + 
Sbjct: 94  VVNKPRGLICQPDKNEKIDTLNNRIKKYLYEKKDKNYLEANLCHRLDKYTTGLCVAAKNQ 153

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQ--DKLNLL------KKGIVIQGICYGDMQV- 177
                L     +    + Y    +G+  +  D L         K+ + I      + ++ 
Sbjct: 154 KTLTELNNLWNTEAVSKYYLCLCYGKFKKKSDTLKDFIFLNEEKQIMEIDRENKFNKEII 213

Query: 178 ---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +  QK   A + + L  GK  +I+         V 
Sbjct: 214 TKYRVIEQKKDMALLEIQLLTGKKHQIRVHMASIGHPVL 252


>gi|325687489|gb|EGD29510.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis SK72]
          Length = 295

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 59/171 (34%), Gaps = 23/171 (13%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRL 114
           VD       E     +  KP G+ +  S  +  +T+ + + + +        +V  V RL
Sbjct: 72  VDKDLSVVYEDEHFLVLDKPAGVASIPS-VNHSNTMANFVKAYYIRHAYENQQVHIVTRL 130

Query: 115 DINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------------QVDQDKLNL 160
           D +T GL+L          L  +L      + Y     G             + ++  ++
Sbjct: 131 DKDTSGLMLFAKHSYAHARLDKQLQKKLIEKRYYALVRGTGDLEEQGEIIAPIGRNPESI 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + + +  +   Y      +  + G    V + L  G+  +I+  F    + 
Sbjct: 191 ITRRVT-EDGKYAHTSYKVIERFGDVYLVDIHLHTGRTHQIRVHFSHIGFP 240


>gi|292487216|ref|YP_003530088.1| tRNA pseudouridine synthase C [Erwinia amylovora CFBP1430]
 gi|292900409|ref|YP_003539778.1| tRNA pseudouridylate synthase C [Erwinia amylovora ATCC 49946]
 gi|291200257|emb|CBJ47385.1| tRNA pseudouridylate synthase C [Erwinia amylovora ATCC 49946]
 gi|291552635|emb|CBA19680.1| tRNA pseudouridine synthase C [Erwinia amylovora CFBP1430]
          Length = 255

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 59/167 (35%), Gaps = 29/167 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V +V RLD  T G+LL+     +A
Sbjct: 11  LVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLMALSSEVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHG----------QVDQDK---LNLLKKG--------IVIQ 168
            +L       Q  + Y     G           + +++    +   +            +
Sbjct: 71  HLLSQQFERHQLQKTYHAVVRGWLEGADTLDYPLTEERDKIADKFSQPEKAPQPAVTHWR 130

Query: 169 GICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKK-VFEFFNWKVN 213
           G+   ++ V +   + S  + V +    G+  ++++ +       + 
Sbjct: 131 GVATAELAVPIGRYETSRYSLVEMQPESGRKHQLRRHMT-HLRHPII 176


>gi|145300305|ref|YP_001143146.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142853077|gb|ABO91398.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 218

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 23/156 (14%), Positives = 59/156 (37%), Gaps = 20/156 (12%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++     P+   +V   +     +  +  RLD++T G++++       R 
Sbjct: 21  IMVVNKPTGLLSVPGRGPENEDSVLHRVKQQHPKAAAAHRLDMSTTGVIVIPLTPNSHRE 80

Query: 134 LELP--STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVI-QGICYGDMQVTL 179
           L       +  + Y     G+ + D                K+ +   +G     +   L
Sbjct: 81  LSRQFRERETEKHYLAWVWGEPEADSGQVDLPLCVDWPNRPKQKVDFEEGRHALTLWEKL 140

Query: 180 DTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
             + G N+ + +  +  G++ +++  + E     + 
Sbjct: 141 KVENG-NSLIKLTPIT-GRSHQLRVHMLE-LGHPIL 173


>gi|187931011|ref|YP_001890995.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. mediasiatica FSC147]
 gi|187711920|gb|ACD30217.1| ribosomal large subunit pseudouridine synthase C [Francisella
           tularensis subsp. mediasiatica FSC147]
          Length = 309

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 82/254 (32%), Gaps = 56/254 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASR------REVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           V E+   QR+   +      SR        + R I +  ++VN   +++ +  V + D +
Sbjct: 9   VAEDVIDQRIDNFL-----LSRFSRLPKSLIYRWIRKGELRVNKKRVKQIS-RVSAGDIV 62

Query: 61  EV-------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
            V       D  P++ ++                  +  KP G+            V   
Sbjct: 63  RVPPFSLEEDSKPIKISQSHLDFLEQRILYENDDYIIVDKPSGMAVHGGSGVNSGLVERL 122

Query: 101 --LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD 156
             L     R+  V RLD  T G +LL                 +  ++Y    HG  D+ 
Sbjct: 123 RQLRPKVRRLDLVHRLDKETSGCVLLAKKHSSLVYFFDIFKQRKVDKIYYSIVHGHWDKK 182

Query: 157 KLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN---------------AWVTVGLREGKNR 199
            + +    + ++     D Q  V +D++ G                 + + + L  G+  
Sbjct: 183 IIKI---DLPLKRTETKDGQRVVKVDSKDGKQALTRIISVRHLQGGFSLLEIKLETGRTH 239

Query: 200 EIKKVFEFFNWKVN 213
           +I+   +     + 
Sbjct: 240 QIRVHTKAMGHPIV 253


>gi|206967734|ref|ZP_03228690.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
 gi|206736654|gb|EDZ53801.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH1134]
          Length = 307

 Score = 57.1 bits (137), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFRKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
             +VT+ L  G+  +I+
Sbjct: 225 TTFVTLQLETGRTHQIR 241


>gi|289525702|emb|CBJ15183.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis Sweden2]
 gi|296435271|gb|ADH17449.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis E/150]
 gi|296438990|gb|ADH21143.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis E/11023]
 gi|297748789|gb|ADI51335.1| Ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D-EC]
 gi|297749669|gb|ADI52347.1| Ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D-LC]
          Length = 335

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 71/183 (38%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
           ++ E  T  R+ K +++  G  SR   ++ I   RV+VNG +  R +  +   D      
Sbjct: 15  VIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEVEL 73

Query: 60  --------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                   +  + +PL K  E   + + +KP  +V   +    + TV   L         
Sbjct: 74  IEEEEPSSLIPEDIPLDKVYEDDMMLVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLK 133

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ 155
              P    R   V RLD +T G LL+T     A+ L      + Q  ++Y         Q
Sbjct: 134 QEFPEEPWRPGIVHRLDKDTSG-LLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQ 192

Query: 156 DKL 158
           +++
Sbjct: 193 ERI 195


>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 = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 1/68 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+   +   G   SR + + +I    V VN   +++    V     I + G  +  
Sbjct: 1  MKKERLDVFLTEQGFFESRSKAQAVIMAGEVLVNDQKIDKPGTMVKPDAKITLLGKKMPF 60

Query: 70 AERTRLWL 77
            R    L
Sbjct: 61 VSRGGYKL 68


>gi|262375074|ref|ZP_06068308.1| 23S rRNA pseudouridylate synthase [Acinetobacter lwoffii SH145]
 gi|262310087|gb|EEY91216.1| 23S rRNA pseudouridylate synthase [Acinetobacter lwoffii SH145]
          Length = 318

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/242 (16%), Positives = 80/242 (33%), Gaps = 55/242 (22%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQDGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLAIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDESAAPVSDKVAQGLLARVIYEDEGLMVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           +           +  + R+D +T GL++++    + + L   L   +  + Y     GQV
Sbjct: 126 IEGLRAATGKKYLELIHRIDRDTSGLVMISKKRSVLKTLQDMLREHKIKKTYAAVVKGQV 185

Query: 154 DQDK--LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW------VTVGLR-----EGKNRE 200
             DK  ++       +            + ++    W      +   L       G+  +
Sbjct: 186 SLDKQLIDAPLHRYELANGERRVCVSPKEGKESKTQWNVQERFMHATLVYASPLSGRTHQ 245

Query: 201 IK 202
           I+
Sbjct: 246 IR 247


>gi|209880932|ref|XP_002141905.1| RNA pseudouridylate synthase family protein [Cryptosporidium muris
           RN66]
 gi|209557511|gb|EEA07556.1| RNA pseudouridylate synthase family protein [Cryptosporidium muris
           RN66]
          Length = 527

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 28/200 (14%), Positives = 65/200 (32%), Gaps = 47/200 (23%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT--RLWLYH--------KPIGLVTT 87
            ++ VNG  +     ++ + D I  + + +         + LY+        KP G+   
Sbjct: 100 GKISVNGKPINSLDHHIFNGDIIRHESLMIELPAPLDNVVILYNNKHFLAVYKPYGIPCH 159

Query: 88  HSDPDGRSTVFDNLPSIFSRV----------------------ISVGRLDINTEGLLLLT 125
                 + ++ + + S + R                         + RLD  T GL++L+
Sbjct: 160 PQGRFHKLSLTNIVMSKYFRSETEVIIDNKAASRIINDDKLYAHPINRLDRVTSGLVILS 219

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------------DKLNLLKKGIVIQGI 170
            +    R+L    ++  + Y     G                    K+  L+ G+ I   
Sbjct: 220 KNCDSTRLLSKVISKSHKYYLAHVEGDFSSLEHVDIGKLFKSTQLVKIQNLEMGLNINFG 279

Query: 171 CYGDMQVTLDTQKGSNAWVT 190
              +  + +   +  ++ +T
Sbjct: 280 IKCEAPLEIIKDRVGDSLMT 299


>gi|330686161|gb|EGG97779.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 284

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/157 (17%), Positives = 51/157 (32%), Gaps = 19/157 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS--VGRLDINTEGLLLL 124
           E   + +  KP G     S      +    V   L     R     V RLD NT G++L 
Sbjct: 80  EDDYIIIVSKPNGQNCAPSREHPHESLVEQVLGYLHHKGERTNPHIVTRLDRNTTGIVLF 139

Query: 125 TNDGGLARVLELPSTQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGD 174
              G +         +  +VY                 + +   +++++ +  +   Y  
Sbjct: 140 AKYGYIHH--LFSKAKMDKVYTCLAYGMTEPSGMIEAPIARSDESIIERCVS-ENGKYAK 196

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  QK + +   V L  G+  +I+  F++    
Sbjct: 197 TVFRTLKQKENVSCCEVQLCTGRTHQIRVHFQYIGHP 233


>gi|311742786|ref|ZP_07716595.1| ribosomal large subunit pseudouridine synthase D [Aeromicrobium
           marinum DSM 15272]
 gi|311314414|gb|EFQ84322.1| ribosomal large subunit pseudouridine synthase D [Aeromicrobium
           marinum DSM 15272]
          Length = 313

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 74/243 (30%), Gaps = 38/243 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----- 61
           V E    +RV   +AR    SR     ++A   V ++G    + +  V+    +E     
Sbjct: 14  VPEGLDGERVDVALARLTGLSRSRASELVADGHVLLDGHRPAK-SERVLFGAVLEATIPA 72

Query: 62  ---------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                             E   + +  KP+G+           TV   L +   R+    
Sbjct: 73  PPVVEVVPIPVDALSIVHEDDDIVVVDKPVGVAAHPGVGWTGPTVLGALAARGYRISTSG 132

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD--KLN 159
                  V RLD+ T GL+ +        VL+         + Y     G  D     ++
Sbjct: 133 APERQGIVHRLDVGTSGLMAVAKSEHAYTVLKQAFRDRVVDKTYHSLVQGHPDPHTGTID 192

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
                      K  +   G        TL+  + + + +T+ L  G+  +I+        
Sbjct: 193 APIARHPKHDFKFTVRADGRASVTHYATLEAHRYA-SLLTIKLETGRTHQIRVHMAAIKH 251

Query: 211 KVN 213
              
Sbjct: 252 PCV 254


>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 = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 78/241 (32%), Gaps = 42/241 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVM-STDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     ++   D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  -----EVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                EVD        G+ +   +   L +  KP G+V   +      T+ + +   F  
Sbjct: 57  DLILPEVDSDIAPEKMGLDIYYEDEDVLIV-DKPAGVVVHPTKRYQSGTLANGVAWYFKD 115

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 +  V RLD  T GL++      +   L        ++Y     G+++ +    L
Sbjct: 116 KGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYL-QIVKPMSKLYFAVVEGKMEGEGRIDL 174

Query: 162 ------KKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 + GI     +          +       + + V +  G+  +I+         +
Sbjct: 175 PISRKPQSGIERMVSEEGDRAITNYKVIKSSERFSLLKVKIETGRTHQIRVHLSHIGHPI 234

Query: 213 N 213
            
Sbjct: 235 V 235


>gi|15605391|ref|NP_220177.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D/UW-3/CX]
 gi|255349046|ref|ZP_05381053.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 70]
 gi|255503584|ref|ZP_05381974.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis 70s]
 gi|255507264|ref|ZP_05382903.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           trachomatis D(s)2923]
 gi|3329108|gb|AAC68253.1| Pseudouridine Synthase [Chlamydia trachomatis D/UW-3/CX]
          Length = 334

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/183 (22%), Positives = 71/183 (38%), Gaps = 32/183 (17%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
           ++ E  T  R+ K +++  G  SR   ++ I   RV+VNG +  R +  +   D      
Sbjct: 14  VIDEQLTG-RLDKGLVSYNGAYSRAFYQQQIELGRVRVNGRVYTRVSHPLSLGDVVEVEL 72

Query: 60  --------IEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                   +  + +PL K  E   + + +KP  +V   +    + TV   L         
Sbjct: 73  IEEEEPSSLIPEDIPLDKVYEDDMMLVINKPRDMVVHPAPGHTQGTVVHALLHEIGERLK 132

Query: 102 ---PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQ 155
              P    R   V RLD +T G LL+T     A+ L      + Q  ++Y         Q
Sbjct: 133 QEFPEEPWRPGIVHRLDKDTSG-LLITVKTRRAKALYSELFATKQVKKLYVAICINAPSQ 191

Query: 156 DKL 158
           +++
Sbjct: 192 ERI 194


>gi|208434858|ref|YP_002266524.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori G27]
 gi|208432787|gb|ACI27658.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori G27]
          Length = 242

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 32/201 (15%), Positives = 66/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPKNTRFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D L S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YD-LASFFKGWVLLHRLDKETSGVVLLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G V+++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLAIVQGIVEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  + VG++ G+  +I+
Sbjct: 172 IINKKTLLKVGIKTGRTHQIR 192


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

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>gi|224543798|ref|ZP_03684337.1| hypothetical protein CATMIT_03019 [Catenibacterium mitsuokai DSM
           15897]
 gi|224523289|gb|EEF92394.1| hypothetical protein CATMIT_03019 [Catenibacterium mitsuokai DSM
           15897]
          Length = 282

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 73/228 (32%), Gaps = 36/228 (15%)

Query: 14  QRVSKVIARAGIASRREVERMIAQ----QRVKVNGI--------LLERAAVNVMSTD--- 58
            R+ +     GI      ++++        + VNG         +   +   V   +   
Sbjct: 14  MRLDEFFYLHGI-----SKKLVKDSRNHGEILVNGEKRYLCYKTVEGDSVAIVFPKETSN 68

Query: 59  HIEVDGVPLRKA-ERTRLWLYHKPIGLVTT-----HSDPDGRSTVFDN-LPSIFSRVISV 111
            I VD +PL+   E   L +  K   L         ++  G + ++   +  I S +  V
Sbjct: 69  VIPVD-IPLKVVYEDDYLMIIDKQPNLACIPVKKYLTESLGNAIMYYYKVNHIESAIHLV 127

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNL---LKKGI--- 165
            RLD  T GL+++     +         Q  RVY     G   Q  +N      +G    
Sbjct: 128 NRLDKETSGLMMIAKSRYVHDAFSHDIKQVKRVYHALVKGNPGQGTVNAPIDHAEGHGTK 187

Query: 166 --VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             V +G              G  + V   L  G+  +I+    +    
Sbjct: 188 REVREGGKEAITHYRTIKTTGEYSLVECKLETGRTHQIRVHMAYLGCP 235


>gi|212530788|ref|XP_002145551.1| DRAP deaminase (Rib2), putative [Penicillium marneffei ATCC 18224]
 gi|210074949|gb|EEA29036.1| DRAP deaminase (Rib2), putative [Penicillium marneffei ATCC 18224]
          Length = 511

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/152 (17%), Positives = 51/152 (33%), Gaps = 23/152 (15%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ I   RV V G +       V +   +          V   P+    E   + +  KP
Sbjct: 70  KKAIEDGRVLVGGKVA-NLETIVPNGAIVSHSTHRHEPPVSSRPIGIIHEDDDMIVIDKP 128

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVGRLDINTEGLLLLTNDGGLARV--LELP 137
            G+    +     +T+ + + +           RLD  T G++ +  +   A    L+L 
Sbjct: 129 AGIPVHGAGRYHFNTILEIMKADRPGFKPLPCNRLDRLTSGVMFIAKNPKAAEKFALQLK 188

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
           S    + Y  R  G+           G+V+  
Sbjct: 189 SRTLQKEYVARVSGRFPD--------GVVLCD 212


>gi|15894302|ref|NP_347651.1| pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|15023925|gb|AAK78991.1|AE007617_3 Pseudouridylate synthase [Clostridium acetobutylicum ATCC 824]
 gi|325508430|gb|ADZ20066.1| Pseudouridylate synthase [Clostridium acetobutylicum EA 2018]
          Length = 318

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/259 (13%), Positives = 84/259 (32%), Gaps = 56/259 (21%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K ++  N   QRV K I       R+ ++        +   +  V +NG   ++   ++ 
Sbjct: 2   KIVIGPNEAGQRVDKFI-------RKWLKDVPLSAIYKAFRKGDVIINGAKCKKEKYSLE 54

Query: 56  STDHIEVDGVPLRKAERTRL---------------WLYHKPIGLVTTHSDPDGRSTVFDN 100
             D +E+  +     ++                   L  K  G++          T+ D 
Sbjct: 55  EGDVLEIKYIRSDAKKKKFTRIENNFKVTYEDENMLLVEKWPGVLVHSDKEKTSPTLTDY 114

Query: 101 LPSIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVY 145
           + S                      RLD NT G+++   +    + L   +   +  + Y
Sbjct: 115 VLSYLYDKGDYAPENEVTFTPSPCNRLDRNTSGIVIYGKNFEALKCLNEMIRERRIKKYY 174

Query: 146 RVRFHGQVDQDKLNL-LKKGI------VIQGICYGDMQVTLDTQKGSN----AWVTVGLR 194
                G++        +KK +      +I     G  Q++++ +        +++ + L 
Sbjct: 175 YALVKGKIKDGIYEAYIKKDVSSNKSEIINTPAPGAKQISMEIKCVETCGTFSFIEIELL 234

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G++ +++         + 
Sbjct: 235 TGRSHQLRAHLSHLGNPIL 253


>gi|281357295|ref|ZP_06243784.1| pseudouridine synthase, RluA family [Victivallis vadensis ATCC
           BAA-548]
 gi|281316326|gb|EFB00351.1| pseudouridine synthase, RluA family [Victivallis vadensis ATCC
           BAA-548]
          Length = 323

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 56/346 (16%), Positives = 103/346 (29%), Gaps = 87/346 (25%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  K +   ++      R+ + ++R   G  SR  ++R+I    VK +G+ LE     V 
Sbjct: 1   MNRKTLTFQIEAGDAGTRLDRCLSRLIPGE-SRSFLQRLIRDGLVKADGVALEVPRYPVR 59

Query: 56  STDHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
           +   I V+                    E   + +  KP G+V   +  +   TV + L 
Sbjct: 60  AGMSIAVELPEEESPEPAAEPFEFPILYEDDVMLVIDKPAGVVVHPAAGNPTGTVVNALL 119

Query: 103 SIFSRV-----------ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRF 149
             + ++             V RLD +T G L +         L       +  + Y    
Sbjct: 120 GRYPQLAEQLACTTSRPGIVHRLDKDTSGCLAVAKTANAQFKLSTAFAGRETRKTYLAIT 179

Query: 150 HG----------------QVDQDKLNLL-KKGI------------VIQGICYGDMQVTLD 180
            G                 V + K+ ++ + G             ++ G+  G + V + 
Sbjct: 180 RGVPIRRSGELSTLIGRHPVSRQKMAVVERNGKLAITRYRVEYTGMLDGVEIGVLAVRIL 239

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI 240
           T              G+  +I+         V            LG  + G  R     +
Sbjct: 240 T--------------GRTHQIRVHLASLGVPV------------LGDAVYGGARTAVAGV 273

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMK 286
            R+ L    L         P+  +     D   I+  +     R  
Sbjct: 274 ERQLLHAWKLCVPHPATGTPMEFTAPPPEDIRRILERIGVKTLREP 319


>gi|156537257|ref|XP_001605561.1| PREDICTED: similar to ribosomal pseudouridine synthase [Nasonia
           vitripennis]
          Length = 552

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 91/248 (36%), Gaps = 33/248 (13%)

Query: 32  ERMIAQQRVKVNGILLE--------RAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   ++            NV+    + V   P+        + + +KP 
Sbjct: 158 ERCIRAGTLTVNYQKVDVDYRLRHNDLLANVVHRHEVPVTSEPITVIHMDEDVVVVNKPA 217

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   +    + ++ RLD  T G+LL       AR +E    +
Sbjct: 218 SIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGILLFGRTPKKARQMEHQIRN 277

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----------GSNA 187
            Q  + Y  R  G+  ++++ +  + I +     G  +V+   +            G ++
Sbjct: 278 RQVQKQYVCRVEGEFPEEEI-VCSEAIEVVSYKIGVCKVSDKGKDCITKFKRLSYNGKSS 336

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNR--L-IRISYGPFQLGTLLAGSTREVSKKIL-RE 243
            V    + G+  +I+   ++  + V    L   + +GP +      G     + + L R+
Sbjct: 337 VVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVFGPHKGKGGNIGK----TDEELVRD 392

Query: 244 QLGPHLLE 251
            +G H  E
Sbjct: 393 LIGIHNAE 400


>gi|88857814|ref|ZP_01132456.1| tRNA pseudouridine synthase C [Pseudoalteromonas tunicata D2]
 gi|88819431|gb|EAR29244.1| tRNA pseudouridine synthase C [Pseudoalteromonas tunicata D2]
          Length = 244

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 46/160 (28%), Gaps = 27/160 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +        KP GL+   S  D          L       V  V RLD  T G+LL    
Sbjct: 7   QDEHFVAIDKPSGLLVHRSFLDKHETQFAMQMLRDQLGQHVFPVHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM- 175
              AR +       +  + Y     G             ++L+ +      Q        
Sbjct: 67  SDAARKMNEQFSDHRVTKRYLALVRGFAPDYRLLDRPLKEELDKIADKYADQNKAPQAAQ 126

Query: 176 -------QVTLDTQKGSNAWVTVGLRE-----GKNREIKK 203
                  QVTL    G    +   L E     G+  +I++
Sbjct: 127 TEFRCLQQVTLPIALGKYPTIRYSLVECFPKTGRKHQIRR 166


>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 = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M  K    +    +R+  +I   G+  SR + +R+I    V V+G+ + + A NV +   
Sbjct: 1  MAGKPPDVKGVGMERLDALIVGLGLVPSRSKAQRLIRDGHVLVDGVAVTKPAANVATASS 60

Query: 60 IEVD 63
          I VD
Sbjct: 61 ITVD 64


>gi|310828904|ref|YP_003961261.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           limosum KIST612]
 gi|308740638|gb|ADO38298.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           limosum KIST612]
          Length = 307

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/242 (16%), Positives = 81/242 (33%), Gaps = 36/242 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------ILLERAAVNV 54
           V E     R+    A      SR  ++ ++ +  VKV+G             +    +  
Sbjct: 8   VSEEKAGVRLDAYCAEQEPDFSRGYIKNLLNEGAVKVDGGQKKASYKLKGKEIITMEIPE 67

Query: 55  MSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--------- 104
            +   IE + +PL    E   + + +KP G+V   +      T+ + L            
Sbjct: 68  PAESTIEPENIPLEIIYEDEDVIVVNKPKGMVVHPAPGSPSGTLVNALMHHTGALSNING 127

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG----------- 151
             R   + R+D +T GLL++  +    + L   L +    R Y+    G           
Sbjct: 128 VYRPGIIHRIDKDTSGLLMVAKNNAAHQNLTEQLKAHTITRQYKALVKGIMENNRGTIDM 187

Query: 152 QVDQDKLNLLKKGIVIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            + +   + ++  +V +          TL         +   L  G+  +I+   +   +
Sbjct: 188 PIGRHPKDRVRMAVVKENSKEAVTHFETLKRYAEGYTLMQFRLETGRTHQIRVHMQAIGY 247

Query: 211 KV 212
            +
Sbjct: 248 PI 249


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

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAASPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>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 = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 19/78 (24%), Positives = 31/78 (39%), Gaps = 1/78 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ +++ + GI  SR +   +I + +V VNG  +E+    V     I + G  L    R 
Sbjct: 4  RLDQLLFKKGITESREKARALIIEGKVIVNGHKIEKPGTMVDENSEITICGETLPYVSRG 63

Query: 74 RLWLYHKPIGLVTTHSDP 91
             L H          D 
Sbjct: 64 GFKLEHAIKEFSIDVKDK 81


>gi|297588274|ref|ZP_06946917.1| possible RluA protein [Finegoldia magna ATCC 53516]
 gi|297573647|gb|EFH92368.1| possible RluA protein [Finegoldia magna ATCC 53516]
          Length = 321

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 88/245 (35%), Gaps = 45/245 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+  NI   N + QRV + I +     S+  ++++I  ++VKVN         N+   D 
Sbjct: 1   MRHINIDNSN-SNQRVDRFIMKLMPKMSKNHIQKLIRTKKVKVNKKR-TEPDYNLKIDDV 58

Query: 60  IEV---DGVPLRKAERTRL----------------WLYHKPIGLVTTHSDPDGR-STVFD 99
           + +   D V  +  +                     L +K  G+++  ++P      + D
Sbjct: 59  VNIYLYDEVIEKYQDNKVYTAEDFNLDIIYEDDDLILINKKTGVLSHAANPQDYGKNIVD 118

Query: 100 -----------NLPSIFSRVIS--VGRLDINTEGLLL--LTNDGGLARVLELPSTQWLRV 144
                        P+  S      V RLD NT G+++   T D            +  ++
Sbjct: 119 MMVSYLIKTNQFTPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFKKHEITKI 178

Query: 145 YRVRFHGQVDQDKLN-LLKKGI-----VIQGICYGDMQVTLDTQK-GSNAWVTVGLREGK 197
           Y     G +    ++  L+K I     VI       M    + +  G  + V V L  G+
Sbjct: 179 YETIVVGNLKDQTIDLALEKDIDKNKSVINSSGKKSMTKVWNVKNFGKYSLVNVDLLTGR 238

Query: 198 NREIK 202
             +I+
Sbjct: 239 THQIR 243


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

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L+L    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVLARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>gi|315302419|ref|ZP_07873284.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
 gi|313629211|gb|EFR97479.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria ivanovii FSL F6-596]
          Length = 296

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 44/292 (15%), Positives = 94/292 (32%), Gaps = 52/292 (17%)

Query: 17  SKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA 70
           +K I++  +       +     +++VNG         V   D + +          L   
Sbjct: 22  NKHISKQLLT----AVKYSDDGKIEVNGTEQNVL-YQVEIGDEVCLTFPREQQNERLLAE 76

Query: 71  --------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDI 116
                   E   L + +KP G+ +  S      +V + +   + +      +  V RLD 
Sbjct: 77  YTALEIIFEDEFLLIINKPAGMASIPSQYHPSGSVANFVKGHYEKQGLTSAIHIVTRLDR 136

Query: 117 NTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKK 163
            T GL+L+  +      L   L      R Y+    G            + +  ++++++
Sbjct: 137 ETSGLMLIAKNRFAHARLSTFLQQGLLKRRYQAFTSGVLNNRIGSIEAPIGRKTVSIMER 196

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            +  +G         L   +  +  V + L  G+  +I+  F +    +        G  
Sbjct: 197 FVTPEGKYAKTNYEVLKRYEAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG-- 246

Query: 224 QLGTLLAGSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLVRDRPN 273
               +  G T  + ++ L        H L E  +  D P+      +  +  
Sbjct: 247 --DDMYGGDTTLLKRQALHSCHLHLIHPLTEEYLTFDLPLPKDMEEIIPKSK 296


>gi|295426413|ref|ZP_06819063.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
 gi|295063781|gb|EFG54739.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           amylolyticus DSM 11664]
          Length = 294

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 83/249 (33%), Gaps = 44/249 (17%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ----QRVKVNGILLERAAVNVMS 56
           M    +  +   P+++   + + G  S    + +I        V VN       + ++ +
Sbjct: 1   MTSFKLFVQEKDPKKLGSFLLKNGF-SH---QALIKARHHGGLVLVNHKR-RYNSFHLRA 55

Query: 57  TDHIEV-------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            D +                  P++   E     + +K  G+++  S  +    + +   
Sbjct: 56  GDEVIFIPGHEKENHWLRPSEEPIKIVKETPNYLIVNKEAGVLSIPSRYEDSDALVNRAM 115

Query: 103 SIFSRV-------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-WLRVYRVRFHGQVD 154
             F +          V RLD +T GL+L+  +            + +++ Y     G   
Sbjct: 116 CYFEKQNEAGLKPHVVTRLDRDTSGLVLIGKNSVAHARFSKMDKENFVKKYHAIVAGNFS 175

Query: 155 QDKLNLL------KKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            ++L  L      K+G      ++  G      +  +  QK + + V + L  G+  +I+
Sbjct: 176 SNELKGLIDQPIGKEGSGVKRQVMSTGQKAQT-EYQVLAQKNNASLVELRLLTGRTHQIR 234

Query: 203 KVFEFFNWK 211
               +    
Sbjct: 235 VHMAYIGHP 243


>gi|240949614|ref|ZP_04753949.1| tRNA pseudouridine synthase C [Actinobacillus minor NM305]
 gi|240295872|gb|EER46548.1| tRNA pseudouridine synthase C [Actinobacillus minor NM305]
          Length = 242

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 69/200 (34%), Gaps = 35/200 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V  + RLD  T G+LL   +  +A
Sbjct: 12  LIAINKPAGMLVHRSWLDKAETVFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALNSDMA 71

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--- 186
           R +     + Q  + Y     G ++          +++  +     Q     +  ++   
Sbjct: 72  RTMCELFENHQVKKGYLAIVRGYLEGKARVDYPLKVILDKVADRFSQEKEPQEAITDYQG 131

Query: 187 -AWVTV------------GLRE-----GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
            A V +             L E     G+  ++++  +     +        G  + G L
Sbjct: 132 LATVEMPYPAGKFQTARYSLVELQPQTGRKHQLRRHLKHLFHPI-------MGDTKYGDL 184

Query: 229 LAGSTREVSKKILREQLGPH 248
                R ++++   E+L  H
Sbjct: 185 H--QNRTLAEQSGVERLMLH 202


>gi|145634988|ref|ZP_01790695.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittAA]
 gi|145267854|gb|EDK07851.1| tRNA pseudouridine synthase C [Haemophilus influenzae PittAA]
          Length = 239

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/181 (14%), Positives = 52/181 (28%), Gaps = 29/181 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  +  LD  T G+LL    
Sbjct: 7   QDEFLVAVNKPDGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHCLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQ 176
             +A ++          + Y     G +            +L+ +      +     +  
Sbjct: 67  SEIANLMCEQFEQKCVQKSYLAVVRGYLQGKERIDYPLKIQLDKIADKFSQEDKEPQEAV 126

Query: 177 VTLDT-------------QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
              +              Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYEGLKIVEMPYPAGRYQTARYSLVKLIPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 Q 224
            
Sbjct: 185 H 185


>gi|270284819|ref|ZP_06194213.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum Nigg]
 gi|270288848|ref|ZP_06195150.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum Weiss]
 gi|301336199|ref|ZP_07224401.1| ribosomal large subunit pseudouridine synthase D [Chlamydia
           muridarum MopnTet14]
          Length = 338

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 63/174 (36%), Gaps = 31/174 (17%)

Query: 15  RVSK--VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ K  V+      SR   ++ I   RV+VNG +  RA+  +   D +++          
Sbjct: 26  RLDKGLVLHNNAY-SRAFYQQQIDLGRVRVNGRVQTRASYLLSQGDLVDLELVEEETPSS 84

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFS 106
              + +PL K  E   + + +KP  +V   +    + TV   L            P    
Sbjct: 85  LTPENIPLDKVYEDNMILVINKPRNMVVHPAPGHVQGTVVHALLHEIGERLKQEFPEEPW 144

Query: 107 RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
           R   V RLD +T GLL+   T            S Q  ++Y         Q  +
Sbjct: 145 RPGIVHRLDKDTSGLLITVKTRRAKAVYSELFSSKQMKKMYIAICINSPAQKHI 198


>gi|156055472|ref|XP_001593660.1| hypothetical protein SS1G_05088 [Sclerotinia sclerotiorum 1980]
 gi|154702872|gb|EDO02611.1| hypothetical protein SS1G_05088 [Sclerotinia sclerotiorum 1980
           UF-70]
          Length = 399

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 25/143 (17%), Positives = 53/143 (37%), Gaps = 15/143 (10%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHK 80
           V+  + +  + VNG  +E  +  + + D I          V  +P+    E   + + +K
Sbjct: 25  VKDAMERGAIAVNGKPVESTSQIIKNGDVISHTLHRHEPPVTALPISIVHEDEDIIVINK 84

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLELP 137
           P G+    +     ++V + + +            RLD  T G++ +      A  L L 
Sbjct: 85  PSGVPVHPAGRYNYNSVVEIMRAERGHGWNPLPCNRLDRLTSGIMFIGKHAKAAEALSLQ 144

Query: 138 STQ--WLRVYRVRFHGQVDQDKL 158
            +     + Y  R  G+    ++
Sbjct: 145 ISGRTVRKEYIARVKGKFPDGEV 167


>gi|329577702|gb|EGG59129.1| S4 domain protein [Enterococcus faecalis TX1467]
          Length = 64

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 1/59 (1%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST-DHIEVDGVPLRKAE 71
           R+ K++      SR+ V+R+I  ++V V+GI+    + NV +    I+V G  +    
Sbjct: 1  MRLDKLLEELQFGSRKTVKRLIKGKQVTVDGIVTLNESQNVDAQLQMIKVKGQLISHRP 59


>gi|293610198|ref|ZP_06692499.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292827430|gb|EFF85794.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 310

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 84/242 (34%), Gaps = 56/242 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLEIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVINKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             DK  ++       L  G     +  +G       V  +  K +   V      G+  +
Sbjct: 186 SLDKQLIDAPLFRYELANGERRVRVSKEGKPSKTEWVVAERFKNAT-LVHASPLSGRTHQ 244

Query: 201 IK 202
           I+
Sbjct: 245 IR 246


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

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 88/250 (35%), Gaps = 62/250 (24%)

Query: 7   VQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           V+E+    R+ +        +   G      +++++   +V+V+G  ++ A + +++   
Sbjct: 9   VEEDENGMRLDRWFKVHYPGL---GFG---YLQKILRSGQVRVDGGRVK-ANMRLVTGQS 61

Query: 60  IEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGR 94
           I V                      DG  L+K    E  ++++++KP GL         R
Sbjct: 62  IRVPSFFIESKRNISITSKVISQQDDGDLLKKMLLYEDPKIFVFNKPAGLAVQGGSGLTR 121

Query: 95  STVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
                       +      V RLD  T GLL++      A+ L     + +  ++Y    
Sbjct: 122 HVDGMLEAWRNKKGEKPRLVHRLDRETSGLLVVARSRSAAQALTAAFRTREMKKIYWALV 181

Query: 150 HGQVDQ-----------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
            G   +                 DK+ + + G  +           LDT+  + +W+ + 
Sbjct: 182 RGVPRKKQEKISTWMAKETTAQGDKMRVCEHG-ELDANHAVSYYRILDTRARALSWLEME 240

Query: 193 LREGKNREIK 202
              G+  +++
Sbjct: 241 PYTGRTHQLR 250


>gi|11279841|pir||A81748 ribosomal large chain pseudouridine synthase D TC0029 [imported] -
           Chlamydia muridarum (strain Nigg)
          Length = 345

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 63/174 (36%), Gaps = 31/174 (17%)

Query: 15  RVSK--VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
           R+ K  V+      SR   ++ I   RV+VNG +  RA+  +   D +++          
Sbjct: 33  RLDKGLVLHNNAY-SRAFYQQQIDLGRVRVNGRVQTRASYLLSQGDLVDLELVEEETPSS 91

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFS 106
              + +PL K  E   + + +KP  +V   +    + TV   L            P    
Sbjct: 92  LTPENIPLDKVYEDNMILVINKPRNMVVHPAPGHVQGTVVHALLHEIGERLKQEFPEEPW 151

Query: 107 RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
           R   V RLD +T GLL+   T            S Q  ++Y         Q  +
Sbjct: 152 RPGIVHRLDKDTSGLLITVKTRRAKAVYSELFSSKQMKKMYIAICINSPAQKHI 205


>gi|329737381|gb|EGG73635.1| putative pseudouridine synthase B, ribosomal large subunit
           [Staphylococcus epidermidis VCU028]
          Length = 49

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQ 254
           +FE+F  +VN+L RI +GP  L  L AG  R ++   ++     HL E  +
Sbjct: 1   MFEYFGHQVNKLTRIQFGPIDLKGLNAGEGRVLTPHEVKIL--RHLAENGK 49


>gi|296129452|ref|YP_003636702.1| pseudouridine synthase, RluA family [Cellulomonas flavigena DSM
           20109]
 gi|296021267|gb|ADG74503.1| pseudouridine synthase, RluA family [Cellulomonas flavigena DSM
           20109]
          Length = 311

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 82/243 (33%), Gaps = 42/243 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +    +RV   +AR    SR     + AQ  V+V+G  + ++   V +   +EVD   
Sbjct: 9   VPDGLAGERVDAALARLLGLSRTRAAELAAQGAVRVDGRAVGKSDRLV-AGSFLEVDLSL 67

Query: 64  --------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                         G+ +   +   + +   P+G+    S      TV   L +   R+ 
Sbjct: 68  PVPTAPVVVPEPVPGMRIVHDDDDLVVVDK-PVGVAAHPSPGWSGPTVVGALAAAGYRIS 126

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--D 156
                     V RLD  T GL+++        VL+    +    +VY     G       
Sbjct: 127 TSGSAERQGVVHRLDAGTSGLMVVAKSEHAYTVLKRAFKERTVEKVYHALAQGHPSPTTG 186

Query: 157 KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            ++           K  +V  G         L+   G+ + V V L  G+  +I+  F  
Sbjct: 187 TIDAPIGRHPSSDWKFAVVADGKPSVTHYEVLEMLPGA-SLVEVHLETGRTHQIRVHFAA 245

Query: 208 FNW 210
              
Sbjct: 246 LRH 248


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

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>gi|261414458|ref|YP_003248141.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|261370914|gb|ACX73659.1| pseudouridine synthase [Fibrobacter succinogenes subsp.
           succinogenes S85]
 gi|302326709|gb|ADL25910.1| putative pseudouridine synthase, RluD family [Fibrobacter
           succinogenes subsp. succinogenes S85]
          Length = 321

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 43/265 (16%), Positives = 82/265 (30%), Gaps = 52/265 (19%)

Query: 24  GIASRREVERMIAQ---QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE--------- 71
              SR   E  I +     V +NG             D +        + E         
Sbjct: 32  TYHSR---EDWIDRLTRGLVTINGATA-NVETVAHRGDKVVYHVENYSEPEVPTDFETVF 87

Query: 72  -RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
                 L  KP G+   H+     +T    +   F       + RLD +T GL+L    G
Sbjct: 88  EDDEFILVAKPAGVPVHHTGRIFYNTFAAIIRREFDSETATPMHRLDRDTGGLILFARYG 147

Query: 129 GLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
             A   +    + L  + Y     G+  + ++      + ++      +++ +  ++G  
Sbjct: 148 ETAARFQKNLDRILLRKFYLAVVRGKFPEGEVE---CHMPLREDPEDPIRLRMHHREGGK 204

Query: 187 AWV----------------TVGLRE-----GKNREIKKVFEFFNWKVNRLIRISY--GPF 223
                               + L E     G+  +I+       + +    R+ Y  G F
Sbjct: 205 ECFTRFKLVRHLDCPEIAPELSLVEAELITGRKHQIRAHLAEMGYPIVG-DRLYYRDGEF 263

Query: 224 QLGTLLAGSTREVSKKILREQLGPH 248
               L  G   E++ + ++  LG H
Sbjct: 264 Y-QKLAQGG--ELTDEDIK-VLGAH 284


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

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 35/185 (18%), Positives = 62/185 (33%), Gaps = 40/185 (21%)

Query: 6   IVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
            V E+    RV +        +A + +A      ++  +  V+V+G  +E  +  +    
Sbjct: 14  TVTEDEAGMRVDRWFKRRYPTLALSHLA------KICRKGEVRVDGKRVET-STRLEEGQ 66

Query: 59  HIEVDGVPLRKAERTRL----------------------WLYHKPIGLVTTHSDPDGRST 96
            + V  + +   E   +                       + +KP GL T       R  
Sbjct: 67  KVRVPPLRIEAPEAPAVKRASPEDAQALKAMTLFEDKDVLVLNKPWGLATQGGSGQKRHV 126

Query: 97  VFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
                 L    SR + V RLD +T G+LL+     +A  L     S Q  ++Y     G 
Sbjct: 127 DGMLESLARGDSRPVLVHRLDRDTSGVLLVAKTRRMAADLGEIFRSRQAKKIYWALVEGV 186

Query: 153 VDQDK 157
               +
Sbjct: 187 PKPAQ 191


>gi|260818260|ref|XP_002604301.1| hypothetical protein BRAFLDRAFT_88590 [Branchiostoma floridae]
 gi|229289627|gb|EEN60312.1| hypothetical protein BRAFLDRAFT_88590 [Branchiostoma floridae]
          Length = 369

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 26/141 (18%), Positives = 50/141 (35%), Gaps = 17/141 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD-----------HIEVDGVPLRKAERTRLWLYHK 80
           E+ I   R+ +NG  ++     +   D            +  D V +   E   L + +K
Sbjct: 53  EKAIKLGRLLLNGECVK-LDTVLKDNDFMQNTVHRHEPPVVADPVQIV-EETDDLVVINK 110

Query: 81  PIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--EL 136
           P  +          ++V   L     F  +  + RLD  T G+L+   +      L  ++
Sbjct: 111 PASMPVHPCGGYRHNSVIFVLGKEHGFQNLHPIHRLDRLTSGILIFAKNLETKHRLDAQI 170

Query: 137 PSTQWLRVYRVRFHGQVDQDK 157
              +  +VY  R  G+  +  
Sbjct: 171 KGREVKKVYLARVEGEFPEKA 191


>gi|254419052|ref|ZP_05032776.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
 gi|196185229|gb|EDX80205.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
          Length = 339

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 76/236 (32%), Gaps = 51/236 (21%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------EVDG 64
           R+ K +A A    SR  ++ ++A+  V+ +G++L   +       ++             
Sbjct: 32  RLDKALAEAFPTLSRARLQALLAEGAVRRDGLVLTAGSAKAQPGLYVVALPPVAPATPQP 91

Query: 65  VPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISV 111
             +      E   L +  KP G+    +      T+ + L +            +R   V
Sbjct: 92  EAIPLTVLYEDADLIVIDKPAGMAAHPAPGCETGTLVNALLAHCGDSLSGIGGVARPGIV 151

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQV---------------- 153
            RLD +T G+++   T+           +    R Y     G                  
Sbjct: 152 HRLDKDTSGVMVAAKTDRAHQGLSALFATHDIERTYIALTRGAPSPSRGRIETRIGRSTG 211

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------AWVTVGLREGKNREIK 202
           D+ K+ +LK G         D  V     + +        A V   L  G+  +I+
Sbjct: 212 DRKKIAVLKAG---GREAITDYVVQAIFGEPAKASGAPLAARVACTLHTGRTHQIR 264


>gi|238783433|ref|ZP_04627456.1| Pseudouridine synthase [Yersinia bercovieri ATCC 43970]
 gi|238715678|gb|EEQ07667.1| Pseudouridine synthase [Yersinia bercovieri ATCC 43970]
          Length = 267

 Score = 56.7 bits (136), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 70/209 (33%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 47  PCHDKIE------TLYQDDHLVLINKPAGLLSLSGKNPQNIDSVHHRLVQIFPGCTLVHR 100

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 101 LDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDN------QGVIDAAIA 154

Query: 172 YGDMQVTLDT-----QKGSNAWVTVG---LRE------------------GKNREIKKVF 205
                  L +      K + +   V      E                  G+  +++   
Sbjct: 155 KDPALFPLMSICSIHGKPARSRYRVVERFYHELEDRTLLPLTRVQLTPETGRTHQLRIHC 214

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +       YG    G LL G+ R
Sbjct: 215 QQLGHPIWGCD--LYG----GRLLPGTER 237


>gi|297182825|gb|ADI18977.1| pseudouridylate synthases, 23S RNA-specific [uncultured delta
           proteobacterium HF0010_10I05]
          Length = 316

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 65/202 (32%), Gaps = 43/202 (21%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE----------VDGVPLRKAERTRLWLYHKPIGL 84
           I    + V+G   + A   + +   +           VD       E   L   +K   L
Sbjct: 42  IKSGHLLVDGQQGK-AGQKLRNNQRVVYLRPDSLEPSVDADYEVLFEDEWLIGLNKSGDL 100

Query: 85  VTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
            T+ S    ++T+   +   F   ++ ++ RLD  T G++L      +A+ +       Q
Sbjct: 101 PTSPSGRYFKNTLMHLVRERFGWQKLYTIHRLDRETSGVVLFAKTHQMAQQMAALFRDKQ 160

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--------MQVTLDTQKGSNAWVTV- 191
             + YR      + ++++        +     G          Q   +  K S       
Sbjct: 161 IRKEYRAVVTTPLPKEEI--------LVSKPIGPDRSSSIRIKQSVCEDGKPSETRFRQL 212

Query: 192 -GLRE----------GKNREIK 202
             +RE          G+  +I+
Sbjct: 213 KTIRECAYLQIHPMTGRTHQIR 234


>gi|256379746|ref|YP_003103406.1| pseudouridine synthase, RluA family [Actinosynnema mirum DSM 43827]
 gi|255924049|gb|ACU39560.1| pseudouridine synthase, RluA family [Actinosynnema mirum DSM 43827]
          Length = 310

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 72/253 (28%), Gaps = 57/253 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----------MS 56
           V +     RV   +A+    SR  +  +     V ++G +  ++   V            
Sbjct: 10  VPDGLDGMRVDAGLAKLLGLSRTVIASLAESGDVVLDGRVAGKSDRLVAGSWLELTLPEP 69

Query: 57  TDHIEVDGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PS 103
              ++V  VP+       E   + +  KP+G+    S      TV   L           
Sbjct: 70  ERPVQVQAVPVEGMIVLHEDDDVIVVDKPVGVAVHPSPGWTGPTVVGGLAAAGVRVSTSG 129

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD+ T G++++        VL+         ++Y     G  D       
Sbjct: 130 AAERQGVVHRLDVGTTGVMVVAKSEHAYSVLKQAFKDRTVDKLYHALVQGHPDP------ 183

Query: 162 KKGIVIQGICYGDMQ---------VTLDTQKGSNAWVTVG------------LREGKNRE 200
                I+G     +            +   K S     V             L  G+  +
Sbjct: 184 -----IKGTIDAPIDRHPKHDYKFAVMAGGKPSITHYEVVEAFRAASLLDVHLETGRTHQ 238

Query: 201 IKKVFEFFNWKVN 213
           I+  F        
Sbjct: 239 IRVHFSALKHPCV 251


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

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>gi|299535937|ref|ZP_07049256.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus fusiformis
           ZC1]
 gi|298728542|gb|EFI69098.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus fusiformis
           ZC1]
          Length = 311

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 29/163 (17%), Positives = 58/163 (35%), Gaps = 22/163 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLL 124
           E   + + +KP    T  S     +++ + +   F +         V RLD +T GLL +
Sbjct: 95  EDDAILVLNKPAHQSTIPSREHPTNSIANLVCGYFQKQGLASTAHIVTRLDRDTSGLLCI 154

Query: 125 TNDGGLARV--LELPSTQWLRVYRVRFHGQVDQDKLNLL-----KKGIVI-----QGICY 172
                +  +  L     +  R Y    HG ++Q+  +++     K+G +I     +   Y
Sbjct: 155 AKHAHIHHLTGLAQRKREISRQYEAIVHGHIEQNFQSIIAPIGRKEGSIIEREVREDGQY 214

Query: 173 GDMQVTLDTQ----KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               V +  +          V + L  G+  +I+         
Sbjct: 215 AHTDVKVLKRFSLGAEPMTHVRLQLHTGRTHQIRVHMSHLGHP 257


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

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAADPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>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 = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 77/209 (36%), Gaps = 36/209 (17%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------------GVPLRKAER 72
           S R V + +   R+ VNG  + +    +   D IE+                + +   + 
Sbjct: 29  SGRFVRKAVRDGRIFVNGEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDINIEIVYEDS 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTN 126
             + +  KP G+V   +      T+ + +   F +      V  V RLD +T GL+++  
Sbjct: 88  DIIVINKKP-GIVVHPTKSHSTGTLSNGILYHFKKKGEKSIVRLVNRLDRDTSGLVIVAK 146

Query: 127 DGGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYG 173
           +      L    ++  + ++Y    HG            + +++   +K+ IV +     
Sbjct: 147 NQFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEENESIKR-IVDERGQES 205

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +  +    + V + L  G+  +I+
Sbjct: 206 ITTYEVLEELSKGSVVKLELETGRTHQIR 234


>gi|148543809|ref|YP_001271179.1| RluA family pseudouridine synthase [Lactobacillus reuteri DSM
           20016]
 gi|184153213|ref|YP_001841554.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227365096|ref|ZP_03849120.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|325681570|ref|ZP_08161092.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri MM4-1A]
 gi|148530843|gb|ABQ82842.1| pseudouridine synthase, RluA family [Lactobacillus reuteri DSM
           20016]
 gi|183224557|dbj|BAG25074.1| pseudouridylate synthase [Lactobacillus reuteri JCM 1112]
 gi|227069874|gb|EEI08273.1| RluA family pseudouridine synthase [Lactobacillus reuteri MM2-3]
 gi|324979111|gb|EGC16056.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           reuteri MM4-1A]
          Length = 301

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/185 (17%), Positives = 61/185 (32%), Gaps = 35/185 (18%)

Query: 55  MSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
            + D+++V   P+    E     + +KP G+ T    P     V D+L +          
Sbjct: 66  TANDNVDVSEAPIDIIYEDQDFLIMNKPAGVATV---PAHNVPVADSLVNRVKGYYKRQN 122

Query: 109 ------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQD--- 156
                     RLD +T GL++       A  +     +     + Y     G+V  +   
Sbjct: 123 YENQVTHVATRLDRDTSGLVVFPKH-RFAHAVLDEQLKKHLVKKNYLALIKGKVPAEHGY 181

Query: 157 -------KLNLLKKGIVIQGICYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFE 206
                    N   K +V      G   VT   ++  N   + + + L  G+  +I+  F 
Sbjct: 182 IDAPIQRDPNSFVKRMV---GKEGKASVTEYWRQECNVQASLIKIRLHTGRTHQIRVHFA 238

Query: 207 FFNWK 211
              + 
Sbjct: 239 SLGFP 243


>gi|326571595|gb|EGE21610.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC7]
          Length = 258

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 29/166 (17%)

Query: 76  WLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP  ++   S  D      V   L +     V  V RLD  T G+L+   D   A 
Sbjct: 27  VIINKPANMLVHRSWLDKHETCFVMQTLRNQINQHVYPVHRLDRPTSGVLVFALDSQTAG 86

Query: 133 VLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGDMQVT 178
           +L     +    + Y     G +                 +              D QV 
Sbjct: 87  LLAKQFENHHIQKSYLAVVRGIIGTGRIDYALKPRLDKIADKFSNPNKASKSAITDYQVL 146

Query: 179 LDTQKG-------SNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
             TQ+         ++  ++     +  G+  ++++  +     + 
Sbjct: 147 ATTQQPFISCRRFDSSRYSLVCLTPIT-GRKHQLRRHMKHIFHPIV 191


>gi|326571287|gb|EGE21309.1| tRNA pseudouridine synthase C [Moraxella catarrhalis BC1]
          Length = 254

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 29/166 (17%)

Query: 76  WLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP  ++   S  D      V   L +     V  V RLD  T G+L+   D   A 
Sbjct: 23  VIINKPANMLVHRSWLDKHETCFVMQTLRNQINQHVYPVHRLDRPTSGVLVFALDSQTAG 82

Query: 133 VLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGDMQVT 178
           +L     +    + Y     G +                 +              D QV 
Sbjct: 83  LLAKQFENHHIQKSYLAVVRGIIGTGRIDYALKPRLDKIADKFSNPNKASKSAITDYQVL 142

Query: 179 LDTQKG-------SNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
             TQ+         ++  ++     +  G+  ++++  +     + 
Sbjct: 143 ATTQQPFISCRRFDSSRYSLVCLTPIT-GRKHQLRRHMKHIFHPIV 187


>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 = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 78/241 (32%), Gaps = 42/241 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVM-STDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     ++   D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  -----EVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                EVD        G+ +   +   L +  KP G+V   +      T+ + +   F  
Sbjct: 57  DLILPEVDSDIAPEKMGLDIYYEDEDVLIV-DKPAGVVVHPTKRYQSGTLANGVAWYFKD 115

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 +  V RLD  T GL++      +   L        ++Y     G+++ +    L
Sbjct: 116 KGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYL-QIVKPMSKLYFAVVEGKMEGEGRIDL 174

Query: 162 ------KKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 + GI     +          +       + + V +  G+  +I+         +
Sbjct: 175 PISRKPQSGIERMVSEEGDRAITNYKVIKSSERFSLLKVKIETGRTHQIRVHLSHIGHPI 234

Query: 213 N 213
            
Sbjct: 235 V 235


>gi|254457610|ref|ZP_05071038.1| tRNA pseudouridine synthase C [Campylobacterales bacterium GD 1]
 gi|207086402|gb|EDZ63686.1| tRNA pseudouridine synthase C [Campylobacterales bacterium GD 1]
          Length = 250

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/173 (18%), Positives = 56/173 (32%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP GL+   S  D     F        I   V  + RLD  T G+LL   D
Sbjct: 12  QDGYLVCINKPSGLLVHKSMIDRHEIYFAMKMLRDQIGQWVYPIHRLDKPTSGVLLFALD 71

Query: 128 GGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQ 182
              A  L     +     + Y     G  +   L  + LK+   +  I   D +   + Q
Sbjct: 72  KETA-KLMSEQFKEHTTKKTYICVVRGYTEVFGLIDHALKE--KLDKIADKDAKEEKEAQ 128

Query: 183 KGSN----------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + +                       + V V  + G+  +I++  +  +  + 
Sbjct: 129 EAATEYERLDTVELDFAVGRYDKTRYSLVKVKPKTGRKHQIRRHMKHISHHIL 181


>gi|332184772|gb|AEE27026.1| Ribosomal large subunit pseudouridine synthase [Francisella cf.
           novicida 3523]
          Length = 307

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/222 (14%), Positives = 72/222 (32%), Gaps = 45/222 (20%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAERTR----------- 74
           R I +  ++VN   +++ +  + + D + V       D  P++ ++              
Sbjct: 36  RWIRKGELRVNKKRVKQTS-RISAGDIVRVPPFSLEEDSKPIKISQSHLDFLEQRILYEN 94

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +  KP G+            V     L     R+  V RLD  T G ++L      
Sbjct: 95  DDYIIVDKPSGMAVHGGSGINSGLVERLRQLRPKARRLDLVHRLDKETSGCVILAKKHSS 154

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSN 186
                      +  ++Y    HG  D+  + +    + ++     D Q  V +D++ G  
Sbjct: 155 LVYFFDIFKQRKVDKIYYAIVHGHWDKKIITI---DLPLKRTETKDGQRVVKVDSKDGKR 211

Query: 187 ---------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                          + + + L  G+  +I+   +     + 
Sbjct: 212 ALTRIISVRHLQGGFSLLEIKLETGRTHQIRVHTKAMGHPIV 253


>gi|320332730|ref|YP_004169441.1| RluA family pseudouridine synthase [Deinococcus maricopensis DSM
           21211]
 gi|319754019|gb|ADV65776.1| pseudouridine synthase, RluA family [Deinococcus maricopensis DSM
           21211]
          Length = 318

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 34/194 (17%), Positives = 65/194 (33%), Gaps = 29/194 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-----------RLWLYHKPIG 83
           +A+  V ++G  ++     ++    + V   P    E T            L    KP G
Sbjct: 60  VARGEVTLDGAPID--GHEILQAGQVLVWNRPPWDEEATPRTFDIAYLDDALLAVIKPSG 117

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
           L T H      +T+   + +       + RL   T GL+L       A  L         
Sbjct: 118 LPTMHGGGFLENTLLSLVRAQHPEATPLHRLGRATSGLVLFARTHAAASRLSEAWRMHHV 177

Query: 142 LRVYRVRFHGQVDQDKLNLLK-------------KGIVIQGICYGDMQVTLDTQKGSNAW 188
            + YR    G + QD++ +                G+   G     +   L+ ++ +   
Sbjct: 178 EKRYRALASGVLAQDRVTIEAPIGPVPHPRLGTVHGVSATGKASRSVACVLERREDAT-L 236

Query: 189 VTVGLREGKNREIK 202
           + V +  G+  +I+
Sbjct: 237 LQVDIFTGRPHQIR 250


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

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/223 (16%), Positives = 76/223 (34%), Gaps = 58/223 (26%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRK-------- 69
           ++++   +V+V+G  ++     V     + V               G  L+         
Sbjct: 35  QKLLRSGQVRVDGGRVKS-DARVQPGQTVRVPPLDVDAKLKSGPIAGKDLKHSSDFDLLS 93

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDIN 117
                E  ++ + +KP G+        G S V  ++  +     S        V RLD +
Sbjct: 94  RMVLHEDEKVIVLNKPPGIAV-----QGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRD 148

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKLNLL----------KK 163
           T G+L++    G A+ L          + Y     G     +DK++            + 
Sbjct: 149 TSGVLVIARTRGAAQKLTAAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEATADGDRM 208

Query: 164 GIVIQGICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIK 202
            I   G    D  ++    L+T   + AW+ +    G+  +++
Sbjct: 209 RIAKHGEDGADHAISFYRVLETAAQNLAWLEMEPYTGRTHQLR 251


>gi|152981434|ref|YP_001352926.1| pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp.
           Marseille]
 gi|151281511|gb|ABR89921.1| Pseudouridylate synthases, 23S RNA-specific [Janthinobacterium sp.
           Marseille]
          Length = 223

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 68/176 (38%), Gaps = 30/176 (17%)

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFS 106
            R    V  T    VD + +   +   + L +KP GL+T +  +P    +V   L   F 
Sbjct: 3   TRIDTFVAPT---CVDEIEIIYQDEA-ILLINKPSGLLTLSGKNPLNLDSVHHRLVQQFP 58

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           + + + RLD+ T GLL++  +  +A  +          + Y+    GQV +D        
Sbjct: 59  QALMIHRLDLGTSGLLVVALNKAVAANINRQFQLRTVAKTYQAVLAGQVAEDHGK----- 113

Query: 165 IVI----QGICYGDMQVTLDTQKGSNAWVTV--------------GLREGKNREIK 202
           I +      + +  +++ L + K +++   V                  G+  +++
Sbjct: 114 ITLPIAKDPLNFPKLKICLASGKAASSHYEVLDRQVDADTTRVLFTPHTGRTHQLR 169


>gi|317011193|gb|ADU84940.1| hypothetical protein HPSA_04800 [Helicobacter pylori SouthAfrica7]
          Length = 242

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 35/235 (14%), Positives = 73/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V + G  L  A   +       V     P    E   +
Sbjct: 6   KLLSIQENISHKKAKALIDLGLVSIGGKKLMVARKELPQNTRFNVQKIEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F     + RLD  T G++LL  +        
Sbjct: 66  LALLKPPFIES-----------YDLV-SFFKGWTLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G V+++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIVEEE--QEINAPILTIKTTKAFSKISKKGQEAITIIAPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  + V ++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKVEIKTGRTHQIRVHLKHINHPI-------IGD-TLYNDEPGSAKRL 218


>gi|1491643|emb|CAA61435.1| ORFA [Chloroflexus aurantiacus J-10-fl]
          Length = 253

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 61/163 (37%), Gaps = 21/163 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLL 122
           E   + + +KP G+V   +    R T+ + L + +         R   V RLD +T GLL
Sbjct: 33  EDADIAVINKPAGMVVHPAPGHPRGTLVNALLARYPDLAIGGELRPGIVHRLDRDTSGLL 92

Query: 123 LLTNDGGLARVLELPST--QWLRVYRVRFHGQVDQ----------DKLNLLKKGIVIQGI 170
           ++       R L       +  ++Y+    G+  +          D  + L+  +V  G 
Sbjct: 93  VIARHDQAMRSLVDQQQARRMRKIYQALVIGRPPETGTIDAPIGRDPRDRLRMAVVPDGR 152

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   LDT  G  + + V L  G+  +I+       + + 
Sbjct: 153 PARTHYRLLDT-FGDYSLLEVQLETGRTHQIRVHLRHLGYPIV 194


>gi|302550785|ref|ZP_07303127.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           viridochromogenes DSM 40736]
 gi|302468403|gb|EFL31496.1| ribosomal large subunit pseudouridine synthase [Streptomyces
           viridochromogenes DSM 40736]
          Length = 314

 Score = 56.7 bits (136), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 83/249 (33%), Gaps = 44/249 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM---- 55
           V +    +RV   I+R    SR +   + A  +V V+G ++ +       A + V     
Sbjct: 12  VPDGLEGERVDAAISRMFGFSRTKAAELAAGGKVTVDGSVVGKSERVHGGAWLEVEMPQA 71

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
                 +   V+G+ +   +   + +  KP+G+    S      TV   L +   R+   
Sbjct: 72  PAPVQVVAEPVEGMEIVHDDDDVVVIA-KPVGVAAHPSPGWTGPTVIGGLAAAGYRISTS 130

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKL 158
                   V RLD+ T GL+++         L+    +    + Y     G  D     +
Sbjct: 131 GAAERQGIVHRLDVGTSGLMVVAKSEYAYTSLKRQFKERTVDKRYHTLVQGHPDPTSGTI 190

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSN-----------AWVTVGLREGKNREIK-KVFE 206
           +            +    VT D +               + + V L  G+  +I+  +  
Sbjct: 191 DAPIGRHPQHDYKWA---VTADGKPSVTHYDLIEAFRAASLLDVKLETGRTHQIRVHMAA 247

Query: 207 FFNWKVNRL 215
             +  V  L
Sbjct: 248 HRHPCVGDL 256


>gi|309799108|ref|ZP_07693361.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus infantis SK1302]
 gi|308117343|gb|EFO54766.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus infantis SK1302]
          Length = 291

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP  + T  + P+  + +      +      V RLD  T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEDMKTHGNQPEEITLLNHVSAYVGQTCYVVHRLDKETSGLILFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G+V   +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVEGKVGSKELIFRDKIGRDRHDRRKRVVDFKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             VT   Q +   + V   L+ G+  +I+
Sbjct: 203 THVTRLKQFQNKTSLVRCRLKTGRTHQIR 231


>gi|238060235|ref|ZP_04604944.1| 50S ribosomal pseudouridine synthase D [Micromonospora sp. ATCC
           39149]
 gi|237882046|gb|EEP70874.1| 50S ribosomal pseudouridine synthase D [Micromonospora sp. ATCC
           39149]
          Length = 311

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 59/176 (33%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +     R+ + ++R    SR     ++      V+G +    +  V +   ++V    
Sbjct: 13  VPDGLDGMRLDQAVSRLFGLSRTAAANLVDAGDALVDG-VARPNSHKVKTGSWLDVTLPT 71

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI- 109
                        G+ +  A+   + +  KP+G+    S      TV   L  I  R+  
Sbjct: 72  PAAPPTMVPQAVPGLTVVYADDDIVVV-DKPVGVAAHPSPGWTGPTVIGGLAGIGHRIST 130

Query: 110 --------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
                    V RLD+ T G++++         L+      +  + Y     G  D 
Sbjct: 131 SGAAERQGVVHRLDVGTTGIMVVAKSEQAYTALKRAFKYREVEKRYHAVVQGHPDP 186


>gi|255505900|ref|ZP_05348786.3| pseudouridine synthase, RluA family [Bryantella formatexigens DSM
           14469]
 gi|255265256|gb|EET58461.1| pseudouridine synthase, RluA family [Bryantella formatexigens DSM
           14469]
          Length = 342

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 87/261 (33%), Gaps = 67/261 (25%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGI-------LLE 48
           MK+  IV+EN   QR+ K++AR  +    +       +M+ ++ + +NG          +
Sbjct: 1   MKE-IIVRENEAGQRLDKLLARY-LC---QAPKSFLYKMLRKKNITLNGKKASGNEITAK 55

Query: 49  RAAVNVMSTDH-------------IEVDG---VPLRKAERTRLWLYHKPIGLVTTHSDPD 92
              + +  +D              I   G         E   + + +KP G+++  S P+
Sbjct: 56  EDCIRIFLSDETYEKFSAGEEAPPIRHTGALTKEQIIYEDGDILVLNKPAGMLSQKSRPE 115

Query: 93  GRSTVFDNLPSIFS------------RVISVGRLDINTEGLLLL--TNDGGLARVLELPS 138
             S     L  +                    RLD NT GLLL   +  G  A    L  
Sbjct: 116 DVSANEYFLSYLLETGQISAQELRTFHPSICNRLDRNTSGLLLAGKSLAGLQAMAEALKD 175

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL------DTQKGSN------ 186
               + Y     G + +       +G +++      +++        + +  S       
Sbjct: 176 RSLHKYYLCLVSGSLTKGAR---LEGFLVKDEAANKVKICATDMGDKEAKPISTQYVPLW 232

Query: 187 -----AWVTVGLREGKNREIK 202
                  + + L  G+  +I+
Sbjct: 233 TDGKVTLLKIWLITGRAHQIR 253


>gi|332753507|gb|EGJ83887.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           4343-70]
 gi|333000233|gb|EGK19816.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-218]
          Length = 260

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRYLAHLRHPII 176


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

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/260 (15%), Positives = 89/260 (34%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV  +    R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDASEAGMRLDRWFKIHYPGL---GFG---HLQKLLRAGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHG-----------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
             + Y     G                   D DK+ + + G       +      +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMRVCQHGEP--DSNHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>gi|78044542|ref|YP_359965.1| ribosomal large subunit pseudouridine synthase A [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996657|gb|ABB15556.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Carboxydothermus hydrogenoformans Z-2901]
          Length = 301

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 83/243 (34%), Gaps = 35/243 (14%)

Query: 44  GILLERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTT----HSDPDGRSTVF 98
           G ++ +    +     ++    P++   E   L +  KP G++      H  P  +    
Sbjct: 56  GEVVIKLPHTLPPA--VQSQNAPVKVLYEDDYLIVIDKPAGVLAHPVKNHFAPSMQELTL 113

Query: 99  DNLPS---IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                   IF     + RLD NT G +L+     +A +L   L   Q  ++Y     G +
Sbjct: 114 SYYRDKGRIFEGFYPIYRLDRNTSGPMLIAKFSLIAEMLNNSLRKRQINKIYLALIEGPL 173

Query: 154 DQD--KLNL---LKKGIVIQ-----GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK 203
                 +NL   L +G +I+     G      +        ++  + V L  G+  +I+ 
Sbjct: 174 ADKSGIINLPLGLLEGSIIKRAVVPGGQPACTKYQTVKAFPTHTLLKVELLTGRTHQIRA 233

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL--GPHLLEEAQVNLDAPI 261
            F                P     L  G    + ++ L       PH + +  ++L AP+
Sbjct: 234 HFAAIGH-----------PLAGDDLYGGKMDLIERQALHLYYISFPHPITKKTISLYAPL 282

Query: 262 YSS 264
              
Sbjct: 283 PRD 285


>gi|259503014|ref|ZP_05745916.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
 gi|259169025|gb|EEW53520.1| ribosomal large subunit pseudouridine synthase [Lactobacillus antri
           DSM 16041]
          Length = 297

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 80/234 (34%), Gaps = 45/234 (19%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMI-AQQRVKVNGILLERAAVNVMSTDHI------ 60
            ++ TP+++   +  +G+ S   ++  I    ++ +NG     AA  V   D        
Sbjct: 7   YDHATPRKLRAALKMSGVTS-SLMKAAIYHGGQLLINGEP-RWAADQVQPGDEYSIVLPP 64

Query: 61  -----EVDG--VPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
                +VD    P+  A   R   + +KP G+ T    P     V D+L +   R     
Sbjct: 65  EQANDQVDESAAPIEIAYEDRDFLVLNKPAGVATV---PAHNVPVADSLVNRVKRYYREQ 121

Query: 109 -------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQW---LRVYRVRFHGQVDQDKL 158
                      RLD +T GL++       A  +     +     + Y    +G++    +
Sbjct: 122 GYENRVTHVATRLDKDTSGLVVFPKH-RFAHAVLDRQLKHHAVKKNYYALVNGRLGSQHV 180

Query: 159 ----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     +   K +V         +  L+      + V + L  G+  +I+
Sbjct: 181 YIDAPIRRDPDSFVKRVVAPDGKPSVTEYWLERSCTEWSLVRIRLHTGRTHQIR 234


>gi|309812701|ref|ZP_07706445.1| pseudouridine synthase, RluA family [Dermacoccus sp. Ellin185]
 gi|308433396|gb|EFP57284.1| pseudouridine synthase, RluA family [Dermacoccus sp. Ellin185]
          Length = 309

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 77/246 (31%), Gaps = 61/246 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
            V E    +RV   IAR    SR     + A+  V V+G  + + +  V +   +EV   
Sbjct: 8   FVPEGLEGERVDAAIARLLGFSRTRAAELAAEGAVSVDGKRVAK-SERVSAGAWLEVAMP 66

Query: 63  ----------DGVPLRK----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                        P+       + T + +  KP G+    S       V   L +   R+
Sbjct: 67  ERTGPREATPRVEPVPGMNIVHDDTEIVVVDKPAGVAAHPSVGWDGPDVVGGLAAAGYRI 126

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
            + G         RLD+ T GL+++        +L+         + Y     G  D   
Sbjct: 127 STSGAPERQGIVQRLDVGTSGLMVVAKSERAYTLLKQAFRDRTVDKTYHALVQGLPDP-- 184

Query: 158 LNLLKKGIVIQGICYGD---------MQVTLDTQKG------------SNAWVTVGLREG 196
                    I+G                  +D+ +             S + + + L  G
Sbjct: 185 ---------IEGTIDAPIGRHPNHDYKFAVMDSGRASVTHYELLEAFRSASLLEIHLETG 235

Query: 197 KNREIK 202
           +  +I+
Sbjct: 236 RTHQIR 241


>gi|242373163|ref|ZP_04818737.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
 gi|242349114|gb|EES40715.1| pseudouridylate synthase [Staphylococcus epidermidis M23864:W1]
          Length = 284

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 63/188 (33%), Gaps = 30/188 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLL 124
           E   L + +KP       S      ++ + +          S    V RLD NT G+++ 
Sbjct: 80  EDDFLVIVNKPQYQNCAPSREHPHESLVEQVLAYLINKGEKSNPHIVTRLDRNTMGIVVF 139

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGD 174
              G +         ++ + Y    +G           + +D  +++ + I   G     
Sbjct: 140 AKYGHVHH--LFSKVKFEKEYVCLAYGRTKSKGVIEAPIARDNKSIITRKISKDGKYAKT 197

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
              TL  QK + +   V L  G+  +I+  F+     +               L  G  R
Sbjct: 198 SYYTL-VQKDNASLCKVKLHTGRTHQIRVHFQHIEHPIVG-----------DDLYGGHHR 245

Query: 235 EVSKKILR 242
           ++  + L+
Sbjct: 246 QIKGQSLQ 253


>gi|37681108|ref|NP_935717.1| pseudouridylate synthase [Vibrio vulnificus YJ016]
 gi|37199858|dbj|BAC95688.1| pseudouridylate synthase [Vibrio vulnificus YJ016]
          Length = 250

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 30/175 (17%), Positives = 59/175 (33%), Gaps = 45/175 (25%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++     P+   +++  L   +  +  V RLD++T GL++   +  
Sbjct: 19  EDDHILAVNKPSGLLSVPGRLPEHHDSMWSRLQEQYPEIQVVHRLDMSTSGLMVFAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV 177
                       L        ++Y  R  G V+ D       G++    I       MQ 
Sbjct: 79  AEAALKKQFQYRLTH------KIYYARVWGHVETD------SGMIDLPLICDWPNRPMQK 126

Query: 178 TL-DTQKGSNAWVTVGLRE-----------------GKNREIK-KVFEFFNWKVN 213
              +  K S     V  RE                 G++ +++  + +     + 
Sbjct: 127 VCHEHGKPSQTEFQVAKREVHANGAQTTIMRLLPVTGRSHQLRVHM-QALGHPIV 180


>gi|330448797|ref|ZP_08312444.1| 23S rRNA and tRNA pseudouridine synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
 gi|328492988|dbj|GAA06941.1| 23S rRNA and tRNA pseudouridine synthase [Photobacterium leiognathi
           subsp. mandapamensis svers.1.1.]
          Length = 232

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 59/154 (38%), Gaps = 16/154 (10%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +   +KP G+++     P+   ++F  + +       V RLD+ T GL++L  +    R 
Sbjct: 23  IIAVNKPSGILSNPGRAPEHHDSIFARVLAEHPESQIVHRLDMGTSGLIVLALNKNSERH 82

Query: 134 LELP--STQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
           L+      +  +VY  R  G + QD     L L+       ++ +             + 
Sbjct: 83  LKAQFRERETQKVYYARVWGHIAQDTGTVDLPLICDWPNRPRQKVCFDNGKPSVTHYEVV 142

Query: 181 TQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
           ++      V +    G++ +++  + +     + 
Sbjct: 143 SRDEKTTLVRLLPVTGRSHQLRVHM-QALGHPIL 175


>gi|320457791|dbj|BAJ68412.1| conserved hypothetical protein [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 317

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 36/225 (16%), Positives = 72/225 (32%), Gaps = 35/225 (15%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRKAERT 73
           A+    SR +   ++   + +V G  + R++  + + + +E D         P+      
Sbjct: 18  AKMLGISRSKAADLVDSGQARVLGREVARSST-LQAGETVEFDLAEEQAGPEPIATDMAV 76

Query: 74  RL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTE 119
                   +  KP+G+    S      TV  +L      + S G         RLD+ T 
Sbjct: 77  VYEDDDVIVVDKPVGVAAHASVGWTGPTVLGSLRDRGVHIASYGAAGREGIVSRLDVGTS 136

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIV 166
           GL+L+         +       +  + Y     G            + + K++  +  + 
Sbjct: 137 GLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATIEAPIGRAKVSDFRFCVT 196

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G         L+        V+V L  G+  +I+  F      
Sbjct: 197 PAGKPAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHP 241


>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 = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 78/241 (32%), Gaps = 42/241 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVM-STDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     ++   D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  -----EVD--------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                EVD        G+ +   +   L +  KP G+V   +      T+ + +   F  
Sbjct: 57  DLILPEVDSDIAPEKMGLDIYYEDEDVLIV-DKPAGVVVHPTKRYQSGTLANGVAWYFKD 115

Query: 108 ------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
                 +  V RLD  T GL++      +   L        ++Y     G+++ +    L
Sbjct: 116 KGIKALIRPVNRLDKGTSGLVVFAKRPFMQYYL-QIVKPMSKLYFAVVEGKMEGEGRIDL 174

Query: 162 ------KKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                 + GI     +          +       + + V +  G+  +I+         +
Sbjct: 175 PISRKPQSGIERMVSEEGDRAITNYKVVKSSERFSLLKVKIETGRTHQIRVHLSHIGHPI 234

Query: 213 N 213
            
Sbjct: 235 V 235


>gi|329770323|ref|ZP_08261706.1| hypothetical protein HMPREF0433_01470 [Gemella sanguinis M325]
 gi|328836681|gb|EGF86337.1| hypothetical protein HMPREF0433_01470 [Gemella sanguinis M325]
          Length = 254

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 16/149 (10%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN 126
           ++ E   L +  KP G+ T  +D      T+ + L S +  +  + RLDI+T GL++ + 
Sbjct: 50  KEYEDPYLLIVSKPFGIKTHPNDISIEDDTLVNYLISDYQYLEPIHRLDIDTCGLVIFSK 109

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYG 173
              +   L   L + +  R Y       +    +             +   +  +G    
Sbjct: 110 TPLIKSKLDQMLKNREIKRYYTALTKNNIKPKTIKTNIGRDIREKNKMA--VTNKGKQAT 167

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              ++ +    +   VT+ L  G+  +I+
Sbjct: 168 TNILSCEKIDQNKFVVTISLETGRTHQIR 196


>gi|159029331|emb|CAO90197.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 302

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 26/215 (12%), Positives = 64/215 (29%), Gaps = 43/215 (20%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           + + ++++ A                + VNG         +     +     P  +    
Sbjct: 36  EWLDRILSAA----------------ILVNGRPAY-PDTVLEIGQQLTYQRPPWTEPDVP 78

Query: 71  -------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGL 121
                  E T + +  KP GL           T+   +   ++ V    + RL   T G+
Sbjct: 79  LFFEVLYEDTEVLVVAKPSGLPVLAGGGFLEHTLIHLVHQHYADVTPYPIHRLGRGTSGI 138

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRF-HGQVDQDK-----LNLLKKGIV------I 167
           +L+         L       +  ++YR     G +  +      +  +   I+      +
Sbjct: 139 VLMAKSKPARSKLSQQMREGKITKIYRALVGQGDIPDNFTINQAIGKIAHPILGYVYGAL 198

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   +  +  +   +  + V +  G+  +I+
Sbjct: 199 TDGLSARSEGRVLKKHLDSTLLEVEIFTGRPHQIR 233


>gi|88597629|ref|ZP_01100862.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
 gi|88189933|gb|EAQ93909.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 84-25]
          Length = 281

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 75/201 (37%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+T +      L+        
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILITKNKKAQIDLKSLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      +    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALAHGKIEENFIVD--KAINLTKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>gi|323704717|ref|ZP_08116295.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323536179|gb|EGB25952.1| pseudouridine synthase, RluA family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 286

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 29/212 (13%), Positives = 72/212 (33%), Gaps = 35/212 (16%)

Query: 34  MIAQ----QRVKVNGILLERAAVNVMSTDHIEV--DGVPLRK----------AERTRLWL 77
           +I +     ++ VNG +       V   D +E+  D                 E   + +
Sbjct: 27  LIRKYKNRGKMLVNGEI-SIVNRIVFEGDTVELLLDDENTSVSPEKMDLHICYEDEDILV 85

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLA 131
            +K  G+V   +      T+ + +   + +      +  V RLD +T GL++   +  + 
Sbjct: 86  VNKDAGIVVHPTAGHPDGTLVNGVAWYYEKNNIKAPIRPVNRLDRDTSGLIIFAKNPFMQ 145

Query: 132 RVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
             L++      ++Y     G           + +   + +++ +  +G         L  
Sbjct: 146 NYLQIVCP-MKKLYIAIVEGDMDGRGTIDLPIKRKPGSTIERMVDDEGDTAVTDFYVLKR 204

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +   + V + L+ G+  +I+         + 
Sbjct: 205 SE-KLSLVKLELKTGRTHQIRVHLSHIGHPII 235


>gi|168242726|ref|ZP_02667658.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|194451570|ref|YP_002046934.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194409874|gb|ACF70093.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|205338110|gb|EDZ24874.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
          Length = 260

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 THYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|161615893|ref|YP_001589858.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|168261891|ref|ZP_02683864.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|197262707|ref|ZP_03162781.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198243086|ref|YP_002216938.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|204928136|ref|ZP_03219336.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205353907|ref|YP_002227708.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858230|ref|YP_002244881.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|161365257|gb|ABX69025.1| hypothetical protein SPAB_03686 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|197240962|gb|EDY23582.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197937602|gb|ACH74935.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|204322458|gb|EDZ07655.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205273688|emb|CAR38681.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205349202|gb|EDZ35833.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710033|emb|CAR34388.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|322614227|gb|EFY11159.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322620959|gb|EFY17817.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322624022|gb|EFY20856.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322628239|gb|EFY25028.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322633358|gb|EFY30100.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636065|gb|EFY32773.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322639401|gb|EFY36089.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322643737|gb|EFY40288.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322648849|gb|EFY45296.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322655158|gb|EFY51468.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322658011|gb|EFY54279.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322664112|gb|EFY60311.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322667081|gb|EFY63253.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322673129|gb|EFY69236.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322677880|gb|EFY73943.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322681054|gb|EFY77087.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322685651|gb|EFY81645.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|323194790|gb|EFZ79977.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196541|gb|EFZ81689.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323205046|gb|EFZ90029.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323207753|gb|EFZ92699.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212695|gb|EFZ97512.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323214822|gb|EFZ99570.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222551|gb|EGA06916.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323226431|gb|EGA10639.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323230690|gb|EGA14808.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323234959|gb|EGA19045.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323238998|gb|EGA23048.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323244644|gb|EGA28650.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323247260|gb|EGA31226.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323251792|gb|EGA35657.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323257479|gb|EGA41169.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323263264|gb|EGA46801.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267516|gb|EGA51000.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323272705|gb|EGA56111.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326624702|gb|EGE31047.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629020|gb|EGE35363.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
          Length = 260

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 TQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|169775969|ref|XP_001822451.1| DRAP deaminase (Rib2) [Aspergillus oryzae RIB40]
 gi|238502633|ref|XP_002382550.1| DRAP deaminase (Rib2), putative [Aspergillus flavus NRRL3357]
 gi|83771186|dbj|BAE61318.1| unnamed protein product [Aspergillus oryzae]
 gi|220691360|gb|EED47708.1| DRAP deaminase (Rib2), putative [Aspergillus flavus NRRL3357]
          Length = 522

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 47/148 (31%), Gaps = 25/148 (16%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------L 75
           RE    +   RV VNG         V + D I      L + E                L
Sbjct: 82  REA---LEAGRVCVNGKPA-GPDTKVKNGDVIS---HTLHRHEPPVTSQEIGIIHEDDGL 134

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLAR 132
            +  KP G+    +     ++V + L S            RLD  T G++ +  +   A 
Sbjct: 135 IVIDKPAGVPVHSAGRYHYNSVIEILRSERGGGWVPRPCNRLDRLTSGVMFIAKEPKAAE 194

Query: 133 VLELPSTQ--WLRVYRVRFHGQVDQDKL 158
           ++     +    + Y  R  G+     +
Sbjct: 195 MVARRLKERTVHKEYVTRVKGKFPDGVV 222


>gi|16766270|ref|NP_461885.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|167550169|ref|ZP_02343926.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167993457|ref|ZP_02574551.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|34582459|sp|Q8ZMD5|TRUC_SALTY RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|16421515|gb|AAL21844.1| putative synthase [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|205324883|gb|EDZ12722.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205328453|gb|EDZ15217.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|261248101|emb|CBG25936.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. D23580]
 gi|267995101|gb|ACY89986.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301159525|emb|CBW19044.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. SL1344]
 gi|312913986|dbj|BAJ37960.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|321225646|gb|EFX50700.1| tRNA pseudouridine synthase C ; tRNA Psi65 [Salmonella enterica
           subsp. enterica serovar Typhimurium str. TN061786]
 gi|323131322|gb|ADX18752.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|332989835|gb|AEF08818.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 260

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 TQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|238795691|ref|ZP_04639205.1| Pseudouridine synthase [Yersinia mollaretii ATCC 43969]
 gi|238720417|gb|EEQ12219.1| Pseudouridine synthase [Yersinia mollaretii ATCC 43969]
          Length = 232

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 42/220 (19%), Positives = 73/220 (33%), Gaps = 52/220 (23%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIE------TLYQDDHLVLINKPAGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG---LRE------------------GKNREIKKVF 205
                     +     K + +   V      E                  G+  +++   
Sbjct: 120 KDPALFPLMSICAIHGKPARSGYRVVERFYHELEDGTLLPLTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
           +     +       YG    G LL G     +++ LR  L
Sbjct: 180 QQLGHPILGCD--LYG----GRLLPG-----TERTLRLML 208


>gi|270719457|ref|ZP_06223312.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae HK1212]
 gi|270315435|gb|EFA27693.1| ribosomal large subunit pseudouridine synthase D [Haemophilus
           influenzae HK1212]
          Length = 162

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 31/138 (22%), Positives = 55/138 (39%), Gaps = 20/138 (14%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           VQ     QR+ + +A      SR  ++  I    VK+N  +       V+  + IE+   
Sbjct: 6   VQPEQMGQRLDQTLAELFPEYSRSRLKTWIEADLVKLNDRITNIPREKVLGGERIEIIVE 65

Query: 63  ---------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                    + +PL    E   + + +KP  LV      +   TV + L   +  ++   
Sbjct: 66  VEDETRFEAENIPLNIVYEDDDIIVINKPKDLVVHPGAGNPNGTVLNALLYHYPPIVEVP 125

Query: 110 ---SVGRLDINTEGLLLL 124
               V RLD +T GL+++
Sbjct: 126 RAGIVHRLDKDTTGLMVV 143


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

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 43/262 (16%), Positives = 78/262 (29%), Gaps = 63/262 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E+    R+ +         RR         ++++    +V+V+G   E  +  ++  
Sbjct: 7   TVSEDEADIRLDRWF-------RRHYPHLTQGALQKLCRTGQVRVDGKRAET-STRLLPG 58

Query: 58  DHIEV-----------------DGVPLRKAERTRLW------LYHKPIGLVTTHSDP--D 92
             + V                 D   +R+     ++      + +KP GL          
Sbjct: 59  QAVRVPPIPGASRPAPPPRPVLDERLVREIRGMVIYSDDQVIVLNKPAGLPVQGGPGIIH 118

Query: 93  GRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
               + D L       R   V R+D +T GLLLL    G+A  L          + Y   
Sbjct: 119 HVDAMLDGLKDQDDDPRPRLVHRIDRDTSGLLLLARTPGVAAKLAASFRGRDVRKTYWAI 178

Query: 149 FHGQVDQDK------LNLLKKG-----IVIQGICYGDMQV-----TLDTQKGSNAWVTVG 192
             G+           L  L  G     +V                 LD      +W+ + 
Sbjct: 179 VVGRPSPASGVIDQPLARLGAGPGALTVVASRKDADAAHALSEYEVLDAAGRKLSWLALS 238

Query: 193 -LREGKNREIKKVFEFFNWKVN 213
            L  G+  +++   E     + 
Sbjct: 239 PLT-GRTHQLRVHCEALGTPIL 259


>gi|170720703|ref|YP_001748391.1| RluA family pseudouridine synthase [Pseudomonas putida W619]
 gi|169758706|gb|ACA72022.1| pseudouridine synthase, RluA family [Pseudomonas putida W619]
          Length = 333

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 77/239 (32%), Gaps = 49/239 (20%)

Query: 7   VQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
           V      QR+   +  A  G+  R  V R++ +  V+VN G +  +    + + D + V 
Sbjct: 31  VAPELAGQRIDNFLITALKGV-PRTLVYRILRKGEVRVNKGRV--KPEYKIQAGDIVRVP 87

Query: 64  GVPLRKA--------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--L 101
            V L +                     E   L + +KP G+            +     L
Sbjct: 88  PVRLPERDEPAPVAQGLLQRLEAAIVYEDKALIVMNKPAGIAVHGGSGLSFGVIEALRQL 147

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG--QVDQDK 157
                 +  V RLD +T GLL++     + R L   L      + Y     G     + +
Sbjct: 148 RPDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMALVRGHWPTSKKQ 207

Query: 158 LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           +N       L+ G     +  +G     +   L         V    +    G+  +I+
Sbjct: 208 VNAPLLKSNLRSGERMVEVNDEGKEALTLFRVLRRFGEFATIVEARPIT---GRTHQIR 263


>gi|32266140|ref|NP_860172.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
 gi|32262190|gb|AAP77238.1| ribosomal pseudouridine synthase [Helicobacter hepaticus ATCC
           51449]
          Length = 245

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 37/215 (17%), Positives = 74/215 (34%), Gaps = 27/215 (12%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRL 75
           KV+AR    S  + + +I +  V   G  +   R  + + +   I     P        +
Sbjct: 8   KVLARTHNISHNQAKSLIDKGLVFAAGKKVNIARLEIPIHTAFEILKPKKPKVLFTDEHI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D L ++F     + RLD  T G++LL  +G       
Sbjct: 68  LALEKPPFIES-----------YD-LSNMFEGWHLLHRLDRETSGVILLIKEGSAFHIKA 115

Query: 133 VLELPSTQWLRVYRVRFHGQVDQ-----DKLNLLKKGI---VIQGICYGDMQ-VTLDTQK 183
                + +  + Y    HG +         ++  K+G     I       +  +T  +  
Sbjct: 116 KEAFKNQEVYKEYVCLVHGILADSIEINKAISTTKRGFAKSRIDKKGLNALTLLTPLSIM 175

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
           G    +   ++ G+  +I+   +  N  +    RI
Sbjct: 176 GKKTLLKALIKTGRTHQIRVHCQSINHPILG-DRI 209


>gi|254476979|ref|ZP_05090365.1| pseudouridine synthase, RluD [Ruegeria sp. R11]
 gi|214031222|gb|EEB72057.1| pseudouridine synthase, RluD [Ruegeria sp. R11]
          Length = 348

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 68/200 (34%), Gaps = 50/200 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E+   QR+ + +       RR         +E+M  +  ++++G  ++ A+  V + 
Sbjct: 8   TVTEDDAGQRIDRWL-------RRLFPHVSQGRIEKMCRKGELRLDGGRVK-ASSRVEAG 59

Query: 58  DHIEV------DGVPLRKAERTR------------------LWLYHKPIGLVT-----TH 88
             + V      D  P     R                    + + +KP GL       T 
Sbjct: 60  QTVRVPPLPASDLKPAEAPSRRISDADAKMIRGCVIYKDDAVIVLNKPAGLAVQGGSGTT 119

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYR 146
              DG S           R+  V RLD +T G+L+L      A+ L          ++Y 
Sbjct: 120 KHVDGLSEALKFDAEEKPRL--VHRLDKDTSGVLVLARTRQAAQALTAAFRHHATRKIYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIV 166
               G      L  +K G+V
Sbjct: 178 ALVAGVPTP-YLGEIKCGLV 196


>gi|62181474|ref|YP_217891.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|168231056|ref|ZP_02656114.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168463884|ref|ZP_02697801.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|194443144|ref|YP_002042215.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194468534|ref|ZP_03074518.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|200386574|ref|ZP_03213186.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|224584754|ref|YP_002638552.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238909744|ref|ZP_04653581.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|62129107|gb|AAX66810.1| putative synthase [Salmonella enterica subsp. enterica serovar
           Choleraesuis str. SC-B67]
 gi|194401807|gb|ACF62029.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194454898|gb|EDX43737.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195633159|gb|EDX51573.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|199603672|gb|EDZ02217.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|205334611|gb|EDZ21375.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|224469281|gb|ACN47111.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|322715958|gb|EFZ07529.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
          Length = 260

 Score = 56.3 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 TQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|119775123|ref|YP_927863.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119767623|gb|ABM00194.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           amazonensis SB2B]
          Length = 330

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 88/249 (35%), Gaps = 48/249 (19%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + E+   QR+   + A+     +  + R++ +  V+VN   ++     + + D + V  V
Sbjct: 25  IDEDGAGQRIDNFLLAKLKGVPKSMIYRIVRKGEVRVNKKRIK-PEYKLAAGDEVRVPPV 83

Query: 66  PLRKA----------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--L 101
            + +                       E  ++ + +KP G+            +     L
Sbjct: 84  RVAEKDYRTAPSANLNRVAQLEDRILFEDKQIIVLNKPAGIAVHGGSGVDYGVIESLRSL 143

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL- 158
                 +  V RLD +T G+LL+       R L     + Q  +VY+    GQ  +    
Sbjct: 144 RPTCKFLELVHRLDRDTSGVLLIAKKRMALRHLHDQLRNKQMQKVYQALVRGQWQEHDRV 203

Query: 159 --NLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV-------GLRE-----GKNREIKK 203
               L K I ++    G+  V ++++ K S     V        L E     G+  +I+ 
Sbjct: 204 VKAPLLK-ITLK---SGERIVRVNSEGKPSETRFRVLRRFDEASLVEASPVTGRTHQIRV 259

Query: 204 VFEFFNWKV 212
             ++    +
Sbjct: 260 HCQYQGHPI 268


>gi|197248998|ref|YP_002147874.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197212701|gb|ACH50098.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
          Length = 260

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 THYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|146296964|ref|YP_001180735.1| RluA family pseudouridine synthase [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410540|gb|ABP67544.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 292

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/185 (11%), Positives = 62/185 (33%), Gaps = 17/185 (9%)

Query: 45  ILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
             +    +  + ++ + + G      E       +KP G+ +  S      T+ +N+   
Sbjct: 56  ESIIELELKDVYSNIVPIKGSIDILFEDQFFLFVNKPSGIPSHPSKGHYFDTLANNVEWY 115

Query: 105 FSRV----ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD---- 154
            +        + RLD +T G+++   +     ++     +    + Y     G +     
Sbjct: 116 LNSQGVTSHIINRLDKDTSGIVVFAKNSYFHSIVSSEFEKRTIEKTYIAVVDGILTKKSG 175

Query: 155 --QDKLNLLKKGI--VI-QGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFF 208
             +  ++    GI   I +   Y      +   K + + + +  +  G+  +++      
Sbjct: 176 FIEKPISRSNDGIKREINEDGDYAITYYEVVDYKNNYSILKLKPIT-GRTHQLRVHLASI 234

Query: 209 NWKVN 213
            + + 
Sbjct: 235 GYPIV 239


>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 = 56.3 bits (135), Expect = 7e-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|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 = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 35/240 (14%), Positives = 76/240 (31%), Gaps = 40/240 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVM-STDHI 60
           IV EN     +   +   G       +R+I     Q  + VNG  ++     ++   D I
Sbjct: 4   IVGENEKGVILENFLRNKGF-----SKRLIRIYKWQGEILVNG--VKENVQRILQPGDVI 56

Query: 61  EV----DGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
           ++    +   +           E   + + +KP  +V   +      T+ + +   F   
Sbjct: 57  DLILPENDSNIAPEKMGLDIYYEDEEILIVNKPANMVVHPTKRYQSGTLANGVAWYFKDK 116

Query: 108 -----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL- 161
                +  V RLD  T GL++      +   L        ++Y     G+++ +    L 
Sbjct: 117 GIKALIRPVNRLDKGTSGLVVFAKRPFMQYYL-QILKPMSKLYFAVVEGKMEGEGRIDLP 175

Query: 162 -----KKGIV---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                + GI     +          +       + + V +  G+  +I+         + 
Sbjct: 176 ISRKPQSGIERMVSEEGDRAITNYKVVKSSKRFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|56419366|ref|YP_146684.1| hypothetical protein GK0831 [Geobacillus kaustophilus HTA426]
 gi|56379208|dbj|BAD75116.1| hypothetical conserved protein [Geobacillus kaustophilus HTA426]
          Length = 303

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 59/160 (36%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP GL T  S      T+ + L   + +      V  V RLD +T GL+L+
Sbjct: 87  EDDYVLVVNKPAGLATIPSRHHPGGTLANGLLHHYRKQQLDSTVHIVTRLDRDTSGLVLV 146

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNL---------LKKGIVIQGIC 171
                +  +L         +R Y    HG +  D+  ++          + + +   G  
Sbjct: 147 AKHRHVHHLLSALQQKGHVVRTYEAICHGVIVEDEGTIDAPIGRQSDSIIAREVREDGKP 206

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  L+   G   +V++ L  G+  +I+    +    
Sbjct: 207 AVTHFRVLERLYGYT-YVSLRLETGRTHQIRVHLAYLGHP 245


>gi|255009494|ref|ZP_05281620.1| putative RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
          Length = 302

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 37/221 (16%), Positives = 75/221 (33%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP 66
            P  +   +A +   ASR +++ +++++ V V+ ++  +    +     + +    +   
Sbjct: 20  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNKKE 79

Query: 67  LRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
            R        E   + +  K  GL++  +D     T    L          +R+  V RL
Sbjct: 80  FRHPLLKIVYEDAYIIVVEKKEGLLSVGTDRQKERTAQHILSEYVGRSGRGNRIFVVHRL 139

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D    R L          R Y     G+           +    L + 
Sbjct: 140 DRDTSGLMMFAKDEKTQRTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTLYVS 199

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 200 SSSYDDGGSKSITHYRTIKRANGY-SLVELRLETGRKNQIR 239


>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 = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+  SR   +RMI    V V+G  +++A   V     I + G  +  
Sbjct: 1  MAKERLDILLVERGLAGSRERAKRMIMAGEVLVDGQKIDKAGTTVKPEAEIRLLGHDIPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|261419065|ref|YP_003252747.1| pseudouridine synthase [Geobacillus sp. Y412MC61]
 gi|319765882|ref|YP_004131383.1| pseudouridine synthase [Geobacillus sp. Y412MC52]
 gi|261375522|gb|ACX78265.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC61]
 gi|317110748|gb|ADU93240.1| pseudouridine synthase, RluA family [Geobacillus sp. Y412MC52]
          Length = 304

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 59/160 (36%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP GL T  S      T+ + L   + +      V  V RLD +T GL+L+
Sbjct: 87  EDDYVLVVNKPAGLATIPSRHHPGGTLANGLLHHYRKQQLDSTVHIVTRLDRDTSGLVLV 146

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNL---------LKKGIVIQGIC 171
                +  +L         +R Y    HG +  D+  ++          + + +   G  
Sbjct: 147 AKHRHVHHLLSALQQKGHVVRTYEAICHGVIVEDEGTIDAPIGRQSDSIIAREVREDGKP 206

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  L+   G   +V++ L  G+  +I+    +    
Sbjct: 207 AVTHFRVLERLYGYT-YVSLRLETGRTHQIRVHLAYLGHP 245


>gi|158320206|ref|YP_001512713.1| RluA family pseudouridine synthase [Alkaliphilus oremlandii OhILAs]
 gi|158140405|gb|ABW18717.1| pseudouridine synthase, RluA family [Alkaliphilus oremlandii
           OhILAs]
          Length = 305

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 74/209 (35%), Gaps = 34/209 (16%)

Query: 35  IAQQR-VKVNGILLERAAVNVMSTDHIEV-----------DGVPLRKA-ERTRLWLYHKP 81
           + + + + VNG  L+     + + D I++             VP     E   L L +K 
Sbjct: 43  VKRGKTIFVNGEYLKYHET-INAGDEIKIVMEDEPNHFTLQDVPFEAVYEDVDLILVNKE 101

Query: 82  IGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+VT  +      T+      +     I  +V  V RLD++T GLL++  +   A  + 
Sbjct: 102 PGIVTHPTKSHPDWTIANGAALYLKSKGIDCKVRFVNRLDMDTSGLLIIAKN-AYAHHVL 160

Query: 136 LPSTQ---WLRVYRVRFHGQVDQDKLNLLK----------KGIVIQGICYGDMQVTLDTQ 182
               Q     + Y     G + +D+  +            K +V +       +  +  +
Sbjct: 161 SEQMQEDRIEKKYIAFVWGVIKEDEGRIEAPIYRTTMDSIKRVVDERGQESITEFKVLER 220

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +   V V L  G+  +I+   E     
Sbjct: 221 YKNATMVEVKLLTGRTHQIRVHMEHLGHP 249


>gi|253682033|ref|ZP_04862830.1| pseudouridine synthase, RluA family [Clostridium botulinum D str.
           1873]
 gi|253561745|gb|EES91197.1| pseudouridine synthase, RluA family [Clostridium botulinum D str.
           1873]
          Length = 323

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 88/262 (33%), Gaps = 63/262 (24%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           +  N + QR+ K         R+ +E        + + +  ++VNG   ++    +   D
Sbjct: 5   IGPNESGQRLDKF------C-RKWLEDVPLGAIFKALRKGDIRVNGKKAKQ-NYFLQEED 56

Query: 59  HIE--------------------VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            IE                    VD   ++   E   + +  K  G++      +G  T+
Sbjct: 57  IIETKYIETYKQNKKDIPKKFQEVDFSSIKISYEDENILIIEKWPGVLVHSDKKNGEPTL 116

Query: 98  FDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S   +                  RLD NT G+++   +    ++L   +   +  
Sbjct: 117 TDYVLSYLFQKGDYDPQKEVTFTPAPCNRLDRNTSGMVIFGKNFKTLKILNAMIRERKIK 176

Query: 143 RVYRVRFHGQVDQDKLNL--LKKGI----VIQGICYG-----DMQVTLDTQKGSNAWVTV 191
           + Y     G++ +       LK  +     I            M+V +    G+ +++ +
Sbjct: 177 KYYNALVKGKIKEGYYEAYILKDQVNNISEIHKEEKQNSKRIAMEVKVIDTVGTFSFLEL 236

Query: 192 GLREGKNREIKKVFEFFNWKVN 213
            L  G++ +++    +    + 
Sbjct: 237 DLLTGRSHQLRAHLAYLGNPII 258


>gi|146328747|ref|YP_001209889.1| ribosomal large subunit pseudouridine synthase, RluC [Dichelobacter
           nodosus VCS1703A]
 gi|146232217|gb|ABQ13195.1| ribosomal large subunit pseudouridine synthase, RluC [Dichelobacter
           nodosus VCS1703A]
          Length = 313

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 69/212 (32%), Gaps = 50/212 (23%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV---------D-------GVPLRKA---ERT 73
           +M+ +  V+ N   ++     + + D I +         D          +  A   E  
Sbjct: 41  QMLRKGEVRRNKKRVK-PTDKICAGDVIRLPPIINAQRADVAIPIYWQKRIEAAVLYEDD 99

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLA 131
              + +KP G+V  H        V D + SI+    +    RLD +T G+L+L       
Sbjct: 100 HFLILNKPAGIVV-HGGSGHEFGVIDVVRSIWGENYAELAHRLDGDTSGVLVLGKHRQAL 158

Query: 132 RVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-------LDTQ 182
              +    +    + Y     G   +++  ++        +    + V        L+  
Sbjct: 159 NAFQTAMNEGTVEKRYWALVDGVWTREEAEVVVH------LTKAPLNVREKMQVSELENA 212

Query: 183 KGSNAWVTV-------GLRE-----GKNREIK 202
           + +  W  V        L E     G+  +I+
Sbjct: 213 QFARTWFYVLQRWQDATLMEAVLDTGRTHQIR 244


>gi|145300070|ref|YP_001142911.1| tRNA pseudouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142852842|gb|ABO91163.1| tRNA pseudouridine synthase C [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 246

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 34/170 (20%), Positives = 61/170 (35%), Gaps = 33/170 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L   +KP GL+   S  D   T F      D +      V  V RLD  T G+LL   D 
Sbjct: 12  LVAVNKPSGLLVHRSWLDKAETRFAMQMTRDLIGG--RHVYPVHRLDRPTSGVLLFALDP 69

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM-- 175
            +AR+L     + Q  + Y     G   +         ++L+ +   +        +   
Sbjct: 70  AVARILTEAFAARQVHKEYLALVRGWAPEQGVIDYPLKEQLDKIADAMSNPDRPAQEAVT 129

Query: 176 ------QVTLD---TQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVN 213
                 QV L    ++K   +  ++  L  + G+  ++++  E     + 
Sbjct: 130 AFRCLHQVELPHAVSKKHPTSRYSLVKLFPKTGRKHQLRRHMEHLFHPIV 179


>gi|330831288|ref|YP_004394240.1| ribosomal large subunit pseudouridine synthase A [Aeromonas veronii
           B565]
 gi|328806424|gb|AEB51623.1| Ribosomal large subunit pseudouridine synthase A [Aeromonas veronii
           B565]
          Length = 218

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 22/161 (13%), Positives = 59/161 (36%), Gaps = 30/161 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++     P+   +V   +     +  +  RLD++T G++++  +    R 
Sbjct: 21  IMVVNKPTGLLSVPGRGPENEDSVLHRVKQQHPKAAAAHRLDMSTTGVIVIPLNPNSHRE 80

Query: 134 LELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----------------QGICYGD 174
           L       +  + Y     G+ + D        + +                 +G     
Sbjct: 81  LSRQFRERETEKHYLAWVWGEPELDAGE-----VDLPLCVDWPNRPKQKVDHEEGRHALT 135

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
           +   L  + G N+ + +  +  G++ +++  + E     + 
Sbjct: 136 LWQKLKVENG-NSLIKLTPIT-GRSHQLRVHMLE-LGHPIL 173


>gi|289422957|ref|ZP_06424779.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
 gi|289156637|gb|EFD05280.1| ribosomal large subunit pseudouridine synthase D
           [Peptostreptococcus anaerobius 653-L]
          Length = 307

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/234 (16%), Positives = 78/234 (33%), Gaps = 51/234 (21%)

Query: 22  RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------EVDGVPLRKA-- 70
             G  S R + R+  ++ + VNG    +  ++V   D I         + +G  L     
Sbjct: 29  ELGF-SARSISRLKREKNIYVNGK-YTKPTLHVDKGDIIEIPIIEEGSDFEGQDLNVRVL 86

Query: 71  -ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLL 123
            E   L +  KP  +V   +    ++T+ ++L           RV  V RLD+NT GL++
Sbjct: 87  YEDFDLVVVDKPPFMVVHPTKSHYQNTLANHLSYHLDQEGQDVRVRFVNRLDMNTSGLVI 146

Query: 124 LTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
           +  +      L    +     + Y    +G  D  +         I    Y + + ++  
Sbjct: 147 VAKNAYAHHKLSSDMSDKLVEKEYYAIVNGVPDHKEA-------TIDQPIYRETEDSIKR 199

Query: 182 QKGSN----------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                                      + + + L  G+  +I+   ++    + 
Sbjct: 200 IVDPRGQRSITHYSLIGSYKDCEGHLISLLRISLETGRTHQIRVHMDYIGHPIV 253


>gi|168820315|ref|ZP_02832315.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205342862|gb|EDZ29626.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|320087390|emb|CBY97155.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
          Length = 260

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 TQYRGLATVEMAVPTGRYPTTRYGLVELEPRTGRKHQLRRHLAHLRHPII 176


>gi|322391241|ref|ZP_08064713.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
 gi|321145994|gb|EFX41383.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           peroris ATCC 700780]
          Length = 291

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 29/146 (19%), Positives = 58/146 (39%), Gaps = 14/146 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L + +KP G+ T  + PD  + +      +      + RLD  T GL+L   +  +
Sbjct: 86  QDQHLIVVNKPEGMKTHGNQPDEIALLNHVSAYVGQTCYVIHRLDKETSGLVLFAKNPFI 145

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
             +L   L   +  R Y     G+++  +L           +  K+ +  +     + QV
Sbjct: 146 LPILNRLLEKKEISREYWALVDGKIEAKELIFRDKLGRNRHDRRKRIVDPKNGQCAETQV 205

Query: 178 TLDTQ-KGSNAWVTVGLREGKNREIK 202
           T   Q +   + V   L+ G+  +I+
Sbjct: 206 TRLKQFQNKTSLVRCKLKTGRTHQIR 231


>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 = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   I   G   SR   ++ I    VKVNG ++ +A+ +V + D IEV
Sbjct: 1  MRLDAYIVDMGHFKSRGRAKKAILAGNVKVNGAVITKASRDVSTDDIIEV 50


>gi|46201801|ref|ZP_00054336.2| COG0564: Pseudouridylate synthases, 23S RNA-specific
           [Magnetospirillum magnetotacticum MS-1]
          Length = 324

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 42/212 (19%), Positives = 66/212 (31%), Gaps = 41/212 (19%)

Query: 32  ERMIAQQRVKVNGILLER-------AAVNVM--STDH--------IEVDGVPLRKAERTR 74
           E+ +    V+V+G   +         A+ V     D         + VD    R      
Sbjct: 29  EKWLRAGNVRVDGKRAKSNQRLEAGQAIRVPPLPADEAPVREAKPVVVDEKIARMLRDAV 88

Query: 75  LWL------YHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL- 124
           L++       +KP GL     T           D L     R   V RLD +T G+LLL 
Sbjct: 89  LYMDDDVIALNKPPGLAVQGGTGMADKHLDAWLDALCFGAGRPKLVHRLDKDTSGVLLLG 148

Query: 125 -TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLL--KKGIVI-----QGI 170
            T +          S    + Y     G            L  L  K G  +     +G 
Sbjct: 149 RTANAASKLAAAFKSRSARKCYWALVAGVPRYPQGRIDAPLAKLPGKAGEKMAVDKEEGK 208

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   +D+     AW+ +  R G+  +++
Sbjct: 209 HAVTYYRVVDSTLKRAAWLEMEPRTGRTHQLR 240


>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 = 56.3 bits (135), Expect = 7e-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 = 56.3 bits (135), Expect = 7e-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|71908482|ref|YP_286069.1| tRNA pseudouridine synthase C [Dechloromonas aromatica RCB]
 gi|71848103|gb|AAZ47599.1| tRNA pseudouridine synthase C [Dechloromonas aromatica RCB]
          Length = 242

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 42/226 (18%), Positives = 72/226 (31%), Gaps = 46/226 (20%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLL 122
           P+   +   + +  KP GL+   S+ D   T F        I  RV    RLD  T G+L
Sbjct: 6   PILYRDEHVVVI-DKPSGLLVHRSEIDRHETRFAIQILRDQIGQRVWPAHRLDRGTSGVL 64

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD-----QDKLNLLKKGIVIQGICYGD- 174
           L   +  +A  L  +       + Y     G           L   +     +G      
Sbjct: 65  LFGLNPAMASQLGKQFEQGTVEKAYWAVVRGYPPASGSIDHPLTRQRDPYEFKGEQCSTE 124

Query: 175 ---------------MQVTLDTQKGSN-AWVTVG-LREGKNREIKKVFEFFNWKVNRLIR 217
                          + V +D    S  A + +  +  G+  +I++  +     +     
Sbjct: 125 AQPALTHFRKLAEIELPVEVDRYPSSRYALLELEPIT-GRRHQIRRHLKHLAHPII---- 179

Query: 218 ISYGPFQLGTLLAGSTREVSKKILREQLGPH--LLEEAQVNLDAPI 261
                   G    G  R    +   EQLG H  LL   +++ + P+
Sbjct: 180 --------GDATYGKGRH--NRYFAEQLGCHRLLLACIRLSFNHPV 215


>gi|297530964|ref|YP_003672239.1| pseudouridine synthase [Geobacillus sp. C56-T3]
 gi|297254216|gb|ADI27662.1| pseudouridine synthase, RluA family [Geobacillus sp. C56-T3]
          Length = 304

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 31/160 (19%), Positives = 59/160 (36%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP GL T  S      T+ + L   + +      V  V RLD +T GL+L+
Sbjct: 87  EDDYVLVVNKPAGLATIPSRHHPGGTLANGLLHHYRKQQLDSTVHIVTRLDRDTSGLVLV 146

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNL---------LKKGIVIQGIC 171
                +  +L         +R Y    HG +  D+  ++          + + +   G  
Sbjct: 147 AKHRHVHHLLSALQQKGHVVRTYEAICHGVIVEDEGTIDAPIGRQSDSIIAREVREDGKP 206

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  L+   G   +V++ L  G+  +I+    +    
Sbjct: 207 AVTHFRVLERLYGYT-YVSLRLETGRTHQIRVHLAYLGHP 245


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

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/223 (17%), Positives = 76/223 (34%), Gaps = 58/223 (26%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRK-------- 69
           ++++   +V+V+G  ++     V     + V               G  L+         
Sbjct: 35  QKLLRSGQVRVDGGRVKS-DARVQPGQTVRVPPMDVDAKLKSGPIAGKDLKHSTDFELLS 93

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDIN 117
                E  ++ + +KP GL        G S V  ++  +     S        V RLD +
Sbjct: 94  RMVLHEDEKVIVLNKPPGLAV-----QGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRD 148

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKLNLL----------KK 163
           T G+L++    G A+ L          + Y     G     +DK++            + 
Sbjct: 149 TSGVLVIARTRGAAQKLTAAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEPTADGDRM 208

Query: 164 GIVIQGICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIK 202
            I   G    D  ++    L+T   + AW+ +    G+  +++
Sbjct: 209 RIAKHGEDGADHAISFYRVLETAAQNLAWLEMEPYTGRTHQLR 251


>gi|332298019|ref|YP_004439941.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
 gi|332181122|gb|AEE16810.1| pseudouridine synthase [Treponema brennaborense DSM 12168]
          Length = 336

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 77/253 (30%), Gaps = 74/253 (29%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           R+ K+I       R+         +   I +  V+VNG     AA  V   D I++    
Sbjct: 16  RLDKII-------RKFLPNAPLSAIYSYIRKSLVRVNGKK-TDAAARVNEGDLIDIADFL 67

Query: 67  LRK--------AERTR-----------------LWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           L+          E  R                 L + +KP  +         R ++ D +
Sbjct: 68  LQPQPAELPSEPEPARSRPAAFPALDDVFCNDFLRVINKPYDIPVQG-CRGARVSIADIV 126

Query: 102 PSIFS----------RVISVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVYRVRF 149
            + ++          +   + RLD  T GLL+ + +  G       +      + Y    
Sbjct: 127 QAEYAETARASSLSFKPGPLHRLDRKTTGLLVCSRNLEGARWFSAAVRDHLLQKRYAAIV 186

Query: 150 HGQVDQD-----KLNLLKKGIV------------IQGICYGDMQVTLDT---QKGSNAWV 189
            G ++ +     K+    +G+              +G       V L     +      V
Sbjct: 187 QGCLETERIWTDKIERETEGLHRFRRSLACRSGGSEGKTADTRAVPLAHGSYEGEPVTLV 246

Query: 190 TVGLREGKNREIK 202
              +  G+  +I+
Sbjct: 247 LFSIGSGRTHQIR 259


>gi|285018394|ref|YP_003376105.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylate
           synthase) protein [Xanthomonas albilineans GPE PC73]
 gi|283473612|emb|CBA16115.1| probable pseudouridine synthase (rna-uridine isomerase) (rna
           pseudouridylate synthase) protein [Xanthomonas
           albilineans]
          Length = 330

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 89/250 (35%), Gaps = 47/250 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E+   QRV   +  +   A R  + +++   +V+VNG    +A   +   D + +  V
Sbjct: 23  VPEDRAGQRVDNFLLGQLKGAPRSLIYKLMRSGQVRVNGGR-TKAERKLEVGDEVRIPPV 81

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNLP 102
            L++                     E  RL   +KP G+ +            T+    P
Sbjct: 82  RLQEEGEKTAPPAAFMERLEAAIVYEDARLLALNKPSGVASHGGSGISFGAIETLRALRP 141

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGG---LARVLELPSTQWL-----RVYRVRFHGQVD 154
           +    +  V RLD +T GLL++          + L     Q       + Y     G++ 
Sbjct: 142 N--QTLELVHRLDRDTSGLLIVAKKRSALTELQALMREDDQVQGRGIGKRYLTLLVGRLP 199

Query: 155 QDKLNL-------LKKGIVIQGICYGDMQVTL-----DTQKGSNAWVTVGLREGKNREIK 202
              + +       L++G       +   + +L       ++G +++  V +  G+  +I+
Sbjct: 200 DGTMTVEVPLHIGLRQGGERHVQVHAAGKPSLSHFRMLERRGGHSYCEVRIETGRTHQIR 259

Query: 203 KVFEFFNWKV 212
              +   + V
Sbjct: 260 VHAQHLGYPV 269


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

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 38/223 (17%), Positives = 76/223 (34%), Gaps = 58/223 (26%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRK-------- 69
           ++++   +V+V+G  ++     V     + V               G  L+         
Sbjct: 35  QKLLRSGQVRVDGGRVKS-DARVQPGQTVRVPPMDVDAKLKSGPIAGKDLKHSSDFQLLS 93

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDIN 117
                E  ++ + +KP GL        G S V  ++  +     S        V RLD +
Sbjct: 94  RMVLHEDDKVIVLNKPPGLAV-----QGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRD 148

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKLNLL----------KK 163
           T G+L++    G A+ L          + Y     G     +DK++            + 
Sbjct: 149 TSGVLVIARTRGAAQKLTAAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEPTADGDRM 208

Query: 164 GIVIQGICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIK 202
            I   G    D  ++    L+T   + AW+ +    G+  +++
Sbjct: 209 RIAKHGEDGADHAISFYRVLETAAQNLAWLEMEPYTGRTHQLR 251


>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 = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 52/285 (18%), Positives = 84/285 (29%), Gaps = 81/285 (28%)

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  VPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------ 106
               +A            E   + +  KP G+VT  S    R T+ + +           
Sbjct: 123 ERRSEAIPEPSIELDIVYEDESVLVVCKPAGMVTHPSAGHARGTLVNAVLGHCDLPELVV 182

Query: 107 -------------------------------------------RVISVGRLDINTEGLLL 123
                                                      R   V RLD  T G+++
Sbjct: 183 PTGRVSNRMNEDGDFDDDDGPSTSESDSDAESASDSDDDAGSIRPGIVHRLDRGTSGVMV 242

Query: 124 LTNDGGLARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGI 170
           +  D      L     S    R Y     G            V +D  + L+  +     
Sbjct: 243 VAKDASAHNSLCNQFASRTVRRRYVAILSGVPKTSKGRIEAPVGRDPKDRLRMAVTPGSG 302

Query: 171 CYGDM--QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            Y     +V      G+ + V   L  G+  +I+   +     + 
Sbjct: 303 RYAASNYEVIATLASGNASLVEWRLETGRTHQIRVHAKHIGHPIL 347


>gi|229078576|ref|ZP_04211134.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
 gi|228704720|gb|EEL57148.1| Pseudouridine synthase [Bacillus cereus Rock4-2]
          Length = 307

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLVVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +               ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGKIDAAIGRDRHHATRRRISSKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
             +VT+ L  G+  +I+
Sbjct: 225 TTFVTLQLETGRTHQIR 241


>gi|168236011|ref|ZP_02661069.1| tRNA pseudouridine synthase C (tRNA-uridine isomerase C)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|194734776|ref|YP_002115916.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194710278|gb|ACF89499.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197290820|gb|EDY30174.1| tRNA pseudouridine synthase C (tRNA-uridine isomerase C)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
          Length = 260

 Score = 56.3 bits (135), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 48/166 (28%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM----- 175
           R L          + Y     G +  D +         + +      +            
Sbjct: 71  RRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAVTQYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|294792069|ref|ZP_06757217.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
 gi|294457299|gb|EFG25661.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           6_1_27]
          Length = 321

 Score = 56.3 bits (135), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 21/143 (14%), Positives = 46/143 (32%), Gaps = 19/143 (13%)

Query: 28  RREVERMIAQQRVKVNGILLE---------RAAVNVMSTDHIEVDGVPLRK-AERTRLWL 77
           RR   R+ +   + +NG                + +       +  + L    E   + +
Sbjct: 34  RR---RLRSDGIITINGKPATWNTLIHGGDHLIMKLTPEQEFSLSPMELDIIYEDEYILV 90

Query: 78  YHKPIGLV----TTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA 131
            +K  G++    +T  D    + V               V RLD +T G++++     + 
Sbjct: 91  INKAAGILMHPTSTVRDHTLANGVLHYYQETNQHYDFHPVHRLDKDTSGIVIIAKTSVVQ 150

Query: 132 RVLELPSTQWLRVYRVRFHGQVD 154
              +   T + + Y     G + 
Sbjct: 151 HAFDKKHTYFYKSYDAIVEGHLP 173


>gi|260599139|ref|YP_003211710.1| tRNA pseudouridine synthase C [Cronobacter turicensis z3032]
 gi|260218316|emb|CBA33307.1| tRNA pseudouridine synthase C [Cronobacter turicensis z3032]
          Length = 262

 Score = 56.3 bits (135), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 29/167 (17%), Positives = 50/167 (29%), Gaps = 29/167 (17%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 12  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDMQVTLD 180
           R+L       Q  + Y     G +           ++L+ +      Q        VT  
Sbjct: 72  RLLAQQFEQHQIQKRYHAIVRGWLTDSAVLDYPLVEELDKIADKFSRQDKEPQPA-VTHY 130

Query: 181 TQKGSNAW---------VTVGLRE-----GKNREIKKVFEFFNWKVN 213
               +            V   L E     G+  ++++        + 
Sbjct: 131 RGLATTTQPVAVGRYESVRYSLVEMLPQTGRKHQLRRHMAHLRHPII 177


>gi|291557471|emb|CBL34588.1| hemolysin TlyA family protein [Eubacterium siraeum V10Sc8a]
          Length = 241

 Score = 56.3 bits (135), Expect = 8e-06,   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|209549478|ref|YP_002281395.1| pseudouridine synthase [Rhizobium leguminosarum bv. trifolii
           WSM2304]
 gi|209535234|gb|ACI55169.1| pseudouridine synthase, RluA family [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 329

 Score = 56.3 bits (135), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/222 (16%), Positives = 76/222 (34%), Gaps = 57/222 (25%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRK--------- 69
           ++++   +V+V+G  ++     V     + V              G  L+          
Sbjct: 35  QKLLRSGQVRVDGGRVKS-DARVQPGQTVRVPPLDVDAKKSGPIAGKDLKHSSDFELLSR 93

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINT 118
               E  ++ + +KP G+        G S V  ++  +     S        V RLD +T
Sbjct: 94  MVLHEDDKVIVLNKPPGIAV-----QGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRDT 148

Query: 119 EGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKLNLL----------KKG 164
            G+L++    G A+ L          + Y     G     +DK++            +  
Sbjct: 149 SGVLVIARTRGAAQKLTAAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEPTADGDRMR 208

Query: 165 IVIQGICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIK 202
           I   G    D  ++    ++T   + AW+ +    G+  +++
Sbjct: 209 IAKHGEDGADHAISFYRVIETAAQNLAWLEMEPYTGRTHQLR 250


>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 = 56.3 bits (135), Expect = 8e-06,   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|302380202|ref|ZP_07268674.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311985|gb|EFK93994.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 273

 Score = 56.3 bits (135), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 86/239 (35%), Gaps = 43/239 (17%)

Query: 4   KNIVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           K I        R+ + +     +     S       I +  + +NG   +R +  +   D
Sbjct: 2   KQISFNVDKKIRLDEFLKKNHISHNLFIS-------IYKDDIFINGKHAKRNS-KLEKGD 53

Query: 59  HIEVDGVPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNL-- 101
            + ++   LR  E                  +++ +KP   +T + D +     F +   
Sbjct: 54  IVTIN---LRDEENKYEPINMDIEVLYEDDDIFVLNKP-DKLTMNKDGEKSLANFVSYLF 109

Query: 102 --PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
              +I  +V  + RLD +T G++++  +       +  S +  + Y     G     K+ 
Sbjct: 110 KQRNIKQKVRFINRLDQDTSGVVMVAKNKIAQAYYQKNSFK--KKYLAIVKGNPKDQKIE 167

Query: 160 LL--KKGIVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           L   + GI  +    G   VT+       G  + V++ L  G+  +I+   E+ N  + 
Sbjct: 168 LNLKRDGIKTEIDENGKKSVTILENLKNYGDYSLVSLELLTGRTHQIRVSMEYINCPIV 226


>gi|239636478|ref|ZP_04677480.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus warneri
           L37603]
 gi|239597833|gb|EEQ80328.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus warneri
           L37603]
          Length = 284

 Score = 56.3 bits (135), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 26/157 (16%), Positives = 55/157 (35%), Gaps = 19/157 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLPSIFSRVISVGRLDINTEGLLLL 124
           E   + +  KP       S      ++ +            +    V RLD NT G++L 
Sbjct: 80  EDDYIIIVSKPNRQNCAPSCEHPHESLVEQVLGYLLHKGEHTNPHIVTRLDRNTTGIVLF 139

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGD 174
              G +        T+  +VY    HG           + +++ +++++ +  +   Y  
Sbjct: 140 AKYGYIHH--LFSKTKMDKVYTCLAHGITEPSGVIEAPIARNEASIIERQVS-ENGKYAK 196

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  QK + +   V L  G+  +I+  F++    
Sbjct: 197 TLYRTIKQKENVSCCEVQLCTGRTHQIRVHFQYIGHP 233


>gi|221065999|ref|ZP_03542104.1| pseudouridine synthase [Comamonas testosteroni KF-1]
 gi|220711022|gb|EED66390.1| pseudouridine synthase [Comamonas testosteroni KF-1]
          Length = 250

 Score = 56.3 bits (135), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 26/172 (15%), Positives = 51/172 (29%), Gaps = 37/172 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   +  D   T F        +   V  V RLD  T G+LL+  +
Sbjct: 15  QDEHLVAVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGRHVWPVHRLDKGTCGVLLMALN 74

Query: 128 GGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
              A+ L          + YR    G + +         + +      D        + +
Sbjct: 75  KEAAQALAARFAAHETRKEYRALVRGWLPEV--------VEVDHPLKPDDAPEDAPVQEA 126

Query: 186 NAWV-------------------TVGLRE-----GKNREIKKVFEFFNWKVN 213
           +  +                    + L E     G+  +I++  +     + 
Sbjct: 127 HTRLRCLARLSWPESWDGRHPETRISLVEALPTTGRRHQIRRHLKHVAHPII 178


>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 = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 47/133 (35%), Gaps = 15/133 (11%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + +   G+  SR   +R+I + +VKV+G  + + +  V     + ++G  + +   
Sbjct: 1   MRLDEYLVSEGLVPSRSRAKRLIEKGQVKVDGKAVLKPSQKVEYGRKVAIEGEDMPEG-- 58

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                Y K  G+            V D   S    ++    +     G+         +R
Sbjct: 59  -----YFKLKGIQEASGILRPGDVVLDIGSSAGGFLMFASGIASRVVGI-------EFSR 106

Query: 133 VLELPSTQWLRVY 145
               P +   + Y
Sbjct: 107 EFLEPLSNVEKEY 119


>gi|213691700|ref|YP_002322286.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           infantis ATCC 15697]
 gi|213523161|gb|ACJ51908.1| pseudouridine synthase, RluA family [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 320

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/225 (16%), Positives = 72/225 (32%), Gaps = 35/225 (15%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRKAERT 73
           A+    SR +   ++   + +V G  + R++  + + + +E D         P+      
Sbjct: 21  AKMLGISRSKAADLVDSGQARVLGREVARSST-LQAGETVEFDLAEEQAGPEPIATDMAV 79

Query: 74  RL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTE 119
                   +  KP+G+    S      TV  +L      + S G         RLD+ T 
Sbjct: 80  VYEDDDVIVVDKPVGVAAHASVGWTGPTVLGSLRDRGVHIASYGAAGREGIVSRLDVGTS 139

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIV 166
           GL+L+         +       +  + Y     G            + + K++  +  + 
Sbjct: 140 GLMLVCKSDLAYTEMRRQFAEHEVKKTYHALVQGGLKENKATIEAPIGRAKVSDFRFCVT 199

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G         L+        V+V L  G+  +I+  F      
Sbjct: 200 PAGKPAVTHWDVLERFGHEATLVSVNLETGRTHQIRVHFSSIGHP 244


>gi|149196356|ref|ZP_01873411.1| ribosomal large subunit pseudouridine synthase C [Lentisphaera
           araneosa HTCC2155]
 gi|149140617|gb|EDM29015.1| ribosomal large subunit pseudouridine synthase C [Lentisphaera
           araneosa HTCC2155]
          Length = 328

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/216 (16%), Positives = 73/216 (33%), Gaps = 31/216 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LW 76
           SR + +  +     ++NG  +E     + + D I +D   + + +  R          + 
Sbjct: 44  SREDWQEALLDGSSQINGKQVEDYNAILKAGDVISLDVTKIPEPDIDRDFKVVYEDDDIL 103

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL-- 134
           +  K   L    +    ++T++  L   F  V  + RLD  T GL+L+      A VL  
Sbjct: 104 MVEKTGDLPVHPAGSFFKNTLWYMLVKQFGNVHIMNRLDRETSGLVLIARHHKAASVLGK 163

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLL-------------------KKGIVIQGICYGDM 175
           +    Q  + Y V   G V  D+ + L                    +     G      
Sbjct: 164 QFERRQVGKEYDVLVEGLVSWDQYDALGYMGPAVSSKIRKKFSFTEAEDWQDYGKHSART 223

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           + ++  +    + +   L  G+  +I+       + 
Sbjct: 224 EFSVLRRSHELSHLHCRLHTGRTHQIRATLLSLGFP 259


>gi|194467694|ref|ZP_03073681.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
 gi|194454730|gb|EDX43627.1| pseudouridine synthase, RluA family [Lactobacillus reuteri 100-23]
          Length = 301

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/182 (16%), Positives = 57/182 (31%), Gaps = 29/182 (15%)

Query: 55  MSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
            + D+++V   P+    E     + +KP G+ T    P     V D+L +          
Sbjct: 66  TANDNVDVSEAPIDIIYEDQDFLIMNKPAGVATV---PAHNVPVADSLVNRVKGYYKRQD 122

Query: 109 ------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVD----- 154
                     RLD +T GL++       A  +     +     + Y     G+V      
Sbjct: 123 YENQVTHVATRLDRDTSGLVVFPKH-RFAHAVLDEQLKKHLVKKNYLALIKGKVPVEHGY 181

Query: 155 -----QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                Q   N   K +V +       +          + + + L  G+  +I+  F    
Sbjct: 182 IDAPIQRDPNSFVKRMVGKEGKASVTEYWCQECNVQASLIKIRLHTGRTHQIRVHFASLG 241

Query: 210 WK 211
           + 
Sbjct: 242 FP 243


>gi|317496022|ref|ZP_07954384.1| RluA family pseudouridine synthase [Gemella moribillum M424]
 gi|316913926|gb|EFV35410.1| RluA family pseudouridine synthase [Gemella moribillum M424]
          Length = 294

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/269 (15%), Positives = 87/269 (32%), Gaps = 52/269 (19%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRKAERTRLWLYHKPI 82
              +KVN    E     + + D + +              +G      E     + +KP 
Sbjct: 38  DGSIKVNDK-EENVRYILKNGDKVTITLPSEKFSEHVRFIEGNLDIIYEDEYFLVVNKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLEL 136
            L +  S  +G +++ + + + F           V RLD NT GL+L+            
Sbjct: 97  NLPSIPSRNEGDASLLEIVNTYFHDNNYVTIPHIVTRLDKNTTGLVLI-----AKHRHIH 151

Query: 137 P---STQWLRVYRVRFHGQVDQDKLNL--------LKKGIVIQGICYGDMQVTLDT--QK 183
                T   + Y     G+V    +          +    V +   Y   Q+ L    +K
Sbjct: 152 ALFGKTDINKFYLALTKGKVADQVIEANIKREADSIITRCVAEDGDYAKTQIWLVKYYEK 211

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL-- 241
              + V + L  G+  +I+         +               L  G+   ++++ L  
Sbjct: 212 NDVSLVKLKLFTGRTHQIRVHMSHLGHPLLG-----------DELYGGNKDLIARQALHC 260

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRD 270
                 H + + +++L+AP+      + D
Sbjct: 261 HNLQFKHPITQKELSLEAPLAGDIKNITD 289


>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 = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 85/255 (33%), Gaps = 64/255 (25%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+++G   + A   + 
Sbjct: 5   EQKIVDTGEAGMRLDRWFKVHYPGL---GFG---HLQKLLRSGQVRIDGSRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQTVRIPPLGVDEKAVGPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGS 117

Query: 91  PDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY 145
              R               +   V R+D +T G+L++    G A+ L          + Y
Sbjct: 118 GVSRHVDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTTAFRERDTKKTY 177

Query: 146 RVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQKGSN-A 187
                G     +DK+            + ++  +   G    D  V    +  + G+N  
Sbjct: 178 WALVKGVPRKREDKISTWLVREQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKAGNNLT 235

Query: 188 WVTVGLREGKNREIK 202
           W+ +    G+  +++
Sbjct: 236 WLEMEPYTGRTHQLR 250


>gi|27904809|ref|NP_777935.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
 gi|34395769|sp|Q89AH2|RLUC_BUCBP RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|27904207|gb|AAO27040.1| ribosomal large subunit pseudouridine synthase D [Buchnera
           aphidicola str. Bp (Baizongia pistaciae)]
          Length = 315

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 78/243 (32%), Gaps = 57/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAVNVMSTD 58
           + EN   QR+   +       R+  +R+        I   ++++N   + +    +   D
Sbjct: 13  ITENSEKQRIDNFL-------RKTFKRLPFNLICKIIRTGQIRINKKRINQ-NYKLKLGD 64

Query: 59  HIEVDGVPLRK---------------------AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            + +  + ++                       E     + +KP G+            +
Sbjct: 65  SVRIPPITIQSDSNKKIKLNTRLSIIFNNMILYEDNYFLILNKPSGMSVHSGSGINYGMI 124

Query: 98  FDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
            +   L      +  V RLD +T G+L++     + R L   L   +  + Y    HG  
Sbjct: 125 ENLRILRPYNRYLDLVHRLDRDTSGVLIIAKKRSILRNLHEQLREKKIKKKYVALVHGVW 184

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------------SNAWVTVG-LREGKNR 199
             D L  + K ++          V +D +                N  +++  +  G+  
Sbjct: 185 P-DILKSISKPLLKTSSRKNKNIVKIDPKGKESITHFNIKKKYTKNTLISITPIT-GRTH 242

Query: 200 EIK 202
           +I+
Sbjct: 243 QIR 245


>gi|330723209|gb|AEC45579.1| ribosomal large subunit pseudouridine synthase D [Mycoplasma
           hyorhinis MCLD]
          Length = 294

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 85/239 (35%), Gaps = 42/239 (17%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------ 62
           R+   + +    SR  V+ +IA  +V V+  ++ +    +     IEV            
Sbjct: 10  RLDIFLRKKLELSRVFVQEIIANNQVWVDNQIVNKKNFILKQGSQIEVHYQEKEQNIIAK 69

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---------SV 111
             D       E   + +  KP  +V   +  +  +T+ + L   F+++           V
Sbjct: 70  AQDIELKIVFEDENVIVVDKPTNMVVHPAPGNYENTLVNALVYKFAQLSNVNGSLRPGIV 129

Query: 112 GRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            RLD +T GL+L+  +  +   L   L   +  R Y     GQ+ +++++ +   I    
Sbjct: 130 HRLDKDTSGLMLVAKNDKMHNFLAQQLKERKIKRKYYAIIEGQL-ENQISHINLPIARDE 188

Query: 170 ICYGDMQVT----------------LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                M V+                   +K   ++V   L  G+  +I+    +    V
Sbjct: 189 KNRKKMSVSHFNSKEAITHVFVEKYFHYKKKVFSFVRCELETGRTHQIRVHLAYIKHPV 247


>gi|261342219|ref|ZP_05970077.1| tRNA pseudouridine synthase [Enterobacter cancerogenus ATCC 35316]
 gi|288315555|gb|EFC54493.1| tRNA pseudouridine synthase [Enterobacter cancerogenus ATCC 35316]
          Length = 261

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 52/168 (30%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 12  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + +         ++L+ +                   
Sbjct: 72  RLLSQQFEQHQMQKRYHAIVRGWLTESGTLDYPLVEELDKIADKFARDDKGPQPAVTDYR 131

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ + T K      ++   E     G+  ++++        + 
Sbjct: 132 AMATTEMPVATSKFPTTRYSLV--ELLPKTGRKHQLRRHLAHLRHPII 177


>gi|86158324|ref|YP_465109.1| ribosomal large subunit pseudouridine synthase D [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774835|gb|ABC81672.1| ribosomal large subunit pseudouridine synthase D [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 353

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 43/227 (18%), Positives = 78/227 (34%), Gaps = 40/227 (17%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+   + R A   SR  V+R++   RV+V+G   + A+  +   + I ++  P       
Sbjct: 36  RLDAALVRLAPELSRARVQRLVEAGRVQVDGRAAK-ASARLRGGEAIALEIPPPEPSGLV 94

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSRV 108
                     E   L +  K  G+V   +     STV + L                 R+
Sbjct: 95  AQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPHSTVVNALLHRLGLPAAAGPDGALPRL 154

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFH------GQVDQDKLNL 160
             V RLD +T G L++  T     A   +       +VY    H      G++D      
Sbjct: 155 GLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRSVEKVYLALCHGALAAAGRLDTPYGRH 214

Query: 161 LKKGIVIQGICYGDMQVTLDTQ-----KGSNAWVTVGLREGKNREIK 202
            +  +   G      +   + +       + +   V L  G+  +I+
Sbjct: 215 PRDRLRFTGRLASSRRAITEWRVREAFGPAASLAEVTLHTGRTHQIR 261


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

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 37/223 (16%), Positives = 76/223 (34%), Gaps = 58/223 (26%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRK-------- 69
           ++++   +V+V+G  ++     V     + V               G  L+         
Sbjct: 35  QKLLRSGQVRVDGGRVKS-DARVQPGQTVRVPPLDVDAKLKSGPIAGKDLKHSSDFELLS 93

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDIN 117
                E  ++ + +KP G+        G S V  ++  +     S        V RLD +
Sbjct: 94  RMVLHEDDKVIVLNKPPGIAV-----QGGSGVARHIDQMLEAWTSPKGEKPRLVHRLDRD 148

Query: 118 TEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKLNLL----------KK 163
           T G+L++    G A+ L          + Y     G     +DK++            + 
Sbjct: 149 TSGVLVIARTRGAAQKLTAAFRERDTKKTYWALVKGVPRKHEDKISTWLVKEATADGDRM 208

Query: 164 GIVIQGICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIK 202
            I   G    D  ++    L+T   + AW+ +    G+  +++
Sbjct: 209 RIAKHGEDGADHAISFYRVLETAAQNLAWIEMEPYTGRTHQLR 251


>gi|117618521|ref|YP_855405.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
 gi|117559928|gb|ABK36876.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 218

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 21/161 (13%), Positives = 58/161 (36%), Gaps = 30/161 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++     P+   +V   +     +  +  RLD++T G++++  +    R 
Sbjct: 21  IMVVNKPTGLLSVPGRGPENEDSVLHRVKQQHPKAAAAHRLDMSTTGVIVIPLNPNSHRE 80

Query: 134 LELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI-----------------QGICYGD 174
           L       +  + Y     G+ +          + +                 +G     
Sbjct: 81  LSRQFRERETEKHYLAWVWGEPEAASGQ-----VDLPLCVDWPNRPKQKVDHEEGRHALT 135

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
           +   L  + G N+ + +  +  G++ +++  + E     + 
Sbjct: 136 LWEKLKVENG-NSLIKLTPIT-GRSHQLRVHMLE-LGHPIL 173


>gi|262276531|ref|ZP_06054340.1| tRNA pseudouridine synthase C [Grimontia hollisae CIP 101886]
 gi|262220339|gb|EEY71655.1| tRNA pseudouridine synthase C [Grimontia hollisae CIP 101886]
          Length = 243

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 24/168 (14%), Positives = 50/168 (29%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D      V   L       V  + RLD  T G+LL      +A
Sbjct: 14  LVAVNKPSGMLVHRSWLDKGETRFVMQTLRDQIGQHVFPLHRLDRPTSGVLLFALSSEMA 73

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDK-LN-LLKKGIVIQGICYGDMQVTLDTQKGSN- 186
             +          + Y     G + ++  L+  LK+   +  +         + ++    
Sbjct: 74  AEMMPKFAGRDIHKTYHAVVRGWIQEEATLDYPLKE--ELDKVADKYATAEPEAKEAVTE 131

Query: 187 ---------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                                  V +    G+  ++++     +  + 
Sbjct: 132 YRPVAHAELPIPLGRYQSCRYTLVEMKPHTGRKHQLRRHMHHLSHPII 179


>gi|169826808|ref|YP_001696966.1| putative RNA pseudouridine synthase yjbO [Lysinibacillus sphaericus
           C3-41]
 gi|168991296|gb|ACA38836.1| Hypothetical RNA pseudouridine synthase yjbO [Lysinibacillus
           sphaericus C3-41]
          Length = 293

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 34/202 (16%), Positives = 69/202 (34%), Gaps = 39/202 (19%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRKAERTRLWLYHKPIG 83
             + VNG +       +   D +EV               G      E   + + +KP  
Sbjct: 31  GLLTVNG-IERNVRYALQVDDCVEVTFPPEEKSEGLTSEHGDLAIVYEDDTILVLNKPAN 89

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARV--LE 135
             T  S     +++ + +   F +         + RLD +T GLL +     +  +  L 
Sbjct: 90  QSTIPSREHPTNSIANLVCGYFEQQGLASTAHIITRLDRDTSGLLCIAKHAHIHHLTGLA 149

Query: 136 LPSTQWLRVYRVRFHGQVDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQ-- 182
             + +  R Y    HG V QD           + +++++ +  +   Y    VT+  +  
Sbjct: 150 QRNGEISRKYEAIVHGHVHQDSQSIVAPIGRKETSIIEREVR-EDGQYAHTDVTVIQRFY 208

Query: 183 --KGSNAWVTVGLREGKNREIK 202
                   + + L  G+  +I+
Sbjct: 209 LGAEPMTHIGLTLHTGRTHQIR 230


>gi|322388362|ref|ZP_08061965.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
 gi|321140675|gb|EFX36177.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           infantis ATCC 700779]
          Length = 291

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + PD  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPDEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G++    L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGRLGAKDLIYRDKIGRNRHDRRKRIVDQKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             VT   Q +   + V   L+ G+  +I+
Sbjct: 203 THVTRLKQFQNKTSLVRCRLKTGRTHQIR 231


>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 = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 34/86 (39%), Gaps = 1/86 (1%)

Query: 7  VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
          ++  F  +R+  ++   G   SR + +R I    V V+    ++A   V +   IEV G 
Sbjct: 1  MKGKFMKKRIDVLLVEQGFFESREKAKRSIMAGLVFVDNQKCDKAGTEVKTDAKIEVKGN 60

Query: 66 PLRKAERTRLWLYHKPIGLVTTHSDP 91
          P+    R  L L         T  D 
Sbjct: 61 PIPYVSRGGLKLEKAMKNFDITLQDK 86


>gi|119944340|ref|YP_942020.1| pseudouridine synthase [Psychromonas ingrahamii 37]
 gi|119862944|gb|ABM02421.1| ribosomal large subunit pseudouridine synthase A [Psychromonas
           ingrahamii 37]
          Length = 222

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 27/137 (19%), Positives = 52/137 (37%), Gaps = 23/137 (16%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++        R ++   +  ++     V RLD+ T GLL+LT        
Sbjct: 23  IVVLNKPYGLLSVPGRAKKNRDSLALRILRVWPNASVVHRLDMATSGLLILTMRKSAQSH 82

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           +          + Y  R  G + +D       G++       D+ +  D +      V  
Sbjct: 83  IGRQFQQKIIDKTYYARVEGIIKED------NGVI-------DLPIRCDWENRPRQIVDF 129

Query: 192 GLREGKNRE-----IKK 203
              EGK+ +     +K+
Sbjct: 130 --AEGKSSQTEWSVVKR 144


>gi|298694246|gb|ADI97468.1| probable RNA pseudoridylate synthase [Staphylococcus aureus subsp.
           aureus ED133]
          Length = 284

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 61/195 (31%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP       S    
Sbjct: 43  VTVRKQLMPNDILEIHLPQEIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCIPSREHP 102

Query: 94  RSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +  +    + +  ++Y  
Sbjct: 103 HESLIEQVLYHCQVHGENINPHIVTRLDRNTTGIVIFAKYGHIHHLFSKGNLK--KIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHSSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|331696640|ref|YP_004332879.1| RluA family pseudouridine synthase [Pseudonocardia dioxanivorans
           CB1190]
 gi|326951329|gb|AEA25026.1| pseudouridine synthase, RluA family [Pseudonocardia dioxanivorans
           CB1190]
          Length = 312

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 49/301 (16%), Positives = 95/301 (31%), Gaps = 52/301 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV------------ 54
           V +     RV   ++R    SR  V  +  + RV V+G    ++                
Sbjct: 11  VPDGLDGMRVDAGLSRLLGLSRTVVATLAEEGRVAVDGRAAGKSDRLAAGGWLEIELPDP 70

Query: 55  -MSTDHIE-----VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------- 101
              +D I      V G+ +   +   + +  KP+G+    S      TV   L       
Sbjct: 71  ERESDGITGPVEVVAGLTILHEDDDIVVV-DKPVGVAAHPSPGWTGPTVVGGLAALGVRV 129

Query: 102 --PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG------ 151
                  R   V RLD  T G++++         L+    +    + Y     G      
Sbjct: 130 ATSGAAERQGIVHRLDAGTTGVMVVAKSESAYSELKRAFKERTVDKRYHAVVQGHPDPSR 189

Query: 152 -----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFE 206
                 +D+   +  +  +V  G        T++  + + + + + L  G+  +I+  F 
Sbjct: 190 GTIDAPIDRHPRHDWRFAVVEGGRPSVTHYDTIEAFRAA-SLLDIRLETGRTHQIRVHFS 248

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTR-EVSKKIL--REQLGPHLLEEAQVNLDAPIYS 263
                         G    G     + R  + ++ L  RE    H  +  +V   +P  +
Sbjct: 249 AMRHPCV-------GDLTYGADPTLAKRLHLDRQWLHARELGFAHPADGRRVEFTSPYPA 301

Query: 264 S 264
            
Sbjct: 302 D 302


>gi|329894956|ref|ZP_08270755.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC3088]
 gi|328922685|gb|EGG30020.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC3088]
          Length = 321

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 76/243 (31%), Gaps = 57/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA----SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           +  +   QR+   + R   A    SR  V + I    V+VN          ++  D I +
Sbjct: 18  IDADEAGQRLDNFLLRW-FAQVPKSR--VYKAIRGGEVRVNKGRANAM-YKLLEGDDIRI 73

Query: 63  ----------DGVPLRKA-----------ERTRLWLYHKPIGLVTTHSD--PDGRSTVFD 99
                     +G  + K            E     + +KP GL          G   V  
Sbjct: 74  PPLGERALQMEGALVAKHWLDSVERGVLYEDADFMIINKPSGLAVHGGSGLKYGLIEVLR 133

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK 157
            L     R+  V RLD +T G +++       R L   L   +  + Y     G+  + +
Sbjct: 134 QLRPEARRLELVHRLDRDTSGCIMIAKKNSALRHLHALLRDRKLTKRYHALVFGKWPRAQ 193

Query: 158 ------LNL--LKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNR 199
                 L    L  G  I     +G        TL+   G      + L E     G+  
Sbjct: 194 RLVDAPLKKFALASGERIVRVNEEGQKAKTEFATLNRYPG------LTLVEAKPITGRTH 247

Query: 200 EIK 202
           +I+
Sbjct: 248 QIR 250


>gi|301629906|ref|XP_002944074.1| PREDICTED: ribosomal large subunit pseudouridine synthase C-like
           [Xenopus (Silurana) tropicalis]
          Length = 541

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 39/265 (14%), Positives = 70/265 (26%), Gaps = 70/265 (26%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V    + QR+   + R      +  V R+I    V+VN G     A   V   D + +  
Sbjct: 31  VDAESSGQRLDNFLLRQLKGVPKTHVYRIIRSGEVRVNRGR--ASAGTRVAEGDQVRLPP 88

Query: 65  VPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           V + +                   E  +L    KP G+        G S V   +     
Sbjct: 89  VRVSEKVALKAGHPAPARAFALLLEDEQLIAIDKPAGVAV-----HGGSGVSFGVIEQLR 143

Query: 107 RVIS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
           +          V RLD  T G+LL+         L+         + Y     G      
Sbjct: 144 QARPQAPFLELVHRLDRETSGILLVAKKRSALHQLQDQFRERATGKTYLALVQGSWPAAH 203

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSN---------------------------AW 188
             ++     + +      D +  +      N                             
Sbjct: 204 KVID-----LPLHKYLLPDGERRVRVTTPENPDGMRALTLVKLRAHLPPRPLQGLPAMTL 258

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           + V ++ G+  +I+         + 
Sbjct: 259 LEVTIKTGRTHQIRVHLASQGHPIV 283


>gi|288960501|ref|YP_003450841.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
 gi|288912809|dbj|BAI74297.1| ribosomal large subunit pseudouridine synthase D [Azospirillum sp.
           B510]
          Length = 226

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 34/154 (22%), Positives = 52/154 (33%), Gaps = 19/154 (12%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVIS-VGRLDINTEGLLLLTNDGGLA 131
            +  KP G +  H+ P G   +   FD L   F +  S   RLD +T G L+L       
Sbjct: 18  LILDKPAG-LPVHAGPAGGPNLERHFDALRFGFPKPPSLAHRLDRDTSGCLILGRHAKAL 76

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDK------LNLLKK---GIVIQGICYGDMQVT-- 178
           R +     + +  + Y     G   QD       L  +     G  I G   G   VT  
Sbjct: 77  RKIGILFQNGKVDKTYWAVVAGGPPQDSGRIELPLAKISNKTGGWRIVGSPDGQSAVTDY 136

Query: 179 -LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +  Q     W+ +    G+  +I+         
Sbjct: 137 VVRGQADGLTWLELTPHTGRTHQIRVHCASIGCP 170


>gi|239500866|ref|ZP_04660176.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB900]
          Length = 310

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 84/242 (34%), Gaps = 56/242 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLAIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             DK  ++       L  G     +  +G       V  +  K +   V      G+  +
Sbjct: 186 SLDKQLIDAPLFRYELANGERRVRVSKEGKPSKTEWVVAERFKNAT-LVHASPLSGRTHQ 244

Query: 201 IK 202
           I+
Sbjct: 245 IR 246


>gi|296120899|ref|YP_003628677.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
 gi|296013239|gb|ADG66478.1| pseudouridine synthase [Planctomyces limnophilus DSM 3776]
          Length = 269

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 52/175 (29%), Gaps = 29/175 (16%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV---------GRLD 115
            P    E   L    KP GL+T    P G  T+ + + +      +           RLD
Sbjct: 19  EPQILLEDGPLLAIWKPAGLLTQGV-PQGLPTLENWVKNWIREKYAKPGNVYLGIPHRLD 77

Query: 116 INTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
               G++L   +   A  L       +  + Y     G   Q    L     +++     
Sbjct: 78  RPVSGVMLFARNSKAAARLAEVFRDRRVKKTYTAVVEGMPPQTTGRLTNY--LLKDPQAA 135

Query: 174 DMQVTLDTQKGS---------------NAWVTVGLREGKNREIKKVFEFFNWKVN 213
             Q+  +   GS                + + + L+ G+  +I+         V 
Sbjct: 136 HSQIVAEGTPGSKSAILDYRLLGTVAGRSLLEIELQTGRMHQIRVQMAAMGCPVV 190


>gi|27364845|ref|NP_760373.1| ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
 gi|34395775|sp|Q8DCG0|RLUA_VIBVU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|27360990|gb|AAO09900.1| Ribosomal large subunit pseudouridine synthase A [Vibrio vulnificus
           CMCP6]
          Length = 250

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/175 (17%), Positives = 59/175 (33%), Gaps = 45/175 (25%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++     P+   +++  L   +  +  V RLD++T GL++   +  
Sbjct: 19  EDDHILAVNKPSGLLSVPGRLPEHHDSMWSRLQEQYPEIQVVHRLDMSTSGLMVFAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV 177
                       L        +VY  R  G V+ D       G++    I       MQ 
Sbjct: 79  AEAALKKQFQYRLTH------KVYYARVWGHVEAD------SGMIDLPLICDWPNRPMQK 126

Query: 178 TL-DTQKGSNAWVTVGLRE-----------------GKNREIK-KVFEFFNWKVN 213
              +  K S     V  RE                 G++ +++  + +     + 
Sbjct: 127 VCHEHGKPSQTAFQVAKREVHANGAQTTIMRLLPVTGRSHQLRVHM-QALGHPIV 180


>gi|326577536|gb|EGE27413.1| tRNA pseudouridine synthase C [Moraxella catarrhalis O35E]
          Length = 258

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 29/166 (17%)

Query: 76  WLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP  ++   S  D      V   L +     V  V RLD  T G+L+   D   A 
Sbjct: 27  VIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVFALDSQTAG 86

Query: 133 VLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGDMQVT 178
           +L     +    + Y     G +                 +              D QV 
Sbjct: 87  LLAKQFENHHIQKSYLAVVRGIIGTGRIDYALKPRLDKIADKFSNPNKASKSAITDYQVL 146

Query: 179 LDTQKG-------SNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
             TQ+         ++  ++     +  G+  ++++  +     + 
Sbjct: 147 ATTQQPFISCRRFDSSRYSLVCLTPIT-GRKHQLRRHMKHIFHPIV 191


>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 = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 12 TPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          T +R+   +   G  S R +    +    V V+   +++    V    H++V G PL   
Sbjct: 4  TKERLDVYLVNHGYFSSREKARAAVMAGLVFVDNRRVDKPGYPVKPDAHVQVQGDPLPYV 63

Query: 71 ER 72
           R
Sbjct: 64 SR 65


>gi|310764748|gb|ADP09698.1| Pseudouridine synthase [Erwinia sp. Ejp617]
          Length = 232

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/209 (20%), Positives = 73/209 (34%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE+        +  RL L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIEI------LYQDDRLVLINKPAGLLSLSGKNPQNIDSVHYRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIA 119

Query: 172 YGDMQVTLDT-----QKGSNAWVTVG--------------LR------E-GKNREIKKVF 205
                  L +      K + +   V               L       E G+  +++   
Sbjct: 120 KDPALFPLMSICSIHGKPARSRYRVVERFYHPLENRTLLPLTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +       YG    G LL G+ R
Sbjct: 180 QQLGHPILGCD--LYG----GRLLPGTER 202


>gi|296112643|ref|YP_003626581.1| tRNA pseudouridine synthase C [Moraxella catarrhalis RH4]
 gi|295920337|gb|ADG60688.1| tRNA pseudouridine synthase C [Moraxella catarrhalis RH4]
 gi|326563862|gb|EGE14113.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 46P47B1]
 gi|326566871|gb|EGE17010.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 103P14B1]
 gi|326576787|gb|EGE26694.1| tRNA pseudouridine synthase C [Moraxella catarrhalis 101P30B1]
          Length = 254

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 29/166 (17%)

Query: 76  WLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP  ++   S  D      V   L +     V  V RLD  T G+L+   D   A 
Sbjct: 23  VIINKPANMLVHRSWLDKHETCFVVQTLRNQINQHVYPVHRLDRPTSGVLVFALDSQTAG 82

Query: 133 VLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGDMQVT 178
           +L     +    + Y     G +                 +              D QV 
Sbjct: 83  LLAKQFENHHIQKSYLAVVRGIIGTGRIDYALKPRLDKIADKFSNPNKASKSAITDYQVL 142

Query: 179 LDTQKG-------SNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
             TQ+         ++  ++     +  G+  ++++  +     + 
Sbjct: 143 ATTQQPFISCRRFDSSRYSLVCLTPIT-GRKHQLRRHMKHIFHPIV 187


>gi|260549179|ref|ZP_05823400.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter sp.
           RUH2624]
 gi|260407907|gb|EEX01379.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter sp.
           RUH2624]
          Length = 310

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 84/242 (34%), Gaps = 56/242 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLAIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             DK  ++       L  G     +  +G       V  +  K +   V      G+  +
Sbjct: 186 SLDKQLIDAPLFRYELANGERRVRVSKEGKPSKTEWVVAERFKNAT-LVHASPLSGRTHQ 244

Query: 201 IK 202
           I+
Sbjct: 245 IR 246


>gi|260577148|ref|ZP_05845125.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
 gi|259020622|gb|EEW23941.1| pseudouridine synthase, RluA family [Rhodobacter sp. SW2]
          Length = 349

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/152 (21%), Positives = 51/152 (33%), Gaps = 30/152 (19%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRKA------ 70
           VE+M    +V+V+G   + A+  V+    I V              DGV           
Sbjct: 34  VEKMCRTGQVRVDGARAK-ASDRVVPGMEIRVPPLPDSEAPSRPLRDGVSAADTKMIQSC 92

Query: 71  ---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP----SIFSRVISVGRLDINTEGLLL 123
              +   + + +KP GL +      G   V             R   V RLD +T G+L+
Sbjct: 93  VLFKDEHIIVLNKPPGLPSQGGSGQGDRHVDGLTEALKFGYKERPKLVHRLDKDTSGVLI 152

Query: 124 LTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
           L     +AR L          ++Y     G  
Sbjct: 153 LARTDRVARALSEAFRHRNTRKIYWALVAGVP 184


>gi|170759197|ref|YP_001786899.1| RluA family pseudouridine synthase [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169406186|gb|ACA54597.1| pseudouridine synthase, RluA family [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 305

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 81/234 (34%), Gaps = 42/234 (17%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           V++ F   R+   +  + I    SR  ++ +I +  V VN    ++    +   D+IE+ 
Sbjct: 8   VEKEFDNVRLD--LCLSKIFEDKSRSYLQGIIDEGNVLVNNK-EKKRNYKLKVGDNIEIN 64

Query: 63  ------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                       D       E   + + +KP  +V   +      T+ + L      +  
Sbjct: 65  IPEPKLLQIEPEDVKLDVIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCKDLSG 124

Query: 111 ---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK-- 157
                    V R+D +T G+L++  +      L          RVY     G +  ++  
Sbjct: 125 INGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKNEQGT 184

Query: 158 ---------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    ++ +K  +V +   +      +  +  ++  V   L  G+  +I+
Sbjct: 185 IEAPIGRHPVDRIKMAVV-KDGRHAVTHYKVIKRFKNHTLVECRLETGRTHQIR 237


>gi|169634491|ref|YP_001708227.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii SDF]
 gi|169153283|emb|CAP02389.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii]
          Length = 310

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 84/242 (34%), Gaps = 56/242 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLAIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             DK  ++       L  G     +  +G       V  +  K +   V      G+  +
Sbjct: 186 SLDKQLIDAPLFRYELANGERRVRVSKEGKPSKTEWVVAERFKNAT-LVHASPLSGRTHQ 244

Query: 201 IK 202
           I+
Sbjct: 245 IR 246


>gi|153853142|ref|ZP_01994551.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814]
 gi|149753928|gb|EDM63859.1| hypothetical protein DORLON_00536 [Dorea longicatena DSM 13814]
          Length = 272

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/214 (15%), Positives = 66/214 (30%), Gaps = 41/214 (19%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLR-KAERTRLWLYHKPI 82
            +  VKVN   ++     +   D +EV            + +PL    E   + + +KP 
Sbjct: 2   KEGYVKVNQKPVKS-NYRLSFGDSVEVTLPEAKEPDIVPENIPLDILYEDQDIIMINKPK 60

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS----------RVISVGRLDINTEGLLLLTNDGGLAR 132
            +V   +      T+ + L               R   V R+D++T G L++  +    +
Sbjct: 61  QMVVHPAPGHYSGTLVNALMYHCGDELSGINGCMRPGIVHRIDMDTTGSLVVCKNDKAHQ 120

Query: 133 VLE--LPSTQWLRVYRVRFHGQVDQD-------------KLNLLKKGIVIQGICYGDMQV 177
            L   L      R+Y    HG + +D                 +      +         
Sbjct: 121 SLSEQLKVHSIRRIYVAIVHGNIKEDSGTVNAPIGRHPTDRKKMSTHC--KNGRDAVTHY 178

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +  + G   ++   L  G+  +I+         
Sbjct: 179 KVLERFGDYTYIQCELETGRTHQIRVHMASIGHP 212


>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 = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 25/62 (40%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          M            +R+  V+A A   SR + +R+I   +V VNG    + A  V     I
Sbjct: 1  MTHMEYEHTGMREERLDVVVANATGESRSKAQRLIKTGKVHVNGHPQTKPAYAVQPESTI 60

Query: 61 EV 62
           V
Sbjct: 61 SV 62


>gi|108758809|ref|YP_633659.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108462689|gb|ABF87874.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 306

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 41/252 (16%), Positives = 78/252 (30%), Gaps = 48/252 (19%)

Query: 2   KDKNIVQENFTPQRVSKVIARA--GI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           + K  V      +R+ + +++   GI   R     +I    V++ G   +     +   +
Sbjct: 3   QQKVQVPREAAGERLDRFLSKQVPGINLER--ARALIDSGAVRIRGKRCQ-PTRKLWGGE 59

Query: 59  HIEV-------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGR-STVFDNLPS 103
            IE+             +G  L    + + L + +KP G+V    +P+GR ++V   L +
Sbjct: 60  EIELERPEPRAASVAASEGPVLPVLHDDSALVIVNKPPGIVV---EPEGRAASVVGLLAA 116

Query: 104 IFSRVI--------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
                          V RLD  T G L        A  L       +  + Y     GQ 
Sbjct: 117 QRPPFDVEGLAQPGVVHRLDRETSGCLAFARTDTAAAALLRSFQEKRVDKRYWTLVLGQP 176

Query: 154 ------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                       D          +         +   +  +    A + V L  G+  ++
Sbjct: 177 PAQGRLEGPYARDPADPRRFTTRVP--SARRAALSFEVRERFADAALLEVDLDTGRTHQV 234

Query: 202 KKVFEFFNWKVN 213
           +       + V 
Sbjct: 235 RVQLSEAGFPVL 246


>gi|226327118|ref|ZP_03802636.1| hypothetical protein PROPEN_00983 [Proteus penneri ATCC 35198]
 gi|225204336|gb|EEG86690.1| hypothetical protein PROPEN_00983 [Proteus penneri ATCC 35198]
          Length = 217

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 61/164 (37%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   +   +KP GL++     P+   ++   + + F     V RLD+ T G++++  +  
Sbjct: 18  QDEHIIAVNKPSGLLSVPGKAPEHNDSIMSRIKAEFPNAECVHRLDMATSGVIVVALNKE 77

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQVTL-DTQ 182
             R L+    +    + Y  R  G V+++      +G+V    I        Q    +T 
Sbjct: 78  AERELKRQFREREPKKTYIARVWGHVEKE------EGLVDLPLICDWPNRPKQKVCHETG 131

Query: 183 KGSNAWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
           K +  +  V   E            G++ +++  +       + 
Sbjct: 132 KAAQTFYEVLEYEENATRVKLSPITGRSHQLRVHML-ALGHPIL 174


>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 = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 78/241 (32%), Gaps = 55/241 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKPI 82
           +++ + R++VN  + ++    +   D I  D       ++            + +  KP 
Sbjct: 34  KLLRKGRIRVNFEVAQK-GQILQFGDLISFDIEEKYLDQKKVEISKVYEDDNIIVIDKPY 92

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLEL--P 137
           G + +H D +   +V + +   +S         RLD NT GL+++  +  +   +     
Sbjct: 93  G-IPSHPDTNNEYSVVNWIEDNYSGNQLPALCHRLDRNTSGLMIIAKNRQVLNEMLKYMS 151

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVI-------------------QGICYGDMQVT 178
                + Y            ++L K G+++                   +G      +  
Sbjct: 152 RRAIKKKYLCITKK------VDLPKSGVLVHYLKKDSKKSKVYISDLPAEGYSEIVTRYK 205

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
           +   K     V V +  GK  +I+         +            LG    G    ++K
Sbjct: 206 IIRGKDDLLLVDVEIETGKTHQIRSQLAHVGLCI------------LGDSKYGDW-ALNK 252

Query: 239 K 239
           K
Sbjct: 253 K 253


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

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 41/260 (15%), Positives = 91/260 (35%), Gaps = 74/260 (28%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +V+V+G   + A   + 
Sbjct: 5   EQKIVDAGEAGMRLDRWFKIHYPGL---GFG---HLQKLLRSGQVRVDGGRAK-ADTRIQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQMLLYEDPKIFVFNKPAGLAV---- 113

Query: 91  PDGRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
             G S V  ++  +     S        V R+D +T G+L++    G A+ L        
Sbjct: 114 -QGGSGVTRHIDGMLEAWRSKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTASFRERD 172

Query: 141 WLRVYRVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQK 183
             + Y     G     +DK+            + ++  +   G    D  V    +  + 
Sbjct: 173 TKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKA 230

Query: 184 GSN-AWVTVGLREGKNREIK 202
           G+N AW+ +    G+  +++
Sbjct: 231 GNNLAWLEMEPYTGRTHQLR 250


>gi|56414914|ref|YP_151989.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197363842|ref|YP_002143479.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129171|gb|AAV78677.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|197095319|emb|CAR60877.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
          Length = 260

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 48/166 (28%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM----- 175
           R L          + Y     G +  D +         + +      +            
Sbjct: 71  RRLAQQFEQHHIRKRYHAIVRGWLMDDAVLDYPLVEERDKIADKFAREDKAPQPAVTQYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|331084165|ref|ZP_08333271.1| hypothetical protein HMPREF0992_02195 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330402020|gb|EGG81593.1| hypothetical protein HMPREF0992_02195 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 224

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 23/163 (14%), Positives = 47/163 (28%), Gaps = 22/163 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS-----DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E   + +  KP G           D +     +         V  + RLD   +G+L+  
Sbjct: 13  EDKYILVCQKPAGFPVQSKRLGTLDMECALRNYLAKKGQEPYVAVIHRLDQPVQGVLVFA 72

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------------- 170
            D   A  L       ++ + Y     G     K   L   +   G              
Sbjct: 73  KDKESAAKLSKQMQQGKFEKTYLAYTQGH-TDKKQETLIDELEKDGGTNTSKVVAKKTAN 131

Query: 171 -CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               ++   +  +    + + V L+ G++ +I+         +
Sbjct: 132 SKRAELSYKVLKETEEGSLLEVSLKTGRHHQIRVQLAHAGLPI 174


>gi|323453124|gb|EGB08996.1| hypothetical protein AURANDRAFT_25466 [Aureococcus anophagefferens]
          Length = 361

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 77/246 (31%), Gaps = 46/246 (18%)

Query: 13  PQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLER--------------AAVNVMST 57
           P R+   +A      +RRE    I    V+VNG +  R              A     + 
Sbjct: 54  PARLDAFLAAQFPERTRREWAEAIGGGAVRVNGAVATRKSASVAAGDGVAADAFAAEPAG 113

Query: 58  DH-IEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
           D  +E + +PL    +     + +K  G+VT  +    R T+ + +              
Sbjct: 114 DKPVEAEDLPLDVLVDDASFLVVNKAAGMVTHPAPGARRGTLANAVAHRCGGGGVFAEAT 173

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF-------------- 149
            R   V RLD  T G +++  +    R L+    +    ++Y                  
Sbjct: 174 PRPGIVHRLDRYTSGAIVVARNARATRRLQAQFKARTVAKLYLAVLARPPPPPPDGADEL 233

Query: 150 --HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
                + +      +K  V+ G      +V +    G      V +  G+  +I+     
Sbjct: 234 VIDAPIGRHPARR-EKMAVVPGGRPAVSRVRVLASDGRRCVAQVAIDTGRTHQIRVHLAH 292

Query: 208 FNWKVN 213
               V 
Sbjct: 293 VGSPVL 298


>gi|319401727|gb|EFV89935.1| pseudouridine synthase, RluA family protein [Staphylococcus
           epidermidis FRI909]
          Length = 284

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 59/173 (34%), Gaps = 19/173 (10%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS 110
            S + I  D       E   L + +KP       S      +    V         ++  
Sbjct: 64  PSENLIPYDKELEVIYEDAYLIIVNKPQMQNCAPSREHPHGSLVEQVLAYYTKKGEKINP 123

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLL-- 161
             V RLD NT GL++    G +  +      +  + Y    +GQ     V +  +  L  
Sbjct: 124 HIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFK--KEYVALAYGQTQSSGVIEAPIARLSD 181

Query: 162 ---KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              K+ +  +G C   +   L  Q  + +   + L  G+  +I+  FE+    
Sbjct: 182 SIIKREVNEKGKCAKTVYQKLM-QNETASLCKIKLLTGRTHQIRVHFEYIGHP 233


>gi|77460386|ref|YP_349893.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf0-1]
 gi|77384389|gb|ABA75902.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens Pf0-1]
          Length = 320

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 83/238 (34%), Gaps = 46/238 (19%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V   +  QR+   + AR     +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRI--KPEYKLQAGDIVRVPP 73

Query: 65  VPLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTV--FDNLP 102
           V + + +                       L + +KP G+            +  F  L 
Sbjct: 74  VRVPERDEPVPLAQGLLQRLEASIVYEDKALIVINKPAGIAVHGGSGLNYGVIEAFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T GLL++     + R L   L      + Y     G      +  
Sbjct: 134 PDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHAALRGDGVDKRYMALVRGNW-ATSIKQ 192

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-----------GLRE-----GKNREIK 202
           ++  +    +  G+  V +D ++G  + VTV            L E     G+  +I+
Sbjct: 193 VRAALGKSNLRSGERMVEVDEEEGKES-VTVFKVLRRFGDFATLIEAKPITGRTHQIR 249


>gi|317495180|ref|ZP_07953550.1| RNA pseudouridylate synthase [Gemella moribillum M424]
 gi|316914602|gb|EFV36078.1| RNA pseudouridylate synthase [Gemella moribillum M424]
          Length = 282

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 32/191 (16%), Positives = 65/191 (34%), Gaps = 32/191 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVP-------------LRKAERTRLWLYHKPIGLVT 86
           + +NG         +   D++E++                +++ E   L +  KP G+ T
Sbjct: 41  IIINGQSA-DLQSKLNKDDNLEINIELGTSNYIANNSLSIIKEYEDDYLLIASKPFGIKT 99

Query: 87  THSD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
             +D  D  +T+ + L + +  +  + RLD +T GL++      +   L   L      R
Sbjct: 100 HPNDITDENNTLVNYLITDYPYLEPIHRLDTDTCGLVIFAKTPFVKSKLDQMLEHRVIKR 159

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV------------TV 191
            Y       +    +  +   I         M VT   +      +            T+
Sbjct: 160 FYTALVKNNI---HVQTINTNIGRDNREKNKMAVTNKGKNAITNILSCEKIEQNKFATTI 216

Query: 192 GLREGKNREIK 202
            L  G+  +I+
Sbjct: 217 SLETGRTHQIR 227


>gi|169797345|ref|YP_001715138.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|184156731|ref|YP_001845070.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213155841|ref|YP_002317886.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii AB0057]
 gi|215484783|ref|YP_002327018.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260556236|ref|ZP_05828455.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii ATCC 19606]
 gi|301345638|ref|ZP_07226379.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB056]
 gi|301511837|ref|ZP_07237074.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB058]
 gi|301597322|ref|ZP_07242330.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB059]
 gi|332852954|ref|ZP_08434464.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332867958|ref|ZP_08437946.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332873142|ref|ZP_08441099.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6014059]
 gi|169150272|emb|CAM88169.1| 23S rRNA pseudouridylate synthase [Acinetobacter baumannii AYE]
 gi|183208325|gb|ACC55723.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213055001|gb|ACJ39903.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii AB0057]
 gi|213987620|gb|ACJ57919.1| pseudouridine synthase, RluA family protein [Acinetobacter
           baumannii AB307-0294]
 gi|260410291|gb|EEX03590.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           baumannii ATCC 19606]
 gi|322506621|gb|ADX02075.1| rluC [Acinetobacter baumannii 1656-2]
 gi|323516497|gb|ADX90878.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332728890|gb|EGJ60245.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013150]
 gi|332733659|gb|EGJ64818.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6013113]
 gi|332738654|gb|EGJ69524.1| rRNA pseudouridylate synthase [Acinetobacter baumannii 6014059]
          Length = 310

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 84/242 (34%), Gaps = 56/242 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLAIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAVPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             DK  ++       L  G     +  +G       V  +  K +   V      G+  +
Sbjct: 186 SLDKQLIDAPLFRYELANGERRVRVSKEGKPSKTEWVVAERFKNAT-LVHASPLSGRTHQ 244

Query: 201 IK 202
           I+
Sbjct: 245 IR 246


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

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 40/256 (15%), Positives = 88/256 (34%), Gaps = 66/256 (25%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           +   V+ +    R+ +        +   G      +++++   +++V+G  ++ A   + 
Sbjct: 5   EIKKVETDENGMRLDRWFKVHYPGL---GFG---ALQKLLRSGQIRVDGGRVK-ADTRLC 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTT--- 87
               + V                      DG  L+K    E  ++++++KP GL      
Sbjct: 58  MGQSVRVPPLPLDNMISLPITDKTLRGQDDGTILKKMLLYEDPKVFVFNKPAGLAVQGGS 117

Query: 88  --HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLR 143
                 D    V+ N      R+  V RLD  T G+L++    G A+ L       +  +
Sbjct: 118 GLTRHIDSMLEVWRNKKGEKPRL--VHRLDRETSGVLIVARSRGAAQALTAAFRERETKK 175

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----------------- 186
            Y     G V + K + +   +V +    GD     D  +  +                 
Sbjct: 176 TYWALVRG-VPKKKQDKISTWMVKEMTAQGDKMRVCDHGEPDSHHAVSYYRVLDTRGRTL 234

Query: 187 AWVTVGLREGKNREIK 202
           +W+ +    G+  +++
Sbjct: 235 SWLEMEPYTGRTHQLR 250


>gi|322817842|gb|EFZ25435.1| hypothetical protein TCSYLVIO_8401 [Trypanosoma cruzi]
          Length = 733

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/173 (19%), Positives = 56/173 (32%), Gaps = 36/173 (20%)

Query: 71  ERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFS--------RVISVGRL 114
           E   + + +KP  L         T  +D      V   L S  +        R   V RL
Sbjct: 513 EDNDILVLNKPPHLASSRHALSCTQMNDKRATDVVSLILASTKNGETMRGVFRQGQVHRL 572

Query: 115 DINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           D  T G L++      A  L          +Q  +VY       V +  L      I ++
Sbjct: 573 DAETSGCLVMAKTDCAADSLRHQMGTSAAYSQCNKVYLALCA--VMEPDLRR----IPLR 626

Query: 169 GICYGDMQVTLDTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G+    M   + T+        K   A +   +++GK  +I++        + 
Sbjct: 627 GVLRDPMDPKISTKYRVIRFFRKARVALLECRIQQGKKHQIRRHLAAAGLPIL 679


>gi|262370010|ref|ZP_06063337.1| 23S rRNA pseudouridylate synthase [Acinetobacter johnsonii SH046]
 gi|262315049|gb|EEY96089.1| 23S rRNA pseudouridylate synthase [Acinetobacter johnsonii SH046]
          Length = 312

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 39/242 (16%), Positives = 83/242 (34%), Gaps = 56/242 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETKLSIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDENAAPVSDKVAQSLLSRVVYEDEGLMVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           +           +  + R+D +T GL++++    + + L   L   +  + Y     G V
Sbjct: 126 IEGLRAATGKKYLELIHRIDRDTSGLVMISKKRSVLKSLQDMLREHKIKKTYAAVVKGVV 185

Query: 154 DQDK--LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW------VTVGLR-----EGKNRE 200
             DK  ++       +       ++V+ + ++    W      +   L       G+  +
Sbjct: 186 SLDKQLIDAPLHRYELANGERR-VRVSSEGKESKTQWNVAERFMHATLVYASPLSGRTHQ 244

Query: 201 IK 202
           I+
Sbjct: 245 IR 246


>gi|254785816|ref|YP_003073245.1| pseudouridine synthase for 23S rRNA and tRNAphe [Teredinibacter
           turnerae T7901]
 gi|237686915|gb|ACR14179.1| pseudouridine synthase for 23S rRNA and tRNAphe [Teredinibacter
           turnerae T7901]
          Length = 208

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/150 (16%), Positives = 52/150 (34%), Gaps = 22/150 (14%)

Query: 71  ERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           +   +   +KP GL+T    + PD     FD L         V RLD+ T GL++     
Sbjct: 9   QDDHIIAINKPAGLLTVPGLATPDN---AFDQLVHQHPNSRVVHRLDMATSGLVIFPQSH 65

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGDM 175
                        +  + Y     G V +D+               K+ + ++   +   
Sbjct: 66  ESLVRFGRLFEQRKMTKTYTATVAGIVAEDRGEITLPLICDWPNRPKQKVDLEQGKHAHT 125

Query: 176 QVTLDTQKGS--NAWVTVG-LREGKNREIK 202
           Q  +  ++       + +  +  G++ +++
Sbjct: 126 QYKVLERRLDLQTTRIELTPIT-GRSHQLR 154


>gi|294793936|ref|ZP_06759073.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
 gi|294455506|gb|EFG23878.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
          Length = 321

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 19/134 (14%), Positives = 43/134 (32%), Gaps = 16/134 (11%)

Query: 37  QQRVKVNGILLE---------RAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLV- 85
           +  + VNG                + +       +  + L    E   + + +K  G++ 
Sbjct: 40  EGIITVNGKFATWNTLIHGGDHLVMKLTPEQEFSLSPMSLDIIYEDEYILVINKAAGILM 99

Query: 86  ---TTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
              +T  +    + V               V RLD NT G++++     +    +   T 
Sbjct: 100 HPTSTVRNHTLANGVLHYYQETNQHYDFHPVHRLDKNTSGIVIIAKTSVVQHAFDKKHTH 159

Query: 141 WLRVYRVRFHGQVD 154
           + ++Y     G + 
Sbjct: 160 FYKIYDAIVEGHLP 173


>gi|194246668|ref|YP_002004307.1| Pseudouridine synthase [Candidatus Phytoplasma mali]
 gi|193807025|emb|CAP18461.1| Pseudouridine synthase [Candidatus Phytoplasma mali]
          Length = 299

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 82/241 (34%), Gaps = 47/241 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++  + +     R+   + +    S+   +++I   ++ VN    ++ +  +   DHI
Sbjct: 1   MGEEFFIIDVEKGMRLDHFLNKKINFSKNRCQKLIILGKILVNNKPSKK-SYILKENDHI 59

Query: 61  EV-------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           +V             D       E   L +  KP  LV   S      T+ + L      
Sbjct: 60  KVFIPSTPLNVLQPIDLNLEIIYEDEFLAVIDKPKNLVIHPSITFSGVTLINGLLFQIKN 119

Query: 107 -------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                  R   V RLD +T GL+L+  + +      L +   +  R Y    HG ++   
Sbjct: 120 FRKMDGLRPGIVHRLDKDTTGLILVAKSEEIRQQLQLSIQKREIKRYYWALIHGHLE--- 176

Query: 158 LNLLKKGIVIQGICYGD----MQVTLDTQKGSNAWVTV-------GLRE-----GKNREI 201
               K+G +I  I            +   K S  +  V        L E     G+  +I
Sbjct: 177 ----KQGKIILPIGRHPHNRIKMAVVKNGKPSITYFKVLKYFNNFSLIECQLETGRTHQI 232

Query: 202 K 202
           +
Sbjct: 233 R 233


>gi|187934776|ref|YP_001887060.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722929|gb|ACD24150.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
          Length = 322

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 37/254 (14%), Positives = 82/254 (32%), Gaps = 67/254 (26%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + ++ ++VNG         + 
Sbjct: 2   KIEIGANEAGQRLDKFL-------RKLLKDVPLSAIFKALRKKDIRVNGKKQSE-KYFLE 53

Query: 56  STDHIEVDGVPLRKAERTRLWLYH-----------------KPIGLVTTHSDPDGRSTVF 98
             D +E+  +     ++ +    +                 K  G++      +   T+ 
Sbjct: 54  EGDIVEIKYIKSNPEKKEKFIQVNFSGMKTAYEDENLLVVEKWPGILVHPDKDEKDPTLT 113

Query: 99  DNLPSIFSRVI-------------SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLR 143
           D + S                      RLD NT GL++   T +G  +    +   +  +
Sbjct: 114 DYVLSYLKEKGSYVPENEITFTPAPCNRLDRNTSGLVMFGKTFEGLKSINETIREDRVRK 173

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYG---------------DMQVTLDTQKGSNAW 188
            Y     G+V       L  G +++                     M+VT     G+ + 
Sbjct: 174 YYVALVKGKVQDG----LHTGYILKNQDTNISKVYEKEVPDSKKIAMEVTTTQTNGAYSL 229

Query: 189 VTVGLREGKNREIK 202
           + + L  G++ +I+
Sbjct: 230 LEINLITGRSHQIR 243


>gi|312829403|emb|CBX34245.1| RNA pseudouridylate synthase family protein [Staphylococcus aureus
           subsp. aureus ECT-R 2]
          Length = 284

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 31/195 (15%), Positives = 59/195 (30%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  KP     T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPREIPSVNLIPYARKLEVLYEDAFIIIVTKPNNQNCTPSREHL 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDHNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|314933208|ref|ZP_07840573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
 gi|313653358|gb|EFS17115.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus caprae C87]
          Length = 284

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 32/195 (16%), Positives = 64/195 (32%), Gaps = 42/195 (21%)

Query: 42  VNGILLE---RAAVNVMSTDHIEVDGVPLRKA---------------ERTRLWLYHKPIG 83
           VNG  +      AV     D  EV  +P+ +                E   + + +KP  
Sbjct: 38  VNGHPVTVRKEMAV----GDQFEVH-MPIEEPSSNLLPYPKPLDIVFEDEFILIVNKPQS 92

Query: 84  LVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
                S      ++ + +        + +    V RLD NT GL+L    G +       
Sbjct: 93  QNCAPSREHPHESLVEQVLAYLMNKDVQTNPHIVTRLDRNTSGLVLFAKFGHIHH--LFS 150

Query: 138 STQWLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             ++ + Y                 + +D  +++ + +  +G        T+  Q  + +
Sbjct: 151 KVKFEKEYICLAYGRTQPEGVVEAPIARDSDSIITRKVSDKGKYAKTSYYTI-VQNNTLS 209

Query: 188 WVTVGLREGKNREIK 202
              V L  G+  +I+
Sbjct: 210 LCKVKLHTGRTHQIR 224


>gi|226223587|ref|YP_002757694.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes Clip81459]
 gi|225876049|emb|CAS04755.1| Putative ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes serotype 4b str. CLIP 80459]
          Length = 296

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 88/264 (33%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A+ +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  AEGKIEVNNKEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTNLDIIFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEKYMAFDLPLPAD 287


>gi|152978874|ref|YP_001344503.1| tRNA pseudouridine synthase C [Actinobacillus succinogenes 130Z]
 gi|150840597|gb|ABR74568.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 238

 Score = 56.0 bits (134), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 33/222 (14%), Positives = 71/222 (31%), Gaps = 39/222 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G++   S  D      V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFIVAVNKPAGMLVHRSWLDRHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALH 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQ------------ 168
             +A +L          + Y     G +  +      L + +  I  +            
Sbjct: 67  SDIANLLCRQFEGKTVRKSYLAVVRGYLSGEARIDYALKIRRDKIADKFSQENKEAQAAV 126

Query: 169 ----GICYGDMQVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
               G+   +M   +   Q    + V +    G+  ++++  +     +  L    YG  
Sbjct: 127 TDYTGLQTAEMPWAVGKYQTCRYSLVRLMPHTGRKHQLRRHMKHIFHPI--LGDTQYGDL 184

Query: 224 QLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSE 265
                     R ++++    Q+   +L   ++  + P+  + 
Sbjct: 185 H-------QNRALAEQT---QVSRLMLHAEKLAFNHPVNQTR 216


>gi|332999543|gb|EGK19128.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           VA-6]
          Length = 260

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +V RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|313147267|ref|ZP_07809460.1| RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
 gi|313136034|gb|EFR53394.1| RNA pseudouridylate synthase [Bacteroides fragilis 3_1_12]
          Length = 305

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/221 (16%), Positives = 75/221 (33%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP 66
            P  +   +A +   ASR +++ +++++ V V+ ++  +    +     + +    +   
Sbjct: 23  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNKKE 82

Query: 67  LRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
            R        E   + +  K  GL++  +D     T    L          +R+  V RL
Sbjct: 83  FRHPLLKIVYEDAYIIVVEKKEGLLSVGTDRQKERTAQHILSEYVGRSGRGNRIFVVHRL 142

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D    R L          R Y     G+           +    L + 
Sbjct: 143 DRDTSGLMMFAKDEKTQRTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTLYVS 202

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 203 SSSYDDGGSKSITHYRTIKRANGY-SLVELRLETGRKNQIR 242


>gi|226312125|ref|YP_002772019.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226095073|dbj|BAH43515.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 302

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 83/244 (34%), Gaps = 46/244 (18%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTR 74
           R++V  +   + V ++G  + +  V   +   I +                P    E   
Sbjct: 36  RKQVHLLFQHKEVLLDGEPVAQHVVG-KAGQEIRLRMCKPEALGLDPASEAPEILYEDDH 94

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDG 128
           L + +KP+GL+   ++     T+   +   F R      V  V RLD +T G++L     
Sbjct: 95  LLIVNKPVGLLLHPTERYHHVTLDHLVSGHFFRTGLEAKVRHVHRLDQDTSGVVLYAKHP 154

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL-----------LKKGIVIQGICYGDM 175
             + +L   L      R Y     GQ+ +++  +            ++ +   G      
Sbjct: 155 WASALLDEMLRERTIKRTYVAYVSGQMPKERGKINEPIGKDRNHGTRRRVTPNGDPAITH 214

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +  +  +   V   L  G+  +I+  F      +            LG  L G  RE
Sbjct: 215 -YQVKERFQTATKVECQLETGRTHQIRVHFSHIGHPL------------LGDELYGGKRE 261

Query: 236 VSKK 239
           + K+
Sbjct: 262 LIKR 265


>gi|114327513|ref|YP_744670.1| ribosomal large subunit pseudouridine synthase D [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315687|gb|ABI61747.1| ribosomal large subunit pseudouridine synthase D [Granulibacter
           bethesdensis CGDNIH1]
          Length = 330

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 77/244 (31%), Gaps = 60/244 (24%)

Query: 8   QENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--------- 57
             +  P+R+ + +A      SR  ++ +I    V  +G  +   A  V            
Sbjct: 18  APDAVPERIDRFLAIHLPDMSRSRLKSLIESGAVHRDGQSVRGPAEMVRPGSLYRLRLPT 77

Query: 58  --------DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNL 101
                    HI     P+   +   L +  KP G+V   +      T+         +NL
Sbjct: 78  PAPAIPIAQHIAF---PILFEDDD-LIVLDKPAGMVVHPAPGSPDGTLVNALLAYCGENL 133

Query: 102 PSI--FSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
           P I    R   V RLD +T G++++  T     A      +    R+Y     G +    
Sbjct: 134 PGIGGEKRPGIVHRLDKDTSGVMVVAKTEFALAALSALFAARDLERLYTALAWGVLTP-- 191

Query: 158 LNLLKKGIVIQGICYGD-------------MQVTLDTQKGSNAWV------TVGLREGKN 198
               ++G  I+G    D              +  L   +    W          L  G+ 
Sbjct: 192 ----REG-DIEGAIGRDPRDRKRMAIVRHGGKPALTHYRAMATWYDAVTRMECKLATGRT 246

Query: 199 REIK 202
            +I+
Sbjct: 247 HQIR 250


>gi|310659241|ref|YP_003936962.1| ribosomal large subunit pseudouridylate synthase d [Clostridium
           sticklandii DSM 519]
 gi|308826019|emb|CBH22057.1| ribosomal large subunit pseudouridylate synthase D [Clostridium
           sticklandii]
          Length = 301

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 70/206 (33%), Gaps = 32/206 (15%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPI 82
             +++ VN     +    V   D IEV+              + L   E   L +  K  
Sbjct: 42  KDKQIFVN-KKFYKMHEIVNIGDIIEVNLPDEANEYDAEDMDIKLLY-EDADLMVIEKEP 99

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            +V   +    R+T+ + L  +F       ++  V RLD +T G+L++  +     +L  
Sbjct: 100 FIVVHPTKGHQRNTLANGLIKLFKDKSINSKIRFVNRLDRDTSGILIVAKNSYCHSILTK 159

Query: 137 PS--TQWLRVYRVRFHGQVDQDK------LNLLKKG---IVIQGICYGDMQVTLDTQKGS 185
                +  + Y     G +D+        ++  + G   IV         +  +  +   
Sbjct: 160 NDAMHEMEKKYYAVVSGHLDKASGVIDLPIDKSEDGIRRIVSDKGQRAVTRYKVIDKLKY 219

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWK 211
              + + L  G+  +I+  F      
Sbjct: 220 ATLLEISLETGRTHQIRVHFSHIGHP 245


>gi|169824723|ref|YP_001692334.1| putative 23S RNA-specific pseudouridylate synthase [Finegoldia
           magna ATCC 29328]
 gi|167831528|dbj|BAG08444.1| putative 23S RNA-specific pseudouridylate synthase [Finegoldia
           magna ATCC 29328]
          Length = 273

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/232 (16%), Positives = 84/232 (36%), Gaps = 43/232 (18%)

Query: 11  FTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
               R+ + +     +     S       I +  + +NG   +R +  +   D + ++  
Sbjct: 9   DKKIRLDEFLKKNHISHNLFIS-------IYKDDIFINGKHAKRNS-KLEKGDIVTIN-- 58

Query: 66  PLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNL----PSIFS 106
            LR  E                  +++ +KP   +T + D +     F +      +I  
Sbjct: 59  -LRDEENKYEPINMDIEVLYEDDDIFVLNKP-DKLTMNKDGEKSLANFVSYLFEQRNIKQ 116

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL--KKG 164
           +V  + RLD +T G++++  +       +  S +  + Y     G     K+ L   + G
Sbjct: 117 KVRFINRLDQDTSGVVMVAKNKIAQAYYQKNSFK--KKYLAIVKGNPKDQKIELNLKRDG 174

Query: 165 IVIQGICYGDMQVTL---DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           I  +    G   VT+       G  + V++ L  G+  +I+   E+ N  + 
Sbjct: 175 IKTEIDENGKKSVTILENLKNYGDYSLVSLELLTGRTHQIRVSMEYINCPIV 226


>gi|167771389|ref|ZP_02443442.1| hypothetical protein ANACOL_02755 [Anaerotruncus colihominis DSM
           17241]
 gi|167666029|gb|EDS10159.1| hypothetical protein ANACOL_02755 [Anaerotruncus colihominis DSM
           17241]
          Length = 292

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/192 (18%), Positives = 63/192 (32%), Gaps = 40/192 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----------VGRLDINTEG 120
           E + + +Y+KP  +         R      L ++F+R  +          VGRLD +T G
Sbjct: 86  EDSDVIVYNKPAAMAC----HPVRGLRQGTLANVFARDCAANGESCACRLVGRLDRDTSG 141

Query: 121 LLLLTNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQG 169
            +++  +   A VL        + Y     G            + Q      ++ IV  G
Sbjct: 142 AVVIAKNARAAAVLTG---HVEKQYIALVTGMPNPKHGVIDAPIGQPDRKNPRRMIVANG 198

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLL 229
                   T    +G  + V   LR G+  +I+         +              TL 
Sbjct: 199 KPAVTEYETQIRCEGY-SVVHCVLRTGRTHQIRVHMASIGCPLLG-----------DTLY 246

Query: 230 AGSTREVSKKIL 241
            G T  + ++ L
Sbjct: 247 GGETERIERQAL 258


>gi|47093663|ref|ZP_00231418.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|47017959|gb|EAL08737.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 4b H7858]
 gi|328466988|gb|EGF38091.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes 1816]
          Length = 296

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 88/264 (33%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A+ +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  AEGKIEVNNKEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTDLDIIFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEKYMAFDLPLPAD 287


>gi|116495316|ref|YP_807050.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           ATCC 334]
 gi|239629769|ref|ZP_04672800.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|301066888|ref|YP_003788911.1| 23S RNA-specific pseudouridylate synthase [Lactobacillus casei str.
           Zhang]
 gi|116105466|gb|ABJ70608.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           casei ATCC 334]
 gi|239527381|gb|EEQ66382.1| pseudouridylate synthase [Lactobacillus paracasei subsp. paracasei
           8700:2]
 gi|300439295|gb|ADK19061.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus casei
           str. Zhang]
          Length = 293

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 72/222 (32%), Gaps = 32/222 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKA---- 70
           + +A  G+ S R  ++M+A   + V+G         V +   I  +      L       
Sbjct: 17  RWLAEQGV-SHRLFKKMLADHLIWVDGQ--ASGNGPVEAGQIIRFEIPTSKTLTPEFAPL 73

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTE 119
               E     +  KP GL +        S++ + +            +   + RLD +T 
Sbjct: 74  EVIYEDANWLIVSKPAGLTSVPGPHTPNSSLLNRIAGYLVEQKIDAPQPAIMTRLDRDTV 133

Query: 120 GLLLLTNDGGLARVLELPSTQWL-RVYRVRFHGQVD------QDKLNLLKKG---IVIQG 169
           GL+L           +    + L + Y     G++          L L   G   IV   
Sbjct: 134 GLVLAAKHPYAQGRFDQAHQRTLTKHYLAVVSGKLPSPKGEIDAPLKLAADGIHRIVAAD 193

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +  +K +N  V V L  G+  +I+  F      
Sbjct: 194 GQTALTKYRVLKEK-TNTLVDVQLLTGRTHQIRVHFASLGHP 234


>gi|258647058|ref|ZP_05734527.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           tannerae ATCC 51259]
 gi|260853174|gb|EEX73043.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           tannerae ATCC 51259]
          Length = 360

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 76/238 (31%), Gaps = 42/238 (17%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------- 62
           RV K + A     SR  +++      + +NG   E++   V   D + +           
Sbjct: 43  RVDKFLMAHLPDTSRNRIQQAAKAGFIHINGRP-EKSNYRVKPHDVVTLLLDRPRYENLI 101

Query: 63  --DGVPLR-KAERTRLWLYHKPIGLV----------TTHSDPDGRSTVFDNLPSIFSRVI 109
             + +PL    E   L + +K  GLV          T  +          +       V 
Sbjct: 102 EPENIPLDIVYEDEALIVVNKSAGLVVHPGFGNYTGTLVNALAYHLKDVADYDPNDPGVG 161

Query: 110 SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL--------- 158
            V R+D +T GLL++  T D      ++  +    R Y     G V  D+          
Sbjct: 162 LVHRIDKDTSGLLVIAKTPDAKSKLGVQFFNKTTRRRYEALVWGNVKTDEGRIEGNIARD 221

Query: 159 --NLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             + L+  +       G   VT   +  + G    +   L  G+  +I+         
Sbjct: 222 PHDRLQMAVFAPDSGIGKPAVTHYKVLKRFGYVTLIECQLETGRTHQIRTHMRHIGHP 279


>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 = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/126 (20%), Positives = 49/126 (38%), Gaps = 15/126 (11%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           +R+ + IA  G  SR    R +    V ++G   + +   + +   + V+     +A   
Sbjct: 15  ERLDRFIAARGGVSRGAARRALDSGGVFLDGRRCKVSGRLLQAGQKVVVNLEEAGRAAPA 74

Query: 74  R--------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINT 118
           R              L    KP G+ +  +    R T+ + +  +  + V  V RLD  T
Sbjct: 75  RSALERARLLYADQDLVAVDKPAGVPSQPTLTTDRGTLPELVSDLLGAPVTLVHRLDRET 134

Query: 119 EGLLLL 124
            G+ +L
Sbjct: 135 SGVTVL 140


>gi|325289846|ref|YP_004266027.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324965247|gb|ADY56026.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 299

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/303 (13%), Positives = 98/303 (32%), Gaps = 51/303 (16%)

Query: 1   MKDKN------IVQENFTPQRVSKVIARAGIASRREVERMIAQQ-RVKVNGI-------- 45
           M +K+       + EN   +++ +++ R    SR+ ++++      V ++G         
Sbjct: 1   MPEKDQDRFIYCLTENDENRKLEEILRRQFHFSRKLIQKL-KTGEHVWLDGKFSYLNIRG 59

Query: 46  -LLERAAVNVMSTDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
              +   ++    + + V           E   L   +KP G V   +      T+ + +
Sbjct: 60  RSGQTLTIDFAEEEDVSVSPEDADLDLLFEDKILLAVNKPAGQVVHPTSVYRSGTLANAV 119

Query: 102 PSIFSR------VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
              + +         + R+D NT G++++  +    + L          + Y    HG +
Sbjct: 120 TGYWKKNGLSLPFRPISRIDRNTSGIVMIAKNRYAHQQLAWMSQHHLVGKKYLGLVHGHL 179

Query: 154 DQDKLN-----LLKKGIVIQGICYGDMQ-----VTLDTQKGSNAWVTVGLREGKNREIKK 203
                       L     I    + D Q       +  +    + +   L  G+  +I+ 
Sbjct: 180 KSSAGEIALPLRLAPDSRIVRETHPDGQQSLTLYKVLEEYPYYSLLEFTLVTGRTHQIRA 239

Query: 204 VFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP--HLLEEAQVNLDAPI 261
             +     +               L  G T  ++++ L        H +    + ++AP+
Sbjct: 240 HCQAIGHSLVG-----------DDLYGGQTELIARQALHAFHYSFIHPISGQPIKIEAPL 288

Query: 262 YSS 264
            + 
Sbjct: 289 PAD 291


>gi|224534166|ref|ZP_03674746.1| RNA pseudouridine synthase family protein [Borrelia spielmanii
           A14S]
 gi|224514591|gb|EEF84905.1| RNA pseudouridine synthase family protein [Borrelia spielmanii
           A14S]
          Length = 315

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 85/237 (35%), Gaps = 49/237 (20%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DG 64
           N   +R+  ++ +    S+  + + I +  +++NGI     +  V   D I +      G
Sbjct: 14  NDNGKRLDSILIKILNLSKARIIKHIRKGDIRLNGIKP-HFSYRVCKGDKIYLYKSLAQG 72

Query: 65  VPLRKAERTR------------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           + L   E  +                  L + +K  G++        R+++   + +  S
Sbjct: 73  LNLTINECYKSDLDFQYIRERIIYEDSDLLVLNKQRGILVHGD----RNSLDFLVNAYLS 128

Query: 107 RVI---------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD- 154
           R           +V RLD NT G+++   +   AR L          + Y     G+V  
Sbjct: 129 REDLRSLSFKPSAVHRLDRNTSGIIVFAKNIDTARKLSILFSRGFVTKKYFAILFGEVKS 188

Query: 155 ----QDKL---NLLKKGIVIQGICY--GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               ++ L     L+K  V++G  +     +V           V + ++ G   +I+
Sbjct: 189 TVVYENHLFRNKRLRKTFVLEGKDFINAITKVNPILSSKRATLVEIIIKTGFTHQIR 245


>gi|89075565|ref|ZP_01161970.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
 gi|89048705|gb|EAR54277.1| putative ribosomal large subunit pseudouridine synthase A
           [Photobacterium sp. SKA34]
          Length = 233

 Score = 56.0 bits (134), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/154 (14%), Positives = 59/154 (38%), Gaps = 16/154 (10%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT-NDGGLAR 132
           +   +KP G+++     P+   ++F  +   + +   V RLD+ T GL++L  N      
Sbjct: 26  IIAVNKPAGILSNPGRAPEHHDSIFARVLEKYPKSQIVHRLDMGTSGLIVLALNKKAECH 85

Query: 133 -VLELPSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
              +    +  +VY  R  G + Q+     L L+       ++ +             + 
Sbjct: 86  LKAQFRERETQKVYYARVWGHIKQNTGTVDLPLICDWPNRPRQKVCFDDGKPSVTHYEVL 145

Query: 181 TQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
           ++   +  V +    G++ +++  + +     + 
Sbjct: 146 SRDEKSTLVRLLPVTGRSHQLRVHM-QALGHSIL 178


>gi|323496130|ref|ZP_08101190.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
 gi|323318874|gb|EGA71825.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           sinaloensis DSM 21326]
          Length = 245

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 25/153 (16%), Positives = 55/153 (35%), Gaps = 28/153 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   + + +KP GL++      +   +++  L + +  +  V RLD++T GL+LL     
Sbjct: 19  EDEHILVANKPSGLLSVPGRLAEHHDSLWSRLVAAYPDIQVVHRLDMDTSGLMLLAKHKE 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGI 170
                       L        +VY  R  G   Q           D  N  ++ +     
Sbjct: 79  AERSLKKQFQYRLTH------KVYYARVWGHPAQPQGEVDLPLICDWPNRPRQKVCFVDG 132

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
                   +  ++   + V +  +  G++ +++
Sbjct: 133 KPSTTLYQVAKREEHTSIVRLLPIT-GRSHQLR 164


>gi|170117367|ref|XP_001889871.1| predicted protein [Laccaria bicolor S238N-H82]
 gi|164635211|gb|EDQ99522.1| predicted protein [Laccaria bicolor S238N-H82]
          Length = 478

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/140 (21%), Positives = 48/140 (34%), Gaps = 17/140 (12%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKAERTRLWLYH----------KPI 82
           +      VNG + +     +   D IE  V              LYH          KP 
Sbjct: 58  LESGVTTVNGQIAK-PDTKLRDGDRIENIVHRHEPPVTSTPVKVLYHDVEREFLVVDKPG 116

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +    S    R+T+ + L + F   +     RLD  T GL+++      ARVL     +
Sbjct: 117 SIPVHASGRYYRNTLIEILVNDFGYKKCYPANRLDRLTSGLMIIPLSPDRARVLTDEFTT 176

Query: 139 TQWLRVYRVRFHGQVDQDKL 158
               + Y  R  G+    ++
Sbjct: 177 GTVRKEYVARVRGRFPAQEI 196


>gi|307634844|gb|ADI84260.2| rRNA methyltransferase, YqxC-related, putative [Geobacter
          sulfurreducens KN400]
          Length = 263

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 31/73 (42%), Gaps = 1/73 (1%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M   + +    + +R+ K++   G+  SR     +I   +V VN  L ++A + V     
Sbjct: 1  MTASSTLNTAKSRERLDKLLVDRGLVQSRERARALIMAGQVVVNDHLADKAGLQVPVEAE 60

Query: 60 IEVDGVPLRKAER 72
          I + G  +    R
Sbjct: 61 IRLKGEDIPFVSR 73


>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 = 55.6 bits (133), Expect = 1e-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|295105662|emb|CBL03206.1| Uncharacterized conserved protein, contains S4-like domain
           [Faecalibacterium prausnitzii SL3/3]
          Length = 272

 Score = 55.6 bits (133), Expect = 1e-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|158298572|ref|XP_553504.3| AGAP009693-PA [Anopheles gambiae str. PEST]
 gi|157013948|gb|EAL39149.3| AGAP009693-PA [Anopheles gambiae str. PEST]
          Length = 494

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P+        + + +KP 
Sbjct: 99  ERCIKAGTLTVNYEKVPTDYRLKHNDLLANIVHRHEVPVTSQPITIVHMDDDIVVVNKPA 158

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   +    + ++ RLD  T GLLL       AR +E    +
Sbjct: 159 SIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRN 218

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------ 192
            Q  + Y  R  G+     +   K+ I +     G  +V+   ++ +  +  +G      
Sbjct: 219 RQVQKEYICRVEGEFPDGIIE-CKEPIEVVSYKIGVCKVSPKGKECTTTFQKLGFNGNSS 277

Query: 193 ------LREGKNREIKKVFEFFNWKVNR 214
                 L  G+  +I+   ++  + V  
Sbjct: 278 VVLCKPLT-GRMHQIRVHLQYLGYPVVN 304


>gi|311279889|ref|YP_003942120.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308749084|gb|ADO48836.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 232

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 70/209 (33%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE+        +  +L + +KP GL++ +  +P    +V   L  +F     V R
Sbjct: 12  PCHDEIEI------LWQDAQLVIINKPAGLLSLSGKNPQNLDSVHYRLVKLFPGCALVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  D  +   L    +Q    +VY     G ++++      +G V   I 
Sbjct: 66  LDFGTSGLIVVARDKAVNAALCQQFSQRAVSKVYTALLCGHLEEN------EGTVDAPIA 119

Query: 172 YGDM--------------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVF 205
                                         Q   D ++     V +  + G+  +++   
Sbjct: 120 KDPALFPRMSICATHGKPARSRFQVVERFTQRLEDGRELPLTRVMLTPQTGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +       YG      L  G+ R
Sbjct: 180 QHLGHPILGCD--LYGGL----LPPGTGR 202


>gi|154302617|ref|XP_001551718.1| hypothetical protein BC1G_09885 [Botryotinia fuckeliana B05.10]
 gi|150855374|gb|EDN30566.1| hypothetical protein BC1G_09885 [Botryotinia fuckeliana B05.10]
          Length = 453

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/138 (17%), Positives = 50/138 (36%), Gaps = 15/138 (10%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKPIGLV 85
            +  + VNG  +E  +  + + D I          V  +P+    E   + + +KP G+ 
Sbjct: 87  ERGAIAVNGKPVESISQIIKNGDVISHTLHRHEPPVTALPISIVHEDEDIIVINKPSGVP 146

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLELPSTQ-- 140
              +     ++V + + +            RLD  T G++ +      A  L L  +   
Sbjct: 147 VHPAGRYNYNSVVEIMRAERGHGWNPLPCNRLDRLTSGIMFIGKHAKAAEALSLQISGRT 206

Query: 141 WLRVYRVRFHGQVDQDKL 158
             + Y  R  G+    ++
Sbjct: 207 VRKEYIARVKGKFPDGEV 224


>gi|53713831|ref|YP_099823.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46]
 gi|52216696|dbj|BAD49289.1| RNA pseudouridylate synthase [Bacteroides fragilis YCH46]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/221 (15%), Positives = 78/221 (35%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP 66
            P  +   +A +   ASR +++ +++++ V V+ ++  +    +     + +    +   
Sbjct: 25  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNKKE 84

Query: 67  LRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
            R        E   + +  K  GL++  ++     T    L          +R+  V RL
Sbjct: 85  FRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSGRGNRIYVVHRL 144

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVIQGICY 172
           D +T GL++   D      L          R Y     G++++D  + +   +  + +  
Sbjct: 145 DRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEIEKDS-DTVVSWLTDRTLYV 203

Query: 173 GDMQVTLDTQKGSNAWVTV------GLRE-----GKNREIK 202
                     K    + T+       L E     G+  +I+
Sbjct: 204 SSSSYDDGGSKSITHYRTIKRANGYSLVELRLETGRKNQIR 244


>gi|308178003|ref|YP_003917409.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
 gi|307745466|emb|CBT76438.1| pseudouridylate synthase [Arthrobacter arilaitensis Re117]
          Length = 321

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 77/240 (32%), Gaps = 51/240 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMST 57
           ++    T +R+ K +       R  ++        +++ + +++VNG  ++     + + 
Sbjct: 22  VIDSEHTGRRIEKYL-------RSALKSMPAGQMFKLMRKGQLRVNGKKVQE-GYRLAAN 73

Query: 58  DHIE---VDGVPLRKA------------------ERTRLWLYHKPIGLVTT--HSDPDGR 94
           D I        P R+                   E   + +  KP G+       +P G 
Sbjct: 74  DKITLPAFHAQPTREPRIEVPPALLKRLRNTVVHEDEDVLVIDKPAGIPVHKGTDNPAGV 133

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE----LPSTQWLRVYRVRFH 150
              F  L      +    RLD +T GLL+L     + R L         +  R Y     
Sbjct: 134 IEAFRQLRPELPDLELSHRLDRDTSGLLVLAKTPSILRYLHEMLRDREDEIERHYLALVA 193

Query: 151 GQVDQDK------LNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWVTVGLREGKNREIK 202
           G  ++D       L  L   +V               Q+       + V L  G+  +I+
Sbjct: 194 GSWNEDTAVIHTPLLRLADRMVADPTGQRAETRVWVQQRVGKRATILDVQLMTGRKHQIR 253


>gi|288802331|ref|ZP_06407771.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
 gi|288335298|gb|EFC73733.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           melaninogenica D18]
          Length = 296

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/213 (18%), Positives = 78/213 (36%), Gaps = 31/213 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----------VPL 67
           ++A     S+ +V+  +  + +KVNG  + +    + + D I V             V +
Sbjct: 27  LLANLNE-SKSKVKATLQNRGIKVNGKCVTQFDHPLKAGDKISVSKSKKNDLFRSRYVKI 85

Query: 68  RKAERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLL 122
              +R  + +  K IG+++           TV D+      +      V RLD +T GL+
Sbjct: 86  VYEDRFLVVI-EKNIGILSMAAGHSSLNVKTVLDDYFRKTKQKCTAHVVHRLDRDTSGLM 144

Query: 123 LLTNDGGLARVLELPSTQW--LRVYRVRFHGQV--DQDKLNLLKKGI---------VIQG 169
           +   D    ++LE         R Y     G++  D+  +    K           V  G
Sbjct: 145 IYAKDIQTEQLLEHDWHNIVYDRRYVAVVSGEMEHDEGTIANWLKDNKSYVTYSSPVDNG 204

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             Y      +  +  +++ V   L  G+  +I+
Sbjct: 205 GKYAVTHFHVLDRTVAHSLVEYQLETGRKNQIR 237


>gi|52144044|ref|YP_082785.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           E33L]
 gi|51977513|gb|AAU19063.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           E33L]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGGTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|308187414|ref|YP_003931545.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
 gi|308057924|gb|ADO10096.1| ribosomal large subunit pseudouridine synthase A [Pantoea vagans
           C9-1]
          Length = 243

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/186 (17%), Positives = 61/186 (32%), Gaps = 37/186 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L + +KP GL++ +  +P    +V   L   F     V RLD  T GL+++  +  
Sbjct: 33  QDDHLLVINKPGGLLSLSGKNPQNLDSVHHRLVKRFPGCTLVHRLDFGTSGLMVVARNKA 92

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQ- 182
           +   L    +Q    + Y+    G +  D      +G+    + +        V    Q 
Sbjct: 93  INAALCQQFSQRTVSKTYQALLCGHLADD------EGVIDAAIAKDPALFPRMVICAAQG 146

Query: 183 KGSNAWVTVG-------------------LR-E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V                    L  E G+  +++   +     +       YG
Sbjct: 147 KPARSRYRVTERSFYRRKEGKELPVTRVELTPETGRTHQLRIHCQQLGHPILGCD--LYG 204

Query: 222 PFQLGT 227
              L  
Sbjct: 205 GLVLPG 210


>gi|300173026|ref|YP_003772192.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299887405|emb|CBL91373.1| ribosomal large subunit pseudouridine synthase D [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 300

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 57/183 (31%), Gaps = 27/183 (14%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
            S D +  D  PL        WL   KP GL T     D   T+ + +      +     
Sbjct: 66  KSNDLVVADYNPLTIIFENEHWLVVDKPYGLTTVPGHADRLHTLVNQVKGHLEEINAEDL 125

Query: 109 --ISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD------- 156
               V RLD +T G++LL      A  +    L      + Y     G + +D       
Sbjct: 126 VPHVVTRLDRDTSGIVLLAKH-RFAHAVMDQQLQEHTVEKFYVAYVSGILSEDHGDIHAP 184

Query: 157 ----KLNLLKKGIVIQGICYGD----MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                 + +K+ +   G          +   D        V V L  G+  +I+  F+  
Sbjct: 185 IGRMDDDFIKREVRDDGKPSRTEYWVERRYDDGGVQPMTRVKVQLHTGRTHQIRVHFQNI 244

Query: 209 NWK 211
              
Sbjct: 245 GHP 247


>gi|308235820|ref|ZP_07666557.1| pseudouridine synthase, RluA family protein [Gardnerella vaginalis
           ATCC 14018]
 gi|311114402|ref|YP_003985623.1| ribosomal large subunit pseudouridine synthase D [Gardnerella
           vaginalis ATCC 14019]
 gi|310945896|gb|ADP38600.1| ribosomal large subunit pseudouridine synthase D [Gardnerella
           vaginalis ATCC 14019]
          Length = 310

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 88/254 (34%), Gaps = 43/254 (16%)

Query: 1   MKD-KNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M D +  V   F   R    +++    SR     +I   + K+     ++++  +   D 
Sbjct: 1   MSDIRFTVTSQFAGCRFDVCLSKLMGVSRANAISLIDSGKAKILDRKSQKSST-LQDGDV 59

Query: 60  I-----EVDGVPLRKAERTRL----WLYH--------KPIGLVTTHSDPDGRSTVFDNLP 102
           I     EVD    +   ++ +     +Y+        KP+G+    +      TV + L 
Sbjct: 60  IVINQEEVDDQKEKSTSKSTICNIPIVYNDEDIVVVDKPVGVAAHSAKGWDGPTVPECLE 119

Query: 103 S----------IFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFH 150
           +            SR   V RLD+ T GL+L+  T+        +  +    ++Y     
Sbjct: 120 ASGVEIKTTVCDESRKGIVSRLDVGTSGLMLVCKTDFAYEEMKKQFANHSVKKIYHALVQ 179

Query: 151 G-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G            + + K++  +  I   G         ++  KG+   V V L  G+  
Sbjct: 180 GNLKQNKATIDAPIGRAKVSDFRFTITKSGKPAITHWDVIERFKGAT-LVKVNLETGRTH 238

Query: 200 EIKKVFEFFNWKVN 213
           +I+  F      V 
Sbjct: 239 QIRVHFSSIGHPVV 252


>gi|260587511|ref|ZP_05853424.1| pseudouridine synthase, RluA family [Blautia hansenii DSM 20583]
 gi|260541776|gb|EEX22345.1| pseudouridine synthase, RluA family [Blautia hansenii DSM 20583]
          Length = 244

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 23/163 (14%), Positives = 47/163 (28%), Gaps = 22/163 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS-----DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           E   + +  KP G           D +     +         V  + RLD   +G+L+  
Sbjct: 33  EDKYILVCQKPAGFPVQSKRLGTLDMECALRNYLAKKGQEPYVAVIHRLDQPVQGVLVFA 92

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI------------- 170
            D   A  L       ++ + Y     G     K   L   +   G              
Sbjct: 93  KDKESAAKLSKQMQQGKFEKTYLAYTQGH-TDKKQETLIDELEKDGRTNTSKVVAKKTAN 151

Query: 171 -CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               ++   +  +    + + V L+ G++ +I+         +
Sbjct: 152 SKRAELSYKVLKETEEGSLLEVSLKTGRHHQIRVQLAHAGLPI 194


>gi|225682103|gb|EEH20387.1| DRAP deaminase [Paracoccidioides brasiliensis Pb03]
          Length = 525

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/163 (16%), Positives = 53/163 (32%), Gaps = 24/163 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ I    V +NG  +      + + D I          V   P+    E   + +  KP
Sbjct: 81  KKAIEDGAVCINGKAVT-IDTKIQNGDVISHTLHRHEPPVTSQPIGVIHEDNDMIVIDKP 139

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     ++V + + +            RLD  T G++ +      A  +  +L
Sbjct: 140 AGVPVHPAGRYNYNSVLEIMKAERGHGWVPYPCNRLDRLTSGVMFVGKHPKGAEQIGEKL 199

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
            S    + Y  R  G+           G+V+       +   L
Sbjct: 200 RSRTVRKEYVARVKGKFPD--------GVVLCDQPMLKISPIL 234


>gi|24214190|ref|NP_711671.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
 gi|24195091|gb|AAN48689.1| ribosomal large subunit pseudouridine synthase [Leptospira
           interrogans serovar Lai str. 56601]
          Length = 365

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/167 (16%), Positives = 64/167 (38%), Gaps = 20/167 (11%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++ +  +  R+   +++     SR   ++ I + R+ ++   ++   V++   D I    
Sbjct: 18  LISKEESGTRLDHFLSKKFTYHSRTTWQKEITEGRILISSKTVK-PGVSLKEGDLISYH- 75

Query: 65  VPLRKAERTR---LWLYH---------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVIS 110
            P++K E        + +         KP  L    +    +  +   L     F  + +
Sbjct: 76  -PIQKEEPPVRNDYKILYEDEFFVAVDKPGDLPIHPAGIYRKGNLLTFLKESGKFKDLFT 134

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRFHGQVDQ 155
           V RLD  T G++L   +  +A +L    +     + Y  + HG   +
Sbjct: 135 VHRLDRETSGVILFAKNSEIASILSKSFSLGNIQKYYITKVHGNFPK 181


>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 = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+A SR     MI + RV V+G  +E+A   V     + + G  +  
Sbjct: 1  MAKERLDVLLVERGLAASRERARTMIMEGRVLVDGKKVEKAGTGVKPEAELRLLGEEMPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|171911749|ref|ZP_02927219.1| hemolysin A [Verrucomicrobium spinosum DSM 4136]
          Length = 245

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+  ++   G+  SR + +R+I    V VN + + +A   V     I V
Sbjct: 1  MAKQRLDHLLVARGLCASREQGKRLILAGDVLVNDVPVTKAGQLVPEDSVIRV 53


>gi|89095308|ref|ZP_01168227.1| putative pseudouridine synthase Rlu family protein [Oceanospirillum
           sp. MED92]
 gi|89080427|gb|EAR59680.1| putative pseudouridine synthase Rlu family protein [Oceanospirillum
           sp. MED92]
          Length = 250

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/174 (16%), Positives = 57/174 (32%), Gaps = 36/174 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTN 126
           E   L   +KP GL+   S   P G   +   L   F       + RLD  T G++L   
Sbjct: 9   EDDHLIAINKPSGLLVHPSWVAPRGTPNLASMLKVYFEGGSPYTIHRLDRPTSGVILFGK 68

Query: 127 DGGLARV--LELPSTQWLRVYRVRFHG-QVDQDKLN-LLKKGIVIQGI------------ 170
              +A+   L        + Y     G   + D ++  LK+   +  I            
Sbjct: 69  SKEVAQKMNLIFAERDVSKTYLCMCRGYTPEADTIDYALKE--QLDKIADKHANQDKEAQ 126

Query: 171 -------CYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKV 212
                    G +++ +   +   +  ++   E     G+  +I++  +     +
Sbjct: 127 EAVSHYRRLGTVELDIPIGRYDKSRYSLV--EVKPETGRKHQIRRHMKHIFHPI 178


>gi|331004271|ref|ZP_08327749.1| hypothetical protein HMPREF0491_02611 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411436|gb|EGG90848.1| hypothetical protein HMPREF0491_02611 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 338

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 86/256 (33%), Gaps = 65/256 (25%)

Query: 6   IVQENFTPQRVSKVI------ARAGIASRREVERMIAQQRVKVNGILL------------ 47
           IV +N   QR+ +V+      A AG      + +M+ ++ + +N                
Sbjct: 5   IVGKNEDGQRLERVLEKIFVNANAGF-----IFKMLRKKNITLNDKKADGKERLVAGSSI 59

Query: 48  ----------ERAAVNVMSTDHIE---VDGVPLRK------AERTRLWLYHKPIGLVTTH 88
                     + +   V +T  ++    D   + K       E     + +KP G+++  
Sbjct: 60  KLWFSDESFEKLSGKKVENT-KVKNNCTDKKNVEKFNSYIVYEDDNTIILNKPEGILSQK 118

Query: 89  S---DPDGRSTVFDNLPSIFSRVI-----SVGRLDINTEGLLLL--TNDGGLARVLELPS 138
           S   D      + + L    S +         RLD NT GLL+   + +G       + +
Sbjct: 119 SNIKDASINDMLLEYLDFDDSVLNTFKPSICNRLDRNTTGLLVCGKSLEGLRVNNELIKT 178

Query: 139 TQWLRVYRVRFHGQVDQDKL-------NLLKKGIVIQGICYGDM-----QVTLDTQKGSN 186
               + Y     G + +  L       +     ++I+   +        +  +     +N
Sbjct: 179 KAVDKFYLALVKGYIKEKCLISGWLYKDESSNKVIIKNKAFEAADFIQTEYEVLDYFENN 238

Query: 187 AWVTVGLREGKNREIK 202
             + V L  GK  +I+
Sbjct: 239 TLLLVKLITGKTHQIR 254


>gi|331083782|ref|ZP_08332891.1| hypothetical protein HMPREF0992_01815 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330403207|gb|EGG82767.1| hypothetical protein HMPREF0992_01815 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 337

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 55/360 (15%), Positives = 113/360 (31%), Gaps = 87/360 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +V+E  + QR+ K + +      +E       +M+ ++ + +NG         +   D I
Sbjct: 5   VVKEIESGQRLDKFLGKYL----KEAPKSFLYKMLRKKNITLNGKKAT-GNEKLQPNDEI 59

Query: 61  EV---DGVPLRK---------------AERTRLWLYHKPIGLVTTHSDPD-----GRSTV 97
           ++   D    +                 E   +   +KP+G+++  ++ +        T 
Sbjct: 60  KLFLSDDTLEKFCGEEKSSSRTELDIVYENNHVLFVNKPVGMLSQKAEKEDVSLVEYITG 119

Query: 98  FDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGLARVLELPST-----QWLRVY 145
           +       +       R     RLD NT G++     G   + L+  S         + Y
Sbjct: 120 YLLEEKFLTKEDLRTFRPGVCNRLDRNTSGIVAA---GKTVQGLQEMSQWFKERNLHKYY 176

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----------------NAWV 189
                G+V++       KG + +      + V  + ++GS                +  +
Sbjct: 177 LTLVKGKVER---PAHVKGYLWKDEKKNKVAVFPEKREGSLPIETKYEPLGISKNGDTLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLG 246
            V L  G++ +I+         V                  G  +  SK+     R++ G
Sbjct: 234 KVELLTGRSHQIRSHLAGLGHPVI-----------------GDWKYGSKEKNENFRKKYG 276

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                     L  P             I ++VP+ F +  K        S++ K     H
Sbjct: 277 IEFQLLHAWKLSFPKTEGILKELSLKTITADVPEKFQKALKGEGLLEFTSEKNKGDVKKH 336


>gi|295661807|ref|XP_002791458.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb01]
 gi|226280015|gb|EEH35581.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb01]
          Length = 525

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/163 (16%), Positives = 53/163 (32%), Gaps = 24/163 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           ++ I    V +NG  +      + + D I          V   P+    E   + +  KP
Sbjct: 81  KKAIEDGAVCINGKAVT-IDTKIQNGDVISHTLHRHEPPVTSQPIGLIHEDNDMIVIDKP 139

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     ++V + + +            RLD  T G++ +      A  +  +L
Sbjct: 140 AGVPVHPAGRYNYNSVLEIMKAERGHGWVPYPCNRLDRLTSGVMFIGKHPRGAEQIGEKL 199

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
            S    + Y  R  G+           G+V+       +   L
Sbjct: 200 RSRTVRKEYVARVKGKFPD--------GVVLCDQPMLKISPIL 234


>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 = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+ K++A  G+A SR   + +I   RV VN   + +    V     + + G  LR   R
Sbjct: 4  RLDKLVAEQGLAASRERAQALILAGRVLVNEQKITKPGHAVDEAATLRLLGEDLRYVSR 62


>gi|296111875|ref|YP_003622257.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
 gi|295833407|gb|ADG41288.1| pseudouridylate synthase [Leuconostoc kimchii IMSNU 11154]
          Length = 300

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 57/182 (31%), Gaps = 27/182 (14%)

Query: 56  STDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---- 110
           S D +  D  PL        WL   KP G+ T     D   T+ + +        +    
Sbjct: 67  SNDLVVPDYKPLDIIFENEHWLVVDKPYGITTVPGHADRLHTLVNQVKGHLEETHAEDLV 126

Query: 111 ---VGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQD-------- 156
              V RLD +T G++LL      A  +    L      + Y     G +  D        
Sbjct: 127 PHVVTRLDRDTSGIVLLAKH-RFAHAVMDQQLQEHTVEKFYLAYTSGILPDDHGDIQAPI 185

Query: 157 ---KLNLLKKGIVIQGICYGD----MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
                + +K+ +   G          +   +  +     V V L  G+  +I+  F+   
Sbjct: 186 GRVDGDFIKREVRDDGKPSRTEYWVERRYDENGQQPMTRVKVQLHTGRTHQIRVHFQNIG 245

Query: 210 WK 211
             
Sbjct: 246 HP 247


>gi|196004434|ref|XP_002112084.1| hypothetical protein TRIADDRAFT_1807 [Trichoplax adhaerens]
 gi|190585983|gb|EDV26051.1| hypothetical protein TRIADDRAFT_1807 [Trichoplax adhaerens]
          Length = 418

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 66/197 (33%), Gaps = 35/197 (17%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------LWLYHKP 81
           I   ++ VN  +   A   V   D I      + + E                + + +KP
Sbjct: 60  IQNGKITVNNKIP-SANTIVRDNDVIR---NTVHRHEPPVTANPIQIIKMDDDIVVINKP 115

Query: 82  IGL-VTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             + V         S VF          + ++ RLD  T G+L+       A+ LE    
Sbjct: 116 ASIPVHPCGRYRHNSVVFMLARDYGLQNLHTIHRLDRLTSGILIFARTLQKAQELEKQVR 175

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-----------KGSN 186
             Q  + Y  R  G+   + ++  K+ I +     G  +V+   +            G  
Sbjct: 176 DRQIEKQYVCRVDGEFPTETID-CKEPIDVVSHKLGVCRVSPKGKSCQTIFQRLSYNGKT 234

Query: 187 AWVT-VGLREGKNREIK 202
           + V  + L  G+  +I+
Sbjct: 235 SLVKCIPLT-GRMHQIR 250


>gi|317472795|ref|ZP_07932106.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
 gi|316899714|gb|EFV21717.1| RluA family pseudouridine synthase [Anaerostipes sp. 3_2_56FAA]
          Length = 305

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 80/249 (32%), Gaps = 41/249 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +  V +  T  R+   +A R    +R  ++++     V V+    +++   V   + +
Sbjct: 4   ERQFTVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDA-EKKSNYKVREGERV 62

Query: 61  --------EVDGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                   E+   P +       E   + L +KP  +V   +      T+ + L      
Sbjct: 63  ILKVPKPTELSIKPEKMDLDIVYEDRDIILINKPKNMVVHPAPGHYEGTLVNGLMEHCRD 122

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVD 154
                    R   V R+D +T G+L++  +  +A       L      R Y    +  + 
Sbjct: 123 ELSGINGVLRPGIVHRIDKDTTGILIVCKN-DMAHQCLAEQLKDHTITRRYHAIVYHNIK 181

Query: 155 QDKL---------NLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++              +K + I    G         L+  K    ++   L  G+  +I+
Sbjct: 182 EESGTVDAPIARSRKERKKMAIDREAGRRAVTHYRVLERLKEGFTYIECSLETGRTHQIR 241

Query: 203 KVFEFFNWK 211
                    
Sbjct: 242 VHMASIGHP 250


>gi|313677829|ref|YP_004055825.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
 gi|312944527|gb|ADR23717.1| pseudouridine synthase [Marivirga tractuosa DSM 4126]
          Length = 300

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/215 (14%), Positives = 68/215 (31%), Gaps = 33/215 (15%)

Query: 32  ERMIAQ----QRVKVNGILLERAAVNVMSTDHIEVD----GVPLRKA------ERTRLWL 77
           + ++ Q     ++++NG ++ +    +   D I+++       ++        E   L  
Sbjct: 36  KALLKQVMGGGQIRINGDVITQFNHPLKKGDEIQINWAKPSKKVKLQKLNIIYEDQHLIA 95

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS------VGRLDINTEGLLLLTNDGGLA 131
             K  GL++  S  +        L      +        + RL+    G+LL      + 
Sbjct: 96  IEKEAGLLSVASLKEKTKNAVQILKEHMEAIDPRNKVYIIHRLEREASGVLLFAKSKEVQ 155

Query: 132 RVLELP--STQWLRVYRVRFHGQVDQD---KLNLLK----KGIVIQGICYGDMQV----T 178
             L+         R Y     G++ +      N L+      + I        +      
Sbjct: 156 EQLQNHWEDYIIDRKYVAVVEGKIKESSHTLRNYLRSNKHNQVFIVNTAENATEAITHFK 215

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           L  Q  + + +   L  G   +I+     F + V 
Sbjct: 216 LLKQSNAYSMLEFKLETGFKNQIRVQMAHFGFPVT 250


>gi|226289283|gb|EEH44795.1| RNA pseudouridylate synthase domain-containing protein
           [Paracoccidioides brasiliensis Pb18]
          Length = 525

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/163 (16%), Positives = 53/163 (32%), Gaps = 24/163 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ I    V +NG  +      + + D I          V   P+    E   + +  KP
Sbjct: 81  KKAIEDGAVCINGKAVT-IDTKIQNGDVISHTLHRHEPPVTSQPIGVIHEDNDMIVIDKP 139

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     ++V + + +            RLD  T G++ +      A  +  +L
Sbjct: 140 AGVPVHPAGRYNYNSVLEIMKAERGHGWVPYPCNRLDRLTSGVMFVGKHPKGAEQIGEKL 199

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
            S    + Y  R  G+           G+V+       +   L
Sbjct: 200 RSRTVRKEYVARVKGKFPD--------GVVLCDQPMLKISPIL 234


>gi|229029062|ref|ZP_04185161.1| Pseudouridine synthase [Bacillus cereus AH1271]
 gi|228732342|gb|EEL83225.1| Pseudouridine synthase [Bacillus cereus AH1271]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 92/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFVEEEYDVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVD-----------QDKLNLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V            +D+ +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKGKQGTVDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+    +              P     L  G T+ ++ + L    
Sbjct: 225 VTFVTLQLETGRTHQIRVHMSYHGN-----------PLVGDVLYGGQTKHMTGQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   + T
Sbjct: 274 IHFLHPITKEEIEVDVPFPTKLNNT 298


>gi|256830871|ref|YP_003159599.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
 gi|256580047|gb|ACU91183.1| pseudouridine synthase [Desulfomicrobium baculatum DSM 4028]
          Length = 306

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/199 (17%), Positives = 67/199 (33%), Gaps = 31/199 (15%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT--------------RLWLY 78
           R++   +V+++G   +     V++   + V  V +++ E++               + + 
Sbjct: 40  RLVRTGQVRIDGRRCK-PFDRVLTGQTVRVPPVTVQRKEKSLRDLPGLRGVFENDEMLVI 98

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVL 134
            K  G +  H       +V D L + F+      I V RLD +T GLLL        R +
Sbjct: 99  DKLAG-LPVHGGTGWTDSVHDRLKACFAGQAFVPIPVHRLDRDTSGLLLCAKTHDFLRAM 157

Query: 135 ELPSTQWLRVYRVRFHGQVDQD-------KLNLLKKG----IVIQGICYGDMQVTLDTQK 183
                   + Y     G            +L   + G    +V          V      
Sbjct: 158 HASWPTLTKGYLCWVEGAWAAAGWRTVVSELAKAQTGSGEQVVSGQGKRAVSHVHPVLVT 217

Query: 184 GSNAWVTVGLREGKNREIK 202
              + + V L  G+  +I+
Sbjct: 218 AGKSLLLVVLGTGRTHQIR 236


>gi|324119833|gb|EGC13712.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 260

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +    V +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFVREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|229160344|ref|ZP_04288342.1| Pseudouridine synthase [Bacillus cereus R309803]
 gi|228623068|gb|EEK79896.1| Pseudouridine synthase [Bacillus cereus R309803]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 91/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNEPLKEGDKLQVHMFMEEEYGVDPEYGELHVIFEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K  
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDEAITYYKVEKYFKKQD 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+      +   N        P     L  G T+ +S + L    
Sbjct: 225 ITFVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSAQALHAMR 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   + T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNNT 298


>gi|304320252|ref|YP_003853895.1| putative ribosomal large subunit pseudouridine synthase protein
           [Parvularcula bermudensis HTCC2503]
 gi|303299154|gb|ADM08753.1| putative ribosomal large subunit pseudouridine synthase protein
           [Parvularcula bermudensis HTCC2503]
          Length = 338

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/293 (15%), Positives = 84/293 (28%), Gaps = 70/293 (23%)

Query: 1   MKDKN----IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVM 55
           M D       V E     R+ K IA    A SR  ++ +I    +  +          + 
Sbjct: 1   MSDTEPLSFTVAEADVGARLDKWIADQTDAYSRARIKALIEGGALTKDAAPFTDPKWKLR 60

Query: 56  STDHIEV------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             +   +            + +PL    E   L + +KP GLV   +  +   T+ + L 
Sbjct: 61  QGEVFTLVPPPPEDPTPKPEDIPLTVLFEDGDLIVINKPAGLVVHPAAGNWTGTLVNALL 120

Query: 103 SIFS----------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR---- 146
                         R   V RLD +T G++++  +    + L     +    R Y     
Sbjct: 121 HHCGDTLSGIGGVIRPGIVHRLDKDTSGVMVIAKNDHAHQGLSALFAAHDIDRAYLALCE 180

Query: 147 --------------------------VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
                                     V       ++ +    +   +     G  ++  D
Sbjct: 181 GSPRPTSGTITWPLARSSGDRKKMTVVGVDRPEGKEAITHFAR---LDAYGIGRAKLPGD 237

Query: 181 TQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVNRLIRISYGPFQLGTLLAGS 232
                 + V   L  G+  +I+  +       +  L    YG   L  L  G 
Sbjct: 238 ALA---SLVECRLETGRTHQIRVHM-SHIGHPL--LGDPVYGRSGLAGLKPGD 284


>gi|195471882|ref|XP_002088231.1| GE18464 [Drosophila yakuba]
 gi|194174332|gb|EDW87943.1| GE18464 [Drosophila yakuba]
          Length = 939

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 73/212 (34%), Gaps = 35/212 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 575 ERSLEAGKLTVNYEKVPK-DYKIKHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKP 633

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARV-----L 134
             +          +TV   L        + ++ RLD  T GLLL    G  A       L
Sbjct: 634 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLF---GRTAERARELEL 690

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-- 192
           ++ + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G  
Sbjct: 691 QIRTRQVQKEYVCRVEGRFPDGTVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEV 749

Query: 193 ----------LREGKNREIKKVFEFFNWKVNR 214
                     L  G+  +I+   ++  + ++ 
Sbjct: 750 GSDSIVLCKPLT-GRMHQIRVHLQYLGYPISN 780


>gi|184157114|ref|YP_001845453.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|183208708|gb|ACC56106.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
          Length = 350

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 94/256 (36%), Gaps = 50/256 (19%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           + E++  QR+ +V A      SR ++++ + +  + VNG +++         + + ++  
Sbjct: 43  LDESYLGQRIDQVAAMLWSEFSREKLKQWMKEGHLLVNGNIVK-PKYRCEGNETLTLNVE 101

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFS 106
                      +PL    E   + + +KP+G+V      +   T+ + L       +  S
Sbjct: 102 LEAQTNSQPENIPLDIVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYHSPKSAELS 161

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           R   V R+D +T GLL++ N+      L   L      R+Y +  +G +       +  G
Sbjct: 162 RAGLVHRIDKDTSGLLVVANNLEAQFSLSKQLGDKSVYRIYDLVTYGNI-------IAGG 214

Query: 165 IVIQGICYGDMQ----VTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFF 208
            + + I    +       L   + +     V             L  G+  +I+  F + 
Sbjct: 215 TIDEPIKRHPVDRVKMAILPGGRDAVTHYNVKERFRDFTRVQAQLETGRTHQIRVHFSYI 274

Query: 209 NWKV----NRLIRISY 220
              +      + R+  
Sbjct: 275 GHGLVGDQVYMNRVRI 290


>gi|324999316|ref|ZP_08120428.1| ribosomal large subunit pseudouridine synthase [Pseudonocardia sp.
           P1]
          Length = 310

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 62/177 (35%), Gaps = 29/177 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNG-----------------ILLER 49
           V +     R+   ++R    SR  V  +  + R++V+G                  L + 
Sbjct: 9   VPDGLDGMRIDAGLSRLLGLSRTVVAGLAEEGRIQVDGRDAGKSDRLPGGSWLEVELPDA 68

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
           AA  V+      V G+ +   +   + +  KP+G+    S      TV   L ++  R+ 
Sbjct: 69  AAPAVIEGPAEVVAGLSVLHDDEDIVVV-DKPVGVAAHPSPGWTGPTVTGGLAALGYRLS 127

Query: 110 ---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
                     V RLD+ T G++++         L+    +    + Y     G  D 
Sbjct: 128 TSGAAERQGIVHRLDVGTTGVMVVATSEHAYTALKRAFKERTVEKRYHAVVQGHPDP 184


>gi|162454763|ref|YP_001617130.1| hypothetical protein sce6481 [Sorangium cellulosum 'So ce 56']
 gi|161165345|emb|CAN96650.1| hypothetical protein predicted by Glimmer/Critica [Sorangium
           cellulosum 'So ce 56']
          Length = 368

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/153 (24%), Positives = 61/153 (39%), Gaps = 34/153 (22%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH-- 59
           K  + E     R+ K++ +   G+  R   +R+ ++ RV+V G+    A       D   
Sbjct: 56  KITITELDAGTRLDKLLVQLLPGLG-RAGAKRLFSEGRVRVLGVGKSGAGRRASKGDVAA 114

Query: 60  ----IEVDGVPLRKA---------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
               +EVD  P   +               ER  L + +KP G+ T    P  R TV + 
Sbjct: 115 AGEVLEVDVEPTEASGAATPDPSAPLDVVLERDDLVVVNKPAGVPTAPLHPGERGTVANA 174

Query: 101 LPSIFSRVISVG----------RLDINTEGLLL 123
           L + +  +  +G          RLD +T GL+L
Sbjct: 175 LVARYPEMAGIGFSPREPGLCHRLDTDTSGLVL 207


>gi|119511719|ref|ZP_01630823.1| Hemolysin A [Nodularia spumigena CCY9414]
 gi|119463628|gb|EAW44561.1| Hemolysin A [Nodularia spumigena CCY9414]
          Length = 270

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+  ++    + S R   +R+I    V VN  ++++A   V +   I+V
Sbjct: 1  MVKQRLDTLLVDLNLCSSRALAQRLIQAGEVTVNQQVVDKAGTEVDTAAQIKV 53


>gi|108800058|ref|YP_640255.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           MCS]
 gi|119869184|ref|YP_939136.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           KMS]
 gi|108770477|gb|ABG09199.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           MCS]
 gi|119695273|gb|ABL92346.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           KMS]
          Length = 304

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 77/243 (31%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---------AAVNVMS- 56
           V E     RV   ++R    SR     +     V ++G    +           V +   
Sbjct: 3   VPEGLGGMRVDAGLSRLLGLSRTAAAAIAEDGGVDIDGAPAGKSDRLTAGAWLEVRLPEA 62

Query: 57  -----TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   +E++G+ +  ++   +    KP G+    +      TV   L          
Sbjct: 63  PPPVENTPVEIEGMAVLYSDDD-IVAVDKPPGVAAHATVGWHGPTVLGGLAAAGFRISTS 121

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQD--KL 158
            I  R   V RLD+ T G++++        VL+    Q    + Y     G  D     +
Sbjct: 122 GIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHPDPSSGTI 181

Query: 159 NL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
           +           K  +   G        TL+  + + + + + L  G+  +I+  F   +
Sbjct: 182 DAPIGRHRGHDWKFAVTEGGRHSVTHYDTLEAFQAA-SLLDIELETGRTHQIRVHFAALH 240

Query: 210 WKV 212
              
Sbjct: 241 HPC 243


>gi|289674871|ref|ZP_06495761.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 256

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/184 (21%), Positives = 67/184 (36%), Gaps = 25/184 (13%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTT----HSDPDGRSTVFDNLPSIF--SRVISV 111
             IE+D       E  ++ + +KP GLV      H+D    + +  ++P I    R   V
Sbjct: 15  QDIELD----IIYEDDQILVINKPAGLVVHPAAGHADGTLLNALLHHVPDIINVPRAGIV 70

Query: 112 GRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---------KLNL 160
            RLD +T GL+++  T       V +L S    R+Y     G V                
Sbjct: 71  HRLDKDTTGLMVVAKTIQAQTQLVTQLQSRSVSRIYECIVIGVVTAGGKIDAPIGRHGQQ 130

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN----RLI 216
            ++  V++G         +  +  S+  V V L  G+  +I+      N+ +        
Sbjct: 131 RQRMAVMEGGKQAVSHYRVLERFRSHTHVRVKLETGRTHQIRVHMAHINYPLVGDPAYGG 190

Query: 217 RISY 220
           R   
Sbjct: 191 RFRI 194


>gi|302346727|ref|YP_003815025.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
 gi|302151131|gb|ADK97392.1| pseudouridine synthase, RluA family [Prevotella melaninogenica ATCC
           25845]
          Length = 296

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/213 (18%), Positives = 78/213 (36%), Gaps = 31/213 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-----------VPL 67
           ++A     S+ +V+  +  + +KVNG  + +    + + D I V             V +
Sbjct: 27  LLANLNE-SKSKVKATLQNRGIKVNGKCVTQFDHPLKAGDKISVSKSKKNDLFRSRYVKI 85

Query: 68  RKAERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLL 122
              +R  + +  K IG+++           TV D+      +      V RLD +T GL+
Sbjct: 86  VYEDRFLVVI-EKNIGILSMAAGHSSLNVKTVLDDYFRKTKQKCTAHVVHRLDRDTSGLM 144

Query: 123 LLTNDGGLARVLELPSTQW--LRVYRVRFHGQV--DQDKLNLLKKGI---------VIQG 169
           +   D    ++LE         R Y     G++  D+  +    K           V  G
Sbjct: 145 IYAKDIQTEQLLEHDWHNIVYDRRYVAVVSGEMEHDEGTIANWLKDNKSYVTYSSPVDNG 204

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             Y      +  +  +++ V   L  G+  +I+
Sbjct: 205 GKYAVTHFHVLDRTVAHSLVEYQLETGRKNQIR 237


>gi|257056703|ref|YP_003134535.1| ribosomal large subunit pseudouridine synthase D [Saccharomonospora
           viridis DSM 43017]
 gi|256586575|gb|ACU97708.1| ribosomal large subunit pseudouridine synthase D [Saccharomonospora
           viridis DSM 43017]
          Length = 308

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/176 (18%), Positives = 60/176 (34%), Gaps = 29/176 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE----- 61
           V +     RV   +A+    SR  V  + A   V ++G +  ++   + + D +E     
Sbjct: 8   VPDGLDGMRVDVGLAKLLGLSRTVVAELAASGDVLIDGKVASKSD-RLTAGDLLEVTLPE 66

Query: 62  -----------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                      V+G+ +   +   + +  KP+G+    S      TV   L         
Sbjct: 67  PDTPAEVSAEPVEGLRILHEDDDIVVV-DKPVGVAVHPSPGWTGPTVVGGLAAAGLRIST 125

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ 155
                R   V RLD  T G++++        VL+    +    + Y     G  D 
Sbjct: 126 SGAAERQGVVHRLDAGTTGVMVVAKSEHAYSVLKRAFKERTVSKGYHALVQGHPDP 181


>gi|296133201|ref|YP_003640448.1| hemolysin A [Thermincola sp. JR]
 gi|296031779|gb|ADG82547.1| hemolysin A [Thermincola potens JR]
          Length = 271

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
              R+  ++   G+  SR + +  I    V V+G  +++A   V  +  IEV G P+  
Sbjct: 1  MEKMRLDMLLVEKGLFPSREKAKSAIMAGLVFVDGQRVDKAGTTVSVSADIEVQGNPIPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|308806025|ref|XP_003080324.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
 gi|116058784|emb|CAL54491.1| RNA pseudouridylate synthases (ISS) [Ostreococcus tauri]
          Length = 434

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 27/152 (17%), Positives = 48/152 (31%), Gaps = 27/152 (17%)

Query: 80  KPIGLVTTHSDPDGRSTVFD------------NLPSIFSRVISVGRLDINTEGLLLLTND 127
           KP G++T  ++    +++ D            +L     R   V RLD  T G++LL   
Sbjct: 216 KPAGVLTHPAEGGAATSLMDAALARFGDTGLSDLNGSDKR-GIVSRLDKPTSGVILLARH 274

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                 L       +  + Y V   G    +      +G V   I            +  
Sbjct: 275 NAAHAKLVTDFYQRRVSKTYIVLVDGAPTDE------RGTVTAPIDDRPATSEYKVLERF 328

Query: 186 NA------WVTVGLREGKNREIKKVFEFFNWK 211
           N+       V V  + G+  +I++        
Sbjct: 329 NSASCSYALVRVKPKSGRKHQIRRHMAMIGCP 360


>gi|16803009|ref|NP_464494.1| hypothetical protein lmo0969 [Listeria monocytogenes EGD-e]
 gi|224502716|ref|ZP_03671023.1| hypothetical protein LmonFR_09374 [Listeria monocytogenes FSL
           R2-561]
 gi|254827914|ref|ZP_05232601.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
 gi|16410371|emb|CAC99047.1| lmo0969 [Listeria monocytogenes EGD-e]
 gi|258600295|gb|EEW13620.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL N3-165]
          Length = 296

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 87/264 (32%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTNLDIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFISGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEEYMAFDLPLPAD 287


>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 = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/255 (14%), Positives = 85/255 (33%), Gaps = 64/255 (25%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           ++ IV       R+ +        +   G      +++++   +++++G   + A   V 
Sbjct: 5   EQKIVDTGEAGMRLDRWFKVHYPGL---GFG---HLQKLLRSGQIRIDGSRAK-ADTRVQ 57

Query: 56  STDHIEV----------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSD 90
           +   + +                      DG  L +    E  ++++++KP GL      
Sbjct: 58  AGQTVRIPPLGVDEKATGPVTARTIRSQQDGDVLSQMLLYEDPKVYVFNKPAGLAVQGGS 117

Query: 91  PDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY 145
              R            +      V R+D +T G+L++    G A+ L          + Y
Sbjct: 118 GVTRHIDGMLEAWRNKKGEKPRLVHRIDRDTSGVLVVARTRGAAQALTAAFRERDTKKTY 177

Query: 146 RVRFHGQV--DQDKL------------NLLKKGIVIQGICYGDMQV---TLDTQKGSN-A 187
                G     +DK+            + ++  +   G    D  V    +  + G+N  
Sbjct: 178 WALVKGVPRKREDKISTWLVKDQTPDGDKMR--VCQHGEPDSDHAVSYYRIIEKAGNNLT 235

Query: 188 WVTVGLREGKNREIK 202
           W+ +    G+  +++
Sbjct: 236 WLEMEPYTGRTHQLR 250


>gi|47096256|ref|ZP_00233854.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|254898858|ref|ZP_05258782.1| hypothetical protein LmonJ_03555 [Listeria monocytogenes J0161]
 gi|254911653|ref|ZP_05261665.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
 gi|254935979|ref|ZP_05267676.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|47015401|gb|EAL06336.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes str. 1/2a F6854]
 gi|258608567|gb|EEW21175.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes F6900]
 gi|293589602|gb|EFF97936.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes J2818]
          Length = 296

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 87/264 (32%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTNLDIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFISGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEEYMAFDLPLPAD 287


>gi|332141130|ref|YP_004426868.1| ribosomal large subunit pseudouridine synthase C [Alteromonas
           macleodii str. 'Deep ecotype']
 gi|327551152|gb|AEA97870.1| ribosomal large subunit pseudouridine synthase C [Alteromonas
           macleodii str. 'Deep ecotype']
          Length = 313

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/260 (16%), Positives = 84/260 (32%), Gaps = 70/260 (26%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMS 56
            V  +   QR+   +       R +++        R++ +  V+VN G +  +    + +
Sbjct: 13  TVDADLAGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKGRV--KPEYKLQA 63

Query: 57  TDHIEV------DGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
            D + +      +G P                  E  R+ + +KP G+        G S 
Sbjct: 64  DDIVRIPPVRVSEGAPAPSPKLDKIAALESHILFEDDRILVMNKPSGMAV-----HGGSG 118

Query: 97  VFDNLPSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV 147
           +   L      +         V RLD +T G +L+       R +   L + +  + Y  
Sbjct: 119 LSFGLIEGLRALRPDAKFMELVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYNA 178

Query: 148 RFHGQVDQDKLN---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-- 195
              G+  +++      L+K ++  G     M    D  K S     +        L E  
Sbjct: 179 LVAGEWPKNRFKVKAPLRKNVLQSGER---MVSVSDDGKPSETRYRILEEYAGATLVEAS 235

Query: 196 ---GKNREIKKVFEFFNWKV 212
              G+  +I+         +
Sbjct: 236 PITGRTHQIRVHCLHAGHPI 255


>gi|325841309|ref|ZP_08167410.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|325489990|gb|EGC92337.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 297

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 55/149 (36%), Gaps = 18/149 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +KP G+ T  S      T+ + L   ++       +  V RLD +T GLL++
Sbjct: 86  EDEYLLVINKPAGIPTIPSLRHPEKTLANALIHYYNEHEIASTIHFVNRLDRDTSGLLMV 145

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKG-----IVIQGICYG 173
                +  +L     Q  R Y     G ++++       +    +G     +   G    
Sbjct: 146 AKYRHIHHLLTKDVKQIKRKYYTLVKGVMEKNSGTVHAPIARESEGNVRRCVRADGDDSI 205

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                L+  + S   V   L  G+  +I+
Sbjct: 206 THYQVLEVWEKST-LVECELETGRTHQIR 233


>gi|291531061|emb|CBK96646.1| hemolysin TlyA family protein [Eubacterium siraeum 70/3]
          Length = 241

 Score = 55.6 bits (133), Expect = 1e-05,   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|154345323|ref|XP_001568603.1| hypothetical protein [Leishmania braziliensis MHOM/BR/75/M2904]
 gi|134065940|emb|CAM43722.1| conserved hypothetical protein [Leishmania braziliensis
           MHOM/BR/75/M2904]
          Length = 754

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 40/122 (32%), Gaps = 22/122 (18%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS------TQWLRVYRV-RFHGQVDQDKLN 159
           R   V RLD+ T G LL+      A  L          +   ++Y       +       
Sbjct: 568 RQGQVHRLDVETSGCLLIAKSNVAADSLRHQIGTSAAFSHHTKIYHALCVVLEPS----- 622

Query: 160 LLKKGIVIQGICYGDMQVTLDTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            L+  + + G         + T+        K    WV   +++GK  +I++      + 
Sbjct: 623 -LRN-VRLHGDIIDAADPKIKTRYRVIRFFPKHRIVWVECRIQQGKKHQIRRHLASRGFP 680

Query: 212 VN 213
           + 
Sbjct: 681 IL 682


>gi|42780396|ref|NP_977643.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|42736315|gb|AAS40251.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
          Length = 297

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/267 (16%), Positives = 86/267 (32%), Gaps = 50/267 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + + V             + +PL    E   + + +K   
Sbjct: 41  GAIEVNGQHA-SVRYQLQAGEELRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 99

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L S + +      V  V RLD +T GL+L+  +      L   
Sbjct: 100 MSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSK 158

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                   R Y    HG            + +   +++++ +   G         +D+  
Sbjct: 159 QHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEDGQRAVTHFRVIDSAN 218

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
                V++ L  G+  +I+         +               L  G   E+ ++ L  
Sbjct: 219 HKTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHS 266

Query: 243 -EQLGPHLLEEAQVNLDAPIYSSETLV 268
                 H + E +++   PI S    V
Sbjct: 267 TSLTFYHPILEKEMSFTTPIPSDMQAV 293


>gi|224534885|ref|ZP_03675454.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           spielmanii A14S]
 gi|224513825|gb|EEF84150.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           spielmanii A14S]
          Length = 328

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/248 (17%), Positives = 83/248 (33%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++      +R +    I ++ V    K NG   + + +  V
Sbjct: 4   LKKEFTVKENAL--RLDLYLSNNLEGFTRSQ----IKRRNVEAFKKNNGKFFKIKLSKPV 57

Query: 55  MSTDH--IEVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D   IE D             +P+    E   + + +KP G+++         TV +
Sbjct: 58  FKDDEMLIEFDEESSQIDCLRPSNIPIAIIYEDPNIIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKGLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL------------R 194
               G  +   +  ++  I           V+ D  K +     + L            +
Sbjct: 178 AIVKGNFN-SFIGSIESFIDRDKYNRKKFSVSKDKGKKALTEYKLLLNFGGYSLLALKPK 236

Query: 195 EGKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>gi|206977555|ref|ZP_03238449.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|217958867|ref|YP_002337415.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|222095026|ref|YP_002529086.1| ribosomal large subunit pseudouridine synthase d [Bacillus cereus
           Q1]
 gi|229138078|ref|ZP_04266676.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
 gi|206744273|gb|EDZ55686.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|217063723|gb|ACJ77973.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|221239084|gb|ACM11794.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           Q1]
 gi|228645423|gb|EEL01657.1| Pseudouridine synthase [Bacillus cereus BDRD-ST26]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFRKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGGTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|228938507|ref|ZP_04101115.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|228971386|ref|ZP_04132012.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977999|ref|ZP_04138378.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228781660|gb|EEM29859.1| Pseudouridine synthase [Bacillus thuringiensis Bt407]
 gi|228788253|gb|EEM36206.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228821105|gb|EEM67122.1| Pseudouridine synthase [Bacillus thuringiensis serovar berliner
           ATCC 10792]
 gi|326939015|gb|AEA14911.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar chinensis CT-43]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/261 (17%), Positives = 87/261 (33%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLEAKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQV--DQDKLNLL---------KKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V   Q  ++           ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKGKQGTIDAAIGRDRHHATRRRISPKGNQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|330002097|ref|ZP_08304182.1| pseudouridine synthase, RluA family [Klebsiella sp. MS 92-3]
 gi|328537466|gb|EGF63703.1| pseudouridine synthase, RluA family [Klebsiella sp. MS 92-3]
          Length = 232

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 70/210 (33%), Gaps = 48/210 (22%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   F     V RLD  T GL+++  + G
Sbjct: 22  QDEHLVLINKPAGLLSLSGKDPRNLDSVHHRLVQRFPGCPLVHRLDFGTSGLMVIARNKG 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +           
Sbjct: 82  INALLCQQFSQRTVEKVYTALLCGHLAED------EGIVEAAIAKDPARFPRMALCARHG 135

Query: 183 KGSNAWV-------------------TVGLR-E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +                      V L  E G+  +++   +   + +         
Sbjct: 136 KPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILGC------ 189

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLE 251
                 L  G  RE+       +L  H  E
Sbjct: 190 -----DLYGG--RELPGTECASRLMLHASE 212


>gi|258545740|ref|ZP_05705974.1| pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
 gi|258518985|gb|EEV87844.1| pseudouridine synthase A [Cardiobacterium hominis ATCC 15826]
          Length = 205

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/159 (15%), Positives = 54/159 (33%), Gaps = 14/159 (8%)

Query: 69  KAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
             E   +++ +KP GL++      D   +V           ++  RLD+ T GLLL+   
Sbjct: 6   HYEDPDIYVINKPAGLLSVPGRGDDKYDSVQSRCQISAPAAMAAHRLDMATSGLLLIAKH 65

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQD--KLN---------LLKKGIVIQGICYGD 174
               R  +    + +  + Y    HG +  D   +            ++ I  +      
Sbjct: 66  KAAERHYKQEFAARRVEKRYIAVVHGSLADDRGDIEYPLITDWERRPRQKICYEHGKTAH 125

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               +  + G+   V +    G++ +++         + 
Sbjct: 126 TSYEVLARDGATTRVALTPHTGRSHQLRVHLAAIGHPIL 164


>gi|323356542|ref|YP_004222938.1| pseudouridylate synthase, 23S RNA-specific [Microbacterium
           testaceum StLB037]
 gi|323272913|dbj|BAJ73058.1| pseudouridylate synthase, 23S RNA-specific [Microbacterium
           testaceum StLB037]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 77/238 (32%), Gaps = 39/238 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           V +     RV + +A+    SR     +     V V+G  + R+   + +   + V+  P
Sbjct: 8   VPDGLDGTRVDQALAKMLGFSRTFAAEIADAGGVSVDGRTVARSD-RLRAGGWLSVEWEP 66

Query: 67  LRKAE--------------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------PS 103
            R+ E                 + +  KP G+    S      TV   L           
Sbjct: 67  KREPEIVPVEVADLGIVWDDDDIVVVDKPAGVAAHPSVGWEGPTVLGALAAAGFRIATSG 126

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DKLN 159
              R   V RLD  T GL+++        +L+      +  ++Y     G  D     ++
Sbjct: 127 PAERRGVVHRLDAGTSGLMVVAKTERAYTLLKSAFKEREVDKIYHAVVQGHPDPLSGTID 186

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF 207
                      K  +V  G        TL+    + + + + L  G+  +I+  +   
Sbjct: 187 APIGRHPHHSWKFAVVPDGKDSVTHYETLEAFPRA-SLLEIHLETGRTHQIRVHMAAH 243


>gi|319950238|ref|ZP_08024165.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
 gi|319436142|gb|EFV91335.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
          Length = 297

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/211 (20%), Positives = 70/211 (33%), Gaps = 48/211 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKAERTRLWLYH--------- 79
           +++ Q R++VNG   E+    +   D I++     G P     R    L           
Sbjct: 8   KLLRQGRLRVNGRRAEQ-NYRLAEGDVIDLPAMQAGAPATTVTRPPTALLDRMAKTVLYE 66

Query: 80  --------KPIGLVTTH-SD-PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
                   KP G+     SD P G       L      +    RLD +T G+L+LT    
Sbjct: 67  DSNLLVVDKPAGVAVHRGSDMPAGVIETLRFLCPDLPGLELGHRLDRDTSGVLVLTKTPP 126

Query: 130 LARVLE----LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD--TQK 183
           + R L         +  R Y     GQ   +       G++   +   D  V +D   Q+
Sbjct: 127 MLRHLHEMLRDREKEIERHYLAIVAGQWPANL------GVLEAPLRRRDADVVVDPRGQR 180

Query: 184 GSNA---------WVTVG---LREGKNREIK 202
                        W T+    L  G+  +I+
Sbjct: 181 AETHVRVRRRVGDWATLVDVRLFTGRKHQIR 211


>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 = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 77/238 (32%), Gaps = 40/238 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M    +V E+    R    ++R    SR +   +I Q ++ + G      +  + S D I
Sbjct: 1   MNKVTMVPEDLVGVRFDLAVSRMMGLSRSKAANLIDQGQISLIGR-CGLKSEKLQSGDSI 59

Query: 61  EVD-------GVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            V          P+              +  KP+G+    S     STV  +L +    +
Sbjct: 60  RVSLTTSEKAPEPIDYDMGIVYEDGDLVVVDKPVGMAAHQSVGWTGSTVLGSLKARGVHI 119

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYR----------- 146
              G         RLD+ T GL+L+       + +    +Q    + Y            
Sbjct: 120 TDYGPQGRQGIVSRLDVGTSGLMLVCKSQMAYKEMRRQFSQHEVKKTYYALAQGNLKEDK 179

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--GSNAWVTVGLREGKNREIK 202
                 + +D     +  I   G          D  +  G   +++V L  G+  +I+
Sbjct: 180 ATVDAPIGRDSAADFRFTITPAG---KPAITHWDVIERFGQATYISVNLETGRTHQIR 234


>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 = 55.6 bits (133), Expect = 1e-05,   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|227534246|ref|ZP_03964295.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|227188136|gb|EEI68203.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
          Length = 315

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 72/222 (32%), Gaps = 32/222 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---GVPLRKA---- 70
           + +A  G+ S R  ++M+A   + V+G         V +   I  +      L       
Sbjct: 39  RWLAEQGV-SHRLFKKMLADHLIWVDGQ--ASGNGPVEAGQIIRFEIPTSKTLTPEFAPL 95

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRVISVGRLDINTE 119
               E     +  KP GL +        S++ + +            +   + RLD +T 
Sbjct: 96  EVIYEDANWLIVSKPAGLTSVPGPHTPNSSLLNRIAGYLVEQKIDAPQPAIMTRLDRDTV 155

Query: 120 GLLLLTNDGGLARVLELPSTQWL-RVYRVRFHGQVD------QDKLNLLKKG---IVIQG 169
           GL+L           +    + L + Y     G++          L L   G   IV   
Sbjct: 156 GLVLAAKHPYAQGRFDQAHQRTLTKHYLAVVSGKLPSPKGEIDAPLKLAADGIHRIVAAD 215

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +  +K +N  V V L  G+  +I+  F      
Sbjct: 216 GQTALTKYRVLKEK-TNTLVDVQLLTGRTHQIRVHFASLGHP 256


>gi|15603701|ref|NP_246775.1| hypothetical protein PM1836 [Pasteurella multocida subsp. multocida
           str. Pm70]
 gi|34395822|sp|Q9CK02|RLUA_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|12722261|gb|AAK03920.1| RsuA [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 219

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/224 (14%), Positives = 74/224 (33%), Gaps = 43/224 (19%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           D +  D             + +KP GL++   + P    +    +   +       RLD+
Sbjct: 15  DIVHYDD---------HFVVINKPSGLLSVPGNQPQYYDSAMSRVKEKYGFCEPAHRLDM 65

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLN-----------LLKK 163
           +T GL+L        R L+    +    + Y+    G +++D+               ++
Sbjct: 66  STSGLILFALSKVADRELKRQFREREPKKHYQALVWGHLEEDQGEVNLPLICDWENRPRQ 125

Query: 164 GIVIQ-GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVNRLIRISYG 221
            I  + G     +   L     +   V +  +  G++ +++         +         
Sbjct: 126 KICFERGKPALTLYEVLARYPNNTTRVKLTPIT-GRSHQLRLHMLALGHPI--------- 175

Query: 222 PFQLGT--LLAGSTREVSKKIL--REQLG-PHLLEEAQVNLDAP 260
              LG         + +S ++    EQL   H + +  ++  AP
Sbjct: 176 ---LGDKFYAPPQAKALSPRLCLHAEQLAFRHPITQEWLSFSAP 216


>gi|229195588|ref|ZP_04322354.1| Pseudouridine synthase [Bacillus cereus m1293]
 gi|228587837|gb|EEK45889.1| Pseudouridine synthase [Bacillus cereus m1293]
          Length = 307

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFRKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGGTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|110639414|ref|YP_679623.1| pseudouridylate synthase [Cytophaga hutchinsonii ATCC 33406]
 gi|110282095|gb|ABG60281.1| pseudouridylate synthase [Cytophaga hutchinsonii ATCC 33406]
          Length = 240

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/159 (16%), Positives = 53/159 (33%), Gaps = 23/159 (14%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEG 120
           +VD   L   E    +  +KP  + +      G  ++       +       R+D  T G
Sbjct: 3   KVDIKDLIIFENDDYFFINKPPFISSLDERTGGAPSIIRMAKEYWPDAQLCHRIDKETSG 62

Query: 121 LLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT 178
           +L +  +    R L +   S    + Y    +G  D D ++     + +  +      V 
Sbjct: 63  VLAVAKNPAAYRHLSMAFESRNVTKEYHAVVNGTHDLDGVD-----VYLPILVLPTGTVK 117

Query: 179 LDTQKGS---NAWVTVG------------LREGKNREIK 202
           +D  KG      + T+             +  G+  +I+
Sbjct: 118 IDKSKGKLAETIFFTIQAYKKATLVRCLPIT-GRMHQIR 155


>gi|283783562|ref|YP_003374316.1| pseudouridine synthase, RluA family [Gardnerella vaginalis 409-05]
 gi|283441085|gb|ADB13551.1| pseudouridine synthase, RluA family [Gardnerella vaginalis 409-05]
          Length = 321

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 84/236 (35%), Gaps = 46/236 (19%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           +SK++   G+ SR     +I + + K+ G   +++++ +   D I VD     + +  + 
Sbjct: 30  LSKLM---GV-SRASAISLIERNQAKILGRKSQKSSI-LQDGDTIVVDQKESAEQKEEQN 84

Query: 76  ---------WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS----------IFSRV 108
                     +Y+        KP+G+ +  +      TV + L +            SR 
Sbjct: 85  NESSVCNIPIIYNDDDVVVIDKPVGVASHAAKGWSGPTVPECLEAVGIDIKTTLCDESRK 144

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQ 155
             V RLD+ T GL+L+  T+        +       + Y     G            + +
Sbjct: 145 GIVSRLDVGTSGLMLVCKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATIDAPIGR 204

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            K++  +  I   G         L+    +   V+V L  G+  +I+  F      
Sbjct: 205 AKVSDFRFTITSDGKPAVTHWDVLERFSQAT-LVSVNLETGRTHQIRVHFSSIGHP 259


>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 = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+  ++    +  SR   +R+I    V VN  ++++    V     I++
Sbjct: 1  MAKQRLDNLLVELNLCNSRTLAQRLIQAGEVTVNEQVIDKPGTEVDVAAQIKI 53


>gi|328725051|ref|XP_001944933.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Acyrthosiphon pisum]
          Length = 522

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 73/209 (34%), Gaps = 27/209 (12%)

Query: 32  ERMIAQQRVKVNGILLE--------RAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   ++            NV+    + V   P+        + + +KP 
Sbjct: 142 ERCIKSGSLTVNYQKVDTQYKLKHNDLLANVVHRHEVPVTNDPITIVHMDDDIVVVNKPA 201

Query: 83  GLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPS 138
            +          +TV   L        + ++ RLD  T GLL+       AR++E  + +
Sbjct: 202 SIPVHPCGRYRHNTVVFVLAKEHNLRNLRTIHRLDRLTSGLLMFGRTPRYARIMEAQIRN 261

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW---------- 188
            Q  + Y  R  G+  +  +      I +     G  +V+   +  S  +          
Sbjct: 262 RQVNKQYVCRVEGRFPEQTIE-CNHPIEVVSYKIGVCKVSNKGKNCSTTFQLVGYNEKTN 320

Query: 189 VTVGL---REGKNREIKKVFEFFNWKVNR 214
           ++V L     G+  +I+   ++  + V  
Sbjct: 321 ISVVLCFPHSGRMHQIRVHLQYLGFPVKN 349


>gi|218296418|ref|ZP_03497161.1| hemolysin A [Thermus aquaticus Y51MC23]
 gi|218243212|gb|EED09743.1| hemolysin A [Thermus aquaticus Y51MC23]
          Length = 235

 Score = 55.6 bits (133), Expect = 1e-05,   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|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 (132), Expect = 1e-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|319949599|ref|ZP_08023642.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
 gi|319436736|gb|EFV91813.1| pseudouridine synthase, RluA family protein [Dietzia cinnamea P4]
          Length = 308

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 81/244 (33%), Gaps = 41/244 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--- 63
           V +     RV   ++R    SR  V  +  + +V ++G  + ++   +     IEV+   
Sbjct: 9   VPDGLDGMRVDAGVSRLLGISRTAVADLAGEGKVLLDGRTVGKSD-KLTGMSWIEVEMPE 67

Query: 64  -------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
                        G+ +  ++   + +  KP+G+    S      TV   L         
Sbjct: 68  PRAEPAVVAEPVAGMAVVYSDADIVVV-DKPVGVAAHASVGWTGPTVIGGLAAAGYRIST 126

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DK 157
                R   V RLD+ T GL+++        +L+         + Y     G  D     
Sbjct: 127 SGPPERKGIVHRLDVGTSGLMVVAASERAYTLLKRAFRDRTVDKTYHALVQGHPDPLSGT 186

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
           ++           +  ++  G        TL+  + +   V V L  G+  +I+  F   
Sbjct: 187 IDAPIGRHTSNDWRFAVISDGKPSITHYDTLEAHQAAT-LVEVKLETGRTHQIRVHFSAL 245

Query: 209 NWKV 212
           +   
Sbjct: 246 HHPC 249


>gi|313609638|gb|EFR85147.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria monocytogenes FSL F2-208]
          Length = 296

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/264 (15%), Positives = 87/264 (32%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTDLDIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPSGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L+  
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLAAQEGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLERY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 TAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTTLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H + E  +  D P+ + 
Sbjct: 264 SCHLHLVHPVTEEYMAFDLPLPAD 287


>gi|88801297|ref|ZP_01116825.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
 gi|88781955|gb|EAR13132.1| ribosomal large subunit pseudouridine synthase D [Polaribacter
           irgensii 23-P]
          Length = 228

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/188 (17%), Positives = 57/188 (30%), Gaps = 37/188 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   + + +K  G +T   D  G   + D +               + +V RLD  T G+
Sbjct: 13  EDNHIIIINKRAGDITQG-DKTGDKPLSDVIKEYIKEKYNKPGEVFIGTVHRLDRPTSGI 71

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV---DQDKLNLLKKGI----------V 166
           ++          L   L      + Y                N LKK             
Sbjct: 72  VIFARTSKALTRLNKMLRDKVIDKTYWALVKNAPIKATDTITNFLKKDTKKNKSFVYKKE 131

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
           I+G     +   +  +  S   + + L  G++ +I+           +L     G    G
Sbjct: 132 IEGCKKAVLHYKILQKLESYCLLEIDLETGRHHQIR----------TQL--SHIGSVIKG 179

Query: 227 TLLAGSTR 234
            L  G++R
Sbjct: 180 DLKYGASR 187


>gi|300174185|ref|YP_003773351.1| ribosomal large subunit pseudouridine synthase A [Leuconostoc
           gasicomitatum LMG 18811]
 gi|299888564|emb|CBL92532.1| Ribosomal large subunit pseudouridine synthase A [Leuconostoc
           gasicomitatum LMG 18811]
          Length = 306

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/216 (17%), Positives = 64/216 (29%), Gaps = 47/216 (21%)

Query: 42  VNG-ILLERAAVNVMSTDHIEVDGVPLRKAERTR----------------LWLYHKPIGL 84
           VNG  +     + V     +  D    R +E                     + +KP G+
Sbjct: 45  VNGNEVPTSYELQVNDKLTLRFDQEDFRTSESHYPPNGMQRVGIVFESEDFVVVNKPAGM 104

Query: 85  VTTHSDPDGRSTVFDNLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARV 133
                      T+ + L + FS           R   V RLD  T G +++  +  +  +
Sbjct: 105 KMHPHTLTENDTLLNYLAADFSERHLVSAGVVARPYMVHRLDRETSGAVIVAKNPVVVPI 164

Query: 134 L--ELPSTQWLRVYRVRFHGQVD--------------QDKLNLLKKGIVIQGICYGDMQV 177
           L   L      R Y    +G++                D    +  GI  Q       Q+
Sbjct: 165 LNRMLADKDIKRTYLAWVNGKMTGNSGTINAPIGVDLDDDRKRMVNGIDEQLAITHWTQI 224

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +  QK     + V L  G+  +I+         + 
Sbjct: 225 HMVFQK---TLLRVQLETGRMHQIRVHLAAIGHPII 257


>gi|300718134|ref|YP_003742937.1| tRNA pseudouridine synthase C [Erwinia billingiae Eb661]
 gi|299063970|emb|CAX61090.1| tRNA pseudouridine synthase C [Erwinia billingiae Eb661]
          Length = 259

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/155 (19%), Positives = 48/155 (30%), Gaps = 31/155 (20%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D   TVF        I   V +V RLD  T G+LLL     +A
Sbjct: 11  LVAVNKPAGWLVHRSWLDRHETVFVMQTLRDQIGQHVFTVHRLDRPTSGVLLLALSSEVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDMQVTLD 180
           R+L          + Y     G ++          ++L+ +                   
Sbjct: 71  RLLSQQFEQHAMQKTYHAVVRGWLEGEETLDYALTEELDKIAD--KFTNPDKAPQPAVTH 128

Query: 181 TQKGSNAWV----------TVGLRE-----GKNRE 200
            +  + A +             L E     G+  +
Sbjct: 129 WKSLAKAELPVAVSRYDSSRFSLVELKPETGRKHQ 163


>gi|313674292|ref|YP_004052288.1| tRNA pseudouridine synthase c [Marivirga tractuosa DSM 4126]
 gi|312940990|gb|ADR20180.1| tRNA pseudouridine synthase C [Marivirga tractuosa DSM 4126]
          Length = 233

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/162 (17%), Positives = 52/162 (32%), Gaps = 22/162 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP GL+   +     + VF    L      RV  V R+D  T G+LL   D
Sbjct: 11  QDDYLVAINKPHGLLVHRTKIATETDVFALQLLRDQLGQRVYPVHRIDRKTSGVLLFALD 70

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD-----KLN----LLKKGIVIQGICYGDMQ 176
                         Q  + Y     G  D +      L      L++ +          +
Sbjct: 71  EENNSKTTALFRDQQIEKTYLAIVRGFTDSEGTIDYALRKESGQLQESVT-HYKTLAKTE 129

Query: 177 VTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
           + +   K   +  ++   E     G+  +I+K     +  + 
Sbjct: 130 IPVPLGKFETSRYSLV--EVRPETGRMHQIRKHLAHIHHPII 169


>gi|312114651|ref|YP_004012247.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219780|gb|ADP71148.1| pseudouridine synthase, RluA family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 358

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 57/184 (30%), Gaps = 37/184 (20%)

Query: 8   QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKV------NGILLERAAVNVMSTDHI 60
            E+    R+ + +A      SR  ++ +I    V V      +       +  V   D  
Sbjct: 14  SEDDAGVRLDRFLASRIETQSRVRLQELIRAGHV-VRLAAGRDAETSTDPSAKVRLGDTF 72

Query: 61  EV----------DGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-- 105
           EV          +G  +      E   L +  KP GLV      +   T+ + L +    
Sbjct: 73  EVTTPPAENYAVEGEAIELNVVYEDASLIVIDKPAGLVVHPGAGNPNGTLVNALIAHCGD 132

Query: 106 --------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW------LRVYRVRFHG 151
                   +R   V RLD NT GL+++       R L              R Y     G
Sbjct: 133 SLSGIGGVTRPGIVHRLDKNTSGLMVVAKTDKAHRSLSAQFADHGRTGALRREYLALVWG 192

Query: 152 QVDQ 155
           +   
Sbjct: 193 EPQP 196


>gi|293401387|ref|ZP_06645530.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 5_2_54FAA]
 gi|291305025|gb|EFE46271.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Erysipelotrichaceae bacterium 5_2_54FAA]
          Length = 293

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 28/153 (18%), Positives = 53/153 (34%), Gaps = 24/153 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL 124
           E   L   +KP  L+      D   T+ + +   +      + V  + RLD  T G++L 
Sbjct: 86  EDELLLAVNKPSHLLVHSDGVDTSHTLCNRVQGYYLMQGITAPVRPLHRLDKETSGIVLF 145

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQV-------------DQDKLNLLKKGIVIQG 169
                   +L+      Q  R Y     G +             D+     ++  +   G
Sbjct: 146 CKIPFFQPLLDHMMKEKQIQREYEAIVEGSIHQKKQTITYPIARDRHDARKMR--VSATG 203

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +    +TL    G+ +W+   L  G+  +I+
Sbjct: 204 -KHAKTTITLQKNYGAYSWIHARLFTGRTHQIR 235


>gi|217964932|ref|YP_002350610.1| pseudouridine synthase, RluA family [Listeria monocytogenes HCC23]
 gi|217334202|gb|ACK39996.1| pseudouridine synthase, RluA family [Listeria monocytogenes HCC23]
 gi|307570509|emb|CAR83688.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes L99]
          Length = 296

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/264 (15%), Positives = 87/264 (32%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTDLDIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPSGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L+  
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLATQEGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLERY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 TAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTTLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H + E  +  D P+ + 
Sbjct: 264 SCHLHLVHPVTEEYMAFDLPLPAD 287


>gi|88608500|ref|YP_506438.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           sennetsu str. Miyayama]
 gi|88600669|gb|ABD46137.1| ribosomal large subunit pseudouridine synthase C [Neorickettsia
           sennetsu str. Miyayama]
          Length = 305

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/246 (16%), Positives = 81/246 (32%), Gaps = 50/246 (20%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE------------ 61
           R+ K +    G   +  +++ + ++ V++N  +++ A+  V+  D +             
Sbjct: 12  RLDKYLRDTFGQFPQSALQKALRKKAVRLNNSVVK-ASAAVLKGDSLTLSANFLQILSSP 70

Query: 62  ----------VDGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-LPSI 104
                     VD   +         E   +    KP G         G +   DN + SI
Sbjct: 71  REIPSDSSKVVDSKFVEFIASLMLYEDENVLAISKPFGFPVQS--GYGITASIDNAMKSI 128

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL---- 158
                 V RLD +T G+L+       AR L     +    + Y     G++ + K     
Sbjct: 129 NPEYRVVHRLDKHTTGVLIFAKTLDAARELWRLFSNRLVKKSYLAIVIGELKEKKGVVDC 188

Query: 159 ---NLLKKGIV------IQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFF 208
               +L KG        I    +   Q  +  +  + + + +  L  G+  +I+      
Sbjct: 189 YINKVLFKGEEVMQCNNIGNGEHAITQFHVIKKFKNTSLIELFPLT-GRKHQIRSQMASI 247

Query: 209 NWKVNR 214
              V  
Sbjct: 248 GHPVLN 253


>gi|332976359|gb|EGK13213.1| ribosomal large subunit pseudouridine synthase D [Desmospora sp.
           8437]
          Length = 270

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/214 (14%), Positives = 67/214 (31%), Gaps = 40/214 (18%)

Query: 35  IAQQRVKVNGILLER---------AAVNVMSTDHIEVDGVPLRKA---ERTRLWLYHKPI 82
           I + RV+V+G +++            V V   +  EV    L      E   + + +KP 
Sbjct: 1   IREHRVRVDGRIVKSNHRLQGGEQVEVAVPPPEEAEVKPEALPLEVVFEDGDVIMVNKPR 60

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTEGLLLLTNDGGLARV 133
           G+V   +      T+ + L +    +  +G         R+D +T GL+++  +   A  
Sbjct: 61  GMVVHPAPGSPSGTLVNALLAHCDDLSGIGGVLRPGIVHRIDKDTSGLIMVAKN-DFAHR 119

Query: 134 LE---LPSTQWLRVYRVRFHGQVDQD-------------KLNLLKKGIVIQGICYGDMQV 177
                L +    R Y     G +  D                 +   +  +         
Sbjct: 120 SLAAQLKNHTVDREYTALVQGNIPHDRGTVDAPIGRDPHHRKRMA--VEHRHGKPAVTHF 177

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +  +      +   L  G+  +I+   +     
Sbjct: 178 EVIERFSRATLIRCRLETGRTHQIRVHMKSIGHP 211


>gi|221638823|ref|YP_002525085.1| Ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides KD131]
 gi|221159604|gb|ACM00584.1| Ribosomal large subunit pseudouridine synthase D [Rhodobacter
           sphaeroides KD131]
          Length = 322

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 48/270 (17%), Positives = 84/270 (31%), Gaps = 67/270 (24%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEVD----------GVPLRKA-ERT 73
           SR  + ++I +  V++ G  +      V       I +D           +PL    E  
Sbjct: 11  SRSRLMKLIGEGAVRLEGAPVTDPKAKVAEGQVYEIALDAPAEVEARPEAIPLSVVWEDE 70

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRLDINTEGLLL 123
            L +  KP+G+V   +      T+ + L               R   V R+D +T GLL+
Sbjct: 71  DLIVIDKPVGMVVHPAPGQWTGTLVNALLHHCGESLSGIGGEKRPGIVHRIDKDTSGLLV 130

Query: 124 L--TNDGGLARVLELPSTQWLRVYRVRFHG--QVDQDKLN-------------LLKKG-- 164
           +  T+        +  +    R Y    HG  +V   +L               +  G  
Sbjct: 131 VAKTDRAHQGLAAQFEAHTVERRYLALVHGVPEVSDPRLRGVRGTSFEPGGVLRIATGLA 190

Query: 165 ----------IVIQGICYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFEFFNWK 211
                     +  +G  +   +  L  + G     A V   L  G+  +I+         
Sbjct: 191 RHRTDRQRQAVTFEGGRHAVTRARLLERFGMPPVLALVECRLETGRTHQIRVHMAHAGHG 250

Query: 212 VNRLIRISYGPFQLGTLLAGSTREVSKKIL 241
           +             G    G  R++S K L
Sbjct: 251 LI------------GDQTYGGRRKLSPKAL 268


>gi|157116527|ref|XP_001658535.1| ribosomal pseudouridine synthase [Aedes aegypti]
 gi|108883445|gb|EAT47670.1| ribosomal pseudouridine synthase [Aedes aegypti]
          Length = 516

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/208 (17%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P+        + + +KP 
Sbjct: 99  ERCIKAGTLTVNYEKVPTDYRLKHNDLLANIVHRHEVPVTSQPITIVHMDDDIVVVNKPA 158

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   +    + ++ RLD  T GLLL       AR +E    +
Sbjct: 159 SIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRN 218

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------ 192
            Q  + Y  R  G+     +   K+ I +     G  +V+   ++ +  +  +G      
Sbjct: 219 RQVQKEYICRVEGEFPDGIIE-CKEPIEVVSYKIGVCKVSPKGKECTTTFQKLGYNGTSS 277

Query: 193 ------LREGKNREIKKVFEFFNWKVNR 214
                 L  G+  +I+   ++  + V  
Sbjct: 278 VVLCKPLT-GRMHQIRVHLQYLGYPVVN 304


>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 = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 31/200 (15%), Positives = 60/200 (30%), Gaps = 28/200 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--ERTRL 75
           K++A+    S    + MI +  V V    +  A   +       +  V   K   E   +
Sbjct: 8   KLLAQQEGISNSNAKSMIDRGLVYVGNKKVMIARGEIDERTVFRIQKVEKVKPIFENDDI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            +  KP  + +            D +   F   + + RLD  T G+L+L  +    +   
Sbjct: 68  IVVDKPAHVNS------------DEIERQFKPAVLLHRLDRETSGVLMLVKNEDFRQRAI 115

Query: 136 LP--STQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQVTLDTQ 182
                 +  + Y     G + +            K N     +  +G          D  
Sbjct: 116 KEFRDDKVYKEYIAWVEGIMTEPIEVDKAITTQKKNNKAYSNVSPKGKPARTEFFP-DIV 174

Query: 183 KGSNAWVTVGLREGKNREIK 202
                 V   +  G+  +I+
Sbjct: 175 SAKKTKVKCIIHNGRTHQIR 194


>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 = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 87/252 (34%), Gaps = 47/252 (18%)

Query: 1   MK-DKNIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAA--- 51
           MK   N +       ++   + + GI SRR    ++A+      ++ +NG    +     
Sbjct: 1   MKMQINWIYSEDVSCKLKTFLKKQGI-SRR----LLAKVRYSDGKILINGKSGRKIDKIK 55

Query: 52  -----VNVMSTDH----IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
                  V+  +     +    VP++   E     L  KP  + +  S      ++ + +
Sbjct: 56  KNDKITLVVPDEEFRRSVPPSFVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRV 115

Query: 102 PSIF-----SRVIS--VGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHG 151
              +       +I   V RLD +T G+++       A  L        +  + Y     G
Sbjct: 116 VGYYQIRGYRGIIPHIVTRLDRDTSGIVIFAKH-RYAHALLDSQLKEHKISKTYTAILSG 174

Query: 152 -----------QVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
                       + +D  +L+K+ ++  +       ++ ++ +   N    + L  G+  
Sbjct: 175 ILHNNHYIIDLPIGRDSTSLIKRKVLFSEKAKRSKTEIFVEERIRDNTLCKIKLHTGRTH 234

Query: 200 EIKKVFEFFNWK 211
           +I+    +  + 
Sbjct: 235 QIRVHCSYLGYP 246


>gi|50955140|ref|YP_062428.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli
           subsp. xyli str. CTCB07]
 gi|50951622|gb|AAT89323.1| ribosomal large subunit pseudouridine synthase [Leifsonia xyli
           subsp. xyli str. CTCB07]
          Length = 306

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 37/231 (16%), Positives = 69/231 (29%), Gaps = 36/231 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAV-----------NVM 55
           + +     RV   +A+    SR     +     V V+G    ++                
Sbjct: 8   IPDGLGGVRVDAGLAKLLGFSRSFAAEVAESGGVTVDGREAGKSDRLPAGSWLDVTWQPR 67

Query: 56  STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---- 109
               I   V        E   + +  KP G+    S      TV   L +   R+     
Sbjct: 68  EEPRIVPIVVSELTIVHEDDDIVVLDKPAGVAAHPSIGWEGPTVLGALAAAGFRISTSGA 127

Query: 110 -----SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--DKLNL 160
                 V RLD  T GL+++        VL+         ++Y     G  D     ++ 
Sbjct: 128 PERAGIVHRLDAGTSGLMVVAKSEHAYTVLKRAFHDRTVEKIYHAVVQGHPDPLTGTIDA 187

Query: 161 ---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     +  +V  G        T++    + + + + L  G+  +I+
Sbjct: 188 PIGRHPKSDWRFAVVAGGKPSVTHYETIEAFPAA-SLLEIHLETGRTHQIR 237


>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 = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 82/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVAVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG +++      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLEE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYNGADLVECLLETGRTHQIR 233


>gi|297172088|gb|ADI23070.1| pseudouridylate synthases, 23S RNA-specific [uncultured gamma
           proteobacterium HF0770_07M15]
          Length = 277

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 32/163 (19%), Positives = 55/163 (33%), Gaps = 21/163 (12%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV---FDNLPSIFSRVISVGRLDIN 117
            V+ +     E   L + +KP GLV   +  D RS++                + RLD  
Sbjct: 28  RVNDLFEILHEDDDLLVINKPAGLVCHPTKGDERSSLAGRLRLYRGAEQSAHLINRLDRE 87

Query: 118 TEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---NLL----KKGIVIQ 168
           T G++ +      AR L     S +  + Y    HG V + +      L       +V++
Sbjct: 88  TSGVVCVGKTDEAARELRRLWESREVDKYYWAIVHGHVPESEGTIDAPLGSDDASEVVVK 147

Query: 169 GICYGDM---------QVTLDTQKGSNAWVTVGLREGKNREIK 202
                D          Q   +       W+ V    G+  +I+
Sbjct: 148 DCVRDDGHPSQTRYWTQWKFERDDEKFTWLRVAPVTGRKHQIR 190


>gi|242212124|ref|XP_002471897.1| predicted protein [Postia placenta Mad-698-R]
 gi|220728995|gb|EED82877.1| predicted protein [Postia placenta Mad-698-R]
          Length = 435

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/207 (17%), Positives = 74/207 (35%), Gaps = 31/207 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE--VDG----------VPLRKAERTRLWLYHKPI 82
           +      +NG + +     V + D IE  V              +         +  KP 
Sbjct: 46  LESGVTTINGTIAK-PDTIVQNGDRIENVVHRHEPPVTSTPVRIIHYDREREFIIIDKPG 104

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +    S    R+++ + L + F   +V ++ RLD  T GL+++     +A  L     +
Sbjct: 105 SIPVHASGRFFRNSLVEILKNDFGFKKVYTINRLDRLTSGLMIIPLSSSMANTLTQEFAA 164

Query: 139 TQWLRVYRVRFHGQVDQDKLN----LL----KKGIVI---QGICYGDMQVTLD-TQKGSN 186
               + Y  R  GQ  +++L     LL    + G+ +   +G     +   +        
Sbjct: 165 GTIRKEYIARCRGQFPKEELACEVPLLTIDRQMGLNVVHPEGKPAKTIFKRMHYDANTDT 224

Query: 187 AWVTVG-LREGKNREIKKVFEFFNWKV 212
           + V    L  G++ +I+   ++    V
Sbjct: 225 SVVHCKPLT-GRSHQIRVHLQYLGHPV 250


>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 = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 39/85 (45%), Gaps = 10/85 (11%)

Query: 5   NIVQENFTPQRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
            +++ +    R+  VIA  G   SR  +   I   +V VNG ++   A N+ + D I V 
Sbjct: 165 EVIKGSVASLRLDAVIA-LGFNGSRSHITSYIIDGKVSVNGRIITSNAYNLKAGDIISVH 223

Query: 64  GV-------PLRKAERTRLWL-YHK 80
           G+        L + ++ R+ +  +K
Sbjct: 224 GLGKIRYMDTLSETKKGRIMITINK 248


>gi|290893473|ref|ZP_06556457.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
 gi|290556974|gb|EFD90504.1| ribosomal large subunit pseudouridine synthase [Listeria
           monocytogenes FSL J2-071]
          Length = 296

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 41/264 (15%), Positives = 87/264 (32%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNNEEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTDLDIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPSGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L+  
Sbjct: 156 TFLQKGLLKRCYQAFTSGVLASQEGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLERY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
              +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 TAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTTLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H + E  +  D P+ + 
Sbjct: 264 SCHLHLVHPVTEEYMAFDLPLPAD 287


>gi|282880676|ref|ZP_06289379.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281305459|gb|EFA97516.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 315

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 69/203 (33%), Gaps = 45/203 (22%)

Query: 37  QQR-VKVNGILLERAAVNVMSTDHIEVDG-----------VPLRKAERTRLWLYHKPIGL 84
             R + VNG  + +    V     I +             V +   +R  L +  K  G+
Sbjct: 42  AGRGIIVNGKQITQFDYPVTPGTKIAISKSKKNTLFKSKYVKIVYEDR-YLVVIEKQAGI 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPS 138
           ++  +       V   L S F +         V RLD +T GL++   D   A++LE   
Sbjct: 101 LS-MAAGHASLNVKKVLDSYFKQSKQKCTAHVVHRLDRDTSGLMIYAKDIQTAQLLEHDW 159

Query: 139 TQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---- 192
               + R Y     G+++QD      +G +   +      +T  + + +     V     
Sbjct: 160 HHNVYDRRYVAVVSGEMEQD------EGTIANWLKDNRAYITYSSPEDNGGKFAVTHFHT 213

Query: 193 --------LRE-----GKNREIK 202
                   L E     G+  +I+
Sbjct: 214 LNRTTEHSLVEYRLETGRKNQIR 236


>gi|224065743|ref|XP_002301949.1| predicted protein [Populus trichocarpa]
 gi|222843675|gb|EEE81222.1| predicted protein [Populus trichocarpa]
          Length = 444

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 84/255 (32%), Gaps = 68/255 (26%)

Query: 15  RVSKVIAR--AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI------------ 60
           R+   I+   +GI SR  V+  I    V VNG ++++ + NV + D +            
Sbjct: 95  RLDSWISSRISGI-SRARVQSSIKSGLVSVNGKVIDKVSHNVKAGDKVNCVISELQPLRA 153

Query: 61  EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------------- 106
           E + +PL    E   + + +KP  +V   +  +   T+ + +    S             
Sbjct: 154 EPENIPLDIVYEDENVLVVNKPAHMVVHPAPGNATGTLVNGILHHCSLPTVSSQEVLSGA 213

Query: 107 --------------------RVISVGRLDINTEGLLLLTNDGGLARVLELP-STQWLRVY 145
                               R   V RLD  T GLL++  D      L        ++  
Sbjct: 214 EDVSDDDDEGLCSSSYAASVRPGIVHRLDKGTSGLLVVAKDEHSHAHLSEQFKLHTIKRV 273

Query: 146 RVRF------------HGQVDQDKLNLLKKGIVIQ---GICYGDM---QVTLDTQKGSNA 187
            V                 + +D  N ++   +++   G         +V      G +A
Sbjct: 274 YVSLTCGVPAPMAGRIDVPIGRDVSNRIRMAAIVEPNRGQARHAASRYKVIEILAGGGSA 333

Query: 188 WVTVGLREGKNREIK 202
            V   L  G+  +I+
Sbjct: 334 LVEWRLETGRTHQIR 348


>gi|84394045|ref|ZP_00992782.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
 gi|84375331|gb|EAP92241.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           12B01]
          Length = 244

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/149 (17%), Positives = 61/149 (40%), Gaps = 28/149 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND------ 127
           + + +KP GL++     P+   +++  L   F+ +  V RLD++T GL+LL         
Sbjct: 23  ILVVNKPAGLLSVPGRLPEHYDSMWSRLVVEFAEIQVVHRLDMSTSGLMLLAKHKQAERH 82

Query: 128 --GGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGD 174
                   L        ++Y  R  G V++      L L+       ++ +  +      
Sbjct: 83  LKKQFQYRLTH------KLYYARVWGSVEEAEGLIDLPLICDWPNRPRQKVCFEDGKPSQ 136

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +  ++ Q+   A + +  +  G++ +++
Sbjct: 137 TRYVVERQEAQTALLKLLPIT-GRSHQLR 164


>gi|332704296|ref|ZP_08424384.1| pseudouridine synthase [Desulfovibrio africanus str. Walvis Bay]
 gi|332554445|gb|EGJ51489.1| pseudouridine synthase [Desulfovibrio africanus str. Walvis Bay]
          Length = 278

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/163 (23%), Positives = 60/163 (36%), Gaps = 30/163 (18%)

Query: 14  QRVSKVI-------ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DG 64
           QR+ +++       +  G   RR   R+I   +  V+G   + A   V     I V  D 
Sbjct: 18  QRLDRLLERIVPELSLRG---RR---RLIDLGKALVDGQP-KPAGFKVGPGQTITVRMDD 70

Query: 65  VPLR---------KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGR 113
            P                R    +KP G+ +  S   G   +   LP +  R  +  V R
Sbjct: 71  TPASDASASGPYVVQADERFAAVYKPAGMHS-ESLAGGGQGLDALLPELLGRTDARLVNR 129

Query: 114 LDINTEGLLLLT--NDGGLARVLELPSTQWLRVYRVRFHGQVD 154
           LD+ T G++L     D          + Q  + Y V  HG+V+
Sbjct: 130 LDLPTSGIVLAALGADAEQEFRKLENAGQVRKEYAVLVHGRVE 172


>gi|291618642|ref|YP_003521384.1| TruC [Pantoea ananatis LMG 20103]
 gi|291153672|gb|ADD78256.1| TruC [Pantoea ananatis LMG 20103]
          Length = 259

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 50/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D      V   +       V +  RLD  T G+LL+     + 
Sbjct: 11  LVAVNKPAGWLVHRSWLDRHETQFVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEVG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G ++          ++L+ +    V              
Sbjct: 71  RLLSQQFEHHQMEKTYHAVVRGWLEGRDRLDYPLVEELDKIADKFVSDPRAPQPAVTDYA 130

Query: 176 -------QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   V +        + + +  + G+  ++++        + 
Sbjct: 131 SLATVEMPVAVSRYPTARYSLIELKPKSGRKHQLRRHMSHLRHPII 176


>gi|83648421|ref|YP_436856.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83636464|gb|ABC32431.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 248

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 33/163 (20%), Positives = 55/163 (33%), Gaps = 26/163 (15%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L    KP GL+   S+ D   T+F        I  RV  + RLD  T G+L+   D   A
Sbjct: 13  LVAIDKPSGLLVHRSEIDRHETLFAIQLLRDQIGRRVYPLHRLDKPTSGVLMFALDSDTA 72

Query: 132 RVL-ELPSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM------ 175
           +   E   T   + Y     G   ++ +         + L    V +             
Sbjct: 73  KKCGESWETGVDKAYLAIVRGVPAEEGVIDKPLKEPWDRLGDRNVSKDKPEQPAVTHYQR 132

Query: 176 ------QVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
                    +D    S  A + V  + G+  +I++ F+  +  
Sbjct: 133 LAECELPYAVDRYPTSRYALLKVRPQTGRRHQIRRHFKSLSHP 175


>gi|229016637|ref|ZP_04173574.1| Pseudouridine synthase [Bacillus cereus AH1273]
 gi|229022852|ref|ZP_04179372.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228738387|gb|EEL88863.1| Pseudouridine synthase [Bacillus cereus AH1272]
 gi|228744627|gb|EEL94692.1| Pseudouridine synthase [Bacillus cereus AH1273]
          Length = 307

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 49/268 (18%), Positives = 92/268 (34%), Gaps = 51/268 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           + VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  ITVNGEQ-RRWDELLKEGDKLQVHMFMEEEYGVDPQYGELDVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+ +G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKNGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V     K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFNKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S + L    
Sbjct: 225 ATLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSHQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSETLVR 269
              L P   EE  V++  P   + T+ +
Sbjct: 274 INFLHPITKEEIMVDVPFPAKLNNTMKK 301


>gi|163790745|ref|ZP_02185172.1| hypothetical protein CAT7_01150 [Carnobacterium sp. AT7]
 gi|159874046|gb|EDP68123.1| hypothetical protein CAT7_01150 [Carnobacterium sp. AT7]
          Length = 309

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/225 (11%), Positives = 74/225 (32%), Gaps = 32/225 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVP 66
           +++     SR  V+ ++ + +V V+  + ++    ++    + +             G+ 
Sbjct: 37  LLSVMTHTSRNSVKSILTRGQVTVDEKMTKKHNFPLLPGQVVAIQSNKAAIKETALIGMT 96

Query: 67  LRKAERTRLWLYHKPIGLVTTHS----DPDGRSTVFDNLP--SIFSRVISVGRLDINTEG 120
           +   +   + +  K  GL++  +    +      + + +   +  +R+  V RLD +T G
Sbjct: 97  ILYEDDA-IIVIDKEAGLLSIAAKFAQELTAHRQLINYVKQENQNNRIYVVHRLDRDTSG 155

Query: 121 LLLLTNDGGLARVLELPSTQWLRV--YRVRFHGQV-----------DQDKLNLLKKGIVI 167
           +++      + + ++    + ++   Y     G V            + K   +      
Sbjct: 156 VMVFAKTEKIKQDMQENWKEIVKERIYTALVEGVVREDEGTIKTWLTESKAMKVHSATYD 215

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
            G                   +   L  G+  +I+   E     V
Sbjct: 216 NGGKLAITHYKKIRNNEDFTLLEARLETGRKNQIRVHMETLGHPV 260


>gi|90962277|ref|YP_536193.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
 gi|90821471|gb|ABE00110.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius UCC118]
          Length = 295

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/247 (14%), Positives = 85/247 (34%), Gaps = 46/247 (18%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAA-------- 51
           N +       ++   + + GI SRR    ++A+      ++ +NG    +          
Sbjct: 4   NWIYSEDVSCKLKTFLKKQGI-SRR----LLAKVRYSDGKILINGKSGRKIDKIKKNDKI 58

Query: 52  VNVMSTDH----IEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
             V+  +     +    VP++   E     L  KP  + +  S      ++ + +   + 
Sbjct: 59  TLVVPDEEFRRSVPPSFVPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQ 118

Query: 106 ----SRVIS--VGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHG----- 151
                 +I   V RLD +T G+++       A  L        +  + Y     G     
Sbjct: 119 IRGYRGIIPHIVTRLDRDTSGIVIFAKH-RYAHALLDSQLKEHKISKTYTAILSGILHNN 177

Query: 152 ------QVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKV 204
                  + +D  +L+K+ ++  +       ++ ++ +   N    + L  G+  +I+  
Sbjct: 178 HYIIDLPIGRDSTSLIKRKVLFSEKAKRSKTEIFVEERIRDNTLCKIKLHTGRTHQIRVH 237

Query: 205 FEFFNWK 211
             +  + 
Sbjct: 238 CSYLGYP 244


>gi|148977837|ref|ZP_01814392.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
 gi|145962906|gb|EDK28177.1| ribosomal large subunit pseudouridine synthase A [Vibrionales
           bacterium SWAT-3]
          Length = 244

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/149 (17%), Positives = 60/149 (40%), Gaps = 28/149 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND------ 127
           + + +KP GL++     P+   +++  L   F+ +  V RLD++T GL+LL         
Sbjct: 23  ILVVNKPAGLLSVPGRLPEHHDSMWSRLVEEFADIQVVHRLDMSTSGLMLLAKHKQAERH 82

Query: 128 --GGLARVLELPSTQWLRVYRVRFHGQVD-QDKLNLL----------KKGIVIQGICYGD 174
                   L        ++Y  R  G V+ ++ L  L          K+ +  +      
Sbjct: 83  LKKQFQYRLTH------KLYYARVWGAVEHKEGLIDLPLICDWPNRPKQKVCFEDGKSSQ 136

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +  ++ Q+     + +  +  G++ +++
Sbjct: 137 TRYVVEQQEPQTTLLKLLPIT-GRSHQLR 164


>gi|116492962|ref|YP_804697.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116103112|gb|ABJ68255.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 253

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/183 (15%), Positives = 57/183 (31%), Gaps = 30/183 (16%)

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------S 106
            S  H+ +  VP+  + E     + +KP  L T  S  + + T+ + + + +        
Sbjct: 16  PSNPHVGLSDVPIDVRYEDADYLIVNKPPFLPTVQSAANQKDTLVNRVKNYYVKNNYESR 75

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVD--------- 154
            V  V RLD +T GL++       A  +        +  ++Y     G            
Sbjct: 76  VVHVVTRLDQDTSGLVIFAKH-RFAHTVMDQDLRQRKINKMYLTIVEGTFTNQHGIIETP 134

Query: 155 -----QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFF 208
                   +  +   +   G     +          N   + V L  G+  +I+  F   
Sbjct: 135 IQRDPDSFIKRM---VAPMGEGKPSLTEYWVEDTFKNFTLLKVKLHSGRTHQIRVHFSSI 191

Query: 209 NWK 211
              
Sbjct: 192 GHP 194


>gi|304321305|ref|YP_003854948.1| Hemolysin HlyA [Parvularcula bermudensis HTCC2503]
 gi|303300207|gb|ADM09806.1| Hemolysin HlyA [Parvularcula bermudensis HTCC2503]
          Length = 243

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+   +  AG   SR   +++I    V VNG+ + +A  ++  TD +E  G       R
Sbjct: 1  MRLDSYLVEAGHVRSRERAKKVIGDGYVWVNGVQVRKAGRSLQPTDRVEFRGEDFAYVSR 60

Query: 73 TRLWLY 78
              L 
Sbjct: 61 AAFKLL 66


>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 = 55.2 bits (132), Expect = 1e-05,   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|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 = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 82/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVAVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG +++      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLEE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYNGADLVECLLETGRTHQIR 233


>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 = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 82/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVAVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG +++      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLEE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYNGADLVECLLETGRTHQIR 233


>gi|330718647|ref|ZP_08313247.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc fallax KCTC
           3537]
          Length = 301

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/174 (18%), Positives = 56/174 (32%), Gaps = 27/174 (15%)

Query: 55  MSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
            S D +  D  P+    E     + +KP G+ T     D   T+ + +      +     
Sbjct: 66  ESNDLVVPDYRPMDIIFENEHWLIVNKPFGVTTVPGHADRLHTLVNQVKGHLEEIEAEDL 125

Query: 109 --ISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQD------- 156
               V RLD +T GL+LL      A  +        +  + Y     G ++Q+       
Sbjct: 126 VPHVVTRLDRDTSGLVLLAKH-RFAHAVLDDQLQRHEVEKFYVAYPSGILEQNHGEINAP 184

Query: 157 ----KLNLLKKGIVIQGICYGDMQVTLDTQKGSN----AWVTVGLREGKNREIK 202
                 + +K+ +   G          D            V V L  G+  +I+
Sbjct: 185 IGRMDGDFIKREVREDGKPSLTEYWVEDVIGADTPHPMTRVKVQLHTGRTHQIR 238


>gi|307705695|ref|ZP_07642541.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
 gi|307620709|gb|EFN99799.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK597]
          Length = 278

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +   +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNISSKELVFKDKIGRDRHDRRKRVVDTKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     + V   L+ G+  +I+
Sbjct: 190 THVSRLKQFPNKTSLVRCKLKTGRTHQIR 218


>gi|293374677|ref|ZP_06620987.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|292646694|gb|EFF64694.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
          Length = 297

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/154 (19%), Positives = 55/154 (35%), Gaps = 28/154 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +KP G+ T  S      T+ + L   ++       +  V RLD +T GLL++
Sbjct: 86  EDEYLLVINKPAGIPTIPSLRHPEKTLANALIHYYNEHEIASTIHFVNRLDRDTSGLLMV 145

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKG-----IVIQGICYG 173
                +  +L     Q  R Y     G ++++       +    +G     +   G    
Sbjct: 146 AKYRHIHHLLTKDVKQIKRKYYTLVKGVMEKNSGTVHAPIARESEGNVRRCVRADGDDSI 205

Query: 174 DMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
                L+       W  + L E     G+  +I+
Sbjct: 206 THYQVLEV------WEKLTLVECELETGRTHQIR 233


>gi|268678698|ref|YP_003303129.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
 gi|268616729|gb|ACZ11094.1| pseudouridine synthase [Sulfurospirillum deleyianum DSM 6946]
          Length = 302

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 79/209 (37%), Gaps = 27/209 (12%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA-ERT 73
           + +      S +E +++I ++RV V    L R +  +     + V   D   LR   E  
Sbjct: 18  RFLMDTFGISMKEAQKIIDKRRVFVEDEQLMRKSTLISGKIGVVVFEGDSKGLRPIFETE 77

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND--GGL 130
              ++ KP G++          T+ D + S++     +  R+D +T GL+L+       +
Sbjct: 78  DFAVFDKPSGVMIHPRKRSDGYTLNDEIKSLYGKDANAAHRIDKSTSGLVLVGKHKQSEI 137

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
           A      + +  + Y     G + ++ L    LK+ +    I     +V +D +   +  
Sbjct: 138 ALKEIFATRKVQKSYIALVKGHLKEELLIDEKLKRDVETSQIRL---KVHVDERGKPSQT 194

Query: 189 VTVGLR--E-------------GKNREIK 202
             + L   E             G+  +I+
Sbjct: 195 KVIPLHYFEDKDATLVQAFPYTGRQHQIR 223


>gi|16761743|ref|NP_457360.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|29143227|ref|NP_806569.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|213162034|ref|ZP_03347744.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E00-7866]
 gi|213424905|ref|ZP_03357655.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213622998|ref|ZP_03375781.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213648743|ref|ZP_03378796.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|289829830|ref|ZP_06547345.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|34582455|sp|Q8Z439|TRUC_SALTI RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|25322427|pir||AG0861 probable RNA pseudouridylate synthase yqcB [imported] - Salmonella
           enterica subsp. enterica serovar Typhi (strain CT18)
 gi|16504044|emb|CAD06078.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhi]
 gi|29138860|gb|AAO70429.1| putative RNA pseudouridylate synthase [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 260

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 7   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 67  SEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAREDKAPQPAV 126

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 127 TQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|313892058|ref|ZP_07825656.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
 gi|313119510|gb|EFR42704.1| pseudouridine synthase, RluA family [Dialister microaerophilus UPII
           345-E]
          Length = 328

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/224 (16%), Positives = 75/224 (33%), Gaps = 58/224 (25%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG-------RLDIN 117
             +   E   + + +KP G+++   D   + ++ D L          G       RLD N
Sbjct: 90  KDIILYENEDIIVVNKPKGMLSQR-DISRQKSLNDYLLEYIKNSNYSGFKPSICNRLDKN 148

Query: 118 TEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-- 173
           T G L+      +AR +   + +    + Y     G +  D        + ++   +   
Sbjct: 149 TSGTLICAKTFKIAREINELIKNHVINKKYLCLVFGDIKDD--------LYLKDYLFKNV 200

Query: 174 ---DMQVTLDTQKG-------------------SNAWVTVGLREGKNREIKKVFEFFNWK 211
                 V+ + ++G                      ++ V L  GK  +I+      ++ 
Sbjct: 201 ENNKAIVSNEKKEGFLEIKTKVHVIKSFKLHEYPVTFLEVTLLTGKFHQIR---AHLSY- 256

Query: 212 VNRLIRISYGPFQLGTLLAG--STREVSK--KILREQLGPHLLE 251
                    G   LG    G   + E+SK  +I R+ L  + +E
Sbjct: 257 --------IGHPILGDRKYGNNESLEISKILEIGRQLLHSYSIE 292


>gi|296104461|ref|YP_003614607.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295058920|gb|ADF63658.1| tRNA pseudouridine synthase C [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 261

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 53/168 (31%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 12  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + +         ++L+ +                   
Sbjct: 72  RLLAQQFEQHQIQKRYHAIVRGWLTEAATLDYPLVEELDKIADKFARDDKGPQPAVTEYR 131

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ + T K      ++   E     G+  ++++  +     + 
Sbjct: 132 GMATTEMPVATSKFPTTRYSLV--ELLPKTGRKHQLRRHLKHLRHPII 177


>gi|253702213|ref|YP_003023402.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251777063|gb|ACT19644.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 297

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/203 (17%), Positives = 68/203 (33%), Gaps = 32/203 (15%)

Query: 28  RREVER---MIAQQRVKVNGILLERA---AVNVMSTDH-IE-VDGVPLRKAERTRLWLYH 79
           RR ++     ++Q  V+V    ++     A+ +M  +  IE V        E       +
Sbjct: 33  RRIIDWGGCYLSQTLVRVASRTVKEGEEIALGIMEAERCIELVYKKEELLYEDKDFLAVY 92

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARV 133
           K  G  +  +    + TV   +      +        V RLD  T G++        A +
Sbjct: 93  KAAGFNSQRTPYQLKGTVEYAVECYMKSIGLRDPSRVVHRLDRGTSGVMFFPKHKQAATL 152

Query: 134 L--ELPSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +   L   +  + Y     G  DQ          K++  K G+ + G     +   +   
Sbjct: 153 ISNLLKDGKVQKTYWALVSGSPDQQSWKVEAPLGKVSKFKYGVALNGKPARTLFRVVGEG 212

Query: 183 KGSNAWVT---VGLREGKNREIK 202
            G  A V    +    G+  +I+
Sbjct: 213 AGVTA-VEAKPLT---GRTHQIR 231


>gi|15606155|ref|NP_213532.1| hemolysin [Aquifex aeolicus VF5]
 gi|2983347|gb|AAC06935.1| hemolysin [Aquifex aeolicus VF5]
          Length = 258

 Score = 55.2 bits (132), Expect = 2e-05,   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|213583042|ref|ZP_03364868.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 259

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 49/170 (28%), Gaps = 27/170 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+   
Sbjct: 6   QDPWLVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLS 65

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM- 175
               R L          + Y     G +  D +         + +      +        
Sbjct: 66  SEAGRRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAREDKAPQPAV 125

Query: 176 ---------QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                    ++ + T +       +   E   G+  ++++        + 
Sbjct: 126 TQYRGLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 175


>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 = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 82/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVAVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG +++      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLEE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYEGADLVECLLETGRTHQIR 233


>gi|240013751|ref|ZP_04720664.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae DGI18]
 gi|240120819|ref|ZP_04733781.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID24-1]
          Length = 307

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPIHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLARGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>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 = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 24/57 (42%), Gaps = 1/57 (1%)

Query: 7  VQENFTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             N    R+ K++   G+AS R + + +I+   V VNG     +   V     + V
Sbjct: 3  TPSNQDSIRLDKLMVELGLASSREKAQALISSGLVTVNGEKARSSDQRVRRGTKVIV 59


>gi|229817354|ref|ZP_04447636.1| hypothetical protein BIFANG_02616 [Bifidobacterium angulatum DSM
           20098]
 gi|229785143|gb|EEP21257.1| hypothetical protein BIFANG_02616 [Bifidobacterium angulatum DSM
           20098]
          Length = 314

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/219 (15%), Positives = 71/219 (32%), Gaps = 35/219 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRKAERTRL---- 75
           SR +   +I   +V+V    + + +  + + + +E+D         P+            
Sbjct: 27  SRSKAATLIDTGQVRVLDREITK-STTLQAGETVEIDLVEERKEPEPIANDMAIVYEDDD 85

Query: 76  -WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTEGLLLLT 125
             +  KP+G+    S      TV  +L      + + G         RLD+ T GL+L+ 
Sbjct: 86  VVVVDKPVGVAAHASVGWTGPTVLGSLLDRGVHITAYGAAGRQGIVSRLDVGTSGLMLVC 145

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD-----------KLNLLKKGIVIQGICY 172
                   +       + ++ Y     G + +D           K++  +  +   G   
Sbjct: 146 KSDLAYVEMRRQFAEHEVVKTYHALVQGNLKEDRATIEAPIGRAKVSDFRFCVTPAGKPA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 ++        V V L  G+  +I+  F      
Sbjct: 206 ITHWDVMERFGSEATLVKVNLETGRTHQIRVHFSSIGHP 244


>gi|157372031|ref|YP_001480020.1| tRNA pseudouridine synthase C [Serratia proteamaculans 568]
 gi|157323795|gb|ABV42892.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 256

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/160 (16%), Positives = 52/160 (32%), Gaps = 27/160 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D      V   +       V +V RLD  T G+LL+   
Sbjct: 7   QDEHLVAVNKPSGWLVHRSWLDRHETRFVMQTVRDQIGQHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM- 175
             +AR+L       Q  + Y     G V +         ++L+ +      +        
Sbjct: 67  SEVARLLSQQFEQHQMQKTYHAVVRGYVLEGATIDYPLTEELDKIADKFASKDKGPQPAV 126

Query: 176 -----------QVTLDT-QKGSNAWVTVGLREGKNREIKK 203
                       V +   +    + V +    G+  ++++
Sbjct: 127 THYRPLARVEMPVAIGRYESARYSLVELKPENGRKHQLRR 166


>gi|312884626|ref|ZP_07744329.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
 gi|309367718|gb|EFP95267.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           caribbenthicus ATCC BAA-2122]
          Length = 256

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/156 (18%), Positives = 56/156 (35%), Gaps = 34/156 (21%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E   +   +K  GL++      +   +++  L   +  V  + RLD++T GL++L  +  
Sbjct: 30  EDDAILAVNKQPGLLSVPGRKVEHHDSIYTRLVERWPEVQVIHRLDMDTSGLMVLAKNKP 89

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQV--DQDKLNLLKKGIVIQGICYGDM-QVT 178
                       L        +VY  R  G V  D+  ++      +I         +V 
Sbjct: 90  AERALKKQFQYRLTH------KVYYARVWGNVAADEGTIDAP----LICDWPNRPKQKVC 139

Query: 179 LDTQKGSNAWVTVGLRE------------GKNREIK 202
            +T K S     V  RE            G++ +++
Sbjct: 140 YETGKSSQTHFQVVKRESQTTIVRLLPITGRSHQLR 175


>gi|300741275|ref|ZP_07071296.1| RNA pseudouridine synthase, RluA family [Rothia dentocariosa M567]
 gi|300380460|gb|EFJ77022.1| RNA pseudouridine synthase, RluA family [Rothia dentocariosa M567]
          Length = 302

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 70/234 (29%), Gaps = 51/234 (21%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKV----N------------GILL-------ERA 50
            R+   +A A    R      I    V+V    N            G  +          
Sbjct: 1   MRLDAALAGALEIPRTRASGWIRDGHVRVVQRGNELKIGKSHKLSAGETVFVNAPAPRDL 60

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------- 101
           A         +VDG  +   +   + +  KP G+    S      TV   L         
Sbjct: 61  ADIQPE----KVDGFGIVYCDDDIVVV-DKPAGVAAHPSHGWHGPTVLSALLGEGVTVAT 115

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DK 157
                R   V RLD+ T GL+++         L+         +VY     G  D     
Sbjct: 116 SGAAERQGIVHRLDVGTSGLMVVARSERAYTELKRAFKDRTVEKVYHTLVQGLPDPLMGT 175

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++           K  ++  G        TL++  GS + V V L  G+  +I+
Sbjct: 176 IDAPIGRHPGHEWKFAVIEDGRSSITHYETLES-FGSASLVEVHLETGRTHQIR 228


>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 = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   +   G+  SR + +R+IA  +V VNG+ + +A+  V   D I  D
Sbjct: 11 RLDVALLERGLTDSRSKAQRLIADGKVSVNGVTVTKASAKVGGDDVIAAD 60


>gi|50312303|ref|XP_456184.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49645320|emb|CAG98892.1| KLLA0F24794p [Kluyveromyces lactis]
          Length = 597

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 63/205 (30%), Gaps = 28/205 (13%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           IA  +V +N  +       V + D I          V    ++   E   L +  KP G+
Sbjct: 132 IAAGKVYLNDSVA-DLDSVVRNGDLITHEIHRHEPSVTSRLIKTVFEDDDLLVIDKPSGI 190

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
               +     +TV   L       V    RLD  T GL+ L  +   A  +     + + 
Sbjct: 191 PVHPTGRYRFNTVTKILEKERGYTVHPCNRLDRLTSGLMFLAKNPRGADRMADQMKAREV 250

Query: 142 LRVYRVRFHGQVDQDKL---NLLKK-----G------IVIQGICYGDMQVTLDTQKGSNA 187
            + Y  R  G+     +     L+      G      I  +G           +  G  +
Sbjct: 251 SKEYVARVVGEFPVGLIVVDKPLRTVDPKVGLNVTCKITDEGAKEARTSFERISFDGKTS 310

Query: 188 WVTVGLREGKNREIKKVFEFFNWKV 212
            V      G+  +I+   +     +
Sbjct: 311 IVRCKPFTGRTHQIRVHLQHLGHPI 335


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

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/255 (14%), Positives = 89/255 (34%), Gaps = 64/255 (25%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLER------ 49
           +   V+E  +  R+ +        +A  G       ++++   +++V+G  ++       
Sbjct: 4   EIKKVEEGESGMRLDRWFKVHYPGLA-FGYL-----QKLLRSGQIRVDGRRVKTDIRLIV 57

Query: 50  ------AAVNVMSTDHIEVDGVPLRKAER------------TRLWLYHKPIGLVTTHS-- 89
                   ++V +  ++ V    +    +             ++++ +KP GL       
Sbjct: 58  GQSIRVPFLSVDNKKNLSVTDKTIHDQAKLAILEKMLLYKDPKIFVLNKPAGLAVQGGSG 117

Query: 90  ---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
                DG   V+ N      R+  V RLD  T G+L++    G A+ L     + +  + 
Sbjct: 118 LTCHIDGMLEVWRNKKGEKPRL--VHRLDRETSGVLIIARSRGAAQALTAAFRARETKKT 175

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----------------A 187
           Y     G V + K + +   +V +    GD     +  +  +                 +
Sbjct: 176 YWALVRG-VPRKKQDKISTWMVKETTAQGDKMRVCEHGEPDSNHAVSYYRVLDTRGRALS 234

Query: 188 WVTVGLREGKNREIK 202
           W+ +    G+  +++
Sbjct: 235 WLEMEPYTGRTHQLR 249


>gi|260654228|ref|ZP_05859718.1| ribosomal large subunit pseudouridine synthase C [Jonquetella
           anthropi E3_33 E1]
 gi|260630861|gb|EEX49055.1| ribosomal large subunit pseudouridine synthase C [Jonquetella
           anthropi E3_33 E1]
          Length = 276

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 68/210 (32%), Gaps = 32/210 (15%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVP-LRKAERTR--------LWLY 78
           +   +  V+++G         V +   + V     D  P ++   R          + + 
Sbjct: 3   KFFRKGSVRLDGARA-DFRTKVAAGQMVFVPWEAPDAQPEVQVRHRPLDVLYRSDSVLVI 61

Query: 79  HKPIGLVTTHSDPDGRSTV----FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           +KP GL++   D  G  +V                 V RLD NT G+++L  DG   R L
Sbjct: 62  NKPAGLLSQP-DTKGEDSVATRALGYASDPAFGAQLVHRLDRNTSGVMILALDGQALRSL 120

Query: 135 ELPSTQWL--RVYRVRFHGQVDQD---KLNLLKK------GIVIQGICYGDMQVTLDTQK 183
            +   +    + Y     GQ+         LLK        +   G         L T  
Sbjct: 121 MVCFKERTANKTYLALVSGQLPPSGQIDAPLLKDPDKKLVRVASNGERAVTRFRRLAT-D 179

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           G  +   V +  G+  +I+         + 
Sbjct: 180 GQFSLAEVEILTGRTHQIRVHMNHIGHPIL 209


>gi|188534848|ref|YP_001908645.1| tRNA pseudouridine synthase C [Erwinia tasmaniensis Et1/99]
 gi|188029890|emb|CAO97774.1| tRNA pseudouridine synthase C [Erwinia tasmaniensis Et1/99]
          Length = 255

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/168 (19%), Positives = 60/168 (35%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  D   TVF        I   V +V RLD  T G+LL+     +A
Sbjct: 11  LVAVNKPSGMLVHRSWLDRHETVFAMQTVRDQIGQHVFTVHRLDRPTSGVLLMALSSDVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIV------------I 167
           R+L       Q  + Y     G           + ++ L+ +                  
Sbjct: 71  RLLSQQFELHQLQKTYHAVVRGWLAGAETLDYPLTEE-LDKIADKFSQPEKAPQPAVTHW 129

Query: 168 QGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKK-VFEFFNWKVN 213
           +GI   ++ V +   + S  + V +    G+  ++++ +       + 
Sbjct: 130 RGIATAELPVPVGRYETSRYSLVEMLPESGRKHQLRRHMT-HLRHPII 176


>gi|170017524|ref|YP_001728443.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
 gi|169804381|gb|ACA82999.1| Pseudouridylate synthase, 23S RNA-specific [Leuconostoc citreum
           KM20]
          Length = 300

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/181 (18%), Positives = 57/181 (31%), Gaps = 27/181 (14%)

Query: 57  TDHIEVDGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------- 108
            D +  D  PL        WL   KP G+ T     D   T+ + +      +       
Sbjct: 68  NDLVVPDYRPLDIIFENEHWLVVDKPYGVTTVPGHADRLHTLVNQVKGHLEEINAEDLVP 127

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVDQDK-------- 157
             V RLD +T G++LL      A  +    L      + Y     G + +D         
Sbjct: 128 HVVTRLDRDTSGIVLLAKH-RFAHAVLDQQLQDHTVEKFYLAYPSGILTEDHGDINAPIG 186

Query: 158 ---LNLLKKGIVIQGICYGD----MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
               + +K+ +   G          +   +  +     V V L  G+  +I+  F+    
Sbjct: 187 RVEGDFIKREVRDDGKPSRTEYWVERRYDENGEQPMTRVKVQLHTGRTHQIRVHFKNIGH 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|144897601|emb|CAM74465.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 230

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 49/156 (31%), Gaps = 17/156 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSI----FSRVISVGRLDINTEGLLLLTNDGGL 130
           + +  KP GL       DG   + D L  +            RLD +T G L+L      
Sbjct: 17  VLIIDKPAGLAVHAGARDGSHHLMDLLEPLRFGLPRNPELAHRLDRDTSGCLVLGRHRKA 76

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQD------KLNLL--KKG---IVIQGICYGDMQV 177
              L      ++  + Y     G+   +      +L  L  + G   +V         + 
Sbjct: 77  LARLGEIFAGSEAQKTYWAVVVGKPPAESGIIDKRLKKLERRHGWRMVVDDKGQDAVTEY 136

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +    G  +W+    R G+  +I+         + 
Sbjct: 137 RVLGGNGRLSWIEAKPRTGRTHQIRVHLAAIGCPIV 172


>gi|45658116|ref|YP_002202.1| ribosomal large subunit pseudouridine synthase C [Leptospira
           interrogans serovar Copenhageni str. Fiocruz L1-130]
 gi|45601358|gb|AAS70839.1| ribosomal large subunit pseudouridine synthase C [Leptospira
           interrogans serovar Copenhageni str. Fiocruz L1-130]
          Length = 394

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/167 (16%), Positives = 64/167 (38%), Gaps = 20/167 (11%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           ++ +  +  R+   +++     SR   ++ I + R+ ++   ++   V++   D I    
Sbjct: 47  LISKEESGTRLDHFLSKKFTYHSRTTWQKEITEGRILISSKTVK-PGVSLKEGDLISYH- 104

Query: 65  VPLRKAERTR---LWLYH---------KPIGLVTTHSDPDGRSTVFDNLPS--IFSRVIS 110
            P++K E        + +         KP  L    +    +  +   L     F  + +
Sbjct: 105 -PIQKEEPPVRNDYKILYEDEFFVAVDKPGDLPIHPAGIYRKGNLLTFLKESGKFKDLFT 163

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRFHGQVDQ 155
           V RLD  T G++L   +  +A +L    +     + Y  + HG   +
Sbjct: 164 VHRLDRETSGVILFAKNSEIASILSKSFSLGNIQKYYITKVHGNFPK 210


>gi|329120908|ref|ZP_08249540.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
 gi|327471367|gb|EGF16818.1| tRNA pseudouridine synthase A [Dialister micraerophilus DSM 19965]
          Length = 328

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 85/262 (32%), Gaps = 78/262 (29%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT 86
           S++E +  I +  ++                D I  +   +         + +KP G+++
Sbjct: 72  SKKESKE-ILKGNIE-----------KFSFKDIILYENEDI--------IVVNKPKGMLS 111

Query: 87  THSDPDGRSTVFDNLPSIFSRVISVG-------RLDINTEGLLLLTNDGGLARVL--ELP 137
              D   + ++ D L          G       RLD NT G L+      +AR +   + 
Sbjct: 112 QR-DISRQKSLNDYLLEYIKNSNYSGFKPSICNRLDKNTSGTLICAKTFKIAREINELIK 170

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG-----DMQVTLDTQKG-------- 184
           +    + Y     G +  D        + ++   +         V+ + ++G        
Sbjct: 171 NHVINKKYLCLVFGDIKDD--------LYLKDYLFKNVENNKAIVSNEKKEGFLEIKTKV 222

Query: 185 -----------SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG-- 231
                         ++ V L  GK  +I+      ++          G   LG    G  
Sbjct: 223 HVIKSFKLHEYPVTFLEVTLLTGKFHQIR---AHLSY---------IGHPILGDRKYGNN 270

Query: 232 STREVSK--KILREQLGPHLLE 251
            + E+SK  +I R+ L  + +E
Sbjct: 271 ESLEISKILEIGRQLLHSYSIE 292


>gi|319776874|ref|YP_004136525.1| ribosomal large subunit pseudouridine synthase c [Mycoplasma
           fermentans M64]
 gi|318037949|gb|ADV34148.1| Ribosomal large subunit pseudouridine synthase C [Mycoplasma
           fermentans M64]
          Length = 280

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/254 (14%), Positives = 77/254 (30%), Gaps = 59/254 (23%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-----------------L 75
           +++  + +K+NG+ +      +   D I++ G+     +  +                 +
Sbjct: 33  KILRNKDIKINGVRINDPQYIINEKDIIQIYGIEANDYQNKKFENSAKKDFKIIYEDDNI 92

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLL-------- 124
            +  KPI L     +      V   L        +   VGRLD  T GL++         
Sbjct: 93  LIVSKPINLAVHSENNCLDKQVLSYLKYNQKDSFKPSHVGRLDKVTSGLMIYAKNYATLV 152

Query: 125 -----TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
                T        L+    +  ++  +        +KL+ +    V+       +  TL
Sbjct: 153 ELNYKTGFFEKIYKLKSDFNEVKKLVEINIQH---DEKLHKM----VVTNNAKDPLAKTL 205

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV-------------NRLIRISYGPFQLG 226
              K +  + ++ L  GK  +I+         +               L   S     L 
Sbjct: 206 FYTKNNEIFASI-LT-GKKHQIRLSMSHLKTPIYGDIKYDGKKADRLYLHCYSITFKNLD 263

Query: 227 TLLAGSTREVSKKI 240
                S + ++ K 
Sbjct: 264 N----SLKYLNNKE 273


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

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/224 (16%), Positives = 81/224 (36%), Gaps = 61/224 (27%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV----------------------DGVPLRK 69
           ++++   +V+V+G   + A   + +   + +                      DG  L +
Sbjct: 27  QKLLRAGQVRVDGGRAK-ADTRIQAGQAVRIPPLGVDEKAAGPMTAKTIRNQQDGDVLSQ 85

Query: 70  ---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--------VGRLDINT 118
               E  ++++++KP GL        G S V  ++  +     S        V R+D +T
Sbjct: 86  MLLYEDPKIFVFNKPAGLAV-----QGGSGVTRHIDGMLEAWRSTKGEKPRLVHRIDRDT 140

Query: 119 EGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKL------------NLLK 162
            G+L++    G A+ L          + Y     G     +DK+            + ++
Sbjct: 141 SGVLVVARTRGAAQALTASFRERDTKKTYWALVKGVPRKREDKISTWLVKEQTPDGDKMR 200

Query: 163 KGIVIQGICYGDMQV---TLDTQKGSN-AWVTVGLREGKNREIK 202
             +   G    D  V    +  + G+N AW+ +    G+  +++
Sbjct: 201 --VCQHGEPDSDHAVSYYRIIEKAGNNLAWLEMEPYTGRTHQLR 242


>gi|126737039|ref|ZP_01752774.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           SK209-2-6]
 gi|126721624|gb|EBA18327.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           SK209-2-6]
          Length = 348

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 45/272 (16%), Positives = 83/272 (30%), Gaps = 77/272 (28%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E    QR+ + +       RR         +E+M  +  ++++G  ++ A+  V + 
Sbjct: 8   TVTEEDDDQRIDRWL-------RRLFPHVNQGRIEKMCRKGELRLDGGRVK-ASTRVATG 59

Query: 58  DHIEV---------------------DGVPLRK---AERTRLWLYHKPIGLVT-----TH 88
             + V                     D   +R     +   + + +KP GL       T 
Sbjct: 60  QVVRVPPLPASDLKPAEPRATKISDADAKMIRGCVIYKDDDVIVLNKPAGLAVQGGSGTT 119

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
              DG S           R+  V RLD +T G+L+L  +   A+ L          ++Y 
Sbjct: 120 RHVDGLSEALRLEAEEKPRL--VHRLDKDTSGVLVLARNRKAAQALTAAFRHKNTRKIYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIV---------------------IQGICYGDMQ----VTLDT 181
               G      L  +K G+V                     I              TL  
Sbjct: 178 ALVAGVPTP-YLGEIKTGLVKAPGHGRSGEGEKMIPVHPRDIDDTPGAKRAHTHYATLYR 236

Query: 182 QKGSNAWVTVG-LREGKNREIKKVFEFFNWKV 212
                +WV +  +  G+  +++         +
Sbjct: 237 VASRASWVAMEPIT-GRTHQLRAHMAAIGHPI 267


>gi|238809659|dbj|BAH69449.1| hypothetical protein [Mycoplasma fermentans PG18]
          Length = 296

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/254 (14%), Positives = 77/254 (30%), Gaps = 59/254 (23%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-----------------L 75
           +++  + +K+NG+ +      +   D I++ G+     +  +                 +
Sbjct: 49  KILRNKDIKINGVRINDPQYIINEKDIIQIYGIEANDYQNKKFENSAKKDFKIIYEDDNI 108

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLL-------- 124
            +  KPI L     +      V   L        +   VGRLD  T GL++         
Sbjct: 109 LIVSKPINLAVHSENNCLDKQVLSYLKYNQKDSFKPSHVGRLDKVTSGLMIYAKNYATLV 168

Query: 125 -----TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
                T        L+    +  ++  +        +KL+ +    V+       +  TL
Sbjct: 169 ELNYKTGFFEKIYKLKSDFNEVKKLVEINIQH---DEKLHKM----VVTNNAKDPLAKTL 221

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV-------------NRLIRISYGPFQLG 226
              K +  + ++ L  GK  +I+         +               L   S     L 
Sbjct: 222 FYTKNNEIFASI-LT-GKKHQIRLSMSHLKTPIYGDIKYDGKKADRLYLHCYSITFKNLD 279

Query: 227 TLLAGSTREVSKKI 240
                S + ++ K 
Sbjct: 280 N----SLKYLNNKE 289


>gi|291287096|ref|YP_003503912.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
 gi|290884256|gb|ADD67956.1| pseudouridine synthase [Denitrovibrio acetiphilus DSM 12809]
          Length = 248

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/157 (18%), Positives = 56/157 (35%), Gaps = 30/157 (19%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLER------------AAVN---VMSTD 58
            R S+ ++     S R  ++ I    V ++GI+  +            A      V   D
Sbjct: 1   MRYSRRLSEQYGLSVRMAKKYIKDGMVALDGIVTTKDLDSDEGFLELTAETKRPDVTPAD 60

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           +I          E   +  + KP  + T    PD   T+ D + +  +    + RLD  T
Sbjct: 61  YIV--------KEFDHIVFFDKPAFMHTDLQKPDDPITMTDVIMAYSNEFSFISRLDYTT 112

Query: 119 EGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
           +G++    D            +  +VY     G++++
Sbjct: 113 DGVIAAVRDDFFV-------FETRKVYLAHVEGKIEK 142


>gi|260587780|ref|ZP_05853693.1| pseudouridylate synthase [Blautia hansenii DSM 20583]
 gi|260542045|gb|EEX22614.1| pseudouridylate synthase [Blautia hansenii DSM 20583]
          Length = 337

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 55/360 (15%), Positives = 113/360 (31%), Gaps = 87/360 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +V+E  + QR+ K + +      +E       +M+ ++ + +NG         +   D I
Sbjct: 5   VVKEIESGQRLDKFLGKYL----KEAPKSFLYKMLRKKNITLNGKKAT-GNEKLQPNDEI 59

Query: 61  EV---DGVPLRK---------------AERTRLWLYHKPIGLVTTHSDPD-----GRSTV 97
           ++   D    +                 E   +   +KP+G+++  ++ +        T 
Sbjct: 60  KLFLSDDTLEKFCGEEKSSSRTELDIVYENNHVLFVNKPVGMLSQKAEKEDVSLVEYITG 119

Query: 98  FDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGLARVLELPST-----QWLRVY 145
           +       +       R     RLD NT G++     G   + L+  S         + Y
Sbjct: 120 YLLEEKFLTKEDLRTFRPGVCNRLDRNTSGIVAA---GKTVQGLQEMSQWFKERNLHKYY 176

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS----------------NAWV 189
                G+V++       KG + +      + V  + ++GS                +  +
Sbjct: 177 LTLVKGKVER---PAHVKGYLWKDEKKNKVAVFQEKREGSLPIETKYEPLGISKNGDTLL 233

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQLG 246
            V L  G++ +I+         V                  G  +  SK+     R++ G
Sbjct: 234 KVELLTGRSHQIRSHLAGLGHPVI-----------------GDWKYGSKEKNENFRKKYG 276

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
                     L  P             I ++VP+ F +  K        S++ K     H
Sbjct: 277 IEFQLLHAWKLSFPKTEGILKELSLKTITADVPEKFQKALKGEGLLEFTSEKNKGDVKKH 336


>gi|167464208|ref|ZP_02329297.1| pseudouridine synthase, RluA family protein [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322383741|ref|ZP_08057492.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321151953|gb|EFX44896.1| pseudouridylate synthase-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 310

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 91/251 (36%), Gaps = 48/251 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M  K+I+Q+     R  K+++R          ++  +  + VNG   +  +V V + D +
Sbjct: 18  MLLKSIIQKRLKVSR--KLLSRL---------KLTEKG-IMVNGTR-QYISVKVKTGDLV 64

Query: 61  EV-------DGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
           E+       D +  +        E  +L + +K  G++   +     +TV + +   +  
Sbjct: 65  ELRMEQETSDDILPQSIPLNILHEDEQLLVLNKEAGMIVHPTHGHYVNTVANAVVFHWQQ 124

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHG-------- 151
                R   V RLD  T G+L +  +  + + +          + Y    +G        
Sbjct: 125 KGICHRFRPVHRLDQETSGVLAIAKNPYVHQQISEQMMMHALDKQYLALVYGVVKEDRGT 184

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D++K N   + +   G         L    G+   V + L  G+  +I+   +  
Sbjct: 185 LDDPIDRNKDNPHIRTVTPSGYPAVTHYEVLKRMNGAT-LVRLWLETGRTHQIRVHMQHL 243

Query: 209 NWKVN--RLIR 217
              +   +L R
Sbjct: 244 GHPLLGDKLYR 254


>gi|229154958|ref|ZP_04283072.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
 gi|228628516|gb|EEK85229.1| Pseudouridine synthase [Bacillus cereus ATCC 4342]
          Length = 307

 Score = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 91/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +  +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKNQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              V + L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVMLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>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 = 55.2 bits (132), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           T +R+ K++   G+A SR   + +I   +V V+  L ++A + V     I + G PL  
Sbjct: 1  MTKERLDKLVLERGLAPSRERAKALIMAGQVVVDDHLADKAGLMVPVEAEIRLKGEPLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>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 = 55.2 bits (132), 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 = 55.2 bits (132), 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|315223482|ref|ZP_07865338.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga ochracea F0287]
 gi|314946517|gb|EFS98509.1| ribosomal large subunit pseudouridine synthase family protein
           [Capnocytophaga ochracea F0287]
          Length = 226

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/189 (14%), Positives = 52/189 (27%), Gaps = 38/189 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   +   +K +G +    D  G + + D +     +         +  V RLD  T G+
Sbjct: 15  EDNHVIAVNKRVGDIVQG-DKTGDTPLSDIVKQYLKQKYNKPGEVFLGVVHRLDRPTTGV 73

Query: 122 LLLTNDGGLARVLE---LPSTQWLRVYRVRFH--GQVDQDKLNLL-------KKGIVIQG 169
           +L          L        +  + Y         V++D L           K +    
Sbjct: 74  VLFAKTSKALARLNTMFSNKQEVQKTYWALVDAKPPVEEDTLTHWLVRNEKQNKSVAYNK 133

Query: 170 ICYGDMQV----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
                 +      L         + + L  G++ +I+         +             
Sbjct: 134 EMQQSKKAVLHYKLLKSYERYYLLEIDLITGRHHQIRAQLAAIGLHIK------------ 181

Query: 226 GTLLAGSTR 234
           G L  G+ R
Sbjct: 182 GDLKYGAKR 190


>gi|229101991|ref|ZP_04232704.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
 gi|228681378|gb|EEL35542.1| Pseudouridine synthase [Bacillus cereus Rock3-28]
          Length = 307

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 70/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D  +V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKFQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQ-----------VDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+           + +D+ +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKKGTIEAAIGRDRHHATRRRVSPKGDEAITYYKVEKYFKKHN 224

Query: 186 NAWVTVGLREGKNREIK 202
             +VT+ L  G+  +I+
Sbjct: 225 TTFVTLQLETGRTHQIR 241


>gi|227545484|ref|ZP_03975533.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           CF48-3A]
 gi|300908150|ref|ZP_07125618.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           SD2112]
 gi|227184534|gb|EEI64605.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           CF48-3A]
 gi|300894715|gb|EFK88069.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus reuteri
           SD2112]
          Length = 301

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/185 (16%), Positives = 61/185 (32%), Gaps = 35/185 (18%)

Query: 55  MSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
            + D++++   P+    E     + +KP G+ T    P     V D+L +          
Sbjct: 66  TANDNVDISEAPIDIIYEDQDFLIMNKPAGVATV---PAHNVPVADSLVNRVKGYYKRQN 122

Query: 109 ------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDK-- 157
                     RLD +T GL++       A  +     +     + Y     G+V  +   
Sbjct: 123 YENQVTHVATRLDRDTSGLVVFPKH-RFAHAVLDEQLKKHLVKKNYLALIKGKVPAEHGY 181

Query: 158 ----LNL----LKKGIVIQGICYGDMQVTLDTQKGSN---AWVTVGLREGKNREIKKVFE 206
               +        K +V      G   VT   ++  N   + + + L  G+  +I+  F 
Sbjct: 182 IDAPIQRDPSSFVKRMV---GKEGKASVTEYWRQECNVQASLIKIRLHTGRTHQIRVHFA 238

Query: 207 FFNWK 211
              + 
Sbjct: 239 SLGFP 243


>gi|300774785|ref|ZP_07084648.1| tRNA pseudouridine synthase C [Chryseobacterium gleum ATCC 35910]
 gi|300506600|gb|EFK37735.1| tRNA pseudouridine synthase C [Chryseobacterium gleum ATCC 35910]
          Length = 231

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/158 (18%), Positives = 58/158 (36%), Gaps = 16/158 (10%)

Query: 72  RTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
              L   +KP GL+   S          + +    I  +V  V RLD  T G+LL T D 
Sbjct: 8   DEHLIAINKPSGLLVHKSFYAGEADTYAIQELKKQIGQKVYPVHRLDRKTSGVLLFTLDK 67

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQDK--------LNLLKKGIVIQGICYGDMQVT 178
              R++     S +  + Y     G   +++         N +++  V         ++ 
Sbjct: 68  DTLRIMSEQFSSREVEKKYLAILRGWTKEEETIDYDLINENEVRQNAVTNYRRLQTSEID 127

Query: 179 LDTQKGSNAWVTVG--LRE-GKNREIKKVFEFFNWKVN 213
           L   K   +  ++   + E G+  +++K F+     + 
Sbjct: 128 LPFLKHQTSRYSLVEAIPETGRFHQLRKHFKHILHPIL 165


>gi|239994407|ref|ZP_04714931.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase [Alteromonas macleodii ATCC
           27126]
          Length = 313

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 83/260 (31%), Gaps = 70/260 (26%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMS 56
            V+ +   QR+   +       R +++        R++ +  V+VN G +  +    + +
Sbjct: 13  TVEADLAGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKGRV--KPEYKLQA 63

Query: 57  TDHIEV------DGVPLRKA--------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
            D I +      +G P                  E  R+ + +KP G+        G S 
Sbjct: 64  DDLIRIPPVRVSEGAPAPSPKLDKIASLESHILFEDDRILVINKPSGMAV-----HGGSG 118

Query: 97  VFDNLPSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV 147
           +   L      +         V RLD +T G +L+       R +   L + +  + Y  
Sbjct: 119 LSFGLIEGLRALRPDAKFMELVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYNA 178

Query: 148 RFHGQVDQ---DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-- 195
              G+  +        L+K ++  G     M    D  K S     +        L E  
Sbjct: 179 LVAGEWPKTRFKVKAALRKNVLQSGER---MVSVSDDGKPSETRYRILEEYAGATLVEAS 235

Query: 196 ---GKNREIKKVFEFFNWKV 212
              G+  +I+         +
Sbjct: 236 PITGRTHQIRVHCLHAGHPI 255


>gi|254493346|ref|ZP_05106517.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 1291]
 gi|226512386|gb|EEH61731.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 1291]
          Length = 307

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPIHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLARGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|322386603|ref|ZP_08060228.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
 gi|321269276|gb|EFX52211.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           cristatus ATCC 51100]
          Length = 296

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/204 (17%), Positives = 70/204 (34%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHI--EVDGVPLRKAE-------------- 71
           R++   +  ++ + VNG  +      V   D I    D     + E              
Sbjct: 28  RKIRHFLRTKKHILVNGESI-HWQTLVKPGDSIQLTFDKEDYPEKELPAGHPHLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ +  ++P   + +      +      V RLD  T G +L   +  + 
Sbjct: 87  DEHLIIVNKPNGMKSHGNEPTEVALLNHVSSYVGQTCYVVHRLDKETSGAILFAKNPFVL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L + +  R Y     G+     +           +  K+ +  +   Y +  VT
Sbjct: 147 PILNRLLENKEISREYWALAQGKFHSKTIVYKDKIGRDRHDRRKRLVDPKKGLYAETHVT 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
                G+   V   L+ G+  +I+
Sbjct: 207 RLKDFGNTTLVKCQLKTGRTHQIR 230


>gi|229095877|ref|ZP_04226855.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
 gi|229114830|ref|ZP_04244243.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228668522|gb|EEL23951.1| Pseudouridine synthase [Bacillus cereus Rock1-3]
 gi|228687501|gb|EEL41401.1| Pseudouridine synthase [Bacillus cereus Rock3-29]
          Length = 307

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 70/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D  +V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKFQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQ-----------VDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+           + +D+ +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKKGTIDAAIGRDRHHATRRRVSPKGDEAITYYKVEKYFKKHN 224

Query: 186 NAWVTVGLREGKNREIK 202
             +VT+ L  G+  +I+
Sbjct: 225 TTFVTLQLETGRTHQIR 241


>gi|163796887|ref|ZP_02190844.1| Pseudouridine synthase, RluD [alpha proteobacterium BAL199]
 gi|159177876|gb|EDP62425.1| Pseudouridine synthase, RluD [alpha proteobacterium BAL199]
          Length = 331

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/215 (16%), Positives = 73/215 (33%), Gaps = 46/215 (21%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------------DGVPLRKAERT 73
           +++   +V+V+G  ++ A   + +   I +                    G      +  
Sbjct: 36  KLLRTGQVRVDGRRVK-AGERLEAGQTIRIPPMDVPAASAEAVKAKPGGKGDAETAEQLR 94

Query: 74  RLWLY--------HKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           RL L+        +KP GL               +   +     R   V RLD +T G+L
Sbjct: 95  RLILHTDRDVLAINKPAGLAVQGGSGITKHVDGALDGLMFDAKERPRLVHRLDKDTSGVL 154

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------QDKLNLL--KKG----IVIQ 168
           L+      AR L     +   +++Y     G+        +  +  L  + G    I ++
Sbjct: 155 LVGRSYQAARRLTEAFRAKSAMKIYWALVVGEPKPNAGSIEGAIGKLPGRAGEKMAIDLE 214

Query: 169 GICYGDMQ-VTLDTQKGSNAWVTVGLREGKNREIK 202
                  + VT++   G   WV +    G+  +++
Sbjct: 215 NGKRAFTRYVTVERLGGKVTWVALFPVTGRTHQLR 249


>gi|297568139|ref|YP_003689483.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
 gi|296924054|gb|ADH84864.1| pseudouridine synthase, RluA family [Desulfurivibrio alkaliphilus
           AHT2]
          Length = 334

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/145 (20%), Positives = 52/145 (35%), Gaps = 15/145 (10%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERT 73
              +R + ++ +   R++VNG  +      + + D +   G  L +           E  
Sbjct: 37  TYLTREQWQQELVDGRLRVNGEPV-PPERLLAAADRVSYRGRELAEPPVASHFSVVYEDD 95

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP  L         R T++  L       + + V RLD  T GL+++      A
Sbjct: 96  DLLVVNKPAPLPCHPGGRYFRHTLWRLLQERCGVPKPLLVNRLDRETSGLVVVAKKRAAA 155

Query: 132 RVLELP--STQWLRVYRVRFHGQVD 154
           R         Q  + Y V   G+  
Sbjct: 156 RDCARQWQEQQVEKRYLVLVEGEFP 180


>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 = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + QR+  ++    +  SR++ +R+I    V+VN  ++++    V     I+V
Sbjct: 1  MSKQRLDTLLVDRQLCDSRQQAQRLIRAGEVRVNQQVIDKPGTEVDVQAQIQV 53


>gi|7440168|pir||JE0399 ribosomal protein S4 - Thermus aquaticus (strain HB8)
          Length = 209

 Score = 54.8 bits (131), 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|312875913|ref|ZP_07735903.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311797394|gb|EFR13733.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 293

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 57/172 (33%), Gaps = 24/172 (13%)

Query: 54  VMSTDHIE-------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           V+  D I        V+G      E       +KP GL +  S      T+ + +    +
Sbjct: 58  VIEVDLISSKSNIAPVEGNIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLN 117

Query: 107 RV----ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD------ 154
                   + RLD +T G+++   +     ++       Q  + Y    HG++       
Sbjct: 118 SKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSHEFEKRQVEKTYIAIVHGRLTKKSGLI 177

Query: 155 QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
           +  +     GI  +      +      +     + + + +  +  G+  +++
Sbjct: 178 EKPIKRSDDGIKREIHQDGSFASTYYEVIDSFENFSLLKLKPIT-GRTHQLR 228


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

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/266 (13%), Positives = 80/266 (30%), Gaps = 63/266 (23%)

Query: 3   DKNIVQENFTPQRVSKVI-AR---AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++  V  +    R+ +   A     G   R  +++++   +V+V+G   E     +    
Sbjct: 5   EQKTVTADEAGMRLDRWFKAHYPGMGFG-R--LQKLLRTGQVRVDGKRAES-NTRIAKGQ 60

Query: 59  HIEV----------DGVPLRKA------------------ERTRLWLYHKPIGLVTTH-- 88
            + +          D    +                    E   + + +KP GL      
Sbjct: 61  TVRIPPLGVELPANDKKNAKPKSSKLMADDKAAIEDMMLFEDNHVMVLNKPAGLAVQGGS 120

Query: 89  ---SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLR 143
                 DG    + N      ++  V RLD  T G++L+      A+ L          +
Sbjct: 121 GLKRHLDGMLEAYTNKKGEKPKL--VHRLDRETSGIILVAKTRKAAQELTKAFRHRNTRK 178

Query: 144 VYRVRFHGQVDQ------------DKLNLLKKGIVIQGICYGDMQVTL----DTQKGSNA 187
           +Y     G                +++  ++  +   G       V+L    +      +
Sbjct: 179 IYWAMLAGVPKPHQGRISTYLARSEEMERMR--VARHGDDEAQHAVSLYSVFEKSAQKLS 236

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVN 213
           WVT+    G+  +++         + 
Sbjct: 237 WVTLKPVTGRTHQLRAHAAHIGHPII 262


>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 = 54.8 bits (131), Expect = 2e-05,   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|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 (131), 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|303314793|ref|XP_003067405.1| ribosomal large subunit pseudouridine synthase D, putative
           [Coccidioides posadasii C735 delta SOWgp]
 gi|240107073|gb|EER25260.1| ribosomal large subunit pseudouridine synthase D, putative
           [Coccidioides posadasii C735 delta SOWgp]
          Length = 531

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 46/141 (32%), Gaps = 20/141 (14%)

Query: 35  IAQQRVKVNGILLERAAV--NVMSTDHIE---------VDGVPL-RKAERTRLWLYHKPI 82
           I    V +NG       V   V + D +          V  +P+    E   + +  KP 
Sbjct: 81  IESGHVTINGKP---GGVDSKVKNGDVVSHTLHRHEPPVTSLPIGVIHEDDEMIVIDKPA 137

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLEL--P 137
           G+    +     +++ + + +            RLD  T G++ +  D   A  +     
Sbjct: 138 GVPVHPAGRYNYNSIIEIMRAERGHGFNPLPCNRLDRLTSGVMFIGKDPKAAERISHGLR 197

Query: 138 STQWLRVYRVRFHGQVDQDKL 158
           +    + Y  R  G+     +
Sbjct: 198 ARTMQKEYIARVKGKFPDGII 218


>gi|119482145|ref|XP_001261101.1| DRAP deaminase (Rib2), putative [Neosartorya fischeri NRRL 181]
 gi|119409255|gb|EAW19204.1| DRAP deaminase (Rib2), putative [Neosartorya fischeri NRRL 181]
          Length = 525

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/141 (17%), Positives = 47/141 (33%), Gaps = 16/141 (11%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKPI 82
           + +A  +V VNG         + + + I          V G  +    E   + +  KP 
Sbjct: 83  QALADGKVTVNGKTAA-PDTVIKNGEIISHTLHRHEPPVTGHEIGIIHEDNDILVIDKPA 141

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE--LP 137
           G+    +     +++ + L S   +        RLD  T G++ +      A  +   L 
Sbjct: 142 GVPVHAAGRYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSGVMFIAKHPKAADAITIKLK 201

Query: 138 STQWLRVYRVRFHGQVDQDKL 158
                + Y  R  G+     +
Sbjct: 202 QRTVQKEYIARVKGRFPDGVV 222


>gi|222147750|ref|YP_002548707.1| hemolysin A [Agrobacterium vitis S4]
 gi|221734738|gb|ACM35701.1| hemolysin A [Agrobacterium vitis S4]
          Length = 263

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/90 (25%), Positives = 37/90 (41%), Gaps = 4/90 (4%)

Query: 9  ENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          ++  PQR+ +++ A    ASR      + +  VKVNG  + + ++       IE+D    
Sbjct: 8  QSLEPQRLDQLLVALNLFASRSRARDAVQRGGVKVNGRTVTKPSLTFSPDVTIEIDDPAQ 67

Query: 68 RKAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
              R  L L     GL     DP G   +
Sbjct: 68 DYVSRAALKLV---AGLDHFKLDPSGHICL 94


>gi|297583854|ref|YP_003699634.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
 gi|297142311|gb|ADH99068.1| pseudouridine synthase [Bacillus selenitireducens MLS10]
          Length = 305

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/220 (18%), Positives = 74/220 (33%), Gaps = 40/220 (18%)

Query: 19  VIARAGIASRR---EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------------- 62
           V+    + SR+   EV+       + VNG      +  V + DHIEV             
Sbjct: 30  VLRNNLMISRKLLAEVK--FQGGALFVNGKNA-NVSDQVFTGDHIEVWFPREDISSSIKM 86

Query: 63  DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLD 115
              PL  + E     +  KP GL+T  ++     +V   +   F           V RLD
Sbjct: 87  SCKPLSIRYEDEWCIVIDKPAGLLTIPNETYENDSVAGRVIGYFKSCDHPATFHPVTRLD 146

Query: 116 INTEGLLLLTNDGGLARVLELPSTQ--WLRVYR-----------VRFHGQVDQDKLNLLK 162
             T GL+L+  D     +           + Y                  + +   ++++
Sbjct: 147 RQTSGLMLIAKDRHSHSLFMKQQCAGLIDKEYVAVTPPGFPWIAATVDAPIARHPDSIIE 206

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + +  +G       V +  +  S + +   L  G+  +I+
Sbjct: 207 RMVHHEGQKAKTRLVKV-NENASGSLIRCKLETGRTHQIR 245


>gi|71649760|ref|XP_813593.1| hypothetical protein [Trypanosoma cruzi strain CL Brener]
 gi|70878491|gb|EAN91742.1| hypothetical protein, conserved [Trypanosoma cruzi]
          Length = 733

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/169 (18%), Positives = 57/169 (33%), Gaps = 28/169 (16%)

Query: 71  ERTRLWLYHKPIGL--------VTTHSDPDGRSTVFDNLPSIFS--------RVISVGRL 114
           E   + + +KP  L         T  +D      V   L S  +        R   V RL
Sbjct: 513 EDNDILVLNKPPHLASSRHALSCTQMNDKTATDVVSLILASTKNGETTRGVFRQGQVHRL 572

Query: 115 DINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRVRFHGQVDQDKLNLL-KKGIV- 166
           D  T G L++      A  L          +Q  +VY       V +  L  +  +G++ 
Sbjct: 573 DAETSGCLVMAKTDCAADSLRHQMGTSAAYSQCNKVYLALCA--VMEPDLRRIPLRGVLR 630

Query: 167 --IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +    Y   +V    +K   A +   +++GK  +I++        + 
Sbjct: 631 DPMDPKIYTKYRVIRFFRKARVALLECRIQQGKKHQIRRHLAAAGLPIL 679


>gi|262280824|ref|ZP_06058607.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           RUH2202]
 gi|262257724|gb|EEY76459.1| 23S rRNA pseudouridylate synthase [Acinetobacter calcoaceticus
           RUH2202]
          Length = 310

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 83/246 (33%), Gaps = 64/246 (26%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIRESQVRVNKKRVK-AETKLEIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETTAPVSDNVAQSLLSRIVYEDEGLLVVNKPSGIAV----HGGSGMAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLR----EG 196
             DK  ++       L  G     +   G       V  +  K +       +      G
Sbjct: 186 SLDKQLIDAPLLRYELANGERRVRVTKDGKPSKTEWVVAERFKNATL-----IHASPLSG 240

Query: 197 KNREIK 202
           +  +I+
Sbjct: 241 RTHQIR 246


>gi|258406577|ref|YP_003199319.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
 gi|257798804|gb|ACV69741.1| pseudouridine synthase [Desulfohalobium retbaense DSM 5692]
          Length = 299

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/226 (15%), Positives = 68/226 (30%), Gaps = 48/226 (21%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG---------- 64
           R+       G   R  + + I   +V+V+     +    V     + +            
Sbjct: 25  RLD------GQVPRSALMKWIRTGQVRVDKKR-TKPFDRVQPGQILRLPPQATLKSASSP 77

Query: 65  ------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLD 115
                    R AE   L +  KP GL        G S V +     P        V RLD
Sbjct: 78  GPPPALKLERIAETETLLVLAKPAGLPVQPGSKHGASLVRELAKAYPETPWPPQPVHRLD 137

Query: 116 INTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL----NLLKKGIVI-- 167
            +T G++L+     + ++++      +  + Y          D +    +  +  I I  
Sbjct: 138 KDTSGIILVAKRADVFQIIQQAWQRGEVQKDYLAWLA---PGDDVGPGWHTWRDRIEICH 194

Query: 168 ----------QGICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIK 202
                     +G     + +    +       V + L  G+  +I+
Sbjct: 195 TDRGEKMCCTEGGKEAILHLRPLRRNSLGEILVAIQLETGRKHQIR 240


>gi|222034482|emb|CAP77224.1| tRNA pseudouridine synthase C [Escherichia coli LF82]
 gi|312947318|gb|ADR28145.1| tRNA pseudouridine synthase C [Escherichia coli O83:H1 str. NRG
           857C]
          Length = 260

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++++ T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMSVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|259907745|ref|YP_002648101.1| Pseudouridine synthase [Erwinia pyrifoliae Ep1/96]
 gi|224963367|emb|CAX54853.1| Pseudouridine synthase [Erwinia pyrifoliae Ep1/96]
 gi|283477602|emb|CAY73518.1| ribosomal large subunit pseudouridine synthase A [Erwinia
           pyrifoliae DSM 12163]
          Length = 232

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/193 (21%), Positives = 69/193 (35%), Gaps = 41/193 (21%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +  RL L +KP GL++ +  +P    +V   L  IF     V RLD  T GL+++  +  
Sbjct: 22  QDDRLVLINKPAGLLSLSGKNPQNIDSVHYRLVQIFPGCTLVHRLDFGTSGLMVIARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +   L    +Q    +VY     G +D +      +G++   I        L +      
Sbjct: 82  INAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIAKDPALFPLMSICSIHG 135

Query: 183 KGSNAWVTVG--------------LR------E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K S +   V               L       E G+  +++   +     +       YG
Sbjct: 136 KPSRSRYRVVERFYHPLENRTLLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCD--LYG 193

Query: 222 PFQLGTLLAGSTR 234
               G LL G+ R
Sbjct: 194 ----GRLLPGTER 202


>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 = 54.8 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 RLDNVVYRLGFAQSRRQARQMVRHGHITVNGRRVDLPAYRVKPGDEIAI 148


>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 = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ +++   G  A+R      I +  VKV+G  + +    V+ T  I VD        R 
Sbjct: 11 RLDQLLVELGLFATRSRARDAIQRGTVKVDGKPVTKPGQTVLRTAKIAVDDPASAYVSRA 70

Query: 74 RLWLY 78
           L L 
Sbjct: 71 ALKLI 75


>gi|300717274|ref|YP_003742077.1| Pseudouridine synthase [Erwinia billingiae Eb661]
 gi|299063110|emb|CAX60230.1| Pseudouridine synthase [Erwinia billingiae Eb661]
          Length = 205

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 49/130 (37%), Gaps = 14/130 (10%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  +P    +V   L  +F     + RLD  T GL+++  +  
Sbjct: 22  QDAYLVLINKPTGLLSLSGKNPQNLDSVHHRLVQLFPGCTLIHRLDFGTSGLMVIARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQ 182
           +   L    +Q    +VY     G + +D       G++   I           +     
Sbjct: 82  INAALCHQFSQRTVTKVYSALLCGHLAEDD------GVIDAAIAKDPALFPLMSICAVNG 135

Query: 183 KGSNAWVTVG 192
           K + +   V 
Sbjct: 136 KPARSRYQVV 145


>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 = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 82/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVAVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG +++      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLEE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYKGADLVECLLETGRTHQIR 233


>gi|288800870|ref|ZP_06406327.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
 gi|288332331|gb|EFC70812.1| ribosomal large subunit pseudouridine synthase D [Prevotella sp.
           oral taxon 299 str. F0039]
          Length = 295

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/205 (18%), Positives = 72/205 (35%), Gaps = 30/205 (14%)

Query: 27  SRREVERMIAQQR-VKVNGILLERAAVNVMSTDHIEVDGVPLR----------KAERTRL 75
           SR +++  I   + +KVNG +  +    +     I +                  E   +
Sbjct: 33  SRNKLKD-ILAGQGIKVNGKITTKYDYPLTPGMKISISKTKRNNLFKSKYVDIVYEDNHI 91

Query: 76  WLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGL 130
            + HK  G+++    H   + ++ + D L     +     V RLD  T GL++   D  +
Sbjct: 92  IVVHKKAGILSMPVGHGSLNVKTVLDDYLMRSKQKCNAHVVHRLDRETSGLMVYAKDKRV 151

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQDK---LNLLKKGIVI--------QGICYGDMQV 177
            R+ E         R Y     G+V +++    N LK   +          G  Y     
Sbjct: 152 ERLFEEDWHNIVYDRRYVAIVSGEVQENEGTIANWLKDNKMFVTYSCPFDNGGKYAVTHF 211

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            +  +   +  V   L  G+  +I+
Sbjct: 212 QVKKRTAYHTLVEYKLETGRKNQIR 236


>gi|153812383|ref|ZP_01965051.1| hypothetical protein RUMOBE_02782 [Ruminococcus obeum ATCC 29174]
 gi|149831545|gb|EDM86632.1| hypothetical protein RUMOBE_02782 [Ruminococcus obeum ATCC 29174]
          Length = 293

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/195 (17%), Positives = 71/195 (36%), Gaps = 35/195 (17%)

Query: 41  KVNGILLERAAVNVMS-TDHIEV--------DGV---PLRKA---ERTRLWLYHKPIGLV 85
            +NG         V+S  DH  V        DG+   PL      E   + + +KP  + 
Sbjct: 43  SLNGQKA--GGRTVLSCGDHFRVRLLETVPADGILPTPLNIPVLYEDEDILVVNKPADMP 100

Query: 86  TTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
              S  +  +T+ + + +             + RLD +T G L+L  +   A +L +   
Sbjct: 101 VHPSLGNYTNTLANGVAAYLETKGESCPFRCINRLDRDTSGALILAKNALSAAILSVQMR 160

Query: 138 STQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           + Q  R Y     G           + +   +++++ I  +          L   K +++
Sbjct: 161 NRQISRTYLAVVEGIPRQSGTISAPISRAADSVIERRIDFENGESAITHYQLLEVKNNHS 220

Query: 188 WVTVGLREGKNREIK 202
            + + L  G+  +I+
Sbjct: 221 LLEIHLETGRTHQIR 235


>gi|119175237|ref|XP_001239884.1| hypothetical protein CIMG_09505 [Coccidioides immitis RS]
 gi|320037744|gb|EFW19681.1| DRAP deaminase [Coccidioides posadasii str. Silveira]
          Length = 531

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/141 (16%), Positives = 46/141 (32%), Gaps = 20/141 (14%)

Query: 35  IAQQRVKVNGILLERAAV--NVMSTDHIE---------VDGVPL-RKAERTRLWLYHKPI 82
           I    V +NG       V   V + D +          V  +P+    E   + +  KP 
Sbjct: 81  IESGHVTINGKP---GGVDSKVKNGDVVSHTLHRHEPPVTSLPIGVIHEDDEMIVIDKPA 137

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLEL--P 137
           G+    +     +++ + + +            RLD  T G++ +  D   A  +     
Sbjct: 138 GVPVHPAGRYNYNSIIEIMRAERGHGFNPLPCNRLDRLTSGVMFIGKDPKAAERISHGLR 197

Query: 138 STQWLRVYRVRFHGQVDQDKL 158
           +    + Y  R  G+     +
Sbjct: 198 ARTMQKEYIARVKGKFPDGII 218


>gi|326790893|ref|YP_004308714.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
 gi|326541657|gb|ADZ83516.1| pseudouridine synthase [Clostridium lentocellum DSM 5427]
          Length = 322

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 79/239 (33%), Gaps = 55/239 (23%)

Query: 14  QRVSKVIARAGIASRREV-ERMIAQQ----RVKVNGILLERAAVNVMSTDHI-------- 60
           QR+ K + +       E  +  I +     ++K NG   +     +   D I        
Sbjct: 13  QRLDKFLMKYL----NECPKSFIYKGMRTKKIKYNGKKPQ-GNEILQEGDEIKIFFTEEQ 67

Query: 61  --------EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRST---VFDNLPSIFS 106
                   EV  VP+      E   + + +KP+GL+T      G S    V   L    S
Sbjct: 68  FKTFSSEKEVKKVPISFQTVYEDEHILIVNKPMGLLTQKDTATGHSLADEVLSYLKDNGS 127

Query: 107 RVI---------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
                          RLD NT G++L+       +VL   L + Q  + Y     G+V  
Sbjct: 128 YDPKTSKGFTPAPCNRLDRNTAGIVLVGKHIPAVQVLGEMLQTKQISKYYMSIVLGRVTA 187

Query: 156 DKL-------NLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +          K  + I     +G    + ++      G    V V L  GK  +I+
Sbjct: 188 PMILKGYHIKQEGKNEVKITTEYVEGAKPVETRILPLKTNGRYTLVEVQLVTGKTHQIR 246


>gi|224825896|ref|ZP_03699000.1| pseudouridine synthase [Lutiella nitroferrum 2002]
 gi|224602120|gb|EEG08299.1| pseudouridine synthase [Lutiella nitroferrum 2002]
          Length = 253

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/169 (19%), Positives = 50/169 (29%), Gaps = 27/169 (15%)

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
             RL   HKP GL+   +  D          L      RV  V RLD  T G+LL   D 
Sbjct: 8   DERLIAIHKPSGLLVHRTVLDRHETRFAIQLLRDQIGQRVYPVHRLDKGTSGVLLFALDR 67

Query: 129 GLARVLE--LPSTQWLRVYRVRFHGQVDQD-----KLNLLKKGIVIQGICYGDMQVTLDT 181
            + R +       Q  + Y     G  D+       L      +   G           T
Sbjct: 68  DMGREMSWQFERQQVDKRYLAVVRGWPDEQGEIEHALTRRPDDLEWVGEKVDTAPQAALT 127

Query: 182 QKGSNAWVTV------------GLRE-----GKNREIKKVFEFFNWKVN 213
           +    A V +             L E     G+  ++++  +     + 
Sbjct: 128 RFRRLATVELPYAVDKYPHSRYALVELTPETGRRHQLRRHLKHIAHPII 176


>gi|67595791|ref|XP_666024.1| N-terminal part related to RNA:pseudouridine (psi)-synthases
           C-terminal portion contains the deaminase domain
           implicated in Riboflavin synthesis; Rib2p
           [Cryptosporidium hominis TU502]
 gi|54656925|gb|EAL35796.1| N-terminal part related to RNA:pseudouridine (psi)-synthases
           C-terminal portion contains the deaminase domain
           implicated in Riboflavin synthesis; Rib2p
           [Cryptosporidium hominis]
          Length = 481

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 69/193 (35%), Gaps = 36/193 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPI 82
           R+I Q+R+ VN          V + D I+   + +             + + L    KP 
Sbjct: 82  RLIDQRRLSVNDTPANSLDYIVRNGDKIKHRSLFIELPVATDKVKILYDSSTLLAVFKPC 141

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           G+         + ++   + S +        + +  + RLD  T GL+LL+ D    + L
Sbjct: 142 GIPCHPQGRFNKLSLTKLIQSEYLSKLNTNSTYIHPINRLDRVTSGLVLLSKDSSTTKNL 201

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI---VIQGICYGDMQVTLDTQKGSNAWV-- 189
                   + Y    +     +  +     +    I+G+     +++LD   G  + V  
Sbjct: 202 SSKVQFAHKYYLAMIN-----ESASNFISHVSQSSIEGVSIR--ELSLDESHGITSHVIK 254

Query: 190 -TVGL-----REG 196
             +GL     REG
Sbjct: 255 CEIGLKTLKDREG 267


>gi|262193432|ref|YP_003264641.1| pseudouridine synthase [Haliangium ochraceum DSM 14365]
 gi|262076779|gb|ACY12748.1| pseudouridine synthase, RluA family [Haliangium ochraceum DSM
           14365]
          Length = 304

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/207 (18%), Positives = 70/207 (33%), Gaps = 33/207 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------GVPLRKA-ERTRLW 76
           SR    +++   +V ++G     A   + +   + +          G  +R A E   + 
Sbjct: 23  SR--ARQLVGTGKVFIDGSRCTDAGQRLRAGQEVGLHMSAPRPQTRGARVRIAYEDAHVV 80

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLL--T 125
           +  KP+ + +   +     T  D L   + ++           V R+D  T GLL    T
Sbjct: 81  VIDKPVDVSSVPYERRETGTAMDLLREAWRKLRPDAGRTPLHVVHRIDKATSGLLAFAKT 140

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-LL--KKGIVIQGICYGDMQ------ 176
               L    +       R Y    HG V   ++   L   +G  ++G      Q      
Sbjct: 141 KRAELGLAAQFRQHTLERAYLCVAHGAVRAQRIESRLVRDRGDGLRGSTRAPNQGKRAVT 200

Query: 177 -VTLDTQKGSNAWVTVGLREGKNREIK 202
            V +  +    +   V L  GK  +I+
Sbjct: 201 HVEVLEELARASLCQVRLETGKTHQIR 227


>gi|15806687|ref|NP_295407.1| pseudouridine synthase [Deinococcus radiodurans R1]
 gi|6459452|gb|AAF11241.1|AE002010_4 pseudouridine synthase, putative [Deinococcus radiodurans R1]
          Length = 321

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 59/201 (29%), Gaps = 25/201 (12%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           +A   V V+G+ +      +     +     P  +           E   L    KP GL
Sbjct: 63  LAAGEVTVDGLTVR-GDETLRPGQMLVWQRPPWAEPDAPLHFDVIYEDADLLAVSKPSGL 121

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
            T         T+   +   +     + RL   T GL+L +        L     + +  
Sbjct: 122 PTMPGGGFLEHTLLHQVRGRWPDASPLHRLGRGTSGLVLFSLTSQAGAALLKDWRAGRVQ 181

Query: 143 RVYRVRFHGQVDQDK---------LNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVT 190
           +VYR    G  +QD+         +   + G V            +  +  ++       
Sbjct: 182 KVYRALSAGVAEQDEYDITVPIGPVAHPRLGQVFAASTAGKTAHSRARVLERREDTTLFE 241

Query: 191 VGLREGKNREIKKVFEFFNWK 211
           V +  G+  +I+         
Sbjct: 242 VEIFTGRPHQIRIHLASLGLP 262


>gi|152967132|ref|YP_001362916.1| pseudouridine synthase [Kineococcus radiotolerans SRS30216]
 gi|151361649|gb|ABS04652.1| pseudouridine synthase, RluA family [Kineococcus radiotolerans
           SRS30216]
          Length = 307

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 80/252 (31%), Gaps = 41/252 (16%)

Query: 1   MKDKNI--VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M ++    V +    +RV   ++R    SR     + A   V V+G  + ++   + +  
Sbjct: 1   MPEQRSLPVPDGLEGERVDAALSRLLGLSRTRAADIAAAGHVLVDGRAVGKSD-RLTAGA 59

Query: 59  HIEVD-----GVPLRKAERTRLWLY----------HKPIGLVTTHSDPDGRSTVFDNLP- 102
            +EV+     G P   AER                 KP+G+    S      TV   L  
Sbjct: 60  WLEVEVPDAPGAPTAVAERIEGLTIVHDDDDLVVVDKPVGVAAHPSPGWTGPTVVGGLMG 119

Query: 103 --------SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
                       R   V RLD+ T GL+++         L+    +    +VY     G 
Sbjct: 120 AGYTIATSGSAERQGVVHRLDVGTSGLMVVAKSEHAYSALKRAFKERTVEKVYHALVQGH 179

Query: 153 VD------QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            D         +     G     +  +G         L+  + + A   V L  G+  +I
Sbjct: 180 PDPLRGTIDAPIGRHPGGTYKFAVTAEGKPSVTHYEVLEAFRAA-ALCEVHLETGRTHQI 238

Query: 202 KKVFEFFNWKVN 213
           +  F        
Sbjct: 239 RVHFSALRHPCV 250


>gi|307707719|ref|ZP_07644198.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
 gi|307616217|gb|EFN95411.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus mitis NCTC 12261]
          Length = 291

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 58/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y  +  G ++  +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWAQVDGHINSKELVFKDKIGRDRHDRRKRIVDTKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     + V   L+ G+  +I+
Sbjct: 203 THVSRLKQFPNKTSLVRCKLKTGRTHQIR 231


>gi|299771717|ref|YP_003733743.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. DR1]
 gi|298701805|gb|ADI92370.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. DR1]
          Length = 310

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 52/284 (18%), Positives = 94/284 (33%), Gaps = 68/284 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIRESQVRVNKKRVK-AETKLEIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAAPVSDSVAQGLLSRVVYEDEGLLVVNKPSGIAV----HGGSGMAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      + L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKQLQDMLREHKIRKTYAAIVKGQV 185

Query: 154 DQDK--LNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             DK  ++       L  G     +   G       V  +  K +   V      G+  +
Sbjct: 186 SLDKQLIDAPLLRYELANGERRVRVTKDGKPSKTEWVVAERFKNAT-LVHASPLSGRTHQ 244

Query: 201 IKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ 244
           I+         V+ L   S G   +G    G T E +    R  
Sbjct: 245 IR---------VHGL---SIGHPLIGDDKYGHTTEYTGPEARRL 276


>gi|262041866|ref|ZP_06015050.1| ribosomal large subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|259040771|gb|EEW41858.1| ribosomal large subunit pseudouridine synthase A [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
          Length = 232

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 70/210 (33%), Gaps = 48/210 (22%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   F     V RLD  T GL+++  + G
Sbjct: 22  QDEHLVLINKPAGLLSLSGKDPRNLDSVHHRLVQRFPGCTLVHRLDFGTSGLMVIARNKG 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +           
Sbjct: 82  INALLCQQFSQRTVDKVYTALLCGHLAED------EGIVEAAIAKDPARFPRMALCARHG 135

Query: 183 KGSNAWV-------------------TVGLR-E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +                      V L  E G+  +++   +   + +         
Sbjct: 136 KPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILGC------ 189

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLE 251
                 L  G  RE+       +L  H  E
Sbjct: 190 -----DLYGG--RELPGTECASRLMLHASE 212


>gi|86134338|ref|ZP_01052920.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
 gi|85821201|gb|EAQ42348.1| RNA pseudouridylate synthase [Polaribacter sp. MED152]
          Length = 228

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/155 (14%), Positives = 55/155 (35%), Gaps = 23/155 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   + + +K  G +T       +     V + +   +++     +  V RLD  T G++
Sbjct: 13  EDNHIIIVNKRSGDITQGDKTGDKPLSDVVKEYIKEKYNKAGNVFLGVVHRLDRPTSGVI 72

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---LNLLKKG----------IVI 167
           +          L   L   +  + Y         ++K   +N L+K             I
Sbjct: 73  IFARTSKALERLNKMLRDKEIHKTYWAVVKNHPKKEKATLINYLRKNPKNNKSSVFQKEI 132

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +G     +  +   +  + + + + L  G++ +I+
Sbjct: 133 EGSKKAILHYSTLKKLDNYSLLEIDLETGRHHQIR 167


>gi|301794949|emb|CBW37412.1| RNA pseudouridylate synthase [Streptococcus pneumoniae INV104]
          Length = 278

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQYLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 TYVSRLKQFSNKTSLARCKLKTGRTHQIR 218


>gi|315586901|gb|ADU41282.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           pylori 35A]
          Length = 242

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 75/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  +  G++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKAGIKTGRTHQIRIHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|183602394|ref|ZP_02963760.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683291|ref|YP_002469674.1| pseudouridine synthase RluD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191252|ref|YP_002968646.1| hypothetical protein Balac_1228 [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|241196658|ref|YP_002970213.1| hypothetical protein Balat_1228 [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|183218313|gb|EDT88958.1| hypothetical protein BIFLAC_05095 [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219620941|gb|ACL29098.1| pseudouridine synthase RluD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249644|gb|ACS46584.1| hypothetical protein Balac_1228 [Bifidobacterium animalis subsp.
           lactis Bl-04]
 gi|240251212|gb|ACS48151.1| hypothetical protein Balat_1228 [Bifidobacterium animalis subsp.
           lactis DSM 10140]
 gi|289177367|gb|ADC84613.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           animalis subsp. lactis BB-12]
 gi|295794245|gb|ADG33780.1| hypothetical protein BalV_1192 [Bifidobacterium animalis subsp.
           lactis V9]
          Length = 317

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/223 (17%), Positives = 79/223 (35%), Gaps = 37/223 (16%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------- 74
            GI SR +   +I   + +V G  + ++A  + + D +E+D    R+             
Sbjct: 24  MGI-SRAKATELIETGQARVIGRDIHKSAT-LQAGDTVEIDVREERREPEPVSNEMTIAY 81

Query: 75  ----LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTEGL 121
               + +  KP+G+    S      TV  +L      + S+G         RLD+ T GL
Sbjct: 82  EDDDIVVVDKPVGVAAHASVGWTGPTVLGSLIQRGVHITSMGAAGRQGIVSRLDVGTSGL 141

Query: 122 LLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           +L+       + +    ++    + Y     G + +DK   ++  I    +      VT 
Sbjct: 142 MLVCKSDLAYKEMRRQFSEHEVKKTYHALVQGNLKEDK-ATIEAPIGRAKVSDFRFTVTP 200

Query: 180 DTQKGSNAW-----------VTVGLREGKNREIKKVFEFFNWK 211
             ++    W            ++ L  G+  +I+  F      
Sbjct: 201 AGKEAVTHWDVMERFGEATLASINLETGRTHQIRVHFSSIGHP 243


>gi|313899281|ref|ZP_07832797.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
 gi|312955961|gb|EFR37613.1| pseudouridine synthase, RluA family [Clostridium sp. HGF2]
          Length = 317

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/271 (16%), Positives = 85/271 (31%), Gaps = 76/271 (28%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLE-RAA 51
           MK+  I+ EN   QRV K I +        ++        + I  +++KVN    E    
Sbjct: 1   MKEF-IINENDADQRVDKFIQKT-------MKTMPKSLMYKYIRNKKIKVNRKRCEISQR 52

Query: 52  VNVMSTDH----------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
           + V  T                  ++V        E   + L +KP GL       + + 
Sbjct: 53  LQVGDTMQCYIPEEFYEVATMRSFLQVPNALDVVYEDDAVLLMNKPKGLRAHSDTSEVQD 112

Query: 96  TVFDNL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ-- 140
            + D L           P+           R+D NT+GL++       A  L   + +  
Sbjct: 113 NLADRLLHYLYCKKEYDPTTEQSFTPALCHRIDRNTQGLVIAA---KTAAALRCMNEKIA 169

Query: 141 ---WLRVYRVRFHGQV-----------------DQDKLNLLKKGIVIQGICYGDMQVTLD 180
                + Y     G++                   + ++  +     +G    +    + 
Sbjct: 170 LRQVEKKYLCIVQGKLKKKQDHIVLYHRKNEQNTAEVIDRER-----EGYTRMETGYRVL 224

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +    + V V L  GK+ +I+ +  +    
Sbjct: 225 QEAERYSLVEVELHSGKSHQIRALMSWLGHP 255


>gi|253565801|ref|ZP_04843256.1| RNA pseudouridylate synthase [Bacteroides sp. 3_2_5]
 gi|265764176|ref|ZP_06092744.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_16]
 gi|251946080|gb|EES86487.1| RNA pseudouridylate synthase [Bacteroides sp. 3_2_5]
 gi|263256784|gb|EEZ28130.1| RNA pseudouridylate synthase [Bacteroides sp. 2_1_16]
 gi|301163522|emb|CBW23073.1| putative RNA pseudouridylate synthase [Bacteroides fragilis 638R]
          Length = 307

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/221 (15%), Positives = 74/221 (33%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP 66
            P  +   +A +   ASR +++ +++++ V V+ ++  +    +     + +    +   
Sbjct: 25  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNKKE 84

Query: 67  LRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
            R        E   + +  K  GL++  ++     T    L          +R+  V RL
Sbjct: 85  FRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSGRGNRIYVVHRL 144

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D      L          R Y     G+           +    L + 
Sbjct: 145 DRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTLYVS 204

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 205 SSSYDDGGSKSITHYRTIKRANGY-SLVELRLETGRKNQIR 244


>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 = 54.8 bits (131), Expect = 2e-05,   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|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 = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 82/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVSVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG +++      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLEE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYNGADLVECLLETGRTHQIR 233


>gi|145294446|ref|YP_001137267.1| hypothetical protein cgR_0401 [Corynebacterium glutamicum R]
 gi|140844366|dbj|BAF53365.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 294

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 76/228 (33%), Gaps = 47/228 (20%)

Query: 15  RVSKVI-ARAGIASRREVERMI----AQQRVKVNGILLERAAVNVMSTDHIE-------- 61
           R+ K + A+    S      +I     +  ++VNG  +      +   D I         
Sbjct: 16  RIDKFLRAQLKGVS----ASLIFRQMRKGDIRVNGRKV-DPNYRLQEGDRIRMWQMDLPA 70

Query: 62  -----VDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-- 107
                V    + KA       E   L + +KP G +  H        V + L   F +  
Sbjct: 71  DLPPPVVDKHIFKAVADSVLFEDAELLVINKPAG-IPVHGGTGHGGGVIEALRQKFPQER 129

Query: 108 -VISVGRLDINTEGLLLLTNDG----GLARVLELPSTQWLRVYRVRFHGQVDQDK----- 157
            +  V RLD +T GLLL++        L  +L     +  R Y ++  G    D      
Sbjct: 130 DLELVHRLDRDTSGLLLVSKTTSVLRELQEILRDREEEIFRGYLLKVEGAWPGDLRQIDV 189

Query: 158 -LNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L   +  +V    G+        +    G+   V   L  G+  +I+
Sbjct: 190 PLKRTETTVVPHSDGLRARTYFEVVKRLPGAT-LVKAQLATGRKHQIR 236


>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 = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          QR+ K++   G+A SR + + +I   +V V+  + ++A   V     I V G  L    R
Sbjct: 5  QRLDKLVLERGLAPSREKAQALIMAGQVIVDDHVADKAGQQVAVDAEIRVRGETLPFVSR 64


>gi|306826329|ref|ZP_07459662.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|304431442|gb|EFM34425.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
          Length = 291

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 59/149 (39%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIVVNKPEGMKTHGNQPNEIALLNHISAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G+V+  +L           +  K+ +  +   + +
Sbjct: 143 PFILPILNRLLEKKEIAREYWALVEGRVESKELVFRDKIGRDRHDRRKRVVDPKNGQHAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
            QV+   Q     + V   L+ G+  +I+
Sbjct: 203 TQVSRLKQFPNKTSLVRCKLKTGRTHQIR 231


>gi|306830219|ref|ZP_07463402.1| ribosomal large subunit pseudouridine synthase [Streptococcus mitis
           ATCC 6249]
 gi|304427586|gb|EFM30683.1| ribosomal large subunit pseudouridine synthase [Streptococcus mitis
           ATCC 6249]
          Length = 278

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/149 (20%), Positives = 58/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + PD  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQYLIVVNKPEGMKTHGNQPDEIALLNHVSSYVGHTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     GQV   +L           +  K+ +  +   + +
Sbjct: 130 PFILPILNRLLEKKEIAREYWALVEGQVGSKELIFRDKIGRDRHDRRKRVVDPKNGQHAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
            QV+   Q     + V   L+ G+  +I+
Sbjct: 190 TQVSRLKQFPNKTSLVRCKLKTGRTHQIR 218


>gi|225351455|ref|ZP_03742478.1| hypothetical protein BIFPSEUDO_03050 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157799|gb|EEG71082.1| hypothetical protein BIFPSEUDO_03050 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 312

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/231 (16%), Positives = 75/231 (32%), Gaps = 48/231 (20%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRKAERT 73
           A+    SR +   +I   + +V G  + +++  + S + +E D         P+ +    
Sbjct: 21  AKMLGISRAKAAELIESGQARVLGRDISKSST-LQSGETVEFDIVEERTEPEPIARDMAV 79

Query: 74  RL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTE 119
                   +  KP+G+    S      TV  +L      + S G         RLD+ T 
Sbjct: 80  VYEDDDVIVVDKPVGVAAHASVGWTGPTVLGSLLDRGVHITSYGAAGRQGIVSRLDVGTS 139

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           GL+L+         +       + ++ Y     G + ++K         I+         
Sbjct: 140 GLMLVCKSDLAYVEMRRQFAEHEVVKTYHALVQGNLKENKA-------TIEAPIGRAKVS 192

Query: 177 -----VTLDTQKGSNAW-----------VTVGLREGKNREIKKVFEFFNWK 211
                VT   ++    W           V+V L  G+  +I+  F      
Sbjct: 193 DFRFCVTPAGKEAITHWDVMERFGEATLVSVNLETGRTHQIRVHFSSIGHP 243


>gi|183220733|ref|YP_001838729.1| putative ribosomal large subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
 gi|189910834|ref|YP_001962389.1| pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167775510|gb|ABZ93811.1| Pseudouridylate synthase [Leptospira biflexa serovar Patoc strain
           'Patoc 1 (Ames)']
 gi|167779155|gb|ABZ97453.1| Putative ribosomal large subunit pseudouridine synthase [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 320

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/139 (17%), Positives = 50/139 (35%), Gaps = 17/139 (12%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------LWLYHKP 81
           ++ + R+ V+G L       ++  + IE + +P R  E                    KP
Sbjct: 36  LVEEGRITVSGNLA-SMHKPLLDGEVIEYNPIPGRIKEPEVDTNYSILKETEDFLFVEKP 94

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ- 140
             L    +      T+   L + + ++I V RLD  T G+++       +R       + 
Sbjct: 95  GNLPMHPAGRYRTKTLLSFLETKYPKIIPVHRLDRETSGIVIFAKS-EESRKWLQKKFET 153

Query: 141 --WLRVYRVRFHGQVDQDK 157
               + Y     G+  +++
Sbjct: 154 RVVYKEYFAIVLGKFTKEQ 172


>gi|154148734|ref|YP_001407253.1| RNA pseudouridine synthase [Campylobacter hominis ATCC BAA-381]
 gi|153804743|gb|ABS51750.1| hypothetical RNA pseudouridine synthase (RNA-uridine isomerase)
           (RNA pseudouridylate synthase) [Campylobacter hominis
           ATCC BAA-381]
          Length = 304

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 61/151 (40%), Gaps = 16/151 (10%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA-----ERT 73
           ++   G    ++ +R+I ++R+   G +       +++ +   +D   + +      E  
Sbjct: 19  ILINCGFC-MKDSQRLIDKKRIFC-GPVSVDTKNEILNGEIFMIDYECMSRGIYPIFEND 76

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGG 129
              ++ KP G+++    P+GR   +     I+           RLD  T GLL+ + +  
Sbjct: 77  DFAVFDKPSGILS---HPNGRHCEYSLCDEIWTLFGKNANVAHRLDRETSGLLIASKNPK 133

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDKL 158
            A  L          ++Y     G+V+++ +
Sbjct: 134 SADELKNMFEKKTVQKIYFALVSGRVNENFI 164


>gi|50291713|ref|XP_448289.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49527601|emb|CAG61250.1| unnamed protein product [Candida glabrata]
          Length = 457

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 68/208 (32%), Gaps = 32/208 (15%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           I +  V +N       ++ + + D I          V   P+    E   + + +KP G+
Sbjct: 152 IERGAVLLNDKPATLESI-IKNGDLITHKVHRHEPPVTSRPIEIVFEDNDILVINKPSGI 210

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
               +     +T+   L      V     RLD  T GL+ L      A  +  +L + + 
Sbjct: 211 PVHPTGRYRFNTITKALEKERGYVVHPCNRLDRMTSGLMFLAKTSKGADKIGDQLKAREV 270

Query: 142 LRVYRVRFHGQVDQDK------LNLLKKGIVIQ------GICYGDMQVTLDT----QKGS 185
            + Y  +  G+  +        L LL+  + +              +   +     +   
Sbjct: 271 EKEYLAKVVGEFPEGTTVVDKPLKLLEPRLTLNVVCEETDPDAKHARTIFERVSVSKDKQ 330

Query: 186 NAWVTVG-LREGKNREIKKVFEFFNWKV 212
            + V    L  G++ +I+   +     +
Sbjct: 331 TSIVKCKPLT-GRSHQIRVHLQHLGHPI 357


>gi|317009613|gb|ADU80193.1| hypothetical protein HPIN_04885 [Helicobacter pylori India7]
          Length = 242

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/203 (14%), Positives = 67/203 (33%), Gaps = 34/203 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----ERT 73
           K+++     S ++ + +I    V + G  L  A   +       V    + K     E  
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSIGGKKLMVARKELPQNTRFSV--QKIEKPGVIFEDE 63

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR- 132
            +    KP  + +           +D + S F   + + RLD  T G++LL  +      
Sbjct: 64  NILALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVVLLVKENSEFHL 111

Query: 133 --VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG------ 184
                       + Y     G ++++    +   I+         +++   Q+       
Sbjct: 112 KAKKAFKDRAVKKEYLALAQGIIEEE--REINAPILTIKTTKAFSKISKKGQEAVTIITP 169

Query: 185 -----SNAWVTVGLREGKNREIK 202
                    + VG++ G+  +I+
Sbjct: 170 LKIINKKTLLKVGIKTGRTHQIR 192


>gi|49184224|ref|YP_027476.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|65318659|ref|ZP_00391618.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|165870408|ref|ZP_02215063.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167634370|ref|ZP_02392691.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167639342|ref|ZP_02397614.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170686762|ref|ZP_02877982.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|170706270|ref|ZP_02896731.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|177651449|ref|ZP_02934238.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190568721|ref|ZP_03021625.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|218902499|ref|YP_002450333.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|227815867|ref|YP_002815876.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|228913961|ref|ZP_04077585.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229604571|ref|YP_002865810.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|254682548|ref|ZP_05146409.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254726210|ref|ZP_05187992.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
 gi|254733966|ref|ZP_05191680.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254740346|ref|ZP_05198037.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254753734|ref|ZP_05205769.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|254758830|ref|ZP_05210857.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
 gi|270000596|ref|YP_003329034.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612209|ref|YP_003541023.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178151|gb|AAT53527.1| RNA pseudouridylate synthase [Bacillus anthracis str. Sterne]
 gi|164713903|gb|EDR19425.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|167512781|gb|EDR88155.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167530258|gb|EDR92984.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170128804|gb|EDS97670.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|170669285|gb|EDT20028.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172082727|gb|EDT67790.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|190560137|gb|EDV14118.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|218535216|gb|ACK87614.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|224552848|gb|ACN55061.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|227003057|gb|ACP12800.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|228845683|gb|EEM90710.1| Pseudouridine synthase [Bacillus thuringiensis serovar pulsiensis
           BGSC 4CC1]
 gi|229268979|gb|ACQ50616.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850296|gb|ACZ49998.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 307

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 94/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTFVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDIPFPTKLNDT 298


>gi|195146686|ref|XP_002014315.1| GL19017 [Drosophila persimilis]
 gi|194106268|gb|EDW28311.1| GL19017 [Drosophila persimilis]
          Length = 644

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/208 (19%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAERTR-LWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       L + +KP 
Sbjct: 336 ERCIQAGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMNEDLVVVNKPA 395

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 396 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 455

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G    + +   K+ I +     G  +V+             +Q G  +
Sbjct: 456 RQVEKEYICRVEGIFPDEIVE-CKEPIEVVSYKIGVCKVSQRGKDCTTTFQKISQNGKTS 514

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR 214
            V    L  G+  +I+   ++  + +  
Sbjct: 515 VVLCKPLT-GRMHQIRVHLQYLGYPILN 541


>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 = 54.8 bits (131), Expect = 2e-05,   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|166364334|ref|YP_001656607.1| pseudouridine synthase [Microcystis aeruginosa NIES-843]
 gi|166086707|dbj|BAG01415.1| pseudouridine synthase [Microcystis aeruginosa NIES-843]
          Length = 299

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/245 (13%), Positives = 72/245 (29%), Gaps = 52/245 (21%)

Query: 14  QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           + + ++++ A                + VNG         +     +     P  + E  
Sbjct: 36  EWLDRILSAA----------------ILVNGRPAC-PDTVLEIGQQLTYQRPPWTEPEVP 78

Query: 74  RLW--LYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGL 121
             +  LY         KP GL           T+   +   ++ V    + RL   T G+
Sbjct: 79  LFFEVLYEDAEVLVVAKPSGLPVLAGGGFLEHTLIHLVHQHYAEVTPYPIHRLGRGTSGI 138

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRF-HGQVDQDK-----LNLLKKGIV------I 167
           +L+         L       +  ++YR     G +  +      +  +   I+      +
Sbjct: 139 VLMAKSKPARAKLSQQMREGKITKIYRALVGQGDIPDNFTINQAIGKIAHPILGHVYGAL 198

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP--FQL 225
                      +  +   +  + V +  G+  +I+    FF + +        G   + L
Sbjct: 199 TDGLSARSDGRVLKKHPDSTLLEVRIFTGRPHQIRIHLAFFGYPL-------IGDPLYGL 251

Query: 226 GTLLA 230
           G L  
Sbjct: 252 GGLPR 256


>gi|60682049|ref|YP_212193.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC
           9343]
 gi|60493483|emb|CAH08269.1| putative RNA pseudouridylate synthase [Bacteroides fragilis NCTC
           9343]
          Length = 305

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/221 (15%), Positives = 74/221 (33%), Gaps = 31/221 (14%)

Query: 12  TPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVP 66
            P  +   +A +   ASR +++ +++++ V V+ ++  +    +     + +    +   
Sbjct: 23  EPMELMDFLAAKMPDASRTKLKSLLSKRIVLVDNVITTQFNFPLQPGMKVLISKDKNKKE 82

Query: 67  LRKA------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRL 114
            R        E   + +  K  GL++  ++     T    L          +R+  V RL
Sbjct: 83  FRHPLLKIVYEDAYIIVVEKKEGLLSVGTERQKERTAQHILSEYVGRSGRGNRIYVVHRL 142

Query: 115 DINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ-----------VDQDKLNLL 161
           D +T GL++   D      L          R Y     G+           +    L + 
Sbjct: 143 DRDTSGLMMFAKDEKTQYTLRDHWHDIVTDRRYVAVVTGEMEKDSDTVVSWLTDRTLYVS 202

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G        T+    G  + V + L  G+  +I+
Sbjct: 203 SSSYDDGGSKSITHYRTIKRANGY-SLVELRLETGRKNQIR 242


>gi|116490290|ref|YP_809834.1| pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290889676|ref|ZP_06552765.1| hypothetical protein AWRIB429_0155 [Oenococcus oeni AWRIB429]
 gi|116091015|gb|ABJ56169.1| Pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290480673|gb|EFD89308.1| hypothetical protein AWRIB429_0155 [Oenococcus oeni AWRIB429]
          Length = 302

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/165 (20%), Positives = 57/165 (34%), Gaps = 23/165 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN----LPSIFSRVIS-----VGRLDINTEGL 121
           E+    L  KP G+      P+   T+ +     L    SR        V R+D +T G+
Sbjct: 89  EKEDYLLVDKPAGMKMHPHSPNETDTLLNYVEAQLKGHLSRSCPAHAFMVHRIDRDTSGV 148

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           +++  +     +L   L   +  R Y     G + ++K   + + I +  I      V  
Sbjct: 149 VIIAKNPLAVGILDQLLAKKRIKRTYLAWVSGNL-ENKKGSIDQAIAVDPINPYKRIVDQ 207

Query: 180 DTQKGSNAW-----------VTVGLREGKNREIKKVFEFFNWKVN 213
             QK    W           V V L  G+  +I+  F      + 
Sbjct: 208 AGQKAVTHWTKIHTVYQNTLVRVSLETGRTHQIRVHFAAIGHPIV 252


>gi|330836420|ref|YP_004411061.1| pseudouridine synthase, RluA family [Spirochaeta coccoides DSM
           17374]
 gi|329748323|gb|AEC01679.1| pseudouridine synthase, RluA family [Spirochaeta coccoides DSM
           17374]
          Length = 329

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 47/278 (16%), Positives = 86/278 (30%), Gaps = 80/278 (28%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERMI--AQQRVKVNGILLERAAVNVMSTD-- 58
           +  +  +    QRV   +A A   SR     +I  A  R+ VNG  ++R+   +   D  
Sbjct: 6   ESIVPDDADGKQRVDAYLAAASGVSRS----IIGDASSRIMVNGREVKRSKA-IAPGDAV 60

Query: 59  ----------HIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----P 102
                     +IE   +PL    E   +    KP G+V      +   TV + L     P
Sbjct: 61  ILYWQENPPGNIEPQDIPLDILYEDDDILFIDKPQGIVVHPGAGNPDGTVVNALVFRYGP 120

Query: 103 SIFS-------------------------RVISVGRLDINTEGLLLLT----NDGGLARV 133
                                        R   V RLD +T G++++       G +AR 
Sbjct: 121 DFIRAYGGQDEHEDAGDETDEAVDRTDFLRPGIVHRLDKDTSGVMVIARTRLAHGYMARQ 180

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------------QGICYGDM 175
                   ++ Y     G +  D      +G++I                  +     + 
Sbjct: 181 FS--EHTAVKHYIALVEGSMKDD------EGVIITNLARDRNDRKKFRVSTGKEGKRAET 232

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +  +  + G    + + +  G+  +I+         V 
Sbjct: 233 RWRVVARYGVCTLLRIRIMTGRTHQIRVHMAHLGHPVV 270


>gi|254449547|ref|ZP_05062984.1| ribosomal large subunit pseudouridine synthase C [Octadecabacter
           antarcticus 238]
 gi|198263953|gb|EDY88223.1| ribosomal large subunit pseudouridine synthase C [Octadecabacter
           antarcticus 238]
          Length = 347

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/171 (18%), Positives = 57/171 (33%), Gaps = 35/171 (20%)

Query: 14  QRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
           QR+ + I    A+        +E+M  +  ++V+G  ++     V     +         
Sbjct: 16  QRLDRWIKRRFAQLQQG---GIEKMCRKGEIRVDGGRVKS-NTRVEVGQTVRIPPLPDAD 71

Query: 61  EVDGVP-------LRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFD---NLPSI 104
           EVD  P       ++  +   ++      + +KP GL T       R             
Sbjct: 72  EVDDRPRDMTKADIQLIQGCVIYKDDHVIVLNKPAGLPTQGGSKQLRHVDGMAEALRFGY 131

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
             R   V RLD +T G+L+L      A+ L          ++Y     G  
Sbjct: 132 DERPRLVHRLDKDTSGVLVLARTRMAAKSLTEAFRHRNTEKIYWALVAGVP 182


>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 (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 86/238 (36%), Gaps = 43/238 (18%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKV-------NGILLE------------RAAVNVM 55
           R+   +A+    SR + +R+I  ++VK+       N  +++              + ++ 
Sbjct: 15  RLDTYVAKKCNISRSKAQRLIQNEQVKLLGIPIINNDHIVKPGEEYVVHLIQPDISTSIE 74

Query: 56  ST-----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRV 108
                  D +  D   +  ++++RL + H   G   T++D    + +     +P   +R 
Sbjct: 75  PNYDIKLDIVYEDDDIIVLSKQSRLTV-HPGAG---TNNDTLLNAVIAHLGKIPYTNTRP 130

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD------QDKLNL 160
             V RLD +T GL+++  +      L   L + +  R Y     G +       +  +  
Sbjct: 131 GIVHRLDKDTSGLMVIAKNEQSHSFLSELLSNRKIKREYLAVIWGALPNLQGTVKTHIAP 190

Query: 161 LKKGIVIQGICYGDMQV-----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +    +  +     ++     ++    G  + V   L  G+  +I+         V 
Sbjct: 191 KRSNKEMMCVTKTAGKLAITHYSVKKIIGQASLVKCTLETGRTHQIRVHMSHIGHSVV 248


>gi|168010811|ref|XP_001758097.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162690553|gb|EDQ76919.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 361

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/244 (16%), Positives = 80/244 (32%), Gaps = 48/244 (19%)

Query: 106 SRVISVGRLDINTEGLLLLTNDG----GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL 161
            +V  V RLD    G ++ +            L  P+   ++ Y V   G      +   
Sbjct: 115 QKVSPVHRLDRPASGAIIFSKSAVATRAAQASLSHPA--CIKEYVVLARGTTPDFFICD- 171

Query: 162 KKGIVIQGICYGD------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRL 215
                +              +  LD  +   + + V ++ G+  +I+K     N +    
Sbjct: 172 ---EPVNDEKGAPKSAVSQCEKILDLPESRCSLLKVVIKTGRWHQIRK---HLNHR---- 221

Query: 216 IRISYGPFQLGTLLAGS------TREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                    +G +  G        RE + K+L    G   L  A++    P++ S+    
Sbjct: 222 -----AHHVVGDVKHGKGKTNRFFRE-NHKMLS---GRIFLHAARLTFPHPLHLSQEKWT 272

Query: 270 DRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSG 329
                 SE  DD   +  ++S          ++         S++WM+   ++SF  D  
Sbjct: 273 PASKHPSESSDDI-DLYSSASDLEDFESTSSVSA-------DSSIWMSP--NTSFSEDPK 322

Query: 330 QREE 333
            R +
Sbjct: 323 TRRQ 326


>gi|116872369|ref|YP_849150.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|116741247|emb|CAK20369.1| ribosomal large subunit pseudouridine synthase [Listeria welshimeri
           serovar 6b str. SLCC5334]
          Length = 296

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 75/209 (35%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN    +     V + D++ +          L           E   L + +KP
Sbjct: 37  ADGKIEVN-RTEQNVLYQVQTGDNVRLTFPTEQQNERLLAEYTKLEVIFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +      S +  V RLD +T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPSGSVANFVKGHYEAQGLTSAIHIVTRLDRDTSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQQGLLKRRYQALTSGVLQEEAGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLKRY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +G +  V + L  G+  +I+  F +    
Sbjct: 216 RGFDH-VAIQLETGRTHQIRVHFSYIGHP 243


>gi|71002582|ref|XP_755972.1| DRAP deaminase (Rib2) [Aspergillus fumigatus Af293]
 gi|66853610|gb|EAL93934.1| DRAP deaminase (Rib2), putative [Aspergillus fumigatus Af293]
 gi|159130027|gb|EDP55141.1| DRAP deaminase (Rib2), putative [Aspergillus fumigatus A1163]
          Length = 526

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/141 (17%), Positives = 47/141 (33%), Gaps = 16/141 (11%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKPI 82
           + +A  +V VNG         + + + I          V G  +    E   + +  KP 
Sbjct: 83  QALADGKVTVNGKTAA-PDTVIKNGEVISHTLHRHEPPVTGHEIGIIHEDNDILVIDKPA 141

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE--LP 137
           G+    +     +++ + L S   +        RLD  T G++ +      A  +   L 
Sbjct: 142 GVPVHAAGRYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSGVMFIAKHPKAADAITIKLK 201

Query: 138 STQWLRVYRVRFHGQVDQDKL 158
                + Y  R  G+     +
Sbjct: 202 QRTVQKEYIARVKGRFPDGVV 222


>gi|167757078|ref|ZP_02429205.1| hypothetical protein CLORAM_02627 [Clostridium ramosum DSM 1402]
 gi|167703253|gb|EDS17832.1| hypothetical protein CLORAM_02627 [Clostridium ramosum DSM 1402]
          Length = 278

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/212 (18%), Positives = 76/212 (35%), Gaps = 32/212 (15%)

Query: 19  VIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------DGVPLR 68
            +++    S ++  ++I    ++ VNG   +     +   D +E+         +  PL 
Sbjct: 17  FLSQQ-ELS-KKAVKLIKMHGKILVNGQR-QTVRYCLRYGDVVELLWPEEVSTMEPYPLA 73

Query: 69  KA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTE 119
                E     +  KP GL +  +    R+T+ + +   +        V  V RLD +T+
Sbjct: 74  LKICYEDENFLVIDKPAGLPSIPTKRYPRNTLANAVVYYYQSQGIKATVHLVNRLDKDTQ 133

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGI 170
           GLLL+  +     +L     Q  RVY     G +                +K+ I   G 
Sbjct: 134 GLLLIAKNSYAHYLLSRDIKQVRRVYHCVVEGVLTGQGTITAPIIKDKKSVKRLIHPAGK 193

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   L+    + + +   L  G+  +I+
Sbjct: 194 FAVTHYRGLEV-SANQSKIECILETGRTHQIR 224


>gi|153835569|ref|ZP_01988236.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           HY01]
 gi|148867844|gb|EDL67073.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           HY01]
          Length = 250

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/170 (15%), Positives = 62/170 (36%), Gaps = 35/170 (20%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E  ++   +KP GL++      +   +++  L   +  +  V RLD++T GL++L  +  
Sbjct: 19  EDEQILAVNKPSGLLSVPGRLAEHYDSMWSRLTEQYPDIQVVHRLDMSTSGLMVLAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLN------------LLKKGIVIQG 169
                       L        ++Y  R  G ++Q++               L+K     G
Sbjct: 79  AESALKKQFQYRLTH------KIYYARVWGHIEQEEGEIDLPLICDWPNRPLQKVCFEDG 132

Query: 170 ICYGDM-QVTLDTQKGSNAWVTVG----LREGKNREIK-KVFEFFNWKVN 213
                + QV    +    +  T+     +  G++ +++  + +     + 
Sbjct: 133 KPSKTLFQVAKREEHPDGSKTTIVRLLPIT-GRSHQLRVHM-QALGHPIV 180


>gi|1361308|pir||S57527 DNA helicase II - Vibrio cholerae
          Length = 611

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI 218
               +GI +       +  TL+    S   V + + EGK  ++K++       V +  R+
Sbjct: 134 EQFNRGIELLVEAELTLGATLEV--ISETEVLLTIHEGKYHQVKRM---LPLWVTK-HRV 187


>gi|223039515|ref|ZP_03609803.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter rectus RM3267]
 gi|222879311|gb|EEF14404.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Campylobacter rectus RM3267]
          Length = 252

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 68/204 (33%), Gaps = 37/204 (18%)

Query: 18  KVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTR 74
           K++A + GI S  E + +I    V   G  +  A   + +     V     P    E   
Sbjct: 8   KLLAIQEGI-SNNEAKELIDAGLVSAKGQRIAVARTVMSAATKFNVQKLPRPSVIFEDEN 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L    KP  L +                S   +   + RLD  T G+LLL  +    +  
Sbjct: 67  LIAVDKPAFLTSEK-------------VSEIYKFPLLHRLDKETSGVLLLVKNEEFQKKA 113

Query: 135 ELP--STQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDMQ---------VT 178
                + +  + Y     G V ++      +  LK     +G  +  +          VT
Sbjct: 114 IEEFKNCRVKKEYVAAVKGIVSEEFSVNEPIITLKN----RGGAFSKISPNGKDALSIVT 169

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
                G  + V V ++ G+  +I+
Sbjct: 170 PVMVAGKKSLVKVEIKTGRTHQIR 193


>gi|118587136|ref|ZP_01544565.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
 gi|118432415|gb|EAV39152.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
          Length = 302

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/165 (20%), Positives = 57/165 (34%), Gaps = 23/165 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN----LPSIFSRVIS-----VGRLDINTEGL 121
           E+    L  KP G+      P+   T+ +     L    SR        V R+D +T G+
Sbjct: 89  EKEDYLLVDKPAGMKMHPHSPNETDTLLNYVEAQLKGHLSRSCPAHAFMVHRIDRDTSGV 148

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
           +++  +     +L   L   +  R Y     G + ++K   + + I +  I      V  
Sbjct: 149 VIIAKNPLAVGILDQLLAKKRIKRTYLAWVSGNL-ENKKGSIDQAIAVDPINPYKRIVDQ 207

Query: 180 DTQKGSNAW-----------VTVGLREGKNREIKKVFEFFNWKVN 213
             QK    W           V V L  G+  +I+  F      + 
Sbjct: 208 AGQKAVTHWTKIHTVYQNTLVRVSLETGRTHQIRVHFAAIGHPIV 252


>gi|26249194|ref|NP_755234.1| tRNA pseudouridine synthase C [Escherichia coli CFT073]
 gi|34582426|sp|Q8FEF9|TRUC_ECOL6 RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|26109601|gb|AAN81804.1|AE016765_206 Hypothetical protein yqcB [Escherichia coli CFT073]
          Length = 260

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLAEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|253989177|ref|YP_003040533.1| 23S rRNA pseudouridylate synthase C [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253780627|emb|CAQ83789.1| 23S rRNA pseudouridine synthase [Photorhabdus asymbiotica]
          Length = 319

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 80/238 (33%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN------------GILLERAAV 52
            + ++   QRV   + AR     +  + R++ +  V+VN            G ++    V
Sbjct: 12  TIDDDEAGQRVDNFLLARLKGVPKSMIYRIVRKGEVRVNKGRVKPEYKLSAGDVVRIPPV 71

Query: 53  NVMSTDHIEV----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
            V     I V          DG  L   E   + + +KP G             +     
Sbjct: 72  RVAERQEIAVSAKLHKVAALDGCIL--YEDDYILVINKPSGTAVHGGSGLSFGVIEGLRV 129

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+     + R L   L   Q  + Y     GQ  Q   
Sbjct: 130 LRPEAKFLELVHRLDRDTSGILLIAKKRSVLRALHEQLRLKQMQKDYLALVRGQW-QSHC 188

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++ I     ++   + +G  +     + E              G+  +I+
Sbjct: 189 KVVQAPL-LKNILQSGERIVKVSGEGKPSETRFKIEERFTNATLVRASPITGRTHQIR 245


>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 = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/224 (19%), Positives = 81/224 (36%), Gaps = 57/224 (25%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G++SR     +I      +R+KV+G+ ++     V + + I+++              
Sbjct: 24  ELGLSSR-----LIRSAAIDKRIKVDGVAVK-MNYVVKTGEEIKIELSKKESQNIEPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSR----VISVGRLDINT 118
            + +   +   L L  KP  +V  T S P+G            S     V  V RLD+NT
Sbjct: 78  DIEIVYEDSDILVLNKKPFMVVHPTRSHPNGTLANGILYYFKESNQDCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM 175
            GL+++  +   A ++     +     + Y    HG + +      K+G  I    Y   
Sbjct: 138 SGLIIIGKN-QYAHMVLSNEMKTDKFQKRYLAIVHGNLAE------KEG-TINRPIYRPA 189

Query: 176 Q-----VTLDTQKGSNAWVTVG-------LRE-----GKNREIK 202
           +     V  +  + S     V        L E     G+  +I+
Sbjct: 190 EDTIKRVVDERGQESITHYKVIESYNGADLVECLLETGRTHQIR 233


>gi|163755046|ref|ZP_02162167.1| guanosine 5'-monophosphate oxidoreductase [Kordia algicida OT-1]
 gi|161325113|gb|EDP96441.1| guanosine 5'-monophosphate oxidoreductase [Kordia algicida OT-1]
          Length = 231

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/166 (12%), Positives = 53/166 (31%), Gaps = 23/166 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   + + +K  G +        +     V + +   +++     +  V RLD  T G++
Sbjct: 16  EDNHIIIVNKRAGDIVQGDKTGDKPLSDVVKEYIAEKYNKPGNVFLGVVHRLDRPTTGII 75

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK---LNLLKKG----------IVI 167
           +          L       +  + Y    +    + +   ++ L+K             I
Sbjct: 76  VFARTSKALPRLNKLFAEKKAKKTYWAIVNNMPPKQQDTLIHWLRKNPKNNKSTAFNKEI 135

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            G     +  T+  +      + + L  G++ +I+        K+ 
Sbjct: 136 PGSKKAILDYTVQKKLDRYVLLEIALHTGRHHQIRTQLSAIGCKIK 181


>gi|197122384|ref|YP_002134335.1| pseudouridine synthase [Anaeromyxobacter sp. K]
 gi|196172233|gb|ACG73206.1| pseudouridine synthase, RluA family [Anaeromyxobacter sp. K]
          Length = 353

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/227 (18%), Positives = 78/227 (34%), Gaps = 40/227 (17%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   + R A   SR  V+R++    V+V+G   + A+  +   + I ++          
Sbjct: 36  RLDAALVRLAPELSRARVQRLVEAGLVQVDGRGAK-ASARLRGGEAIALELPPPEPSGLV 94

Query: 64  --GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSRV 108
              +PL    E   L +  K  G+V   +     STV + L                 R+
Sbjct: 95  AQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPHSTVVNALLHRLGLPGAAGPDGALPRL 154

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------KLNL 160
             V RLD +T G L++  T     A   +       +VY    HG +  +          
Sbjct: 155 GLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRSVEKVYLALCHGALAPEGRLDTPYGRH 214

Query: 161 LKKGIVIQGICYGDMQVTLDTQ-----KGSNAWVTVGLREGKNREIK 202
            +  +   G      +   + +       + +   V L  G+  +I+
Sbjct: 215 PRDRLRFTGRVTSSRRAVTEWRVREAFGAAASLAEVTLHTGRTHQIR 261


>gi|189425760|ref|YP_001952937.1| hemolysin A [Geobacter lovleyi SZ]
 gi|189422019|gb|ACD96417.1| hemolysin A [Geobacter lovleyi SZ]
          Length = 249

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 37/87 (42%), Gaps = 4/87 (4%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          + QR+ K++   G+A SR + + +I   +V V     ++A   V     I + G  L   
Sbjct: 3  SKQRLDKLMVERGLAPSREKAQALIMAGQVVVGDHAAQKAGQQVTDEVEIRIKGELLPYV 62

Query: 71 ERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           R  L L     GL     DP GR  +
Sbjct: 63 SRGGLKLA---QGLDAFGIDPAGRIAI 86


>gi|304386318|ref|ZP_07368651.1| ribosomal large subunit pseudouridine synthase [Pediococcus
           acidilactici DSM 20284]
 gi|304327675|gb|EFL94902.1| ribosomal large subunit pseudouridine synthase [Pediococcus
           acidilactici DSM 20284]
          Length = 304

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 76/222 (34%), Gaps = 36/222 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------------VDGVPLRKA-- 70
           SR+ V  +  ++RV VN    +  +  V + D I                D    +    
Sbjct: 29  SRKVVHFLRTERRVLVN-QRYQPVSTVVRTGDLISLTFKESDFSTPLPPFDPDSSQSPDV 87

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLL 124
             E   L + +KP G+ T  + P    ++ + L + F++  S    V RLD  T G LL+
Sbjct: 88  LFENDDLLVVNKPAGIKTHANQPHELGSMINFLQAYFAKKDSNAYNVHRLDQWTSGALLV 147

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHGQV-DQDKLNLLKKGI--------VIQGICYG 173
             +  +  +L    +Q    R Y     G +  +     L  G+         I G    
Sbjct: 148 AKNPVVVPILSRQISQKLIQRTYLCMVEGHLKSRSGTITLPIGLDPHDQRKRQINGPGAQ 207

Query: 174 DMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +  +    + + V L  G+  +I+         + 
Sbjct: 208 PATTHYQVVREFVERSLLRVQLATGRTHQIRVHLAALGHPIV 249


>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 = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+  ++    +  SR++ +R+I    VKVN  ++++    V  T  I+V
Sbjct: 1  MAKQRLDTLLVSLELCTSRQQAQRVIRAGEVKVNDQIIDKPGTEVQLTAEIQV 53


>gi|119478011|ref|ZP_01618111.1| 23S rRNA pseudouridylate 746 synthase [marine gamma proteobacterium
           HTCC2143]
 gi|119448924|gb|EAW30166.1| 23S rRNA pseudouridylate 746 synthase [marine gamma proteobacterium
           HTCC2143]
          Length = 221

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 45/127 (35%), Gaps = 18/127 (14%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GL++     P  +  +   +   ++    V RLD++T G+++L       R 
Sbjct: 24  LLLVNKPAGLLSVPGRHPANKDCLITRVQRQYADARIVHRLDMDTSGIMVLALSADSHRA 83

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
           L       + ++ Y    +G +             I      D+ +  D        V  
Sbjct: 84  LSQLFAERKIIKEYEANVYGTI-------------IDDHRLIDLPLLCDWPNRPRQKVDF 130

Query: 192 GLREGKN 198
               GKN
Sbjct: 131 --HHGKN 135


>gi|322832332|ref|YP_004212359.1| pseudouridine synthase [Rahnella sp. Y9602]
 gi|321167533|gb|ADW73232.1| pseudouridine synthase [Rahnella sp. Y9602]
          Length = 232

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 77/235 (32%), Gaps = 51/235 (21%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
           G      +   L L +KP GL++ +  +P    +V   L  IF     V RLD  T GL+
Sbjct: 15  GQIETLYQDEHLVLINKPTGLLSLSGKNPQNLDSVHHRLVKIFPGCTLVHRLDFGTSGLM 74

Query: 123 LLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           ++  +  +   L    +Q    +VY     G +         +G+    I        L 
Sbjct: 75  VIARNKAINAALCHQFSQRTVTKVYSALLCGHL------QHNEGVTDAPIAKDPALFPLM 128

Query: 181 T-----QKGSNAWVTVG---LRE------------------GKNREIKKVFEFFNWKVNR 214
           +      K + +   V     RE                  G+  +++   ++    +  
Sbjct: 129 SICAVHGKPARSGYRVVERFYREQENGELLPLTRVLLTPQTGRTHQLRIHCQYLGHPILG 188

Query: 215 LIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                YG    G LL G+          EQ    +L  ++++   P+       R
Sbjct: 189 CD--LYG----GRLLPGT----------EQTPRLMLHASELHFVHPVSGERIEAR 227


>gi|298492205|ref|YP_003722382.1| hemolysin A ['Nostoc azollae' 0708]
 gi|298234123|gb|ADI65259.1| hemolysin A ['Nostoc azollae' 0708]
          Length = 270

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             QR+  ++   G++ SR++ +R+I    V+VN  ++++A   V  T  I+V   P
Sbjct: 1  MVKQRLDTLLVDLGLSPSRQQAQRLIQAGEVRVNQQVIDKAGTEVDITAQIQVKQRP 57


>gi|196040729|ref|ZP_03108028.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|228932672|ref|ZP_04095546.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|229090345|ref|ZP_04221588.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|196028519|gb|EDX67127.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|228692928|gb|EEL46646.1| Pseudouridine synthase [Bacillus cereus Rock3-42]
 gi|228826990|gb|EEM72750.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 307

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDIPFPTKLNDT 298


>gi|154504965|ref|ZP_02041703.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149]
 gi|153794848|gb|EDN77268.1| hypothetical protein RUMGNA_02475 [Ruminococcus gnavus ATCC 29149]
          Length = 321

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 33/226 (14%), Positives = 71/226 (31%), Gaps = 51/226 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRK----------------AERTR 74
           +M+ ++ + +NG         +   D +++      ++K                 E   
Sbjct: 33  KMLRKKNITLNGKKA-SGNEKLAKGDCVKLFLSDETIQKFSETFSGYTNVSLDILYEDED 91

Query: 75  LWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLL 122
           + L +KP+G+++     SD      +   L    +         R     RLD NT G++
Sbjct: 92  IILINKPVGMLSQKAARSDESLVEHLISYLIQSHALTEEDLRTFRPSICNRLDRNTSGIV 151

Query: 123 LL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
               +  G  +           + Y     G +++       +G + +      +++   
Sbjct: 152 AAGKSMAGLQSLSQMFHDRTIGKYYLCLTAGIIEKPSR---VEGWLFKDERTNKVEILFQ 208

Query: 181 TQKGSNAWVT----------VGLRE-----GKNREIKKVFEFFNWK 211
            + GS   +T          V L E     GK  +I+         
Sbjct: 209 ERPGSARIITEYRPIKSHDGVTLLEVHLITGKTHQIRAHLASVGHP 254


>gi|118587355|ref|ZP_01544781.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
 gi|118432179|gb|EAV38919.1| pseudouridine synthase [Oenococcus oeni ATCC BAA-1163]
          Length = 301

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 85/237 (35%), Gaps = 48/237 (20%)

Query: 7   VQENFTPQ--RVSKVIARAGIASR--REVE----RMIAQQR-------VKVNGILLERAA 51
           + E   P+  R+   +   G++ R   +++    +++ + R       VK NG  +    
Sbjct: 8   ISETKEPEKVRL--FLKARGVSHRMFSQIKHFGGKIVVEGREVFTNDYVK-NGEKITI-- 62

Query: 52  VNVMSTDHIEVDGV---PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                 +++E+D     PL+   E     +  KP  + T     D ++T+ + + +   +
Sbjct: 63  FMPPERENVELDADFTDPLKVVFEDKNFLIVDKPAFVTTVPGHADRKTTLVNMIKAHLIQ 122

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLEL----PSTQWLRVYRVRFHGQVDQD 156
                     V RLD +T GL+LL      A  L            + Y     G   +D
Sbjct: 123 EKADSLVPHVVTRLDRDTSGLVLLAKH-KFAHALLNDALMEHHDIEKFYVALVSGNFQED 181

Query: 157 KL-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        + +++ +   G      +  ++ +  +   + + L  G+  +I+
Sbjct: 182 HGMIDEPIGRIEGDFIRRQVRQDGKRSVT-EYWIEKRFDNFTQLRIQLHTGRTHQIR 237


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

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/264 (14%), Positives = 84/264 (31%), Gaps = 58/264 (21%)

Query: 3   DKNIVQENFTPQRVSKVI-AR---AGIASRREVERMIAQQRVKVNGILLER--------- 49
           ++  V  +    R+ +   A     G   R  +++++   +V+V+G   E          
Sbjct: 5   EQKKVTADEAGMRLDRWFKAHYPGLGFG-R--LQKLLRTGQVRVDGKRAESNTRIAKGQI 61

Query: 50  -----AAVNVMSTDH----------IEVDGVPLR---KAERTRLWLYHKPIGLVTTH--- 88
                  V + + D           I  D   +      E  ++ + +KP GL       
Sbjct: 62  IRIPPLGVELPADDKKNARPKSTKLIADDKKAIEDMLLYEDNQVMVLNKPAGLAVQGGSG 121

Query: 89  --SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
                DG    F +      R+  V RLD  T G++L+      A+ L          +V
Sbjct: 122 LKRHLDGMLDAFTDQKGNKPRL--VHRLDRETSGIILVARTRQAAQELTKAFRHRNTRKV 179

Query: 145 YRVRFHGQV---------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           Y     G                 +++++ ++++G          +    +      +WV
Sbjct: 180 YWTILAGVPKPHQGRISTFLARDEEEERMQVVRQGGADDAQHAVSLYSVFEKSGQKLSWV 239

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
           T+    G+  +++         + 
Sbjct: 240 TMKPVTGRTHQLRAHAAHIGHPII 263


>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 = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 80/222 (36%), Gaps = 36/222 (16%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA---------ERTRL 75
           R  ++++I +  V VN IL+++    V   D IE+   +G               E   +
Sbjct: 29  RNFIQKIIEKGFVYVNNILIKK-NYIVKINDVIEIFLPEGKKNIIPENLKINIFYEDEYV 87

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNL-------PSIFSRVIS-VGRLDINTEGLLLLTND 127
            + +K  GLV      +   T+ + L        +I++++   V R+D  T GL+L+  D
Sbjct: 88  IIINKQSGLVVHPGKGNESMTLINGLHFYFLKKKNIYNKIPILVHRIDKGTSGLILVAKD 147

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDK-------LNLLKKGIVIQ---GICYGDM 175
             +   +          R Y     G +  +K          LK  I +       YG  
Sbjct: 148 KNILEKISKQFYINHIKRKYITLVWGYIKNNKGTIICNIGRSLKNRIYMNVFPNGIYGKF 207

Query: 176 QVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            +T   +  +      +   L  G+  +I+   ++    +  
Sbjct: 208 SITHYKVLERFKYVTLLKCTLETGRTHQIRVHLKYIGHPILN 249


>gi|264679457|ref|YP_003279364.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262209970|gb|ACY34068.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
          Length = 255

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/164 (17%), Positives = 55/164 (33%), Gaps = 21/164 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   + + +KP G +   +  D   T F        +   V  V RLD  T G+LL+   
Sbjct: 20  QDEHMVVVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGHHVWPVHRLDKGTCGVLLMALH 79

Query: 128 GGLARVLELPSTQWL--RVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGDMQVTL---- 179
              A+ L          + YR    G + +  +  + LK     +     D    L    
Sbjct: 80  KQAAQALAASFAAHETRKEYRALVRGWLPETLEVDHPLKPDDAPEDAPVQDAHTHLRCLA 139

Query: 180 -----DTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++  G +    + L E     G+  +I++  +     + 
Sbjct: 140 RLSWPESYDGRHPETRISLVEALPTTGRRHQIRRHLKHVAHPII 183


>gi|210615096|ref|ZP_03290443.1| hypothetical protein CLONEX_02657 [Clostridium nexile DSM 1787]
 gi|210150445|gb|EEA81454.1| hypothetical protein CLONEX_02657 [Clostridium nexile DSM 1787]
          Length = 303

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/160 (15%), Positives = 59/160 (36%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +KP  +    S  +  +T+ + +   +++         + RLD +T GLL+L
Sbjct: 86  EDEDLMVINKPADMPIHPSQGNYDNTLANAVAYYYAQKGEPFTYRCINRLDRDTTGLLIL 145

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICY 172
                 A +L     + +  R Y     G           + +   + +++ +  +   Y
Sbjct: 146 AKHMYSASLLSDMVKNRKIHREYLAVAEGKTPSSGIIDAPIGRVDGSTIERQVDYEQGDY 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
                     K   + V++ L+ G+  +I+  + +     
Sbjct: 206 ACTHYKRLCYKNGYSLVSLTLKTGRTHQIRVHM-KHVGHP 244


>gi|270264826|ref|ZP_06193090.1| tRNA pseudouridine synthase C [Serratia odorifera 4Rx13]
 gi|270041124|gb|EFA14224.1| tRNA pseudouridine synthase C [Serratia odorifera 4Rx13]
          Length = 257

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/160 (20%), Positives = 52/160 (32%), Gaps = 27/160 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G +   S  D   T F        I   V +V RLD  T G+LL+   
Sbjct: 7   QDEHLVAVNKPSGWLVHRSWLDRHETRFMMQTVRDQIGQHVFTVHRLDRPTSGVLLMALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD-- 174
             +AR+L       Q  + Y     G V +         ++L+ +               
Sbjct: 67  SEVARLLSQQFEQHQVQKTYHAVVRGYVQEGATLDYPLTEELDKIADKHTAVDKGPQPAV 126

Query: 175 ------MQVTLDTQKGSNAWVTVGLRE-----GKNREIKK 203
                  QV +    G        L E     G+  ++++
Sbjct: 127 THYRPLAQVEMPVAIGRYDSARYSLMELKPENGRKHQLRR 166


>gi|87311869|ref|ZP_01093981.1| putative 23S rRNA pseudouridine synthase [Blastopirellula marina
           DSM 3645]
 gi|87285400|gb|EAQ77322.1| putative 23S rRNA pseudouridine synthase [Blastopirellula marina
           DSM 3645]
          Length = 250

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/165 (17%), Positives = 58/165 (35%), Gaps = 24/165 (14%)

Query: 80  KPIGLVTTHSDP----DGRSTVFDNLPSIFSRVISVG---RLDINTEGLLLLTNDGGLAR 132
           KP GL+T         + R   F       +  + +G   RLD    G+L    +   AR
Sbjct: 23  KPAGLLTQAPPHIDSLESRFKAFIRQRDFKTGKVYLGVPHRLDRPVSGVLTFARNVRAAR 82

Query: 133 VLEL--PSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQ-------GICYGDMQV 177
            +     +    ++Y     GQ   D+      +  +    + +       G  +  ++ 
Sbjct: 83  RISQQFETRLVRKLYWAFVAGQPPDDQGVWEDPIRKIPDVAMAEIVSPSDPGARWAKLKY 142

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
            +  +    AW+ + L  G+  +I+       + +  L  +SYG 
Sbjct: 143 EVLQRTEQGAWLEIELDTGRYHQIRVQCASRGFPI--LGDVSYGG 185


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

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 78/254 (30%), Gaps = 51/254 (20%)

Query: 6   IVQENFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            V E+    R+ +     +   G A+   V R     +++V+G   +     +     + 
Sbjct: 17  TVAEDDEGVRLDRWFKRHLPEVGFAT---VARWARTGQIRVDGARAK-PDDRLTQGQVLR 72

Query: 62  VD-GVPLRKAERTRL----------------------WLYHKPIGLVTTH--SDPDGRST 96
           +  G P R     R                        + +KP GL T            
Sbjct: 73  IPPGNPARAKTPPRRRELTEDQKAQARAMVIKETPNAIVLNKPPGLATQGGSKTFSHVDG 132

Query: 97  VFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
           + D  +     R   V RLD +T G+LL+    G A             +VY     G  
Sbjct: 133 LLDAFVEGDGPRPRLVHRLDKDTSGVLLIARTPGSAAAFSKRFAGRSAKKVYWALVVGVP 192

Query: 154 DQ---DKLNLLKK---------GIVIQGICYGDMQVTLDTQKGSN-AWVTVG-LREGKNR 199
           +Q   +    L K          +  +G      +  +  + G+  AW+ +  L  G+  
Sbjct: 193 EQHVGEIDAPLAKQPGTGGEKMHVDTEGGQPAKTRYRVVERAGNRAAWLELEPLT-GRTH 251

Query: 200 EIKKVFEFFNWKVN 213
           +++         + 
Sbjct: 252 QLRVHCAAMGHPIV 265


>gi|258566750|ref|XP_002584119.1| hypothetical protein UREG_04808 [Uncinocarpus reesii 1704]
 gi|237905565|gb|EEP79966.1| hypothetical protein UREG_04808 [Uncinocarpus reesii 1704]
          Length = 537

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/142 (16%), Positives = 49/142 (34%), Gaps = 16/142 (11%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           +  I    V +NG         VM+ D +          V  +P+    E  ++ +  KP
Sbjct: 84  KEAIESGHVAINGKPG-NLDTRVMNGDMVSHTLHRHEPPVTSLPIGVIHEDDKMIVIDKP 142

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLE--L 136
            G+    +     +++ + + +            RLD  T G++ +  D   A  +   L
Sbjct: 143 AGVPVHPAGRYNYNSIIEIMRAERGHSFNPRPCNRLDRLTSGVMFIGKDPKAAEKIAEGL 202

Query: 137 PSTQWLRVYRVRFHGQVDQDKL 158
            +    + Y  R  G+     +
Sbjct: 203 RARTMQKEYIARVKGKFPDGII 224


>gi|229084299|ref|ZP_04216581.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-44]
 gi|228699010|gb|EEL51713.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-44]
          Length = 297

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/264 (16%), Positives = 87/264 (32%), Gaps = 44/264 (16%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPLRKA-ERTRLWLYHKPIGL 84
             ++VNG     R  +       +             + +PL    E   + + +K   +
Sbjct: 43  GAIEVNGKHATVRHVLQAGEELQVFFPLEERSEGMLAENIPLNVVYEDDSVLVMNKAPYM 102

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--L 136
            T  S      +V + L   + +      V  V RLD +T GL+L+  +  +  +L    
Sbjct: 103 STIPSREHPAGSVANALLYHYDKQHLASTVHIVTRLDRDTSGLMLVAKNRFIHHLLSKQH 162

Query: 137 PSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
              Q  R Y    HG++ ++          K + + +  V +          +  +    
Sbjct: 163 QEKQVQRTYEAIVHGELVEESGTIDAPIGRKSDSIIERTVCEDGQKAVTHFQVLERFPDK 222

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--EQ 244
             V++ L  G+  +I+    +    +               L  GST E+ ++ L     
Sbjct: 223 TRVSLQLETGRTHQIRVHMAYVGHPLLG-----------DDLYGGSTSEMKRQALHSTSL 271

Query: 245 LGPHLLEEAQVNLDAPIYSSETLV 268
              H + E Q+   A +      V
Sbjct: 272 TFYHPILEKQMTFHADVPKDMKEV 295


>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 = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/79 (17%), Positives = 33/79 (41%), Gaps = 6/79 (7%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            +++   + +R+  V + A   SR +++  I    V VNG  +  A   +   D + V G
Sbjct: 173 RVIRTTESSKRLDSVGSAALGISRSKMQSYIKAGVVTVNGKKVYDAHYELEEGDIVIVQG 232

Query: 65  ------VPLRKAERTRLWL 77
                   +   ++ + ++
Sbjct: 233 LGNFKINKINVTQKGKFYM 251


>gi|194377234|dbj|BAG63178.1| unnamed protein product [Homo sapiens]
          Length = 524

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 45/292 (15%), Positives = 96/292 (32%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+++N   ++   + +   D +          V   P+R  AE   + +  KP
Sbjct: 158 EAAVRAGRLQLNEKPVQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 217

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 218 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 277

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 278 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGQSS 337

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI- 240
            V    +    G+  +I+   +F    +        +++GP +      G     + +  
Sbjct: 338 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSR----GRGGYIPKTNEEL 390

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       ++QK
Sbjct: 391 LRDLVAEHQAKQSLDVLDLCEGDLSPGLTDSTAPSSELGKDDLEELAAAAQK 442


>gi|206577943|ref|YP_002236857.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae 342]
 gi|288933804|ref|YP_003437863.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|290511116|ref|ZP_06550485.1| tRNA pseudouridine synthase C [Klebsiella sp. 1_1_55]
 gi|206567001|gb|ACI08777.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae 342]
 gi|288888533|gb|ADC56851.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|289776109|gb|EFD84108.1| tRNA pseudouridine synthase C [Klebsiella sp. 1_1_55]
          Length = 264

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +  +          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMDEALLDYPLVEELDKIADKFAREDKDPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPIL 176


>gi|195118760|ref|XP_002003904.1| GI18161 [Drosophila mojavensis]
 gi|193914479|gb|EDW13346.1| GI18161 [Drosophila mojavensis]
          Length = 545

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/208 (14%), Positives = 67/208 (32%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRKAE-RTRLWLYHKP 81
           +R I    + VN   +      +   D          + V   P+        + + +KP
Sbjct: 181 KRSIEAGNLTVNYEKV-PVDYRLKHNDLLANTVHRHEVPVTAQPISIVHIDDDILVVNKP 239

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L   +    + ++ RLD  T GLLL   +   AR +E    
Sbjct: 240 ASIPVHPCGRYRHNTVIFILAKEYNLKNLRTIHRLDRLTSGLLLFGRNSEKARQMEQQIR 299

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------ 191
           + Q  + Y     G      +    + I +     G  +V+   +     +  +      
Sbjct: 300 NRQVQKEYVCCVEGHFPDGIIE-CNEPIEVVSYKIGVCKVSKKGKDCQTTFKRIAQAGDY 358

Query: 192 GLRE-----GKNREIKKVFEFFNWKVNR 214
            + +     G+  +I+   ++  + +  
Sbjct: 359 SIVQCKPLTGRMHQIRVHLQYLGYPIVN 386


>gi|110642932|ref|YP_670662.1| tRNA pseudouridine synthase C [Escherichia coli 536]
 gi|191171222|ref|ZP_03032772.1| tRNA pseudouridine synthase C [Escherichia coli F11]
 gi|227888331|ref|ZP_04006136.1| TruC protein [Escherichia coli 83972]
 gi|300976014|ref|ZP_07173255.1| tRNA pseudouridine synthase [Escherichia coli MS 45-1]
 gi|300976318|ref|ZP_07173382.1| tRNA pseudouridine synthase [Escherichia coli MS 200-1]
 gi|301049449|ref|ZP_07196408.1| tRNA pseudouridine synthase [Escherichia coli MS 185-1]
 gi|331648518|ref|ZP_08349606.1| tRNA pseudouridine synthase C [Escherichia coli M605]
 gi|331658904|ref|ZP_08359846.1| tRNA pseudouridine synthase C [Escherichia coli TA206]
 gi|110344524|gb|ABG70761.1| hypothetical protein YqcB (putative RNA pseudouridylate synthase)
           [Escherichia coli 536]
 gi|190908522|gb|EDV68111.1| tRNA pseudouridine synthase C [Escherichia coli F11]
 gi|227834600|gb|EEJ45066.1| TruC protein [Escherichia coli 83972]
 gi|281179792|dbj|BAI56122.1| putative pseudouridine synthase [Escherichia coli SE15]
 gi|300298765|gb|EFJ55150.1| tRNA pseudouridine synthase [Escherichia coli MS 185-1]
 gi|300308560|gb|EFJ63080.1| tRNA pseudouridine synthase [Escherichia coli MS 200-1]
 gi|300410152|gb|EFJ93690.1| tRNA pseudouridine synthase [Escherichia coli MS 45-1]
 gi|307554763|gb|ADN47538.1| tRNA pseudouridine synthase C [Escherichia coli ABU 83972]
 gi|315293748|gb|EFU53100.1| tRNA pseudouridine synthase [Escherichia coli MS 153-1]
 gi|315298808|gb|EFU58062.1| tRNA pseudouridine synthase [Escherichia coli MS 16-3]
 gi|324015525|gb|EGB84744.1| tRNA pseudouridine synthase [Escherichia coli MS 60-1]
 gi|331042265|gb|EGI14407.1| tRNA pseudouridine synthase C [Escherichia coli M605]
 gi|331053486|gb|EGI25515.1| tRNA pseudouridine synthase C [Escherichia coli TA206]
          Length = 260

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|317177743|dbj|BAJ55532.1| hypothetical protein HPF16_0935 [Helicobacter pylori F16]
          Length = 242

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 66/201 (32%), Gaps = 30/201 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V G  L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGGKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIITPLK 171

Query: 185 ---SNAWVTVGLREGKNREIK 202
                  +  G++ G+  +I+
Sbjct: 172 IINKKTLLKAGIKTGRTHQIR 192


>gi|293412139|ref|ZP_06654862.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291468910|gb|EFF11401.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 260

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RMLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|269103546|ref|ZP_06156243.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163444|gb|EEZ41940.1| ribosomal large subunit pseudouridine synthase A [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 241

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 58/160 (36%), Gaps = 28/160 (17%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +   +KP GL++    DP    +++  +     +   V RLD+ T GL++L  +    R 
Sbjct: 36  IIAVNKPSGLLSVPGRDPAHYDSIYSRVLRDHPKSQIVHRLDMTTSGLIVLAINKNAERH 95

Query: 134 LELP--STQWLRVYRVRFHGQVDQDKLNLLKKG-IVI----QGICYGDMQVTLDTQKGSN 186
           L+      Q  +VY  R  G ++Q      + G + +            +V  +  K S 
Sbjct: 96  LKAQFRERQTHKVYYARVWGHLEQ------QHGSVDLPLICDWPNRPKQKVCYEEGKPSL 149

Query: 187 AWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
               V   E            G++ +++  +       + 
Sbjct: 150 THYEVVRYEENATLVRLLPVTGRSHQLRVHMM-AIGHPIL 188


>gi|90407469|ref|ZP_01215652.1| pseudouridine synthase Rlu family protein [Psychromonas sp. CNPT3]
 gi|90311390|gb|EAS39492.1| pseudouridine synthase Rlu family protein [Psychromonas sp. CNPT3]
          Length = 253

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/171 (14%), Positives = 53/171 (30%), Gaps = 30/171 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND 127
           +   +   +KP GL+   S  DP         L       V    RLD  T G+LL   D
Sbjct: 23  QDEAVVAINKPPGLLVHRSWLDPHATEFAIQKLRDQIGVHVYPAHRLDRPTSGVLLFLLD 82

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQ--------DKLNLLKKGIVIQGICYGDM-- 175
               + +       +  + Y     G + +         KL+ +    V++         
Sbjct: 83  KNYLKPVMAQFAEQKIEKRYLAIVRGHIGEGIIDYALKKKLDKIAHKHVLREPEAQSAVT 142

Query: 176 --------QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                   +V +  +    +  ++   E     G+  ++++  +     + 
Sbjct: 143 HYRNMAHCEVDIGVRPYPTSRYSLV--ELSPKTGRRHQLRRHMKHVFHPII 191


>gi|228926422|ref|ZP_04089494.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229120931|ref|ZP_04250173.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228662591|gb|EEL18189.1| Pseudouridine synthase [Bacillus cereus 95/8201]
 gi|228833246|gb|EEM78811.1| Pseudouridine synthase [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 307

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|254512315|ref|ZP_05124382.1| ribosomal large subunit pseudouridine synthase C [Rhodobacteraceae
           bacterium KLH11]
 gi|221536026|gb|EEE39014.1| ribosomal large subunit pseudouridine synthase C [Rhodobacteraceae
           bacterium KLH11]
          Length = 347

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 73/268 (27%), Gaps = 68/268 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E    QR+ + +       RR         +E+M  +  ++V+G  ++ A+  +   
Sbjct: 8   TVAEGDGDQRLDRWL-------RRLFPHVSQGRIEKMCRKGELRVDGGRVK-ASTRLEVG 59

Query: 58  DHIEV------DGVPLRKAERT-----------------RLWLYHKPIGLVTTHSDPDGR 94
             + V      D  P     R                  ++   +KP GL         R
Sbjct: 60  QVVRVPPLPDADHKPAVVRHRVSDADAKMIQSCVIYKDDQVLALNKPHGLPVQGGSGQTR 119

Query: 95  STVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
                              V RLD +T G+LL+      A+ L          ++Y    
Sbjct: 120 HVDSLSEALRFGYDENPRLVHRLDKDTSGVLLMARTRDAAKALTAAFRHRNTRKIYWALV 179

Query: 150 HGQVDQ-------DKLNLLKKGIVIQGIC-----------------YGDMQVTLDTQKGS 185
            G             +     G   +G                      +  TL    G 
Sbjct: 180 AGVPTPYLGEIKTGLVKASGHGKQGEGEKMIALHPSEVNDTPGAKRAHTLYATLYRVAGR 239

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
            AWV +    G+  +++         + 
Sbjct: 240 AAWVAMEPVTGRTHQLRAHMAAIGHPII 267


>gi|220917166|ref|YP_002492470.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219955020|gb|ACL65404.1| pseudouridine synthase, RluA family [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 352

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 44/227 (19%), Positives = 78/227 (34%), Gaps = 40/227 (17%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   + R A   SR  V+R++    V+V+G   + A+  +   + I ++          
Sbjct: 36  RLDAALVRLAPDLSRARVQRLVEAGLVQVDGRGAK-ASARLRGGEAIALELPPPEPSGLV 94

Query: 64  --GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------------PSIFSRV 108
              +PL    E   L +  K  G+V   +     STV + L                 R+
Sbjct: 95  AQDLPLAVLHEDADLIVLDKAPGMVVHPARGTPHSTVVNALLHRLGLPGAAGPDGGLPRL 154

Query: 109 ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK--------- 157
             V RLD +T G L++  T     A   +       +VY    HG +  +          
Sbjct: 155 GLVHRLDKDTSGCLVVAKTEAALAALQAQWKGRSVEKVYLALCHGALAPEGRLDTPYGRH 214

Query: 158 -LNLLK-KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             + L+  G V             +    + +   V L  G+  +I+
Sbjct: 215 PRDRLRFTGRVTSSRRALTEWRVREAFGAAASLAEVTLHTGRTHQIR 261


>gi|16130698|ref|NP_417271.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           MG1655]
 gi|24114075|ref|NP_708585.1| tRNA pseudouridine synthase C [Shigella flexneri 2a str. 301]
 gi|30064136|ref|NP_838307.1| tRNA pseudouridine synthase C [Shigella flexneri 2a str. 2457T]
 gi|74313363|ref|YP_311782.1| tRNA pseudouridine synthase C [Shigella sonnei Ss046]
 gi|89109577|ref|AP_003357.1| tRNA pseudouridine synthase [Escherichia coli str. K-12 substr.
           W3110]
 gi|157162245|ref|YP_001459563.1| tRNA pseudouridine synthase C [Escherichia coli HS]
 gi|170018963|ref|YP_001723917.1| tRNA pseudouridine synthase C [Escherichia coli ATCC 8739]
 gi|170082362|ref|YP_001731682.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170682843|ref|YP_001744955.1| tRNA pseudouridine synthase C [Escherichia coli SMS-3-5]
 gi|187734142|ref|YP_001881468.1| tRNA pseudouridine synthase C [Shigella boydii CDC 3083-94]
 gi|188493340|ref|ZP_03000610.1| tRNA pseudouridine synthase C [Escherichia coli 53638]
 gi|194439667|ref|ZP_03071738.1| tRNA pseudouridine synthase C [Escherichia coli 101-1]
 gi|215488108|ref|YP_002330539.1| tRNA pseudouridine synthase C [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218690914|ref|YP_002399126.1| tRNA pseudouridine synthase C [Escherichia coli ED1a]
 gi|218706287|ref|YP_002413806.1| tRNA pseudouridine synthase C [Escherichia coli UMN026]
 gi|238901929|ref|YP_002927725.1| tRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|253772358|ref|YP_003035189.1| tRNA pseudouridine synthase C [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037844|ref|ZP_04871902.1| tRNA pseudouridine synthase C [Escherichia sp. 1_1_43]
 gi|254162717|ref|YP_003045825.1| tRNA pseudouridine synthase C [Escherichia coli B str. REL606]
 gi|256024706|ref|ZP_05438571.1| tRNA pseudouridine synthase C [Escherichia sp. 4_1_40B]
 gi|291284120|ref|YP_003500938.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. CB9615]
 gi|293406283|ref|ZP_06650209.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1412]
 gi|293416038|ref|ZP_06658678.1| tRNA pseudouridine synthase C [Escherichia coli B185]
 gi|297517184|ref|ZP_06935570.1| tRNA pseudouridine synthase C [Escherichia coli OP50]
 gi|298382019|ref|ZP_06991616.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1302]
 gi|300898152|ref|ZP_07116515.1| tRNA pseudouridine synthase [Escherichia coli MS 198-1]
 gi|300920353|ref|ZP_07136791.1| tRNA pseudouridine synthase [Escherichia coli MS 115-1]
 gi|300931251|ref|ZP_07146591.1| tRNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|300936292|ref|ZP_07151224.1| tRNA pseudouridine synthase [Escherichia coli MS 21-1]
 gi|300950522|ref|ZP_07164431.1| tRNA pseudouridine synthase [Escherichia coli MS 116-1]
 gi|300958108|ref|ZP_07170267.1| tRNA pseudouridine synthase [Escherichia coli MS 175-1]
 gi|301026250|ref|ZP_07189710.1| tRNA pseudouridine synthase [Escherichia coli MS 196-1]
 gi|301027548|ref|ZP_07190883.1| tRNA pseudouridine synthase [Escherichia coli MS 69-1]
 gi|301645242|ref|ZP_07245195.1| tRNA pseudouridine synthase [Escherichia coli MS 146-1]
 gi|307139477|ref|ZP_07498833.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|312964939|ref|ZP_07779179.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|312972991|ref|ZP_07787164.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|331643478|ref|ZP_08344609.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|331654276|ref|ZP_08355276.1| tRNA pseudouridine synthase C [Escherichia coli M718]
 gi|331674285|ref|ZP_08375045.1| tRNA pseudouridine synthase C [Escherichia coli TA280]
 gi|92090982|sp|P0AA42|TRUC_SHIFL RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|108936020|sp|P0AA41|TRUC_ECOLI RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|882686|gb|AAB40441.1| corresponds to hypothetical protein from E. carotovora PIR
           Accession Number S45108; 2 ORFs in E. coli; ORF_f260
           [Escherichia coli str. K-12 substr. MG1655]
 gi|1789155|gb|AAC75833.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           MG1655]
 gi|24053203|gb|AAN44292.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
 gi|30042392|gb|AAP18117.1| hypothetical protein S2998 [Shigella flexneri 2a str. 2457T]
 gi|73856840|gb|AAZ89547.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|85675610|dbj|BAE76863.1| tRNA pseudouridine synthase [Escherichia coli str. K12 substr.
           W3110]
 gi|157067925|gb|ABV07180.1| tRNA pseudouridine synthase C [Escherichia coli HS]
 gi|169753891|gb|ACA76590.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169890197|gb|ACB03904.1| tRNA U65 pseudouridine synthase [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170520561|gb|ACB18739.1| tRNA pseudouridine synthase C [Escherichia coli SMS-3-5]
 gi|187431134|gb|ACD10408.1| tRNA pseudouridine synthase C [Shigella boydii CDC 3083-94]
 gi|188488539|gb|EDU63642.1| tRNA pseudouridine synthase C [Escherichia coli 53638]
 gi|194421414|gb|EDX37430.1| tRNA pseudouridine synthase C [Escherichia coli 101-1]
 gi|209761378|gb|ACI79001.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761384|gb|ACI79004.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|215266180|emb|CAS10606.1| tRNA pseudouridine synthase [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218428478|emb|CAR09404.2| tRNA pseudouridine synthase [Escherichia coli ED1a]
 gi|218433384|emb|CAR14286.1| tRNA pseudouridine synthase [Escherichia coli UMN026]
 gi|226839468|gb|EEH71489.1| tRNA pseudouridine synthase C [Escherichia sp. 1_1_43]
 gi|238863710|gb|ACR65708.1| tRNA pseudouridine synthase [Escherichia coli BW2952]
 gi|242378338|emb|CAQ33115.1| tRNA pseudouridine 65 synthase [Escherichia coli BL21(DE3)]
 gi|253323402|gb|ACT28004.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253974618|gb|ACT40289.1| tRNA pseudouridine synthase [Escherichia coli B str. REL606]
 gi|253978783|gb|ACT44453.1| tRNA pseudouridine synthase [Escherichia coli BL21(DE3)]
 gi|260448158|gb|ACX38580.1| pseudouridine synthase [Escherichia coli DH1]
 gi|281602151|gb|ADA75135.1| tRNA pseudouridine synthase C [Shigella flexneri 2002017]
 gi|284922729|emb|CBG35817.1| tRNA pseudouridine synthase C [Escherichia coli 042]
 gi|290763993|gb|ADD57954.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. CB9615]
 gi|291426289|gb|EFE99321.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1412]
 gi|291432227|gb|EFF05209.1| tRNA pseudouridine synthase C [Escherichia coli B185]
 gi|298277159|gb|EFI18675.1| tRNA pseudouridine synthase C [Escherichia coli FVEC1302]
 gi|299879762|gb|EFI87973.1| tRNA pseudouridine synthase [Escherichia coli MS 196-1]
 gi|300315205|gb|EFJ64989.1| tRNA pseudouridine synthase [Escherichia coli MS 175-1]
 gi|300358142|gb|EFJ74012.1| tRNA pseudouridine synthase [Escherichia coli MS 198-1]
 gi|300394909|gb|EFJ78447.1| tRNA pseudouridine synthase [Escherichia coli MS 69-1]
 gi|300412678|gb|EFJ95988.1| tRNA pseudouridine synthase [Escherichia coli MS 115-1]
 gi|300450155|gb|EFK13775.1| tRNA pseudouridine synthase [Escherichia coli MS 116-1]
 gi|300458544|gb|EFK22037.1| tRNA pseudouridine synthase [Escherichia coli MS 21-1]
 gi|300460905|gb|EFK24398.1| tRNA pseudouridine synthase [Escherichia coli MS 187-1]
 gi|301076512|gb|EFK91318.1| tRNA pseudouridine synthase [Escherichia coli MS 146-1]
 gi|309703149|emb|CBJ02483.1| tRNA pseudouridine synthase C [Escherichia coli ETEC H10407]
 gi|310332933|gb|EFQ00147.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|312290495|gb|EFR18375.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|313647852|gb|EFS12298.1| RNA pseudouridylate synthase family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315137398|dbj|BAJ44557.1| tRNA pseudouridine synthase C [Escherichia coli DH1]
 gi|315615179|gb|EFU95816.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320173224|gb|EFW48434.1| tRNA pseudouridine synthase C [Shigella dysenteriae CDC 74-1112]
 gi|320640440|gb|EFX09979.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. G5101]
 gi|320645686|gb|EFX14671.1| tRNA pseudouridine synthase C [Escherichia coli O157:H- str.
           493-89]
 gi|320650986|gb|EFX19426.1| tRNA pseudouridine synthase C [Escherichia coli O157:H- str. H
           2687]
 gi|320656482|gb|EFX24378.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. 3256-97
           TW 07815]
 gi|320662378|gb|EFX29775.1| tRNA pseudouridine synthase C [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320667076|gb|EFX34039.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323167869|gb|EFZ53560.1| RNA pseudouridylate synthase family protein [Shigella sonnei 53G]
 gi|323172906|gb|EFZ58537.1| RNA pseudouridylate synthase family protein [Escherichia coli
           LT-68]
 gi|323188791|gb|EFZ74076.1| RNA pseudouridylate synthase family protein [Escherichia coli
           RN587/1]
 gi|323935847|gb|EGB32150.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323941527|gb|EGB37709.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323960691|gb|EGB56315.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323971607|gb|EGB66838.1| RNA pseudouridylate synthase [Escherichia coli TA007]
 gi|324005662|gb|EGB74881.1| tRNA pseudouridine synthase [Escherichia coli MS 57-2]
 gi|331036949|gb|EGI09173.1| tRNA pseudouridine synthase C [Escherichia coli H736]
 gi|331047658|gb|EGI19735.1| tRNA pseudouridine synthase C [Escherichia coli M718]
 gi|331068379|gb|EGI39774.1| tRNA pseudouridine synthase C [Escherichia coli TA280]
 gi|332087547|gb|EGI92675.1| RNA pseudouridylate synthase family protein [Shigella boydii
           5216-82]
 gi|332344684|gb|AEE58018.1| conserved hypothetical protein [Escherichia coli UMNK88]
 gi|332753644|gb|EGJ84023.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-671]
 gi|332754556|gb|EGJ84922.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           2747-71]
 gi|332765743|gb|EGJ95956.1| tRNA pseudouridine 65 synthase [Shigella flexneri 2930-71]
 gi|333015363|gb|EGK34703.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-304]
          Length = 260

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|307718151|ref|YP_003873683.1| ribosomal large subunit pseudouridine synthase C [Spirochaeta
           thermophila DSM 6192]
 gi|306531876|gb|ADN01410.1| ribosomal large subunit pseudouridine synthase C [Spirochaeta
           thermophila DSM 6192]
          Length = 300

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 77/238 (32%), Gaps = 43/238 (18%)

Query: 1   MKDKNIVQ--ENFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNV 54
           M+D  + +   +   +R+ ++    ++   + SR  V R +    + + G  +   +  V
Sbjct: 1   MEDYQVFESGPDDHGKRLDRIVRTLLSHIPL-SR--VFRALRTGEILLEGKRV-PPSTRV 56

Query: 55  MSTDHIEVDGVPLRKAERTRLW---------------LYHKPIGLVT----THSDPDGRS 95
                I +    L + E  + W               + +KP G V     + +D   RS
Sbjct: 57  SRGARIHIHRSLLPEREPRQKWEPRALPILLETDHLLILNKPPGAVVHGPGSLTD-QVRS 115

Query: 96  TVFDNLPSIFSRVI-SVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQ 152
            + D +P   +     + RLD  T G+L+   +  G       L      + Y     G 
Sbjct: 116 YLKDRIPPSLAFTPSPLHRLDRLTSGILVFSRSIHGARWFTRALREGGIEKTYLALLEGT 175

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQ--------VTLDTQKGSNAWVTVGLREGKNREIK 202
           + +      +  +  +G               V       +       +  G+  +I+
Sbjct: 176 LAEP--ARWEDLLTREGRRSRPSPHGRPALTDVRPLLAAPTATLALCIIHTGRMHQIR 231


>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 = 54.4 bits (130), Expect = 2e-05,   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|281338228|gb|EFB13812.1| hypothetical protein PANDA_001071 [Ailuropoda melanoleuca]
          Length = 545

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 46/292 (15%), Positives = 97/292 (33%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWLYH-------K 80
           E  + + R+ +N   ++  ++ +   D     +     P+  AE  RL   +       K
Sbjct: 179 EAAVREGRLHLNEEPVQDLSIVLKDNDFLRNRVHRHEPPVT-AEPVRLLAENEDMVVVDK 237

Query: 81  PIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP- 137
           P  +          +TV   L        +  + RLD  T G+L+      ++  +    
Sbjct: 238 PSSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQV 297

Query: 138 -STQWLRVYRVRFHGQ-VDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ--KGSN 186
              Q  + Y  R  G+   ++ +          K G+          +         G +
Sbjct: 298 RDRQLEKEYVCRVEGEFPTEEVICKEPILVVSYKVGVCRVDARGKPCETVFQRLSYNGHS 357

Query: 187 AWVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI 240
           + V    +    G+  +I+   +F    +        +++GP        G   +  +++
Sbjct: 358 SVVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGP---SRGRCGHIPKTDEEL 411

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       S+QK
Sbjct: 412 LRDLVAEHQAKQSLDVLDLCEGDLSPGLIDSTAPSSELGKDHLEELATSAQK 463


>gi|86147828|ref|ZP_01066134.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
 gi|85834355|gb|EAQ52507.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp.
           MED222]
          Length = 244

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/149 (16%), Positives = 57/149 (38%), Gaps = 28/149 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND------ 127
           + + +KP GL++     P+   +++  L   F  +  V RLD++T GL+LL         
Sbjct: 23  ILVVNKPAGLLSVPGRLPEHYDSMWSRLVVEFPEIQVVHRLDMSTSGLMLLAKHKQAERH 82

Query: 128 --GGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGD 174
                   L        ++Y  R  G ++       L L+       ++ +         
Sbjct: 83  LKKQFQYRLTH------KLYYARVWGSMEDKAGLIDLPLICDWTNRPRQKVCFDDGKPSQ 136

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +  ++ Q+     + +  +  G++ +++
Sbjct: 137 TRYVVEQQEPQTTLLKLLPIT-GRSHQLR 164


>gi|323966769|gb|EGB62200.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323978598|gb|EGB73680.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|327251531|gb|EGE63217.1| RNA pseudouridylate synthase family protein [Escherichia coli
           STEC_7v]
          Length = 260

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|296271632|ref|YP_003654263.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
 gi|296095807|gb|ADG91757.1| pseudouridine synthase [Arcobacter nitrofigilis DSM 7299]
          Length = 300

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 34/197 (17%), Positives = 72/197 (36%), Gaps = 30/197 (15%)

Query: 31  VERMIAQQRVKVNGILLERAAV-NVMSTDHIE---VDG--VPLRKAERTRLW-LYHKPIG 83
            ++ I++ RV             +++ +D I     +G    L+   +T  + ++ KP G
Sbjct: 31  AQKSISKGRVF--DEAFNTLKYGDIIDSDLIYMAQFEGHTRGLKPLFQTNYFAIFEKPSG 88

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLLTNDGGLARVL--ELP 137
           +V     P  ++T +  L  +          V R+D  T GL++   D  +   L     
Sbjct: 89  IVV---HPISKNTEYCLLDEVRYHFGPDANLVHRIDAETSGLIMCAKDRDIESKLKLMFE 145

Query: 138 STQWLRVYRVRFHGQVDQDKL--NLLKK-----GIVIQGICYGDMQVTLDTQKGSNAWVT 190
             ++ + Y     G + +  +    ++K     G+ +     G    T+      N    
Sbjct: 146 EKKYQKSYLAIVRGHIKESVIIDTSIQKEGKNIGVRMAAGAEGKKSKTIINPIKYNEKKD 205

Query: 191 VGLRE-----GKNREIK 202
           + L E     G+  +I+
Sbjct: 206 LTLIEAIPVTGRQHQIR 222


>gi|315500130|ref|YP_004088933.1| pseudouridine synthase, rlua family [Asticcacaulis excentricus CB
           48]
 gi|315418142|gb|ADU14782.1| pseudouridine synthase, RluA family [Asticcacaulis excentricus CB
           48]
          Length = 335

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 37/261 (14%), Positives = 70/261 (26%), Gaps = 63/261 (24%)

Query: 7   VQENFTPQRVSKVIARAGIASRR-------EVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           V E     R+ K         RR       ++ +++   +V+V+G   + A   + +   
Sbjct: 10  VAEGEDGVRIDKFFK------RRWPHLNHIQLNKLLRSGQVRVDGARAK-ADTRLSTGQS 62

Query: 60  IEV-------------------------DGVPLRKAERTRLWLYHKPIGLVTT--HSDPD 92
           + V                             L   E   +   +KP GL         +
Sbjct: 63  VRVPPLPDAPSEEQQKRERAELSPQEVRYAKSLVLYEDEDVIAINKPSGLAVQGGTKTKN 122

Query: 93  GRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFH 150
               +         R   V RLD +T G+LLL  +              +  + Y     
Sbjct: 123 HIDRLLSAWGEGLERPRLVHRLDRDTSGVLLLGKSPSAAARLAGAFAKRKAYKTYWALVA 182

Query: 151 GQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL------------- 193
           G  D       + L+KKGI                 + +     V +             
Sbjct: 183 GTPDPKEGVIDVPLVKKGIN-DREMVMPADPKEPGAEAAETEY-VTISRAAHRLAWMALR 240

Query: 194 -REGKNREIKKVFEFFNWKVN 213
              G+  +++   +     + 
Sbjct: 241 PHTGRTHQLRAHMQAIGHCIL 261


>gi|296445496|ref|ZP_06887453.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
 gi|296257062|gb|EFH04132.1| pseudouridine synthase, RluA family [Methylosinus trichosporium
           OB3b]
          Length = 338

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 76/243 (31%), Gaps = 46/243 (18%)

Query: 15  RVSKVIAR-----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
           R+ + +A      A   SR  ++ +I   R+ +       AA  + + D + +       
Sbjct: 26  RLDRFLAERPEIVAASLSRTRLKALIEDGRLTIGPAPTRDAARKLAAGDRVSLAVPPPQP 85

Query: 63  -----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------S 106
                + +PL  + E   L +  KP GLV   +      T+ + L               
Sbjct: 86  PEPQPENIPLDIRFEDAHLIVVDKPAGLVVHPAHGHESGTLVNALLGHCGDSLSGIGGVK 145

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRVRFHG--------- 151
           +   V R+D +T GLL++       + L         S   +R Y     G         
Sbjct: 146 KPGIVHRIDKDTSGLLVVAKTDAAHKGLSRLFEDHGRSLGLMREYLAFVWGVPERARGTV 205

Query: 152 --QVDQDKLNLLKKGIVIQG-ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
              + +  +   +  +V +           L    G  + V   L  G+  +I+      
Sbjct: 206 EAPIGRHSIQRERMAVVSEERGREAITHWELIESFGVVSLVACRLETGRTHQIRVHMAHI 265

Query: 209 NWK 211
              
Sbjct: 266 GHP 268


>gi|218701508|ref|YP_002409137.1| tRNA pseudouridine synthase C [Escherichia coli IAI39]
 gi|218371494|emb|CAR19332.1| tRNA pseudouridine synthase [Escherichia coli IAI39]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIDQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|134102271|ref|YP_001107932.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291003766|ref|ZP_06561739.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133914894|emb|CAM05007.1| ribosomal large subunit pseudouridine synthase [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 310

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 79/244 (32%), Gaps = 39/244 (15%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV---------MST 57
           V +     RV   +++    SR  V  +     V ++G    ++   V            
Sbjct: 9   VPDGLDGMRVDAGLSKLLGLSRTIVAGLAESGDVVLDGTPAGKSDRLVAGAWLEVTLPPA 68

Query: 58  DH------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
           +       + V+G+ +   +   + +  KPIG+    S      TV   L +   R+   
Sbjct: 69  EQPLEVVAVPVEGLRILHQDDDIVVV-DKPIGVAVHPSPGWEGPTVVGGLAAAGVRIATS 127

Query: 109 ------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG--------- 151
                   V RLD  T G++++         L+    +    + Y     G         
Sbjct: 128 GASERQGVVHRLDAGTTGVMVVAKSEHAYSTLKRAFKERTVDKRYHALVQGHPDPSRGTI 187

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              +D+   +  K  +V  G        T++  + + + V V L  G+  +I+  F    
Sbjct: 188 DAPIDRHPRHDYKFAVVAGGKPSITHYETVEAFRAA-SLVDVKLETGRTHQIRVHFAAVR 246

Query: 210 WKVN 213
               
Sbjct: 247 HPCV 250


>gi|303231322|ref|ZP_07318057.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514002|gb|EFL56009.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-049-V-Sch6]
          Length = 335

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/146 (18%), Positives = 51/146 (34%), Gaps = 18/146 (12%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLR-----KAERTRL 75
           R+ + ++  ++ + VNG         V   D I       ++D  P+        E   L
Sbjct: 43  RKAMVKLFDEKLIHVNGHKAT-PHTEVAVDDEIWIAMAKEKIDHEPIAMDLHILYEDDDL 101

Query: 76  WLYHKPIGLVTTHSDP---DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--GL 130
            +  KP G+     D          +     I  +V  + RLD +T G +++   G    
Sbjct: 102 LIVDKPAGVTVNSKDKVSLANGIAHYFMEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQS 161

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQD 156
               ++    + + Y     G V+ D
Sbjct: 162 LYQQQMDDNTFEKWYMAIVEGLVESD 187


>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 = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/229 (13%), Positives = 70/229 (30%), Gaps = 38/229 (16%)

Query: 16  VSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEV----DGVPL 67
           +   +   G       +R+I     Q  + VNGI        +   D I++    +   +
Sbjct: 14  LENFLRNKGF-----SKRLIRIYKWQGEILVNGIK-SNVKRILQPGDVIDLILPENDSNI 67

Query: 68  RKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGR 113
                      E   + + +KP  +V   +      T+ + +   F        +  V R
Sbjct: 68  APEKLDLDICYEDEEILIVNKPANMVVHPTKGYQSGTLANGIAWYFKDKGLKALIRPVNR 127

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL------KKGIV- 166
           LD  T GL++      +   L        ++Y     G+++ +    L      + GI  
Sbjct: 128 LDRGTSGLVVFAKLPFMQYYL-QIVKPMSKLYFAVVEGKMEGEGRINLPISRKPQSGIER 186

Query: 167 --IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +          +       + + V +  G+  +I+         + 
Sbjct: 187 MVSEEGEIAITNYKVVKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>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 = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 13 PQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          P R+   +   G   SR   +  I   +VKVNGI + + + +V   D IEV
Sbjct: 13 PMRLDAYLVEMGHFKSRGRAKTAILDGKVKVNGIAVTKVSRDVSIDDTIEV 63


>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 = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          T +R+   +   G   SR +    +    V V+G  +++    V +   I+V G  L   
Sbjct: 4  TKERLDVYLVNNGFFPSREKARAAVMAGLVFVDGERVDKPGHQVKAEVSIQVQGKTLPFV 63

Query: 71 ER 72
           R
Sbjct: 64 SR 65


>gi|238791583|ref|ZP_04635221.1| Pseudouridine synthase [Yersinia intermedia ATCC 29909]
 gi|238729199|gb|EEQ20715.1| Pseudouridine synthase [Yersinia intermedia ATCC 29909]
          Length = 232

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 71/209 (33%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE+        +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIEI------LYQDDHLVLINKPAGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKVINAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIA 119

Query: 172 YGDMQVTLDT-----QKGSNAWVTVG---LRE------------------GKNREIKKVF 205
                  L +      K + +   V      E                  G+  +++   
Sbjct: 120 KDPALFPLMSICSIHGKPARSHYQVVERFYHELEDSTLLPLTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +       YG    G LL G+ R
Sbjct: 180 QQLGHPILGCD--LYG----GRLLPGTER 202


>gi|332993476|gb|AEF03531.1| ribosomal large subunit pseudouridine synthase C [Alteromonas sp.
           SN2]
          Length = 314

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 85/250 (34%), Gaps = 70/250 (28%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMS 56
            V+ +   QRV   +       R +++        R++ +  V+VN G +  +    +++
Sbjct: 13  TVEPDLAGQRVDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKGRV--KPEYKLVA 63

Query: 57  TDHIEVDGVPLRKA--------------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
            D + +  V + +                     E  R+ + +KP G+        G S 
Sbjct: 64  DDVVRIPPVRVSEGTPGPSPKLDKIAALESQILFEDERIIVINKPSGIAV-----HGGSG 118

Query: 97  VFDNLPSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV 147
           +   L      +         V RLD +T G +L+       R +   L + +  + Y+ 
Sbjct: 119 LSFGLIEGLRALRPDANFMELVHRLDRDTSGCILIAKKRSALRHMHEQLRTGKMDKRYQA 178

Query: 148 RFHGQVDQDKLN---LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-- 195
              GQ   ++      L+K ++  G     M    +  K S     +        L E  
Sbjct: 179 LVAGQWPDNRFKVKAPLRKNVLQSGER---MVSVSEDGKPSETRYRILQKFDTATLVEAS 235

Query: 196 ---GKNREIK 202
              G+  +I+
Sbjct: 236 PITGRTHQIR 245


>gi|261339742|ref|ZP_05967600.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
 gi|288318572|gb|EFC57510.1| pseudouridine synthase A [Enterobacter cancerogenus ATCC 35316]
          Length = 228

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 60/178 (33%), Gaps = 33/178 (18%)

Query: 75  LWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L L +KP GL++ +  +P    +V   L   F     V RLD  T G++++  +  +   
Sbjct: 26  LILINKPSGLLSLSGKNPQNLDSVHYRLVQTFPGCTLVHRLDFGTSGIMVIARNKAINAA 85

Query: 134 LELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQKGSN 186
           L    +Q    + Y     G V  D      +GI+   I           +   + K + 
Sbjct: 86  LCHQFSQRAVSKAYTALLCGHVKDD------EGIIDAPIAKDPALFPLMSICAISGKPAR 139

Query: 187 AWVTVG----------------LRE-GKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
           +   V                 + E G+  +++   +     +       YG  ++  
Sbjct: 140 SRFRVVERIDKDEELPLTRVELIPETGRTHQLRIHCQQLGHSILGCD--LYGGLEMPG 195


>gi|313886583|ref|ZP_07820296.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|332300873|ref|YP_004442794.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
 gi|312923939|gb|EFR34735.1| pseudouridine synthase, RluA family [Porphyromonas asaccharolytica
           PR426713P-I]
 gi|332177936|gb|AEE13626.1| pseudouridine synthase [Porphyromonas asaccharolytica DSM 20707]
          Length = 228

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/194 (17%), Positives = 56/194 (28%), Gaps = 49/194 (25%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   L + +KP G++       D      V   L   + +     V    R+D  T G +
Sbjct: 9   EDNHLLIVNKPAGMLVQGDSTGDTPLSELVERYLIDKYDKPGRAFVGVTHRIDRPTSGAV 68

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---- 176
           L          L       +  +VY     G   Q            + + Y + +    
Sbjct: 69  LFAKTSKALARLNAMFQRREIHKVYHAVVCGAFPQKAGEA-------KDLLYRNRKQNKS 121

Query: 177 --VTLDTQKGSNAWVT--------------VGLREGKNREIKKVFEFFNWKVNRLIRISY 220
             VT    +   AW+T              V L  G++ +I+       + +        
Sbjct: 122 YVVTEAHAEAKRAWLTYERLAVGDRYSLLAVTLHTGRHHQIRTQLSHMGFPIK------- 174

Query: 221 GPFQLGTLLAGSTR 234
                G L  G+ R
Sbjct: 175 -----GDLKYGAPR 183


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

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 62/186 (33%), Gaps = 41/186 (22%)

Query: 6   IVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
            V E+    R+ +        +A + +A      ++  +  V+V+G  ++  A  +    
Sbjct: 18  TVTEDEAGLRLDRWFKRRFPALALSHLA------KICRKGEVRVDGKRVDT-ATRLEQDQ 70

Query: 59  HIEVDGVPLRKA-----------------------ERTRLWLYHKPIGLVTTHSDPDGRS 95
            I V  + L  A                       E   L + +KP GL         R 
Sbjct: 71  KIRVPPLKLEAAAAAPTILRASPEDARALADMTLYEDASLLVLNKPYGLAVQGGSGMTRH 130

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG 151
                  L    +R + V RLD +T G+LL+  +   A  L     S Q  ++Y     G
Sbjct: 131 IDGMLESLAKGDTRPVLVHRLDRDTSGVLLIAKNRRTAADLGEIFRSRQAKKIYWALVEG 190

Query: 152 QVDQDK 157
                +
Sbjct: 191 VPKPAQ 196


>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 = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+   +   G+  SR + +  IA   V VNG  + +A++ V   D IEV G       R
Sbjct: 1  MRLDVALVERGLEPSRAKAKASIAAGLVFVNGRNVTKASLGVDDGDAIEVQGTACAYVGR 60

Query: 73 TRLWLYH 79
            L L H
Sbjct: 61 GGLKLEH 67


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

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/265 (15%), Positives = 83/265 (31%), Gaps = 61/265 (23%)

Query: 3   DKNIVQENFTPQRVSKVI-AR---AGIASRREVERMIAQQRVKVNGILLER--------- 49
           ++  V  +    R+ +   +     G      +++++   +V+V+G   E          
Sbjct: 21  EQKQVTADEAGMRLDRWFKSHYPGLGFG---HLQKLLRTGQVRVDGKRAETNTRIAKGQM 77

Query: 50  -----AAVNVMSTDH----------IEVDGVPLRKA---ERTRLWLYHKPIGLVTTH--- 88
                  V + + D           I  D   +      E +++ + +KP GL       
Sbjct: 78  IRIPPLGVELPADDKKNAKPKSTKLIADDRKAIEDMLLFEDSQVMVLNKPAGLAVQGGSG 137

Query: 89  --SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
                DG    + +      R+  V RLD  T G++L+      A+ L          ++
Sbjct: 138 LKRHLDGMLDAYTDRKGNKPRL--VHRLDRETSGIILVARTRQAAQELTKAFRHRNTRKI 195

Query: 145 YRVRFHGQVDQ------------DKLNLLKKGIVIQGICYGDMQVTL----DTQKGSNAW 188
           Y     G                D    ++  +V QG       V+L    +      +W
Sbjct: 196 YWAILAGVPKPFQGRISTFLARNDGEERMQ--VVRQGEDEAQHAVSLYSVFEKSGQKLSW 253

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           VT+    G+  +++         + 
Sbjct: 254 VTMKPVTGRTHQLRAHAAHIGHPII 278


>gi|117619994|ref|YP_855705.1| RNA pseudouridine synthase family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
 gi|117561401|gb|ABK38349.1| RNA pseudouridine synthase family protein [Aeromonas hydrophila
           subsp. hydrophila ATCC 7966]
          Length = 257

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/170 (19%), Positives = 60/170 (35%), Gaps = 33/170 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L   +KP GL+   S  D   T F      D +      V  V RLD  T G+LL   D 
Sbjct: 23  LVAVNKPSGLLVHRSWLDKAETRFAMQMTRDLIGG--RHVYPVHRLDRPTSGVLLFALDP 80

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM-- 175
            +AR L     + Q  + Y     G   +         ++L+ +   +        +   
Sbjct: 81  AVARTLTEAFAARQVHKEYLALVRGWAPEQGLIDYPLKEQLDKIADAMSDPDRPAQEAVT 140

Query: 176 ------QVTLD---TQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVN 213
                 QV L    ++K   +  ++  L  + G+  ++++  +     + 
Sbjct: 141 AFRRLHQVELPHAVSKKHPTSRYSLVRLFPKTGRKHQLRRHMDHLFHPIV 190


>gi|195339845|ref|XP_002036527.1| GM11650 [Drosophila sechellia]
 gi|194130407|gb|EDW52450.1| GM11650 [Drosophila sechellia]
          Length = 739

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 56/307 (18%), Positives = 110/307 (35%), Gaps = 46/307 (14%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 333 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPA 392

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 393 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 452

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G+ +
Sbjct: 453 RQVEKEYICRVEGVFPDGIVE-CKEPIEVVSYKIGVCKVSPKGKDCTTTFQKLSQNGTTS 511

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR--L--IRISYGPF--QLGTLLAGSTREVSKKI 240
            V    L  G+  +I+   ++  + +    L    + +GP   + G +  G +    +++
Sbjct: 512 VVLCKPLT-GRMHQIRVHLQYLGYPILNDPLYNHEV-FGPLKGRSGDIG-GKS---DEEL 565

Query: 241 LREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +R+ +  H  E       + D  ++ S     DR ++ SE          + S  +G + 
Sbjct: 566 IRDLINIHNAENWLGIDCDSDISMFKSTKDEADRESLSSEHTSVV-----HHSDDDGCAN 620

Query: 298 QKKLATP 304
            ++   P
Sbjct: 621 SRETTPP 627


>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 = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 29/50 (58%), Gaps = 1/50 (2%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          R+   +   G+  SR + +R+I   +V+VNG +  +A++ V + D ++ D
Sbjct: 10 RLDIALVERGVTDSRSKAQRLIESGKVRVNGTVASKASLKVTAADTLDAD 59


>gi|77919951|ref|YP_357766.1| 23S RNA-specific pseudouridylate synthase [Pelobacter carbinolicus
           DSM 2380]
 gi|77546034|gb|ABA89596.1| 23S RNA-specific pseudouridylate synthase [Pelobacter carbinolicus
           DSM 2380]
          Length = 296

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 51/292 (17%), Positives = 95/292 (32%), Gaps = 44/292 (15%)

Query: 28  RREVERMIAQQRVKVNGILLERA-------AVNVMSTDH---IEVDGVPLRKA--ERTRL 75
           R  + +++   +++ NG +L          ++ +  +     +  D VP      E    
Sbjct: 28  RSYLRQLLRSGKIRCNGSILTENICLRGHESLQLPDSKRLREVCTDRVPELTILLETDEF 87

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGG 129
               KP GL    S       + D L +         R+  V RLDI T G ++      
Sbjct: 88  LAVFKPAGLAVHSSVGHTEDNLTDRLKAWIKQCKAPYRIAPVHRLDIGTSGPVIFGKGRK 147

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKGSN 186
               L   L +    + Y    +G   +  +  +   + +QG       +  +  +  S 
Sbjct: 148 ATAELGRLLQNGHMSKTYLALVNGHPPETGM--MVTSVRVQGKPKQAATRFRVLGRHASA 205

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
           A + + L  G+  +I++      W +    R  YG  +L                R++L 
Sbjct: 206 ALLELELLSGRKHQIRQQCADAGWPLYGDHR--YGGPELPG--------------RDRLF 249

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
            H  + A      PI   +   R    +  E+    T M   S   N   + 
Sbjct: 250 LHCWQLAW-----PIQGDQPSHRITSPLPEELSVILTSMDIESPAPNRKPES 296


>gi|14043412|gb|AAH07697.1| RPUSD2 protein [Homo sapiens]
          Length = 554

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/292 (15%), Positives = 96/292 (32%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+++N   ++   + +   D +          V   P+R  AE   + +  KP
Sbjct: 188 EAAVRAGRLQLNEKPVQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 247

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 248 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 307

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 308 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGQSS 367

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI- 240
            V    +    G+  +I+   +F    +        +++GP +      G     + +  
Sbjct: 368 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSR----GRGGYIPKTNEEL 420

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       ++QK
Sbjct: 421 LRDLVAEHQAKQSLDVLDLCEGDLSPGLTDSTAPSSELGKDDLEELAAAAQK 472


>gi|82778170|ref|YP_404519.1| tRNA pseudouridine synthase C [Shigella dysenteriae Sd197]
 gi|309786089|ref|ZP_07680718.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|81242318|gb|ABB63028.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|308926200|gb|EFP71678.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +  +    +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPSTRYGLVELEPKTGRKHQLRRHLAHLCHPII 176


>gi|313108160|ref|ZP_07794295.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa 39016]
 gi|310880797|gb|EFQ39391.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa 39016]
          Length = 326

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 76/239 (31%), Gaps = 48/239 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V      QR+   + AR   A +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 24  VPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRI--KPDYRLQAGDQVRVPP 81

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLP 102
           + L +                     E   L + +KP G+          G   VF  L 
Sbjct: 82  LRLAERDEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHGGSGVSAGVIEVFRQLR 141

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDK-- 157
                +  V RLD +T GLL++     + R L           + Y     G     K  
Sbjct: 142 PDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVDKRYHALVRGHWPAGKKN 201

Query: 158 ------LNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
                  N L+ G     + ++G         L         V    +    G+  +I+
Sbjct: 202 VRAPLLKNNLRSGERMVEVNVEGKDALTEFRVLRRFGDFATLVEARPIT---GRTHQIR 257


>gi|296164416|ref|ZP_06846990.1| RluA family RNA pseudouridine synthase [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295900198|gb|EFG79630.1| RluA family RNA pseudouridine synthase [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 308

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 84/250 (33%), Gaps = 40/250 (16%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-------V 52
           M D+++ V E     RV   +AR    SR     +     V+++G+   ++        +
Sbjct: 1   MTDRSMPVPEGLAGMRVDAGLARLLGLSRSAAAAIAEDGGVELDGVQAGKSDRLTGGAWL 60

Query: 53  NVM--------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            V             ++++G+ +  ++   +    KP  +    S      TV   L + 
Sbjct: 61  QVRLPEAPPPVENTPVDIEGMTILYSDED-IVAVDKPAAVAAHASVGWTGPTVLGGLAAA 119

Query: 105 FSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
             R+           V RLD+ T G++++        VL+    Q    + Y     G  
Sbjct: 120 GYRITTSGVPERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVDKRYHALVQGHP 179

Query: 154 D------QDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D         +   + G     +   G        T++    + + + V L  G+  +I+
Sbjct: 180 DPSSGTIDAPIGRHRGGEWKFAVTTNGRHSLTHYDTIEAFTAA-SLLDVHLETGRTHQIR 238

Query: 203 KVFEFFNWKV 212
             F   +   
Sbjct: 239 VHFSALHHPC 248


>gi|270293436|ref|ZP_06199644.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
 gi|270278098|gb|EFA23947.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M143]
          Length = 291

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/146 (21%), Positives = 57/146 (39%), Gaps = 14/146 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L + +KP G+ T  + PD  + +      +      V RLD+ T GL+L   +  +
Sbjct: 86  QDQHLIIVNKPEGMKTHGNQPDEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKNPFI 145

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
             +L   L   +  R Y     GQV   +L           +  K+ +  +   Y + QV
Sbjct: 146 LPILNRLLEKKEIAREYWALVEGQVGSKELIFRDKIGRDRHDRRKRVVDAKSGQYAETQV 205

Query: 178 TLDTQ-KGSNAWVTVGLREGKNREIK 202
               Q     + V   L+ G+  +I+
Sbjct: 206 RRLKQFLNKTSLVRCKLKTGRTHQIR 231


>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 = 54.4 bits (130), 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|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 = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          QR+  ++    +  SR++ +R+I    V+VN  L+++    + +T  I+++
Sbjct: 3  QRLDTLLVDLNLCESRQQAQRLILAGEVRVNQQLVDKPGTEIETTAEIKIN 53


>gi|194376328|dbj|BAG62923.1| unnamed protein product [Homo sapiens]
          Length = 538

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/292 (15%), Positives = 96/292 (32%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+++N   ++   + +   D +          V   P+R  AE   + +  KP
Sbjct: 172 EAAVRAGRLQLNEKPVQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 231

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 232 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 291

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 292 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGQSS 351

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI- 240
            V    +    G+  +I+   +F    +        +++GP +      G     + +  
Sbjct: 352 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSR----GRGGYIPKTNEEL 404

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       ++QK
Sbjct: 405 LRDLVAEHQAKQSLDVLDLCEGDLSPGLTDSTAPSSELGKDDLEELAAAAQK 456


>gi|78776810|ref|YP_393125.1| pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497350|gb|ABB43890.1| tRNA pseudouridine synthase C [Sulfurimonas denitrificans DSM 1251]
          Length = 241

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/192 (16%), Positives = 61/192 (31%), Gaps = 44/192 (22%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   L   +KP GL+   S  D   T F    L +   R V  + RLD  T G+LL   D
Sbjct: 7   QDEHLVAINKPSGLLVHRSPIDRHETEFAIQTLRNQLGRFVYPIHRLDKPTSGVLLFALD 66

Query: 128 GGLARVLELPS---TQWLRVYRVRFHG------QVDQDKLNLLKKGIVIQG--------- 169
              +  +        +  + Y     G      ++D        K I  +          
Sbjct: 67  -KESAKIMGEKFMAHEAKKSYIAVVRGYTLQSGEIDYALSIKFDK-IADKDSSSDKEPQE 124

Query: 170 -----ICYGDMQVTLDTQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN------- 213
                     +++  +  K      ++     L  G+  ++++  +  +  +        
Sbjct: 125 ALTHYKRLATVELDFEVGKYDKTRYSLVKLNPLT-GRKHQLRRHMKHISHHILGDTKYGR 183

Query: 214 ----RLIRISYG 221
               +LIR  +G
Sbjct: 184 GEHNKLIRQEFG 195


>gi|82548298|gb|ABB82988.1| putative RNA pseudouridylate synthase [uncultured organism
           HF10_3D09]
          Length = 294

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 71/217 (32%), Gaps = 35/217 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------------- 74
            +M+  +R+ V   ++ RA   V++ + +E+   P    E TR                 
Sbjct: 28  RKMLTNRRITVEEKIIHRAKHPVLAGETVEIRPKPKLSIEETRQTSAETHSLDIIFEDDA 87

Query: 75  LWLYHKPIGLVTTHSDP------DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TN 126
           + +  KP GL++  +D         R   +       +    V RLD  T GL++   T 
Sbjct: 88  ILVVEKPAGLLSVATDRLEVDTLHNRCVEYCRELKKKAWCFIVHRLDKATSGLMVFAKTE 147

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-------NLLKKGIVIQGICYGDMQVT- 178
           D       +       R Y     G  +  +          L+  +  +        +T 
Sbjct: 148 DVKRDLQEQFAERLVHRHYVALVEGVAEPGQAIQHLVEDRNLRVFVSDKKTKTSKHAITT 207

Query: 179 --LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  +   +  ++V +  G+  +I+         V 
Sbjct: 208 WDILEKGDESTLLSVVIETGRRHQIRVAMAENGTPVM 244


>gi|331664352|ref|ZP_08365258.1| tRNA pseudouridine synthase C [Escherichia coli TA143]
 gi|331058283|gb|EGI30264.1| tRNA pseudouridine synthase C [Escherichia coli TA143]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFAQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|301169114|emb|CBW28711.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae 10810]
          Length = 322

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ T QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDETGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|237735851|ref|ZP_04566332.1| pseudouridine synthase [Mollicutes bacterium D7]
 gi|229381596|gb|EEO31687.1| pseudouridine synthase [Coprobacillus sp. D7]
          Length = 278

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/212 (18%), Positives = 76/212 (35%), Gaps = 32/212 (15%)

Query: 19  VIARAGIASRREVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------DGVPLR 68
            +++    S ++  ++I    ++ VNG   +     +   D +E+         +  PL 
Sbjct: 17  FLSQQ-ELS-KKAVKLIKMHGKILVNGQR-QTVRYCLRYGDVVELLWPEEVSTMEPYPLA 73

Query: 69  KA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTE 119
                E     +  KP GL +  +    R+T+ + +   +        V  V RLD +T+
Sbjct: 74  LKISYEDENFLVIDKPAGLPSIPTKRYPRNTLANAVVYYYQSQGIKATVHLVNRLDKDTQ 133

Query: 120 GLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGI 170
           GLLL+  +     +L     Q  RVY     G +                +K+ I   G 
Sbjct: 134 GLLLIAKNSYAHYLLSRDIKQVRRVYHCVVEGVLTGQGTITAPIIKDKKSVKRLIHPAGK 193

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   L+    + + +   L  G+  +I+
Sbjct: 194 FAVTHYRGLEV-SANQSKIECILETGRTHQIR 224


>gi|121716811|ref|XP_001275916.1| DRAP deaminase (Rib2), putative [Aspergillus clavatus NRRL 1]
 gi|119404073|gb|EAW14490.1| DRAP deaminase (Rib2), putative [Aspergillus clavatus NRRL 1]
          Length = 538

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/141 (17%), Positives = 47/141 (33%), Gaps = 16/141 (11%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKPI 82
           + +   RV VNG         + + + I          V G  +    E   + +  KP 
Sbjct: 83  QALTDGRVTVNGKTAA-PNTVIKNGEIISHTLHRHEPPVTGHEIGVIHEDNDILVIDKPA 141

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLELPST 139
           G+    +     +++ + L S   +        RLD  T G++ +      A ++     
Sbjct: 142 GVPVHAAGRYHYNSIVEILRSQRGQEFVPRPCNRLDRLTSGVMFIAKHPQGADMITRKLK 201

Query: 140 Q--WLRVYRVRFHGQVDQDKL 158
           Q    + Y  R  G+     +
Sbjct: 202 QRTVQKEYIARVKGRFPDGVV 222


>gi|291277548|ref|YP_003517320.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290964742|emb|CBG40597.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 245

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 30/208 (14%), Positives = 61/208 (29%), Gaps = 44/208 (21%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILL----------ERAAVNVMSTDHIEVDGVPL 67
           K+++     S  + + +I +  V V G  +              V       I      L
Sbjct: 7   KILSLQKKISHNKAKELIDKGLVSVAGKKVGIARAEYPSHTLFDVAPPPKPEILFQDENL 66

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--- 124
                       KP  L +           +D L  +F   + + RLD  T G++LL   
Sbjct: 67  --------LALIKPAFLES-----------YD-LAEMFDGWVLLHRLDKETSGVILLVRG 106

Query: 125 -TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGD 174
            ++    A+       +  + Y     G + + +              K  + Q      
Sbjct: 107 ESDFHKRAKK-AFKDQEVYKEYIALVSGFLSEPQTITAPILTTKKGFAKSRIHQDGLSAV 165

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +      G    +   ++ G+  +I+
Sbjct: 166 TYIDPLKIIGKKTLIKAVIQTGRTHQIR 193


>gi|121591256|ref|ZP_01678555.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|229527559|ref|ZP_04416951.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|262401797|ref|ZP_06078362.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|297581352|ref|ZP_06943275.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|121546902|gb|EAX57056.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           2740-80]
 gi|229335191|gb|EEO00676.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           12129(1)]
 gi|262351769|gb|EEZ00900.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC586]
 gi|297534190|gb|EFH73028.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC385]
 gi|327484993|gb|AEA79400.1| Ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           LMA3894-4]
          Length = 245

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 57/164 (34%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN--- 126
           E   +   +KP GL++    P +   +++  L      V  V RLD++T GL+L      
Sbjct: 19  EDEHIIAANKPSGLLSVPGRPVEHYDSMWARLVDYCPDVKVVHRLDMSTSGLILFAKGKH 78

Query: 127 -----DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGI 170
                       L        ++Y  R  G ++QD+               K+ +  +  
Sbjct: 79  MESALKKQFQYRLTH------KIYYARVWGVMEQDEGEVNLPLCCDWPNRPKQKVCFEEG 132

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                +  +  ++     V +  +  G++ +++   +     + 
Sbjct: 133 RDSLTRYQVVKREEKTTVVRLIPIT-GRSHQLRVHMQSLGHPIV 175


>gi|21672612|ref|NP_660679.1| ribosomal large subunit pseudouridine synthase [Buchnera aphidicola
           str. Sg (Schizaphis graminum)]
 gi|25091178|sp|Q8K9J8|RLUC_BUCAP RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|21623244|gb|AAM67890.1| ribosomal large subunit pseudouridine synthase [Buchnera aphidicola
           str. Sg (Schizaphis graminum)]
          Length = 314

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/269 (14%), Positives = 85/269 (31%), Gaps = 46/269 (17%)

Query: 1   MKDKNI------VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVN 53
           MK K        + E+   QR+   + +      R  + R+I   ++++N   ++     
Sbjct: 1   MKYKTTSVSIIYINEDMINQRIDNFLQKKLKNVPRSMIYRIIRTGKIRINKKRIK-PDYK 59

Query: 54  VMSTDHIEVDGVPL--------------------RKAERTRLWLYHKPIGLVTTHSDPDG 93
           +   D + +  + +                       E   L + +KP G+         
Sbjct: 60  LKIGDKLRIPPIKILCEKKSSLLTTEYKKNLLNNILYEDNYLLIINKPSGIAVHGGSGIN 119

Query: 94  RSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
              +  F  +  +   +  V R+D +T G+L+L         L       +  + Y    
Sbjct: 120 LGVIEYFRKIRPLEKFLELVHRIDRDTSGVLMLAKKRRSLLSLHKQIREKKVQKKYIALV 179

Query: 150 HG-----------QVDQDKLNLLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
           HG            + +  L   ++ I+I +     +    +  Q      V++  + G+
Sbjct: 180 HGLWPLSLRKVSEPLLKTHLKNKQRKILINKEGKPAETYFKIKKQYLFTTLVSITPKTGR 239

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLG 226
             +I+         +    R  YG   L 
Sbjct: 240 THQIRVHTLHAGHPILFDKR--YGKRDLD 266


>gi|320182406|gb|EFW57303.1| tRNA pseudouridine synthase C [Shigella boydii ATCC 9905]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G   ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWFMEEAVLDYPLVEELDKIADKFACEDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|226357282|ref|YP_002787022.1| RNA pseudouridine synthase [Deinococcus deserti VCD115]
 gi|226319272|gb|ACO47268.1| putative RNA pseudouridine synthase [Deinococcus deserti VCD115]
          Length = 298

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 66/195 (33%), Gaps = 31/195 (15%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           +AQ  V+V+G+ ++     + +   +     P ++           E   L   HKP GL
Sbjct: 40  LAQGEVQVDGLTVQ-GHERLRAGQTLVWHRPPWQEESVPLHFEVLHEDASLLAVHKPSGL 98

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
            T         T+   + + F     + RL   T G++L    G     L          
Sbjct: 99  PTLPGGGFLEHTLLTVVRAQFPGASPLHRLGRGTSGVVLFARTGAAGSALARAWREQDVR 158

Query: 143 RVYRVRFHGQVDQDKLNLLKKGIVIQGIC---YGDMQVTLDTQKGSNAWVTVG------- 192
           ++YR    G   QD+  +    + I  +     G++     T K S +   V        
Sbjct: 159 KMYRALASGVATQDETEIT---VSIGPVPHPRLGEVFAACPTGKPSRSVARVVERCSGTT 215

Query: 193 -----LREGKNREIK 202
                +  G+  +I+
Sbjct: 216 LFDVQIFTGRPHQIR 230


>gi|50285951|ref|XP_445404.1| hypothetical protein [Candida glabrata CBS 138]
 gi|49524708|emb|CAG58310.1| unnamed protein product [Candida glabrata]
          Length = 584

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/197 (18%), Positives = 65/197 (32%), Gaps = 31/197 (15%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           IA+  V VNG         + + + I          V   P++   E   + +  KP G+
Sbjct: 123 IAKGAVSVNGKPA-NLETILRNGEMITHKMHRHEPPVTSRPIKIVFENDDILVIDKPGGI 181

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLL--TNDGGLARVLELPSTQW 141
               +     +T+   L     R V    RLD  T GL+ L  T +G      ++ + + 
Sbjct: 182 PVHPTGRYRYNTITKILEKQMKRSVHPCNRLDRLTSGLMFLAKTPEGADQMADQMKTREV 241

Query: 142 LRVYRVRFHGQVDQDKL---NLLKK---GIVI---------QGICYGDMQVTLDTQKGSN 186
            + Y  R  G+    ++     LK     + +                      +  G  
Sbjct: 242 TKEYIARVVGEFPTGEITVEKPLKSYDPKVSLNIICDDTNEDDAKPAKTVFQRISFDGQT 301

Query: 187 AWVTVG-LREGKNREIK 202
           + V    L  G+  +I+
Sbjct: 302 SIVKCKPLT-GRTHQIR 317


>gi|331005540|ref|ZP_08328915.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC1989]
 gi|330420660|gb|EGG94951.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC1989]
          Length = 237

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/179 (13%), Positives = 49/179 (27%), Gaps = 45/179 (25%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTND 127
           +   L   HKP GL+   S  D          L     +    + RLD  T G+LL    
Sbjct: 8   QDEYLVAIHKPAGLLVHKSLIDKHESQYAMQILRDQIGQWVYPLHRLDRPTSGVLLF-GL 66

Query: 128 GGLARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                 L     +     + Y     G ++++ +        I            D Q+ 
Sbjct: 67  SKEVAQLMGEQFEQRLLQKTYWAIVRGYINKEGI--------IDHPIKPTADFKRDKQRI 118

Query: 185 SN------------------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
           +                               + V +  + G+  +++K  +  +  + 
Sbjct: 119 AQKEAQEAITGYRRLGTLELPYCVDQFPISRYSLVELSPQTGRKHQLRKHMKHLSHPII 177


>gi|302338972|ref|YP_003804178.1| pseudouridine synthase [Spirochaeta smaragdinae DSM 11293]
 gi|301636157|gb|ADK81584.1| pseudouridine synthase, RluA family [Spirochaeta smaragdinae DSM
           11293]
          Length = 319

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 79/241 (32%), Gaps = 49/241 (20%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ + ++  AG+ +R ++ +     R  +NG +++ A+  V + D I +      +    
Sbjct: 23  RIDRYVSEVAGLFARSQLRQ--RNPRFFINGKVVK-ASSRVYTGDRIALMYEDQPEPSFG 79

Query: 71  ----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----------RVI 109
                     E   + +  KP GLV   +  +   T+   L                R  
Sbjct: 80  AQAIDLSIIYEDEHVIVVDKPQGLVVHPAAGNWSGTLVQGLLYHCRELGERFGEDTVRPG 139

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            V RLD +T G+L+   D    + L     + +  + Y     G +       ++ GI+ 
Sbjct: 140 IVHRLDKDTSGVLIAAKDPETRQFLAEQFANRRCKKRYIALVKGDLSNAT-GRMESGIIR 198

Query: 168 Q------------GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK---KVFEFFNWKV 212
                        G      + T   +    +     L  G+  +I+    +       V
Sbjct: 199 DPKNRKRFTWTMSGGKPAVTEYTRLRRGNDCSLAAFNLLTGRTHQIRVHTLM---LGHPV 255

Query: 213 N 213
            
Sbjct: 256 I 256


>gi|92115011|ref|YP_574939.1| tRNA pseudouridine synthase C [Chromohalobacter salexigens DSM
           3043]
 gi|91798101|gb|ABE60240.1| tRNA pseudouridine synthase C [Chromohalobacter salexigens DSM
           3043]
          Length = 261

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 34/168 (20%), Positives = 56/168 (33%), Gaps = 27/168 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIF-SRVISVGRLDINTEGLLLLTND 127
           +  R+    KP G++   S     + VF    L +     V  V RLD  T GLLL   D
Sbjct: 10  QDERMVAVQKPSGMLVHRSPIARDARVFALQTLRNQLGRHVYPVHRLDRPTSGLLLFALD 69

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------- 176
             +A+ L  E  + +  + Y     G   +  L  L  G+  +       +         
Sbjct: 70  PEMAQALGEEFTAHRVHKRYLAVVRGVGPEQDL--LDYGLREEDGSRPKAEMPELEAWTA 127

Query: 177 ------VTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                 V L  +      V   L E     G+  +I++      + + 
Sbjct: 128 VRRLDSVELPVRIDRYPQVRYSLMEARPWTGRRHQIRRHLARRGYPII 175


>gi|157157184|ref|YP_001464113.1| tRNA pseudouridine synthase C [Escherichia coli E24377A]
 gi|191168568|ref|ZP_03030353.1| tRNA pseudouridine synthase C [Escherichia coli B7A]
 gi|193065141|ref|ZP_03046215.1| tRNA pseudouridine synthase C [Escherichia coli E22]
 gi|193071106|ref|ZP_03052031.1| tRNA pseudouridine synthase C [Escherichia coli E110019]
 gi|194426330|ref|ZP_03058885.1| tRNA pseudouridine synthase C [Escherichia coli B171]
 gi|209920242|ref|YP_002294326.1| tRNA pseudouridine synthase C [Escherichia coli SE11]
 gi|218555342|ref|YP_002388255.1| tRNA pseudouridine synthase C [Escherichia coli IAI1]
 gi|218696390|ref|YP_002404057.1| tRNA pseudouridine synthase C [Escherichia coli 55989]
 gi|256019422|ref|ZP_05433287.1| tRNA pseudouridine synthase C [Shigella sp. D9]
 gi|260845437|ref|YP_003223215.1| tRNA pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|260856901|ref|YP_003230792.1| tRNA pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|260869469|ref|YP_003235871.1| tRNA pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|300815791|ref|ZP_07096015.1| tRNA pseudouridine synthase [Escherichia coli MS 107-1]
 gi|300820579|ref|ZP_07100730.1| tRNA pseudouridine synthase [Escherichia coli MS 119-7]
 gi|300906681|ref|ZP_07124370.1| tRNA pseudouridine synthase [Escherichia coli MS 84-1]
 gi|300923234|ref|ZP_07139288.1| tRNA pseudouridine synthase [Escherichia coli MS 182-1]
 gi|301304561|ref|ZP_07210671.1| tRNA pseudouridine synthase [Escherichia coli MS 124-1]
 gi|301325733|ref|ZP_07219190.1| tRNA pseudouridine synthase [Escherichia coli MS 78-1]
 gi|307312780|ref|ZP_07592410.1| pseudouridine synthase [Escherichia coli W]
 gi|309795259|ref|ZP_07689678.1| tRNA pseudouridine synthase [Escherichia coli MS 145-7]
 gi|331669526|ref|ZP_08370372.1| tRNA pseudouridine synthase C [Escherichia coli TA271]
 gi|331678771|ref|ZP_08379445.1| tRNA pseudouridine synthase C [Escherichia coli H591]
 gi|332280540|ref|ZP_08392953.1| tRNA pseudouridine synthase C [Shigella sp. D9]
 gi|157079214|gb|ABV18922.1| tRNA pseudouridine synthase C [Escherichia coli E24377A]
 gi|190901415|gb|EDV61179.1| tRNA pseudouridine synthase C [Escherichia coli B7A]
 gi|192927272|gb|EDV81892.1| tRNA pseudouridine synthase C [Escherichia coli E22]
 gi|192955567|gb|EDV86045.1| tRNA pseudouridine synthase C [Escherichia coli E110019]
 gi|194415638|gb|EDX31905.1| tRNA pseudouridine synthase C [Escherichia coli B171]
 gi|209913501|dbj|BAG78575.1| putative pseudouridine synthase [Escherichia coli SE11]
 gi|218353122|emb|CAU98959.1| tRNA pseudouridine synthase [Escherichia coli 55989]
 gi|218362110|emb|CAQ99719.1| tRNA pseudouridine synthase [Escherichia coli IAI1]
 gi|257755550|dbj|BAI27052.1| tRNA pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|257760584|dbj|BAI32081.1| tRNA pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|257765825|dbj|BAI37320.1| tRNA pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|300401582|gb|EFJ85120.1| tRNA pseudouridine synthase [Escherichia coli MS 84-1]
 gi|300420473|gb|EFK03784.1| tRNA pseudouridine synthase [Escherichia coli MS 182-1]
 gi|300526843|gb|EFK47912.1| tRNA pseudouridine synthase [Escherichia coli MS 119-7]
 gi|300531720|gb|EFK52782.1| tRNA pseudouridine synthase [Escherichia coli MS 107-1]
 gi|300840165|gb|EFK67925.1| tRNA pseudouridine synthase [Escherichia coli MS 124-1]
 gi|300847483|gb|EFK75243.1| tRNA pseudouridine synthase [Escherichia coli MS 78-1]
 gi|306907215|gb|EFN37721.1| pseudouridine synthase [Escherichia coli W]
 gi|308121230|gb|EFO58492.1| tRNA pseudouridine synthase [Escherichia coli MS 145-7]
 gi|315062072|gb|ADT76399.1| tRNA pseudouridine synthase [Escherichia coli W]
 gi|315256652|gb|EFU36620.1| tRNA pseudouridine synthase [Escherichia coli MS 85-1]
 gi|320202437|gb|EFW77007.1| tRNA pseudouridine synthase C [Escherichia coli EC4100B]
 gi|323154837|gb|EFZ41030.1| RNA pseudouridylate synthase family protein [Escherichia coli
           EPECa14]
 gi|323159892|gb|EFZ45862.1| RNA pseudouridylate synthase family protein [Escherichia coli
           E128010]
 gi|323180223|gb|EFZ65775.1| RNA pseudouridylate synthase family protein [Escherichia coli 1180]
 gi|323183332|gb|EFZ68729.1| RNA pseudouridylate synthase family protein [Escherichia coli 1357]
 gi|323377345|gb|ADX49613.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323946486|gb|EGB42512.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|324016355|gb|EGB85574.1| tRNA pseudouridine synthase [Escherichia coli MS 117-3]
 gi|331063194|gb|EGI35107.1| tRNA pseudouridine synthase C [Escherichia coli TA271]
 gi|331073601|gb|EGI44922.1| tRNA pseudouridine synthase C [Escherichia coli H591]
 gi|332102892|gb|EGJ06238.1| tRNA pseudouridine synthase C [Shigella sp. D9]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGSQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


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

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/264 (14%), Positives = 80/264 (30%), Gaps = 63/264 (23%)

Query: 5   NIVQENFTPQRVSKVI-AR---AGIASRREVERMIAQQRVKVNGILLER----------- 49
             V  +    R+ +   +     G      +++++   +V+V+G   +            
Sbjct: 7   KTVTADEAGMRLDRWFKSHYPGLGFG---HLQKLLRTGQVRVDGKRADSATRLATGQSVR 63

Query: 50  ---AAVNVMSTDH----------IEVDGVPLR---KAERTRLWLYHKPIGLVTTH----- 88
                V V + D           I  D   +      E  ++ + +KP GL         
Sbjct: 64  VPPLGVVVAADDTKNARPKSSRLIADDRKAVEDMILYEDDQVMVLNKPAGLAVQGGSGLS 123

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
              DG    F N      R+  V RLD  T G+LL+      A+ L          ++Y 
Sbjct: 124 RHLDGMLDAFTNKKGEKPRL--VHRLDRETSGVLLVAKTRKAAQELTRAFRQRSTRKIYW 181

Query: 147 VRFHGQVDQ---------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AWV 189
               G                   +K+ + + G          + +    ++ +   AWV
Sbjct: 182 ALLAGVPKPRQGRISTYLARDEGSEKMKVARHG---DDEAQHAVSLYSVVEQSAQKLAWV 238

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
           ++    G+  +++         + 
Sbjct: 239 SLRPVTGRTHQLRAHAAHIGHPIV 262


>gi|261344629|ref|ZP_05972273.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
 gi|282567545|gb|EFB73080.1| pseudouridine synthase A [Providencia rustigianii DSM 4541]
          Length = 232

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 53/136 (38%), Gaps = 15/136 (11%)

Query: 66  PLRK-AERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           P+    +   L L +KP GL++ +  +P    +V   +  IF     V RLD  T GL++
Sbjct: 16  PIEYLYQDDHLILINKPSGLLSLSGKNPQNLDSVHHRMVKIFPECTLVHRLDFGTSGLMV 75

Query: 124 LTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----Q 176
           +  +  +   L    +Q    ++Y     G +D D      +G++   I           
Sbjct: 76  VARNKAINAALCHQFSQRTVGKMYSALLCGHLDDD------EGVIDAPIAKDPALFPLMS 129

Query: 177 VTLDTQKGSNAWVTVG 192
           ++    K + +   V 
Sbjct: 130 ISAINGKPARSHYRVI 145


>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 = 54.4 bits (130), Expect = 3e-05,   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|332843544|ref|XP_510311.3| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           isoform 2 [Pan troglodytes]
          Length = 545

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/292 (15%), Positives = 96/292 (32%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+++N   ++   + +   D +          V   P+R  AE   + +  KP
Sbjct: 179 EAAVRAGRLQLNEKPVQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 238

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 239 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 298

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 299 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGQSS 358

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI- 240
            V    +    G+  +I+   +F    +        +++GP +      G     + +  
Sbjct: 359 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSR----GRGGYIPKTNEEL 411

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       ++QK
Sbjct: 412 LRDLVAEHQAKQSLDVLDLCEGDLSPGLTDSTAPSSELGKDDLEELAAAAQK 463


>gi|169335105|ref|ZP_02862298.1| hypothetical protein ANASTE_01512 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257843|gb|EDS71809.1| hypothetical protein ANASTE_01512 [Anaerofustis stercorihominis DSM
           17244]
          Length = 305

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/211 (13%), Positives = 77/211 (36%), Gaps = 33/211 (15%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEV------------DGVPLRKAERTRLWLYHKP 81
           +I + R+ +N        + +   D I+V            D       E   + + +K 
Sbjct: 43  IIREGRLLINDKDAMFVDI-LKEEDIIKVSFPVEEADAPSTDMKIDIIYEDDDIAVINKK 101

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVL- 134
            G+V   +      T+ + +   +       +   V RLD++T G++++  +  +   + 
Sbjct: 102 PGMVVHVTKSHPLDTLQNAIYHKWEIEKKHFKTRFVNRLDMDTSGIVVIAKNKYVHHFIQ 161

Query: 135 -ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
            +  + Q  + Y +   G            + + + + L++ IV +       +  +  +
Sbjct: 162 NQSINNQIDKKYVLIVDGIMDQKEGYINAPIKRAEGHPLRR-IVAEDGKECITKYKVIEE 220

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +++ V   L  G+  +++  F +    + 
Sbjct: 221 FKNHSLVEAKLITGRTHQLRVHFSYVGHPIL 251


>gi|157375387|ref|YP_001473987.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157317761|gb|ABV36859.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 238

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/104 (24%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D IE+        +   L L +KP GL++ +   PD + +V   L   F     + RLD
Sbjct: 14  HDEIEI------LYQDEALILINKPSGLLSLSGKHPDNKDSVHFRLVQDFPSCTMIHRLD 67

Query: 116 INTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK 157
             T G++L+  +  +   L    ++    + Y    HG +  D+
Sbjct: 68  FGTSGIMLVAMNKQVNAQLCKQFSERTVSKRYTALLHGHLKMDE 111


>gi|87118928|ref|ZP_01074826.1| ribosomal large subunit pseudouridine synthase C [Marinomonas sp.
           MED121]
 gi|86165319|gb|EAQ66586.1| ribosomal large subunit pseudouridine synthase C [Marinomonas sp.
           MED121]
          Length = 322

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 75/236 (31%), Gaps = 39/236 (16%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           N + EN   QR+   + A+     +  +  ++ +  ++VN   ++     + S D + + 
Sbjct: 17  NTIDENNHDQRIDNYLMAQLKGVPKGRIYNLLRKGEIRVNKKRVK-PDTRIYSGDIVRIA 75

Query: 64  GVPLRKA--------------------ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNL 101
            + +                       E   L + +KP GL          G   V   L
Sbjct: 76  PIVVEPPKEASPVPHKLMQLIESRIVYEDAGLMVVNKPSGLAVHGGSGLNFGLVEVVRQL 135

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDG---GLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
            S    +  V RLD +T GL++++                    + Y+   +G   + K 
Sbjct: 136 RSKEKSIELVHRLDRDTSGLIMISKKRSVLKQLHAALREKEGVQKTYQALVYGSWPKRKQ 195

Query: 159 N--------LLKKGIVIQGICYGDMQ----VTLDTQKGSNAWVTVGLREGKNREIK 202
                     LK G  I  +     +      L  Q    + V      G+  +I+
Sbjct: 196 QVNAPLLKNELKSGERIVKVHTEGKESLTRFKLLRQFEGYSLVECEPVTGRTHQIR 251


>gi|300854916|ref|YP_003779900.1| putative ribosomal large subunit pseudouridine synthase D
           [Clostridium ljungdahlii DSM 13528]
 gi|300435031|gb|ADK14798.1| predicted ribosomal large subunit pseudouridine synthase D
           [Clostridium ljungdahlii DSM 13528]
          Length = 319

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/263 (14%), Positives = 84/263 (31%), Gaps = 76/263 (28%)

Query: 7   VQENFTPQRVSKVIARAGIASR---REVE-----RMIAQQRVKVNGILLERAAVNVMSTD 58
           + +N   QR+ K        SR   R+V      R I +  +KVNG   +     ++  D
Sbjct: 5   IGKNEAGQRLDKF-------SRKWLRDVPLSGIYRAIRKGDIKVNGKKAKE-KYFLLEGD 56

Query: 59  HI---------------EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
            +                +D   L+   E   + L  K  G++         +T+ D + 
Sbjct: 57  IVNAEYITSKETKSKFERIDNAFLKIIYEDKNMLLVEKWPGVLVHSDKNSKDATLTDYVL 116

Query: 103 SIFSRV-------------ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV 147
           S                      RLD NT G+++   +    ++L   +      + Y  
Sbjct: 117 SHLYDRGEFNPEEEVTFTPSPCNRLDRNTSGIVIYGKNYESLKLLNEMIRERSIKKYYIA 176

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGD----------------MQVTLDTQKGSN----A 187
              G++        K G+  +G    D                 ++++  +  +     +
Sbjct: 177 LVIGKI--------KDGVY-EGYIKKDRTNNKSSVSNTPEKDSKKISMRVKNVNTCGIYS 227

Query: 188 WVTVGLREGKNREIKKVFEFFNW 210
            + + L  G++ +++    +   
Sbjct: 228 LIQLELITGRSHQLRAHLAYLGN 250


>gi|323339779|ref|ZP_08080049.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           ruminis ATCC 25644]
 gi|323092858|gb|EFZ35460.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           ruminis ATCC 25644]
          Length = 301

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 77/239 (32%), Gaps = 49/239 (20%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERMIAQ-----QRVKVNGILLERAAVNVMSTDHI 60
           +V +   P  +   + + GI SR     ++A+       + V+G    +  + +     +
Sbjct: 5   LVYQGENPCHLKTFLRQQGI-SR----GLLAKIRHEGGAIDVDGTSGRKLDM-IFPNAVV 58

Query: 61  E-------VDGVPLRK--------AERTRLWLYHKPIGLVTTHS-DPDGRS-TVFDNLPS 103
                   V   P+           E     +  KP  L T  S D   R  ++ + +  
Sbjct: 59  TLTMPPEKVRKEPVIPSYVPLKILYEDRDFLIVDKPAHLATIPSPDKKHRYDSLVNRVVG 118

Query: 104 IFSR-------VISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQV 153
            +         V  + RLD +T G++L+      A  L           + Y     G+V
Sbjct: 119 YYELRGIKDTVVHVITRLDRDTTGIVLIAKH-RYAHALIDKQVHDHSIKKEYLALLSGKV 177

Query: 154 DQDKL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D+               + K  + +       +  L+ +    +   V L  G+  +I+
Sbjct: 178 DRRHFFVNLPIGREPGSMIKRTITEDGKPSSSEYFLEKKLRDASLYRVRLHSGRTHQIR 236


>gi|320194932|gb|EFW69561.1| tRNA pseudouridine synthase C [Escherichia coli WV_060327]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMLVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|315453301|ref|YP_004073571.1| ribosomal pseudouridine synthase [Helicobacter felis ATCC 49179]
 gi|315132353|emb|CBY82981.1| ribosomal pseudouridine synthase [Helicobacter felis ATCC 49179]
          Length = 302

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/164 (13%), Positives = 54/164 (32%), Gaps = 24/164 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
               +Y+KP  L +   +     ++++++ +       + RLD  T GL++++       
Sbjct: 78  PYFDIYYKPKNLYSHPKNYKSH-SLYESVYAHNPEARLIHRLDYETSGLVMVSTQKRYEN 136

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDK-------LNLLKKGIVIQGICYG-DMQVTLDTQ 182
            L     + Q  + Y     G V           L +L+  I I+        Q+  + +
Sbjct: 137 ALRELFSARQIKKTYEAWVQGDVRAYAQGPFSVILRILEPKIKIKHADLAIRCQIAKEGK 196

Query: 183 KGSNAW-------------VTVGLREGKNREIKKVFEFFNWKVN 213
             +                + +    G+  +I+       + + 
Sbjct: 197 PSATTIEILNFCPHTQRTHLKITPLSGRTHQIRLHLSALGFPIV 240


>gi|293449117|ref|ZP_06663538.1| tRNA pseudouridine synthase C [Escherichia coli B088]
 gi|291322207|gb|EFE61636.1| tRNA pseudouridine synthase C [Escherichia coli B088]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGSQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|282852228|ref|ZP_06261580.1| S4 domain protein [Lactobacillus gasseri 224-1]
 gi|282556647|gb|EFB62257.1| S4 domain protein [Lactobacillus gasseri 224-1]
          Length = 163

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/134 (23%), Positives = 56/134 (41%), Gaps = 26/134 (19%)

Query: 15  RVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK---- 69
           R+ KVIA      SR +++ ++  + + VN    E+ +  V + D I++   P +     
Sbjct: 15  RLDKVIAEKLKDLSRTKIKELVNDKNILVNHK-AEKVSYKVQAGDSIDITVPPAKPLSLE 73

Query: 70  ---------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----------PSIFSRVIS 110
                     E   + + +KP G+V   S      T+ + L          P  F R   
Sbjct: 74  AQNLNLDIVYEDADVIVVNKPQGMVVHPSAGHPDHTLVNGLLYHTHELADSPEGF-RPGI 132

Query: 111 VGRLDINTEGLLLL 124
           V R+D +T GLL++
Sbjct: 133 VHRIDKDTSGLLMV 146


>gi|167745608|ref|ZP_02417735.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662]
 gi|167654920|gb|EDR99049.1| hypothetical protein ANACAC_00300 [Anaerostipes caccae DSM 14662]
          Length = 305

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 79/249 (31%), Gaps = 41/249 (16%)

Query: 2   KDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           + +  V +  T  R+   +A R    +R  ++++     V V+    +++   V   + +
Sbjct: 4   ERQFTVSQKETGSRLDVCLAGRFPEFTRSYLQKLCKDSAVLVDDA-EKKSNYKVREGERV 62

Query: 61  --------EVDGVPLR-----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                   E+   P +       E   + L +KP  +V   +      T+ + L      
Sbjct: 63  ILKVPKPTELSIKPEKMDLDIVYEDRDIILINKPKNMVVHPAPGHYEGTLVNGLMEHCRD 122

Query: 107 ---------RVISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQVD 154
                    R   V R+D +T G+L++  +  +A       L      R Y       + 
Sbjct: 123 ELSGINGVLRPGIVHRIDKDTTGILIVCKN-DMAHQCLAEQLKDHTITRRYHAIVCHNIK 181

Query: 155 QDKL---------NLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++              +K + I    G         L+  K    ++   L  G+  +I+
Sbjct: 182 EESGTVDAPIARSRKDRKKMAIDREAGRRAVTHYRVLERLKEGFTYIECRLETGRTHQIR 241

Query: 203 KVFEFFNWK 211
                    
Sbjct: 242 VHMASIGHP 250


>gi|15803313|ref|NP_289346.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 EDL933]
 gi|15832905|ref|NP_311678.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. Sakai]
 gi|168751005|ref|ZP_02776027.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|168758485|ref|ZP_02783492.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|168764507|ref|ZP_02789514.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|168766761|ref|ZP_02791768.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4486]
 gi|168777585|ref|ZP_02802592.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4196]
 gi|168778782|ref|ZP_02803789.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4076]
 gi|168788052|ref|ZP_02813059.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC869]
 gi|168802525|ref|ZP_02827532.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC508]
 gi|195936394|ref|ZP_03081776.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4024]
 gi|208807818|ref|ZP_03250155.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208813945|ref|ZP_03255274.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821365|ref|ZP_03261685.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209397015|ref|YP_002272257.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|217327006|ref|ZP_03443089.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254794732|ref|YP_003079569.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14359]
 gi|261226091|ref|ZP_05940372.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256654|ref|ZP_05949187.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           FRIK966]
 gi|34582446|sp|Q8X6T6|TRUC_ECO57 RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
 gi|12517267|gb|AAG57905.1|AE005507_6 hypothetical protein Z4107 [Escherichia coli O157:H7 str. EDL933]
 gi|13363123|dbj|BAB37074.1| hypothetical protein [Escherichia coli O157:H7 str. Sakai]
 gi|187767213|gb|EDU31057.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4196]
 gi|188014875|gb|EDU52997.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003616|gb|EDU72602.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4076]
 gi|189354717|gb|EDU73136.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4401]
 gi|189363807|gb|EDU82226.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4486]
 gi|189365505|gb|EDU83921.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4501]
 gi|189372179|gb|EDU90595.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC869]
 gi|189375502|gb|EDU93918.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. EC508]
 gi|208727619|gb|EDZ77220.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735222|gb|EDZ83909.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741488|gb|EDZ89170.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4042]
 gi|209158415|gb|ACI35848.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC4115]
 gi|209761380|gb|ACI79002.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761382|gb|ACI79003.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|209761386|gb|ACI79005.1| hypothetical protein ECs3651 [Escherichia coli]
 gi|217319373|gb|EEC27798.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           TW14588]
 gi|254594132|gb|ACT73493.1| tRNA U65 pseudouridine synthase [Escherichia coli O157:H7 str.
           TW14359]
 gi|320189127|gb|EFW63786.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str.
           EC1212]
 gi|326339134|gb|EGD62949.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. 1044]
 gi|326342983|gb|EGD66751.1| tRNA pseudouridine synthase C [Escherichia coli O157:H7 str. 1125]
          Length = 260

 Score = 54.4 bits (130), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|291519368|emb|CBK74589.1| pseudouridine synthase, RluA family [Butyrivibrio fibrisolvens
           16/4]
          Length = 311

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 32/200 (16%), Positives = 62/200 (31%), Gaps = 48/200 (24%)

Query: 54  VMSTDHIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTH---SDPDGRSTVFDNL---- 101
           V   D +      ++       E   + + +KP G+ +     SD          +    
Sbjct: 74  VSERDELYYSIKEIKPNINIVFEDDDMIIINKPAGVKSQKDSPSDISINEMAISYMIASN 133

Query: 102 ---PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
                 F         RLD NT G++L   +   A+ L   L      ++YR    G+VD
Sbjct: 134 QLSEESFKHFHPSVCNRLDRNTSGIVLFAKNLHAAQSLGQALKERSCKKLYRAVVLGKVD 193

Query: 155 QDKLNLLKKGIVIQGICYGDM---QVTLDTQKGSNA------------------WVTVGL 193
             +         I+G  + D    +VT+   +  ++                   + + L
Sbjct: 194 SKQ--------QIEGFLWKDEATNKVTISKNEIPDSKPIKTAYNPIKNIGDKFTLLEIHL 245

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +I+         + 
Sbjct: 246 ITGRTHQIRAHLASIGHPIL 265


>gi|118602128|ref|YP_903343.1| ribosomal large subunit pseudouridine synthase C [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567067|gb|ABL01872.1| ribosomal large subunit pseudouridine synthase C [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 303

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/246 (16%), Positives = 82/246 (33%), Gaps = 64/246 (26%)

Query: 5   NIVQENFTPQRVSKVI-------ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMS 56
            IV E    QR+   +        ++ I       R+I +  V+VN G   ++ +  ++ 
Sbjct: 6   QIVDEFSEGQRLDNYLLKILKGVPKSHIC------RVIRKGWVRVNKGR--KKVSYKLIL 57

Query: 57  TDHIEVDGVPLRKAERTRL-------------------WLYHKPIGLVTTHSDPDGRSTV 97
            D + +  + +   +   +                    + +KP G ++ HS       +
Sbjct: 58  NDIVRIPPIKVSIIKSIYISDSLKKLLIDAKLYEDKGLLIINKPSG-LSVHSGSGVDVGI 116

Query: 98  FDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
            + L  I+ + +  V RLD  T G+LL+     + + L   L      + Y     G   
Sbjct: 117 IEALRQIYKKPIELVHRLDRATSGVLLIAKKRSVLKNLHEQLSQHTVEKRYTALVKGVWS 176

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKG------------------SNAWVTVGLREG 196
           +           I    Y + +  +   KG                  S + V + +  G
Sbjct: 177 KKC-------HTIDAPLYQNSRYIMVDAKGKYAISHFQPLKNFSDGGFSASLVEISIETG 229

Query: 197 KNREIK 202
           +  +I+
Sbjct: 230 RTHQIR 235


>gi|49083776|gb|AAT51141.1| PA2975 [synthetic construct]
          Length = 319

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 76/239 (31%), Gaps = 48/239 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V      QR+   + AR   A +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRI--KPDYRLQAGDQVRVPP 73

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLP 102
           + L +                     E   L + +KP G+          G   VF  L 
Sbjct: 74  LRLAERDEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHGGSGVSAGVIEVFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDK-- 157
                +  V RLD +T GLL++     + R L           + Y     G     K  
Sbjct: 134 PDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVDKRYHALVRGHWPAGKKN 193

Query: 158 ------LNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
                  N L+ G     + ++G         L         V    +    G+  +I+
Sbjct: 194 VRAPLLKNNLRSGERMVEVNVEGKDALTEFRVLRRFGDFATLVEARPIT---GRTHQIR 249


>gi|114570313|ref|YP_756993.1| ribosomal large subunit pseudouridine synthase C [Maricaulis maris
           MCS10]
 gi|114340775|gb|ABI66055.1| ribosomal large subunit pseudouridine synthase C [Maricaulis maris
           MCS10]
          Length = 330

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/152 (16%), Positives = 46/152 (30%), Gaps = 26/152 (17%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------------------DGVPLRK 69
           V+++  + +++V+G  ++     V     I +                         L  
Sbjct: 34  VQKLCRKGQIRVDGGRVK-GDSRVHEGQEIRIPPLPEPGERPPVNRMSDEDIAYVKSLVI 92

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRST--VFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            +   L  ++KP GL         R    + D       R   V RLD +T G+L++   
Sbjct: 93  YQDDELIAFNKPAGLAVQGGSKTTRHLDGMLDAFGEGLDRPRLVHRLDKDTSGILIVGKG 152

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
                 L     S +  + Y     G      
Sbjct: 153 PKATARLAKAFQSHKTRKTYWAIAIGVPKPKM 184


>gi|90408903|ref|ZP_01217040.1| putative ribosomal large subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
 gi|90309987|gb|EAS38135.1| putative ribosomal large subunit pseudouridine synthase A
           [Psychromonas sp. CNPT3]
          Length = 219

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 79/210 (37%), Gaps = 38/210 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++    +   R ++   +  ++     V RLD+ T GL++L         
Sbjct: 23  IVVLNKPAGLLSVPGREIKHRDSLALRILRVWPNACVVHRLDLATSGLIVLAMRKSAQSH 82

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTLD 180
           +          + Y  R  G + +D             N  ++ +  +       Q  + 
Sbjct: 83  IGRQFQQKVIAKTYFARVEGYIKEDAGLVDLPIRCDWENRPRQIVDFEQGKSSQTQWKVV 142

Query: 181 TQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           +++  +  V +  L  G+  +++      + +         G   LG    GS  E++KK
Sbjct: 143 SRENDSTLVELTPLT-GRTHQLR-----VHMQ-------QIGHPILGDDFYGS--ELAKK 187

Query: 240 ILREQLGPHLLE--------EAQVNLDAPI 261
           +  ++L  H  +        E +++ D P+
Sbjct: 188 LSTQRLALHAAKISLIHPTTEERISFDCPV 217


>gi|147673149|ref|YP_001218003.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|153829796|ref|ZP_01982463.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|229513432|ref|ZP_04402896.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|254225904|ref|ZP_04919506.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|254291423|ref|ZP_04962215.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|258622801|ref|ZP_05717819.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|258625826|ref|ZP_05720705.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|262166537|ref|ZP_06034274.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
 gi|262167535|ref|ZP_06035240.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|262170551|ref|ZP_06038229.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|125621530|gb|EAZ49862.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           V51]
 gi|146315032|gb|ABQ19571.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|148874714|gb|EDL72849.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           623-39]
 gi|150422613|gb|EDN14568.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           AM-19226]
 gi|227014395|gb|ACP10605.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O395]
 gi|229349309|gb|EEO14265.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TMA 21]
 gi|258582064|gb|EEW06934.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM603]
 gi|258584989|gb|EEW09720.1| Ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM573]
 gi|261891627|gb|EEY37613.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           MB-451]
 gi|262023988|gb|EEY42684.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC27]
 gi|262026253|gb|EEY44921.1| ribosomal large subunit pseudouridine synthase A [Vibrio mimicus
           VM223]
          Length = 245

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 57/164 (34%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN--- 126
           E   +   +KP GL++    P +   +++  L      V  V RLD++T GL+L      
Sbjct: 19  EDEHIIAANKPSGLLSVPGRPVEHYDSMWARLVDYCPDVKVVHRLDMSTSGLILFAKGKH 78

Query: 127 -----DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGI 170
                       L        ++Y  R  G ++QD+               K+ +  +  
Sbjct: 79  MESALKKQFQYRLTH------KIYYARVWGVMEQDEGEVNLPLCCDWPNRPKQKVCFEEG 132

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                +  +  ++     V +  +  G++ +++   +     + 
Sbjct: 133 RDSLTRYQVVKREEKTTVVRLIPIT-GRSHQLRVHMQSLGHPIV 175


>gi|55980515|ref|YP_143812.1| hemolysin [Thermus thermophilus HB8]
 gi|55771928|dbj|BAD70369.1| hemolysin [Thermus thermophilus HB8]
          Length = 235

 Score = 54.0 bits (129), Expect = 3e-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|328948139|ref|YP_004365476.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
 gi|328448463|gb|AEB14179.1| pseudouridine synthase, RluA family [Treponema succinifaciens DSM
           2489]
          Length = 326

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/240 (15%), Positives = 79/240 (32%), Gaps = 56/240 (23%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRV--KVNGILLERAAVNVMSTDHIEV-------- 62
            R+ K IA      +R +    +    V  +VNG   ++ +  V + D I++        
Sbjct: 16  IRLDKYIASLPNGMNRSK----LKSGIVCIQVNGKK-QKISCQVKANDIIDIQWEENVPD 70

Query: 63  ----DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------------ 105
               + +PL    E   + + +K  G+VT  +  + + T+ + L   +            
Sbjct: 71  NIEPENIPLDTIYEDENVCVVNKKQGMVTHPAAGNWKGTLVNALLYHWGRESIPELKEGQ 130

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQV-- 153
                   R   V RLD  T G+++   +      L       +  ++ Y     G+   
Sbjct: 131 VSKILSNRRPGIVHRLDKETSGIIITAKNHDTEEFLSAQFRNHSSIVKEYIAICIGRPQH 190

Query: 154 -----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      D  +    K  +  +     +      +  G  + + V +  G+  +I+
Sbjct: 191 QHGIIQTNIIRDPKERKRFKAVVGTEEGKPAESYYECISCYGEYSLMKVRINTGRTHQIR 250


>gi|223042701|ref|ZP_03612749.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus capitis
           SK14]
 gi|222443555|gb|EEE49652.1| pseudouridylate synthase, 23S RNA-specific [Staphylococcus capitis
           SK14]
          Length = 284

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/148 (17%), Positives = 52/148 (35%), Gaps = 19/148 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS--VGRLDINTEGLLLL 124
           E   + + +KP       S      +    V   L +   +     V RLD NT GL+L 
Sbjct: 80  EDEFILIVNKPQLQNCAPSREHPHESLVEQVLAYLMNKDEQTNPHIVTRLDRNTSGLVLF 139

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGD 174
              G +         ++ + Y    +G           + +D  +++ + +  +G     
Sbjct: 140 AKFGHIHH--LFSKVKFEKEYICLAYGRTQSEGVIEAPIARDNESIITRKVSDKGKYAKT 197

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
              T+  Q  + +   V L  G+  +I+
Sbjct: 198 SYYTI-AQNNNLSLCKVKLHTGRTHQIR 224


>gi|325106618|ref|YP_004267686.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324966886|gb|ADY57664.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
          Length = 296

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/167 (16%), Positives = 56/167 (33%), Gaps = 25/167 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   +   +KP G+++  S P G   + D + +             +  V RLD    G+
Sbjct: 64  EDGPVVAVNKPAGMLSQGS-PQGVFCLPDYVKAYLKHKYEKPGNVYLGVVHRLDRPVTGV 122

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGI------VIQGIC 171
           ++ + +   A  L       +  +VY        D  +  L    + +      VI+   
Sbjct: 123 VVFSRNSKGAARLAEQFREREVQKVYLALLENVPDQPEGTLKDFIRKVPEQARAVIEPGE 182

Query: 172 YGDMQV-----TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             + +       +    G  A V V  + G+  +I+  F      + 
Sbjct: 183 TQEAKAAELSYRVLASDGKYALVEVLPKTGRMHQIRIQFASRGCPIV 229


>gi|238018437|ref|ZP_04598863.1| hypothetical protein VEIDISOL_00263 [Veillonella dispar ATCC 17748]
 gi|237864908|gb|EEP66198.1| hypothetical protein VEIDISOL_00263 [Veillonella dispar ATCC 17748]
          Length = 289

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/214 (16%), Positives = 79/214 (36%), Gaps = 29/214 (13%)

Query: 29  REVERMIAQQRVKVNGILL------ERAA--VNVMSTDH---IEVDGVPLRK-AERTRLW 76
           R+++ M  ++RVKVN  +       ++       +  D    ++V+  P+    E     
Sbjct: 29  RDIQMMFRKKRVKVNSRVAHSQRSLKKGDVLTLELPQDKDYGVDVEKGPITVLYEDAHTL 88

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLL--TNDG 128
           +  K   ++   +      T+ + +   +       +V  V RLD +T G +L   T + 
Sbjct: 89  VVDKAPFMLVHPAGQTKSGTLSNYVAGYYAKKGVVHKVRPVHRLDRDTSGCILFGKTKEA 148

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG---------IVIQGICYGDMQVTL 179
                 EL + +  R+Y     G+++ D +     G         ++ +       + T+
Sbjct: 149 QQYYTDELQAGRIDRIYTGLVEGRINSDGVVDAPIGVDPVFDNRRVIDEFGQPAQTEYTV 208

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +G +  +   L  G+  +I+   E     + 
Sbjct: 209 LGHEGEHTLLKFKLLTGRTHQIRVHMEHIGHPIV 242


>gi|269121328|ref|YP_003309505.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268615206|gb|ACZ09574.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 285

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/141 (19%), Positives = 52/141 (36%), Gaps = 15/141 (10%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLARV 133
            + +KP G V  H     +  + +   SI+    +    R+D  T+GLLL   +    R 
Sbjct: 96  LIINKP-GGVAVHKGTGNQYGLAEVYKSIYKNENLNFANRIDKETKGLLLGAKNLKFLRY 154

Query: 134 LELP--STQWLRVYRVRFHGQVDQD------KLNLLKKGIVI----QGICYGDMQVTLDT 181
           L     + +  + Y     G + +D       L   +  +V+     G     +   + T
Sbjct: 155 LTEKIRNNELEKRYIAVVSGIITEDEFTIDNFLETKENKVVVSDKENGKAAKAVFKKIKT 214

Query: 182 QKGSNAWVTVGLREGKNREIK 202
            K     + V L  G+  +I+
Sbjct: 215 IKNKYTVLEVELITGRKHQIR 235


>gi|153215725|ref|ZP_01950106.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|153801105|ref|ZP_01955691.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|229521570|ref|ZP_04410988.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|261211068|ref|ZP_05925357.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|262191021|ref|ZP_06049230.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
 gi|124114643|gb|EAY33463.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           1587]
 gi|124123338|gb|EAY42081.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MZO-3]
 gi|229341164|gb|EEO06168.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           TM 11079-80]
 gi|260839569|gb|EEX66180.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. RC341]
 gi|262033084|gb|EEY51613.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           CT 5369-93]
          Length = 245

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 57/164 (34%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN--- 126
           E   +   +KP GL++    P +   +++  L      V  V RLD++T GL+L      
Sbjct: 19  EDEHIIAANKPSGLLSVPGRPVEHYDSMWARLVDYCPDVKVVHRLDMSTSGLILFAKGKH 78

Query: 127 -----DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGI 170
                       L        ++Y  R  G ++QD+               K+ +  +  
Sbjct: 79  MESALKKQFQYRLTH------KIYYARVWGVMEQDEGEVNLPLCCDWPNRPKQKVCFEEG 132

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                +  +  ++     V +  +  G++ +++   +     + 
Sbjct: 133 RDSLTRYQVVKREEKTTVVRLIPIT-GRSHQLRVHMQSLGHPIV 175


>gi|107102524|ref|ZP_01366442.1| hypothetical protein PaerPA_01003588 [Pseudomonas aeruginosa PACS2]
          Length = 318

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 76/239 (31%), Gaps = 48/239 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V      QR+   + AR   A +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRI--KPDYRLQAGDQVRVPP 73

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLP 102
           + L +                     E   L + +KP G+          G   VF  L 
Sbjct: 74  LRLAERDEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHGGSGVSAGVIEVFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDK-- 157
                +  V RLD +T GLL++     + R L           + Y     G     K  
Sbjct: 134 PDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVDKRYHALVRGHWPAGKKN 193

Query: 158 ------LNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
                  N L+ G     + ++G         L         V    +    G+  +I+
Sbjct: 194 VRAPLLKNNLRSGERMVEVNVEGKDALTEFRVLRRFGDFATLVEARPIT---GRTHQIR 249


>gi|15598171|ref|NP_251665.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAO1]
 gi|116050977|ref|YP_790198.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|218890827|ref|YP_002439691.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa LESB58]
 gi|254235949|ref|ZP_04929272.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa C3719]
 gi|296388532|ref|ZP_06878007.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAb1]
 gi|34395830|sp|Q9HZM9|RLUC_PSEAE RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|9949074|gb|AAG06363.1|AE004723_7 ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PAO1]
 gi|115586198|gb|ABJ12213.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|126167880|gb|EAZ53391.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa C3719]
 gi|218771050|emb|CAW26815.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa LESB58]
          Length = 318

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 76/239 (31%), Gaps = 48/239 (20%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V      QR+   + AR   A +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRI--KPDYRLQAGDQVRVPP 73

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLP 102
           + L +                     E   L + +KP G+          G   VF  L 
Sbjct: 74  LRLAERDEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHGGSGVSAGVIEVFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDK-- 157
                +  V RLD +T GLL++     + R L           + Y     G     K  
Sbjct: 134 PDAKDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVDKRYHALVRGHWPAGKKN 193

Query: 158 ------LNLLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVT---VGLREGKNREIK 202
                  N L+ G     + ++G         L         V    +    G+  +I+
Sbjct: 194 VRAPLLKNNLRSGERMVEVNVEGKDALTEFRVLRRFGDFATLVEARPIT---GRTHQIR 249


>gi|198477421|ref|XP_002136622.1| GA24957 [Drosophila pseudoobscura pseudoobscura]
 gi|198142914|gb|EDY71626.1| GA24957 [Drosophila pseudoobscura pseudoobscura]
          Length = 540

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/196 (20%), Positives = 68/196 (34%), Gaps = 27/196 (13%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAERTR-LWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       L + +KP 
Sbjct: 336 ERRIQAGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMNEDLVVVNKPA 395

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 396 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 455

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G    + +   K+ I +     G  +V+             +Q G  +
Sbjct: 456 RQVEKEYICRVEGIFPDEIVE-CKEPIEVVSYKIGVCKVSQRGKDCTTTFQKISQNGKTS 514

Query: 188 WVTVG-LREGKNREIK 202
            V    L  G+  +I+
Sbjct: 515 VVLCKPLT-GRMHQIR 529


>gi|118602363|ref|YP_903578.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
 gi|118567302|gb|ABL02107.1| ribosomal large subunit pseudouridine synthase D [Candidatus Ruthia
           magnifica str. Cm (Calyptogena magnifica)]
          Length = 314

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/234 (17%), Positives = 82/234 (35%), Gaps = 44/234 (18%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQ-------------RVKVNGILLERAA 51
           I+   F  QR+   +A+     SR ++   I                +V + G ++   +
Sbjct: 7   IIPNRFIGQRIDAAMAQMLPNYSRVKITYWIKSGDALIHHKTFKPKEKV-LGGEVIT-LS 64

Query: 52  VNVMST-----DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV------FDN 100
           + +  T       I +D       E   + + +KP+ LVT     +   T+      +D+
Sbjct: 65  IKIEKTNAWLAQDIVID----VVYEDEAIIIVNKPVNLVTHPGVSNWTGTLANALLHYDS 120

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVR---------- 148
             +   R   V RLD NT GL+++       + L     +    R Y             
Sbjct: 121 SLANLDRAGIVHRLDKNTSGLMVVARSEYAQKYLTRQLQTHSISREYSAIVYGHMISGGT 180

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +D  + +++ +   G         ++ +   +  V V L  G+  +I+
Sbjct: 181 VDKPIGRDPKDRIRQTVTESGKDALTHYRVIE-RFAHHTHVKVMLETGRTHQIR 233


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

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 35/255 (13%), Positives = 91/255 (35%), Gaps = 64/255 (25%)

Query: 3   DKNIVQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVN------------ 43
           +   V+ + +  R+ +        +   G      +++++   +++V+            
Sbjct: 5   EIKKVEADESGMRLDRWFKVYYPGL---GFG---YLQKLLRSGQIRVDGGRVKADTRLLI 58

Query: 44  GILLERAAVNVMSTDHIEVDGVPLRKA------------ERTRLWLYHKPIGLVTTHSDP 91
           G ++    + V   + + V    +R+             E +++++++KP GL       
Sbjct: 59  GQVVRVPPLLVDEKESLPVTDKIIREQDDRVILKKMLLYEDSKIFVFNKPAGLAVQG--G 116

Query: 92  DGRSTVFDNLPSIFSRVIS-----VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
            G +  FD++  ++          V RLD  T G+L++    G A+ L     + +  + 
Sbjct: 117 SGLTRHFDSMLEVWRNKKGEKPRLVHRLDRETSGVLIVARSRGAAQTLTAAFRARETKKT 176

Query: 145 YRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-----------------A 187
           Y     G V + K + +   +V      GD     +  +  +                 +
Sbjct: 177 YWALVRG-VPKKKQDKISTWVVKDITAQGDKMCVCEHGEPDSNHAVSYYRVLDTRGRALS 235

Query: 188 WVTVGLREGKNREIK 202
           W+ +    G+  +++
Sbjct: 236 WLEMEPYTGRTHQLR 250


>gi|304397365|ref|ZP_07379243.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304354983|gb|EFM19352.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 232

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/146 (18%), Positives = 51/146 (34%), Gaps = 20/146 (13%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D I          +   L + +KP GL++ +  +P    +V   L  +F     V R
Sbjct: 12  PCFDEITF------LFQDAHLLVINKPGGLLSLSGKNPQNLDSVHHRLVGLFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    + Y+    G +  D      +G++   I 
Sbjct: 66  LDFGTSGLMVVARNKAINAALCQQFSQRSVNKTYQALLCGHLSDD------EGVIDAAIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG 192
                     +     K + +   V 
Sbjct: 120 KDPALFPRMTICTIRGKPARSRYRVT 145


>gi|240144135|ref|ZP_04742736.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|257203836|gb|EEV02121.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis L1-82]
 gi|291538917|emb|CBL12028.1| Pseudouridylate synthases, 23S RNA-specific [Roseburia intestinalis
           XB6B4]
          Length = 329

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/276 (15%), Positives = 85/276 (30%), Gaps = 66/276 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M++  I  EN   QR  K + +  G A    + +M+ ++ + +NG         +   D 
Sbjct: 1   MREFKI-NENEAGQRFDKYLKKLLGNAPGSFIYKMLRKKNITLNGKKA-DGTEKLNQGDD 58

Query: 60  IEV-------------------------------DGV---PLRKAERTRLWLYHKPIGLV 85
           I++                                G    P+   ++  +++ +KP G++
Sbjct: 59  IKLFFSDETFEKFSGSGTPDSEFEALKVLSREFTSGKRKLPVVYEDKDVIFI-NKPTGML 117

Query: 86  TTHSDPDG---RSTVFDNLPSIFS---------RVISVGRLDINTEGLLLL--TNDGGLA 131
           +  + P+       +   L +            R     RLD NT GLL    T  G   
Sbjct: 118 SQKAKPEDISANEYILAYLIAKGELTESSFRTFRPSICNRLDRNTSGLLAAGKTLKGLQE 177

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQD-----KLNL--------LKKGIVIQGICYG-DMQV 177
               L      + YR    G V +       L          +++    +G     + + 
Sbjct: 178 MAKALKERSVQKYYRCIVKGTVKEASYLKGYLQKDESSNQVLIRRTKPSEGEWLPIETEY 237

Query: 178 TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 G      V L  G++ +I+         + 
Sbjct: 238 KPIRCMGGYTEFEVHLMTGRSHQIRAHLASIGHPII 273


>gi|94676891|ref|YP_588880.1| ribosomal large subunit pseudouridine synthase C [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
 gi|94220041|gb|ABF14200.1| ribosomal large subunit pseudouridine synthase C [Baumannia
           cicadellinicola str. Hc (Homalodisca coagulata)]
          Length = 322

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 73/239 (30%), Gaps = 61/239 (25%)

Query: 12  TPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTDHIE-- 61
             QR+   +       R +++        R+I +  V++N   ++     + S D I   
Sbjct: 18  AGQRIDNFL-------RTKLKGVPKSLIYRIIRKGEVRINKKRIK-PQYKLQSGDQIRLP 69

Query: 62  -VDGVPLRK-----------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--L 101
            V    + +                  E   + + +KP G             +     L
Sbjct: 70  PVWRNNITQLFSPQLKKVAVLADTILYEDDYILVLNKPAGTAVHGGYKLSFGVIEGLRAL 129

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQDKL 158
                 +  + RLD +T G LL+      A  L           + Y     GQ + D +
Sbjct: 130 WPFAKFLELIHRLDRDTSGALLVA-KKRSALRLMHEQLRMKNINKHYLALVRGQWESDTV 188

Query: 159 NL--LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-------------LREGKNREIK 202
               L K I   G     +QV+ D  K S  +  +              +  G+  +I+
Sbjct: 189 VEVPLMKKIQSNGKHI--VQVSSDG-KMSKTFFKIEENFTIATLVNASPIT-GRTHQIR 243


>gi|323488794|ref|ZP_08094034.1| putative RNA pseudouridine synthase yjbO [Planococcus donghaensis
           MPA1U2]
 gi|323397492|gb|EGA90298.1| putative RNA pseudouridine synthase yjbO [Planococcus donghaensis
           MPA1U2]
          Length = 291

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 72/208 (34%), Gaps = 37/208 (17%)

Query: 38  QRVKVNGILLERAAVNVMST-DHIEV--------------DGVPLRKAERTRLWLYHKPI 82
            ++ VNG  +     +V+   D + V              DG      E   L +  KP 
Sbjct: 38  GQILVNGQEVT--VRHVLEKGDAVTVIFPNEEHGKGLLAEDGDLEIVYEDEVLLIVEKPP 95

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE- 135
              T  S      ++ + +   F+       +    RLD +T GL+ +  +  +  ++  
Sbjct: 96  LQNTIPSREHPFGSLANIVAKHFNDHGIPSTLHIATRLDRDTSGLVCIAKNRHIHHMISQ 155

Query: 136 -LPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGDMQVTLDTQK 183
                +  R Y    HGQ+D+ +             ++++ +  +   + + +V +    
Sbjct: 156 QQQEKKMKRRYEALVHGQIDKTEFTITAPIGRKNTSIIEREVR-EDGQFAETEVRVLENL 214

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWK 211
              A V++ L  G+  +I+         
Sbjct: 215 QGYAHVSLQLNTGRTHQIRVHLAHIGHP 242


>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 = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 16 VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          + + ++     SR + +R+I Q +V VNG+++ +A+  V   D I  D
Sbjct: 17 LDRGLSD----SRSKAQRLIVQGKVSVNGVVVSKASAKVSDDDVIAAD 60


>gi|299530540|ref|ZP_07043960.1| pseudouridine synthase [Comamonas testosteroni S44]
 gi|298721516|gb|EFI62453.1| pseudouridine synthase [Comamonas testosteroni S44]
          Length = 255

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/164 (17%), Positives = 55/164 (33%), Gaps = 21/164 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   + + +KP G +   +  D   T F        +   V  V RLD  T G+LL+   
Sbjct: 20  QDEHMVVVYKPAGWLVHRTGLDAHETRFVMQTLRDQLGHHVWPVHRLDKGTCGVLLMALH 79

Query: 128 GGLARVLELPSTQWL--RVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGDMQVTL---- 179
              A+ L          + YR    G + +  +  + LK     +     D    L    
Sbjct: 80  KQAAQALAASFAAHETRKEYRALVRGWLPETLEVDHPLKPDDAPEDAPVQDAHTHLRCLA 139

Query: 180 -----DTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++  G +    + L E     G+  +I++  +     + 
Sbjct: 140 RLSWPESYDGRHPETRISLVEALPTTGRRHQIRRHLKHVAHPII 183


>gi|294675889|ref|YP_003576504.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           capsulatus SB 1003]
 gi|294474709|gb|ADE84097.1| ribosomal large subunit pseudouridine synthase C [Rhodobacter
           capsulatus SB 1003]
          Length = 355

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/269 (15%), Positives = 83/269 (30%), Gaps = 64/269 (23%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           V E+    R+ + + +   + ++  VE+M    +++V+G  ++ A+  +     + V   
Sbjct: 9   VTEDEGESRLDRWLKKKFPVLTQGAVEKMCRTGQLRVDGGRVK-ASDRIGPGMEVRVPPL 67

Query: 63  ------------------------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRS 95
                                   D   ++ A   +   +   +KP GL +      G  
Sbjct: 68  PEAGAKAPESRSEARRDATQISPADEKMIQAAVLWKDEHIIALNKPAGLPSQGGSGQGDR 127

Query: 96  TVFDNLP----SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
            V   L         R   V RLD +T G+LL+     +AR L          ++Y    
Sbjct: 128 HVDGLLEALKFGYKDRPKMVHRLDKDTSGVLLIARTDRVARALSESFRLKTTRKIYWAAV 187

Query: 150 HGQVDQDK-------LNLLKKGIVIQGIC-----------YGDMQ------VTLDTQKGS 185
            G     K       +     G   +G               D +        +D     
Sbjct: 188 AGVPSPKKGTIRYGLVKAPGHGRGGEGEKMLCIHPSKVDATPDAKRATTDFAVIDGLGSR 247

Query: 186 NAWVTVG-LREGKNREIKKVFEFFNWKVN 213
            +WV +  +  G+  +++         + 
Sbjct: 248 VSWVGLVPIT-GRTHQLRAHMAELGHPIV 275


>gi|239637869|ref|ZP_04678830.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus warneri L37603]
 gi|239596432|gb|EEQ78968.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus warneri L37603]
          Length = 276

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 84/234 (35%), Gaps = 39/234 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAERTRL-----WLYHKPIGLVTT 87
           + +N     R +  V S D + +       + +P  +  +         +  KP G+ T 
Sbjct: 37  ITINKET-SRLSDKVNSGDEVFIPTPEEKSNYLPSYRYAQVYYENDDFAIVLKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ ++L        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHLIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEENDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  KK I   G       ++ +  K +   + + 
Sbjct: 156 IYKAHVKALLPIKPQTIDKPIGKDKFHPNKKRISNTGQRAITHILSSNMVKENVCELEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKK 239
           L  G+  +I+         V    L    YG   L  L   S +      ++K+
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELHSYKIELEHPLTKE 265


>gi|164687826|ref|ZP_02211854.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM
           16795]
 gi|164603101|gb|EDQ96566.1| hypothetical protein CLOBAR_01470 [Clostridium bartlettii DSM
           16795]
          Length = 307

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 49/225 (21%), Positives = 88/225 (39%), Gaps = 39/225 (17%)

Query: 15  RVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD---------- 63
           R+   + ++ G  SR  ++++I  ++VKVNG + E+A   V   D + ++          
Sbjct: 21  RLDVYLSSQLGEMSRSYIQKIIKDKKVKVNGKI-EKAKYAVKEDDSVVIEIPAPKLLEVI 79

Query: 64  --GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVF--------DNLPSIFSRVIS-- 110
              +P+    E   L + +KP  +V   +  +  +T+         DNL SI   +    
Sbjct: 80  PQDIPIDIVYEDDDLLIVNKPQDMVVHPAPGNYENTLVNAILYHCKDNLSSINGVIRPGI 139

Query: 111 VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL---------- 158
           V R+D +T G+L++  +      L   L      R Y    HG V +DK+          
Sbjct: 140 VHRIDKDTSGILMIAKNNNAHNSLAEQLKDHSITREYEFICHGVVKEDKITVDRPIGRNP 199

Query: 159 -NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + LK  IV  G         +   +         L  G+  +I+
Sbjct: 200 KDRLKMAIVKDGKRAVTHFEVIKRYENFTHM-KANLETGRTHQIR 243


>gi|240112543|ref|ZP_04727033.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|240125374|ref|ZP_04738260.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
 gi|268598611|ref|ZP_06132778.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|268683976|ref|ZP_06150838.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
 gi|268582742|gb|EEZ47418.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae MS11]
 gi|268624260|gb|EEZ56660.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-92-679]
          Length = 307

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLARGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|170766087|ref|ZP_02900898.1| tRNA pseudouridine synthase C [Escherichia albertii TW07627]
 gi|170125233|gb|EDS94164.1| tRNA pseudouridine synthase C [Escherichia albertii TW07627]
          Length = 260

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKCYHAIVRGWLMEEAELDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|254832286|ref|ZP_05236941.1| hypothetical protein Lmon1_13109 [Listeria monocytogenes 10403S]
 gi|284801300|ref|YP_003413165.1| hypothetical protein LM5578_1050 [Listeria monocytogenes 08-5578]
 gi|284994442|ref|YP_003416210.1| hypothetical protein LM5923_1004 [Listeria monocytogenes 08-5923]
 gi|284056862|gb|ADB67803.1| hypothetical protein LM5578_1050 [Listeria monocytogenes 08-5578]
 gi|284059909|gb|ADB70848.1| hypothetical protein LM5923_1004 [Listeria monocytogenes 08-5923]
          Length = 296

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 87/264 (32%), Gaps = 48/264 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A  +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  ADGKIEVNSEEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTNLDIVFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYEAQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFISGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
           +  +  V + L  G+  +I+  F +    +        G      +  G T  + ++ L 
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTNLLKRQALH 263

Query: 243 --EQLGPHLLEEAQVNLDAPIYSS 264
                  H L E  +  D P+ + 
Sbjct: 264 SCHLHLVHPLTEEYMAFDLPLPAD 287


>gi|149011862|ref|ZP_01833010.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP19-BS75]
 gi|194398411|ref|YP_002038593.1| RluD subfamily ribosomal large subunit pseudouridine synthase
           [Streptococcus pneumoniae G54]
 gi|237650123|ref|ZP_04524375.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974]
 gi|237821869|ref|ZP_04597714.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae CCRI 1974M2]
 gi|147763817|gb|EDK70750.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP19-BS75]
 gi|194358078|gb|ACF56526.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae G54]
          Length = 291

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 THVSRLKQFSNKTSLARCKLKTGRTHQIR 231


>gi|223998226|ref|XP_002288786.1| hypothetical protein THAPSDRAFT_261746 [Thalassiosira pseudonana
           CCMP1335]
 gi|220975894|gb|EED94222.1| hypothetical protein THAPSDRAFT_261746 [Thalassiosira pseudonana
           CCMP1335]
          Length = 383

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 24/161 (14%), Positives = 57/161 (35%), Gaps = 39/161 (24%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL--------------- 75
           ++++I  + +KVNG+ + ++   +   D +E     +   E   +               
Sbjct: 40  MQQLIDARLIKVNGVPVSKSDGLLQKEDTVE---RVVHWHEPPIIVPETISLTKHSLPDT 96

Query: 76  --------WLYHKPIGLVTTHSDPDGRSTVFDNLPSI----FSRVISVGRLDINTEGLLL 123
                   +  +KP  +    S P   +++   + +        ++   R+D  T G+LL
Sbjct: 97  ANCGNGILYCINKPASVPVYPSGPYYSNSLLMMVEAQEGLPPKSLVPCHRIDRATSGVLL 156

Query: 124 LTNDGGLARVLELP---------STQWLRVYRVRFHGQVDQ 155
            T D  ++R ++                ++Y  R  G+   
Sbjct: 157 CTIDSKVSRAVQGRMASRNEVGTQHPIKKLYLARVQGKFPD 197


>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 = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+ K++   G+  SR     +I   +V VN  L ++A   V     I + G  +    R
Sbjct: 14 ERLDKLLVDRGLVQSRERARALIMAGQVVVNDHLADKAGTQVPLDADIRLKGEDIPFVSR 73


>gi|332971512|gb|EGK10462.1| RNA pseudouridine synthase [Kingella kingae ATCC 23330]
          Length = 305

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 31/181 (17%), Positives = 59/181 (32%), Gaps = 25/181 (13%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-------R 107
                I  D   L   E   L +  KP  L    S    R T+   L    +        
Sbjct: 84  DDEPRIPFDEKILLLDEH--LIVVDKPHFLPVIPSGRFLRETLLTRLRLHPNLQHLNVAD 141

Query: 108 VISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRVRFHGQVDQDK----LNLL 161
           +  + RLD +T G++LL+++     A           + Y      ++D        + L
Sbjct: 142 ITPIHRLDKDTAGVMLLSHNPQTRAAYQQLFQQKVIQKTYHALAPTRLDLAYPLTVQSRL 201

Query: 162 KKG------IVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
            +G        I G      ++ L  Q+G ++   +  +  GK  +++  +       + 
Sbjct: 202 VRGDSFFLTKQIDGEPNSQTEIRLLEQRGKHSLYELRPIT-GKKHQLRVHMM-HLGMPLL 259

Query: 214 R 214
            
Sbjct: 260 N 260


>gi|23308689|ref|NP_689473.1| RNA pseudouridylate synthase domain-containing protein 2 [Homo
           sapiens]
 gi|158563848|sp|Q8IZ73|RUSD2_HUMAN RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 2
 gi|16550833|dbj|BAB71059.1| unnamed protein product [Homo sapiens]
 gi|119612834|gb|EAW92428.1| RNA pseudouridylate synthase domain containing 2 [Homo sapiens]
 gi|127796558|gb|AAH16967.2| RNA pseudouridylate synthase domain containing 2 [Homo sapiens]
          Length = 545

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/292 (15%), Positives = 96/292 (32%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+++N   ++   + +   D +          V   P+R  AE   + +  KP
Sbjct: 179 EAAVRAGRLQLNEKPVQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 238

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 239 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 298

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 299 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGQSS 358

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI- 240
            V    +    G+  +I+   +F    +        +++GP +      G     + +  
Sbjct: 359 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSR----GRGGYIPKTNEEL 411

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       ++QK
Sbjct: 412 LRDLVAEHQAKQSLDVLDLCEGDLSPGLTDSTAPSSELGKDDLEELAAAAQK 463


>gi|319440272|ref|ZP_07989428.1| pseudouridylate synthase [Corynebacterium variabile DSM 44702]
          Length = 311

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 77/255 (30%), Gaps = 46/255 (18%)

Query: 1   MKDKNI----VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-- 54
           M D+      V       RV   +++    SR  V  +     +  +G    ++   V  
Sbjct: 1   MSDRESRMMPVPGGLAGMRVDAGLSKLLGLSRTVVAELAEAGDIVQDGKTAGKSDRLVDG 60

Query: 55  ---------MSTD------HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
                       D       + V+G+ +  ++   + +  KP+G+    +      TV  
Sbjct: 61  AWLDVTLPAPPRDLAAEPARV-VEGMDILYSDDD-VIVVDKPVGVAAHPTIGWEGPTVTS 118

Query: 100 NL---------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
            L              R   V RLD+ T G++ +        VL+         + Y   
Sbjct: 119 GLAAAGYRISTSGPPERKGIVHRLDVGTSGVMAVAASERAYTVLKRAFRDRTVDKTYHAL 178

Query: 149 FHGQVDQDK--LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
             G  D     ++           K  +   G        T++  + +   V V L  G+
Sbjct: 179 VQGHPDPTDGTIDAPIARHPGHGWKFAVQDGGRHAVTHYETIEAFREAT-LVRVHLETGR 237

Query: 198 NREIKKVFEFFNWKV 212
             +I+  F   +   
Sbjct: 238 THQIRVHFSALHHPC 252


>gi|77360755|ref|YP_340330.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76875666|emb|CAI86887.1| 23S rRNA pseudouridylate synthase, in E. coli modifies positions
           955, 2504, and 2580 in 23 S ribosomal RNA
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 319

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 80/248 (32%), Gaps = 48/248 (19%)

Query: 1   MKDKNIVQ-------ENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           M +KN +Q       E+   QR+   +        +  + +++ +  V+VN   ++    
Sbjct: 1   MSEKNDLQVTYVTINEDHLGQRIDNFLITHLKGVPKSAIYKLLRKGEVRVNKKRIK-PVY 59

Query: 53  NVMSTDHIEVDGVPLRKAER--------------------TRLWLYHKPIGLVTTHSDPD 92
            +   D + +  + + + E                       L + +KP G+        
Sbjct: 60  KLQLEDVLRIAPIRVAEREEFVPSKLDKVTRLENDIIFEDKYLIVINKPSGMAVHGGSGL 119

Query: 93  GRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVR 148
               +     L      +  V RLD +T G LL+     +   L   L      + Y   
Sbjct: 120 SYGLIEALRVLRPEERSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWAL 179

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------- 195
             GQ D      + +G+    +  G+  V +D  +G  +     + E             
Sbjct: 180 VDGQWDSKT-KNVTEGLRKNTLKSGERVVRVDNTEGKPSHTRFKVLERFNECSLVQASPV 238

Query: 196 -GKNREIK 202
            G+  +I+
Sbjct: 239 TGRTHQIR 246


>gi|256617567|ref|ZP_05474413.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
 gi|256597094|gb|EEU16270.1| pseudouridine synthase [Enterococcus faecalis ATCC 4200]
          Length = 287

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 43/209 (20%), Positives = 78/209 (37%), Gaps = 36/209 (17%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVM----STDHIE--VD-GVPLRKA---ER 72
           R+V   +  ++ VK+NG         +A   V      TD++   V  G   R     E 
Sbjct: 28  RKVRHFLRTRKNVKINGETAAFHFPVQAGDCVTLTFEETDYVRPTVHLGEATRVKVLYED 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDG 128
             L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++ T + 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFTKNP 147

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYG 173
            +  +L   L + Q  R Y+    G  +Q +   + + I               +G    
Sbjct: 148 FVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSAI 206

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                + T   +   VT  L  G+  +I+
Sbjct: 207 THVQVVQTLSNNQTAVTCVLETGRTHQIR 235


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

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 87/256 (33%), Gaps = 72/256 (28%)

Query: 7   VQENFTPQRVSKV-------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           V+ +    R+ +        +   G     ++++++   +V+V+G  ++     V     
Sbjct: 9   VEPDEAGMRLDRWFKVHFPGL---GFG---QLQKLMRSGQVRVDGGRVKT-DARVQPGQI 61

Query: 60  IEV------------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPD 92
           + V                        D   L +    E  ++++ +KP GL        
Sbjct: 62  VRVPPLDVDAKGPKSGPIGNKDMKHSSDADLLARMLLHEDEKVFVLNKPAGLAV-----Q 116

Query: 93  GRSTVFDNLPSIFSRVIS--------VGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
           G S +  +L  +     S        V RLD +T G+L++    G A+ L          
Sbjct: 117 GGSGLTRHLDKMLEAWTSKKGEKPRLVHRLDRDTSGVLVVARTRGAAQKLTAAFRERDTK 176

Query: 143 RVYRVRFHGQV--DQDKLNLL----------KKGIVIQGICYGDMQVT----LDTQKGSN 186
           + Y     G     +DK++            +  I   G    D  +T    L+T   S 
Sbjct: 177 KTYWSLVKGVPRKHEDKISTWLVKEATADGDRMRIAKHGEDGADHAITYYRVLETAAQSL 236

Query: 187 AWVTVGLREGKNREIK 202
           AW+ +    G+  +++
Sbjct: 237 AWLEMEPYTGRTHQLR 252


>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 = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 4/48 (8%)

Query: 16 VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          + + ++     SR + +R+I Q +V VNG+++ +A+  V   D I  D
Sbjct: 17 LDRGLSD----SRSKAQRLIVQGKVSVNGVVVSKASAKVSDDDVIAAD 60


>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 = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          + T +R+ K +   G+  SR     +I    V VN  ++++A   V     I V G  L 
Sbjct: 2  SATKERLDKRVVELGLCRSRERARALIMSGNVLVNETVIDKAGTRVAVDAAIRVRGGDLP 61

Query: 69 KAER 72
             R
Sbjct: 62 YVSR 65


>gi|212696263|ref|ZP_03304391.1| hypothetical protein ANHYDRO_00799 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676892|gb|EEB36499.1| hypothetical protein ANHYDRO_00799 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 282

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/209 (13%), Positives = 61/209 (29%), Gaps = 36/209 (17%)

Query: 35  IAQQRVKVNGILL-ERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIG 83
           I    V VN   + +   +       I ++   L             E   +    KP  
Sbjct: 31  IINNLVYVNDEKISKNIGLKAGDKVKILIEDENLNYEPINKKIKILYEDKDIVAVDKPPN 90

Query: 84  LVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG----GLARVLEL 136
           L     + +  S              ++  + RLD+NT G++L+  +          +  
Sbjct: 91  LTVNSKNQESLSNYLAYYFKENKIKSQIRLINRLDMNTSGIMLVAKNPFSHAYYQNQI-- 148

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN--------- 186
            + +  + Y     G +    ++   + I I        M+V  D               
Sbjct: 149 ENNELDKEYLALVEGNL---IIDDFCE-IDIDYDKENKKMKVVSDKNHVKTYFKTLKNYG 204

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVN 213
             + +   +  GK  +I+    + N  + 
Sbjct: 205 KFSLIYCKIYTGKTHQIRLSLAYLNHPIL 233


>gi|167949147|ref|ZP_02536221.1| Pseudouridylate synthase [Endoriftia persephone 'Hot96_1+Hot96_2']
          Length = 154

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 35/93 (37%), Gaps = 5/93 (5%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTND 127
           +   +   +KP GL+   S  D     +    L     R    V RLD  T G+LL   +
Sbjct: 9   QDQAIVAINKPAGLLVHPSLVDRYETRSAMKLLRDQLGRWVYPVHRLDKPTSGVLLFALN 68

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL 158
             +A+ L  +       + Y     G  DQ ++
Sbjct: 69  SEVAQRLGEQFEGRGVEKRYLAVVRGHPDQQEV 101


>gi|118476866|ref|YP_894017.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196046511|ref|ZP_03113736.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225863254|ref|YP_002748632.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|229183584|ref|ZP_04310807.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
 gi|118416091|gb|ABK84510.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196022695|gb|EDX61377.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225789436|gb|ACO29653.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|228599827|gb|EEK57424.1| Pseudouridine synthase [Bacillus cereus BGSC 6E1]
          Length = 307

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  K+ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATKRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|157803478|ref|YP_001492027.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           canadensis str. McKiel]
 gi|157784741|gb|ABV73242.1| ribosomal large subunit pseudouridine synthase C [Rickettsia
           canadensis str. McKiel]
          Length = 303

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 33/175 (18%), Positives = 59/175 (33%), Gaps = 42/175 (24%)

Query: 15  RVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV--- 65
           R+ K + R       G+     +E+ + Q+++ VN      A++ V+  D I +      
Sbjct: 12  RLDKYLKRLYPLLTQGV-----IEKALRQKQIIVNARKA-EASLRVIDGDKIFISDKFNL 65

Query: 66  PLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VFDN 100
           P+++ E+                         L   +KP GL T        S       
Sbjct: 66  PVKQPEKLVFTDAEIKLAKKITTDYLIYEDDNLIAINKPAGLATQGGSKINLSIDSALKY 125

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
           L    +    V RLD  T GLLL+  +   +            ++ Y    +G+ 
Sbjct: 126 LNYKGADFKLVHRLDKETSGLLLIAKNYLSSIKFHDAFKDKLVVKTYFAVTYGKP 180


>gi|325292121|ref|YP_004277985.1| hemolysin [Agrobacterium sp. H13-3]
 gi|325059974|gb|ADY63665.1| hemolysin [Agrobacterium sp. H13-3]
          Length = 250

 Score = 54.0 bits (129), Expect = 3e-05,   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|312885611|ref|ZP_07745247.1| tRNA pseudouridine synthase C [Mucilaginibacter paludis DSM 18603]
 gi|311301923|gb|EFQ78956.1| tRNA pseudouridine synthase C [Mucilaginibacter paludis DSM 18603]
          Length = 234

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/159 (16%), Positives = 47/159 (29%), Gaps = 22/159 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L   +KP GL+   S      T F        +   V    RLD  T G+LL   D   
Sbjct: 12  YLVAINKPHGLLVHRSSIAHDVTEFALQILRDQLNRHVFPAHRLDRKTGGVLLFALD-KE 70

Query: 131 ARVLEL---PSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQG-----ICYGDMQV 177
              L           + Y     G    ++     L   + G  +Q            ++
Sbjct: 71  TEKLMQTQFMENAVKKKYLALVRGHTPDEQEIDYPLRK-ENG-TLQDAFTRYKTLARAEL 128

Query: 178 TLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
            +       +  ++   +   G+  +++K F      + 
Sbjct: 129 KVPLGNHPTSRYSLIEAQPETGRMHQLRKHFSHIFHPII 167


>gi|237729755|ref|ZP_04560236.1| tRNA pseudouridine synthase C [Citrobacter sp. 30_2]
 gi|226908361|gb|EEH94279.1| tRNA pseudouridine synthase C [Citrobacter sp. 30_2]
          Length = 260

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 49/168 (29%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGRHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +  D          L+ +                   
Sbjct: 71  RLLSQQFEHHQIQKRYHAIVRGWLMDDAVLDYPLVEELDKIADKFARDDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E     G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLV--ELDPKTGRKHQLRRHLAHLRHPII 176


>gi|146418802|ref|XP_001485366.1| hypothetical protein PGUG_03095 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 390

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 55/162 (33%), Gaps = 20/162 (12%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDIN 117
           I   G      +   L + +KP G+ T  S     ++V + + +      +    RLD  
Sbjct: 96  IVWSGPISIIYQDPSLIVVNKPSGIPTHPSGNFRYNSVTEIVKAQLHLESIFPCHRLDKA 155

Query: 118 TEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGI 170
           T G+L+L         +           + Y  R  G+    +L + +  + +     G 
Sbjct: 156 TSGILMLATTSAACSNIQKQLQERKDVKKEYIARVKGKFPPSQL-VHQDPVFLLNSTAGY 214

Query: 171 CYGDMQVTLDTQ----------KGSNAWVTVGLREGKNREIK 202
                 V++D+           +   + V+     GK  +I+
Sbjct: 215 IMPGRYVSIDSSTTFTRLKYNLELDESIVSCEPHSGKMHQIR 256


>gi|325962959|ref|YP_004240865.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469046|gb|ADX72731.1| ribosomal large subunit pseudouridine synthase D [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 308

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 80/250 (32%), Gaps = 41/250 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           M ++ +V E F   R    +A     SR     ++A+  V   G  L ++A  V + D +
Sbjct: 1   MPERMVVTEEFGGARADAGLAALLGVSRSVAASLLAEGHVLAKGKPLGKSAKLV-AGDVL 59

Query: 61  EVD----------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +V                 G+ +   +     +  KP+G+    S      TV   L   
Sbjct: 60  QVSMPERRDPLEVVEEVVEGLKILLDDED-FAVVDKPVGVAAHPSPGWVGPTVVGGLAGA 118

Query: 105 FSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
             R+           V RLD+ T G++++         L+         +VY     G +
Sbjct: 119 GYRISTSGSPERAGIVHRLDVGTSGVMVVAKSERAYTALKRAFKERSVDKVYHAVVQG-L 177

Query: 154 DQDKLNLLKKGI-----------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +  +   I           VI+          +    G  + V V L  G+  +I+
Sbjct: 178 PDPVVGTIDAPIGRHPGHDWRFAVIEDGRPSITHYEVLEAFGKASLVEVHLETGRTHQIR 237

Query: 203 KVFEFFNWKV 212
             F       
Sbjct: 238 VHFSALRHPC 247


>gi|190346820|gb|EDK38997.2| hypothetical protein PGUG_03095 [Meyerozyma guilliermondii ATCC
           6260]
          Length = 390

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 55/162 (33%), Gaps = 20/162 (12%)

Query: 60  IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS--IFSRVISVGRLDIN 117
           I   G      +   L + +KP G+ T  S     ++V + + +      +    RLD  
Sbjct: 96  IVWSGPISIIYQDPSLIVVNKPSGIPTHPSGNFRYNSVTEIVKAQLHLESIFPCHRLDKA 155

Query: 118 TEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGI 170
           T G+L+L         +           + Y  R  G+    +L + +  + +     G 
Sbjct: 156 TSGILMLATTSAACSNIQKQLQERKDVKKEYIARVKGKFPPSQL-VHQDPVFLLNSTAGY 214

Query: 171 CYGDMQVTLDT----------QKGSNAWVTVGLREGKNREIK 202
                 V++D+           +   + V+     GK  +I+
Sbjct: 215 IMPGRYVSIDSSTTFTRLKYNSELDESIVSCEPHSGKMHQIR 256


>gi|168186684|ref|ZP_02621319.1| pseudouridine synthase, RluA family [Clostridium botulinum C str.
           Eklund]
 gi|169295320|gb|EDS77453.1| pseudouridine synthase, RluA family [Clostridium botulinum C str.
           Eklund]
          Length = 323

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 90/252 (35%), Gaps = 65/252 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           +  N   QR+ K         R+ +E        + + +  ++VNG   ++    +   D
Sbjct: 5   IGPNEAGQRLDKF------C-RKWLEDVPLGAIFKALRKGDIRVNGKKAKQ-NYFLEEED 56

Query: 59  HIE--------------------VDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            +E                    V+   ++ A E   + +  K  G++      DG  T+
Sbjct: 57  VVETKYIESYKKNKNNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPTL 116

Query: 98  FDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                      RLD NT G+++   +    ++L   +   +  
Sbjct: 117 TDYVLSYLFNKGEYIPEKEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKIS 176

Query: 143 RVYRVRFHGQVDQ---------DKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVT 190
           + Y     G++ +         D++N + + I +          M+V++    G+ +++ 
Sbjct: 177 KYYNALVKGKIKEGRYEAYISKDQINNISE-IHLDKKPNSKKIAMEVSVIDTVGTFSFLE 235

Query: 191 VGLREGKNREIK 202
           + L  G++ +++
Sbjct: 236 LDLITGRSHQLR 247


>gi|303228653|ref|ZP_07315478.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516633|gb|EFL58550.1| pseudouridine synthase, RluA family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 335

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/146 (18%), Positives = 51/146 (34%), Gaps = 18/146 (12%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLR-----KAERTRL 75
           R+ + ++  ++ + VNG         V   D I       ++D  P+        E   L
Sbjct: 43  RKAMVKLFDEKLIHVNGHKAT-PHTEVAVDDEIWIAMAKEKIDHEPIAMDLHILYEDDDL 101

Query: 76  WLYHKPIGLVTTHSDP---DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--GL 130
            +  KP G+     D          +     I  +V  + RLD +T G +++   G    
Sbjct: 102 LIVDKPAGVTVNSKDQVSLANGIAHYFMEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQS 161

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQD 156
               ++    + + Y     G V+ D
Sbjct: 162 LYQQQMDDNTFEKWYMAIVEGLVESD 187


>gi|108759922|ref|YP_634049.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108463802|gb|ABF88987.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 318

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 36/261 (13%), Positives = 75/261 (28%), Gaps = 66/261 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++ +    R+ K +       R+         + +MI  ++V+VNG   +     +   D
Sbjct: 6   IEADTAGMRLDKHL-------RKRLPNVPVSHLFKMIRTKKVRVNGKRAQ-PEQLLSEGD 57

Query: 59  HIEVDG-----------------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
            + + G                         +   E   L    KP G+           
Sbjct: 58  VLTIRGDEQQLVGAERPKVDPPPPPVDPSRLVILREDDWLMAVDKPSGMAVHTGSGITGG 117

Query: 96  TVFDNLPSIFSRV--------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVY 145
           T+ D + +                 RLD  T G++L+              T     + Y
Sbjct: 118 TLVDYVRAYLGPKAVRNDFAASPAHRLDRETSGVILVAKRRPAMVHFTEVFTHGLSRKRY 177

Query: 146 RVRFHGQVDQD--------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                G++ +D                +  ++G+ +Q        V    Q    A ++ 
Sbjct: 178 LTLVKGKMPRDSGVIDLPLSEHQQTAESKARRGVNMQAAVTRWKVVK---QSSEAALLSC 234

Query: 192 GLREGKNREIKKVFEFFNWKV 212
            +  G+  +I++        V
Sbjct: 235 AIETGRTHQIRRHLAAIGHPV 255


>gi|152986000|ref|YP_001347558.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PA7]
 gi|150961158|gb|ABR83183.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           aeruginosa PA7]
          Length = 318

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 81/237 (34%), Gaps = 44/237 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V      QR+   + AR   A +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VPPELAGQRIDNFLIARLKGAPKTLIYRILRKGEVRVNKGRI--KPDYRLQAGDQVRVPP 73

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLP 102
           + L +                     E   L + +KP G+          G   VF  L 
Sbjct: 74  LRLAERDEPAPLAQGLLERMEAAIVYEDKALIVVNKPAGIAVHGGSGVSAGVIEVFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKLN 159
                +  V RLD +T GLL++     + R L           + Y     G     K  
Sbjct: 134 PEARDIELVHRLDRDTSGLLMIAKKRSMLRHLHEALRGEKIVDKRYHALVRGHWPAGK-K 192

Query: 160 LLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV--------GLRE-----GKNREIK 202
            ++  ++   +  G+  V ++ + K +     V         L E     G+  +I+
Sbjct: 193 NIRAPLLKNNLRSGERMVEVNVEGKDALTEFRVLRRFGDFATLVEARPITGRTHQIR 249


>gi|116491175|ref|YP_810719.1| pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290890691|ref|ZP_06553761.1| hypothetical protein AWRIB429_1151 [Oenococcus oeni AWRIB429]
 gi|116091900|gb|ABJ57054.1| Pseudouridylate synthase, 23S RNA-specific [Oenococcus oeni PSU-1]
 gi|290479666|gb|EFD88320.1| hypothetical protein AWRIB429_1151 [Oenococcus oeni AWRIB429]
          Length = 299

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 85/237 (35%), Gaps = 48/237 (20%)

Query: 7   VQENFTPQ--RVSKVIARAGIASR--REVE----RMIAQQR-------VKVNGILLERAA 51
           + E   P+  R+   +   G++ R   +++    +++ + R       VK NG  +    
Sbjct: 6   ISETKEPEKVRL--FLKARGVSHRMFSQIKHFGGKIVVEGREVFTNDYVK-NGEKITI-- 60

Query: 52  VNVMSTDHIEVDGV---PLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                 +++E+D     PL+   E     +  KP  + T     D ++T+ + + +   +
Sbjct: 61  FMPPERENVELDADFTDPLKVVFEDKNFLIVDKPAFVTTVPGHADRKTTLVNMIKAHLIQ 120

Query: 108 -------VISVGRLDINTEGLLLLTNDGGLARVLEL----PSTQWLRVYRVRFHGQVDQD 156
                     V RLD +T GL+LL      A  L            + Y     G   +D
Sbjct: 121 EKADSLVPHVVTRLDRDTSGLVLLAKH-KFAHALLNDALMEHHDIEKFYVALVSGNFQED 179

Query: 157 KL-----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        + +++ +   G      +  ++ +  +   + + L  G+  +I+
Sbjct: 180 HGMIDEPIGRIEGDFIRRQVRQDGKRSVT-EYWVEKRFDNFTQLRIQLHTGRTHQIR 235


>gi|302874505|ref|YP_003843138.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
 gi|307690886|ref|ZP_07633332.1| pseudouridine synthase, RluA family protein [Clostridium
           cellulovorans 743B]
 gi|302577362|gb|ADL51374.1| pseudouridine synthase, RluA family [Clostridium cellulovorans
           743B]
          Length = 321

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 43/267 (16%), Positives = 84/267 (31%), Gaps = 70/267 (26%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVERMI------------AQQRVKVNGILLERAA 51
           +  +  N   QR  K            V + +             +  ++VNG  ++   
Sbjct: 2   RITIGTNEQGQRTDKF-----------VRKWLQDLPLSALYKAFRKGDIRVNGKKVKE-N 49

Query: 52  VNVMSTDHIE-----------------VDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDG 93
             +   D +E                 ++ V L+   E   + L  K  G++      +G
Sbjct: 50  YFLQEGDVVETSKYVQASPKKELNFQKIENVHLKITFEDENILLVEKWPGVLVHADKKNG 109

Query: 94  RSTVF-----------DNLPSIFSRVIS--VGRLDINTEGLLLL--TNDGGLARVLELPS 138
             T+            D LP            RLD NT G+++   T +G  A    +  
Sbjct: 110 DPTLTDYVLSYLHDKGDYLPENEVTFTPASCNRLDRNTSGIVIFGKTFEGLKALNEMVRD 169

Query: 139 TQWLRVYRVRFHGQ---------VDQDKLNLLKKGIVIQGICYGD---MQVTLDTQKGSN 186
            +  + Y     G+         + +D+   L K I  +G        M+V      GS 
Sbjct: 170 RRIQKYYMALVQGKLKDGRYDAYISKDESQNLSK-IYNEGGADRKKISMEVKTLETVGSY 228

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
           + + + L  G++ +++         + 
Sbjct: 229 SLLDIELITGRSHQLRAHLSHLGNPIV 255


>gi|224371098|ref|YP_002605262.1| RluC [Desulfobacterium autotrophicum HRM2]
 gi|223693815|gb|ACN17098.1| RluC [Desulfobacterium autotrophicum HRM2]
          Length = 295

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 22/122 (18%), Positives = 38/122 (31%), Gaps = 15/122 (12%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ--DKLNLLK 162
           ++  V RLD  T GL+L+  D    R L          + Y    HG  D   D   +  
Sbjct: 114 QIHPVHRLDQETSGLILVATDPDRLRYLSNLFQQGAVQKHYIALVHGNFDPPCDPFQVWD 173

Query: 163 KGI-VIQGICYGDM----------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +    G                +  +  Q      + + L  G+  +I++  +     
Sbjct: 174 TPLSKQAGGRTDPRGKGKRVRSETRYRIMDQSPHYTLLEIELVTGRKHQIRRHAKLAGHP 233

Query: 212 VN 213
           V 
Sbjct: 234 VT 235


>gi|157148329|ref|YP_001455648.1| tRNA pseudouridine synthase C [Citrobacter koseri ATCC BAA-895]
 gi|157085534|gb|ABV15212.1| hypothetical protein CKO_04146 [Citrobacter koseri ATCC BAA-895]
          Length = 260

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 50/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +  +          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMDEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|91212158|ref|YP_542144.1| tRNA pseudouridine synthase C [Escherichia coli UTI89]
 gi|117625019|ref|YP_854007.1| tRNA pseudouridine synthase C [Escherichia coli APEC O1]
 gi|218559779|ref|YP_002392692.1| tRNA pseudouridine synthase C [Escherichia coli S88]
 gi|237706579|ref|ZP_04537060.1| tRNA pseudouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|331684413|ref|ZP_08385005.1| tRNA pseudouridine synthase C [Escherichia coli H299]
 gi|91073732|gb|ABE08613.1| hypothetical protein UTI89_C3161 [Escherichia coli UTI89]
 gi|115514143|gb|ABJ02218.1| tRNA pseudouridine synthase [Escherichia coli APEC O1]
 gi|218366548|emb|CAR04301.1| tRNA pseudouridine synthase [Escherichia coli S88]
 gi|226899619|gb|EEH85878.1| tRNA pseudouridine synthase C [Escherichia sp. 3_2_53FAA]
 gi|294489605|gb|ADE88361.1| tRNA pseudouridine synthase C [Escherichia coli IHE3034]
 gi|307625640|gb|ADN69944.1| tRNA pseudouridine synthase C [Escherichia coli UM146]
 gi|315289310|gb|EFU48705.1| tRNA pseudouridine synthase [Escherichia coli MS 110-3]
 gi|323950992|gb|EGB46868.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323957197|gb|EGB52921.1| RNA pseudouridylate synthase [Escherichia coli H263]
 gi|331078028|gb|EGI49234.1| tRNA pseudouridine synthase C [Escherichia coli H299]
          Length = 260

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +  +    V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDLIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|240080333|ref|ZP_04724876.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
 gi|268596481|ref|ZP_06130648.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
 gi|268550269|gb|EEZ45288.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae FA19]
          Length = 307

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPIDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLARGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|437185|gb|AAA64631.1| C-terminal sequence of ORF C product shows homology to several
           bacterial ORFs (accession numbers M87501, M59757,
           D10483, M62747, M96791, X57620, Z12154) and human EST
           cDNA (Z13254) [Leishmania donovani]
          Length = 741

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 38/122 (31%), Gaps = 22/122 (18%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS------TQWLRVYRV-RFHGQVDQDKLN 159
           R   V RLD  T G LL+      A  L          +   ++Y       +       
Sbjct: 568 RQGQVHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS----- 622

Query: 160 LLKKGIVIQGICYGDMQVTLDTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            L+  + +           + T+        K   AWV   +++GK  +I++        
Sbjct: 623 -LRN-VRLHDDIIDAADPKIRTRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHLASRGLP 680

Query: 212 VN 213
           + 
Sbjct: 681 IL 682


>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 = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/195 (15%), Positives = 58/195 (29%), Gaps = 23/195 (11%)

Query: 40  VKV------NGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           V V      N IL       + S + I          E   + +  K      T S    
Sbjct: 43  VTVRKQLMPNDILEIHLPQEIPSVNLIPYARKLEVLYEDAFIIIVTKLNNQNCTPSREHP 102

Query: 94  RSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRV 147
             ++ + +               V RLD NT G+++    G +            ++Y  
Sbjct: 103 HESLIEQVLYHCQEHGENINPHIVTRLDRNTTGIVIFAKYGHIHH--LFSKVNLKKIYTC 160

Query: 148 RFHGQ-----VDQDKLNLLKKGIVIQ----GICYGDMQVTLDTQKGSNAWVTVGLREGKN 198
             +G+     + +  +   K  I+ +       Y      +  Q    +   V L  G+ 
Sbjct: 161 LVYGKTHTSGIIEANIRRSKDSIITREVASDGKYAKTSYEVINQNDKYSLCKVHLHTGRT 220

Query: 199 REIKKVFEFFNWKVN 213
            +I+  F+     + 
Sbjct: 221 HQIRVHFQHIGHPIV 235


>gi|113460859|ref|YP_718926.1| 23S rRNA pseudouridylate synthase C [Haemophilus somnus 129PT]
 gi|112822902|gb|ABI24991.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           somnus 129PT]
          Length = 326

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/239 (14%), Positives = 78/239 (32%), Gaps = 47/239 (19%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TINEDESGQRIDNFLLAKLKSVPKSLIYRILRKGEVRVNKGRI--KPEYKLQNGDIVRIP 74

Query: 64  GVPLRKAERT---------------------RLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
            V + + E T                      L + +KP GL            +     
Sbjct: 75  PVRIAEKEHTPISKKLNKVAQLEQQIIFEDNYLLVLNKPSGLAVHGGSGLNFGAIEALRT 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK 157
           L      +  V RLD +T G+LL+      A              + Y     G   Q  
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIA-KKRSALRSLHEQLREKTIQKEYLALVRGHW-QSH 192

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
             +++  + ++       ++    ++G  +     + E              G+  +I+
Sbjct: 193 CKMIQAPL-LKNELTSGERIVKVNEQGKPSETKFSVEERYNNATLVKASPITGRTHQIR 250


>gi|182684947|ref|YP_001836694.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae CGSP14]
 gi|303253824|ref|ZP_07339955.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|303260789|ref|ZP_07346745.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|303263120|ref|ZP_07349049.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|303265168|ref|ZP_07351080.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
 gi|303267680|ref|ZP_07353509.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|303270027|ref|ZP_07355752.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|182630281|gb|ACB91229.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CGSP14]
 gi|302599211|gb|EFL66226.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae BS455]
 gi|302635742|gb|EFL66248.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP14-BS292]
 gi|302638071|gb|EFL68550.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP-BS293]
 gi|302640439|gb|EFL70861.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS458]
 gi|302642786|gb|EFL73104.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS457]
 gi|302645249|gb|EFL75484.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae BS397]
          Length = 291

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 TYVSRLKQFSNKTSLARCKLKTGRTHQIR 231


>gi|160915826|ref|ZP_02078034.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991]
 gi|158432302|gb|EDP10591.1| hypothetical protein EUBDOL_01842 [Eubacterium dolichum DSM 3991]
          Length = 313

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/252 (16%), Positives = 90/252 (35%), Gaps = 47/252 (18%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH----- 59
           ++ +N   QRV K +++A     +  + + I  +++KVN       +  +   D      
Sbjct: 5   VIGKNDCDQRVDKFLSKALPTLPKSLMYKAIRNKKIKVNRKRC-EISQRLQEGDTMQLFL 63

Query: 60  -------------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL----- 101
                        ++V        E   L + +K  GL+       G+  + D +     
Sbjct: 64  AEEFFMTQIDTAFLKVPSELDIVYEDENLLIVNKAKGLLAHRDQKVGQDNLMDRILHYLY 123

Query: 102 ------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG 151
                 P + +  +     R+D NT+GL++   +    R +   +   +  + Y     G
Sbjct: 124 IHKEYDPRMENSFVPALCHRIDRNTQGLVIAAKNAASLRAMNAHIKQRKVRKKYVCIAQG 183

Query: 152 QVDQDKLNLLKKGIVIQG----------ICYGDMQV--TLDTQKGSNAWVTVGLREGKNR 199
             D+ + ++L      +             Y  +++   +  QK   A V V L  GK+ 
Sbjct: 184 VFDKRQEHVLLYHCKTKDNVAHILPYPKEGYKPIEINYQIKEQKKQYALVEVELLSGKSH 243

Query: 200 EIKKVFEFFNWK 211
           +I+ +  + +  
Sbjct: 244 QIRAMLAYLSHP 255


>gi|148244467|ref|YP_001219161.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326294|dbj|BAF61437.1| ribosomal large subunit pseudouridine synthase D [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 314

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 42/229 (18%), Positives = 82/229 (35%), Gaps = 34/229 (14%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           I+   F  QRV   +A+     SR ++   I      +      +    V+  + + +  
Sbjct: 7   IIPNRFINQRVDVAMAQMLPNYSRTKITYWIKSGNALI-HRKTFKPKEKVLGGEMVNLLI 65

Query: 63  -----------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIF 105
                      D       E + + + +KP+GLVT     +   T+      +D+  +  
Sbjct: 66  KTKKANSWLAEDAAIDVVYEDSEIIIVNKPVGLVTHPGASNWTGTLANALLHYDSSLANL 125

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG----------QV 153
            R   V RLD NT GL+++       + L   L +    R Y    +G           +
Sbjct: 126 DRAGIVHRLDKNTSGLMVVARSEYAQKYLTKQLQTHSISREYSAIVYGYMISGGSVDAPI 185

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D  + +K+ +V +   Y      +  +   +  V   L  G+  +I+
Sbjct: 186 GRDPKDRIKQAVV-KDGKYALTHYRIIERFTHHTHVKAILETGRTHQIR 233


>gi|269118930|ref|YP_003307107.1| pseudouridine synthase [Sebaldella termitidis ATCC 33386]
 gi|268612808|gb|ACZ07176.1| pseudouridine synthase, RluA family [Sebaldella termitidis ATCC
           33386]
          Length = 283

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/189 (16%), Positives = 67/189 (35%), Gaps = 35/189 (18%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS 95
            Q  +KV   + +    N+     I +D       E   + + +K   LVT  +      
Sbjct: 50  KQGLLKV---VEKEKGTNIKPI-KIPLD----IVFEDEDILVVNKQPYLVTHPTKKKVDV 101

Query: 96  TVFDNLPSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVR 148
           T+ + +   F              RLD++T GL+++  +    +          + Y   
Sbjct: 102 TLANGIVYYFQEKYGKEMVPRFYNRLDMDTSGLIIIAKN-SFTQAFLQNFGDVKKYYMAL 160

Query: 149 FHGQVDQDKL----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--- 195
            HG + ++ +          + L++ I+ +G     +  T+   +  N    + L E   
Sbjct: 161 VHGIIKEEMINIEKPIARVGDDLRRKILDEGQYAKTVVKTIKRNEEKN----ITLTECEL 216

Query: 196 --GKNREIK 202
             G+  +I+
Sbjct: 217 FTGRTHQIR 225


>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 = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           + +R+  ++   G+A SR + + +I    V V+G   ++A  +   T  IEV G  L+ 
Sbjct: 1  MSKERLDVLLVNKGLATSREKAKAIIMSGNVYVDGQKEDKAGQSFPDTAVIEVRGTTLKY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|225568048|ref|ZP_03777073.1| hypothetical protein CLOHYLEM_04121 [Clostridium hylemonae DSM
           15053]
 gi|225163144|gb|EEG75763.1| hypothetical protein CLOHYLEM_04121 [Clostridium hylemonae DSM
           15053]
          Length = 341

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 55/355 (15%), Positives = 119/355 (33%), Gaps = 88/355 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVER--------MIAQQRVKVNGILLERAAVNVMST 57
           I++ N + QR+ K +       ++ + R        M+ ++ + +NG         + + 
Sbjct: 5   IIKPNESEQRLDKFL-------KKYMNRAPGSFLYKMLRKKNITLNGRRA-GGNEKLHTG 56

Query: 58  DHIEV------------DGVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGR 94
           D + +            D  P+  A           E + +   +KP G+++  ++    
Sbjct: 57  DEVRLFLSDETIEKFTGDDEPVAGAKGRNTTLDIIYEDSHVLFVNKPAGMLSQKAEKTDI 116

Query: 95  STVFDNLPSIFS------------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQ 140
           S V   +  +              R     RLD NT GL+    T  G            
Sbjct: 117 SLVEHIISYLLDSGQLTREELRTFRPSVCNRLDRNTSGLVAAGKTLAGLQMFGSLFRDRN 176

Query: 141 WLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICY----------GDMQVTLDTQKGS---- 185
             + Y     G+VD    +    KG +I+               +    ++T+       
Sbjct: 177 LRKYYLCIVKGKVDKPSHI----KGYLIKNEQTNEVRIVTSGEAEKAAPIETEYIPLAYS 232

Query: 186 --NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILRE 243
             ++ + V L  G+  +I+    + +  +        G ++ G       R+V+++  R+
Sbjct: 233 REHSLLRVHLITGRTHQIRAHLAYVSHPLC-------GDYKYGD------RDVNERY-RK 278

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           + G          L  P+   E          + VP  F ++ K ++ ++G  + 
Sbjct: 279 KYGVTSQMLHSYELVLPVLEGEFAALSERTFRAPVPALFQKVIKETAWEHGTQEA 333


>gi|291544840|emb|CBL17949.1| hemolysin TlyA family protein [Ruminococcus sp. 18P13]
          Length = 261

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 1/67 (1%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+   +   G+AS R   + +I   ++ VNG+   +A+  V  +D I   G  L    R
Sbjct: 3  MRLDSRLVTLGLASSRARAKELICGGQITVNGVPARKASAEVSDSDEILCTGGQLPFVGR 62

Query: 73 TRLWLYH 79
            L L H
Sbjct: 63 GGLKLAH 69


>gi|149007842|ref|ZP_01831438.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP18-BS74]
 gi|298229086|ref|ZP_06962767.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae str. Canada MDR_19F]
 gi|298254837|ref|ZP_06978423.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae str. Canada MDR_19A]
 gi|298501509|ref|YP_003723449.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
 gi|147760692|gb|EDK67665.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP18-BS74]
 gi|298237104|gb|ADI68235.1| pseudouridylate synthase [Streptococcus pneumoniae TCH8431/19A]
          Length = 291

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/150 (17%), Positives = 55/150 (36%), Gaps = 16/150 (10%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 G---GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYG 173
                +   L     +  R Y     G +++ +L           +  K+ +  +   Y 
Sbjct: 143 PFILPILNRLL-EKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYA 201

Query: 174 DMQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
           +  V+   Q     +     L+ G+  +I+
Sbjct: 202 ETYVSRLKQFSNKTSLAHCKLKTGRTHQIR 231


>gi|221135371|ref|ZP_03561674.1| ribosomal large subunit pseudouridine synthase C (pseudouridylate
           synthase) (uracil hydrolyase [Glaciecola sp. HTCC2999]
          Length = 316

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/224 (17%), Positives = 73/224 (32%), Gaps = 53/224 (23%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--------------------ER 72
           R++ +  V+VN   ++     + + D I V  + +  A                    E 
Sbjct: 42  RILRKGEVRVNKKRIK-PEYKLQAHDVIRVPPIRVSDAPEPVNVKLDKVAVMQDYIIYED 100

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VGRLDINTEGLLLLT 125
            R+ + +KP GL        G S +   L      +         V R+D +T G+LL+ 
Sbjct: 101 DRIMVINKPSGLAV-----HGGSGLSFGLIEGLRALRPDAKFMELVHRIDRDTSGILLVA 155

Query: 126 NDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN---LLKKGIVIQGICYGDMQVTLD 180
                 R L   L   +  + Y     GQ  +++      L K ++  G    ++     
Sbjct: 156 KRRSALRHLHEQLRDKKMQKRYHALVWGQWPENRFKVKAPLLKNVLKSGERIVNVNPE-- 213

Query: 181 TQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKV 212
             K S     V        L E     G+  +I+       + +
Sbjct: 214 -GKPSETRYRVLQAFAQTTLVEASPITGRTHQIRVHCLHAGFPI 256


>gi|269468168|gb|EEZ79867.1| pseudouridylate synthase, 23S RNA-specific [uncultured SUP05
           cluster bacterium]
          Length = 303

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 78/234 (33%), Gaps = 40/234 (17%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN------------GILLERAA 51
             V E    QR+   + +      +  + R+I +  V+VN              ++    
Sbjct: 6   KTVDEFSEGQRLDNYLLKHLKGVPKSHIYRVIRKGEVRVNKGRKKAEYKLQLDDVVRIPP 65

Query: 52  VNVMSTDHIEVDGVPLRK------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           + V  +  + V     +        E   L + +KP G +  HS       V + L  ++
Sbjct: 66  IRVSESIQVVVSDSLKQLLSDAILYEDKGLLIINKPSG-LAVHSGSGVAVGVIEALRGMY 124

Query: 106 SR-VISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD------QD 156
              V  V RLD +T G+LL+     + + L   L   Q  + Y     G           
Sbjct: 125 KEPVELVHRLDRSTSGVLLIAKKRSVLKNLHEQLSQHQMEKRYTALVKGTWSKKRHTIDA 184

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSN--------AWVTVGLREGKNREIK 202
            L    +G+VI        Q     Q   N        + V V +  G+  +I+
Sbjct: 185 PLYQNSRGVVID---AKGKQAVSHFQPLKNFHNDEFEASLVEVLIETGRMHQIR 235


>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 = 54.0 bits (129), Expect = 4e-05,   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  MRLDIYLVEIA-GSRSKAVHLIKSGKVMVNGAVCRKQSYRVKPGDRVEI 50


>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 = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+ +V+   G+A +R   + +I   +V VNG +  +A   +     +EV
Sbjct: 1  MPRQRLDQVLVSRGLAETRARAQALIMAGQVLVNGQVQTKAGTLIADDASVEV 53


>gi|325971290|ref|YP_004247481.1| pseudouridine synthase [Spirochaeta sp. Buddy]
 gi|324026528|gb|ADY13287.1| pseudouridine synthase, RluA family [Spirochaeta sp. Buddy]
          Length = 333

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 47/268 (17%), Positives = 88/268 (32%), Gaps = 62/268 (23%)

Query: 1   MKDKN-----IVQENFTPQRVSKVIA--RAGIASRREVERMIAQQRVKVNGILLERAAVN 53
           M  K      +V+ +    R+   IA  +  + SR ++     +  + +NG  ++++ + 
Sbjct: 1   MPTKERILEMVVENDSEAMRLDIYIATKQQSV-SRSQLSE--EKTHLFLNGKEVKKSKL- 56

Query: 54  VMSTDHIEV------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           V + D I+V              +PL    E   L + +K  G+V   +  +   T+ + 
Sbjct: 57  VKAGDCIKVIYYEDFFEGIIAQDIPLDVLYEDQDLLIINKKQGMVVHPAAGNYEDTLVNA 116

Query: 101 L----------------------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP- 137
           L                      P +  R   V RLD +T G+L++  +    R L    
Sbjct: 117 LLFRYGQDFSPSLEDDEETEVESPDMALRPGIVHRLDKDTSGVLVIARNRQSHRNLSQQF 176

Query: 138 -STQWLRVYRVRFHGQV-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                 +VY     G               D +           +G        T+  Q 
Sbjct: 177 KDRTTHKVYIALAKGNFKGTEGSIRANLKRDSNDRKKFTTCSDTEGRDART-DYTVLRQY 235

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWK 211
              A V + L  G+  +I+  F+     
Sbjct: 236 RDFALVRITLFTGRTHQIRVHFKSIGHP 263


>gi|257900349|ref|ZP_05680002.1| pseudouridine synthase [Enterococcus faecium Com15]
 gi|257838261|gb|EEV63335.1| pseudouridine synthase [Enterococcus faecium Com15]
          Length = 285

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 58/159 (36%), Gaps = 16/159 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 86  EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVLFAK 145

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D+           +  K+ +  +      
Sbjct: 146 NPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDRTITNKIGRDRHDRRKRVVDDKNGQNAL 205

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             VT+D        V   L  G+  +I+         + 
Sbjct: 206 THVTVDKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIV 244


>gi|119383542|ref|YP_914598.1| RluA family pseudouridine synthase [Paracoccus denitrificans
           PD1222]
 gi|119373309|gb|ABL68902.1| ribosomal large subunit pseudouridine synthase C [Paracoccus
           denitrificans PD1222]
          Length = 348

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 57/178 (32%), Gaps = 37/178 (20%)

Query: 9   ENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
           E+   QR+ + +     +        VE+M    +++V+G  ++ A   +     + V  
Sbjct: 11  EDEGEQRIDRWLKKRFPQLTQG---AVEKMCRTGQLRVDGGRVK-ANTRIEPGQEVRVPP 66

Query: 63  ------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTV---- 97
                             D   ++         +   +KP GL +      G   V    
Sbjct: 67  LPEGAPPPAAPKASVKQSDAEMIQSCVLWRDEHIIALNKPPGLPSQGGSGQGDRHVDGLT 126

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
              +     R   V RLD +T G+LLL     +AR L          ++Y     G  
Sbjct: 127 TALMFGYKDRPKLVHRLDKDTSGVLLLARTDRIARALSEAFRHRLTRKIYWAAVAGVP 184


>gi|330684742|gb|EGG96437.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU121]
          Length = 276

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 84/234 (35%), Gaps = 39/234 (16%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAERTRL-----WLYHKPIGLVTT 87
           + +N     R +  V S D + +       + +P  +  +         +  KP G+ T 
Sbjct: 37  ITIN-KQTSRLSDKVNSGDEVFIPTPEEKSNYLPSYRYAQVYYENDDFAIVLKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ ++L        V  + RLD  T GLL++  +  + ++L   L      R
Sbjct: 96  PNDLKESNTLMNHLIYTIDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEENDITR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  KK I   G       ++ +  K +   + + 
Sbjct: 156 IYKAHVKALLPIKPQTIDMPIGKDKFHPNKKRISNTGQRAITHILSSNMIKENVCELEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVSKK 239
           L  G+  +I+         V    L    YG   L  L   S +      ++K+
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVIGDPL----YGDSTLRQLELHSYKIELEHPLTKE 265


>gi|319946086|ref|ZP_08020334.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
 gi|319747732|gb|EFV99977.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           australis ATCC 700641]
          Length = 278

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 75/203 (36%), Gaps = 29/203 (14%)

Query: 29  REVERMIA-QQRVKVNGILL---------ERAAVNVMSTDHIEVD------GVPLRKAER 72
           R++   +  ++ V+VNG  +         ++  +     D+ E D       +     E 
Sbjct: 15  RKIRHFLRTKKHVQVNGETVHWQSMLQAGDQLTLTFDPEDYEEKDLLAGDASLVETLYED 74

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             L + +KP G+ T  + PD  + +      +      V RLD  T G L+   +  +  
Sbjct: 75  EHLIIVNKPEGMKTHANQPDEIALLNHVSTYVGKTCYVVHRLDKETSGALVFAKNPFVLP 134

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           VL   L   +  R Y     G + + +L           +  K+ +  +   Y +  VT+
Sbjct: 135 VLNRLLEDKKIQRDYWALILGSLPKKQLVYKDKLGRDRHDRRKRIVDPRKGLYAETHVTI 194

Query: 180 DTQKGSNAWVTVGLREGKNREIK 202
                  + V   L+ G+  +I+
Sbjct: 195 LKTFKRTSLVNCQLQTGRTHQIR 217


>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 = 54.0 bits (129), Expect = 4e-05,   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|332535383|ref|ZP_08411176.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332035211|gb|EGI71720.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 319

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 80/248 (32%), Gaps = 48/248 (19%)

Query: 1   MKDKNIVQ-------ENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAV 52
           M +KN +Q       E+   QR+   +        +  + +++ +  V+VN   ++    
Sbjct: 1   MSEKNDLQVTYVTINEDHLGQRIDNFLITHLKGVPKSAIYKLLRKGEVRVNKKRIK-PVY 59

Query: 53  NVMSTDHIEVDGVPLRKAER--------------------TRLWLYHKPIGLVTTHSDPD 92
            +   D + +  + + + E                       L + +KP G+        
Sbjct: 60  KLQLDDVLRIAPIRVAEREEFVPSKLDKVTRLENDILFEDKYLIVINKPSGMAVHGGSGL 119

Query: 93  GRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVR 148
               +     L      +  V RLD +T G LL+     +   L   L      + Y   
Sbjct: 120 SYGLIEALRALRPEERSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWAL 179

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------- 195
             GQ D      + +G+    +  G+  V +D  +G  +     + E             
Sbjct: 180 VEGQWDSKT-KNVTEGLRKNTLKSGERVVRVDNTEGKPSHTRFKVLERFNDCSLVQASPV 238

Query: 196 -GKNREIK 202
            G+  +I+
Sbjct: 239 TGRTHQIR 246


>gi|310820148|ref|YP_003952506.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|309393220|gb|ADO70679.1| Pseudouridine synthase, RluA family [Stigmatella aurantiaca
           DW4/3-1]
          Length = 304

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 85/254 (33%), Gaps = 59/254 (23%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           IV    + +R+ K +++   G+ S     ++IAQ  V++ G   +     +   + IE+ 
Sbjct: 2   IVAREASGERLDKHLSKHVPGL-SLERARQLIAQGNVRIRGKKCQ-PTRKLWGGEEIELS 59

Query: 64  ----------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS- 106
                           G+P+   +   + +  KP+GLV       G  +V + L +    
Sbjct: 60  LPPPRVPQGTAAVEGPGLPVLHDDPDMVIV-DKPVGLVV--EPGGGAPSVVELLAAQRPP 116

Query: 107 -------RVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                  R   V RLD  T G L+   T+    A        +  + Y     G+  + +
Sbjct: 117 FDVEGVARPGVVHRLDRETSGCLMFARTDAAAAALDQAFQQKRVDKRYWTLVLGETPEHE 176

Query: 158 LNLLKKGIVIQGI----CYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNR 199
                    ++G          + T   +    A ++  +RE              G+  
Sbjct: 177 --------RLEGPYGRDPQDPRKFTTRVKSARRAALSFEVRERLRGATLLEVRLETGRTH 228

Query: 200 EIKKVFEFFNWKVN 213
           +I+       + V 
Sbjct: 229 QIRVQLSEAGFPVL 242


>gi|148998774|ref|ZP_01826211.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP11-BS70]
 gi|168576962|ref|ZP_02722796.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|307068624|ref|YP_003877590.1| 23S RNA-specific pseudouridylate synthase [Streptococcus pneumoniae
           AP200]
 gi|147755335|gb|EDK62385.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP11-BS70]
 gi|183577335|gb|EDT97863.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae MLV-016]
 gi|306410161|gb|ADM85588.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus
           pneumoniae AP200]
          Length = 291

 Score = 54.0 bits (129), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 TYVSRLKQFSNKTSLARCKLKTGRTHQIR 231


>gi|289167119|ref|YP_003445386.1| 23S_rRNA pseudouridine synthase [Streptococcus mitis B6]
 gi|288906684|emb|CBJ21518.1| 23S rRNA pseudouridine synthase [Streptococcus mitis B6]
          Length = 291

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/149 (17%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYVGQTCYVVHRLDMETSGLILFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G ++  +L           +  K+ +  +     +
Sbjct: 143 PFILPILNRLLEKKKISREYWALVDGNINSKELVFRDKIGRDRHDRRKRVVDTKNGQSAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             ++   Q     + V   L+ G+  +I+
Sbjct: 203 THISRLKQFPNKTSLVRCKLKTGRTHQIR 231


>gi|255321251|ref|ZP_05362417.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SK82]
 gi|262380064|ref|ZP_06073219.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SH164]
 gi|255301805|gb|EET81056.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SK82]
 gi|262298258|gb|EEY86172.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           radioresistens SH164]
          Length = 312

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 42/246 (17%), Positives = 85/246 (34%), Gaps = 64/246 (26%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D + V 
Sbjct: 15  VDEHQAGQRIDNFLFSRLKGVPKSR--IYRLIREGQVRVNKKRIK-AESKLAIGDQVRVA 71

Query: 63  -------DGVPLRKAERTR-------------LWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                  D  P+  +++               L + +KP G+        G    +  + 
Sbjct: 72  PIRFEPKDETPVPVSDKVAQGLLSRVIYEDEGLMVVNKPSGIAV----HGGSGVAYGLIE 127

Query: 103 S-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV-- 153
                     +  V R+D +T GL++++    + + L   L   +  + Y     GQV  
Sbjct: 128 GLRAATGKKYLELVHRIDRDTSGLVMISKKRSVLKTLQDLLREHKIKKTYAAIVKGQVSL 187

Query: 154 DQDKLNL------LKKGIVIQGICYGDMQVTLDTQKGSNAW------VTVGLR-----EG 196
           DQ  ++       L  G          ++V+ + +     W      +   L       G
Sbjct: 188 DQQLIDAPLYRYELANG-------ERRVRVSKEGKDSKTQWNVAERFMHATLVYASPLSG 240

Query: 197 KNREIK 202
           +  +I+
Sbjct: 241 RTHQIR 246


>gi|134301061|ref|YP_001114557.1| RluA family pseudouridine synthase [Desulfotomaculum reducens MI-1]
 gi|134053761|gb|ABO51732.1| pseudouridine synthase, RluA family [Desulfotomaculum reducens
           MI-1]
          Length = 320

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/226 (13%), Positives = 69/226 (30%), Gaps = 48/226 (21%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R+++++  ++ + +NG  +      + + D + +              G      E  
Sbjct: 51  SGRKIQKLTRRKGILLNGKTVY-LQKKLNAEDTLSILDLEDTNYGVQPEKGAIEVLYEDD 109

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            L + +KP   +   +    R T+ + L     +      +  V RLD  T G ++   D
Sbjct: 110 FLLVLNKPAHQLVHPTGQTTRGTMANYLAYYLKQRNVVSAIRPVHRLDRETSGCVIFAKD 169

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                +LE    +    R Y     G V          G +      G      + +  +
Sbjct: 170 SRSQFILEQQLKERTLKRTYWALVKGIVHPP------SGTI--DAPIGPHPSLANRRAIN 221

Query: 186 N------------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
                              + + + L  G+  +I+       + + 
Sbjct: 222 EHGEQSITHYQTLRSFPEISLLKLNLDTGRTHQIRLHLAHLGYPII 267


>gi|312130454|ref|YP_003997794.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
 gi|311907000|gb|ADQ17441.1| pseudouridine synthase [Leadbetterella byssophila DSM 17132]
          Length = 250

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/197 (16%), Positives = 61/197 (30%), Gaps = 38/197 (19%)

Query: 62  VDGVPLRKAERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTE 119
           +D   L   E     + +KP   V +  +   D   ++       +  +    RLD  T 
Sbjct: 13  LDIKDLVIFENEHYVVINKPP-FVPSLDERTADKSLSILKLAREAYGDIQLCHRLDKETS 71

Query: 120 GLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ- 176
           G L+L  +    R L +     +  + Y    +G  D D +     G+ +      D   
Sbjct: 72  GALVLAKNPEAYRNLAMQFEHREVQKEYHAVVNGAHDFDSI-----GVFLPIAILKDGTA 126

Query: 177 VTLDTQKGS--------------NAWVTVG-LREGKNREIKKVFEFFNWKVNRLIRISYG 221
           V +D QKG               +  V    +  G+  +I+      + +          
Sbjct: 127 VRIDRQKGKLAETIFFTLQKFQRHTLVRCVPIT-GRMHQIR-----VHLQCLN------A 174

Query: 222 PFQLGTLLAGSTREVSK 238
           P        G    +S+
Sbjct: 175 PIVCDPTYGGDYIFLSQ 191


>gi|188995238|ref|YP_001929490.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas gingivalis ATCC 33277]
 gi|188594918|dbj|BAG33893.1| putative ribosomal large subunit pseudouridine synthase D
           [Porphyromonas gingivalis ATCC 33277]
          Length = 227

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 22/166 (13%), Positives = 49/166 (29%), Gaps = 23/166 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   L + +K +G +       D     TV   +   +++     +    RLD    GL+
Sbjct: 6   EDNHLIIVNKAVGEIVQGDKTGDSPLSETVKQWIKEKYAKPGKVFLGVAHRLDRPVAGLV 65

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ------------DKLNL-LKKGIVI 167
           +          L       +  +VYR     +  +            ++LN        +
Sbjct: 66  VFAKTSKALARLNNMFRDGKVQKVYRAIVKQRPPKDGDTLVHYISRNERLNKSFASVCKV 125

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +   L     +   + + L  G++ +I+         + 
Sbjct: 126 PNSKKASLSYRLLASSDNYHLLEIELHTGRHHQIRCQLAAMGCPIK 171


>gi|196035329|ref|ZP_03102734.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|195992006|gb|EDX55969.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
          Length = 307

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVRMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|134045627|ref|YP_001097113.1| RluA family pseudouridine synthase [Methanococcus maripaludis C5]
 gi|132663252|gb|ABO34898.1| pseudouridine synthase, RluA family [Methanococcus maripaludis C5]
          Length = 298

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/203 (16%), Positives = 76/203 (37%), Gaps = 34/203 (16%)

Query: 33  RMIA----QQRVKVNGILLERAAVNVMSTDHIEV---------DGVPL---RKAERTRLW 76
           +MI     ++++ VN   +      +   + + V         D   L      E   L 
Sbjct: 34  KMIKKFDKEKKIFVNSKNI-SLKSKLKENETVSVEIDCGINNIDPEKLLLCVIYEDDDLL 92

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGL 130
           +  KP  +V   +      T+ + + +         ++  V RLD++T GLL++  +   
Sbjct: 93  IVDKPKNMVVHPTKNVLSGTLANAISNHQKINNQNYKIRFVNRLDMDTTGLLIIAKNSYS 152

Query: 131 ARVLELPSTQ--WLRVYRVRFHGQVD------QDKLNLLKKGIVIQ---GICYGDMQVTL 179
            + L     +    ++Y V  +G +D      +D ++L   GI  +          +  +
Sbjct: 153 HQQLAKQMDEGILEKIYIVVVNGHLDSKEGVIEDSIDLNDDGIKRELSTFGKISKTKYKV 212

Query: 180 DTQKGSNAWVTVGLREGKNREIK 202
             +  + + + + L  G+  +I+
Sbjct: 213 IEEFNNVSVLEIKLLTGRTHQIR 235


>gi|313683666|ref|YP_004061404.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
 gi|313156526|gb|ADR35204.1| pseudouridine synthase [Sulfuricurvum kujiense DSM 16994]
          Length = 305

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 47/231 (20%), Positives = 78/231 (33%), Gaps = 44/231 (19%)

Query: 6   IVQENFTPQR---VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--I 60
           I ++ F+P R   +S  +      SR E +R+IA+ R+  NG +++      +  D   I
Sbjct: 4   ITKKLFSPVRQMALS-FLMNELGLSRSEGQRLIARGRLSQNGSVMDD-QFGFIEGDCEFI 61

Query: 61  EVDGVPLRKAERTR---LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDI 116
             +                +Y KP GL           T+ D +   F     +  R+D 
Sbjct: 62  CFEPDTRGFKPMFVANDFVIYDKPSGLSVHPHSRQSPYTLNDEIKHQFGDEANATHRIDQ 121

Query: 117 NTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
            T GL+L++       VL+         + Y     G V        +  I IQ   Y  
Sbjct: 122 ETSGLVLVSRHKKSESVLKRLFSERAITKRYLAMVKGCV--------EHPIDIQEPLYRK 173

Query: 175 --------MQVTLDTQKGSNAWVT----------VGLRE-----GKNREIK 202
                   M V +D +      V           + L E     G+  +I+
Sbjct: 174 DHPNLLISMVVKVDPKGKPAHTVINPLRYFPEHDMTLVEASPLTGRTHQIR 224


>gi|169838496|ref|ZP_02871684.1| pseudouridine synthase [candidate division TM7 single-cell
          isolate TM7a]
          Length = 44

 Score = 53.6 bits (128), Expect = 4e-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  ETGFCSRRKADELINEGRVTVNKQEAI-IGMDIKPEDVVRIDGKE 44


>gi|94992202|ref|YP_600301.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94545710|gb|ABF35757.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 223

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 64/164 (39%), Gaps = 23/164 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGL 121
           E   L + +KP G+V   S      T+ + L      + S         V R+D +T GL
Sbjct: 6   EDDALAIINKPQGMVVHPSAGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGL 65

Query: 122 LLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQ 168
           L++  T+    A   EL + + LR Y    HG            + + + +  K+ +  +
Sbjct: 66  LMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKDRKKQAVTAK 125

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 126 GKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 168


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

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 85/246 (34%), Gaps = 60/246 (24%)

Query: 10  NFTPQRVSKVI-AR---AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + +  R+ +   A     G      +++++   +++++G  ++ A   ++    + +   
Sbjct: 12  DESGMRLDRWFKAHYPGLGFG---HLQKLLRSGQIRIDGRRVK-ADTRLLMGQVVRIPPL 67

Query: 63  ------------------DGVPLRKA----ERTRLWLYHKPIGLVTT-----HSDPDGRS 95
                             D   + K     E  ++++++KP GL            D   
Sbjct: 68  PVNDMGSLPVTDKTLRGQDDEVILKKMLLYEDPKIFVFNKPAGLAVQGGSGLTRHVDSML 127

Query: 96  TVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
            V+ N      R+  V RLD  T G+L++    G A+ L     + +  + Y     G  
Sbjct: 128 RVWRNKKGEKPRL--VHRLDRETSGVLIVARSRGAAQALTTAFRTRETKKTYWALVRGVP 185

Query: 154 DQ-----------------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +                 DK+ + + G              +DT+  + +W+ +    G
Sbjct: 186 KKKQDKISTWMVKDISTQVDKMRVCEHG-EPDSYHAVSYYRVVDTRGRALSWLEMEPYTG 244

Query: 197 KNREIK 202
           +  +++
Sbjct: 245 RTHQLR 250


>gi|228990395|ref|ZP_04150360.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
 gi|228996496|ref|ZP_04156135.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|229004147|ref|ZP_04161948.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228757008|gb|EEM06252.1| Pseudouridine synthase [Bacillus mycoides Rock1-4]
 gi|228763128|gb|EEM12036.1| Pseudouridine synthase [Bacillus mycoides Rock3-17]
 gi|228768921|gb|EEM17519.1| Pseudouridine synthase [Bacillus pseudomycoides DSM 12442]
          Length = 307

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/196 (17%), Positives = 68/196 (34%), Gaps = 34/196 (17%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           + VNG   +R +  +   D ++V              G      E   + + +KP  + T
Sbjct: 47  IIVNGER-KRWSEPLAEGDKLQVHMFIQEEYGVQPEFGDLEVIFEDDHVLIVNKPAHMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
             S   G  T+ + +           +V  + RLD +T G ++    G    ++   L  
Sbjct: 106 HPSSKGGTGTLANLVAFHLQMQGVETKVRHIHRLDKDTTGGVVFAKHGIAGAIMDRLLME 165

Query: 139 TQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDM-QVTLDTQKGSN 186
               R Y     G+V + +            +  ++ + ++G       +V    +    
Sbjct: 166 RNIKRTYLALVEGKVKKKQGIIDAAIGRDRHHATRRRVSLKGDQAVTHYRVEKYFKHQDV 225

Query: 187 AWVTVGLREGKNREIK 202
             VT+ L  GK  +I+
Sbjct: 226 TLVTLQLETGKTHQIR 241


>gi|196036248|ref|ZP_03103647.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
 gi|195991223|gb|EDX55192.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus W]
          Length = 297

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 44/267 (16%), Positives = 87/267 (32%), Gaps = 50/267 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + I V             + +PL    E   + + +K   
Sbjct: 41  GAIEVNGQHA-SVRHQLQAGEEIRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 99

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L S + +      V  V RLD +T GL+L+  +      L   
Sbjct: 100 MSTIPSREHSSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSK 158

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                   R Y    HG            + +   +++++ +  +G         +D+  
Sbjct: 159 QHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSAN 218

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
                V++ L  G+  +I+         +               L  G   E+ ++ L  
Sbjct: 219 HKTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHS 266

Query: 243 -EQLGPHLLEEAQVNLDAPIYSSETLV 268
                 H + E +++  A I S    V
Sbjct: 267 TSLTFYHPILEKEMSFAAMIPSDMQEV 293


>gi|84683903|ref|ZP_01011805.1| ribosomal large subunit pseudouridine synthase A [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84667656|gb|EAQ14124.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium HTCC2654]
          Length = 215

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 61/156 (39%), Gaps = 16/156 (10%)

Query: 72  RTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
              + + +KP GL++     +     +   L + F  V+ V RLD +T G+++       
Sbjct: 18  DHEILVVNKPSGLLSVPGKGEHLADCLIARLQTAFPEVLLVHRLDRDTSGVMVFALTPHA 77

Query: 131 ARVLEL--PSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQV 177
            R L L     Q  + Y  R  G V +D     L L+       ++ +  +         
Sbjct: 78  QRHLGLQFEKRQVKKTYVARVWGDVQEDTGTVDLPLIVDWPNRPRQHVDFEKGKPAVTDW 137

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKV 212
            +  ++G+   + +  + G++ +++  + E     +
Sbjct: 138 KVLKREGATTRMRLFPQTGRSHQLRVHMLE-LGHPI 172


>gi|329920350|ref|ZP_08277082.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
 gi|328936026|gb|EGG32479.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           1401G]
          Length = 307

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/181 (17%), Positives = 60/181 (33%), Gaps = 28/181 (15%)

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRV 108
                ++   +P+    E     + +K   L+T  S  +   +V   L     P    ++
Sbjct: 78  KPNATLKFSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKI 137

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
               + RLD +T GL+L+  +             + ++ Y    HG     +L     G+
Sbjct: 138 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYHAIVHGNFSPSQLQ----GV 193

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVG-------LRE-----GKNREIKKVFEFFNW 210
           +   I   D  V    ++  K S     V        L E     G+  +I+   ++   
Sbjct: 194 IDAPIGKKDDPVKRYIMEGGKESVTKYRVIKQVAGASLVELQLFTGRTHQIRVHMQYLGH 253

Query: 211 K 211
            
Sbjct: 254 P 254


>gi|302187286|ref|ZP_07263959.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. syringae 642]
          Length = 318

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 70/207 (33%), Gaps = 38/207 (18%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAW 188
           R L   L      + Y     G      L  ++  ++   +  G+  V + D  K +   
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNW-ATALKQVRAPLMKSNLRSGERMVEVNDEGKEALTI 221

Query: 189 VTV--------GLRE-----GKNREIK 202
             V         + E     G+  +I+
Sbjct: 222 FKVLRRFGDFATMVEAKPVTGRTHQIR 248


>gi|167032492|ref|YP_001667723.1| RluA family pseudouridine synthase [Pseudomonas putida GB-1]
 gi|166858980|gb|ABY97387.1| pseudouridine synthase, RluA family [Pseudomonas putida GB-1]
          Length = 333

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 67/211 (31%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKA--------------------E 71
           R++ +  V+VN G +  +    + + D + V  V L +                     E
Sbjct: 58  RILRKGEVRVNKGRV--KPEYKIQAGDIVRVPPVRLPERDEPAPVAQGLLQRLEAAIVYE 115

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 116 DKALIVMNKPAGIAVHGGSGLSFGVIEALRQLRPDAKELELVHRLDRDTSGLLMIAKKRS 175

Query: 130 LARVL--ELPSTQWLRVYRVRFHG--QVDQDKLNL------LKKG-----IVIQGICYGD 174
           + R L   L      + Y     G     + ++N       L+ G     +  +G     
Sbjct: 176 MLRHLHAALRGDGVDKRYMALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVSDEGKEALT 235

Query: 175 MQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           +   L         V    +    G+  +I+
Sbjct: 236 LFRVLRRFGEFATIVEARPIT---GRTHQIR 263


>gi|329729823|gb|EGG66216.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU144]
          Length = 284

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 31/173 (17%), Positives = 57/173 (32%), Gaps = 19/173 (10%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS 110
            S + I  D       E   L + +KP       S      +    V         ++  
Sbjct: 64  PSENLIPYDKELEVIYEDAYLIIVNKPQMQNCAPSREHPHGSLVEQVLAYYTKKGEKINP 123

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNL--- 160
             V RLD NT GL++    G +  +      +  + Y    +G      V ++ +     
Sbjct: 124 HIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFK--KEYVALAYGHTQSSGVIEEPIARRSD 181

Query: 161 --LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             +K+ +  +G  Y         Q  + +   V L  G+  +I+  FE+    
Sbjct: 182 SIIKREVNDKG-KYAKTVYQRLMQNETASLCKVKLLTGRTHQIRVHFEYIGHP 233


>gi|228470977|ref|ZP_04055822.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
 gi|228307374|gb|EEK16388.1| ribosomal large subunit pseudouridine synthase family protein
           [Porphyromonas uenonis 60-3]
          Length = 228

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/194 (17%), Positives = 56/194 (28%), Gaps = 49/194 (25%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   L + +KP G++       D      V   L   + +     V    R+D  T G +
Sbjct: 9   EDNHLLIVNKPAGMLVQGDSTGDTPLSELVERYLIDKYDKPGRAFVGVTHRIDRPTSGAV 68

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ---- 176
           L          L       +  +VY     G   Q            + + Y + +    
Sbjct: 69  LFAKTSKALARLNAMFQRREIHKVYHAVVCGAFPQKAGEA-------KNLLYRNRKQNKS 121

Query: 177 --VTLDTQKGSNAWVT--------------VGLREGKNREIKKVFEFFNWKVNRLIRISY 220
             VT    +   AW+T              V L  G++ +I+       + +        
Sbjct: 122 YVVTEPHAEAKRAWLTYERLSVGDRYSLLAVTLHTGRHHQIRTQLSHMGYPIK------- 174

Query: 221 GPFQLGTLLAGSTR 234
                G L  G+ R
Sbjct: 175 -----GDLKYGAPR 183


>gi|256851497|ref|ZP_05556886.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 27-2-CHN]
 gi|260660920|ref|ZP_05861835.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 115-3-CHN]
 gi|282931931|ref|ZP_06337399.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|297206310|ref|ZP_06923705.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
 gi|256616559|gb|EEU21747.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 27-2-CHN]
 gi|260548642|gb|EEX24617.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii 115-3-CHN]
 gi|281303947|gb|EFA96081.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|297149436|gb|EFH29734.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           jensenii JV-V16]
          Length = 297

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/167 (16%), Positives = 55/167 (32%), Gaps = 30/167 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------ISVGRLDINTEG 120
           E     + +KP  +++  S  + +  V + +   F++             V RLD +T G
Sbjct: 84  ETDNYLVINKPAAVLSIPSRYEDKDAVVNRVMGYFAKKKSSEQAFLKPHIVTRLDRDTSG 143

Query: 121 LLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLLKKGIV------IQG---- 169
           L+L+  +               ++ Y    HG  + +     +KG++      I      
Sbjct: 144 LVLVGKNAVAHSKFSELKKDVFVKEYHAIVHGNFNSEH----QKGLITAPIGKIDDSVKR 199

Query: 170 -----ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                      Q  +  QK   + V + L  G+  +I+         
Sbjct: 200 YVTPNGQKSVTQYEVLAQKDDASLVKLRLFTGRTHQIRVHMAHIGHP 246


>gi|162148037|ref|YP_001602498.1| ribosomal large subunit pseudouridine synthase D [Gluconacetobacter
           diazotrophicus PAl 5]
 gi|161786614|emb|CAP56196.1| putative ribosomal large subunit pseudouridine synthase D
           [Gluconacetobacter diazotrophicus PAl 5]
          Length = 295

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/218 (18%), Positives = 70/218 (32%), Gaps = 41/218 (18%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA------------- 70
           G  SR  V+ ++    V  +G +L   A  V +    E+   P   A             
Sbjct: 3   GTLSRSRVKALMEGGHVLRDGHVLREPADPVRAGLCYEIRMPPAIPATPRAQAIPFAILY 62

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRLDINTEG 120
           E + L +  KP GLV   +  +   T+ + L +             R   V RLD +T G
Sbjct: 63  EDSDLIVLDKPAGLVVHPAPGNEDGTLVNALLAHCGDSLTGIGGERRPGIVHRLDKDTSG 122

Query: 121 LLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD-------------KLNLLKKGI 165
           ++++         L     +    R Y     G +                    +   +
Sbjct: 123 VMVVAKTEQAHTALSDAFAARDIDRTYLALAWGILSPASGTFEGAIGRDRRDRKRMA--V 180

Query: 166 VIQGICYG-DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           V  G  +      TL +  G  + V   L  G+  +I+
Sbjct: 181 VTHGGKHAMTHYRTLHSFHGGISSVECRLATGRTHQIR 218


>gi|169614099|ref|XP_001800466.1| hypothetical protein SNOG_10184 [Phaeosphaeria nodorum SN15]
 gi|160707276|gb|EAT82519.2| hypothetical protein SNOG_10184 [Phaeosphaeria nodorum SN15]
          Length = 474

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 52/148 (35%), Gaps = 27/148 (18%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-------------RLWLY 78
           E+ I + RV VNG  +      + + D I      L + E                L + 
Sbjct: 86  EKAIVEGRVVVNGQPVPSTKTTIKNGDIIS---HTLHRHEPPCTATPIGIVHEDDNLIVI 142

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G+    +     +++ + L +            RLD  T G++ +   G   +  E
Sbjct: 143 NKPAGMPVHPAGRYNFNSIIEILRADRGYGWNPLPCNRLDRLTSGIMFI---GKHRQAAE 199

Query: 136 LPSTQ-----WLRVYRVRFHGQVDQDKL 158
             S Q       + Y  R  G+  + ++
Sbjct: 200 DMSAQIRTRTVKKEYITRVAGEFPEGEV 227


>gi|145224223|ref|YP_001134901.1| RluA family pseudouridine synthase [Mycobacterium gilvum PYR-GCK]
 gi|315444557|ref|YP_004077436.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           Spyr1]
 gi|145216709|gb|ABP46113.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           gilvum PYR-GCK]
 gi|315262860|gb|ADT99601.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium sp.
           Spyr1]
          Length = 309

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 83/250 (33%), Gaps = 40/250 (16%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM---- 55
           M  +++ V +     RV   +AR    SR     +  +  V ++G    ++   V     
Sbjct: 1   MTTRSMPVPDGLAGMRVDAGLARLLGLSRTAAAAIAEEGGVDIDGAPAAKSDKLVAGAWL 60

Query: 56  -----------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
                          ++++G+ +  ++   +    KP G+    +      TV   L   
Sbjct: 61  EVRLPPPPAPVENTPVDIEGMGILYSDDD-IVAVDKPPGVAAHATVGWHGPTVLGGLAAA 119

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                   I  R   V RLD+ T G++++        VL+    Q    + Y     G  
Sbjct: 120 GFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVEKRYHALVQGHP 179

Query: 154 DQD--KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +V  G        TL+  + + + + + L  G+  +I+
Sbjct: 180 DPSSGTIDAPIGRHRGHDWKFAVVEDGRHSITHYDTLEAHQAA-SLLDIELETGRTHQIR 238

Query: 203 KVFEFFNWKV 212
             F   +   
Sbjct: 239 VHFAALHHPC 248


>gi|74316828|ref|YP_314568.1| ribosomal large subunit pseudouridine synthase D [Thiobacillus
           denitrificans ATCC 25259]
 gi|74056323|gb|AAZ96763.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC
           25259]
          Length = 318

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/164 (20%), Positives = 64/164 (39%), Gaps = 24/164 (14%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--- 70
           R+ + ++      SR  ++  I  +++ V+        + V   + + V   P   A   
Sbjct: 26  RLDQALSALLPEFSRNRIQNWIRARKIVVDDAWGTT-KMKVSGGESVRVQVEPDPGATPD 84

Query: 71  -----------ERTRLWLYHKPIGLV----TTHSDPDGRSTVFDNLPS--IFSRVISVGR 113
                      E + L + +KP+GLV    + + D    + +   +P      R   V R
Sbjct: 85  APEAIPLDVVYEDSMLLVINKPVGLVVHPGSGNRDGTLLNALLHRVPQVAELPRAGIVHR 144

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQ 155
           LD +T GLL++         L  +L +    R Y    +G+VD+
Sbjct: 145 LDKDTSGLLVVAKTLRAHTDLVRQLQARTVKREYLALVYGEVDR 188


>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 = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 42/261 (16%), Positives = 81/261 (31%), Gaps = 56/261 (21%)

Query: 3   DKNIVQENFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
            + +V  +    R+ +     + + G A+   V R     +++V+G         ++   
Sbjct: 11  RQFVVGRDDDGVRLDRWFKRHLPQVGFAT---VSRWARTGQIRVDGKRA-DVDTRLVPGQ 66

Query: 59  HIEV----------DG---------------VPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
            + V           G                 +   +     + +KP GL T       
Sbjct: 67  TLRVPPGGTQAPGSRGPRTRKPLTEEEMALAERIVLTQDRAAIVLNKPPGLATQGG-SGT 125

Query: 94  RSTVFDNLP----SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRV 147
            S V   L         R   V RLD +T G+LL+    G A       +     ++Y  
Sbjct: 126 HSHVDGLLDAYAGDNDPRPRLVHRLDKDTSGVLLIARTPGSAAYFSRHFSGRSAKKIYWA 185

Query: 148 RFHG--QVDQDKLNL-LKK-----GIVI------QGICYGDMQVTLDTQKGSNAWVTVG- 192
              G  +++   ++L L K     G  +      +G         +D      AWV +  
Sbjct: 186 LVMGIPEINDGYIDLPLAKQPGTGGEKMMVDESGEGQTARTRYRVIDRAGNRAAWVELQP 245

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           L  G+  +++         + 
Sbjct: 246 LT-GRTHQLRVHMAAIGHPIV 265


>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 = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/229 (13%), Positives = 70/229 (30%), Gaps = 38/229 (16%)

Query: 16  VSKVIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEV----DGVPL 67
           +   +   G       +R+I     Q  + VNGI        +   D I++    +   +
Sbjct: 14  LENFLRNRGF-----SKRLIRIYKWQGEILVNGIK-SNVKRILQPGDVIDLILPENDSNI 67

Query: 68  RKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGR 113
                      E   + + +KP  +V   +      T+ + +   F        +  V R
Sbjct: 68  APEKLDLDICYEDEEILIVNKPANMVVHPTKGYQSGTLANGVAWYFKDKGLKALIRPVNR 127

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLL------KKGIV- 166
           LD  T GL++      +   L        ++Y     G+++ +    L      + GI  
Sbjct: 128 LDRGTSGLVVFAKLPFMQYYL-QIVKPMSKLYFAVVEGKMEGEGRINLPISRKPQSGIER 186

Query: 167 --IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +          +       + + V +  G+  +I+         + 
Sbjct: 187 MVSEEGDRAITNYKVVKSSERFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|121534494|ref|ZP_01666317.1| hemolysin A [Thermosinus carboxydivorans Nor1]
 gi|121306987|gb|EAX47906.1| hemolysin A [Thermosinus carboxydivorans Nor1]
          Length = 268

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++ + G+AS RE  +  I    V+V+G  +++A   V     I V G  +  
Sbjct: 1  MPKERLDVLLVKRGLASSRERAKAWIMAGLVRVDGQRVDKAGAMVPLMADIVVTGDNIGY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|28316862|gb|AAO39454.1| RH45372p [Drosophila melanogaster]
          Length = 739

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 56/307 (18%), Positives = 109/307 (35%), Gaps = 46/307 (14%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 334 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPA 393

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 394 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 453

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-----------DTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G+ +
Sbjct: 454 RQVEKEYICRVEGVFPDGIVE-CKEPIEVVSYKIGVCKVSAKGKDCTTTFQKLSQNGTTS 512

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR--L--IRISYGPF--QLGTLLAGSTREVSKKI 240
            V    L  G+  +I+   ++  + +    L    + +GP   + G +  G +    +++
Sbjct: 513 VVLCKPLT-GRMHQIRVHLQYLGYPILNDPLYNHEV-FGPLKGRSGDIG-GKS---DEEL 566

Query: 241 LREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +R+ +  H  E       + D  ++ S     DR ++ SE          + S  +G   
Sbjct: 567 IRDLINIHNAENWLGIDCDSDISMFKSTKDEADRESLSSEHTSVV-----HHSDDDGCVN 621

Query: 298 QKKLATP 304
            ++   P
Sbjct: 622 SRETTPP 628


>gi|24583445|ref|NP_723592.1| RluA-1, isoform A [Drosophila melanogaster]
 gi|24583447|ref|NP_723593.1| RluA-1, isoform B [Drosophila melanogaster]
 gi|24583449|ref|NP_723594.1| RluA-1, isoform C [Drosophila melanogaster]
 gi|22946167|gb|AAF52959.2| RluA-1, isoform A [Drosophila melanogaster]
 gi|22946168|gb|AAF52960.2| RluA-1, isoform B [Drosophila melanogaster]
 gi|22946169|gb|AAN10755.1| RluA-1, isoform C [Drosophila melanogaster]
 gi|206725570|gb|ACI16540.1| FI04540p [Drosophila melanogaster]
          Length = 739

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 56/307 (18%), Positives = 109/307 (35%), Gaps = 46/307 (14%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 334 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPA 393

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 394 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 453

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-----------DTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G+ +
Sbjct: 454 RQVEKEYICRVEGVFPDGIVE-CKEPIEVVSYKIGVCKVSAKGKDCTTTFQKLSQNGTTS 512

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR--L--IRISYGPF--QLGTLLAGSTREVSKKI 240
            V    L  G+  +I+   ++  + +    L    + +GP   + G +  G +    +++
Sbjct: 513 VVLCKPLT-GRMHQIRVHLQYLGYPILNDPLYNHEV-FGPLKGRSGDIG-GKS---DEEL 566

Query: 241 LREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +R+ +  H  E       + D  ++ S     DR ++ SE          + S  +G   
Sbjct: 567 IRDLINIHNAENWLGIDCDSDISMFKSTKDEADRESLSSEHTSVV-----HHSDDDGCVN 621

Query: 298 QKKLATP 304
            ++   P
Sbjct: 622 SRETTPP 628


>gi|224476102|ref|YP_002633708.1| putative pseudouridylate synthase [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222420709|emb|CAL27523.1| putative pseudouridylate synthase [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 294

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 29/192 (15%), Positives = 56/192 (29%), Gaps = 32/192 (16%)

Query: 46  LLERAAVN-----VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +++          V     I+V        E        K        S      ++ + 
Sbjct: 56  VVKLPDEQASENLVPDYQPIDV------LFEDQYFIAVSKGKKQNCAPSREHPHGSLIEQ 109

Query: 101 LPSIFSRV----------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFH 150
           +                   V RLD +T G++L    G L   +    T+  +VY    +
Sbjct: 110 VIGYLKDQAADGNYQSIPHIVTRLDRDTSGIVLFAKHGHLHHRMSS--TEMKKVYHCICN 167

Query: 151 GQV---DQDKLNLLKKGIVI------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           G++    +    +++ G  I      Q   Y                  V L  G+  +I
Sbjct: 168 GKLENTSKIVAPIMRAGDSIIERKVDQAGKYAATSYQPINASEQYTLCEVRLHTGRTHQI 227

Query: 202 KKVFEFFNWKVN 213
           +  F++ N  + 
Sbjct: 228 RVHFQYINHPIV 239


>gi|163745572|ref|ZP_02152932.1| ribosomal large subunit pseudouridine synthase C [Oceanibulbus
           indolifex HEL-45]
 gi|161382390|gb|EDQ06799.1| ribosomal large subunit pseudouridine synthase C [Oceanibulbus
           indolifex HEL-45]
          Length = 348

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 26/154 (16%), Positives = 50/154 (32%), Gaps = 30/154 (19%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------------DGVPLRK- 69
           +E+M  +  ++V+G  ++ A   + +   + V                    D   +R  
Sbjct: 34  IEKMCRKGEIRVDGGRVK-ANTRLEAGQEVRVPPLPDSAPPPPPKRTRITDADAKMIRNC 92

Query: 70  --AERTRLWLYHKPIGLV----TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
                  +   +KP GL     +  +D    +     +     +   V RLD +T G+LL
Sbjct: 93  VIYRDEHVIALNKPPGLAVQGGSGQADRHVDALSEALIFDAEEKPRLVHRLDRDTSGVLL 152

Query: 124 LTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ 155
           L      A+ L          ++Y     G    
Sbjct: 153 LARTRLAAKALTAAMRHRETRKIYWAIVAGVPTP 186


>gi|306812329|ref|ZP_07446527.1| tRNA pseudouridine synthase C [Escherichia coli NC101]
 gi|305854367|gb|EFM54805.1| tRNA pseudouridine synthase C [Escherichia coli NC101]
          Length = 260

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFARKDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|304399240|ref|ZP_07381107.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304353294|gb|EFM17674.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 259

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/168 (16%), Positives = 55/168 (32%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D   TVF        I   V +  RLD  T G+LL+     + 
Sbjct: 11  LVAVNKPSGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDKPTSGVLLMGLSSEVG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L L     Q  + Y     G ++          ++L+ +      +            
Sbjct: 71  RLLSLQFEQHQMQKTYHAVVRGWLESSGTIDYPLVEELDKIADKHATEARTAQPAVTDYQ 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ +   +   +  ++   E     G+  ++++        + 
Sbjct: 131 SLATVEMPVGIGRYPTSRYSLV--EMAPKTGRKHQLRRHMSHLRHPII 176


>gi|169846844|ref|XP_001830136.1| tRNA-pseudouridine synthase [Coprinopsis cinerea okayama7#130]
 gi|116508906|gb|EAU91801.1| tRNA-pseudouridine synthase [Coprinopsis cinerea okayama7#130]
          Length = 583

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/196 (17%), Positives = 67/196 (34%), Gaps = 29/196 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR---KAERTRLWLYHKPI 82
           +      VNG +       +   D IE         V   P+R   + +     +  KP 
Sbjct: 106 LESGVTTVNGQVA-SPTTILKDGDRIENVVHRHEPPVTDTPVRILHRDDEREFIVVDKPG 164

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
            +    S    ++T+ + L   F   +     RLD  T GL+++      AR L    T 
Sbjct: 165 SIPVHASGRYYKNTLIEILVHDFGIKKCYPANRLDRLTSGLMIMPLSPERARTLTEEFTA 224

Query: 141 --WLRVYRVRFHGQVDQDKL---NLL-----KKGIVI---QGICYGDMQVTLDTQKGSN- 186
               + Y  R  G+  +  +     L     + G+ I    G     +   +   + +N 
Sbjct: 225 GTVKKEYVARVKGKFPEGSVVCEQPLLTVDRQMGLNIVHPDGKPAKTVFTLIRYDENTNS 284

Query: 187 AWVTVGLREGKNREIK 202
           + V      G++ +++
Sbjct: 285 SVVKCEPHTGRSHQLR 300


>gi|330830764|ref|YP_004393716.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805900|gb|AEB51099.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 257

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/170 (20%), Positives = 60/170 (35%), Gaps = 33/170 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           L   +KP GL+   S  D   T F      D +   +  V  V RLD  T G+LL   D 
Sbjct: 23  LVAVNKPSGLLVHRSWLDKGETRFAMQMTRDLIGGRY--VYPVHRLDRPTSGVLLFALDP 80

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM-- 175
            +AR L       Q  + Y     G   +         ++L+ +   +        D   
Sbjct: 81  VIARALTEAFTQRQVHKEYLALVRGWAPEQGVIDYPLKEQLDKIADAMSNPDRPAQDAVT 140

Query: 176 ------QVTLD---TQKGSNAWVTVG-L--REGKNREIKKVFEFFNWKVN 213
                 QV L    ++K   +  ++  L  + G+  ++++  +     + 
Sbjct: 141 TFRRLHQVELPHAVSKKHPTSRYSLVRLFPKTGRKHQLRRHMDHLFHPIV 190


>gi|315931284|gb|EFV10253.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 327]
          Length = 281

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      I    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALAHGKIEENFIVD--KAINLTKNYDDIKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>gi|228944990|ref|ZP_04107351.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
 gi|228814659|gb|EEM60919.1| Pseudouridine synthase [Bacillus thuringiensis serovar monterrey
           BGSC 4AJ1]
          Length = 307

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVRMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEEYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|194434667|ref|ZP_03066921.1| tRNA pseudouridine synthase C [Shigella dysenteriae 1012]
 gi|194417064|gb|EDX33179.1| tRNA pseudouridine synthase C [Shigella dysenteriae 1012]
 gi|332089085|gb|EGI94195.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           155-74]
          Length = 260

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQYVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +      ++   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYSLVELEPKTGRKHQLRRHLAHLRHPII 176


>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 = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 12 TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + +R+  ++  +G+A SR + +R+I    V VN   +++A   V    +I + G
Sbjct: 3  SKERLDVLLFESGMAESREKAKRLIMAGVVFVNDQRVDKAGTKVDIYSNIIIKG 56


>gi|121613293|ref|YP_999742.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
 gi|218561715|ref|YP_002343494.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|112359421|emb|CAL34203.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni NCTC 11168]
 gi|121504235|gb|EAQ72031.2| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 300

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLV 147

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      +    MQ+    ++G  A     + E  
Sbjct: 148 QKEYLALAHGKIEENFIVD--KAINLTKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 201

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 202 PKINATLLLCKPLTGRQHQIR 222


>gi|163733779|ref|ZP_02141221.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           litoralis Och 149]
 gi|161392890|gb|EDQ17217.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           litoralis Och 149]
          Length = 346

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 61/184 (33%), Gaps = 40/184 (21%)

Query: 6   IVQENFTPQRVSKV------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            V E+   QR+ +       +   G   R  VE+M  +  ++V+G  ++ AA  +     
Sbjct: 8   TVGEDEGDQRLDRWFKKQFPLISQG---R--VEKMCRKGEIRVDGGRVK-AATRLEVGQQ 61

Query: 60  IEV--------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRST 96
           + +                    D   ++         +   +KP GL T       R  
Sbjct: 62  VRIPPLPDTAAPAPVARSAVSAADAKLIQSCVIYRDDHIIAINKPAGLPTQGGSGQTRHV 121

Query: 97  --VFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG 151
             + + L   F  +   V RLD +T G+LLL      A+ L          ++Y     G
Sbjct: 122 DGLSEALKFGFEDKPRLVHRLDKDTSGVLLLARTRMAAKALTTAMRHKETRKIYWALVAG 181

Query: 152 QVDQ 155
               
Sbjct: 182 VPTP 185


>gi|222054127|ref|YP_002536489.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
 gi|221563416|gb|ACM19388.1| pseudouridine synthase, RluA family [Geobacter sp. FRC-32]
          Length = 319

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 85/242 (35%), Gaps = 44/242 (18%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           M D  + V EN   +R+   IAR  +   +R  V+R++    + VNG+  +  ++ +   
Sbjct: 1   MTDIELTVPENTEAERLDSYIAR-TVETLTRAAVQRLMESGMITVNGMPPK-PSLKLKGG 58

Query: 58  DHIEV------------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           + +++            + +PL    E   L + +K  G+V      +   T+ + L   
Sbjct: 59  EQLKIAVPPPVEAGPAPENIPLEILYEDRDLVVVNKGAGMVVHPGAGNSGGTLVNALLGH 118

Query: 105 FSRVISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
            + +  +G         R+D +T G+L++  +      L          R+Y    +G  
Sbjct: 119 CTDLSGIGGELRPGIVHRIDKDTSGILVVAKNDASHLALSEQFREHSIKRIYIAIVYGSP 178

Query: 154 DQD-------------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             D                 +  G    G         +    G    + + L  G+  +
Sbjct: 179 KTDSGRLESIIGRHPVDRKRM-SGKARHGKHAVTHWRVIGRYPGM-CLIRLRLETGRTHQ 236

Query: 201 IK 202
           I+
Sbjct: 237 IR 238


>gi|74317581|ref|YP_315321.1| ribosomal large subunit pseudouridine synthase C [Thiobacillus
           denitrificans ATCC 25259]
 gi|74057076|gb|AAZ97516.1| pseudouridine synthase, RluD [Thiobacillus denitrificans ATCC
           25259]
          Length = 322

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 49/303 (16%), Positives = 91/303 (30%), Gaps = 64/303 (21%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
           + E    QR+   +         SR  + +++    V++NG  +      +   D + + 
Sbjct: 16  IDEGADDQRLDNYLMARLKGVPKSR--IYKLVRGGEVRINGGRV-DVGYRLKVGDEVRIP 72

Query: 63  ----------------DG----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                            G    +PL       L   +KP G+         R  +     
Sbjct: 73  PVRMAAPVITPATHLPQGGLRLLPLILYRDDALIALNKPAGMAVHGGSGISRGVIEQLRL 132

Query: 101 -LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD--- 154
            LP     +  V RLD  T G+LL+         L       +  + Y     G+     
Sbjct: 133 ELPEC-RYMELVHRLDRETSGVLLVALKRRALVGLHAAMRDGKIEKRYLTLVAGRWPNPL 191

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV-------TVGLRE-----GKNREIK 202
           Q     L K +  +G     ++   DT + ++             L E     G+  +I+
Sbjct: 192 QHVKLPLHKRVTEEGEKRVTVR---DTGQTAHTIFRRLRGYAEFTLLEAELKTGRTHQIR 248

Query: 203 KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIY 262
                  + +             G    G   E++K++ +  L    L  A++    PI 
Sbjct: 249 VHTSHLGFPIA------------GDDKYGDF-ELNKRLAKRGLKRMFLHAAKLAFAHPIS 295

Query: 263 SSE 265
              
Sbjct: 296 GER 298


>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 = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          QR+  ++ + G  ASR      + +  V V+G++  +   +V+   H+ +D        R
Sbjct: 11 QRLDDLLVQRGLFASRSRARDAVERGTVTVDGVIARKPGQSVLPQCHVAIDDPAQGYVSR 70

Query: 73 TRLWLY 78
            L L 
Sbjct: 71 AALKLI 76


>gi|84515664|ref|ZP_01003025.1| ribosomal large subunit pseudouridine synthase C [Loktanella
           vestfoldensis SKA53]
 gi|84510106|gb|EAQ06562.1| ribosomal large subunit pseudouridine synthase C [Loktanella
           vestfoldensis SKA53]
          Length = 351

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 27/188 (14%), Positives = 59/188 (31%), Gaps = 47/188 (25%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMS 56
             +  +   QR+ + +       RR         +E++  +  ++V+G  ++  +  +  
Sbjct: 7   RTIGPDDGDQRLDRYL-------RRLFPHLTQGRIEKLCRKGELRVDGGRVKT-STRLEV 58

Query: 57  TDHIEV-----------------------DGVPLRK---AERTRLWLYHKPIGLVT---T 87
              + +                       D   ++         +   +KP GL T   T
Sbjct: 59  GQKVRIPPLPTEQEAAAAATLARHGVTKADAKLIQSCVIYRDDHIIAINKPHGLATQGGT 118

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVY 145
           ++           +     +   V RLD +T G+LLL     +A+ L          ++Y
Sbjct: 119 NTTRHVDGMAEALMFGYDEKPRLVHRLDRDTSGVLLLARTRMMAKQLTENLKHRETRKIY 178

Query: 146 RVRFHGQV 153
                G  
Sbjct: 179 WAAVAGVP 186


>gi|330718578|ref|ZP_08313178.1| pseudouridylate synthase, 23S RNA-specific [Leuconostoc fallax KCTC
           3537]
          Length = 258

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 42/199 (21%), Positives = 73/199 (36%), Gaps = 31/199 (15%)

Query: 41  KVN-G--ILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRST 96
           KVN G  I++    V       IE + +PL    E   L + +KP G+V   S      T
Sbjct: 6   KVNKGDIIVITPPKVQAT---TIEPEAIPLNIVYEDDDLLVVNKPQGMVVHPSAGHSSGT 62

Query: 97  VFDNLPSIFS--------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYR 146
           + + L             R   V R+D +T GLL++  +    + L   L + +  R+Y 
Sbjct: 63  LVNALLHHAPLSTINGEFRPGIVHRIDRDTSGLLMVAKNDTAHQALSAQLKAHKNQRIYY 122

Query: 147 VRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
               G            + + K++  K+ IV  G         +    G    + V L  
Sbjct: 123 ALVRGEFKENSGTVNAPIARHKIDRKKQAIVSDGKPAVTHFEVVQRYVGYT-LLKVRLET 181

Query: 196 GKNREIK-KVFEFFNWKVN 213
           G+  +I+  +  +    + 
Sbjct: 182 GRTHQIRVHMT-YIGHPIV 199


>gi|224370646|ref|YP_002604810.1| TruC [Desulfobacterium autotrophicum HRM2]
 gi|223693363|gb|ACN16646.1| TruC [Desulfobacterium autotrophicum HRM2]
          Length = 260

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/166 (13%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP GL+   +      T F            V  V RLD  T+G+LL   +  +A
Sbjct: 22  LVAVNKPPGLLVHRTALATHETRFALQMVRDQTQGHVFPVHRLDRPTQGVLLFARNRNMA 81

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ--------------DKLNLLKKGIVIQG-----I 170
             +     + +  + Y     G V +                   +   + I        
Sbjct: 82  TRMSHLFQTGKIQKTYLAVVRGHVKERGTIVHPLKNIKHPQDNKRINHSLKIDDAVTDYA 141

Query: 171 CYGDMQVTLDTQKGSNAWVTVG--L-REGKNREIKKVFEFFNWKVN 213
           C   +++     +       +   + + G+  ++++  +  +  + 
Sbjct: 142 CLASVELPFYVDRYPTTRYCLVALIPKTGRRHQLRRHMKHISHPIV 187


>gi|72549946|ref|XP_843613.1| hypothetical protein [Leishmania major strain Friedlin]
 gi|323364132|emb|CBZ13139.1| conserved hypothetical protein [Leishmania major strain Friedlin]
          Length = 741

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 39/122 (31%), Gaps = 22/122 (18%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS------TQWLRVYRV-RFHGQVDQDKLN 159
           R   V RLD  T G LL+      A  L          +   ++Y       +       
Sbjct: 568 RQGQVHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS----- 622

Query: 160 LLKKGIVIQGICYGDMQVTLDTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            L+  + +           + T+        K   AWV   +++GK  +I++      + 
Sbjct: 623 -LRN-VRLHDDIIDAADPKIRTRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHLASRGFP 680

Query: 212 VN 213
           + 
Sbjct: 681 IL 682


>gi|312874385|ref|ZP_07734416.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
 gi|311090151|gb|EFQ48564.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2052A-d]
          Length = 307

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 47  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 105

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 106 ADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITRLDRDTSGLVLVGKNAVAHARF 165

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  V    ++  K S     
Sbjct: 166 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPVKRYIMEGGKESVTKYR 221

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 222 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 254


>gi|257891490|ref|ZP_05671143.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
 gi|257827850|gb|EEV54476.1| pseudouridine synthase [Enterococcus faecium 1,231,410]
          Length = 285

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 32/148 (21%), Positives = 57/148 (38%), Gaps = 16/148 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 86  EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVLFAK 145

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++D+D            +  K+ +  +      
Sbjct: 146 NPFVLPILGRMLEQKMIYRRYQAIVWGEIDKDMTITNKIGRDRHDRRKRVVDDKNGQSAL 205

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             VT++        V   L  G+  +I+
Sbjct: 206 THVTVNKVLSEQTQVYCVLETGRTHQIR 233


>gi|109391494|gb|ABG33874.1| Yen4 [Yersinia sp. MH-1]
          Length = 232

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/210 (15%), Positives = 62/210 (29%), Gaps = 59/210 (28%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIE------NLYQDDHLVLINKPSGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK-------------- 157
           LD  T GL+++  +  +   L    ++    +VY     G +D D+              
Sbjct: 66  LDFGTSGLMVIARNKAINAALCQQFSRRTVTKVYSALLCGHLDNDEGVIDAAIAKDAALF 125

Query: 158 -------------------LNLLKKGIVIQGICYGDM-QVTLDTQKGSNAWVTVGLREGK 197
                              +    +   ++      + +V L  + G    + +      
Sbjct: 126 PLMSICSIRGKPARSHYRVVERFYR--ELEDGRLLPLTRVRLIPETGRTHQLRIH----- 178

Query: 198 NREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                   +     +       YG  +L  
Sbjct: 179 -------CQQLGHPILGCD--LYGGLRLPG 199


>gi|320583405|gb|EFW97618.1| DRAP deaminase, putative [Pichia angusta DL-1]
          Length = 569

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 44/279 (15%), Positives = 89/279 (31%), Gaps = 47/279 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKPIGL 84
           + + RV +N   +      + + D I          V   P++   E   L +  KP G+
Sbjct: 111 LEKGRVTIN-EKVANIDTILKNGDLISHRMHRHEPPVTSRPVKIVHEDDELVVIDKPSGI 169

Query: 85  VTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQW 141
               +     +TV F     +  +     RLD  T GL+ L  T  G    V ++   + 
Sbjct: 170 PVHPTGRYRHNTVTFILEREMGIKAHPCNRLDRLTSGLMFLGKTAAGAEKMVKQMREREV 229

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---------VG 192
            + Y  +  G+    +  + ++ +           V  +  K +              + 
Sbjct: 230 SKEYIAKVVGEFPAQREIVCEEPLRTVDPRIAFNIVDRENGKEAKTVFKRLSYDGVTSLV 289

Query: 193 LR---EGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHL 249
           +     G+  +I+   ++    +               L +      S KI     GP L
Sbjct: 290 ICKPLTGRTHQIRVHLQYLGHPIVN-----------DPLYS------SPKIW----GPSL 328

Query: 250 LEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKN 288
            + A  ++DA       + +  P      P+D   ++  
Sbjct: 329 GKGADFDIDAIAEKLSKIGKTEPATSWLHPNDDGEIQST 367


>gi|300214932|gb|ADJ79348.1| Pseudouridine synthase [Lactobacillus salivarius CECT 5713]
          Length = 295

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 34/230 (14%), Positives = 76/230 (33%), Gaps = 46/230 (20%)

Query: 22  RAGIASRREVERMIAQ-----QRVKVNGILLERAA--------VNVMSTDHIEVDG---- 64
           + GI SRR    ++A+      ++ +NG    +            V+  +    +     
Sbjct: 21  KQGI-SRR----LLAKVRYSDGKILINGKSGRKIDKIKKNDKITLVVPDEEFRRNVPPSF 75

Query: 65  VPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVIS--VGRLDI 116
           VP++   E     L  KP  + +  S      ++ + +   +       +I   V RLD 
Sbjct: 76  VPIKILYEDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQIRGYRGIIPHIVTRLDR 135

Query: 117 NTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHG-----------QVDQDKLNLLK 162
           +T G+++       A  L        +  + Y     G            + +D  +L+K
Sbjct: 136 DTSGIVIFAKH-RYAHALLDSQLKEHKISKTYTAILSGILHNNHYIIDLPIGRDSTSLIK 194

Query: 163 KGIVIQGICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWK 211
           + ++               ++   N    + L  G+  +I+    +  + 
Sbjct: 195 RKVLFSEKAKRSKTEIFVKERIRDNTLCKIKLHTGRTHQIRVHCSYLGYP 244


>gi|228932580|ref|ZP_04095460.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228827098|gb|EEM72852.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
          Length = 292

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 96  STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 154

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 155 HQQKAVKRTYEAIVHGEMVEREGTIGAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 214

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 215 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 262

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 263 SLTFYHPILEKEMSFAAMIPSDMQEV 288


>gi|324325409|gb|ADY20669.1| ribosomal large subunit pseudouridine synthase D [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 307

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 92/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELHVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFRKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGGTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++ 
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDK 298


>gi|307822685|ref|ZP_07652916.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
 gi|307736289|gb|EFO07135.1| pseudouridine synthase, RluA family [Methylobacter tundripaludum
           SV96]
          Length = 319

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 81/250 (32%), Gaps = 47/250 (18%)

Query: 5   NIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV 62
            I +EN   QR+   + AR     +  + R++ +  V+VN G +       +++ D + +
Sbjct: 16  EITEENCD-QRLDNFLIARLKGVPKSRIYRIVRKGEVRVNKGRV--DVKYRLVAGDIVRI 72

Query: 63  DGVPLRKAERTRL--------------------WLYHKPIGLVTTHSDPDGRSTV--FDN 100
             V + +                           + +KP G             +     
Sbjct: 73  PPVRVAERSEESYVPQGLQAALQQGILFEDEGFLIVNKPAGFAVHGGSGVSSGIIEGLRL 132

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK 157
           +      +  V RLD +T G L++      A  L           + Y     GQ  + K
Sbjct: 133 IRPEAHFLELVHRLDKDTSGCLIIA-KKRSALKLLHELFRDNHIHKTYLALLAGQWARKK 191

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-----VTV----GLRE-----GKNREIKK 203
           L +     +++ +  G  ++ + +Q G  A      V +     L E     G+  +I+ 
Sbjct: 192 LVVTAP--LLKNVAKGGERMVVISQSGKEAETLFRRVKLFSDSTLVEASPKTGRTHQIRV 249

Query: 204 VFEFFNWKVN 213
                   + 
Sbjct: 250 HAASLGHPIV 259


>gi|270290798|ref|ZP_06197022.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
 gi|270280858|gb|EFA26692.1| ribosomal large subunit pseudouridine synthase D [Pediococcus
           acidilactici 7_4]
          Length = 304

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 42/222 (18%), Positives = 76/222 (34%), Gaps = 36/222 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE--------------VDGVPLRKA-- 70
           SR+ V  +  ++RV VN    +  +  V + D I                D    +    
Sbjct: 29  SRKVVHFLRTERRVLVN-QRYQPVSTVVRTGDLISLTFKESDFSTPLPPFDPDSSQSPDV 87

Query: 71  --ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS----VGRLDINTEGLLLL 124
             E   L + +KP G+ T  + P    ++ + L + F++  S    V RLD  T G LL+
Sbjct: 88  LFENDDLLVVNKPAGIKTHANQPHELGSMINFLQAYFAKKDSNAYNVHRLDQWTSGALLV 147

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHGQV-DQDKLNLLKKGI--------VIQGICYG 173
             +  +  +L    +Q    R Y     G +  +     L  G+         I G    
Sbjct: 148 AKNPVVVPILSRQISQKLIQRTYLCVVEGHLKSRSGTITLPIGLDPHDQRKRQINGPGAQ 207

Query: 174 DMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  +  +    + + V L  G+  +I+         + 
Sbjct: 208 PATTHYQVVREFVERSLLRVQLATGRTHQIRVHLAALGHPIV 249


>gi|110678758|ref|YP_681765.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           denitrificans OCh 114]
 gi|109454874|gb|ABG31079.1| ribosomal large subunit pseudouridine synthase C [Roseobacter
           denitrificans OCh 114]
          Length = 346

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 35/184 (19%), Positives = 61/184 (33%), Gaps = 40/184 (21%)

Query: 6   IVQENFTPQRVSKV------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
            V E+   QR+ +       +   G   R  VE+M  +  ++V+G  ++ AA  +     
Sbjct: 8   TVGEDEGDQRLDRWFKKQFPLISQG---R--VEKMCRKGEIRVDGGRVK-AATRLEVGQQ 61

Query: 60  IEV--------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRST 96
           + +                    D   ++         +   +KP GL T       R  
Sbjct: 62  VRIPPLPDTAAPAPVARSAVSAADARMIQSCVIYRDDHIIAINKPAGLPTQGGSGQTRHV 121

Query: 97  --VFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG 151
             + + L   F  +   V RLD +T G+LLL      A+ L          ++Y     G
Sbjct: 122 DGLAEALKFGFEDKPRLVHRLDKDTSGVLLLARTRMAAKALTTAMRHKETRKIYWALVAG 181

Query: 152 QVDQ 155
               
Sbjct: 182 VPTP 185


>gi|319900985|ref|YP_004160713.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
 gi|319416016|gb|ADV43127.1| ribosomal large subunit pseudouridine synthase D [Bacteroides
           helcogenes P 36-108]
          Length = 223

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 21/166 (12%), Positives = 51/166 (30%), Gaps = 23/166 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   + + +K    +       D     TV   L   + +     +    RLD    GL+
Sbjct: 6   EDNHIIIVNKTASEIVQGDKTGDTPLSETVKQYLKEKYDKPGNVFIGVTHRLDRPVSGLV 65

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ------------ 168
           +    G     L     +++  + Y      Q  +++  L+   +  +            
Sbjct: 66  VFAKTGKALSRLNEMFKNSEVKKTYWAVVKNQPPEEEGELVNYMVRNEKQNKSYAYDKER 125

Query: 169 -GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            G     +   L  +  +   + + L+ G++ +I+         + 
Sbjct: 126 PGSKRAILHYRLIGKSQNYYLLEIDLKTGRHHQIRCQLAKIGCPIK 171


>gi|281211774|gb|EFA85936.1| pseudouridine synthase family protein [Polysphondylium pallidum
           PN500]
          Length = 530

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/138 (21%), Positives = 50/138 (36%), Gaps = 15/138 (10%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKPIGL 84
           I    +KVNG ++      + + D IE         V G P+   A    + +  KP  +
Sbjct: 191 IKLGWIKVNGKIV-SPNYKLTNKDEIEHRVHRHEPPVSGAPIHVVAVDDDVVVVDKPSSI 249

Query: 85  VTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQ 140
                     +T+   L +   ++R+  V RLD  T GLL+L      A        S  
Sbjct: 250 PIHPCGRFRHNTLIYILAAELGYNRLYGVHRLDRLTSGLLILARSPAAATKKSEAIMSGN 309

Query: 141 WLRVYRVRFHGQVDQDKL 158
             + Y  +  G+     +
Sbjct: 310 VTKRYVAQVRGRFPDGDI 327


>gi|224282575|ref|ZP_03645897.1| hypothetical protein BbifN4_01992 [Bifidobacterium bifidum NCIMB
           41171]
 gi|313139732|ref|ZP_07801925.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
 gi|313132242|gb|EFR49859.1| conserved hypothetical protein [Bifidobacterium bifidum NCIMB
           41171]
          Length = 313

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/225 (17%), Positives = 75/225 (33%), Gaps = 36/225 (16%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----W 76
           ++    SR +   +I   + +V    + ++   ++  + +E D    R            
Sbjct: 21  SKMLGISRAKAADLIESGQARVLDRAIAKSGT-LLYGETVEFDIAEERHEPEPVCLDMAI 79

Query: 77  LYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTE 119
            Y         KP+G+    S      TV  +L     R+ S G         RLD+ T 
Sbjct: 80  AYEDDDVVVVDKPVGVAAHASAGWTGPTVLGSLLKRGVRITSYGAPGRQGIVSRLDVGTS 139

Query: 120 GLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD-----------KLNLLKKGIV 166
           GL+L+       + +    ++    + Y     G + +D           K++  +  + 
Sbjct: 140 GLMLVCKSELAYKEMRRQFSEHEVVKTYHAMVQGNLKEDKATIEAPIGRAKVSDFRFCVT 199

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G         LD + G    V+V L  G+  +I+  F      
Sbjct: 200 PSGKPAVTHWDVLD-RFGEATLVSVNLETGRTHQIRVHFSSIGHP 243


>gi|169824298|ref|YP_001691909.1| putative ribosomal large subunit pseudouridine synthase [Finegoldia
           magna ATCC 29328]
 gi|167831103|dbj|BAG08019.1| putative ribosomal large subunit pseudouridine synthase [Finegoldia
           magna ATCC 29328]
          Length = 321

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 51/280 (18%), Positives = 100/280 (35%), Gaps = 56/280 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTD 58
           M+  NI   N + QRV + + +     S+  ++++I  +++KVN    E    + +    
Sbjct: 1   MRHINIDNSN-SNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVV 59

Query: 59  HIEVDGVPLRKAERTRLW-----------------LYHKPIGLVTTHSDPDGR-STVFDN 100
           +I +    + K +  +++                 L +K  G+++  ++P      + D 
Sbjct: 60  NIYLYDEVIEKYQDNKIYTADDFNLDIIYEDDDLILINKKTGVLSHAANPQDYGKNIVDM 119

Query: 101 L-----------PSIFSRVIS--VGRLDINTEGLLL--LTNDGGLARVLELPSTQWLRVY 145
           +           P+  S      V RLD NT G+++   T D            +  ++Y
Sbjct: 120 MVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFKKHEITKIY 179

Query: 146 RVRFHGQVDQDKLNLL------KKGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKN 198
                G +    ++L       K   VI       M    + +  G  + V V L  G+ 
Sbjct: 180 ETIVVGNLKDQTIDLALEKDNDKNKSVINSSGKKSMTKVWNVKNFGKYSLVNVDLLTGRT 239

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +I+      N  +        G  + G       REV+K
Sbjct: 240 HQIRAHLSHINHPI-------IGDIKYGN------REVNK 266


>gi|301052847|ref|YP_003791058.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|300375016|gb|ADK03920.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
          Length = 297

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 41  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 101 STIPSREHPSGSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 268 SLTFYHPILEKEMSFAAMIPSDMQEV 293


>gi|228944912|ref|ZP_04107274.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|229120827|ref|ZP_04250069.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           95/8201]
 gi|228662487|gb|EEL18085.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           95/8201]
 gi|228814780|gb|EEM61039.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
          Length = 292

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 96  STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 154

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 155 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 214

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 215 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 262

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 263 SLTFYHPILEKEMSFAAMIPSDMQEV 288


>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 = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 80/222 (36%), Gaps = 36/222 (16%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA---------ERTRL 75
           R  ++++I +  V VN IL+++    V   D IE+   +G               E   +
Sbjct: 53  RNFIQKIIEKGFVYVNNILIKK-NYIVKINDVIEIFLPEGKKNIIPENLKINIFYEDEYV 111

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNL-------PSIFSRVIS-VGRLDINTEGLLLLTND 127
            + +K  GLV      +   T+ + L        +I++++   V R+D  T GL+L+  D
Sbjct: 112 IIINKQSGLVVHPGKGNESMTLINGLHFYFLKKKNIYNKIPILVHRIDKGTSGLILVAKD 171

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDK-------LNLLKKGIVIQ---GICYGDM 175
             +   +          R Y     G +  +K          LK  I +       YG  
Sbjct: 172 KNILEKIYKQFYINHIKRKYITLVWGYIKNNKGTIICNIGRSLKNRIYMNVFPNGIYGKF 231

Query: 176 QVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            +T   +  +      +   L  G+  +I+   ++    +  
Sbjct: 232 SITHYKVLERFKYVTLLKCTLETGRTHQIRVHLKYIGHPILN 273


>gi|255994432|ref|ZP_05427567.1| pseudouridylate synthase [Eubacterium saphenum ATCC 49989]
 gi|255993145|gb|EEU03234.1| pseudouridylate synthase [Eubacterium saphenum ATCC 49989]
          Length = 331

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 41/256 (16%), Positives = 79/256 (30%), Gaps = 71/256 (27%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILL-----------------ERAAVNVMST 57
           R    IA A   SR +  ++     V ++GI +                   A ++    
Sbjct: 13  RADVYIAGALKISRAKAAKLCDVGSVTLDGIKISKNHRMNANDLLEISDDREAGLHQSEQ 72

Query: 58  D----HIEVDGVPLRKA---------------------ERTRLWLYHKPIGLVTTHS-DP 91
           D    HI  D V + K                      E   + +  KP GL+T    D 
Sbjct: 73  DSTGVHISSDDVEVIKVPEDNDLYNANEEGILKIGILYEDDYIIVVDKPAGLLTHAKGDK 132

Query: 92  DGRSTVFDNLPSI----------FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PST 139
               T+ D +              +R   V RLD  T G++++       + L       
Sbjct: 133 SCECTLSDKILEYTEGSLANGSGANRPGVVHRLDRGTCGVMVMAKTDTALKHLTEAFEKQ 192

Query: 140 QWLRVYRVRFHGQVDQD------KLN-------LLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +  + Y    +  + +D      K+         +  G           +  +  + G  
Sbjct: 193 EVSKEYEAIVYDNIVRDSGVITAKIERNKKNRLKMSAG---DEGREAHTEFKVIERFGKF 249

Query: 187 AWVTVGLREGKNREIK 202
            +V++ ++ G+  +I+
Sbjct: 250 TYVSLVIKSGRTHQIR 265


>gi|228926342|ref|ZP_04089415.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228833334|gb|EEM78898.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
          Length = 292

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 44/267 (16%), Positives = 87/267 (32%), Gaps = 50/267 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + I V             + +PL    E   + + +K   
Sbjct: 36  GAIEVNGQHA-SVRHQLQAGEEIRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 94

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L S + +      V  V RLD +T GL+L+  +      L   
Sbjct: 95  MSTIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSK 153

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                   R Y    HG            + +   +++++ +  +G         +D+  
Sbjct: 154 QHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSAN 213

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
                V++ L  G+  +I+         +               L  G   E+ ++ L  
Sbjct: 214 HKTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHS 261

Query: 243 -EQLGPHLLEEAQVNLDAPIYSSETLV 268
                 H + E +++  A I S    V
Sbjct: 262 TSLTFYHPILEKEMSFAAMIPSDMQEV 288


>gi|253700204|ref|YP_003021393.1| hemolysin A [Geobacter sp. M21]
 gi|251775054|gb|ACT17635.1| hemolysin A [Geobacter sp. M21]
          Length = 257

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           T +R+ K++   G+A SR   + +I   +V V+  L ++A + V     I + G PL  
Sbjct: 1  MTKERLDKLVLERGLAPSRERAKALIMAGQVVVDDHLADKAGLMVSIEAEIRLKGEPLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|49477132|ref|YP_035440.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|49328688|gb|AAT59334.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis serovar konkukian str. 97-27]
          Length = 297

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 41  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 101 STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 268 SLTFYHPILEKEMSFTAMIPSDMQEV 293


>gi|88798806|ref|ZP_01114389.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp.
           MED297]
 gi|88778569|gb|EAR09761.1| ribosomal large subunit pseudouridine synthase C [Reinekea sp.
           MED297]
          Length = 313

 Score = 53.6 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 67/229 (29%), Gaps = 58/229 (25%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------------ 74
           R+I +  V+VN    +     +   D + V   P+  AE+T                   
Sbjct: 36  RIIRKGEVRVNKKRAK-PDTKLSEGDVVRV--PPVTMAEKTIENPQPSAGLRKALDHAIV 92

Query: 75  -----LWLYHKPIGLVTTHSDPDGRSTVFDNLP------SIFSRVISVGRLDINTEGLLL 123
                L   +KP GL        G       +            +  V RLD +T G++L
Sbjct: 93  FEDSALLAVNKPSGLAV----HGGSGLKLGLIEALRAQRESEPFLELVHRLDRDTSGVVL 148

Query: 124 LTNDGGLARVLELP---STQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQ 176
           +        +L+      T+  + Y     G            LL+      G     +Q
Sbjct: 149 VAKKRKSLTLLQDEFRQKTRVRKTYWCLVKGHWPDGCSVVDAPLLRHEESASGERRVSVQ 208

Query: 177 V---------TLDTQKGSNAWVT---VGLREGKNREIKKVFEFFNWKVN 213
                      +  Q    AWV    +    G+  +I+   ++    + 
Sbjct: 209 ANGKPSRTHFRVLKQYQDCAWVEALPIT---GRTHQIRVHCQYVGCPIL 254


>gi|315641865|ref|ZP_07896857.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           italicus DSM 15952]
 gi|315482433|gb|EFU72973.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           italicus DSM 15952]
          Length = 316

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/218 (17%), Positives = 74/218 (33%), Gaps = 34/218 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKA---E 71
           R+V   +  ++ V VN  L       V + D I +              G   R +   E
Sbjct: 54  RKVRHFLRIRKNVWVNDQLA-LFHQEVRAGDRITLRLEADDYSYQPVALGQASRVSVLFE 112

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTND 127
              L L +KP G+ T  + P+   T+ +++ +       +   V RLD  T G++L   +
Sbjct: 113 DEHLLLVNKPAGIKTHPNQPNEDDTLLNDIKAYLAPKQQQAYVVHRLDKETSGVILFAKN 172

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--------- 176
             +  +L   L   +  R Y+    G++ ++     K G          +          
Sbjct: 173 PLVLPILGRLLEQKKIYRTYQAIVTGKLTKNCTIRKKIGRDRHDRRKRVIDERHGQQAVT 232

Query: 177 -VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            V +         +T  L  G+  +I+         + 
Sbjct: 233 HVQVIQVHSQTTNITCQLETGRTHQIRVHLASIGHPII 270


>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 = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 80/222 (36%), Gaps = 36/222 (16%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA---------ERTRL 75
           R  ++++I +  V VN IL+++    V   D IE+   +G               E   +
Sbjct: 52  RNFIQKIIEKGFVYVNNILIKK-NYIVKINDVIEIFLPEGKKNIIPENLKINIFYEDEYV 110

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNL-------PSIFSRVIS-VGRLDINTEGLLLLTND 127
            + +K  GLV      +   T+ + L        +I++++   V R+D  T GL+L+  D
Sbjct: 111 IIINKQSGLVVHPGKGNESMTLINGLHFYFLKKKNIYNKIPILVHRIDKGTSGLILVAKD 170

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDK-------LNLLKKGIVIQ---GICYGDM 175
             +   +          R Y     G +  +K          LK  I +       YG  
Sbjct: 171 KNILEKIYKQFYINHIKRKYITLVWGYIKNNKGTIICNIGRSLKNRIYMNVFPNGIYGKF 230

Query: 176 QVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
            +T   +  +      +   L  G+  +I+   ++    +  
Sbjct: 231 SITHYKVLERFKYVTLLKCTLETGRTHQIRVHLKYIGHPILN 272


>gi|118476779|ref|YP_893930.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196044122|ref|ZP_03111358.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225863156|ref|YP_002748534.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
 gi|118416004|gb|ABK84423.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           thuringiensis str. Al Hakam]
 gi|196024761|gb|EDX63432.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB108]
 gi|225788401|gb|ACO28618.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus 03BB102]
          Length = 297

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 41  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 101 STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 268 SLTFYHPILEKEMSFTAMIPSDMQEV 293


>gi|51473455|ref|YP_067212.1| pseudouridine synthase [Rickettsia typhi str. Wilmington]
 gi|81692307|sp|Q68XB2|RLUC_RICTY RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|51459767|gb|AAU03730.1| Pseudouridine synthase [Rickettsia typhi str. Wilmington]
          Length = 303

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/177 (19%), Positives = 59/177 (33%), Gaps = 42/177 (23%)

Query: 13  PQRVSKVIAR------AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-- 64
           P R+ K + R       G+     +E+ + Q++V VN      A + V   D I ++   
Sbjct: 10  PFRLDKYLKRLYPSLTQGV-----IEKALRQKQVTVNFQKA-EANLRVKEGDTIFINDYF 63

Query: 65  -VPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRST--VF 98
            +P+ + E                          L   +KP  L T        S     
Sbjct: 64  NLPVTQHETLVFADAEIKLAKKILTDYLIYEDDHLIAINKPASLATQGGSKINLSIDSAL 123

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
             L    +    V RLD  T GLLL+  +   +  L     +   ++ Y    +G+ 
Sbjct: 124 KYLNYQGADFKLVHRLDKETSGLLLIAKNYLSSVKLHDAFKEKLVIKKYFAITYGRP 180


>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 = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/213 (14%), Positives = 67/213 (31%), Gaps = 33/213 (15%)

Query: 32  ERMIA----QQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKA--------ERTRL 75
           +R+I     Q  + VNGI        +   D I++    +   +           E   +
Sbjct: 25  KRLIRIYKWQGEILVNGIK-SNVKRILQPGDVIDLILPENDSNIAPEKLDLDICYEDEEI 83

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGG 129
            + +KP  +V   +      T+ + +   F        +  V RLD  T GL++      
Sbjct: 84  LIVNKPANMVVHPTKRYQSGTLANGVAWYFKEKGLKALIRPVNRLDRGTSGLVVFAKRPF 143

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLL------KKGIV---IQGICYGDMQVTLD 180
           +   L        ++Y     G+++ +    L      + GI     +          + 
Sbjct: 144 MQYYL-QIIKPMTKLYFAVVEGKMEGEGRIDLPISRKPQSGIERMVSEEGDRAITNYKVV 202

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 + + V +  G+  +I+         + 
Sbjct: 203 KSSKRFSLLKVKIETGRTHQIRVHLSHIGHPIV 235


>gi|308187954|ref|YP_003932085.1| tRNA pseudouridine synthase C [Pantoea vagans C9-1]
 gi|308058464|gb|ADO10636.1| tRNA pseudouridine synthase C [Pantoea vagans C9-1]
          Length = 259

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/168 (16%), Positives = 55/168 (32%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D   TVF        I   V +  RLD  T G+LL+     + 
Sbjct: 11  LVAVNKPSGWLVHRSWLDRHETVFVMQTVRDQIGQHVFTAHRLDKPTSGVLLMGLSSEVG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L L     Q  + Y     G ++          ++L+ +      +            
Sbjct: 71  RLLSLQFEQHQMQKTYHAVVRGWLESSGTLDYPLVEELDKIADRHATEARTAQPAVTDYQ 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ +   +   +  ++   E     G+  ++++        + 
Sbjct: 131 SLATVEMPVGIGRYPTSRYSLV--EMAPKTGRKHQLRRHMSHLRHPII 176


>gi|240123126|ref|ZP_04736082.1| Pseudouridine synthase [Neisseria gonorrhoeae PID332]
 gi|260440900|ref|ZP_05794716.1| Pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268681754|ref|ZP_06148616.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID332]
 gi|291044222|ref|ZP_06569931.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
 gi|268622038|gb|EEZ54438.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID332]
 gi|291011116|gb|EFE03112.1| pseudouridine synthase [Neisseria gonorrhoeae DGI2]
          Length = 307

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      +       D ++
Sbjct: 142 EDITPIHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTKTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|254445726|ref|ZP_05059202.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
 gi|198260034|gb|EDY84342.1| pseudouridine synthase, RluA family [Verrucomicrobiae bacterium
           DG1235]
          Length = 324

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/156 (17%), Positives = 53/156 (33%), Gaps = 26/156 (16%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAERT-----------RLWL 77
           +    I   +V ++G  +   A  V +   IE+    P ++ E              + +
Sbjct: 39  KARAWIDTGKVFIDGNCVSDQAFAVAAGSRIELRMSQPKKRPEPKIPDAAIVYFDEHIVV 98

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI------------SVGRLDINTEGLLLLT 125
            +K  GL+T        +   D L + + R+              V R+D +T GL++  
Sbjct: 99  VNKAAGLMTVPHPESDETETLDRLVNDYLRIRDPDAKTNRASLGVVHRIDKDTSGLVVFA 158

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN 159
                 R L     +    R Y    HG++    + 
Sbjct: 159 RTFLAKRALSEQFRAHSIERRYLAIVHGELKAQSIR 194


>gi|163802917|ref|ZP_02196805.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. AND4]
 gi|159173324|gb|EDP58150.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. AND4]
          Length = 250

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 28/173 (16%), Positives = 59/173 (34%), Gaps = 41/173 (23%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E  ++   +KP GL++      +   ++   L   +  +  V RLD++T GL++L  +  
Sbjct: 19  EDEQILAVNKPSGLLSVPGRLAEHHDSMSSRLEKEYPEIQVVHRLDMSTSGLMVLAKNKL 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI---VIQGICYGDM-QV 177
                       L        ++Y  R  G V Q++       +   +I       + +V
Sbjct: 79  AESALKKQFQYRLTH------KIYYARVWGHVAQEEGE-----VDLPLICDWPNRPLQKV 127

Query: 178 TLDTQKGSNAWVTVGLRE-----------------GKNREIKKVFEFFNWKVN 213
             +  K S     V  RE                 G++ +++   +     + 
Sbjct: 128 CFEDGKPSKTLFQVAKREEHADGLKTTIVRLLPITGRSHQLRVHMQALGHPIV 180


>gi|59800875|ref|YP_207587.1| hypothetical protein NGO0433 [Neisseria gonorrhoeae FA 1090]
 gi|194098179|ref|YP_002001227.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|240016189|ref|ZP_04722729.1| Pseudouridine synthase [Neisseria gonorrhoeae FA6140]
 gi|240115283|ref|ZP_04729345.1| Pseudouridine synthase [Neisseria gonorrhoeae PID18]
 gi|240117570|ref|ZP_04731632.1| Pseudouridine synthase [Neisseria gonorrhoeae PID1]
 gi|268600964|ref|ZP_06135131.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID18]
 gi|268603274|ref|ZP_06137441.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID1]
 gi|59717770|gb|AAW89175.1| conserved hypothetical protein [Neisseria gonorrhoeae FA 1090]
 gi|193933469|gb|ACF29293.1| Pseudouridine synthase [Neisseria gonorrhoeae NCCP11945]
 gi|268585095|gb|EEZ49771.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID18]
 gi|268587405|gb|EEZ52081.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae PID1]
          Length = 307

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      +       D ++
Sbjct: 142 EDITPIHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTKTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|295100786|emb|CBK98331.1| Uncharacterized conserved protein, contains S4-like domain
           [Faecalibacterium prausnitzii L2-6]
          Length = 273

 Score = 53.6 bits (128), Expect = 5e-05,   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|197119918|ref|YP_002140345.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
 gi|197089278|gb|ACH40549.1| RNA pseudouridine synthase, RluA family [Geobacter bemidjiensis
           Bem]
          Length = 297

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/203 (17%), Positives = 68/203 (33%), Gaps = 32/203 (15%)

Query: 28  RREVER---MIAQQRVKVNGILLERA---AVNVMSTDH-IEV-DGVPLRKAERTRLWLYH 79
           RR ++     ++Q  V+V    ++     A+ +M  +  IE+         E       +
Sbjct: 33  RRIIDWGGCYLSQTLVRVASRTVKEGEEIALGIMEAERCIELAYKKEELLYEDKDFLAVY 92

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARV 133
           K  G  +  +    + TV   +      +        V RLD  T G++        A +
Sbjct: 93  KAAGFNSQRTPYQLKGTVEYAVECYMKSIGLRDPSRVVHRLDRGTSGVMFFPKHKQAATL 152

Query: 134 L--ELPSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
           +   L   +  + Y     G  DQ          K++  K G+ + G     +   +   
Sbjct: 153 ISNLLKDGKVQKTYWALVAGSPDQQSWKVDAPLGKVSKFKYGVALNGKPARTLFRVVGEG 212

Query: 183 KGSNAWVT---VGLREGKNREIK 202
            G  A V    +    G+  +I+
Sbjct: 213 AGVTA-VEAKPLT---GRTHQIR 231


>gi|110806543|ref|YP_690063.1| tRNA pseudouridine synthase C [Shigella flexneri 5 str. 8401]
 gi|110616091|gb|ABF04758.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
          Length = 260

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFARKDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|320333923|ref|YP_004170634.1| pseudouridine synthase [Deinococcus maricopensis DSM 21211]
 gi|319755212|gb|ADV66969.1| pseudouridine synthase [Deinococcus maricopensis DSM 21211]
          Length = 294

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 53/161 (32%), Gaps = 28/161 (17%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVISVGRLDINTEGLLLLTNDGG 129
             + +KP   +T       R  V D L           +    RLD  T G+L+LT    
Sbjct: 69  YHVLNKPPLWLTHQ--VHARFEVPDALGWARATLGEPELAPAHRLDRETSGVLILTRSSS 126

Query: 130 LA---RVLELPSTQWLRVYRVRFHGQVDQDKLN----------------LLKKGIVIQGI 170
            A     L L   +  + Y    HGQ   +++                  +++G+V  G 
Sbjct: 127 AARGFHRLFL-DRRVEKTYLAIVHGQPAWEEVTLDAPLGFLGLSDTNSIRVRQGVVPDGK 185

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   +  ++G+ A +    R G+  +++         
Sbjct: 186 PAVTHF-EVLGRRGAYALLRCSPRTGRMHQLRAHLAHLGHP 225


>gi|303234009|ref|ZP_07320658.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
 gi|302494934|gb|EFL54691.1| pseudouridine synthase, RluA family [Finegoldia magna BVS033A4]
          Length = 321

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 50/280 (17%), Positives = 99/280 (35%), Gaps = 56/280 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTD 58
           M+  NI   N + QRV + + +     S+  ++++I  +++KVN    E    + +    
Sbjct: 1   MRHINIDNSN-SNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVV 59

Query: 59  HIEVDGVPLRKAERTRLW-----------------LYHKPIGLVTTHSDPDGR-STVFDN 100
           +I +    + K +  +++                 L +K  G+++  ++P      + D 
Sbjct: 60  NIYLYDEVIEKYQDNKIYTADDFNLDIIYEDNDLILINKKTGVLSHAANPQDYGENIVDM 119

Query: 101 L-----------PSIFSRVIS--VGRLDINTEGLLL--LTNDGGLARVLELPSTQWLRVY 145
           +           P+  S      V RLD NT G+++   T D            +  ++Y
Sbjct: 120 MVSYLIKTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNGLFKKHEITKIY 179

Query: 146 RVRFHGQVDQDKLNLL------KKGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKN 198
                G +    ++        K   VI       M    + +  G  + V V L  G+ 
Sbjct: 180 ETIVVGNLKDQTIDFALEKDNDKNKSVINSSGKKSMTKVWNVKNFGKYSLVNVDLLTGRT 239

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
            +I+      N  +        G  + G       REV+K
Sbjct: 240 HQIRAHLSHINHPI-------IGDIKYGN------REVNK 266


>gi|283956200|ref|ZP_06373685.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
 gi|283792354|gb|EFC31138.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 1336]
          Length = 300

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYKNNPKGVEIVF-ENEDFAILEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLV 147

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      +    MQ+    ++G  A     + E  
Sbjct: 148 QKEYLALAHGKIEENFIVD--KAINLTKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 201

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 202 PKINATLLLCKPLTGRQHQIR 222


>gi|144899540|emb|CAM76404.1| ribosomal large subunit pseudouridine synthase C [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 333

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/216 (17%), Positives = 67/216 (31%), Gaps = 46/216 (21%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKAERTR------------- 74
           E+ +   +V+V+G   + A   +    HI V    +G   +     R             
Sbjct: 35  EKWLRTGQVRVDGKRAK-ANQRLSPGLHIRVPPVPEGEAPKANPENRRPAVDEKIARMLR 93

Query: 75  ---------LWLYHKPIGLV----TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
                    +   +KP G+     T   D    + +   +     R   V RLD +T G+
Sbjct: 94  DAVLYMDDDVIALNKPAGIAVQGGTGTGDKHIDAWLDALMFDRDDRPRLVHRLDKDTSGV 153

Query: 122 LLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLL--KKGIVI---- 167
           LLL  + +          S    + Y     G            L  L  + G  +    
Sbjct: 154 LLLGRSANAAAKLAAAFKSRAARKCYWALVVGVPKLRQGRIDAALAKLPGRAGEKMAVDE 213

Query: 168 -QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +G         +D      AW+ +  R G+  +++
Sbjct: 214 DEGKRAVTWYRVVDNALRKAAWLEMEPRTGRTHQLR 249


>gi|146312885|ref|YP_001177959.1| tRNA pseudouridine synthase C [Enterobacter sp. 638]
 gi|145319761|gb|ABP61908.1| Pseudouridylate synthase [Enterobacter sp. 638]
          Length = 261

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           +   +KP G +   S  D D +  V   +       V +V RLD  T G+LL+       
Sbjct: 12  IVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTVHRLDRPTSGVLLMGLSSEAG 71

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +  +          L+ +      +            
Sbjct: 72  RLLSQQFEQHQIQKRYHAIVRGWLMDEATLDYPLVEELDKIADKFARENKDPQPAVTDYR 131

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T K       +   E   G+  ++++        + 
Sbjct: 132 GLATVEMPVATGKFPTTRYGLVELEPKTGRKHQLRRHLSHLRHPII 177


>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 = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/271 (14%), Positives = 91/271 (33%), Gaps = 77/271 (28%)

Query: 4   KNIVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVM 55
           K  +  N   QR+ K +       R+ ++        + + ++ ++VNG         + 
Sbjct: 2   KIEIGPNEAGQRLDKFL-------RKLLKDVPLSAIFKALRKKDIRVNGTKQNE-KYFLQ 53

Query: 56  STDHIE-----------------VDGVPLRKA-ERTRLWLYHK-PIGLVTTHSDPDGRST 96
             D +E                 VD   ++ A E   + +  K P  LV + S+     T
Sbjct: 54  EGDVVEIKYIQSNKEDKKEKFIKVDPKRIKIAYEDENVVVIEKWPDVLVHSDSNNSEEPT 113

Query: 97  VFDNLPSIFSRVI-------------SVGRLDINTEGLLLL--TNDGGLARVLELPSTQW 141
           + D + S  +                +  RLD NT G+++   T +G  A    +   + 
Sbjct: 114 LTDYVLSYLNDKGDYIPENEITFTPAACNRLDRNTSGMVMFGKTFEGLKAINEAIREDEI 173

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGD---------------MQVTLDTQ 182
            + Y     G++        + G+    +++                     M++++   
Sbjct: 174 RKYYYALAKGKI--------RAGLYEAYILKNPETNTSKIYDTEVKNSKKISMEISIVES 225

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            G+ + + + L  G++ +I+         + 
Sbjct: 226 NGAYSLLEIHLITGRSHQIRAHLAHLGNPII 256


>gi|170717346|ref|YP_001784455.1| 23S rRNA pseudouridylate synthase C [Haemophilus somnus 2336]
 gi|168825475|gb|ACA30846.1| pseudouridine synthase, RluA family [Haemophilus somnus 2336]
          Length = 326

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/239 (15%), Positives = 79/239 (33%), Gaps = 47/239 (19%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + S D + + 
Sbjct: 17  TINEDESGQRIDNFLLAKLKSVPKSLIYRILRKGEVRVNKGRI--KPEYKLQSGDIVRIP 74

Query: 64  GVPLRKAERT---------------------RLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
            V + + E T                      L + +KP GL            +     
Sbjct: 75  PVRIAEKEHTPISKKLNKVAQLEQQIIFEDNYLLVLNKPSGLAVHGGSGLNFGAIEALRT 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDK 157
           L      +  V RLD +T G+LL+      A              + Y     G   Q  
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIA-KKRSALRSLHEQLREKTIQKEYLALVRGHW-QSH 192

Query: 158 LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
             +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 193 CKMIQAPL-LKSELTSGERIVKVSEQGKPSETKFSVEERYNNATLVKASPITGRTHQIR 250


>gi|257461315|ref|ZP_05626412.1| pseudouridine synthase [Campylobacter gracilis RM3268]
 gi|257441343|gb|EEV16489.1| pseudouridine synthase [Campylobacter gracilis RM3268]
          Length = 249

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 38/203 (18%), Positives = 67/203 (33%), Gaps = 35/203 (17%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTRL 75
           K++A     S  E + +I    V   G  +  A   +       V     P    E   +
Sbjct: 7   KLLAAQENISHNEAKALIDAGLVSARGAKIALAREMLGENTKFSVMKPAKPAIIYEDENV 66

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARV 133
              +KP  + +            +NL  I+     + RLD  T G++LL    +   A +
Sbjct: 67  LAVNKPPFMSS------------ENLEKIYK-FGLLNRLDKETSGVVLLYKNEEFREAAI 113

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICY--------------GDMQVTL 179
            E  + +  + Y     G V ++    +K G  I  I                   +V  
Sbjct: 114 AEFKNLRVKKSYIAIVKGIVSEE----MKFGEPILTIKTRSGAFSKISPNGKSAFSEVYP 169

Query: 180 DTQKGSNAWVTVGLREGKNREIK 202
               G  + V V +  G+  +I+
Sbjct: 170 LMVSGKKSLVKVRIETGRTHQIR 192


>gi|82545090|ref|YP_409037.1| tRNA pseudouridine synthase C [Shigella boydii Sb227]
 gi|81246501|gb|ABB67209.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|332091999|gb|EGI97077.1| RNA pseudouridylate synthase family protein [Shigella boydii
           3594-74]
          Length = 260

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/162 (14%), Positives = 51/162 (31%), Gaps = 27/162 (16%)

Query: 79  HKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G +   S  D D +  V   + +     V +  RLD  T G+LL+       R+L 
Sbjct: 15  NKPSGWLVHRSWLDRDEKVVVMQTVRNQIGQHVFTAHRLDRPTSGVLLMGLSSEAGRLLA 74

Query: 136 L--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM--------- 175
                 Q  + Y     G + ++          L+ +      +                
Sbjct: 75  QQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYRGLAT 134

Query: 176 -QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
            ++ + T +       +   E   G+  ++++        + 
Sbjct: 135 VEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|152971656|ref|YP_001336765.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|238896253|ref|YP_002920989.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae NTUH-K2044]
 gi|262041533|ref|ZP_06014730.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|330012185|ref|ZP_08307318.1| RNA pseudouridine synthase [Klebsiella sp. MS 92-3]
 gi|150956505|gb|ABR78535.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae MGH
           78578]
 gi|238548571|dbj|BAH64922.1| pseudouridine synthase [Klebsiella pneumoniae subsp. pneumoniae
           NTUH-K2044]
 gi|259041094|gb|EEW42168.1| tRNA pseudouridine synthase C [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|328533887|gb|EGF60555.1| RNA pseudouridine synthase [Klebsiella sp. MS 92-3]
          Length = 264

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 54/168 (32%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKL-------------NLLKKGIVIQGIC----- 171
           R+L       Q  + Y     G + ++ L             +   +    +G       
Sbjct: 71  RLLAQQFEQHQIRKRYHAIVRGWLMEEALLDYPLVEELDRIADKFAR--EDKGPQPAVTH 128

Query: 172 ---YGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                 +++ + T +   +   +   E   G+  ++++        + 
Sbjct: 129 YRGLATVEMPVATGRYPTSRYGLVELEPKTGRKHQLRRHLAHLRHPIL 176


>gi|301052930|ref|YP_003791141.1| ribosomal large subunit pseudouridylate synthase D [Bacillus
           anthracis CI]
 gi|300375099|gb|ADK04003.1| ribosomal large subunit pseudouridylate synthase D [Bacillus cereus
           biovar anthracis str. CI]
          Length = 307

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   +       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHYQMKGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEGYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDVLYGGQTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|239998629|ref|ZP_04718553.1| Pseudouridine synthase [Neisseria gonorrhoeae 35/02]
 gi|268594485|ref|ZP_06128652.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 35/02]
 gi|268547874|gb|EEZ43292.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae 35/02]
 gi|317163901|gb|ADV07442.1| hypothetical protein NGTW08_0470 [Neisseria gonorrhoeae
           TCDC-NG08107]
          Length = 307

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      +       D ++
Sbjct: 142 EDITPIHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTKTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|196037436|ref|ZP_03104747.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
 gi|196031678|gb|EDX70274.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus NVH0597-99]
          Length = 297

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 41  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 101 STIPSREHPSGSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 268 SLTFYHPILEKEMSFTAMIPSDMQEV 293


>gi|197119760|ref|YP_002140187.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           bemidjiensis Bem]
 gi|197089120|gb|ACH40391.1| ribosomal large subunit pseudouridine synthase D [Geobacter
           bemidjiensis Bem]
          Length = 319

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 78/242 (32%), Gaps = 52/242 (21%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--------- 59
           +  P+R+   I+R+    +R    R+I      VNG   ++ A+ +   +          
Sbjct: 11  DSDPERLDSFISRSVPELTRSAALRLIETGFATVNGSK-QKPALKLKGGEVVQVVVPPPT 69

Query: 60  ----------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                     IEV        E   L + +K  G+V      +   T+ + L +    + 
Sbjct: 70  PAEPQPEEIPIEV------LYEDAELVVVNKGAGMVVHPGAGNPEGTLVNALLAHCKDLS 123

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
            +G         R+D +T G L++         L          RVY    +G   +DK 
Sbjct: 124 GIGGELRPGIVHRIDKDTSGTLVVAKCDRAHNALAEQFKEHSIKRVYLALVYGSPKEDK- 182

Query: 159 NLLKKGIVIQGICYGDMQVTLD-TQKGSNAW-----------VTVGLREGKNREIK-KVF 205
             ++  I         M       ++    W           + + L  G+  +I+  + 
Sbjct: 183 GRIESTIGRHPTDRKKMSAKARHGKQAVTHWRVVARYPGITLIRLRLETGRTHQIRVHMS 242

Query: 206 EF 207
           E 
Sbjct: 243 EA 244


>gi|15903866|ref|NP_359416.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116515727|ref|YP_817230.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
 gi|15459512|gb|AAL00627.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae R6]
 gi|116076303|gb|ABJ54023.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae D39]
          Length = 291

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGKYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 231


>gi|240127829|ref|ZP_04740490.1| Pseudouridine synthase [Neisseria gonorrhoeae SK-93-1035]
 gi|268686227|ref|ZP_06153089.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-93-1035]
 gi|268626511|gb|EEZ58911.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae SK-93-1035]
          Length = 307

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      +       D ++
Sbjct: 142 EDITPIHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTKTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|299822427|ref|ZP_07054313.1| 23S rRNA pseudouridylate synthase RluD [Listeria grayi DSM 20601]
 gi|299815956|gb|EFI83194.1| 23S rRNA pseudouridylate synthase RluD [Listeria grayi DSM 20601]
          Length = 298

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 33/224 (14%), Positives = 68/224 (30%), Gaps = 43/224 (19%)

Query: 28  RREVERMI-------AQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLR----- 68
           R+ + +++          R+ VN          V S D + V       +   +      
Sbjct: 22  RKHISKLLLTAIKYHEGGRIAVNNATENVL-YRVRSGDKVSVMLPEEKQNEQLIAEHTDL 80

Query: 69  --KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEG 120
             + E   + + +KP G+ +  S      +V + +   +        V  V RLD  T G
Sbjct: 81  DIRYEDDFVIVLNKPAGMPSIPSQYHPTGSVANFIKGHYQEQNLTNAVHIVTRLDRETSG 140

Query: 121 LLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIV 166
           L+L+         L          R Y+    G +                ++++ + + 
Sbjct: 141 LMLIAKTRFAHARLSSFLQKGDLKRKYQALTMGDLANKAGYIEAPIGRDSDISIMARKVT 200

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
            +   Y      +         V + L  G+  +I+  F     
Sbjct: 201 -ETGKYAKTNYQVIASYPDFEHVDIQLETGRTHQIRVHFSHIGH 243


>gi|71083779|ref|YP_266499.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1062]
 gi|91763185|ref|ZP_01265149.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1002]
 gi|71062892|gb|AAZ21895.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1062]
 gi|91717598|gb|EAS84249.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter ubique HTCC1002]
          Length = 304

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 22/173 (12%), Positives = 58/173 (33%), Gaps = 15/173 (8%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS---IFSRV 108
           +  + ++ +  +   L         + +K  G+         ++ V     S     ++ 
Sbjct: 76  IKFVPSEEVIKENEELIIDNNDDFIVLNKSSGISVQGGTKSKKNLVDIFARSEIFQDTKP 135

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ------DKLNL 160
            SV RLD +T G+ ++      A++L       +  + Y    HG++ +      D L  
Sbjct: 136 FSVHRLDKDTSGVFIMAKHRQSAQLLTSLFRLRKVHKTYLAICHGELQKDSGEWNDDLTR 195

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKV 212
                 +  +        +  +    + V +  +  G+  +++K        +
Sbjct: 196 YDNDREV--VEKARTLYKVLDKNSICSLVEMKPIT-GRKHQLRKQLYAVGCPI 245


>gi|42524230|ref|NP_969610.1| pseudouridylate synthase, 23S RNA-specific [Bdellovibrio
           bacteriovorus HD100]
 gi|39576438|emb|CAE80603.1| Pseudouridylate synthase, 23S RNA-specific [Bdellovibrio
           bacteriovorus HD100]
          Length = 230

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/152 (17%), Positives = 54/152 (35%), Gaps = 19/152 (12%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------PSIFSRVISVGRLDINTEGL 121
            E   + + +K  G++T  +  D  +TV + L        P     V  V RLD  T G+
Sbjct: 17  HEDLDVIVGNKAAGVLTVAAKWDRDNTVHNLLNLYVRKGNPRSNKCVYVVHRLDQATTGV 76

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD------KLNLLKKGIVI-----QGI 170
           L+      +   L+      ++ Y    HG++ +        L   +  +V         
Sbjct: 77  LIFAKTEQVQHFLKDDWKSTIKTYYAIVHGKMPKKSGTITSYLEEDENYVVHSSKDSDKG 136

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                +  +  +    + + + L  GK  +I+
Sbjct: 137 KLAITEYEVLKETEKFSLLKINLLTGKKNQIR 168


>gi|19551566|ref|NP_599568.1| 23S RNA-specific pseudouridylate synthase [Corynebacterium
           glutamicum ATCC 13032]
 gi|62389214|ref|YP_224616.1| ribosomal large subunit pseudouridine synthase C [Corynebacterium
           glutamicum ATCC 13032]
 gi|21323080|dbj|BAB97709.1| Pseudouridylate synthases, 23S RNA-specific [Corynebacterium
           glutamicum ATCC 13032]
 gi|41324547|emb|CAF18887.1| RIBOSOMAL LARGE SUBUNIT PSEUDOURIDINE SYNTHASE C [Corynebacterium
           glutamicum ATCC 13032]
          Length = 294

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 47/230 (20%), Positives = 79/230 (34%), Gaps = 51/230 (22%)

Query: 15  RVSKVI-ARA-GI-ASRREVERMI----AQQRVKVNGILLERAAVNVMSTDHIE------ 61
           R+ K + A+  G+ AS      +I     +  ++VNG  +      +   D I       
Sbjct: 16  RIDKFLRAQLKGVPAS------LIFRQMRKGDIRVNGRKV-DPNYRLQEGDRIRMWQMDL 68

Query: 62  -------VDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
                  V    + KA       E   L + +KP G +  H        V + L   F +
Sbjct: 69  LADLPPPVVDKHIFKAVADSVLFEDAELLVINKPAG-IPVHGGTGHGGGVIEALRQKFPQ 127

Query: 108 ---VISVGRLDINTEGLLLLTNDG----GLARVLELPSTQWLRVYRVRFHGQVDQDK--- 157
              +  V RLD +T GLLL++        L  +L     +  R Y ++  G    D    
Sbjct: 128 ERDLELVHRLDRDTSGLLLVSKTTSVLRELQEILRDREEEIFRGYLLKVEGAWPGDLRQI 187

Query: 158 ---LNLLKKGIV--IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              L   +  +V    G+        +    G+   V   L  G+  +I+
Sbjct: 188 DVPLKRTETTVVPHSDGLRARTYFEVVKRLPGAT-LVKAQLATGRKHQIR 236


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

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 86/249 (34%), Gaps = 56/249 (22%)

Query: 5   NIVQENFTPQRVSK----VIARAGIASRREVERMIAQQRVKVNGILLER-------AAVN 53
             V+ + +  R+ +         G      +++++   +++++G  ++         ++ 
Sbjct: 7   RKVEADESGMRLDRWFKIYYPNVGFG---YLQKLLRSGQIRIDGGRVKNDMRLVVGQSIR 63

Query: 54  VMS-------------------TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
           V                      D I +    +   E +++++++KP GL         R
Sbjct: 64  VPPLFTDKKDGFPVINKTICGQDDRITL--KNILLYEDSKIFVFNKPAGLAVQGGSGLTR 121

Query: 95  STVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
                       +      V RLD  T G+L++    G A+VL     + +  + Y    
Sbjct: 122 HVDSMLEAWRNKKGEKPRLVHRLDRETSGILVVARSRGAAQVLTAAFRARETKKTYWALV 181

Query: 150 HGQV--DQDKLNL-LKKGIVIQGICYGDMQ-------------VTLDTQKGSNAWVTVGL 193
            G     QDK++  + + I  Q       +               LDT+  S +W+ +  
Sbjct: 182 RGVPRKKQDKISTWMAREITTQADKMRVCEHRQPDSNHAISYYRVLDTRGKSLSWLEMEP 241

Query: 194 REGKNREIK 202
             G+  +++
Sbjct: 242 YTGRTHQLR 250


>gi|169833510|ref|YP_001695365.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae Hungary19A-6]
 gi|168996012|gb|ACA36624.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Hungary19A-6]
          Length = 278

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLARCKLKTGRTHQIR 218


>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 = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
              R+  ++   G+  SR++ +R+I    V+V   ++++    V     IEV   P
Sbjct: 1  MAKHRLDALLVERGLCPSRQQAQRLIRAGEVRVAQAIVDKPGSLVAEDAVIEVAAKP 57


>gi|283835440|ref|ZP_06355181.1| tRNA pseudouridine synthase [Citrobacter youngae ATCC 29220]
 gi|291068616|gb|EFE06725.1| tRNA pseudouridine synthase [Citrobacter youngae ATCC 29220]
          Length = 260

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 26/168 (15%), Positives = 50/168 (29%), Gaps = 31/168 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G +  D          L+ +      +            
Sbjct: 71  RLLAQQFEHHQIQKRYHAIVRGWLMDDAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E     G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLV--ELDPKTGRKHQLRRHLAHLRHPII 176


>gi|195434112|ref|XP_002065047.1| GK15252 [Drosophila willistoni]
 gi|194161132|gb|EDW76033.1| GK15252 [Drosophila willistoni]
          Length = 532

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 68/205 (33%), Gaps = 27/205 (13%)

Query: 35  IAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPIGLV 85
           I   ++ VN  ++             NV+    + V   P+R       + + +KP  + 
Sbjct: 176 IEAGKLTVNHEIVPADYSLKHNDLLANVVHRHEVPVTAQPIRIIHMDEDIVVVNKPASIP 235

Query: 86  TTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                    +TV   L   F    + ++ RLD  T GLLL   +   AR LE      Q 
Sbjct: 236 VHPCGRYRHNTVVFILAKEFNLKDLRTIHRLDRLTSGLLLFGRNANKARELEQQIRQRQV 295

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG--------- 192
            + Y     G+     +    + I +     G  +V+   +     +  +          
Sbjct: 296 QKEYVCLVEGKFPDGIIE-CNESIEVVSYKIGVCRVSPKGKDCKTTFQRLSNVGDSSLVL 354

Query: 193 ---LREGKNREIKKVFEFFNWKVNR 214
              L  G+  +I+   ++  + +  
Sbjct: 355 CKPLT-GRMHQIRVHLQYLGYPIVN 378


>gi|148259184|ref|YP_001233311.1| RluA family pseudouridine synthase [Acidiphilium cryptum JF-5]
 gi|326402337|ref|YP_004282418.1| pseudouridine synthase [Acidiphilium multivorum AIU301]
 gi|146400865|gb|ABQ29392.1| ribosomal large subunit pseudouridine synthase C [Acidiphilium
           cryptum JF-5]
 gi|325049198|dbj|BAJ79536.1| pseudouridine synthase [Acidiphilium multivorum AIU301]
          Length = 324

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/266 (15%), Positives = 77/266 (28%), Gaps = 62/266 (23%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ + + +     ++  +++     +V+V+G     A+ ++ +   + +  VP   A +
Sbjct: 15  MRLDRFLRSLHPGLTQGAIQKFCRTGQVRVDGKRA-EASTHLAAGQAVRIPPVPETPAPK 73

Query: 73  TR-----------------------LWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFS 106
            R                       + +  KP GL T       R     +         
Sbjct: 74  PRQTVVANEWDVKELNARILHRDADVLVIDKPAGLATQGGKGIARHLDGMLDALRFDAAE 133

Query: 107 RVISVGRLDINTEGLLLLT--NDGGLARVLELPSTQWLRVYRVRFHG-QVDQD---KLNL 160
           R   V RLD +T G+L+L                    + Y     G  +  +    L L
Sbjct: 134 RPRLVHRLDRDTSGVLVLARNAFAANRLAAAFRGRDMEKTYWAIVVGLPIPMEGQIDLPL 193

Query: 161 LKKGIVIQGICYGDMQ-------------VTLDTQKGSNAWVTVG-LREGKNREIKKVFE 206
            + G   QG                     TLD      +W+ +  L  G+  +++    
Sbjct: 194 ARIG-GAQGARTRPADRDDEDAAKAITDYRTLDHAGRKFSWLELHPLT-GRTHQLRAHCA 251

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGS 232
                +            LG    G 
Sbjct: 252 AIGTPI------------LGDAPYGE 265


>gi|302380688|ref|ZP_07269153.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311631|gb|EFK93647.1| pseudouridine synthase, RluA family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 321

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 47/274 (17%), Positives = 98/274 (35%), Gaps = 55/274 (20%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEVDG 64
           + ++ + QRV + + +     S+  ++++I  +++KVN    E    + +    +I +  
Sbjct: 6   IDDSNSNQRVDRFLMKLMPKMSKNHIQKLIRTKKIKVNKKRTEPDYDLKIDDVVNIYLYD 65

Query: 65  VPLRKAERTRLW-----------------LYHKPIGLVTTHSDPDGR-STVFDNL----- 101
             + K +  +++                 L +K  G+++  ++P      + D +     
Sbjct: 66  EVIEKYQDNKIYTADDFNLDIIYEDDDLILINKKTGVLSHAANPQDYGKNIVDMMVSYLI 125

Query: 102 ------PSIFSRVIS--VGRLDINTEGLLL--LTNDGGLARVLELPSTQWLRVYRVRFHG 151
                 P+  S      V RLD NT G+++   T D            +  ++Y     G
Sbjct: 126 KTNQFKPTQNSTFTPALVNRLDRNTSGIVVGAKTYDSLKYFNDLFKKHEITKIYETIVVG 185

Query: 152 QVDQDKLNLL------KKGIVIQGICYGDMQVTLDTQK-GSNAWVTVGLREGKNREIKKV 204
            +    ++L       K   VI       M    + +  G  + V V L  G+  +I+  
Sbjct: 186 NLKDQTIDLALEKDNDKNKSVINSSGKKSMTKVWNVKNFGKYSLVNVDLLTGRTHQIRAH 245

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSK 238
               N  +        G  + G       REV+K
Sbjct: 246 LSHINHPI-------IGDIKYGN------REVNK 266


>gi|238749676|ref|ZP_04611181.1| Ribosomal large subunit pseudouridine synthase C [Yersinia rohdei
           ATCC 43380]
 gi|238712331|gb|EEQ04544.1| Ribosomal large subunit pseudouridine synthase C [Yersinia rohdei
           ATCC 43380]
          Length = 319

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 64/211 (30%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDHIEVDGVPLRKA--------ER 72
           R++ +  V+VN            G ++    V V   D I+V     + A        E 
Sbjct: 40  RIVRKGEVRVNKGRIKPEYKLADGDVVRIPPVRVAERDEIQVSAKLDKVAALADCILFED 99

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G             +     L      +  V RLD +T G+LL+      
Sbjct: 100 DYLLVLNKPSGTAVHGGSGLSFGVIEALRALRPEARFLELVHRLDRDTSGVLLVA-KKRS 158

Query: 131 ARVLELPS---TQWLRVYRVRFHG---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           A              + Y     G      +     L K I+  G     ++V+ +  K 
Sbjct: 159 ALRSLHEQLRLKGMQKDYLALVRGQWQPHCKAVQAPLLKNIMQSGERM--VKVSSEG-KP 215

Query: 185 SNAWVTVG-------------LREGKNREIK 202
           S     +              +  G+  +I+
Sbjct: 216 SETRFKIEERFEHATLVKASPIT-GRTHQIR 245


>gi|229183506|ref|ZP_04310730.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BGSC 6E1]
 gi|228599916|gb|EEK57512.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BGSC 6E1]
          Length = 292

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 96  STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 154

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 155 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 214

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 215 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 262

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 263 SLTFYHPILEKEMSFTAMIPSDMQEV 288


>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 = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ +++ + G+A +R   + +I    V+VNG+   +    V     IEV G  L    R 
Sbjct: 6  RLDQLLVQRGLAETRARAQALILAGEVRVNGVTRHKGGELVPDDAEIEVIG-ALPYVSRG 64

Query: 74 RLWLYH 79
             L H
Sbjct: 65 GYKLAH 70


>gi|114766871|ref|ZP_01445793.1| ribosomal large subunit pseudouridine synthase C [Pelagibaca
           bermudensis HTCC2601]
 gi|114540917|gb|EAU43977.1| ribosomal large subunit pseudouridine synthase C [Roseovarius sp.
           HTCC2601]
          Length = 350

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/190 (18%), Positives = 62/190 (32%), Gaps = 44/190 (23%)

Query: 14  QRVSKVIA------RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           QR+ + +       + G   R  +E+M  +  ++V+G   + AA  +     + V     
Sbjct: 16  QRLDRWLKRQFPHLQQG---R--IEKMCRKGELRVDGGRCK-AATRLEVGQQVRVPPLPE 69

Query: 63  ------------------DGVPLRKAERTR---LWLYHKPIGLVTTHSDPDGRSTVF--- 98
                             D   +R A   R   +   +KP GL         R       
Sbjct: 70  PGETPAPAAKPKATVSDADAKMIRDAVIYRDDHIIALNKPPGLPVQGGSKQERHVDGLAE 129

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD 156
                   +   V RLD +T G+LLL     +A+ L          ++Y     G     
Sbjct: 130 ALRFDYDEKPRLVHRLDKDTSGVLLLARTREIAQALTGAIRHKQTRKIYWAVVAGVPTP- 188

Query: 157 KLNLLKKGIV 166
            L  ++ G+V
Sbjct: 189 YLGEIRFGLV 198


>gi|167004717|ref|ZP_02270475.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 81-176]
          Length = 281

 Score = 53.6 bits (128), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      +    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALAHGKIEENFIVD--KAINLTKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>gi|194862300|ref|XP_001969970.1| GG10383 [Drosophila erecta]
 gi|190661837|gb|EDV59029.1| GG10383 [Drosophila erecta]
          Length = 721

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 56/316 (17%), Positives = 111/316 (35%), Gaps = 46/316 (14%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 316 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTSQPIKIVHMDEDIVVVNKPA 375

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 376 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 435

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G+ +
Sbjct: 436 RQVEKEYICRVEGVFPDGIVE-CKEPIEVVSYKIGVCKVSSKGKDCTTTFQKLSQNGTTS 494

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR--L--IRISYGPF--QLGTLLAGSTREVSKKI 240
            V    L  G+  +I+   ++  + +    L    + +GP   + G +  G +    +++
Sbjct: 495 VVLCKPLT-GRMHQIRVHLQYLGYPILNDPLYNHEV-FGPLKGRSGDIG-GKS---DEEL 548

Query: 241 LREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +R+ +  H  E       + D  ++ +     DR ++ SE          + S  +G   
Sbjct: 549 IRDLINIHNAENWLGIDCDSDISMFKNTKDEADRESLSSEHTSVV-----HHSDDDGCVN 603

Query: 298 QKKLATPVHRRNLASN 313
            ++   P      + N
Sbjct: 604 SRETTPPCTEAQQSEN 619


>gi|157414343|ref|YP_001481599.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
 gi|157385307|gb|ABV51622.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni 81116]
          Length = 281

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/201 (17%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      I    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALAHGKIEENFIVD--KAINLTKNYDDIKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>gi|309804686|ref|ZP_07698751.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
 gi|308166078|gb|EFO68296.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           09V1-c]
          Length = 274

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 42  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 100

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 101 ADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITRLDRDTSGLVLVGKNAVAHARF 160

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 161 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKNSVTKYR 216

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 217 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 249


>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 = 53.3 bits (127), Expect = 5e-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|260906535|ref|ZP_05914857.1| ribosomal large subunit pseudouridine synthase D [Brevibacterium
           linens BL2]
          Length = 307

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 46/262 (17%), Positives = 94/262 (35%), Gaps = 49/262 (18%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M +++I V E    QRV   +++    SR     + A+  V+++G ++ ++   V + + 
Sbjct: 1   MAERSILVPEGLEGQRVDSALSKLLGLSRTAAADICAEGGVQLSGQVVAKSD-RVSAGER 59

Query: 60  IEVD----------------GVPLRKAERTRLWLYHKPIGLVTTHS-DPDGRSTVFDNLP 102
           ++++                G+ +   E + + +  KP+G+    +    GR+ V     
Sbjct: 60  LDIEMPEPPRPLEVVPDPVPGMKVVHDEDSFVVV-DKPVGVAAHPALGWKGRTVVGGLAA 118

Query: 103 SIFS--------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
           + F         R   V RLD+ T GL+++        VL+    +    + Y     G 
Sbjct: 119 AGFRIATSGAPERQGIVQRLDVGTSGLMVIAKSEYAYSVLKRAFKERTVEKTYHAVVQG- 177

Query: 153 VDQDKLNLLKKGI-----------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +    L  +   I           V  G         +       + V V L  G+  +I
Sbjct: 178 LPDPVLGTIDAPIARNPRHDGLYAVHSGGKNAITHYEVLEAHRRASLVEVHLETGRTHQI 237

Query: 202 KKVFEFFNWKVNRLIRISYGPF 223
           +      ++  + L R   G  
Sbjct: 238 R-----VHF--SALKRPCVGDL 252


>gi|282881245|ref|ZP_06289932.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
 gi|281305049|gb|EFA97122.1| pseudouridine synthase, RluA family [Prevotella timonensis CRIS
           5C-B1]
          Length = 566

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 29/178 (16%), Positives = 60/178 (33%), Gaps = 26/178 (14%)

Query: 51  AVNVMSTDHI-EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--- 106
            + V +   + E         E   L +  KP G+++       R +V+  L S      
Sbjct: 335 GLKVDAEQSVAEQHSQLHVVYEDDALIVVDKPAGILSVPGRSQ-RPSVYSILRSQMPSSV 393

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QV 153
            + SV RLD+ T GLL+L  +  + R L+    +    + Y     G            +
Sbjct: 394 ELFSVHRLDMATSGLLILAKNSVVYRHLQRQFRTHHIQKEYIAILEGALSQREGVVTLPL 453

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV---GLREGKNREIKKV-FEF 207
             D  +  ++ +  +          +   +    WV +       G+  ++ ++    
Sbjct: 454 RPDPFDRPRQVVDWEHGKKAVTSYRVLNVRHGKTWVALFPET---GRTHQL-RMHCAH 507


>gi|319951753|ref|YP_004163020.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
 gi|319420413|gb|ADV47522.1| pseudouridine synthase [Cellulophaga algicola DSM 14237]
          Length = 269

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/213 (17%), Positives = 73/213 (34%), Gaps = 44/213 (20%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------GVPLRKA-----ERTRLWLYH 79
           ++ I ++ + +NGI     A  +   + I +           L        E   L + H
Sbjct: 14  KKAIKKRYITINGIAATT-ATFIQGGERISLYIPEETTASKTLIFPLKVLFEDDYLAIIH 72

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLLLLTNDGGLA 131
           KP G++ +    +   T+ + L    S        +   V RLD  T G+LL    G  +
Sbjct: 73  KPGGILVSG---NSFKTIANALTQNLSPSTLPDATKPQPVHRLDYATTGILLA---GKTS 126

Query: 132 RVL-----ELPSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +          +  + Y     G +D + +++       I       M  T+ T   S
Sbjct: 127 SSIRALNKMFEDKKVAKTYYAVTIGTMDVEGEIST-----TIDDKPSYSM-YTVITSAPS 180

Query: 186 NAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
             + T+ L +     G+  +++K        + 
Sbjct: 181 KRFGTLNLVQLDPKTGRRHQLRKHLSSIGNPIL 213


>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 (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +  R+   +   G+  SR + + ++   RV V+G    +A+  V  T ++E++G
Sbjct: 1  MSGVRLDAALVARGLVRSRAQAKELLDAGRVLVDGKAEAKASTKVSDTQNVEIEG 55


>gi|325677946|ref|ZP_08157588.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
 gi|324110500|gb|EGC04674.1| pseudouridine synthase, RluA family [Ruminococcus albus 8]
          Length = 321

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/264 (14%), Positives = 78/264 (29%), Gaps = 66/264 (25%)

Query: 6   IVQENFTPQRVSKVIA--------RAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
            + +N   QR+ K +                    + I  +R+K+NG      +  +   
Sbjct: 5   TISKNDADQRMDKFLTKAVPALPKNLLY-------KYIRLKRIKLNGKRC-EISTRLKDG 56

Query: 58  DHI--EVDGV--PLRKAERTR----------------LWLYHKPIGLVTTHSDPDGRSTV 97
           D +   ++    P ++    R                + L +KP GLV    +     T+
Sbjct: 57  DIVQLYINDEFFPEKRDAAHRFLNAPKDIEVVYEDDDVILCNKPCGLVVHEDESGESDTL 116

Query: 98  FDNL-----------PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
            D +           P            R+D NT G+++   +    R+L       +  
Sbjct: 117 IDRILHYLYDKGEYDPDSELSFTPALCNRIDRNTAGIVICAKNAESLRILNQKVKDRELE 176

Query: 143 RVYRVRFHGQV---DQDKLNLLKKGIVIQGICYGDM------------QVTLDTQKGSNA 187
           + Y     G       +     ++    + +   D             +V  + ++   A
Sbjct: 177 KKYLCVTVGVPKAKSAELKAYHRRNEQTKTVKVADKPFDGCKTMITRYKVLEENKQSGLA 236

Query: 188 WVTVGLREGKNREIKKVFEFFNWK 211
            + V L  G+  +I+         
Sbjct: 237 LLEVDLVTGRTHQIRAHLAHIGCP 260


>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 (127), Expect = 5e-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|218232731|ref|YP_002366075.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|229108847|ref|ZP_04238452.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
 gi|229149592|ref|ZP_04277824.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|218160688|gb|ACK60680.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus B4264]
 gi|228633938|gb|EEK90535.1| Pseudouridine synthase [Bacillus cereus m1550]
 gi|228674616|gb|EEL29855.1| Pseudouridine synthase [Bacillus cereus Rock1-15]
          Length = 307

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 88/261 (33%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGSIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQ-----------VDQDKLNLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+           + +D+ +  ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKKGKIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|119469426|ref|ZP_01612365.1| 23S rRNA pseudouridylate synthase [Alteromonadales bacterium TW-7]
 gi|119447290|gb|EAW28559.1| 23S rRNA pseudouridylate synthase [Alteromonadales bacterium TW-7]
          Length = 320

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 76/236 (32%), Gaps = 41/236 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + E+   QR+   +        +  + +++ +  V+VN   ++     +   D I +  
Sbjct: 13  TINEDHLGQRIDNFLITHLKGVPKSAIYKILRKGEVRVNKKRIK-PVYKLQLDDIIRIPP 71

Query: 65  VPLRKAER--------------------TRLWLYHKPIGLVTTHSDPDGRSTVFDN--LP 102
           + + + E                       L + +KP G+            +     L 
Sbjct: 72  IKVAEREEFVPSKLDKVTRLEDDILFEDKYLIVINKPSGMAVHGGSGLSYGLIEALRVLR 131

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T G LL++    +   L   L      + Y     GQ D      
Sbjct: 132 PEERNLELVHRLDRDTSGCLLISKRRSVLTSLHEQLREKTMEKNYWALVDGQWDGKT-KN 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           + +G+    +  G+  V +D  +G  +     + E              G+  +I+
Sbjct: 191 VTEGLRKNTLKSGERVVRVDNVEGKPSHTRFKVLERFNECSLVQASPVTGRTHQIR 246


>gi|91793876|ref|YP_563527.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91715878|gb|ABE55804.1| Pseudouridylate synthase [Shewanella denitrificans OS217]
          Length = 230

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 24/155 (15%), Positives = 55/155 (35%), Gaps = 19/155 (12%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++     P+   T    L  ++   I + RLD +T G+++   +      
Sbjct: 36  IIVINKPSGLLSNPGRAPETYDTAITRLQRLYPETILIHRLDCDTSGIMIFARNKKAESN 95

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLN------------LLKKGIVIQGICYGDMQVTL 179
           L+    + Q  +VY     G  +                   ++  VI+          L
Sbjct: 96  LKTQFQNRQAKKVYIAEVSGCFEHQDGKVNFPLGPDPMTPPFQQ--VIESGKPALTYYRL 153

Query: 180 DTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
              + S + V +    G+  +++  + +     + 
Sbjct: 154 LEHRASTSLVELKPHTGRTHQLRVHM-KALGHTII 187


>gi|301754896|ref|XP_002913309.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Ailuropoda melanoleuca]
          Length = 511

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 46/292 (15%), Positives = 97/292 (33%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWLYH-------K 80
           E  + + R+ +N   ++  ++ +   D     +     P+  AE  RL   +       K
Sbjct: 145 EAAVREGRLHLNEEPVQDLSIVLKDNDFLRNRVHRHEPPVT-AEPVRLLAENEDMVVVDK 203

Query: 81  PIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP- 137
           P  +          +TV   L        +  + RLD  T G+L+      ++  +    
Sbjct: 204 PSSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQV 263

Query: 138 -STQWLRVYRVRFHGQ-VDQDKLNL-------LKKGIVIQGICYGDMQVTLDTQ--KGSN 186
              Q  + Y  R  G+   ++ +          K G+          +         G +
Sbjct: 264 RDRQLEKEYVCRVEGEFPTEEVICKEPILVVSYKVGVCRVDARGKPCETVFQRLSYNGHS 323

Query: 187 AWVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI 240
           + V    +    G+  +I+   +F    +        +++GP        G   +  +++
Sbjct: 324 SVVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGP---SRGRCGHIPKTDEEL 377

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SE+  D       S+QK
Sbjct: 378 LRDLVAEHQAKQSLDVLDLCEGDLSPGLIDSTAPSSELGKDHLEELATSAQK 429


>gi|225019500|ref|ZP_03708692.1| hypothetical protein CLOSTMETH_03453 [Clostridium methylpentosum
           DSM 5476]
 gi|224947721|gb|EEG28930.1| hypothetical protein CLOSTMETH_03453 [Clostridium methylpentosum
           DSM 5476]
          Length = 299

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/204 (19%), Positives = 67/204 (32%), Gaps = 40/204 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L L +KP G     S      ++ +     +++         V RLD  T GLL +
Sbjct: 85  EDDDLLLVNKPAGTPVHPSPGHYEDSLANYSAWQYAQRREQLVFRPVNRLDRGTSGLLCV 144

Query: 125 TNDGGLARVLELPST--QWLRVYRVRFHGQVDQDK--LNL---------LKKGIVIQGIC 171
             +      L        + R+Y     G        ++L         LK+ +  QG  
Sbjct: 145 AKNAHAQARLSQQLHTGAFERIYYAVVCGAPSPAAGTIDLPIGRTPGSVLKRRVDPQGAR 204

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT---- 227
                 T+    G+   + + L  G+  +I+  F      +       +G F  GT    
Sbjct: 205 AVTHYETV-RVNGAYTLLKIRLETGRTHQIRVHFAHLGCPL-------FGDFLYGTERRD 256

Query: 228 ------LLAGSTR---EVSKKILR 242
                 L +G  R    +S + +R
Sbjct: 257 VVEGHALHSGEIRLLHPISGEEIR 280


>gi|27467615|ref|NP_764252.1| hypothetical protein SE0697 [Staphylococcus epidermidis ATCC 12228]
 gi|251810369|ref|ZP_04824842.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|282875499|ref|ZP_06284370.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|293367012|ref|ZP_06613686.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|27315159|gb|AAO04294.1|AE016746_84 conserved hypothetical protein [Staphylococcus epidermidis ATCC
           12228]
 gi|251806106|gb|EES58763.1| pseudouridylate synthase [Staphylococcus epidermidis BCM-HMP0060]
 gi|281295526|gb|EFA88049.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           SK135]
 gi|291318867|gb|EFE59239.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|329733393|gb|EGG69726.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU028]
 gi|329738101|gb|EGG74319.1| pseudouridine synthase, RluA family [Staphylococcus epidermidis
           VCU045]
          Length = 284

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 30/173 (17%), Positives = 57/173 (32%), Gaps = 19/173 (10%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS 110
            S + I  D       E   L + +KP       S      +    V         ++  
Sbjct: 64  PSENLIPYDKELEVIYEDAYLIIVNKPQMQNCAPSREHPHGSLVEQVLAYYTKKGEKINP 123

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
             V RLD NT GL++    G +  +      +  + Y    +G           + +   
Sbjct: 124 HIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFK--KEYVALAYGHTQSSGVIEAPIARRSD 181

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +++K+ +  +G  Y         Q  + +   V L  G+  +I+  FE+    
Sbjct: 182 SIIKREVNDKG-KYAKTVYQRLMQNETASLCKVKLLTGRTHQIRVHFEYIGHP 233


>gi|254491706|ref|ZP_05104885.1| pseudouridine synthase, RluA family [Methylophaga thiooxidans
           DMS010]
 gi|224463184|gb|EEF79454.1| pseudouridine synthase, RluA family [Methylophaga thiooxydans
           DMS010]
          Length = 318

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 72/209 (34%), Gaps = 43/209 (20%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKAERTR----------------- 74
           R I +  V+VN G +  +    + + D + V  + + + E                    
Sbjct: 43  RAIRKGEVRVNKGRI--KQTYKIQAGDIVRVPPLRVAEREAPTHVSESLRQQLLQDIIFE 100

Query: 75  ---LWLYHKPIG--LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              + + +KP G  +        G    F  +    + +  V RLD +T G LLL     
Sbjct: 101 DDSMLVLNKPSGLAVHAGSQIQVGVIEAFRIIKPELAFLELVHRLDRDTSGCLLLAKSRD 160

Query: 130 LARVLELP--STQWLRVYRVRFHGQVD--QDKLNL-LKKGIVIQGICYGDMQVTLDTQKG 184
               L+    S Q  + Y     G +   ++ +   L K  V  G     ++VT D ++ 
Sbjct: 161 SLLNLQQQMLSDQIDKRYLTLLKGILPNAEELVEQPLLKNTVSSGERM--VKVTPDGKRA 218

Query: 185 SNAWV-----------TVGLREGKNREIK 202
              ++            V L  G+  +I+
Sbjct: 219 KTLFIRQQDLSLAQLTEVKLYTGRTHQIR 247


>gi|309808775|ref|ZP_07702661.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
 gi|308168011|gb|EFO70143.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           01V1-a]
          Length = 302

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 42  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 100

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 101 ADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITRLDRDTSGLVLVGKNAVAHARF 160

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  V    ++  K S     
Sbjct: 161 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPVKRYIMEGGKESVTKYR 216

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 217 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 249


>gi|229172031|ref|ZP_04299596.1| Pseudouridine synthase [Bacillus cereus MM3]
 gi|228611374|gb|EEK68631.1| Pseudouridine synthase [Bacillus cereus MM3]
          Length = 307

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 47/265 (17%), Positives = 92/265 (34%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           + VNG    R    +   D ++V              G      E   + + +KP  + T
Sbjct: 47  ITVNGEQ-RRWNELLKEGDKLQVHMFMEEEYDVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQV--DQDKLNLL---------KKGIVIQGICY-GDMQVTLDTQKGS 185
             +  R Y     G+V   Q  ++           ++ +  +G       +V    +  +
Sbjct: 165 ERKIKRTYAALVEGKVKGKQGTIDAAIGRDRHHATRRRVSPKGDQAITFYKVEKYFKNQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
             +VT+ L  G+  +I+    +              P     L  G T+ +S++ L    
Sbjct: 225 VTFVTLQLETGRTHQIRVHMSYHGN-----------PLVGDVLYGGQTQYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPAKLNDT 298


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

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 63/192 (32%), Gaps = 43/192 (22%)

Query: 1   MKDKNIVQE-NFTPQRVSKV---------IARAGIASRREVERMIAQQRVKVNGILLERA 50
           M  K +  + +    R+ +          ++           +++   +V+V+G  ++ A
Sbjct: 1   MSAKTLTVDTDEEGMRLDRWFKRRLPDLSLSHLN--------KIVRTGQVRVDGARVKTA 52

Query: 51  -------AVNVMSTD----------HIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHS- 89
                  +V V   D           +  D   LR+    E   L + +KP GL      
Sbjct: 53  TRLAAGQSVRVPPLDLPERPLEKPAIVSADAQALREMILFEDRDLMVLNKPFGLAVQGGS 112

Query: 90  --DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVY 145
                    +         R + V RLD +T G+LL+     +A  L     S Q  ++Y
Sbjct: 113 GMTHHIDKMLASLPNERGDRPVLVHRLDRDTSGVLLVAKTRRMAAELGEIFRSRQARKIY 172

Query: 146 RVRFHGQVDQDK 157
                G     +
Sbjct: 173 WAVVEGVPKPAQ 184


>gi|148989706|ref|ZP_01821015.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP6-BS73]
 gi|147924822|gb|EDK75905.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP6-BS73]
          Length = 291

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 231


>gi|257468012|ref|ZP_05632108.1| tRNA pseudouridine synthase A [Fusobacterium ulcerans ATCC 49185]
 gi|317062298|ref|ZP_07926783.1| rRNA pseudouridylate synthase C [Fusobacterium ulcerans ATCC 49185]
 gi|313687974|gb|EFS24809.1| rRNA pseudouridylate synthase C [Fusobacterium ulcerans ATCC 49185]
          Length = 290

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 80/241 (33%), Gaps = 53/241 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAVNVMST 57
           IV + F   R+ K +       R++ E +        I   ++KVNG   +     +   
Sbjct: 4   IVDKEFEDVRLDKFL-------RKKYEDIPLTEIFKGIRTGKIKVNGKKSKE-NYRLQLN 55

Query: 58  DHI---------------EVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRST 96
           D I               EV+   + K +++ ++      +++K    +  H        
Sbjct: 56  DEIKVFFKGGETKEEKLLEVEDKEIEKIKKSIVYENENVLIFNK-KNNMVMHKGSGYDFG 114

Query: 97  VFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
           + + L           V R+D  T GL++       AR L     +    + Y +   G+
Sbjct: 115 ISELLKGYLKNPNFNFVNRIDKATSGLIIGAKSLVTARELAEEIRNRNIDKRYYILVEGK 174

Query: 153 VDQDK------LNLLK-KGIVIQGICYGDMQ----VTLDTQKGSNAWVTVGLREGKNREI 201
           V   +      L  ++ K I ++    G  +      +         +   L  G+  ++
Sbjct: 175 VKDKEFTIKSYLKKIEDKVIEVEKFEEGAKESLSFFKVKKYGKDCTLLEGTLGSGRTHQL 234

Query: 202 K 202
           +
Sbjct: 235 R 235


>gi|237785359|ref|YP_002906064.1| pseudouridylate synthase [Corynebacterium kroppenstedtii DSM 44385]
 gi|237758271|gb|ACR17521.1| pseudouridylate synthase [Corynebacterium kroppenstedtii DSM 44385]
          Length = 313

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 81/235 (34%), Gaps = 39/235 (16%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLER---------AAVNVMSTDHI----- 60
           RV   +++    SR  V  + +   + ++G+   +           V +  +  I     
Sbjct: 17  RVDSGLSKLLGLSRTVVADLASSGDILIDGVPASKSDRLTTDSWLDVTLPESRSIADEPA 76

Query: 61  -EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
            EV+G+ +  ++   + +  KP+G+    +      TV   L +   RV + G       
Sbjct: 77  REVEGMDILYSDSD-VIVVDKPVGVAAHPTMGWDGPTVTSGLRAAGFRVSTSGPPERQGI 135

Query: 113 --RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------QDKLNL-- 160
             RLD+ T G++++        +L+         + Y     G  D         +    
Sbjct: 136 VQRLDVGTSGVMIVAASERAYSLLKQAFRDRTVDKTYHALVQGHPDPTVGTIDAPIARHP 195

Query: 161 ---LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               K  +   G        T++  + +   V+V L  G+  +I+  F   +   
Sbjct: 196 GAGWKFAVRSDGKRAVTHYSTMEAFREAT-LVSVHLETGRTHQIRVHFSALHHPC 249


>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 = 53.3 bits (127), Expect = 5e-05,   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 +   +I   RV VN  +  +AA  +   D + V
Sbjct: 6  RLDAELVRRGMARSREQARELIESGRVTVNKQVARKAANQIDPADPVHV 54


>gi|238018444|ref|ZP_04598870.1| hypothetical protein VEIDISOL_00271 [Veillonella dispar ATCC 17748]
 gi|237864915|gb|EEP66205.1| hypothetical protein VEIDISOL_00271 [Veillonella dispar ATCC 17748]
          Length = 334

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/148 (16%), Positives = 52/148 (35%), Gaps = 18/148 (12%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLR-----KAERTR 74
           SR+ + ++  ++ + +NG         +   D I       ++D  P+        E   
Sbjct: 41  SRKSLVKLFEEKLIHINGHKAT-PKDVISEGDEIWIAMAKEKIDYEPIEMDLHILYEDDD 99

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDG--G 129
           L +  KP G+     D    +              +V  + RLD +T G +++   G   
Sbjct: 100 LLIVDKPAGVTVNSKDQVSLANGVAYYFKENGIKRKVRFLNRLDRDTTGCIVIAKSGLAQ 159

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK 157
                ++    + + Y     G V+ D+
Sbjct: 160 SLYQQQMDDNTFEKWYMATVEGIVEADE 187


>gi|46198486|ref|YP_004153.1| hemolysin [Thermus thermophilus HB27]
 gi|46196108|gb|AAS80526.1| hemolysin [Thermus thermophilus HB27]
          Length = 235

 Score = 53.3 bits (127), Expect = 5e-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|310816979|ref|YP_003964943.1| RluA family pseudouridine synthase [Ketogulonicigenium vulgare Y25]
 gi|308755714|gb|ADO43643.1| RluA family pseudouridine synthase [Ketogulonicigenium vulgare Y25]
          Length = 347

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/182 (17%), Positives = 60/182 (32%), Gaps = 47/182 (25%)

Query: 15  RVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           R+ + +       R+        ++E+M  +  ++V+G  ++  A  +    ++ +    
Sbjct: 17  RLDRWL-------RKKFPNLTQGQIEKMCRKGELRVDGGRVKSNA-RLEDGQNVRIPPLG 68

Query: 63  ------------------DGVPLRKA---ERTRLWLYHKPIGLVTTHS----DPDGRSTV 97
                             D   ++ A   +   + + +KP GL +       D       
Sbjct: 69  AEIEQQAPMAVRTRVTRSDAEMIQAAVLWKDEHIIVLNKPPGLPSQGGSGLGDRHVDGLT 128

Query: 98  FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQ 155
              +     R   V RLD +T GLLLL     +AR L   L      ++Y     G    
Sbjct: 129 EALMFGYKDRPKLVHRLDKDTSGLLLLARTDRVARALSEALRHRNVRKIYWAAVAGIPTP 188

Query: 156 DK 157
             
Sbjct: 189 WA 190


>gi|305432550|ref|ZP_07401711.1| RNA pseudouridine synthase [Campylobacter coli JV20]
 gi|304444261|gb|EFM36913.1| RNA pseudouridine synthase [Campylobacter coli JV20]
          Length = 334

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 53/137 (38%), Gaps = 9/137 (6%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKA---ERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     ++  D   I  +  P       E     +  K  G+
Sbjct: 65  EAQKLIDKKRLFCDGILVEE-KNKILKGDVELIVYENNPKGVEIVFENEDFAILEKESGI 123

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +      +     RLD  T GL+L+         L       Q 
Sbjct: 124 LSHPNGRHCKYSLSDEIWHLWGKKACVAHRLDKETSGLILVAKHKEAQIELKTMFEKKQI 183

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y     G++  + +
Sbjct: 184 QKEYLALASGEIKVNFI 200


>gi|310287036|ref|YP_003938294.1| Ribosomal large subunit pseudouridine synthase [Bifidobacterium
           bifidum S17]
 gi|291045148|dbj|BAI82361.1| pseudouridine synthase [Bifidobacterium bifidum]
 gi|309250972|gb|ADO52720.1| Ribosomal large subunit pseudouridine synthase [Bifidobacterium
           bifidum S17]
          Length = 313

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 39/225 (17%), Positives = 76/225 (33%), Gaps = 36/225 (16%)

Query: 21  ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----W 76
           ++    SR +   +I   + +V    + ++   ++  + +E D    R            
Sbjct: 21  SKMLGISRAKAADLIESGQARVLDRAIAKSGT-LLYGETVEFDIAEERHEPEPVCLDMAI 79

Query: 77  LYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTE 119
           +Y         KP+G+    S      TV  +L     R+ S G         RLD+ T 
Sbjct: 80  VYEDDDVVVVDKPVGVAAHASAGWTGPTVLGSLLKRGVRITSYGAPGRQGIVSRLDVGTS 139

Query: 120 GLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD-----------KLNLLKKGIV 166
           GL+L+       + +    ++    + Y     G + +D           K++  +  + 
Sbjct: 140 GLMLVCKSELAYKEMRRQFSEHEVVKTYHAMVQGNLKEDKATIEAPIGRAKVSDFRFCVT 199

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G         LD + G    V+V L  G+  +I+  F      
Sbjct: 200 PSGKPAVTHWDVLD-RFGEATLVSVNLETGRTHQIRVHFSSIGHP 243


>gi|259501034|ref|ZP_05743936.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
 gi|302190517|ref|ZP_07266771.1| pseudouridine synthase, RluA family protein [Lactobacillus iners
           AB-1]
 gi|259167728|gb|EEW52223.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners DSM 13335]
          Length = 300

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 31/181 (17%), Positives = 60/181 (33%), Gaps = 28/181 (15%)

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRV 108
                ++   +P+    E     + +K   L+T  S  +   +V   L     P    ++
Sbjct: 71  KPNATLKFSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALIKI 130

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
               + RLD +T GL+L+  +             + ++ Y    HG     +L     G+
Sbjct: 131 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYHAIVHGNFSPSQLQ----GV 186

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVG-------LRE-----GKNREIKKVFEFFNW 210
           +   I   D  V    ++  K S     V        L E     G+  +I+   ++   
Sbjct: 187 IDAPIGKKDDPVKRYIMEGGKESVTKYRVIKQIAGASLVELQLLTGRTHQIRVHMQYLGH 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|194206789|ref|XP_001501154.2| PREDICTED: similar to RPUSD2 protein [Equus caballus]
          Length = 559

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 47/291 (16%), Positives = 97/291 (33%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDG-VPLRKAERTRLWLYH-------KP 81
           E  +   R+ +N   ++  ++ +   D +   V    P   AE  RL   +       KP
Sbjct: 193 EAAVRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPVRLLAENEDMVVVDKP 252

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 253 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 312

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 313 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDTRGKPCETVFQRLSYNGHSS 372

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +        +++GP +      G   +  +++L
Sbjct: 373 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSRGRG---GHIPKTDEQLL 426

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +++   LD         + D     SE+  D       S+QK
Sbjct: 427 RDLVAEHQAKQSLDVLDLCEGDLSPGLSDTTAPSSELGKDCLEELTASAQK 477


>gi|183603679|ref|ZP_02718812.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
 gi|183575456|gb|EDT95984.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC3059-06]
          Length = 278

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 TYVSRLKQFSNKTSLARCKLKTGRTHQIR 218


>gi|28899453|ref|NP_799058.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|260363379|ref|ZP_05776231.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
 gi|260879313|ref|ZP_05891668.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|260895728|ref|ZP_05904224.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|34395765|sp|Q87LD3|RLUA_VIBPA RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|28807689|dbj|BAC60942.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|308087397|gb|EFO37092.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus Peru-466]
 gi|308093125|gb|EFO42820.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AN-5034]
 gi|308111223|gb|EFO48763.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus K5030]
          Length = 250

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/169 (15%), Positives = 60/169 (35%), Gaps = 33/169 (19%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++      +   +++  L   +  +  V RLD++T GL++L  +  
Sbjct: 19  EDDHILAVNKPSGLLSVPGRLAEHHDSMWSRLQEEYPDIQVVHRLDMSTSGLMVLAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLN------------LLKKGIVIQG 169
                       L        ++Y  R  G V+Q++               L+K     G
Sbjct: 79  AESALKKQFQFRLTH------KIYYARVWGHVEQEEGEIDLPLICDWPNRPLQKVCFEDG 132

Query: 170 ICYGDM-QVTLDTQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
                + QV    ++      T+     +  G++ +++   +     + 
Sbjct: 133 KPSKTLFQVAKREEQEDGTKTTIVRLLPIT-GRSHQLRVHMQALGHPIV 180


>gi|309803082|ref|ZP_07697181.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
 gi|308164863|gb|EFO67111.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           11V1-d]
          Length = 307

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 60/181 (33%), Gaps = 28/181 (15%)

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRV 108
              + ++   +P+    E     + +K   L+T  S  +   +V   L     P     +
Sbjct: 78  KPNETLKFSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLNI 137

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
               + RLD +T GL+L+  +             + ++ Y    HG     +L     G+
Sbjct: 138 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYHAIVHGNFSPSQLQ----GV 193

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVG-------LRE-----GKNREIKKVFEFFNW 210
           +   I   D  +    ++  K S     V        L E     G+  +I+   ++   
Sbjct: 194 IDAPIGKKDDPIKRYIMEGGKDSVTKYRVIKQVAGASLVELQLLTGRTHQIRVHMQYLGH 253

Query: 211 K 211
            
Sbjct: 254 P 254


>gi|255994608|ref|ZP_05427743.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saphenum ATCC 49989]
 gi|255993321|gb|EEU03410.1| ribosomal large subunit pseudouridine synthase D [Eubacterium
           saphenum ATCC 49989]
          Length = 322

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 53/299 (17%), Positives = 95/299 (31%), Gaps = 87/299 (29%)

Query: 4   KNIVQENFTPQRVS----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           K  + EN   QR+     K    A +A    + ++I +  VKVNG   ++    + + D 
Sbjct: 3   KFTITENDAGQRLDRFFKKYYCNASLA---YIYKLIRK-DVKVNGKKCKQ-NFLLNAGDA 57

Query: 60  IEVD--------------GVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           + +               GV ++ +     E   L + +K  GL+T  S  + + T+ + 
Sbjct: 58  VHIYISDDEHKRMILKDKGVQIKPSFKIIFEDDNLLVVYKRAGLLTHGSSTEKKRTLLNE 117

Query: 101 LPSIFSR-------------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVY 145
           + +   +             + +  RLD NTEGL+ +  +    R L     +    R Y
Sbjct: 118 VKTYLIQKGEYDPGFEKTFSLATSNRLDRNTEGLIAIAKNAASQRELNAAFKEGRIERYY 177

Query: 146 RVRFHGQVDQDKLNLLKKGIVIQGICYG----------------------------DMQV 177
                G+V  D        + I    Y                              ++V
Sbjct: 178 VAEVVGEVRGD--------VTIDYPLYKSAKNNTVFADKDGSVPPDVTKEAITKVHPIRV 229

Query: 178 TLDTQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVNRLIR--ISYGPFQLGTLLA 230
               + GS    TV     L  G+  +I+         +    R  + Y       L  
Sbjct: 230 NRIDKNGSEFTYTVVRVKLLT-GRTHQIRVHLAAIGHPLVN-DRKYLKYANVSSKYLNP 286


>gi|254455970|ref|ZP_05069399.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter sp. HTCC7211]
 gi|207082972|gb|EDZ60398.1| ribosomal large subunit pseudouridine synthase C [Candidatus
           Pelagibacter sp. HTCC7211]
          Length = 292

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 23/172 (13%), Positives = 55/172 (31%), Gaps = 11/172 (6%)

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---SR 107
            +    +  I                + +K  G+         ++ V     S     ++
Sbjct: 62  KIKFEPSKEIIKSNEDQIIDNNENFIVLNKSSGISVQGGTKSKKNLVDIFAKSEIFQGTK 121

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
             SV RLD +T G+ ++      A++L       +  + Y    HG++++D        I
Sbjct: 122 PYSVHRLDKDTSGVFIMAKTRQSAQLLTSLFRLRKVHKTYLAICHGELNKDSGEWNDDLI 181

Query: 166 VIQGICYGDMQVT----LDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKV 212
              G      +      +  +    + V +  +  G+  +++K        +
Sbjct: 182 RYDGEKKIIEKAKTIYRVLDKNSEASLVELKPIT-GRKHQLRKQLYALGQPI 232


>gi|195118758|ref|XP_002003903.1| GI20532 [Drosophila mojavensis]
 gi|193914478|gb|EDW13345.1| GI20532 [Drosophila mojavensis]
          Length = 798

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 62/349 (17%), Positives = 116/349 (33%), Gaps = 46/349 (13%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P+        + + +KP 
Sbjct: 393 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPA 452

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 453 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 512

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G  +
Sbjct: 513 RQVEKEYICRVEGIFPDGVVE-CKEPIEVVSYKIGVCKVSQKGKDCTTTFQKLSQNGKTS 571

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR--L--IRISYGPFQLGTLLAGSTREVSKKIL- 241
            V    L  G+  +I+   ++  + +    L    + +GP +     AG     +   L 
Sbjct: 572 VVLCKPLT-GRMHQIRVHLQYLGFPILNDPLYNHEV-FGPLK---GRAGDIGGKTDDELI 626

Query: 242 REQLGPHLLEE-AQVNLDAPIY---------SSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           R+ +  H  E    ++ D+ I            E+L  D+   +    DD     + ++ 
Sbjct: 627 RDLINIHNAENWLGIDCDSDISLFKNTKDETDLESLSSDQTFAVHHSDDDVGVNSRETTP 686

Query: 292 KNGLSKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPS 340
               ++Q   A        +S V  AK   ++  S   +   +   +  
Sbjct: 687 PCSENQQSAEALKQLHSTNSSPVLPAKADAATEPSVPNEVPTDQAVASD 735


>gi|172079581|ref|ZP_02709037.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|172042644|gb|EDT50690.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1873-00]
 gi|301802690|emb|CBW35457.1| RNA pseudouridylate synthase [Streptococcus pneumoniae INV200]
 gi|332199159|gb|EGJ13238.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA47368]
          Length = 278

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 TYVSRLKQFSNKTSLARCKLKTGRTHQIR 218


>gi|54023755|ref|YP_117997.1| putative RNA pseudouridine synthase [Nocardia farcinica IFM 10152]
 gi|54015263|dbj|BAD56633.1| putative RNA pseudouridine synthase [Nocardia farcinica IFM 10152]
          Length = 308

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 40/250 (16%), Positives = 81/250 (32%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA------- 51
           M++   +   +     RV   ++R    SR  V  + A+  V+++G+   ++        
Sbjct: 1   MRETRAMPVPDGLDGMRVDAGLSRLLGLSRTAVAALTAEGSVQLDGVPAGKSDRLTAGAW 60

Query: 52  VNV---MSTDHIEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
           + V        + V+  P+   +       +    KP+G+           TV   L   
Sbjct: 61  LEVEFPEPKRELTVEAAPVEGMKILYADDDIVAVDKPVGVAAHTGVGWSGPTVVGGLAAA 120

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                      R   V RLD+ T G++++        VL+    Q    + Y     G  
Sbjct: 121 GYRISTSGAHERQGIVHRLDVGTSGVMVVAQSEHAYTVLKRAFKQRTVSKRYHALVQGHP 180

Query: 154 DQ-----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D             + N  K  +   G        T++  + + + + + L  G+  +I+
Sbjct: 181 DPSSGTIDAPIGRARGNDWKFAVTADGRPSVTHYDTIEAFQAA-SLLDIHLETGRTHQIR 239

Query: 203 KVFEFFNWKV 212
             F       
Sbjct: 240 VHFSAIRHPC 249


>gi|260432477|ref|ZP_05786448.1| ribosomal large subunit pseudouridine synthase C [Silicibacter
           lacuscaerulensis ITI-1157]
 gi|260416305|gb|EEX09564.1| ribosomal large subunit pseudouridine synthase C [Silicibacter
           lacuscaerulensis ITI-1157]
          Length = 347

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/260 (13%), Positives = 69/260 (26%), Gaps = 68/260 (26%)

Query: 14  QRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           QR+ + +       RR         +E+M  +  ++V+G  ++  +  + +   + V   
Sbjct: 16  QRLDRWL-------RRLFPHVSQGRIEKMCRKGELRVDGGRVK-GSTRLQAGQVVRVPPL 67

Query: 63  ---DGVPLRKAERT-----------------RLWLYHKPIGLVTTHSDPDGRSTVF---D 99
              D  P     R                   +   +KP GL         R        
Sbjct: 68  PDPDHKPAPTRPRVTDADAKMIQSCVIYRDDHVLALNKPHGLPVQGGSGQARHVDGLAEA 127

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ-- 155
                      V RLD +T G+LL+      A+ L          ++Y     G      
Sbjct: 128 LRFGYDENPRLVHRLDKDTSGVLLMARTREAAKGLTAAFRHRNTRKIYWALVAGVPTPYL 187

Query: 156 -----DKLNLLKKGIVIQGIC-----------------YGDMQVTLDTQKGSNAWVTVGL 193
                  +     G   +G                      +  TL       +WV +  
Sbjct: 188 GEIKTGLVKAPGHGKQGEGEKMIAVHLNEIDSTPGAKRAHTLYATLFRVASRASWVAMEP 247

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +++         + 
Sbjct: 248 VTGRTHQLRAHMAAIGHPII 267


>gi|322420039|ref|YP_004199262.1| hemolysin A [Geobacter sp. M18]
 gi|320126426|gb|ADW13986.1| hemolysin A [Geobacter sp. M18]
          Length = 256

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+ K++   G+A SR   + +I   +V V+  L ++A + V     I + G PL  
Sbjct: 1  MAKERLDKLVLERGLAPSRERAKALIMAGQVVVDDHLADKAGLMVPLEAEIRLKGEPLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|148985947|ref|ZP_01819000.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP3-BS71]
 gi|168492590|ref|ZP_02716733.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
 gi|147921920|gb|EDK73045.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP3-BS71]
 gi|183573261|gb|EDT93789.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC0288-04]
          Length = 291

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 231


>gi|254479301|ref|ZP_05092641.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
 gi|214034749|gb|EEB75483.1| pseudouridine synthase, RluA family [Carboxydibrachium pacificum
           DSM 12653]
          Length = 285

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 77/216 (35%), Gaps = 40/216 (18%)

Query: 19  VIARAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEV-------DGVPL 67
            + R G ++R     +I        ++VNG   E     +   D IE+       D +P 
Sbjct: 17  FLKRKGFSTR-----LIKMYKWHGEMRVNGEK-ENVKRVLKEGDVIELSLFDTSSDILPQ 70

Query: 68  RK-----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDI 116
                   E   + +  KP G+V   +      T+ + +   F +      +  V RLD 
Sbjct: 71  EMDLSICYEDDEILIVDKPAGMVVHPTRRYREGTLANGVAYYFEKKGIKTLIRPVNRLDK 130

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIV 166
            T G+++   +  +   L        + Y    +G+++ + +            +++ + 
Sbjct: 131 GTSGIVIFAKEPFMQYYL-QIVKPMSKFYYAIVNGKLEGEGIIDVPIKRKSFMTIEREVS 189

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +G        +L   +   + + + +  G+  +I+
Sbjct: 190 EEGDRAITYYKSLKATEEF-SLLKIKIATGRTHQIR 224


>gi|15901834|ref|NP_346438.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae TIGR4]
 gi|148992153|ref|ZP_01821927.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP9-BS68]
 gi|14973521|gb|AAK76078.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae TIGR4]
 gi|147929202|gb|EDK80213.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Streptococcus pneumoniae SP9-BS68]
          Length = 291

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 203 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 231


>gi|333001149|gb|EGK20719.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-272]
 gi|333015787|gb|EGK35124.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-227]
          Length = 260

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  +   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVLMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>gi|312870695|ref|ZP_07730803.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
 gi|311093806|gb|EFQ52142.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           3008A-a]
          Length = 307

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 47  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 105

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 106 ADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITRLDRDTSGLVLVGKNAVAHARF 165

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 166 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKNSVTKYR 221

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 222 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 254


>gi|293375853|ref|ZP_06622121.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325844995|ref|ZP_08168320.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
 gi|292645532|gb|EFF63574.1| pseudouridine synthase, RluA family [Turicibacter sanguinis PC909]
 gi|325488968|gb|EGC91358.1| pseudouridine synthase, RluA family [Turicibacter sp. HGF1]
          Length = 299

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 79/240 (32%), Gaps = 58/240 (24%)

Query: 28  RREVERMIAQQRVKVNGILLE-----RAA----VNVMSTDHIEVDGVPLR---KAERTRL 75
           R+++  +   ++V++N  + +            + V  ++ I+     +      E   L
Sbjct: 34  RKKIHELYMSKKVQLNAQIADFNKILEVGDILLIPVFESEGIDFKPQKMNLDIVYEDEHL 93

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGG 129
            + +KP G++      DG +T+ + +   +       R+  + R+D +T G ++      
Sbjct: 94  LILNKPAGVMVHPDQKDGLNTLVNGVAYYYEQKGFNERIRYIHRIDTDTSGGIIFAKH-F 152

Query: 130 LARVLE---LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
           +A  L    L   Q  R Y     G +        +KG  I      D       +   N
Sbjct: 153 MAHSLMDYQLSEKQIRRWYLALVSGNL------KTRKG-RIDAPIGKDRHHRARRRVAKN 205

Query: 187 -----------------AWVTVGLREGKNREIKKVFEFFNW------------KVNRLIR 217
                            + V + L+ G+  +I+                    KV +L R
Sbjct: 206 GDQAVTLYEVKKQFKTYSLVELELKTGRTHQIRVHMSHLGHPLLGDVLYGGVAKVGKLKR 265


>gi|254993270|ref|ZP_05275460.1| ribosomal large subunit pseudouridine synthetase [Listeria
           monocytogenes FSL J2-064]
          Length = 243

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/209 (15%), Positives = 71/209 (33%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKP 81
           A+ +++VN         +V   D + +          L           E   L + +KP
Sbjct: 37  AEGKIEVNNKEQNVL-YHVKVGDKVRLTFPTEQQNERLLAEYTDLDIIFEDDFLLIINKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE 135
            G+ +  S      +V + +   +        +  V RLD  T GL+L+  +      L 
Sbjct: 96  AGMASIPSQYHPNGSVANFVKGHYETQGLTNAIHIVTRLDRETSGLMLIAKNRFAHARLS 155

Query: 136 --LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             L      R Y+    G            + + +++++++ +  +G         L   
Sbjct: 156 TFLQKGLLKRRYQAFTSGVLVEQKGSIEAPIGRKEVSIMERFVTPEGKYAKTNYEVLARY 215

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +  +  V + L  G+  +I+  F +    
Sbjct: 216 RAFDH-VAIQLETGRTHQIRVHFSYIGHP 243


>gi|238895332|ref|YP_002920067.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae NTUH-K2044]
 gi|238547649|dbj|BAH64000.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044]
          Length = 232

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/186 (19%), Positives = 65/186 (34%), Gaps = 37/186 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   F     V RLD  T GL+++  + G
Sbjct: 22  QDEHLLLINKPAGLLSLSGKDPRNLDSVHHRLVQRFPGCTLVHRLDFGTSGLMVIARNKG 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +           
Sbjct: 82  INALLCQQFSQRTVDKVYTALLCGHLAED------EGIVEAAIAKDPARFPRMALCARHG 135

Query: 183 KGSNAWV-------------------TVGLR-E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +                      V L  E G+  +++   +   + +       YG
Sbjct: 136 KPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILGCD--LYG 193

Query: 222 PFQLGT 227
             +L  
Sbjct: 194 GRELPG 199


>gi|254436973|ref|ZP_05050467.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
 gi|198252419|gb|EDY76733.1| pseudouridine synthase, RluA family [Octadecabacter antarcticus
           307]
          Length = 347

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 46/256 (17%), Positives = 81/256 (31%), Gaps = 61/256 (23%)

Query: 14  QRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--------- 60
           QR+ + I    A         +E+M  +  ++V+G  ++     V     I         
Sbjct: 16  QRLDRWIKRRFAHLQQG---GIEKMCRKGEIRVDGGRVKT-NTRVEVGQKIRIPPLPDAN 71

Query: 61  EVDGVP-------LRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFD---NLPSI 104
           EVD  P       ++  +   ++        +KP GL T       R             
Sbjct: 72  EVDERPRDMTKADIQLIQGCVIYKDDHVIALNKPAGLPTQGGSKQLRHVDGMAEALRFGY 131

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLK 162
             +   V RLD +T G+L+L      A+ L          ++Y     G V   KL  +K
Sbjct: 132 DEKPRLVHRLDKDTSGVLILARTRMAAKSLTDAFRHRNTEKIYWALVAG-VPIPKLGSVK 190

Query: 163 KGIVIQG-------------ICYGDMQVTLDTQKG------------SNAWVTVGLREGK 197
            G+V QG             +   D+  T   ++               AWV +    G+
Sbjct: 191 YGLVKQGGHGGKGDNERMKCVHPKDVDKTFGAKRALTNYTVLTSLADRTAWVALTPVTGR 250

Query: 198 NREIKKVFEFFNWKVN 213
             +++         + 
Sbjct: 251 THQLRAHMAEIGHPIV 266


>gi|121634642|ref|YP_974887.1| hypothetical protein NMC0808 [Neisseria meningitidis FAM18]
 gi|120866348|emb|CAM10091.1| hypothetical protein NMC0808 [Neisseria meningitidis FAM18]
          Length = 307

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 41/109 (37%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALALTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G        ++G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEVEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|28849821|gb|AAN64577.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii]
          Length = 290

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 69/205 (33%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTD--HIEVD-----------GVP---LRKAE 71
           R++   +  ++ V VN   +      + + D   +  D           G P       +
Sbjct: 28  RKIRHFLRTKKHVLVNDQTI-NWQSKIQAGDLLSLTFDEEDYPAKAILMGKPELVQELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHG------QVDQDKLNLLKKG-----IVIQGICYGDMQV 177
            +   L   +    R Y     G      ++ +DK+   +       +  +   Y +  V
Sbjct: 147 PILNRLL-ENKDIQREYWALVDGKFIEKSRIYKDKIGRDRHNRRKRLVDNKHGQYAETHV 205

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T     G    V   L+ G+  +I+
Sbjct: 206 TRLKSFGQKTLVKCQLKTGRTHQIR 230


>gi|45200963|ref|NP_986533.1| AGL134Cp [Ashbya gossypii ATCC 10895]
 gi|74692056|sp|Q750S3|PUS5_ASHGO RecName: Full=Pseudouridylate synthase PUS5; AltName:
           Full=Pseudouridine synthase 5; AltName: Full=Uracil
           hydrolyase PUS5
 gi|44985733|gb|AAS54357.1| AGL134Cp [Ashbya gossypii ATCC 10895]
          Length = 260

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/166 (17%), Positives = 53/166 (31%), Gaps = 31/166 (18%)

Query: 70  AERTRLWLYHKPIGLVTTHSD--------PDGRSTVFDNLPSIFSR-----VISVGRLDI 116
            E    ++ +K  G+V    D              + D L             +V RLD 
Sbjct: 10  HEHKHYYIVNKVHGIVCQPPDLRTWYKYHDYEPPVLLDLLRKQHPNFGGEVWRTVHRLDE 69

Query: 117 NTEGLLLLTNDGGLARVLELP-------STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
              G +L++ +   A +                R Y      +          KG+  +G
Sbjct: 70  PVTGGVLVSRNKRAAAMFSRSLALGGNRGFPLTRRYVALLARE---------AKGLPSEG 120

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKK-VFEFFNWKVNR 214
                  +T D ++  N  V + L+ G+  +I+K + + F   V  
Sbjct: 121 RITMGDMIT-DYKRLENDLVLLQLQTGRKHQIRKQMAQVFGQPVVN 165


>gi|325127991|gb|EGC50890.1| RNA pseudouridine synthase [Neisseria meningitidis N1568]
          Length = 307

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/109 (18%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTN--DGGLARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL++  D   A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPDTRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|148549014|ref|YP_001269116.1| RluA family pseudouridine synthase [Pseudomonas putida F1]
 gi|148513072|gb|ABQ79932.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           putida F1]
          Length = 333

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 67/211 (31%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKA--------------------E 71
           R++ +  V+VN G +  +    + + D + V  V L +                     E
Sbjct: 58  RILRKGEVRVNKGRV--KPEYKIQAGDIVRVPPVRLPERDEPAPVAQGLLQRLEAAIVYE 115

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 116 DKALIVMNKPAGIAVHGGSGLSFGVIEALRQLRPDAKELELVHRLDRDTSGLLMIAKKRS 175

Query: 130 LARVL--ELPSTQWLRVYRVRFHG--QVDQDKLNL------LKKG-----IVIQGICYGD 174
           + R L   L      + Y     G     + ++N       L+ G     +  +G     
Sbjct: 176 MLRHLHAALRGDGVDKRYMALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVNDEGKEALT 235

Query: 175 MQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           +   L         V    +    G+  +I+
Sbjct: 236 LFRVLRRFGDFATIVEARPIT---GRTHQIR 263


>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 = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 58/161 (36%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K  G+    S  + R+++ + L   + +           RLD +T GL ++
Sbjct: 36  EDEDIIVINKAAGMPIHPSLNNYRNSLANALMWYYEQQNKPFIFRCTNRLDRDTSGLTVV 95

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQVD--QDKLNL---------LKKGIVIQGIC 171
                 + +L       Q  R Y     G V   +  +N          +++ I  +   
Sbjct: 96  AKHMVSSNILSSMTARHQIEREYLAIVRGHVTPFEGTINAPIGRTGSSLIERKIDFENGE 155

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
           +         +K   + V++ L  G+  +I+  + +   + 
Sbjct: 156 HAITHYHTVFEKNGLSLVSLILETGRTHQIRVHM-KHLGFP 195


>gi|295107941|emb|CBL21894.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 342

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 37/94 (39%), Gaps = 8/94 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLL 124
           E   +   +KP G++T  S      T+ + +   F       RV  +GRLD  T G++L 
Sbjct: 91  EDEDILAVNKPAGILTHPSGAHYADTLSNQVAGYFHKKKLSCRVRPIGRLDKETSGIVLF 150

Query: 125 TNDGGLARVL-ELPSTQWL-RVYRVRFHGQVDQD 156
             +   A+ L     +  L + Y     G    D
Sbjct: 151 AKNQVSAQRLQTQRESGILHKQYIAVVKGDFSDD 184


>gi|227550294|ref|ZP_03980343.1| pseudouridylate synthase RluD [Enterococcus faecium TX1330]
 gi|227180554|gb|EEI61526.1| pseudouridylate synthase RluD [Enterococcus faecium TX1330]
          Length = 299

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 58/159 (36%), Gaps = 16/159 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 100 EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVLFAK 159

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D+           +  K+ +  +      
Sbjct: 160 NPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDRTITNKIGRDRHDRRKRVVDDKNGQNAL 219

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             VT+D        V   L  G+  +I+         + 
Sbjct: 220 THVTVDKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIV 258


>gi|222150872|ref|YP_002560025.1| truncated ribosomal large subunit pseudouridine synthase
           [Macrococcus caseolyticus JCSC5402]
 gi|222119994|dbj|BAH17329.1| truncated ribosomal large subunit pseudouridine synthase
           [Macrococcus caseolyticus JCSC5402]
          Length = 235

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 71/217 (32%), Gaps = 40/217 (18%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVP--------- 66
            +      SR+ +  +     + VNG  +      +   D + V   D            
Sbjct: 10  FLQNHQY-SRKSISAIKQNGALLVNGHQVT-VRYEMHKHDTLTVQLPDESRSKTLIPSHI 67

Query: 67  --LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINT 118
             L   +   L +  KP  + T  S      ++ + +            +  V RLD +T
Sbjct: 68  PILIHYDDEYLIIVSKPPFMNTIPSKQHPHDSLIEAVYGHLETHDDKSVLHPVSRLDRDT 127

Query: 119 EGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG----------QVDQDKLNLLKKGIV 166
            GL++ +        L     + +  + Y +   G           +D+ + +++ + + 
Sbjct: 128 SGLVVFS-----KHQLTHHLLTGKIEKFYLLIAAGHVKDHGNYVYPIDRREDSIITRTVN 182

Query: 167 IQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
           + G         +D     + + V V L  G+  +I+
Sbjct: 183 VHGQHARTEYHLIDYDAEFDVSLVHVKLHTGRTHQIR 219


>gi|172040870|ref|YP_001800584.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109]
 gi|171852174|emb|CAQ05150.1| pseudouridylate synthase D [Corynebacterium urealyticum DSM 7109]
          Length = 314

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 80/234 (34%), Gaps = 40/234 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-----------M 55
           V +     RV   +++    SR  V  + A   +   G  L ++   V            
Sbjct: 11  VPDGLAGMRVDAGLSKLLGLSRTVVADLAAAGDITAEGKSLGKSDRLVAGQWLDVTLPAP 70

Query: 56  STDHIE-----VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
             D        V+G+ +  ++   +   +KP+G+    +      TV   L +   R+ +
Sbjct: 71  ERDLAAEPPQLVEGMDILYSDDD-VIAVNKPVGVAAHPTLGWEGPTVTAGLAAAGFRIST 129

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ--DK 157
            G         RLD+ T G++++         L+    + +  ++Y     G  D     
Sbjct: 130 SGPPERKGIVQRLDVGTSGVMIVAASERAYTHLKRAFRNREVQKIYHALVQGHPDPTSGT 189

Query: 158 LNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++           +  +   G        TL+  + + + + V L  G+  +I+
Sbjct: 190 IDAPIGRHPSAGWRFAVRDDGKHAVTHYDTLEAHRQA-SLLRVNLETGRTHQIR 242


>gi|325474713|gb|EGC77899.1| RNA pseudouridylate synthase [Treponema denticola F0402]
          Length = 244

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLL 124
           E   + + +K   L+      D  +   D +           ++  V RLD  T GL++ 
Sbjct: 11  EDKDILIVNKSADLLVGADRWDSEAPRLDKILEELYKDKGERKIYPVHRLDKETSGLIIY 70

Query: 125 TNDGGLARVLELPST---QWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
             +   A  +        +  ++Y     G   ++      K + I G      +  +D 
Sbjct: 71  ALNAE-AHKILNDDFQNRKIEKIYHAVSAGIPQEENFKTEAK-LRIDGDKL--HRTVIDE 126

Query: 182 QKGSNAWVTVG---------LRE-----GKNREIKKVFEFFNWKVN 213
           +KG  +              L E     G+  +I+   +     + 
Sbjct: 127 KKGKESLTEFSLLKKFSRFCLLEARPITGRTHQIRAHLKHLGLPIL 172


>gi|325206298|gb|ADZ01751.1| RNA pseudouridine synthase [Neisseria meningitidis M04-240196]
          Length = 307

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 41/109 (37%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALALTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G        ++G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEVEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|309807023|ref|ZP_07701005.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
 gi|308166643|gb|EFO68840.1| pseudouridine synthase, RluA family [Lactobacillus iners LactinV
           03V1-b]
          Length = 302

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 42  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 100

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 101 ADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITRLDRDTSGLVLVGKNAVAHARF 160

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 161 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKDSVTKYR 216

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 217 VIKQVAGASLVELQLFTGRTHQIRVHMQYLGHP 249


>gi|307128211|ref|YP_003880242.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
 gi|306485273|gb|ADM92142.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 670-6B]
          Length = 278

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|238755849|ref|ZP_04617179.1| Pseudouridine synthase [Yersinia ruckeri ATCC 29473]
 gi|238705934|gb|EEP98321.1| Pseudouridine synthase [Yersinia ruckeri ATCC 29473]
          Length = 232

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/209 (19%), Positives = 69/209 (33%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIE------NLYQDDHLVLINKPAGLLSLSGKNPQNLDSVHYRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKAINAALCQQFSQRSVTKVYSALLCGHLDDN------EGVIDAAIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG---LRE------------------GKNREIKKVF 205
                     +     K + +   V      E                  G+  +++   
Sbjct: 120 KDPALFPRMSICATHGKPARSGYRVVERFYHELEDGTLLPLTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +       YG    G LL G+ R
Sbjct: 180 QQLGHPIWGCD--LYG----GRLLPGTER 202


>gi|88856520|ref|ZP_01131177.1| ribosomal large subunit pseudouridine synthase [marine
           actinobacterium PHSC20C1]
 gi|88814174|gb|EAR24039.1| ribosomal large subunit pseudouridine synthase [marine
           actinobacterium PHSC20C1]
          Length = 301

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 77/232 (33%), Gaps = 38/232 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILL-------ERAAVNV----- 54
           V E    QRV   +A+    SR     +  +  V +NG+++         A + V     
Sbjct: 3   VPEGLAGQRVDAALAKLLGFSRTFAAEVAEEGGVTMNGVVVGKSDRLSAEAWLEVSWVSK 62

Query: 55  MSTDHIEV--DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--- 109
                + V  D + +   +   + +  KP G+    S      TV   L     R+    
Sbjct: 63  SEPQIVPVVLDTLGIVYDDEHIVVI-DKPAGVAAHPSIGWDGVTVLGALAGAGYRISTSG 121

Query: 110 ------SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ--DKLN 159
                  V RLD  T GL+++         L+      +  ++Y     G  D     ++
Sbjct: 122 AAERAGIVHRLDAGTSGLMVVAKSELAYTELKRAFHDREVNKIYHSIVQGHPDPLMGTID 181

Query: 160 L---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      K  +V  G        TL+    S + V V L  G+  +I+
Sbjct: 182 APIGRHPGSSWKFAVVAGGKDSITHYETLEA-FPSASLVEVQLETGRTHQIR 232


>gi|330811001|ref|YP_004355463.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327379109|gb|AEA70459.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 322

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 82/236 (34%), Gaps = 43/236 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V   +  QR+   + AR     +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 20  VSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRI--KPEYKLQAGDIVRVPP 77

Query: 65  VPLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTV--FDNLP 102
           V + + +                       L + +KP G+            +  F  L 
Sbjct: 78  VRVPERDEPVPLAQGLLQRLEASIIYEDKALIVINKPAGIAVHGGSGLNFGVIEAFRQLR 137

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T GLL++     + R L   L      + Y     G+  +  +  
Sbjct: 138 PDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHEQLRGDGVDKRYMALVRGRW-ETSIKQ 196

Query: 161 LKKGIVIQGICYGDMQVTL-DTQKGSNAWVTV--------GLRE-----GKNREIK 202
           ++  ++   +  G+  V + +  K +     V         L E     G+  +I+
Sbjct: 197 VRAPLLKSNLRSGERMVEVNEEGKEALTVFKVLRRFDDFATLIEAKPVTGRTHQIR 252


>gi|56551335|ref|YP_162174.1| RluA family pseudouridine synthase [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241760988|ref|ZP_04759077.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260753046|ref|YP_003225939.1| pseudouridine synthase [Zymomonas mobilis subsp. mobilis NCIMB
           11163]
 gi|56542909|gb|AAV89063.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374607|gb|EER64068.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552409|gb|ACV75355.1| pseudouridine synthase, RluA family [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 374

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 82/251 (32%), Gaps = 58/251 (23%)

Query: 14  QRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
            R+ +     +   G A  R   R     +++++G         VM+   I V       
Sbjct: 17  IRLDRWFQRHLPDTGFA--RIA-RWTRTGQIRLDGRRAT-PGSRVMAGQSIRVPPAEPNL 72

Query: 63  -DGVP------------LRKAERTRL------WLYHKPIGLVTTHSDPDGRST--VFDNL 101
            D  P            +  A+   +       + +KP GL T            + D L
Sbjct: 73  QDNRPTKPSRPELTEAEIEFAQSLVIHRDKAAIVVNKPAGLATQGGTKTHYHLDGLLDAL 132

Query: 102 P-SIFSRVISVGRLDINTEGLLLL----TNDGGLARVLELPSTQWLRVYRVRFHGQ--VD 154
                SR   V RLD +T G+LLL     N G  ++     +    +VY     G   + 
Sbjct: 133 QFEAPSRPKLVHRLDKDTSGVLLLARSANNAGYFSKAFSGRTAH--KVYWALVVGVPSIT 190

Query: 155 QDKLNL-LKK-----GIVIQ-----GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
           +  ++L L +     G  +      G     +   ++    +  W+ +  L  G+  +++
Sbjct: 191 EGLIDLPLARQPGSGGEKMHVDEENGATAKTLYRVIERAGNAACWLELQPLT-GRTHQLR 249

Query: 203 KVFEFFNWKVN 213
                  + + 
Sbjct: 250 AHLSAIGFPIV 260


>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 = 53.3 bits (127), Expect = 6e-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|84499811|ref|ZP_00998099.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           batsensis HTCC2597]
 gi|84392955|gb|EAQ05166.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           batsensis HTCC2597]
          Length = 347

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 34/187 (18%), Positives = 61/187 (32%), Gaps = 46/187 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVN-GILLERAAVNVMS 56
            V      QR+ + +       RR         +E+M  +  ++V+ G +  +++  + +
Sbjct: 8   TVAPEDAGQRLDRWL-------RRLFPQVTQGRIEKMCRKGDLRVDKGRV--KSSTRLEA 58

Query: 57  TDHIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDG 93
              + V  +P   A                           +   +KP GL T       
Sbjct: 59  GQVVRVPPLPESAAPEPAPRDAVSEADARLIRDCVLWSDDHIVALNKPAGLPTQGGSKQS 118

Query: 94  RSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVR 148
           R         +P+   +   V RLD +T G+LLL      A+ L   L   Q  ++Y   
Sbjct: 119 RHVDGLSQALVPAGAEKPRLVHRLDKDTSGVLLLARTRVAAQGLTAALRHKQTRKIYWAL 178

Query: 149 FHGQVDQ 155
             G    
Sbjct: 179 VAGVPTP 185


>gi|332199442|gb|EGJ13518.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA47901]
          Length = 278

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 TYVSRLKQFSNKTSLARCKLKTGRTHQIR 218


>gi|295110320|emb|CBL24273.1| pseudouridine synthase, RluA family [Ruminococcus obeum A2-162]
          Length = 293

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 67/176 (38%), Gaps = 26/176 (14%)

Query: 52  VNVMSTDHIEVDG-VPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTV------FD 99
             V   + ++ DG VP+        E   + + +KP  +    S  +  +T+      + 
Sbjct: 61  FRVRLLETVDSDGIVPVSMPLSILYEDEDILVINKPADMPVHPSIGNYTNTLANGVAAYL 120

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG------ 151
           +     S    + RLD +T G L+L  +   A VL     + Q  R Y     G      
Sbjct: 121 DAKDEHSPFRCINRLDRDTSGALILAKNAFSAAVLSTQMRNRQIRRTYLAVVEGITPPNG 180

Query: 152 ----QVDQDKLNLLKKGI-VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                + +   +++++ +  ++G         L+ +   ++ + + L  G+  +I+
Sbjct: 181 TISAPISRVDDSVIERHVDFLRGEPAVTHYERLEVKNE-HSLLEIHLETGRTHQIR 235


>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 (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 1/63 (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  RLW 76
           R +
Sbjct: 159 RRF 161


>gi|322495754|emb|CBZ31060.1| conserved hypothetical protein [Leishmania mexicana
           MHOM/GT/2001/U1103]
          Length = 741

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 39/122 (31%), Gaps = 22/122 (18%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS------TQWLRVYRV-RFHGQVDQDKLN 159
           R   V RLD  T G LL+      A  L          +   ++Y       +       
Sbjct: 568 RQGQVHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS----- 622

Query: 160 LLKKGIVIQGICYGDMQVTLDTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            L+  + +           + T+        K   AWV   +++GK  +I++      + 
Sbjct: 623 -LRN-VRLHDDIIDAADPKIRTRYRVIRFFPKHRVAWVECRIQQGKKHQIRRHLASRGFP 680

Query: 212 VN 213
           + 
Sbjct: 681 IL 682


>gi|145492917|ref|XP_001432455.1| hypothetical protein [Paramecium tetraurelia strain d4-2]
 gi|124399567|emb|CAK65058.1| unnamed protein product [Paramecium tetraurelia]
          Length = 469

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 43/303 (14%), Positives = 92/303 (30%), Gaps = 53/303 (17%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKP 81
           E  I + ++ VN + +      +     IE     +             E     +  KP
Sbjct: 54  ENAINEGKITVNSVRV-SPEYKLEHGMQIEHATTRVEPPILDLPVDIVFEDDSFVVVSKP 112

Query: 82  IGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
             ++         + +    +       +  + RLD  T GLL+ + +  LA+     ++
Sbjct: 113 PSMIVHTGGGYHYNCLSAILHFEHGLKDLYVLHRLDRLTSGLLIFSKNRLLAQKFHDANS 172

Query: 140 Q--WLRVYRVRFHGQVDQDKLNL--------LKKGI----------VIQGICYGDMQVTL 179
           +    + Y  R  G   +D            +K  I           +           L
Sbjct: 173 KLNVQKTYLARVQGNFSEDIKENNKPQYCVSMKDAIFACCTEEDAQKLDAKSATTKFEKL 232

Query: 180 DTQKGSNAWVT----VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-------- 227
                S++ +     +    G+  +I+         +  L  I YG   +G         
Sbjct: 233 WYDPISDSSLLECKPIT---GRTHQIRVHLADLGHPI--LNDIGYGGKFIGNEIVNRNFK 287

Query: 228 -LLAGSTR--EVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
            L   S R  +V +  + E +G  +    Q +      + E   ++ P+++     +   
Sbjct: 288 GLKQESIRQKDVLEGEVVEIVGKKVKLNTQEDEQQKEKNKEDQNQEEPSLLQNEQQEVAG 347

Query: 285 MKK 287
            +K
Sbjct: 348 QEK 350


>gi|332235181|ref|XP_003266785.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein 2
           [Nomascus leucogenys]
          Length = 545

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 46/291 (15%), Positives = 98/291 (33%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++   V +   D +          V   P+R  AE   + +  KP
Sbjct: 179 EAAVRAGRLHLNEKPVQDLNVVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 238

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 239 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 298

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 299 DRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGQSS 358

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +        +++GP +      G   + ++++L
Sbjct: 359 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSRGRG---GHIPKTNEELL 412

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +++   LD         + D     SE+  D       ++QK
Sbjct: 413 RDLVAEHQAKQSLDVLDLYEGDLSPGLTDSTAPSSELGKDNLEELAAAAQK 463


>gi|261326897|emb|CBH09870.1| hypothetical protein, conserved [Trypanosoma brucei gambiense
           DAL972]
          Length = 828

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/260 (15%), Positives = 68/260 (26%), Gaps = 88/260 (33%)

Query: 18  KVIARAGIAS--------RREVERMIAQ--QRVKVNGILLERAAVNVMSTDHIEVD---- 63
           +++A A   S        R E   ++A     V+V        AV +       V     
Sbjct: 537 QLLALAPHCSYWRTLLEKRPECADIVAAPEGHVRV--------AVRLPPEHE-CVRAAET 587

Query: 64  ---GVPLRKA--------ERTRLWLYHKPIGLVTTHS--------DPDGRSTVFDNLPSI 104
              G PL+          E   L + +KP  + T+          D      V   L   
Sbjct: 588 MRAGDPLKSPLPIFPVVYEDDDLLVINKPPHVATSRHALSCSQLCDDKATDIVSLQLTCK 647

Query: 105 FS--------RVISVGRLDINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRV--- 147
                     R   V RLD  T G L++      A  L          +Q  ++Y     
Sbjct: 648 KRGDVMRRVFRQGQVHRLDTETSGCLIMAKSDVAASSLRHQMGTSAAYSQSSKIYLALCA 707

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG--------------L 193
                +           I + G+        +           +               +
Sbjct: 708 VVESNLTN---------IPLNGVLRDPADAKI------TTKYRIVHFYKRFRVALVEARI 752

Query: 194 REGKNREIKKVFEFFNWKVN 213
           ++GK  +I++        + 
Sbjct: 753 QQGKKHQIRRHLAAVGLPIL 772


>gi|222823069|ref|YP_002574642.1| ribosomal pseudouridine synthase [Campylobacter lari RM2100]
 gi|222538290|gb|ACM63391.1| putative ribosomal pseudouridine synthase [Campylobacter lari
           RM2100]
          Length = 300

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/140 (20%), Positives = 53/140 (37%), Gaps = 15/140 (10%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  NG L+E     +     + V      G+ +   E     +  KP G+
Sbjct: 29  EAQKLIDKKRLFCNGNLVEEKNKFLDGLVELIVYENNPKGLEIVF-ENEDFAIVEKPSGV 87

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
           +T    P+GR+  +     I+           RLD  T GLLL+         L      
Sbjct: 88  LT---HPNGRNCTYSLCDEIWHLWGQNACVAHRLDKETSGLLLIAKHKNAQIELKTMFEK 144

Query: 139 TQWLRVYRVRFHGQVDQDKL 158
               + Y     G+  ++ +
Sbjct: 145 RLVQKSYLALVKGKTKEEFI 164


>gi|153815705|ref|ZP_01968373.1| hypothetical protein RUMTOR_01942 [Ruminococcus torques ATCC 27756]
 gi|317501908|ref|ZP_07960092.1| RluA family Pseudouridine synthase [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|145846946|gb|EDK23864.1| hypothetical protein RUMTOR_01942 [Ruminococcus torques ATCC 27756]
 gi|316896588|gb|EFV18675.1| RluA family Pseudouridine synthase [Lachnospiraceae bacterium
           8_1_57FAA]
          Length = 295

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 25/161 (15%), Positives = 58/161 (36%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K  G+    S  + R+++ + L   + +           RLD +T GL ++
Sbjct: 86  EDEDIIVINKAAGMPIHPSLNNYRNSLANALMWYYEQQNKPFIFRCTNRLDRDTSGLTVV 145

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQVD--QDKLNL---------LKKGIVIQGIC 171
                 + +L       Q  R Y     G V   +  +N          +++ I  +   
Sbjct: 146 AKHMVSSNILSSMTARHQIEREYLAIVRGHVTPFEGTINAPIGRTGSSLIERKIDFENGE 205

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
           +         +K   + V++ L  G+  +I+  + +   + 
Sbjct: 206 HAITHYHTVFEKNGLSLVSLILETGRTHQIRVHM-KHLGFP 245


>gi|85713201|ref|ZP_01044230.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85692974|gb|EAQ30943.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 315

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 81/234 (34%), Gaps = 40/234 (17%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V  +   QR+   + AR     +  V R++ +  V+VN     +    + + D I +  V
Sbjct: 13  VARDEAGQRIDNFLIARLRGVPKSLVYRILRKGEVRVNKKR-TKPDYKIKAGDAIRIPPV 71

Query: 66  PLRKA--------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPS 103
            +                       E     + +KP GL            +     L  
Sbjct: 72  KVSPKPELPSPKLAKVAELEQAIVYEDDAFMIVNKPSGLAVHGGSGLNFGLIEGLRALRP 131

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLL 161
             + +  V RLD +T GL+++     + +VL   L   +  + Y     GQ  Q  +  +
Sbjct: 132 QDNALELVHRLDRDTSGLIMIAKKRSVLKVLHAQLRDKEMNKQYLALVRGQW-QKNVRNV 190

Query: 162 KKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV-------GLRE-----GKNREIK 202
           +  +    +  G+  V +D + K S+    +        L E     G+  +I+
Sbjct: 191 EAPLKKNTLKSGERIVRVDAEGKPSHTRFRINQRYAEATLVEASPVTGRTHQIR 244


>gi|325921580|ref|ZP_08183425.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           gardneri ATCC 19865]
 gi|325547934|gb|EGD18943.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           gardneri ATCC 19865]
          Length = 331

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 61/322 (18%), Positives = 110/322 (34%), Gaps = 43/322 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-----RAAVNVMSTDH 59
           IV +N   +R   V+A      SR  +   I      +NG +       R   +V     
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLNGEMARPRDTLRGGESVQVQVV 76

Query: 60  IEVD------GVPLRK-AERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIF----S 106
           +E+        +PL    E  ++ +  KP GLV      +PDG                 
Sbjct: 77  LEIQTHSEPQDIPLSVLYEDDQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDPALAAVP 136

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVD 154
           R   V RLD +T G++++         L  +L +    R Y     G           +D
Sbjct: 137 RAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGTANAPID 196

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           +   + LK  +   G          +  +   A +   L  G+  +I+         +  
Sbjct: 197 RHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHLKSPIVG 255

Query: 215 --LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVR 269
             L    YG   L  L  G++ E+  ++    R+ L    LE        P+ +S  +  
Sbjct: 256 DPL----YGG-ALK-LPKGASDELVHELRTFKRQALHAETLEFLHPVSGEPVRASAPVPV 309

Query: 270 DRPNIISEVPDDFTRMKKNSSQ 291
           D   +++ + +D  R  + + +
Sbjct: 310 DLQRLMTALREDSVRAAEQARR 331


>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 = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|225861831|ref|YP_002743340.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|225728075|gb|ACO23926.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|327389005|gb|EGE87352.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA04375]
          Length = 278

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 TYVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>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 = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 76/218 (34%), Gaps = 35/218 (16%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHGQV------------DQDKLNLLKKGIVIQGICYG 173
                 L    ++  + ++Y    HG +            ++++   +K+ IV +     
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYNEEESESIKR-IVDERGQES 206

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +  +    + V + L  G+  +I+         
Sbjct: 207 ITTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|145634591|ref|ZP_01790300.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittAA]
 gi|148825307|ref|YP_001290060.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittEE]
 gi|148827612|ref|YP_001292365.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittGG]
 gi|229846499|ref|ZP_04466607.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 7P49H1]
 gi|319775660|ref|YP_004138148.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3047]
 gi|329122287|ref|ZP_08250875.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
 gi|145268136|gb|EDK08131.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittAA]
 gi|148715467|gb|ABQ97677.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae PittEE]
 gi|148718854|gb|ABQ99981.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae PittGG]
 gi|229810592|gb|EEP46310.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 7P49H1]
 gi|317450251|emb|CBY86467.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3047]
 gi|327473848|gb|EGF19265.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           aegyptius ATCC 11116]
          Length = 322

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|66044884|ref|YP_234725.1| pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|289671959|ref|ZP_06492849.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. syringae FF5]
 gi|63255591|gb|AAY36687.1| Pseudouridine synthase, RluD [Pseudomonas syringae pv. syringae
           B728a]
 gi|330900159|gb|EGH31578.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. japonica str. M301072PT]
 gi|330952677|gb|EGH52937.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae Cit 7]
 gi|330973866|gb|EGH73932.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aceris str. M302273PT]
 gi|330975220|gb|EGH75286.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aptata str. DSM 50252]
          Length = 318

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 39/207 (18%), Positives = 70/207 (33%), Gaps = 38/207 (18%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAW 188
           R L   L      + Y     G      L  ++  ++   +  G+  V + +  K +   
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNW-ATALKQVRAPLMKSNLRSGERMVEVNEEGKEALTI 221

Query: 189 VTV--------GLRE-----GKNREIK 202
             V         + E     G+  +I+
Sbjct: 222 FKVLRRFGDFATMVEAKPVTGRTHQIR 248


>gi|327395022|dbj|BAK12444.1| tRNA pseudouridine synthase C TruC [Pantoea ananatis AJ13355]
          Length = 259

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 50/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D      V   +       V +  RLD  T G+LL+     + 
Sbjct: 11  LVAVNKPAGWLVHRSWLDRHETQFVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEVG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G ++          ++L+ +    V              
Sbjct: 71  RLLSQQFEHHQMEKTYHAVVRGWLEGRDRLDYPLVEELDKIADKFVSDPRAPQPAVTDYA 130

Query: 176 -------QVTLDT-QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                   V +        + + +  + G+  ++++        + 
Sbjct: 131 SLATVEMPVAVSRYPTARYSLIELKPKTGRKHQLRRHMSHLRHPII 176


>gi|289522930|ref|ZP_06439784.1| ribosomal large subunit pseudouridine synthase D [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
 gi|289503954|gb|EFD25118.1| ribosomal large subunit pseudouridine synthase D [Anaerobaculum
           hydrogeniformans ATCC BAA-1850]
          Length = 299

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 78/236 (33%), Gaps = 52/236 (22%)

Query: 6   IVQENFTPQRVS----KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV------- 54
           +V + F  +R+     K+ AR    SR +++R +             + ++ V       
Sbjct: 8   VVSDEFIGERLDVAVSKITAR----SRSQIQRAMR--------EAGFKPSMKVREAMNLE 55

Query: 55  ----MSTDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVF--------D 99
                      ++  P+      E   + +  KP  LV   +      T+         +
Sbjct: 56  LSFHDEEKEATLEPEPVNFEVLYEDADIIIIDKPAPLVVHPAVGHWYGTLVHGLVYRYPE 115

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
              S   R   V RLD  T GL+++  +    + L     +    + Y    +G  +++K
Sbjct: 116 LADSDMRRPGIVHRLDAGTSGLMVIARNLFSKQKLTDAFKARSVKKEYLALVYGSPNKEK 175

Query: 158 -----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       N LK  +V  G      +  +       +++   +  G+  +I+
Sbjct: 176 GTIASPIGRHPKNRLKMAVV-SGGREAVTEYEVLWSNDKFSFLRCTIHTGRTHQIR 230


>gi|260460313|ref|ZP_05808565.1| hemolysin A [Mesorhizobium opportunistum WSM2075]
 gi|259033958|gb|EEW35217.1| hemolysin A [Mesorhizobium opportunistum WSM2075]
          Length = 254

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          QR+  ++ + G  ASR      + +  V V+G++  +   NV     + +D        R
Sbjct: 11 QRLDDLLVQRGLFASRSRARDAVERGTVTVDGVIARKPGQNVSLQCLVTIDDPAQGYVSR 70

Query: 73 TRLWLY 78
            L L 
Sbjct: 71 AALKLL 76


>gi|219684788|ref|ZP_03539730.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia garinii PBr]
 gi|219685395|ref|ZP_03540214.1| ribosomal large subunit pseudouridine synthase D [Borrelia garinii
           Far04]
 gi|219671733|gb|EED28788.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia garinii PBr]
 gi|219673168|gb|EED30188.1| ribosomal large subunit pseudouridine synthase D [Borrelia garinii
           Far04]
          Length = 326

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 84/254 (33%), Gaps = 65/254 (25%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG   + + +  V
Sbjct: 4   LKKEFTVKENAL--RLDLYLSNNLEVFTRSQ----IKRRNVEAFKKSNGKFFKIKLSKPV 57

Query: 55  MSTDH--IEVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D   IE D             +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKNDEMLIEFDEESNQIDCLRPNNIPIAIIYEDSNIIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFSRVIS-----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L     R+             V RLD +T G+L+   +      L       +  +VY 
Sbjct: 118 FLLYHIKRLKINFNEEKVRPGIVHRLDKDTSGVLICAKNINTLSFLAQQFKDKKTNKVYI 177

Query: 147 VRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL------- 193
               G  +      +  ++                 V+ D  K +     + L       
Sbjct: 178 AIVKGNFNSFSGSIESFIDR-------DKYNRKKFSVSKDRGKKALTEYRLLLNFGGYSL 230

Query: 194 -----REGKNREIK 202
                + G+  +++
Sbjct: 231 LALKPKTGRTHQLR 244


>gi|320544924|ref|NP_001188782.1| RluA-2, isoform B [Drosophila melanogaster]
 gi|318068416|gb|ADV37032.1| RluA-2, isoform B [Drosophila melanogaster]
          Length = 583

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 68/197 (34%), Gaps = 29/197 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 209 ERSLEAGKLTVNSEKVPK-DYKIKHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKP 267

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        + ++ RLD  T GLLL       AR LEL   
Sbjct: 268 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIR 327

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----- 192
           + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G     
Sbjct: 328 TRQVQKEYVCRVEGRFPDGIVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEVGSD 386

Query: 193 -------LREGKNREIK 202
                  L  G+  +I+
Sbjct: 387 SIVLCKPLT-GRMHQIR 402


>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 = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|325846771|ref|ZP_08169686.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481529|gb|EGC84570.1| pseudouridine synthase, RluA family [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 264

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 29/209 (13%), Positives = 61/209 (29%), Gaps = 36/209 (17%)

Query: 35  IAQQRVKVNGILL-ERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIG 83
           I    V VN   + +   +       I ++   L             E   +    KP  
Sbjct: 31  IINNLVYVNDEKINKNIGLKAGDKVKILIEDENLNYEPINKKIKILYEDKDIVAVDKPPN 90

Query: 84  LVTTHSDPDGRSTVFDNLPSIFS---RVISVGRLDINTEGLLLLTNDG----GLARVLEL 136
           L     + +  S              ++  + RLD+NT G++L+  +          +  
Sbjct: 91  LTVNSKNQESLSNYLAYYFKENKIKSQIRLINRLDMNTSGIMLVAKNPFSHAYYQNQI-- 148

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-GICYGDMQVTLDTQKGSN--------- 186
            + +  + Y     G +    ++   + I I        M+V  D               
Sbjct: 149 ENNELDKEYLALVEGNL---IIDDFCE-IDIDYDKENKKMKVVSDKNHVKTYFKTLKNYG 204

Query: 187 --AWVTVGLREGKNREIKKVFEFFNWKVN 213
             + +   +  GK  +I+    + N  + 
Sbjct: 205 KFSLIYCKIYTGKTHQIRLSLAYLNHPIL 233


>gi|325911465|ref|ZP_08173877.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
 gi|325476815|gb|EGC79969.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII
           143-D]
          Length = 309

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 49  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 107

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 108 ADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITRLDRDTSGLVLVGKNAVAHARF 167

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 168 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKNSVTKYR 223

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 224 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 256


>gi|301166303|emb|CBW25879.1| putative pseudouridylate synthase [Bacteriovorax marinus SJ]
          Length = 230

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 43/184 (23%), Positives = 69/184 (37%), Gaps = 23/184 (12%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           AE     L +KP G ++ H+D     +V +        +    R+D  T GLLLLT +  
Sbjct: 11  AEDQSWILINKP-GAMSVHNDSK---SVIEYFKQRNINLTPPHRIDKETSGLLLLTKEKN 66

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGDMQVTLDT-- 181
                +       + Y     GQV  D       L+   +G         D ++ L    
Sbjct: 67  EVSNHQQQLKNASKYYIAICRGQVKADNGKWEQPLSDKAEGHKNPAGKKSDQKICLTNWW 126

Query: 182 QKGSNAWVTVGLR--E-GKNREIKKVFEFFNWKVNRLIRISYG--------PFQLGTLLA 230
           +  SN +VT+ L   E G+  +I+K       ++    R   G         +QL ++L 
Sbjct: 127 KVSSNQYVTLILFKIETGRTHQIRKHCALNGHEILGDKRYGQGKYQKIIKDKYQLDSMLL 186

Query: 231 GSTR 234
            S R
Sbjct: 187 HSYR 190


>gi|311063909|ref|YP_003970634.1| ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
 gi|310866228|gb|ADP35597.1| Ribosomal large subunit pseudouridine synthase D [Bifidobacterium
           bifidum PRL2010]
          Length = 313

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 76/226 (33%), Gaps = 38/226 (16%)

Query: 21  ARAGIASRREVERMIAQQRVKV-NGILLERAAVNVMSTDHIEVDGVPLRKAERTRL---- 75
           ++    SR +   +I   + +V N  + +   +  +  + +E D    R           
Sbjct: 21  SKMLGISRAKAADLIESGQARVLNRAIAKSGTL--LYGETVEFDIAEERHEPEPVCLDMA 78

Query: 76  WLYH--------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG---------RLDINT 118
            +Y         KP+G+    S      TV  +L     R+ S G         RLD+ T
Sbjct: 79  IVYEDDDVVVVDKPVGVAAHASAGWTGPTVLGSLLKRGVRITSYGAPGRQGIVSRLDVGT 138

Query: 119 EGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD-----------KLNLLKKGI 165
            GL+L+       + +    ++    + Y     G + +D           K++  +  +
Sbjct: 139 SGLMLVCKSELAYKEMRRQFSEHEVVKTYHAMVQGNLKEDKATIEAPIGRAKVSDFRFCV 198

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              G         LD + G    V+V L  G+  +I+  F      
Sbjct: 199 TPSGKPAVTHWDVLD-RFGEATLVSVNLETGRTHQIRVHFSSIGHP 243


>gi|226324582|ref|ZP_03800100.1| hypothetical protein COPCOM_02366 [Coprococcus comes ATCC 27758]
 gi|225207030|gb|EEG89384.1| hypothetical protein COPCOM_02366 [Coprococcus comes ATCC 27758]
          Length = 302

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 77/197 (39%), Gaps = 34/197 (17%)

Query: 40  VKVNGILL---------ERAAVNVMST---DHIEVDGVPLR-KAERTRLWLYHKPIGLVT 86
           +++NG  +         ++ A+ +  T   ++I    +PL    E   L + +KP G+  
Sbjct: 50  IRLNGEPVLARTLLTPGDQLAIRITETKFSENIVPSDLPLSIVYEDPDLLVINKPAGMPI 109

Query: 87  THSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
             S  +  +T+ +     F           + RLD +T GLL++      A +L   +  
Sbjct: 110 HPSQGNYDNTLANACAWYFKEKGEPFVYRCINRLDRDTTGLLIIARHLYSASLLSAMMAR 169

Query: 139 TQWLRVYRVRFHGQVDQDKLNLL----KKGIVIQ---GICYGD------MQVTLDTQKGS 185
            +  R Y     G V +D +       K+G  I+      +G+       ++++      
Sbjct: 170 REIHREYLALATGIVPEDGIITAPIARKEGSTIERMVDFKHGEYACTHYRRISITNTDPV 229

Query: 186 NAWVTVGLREGKNREIK 202
            + V + L  G+  +I+
Sbjct: 230 YSLVALKLDTGRTHQIR 246


>gi|94984711|ref|YP_604075.1| pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
 gi|94554992|gb|ABF44906.1| Pseudouridine synthase, RluD [Deinococcus geothermalis DSM 11300]
          Length = 341

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 42/259 (16%), Positives = 71/259 (27%), Gaps = 65/259 (25%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIA------------------QQRVKVNGILLERAA 51
             TP R+  V+A     SR +    IA                  +      G  L    
Sbjct: 28  TATPGRLDSVLADLTGVSRSQAAGWIAGGQVEVGGVVVQKASLKLKG-----GETLR--- 79

Query: 52  VNVMSTDHIEVDGVPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD------NLP 102
           V V       V    +      E   L   +KP G+VT  +      T+ +       LP
Sbjct: 80  VQVPPPPDATVSPEAVPLDVLYEDEHLIAVNKPPGMVTHPAPGVTSGTLVNALLGRLTLP 139

Query: 103 SIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR------- 146
                V         V RLD +T G++++         L          + Y        
Sbjct: 140 EQPGAVGPDGYRPGIVHRLDKDTSGVIVVAKTVEAHARLAAAFKDRSTHKTYLAIAAGMW 199

Query: 147 -----VRFHGQVDQDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGL-----R 194
                V  +  V +      ++ + + G+   + Q   T           T+ L      
Sbjct: 200 KAQGPVSVNAPVGRH--PTARQRMTVGGVGPREAQTLFTPLATHPDGHGRTLALVRAQPH 257

Query: 195 EGKNREIKKVFEFFNWKVN 213
            G+  +I+         + 
Sbjct: 258 TGRTHQIRVHLAHLGSPIL 276


>gi|145636319|ref|ZP_01791988.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittHH]
 gi|145270484|gb|EDK10418.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittHH]
          Length = 322

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRIKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|37524616|ref|NP_927960.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36784040|emb|CAE12909.1| ribosomal large subunit pseudouridine synthase A (pseudouridylate
           synthase) (uracil hydrolyase) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 216

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 26/157 (16%), Positives = 59/157 (37%), Gaps = 27/157 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TND 127
           +   + + +KP GL++      + + ++   +   F    SV RLD+ T G++++  T D
Sbjct: 17  QDQYIIVVNKPSGLLSVPGRAAEHKDSIMTRIQQQFPAAESVHRLDMATSGVMVVALTKD 76

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVTLDTQ 182
                  +    +  + Y  R  G+++ +       G+V    I         +V  +T 
Sbjct: 77  AERELKRQFREREPEKTYIARVWGRLEPET------GLVDLPLICDWPNRPKQKVCFETG 130

Query: 183 KGSNAWVTVGLRE------------GKNREIK-KVFE 206
           K +     V   E            G++ +++  +  
Sbjct: 131 KSAQTEYEVLAYEDEATRIKLSPITGRSHQLRVHMLA 167


>gi|15642501|ref|NP_232134.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|153817992|ref|ZP_01970659.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|153822421|ref|ZP_01975088.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227082624|ref|YP_002811175.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229507437|ref|ZP_04396942.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229509638|ref|ZP_04399119.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229516763|ref|ZP_04406209.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229606943|ref|YP_002877591.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254851050|ref|ZP_05240400.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255744517|ref|ZP_05418469.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262154659|ref|ZP_06028785.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|298500664|ref|ZP_07010468.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
 gi|34395834|sp|Q9KP71|RLUA_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|9657087|gb|AAF95647.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|126511427|gb|EAZ74021.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           NCTC 8457]
 gi|126520064|gb|EAZ77287.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|227010512|gb|ACP06724.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           M66-2]
 gi|229345826|gb|EEO10798.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           RC9]
 gi|229353112|gb|EEO18051.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           B33]
 gi|229354942|gb|EEO19863.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           BX 330286]
 gi|229369598|gb|ACQ60021.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MJ-1236]
 gi|254846755|gb|EET25169.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MO10]
 gi|255738042|gb|EET93435.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholera
           CIRS 101]
 gi|262030499|gb|EEY49137.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           INDRE 91/1]
 gi|297540833|gb|EFH76890.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           MAK 757]
          Length = 245

 Score = 53.3 bits (127), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 24/164 (14%), Positives = 57/164 (34%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN--- 126
           E   +   +KP GL++    P +   +++  L      V  V RLD++T GL+L      
Sbjct: 19  EDEHIIAANKPSGLLSVPGRPVEHYDSMWARLVDYCPDVKVVHRLDMSTSGLILFAKGKH 78

Query: 127 -----DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGI 170
                       L        ++Y  R  G ++Q++               K+ +  +  
Sbjct: 79  MESALKKQFQYRLTH------KIYYARVWGVMEQNEGEVNLPLCCDWPNRPKQKVCFEEG 132

Query: 171 CYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                +  +  ++     V +  +  G++ +++   +     + 
Sbjct: 133 RDSLTRYQVVKREEKTTVVRLIPIT-GRSHQLRVHMQSLGHPIV 175


>gi|331269001|ref|YP_004395493.1| RluA family pseudouridine synthase [Clostridium botulinum
           BKT015925]
 gi|329125551|gb|AEB75496.1| pseudouridine synthase, RluA family [Clostridium botulinum
           BKT015925]
          Length = 323

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 39/265 (14%), Positives = 89/265 (33%), Gaps = 69/265 (26%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           +  N   QR+ K         R+ +E        + + +  ++VNG   ++    +   D
Sbjct: 5   IGPNEAGQRLDKF------C-RKWLEDVPLGAIFKALRKGDIRVNGKKAKQ-NYFLQEED 56

Query: 59  HIE--------------------VDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            IE                    VD   ++   E   + +  K  G++      DG  T+
Sbjct: 57  IIETKYIETYKQNKKNMPKKFQEVDFSSIKISYEDENMLIIEKWPGVLVHSDKKDGEPTL 116

Query: 98  FDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S   +                  RLD NT G+++   +    ++L   +   +  
Sbjct: 117 TDYVLSYLFQKGDYDPQKEVTFTPAPCNRLDRNTSGMVIFGKNFKTLKILNAMIRERKIK 176

Query: 143 RVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYG-----DMQVTLDTQKGSNAW 188
           + Y     G++ +         D++N +     I            M+V +    G+ ++
Sbjct: 177 KYYNALVKGKIKEGYYEAYISKDQVNNIS---EIHKEKKQNSKKIAMEVNVIDTVGTFSF 233

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           + + L  G++ +++    +    + 
Sbjct: 234 LELDLLTGRSHQLRAHLAYLGNPII 258


>gi|313624349|gb|EFR94381.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria innocua FSL J1-023]
          Length = 208

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/211 (15%), Positives = 70/211 (33%), Gaps = 33/211 (15%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDG 128
           L + +KP G+ +  S      +V + +   +        +  V RLD  T GL+L+  + 
Sbjct: 1   LLIINKPAGMASIPSQYHPTGSVANFVKGHYENQGLTSAIHIVTRLDRETSGLMLIAKNR 60

Query: 129 GLARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDM 175
                L          R Y+    G            + +  ++++++ +  +G      
Sbjct: 61  YAHARLSSFLQQGLLKRRYQAFTSGTLEEAAGSIEAPIGRKDVSIMERFVTPEGKYAKTN 120

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              L    G +  + + L  G+  +I+  F +    +        G      +  G    
Sbjct: 121 YEVLMRYNGFDH-LAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDQEL 168

Query: 236 VSKKILR--EQLGPHLLEEAQVNLDAPIYSS 264
           + ++ L        H + E  +  D P+   
Sbjct: 169 LKRQALHSCHLHLVHPVTEEYMAFDLPLPED 199


>gi|308273177|emb|CBX29780.1| hypothetical protein N47_F14750 [uncultured Desulfobacterium sp.]
          Length = 271

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/159 (15%), Positives = 57/159 (35%), Gaps = 22/159 (13%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------PSIFSRVISVGRLD 115
           G+ +   +R  + +  K  GL++  ++ +  +T  + L        P     +  V RLD
Sbjct: 41  GLRILYEDRD-IIVIDKSSGLLSVEANYEAENTAHNLLTNYVRKGNPKARINLFVVHRLD 99

Query: 116 INTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD--KLNL-LKKG-------- 164
             T G+L+      +            + Y    +G + +    +   L +G        
Sbjct: 100 RETSGVLIFAKSLEIREKFAAQWKNVEKKYIALVYGNLTKKSGIIESYLAEGDNYKVQSV 159

Query: 165 -IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              I+G      +  +  +  + + + + L  GK  +I+
Sbjct: 160 KNPIEG-KLAITKYKVIKESKNYSLLEIDLLTGKKNQIR 197


>gi|262283613|ref|ZP_06061378.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           2_1_36FAA]
 gi|262260670|gb|EEY79371.1| ribosomal large subunit pseudouridine synthase D [Streptococcus sp.
           2_1_36FAA]
          Length = 290

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/205 (16%), Positives = 68/205 (33%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTD--HIEVDGV--------------PLRKAE 71
           R++   +  ++ V VN   +      + + D   +  D                     +
Sbjct: 28  RKIRHFLRTKKHVLVNNQTI-NWQSKIQAGDLLSLTFDEEDYPAKDILMGHPELVQELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGAVLFAKNPFVL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVD------QDKL-----NLLKKGIVIQGICYGDMQV 177
            +   L   +    R Y     G+        +DK+     +  K+ +  +   Y +  V
Sbjct: 147 PILNRLL-ENKDIQREYWALVDGKFPVKNRVFKDKIGRDRHDRRKRLVDSKHGQYAETHV 205

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T     G    +   L+ G+  +I+
Sbjct: 206 TRLKSFGQKTLIKCQLKTGRTHQIR 230


>gi|19921090|ref|NP_609411.1| RluA-2, isoform A [Drosophila melanogaster]
 gi|16198203|gb|AAL13915.1| LD40728p [Drosophila melanogaster]
 gi|22946170|gb|AAF52961.2| RluA-2, isoform A [Drosophila melanogaster]
 gi|220946196|gb|ACL85641.1| RluA-2-PA [synthetic construct]
 gi|220955960|gb|ACL90523.1| RluA-2-PA [synthetic construct]
          Length = 547

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 68/197 (34%), Gaps = 29/197 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 173 ERSLEAGKLTVNSEKVPK-DYKIKHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKP 231

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        + ++ RLD  T GLLL       AR LEL   
Sbjct: 232 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIR 291

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----- 192
           + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G     
Sbjct: 292 TRQVQKEYVCRVEGRFPDGIVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEVGSD 350

Query: 193 -------LREGKNREIK 202
                  L  G+  +I+
Sbjct: 351 SIVLCKPLT-GRMHQIR 366


>gi|296102445|ref|YP_003612591.1| pseudouridylate synthase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
 gi|295056904|gb|ADF61642.1| pseudouridylate synthase [Enterobacter cloacae subsp. cloacae ATCC
           13047]
          Length = 228

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/187 (17%), Positives = 62/187 (33%), Gaps = 37/187 (19%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE+        +   L L +KP GL++ +  +P    +V   L   F     V R
Sbjct: 12  PCHDDIEI------LWQDEHLLLINKPSGLLSLSGKNPQNLDSVHYRLVQSFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G ++ +      +GI+   I 
Sbjct: 66  LDFGTSGLMVIARNKPINAALCQQFSQRSVEKVYSALLCGHLENN------EGIIDAPIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG--LRE---------------GKNREIKKVFEFFN 209
                     +     K + +   V   L +               G+  +++   +   
Sbjct: 120 KDPALFPLMSICAVNGKPARSRYRVVERLYQNAAMPLTRVELTPETGRTHQLRIHCQLLG 179

Query: 210 WKVNRLI 216
             +    
Sbjct: 180 HPILGCD 186


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+ +++   G  A+R      I +  VKV+G  + +    V+   +I VD        R 
Sbjct: 11 RLDQLLVELGLFATRSRARDAIQRGTVKVDGKPVTKPGQTVLRNANIAVDDPASAYVSRA 70

Query: 74 RLWLY 78
           L L 
Sbjct: 71 ALKLI 75


>gi|218896324|ref|YP_002444735.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228899971|ref|ZP_04064209.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
 gi|218541071|gb|ACK93465.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus G9842]
 gi|228859657|gb|EEN04079.1| Pseudouridine synthase [Bacillus thuringiensis IBL 4222]
          Length = 307

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 86/261 (32%), Gaps = 49/261 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +K   + T
Sbjct: 47  VTVNGEQ-RRWNELLKENDKLQVHMFAEEEYGVDPEYGELHVVYEDDHVLIVNKLEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGNGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ I  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRISPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
             +VT+ L  G+  +I+                   P     L  G T+ +S + L    
Sbjct: 225 TTFVTLQLETGRTHQIRVHMSHNGN-----------PLVGDVLYGGQTKYMSSQALHAMK 273

Query: 246 GP--HLLEEAQVNLDAPIYSS 264
               H + +  + +D P  + 
Sbjct: 274 INFLHPITKEAIEVDVPFPTK 294


>gi|27804835|gb|AAO22876.1| AgmF [Myxococcus xanthus]
          Length = 264

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 72/226 (31%), Gaps = 40/226 (17%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           +RV + +ARA    +R  +  +I    V  +G   +  A  +   + + +          
Sbjct: 18  ERVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAK-PARRLRGGELLVLHIPAPVPAVP 76

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
                      E   L +  K  G+V          T+ + L      +  VG       
Sbjct: 77  LAEELPLALLHEDRDLVVVDKAAGMVVHPGAGHASGTLVNALLHRVKDLAGVGGELRPGI 136

Query: 113 --RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD------------ 156
             RLD +T G L++  +      L+    +    + Y    HG    +            
Sbjct: 137 VHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGVPPAEGRIETLYGRHPI 196

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G V +G         L+T  G+ A V V L  G+  +I+
Sbjct: 197 HRQRFT-GKVKEGKNAITEYRVLETFDGA-ALVEVDLLTGRTHQIR 240


>gi|268315647|ref|YP_003289366.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262333181|gb|ACY46978.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 235

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 36/160 (22%), Positives = 54/160 (33%), Gaps = 21/160 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGG 129
           E   L   HKP GL         R +    L +    R+  V RLD    G+LL   +  
Sbjct: 8   EDDDLLAVHKPEGLAAIPERDPSRPSARRLLEAARGERLWVVHRLDKEASGVLLFARNAE 67

Query: 130 LARVLEL---PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            A           Q  +VYR   HG+++  +   ++  I + G   G M V  +  K S 
Sbjct: 68  -AHRYMNTLFEQRQVRKVYRALVHGRLEPGQ-GQIRAPIRMYG--SGRMGVDPERGKPSE 123

Query: 187 AWVTV--------GLRE-----GKNREIKKVFEFFNWKVN 213
               V         L E     G+  +I+         + 
Sbjct: 124 TRYRVLEYLDEAYSLIEALPLTGRRHQIRVHCYHIGHPIV 163


>gi|237750207|ref|ZP_04580687.1| predicted protein [Helicobacter bilis ATCC 43879]
 gi|229374101|gb|EEO24492.1| predicted protein [Helicobacter bilis ATCC 43879]
          Length = 671

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 41/101 (40%), Gaps = 5/101 (4%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDG 128
                  +++KP  L+T   +     ++ D+L   F        RLD  T GLL+ + D 
Sbjct: 96  QNPPYFCVFNKPSKLLTHPKNLADSKSILDSLRYYFGKHANPCHRLDYETSGLLVCSIDK 155

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
               +L+         + Y    HG+V +  L  ++ GI+ 
Sbjct: 156 QSEVMLKNLFLQKGVEKSYMAILHGEVKESLL--IESGIIF 194


>gi|149907559|ref|ZP_01896306.1| Pseudouridylate synthase [Moritella sp. PE36]
 gi|149809229|gb|EDM69158.1| Pseudouridylate synthase [Moritella sp. PE36]
          Length = 251

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/173 (17%), Positives = 53/173 (30%), Gaps = 32/173 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTND 127
           +   L    KP GL+   S  D   T F        I   V +V RLD  T G+LL    
Sbjct: 7   QDEYLVAIDKPAGLLVHRSWLDSHETQFAMQMVRDQIGQHVYTVHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-- 183
             +AR +     +    + Y     G +++         + +      D Q T D +   
Sbjct: 67  SEVARQMSEIFQAHALTKRYLAVVRGWINEAGTLDYALKVELD--KIADKQATQDKEAQE 124

Query: 184 -----GSNAWVTV-------------GLRE-----GKNREIKKVFEFFNWKVN 213
                     V +              L E     G+  ++++  +     + 
Sbjct: 125 AVTHYKPLHQVEIPYPISKNHPTSRYCLMELEPQTGRKHQLRRHMKHLFHPIV 177


>gi|145630415|ref|ZP_01786196.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R3021]
 gi|145638677|ref|ZP_01794286.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittII]
 gi|229844426|ref|ZP_04464566.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 6P18H1]
 gi|144984150|gb|EDJ91587.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R3021]
 gi|145272272|gb|EDK12180.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae PittII]
 gi|229812675|gb|EEP48364.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae 6P18H1]
 gi|309750170|gb|ADO80154.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R2866]
          Length = 322

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRIKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|309810028|ref|ZP_07703875.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169668|gb|EFO71714.1| pseudouridine synthase, RluA family [Lactobacillus iners SPIN
           2503V10-D]
          Length = 302

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 42  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 100

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 101 ADLLTIPSKNEDNDSVVGRLLHYLNPDALIKIKPHIITRLDRDTSGLVLVGKNAVAHARF 160

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 161 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKNSVTKYR 216

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 217 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 249


>gi|300784875|ref|YP_003765166.1| ribosomal large subunit pseudouridine synthase D [Amycolatopsis
           mediterranei U32]
 gi|299794389|gb|ADJ44764.1| ribosomal large subunit pseudouridine synthase D [Amycolatopsis
           mediterranei U32]
          Length = 309

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 71/249 (28%), Gaps = 49/249 (19%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA----------VNVMS 56
           V +     RV   +A+    SR  V  +     V ++G    ++                
Sbjct: 8   VPDGLDGMRVDAGLAKLLGLSRTVVAELAESGDVLLDGRPAGKSDRLSGGGLLEITLPEP 67

Query: 57  TDHIE-----VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
            + +E     VDG+ +   +   + +  KP+G+    S      TV   L          
Sbjct: 68  ANPVEVVAQPVDGMQILHDDDDIVVI-SKPVGVAVHPSPGWTGPTVVGGLAAAGLRIATS 126

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNL 160
               R   V RLD  T G++++        VL+    +    + Y     G  D      
Sbjct: 127 GAAERQGVVHRLDAGTTGVMVVAKSEHAYTVLKRAFKERTVDKGYHAIVQGHPDP----- 181

Query: 161 LKKGIVIQGICYGD----MQVTLDTQKGSNAWVTVG------------LREGKNREIKKV 204
             +G +   I            +   + S     V             L  G+  +I+  
Sbjct: 182 -MRGTIDAPIDRHPRHDYKFAVVQGGRPSVTHYEVVEAFRAASLTHIKLETGRTHQIRVH 240

Query: 205 FEFFNWKVN 213
           F        
Sbjct: 241 FSALRHPCV 249


>gi|260582324|ref|ZP_05850117.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|319898067|ref|YP_004136264.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3031]
 gi|260094692|gb|EEW78587.1| pseudouridylate synthase [Haemophilus influenzae NT127]
 gi|309972429|gb|ADO95630.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae R2846]
 gi|317433573|emb|CBY81957.1| 23S rRNA pseudouridylate synthase [Haemophilus influenzae F3031]
          Length = 322

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|332161266|ref|YP_004297843.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318605161|emb|CBY26659.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665496|gb|ADZ42140.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330860585|emb|CBX70883.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           enterocolitica W22703]
          Length = 232

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/190 (19%), Positives = 65/190 (34%), Gaps = 41/190 (21%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  +P    +V   L  IF     V RLD  T GL+++  +  
Sbjct: 22  QDDHLVLINKPTGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHRLDFGTSGLMVIARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +   L    +Q    +VY     G +D +      +G++   I        L +      
Sbjct: 82  INAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIAKDPALFPLMSICATHG 135

Query: 183 KGSNAWVTVG---LRE------------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V      E                  G+  +++   +     +       YG
Sbjct: 136 KPARSGYRVVERFYHELEDGRLLPLTRVQLTPETGRTHQLRIHCQQLGHPIWGCD--LYG 193

Query: 222 PFQLGTLLAG 231
               G LL G
Sbjct: 194 ----GRLLPG 199


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 65/208 (31%), Gaps = 35/208 (16%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------LWLYHKP 81
           ++++ VNG  L      V   D IE+    +   ++                 + + +KP
Sbjct: 39  EKKILVNGKYL-PLNFLVKPGDKIEIQLDHIESDQQPYPASGKLPKVVYEDNDILVINKP 97

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL----ARVLELP 137
            G  T  +  +  + + D    +      V RLD+ T GLLL+  +  +     R L   
Sbjct: 98  AGQKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDK 157

Query: 138 STQWLRVYRVRF------------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +    R Y                   +  D  +  K+ +   G         +  +   
Sbjct: 158 TLH--REYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVRQDGQKAVTH-YEVIKRDKD 214

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
              V + L  G+  +I+         + 
Sbjct: 215 RILVKLTLETGRTHQIRVHLAALGAPII 242


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 80/256 (31%), Gaps = 47/256 (18%)

Query: 1   MKDKNIV--QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M D   +   E    +RV   I+R    SR     + A   V VNG  + + +  V   D
Sbjct: 4   MSDSRTMLVPEGLQGERVDAAISRLFGLSRTRAADLAADGGVAVNGASVGK-SHRVHGGD 62

Query: 59  -------------HIEVDGVPLR----KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
                         +EV   P+       +   + +  KP+G+    S      TV   L
Sbjct: 63  LLELTLPSNDASPTLEVIAEPVPGMSIIHDDDDIVVVDKPVGVAAHPSVGWTGPTVLGGL 122

Query: 102 PSIFSRVISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFH 150
            +   R+ + G         RLD+ T GL+++        VL+    +    + Y     
Sbjct: 123 AAAGYRISTSGASERQGIVSRLDVGTSGLMVVCKSERGYSVLKRAFKERTVEKTYHTLVQ 182

Query: 151 GQVDQ--DKLN-----------LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
           G  D     ++                 V++   +      L       + + + L  G+
Sbjct: 183 GLPDPLVGTIDAPIARHPGHDYKFA---VMESGKHAVTHYELIEAFRYASLLDIRLETGR 239

Query: 198 NREIKKVFEFFNWKVN 213
             +I+  F        
Sbjct: 240 THQIRVHFSALRHPCV 255


>gi|166154327|ref|YP_001654445.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|166155202|ref|YP_001653457.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335578|ref|ZP_07223822.1| tRNA pseudouridine synthase A [Chlamydia trachomatis L2tet1]
 gi|165930315|emb|CAP03801.1| tRNA pseudouridine synthase A [Chlamydia trachomatis 434/Bu]
 gi|165931190|emb|CAP06755.1| tRNA pseudouridine synthase A [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 274

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 43/124 (34%), Gaps = 23/124 (18%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  +   D + +    +  +    LW      +Y+KP     T  D   +
Sbjct: 40  RVNGRIERFESYKLQPGDRVSL--QIIEHSSPQLLWEDEHLCIYNKPAK--QTSEDLAHQ 95

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             V             V RLD +T G +L       + ++     + +  + Y     GQ
Sbjct: 96  LNV-----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQ 144

Query: 153 VDQD 156
             Q+
Sbjct: 145 PRQE 148


>gi|312374039|gb|EFR21691.1| hypothetical protein AND_16535 [Anopheles darlingi]
          Length = 912

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 46/275 (16%), Positives = 101/275 (36%), Gaps = 30/275 (10%)

Query: 92  DGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVR 148
              + VF          + ++ RLD  T GLLL       AR +E    + Q  + Y  R
Sbjct: 22  RHNTVVFILAKEYNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEHQIRNRQVQKEYICR 81

Query: 149 FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------------LREG 196
             G+     +   K+ I +     G  +V+   ++ +  +  +G            L  G
Sbjct: 82  VEGEFPDGVIE-CKEPIEVVSYKIGVCKVSPKGKECTTTFQKLGFNGSSSVVLCKPLT-G 139

Query: 197 KNREIKKVFEFFNWKVNR--L--IRISYGPFQ-LGTLLAGSTREVSKKILREQLGPHLLE 251
           +  +I+   ++  + V    L    + +GP +  G  + G +     +++++ +  H  E
Sbjct: 140 RMHQIRVHLQYLGYPVVNDPLYNHEV-FGPAKGRGGDIGGKS---DDQLVKDLINIHNAE 195

Query: 252 E-AQVNLDAPIYSSETLVRDRPNIISE--VPDDFTRMKKNSSQKNGLSKQKKLATPVHRR 308
               ++ D+ +   + +  D  ++  +    DD   + + +S  +   +   L +     
Sbjct: 196 NWLGIDGDSDLSMFKPMKNDLDDVKGQLLSDDDSESVSREASPCSESPRPVSLGSESPHE 255

Query: 309 NLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPS 343
           NL S++ M+    S+     G        S +   
Sbjct: 256 NLCSSILMS-NAMSAVSGTGGVVVVGTNSSSAGVG 289


>gi|312874750|ref|ZP_07734769.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
 gi|311089495|gb|EFQ47920.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2053A-b]
          Length = 302

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/181 (17%), Positives = 60/181 (33%), Gaps = 28/181 (15%)

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRV 108
                ++   +P+    E     + +K   L+T  S  +   +V   L     P    ++
Sbjct: 73  KPNATLKFSNLPIAIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLKI 132

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
               + RLD +T GL+L+  +             + ++ Y    HG     +L     G+
Sbjct: 133 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYHAIVHGNFSPSQLQ----GV 188

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVG-------LRE-----GKNREIKKVFEFFNW 210
           +   I   D  V    ++  K S     V        L E     G+  +I+   ++   
Sbjct: 189 IDAPIGKKDDPVKRYIMEGGKESVTKYRVIKQVAGASLVELQLLTGRTHQIRVHMQYLGH 248

Query: 211 K 211
            
Sbjct: 249 P 249


>gi|304387818|ref|ZP_07369992.1| RNA pseudouridine synthase [Neisseria meningitidis ATCC 13091]
 gi|304338083|gb|EFM04219.1| RNA pseudouridine synthase [Neisseria meningitidis ATCC 13091]
          Length = 307

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 41/109 (37%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALALTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G        ++G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEVEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|195384880|ref|XP_002051140.1| GJ14588 [Drosophila virilis]
 gi|194147597|gb|EDW63295.1| GJ14588 [Drosophila virilis]
          Length = 552

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 68/208 (32%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD---------HIEVDGVPLRKAE-RTRLWLYHKP 81
           +R I    + VN   +      +   D          + V   P+        + + +KP
Sbjct: 183 KRSIEAGTLTVNYEKV-PIDYKLKHNDLLANTVHRHEVPVTSQPITIVHMDEDILVVNKP 241

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L   F    + ++ R+D  T GLLL   +   AR +E    
Sbjct: 242 ASIPVHPCGRYRHNTVIFILAKEFNLKNLRTIHRIDRLTSGLLLFGRNSEKARQMEQQIR 301

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------ 191
           + Q  + Y     GQ     +    + I +     G  +V+   +     +  +      
Sbjct: 302 NRQVQKEYICCVEGQFPDGIIE-CNEPIEVVSYKIGVCKVSPKGKDCKTTFKRIAQAGDY 360

Query: 192 GLRE-----GKNREIKKVFEFFNWKVNR 214
            + +     G+  +I+   ++  + +  
Sbjct: 361 SIVQCKPLTGRMHQIRVHLQYLGYPIVN 388


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 26/73 (35%), Gaps = 10/73 (13%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M DK         +R+  ++   G   SR + +  I    V VN   +++  + +     
Sbjct: 1  MSDK---------ERIDVLLVEQGYYESREKAKAAIMAGLVFVNEESVDKPGIKICRKAD 51

Query: 60 IEVDGVPLRKAER 72
          I V G       R
Sbjct: 52 IRVKGAVHPYVSR 64


>gi|163841219|ref|YP_001625624.1| ribosomal large subunit pseudouridine synthase D [Renibacterium
           salmoninarum ATCC 33209]
 gi|162954695|gb|ABY24210.1| ribosomal large subunit pseudouridine synthase D [Renibacterium
           salmoninarum ATCC 33209]
          Length = 308

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/256 (16%), Positives = 73/256 (28%), Gaps = 48/256 (18%)

Query: 1   MKDKNI---VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI------------ 45
           M +  +   V + F   R    +A+    SR     ++    V   G             
Sbjct: 1   MPEDKVRLSVTDEFDGVRADAALAQLLEISRSAAAVLLNGGHVSSEGKSLGKSARLFTGM 60

Query: 46  --LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
             L+            +E         +     +  KP+G+    S      TV   L +
Sbjct: 61  SVLVSIPEQRDPLAVVVEAVDDLNILLDDDAFVVIDKPVGVAAHPSPGWVGPTVVGALAA 120

Query: 104 IFSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
              R+           V RLD+ T G++++        VL+    +    +VY     G 
Sbjct: 121 AGYRISTSGAAERAGIVHRLDVGTSGVMVVAKTEQAYTVLKRAFKERTVNKVYYAVVQGL 180

Query: 153 VDQDKLNLLKKGI---------------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
            D      L+  +               VI+          +    G  + + V L  G+
Sbjct: 181 PDP-----LRGTVDAPIGRHPGHDWRFAVIEDGRPSVTHYEVLEAFGKASLLEVHLETGR 235

Query: 198 NREIKKVFEFFNWKVN 213
             +I+  F   N    
Sbjct: 236 THQIRVHFSALNHPCV 251


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 61/178 (34%), Gaps = 25/178 (14%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDN 100
           +VNG L    +  V   D I +      ++E   LW             D    +T  D 
Sbjct: 40  RVNGRLERFESYKVQPGDCIAL--TLQIRSEPKILW-----EDQHCCIYDKPTHTTTEDL 92

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL 158
             +  + +  V RLD +T G +L   +   A  L       +  + Y     G   +   
Sbjct: 93  --AKTTGLHIVHRLDRDTTGCILFAKNTNSAHALSELFKKRKIHKQYTALVFGHPKKSSG 150

Query: 159 NLL--------KKGIVIQG---ICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIK 202
            L+        + G VI G      G + +T  +   S    T+ L +   G+  +I+
Sbjct: 151 TLISYTAPKSRRCGAVIFGNTDKHSGKLTITHWSVLHSYKHYTLMLCQPFTGRTHQIR 208


>gi|329895229|ref|ZP_08270893.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC3088]
 gi|328922467|gb|EGG29809.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium IMCC3088]
          Length = 317

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 47/277 (16%), Positives = 91/277 (32%), Gaps = 44/277 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLE-RAAVNVMS--------TDHIEVDGVPLR---KAERTR 74
           SR +++  I    + V+G   + + +V+V S           +      +      E   
Sbjct: 32  SRGKLQEWIKSGALLVDGNTAKPKQSVDVDSVLTLSADLEPAVHWQPQAIPMDIVYEDED 91

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDG 128
           + + +KP+GLV   +  +   T+ + L +         R   V RLD +T GL+++    
Sbjct: 92  VIVVNKPVGLVVHPAAGNWDGTLVNALLAHDASLEQVPRAGVVHRLDKDTSGLMVVAKTL 151

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGD 174
                L   L   +  R Y    HG +                   +   +V  G     
Sbjct: 152 QSHTALVEALQQREVSRQYIAIAHGSMTGGGVVDAPIGRHPTMRQKMA--VVASGKPART 209

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEF----FNWKVNRLIRISYGPFQLGTLL 229
              +L  +      + + L  G+  +I+  +           V    R          L 
Sbjct: 210 H-YSLGQRFKHFTELHLKLETGRTHQIRVHMAHKKHPLVGDSV-YGGRARVPGNSAPEL- 266

Query: 230 AGSTREVSKKIL--REQLGPHLLEEAQVNLDAPIYSS 264
             + RE  ++ L  +     H + +  ++ DAPI   
Sbjct: 267 VNAIREFPRQALHAKALAFFHPISDEWMSFDAPIPDD 303


>gi|325285555|ref|YP_004261345.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
 gi|324321009|gb|ADY28474.1| pseudouridine synthase [Cellulophaga lytica DSM 7489]
          Length = 287

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/209 (13%), Positives = 73/209 (34%), Gaps = 42/209 (20%)

Query: 24  GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-------VPLRKA-----E 71
           GI+++  +++ I +  + ++          +  ++ I  +          L        +
Sbjct: 28  GISTKSALKKAIKKGLIYIDEKKAST-GTFIYGSEKITFNKPEENNTKKRLNLKLEVVFQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN------LPSIFSRVISVGRLDINTEGLLLLT 125
              L + +KP G++ + +         +       LP   ++   V RLD  T GLL++ 
Sbjct: 87  DNYLAIINKPPGILVSGNTFKTIDNALEQNITKSSLPDA-TKPRPVHRLDFPTTGLLII- 144

Query: 126 NDGGLARVLEL-----PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
             G  +  +        + +  + Y     G        ++KKG +   +   +   T +
Sbjct: 145 --GKTSASILALNKLFENKKIQKTYLAVTIG-------EMIKKGTINTNVDNKEAFTTYN 195

Query: 181 TQKGSNA-------WVTVGLREGKNREIK 202
             K   +        V +  + G+  +++
Sbjct: 196 VLKTVTSNKFNYLNLVKLEPKTGRKHQLR 224


>gi|293379048|ref|ZP_06625201.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
 gi|292642327|gb|EFF60484.1| pseudouridine synthase, RluA family [Enterococcus faecium PC4.1]
          Length = 285

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 58/159 (36%), Gaps = 16/159 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 86  EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVLFAK 145

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D+           +  K+ +  +      
Sbjct: 146 NPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDRTITNKIGRDRHDRRKRVVDDKNGQNAL 205

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             VT+D        V   L  G+  +I+         + 
Sbjct: 206 THVTVDKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIV 244


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   G   SR + + +I    V VNG   ++A         IEV G  L+   R
Sbjct: 3  ERLDVLLTERGFFVSREKAKAVIMAGEVFVNGQREDKAGSKFDREAEIEVKGKVLKYVSR 62


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 8/82 (9%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           ++      R+  +++    ASR ++  +I   RV VNG L+   + NV   D + V    
Sbjct: 168 IKGTVASVRLDSLLSLVFPASRSKLVPLIEGGRVFVNGKLITTNSYNVKENDIVSVRKLG 227

Query: 63  ----DGVPLRKAERTRLWLYHK 80
                GV  +  +     L  K
Sbjct: 228 RFRYKGVLSQTKKGRYYVLLEK 249


>gi|325913175|ref|ZP_08175545.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
 gi|325477596|gb|EGC80738.1| pseudouridine synthase, RluA family [Lactobacillus iners UPII 60-B]
          Length = 309

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 49  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 107

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 108 ADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITRLDRDTSGLVLVGKNAVAHARF 167

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 168 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKNSVTKYR 223

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 224 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 256


>gi|261749573|ref|YP_003257259.1| ribosomal large subunit pseudouridine synthase D [Blattabacterium
           sp. (Periplaneta americana) str. BPLAN]
 gi|261497666|gb|ACX84116.1| ribosomal large subunit pseudouridine synthase D [Blattabacterium
           sp. (Periplaneta americana) str. BPLAN]
          Length = 344

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/180 (19%), Positives = 69/180 (38%), Gaps = 30/180 (16%)

Query: 2   KDKNIVQENFTPQRVSKVI--ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           K K  V++     R+ K +  +   I SR ++++     ++ VN  ++++    +   D 
Sbjct: 5   KFKFFVEKYQKTIRIDKFLRKSIQNI-SRNQIQKATNSGKILVNQCIIKK-NYKIKPFDL 62

Query: 60  IE--------VD---------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           +E        +D          +PL    E   + + +K  G+V      + + T+   +
Sbjct: 63  VEAEIYYPPILDSEYKNIIAENIPLNILYEDEDILVINKAAGMVVHPGFGNEKGTLIHGI 122

Query: 102 PSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
              F       R+  V R+D +T GLL+L  +    + L     S    R Y     G +
Sbjct: 123 KYHFKNNHQLYRLGLVHRIDKDTTGLLVLAKNEYAQKYLFQQFISKTIQRKYLALVWGNI 182


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+  SR++ + +I   +V V G  +++A      T  IEV G  L  
Sbjct: 1  MAKKRLDVLLCERGLMESRQKAQAVIMAGQVYVGGQKVDKAGAQTEETAEIEVRGKTLAY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|89098123|ref|ZP_01171009.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Bacillus sp. NRRL B-14911]
 gi|89087286|gb|EAR66401.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Bacillus sp. NRRL B-14911]
          Length = 295

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/257 (15%), Positives = 87/257 (33%), Gaps = 48/257 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLR-KAERTRLWLYHKPIG 83
            +++VNG   E     +   D + V             + +PL    E   + + +KP  
Sbjct: 41  GKIEVNGN-EENVRYMLKEGDCLSVRFPSEMPSPGMEAEDIPLAIVYEDPYVLVVNKPAA 99

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVL--E 135
           + T  S    R ++ + L   + ++        V RLD +T GL+L+     +  ++   
Sbjct: 100 MSTIPSREHPRGSLANALIGYYRKIDLASTVHIVTRLDRDTSGLVLVAKHRHVHHLMSTL 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
               +  R Y     G            + + K +++++ +      Y      +    G
Sbjct: 160 QREGRVKRTYEAFAEGKLFPVEGSIEAPIARKKDSIIEREVNFLEGQYACTHYKVKG-TG 218

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL--R 242
              +  + L  G+  +I+         +               L  G+  ++S++ L  R
Sbjct: 219 EFTYAELVLETGRTHQIRVHLSHLGHPLLG-----------DGLYGGNKNQISRQALHCR 267

Query: 243 EQLGPHLLEEAQVNLDA 259
           E    H   E ++   A
Sbjct: 268 ELRFFHPFLERELCFSA 284


>gi|67900736|ref|XP_680624.1| hypothetical protein AN7355.2 [Aspergillus nidulans FGSC A4]
 gi|40742536|gb|EAA61726.1| hypothetical protein AN7355.2 [Aspergillus nidulans FGSC A4]
          Length = 1054

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 25/142 (17%), Positives = 46/142 (32%), Gaps = 16/142 (11%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ +    V VNG         + + + I          V G  +    E   L +  KP
Sbjct: 564 KKALESGNVCVNGKPA-GPHTVLKNGEVISHTLHRHEPPVTGNEIGIIHETDDLLVIDKP 622

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLL--TNDGGLARVLEL 136
            G+    +     ++V + L              RLD  T G++ +  T  G     ++L
Sbjct: 623 AGVPVHSTGRYHYNSVMEILRIQNGGAYVPRPCNRLDRLTSGVMFVGKTAQGADRMTVKL 682

Query: 137 PSTQWLRVYRVRFHGQVDQDKL 158
                 + Y  R  G+     +
Sbjct: 683 KERTVQKEYVARVKGRFPDGVV 704


>gi|320544926|ref|NP_001188783.1| RluA-2, isoform C [Drosophila melanogaster]
 gi|318068417|gb|ADV37033.1| RluA-2, isoform C [Drosophila melanogaster]
          Length = 543

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/197 (18%), Positives = 68/197 (34%), Gaps = 29/197 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 173 ERSLEAGKLTVNSEKVPK-DYKIKHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKP 231

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        + ++ RLD  T GLLL       AR LEL   
Sbjct: 232 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIR 291

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----- 192
           + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G     
Sbjct: 292 TRQVQKEYVCRVEGRFPDGIVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEVGSD 350

Query: 193 -------LREGKNREIK 202
                  L  G+  +I+
Sbjct: 351 SIVLCKPLT-GRMHQIR 366


>gi|283780201|ref|YP_003370956.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
 gi|283438654|gb|ADB17096.1| pseudouridine synthase, RluA family [Pirellula staleyi DSM 6068]
          Length = 313

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/168 (22%), Positives = 64/168 (38%), Gaps = 30/168 (17%)

Query: 15  RVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-------- 63
           R+    K ++  G  SR +V  ++  Q VK+NG + +     +   D IE+         
Sbjct: 20  RLDLAVKQLS--GF-SREQVRGLLDHQCVKLNGAVTDEPGQPLSVDDRIEIAFDPHHRYH 76

Query: 64  -GVPLRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVI 109
               +R         E   L +  KP  L+T  +  + R T+ + + +            
Sbjct: 77  PKKKIRGGLGFGIVYEDRHLIVVEKPAALLTVPTPKNDRGTLLERVANYVKIVSRGKGAF 136

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ 155
            V RLD    GLL+      LA++L       +  R Y     G++D+
Sbjct: 137 QVHRLDRGVSGLLIFGKTTELAQMLRDQFAMHKPEREYVAIVRGKLDK 184


>gi|153839608|ref|ZP_01992275.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|260900301|ref|ZP_05908696.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
 gi|149746879|gb|EDM57867.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ3810]
 gi|308107572|gb|EFO45112.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus AQ4037]
          Length = 250

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 61/171 (35%), Gaps = 37/171 (21%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++      +   +++  L   +  +  V RLD++T GL++L  +  
Sbjct: 19  EDDHILAVNKPSGLLSVPGRLAEHHDSMWSRLQEEYPDIQVVHRLDMSTSGLMVLAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDM-QVTL 179
                       L        ++Y  R  G V+Q++  + L    +I       + +V  
Sbjct: 79  AESALKKQFQFRLTH------KIYYARVWGHVEQEEGEIDLP---LICDWPNRPLQKVCF 129

Query: 180 DTQKGSNAWVTVGLRE-----------------GKNREIKKVFEFFNWKVN 213
           +  K S     V  RE                 G++ +++   +     + 
Sbjct: 130 EDGKPSKTLFQVAKREEHEDGTKTTIVRLLPITGRSHQLRVHMQALGHPIV 180


>gi|149280788|ref|ZP_01886893.1| tRNA pseudouridine synthase C [Pedobacter sp. BAL39]
 gi|149228467|gb|EDM33881.1| tRNA pseudouridine synthase C [Pedobacter sp. BAL39]
          Length = 235

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 48/167 (28%), Gaps = 32/167 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTND 127
           E   L   +KP GL+   S    D +      L       V  V RLD  T G+LL   D
Sbjct: 7   EDEHLIAINKPHGLLVHRSSIANDAKEFALQLLRDQVNKHVSPVHRLDRKTGGILLFAFD 66

Query: 128 GGLARVLELPST---QWLRVYRVRFHGQVDQDK-------------LNLLKKGIVIQGIC 171
              A +         +  + Y     G                          + +    
Sbjct: 67  -KEAEIAMHQQFQNGEVTKKYMAILRGHAPDQMDINYPLAKENGTIQEAFTSFVTLD--- 122

Query: 172 YGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
               ++ +   K   +  ++   E     G+  ++++ F    + + 
Sbjct: 123 --RAELAVPFGKHETSRYSLV--EASPTTGRMHQLRRHFAHIFYPII 165


>gi|183603400|ref|ZP_02712152.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
 gi|183569583|gb|EDT90111.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae CDC1087-00]
          Length = 278

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|76788821|ref|YP_327907.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|237802537|ref|YP_002887731.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
 gi|237804454|ref|YP_002888608.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|76167351|gb|AAX50359.1| tRNA pseudouridine synthase A [Chlamydia trachomatis A/HAR-13]
 gi|231272754|emb|CAX09659.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273771|emb|CAX10553.1| tRNA pseudouridine synthase A [Chlamydia trachomatis B/Jali20/OT]
          Length = 274

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 43/124 (34%), Gaps = 23/124 (18%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  +   D + +    +  +    LW      +Y+KP     T  D   +
Sbjct: 40  RVNGRIERFESYKLQPGDRVSL--QIIEHSSPQLLWEDEHLCIYNKPAK--QTSEDLAHQ 95

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             V             V RLD +T G +L       + ++     + +  + Y     GQ
Sbjct: 96  LNV-----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNPEIDKRYIALVFGQ 144

Query: 153 VDQD 156
             Q+
Sbjct: 145 PRQE 148


>gi|257889020|ref|ZP_05668673.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257897615|ref|ZP_05677268.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|293571088|ref|ZP_06682128.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
 gi|257825083|gb|EEV52006.1| pseudouridine synthase [Enterococcus faecium 1,141,733]
 gi|257834180|gb|EEV60601.1| pseudouridine synthase [Enterococcus faecium Com12]
 gi|291608818|gb|EFF38100.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E980]
          Length = 285

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 58/159 (36%), Gaps = 16/159 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 86  EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKKQRPYVVHRLDKETSGAVLFAK 145

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D+           +  K+ +  +      
Sbjct: 146 NPFVLPILGRMLEQKMIYRRYQAIVWGKIAKDRTITNKIGRDRHDRRKRVVDDKNGQNAL 205

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             VT+D        V   L  G+  +I+         + 
Sbjct: 206 THVTVDKVLSGKTQVYCVLETGRTHQIRVHLAHIGHPIV 244


>gi|228913878|ref|ZP_04077503.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|228845817|gb|EEM90843.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
          Length = 292

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 96  STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 154

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 155 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 214

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 215 KTH-VSLELDTGRTHQIRVHLAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 262

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 263 SLTFYHPILEKEMSFAAMIPSDMQEV 288


>gi|42528076|ref|NP_973174.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
 gi|41819121|gb|AAS13093.1| RNA pseudouridylate synthase family protein [Treponema denticola
           ATCC 35405]
          Length = 244

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 55/165 (33%), Gaps = 25/165 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLL 124
           E   + + +K  GL+      D  +   D +           ++  V RLD  T GL++ 
Sbjct: 11  EDKDILIVNKNAGLLVGADRWDSEAPRLDKILEELYKDKGERKIYPVHRLDKETSGLIIY 70

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
             +    + L     + +  ++Y     G   ++     +K + I G      +  +D +
Sbjct: 71  ALNAEAHKTLNDDFQNRKIEKIYHAVSAGIPQEENFKAEEK-LRIDGDKL--HRTVIDEK 127

Query: 183 KGSNAWVTVG---------LRE-----GKNREIKKVFEFFNWKVN 213
           KG  +              L E     G+  +I+   +     + 
Sbjct: 128 KGKESLTEFSLLKRFSRFCLLEARPITGRTHQIRAHLKHLGLPIL 172


>gi|317049313|ref|YP_004116961.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316950930|gb|ADU70405.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 259

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 26/182 (14%), Positives = 57/182 (31%), Gaps = 34/182 (18%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D   +  V   +       V +  RLD  T G+LL+     + 
Sbjct: 11  LVAVNKPAGWLVHRSWLDRKEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEVG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + +         ++L+ +      +            
Sbjct: 71  RLLAQQFEQHQIRKTYHAVLRGWLMESGTLDYPLVEELDKIADKFATEPRGPQPAVTDFQ 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
                ++ +   + + A  ++   +   G+  ++++        +        G    G 
Sbjct: 131 MLAHTEMPVAIGRYATARYSLVEMQPRTGRKHQLRRHMAHLRHPI-------IGDTTHGD 183

Query: 228 LL 229
           L 
Sbjct: 184 LR 185


>gi|237744439|ref|ZP_04574920.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
 gi|229431668|gb|EEO41880.1| tRNA pseudouridine synthase A [Fusobacterium sp. 7_1]
          Length = 292

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 97/254 (38%), Gaps = 55/254 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
           I+ E++   RV + +       R+        E+ +M+ + ++KVN   + +    ++  
Sbjct: 5   IIDEDYESVRVDRFL-------RKHLKNINLSEIYKMLRKGKIKVNNKKISQ-DYRLVLG 56

Query: 58  DHI--------------------EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGR 94
           D I                    ++    L++    E   L++ +KP+G V  H      
Sbjct: 57  DIIFIFLPETFKEQNEEKFIEISQIRKEKLKQMIVFENDNLFVINKPLGDVV-HKGSGHD 115

Query: 95  STVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH 150
            ++ +   S +S   +  V R+D  T GL++   +   AR +  E+ +   ++ Y +  +
Sbjct: 116 ISLLEEFRSYYSNNNINFVNRIDKLTSGLVIGAKNIKTAREIAKEIQTGNIVKKYYILVN 175

Query: 151 GQVDQD------KLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G++++D       L   ++ +++     +G            +      +   L+ G+  
Sbjct: 176 GKIEKDNFILENYLKKDEERVIVSDIEKEGYKKSITYFKKIKEYDKYTLLEAELKTGRTH 235

Query: 200 EIKKVFEFFNWKVN 213
           +++   +     + 
Sbjct: 236 QLRAQLDHLGNNIV 249


>gi|118444019|ref|YP_877712.1| ribosomal large subunit pseudouridine synthase C [Clostridium novyi
           NT]
 gi|118134475|gb|ABK61519.1| ribosomal large subunit pseudouridine synthase C, putative
           [Clostridium novyi NT]
          Length = 323

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 89/252 (35%), Gaps = 65/252 (25%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           +  N   QR+ K         R+ +E        + + +  ++VNG   ++    +   D
Sbjct: 5   IGPNEAGQRLDKF------C-RKWLEDVPLGAIFKALRKGDIRVNGKKAKQ-NYFLEEED 56

Query: 59  HIE--------------------VDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTV 97
            +E                    V+   ++ A E   + +  K  G++      DG  T+
Sbjct: 57  VVETKYIESYKKNKKNVPKKFQEVNFSSIKIAYEDENMLIIEKWPGVLVHSDKKDGDPTL 116

Query: 98  FDNLPSIFSRVI-------------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWL 142
            D + S                      RLD NT G+++   +    ++L   +   +  
Sbjct: 117 TDYVLSYLFNKGEYIPENEVTFTPAPCNRLDRNTSGMVIFGKNFKSLKLLNEMIRERKIS 176

Query: 143 RVYRVRFHGQ---------VDQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVT 190
           + Y     G+         + +D++N + + I +          M+V +    G+ +++ 
Sbjct: 177 KYYNALVKGKIREGRYEAYISKDQINNISE-IHLNKKPNSKKIAMEVKVIDTVGTFSFLE 235

Query: 191 VGLREGKNREIK 202
           + L  G++ +++
Sbjct: 236 LDLITGRSHQLR 247


>gi|49184141|ref|YP_027393.1| pseudouridine synthetase [Bacillus anthracis str. Sterne]
 gi|167636101|ref|ZP_02394406.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|167641221|ref|ZP_02399475.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|170686706|ref|ZP_02877926.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|177654397|ref|ZP_02936294.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|227815949|ref|YP_002815958.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|229600901|ref|YP_002865732.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|254682628|ref|ZP_05146489.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. CNEVA-9066]
 gi|254725424|ref|ZP_05187206.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. A1055]
 gi|254734046|ref|ZP_05191760.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Western North America USA6153]
 gi|254740807|ref|ZP_05198496.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Kruger B]
 gi|254753650|ref|ZP_05205686.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Vollum]
 gi|254758747|ref|ZP_05210774.1| ribosomal large subunit pseudouridine synthase, RluA family protein
           [Bacillus anthracis str. Australia 94]
 gi|270000595|ref|YP_003329033.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. Ames]
 gi|291612207|ref|YP_003541021.1| ribosomal large subunit pseudouridine synthase [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178068|gb|AAT53444.1| pseudouridine synthetase [Bacillus anthracis str. Sterne]
 gi|167510862|gb|EDR86254.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0193]
 gi|167528455|gb|EDR91220.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0442]
 gi|170669229|gb|EDT19972.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0465]
 gi|172080681|gb|EDT65763.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0174]
 gi|224552858|gb|ACN55068.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. 'Ames Ancestor']
 gi|227004816|gb|ACP14559.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. CDC 684]
 gi|229265309|gb|ACQ46946.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0248]
 gi|269850244|gb|ACZ49984.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. Ames]
          Length = 297

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 41  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 101 STIPSREHPSGSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHLAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 268 SLTFYHPILEKEMSFAAMIPSDMQEV 293


>gi|56807621|ref|ZP_00365521.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
          Length = 218

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/164 (21%), Positives = 63/164 (38%), Gaps = 23/164 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGL 121
           E   L + +KP G+V   S      T+ + L              R   V R+D +T GL
Sbjct: 1   EDDTLAIINKPQGMVVHPSVGHPSGTMVNALMYHIKDLSSINGVVRPGIVHRIDKDTSGL 60

Query: 122 LLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQ 168
           L++  T+    A   EL + + LR Y    HG            + + + +  K+ +  +
Sbjct: 61  LMVAKTDAAHQALAEELKAKKSLRKYLAIVHGNLPNDRGMIEAPIGRSEKDRKKQAVTAK 120

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
           G      + T+  + G  + V + L  G+  +I+    +    V
Sbjct: 121 GKEAVT-RFTVLERFGDYSLVELQLETGRTHQIRVHMAYIGHPV 163


>gi|259416795|ref|ZP_05740715.1| ribosomal large subunit pseudouridine synthase C [Silicibacter sp.
           TrichCH4B]
 gi|259348234|gb|EEW60011.1| ribosomal large subunit pseudouridine synthase C [Silicibacter sp.
           TrichCH4B]
          Length = 348

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 69/200 (34%), Gaps = 50/200 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E+   QR+ + +       RR         +E+M  +  ++++G  ++ A   V + 
Sbjct: 8   TVTEDDGGQRIDRWL-------RRLFPHVNQGRIEKMCRKGELRLDGGRVK-ANTRVEAG 59

Query: 58  DHIEV---------------------DGVPLR---KAERTRLWLYHKPIGLVT-----TH 88
             + V                     D   +R     +   + + +KP GL       T 
Sbjct: 60  QVVRVPPLAKSDMKPAEARPVKISDADAKMIRDCVVYKDDDVLVINKPAGLAVQGGSGTT 119

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
              DG S           R+  V RLD +T GLL+L  +   A+ L          ++Y 
Sbjct: 120 KHVDGLSEALRFDAEDKPRL--VHRLDKDTSGLLVLARNRKAAQGLTAAFRHKNTRKIYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIV 166
               G      L  +K G+V
Sbjct: 178 ALVAGVPTP-YLGEIKTGLV 196


>gi|258544039|ref|ZP_05704273.1| ribosomal large subunit pseudouridine synthase C [Cardiobacterium
           hominis ATCC 15826]
 gi|258520667|gb|EEV89526.1| ribosomal large subunit pseudouridine synthase C [Cardiobacterium
           hominis ATCC 15826]
          Length = 311

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 74/238 (31%), Gaps = 48/238 (20%)

Query: 6   IVQENFTPQRVSKVIAR---AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            V  +   QR+   + +   A   SR  + +M+ +  V+VN    +   + V + D + +
Sbjct: 10  TVTADDAGQRLDNFLRKRYPALPKSR--IYQMLRRGEVRVNKKRAK-PELRVAAGDELRL 66

Query: 63  ----------DGVPLRKAERTR---------LWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
                       VP    ER             + +KP G+            V D +  
Sbjct: 67  PPLADATRPPQDVPAFWCERIAGAVLYEDDDFLMLNKPAGIAVHGGSEQPYG-VIDAVRQ 125

Query: 104 IFSRVIS--VGRLDINTEGLLLLTNDGGLARVL-----ELPSTQWLRVYRVRFHGQVDQD 156
           ++    +    RLD +T G+L+L   G     L      + +    + Y     G  +  
Sbjct: 126 VWGAGYAELAHRLDRDTSGVLVL---GKNRAALAGFQALMQAGGVEKRYLCLVDGHWNPA 182

Query: 157 KLN--------LLKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                       L+ G    +          +  L       + +   L  G+  +I+
Sbjct: 183 TREVRLHLAKAQLQGGERMVVGAADGQEARTRFRLLQTFADASLLEATLDTGRTHQIR 240


>gi|52144130|ref|YP_082698.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
 gi|51977599|gb|AAU19149.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           E33L]
          Length = 297

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 85/266 (31%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 41  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 100

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 101 STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++    I +    V
Sbjct: 268 SLTFYHPILEKEMSFTTTIPNDMQAV 293


>gi|226951907|ref|ZP_03822371.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ATCC 27244]
 gi|294649166|ref|ZP_06726607.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           haemolyticus ATCC 19194]
 gi|226837447|gb|EEH69830.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ATCC 27244]
 gi|292824964|gb|EFF83726.1| ribosomal large subunit pseudouridine synthase C [Acinetobacter
           haemolyticus ATCC 19194]
          Length = 310

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 41/224 (18%), Positives = 75/224 (33%), Gaps = 56/224 (25%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQDGQRIDNFLFTRLKGVPKSR--IYRLIREGQVRVNKKRIK-AETRLQIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDETAAPVSDSVAQSLLSRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPS-----IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + +         +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEALRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIQKTYAAIVKGQV 185

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
             DK                D  +           V V  +EGK
Sbjct: 186 SLDK-------------QLIDAPLLRYELANGERRVRVT-KEGK 215


>gi|145628779|ref|ZP_01784579.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.1-21]
 gi|145640373|ref|ZP_01795957.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae R3021]
 gi|144979249|gb|EDJ88935.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.1-21]
 gi|145274959|gb|EDK14821.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 22.4-21]
          Length = 322

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 84/238 (35%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  + VP+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDVPISKNLNKVTALENQILFEDDCLIVLNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYTNATLVKASPVTGRTHQIR 250


>gi|84685385|ref|ZP_01013283.1| ribosomal large subunit pseudouridine synthase C [Maritimibacter
           alkaliphilus HTCC2654]
 gi|84666542|gb|EAQ13014.1| ribosomal large subunit pseudouridine synthase C [Rhodobacterales
           bacterium HTCC2654]
          Length = 350

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 50/153 (32%), Gaps = 33/153 (21%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------------DGVPLR-- 68
           VE+M  +  ++V+G  ++ A+  V     + +                    D   +R  
Sbjct: 34  VEKMCRKGEIRVDGGRVK-ASTRVEVGQEVRIPPLPDPGERPAAPRPSVTDKDAQMIRDC 92

Query: 69  -KAERTRLWLYHKPIGLVTTHSDPDGRST-----VFDNLPSIFSRVISVGRLDINTEGLL 122
                  +   +KP GL T       R       V         R+  V RLD +T G+L
Sbjct: 93  VIYRDDHIIALNKPPGLPTQGGSKQTRHVDGLAEVLTFGYDDKPRL--VHRLDKDTSGVL 150

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
           LL     +A+ L          ++Y     G  
Sbjct: 151 LLARTRQVAKDLTDAFRHRNTRKIYWAVVAGVP 183


>gi|325265622|ref|ZP_08132312.1| tRNA pseudouridine synthase C [Kingella denitrificans ATCC 33394]
 gi|324982892|gb|EGC18514.1| tRNA pseudouridine synthase C [Kingella denitrificans ATCC 33394]
          Length = 242

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 23/167 (13%), Positives = 45/167 (26%), Gaps = 28/167 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
               +KP  ++   +      TVF        +   V  V RLD  T G++L       A
Sbjct: 11  YIAVNKPADMLVHRTWLSCGETVFLLQTLRDQLGRHVFPVHRLDRPTSGIMLFALHREAA 70

Query: 132 RVLELP--STQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGDMQVTLD 180
           +       S    + Y     G  D          ++L+ +                   
Sbjct: 71  QYFTGQFGSRLVRKTYLAIARGWTDDAGCIDYPLKEQLDKIADQHADGDKPAQAACTEYR 130

Query: 181 TQKGSN--------------AWVTVGLREGKNREIKKVFEFFNWKVN 213
           T   S               + + +    G+  +I++  +     + 
Sbjct: 131 TLARSELPIVSTPRYATSRYSLLRLMPHTGRKHQIRRHLKHIFHPIV 177


>gi|325989585|ref|YP_004249284.1| pseudouridine synthase, RluA family [Mycoplasma suis KI3806]
 gi|323574670|emb|CBZ40326.1| similar to pseudouridine synthase, RluA family [Mycoplasma suis]
          Length = 231

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 53/146 (36%), Gaps = 16/146 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E     +  K  G++  H D    G+ T+ D L   +   +  V RLD NT GLLL+   
Sbjct: 8   ETKHYLIVDKDSGILV-HKDKYTRGKDTLIDILKEEYGENIYLVNRLDKNTSGLLLIA-K 65

Query: 128 GGLA---RVLELPSTQWLRVYRVRFHGQVDQDKLN-LLK----KGIVIQGICYGDMQVTL 179
           G L+           +  + Y       +   K+         KG  ++       +   
Sbjct: 66  GKLSLLTLKALFEEQKIDKKYLAILSSPLPHPKIKITFSLGRDKGKKLRFTATNSKKYKT 125

Query: 180 D---TQKGSNAWVTVGLREGKNREIK 202
                +  ++  V + L+ G+  +++
Sbjct: 126 ALTYAETINSQLVLLSLKTGRTHQLR 151


>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 = 52.9 bits (126), Expect = 7e-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|16272361|ref|NP_438574.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae Rd
           KW20]
 gi|260580525|ref|ZP_05848353.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae RdAW]
 gi|1175639|sp|P44433|RLUC_HAEIN RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|1573385|gb|AAC22071.1| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
 gi|260092867|gb|EEW76802.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae RdAW]
          Length = 322

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 74

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 75  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 134

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 135 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHI 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 194 KVIQASL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|332525768|ref|ZP_08401915.1| RluA family pseudouridine synthase [Rubrivivax benzoatilyticus JA2]
 gi|332109325|gb|EGJ10248.1| RluA family pseudouridine synthase [Rubrivivax benzoatilyticus JA2]
          Length = 305

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 76/242 (31%), Gaps = 49/242 (20%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHI 60
            +  V E    QR+   + R      +  V R+I    V+VN G     A   V + D I
Sbjct: 2   QRITVDEESAGQRLDNFLLRHLKGVPKTHVYRVIRSGEVRVNKGR--ASADTRVAAGDEI 59

Query: 61  EVDGVPLRKA---------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            V  + + +                E   L    KP G+        G S V   +    
Sbjct: 60  RVPPMRIAEKPAAAAVPAREFPVLFEDEHLLAIAKPAGVAV-----HGGSGVSSGVIEQL 114

Query: 106 SRVIS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
            R          V RLD  T G+LLL         L+    +    + Y     G   + 
Sbjct: 115 RRARPDARFLELVHRLDKETSGVLLLAKKRSALTALQDQFRARDTGKNYLALVVGVWPKK 174

Query: 157 --KLN-LLKKGIVIQGICY-----GDMQ--------VTLDTQKGSNAWVTVGLREGKNRE 200
              L+  L KG    G  +      D          V      G  + + +GL+ G+  +
Sbjct: 175 LKVLDLALHKGTDAAGERHVRVVAADAPDARRSITVVRSVRAVGPYSLLEIGLKTGRTHQ 234

Query: 201 IK 202
           I+
Sbjct: 235 IR 236


>gi|325288659|ref|YP_004264840.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964060|gb|ADY54839.1| pseudouridine synthase, RluA family [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 295

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/162 (17%), Positives = 56/162 (34%), Gaps = 20/162 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +KP GL+   +      T+ + L   F +      +  + RLD +T G L+ 
Sbjct: 85  EDESLIVLNKPAGLLVHPAGMTTSGTLANYLADYFRQLGVICTIRPLHRLDRDTSGCLVF 144

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGIC 171
                +   +   L + +  R Y     G            +  D     ++ +  +G  
Sbjct: 145 AKGPVVQSKMEDLLAAGKIKRTYLALAEGLIIPAEGTISAPIASDPAKPNRRMVSEKGSQ 204

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  L T  G N+ V + L  G+  +I+    +    + 
Sbjct: 205 AITHYRKLKT-FGQNSLVELNLETGRTHQIRVHLAYLGHPIL 245


>gi|300812735|ref|ZP_07093142.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
 gi|300496275|gb|EFK31390.1| pseudouridine synthase, RluA family [Lactobacillus delbrueckii
           subsp. bulgaricus PB2003/044-T3-4]
          Length = 297

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 83/245 (33%), Gaps = 46/245 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE---VERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
           ++     P ++S  + + G  SRR     +       + VN       +  +   D +  
Sbjct: 1   MIVAKNDPGQLSHFLLKKGF-SRRAVNNCKN--HGGMMSVNHHR-RNGSYRLKEGDVVHF 56

Query: 61  -----------EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                      +V   PL   E T    + +KP GL++  S       V + + + F + 
Sbjct: 57  LMGQEPVNPWLKVSRRPLDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQ 116

Query: 109 ---------ISVGRLDINTEGLLLLTNDGGLARVLE-LPSTQWLRVYRVRFHGQVDQDKL 158
                      V RLD +T GL+LL  +         L    +++ Y    HG   +  L
Sbjct: 117 GVNPAYVKPHIVTRLDQDTSGLVLLGKNAIAHDRFSKLGKDDFIKKYHAIVHGNFAEGDL 176

Query: 159 NLL------------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVF 205
           + L            K+ +  +G         LD   G+ + + + L  G+  +I+  + 
Sbjct: 177 SGLIDKPLARVGDTVKREVNPKGQRALTEYRVLDQVPGA-SLIELRLLTGRTHQIRIHM- 234

Query: 206 EFFNW 210
                
Sbjct: 235 ASIGH 239


>gi|289805997|ref|ZP_06536626.1| tRNA pseudouridine synthase C [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 201

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 24/166 (14%), Positives = 48/166 (28%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 3   LVAVNKPAGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 62

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDM----- 175
           R L          + Y     G +  D +         + +      +            
Sbjct: 63  RRLAQQFEQHHIRKRYHAIVRGWLIDDAVLDYPLVEERDKIADKFAREDKAPQPAVTQYR 122

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 123 GLATVEMAVPTGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 168


>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 = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 36/82 (43%), Gaps = 8/82 (9%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV- 65
           ++      R+  V++ A   SR ++   I   +V VNG L+     ++  +D I V G+ 
Sbjct: 168 MKGTVPSVRLDTVLSVAWPLSRSKLTAYIEGGKVFVNGKLITSNGYHLKESDRISVRGMG 227

Query: 66  ------PLRKAERTRLWL-YHK 80
                  L + ++ R  +  HK
Sbjct: 228 RLTYEGILSQTKKGRYMISVHK 249


>gi|90407030|ref|ZP_01215220.1| Predicted pseudouridylate synthase, Rlu family protein
           [Psychromonas sp. CNPT3]
 gi|90311901|gb|EAS39996.1| Predicted pseudouridylate synthase, Rlu family protein
           [Psychromonas sp. CNPT3]
          Length = 303

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 33/206 (16%), Positives = 67/206 (32%), Gaps = 40/206 (19%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--------------------ER 72
           R+I +  V+VN   ++     +   D + +  V +                       E 
Sbjct: 31  RIIRKGEVRVNKKRIK-PDYKLQPGDIVRIPPVKVSAENPLPSPKLNAIAQLESRIVYED 89

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
             L + +KP G+            +     L      +  V RLD  T G LL+     +
Sbjct: 90  DALLILNKPSGIAVHGGSGLSFGAIEGLRALRPDARFLELVHRLDKATSGCLLIAKKRSM 149

Query: 131 ARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            R L   L +    + Y     G  D+   ++  K  +++      ++V+   ++ +   
Sbjct: 150 LRALHEQLRNKTMNKQYLALVKGSWDKKDRSV--KEPLLKDSQNSVVKVSALGKQ-AETR 206

Query: 189 VTV-------GLRE-----GKNREIK 202
             +        L E     G+  +I+
Sbjct: 207 FKIMQRYHGATLVEASPVTGRTHQIR 232


>gi|254229275|ref|ZP_04922693.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262393167|ref|YP_003285021.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. Ex25]
 gi|151938199|gb|EDN57039.1| RNA pseudouridine synthase family [Vibrio sp. Ex25]
 gi|262336761|gb|ACY50556.1| ribosomal large subunit pseudouridine synthase A [Vibrio sp. Ex25]
          Length = 250

 Score = 52.9 bits (126), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 56/163 (34%), Gaps = 43/163 (26%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E   +   +KP GL++      +   +++  L  +   +  V RLD++T GL+LL  +  
Sbjct: 19  EDDDILAVNKPSGLLSVPGRLAEHYDSMWSRLKEVHPEIQVVHRLDMSTSGLMLLAKNKP 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVI----QGICYGDMQ 176
                       L        +VY  R  G V+       ++G I +            +
Sbjct: 79  SERALKKQFQYRLTH------KVYYARVWGHVEP------QEGNIDLPLICDWPNRPRQK 126

Query: 177 VTLDTQKGSNAWVTVGLRE-----------------GKNREIK 202
           V  D  K S     V  RE                 G++ +++
Sbjct: 127 VCFDDGKPSQTLFQVVKREVHSDGTHTTVVRLLPITGRSHQLR 169


>gi|307293091|ref|ZP_07572937.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
 gi|306881157|gb|EFN12373.1| pseudouridine synthase, RluA family [Sphingobium chlorophenolicum
           L-1]
          Length = 316

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 83/249 (33%), Gaps = 49/249 (19%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            + E     R+ K +A      SR  ++ +I   +V  +G      ++ V       +  
Sbjct: 11  TIGEAQDGMRLDKALAELVPDLSRERLKALIVDGQVTSSGR-APNPSLKVTMGQAFAIAL 69

Query: 63  ----------DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +PL    E   L +  KP GLV   +  +   T+ + L          
Sbjct: 70  PPPVEAEAVAQNIPLAIVHEDADLIVIDKPAGLVVHPAAGNLDGTLVNALLHHCQGQLSG 129

Query: 107 -----RVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV------ 153
                R   V R+D +T GLL++         L     +    R+Y    +G        
Sbjct: 130 IGGVARPGIVHRIDKDTSGLLVVAKSDRAHEGLAQQFAAHSIDRLYAAIVYGAPQPAAGT 189

Query: 154 ----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK- 202
                     D+ K+ + ++G   +G        TL+  +G+ A V   L  G+  +++ 
Sbjct: 190 VDSWIGRSDADRKKMAVCREG---RGKHAVTHYRTLEKLRGA-ALVECRLETGRTHQVRV 245

Query: 203 KVFEFFNWK 211
            + +     
Sbjct: 246 HMTQ-LGHP 253


>gi|262275057|ref|ZP_06052868.1| ribosomal large subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
 gi|262221620|gb|EEY72934.1| ribosomal large subunit pseudouridine synthase A [Grimontia
           hollisae CIP 101886]
          Length = 240

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/155 (16%), Positives = 59/155 (38%), Gaps = 18/155 (11%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +   +KP GL+T    DP    + +  + + +     V RLD++T GL++        R 
Sbjct: 23  IIAINKPSGLLTNPGRDPAHYDSAWSRIKAEYPDAELVHRLDMSTSGLIVFAKHKEAERH 82

Query: 134 LELPSTQ--WLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGDMQVTLD 180
           L+    +    ++Y  R  G V+Q+K               K+ +  +          + 
Sbjct: 83  LKAQFRERVTHKLYYARVWGHVEQEKGRVDLPLICDWPNRPKQKVCFENGKPSVTDYEVI 142

Query: 181 TQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
            ++     V +  +  G++ +++  +    +  + 
Sbjct: 143 KREKKTTLVRLLPIT-GRSHQLRVHML-ALDHPIV 175


>gi|205355761|ref|ZP_03222531.1| hypothetical protein Cj8421_0022c [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|205346538|gb|EDZ33171.1| hypothetical protein Cj8421_0022c [Campylobacter jejuni subsp.
           jejuni CG8421]
          Length = 300

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 75/201 (37%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E   L +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEEKNEILNGLVELIVYENNPKGVEIVF-ENEDLAILEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L         
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLV 147

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    +G+++++ +  + K I +      +    MQ+    ++G  A     + E  
Sbjct: 148 QKEYLALANGKIEENFI--IDKAINLAKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 201

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 202 PKINATLLLCKPLTGRQHQIR 222


>gi|328471410|gb|EGF42305.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           parahaemolyticus 10329]
          Length = 250

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 29/171 (16%), Positives = 61/171 (35%), Gaps = 37/171 (21%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++      +   +++  L   +  +  V RLD++T GL++L  +  
Sbjct: 19  EDDHILAVNKPSGLLSVPGRLAEHHDSMWSRLQEEYPDIQVVHRLDMSTSGLMVLAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLNL-LKKGIVIQGICYGDM-QVTL 179
                       L        ++Y  R  G V+Q++  + L    +I       + +V  
Sbjct: 79  AESALKKQFQFRLTH------KIYYARVWGHVEQEEGEIDLP---LICDWPNRPLQKVCF 129

Query: 180 DTQKGSNAWVTVGLRE-----------------GKNREIKKVFEFFNWKVN 213
           +  K S     V  RE                 G++ +++   +     + 
Sbjct: 130 EDGKPSKTLFQVAKREEHEDGTKTTIVRLLPITGRSHQLRVHMQALGHPIV 180


>gi|289434238|ref|YP_003464110.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
 gi|289170482|emb|CBH27022.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Listeria seeligeri serovar 1/2b str. SLCC3954]
          Length = 296

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 68/199 (34%), Gaps = 35/199 (17%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKA--------ERTRLWLYHKPI 82
             +++VNG         V + D + +          L           E   L + +KP 
Sbjct: 38  DGKIEVNGTEQNVL-YEVQTGDEVRLTFPTEQQNERLLAEYTDLEIVFEDDFLLIINKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVLE- 135
           G+ +  S      +V + +   +      S +  V RLD  T GL+L+  +      L  
Sbjct: 97  GMASIPSQYHPSGSVANFVKGHYEAQGLTSAIHIVTRLDRETSGLMLIAKNRFAHARLST 156

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
            L      R Y+    G            + +  ++++++ +  +G         L   +
Sbjct: 157 FLQQGLLKRSYQAFVSGELVKQVGSIEAPIGRKAVSIMERVVTPEGKYAKTNYQVLARYQ 216

Query: 184 GSNAWVTVGLREGKNREIK 202
             +  V + L  G+  +I+
Sbjct: 217 AFDH-VALQLETGRTHQIR 234


>gi|262166132|ref|ZP_06033869.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM223]
 gi|262025848|gb|EEY44516.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM223]
          Length = 316

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKTIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAE-----------------------RTRLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEATPPSTKLNKVAELEHCIVYEDEHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDPEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFTEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|255317207|ref|ZP_05358453.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           6276s]
          Length = 303

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 60/202 (29%), Gaps = 51/202 (25%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  +   D + +    +  +    LW      +Y+KP     T  D   +
Sbjct: 40  RVNGRIERFESYKLQPGDRVSL--QIIEHSSPQLLWEDEHLCIYNKPAK--QTSEDLAHQ 95

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             V             V RLD +T G +L       + ++     +    + Y     GQ
Sbjct: 96  LNV-----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNRGIDKRYIALVFGQ 144

Query: 153 VDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLR--E------------- 195
             Q+       GI       CY  +   L      N+   + +   E             
Sbjct: 145 PRQE------SGIITTYTAPCYRRIGAVLFGNTDQNSG-KITITKWEILTRYPKYTLLLC 197

Query: 196 ----GKNREIKKVFEFFNWKVN 213
               G+  +I+   +     + 
Sbjct: 198 RPVTGRTHQIRLHMKTIGHPIV 219


>gi|254578372|ref|XP_002495172.1| ZYRO0B05082p [Zygosaccharomyces rouxii]
 gi|238938062|emb|CAR26239.1| ZYRO0B05082p [Zygosaccharomyces rouxii]
          Length = 611

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/196 (18%), Positives = 62/196 (31%), Gaps = 30/196 (15%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           IA   V +N          + + D I          V   P++   E   L +  KP G+
Sbjct: 146 IAGGSVYLNDEPA-NLESIIRNGDCIRHKIHRHEPPVTSRPIKVVYEDENLLVIDKPSGI 204

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELPST--QW 141
               +     +T+   L     R V    RLD  T GL+ +      A  +       + 
Sbjct: 205 PVHPTGRYRFNTITKILEKKLGRTVHPCNRLDRLTSGLMFMAKTPKGADEMADQLKAREV 264

Query: 142 LRVYRVRFHGQVD------QDKLNLLK--------KGIVIQGICYGDMQVTLDTQKGSNA 187
            + Y  R  G+         + L  L+         G+  +G  +        +  G  +
Sbjct: 265 TKEYVARVVGEFPVGEVVVDNPLKSLEPKLGLNVVCGMDEEGAKHAKTVFRRVSYDGETS 324

Query: 188 WVTVG-LREGKNREIK 202
            V    L  G+  +I+
Sbjct: 325 IVKCKPLT-GRTHQIR 339


>gi|227873687|ref|ZP_03991921.1| hemolysin A [Oribacterium sinus F0268]
 gi|227840476|gb|EEJ50872.1| hemolysin A [Oribacterium sinus F0268]
          Length = 275

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   G+  SR + +R I    V VNG   ++A  +      I V G  L    R
Sbjct: 6  ERLDVLLVERGLMESREKAKRAIMAGLVFVNGEKEDKAGSSFPEEAEILVKGKALPYVSR 65


>gi|74000106|ref|XP_544620.2| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Canis familiaris]
          Length = 518

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 47/292 (16%), Positives = 97/292 (33%), Gaps = 38/292 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWLYH-------K 80
           E  +   R+ +N   ++  ++ +   D     +     P+  AE  RL   +       K
Sbjct: 152 EAAVRAGRLHLNEEPVQDLSIMLKDNDFLRNRVHRHEPPVT-AEPVRLLAENEDVVVVDK 210

Query: 81  PIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP- 137
           P  +          +TV   L        +  + RLD  T G+L+      ++  +    
Sbjct: 211 PSSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQV 270

Query: 138 -STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSN 186
              Q  + Y  R  G+   +++           K G+          +         G +
Sbjct: 271 RDRQLEKEYVCRVEGEFPTEEVTCKEPILVVSYKVGVCRVDTRGKPCETVFQRLSYNGHS 330

Query: 187 AWVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKI 240
           + V    +    G+  +I+   +F    +        +++GP +      G   +  +++
Sbjct: 331 SVVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVAWGPSRGRG---GHIPKTDEEL 384

Query: 241 LREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           LR+ +  H  +++   LD         + D     SEV  D       S+QK
Sbjct: 385 LRDLVAEHQAKQSLDVLDLCEGDLPPGLIDSTAPSSEVGKDHIEELAASAQK 436


>gi|70726951|ref|YP_253865.1| ibosomal large subunit pseudouridine synthase RluD subfamily
           protein [Staphylococcus haemolyticus JCSC1435]
 gi|68447675|dbj|BAE05259.1| hypothetical protein, ribosomal large subunit pseudouridine
           synthase, RluD subfamily [Staphylococcus haemolyticus
           JCSC1435]
          Length = 287

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 58/160 (36%), Gaps = 22/160 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---------LPSIFSRVISVGRLDINTEGL 121
           E   L +  KP  L +T S      ++ +          L         V RLD NT+G+
Sbjct: 80  EDDYLIIVSKPNYLNSTPSREHPHDSLIERVLYYLNVGQLIDTSIVPHIVTRLDRNTKGI 139

Query: 122 LLLTNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGIC 171
           ++    G +  ++   ++   + Y    +G           + +D  +++ + +   G  
Sbjct: 140 VIFAKHGHIHHLMT--TSAIDKRYMCVCYGQMQLSGVIEEPIARDSQSIITRKVDASGKY 197

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 T+ T+  + +   + L  G+  +I+  F +    
Sbjct: 198 AKTSYETVMTKPEA-SLCEIKLHTGRTHQIRVHFNYVGHP 236


>gi|325264047|ref|ZP_08130779.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium sp. D5]
 gi|324030531|gb|EGB91814.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium sp. D5]
          Length = 296

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 35/233 (15%), Positives = 84/233 (36%), Gaps = 42/233 (18%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQR----VKVNGILLE---------RAAVN 53
           +++N    RV + + R G  SR   + ++  ++    V VNG                V+
Sbjct: 9   IRKNDDGLRVEQYLRRQGY-SR---QNLVELKKMPQSVLVNGCFCRLNERLANHNTLTVH 64

Query: 54  VMSTDHIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR- 107
           +   +   +  +P+        E   + + +KP G+    S  +  +T+ + L   +   
Sbjct: 65  IQERES-SLQILPVLLPLDIIYEDEDIIVINKPAGMPVHPSMNNYSNTLANGLAWYYQEQ 123

Query: 108 -----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG--------- 151
                     RLD +T GL ++      + +L   + +    R Y     G         
Sbjct: 124 GKPFIFRCTNRLDRDTSGLTVIAKHMLSSNILSRMTVRHEITREYLAVVRGSVRPSEGII 183

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              + +   +++++ +  +             +K  ++ V++ L  G+  +I+
Sbjct: 184 CAPLSRKPGSIIERTVDFENGEKAVTHYHAVEEKNGHSLVSLVLETGRTHQIR 236


>gi|292489024|ref|YP_003531911.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|292900157|ref|YP_003539526.1| RNA pseudouridylate synthase [Erwinia amylovora ATCC 49946]
 gi|291200005|emb|CBJ47129.1| putative RNA pseudouridylate synthase [Erwinia amylovora ATCC
           49946]
 gi|291554458|emb|CBA21962.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           CFBP1430]
 gi|312173188|emb|CBX81443.1| ribosomal large subunit pseudouridine synthase A [Erwinia amylovora
           ATCC BAA-2158]
          Length = 232

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 42/209 (20%), Positives = 72/209 (34%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IEV        +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDEIEV------LCQDEHLVLINKPAGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++     +   L    +Q    +VY     G ++ +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARTKAINAALCQQFSQRTVTKVYCALLCGHLNDN------EGVIDAAIA 119

Query: 172 YGDMQVTLDT-----QKGSNAWVTV-----------GL-----RE-----GKNREIKKVF 205
                  L +      K + +   V            L      E     G+  +++   
Sbjct: 120 KDPALFPLMSICSIHGKPARSRYRVLQRCYHALQDGTLLPLTRVELTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +   + +       YG    G LL G+ R
Sbjct: 180 QQLGYPILGCD--LYG----GRLLPGTER 202


>gi|221232733|ref|YP_002511887.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225855502|ref|YP_002737014.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
 gi|220675195|emb|CAR69781.1| RNA pseudouridylate synthase [Streptococcus pneumoniae ATCC 700669]
 gi|225723486|gb|ACO19339.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae JJA]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGKYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|296314658|ref|ZP_06864599.1| RNA pseudouridine synthase [Neisseria polysaccharea ATCC 43768]
 gi|296838567|gb|EFH22505.1| RNA pseudouridine synthase [Neisseria polysaccharea ATCC 43768]
          Length = 307

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 38/109 (34%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+ +     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSQNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|223999397|ref|XP_002289371.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220974579|gb|EED92908.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 543

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/202 (18%), Positives = 64/202 (31%), Gaps = 51/202 (25%)

Query: 8   QENFTPQRVSKVIA-RAGIA------SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
           +E    +R+ K +  +   A      S+ + E  I   RV VN  ++  ++  V   D I
Sbjct: 189 EEFADSKRL-KWLCRQQNFALSKFIRSKSQCEDAIKNGRVFVNRCVVMDSSRIVRENDVI 247

Query: 61  EV-----------------DG-----------VPLRKAERTRLWLYHKPIGLVTTHSDPD 92
            +                 D              L   +   L + HKP+G+    S   
Sbjct: 248 TLVEEYALVSTSTNNINANDNDSNSSEKVKVVKELLINKDVTLVVVHKPVGMRCVGS--F 305

Query: 93  GRSTVFDNLPSIFSRVISVG--------RLDINTEGLLLLTNDGGLARVLELPSTQWLRV 144
             +T+       +  +  V         +LD  + GL LLT          L S + +  
Sbjct: 306 SHTTLEMITKRQYETIRGVNGLSCNVISKLDTGSAGLCLLTVSSSTVDNGILDSVKAVYT 365

Query: 145 YRVRFHGQVDQDKLNLLKKGIV 166
           + V  HG          K G+ 
Sbjct: 366 FTVLVHGCP-----ENWKSGVY 382


>gi|139438597|ref|ZP_01772113.1| Hypothetical protein COLAER_01111 [Collinsella aerofaciens ATCC
           25986]
 gi|133776136|gb|EBA39956.1| Hypothetical protein COLAER_01111 [Collinsella aerofaciens ATCC
           25986]
          Length = 205

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 24/154 (15%), Positives = 51/154 (33%), Gaps = 28/154 (18%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGLLLLTN 126
               KP G++  H D  G  T+ D    +          + +  + RLD NT G++L + 
Sbjct: 1   MAIDKPAGMIV-HGDGTGERTLTDYASDLLLAMGDGFAATDMQPLNRLDRNTTGVVLFSL 59

Query: 127 DGGLARVLELPSTQW--LRVYRVRFHGQV-------------DQDKLNLLKKGIVIQGIC 171
           D       +         + Y     G++             D+     ++ G   +   
Sbjct: 60  DKQTQPAFDQMVNDHAFEKHYLALAEGKIDWNEKLIDKPIARDRHDSRKMRVGASGKPSQ 119

Query: 172 YGDMQVTLDTQK---GSNAWVTVGLREGKNREIK 202
                +     +    + +++ V L  G+  +I+
Sbjct: 120 TRVKVLKRLKSRRGLPTRSYIDVELLTGRKHQIR 153


>gi|73662254|ref|YP_301035.1| pseudouridylate synthase [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494769|dbj|BAE18090.1| putative pseudouridylate synthase [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
          Length = 275

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 70/201 (34%), Gaps = 28/201 (13%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAERTRL-----WLYHKPIGLVTT 87
           + +N          V + D++ +       + +P  +  +         +  KP G+ T 
Sbjct: 37  ITIN-ESPGTLTTKVNTGDNVYIPTPDEVSNYLPSYRFAQIYYEDDDIAIVMKPKGVKTH 95

Query: 88  HSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
            +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   L   +  R
Sbjct: 96  PNDLKESNTLMNHVIYTIKSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRMLEENKIDR 155

Query: 144 VYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG 192
           +Y+                 + +DK +  K+ +   G       +     K     + + 
Sbjct: 156 IYKANVHSLLPIKPQTIDMPIGKDKFHSNKRRVSSTGQSAITHILNSKMIKEDVCELEIK 215

Query: 193 LREGKNREIKKVFEFFNWKVN 213
           L  G+  +I+         V 
Sbjct: 216 LDTGRTHQIRVHLAEIGHPVI 236


>gi|315653906|ref|ZP_07906822.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
 gi|315488602|gb|EFU78248.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           iners ATCC 55195]
          Length = 300

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 65/213 (30%), Gaps = 42/213 (19%)

Query: 36  AQQRVKVN-------------GILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKP 81
               V VN               ++            ++   +P+    E     + +K 
Sbjct: 40  RGGNVLVNHRRRYNNYLLHDGDEVIFILG-KEKPNATLKFSNLPIAIVQETANYLIVNKE 98

Query: 82  IGLVTTHSDPDGRSTVFDNL-----PSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL 134
             L+T  S  +   +V   L     P    ++    + RLD +T GL+L+  +       
Sbjct: 99  ADLLTIPSKNEDNDSVVGRLLHYLNPDALLKIKPHIITRLDRDTSGLVLVGKNAVAHARF 158

Query: 135 E-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + ++ Y    HG     +L     G++   I   D  +    ++  K S     
Sbjct: 159 NVSDKQRTIKKYHAIVHGNFSPSQLQ----GVIDAPIGKKDDPIKRYIMEGGKNSVTKYR 214

Query: 191 VG-------LRE-----GKNREIKKVFEFFNWK 211
           V        L E     G+  +I+   ++    
Sbjct: 215 VIKQVAGASLVELQLLTGRTHQIRVHMQYLGHP 247


>gi|298252641|ref|ZP_06976435.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           5-1]
 gi|297533005|gb|EFH71889.1| pseudouridylate synthase, 23S RNA-specific [Gardnerella vaginalis
           5-1]
          Length = 288

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 79/229 (34%), Gaps = 43/229 (18%)

Query: 23  AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL------- 75
            G+ SR     +I + + K+ G   +++++ +   D I VD     + +  +        
Sbjct: 1   MGV-SRASAISLIERNQAKILGRKSQKSSI-LQDGDTIVVDQKESAEQKEEQNNESSVCN 58

Query: 76  --WLYH--------KPIGLVTTHSDPDGRSTVFDNLPS----------IFSRVISVGRLD 115
              +Y+        KP+G+ +  +      TV + L +            SR   V RLD
Sbjct: 59  IPIIYNDDDVVVIDKPVGVASHAAKGWSGPTVPECLEAVGIDIKTTLCDESRKGIVSRLD 118

Query: 116 INTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLK 162
           + T GL+L+  T+        +       + Y     G            + + K++  +
Sbjct: 119 VGTSGLMLVCKTDFAYEVMKNQFAKHIVKKTYHALVQGDLAQDKATIDAPIGRAKVSDFR 178

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             I   G         L+    +   V+V L  G+  +I+  F      
Sbjct: 179 FTITSDGKPAVTHWDVLERFSQAT-LVSVNLETGRTHQIRVHFSSIGHP 226


>gi|258511286|ref|YP_003184720.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478012|gb|ACV58331.1| pseudouridine synthase, RluA family [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 314

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 78/253 (30%), Gaps = 54/253 (21%)

Query: 7   VQENFTPQRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVN----VMST 57
           V      +R+ + +           SR +V+R +    ++          +     V + 
Sbjct: 11  VSAEDAGERLDRWLTDRLQEDDIEVSRTQVQRWLDDGFIR----RARPGRLKASDPVEAG 66

Query: 58  DHIEVD-------------GVP-LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D  EVD             GVP +   E   + +  KP G+V        R T+ + L +
Sbjct: 67  DLYEVDVPEEEPLELVPDDGVPFVVAYEDDDVIVVDKPRGVVVHPGAGHMRGTLVNGLLA 126

Query: 104 IFSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
             + +           V R+D +T GL++        R L     +    R Y    HG+
Sbjct: 127 RGTPLCTLAGALRPGVVHRIDKDTSGLVVFAKSDRAYRALVEAFRAHDVEREYVAIAHGR 186

Query: 153 V-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +             D      +    V QG         +       +++ + L  G+  
Sbjct: 187 MPHREGTIDMPIARDPADRQRMA---VRQGGKRAVTHFEVLESFAKYSYLRLRLETGRTH 243

Query: 200 EIKKVFEFFNWKV 212
           +I+         +
Sbjct: 244 QIRVHLAAIGHPI 256


>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 = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|154175159|ref|YP_001407354.1| putative prophage LambdaCh01, recombination protein Bet
           [Campylobacter curvus 525.92]
 gi|112802454|gb|EAT99798.1| putative prophage LambdaCh01, recombination protein Bet
           [Campylobacter curvus 525.92]
          Length = 305

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 59/138 (42%), Gaps = 9/138 (6%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV-----PLRKAERTRLWLYHKPIG 83
           RE +R+I + R+  +G ++      V+S +   +D            E     ++ KP G
Sbjct: 28  REAQRLIDKGRLLCDGAVVSE-KNAVLSGEICLIDYEMNPRGLSPIFECDEFAVFDKPSG 86

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
           +++  +      ++ D +  ++ R  +V  RLD  T GL++++ +    + L     S  
Sbjct: 87  VLSHPNGRRCEYSLNDEIWHLYGREAAVTHRLDRETSGLIVVSKNLAAQKELKAMFESRA 146

Query: 141 WLRVYRVRFHGQVDQDKL 158
             + Y     G++ +  +
Sbjct: 147 VKKRYVALAGGEICEPFI 164


>gi|87119407|ref|ZP_01075304.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp.
           MED121]
 gi|86164883|gb|EAQ66151.1| ribosomal large subunit pseudouridine synthase D [Marinomonas sp.
           MED121]
          Length = 322

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/208 (15%), Positives = 63/208 (30%), Gaps = 34/208 (16%)

Query: 27  SRREVERMIAQQRVKVNGIL-----------LERAAVNVMSTDHIEVDGVPLR-KAERTR 74
           SR  ++  I +  + V+G             +      V   D  + + +PL    E   
Sbjct: 32  SRSRIQAWIKEGVLLVDGKKSKAKEKLFVGEVISLETLVEDIDDHQPEDIPLDIVYEDED 91

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFSRVISVGRLDINTEGLLLLTNDG 128
           + + +KP GLV   +      T+ + +       +   R   V RLD  T GL+++    
Sbjct: 92  ILVVNKPSGLVVHPAVGHRSGTLMNAILFHCPESAHVPRAGIVHRLDKETTGLMVVAKTL 151

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVD------------QDKLNLLKKGIVIQGICYGD 174
                L          R Y     G +                   +   +         
Sbjct: 152 AAQTELVSQLQDRSMGREYEAVAIGIMTGGGTVNEPIGRHPQNRQKMA--VEPLNGKDAV 209

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
               L  +  ++  + + L  G+  +I+
Sbjct: 210 THYRLLQRFKNHTHIRLKLETGRTHQIR 237


>gi|99080132|ref|YP_612286.1| ribosomal large subunit pseudouridine synthase C [Ruegeria sp.
           TM1040]
 gi|99036412|gb|ABF63024.1| ribosomal large subunit pseudouridine synthase C [Ruegeria sp.
           TM1040]
          Length = 348

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/200 (20%), Positives = 69/200 (34%), Gaps = 50/200 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E+   QR+ + +       RR         +E+M  +  ++++G  ++ A   V + 
Sbjct: 8   TVTEDDGGQRIDRWL-------RRLFPHVNQGRIEKMCRKGELRLDGGRVK-ANTRVEAG 59

Query: 58  DHIEV---------------------DGVPLR---KAERTRLWLYHKPIGLVT-----TH 88
             + V                     D   +R     +   + + +KP GL       T 
Sbjct: 60  QVVRVPPLAESDMKPAEARPVKISDADAKMIRDCVIYKDDDVLVINKPAGLAVQGGSGTT 119

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
              DG S           R+  V RLD +T GLL+L  +   A+ L          ++Y 
Sbjct: 120 KHVDGLSEALRFDAEDKPRL--VHRLDKDTSGLLVLARNRKAAQGLTAAFRHKNTRKIYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIV 166
               G      L  +K G+V
Sbjct: 178 ALVAGVPTP-YLGEIKTGLV 196


>gi|332199087|gb|EGJ13167.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA41317]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|315126331|ref|YP_004068334.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315014845|gb|ADT68183.1| 23S rRNA pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 319

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 75/236 (31%), Gaps = 41/236 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + E+   QR+   +        +  V +++ +  V+VN   ++     +   D I +  
Sbjct: 13  TINEDHLGQRIDNFLITHLKGVPKSAVYKILRKGEVRVNKKRIK-PVYKLQLDDVIRIPP 71

Query: 65  VPLRKAER--------------------TRLWLYHKPIGLVTTHSDPDGRSTVFDN--LP 102
           + + + E                       L + +KP G+            +     L 
Sbjct: 72  IRVSEREEFVPSKLDKVTRLEDYILFEDKYLMVINKPSGMAVHGGSGLSYGLIEALRVLR 131

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T G LL+     +   L   L      + Y     GQ D      
Sbjct: 132 PEERSLELVHRLDRDTSGCLLIAKRRSVLTALHEQLREKTMEKNYWALVEGQWDSKT-KN 190

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           + +G+    +  G+  V +D  +G  +     + E              G+  +I+
Sbjct: 191 VTEGLRKNTLKSGERVVRVDNTEGKPSHTRFKVLERFNDCSLVQASPVTGRTHQIR 246


>gi|224013560|ref|XP_002296444.1| hypothetical protein THAPSDRAFT_263801 [Thalassiosira pseudonana
           CCMP1335]
 gi|220968796|gb|EED87140.1| hypothetical protein THAPSDRAFT_263801 [Thalassiosira pseudonana
           CCMP1335]
          Length = 341

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/215 (16%), Positives = 63/215 (29%), Gaps = 65/215 (30%)

Query: 44  GILLERAAVNVMSTDHI-----------EVDGVPLRKA--------ERTRLWLYHKPIGL 84
           G ++      V   D I            + GVP R          E   + + +KP G+
Sbjct: 43  GKVIT----RVYPGDTIGFQRRAGSDYYALQGVPYRLPPFEVPVVYEDDHMAIVNKPSGV 98

Query: 85  V---------TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
           V             D D    V         R   V RLD  T GL+++      A  L 
Sbjct: 99  VLYRAEGGRGGGARDEDTPQNV------PLKRPQPVHRLDRPTSGLVVVAKTKLAAVHLS 152

Query: 136 L--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV---- 189
                 +  + Y    +G   Q        G+  + + +  +   L+ +     W     
Sbjct: 153 QQFEFRKAEKTYVAIVNGIPRQ-------SGVRAEPMQWNTIDYDLEEKTAVTRWRVLRK 205

Query: 190 ---------TVGLRE-----GKNREIKKVFEFFNW 210
                    T+ L E     G+  ++++   +   
Sbjct: 206 VKSLHGNDGTLTLVEMKPKTGRYHQLRRHCAWVCN 240


>gi|32474288|ref|NP_867282.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
 gi|32444826|emb|CAD74828.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica SH 1]
          Length = 256

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/176 (15%), Positives = 54/176 (30%), Gaps = 41/176 (23%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   L + +KP  L T  +   G+ T+         R         +  V RLD  T G+
Sbjct: 34  EDNHLLVVNKPTKLATMGA--AGQPTLHSLGCDYIRRTCNKPNKVYLGIVSRLDSMTSGV 91

Query: 122 LLLTNDGGLARVLE-----LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++      A  L             + Y     G+V+Q      ++G ++  +   D  
Sbjct: 92  IVMARTSKAASRLTPQFANHSGDGAKKTYLAVVSGRVEQ------QQGTLVDDVYKDDAA 145

Query: 177 VTLDTQKGSNA-------WVTV-----GLR-------EGKNREIKKVFEFFNWKVN 213
             +     S +          V      L         G+  +I+  +    + + 
Sbjct: 146 HRMRVAHHSRSDAKEARLEYEVLGCDRELTLLMVKPLTGRKHQIRLQWAEVGFPIL 201


>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 = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   GI  SR + +  I + RV VNG  +++A   V     IE  G  L+   R
Sbjct: 6  ERLDILLVEKGIITSREKAKACIMEGRVYVNGQKVDKAGEKVGVDSDIEYRGDTLKYVSR 65


>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 = 52.9 bits (126), Expect = 8e-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|307151795|ref|YP_003887179.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
 gi|306982023|gb|ADN13904.1| pseudouridine synthase [Cyanothece sp. PCC 7822]
          Length = 562

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 31/164 (18%), Positives = 57/164 (34%), Gaps = 25/164 (15%)

Query: 61  EVDGVPLRK--AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFS---RVISVGRL 114
            V+   +     E   L   +KP GL++          +V   +  + +   + + V RL
Sbjct: 348 TVNAKEILPIIYEDEYLIAINKPEGLLSVPGRGSHQYDSVISRITHLLADGDQCMVVHRL 407

Query: 115 DINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK----LNLL------- 161
           D +T G+LLL     +   L       +  +VY     G V   K    L L        
Sbjct: 408 DQDTSGILLLARHRQIYNHLAQQFRQRKIHKVYHALVKGGVSAQKGTINLPLWGDPNTRP 467

Query: 162 KKGIVIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
           ++ +     CYG   +T   +     +   +      G+  +I+
Sbjct: 468 RQKV---DFCYGKESITHFQVIAVAENFTRLEFIPVTGRTHQIR 508


>gi|167521497|ref|XP_001745087.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163776701|gb|EDQ90320.1| predicted protein [Monosiga brevicollis MX1]
          Length = 401

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/183 (19%), Positives = 56/183 (30%), Gaps = 26/183 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKPIGL 84
           I +  + VN   +      + +   I          V   PL    E   L    KP  +
Sbjct: 72  ITEGLITVNSERV-PLDFIIDNNHIILNKVHRHEPPVTNDPLSIVGETPDLLAIDKPASI 130

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQ 140
                     +TV   L     R       RLD  T GLL+   +  +A+  E      Q
Sbjct: 131 PVHPCGRYRHNTVQAILGHEHDRWRVYPCHRLDRLTSGLLIFCKNPAMAKQFEQWITQHQ 190

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             + Y  R  G+V+Q  L      + I     G   V  + +              + R 
Sbjct: 191 VEKQYICRVQGRVEQSVL-FCDAPLKICDQRLGLCCVHPEGKASLT----------RFRV 239

Query: 201 IKK 203
           I++
Sbjct: 240 IRR 242


>gi|78224034|ref|YP_385781.1| pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
 gi|78195289|gb|ABB33056.1| Pseudouridine synthase, RluD [Geobacter metallireducens GS-15]
          Length = 296

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 43/228 (18%), Positives = 80/228 (35%), Gaps = 42/228 (18%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKA------- 70
           +A  G  +R           + VNG+ +      +++ D + +   G             
Sbjct: 28  LAYLGKLTR--------GGHLTVNGLPVT-PDTLLVTGDTMALKESGRTRELLAAKRPSL 78

Query: 71  ----ERTRLWLYHKPIGLVTTHSDPDGRSTV-----FDNLPSIFSRVISVGRLDINTEGL 121
               E  R+ + +KP GL    +  D ++ V     F       +++  V RLD  T G 
Sbjct: 79  DILFEDDRIVVVNKPPGLPVHRTAEDEQTLVDVAERFLAQRGTPAKLRPVNRLDRGTSGA 138

Query: 122 LLL----TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQGICYGDMQ 176
            +L    T+ G   R ++   T   ++Y     G++  +  ++       ++G       
Sbjct: 139 TILAKSATSAGMFGRFVK--ETGLGKLYLAVADGKLPAEGTIDT-----PLEGKEAQTQY 191

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
            TL  Q  S A + V  +  G+  +I+K        V    R    P 
Sbjct: 192 RTL-FQGKSAALLLVTPIT-GRTHQIRKHLALTGHPVRGDRRYRGAPL 237


>gi|332071723|gb|EGI82215.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA17545]
          Length = 286

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGKYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|296436545|gb|ADH18715.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/11222]
          Length = 303

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 61/202 (30%), Gaps = 51/202 (25%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  +   D + +    +  +    LW      +Y+KP     T  D   +
Sbjct: 40  RVNGRIERFESYKLQPGDRVSL--QIIEHSSPQLLWEDEHLCIYNKPAK--QTSEDLAHQ 95

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             V             V RLD +T G +L       + ++     + +  + Y     GQ
Sbjct: 96  LNV-----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQ 144

Query: 153 VDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLR--E------------- 195
             Q+       GI       CY  +   L      N+   + +   E             
Sbjct: 145 PRQE------SGIITTYTAPCYRRIGAVLFGNTDQNSG-KITITKWEILTRYPKYTLLLC 197

Query: 196 ----GKNREIKKVFEFFNWKVN 213
               G+  +I+   +     + 
Sbjct: 198 RPVTGRTHQIRLHMKTIGHPIV 219


>gi|253988053|ref|YP_003039409.1| ribosomal large subunit pseudouridine synthase A [Photorhabdus
           asymbiotica subsp. asymbiotica ATCC 43949]
 gi|253779503|emb|CAQ82664.1| ribosomal large subunit pseudouridine synthase A [Photorhabdus
           asymbiotica]
          Length = 230

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/156 (16%), Positives = 57/156 (36%), Gaps = 25/156 (16%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TND 127
           +   + + +KP GL++      + + ++   +   F    SV RLD+ T G++++  T D
Sbjct: 31  QDQHIIVVNKPSGLLSVPGRAEEHKDSIMTRIQQQFPAAESVHRLDMATSGIMVVALTKD 90

Query: 128 GGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTLDTQK 183
                  +    +  + Y  R  G +  +     L L+              +V  DT K
Sbjct: 91  AERELKRQFREREPKKTYIARVWGYLKPETGTVDLPLIC-----DWPNRPKQKVCFDTGK 145

Query: 184 GSNAWVTVGLRE------------GKNREIK-KVFE 206
            +     V + E            G++ +++  +  
Sbjct: 146 SAQTEYEVLVYEDQATRVKLSPITGRSHQLRVHMLA 181


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

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 71/218 (32%), Gaps = 48/218 (22%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRK-------- 69
           ++++   +V+V+G  ++     V     + V               G  L+         
Sbjct: 20  QKLLRSGQVRVDGGRVKS-DARVQPGQMVRVPPLDVDAKLKSGPIAGKDLKHSSDFELLS 78

Query: 70  ----AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLL 122
                E  ++ + +KP GL         R         +     +   V RLD +T G+L
Sbjct: 79  RMVLHEDEKVIVLNKPPGLAVQGGSGVARHIDQMLEAWISPKGEKPRLVHRLDRDTSGVL 138

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQV--DQDKLNLL----------KKGIVIQ 168
           ++    G A+ L          + Y     G     +DK++            +  I   
Sbjct: 139 VIARTRGAAQKLTAAFRERDTKKTYWSLVKGVPRKHEDKISTWLVKEPTADGDRMRIAKH 198

Query: 169 GICYGDMQVT----LDTQKGSNAWVTVGLREGKNREIK 202
           G    D  V+    ++T     AW+ +    G+  +++
Sbjct: 199 GEDGADHAVSYYRVVETAAQRLAWLEMEPYTGRTHQLR 236


>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 = 52.9 bits (126), Expect = 8e-05,   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|301300163|ref|ZP_07206378.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300852251|gb|EFK79920.1| pseudouridine synthase, RluA family [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 295

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 23/163 (14%), Positives = 52/163 (31%), Gaps = 23/163 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-----SRVIS--VGRLDINTEGLLL 123
           E     L  KP  + +  S      ++ + +   +       +I   V RLD +T G+++
Sbjct: 83  EDDNYLLVDKPAFVASIPSPLHPNDSLVNRVVGYYQIRGYRGIIPHIVTRLDRDTSGIVI 142

Query: 124 LTNDGGLARVLELP---STQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQG 169
                  A  L        +  + Y     G            + +D  +L+K+ ++   
Sbjct: 143 FAKH-RYAHALLDSQLKEHKISKTYTAILSGILHNNHYIIDLPIGRDSTSLIKRKVLFSE 201

Query: 170 ICYGDMQVTLDTQKG-SNAWVTVGLREGKNREIKKVFEFFNWK 211
                       ++   N    + L  G+  +I+    +  + 
Sbjct: 202 KAKRSKTEIFVKERIRDNTLCKIKLHTGRTHQIRVHCSYLGYP 244


>gi|294140341|ref|YP_003556319.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
 gi|293326810|dbj|BAJ01541.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           violacea DSS12]
          Length = 218

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/166 (16%), Positives = 58/166 (34%), Gaps = 26/166 (15%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +R  +R  + + +KP GL++      +        L   +  +I V RLD  T G+++  
Sbjct: 16  IRYQDRD-ILVINKPSGLLSNPGRAANTYDCALTRLLQRYPEIILVHRLDCATSGIMVFA 74

Query: 126 -NDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTL 179
            N    + +      +   + Y     GQ++QD      +G++            +Q   
Sbjct: 75  LNKKAESNIKTQFQNRMSKKTYIAEVLGQLNQD------QGVIDLAMKADKIRPPLQEIA 128

Query: 180 DTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVN 213
           +  K S  +  V        L E     G+  +++         + 
Sbjct: 129 EDGKVSKTYYKVLERRETSTLVELKPVTGRTHQLRLHMLALGHPIL 174


>gi|65318577|ref|ZP_00391536.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Bacillus
           anthracis str. A2012]
 gi|165872829|ref|ZP_02217455.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|170708875|ref|ZP_02899309.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|190569145|ref|ZP_03022043.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
 gi|164711406|gb|EDR16957.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0488]
 gi|170126191|gb|EDS95084.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis str. A0389]
 gi|190559728|gb|EDV13715.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus anthracis Tsiankovskii-I]
          Length = 292

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 45/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 96  STIPSREHPSGSVANALLSHYDKQYLPSTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 154

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 155 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 214

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 215 KTH-VSLELDTGRTHQIRVHLAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 262

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 263 SLTFYHPILEKEMSFAAMIPSDMQEV 288


>gi|254294726|ref|YP_003060749.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
 gi|254043257|gb|ACT60052.1| pseudouridine synthase [Hirschia baltica ATCC 49814]
          Length = 219

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/171 (16%), Positives = 61/171 (35%), Gaps = 17/171 (9%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           D   +   E     +  KP GL++     P+    +     +++    +V RLD+ T G+
Sbjct: 12  DPSIVVIYEDEAFLVLDKPSGLLSVPGKPPEHSDCLETRAQAVYPEARTVHRLDMATSGV 71

Query: 122 LLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQ 168
            ++  +  + R L L        + Y  R  G ++ D+            N  K+ I  +
Sbjct: 72  WVMAREHAMMRHLGLQFERRHTSKTYIARVWGDIEDDEGFIDEPIICDWPNRPKQMICYE 131

Query: 169 GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVNRLIRI 218
                  +  +  +K     V +  +  G+  +++   +     +    RI
Sbjct: 132 KGKPSQTKWKVIERKDGITRVELTPIT-GRTHQLRLHMQHIGHPILA-DRI 180


>gi|238757890|ref|ZP_04619072.1| Pseudouridine synthase [Yersinia aldovae ATCC 35236]
 gi|238703875|gb|EEP96410.1| Pseudouridine synthase [Yersinia aldovae ATCC 35236]
          Length = 232

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 30/146 (20%), Positives = 54/146 (36%), Gaps = 20/146 (13%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L + +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIE------NLYQDDHLLVINKPTGLLSLSGKNPQNLDSVHHRLVQIFPSCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG 192
                     +     K + ++  V 
Sbjct: 120 KDPALFPLMSICAIHGKPARSYYRVV 145


>gi|15604825|ref|NP_219609.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           D/UW-3/CX]
 gi|255348466|ref|ZP_05380473.1| pseudouridine synthetase family protein [Chlamydia trachomatis 70]
 gi|255503008|ref|ZP_05381398.1| pseudouridine synthetase family protein [Chlamydia trachomatis 70s]
 gi|255506680|ref|ZP_05382319.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           D(s)2923]
 gi|3328503|gb|AAC67697.1| predicted pseudouridine synthetase family [Chlamydia trachomatis
           D/UW-3/CX]
 gi|289525149|emb|CBJ14622.1| tRNA pseudouridine synthase A [Chlamydia trachomatis Sweden2]
 gi|296434693|gb|ADH16871.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           E/150]
 gi|296435622|gb|ADH17796.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/9768]
 gi|296437482|gb|ADH19643.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/11074]
 gi|296438411|gb|ADH20564.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           E/11023]
 gi|297139981|gb|ADH96739.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           G/9301]
 gi|297748235|gb|ADI50781.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-EC]
 gi|297749115|gb|ADI51793.1| tRNA pseudouridine synthase A [Chlamydia trachomatis D-LC]
          Length = 303

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 32/202 (15%), Positives = 61/202 (30%), Gaps = 51/202 (25%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  +   D + +    +  +    LW      +Y+KP     T  D   +
Sbjct: 40  RVNGRIERFESYKLQPGDRVSL--QIIEHSSPQLLWEDEHLCIYNKPAK--QTSEDLAHQ 95

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             V             V RLD +T G +L       + ++     + +  + Y     GQ
Sbjct: 96  LNV-----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNREIDKRYIALVFGQ 144

Query: 153 VDQDKLNLLKKGI--VIQGICYGDMQVTLDTQKGSNAWVTVGLR--E------------- 195
             Q+       GI       CY  +   L      N+   + +   E             
Sbjct: 145 PRQE------SGIITTYTAPCYRRIGAVLFGNTDQNSG-KITITKWEILTRYPKYTLLLC 197

Query: 196 ----GKNREIKKVFEFFNWKVN 213
               G+  +I+   +     + 
Sbjct: 198 RPVTGRTHQIRLHMKTIGHPIV 219


>gi|322807303|emb|CBZ04877.1| similar to ribosomal large subunit pseudouridine synthase D,
           CAC1266-type [Clostridium botulinum H04402 065]
          Length = 300

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|312872564|ref|ZP_07732632.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
 gi|311091926|gb|EFQ50302.1| pseudouridine synthase, RluA family [Lactobacillus iners LEAF
           2062A-h1]
          Length = 300

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 30/181 (16%), Positives = 59/181 (32%), Gaps = 28/181 (15%)

Query: 55  MSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRV 108
                ++   +P+    E     + +K   L+T  S  +   +V   L     P     +
Sbjct: 71  KPNATLKFSNLPITIVQETANYLIVNKEADLLTIPSKNEDNDSVVGRLLHYLNPDALLNI 130

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKGI 165
               + RLD +T GL+L+  +             + ++ Y    HG     +L     G+
Sbjct: 131 KPHIITRLDRDTSGLVLVGKNAVAHARFNVSDKQRTIKKYHAIVHGNFSPSQLQ----GV 186

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVG-------LRE-----GKNREIKKVFEFFNW 210
           +   I   D  +    ++  K S     V        L E     G+  +I+   ++   
Sbjct: 187 IDAPIGKKDDPIKRYIMEGGKDSVTKYRVIKQVAGASLVELQLLTGRTHQIRVHMQYLGH 246

Query: 211 K 211
            
Sbjct: 247 P 247


>gi|307709867|ref|ZP_07646315.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
 gi|307619357|gb|EFN98485.1| pseudouridine synthase, RluA family protein [Streptococcus mitis
           SK564]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 55/149 (36%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +   +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNISSKELVFRDKIGRDRHDRRKRIVDAKHGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V    Q     + V   L+ G+  +I+
Sbjct: 190 THVNRLKQFPNKTSLVRCKLKTGRTHQIR 218


>gi|254994901|ref|ZP_05277091.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Mississippi]
          Length = 296

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 82/243 (33%), Gaps = 48/243 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK + +V+      RV + +   G+    ++  +ER++ +  + +N    +  +  V + 
Sbjct: 1   MKREYLVEGTCFEVRVDRYL--RGLLPGVTQSFIERLLRRGEILLNNTKAKS-STRVSNG 57

Query: 58  DHIEV---DGVPLRKAE--------------------RTRLWLYHKPIGLVTTHSDPDGR 94
           D + +   D + LR+ E                       +   +KP G+         +
Sbjct: 58  DVLSIKHADRIALREKEIHALQHVPLLDLISGSILYEDKNIIAINKPAGVSVQGG-SKVK 116

Query: 95  STVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
            ++ D L  I        V RLD +T G+L+L  +  +AR L       +  + Y     
Sbjct: 117 VSIDDVLDKIKPGECCRIVHRLDKDTSGVLVLARNLDVARYLAREFRERRVKKEYIAVTR 176

Query: 151 GQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGKNR 199
           G               K+       +I+        V       +   +  V    G+  
Sbjct: 177 GVPQPASGEVSTPIFYKVRSATGESMIEKEAKTFFSVMRILGDCAVVLLRPVT---GRKH 233

Query: 200 EIK 202
           +++
Sbjct: 234 QLR 236


>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 (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           T  R+ + + R G+A SR    R+I   RV V G + E+ A  V +   I V
Sbjct: 1  MTRVRLDRELVRRGLARSREHAARLIEAGRVYVRGSVAEKPATQVDTGAPIVV 53


>gi|283953645|ref|ZP_06371176.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
 gi|283794686|gb|EFC33424.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 414]
          Length = 300

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/199 (14%), Positives = 68/199 (34%), Gaps = 31/199 (15%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + +      GV +   E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILIEEKNKILNGLVELIIYENNPKGVKIVF-ENEDFAVLEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILVAKNKKAQINLKSLFEKKLV 147

Query: 142 LRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---- 195
            + Y     G++ ++ +    +        +    MQ+    ++         + E    
Sbjct: 148 QKEYLALASGEITENFIVDKAMDLAKNYDDVKTR-MQICAQGKQAIT---EFEILEYFPT 203

Query: 196 ------------GKNREIK 202
                       G+  +I+
Sbjct: 204 LNATLLLCKPLTGRQHQIR 222


>gi|145632659|ref|ZP_01788393.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 3655]
 gi|144986854|gb|EDJ93406.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 3655]
          Length = 322

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 82/237 (34%), Gaps = 43/237 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN   ++     + + D + +  
Sbjct: 17  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKSRIK-PEYKLQTGDVVRIPP 75

Query: 63  ------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--L 101
                 +  P+ K              E   L + +KP G+            +     L
Sbjct: 76  VRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRAL 135

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN 159
                 +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  + 
Sbjct: 136 RPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHIK 194

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 195 VIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 250


>gi|332071869|gb|EGI82358.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA41301]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|327484563|gb|AEA78970.1| Ribosomal large subunit pseudouridine synthase C LSU Psi955,
           Psi2504 and Psi2580 [Vibrio cholerae LMA3894-4]
          Length = 321

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/266 (14%), Positives = 81/266 (30%), Gaps = 58/266 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-SNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQL 225
           +I+   ++    +    R+      L
Sbjct: 242 QIRVHTQYMGHPIAWDDRMVIAALML 267


>gi|325973143|ref|YP_004250207.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
 gi|323651745|gb|ADX97827.1| tRNA pseudouridine synthase [Mycoplasma suis str. Illinois]
          Length = 231

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/146 (19%), Positives = 53/146 (36%), Gaps = 16/146 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           E     +  K  G++  H D    G+ T+ D L   +   +  V RLD NT GLLL+   
Sbjct: 8   ETKHYLIVDKDSGILV-HKDKYTRGKDTLIDILKEEYGEDIYLVNRLDKNTSGLLLIA-K 65

Query: 128 GGLA---RVLELPSTQWLRVYRVRFHGQVDQDKLN-LLK----KGIVIQGICYGDMQVTL 179
           G L+           +  + Y       +   K+         KG  ++       +   
Sbjct: 66  GKLSLLTLKALFEEQKIDKKYLAILSSPLPHPKIKITFSLGRDKGKKLRFTATNSKKYKT 125

Query: 180 D---TQKGSNAWVTVGLREGKNREIK 202
                +  ++  V + L+ G+  +++
Sbjct: 126 ALTYAETINSQLVLLSLKTGRTHQLR 151


>gi|223937244|ref|ZP_03629150.1| pseudouridine synthase, RluA family [bacterium Ellin514]
 gi|223894029|gb|EEF60484.1| pseudouridine synthase, RluA family [bacterium Ellin514]
          Length = 599

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 40/199 (20%), Positives = 66/199 (33%), Gaps = 30/199 (15%)

Query: 32  ERMIAQQR-VKVNGILLERAAVNVMSTDHI----------EVDGVPLRKAERTRLWLYHK 80
           E + AQ   V  + + +      V +   I          EV+G      E   L + +K
Sbjct: 335 EGLAAQGLLVTDDHLPVT-GKHIVSAGKRILQKMPNLTEPEVNGDIQILHEDEALIVLNK 393

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVL--EL 136
           P  L         R+T+   L  ++         RLD NT G++L+T     A  L  + 
Sbjct: 394 PAPLPMHAGGRFNRNTLEYILHQVYHPQKPRAAHRLDANTSGVVLVTRTRHFASHLQPQF 453

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV----- 191
              +  + Y V+  G   +D        I  +    G  +V  +    S     V     
Sbjct: 454 AHGEVGKFYLVKVQGTPKEDSF-SCNAPISAEPSEAGAREVDFEEGLPSRTEFRVLQRNA 512

Query: 192 ---GLRE-----GKNREIK 202
               L E     G+  +I+
Sbjct: 513 DGTTLLEARPLTGRTNQIR 531


>gi|68249014|ref|YP_248126.1| 23S rRNA pseudouridylate synthase C [Haemophilus influenzae
           86-028NP]
 gi|68057213|gb|AAX87466.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           influenzae 86-028NP]
          Length = 331

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 83/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + E+ + QR+   + A+     +  + R++ +  V+VN G +  +    + + D + + 
Sbjct: 26  TISEDESGQRIDNYLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQTGDVVRIP 83

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+ K              E   L + +KP G+            +     
Sbjct: 84  PVRVAEKNDAPISKNLNKVAALENQILFEDDCLIILNKPSGIAVHGGSGLNFGVIEALRA 143

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 144 LRPEARFLELVHRLDRDTSGILLIAKKRSALRNLHEQLRVKTVQKDYLALVRGQW-QSHI 202

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            +++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 203 KVIQAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYINATLVKASPVTGRTHQIR 259


>gi|322378277|ref|ZP_08052759.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
 gi|321280779|gb|EFX57797.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. M334]
          Length = 291

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G  ++ +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEISREYWALVDGNTNKKELVFKDKIGRDRHDRRKRIVDTKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     + V   L+ G+  +I+
Sbjct: 203 THVSRLKQFPNKTSLVRCKLKTGRTHQIR 231


>gi|225857586|ref|YP_002739097.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|225726338|gb|ACO22190.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae P1031]
 gi|301800771|emb|CBW33421.1| RNA pseudouridylate synthase [Streptococcus pneumoniae OXC141]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|225859768|ref|YP_002741278.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
 gi|225720831|gb|ACO16685.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae 70585]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|83644955|ref|YP_433390.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83632998|gb|ABC28965.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 315

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/245 (15%), Positives = 75/245 (30%), Gaps = 59/245 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMST 57
            +      QR+   +        RE++        ++I +  V++N    +     +   
Sbjct: 16  TIDSGSDGQRLDNFLV-------RELKGVPKGKIYKIIRKGEVRINKGRCK-PETKLKDG 67

Query: 58  DHIEV------DGVPLRKA---------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           D + +      +G  L                  E   L + +KP G+            
Sbjct: 68  DQVRIPPIRVSEGDSLEPVIPAGLIELVSQSTLFENDELLIINKPCGVAVHGGSGVSFGV 127

Query: 97  VFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG--LARVLELPSTQWLRVYRVRFHGQ 152
           +            +    RLD +T G+L+L       +     L + +  ++Y     G+
Sbjct: 128 IEILRAARQDIRFLELAHRLDRDTSGVLVLAKKRRALVQFHDMLKTGRVEKIYHAWVCGK 187

Query: 153 VDQDK---LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GK 197
             + K      LKK ++  G    ++    +  K S     V        L E     G+
Sbjct: 188 WPKHKSVITAPLKKNVLRSGERMVNVS---EDGKPSETRFRVLYSGAGRTLVEAQPITGR 244

Query: 198 NREIK 202
             +I+
Sbjct: 245 THQIR 249


>gi|53804663|ref|YP_113451.1| ribosomal large subunit pseudouridine synthase D [Methylococcus
           capsulatus str. Bath]
 gi|53758424|gb|AAU92715.1| ribosomal large subunit pseudouridine synthase D [Methylococcus
           capsulatus str. Bath]
          Length = 334

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 37/230 (16%), Positives = 71/230 (30%), Gaps = 36/230 (15%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILL---------ERAAVNVMSTDHIEVDG 64
           R+ + +A      SR  ++  I      ++GI +         ER  +   +   +E + 
Sbjct: 38  RLDQALAVLFPDFSRARLQTWIKDGHALLDGIQVAPRQKLLGGERVELRAEADAAVECEA 97

Query: 65  VPLR---KAERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLD 115
             +          +++  KP GLV   +      T+       D   +   R   V RLD
Sbjct: 98  EAIPLTVVHADESIFVIDKPAGLVVHPAAGHPAGTLQNALLHLDPALAAIPRCGIVHRLD 157

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD------------QDKLNLL 161
            +T GLL++       + L  +L      R Y     G V                    
Sbjct: 158 KDTSGLLVVARTLEAHKSLVDQLKDRSVNREYLALVQGMVTAGATVDEPIGRHPADRKRF 217

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +   G         ++ +   +  + V L  G+  +I+      +  
Sbjct: 218 A--VRPDGRESVTH-YRVEERFLHHTLLRVRLETGRTHQIRVHMAHLHHP 264


>gi|50085931|ref|YP_047441.1| ribosomal large subunit pseudouridine synthase D (pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1]
 gi|49531907|emb|CAG69619.1| ribosomal large subunit pseudouridine synthase D (Pseudouridylate
           synthase) (Uracil hydrolyase) [Acinetobacter sp. ADP1]
          Length = 350

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 31/171 (18%), Positives = 68/171 (39%), Gaps = 27/171 (15%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +  ++  QR+ +V   A +    SR ++++ +    + VNG +++         + + ++
Sbjct: 43  LDPDYLGQRIDQV--AATVWNEFSREKLKQWMKDGHLLVNGEVVK-PKYRCEGNELLTLN 99

Query: 64  ------------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                        +PL    E   + + +KP G+V      +   T+ + L   +     
Sbjct: 100 VELEAQTTSQPENIPLDIVYEDQDILVINKPAGMVVHPGAGNPSGTLVNALLYHYPKAVE 159

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
             R   V R+D +T GLL++  +      L   L      R+Y +  +G +
Sbjct: 160 LSRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLADKSVYRIYDLVVYGNI 210


>gi|111657101|ref|ZP_01407890.1| hypothetical protein SpneT_02001674 [Streptococcus pneumoniae
           TIGR4]
 gi|183603313|ref|ZP_02714103.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|183571639|gb|EDT92167.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus pneumoniae SP195]
 gi|332071803|gb|EGI82293.1| RNA pseudouridylate synthase family protein [Streptococcus
           pneumoniae GA17570]
          Length = 278

 Score = 52.9 bits (126), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 57/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPNEIALLNHVSTYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G +++ +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWALVDGNINRKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     +     L+ G+  +I+
Sbjct: 190 THVSRLKQFSNKTSLAHCKLKTGRTHQIR 218


>gi|258625453|ref|ZP_05720346.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM603]
 gi|258582257|gb|EEW07113.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM603]
          Length = 316

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKTIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAE-----------------------RTRLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEATPPSTKLNKVAELEHCIVYEDEHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDPEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFTEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 44/253 (17%), Positives = 80/253 (31%), Gaps = 54/253 (21%)

Query: 7   VQENFTPQRVSKVIARAGI-----ASRREVERMIAQQRVKVNGILLERAAVN----VMST 57
           V      +R+ + +           SR +V+R I+   V+          +     V + 
Sbjct: 11  VSAEDAGERLDRWLTDRLQEDEIEVSRTQVQRWISDGCVR----RARPGRLKASDPVEAG 66

Query: 58  DHIEVD-------------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D  EVD             GVP   A E   + +  KP G+V        R T+ + L +
Sbjct: 67  DLYEVDVPEEEPMELAPDAGVPFAVAYEDDDVVVVDKPRGVVVHPGAGHMRGTLVNGLLA 126

Query: 104 IFSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
             +++           V R+D +T GL++        R L     +    R Y    HG+
Sbjct: 127 RGTQLCTLAGAMRPGVVHRIDKDTSGLVVFAKSDRAYRWLVEAFRAHDVEREYVAIAHGR 186

Query: 153 V-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           +             D      +    V QG         +       +++ + L  G+  
Sbjct: 187 MSHREGTIDMPIARDPADRQRMA---VRQGGKRAVTHFEVLESFAKYSYLRLRLETGRTH 243

Query: 200 EIKKVFEFFNWKV 212
           +I+         +
Sbjct: 244 QIRVHLAAIGHPI 256


>gi|198414279|ref|XP_002128102.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 2 [Ciona intestinalis]
          Length = 456

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 31/200 (15%), Positives = 70/200 (35%), Gaps = 30/200 (15%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHI----------EVDGVPLRKAERTRLWLYHKP 81
           ER + +  VKVN   +    V +   D I           +D       + ++  + +KP
Sbjct: 139 ERAVLEGGVKVNLKPVVSLDVKLRDNDMISARLHRHEAPVLDTKVEIIEDNSKYVVVNKP 198

Query: 82  IGL-VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELP 137
             + +         S V+       +  ++   R+D  T G+++      +A  +  E+ 
Sbjct: 199 SSIPIHPCGRFRNNSLVYILAKDLGYQGLLGCHRIDRLTSGIVIFGKTKNIAHKVAKEIS 258

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG---DMQVTLDTQKGSNAWVT---- 190
             +  + Y  +  G+     + +  + + +     G     +V     K ++ W T    
Sbjct: 259 ERKVEKQYVCKVVGEFPSTDI-VCNEPVSLFNRKLGYAVAWKVEGVVGKEASTWFTRMSY 317

Query: 191 -----VGL---REGKNREIK 202
                V L   + G+  +I+
Sbjct: 318 DGTNSVVLCKPKTGRTHQIR 337


>gi|149178869|ref|ZP_01857448.1| ribosomal large subunit pseudouridine synthase D [Planctomyces
           maris DSM 8797]
 gi|148842281|gb|EDL56665.1| ribosomal large subunit pseudouridine synthase D [Planctomyces
           maris DSM 8797]
          Length = 317

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 37/180 (20%), Positives = 64/180 (35%), Gaps = 28/180 (15%)

Query: 6   IVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
           IV++     R+ + ++R     ++ R ++R++     KVNGI        V     I   
Sbjct: 10  IVEDYLDGARIDRFLSRHFRNYSTHR-LQRIVQAGFAKVNGIPA-DPLQRVFRGQQINIR 67

Query: 61  -------EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---- 106
                    D  PL      E   L + +KP G++   +      TV + L         
Sbjct: 68  LPEPPDKTYDPEPLPLEVLYEDAWLIIVNKPPGMIAHPAGNILSGTVANALQYYLDQQTG 127

Query: 107 -----RVISVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                R   V RLD  T G+L++  +  G  +  ++    +  + Y      Q  QD   
Sbjct: 128 VRSLLRPGIVHRLDQFTSGILIVAKEHLGHRSLSIQFQQNRVSKSYLAIVRDQPKQDLFE 187


>gi|298373557|ref|ZP_06983546.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroidetes oral taxon 274 str. F0058]
 gi|298274609|gb|EFI16161.1| ribosomal large subunit pseudouridine synthase family protein
           [Bacteroidetes oral taxon 274 str. F0058]
          Length = 223

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 22/163 (13%), Positives = 44/163 (26%), Gaps = 25/163 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   +   +K    +        +    TV + L   +S+        V RLD    G++
Sbjct: 6   EDNHIIAINKSSSDIVQGDKTGDKPLVDTVREYLKERYSKSGNVFCGVVHRLDRPVSGVV 65

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI--------------V 166
           L          L   L   +  + Y         Q++   LK  +               
Sbjct: 66  LFAKTSKALARLNEMLRGHEIKKKYWAIVVKPP-QEQEATLKHYLVRNEKQNKSYAYTTE 124

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
            +      +      +      + V L  G++ +I+       
Sbjct: 125 KKDSKLAVLHYVTIGKSERYTLLEVDLHTGRHHQIRCQLAAVG 167


>gi|268319938|ref|YP_003293594.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
 gi|262398313|emb|CAX67327.1| pseudouridine synthase, RluA family [Lactobacillus johnsonii
           FI9785]
          Length = 282

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 34/208 (16%), Positives = 66/208 (31%), Gaps = 35/208 (16%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------LWLYHKP 81
           ++++ VNG  L      V   D IE+    +   ++T                + + +KP
Sbjct: 39  EKKILVNGKYL-PLNFLVKPGDKIEIQLDHIESDQQTYPASGKLPKVVYEDNDILVINKP 97

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA----RVLELP 137
            G  T  +  +  + + D    +      V RLD+ T GLLL+  +  +     R L   
Sbjct: 98  AGQKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDK 157

Query: 138 STQWLRVYRVRF------------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +    R Y                   +  D  +  K+ +   G         +  +   
Sbjct: 158 TLH--REYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVRQDGQKAVTH-YEVIKRDKD 214

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
              V + L  G+  +I+         + 
Sbjct: 215 RILVKLTLETGRTHQIRVHLAALGAPII 242


>gi|209529662|ref|NP_001129317.1| RNA pseudouridylate synthase domain-containing protein 2 [Rattus
           norvegicus]
 gi|149022995|gb|EDL79889.1| RNA pseudouridylate synthase domain containing 2 (predicted)
           [Rattus norvegicus]
          Length = 553

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 51/349 (14%), Positives = 107/349 (30%), Gaps = 54/349 (15%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++   + +   D +          V   P+R  AE   + +  KP
Sbjct: 192 EAAVRAGRLHLNEEPVQDLNIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENDDVVVIDKP 251

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 252 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVR 311

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+    ++           K G+          +         G ++
Sbjct: 312 DRQLEKEYVCRVAGEFPDKEVICKEPILVVSYKVGVCRVDPQGKPCETVFQRLSYNGRSS 371

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +         ++GP +      G   +  +++L
Sbjct: 372 VVQCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSTAWGPSRGQG---GHIPKTDEELL 425

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKL 301
           R+ +  H  +E+   LD         + D     SE+  D       ++QK         
Sbjct: 426 RDLVAEHQAKESLSMLDLCEGDLAPGLIDSTAPSSELGKDSLEGLATAAQKIDG------ 479

Query: 302 ATPVHRRNLASNVWMAKGIHSSFLSDSGQREENHRRSPSFPSKRSLRRT 350
                       +      H      + + + + +  P     R LR+ 
Sbjct: 480 ------------MVDEASQHPDTPGKAAKADVSQQTDPLCAECRVLRQD 516


>gi|78355167|ref|YP_386616.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
 gi|78217572|gb|ABB36921.1| ribosomal large subunit pseudouridine synthase C [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 332

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 71/239 (29%), Gaps = 66/239 (27%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------------ 74
           R+I +  V+VN    +     V   D + +   P+R A                      
Sbjct: 42  RIIRKGEVRVNKGRAK-PYDRVSEGDVVRI--PPVRPAAEPSCDAACAVPAVSASPLPQI 98

Query: 75  ------LWLYHKPIGL----VTTHSDPDGRSTVFDNLPSIFS----RVISVGRLDINTEG 120
                 L + +KP GL     T H+D      V   L + F+          RLD NT G
Sbjct: 99  IASGDGLLVINKPAGLPVQPGTGHTD-----CVTARLAAHFAGADFMPAPAHRLDKNTSG 153

Query: 121 LLLL-TNDG--GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--- 174
           LLL  T        + L       ++ Y     G   + +   L   +V +G    +   
Sbjct: 154 LLLAGTTYTALRTLQDLFRNGHSLIKDYCAWVCGIWPEQEALTLTDVLVKEGTPGKEKIH 213

Query: 175 --------------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                                QV    +  +   + + L  G+  +I+      N  V 
Sbjct: 214 ALPAGSAQPHTAPPKGREALCQVVPLLRLDNATLLGIRLATGRTHQIRVQLASRNHPVI 272


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 36/85 (42%), Gaps = 6/85 (7%)

Query: 12 TPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA 70
          T QR+  ++ + G  ASR      + +  V V+G++  +   NV     + +D       
Sbjct: 9  TRQRLDDLLVQRGLFASRSRARDAVERGTVTVDGVMARKPGQNVSPQCLVAIDDPAQGYV 68

Query: 71 ERTRLWLYHKPIGLVTTHS-DPDGR 94
           R  L    K IG +   S DP GR
Sbjct: 69 SRAAL----KLIGGLDHFSLDPAGR 89


>gi|330502588|ref|YP_004379457.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina NK-01]
 gi|328916874|gb|AEB57705.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           mendocina NK-01]
          Length = 317

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 79/236 (33%), Gaps = 43/236 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV-- 62
           V      QR+   + A+     +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VAPELAGQRIDNFLRAQLKGVPKTLIYRILRKGEVRVNKGRI--KPEYKLQAGDVVRVPP 73

Query: 63  -------DGVPLRK-----------AERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLP 102
                  +  PL +            E   L + +KP G+            +  F  L 
Sbjct: 74  LRLAERDEPEPLAQGLLERLEAAIVYEDKALIVLNKPAGIAVHGGSGLNYGVIEAFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T GLL++     + R L   L      + Y     G     K   
Sbjct: 134 PDAKDLELVHRLDRDTSGLLMIAKKRSMLRHLHEQLRGDGVDKRYMALVRGHWATAK-KQ 192

Query: 161 LKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV--------GLRE-----GKNREIK 202
           +   +    +  G+  V +D + K +     V         L E     G+  +I+
Sbjct: 193 VNAPLQKSNLRSGERMVEVDGEGKEALTLFRVLRRFGEFATLVEAKPVTGRTHQIR 248


>gi|302795552|ref|XP_002979539.1| hypothetical protein SELMODRAFT_36043 [Selaginella moellendorffii]
 gi|300152787|gb|EFJ19428.1| hypothetical protein SELMODRAFT_36043 [Selaginella moellendorffii]
          Length = 229

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 34/180 (18%), Positives = 59/180 (32%), Gaps = 31/180 (17%)

Query: 6   IVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--EV 62
            + E     R+   ++ +    SR  V+  I +    VNG  + + +  V+  D +   +
Sbjct: 12  TIPEETVSTRIDVWLSGQLPHTSRARVQDSIRKGLALVNGKTITKPSFPVIGGDEVVCTL 71

Query: 63  DG-VPLRK----------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
            G  PL             E   + + +K   +V   +      T+ + +         P
Sbjct: 72  CGAAPLEATPEKIQLDIVHEDDHVIVVNKAADMVVHPAPGHYGGTLVNAILHHCGLPATP 131

Query: 103 SIFSRVIS------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
           S F           V RLD  T GL+++  D      L     S +  R Y     G   
Sbjct: 132 SRFRGPRPVIRPGIVHRLDKGTSGLIVVAKDEQSQLSLSEQFKSRKVRRTYLSLTCGTPS 191


>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 = 52.5 bits (125), Expect = 9e-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|149197335|ref|ZP_01874386.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Lentisphaera araneosa HTCC2155]
 gi|149139353|gb|EDM27755.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           protein [Lentisphaera araneosa HTCC2155]
          Length = 218

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 50/144 (34%), Gaps = 13/144 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV-FDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E+  L + +KP  L +T    D    + +  +    + V +V +LD +T G+ L   +  
Sbjct: 12  EKDGLLVLNKPYDLPSTGRKLDDDDCLQYWLIQRQGAMVWAVHQLDADTSGINLFVTEKK 71

Query: 130 L--ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKK---------GIVIQGICYGDMQVT 178
           L       L   Q  + Y    HG     +     +         GI  +G         
Sbjct: 72  LVKYYKELLEQAQADKQYLAIVHGVPSWKQCEEHGRIGKVDARSLGIHAEG-KTAHSHFE 130

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
           +       + + V +  G+  +I+
Sbjct: 131 VIGSVKDFSLIKVKIFTGRTHQIR 154


>gi|123442854|ref|YP_001006830.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|122089815|emb|CAL12670.1| putative ribosomal large subunit pseudouridine synthase [Yersinia
           enterocolitica subsp. enterocolitica 8081]
          Length = 232

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 67/204 (32%), Gaps = 47/204 (23%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D IE         +   L L +KP GL++ +  +P    +V   L  IF     V RLD
Sbjct: 14  HDKIE------TLYQDDHLVLINKPTGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHRLD 67

Query: 116 INTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
             T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I   
Sbjct: 68  FGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIAKD 121

Query: 174 DMQVTLDT-----QKGSNAWVTVG---LRE------------------GKNREIKKVFEF 207
                L        K + +   V      E                  G+  +++   + 
Sbjct: 122 PALFPLMLICATHGKPARSGYRVVERFYHELEDGRSLPLTRVQLIPETGRTHQLRIHCQQ 181

Query: 208 FNWKVNRLIRISYGPFQLGTLLAG 231
               +       YG    G LL G
Sbjct: 182 LGHPIWGCD--LYG----GRLLPG 199


>gi|57236934|ref|YP_178049.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
 gi|57165738|gb|AAW34517.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           RM1221]
          Length = 300

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEEKNEILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L         
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLV 147

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    +G+++++ +  + K I +      +    MQ+    ++G  A     + E  
Sbjct: 148 QKEYLALANGKIEENFI--IDKAINLAKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 201

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 202 PKINATLLLCKPLTGRQHQIR 222


>gi|254445479|ref|ZP_05058955.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
 gi|198259787|gb|EDY84095.1| RNA pseudouridine synthase family [Verrucomicrobiae bacterium
           DG1235]
          Length = 262

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 33/175 (18%), Positives = 54/175 (30%), Gaps = 24/175 (13%)

Query: 46  LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
                   V   +                + L +KP  LV   S     S++        
Sbjct: 2   PATEWGWLVTPEEL-----ETWILQNDDHVLLINKPALLVCHPSKNGPWSSLAGACREYL 56

Query: 106 S--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL 161
              R   V RLD  T G++L       +R L   L   +  + Y     G++ ++ L   
Sbjct: 57  QSERSHLVSRLDRETSGIVLFAKHRLKSRHLQMALEQRKVSKTYLAILEGELKEETLVDA 116

Query: 162 KKGIVIQGICYGDMQVTLDTQK----------GSNAWVTVG----LREGKNREIK 202
             G   Q I +    V  D +K           SN   T+     +  G+  +I+
Sbjct: 117 PLGPDTQSIVHSKNTVRRDGRKQEAQTKYTPLHSNGRYTLAKVDPIT-GRKHQIR 170


>gi|255310907|ref|ZP_05353477.1| pseudouridine synthetase family protein [Chlamydia trachomatis
           6276]
          Length = 303

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 23/124 (18%), Positives = 42/124 (33%), Gaps = 23/124 (18%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  +   D + +    +  +    LW      +Y+KP     T  D   +
Sbjct: 40  RVNGRIERFESYKLQPGDRVSL--QIIEHSSPQLLWEDEHLCIYNKPAK--QTSEDLAHQ 95

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             V             V RLD +T G +L       + ++     +    + Y     GQ
Sbjct: 96  LNV-----------HLVHRLDRDTSGCILFAKHAKASSLITQLFKNRGIDKRYIALVFGQ 144

Query: 153 VDQD 156
             Q+
Sbjct: 145 PRQE 148


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 33/87 (37%), Gaps = 5/87 (5%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+   + R G   SR +    I    + VN   +++A   V S   +EV G  L+   R
Sbjct: 6  ERLDNFLVREGFFPSREKARSAIMAGLIYVNDQRMDKAGTQVSSGVQVEVRGNALKYVSR 65

Query: 73 TRLWLYHKPIGLVTTHSDPDGRSTVFD 99
            L    K    +T  S       V D
Sbjct: 66 GGL----KLEKAITAFSIDMRERIVLD 88


>gi|72386765|ref|XP_843807.1| hypothetical protein [Trypanosoma brucei TREU927]
 gi|62359821|gb|AAX80250.1| hypothetical protein, conserved [Trypanosoma brucei]
 gi|70800339|gb|AAZ10248.1| hypothetical protein, conserved [Trypanosoma brucei brucei strain
           927/4 GUTat10.1]
          Length = 828

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 25/182 (13%), Positives = 46/182 (25%), Gaps = 54/182 (29%)

Query: 71  ERTRLWLYHKPIGLVTTHS--------DPDGRSTVFDNLPSIFS--------RVISVGRL 114
           E   L + +KP  + T+          D      V   L             R   V RL
Sbjct: 606 EDDDLLVINKPPHVATSRHALSCSQLCDDKATDIVSLQLTCKKRGDVMRRVFRQGQVHRL 665

Query: 115 DINTEGLLLLTNDGGLARVLEL------PSTQWLRVYRV---RFHGQVDQDKLNLLKKGI 165
           D  T G L++      A  L          +Q  ++Y          +           I
Sbjct: 666 DTETSGCLIMAKSDVAASSLRHQMGTSAAYSQSSKIYLALCAVVESNLTN---------I 716

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVG--------------LREGKNREIKKVFEFFNWK 211
            + G+        +           +               +++GK  +I++        
Sbjct: 717 PLNGVLRDPADAKI------TTKYRIVHFYKRFRVALVEARIQQGKKHQIRRHLAAVGLP 770

Query: 212 VN 213
           + 
Sbjct: 771 IL 772


>gi|87309950|ref|ZP_01092084.1| ribosomal large subunit pseudouridine synthase [Blastopirellula
           marina DSM 3645]
 gi|87287714|gb|EAQ79614.1| ribosomal large subunit pseudouridine synthase [Blastopirellula
           marina DSM 3645]
          Length = 281

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 47/300 (15%), Positives = 96/300 (32%), Gaps = 64/300 (21%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-------------RLWLYHKPIGLVTT 87
            ++G   +  A  + + + + V  +     E+              R+ + +KP G++T 
Sbjct: 2   TIDGEPCK-PAHKLSAGEQLIVKPIAAYSDEQIGVNVHLDIIYQDDRIAVINKPAGMITH 60

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVG---------RLDINTEGLLLLTNDGGLARVLELPS 138
            +    + T+ + L   F ++ ++G         RLD +T G++++  D   A       
Sbjct: 61  PAKGHWKGTLTEGLKGQFPQLSTIGGPTRPGIVHRLDRDTSGVIVIAKD-DAAHEFLKTQ 119

Query: 139 TQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            Q     + Y     G  D+D+ +L+ + +         M +     +G +A       E
Sbjct: 120 FQDRLTEKEYFAMVIGAPDRDR-DLINEPVGPHPKIRERMAIRRGDDEGKDAQ---TFYE 175

Query: 196 -----------------GKNREIK--KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                            G+  +I+   +       V            L   L GS R +
Sbjct: 176 VLERYQGFAAIKALPKTGRTHQIRVHLM--HAGHPV------------LCDPLYGSRRFL 221

Query: 237 SKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLS 296
           S   L+      +L          I  +     +    I+ +P D  R +    Q     
Sbjct: 222 SLGELQHDDDRTVLLNRTALHAHRIAIAHPDDGEIREFIAPLPADLERTQNMLRQLRPAR 281


>gi|77412972|ref|ZP_00789175.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
 gi|77160984|gb|EAO72092.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 515]
          Length = 342

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 76  RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 134

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 135 DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 194

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 195 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 251

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 252 IIDVLKYIQNSSLIKCRLETGRTHQIR 278


>gi|77409155|ref|ZP_00785868.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
 gi|77172239|gb|EAO75395.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae COH1]
          Length = 342

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 76  RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 134

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 135 DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 194

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 195 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 251

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 252 IIDVLKYIQNSSLIKCRLETGRTHQIR 278


>gi|262170983|ref|ZP_06038661.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           MB-451]
 gi|261892059|gb|EEY38045.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           MB-451]
          Length = 316

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKTIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAE-----------------------RTRLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEATPPSTKLNKVAELEHCIVYEDEHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDPEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFTEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|227889491|ref|ZP_04007296.1| pseudouridylate synthase RluD [Lactobacillus johnsonii ATCC 33200]
 gi|227849969|gb|EEJ60055.1| pseudouridylate synthase RluD [Lactobacillus johnsonii ATCC 33200]
          Length = 266

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 33/208 (15%), Positives = 65/208 (31%), Gaps = 35/208 (16%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------LWLYHKP 81
           ++++ VNG  L      V   D IE+    +   ++                 + + +KP
Sbjct: 23  EKKILVNGKYL-PLNFLVKPGDKIEIQLDHIESDQQPYPASGKLPKVVYEDNDILVINKP 81

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL----ARVLELP 137
            G  T  +  +  + + D    +      V RLD+ T GLLL+  +  +     R L   
Sbjct: 82  TGQKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDK 141

Query: 138 STQWLRVYRVRF------------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
           +    R Y                   +  D  +  K+ +   G         +  +   
Sbjct: 142 TLH--REYLAWISNSPQIKYTGIIDLPIGHDPHDQRKRMVRQDGQKAVTH-YEVIKRDKD 198

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
              V + L  G+  +I+         + 
Sbjct: 199 RILVKLTLETGRTHQIRVHLAALGAPII 226


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+  ++   G   SR   ++ I    V V+    ++A   V    +IEV G P+    R
Sbjct: 4  RIDVLLVEQGYFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDANIEVKGNPIPYVSR 62


>gi|302840927|ref|XP_002952009.1| pseudouridine synthase [Volvox carteri f. nagariensis]
 gi|300262595|gb|EFJ46800.1| pseudouridine synthase [Volvox carteri f. nagariensis]
          Length = 367

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 25/127 (19%), Positives = 35/127 (27%), Gaps = 22/127 (17%)

Query: 31  VERM---IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----------WL 77
            E     I   +V +NG  +      +   D +     P R+                  
Sbjct: 48  CEEWTSRIVGGQVAINGSTVLEPDHVLRVGDVVSYTRRPWREPPSPSYVDVLYEDDDVVA 107

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGLLLLTNDG 128
             KP GL    +    + TV   L   +           V  V RL   T GLLL     
Sbjct: 108 LCKPAGLQVLPAAMLHQRTVLTLLQHHYGNPPGTRACVAVAPVHRLGRGTSGLLLCARTT 167

Query: 129 GLARVLE 135
              + L 
Sbjct: 168 HARQRLT 174


>gi|269963388|ref|ZP_06177716.1| Ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
 gi|269831867|gb|EEZ85998.1| Ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           1DA3]
          Length = 250

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/170 (15%), Positives = 60/170 (35%), Gaps = 35/170 (20%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E  ++   +KP GL++      +   +++  L   +  +  V RLD+ T GL++L  +  
Sbjct: 19  EDEQILAVNKPSGLLSVPGRLAEHHDSMWSRLTEQYPDIQVVHRLDMCTSGLMVLAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLN------------LLKKGIVIQG 169
                       L        ++Y  R  G + Q++               L+K     G
Sbjct: 79  AESALKKQFQYRLTH------KIYYARVWGHLKQEEGEIDLPLICDWPNRPLQKVCFEDG 132

Query: 170 ICYGDM-QVTLDTQKGSNAWVTVG----LREGKNREIK-KVFEFFNWKVN 213
                + QV    +    +  T+     +  G++ +++  + +     + 
Sbjct: 133 KPSKTLFQVAKREEHPDGSKTTIVRLLPIT-GRSHQLRVHM-QALGHPIV 180


>gi|195339847|ref|XP_002036528.1| GM18469 [Drosophila sechellia]
 gi|194130408|gb|EDW52451.1| GM18469 [Drosophila sechellia]
          Length = 537

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 73/209 (34%), Gaps = 29/209 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 173 ERSLEAGKLTVNSEKVPK-DYRIKHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKP 231

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        + ++ RLD  T GLLL       AR LEL   
Sbjct: 232 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIR 291

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----- 192
           + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G     
Sbjct: 292 TRQVQKEYVCRVEGRFPDGIVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEVGSD 350

Query: 193 -------LREGKNREIKKVFEFFNWKVNR 214
                  L  G+  +I+   ++  + ++ 
Sbjct: 351 SIVLCKPLT-GRMHQIRVHLQYLGYPISN 378


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNEEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEKRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYKVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++ R G+  SR +    I    V VN + +++    V  T  I + G  L  
Sbjct: 1  MAKERLDLLLVRRGLYPSREQARTAIMAGEVLVNDVPVDKPGAAVPDTATIRLLGQHLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|166031887|ref|ZP_02234716.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC
           27755]
 gi|166028340|gb|EDR47097.1| hypothetical protein DORFOR_01588 [Dorea formicigenerans ATCC
           27755]
          Length = 335

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 39/265 (14%), Positives = 88/265 (33%), Gaps = 61/265 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR---AGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK+  I++EN + QR+ K + +       S   + +M+ ++ + +NG         + + 
Sbjct: 1   MKE-TIIKENESGQRLDKYLKKYLPQAPGS--FIYKMLRKKNITLNGKKAA-GQEKLNTG 56

Query: 58  DHIEV-----------------DGVPLRK-----AERTRLWLYHKPIGLVTTHSDPDGRS 95
           D I+                  +  P++K      E   + L +KP G+++  +  +  S
Sbjct: 57  DSIKFFLAEETIDKFTGNAAASESYPVKKDLEIIYEDDNILLINKPAGMLSQKAKKEDVS 116

Query: 96  TVFDNLPSIFS------------RVISVGRLDINTEGLLLLTNDGGLAR--VLELPSTQ- 140
            V   +  + S                  RLD NT G+++    G       +   + + 
Sbjct: 117 LVEYVIGYLLSNGSVTKEELLTFHPGICNRLDRNTSGMVVA---GKSLAGLQIMGEAFKE 173

Query: 141 --WLRVYRVRFHGQV------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
               + Y     G +            D+    ++    + +G    + +      +   
Sbjct: 174 RTLAKYYLCLVKGCIKETSHIRGYLKKDEKTNKVMISRKMSEGAAAIETEYEPVAYQKEL 233

Query: 187 AWVTVGLREGKNREIKKVFEFFNWK 211
             + V L  G+  +I+         
Sbjct: 234 TLLKVHLITGRTHQIRAHLASIGHP 258


>gi|160892611|ref|ZP_02073401.1| hypothetical protein CLOL250_00141 [Clostridium sp. L2-50]
 gi|156865652|gb|EDO59083.1| hypothetical protein CLOL250_00141 [Clostridium sp. L2-50]
          Length = 328

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 30/169 (17%), Positives = 55/169 (32%), Gaps = 32/169 (18%)

Query: 75  LWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLL 122
           + +  KP G+++   +  D      + D L              R     RLD NT GL+
Sbjct: 98  ILIADKPAGVLSQKASKDDYSFNEALIDYLLDSGHITTEELRTYRPSVCNRLDRNTSGLI 157

Query: 123 LL----TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------KLNLLKKGIVIQGIC 171
           L     T    L+R++        + Y     G++ Q        + +  K  + I    
Sbjct: 158 LCGVSLTGSQELSRII--REHLLHKYYYTLVRGRLTQKLDSTCYLQKDNAKNKVRISDRP 215

Query: 172 YGDMQVTLD-------TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +   +            +      V V L  GK+ +I+   +   + V 
Sbjct: 216 WEQGKSEEIHSIFYPVKKNDDYTLVKVELITGKSHQIRAQLKHLGYPVV 264


>gi|315042395|ref|XP_003170574.1| DRAP deaminase [Arthroderma gypseum CBS 118893]
 gi|311345608|gb|EFR04811.1| DRAP deaminase [Arthroderma gypseum CBS 118893]
          Length = 516

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 64/218 (29%), Gaps = 47/218 (21%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKP 81
           +  I   R+ ++G +   A   + +   I          V    ++   E   + +  KP
Sbjct: 80  KAAIDNGRITIDGKIAT-ADSIINNGQVISHTLHRHEPPVTSQRIKIIHEDDDIIVIDKP 138

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLELP- 137
            G+    +     +++ + L +            RLD  T G++ L      A  +    
Sbjct: 139 AGIPVHPAGRYNYNSIIEILRAERGVGWVPYPCNRLDRLTSGIMFLGKHPKAAEQMAHSL 198

Query: 138 -STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            S    + Y  R  G            G+V+       +   L                G
Sbjct: 199 RSRTLQKEYIARVKGYFPD--------GVVLCDQPMLKVSPIL----------------G 234

Query: 197 KNREIKKVFEFFNWKV-NRLIRIS-YGPFQLGTLLAGS 232
            NR ++            +  RI+ Y P + G    G 
Sbjct: 235 LNR-VR----ATGKDAQTKFRRIAYYPPVKKGDESNGE 267


>gi|309379425|emb|CBX21992.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 307

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|302682125|ref|XP_003030744.1| hypothetical protein SCHCODRAFT_16635 [Schizophyllum commune H4-8]
 gi|300104435|gb|EFI95841.1| hypothetical protein SCHCODRAFT_16635 [Schizophyllum commune H4-8]
          Length = 506

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 26/143 (18%), Positives = 50/143 (34%), Gaps = 23/143 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR---------------LWLYH 79
           +      +NG +       + + D IE     + + E                    + +
Sbjct: 62  LESGVTTINGKVAR-PDTIIRNGDRIE---NVVHRHEPPVTSTPVRVLLHDTERGFIVVN 117

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           KP  +    +    R+++   L     F +V +V RLD  T GL+++  +  LAR L   
Sbjct: 118 KPGSIPVHAAGRYNRNSLIHILMHEMGFKKVYTVNRLDRLTSGLMIIPLNADLARSLTKE 177

Query: 138 --STQWLRVYRVRFHGQVDQDKL 158
                  + Y  R  G+    ++
Sbjct: 178 FIEGSVRKEYVARVKGKFPDGEV 200


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           ++  ++  AG+  +  E + +I    VKVNG +         + D +E+DG  ++ AE
Sbjct: 11 IKLDALLKFAGLCETGGEAKELIQGGAVKVNGEVCTMRGKKCRAGDTVELDGRTVQVAE 69


>gi|159027410|emb|CAO86894.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 501

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 29/152 (19%), Positives = 51/152 (33%), Gaps = 26/152 (17%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++      D +  V +        +I V RLD  T G+LLL     
Sbjct: 305 EDEGIIAINKPAGLLSVAGRYQDSQDAVVNRFRRQGKNLIPVHRLDRETSGILLLAKSLD 364

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQ 182
           + R L       +  ++Y       ++++       GI+   +           V     
Sbjct: 365 IYRCLSQQFQRREVEKIYEAILSEIIERE------SGIIDLPLWGNPQNRPYQTVDWQRG 418

Query: 183 KGSNAWVTVGLREGKN------------REIK 202
           K S  +  V  +EG               +I+
Sbjct: 419 KASQTYFKVVGKEGNYSRLEFIPYTGRTHQIR 450


>gi|290508924|ref|ZP_06548295.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
 gi|289778318|gb|EFD86315.1| ribosomal large subunit pseudouridine synthase A [Klebsiella sp.
           1_1_55]
          Length = 263

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 65/186 (34%), Gaps = 37/186 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   F     V RLD  T GL+++  +  
Sbjct: 53  QDEHLLLINKPAGLLSLSGKDPRNLDSVHHRLVQRFPGCTLVHRLDFGTSGLMVVARNKD 112

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +    +      
Sbjct: 113 VNALLCQQFSQRTVAKVYTALLCGHLAED------EGIVEAAIAKDPARFPRMSLCARHG 166

Query: 183 KGSNAWVTVG--LRE-------------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V   L +                   G+  +++   +   + +       YG
Sbjct: 167 KPARSRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQLLGYPILGCD--LYG 224

Query: 222 PFQLGT 227
             +L  
Sbjct: 225 GRELPG 230


>gi|113477291|ref|YP_723352.1| hemolysin A [Trichodesmium erythraeum IMS101]
 gi|110168339|gb|ABG52879.1| hemolysin A [Trichodesmium erythraeum IMS101]
          Length = 284

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 1/65 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             QR+  ++    + S R++ + +I    V VN  ++++    V    +I+V    L  
Sbjct: 1  MPKQRLDVLLVERNLCSSRQKAQVLIRAGEVMVNQQIVDKPGTEVDLESNIKVKQKSLYV 60

Query: 70 AERTR 74
          +    
Sbjct: 61 SRGGY 65


>gi|312793590|ref|YP_004026513.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312180730|gb|ADQ40900.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 293

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 57/172 (33%), Gaps = 24/172 (13%)

Query: 54  VMSTDHIE-------VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           V+  D I        V+G      E       +KP GL +  S      T+ + +    +
Sbjct: 58  VIEVDLISSKSNIAPVEGNIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLN 117

Query: 107 RV----ISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD------ 154
                   + RLD +T G+++   +     ++       Q  + Y    HG++       
Sbjct: 118 SKNLTSHIINRLDKDTSGIVVFAKNSYFHSIVSHEFEKRQVEKTYIAIVHGRLAKKSGLI 177

Query: 155 QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
           +  +     GI  +      +      +     + + + +  +  G+  +++
Sbjct: 178 EKPIKRSDDGIKREIHQDGSFASTYYEVIDSFENFSLLKLKPIT-GRTHQLR 228


>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 = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   GI  SR + +  I + +V V+G  +++A   V S  +IE  G  L+   R
Sbjct: 6  ERLDLLLVEKGIINSREKAKACIMEGKVYVDGQKVDKAGEKVSSNANIEYRGETLKYVSR 65


>gi|196232099|ref|ZP_03130954.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
 gi|196223821|gb|EDY18336.1| pseudouridine synthase [Chthoniobacter flavus Ellin428]
          Length = 265

 Score = 52.5 bits (125), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 33/169 (19%), Positives = 57/169 (33%), Gaps = 39/169 (23%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGLAR 132
           KP  +    S P+GR T++D L  + +       +V  + RLD  T GL L+      AR
Sbjct: 27  KPPFMEAHPSKPNGRPTLWDGLRGLLAYEIVNGGQVSIINRLDRETSGLTLVAKHRAAAR 86

Query: 133 VLELP--STQWLRVYRVRFHGQVDQD----KLNLLKKG------IVIQGICYGDMQVTLD 180
            L L     +  + Y     G  +++       +L++G      I ++   + D      
Sbjct: 87  ELHLQMQGRRVEKEYLALVWGWPERETFTIDAPILRQGECMPSPIHLKQAVHPDGAA--- 143

Query: 181 TQKGSNAWVTVGLRE----------------GKNREIKKVFEFFNWKVN 213
            +       T  L E                G+  +I+         V 
Sbjct: 144 ARTRFQVECTFTL-ETSNGNRFALVRAFPETGRTHQIRVHLAHAGHPVV 191


>gi|332994209|gb|AEF04264.1| Pseudouridylate synthase [Alteromonas sp. SN2]
          Length = 265

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 34/88 (38%), Gaps = 5/88 (5%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRST---VFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +    KP GL+   S  D   T   V      +   V    RLD  T G+LL + D
Sbjct: 33  QDEHIVAIDKPPGLLVHRSPIDRHETRFAVQTLRDQLNKHVFPAHRLDRPTSGVLLFSFD 92

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQV 153
              A +L  +L + Q  + Y     G V
Sbjct: 93  SKTAALLGQQLMNKQVQKQYHAIVRGYV 120


>gi|330995758|ref|ZP_08319655.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329574488|gb|EGG56053.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 522

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 6/102 (5%)

Query: 61  EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDIN 117
            +D  P    E   +   +KP G+++     D   +V+    + F        V RLD++
Sbjct: 314 HLDHEPELVYEDEWMVAVNKPAGMLSVPGKGDA-PSVWSWARAHFPEATGPLLVHRLDMD 372

Query: 118 TEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
           T G+LL+  D    R L+    +    + Y     G V  D+
Sbjct: 373 TSGVLLIAKDPETHRQLQQLFETRHIKKRYVALLDGTVTDDE 414


>gi|27734094|ref|NP_775626.1| RNA pseudouridylate synthase domain-containing protein 2 [Mus
           musculus]
 gi|158564131|sp|Q149F1|RUSD2_MOUSE RecName: Full=RNA pseudouridylate synthase domain-containing
           protein 2
 gi|26336789|dbj|BAC32077.1| unnamed protein product [Mus musculus]
 gi|126540740|emb|CAM45958.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/291 (15%), Positives = 95/291 (32%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++  ++ +   D +          V   P+   AE   + +  KP
Sbjct: 192 EAAVRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPIHLLAENNDVVVIDKP 251

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 252 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVR 311

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+    ++           K G+          +         G ++
Sbjct: 312 DRQLEKEYVCRVAGEFPDKEVICKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGRSS 371

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +         ++GP +      G   +  +++L
Sbjct: 372 VVQCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSTAWGPSRGQG---GHIPKTDEELL 425

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +E+   LD         + D     SE+  D       ++QK
Sbjct: 426 RDLVAEHQAKESLSMLDLCESDLTPGLIDSTAPSSELAKDSLEGLATAAQK 476


>gi|255263430|ref|ZP_05342772.1| ribosomal large subunit pseudouridine synthase C [Thalassiobium sp.
           R2A62]
 gi|255105765|gb|EET48439.1| ribosomal large subunit pseudouridine synthase C [Thalassiobium sp.
           R2A62]
          Length = 347

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/191 (16%), Positives = 59/191 (30%), Gaps = 44/191 (23%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNV 54
            K IV E    QRV + +       RR         +E+M  +  ++V+G  ++     V
Sbjct: 5   QKIIVAEGDGDQRVDRWL-------RRLFPHVSQGRIEKMCRKGDLRVDGGRVKS-NTRV 56

Query: 55  MSTDHIEVDGVP-----------------------LRKAERTRLWLYHKPIGLVTTHSDP 91
                + V  +P                       L   +   +   +KP G+ +     
Sbjct: 57  EVGQEVRVPPLPDADEITAGPVTKITSADAEMMRSLVIYKDDHIIALNKPSGIASQGGSK 116

Query: 92  DGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYR 146
             R             F +   V RLD +T G+ ++     +A+ +     +    ++Y 
Sbjct: 117 QVRHLDGLAEALKFDYFEKPRLVHRLDRDTSGVFIMARTREIAKAMSDAFKERETRKIYW 176

Query: 147 VRFHGQVDQDK 157
               G      
Sbjct: 177 AAVGGVPHPAM 187


>gi|194015110|ref|ZP_03053727.1| pseudouridylate synthase [Bacillus pumilus ATCC 7061]
 gi|194014136|gb|EDW23701.1| pseudouridylate synthase [Bacillus pumilus ATCC 7061]
          Length = 288

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 43/264 (16%), Positives = 90/264 (34%), Gaps = 50/264 (18%)

Query: 42  VNGILLERAAVNVMSTDHIEV--------DGVP-------LRKAERTRLWLYHKPIGLVT 86
           +NG  +      + + D + +        +G+        +   +   L L  KP     
Sbjct: 36  INGEHVT-VRYKLHNGDRLTILFPEEKVSEGLKPAPIPLDILFEDDHVLVLNKKPYIPSI 94

Query: 87  THSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ- 140
              +    S     L     +     V  V RLD +T G++L+      A  L   + + 
Sbjct: 95  PSREHPEHSIANGLLHHYAEQSVRLTVHLVNRLDRDTSGVMLVAKH-RFAHSLLSKAQKS 153

Query: 141 --WLRVYRVRFHGQVDQDK----LNLLKKG-IVIQGICYGDMQ-------VTLDTQKGSN 186
               R YR   HG + +        + +KG  +I+ +     Q       V     + + 
Sbjct: 154 GAVKRTYRAFTHGMIREKHGTIRAKIARKGDSIIERMVNETGQEAVTHFTVRAVDAELNM 213

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL--REQ 244
           + V + L  G+  +I+   ++  + +        G     TL  G+   ++++ L     
Sbjct: 214 SDVRLTLETGRTHQIRVHMQYLGYPL-------IG----DTLYGGTNERMNRQALHSETL 262

Query: 245 LGPHLLEEAQVNLDAPIYSSETLV 268
           + PH +   ++   AP+      +
Sbjct: 263 VFPHPMTGEEMTFSAPLPEDMKSL 286


>gi|94501303|ref|ZP_01307824.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
 gi|94426574|gb|EAT11561.1| Pseudouridylate synthases, 23S RNA-specific [Oceanobacter sp.
           RED65]
          Length = 322

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/220 (18%), Positives = 79/220 (35%), Gaps = 34/220 (15%)

Query: 15  RVSKVIARAGI--ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------GVP 66
           R+ + IA       SR  ++  I    +K++G  + +    ++  + + +D      G  
Sbjct: 19  RLDQ-IAAQLFPDYSRARLQSWIKDGELKIDGA-VRKPKDKLIGGETLTLDVTLQAEGEW 76

Query: 67  LRK-------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGR 113
           + +        E   + +  KP  LV   +  +   T+ + L           R   V R
Sbjct: 77  IAEDIDFPIVYEDEHIIVIDKPADLVVHPAAGNLTGTLLNGLLHHCPSLETIPRAGIVHR 136

Query: 114 LDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH------GQVDQDKLNLLKKGI 165
           LD +T GL+++         L  +L S Q  R Y           G++ +      K   
Sbjct: 137 LDKDTTGLMVVAKTLQAQNHLVEQLQSRQMGREYEAVIQGKMTGGGKISEPIARHSKDRT 196

Query: 166 VIQGICYGDMQVT---LDTQKGSNAWVTVGLREGKNREIK 202
            +     G   +T   +  Q  ++  + V L  G+  +I+
Sbjct: 197 KMAVHPTGKEAITHYRVVKQYPAHTHIRVKLETGRTHQIR 236


>gi|317056623|ref|YP_004105090.1| hemolysin A [Ruminococcus albus 7]
 gi|315448892|gb|ADU22456.1| hemolysin A [Ruminococcus albus 7]
          Length = 263

 Score = 52.5 bits (125), Expect = 1e-04,   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|293399421|ref|ZP_06643574.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae F62]
 gi|291609990|gb|EFF39112.1| YabO/YceC/SfhB family protein [Neisseria gonorrhoeae F62]
          Length = 307

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|312114370|ref|YP_004011966.1| pseudouridine synthase [Rhodomicrobium vannielii ATCC 17100]
 gi|311219499|gb|ADP70867.1| pseudouridine synthase, RluA family [Rhodomicrobium vannielii ATCC
           17100]
          Length = 326

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/261 (13%), Positives = 85/261 (32%), Gaps = 73/261 (27%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRRE---------VERMIAQQRVKVNGILLERAAVN 53
           +K  V+ +    R+ + +        ++         V++++   +V+V+G  ++ A   
Sbjct: 4   EKRAVRTDDDGLRLDRWL--------KKNYPTLPHTLVQKLVRTGQVRVDGGRVK-ADSR 54

Query: 54  VMSTDHIEV------------------------DG---VPLRKAERTRLWLYHKPIGLVT 86
           + +   + V                        D      +   E   +++ +KP G+  
Sbjct: 55  LSTGQEVRVPTHFAEPENAPQPSLKPPPGLSKADRDFIERMIVFENDEMFILNKPFGIAV 114

Query: 87  THSDPDGRST------VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPS 138
                  R        + D       R+  V RLD +T G+L +  D   A  L     +
Sbjct: 115 QGGTKTTRHIDGLLAGMADRFGGERPRL--VHRLDRDTTGILAVAKDRQTAARLGRLFQT 172

Query: 139 TQWLRVYRVRFHGQ-----------------VDQDKLNLLKKGIVIQGICYGDMQVTLDT 181
               ++Y     G                   D D++   + G   +   +     ++  
Sbjct: 173 RSVQKIYWAITRGIPKPTQGKVEAALVKASGPDGDRVRKARPG-EQELAQHATTFYSVID 231

Query: 182 QKGSNAWVTVGLREGKNREIK 202
           +  + AWV++    G+  +++
Sbjct: 232 RAANMAWVSLKPVTGRQHQLR 252


>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 = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KHKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDRFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|86153961|ref|ZP_01072163.1| ribosomal large subunit pseudouridylate synthase D [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|85842499|gb|EAQ59712.1| ribosomal large subunit pseudouridylate synthase D [Campylobacter
           jejuni subsp. jejuni HB93-13]
 gi|284925325|gb|ADC27677.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni IA3902]
 gi|315057463|gb|ADT71792.1| Putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni S3]
          Length = 281

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNEILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L         
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILVAKNKKAQIDLKALFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    +G+++++ +  + K I +      +    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALANGKIEENFI--IDKAINLAKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>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 = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/308 (12%), Positives = 103/308 (33%), Gaps = 75/308 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR---------EVERMIAQQRVKVNG------------ 44
           ++ E     R+ + +       RR         E++RM     + VNG            
Sbjct: 8   LITEKEDGLRIEQFL-------RRKGYSGQNLAEIKRMPKS--ILVNGVHYYMRQTLTAG 58

Query: 45  ---ILL---ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
               ++    + +  +     I +D       E   + + +KP G+    S  +  +++ 
Sbjct: 59  DILKVIICETKCSEKIPPV-EIPLD----IIYEDEDIIVINKPAGMPIHPSMNNYYNSLA 113

Query: 99  DNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH 150
           + L   + +           RLD +T GL +++       +L     + +  R Y     
Sbjct: 114 NALAWYYQKQDKPFIFRCCNRLDRDTSGLTVVSKHLVSGSILSTMTKNREVHREYLAVVK 173

Query: 151 GQVDQ-----------DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G+V              +  ++++ +  +          L  +   ++ V++ L  G+  
Sbjct: 174 GRVTPSSGTICAPLARKEGTIIERMVDFEHGEEAITHYKLIREANGHSLVSLKLETGRTH 233

Query: 200 EIK-KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP--HLLEEAQVN 256
           +I+  + ++  + +        G +    L       ++++ L        H +    ++
Sbjct: 234 QIRIHM-KYLGFPL-------IGDY----LYNPDMEHMTRQALHSHHMEFAHPITGEWMS 281

Query: 257 LDAPIYSS 264
             AP+ + 
Sbjct: 282 FTAPLPAD 289


>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 = 52.5 bits (125), Expect = 1e-04,   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|303239847|ref|ZP_07326370.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
 gi|302592557|gb|EFL62282.1| pseudouridine synthase, RluA family [Acetivibrio cellulolyticus
           CD2]
          Length = 337

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 76/217 (35%), Gaps = 39/217 (17%)

Query: 32  ERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRK-AERT 73
           ER+I     Q ++  N   +   AV V S D IEV+              +P+    E  
Sbjct: 28  ERLIKKLKYQSKILCNKQPVFVNAV-VKSGDVIEVEIEYDEELEGLVPQDLPIDIIYEDD 86

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTND 127
            L + +K   +V   +      T+ + +           ++  V RLD NT G+++   +
Sbjct: 87  CLIVINKAPDIVVHPTCSHPDGTLANAVAYHLQKSGVAKKIRPVIRLDRNTSGIIIFAKN 146

Query: 128 GGLARVLELPSTQW--LRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L         ++ Y    +G            +++ + +++ + + + G     
Sbjct: 147 SFSQESLIRQMNTKTFVKEYIGIVYGILKNTRGTIDLPIERKEGSIMLRHVSLSGDRSVT 206

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              TL+    + + +   L  G+  +I+   +     
Sbjct: 207 HFETLEVLN-NTSLLKFRLETGRTHQIRVHCQAIGHP 242


>gi|268608473|ref|ZP_06142200.1| hemolysin A [Ruminococcus flavefaciens FD-1]
          Length = 261

 Score = 52.5 bits (125), 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|108757849|ref|YP_631549.1| RluA family pseudouridine synthase [Myxococcus xanthus DK 1622]
 gi|108461729|gb|ABF86914.1| pseudouridine synthase, RluA family [Myxococcus xanthus DK 1622]
          Length = 346

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 72/226 (31%), Gaps = 40/226 (17%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           +RV + +ARA    +R  +  +I    V  +G   +  A  +   + + +          
Sbjct: 18  ERVDQYLARAFPDLTRSRIHGLIEAGHVLADGQPAK-PARRLRGGELLVLHIPAPVPAVP 76

Query: 64  ----GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVG------- 112
                      E   L +  K  G+V          T+ + L      +  VG       
Sbjct: 77  LAEELPLALLHEDRDLVVVDKAAGMVVHPGAGHASGTLVNALLHRVKDLAGVGGELRPGI 136

Query: 113 --RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD------------ 156
             RLD +T G L++  +      L+    +    + Y    HG    +            
Sbjct: 137 VHRLDKDTTGCLVVAKNEQALVALQKAFKTRAVEKTYLALVHGVPPAEGRIETLYGRHPI 196

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  G V +G         L+T  G+ A V V L  G+  +I+
Sbjct: 197 HRQRFT-GKVKEGKNAITEYRVLETFDGA-ALVEVDLLTGRTHQIR 240


>gi|325275825|ref|ZP_08141690.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas sp.
           TJI-51]
 gi|324099044|gb|EGB97025.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas sp.
           TJI-51]
          Length = 318

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 64/211 (30%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKA--------------------E 71
           R++ +  V+VN G +  +    + + D + V  V L +                     E
Sbjct: 43  RILRKGEVRVNKGRV--KPEYKIQAGDIVRVPPVRLPERDEPAPVAQGLLQRLEAAIVYE 100

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 101 DKALIVMNKPAGIAVHGGSGLSFGVIEALRQLRPDAKELELVHRLDRDTSGLLMIAKKRS 160

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGD 174
           + R L   L      + Y     G     K           L+ G     +  +G     
Sbjct: 161 MLRHLHAALRGDGVDKRYMALVRGHWPTAKKQVNAPLLKSNLRSGERMVEVNDEGKEALT 220

Query: 175 MQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           +   L         V    +    G+  +I+
Sbjct: 221 LFRVLRRFGDFATIVEARPIT---GRTHQIR 248


>gi|315928439|gb|EFV07751.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni DFVF1099]
          Length = 281

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNEILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L         
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILVAKNKKAQIDLKTLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    +G+++++ +  + K I +      +    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALANGKIEENFI--IDKAINLAKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>gi|298372061|ref|ZP_06982051.1| ribosomal large subunit pseudouridine synthase D [Bacteroidetes
           oral taxon 274 str. F0058]
 gi|298274965|gb|EFI16516.1| ribosomal large subunit pseudouridine synthase D [Bacteroidetes
           oral taxon 274 str. F0058]
          Length = 357

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 72/240 (30%), Gaps = 43/240 (17%)

Query: 14  QRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------- 62
            R+ K +    G  SR   +       + VNG  ++  +  V   D I +          
Sbjct: 39  IRIDKYLTNLLGGVSRTRFQNAADFGFITVNGDTVKS-SYRVKPLDEIVISLETPPSDYT 97

Query: 63  ---DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRV 108
                +PL    E   + + +K   +V      +   T+ + +               RV
Sbjct: 98  IVPQDIPLSVVFEDDDIMVVNKTPDMVVHPGVGNLDGTLLNAIAWYLRDNPKFDVNNPRV 157

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK--------- 157
             V R+D +T GLLL+  +      L  +       R Y     G V +D          
Sbjct: 158 GLVHRIDKDTSGLLLIAKNEQAKSFLGKQFQDKTTKRTYNALVWGIVKEDNGTVDGALAR 217

Query: 158 --LNLLKKGIVIQGI-CYGDMQVT---LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              + ++  +            VT   +  +      +   L  G+  +I+   +     
Sbjct: 218 NPKDRMQFCVFDPDENPLAKHAVTHYRVLRRFKYTTLLECNLETGRTHQIRVHMKHIGHT 277


>gi|307710900|ref|ZP_07647326.1| RNA pseudouridylate synthase family protein [Streptococcus mitis
           SK321]
 gi|307617256|gb|EFN96430.1| RNA pseudouridylate synthase family protein [Streptococcus mitis
           SK321]
          Length = 278

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 58/149 (38%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P+  + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLVIVNKPEGMKTHGNQPNETALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y  +  G ++  ++           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEISREYWAQVDGYINSKEIVFKDKIGRDRHDRRKRIVDTKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q     + V   L+ G+  +I+
Sbjct: 190 THVSRLKQFPNKTSLVRCKLKTGRTHQIR 218


>gi|254458808|ref|ZP_05072232.1| pseudouridine synthase [Campylobacterales bacterium GD 1]
 gi|207084574|gb|EDZ61862.1| pseudouridine synthase [Campylobacterales bacterium GD 1]
          Length = 244

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/204 (15%), Positives = 60/204 (29%), Gaps = 36/204 (17%)

Query: 18  KVIA-RAGIASRREVERMIAQQRVKVNGILLE----RAAVN-VMSTDHIEVDGVPLRKAE 71
           K++A + G+ S  E + MI +    V    +           V     IE         E
Sbjct: 8   KILALQQGV-SNNEAKSMIDRGLAYVGNKKVMIARGELDTKTVFKVQKIE---KIKPIFE 63

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + +  KP  + +   +   +  V             + RLD  T G+L+L  D    
Sbjct: 64  NDEIIVVDKPAFVNSDEIERQLKPAVL------------LHRLDRETSGVLMLVKDEEFR 111

Query: 132 RVLELPSTQ--WLRVYRVRFHGQV-----------DQDKLNLLKKGIVIQGICYGDMQVT 178
           +       +    + Y     G +            Q K N     +  +G         
Sbjct: 112 QKAIKEFKKDNVYKEYIAWVEGIISEPVEVDKPILTQKKNNKAYSNVSGKGKPARTEFFP 171

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
            D    +   +   +  G+  +I+
Sbjct: 172 -DLVSANKTKIKCIIHHGRTHQIR 194


>gi|91202037|emb|CAJ75097.1| similar to pseudouridine synthase C [Candidatus Kuenenia
           stuttgartiensis]
          Length = 244

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/151 (17%), Positives = 52/151 (34%), Gaps = 19/151 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--------RVISVGRLDINTEGLL 122
           E   + +  KP GL+T  +D +   T +  L              V  + RLD +  GLL
Sbjct: 21  EDEDILVIDKPAGLLTMGTDTNKTKTAYYMLNDYVRKGCVKSRKHVFIIHRLDRDASGLL 80

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICYGDMQ 176
           L   +      L+       + Y    HG++ +        L   K  +V         +
Sbjct: 81  LFAKNIRSKLNLQSQWQNTEKKYLTVVHGRLAKKAGTISTYLAENKAQVVYSTSDTKKGK 140

Query: 177 V-----TLDTQKGSNAWVTVGLREGKNREIK 202
           +      +  +    + + + L  G+  +I+
Sbjct: 141 LSHTVYRVLKETKYFSLLEIKLLTGRKNQIR 171


>gi|32266234|ref|NP_860266.1| hypothetical protein HH0735 [Helicobacter hepaticus ATCC 51449]
 gi|32262284|gb|AAP77332.1| conserved hypothetical protein [Helicobacter hepaticus ATCC 51449]
          Length = 303

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 56/156 (35%), Gaps = 20/156 (12%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL- 134
           +Y KP  L+T         ++ D L   F     ++ RLD  T GL+L   +      L 
Sbjct: 80  VYDKPHNLLTHPKGRFYHYSLNDALKLRFGNYANAIHRLDKQTSGLVLCAINPQSEPELK 139

Query: 135 -ELPSTQWLRVYRVRFHGQVDQDKL----NLLK--KGIVIQ--------GICYGDMQVTL 179
             + + Q L+ Y     G++ Q+ L      L+  KG  +         G         L
Sbjct: 140 ELISTRQILKTYYAIVEGKLTQECLIDEPIALQKYKGTDLSIKSIISPYGKPSRTKLYPL 199

Query: 180 DTQKGSNAWVT--VGLREGKNREIKKVFEFFNWKVN 213
                +++ +   + L  G+  +I+        ++ 
Sbjct: 200 AYHSPTDSTLIRVLPLT-GRTHQIRLHCAHIGHRIL 234


>gi|296332584|ref|ZP_06875045.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305673865|ref|YP_003865537.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
 gi|296150502|gb|EFG91390.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305412109|gb|ADM37228.1| pseudouridylate synthase [Bacillus subtilis subsp. spizizenii str.
           W23]
          Length = 299

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 90/256 (35%), Gaps = 58/256 (22%)

Query: 46  LLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
           +++     V  T  + V+ VPL    E   + + +K   + +  S      ++ + +   
Sbjct: 63  VVKFPEEQVSET--LLVEPVPLDILYEDEHVLVINKQPYVSSIPSREHPSGSIANGIIHH 120

Query: 105 FSR------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQ 155
           + +      V  V RLD +T G++L+      A  +   + +     R Y    HG++ Q
Sbjct: 121 YQKNGVRATVHLVTRLDRDTSGVMLVAKH-RFAHSILSSAQKNGLVKRRYAAVVHGRLTQ 179

Query: 156 DKLNLLKKGIVIQGICYGDM----------QVTLDTQKGSNAWV---------TVGLR-E 195
                       +G     +           VT D QK    +          +V L+ E
Sbjct: 180 A-----------EGTIDAPIGRHPDSIIERTVTPDGQKAVTHFYVTCANDDMTSVTLQLE 228

Query: 196 -GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-EQLGP-HLLEE 252
            G+  +I+    +              P    TL  G+ RE+ ++ L  EQL   H L +
Sbjct: 229 TGRTHQIRVHMSYLGH-----------PLCGDTLYGGTRREIGRQALHSEQLSFIHPLTQ 277

Query: 253 AQVNLDAPIYSSETLV 268
            ++   A +      +
Sbjct: 278 EKMTFHASLPQDMKEL 293


>gi|91775675|ref|YP_545431.1| pseudouridine synthase, RluD [Methylobacillus flagellatus KT]
 gi|91709662|gb|ABE49590.1| Pseudouridine synthase, RluD [Methylobacillus flagellatus KT]
          Length = 326

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 51/318 (16%), Positives = 98/318 (30%), Gaps = 62/318 (19%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + E    QRV   +A+      +  + R++    V+VN   +  ++  +   D + V  
Sbjct: 20  TIDEASEGQRVDNFLAKILKGVPKSHIYRILRSGEVRVNSKRV-DSSCKLNLGDQVRVPP 78

Query: 65  VPLRKA-------------------ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPS 103
           V + +                    E   L +  KP G          R  +        
Sbjct: 79  VRMAQPQAESVARPQASRFEGAIIFEDEALLVIDKPAGFAVHGGSGISRGVIEQLRLERP 138

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL 161
               +  V RLD  T G+LLL         L     + Q  + Y V  HG+         
Sbjct: 139 HAKFLELVHRLDRETSGVLLLAKKRVALVNLHDAIRNNQTDKRYLVLVHGKWTD---QKR 195

Query: 162 KKGIVIQGICYGDMQVTLDTQKG---SNAWV-------TVGLRE-----GKNREIKKVFE 206
           +  + +        +  +  Q G   S+             L E     G+  +++    
Sbjct: 196 RVKLPLHKFVLPSGERRVAVQDGGQNSDTIFYLRKPLGEFTLLEAQLVTGRTHQLRVQLS 255

Query: 207 FFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSET 266
              + +             G    G    ++K + +  L    L  A+ NL  P+     
Sbjct: 256 HLGFPIA------------GDDKYGDF-ALNKSLQKRGLKRMFLHSAETNLRHPVSG--- 299

Query: 267 LVRDRPNIISEVPDDFTR 284
              ++  +I+ +PD+  +
Sbjct: 300 ---EKLKLIAPLPDELNK 314


>gi|328857444|gb|EGG06560.1| hypothetical protein MELLADRAFT_116466 [Melampsora larici-populina
           98AG31]
          Length = 486

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/326 (13%), Positives = 102/326 (31%), Gaps = 41/326 (12%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAER---TRLWLYHK 80
           + +A   +K+NG  + +  + + + D I          V G P+R   R     L +  K
Sbjct: 69  QAVASGVIKINGKTITQ-DLIIRNGDLITNTLHRHEPPVIGDPVRILHRDDVKGLLVVEK 127

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLE--- 135
           P  +    +     +T+   L   +    V +  RLD  T G+++       +R L    
Sbjct: 128 PGSMPIHPTGRYNYNTLLSILKFDYDLPLVHTSNRLDRLTSGVMICALTIEASRGLSAYF 187

Query: 136 LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQVTLDTQKGSNAWVT 190
                  + Y  R  G    +++   +  + I       + + + ++ L  +  +     
Sbjct: 188 GQEGAVKKEYIARCRGNFPDEEIVCEEPLLTIDRQVGLNVVHPEGKLPLLGRPIT----- 242

Query: 191 VGLREGKNREIKKVFEFFNWK----VNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG 246
                G++ +I+   +F        V     +++GP        G     + +  +    
Sbjct: 243 -----GRSHQIRVHLQFLGHPILNDVIYCSNVAWGP---EGGKGGIFSSPTDQRPKSSEK 294

Query: 247 PHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATPVH 306
              +E     +        +    RP           R ++    +N   K+ +L     
Sbjct: 295 EEAIESVAHEVPIEANLEASEENSRPKRSGSAI-KLGRGQRQGISQNDSGKRARLNPEDP 353

Query: 307 RRNLASNVWMAKGIHSSFLSDSGQRE 332
                S +   +   +        R+
Sbjct: 354 DSGNCSGIAFNETARAVVNELRKARD 379


>gi|301168229|emb|CBW27818.1| putative ribosomal large subunit pseudouridine synthase D
           [Bacteriovorax marinus SJ]
          Length = 333

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 80/236 (33%), Gaps = 52/236 (22%)

Query: 14  QRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV------ 62
            R+ + +    A     SR +V++ IA   + + G   + R +  + + D I +      
Sbjct: 1   MRLDQYLQIYLASW---SREQVKKKIAGGDILIKGRPGKHRPSTKIYTRDIITLVTVKTE 57

Query: 63  ------DGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-V 108
                 +G  L          E   L +  KP  + T  +     +       S++ + V
Sbjct: 58  HEDEYWNGELLELELKPSIIFEDDELIIISKPPYMSTHPTGKHLFNCATVYFESLYKKTV 117

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVR-----FHGQVDQDKLNLL 161
            S+ RLD  T G+L+L      A+ +     +    + Y        ++G+   +  + L
Sbjct: 118 HSIHRLDRETSGVLMLAKTPKCAQSMTDCFEKDLVRKCYFFIAYNKSWNGEQSFEDNHRL 177

Query: 162 ---KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------GKNREIK 202
              ++G  ++ +            K +     V   E            G+  +I+
Sbjct: 178 GASEEG--LKRVYINHFPKESSEGKSARTLFRVIHSEGDYVLGLAFPITGRQHQIR 231


>gi|237653878|ref|YP_002890192.1| transaldolase [Thauera sp. MZ1T]
 gi|237625125|gb|ACR01815.1| transaldolase [Thauera sp. MZ1T]
          Length = 648

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/86 (27%), Positives = 32/86 (37%), Gaps = 5/86 (5%)

Query: 75  LWLYHKPIGLVTTHSD---PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   HKP GL+   S     + R  V      +  RV    RLD  T G+LL   D  +A
Sbjct: 11  LVAIHKPSGLLVHRSPIAAHEERFAVQLLRDQLGRRVYPAHRLDRGTSGVLLFALDREVA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ 155
           R L     +    + Y     G   +
Sbjct: 71  RTLAQRFEAQAVDKRYLAVVRGHPPE 96


>gi|126663902|ref|ZP_01734897.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteria bacterium BAL38]
 gi|126624166|gb|EAZ94859.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteria bacterium BAL38]
          Length = 231

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/167 (13%), Positives = 55/167 (32%), Gaps = 23/167 (13%)

Query: 70  AERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGL 121
            E   + + +K +G +       D      V + +   +++     +  V RLD  T G+
Sbjct: 16  HEDNHIIVVNKRVGDIVQGDITGDKPLSDVVKEYIKIKYNKPGDVFLGVVHRLDRPTTGI 75

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK--LNLLKKGIVIQGICYGDMQV 177
           ++          L     + +  + Y         ++K  L    K           ++ 
Sbjct: 76  VVFAKTSKALTRLNESFKNRETQKTYWAVVKNTPPKEKDTLTHFLKRNSKNNTSKAHLKE 135

Query: 178 TLDTQKGSNAW-----------VTVGLREGKNREIKKVFEFFNWKVN 213
             D++K S ++           + + L  G++ +I+   +     + 
Sbjct: 136 IPDSKKASLSYQIIKKLDNYFALEIDLHTGRHHQIRAQLQAIGCPIK 182


>gi|332185831|ref|ZP_08387578.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
 gi|332014189|gb|EGI56247.1| pseudouridine synthase, RluA family protein [Sphingomonas sp. S17]
          Length = 315

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 72/224 (32%), Gaps = 36/224 (16%)

Query: 15  RVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTD--HIEV--------- 62
           R+ + +A A    SR  ++ +IA   V   G++    A    + D   + V         
Sbjct: 20  RLDRALADAVPTLSRERLKVLIASGAVTREGVMARDPAKRAAAGDLFQVAVPAPTPAHNE 79

Query: 63  --DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVIS 110
             D   +   E   L +  KP GLV   +  +   T+ + L              +R   
Sbjct: 80  AQDIPLVIAYEDEHLIVIDKPAGLVVHPAAGNLDGTLVNALLHYCGGSLSGIGGVARPGI 139

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN--------- 159
           V R+D +T GL++          L     +    R YR    G                 
Sbjct: 140 VHRIDKDTSGLMVAAKTDRTHEGLAKQFAAHSIDRRYRAITGGIPRPADGTVDAPLARSP 199

Query: 160 LLKKGIVI-QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +K + I QG            +  + A V   L  G+  +++
Sbjct: 200 QNRKKVAIVQGGKRAVTHYRTIEKLNNAALVECRLETGRTHQVR 243


>gi|206579623|ref|YP_002237870.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
 gi|206568681|gb|ACI10457.1| pseudouridine synthase, RluA family [Klebsiella pneumoniae 342]
          Length = 232

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 66/186 (35%), Gaps = 37/186 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   F     V RLD  T GL+++  + G
Sbjct: 22  QDEHLLLINKPAGLLSLSGKDPRNLDSVHHRLVQRFPGCTLVHRLDFGTSGLMVIARNKG 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +    +      
Sbjct: 82  INALLCQQFSQRTVAKVYTALLCGHLAED------EGIVEAAIAKDPARFPRMSLCARHG 135

Query: 183 KGSNAWVTVG--LRE-------------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V   L +                   G+  +++   +   + +       YG
Sbjct: 136 KPARSRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQLLGYPILGCD--LYG 193

Query: 222 PFQLGT 227
             +L  
Sbjct: 194 GRELPG 199


>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 (125), 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|56416692|ref|YP_153766.1| ribosomal large subunit pseudouridine synthase [Anaplasma marginale
           str. St. Maries]
 gi|222475057|ref|YP_002563472.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Florida]
 gi|255003036|ref|ZP_05278000.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Puerto Rico]
 gi|255004159|ref|ZP_05278960.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Virginia]
 gi|56387924|gb|AAV86511.1| ribosomal large subunit pseudouridine synthase [Anaplasma marginale
           str. St. Maries]
 gi|222419193|gb|ACM49216.1| ribosomal large subunit pseudouridine synthase (rluC) [Anaplasma
           marginale str. Florida]
          Length = 296

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 82/243 (33%), Gaps = 48/243 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           MK + +V+      RV + +   G+    ++  +ER++ +  + +N    +  +  V + 
Sbjct: 1   MKREYLVEGTCFEVRVDRYL--RGLLPGVTQSFIERLLRRGEILLNNTKAKS-STRVSNG 57

Query: 58  DHIEV---DGVPLRKAE--------------------RTRLWLYHKPIGLVTTHSDPDGR 94
           D + +   D + LR+ E                       +   +KP G+         +
Sbjct: 58  DVLSIKHADRIALREKEIRALQHVPLLDLISGSILYEDKNIIAINKPAGVSVQGG-SKVK 116

Query: 95  STVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
            ++ D L  I        V RLD +T G+L+L  +  +AR L       +  + Y     
Sbjct: 117 VSIDDVLDKIKPGECCRIVHRLDKDTSGVLVLARNLDVARYLAREFRERRVKKEYIAVTR 176

Query: 151 GQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT-VGLREGKNR 199
           G               K+       +I+        V       +   +  V    G+  
Sbjct: 177 GVPQPASGEVSTPIFYKVRSATGESMIEKEAKTFFSVMRILGDCAVVLLRPVT---GRKH 233

Query: 200 EIK 202
           +++
Sbjct: 234 QLR 236


>gi|304309991|ref|YP_003809589.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HdN1]
 gi|301795724|emb|CBL43923.1| Ribosomal large subunit pseudouridine synthase D [gamma
           proteobacterium HdN1]
          Length = 318

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 83/237 (35%), Gaps = 32/237 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGIL--LER---------AAVN 53
            + ++ + +R+ +  A+     SR  ++  I    + +N  +   +           +V 
Sbjct: 9   TIPDDLSGKRLDQAAAQLFPDYSRARLQEWIKMGALTINQQVGVAKEKVIGGEQLFLSVE 68

Query: 54  VMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI------FS 106
           + + + ++   + L    E   L + +KP GLV          T+ + L +         
Sbjct: 69  LQADERVKPQNISLDIVHEDDSLLIINKPAGLVVHPGSGHSEGTLVNALVNHAPKLAELP 128

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVD 154
           R   V R+D +T GLL++         L  +L +    R Y     G           + 
Sbjct: 129 RAGLVHRIDKDTTGLLVVAKTLEAHTDLVAQLQAKLVKREYEAIAQGVMTGGGKVDAPIG 188

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +      K+ +V  G         +  +  ++  + + L  G+  +I+      ++ 
Sbjct: 189 RHPTQRTKQAVVSSGREAVTH-YRVVARYRAHTHIRLALETGRTHQIRVHMAHIHYP 244


>gi|109730743|gb|AAI17829.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
 gi|109734876|gb|AAI17828.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 46/291 (15%), Positives = 97/291 (33%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++  ++ +   D +          V   P+R  AE   + +  KP
Sbjct: 192 EAAVRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENNDVVVIDKP 251

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 252 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVR 311

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
             Q  + Y  R  G+    ++           K G+          +      +  G ++
Sbjct: 312 DRQLEKEYVCRVAGEFPDKEVICKEPILVVSYKVGVCRVDPRGKPCETMFQRLSYNGRSS 371

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +         ++GP +      G   +  +++L
Sbjct: 372 VVQCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSTAWGPSRGQG---GHIPKTDEELL 425

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +E+   LD         + D     SE+  D       ++QK
Sbjct: 426 RDLVAEHQAKESLSMLDLCESDLTPGLIDSTAPSSELAKDSLEGLATAAQK 476


>gi|225028057|ref|ZP_03717249.1| hypothetical protein EUBHAL_02326 [Eubacterium hallii DSM 3353]
 gi|224954657|gb|EEG35866.1| hypothetical protein EUBHAL_02326 [Eubacterium hallii DSM 3353]
          Length = 237

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 59/168 (35%), Gaps = 29/168 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------SRVISVGRLDINTEGL 121
           E   + +  KP G+    SD      V   L               +  V RLD    GL
Sbjct: 12  EDDAVIVCEKPAGM-PVQSDHTRDMDVLTILKHHIFEEQNSEEEPYLAVVHRLDRPVGGL 70

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN----LLKKGI-----VIQGI 170
           ++L      A  L     + ++ + Y+    G + +D       LLK G      V++  
Sbjct: 71  MVLAKTKEAAANLSEQIQNFEFEKNYQAVVCGNLREDFGTFEDYLLKNGKTNKTEVVKAG 130

Query: 171 CYGDMQVTLD--------TQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             G  +  LD        T++G   W+ V L  G++ +I+  F     
Sbjct: 131 TPGARKAELDYELIDCIETKEGVLTWILVILHTGRHHQIRVQFASRGL 178


>gi|313668670|ref|YP_004048954.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylat
           synthase) [Neisseria lactamica ST-640]
 gi|313006132|emb|CBN87593.1| pseudouridine synthase (rna-uridine isomerase) (rna pseudouridylat
           synthase) [Neisseria lactamica 020-06]
          Length = 307

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPIDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G+      V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGVPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|304407496|ref|ZP_07389148.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304343447|gb|EFM09289.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 308

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/160 (17%), Positives = 51/160 (31%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDINTEGLLLL 124
           E   + + HKP G+    S P  R T+                V  + RLD  T G +L 
Sbjct: 90  EDDSILVMHKPAGVPVHPSRPGERGTLDEAAARHMLKKGDPLPVRHIHRLDQETSGPVLY 149

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGIC 171
           + +      L   +      RVY     G            + +D+    ++ ++  G  
Sbjct: 150 SKNDLAQLRLDEAMRQKTIERVYLAFVQGKISKPRGVIDAPIGRDRHQPARRRVIANGDH 209

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 T++    +   V + L  G+  +I+         
Sbjct: 210 AVTRYETMERYSKAT-LVRIRLETGRTHQIRVHMSHLGHP 248


>gi|291535586|emb|CBL08698.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis M50/1]
          Length = 217

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 56/169 (33%), Gaps = 20/169 (11%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHS-----DPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            P    E   + +  KP G+ T        D +     +         +  V RLD   E
Sbjct: 2   QPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPVE 61

Query: 120 GLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----NLLKKG------IVI 167
           G+++   +   A  L          + Y     G  ++ K      LL+ G      +V 
Sbjct: 62  GIMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNTSEVVE 121

Query: 168 QGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +G     +  +   +  Q G +A + + L  G++ +I+         + 
Sbjct: 122 RGTPQAKHASLSYEVVEQDGKHAVLRIKLDTGRHHQIRVQLAHAGMPIV 170


>gi|282878833|ref|ZP_06287600.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281299041|gb|EFA91443.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 516

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 6/92 (6%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLLLLTND 127
           E   L + +KP GL++       R +V   L  +  + +    V RLD+ T GLL++  +
Sbjct: 312 EDDDLVVVNKPAGLLSVPG-RSSRPSVLTILQEMMPQDMPLHAVHRLDMATSGLLIVAKN 370

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
             +   L+    +    + Y     G+V Q  
Sbjct: 371 MKVYHHLQAQFKAHTIQKEYIAVLDGKVTQTD 402


>gi|221123607|ref|XP_002156005.1| PREDICTED: similar to RNA pseudouridylate synthase domain
           containing 4 [Hydra magnipapillata]
          Length = 329

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/155 (22%), Positives = 55/155 (35%), Gaps = 31/155 (20%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VISVGRLDINTEGLLLLTND 127
           L   HKP G +  H  P  + ++ D LP++  +       +    RLD NT G+LLLT  
Sbjct: 38  LLAIHKPYG-IPVHGGPKIKLSIADFLPALEQKHGLLAGSLELAHRLDKNTSGVLLLTYK 96

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQ-------DKLNLLKKG---IVIQGICYGDM 175
             +A+ L     + Q  + Y     G V +       +    L+ G     I  I     
Sbjct: 97  KEMAKYLADLHENRQIEKSYLAILLGNVSRVTGVLNGELHETLRNGQFKQTINEISINKS 156

Query: 176 QV----TLDTQKGSNAWV----TVGLREGKNREIK 202
            V    T+         +    T     G   +I+
Sbjct: 157 SVETNYTILDSNQDTCMLCLFKTFT---GNKHQIR 188


>gi|149237721|ref|XP_001524737.1| DRAP deaminase [Lodderomyces elongisporus NRRL YB-4239]
 gi|146451334|gb|EDK45590.1| DRAP deaminase [Lodderomyces elongisporus NRRL YB-4239]
          Length = 622

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/140 (17%), Positives = 45/140 (32%), Gaps = 14/140 (10%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHI-----EVDGVPLRKAERTRL-----WLYHKP 81
           ++ I    V +N       +  V + D I       +G    K  +         +  KP
Sbjct: 146 KKAIESGMVCINSKPA-DLSTIVRNGDLISHRGFRREGHVSSKEIKIVYQDDDLLVIDKP 204

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLE--LPS 138
            G+    S     ++V   L       +    RLD  T GL+ L      +  L   +  
Sbjct: 205 SGIPAHPSGRYRYNSVTKILQHEMGIVLHPCNRLDRLTSGLMFLGKTAKGSTKLMTQIKD 264

Query: 139 TQWLRVYRVRFHGQVDQDKL 158
               + Y  R  G+  ++ +
Sbjct: 265 RNVSKEYIARVKGKFPKESI 284


>gi|146291939|ref|YP_001182363.1| pseudouridylate synthase [Shewanella putrefaciens CN-32]
 gi|145563629|gb|ABP74564.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           putrefaciens CN-32]
          Length = 226

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 30/165 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G+++L     
Sbjct: 20  QDKDIIVINKPSGLLSVPGRDPAHYDSVYARVKAEHPHCQIVHRLDMATSGVIVLALIRS 79

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV------ 177
             R L+      +  + Y  R  G +  D       G +    I        Q       
Sbjct: 80  AERELKRQFHDRETSKTYIARVAGHIKHDT------GSIDYPLICDWPNRPKQKVDHFVG 133

Query: 178 -------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                   + ++   +  V +  +  G++ +++  +       + 
Sbjct: 134 KPSLTHYQVMSRAKRSTLVKLTPIT-GRSHQLRVHMM-AIGHPIL 176


>gi|327312402|ref|YP_004327839.1| RluA family pseudouridine synthase [Prevotella denticola F0289]
 gi|326945177|gb|AEA21062.1| pseudouridine synthase, RluA family [Prevotella denticola F0289]
          Length = 319

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/213 (17%), Positives = 77/213 (36%), Gaps = 31/213 (14%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKAERT 73
           ++A     S+ +V+  +  + ++VNG  + +    + + D + V     +G    +  + 
Sbjct: 50  LLANLKE-SKSKVKATLQNRGIRVNGSCVTQFDRQLKAGDKVSVSKSKKNGQFRSRYVKI 108

Query: 74  RL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLL 122
                   +  K IG+++  +       V   L   F +         V RLD +T GL+
Sbjct: 109 VYEDRFLVVVEKNIGILS-MAAGHASLNVKSILDDYFYKTRQKCTAHVVHRLDRDTSGLM 167

Query: 123 LLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------LNLLKKGIVI-----QG 169
           +   D    ++ E         R Y     G+++QD+      L   K  +        G
Sbjct: 168 IYAKDMQTEQLFEHDWHNIVYDRRYVGVVSGEMEQDEGTVANWLKDNKAYVTYSSPVDNG 227

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             Y      +  +  + + V   L  G+  +I+
Sbjct: 228 GKYAVTHFYVLDRTVAYSLVEYRLETGRKNQIR 260


>gi|324111198|gb|EGC05181.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
          Length = 260

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKYAREDKGPQPAVTQYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>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 = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
           +  R+ + + + G+  SR   + +I    V V+   +++A   +     +EV G  +  
Sbjct: 1  MSKIRLDQYLCQHGLVQSRERAKALIMSGIVFVDEQKVDKAGEMIAEDAKVEVRGHDIGY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|115452369|ref|NP_001049785.1| Os03g0288500 [Oryza sativa Japonica Group]
 gi|113548256|dbj|BAF11699.1| Os03g0288500 [Oryza sativa Japonica Group]
          Length = 162

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/115 (17%), Positives = 34/115 (29%), Gaps = 25/115 (21%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           I   ++ V+G +     + +     +    +P ++           E   +   +KP GL
Sbjct: 13  IRDGQITVDGEVATDPDMILREGSKLVYHRLPWQEPFAPHLLDVLYEDDDMIALNKPSGL 72

Query: 85  VTTHSDPDGRSTVFDNL---------------PSIFSRVISVGRLDINTEGLLLL 124
                    + TV   L                   S  + V RL   T GL L 
Sbjct: 73  QVLPKGLFQQRTVLAQLQLKDWKMPSSFCSKRKDAQSHPVPVHRLGRGTSGLFLC 127


>gi|120600133|ref|YP_964707.1| pseudouridylate synthase [Shewanella sp. W3-18-1]
 gi|120560226|gb|ABM26153.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           W3-18-1]
          Length = 226

 Score = 52.5 bits (125), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 30/165 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G+++L     
Sbjct: 20  QDKDIIVINKPSGLLSVPGRDPAHYDSVYARVKAEHPHCQIVHRLDMATSGVIVLALIRS 79

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV------ 177
             R L+      +  + Y  R  G +  D       G +    I        Q       
Sbjct: 80  AERELKRQFHDRETSKTYIARVAGHIKHDT------GSIDYPLICDWPNRPKQKVDHFVG 133

Query: 178 -------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                   + ++   +  V +  +  G++ +++  +       + 
Sbjct: 134 KPSLTHYQVMSRAKRSTLVKLTPIT-GRSHQLRVHMM-AIGHPIL 176


>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 = 52.5 bits (125), Expect = 1e-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|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 = 52.5 bits (125), Expect = 1e-04,   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|319425230|gb|ADV53304.1| pseudouridine synthase [Shewanella putrefaciens 200]
          Length = 225

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/165 (15%), Positives = 57/165 (34%), Gaps = 30/165 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G+++L     
Sbjct: 19  QDKDIIVINKPSGLLSVPGRDPAHYDSVYARVKAEHPHCQIVHRLDMATSGVIVLALIRS 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV------ 177
             R L+      +  + Y  R  G +  D       G +    I        Q       
Sbjct: 79  AERELKRQFHDRETSKTYIARVAGHIKHDT------GSIDYPLICDWPNRPKQKVDHFVG 132

Query: 178 -------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                   + ++   +  V +  +  G++ +++  +       + 
Sbjct: 133 KPSLTHYQVMSRAKRSTLVKLTPIT-GRSHQLRVHMM-AIGHPIL 175


>gi|291615429|ref|YP_003525586.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
 gi|291585541|gb|ADE13199.1| pseudouridine synthase [Sideroxydans lithotrophicus ES-1]
          Length = 208

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 51/160 (31%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLV-TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL+       D +  +   L   F   + V RLD+ T GL++      
Sbjct: 12  QDDYLLLVNKPAGLLAVPGRGADKQDCLSARLQLQFPDALVVHRLDMATSGLMVFARGAR 71

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQDKLN------------LLKKGIVIQGICYGD- 174
           +   L       +  + Y     G+++ +                L+K   I        
Sbjct: 72  MQSRLSNMFRDREVGKRYVAVVAGRLEPETGEVDLPIAADWPKRPLRK---IDSELGKPS 128

Query: 175 -MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
             +  L     S + V +    G+  +++         + 
Sbjct: 129 LTRYRLLELDVSASRVELEPFTGRTHQLRVHMAAIGHPIL 168


>gi|218547690|ref|YP_002381481.1| tRNA pseudouridine synthase C [Escherichia fergusonii ATCC 35469]
 gi|218355231|emb|CAQ87838.1| tRNA pseudouridine synthase [Escherichia fergusonii ATCC 35469]
 gi|325496166|gb|EGC94025.1| tRNA pseudouridine synthase C [Escherichia fergusonii ECD227]
          Length = 260

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/166 (15%), Positives = 51/166 (30%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDK---------LNLLKKGIVIQGICYGDM----- 175
           R+L       Q  + Y     G + ++          L+ +      +            
Sbjct: 71  RLLAQQFEQHQIQKRYHAIVRGWLMEEAVLDYPLVEELDKIADKYAREDKGPQPAVTQYR 130

Query: 176 -----QVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
                ++ + T +       +   E   G+  ++++        + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELEPKTGRKHQLRRHLAHLRHPII 176


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/233 (15%), Positives = 85/233 (36%), Gaps = 40/233 (17%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGI---------LLERAAVNV 54
           V++ F   R+   +++  I    SR  ++ +I +  V VN           + +   VN+
Sbjct: 8   VEKEFDNVRLDLYLSK--IFEDKSRSYLQGIIDEGNVLVNNKKKKRNYKLKVGDNIEVNI 65

Query: 55  MSTDHIEVDGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS- 110
                +E++   ++     E   + + +KP  +V   +      T+ + L +    +   
Sbjct: 66  PEPKLLEIEPEDIKLDIIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLNHCKDLSGI 125

Query: 111 --------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK--- 157
                   V R+D +T G+L++  +      L          RVY     G +  ++   
Sbjct: 126 NGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKDEQGTI 185

Query: 158 --------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   ++ +K  +V +   +      +  +  ++  V   L  G+  +I+
Sbjct: 186 EAPIGRHPVDRIKMAVV-KDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIR 237


>gi|78485049|ref|YP_390974.1| pseudouridine synthase, RluD [Thiomicrospira crunogena XCL-2]
 gi|78363335|gb|ABB41300.1| ribosomal large subunit pseudouridine synthase C [Thiomicrospira
           crunogena XCL-2]
          Length = 312

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 72/209 (34%), Gaps = 44/209 (21%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDHIEVDGVPLRKAERTRLW---- 76
           R+I +  V+VN            G  +    + V     + V    +++ E + L+    
Sbjct: 35  RIIRKGEVRVNKGRVKQNTRLNDGDTVRVPPIRVPEKTEVTVPTNQMQRIEDSILYEDND 94

Query: 77  --LYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + +KP G+          G   +   L  +  R+  V R+D +T G +LL     + +
Sbjct: 95  LLVINKPSGIAVHGGSGIQWGLIEIVRALRPLAKRLELVHRIDRDTSGCILLAKKASVLK 154

Query: 133 VLELP--STQWLRVYRVRFHGQVDQD----KLNLLKKGIVIQGICYGDMQVTL-DTQKGS 185
            L       +  + Y         +      L LLK       +  G+  V + D  K S
Sbjct: 155 ALHEQIRENKMTKEYLALVAHHWPKGLEKIDLPLLKN-----TLKSGERVVKVSDEGKPS 209

Query: 186 NAWVTVG------------LREGKNREIK 202
            ++  V             L+ G+  +I+
Sbjct: 210 VSYFRVVERYQECDLVAVRLKTGRTHQIR 238


>gi|71065814|ref|YP_264541.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           arcticus 273-4]
 gi|71038799|gb|AAZ19107.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           arcticus 273-4]
          Length = 400

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 83/233 (35%), Gaps = 38/233 (16%)

Query: 6   IVQENFTPQRVSKVIARAGIA--SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
            V E     R+ K +A       SR +++  ++   +  NG  +++  + V + D + + 
Sbjct: 88  TVTEEEAGLRIDK-LASKIFIDFSRVQLQGWVSDGSLLYNGS-VQKPKIRVKAGDVLHLS 145

Query: 63  -----------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
                      + + +    E   + + +KP+G+V      +   T+ + L   + +   
Sbjct: 146 TILEQHSADQPEDIAIDVVYEDDEVLVINKPVGMVVHPGAGNQAGTLVNALLYHYPQHHH 205

Query: 111 ------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG----------- 151
                 V R+D +T GLLL+         L   L      R Y+    G           
Sbjct: 206 LPRAGLVHRIDKDTSGLLLIGKTKPAQLALMEQLKDKSVYRHYQCVVAGDAASLLRHRRI 265

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              + + +    K  ++  G       + +    G+   + VGL  G+  +I+
Sbjct: 266 DAPIGRHRNQRTKMTVMTAGREAVTHLLNVTALNGNYCLLDVGLETGRTHQIR 318


>gi|93005955|ref|YP_580392.1| pseudouridine synthase, RluD [Psychrobacter cryohalolentis K5]
 gi|92393633|gb|ABE74908.1| ribosomal large subunit pseudouridine synthase D [Psychrobacter
           cryohalolentis K5]
          Length = 396

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 84/235 (35%), Gaps = 38/235 (16%)

Query: 4   KNIVQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K+ V E+    R+ K +A       SR +++  ++   +  NG + ++  + V + D + 
Sbjct: 82  KHTVIEDEAGLRIDK-LASKIFTDFSRVQLQGWVSDGSLLYNGSI-QKPKIRVKAGDILH 139

Query: 62  V--------DGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
           +        +  P   A           + +KP+G+V      +   T+ + L   + + 
Sbjct: 140 LSTTLEQHSEDQPEDIAIDVVYEDDDVLVINKPVGMVVHPGAGNQTGTLVNALLYHYPQQ 199

Query: 109 IS------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHG--------- 151
                   V R+D +T GLLL+         L   L      R Y+    G         
Sbjct: 200 HHLPRAGLVHRIDKDTSGLLLIGKTKPAQLALMEQLKDKSVYRHYQCVVAGDAASLSRHR 259

Query: 152 ----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                + + +    K  ++  G       + +    G+   + +GL  G+  +I+
Sbjct: 260 RIDAPIGRHRNQRTKMTVMTAGREAVTHLLNVTALNGNYCLLDIGLETGRTHQIR 314


>gi|313637033|gb|EFS02602.1| S4 domain-containing protein [Listeria seeligeri FSL S4-171]
          Length = 259

 Score = 52.1 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|260914556|ref|ZP_05921024.1| pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
 gi|260631347|gb|EEX49530.1| pseudouridine synthase A [Pasteurella dagmatis ATCC 43325]
          Length = 228

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/172 (13%), Positives = 58/172 (33%), Gaps = 26/172 (15%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           D +  D             + +KP GL++   + P    +    +   +       RLD+
Sbjct: 24  DIVHYDD---------HFVVVNKPSGLLSVPGNQPQYYDSAMSRVKEKYGFCEPAHRLDM 74

Query: 117 NTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLN-----------LLKK 163
           +T GL+L        R L+    +    + Y+    G +++D+               ++
Sbjct: 75  STSGLILFALSKAADRELKRQFREREPKKHYQALVWGHLEEDQGKINLPLICDWENRPRQ 134

Query: 164 GIVIQ-GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
            I  + G     +   L+    +   V +  +  G++ +++         + 
Sbjct: 135 KICFERGKSAVTLYEVLERYPNNTTRVKLTPIT-GRSHQLRLHMLALGHPIL 185


>gi|195578239|ref|XP_002078973.1| GD23709 [Drosophila simulans]
 gi|194190982|gb|EDX04558.1| GD23709 [Drosophila simulans]
          Length = 541

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 73/209 (34%), Gaps = 29/209 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 173 ERSLEAGKLTVNSEKVPK-DYRIKHNDLLANVVHRHEVPVTSQPIKIVFMDKDIVVVNKP 231

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        + ++ RLD  T GLLL       AR LEL   
Sbjct: 232 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFGRTAEKARELELQIR 291

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----- 192
           + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G     
Sbjct: 292 TRQVQKEYVCRVEGRFPDGIVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEVGSD 350

Query: 193 -------LREGKNREIKKVFEFFNWKVNR 214
                  L  G+  +I+   ++  + ++ 
Sbjct: 351 SIVLCKPLT-GRMHQIRVHLQYLGYPISN 378


>gi|156975908|ref|YP_001446815.1| ribosomal large subunit pseudouridine synthase A [Vibrio harveyi
           ATCC BAA-1116]
 gi|156527502|gb|ABU72588.1| hypothetical protein VIBHAR_03674 [Vibrio harveyi ATCC BAA-1116]
          Length = 250

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/170 (15%), Positives = 60/170 (35%), Gaps = 35/170 (20%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E  ++   +KP GL++      +   +++  L   +  +  V RLD+ T GL++L  +  
Sbjct: 19  EDEQILAVNKPSGLLSVPGRLAEHYDSMWSRLTEQYPDIQVVHRLDMCTSGLMVLAKNKR 78

Query: 130 --------LARVLELPSTQWLRVYRVRFHGQVDQDKLN------------LLKKGIVIQG 169
                       L        ++Y  R  G ++Q++               L+K     G
Sbjct: 79  AESALKKQFQYRLTH------KIYYARVWGHIEQEEGEIDLPLICDWPNRPLQKVCFEDG 132

Query: 170 ICYGDMQVTLDTQKGS----NAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                +      +K S       V +  +  G++ +++  + +     + 
Sbjct: 133 KPSKTLFQVAKREKHSDGSKTTIVRLLPIT-GRSHQLRVHM-QALGHPIV 180


>gi|313632501|gb|EFR99511.1| S4 domain-containing protein [Listeria seeligeri FSL N1-067]
          Length = 258

 Score = 52.1 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|192361541|ref|YP_001981578.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
 gi|190687706|gb|ACE85384.1| ribosomal large subunit pseudouridine synthase A [Cellvibrio
           japonicus Ueda107]
          Length = 221

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/166 (17%), Positives = 59/166 (35%), Gaps = 30/166 (18%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT-ND 127
            E     L HKP  L++     P  R +V   L   +     V RLD +T G++++  N 
Sbjct: 22  REDEDFLLIHKPTRLLSVPGRHPQNRDSVIARLLPDYPGATIVHRLDFDTSGVMVIPLNK 81

Query: 128 GGLARVLEL-PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI------QGICYGDM----- 175
             L+ + +   +    + Y     G V Q+      +G++       +G  Y        
Sbjct: 82  PALSHISKQFQARSVSKHYTAVVAGLVGQE------QGVIDLPIASGEGPTYKICRTSGK 135

Query: 176 ------QVTLDTQKGSNAWVTVGLR--EGKNREIKKVFEFFNWKVN 213
                 +V    Q  + +   + L    G++ +++   +     + 
Sbjct: 136 PSVTEFRVLARDQAANTS--RLVLHPITGRSHQLRLHLQAIGHPIL 179


>gi|149212744|ref|NP_439586.2| hypothetical protein HI1435 [Haemophilus influenzae Rd KW20]
 gi|262021233|gb|AAC23084.2| conserved hypothetical protein [Haemophilus influenzae Rd KW20]
          Length = 182

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 49/135 (36%), Gaps = 12/135 (8%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  DP     V   L       V  + RLD  T G+LL      +A
Sbjct: 11  LVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALSSEIA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            ++          + Y     G +  +++++   K I +  I     Q   + Q+    +
Sbjct: 71  NLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEAITDY 129

Query: 189 VTVGLRE-----GKN 198
             + + E     G+ 
Sbjct: 130 EGLKIVEMPYPAGRY 144


>gi|153820359|ref|ZP_01973026.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           NCTC 8457]
 gi|126509095|gb|EAZ71689.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           NCTC 8457]
          Length = 310

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 8   IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 59

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 60  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 119

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 120 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 179

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 180 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFAEATLVQASPVTGRTH 236

Query: 200 EIK 202
           +I+
Sbjct: 237 QIR 239


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/218 (16%), Positives = 69/218 (31%), Gaps = 42/218 (19%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLRKAERTRLWL 77
           ++I    V+VN   ++     +   D + +               +  P    E   L +
Sbjct: 38  KIIRNGEVRVNKKRVKTL-YKLKINDVVRIPPIEFIEKKEKKPSDNFKPHIIYEDEWLLV 96

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSI------FSRVISVGRLDINTEGLLLLTNDGGLA 131
            +KP GL        G    F  +  +      +  +  V R+D NT G++++       
Sbjct: 97  VNKPSGLAV----HGGSGIDFGLIEHMRHIKPEYKFLELVHRIDKNTSGVIVIAKKRSAL 152

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN---LLKKGIVIQG-----------ICYGDM 175
           R +     + +  + Y V   G  D  K      L+K    +G                 
Sbjct: 153 RSMQELFRNKKIKKNYLVAVKGNWDSKKKEVSLRLEKKQTSEGHHVNVVEDPLRGKLSKS 212

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              L  Q    + ++  +  G+  +I+    F  + V 
Sbjct: 213 IFYLVKQMQKQSLLSAQIITGRTHQIRVQLAFLGFPVL 250


>gi|217958782|ref|YP_002337330.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
 gi|217067935|gb|ACJ82185.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH187]
          Length = 297

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 74/220 (33%), Gaps = 35/220 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L S + +      V  V RLD +T GL+L+
Sbjct: 87  EDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLI 146

Query: 125 TNDGGLARVLE---LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGI 170
             +      L           R Y    HG            + +   +++++ +  +G 
Sbjct: 147 AKN-RFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQ 205

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +D+       V++ L  G+  +I+    +    +               L  
Sbjct: 206 RAVTHFRVIDSVNHKTH-VSLELDTGRTHQIRVHMAYIGHPLLG-----------DNLYG 253

Query: 231 GSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLV 268
           G   E+ ++ L        H + E +++   PI S    V
Sbjct: 254 GKRDEMKRQALHSTSLTFYHPILEKEMSFTTPIPSDMQAV 293


>gi|328948215|ref|YP_004365552.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
 gi|328448539|gb|AEB14255.1| pseudouridine synthase [Treponema succinifaciens DSM 2489]
          Length = 314

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 23/168 (13%), Positives = 53/168 (31%), Gaps = 17/168 (10%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             ++     ST  I  D       +   LW+ +K  G+    S  +    + D +     
Sbjct: 75  ARKSKTEKKSTQKIHGDISLQTAFKNEHLWIINKQSGIEVQPS-KNSSFCLADFVAQNTK 133

Query: 107 ------RVISVGRLDINTEGLLLLTND--GGLARVLELPSTQWLRVYRVRFHGQVDQDKL 158
                 R   + R+D  T GL+  +    G       + +    + Y       + +++L
Sbjct: 134 NASLSFRPGPLHRIDKFTTGLITFSQSLQGAKWFSENIKNHSIKKTYLAVVENFLPENEL 193

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKG----SNAWVTVGLREGKNREIK 202
            +      I+       ++    Q        +   + +  G+  +I+
Sbjct: 194 AIYD---TIE-EKTACTKIKKIAQGIFCGKEISLAKIQIETGRKHQIR 237


>gi|255712643|ref|XP_002552604.1| KLTH0C08756p [Lachancea thermotolerans]
 gi|238933983|emb|CAR22166.1| KLTH0C08756p [Lachancea thermotolerans]
          Length = 610

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/195 (18%), Positives = 63/195 (32%), Gaps = 28/195 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           IA+  V +N          V + D I          V   P++   E   L++  KP G+
Sbjct: 144 IARGAVFLNENPA-NLESIVRNGDLISHKIHRHEPPVTSRPIKIVFEDQDLFVIDKPSGI 202

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELPST--QW 141
               +     +T+   L    +  V    RLD  T GL+ L      A  +       + 
Sbjct: 203 PVHPTGRYRFNTITKILQKQINGSVHPCNRLDRLTSGLMFLAKTPRGADHMANQLKAREV 262

Query: 142 LRVYRVRFHGQVDQDKL-----------NLLKKGI---VIQGICYGDMQVTLDTQKGSNA 187
            + Y  R  G+   +++            L   G+     +G        T  +  G  +
Sbjct: 263 KKEYIARVVGEFPAERISVEKPLKCVEPRLALNGVCNSEEEGAKEAKTVFTRVSFDGETS 322

Query: 188 WVTVGLREGKNREIK 202
            V      G+  +I+
Sbjct: 323 LVKCQPHTGRTHQIR 337


>gi|237800339|ref|ZP_04588800.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. oryzae str. 1_6]
 gi|331023196|gb|EGI03253.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. oryzae str. 1_6]
          Length = 318

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RIVRKGEVRVNKGRTKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWAAAQKQVRAPLLKSNLRSGERMVEVNEEGKEALTIF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|229137994|ref|ZP_04266592.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST26]
 gi|229195503|ref|ZP_04322271.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1293]
 gi|228588043|gb|EEK46093.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           m1293]
 gi|228645339|gb|EEL01573.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST26]
          Length = 292

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/220 (16%), Positives = 74/220 (33%), Gaps = 35/220 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L S + +      V  V RLD +T GL+L+
Sbjct: 82  EDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLI 141

Query: 125 TNDGGLARVLE---LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGI 170
             +      L           R Y    HG            + +   +++++ +  +G 
Sbjct: 142 AKN-RFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQ 200

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +D+       V++ L  G+  +I+    +    +               L  
Sbjct: 201 RAVTHFRVIDSVNHKTH-VSLELDTGRTHQIRVHMAYIGHPLLG-----------DNLYG 248

Query: 231 GSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLV 268
           G   E+ ++ L        H + E +++   PI S    V
Sbjct: 249 GKRDEMKRQALHSTSLTFYHPILEKEMSFTTPIPSDMQAV 288


>gi|62185009|ref|YP_219794.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           abortus S26/3]
 gi|62148076|emb|CAH63831.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           abortus S26/3]
          Length = 274

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/201 (15%), Positives = 58/201 (28%), Gaps = 49/201 (24%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGR 94
           +VNG +    +  V   D I +      + E   LW      +Y+KP    T+  D    
Sbjct: 40  RVNGRVERFESYRVQPGDRITL--TVQTRLEPQILWEDAHCCIYNKPS--HTSTEDL--- 92

Query: 95  STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
                   +  +R+  V RLD +T G +L       A  L       +  + Y     G 
Sbjct: 93  --------AKITRLNIVHRLDRDTTGCILFAKHASAANALSELFKKRKIHKQYTALVFGH 144

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQV-TLDTQKGSNAWVTVGLRE---------------- 195
             +        G VI        +  ++           + + +                
Sbjct: 145 PKK------SSGTVISYTAPKSRRCGSVIFGNTPKNQGKLTITQWSILRTYKQYTLMRCE 198

Query: 196 ---GKNREIKKVFEFFNWKVN 213
              G+  +I+   +     + 
Sbjct: 199 PITGRTHQIRLHMQTLGHPIV 219


>gi|89097691|ref|ZP_01170579.1| ribosomal large subunit pseudouridine synthase [Bacillus sp. NRRL
           B-14911]
 gi|89087550|gb|EAR66663.1| ribosomal large subunit pseudouridine synthase [Bacillus sp. NRRL
           B-14911]
          Length = 285

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/159 (18%), Positives = 55/159 (34%), Gaps = 34/159 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTV-----FDNL-PSIFSRVISVGRLDINTEGLLLL 124
           E   + + +KP G+ T  ++P    T+     F  L    + +V  + RLD +T G +L 
Sbjct: 70  EDDHMLILNKPAGMDTHPNEPMQEDTLANAAAFHLLAKGEYRQVKHIHRLDKDTTGAVLF 129

Query: 125 TND---GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ----GICYGDMQV 177
                 GG+   L     +  R Y     G + Q      KKG++ +       +   + 
Sbjct: 130 AKHALAGGMLDQLL-KERKIKRTYIAMADGVIKQ------KKGVIRKPIGRDRHHPTRRR 182

Query: 178 TLDTQKGSNAWVTV---------GLRE-----GKNREIK 202
                + +     V          L       G+  +I+
Sbjct: 183 VSPGGQDAVTHYEVAAIFPREQQTLVSCRLETGRTHQIR 221


>gi|328786842|ref|XP_624656.2| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Apis mellifera]
          Length = 535

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/289 (15%), Positives = 101/289 (34%), Gaps = 34/289 (11%)

Query: 32  ERMIAQQRVKVNGILLE--------RAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   ++            NV+    + V   P+        + + +KP 
Sbjct: 156 ERCIRAGTLTVNYQKVDVDYRLRHNDLLANVVHRHEVPVTSEPITVIHMDEDVVVVNKPA 215

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   +    + ++ RLD  T G+LL       AR +E    +
Sbjct: 216 SIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGILLFGRTPKKARQMEHQIRN 275

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK-----------GSNA 187
            Q  + Y  R  G+  ++++ +  + I +     G  +++   +            G ++
Sbjct: 276 RQVHKQYVCRVEGEFPEEEV-VCSEPIEVVSYKIGVCKISEKGKDCVTRFKRLSYNGKSS 334

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNR--L-IRISYGPFQLGTLLAGSTREVSKKIL-RE 243
            V    + G+  +I+   ++  + V    L   + +GP +      G     + + L R+
Sbjct: 335 VVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVFGPEKGKGGNIGK----TDQELVRD 390

Query: 244 QLGPHLLEE-AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
            +  H  E    ++ D+ +   +  +     +      D      ++  
Sbjct: 391 LISIHNAENWLGMDGDSEMSLFKPKLDMEDRVSLSNDKDVASSPSSTPG 439


>gi|257413410|ref|ZP_04742958.2| ribosomal large subunit pseudouridine synthase family protein
           [Roseburia intestinalis L1-82]
 gi|257203607|gb|EEV01892.1| ribosomal large subunit pseudouridine synthase family protein
           [Roseburia intestinalis L1-82]
          Length = 221

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 56/169 (33%), Gaps = 20/169 (11%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHS-----DPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            P    E   + +  KP G+ T        D +     +         +  V RLD   E
Sbjct: 6   QPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPVE 65

Query: 120 GLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----NLLKKG------IVI 167
           G+++   +   A  L          + Y     G  ++ K      LL+ G      +V 
Sbjct: 66  GIMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNTSEVVE 125

Query: 168 QGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +G     +  +   +  Q G +A + + L  G++ +I+         + 
Sbjct: 126 RGTPQAKHASLSYEVVEQDGKHAVLRIKLDTGRHHQIRVQLAHAGMPIV 174


>gi|126728208|ref|ZP_01744024.1| ribosomal large subunit pseudouridine synthase C [Sagittula
           stellata E-37]
 gi|126711173|gb|EBA10223.1| ribosomal large subunit pseudouridine synthase C [Sagittula
           stellata E-37]
          Length = 347

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/173 (18%), Positives = 60/173 (34%), Gaps = 34/173 (19%)

Query: 14  QRVSKVIARA--GIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------- 62
           QR+ + + R    +A SR  +E+M  +  ++++G   + A+  V +   + +        
Sbjct: 16  QRLDRWLKRLFPHVAQSR--IEKMCRKGELRLDGGRCK-ASSRVETGMQVRIPPLPEPGQ 72

Query: 63  ------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSI 104
                       D   +R     +   +   +KP GL T       R            +
Sbjct: 73  VDSAPKPSFNEKDAEMIRACVLWKDDHIIALNKPPGLATQGGSGQTRHVDGLSEALTFGM 132

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ 155
             +   V RLD +T G+LLL     +A+ L          ++Y     G    
Sbjct: 133 DEKPRLVHRLDKDTSGVLLLARTRAVAKALTEAIRHREARKIYWALVAGVPTP 185


>gi|78776648|ref|YP_392963.1| pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
 gi|78497188|gb|ABB43728.1| Pseudouridine synthase [Sulfurimonas denitrificans DSM 1251]
          Length = 244

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/206 (16%), Positives = 65/206 (31%), Gaps = 40/206 (19%)

Query: 18  KVIARAGIASRREVERMIAQQRV-----KV---NGILLERAAVNVMSTDHIEVDGVPLRK 69
           K++A     S  E + MI +  V     KV    G +  +    V   + I     P+ +
Sbjct: 8   KLLAAQEGISNSEAKSMIDRGLVYAANKKVMIARGDIDTKTLFKVEKVEKIR----PIFE 63

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            +   +    KP  + +            D +   F   + + RLD  T G+L+L  +  
Sbjct: 64  NDDLVVV--DKPAHVNS------------DEIERQFKPAVLLHRLDKETSGVLMLVKNEE 109

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
                     +    + Y     G + +            K N     +  +G      +
Sbjct: 110 FREKAIQEFKKDRVYKEYIAWIEGILSEPVDIDRPILTTKKNNRASSNVSSKGKPART-E 168

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK 202
           V  D    +   V   +  G+  +I+
Sbjct: 169 VFPDLVSANKTKVKCIIHHGRTHQIR 194


>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 = 52.1 bits (124), Expect = 1e-04,   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|289624528|ref|ZP_06457482.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. NCPPB3681]
 gi|330869277|gb|EGH03986.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. 0893_23]
          Length = 318

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLMKSNLRSGERMVEVNEEGKKALTIF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|225556035|gb|EEH04325.1| DRAP deaminase [Ajellomyces capsulatus G186AR]
          Length = 545

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/163 (15%), Positives = 53/163 (32%), Gaps = 24/163 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKP 81
           ++ I    V +NG  +      + + D I          V   P+    E   + +  KP
Sbjct: 82  QKAIEDGAVCINGKAV-SIDTKIQNGDVISHTLHRHEPPVTSQPISIIHEDDDMIVIDKP 140

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     +++ + + +            RLD  T G++ +      A  +  +L
Sbjct: 141 AGVPVHPAGRYNYNSILEIMKAERGNGWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKL 200

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
            S    + Y  R  G+           G+V+       +   L
Sbjct: 201 RSRTVRKEYVARVKGKFPD--------GVVLCDQPMLKISPIL 235


>gi|311746883|ref|ZP_07720668.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
 gi|126578569|gb|EAZ82733.1| RNA pseudouridine synthase family protein [Algoriphagus sp. PR1]
          Length = 237

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/176 (17%), Positives = 50/176 (28%), Gaps = 47/176 (26%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTND 127
           E   +   +KP GL+   +    + TVF        I   V  V RLD  T G+LL    
Sbjct: 8   EDDSIIAINKPAGLLVHRTSIAAQETVFALQILRDQIGMHVHPVHRLDRPTSGILLFAKK 67

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ--- 182
             +   L+      Q  + Y     G  +Q K                D  +  +     
Sbjct: 68  EEILPHLKNLFSERQIKKNYLTIVRGIPEQKK-------------ALIDHPLKSERSGRL 114

Query: 183 KGSNAWVTVGLRE--------GKN-----------------REIKKVFEFFNWKVN 213
           + +  W  V + E        G+                   +I++        + 
Sbjct: 115 QEAQTWYKV-ISETEIPFDTTGRYPTSRYSLLSVNPETGRTHQIRRHLAHIRHYII 169


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+  ++    + S R   +R+I    V VN  L+++    V  +  I +
Sbjct: 1  MAKQRLDTLLVELNLCSSRALAQRLIQAGEVTVNQQLVDKPGTEVDISAQINI 53


>gi|297579532|ref|ZP_06941460.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC385]
 gi|297537126|gb|EFH75959.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC385]
          Length = 315

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|289667068|ref|ZP_06488143.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. musacearum NCPPB4381]
          Length = 331

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 59/328 (17%), Positives = 106/328 (32%), Gaps = 55/328 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------------ILL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQVQVV 76

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSI 104
                +    D       PL    E  ++ +  KP GLV      +PDG           
Sbjct: 77  LETQTHAAPQDI------PLSVLYEDEQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDP 130

Query: 105 F----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
                 R   V RLD +T G++++         L  +L +    R Y     G       
Sbjct: 131 ALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGT 190

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D+   + LK  +   G          +  +   A +   L  G+  +I+      
Sbjct: 191 ANAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHL 249

Query: 209 NWKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYS 263
              +    L    YG   L  L  G+T E+  ++    R+ L    LE        P+ +
Sbjct: 250 KSPIVGDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLEFRHPVSGEPVRA 303

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           S  +  D   +++ + +D  R  + + +
Sbjct: 304 SAPVPADLQRLMTALREDSARAAEMARR 331


>gi|313499940|gb|ADR61306.1| RluA family pseudouridine synthase [Pseudomonas putida BIRD-1]
          Length = 318

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/211 (17%), Positives = 67/211 (31%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKA--------------------E 71
           R++ +  V+VN G +  +    + + D + V  V L +                     E
Sbjct: 43  RILRKGEVRVNKGRV--KPEYKIQAGDIVRVPPVRLPERDEPAPVAQGLLQRLEAAIVYE 100

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 101 DKALIVMNKPAGIAVHGGSGLSFGVIEALRQLRPDAKELELVHRLDRDTSGLLMIAKKRS 160

Query: 130 LARVL--ELPSTQWLRVYRVRFHG--QVDQDKLNL------LKKG-----IVIQGICYGD 174
           + R L   L      + Y     G     + ++N       L+ G     +  +G     
Sbjct: 161 MLRHLHAALRGDGVDKRYMALVRGHWPTSKKQVNAPLLKSNLRSGERMVEVNDEGKEALT 220

Query: 175 MQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           +   L         V    +    G+  +I+
Sbjct: 221 LFRVLRRFGDFATIVEARPIT---GRTHQIR 248


>gi|261400179|ref|ZP_05986304.1| RNA pseudouridine synthase [Neisseria lactamica ATCC 23970]
 gi|269210178|gb|EEZ76633.1| RNA pseudouridine synthase [Neisseria lactamica ATCC 23970]
          Length = 307

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|261392780|emb|CAX50356.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis 8013]
          Length = 307

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|288934799|ref|YP_003438858.1| pseudouridine synthase [Klebsiella variicola At-22]
 gi|288889508|gb|ADC57826.1| pseudouridine synthase [Klebsiella variicola At-22]
          Length = 232

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 66/186 (35%), Gaps = 37/186 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   F     V RLD  T GL+++  + G
Sbjct: 22  QDEHLLLINKPAGLLSLSGKDPRNLDSVHHRLVQRFPGCTLVHRLDFGTSGLMVIARNKG 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +    +      
Sbjct: 82  INALLCQQFSQRTVAKVYTALLCGHLAED------EGIVEAAIAKVPARFPRMSLCARHG 135

Query: 183 KGSNAWVTVG--LRE-------------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V   L +                   G+  +++   +   + +       YG
Sbjct: 136 KPARSRYRVIDRLYQSRDGERALALTRVALTPETGRTHQLRIHCQLLGYPILGCD--LYG 193

Query: 222 PFQLGT 227
             +L  
Sbjct: 194 GRELPG 199


>gi|269968014|ref|ZP_06182052.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
 gi|269827371|gb|EEZ81667.1| Ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 40B]
          Length = 250

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 56/163 (34%), Gaps = 43/163 (26%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E   +   +KP GL++      +   +++  L  +   +  V RLD++T GL+LL  +  
Sbjct: 19  EDDDILAVNKPSGLLSVPGRLAEHYDSMWSRLKELHPEIQVVHRLDMSTSGLMLLAKNKP 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVI----QGICYGDMQ 176
                       L        +VY  R  G V+       ++G I +            +
Sbjct: 79  AERALKKQFQYRLTH------KVYYARVWGHVEP------QEGNIDLPLICDWPNRPRQK 126

Query: 177 VTLDTQKGSNAWVTVGLRE-----------------GKNREIK 202
           V  D  K S     V  RE                 G++ +++
Sbjct: 127 VCFDDGKPSQTLFQVVKREVHPDGTHTTVVRLLPITGRSHQLR 169


>gi|83859151|ref|ZP_00952672.1| ribosomal large subunit pseudouridine synthase d [Oceanicaulis
           alexandrii HTCC2633]
 gi|83852598|gb|EAP90451.1| ribosomal large subunit pseudouridine synthase d [Oceanicaulis
           alexandrii HTCC2633]
          Length = 310

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 48/149 (32%), Gaps = 26/149 (17%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD------------GVPLRKA-ERT 73
           SR   + ++ Q  + V+G  L   +  V       +D             +PL    E  
Sbjct: 9   SRSRCKALVEQGCLFVDGEALTDPSAKVREG-VYRLDVPAPVEATPKPEDIPLEVLFEDD 67

Query: 74  RLWLYHKPIGLVTTHSDPDGRST-VFDNLPSIF---------SRVISVGRLDINTEGLLL 123
            L + +KP G+    +  +   T V   L              R   V RLD +T G+++
Sbjct: 68  HLIVINKPAGMAVHPAAGNWTGTLVHALLFHCAGSLSGIGGVERPGIVHRLDKDTSGVMV 127

Query: 124 L--TNDGGLARVLELPSTQWLRVYRVRFH 150
              T+        +  +    R Y     
Sbjct: 128 AAKTDKAHQGLSAQFAAHTVERAYLAFTR 156


>gi|332664097|ref|YP_004446885.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
 gi|332332911|gb|AEE50012.1| pseudouridine synthase [Haliscomenobacter hydrossis DSM 1100]
          Length = 237

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/155 (16%), Positives = 48/155 (30%), Gaps = 20/155 (12%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLAR 132
           +L  ++KP G + T +D  G  ++           V  V RLD    G++L++       
Sbjct: 27  QLIAFNKPAG-IPTQTDKTGDKSLLQLAEIFTKSAVQLVHRLDRPASGIVLVSKTAKALA 85

Query: 133 VLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC---------------YGDM 175
            L     + Q  + Y       +  +    L+  I   G                    +
Sbjct: 86  NLNEQFRNRQIQKTYLAVVE-ALPAEPKGRLEHWIWKNGQTNRSVISTEKGHANAQEAIL 144

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
           +  L         + V L  G++ +I+        
Sbjct: 145 EYQLLGSSDRYHLLEVKLLTGRHHQIRAQLAAMGC 179


>gi|313672668|ref|YP_004050779.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
 gi|312939424|gb|ADR18616.1| pseudouridine synthase [Calditerrivibrio nitroreducens DSM 19672]
          Length = 211

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/150 (16%), Positives = 53/150 (35%), Gaps = 14/150 (9%)

Query: 75  LWLYHKPIGLVTTHSDPDGR-STVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +K  GL+      D     + D L  I+ R+  V RLD  T G+++   +    R 
Sbjct: 12  ILVVNKGHGLLVVPDRYDKDLPNLKDLLTEIYGRIFVVHRLDYGTSGIMVFAKNERSHRS 71

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLNLL---------KKGIVIQGICYGDMQVTLDTQ 182
           L +    ++  + Y     G    D   +L         +  I  +         ++  +
Sbjct: 72  LSIQFERSEVDKRYYAICKGVFPADLTCMLPISKVNYHGRYKINFKSGRKALTSFSVLDR 131

Query: 183 KGSNAWVTVG-LREGKNREIKKVFEFFNWK 211
                 + V  L  G++ +I+   +   + 
Sbjct: 132 FSDKTLIDVVPLT-GRSHQIRVHLKALGYP 160


>gi|292490642|ref|YP_003526081.1| pseudouridine synthase [Nitrosococcus halophilus Nc4]
 gi|291579237|gb|ADE13694.1| pseudouridine synthase, RluA family [Nitrosococcus halophilus Nc4]
          Length = 325

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/246 (15%), Positives = 76/246 (30%), Gaps = 46/246 (18%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           +Q     QR+   +         SR  + R + +  V+VN   +   +  +   D + + 
Sbjct: 17  IQLEQAGQRIDNFLLSQLKGVPKSR--IYRCLRRGEVRVNKSRVAS-SYRLEQGDQVRIP 73

Query: 64  GVPLRKA--------------------ERTRLWLYHKPIG--LVTTHSDPDGRSTVFDNL 101
            + +                       E   L + +KP G  + +  S   G      +L
Sbjct: 74  PLRVSHPSVKEPVAPSLLHLIESSLLYEDKHLLILNKPAGIAVHSGSSISYGVIETLRHL 133

Query: 102 PSIFSRVISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                 +  V RLD  T G L++  T    LA           + Y     G+  ++   
Sbjct: 134 RPEAPFLELVHRLDRETSGCLMVAKTRSTLLALQSMQREQLIHKRYLALVKGRWPRNIGQ 193

Query: 160 ---LLKKGIVIQGICYGDMQVTLDTQKGSNA-----------WVTVGLREGKNREIKKVF 205
               L K I+  G     ++V+   +  ++             + + L  G+  +I+   
Sbjct: 194 VNLPLLKNILQSGERV--VKVSATGKPAASHFHPKQLYKEATLMEITLETGRTHQIRVHA 251

Query: 206 EFFNWK 211
                 
Sbjct: 252 AHLGHP 257


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

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/188 (15%), Positives = 62/188 (32%), Gaps = 37/188 (19%)

Query: 3   DKNIVQENFTPQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           ++  V       R+ +         G     ++++++   +V+V+G   + A   V +  
Sbjct: 5   EQIEVDSGEAGMRLDRWFKTHYPGLGFG---QLQKLLRTGQVRVDGGRAK-ADTRVQAGQ 60

Query: 59  HIEV---------------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGR 94
            I V                     D   L +    E  ++++++KP GL         R
Sbjct: 61  MIRVPPLAVDHKGAPATIRTMRDRGDAEVLSQMLIHEDEKVFVFNKPAGLAVQGGSGVNR 120

Query: 95  STVFDNLPSIFSR---VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
                       R      V RLD +T G+L++      A  L     + +  ++Y    
Sbjct: 121 HVDGMLEAWRNKRGEKPRLVHRLDRDTSGVLVVARTRLAAVKLTESFRARETKKIYWALI 180

Query: 150 HGQVDQDK 157
            G   + +
Sbjct: 181 KGVPKKAE 188


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KNKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>gi|289550433|ref|YP_003471337.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
 gi|289179965|gb|ADC87210.1| Putative ribosomal large subunit pseudouridine synthase D
           [Staphylococcus lugdunensis HKU09-01]
          Length = 278

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/204 (16%), Positives = 68/204 (33%), Gaps = 28/204 (13%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGL 84
            + + +N       +  V + D +E+  D          R    +          KP G+
Sbjct: 34  SKEITINNAPAR-LSNQVHTMDCVEIPTDEEKSNYLPSYRYAQIYYEDDDLAIVMKPKGV 92

Query: 85  VTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
            T  +D    +T+ +++           + RLD  T GLL++  +  + ++L   L   +
Sbjct: 93  KTHPNDLKESNTLMNHIIYTLDSEYAEPIHRLDQETVGLLIIAKNPLMKKILDRMLEDNK 152

Query: 141 WLRVYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             R+Y+                 + +DK +  K+ I   G       +     K     +
Sbjct: 153 ITRIYKANVNALLPIKPQTIDMPIGKDKFHPNKRRISNTGQRAITHILASTMLKEGVCQL 212

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G+  +I+         V 
Sbjct: 213 DIKLDTGRTHQIRVHLAEIGHPVI 236


>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 (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|183982375|ref|YP_001850666.1| RluA family pseudouridine synthase [Mycobacterium marinum M]
 gi|183175701|gb|ACC40811.1| pseudouridine synthase, RluA-family [Mycobacterium marinum M]
          Length = 303

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-------VNV----- 54
           V E     RV   +AR    SR  V  +     V+++G+   ++        ++V     
Sbjct: 3   VPEGLAGMRVDAGLARLLGLSRSAVAVIAENGGVELDGVPAGKSDRLTAGAWLHVQLPEA 62

Query: 55  ---MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   +E++G+ +  ++   +    KP  +    S      TV   L          
Sbjct: 63  PPPPENTPVEIEGMTILYSDDD-IVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRISTS 121

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNL 160
            +  R   V RLD+ T G++++        VL+    Q    + Y     G  D      
Sbjct: 122 GVHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVDKRYHALVQGHPDP----- 176

Query: 161 LKKGIVIQ-------GICYGDMQVTLDTQKGSN----------AWVTVGLREGKNREIKK 203
              G  I        G  +            ++          + + V L  G+  +I+ 
Sbjct: 177 -SSG-TIDAPIGRHPGGEWKFAVTKNGRHSLTHYDTVEAFVAASLLDVHLETGRTHQIRV 234

Query: 204 VFEFFNWKV 212
            F   +   
Sbjct: 235 HFAALHHPC 243


>gi|149019517|ref|ZP_01834836.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP23-BS72]
 gi|147930892|gb|EDK81872.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pneumoniae SP23-BS72]
          Length = 237

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/160 (20%), Positives = 61/160 (38%), Gaps = 23/160 (14%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---------VGRLDINTEGLLLL- 124
           + + +KP G+V   S      T+ + L      +           V R+D +T GLL++ 
Sbjct: 25  VAVVNKPQGMVVHPSAGHTSGTLVNALMYHIKDLSGINGVLRPGIVHRIDKDTSGLLMIA 84

Query: 125 -TNDGGLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICY 172
             +D  LA   EL   + LR Y    HG            + + + +  K+ +  +G   
Sbjct: 85  KNDDAHLALAQELKDKKSLRKYWAIVHGNLPNDRGVIEAPIGRSEKDRKKQAVTAKGKPA 144

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
              +  +  + G  + V + L  G+  +I+    +    V
Sbjct: 145 VT-RFHVLERFGDYSLVELQLETGRTHQIRVHMAYIGHSV 183


>gi|2828514|sp|P44197|TRUC_HAEIN RecName: Full=tRNA pseudouridine synthase C; AltName: Full=tRNA
           pseudouridylate synthase C; AltName: Full=tRNA-uridine
           isomerase C
          Length = 239

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/135 (20%), Positives = 49/135 (36%), Gaps = 12/135 (8%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   S  DP     V   L       V  + RLD  T G+LL      +A
Sbjct: 11  LVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALSSEIA 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            ++          + Y     G +  +++++   K I +  I     Q   + Q+    +
Sbjct: 71  NLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEAITDY 129

Query: 189 VTVGLRE-----GKN 198
             + + E     G+ 
Sbjct: 130 EGLKIVEMPYPAGRY 144


>gi|153216570|ref|ZP_01950521.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           1587]
 gi|229513684|ref|ZP_04403146.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TMA 21]
 gi|229521940|ref|ZP_04411357.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TM 11079-80]
 gi|229524038|ref|ZP_04413443.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           bv. albensis VL426]
 gi|254226963|ref|ZP_04920527.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V51]
 gi|254286849|ref|ZP_04961802.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           AM-19226]
 gi|124114199|gb|EAY33019.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           1587]
 gi|125620503|gb|EAZ48873.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V51]
 gi|150423140|gb|EDN15088.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           AM-19226]
 gi|229337619|gb|EEO02636.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           bv. albensis VL426]
 gi|229340865|gb|EEO05870.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TM 11079-80]
 gi|229348865|gb|EEO13822.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           TMA 21]
          Length = 315

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|255532252|ref|YP_003092624.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
 gi|255345236|gb|ACU04562.1| pseudouridine synthase [Pedobacter heparinus DSM 2366]
          Length = 225

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/162 (17%), Positives = 53/162 (32%), Gaps = 22/162 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLT-- 125
           +   L   +KP GL+   S    D +      L       V  V RLD  T GLLL    
Sbjct: 7   QDDHLIAINKPHGLLVHRSSIANDAKEFALQLLRDQVNRHVSPVHRLDRKTGGLLLFAFE 66

Query: 126 NDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQG----ICYGDMQ 176
            D   A   +  + +  + Y     G           L   + G + +     +     +
Sbjct: 67  KDVETAMQQKFMNGEVQKKYLAVLRGYAPDQMAIDYPLAK-ENGTIQEAFTAFVTLKRAE 125

Query: 177 VTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
           + +   K   +  ++   E     G+  +++K F    + + 
Sbjct: 126 LDIAFGKHPTSRYSLV--EASPTTGRMHQLRKHFAHIFYPII 165


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/217 (16%), Positives = 74/217 (34%), Gaps = 33/217 (15%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLRKAERT 73
           S R + + +   RV VN   + +    +   D IE+             D       E  
Sbjct: 29  SGRFIRKAVRDGRVFVNKEKVIK-KNKLSQDDLIEIYMQEDEHQNIEPEDMNIEIVYEDN 87

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTND 127
            + + +K  G+V   +      T+ + +   F +      V  V RLD +T GL+++  +
Sbjct: 88  DIIVINKRPGIVVHPTKGHPTGTLSNGILYHFKKNGEKSIVRLVSRLDRDTSGLIIIAKN 147

Query: 128 GGLARVLELPSTQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGD 174
                 L    ++  + ++Y    HG            + +++ +   K IV +      
Sbjct: 148 QFSHMRLASDMSKDSFRKIYIAVVHGSMKEKEGRINLPIYKEEESESIKRIVDERGQESI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +  +    + V + L  G+  +I+         
Sbjct: 208 TTYEVLEELSKGSVVRLELETGRTHQIRVHMSHLGHP 244


>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 = 52.1 bits (124), Expect = 1e-04,   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|325852028|ref|ZP_08171111.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
 gi|325484584|gb|EGC87500.1| pseudouridine synthase, RluA family [Prevotella denticola CRIS
           18C-A]
          Length = 319

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 74/205 (36%), Gaps = 30/205 (14%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKAERTRL-----W 76
           S+ +V+  +  + ++VNG  + +    + + D + V     +G    +  +         
Sbjct: 57  SKSKVKATLQNRGIRVNGSCVTQFDRQLKAGDKVSVSKSKKNGQFRSRYVKIVYEDRFLV 116

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGL 130
           +  K IG+++  +       V   L   F +         V RLD +T GL++   D   
Sbjct: 117 VVEKNIGILS-MAAGHASLNVKSILDDYFYKTRQKCTAHVVHRLDRDTSGLMIYAKDMQT 175

Query: 131 ARVLELPSTQW--LRVYRVRFHGQVDQDK------LNLLKKGIVI-----QGICYGDMQV 177
            ++ E         R Y     G+++QD+      L   K  +        G  Y     
Sbjct: 176 EQLFEHDWHNIVYDRRYVGVVSGEMEQDEGTVANWLKDNKAYVTYSSPVDNGGKYAVTHF 235

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            +  +  + + V   L  G+  +I+
Sbjct: 236 HVLDRTVAYSLVEYRLETGRKNQIR 260


>gi|291540830|emb|CBL13941.1| ribosomal large subunit pseudouridine synthase D [Roseburia
           intestinalis XB6B4]
          Length = 221

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 56/169 (33%), Gaps = 20/169 (11%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHS-----DPDGRSTVFDNLPSIFSRVISVGRLDINTE 119
            P    E   + +  KP G+ T        D +     +         +  V RLD   E
Sbjct: 6   QPAIIYEDEDIIVCKKPAGVATQTRRIGQADMESLLKNYRASKGELPYIGVVHRLDQPVE 65

Query: 120 GLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL----NLLKKG------IVI 167
           G+++   +   A  L          + Y     G  ++ K      LL+ G      +V 
Sbjct: 66  GVMVFAKNKEAAADLSRQIKTKLADKYYYAMTDGVPEKKKGTLEDELLQNGKTNASEVVE 125

Query: 168 QGI---CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +G     +  +   +  Q G +A + + L  G++ +I+         + 
Sbjct: 126 RGTPQAKHASLSYEVVEQDGKHAVLRIKLDTGRHHQIRVQLAHAGMPIV 174


>gi|254673322|emb|CBA08488.1| pseudouridylate synthase [Neisseria meningitidis alpha275]
 gi|325202346|gb|ADY97800.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240149]
 gi|325207901|gb|ADZ03353.1| RNA pseudouridine synthase [Neisseria meningitidis NZ-05/33]
          Length = 307

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +R+ K++   G+  SR + +R+I    V VN   +++    +    +I
Sbjct: 5  ERIDKLLVERGLVESREKAQRLIMAGCVFVNDQRVDKPGTKIPVDANI 52


>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 = 52.1 bits (124), Expect = 1e-04,   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|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 = 52.1 bits (124), Expect = 1e-04,   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|302871790|ref|YP_003840426.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302574649|gb|ADL42440.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 293

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/160 (13%), Positives = 53/160 (33%), Gaps = 17/160 (10%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRL 114
            + V+G      E       +KP GL +  S      T+ + +    +        + RL
Sbjct: 70  IVPVEGSIDILYEDNFFLFVNKPSGLPSHPSKGHYSDTIANYVEYYLNSKNLTSHIINRL 129

Query: 115 DINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------QDKLNLLKKGIV 166
           D  T G+++   +     ++       Q  + Y    HG++       +  +   + GI 
Sbjct: 130 DKETSGIVVFAKNSYFHSIVSREFEKRQVEKTYIAIVHGRLTKKSGLIEKPIKRSQDGIK 189

Query: 167 IQ---GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +      +      +     +   + +  +  G+  +++
Sbjct: 190 REIHQDGSFASTYYEVIDCFENFTLLKLKPIT-GRTHQLR 228


>gi|223038326|ref|ZP_03608620.1| RNA pseudouridine synthase family [Campylobacter rectus RM3267]
 gi|222880183|gb|EEF15270.1| RNA pseudouridine synthase family [Campylobacter rectus RM3267]
          Length = 303

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 53/282 (18%), Positives = 108/282 (38%), Gaps = 36/282 (12%)

Query: 29  REVERMIAQQRVKVNGILL-ERAAVNVMSTDHIEVDGVP--LRKA-ERTRLWLYHKPIGL 84
           RE +R+I + R+  +G ++ E+ A+       IE +  P  LR   E  +  ++ KP G+
Sbjct: 28  RETQRLIDKGRLTCDGAVVGEKNALLSGEICLIEYETNPRGLRPIFECEKFAVFDKPNGV 87

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +      ++ D + S++ R  SV  RLD  T GL+++  D      L     + Q 
Sbjct: 88  LSHPNGRHCEYSLNDEIWSLYGREASVAHRLDCETSGLIVVGKDKNTVVNLKKLFENRQV 147

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTV--------- 191
            + Y     G++ ++    ++  + +    Y D+++ +   + G +A   +         
Sbjct: 148 YKSYVALAQGKISENL--RIEANMDLAN-DYDDVKMRMRICEDGKSAVTEISPIEYFADI 204

Query: 192 --GLRE-----GKNREIK-KVF--EF--FNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
              L +     G+  +I+  +F  E       +  L+R          +     R ++  
Sbjct: 205 DATLVQAVPLTGRQHQIRLHLFHVEHKILGEPLYGLMRSQIEKILDKEMSEAE-RILTTG 263

Query: 240 ILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD 281
             R  L     +E +   D   Y   +    R      V  D
Sbjct: 264 APRLLLH---ADEIRFKFDGIEYEIRSEFDARNEFYQSVKSD 302


>gi|328914578|gb|AEB55411.1| ribosomal large subunit pseudouridine synthase C [Chlamydophila
           psittaci 6BC]
          Length = 279

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 38/119 (31%), Gaps = 19/119 (15%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDG----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           +VNG L    +  V   D + +       P    E     +Y+KP    T+  D      
Sbjct: 44  RVNGRLERFESYRVQPGDRVTLTVQTRLEPQILWEDEHYCIYNKPS--HTSTEDL----- 96

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                 +  + +  V RLD +T G +L       A  L       +  + Y     G  
Sbjct: 97  ------AKITGLNIVHRLDRDTTGCILFAKHASAAHALSELFKKRKIHKQYTALVFGHP 149


>gi|312962573|ref|ZP_07777063.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens WH6]
 gi|311283153|gb|EFQ61744.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens WH6]
          Length = 319

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 80/236 (33%), Gaps = 43/236 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V   +  QR+   + AR     +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRI--KPEYKLQAGDIVRVPP 73

Query: 65  VPLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTV--FDNLP 102
           V + + +                       L + +KP G+            +  F  L 
Sbjct: 74  VRVPERDEPVPLAQGLLQRLEASIVFEDNKLIVINKPCGIAVHGGSGLNFGVIEAFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T GLL++     + R L   L      + Y     G      +  
Sbjct: 134 PDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHTALRGDGVDKRYMALVRGNW-ASSIKS 192

Query: 161 LKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV--------GLRE-----GKNREIK 202
           ++  +    +  G+  V +D + K +     V         + E     G+  +I+
Sbjct: 193 VRAPLQKSNLRSGERMVEVDEEGKEALTLFKVLRRFGDFATMVEAKPVTGRTHQIR 248


>gi|229592115|ref|YP_002874234.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens SBW25]
 gi|229363981|emb|CAY51520.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           fluorescens SBW25]
          Length = 319

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/236 (16%), Positives = 80/236 (33%), Gaps = 43/236 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V   +  QR+   + AR     +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  VSPEYAGQRIDNFLLARLKGVPKTLIYRILRKGEVRVNKGRI--KPEYKLQAGDIVRVPP 73

Query: 65  VPLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTV--FDNLP 102
           V + + +                       L + +KP G+            +  F  L 
Sbjct: 74  VRVPERDEPVPLAQGLLQRLEASIVFEDNKLIVINKPCGIAVHGGSGLNFGVIEAFRQLR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T GLL++     + R L   L      + Y     G      +  
Sbjct: 134 PDAKELELVHRLDRDTSGLLMIAKKRSMLRHLHTALRGDGVDKRYMALVRGNW-ASSIKS 192

Query: 161 LKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV--------GLRE-----GKNREIK 202
           ++  +    +  G+  V +D + K +     V         + E     G+  +I+
Sbjct: 193 VRAPLQKSNLRSGERMVEVDEEGKEALTLFKVLRRFGDFATMVEAKPVTGRTHQIR 248


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/82 (21%), Positives = 31/82 (37%), Gaps = 1/82 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++ + G+AS R + + +I    V V+G   ++A         I V G  L+ 
Sbjct: 1  MKKERLDVLLVKKGLASSREKAKAIIMSGIVFVDGQREDKAGSTFDEKQEIIVKGKTLKY 60

Query: 70 AERTRLWLYHKPIGLVTTHSDP 91
            R  L L            D 
Sbjct: 61 VSRGGLKLEKAMKNFDIVLKDK 82


>gi|166365046|ref|YP_001657319.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
 gi|166087419|dbj|BAG02127.1| ribosomal large subunit pseudouridine synthase D [Microcystis
           aeruginosa NIES-843]
          Length = 501

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/152 (19%), Positives = 51/152 (33%), Gaps = 26/152 (17%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   +   +KP GL++      D +  V +        +I V RLD  T G+LLL     
Sbjct: 305 EDEGIIAINKPAGLLSVAGRYQDSQDAVVNRFRRQGKNLIPVHRLDRETSGILLLAKSLD 364

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDTQ 182
           + R L       +  ++Y       ++++       GI+   +           V     
Sbjct: 365 IYRCLSQQFQRREVEKIYEAILSEIIERE------SGIIDLPLWGNPQNRPYQTVDWQRG 418

Query: 183 KGSNAWVTVGLREGKN------------REIK 202
           K S  +  V  +EG               +I+
Sbjct: 419 KASQTYFKVVGKEGNYSRLEFIPYTGRTHQIR 450


>gi|332140394|ref|YP_004426132.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           str. 'Deep ecotype']
 gi|327550416|gb|AEA97134.1| pseudouridylate synthase, 23S RNA-specific [Alteromonas macleodii
           str. 'Deep ecotype']
          Length = 265

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/100 (26%), Positives = 37/100 (37%), Gaps = 8/100 (8%)

Query: 62  VDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLD 115
           V+  PL      +   +    KP GL+   S  D   TVF        I   V    RLD
Sbjct: 21  VEHQPLHLPVLYQDEHIIAIDKPPGLLVHRSPIDKHETVFAVQTLRDQIGQHVFPAHRLD 80

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
             T G+L+ +     A  L  ++   Q ++ Y     G V
Sbjct: 81  RPTSGVLVFSFSADTAAKLGKQMMDKQVVKQYHAIVRGFV 120


>gi|15642030|ref|NP_231662.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121729883|ref|ZP_01682310.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V52]
 gi|147673109|ref|YP_001217555.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|227082155|ref|YP_002810706.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           M66-2]
 gi|229507883|ref|ZP_04397388.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           BX 330286]
 gi|229511882|ref|ZP_04401361.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|229519018|ref|ZP_04408461.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC9]
 gi|229607428|ref|YP_002878076.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MJ-1236]
 gi|254849115|ref|ZP_05238465.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MO10]
 gi|255745223|ref|ZP_05419172.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholera
           CIRS 101]
 gi|262167652|ref|ZP_06035355.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC27]
 gi|298497942|ref|ZP_07007749.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MAK 757]
 gi|14423896|sp|Q9KQH0|RLUC_VIBCH RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|9656573|gb|AAF95176.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O1 biovar El Tor str. N16961]
 gi|121628373|gb|EAX60874.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           V52]
 gi|146314992|gb|ABQ19531.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|227010043|gb|ACP06255.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           M66-2]
 gi|227013925|gb|ACP10135.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           O395]
 gi|229343707|gb|EEO08682.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC9]
 gi|229351847|gb|EEO16788.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|229355388|gb|EEO20309.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           BX 330286]
 gi|229370083|gb|ACQ60506.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MJ-1236]
 gi|254844820|gb|EET23234.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MO10]
 gi|255737053|gb|EET92449.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholera
           CIRS 101]
 gi|262023857|gb|EEY42555.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           RC27]
 gi|297542275|gb|EFH78325.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MAK 757]
          Length = 315

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>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 (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+   +   G+A SR++ + +I   +V V+   +++A   V     I+V G  LR   R
Sbjct: 6  RLDVAMVERGLAESRQKAQAIIMAGQVYVDDQKVDKAGAPVKEEQVIQVRGKTLRYVSR 64


>gi|237751452|ref|ZP_04581932.1| conserved hypothetical protein [Helicobacter bilis ATCC 43879]
 gi|229372818|gb|EEO23209.1| conserved hypothetical protein [Helicobacter bilis ATCC 43879]
          Length = 279

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/199 (18%), Positives = 70/199 (35%), Gaps = 28/199 (14%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-LRKAERTRLW 76
           K++A     S  + + +I   RV + G  L  A   +      EV   P +   E   + 
Sbjct: 40  KLLALQRNISTNKAKDLIDSGRVSIKGKRLLIARTLLPLNTKFEVLTTPCVVIFEDDDIL 99

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
              K +G+ +           +  L   +     + RLD +T G++LL  +  + +    
Sbjct: 100 ALDKSVGIES-----------YSLL-KTYPHYKLINRLDKDTSGVILLAKNEKMRQKAIQ 147

Query: 137 P--STQWLRVYRVRFHGQVDQDKLNLLKKGI-----------VIQGICYGDMQVTLDTQK 183
                +  ++Y     G+V ++    ++K I           V     Y    VT     
Sbjct: 148 AFKQKEVEKMYFALIEGKVYEEI--NIEKKISTQKDSKAKSYVDNEGLYAQSIVTPLQTF 205

Query: 184 GSNAWVTVGLREGKNREIK 202
                V+V +  G+  +I+
Sbjct: 206 THTTLVSVQIPTGRTHQIR 224


>gi|167041971|gb|ABZ06708.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_141E02]
          Length = 320

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 41/245 (16%), Positives = 81/245 (33%), Gaps = 48/245 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           + +K IV  +    R+   + +       SR  + RMI +  V++N    +     V   
Sbjct: 6   INNKVIVSRDDDGMRLDNYLIKIIKGMPKSR--IYRMIRKGEVRINSKRAK-PRSRVHVN 62

Query: 58  DHIEV----------DGVPLRKAERTRL-----------WLYHKPIGLVTTHSDPDGRST 96
           D + +          +   +RK +  R+            L +KP G +  H        
Sbjct: 63  DTVRIPPYALNEPKTNVSSVRKDDFRRINNIVIFENDSFLLVNKPSG-LAVHGGSGIHLG 121

Query: 97  VFDNL----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
           + + L          +  V RLD +T G LL++      R L       +  + Y     
Sbjct: 122 LIELLRSFREQRNEHLELVHRLDKDTSGCLLVSKKKSKLRKLHEYFREGKVQKTYLGLMV 181

Query: 151 GQVDQ---------DKLNLLKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGK 197
           G+  Q           ++  + G   +          +  L  +  ++A   +  +  GK
Sbjct: 182 GKFTQTVYEIDQPLKIISTPENGRLAVPDDSGTKAKTKFFLMEKYKNSALFKIEPIT-GK 240

Query: 198 NREIK 202
             +I+
Sbjct: 241 THQIR 245


>gi|160900713|ref|YP_001566295.1| RluA family pseudouridine synthase [Delftia acidovorans SPH-1]
 gi|160366297|gb|ABX37910.1| pseudouridine synthase, RluA family [Delftia acidovorans SPH-1]
          Length = 362

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 53/334 (15%), Positives = 105/334 (31%), Gaps = 85/334 (25%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V ++   QR+   + R      +  V R+I    V++N G +   A   V + D + +  
Sbjct: 55  VDDDSAGQRLDNFLIRHLKGVPKTHVYRIIRSGEVRINKGRV--SAETRVSTGDIVRIPP 112

Query: 65  VPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           V + +                   E   L    KP G+        G S V   +     
Sbjct: 113 VRISEKVAEKAERPAPARDFPSLLEDEHLIAIDKPAGVAV-----HGGSGVSFGVIEQLR 167

Query: 107 RVIS-------VGRLDINTEGLLLLTNDGGLARVLEL-----PSTQWLRVYRVRFHGQVD 154
           +          V RLD  T G+LL+         L          +  + Y     G   
Sbjct: 168 QARPQSRFLELVHRLDRETSGILLVA---KKRSALTHLQDQFRERETGKTYLALVQGTWP 224

Query: 155 QDK--LNL-LKKGIVIQG-----ICYGDMQ-----VTLDTQK-----------GSNAWVT 190
            +   ++L L K +   G     +   D       VTL   +            + + + 
Sbjct: 225 ANHKVIDLPLHKYLQADGERRVRVTTADDPDGMRSVTLVRVRSTLAPQPLLGLPAMSLLE 284

Query: 191 VGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLL 250
           V ++ G+  +I+         +             G    G   ++++++ ++ L    L
Sbjct: 285 VTIKTGRTHQIRVHLSSQGHPIA------------GDDKYGDF-DLNRRLQKQGLKRMFL 331

Query: 251 EEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTR 284
              ++    P         +R  + +E+P++  R
Sbjct: 332 HAWRLQFTHPASG------ERVELRAELPEELAR 359


>gi|91215096|ref|ZP_01252068.1| hypothetical protein P700755_12402 [Psychroflexus torquis ATCC
           700755]
 gi|91186701|gb|EAS73072.1| hypothetical protein P700755_12402 [Psychroflexus torquis ATCC
           700755]
          Length = 292

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/220 (12%), Positives = 63/220 (28%), Gaps = 31/220 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY------------H 79
           ++ I +  + ++G + E +   +     +E+    L   ++                  +
Sbjct: 42  KKAIKKGLLFLDGRVAETSD-WIEEGQVLELFAEELLYKKKVFPLQLKVIFEDDSMAVVN 100

Query: 80  KPIGLVTTHSDPDGRSTVFDN------LPSIFSRVISVGRLDINTEGLLLL--TNDGGLA 131
           KP G  T  +                           V RLD  T GLL++  T      
Sbjct: 101 KPEGYPTNGNYFKTIENALTYNLKTSSEKDKLPYPQPVHRLDNPTSGLLIIAKTLSSKSY 160

Query: 132 RVLELPSTQWLRVYRVRFHGQVDQ-DKLNLLKKGIVIQGICYGD---MQVTLDTQKGSNA 187
             +     +  ++Y     G  +    +  L     I G        ++      +   +
Sbjct: 161 LSVLFEHNKVHKIYLAIVEGHFEGLSDIISL----DIDGKQSSTNYGVEKMFKINQDEFS 216

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            +++    G+  +++         +      +YG   L  
Sbjct: 217 LLSLKPSSGRTHQLRIHLSKIGHPIVGDK--TYGSLTLSN 254


>gi|228990288|ref|ZP_04150255.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           pseudomycoides DSM 12442]
 gi|228769455|gb|EEM18051.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           pseudomycoides DSM 12442]
          Length = 286

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/159 (18%), Positives = 57/159 (35%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L   + R      V  V RLD +T GL+L+
Sbjct: 78  EDESVMVINKEPYMSTIPSREHPAGSVANALLYHYDRQNLASTVHIVTRLDRDTSGLMLI 137

Query: 125 TNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVI------QGICY 172
             +  +  +L       Q  R Y    HG++ ++       + +KG  I      +    
Sbjct: 138 AKNRFIHHLLSKQHQQKQVQRTYEAIVHGELLEESGTIDAPIGRKGDSIIERMVCEDGQK 197

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +      V++ L  G+  +I+    +    
Sbjct: 198 AVTHFQVMERFPDKTRVSLQLETGRTHQIRVHMAYLGHP 236


>gi|222094929|ref|YP_002528989.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
 gi|221238987|gb|ACM11697.1| pseudouridylate synthase (pseudouridine synthase) [Bacillus cereus
           Q1]
          Length = 297

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 74/220 (33%), Gaps = 35/220 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L S + +      V  V RLD +T GL+L+
Sbjct: 87  EDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLI 146

Query: 125 TNDGGLARVLE---LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGI 170
             +      L           R Y    HG            + +   +++++ +  +G 
Sbjct: 147 AKN-RFVHHLLSKQHQQKAVKRTYEAIVHGEMVEKEGTIDAPIGRKSDSIIERTVCEEGQ 205

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +D+       V++ L  G+  +I+    +    +               L  
Sbjct: 206 RAVTHFRVIDSVNHKTH-VSLELDTGRTHQIRVHMAYIGHPLLG-----------DNLYG 253

Query: 231 GSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLV 268
           G   E+ ++ L        H + E +++   PI S    +
Sbjct: 254 GKRDEMKRQALHSTSLTFYHPILEKEMSFTTPIPSDMQAI 293


>gi|57866557|ref|YP_188179.1| ribosomal large subunit pseudouridine synthase D [Staphylococcus
           epidermidis RP62A]
 gi|57637215|gb|AAW54003.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus epidermidis RP62A]
          Length = 284

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/172 (18%), Positives = 55/172 (31%), Gaps = 17/172 (9%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS 110
            S + I  D       E   L + +KP       S      +    V         ++  
Sbjct: 64  PSENLIPYDKELEVIYEDAYLIIVNKPQMQNCAPSREHPHGSLVEQVLAYYTKKGEKINP 123

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQ-----VDQDKLNLLKK 163
             V RLD NT GL++    G +  +      +  + Y    +GQ     V +  +  L  
Sbjct: 124 HIVTRLDRNTSGLVVFAKFGHVHNLFSKVKFK--KEYVALAYGQTQSSGVIEVPIARLSD 181

Query: 164 GIVI----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            I+     +   Y         Q  + +   + L  G+  +I+  FE+    
Sbjct: 182 SIIKREVNEKGKYAKTVYQKLMQNETASLCKINLLTGRTHQIRVHFEYIGHP 233


>gi|268563128|ref|XP_002646857.1| Hypothetical protein CBG19546 [Caenorhabditis briggsae]
          Length = 356

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/141 (19%), Positives = 48/141 (34%), Gaps = 14/141 (9%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHK 80
            +      R+ VNG  +      + + D +E         V  +P+R  +E   L +  K
Sbjct: 109 AKVACKMGRIYVNGEQMTDVDYVMKNGDRVEHWVHRHEHPVRDLPIRIISETDDLLVIEK 168

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDGGLA--RVLEL 136
           P  L           TV   L     +  +  + RLD  T G+LL   +          L
Sbjct: 169 PPSLPVHTCGQYAIHTVLGQLRENEEKTGLRVLHRLDRATSGVLLFAKNYETDLEFKTTL 228

Query: 137 PSTQWLRVYRVRFHGQVDQDK 157
              +W + Y  +  G    ++
Sbjct: 229 KQGEWSKEYVCKVDGVFPDEE 249


>gi|302528436|ref|ZP_07280778.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           AA4]
 gi|302437331|gb|EFL09147.1| ribosomal large subunit pseudouridine synthase [Streptomyces sp.
           AA4]
          Length = 308

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 78/243 (32%), Gaps = 39/243 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-------VNVM---- 55
           V +     RV   +A+    SR  V  + A   V ++G    ++        + V     
Sbjct: 8   VPDGLDGMRVDAGLAKLLGLSRTAVADLAAAGDVLLDGRPAGKSDRLAAGGLLEVTLPEP 67

Query: 56  --STDHIE--VDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
               + +   VDG+ +   +   + +  KP+G+    S      TV   L          
Sbjct: 68  ERPAEIVAEPVDGMKILHDDDDIVVI-SKPVGVAVHPSPGWTGPTVVGGLAAAGLRISTS 126

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG--------- 151
               R   V RLD  T G++++        VL+    +    + Y     G         
Sbjct: 127 GAAERQGVVHRLDAGTTGVMVVAKSEHAYTVLKRAFKERTVDKGYHAVVQGHPDPTRGTI 186

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              +D+   +  K  +V  G         ++  + + +   V L  G+  +I+  F    
Sbjct: 187 DAPIDRHPRHDYKFAVVAGGRPSVTHYEVVEAFRAA-SLAHVKLETGRTHQIRVHFSALR 245

Query: 210 WKV 212
              
Sbjct: 246 HPC 248


>gi|153830613|ref|ZP_01983280.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           623-39]
 gi|148873911|gb|EDL72046.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           623-39]
          Length = 315

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 74/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R + +        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQXKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|146319641|ref|YP_001199353.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|146321839|ref|YP_001201550.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|253752639|ref|YP_003025780.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|253754465|ref|YP_003027606.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|253756398|ref|YP_003029538.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|145690447|gb|ABP90953.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           05ZYH33]
 gi|145692645|gb|ABP93150.1| Pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           98HAH33]
 gi|251816928|emb|CAZ52577.1| RNA pseudouridylate synthase [Streptococcus suis SC84]
 gi|251818862|emb|CAZ56705.1| RNA pseudouridylate synthase [Streptococcus suis BM407]
 gi|251820711|emb|CAR47473.1| RNA pseudouridylate synthase [Streptococcus suis P1/7]
 gi|292559258|gb|ADE32259.1| Pseudouridylate synthase [Streptococcus suis GZ1]
 gi|319759055|gb|ADV70997.1| pseudouridylate synthase, 23S RNA-specific [Streptococcus suis
           JS14]
          Length = 288

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 78/204 (38%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTD--HIEVDGV-------PLRKAE------- 71
           R++   +  +++V+VNG L+      + + D   +  D         PL +A+       
Sbjct: 28  RKIRHFLRTKKQVRVNGELI-NWQCPITAGDLLELTFDQEDYPEKSIPLGQADLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  +DP   + +      +      V RLD+ T G +L   +  + 
Sbjct: 87  DEHLIIVNKPEGMKTHGNDPTEIALLNHVSAYVGQTCYVVHRLDMETSGAILFAKNPFIL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQV--DQDKL---------NLLKKGIVIQGICYGDMQVT 178
            +L   L      R Y     GQ+      +         +  K+ +  +       QV 
Sbjct: 147 PILNRLLEDKVIYRDYLALCQGQLKMTDWTITDKIGRDRHDRRKRVVDNRKGQTALTQVR 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
           L    G N+ V+  L+ G+  +I+
Sbjct: 207 LLKTLGKNSLVSCRLQTGRTHQIR 230


>gi|329897136|ref|ZP_08271879.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC3088]
 gi|328921394|gb|EGG28785.1| tRNA pseudouridine synthase C [gamma proteobacterium IMCC3088]
          Length = 239

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/123 (19%), Positives = 38/123 (30%), Gaps = 13/123 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G++   +  D   TVF        +  RV  + RLD  T G+L       +A
Sbjct: 17  LVAINKPPGMLVHRTKLDAHETVFALQWVRDHVGQRVYPLHRLDKATSGVLAFAKSSKVA 76

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           R       +    + Y     G  +        KG  I              +K +    
Sbjct: 77  RHWSDAWHTDAVHKDYLALVRGWPN-------SKG-TIDHPLRDPDSAPDSPRKEAETTF 128

Query: 190 TVG 192
            + 
Sbjct: 129 EII 131


>gi|260664193|ref|ZP_05865046.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii SJ-7A-US]
 gi|260562079|gb|EEX28048.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           jensenii SJ-7A-US]
          Length = 297

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 57/172 (33%), Gaps = 25/172 (14%)

Query: 64  GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------ISVG 112
             P+    E     + +KP  +++  S  +    V + +   FS+             V 
Sbjct: 76  NKPIEIVLETDNYLVINKPANVLSIPSRYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVT 135

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLL---------- 161
           RLD +T GL+L+  +               ++ Y    H   + ++   L          
Sbjct: 136 RLDRDTSGLVLVGKNAVAHSKFSELKKDVFVKEYHAIVHSNFNPEEQAGLIDAPIGKIDD 195

Query: 162 --KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ ++  G  +   Q  +  QK   + V + L  G+  +I+         
Sbjct: 196 SVKRYVIPNGQKFLT-QYEVLAQKEGASLVKLRLFTGRTHQIRVHMAHIGHP 246


>gi|327539595|gb|EGF26204.1| ribosomal large subunit pseudouridine synthase D [Rhodopirellula
           baltica WH47]
          Length = 231

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/177 (15%), Positives = 54/177 (30%), Gaps = 43/177 (24%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   L + +KP  L T  +   G+ T+         R         +  V RLD  T G+
Sbjct: 9   EDNHLLVVNKPTKLATMGA--AGQPTLHSLGCDYIRRTCNKPNKVYLGIVSRLDSMTSGV 66

Query: 122 LLLTNDGGLARVLE-----LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ 176
           +++      A  L             + Y     G+V+Q      ++G ++  +   D  
Sbjct: 67  IVMARTSKAASRLTPQFANHSGDGAKKTYLAVVPGRVEQ------QQGTLVDDVYKDDAA 120

Query: 177 VTLDTQKGSNA-------WVTVG-------------LREGKNREIKKVFEFFNWKVN 213
             +     S +          V              L  G+  +I+  +    + + 
Sbjct: 121 YRMRVAHHSRSDAKEARLEYEVSGYDRELTLLKVKPLT-GRKHQIRLQWAEAGFPIL 176


>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 = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+A SR   +R+I   +V VN   +++A   V +   + V G  L  
Sbjct: 1  MKKERLDVLLTVQGLAPSRERAKRLIMAGQVLVNEQRVDKAGATVPADAVLRVVGEDLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|301622434|ref|XP_002940545.1| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Xenopus (Silurana) tropicalis]
          Length = 497

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 49/329 (14%), Positives = 111/329 (33%), Gaps = 32/329 (9%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE--VDG-VPLRKAERTRLWLYH-------KP 81
           E+     R+++N   +    V + + D +   V    P   AE  R+   +       KP
Sbjct: 126 EQAAQAGRLRLNEETVRDLNVVLKNNDFLRNTVHRHEPPVTAEPLRILAENDEMVVIDKP 185

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELP 137
             L          +TV   L   +    + ++ RLD  T G+L+      +++ +  ++ 
Sbjct: 186 SSLPVHPCGRFRHNTVIFILGKEYNLKGLHTIHRLDRMTSGVLMFAKTLEVSKKIDEQVR 245

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+  ++++           K G+          +         G ++
Sbjct: 246 QRQLEKEYVCRVCGEFPKEEVTCEEPIFVVSYKIGVCRVDPKGKPCKTVFQRLSYNGKSS 305

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKILREQ 244
            V      G+  +I+   ++    +         ++GP +      G      + +LR  
Sbjct: 306 VVKCFPYTGRTHQIRVHLQYLGHPIVNDPIYNTEAWGPNRGKG---GEINRTDEDLLRAL 362

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQKKLATP 304
           +  H  +++   LD      + ++ +     S  P      +    Q    +++ KL   
Sbjct: 363 VDVHKSKQSLDILDISEEDLQPIMENAGLKSSTEPVQKEASEPADPQPKDEAQECKLTEN 422

Query: 305 VHRRNLASNVWMAKGIHSSFLSDSGQREE 333
           V   +  ++   +     +  S  G R+ 
Sbjct: 423 VTNSSQDTD--SSAACRITEESSQGSRDS 449


>gi|253998975|ref|YP_003051038.1| RluA family pseudouridine synthase [Methylovorus sp. SIP3-4]
 gi|253985654|gb|ACT50511.1| pseudouridine synthase, RluA family [Methylovorus sp. SIP3-4]
          Length = 333

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 76/248 (30%), Gaps = 47/248 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E    QR+   + +      +  V R++    V+VN   +  A   +   D + V  
Sbjct: 24  TVDEGSAGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNSKRI-DATYRLQLGDLVRVPP 82

Query: 65  VPLRKA-------------------ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPS 103
           + ++                     E   + +  KP G          R  +        
Sbjct: 83  IRVQPQPVAEETRPVAARFEEAVIFEDEAMLVIDKPAGFAVHGGSGVSRGVIEQLRLERP 142

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDKLN- 159
               +  V RLD  T G+L++      A V       +    + Y +   G   + K   
Sbjct: 143 HAKFLELVHRLDRETSGVLMVA-KKRSALVGLHEAMRANHMDKRYLMLVSGDWKEKKKRV 201

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWV--------TVGLRE-----GKNREIKKV 204
              L+K +   G      +VT++ +  ++  +           L E     G+  +++  
Sbjct: 202 VLALQKHVTANGER----KVTVEEEGQNSETIFHLKKSYGEFTLLEAQLITGRTHQLRVQ 257

Query: 205 FEFFNWKV 212
                + +
Sbjct: 258 LAHLGFPI 265


>gi|163739478|ref|ZP_02146888.1| Pseudouridine synthase, RluD [Phaeobacter gallaeciensis BS107]
 gi|163740271|ref|ZP_02147665.1| ribosomal large subunit pseudouridine synthase C [Phaeobacter
           gallaeciensis 2.10]
 gi|161386129|gb|EDQ10504.1| ribosomal large subunit pseudouridine synthase C [Phaeobacter
           gallaeciensis 2.10]
 gi|161387231|gb|EDQ11590.1| Pseudouridine synthase, RluD [Phaeobacter gallaeciensis BS107]
          Length = 348

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 41/201 (20%), Positives = 67/201 (33%), Gaps = 52/201 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQ-------RVKVN-----GI 45
            V E+   QR+ + +       RR         +E+M  +        RVK N     G 
Sbjct: 8   TVSEDDADQRIDRWL-------RRLFPHVSQGRIEKMCRKGELRLDGGRVKANSRVAAGQ 60

Query: 46  LLERA-------------AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-----T 87
           ++                +  +   D   + G  + K +   + + +KP GL       T
Sbjct: 61  VVRVPPLGASDLKPAEAPSYRISEADAKMIRGCVIYKDDA--VIVLNKPAGLAVQGGSGT 118

Query: 88  HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVY 145
               DG S           R+  V RLD +T G+L+L      A+ L          ++Y
Sbjct: 119 TKHVDGLSAALQFDAEEKPRL--VHRLDKDTSGVLVLARTRLAAQSLTAAFRHRATRKIY 176

Query: 146 RVRFHGQVDQDKLNLLKKGIV 166
                G      L  +K G+V
Sbjct: 177 WALVAGVPTP-YLGEIKCGLV 196


>gi|33151828|ref|NP_873181.1| 23S rRNA pseudouridylate synthase C [Haemophilus ducreyi 35000HP]
 gi|34395752|sp|P59835|RLUC_HAEDU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|33148049|gb|AAP95570.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           ducreyi 35000HP]
          Length = 320

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 81/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV- 62
            + ++   QR+   + A+     +  + R++ +  V+VN G +  +    +   D + + 
Sbjct: 15  TISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRV--KPDYKLQHNDIVRIP 72

Query: 63  -------DGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
                  +  P+                E   + + +KP G+            +     
Sbjct: 73  LVRVTPKNEAPISTKLNKVAELEQHILYEDDVMLVLNKPSGIGVHGGSGLSFGVIEALRA 132

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V R+D +T G+LL+       R L   L      + Y     GQ  Q  +
Sbjct: 133 LRPQARFLELVHRIDRDTSGILLVAKKRSALRALHEQLREKVVQKDYLALVRGQW-QAHI 191

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           N++K  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 192 NVIKAPL-LKNELQSGERIVKVSEQGKPSETRFSIEERYPNATLIKASPITGRTHQIR 248


>gi|317502895|ref|ZP_07960993.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
 gi|315666001|gb|EFV05570.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           salivae DSM 15606]
          Length = 300

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 37/196 (18%), Positives = 62/196 (31%), Gaps = 30/196 (15%)

Query: 37  QQR-VKVNGILLERAAVNVMSTDHIEVDGVPLR-----------KAERTRLWLYHKPIGL 84
           Q R +KV   ++ +    V     I V                   E   L +  K IG+
Sbjct: 45  QGRGIKVESKVITKFDYPVSPGMKISVSRTKRNNDIFKSRYVKIVYEDRYLVVVEKNIGI 104

Query: 85  VT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLELPST 139
           ++    HS  + ++ + D       +     V RLD +T GL++   D     +LE    
Sbjct: 105 LSMAAGHSTLNVKTILDDYFKKSRQKCTAHVVHRLDRDTSGLMIYAKDKQTEMLLEQDWH 164

Query: 140 QW--LRVYRVRFHGQV--DQDKLNLLKKGI---------VIQGICYGDMQVTLDTQKGSN 186
                R Y     G +   +  +    K           V  G  Y      +  Q    
Sbjct: 165 HIVYDRRYVAVVSGVIEAPEGTIANWLKDNKAYITYSSPVDNGGKYAVTHFHVLGQNNDY 224

Query: 187 AWVTVGLREGKNREIK 202
           + V   L  G+  +I+
Sbjct: 225 SLVEYKLETGRKNQIR 240


>gi|294666973|ref|ZP_06732202.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
 gi|292603262|gb|EFF46684.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 10535]
          Length = 331

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 58/323 (17%), Positives = 111/323 (34%), Gaps = 45/323 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           IV +N   +R   V+A      SR  +   I      ++G +       +   + ++V  
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMAR-PRDTLRGGESVQVQV 75

Query: 64  -----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIF 105
                       +PL    E  ++ +  KP GLV      +   T+       D   +  
Sbjct: 76  VLETQTHAAPQDIPLSVLYEDEQVLVIDKPAGLVVHPGAGNPDRTLVNALLFRDPALASV 135

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD +T G++++         L  +L + +  R Y     G           +
Sbjct: 136 PRSGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREVHRQYLAVVVGALVSGGTANAPI 195

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D+   + LK  +   G          +  +   A +   L  G+  +I+         + 
Sbjct: 196 DRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHLKSPIV 254

Query: 214 R--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLV 268
              L    YG   L  L  G+T E+  ++    R+ L    LE        P+ +S  + 
Sbjct: 255 GDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLEFLHPVSGEPVRASAPVP 308

Query: 269 RDRPNIISEVPDDFTRMKKNSSQ 291
            D   +++ + +D  R  + + +
Sbjct: 309 ADLQRLMTVLREDSARAAELARR 331


>gi|153952071|ref|YP_001397292.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
 gi|152939517|gb|ABS44258.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. doylei 269.97]
          Length = 300

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 72/199 (36%), Gaps = 31/199 (15%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEEKNKILKGLVELIVYENNPKGVEIVF-ENENFAILEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKGACVAHRLDKETSGLILVAKNKKAQIDLKSLFEKKLV 147

Query: 142 LRVYRVRFHGQVDQDKL--NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---- 195
            + Y    HG+++++ +    +        +    MQ+    ++G  A     + E    
Sbjct: 148 QKEYLALAHGKIEKNFIVDKAINLAKNYDDVKTR-MQI---CKEGKQAITEFKILEYFPK 203

Query: 196 ------------GKNREIK 202
                       G+  +I+
Sbjct: 204 INATLLLCKPLTGRQHQIR 222


>gi|314938511|ref|ZP_07845796.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|314942472|ref|ZP_07849312.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|314949504|ref|ZP_07852839.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
 gi|314952915|ref|ZP_07855882.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|314992184|ref|ZP_07857627.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|314995258|ref|ZP_07860370.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313590514|gb|EFR69359.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a01]
 gi|313593242|gb|EFR72087.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133B]
 gi|313594987|gb|EFR73832.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133A]
 gi|313598780|gb|EFR77625.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0133C]
 gi|313642139|gb|EFS06719.1| pseudouridine synthase, RluA family [Enterococcus faecium
           TX0133a04]
 gi|313644118|gb|EFS08698.1| pseudouridine synthase, RluA family [Enterococcus faecium TX0082]
          Length = 299

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 56/148 (37%), Gaps = 16/148 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 100 EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVLFAK 159

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D            +  K+ +  +      
Sbjct: 160 NPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDMTITNKIGRDRHDRRKRVVDDKNGQSAL 219

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             VT++        V   L  G+  +I+
Sbjct: 220 THVTVNKVLSEQTQVYCVLETGRTHQIR 247


>gi|21243943|ref|NP_643525.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|294625813|ref|ZP_06704430.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
 gi|34395784|sp|Q8PHN2|RLUD_XANAC RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21109553|gb|AAM38061.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           axonopodis pv. citri str. 306]
 gi|292599888|gb|EFF44008.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           fuscans subsp. aurantifolii str. ICPB 11122]
          Length = 331

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 58/323 (17%), Positives = 111/323 (34%), Gaps = 45/323 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           IV +N   +R   V+A      SR  +   I      ++G +       +   + ++V  
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMAR-PRDTLRGGESVQVQV 75

Query: 64  -----------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIF 105
                       +PL    E  ++ +  KP GLV      +   T+       D   +  
Sbjct: 76  VLETQTHAAPQDIPLSVLYEDEQVLVIDKPAGLVVHPGAGNPDRTLVNALLFRDPALASV 135

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QV 153
            R   V RLD +T G++++         L  +L + +  R Y     G           +
Sbjct: 136 PRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREVHRQYLAVVVGALVSGGTANAPI 195

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           D+   + LK  +   G          +  +   A +   L  G+  +I+         + 
Sbjct: 196 DRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHLKSPIV 254

Query: 214 R--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLV 268
              L    YG   L  L  G+T E+  ++    R+ L    LE        P+ +S  + 
Sbjct: 255 GDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLEFLHPVSGEPVRASAPVP 308

Query: 269 RDRPNIISEVPDDFTRMKKNSSQ 291
            D   +++ + +D  R  + + +
Sbjct: 309 ADLQRLMTVLREDSARAAELARR 331


>gi|256027210|ref|ZP_05441044.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289765187|ref|ZP_06524565.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
 gi|289716742|gb|EFD80754.1| tRNA pseudouridine synthase A [Fusobacterium sp. D11]
          Length = 304

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 96/254 (37%), Gaps = 55/254 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
           I+ E++   RV + +       R+        E+ +M+ + ++KVN   + +    ++  
Sbjct: 5   IIDEDYESVRVDRFL-------RKHLKNINLSEIYKMLRKGKIKVNNKKISQ-DYRLVLG 56

Query: 58  DHI--------------------EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGR 94
           D I                    +V    L++    +   L++ +KP+G V  H      
Sbjct: 57  DIIFIFLPETFKEQNEEKFIELSQVRKEKLKQMIVFQNDNLFVINKPLGDVV-HKGSGHD 115

Query: 95  STVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH 150
            ++ +   S +S   +  V R+D  T GL++   +   AR +  E+ +   ++ Y +  +
Sbjct: 116 ISLLEEFRSYYSNNNINFVNRIDKLTSGLVIGAKNIKTAREIAKEIQTGNIVKKYYILVN 175

Query: 151 GQVDQD------KLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G++++D       L   ++ +++     +G            +      +   L+ G+  
Sbjct: 176 GKIEKDNFILENYLKKDEERVIVSDIEKEGYKKSITYFKKIKEYDKYTLLEAELKTGRTH 235

Query: 200 EIKKVFEFFNWKVN 213
           +++         + 
Sbjct: 236 QLRAQLNHLGNNIV 249


>gi|261200229|ref|XP_002626515.1| DRAP deaminase [Ajellomyces dermatitidis SLH14081]
 gi|239593587|gb|EEQ76168.1| DRAP deaminase [Ajellomyces dermatitidis SLH14081]
 gi|239607533|gb|EEQ84520.1| DRAP deaminase [Ajellomyces dermatitidis ER-3]
 gi|327352524|gb|EGE81381.1| DRAP deaminase [Ajellomyces dermatitidis ATCC 18188]
          Length = 549

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/163 (16%), Positives = 53/163 (32%), Gaps = 24/163 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ I    V +NG  +      + + D I          V   P+    E   + +  KP
Sbjct: 82  QKAIEDGAVCINGKAV-SIDTKIQNGDVISHTLHRHEPPVTSQPIGIIHEDNDMIVIDKP 140

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     ++V + + +            RLD  T G++ +      A  +  +L
Sbjct: 141 AGVPVHPAGRYNYNSVLEIMKAERGNGWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKL 200

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
            S    + Y  R  G+           G+V+       +   L
Sbjct: 201 RSRTVRKEYVARVKGKFPD--------GVVLCDQPMLKISPIL 235


>gi|225619476|ref|YP_002720733.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           hyodysenteriae WA1]
 gi|225214295|gb|ACN83029.1| ribosomal large subunit pseudouridine synthase C [Brachyspira
           hyodysenteriae WA1]
          Length = 345

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/239 (16%), Positives = 74/239 (30%), Gaps = 42/239 (17%)

Query: 5   NIVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI--- 60
            I ++     R+ K +       SR + + +I Q  V +N   ++     V   D I   
Sbjct: 25  RIEEDVEENTRIDKYMGDRFSYYSRNKWQDLIGQGLVLLNNSKVKYTRT-VKKGDEIAYH 83

Query: 61  -------EVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVG 112
                  EVD       +   L + +KP  L    S     +T+   + ++  S +  + 
Sbjct: 84  IIGMKEPEVDKNVTIVYDDGDLIIANKPANLPVIPSGKYYHNTLHTIVKNMLNSNINMLN 143

Query: 113 RLDINTEGLLLLTNDGGLARVLELP------------STQWLRVYRVRFH--GQVDQDKL 158
           R+D  T G ++L+     A                       + Y         ++    
Sbjct: 144 RIDRETSGCVVLSRSSKSASNFCAMLAGRKVNGKQYKRNSIKKTYIAVIENAKDIEDKFT 203

Query: 159 N---LLKKGIV------------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +L+ G              ++G  Y         + G  A V   L  G+  +I+
Sbjct: 204 VEGYMLESGHEYYRRFQTLHKENVEGSKYSKTSFKTIKRIGDYAVVMARLYTGRMHQIR 262


>gi|193076604|gb|ABO11275.2| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 17978]
          Length = 350

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 94/256 (36%), Gaps = 50/256 (19%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           + E++  QR+ +V A      SR ++++ + +  + VNG +++         + + ++  
Sbjct: 43  LDESYLGQRIDQVAAMVWSEFSREKLKQWMKEGHLLVNGNIVK-PKYRCEGNETLTLNVE 101

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFS 106
                      +PL    E   + + +KP+G+V      +  ST+ + L       +  S
Sbjct: 102 LEAQTNSQPENIPLDIVYEDEDILVINKPVGMVVHPGAGNTSSTLVNALLYHSPKSAELS 161

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           R   V R+D +T GLL++  +      L   L      R+Y +  +G +       +  G
Sbjct: 162 RAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYGNI-------IAGG 214

Query: 165 IVIQGICYGDMQ----VTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFF 208
            + + I    +       L   + +     V             L  G+  +I+  F + 
Sbjct: 215 TIDEPIKRHPVDRVKMAILPGGRDAVTHYNVKERFRDFTRVQAQLETGRTHQIRVHFSYI 274

Query: 209 NWKV----NRLIRISY 220
              +      + R+  
Sbjct: 275 GHGLVGDQVYMNRVRI 290


>gi|78048898|ref|YP_365073.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325929044|ref|ZP_08190199.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           perforans 91-118]
 gi|78037328|emb|CAJ25073.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325540577|gb|EGD12164.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           perforans 91-118]
          Length = 331

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 58/328 (17%), Positives = 108/328 (32%), Gaps = 55/328 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGI-----------------LL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGEMARPRDTLRGGESVQLQVV 76

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF------DN 100
                +    D       PL    E  ++ +  KP GLV      +   T+       D 
Sbjct: 77  LETQTHAAPQDI------PLSVLYEDEQVLVIDKPAGLVVHPGAGNPDQTLVNALLFRDP 130

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
             +   R   V RLD +T G++++         L  +L + +  R Y     G       
Sbjct: 131 ALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSAREVHRQYLAVVVGALVSGGT 190

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D+   + LK  +   G          +  +   A +   L  G+  +I+      
Sbjct: 191 VNAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHL 249

Query: 209 NWKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYS 263
              +    L    YG   L  L  G+T E+  ++    R+ L    LE        P+ +
Sbjct: 250 KSPIVGDPL----YGG-ALK-LPKGATDELVHELRSFKRQALHAETLEFLHPVSGEPVRA 303

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           S  +  D   +++ + +D  R  + + +
Sbjct: 304 SAPVPADLQRLMTVLREDSARAAELARR 331


>gi|254525135|ref|ZP_05137190.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
 gi|219722726|gb|EED41251.1| pseudouridylate synthase [Stenotrophomonas sp. SKA14]
          Length = 247

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/156 (21%), Positives = 55/156 (35%), Gaps = 29/156 (18%)

Query: 72  RTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
             RL + +KP GL+   S         + D L     R +  V RLD  T G LLL  D 
Sbjct: 24  DERLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLLLAFDR 83

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGD--MQVTLDTQ 182
             A  L   L   + L+ Y     G   +   +++       + G            D Q
Sbjct: 84  DTASALGKALMGGEVLKDYLTVCRGWPAELSWQVDH-----DLDGGPGKPVKKPAITDFQ 138

Query: 183 KGSNAWVTVGLRE---------------GKNREIKK 203
           + +   ++V + E               G+ R+I++
Sbjct: 139 RLATGELSVPIGEFSSSRYALLRCQPQTGRFRQIRR 174


>gi|157149723|ref|YP_001451260.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii str. Challis substr. CH1]
 gi|157074517|gb|ABV09200.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gordonii str. Challis substr. CH1]
          Length = 290

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/205 (17%), Positives = 70/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTD--HIEVD-----------GVP---LRKAE 71
           R++   +  ++ V VN   +      + + D   +  D           G P       +
Sbjct: 28  RKIRHFLRTKKHVLVNDQTI-NWQSKIQAGDLLSLTFDEEDYPAKAILMGQPELVQELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ T  ++P   + +      +      V RLD  T G +L   +    
Sbjct: 87  DQHLIIVNKPEGMKTHANEPTELALLNHVSAYVGETCYVVHRLDKETSGTVLFAKNPFVL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQV 177
            +   L   +    R Y     G           ++ +D+ +  K+ +  +   Y +  V
Sbjct: 147 PILNRLL-ENKDIQREYWALVDGKFIEKSRIYKDKIGRDRHDRRKRLVDNKHGQYAETHV 205

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
           T     G    V   L+ G+  +I+
Sbjct: 206 TRLKSFGQKTLVKCQLKTGRTHQIR 230


>gi|57169014|ref|ZP_00368142.1| RNA pseudouridylate synthase family [Campylobacter coli RM2228]
 gi|57019559|gb|EAL56249.1| RNA pseudouridylate synthase family [Campylobacter coli RM2228]
          Length = 336

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 53/137 (38%), Gaps = 9/137 (6%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKA---ERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     ++  D   I  +  P       E     +  K  G+
Sbjct: 67  EAQKLIDKKRLFCDGILVEE-KNKILKGDVELIVYENNPKGVEIVFENEDFAVLEKESGI 125

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +      +     RLD  T GL+L+         L       Q 
Sbjct: 126 LSHPNGRHCKYSLSDEIWHLWGKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQI 185

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y     G++  + +
Sbjct: 186 QKEYLALASGEIKVNFI 202


>gi|319787308|ref|YP_004146783.1| pseudouridine synthase [Pseudoxanthomonas suwonensis 11-1]
 gi|317465820|gb|ADV27552.1| pseudouridine synthase, RluA family [Pseudoxanthomonas suwonensis
           11-1]
          Length = 319

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 47/250 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E+   QR+   +  +   A R  V +++   +V+VNG   + A   +   D + +  
Sbjct: 14  TVPEDRDGQRLDNFLLGQLKGAPRSLVYKLVRSGQVRVNGGRAK-AERKLAGGDEVRIPP 72

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP---DGRSTVFDNL 101
           V +                       E  R+ +  KP G+ +            T+    
Sbjct: 73  VRVETEAERGTPAPGLLQRMEASIVFEDARILVIDKPSGVASHGGSGISFGAIETLRALR 132

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE------LPSTQWLRVYRVRFHGQVDQ 155
           P     +    RLD +T G+L++         L+             + Y     G++  
Sbjct: 133 PG--QTLELAHRLDRDTSGILVVAKKRSALAELQALMREGGSGGGIRKRYLTLLAGRMPD 190

Query: 156 DKLNL-------LKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
             +++       L++G      +   G         L+ + G  ++  V +  G+  +I+
Sbjct: 191 GTMSVDAPLHVGLRQGGERHVQVNQAGKPSVSHFRALERRGG-QSYCEVRIETGRTHQIR 249

Query: 203 KVFEFFNWKV 212
              +     V
Sbjct: 250 VHAQHIGHPV 259


>gi|152974818|ref|YP_001374335.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152023570|gb|ABS21340.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 307

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VN    +R +  +   D ++V              G      E   + + +KP  + T
Sbjct: 47  VIVNNEQ-KRWSELLKEGDKLQVHMFIPEEYGVIPEFGELDVVFEDDHVLIVNKPEQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+ +G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKNGTGTLANLIAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRLAGAIMDQLL-M 164

Query: 138 STQWLRVYRVRFHGQ-----------VDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKGS 185
                R Y     G+           + +D+ +  ++ +  +G        V    ++  
Sbjct: 165 ERNIKRTYMALVEGKMKKRKGTIDAAIGRDRHHATRRRVSPKGDRAVTHYTVEEYFKRQD 224

Query: 186 NAWVTVGLREGKNREIK 202
              VTV L  G+  +I+
Sbjct: 225 TTLVTVQLETGRTHQIR 241


>gi|116492157|ref|YP_803892.1| pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
 gi|116102307|gb|ABJ67450.1| Pseudouridylate synthase, 23S RNA-specific [Pediococcus pentosaceus
           ATCC 25745]
          Length = 296

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 87/229 (37%), Gaps = 40/229 (17%)

Query: 11  FTPQRVSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVDGV---- 65
           + PQ + +++ R  + SR+ V  + I + RV VNG  +      V   D IE++      
Sbjct: 13  YQPQSLRELLQRTWLLSRKIVHFLRINE-RVLVNGKYV-PVNTIVQGGDLIELNFESSDF 70

Query: 66  --------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV--- 108
                         P+   E + L + +KP G+ T  + P    ++ + L + F      
Sbjct: 71  DTPLPPFDPDFTQAPIILYENSDLMVVNKPTGVKTHANQPHELGSMMNFLQAYFKDTENE 130

Query: 109 -ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGI 165
             +V RLD  T G LL+  +  +  +L    +     R Y     G ++Q K   +   I
Sbjct: 131 AYNVHRLDQFTSGALLVAKNPVVVPILNRQISTKVINRTYLCVVSGHLEQSK-GTINVPI 189

Query: 166 VIQGICYGDMQV------------TLDTQKGSNAWVTVGLREGKNREIK 202
                     Q+             +  Q  +++ + V L  G+  +I+
Sbjct: 190 GFDPDDKRKRQINGLNPLSAITHYQVLAQYENSSLIQVDLETGRTHQIR 238


>gi|332686149|ref|YP_004455923.1| ribosomal large subunit pseudouridine synthase D [Melissococcus
           plutonius ATCC 35311]
 gi|332370158|dbj|BAK21114.1| similar to ribosomal large subunit pseudouridine synthase D
           [Melissococcus plutonius ATCC 35311]
          Length = 290

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 40/213 (18%), Positives = 75/213 (35%), Gaps = 43/213 (20%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------------E 71
           R+V   +  ++ V +N   +      V + D I +                        E
Sbjct: 28  RKVRHFLRIRKNVLLNNQPV-LFHQTVSANDQITLKFEKEDYQIPTIHAGNSKLVHVLFE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP+G+ T  + PD   T+ ++L +           V RLD  T G +L   +
Sbjct: 87  DEHLIIINKPVGMKTHPNQPDENDTLLNHLTAYLKPKQQIPYVVHRLDKETSGAILFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
             +  +L   L   Q  R Y+    G V ++   + KK   I    +   +  +D++ G 
Sbjct: 147 PFVLPILGRMLEKKQIYRCYQAIVDGIVLKNTWTITKK---IGRDRHDRRKRIIDSKHGM 203

Query: 186 NAWVTV----GLRE------------GKNREIK 202
            A   +     L +            G+  +I+
Sbjct: 204 IAITHIQKAFTLTQENKTALLCRLETGRTHQIR 236


>gi|319779244|ref|YP_004130157.1| Ribosomal large subunit pseudouridine synthase C [Taylorella
           equigenitalis MCE9]
 gi|317109268|gb|ADU92014.1| Ribosomal large subunit pseudouridine synthase C [Taylorella
           equigenitalis MCE9]
          Length = 310

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/204 (15%), Positives = 65/204 (31%), Gaps = 37/204 (18%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKAERT---------------RLW 76
           + I   +V+VN G +       + + D I +    L + +                    
Sbjct: 40  KAIRSGQVRVNKGRVNSE--CRIHTGDEIRIPPFRLPQEQPKSFIPTRNFDIIFEDDYFL 97

Query: 77  LYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           + +KP G+            +            +  V RLD  T GLL++         L
Sbjct: 98  IINKPAGVAVHGGSGVSYGVIEQIRTSRPDSKFLELVHRLDKETSGLLIIAKKRSALVAL 157

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDKLNLLK---------KG-----IVIQGICYGDMQVT 178
              +  ++  + Y     G    +KL  +K         +G     +  +   Y   +V 
Sbjct: 158 QDMIRQSKLHKSYYALIKGNWP-EKLKDIKLPLYKYLTPQGERRVKVDAENGKYAHSKVR 216

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
              + G    ++V +  G+  +I+
Sbjct: 217 KVEKVGEFELLSVQILTGRTHQIR 240


>gi|332876323|ref|ZP_08444096.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6014059]
 gi|322507012|gb|ADX02466.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 1656-2]
 gi|323516880|gb|ADX91261.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332735474|gb|EGJ66528.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii 6014059]
          Length = 350

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 42/256 (16%), Positives = 93/256 (36%), Gaps = 50/256 (19%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-- 63
           + E++  QR+ +V A      SR ++++ + +  + VNG +++         + + ++  
Sbjct: 43  LDESYLGQRIDQVAAMLWSEFSREKLKQWMKEGHLLVNGNIVK-PKYRCEGNETLTLNVE 101

Query: 64  ----------GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL------PSIFS 106
                      +PL    E   + + +KP+G+V      +   T+ + L       +  S
Sbjct: 102 LEAQTNSQPENIPLDIVYEDEDILVINKPVGMVVHPGAGNTSGTLVNALLYHSPKSAELS 161

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKG 164
           R   V R+D +T GLL++  +      L   L      R+Y +  +G +       +  G
Sbjct: 162 RAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLGDKSVYRIYDLVTYGNI-------IAGG 214

Query: 165 IVIQGICYGDMQ----VTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFF 208
            + + I    +       L   + +     V             L  G+  +I+  F + 
Sbjct: 215 TIDEPIKRHPVDRVKMAILPGGRDAVTHYNVKERFRDFTRVQAQLETGRTHQIRVHFSYI 274

Query: 209 NWKV----NRLIRISY 220
              +      + R+  
Sbjct: 275 GHGLVGDQVYMNRVRI 290


>gi|269791933|ref|YP_003316837.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269099568|gb|ACZ18555.1| pseudouridine synthase [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 302

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 85/258 (32%), Gaps = 55/258 (21%)

Query: 7   VQENFTPQRVSKVI------ARAGIASRREVERM--IAQQRVKVNGILLERAAVNVMSTD 58
           +  +   +R+ ++I         G+       RM  I + +V+++G  +   +  ++   
Sbjct: 6   IPPDQEGRRLDRLIREWWPEVNMGL-------RMGAIRRGQVRLDGRRV-PCSQRLLEGQ 57

Query: 59  HIEV-----------------DGVPLRK---AERTRLWLYHKPIGLVTTHSDPDGRST-- 96
            + V                 +G  L +       RL + +KP G +       G S   
Sbjct: 58  ELTVPWDQEPRRSGSGTPCPAEGRELPRWVIHWDRRLLVANKPAGWICQPGGGRGTSLPE 117

Query: 97  -VFDNLPSIFSRVISVGRLDINTEGLLLLTND---GGLARVLELPSTQWLRVYRVRFHGQ 152
            V+  L  +    +   RLD+NT G++L+  D   G     L    T   ++Y     G 
Sbjct: 118 EVWRLL-GVDRGPVPSHRLDVNTTGVVLVPLDGALGRELHRLFREGT-IRKLYWALVRGT 175

Query: 153 VDQDKLNLLK-----KGIVIQGICYGDMQ--VTLDTQKGSNAWVTVGLREGKNREIKKVF 205
              + L  L      +G V         +  V     +G  + V V L  G+  + +   
Sbjct: 176 CVGEALVDLPLSKDGRGNVTPSPSGQPARSVVRPLAVRGGFSLVEVELLTGRQHQARVHL 235

Query: 206 EFFNWK----VNRLIRIS 219
                     V   +R  
Sbjct: 236 AHLGLPILGDVRYGVRFR 253


>gi|15827611|ref|NP_301874.1| pseudouridine synthase [Mycobacterium leprae TN]
 gi|221230088|ref|YP_002503504.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
 gi|4539134|emb|CAB39580.1| putative pseudouridine synthase [Mycobacterium leprae]
 gi|13093162|emb|CAC31581.1| putative pseudouridine synthase [Mycobacterium leprae]
 gi|219933195|emb|CAR71295.1| putative pseudouridine synthase [Mycobacterium leprae Br4923]
          Length = 308

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 89/260 (34%), Gaps = 45/260 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-------V 52
           M D+++ + E     RV   +AR    SR  V  +     V+++G+   ++        +
Sbjct: 1   MTDRSMPIPEGLAGMRVDAGLARLLGLSRTAVAALAEDGGVELDGVQAGKSDRLTSGAWL 60

Query: 53  NV--------MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            V        +    ++++ + +  ++   +    KP  +    S      TV   L + 
Sbjct: 61  QVRLCEAPAPLENTPVDIEDMTILYSDDD-IVAVDKPAAVAAHASVGWAGPTVLGGLAAA 119

Query: 105 FSRVI---------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
             R+           V RLD+ T G++L+        VL+         + Y     G  
Sbjct: 120 GYRITTSGVPERQGIVHRLDVGTSGVMLVAISERAYTVLKRAFKCRTVDKRYHALVQGHP 179

Query: 154 DQDKLNLLK-----KGIVIQGICYGDMQVTL---DTQKG--SNAWVTVGLREGKNREIKK 203
           D     +       +G   +     D + ++   DT +   + + + V L  G+  +I+ 
Sbjct: 180 DPSSGTIDAPIGRHRGHTWKFAVTKDGRHSITHYDTLEAFVAASLLDVHLETGRTHQIR- 238

Query: 204 VFEFFNWKVNRLIRISYGPF 223
               F      L R   G  
Sbjct: 239 --AHF----AELHRPCCGDL 252


>gi|84500882|ref|ZP_00999117.1| putative Pseudouridine synthase, Rlu [Oceanicola batsensis
           HTCC2597]
 gi|84390949|gb|EAQ03367.1| putative Pseudouridine synthase, Rlu [Oceanicola batsensis
           HTCC2597]
          Length = 339

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 76/254 (29%), Gaps = 56/254 (22%)

Query: 13  PQRVSKVIAR----AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------ 62
           P R+ K +AR    A   SR  + R+IA   V   G  +      V   D IE+      
Sbjct: 17  PARLDKALARDVPEAAALSRTRIARLIAGGAVARAGAAVTDPKARVAEGDVIEITLGAAA 76

Query: 63  ------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF---------- 105
                   +PL    E   L +  KP+G+V   +      T+ + L              
Sbjct: 77  EVETRPQAIPLDVVYEDAALIVVDKPVGMVVHPAPGTPEGTLVNALLHHCGDSLSGIGGE 136

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKLNL--- 160
            R   V R+D +T GLL+          L     +    R Y    HG  D     L   
Sbjct: 137 RRPGIVHRIDKDTSGLLVAAKTDRAHHALAAQFERHSAERAYLAICHGVPDAADPRLRGV 196

Query: 161 ----LKKG--------------------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
                + G                    +  +G  +   +  +    G  A +   L  G
Sbjct: 197 RGASFEPGGVLKLTTQLARHRTDRQRQAVCFEGGRHAVTRARVLEGFGGAALLECRLETG 256

Query: 197 KNREIKKVFEFFNW 210
           +  +I+        
Sbjct: 257 RTHQIRVHMAHAGH 270


>gi|325684453|gb|EGD26617.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp. lactis
           DSM 20072]
          Length = 302

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 47/255 (18%), Positives = 85/255 (33%), Gaps = 56/255 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE---VERMIAQQRVKVNGILLERAAVNVMST 57
           M+   ++     P ++S  + + G  SRR     +       + VN       +  +   
Sbjct: 1   MQVYKMIVAKNDPGQLSHFLLKKGF-SRRAVNNCKN--HGGMMLVNHHR-RNGSYRLKEG 56

Query: 58  DHI-------------EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D +             +V  +PL   E T    + +KP GL++  S       V + + +
Sbjct: 57  DVVHFLMGQEPVNPWLKVSRLPLDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLA 116

Query: 104 IFSRV---------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVR 148
            F +            V RLD +T GL+LL   G     +       L      + Y   
Sbjct: 117 YFEKQGVNPAYVKPHIVTRLDQDTSGLVLL---GK--NAIAHDRFSKLGKDAFIKKYHAI 171

Query: 149 FHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            HG   +  L+ L            K+ +  +G         LD   G+ + V + L  G
Sbjct: 172 VHGNFAEGDLSGLIDKPLARVGDTVKREVNPKGQRALTEYRVLDQVPGA-SLVELRLLTG 230

Query: 197 KNREIK-KVFEFFNW 210
           +  +I+  +      
Sbjct: 231 RTHQIRIHM-ASIGH 244


>gi|308049100|ref|YP_003912666.1| ribosomal large subunit pseudouridine synthase C [Ferrimonas
           balearica DSM 9799]
 gi|307631290|gb|ADN75592.1| ribosomal large subunit pseudouridine synthase C [Ferrimonas
           balearica DSM 9799]
          Length = 320

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 77/243 (31%), Gaps = 56/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R  ++        R++ +  V+VN   ++     +   D
Sbjct: 17  ITEDHAGQRIDNFL-------RTFLKGVPKSLIYRLLRKGEVRVNKKRIK-PEYKLADGD 68

Query: 59  HIEVDGVPLRKA----------------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
            I +  + + +                       E   + + +KP G+            
Sbjct: 69  QIRIAPIRVSERDETVAPSAKLEKVAQLESQIVYEDKVMLVINKPSGIAVHGGSGINFGV 128

Query: 97  VFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
           +     L     ++  V RLD  T GLL++       + L+         + Y     GQ
Sbjct: 129 IEALRALRPNERQLELVHRLDRATSGLLMVAKRRSALKHLQDQLREKTMRKQYLALVKGQ 188

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLD-TQKGSNAWVTV-------GLRE-----GKNR 199
            +      ++  ++   +  G+  V +D   K S     +        L E     G+  
Sbjct: 189 WNPKT-RAVQAPLLKNTLGTGERLVRVDAAGKPSETRFRIVENFAEGTLVECSPITGRTH 247

Query: 200 EIK 202
           +I+
Sbjct: 248 QIR 250


>gi|188996824|ref|YP_001931075.1| hemolysin A [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188931891|gb|ACD66521.1| hemolysin A [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 268

 Score = 52.1 bits (124), Expect = 1e-04,   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|330720408|gb|EGG98730.1| Ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium IMCC2047]
          Length = 330

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 85/241 (35%), Gaps = 54/241 (22%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN------------GILLERAAVN 53
           + E+   QR+   + AR     R  + R++ +  V+VN            G ++    + 
Sbjct: 29  ITEDSAGQRIDNFLCARLKGVPRTRIYRIVRKGEVRVNKGRIKADYKLQSGDVVRVPPIR 88

Query: 54  VMSTDHIEVDGVPLRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           V   + +   G  L++A       E   L + +KP GL        G S +   L     
Sbjct: 89  VAEANELPQAGKGLKEALEQAVLYEDDSLLIINKPSGLAV-----HGGSGIKLGLIETLR 143

Query: 107 RVIS-------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------ 151
           ++         V RLD +T G +++     + R L   L +    + Y+    G      
Sbjct: 144 QLRPEARFLELVHRLDRDTSGCVMVAKKRSMLRYLHDLLRTNGVTKHYQALVVGKWPTRK 203

Query: 152 -----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREI 201
                 + ++ L   ++ +V       D + +L   +    +    L +     G+  +I
Sbjct: 204 HKVDVPLQKNTLQSGERMVVAD----PDGKPSLTRYEVRQRFSGYTLVQAYPVSGRTHQI 259

Query: 202 K 202
           +
Sbjct: 260 R 260


>gi|295114100|emb|CBL32737.1| pseudouridine synthase, RluA family [Enterococcus sp. 7L76]
          Length = 283

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 24  RKVRHFLRTRKNVKINGETAT-FHFPVQAGDCVTLTFEETDYVFPTIHLGEATRVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>gi|254448155|ref|ZP_05061618.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HTCC5015]
 gi|198262281|gb|EDY86563.1| ribosomal large subunit pseudouridine synthase C [gamma
           proteobacterium HTCC5015]
          Length = 321

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 56/303 (18%), Positives = 90/303 (29%), Gaps = 70/303 (23%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTD- 58
            K  V +    QR+   +   G      R  V R++ +  V+VNG   ++    + S D 
Sbjct: 13  QKLTVPDEAVGQRIDNFL--MGYWKGVPRSRVYRVLRKGEVRVNGGR-KKPIYKLKSGDL 69

Query: 59  ------HIEVDGVPLRKA------------ERTRLWLYHKPIGLVTTHSD--PDGRSTVF 98
                  IE  G     A            E  RL + +KP G+        P G +   
Sbjct: 70  LRLPPVRIEPQGETEVPAGAWREIAQRILFEDERLLVINKPSGMAAHAGSGVPFGIAEAV 129

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD 156
                   R   V RLD  T G LLL     +  VL+      +  + Y     G +   
Sbjct: 130 HQHHCDGKRTELVHRLDRETSGCLLLAKGRSVLNVLQDSFRQRETHKQYLALLVGDLKGS 189

Query: 157 KLNLLKKGIVIQGICY-GDMQVTLDTQKGSN-----------------AWVTVGLREGKN 198
           +   L     +Q     G+  V +D    S                      V +  G+ 
Sbjct: 190 RRVDLA----LQKTKLSGEAMVVVDEAGKSALSDFEPLAHYPWNDRTLTLARVTIHTGRT 245

Query: 199 REIK---KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQV 255
            +I+   +        +            LG    G  R +++   R+ L    L    +
Sbjct: 246 HQIRVHAR---ALGLPL------------LGDDKYGDER-LNRDAKRQGLKRLFLHAESI 289

Query: 256 NLD 258
              
Sbjct: 290 RFP 292


>gi|300727932|ref|ZP_07061310.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
 gi|299774774|gb|EFI71388.1| ribosomal large subunit pseudouridine synthase D [Prevotella
           bryantii B14]
          Length = 298

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/201 (16%), Positives = 65/201 (32%), Gaps = 28/201 (13%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGLVT--T 87
           ++V   ++ +    +     I +       A          E   L +  K  G+++   
Sbjct: 49  IRVGSKVITKFDYPLKPGMKIHISKNKRNNAFKSKWMKIVYEDQYLVVIEKNAGILSMAA 108

Query: 88  HSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWL 142
                   TV D   +   +      V RLD +T GL++   D      LE    +T + 
Sbjct: 109 GHSSLNCKTVLDQYFNETRQHCQAHVVHRLDRDTSGLMIYAKDKKTELSLEEDWHNTVYD 168

Query: 143 RVYRVRFHGQVDQDK------LNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTV 191
           R Y     G++ +D+      L   +  I        G  Y      +  +  +++ V  
Sbjct: 169 RRYVAVVSGEMREDEGTVANWLKDNRAYITFSSPVDNGGKYAVTHFRVLDRTPNHSLVEF 228

Query: 192 GLREGKNREIKKVFEFFNWKV 212
            L  G+  +I+         V
Sbjct: 229 KLETGRKNQIRVHTADMGHPV 249


>gi|257457444|ref|ZP_05622614.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
 gi|257445173|gb|EEV20246.1| ribosomal large subunit pseudouridine synthase D [Treponema
           vincentii ATCC 35580]
          Length = 246

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 26/159 (16%), Positives = 57/159 (35%), Gaps = 27/159 (16%)

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSI--------FSRVISVGRLDINTEGLLLLTNDGGL 130
           +K  GL+      D  +   D L            +++ +V R+D +T G+LL   +   
Sbjct: 19  NKAAGLLVAADRWDAEAPRLDLLIQKELPQIAPSCNKLYAVHRIDKDTSGILLYALNAEA 78

Query: 131 ARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            R L     + +  + YR+  HG+V ++        + ++       +  +D ++G  A 
Sbjct: 79  HRTLNTAFQNREIKKTYRLLIHGRVSEE---QFTVDLPLRADGDALHRTVVDKRRGKEAV 135

Query: 189 VTVGLRE--------------GKNREIKKVFEFFNWKVN 213
               + E              G+  +I+       + + 
Sbjct: 136 THFTVLETFRQFSLLEACPVTGRTHQIRAHLAAAGYPIV 174


>gi|242242285|ref|ZP_04796730.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
 gi|242234241|gb|EES36553.1| pseudouridylate synthase [Staphylococcus epidermidis W23144]
          Length = 284

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 30/173 (17%), Positives = 57/173 (32%), Gaps = 19/173 (10%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFSRVIS 110
            S + I  D       E   L + +KP       S      +    V         ++  
Sbjct: 64  PSENLIPYDKELEVIYEDAYLIIVNKPQMQNCAPSREHPHGSLVEQVLAYYTKKGEKINP 123

Query: 111 --VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHG----------QVDQDKL 158
             V RLD NT GL++    G +  +      +  + Y    +G           + +   
Sbjct: 124 HIVTRLDRNTSGLVVFAKFGHVHHLFSKVKFK--KEYVALAYGHTQSSGVIEAPIARRSD 181

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +++K+ +  +G  Y         Q  + +   V L  G+  +I+  FE+    
Sbjct: 182 SIIKREVNDKG-KYAITVYQRLMQNETASLCKVKLLTGRTHQIRVHFEYIGHP 233


>gi|218767979|ref|YP_002342491.1| hypothetical protein NMA1085 [Neisseria meningitidis Z2491]
 gi|121051987|emb|CAM08296.1| hypothetical protein NMA1085 [Neisseria meningitidis Z2491]
 gi|308389039|gb|ADO31359.1| YabO/YceC/SfhB family protein [Neisseria meningitidis alpha710]
 gi|316985760|gb|EFV64704.1| RNA pseudouridylate synthase family protein [Neisseria meningitidis
           H44/76]
 gi|319410229|emb|CBY90568.1| putative RNA pseudouridine synthase (RNA-uridine isomerase; RNA
           pseudouridylate synthase) [Neisseria meningitidis WUE
           2594]
 gi|325130001|gb|EGC52795.1| RNA pseudouridine synthase [Neisseria meningitidis OX99.30304]
 gi|325139980|gb|EGC62509.1| RNA pseudouridine synthase [Neisseria meningitidis CU385]
 gi|325200448|gb|ADY95903.1| RNA pseudouridine synthase [Neisseria meningitidis H44/76]
 gi|325203940|gb|ADY99393.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240355]
          Length = 307

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|311032387|ref|ZP_07710477.1| pseudouridine synthase, RluA family protein [Bacillus sp. m3-13]
          Length = 307

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 65/198 (32%), Gaps = 33/198 (16%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKA-------ERTRLWLYHKPIGL 84
            ++V VNG         +   D + V     D  P+          E   L + +K  G+
Sbjct: 39  SKKVMVNGENP-NWTHLLKEGDRVSVPILPEDITPIATEMDIKIIYETEHLLVINKEAGM 97

Query: 85  VTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVL--EL 136
            T  S      ++ + +   F      S+V  + RLD +T G +L         +L   L
Sbjct: 98  DTHPSSDQDFRSLSNGVAHYFNNNGISSKVRHIHRLDQDTSGAILFAKHAISGAILDRML 157

Query: 137 PSTQWLRVYRVRFHGQV--DQDKLNLL---------KKGIVIQGICYGDM-QVTLDTQKG 184
              +  R Y     G V   +  ++           ++ +   G       +V     K 
Sbjct: 158 EERKVKRTYLALVEGIVKTPEGTIDKPIGKDRHHASRRRVSPNGQKAITHYKVVKTYPKE 217

Query: 185 SNAWVTVGLREGKNREIK 202
               V + L  G+  +I+
Sbjct: 218 QLTLVELTLDTGRTHQIR 235


>gi|254804732|ref|YP_003082953.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
 gi|254668274|emb|CBA05164.1| pseudouridylate synthase [Neisseria meningitidis alpha14]
          Length = 307

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|229016558|ref|ZP_04173498.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1273]
 gi|229022765|ref|ZP_04179289.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1272]
 gi|228738577|gb|EEL89049.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1272]
 gi|228744734|gb|EEL94796.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH1273]
          Length = 292

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 34/205 (16%), Positives = 67/205 (32%), Gaps = 31/205 (15%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHI-----------EVDGVPLR-KAERTRLWLYHKPIGL 84
             ++VNG     R  +       +           EV+ +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHKLQAGEELQVFFPFEERSEGMEVEDIPLNIVYEDDAVLVVNKEAYM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--L 136
            T  S      +V + L   + +      V  V RLD +T GL+L+  +  +  +L    
Sbjct: 96  STIPSREHPSGSVANALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKNRFVHNLLSKQH 155

Query: 137 PSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
                 R Y    HG + ++          K + + +  V +          +     + 
Sbjct: 156 QQKGVKRTYEALVHGMILEEIGTIDAPIGRKADSIIERTVCEDGQRAVTHFKVMESSSNK 215

Query: 187 AWVTVGLREGKNREIKKVFEFFNWK 211
             V + L  G+  +I+         
Sbjct: 216 THVALELETGRTHQIRVHMAHIGHP 240


>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 = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 11 FTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
              R+  ++ AR   ASR    R I    V+V+G+  ++    V    H+EV+
Sbjct: 1  MNKTRLDLLLVARGLYASREAARRAIMAGLVRVDGVRADKPGFKVAEDAHVEVE 54


>gi|161869801|ref|YP_001598969.1| YabO/YceC/SfhB family protein [Neisseria meningitidis 053442]
 gi|161595354|gb|ABX73014.1| YabO/YceC/SfhB family protein [Neisseria meningitidis 053442]
          Length = 307

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|324325321|gb|ADY20581.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus thuringiensis serovar finitimus YBT-020]
          Length = 297

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 74/220 (33%), Gaps = 35/220 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L S + +      V  V RLD +T GL+L+
Sbjct: 87  EDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKRHLASTVHIVTRLDRDTSGLMLI 146

Query: 125 TNDGGLARVLE---LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGI 170
             +      L           R Y    HG            + +   +++++ +  +G 
Sbjct: 147 AKN-RFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQ 205

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +D+       V++ L  G+  +I+    +    +               L  
Sbjct: 206 RAVTHFRVIDSVNHKTH-VSLELDTGRTHQIRVHMAYIGHPLLG-----------DNLYG 253

Query: 231 GSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLV 268
           G   E+ ++ L        H + E +++   PI S    +
Sbjct: 254 GKRDEMKRQALHSTSLTFYHPILEKEMSFTTPIPSDMQAI 293


>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 = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 24/119 (20%), Positives = 38/119 (31%), Gaps = 19/119 (15%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDG----VPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           +VNG L    +  V   D + +       P    E     +Y+KP    T+  D      
Sbjct: 40  RVNGRLERFESYRVQPGDRVTLTVQTRLEPQILWEDEHYCIYNKPS--HTSTEDL----- 92

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
                 +  + +  V RLD +T G +L       A  L       +  + Y     G  
Sbjct: 93  ------AKITGLNIVHRLDRDTTGCILFAKHASAAHALSELFKKRKIHKQYTALVFGHP 145


>gi|295101862|emb|CBK99407.1| Uncharacterized conserved protein [Faecalibacterium prausnitzii
          L2-6]
          Length = 71

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
           ++  ++  AG+  +  E + ++    VKVNG +           D +E+DG  + 
Sbjct: 11 IKLDALLKYAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRPGDTVELDGQTIE 66


>gi|15676763|ref|NP_273908.1| YabO/YceC/SfhB family protein [Neisseria meningitidis MC58]
 gi|7226104|gb|AAF41278.1| YabO/YceC/SfhB family protein [Neisseria meningitidis MC58]
          Length = 307

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|257454043|ref|ZP_05619317.1| ribosomal large subunit pseudouridine synthase C [Enhydrobacter
           aerosaccus SK60]
 gi|257448521|gb|EEV23490.1| ribosomal large subunit pseudouridine synthase C [Enhydrobacter
           aerosaccus SK60]
          Length = 365

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 73/248 (29%), Gaps = 53/248 (21%)

Query: 14  QRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QRV   +  R     R  V  MI    ++VNG   +     +   D + +  + L   E+
Sbjct: 68  QRVDNFLLGRLKGLPRSHVYNMIRSDEIRVNGKRCK-PHDKLQRNDVVRIAPIKLATREK 126

Query: 73  TRL-------------------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVG 112
             +                    + +KP G+       +    +     +   + +  V 
Sbjct: 127 PVISPDFAQSLLERIVYEDEGLIVLNKPSGMAVHGGSGESFGVIEAMREATGKKYLELVH 186

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD-----------KLN 159
           R+D +T GLL++       + L   L      + Y     G +  +            L 
Sbjct: 187 RIDKDTSGLLMIAKKRSTLKTLQEHLREKTLQKTYLCLVVGWISSETQTIDKPLLKYTLP 246

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWV-----------TVGLRE-----GKNREIKK 203
             ++G    G     + V  +  K S   +            V L E     G+  +I+ 
Sbjct: 247 ATQEGKS--GERRVKVDVKSEDSKPSQTQINVLQKFELNGQKVSLIEAKPLTGRTHQIRV 304

Query: 204 VFEFFNWK 211
                   
Sbjct: 305 HLASIGHP 312


>gi|226197455|ref|ZP_03793032.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
 gi|225930834|gb|EEH26844.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pakistan 9]
          Length = 389

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>gi|16124708|ref|NP_419272.1| ribosomal large subunit pseudouridine synthase d [Caulobacter
           crescentus CB15]
 gi|221233422|ref|YP_002515858.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus NA1000]
 gi|13421626|gb|AAK22440.1| ribosomal large subunit pseudouridine synthase d [Caulobacter
           crescentus CB15]
 gi|220962594|gb|ACL93950.1| ribosomal large subunit pseudouridine synthase D [Caulobacter
           crescentus NA1000]
          Length = 342

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 60/179 (33%), Gaps = 35/179 (19%)

Query: 7   VQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           + EN   QR+ KV+A      SR  ++ +IA+ R+  +G  +  A+    +     V  +
Sbjct: 31  LPENLAGQRLDKVLAPLFPDLSRARLQALIAEGRLTFDGETVADASRKARAG----VYSL 86

Query: 66  PLRKA----------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRV 108
            +                   E   L +  K  G+    +      T+ +  L    + +
Sbjct: 87  VVPPPAPADPEPEALPLSILYEDAHLIVVDKAAGMAVHPAPGTYNGTLVNALLHHCGASL 146

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQ 155
             VG         RLD +T G+++       A         +    R+Y     G  + 
Sbjct: 147 SGVGGVARPGIVHRLDKDTSGVMVAAKS-DAAHRGLSTLFATHDIDRLYVALTRGAPNP 204


>gi|325144100|gb|EGC66407.1| RNA pseudouridine synthase [Neisseria meningitidis M01-240013]
          Length = 307

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPIDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|254670442|emb|CBA06065.1| pseudouridylate synthase [Neisseria meningitidis alpha153]
 gi|325135925|gb|EGC58535.1| RNA pseudouridine synthase [Neisseria meningitidis M0579]
          Length = 307

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|24380298|ref|NP_722253.1| putative pseudouridylate synthase [Streptococcus mutans UA159]
 gi|24378312|gb|AAN59559.1|AE015019_4 putative pseudouridylate synthase [Streptococcus mutans UA159]
          Length = 288

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 33/206 (16%), Positives = 75/206 (36%), Gaps = 34/206 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRK------------AE 71
           R++   +  ++ V VN   +   ++ V   D I+++      P++K             +
Sbjct: 28  RKIRHFLRIKKNVTVNSQAVNWQSL-VRRGDIIQLNFDNTDYPIKKIPMGNKTLIDCLYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +K  G+ T  +DP+  + +      +      V RLD+ T G ++   +    
Sbjct: 87  DEHLIIVNKIEGMKTHANDPNEIALLNHVSAYVGQTCYVVHRLDMKTSGTVMFAKNPFIL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L   +    R Y     GQ  +  +           +  K+ +  +       QV
Sbjct: 147 PILNRLL-ENKSIKREYWALAQGQFSEHAIIYREPIGRDRHDRRKRVVDHKHGQTAITQV 205

Query: 178 TLDTQ-KGSNAWVTVGLREGKNREIK 202
           +L      + + +   L+ G+  +I+
Sbjct: 206 SLLKHFSNNTSLIKCQLQTGRTHQIR 231


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

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 40/249 (16%), Positives = 91/249 (36%), Gaps = 60/249 (24%)

Query: 7   VQENFTPQRVSK----VIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM 55
           V+ + +  R+ +         G      +++++   +++V+G  ++         ++ V 
Sbjct: 9   VEADESGMRLDRWFKVYYPDVGFG---YLQKLLRSGQIRVDGGRVKNDMRLVVGQSIRVP 65

Query: 56  S-------------------TDHIEVDGVPLRKAERTRLWLYHKPIGLVTT-----HSDP 91
                                D I +  + L   E +++++++KP GL            
Sbjct: 66  PLLIDKEDSFSVINKIVCGRDDDIILKDMLL--YEDSKIFVFNKPAGLAVQGGSGLTRHI 123

Query: 92  DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
           D    V+ N      R+  V R+D  T G+L++    G A+ L     + +  + Y    
Sbjct: 124 DNMLEVWRNKKGEKPRL--VHRIDRETSGILVVARSRGAAQALTAAFRTRETKKTYWALV 181

Query: 150 HGQV--DQDKLNL-LKKGIVIQGICYGDMQVT-------------LDTQKGSNAWVTVGL 193
            G     QDK++  + + I  QG      +               LDT+  + +W+ +  
Sbjct: 182 RGVPRKKQDKISTWMVREITAQGDKMRVCERRQPDSNHAVSYYRVLDTRGKALSWLEMEP 241

Query: 194 REGKNREIK 202
             G+  +++
Sbjct: 242 YTGRTHQLR 250


>gi|240167932|ref|ZP_04746591.1| RluA family pseudouridine synthase [Mycobacterium kansasii ATCC
           12478]
          Length = 308

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 80/256 (31%), Gaps = 52/256 (20%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-------V 52
           M D+++ V E     RV   +AR    SR  V  +     V+++G+   ++        +
Sbjct: 1   MPDRSMPVPEGLAGLRVDAGLARLLGLSRSAVAAIAEGGGVQLDGVPAGKSDRLTSGAWL 60

Query: 53  NVM--------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
            V             ++++G+ +  ++   +    KP  +    S      TV   L   
Sbjct: 61  QVRLPEAPPPLENTPVDIEGMTILYSDDD-IVAVDKPAAVAAHASVGWTGPTVLGGLAAA 119

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                   +  R   V RLD+ T G++++        VL+         + Y     G  
Sbjct: 120 GYRITTSGVHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKHRTVEKRYHALVQGHP 179

Query: 154 DQDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNA--------------WVTVGLREG 196
           D         G  I    G   G       T  G ++               + + L  G
Sbjct: 180 DP------SSG-TIDAPIGRHPGPEWKFAVTTNGRHSVTHYDTIEAFVAASLLDIELETG 232

Query: 197 KNREIKKVFEFFNWKV 212
           +  +I+  F       
Sbjct: 233 RTHQIRVHFAALRHPC 248


>gi|210623700|ref|ZP_03293984.1| hypothetical protein CLOHIR_01934 [Clostridium hiranonis DSM 13275]
 gi|210153388|gb|EEA84394.1| hypothetical protein CLOHIR_01934 [Clostridium hiranonis DSM 13275]
          Length = 303

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 40/229 (17%), Positives = 76/229 (33%), Gaps = 44/229 (19%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLR 68
           + K+    G  S R + +M  ++ V VNG    +  ++V   D IEV       +  P  
Sbjct: 27  LDKL----GF-SVRSISKMKRERTVNVNGE-YRKPTLDVKKGDLIEVEINEDMANFEPQN 80

Query: 69  KA-----ERTRLWLYHKPIGLVTTHSDPDGRSTV------FDNLPSIFSRVISVGRLDIN 117
                  +   + +  KP  +V   +      TV      F        +V  V RLD+N
Sbjct: 81  LEMGILYDDFDIIMVDKPPYMVVHPTKSHFDGTVANGVTDFIIKKDEKVKVRFVNRLDMN 140

Query: 118 TEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHG--------------QVDQDKLNLL 161
           T GL+++  +     VL    ++    + Y     G              +   D +   
Sbjct: 141 TSGLVIVAKNAYAHHVLSTDMSENLVEKKYIAVVKGVMKEDKGTIDAPIYRPTDDSIKR- 199

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
              +V +         ++  +      V + L  G+  +I+       +
Sbjct: 200 ---VVDERGQRSITHYSVIERLDDATVVELKLETGRTHQIRVHLAHLGY 245


>gi|148695986|gb|EDL27933.1| RNA pseudouridylate synthase domain containing 2 [Mus musculus]
          Length = 553

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/291 (15%), Positives = 96/291 (32%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++  ++ +   D +          V   P+   AE   + +  KP
Sbjct: 192 EAAVRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPIHLLAENNDVVVIDKP 251

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 252 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSEKIHEQVR 311

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQ--VTLDTQKGSNA 187
             Q  + Y  R  G+    ++           K G+          +      +  G ++
Sbjct: 312 DRQLEKEYVCRVAGEFPDKEVICKEPILVVSYKVGVCRVDPRGKPCETMFQRLSYNGRSS 371

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +         ++GP +      G   +  +++L
Sbjct: 372 VVQCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSTAWGPSRGQG---GHIPKTDEELL 425

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +E+   LD         + D     SE+  D       ++QK
Sbjct: 426 RDLVAEHQAKESLSMLDLCESDLTPGLIDSTAPSSELAKDSLEGLATAAQK 476


>gi|188533189|ref|YP_001906986.1| Pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
 gi|188028231|emb|CAO96089.1| Pseudouridylate synthase [Erwinia tasmaniensis Et1/99]
          Length = 232

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/193 (19%), Positives = 65/193 (33%), Gaps = 41/193 (21%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  +P    +V   L  IF     V RLD  T GL+L+  +  
Sbjct: 22  QDEHLALINKPAGLLSLSGKNPQNIDSVHHRLVRIFPGCTLVHRLDFGTSGLMLIARNKA 81

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQ 182
           +   L       +  ++Y     G +D D       G++   I           +     
Sbjct: 82  INAALCQQFSQRKVAKMYSALLCGHLDND------GGVIDAAIAKDPALFPLMSICAIHG 135

Query: 183 KGSNAWVTVG--------------LR------E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V               L       E G+  +++   +     +       YG
Sbjct: 136 KPARSRYQVTARFYHALQDGTRLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCD--LYG 193

Query: 222 PFQLGTLLAGSTR 234
               G LL G+ R
Sbjct: 194 ----GRLLPGTER 202


>gi|237752561|ref|ZP_04583041.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376050|gb|EEO26141.1| ribosomal large subunit pseudouridine synthase C [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 290

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/220 (14%), Positives = 70/220 (31%), Gaps = 44/220 (20%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--------LLERAAVNVMSTDHIEVDGVPLRK 69
           K++A     S  E + +I +  V V G         L      N+     I      +  
Sbjct: 50  KLLALQENISNNEAKALIDRGLVNVKGKKILIARGLLAPNTRFNIQQIQTI----KEIFC 105

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   +    KP  L +            + +   + +   + RLD  T G+LLL  +  
Sbjct: 106 NEN--ILALEKPAFLTS------------EEIVKSYPQWTLLHRLDKETSGILLLVKENS 151

Query: 130 LARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK--- 183
              +    + +    L+ Y     G +D++    +   ++I+      + ++   +    
Sbjct: 152 SFHLKAKEAFKQLQVLKQYTAIVEGILDEEC--EITAPLIIKKGKSAKVSISKTNEGQKA 209

Query: 184 ----------GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                     G    + + ++ GK  +I+         + 
Sbjct: 210 ITHITPLEIFGKKTKLDIEIKTGKTHQIRAHLAHIKHPII 249


>gi|217421724|ref|ZP_03453228.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
 gi|217395466|gb|EEC35484.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 576]
          Length = 395

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 66  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 124

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 125 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 184

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 185 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 244

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 245 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 302


>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 = 51.7 bits (123), Expect = 2e-04,   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|113970739|ref|YP_734532.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-4]
 gi|114047966|ref|YP_738516.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-7]
 gi|113885423|gb|ABI39475.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-4]
 gi|113889408|gb|ABI43459.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           MR-7]
          Length = 329

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/219 (15%), Positives = 71/219 (32%), Gaps = 41/219 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVPLRKA-------------- 70
           R++ +  V+VN   ++     +   D + V        D      A              
Sbjct: 52  RIVRKGEVRVNKKRIK-PEYKLQIGDVVRVPPVRMAEQDNRTAPSANLSKVSQLEDRILH 110

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 111 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 170

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGS 185
              + L       +  + Y     G+       ++K+ ++   +  G+  V ++ + K S
Sbjct: 171 SALKHLHDQLRQKKMQKDYLALVKGEWSAQD-KVVKQPLLKLTLKSGERIVRVNGEGKPS 229

Query: 186 NAWVTV-------GLRE-----GKNREIKKVFEFFNWKV 212
                +        L +     G+  +I+   ++    +
Sbjct: 230 ETRFKIVQRYQGCTLVQASPVTGRTHQIRVHCQYMGHPI 268


>gi|257886368|ref|ZP_05666021.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
 gi|257822224|gb|EEV49354.1| pseudouridine synthase [Enterococcus faecium 1,231,501]
          Length = 285

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 56/148 (37%), Gaps = 16/148 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 86  EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVLFAK 145

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D            +  K+ +  +      
Sbjct: 146 NPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDMTITNKIGRDRHDRRKRVVDDKNGQSAL 205

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             VT++        V   L  G+  +I+
Sbjct: 206 THVTVNKVLSEQTQVYCVLETGRTHQIR 233


>gi|332977573|gb|EGK14343.1| hemolysin A [Desmospora sp. 8437]
          Length = 64

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/55 (20%), Positives = 25/55 (45%), Gaps = 1/55 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
             +R+  V+   G   +R++ +R +    V+V+G   ++    +     +EV G
Sbjct: 1  MAKERLDLVLVNKGYFPTRQQAQRAVMAGLVRVDGERADKPGTRIPPEATVEVAG 55


>gi|332306496|ref|YP_004434347.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173825|gb|AEE23079.1| pseudouridine synthase, RluA family [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 318

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/244 (15%), Positives = 81/244 (33%), Gaps = 60/244 (24%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           ++ +   QR+   +       R  ++        R++ +  ++VN   ++     + + D
Sbjct: 15  IEPDLEGQRIDNFL-------RTLLKGVPKSLIYRIVRKGEIRVNKKRVK-PEYKLQAHD 66

Query: 59  HIEVDGVPLRKA--------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
            + +  + + +                     E   L + +KP G+            + 
Sbjct: 67  QLRIPPIRVSEPNAAPSTKLDKVASLESHILFEDDLLIVLNKPSGMAVHGGSGLSFGVIE 126

Query: 99  DN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
               L      +  V RLD +T G L++       + L   L   +  + Y     G+  
Sbjct: 127 ALRALRPQARFLELVHRLDRDTSGCLVIAKKRSALKNLHEQLRDKKMDKRYHALVVGEWP 186

Query: 155 QDKLN---LLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV-------GLRE-----GKN 198
           +++      L K I+  G       V++D++ K S     V        L E     G+ 
Sbjct: 187 ENRYKVNAPLLKNILKSGERL----VSVDSEGKPSETRFRVLERYVGATLVEASPITGRT 242

Query: 199 REIK 202
            +I+
Sbjct: 243 HQIR 246


>gi|325661187|ref|ZP_08149814.1| hypothetical protein HMPREF0490_00547 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325472694|gb|EGC75905.1| hypothetical protein HMPREF0490_00547 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 323

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 85/255 (33%), Gaps = 62/255 (24%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           M++  + + N   QR+ K++A+       E       +M+ ++ + +NG         + 
Sbjct: 1   MQEIKVTK-NEAGQRLDKLLAKYL----NEAPKSFFYKMMRKKNIVLNGKKAT-GNEKLE 54

Query: 56  STDHIE--VDGVPLRK----------------AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
             D ++  +    +RK                 E   + L +KP+G+++  +     S V
Sbjct: 55  EGDIVKLFLADETIRKFSSVKIQRTKTNLSVIYEDQDVVLINKPVGMLSQKAKESDVSLV 114

Query: 98  FDNLPSIFS------------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
              +  +F             R     RLD NT G+++        + +          +
Sbjct: 115 EHLISYLFDAGELSEETLKSFRPSICNRLDRNTSGIVVAGKSLPGLQKMGELFKERTLHK 174

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----------------A 187
            YR    G + +D      KG + +      +Q+       S+                 
Sbjct: 175 YYRCLVQGVIRED---QYLKGWLKKDEKTNKVQILDRPSDPSDQPIETEYHPLWTKEGVT 231

Query: 188 WVTVGLREGKNREIK 202
            + V L  GK  +I+
Sbjct: 232 LLEVRLITGKTHQIR 246


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +R+  ++   G   SR + +  +    V VN   +++  + V     I+V G
Sbjct: 7  ERIDVLLVERGFYESREKAKAAVMAGLVLVNNEPVDKGGMKVPREAEIKVKG 58


>gi|91794398|ref|YP_564049.1| pseudouridylate synthase [Shewanella denitrificans OS217]
 gi|91716400|gb|ABE56326.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           denitrificans OS217]
          Length = 225

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 59/165 (35%), Gaps = 28/165 (16%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +   + + +KP GL++    DP    +++  + + F     V RLD+ T G++++    
Sbjct: 18  HQDKDVLVVNKPSGLLSVPGRDPAHSDSIYSRVLAQFPNAHIVHRLDMATSGVMVVALRR 77

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQV----DQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
              R L+      +  +VY  R  G +     +  L L+              +V     
Sbjct: 78  SAERELKRQFHDRETKKVYYARVAGHLSPVHTRVDLPLIC-----DWPNRPKQKVDHKLG 132

Query: 183 KGSNAWVTVG-------------LREGKNREIK-KVFEFFNWKVN 213
           K S+  V +              +  G++ +++  +       + 
Sbjct: 133 KPSSTLVKIISYGKRSTLVKLSPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|325282268|ref|YP_004254809.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
 gi|324314077|gb|ADY25192.1| pseudouridine synthase, RluA family [Deinococcus proteolyticus MRP]
          Length = 305

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/192 (17%), Positives = 63/192 (32%), Gaps = 25/192 (13%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGL 84
           +A   V++NG      + ++   D +     P  +           E   +   HKP GL
Sbjct: 46  LAAGEVELNGHPAA-GSESLRPGDRLAWHRPPWAEEAVPLHFSVLYEDAHILAVHKPSGL 104

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWL 142
            T  +      T+   L   +     + RL   T GL+L +        L       +  
Sbjct: 105 PTLPAGGFLDHTLLALLRRQWPAATPLHRLGRGTSGLVLCSLTPAAGSRLTADWREGRIH 164

Query: 143 RVYRVRFHGQVDQDKLNLLKK-GIVIQ---GICYGDMQ--------VTLDTQKGSNAWVT 190
           + YR    G   Q+K ++    G+V     G  Y              +  ++  +    
Sbjct: 165 KRYRALSAGVAAQEKYDITAPIGLVDHPRLGQIYAATPAGKPSRSRAQVLERRDGSTLFQ 224

Query: 191 VGLREGKNREIK 202
           V +  G+  +I+
Sbjct: 225 VDIETGRPHQIR 236


>gi|167893970|ref|ZP_02481372.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 7894]
 gi|167918689|ref|ZP_02505780.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei BCC215]
 gi|237812527|ref|YP_002896978.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei MSHR346]
 gi|254179573|ref|ZP_04886172.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|184210113|gb|EDU07156.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1655]
 gi|237504431|gb|ACQ96749.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei MSHR346]
          Length = 389

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>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 = 51.7 bits (123), Expect = 2e-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|326382577|ref|ZP_08204268.1| pseudouridine synthase, RluA family protein [Gordonia neofelifaecis
           NRRL B-59395]
 gi|326198696|gb|EGD55879.1| pseudouridine synthase, RluA family protein [Gordonia neofelifaecis
           NRRL B-59395]
          Length = 308

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/182 (18%), Positives = 59/182 (32%), Gaps = 27/182 (14%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--------- 49
           M+D   +   +     RV   +AR    SR  V  +     + V+G+ + +         
Sbjct: 1   MRDSRAMPVPDGLHGMRVDAGVARVLGLSRTVVATLADAGDITVDGVSVGKSHKLAAGSW 60

Query: 50  AAVNVM-STDHIEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
             V +      + V+  P+   E       + +  KP G+    S      TV   L   
Sbjct: 61  LDVLLPEPEQPLTVEPTPVEDLEVIYHDSDIIVVDKPAGVAAHPSLGWSGPTVIGALAAA 120

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                      R   V RLD  T G++++        +L+    Q    + Y     G +
Sbjct: 121 GFRISTSGAHERQGIVHRLDAGTSGVMVVAASERAYTLLKRAFKQRTVDKRYHALVQGHL 180

Query: 154 DQ 155
           D 
Sbjct: 181 DP 182


>gi|260912693|ref|ZP_05919179.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
 gi|260633071|gb|EEX51236.1| ribosomal large subunit pseudouridine synthase C [Pasteurella
           dagmatis ATCC 43325]
          Length = 381

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 81/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
            + E    QR+   + A+     +  + R++ +  V+VN G +  +    + ++D + V 
Sbjct: 78  TISEEEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRI--KPEYKLQASDIVRVP 135

Query: 64  GVPLRKAERTRL---------------------WLYHKPIGLVTTHSDPDGRSTVFDN-- 100
            V + + E+  +                      + +KP G+            +     
Sbjct: 136 PVRVSEKEQAPVSTKLNKVNQLENQILFEDDCLLVLNKPSGIAVHGGSGLNFGVIEALRA 195

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q   
Sbjct: 196 LRPEARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLALVRGQW-QSHC 254

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            ++K  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 255 KVVKAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYENATLVKASPVTGRTHQIR 311


>gi|261207216|ref|ZP_05921905.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289566649|ref|ZP_06447067.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|293557194|ref|ZP_06675744.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
 gi|294614335|ref|ZP_06694252.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|260078844|gb|EEW66546.1| pseudouridine synthase [Enterococcus faecium TC 6]
 gi|289161549|gb|EFD09431.1| pseudouridine synthase [Enterococcus faecium D344SRF]
 gi|291592807|gb|EFF24399.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1636]
 gi|291600646|gb|EFF30948.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1039]
          Length = 285

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/149 (20%), Positives = 56/149 (37%), Gaps = 16/149 (10%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLT 125
            E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L  
Sbjct: 85  HEDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVLFA 144

Query: 126 NDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYG 173
            +  +  +L   L      R Y+    G++ +D            +  K+ +  +     
Sbjct: 145 KNPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDMTITNKIGRDRHDRRKRVVDDKNGQSA 204

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
              VT++        V   L  G+  +I+
Sbjct: 205 LTHVTVNKVLSEQTQVYCVLETGRTHQIR 233


>gi|206977693|ref|ZP_03238585.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
 gi|206744121|gb|EDZ55536.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus H3081.97]
          Length = 292

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 74/220 (33%), Gaps = 35/220 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L S + +      V  V RLD +T GL+L+
Sbjct: 82  EDDAVLVINKEANMSTIPSREHPAGSVANALLSHYDKRHLTSTVHIVTRLDRDTSGLMLI 141

Query: 125 TNDGGLARVLE---LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGI 170
             +      L           R Y    HG            + +   +++++ +  +G 
Sbjct: 142 AKN-RFVHHLLSKQHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQ 200

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLA 230
                   +D+       V++ L  G+  +I+    +    +               L  
Sbjct: 201 RAVTHFRVIDSVNHKTH-VSLELDTGRTHQIRVHMAYIGHPLLG-----------DNLYG 248

Query: 231 GSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSSETLV 268
           G   E+ ++ L        H + E +++   PI S    +
Sbjct: 249 GKRDEMKRQALHSTSLTFYHPILEKEMSFTTPIPSDMQAI 288


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 82/238 (34%), Gaps = 50/238 (21%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKV--------------NGILLER 49
           V++ F   R+   +++  I    SR  ++ +I Q  V V              + I +  
Sbjct: 8   VEKEFDNVRLDLYLSK--IFEDKSRSYLQGIIDQGSVLVNNKKKKRNYKLKVGDNIEVNI 65

Query: 50  AA---VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                + +   D I++D       E   + + +KP  +V   +      T+ + L     
Sbjct: 66  PEPKLLQIEPED-IKLD----IIYEDKDVIVVNKPQEMVVHPAPGVYSGTLVNALLHHCK 120

Query: 107 RVIS---------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQ 155
            +           V R+D +T G+L++  +      L          RVY     G +  
Sbjct: 121 DLSGINGVARPGIVHRIDKDTSGILVVAKNDISHNNLAAQFKEHSISRVYMALVEGIIKD 180

Query: 156 DK-----------LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++           ++ +K  +V +   +      +  +  ++  V   L  G+  +I+
Sbjct: 181 EQGTIEAPIGRHPVDRIKMAVV-KDGRHAVTHYKVIERFKNHTLVECRLETGRTHQIR 237


>gi|83589720|ref|YP_429729.1| ribosomal large subunit pseudouridine synthase D [Moorella
           thermoacetica ATCC 39073]
 gi|83572634|gb|ABC19186.1| ribosomal large subunit pseudouridine synthase D [Moorella
           thermoacetica ATCC 39073]
          Length = 306

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 83/238 (34%), Gaps = 42/238 (17%)

Query: 15  RVSKVIA-RAGIASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEV--------- 62
           R+   +A      SR  +++++    + +   G L  +A   +   + + V         
Sbjct: 13  RIDAWLAGELPEVSRSRIQQLLEAGEITLALPGRL--KANYRLRGGERVRVRLPEPTLLA 70

Query: 63  ---DGVPLR-KAERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFS--------RVI 109
              + +PL    E   + + +KP G+V   +   +G + V   L             R  
Sbjct: 71  ARPEAIPLDILYEDEDIIVVNKPQGMVVHPAPGSEGGTLVNALLYHCGDLSGINGVLRPG 130

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI 167
            V RLD +T G+L+   +    R L   +      R+Y    HG+V  +    ++  I  
Sbjct: 131 IVHRLDKDTSGILVAAKNDAAHRGLAAQIKDHSMKRIYLALVHGEV-AEPRGRVEAPIGR 189

Query: 168 QGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVN 213
             +    M VTL   + +     V        L E     G+  +I+    F    V 
Sbjct: 190 HPVDRQRMAVTLKNSRPAVTHYRVVEHFPGYTLLEARLETGRTHQIRVHMAFIGHPVV 247


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          QR+   +       +R +   +I + RV VN   + + +  V  TD +E+    +    +
Sbjct: 3  QRLDHYLKNTNQCETRSKAIDLIKRGRVFVNNFQVLKPSFLVKQTDSVEIKNDEMYFVSK 62

Query: 73 TRLWLYH 79
              L  
Sbjct: 63 GGYKLLK 69


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              R+  ++    +A SR +   MI    V+VNG ++++    V     IE+
Sbjct: 1  MARIRLDSLLYDKALAPSREKARAMILAGEVRVNGQMVDKPGTTVDEEARIEL 53


>gi|303325510|ref|ZP_07355953.1| RNA pseudouridine synthase family protein [Desulfovibrio sp.
           3_1_syn3]
 gi|302863426|gb|EFL86357.1| RNA pseudouridine synthase family protein [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 63/179 (35%), Gaps = 30/179 (16%)

Query: 1   MKDKNI-VQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVKVNGILLERAAVNVM 55
           M  + + V      QR+ + +A      G+  RR   R+IA+  V VNG +   A   + 
Sbjct: 1   MNARELRVDAALAGQRLDQALAALTPELGLRGRR---RLIARGAVLVNGRVG-DAGCRLR 56

Query: 56  STDHIEVDG-------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             D + + G             +P   + +      +KP GL +     D   ++   LP
Sbjct: 57  PGDVLALRGTEDGTGATPCSADMPRLLSRQGDYCFLYKPAGLHSAALAGDNGLSLEALLP 116

Query: 103 SIFSRVISVG------RLDINTEGLL--LLTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
            + S            RLD  T G++   L      A  +   + +  + Y     G +
Sbjct: 117 VLLSEESEGRAPRLMQRLDYGTSGIVCAALGAKAAQAFRVAERAGRCEKRYLALLRGTL 175


>gi|224436535|ref|ZP_03657544.1| hypothetical protein HcinC1_01225 [Helicobacter cinaedi CCUG
          18818]
          Length = 240

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 7/57 (12%)

Query: 14 QRVS---KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+    K +      SR + +  I    VKVNG ++++ +  +   D + VD   L
Sbjct: 1  MRLDIYVKSLCS----SRTKAKEAIESGCVKVNGAVVKKGSFLLEKDDEVGVDSKDL 53


>gi|118617189|ref|YP_905521.1| RluA family pseudouridine synthase [Mycobacterium ulcerans Agy99]
 gi|118569299|gb|ABL04050.1| pseudouridine synthase, RluA-family [Mycobacterium ulcerans Agy99]
          Length = 345

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 77/249 (30%), Gaps = 51/249 (20%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAA-------VNV----- 54
           V E     RV   +AR    SR  V  +     V+++G+   ++        ++V     
Sbjct: 9   VPEGLAGMRVDAGLARLLGLSRSAVAVIAENGGVELDGVPAGKSDRLTAGAWLHVQLPEA 68

Query: 55  ---MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL---------P 102
                   +E++G+ +  ++   +    KP  +    S      TV   L          
Sbjct: 69  PPPPENTPVEIEGMTILYSDDD-IVAVDKPAAVAAHASVGWTGPTVLGGLAAAGYRISTS 127

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNL 160
            +  R   V RLD+ T G++++        VL+    Q    + Y     G  D      
Sbjct: 128 GVHERQGIVHRLDVGTSGVMVVALSERAYTVLKRAFKQRTVDKRYHALVQGHPDP----- 182

Query: 161 LKKGIVIQ-------GICYGDMQVTLDTQKGSN----------AWVTVGLREGKNREIKK 203
              G  I        G  +            ++          + + V L  G+  +I+ 
Sbjct: 183 -SSG-TIDAPIGRHPGGEWKFAVTKNGRHSLTHYDTVEAFVAASLLDVHLETGRTHQIRV 240

Query: 204 VFEFFNWKV 212
            F   +   
Sbjct: 241 HFAALHHPC 249


>gi|114327246|ref|YP_744403.1| ribosomal large subunit pseudouridine synthase C [Granulibacter
           bethesdensis CGDNIH1]
 gi|114315420|gb|ABI61480.1| ribosomal large subunit pseudouridine synthase C [Granulibacter
           bethesdensis CGDNIH1]
          Length = 366

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 51/292 (17%), Positives = 99/292 (33%), Gaps = 75/292 (25%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMS 56
             V ++    R+ +         RR         +++M    +++V+G     AA  +  
Sbjct: 37  RQVTDDEADIRLDRWF-------RRHYPSLTQVAIQKMCRTGQIRVDGARA-EAATRLQP 88

Query: 57  TDHIEV-----------DGV------PLRKAE--------RTRLWLYHKPIGLVTTHSDP 91
              + +           +G       P+++ E           L + +KP GL +     
Sbjct: 89  GQSVRIPPLKVPSAAEQEGEGPRALDPIQQKELESWILYKDDHLIVLNKPSGLPSQGGPG 148

Query: 92  DGRST--VFDNLP-SIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYR 146
             R    + D L      R   V RLD +T G++++    G+A  L     + +  +VY 
Sbjct: 149 ITRHLDGLLDGLRFGRDDRPRLVHRLDRDTSGVIVIARSPGVAAKLAALFRTRETEKVYW 208

Query: 147 -------VRFHGQVDQDKLNL--LKKGIVIQGICYGDMQ------VTLDTQKGSNAWVTV 191
                  V   G++D+  L      + +V+      D         TLD      AW+ +
Sbjct: 209 AVVAGRPVPVEGRIDRPLLRQNDRNEPVVLADRKDRDKVTAITDYRTLDHAARKLAWLEL 268

Query: 192 G-LREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR 242
             L  G+  +++      +  +            LG    GS R   ++ +R
Sbjct: 269 RPLT-GRMHQLRVHCAAMDAPI------------LGDERYGSWRNTDERGVR 307


>gi|15674094|ref|NP_268269.1| pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
 gi|12725167|gb|AAK06210.1|AE006439_7 pseudouridine synthase [Lactococcus lactis subsp. lactis Il1403]
          Length = 288

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 59/189 (31%), Gaps = 29/189 (15%)

Query: 42  VNGILLERAAVNVMSTDHIE--VDGVPLRK--------------AERTRLWLYHKPIGLV 85
           VN  L+    + V + D I    D                     E   L + +KP G+ 
Sbjct: 42  VNNKLINENQL-VHAGDKITLIFDNEDFSNLSLKFGSANLADILYEDEHLIVVNKPEGMK 100

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
           T  +  D  +       +I   V  V RLD  T G +L   +  +  +L       +  R
Sbjct: 101 THGNTADELALQNHVAAAINQEVFVVHRLDQATSGAVLFAKNQFVLPILGKMFEENKIHR 160

Query: 144 VYRVRFHGQVDQDKLNLLK----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            Y     G   +++  + +          K I+          V +  +      V   L
Sbjct: 161 EYLALVKGHFSENQFTIDRAIGQNRHDKNKRILSAKGQKAVTHVEIIKKFTDKTLVKCTL 220

Query: 194 REGKNREIK 202
             G+  +I+
Sbjct: 221 DTGRTHQIR 229


>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 = 51.7 bits (123), Expect = 2e-04,   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|312135211|ref|YP_004002549.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           owensensis OL]
 gi|311775262|gb|ADQ04749.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           owensensis OL]
          Length = 293

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/160 (13%), Positives = 54/160 (33%), Gaps = 17/160 (10%)

Query: 59  HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRL 114
            + V+G      E       +KP GL +  S      T+ + +    +        + RL
Sbjct: 70  IVPVEGSIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLNSKNLTSHIINRL 129

Query: 115 DINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD------QDKLNLLKKGIV 166
           D  T G+++   +     ++       Q  + Y    HG++       +  +   + GI 
Sbjct: 130 DKETSGIVVFAKNSYFHSIVSREFEKRQVEKTYIAIVHGKLTKKSGLIEKPIKRSQDGIK 189

Query: 167 IQ---GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +      +      +     + + + +  +  G+  +++
Sbjct: 190 REIHQDGSFASTYYEVIDSFENFSVLKLKPIT-GRTHQLR 228


>gi|311278253|ref|YP_003940484.1| pseudouridine synthase [Enterobacter cloacae SCF1]
 gi|308747448|gb|ADO47200.1| pseudouridine synthase [Enterobacter cloacae SCF1]
          Length = 260

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/166 (16%), Positives = 52/166 (31%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   S  D D +  V   +       V +  RLD  T G+LL+       
Sbjct: 11  LVAVNKPSGWLVHRSWLDRDEKVVVMQTVRDQIGQHVFTAHRLDRPTSGVLLMGLSSEAG 70

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ---------DKLNLLKKGIVIQGICYGD------ 174
           R+L       Q  + Y     G + +         ++L+ +      +            
Sbjct: 71  RLLAQQFEQHQIHKRYHAIVRGWLSEEGILDYPLVEELDKIADKFAREDKGPQPAVTHYR 130

Query: 175 --MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
               V +    G       GL E     G+  ++++  +     + 
Sbjct: 131 GLATVEMPVATGRYPTTRYGLVELDPKTGRKHQLRRHLKHLRHPII 176


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 85/252 (33%), Gaps = 52/252 (20%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRKAERTRLWL-------- 77
           R+I   +++V+   +   +  V   D I++           +    +   W+        
Sbjct: 46  RLIRIGKIRVDDSKV-NPSYRVQKEDLIKIPISLSYSQDKSISIQRKNFYWIKKRILYED 104

Query: 78  -----YHKPIGLVTTHSDPDGRSTVFDNLPSIF---SRVISVGRLDINTEGLLLLTNDGG 129
                 +KP G +  HS       + + L  ++     +  + R+D  T G+LL+     
Sbjct: 105 SEILVLNKPSG-IAVHSGSKFSFGIIEILREVYFQSKYLELIHRIDKETSGILLIAKSRN 163

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           + ++++    S +  + Y V  HG     K+  +    + + I     +     + G  +
Sbjct: 164 ILQLIQKQFCSQKIFKKYIVLVHGVWP-SKIKRISC-FLEKKISQKKEKKIEIKKNGRMS 221

Query: 188 WVTVGLRE--------------GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                ++E              G+  +I+   +  N  +    R  YG  +L        
Sbjct: 222 ETLFQIKERFASFTLMLATPITGRKHQIRLHTKKINHPIVLDKR--YGNRKLD------- 272

Query: 234 REVSKKILREQL 245
           R + +  L+   
Sbjct: 273 RNLKESGLKRLF 284


>gi|262404383|ref|ZP_06080938.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. RC586]
 gi|262349415|gb|EEY98553.1| ribosomal large subunit pseudouridine synthase C [Vibrio sp. RC586]
          Length = 315

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKTIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEATPPSTKLNKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFTEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|213023738|ref|ZP_03338185.1| 23S rRNA pseudouridine synthase D [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 282

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/192 (16%), Positives = 62/192 (32%), Gaps = 32/192 (16%)

Query: 42  VNGILLERAAVNVMSTDHIEVD---GVPLRKA----------ERTRLWLYHKPIGLVTTH 88
           VNG L ++    V+  + + +D      +R            E   + + +KP  LV   
Sbjct: 3   VNGQLCDKPKEKVLGGERVAIDAEIDEEIRFEAQDIPLDIVYEDDDILVINKPRDLVVHP 62

Query: 89  SDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
              +   TV + L   +       R   V RLD +T GL+++         L   L   +
Sbjct: 63  GAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLRE 122

Query: 141 WLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             R Y              +  + +         +   G         ++  +  +  + 
Sbjct: 123 ITREYEAVAIGHMTAGGTVNEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRV-HTRLR 181

Query: 191 VGLREGKNREIK 202
           + L  G+  +I+
Sbjct: 182 LRLETGRTHQIR 193


>gi|109898450|ref|YP_661705.1| RluA family pseudouridine synthase [Pseudoalteromonas atlantica
           T6c]
 gi|109700731|gb|ABG40651.1| ribosomal large subunit pseudouridine synthase C [Pseudoalteromonas
           atlantica T6c]
          Length = 318

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 83/254 (32%), Gaps = 60/254 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           ++ +   QR+   +       R  ++        R++ +  ++VN   ++     + + D
Sbjct: 15  IEPDLEGQRIDNFL-------RTLLKGVPKSLIYRIVRKGEIRVNKKRVK-PEYKLQAHD 66

Query: 59  HIEVDGVPLRKA--------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
            + +  + + +                     E   L + +KP G+            + 
Sbjct: 67  QLRIPPIRVSEPNEAPSTKLDKVASLESHILFEDDLLIVLNKPSGMAVHGGSGLSFGVIE 126

Query: 99  DN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVD 154
               L      +  V RLD +T G L++       + L   L   +  + Y+    G+  
Sbjct: 127 ALRALRPQARFLELVHRLDRDTSGCLVIAKKRSALKNLHEQLRDKKMDKRYQALVVGEWP 186

Query: 155 QDKLN---LLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV-------GLRE-----GKN 198
           +++      L K I+  G       V++DT+ K S     V        L E     G+ 
Sbjct: 187 ENRYKVNAPLLKNILKSGERL----VSVDTEGKPSETRFRVLDRFSGATLVEASPITGRT 242

Query: 199 REIKKVFEFFNWKV 212
            +I+         +
Sbjct: 243 HQIRVHCLHAGHPI 256


>gi|325133994|gb|EGC56649.1| RNA pseudouridine synthase [Neisseria meningitidis M13399]
          Length = 307

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPLDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|229528953|ref|ZP_04418343.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           12129(1)]
 gi|229332727|gb|EEN98213.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           12129(1)]
          Length = 315

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-SNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|223986739|ref|ZP_03636725.1| hypothetical protein HOLDEFILI_04048 [Holdemania filiformis DSM
           12042]
 gi|223961305|gb|EEF65831.1| hypothetical protein HOLDEFILI_04048 [Holdemania filiformis DSM
           12042]
          Length = 295

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/221 (19%), Positives = 72/221 (32%), Gaps = 42/221 (19%)

Query: 19  VIARAGIASRREVERM---IAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVPL 67
           ++A  G  S  +  R    I Q ++ +NG  + ++A  V   D + +        D VP 
Sbjct: 26  LLAPWG-CS--KAARYKLEIEQ-KITLNGQPVRQSA-KVKVGDELALKVFQQEESDFVPW 80

Query: 68  RKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDI 116
               R            KP G++    +     T+ + + + + R      V  + RLD 
Sbjct: 81  AIPVRILYEDELILAVSKPAGMIVHPDNKGKTGTLANAVAAYYLRTGQHCTVRPIHRLDE 140

Query: 117 NTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
            T G++L +        L   L   Q  R Y     G +       L K I         
Sbjct: 141 GTSGIVLFSKCPFFQPKLDQALAQKQIARTYLAVVSGVMKPKDRLTLDKPIGRDRHNAKA 200

Query: 175 -------------MQVTLDTQKGSNAWVTVGLREGKNREIK 202
                        ++V    QK     V   L  G+  +I+
Sbjct: 201 YRISPTGKPAVTHVEVLRCRQKEKQTLVRCQLETGRTHQIR 241


>gi|296123212|ref|YP_003630990.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
 gi|296015552|gb|ADG68791.1| pseudouridine synthase, RluA family [Planctomyces limnophilus DSM
           3776]
          Length = 623

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 56/149 (37%), Gaps = 18/149 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDG 128
           E   + + +KP  L    S    R+T+   L  I+         RLD  T G+L+L+   
Sbjct: 408 EDESIVVINKPAPLPVHASGRFHRNTLQYLLAQIYDPQSPRAAHRLDAMTTGVLVLSRTR 467

Query: 129 GLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLK-----KGIV----IQ---GICYGD 174
            +A  L+      +  +VY  R  G+  ++            G++    I    G+    
Sbjct: 468 HMAGRLQPQFSRREVEKVYLARVQGEPAEESFECHAPMTDVAGVMGSRDIDESGGVEAST 527

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK 202
           +   +   +   + + V  +  G+  +I+
Sbjct: 528 LFRLVQRLEDGTSLLEVRPIT-GRTNQIR 555


>gi|194862296|ref|XP_001969969.1| GG23644 [Drosophila erecta]
 gi|190661836|gb|EDV59028.1| GG23644 [Drosophila erecta]
          Length = 537

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 73/209 (34%), Gaps = 29/209 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD----HIEVDGVPLRKAERTRLWL------YHKP 81
           ER +   ++ VN   + +    +   D     +    VP+       +++       +KP
Sbjct: 173 ERSLEAGKLTVNYEKVPK-DYKIKHNDLLANVVHRHEVPVTSQPIKIVYMDKDIVVVNKP 231

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        + ++ RLD  T GLLL       AR LEL   
Sbjct: 232 ASIPVHPCGRYRHNTVVFILAKEHNLKNLRTIHRLDRLTSGLLLFGRTAERARELELQIR 291

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG----- 192
           + Q  + Y  R  G+     +   +K I +     G  +V+   +     +  +G     
Sbjct: 292 TRQVQKEYVCRVEGRFPDGIVECNEK-IDVVSYKIGVCKVSPKGKDCKTTFKRIGEVGSD 350

Query: 193 -------LREGKNREIKKVFEFFNWKVNR 214
                  L  G+  +I+   ++  + ++ 
Sbjct: 351 SIVLCKPLT-GRMHQIRVHLQYLGYPISN 378


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 21/48 (43%), Gaps = 1/48 (2%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
          R+ K++   G   SR   +  +   +V VNG + ++    V     IE
Sbjct: 37 RIDKLLVERGLFDSRARAQAAVLAGQVSVNGAVAKKPGQEVDEDAQIE 84


>gi|195952821|ref|YP_002121111.1| hemolysin A [Hydrogenobaculum sp. Y04AAS1]
 gi|195932433|gb|ACG57133.1| hemolysin A [Hydrogenobaculum sp. Y04AAS1]
          Length = 246

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
          R+  ++   G ++SR + +  I + RV VNG  + +A   V   D IE+ G  
Sbjct: 4  RLDLLLVEKGLVSSREKAQAFIMEGRVFVNGKAVLKAGTLVQEEDGIELLGEE 56


>gi|149913096|ref|ZP_01901630.1| hypothetical protein RAZWK3B_03870 [Roseobacter sp. AzwK-3b]
 gi|149813502|gb|EDM73328.1| hypothetical protein RAZWK3B_03870 [Roseobacter sp. AzwK-3b]
          Length = 348

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/271 (14%), Positives = 77/271 (28%), Gaps = 73/271 (26%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE--------VERMIAQQRVKVNGILLERAAVNVMST 57
            V E    QR+ + +       RR         +E++  +  ++V+G  ++ A+  +   
Sbjct: 8   TVTEGDADQRLDRWL-------RRHFPHVSQGRIEKLCRKGELRVDGGRVK-ASTRLEVG 59

Query: 58  DHIEV---------------------DGVPLRKAERTR---LWLYHKPIGLVTTHSDPDG 93
             + +                     D   ++ A   R   +   +KP GL         
Sbjct: 60  QQVRIPPLPDPGQIDSASPHSRISDADARMIQSAVIYRDDHIIALNKPPGLPVQGGSKQT 119

Query: 94  RSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYR 146
           R    D L          +   V RLD +T G+L+L     +A+ L          ++Y 
Sbjct: 120 RHV--DGLADALRFGAEEKPRLVHRLDKDTSGVLILARSRAVAKTLTAGFRHRDTRKIYW 177

Query: 147 VRFHGQVDQDK-------LNLLKKGIVIQGIC-----------------YGDMQVTLDTQ 182
               G             +     G   +G                          +++ 
Sbjct: 178 AAVAGVPSPRMGTIRFGLVKAPGHGAQGEGEKMLCLHPEAVDSTPGAKRATTDFAVIESA 237

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               AWV +    G+  +++         + 
Sbjct: 238 GARCAWVALVPVTGRTHQLRAHMAEIGHPIV 268


>gi|69244119|ref|ZP_00602655.1| Pseudouridine synthase, RluD [Enterococcus faecium DO]
 gi|257880479|ref|ZP_05660132.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257883291|ref|ZP_05662944.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257894567|ref|ZP_05674220.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|258614127|ref|ZP_05711897.1| RNA pseudouridylate synthase [Enterococcus faecium DO]
 gi|260562478|ref|ZP_05832988.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|293559878|ref|ZP_06676390.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
 gi|293568196|ref|ZP_06679530.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|294617460|ref|ZP_06697092.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|294620663|ref|ZP_06699873.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|68196576|gb|EAN11002.1| Pseudouridine synthase, RluD [Enterococcus faecium DO]
 gi|257814707|gb|EEV43465.1| pseudouridine synthase [Enterococcus faecium 1,230,933]
 gi|257818949|gb|EEV46277.1| pseudouridine synthase [Enterococcus faecium 1,231,502]
 gi|257830946|gb|EEV57553.1| pseudouridine synthase [Enterococcus faecium 1,231,408]
 gi|260073163|gb|EEW61508.1| pseudouridine synthase [Enterococcus faecium C68]
 gi|291589096|gb|EFF20910.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1071]
 gi|291596267|gb|EFF27528.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1679]
 gi|291599760|gb|EFF30767.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium U0317]
 gi|291606150|gb|EFF35572.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecium E1162]
          Length = 285

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/148 (20%), Positives = 56/148 (37%), Gaps = 16/148 (10%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTN 126
           E   L +  KP G+ T  ++P   ST+ ++L +       R   V RLD  T G +L   
Sbjct: 86  EDEHLIIVDKPAGMKTHPNEPTENSTLLNHLAAYLDTKQQRPYVVHRLDKETSGAVLFAK 145

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGD 174
           +  +  +L   L      R Y+    G++ +D            +  K+ +  +      
Sbjct: 146 NPFVLPILGRMLEQKMIYRRYQAIVWGEIAKDMTITNKIGRDRHDRRKRVVDDKNGQSAL 205

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
             VT++        V   L  G+  +I+
Sbjct: 206 THVTVNKVLSEQTQVYCVLETGRTHQIR 233


>gi|194363955|ref|YP_002026565.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
 gi|194346759|gb|ACF49882.1| pseudouridine synthase [Stenotrophomonas maltophilia R551-3]
          Length = 253

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/167 (22%), Positives = 60/167 (35%), Gaps = 26/167 (15%)

Query: 60  IEVDGVPLRKAE-RTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSR-VISVGRLD 115
           +E D  PL+      RL + +KP GL+   S         + D L     R +  V RLD
Sbjct: 19  VETDTAPLQLLHLDERLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLD 78

Query: 116 INTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
             T G LLL  D   A +L   L   + L+ Y     G   +      +    + G    
Sbjct: 79  RATSGCLLLAFDRDTASLLGKALMGGEVLKDYLTVCRGWPAE---LSWRVDHDLDGGPGK 135

Query: 174 D--MQVTLDTQKGSNAWVTVGLRE---------------GKNREIKK 203
                   D Q+ +   ++V + E               G+ R+I++
Sbjct: 136 PVKKPAVTDFQRLATGELSVPIGEFTSSRYALLRCQPQTGRFRQIRR 182


>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 = 51.7 bits (123), Expect = 2e-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|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 = 51.7 bits (123), Expect = 2e-04,   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|253702050|ref|YP_003023239.1| pseudouridine synthase [Geobacter sp. M21]
 gi|251776900|gb|ACT19481.1| pseudouridine synthase, RluA family [Geobacter sp. M21]
          Length = 319

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 78/242 (32%), Gaps = 52/242 (21%)

Query: 10  NFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH--------- 59
           +  P+R+   I+R     +R    R+I      VNG   ++ A+ +   +          
Sbjct: 11  DSDPERLDSFISRNVPELTRSAALRLIETGFATVNGSK-QKPALKLKGGEVVQVVVPPPV 69

Query: 60  ----------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
                     IEV        E   L + +K  G+V      +   T+ + L +    + 
Sbjct: 70  PAEPQPEEIPIEV------LYEDGELVVVNKGAGMVVHPGAGNPEGTLVNALLAHCKDLS 123

Query: 110 SVG---------RLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDKL 158
            +G         R+D +T G L++         L     +    RVY    +G   +DK 
Sbjct: 124 GIGGELRPGIVHRIDKDTSGTLVVAKSDRAHNALAEQFKEHTIKRVYLALVYGSPKEDK- 182

Query: 159 NLLKKGIVIQGICYGDMQVTLD-TQKGSNAW-----------VTVGLREGKNREIK-KVF 205
             ++  I         M       ++    W           + + L  G+  +I+  + 
Sbjct: 183 GRIESSIGRHPTDRKKMSAKARHGKQAVTHWRVVARYPGITLIRLRLETGRTHQIRVHMS 242

Query: 206 EF 207
           E 
Sbjct: 243 EA 244


>gi|182419830|ref|ZP_02951070.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium butyricum 5521]
 gi|237666579|ref|ZP_04526564.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
 gi|182376378|gb|EDT73960.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Clostridium butyricum 5521]
 gi|237657778|gb|EEP55333.1| ribosomal large subunit pseudouridine synthase D [Clostridium
           butyricum E4 str. BoNT E BL5262]
          Length = 301

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/219 (15%), Positives = 77/219 (35%), Gaps = 45/219 (20%)

Query: 22  RAGIASRREVERMIA----QQRVKVNGILLERAAVNVMSTDHIEVD-------------- 63
             G+++R     +I      +R+ VN I ++     +   + I++D              
Sbjct: 24  EMGLSTR-----LIRSASIDKRIFVNDIPVK-MNRVINEGEVIKIDLAKDESQDIAPEKM 77

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST---VFDNLPSIFSRVIS--VGRLDINT 118
            + +   +   L +  KP  +V         +    V +         I   V RLD+NT
Sbjct: 78  DIEIIYEDEDILVVNKKPFMVVHPTKSYQSGTLANGVINYFMESGQNCIVRLVSRLDMNT 137

Query: 119 EGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQVDQDKLNLLK-----KGIVIQGI 170
            GL+++  +   +  +        +  + Y    HG ++ ++  + +     +GI    +
Sbjct: 138 SGLIIIAKN-QFSHGMLSKEMTENKVTKRYLAVVHGILENEEGTIDRPIYRPEGIDFGIM 196

Query: 171 CYGDMQ-------VTLDTQKGSNAWVTVGLREGKNREIK 202
              D +         +  +  + + V   L  G+  +I+
Sbjct: 197 RIVDERGQRSITHYKVIEKYENASLVECTLETGRTHQIR 235


>gi|224532212|ref|ZP_03672844.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia valaisiana VS116]
 gi|224511677|gb|EEF82083.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia valaisiana VS116]
          Length = 326

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/188 (19%), Positives = 69/188 (36%), Gaps = 40/188 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   LKREFTVKENAL--RLDLYLSSNLEVLTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHIEV--------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I +              + +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEEISQIDCLRPNNIPIAIIYEDSNIIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKIDFNGEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFRDKRTNKVYI 177

Query: 147 VRFHGQVD 154
               G  +
Sbjct: 178 AIVKGNFN 185


>gi|50555826|ref|XP_505321.1| YALI0F12199p [Yarrowia lipolytica]
 gi|49651191|emb|CAG78128.1| YALI0F12199p [Yarrowia lipolytica]
          Length = 605

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/137 (21%), Positives = 51/137 (37%), Gaps = 14/137 (10%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKPIGL 84
           I   +V +NG + +  +V V + D I+         V    +    E   L +  KP G+
Sbjct: 130 IENGQVLLNGKVAQVDSV-VRNGDAIQHRSHKHEPPVTDQEIDIVHEDDDLVVIDKPSGM 188

Query: 85  VTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
               +     +T  + L  +    V    RLD  T GL+ +  +   A     +L   Q 
Sbjct: 189 PVHPAGRYRFNTAVNILKHVNGLHVHPCNRLDRLTSGLMFMAKNPKSADKFGAQLRDRQV 248

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y  R  G+    ++
Sbjct: 249 QKQYVARVVGKFPDGEI 265


>gi|34763384|ref|ZP_00144336.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
 gi|27886957|gb|EAA24077.1| Ribosomal large subunit pseudouridine synthase D [Fusobacterium
           nucleatum subsp. vincentii ATCC 49256]
          Length = 214

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/113 (15%), Positives = 35/113 (30%), Gaps = 19/113 (16%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL------ 158
           R   + RLD +T GL+L+  +      L          + Y     G   ++ L      
Sbjct: 33  RPGIIHRLDKDTSGLILVAKNNYAHAKLASMFTDKTIHKTYLCIVKGNFSEENLNGRIEN 92

Query: 159 ---------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                      +   +V +          +  Q    + V + +  G+  +I+
Sbjct: 93  LIGRDSKDRKKMA--VVKENGKTAISNYKVIEQVDGYSLVEIAIETGRTHQIR 143


>gi|330997883|ref|ZP_08321717.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
 gi|329569487|gb|EGG51257.1| pseudouridine synthase, RluA family [Paraprevotella xylaniphila YIT
           11841]
          Length = 313

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/226 (14%), Positives = 73/226 (32%), Gaps = 28/226 (12%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKA 70
           +  ++      SR + + ++    + VN   + +    +     + V     +     K 
Sbjct: 26  LDFIMESMNGISRNKAKDILTGHGITVNKKSVSQYNYELRPGMVVRVSKHKRNNELKNKY 85

Query: 71  ERTRL-----WLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEG 120
            +         +  K  G+++    +      TV D   +          V RLD +T G
Sbjct: 86  VKIVYEDKDLIVIEKSAGILSMPAVAQQFSIKTVLDEYFTRRHFKCTAHVVHRLDRDTSG 145

Query: 121 LLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------LNLLKKGIVI----- 167
           L++   +  + R+LE    +    R Y     G+++++       L   K  +       
Sbjct: 146 LMMYAKNIEVQRILEEHWQEIVTDRRYVAIVSGKMEKEGGTISSWLKDNKAYVTYSSPTD 205

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            G  Y          +   + V + L  G+  +I+   +     V 
Sbjct: 206 NGGKYAVTHFHTLDARERYSLVELKLETGRKNQIRVHMQDIGHPVV 251


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+A SR   +R+I   +V V+   +++A   V +   + V G  L  
Sbjct: 1  MKKERLDLLLVAQGLAPSRERAKRLIMAGQVLVDERRVDKAGTTVDADASLRVTGEDLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|295133553|ref|YP_003584229.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
 gi|294981568|gb|ADF52033.1| pseudouridylate synthase [Zunongwangia profunda SM-A87]
          Length = 235

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/167 (12%), Positives = 49/167 (29%), Gaps = 23/167 (13%)

Query: 70  AERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGL 121
            E   + + +K +G +       D      V   L    ++     +  V RLD  T G+
Sbjct: 16  HEDNHIIIVNKRVGDIVQGDKTGDKPLSEVVKAYLKEKHNKPGNVYLGVVHRLDRPTSGI 75

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK------LNL-------LKKGIV 166
           +L +        L          + Y      +  +D+      L               
Sbjct: 76  VLFSKTSKALPRLNKLFQQKDAKKTYWAVVKNRPPKDQDILVHYLKRNPKQNKSFAHKNE 135

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +       ++  +  +  +   + V L+ G++ +I+         + 
Sbjct: 136 VPDSKKAILEYRILKELDNYFLLEVDLKTGRHHQIRSQLSAIGCPIK 182


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G  S R E  +++      VNG  ++ A+  V + D I V     R  E+
Sbjct: 98  MRLDNVVYRLGFGSSRSEARQLVTHGHFLVNGKKVDIASFKVSAGDVITVR-EKSRGTEK 156

Query: 73  TRLWLYH 79
            + +  +
Sbjct: 157 FKTFAEN 163


>gi|253583482|ref|ZP_04860680.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
 gi|251834054|gb|EES62617.1| pseudouridylate synthase [Fusobacterium varium ATCC 27725]
          Length = 290

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 76/241 (31%), Gaps = 53/241 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAVNVMST 57
           IV + F   R+ K +       R++ E +        I   ++KVNG   +     +   
Sbjct: 4   IVDKEFEDVRLDKFL-------RKKYENIPLTEIFKGIRTGKIKVNGKKSKE-NYRLQLN 55

Query: 58  DHIEV---DGVPLRKA------------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           D I+V   DG    +                   E   + +++K    +  H        
Sbjct: 56  DKIKVFFKDGETKEEKLLEIEDREIEKIKKSIVYEDENILIFNK-KNNMVMHKGSGYDFG 114

Query: 97  VFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ 152
           + + L           V R+D  T GL++       AR L     +    + Y +   G 
Sbjct: 115 ISELLKGYLKNPNFNFVNRIDKATSGLIIGAKSLVAARELAEEIRNRNIEKKYYILVEGI 174

Query: 153 VD------QDKLNLLK-KGIVIQGICYGDMQ----VTLDTQKGSNAWVTVGLREGKNREI 201
           +       +  L  ++ K I ++    G  +      +         +   L  G+  ++
Sbjct: 175 IKNREFTIKSYLKKIEDKVIEVEEFEEGAKESISYFKIKKYGKDCTLLEGTLGSGRTHQL 234

Query: 202 K 202
           +
Sbjct: 235 R 235


>gi|217966766|ref|YP_002352272.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
 gi|217335865|gb|ACK41658.1| pseudouridine synthase [Dictyoglomus turgidum DSM 6724]
          Length = 226

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/230 (14%), Positives = 70/230 (30%), Gaps = 50/230 (21%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLD 115
            P    E   L + +KP G++    D    +T+ +   +             +  V RLD
Sbjct: 6   RPEIIYEDNHLLVVNKPAGVLVQG-DITKSTTLLEISKAYIKEKYQKAGNVFLAIVHRLD 64

Query: 116 INTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
               G+++   +   A  L       +  + Y     G         +KKG + + + + 
Sbjct: 65  KPVSGVVIFARNSKSAGRLSEAFRERKVEKEYLAICEGIF------KIKKGTINESLFWD 118

Query: 174 DMQVTLDTQKGSNAWVTVGLRE-----------------GKNREIKKVFEFFNWKVNRLI 216
           + +        + + V +   E                 G+  +++      ++      
Sbjct: 119 ERERKAKISNKAESRVAITHYEVLEEFKNLSLVRLIPETGRKHQLR---AHLSY------ 169

Query: 217 RISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYS 263
               G   LG    G  R    KI    R    PH +++  +     + +
Sbjct: 170 ---IGHPILGDEKYGGVRIFKDKIFLHCRRMRIPHPVKKEIMEFKTEVPN 216


>gi|291521873|emb|CBK80166.1| SSU ribosomal protein S4P [Coprococcus catus GD/7]
          Length = 197

 Score = 51.7 bits (123), Expect = 2e-04,   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|255323619|ref|ZP_05364749.1| RNA pseudouridine synthase family protein [Campylobacter showae
           RM3277]
 gi|255299333|gb|EET78620.1| RNA pseudouridine synthase family protein [Campylobacter showae
           RM3277]
          Length = 307

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 42/221 (19%), Positives = 87/221 (39%), Gaps = 32/221 (14%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKA-ERTRLWLYHKPI 82
           REV+R+I + R+  +G ++     N + +  I +     +   L+   E  +  ++ KP 
Sbjct: 28  REVQRLIDKGRLTCDGAVVSE--KNALLSGEICLIDYETNPRGLQPIFECDKFAVFDKPS 85

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISV-GRLDINTEGLLLLTNDGGLARVL--ELPST 139
           G+++  +      ++ D + S++ R  SV  RLD  T GL+++  D      L     + 
Sbjct: 86  GVLSHPNGRHCEYSLNDEIWSLYGREASVAHRLDCETSGLIVVGKDKNAVVNLKKLFENR 145

Query: 140 QWLRVYRVRFHGQVDQD-------KLN------LLKKGIVIQGICYGDMQVTLD-TQKGS 185
           Q  + Y    +G++ ++        L        ++  I   G       + ++      
Sbjct: 146 QVYKSYVALVYGKISENLHIEANMDLANDYDDVKMRMRICEDGKGAVTEILPIEYFADID 205

Query: 186 NAWVT-VGLREGKNREIK-KVF--EF--FNWKVNRLIRISY 220
              V  V L  G+  +I+  +F  E       +  L R+  
Sbjct: 206 ATLVRAVPLT-GRQHQIRLHLFHVEHKILGEPLYGLSRLQI 245


>gi|53719166|ref|YP_108152.1| putative ribosomal large subunit pseudouridine synthase D
           [Burkholderia pseudomallei K96243]
 gi|126454439|ref|YP_001066469.1| RluA family pseudouridine synthase [Burkholderia pseudomallei
           1106a]
 gi|242316335|ref|ZP_04815351.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
 gi|52209580|emb|CAH35533.1| putative ribosomal large subunit pseudouridine synthase D
           [Burkholderia pseudomallei K96243]
 gi|126228081|gb|ABN91621.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106a]
 gi|242139574|gb|EES25976.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1106b]
          Length = 395

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 77/238 (32%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 66  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 124

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 125 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 184

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L     +    R Y     G++  +            
Sbjct: 185 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 244

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 245 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 302


>gi|325142086|gb|EGC64512.1| RNA pseudouridine synthase [Neisseria meningitidis 961-5945]
          Length = 307

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPIDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|154275958|ref|XP_001538824.1| hypothetical protein HCAG_06429 [Ajellomyces capsulatus NAm1]
 gi|150413897|gb|EDN09262.1| hypothetical protein HCAG_06429 [Ajellomyces capsulatus NAm1]
          Length = 545

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/163 (15%), Positives = 53/163 (32%), Gaps = 24/163 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ I    V +NG  +      + + D I          V   P+    E   + +  KP
Sbjct: 82  QKAIEDGAVCINGKAV-SIDTKIQNGDVISHTLHRHEPPVTSQPIGIIHEDDDMIVIDKP 140

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     +++ + + +            RLD  T G++ +      A  +  +L
Sbjct: 141 AGVPVHPAGRYNYNSILEIMKAERGNGWVPYPCNRLDRLTSGVMFIGKHPKGAEQIGEKL 200

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTL 179
            S    + Y  R  G+           G+V+       +   L
Sbjct: 201 RSRTVRKEYVARVKGKFPD--------GVVLCDQPMLKISPIL 235


>gi|45358573|ref|NP_988130.1| RluA family pseudouridine synthase [Methanococcus maripaludis S2]
 gi|44921331|emb|CAF30566.1| Pseudouridine synthase:Pseudouridine synthase, Rlu. Related protein
           [Methanococcus maripaludis S2]
          Length = 297

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 46/261 (17%), Positives = 102/261 (39%), Gaps = 51/261 (19%)

Query: 42  VNGILLERAAVNV--MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           +N I  E   +NV     D + VD        +++  + H    +++         +   
Sbjct: 72  INNITPENLTLNVIYEDDDLLIVD--------KSKNMVVHPTKNVLSGT--LANAISNHQ 121

Query: 100 NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD--- 154
            + +   ++  V RLD++T GLL++  +    + L     +    ++Y    +G +D   
Sbjct: 122 KINNQNYKIRFVNRLDMDTTGLLIVAKNSYSHQQLAKQMDEGILEKIYIAVVNGHLDLKE 181

Query: 155 ---QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
              +D ++L + GI  +          +  +  +  + + + + L  G+  +I+      
Sbjct: 182 GIIEDSIDLNENGIKRELSNFGKISKTKYKVIEELKNASVLEINLLTGRTHQIR------ 235

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL-REQLGPHLLEEAQVNLDAPIYSSETL 267
                 +   S G + +G  L G     + K++ R+ L  H+L                +
Sbjct: 236 ------VHLSSTGNYIIGDTLYGE----TSKLIDRQALHSHIL-----------RFIHPI 274

Query: 268 VRDRPNIISEVPDDFTRMKKN 288
            +++  IIS++PDD   + KN
Sbjct: 275 TKEKIEIISKLPDDMKNLIKN 295


>gi|153810915|ref|ZP_01963583.1| hypothetical protein RUMOBE_01301 [Ruminococcus obeum ATCC 29174]
 gi|149832803|gb|EDM87886.1| hypothetical protein RUMOBE_01301 [Ruminococcus obeum ATCC 29174]
          Length = 334

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/119 (21%), Positives = 47/119 (39%), Gaps = 17/119 (14%)

Query: 56  STDHI--------EVDGVPL-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
            TD I        ++ G  L    E   +   +KP G++T  +      ++ + + + F 
Sbjct: 67  ETDEIQSAQLVLAKIQGERLCILYEDEDILAVNKPAGVLTHPAGMHYSDSLANQVAAYFQ 126

Query: 107 R------VISVGRLDINTEGLLLLTNDGGLARVL-ELPSTQW-LRVYRVRFHGQVDQDK 157
                  +  +GRLD  T G++L   +   A+ L E   T    + Y     G + +D+
Sbjct: 127 ERNLSVCIRPIGRLDKETSGIVLFAKNQVAAQRLQEQRETGVLEKQYLALVDGNLPKDQ 185


>gi|229541367|ref|ZP_04430427.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
 gi|229325787|gb|EEN91462.1| pseudouridine synthase, RluA family [Bacillus coagulans 36D1]
          Length = 290

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/199 (16%), Positives = 66/199 (33%), Gaps = 33/199 (16%)

Query: 36  AQQRVKVNGILLE--------RAAVNVMSTDH----IEVDGVPL-RKAERTRLWLYHKPI 82
               + VNG  +          AA  V   +     +  + +P     E   + +  KP 
Sbjct: 37  RGGMILVNGREVTVRYRLQPGDAAAIVFPKETPSPNLTPENIPFGHVYEDESVLVADKPA 96

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLAR--VL 134
            + T  S     +++ + +   + +      V  V RLD NT GL+L+  +  +     L
Sbjct: 97  FMNTIPSREHPSASLANAVLGHYRKNGIESAVHVVTRLDRNTSGLVLIAKNRYIHHLCSL 156

Query: 135 ELPSTQWLRVYRVRFHGQVDQD--KLNL---------LKKGIVIQGICYGDMQVTLDTQK 183
                   R Y     G   +    +           +++G+      +      +  Q 
Sbjct: 157 MQQKHVICRTYEALAEGAFTEKSGTIEAPIGRKETSIIERGVR-DDGQFARTHYEVVRQF 215

Query: 184 GSNAWVTVGLREGKNREIK 202
            + A V + L  G+  +I+
Sbjct: 216 PAYAHVRLRLDTGRTHQIR 234


>gi|126438505|ref|YP_001059203.1| RluA family pseudouridine synthase [Burkholderia pseudomallei 668]
 gi|167738292|ref|ZP_02411066.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 14]
 gi|167815478|ref|ZP_02447158.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 91]
 gi|167845428|ref|ZP_02470936.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei B7210]
 gi|126217998|gb|ABN81504.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 668]
          Length = 389

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 77/238 (32%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L     +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G  S R E  +++      VNG  ++ A+  V + D I V     R  E+
Sbjct: 98  MRLDNVVYRLGFGSSRSEARQLVTHGHFLVNGKKVDIASFKVSAGDVITVR-EKSRGTEK 156

Query: 73  TRLWLYH 79
            + +  +
Sbjct: 157 FKTFAEN 163


>gi|315222228|ref|ZP_07864135.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
 gi|315188731|gb|EFU22439.1| pseudouridine synthase, RluA family [Streptococcus anginosus F0211]
          Length = 286

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/215 (15%), Positives = 75/215 (34%), Gaps = 31/215 (14%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGVPLRKA--------------E 71
           R++   +  ++ V VN   +      V   D I    D     +               +
Sbjct: 28  RKIRHFLRIKKHVLVNQHPI-NWQSQVHPADVITLIFDEEDYPQKSILMGNASLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              + + +KP G+ T  ++P   + +      + +    V RLD  T G +L   +  + 
Sbjct: 87  DEHITIVNKPEGMKTHANEPTELALLNHVSAYVGNTCYVVHRLDKETSGAVLFAKNPFIL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQ------DKL-----NLLKKGIVIQGICYGDMQVT 178
            +L   L + +  R Y     G   Q      DK+     +  K+ +  +   Y +  ++
Sbjct: 147 PILNRLLENKEISREYWALVQGAFPQKRQIYTDKIGRDRHDRRKRLVDNKNGQYAETHIS 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +  +   V+  L+ G+  +I+       + + 
Sbjct: 207 KLKEFENKTLVSCQLKTGRTHQIRVHLAHHGYPII 241


>gi|281492772|ref|YP_003354752.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
 gi|281376424|gb|ADA65910.1| Ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis KF147]
          Length = 288

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/189 (17%), Positives = 59/189 (31%), Gaps = 29/189 (15%)

Query: 42  VNGILLERAAVNVMSTDHIE--VDGVPLRK--------------AERTRLWLYHKPIGLV 85
           VN  L+    + V + D I    D                     E   L + +KP G+ 
Sbjct: 42  VNNKLINENQL-VHAGDKITLIFDNEDFSNLSLKFGSVNLADILYEDEHLIVVNKPEGMK 100

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
           T  +  D  +       +I   V  V RLD  T G +L   +  +  +L       +  R
Sbjct: 101 THGNTADELALQNHVAAAINQEVFVVHRLDHATSGAVLFAKNQFVLPILGKMFEENKIHR 160

Query: 144 VYRVRFHGQVDQDKLNLLK----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            Y     G   +++  + +          K I+          V +  +      V   L
Sbjct: 161 EYLALVKGHFSENQFTIDRAIGQNRHDKNKRILSAKGQKAVTHVEIIKKFTDKTLVKCTL 220

Query: 194 REGKNREIK 202
             G+  +I+
Sbjct: 221 DTGRTHQIR 229


>gi|260912603|ref|ZP_05919132.1| ribosomal large subunit pseudouridine synthase [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260633281|gb|EEX51442.1| ribosomal large subunit pseudouridine synthase [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 229

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/192 (13%), Positives = 51/192 (26%), Gaps = 37/192 (19%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
           +   E   + +  K  G +   SD  G   + D + +             +  V RLD  
Sbjct: 10  IPVYEDNHIIIVSKHSGEIVQ-SDKTGDVPLVDIVKNYLKEKYAKPGNVFLGVVHRLDRP 68

Query: 118 TEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL-------------K 162
             GL+           +     +    + Y        + +   L+              
Sbjct: 69  VWGLVAFAKTSKALSRMNALFRTGDVEKTYWAIVQSPPENESGELVHWLTRNEKQNKSYA 128

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
               + G     +   +  Q  +   + V L  G++ +I+         +          
Sbjct: 129 HNHEVAGAKKAILSYKVIGQSENYTLLEVQLMTGRHHQIRCQLAAMGCPIK--------- 179

Query: 223 FQLGTLLAGSTR 234
              G L  G+ R
Sbjct: 180 ---GDLKYGAKR 188


>gi|229553304|ref|ZP_04442029.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|258540084|ref|YP_003174583.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
 gi|229313390|gb|EEN79363.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus rhamnosus
           LMS2-1]
 gi|257151760|emb|CAR90732.1| Ribosomal large subunit pseudouridine synthase D [Lactobacillus
           rhamnosus Lc 705]
          Length = 289

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/221 (15%), Positives = 73/221 (33%), Gaps = 30/221 (13%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI----LLERAAVNV----MSTDHIEVDGVPLRK 69
           + +A+ G+ S R  ++M+A   + ++G        +A   V     +T  +  +   L  
Sbjct: 17  RWLAKQGV-SHRLFKKMLANHLLWLDGHRTGNTAIQAGQTVRFAIPTTMTVTPEKASLDV 75

Query: 70  AERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VGRLDINTEGL 121
               + WL  +KP  L +     D   ++ + +     +          + RLD +T GL
Sbjct: 76  LYEDQNWLIINKPAHLTSVPGPHDPHHSLLNRIVWYLQQQKVTEPQPAIITRLDRDTVGL 135

Query: 122 LLLTNDGGLARVLELPSTQ-WLRVYRVRFHGQVDQDKLNLLKKGIVI----------QGI 170
           +L           +        + Y     G +       ++  I +          +  
Sbjct: 136 VLAAKHPYAQGRFDQAHHATLKKEYLAVVAGHLSHAT-ETIEAPIGLGPDGIHRMVTENG 194

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                +  +  ++  N  V V L  G+  +I+  F      
Sbjct: 195 QSAITKYQVL-KEAVNTLVEVQLLTGRTHQIRVHFASLGHP 234


>gi|115375226|ref|ZP_01462492.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|310818943|ref|YP_003951301.1| pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
 gi|115367788|gb|EAU66757.1| ribosomal large subunit pseudouridine synthase D [Stigmatella
           aurantiaca DW4/3-1]
 gi|309392015|gb|ADO69474.1| Pseudouridine synthase [Stigmatella aurantiaca DW4/3-1]
          Length = 345

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/230 (16%), Positives = 70/230 (30%), Gaps = 38/230 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           +V+ N+   R+ + +       SR  ++R+I +  V        + +  V       +  
Sbjct: 28  VVEPNYAGWRLDRYLGEKIRRLSRPRIQRIIQRGLVC---ERRLKPSTLVFPGLTFSIRR 84

Query: 65  VPLRKAERTR----------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI--SVG 112
               + E             L +  KP GL    +    + T+   L   F         
Sbjct: 85  SLSTEPETPTELPIVYQDDWLLVLDKPAGLPIHPTARYQKGTLVSLLRERFGERFAEPAH 144

Query: 113 RLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGI 170
           RLD  T GL++        RVL     S    + Y     G   +D         + +G 
Sbjct: 145 RLDRETSGLVVCGRTTEACRVLGRLFLSRDVHKEYLAVCEGHPPEDT--FFVDAPIAEGT 202

Query: 171 CYGDMQVTLDTQKGSNAWVTVGLRE------------------GKNREIK 202
               + V +D  +G  +     + +                  G+  +I+
Sbjct: 203 ELIRIAVRIDRAEGKESRTRFQVLQRFVRDGAPFALLRCYPETGRQHQIR 252


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+   +   G   SR   +  I    VKVNGI + + + +V   D IEV
Sbjct: 1  MRLDAYLVEMGHFKSRGRAKTAILDGNVKVNGITVTKVSRDVSIDDVIEV 50


>gi|325198068|gb|ADY93524.1| RNA pseudouridine synthase [Neisseria meningitidis G2136]
          Length = 307

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++     A      +    + Y      R       D ++
Sbjct: 142 EDITPLHRLDKDTAGVMLLSHNPATRGAYQTMFQNKTVWKTYEALAPTRTDLPYPIDVVS 201

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 202 RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 250


>gi|319649950|ref|ZP_08004100.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
 gi|317398388|gb|EFV79076.1| pseudouridine synthase [Bacillus sp. 2_A_57_CT2]
          Length = 212

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/142 (19%), Positives = 49/142 (34%), Gaps = 23/142 (16%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-----------DGVPLRK---AERTRLWLYHKPIG 83
             +KVN   +      +   D ++V            G  L      E   L + +KP G
Sbjct: 41  GFIKVNNQEV-NVRYELKEGDILQVGFPEEVPSKGMKGEDLPLDILYEDAYLLIVNKPAG 99

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRV------ISVGRLDINTEGLLLLTNDGGLARVLELP 137
           + T  S      ++ + L   + R+        V RLD +T GL+L+     +  +    
Sbjct: 100 VSTIPSREHPSGSLANRLIGYYQRIGLKSAAHIVTRLDRDTSGLVLIAKHRHVHHLFSQQ 159

Query: 138 S--TQWLRVYRVRFHGQVDQDK 157
               +  R Y     G + +D 
Sbjct: 160 QRFRKIQRTYEAFAEGTISRDA 181


>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 = 51.7 bits (123), Expect = 2e-04,   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|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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/86 (29%), Positives = 35/86 (40%), Gaps = 5/86 (5%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+   + R G A SR E    IA  RV V G +  + +  V     + V    L     +
Sbjct: 5  RLDAELVRRGHARSRAEAAEFIAAGRVLVAGQVATKPSTAVDPAVALLVRDADLDPRWAS 64

Query: 74 RLWLYHKPIGLVTTHSD--PDGRSTV 97
          R    HK IG +   +D   DGR  +
Sbjct: 65 RGA--HKLIGALDAFTDVVVDGRRCL 88


>gi|288576272|ref|ZP_06394280.1| RNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
 gi|288565855|gb|EFC87415.1| RNA pseudouridine synthase [Neisseria mucosa ATCC 25996]
          Length = 169

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/122 (13%), Positives = 41/122 (33%), Gaps = 20/122 (16%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLA--RVLELPSTQWLRVYRVRFHGQVDQDKLN---- 159
           + +  + RLD +T G++LL+++            +    + Y         +  L     
Sbjct: 4   ADITPIHRLDKDTAGVMLLSHNPATRRDYQTMFQNKTVCKTYEAIA---PTRTDLAYPLN 60

Query: 160 ---LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFN 209
               + +G      + ++G       V L   +G+ +   +    GK  +++  +     
Sbjct: 61  ISSRMVRGEKFFTTLEVEGEPNAHTTVELIENRGAFSLYRLTPHTGKKHQLRVHMM-SLG 119

Query: 210 WK 211
             
Sbjct: 120 MP 121


>gi|148264094|ref|YP_001230800.1| hemolysin A [Geobacter uraniireducens Rf4]
 gi|146397594|gb|ABQ26227.1| hemolysin A [Geobacter uraniireducens Rf4]
          Length = 250

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             +R+ K++   G+A SR   + +I   +V V+  L ++A   V     I + G  
Sbjct: 1  MAKERLDKILLDRGLAQSRERAKALIMAGQVVVDDHLADKAGQMVALEAEIRLKGEV 57


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+   + R G+A SR     +IA  RV+V G    + A  V   D + + G       R 
Sbjct: 6  RLDAELVRRGLARSRAHAAELIAAGRVRVRGFTATKPAAGVDPADPVLLAGDGDDYVSRG 65

Query: 74 RLWLYHKPIGLVTTHSD 90
               HK +G ++  +D
Sbjct: 66 A----HKLVGALSAFAD 78


>gi|222153833|ref|YP_002563010.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
 gi|222114646|emb|CAR43689.1| RNA pseudouridylate synthase [Streptococcus uberis 0140J]
          Length = 294

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/215 (15%), Positives = 72/215 (33%), Gaps = 34/215 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV---------------DGVPLR-KAE 71
           R++   +  ++ + +N  ++      V + DHI +               D   +    +
Sbjct: 34  RKIRHFLRIKKHILINHQMV-NWQNQVQTGDHITLIFDEEDYPSKVIAFGDPKLVDCLYQ 92

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +KP G+ +  + PD  + +      +      + RLD  T G +L   +    
Sbjct: 93  DEHLIVVNKPEGMKSHANQPDELALLNHVSAYVGKTCYIIHRLDKETSGTILFAKNPFIL 152

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQ-GICYGDMQ 176
            +     L +    R Y     G + + KL           +  K+ + ++ G     + 
Sbjct: 153 PIMNR-MLENRDISRTYWAFVSGTIKEKKLTIQKPIGRHRHDRRKRVVDMKQGQKAITIV 211

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             L     S   V   L+ G+  +I+   +     
Sbjct: 212 KKLKNDSSSFTLVECHLKTGRTHQIRVHMDAIGHP 246


>gi|254189036|ref|ZP_04895547.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
 gi|157936715|gb|EDO92385.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           Pasteur 52237]
          Length = 395

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 77/238 (32%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 66  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 124

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 125 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 184

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L     +    R Y     G++  +            
Sbjct: 185 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 244

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 245 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 302


>gi|160876810|ref|YP_001556126.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|160862332|gb|ABX50866.1| pseudouridine synthase [Shewanella baltica OS195]
 gi|315269012|gb|ADT95865.1| pseudouridine synthase [Shewanella baltica OS678]
          Length = 225

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 57/165 (34%), Gaps = 30/165 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G++++     
Sbjct: 19  QDKDIIVINKPSGLLSVPGRDPAHYDSVYARVKAEHPHSQIVHRLDMATSGVIVVALIRS 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV------ 177
             R L+      +  + Y  R  G V  D       G V    I        Q       
Sbjct: 79  AERELKRQFHDRETSKTYFARVAGHVKNDT------GSVDYPLICDWPNRPKQKVDHLVG 132

Query: 178 -------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                   + ++   +  V +  +  G++ +++  +       + 
Sbjct: 133 KPSLTHYQVISRAKRSTLVKLTPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|321257772|ref|XP_003193704.1| hypothetical protein CGB_D5020C [Cryptococcus gattii WM276]
 gi|317460174|gb|ADV21917.1| Conserved hypothetical protein [Cryptococcus gattii WM276]
          Length = 497

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/139 (21%), Positives = 56/139 (40%), Gaps = 16/139 (11%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHI--EV---------DGVPLRKAERTR-LWLYHKPI 82
           +     +VNG++     + + + D I   V         D + +   +R R   +  KP 
Sbjct: 63  LESGVTRVNGVVAR-PDLILRNGDRIDNTVHRHEPPVTNDPILILHIDREREFIVISKPG 121

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELP--ST 139
            L    +    + TV + + S +  +  SV RLD  T GL++L   G  A  L       
Sbjct: 122 SLPVHAAGRYFKHTVLEMMESDYGLKCYSVNRLDRLTSGLMILALSGKAASKLAREFVEG 181

Query: 140 QWLRVYRVRFHGQVDQDKL 158
           +  + Y  R  G+  ++++
Sbjct: 182 KVKKEYVARVKGKFPEEEV 200


>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 = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 36/94 (38%), Gaps = 13/94 (13%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M+   I++      R+ + + + G+  SR   + MI    V VN   +++A   +     
Sbjct: 1  MERSRILK-----IRLDQYLVQHGLIQSRERAKAMIMSGVVFVNEQKVDKAGEMIKEDAK 55

Query: 60 IEVDGVPLRKAERTRLWLYHK-------PIGLVT 86
          +EV G  +    R  L L          P G V 
Sbjct: 56 VEVRGHDIGYVSRGGLKLEKAMQCFPLTPKGKVC 89


>gi|119384947|ref|YP_916003.1| RluA family pseudouridine synthase [Paracoccus denitrificans
           PD1222]
 gi|119374714|gb|ABL70307.1| ribosomal large subunit pseudouridine synthase D [Paracoccus
           denitrificans PD1222]
          Length = 341

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 52/281 (18%), Positives = 90/281 (32%), Gaps = 65/281 (23%)

Query: 1   MKDKNIVQENFTPQRVSKVIA----RAGIASRREVERMIAQQRVK-----V-NGILLERA 50
           M +  I       +R+ K +A         SR  + ++IA+  V      V +G +    
Sbjct: 1   MAEILITIPEGLSERLDKALALAAPEQAALSRSRLAKLIAEGAVLGPSGPVTDGKVRAET 60

Query: 51  A---VNVMSTDHIEVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
               V +++ + +E    P+  A   E   L +  KP G+V   +      T+ + L + 
Sbjct: 61  GDYRVRIVAPEPLEAQPEPIPLAVAYEDAELIVVDKPAGMVVHPAPGAPSGTLVNALLAH 120

Query: 105 FS----------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQ 152
            +          R   V R+D  T GLL++       + L          R Y    HG 
Sbjct: 121 CAGSLSGIGGAARPGIVHRIDKETSGLLVVAKTDRAHQGLARQFADHTARRRYLAIAHGM 180

Query: 153 VDQDKLNLLKK--GI-----------VIQGICYGDMQ---VTLDTQKGSNAWVTVG---- 192
           +D      L+   G+            + G   GD Q   V+    + +     V     
Sbjct: 181 IDPAD-ARLRGLPGVGFEPGGVLRIATLIGRHPGDRQRQAVSFQNGRHAVTRARVVETFG 239

Query: 193 ------LRE-----GKNREIK-KVFEF----FNWKVNRLIR 217
                 L E     G+  +I+  +           V    R
Sbjct: 240 TPPAAMLVECRLETGRTHQIRVHMAHAGLGLVGDPVYGGNR 280


>gi|289649339|ref|ZP_06480682.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. aesculi str. 2250]
          Length = 318

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLMKSNLRSGERMVEVNEEGKEALTIF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|145299818|ref|YP_001142659.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142852590|gb|ABO90911.1| ribosomal large subunit pseudouridine synthase A [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 232

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 76/228 (33%), Gaps = 51/228 (22%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   L L +KP GL++ +  +P    +V   L   +     V RLD  T G++++  +  
Sbjct: 22  EDEHLLLINKPSGLLSLSGKNPQNLDSVHYRLVQDYPGCTLVHRLDFGTSGIMVVARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQ 182
           +  +L    +Q    + Y       +  D      +G++   I          ++   + 
Sbjct: 82  INALLCQQFSQRAVSKAYSALLCDHLTDD------EGMIDAPIAKDPALFPLMKICAASG 135

Query: 183 KGSNAWVTVG---LRE------------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V     RE                  G+  +++   +     +       YG
Sbjct: 136 KPARSRYEVEDRLCRESEHGETQLLTRVRLVPETGRTHQLRIHCQLVGHPILGCD--LYG 193

Query: 222 PFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                 LL G           EQ    +L  ++++L  P+      VR
Sbjct: 194 GL----LLPGC----------EQAPRLMLHASELDLVHPVSGEPMAVR 227


>gi|104773696|ref|YP_618676.1| pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103422777|emb|CAI97416.1| Pseudouridylate synthase [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125343|gb|ADY84673.1| Ribosomal large subunit pseudouridine synthase [Lactobacillus
           delbrueckii subsp. bulgaricus 2038]
          Length = 302

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 83/255 (32%), Gaps = 56/255 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRRE---VERMIAQQRVKVNGILLERAAVNVMST 57
           M+   ++     P ++S  + + G  SRR     +       + VN       +  +   
Sbjct: 1   MQVYKMIVAKNDPGQLSHFLLKKGF-SRRAVNNCKN--HGGMMLVNHHR-RNGSYRLKEG 56

Query: 58  DHI-------------EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D +             +V   PL   E T    + +KP GL++  S       V + + +
Sbjct: 57  DVVHFLMGQEPVNPWLKVSRRPLDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLA 116

Query: 104 IFSRV---------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVR 148
            F +            V RLD +T GL+LL   G     +       L      + Y   
Sbjct: 117 YFEKQGVNPAYVKPHIVTRLDQDTSGLVLL---GK--NAIAHDRFSKLGKDAFIKKYHAI 171

Query: 149 FHGQVDQDKLNLL------------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            HG   +  L+ L            K+ +  +G      +  +  Q    + V + L  G
Sbjct: 172 VHGNFAEGDLSGLIDKPLARVGDTVKREVNPKGQRALT-EYRVLNQVPGASLVELRLLTG 230

Query: 197 KNREIK-KVFEFFNW 210
           +  +I+  +      
Sbjct: 231 RTHQIRIHM-ASIGH 244


>gi|254297450|ref|ZP_04964903.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           406e]
 gi|157806772|gb|EDO83942.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           406e]
          Length = 389

 Score = 51.7 bits (123), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 77/238 (32%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L     +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLIRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>gi|312622364|ref|YP_004023977.1| pseudouridine synthase, rlua family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202831|gb|ADQ46158.1| pseudouridine synthase, RluA family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 293

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/173 (11%), Positives = 56/173 (32%), Gaps = 19/173 (10%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +    +    ++ + V+G      E       +KP GL +  S      T+ + +    +
Sbjct: 58  VIEVDLIFSKSNIVPVEGSIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLN 117

Query: 107 RV----ISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVD----- 154
                   + RLD +T G+++   +      +        +  + Y    HG +      
Sbjct: 118 SKNLTSHIINRLDKDTSGIVVFAKN-SYFHSIVSYEFEKRRVDKTYIAIVHGILTKKSGL 176

Query: 155 -QDKLNLLKKGIVIQ---GICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +  +     GI  +      +      +     + + + +  +  G+  +++
Sbjct: 177 IEKPIKRSDDGIKREIHQDGSFAFTYYEVIDTFENFSVLKLKPIT-GRTHQLR 228


>gi|253579159|ref|ZP_04856429.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849257|gb|EES77217.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 233

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 45/218 (20%), Positives = 77/218 (35%), Gaps = 38/218 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHS-----DPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLLL 123
           E   + + HKP GL   ++     D +   ++ +   +P     +  + RLD   EG+L+
Sbjct: 13  EDKDILVCHKPAGLAVQNARVGSMDMESLLKNYIAQKVPGKMPYLGIIHRLDQPVEGVLV 72

Query: 124 LTNDGGLARVLELPST--QWLRVYRVRFHGQV---DQDKLNLLKK-G-----IVIQGICY 172
              +   A  L    T  +  + Y     G V       ++ LKK G      V++G   
Sbjct: 73  FALNPKAAADLSRQMTAGKIKKTYLAVTEGTVKVKSAKLVDWLKKDGRTNSSAVVEGGTS 132

Query: 173 GDMQVTL------------DTQK-GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRI- 218
           G  +  L            D Q  G    + + L  G++ +I+         +    R  
Sbjct: 133 GAKKAILSYEVLETWKNKEDAQDCGERNLIRIDLDTGRHHQIRVQMAHAGMPLVG-DRKY 191

Query: 219 -----SYGPFQLGTLLAGSTREVSKKILREQLGPHLLE 251
                S  P  L +   G    V+KK L  Q+ P  + 
Sbjct: 192 NPGQNSQEPLALCSAKLGFQHPVTKKQLEFQVQPAGMA 229


>gi|167041415|gb|ABZ06167.1| putative RNA pseudouridylate synthase [uncultured marine
           microorganism HF4000_006O13]
          Length = 320

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/245 (16%), Positives = 80/245 (32%), Gaps = 48/245 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMST 57
           + +K IV  +    R+   + +       SR  + RMI +  V++N    +     V   
Sbjct: 6   INNKVIVSRDDDGMRLDNYLIKIIKGMPKSR--IYRMIRKGEVRINSKRAK-PRSRVHVN 62

Query: 58  DHIEV----------DGVPLRKAERTRL-----------WLYHKPIGLVTTHSDPDGRST 96
           D + +          +   +RK +  R+            L +KP G +  H        
Sbjct: 63  DTVRIPPYAVNEPKTNVSSVRKDDFRRINNIVIFENDSFLLVNKPSG-LAVHGGSGIHLG 121

Query: 97  VFDNL----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFH 150
           + + L          +  V RLD +T G LL++      R L       +  + Y     
Sbjct: 122 LIELLRSFREKRNEHLELVHRLDKDTSGCLLVSKKKSKLRKLHEYFREGKVKKTYLGLMV 181

Query: 151 GQVDQ---------DKLNLLKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGK 197
           G+  Q           +   + G   +          +  L  +  ++A   +  +  GK
Sbjct: 182 GKFTQTVYEIDQPLKIITTPENGRLAVPDDSGKKAKTKFFLMEKYKNSALFKIEPIT-GK 240

Query: 198 NREIK 202
             +I+
Sbjct: 241 THQIR 245


>gi|229090249|ref|ZP_04221495.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-42]
 gi|228693095|gb|EEL46810.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           Rock3-42]
          Length = 292

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/266 (16%), Positives = 86/266 (32%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLE-RAAVNVMSTDHIEV-----------DGVPL-RKAERTRLWLYHKPIGL 84
             ++VNG     R  + V     I             + +PL    E   + + +K   +
Sbjct: 36  GAIEVNGQHASVRHQLQVGEELRIFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEANM 95

Query: 85  VTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE--- 135
            T  S      +V + L S + +      V  V RLD +T GL+L+  +      L    
Sbjct: 96  STIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSKQ 154

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +++   
Sbjct: 155 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVINSANH 214

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 215 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 262

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++  A I S    V
Sbjct: 263 SLTFYHPILEKEMSFTAMIPSDMQEV 288


>gi|153827554|ref|ZP_01980221.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-2]
 gi|149738478|gb|EDM52874.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           MZO-2]
          Length = 315

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDAEC--KVVNAPLLKNEVNSIVRVN-PNGKSSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|170660217|ref|YP_001740053.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213969773|ref|ZP_03397908.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato T1]
 gi|301382849|ref|ZP_07231267.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato Max13]
 gi|302062845|ref|ZP_07254386.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato K40]
 gi|302131353|ref|ZP_07257343.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato NCPPB 1108]
 gi|118201620|gb|ABK79683.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato str. DC3000]
 gi|213925581|gb|EEB59141.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tomato T1]
 gi|330878259|gb|EGH12408.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. morsprunorum str. M302280PT]
 gi|331019164|gb|EGH99220.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. lachrymans str. M302278PT]
          Length = 318

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEEGKEALTLF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|85712033|ref|ZP_01043087.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
 gi|85694219|gb|EAQ32163.1| Predicted pseudouridylate synthase, Rlu family protein [Idiomarina
           baltica OS145]
          Length = 239

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/176 (19%), Positives = 55/176 (31%), Gaps = 38/176 (21%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L +  KP GL+   S    D +      L      RV  V RLD  T GLL+    
Sbjct: 12  KDEYLVVIDKPSGLLVHRSWLASDAKRFAMQMLRDQLGQRVYPVHRLDRPTSGLLIFALS 71

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN--LLKKGIVIQGICYGDMQVTLD--- 180
             +AR L          +VY     G VD   +    LK+    +     D Q   D   
Sbjct: 72  SEIARALNEQFAERDIKKVYHAVVRGYVDDAGIIDYALKE----EHDKIADKQAQADKPA 127

Query: 181 -------------------TQKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
                              ++K   +  ++     L  G+  ++++        + 
Sbjct: 128 QEAVTEYQCVARVELPFKVSKKHDTSRYSLVKLMPLT-GRKHQLRRHMSHIRHPII 182


>gi|118588379|ref|ZP_01545788.1| pseudouridine synthase [Stappia aggregata IAM 12614]
 gi|118439085|gb|EAV45717.1| pseudouridine synthase [Stappia aggregata IAM 12614]
          Length = 223

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/153 (15%), Positives = 56/153 (36%), Gaps = 16/153 (10%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L +  KP GL++      +    +       ++    V RLD++T G+++L  +    R 
Sbjct: 28  LLVVDKPSGLLSVPGKAAEHADCIESRAQERYADARIVHRLDMDTSGIMVLARNPAAHRH 87

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGICYGDMQVTLD 180
           L L     + L+ Y     G   +D+               K+ +  +       +  + 
Sbjct: 88  LGLQFERRKTLKTYIADIWGSPSEDEGEVDLPLICDWPNRPKQMVSFEFGKPALTRWQVL 147

Query: 181 TQKGSNAWVTVGLREGKNREIK-KVFEFFNWKV 212
            +K + + V +    G++ +++  +       +
Sbjct: 148 ERKDTTSRVRLFPHTGRSHQLRVHML-ALGHPI 179


>gi|270264957|ref|ZP_06193221.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
 gi|270041255|gb|EFA14355.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera 4Rx13]
          Length = 232

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/209 (20%), Positives = 71/209 (33%), Gaps = 47/209 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF     V R
Sbjct: 12  PCHDKIE------NLYQDESLVLINKPAGLLSLSGKNPQNLDSVHHRLVQIFPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D D      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKTVNAALCQQFSQRTVTKVYSALLCGHLDND------EGVIDAAIA 119

Query: 172 YGDMQVTLDT-----QKGSNAWVTVG---LRE------------------GKNREIKKVF 205
                  L +      K + +   V     RE                  G+  +++   
Sbjct: 120 KDPALFPLMSICATHGKPARSGYRVVERFYRELEGGTLLPVTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTR 234
           +     +       YG    G LL G+ R
Sbjct: 180 QLLGHPILGCD--LYG----GRLLPGTER 202


>gi|315498779|ref|YP_004087583.1| pseudouridine synthase, rlua family [Asticcacaulis excentricus CB
           48]
 gi|315416791|gb|ADU13432.1| pseudouridine synthase, RluA family [Asticcacaulis excentricus CB
           48]
          Length = 334

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 78/254 (30%), Gaps = 52/254 (20%)

Query: 6   IVQENFTPQRVSK-VIARAGIASRREVERMIAQQRVKVNGILLERAAVN---------VM 55
           ++  +    R+ + ++      SR  ++ +I+   +  +G  +               V 
Sbjct: 23  VLTSDMAGDRLDRALLPLLPDLSRARLQALISDGHLSHDGQTIADGKHKARAGLYRLFVP 82

Query: 56  -STDHI-EVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD-NLPSIFSRVISV 111
                I E   +PL    E   L + +KP G+    +      T+ +  L      +  +
Sbjct: 83  APVSAIPEAQNLPLEVLYEDAHLIVVNKPAGMAAHPAPGTADGTLVNALLFHCGESLSGI 142

Query: 112 G---------RLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQV------ 153
           G         RLD +T G+++       A              R Y     G        
Sbjct: 143 GGVLRPGIVHRLDKDTSGVMVAAKS-DAAHRGLSELFSRHDIDRAYEALVRGAPKTASGT 201

Query: 154 ----------DQDKLNLLKKGIVIQGICYGDMQVTLD---TQKGSNAWVTVGLREGKNRE 200
                     D+ K+ +LK G    G        TL+    +K   A V   L  G+  +
Sbjct: 202 VTTRIGRSPHDRKKMAVLKSG----GREAISHYRTLNSFGGEKPVAARVRCTLETGRTHQ 257

Query: 201 IK-KVFEFFNWKVN 213
           I+  +  +      
Sbjct: 258 IRVHM-AYLGCPCL 270


>gi|227522958|ref|ZP_03953007.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
 gi|227089776|gb|EEI25088.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus hilgardii
           ATCC 8290]
          Length = 299

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 77/237 (32%), Gaps = 36/237 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +++  P+ + K +   GI S R  + +    +V +N      +   +   D + V     
Sbjct: 15  KQSNEPKTLKKFLNTHGI-SHRMYKNIKTSGQVLINSRS-SDSQTKLADGDQVTVILPDE 72

Query: 63  --------DGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR------ 107
                      P++       WL   KP GL       +   T+ + +     R      
Sbjct: 73  AGDPNVAVSEQPIKVVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVKGYLVRAGATDM 132

Query: 108 -VISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDK------ 157
               + RLD  T GL+L+     LA  L    L + Q  + Y     G    D       
Sbjct: 133 VPHIITRLDRFTSGLVLIAKH-RLANSLANELLAAKQLHKRYLAVVSGVGLPDHGRIQKP 191

Query: 158 LNLLKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +     G   I+     + D +  +  +   +  V V L  G+  +I+  F      
Sbjct: 192 IAKDPNGYGQIISDDGRFSDTEYWVRQRLNDDMLVEVALHTGRTHQIRVHFASIGHP 248


>gi|166713128|ref|ZP_02244335.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzicola BLS256]
          Length = 331

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 57/327 (17%), Positives = 104/327 (31%), Gaps = 53/327 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------------ILL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQVQVV 76

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIF 105
                +    D            E  ++ +  KP GLV      +PDG            
Sbjct: 77  LETQTHAAPQDI-----ALSVLYEDAQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDPA 131

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-------- 151
                R   V RLD +T G++++         L  +L +    R Y     G        
Sbjct: 132 LASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGTA 191

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              +D+   + LK  +   G          +  +   A +   L  G+  +I+       
Sbjct: 192 NAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHLK 250

Query: 210 WKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSS 264
             +    L    YG   L  L  G+T E+  ++    R+ L    LE        P+ +S
Sbjct: 251 SPIVGDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLEFLHPVSGEPVRAS 304

Query: 265 ETLVRDRPNIISEVPDDFTRMKKNSSQ 291
             +  D   +++ + +D  R  + + +
Sbjct: 305 APVPADLQRLMTALREDSARAAELARR 331


>gi|222151816|ref|YP_002560976.1| ribosomal large subunit pseudouridine synthase homolog [Macrococcus
           caseolyticus JCSC5402]
 gi|222120945|dbj|BAH18280.1| ribosomal large subunit pseudouridine synthase homolog [Macrococcus
           caseolyticus JCSC5402]
          Length = 273

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/160 (21%), Positives = 59/160 (36%), Gaps = 15/160 (9%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTN 126
           K E   L +  KP G+ T  +D    +T+ ++         V  + RLD  T GLLL+  
Sbjct: 77  KYEDEYLAILVKPKGVKTHPNDMSESNTLLNHAIYTLDSEYVEPIHRLDQETVGLLLVAK 136

Query: 127 DGGLARVL--ELPSTQWLRVYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYG 173
           +  + ++L   L      R YR +               + +DK +  K+ +   G    
Sbjct: 137 NPFIKKILDRMLEERLIKRTYRAKVKSHLPLKHQTIDMPIGKDKFHPNKRRVSQTGDRAV 196

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              V+    +   A V + L  G+  +I+         V 
Sbjct: 197 THIVSSKANRDGTADVELQLETGRTHQIRVHLAEIGHPVI 236


>gi|270157796|ref|ZP_06186453.1| RluA family pseudouridine synthase [Legionella longbeachae D-4968]
 gi|289163935|ref|YP_003454073.1| Ribosomal large subunit pseudouridine synthase [Legionella
           longbeachae NSW150]
 gi|269989821|gb|EEZ96075.1| RluA family pseudouridine synthase [Legionella longbeachae D-4968]
 gi|288857108|emb|CBJ10923.1| Ribosomal large subunit pseudouridine synthase [Legionella
           longbeachae NSW150]
          Length = 318

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 81/245 (33%), Gaps = 51/245 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN------------GILL 47
           +  K I  E    QR+   + R      +  + R+I    V+VN            G  +
Sbjct: 4   VSYKEISNEE-EGQRLDNYLIRVLKGVPKSHIYRIIRAGEVRVNKKRAQINSRLHAGDSV 62

Query: 48  ERAAVNVMSTDHIEVDGVPLRKA-------ERTRLWLYHKPIGL-------VTTHSDPDG 93
               V V     + V G  L K        E + L + +KP G+       ++       
Sbjct: 63  RIPPVRVSEPKEVFV-GNNLAKRLQESIIFEDSSLLVINKPAGIAVHGGSGLSLGVIEAL 121

Query: 94  RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRF-- 149
           R T  D      + +  + RLD  T G LLL     + R +   L + +  + Y      
Sbjct: 122 RKTRSDL-----AYLELIHRLDKETSGCLLLAKKRSVLRAIHALLEAREVQKTYWALLTH 176

Query: 150 -----HGQVDQDKLNL--LKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGK 197
                   + Q  L    LK G  I     +G         L+  + +  WV    + G+
Sbjct: 177 RWEGKKRVIVQAALEKNILKSGERIVKVKEEGKASETAFKLLENYEQA-CWVEASPKTGR 235

Query: 198 NREIK 202
             +I+
Sbjct: 236 THQIR 240


>gi|251793535|ref|YP_003008264.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
 gi|247534931|gb|ACS98177.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           aphrophilus NJ8700]
          Length = 219

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/162 (16%), Positives = 52/162 (32%), Gaps = 29/162 (17%)

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + + +KP GL++   + P    +    +   +       RLD+ T G+LL        R
Sbjct: 22  YIAVVNKPSGLLSVPGNQPQYYDSAMSRVKEKYGFCEPAHRLDMATSGILLFALSKAADR 81

Query: 133 VLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQVT-------- 178
            L+    +    + Y+    G V+QD       G+V    I        Q          
Sbjct: 82  ELKRQFREREPKKYYQALVWGHVEQD------HGVVELPLICDWENRPRQKICFAQGKRA 135

Query: 179 ------LDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                 L     +   V +  +  G++ +++         + 
Sbjct: 136 VTFYDVLQRYPNNTTRVKLTPIT-GRSHQLRLHMLALGHPIL 176


>gi|254569206|ref|XP_002491713.1| Mitochondrial tRNA pseudouridine synthase involved in
           pseudouridylation of mitochondrial tRNAs [Pichia
           pastoris GS115]
 gi|238031510|emb|CAY69433.1| Mitochondrial tRNA pseudouridine synthase involved in
           pseudouridylation of mitochondrial tRNAs [Pichia
           pastoris GS115]
          Length = 358

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/216 (15%), Positives = 75/216 (34%), Gaps = 38/216 (17%)

Query: 15  RVS------KVIARAGIASRREVER------MIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R++      K+I   G+A+ + +++      +I      VN        V +        
Sbjct: 51  RLNIDNGTIKLIRNRGLATEQTIDKSLLYSTLIKSGDCVVNTEHKHEPEVGI-------- 102

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEG 120
            G  +   +   + + +KP G+    +     +T+ + + +    S +    RLD  T G
Sbjct: 103 -GEEIVYQDDN-ILVVNKPCGVPVHPTGKYYYNTMTEIMKNELGVSSLYPCHRLDRLTSG 160

Query: 121 LLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLL------KKGIV 166
           +L++  T         +L      + Y  R  G+         DK+  +      + GI 
Sbjct: 161 ILIIGKTPRAAAKYQTQLKQNSIQKTYIARVDGEFPMGNIVCSDKIVNIDCKRGKENGIT 220

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  + Q    +   + + V    + G+  +I+
Sbjct: 221 EPKEALTNFQRLAYSTSLNQSIVKCSPKTGRTHQIR 256


>gi|126172980|ref|YP_001049129.1| pseudouridine synthase [Shewanella baltica OS155]
 gi|153002090|ref|YP_001367771.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|307304720|ref|ZP_07584470.1| pseudouridine synthase [Shewanella baltica BA175]
 gi|125996185|gb|ABN60260.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           baltica OS155]
 gi|151366708|gb|ABS09708.1| pseudouridine synthase [Shewanella baltica OS185]
 gi|306912122|gb|EFN42546.1| pseudouridine synthase [Shewanella baltica BA175]
          Length = 225

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 57/165 (34%), Gaps = 30/165 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G++++     
Sbjct: 19  QDKDIIVINKPSGLLSVPGRDPAHYDSVYARVKAEHPHSQIVHRLDMATSGVIVVALIRS 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV------ 177
             R L+      +  + Y  R  G V  D       G V    I        Q       
Sbjct: 79  AERELKRQFHDRETSKTYFARVAGHVKNDT------GSVDYPLICDWPNRPKQKVDHLVG 132

Query: 178 -------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                   + ++   +  V +  +  G++ +++  +       + 
Sbjct: 133 KPSLTHYQVISRAKRSTLVKLTPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|330962632|gb|EGH62892.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. maculicola str. ES4326]
          Length = 318

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEEGKEALTLF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|241955527|ref|XP_002420484.1| DRAP deaminase, putative; pseudouridine synthase, putative [Candida
           dubliniensis CD36]
 gi|223643826|emb|CAX41563.1| DRAP deaminase, putative [Candida dubliniensis CD36]
          Length = 589

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/144 (19%), Positives = 47/144 (32%), Gaps = 18/144 (12%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWL 77
           R+ VE       VKVN  +       + + D I          V    ++   E   L +
Sbjct: 128 RKAVEG----GLVKVNSKVA-NLETILRNGDLISHRSYRREPPVSSREIKIVFEDDDLLV 182

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLEL 136
             KP G+    +     +T+         ++     RLD  T GL+ L      A  +  
Sbjct: 183 IDKPSGIPVHPTGRYRYNTITKVFEHEMGKIVHPCNRLDRLTSGLMFLGKSSKGANNMMS 242

Query: 137 P--STQWLRVYRVRFHGQVDQDKL 158
                   + Y  R  G+   ++L
Sbjct: 243 QIRDRNVTKEYIARVKGEFPLERL 266


>gi|251793109|ref|YP_003007835.1| 23S rRNA pseudouridylate synthase C [Aggregatibacter aphrophilus
           NJ8700]
 gi|247534502|gb|ACS97748.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           aphrophilus NJ8700]
          Length = 319

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 76/236 (32%), Gaps = 41/236 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN------------GILLERAAV 52
            + ++   QR+   + AR     +  + R++ +  V+VN              ++    V
Sbjct: 14  TINDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLQADDVVRIPPV 73

Query: 53  NVMSTDHIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LP 102
            V       +     + A        E   L + +KP G+            +     L 
Sbjct: 74  RVAEKAQETISNKLTKVAQLEQQIIFEDNYLLVLNKPSGIAVHGGSGLDFGVIEALRALR 133

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T G+LL+       R L   L      + Y     GQ  Q    +
Sbjct: 134 PEARFLELVHRLDRDTSGILLVAKKRSALRNLHKQLREKTVQKEYLALVRGQW-QSHCKV 192

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           ++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 193 VQAPL-LKNELSSGERIVKVSEQGKPSETRFSVEERYVNATLVKASPVTGRTHQIR 247


>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 = 51.3 bits (122), Expect = 2e-04,   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|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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 22/112 (19%)

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  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
              W   +                  D   ++FS    V  L  +  G LL 
Sbjct: 57  RGYWKLKE-----------------IDEHFNLFSGNEVVLDLGSSAGGFLLY 91


>gi|291563059|emb|CBL41875.1| pseudouridine synthase, RluA family [butyrate-producing bacterium
           SS3/4]
          Length = 334

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/233 (16%), Positives = 78/233 (33%), Gaps = 47/233 (20%)

Query: 19  VIARAGIASRREVERMI-----AQQRVKVNGILLERAAVNVMSTDHIEVD-------GVP 66
            +  +G +SR     ++      +    +NG  +      +   D + V           
Sbjct: 48  FLLDSGYSSR-----LVVHLRNTEGSFLLNGKTVFS-NTVLQPKDQLRVHVTEKKTSDQI 101

Query: 67  LRKA-------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGR 113
           +          E   + +  KP G+    S     +T+ + +   +          +V R
Sbjct: 102 VPVPMDLSVVFEDEHVLVIDKPAGMPVHPSQGHYENTLANGIAWYYRNEATPFVFRAVNR 161

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQD---KLNLLKK-GIVI 167
           LD +T GL+LL  +   + VL          R Y     G+ D      L + +K G  I
Sbjct: 162 LDRDTSGLVLLAKNPYSSCVLSDAVKDHTIHREYAAIVSGKTDASGTIDLPIARKDGSTI 221

Query: 168 QGICYGDMQVTLDT--------QKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
           + +C  +   T  T        +    +++ + L  G+  +I+  + +     
Sbjct: 222 ERVCDPERGETAVTHYRTFAYNKDADISFIRLLLETGRTHQIRVHM-KAIGHP 273


>gi|291403226|ref|XP_002717836.1| PREDICTED: RNA pseudouridylate synthase domain containing 2
           [Oryctolagus cuniculus]
          Length = 561

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 47/314 (14%), Positives = 102/314 (32%), Gaps = 40/314 (12%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE--VDG-VPLRKAERTRLWLYH-------KPIGL 84
           +   R+ +N   ++  ++ +   D +   V    P   AE  RL   +       KP  +
Sbjct: 199 LRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENDDVVVVDKPSSI 258

Query: 85  VTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQ 140
                     +TV   L        +  + RLD  T G+L+      ++  +       Q
Sbjct: 259 PVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVRDRQ 318

Query: 141 WLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNAWVT 190
             + Y  R  G+   +++           K G+          +         G ++ V 
Sbjct: 319 LEKEYVCRVEGEFPVEEVTCKEPILVVSYKVGVCRVDPRGKPCETVFQRLSYNGHSSVVR 378

Query: 191 ---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKILREQ 244
              +    G+  +I+   +F    +        + +GP +      G   +  +++LR+ 
Sbjct: 379 CRPLT---GRTHQIRVHLQFLGHPILNDPIYNSVIWGPSRGRG---GHIPKTDEELLRDL 432

Query: 245 LGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDD----FTRMKKNSSQKNGLSKQKK 300
           +  H  +++   LD         + D     SE+ +D       + K +      S+   
Sbjct: 433 VAEHQAKQSLDVLDLCESDLSPGLTDPTAPSSELGEDGMQKLAAVPKMAGVVEAASQDLD 492

Query: 301 LATPVHRRNLASNV 314
            A     +   ++V
Sbjct: 493 TAASAPEKAPETDV 506


>gi|269214112|ref|ZP_06158361.1| RNA pseudouridine synthase [Neisseria cinerea ATCC 14685]
 gi|269144501|gb|EEZ70919.1| RNA pseudouridine synthase [Neisseria cinerea ATCC 14685]
          Length = 169

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 38/109 (34%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGL--ARVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
             +  + RLD +T G++LL+++            +    + Y      R       D ++
Sbjct: 4   EDITPLHRLDKDTAGVMLLSHNPATRGTYQTMFQNKTVWKTYEALAPTRTDLPYPIDVVS 63

Query: 160 LLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            L +G         +G       V L   +G  +   +    GK  +++
Sbjct: 64  RLVRGEKFFTTQEAEGEPNAHTTVELIENRGEFSLYRLTPHTGKKHQLR 112


>gi|331012623|gb|EGH92679.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tabaci ATCC 11528]
          Length = 318

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLMKSNLRSGERMGEVNEEGKEALTIF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|330966256|gb|EGH66516.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. actinidiae str. M302091]
          Length = 318

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLLKSNLRSGERMVEVNEEGKEALTLF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|89070524|ref|ZP_01157813.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           granulosus HTCC2516]
 gi|89043831|gb|EAR50029.1| ribosomal large subunit pseudouridine synthase C [Oceanicola
           granulosus HTCC2516]
          Length = 348

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 32/179 (17%), Positives = 60/179 (33%), Gaps = 34/179 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V+ +    R+ + + AR    ++  +E+M  +  ++++G  ++     +     + V  
Sbjct: 8   TVEADEADMRLDRWLRARFPQLTQGRIEKMCRKGELRIDGGRVKS-NTRIAPGQQVRV-- 64

Query: 65  VPLRKAERTR-------------------------LWLYHKPIGLVTTHSDPDGRSTV-- 97
            PL      R                         L + +KP GL T       R     
Sbjct: 65  PPLPPPGEVRPAGRDEPSAQDAEMMRAAVLYRDDHLIVLNKPPGLPTQGGSRQTRHVDGL 124

Query: 98  -FDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
                  +  +   V RLD +T G+LLL      A+ L     S +  ++Y     G  
Sbjct: 125 SAALTFGLEEKPRLVHRLDKDTSGILLLARTRAAAKGLTDAFRSRETRKIYWAAVAGVP 183


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G A SR   +R+I   +V V+   +++A   V     + V G  L  
Sbjct: 1  MKKERLDLLLVARGFAASRERAKRLIMAGQVLVDEQRVDKAGTTVSPLSSLRVVGEDLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|284038283|ref|YP_003388213.1| pseudouridine synthase [Spirosoma linguale DSM 74]
 gi|283817576|gb|ADB39414.1| pseudouridine synthase [Spirosoma linguale DSM 74]
          Length = 244

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/165 (15%), Positives = 51/165 (30%), Gaps = 23/165 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           + T L   +KP GL+   S    D        L      RV  V RLD  T G+LL    
Sbjct: 16  QDTELVAINKPHGLLVHRSMIASDASEFAVQLLRDQLGQRVYPVHRLDRKTAGVLLFA-L 74

Query: 128 GGLARVLELPSTQ---WLRVYRVRFHGQVDQD--------------KLNLLKKGIV-IQG 169
                 +           + Y     G    +               + +L++ +  ++ 
Sbjct: 75  SESMNAIMQQQFMEGAVQKTYLAIVRGYTPDELTIDYPLCKDDGNGAVGVLQEAVTHLKT 134

Query: 170 ICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWKVN 213
           +   ++ V       S  + V +    G+  ++++        + 
Sbjct: 135 LRQTEIPVAFGKHPTSRYSLVELTPTTGRMHQLRRHMAHILHPII 179


>gi|20808199|ref|NP_623370.1| pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
 gi|20516793|gb|AAM24974.1| Pseudouridylate synthase, 23S RNA-specific [Thermoanaerobacter
           tengcongensis MB4]
          Length = 268

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/202 (15%), Positives = 72/202 (35%), Gaps = 35/202 (17%)

Query: 33  RMIA----QQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLRK-----AERTRLW 76
           R+I        ++VNG   E     +   D IE+       D +P         E   + 
Sbjct: 9   RLIKMYKWHGEMRVNGEK-ENVKRVLKEGDVIELSLFDTSSDILPQEMDLSICYEDDEIL 67

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGL 130
           +  KP G+V   +      T+ + +   F +      +  V RLD  T G+++   +  +
Sbjct: 68  IVDKPAGMVVHPTRRYREGTLANGVAYYFEKKGIKTLIRPVNRLDKGTSGIVIFAKEPFM 127

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGDMQVTLD 180
              L        + Y    +G+++ + +            +++ +  +G        +L 
Sbjct: 128 QYYL-QIVKPMSKFYYAIVNGKLEGEGIIDVPIKRKSFMTIEREVSEEGDRAITYYKSLK 186

Query: 181 TQKGSNAWVTVGLREGKNREIK 202
             +   + + + +  G+  +I+
Sbjct: 187 ATEEF-SLLKIKIATGRTHQIR 207


>gi|71735436|ref|YP_273876.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|257487558|ref|ZP_05641599.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. tabaci ATCC 11528]
 gi|298486212|ref|ZP_07004275.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|71555989|gb|AAZ35200.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. phaseolicola 1448A]
 gi|298159219|gb|EFI00277.1| Ribosomal large subunit pseudouridine synthase C [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320325303|gb|EFW81370.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. B076]
 gi|320327712|gb|EFW83720.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330877844|gb|EGH11993.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. glycinea str. race 4]
 gi|330891478|gb|EGH24139.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. mori str. 301020]
 gi|330985584|gb|EGH83687.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           syringae pv. lachrymans str. M301315]
          Length = 318

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/209 (18%), Positives = 65/209 (31%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN------------GILLERAAVNVMSTDH-IEVDGVPLRK------AERT 73
           R++ +  V+VN            G ++    V V   D  + V    L++       E  
Sbjct: 43  RILRKGEVRVNKGRIKPEYKLQAGDIVRIPPVRVPERDEPVPVAQALLQRLEAAIVYEDK 102

Query: 74  RLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
            L + +KP G+          G    F  L      +  V RLD +T GLL++     + 
Sbjct: 103 ALIVLNKPAGIAVHGGSGLSFGVIEAFRQLRPDAKELELVHRLDRDTSGLLMIAKKRSML 162

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGDMQ 176
           R L   L      + Y     G     +           L+ G     +  +G     + 
Sbjct: 163 RHLHEALRGDGVDKRYMALVRGNWATAQKQVRAPLMKSNLRSGERMVEVNEEGKEALTIF 222

Query: 177 VTLDTQKGSNAWVT---VGLREGKNREIK 202
             L         V    V    G+  +I+
Sbjct: 223 KVLRRFGDFATMVEAKPVT---GRTHQIR 248


>gi|255732273|ref|XP_002551060.1| DRAP deaminase [Candida tropicalis MYA-3404]
 gi|240131346|gb|EER30906.1| DRAP deaminase [Candida tropicalis MYA-3404]
          Length = 590

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/143 (18%), Positives = 46/143 (32%), Gaps = 17/143 (11%)

Query: 29  REVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLY 78
           RE    +    VKVN  +       + + D I            +R          + + 
Sbjct: 127 REA---VDTGLVKVNSKVA-NLETVLKNGDLISHRSYRREPPVTSRDIKIVYENDDILVI 182

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLELP 137
            KP G+    +     +TV   +   F + V    RLD  T GL+ L      A  +   
Sbjct: 183 DKPSGIPVHPTGRYRYNTVTKIIEQEFGKTVHPCNRLDRLTSGLMFLGKSSKGANEMMSQ 242

Query: 138 --STQWLRVYRVRFHGQVDQDKL 158
                  + Y  R  G+   +++
Sbjct: 243 IRDRNVSKEYIARVKGEFPIERI 265


>gi|209693957|ref|YP_002261885.1| ribosomal large subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
 gi|208007908|emb|CAQ78038.1| ribosomal large subunit pseudouridine synthase A [Aliivibrio
           salmonicida LFI1238]
          Length = 244

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 58/161 (36%), Gaps = 35/161 (21%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT---- 125
           +   +   +KP GL++     P+   +V+  + + F     V RLD++T GL++      
Sbjct: 18  QDEAILAVNKPAGLLSNPGRAPEHYDSVWSRVVAEFPDAQLVHRLDMSTSGLMIFALYKE 77

Query: 126 ----NDGGLARVLELPSTQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDM-QVT 178
                       L        +VY  R  G V+  + +++L     +I         +V 
Sbjct: 78  AERHIKKQFQYRLTH------KVYYARVWGNVEKVEGQIDLP----LICDWPNRPRQKVC 127

Query: 179 LDTQKGSNAWVTVGLRE------------GKNREIK-KVFE 206
            +  K S     V   E            G++ +++  + E
Sbjct: 128 YEHGKSSQTGYEVIQVEEKTTLVRLLPITGRSHQLRVHMME 168


>gi|157373960|ref|YP_001472560.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
 gi|157316334|gb|ABV35432.1| pseudouridylate synthase [Shewanella sediminis HAW-EB3]
          Length = 225

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/159 (15%), Positives = 59/159 (37%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    ++F  + +       V RLD+ T G++++     
Sbjct: 19  QDKDILVVNKPSGLLSVPGRDPAHSDSIFTRVLAEHPNAQIVHRLDMATSGVIVVALRKS 78

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQ 176
             R L+      +  + Y  R  G V  D     L L+       K+ +           
Sbjct: 79  AERELKRQFRDRETKKTYYARVAGHVKADNGSVDLPLICDWPNRPKQKVDHDIGKASLTH 138

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
             + ++   +  V +  +  G++ +++  +       + 
Sbjct: 139 FEVISRAKRSTLVKLTPIT-GRSHQLRVHMM-AVGHPIL 175


>gi|56419100|ref|YP_146418.1| ribosomal large subunit pseudouridine synthase [Geobacillus
           kaustophilus HTA426]
 gi|56378942|dbj|BAD74850.1| ribosomal large subunit pseudouridine synthase [Geobacillus
           kaustophilus HTA426]
          Length = 299

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/160 (18%), Positives = 50/160 (31%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRST----VFDNLPSI--FSRVISVGRLDINTEGLLLL 124
           E   L + +K  G+    S+P    T    V   L S    ++V  + RLD +T G +L 
Sbjct: 89  EDDHLLVLNKEAGIDIHPSEPGQTGTLANAVAFYLQSQAILTKVRHIHRLDRDTSGAILF 148

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL-----------KKGIVIQGIC 171
                    L   L      R Y    HG++      +            ++ +   G  
Sbjct: 149 AKHPLAGATLDRMLAHRAIKRTYVALVHGRLSPKSGTIFAPIGRDRHHPTRRRVSKTGAK 208

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                  +     S + V + L  G+  +I+         
Sbjct: 209 AVTH-YRVIKTFPSTSLVELSLETGRTHQIRVHLAHLGHP 247


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+A SR   +R+I   +V V+   +++A   V +   + V G  L  
Sbjct: 1  MKKERLDLLLVAQGLAPSRERAKRLIMAGQVLVDERRVDKAGTTVDADASLRVTGEDLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|227357295|ref|ZP_03841652.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
 gi|227162558|gb|EEI47547.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           ATCC 29906]
          Length = 217

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 61/160 (38%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++      +   ++   + + F    SV RLD+ T G++++  +  
Sbjct: 18  QDEHIIVVNKPSGLLSVPGKALEHHDSIMSRIKADFPDAESVHRLDMATSGVMVVALNKA 77

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKGSN 186
             R L+    +    + Y  R  G++  +K   L    +I         +V  +T K + 
Sbjct: 78  AERELKRQFREREPKKTYIARVWGKL--EKPQGLVDLPLICDWPNRPKQKVCYETGKSAQ 135

Query: 187 AWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
            +  V   E            G++ +++  +       + 
Sbjct: 136 TFYEVLEYEENATRVKLSPITGRSHQLRVHML-ALGHPIL 174


>gi|317969027|ref|ZP_07970417.1| RNA-binding S4 [Synechococcus sp. CB0205]
          Length = 260

 Score = 51.3 bits (122), Expect = 2e-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|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 = 51.3 bits (122), Expect = 2e-04,   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|145630740|ref|ZP_01786518.1| hypothetical protein CGSHi22421_10087 [Haemophilus influenzae
           R3021]
 gi|144983622|gb|EDJ91082.1| hypothetical protein CGSHi22421_10087 [Haemophilus influenzae
           R3021]
          Length = 152

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/139 (19%), Positives = 50/139 (35%), Gaps = 12/139 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   +KP G++   S  DP     V   L       V  + RLD  T G+LL    
Sbjct: 7   QDEFLVAVNKPAGMLVHRSWLDPHETQFVMQTLRDQIGQHVFPIHRLDRPTSGVLLFALS 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVD-QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +A ++          + Y     G +  +++++   K I +  I     Q   + Q+ 
Sbjct: 67  SEIANLMCEQFEQKYVQKSYLAVVRGYLQGKERIDYPLK-IQLDKIADKFSQEDKEPQEA 125

Query: 185 SNAWVTVGLRE-----GKN 198
              +  + + E     G+ 
Sbjct: 126 VTDYEGLKIVEMPYPAGRY 144


>gi|315611921|ref|ZP_07886839.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis ATCC 49296]
 gi|315315910|gb|EFU63944.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           sanguinis ATCC 49296]
          Length = 291

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/149 (19%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P   + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G+V+  +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEIAREYWALIEGRVESKELVFRDKIGRDRHDRRKRIVDAKHGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             V+   Q       V   L+ G+  +I+
Sbjct: 203 THVSRLKQFPNQTTLVRCKLKTGRTHQIR 231


>gi|325109066|ref|YP_004270134.1| pseudouridine synthase [Planctomyces brasiliensis DSM 5305]
 gi|324969334|gb|ADY60112.1| pseudouridine synthase, RluA family [Planctomyces brasiliensis DSM
           5305]
          Length = 410

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/217 (15%), Positives = 67/217 (30%), Gaps = 49/217 (22%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL-------------WLY--HKPI 82
             + +    ++     +   D I+V    +   E                 W+   +KP 
Sbjct: 113 GAITIRHQPVDLMK-RLYPGDTIQV--RLVEPPETVYEPEPFPLEIEYEDAWMLAVNKPP 169

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLLTNDGGLARV 133
           G++   +      T+ + L + F          +   V RLD  T G++L+       R 
Sbjct: 170 GVIAHPTGNMQSGTLCNYLQAHFDTQSGIPGLLKPGIVHRLDRETSGVMLIAKTHRAHRN 229

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLNL-LKKG---------IVIQGICYGDMQVT--- 178
                  ++  + Y     G V +++  + L  G         +  +G            
Sbjct: 230 FVDAFEHSRVSKTYVALLEGDVAKEEGTIDLPIGQATVDSKVLMSARGDAKNPKPAKTHW 289

Query: 179 -LDTQKGSNAWVT---VGLREGKNREIKKVFEFFNWK 211
            +  + GS+  V    V    G+N +I+  F      
Sbjct: 290 RVLKRLGSHTLVAAKPVT---GRNHQIRVHFATIGHP 323


>gi|295698280|ref|YP_003602935.1| ribosomal large subunit pseudouridine synthase D [Candidatus Riesia
           pediculicola USDA]
 gi|291157095|gb|ADD79540.1| ribosomal large subunit pseudouridine synthase D [Candidatus Riesia
           pediculicola USDA]
          Length = 282

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/209 (12%), Positives = 66/209 (31%), Gaps = 33/209 (15%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA--------------ERTRLWLYHKPI 82
           +++V V+ I + + ++ ++    I +  + L K               E   + +  KP 
Sbjct: 4   KKKVYVDQIPINKPSIRILGEKSILIKDIDLEKKIQCIPKNIPLKILHEDDSIIVIDKPY 63

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            L         ++T+   L   F       R   V RLD +T GL+++     +   +  
Sbjct: 64  NLCVHPGTHHEKNTLMHALMYHFPILKNIPRAGIVHRLDKDTSGLMIVAKKSSIQNQMMK 123

Query: 137 --PSTQWLRVYRVRF----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              S +  + Y                 + +     +K  +   G          +    
Sbjct: 124 LFKSRKVYKEYEAIVYGNINSDGTIDKPIKRHPYERIKNFVCDFGRKAKTHYYVKEKFAN 183

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               + + L  G++ + +   ++    + 
Sbjct: 184 FTRII-LSLESGRHHQARVHMKYIGHPIV 211


>gi|197286175|ref|YP_002152047.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
 gi|194683662|emb|CAR44607.1| ribosomal large subunit pseudouridine synthase A [Proteus mirabilis
           HI4320]
          Length = 216

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 61/160 (38%), Gaps = 20/160 (12%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++      +   ++   + + F    SV RLD+ T G++++  +  
Sbjct: 17  QDEHIIVVNKPSGLLSVPGKALEHHDSIMSRIKADFPDAESVHRLDMATSGVMVVALNKA 76

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKGSN 186
             R L+    +    + Y  R  G++  +K   L    +I         +V  +T K + 
Sbjct: 77  AERELKRQFREREPKKTYIARVWGKL--EKPQGLVDLPLICDWPNRPKQKVCYETGKSAQ 134

Query: 187 AWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
            +  V   E            G++ +++  +       + 
Sbjct: 135 TFYEVLEYEENATRVKLSPITGRSHQLRVHML-ALGHPIL 173


>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 = 51.3 bits (122), Expect = 2e-04,   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|187477608|ref|YP_785632.1| ribosomal large subunit pseudouridine synthase C [Bordetella avium
           197N]
 gi|115422194|emb|CAJ48718.1| ribosomal large subunit pseudouridine synthase C [Bordetella avium
           197N]
          Length = 319

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 41/230 (17%), Positives = 77/230 (33%), Gaps = 47/230 (20%)

Query: 12  TPQRVSKVIARA--GIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEV------ 62
             QR+   + R   G+  +  + + I    V+VN G +   A   ++  D + V      
Sbjct: 27  EGQRLDNFLLRLCKGV-PKSHIYKAIRGGEVRVNKGRI--SADYRLVVGDVVRVPPLRLP 83

Query: 63  ---DGVPLRKAERTRLW------LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS--- 110
                 P+  +E   ++      + +KP G+        G S V   +            
Sbjct: 84  DPGQPKPVPASEFPVVYEDDAMLVINKPAGVAV-----HGGSGVSFGVIEQLRAARPEAR 138

Query: 111 ----VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNLL- 161
               V RLD  T GLL++         L   L   +  + Y     G    D+  + L  
Sbjct: 139 FLELVHRLDRETSGLLMIAKKRSALLALHAMLREGRGSKRYLALVEGDWVNDRQHIRLAL 198

Query: 162 --------KKGIVIQ-GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                   ++ + +          ++L  + G  + V   LR G+  +I+
Sbjct: 199 SKWTTQSGERRVKVDPDGQTAHTVISLKQRFGDYSLVEAELRTGRTHQIR 248


>gi|111114840|ref|YP_709458.1| hypothetical protein BAPKO_0017 [Borrelia afzelii PKo]
 gi|216263838|ref|ZP_03435832.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia afzelii ACA-1]
 gi|110890114|gb|ABH01282.1| conserved hypothetical protein [Borrelia afzelii PKo]
 gi|215979882|gb|EEC20704.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia afzelii ACA-1]
          Length = 326

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 85/247 (34%), Gaps = 51/247 (20%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++      +R +    I ++ V    K NG   + + +  V
Sbjct: 4   LKKEFTVKENAL--RLDLYLSNNLEFFTRSQ----IKKRNVEAFKKSNGEFFKIKLSKPV 57

Query: 55  MSTDH--IEVDGVPLRK-------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D   IE D    +               E + + + +KP G+++        +TV +
Sbjct: 58  FKDDEMLIEFDEESSQIDYLRPNNISIDIIYEDSNIIVLNKPQGILSHPGISHWDNTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKGLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTVRFLAQQFKDRRTNKVYI 177

Query: 147 VRFHGQ-----------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
               G            +D+DK N  K  +          +  L    G  + + +  + 
Sbjct: 178 AIVKGNFNSFFGSIESFIDRDKYNRKKFSVSKDRGKKALTEYKLLLNFGGYSLLALKPKT 237

Query: 196 GKNREIK 202
           G+  +++
Sbjct: 238 GRTHQLR 244


>gi|89056515|ref|YP_511966.1| ribosomal large subunit pseudouridine synthase A [Jannaschia sp.
           CCS1]
 gi|88866064|gb|ABD56941.1| ribosomal large subunit pseudouridine synthase A [Jannaschia sp.
           CCS1]
          Length = 217

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 36/91 (39%), Gaps = 3/91 (3%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E   L L +KP GL++     +     +   L   F  V+ V RLD++T G+++     
Sbjct: 18  HEDHDLLLVNKPAGLLSVPGKGEHLSDCLIARLKIAFPEVLLVHRLDMDTSGVMVFARTP 77

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQDK 157
              R L L        + Y  R  G+V    
Sbjct: 78  HAQRHLGLQFEKRHTKKAYVARVWGEVTDKD 108


>gi|119773744|ref|YP_926484.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119766244|gb|ABL98814.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           amazonensis SB2B]
          Length = 225

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/161 (14%), Positives = 59/161 (36%), Gaps = 21/161 (13%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL---- 124
            +   + + +KP GL++    DP    + +  + +       V RLD+ T G+++     
Sbjct: 19  HQDKDIIVINKPSGLLSVPGRDPIHHDSAWSRIKAEHPNSQVVHRLDMATSGVMVYALRK 78

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD---KLNLL-------KKGIVIQGICYGD 174
           + +  L R      T   + Y  R  G V  +    L L+       ++ +  +      
Sbjct: 79  SAEVELKRQFRDRETH--KTYFARVAGHVKANCSVDLPLICDWPNRPRQKVDHEIGKPSL 136

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
             V + +    +  V +  +  G++ +++  +       + 
Sbjct: 137 THVDVISYGKRSTLVKLTPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|325479463|gb|EGC82559.1| pseudouridine synthase, RluA family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 279

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/228 (17%), Positives = 82/228 (35%), Gaps = 32/228 (14%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH- 59
           M+         T  R  K +   G  S+R VE ++++    +N  L ++ + N+ + D  
Sbjct: 1   MRYIKYELSEKTTVR--KFLLSKGY-SKRSVEAILSEGF-LLNNQLSKK-SKNLKAGDKL 55

Query: 60  -IEVDGVPLRKAE-RTRLWLYHKPIGLVTTHSDP------DGRSTVFDNLPSIFS----- 106
            + +    +     R  L + ++    +    DP       G+ ++ +N+   F      
Sbjct: 56  FVIIRDENIDYEPVRGNLKIIYEDRDTLVISKDPNITVNSKGQISLANNIAYYFKSNNIN 115

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKL---- 158
            +V  V RLD++T GL+L+  +   A      ++ + + ++ Y        + D L    
Sbjct: 116 SKVRFVNRLDMDTSGLILVAKN-KYAHAFYQKQIENNEMIKKYIAIVDPNANLDMLYEEK 174

Query: 159 ----NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  K  +V +                    V   +  GK  +I+
Sbjct: 175 FAYDEKSKSYVVSEDGKTAKTIFKPLKLLKDRTIVECQILTGKTHQIR 222


>gi|289662940|ref|ZP_06484521.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. vasculorum NCPPB702]
          Length = 331

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 59/328 (17%), Positives = 106/328 (32%), Gaps = 55/328 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------------ILL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQVQVV 76

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSI 104
                +    D       PL    E  ++ +  KP GLV      +PDG           
Sbjct: 77  LETQTHAAPQDI------PLSVLYEDEQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDP 130

Query: 105 F----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
                 R   V RLD +T G++++         L  +L +    R Y     G       
Sbjct: 131 ALASVPRAGVVHRLDKDTSGVMVVARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGT 190

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D+   + LK  +   G          +  +   A +   L  G+  +I+      
Sbjct: 191 ANAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHL 249

Query: 209 NWKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYS 263
              +    L    YG   L  L  G+T E+  ++    R+ L    LE        P+ +
Sbjct: 250 KSPIVGDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLEFLHPVSGEPVRA 303

Query: 264 SETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           S  +  D   +++ + +D  R  + + +
Sbjct: 304 SAPVPADLQRLMTALREDSARAAEMARR 331


>gi|229166225|ref|ZP_04293984.1| Pseudouridine synthase [Bacillus cereus AH621]
 gi|228617170|gb|EEK74236.1| Pseudouridine synthase [Bacillus cereus AH621]
          Length = 307

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +K   + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELNVVFEDDHVLIINKQGQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+ +G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKNGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYMALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
              VT+ L  G+  +I+
Sbjct: 225 ATLVTLQLETGRTHQIR 241


>gi|77406648|ref|ZP_00783692.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
 gi|77411850|ref|ZP_00788184.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77162127|gb|EAO73104.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae CJB111]
 gi|77174748|gb|EAO77573.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae H36B]
          Length = 325

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 59  RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 117

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 118 DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 177

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 178 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 234

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 235 IIDVLKYTQNSSLIKCRLETGRTHQIR 261


>gi|312870194|ref|ZP_07730326.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
 gi|311094285|gb|EFQ52597.1| pseudouridine synthase, RluA family [Lactobacillus oris PB013-T2-3]
          Length = 297

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 81/234 (34%), Gaps = 45/234 (19%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMI-AQQRVKVNGIL---------LERAAVNVMS- 56
            ++ TP+++   +  +G+ S   ++  I    ++ +NG            +  ++ +   
Sbjct: 7   YDHATPRKLRSALKMSGVTS-SLMKVAIYHGGQMLINGEPKWAVDLVQPGDEYSIVIPPE 65

Query: 57  --TDHIEVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----- 108
              DH++    P+  A   R   + +KP G+ T    P     V D+L +          
Sbjct: 66  EANDHVDESTAPITIAYEDRDFLVLNKPAGVATV---PAHNVPVADSLVNRVKYYYRERD 122

Query: 109 ------ISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHG-------- 151
                     RLD +T GL++       A  +        +  + Y     G        
Sbjct: 123 YENQVTHVATRLDKDTSGLVVFPKH-RFAHAVLDRQLKRHEVKKNYYALVSGHLHTQHGY 181

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + +D  + +K+ +   G      +  L   +   + V + L  G+  +I+
Sbjct: 182 IDAPIRRDPASFVKREVAPDGKDSVT-EYWLAQAQAERSLVRIRLHTGRTHQIR 234


>gi|227509897|ref|ZP_03939946.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
 gi|227190617|gb|EEI70684.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus brevis subsp.
           gravesensis ATCC 27305]
          Length = 299

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 38/238 (15%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----- 62
           +++  P+ + K +   GI S R  + +    +V +N      +   +   D + V     
Sbjct: 15  KQSNEPKTLKKFLNTHGI-SHRMYKNIKTSGQVLINSRS-SDSQTKLADGDQVTVILPDE 72

Query: 63  --------DGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR------ 107
                      P++       WL   KP GL       +   T+ + +     R      
Sbjct: 73  AGDPNVAVSEQPIKVVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVKGYLVRAGVTDL 132

Query: 108 -VISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRF-------HGQVDQD 156
               + RLD  T GL+L+     LA  L    L + Q  + Y           HG++ Q 
Sbjct: 133 VPHIITRLDRFTSGLVLIAKH-RLANSLANELLAAKQLHKRYLAVVSGGGLPDHGRI-QK 190

Query: 157 KLNLLKKG---IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +     G   I+     + D +  +  +   +  V V L  G+  +I+  F      
Sbjct: 191 PIAKDPNGYGQIISDDGRFSDTEYWVRQRLNDDMLVEVALHTGRTHQIRVHFASIGHP 248


>gi|195051256|ref|XP_001993061.1| GH13618 [Drosophila grimshawi]
 gi|193900120|gb|EDV98986.1| GH13618 [Drosophila grimshawi]
          Length = 753

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/208 (18%), Positives = 69/208 (33%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P+        + + +KP 
Sbjct: 353 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPA 412

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 413 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 472

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV-----------TLDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V              +Q G  +
Sbjct: 473 RQVEKEYICRVEGVFPDGVVE-CKEPIEVVSYKIGVCKVSQKGKDCTTTFKKLSQNGKTS 531

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR 214
            V    L  G+  +I+   ++  + +  
Sbjct: 532 VVLCKPLT-GRMHQIRVHLQYLGYPILN 558


>gi|148926838|ref|ZP_01810517.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
 gi|145844563|gb|EDK21670.1| putative ribosomal pseudouridine synthase [Campylobacter jejuni
           subsp. jejuni CG8486]
          Length = 244

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 53/137 (38%), Gaps = 9/137 (6%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKA---ERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     ++  D   I  +  P       E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEE-KNKILKGDVELIVYENNPKGVEIVFENEDFAVLEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +      +     RLD  T GL+L+         L       Q 
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQI 147

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y     G++  + +
Sbjct: 148 QKEYLALASGEIKVNFI 164


>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 (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 11 FTP--QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
           TP  QR+  ++    +  SR++ +R I    V VN I +++    V     I+V   P
Sbjct: 1  MTPRKQRLDSLLVERHLCESRQQAQRWIRAGAVHVNHIPIDKPGTLVAVDATIQVKAKP 59


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

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 39/249 (15%), Positives = 91/249 (36%), Gaps = 60/249 (24%)

Query: 7   VQENFTPQRVSK----VIARAGIASRREVERMIAQQRVKVNGILLER-------AAVNVM 55
           V+ + +  R+ +         G      +++++   +++V+G  ++         ++ V 
Sbjct: 9   VKADESGMRLDRWFKVYYPDVGFG---YLQKLLRSGQIRVDGRRVKNDVRLVVGQSIRVP 65

Query: 56  S-------------------TDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
                                D + +  + L   E +++++++KP GL         R  
Sbjct: 66  PFLIDKEDSAPVFNKIIFGQEDEVILKDMLL--YEDSKIFVFNKPAGLAVQGGSGLTRHV 123

Query: 97  -----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
                V+ N      R+  V R+D  T G+L++    G A+ L     + +  + Y    
Sbjct: 124 DSMLEVWRNKKGEKPRL--VHRIDRETSGVLVVARSRGAAQALTAAFRTRETKKTYWALV 181

Query: 150 HGQV--DQDKLNL-LKKGIVIQGICYGDMQVT-------------LDTQKGSNAWVTVGL 193
            G     QDK++  + + I  QG      +               LDT+  + +W+ +  
Sbjct: 182 RGVPRKKQDKISTWMVREITEQGDKVRVCERRQADSNHAVSYYRVLDTRGKALSWLEMEP 241

Query: 194 REGKNREIK 202
             G+  +++
Sbjct: 242 YTGRTHQLR 250


>gi|296393841|ref|YP_003658725.1| pseudouridine synthase [Segniliparus rotundus DSM 44985]
 gi|296180988|gb|ADG97894.1| pseudouridine synthase, RluA family [Segniliparus rotundus DSM
           44985]
          Length = 315

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 71/252 (28%), Gaps = 55/252 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVM----------- 55
           V E     R+   +AR    SR +   +       V+G    R+   V            
Sbjct: 13  VPEGLVGLRLDAGLARLLGVSRTKAAELADAGHALVDGKEARRSDRLVEGAWLEVSVPAA 72

Query: 56  -----STDH--------IEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                  D         +      +   E+      H  +G            TV   L 
Sbjct: 73  LPAPVEEDVPEIIAGLNVLFSDEHVVVVEKPAEIAVHPSVGW--------SGPTVVGGLK 124

Query: 103 SIFSRVISVG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
           ++  R+ + G         RLD+ T G+++L        VL+      +  + Y     G
Sbjct: 125 ALGFRIATSGVAERQGVVQRLDVGTSGVMVLAASEHAYTVLKRAFKHREVEKWYEALVQG 184

Query: 152 QVD------QDKLNL-----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
             D         +        +  +   G        TL+   G  + V++ L  G+  +
Sbjct: 185 HPDPSSGTIDAAIGKRPGPGWRFAVTTNGRPSVTHYDTLEA-FGQASLVSIRLETGRTHQ 243

Query: 201 IKKVFEFFNWKV 212
           I+  F       
Sbjct: 244 IRVHFSALRHPC 255


>gi|15888079|ref|NP_353760.1| hemolysin [Agrobacterium tumefaciens str. C58]
 gi|15155705|gb|AAK86545.1| hemolysin [Agrobacterium tumefaciens str. C58]
          Length = 250

 Score = 51.3 bits (122), Expect = 2e-04,   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|114046333|ref|YP_736883.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
 gi|113887775|gb|ABI41826.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-7]
          Length = 225

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/159 (14%), Positives = 58/159 (36%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G++++     
Sbjct: 19  QDKDIIVVNKPSGLLSVPGRDPAHYDSVYARVKAEHPHCQIVHRLDMATSGVMVVALIRS 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQ 176
             R L+      +  + Y  R  G +  D             N  K+ +  +        
Sbjct: 79  AERELKRQFHDRETSKTYLARVAGHIKNDTGSVDYPLICDWPNRPKQKVDHEIGKPSLTH 138

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
             + ++   +  V +  +  G++ +++  +       + 
Sbjct: 139 FEVLSRAKRSTLVKLKPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|309789597|ref|ZP_07684178.1| hemolysin A [Oscillochloris trichoides DG6]
 gi|308228333|gb|EFO81980.1| hemolysin A [Oscillochloris trichoides DG6]
          Length = 261

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              R+ +++   G+A +R + + ++    V+VNG    +    V +   IEV
Sbjct: 1  MPKIRLDQLLVSRGLAETRSKAQALLMAGSVRVNGQPAGKPGAMVDAEVEIEV 53


>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 (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/67 (19%), Positives = 26/67 (38%), Gaps = 1/67 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          QR+   +       +R +   +I + RV VN   + + +  V  TD +E+    +    +
Sbjct: 3  QRLDHYLKNTNQCETRSKAIDLIKRGRVFVNNFEVLKPSFLVKQTDSVEIKNDEMYFVSK 62

Query: 73 TRLWLYH 79
              L  
Sbjct: 63 GGYKLLK 69


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 32/76 (42%), Gaps = 9/76 (11%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV------- 62
             +  R+  V+A A   SR ++   I   +V VNG L+      +   D I V       
Sbjct: 171 TVSSIRLDSVLALAYPLSRSKITAQIEAGKVFVNGKLITSNGYRLKDNDIISVRKMGRIA 230

Query: 63  -DGVPLRKAERTRLWL 77
            DG+ L + ++ R  +
Sbjct: 231 YDGI-LSETKKGRYLI 245


>gi|150015406|ref|YP_001307660.1| RluA family pseudouridine synthase [Clostridium beijerinckii NCIMB
           8052]
 gi|149901871|gb|ABR32704.1| pseudouridine synthase, RluA family [Clostridium beijerinckii NCIMB
           8052]
          Length = 299

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 30/218 (13%), Positives = 71/218 (32%), Gaps = 40/218 (18%)

Query: 33  RMIAQ----QRVKVNGILLERAAVNVMSTDHIEVD--------------GVPLRKAERTR 74
           R+I      +R+ VN  +++     +   + I++D               + +   +   
Sbjct: 30  RLIRSASLGKRIFVNDEVVK-MNRVLNEGEIIKIDLAKDESQDIAPEKMDIDIVYEDEDI 88

Query: 75  LWLYHKPIGLVTTHSDPDGRST---VFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGG 129
           L +  KP  +V         +    V +         I   V RLD+NT GL+++  +  
Sbjct: 89  LVVNKKPFMVVHPTKSYQSGTLANGVINYFMESGQNCIVRLVSRLDMNTSGLIIIAKN-Q 147

Query: 130 LARVLEL---PSTQWLRVYRVRFHGQVDQDKL---------NLLKKG---IVIQGICYGD 174
            +  +        +  + Y    HG + + +            ++ G   +V +      
Sbjct: 148 FSHGMLSKEMSENKVEKKYLALVHGIMKEKQGTIDLPIYKPEGIENGIRRVVDERGQRSI 207

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
               +  +   ++ V   L  G+  +I+         +
Sbjct: 208 THYKVVEEYNESSLVECKLETGRTHQIRVHLSHLGHPI 245


>gi|195471884|ref|XP_002088232.1| GE13593 [Drosophila yakuba]
 gi|194174333|gb|EDW87944.1| GE13593 [Drosophila yakuba]
          Length = 738

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 40/208 (19%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 333 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPA 392

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 393 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 452

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q GS +
Sbjct: 453 RQVEKEYICRVEGVFPDGIVE-CKEPIEVVSYKIGVCKVSSKGKDCTTTFQKLSQNGSTS 511

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR 214
            V    L  G+  +I+   ++  + +  
Sbjct: 512 VVLCKPLT-GRMHQIRVHLQYLGYPILN 538


>gi|91225595|ref|ZP_01260669.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
 gi|91189715|gb|EAS75989.1| ribosomal large subunit pseudouridine synthase A [Vibrio
           alginolyticus 12G01]
          Length = 250

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 31/163 (19%), Positives = 56/163 (34%), Gaps = 43/163 (26%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND-- 127
           E   +   +KP GL++      +   +++  L  +   +  V RLD++T GL+LL  +  
Sbjct: 19  EDDDILAVNKPSGLLSVPGRLAEHYDSMWSRLKELHPEIQVVHRLDMSTSGLMLLAKNKP 78

Query: 128 ------GGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVI----QGICYGDMQ 176
                       L        +VY  R  G V+       ++G I +            +
Sbjct: 79  AERALKKQFQYRLTH------KVYYARVWGHVES------QEGNIDLPLICDWPNRPRQK 126

Query: 177 VTLDTQKGSNAWVTVGLRE-----------------GKNREIK 202
           V  D  K S     V  RE                 G++ +++
Sbjct: 127 VCFDDGKPSQTLFQVVKREVHPDGTHTTVVRLLPITGRSHQLR 169


>gi|325568271|ref|ZP_08144638.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158040|gb|EGC70193.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           casseliflavus ATCC 12755]
          Length = 284

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/178 (19%), Positives = 62/178 (34%), Gaps = 22/178 (12%)

Query: 52  VNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSR 107
           + +   D ++V        E   L + +KP  + T  + P    T+ +     L     +
Sbjct: 73  IQLGQADKVDV------LFEDEHLLVLNKPARVKTHPNQPLEADTLLNDAAAYLAPKQQQ 126

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKG- 164
              V RLD  T G++L   +  +  +L   L + Q  R Y+    G++ QD+    K G 
Sbjct: 127 PYVVHRLDKETSGVVLFAKNPLVLPILGRMLENKQIFRRYQATVLGKLTQDQTIAKKIGR 186

Query: 165 ---------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                    I  +        VT+   +     V   L  G+  +I+         V 
Sbjct: 187 DRHDRRKRIIDSRNGQSAVTHVTIAHAQQKTTNVYCVLETGRTHQIRVHLASIGHPVV 244


>gi|320536301|ref|ZP_08036344.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
 gi|320146861|gb|EFW38434.1| pseudouridine synthase, RluA family [Treponema phagedenis F0421]
          Length = 320

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 42/270 (15%), Positives = 74/270 (27%), Gaps = 64/270 (23%)

Query: 1   MKDKNIVQENF--TPQRVSKVI-ARAGIASRREVERMIAQQR--VKVNGILLERAAVNVM 55
           M++K  V       P+R+     A+  I  R +    +        VNG   +  +  V 
Sbjct: 1   MQNKRFVVSEAYNEPRRLDVFCGAQMNI-PRSK----LKAGLQSAAVNGKQAK-LSTLVR 54

Query: 56  STDHIEV---DGVPLRKA----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             D +E+   D +P              E   +   +K  GLVT  +  +   T+   L 
Sbjct: 55  PNDIVEIKWADPIPEVFIPEEIPLSILFENEDVIAVNKQQGLVTHPASGNWTGTLVQGLA 114

Query: 103 SIFSRVIS-----------------------VGRLDINTEGLLLL--TNDGGLARVLELP 137
                                          V RLD +T G+L+             +  
Sbjct: 115 YYRLHCSPIKDEFSEILQNTQSFQSCFRQGIVHRLDKDTSGVLITERNTRAEEFFKAQFK 174

Query: 138 STQWLRVYRVRFHGQV-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +  ++Y     G               D            +    Y D    +    G
Sbjct: 175 QHKTTKIYLAVVQGCPRTLKGKIETSIYRDPKHRTKFAASSDLSVGRYADTLYRVLKTFG 234

Query: 185 SNAWVTVGLREGKNREIKKVFEFF-NWKVN 213
             + V   L  G+  +I ++   F    + 
Sbjct: 235 KYSIVQFKLGTGRTHQI-RMHAAFIGCPIL 263


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 1/64 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          N   +R+  ++    I  SR + +  I + +V VNG  +++    +     IE  G  + 
Sbjct: 3  NIKSERLDVLLVEKKIFDSREKAKIAIMEGKVFVNGQRVDKCGQKIKVDSEIEFKGEVMP 62

Query: 69 KAER 72
             R
Sbjct: 63 YVSR 66


>gi|154685381|ref|YP_001420542.1| YhcT [Bacillus amyloliquefaciens FZB42]
 gi|154351232|gb|ABS73311.1| YhcT [Bacillus amyloliquefaciens FZB42]
          Length = 302

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/206 (16%), Positives = 67/206 (32%), Gaps = 36/206 (17%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           ++VN     +  + + + D + +D             G P    E   + + +KP G+ T
Sbjct: 45  IQVN-RTPTKNNIILKTGDRLFIDLQEKTGSSVTPEYGEPDILFEDNHMLIANKPAGMPT 103

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ 140
             ++     T+ + +   F       +V  V RLD +T G ++      LA  +     +
Sbjct: 104 HPNEEGQTGTLSNLIAYHFHINGEQAKVRHVHRLDRDTSGAVVFAKH-RLAHAILDRQLE 162

Query: 141 ---WLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTLDTQKGSN 186
                R Y     G+V   K            + +++ +   G          D   G+ 
Sbjct: 163 TKTLKRTYIAAAEGKVTPKKGTVDSPIGRDRSHSVRRRVSPGGQAAVTHYKVKDYHPGAQ 222

Query: 187 -AWVTVGLREGKNREIKKVFEFFNWK 211
                + L  G+  +I+         
Sbjct: 223 LTLAELELETGRTHQIRVHMASIGHP 248


>gi|312135354|ref|YP_004002692.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
 gi|311775405|gb|ADQ04892.1| pseudouridine synthase [Caldicellulosiruptor owensensis OL]
          Length = 311

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 79/238 (33%), Gaps = 49/238 (20%)

Query: 33  RMIAQQRVKVN------GILLERAAV-------NVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +M+ +  + V+      G +L+             +    +E+    ++  E   + +  
Sbjct: 34  KMLRKGEIIVSFLPAQKGQVLKFGDTVSFEIEDRFLEHKKVEI----IKVYEDDNIVVID 89

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLARVLEL 136
           KP G + +H D +   +V   +   +S+        RLD NT GL+++  +  +   +  
Sbjct: 90  KPYG-IPSHPDSNNEYSVVSWIEDNYSKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLK 148

Query: 137 --PSTQWLRVYRVRFHG---QVDQDKLNLLKKG-----IVI-----QGICYGDMQVTLDT 181
                  ++ Y               ++ LKK      + I      G         +  
Sbjct: 149 YMSRRAIIKKYLCITKKADLPESGVLVHYLKKDSKKSKVYISDFPQDGYSEVVTAYKIVR 208

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKK 239
           QK     + V ++ GK  +I+         +            LG    G   E++KK
Sbjct: 209 QKDDLQLLDVEIKSGKTHQIRAQLAHVGLCI------------LGDSKYGDW-ELNKK 253


>gi|306832623|ref|ZP_07465762.1| ribosomal large subunit pseudouridine synthase [Streptococcus bovis
           ATCC 700338]
 gi|304425231|gb|EFM28358.1| ribosomal large subunit pseudouridine synthase [Streptococcus bovis
           ATCC 700338]
          Length = 286

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 24/151 (15%), Positives = 56/151 (37%), Gaps = 25/151 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG- 128
           +   L + +KP G+ T  ++P    T+ +++ +   +    + RLD+ T G ++   +  
Sbjct: 86  QDEHLIIVNKPEGMKTHGNEP-NEITLLNHVSAYVGQTCYVIHRLDMETSGAVMFAKNPF 144

Query: 129 --GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
              +   L   +    R Y     G+ +     + +  I   G    D +  +  +K   
Sbjct: 145 VLPILNRLL-ENKDIAREYWALVQGKFEPKH-QVFQDKI---GRDRHDRRKRVIDRKNGQ 199

Query: 187 AWVTVG---------------LREGKNREIK 202
             +T+                L+ G+  +I+
Sbjct: 200 TALTIVDRLKVFPNGTLVKCRLKTGRTHQIR 230


>gi|300933336|ref|ZP_07148592.1| pseudouridylate synthase [Corynebacterium resistens DSM 45100]
          Length = 339

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/234 (15%), Positives = 78/234 (33%), Gaps = 40/234 (17%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV-----------M 55
           V +     RV   +++    SR  V ++     V + G  + ++   V            
Sbjct: 37  VPDGLAGMRVDAGLSKLLGLSRTVVAQLAESNDVLMEGAPVGKSDRLVAGAWLDITLPEP 96

Query: 56  STD-----HIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS 110
             D        V+G+ +  ++   + +  KP+G+    +      TV   L +   R+ +
Sbjct: 97  PRDLANEPPQLVEGMDILYSDED-VIVVDKPVGVAAHPTLGWEGPTVTAGLAAAGFRIST 155

Query: 111 VG---------RLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD----- 154
            G         RLD+ T G +++        +L+      +  + Y     G  D     
Sbjct: 156 SGPPERKGIVQRLDVGTSGAMVVAASERAYSLLKRAFRDREVDKTYHALVQGHPDPTSGT 215

Query: 155 -QDKLNL-----LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +        +  +   G        TL+  + + + + V L  G+  +I+
Sbjct: 216 IDAPIARHPSAGWRFAVRDDGKHAVTHYDTLEAHRQA-SLLKVKLETGRTHQIR 268


>gi|50083692|ref|YP_045202.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1]
 gi|49529668|emb|CAG67380.1| 23S rRNA pseudouridylate synthase [Acinetobacter sp. ADP1]
          Length = 310

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/184 (18%), Positives = 68/184 (36%), Gaps = 42/184 (22%)

Query: 7   VQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           V E+   QR+   +         SR  + R+I + +V+VN   ++ A   +   D I V 
Sbjct: 15  VDEHQAGQRIDNFLFTRLKGVPKSR--IYRLIREGQVRVNKKRIK-AESKLSIGDQIRV- 70

Query: 64  GVPLRKAERTR-----------------------LWLYHKPIGLVTTHSDPDGRSTVFDN 100
             P+R  ++                         L + +KP G+        G    +  
Sbjct: 71  -APIRYEQKDESDAPVSDQVAKSLLNRVVYEDEGLLVVNKPSGIAV----HGGSGVAYGL 125

Query: 101 LPSIF-----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV 153
           + ++        +  + R+D +T GL++++      ++L   L   +  + Y     GQV
Sbjct: 126 IEAMRAATGKKYLELIHRIDRDTSGLVMISKKRSTLKLLQDLLREHKIRKTYAALVKGQV 185

Query: 154 DQDK 157
             D+
Sbjct: 186 SLDQ 189


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 10/79 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M DK          R+ + +   G+A SR      I +  V V+G + ++  + V  +  
Sbjct: 1  MSDKK---------RLDQRLVELGLAPSRARARDAILRGTVTVDGRIADKPGLAVGPSAA 51

Query: 60 IEVDGVPLRKAERTRLWLY 78
          I +D        R  L L 
Sbjct: 52 IAIDDPARGYVSRAALKLL 70


>gi|307746984|gb|ADN90254.1| Pseudouridine synthase [Campylobacter jejuni subsp. jejuni M1]
          Length = 281

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/201 (16%), Positives = 74/201 (36%), Gaps = 35/201 (17%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            R+D  T GL+L+  +      L+        
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRIDKETSGLILIAKNKKAQIDLKSLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQKGSNAWVTVGLRE-- 195
            + Y    HG+++++ +    K I +      +    MQ+    ++G  A     + E  
Sbjct: 129 QKEYLALAHGKIEENFIVD--KAINLTKNYDDVKTR-MQI---CKEGKQAITEFEILEYF 182

Query: 196 --------------GKNREIK 202
                         G+  +I+
Sbjct: 183 PKINATLLLCKPLTGRQHQIR 203


>gi|255321341|ref|ZP_05362501.1| pseudouridine synthase [Campylobacter showae RM3277]
 gi|255301494|gb|EET80751.1| pseudouridine synthase [Campylobacter showae RM3277]
          Length = 252

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/200 (18%), Positives = 64/200 (32%), Gaps = 29/200 (14%)

Query: 18  KVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG--VPLRKAERTR 74
           K++A + GI S  E + +I    V   G  +  A   + +     V     P    E   
Sbjct: 8   KLLAIQEGI-SNNEAKELIDAGLVSAKGQRIAVARAMMSAATKFNVQKLPRPSVIFEDEN 66

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L    KP  L +                S   +   + RLD  T G+LLL  +    +  
Sbjct: 67  LIAVDKPAFLTSEK-------------VSEIYKFPLLHRLDKETSGVLLLVKNEEFQKKA 113

Query: 135 ELP--STQWLRVYRVRFHGQVDQDK-----LNLLKK--GIVIQ---GICYGDMQVTLDTQ 182
                + +  + Y       V ++      +  LK   G   +           V     
Sbjct: 114 IEEFKNCRVKKEYVAAVKSIVSEEFSINEPIITLKNRGGAFSKISPNGKEAFSHVIPVMV 173

Query: 183 KGSNAWVTVGLREGKNREIK 202
            G  + V V ++ G+  +I+
Sbjct: 174 AGKKSLVKVEIKTGRTHQIR 193


>gi|6320168|ref|NP_010248.1| Pus9p [Saccharomyces cerevisiae S288c]
 gi|3915436|sp|Q12069|PUS9_YEAST RecName: Full=tRNA pseudouridine synthase 9, mitochondrial;
           AltName: Full=tRNA pseudouridylate synthase 9; AltName:
           Full=tRNA-uridine isomerase 9; Flags: Precursor
 gi|1279680|emb|CAA96453.1| unknown [Saccharomyces cerevisiae]
 gi|1431018|emb|CAA98595.1| unnamed protein product [Saccharomyces cerevisiae]
 gi|285810994|tpg|DAA11818.1| TPA: Pus9p [Saccharomyces cerevisiae S288c]
          Length = 462

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRL 75
           RE E     I    V +N       +  + + D I          V   P++   E   +
Sbjct: 139 RESEYYKRTIENGDVHINDETA-DLSTVIRNGDLITHQVHRHEPPVTSRPIKVIFEDDNI 197

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL 134
            +  KP G+    +     +T+   L +    V     RLD  T GL+ L      A  +
Sbjct: 198 MVIDKPSGIPVHPTGRYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPKGADNI 257

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI--------QGICYGDMQVT 178
             +L + +  + Y  +  G+  + +      L L++  + +        +G  +      
Sbjct: 258 GDQLKAREVTKEYVAKVVGEFPETEVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKTVFN 317

Query: 179 LDTQKGSNAWVTVG-LREGKNREIK 202
             +  G  + V    L  G++ +I+
Sbjct: 318 RISYDGKTSIVKCKPLT-GRSHQIR 341


>gi|331265601|ref|YP_004325231.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
 gi|326682273|emb|CBY99890.1| 23S rRNA pseudouridine synthase [Streptococcus oralis Uo5]
          Length = 291

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 29/146 (19%), Positives = 56/146 (38%), Gaps = 14/146 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           +   L + +KP G+ T  + P   + +      +      V RLD+ T GL+L   +  +
Sbjct: 86  QDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKNPFI 145

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
             +L   L   +  R Y     G+V+  +L           +  K+ +  +   Y +  V
Sbjct: 146 LPILNRLLEKKEIAREYWALIEGRVESKELVFRDKIGRDRHDRRKRIVDAKHGQYAETHV 205

Query: 178 TLDTQ-KGSNAWVTVGLREGKNREIK 202
           +   Q       V   L+ G+  +I+
Sbjct: 206 SRLKQFPNQTTLVRCKLKTGRTHQIR 231


>gi|113971474|ref|YP_735267.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
 gi|113886158|gb|ABI40210.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           MR-4]
          Length = 225

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/159 (14%), Positives = 58/159 (36%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G++++     
Sbjct: 19  QDKDIIVVNKPSGLLSVPGRDPAHYDSVYARVKAEHPHCQIVHRLDMATSGVMVVALIRS 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQ 176
             R L+      +  + Y  R  G +  D             N  K+ +  +        
Sbjct: 79  AERELKRQFHDRETSKTYLARVAGHIKNDTGSVDYPLICDWPNRPKQKVDHEIGKPSLTH 138

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
             + ++   +  V +  +  G++ +++  +       + 
Sbjct: 139 FEVLSRAKRSTLVKLKPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|330830420|ref|YP_004393372.1| Pseudouridine synthase [Aeromonas veronii B565]
 gi|328805556|gb|AEB50755.1| Pseudouridine synthase [Aeromonas veronii B565]
          Length = 231

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/227 (16%), Positives = 76/227 (33%), Gaps = 50/227 (22%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   L L +KP GL++ +  +P    +V   L   +     V RLD  T G++++  +  
Sbjct: 22  EDEHLLLINKPSGLLSLSGKNPQNLDSVHYRLVQDYPGCTLVHRLDFGTSGIMVVARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQ 182
           +  +L    +Q    + Y     G +  D      +G++   I          ++   + 
Sbjct: 82  INALLCQQFSQRAVSKAYSALLCGHLIDD------EGVIDAPIAKDPALFPLMKICAASG 135

Query: 183 KGSNAWVTVG--LRE------------------GKNREIKKVFEFFNWKVNRLIRISYGP 222
           K + +   V   L +                  G+  +++   +   + +       YG 
Sbjct: 136 KPARSRYRVIERLAQQIQGQTVPLTRVRLVPETGRTHQLRLHSQLLGYPILGCD--LYGG 193

Query: 223 FQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVR 269
                L  G           EQ    +L  ++++   P+      VR
Sbjct: 194 L----LPPGC----------EQAPRLMLHASKLDFTHPVSGEPMQVR 226


>gi|322412796|gb|EFY03704.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus dysgalactiae subsp. dysgalactiae ATCC
           27957]
          Length = 303

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 74/205 (36%), Gaps = 32/205 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VD-----GVPLR---------KAE 71
           R++   +  ++ V VNG  +   +  V S D +E   D       P+            E
Sbjct: 36  RKIRHFLRTKKNVLVNGSAITWQSA-VNSGDQVELFFDEEDYPDKPIMMGQANKVDCLYE 94

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +             V RLD+ T G+++      + 
Sbjct: 95  DDHLIIVNKPEGMKTHGNEPTELALLNHVSAYTGRTCYVVHRLDMETSGVIVFAKTPFIL 154

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y    HG +   ++           +  K+ + ++        V 
Sbjct: 155 PILNRLLEKREISRDYWALVHGTLSSKEVGYREPIGRHRHDRRKRVVDVKQGQKAITDVK 214

Query: 179 LDTQKGSN-AWVTVGLREGKNREIK 202
           L      N + +   L+ G+  +I+
Sbjct: 215 LLKSFKQNVSLINCRLQTGRTHQIR 239


>gi|295702869|ref|YP_003595944.1| pseudouridine synthase [Bacillus megaterium DSM 319]
 gi|294800528|gb|ADF37594.1| pseudouridine synthase, RluA family [Bacillus megaterium DSM 319]
          Length = 302

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 70/199 (35%), Gaps = 34/199 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLR-KAERTRLWLYHKP 81
               ++VNG         +   D I+V               +PL    E   + + +K 
Sbjct: 40  RGGAIEVNGKHAT-VRYILQKGDEIKVAFPPEKASESLLPKAIPLDIVYEDEYILVLNKQ 98

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + +  S      ++ + +   + +      V  V RLD +T GLL++     +  +  
Sbjct: 99  PNMPSIPSREHLTWSLSNAVLYYYEKNNINSTVHLVNRLDRDTSGLLIVAKHRHVHYLFS 158

Query: 136 LPSTQWL--RVYRVRFHGQ-VDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQK 183
               +    RVYR   HG+ V ++ +           +++ +  +   +     T   Q 
Sbjct: 159 KAQKEHEIKRVYRAFVHGKLVGKETIEAPIGRKESSIIEREVR-EDGQFAITHYTALRQY 217

Query: 184 GSNAWVTVGLREGKNREIK 202
            S   V + L  G+  +I+
Sbjct: 218 SSFTEVALSLETGRTHQIR 236


>gi|259145207|emb|CAY78471.1| Pus9p [Saccharomyces cerevisiae EC1118]
          Length = 462

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRL 75
           RE E     I    V +N       +  + + D I          V   P++   E   +
Sbjct: 139 RESEYYKRTIENGDVHINDETA-DLSTVIRNGDLITHQVHRHEPPVTSRPIKVIFEDDNI 197

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL 134
            +  KP G+    +     +T+   L +    V     RLD  T GL+ L      A  +
Sbjct: 198 MVIDKPSGIPVHPTGRYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPKGADNI 257

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI--------QGICYGDMQVT 178
             +L + +  + Y  +  G+  + +      L L++  + +        +G  +      
Sbjct: 258 GDQLKAREVTKEYVAKVVGEFPETEVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKTVFN 317

Query: 179 LDTQKGSNAWVTVG-LREGKNREIK 202
             +  G  + V    L  G++ +I+
Sbjct: 318 RISYDGKTSIVKCKPLT-GRSHQIR 341


>gi|326317665|ref|YP_004235337.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
 gi|323374501|gb|ADX46770.1| pseudouridine synthase [Acidovorax avenae subsp. avenae ATCC 19860]
          Length = 281

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 27/162 (16%), Positives = 47/162 (29%), Gaps = 25/162 (15%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFD---NLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   +  D   T F        +  RV  V RLD  T G+L++      A
Sbjct: 21  LVAVYKPAGWLVHRTGLDAGETRFVMQALRDQMGRRVYPVHRLDKGTCGVLVMGLHADAA 80

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----------VTL 179
           R L       +  + Y     G         +   +                       L
Sbjct: 81  RALSQAFEHHRVDKRYLALVRGHAPDRV--QVDHALRPDDAPPDAAVQPARTALRCLARL 138

Query: 180 DTQKGSNAWV---TVGLRE-----GKNREIKKVFEFFNWKVN 213
           +  + S+         L E     G+  +I++  +     + 
Sbjct: 139 ELPEASDTRFATTRASLVEALPETGRRHQIRRHLKHIAHPIL 180


>gi|152970825|ref|YP_001335934.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
 gi|150955674|gb|ABR77704.1| putative ribosomal large subunit pseudouridine synthase A
           [Klebsiella pneumoniae subsp. pneumoniae MGH 78578]
          Length = 263

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/186 (19%), Positives = 65/186 (34%), Gaps = 37/186 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  DP    +V   L   +     V RLD  T GL+++  + G
Sbjct: 53  QDEHLVLINKPAGLLSLSGKDPRNLDSVHHRLVQRYPGCTLVHRLDFGTSGLMVIARNKG 112

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +  +L    +Q    +VY     G + +D      +GIV   I     +           
Sbjct: 113 INALLCQQFSQRTVDKVYTALLCGHLAED------EGIVEAAIAKDPARFPRMALCARHG 166

Query: 183 KGSNAWV-------------------TVGLR-E-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +                      V L  E G+  +++   +   + +       YG
Sbjct: 167 KPARSRYRVIDRLYQAREGERALALTRVTLTPETGRTHQLRIHCQLLGYPILGCD--LYG 224

Query: 222 PFQLGT 227
             +L  
Sbjct: 225 GRELPG 230


>gi|228996384|ref|ZP_04156026.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock3-17]
 gi|228763347|gb|EEM12252.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock3-17]
          Length = 286

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/159 (17%), Positives = 56/159 (35%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L   + R      V  V RLD +T GL+L+
Sbjct: 78  EDESVLVINKAPYMSTIPSREHPAGSVANALLYHYDRQNLASTVHIVTRLDRDTSGLMLI 137

Query: 125 TNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVI------QGICY 172
             +  +  +L       +  R Y    HG+  ++       + +KG  I      +    
Sbjct: 138 AKNRFIHHLLSKQHQQKKVKRTYEAIVHGEWLEESGTIDAPIGRKGDSIIERMVCEDGQK 197

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +      V++ L  G+  +I+    +    
Sbjct: 198 AVTHFQVMERFPDKTRVSLQLETGRTHQIRVHMAYLGHP 236


>gi|228475873|ref|ZP_04060583.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus hominis SK119]
 gi|314936097|ref|ZP_07843444.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
 gi|228270028|gb|EEK11498.1| ribosomal large subunit pseudouridine synthase, RluD family
           [Staphylococcus hominis SK119]
 gi|313654716|gb|EFS18461.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Staphylococcus hominis subsp. hominis C80]
          Length = 274

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 37/184 (20%), Positives = 69/184 (37%), Gaps = 26/184 (14%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVL--E 135
           KP G+ T  +D    +T+ +++        V  + RLD  T GLL++  +  + ++L   
Sbjct: 88  KPKGVKTHPNDLKESNTLMNHVIYTMDSDYVEPIHRLDQETVGLLIVAKNPLMKKILDRM 147

Query: 136 LPSTQWLRVYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
           L   Q  R+YR                 + +DK +  K+ I   G       +T    K 
Sbjct: 148 LEENQITRIYRANVKALLPLKPQTIDMPIGKDKFHPNKRRISNTGQRAITHILTSKMIKE 207

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNR--LIRISYGPFQLGTLLAGSTR-----EVS 237
               + + L  G+  +I+         V    L    YG   L  L   S +      ++
Sbjct: 208 GICQLEIKLDTGRTHQIRVHLAEIGHPVIGDPL----YGDATLRQLELNSYKIEFTHPLT 263

Query: 238 KKIL 241
           ++++
Sbjct: 264 QELI 267


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
          +E    +R+ +++   G+  SR +    I   RV V G ++ + +  V     +
Sbjct: 21 EEALARKRIDQLLVDRGVFDSRAKARAAIEAGRVSVAGRVVAKPSEQVDDNAEV 74


>gi|269861115|ref|XP_002650272.1| diaminohydroxyphosphoribosylaminopyrimidine deaminase
           [Enterocytozoon bieneusi H348]
 gi|220066286|gb|EED43774.1| diaminohydroxyphosphoribosylaminopyrimidine deaminase
           [Enterocytozoon bieneusi H348]
          Length = 331

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 35/223 (15%), Positives = 68/223 (30%), Gaps = 49/223 (21%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTD---HIEVDGVPLRKAERTRLW-----LYHKPIG 83
           E  +A   + VN  ++      +   D   HI     P +    T        + +KP G
Sbjct: 37  EDALAIGAITVNDKIVST-EYRMQFNDYFKHIVHQHEPKQPHIPTIYIDDEITVVNKPFG 95

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL-TNDGGLARVLELPSTQWL 142
           +           TV   +      V  V RLDI   G+L++ T +        L S    
Sbjct: 96  IPCHPVGAYHYYTVTKTIFKNKP-VGCVNRLDIPVSGVLIINTCNQKRIHEYLLNSK--- 151

Query: 143 RVYRVRFHGQ--VDQDKLNLLKKGIV----------------IQGICYGDMQVTLDTQKG 184
           ++Y  +  GQ     ++L+ L  GI                 +        +++ D +  
Sbjct: 152 KIYIAKVIGQFIFSDEQLHKL--GIEKRISNGKSIIIVNKSLLLDPKTKKQKISDDGKFA 209

Query: 185 SNAWVTVG-------------LREGKNREIKKVFEFFNWKVNR 214
                 +              +  G+  +I+    +  + +  
Sbjct: 210 ETH-FELVSYQNQYSMIKCYPIT-GRTHQIRVHLAYIGFPILY 250


>gi|218708391|ref|YP_002416012.1| ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           LGP32]
 gi|218321410|emb|CAV17360.1| Ribosomal large subunit pseudouridine synthase A [Vibrio splendidus
           LGP32]
          Length = 244

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 57/149 (38%), Gaps = 28/149 (18%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND------ 127
           + + +KP GL++     P+   +++  L   F  +  V RLD++T GL+LL         
Sbjct: 23  ILVVNKPAGLLSVPGRLPEHYDSMWSRLVVEFPEIQVVHRLDMSTSGLMLLAKHKQAERH 82

Query: 128 --GGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGD 174
                   L        ++Y  R  G V +      L L+       ++ +         
Sbjct: 83  LKKQFQYRLTH------KLYYARVWGSVGEAEGLIDLPLICDWPNRPRQKVCFNEGKPSQ 136

Query: 175 MQVTLDTQKGSNAWVTVG-LREGKNREIK 202
            +  ++ Q+     + +  +  G++ +++
Sbjct: 137 TRYIVEQQEPQTTLLKLLPIT-GRSHQLR 164


>gi|77411416|ref|ZP_00787762.1| ylmH protein [Streptococcus agalactiae CJB111]
 gi|77162502|gb|EAO73467.1| ylmH protein [Streptococcus agalactiae CJB111]
          Length = 262

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 28/50 (56%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+ K++A     SR++  ++I   +VKVN  ++ R +  ++  D I V G
Sbjct: 185 RLDKILATILKISRKQSTKLIEADKVKVNYAIVNRVSEQLVEGDLISVRG 234


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/94 (24%), Positives = 41/94 (43%), Gaps = 8/94 (8%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M++ +  +E    +R+  ++ + G+A SR + + +I    V V+G   ++A      T  
Sbjct: 1  MQNISDYKEKQMKERLDVLVVQKGLAPSREKAKALIMAGCVLVDGEREDKAGTMFAETVQ 60

Query: 60 IEVDGVPLRKAERTRLWL---YHK----PIGLVT 86
          I + G  L+   R  L L     K    P G V 
Sbjct: 61 ITLKGGTLKYVSRGGLKLEKAMEKFSVTPAGKVC 94


>gi|259046558|ref|ZP_05736959.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
 gi|259036723|gb|EEW37978.1| ribosomal large subunit pseudouridine synthase D [Granulicatella
           adiacens ATCC 49175]
          Length = 284

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/154 (14%), Positives = 51/154 (33%), Gaps = 24/154 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-------ISVGRLDINTEGLLL 123
           E   L + +KP+G  +  S      ++ + +   + R          V RLD +T G+++
Sbjct: 69  EDEYLLIINKPVGTASIPSKLHPDHSMANRVKGYYKRRGYADQITHVVTRLDRDTTGVMM 128

Query: 124 LTNDGGLARVLELP---STQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQ 168
                 +               + Y    H              + + + +++ + +   
Sbjct: 129 FAKH-RVVHAWMDQALREKTIQKKYLALVHDTSTLEAHGFIDAPIGRHEGSIINRCVSED 187

Query: 169 GICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           G          +T  G+   V + L  G+  +I+
Sbjct: 188 GKPSLTEYWKKETLVGAE-LVEILLHTGRTHQIR 220


>gi|219119925|ref|XP_002180713.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217408186|gb|EEC48121.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 200

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 36/174 (20%), Positives = 51/174 (29%), Gaps = 41/174 (23%)

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
           + R    +KP G+ T  S  +   +  V   L    SR V  V RLD  T G LL   D 
Sbjct: 4   QDRWVCVNKPAGMSTHRSGGNRSNQFVVSTLLKRQLSRKVFPVHRLDHRTSGALLFAFDS 63

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            +   L          + Y     G  D    N  +           D  +T+D  K S 
Sbjct: 64  EMCASLHDALREQSARKTYVCLVRGFWD----NFFES-----DTATVDKALTVDGTKRSA 114

Query: 187 AWV------TVGL---------------------REGKNREIKKVFEFFNWKVN 213
             V      T+ L                       G+  +I++        V 
Sbjct: 115 TTVFTKLASTIILNNSAYGEKNVPISCSLILAVPTTGRTHQIRRHASAMGMPVL 168


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

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 46/273 (16%), Positives = 90/273 (32%), Gaps = 76/273 (27%)

Query: 7   VQENFTPQRVSKV---------IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST 57
           V E+    R+ +          ++           +++   +V+V+G  ++  A  +   
Sbjct: 8   VAEDEDGLRLDRWFKRRIPALSLSHLN--------KIVRTGQVRVDGARVKT-ATRLAQG 58

Query: 58  DHIEV-------------------DGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRS 95
            ++ V                   D   LR+    E   L + +KP GL         R 
Sbjct: 59  QNVRVPPLNLEAAPEAPVFRISEEDQRDLRQMILFEDKDLMVLNKPYGLAVQGGSGMRRH 118

Query: 96  TVFDN--LPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFH 150
                  LP+    R + V RLD +T G+LL+     +A  L     S Q  ++Y     
Sbjct: 119 IDGMLASLPNERGDRPVLVHRLDRDTSGVLLIAKTRKMAADLGEIFRSRQAQKIYWALVE 178

Query: 151 GQVDQDK--LNLLK---KGIVIQGICYGDMQ------------------------VTLDT 181
           G     +  ++L     +G+  +G    D +                         T+DT
Sbjct: 179 GVPKPAQGKISLFLAKGEGMDARGPRRSDEERASMEKMRVAKHGDEDAQHSVTYYATVDT 238

Query: 182 QKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                AW+++  +  G+  +++   E     + 
Sbjct: 239 FSPRAAWLSMKPIT-GRTHQLRAHAEAIGHPII 270


>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 = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ + + + G+  SR   + +I    V VN   +++A   +     +EV G  +    R
Sbjct: 3  IRLDQYLVQNGLVQSRERAKALIMAGVVFVNQQKVDKAGEMIKEDAVVEVRGHDIGYVSR 62


>gi|116750307|ref|YP_846994.1| RluA family pseudouridine synthase [Syntrophobacter fumaroxidans
           MPOB]
 gi|116699371|gb|ABK18559.1| pseudouridine synthase, RluA family [Syntrophobacter fumaroxidans
           MPOB]
          Length = 300

 Score = 51.3 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 34/200 (17%), Positives = 62/200 (31%), Gaps = 27/200 (13%)

Query: 29  REVERM--IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYH------ 79
            E E M  +    V ++G      +V +     +     P  + +      + H      
Sbjct: 34  SEAEWMARLENGEVCLDGRRAR-GSVVLKPGQWLAWRRPPWEEPDVPLAYAVLHADEDLL 92

Query: 80  ---KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARVL 134
              KP GL T  +     +T+   +         V RL   T G++LL  T         
Sbjct: 93  AVAKPRGLPTVPAGGFLDNTLLALVRRACPEATPVHRLGRGTSGIVLLARTARARSVLAA 152

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVIQGICYGDM--QVTLDTQ 182
            L   +  R YR    G   +D            + L   +             V +  +
Sbjct: 153 ALRRNEVTRTYRALAGGVPGRDAFTVGSPIGPVPHPLLGSVHAANPSGRPALSLVEVLER 212

Query: 183 KGSNAWVTVGLREGKNREIK 202
           +   + V V ++ G+  +I+
Sbjct: 213 RTGCSVVGVRIKTGRPHQIR 232


>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 = 50.9 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 10/75 (13%)

Query: 12  TPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV----- 65
              R+   IA AG   SR ++   I+   V+VN   + +A+ NV S D I   G      
Sbjct: 182 ASMRLD-AIASAGFGISRSKMAEAISAGDVRVNWKEITQASYNVQSGDLITFRGKGRLEV 240

Query: 66  ---PLRKAERTRLWL 77
               + K ER R+ L
Sbjct: 241 GEVAVTKKERYRIQL 255


>gi|254466117|ref|ZP_05079528.1| pseudouridine synthase, RluD [Rhodobacterales bacterium Y4I]
 gi|206687025|gb|EDZ47507.1| pseudouridine synthase, RluD [Rhodobacterales bacterium Y4I]
          Length = 348

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/200 (18%), Positives = 69/200 (34%), Gaps = 50/200 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E+   QR+ + +       RR         +E+M  +  ++++G  ++ A+  V + 
Sbjct: 8   TVSEDDGGQRIDRWL-------RRLFPHVNQGRIEKMCRKGELRLDGARVK-ASSRVEAG 59

Query: 58  DHIEV---------------------DGVPLRKAERTR---LWLYHKPIGLVTTHSDPDG 93
             + V                     D   ++     R   + + +KP GL        G
Sbjct: 60  QVVRVPPLADSDLKPAEPRAMKISDADAKMIQSCVIYRDDDVIVLNKPAGLAVQG--GSG 117

Query: 94  RSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            +   D L          +   V R+D +T G+L+L  +   A+ L          ++Y 
Sbjct: 118 TTKHVDGLAEALKFGLEEKPKLVHRIDKDTSGVLVLARNRKAAQGLTAAFRHKNTRKIYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIV 166
               G      L  +K G+V
Sbjct: 178 ALVAGVPTP-YLGEIKNGLV 196


>gi|56698216|ref|YP_168588.1| ribosomal large subunit pseudouridine synthase A [Ruegeria pomeroyi
           DSS-3]
 gi|56679953|gb|AAV96619.1| ribosomal large subunit pseudouridine synthase A [Ruegeria pomeroyi
           DSS-3]
          Length = 215

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/158 (15%), Positives = 56/158 (35%), Gaps = 14/158 (8%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            E   L + +KP GL++           +   + + F   + V RLD +T G+++     
Sbjct: 16  HEDAELIVLNKPAGLLSVPGRGAHLADCLLSRVQAAFPGALLVHRLDRDTSGVMVFAQTP 75

Query: 129 GLARVLEL--PSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDM 175
              R L       +  + Y  R  G+++       L L+       ++ +  +       
Sbjct: 76  HAQRNLGRQFEERKTRKTYVARLWGRLEPKTGTVDLPLIVDWPNRPRQMVCHETGKPAVT 135

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
              +   +G    V +  R G++ +++   +     + 
Sbjct: 136 DWRVLRYEGDTTRVRLLPRTGRSHQLRVHCQALGHPIL 173


>gi|332975054|gb|EGK11960.1| ribosomal large subunit pseudouridine synthase C [Kingella kingae
           ATCC 23330]
          Length = 334

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 83/254 (32%), Gaps = 66/254 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
            +QE+   QR+   + +      +  + R+I    V+VN G +  +    + + D + + 
Sbjct: 13  TIQEHEAGQRLDNYLIKILKGVPKSHIHRIIRAGEVRVNKGRV--KPDYRIENKDLVRI- 69

Query: 64  GVPLRKAERTR----------------------LWLYHKPIGLVTTHSDPDGRSTVFDNL 101
             P+R AE+                        + + +KP G+        G S V   +
Sbjct: 70  -PPIRIAEKDVSGSLKNAPIPAREFDIVFEDDAMIVINKPSGVAV-----HGGSGVSFGV 123

Query: 102 PSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQ 152
                +          V RLD +T GLL++         L   L +    ++Y     G 
Sbjct: 124 IEQLRQSRPDAKYLELVHRLDRDTSGLLMIAKKRSALVKLHEMLRNDHPKKIYLALGVGT 183

Query: 153 VDQDKL---------------NLLKKGIVIQGICYGDMQVTLDTQKGS---------NAW 188
              +                  +++ G    G     +   L+T  GS          + 
Sbjct: 184 WQPENRHVKLPLIKYTGANGEKMVRVGSDADGQSAHTIFRVLNTFSGSLMHSVGISALSL 243

Query: 189 VTVGLREGKNREIK 202
           V   L+ G+  +I+
Sbjct: 244 VEATLKTGRTHQIR 257


>gi|309389907|gb|ADO77787.1| SSU ribosomal protein S4P [Halanaerobium praevalens DSM 2228]
          Length = 208

 Score = 50.9 bits (121), Expect = 3e-04,   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|261856344|ref|YP_003263627.1| pseudouridine synthase [Halothiobacillus neapolitanus c2]
 gi|261836813|gb|ACX96580.1| pseudouridine synthase, RluA family [Halothiobacillus neapolitanus
           c2]
          Length = 346

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 75/242 (30%), Gaps = 47/242 (19%)

Query: 6   IVQENFTPQRVSKVI-----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            V  ++  QR+   +     A  G   R  + R++    V+VN    +     + + D +
Sbjct: 23  TVDAHYAGQRIDNFLLRELGATHGEVPRSLIYRILRTGEVRVNSQRAK-PTTRLATGDEV 81

Query: 61  EVDGVPLRKA----------------------ERTRLWLYHKPIGLVTTH--SDPDGRST 96
            +  + L+                        E   L   +KP GL      + P G   
Sbjct: 82  RIPPLKLQSPSQESAGVISANWLARAADMIVYEDEALLAVNKPAGLAVHGGSNIPFGLIE 141

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHGQV 153
           +      +  ++    R+D +T GLL+L         L+    P     + Y    HG  
Sbjct: 142 LMRQHTGLGEKLELAHRIDRDTSGLLILAKTRATLHSLQTQFRPEGHAEKQYLAIVHGHW 201

Query: 154 DQDK------LNLLK-KG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
                     L   + +G      +  QG         L   K +   +   L  G+  +
Sbjct: 202 PDKLKRVDAPLEKWQGEGESHRVQVNPQGKEAVTHFAVLAANKNAT-LLRAQLETGRTHQ 260

Query: 201 IK 202
           I+
Sbjct: 261 IR 262


>gi|290579729|ref|YP_003484121.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
 gi|254996628|dbj|BAH87229.1| putative pseudouridylate synthase [Streptococcus mutans NN2025]
          Length = 288

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/206 (16%), Positives = 75/206 (36%), Gaps = 34/206 (16%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEVD----GVPLRK------------AE 71
           R++   +  ++ V VN   +   ++ V   D I+++      P++K             +
Sbjct: 28  RKIRHFLRIKKNVTVNSQAVNWQSL-VRRGDIIQLNFDNTDYPIKKIPMGNKALIDCLYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG--- 128
              L + +K  G+ T  +DP+  + +      +      V RLD+ T G ++   +    
Sbjct: 87  DEHLIIVNKIEGMKTHANDPNEIALLNHASAYVGQTCYVVHRLDMKTSGTVMFAKNPFIL 146

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQV 177
            +   L   +    R Y     GQ  +  +           +  K+ +  +       QV
Sbjct: 147 PILNRLL-ENKSIKREYWALAQGQFSERAIIYREPIGRDRHDRRKRVVDHKHGQTAITQV 205

Query: 178 TLDTQ-KGSNAWVTVGLREGKNREIK 202
           +L      + + +   L+ G+  +I+
Sbjct: 206 SLLKHFPNNTSLIKCQLQTGRTHQIR 231


>gi|241667739|ref|ZP_04755317.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25015]
 gi|254876283|ref|ZP_05248993.1| ribosomal large subunit pseudouridine synthase C [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
 gi|254842304|gb|EET20718.1| ribosomal large subunit pseudouridine synthase C [Francisella
           philomiragia subsp. philomiragia ATCC 25015]
          Length = 309

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 69/212 (32%), Gaps = 48/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKAERTR------------ 74
           R I +  ++VN   +++    V + D + V      + + + K  ++             
Sbjct: 36  RWIRKGELRVNKKRVKQ-TTRVSAGDIVRVPPFSLEENLEIAKVSKSHLDFLEQRILYET 94

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +  KP G+            V     L     R+  V RLD  T G +LL      
Sbjct: 95  DDYIVVDKPSGMAVHGGSGVNSGLVERLRQLRPKVRRLDLVHRLDKETSGCVLLAKKHSS 154

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGDMQ--VTLDTQKG 184
                      +  ++Y    HG  D+  D ++     + +      D Q  V +D ++G
Sbjct: 155 LVYFFDIFKERKVNKIYYALVHGHWDEKVDAID-----LPLSRTETKDGQRIVKVDKREG 209

Query: 185 SN--------------AWVTVGLREGKNREIK 202
                           + + + L  G+  +I+
Sbjct: 210 KRALTRILAVQKIGDYSLLEIKLETGRTHQIR 241


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 29/63 (46%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++   G+A SR   +R+I   +V VN   +++A   V +   + V G  L  
Sbjct: 1  MKKERLDVLLTVQGLAPSRERAKRLIMAGQVLVNEQRVDKAGATVPADAALRVAGEDLPY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>gi|220934229|ref|YP_002513128.1| tRNA pseudouridine synthase C [Thioalkalivibrio sp. HL-EbGR7]
 gi|219995539|gb|ACL72141.1| tRNA pseudouridine synthase C [Thioalkalivibrio sp. HL-EbGR7]
          Length = 235

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/178 (20%), Positives = 61/178 (34%), Gaps = 35/178 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP  ++   S P  R  VF        +  RV +V RLD  T G+LL       A
Sbjct: 16  LVAINKPEQMLVHRS-PISRDEVFVLQRLRDQLGQRVYTVHRLDRPTSGVLLFGLHPAAA 74

Query: 132 RVLEL--PSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDMQVTL 179
             +     + +  + Y     G           ++ +    L++ +           V L
Sbjct: 75  TAMARQFEAGEVHKRYLAVVRGYTEESGEIDHPLESEDGRGLQQAVT---RYRRLATVEL 131

Query: 180 DTQKGSN-----AWVTVGLREGKNREIKKVFEFFNWKV-----------NRLIRISYG 221
           D   G       + + V  R G+  +I++ F+     +           NRL R  +G
Sbjct: 132 DIPVGRYPVARYSLLEVWPRSGRRHQIRRHFKHIFHPLAGDTTYGEGRHNRLFREHFG 189


>gi|197303693|ref|ZP_03168730.1| hypothetical protein RUMLAC_02422 [Ruminococcus lactaris ATCC
           29176]
 gi|197297213|gb|EDY31776.1| hypothetical protein RUMLAC_02422 [Ruminococcus lactaris ATCC
           29176]
          Length = 295

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/151 (15%), Positives = 56/151 (37%), Gaps = 19/151 (12%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +KP G+    S  + ++++ + L   +             RLD +T GL ++
Sbjct: 86  EDDDLLVVNKPAGMPIHPSLNNYKNSLANALMYYYKEQGKPFIFRCTNRLDRDTSGLTVI 145

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--KLNL---------LKKGIVIQGIC 171
                 + +L       +  R Y     G V      +N          +++ +  +   
Sbjct: 146 AKHLVSSSILSFMAVRHEIHREYLAIVRGAVSPASGTINAPLARTGSSIIERKVDFEHGE 205

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +      +  ++  ++ V++ L  G+  +I+
Sbjct: 206 HAVTHYKVLKEQNQHSLVSLILETGRTHQIR 236


>gi|195434114|ref|XP_002065048.1| GK15253 [Drosophila willistoni]
 gi|194161133|gb|EDW76034.1| GK15253 [Drosophila willistoni]
          Length = 761

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 54/338 (15%), Positives = 110/338 (32%), Gaps = 43/338 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P+        + + +KP 
Sbjct: 352 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPA 411

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 412 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 471

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G  +
Sbjct: 472 RQVEKEYICRVEGIFPDGIVE-CKEPIEVVSYKIGVCKVSPRGKDCTTTFQKLSQNGKTS 530

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR--L--IRISYGPF--QLGTLLAGSTREVSKKI 240
            V    L  G+  +I+   ++  + +    L    + +GP   + G +  G T     ++
Sbjct: 531 VVLCKPLT-GRMHQIRVHLQYLGYPILNDPLYNHEV-FGPLKGRSGDIG-GKT---DDEL 584

Query: 241 LREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDF--TRMKKNSSQKNGL 295
           +R+ +  H  E       + D  ++ +     DR ++ S+       +      + +   
Sbjct: 585 IRDLINIHNAENWLGIDCDSDISLFKNTKDETDRESLSSDQTSAIHQSDDDGGINSRETT 644

Query: 296 SKQKKLATPVHRRNLASNVWMAKGIHSSFLSDSGQREE 333
               +        ++  ++       S     S   + 
Sbjct: 645 PPCSESIQQQTTNSVKQHLEHPNTSRSQIEYSSTSDDT 682


>gi|188590633|ref|YP_001919968.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500914|gb|ACD54050.1| pseudouridine synthase, RluA family [Clostridium botulinum E3 str.
           Alaska E43]
          Length = 298

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 40/222 (18%), Positives = 78/222 (35%), Gaps = 49/222 (22%)

Query: 33  RMI----AQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKA--------ERTRL 75
           R+I      QR+ VN  ++      + + D I++D        +           E   +
Sbjct: 30  RLIRSASKDQRIYVNNSVVR-MNYMIKNGDVIKIDLNKNESQNINPEKIDLDIVYEDDDV 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGG 129
            + +K   ++   +      T+ + +   F        V  V RLD+NT GL+++  +  
Sbjct: 89  LVINKQPFIIVHPTKNFQSGTLANGILYYFQETNQNCIVRLVSRLDMNTSGLIIIAKNQF 148

Query: 130 LARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVI-----QGICYGDMQVTLDTQ 182
               L      +  + Y    HG +++      K+G I +     +GI YG  +V  +  
Sbjct: 149 SHSRLSKDMKEKLQKRYLAIVHGNLEE------KEGTIDLPIYKPEGIEYGSRRVIDERG 202

Query: 183 KGSNAWVTVG-------LRE-----GKNREIKKVFEFFNWKV 212
           + S     V        L E     G+  +I+         +
Sbjct: 203 QRSITHYKVIESFEGGDLVECLLETGRTHQIRVHLSHLGHPI 244


>gi|161507907|ref|YP_001577871.1| ribosomal protein large subunit [Lactobacillus helveticus DPC 4571]
 gi|160348896|gb|ABX27570.1| ribosomal protein large subunit [Lactobacillus helveticus DPC 4571]
          Length = 285

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 69/210 (32%), Gaps = 35/210 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRKA----------ERTRLWLYH 79
           I Q  + +NG        NV+  D I+     VD    +            E   L + +
Sbjct: 37  IEQ-NITING-TYRYFNQNVLPGDKIDIILDQVDSAQQKYPASGKLPDIIYEDDNLLIIN 94

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL----ARVLE 135
           K  G  T  +  +  +T+ D    +      V RLD+ T GLLL+  +  +     R L 
Sbjct: 95  KKKGQKTHPNLNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELT 154

Query: 136 LPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
             +    R Y  +                +D D  +  K+ I   G+        L    
Sbjct: 155 SKTFH--RDYLAKVDHADKLSDQGTINQPIDHDPEDQRKRMISPAGLHAVTHYQVLKRND 212

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + A V + L  G+  +I+         + 
Sbjct: 213 NNTAVVKLTLETGRTHQIRVHLASLGTPII 242


>gi|163789051|ref|ZP_02183495.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteriales bacterium ALC-1]
 gi|159875715|gb|EDP69775.1| putative ribosomal large subunit pseudouridine synthase
           [Flavobacteriales bacterium ALC-1]
          Length = 232

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/166 (13%), Positives = 49/166 (29%), Gaps = 23/166 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLL 122
           E   + + +K  G +       D      V + +   +++     +  V RLD  T G++
Sbjct: 16  EDNHIIVANKRAGDIVQGDKTGDKPLSEVVKEYIKDKYNKPGNVYLGVVHRLDRPTTGIV 75

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNLLKK-----------GIVI 167
           L +        L       +  + Y      Q     D L    K              +
Sbjct: 76  LFSKTSKALPRLNKLFAEKKAKKTYWALVKNQPPKTNDTLTHWLKKNPKNNKSTAYHKEV 135

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +G     +   +     +   + + L  G++ +I+         + 
Sbjct: 136 EGSKKAILHYKIIKTLDNFYLLEIDLETGRHHQIRTQLASIGCPIK 181


>gi|329667795|gb|AEB93743.1| hypothetical protein LJP_1421 [Lactobacillus johnsonii DPC 6026]
          Length = 282

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 67/207 (32%), Gaps = 33/207 (15%)

Query: 37  QQRVKVNGI------LLERAAVNVMSTDHIEVDGVPLRK--------AERTRLWLYHKPI 82
           ++++ +NG       L++      +  DHIE D  P            E   + + +KP 
Sbjct: 39  EKKILINGKYLPLNFLVKHGDKIEIQLDHIESDQQPYPASGKLPKVVYEDNDILVINKPA 98

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL----ARVLELPS 138
           G  T  +  +  + + D    +      V RLD+ T GLLL+  +  +     R L   +
Sbjct: 99  GQKTHPNLNEEDTALNDCATYLGYSPFIVHRLDMLTSGLLLVAKNPAVVPILNRQLTDKT 158

Query: 139 TQWLRVYRVRF------------HGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
               R Y                   +  D  +  K+ +   G         +  +    
Sbjct: 159 LH--REYLAWISNSPQIKNTGIIDLPIGHDPHDQRKRMVRQDGQKAVTH-YEVIKRDKDR 215

Query: 187 AWVTVGLREGKNREIKKVFEFFNWKVN 213
             V + L  G+  +I+         + 
Sbjct: 216 ILVKLTLETGRTHQIRVHLAALGAPII 242


>gi|254360710|ref|ZP_04976858.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261496892|ref|ZP_05993260.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
 gi|153091280|gb|EDN73254.1| pseudouridylate synthase [Mannheimia haemolytica PHL213]
 gi|261307416|gb|EEY08751.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           OVINE]
          Length = 217

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/159 (14%), Positives = 47/159 (29%), Gaps = 12/159 (7%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+    R    + +KP GL     + +   T          +V  V RLD  T GLL+L 
Sbjct: 6   PICYQHRD-FIIINKPEGLSVHKDEAEIGLTELVARQLNVKQVWLVHRLDKITSGLLILA 64

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD------KLNLLKKGI-VIQGICYGDMQ 176
            +   A          +  + Y      +  +        +   + G   +         
Sbjct: 65  LNKEAAARFYHLFEQHKIYKTYWALSDKKPKKKQGRIVGDMQKSRNGAWKLCHSKENPAV 124

Query: 177 VTLDTQKGSNAWVTVGL--REGKNREIKKVFEFFNWKVN 213
               +    ++     L  + GK  +++   +     + 
Sbjct: 125 TQFISHSVEDSLRHFILQPKTGKTHQLRVAMKSLGSPIL 163


>gi|86150522|ref|ZP_01068746.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|86152341|ref|ZP_01070551.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|315123634|ref|YP_004065638.1| RNA pseudouridylate synthase family [Campylobacter jejuni subsp.
           jejuni ICDCCJ07001]
 gi|85838974|gb|EAQ56239.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni CF93-6]
 gi|85840638|gb|EAQ57890.1| RNA pseudouridine synthase family protein [Campylobacter jejuni
           subsp. jejuni 260.94]
 gi|315017356|gb|ADT65449.1| RNA pseudouridylate synthase family [Campylobacter jejuni subsp.
           jejuni ICDCCJ07001]
          Length = 298

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 53/137 (38%), Gaps = 9/137 (6%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDH--IEVDGVPLRKA---ERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     ++  D   I  +  P       E     +  K  G+
Sbjct: 29  EAQKLIDKKRLFCDGILVEE-KNKILKGDVELIVYENNPKGVEIVFENEDFAVLEKESGI 87

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
           ++  +    + ++ D +      +     RLD  T GL+L+         L       Q 
Sbjct: 88  LSHPNGRHCKYSLSDEIWHLWGKKACVAHRLDKETSGLILVAKHKKAQIELKTMFEKKQI 147

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y     G++  + +
Sbjct: 148 QKEYLALASGEIKVNFI 164


>gi|293391529|ref|ZP_06635863.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952063|gb|EFE02182.1| ribosomal large subunit pseudouridine synthase A [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 219

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/156 (14%), Positives = 54/156 (34%), Gaps = 17/156 (10%)

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + + +KP GL++   + P    +    +   +       RLD+ T G+LL        R
Sbjct: 22  YIAVVNKPSGLLSVPGNQPQYYDSAMSRVKEKYGFCEPAHRLDMATSGILLFALSKSADR 81

Query: 133 VLELPSTQWL--RVYRVRFHGQVDQDKL-----------NLLKKGIVIQ-GICYGDMQVT 178
            L+    +    + Y+    G ++Q++            N  ++ I  + G         
Sbjct: 82  ELKRQFREREPKKYYQALVWGHLEQEQGVVELPLICDWENRPRQKICFERGKRAVTFYEV 141

Query: 179 LDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
           L     +   + +  +  G++ +++         + 
Sbjct: 142 LQRHPNNTTRIKLTPIT-GRSHQLRLHMLALGHPIL 176


>gi|229004047|ref|ZP_04161850.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock1-4]
 gi|228757200|gb|EEM06442.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           Rock1-4]
          Length = 286

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/159 (17%), Positives = 56/159 (35%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +K   + T  S      +V + L   + R      V  V RLD +T GL+L+
Sbjct: 78  EDESVLVINKAPYMSTIPSREHPAGSVANALLYHYDRQNLASTVHIVTRLDRDTSGLMLI 137

Query: 125 TNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQD----KLNLLKKGIVI------QGICY 172
             +  +  +L       +  R Y    HG+  ++       + +KG  I      +    
Sbjct: 138 AKNRFIHHLLSKQHQQKKVKRTYEAIVHGEWLEESGTIDAPIGRKGDSIIERMVCEDGQK 197

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 +  +      V++ L  G+  +I+    +    
Sbjct: 198 AVTHFQVMERFPDKTRVSLQLETGRTHQIRVHMAYLGHP 236


>gi|190405049|gb|EDV08316.1| tRNA pseudouridine synthase [Saccharomyces cerevisiae RM11-1a]
          Length = 462

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRL 75
           RE E     I    V +N       +  + + D I          V   P++   E   +
Sbjct: 139 RESEYYKRTIENGDVHINDETA-DLSTVIRNGDLITHQVHRHEPPVTSRPIKVIFEDDNI 197

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL 134
            +  KP G+    +     +T+   L +    V     RLD  T GL+ L      A  +
Sbjct: 198 MVIDKPSGIPVHPTGRYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPRGADNI 257

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI--------QGICYGDMQVT 178
             +L + +  + Y  +  G+  + +      L L++  + +        +G  +      
Sbjct: 258 GDQLKAREVTKEYVAKVVGEFPETEVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKTVFN 317

Query: 179 LDTQKGSNAWVTVG-LREGKNREIK 202
             +  G  + V    L  G++ +I+
Sbjct: 318 RISYDGKTSIVKCKPLT-GRSHQIR 341


>gi|146102317|ref|XP_001469333.1| hypothetical protein [Leishmania infantum]
 gi|134073702|emb|CAM72439.1| conserved hypothetical protein [Leishmania infantum JPCM5]
          Length = 741

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/122 (16%), Positives = 38/122 (31%), Gaps = 22/122 (18%)

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVLELPS------TQWLRVYRV-RFHGQVDQDKLN 159
           R   V RLD  T G LL+      A  L          +   ++Y       +       
Sbjct: 568 RQGQVHRLDAETSGCLLIAKSDVAADSLRHQLGTSAAFSHHSKIYHALCVVLEPS----- 622

Query: 160 LLKKGIVIQGICYGDMQVTLDTQ--------KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            L+  + +           + T+        K   AWV   +++GK  ++++        
Sbjct: 623 -LRN-VRLHDDIIDAADPKIRTRYRVIRFFPKHRVAWVECRIQQGKKHQLRRHLASRGLP 680

Query: 212 VN 213
           + 
Sbjct: 681 IL 682


>gi|99034362|ref|ZP_01314387.1| hypothetical protein Wendoof_01000811 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 264

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR--VISVGRLDINTEGLLLLTNDG 128
           E   +   +KP G++        + ++ D L  I        V RLD +T G+++   + 
Sbjct: 50  EDEYILAINKPAGVIVQGG-VKVKISMSDLLDQIREGETFKIVHRLDRDTSGVIIFARNA 108

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQD 156
            +AR L       +  + Y     G   +D
Sbjct: 109 NVARYLMEEFKGRRVKKTYLALTSGIPSKD 138


>gi|328868208|gb|EGG16588.1| pseudouridine synthase family protein [Dictyostelium fasciculatum]
          Length = 558

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/141 (18%), Positives = 43/141 (30%), Gaps = 21/141 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------LWLYHKP 81
           I    ++VNG         V   D IE     + + E                     KP
Sbjct: 208 IENGWIRVNGQQ-TTVDYCVGRKDMIE---HRVHRHEPPVTSAPIKIVANDDEYVAVDKP 263

Query: 82  IGL-VTTHSDPDGRSTVFDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--P 137
             + V         S ++        + +  V RLD  T GLL+L      A+ +     
Sbjct: 264 SSIPVHPCGRFRHNSLIYVLAKEYGLNNLFGVHRLDRLTSGLLILAKSTESAQKMSGAIM 323

Query: 138 STQWLRVYRVRFHGQVDQDKL 158
             +  + Y     G+   D++
Sbjct: 324 KGEVSKRYVALVKGKFSNDEV 344


>gi|270007545|gb|EFA03993.1| hypothetical protein TcasGA2_TC014142 [Tribolium castaneum]
          Length = 552

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/165 (18%), Positives = 57/165 (34%), Gaps = 18/165 (10%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLL 122
             +   E   +    KP  L          +TV   L   +    + ++ RLD  T GLL
Sbjct: 192 KLIHVDEDLVV--LDKPCSLPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGLL 249

Query: 123 LLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           L       AR +E         + Y  R  G+   + +   K+ I +     G  +V+  
Sbjct: 250 LFGRSPKKARQMEHQIRNRLVQKEYVCRVEGEFPDEIIE-CKEPIEVVSYKIGVCKVSPK 308

Query: 181 TQK--------GSNAWVTVGL---REGKNREIKKVFEFFNWKVNR 214
            +         G N   ++ L   + G+  +I+   ++  + V  
Sbjct: 309 GKDCNTIFQKLGFNGKTSIVLCKPKTGRMHQIRVHLQYLGYPVVN 353


>gi|302382665|ref|YP_003818488.1| pseudouridine synthase [Brevundimonas subvibrioides ATCC 15264]
 gi|302193293|gb|ADL00865.1| pseudouridine synthase, RluA family [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 350

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/258 (15%), Positives = 71/258 (27%), Gaps = 59/258 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLER-------AA 51
           V E     R+ +         RR        +V++M    +++V+G  ++        AA
Sbjct: 29  VAEAEDGIRLDRWF-------RRRWPHLSNIQVQKMARGGQIRVDGARIKPEGRLTAGAA 81

Query: 52  VNVMS--TDHIEVDGVPLRKA-------------ERTRLWLYHKPIGLVTTHSDPDGRST 96
           V V       +   G  +                E   +   +KP GL         R  
Sbjct: 82  VRVPPIPEPIVRAPGEHMALTPADIAFAKSMVIYEDDLVIALNKPWGLAVQGGTKTTRHV 141

Query: 97  --VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             +         R   V RLD +T G+LLL      A+ L       Q  + Y     G 
Sbjct: 142 DRLLSAWGEGMERPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWAIVMGL 201

Query: 153 VDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR-------------E 195
                    ++L K GI                 + +     V                 
Sbjct: 202 PKPADGQISVHLKKSGIN-DYEIMRPADPKDPGAEPAETAYAVISHAAQRASWMALRPFT 260

Query: 196 GKNREIKKVFEFFNWKVN 213
           G+  +++   +     + 
Sbjct: 261 GRTHQLRAHMKAIGHPIL 278


>gi|237731372|ref|ZP_04561853.1| pseudouridylate synthase [Citrobacter sp. 30_2]
 gi|226906911|gb|EEH92829.1| pseudouridylate synthase [Citrobacter sp. 30_2]
          Length = 232

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 80/239 (33%), Gaps = 57/239 (23%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  I+     V R
Sbjct: 12  PCHDEIE------TLYQDEHLVLINKPSGLLSLSGKNPQNLDSVHHRLVQIYPGCTLVHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G ++ D      +G++   I 
Sbjct: 66  LDFGTSGLMVVARNKAINAALCQQFSQRTVTKVYSALLCGHLEND------EGVIDAAIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG--------------LR------E-GKNREIKKVF 205
                     +     K + +   V               L       E G+  +++   
Sbjct: 120 KDPALFPLMSICALNGKPARSRYQVVERFYHRQEEGTLLPLTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSS 264
           +     +       YG    G LL G+          EQ    +L  ++++   PI  +
Sbjct: 180 QQLGHPILGCD--LYG----GRLLPGT----------EQTSRLMLHASELHFRHPISEA 222


>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 = 50.9 bits (121), Expect = 3e-04,   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|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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
              QR+  ++   G+  SR   +R+I    VKVN  L+++    V     +E+
Sbjct: 3  KADKQRLDALLVAKGLCESRALAQRLIRAGEVKVNQQLVDKPGTLVTMDVAVEL 56


>gi|307174606|gb|EFN65027.1| RNA pseudouridylate synthase domain-containing protein 2
           [Camponotus floridanus]
          Length = 376

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 42/257 (16%), Positives = 93/257 (36%), Gaps = 31/257 (12%)

Query: 59  HIEVDGVPLRKAERTRLWL------YHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVIS 110
            I +  VP+     T + +       +KP  +          +TV   L   +    + +
Sbjct: 27  DIRIHEVPVTSEPITVIHMDEDVVVVNKPASIPVHPCGRYRHNTVVFILAKEYNLKNLRT 86

Query: 111 VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ 168
           + RLD  T G+LL       AR +E    + Q  + Y  R  G+  ++++ +  + I + 
Sbjct: 87  IHRLDRLTSGILLFGRTPKKARQMEHQIRNRQVHKQYVCRVEGEFPEEEV-ICSEPIEVV 145

Query: 169 GICYGDMQVTLDTQK-----------GSNAWVTVGLREGKNREIKKVFEFFNWKVNR--L 215
               G  +V+   +            G ++ V    + G+  +I+   ++  + V    L
Sbjct: 146 SYKIGVCKVSEKGKDCVTRFKRLSYNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPL 205

Query: 216 -IRISYGPFQLGTLLAGSTREVSKKIL-REQLGPHLLEE-AQVNLDAPIYSSETLVRDRP 272
              + +GP +      G     + + L R+ +  H  E    ++ D+ +   +  +    
Sbjct: 206 YNHVVFGPHKGKGGNIGK----TDEELVRDLISIHNAENWLGMDGDSDMSLFKPKLELEE 261

Query: 273 NIISEVPDDFTRMKKNS 289
            ++    D       +S
Sbjct: 262 RVLGSGNDKDNGSSPSS 278


>gi|229524488|ref|ZP_04413893.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
 gi|229338069|gb|EEO03086.1| ribosomal large subunit pseudouridine synthase A [Vibrio cholerae
           bv. albensis VL426]
          Length = 177

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/96 (22%), Positives = 38/96 (39%), Gaps = 15/96 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP-DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTN--- 126
           E   +   +KP GL++    P +   +++  L      V  V RLD++T GL+L      
Sbjct: 19  EDEHIIAANKPSGLLSVPGRPVEHYDSMWARLVDYCPDVKVVHRLDMSTSGLILFAKGKH 78

Query: 127 -----DGGLARVLELPSTQWLRVYRVRFHGQVDQDK 157
                       L        ++Y  R  G ++QD+
Sbjct: 79  MESALKKQFQYRLTH------KIYYARVWGVMEQDE 108


>gi|52424286|ref|YP_087423.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
 gi|52306338|gb|AAU36838.1| RluA protein [Mannheimia succiniciproducens MBEL55E]
          Length = 219

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/156 (14%), Positives = 50/156 (32%), Gaps = 17/156 (10%)

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + + +KP GL++   + P    +    +   +       RLD+ T G+LL         
Sbjct: 22  HILVVNKPSGLLSVPGNQPRYYDSAMSRVKDKYGFCEPAHRLDMATSGILLFAMSKAADS 81

Query: 133 VLELP--STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQ-GICYGDMQVT 178
            L+      +  + Y     G ++QD                ++ I  + G         
Sbjct: 82  ELKRQFRERETKKYYEALVWGHLEQDSGEVNLPLVCDWENRPRQTICFERGKSAVTKYEV 141

Query: 179 LDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
           L     +   V +  +  G++ +++         + 
Sbjct: 142 LQRLPNNTTRVKLTPIT-GRSHQLRLHMLALGHPIL 176


>gi|328351783|emb|CCA38182.1| hypothetical protein PP7435_Chr2-0494 [Pichia pastoris CBS 7435]
          Length = 327

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 34/216 (15%), Positives = 75/216 (34%), Gaps = 38/216 (17%)

Query: 15  RVS------KVIARAGIASRREVER------MIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R++      K+I   G+A+ + +++      +I      VN        V +        
Sbjct: 20  RLNIDNGTIKLIRNRGLATEQTIDKSLLYSTLIKSGDCVVNTEHKHEPEVGI-------- 71

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEG 120
            G  +   +   + + +KP G+    +     +T+ + + +    S +    RLD  T G
Sbjct: 72  -GEEIVYQDDN-ILVVNKPCGVPVHPTGKYYYNTMTEIMKNELGVSSLYPCHRLDRLTSG 129

Query: 121 LLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVD------QDKLNLL------KKGIV 166
           +L++  T         +L      + Y  R  G+         DK+  +      + GI 
Sbjct: 130 ILIIGKTPRAAAKYQTQLKQNSIQKTYIARVDGEFPMGNIVCSDKIVNIDCKRGKENGIT 189

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  + Q    +   + + V    + G+  +I+
Sbjct: 190 EPKEALTNFQRLAYSTSLNQSIVKCSPKTGRTHQIR 225


>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 = 50.9 bits (121), Expect = 3e-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|85707668|ref|ZP_01038734.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
 gi|85689202|gb|EAQ29205.1| pseudouridylate synthase [Erythrobacter sp. NAP1]
          Length = 395

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 85/260 (32%), Gaps = 54/260 (20%)

Query: 3   DKNIVQENFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
            +  V ++    R+ +     + + G A+   + R     +V+V+G  ++     + +  
Sbjct: 9   RQFTVSDDDDGIRLDRWFKRNLPKIGFAT---ISRWARTGQVRVDGGRVK-PEDRLEAGQ 64

Query: 59  HIEV--DGVPLRKAERTRL---------------------WLYHKPIGLVT-----THSD 90
            + V   G   ++  + R                       + +KP GL T     T   
Sbjct: 65  VLRVPPGGEDQKRGPKPRRPLTEEEIAEARAMVIRETPSAIVLNKPPGLATQGGSKTTKH 124

Query: 91  PDGRSTVF-DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRV 147
            DG    F D+      R   V RLD +T G+LL+    G A       +     +VY  
Sbjct: 125 VDGLLDAFVDDQEEDAPRPRLVHRLDKDTSGVLLIARTPGSAATYSRKFSGRSARKVYWA 184

Query: 148 RF-------HGQVDQDKLNLLKKG-----IVIQGICYGDMQVTLDTQKGSN-AWVTVG-L 193
                     G +D         G     +  +G      +  +  + G+  AWV +  L
Sbjct: 185 LVVGVPEVREGTIDAPLAKQPGTGGEKMHVDEEGGQIAKTRYRVVERAGTRAAWVELEPL 244

Query: 194 REGKNREIKKVFEFFNWKVN 213
             G+  +++         + 
Sbjct: 245 T-GRTHQLRVHLAAIGHPIV 263


>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 = 50.9 bits (121), Expect = 3e-04,   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|223933756|ref|ZP_03625728.1| pseudouridine synthase [Streptococcus suis 89/1591]
 gi|223897560|gb|EEF63949.1| pseudouridine synthase [Streptococcus suis 89/1591]
          Length = 291

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 77/204 (37%), Gaps = 31/204 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTD--HIEVDGV-------PLRKAE------- 71
           R++   +  ++ V+VNG L+      + + D   +  D         PL +A+       
Sbjct: 28  RKIRHFLRTKKHVRVNGELI-NWQSPITAGDLLELTFDQEDYPEKSIPLGQADLVEELYQ 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +      +      V RLD+ T G +L   +  + 
Sbjct: 87  DEHLIIVNKPEGMKTHGNEPTEIALLNHVSAYVGQTCYVVHRLDMETSGAILFAKNPFIL 146

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L      R Y     GQ+ +              +  K+ +  +       QV 
Sbjct: 147 PILNRLLEDKVIYRDYLALCQGQLKETDWTITDKIGRDRHDRRKRMVDNRKGQAALTQVR 206

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
           L    G N+ V+  L+ G+  +I+
Sbjct: 207 LLKPLGKNSLVSCRLQTGRTHQIR 230


>gi|325267840|ref|ZP_08134490.1| ribosomal large subunit pseudouridine synthase C [Kingella
           denitrificans ATCC 33394]
 gi|324980721|gb|EGC16383.1| ribosomal large subunit pseudouridine synthase C [Kingella
           denitrificans ATCC 33394]
          Length = 326

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 80/250 (32%), Gaps = 62/250 (24%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           VQE+ + QR+   + +      +  + R+I    V+VN    +     + + D I +   
Sbjct: 14  VQEHESAQRLDNYLIKILKGVPKSHIHRIIRAGEVRVNKGRAK-PETRIQTGDLIRI--P 70

Query: 66  PLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           P+R AE+T                     L + +KP G+        G S V   +    
Sbjct: 71  PVRTAEKTAKSSLQPVPARHFEIVYEDDALLVVNKPSGVAV-----HGGSGVSFGVIEQL 125

Query: 106 SRVIS-------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRV--------- 147
            R          V RLD +T GLL++         L   L +    ++Y           
Sbjct: 126 RRARPEAKYLELVHRLDKDTSGLLMVAKKRSALVKLHEMLRNDHPKKIYWALGVGTWQPA 185

Query: 148 --RFHGQV---DQDKLNLL-KKGIVIQGICYGDMQVTLDTQKGSN---------AWVTVG 192
                  +          + + G    G     +   LDT  G           + V   
Sbjct: 186 LRHVRLPLVKYTGAAGEKMVRVGSAEDGQSAHTVFRVLDTFSGERPHSVGVSALSLVEAT 245

Query: 193 LREGKNREIK 202
           L+ G+  +I+
Sbjct: 246 LKTGRTHQIR 255


>gi|256761450|ref|ZP_05502030.1| pseudouridine synthase [Enterococcus faecalis T3]
 gi|256682701|gb|EEU22396.1| pseudouridine synthase [Enterococcus faecalis T3]
          Length = 287

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 42/209 (20%), Positives = 77/209 (36%), Gaps = 36/209 (17%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVM----STDHIE--VD-GVPLRKA---ER 72
           R+V   +  ++ VK+NG         +A   V      TD++   V  G   R     E 
Sbjct: 28  RKVRHFLRTRKNVKINGETAAFHFPVQAGDCVTLTFEETDYVRPTVHLGEATRVKVLYED 87

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDG 128
             L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   + 
Sbjct: 88  EHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKNP 147

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICYG 173
            +  +L   L + Q  R Y+    G  +Q +   + + I               +G    
Sbjct: 148 FVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSAI 206

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                + T   +   VT  L  G+  +I+
Sbjct: 207 THVQVVQTLSNNQTAVTCVLETGRTHQIR 235


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

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 39/265 (14%), Positives = 83/265 (31%), Gaps = 65/265 (24%)

Query: 5   NIVQENFTPQRVSKVI----ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             V E+    R+ +         G   R  +++++  ++V+V+G     A+  + +   I
Sbjct: 23  RRVDEDDAGIRLDRWFKENFPELGFG-R--LQKLLRTKQVRVDGKRA-EASTRLEAGQEI 78

Query: 61  EV-------------------------DGVPLRKA---ERTRLWLYHKPIGLVTTH---- 88
            +                         D   + +    E + + + +KP GL        
Sbjct: 79  RIPPLGVELAADDRKNAKPRARKLVDSDREAIEQMMLFEDSHVMVLNKPAGLAVQGGSGL 138

Query: 89  -SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY 145
               DG    F N      R+  V RLD  T G+LL+      A+ L          ++Y
Sbjct: 139 KRHVDGMLDAFTNQKGDKPRL--VHRLDRETSGILLVAKTRRAAQELTKAFRHRNTRKIY 196

Query: 146 RVRFHGQVD---------------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN--AW 188
                G                  ++++ + + G          + +    ++     AW
Sbjct: 197 WAMVAGVPKPRQGRISTYLARDEGEERMRVARHG---DDEAQHAVSLYNVVEQSGQKLAW 253

Query: 189 VTVGLREGKNREIKKVFEFFNWKVN 213
           VT+    G+  +++         + 
Sbjct: 254 VTLKPVTGRTHQLRAHSAHIGHPII 278


>gi|88607689|ref|YP_505141.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           phagocytophilum HZ]
 gi|88598752|gb|ABD44222.1| ribosomal large subunit pseudouridine synthase C [Anaplasma
           phagocytophilum HZ]
          Length = 297

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/211 (14%), Positives = 66/211 (31%), Gaps = 45/211 (21%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIE---VDGVPLRKAERTRL------------ 75
           VE+++ +  +++N      A+  V   D +    VD +  R  E   +            
Sbjct: 19  VEKLLRKGEIRLNSSKA-LASSRVQRGDTVSIRNVDKIASRSKEAKEVHDDALLRLVSDN 77

Query: 76  --------WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT 125
                      +KP G+           ++ D L  I    ++  V RLD +T G+L++ 
Sbjct: 78  IIYKDENIIAINKPAGVNVQGG-TKVSISLSDLLNKIIPGEQLHIVHRLDRDTSGVLIIA 136

Query: 126 NDGGLARVLELPS---TQWLRVYRVRFHGQVDQDKLN-------LLKKGIVIQGICYGDM 175
             G     +        +  + Y     G     K           + G+   G      
Sbjct: 137 -RGQSIARILSEELRFRRVRKEYIAVTKGVPAFSKGEITMPIYCKKQSGV---GETLIPK 192

Query: 176 QVT----LDTQKGSNAWVTVGLREGKNREIK 202
           +      +      +A + +    G+  +++
Sbjct: 193 EAKTVFSVLQSSKRHAVMLLSPVTGRKHQLR 223


>gi|317508658|ref|ZP_07966314.1| RluA family pseudouridine synthase [Segniliparus rugosus ATCC
           BAA-974]
 gi|316253061|gb|EFV12475.1| RluA family pseudouridine synthase [Segniliparus rugosus ATCC
           BAA-974]
          Length = 315

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/245 (14%), Positives = 76/245 (31%), Gaps = 41/245 (16%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGI--------------------- 45
           V E     R+   +AR    SR +   +       ++G                      
Sbjct: 13  VPEGLAGLRLDAGLARLLGVSRTKAAELADAGHALIDGKEAGRSDRLVAGAWLEVSVPSA 72

Query: 46  ---LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL- 101
               +E  A  ++   ++      +   E+      H  +G  +  +   G   +  ++ 
Sbjct: 73  PSAPVEEDAPEIIPGLNVLYSDEHVVVVEKPPEIAVHPSVGW-SGPTVVGGLKALGFHIA 131

Query: 102 -PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQD-- 156
              +  R   V RLD+ T G+++L        VL+      +  + Y     G  D    
Sbjct: 132 TTGVAERQGVVQRLDVGTSGVMVLAASEHAYTVLKRAFKHREVEKWYEALVQGHPDPSSG 191

Query: 157 KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
            ++           +  +  +G        T++   G+ + V+V L  G+  +I+  F  
Sbjct: 192 TIDAPIGKRPGPGWRFAVTTEGRHSVTHYDTIEA-FGAASLVSVKLETGRTHQIRVHFSA 250

Query: 208 FNWKV 212
                
Sbjct: 251 LRHPC 255


>gi|315657924|ref|ZP_07910798.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
 gi|315496960|gb|EFU85281.1| ribosomal large subunit pseudouridine synthase [Staphylococcus
           lugdunensis M23590]
          Length = 278

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/204 (16%), Positives = 68/204 (33%), Gaps = 28/204 (13%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIEV--DGVPLRKAERTRLWLYH----------KPIGL 84
            + + +N       +  V + D +E+  D          R    +          KP G+
Sbjct: 34  SKEITINNAPAR-LSNQVHTMDCVEIPTDEEKSNYLPSYRYAQIYYEDDDLAIVMKPKGV 92

Query: 85  VTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
            T  +D    +T+ +++           + RLD  T GLL++  +  + ++L   L   +
Sbjct: 93  KTHPNDLKESNTLMNHIIYTLDSEYAEPIHRLDQETVGLLIIAKNPLMKKILDRMLEDNK 152

Query: 141 WLRVYRVR-----------FHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             R+Y+                 + +DK +  K+ I   G       +     K     +
Sbjct: 153 ITRIYKANINALLPIKPQTIDMPIGKDKFHPNKRRISNTGQRAITHILASTMLKEGVCQL 212

Query: 190 TVGLREGKNREIKKVFEFFNWKVN 213
            + L  G+  +I+         V 
Sbjct: 213 DIKLDTGRTHQIRVHLAEIGHPVI 236


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+  ++   G   SR   ++ I    V V+    ++A   V     IEV G P+    R
Sbjct: 4  RIDLLLVEQGYFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDCSIEVKGNPIPYVSR 62


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 28/69 (40%), Gaps = 1/69 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          N   +R+  ++    +  SR + +  I + ++ VNG  +++    V     IE  G  + 
Sbjct: 3  NVKSERLDSLLVEKNLFESREKAKIAIMEGKIFVNGQRVDKCGQKVKVDSDIEFKGEVMP 62

Query: 69 KAERTRLWL 77
             R    L
Sbjct: 63 YVSRGGYKL 71


>gi|238854907|ref|ZP_04645237.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|313472401|ref|ZP_07812893.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 1153]
 gi|238832697|gb|EEQ25004.1| pseudouridine synthase, RluA family [Lactobacillus jensenii 269-3]
 gi|239529732|gb|EEQ68733.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Lactobacillus jensenii 1153]
          Length = 297

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 56/172 (32%), Gaps = 25/172 (14%)

Query: 64  GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------ISVG 112
             P+    E     + +KP  +++  S  +    V + +   FS+             V 
Sbjct: 76  NKPIEIVLETDNYLVINKPANVLSIPSRYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVT 135

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLL---------- 161
           RLD +T GL+L+  +               ++ Y    H   + ++   L          
Sbjct: 136 RLDRDTSGLVLVGKNAVAHSKFSELKKDVFVKEYHAIVHSNFNPEEQAGLIDAPIGKIDD 195

Query: 162 --KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ ++  G      Q  +  QK   + V + L  G+  +I+         
Sbjct: 196 SVKRYVIPNGQKSLT-QYEVLAQKEGASLVKLRLFTGRTHQIRVHMAHIGHP 246


>gi|151941961|gb|EDN60317.1| tRNA-pseudouridine synthase [Saccharomyces cerevisiae YJM789]
          Length = 462

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRL 75
           RE E     I    V +N       +  + + D I          V   P++   E   +
Sbjct: 139 RESEYYKRTIENGDVHINDETA-DLSTVIRNGDLITHQVHRHEPPVTSRPIKVIFEDDNI 197

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL 134
            +  KP G+    +     +T+   L +    V     RLD  T GL+ L      A  +
Sbjct: 198 MVIDKPSGIPVHPTGRYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPKGADNI 257

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI--------QGICYGDMQVT 178
             +L + +  + Y  +  G+  + +      L L++  + +        +G  +      
Sbjct: 258 GDQLKAREVTKEYVAKVVGEFPETEVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKTVFN 317

Query: 179 LDTQKGSNAWVTVG-LREGKNREIK 202
             +  G  + V    L  G++ +I+
Sbjct: 318 RISYDGKTSIVKCKPLT-GRSHQIR 341


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 15  RVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+  V+ R GI  +RR+  + +    + VNG  ++  +  V   D IEV    + +  +
Sbjct: 99  RLDNVVYRLGIACTRRQARQFVVHGHIMVNGKKVDIPSYQVNVGDIIEVYSKDIPQIRQ 157


>gi|260103209|ref|ZP_05753446.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|260083000|gb|EEW67120.1| ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus DSM 20075]
 gi|328464673|gb|EGF36019.1| ribosomal protein large subunit [Lactobacillus helveticus MTCC
           5463]
          Length = 285

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 69/210 (32%), Gaps = 35/210 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRKA----------ERTRLWLYH 79
           I Q  + +NG        NV+  D I+     VD    +            E   L + +
Sbjct: 37  IEQ-NITING-TYRYFNQNVLPGDKIDIILDQVDSAQQKYPASGKLPDIIYEDDNLLIIN 94

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL----ARVLE 135
           K  G  T  +  +  +T+ D    +      V RLD+ T GLLL+  +  +     R L 
Sbjct: 95  KKKGQKTHPNLNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELT 154

Query: 136 LPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
             +    R Y  +                +D D  +  K+ I   G+        L    
Sbjct: 155 SKTFH--RDYLAKVDHADKLSDQGTINQPIDHDPEDQRKRMISPAGLHAVTHYQVLKRND 212

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + A V + L  G+  +I+         + 
Sbjct: 213 NNTAVVKLTLETGRTHQIRVHLASLGTPII 242


>gi|116332841|ref|YP_794368.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
 gi|116098188|gb|ABJ63337.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus brevis
           ATCC 367]
          Length = 295

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/209 (19%), Positives = 62/209 (29%), Gaps = 39/209 (18%)

Query: 39  RVKVNGILLERAAVNVMSTDHIE--------------VDG----VPLRKAERTRLWLYHK 80
           RV VNG         V S D ++              VD           E   L + +K
Sbjct: 40  RVLVNGA-YRSMNQLVYSGDTVQLTFLPTDFKEPFPNVDPDSAATVAVLYESADLLVINK 98

Query: 81  PIGLVTTHSDPDGRST----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
             G  T  + P  R T    V   L         + RLD  T G LL+T    +  ++  
Sbjct: 99  TRGSKTHPNQPGERGTTLNHVAAYLGPDQPGPYILSRLDQETTGALLMTKTPAVVPIMVR 158

Query: 137 P--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV--- 191
                Q  R Y    HG++  D +      I    +     QV  D  + +     V   
Sbjct: 159 HIADKQVQRTYLAWVHGRLTGDGV--FTDPIGRDPLDKRKRQVNGDHAQPAVTHYHVCEY 216

Query: 192 ----GLRE-----GKNREIKKVFEFFNWK 211
                L +     G+  +++         
Sbjct: 217 REQATLIQLRLETGRTHQLRVHLAAAGHP 245


>gi|50311419|ref|XP_455734.1| hypothetical protein [Kluyveromyces lactis NRRL Y-1140]
 gi|49644870|emb|CAG98442.1| KLLA0F14553p [Kluyveromyces lactis]
          Length = 377

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/177 (16%), Positives = 62/177 (35%), Gaps = 30/177 (16%)

Query: 46  LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            ++     +    HI   G+P+   +  +L + +KP G+    +    ++T+ + L    
Sbjct: 94  PVKNWGEPICDEKHIM--GIPIVHQDE-QLLVINKPNGIPVHPTAYFYKNTLTELLKDSL 150

Query: 106 SR-VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLK 162
              V    RLD  T GLL+L  +   A  ++         + Y  R  G+  +  ++   
Sbjct: 151 GYPVHPCYRLDKITSGLLILAKNPIDANRVQSKIRDRDMKKYYLARVKGKFPETAVDK-- 208

Query: 163 KGIVIQGICYGDMQVTLDTQKG-SNAWVTVGLRE----------------GKNREIK 202
                  I   D+++  +      +A     L E                G+  +I+
Sbjct: 209 -----SPIYTCDLKIKSEPLSPLKDAHTEFELMEYDAVTDQSIVLCKPFTGRTHQIR 260


>gi|323466046|gb|ADX69733.1| Ribosomal large subunit pseudouridine synthase [Lactobacillus
           helveticus H10]
          Length = 285

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/210 (19%), Positives = 69/210 (32%), Gaps = 35/210 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE-----VDGVPLRKA----------ERTRLWLYH 79
           I Q  + +NG        NV+  D I+     VD    +            E   L + +
Sbjct: 37  IEQ-NITING-TYRYFNQNVLPGDKIDIILDQVDSAQQKYPASGKLPDIIYEDDNLLIIN 94

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL----ARVLE 135
           K  G  T  +  +  +T+ D    +      V RLD+ T GLLL+  +  +     R L 
Sbjct: 95  KKKGQKTHPNLNETNTTLNDCATYLGQSPYIVHRLDMLTGGLLLVAKNPAVVPILNRELT 154

Query: 136 LPSTQWLRVYRVRFHG------------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
             +    R Y  +                +D D  +  K+ I   G+        L    
Sbjct: 155 SKTFH--RDYLAKVDHADKLSDQGTINQPIDHDPEDQRKRMISPAGLHAVTHYQVLKRND 212

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            + A V + L  G+  +I+         + 
Sbjct: 213 NNTAVVKLTLETGRTHQIRVHLASLGTPII 242


>gi|317053991|ref|YP_004118016.1| pseudouridine synthase [Pantoea sp. At-9b]
 gi|316951986|gb|ADU71460.1| pseudouridine synthase [Pantoea sp. At-9b]
          Length = 232

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 67/191 (35%), Gaps = 41/191 (21%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  +P    +V   L  IF     V RLD  T GL+++  +  
Sbjct: 22  QDEHLVLINKPAGLLSLSGKNPQNLDSVHHRLVKIFPGCTLVHRLDFGTSGLMVIARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-----Q 182
           +   L    +Q    +VY     G ++        +G++   I     +  L +      
Sbjct: 82  INAALCQQFSQRSVTKVYSALLCGHLENH------EGVIDAAIAKDPARFPLMSICATHG 135

Query: 183 KGSNAWVTVG------LRE---------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V       L E               G+  +++   +     +       YG
Sbjct: 136 KPARSRYQVVERFNHELEEGTLLPLTRVQLIPETGRTHQLRIHCQLLGHPILGCD--LYG 193

Query: 222 PFQLGTLLAGS 232
               G LL GS
Sbjct: 194 ----GRLLPGS 200


>gi|330946151|ref|XP_003306701.1| hypothetical protein PTT_19907 [Pyrenophora teres f. teres 0-1]
 gi|311315680|gb|EFQ85200.1| hypothetical protein PTT_19907 [Pyrenophora teres f. teres 0-1]
          Length = 475

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/145 (16%), Positives = 48/145 (33%), Gaps = 21/145 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-------------RLWLY 78
           E+ I   RV +NG  +      V + D I      L + E                + + 
Sbjct: 86  EQAIIDGRVVLNGKPVPSTKTIVKNGDVIS---HTLHRHEPPCTAQPIGIVHEDDNMIVI 142

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G+    +     +++ + + +            RLD  T G++ +      A  L 
Sbjct: 143 NKPAGMPVHPAGRYNFNSIIEIMRADRGYGWNPLPCNRLDRLTSGIMFIGKHKQAAEELS 202

Query: 136 LPSTQ--WLRVYRVRFHGQVDQDKL 158
                    + Y  R  G+  + ++
Sbjct: 203 AQIRGRTVKKEYITRVVGEFPEGEI 227


>gi|295091133|emb|CBK77240.1| pseudouridine synthase, RluA family [Clostridium cf.
           saccharolyticum K10]
          Length = 314

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 43/215 (20%), Positives = 78/215 (36%), Gaps = 37/215 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L +  KP G+    S  +  +T+ + +   FS         +V RLD +T GLLL+
Sbjct: 89  EDRDLMVIDKPAGMPVHPSQGNFYNTLANGIAWYFSERGEPFTFRAVNRLDRDTTGLLLI 148

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ---GICYGD 174
              G  A +L   +   +  R Y     G+ D++      +     G  I+       G+
Sbjct: 149 AKHGLCAALLSEMVARKEVRRQYLAIASGKTDEEGTICAPIAR-ADGSTIERCVDETRGE 207

Query: 175 MQVT-----LDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVNRLIRISYGPFQLGTL 228
              T     + + +   + + + L  G+  +I+  + +     +        G F    L
Sbjct: 208 YACTHYRRLVYSSENDCSLLLLTLDTGRTHQIRVHM-KHIGHPLL-------GDF----L 255

Query: 229 LAGSTREVSKKILREQLGP--HLLEEAQVNLDAPI 261
                R   ++ L   L    H L    +N  AP+
Sbjct: 256 YNPDYRLFRRQSLHSFLLSFTHPLTGESLNFSAPL 290


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      VNG  ++  +  V + D I V     +  E+
Sbjct: 98  MRLDNVVYRLGYGNSRTEARQLVTHGHFLVNGKKVDIPSYQVSANDVITVCDKS-KATEK 156

Query: 73  TRLWLYH 79
            + +  +
Sbjct: 157 FKTFAEN 163


>gi|167627177|ref|YP_001677677.1| lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
 gi|167597178|gb|ABZ87176.1| Lysozyme [Francisella philomiragia subsp. philomiragia ATCC 25017]
          Length = 309

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/212 (16%), Positives = 69/212 (32%), Gaps = 48/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV------DGVPLRKAERTR------------ 74
           R I +  ++VN   +++    V + D + V      + + + K  ++             
Sbjct: 36  RWIRKGELRVNKKRVKQ-TTRVSAGDIVRVPPFSLEENLEIAKVSKSHLDFLEQRILYET 94

Query: 75  --LWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               +  KP G+            V     L     R+  V RLD  T G +LL      
Sbjct: 95  DDYIVVDKPSGMAVHGGSGVNSGLVERLRQLRPKVRRLDLVHRLDKETSGCVLLAKKHSS 154

Query: 131 ARVL--ELPSTQWLRVYRVRFHGQVDQ--DKLNLLKKGIVIQGICYGDMQ--VTLDTQKG 184
                      +  ++Y    HG  D+  D ++     + +      D Q  V +D ++G
Sbjct: 155 LVYFFDIFKERKVNKIYYALVHGHWDEKVDAID-----LPLSRTETKDGQRIVKVDKREG 209

Query: 185 SN--------------AWVTVGLREGKNREIK 202
                           + + + L  G+  +I+
Sbjct: 210 KRALTRILAVQKIGDYSLLEIKLETGRTHQIR 241


>gi|160946974|ref|ZP_02094177.1| hypothetical protein PEPMIC_00936 [Parvimonas micra ATCC 33270]
 gi|158447358|gb|EDP24353.1| hypothetical protein PEPMIC_00936 [Parvimonas micra ATCC 33270]
          Length = 318

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 39/246 (15%), Positives = 87/246 (35%), Gaps = 46/246 (18%)

Query: 1   MKDKNIVQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
           M+D  +   N + QR+ + + +    AS   +++ +  +++KVN   +  +   +   D 
Sbjct: 1   MRDIEV-NNNDSGQRIDRFLKKYLNNASTSMIQKFLRTKKIKVNRKKV-DSNYILAENDV 58

Query: 60  I--EVDGVPLRK------------------AERTRLWLYHKPIGLVT---THSDPDGRST 96
           I   +    L K                   E   + + +KP  L++   +  D      
Sbjct: 59  INIFIYEEELEKLIVSKSKKYSYSKKLDIIYEDENIIVMNKPKNLLSHASSKEDYGNNLV 118

Query: 97  VF---------DNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLEL-PSTQWLRV 144
            F         D  P      +   + RLD NT GL++   +    R L         + 
Sbjct: 119 DFMIGYLLEKGDYNPRAEKTFVPAIINRLDRNTSGLVIGAKNSKALRELNRLKENSIEKY 178

Query: 145 YRVRFHGQVDQDKL--NLLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
           Y+    G+V ++ +    L+K        + +       ++ ++      + + + L  G
Sbjct: 179 YKTIVSGKVKKNFVINEKLEKDEEKNKSTISKNGKDSITEIYVEKNNDEFSLLKIKLITG 238

Query: 197 KNREIK 202
           +  +I+
Sbjct: 239 RTHQIR 244


>gi|157363559|ref|YP_001470326.1| hemolysin A [Thermotoga lettingae TMO]
 gi|157314163|gb|ABV33262.1| hemolysin A [Thermotoga lettingae TMO]
          Length = 265

 Score = 50.9 bits (121), Expect = 3e-04,   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|297479512|ref|XP_002690866.1| PREDICTED: RNA pseudouridylate synthase domain containing 2 [Bos
           taurus]
 gi|296483299|gb|DAA25414.1| RNA pseudouridylate synthase domain containing 2 [Bos taurus]
          Length = 518

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 47/291 (16%), Positives = 96/291 (32%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++  ++ +   D +          V   P+R  AE   + +  KP
Sbjct: 152 EAAVRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 211

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 212 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 271

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 272 DRQLEKEYVCRVVGEFPTEEVTCKEPILVVSYKVGVCRVDPQGKPCESVFQRLSYNGHSS 331

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +         ++GP +      G   +  +++L
Sbjct: 332 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSAAWGPSRGRG---GHIPKTDEELL 385

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +++   LD           D     SE+  D       SSQK
Sbjct: 386 RDLVAEHQAKQSLDVLDLYEGDLCPGAPDSTAPSSELSKDCLEEMAASSQK 436


>gi|255729940|ref|XP_002549895.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
 gi|240132964|gb|EER32521.1| conserved hypothetical protein [Candida tropicalis MYA-3404]
          Length = 392

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/162 (17%), Positives = 59/162 (36%), Gaps = 26/162 (16%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGL 121
           G      E   L +  KP G+ T  +     ++V + +   F    + +  RLD  T G+
Sbjct: 104 GRIKSVYEDDELLVVDKPSGVPTHPTGNYYFNSVSEMVKDQFGLEAIWTCHRLDKVTSGV 163

Query: 122 LLL----TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN----LLKKGIVIQGICYG 173
           L+     +     +R+++    Q  + Y  R  G+    KL     +    + + G    
Sbjct: 164 LIFGKTKSAGSKFSRLIKDHKDQTEKTYLARVVGEFPNGKLQYNCPIFA--VNLNGYLVP 221

Query: 174 --DMQVTLDTQKG----------SNAWVT-VGLREGKNREIK 202
               ++ LD+             + + V  + +  GK  +I+
Sbjct: 222 GNSEELPLDSTTIFQKVSYNASLNQSLVKCIPIT-GKFHQIR 262


>gi|224538849|ref|ZP_03679388.1| hypothetical protein BACCELL_03745 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224519524|gb|EEF88629.1| hypothetical protein BACCELL_03745 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 510

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/92 (21%), Positives = 42/92 (45%), Gaps = 6/92 (6%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
           E   L + +KP G+++     + +++++D     +      + V RLD+ T GLL++  D
Sbjct: 312 EDQWLLIINKPAGMLSVPG-KERQTSIYDLAREAYPEAEGPMIVHRLDMATSGLLIIAKD 370

Query: 128 GGLARVLELP--STQWLRVYRVRFHGQVDQDK 157
               + L+    +    + Y     G V +D+
Sbjct: 371 KKTHQHLQAQFKNRSIRKKYIALLDGIVPEDE 402


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      VNG  ++  +  V + D I V     +  E+
Sbjct: 98  MRLDNVVYRLGYGNSRTEARQLVTHGHFLVNGKKVDIPSYQVSANDVITVCDKS-KATEK 156

Query: 73  TRLWLYH 79
            + +  +
Sbjct: 157 FKTFAEN 163


>gi|157961293|ref|YP_001501327.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157846293|gb|ABV86792.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 217

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/159 (15%), Positives = 49/159 (30%), Gaps = 27/159 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           + + +KP GL++     +         L   F   I V RLD  T G+++   +      
Sbjct: 23  IIVINKPSGLLSNPGIAEYTHDCALTRLQQRFKDCILVHRLDCATSGIMVFARNKKAESN 82

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGI----VIQGICYGDMQVTLDTQKGSNA 187
           L+      Q  + Y     G         L+ G+    +         Q+  +  K +  
Sbjct: 83  LKTQFQDRQTQKTYIAEVDGIF------KLQSGVIELSIAADKLNPPKQMVSELGKAAIT 136

Query: 188 WVTV-------GLRE-----GKNREIK-KVFEFFNWKVN 213
              V        L E     G+  +++  +       + 
Sbjct: 137 HYKVLQQKPHSTLVELKPVTGRTHQLRVHML-AIGHPIL 174


>gi|325920613|ref|ZP_08182526.1| tRNA pseudouridine synthase C [Xanthomonas gardneri ATCC 19865]
 gi|325548904|gb|EGD19845.1| tRNA pseudouridine synthase C [Xanthomonas gardneri ATCC 19865]
          Length = 245

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/167 (17%), Positives = 54/167 (32%), Gaps = 31/167 (18%)

Query: 70  AERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTN 126
            +   L + +KP GL+   S         + D L     R +  V RLD  T G LLL  
Sbjct: 12  HQDDVLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLLLAF 71

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--Q 182
           D   A  L   L + +  + Y     G   ++          + G     ++    T  Q
Sbjct: 72  DRESASTLGKALMAGELEKDYLTVCRGWPAEE---QFIVDHDLDGGPGKPVKKPAVTHFQ 128

Query: 183 KGSNAWVTV------------------GLREGKNREIKKVFEFFNWK 211
           + +   + +                      G+ R+I++  +  +  
Sbjct: 129 RLATGELEIPSTGFATSRYALLRCQPQT---GRFRQIRRHMKHLSHH 172


>gi|282931619|ref|ZP_06337112.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
 gi|281304230|gb|EFA96339.1| pseudouridine synthase YjbO [Lactobacillus jensenii 208-1]
          Length = 290

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/172 (16%), Positives = 56/172 (32%), Gaps = 25/172 (14%)

Query: 64  GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----------ISVG 112
             P+    E     + +KP  +++  S  +    V + +   FS+             V 
Sbjct: 69  NKPIEIVLETDNYLVINKPANVLSIPSRYEDGDAVVNRVMGYFSKKKSSEQAFLKPHIVT 128

Query: 113 RLDINTEGLLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLL---------- 161
           RLD +T GL+L+  +               ++ Y    H   + ++   L          
Sbjct: 129 RLDRDTSGLVLVGKNAVAHSKFSELKKDVFVKEYHAIVHSNFNPEEQAGLIDAPIGKIDD 188

Query: 162 --KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             K+ ++  G      Q  +  QK   + V + L  G+  +I+         
Sbjct: 189 SVKRYVIPNGQKSLT-QYEVLAQKEGASLVKLRLFTGRTHQIRVHMAHIGHP 239


>gi|258621208|ref|ZP_05716242.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM573]
 gi|258586596|gb|EEW11311.1| ribosomal large subunit pseudouridine synthase C [Vibrio mimicus
           VM573]
          Length = 316

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 75/243 (30%), Gaps = 58/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKTIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEAPPPSTKLNKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV-------GLRE-----GKNR 199
             D +    +    +++      ++V     K S     +        L +     G+  
Sbjct: 185 HWDSEC--KVVNAPLLKNEVNSIVRVN-PNGKPSETRFRILEKFAEATLVQASPVTGRTH 241

Query: 200 EIK 202
           +I+
Sbjct: 242 QIR 244


>gi|329767055|ref|ZP_08258583.1| hypothetical protein HMPREF0428_00280 [Gemella haemolysans M341]
 gi|328837780|gb|EGF87405.1| hypothetical protein HMPREF0428_00280 [Gemella haemolysans M341]
          Length = 283

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 31/144 (21%), Positives = 55/144 (38%), Gaps = 12/144 (8%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   L +  KP G+ T  +D +    T+ + L S ++ +  + RLDI+T GL++L     
Sbjct: 84  EDEYLLVVSKPFGIKTHPNDIELEDDTLVNYLISNYNYLEPIHRLDIDTCGLVILAKTPL 143

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDKL---------NLLKKGIVIQGICYGDMQVT 178
           +   L   L   Q  R Y       +    +            K  +   G       ++
Sbjct: 144 IKAKLDQMLEQRQIKRYYSALIKNNIKPQTINSNIGRDSKEKNKMAVTKNGKNAITNILS 203

Query: 179 LDTQKGSNAWVTVGLREGKNREIK 202
            +    +   VTV L  G+  +I+
Sbjct: 204 CEKIDQNRFLVTVSLETGRTHQIR 227


>gi|226313676|ref|YP_002773570.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
 gi|226096624|dbj|BAH45066.1| pseudouridine synthase [Brevibacillus brevis NBRC 100599]
          Length = 306

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/222 (19%), Positives = 78/222 (35%), Gaps = 44/222 (19%)

Query: 16  VSKVIARAGIASRREVERMIAQ---QRVKVNGILLERAAVNVMSTDHIEVD--------- 63
           + K   R G+ SRR    +I       +  NG+L+      + + D I V          
Sbjct: 23  LQK---RYGV-SRR---LLIRAKFKGSITRNGVLVF-VNEKLQAGDKIAVMVEEEAEETV 74

Query: 64  ---GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGR 113
               +PL  + E   L +  KP GLV   +      T+ + + + +       +  +V R
Sbjct: 75  APEDMPLSIRYEDEDLMVIAKPAGLVVHPTGNHPSGTLANGMIAYWKKRGENRKFRAVNR 134

Query: 114 LDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRFHGQVDQDKLN-----------L 160
           LD +T GL+++  +                 R YR    G V+ D               
Sbjct: 135 LDKDTSGLMIVAKNQWAHEQFSRMQQIRTLQRTYRAIVQGIVESDDGTINTPIGLAENSF 194

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           + + +   G         L   +G  ++V V L  G+  +I+
Sbjct: 195 ITRQVRPDGQTAVTHYRVLARGEGM-SFVEVKLETGRTHQIR 235


>gi|194670657|ref|XP_583460.4| PREDICTED: RNA pseudouridylate synthase domain containing 2 isoform
           1 [Bos taurus]
          Length = 505

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 47/291 (16%), Positives = 96/291 (32%), Gaps = 36/291 (12%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
           E  +   R+ +N   ++  ++ +   D +          V   P+R  AE   + +  KP
Sbjct: 139 EAAVRAGRLHLNEEPVQDLSIVLKDNDFLRNTVHRHEPPVTAEPIRLLAENEDVVVVDKP 198

Query: 82  IGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
             +          +TV   L        +  + RLD  T G+L+      ++  +     
Sbjct: 199 SSIPVHPCGRFRHNTVIFILGKEHQLKELHPLHRLDRLTSGVLMFAKTAAVSERIHEQVR 258

Query: 138 STQWLRVYRVRFHGQVDQDKLN--------LLKKGIVIQGICYGDMQVTLDTQ--KGSNA 187
             Q  + Y  R  G+   +++           K G+          +         G ++
Sbjct: 259 DRQLEKEYVCRVVGEFPTEEVTCKEPILVVSYKVGVCRVDPQGKPCESVFQRLSYNGHSS 318

Query: 188 WVT---VGLREGKNREIKKVFEFFNWKVNR---LIRISYGPFQLGTLLAGSTREVSKKIL 241
            V    +    G+  +I+   +F    +         ++GP +      G   +  +++L
Sbjct: 319 VVRCRPLT---GRTHQIRVHLQFLGHPILNDPIYNSAAWGPSRGRG---GHIPKTDEELL 372

Query: 242 REQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQK 292
           R+ +  H  +++   LD           D     SE+  D       SSQK
Sbjct: 373 RDLVAEHQAKQSLDVLDLYEGDLCPGAPDSTAPSSELSKDCLEEMAASSQK 423


>gi|145299036|ref|YP_001141877.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           salmonicida subsp. salmonicida A449]
 gi|142851808|gb|ABO90129.1| ribosomal large subunit pseudouridine synthase C [Aeromonas
           salmonicida subsp. salmonicida A449]
          Length = 327

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 67/210 (31%), Gaps = 45/210 (21%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----------------- 75
           R++ +  V+VN   ++     +   D + V   P+R AE+  L                 
Sbjct: 53  RILRKGEVRVNKKRIK-PEYKLCPGDEVRV--PPVRVAEKNELPSANLGSIQRLESQILF 109

Query: 76  -----WLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 110 EDDAMIVLNKPSGMAVHGGSGLSFGVIEGLRALRPDARFLELVHRLDRDTSGVLLVA-KK 168

Query: 129 GLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKG 184
             A        +     + Y     GQ     + ++   +    +  G+  V + +  K 
Sbjct: 169 RSALRSLHEQLRVKTMRKQYLALVRGQWQP-HVKVVNAPLRKNDLQSGERVVRVSSDGKP 227

Query: 185 SNAWVTV-------GLRE-----GKNREIK 202
           S     +        L E     G+  +I+
Sbjct: 228 SETRFRIARQFAEATLVECSPITGRTHQIR 257


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+  ++   G   SR   ++ I    V V+    ++A   V     IEV G P+    R
Sbjct: 4  RIDLLLVEQGYFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDCSIEVKGNPIPYVSR 62


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++ + G  S R + +  I    V V+G   E+A   V     IEV G  L    R
Sbjct: 3  ERIDVLLVKRGFFSSREKAKAAIMAGEVYVDGKRAEKAGEMVKEDSKIEVKGNSLPYVSR 62


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


>gi|304396538|ref|ZP_07378419.1| pseudouridine synthase [Pantoea sp. aB]
 gi|304356047|gb|EFM20413.1| pseudouridine synthase [Pantoea sp. aB]
          Length = 217

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/160 (14%), Positives = 62/160 (38%), Gaps = 19/160 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++      + + +V   +   F +  SV RLD+ T G++++     
Sbjct: 17  QDAHIMVVNKPSGLLSVPGRLDEHKDSVMTRIQRDFPQAESVHRLDMATSGVMVVALTKA 76

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQ 176
             R L+    +    + Y     G  +++     L L+       K+ +  +       +
Sbjct: 77  AERELKRQFREREPSKTYVACIWGHPEKEEGLVDLPLICDWPNRPKQMVCFENGKAAQTE 136

Query: 177 VTLDTQKGSNAWVTVGLR--EGKNREIK-KVFEFFNWKVN 213
             +   +  N+   + L+   G++ +++  +       + 
Sbjct: 137 YQVLEYRADNST-RISLKPITGRSHQLRVHML-ALGHPIL 174


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 179 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 229


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 179 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 229


>gi|51012815|gb|AAT92701.1| YDL036C [Saccharomyces cerevisiae]
          Length = 462

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 71/205 (34%), Gaps = 33/205 (16%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRL 75
           RE E     I    V +N       +  + + D I          V   P++   E   +
Sbjct: 139 RESEYYKRTIENGDVHINDETA-DLSTVIRNGDLITHQVHRHEPPVTSRPIKVIFEDDNI 197

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL 134
            +  KP G+    +     +T+   L +    V     RLD  T GL+ L      A  +
Sbjct: 198 MVIDKPSGIPVHPTGRYRFNTITKMLQNNLGFVVNPCNRLDRLTSGLMFLAKTPKGADNI 257

Query: 135 --ELPSTQWLRVYRVRFHGQVDQDK------LNLLKKGIVI--------QGICYGDMQVT 178
             +L + +  + Y  +  G+  + +      L L++  + +        +G  +      
Sbjct: 258 GDQLKAREVTKEYVAKVVGEFPETEVIVEKPLKLIEPRLALNAVCQMDEKGAKHAKTVFN 317

Query: 179 LDTQKGSNAWVTVG-LREGKNREIK 202
             +  G  + V    L  G++ +I+
Sbjct: 318 RISYDGKTSIVKCKPLT-GRSHQIR 341


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


>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 = 50.9 bits (121), 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  RLDNVLFRLGYGRTRKECRQIVDHKHVLVNGKQVNIPSYQVKAGDVIEI 136


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


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

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 78/254 (30%), Gaps = 50/254 (19%)

Query: 6   IVQENFTPQRVSKV----IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            V+ +    R+ +     + + G  +   V +     +++V+G   +     +     I 
Sbjct: 11  TVEADDDGIRLDRWFKRHLPQIGFGT---VSKWARTGQIRVDGSRAK-PDDRLAQGQQIR 66

Query: 62  V---DGVPLRKAERTRLW--------------------LYHKPIGLVTT--HSDPDGRST 96
           V      P +K ++ R                      + +KP GL T    +  +    
Sbjct: 67  VPPGGDAPHKKPKQKRELTKAEIEQAEAMLIEQTKSALVINKPPGLATQGGTNTFNHVDG 126

Query: 97  VFDNLPSIFSRVIS--VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQ 152
           + D             V RLD +T G+LL+    G A       +     ++Y     G 
Sbjct: 127 LLDAYMEEGEEQRPRLVHRLDKDTSGILLVARTPGSAAFFSKRFSGRSAKKIYWALVVGV 186

Query: 153 VD--QDKLNL-LKK---------GIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNR 199
            D  Q  +   L K          +  +G      +  +    G   AW+ +    G+  
Sbjct: 187 PDIRQGVIEAPLAKQPGSGGEKMHVDHEGGAPAKTKYRVVESAGKKVAWLELQPMTGRTH 246

Query: 200 EIKKVFEFFNWKVN 213
           +++         + 
Sbjct: 247 QLRVHCAAMGHPIV 260


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


>gi|330815964|ref|YP_004359669.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           gladioli BSR3]
 gi|327368357|gb|AEA59713.1| ribosomal large subunit pseudouridine synthase C [Burkholderia
           gladioli BSR3]
          Length = 342

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 38/257 (14%), Positives = 74/257 (28%), Gaps = 67/257 (26%)

Query: 9   ENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMSTDH 59
           E    QR+   +        R  +        R++    V+VN G +   A   +   D 
Sbjct: 32  EEAAGQRIDNFLL-------RVCKGVPKSHIYRILRSGEVRVNKGRI--DAQYRLAYGDV 82

Query: 60  IEVDGVPLRKAERTR------------------LWLYHKPIGLVTTHSDPDGRSTVFDNL 101
           + +  + +  A+ +R                  + + +KP G+        G S V   +
Sbjct: 83  VRIPPIRIAAADPSRESVPVPAAEFAVVFEDEAMLVINKPAGVAV-----HGGSGVSFGV 137

Query: 102 PSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHG 151
                           V RLD  T G+L++      A V         +  + Y    HG
Sbjct: 138 IEQLREARPEARFLELVHRLDRETSGILMIA-KKRSALVGLHEQIRDNRMDKRYYAAVHG 196

Query: 152 QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK---GSNAWVTVG------------LREG 196
           +   D        + +      D +  +  Q     S+    +             L+ G
Sbjct: 197 EWAADWGRRRAVKVPLFKYSTPDGERRVRVQDDGLPSHTVFNLIDRWSDYAFLEAELKTG 256

Query: 197 KNREIKKVFEFFNWKVN 213
           +  +I+         + 
Sbjct: 257 RTHQIRVHLAHLGLPIV 273


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

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 38/225 (16%), Positives = 70/225 (31%), Gaps = 65/225 (28%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEV---------------------DGVPLRK- 69
           ++M+   +++V+G     A   +     I +                     D   L   
Sbjct: 39  QKMLRTGQIRVDGKRA-EANTRLARGQEIRIPPLPEGPAPEPVARDRQVSAEDAKALEAM 97

Query: 70  --AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--------SRVISVGRLDINTE 119
                  +   +KP GL        G   +  +L  +          R   V RLD +T 
Sbjct: 98  ILYRDDYIIALNKPHGLPV-----QGGPNIKKHLDGMLDALTFEKEERPRLVHRLDRDTS 152

Query: 120 GLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD----QDKLNLLKKGIVIQGICYG 173
           G++LL  D   A  L          + Y     GQ      +  + L K+G    G   G
Sbjct: 153 GVILLARDASAAGFLAKAFRGRDAEKTYWAIVVGQPQYQGGRIDMRLAKQG----GGPMG 208

Query: 174 DMQVTLDTQKGSN---------------AWVTVG-LREGKNREIK 202
           +  V  + + G++                W+ +  L  G+  +++
Sbjct: 209 ERVVPAEGRDGAHAITEFDTVDVARRHATWLELRPLT-GRTHQLR 252


>gi|268316750|ref|YP_003290469.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
 gi|262334284|gb|ACY48081.1| pseudouridine synthase [Rhodothermus marinus DSM 4252]
          Length = 242

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/167 (16%), Positives = 57/167 (34%), Gaps = 22/167 (13%)

Query: 74  RLWLYHKPIGLVTTHSDPDGRSTVFDN----LPSIFSR-----VISVGRLDINTEGLLLL 124
            L + +KP GL +   D  G  TV       +   F++     +  V RLD    G+++L
Sbjct: 15  HLLVINKPSGLRSQG-DRSGAPTVLSLGKALIKERFNKPGNVYLGLVHRLDAPVSGVMVL 73

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQVD-----QDKLNLLKKGIVIQGICYGDMQV 177
                 A  L          +VY     G+++     +D +   +  + +    +   + 
Sbjct: 74  ARTSKAAARLMQQFRERTVEKVYLALVEGELEGSGTWEDFIAPARDHMRLVPEDHPFGKR 133

Query: 178 TLDTQKGSNAWVTVGLR----E-GKNREIKKVFEFFNWKVNRLIRIS 219
            +   +       + L     E G+  +I+    F  + +    R  
Sbjct: 134 AVLHWQALMTRNGLTLMRLVPETGRKHQIRVQLAFRGYPILGDRRYR 180


>gi|85058407|ref|YP_454109.1| ribosomal large subunit pseudouridine synthase A [Sodalis
           glossinidius str. 'morsitans']
 gi|84778927|dbj|BAE73704.1| ribosomal large subunit pseudouridine synthase A [Sodalis
           glossinidius str. 'morsitans']
          Length = 217

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 27/147 (18%), Positives = 58/147 (39%), Gaps = 15/147 (10%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           + T +   +KP GL++     P+ R +V   + + F +  SV RLD+ T G+L++     
Sbjct: 17  QDTHIMAVNKPSGLLSVPGRAPEHRDSVMTRIQANFPQAESVHRLDMATSGVLVVALTKA 76

Query: 130 LARVLELPSTQWL--RVYRVRFHGQV--DQDKLN---------LLKKGIVIQ-GICYGDM 175
             R L+    +    + Y    +G    D+  ++           ++ +    G      
Sbjct: 77  AERELKRQFREREPRKTYIASVYGHPACDEGDIDLPLICDWPNRPRQKVCFGTGKAALTH 136

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
              L      +A V +    G++ +++
Sbjct: 137 YEVLSRDPDGSARVRLTPMTGRSHQLR 163


>gi|117921007|ref|YP_870199.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           ANA-3]
 gi|117613339|gb|ABK48793.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           ANA-3]
          Length = 329

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/219 (14%), Positives = 71/219 (32%), Gaps = 41/219 (18%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEV--------DGVPLRKA-------------- 70
           R++ +  V+VN   ++     +   D + V        D      A              
Sbjct: 52  RIVRKGEVRVNKKRIK-PEYKLQIGDVVRVPPVRMAEQDNRTAPSANLSRVSQLEDRILH 110

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 111 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 170

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGS 185
              + +       +  + Y     G+       ++K+ ++   +  G+  V ++ + K S
Sbjct: 171 SALKHMHDQLRYKKMQKDYLALVKGEWSAQD-KVVKQPLLKLTLKSGERIVRVNAEGKPS 229

Query: 186 NAWVTV-------GLRE-----GKNREIKKVFEFFNWKV 212
                +        L +     G+  +I+   ++    +
Sbjct: 230 ETRFKIVQRYQGCTLVQASPVTGRTHQIRVHCQYMGHPI 268


>gi|312953063|ref|ZP_07771913.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|310628972|gb|EFQ12255.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0102]
 gi|315154025|gb|EFT98041.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0031]
          Length = 283

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNHPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 + T   +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQTLSNNQTAVTCVLETGRTHQIR 231


>gi|313201079|ref|YP_004039737.1| RluA family pseudouridine synthase [Methylovorus sp. MP688]
 gi|312440395|gb|ADQ84501.1| pseudouridine synthase, RluA family [Methylovorus sp. MP688]
          Length = 312

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 76/248 (30%), Gaps = 47/248 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V E    QR+   + +      +  V R++    V+VN   +  A   +   D + V  
Sbjct: 3   TVDEGSAGQRIDNFLTKTLKGVPKSHVYRILRSGEVRVNSKRI-DATYRLQLGDLVRVPP 61

Query: 65  VPLRKA-------------------ERTRLWLYHKPIGLVTTHSDPDGRSTV--FDNLPS 103
           + ++                     E   + +  KP G          R  +        
Sbjct: 62  IRVQPQPVAEESRPVAARFEEAVIFEDEAMLVIDKPAGFAVHGGSGVSRGVIEQLRLERP 121

Query: 104 IFSRVISVGRLDINTEGLLLLTNDGGLARVLELP---STQWLRVYRVRFHGQVDQDKLN- 159
               +  V RLD  T G+L++      A V       +    + Y +   G   + K   
Sbjct: 122 HAKFLELVHRLDRETSGVLMVA-KKRSALVGLHEAMRANHMDKRYLMLVSGDWKEKKKRV 180

Query: 160 --LLKKGIVIQGICYGDMQVTLDTQKGSNAWV--------TVGLRE-----GKNREIKKV 204
              L+K +   G      +VT++ +  ++  +           L E     G+  +++  
Sbjct: 181 VLALQKHVTANGER----KVTVEEEGQNSETIFHLKKSYGEFTLLEAQLITGRTHQLRVQ 236

Query: 205 FEFFNWKV 212
                + +
Sbjct: 237 LAHLGFPI 244


>gi|223938948|ref|ZP_03630834.1| hemolysin A [bacterium Ellin514]
 gi|223892375|gb|EEF58850.1| hemolysin A [bacterium Ellin514]
          Length = 252

 Score = 50.9 bits (121), Expect = 3e-04,   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|5420076|emb|CAB46588.1| hypothetical protein [Yersinia enterocolitica]
          Length = 125

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/122 (23%), Positives = 48/122 (39%), Gaps = 15/122 (12%)

Query: 57  TDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
            D IE         +   L L +KP GL++ +  +P    +V   L  IF     V RLD
Sbjct: 15  HDKIE------TLYQDDHLVLINKPTGLLSLSGENPQNLDSVHHRLVQIFPGCTLVHRLD 68

Query: 116 INTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYG 173
             T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I   
Sbjct: 69  FGTSGLMVIARNKAINAALCQQFSQRTVTKVYSALLCGHLDDN------EGVIDAAIAKD 122

Query: 174 DM 175
             
Sbjct: 123 PA 124


>gi|194761916|ref|XP_001963137.1| GF14093 [Drosophila ananassae]
 gi|190616834|gb|EDV32358.1| GF14093 [Drosophila ananassae]
          Length = 755

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 39/208 (18%), Positives = 72/208 (34%), Gaps = 27/208 (12%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 352 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPA 411

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 412 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 471

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G+ +
Sbjct: 472 RQVEKEYICRVEGVFPDGVVE-CKEPIEVVSYKIGVCKVSPKGKDCTTTFQKLSQNGTTS 530

Query: 188 WVTVG-LREGKNREIKKVFEFFNWKVNR 214
            V    L  G+  +I+   ++  + +  
Sbjct: 531 VVLCKPLT-GRMHQIRVHLQYLGYPILN 557


>gi|169350972|ref|ZP_02867910.1| hypothetical protein CLOSPI_01749 [Clostridium spiroforme DSM 1552]
 gi|169292034|gb|EDS74167.1| hypothetical protein CLOSPI_01749 [Clostridium spiroforme DSM 1552]
          Length = 310

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 69/187 (36%), Gaps = 31/187 (16%)

Query: 43  NGILLERAAVNVMSTDHIEVDGVPLRKA-----ERTRLWLYHKPIGLVTTHSDPDGRSTV 97
           N +L +   + + + +   +D VP         E   + + +KPI            +T+
Sbjct: 64  NHLLNKNDHLKIKAFNQESIDYVPQEYPLSIAYENDFILIVNKPINTTIYPETKKELNTL 123

Query: 98  FDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRF 149
            + + + +        +  + RLD +T GL+L      L  +L   + +    R Y    
Sbjct: 124 CNYVANYYLETNQYLLIRHIHRLDKDTTGLVLFCKCPLLQPILDNMMANKLIKRSYIAIC 183

Query: 150 HGQVDQD-----------KLNLLK---KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE 195
            G +D D            +N ++   KG+        ++++    ++ +       L+ 
Sbjct: 184 KGIIDHDLTINRDIARDRHVNKMRITNKGLK----AITEIKIIKHDKQKNYTVCKCDLKT 239

Query: 196 GKNREIK 202
           G+  +I+
Sbjct: 240 GRKHQIR 246


>gi|119897756|ref|YP_932969.1| hypothetical protein azo1465 [Azoarcus sp. BH72]
 gi|119670169|emb|CAL94082.1| hypothetical protein azo1465 [Azoarcus sp. BH72]
          Length = 260

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/178 (14%), Positives = 47/178 (26%), Gaps = 43/178 (24%)

Query: 71  ERTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTND 127
           +   L   HKP GL+   S  D          L       V  V RLD  T G+L+   D
Sbjct: 7   QDEHLVAIHKPSGLLVHRSALDAHEERFAVQLLRDQLGRHVHPVHRLDKGTSGVLVFALD 66

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQVDQD---------------------------KL 158
              A  L     +    + Y     G   +                             +
Sbjct: 67  RDTAGRLATQFETRAVRKQYVAIVRGHPAEAGTIDHPLSRRFDPVEHVAEDKVFAPQPAI 126

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---GKNREIKKVFEFFNWKVN 213
              ++            ++     +   +   +   E   G+  +I++  +  +  + 
Sbjct: 127 TRFRR--------LATAELPWAVDRYPTSRYALLALEPETGRRHQIRRHLKHISHPII 176


>gi|56695430|ref|YP_165778.1| ribosomal large subunit pseudouridine synthase C [Ruegeria pomeroyi
           DSS-3]
 gi|56677167|gb|AAV93833.1| ribosomal large subunit pseudouridine synthase C [Ruegeria pomeroyi
           DSS-3]
          Length = 347

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 59/193 (30%), Gaps = 37/193 (19%)

Query: 6   IVQENFTPQRVSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
            V E    QR+ +   R     G   R  +E+M  +  ++V+G   +  A  +     + 
Sbjct: 8   TVGEGDGDQRLDRWFRRMFPHVGQG-R--IEKMCRKGELRVDGARAK-PATRLEVGQQVR 63

Query: 62  V--------------------DGVPLRKAERTR---LWLYHKPIGLVTTHSDPDGRSTVF 98
           +                    D   +R     R   + + +KP GL         R    
Sbjct: 64  IPPLPAPGERPEPVKSRVSDSDAKLIRACVLHRDDDIIVLNKPAGLAVQGGSGQTRHVDG 123

Query: 99  ---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV 153
                          V RLD +T G+L+L      A  L          ++Y     G  
Sbjct: 124 LSEALRFGNDENPRLVHRLDKDTSGVLVLARTREAAARLTAAFRHRNTRKIYWALVAGVP 183

Query: 154 DQDKLNLLKKGIV 166
               L  +K G+V
Sbjct: 184 TP-YLGEIKTGLV 195


>gi|16801200|ref|NP_471468.1| hypothetical protein lin2134 [Listeria innocua Clip11262]
 gi|16414648|emb|CAC97364.1| lin2134 [Listeria innocua Clip11262]
          Length = 258

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 178 TVSSMRLDVIISNAHHISRQKAKQLVTAGLVKVNWKTVENPDFECEEEDVL 228


>gi|163939103|ref|YP_001643987.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|163861300|gb|ABY42359.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
          Length = 297

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 66/209 (31%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHI-------------EVDGVPL-RKAERTRLWLYHKP 81
               ++VNG         + + + +             EV+ +PL    E   + + +K 
Sbjct: 39  RGGAIEVNGQH-TSVRHKLQAGEELQIFFPVEERSEGMEVEDIPLCIVYEDDAVLVINKE 97

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + T  S      ++ + L   + +      V  V RLD +T GL+L+  +      L 
Sbjct: 98  ANMSTIPSREHPSGSIANALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLL 156

Query: 136 ---LPSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                     R Y    HG + ++          K + + +  V +          +   
Sbjct: 157 SKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKADSIIERTVCEDGQRAVTHFRVMES 216

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 V + L  G+  +I+    +    
Sbjct: 217 SSDKTHVALELETGRTHQIRVHMAYIGHP 245


>gi|262376643|ref|ZP_06069871.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           lwoffii SH145]
 gi|262308353|gb|EEY89488.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           lwoffii SH145]
          Length = 350

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/170 (19%), Positives = 67/170 (39%), Gaps = 25/170 (14%)

Query: 7   VQENFTPQRVSKVIARA--GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD- 63
           + E +  QR+ + IA       SR ++++ I    + VNG  ++         + + ++ 
Sbjct: 43  LDETYIGQRIDQ-IAAMVWNDFSREKLKQWIKDGNLLVNGQPVK-PKFKSDGFETLTLNV 100

Query: 64  -----------GVPL-RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----- 106
                       +PL    E   + + +KP+G+V      +   T+ + L   +      
Sbjct: 101 ELEAQTRSLPEDIPLDIIYEDDDIIVINKPVGMVVHPGAGNSSGTLVNALLHHYPKSAEL 160

Query: 107 -RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
            R   V R+D +T GLL++  +      L   L      R+Y +  +G +
Sbjct: 161 ARAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLEKKSVYRLYDLVVYGNI 210


>gi|264677097|ref|YP_003277003.1| pseudouridine synthase [Comamonas testosteroni CNB-2]
 gi|262207609|gb|ACY31707.1| pseudouridine synthase, RluA family [Comamonas testosteroni CNB-2]
          Length = 346

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 50/316 (15%), Positives = 99/316 (31%), Gaps = 73/316 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIE--- 61
           V E+   QR+   + R      +  V R+I    V++N G +   A   V   D +    
Sbjct: 39  VDEDSAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRINKGRV--SAETRVQPGDVVRLPP 96

Query: 62  --VDGVPLRKAERT-------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             +      KAER               +    KP G+        G S V   +     
Sbjct: 97  VRISDKVAEKAERPAPAKDFPALLDDEHMIALSKPAGVAV-----HGGSGVSFGVIEQLR 151

Query: 107 RVIS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--QVDQ 155
           +          V RLD  T G+LL+         L+      +  + Y     G    ++
Sbjct: 152 QARPDAKFLELVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLALVQGAWPANK 211

Query: 156 DKLNL-LKKGIVIQG-----ICYGD----------MQVTLDTQK------GSNAWVTVGL 193
             ++L L K +   G     +   D          ++V    +        + + + V +
Sbjct: 212 KVIDLPLHKYLQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQGLPAMSLLEVTI 271

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           + G+  +I+         +             G    G   ++++++ ++ L    L   
Sbjct: 272 KTGRTHQIRVHLSSQGHPIV------------GDDKYGDF-DLNRRVQKQGLKRMFLHAW 318

Query: 254 QVNLDAPIYSSETLVR 269
           ++  + P       +R
Sbjct: 319 RLQFNHPASGERVELR 334


>gi|224476909|ref|YP_002634515.1| hypothetical protein Sca_1425 [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421516|emb|CAL28330.1| conserved hypothetical protein [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 275

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/158 (17%), Positives = 59/158 (37%), Gaps = 15/158 (9%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDG 128
           E   + +  KP G+ T  +D    +T+ +++           + RLD  T GLL++  + 
Sbjct: 79  EDNDIAIIKKPKGVKTHPNDLKESNTLMNHVIYTLDSEYAEPIHRLDQETVGLLIVAKNP 138

Query: 129 GLARVL--ELPSTQWLRVYRVRF-----------HGQVDQDKLNLLKKGIVIQGICYGDM 175
            + ++L   L   Q  R+Y+ R               + +DK +  ++ +   G      
Sbjct: 139 LMKKLLDRMLEDNQISRIYKARVKSQLPLKPQTIDKPIGKDKFHSNRRRVSPTGQHAITH 198

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            +     K +   + + L  G+  +I+         V 
Sbjct: 199 ILDSRMIKENECELDIKLDTGRTHQIRVHLAAIGHPVL 236


>gi|167910661|ref|ZP_02497752.1| pseudouridine synthase, RluA family protein [Burkholderia
           pseudomallei 112]
          Length = 389

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 79/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>gi|162447506|ref|YP_001620638.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii
           PG-8A]
 gi|161985613|gb|ABX81262.1| pseudouridylate synthase, 23S RNA-specific [Acholeplasma laidlawii
           PG-8A]
          Length = 277

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/159 (15%), Positives = 50/159 (31%), Gaps = 16/159 (10%)

Query: 71  ERTRLWLYHKPIGLVT----THSDPDGRSTVFDN-LPSIFSRVISVGRLDINTEGLLLLT 125
           E   + + +KP  ++        D   R             +V+   R+D  T G+++  
Sbjct: 81  EDDDIVIVNKPFNVIVHDDGASEDHLTRRVNMHFQYHGYHHQVLPAHRIDKETTGIVVFA 140

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFH-------GQVDQDKLN--LLKKGIVIQGICYGD 174
                   L     S Q ++ Y            G ++   +    L+K +V        
Sbjct: 141 KHFIALAYLSNLFESRQVVKNYICVVENKVKDKTGSIESKLIKDSKLQKMVVSPHGKLAI 200

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               L   + + + + V +  G+  +I+      N  V 
Sbjct: 201 THYELLGYEATRSRLKVQIETGRTHQIRAHMASINHPVV 239


>gi|120403758|ref|YP_953587.1| RluA family pseudouridine synthase [Mycobacterium vanbaalenii
           PYR-1]
 gi|119956576|gb|ABM13581.1| ribosomal large subunit pseudouridine synthase D [Mycobacterium
           vanbaalenii PYR-1]
          Length = 309

 Score = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 83/250 (33%), Gaps = 40/250 (16%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER---------A 50
           M  +++ V E     RV   +AR    SR     +  +  V+++G    +          
Sbjct: 1   MTTRSMPVPEGLAGMRVDAGLARLLGLSRTAAAAIAEEGGVELDGARAAKSDKLTAGAWL 60

Query: 51  AVNVM------STDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
            V +           ++++G+ +  ++   +    KP G+    +      TV   L   
Sbjct: 61  EVRLPEAPAPVENTPVDIEGMGILYSDED-IVAVDKPPGVAAHATVGWHGPTVLGGLAAA 119

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                   I  R   V RLD+ T G++++         L+    Q    + Y     G  
Sbjct: 120 GFRISTSGIHERQGIVHRLDVGTSGVMVVALSERAYTALKRAFKQRTVEKRYHALVQGHP 179

Query: 154 DQD--KLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +V  G        TL+  + + + + + L  G+  +I+
Sbjct: 180 DPSSGTIDAPIGRHRGHDWKFAVVEGGRHSVTHYDTLEAHQAA-SLLDIELETGRTHQIR 238

Query: 203 KVFEFFNWKV 212
             F   +   
Sbjct: 239 VHFAALHHPC 248


>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 = 50.9 bits (121), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 14 QRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
          QR+   + +  ++SR + +  I    V+VNG ++ ++++ + S+D +++D
Sbjct: 2  QRLDIYL-KTLLSSRTKAQEAIESGCVRVNGKVVYKSSLPLKSSDEVDID 50


>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 = 50.9 bits (121), Expect = 3e-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|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 = 50.9 bits (121), Expect = 3e-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|315930644|gb|EFV09666.1| RNA pseudouridine synthase family domain protein [Campylobacter
           jejuni subsp. jejuni 305]
          Length = 54

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 24/47 (51%), Gaps = 3/47 (6%)

Query: 202 KKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKI---LREQL 245
           ++ F  F+ +V  L R+++G   LG L AG  R +       LR+ L
Sbjct: 1   RRFFGHFDLEVMDLKRVAFGALDLGMLKAGKHRYLENGEYEKLRDFL 47


>gi|227512831|ref|ZP_03942880.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
 gi|227083831|gb|EEI19143.1| 23S rRNA pseudouridylate synthase RluD [Lactobacillus buchneri ATCC
           11577]
          Length = 299

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 43/233 (18%), Positives = 74/233 (31%), Gaps = 36/233 (15%)

Query: 12  TPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--------- 62
            P+ + K +   GI S R  + +    +V +N      +   +   D + V         
Sbjct: 19  EPKTLKKFLNTHGI-SHRMYKNIKTSGQVLINSRS-SDSQTKLADGDQVTVILHDEAGDP 76

Query: 63  ----DGVPLRKAERTRLWLY-HKPIGLVTTHSDPDGRSTVFDNLPSIFSR-------VIS 110
                  P++       WL   KP GL       +   T+ + +     R          
Sbjct: 77  NVAVSEQPIKVVYEDDNWLVVDKPAGLTVVPGPANRDDTLVNRVKGYLVRAGATDLVPHI 136

Query: 111 VGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDK------LNLL 161
           + RLD  T GL+L+     LA  L    L + Q  + Y     G    D       +   
Sbjct: 137 ITRLDRFTSGLVLIAKH-RLANSLANELLAAKQLHKRYLAVVSGVGLPDHGRIQKPIAKD 195

Query: 162 KKG---IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
             G   I+     + D +  +  +   +  V V L  G+  +I+  F      
Sbjct: 196 PNGYGQIISDDGRFSDTEYWVRQRLNDDMLVEVALHTGRTHQIRVHFASIGHP 248


>gi|315634769|ref|ZP_07890051.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
 gi|315476321|gb|EFU67071.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           segnis ATCC 33393]
          Length = 349

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 77/236 (32%), Gaps = 41/236 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GI-----------LLERAAV 52
            + ++   QR+   + AR     +  + R++ +  V+VN G            ++    V
Sbjct: 44  TISDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEYKLQAEDVVRIPPV 103

Query: 53  NVMSTDHIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LP 102
            V       V     + A        E   L + +KP G+            +     L 
Sbjct: 104 RVAEKAQETVSHKLTKVAQLEQHIIFEDNYLLVLNKPSGIAVHGGSGLDFGVIEALRALR 163

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLNL 160
                +  V RLD +T G+LL+       R L   L      + Y     GQ  Q    +
Sbjct: 164 PEARFLELVHRLDRDTSGILLVAKKRSALRHLHEQLREKTIQKEYLALVRGQW-QSHCKV 222

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           ++  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 223 VQAPL-LKNELSSGERIVKVSEQGKPSETRFSVEERYVNATLVKASPVTGRTHQIR 277


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ K + R+G+  S  + +  I    V VNG +  R    ++  D +  +G 
Sbjct: 10 IKLDKFLKRSGLVQSGGQAKAFIQSGYVMVNGEIETRRGRKLIEGDRVTFNGE 62


>gi|260893252|ref|YP_003239349.1| hemolysin A [Ammonifex degensii KC4]
 gi|260865393|gb|ACX52499.1| hemolysin A [Ammonifex degensii KC4]
          Length = 276

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 5/63 (7%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  ++   G   SR    + I   +V VNG    +    V   D +EV    LR  E  
Sbjct: 7  RLDILLVEQGYFPSRERARQAILAGQVLVNGQRAAKPGRMVGPEDRVEV----LRGTEEP 62

Query: 74 RLW 76
             
Sbjct: 63 PYV 65


>gi|238916958|ref|YP_002930475.1| ribosomal large subunit pseudouridine synthase C [Eubacterium
           eligens ATCC 27750]
 gi|238872318|gb|ACR72028.1| ribosomal large subunit pseudouridine synthase C [Eubacterium
           eligens ATCC 27750]
          Length = 333

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/273 (13%), Positives = 85/273 (31%), Gaps = 73/273 (26%)

Query: 1   MKDKNIVQE--NFTPQR-VSKVIARA----GIASRREVERMIAQQRVKVNGILLERAAVN 53
           MK+ NI ++       R + + ++ A             +M+ ++ + +N          
Sbjct: 1   MKEINIDEKLAGQKMMRCLERYLSNAPKSFLY-------KMLRKKNITLNNSKAT-GDEK 52

Query: 54  VMSTDHIEV-------------DGVPLRKAERTRLW-------------LYHKPIGLVTT 87
           +   D I++             +   +      R++               +KP G+++ 
Sbjct: 53  LKCGDIIKIFFSDETFEKFSADNNRTVNYDYYNRIYRPLDIIYENSDVIFINKPSGMLSQ 112

Query: 88  HSDPDGRSTVFDNLPSIFSR------------VISVGRLDINTEGLLLL--TNDGGLARV 133
            + P+  S V   +  +  +                 RLD NT G++    T  G     
Sbjct: 113 KAKPEDVSLVEYLIAHLIHKGELNAGDLASFKPGICNRLDRNTSGIVAAGKTTKGLQQLS 172

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT---------LDTQ-- 182
                    + Y     G VD+     L KG + +      + ++         ++T+  
Sbjct: 173 EAFKQRTLGKYYLCIVKGNVDK---RALIKGYLYKDNKTNKVTISRTETKDSLPIETEYI 229

Query: 183 ----KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                G+   + + L  G++ +I+         
Sbjct: 230 PVCSNGNVTLLKIHLLTGRSHQIRAHLASIGHP 262


>gi|223041614|ref|ZP_03611813.1| ribosomal large subunit pseudouridine synthase [Actinobacillus
           minor 202]
 gi|223017589|gb|EEF16001.1| ribosomal large subunit pseudouridine synthase [Actinobacillus
           minor 202]
          Length = 320

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 81/237 (34%), Gaps = 45/237 (18%)

Query: 7   VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           + E+   QR+   + A+     +  + R++ +  V+VN G +  +    + + D + V  
Sbjct: 16  ISEDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQADDIVRVPP 73

Query: 65  VPLRKA---------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--L 101
           V + +                      E   + + +KP G+            +     L
Sbjct: 74  VRVAEKNEAPISTKLNKVAELEHQILYEDDVMLVINKPSGIAVHGGSGLSFGVIEALRAL 133

Query: 102 PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKLN 159
                 +  V R+D +T GLLL+       R L   L      + Y     GQ  Q  + 
Sbjct: 134 RPQARFLELVHRIDRDTSGLLLVAKKRSALRNLHEQLREKVVQKDYLALVRGQW-QSHVK 192

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
           ++K  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 193 VIKAPL-LKNELASGERIVRVSEEGKPSETRFVIEERYPTATLVKASPVTGRTHQIR 248


>gi|94497617|ref|ZP_01304185.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
 gi|94422834|gb|EAT07867.1| pseudouridylate synthase [Sphingomonas sp. SKA58]
          Length = 394

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 48/161 (29%), Gaps = 28/161 (17%)

Query: 76  WLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + +KP GL T   T +D      +   L    SR   V RLD +T G LLL      A 
Sbjct: 188 IVINKPPGLATQGGTKTDEHVDKLLDALLFDAESRPKLVHRLDKDTSGALLLARTSRAAA 247

Query: 133 VLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------------QGICY 172
                  S    +VY     G    +        I +                  +G+  
Sbjct: 248 HFAKAFSSRTARKVYWALVMGVPSIED-----GMIELPIAKQPGTGGEKMHVDEEEGLPA 302

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 ++      AW+ +    G+  +++         + 
Sbjct: 303 RSRYRVIERAGNRAAWIELQPYTGRTHQLRVHMAAIGHPIV 343


>gi|152974728|ref|YP_001374245.1| RluA family pseudouridine synthase [Bacillus cereus subsp.
           cytotoxis NVH 391-98]
 gi|152023480|gb|ABS21250.1| pseudouridine synthase, RluA family [Bacillus cytotoxicus NVH
           391-98]
          Length = 297

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/272 (13%), Positives = 76/272 (27%), Gaps = 52/272 (19%)

Query: 38  QRVKVNGILLE-----------RAAVNVMSTDHIEVDGVP---LRKAERTRLWLYHKPIG 83
             ++VNG               +    V       V       +   +   L +  +P  
Sbjct: 41  GAIEVNGEEATVRHILKTGEILQIFFPVEERSEGMVAEKIPLSIVYEDDAVLVINKEPYM 100

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLTNDGGLARVLE--L 136
                 +    S     L    ++     V  V RLD +T GL+L+  +  +  +L    
Sbjct: 101 STIPSREHPTGSIANALLYHYDTQKLASTVHIVTRLDRDTSGLMLIAKNRFVHHLLSKQH 160

Query: 137 PSTQWLRVYRVRFHGQV--------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQ 182
              Q  R Y    HG++                  +  + +    +          +  +
Sbjct: 161 QQKQVKRTYEAVVHGRMLNESGTIDAPIGRKSDSIIERMVR----EDGQKAVTHFQVRKR 216

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL- 241
             +   V + L  G+  +I+         +               L  G    + ++ L 
Sbjct: 217 YSNKTHVALQLDTGRTHQIRVHMAHIGHPLLG-----------DDLYGGQLDLIKRQALH 265

Query: 242 -REQLGPHLLEEAQVNLDAPIYSSETLVRDRP 272
            +     H + E +++  A I +    V  R 
Sbjct: 266 SKSLTFYHPILEKEMSFSADIPTDMHTVLARE 297


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 4/71 (5%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL---RKA 70
          R+   +   G+  SR +    I + RV ++G + ++ A  V     I + G P+   R A
Sbjct: 3  RLDTALVERGLFESRNKAAEAIRKGRVFLDGHVQKKPAFKVGEETEITLQGGPVYVSRSA 62

Query: 71 ERTRLWLYHKP 81
          ++   +L   P
Sbjct: 63 QKLAGYLQEHP 73


>gi|291519200|emb|CBK74421.1| hemolysin TlyA family protein [Butyrivibrio fibrisolvens 16/4]
          Length = 265

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  V+   G A SR + + MI +  V V G   ++A   +     IE+ G  L+   R
Sbjct: 3  ERLDIVLVDRGFAPSREKAKTMIMEGYVFVKGNREDKAGTKIDVDADIEIHGQQLKYVSR 62


>gi|152979640|ref|YP_001345269.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
 gi|150841363|gb|ABR75334.1| pseudouridine synthase [Actinobacillus succinogenes 130Z]
          Length = 219

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 24/158 (15%), Positives = 52/158 (32%), Gaps = 21/158 (13%)

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT----NDG 128
            + + +KP GL++   + P    +    +   +       RLD+ T G++L       D 
Sbjct: 22  HILVVNKPSGLLSVPGNQPQYYDSAMSRVKEKYGFCEPAHRLDMATSGIILFAMSKLADS 81

Query: 129 GLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQ-GICYGDMQ 176
            L R       Q  + Y+    G   QD             N  ++ I    G       
Sbjct: 82  ELKRQF--RERQTEKFYQAVVWGHPKQDSGTVNLPLICDWENRPRQRIDFNAGKSAVTKF 139

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
             L+    ++  + +  +  G++ +++         + 
Sbjct: 140 EVLERLPNNSTRLKLTPIT-GRSHQLRLHMLALGHPIL 176


>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 = 50.6 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+  V+ R G A SRR+  ++++   ++VNG  ++  +  V   D I V
Sbjct: 99  RLDNVVYRLGFAVSRRQARQLVSHGHIEVNGKKVDIPSFLVKPGDVISV 147


>gi|53723511|ref|YP_102984.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei ATCC 23344]
 gi|76810454|ref|YP_333728.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 1710b]
 gi|52426934|gb|AAU47527.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei ATCC 23344]
 gi|76579907|gb|ABA49382.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 1710b]
          Length = 395

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 79/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 66  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 124

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 125 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 184

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 185 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 244

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 245 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 302


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++   G+  SR + +  I    V +NGI  ++    V     IE+
Sbjct: 1  MEKERLDVLLVNKGLFESREKCKSAIMAGLVWINGIREDKPGTKVPVECEIEI 53


>gi|67641328|ref|ZP_00440109.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei GB8 horse 4]
 gi|121600453|ref|YP_993132.1| RluA family pseudouridine synthase [Burkholderia mallei SAVP1]
 gi|124385530|ref|YP_001026092.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10229]
 gi|126448439|ref|YP_001080638.1| RluA family pseudouridine synthase [Burkholderia mallei NCTC 10247]
 gi|134277051|ref|ZP_01763766.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|167902420|ref|ZP_02489625.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei NCTC 13177]
 gi|254177619|ref|ZP_04884274.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|254199929|ref|ZP_04906295.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|254206262|ref|ZP_04912614.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|254260754|ref|ZP_04951808.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
 gi|254358323|ref|ZP_04974596.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|121229263|gb|ABM51781.1| pseudouridine synthase, RluA family [Burkholderia mallei SAVP1]
 gi|124293550|gb|ABN02819.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10229]
 gi|126241309|gb|ABO04402.1| pseudouridine synthase, RluA family [Burkholderia mallei NCTC
           10247]
 gi|134250701|gb|EBA50780.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei 305]
 gi|147749525|gb|EDK56599.1| pseudouridine synthase, RluA family [Burkholderia mallei FMH]
 gi|147753705|gb|EDK60770.1| pseudouridine synthase, RluA family [Burkholderia mallei JHU]
 gi|148027450|gb|EDK85471.1| pseudouridine synthase, RluA family [Burkholderia mallei
           2002721280]
 gi|160698658|gb|EDP88628.1| pseudouridine synthase, RluA family [Burkholderia mallei ATCC
           10399]
 gi|238522242|gb|EEP85688.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           mallei GB8 horse 4]
 gi|254219443|gb|EET08827.1| pseudouridine synthase, RluA family [Burkholderia pseudomallei
           1710a]
          Length = 389

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 79/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT    +   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWARQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>gi|300175850|emb|CBK21846.2| Pseudouridylate synthase [Blastocystis hominis]
          Length = 273

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 35/224 (15%), Positives = 70/224 (31%), Gaps = 48/224 (21%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------LWLY 78
           E  I   R++VNG  + R    + + D I      + + E                +   
Sbjct: 41  EEAIRNGRIRVNGERVTR-DHILKNGDRIT---HTVHRHEPPVPYSPVVILGETDDIIAV 96

Query: 79  HKPIG--LVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE- 135
           +KP    +    +             +  S    + RLD  T G++LL     +A  L  
Sbjct: 97  NKPAALPVHPCGAYRYNSLETILRKENKLSEFYFIHRLDRVTSGVMLLAKRKDIASKLSE 156

Query: 136 -LPSTQWLRVYRVRFHG------QVDQDKLNLLKKGIVIQG----ICYGDMQVTLDTQKG 184
            L    + +VY     G      ++        + GI +      +   +    +D ++G
Sbjct: 157 QLVKGGFHKVYLAEAEGNCFEKPEIPGVFYTQ-QNGIAVDRNIAVVSQKEGIFKVDEKEG 215

Query: 185 SNAWVTV-----------GLRE-----GKNREIKKVFEFFNWKV 212
             A+  +            L E     G+  +I+   ++    +
Sbjct: 216 KPAYTYLFPLYYSKQSNTTLMECVPITGRTHQIRLHLKYIGHPI 259


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             QR+  ++    + S R   +R+I    V VN  ++++    +     I+V
Sbjct: 1  MAKQRLDTLLIDRNLCSSRHIAQRLIRAGEVMVNQQVIDKPGTEIDLEAQIKV 53


>gi|78485000|ref|YP_390925.1| pseudouridine synthase [Thiomicrospira crunogena XCL-2]
 gi|78363286|gb|ABB41251.1| ribosomal large subunit pseudouridine synthase A [Thiomicrospira
           crunogena XCL-2]
          Length = 241

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 57/154 (37%), Gaps = 17/154 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   + + +KP GL++    D D    +   +       + V RLD++T G+++L     
Sbjct: 32  EDDDIIVVNKPAGLLSVPGKDLDPEMNLLAQVQKHVPTALIVHRLDMDTSGIMILAKHKA 91

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQV--DQDKLNL-LKKG--------IVIQGICYGDMQ 176
             R L +        + Y+    G+    Q  LNL ++          I ++        
Sbjct: 92  SHRHLSIQFQDRLTEKTYQAICFGKPSTSQGHLNLPMRCDWENRPLQIIDLKQGKAASTH 151

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK---KVFEF 207
             L  Q  +   V +    G++ +++   K+   
Sbjct: 152 WKLTAQYDNAFEVNLTPVTGRSHQLRLHMKMLGH 185


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 41/90 (45%), Gaps = 2/90 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  V  R+G+A +RRE  +++    + VNG+ ++  +  V   D IEV       +   
Sbjct: 88  RLDNVAFRSGLARTRREARQIVTHGHLTVNGVQVDIPSYKVSEGDVIEVREKSRSNSLFK 147

Query: 74  RLWLYHKPIGLVT-THSDPDGRSTVFDNLP 102
            +   +   G+V   +SD +    + D  P
Sbjct: 148 AIKETNATFGVVEWLNSDIENLKVIVDRFP 177


>gi|134082733|emb|CAK42625.1| unnamed protein product [Aspergillus niger]
          Length = 484

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 33/203 (16%), Positives = 62/203 (30%), Gaps = 46/203 (22%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
            + +    V VNG         V +   I          V G  +    E   L +  KP
Sbjct: 82  RKALQDGLVAVNGTPA-GPNTVVKNGQIISHTLHRHEPPVTGKEIGIIHEDDDLIVIDKP 140

Query: 82  IGLVTTHSDPDGRSTVFD-----NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            G+    +     ++V +       P    R     RLD  T G++ L   G  A+  E 
Sbjct: 141 AGVPVHSAGRYHYNSVLEIMRSQRHPEWVPR--PCNRLDRLTSGVMFL---GKTAKAAEN 195

Query: 137 PSTQW-----LRVYRVRFHGQVDQDKLNLLKKGIVIQG-------ICYGDMQVTLDTQKG 184
            + +       + Y  R  G+           G+++            G  +V    ++ 
Sbjct: 196 MTGKLKARTLQKEYVARVKGKFPD--------GVIVCDQPIMSVSPKVGLNRVRATGKEA 247

Query: 185 SNAWVTVGLRE-----GKNREIK 202
              +  + +       G+  +I+
Sbjct: 248 KTKFRRLAIVHCLPLTGRTHQIR 270


>gi|58266206|ref|XP_570259.1| hypothetical protein [Cryptococcus neoformans var. neoformans
           JEC21]
 gi|134111034|ref|XP_775981.1| hypothetical protein CNBD3880 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|50258647|gb|EAL21334.1| hypothetical protein CNBD3880 [Cryptococcus neoformans var.
           neoformans B-3501A]
 gi|57226492|gb|AAW42952.1| conserved hypothetical protein [Cryptococcus neoformans var.
           neoformans JEC21]
          Length = 520

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/139 (21%), Positives = 57/139 (41%), Gaps = 16/139 (11%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHI--EV---------DGVPLRKAERTR-LWLYHKPI 82
           +     +VNG++ +   + + + D I   V         D + +   +R R   +  KP 
Sbjct: 63  LESGVTRVNGVVAQ-PDLILRNGDRIDNTVHRHEPPVTNDPILVLHIDREREFIVISKPG 121

Query: 83  GLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLARVLELP--ST 139
            L    +    + TV + + S +  +  SV RLD  T GL++L   G  A  L       
Sbjct: 122 SLPVHAAGRYFKHTVLEMMESDYGLKCYSVNRLDRLTSGLMILALSGKAASKLAREFVEG 181

Query: 140 QWLRVYRVRFHGQVDQDKL 158
           +  + Y  R  G+  ++++
Sbjct: 182 KVKKEYVARVKGKFPKEEI 200


>gi|47568408|ref|ZP_00239109.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
 gi|47554956|gb|EAL13306.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus G9241]
          Length = 297

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/266 (15%), Positives = 88/266 (33%), Gaps = 48/266 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + + V             + +PL    E   + + +K   
Sbjct: 41  GAIEVNGQYA-SVRHQLQAGEELRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 99

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L S + +      V  V RLD +T GL+L+  +  +  +L   
Sbjct: 100 MSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKNRFMHHLLSKQ 159

Query: 136 LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
                  R Y    HG            + +   +++++ +  +G         +D+   
Sbjct: 160 HQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSANH 219

Query: 185 SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR-- 242
               V++ L  G+  +I+         +               L  G   E+ ++ L   
Sbjct: 220 KTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHST 267

Query: 243 EQLGPHLLEEAQVNLDAPIYSSETLV 268
                H + E +++    I +    V
Sbjct: 268 SLTFYHPILEKEMSFTTTIPNDMQAV 293


>gi|254463248|ref|ZP_05076664.1| ribosomal large subunit pseudouridine synthase A [Rhodobacterales
           bacterium HTCC2083]
 gi|206679837|gb|EDZ44324.1| ribosomal large subunit pseudouridine synthase A [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 216

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 77/235 (32%), Gaps = 42/235 (17%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TN 126
            +   + + +KP GL++      +    +   +  +F + + V RLD +T G+++   T 
Sbjct: 16  HDDHEILIVNKPAGLLSVPGKGEELADCLIARIQKVFPQALLVHRLDRDTSGVMVFALTR 75

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
                  L+       + Y  R  G ++              G     + V    +    
Sbjct: 76  HAQRHLGLQFEKRMTQKTYVARVAGVLEPKT-----------GSVELPLIVDWPNRPLQK 124

Query: 187 AWVTVGLRE-GKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTR-EVSKKILR-E 243
                   E GK           +++V       YG         G TR  ++ +  R  
Sbjct: 125 -----VCHETGK-------AAHTDYRVM-----RYG--------EGETRVRLTPRTGRSH 159

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSKQ 298
           QL  H+L      L  P Y+S T + D P ++    +   +     +     +K 
Sbjct: 160 QLRVHMLALGHPILGDPFYASGTDLSDHPRLMLHSEELRLKHPDGGNTHKFRAKA 214


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 1/62 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          I+ +    QR+  ++   G+  SR++ +R+I    VK+   ++++    V +   IE+  
Sbjct: 9  ILLQALAKQRIDILLVEQGLCPSRQQAQRLIRAGEVKIAQQIIDKPGTLVATDAVIELKQ 68

Query: 65 VP 66
           P
Sbjct: 69 KP 70


>gi|167855918|ref|ZP_02478667.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parasuis 29755]
 gi|219871480|ref|YP_002475855.1| 23S rRNA pseudouridylate synthase C [Haemophilus parasuis SH0165]
 gi|167852955|gb|EDS24220.1| ribosomal large subunit pseudouridine synthase C [Haemophilus
           parasuis 29755]
 gi|219691684|gb|ACL32907.1| 23S rRNA pseudouridylate synthase C [Haemophilus parasuis SH0165]
          Length = 319

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 81/238 (34%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
            + ++   QR+   + A+     +  + R++ +  V+VN G +  +    + + D + V 
Sbjct: 15  TISDDEAGQRLDNFLLAKLKGVPKSLIYRIVRKGEVRVNKGRI--KPEYKLQADDIVRVP 72

Query: 64  GVPLRKA---------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
            V + +                      E   + + +KP G+            +     
Sbjct: 73  PVRVAEKNEAPISTKLNKVAELEHQILYEDEVMLVINKPSGIAVHGGSGLSFGVIEALRA 132

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V R+D +T GLLL+       R L   L      + Y     GQ  Q  +
Sbjct: 133 LRPQARFLELVHRIDRDTSGLLLVAKKRSALRSLHEQLREKVVQKDYLALVRGQW-QSHV 191

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            ++K  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 192 KVIKAPL-LKNELASGERIVRVSEEGKPSETRFVIEERYPIATLVKASPVTGRTHQIR 248


>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 = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD 63
           R+   +   G   SR   +  IA  +VK++G ++++A+ +V   + ++V+
Sbjct: 1  MRLDVYLVENGYFTSRGRSKTAIASGKVKIDGRIVKKASKDVKPENKVQVE 51


>gi|229166145|ref|ZP_04293906.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH621]
 gi|228617367|gb|EEK74431.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH621]
          Length = 292

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 66/209 (31%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHI-------------EVDGVPL-RKAERTRLWLYHKP 81
               ++VNG         + + + +             EV+ +PL    E   + + +K 
Sbjct: 34  RGGAIEVNGQH-TSVRHKLQAGEELQIFFPVEERSEGMEVEDIPLCIVYEDDAVLVINKE 92

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + T  S      ++ + L   + +      V  V RLD +T GL+L+  +      L 
Sbjct: 93  ANMSTIPSREHPSGSIANALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLL 151

Query: 136 ---LPSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                     R Y    HG + ++          K + + +  V +          +   
Sbjct: 152 SKQHQQKGVKRTYEAIVHGTILEEVGTIDAQIGRKADSIIERTVCEDGQRAVTHFRVMES 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 V + L  G+  +I+    +    
Sbjct: 212 SSDKTHVALELETGRTHQIRVHMAYIGHP 240


>gi|254419979|ref|ZP_05033703.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
 gi|196186156|gb|EDX81132.1| pseudouridine synthase, RluA family [Brevundimonas sp. BAL3]
          Length = 341

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 37/183 (20%), Positives = 56/183 (30%), Gaps = 41/183 (22%)

Query: 7   VQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLER-------AA 51
           V E+    R+ +         RR        +V++M    +++V+G  ++        AA
Sbjct: 20  VAEDEDGIRLDRWF-------RRRWPHLSNIQVQKMARSGQIRVDGARIKPEGRLTAGAA 72

Query: 52  VNVMS--TDHIEVDG-------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGRST 96
           V V     D     G               L   E   +   +KP GL         R  
Sbjct: 73  VRVPPIPDDTSRQAGDLHTLSERDIAFAKSLVLYEDDMVIAINKPHGLAVQGGTKTSRHV 132

Query: 97  --VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQ 152
             +         R   V RLD +T G+LLL      A+ L       Q  + Y     G 
Sbjct: 133 DRLLSAWGEGMDRPRLVHRLDRDTSGVLLLGKGPEAAKRLAGAFARRQAKKTYWAIVIGN 192

Query: 153 VDQ 155
              
Sbjct: 193 PKP 195


>gi|167823889|ref|ZP_02455360.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei 9]
          Length = 318

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>gi|164687176|ref|ZP_02211204.1| hypothetical protein CLOBAR_00817 [Clostridium bartlettii DSM
           16795]
 gi|164603600|gb|EDQ97065.1| hypothetical protein CLOBAR_00817 [Clostridium bartlettii DSM
           16795]
          Length = 326

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 30/164 (18%), Positives = 56/164 (34%), Gaps = 32/164 (19%)

Query: 75  LWLYHKPIGLVTTHSDPDGRST----VFDNLPSIFS--RVISVGRLDINTEGLLLLTNDG 128
           L +  KP  +V   +     +T    V D +       ++  V RLD+NT GL+++  + 
Sbjct: 118 LIMVDKPPFMVVHPTKSHFENTMANGVTDYIIKKGEDVKIRFVNRLDMNTSGLVIVAKNP 177

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTLDT 181
               VL        + + Y     G +++D      +G  I    Y        +V  + 
Sbjct: 178 FAQHVLSSEMKDDDFEKKYITVVKGIIEED------EG-TINQPIYRPTDDSVKRVVDER 230

Query: 182 QKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVN 213
            + S     V        + E     G+  +I+   E     + 
Sbjct: 231 GQESITHYKVIERLNDATIVEVKLETGRTHQIRVHMEHIGHPII 274


>gi|51598281|ref|YP_072469.1| hypothetical protein BG0018 [Borrelia garinii PBi]
 gi|51572852|gb|AAU06877.1| conserved hypothetical protein [Borrelia garinii PBi]
          Length = 327

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 39/255 (15%), Positives = 84/255 (32%), Gaps = 66/255 (25%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG     + +  V
Sbjct: 4   LKKEFTVKENAL--RLDLYLSNNLEVFTRSQ----IKRRNVEAFKKSNGKFFNIKLSKPV 57

Query: 55  MSTDHIEV---------------DGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
           +  D I +               + +P+    E + + + +KP G+++         TV 
Sbjct: 58  LKNDEILIEFDEEESSQIDYLRPNNIPITIIYEDSNIIVLNKPQGILSHPGISHWDDTVV 117

Query: 99  DNLPSIFSRVIS-----------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVY 145
           + L     R+             V RLD +T G+L+   +      L       +  +VY
Sbjct: 118 NFLLYHIKRLKINFNEEKVRPGIVHRLDKDTSGVLICAKNINTLSFLAQQFKDKRTNKVY 177

Query: 146 RVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGL------ 193
                G  +      +  ++                 V+ D  K +     + L      
Sbjct: 178 IAIVKGNFNSFSGSIESFIDR-------DKYNRKKFSVSKDRGKKALTEYRLLLNFRGYS 230

Query: 194 ------REGKNREIK 202
                 + G+  +++
Sbjct: 231 LLALKPKTGRTHQLR 245


>gi|331085058|ref|ZP_08334145.1| hypothetical protein HMPREF0987_00448 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330408758|gb|EGG88223.1| hypothetical protein HMPREF0987_00448 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 323

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 84/255 (32%), Gaps = 62/255 (24%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVE-----RMIAQQRVKVNGILLERAAVNVM 55
           M++  + + N   QR+ K++A+       E       +M+ ++ + +NG         + 
Sbjct: 1   MQEIKVTK-NEAGQRLDKLLAKYL----NEAPKSFFYKMMRKKNIVLNGKKAT-GNEKLE 54

Query: 56  STDHIE--VDGVPLRK----------------AERTRLWLYHKPIGLVTTHSDPDGRSTV 97
             D ++  +    +RK                 E   + L +KP+G+++  +     S V
Sbjct: 55  EGDIVKLFLADETIRKFSSVKIQRTKTNLSVIYEDQDVVLINKPVGMLSQKAKESDVSLV 114

Query: 98  FDNLPSIFS------------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
              +  +              R     RLD NT G+++        + +          +
Sbjct: 115 EHLISYLLDAGELSEETLKSFRPSICNRLDRNTSGIVVAGKSLPGLQKMGELFKERTLHK 174

Query: 144 VYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN----------------A 187
            YR    G + +D      KG + +      +Q+       S+                 
Sbjct: 175 YYRCLVQGVIRED---QYLKGWLKKDEKTNKVQILDRPSDPSDQPIETEYHPLWTKEGVT 231

Query: 188 WVTVGLREGKNREIK 202
            + V L  GK  +I+
Sbjct: 232 LLEVRLITGKTHQIR 246


>gi|315930491|gb|EFV09543.1| RNA pseudouridylate synthase family protein [Campylobacter jejuni
           subsp. jejuni 305]
          Length = 144

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/136 (18%), Positives = 55/136 (40%), Gaps = 9/136 (6%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKAERTRLWLYHKPIGL 84
           E +++I ++R+  +GIL+E     +     + V      GV +   E     +  K  G+
Sbjct: 10  EAQKLIDKKRLFCDGILVEEKNKILNGLVELIVYENNPKGVEIVF-ENEDFAILEKESGI 68

Query: 85  VTTHSDPDGRSTVFDNLPS-IFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQW 141
           ++  +    + ++ D +            RLD  T GL+L+  +      L+        
Sbjct: 69  LSHPNGRHCKYSLSDEIWHLWGKEACVAHRLDKETSGLILIAKNKKAQIDLKSLFEKKLV 128

Query: 142 LRVYRVRFHGQVDQDK 157
            + Y    HG+++++ 
Sbjct: 129 QKEYLALAHGKIEENF 144


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ + + + G+  SR   + +I    V VN   +++A   +     +EV G  +    R
Sbjct: 3  IRLDQYLVQHGLTQSRERAKALIMSGIVFVNEQKVDKAGEMIKEDAKVEVRGHDIGYVSR 62


>gi|313123295|ref|YP_004033554.1| pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
 gi|312279858|gb|ADQ60577.1| Pseudouridine synthase [Lactobacillus delbrueckii subsp. bulgaricus
           ND02]
          Length = 297

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 83/250 (33%), Gaps = 56/250 (22%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE---VERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
           ++     P ++S  + + G  SRR     +       + VN       +  +   D +  
Sbjct: 1   MIVAKNDPGQLSHFLLKKGF-SRRAVNNCKN--HGGMMLVNHHR-RNGSYRLKEGDVVHF 56

Query: 61  -----------EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                      +V  +PL   E T    + +KP GL++  S       V + + + F + 
Sbjct: 57  LMGQEPVNPWLKVSRLPLDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQ 116

Query: 109 ---------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQV 153
                      V RLD +T GL+LL   G     +       L      + Y    HG  
Sbjct: 117 GVNPAYVKPHIVTRLDQDTSGLVLL---GK--NAIAHDRFSKLGKDAFIKKYHAIVHGNF 171

Query: 154 DQDKLNLL------------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +  L+ L            K+ +  +G         LD   G+ + V + L  G+  +I
Sbjct: 172 AEGDLSGLIDKPLARVGDTVKREVNPKGQRALTEYRVLDQVPGA-SLVELRLLTGRTHQI 230

Query: 202 K-KVFEFFNW 210
           +  +      
Sbjct: 231 RIHM-ASIGH 239


>gi|157376031|ref|YP_001474631.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
 gi|157318405|gb|ABV37503.1| pseudouridine synthase [Shewanella sediminis HAW-EB3]
          Length = 218

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 56/167 (33%), Gaps = 28/167 (16%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +R  +R  + + +KP GL++      +      + L   +   I V RLD  T G+++  
Sbjct: 16  IRYKDRD-IIVINKPSGLLSNPGRAANTFDCAINRLLQRYPEAILVHRLDCATSGIMVFA 74

Query: 126 -NDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQVT 178
            N    + +      +   + Y     G +  +      +G+ I+           +Q  
Sbjct: 75  LNKKAESNIKTQFQNRMSKKTYIAEVQGHIVDE------EGV-IELAMKPDTERPPLQKL 127

Query: 179 LDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVN 213
            +  K S  +  V        L E     G+  +++         + 
Sbjct: 128 AEEGKPSKTYFKVLERRKNSTLVELKPVTGRTHQLRLHMLAIGHPIL 174


>gi|326568395|gb|EGE18475.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC7]
          Length = 382

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 58/177 (32%), Gaps = 26/177 (14%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  N   QRV   + AR     R  + ++I    +++NG   + A   +   D + V  
Sbjct: 64  TVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCK-AHDKLYMGDVVRVAP 122

Query: 65  VPLRKAERTRL-------------------WLYHKPIGLVTTHSDPDGRSTV-FDNLPSI 104
           + L   E   +                    + +KP G+       +    +    L   
Sbjct: 123 IRLSVREAPIISEELAKGLLERIIFEDNGLIVLNKPHGMAVHGGSGESFGIIEAMRLAMG 182

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL 158
              +  + R+D +T GLLL+         +     +     + Y     G V  D++
Sbjct: 183 KKYLELIHRIDKDTSGLLLIA-KKRSTLKILQEQFRKKTIQKRYLCLVMGHVQADEM 238


>gi|312793770|ref|YP_004026693.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312180910|gb|ADQ41080.1| pseudouridine synthase [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 311

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 38/244 (15%), Positives = 77/244 (31%), Gaps = 61/244 (25%)

Query: 33  RMIAQQRVKVN------GILLERAAV-------NVMSTDHIEVDGVPLRKAERTRLWLYH 79
           +M+ +  + V+      G +L              +    +E+    L+  E   + +  
Sbjct: 34  KMLRKGEIIVSFLPAQKGQVLRFGDTVSFEIEDRFLEHKKVEI----LKVYEDDNIVVID 89

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRV---ISVGRLDINTEGLLLLTNDGGLARVLEL 136
           KP G + +H D +   +V   +   +S+        RLD NT GL+++  +  +   +  
Sbjct: 90  KPYG-IPSHPDSNNEYSVVSWIEDNYSKDELPQLCHRLDRNTAGLMIIAKNRQVLSEMLK 148

Query: 137 --PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ------------------ 176
                   + Y              L K G+++  +     +                  
Sbjct: 149 YMSRRAIKKRYLCITKK------AELPKSGVLVHYLKKDPKKSKVYISDFPQDGYSEVVT 202

Query: 177 -VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTRE 235
              +  QK     V V ++ GK  +I+         +            LG    G   E
Sbjct: 203 AYKIVRQKDDLQLVDVEIKTGKTHQIRAQLAHVGLCI------------LGDSKYGDW-E 249

Query: 236 VSKK 239
           ++KK
Sbjct: 250 LNKK 253


>gi|300813392|ref|ZP_07093743.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
 gi|300512535|gb|EFK39684.1| pseudouridine synthase, RluA family [Peptoniphilus sp. oral taxon
           836 str. F0141]
          Length = 316

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/256 (14%), Positives = 79/256 (30%), Gaps = 71/256 (27%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA 50
            K I+  N + QR+ + +           ++             + ++ +KV+G      
Sbjct: 2   RKVIIGPNDSDQRLDRFL-----------KKYFEKAPLSFIYKNLRKKNIKVDGKKA-SP 49

Query: 51  AVNVMSTDHIE--VDGVPLRKAERTRLW-----------------LYHKPIGLVTTHSDP 91
              +     I   +    + K ++ +L                  L  KP+ ++T +   
Sbjct: 50  EDLIKEGQEISLFISDETIEKYKKDKLARNSQKFPQILYEDDNICLMKKPLNMLTHNDKN 109

Query: 92  DGRSTVFDNLPSIF-------------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
             +  + D                    R     RLD NT G+LL   +    R +    
Sbjct: 110 FYQDNMVDRFIDYLIFKEEYSPREENTFRPSICNRLDRNTSGILLGAKNAETLREINKAI 169

Query: 139 TQ--WLRVYRVRFHGQV----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            +    + Y     G+V          ++   N+++K  V +        +      G  
Sbjct: 170 KERLVDKFYLTIVKGKVQKPFEINIKLEKTDKNIMRKSCVGKDSLTKFFPL---ISNGEY 226

Query: 187 AWVTVGLREGKNREIK 202
           + + V L  G+  +I+
Sbjct: 227 SLIKVKLITGRTHQIR 242


>gi|222529402|ref|YP_002573284.1| RluA family pseudouridine synthase [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456249|gb|ACM60511.1| pseudouridine synthase, RluA family [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 293

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/179 (12%), Positives = 60/179 (33%), Gaps = 31/179 (17%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
           +    +    ++ + V+G      E       +KP GL +  S      T+ + +    +
Sbjct: 58  VIEVDLIFSKSNIVPVEGSIDILYEDNFFLFVNKPSGLPSHPSKGHYFDTIANYVEYYLN 117

Query: 107 RV----ISVGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDKLN 159
                   + RLD +T G+++   +      +        +  + Y    HG + +    
Sbjct: 118 SKNLTSHIINRLDKDTSGIVVFAKN-SYFHSIVSYEFEKRRVDKTYIAIVHGILTK---- 172

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKG---SNAWVTVG-------------LREGKNREIK 202
             K G++ + I   D  +  +  +    ++ +  V              +  G+  +++
Sbjct: 173 --KSGLIEKPIKRSDDGIKREIHQDGSFASTYYEVIDSFENFSVLKLKPIT-GRTHQLR 228


>gi|229010596|ref|ZP_04167798.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           DSM 2048]
 gi|228750794|gb|EEM00618.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus mycoides
           DSM 2048]
          Length = 292

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 66/209 (31%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHI-------------EVDGVPL-RKAERTRLWLYHKP 81
               ++VNG         + + + +             EV+ +PL    E   + + +K 
Sbjct: 34  RGGAIEVNGQH-TSVRHKLQAGEELQIFFPVEERSEGMEVEDIPLCIVYEDDAVLVINKE 92

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + T  S      ++ + L   + +      V  V RLD +T GL+L+  +      L 
Sbjct: 93  ANMSTIPSREHPSGSIANALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLL 151

Query: 136 ---LPSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                     R Y    HG + ++          K + + +  V +          +   
Sbjct: 152 SKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKADSIIERTVCEDGQRAVTHFRVMES 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 V + L  G+  +I+    +    
Sbjct: 212 SSDKTHVALELETGRTHQIRVHMAYIGNP 240


>gi|219116402|ref|XP_002178996.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409763|gb|EEC49694.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 424

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/176 (19%), Positives = 55/176 (31%), Gaps = 44/176 (25%)

Query: 71  ERTRLWLYHKPIGLVT--THSDPDGRSTVFDNLP-----------SIFSRVISVGRLDIN 117
           E     L +KP G+V     +   G  TV   LP           S+  R  SV RLD  
Sbjct: 213 EDDHWALVNKPAGIVVYNQRNGGHGIMTVRAALPFVLAPPKVGTISVLRRPASVHRLDKP 272

Query: 118 TEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKLNLLKK------GIVIQ 168
           T G +L       A +            + Y    +G       + +        G+ + 
Sbjct: 273 TSG-ILCIAKTKPAMLCLSRQFHDRIVKKTYFAVINGIPTYSNESKISSKTAYELGVDVD 331

Query: 169 GICYGDMQVT---LDTQKGSNAW--VT-----------VGLRE-----GKNREIKK 203
                D Q+    LD +K    W  V            + L E     G+  ++++
Sbjct: 332 PNDLDDWQLIDSPLDEKKAVTVWRVVRSIKSLHANDGYLTLVELKPKTGRYHQLRR 387


>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 = 50.6 bits (120), Expect = 4e-04,   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|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 = 50.6 bits (120), Expect = 4e-04,   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  KAQKERIDKLLVDKGLVESREKAQVLIMSGVVFVNNQKIDKPGTKVPTDANIHI 55


>gi|189200266|ref|XP_001936470.1| DRAP deaminase [Pyrenophora tritici-repentis Pt-1C-BFP]
 gi|187983569|gb|EDU49057.1| DRAP deaminase [Pyrenophora tritici-repentis Pt-1C-BFP]
          Length = 475

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/145 (16%), Positives = 48/145 (33%), Gaps = 21/145 (14%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT-------------RLWLY 78
           E+ I   RV +NG  +      V + D I      L + E                + + 
Sbjct: 86  EQAIIDGRVVLNGKPVPSTKTIVKNGDVIS---HTLHRHEPPCTAQPIGIVHEDDNMIVI 142

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G+    +     +++ + + +            RLD  T G++ +      A  L 
Sbjct: 143 NKPAGMPVHPAGRYNFNSIIEIMRADRGYGWNPLPCNRLDRLTSGIMFIGKHKQAAEELS 202

Query: 136 LPSTQ--WLRVYRVRFHGQVDQDKL 158
                    + Y  R  G+  + ++
Sbjct: 203 AQIRGRTVKKEYITRVVGEFPEGEI 227


>gi|296113828|ref|YP_003627766.1| RluA family pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|295921522|gb|ADG61873.1| RluA family pseudouridine synthase [Moraxella catarrhalis RH4]
 gi|326562171|gb|EGE12499.1| RluA family pseudouridine synthase [Moraxella catarrhalis 7169]
 gi|326564465|gb|EGE14691.1| RluA family pseudouridine synthase [Moraxella catarrhalis 46P47B1]
 gi|326565646|gb|EGE15809.1| RluA family pseudouridine synthase [Moraxella catarrhalis 12P80B1]
 gi|326572296|gb|EGE22291.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC8]
 gi|326574310|gb|EGE24257.1| RluA family pseudouridine synthase [Moraxella catarrhalis O35E]
 gi|326574892|gb|EGE24822.1| RluA family pseudouridine synthase [Moraxella catarrhalis 101P30B1]
 gi|326576218|gb|EGE26133.1| RluA family pseudouridine synthase [Moraxella catarrhalis CO72]
          Length = 382

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 58/177 (32%), Gaps = 26/177 (14%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  N   QRV   + AR     R  + ++I    +++NG   + A   +   D + V  
Sbjct: 64  TVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCK-AHDKLYMGDVVRVAP 122

Query: 65  VPLRKAERTRL-------------------WLYHKPIGLVTTHSDPDGRSTV-FDNLPSI 104
           + L   E   +                    + +KP G+       +    +    L   
Sbjct: 123 IRLSVREAPIISEELAKGLLERIIFEDDGLIVLNKPHGMAVHGGSGESFGIIEAMRLAMG 182

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL 158
              +  + R+D +T GLLL+         +     +     + Y     G V  D++
Sbjct: 183 KKYLELIHRIDKDTSGLLLIA-KKRSTLKILQEQFRKKTIQKRYLCLVMGHVQADEM 238


>gi|282849749|ref|ZP_06259133.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
 gi|282580686|gb|EFB86085.1| pseudouridine synthase, RluA family [Veillonella parvula ATCC
           17745]
          Length = 372

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/142 (18%), Positives = 50/142 (35%), Gaps = 18/142 (12%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLR-----KAERTRLWLYHK 80
           ++  ++ + +NG         +   D I       ++D  P+        E T L +  K
Sbjct: 85  KLFEEKLIHINGHKAT-PKDTISEGDEIWIAMAKEKIDHDPIEMDLRILYEDTDLLIVDK 143

Query: 81  PIGLVTTHSDPDGRST-VFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG--GLARVLE 135
           P GL     D    +  V           +V  + RLD +T G +++   G        +
Sbjct: 144 PCGLTVNSKDQVSLANGVAHYFKEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQSLYQQQ 203

Query: 136 LPSTQWLRVYRVRFHGQVDQDK 157
           +    + + Y     G V+ D+
Sbjct: 204 MDDNTFEKWYMATVEGIVEADE 225


>gi|330829706|ref|YP_004392658.1| 23S rRNA pseudouridylate synthase C [Aeromonas veronii B565]
 gi|328804842|gb|AEB50041.1| 23S rRNA pseudouridylate synthase C [Aeromonas veronii B565]
          Length = 327

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/210 (16%), Positives = 68/210 (32%), Gaps = 45/210 (21%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----------------- 75
           R++ +  V+VN   ++     + + D + V   P+R AE+  L                 
Sbjct: 53  RILRKGEVRVNKKRIK-PEYKLCAGDEVRV--PPVRVAEKNELPSANLGVIQRLESQILF 109

Query: 76  -----WLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
                 + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 110 EDDAMIVLNKPSGMAVHGGSGLSFGVIEGLRALRPEARFLELVHRLDRDTSGVLLVA-KK 168

Query: 129 GLARVLELPSTQWL---RVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT-QKG 184
             A        +     + Y     G+  Q  + ++   +    +  G+  V +    K 
Sbjct: 169 RSALRSLHEQLRVKTMRKQYLALVRGKW-QAHVKVVNAPLRKNDLQSGERVVRVSADGKP 227

Query: 185 SNAWVTV-------GLRE-----GKNREIK 202
           S     +        L E     G+  +I+
Sbjct: 228 SETRFRIVRQFAEATLVECSPITGRTHQIR 257


>gi|319762713|ref|YP_004126650.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
 gi|317117274|gb|ADU99762.1| pseudouridine synthase [Alicycliphilus denitrificans BC]
          Length = 282

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 45/154 (29%), Gaps = 21/154 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   +     + R  V      I   V  V RLD  T G+L++   
Sbjct: 40  QDEHMVALYKPAGWLVHRTGLDAGETRFVVQALRDQIGRHVYPVHRLDKGTCGVLVMGLH 99

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
              AR L          + Y     G           +  D             +     
Sbjct: 100 PAAARALAGSFARHAVHKRYLALVRGWAPPLADVDHPLRPDDAPQDAPAQPAHTLLTRLA 159

Query: 176 QVTLDTQKGS---NAWVTVGLRE---GKNREIKK 203
           ++ L             ++ L E   G+  +I++
Sbjct: 160 RLELPESSDPRFATTRASLVLAEPTTGRRHQIRR 193


>gi|311067404|ref|YP_003972327.1| putative RNA pseudouridine synthase [Bacillus atrophaeus 1942]
 gi|310867921|gb|ADP31396.1| putative RNA pseudouridine synthase [Bacillus atrophaeus 1942]
          Length = 303

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 39/250 (15%), Positives = 82/250 (32%), Gaps = 41/250 (16%)

Query: 1   MKDKNIVQENFTPQRVS-KVIARAGI----ASRREVERMIAQQRVKVNGILLERAAVNVM 55
           MK K    E    +++  + +         AS+  ++  +  + +KVN          V 
Sbjct: 1   MKQKGRGLELMITEKLDGQWLFSVLKTEVKASKPVIQEWMTTKSIKVNHEPAVH-NFIVK 59

Query: 56  STDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
             D + +D             G      E + + + +KP G+ T  ++     T+ + + 
Sbjct: 60  KGDRLFIDLQEKAESNVIPEYGEIEILFEDSHMLIVNKPAGMPTHPNEEGQTGTLANLIA 119

Query: 103 SIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE---LPSTQWLRVYRVRFHG-- 151
                     +V  V RLD++T G ++      LA  +    L   +  R Y     G  
Sbjct: 120 YHLQANGEQTKVRHVHRLDLDTSGAVVFAKH-RLAHAILDQQLEKKELKRTYIALAEGKL 178

Query: 152 ---------QVDQDKLNLLKKGIVIQGICYGDM-QVTLDTQKGSNAWVTVGLREGKNREI 201
                     + +D+ +  ++ +   G       +V     K   +   + L  G+  +I
Sbjct: 179 KPKKGTIDSPIGRDRSHPTRRRVSPGGQAAVTHFRVKGYHPKAGLSLAELELETGRTHQI 238

Query: 202 KKVFEFFNWK 211
           +         
Sbjct: 239 RVHMASIGHP 248


>gi|16125573|ref|NP_420137.1| hemolysin A [Caulobacter crescentus CB15]
 gi|13422669|gb|AAK23305.1| hemolysin A [Caulobacter crescentus CB15]
          Length = 243

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 10/51 (19%), Positives = 22/51 (43%), Gaps = 1/51 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +R+ +++   G+  SR +    I   RV V G ++ + +  V     +
Sbjct: 1  MARKRIDQLLVDRGVFDSRAKARAAIEAGRVSVAGRVVAKPSEQVDDNAEV 51


>gi|294497498|ref|YP_003561198.1| pseudouridine synthase, RluA family [Bacillus megaterium QM B1551]
 gi|294347435|gb|ADE67764.1| pseudouridine synthase, RluA family [Bacillus megaterium QM B1551]
          Length = 302

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 69/199 (34%), Gaps = 34/199 (17%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEV-------------DGVPLR-KAERTRLWLYHKP 81
               ++VNG         +   D I+V               +PL    E   + + +K 
Sbjct: 40  RGGAIEVNGKHAT-VRYILQKGDEIKVAFPPEKASESLLPRAIPLDIVYEDEYILVLNKQ 98

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + +  S      ++ + +   +        V  V RLD +T GLL++     +  +  
Sbjct: 99  PNMPSIPSREHLTWSLSNAVLYYYEENNINSTVHLVNRLDRDTSGLLIVAKHRHVHYLFS 158

Query: 136 LPSTQWL--RVYRVRFHGQ-VDQDKLNL---------LKKGIVIQGICYGDMQVTLDTQK 183
               +    RVYR   HG+ V ++ +           +++ +  +   +     T   Q 
Sbjct: 159 KAQKEHEIKRVYRAFVHGKLVGKETIEAPIGRKESSIIEREVR-EDGQFAITHYTALRQY 217

Query: 184 GSNAWVTVGLREGKNREIK 202
            S   V + L  G+  +I+
Sbjct: 218 SSFTEVALSLETGRTHQIR 236


>gi|261885552|ref|ZP_06009591.1| pseudouridine synthase [Campylobacter fetus subsp. venerealis str.
           Azul-94]
          Length = 155

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/144 (18%), Positives = 51/144 (35%), Gaps = 17/144 (11%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGI--LLERAAVNVMSTDHIEVDGVPLRKAERTRL 75
           K++A     S  E + +I    V   G   +L R  +N  ++  +     P+   E   +
Sbjct: 8   KLLALQEGISNNEAKELIDSGLVSAGGKRLVLARGLLNENTSFKVTKLAKPVMIYEDDNI 67

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE 135
              +KP   +T+         V +           + RLD  T G++LL  +    +   
Sbjct: 68  VAVNKPP-FITSEK-------VAEIFKFPL-----LNRLDKETSGVILLYKNEEFQKAAI 114

Query: 136 LP--STQWLRVYRVRFHGQVDQDK 157
               +T+  + Y     G V  + 
Sbjct: 115 KEFANTKVKKTYLAIVRGIVVDEF 138


>gi|260654932|ref|ZP_05860420.1| ribosomal large subunit pseudouridine synthase D [Jonquetella
           anthropi E3_33 E1]
 gi|260630247|gb|EEX48441.1| ribosomal large subunit pseudouridine synthase D [Jonquetella
           anthropi E3_33 E1]
          Length = 301

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 82/238 (34%), Gaps = 44/238 (18%)

Query: 2   KDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVK-VNGILLERAAVNVMSTDHI 60
             + +V+ +    R+   ++     SR  V R+I+   V  V G +  +A+  V+S D  
Sbjct: 3   SRRIVVEPSDAGNRLDLYLSGQLELSRSAVGRLISGGLVSGV-GKV--KASRVVVSGDWF 59

Query: 61  EV--------DGVPLRKAERTRL---WL--YHKPIGLVTTHSDPDGRSTV-------FDN 100
           +V          VP     RT     WL    K  G+           T+       F  
Sbjct: 60  DVSMPEPSEESVVPQDVPFRTVYADDWLAVVEKLAGIAVHPGAGRKDGTLVNGLVKTFGP 119

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
           LP    R   V RLDI T GL+++         L+      +  + Y    HG +   + 
Sbjct: 120 LPGAGLRPGIVHRLDIGTSGLMVVARTPQAYLFLQREFSQRRVEKTYLALVHGWIPASQG 179

Query: 159 -----------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG---LREGKNREIK 202
                      + LK  +   G        TL T+      +++    +  G+  +I+
Sbjct: 180 TLDGPIGRSRYDRLKMAVRADGRRAVTRYRTLWTRGS----LSLTACRIETGRTHQIR 233


>gi|259483290|tpe|CBF78558.1| TPA: DRAP deaminase (Rib2), putative (AFU_orthologue; AFUA_2G16360)
           [Aspergillus nidulans FGSC A4]
          Length = 572

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/142 (17%), Positives = 46/142 (32%), Gaps = 16/142 (11%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPL-RKAERTRLWLYHKP 81
           ++ +    V VNG         + + + I          V G  +    E   L +  KP
Sbjct: 82  KKALESGNVCVNGKPA-GPHTVLKNGEVISHTLHRHEPPVTGNEIGIIHETDDLLVIDKP 140

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLL--TNDGGLARVLEL 136
            G+    +     ++V + L              RLD  T G++ +  T  G     ++L
Sbjct: 141 AGVPVHSTGRYHYNSVMEILRIQNGGAYVPRPCNRLDRLTSGVMFVGKTAQGADRMTVKL 200

Query: 137 PSTQWLRVYRVRFHGQVDQDKL 158
                 + Y  R  G+     +
Sbjct: 201 KERTVQKEYVARVKGRFPDGVV 222


>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 = 50.6 bits (120), Expect = 4e-04,   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|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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/85 (25%), Positives = 35/85 (41%), Gaps = 10/85 (11%)

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--------PLRKAERTRLWL 77
            + G          + K ER R+ L
Sbjct: 231 AIRGKGRLQVGDVSITKKERYRIQL 255


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/161 (14%), Positives = 56/161 (34%), Gaps = 21/161 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP G+    S  + R+++ + L   +             RLD +T GL ++
Sbjct: 95  EDEDIIVINKPAGMPIHPSQNNYRNSLANALAWYYQEQGKAFVFRCANRLDRDTSGLTVV 154

Query: 125 TNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN-----------LLKKGIVIQGIC 171
           +       VL          R Y     G +                 ++++ +  +   
Sbjct: 155 SKHMLSGNVLSSMAADRMLHREYLAICRGHITPSAGTIHAPLSRKPGSIIERTVDWEQGE 214

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
                  +  +K  ++ V++ L  G+  +I+  + +   + 
Sbjct: 215 TAITHYCVVDEKNGHSLVSLRLETGRTHQIRIHM-KHLGYP 254


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           ++  ++  AG+  +  E + ++    VKVNG +         + D IE+DG  +   +
Sbjct: 11 IKLDALLKYAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDVIELDGQTVEVGQ 69


>gi|255973763|ref|ZP_05424349.1| pseudouridine synthase [Enterococcus faecalis T2]
 gi|255966635|gb|EET97257.1| pseudouridine synthase [Enterococcus faecalis T2]
          Length = 287

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/215 (17%), Positives = 74/215 (34%), Gaps = 48/215 (22%)

Query: 29  REVERMIA-QQRVKVNGILLE---------------------RAAVNVMSTDHIEVDGVP 66
           R+V   +  ++ VK+NG                         R  +++  T  ++V    
Sbjct: 28  RKVRHFLRTRKNVKINGETAAFHFPVQAGDCVTLTFEETDYVRPTIHLGETTRVKV---- 83

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLL 122
               E   L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G +
Sbjct: 84  --LYEDEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAI 141

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VI 167
           +   +  +  +L   L + Q  R Y+    G  +Q +   + + I               
Sbjct: 142 VFAKNPFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQ 200

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +G         +     +   VT  L  G+  +I+
Sbjct: 201 KGDSAITHVQVVQALSNNQTAVTCVLETGRTHQIR 235


>gi|251783426|ref|YP_002997731.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
 gi|242392058|dbj|BAH82517.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           dysgalactiae subsp. equisimilis GGS_124]
          Length = 341

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/205 (18%), Positives = 74/205 (36%), Gaps = 32/205 (15%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VD-----GVPLR---------KAE 71
           R++   +  ++ V VNG  +   +  V S D +E   D       P+            E
Sbjct: 74  RKIRHFLRTKKNVLVNGSAITWQSA-VNSGDQVELFFDEEDYPDKPIMMGQANKVDCLYE 132

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  ++P   + +             V RLD+ T G+++      + 
Sbjct: 133 DDHLIIVNKPEGMKTHGNEPTELALLNHVSAYTGRTCYVVHRLDMETSGVIVFAKTPFIL 192

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
            +L   L   +  R Y    HG +   ++           +  K+ + ++        V 
Sbjct: 193 PILNRLLEKREISRDYWALVHGTLSSKEVSYREPIGRHRHDRRKRVVDVKQGQKAVTDVK 252

Query: 179 LDTQKGSN-AWVTVGLREGKNREIK 202
           L      N + +   L+ G+  +I+
Sbjct: 253 LLKSFKQNVSLINCRLQTGRTHQIR 277


>gi|291326503|ref|ZP_06124794.2| pseudouridine synthase A [Providencia rettgeri DSM 1131]
 gi|291313961|gb|EFE54414.1| pseudouridine synthase A [Providencia rettgeri DSM 1131]
          Length = 217

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 61/164 (37%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++     P+   ++   +   F    SV RLD+ T G++++     
Sbjct: 18  QDDHIIVVNKPSGLLSVPGKAPEHHDSIMSRVQRDFPAAESVHRLDMATSGVMVVALHKK 77

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVTLDTQ 182
             R L+    +    + Y  R  G ++++      +G+V    I         +V  +T 
Sbjct: 78  AERELKRQFREREPKKFYIARVWGHLEKE------EGLVDLPLICDWPNRPKQKVCFETG 131

Query: 183 KGSNAWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
           K +     V   E            G++ +++  +       + 
Sbjct: 132 KSAQTEYQVLQYEEQATRVKLSPITGRSHQLRVHML-ALGHPIL 174


>gi|254449188|ref|ZP_05062638.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
 gi|198261234|gb|EDY85529.1| ribosomal large subunit pseudouridine synthase A [gamma
           proteobacterium HTCC5015]
          Length = 217

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 55/167 (32%), Gaps = 23/167 (13%)

Query: 66  PLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL 124
            +   +   L++  KP GL++     P  R +V   L   F     V RLD++T G++++
Sbjct: 14  RILYQDEHCLFI-DKPSGLLSVPGRHPANRDSVASRLQQDFPEAHIVHRLDMDTSGVMVI 72

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDK---------------LNLLKKGIVI 167
             +    R L       +  + Y          ++               L  +     I
Sbjct: 73  ALNVESHRFLSRQFQERRSQKRYEAIVSATPTPEQGSVDLPLICDWPNRPLQKVDH--EI 130

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
                   + T   Q G+   V +    G++ +++  +       + 
Sbjct: 131 GKPSLTHYETTGPWQDGAGTRVVLTPHTGRSHQLRVHM-AAIGCPIL 176


>gi|163751081|ref|ZP_02158312.1| RluC [Shewanella benthica KT99]
 gi|161329242|gb|EDQ00241.1| RluC [Shewanella benthica KT99]
          Length = 319

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 76/254 (29%), Gaps = 56/254 (22%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            + E+   QR+   +         SR  + R++ +  V+VN   ++     +   D + +
Sbjct: 14  TIDEDHLGQRIDNYLMTKLKGVPKSR--IYRIVRKGEVRVNKKRIK-PEYKLQDGDIVRI 70

Query: 63  DGVPLRKA----------------------ERTRLWLYHKPIGLVTTHSD--PDGRSTVF 98
             V +                         E   + + +KP G+          G     
Sbjct: 71  PPVRVSDKSDRPGPSAKLTKVSQLEDRIVFEDKFIIVLNKPSGIAVHGGSGVDFGVIEAM 130

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS--TQWLRVYRVRFHGQVD-- 154
             L      +  V RLD +T G+LL+       R L       +  + Y+    G     
Sbjct: 131 RALRPTQKFLELVHRLDKDTSGVLLIAKKRSALRHLHDQLRFKKMQKDYQALVKGTWQAR 190

Query: 155 QDKLNL------LKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKN 198
              +        LK G     +  +G         L   +G+       L +     G+ 
Sbjct: 191 DKVIKAPLLKLTLKSGERIVRVNQEGKECETRFKILQRYQGA------TLVQASPVTGRT 244

Query: 199 REIKKVFEFFNWKV 212
            +I+   ++    +
Sbjct: 245 HQIRVHCQYAGHPI 258


>gi|160916027|ref|ZP_02078235.1| hypothetical protein EUBDOL_02055 [Eubacterium dolichum DSM 3991]
 gi|158432503|gb|EDP10792.1| hypothetical protein EUBDOL_02055 [Eubacterium dolichum DSM 3991]
          Length = 317

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 32/207 (15%), Positives = 71/207 (34%), Gaps = 34/207 (16%)

Query: 29  REVERMIAQQ-RVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL------------ 75
           +++++ + Q  R++VN   +      +   D I +   P    E+  +            
Sbjct: 40  KKMQKQLYQGQRIQVNQQTI-LHNTPLQRKDLIRIQPFPQYDLEKHLIPCFDPLSILYED 98

Query: 76  ---WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTN 126
               + +KP  ++      +  +T++D +   +        V ++ RLD  T G ++   
Sbjct: 99  DLFLIVYKPSFMLVHSDGNETETTLYDIVKGYYLLQGLDIPVRAIHRLDKETSGAVIFCK 158

Query: 127 DGGLARVL--ELPSTQWLRVYRVRFHGQVDQD---------KLNLLKKGIVIQGICYGDM 175
              L  +L   L   Q  R Y       ++ D           +  KK  + +       
Sbjct: 159 IPLLQPLLDYMLQEKQIDRQYLALCAKVLNDDLTIDKQIGRDRHNAKKMRISKQGKSAKT 218

Query: 176 QVTLDTQKGSNAWVTVGLREGKNREIK 202
            V +  Q      +   L +G+  +I+
Sbjct: 219 DVHVIAQYQDYTLIACKLYQGRTHQIR 245


>gi|72162433|ref|YP_290090.1| hemolysin A [Thermobifida fusca YX]
 gi|71916165|gb|AAZ56067.1| hemolysin A [Thermobifida fusca YX]
          Length = 266

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/67 (29%), Positives = 28/67 (41%), Gaps = 4/67 (5%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---DGVPLRKA 70
          R+   + R G A SR     +IA  RV+V G L  +AA  V     I V   D  P+  +
Sbjct: 6  RLDAELVRRGHARSRAHAAELIAAGRVRVAGTLATKAATQVGVDQAIVVEQADDEPVYVS 65

Query: 71 ERTRLWL 77
                +
Sbjct: 66 RGAYKLI 72


>gi|315633348|ref|ZP_07888639.1| pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
 gi|315477848|gb|EFU68589.1| pseudouridine synthase A [Aggregatibacter segnis ATCC 33393]
          Length = 219

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/162 (15%), Positives = 52/162 (32%), Gaps = 29/162 (17%)

Query: 74  RLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
            + + +KP GL++   + P    +    +   +       RLD+ T G+LL        R
Sbjct: 22  YIAVVNKPSGLLSVPGNQPQYYDSAMSRVKEKYGFCEPAHRLDMATSGILLFALSKAADR 81

Query: 133 VLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQVT-------- 178
            L+    +    + Y+    G V+QD       G+V    I        Q          
Sbjct: 82  ELKRQFREREPKKYYQALVWGHVEQD------HGVVELPLICDWENRPRQKICFERGKRA 135

Query: 179 ------LDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVN 213
                 L     +   + +  +  G++ +++         + 
Sbjct: 136 VTFYDVLQRYPNNTTRIKLTPIT-GRSHQLRLHMLALGHPIL 176


>gi|239826305|ref|YP_002948929.1| pseudouridine synthase [Geobacillus sp. WCH70]
 gi|239806598|gb|ACS23663.1| pseudouridine synthase, RluA family [Geobacillus sp. WCH70]
          Length = 298

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/222 (16%), Positives = 76/222 (34%), Gaps = 33/222 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP  + T  S      T+ + L   + +      +  V RLD +T GL+L+
Sbjct: 87  EDEYVLVVNKPPFMATIPSREHPGGTLANALLYHYKKQQLESTIHVVTRLDRDTSGLVLV 146

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLNL---------LKKGIVIQGIC 171
                +  +L       +  R Y    HG +  D+  ++          +++ +   G  
Sbjct: 147 AKHRHVHHLLSTLQQQGKVTRCYEAICHGCLVEDEGTIDAPIARKSDSIIEREVRKDGQR 206

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  L   +    +V++ L  G+  +I+                   P     L  G
Sbjct: 207 AVTHFRVLQRFREYT-YVSLRLETGRTHQIRVHLAHIGH-----------PLAGDELYGG 254

Query: 232 STREVSKKIL--REQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
           S   +S++ L  +E    H ++        P+      + +R
Sbjct: 255 SREAISRQALHSKELSFFHPIKRKIYTFSCPLPDDMKQLMER 296


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   GI  SR + +  I + +V V+G  +++A   V    +IE  G  L+   R
Sbjct: 6  ERLDILLVEKGIITSRDKAKACIMEGKVFVDGQRVDKAGEKVSVIANIEYKGAKLKYVSR 65

Query: 73 TRLWLYHKPIGLVTTHSDP 91
            L L         +  D 
Sbjct: 66 GGLKLEKAMKSYDISLEDK 84


>gi|188989643|ref|YP_001901653.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. B100]
 gi|167731403|emb|CAP49578.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris]
          Length = 258

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/158 (18%), Positives = 51/158 (32%), Gaps = 31/158 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   L +  KP GL+   S         + D L     R +  V RLD  T G LLL  D
Sbjct: 25  QDAVLAVVDKPAGLMVHDSKLARGEDDFLADRLRVQLGRPIFLVHRLDRATSGCLLLAFD 84

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QK 183
              A  L   L + +  + Y     G   ++          + G     ++    T  Q+
Sbjct: 85  RDTASALGKALMAGEVEKDYLAICRGWPAEE---RFIVDHDLDGGPGKPIKKPAVTHFQR 141

Query: 184 GSNAWVTV------------------GLREGKNREIKK 203
            +   + +                      G+ R+I++
Sbjct: 142 LATGELEIPSTGFATSRYALLRCQPQT---GRFRQIRR 176


>gi|103487227|ref|YP_616788.1| pseudouridine synthase, RluD [Sphingopyxis alaskensis RB2256]
 gi|98977304|gb|ABF53455.1| ribosomal large subunit pseudouridine synthase D [Sphingopyxis
           alaskensis RB2256]
          Length = 376

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 81/250 (32%), Gaps = 49/250 (19%)

Query: 6   IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVN--GILLERAAVNVMSTDHIEV 62
            + +     R+ + +A A    SR  ++ +I   RV V+  G +L   A        IE+
Sbjct: 69  TLGDTAAGLRLDRALAEALPNLSRERLKSLIKGGRV-VDAHGAILWDPAAKAAPPATIEI 127

Query: 63  -------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRST-VFDNLPSIFSRV 108
                        D   +   E   L +  KP G+V   +  +   T V   L     ++
Sbjct: 128 RVPAALPAHNAAQDLDLVIAYEDAHLIVIDKPAGMVVHPAAGNLDGTMVNALLHHCAGQL 187

Query: 109 ISVG---------RLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV---- 153
             +G         R+D +T GL++          L     +    R Y     G+     
Sbjct: 188 SGIGGVARPGIVHRIDKDTSGLIVAAKHDKAHEGLAKQFAAHSIDRRYLAIATGRPMPAN 247

Query: 154 ------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
                       ++ K+ ++  G   +G        T++  +G+   +   L  G+  ++
Sbjct: 248 GTVDAALGRSATNRKKMAVVAAG---RGKHALTHYRTVEPLQGAT-LIECRLETGRTHQV 303

Query: 202 KKVFEFFNWK 211
           +         
Sbjct: 304 RVHMAHIGHP 313


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+  ++   G   SR +  R I    V V+   +++    V     I V G PL    R
Sbjct: 4  RIDVLLVDMGFFPSREQARRTIMAGNVFVDNQRVDKPGTMVKDDSEILVKGKPLAYVSR 62


>gi|195578233|ref|XP_002078970.1| GD22253 [Drosophila simulans]
 gi|194190979|gb|EDX04555.1| GD22253 [Drosophila simulans]
          Length = 555

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 53/307 (17%), Positives = 108/307 (35%), Gaps = 46/307 (14%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P++       + + +KP 
Sbjct: 149 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPIKIVHMDEDIVVVNKPA 208

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 209 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 268

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG------ 192
            Q  + Y  R  G      +   K+ I +     G  +V+   +  +  +  +       
Sbjct: 269 RQVEKEYICRVEGVFPDGIVE-CKEPIEVVSYKIGVCKVSPKGKDCTTTFQKLSQNGTTS 327

Query: 193 ------LREGKNREIKKVFEFFNWKVNR--L--IRISYGPF--QLGTLLAGSTREVSKKI 240
                 L  G+  +I+   ++  + +    L    + +GP   + G +  G +    +++
Sbjct: 328 VVLCKPLT-GRMHQIRVHLQYLGYPILNDPLYNHEV-FGPLKGRSGDIG-GKS---DEEL 381

Query: 241 LREQLGPHLLEE---AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQKNGLSK 297
           +R+ +  H  E       + D  ++ S     DR ++ SE          + S  +G + 
Sbjct: 382 IRDLINIHNAENWLGIDCDSDISMFKSTKDEADRESLSSEHTSVV-----HHSDDDGCAN 436

Query: 298 QKKLATP 304
            ++   P
Sbjct: 437 SRETTPP 443


>gi|261868551|ref|YP_003256473.1| 23S rRNA pseudouridylate synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413883|gb|ACX83254.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 319

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 81/249 (32%), Gaps = 49/249 (19%)

Query: 1   MKDKNI--------VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-------- 43
           M +K I        V ++   QR+   + AR     +  + R++ +  V+VN        
Sbjct: 1   MSEKTINPSVQFLTVSDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKARSKPEY 60

Query: 44  ----GILLERAAVNVMSTDHIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDP 91
                 ++    V V       +     + A        E   L + +KP G+       
Sbjct: 61  KLLADDVVRIPPVRVAEKAQDTISNKLTKVAQLEQHIIFEDNYLLVLNKPSGIAVHGGSG 120

Query: 92  DGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV 147
                +     L      +  V RLD +T G+LL+       R L   L      + Y  
Sbjct: 121 LDFGVIEALRALRPAARFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLA 180

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------ 195
              GQ  Q    +++  + ++    G  ++   +++G  +     + E            
Sbjct: 181 LVRGQW-QSHCKVVQAPL-LKNELAGGERIVKVSEQGKPSETRFSVEERYTNATLIKASP 238

Query: 196 --GKNREIK 202
             G+  +I+
Sbjct: 239 VTGRTHQIR 247


>gi|229132186|ref|ZP_04261043.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
 gi|228651234|gb|EEL07212.1| Pseudouridine synthase [Bacillus cereus BDRD-ST196]
          Length = 307

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +K   + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELNVVFEDDHVLIVNKQGQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+ +G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKNGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDKAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
              VT+ L  G+  +I+
Sbjct: 225 ATLVTLQLETGRTHQIR 241


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++ + G+A SR + + +I    V V+G   ++A   V     IE+ G  L+   R
Sbjct: 3  ERLDVLLVKKGLAASREKAKAIIMSGVVFVDGQREDKAGTMVKEELPIEIKGKTLKYVSR 62


>gi|42780479|ref|NP_977726.1| ribosomal large subunit pseudouridine synthase D [Bacillus cereus
           ATCC 10987]
 gi|42736398|gb|AAS40334.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Bacillus cereus ATCC 10987]
          Length = 307

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 48/265 (18%), Positives = 93/265 (35%), Gaps = 51/265 (19%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   + ++V              G      E   + + +KP  + T
Sbjct: 47  VTVNGEQ-RRWNELLKEDEKLQVHMFMEEEYGVEPEYGELDVVYEDDHVLIVNKPEKMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             ++  G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPAEKGGMGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQ- 244
              VT+ L  G+  +I+      +   N        P     L  G T+ +S++ L    
Sbjct: 225 VTLVTLQLETGRTHQIR-----VHMSYNG------NPLVGDILYGGGTKYMSRQALHAMK 273

Query: 245 ---LGPHLLEEAQVNLDAPIYSSET 266
              L P   EE +V++  P   ++T
Sbjct: 274 INFLHPITKEEIEVDVPFPTKLNDT 298


>gi|68482658|ref|XP_714726.1| hypothetical protein CaO19.10687 [Candida albicans SC5314]
 gi|68482929|ref|XP_714595.1| hypothetical protein CaO19.3177 [Candida albicans SC5314]
 gi|46436176|gb|EAK95543.1| hypothetical protein CaO19.3177 [Candida albicans SC5314]
 gi|46436316|gb|EAK95680.1| hypothetical protein CaO19.10687 [Candida albicans SC5314]
          Length = 589

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/137 (18%), Positives = 45/137 (32%), Gaps = 14/137 (10%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           + +  VKVN  +       + + D I          V    ++   E   L +  KP G+
Sbjct: 131 VEEGLVKVNSQVA-NLETILRNGDLISHRSYRREPPVSSRDIKIVFEDDDLLVIDKPGGI 189

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
               +     +TV         ++     RLD  T GL+ L      A  +         
Sbjct: 190 PVHPTGRYRYNTVTKIFEHEKGKIVHPCNRLDRLTSGLMFLGKSSKGANNMMSQIRDRNV 249

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y  R  G+   D++
Sbjct: 250 TKEYIARVKGEFPLDRI 266


>gi|262039482|ref|ZP_06012784.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
 gi|261746463|gb|EEY34000.1| ribosomal large subunit pseudouridine synthase D [Leptotrichia
           goodfellowii F0264]
          Length = 293

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 87/252 (34%), Gaps = 54/252 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERMIAQQR------VKVNGILLE------ 48
           MK K  +++ +   ++S+ +        REV+      R      V +NG  +       
Sbjct: 1   MK-KFKLEKQYQRMKISQYL--------REVQNY--SGRSLRNVEVFLNGKQVRTTKKLP 49

Query: 49  -RAAVNVMSTDHIEVDGVPLRKAERTRL-----WLYHKPIGLVTTHSDPDGRSTVFDNLP 102
               + V+  +    D  P++             + +K   L+T  +      T+ + + 
Sbjct: 50  SSGTLRVIEKEKGT-DIKPIKLDLDIVYEDDDLLVVNKEPFLLTHPTQKKADFTLANGIV 108

Query: 103 SIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQ 155
             F              RLD+NT GL+++  +   A+      + + + Y     G ++ 
Sbjct: 109 YYFKEKYEKETVPRFYNRLDMNTSGLIIIAKN-SFAQAFLQNFSNFEKKYLAIVDGIMET 167

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT---------VGLRE-----GKNREI 201
           D+  +++K I   G      ++  +  + +   V          V L E     G+  +I
Sbjct: 168 DEEIVIEKPIYRDGDKL--ERIIDERGQYAKTIVKPLKKYPEKNVTLAECELFTGRTHQI 225

Query: 202 KKVFEFFNWKVN 213
           +   +     + 
Sbjct: 226 RVHLKSVGHTIV 237


>gi|326773128|ref|ZP_08232411.1| cytotoxin/hemolysin [Actinomyces viscosus C505]
 gi|326636358|gb|EGE37261.1| cytotoxin/hemolysin [Actinomyces viscosus C505]
          Length = 290

 Score = 50.6 bits (120), 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+   + R G+A SR     +IA   V ++G ++ + A  V     IE+
Sbjct: 5  IRIDSELVRRGLARSRTHAATLIADGHVTLDGEVVTKPARQVNPAQAIEI 54


>gi|284007272|emb|CBA72588.1| 23S rRNA pseudouridylate synthase C [Arsenophonus nasoniae]
          Length = 315

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/213 (15%), Positives = 70/213 (32%), Gaps = 50/213 (23%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKAERTR----------------- 74
           R+I +  V++N G +  +    + + D I +   P+R+AE+ +                 
Sbjct: 39  RIIRKGEVRINSGRI--KPEYKIQAGDLIRI--PPVRQAEKQQTVISAKLDKVAALSDCI 94

Query: 75  ------LWLYHKPIGLVTTHSDPDGRSTV--FDNLPSIFSRVISVGRLDINTEGLLLLTN 126
                 L + +KP G+            +     L      +  V RLD  T G+LL+  
Sbjct: 95  LYEDDHLLVLNKPSGMAVHGGSGVNFGIIEALRILRPEARFLELVHRLDRETSGVLLIA- 153

Query: 127 DGGLARVLELPS---TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
               A  +        Q  + Y     GQ     + +++  + ++ I     ++      
Sbjct: 154 KKRSALRVLHQQLRLKQMQKQYLALVKGQWP-SHIKVIQAPL-LKNILQSGERIVKVGTD 211

Query: 184 GSNAWVTVGLRE--------------GKNREIK 202
           G  +     + E              G+  +I+
Sbjct: 212 GKYSETHFKIEERFSNATLVKASPITGRTHQIR 244


>gi|170726105|ref|YP_001760131.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169811452|gb|ACA86036.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 219

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/167 (16%), Positives = 56/167 (33%), Gaps = 28/167 (16%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +R  +R  + + +KP GL++      +        L   +   I V RLD  T G+++  
Sbjct: 16  IRYQDRD-MIVINKPSGLLSNPGRAENTFDCALTRLLQRYPETILVHRLDCATSGIMVFA 74

Query: 126 -NDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNLLKKGIVIQ-----GICYGDMQVT 178
            N    + +      +   + Y     G +D+       +G+ I+           +Q  
Sbjct: 75  LNKKAESNIKTQFQNRLSKKTYIAEVQGHLDK------TEGV-IELAMKADSERPPLQKI 127

Query: 179 LDTQKGSNAWVTV-------GLRE-----GKNREIKKVFEFFNWKVN 213
            +  K S  +  V        L E     G+  +++         + 
Sbjct: 128 AEDGKPSKTYYKVLEKRENSTLVELNPVTGRTHQLRLHMLAIGHPIL 174


>gi|157372174|ref|YP_001480163.1| pseudouridine synthase [Serratia proteamaculans 568]
 gi|157323938|gb|ABV43035.1| pseudouridine synthase [Serratia proteamaculans 568]
          Length = 232

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 33/193 (17%), Positives = 63/193 (32%), Gaps = 41/193 (21%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L +KP GL++ +  +P    +V   L   F     + RLD  T GL+++  +  
Sbjct: 22  QDESLVLINKPTGLLSLSGKNPQNLDSVHHRLVQQFPGCTLIHRLDFGTSGLMVIARNKA 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM-----QVTLDTQ 182
           +   L    +Q    +VY     G +  +      +G++   I           +     
Sbjct: 82  INAALCQQFSQRTVTKVYSALLCGHLADN------EGVIDAAIAKDPALFPLMSICAIHG 135

Query: 183 KGSNAWVTVG---LRE------------------GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V      E                  G+  +++   +     +       YG
Sbjct: 136 KPARSGYQVIERFYHELEDGTSLPLTRVQLTPETGRTHQLRIHCQQLGHPILGCD--LYG 193

Query: 222 PFQLGTLLAGSTR 234
                 LL G+ R
Sbjct: 194 GL----LLPGTER 202


>gi|326567130|gb|EGE17252.1| RluA family pseudouridine synthase [Moraxella catarrhalis BC1]
          Length = 382

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 58/177 (32%), Gaps = 26/177 (14%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  N   QRV   + AR     R  + ++I    +++NG   + A   +   D + V  
Sbjct: 64  TVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCK-AHDKLYMGDVVRVAP 122

Query: 65  VPLRKAERTRL-------------------WLYHKPIGLVTTHSDPDGRSTV-FDNLPSI 104
           + L   E   +                    + +KP G+       +    +    L   
Sbjct: 123 IRLSVREAPIISEELAKGLLERIIFEDDGLIVLNKPHGMAVHGGSGESFGIIEAMRLAMG 182

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL 158
              +  + R+D +T GLLL+         +     +     + Y     G V  D++
Sbjct: 183 KKYLELIHRIDKDTSGLLLIA-KKRSTLKILQEQFRKKTIQKRYLCLVMGHVQADEM 238


>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 = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 56/151 (37%), Gaps = 35/151 (23%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+ +++   G  S R++ +  I ++ V VNG ++ + + +V     I V          
Sbjct: 1   MRLDRLLVIKGYFSSRQKAKEAIRRRFVIVNGKVVTKPSYDVDFDVEIRV---------- 50

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
                  KP G          +    D + ++  +   V  L  +  G LL         
Sbjct: 51  ---LQEEKPKGY--------WKLKELDEMWNLIKKDDIVLDLGSSAGGFLLY-------- 91

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKK 163
                S +  RVY + +  +  +DKL  +++
Sbjct: 92  ----ASEKAERVYGIEYSREF-EDKLKEIER 117


>gi|223940477|ref|ZP_03632327.1| pseudouridine synthase [bacterium Ellin514]
 gi|223890839|gb|EEF57350.1| pseudouridine synthase [bacterium Ellin514]
          Length = 536

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 30/154 (19%), Positives = 50/154 (32%), Gaps = 19/154 (12%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEGLL 122
            L   E   L + +KP G+ T    P     +++ L     R  S   V RLD  T G++
Sbjct: 10  RLILFEDEHLLVVNKPAGMNTHAPSPYAGEGIYEWLKHREPRWASLAIVHRLDKETSGVM 69

Query: 123 LLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
           +        R L     +    + Y +     V      ++   + + G  Y    V   
Sbjct: 70  VFGKTTVANRSLTEQFTNHSIRKKYLLLTDKVVSSQTSTMVSCLVRV-GEKYLSRPVHAG 128

Query: 181 TQKGSNAWVTV-------GLRE-----GKNREIK 202
            +K       V        L E     G+  +I+
Sbjct: 129 GEKAETH-FEVITKAEGGTLVEAEPITGRTHQIR 161


>gi|149923941|ref|ZP_01912327.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
 gi|149815173|gb|EDM74722.1| Pseudouridine synthase, RluD [Plesiocystis pacifica SIR-1]
          Length = 324

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 81/263 (30%), Gaps = 60/263 (22%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIA--------SRREVERMIAQQRVKVNGILLER--- 49
           M    ++ E+   QR+ K +  A  A        SR ++ R  A   V++ G  ++    
Sbjct: 1   MSVTLVLGEDAIGQRLDKALVDA-FARSEAHESLSRSQLARAFAAGEVRIAGRKVKASFR 59

Query: 50  ---AAVNVM-------STDHIEVDGVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVF 98
              A V V           H   + +PL    E   L +  KP G+V          T+ 
Sbjct: 60  LEAAGVCVELRVPAPAPLAHARPEAIPLTVVHEDASLLVLDKPAGMVVHAGPGHDSGTLV 119

Query: 99  -----------DNLP----SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
                      D LP    +   R   V RLD +T GL++         VL         
Sbjct: 120 NAVLHHLQVHADALPVLPGNGPERPGVVHRLDKDTSGLIVFARGLRAQTVLAEQFRDHSI 179

Query: 142 LRVYRVRFHGQV-------------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            R Y     G+              D             QG       + +    G++A 
Sbjct: 180 DRAYLGVVLGRPSFERRRLETTHGRDPADRRRFA---PDQGTRRAVTTMEVLRPLGAHAA 236

Query: 189 V-TVGLREGKNREIK---KVFEF 207
           +    L  G+  +I+   ++   
Sbjct: 237 LARFTLETGRTHQIRMHARMVGH 259


>gi|104780776|ref|YP_607274.1| 23S rRNA pseudouridylate synthase [Pseudomonas entomophila L48]
 gi|95109763|emb|CAK14468.1| 23S rRNA pseudouridylate synthase [Pseudomonas entomophila L48]
          Length = 318

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 67/211 (31%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEVDGVPLRKA--------------------E 71
           R++ +  V+VN G +  +    + + D + V  V L +                     E
Sbjct: 43  RILRKGEVRVNKGRI--KPEYKLQAGDIVRVPPVRLPERDEPAPVAQGLLQRLEAAIVYE 100

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 101 DKALIVMNKPAGIAVHGGSGLSFGVIEALRQLRPDAKELELVHRLDRDTSGLLMIAKKRS 160

Query: 130 LARVL--ELPSTQWLRVYRVRFHG--QVDQDKLNL------LKKG-----IVIQGICYGD 174
           + R L   L      + Y     G     + ++N       L+ G     +  +G     
Sbjct: 161 MLRHLHAALRGDGVDKRYMALVRGHWPTSKKQVNAPLQKSNLRSGERMVEVNDEGKEALT 220

Query: 175 MQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           M   L         V    +    G+  +I+
Sbjct: 221 MFRVLRRFGEFATIVEARPIT---GRTHQIR 248


>gi|256854461|ref|ZP_05559825.1| pseudouridine synthase [Enterococcus faecalis T8]
 gi|256710021|gb|EEU25065.1| pseudouridine synthase [Enterococcus faecalis T8]
          Length = 288

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 29  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVFPTIHLGEATRVKVLYE 87

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 88  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 147

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 148 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 206

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 207 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 236


>gi|302880095|ref|YP_003848659.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
 gi|302582884|gb|ADL56895.1| pseudouridine synthase [Gallionella capsiferriformans ES-2]
          Length = 203

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/153 (15%), Positives = 53/153 (34%), Gaps = 14/153 (9%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L + +KP GL++      D +  +   +   F   + V RLD+ T GLL+      + R 
Sbjct: 11  LLVVNKPAGLLSVPGRGEDKQDCLSSRVQEKFPDALIVHRLDMATSGLLVFARGIEMQRQ 70

Query: 134 L--ELPSTQWLRVYRVRFHGQVDQDKLN-LLKKGIVIQGICYGDM----------QVTLD 180
           L     + +  + Y     G++  D+    L  G          +          +  + 
Sbjct: 71  LSAMFHNREVSKRYVAIVAGKLQPDEGEINLSIGADWNERPLRKIDEATGKPSLTRYRVL 130

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +++     V +    G+  +++         + 
Sbjct: 131 SREADTTRVELEPVTGRTHQLRVHMRAIGHPIL 163


>gi|229546507|ref|ZP_04435232.1| pseudouridylate synthase RluD [Enterococcus faecalis TX1322]
 gi|257089108|ref|ZP_05583469.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|229308407|gb|EEN74394.1| pseudouridylate synthase RluD [Enterococcus faecalis TX1322]
 gi|256997920|gb|EEU84440.1| pseudouridine synthase [Enterococcus faecalis CH188]
 gi|323479863|gb|ADX79302.1| pseudouridine synthase, RluA family protein [Enterococcus faecalis
           62]
          Length = 287

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVFPTIHLGEATRVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 235


>gi|117919251|ref|YP_868443.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
 gi|117611583|gb|ABK47037.1| ribosomal large subunit pseudouridine synthase A [Shewanella sp.
           ANA-3]
          Length = 225

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 24/159 (15%), Positives = 58/159 (36%), Gaps = 18/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP    +V+  + +       V RLD+ T G++++     
Sbjct: 19  QDKDIIVVNKPSGLLSVPGRDPAHYDSVYARVKAEHPHCQIVHRLDMATSGVIVVALIRS 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICYGDMQ 176
             R L+      +  + Y  R  G V             D  N  K+ +  +        
Sbjct: 79  AERELKRQFHDRETSKTYLARVAGHVKNTTGSVDYPLICDWPNRPKQKVDHEIGKPSLTH 138

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
             + ++   +  V +  +  G++ +++  +       + 
Sbjct: 139 FEVLSRAKRSTLVKLKPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|238882595|gb|EEQ46233.1| DRAP deaminase [Candida albicans WO-1]
          Length = 589

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/137 (18%), Positives = 45/137 (32%), Gaps = 14/137 (10%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKA-ERTRLWLYHKPIGL 84
           + +  VKVN  +       + + D I          V    ++   E   L +  KP G+
Sbjct: 131 VEEGLVKVNSQVA-NLETILRNGDLISHRSYRREPPVSSRDIKIVFEDDDLLVIDKPGGI 189

Query: 85  VTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVLELP--STQW 141
               +     +TV         ++     RLD  T GL+ L      A  +         
Sbjct: 190 PVHPTGRYRYNTVTKIFEHEKGKIVHPCNRLDRLTSGLMFLGKSSKGANNMMSQIRDRNV 249

Query: 142 LRVYRVRFHGQVDQDKL 158
            + Y  R  G+   D++
Sbjct: 250 TKEYIARVKGEFPLDRI 266


>gi|119774268|ref|YP_927008.1| pseudouridylate synthase [Shewanella amazonensis SB2B]
 gi|119766768|gb|ABL99338.1| tRNA pseudouridine synthase C [Shewanella amazonensis SB2B]
          Length = 258

 Score = 50.6 bits (120), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 27/173 (15%), Positives = 51/173 (29%), Gaps = 33/173 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVF------DNLPSIFSRVISVGRLDINTEGLLLL 124
           E   +   HKP GL+   +    +   F      D +      V  V RLD  T G+LL 
Sbjct: 15  EDEAMVAIHKPAGLLVHRTYLARKEHWFAMQLTRDLVGC---HVFPVHRLDRPTSGVLLF 71

Query: 125 TNDGGLARVLEL--PSTQWLRVYRVRFHGQV-DQDKLN-LLKKGI-VIQGICYGDMQVTL 179
                +A  L     S    + Y     G + D   L+  LK+ +  +        +   
Sbjct: 72  AKSSEVANSLCGQFASHSIRKHYLALVRGNMFDAGVLDYALKEELDELADKDVDPDKPAQ 131

Query: 180 DTQKGSNAWVTVGL-------------------REGKNREIKKVFEFFNWKVN 213
           +        +   +                   + G+  ++++        + 
Sbjct: 132 EAITAYRPLLNSEIPYSSGRYPSSRFALMHLQPQTGRKHQLRRHMAHLRHPIV 184


>gi|227554793|ref|ZP_03984840.1| pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|257077553|ref|ZP_05571914.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294780463|ref|ZP_06745828.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
 gi|227176092|gb|EEI57064.1| pseudouridylate synthase RluD [Enterococcus faecalis HH22]
 gi|256985583|gb|EEU72885.1| pseudouridine synthase [Enterococcus faecalis JH1]
 gi|294452462|gb|EFG20899.1| pseudouridine synthase, RluA family [Enterococcus faecalis PC1.1]
          Length = 287

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 72/210 (34%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G   Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFSQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 235


>gi|221068709|ref|ZP_03544814.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
 gi|220713732|gb|EED69100.1| pseudouridine synthase, RluA family [Comamonas testosteroni KF-1]
          Length = 346

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 50/316 (15%), Positives = 99/316 (31%), Gaps = 73/316 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIE--- 61
           V E+   QR+   + R      +  V R+I    V++N G +   A   V   D +    
Sbjct: 39  VDEDSAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRINKGRV--SAETRVQPGDVVRLPP 96

Query: 62  --VDGVPLRKAERT-------------RLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
             +      KAER               +    KP G+        G S V   +     
Sbjct: 97  VRISDKVAEKAERPAPAKDFPALLDDEHMLALSKPAGVAV-----HGGSGVSFGVIEQLR 151

Query: 107 RVIS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG--QVDQ 155
           +          V RLD  T G+LL+         L+      +  + Y     G    ++
Sbjct: 152 QARPDAKFLELVHRLDRETSGILLVAKKRSALINLQDQFRERETGKTYLALVQGAWPANK 211

Query: 156 DKLNL-LKKGIVIQG-----ICYGD----------MQVTLDTQK------GSNAWVTVGL 193
             ++L L K +   G     +   D          ++V    +        + + + V +
Sbjct: 212 KVIDLPLHKYLQADGERRVRVTTADDPDGMRSITLVKVRKLIEPRPLQGLPAMSLLEVTI 271

Query: 194 REGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEA 253
           + G+  +I+         +             G    G   ++++++ ++ L    L   
Sbjct: 272 KTGRTHQIRVHLSSQGHPIV------------GDDKYGDF-DLNRRVQKQGLKRMFLHAW 318

Query: 254 QVNLDAPIYSSETLVR 269
           ++  + P       +R
Sbjct: 319 RLQFNHPASGERVELR 334


>gi|255711220|ref|XP_002551893.1| KLTH0B02376p [Lachancea thermotolerans]
 gi|238933271|emb|CAR21455.1| KLTH0B02376p [Lachancea thermotolerans]
          Length = 397

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 2/85 (2%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL 134
           L +  KP G+    +    ++T+ + L S    V    RLD  T G+L+LT +  +A  +
Sbjct: 122 LLVIDKPSGIPIHPTGQYYQNTLVEVLKSHGKTVFPSHRLDKITSGVLILTKNPHMANKI 181

Query: 135 ELPSTQ--WLRVYRVRFHGQVDQDK 157
           +    Q    ++Y  R  G      
Sbjct: 182 QHQIRQRTMSKIYLARVDGAFPMAD 206


>gi|149277745|ref|ZP_01883885.1| pseudouridylate synthase [Pedobacter sp. BAL39]
 gi|149231433|gb|EDM36812.1| pseudouridylate synthase [Pedobacter sp. BAL39]
          Length = 240

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/154 (14%), Positives = 46/154 (29%), Gaps = 20/154 (12%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDG--RSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             +   E     + +KP   V +  +  G     +               RLD  T G +
Sbjct: 7   KDIILFENDDYIVVNKPP-FVASLDERGGSGEVNILRLAKQYSPDAQVCHRLDKETSGAI 65

Query: 123 LLTNDGGLAR--VLELPSTQWLRVYRVRFHGQVDQD----KLNLLKKG---IVIQGICYG 173
           ++       R   ++    +  + Y     GQ   +     L +L  G   + I      
Sbjct: 66  IIAKTPEAYRNVAIQFEKRKINKTYHAIVDGQFSFNDLFIDLPILNDGNKSVTIDRKEGK 125

Query: 174 DMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
             +   ++ K    +    L E     G+  +I+
Sbjct: 126 RAETIFNSIKNYRHY---TLVECKPITGRMHQIR 156


>gi|327438734|dbj|BAK15099.1| pseudouridylate synthase [Solibacillus silvestris StLB046]
          Length = 277

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 34/212 (16%), Positives = 63/212 (29%), Gaps = 41/212 (19%)

Query: 37  QQRVKVNGILL--ERA---AVNV-----------MSTDHIEVDGVPLRKAERTRLWLYHK 80
            + V ++G  +  +        +             TD  +V    +R  E     +  K
Sbjct: 34  AKAVTIDGEPIMWKEPFEKGTKIEFAFDIPASNYTPTDSCDV---KIRY-EDEHCLIVSK 89

Query: 81  PIGLVTTHSDPDGRST----VFDNLPSIFSRV-ISVGRLDINTEGLLLLTNDGGLARVL- 134
           P G+ T  ++P    T    V   +          V RLD  T GLLL+        +  
Sbjct: 90  PKGMATHPNEPTDNDTCMNHVMRYIMDNGGHYAEHVHRLDQGTNGLLLVAKHPVAKSIFD 149

Query: 135 -ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQV------------TLDT 181
             +     +R Y     G + +     +  GI  +   +   +V             +  
Sbjct: 150 RMIEEKTIVRTYAAEVQGNL-RTDSGTINAGIG-KDRHHNTRRVVSPTGQHAVTHYEVVN 207

Query: 182 QKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +      V V L  G+  +I+         + 
Sbjct: 208 RYKGTCVVHVVLETGRTHQIRVHMAHLGHPIV 239


>gi|317035512|ref|XP_001397201.2| DRAP deaminase (Rib2) [Aspergillus niger CBS 513.88]
          Length = 518

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 28/147 (19%), Positives = 46/147 (31%), Gaps = 26/147 (17%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKP 81
            + +    V VNG         V +   I          V G  +    E   L +  KP
Sbjct: 82  RKALQDGLVAVNGTPA-GPNTVVKNGQIISHTLHRHEPPVTGKEIGIIHEDDDLIVIDKP 140

Query: 82  IGLVTTHSDPDGRSTVFD-----NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
            G+    +     ++V +       P    R     RLD  T G++ L   G  A+  E 
Sbjct: 141 AGVPVHSAGRYHYNSVLEIMRSQRHPEWVPR--PCNRLDRLTSGVMFL---GKTAKAAEN 195

Query: 137 PSTQW-----LRVYRVRFHGQVDQDKL 158
            + +       + Y  R  G+     +
Sbjct: 196 MTGKLKARTLQKEYVARVKGKFPDGVI 222


>gi|119898153|ref|YP_933366.1| pseudouridine synthase A [Azoarcus sp. BH72]
 gi|119670566|emb|CAL94479.1| pseudouridine synthase A [Azoarcus sp. BH72]
          Length = 236

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/150 (17%), Positives = 53/150 (35%), Gaps = 16/150 (10%)

Query: 80  KPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL-- 136
           KP GL++      + +  ++  +   F   ++V RLD+ T GL++L  D    R L    
Sbjct: 44  KPSGLLSVPGRGAEKQDCLWRRVVHDFPDALTVHRLDMETSGLMVLARDAETHRRLSGLF 103

Query: 137 PSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLDTQKGS 185
                 + Y     G    D     L LL       ++ +  +G      +  +  +   
Sbjct: 104 HDRLVEKRYVAMVDGLPTSDRGQIDLPLLADWPNRPRQKVDFEGGKPSLTRFEVMARYPD 163

Query: 186 NAWVTVGLR-E-GKNREIKKVFEFFNWKVN 213
                + L  E G++ +++         + 
Sbjct: 164 RDVSRIALMPETGRSHQLRVHLLALGHPIL 193


>gi|109947518|ref|YP_664746.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
 gi|109714739|emb|CAJ99747.1| putative ribosomal pseudouridine synthase [Helicobacter acinonychis
           str. Sheeba]
          Length = 293

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/209 (17%), Positives = 67/209 (32%), Gaps = 43/209 (20%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKAERTRLWLYHK 80
            S +E +R + +QR+K N  ++ ++ +       I        G  +   E     ++ K
Sbjct: 26  CSLKEAQRHLDKQRLKQNQQIVRKSQIIQGIVSLIYFKPNEKQGKLV--FETKDFGIFDK 83

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL--ELP 137
           P  + T         ++ D + S F        RLD  T GL+L+       + L     
Sbjct: 84  PTQVYTHPKGYFYHESLLDCIQSHFGKNAHPAHRLDYETSGLVLVGKTPQSTKDLKALFM 143

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---------KGSNAW 188
             +  + Y    HG +DQ+          I         +  D +         K S   
Sbjct: 144 QKKVKKTYLALVHGLMDQNT--------TIDKPILTPENIQKDLRIRSKISPLGKPSTTL 195

Query: 189 VT--------------VG-LREGKNREIK 202
           V               +  L  G+  +I+
Sbjct: 196 VEPLAYNSFLDVSLLKITPLT-GRTHQIR 223


>gi|307284559|ref|ZP_07564721.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
 gi|306503236|gb|EFM72490.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0860]
          Length = 283

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 37/215 (17%), Positives = 74/215 (34%), Gaps = 48/215 (22%)

Query: 29  REVERMIA-QQRVKVNGILLE---------------------RAAVNVMSTDHIEVDGVP 66
           R+V   +  ++ VK+NG                         R  +++  T  ++V    
Sbjct: 24  RKVRHFLRTRKNVKINGETAAFHFPVQAGDCVTLTFEETDYVRPTIHLGETTRVKV---- 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLL 122
               E   L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G +
Sbjct: 80  --LYEDEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAI 137

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VI 167
           +   +  +  +L   L + Q  R Y+    G  +Q +   + + I               
Sbjct: 138 VFAKNPFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQ 196

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +G         +     +   VT  L  G+  +I+
Sbjct: 197 KGDSAITHVQVVQALSNNQTAVTCVLETGRTHQIR 231


>gi|255971139|ref|ZP_05421725.1| pseudouridine synthase [Enterococcus faecalis T1]
 gi|255962157|gb|EET94633.1| pseudouridine synthase [Enterococcus faecalis T1]
          Length = 287

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHFGEATRVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 235


>gi|299148873|ref|ZP_07041935.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_23]
 gi|298513634|gb|EFI37521.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           3_1_23]
          Length = 612

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/129 (19%), Positives = 53/129 (41%), Gaps = 8/129 (6%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
           E   L + +KP G+++     + R +V+  L   +      + V RLD+ T GLLL+   
Sbjct: 350 EDEWLLVVNKPAGMLSVPGKAEDRDSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKT 409

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQV--DQDKLNLL-KKGIVIQGICYGDMQVTLDTQ 182
             + R L+    +    + Y     G +   + ++  + +K I+I        +     +
Sbjct: 410 KEVHRDLQAQFANRSIKKRYVAVLDGVIIKTEKEIKPIAEKAILIAKETVLTKKTAKAER 469

Query: 183 KGSNAWVTV 191
            G+   + +
Sbjct: 470 TGNTGRIEL 478


>gi|261493419|ref|ZP_05989944.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
 gi|261310913|gb|EEY12091.1| pseudouridylate synthase [Mannheimia haemolytica serotype A2 str.
           BOVINE]
          Length = 217

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 23/159 (14%), Positives = 47/159 (29%), Gaps = 12/159 (7%)

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           P+    R    + +KP GL     + +   T          +V  V RLD  T GLL+L 
Sbjct: 6   PICYQHRD-FIIINKPEGLSVHKDEAEIGLTELVARQLNVKQVWLVHRLDKITSGLLILA 64

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD------KLNLLKKGI-VIQGICYGDMQ 176
            +   A          +  + Y      +  +        +   + G   +         
Sbjct: 65  LNKEAAARFYHLFEQHKIYKTYWALSDKKPKKKQGRIVGDMQKSRNGAWKLCYSKENPAV 124

Query: 177 VTLDTQKGSNAWVTVGL--REGKNREIKKVFEFFNWKVN 213
               +    ++     L  + GK  +++   +     + 
Sbjct: 125 TQFISHSVEDSLRHFILQPKTGKTHQLRVAMKSLGSPIL 163


>gi|257455430|ref|ZP_05620665.1| tRNA pseudouridine synthase C [Enhydrobacter aerosaccus SK60]
 gi|257447392|gb|EEV22400.1| tRNA pseudouridine synthase C [Enhydrobacter aerosaccus SK60]
          Length = 266

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 21/81 (25%), Positives = 31/81 (38%), Gaps = 5/81 (6%)

Query: 79  HKPIGLVTTHS--DPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLE 135
           +KP G++   S  D      V   L    ++ V  + RLD  T G+LL       AR L 
Sbjct: 15  NKPAGMLVHRSWLDRHETEFVMQTLRDQLAQYVYPIHRLDRPTSGVLLFALSSESARQLC 74

Query: 136 L--PSTQWLRVYRVRFHGQVD 154
               + Q  + Y     G + 
Sbjct: 75  EQFENRQVQKSYLAIVRGYLT 95


>gi|228984376|ref|ZP_04144555.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|228775345|gb|EEM23732.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
          Length = 292

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 41/267 (15%), Positives = 86/267 (32%), Gaps = 50/267 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + + V             + +PL    E   + + +K   
Sbjct: 36  GAIEVNGQHA-SVRHQLQAGEELRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 94

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L + + +      V  V RLD +T GL+L+  +      L   
Sbjct: 95  MSTIPSREHPAGSVANALLTHYDKQHLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSK 153

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                   R Y    HG            + +   +++++ +  +G         +D+  
Sbjct: 154 QHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSAN 213

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
                V++ L  G+  +I+         +               L  G   E+ ++ L  
Sbjct: 214 HKTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHS 261

Query: 243 -EQLGPHLLEEAQVNLDAPIYSSETLV 268
                 H + E +++    I S    V
Sbjct: 262 TSLTFYHPILEKEMSFTTTIPSDMQAV 288


>gi|212635834|ref|YP_002312359.1| pseudouridine synthase RluD [Shewanella piezotolerans WP3]
 gi|212557318|gb|ACJ29772.1| Pseudouridine synthase, RluD [Shewanella piezotolerans WP3]
          Length = 308

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 84/247 (34%), Gaps = 42/247 (17%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + E+ T QR+   +  +     +  + R++ +  V+VN   ++     +   D + +  
Sbjct: 3   TIDEDHTGQRIDNFLLTKLKGVPKSMIYRIVRKGEVRVNKKRIK-PEYKLQDGDVVRIPP 61

Query: 65  VPLRK----------------------AERTRLWLYHKPIGLVTTHSD--PDGRSTVFDN 100
           V + +                       E   + + +KP G+          G      +
Sbjct: 62  VRVSESEGRPGPSAKLTKVSQLENRIIYEDKFIIVLNKPSGIAVHGGSGVDFGVIEAMRS 121

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKL 158
           L +    +  V RLD +T GLLL+       + L       +  + Y     G+  +   
Sbjct: 122 LRTQQKFLELVHRLDKDTSGLLLIAKKRSALKHLHDQLRYKKMQKDYLALVRGEWQKHD- 180

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV-------GLRE-----GKNREIKKVF 205
             +K  ++   +  G+  V ++ + K S     +        L +     G+  +I+   
Sbjct: 181 KAVKAPLLKLTLKSGERIVRVNKEGKESETRFKIMQRYSDATLVQASPITGRTHQIRVHC 240

Query: 206 EFFNWKV 212
           ++    +
Sbjct: 241 QYAGHPI 247


>gi|330824854|ref|YP_004388157.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
 gi|329310226|gb|AEB84641.1| pseudouridine synthase [Alicycliphilus denitrificans K601]
          Length = 256

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 25/154 (16%), Positives = 45/154 (29%), Gaps = 21/154 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
           +   +   +KP G +   +     + R  V      I   V  V RLD  T G+L++   
Sbjct: 14  QDEHMVALYKPAGWLVHRTGLDAGETRFVVQALRDQIGRHVYPVHRLDKGTCGVLVMGLH 73

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICYGDM 175
              AR L          + Y     G           +  D             +     
Sbjct: 74  PAAARALAGSFARHAVHKRYLALVRGWAPPLADVDHPLRPDDAPQDAPAQPAHTLLTRLA 133

Query: 176 QVTLDTQKGS---NAWVTVGLRE---GKNREIKK 203
           ++ L             ++ L E   G+  +I++
Sbjct: 134 RLELPESSDPRFATTRASLVLAEPTTGRRHQIRR 167


>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 = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAE 71
           ++  ++  AG+  +  E + ++    VKVNG +         + D +E+DG  +   +
Sbjct: 11 IKLDALLKYAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDVVELDGQTVEVGQ 69


>gi|291086839|ref|ZP_06344600.2| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sp. M62/1]
 gi|291077108|gb|EFE14472.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Clostridium sp. M62/1]
          Length = 331

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 78/215 (36%), Gaps = 37/215 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L +  KP G+    S  +  +T+ + +   FS         +V RLD +T GLL++
Sbjct: 106 EDRDLMVIDKPAGMPVHPSQGNFYNTLANGIAWYFSERGEPFTFRAVNRLDRDTTGLLII 165

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQ---GICYGD 174
              G  A +L   +   +  R Y     G+ D++      +     G  I+       G+
Sbjct: 166 AKHGLCAALLSEMVARKEVRRQYLAIASGKTDEEGTICAPIAR-ADGSTIERCVDETRGE 224

Query: 175 MQVT-----LDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVNRLIRISYGPFQLGTL 228
              T     + + +   + + + L  G+  +I+  + +     +        G F    L
Sbjct: 225 YACTHYRRLVYSSENDCSLLLLTLDTGRTHQIRVHM-KHIGHPLL-------GDF----L 272

Query: 229 LAGSTREVSKKILREQLGP--HLLEEAQVNLDAPI 261
                R   ++ L   L    H L    +N  AP+
Sbjct: 273 YNPDYRLFRRQSLHSFLLSFTHPLTGESLNFSAPL 307


>gi|237653101|ref|YP_002889415.1| pseudouridine synthase [Thauera sp. MZ1T]
 gi|237624348|gb|ACR01038.1| pseudouridine synthase, RluA family [Thauera sp. MZ1T]
          Length = 319

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 69/240 (28%), Gaps = 40/240 (16%)

Query: 7   VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV--- 62
           + E    QR+   + R A    +  V R++    V+VNG  +++    +   D + +   
Sbjct: 16  IDEAAAGQRIDNYLLRIAKGVPKSHVYRILRSGEVRVNGRRVQQ-TYRLQEGDEVRIPPI 74

Query: 63  ------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI--FSR 107
                        G PL    E   L +  KP G             +            
Sbjct: 75  RIAEPTHAAPAPAGKPLPVVYEDEALLVIDKPSGKAVHGGSGVSYGVIEQLRVQRPELRM 134

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR---------------VRFH 150
           +    RLD  T GLL++         L          + Y                V  H
Sbjct: 135 LELAHRLDRETSGLLIVAKKRSALTALHDMMREGSVEKRYLTLVPGRWSNPLQHVKVPLH 194

Query: 151 GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNW 210
             +  +    ++   V          V L  +    + + V L+ G+  +I+       +
Sbjct: 195 KYLTAEGERRVR---VADEGKAAHSIVRLVRRWRDYSLLEVELKTGRTHQIRVHLAHLGF 251


>gi|215485220|ref|YP_002327651.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O127:H6
           str. E2348/69]
 gi|312966179|ref|ZP_07780405.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
 gi|215263292|emb|CAS07607.1| pseudouridine synthase for 23S rRNA (position 746) and tRNAphe
           (position 32) [Escherichia coli O127:H6 str. E2348/69]
 gi|312289422|gb|EFR17316.1| RNA pseudouridylate synthase family protein [Escherichia coli
           2362-75]
          Length = 219

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/174 (14%), Positives = 60/174 (34%), Gaps = 31/174 (17%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           D   +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G+
Sbjct: 11  DPWLIVLYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGV 70

Query: 122 LLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM 175
           +++       R L+    +    + Y  R  G           +G+V    I        
Sbjct: 71  IVVALTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPK 124

Query: 176 -QVTLDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +V  +T K +     V               +  G++ +++  +       + 
Sbjct: 125 QKVCYETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|229010681|ref|ZP_04167879.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
 gi|228750575|gb|EEM00403.1| Pseudouridine synthase [Bacillus mycoides DSM 2048]
          Length = 307

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +K   + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELNVVFEDDHVLIVNKQGQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+ +G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKNGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYMALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
              VT+ L  G+  +I+
Sbjct: 225 ATLVTLQLETGRTHQIR 241


>gi|226330541|ref|ZP_03806059.1| hypothetical protein PROPEN_04459 [Proteus penneri ATCC 35198]
 gi|225201336|gb|EEG83690.1| hypothetical protein PROPEN_04459 [Proteus penneri ATCC 35198]
          Length = 317

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 72/240 (30%), Gaps = 49/240 (20%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN------------GILLERAAV 52
            +  +   QR+   + AR     +  + R+I +  V+VN            G  +    V
Sbjct: 11  TIDGDEAGQRIDNFLLARLKGVPKSMIYRIIRKGEVRVNKGRIKPEYKLNAGDSIRIPPV 70

Query: 53  NVMSTDHIEVDGVPLRK--------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LP 102
            V   + + V     +          E   L L +KP G             +     L 
Sbjct: 71  RVSEKEEVAVSPKLDKVSALANCILYEDDHLMLINKPSGTAVHGGSGLSFGVIEGLRALR 130

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRFHGQV---DQD 156
                +  V RLD +T G+LL+      A           Q  + Y     GQ     + 
Sbjct: 131 PEARFLELVHRLDRDTSGVLLIA-KKRSALRALHEQLRLKQMQKDYLALVRGQWQSHTKV 189

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
               L K I+  G      +V   + +G  +     + E              G+  +I+
Sbjct: 190 VQAPLLKNILQSGE-----RVVKVSNEGKPSETRFKVEERFEFATLVKASPVTGRTHQIR 244


>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 = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLRKAER 72
            L    R
Sbjct: 61 ERLPFVSR 68


>gi|260549688|ref|ZP_05823905.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
 gi|260407205|gb|EEX00681.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter sp.
           RUH2624]
          Length = 212

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 42/117 (35%), Gaps = 16/117 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLAR 132
             + HKP  +++     D   +V   L +I  R + + RLD +T G+L+   +  G  A 
Sbjct: 16  FMVIHKPSDILSVPGKGDLHDSVLTRLVAIEPRTLLIHRLDRDTSGILVFGLSKRGQSAI 75

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +    Q  ++Y     G               + G    D+ V  D  +     V
Sbjct: 76  ARQFQDRQTSKIYEALVAGH--------------LDGEGTVDIPVVYDPSRPPLHIV 118


>gi|256820360|ref|YP_003141639.1| pseudouridine synthase [Capnocytophaga ochracea DSM 7271]
 gi|256581943|gb|ACU93078.1| pseudouridine synthase [Capnocytophaga ochracea DSM 7271]
          Length = 215

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/189 (14%), Positives = 53/189 (28%), Gaps = 38/189 (20%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   +   +K +G +    D  G + + D +     +         +  V RLD  T G+
Sbjct: 4   EDNHVIAVNKRVGDIVQG-DKTGDTPLSDIVKQYLKQKYNKPGEVFLGVVHRLDRPTTGV 62

Query: 122 LLLTNDGGLARVLELP---STQWLRVYRVRFH--GQVDQDKL-----------NLLKKGI 165
           +L          L        +  + Y         V++D L             +    
Sbjct: 63  VLFAKTSKALARLNTMFANKQEVQKTYWALVDAKPPVEEDTLTHWLVRNEKQNKSVAYNK 122

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQL 225
            +Q      +   L         + + L  G++ +I+         +             
Sbjct: 123 EMQHSKKAVLHYKLLKSYERYYLLEIDLITGRHHQIRAQLAAIELHIK------------ 170

Query: 226 GTLLAGSTR 234
           G L  G+ R
Sbjct: 171 GDLKYGAKR 179


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 1/79 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   GI  SR + +  I + +V V+G  +++A   V    +IE  G  L+   R
Sbjct: 6  ERLDILLVEKGIITSRDKAKACIMEGKVFVDGQRVDKAGEKVSVIANIEYKGAKLKYVSR 65

Query: 73 TRLWLYHKPIGLVTTHSDP 91
            L L         +  D 
Sbjct: 66 GGLKLEKAMKSYDISLEDK 84


>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 = 50.2 bits (119), Expect = 5e-04,   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|160879192|ref|YP_001558160.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
 gi|160427858|gb|ABX41421.1| pseudouridine synthase [Clostridium phytofermentans ISDg]
          Length = 237

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/157 (17%), Positives = 60/157 (38%), Gaps = 26/157 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR-----VISVGRLDINTEGLLLLT 125
           E   + +  KPIG+++     +G   +        +      +  V RLD N  G+++  
Sbjct: 7   EDKHIIVCIKPIGVLSQPGQGEGMDMITLLQEYRKNNKESDYIGLVHRLDRNVGGVMVFA 66

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQD------------------KLNLLKKGI 165
                 + L +      + + Y    HG+  +                    +N ++KG+
Sbjct: 67  KTELATKKLSVAIRERNFTKEYMAVIHGRPSESSGILKDLMFKDSSKNKSFVVNRMRKGV 126

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               + Y  ++ T++  KG  +++ V L  G+  +I+
Sbjct: 127 KEASLEYRTIE-TIEVAKGEFSFIRVKLHTGRTHQIR 162


>gi|257453802|ref|ZP_05619080.1| YabO/YceC/SfhB family protein [Enhydrobacter aerosaccus SK60]
 gi|257448729|gb|EEV23694.1| YabO/YceC/SfhB family protein [Enhydrobacter aerosaccus SK60]
          Length = 285

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/179 (15%), Positives = 54/179 (30%), Gaps = 33/179 (18%)

Query: 62  VDGVPLRKAER------TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF-------SRV 108
           V+  P+   E         L +  KP  L  T S      T+   L +         + +
Sbjct: 56  VENEPIIPFEPNILHLDGHLLVVDKPHFLPVTPSGRYVSQTLLAKLRNHPDLQQLAVNDI 115

Query: 109 ISVGRLDINTEGLLLLTNDG--GLARVLELPSTQWLRVYRVRFHGQVDQDKL-------N 159
             + RLD +T G++LL+ +                 + Y         +  L       +
Sbjct: 116 SPLHRLDKDTAGVMLLSVNPSSRACYHALFADRHIHKTYHAIA---PTRSDLCYPFHIHS 172

Query: 160 LLKKGIVI------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
            L++G         QG       + L    G+ +   +    GK  +++  +       
Sbjct: 173 RLERGEPFFLTKTTQGEPNAHTTIELIENNGAFSLYRLTPVTGKKHQLRVHM-ASLGMP 230


>gi|291545451|emb|CBL18559.1| hemolysin TlyA family protein [Ruminococcus sp. SR1/5]
          Length = 269

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 21/78 (26%), Positives = 30/78 (38%), Gaps = 1/78 (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 RLWLYHKPIGLVTTHSDP 91
           L L         T  D 
Sbjct: 64 GLKLEKAMKNFGVTLKDK 81


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 6  IVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +     +  R+ +++   G +ASR      I +  V V+G  + + A    +   I +D 
Sbjct: 1  MSDNKHSTIRLDQLLLNKGLVASRARARDAIQRGTVMVDGRTVTKPATAFAANATITIDD 60

Query: 65 VPLRKAERTRLWL 77
                 R  L L
Sbjct: 61 PAQDYVSRAALKL 73


>gi|195384878|ref|XP_002051139.1| GJ13872 [Drosophila virilis]
 gi|194147596|gb|EDW63294.1| GJ13872 [Drosophila virilis]
          Length = 807

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 39/196 (19%), Positives = 66/196 (33%), Gaps = 27/196 (13%)

Query: 32  ERMIAQQRVKVNGILL--------ERAAVNVMSTDHIEVDGVPLRKAE-RTRLWLYHKPI 82
           ER I    + VN   +             N++    + V   P+        + + +KP 
Sbjct: 398 ERCIQTGTLTVNFEKVPIDYRLKHNDLLANIVHRHEVPVTCQPITIVHMDEDIVVVNKPA 457

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +TV   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 458 SIPVHPCGRYRHNTVVFILAKEFNLKNLRTIHRLDRLTSGLLLFGRSPKKARQMEQQIRN 517

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT-----------LDTQKGSNA 187
            Q  + Y  R  G      +   K+ I +     G  +V+             +Q G  +
Sbjct: 518 RQVEKEYICRVEGIFPDGVVE-CKEPIEVVSYKIGVCKVSQKGKDCTTTFQKLSQNGKTS 576

Query: 188 WVTVG-LREGKNREIK 202
            V    L  G+  +I+
Sbjct: 577 VVLCKPLT-GRMHQIR 591


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++ + G+A SR + + +I    V V+G   ++A   V     IE+ G  L+   R
Sbjct: 3  ERLDVLLVKKGLAASREKAKAIIMSGVVFVDGQREDKAGTMVKEELPIEIKGKTLKYVSR 62


>gi|291617372|ref|YP_003520114.1| RluA [Pantoea ananatis LMG 20103]
 gi|291152402|gb|ADD76986.1| RluA [Pantoea ananatis LMG 20103]
          Length = 232

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/188 (16%), Positives = 62/188 (32%), Gaps = 37/188 (19%)

Query: 71  ERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   L L  KP GL++ +  +P    +V   L +IF     V RLD  T GL+++  +  
Sbjct: 22  QDDHLVLIDKPSGLLSLSGKNPQNLDSVHYRLVTIFPGCTLVHRLDFGTSGLIVVARNKT 81

Query: 130 LARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ-----VTLDTQ 182
           +   L    +     + Y     G +  +      +GI+   I     +     +  +  
Sbjct: 82  INAALSQQFSARTVAKHYSALLCGHLPDE------EGIIDAPIAKDPARFPRMSICAEWG 135

Query: 183 KGSNAWVTVG--------------------LRE-GKNREIKKVFEFFNWKVNRLIRISYG 221
           K + +   V                     + E G+  +++   +     +       YG
Sbjct: 136 KPARSRYRVVERFNLKRDDARVIPLTRVTLIPETGRTHQLRIHCQLLGHPILGCD--LYG 193

Query: 222 PFQLGTLL 229
              L  + 
Sbjct: 194 GLLLPGME 201


>gi|67924151|ref|ZP_00517595.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
 gi|67854003|gb|EAM49318.1| Pseudouridine synthase, RluD [Crocosphaera watsonii WH 8501]
          Length = 302

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 32/199 (16%), Positives = 64/199 (32%), Gaps = 32/199 (16%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR----------LWLYHKP 81
           ER+I   +V V+   +      + +   +     P ++ E             L + +KP
Sbjct: 38  ERII-SGQVLVDEQTV-DPQTVLKTGQRLSYHRPPWQEPEVPLSFEIIYEDDNLLIVNKP 95

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLARVLELP-- 137
            GL           T+   L   + +   I + RL   T GL+L+         L     
Sbjct: 96  SGLPVLPGGGFLEHTLLWQLKKQYPQNEPIPIHRLGRGTSGLMLMGKSAIARSHLTQQMR 155

Query: 138 STQWLRVYRVRFH--------------GQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
             +  +VY+                  G++    L  +  G  + G  Y   +  +  + 
Sbjct: 156 EQKISKVYQGLIGKNNLPDKFSIDHPIGKIPDPVLGYI-YGAKVDG-KYAYSECRVLGRY 213

Query: 184 GSNAWVTVGLREGKNREIK 202
                + V +  G+  +I+
Sbjct: 214 VDKTLLEVTILTGRPHQIR 232


>gi|323692319|ref|ZP_08106558.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
 gi|323503644|gb|EGB19467.1| pseudouridine synthase [Clostridium symbiosum WAL-14673]
          Length = 298

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 75/219 (34%), Gaps = 39/219 (17%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +K  G+    S  +  +T+ + L   F          +V RLD +T GLLL+
Sbjct: 86  EDEDLMVINKAAGMPVHPSQGNFDNTLANGLAWYFKEKGEAFVFRAVNRLDRDTTGLLLI 145

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDK------LNLLKKGIVIQ-------G 169
             +     +L    ++    R YR    G + +++      +    +G  I+       G
Sbjct: 146 AKNMLSGAILSSMVSEKTIRREYRAIVSG-LTEEEGCICRPIAR-AEGSTIERCVDPERG 203

Query: 170 ICYGDMQVTLD-TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT- 227
                    L   +    + + + L  G+  +I+      + K         G   LG  
Sbjct: 204 EYASTRYRRLGYDRDKDCSLLLITLDTGRTHQIR-----VHMKY-------IGHPLLGDF 251

Query: 228 LLAGSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSS 264
           L     R + ++ L        H L    ++  AP+   
Sbjct: 252 LYNPDYRFIKRQSLHSCRLTFTHPLTGEAMDFTAPLPED 290


>gi|315166865|gb|EFU10882.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1341]
 gi|315575307|gb|EFU87498.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309B]
 gi|315581474|gb|EFU93665.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0309A]
          Length = 283

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 72/210 (34%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G   Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFSQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 231


>gi|312900272|ref|ZP_07759584.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
 gi|311292633|gb|EFQ71189.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0470]
          Length = 283

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVCPTIHLGEATRVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>gi|171678031|ref|XP_001903966.1| hypothetical protein [Podospora anserina S mat+]
 gi|170937084|emb|CAP61743.1| unnamed protein product [Podospora anserina S mat+]
          Length = 479

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/147 (17%), Positives = 50/147 (34%), Gaps = 34/147 (23%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK-----------------AERTRLWLY 78
              +V VNG ++        S D++ V+G  +                    E   + + 
Sbjct: 105 ESGQVAVNGKIV--------SPDYVMVNGDLVSHTTHRHEPPVTQDPVQVIHEDDDMIVI 156

Query: 79  HKPIGLVTTHSDPDGRSTVFDNL-----PSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           +KP G+    +     ++V + +     P+   R     RLD  T G++ +      A  
Sbjct: 157 NKPSGVPVHPAGRYHYNSVVEIMKAERGPTFAPR--PCNRLDRLTSGIMFIAKTAKAAES 214

Query: 134 LELPSTQ--WLRVYRVRFHGQVDQDKL 158
           L     +    + Y  R  G+    ++
Sbjct: 215 LSAQIFRRSVRKEYLARVVGRFPDGEV 241


>gi|154505454|ref|ZP_02042192.1| hypothetical protein RUMGNA_02983 [Ruminococcus gnavus ATCC 29149]
 gi|153794247|gb|EDN76667.1| hypothetical protein RUMGNA_02983 [Ruminococcus gnavus ATCC 29149]
          Length = 354

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 37/265 (13%), Positives = 88/265 (33%), Gaps = 49/265 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEV------DGVPLRKAERTRLWLYH--------KPIGLV 85
           V +NGI +     ++ S D + +          +   E     +Y         K  G+ 
Sbjct: 101 VLLNGIWV-HMTHHLTSGDELVIRIVEEQSSERVPPVEHPIHIVYEDEDILVIDKQAGMP 159

Query: 86  TTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELPS- 138
              S  +  +++ + L   F +         V RLD +T GL ++      A +L   + 
Sbjct: 160 IHPSLNNYYNSLANALAWYFEQQKKPFIFRCVNRLDRDTSGLTIIAKHVVSAAILSSMNA 219

Query: 139 -TQWLRVYRVRFHGQVDQD-----------KLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
             +  R YR    G +  +             +++++ +                +K  +
Sbjct: 220 RREIHREYRAIVRGHLTPESGVITAPLGRKDSSIIERTVDFDHGEKAVTYYQFLEEKNGH 279

Query: 187 AWVTVGLREGKNREIK-KVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR--E 243
           + V++ L  G+  +I+  + ++  +           P     L       ++++ L    
Sbjct: 280 SLVSLRLGTGRTHQIRIHM-KYIGF-----------PLVGDYLYNPDMEYITRQALHSYR 327

Query: 244 QLGPHLLEEAQVNLDAPIYSSETLV 268
               H +   +++  AP+      +
Sbjct: 328 LTFLHPITGQKMDFTAPLPDDMKKI 352


>gi|307297424|ref|ZP_07577230.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
 gi|306916684|gb|EFN47066.1| pseudouridine synthase, RluA family [Thermotogales bacterium
           mesG1.Ag.4.2]
          Length = 310

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 82/240 (34%), Gaps = 40/240 (16%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAG--IASRREVERMIAQQRVKVNGILLERAAVNVMSTD 58
           M  + IV       R+ KV+        SR  V+R I   +V VN     + +  V   +
Sbjct: 1   MLQEIIVSSREDGWRLDKVVVEKAPPWVSRTFVQRQIKNSKVFVNSRP-RKPSYKVKIGE 59

Query: 59  HIEVD-------------GVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI 104
            I  D              +PL+   E   + + +K  G++          T+ + L   
Sbjct: 60  SITFDLPEKPKVASVEPEAIPLKIVFEDRDIIVVNKDPGIIVHPLPRKQTGTLVNALLYH 119

Query: 105 FSRVISVG---------RLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQ 152
              +  +G         RLD +T G++++  +  LA V      +     + Y     G+
Sbjct: 120 CKDLQGIGGVTRPGIVHRLDKDTSGIIIVAKN-DLAHVSLSSQFKSRLTAKEYIALVRGK 178

Query: 153 ----------VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                     + +  +N LK  +   G        TL       + + V  R G+  +I+
Sbjct: 179 TPPFGKIDYSIARHPVNRLKMSVNENGKESLTYFQTLSNFSSIASLIIVRPRTGRTHQIR 238


>gi|307277035|ref|ZP_07558141.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|307289950|ref|ZP_07569879.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306499016|gb|EFM68505.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0411]
 gi|306506279|gb|EFM75443.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2134]
 gi|315030583|gb|EFT42515.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4000]
 gi|315159704|gb|EFU03721.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0312]
 gi|315161994|gb|EFU06011.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0645]
 gi|315578744|gb|EFU90935.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0630]
          Length = 283

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVFPTIHLGEATRVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>gi|261339387|ref|ZP_05967245.1| ribosomal large subunit pseudouridine synthase [Enterobacter
           cancerogenus ATCC 35316]
 gi|288318188|gb|EFC57126.1| ribosomal large subunit pseudouridine synthase [Enterobacter
           cancerogenus ATCC 35316]
          Length = 315

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 79/243 (32%), Gaps = 57/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++     + + D
Sbjct: 13  IAEDDAGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKKRVK-PEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERTRL---------------------WLYHKPIGLVTTHSDPDGRSTV 97
            I +  V + + E   +                      + +KP G             +
Sbjct: 65  EIRIPPVRVAEREEEVVSPKLQKVAALSDVILYEDDHILVLNKPSGTAVHGGSGLSFGVI 124

Query: 98  FDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                L      +  V RLD +T G+LL+       R L   L      + Y     GQ 
Sbjct: 125 EGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQW 184

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNR 199
            Q  + +++  + ++ I     ++    Q+G  +     + E              G+  
Sbjct: 185 -QSHVKVVQAPL-LKNILQSGERIVRVNQEGKPSETRFKVEERYEFATLVRCSPVTGRTH 242

Query: 200 EIK 202
           +I+
Sbjct: 243 QIR 245


>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 = 50.2 bits (119), Expect = 5e-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: 97  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGQVVNIPSFQVKAGDVVAV 145


>gi|307719808|ref|YP_003875340.1| pseudouridine synthase [Spirochaeta thermophila DSM 6192]
 gi|306533533|gb|ADN03067.1| pseudouridine synthase [Spirochaeta thermophila DSM 6192]
          Length = 256

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 18/126 (14%), Positives = 34/126 (26%), Gaps = 15/126 (11%)

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVD------ 154
               R+  V RLD  T G++L       A             ++Y               
Sbjct: 46  EAPPRLHLVNRLDRPTSGIVLFARHRKAAGKFSHLFRRRGVYKLYWAVLDAPPPLPSDTV 105

Query: 155 QDKL-------NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEF 207
           +  +                +G  Y  +   +        +V V L  G++ +I+  F  
Sbjct: 106 EHYIVENRRINKSFAFAEKKEGSEYARLSYQVIGSGDRYFFVVVRLHTGRHHQIRAQFSA 165

Query: 208 FNWKVN 213
               + 
Sbjct: 166 LGCHIK 171


>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 = 50.2 bits (119), Expect = 5e-04,   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|288928581|ref|ZP_06422428.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 317 str. F0108]
 gi|288331415|gb|EFC69999.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella sp. oral taxon 317 str. F0108]
          Length = 221

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/192 (13%), Positives = 51/192 (26%), Gaps = 37/192 (19%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDIN 117
           +   E   + +  K  G +   SD  G   + D + S             +  V RLD  
Sbjct: 2   IPVYEDNHIIIVSKHSGEIVQ-SDKTGDVPLVDIVKSYLKEKYAKPGNVFLGVVHRLDRP 60

Query: 118 TEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL-------------K 162
             GL+           +     +    + Y        + +   L+              
Sbjct: 61  VWGLVAFAKTSKALSRMNALFRTGDVEKTYWAIVQSPPENETGELVHWLTRNEKQNKSYA 120

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGP 222
               + G     +   +  +  +   + V L  G++ +I+         +          
Sbjct: 121 HNHEVAGAKKAILSYKVIGRSENYTLLEVQLMTGRHHQIRCQLAAMGCPIK--------- 171

Query: 223 FQLGTLLAGSTR 234
              G L  G+ R
Sbjct: 172 ---GDLKYGARR 180


>gi|256545084|ref|ZP_05472450.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Anaerococcus vaginalis ATCC 51170]
 gi|256399125|gb|EEU12736.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Anaerococcus vaginalis ATCC 51170]
          Length = 286

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 79/218 (36%), Gaps = 45/218 (20%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-------DGVPLR 68
           + + I+       R  +++I    + VN   +E+  + + S D+I++       +  P+ 
Sbjct: 19  LDRNISN------RAYKKIIKN-SILVNDKKIEK-NIKLNSDDNIKIIIEDEILNYEPIN 70

Query: 69  KA-----ERTRLWLYHKPIGLVTTHSDPD---GRSTVFDNLPSIFSRVISVGRLDINTEG 120
           K      E   +    K   L       +      + +    +I S+V  + RLD+NT G
Sbjct: 71  KELEILYEDQDIIAIDKDANLTVNSKGQESLANYISYYFWKNNIKSQVRFINRLDMNTSG 130

Query: 121 LLLLTNDG--GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQ---GICYGDM 175
           ++L+  +          + +  + + Y     G ++ DK       IV++         M
Sbjct: 131 IILIARNPYAQAYYQKLIENNDFDKEYLALVEGNLEIDKT------IVLKINYDENKKKM 184

Query: 176 QVTLDTQKGSN-----------AWVTVGLREGKNREIK 202
           ++  +  +              + +   +  GK  +I+
Sbjct: 185 KIADEGYEIKTYFKNIKLYDKFSLIYCKIFTGKTHQIR 222


>gi|238749474|ref|ZP_04610979.1| Pseudouridine synthase [Yersinia rohdei ATCC 43380]
 gi|238712129|gb|EEQ04342.1| Pseudouridine synthase [Yersinia rohdei ATCC 43380]
          Length = 232

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 79/234 (33%), Gaps = 52/234 (22%)

Query: 55  MSTDHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGR 113
              D IE         +   L L +KP GL++ +  +P    +V   L  IF       R
Sbjct: 12  PCHDKIE------TLYQDDHLVLINKPAGLLSLSGKNPQNLDSVHHRLVQIFPGCTLAHR 65

Query: 114 LDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
           LD  T GL+++  +  +   L    +Q    +VY     G +D +      +G++   I 
Sbjct: 66  LDFGTSGLMVIARNKAVNAALCQQFSQRTVTKVYSALLCGHLDNN------EGVIDAAIA 119

Query: 172 YGDM-----QVTLDTQKGSNAWVTVG--------------LR------E-GKNREIKKVF 205
                     +     K + +   V               L       E G+  +++   
Sbjct: 120 KDPALFPVMSICALHGKPARSGYRVVERFYHPLEDGTLLPLTRVQLTPETGRTHQLRIHC 179

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKIL---REQLGPHLLEEAQVN 256
           +     +       YG    G LL G+ R  + +++    E    H + +  VN
Sbjct: 180 QLLGHPIWGCD--LYG----GRLLPGTER--TPRLMLHASELHFIHPISQEWVN 225


>gi|294657495|ref|XP_459803.2| DEHA2E11374p [Debaryomyces hansenii CBS767]
 gi|199432736|emb|CAG88042.2| DEHA2E11374p [Debaryomyces hansenii]
          Length = 582

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 30/147 (20%), Positives = 49/147 (33%), Gaps = 17/147 (11%)

Query: 29  REVERM---IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRL 75
           R+ +     IA  +V +N          V + D I          V    ++   E   +
Sbjct: 118 RDADFYKKTIAAGQVTLNKKPA-DLDSIVRNGDLISHRCHRHEPSVSSRGIKIVHEDENI 176

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV-ISVGRLDINTEGLLLL--TNDGGLAR 132
               KP G+    +     +T+       F +V     RLD  T GL+ L     G  A 
Sbjct: 177 IAIDKPSGIAVHPTGRYRYNTITKIFQHEFGKVVHPCNRLDRLTSGLMFLGKNAKGADAF 236

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLN 159
           V ++      + Y  R  G+ D   + 
Sbjct: 237 VQQIRDRTVKKEYIARVVGKFDIGDVE 263


>gi|167719292|ref|ZP_02402528.1| ribosomal large subunit pseudouridine synthase D [Burkholderia
           pseudomallei DM98]
          Length = 318

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 80/238 (33%), Gaps = 39/238 (16%)

Query: 12  TPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI---------- 60
             +R+ K +A+     SR  +++ I   RV+V+G   +     V     I          
Sbjct: 60  AGERLDKALAQLFPEFSRSRLQQWIESDRVRVSGAPAK-IRQPVPLGATIELLPELLPEQ 118

Query: 61  ---EVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVIS 110
                + VPL    E   + +  KP GLV   +  +   T+ + L   +       R   
Sbjct: 119 LAFTPEPVPLSIVYEDDTIVVVDKPAGLVVHPAAGNWSGTLLNGLLHRYADAAGLPRAGI 178

Query: 111 VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK----------L 158
           V RLD  T GL+++         L  +L +    R Y     G++  +            
Sbjct: 179 VHRLDKETSGLMVVARTLAAQTDLVRQLQARTVKRRYFALAWGRMPDEGTIDAPIGRDPR 238

Query: 159 NLLKKGIV--IQGICYGDMQVTLDT---QKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
              +  +V    G        T+DT   ++   + +   L  G+  +I+         
Sbjct: 239 ERTRMAVVTGAAGKPARTHFRTVDTTLWERQPVSAIHCDLETGRTHQIRVHCAHVGHP 296


>gi|167622731|ref|YP_001673025.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
 gi|167352753|gb|ABZ75366.1| pseudouridine synthase [Shewanella halifaxensis HAW-EB4]
          Length = 225

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/168 (14%), Positives = 59/168 (35%), Gaps = 34/168 (20%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL---- 124
            +   + + +KP GL++    DP    + ++ + + F     V RLD+ T G++++    
Sbjct: 18  HQDKDIMVVNKPSGLLSVPGRDPAHADSTYNRVLAEFPHAKIVHRLDMATSGVIVVALLR 77

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQV--- 177
           + +  L R       +  + Y  R  G V +        G V    I        Q    
Sbjct: 78  SAESELKRQF--RDRETEKTYYARVAGHVKE------THGTVNLPLICDWPNRPKQKVDH 129

Query: 178 ----------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                      + ++   +  V +  +  G++ +++  +       + 
Sbjct: 130 KIGKPSQTHYEVISRGKRSTLVKLTPIT-GRSHQLRVHMM-ALGHPIL 175


>gi|116513692|ref|YP_812598.1| pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|116093007|gb|ABJ58160.1| Pseudouridylate synthase, 23S RNA-specific [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC BAA-365]
          Length = 297

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 81/250 (32%), Gaps = 56/250 (22%)

Query: 6   IVQENFTPQRVSKVIARAGIASRRE---VERMIAQQRVKVNGILLERAAVNVMSTDHI-- 60
           ++     P ++S  + + G  SRR     +       + VN       +  +   D +  
Sbjct: 1   MIVAKNDPGQLSHFLLKKGF-SRRAVNNCKN--HGGMMLVNHHR-RNGSYRLKEGDVVHF 56

Query: 61  -----------EVDGVPLRKAERTR-LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
                      +V   PL   E T    + +KP GL++  S       V + + + F + 
Sbjct: 57  LMGQEPVNPWLKVSRRPLDIVEETADYLVINKPAGLLSIPSGFHAEDAVINRVLAYFEKQ 116

Query: 109 ---------ISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL------RVYRVRFHGQV 153
                      V RLD +T GL+LL   G     +       L      + Y    HG  
Sbjct: 117 GVNPAYVKPHIVTRLDQDTSGLVLL---GK--NAIAHDRFSKLGKDAFIKKYHAIVHGNF 171

Query: 154 DQDKLNLL------------KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
            +  L+ L            K+ +  +G      +  +  Q    + V + L  G+  +I
Sbjct: 172 AEGDLSGLIDKPLARVGDTVKREVNPKGQRALT-EYRVLNQVPGASLVELRLLTGRTHQI 230

Query: 202 K-KVFEFFNW 210
           +  +      
Sbjct: 231 RIHM-ASIGH 239


>gi|114776527|ref|ZP_01451572.1| pseudouridylate synthase, 23S RNA-specific [Mariprofundus
           ferrooxydans PV-1]
 gi|114553357|gb|EAU55755.1| pseudouridylate synthase, 23S RNA-specific [Mariprofundus
           ferrooxydans PV-1]
          Length = 579

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 31/161 (19%), Positives = 62/161 (38%), Gaps = 28/161 (17%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTEG 120
           G+ +   E  +L + +KP GL++T    +   ++F  L   + ++     V RLD++T G
Sbjct: 373 GIEIVY-EDDQLLVVNKPAGLMSTPG-REIEESLFSRLAQRYPQIPELTLVHRLDMDTSG 430

Query: 121 LLLLTNDGGLARVLELP--STQWLRVYRVRFHGQ----VDQDKLNL-LKKGIVIQGICYG 173
           LLL+  D    + L+         + Y      +     DQ ++ L L+  + +      
Sbjct: 431 LLLVAKDLRTHKRLQKQFIERSVEKCYEAVLVKRLPAQPDQGRIELPLR--VDLDDRPRQ 488

Query: 174 DMQVTLDTQKGSNAWVTVGLRE------------GKNREIK 202
              V     K +     +  RE            G+  +++
Sbjct: 489 --MVCYQHGKPATTRWQIIARENNRTRIWFYPETGRTHQLR 527


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 34/177 (19%), Positives = 70/177 (39%), Gaps = 23/177 (12%)

Query: 47  LERAAVNVMSTDHIEVDGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
           +    +N   +  IE + +PL+ A E + + + +KP  +V   +      T+ + L   F
Sbjct: 60  VIEVKLNKEESQDIEPENIPLKVAYEDSDIIVLNKPPFIVVHPTKNYPYGTLANGLLYYF 119

Query: 106 SR------VISVGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHG------ 151
                   V  V RLD+NT GL+++  +      L+    +    + Y    HG      
Sbjct: 120 KEKGENCIVRLVSRLDMNTSGLIIVAKNQFSHMSLQRDMNKEEFKKQYLAIVHGKMEADF 179

Query: 152 -----QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW-VTVGLREGKNREIK 202
                 + +++   +K+  +I       +      +  SNA  + + L  G+  +I+
Sbjct: 180 GTIDLPIYKEEDEPIKR--IIDDRGQRSITHYKVIETYSNAQLLKLTLETGRTHQIR 234


>gi|163939199|ref|YP_001644083.1| RluA family pseudouridine synthase [Bacillus weihenstephanensis
           KBAB4]
 gi|163861396|gb|ABY42455.1| pseudouridine synthase, RluA family [Bacillus weihenstephanensis
           KBAB4]
          Length = 307

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 69/197 (35%), Gaps = 36/197 (18%)

Query: 40  VKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHKPIGLVT 86
           V VNG    R    +   D ++V              G      E   + + +K   + T
Sbjct: 47  VTVNGEQ-RRWNELLKEGDKLQVHMFMEEEYGVEPEYGELNVVFEDDHVLIVNKQGQMDT 105

Query: 87  THSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTND---GGLARVLELP 137
             S+ +G  T+ + +   F       +V  + RLD +T G ++       G +   L   
Sbjct: 106 HPSEKNGTGTLANLVAFHFQMQGLETKVRHIHRLDKDTTGGVVFAKHRIAGAIMDRLL-M 164

Query: 138 STQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD-MQVTLDTQKGS 185
             +  R Y     G+V + +            +  ++ +  +G       +V    +K +
Sbjct: 165 ERKIKRTYAALVEGKVKKKQGTIDAAIGRDRHHATRRRVSPKGDQAITYYKVEKYFKKQN 224

Query: 186 NAWVTVGLREGKNREIK 202
              VT+ L  G+  +I+
Sbjct: 225 ATLVTLQLETGRTHQIR 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 = 50.2 bits (119), Expect = 5e-04,   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|256957449|ref|ZP_05561620.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|257080924|ref|ZP_05575285.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|257083608|ref|ZP_05577969.1| pseudouridine synthase [Enterococcus faecalis Fly1]
 gi|256947945|gb|EEU64577.1| pseudouridine synthase [Enterococcus faecalis DS5]
 gi|256988954|gb|EEU76256.1| pseudouridine synthase [Enterococcus faecalis E1Sol]
 gi|256991638|gb|EEU78940.1| pseudouridine synthase [Enterococcus faecalis Fly1]
          Length = 287

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATRVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 235


>gi|168018525|ref|XP_001761796.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162686851|gb|EDQ73237.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 346

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/143 (18%), Positives = 51/143 (35%), Gaps = 15/143 (10%)

Query: 32  ERMIAQQRVKVNGILL---------ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPI 82
           E  + + R++V G ++         +  +  V   +   + G  +   E   + +  KP 
Sbjct: 42  EEAVKRGRIRVEGKVVAPSYVVRDSQTMSHFVHRHEPPVLAGRVIVLEEGPDIIVVSKPA 101

Query: 83  GLVTTHSDPDGRST-VFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLA--RVLELP 137
             V  H     R   V   L +      +  V RLD    GLL+L  +   A     E+ 
Sbjct: 102 -TVPVHPCGQYRKNSVISILEAEHKTGPLFPVHRLDRLVSGLLILARNSRTADFFRQEIE 160

Query: 138 STQWLRVYRVRFHGQVDQDKLNL 160
           +    + Y  +  G    +++ L
Sbjct: 161 AGVVQKQYVAKVKGVFPAEEVEL 183


>gi|297619316|ref|YP_003707421.1| pseudouridine synthase [Methanococcus voltae A3]
 gi|297378293|gb|ADI36448.1| pseudouridine synthase [Methanococcus voltae A3]
          Length = 372

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/204 (13%), Positives = 68/204 (33%), Gaps = 38/204 (18%)

Query: 27  SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD-GVPLRKAERTR----------- 74
           SR+ + +    + + VN   +      +   + I +  G  +   E              
Sbjct: 47  SRKSINKFDKNKYILVNNKYI-SLKSKIKDNETITIYLGKNIETDENLINNTELDNTPMD 105

Query: 75  -------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINT 118
                  + + +KP  +V   +      T+ + +    +          +  + R+D++T
Sbjct: 106 IMYEDMDILVVNKPKNMVVHPTKTIKSGTLANAIMDYQNHNKSESERFKIRFINRIDMDT 165

Query: 119 EGLLLLTNDGGLARVLELPSTQW-LRVYRVRFHGQVDQDKLNL-LKKGIV------IQGI 170
            G++L+  +    + +         + Y     G +D D L+  L   +       +   
Sbjct: 166 TGIVLIAKNSFAHQKIANQFQGCMKKEYLAVISGNMDVDNLDTNLNNSLDTELNNNLNDE 225

Query: 171 CY-GDMQVTLDTQKGSNAWVTVGL 193
            Y   + + L   K +N+  +V +
Sbjct: 226 KYNLPLNLRLKIYKENNSKFSVII 249


>gi|319746042|gb|EFV98321.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           agalactiae ATCC 13813]
          Length = 294

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 28  RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 87  DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 146

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 147 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 203

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 204 IIDVLKYIQNSSLIKCRLETGRTHQIR 230


>gi|110833922|ref|YP_692781.1| ribosomal large subunit pseudouridine synthase C [Alcanivorax
           borkumensis SK2]
 gi|110647033|emb|CAL16509.1| Ribosomal large subunit pseudouridine synthase C [Alcanivorax
           borkumensis SK2]
          Length = 317

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 85/236 (36%), Gaps = 44/236 (18%)

Query: 6   IVQENFTPQRVSKVIARAGIA---SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
            + E    QR+   +         SR  V R+I    V+VN    ++    + + D + V
Sbjct: 15  TIDEGRHGQRLDNFLFTHLKGVPKSR--VYRIIRSGEVRVNKGRAKQ-TTRLCTGDVVRV 71

Query: 63  ---------------DG--VPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP 102
                          +G    LR+A   E  +L++++KP G +  H        + + L 
Sbjct: 72  PPIRTSDSTAPAAVSEGLAERLRRACVYEDDQLFVFNKPAG-LAVHGGSGVSLGLIEALR 130

Query: 103 SIFSR---VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG------ 151
            +F +   +  V RLD +T GL+++       R L+      Q  + Y +   G      
Sbjct: 131 VMFPQERELELVHRLDRDTSGLIMVARRRSFLRKLQRLMQGGQIEKRYWLLCQGFKGKER 190

Query: 152 QVDQDKLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +D   L ++     I     +G         L+    +   V   L  G+  +I+
Sbjct: 191 TLDAPLLKMMNGNERIVRVSREGKPSVTHFRLLERFAQAQ-LVEATLETGRTHQIR 245


>gi|76786717|ref|YP_330596.1| ribosomal large subunit pseudouridine synthase A [Streptococcus
           agalactiae A909]
 gi|76561774|gb|ABA44358.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Streptococcus agalactiae A909]
          Length = 294

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 28  RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 87  DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 146

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 147 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 203

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 204 IIDVLKYTQNSSLIKCRLETGRTHQIR 230


>gi|308172908|ref|YP_003919613.1| RNA pseudouridine synthase [Bacillus amyloliquefaciens DSM 7]
 gi|307605772|emb|CBI42143.1| putative RNA pseudouridine synthase [Bacillus amyloliquefaciens DSM
           7]
 gi|328552548|gb|AEB23040.1| RNA pseudouridine synthase [Bacillus amyloliquefaciens TA208]
 gi|328910948|gb|AEB62544.1| putative RNA pseudouridine synthase [Bacillus amyloliquefaciens
           LL3]
          Length = 302

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/169 (15%), Positives = 56/169 (33%), Gaps = 22/169 (13%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDIN 117
           G      E + + + +KP G+ T  ++     T+ + +   F       +V  V RLD +
Sbjct: 81  GEAEILFEDSHMLIANKPAGMPTHPNEEGQTGTLSNLIAYHFQINGEQAKVRHVHRLDRD 140

Query: 118 TEGLLLLTNDGGLARVLELPSTQ---WLRVYRV-----------RFHGQVDQDKLNLLKK 163
           T G ++      LA  +     +     R Y                  + +D+ + +++
Sbjct: 141 TSGAVVFAKH-RLAHAILDRQLETKTLKRTYIAAAEGKVKPKKGTVDSPIGRDRSHSVRR 199

Query: 164 GIVIQGICYGDMQVTLDTQKGSN-AWVTVGLREGKNREIKKVFEFFNWK 211
            +   G              G+  + V + L  G+  +I+         
Sbjct: 200 RVSPGGQAAVTHYKVKGYHPGAQLSLVELELETGRTHQIRVHMASIGHP 248


>gi|183597816|ref|ZP_02959309.1| hypothetical protein PROSTU_01145 [Providencia stuartii ATCC 25827]
 gi|188022571|gb|EDU60611.1| hypothetical protein PROSTU_01145 [Providencia stuartii ATCC 25827]
          Length = 217

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/164 (15%), Positives = 60/164 (36%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   +   +KP GL++     P+   ++   +        SV RLD+ T G++++  +  
Sbjct: 18  QDEHIITVNKPSGLLSVPGKAPEHHDSIMSRIQRDHPHAESVHRLDMATSGVMVVALNKA 77

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVTLDTQ 182
             R L+    +    + Y  R  G +++      ++G+V    I         +V  +T 
Sbjct: 78  AERELKRQFREREPKKHYIARVWGHLEK------QEGLVDLPLICDWPNRPKQKVCFETG 131

Query: 183 KGSNAWVTVGLRE------------GKNREIK-KVFEFFNWKVN 213
           K +     V   E            G++ +++  +       + 
Sbjct: 132 KAAQTEYQVLEYEEQATRVKLSPITGRSHQLRVHML-ALGHPIL 174


>gi|149183528|ref|ZP_01861954.1| ribosomal large subunit pseudouridylate synthase D [Bacillus sp.
           SG-1]
 gi|148848774|gb|EDL62998.1| ribosomal large subunit pseudouridylate synthase D [Bacillus sp.
           SG-1]
          Length = 334

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/153 (18%), Positives = 57/153 (37%), Gaps = 21/153 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPD-GRSTVFDNLPSIFSR------VISVGRLDINTEGLLL 123
           E   + + +KP G+ T  ++P   + T+ + +     +      V  + RLD +T G ++
Sbjct: 117 EDAHMMIVNKPAGMNTHPNNPSLEKDTLANAVAWHLQQKGEKVDVQHIHRLDKDTTGAVV 176

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK--LNLL---------KKGIVIQGI 170
                 +  +L   L   +  R Y    HG +   K  +            ++ +   G 
Sbjct: 177 FAKHALVKGILDRLLAERKIKRTYWAIVHGLITNKKGTITKAIGRDRHHNTRRRVSPSGQ 236

Query: 171 CYGDMQVTLDTQKGSN-AWVTVGLREGKNREIK 202
                   L+  K  N + V + L  G+  +I+
Sbjct: 237 PATTHFQLLEQNKPKNLSLVQLVLDTGRTHQIR 269


>gi|257418294|ref|ZP_05595288.1| pseudouridine synthase [Enterococcus faecalis T11]
 gi|257160122|gb|EEU90082.1| pseudouridine synthase [Enterococcus faecalis T11]
          Length = 287

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P   +T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 235


>gi|218902402|ref|YP_002450236.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
 gi|218537046|gb|ACK89444.1| ribosomal large subunit pseudouridine synthase, RluA family
           [Bacillus cereus AH820]
          Length = 292

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 45/267 (16%), Positives = 87/267 (32%), Gaps = 50/267 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + I V             + +PL    E   + + +K   
Sbjct: 36  GAIEVNGQHA-SVRHQLQAGEEIRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 94

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L S + +      V  V RLD +T GL+L+  +      L   
Sbjct: 95  MSTIPSREHPSGSVANALLSHYDKQYLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSK 153

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                   R Y    HG            + +   +++++ +  +G         + +  
Sbjct: 154 QHQQKAVKRTYEALVHGEMIEQEGTIDAPIGRKSDSIIERTVCEEGQRAITHFRVIASAN 213

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
                V++ L  G+  +I+         +              TL  G   EV ++ L  
Sbjct: 214 HKTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DTLYGGKRDEVKRQALHS 261

Query: 243 -EQLGPHLLEEAQVNLDAPIYSSETLV 268
                 H + E +++  A I S    V
Sbjct: 262 TSLTFYHPILEKEMSFTAMIPSDMQEV 288


>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 = 50.2 bits (119), Expect = 5e-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  QRLDNVVYRMGFASTRAEARQLVSHKAVVVNGQVVNIPSFKVRPEDVVSV 145


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR+E  +++      VNG  +   + NV   D I V     R  E+
Sbjct: 98  MRLDNVVYRLGYGDSRKESRQLVTHGHFLVNGKKVNIPSFNVSVNDVITVS-EKSRATEK 156

Query: 73  TRLWLYH 79
            + ++ +
Sbjct: 157 FKTFIEN 163


>gi|254557295|ref|YP_003063712.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
 gi|254046222|gb|ACT63015.1| pseudouridylate synthase [Lactobacillus plantarum JDM1]
          Length = 300

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 49/145 (33%), Gaps = 17/145 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGL 130
           L +  KP G+ +  + P    ++ ++L +           V RLD  T G +L+  +  +
Sbjct: 93  LLVVDKPAGVKSHPNQPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLVALNPVV 152

Query: 131 ARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQV 177
             +L   +   Q  R Y     G            +  D  +  K+ +            
Sbjct: 153 VPILDRLISDKQIRRTYYAWVRGHFATPTGHFTAPIGHDATDKRKRWVNTADAQPALTDY 212

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            +       + V + L  G+  +++
Sbjct: 213 EVCATTAHQSLVKLTLHTGRTHQLR 237


>gi|300768616|ref|ZP_07078515.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
 gi|300493923|gb|EFK29092.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ATCC 14917]
          Length = 300

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 49/145 (33%), Gaps = 17/145 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGL 130
           L +  KP G+ +  + P    ++ ++L +           V RLD  T G +L+  +  +
Sbjct: 93  LLVVDKPAGVKSHPNQPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLVALNPVV 152

Query: 131 ARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQV 177
             +L   +   Q  R Y     G            +  D  +  K+ +            
Sbjct: 153 VPILDRLISDKQIRRTYYAWVRGHFTTPTGHFTAPIGHDATDKRKRWVNTADAQPALTDY 212

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            +       + V + L  G+  +++
Sbjct: 213 EVCATTAHQSLVKLTLHTGRTHQLR 237


>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 = 50.2 bits (119), Expect = 5e-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|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 = 50.2 bits (119), Expect = 5e-04,   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|195051252|ref|XP_001993060.1| GH13297 [Drosophila grimshawi]
 gi|193900119|gb|EDV98985.1| GH13297 [Drosophila grimshawi]
          Length = 562

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/207 (15%), Positives = 69/207 (33%), Gaps = 25/207 (12%)

Query: 32  ERMIAQQRVKVNGILLE---RAAVNVMSTDHIEVDGVPLRKAERTRLWL------YHKPI 82
           +R I    + VN   +    R   N +  + +    VP+     T + +       +KP 
Sbjct: 190 KRSIEAGSLTVNHEKVPIDYRLKHNDLLANTVHRHEVPVTAHPITIVHMDDDILVVNKPA 249

Query: 83  GLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            +          +T+   L   F    + ++ RLD  T GLLL       AR +E    +
Sbjct: 250 SIPVHPCGRYRHNTMIFILAKEFNMRNLRTIHRLDRLTSGLLLFGRTAEKAREMEQQIRN 309

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV------G 192
            Q  + Y     G      +    + I +     G  +V+   +     +  +       
Sbjct: 310 RQVQKEYVCCVEGCFPDGNIE-CNEPIEVVSYKIGVCKVSPKGKDCKTTFKRLGQVGDYS 368

Query: 193 LRE-----GKNREIKKVFEFFNWKVNR 214
           + +     G+  +I+   ++  + +  
Sbjct: 369 IVQCKPLTGRMHQIRVHLQYLGYPIVN 395


>gi|28379165|ref|NP_786057.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308181361|ref|YP_003925489.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
 gi|28272003|emb|CAD64908.1| pseudouridylate synthase [Lactobacillus plantarum WCFS1]
 gi|308046852|gb|ADN99395.1| pseudouridylate synthase [Lactobacillus plantarum subsp. plantarum
           ST-III]
          Length = 300

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 23/145 (15%), Positives = 49/145 (33%), Gaps = 17/145 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTNDGGL 130
           L +  KP G+ +  + P    ++ ++L +           V RLD  T G +L+  +  +
Sbjct: 93  LLVVDKPAGVKSHPNQPGETGSILNDLAATLQPTQQVPYMVHRLDQMTSGAMLVALNPVV 152

Query: 131 ARVL--ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQV 177
             +L   +   Q  R Y     G            +  D  +  K+ +            
Sbjct: 153 VPILDRLISDKQIRRTYYAWVRGHFATPTGHFTAPIGHDATDKRKRWVNTADAQPALTDY 212

Query: 178 TLDTQKGSNAWVTVGLREGKNREIK 202
            +       + V + L  G+  +++
Sbjct: 213 EVCATTAHQSLVKLTLHTGRTHQLR 237


>gi|304407040|ref|ZP_07388694.1| hemolysin A [Paenibacillus curdlanolyticus YK9]
 gi|304344027|gb|EFM09867.1| hemolysin A [Paenibacillus curdlanolyticus YK9]
          Length = 277

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 1/64 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
              +R+  ++   G   SR + +  +    V V+G  +E++ + V     I V G P  
Sbjct: 2  TIPKERIDVLLVEQGFYESREKAKAAVMAGLVLVDGDRMEKSGMKVPRAATITVKGAPHP 61

Query: 69 KAER 72
             R
Sbjct: 62 YVSR 65


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 1/63 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRK 69
             +R+  ++ +  +A SR + + +I    V VNG   ++A  +   T  IEV G  L+ 
Sbjct: 1  MKKERLDVLMVQRNLAESREKAKALIMSGIVYVNGQKEDKAGTSFEETVQIEVRGNTLKY 60

Query: 70 AER 72
            R
Sbjct: 61 VSR 63


>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 = 50.2 bits (119), Expect = 5e-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  RLDNVLFRMGLGRTRKEARQIVDHKHILVNGKPVNIPSYRVKAGDVIEV 136


>gi|22538202|ref|NP_689053.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           agalactiae 2603V/R]
 gi|22535113|gb|AAN00926.1|AE014285_8 ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus agalactiae 2603V/R]
          Length = 294

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 28  RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 87  DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 146

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 147 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 203

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 204 IIDVLKYIQNSSLIKCRLETGRTHQIR 230


>gi|169795158|ref|YP_001712951.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AYE]
 gi|184158990|ref|YP_001847329.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213158176|ref|YP_002320227.1| pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|215482708|ref|YP_002324906.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|301348011|ref|ZP_07228752.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB056]
 gi|301512677|ref|ZP_07237914.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB058]
 gi|301597067|ref|ZP_07242075.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB059]
 gi|169148085|emb|CAM85948.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AYE]
 gi|183210584|gb|ACC57982.1| Pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           ACICU]
 gi|213057336|gb|ACJ42238.1| pseudouridine synthase A [Acinetobacter baumannii AB0057]
 gi|213988340|gb|ACJ58639.1| Ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii AB307-0294]
 gi|322508972|gb|ADX04426.1| rluA [Acinetobacter baumannii 1656-2]
 gi|323518957|gb|ADX93338.1| pseudouridylate synthase, 23S RNA-specific [Acinetobacter baumannii
           TCDC-AB0715]
          Length = 212

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 43/117 (36%), Gaps = 16/117 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLAR 132
             + HKP  +++     D   +V   L +I  R + + RLD +T G+L+   +  G  A 
Sbjct: 16  FMVIHKPSDILSVPGKGDLHDSVLTRLVAIEPRTLLIHRLDRDTSGILVFGLSKRGQSAI 75

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 76  ARQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVVYDPSRPPLHIV 118


>gi|254303628|ref|ZP_04970986.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
 gi|148323820|gb|EDK89070.1| pseudouridylate synthase [Fusobacterium nucleatum subsp.
           polymorphum ATCC 10953]
          Length = 288

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 37/222 (16%), Positives = 83/222 (37%), Gaps = 41/222 (18%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS-------VGRLDINTEGLLL 123
           E   L + +K   ++   +      T+ + + + F + +          RLD+NT GL++
Sbjct: 78  EDENLLIVNKEPYIIVHPTQKKVDKTLANAVVNYFEKTLGKTLVPRFYNRLDMNTSGLII 137

Query: 124 LTNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL----------NLLKKGIVI---QGI 170
           +  +    +      T+  + Y+V   G +++D            + L++ I +    G 
Sbjct: 138 IAKN-SYTQAFLQDKTEVKKTYKVIVSGIIEEDDFFIEKPIGKIGDDLRR-IELSEENGG 195

Query: 171 CYGDMQVTLDTQ--KGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTL 228
                 + +  +  + +  ++   L  G+  +I+      +           G   +G  
Sbjct: 196 KSAKTHIKVLERNYEKNITFLEARLYTGRTHQIR---AHLSL---------IGHSLVGDE 243

Query: 229 LAGSTREVSKKIL-----REQLGPHLLEEAQVNLDAPIYSSE 265
           L G   E++K+ +      E   P  LE  ++ +D PI   E
Sbjct: 244 LYGGNMELAKRQMLHAYKLEFQNPKTLENLKIEIDIPIDMKE 285


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
          R+  ++ + G+A +R   + +I    V+V+G++  +A   V     IE+ G  L    R 
Sbjct: 6  RLDHLLVQRGLAETRARAQALILAGEVRVDGVVRLKAGELVPEDAGIELAGK-LPYVSRG 64

Query: 74 RLWLYH 79
             L H
Sbjct: 65 GYKLAH 70


>gi|56755719|gb|AAW26038.1| SJCHGC01065 protein [Schistosoma japonicum]
          Length = 438

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 32/222 (14%), Positives = 67/222 (30%), Gaps = 49/222 (22%)

Query: 37  QQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRKAERTRLWL-YHKPIGLVT 86
              + VNG  +      +   D +          V  +P+     +   L  +KP    +
Sbjct: 94  SGDILVNGARV-DPDYVLNDNDLLSQQVHRHEFPVLNLPIEFIHDSHDMLVINKPP---S 149

Query: 87  THSDPDGRSTV----FDNLPSI-FSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PST 139
               P GR T+               +    RLD  T GLLL+  D   +  L+    S 
Sbjct: 150 IPIHPCGRYTLNSITHILAKDYGLRPLRFTHRLDRMTSGLLLIAKDYDTSVRLQSQIASK 209

Query: 140 QWLRVYRVRFHGQVDQDKLN-----LLKKGIVIQGICYGDMQVTLDT----------QKG 184
           +  + Y     G    + ++      +  G+V+     G +   +            +  
Sbjct: 210 EVTKHYICHVDGCFPTEPIDHCTGFEINNGVVVCSQPVGPISPKMGIHAVLPESAGGKPA 269

Query: 185 SNAWVTV-------------GLREGKNREIKKVFEFFNWKVN 213
              ++ +              L  G+  +I+   ++  + + 
Sbjct: 270 RTHFLRLNYNSVTNTSLVICRLFTGRTHQIRIHTQYLGYPIV 311


>gi|86740132|ref|YP_480532.1| ribosomal large subunit pseudouridine synthase D [Frankia sp. CcI3]
 gi|86566994|gb|ABD10803.1| ribosomal large subunit pseudouridine synthase D [Frankia sp. CcI3]
          Length = 313

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 53/324 (16%), Positives = 97/324 (29%), Gaps = 67/324 (20%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV---- 62
           V +     R+   IAR    SR     ++   +  ++G +  R+   V     +EV    
Sbjct: 13  VPDGLDGVRLDAAIARMFGLSRTVAAALVDDGQASLDGKVRGRSD-RVSGGAWLEVRLPA 71

Query: 63  --DGVPLRKAERTRLWLYH---------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVI-- 109
               V +       L + +         KP+G+    +      TV   L +   R+   
Sbjct: 72  PPRPVAVEPTPVEALGILYDDDDIIVVDKPVGVAVHPAPGFTGPTVIGALAAAGYRISTS 131

Query: 110 -------SVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNL 160
                   V RLD+ T G++++        +L+         + YR    G  D      
Sbjct: 132 GAAERQGVVHRLDVGTTGVMVVAKSERAYTLLKRAFRDRTVDKRYRAVVQGHPDP----- 186

Query: 161 LKKGI--VIQGICYGDM--QVTLDTQKGSN-----------AWVTVGLREGKNREIKKVF 205
           L+  +   I           V  D +               + ++V L  G+  +I+   
Sbjct: 187 LRGTVDAPIDRHPRRPGLFAVVADGKPSITHYDLQEAFRAASLLSVRLETGRTHQIRVHM 246

Query: 206 EFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLG--PHLLEEAQVNLDAPIYS 263
                               G L  G+        L E+LG     L  A+++ D P + 
Sbjct: 247 SALRHPCV------------GDLAYGA-----DPTLAERLGLTRQWLHAARLSFDHPGHG 289

Query: 264 SETL-VRDRPNIISEVPDDFTRMK 286
                    P  ++E  +      
Sbjct: 290 GRVEFTSPDPADLAEAVERLRDQP 313


>gi|260494008|ref|ZP_05814139.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
 gi|260198154|gb|EEW95670.1| pseudouridylate synthase [Fusobacterium sp. 3_1_33]
          Length = 304

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 37/254 (14%), Positives = 93/254 (36%), Gaps = 55/254 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
           I+ E++   RV + +       R+        E+ +M+ + ++KVN   + +    ++  
Sbjct: 5   IIDEDYESVRVDRFL-------RKHLKNINLSEIYKMLRKGKIKVNNKKISQ-DYRLVLG 56

Query: 58  DHI--------------------EVDGVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGR 94
           D I                    ++    L++    E   L++ +KP+G V  H      
Sbjct: 57  DIIFIFLPEIFKEKNEEKFIEISQIRKEKLKQMIVFENDNLFVINKPLGDVV-HKGSGHD 115

Query: 95  STVFDNLPSIFS--RVISVGRLDINTEGLLLLTNDGGLARVLELPST--QWLRVYRVRFH 150
            ++ +   S +S   +  V R+D  T GL++   +   AR +         ++ Y +  +
Sbjct: 116 ISLLEEFRSYYSNNNINFVNRIDKLTSGLVIGAKNIKTAREVAKEIQAGNIVKKYYILVN 175

Query: 151 GQVDQD------KLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
           G++++D       L   ++ +++     +G            +      +   L+ G+  
Sbjct: 176 GKIEKDNFILENYLKKDEERVIVSDIEKEGYKKSITYFKKIKEYDKYTLLEAELKTGRTH 235

Query: 200 EIKKVFEFFNWKVN 213
           +++         + 
Sbjct: 236 QLRAQLNHLGNNIV 249


>gi|169632854|ref|YP_001706590.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii SDF]
 gi|239501123|ref|ZP_04660433.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii AB900]
 gi|260556640|ref|ZP_05828858.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
 gi|169151646|emb|CAP00433.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter baumannii]
 gi|193077967|gb|ABO12881.2| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter baumannii ATCC 17978]
 gi|260409899|gb|EEX03199.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           baumannii ATCC 19606]
          Length = 212

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 43/117 (36%), Gaps = 16/117 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLAR 132
             + HKP  +++     D   +V   L +I  R + + RLD +T G+L+   +  G  A 
Sbjct: 16  FMVIHKPSDILSVPGKGDLHDSVLTRLVAIEPRTLLIHRLDRDTSGILVFGLSKRGQSAI 75

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 76  ARQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVVYDPSRPPLHIV 118


>gi|326675673|ref|XP_693475.4| PREDICTED: RNA pseudouridylate synthase domain-containing protein
           2-like [Danio rerio]
          Length = 599

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/138 (20%), Positives = 54/138 (39%), Gaps = 14/138 (10%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKPIGL 84
           + + R+K+N   ++   V + + D +          V G PL+   +   + +  KP  L
Sbjct: 218 VKEGRIKLNETPVDDLNVVLKNNDLLRNTVHRHEPPVCGQPLKLLVDDGEVVVVDKPSSL 277

Query: 85  VTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
                     +TV   L        + +V RLD  T G+LL      +++ L   +   Q
Sbjct: 278 PVHPCGRYRHNTVIFILGKEKGLVGLHTVHRLDRLTSGVLLFARTLEVSKKLDVMVRERQ 337

Query: 141 WLRVYRVRFHGQVDQDKL 158
             + Y  R  G+  + ++
Sbjct: 338 LEKEYVCRVEGEFPEAEV 355


>gi|304404905|ref|ZP_07386565.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
 gi|304345784|gb|EFM11618.1| pseudouridine synthase, RluA family [Paenibacillus curdlanolyticus
           YK9]
          Length = 317

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/195 (16%), Positives = 73/195 (37%), Gaps = 34/195 (17%)

Query: 41  KVNGILLERAAVNVMSTDHIEV------------DGVPLRKA-ERTRLWLYHKPIGLVTT 87
            VNG  +  +   V + D ++V            + +P+    E   L + +KP G++  
Sbjct: 49  TVNGKRVYTSD-RVSTGDLLQVRMEKERSDDILPEPIPIEVVFEDDDLLIVNKPAGIIVH 107

Query: 88  HSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPST 139
            +      T+ + +   +       R   + RLD +T GL+++     + + L   L + 
Sbjct: 108 PTHGHYTGTLANGVVHYWQERGEIVRFRPIHRLDEHTSGLVVIAKTPYVHQQLSEQLQAG 167

Query: 140 QWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNA 187
              + Y    +G            +D+D      + +  +G        T+    +G+ +
Sbjct: 168 TIEKRYLAFVYGKPEPSEGTVNEPIDRDPERPHIRIVTPEGYPSVTHYETIAQYNEGTAS 227

Query: 188 WVTVGLREGKNREIK 202
            V + L  G+  +I+
Sbjct: 228 CVRLNLETGRTHQIR 242


>gi|161503726|ref|YP_001570838.1| 23S rRNA pseudouridylate synthase C [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160865073|gb|ABX21696.1| hypothetical protein SARI_01811 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 317

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 42/272 (15%), Positives = 88/272 (32%), Gaps = 59/272 (21%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           +  +   QR+   +       R +++        R++ +  V+VN   ++     + + D
Sbjct: 13  ITADEAGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKKRIK-PEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT---------------------RLWLYHKPIGLVTTHSDPDGRSTV 97
            + +  V + + E                        L + +KP G             +
Sbjct: 65  EVRIPPVRVAEREEEAVSPHLQKVAALADVILYEDDYLLVLNKPSGTAVHGGSGLSFGVI 124

Query: 98  FDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                L      +  V RLD +T G+LL+       R L   L      + Y     GQ 
Sbjct: 125 EGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQW 184

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNR 199
            Q  +  ++  + ++ I     ++   +Q+G  +     + E              G+  
Sbjct: 185 -QSHVKTVQAPL-LKNILQSGERIVRVSQEGKPSETRFKVEERFAFATLVRCSPVTGRTH 242

Query: 200 EIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
           +I+   ++    +    R  YG  +    LAG
Sbjct: 243 QIRVHTQYVGHPIAFDDR--YGDREFDKQLAG 272


>gi|307269713|ref|ZP_07551043.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|306513823|gb|EFM82425.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4248]
 gi|315034494|gb|EFT46426.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0027]
 gi|315147005|gb|EFT91021.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX4244]
 gi|329576828|gb|EGG58313.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1467]
          Length = 283

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATRVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 231


>gi|21229703|ref|NP_635620.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66766580|ref|YP_241342.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|21111188|gb|AAM39544.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66571912|gb|AAY47322.1| pseudouridylate synthase [Xanthomonas campestris pv. campestris
           str. 8004]
          Length = 245

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 30/158 (18%), Positives = 51/158 (32%), Gaps = 31/158 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTND 127
           +   L +  KP GL+   S         + D L     R +  V RLD  T G LLL  D
Sbjct: 13  QDAVLAVVDKPAGLMVHDSKLARGEDDFLADRLRVQLGRPIFLVHRLDRATSGCLLLAFD 72

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDT--QK 183
              A  L   L + +  + Y     G   ++          + G     ++    T  Q+
Sbjct: 73  RDTASALGKALMAGEVEKDYLAICRGWPAEE---RFIVDHDLDGGPGKPIKKPAVTHFQR 129

Query: 184 GSNAWVTV------------------GLREGKNREIKK 203
            +   + +                      G+ R+I++
Sbjct: 130 LATGELEIPSTGFATSRYALLRCQPQT---GRFRQIRR 164


>gi|83855236|ref|ZP_00948766.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           NAS-14.1]
 gi|83941758|ref|ZP_00954220.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           EE-36]
 gi|83843079|gb|EAP82246.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           NAS-14.1]
 gi|83847578|gb|EAP85453.1| ribosomal large subunit pseudouridine synthase A [Sulfitobacter sp.
           EE-36]
          Length = 215

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/162 (16%), Positives = 55/162 (33%), Gaps = 16/162 (9%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   E   + L  KP GL++     P     +   +   F   + V RLD +T G+++  
Sbjct: 13  VVLHEDAEVLLVDKPAGLLSVPGKGPHLADCLIARVQDAFPDALLVHRLDRDTSGVMIFA 72

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICY 172
                 R L L        + Y  R  G   +      L L+       ++ +  +    
Sbjct: 73  LTPHAQRHLGLQFEKRMTRKTYVARVWGVPQEKTGTIDLPLIVDWPNRPRQMVCHETGKP 132

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
                 +   +G  A V +  + G++ +++  +       + 
Sbjct: 133 AQTDWRVLKDEGDTARVRLSPKTGRSHQLRVHML-SLGHPIL 173


>gi|323487164|ref|ZP_08092469.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
 gi|323399516|gb|EGA91909.1| pseudouridine synthase [Clostridium symbiosum WAL-14163]
          Length = 298

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 37/217 (17%), Positives = 75/217 (34%), Gaps = 35/217 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   L + +K  G+    S  +  +T+ + L   F          +V RLD +T GLLL+
Sbjct: 86  EDEDLMVINKAAGMPVHPSQGNFDNTLANGLAWYFKEKGEAFVFRAVNRLDRDTTGLLLI 145

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHG----------QVDQDKLNLLKKGIVIQGICY 172
             +     +L    ++    R YR    G           + + + + +++ +  +   Y
Sbjct: 146 AKNMLSGAILSSMVSEKTIRREYRAIVSGLTEEEGCICRPIARAEGSTIERCVDPERGEY 205

Query: 173 GDMQVTLDT--QKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT-LL 229
              +       +    + + + L  G+  +I+      + K         G   LG  L 
Sbjct: 206 ACTRYRRLGYDRDKDCSLLLITLDTGRTHQIR-----VHMKY-------IGHPLLGDFLY 253

Query: 230 AGSTREVSKKILR--EQLGPHLLEEAQVNLDAPIYSS 264
               R + ++ L        H L    ++  AP+   
Sbjct: 254 NPDYRFIKRQSLHSCRLTFTHPLTGEAMDFTAPLPED 290


>gi|260945269|ref|XP_002616932.1| hypothetical protein CLUG_02376 [Clavispora lusitaniae ATCC 42720]
 gi|238848786|gb|EEQ38250.1| hypothetical protein CLUG_02376 [Clavispora lusitaniae ATCC 42720]
          Length = 590

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 30/140 (21%), Positives = 46/140 (32%), Gaps = 14/140 (10%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHI---------EVDGVPLRKA-ERTRLWLYHKP 81
            R IA  +V +N          V + D I          V   P+    E       +KP
Sbjct: 131 RRAIAAGQVLLN-KTPTTLDSIVRNGDLISHRCHRHEPAVSSRPIEIVFEDADKIAINKP 189

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLL--TNDGGLARVLELPS 138
            G+    +     +T+       F + V    RLD  T GL+ L     G    V ++  
Sbjct: 190 SGIPVHPTGRYRYNTITKIFQHEFGKTVHPCNRLDRLTSGLMFLGKNARGAEFFVKQIRE 249

Query: 139 TQWLRVYRVRFHGQVDQDKL 158
               + Y  R  G+    +L
Sbjct: 250 RTVRKEYIARVKGKFPLGEL 269


>gi|229829105|ref|ZP_04455174.1| hypothetical protein GCWU000342_01190 [Shuttleworthia satelles DSM
           14600]
 gi|229792268|gb|EEP28382.1| hypothetical protein GCWU000342_01190 [Shuttleworthia satelles DSM
           14600]
          Length = 337

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 46/282 (16%), Positives = 88/282 (31%), Gaps = 85/282 (30%)

Query: 1   MKDKNIVQENFTPQRVSKVIA---RAGIAS----------------RREVERMIAQQ-RV 40
           M++ +I +E    QR+ K +    RA   S                R E   ++++  R+
Sbjct: 1   MREISITKEE-AGQRLDKFLCKYFRAATTSFLYKMLRKKNIVLNQKRAEGRELLSEGDRI 59

Query: 41  KV-----------NGILLERAAVNVMSTD--HIEVDGVPLRKAERTRLWLYHKPIGLVTT 87
           +V            G   ++A   +   D  H+ V        E   +    KP G ++ 
Sbjct: 60  QVFFSDETFERMRGGDHQDQAFFTLKEIDYRHVHV------IYEDEDILALDKPAGCLSQ 113

Query: 88  H---SDPDGRSTVFDNLPS---------IFSRVISVGRLDINTEGLLLL--TNDGGLARV 133
                D      +   L +                  RLD NT GL+L   T  G     
Sbjct: 114 RAGQKDISLNEEMLAYLIAKGALTRESYFLFHPSVANRLDRNTSGLILAGKTLRGQQYLS 173

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDM--------QVTLDTQKGS 185
            +L     +++Y     G++ ++        + + G  Y D+        +   D  +G+
Sbjct: 174 EQLRDRSVIKLYHTIVRGRLTEE--------LQLDGYLYKDVGRNQVLVSEKKEDLPEGA 225

Query: 186 N---------------AWVTVGLREGKNREIKKVFEFFNWKV 212
                             + V L  G++ +I+         +
Sbjct: 226 QEIHTAYRPLDHRKDLTLLEVHLMTGRSHQIRAHLASIGHPI 267


>gi|86158289|ref|YP_465074.1| ribosomal large subunit pseudouridine synthase A [Anaeromyxobacter
           dehalogenans 2CP-C]
 gi|85774800|gb|ABC81637.1| ribosomal large subunit pseudouridine synthase A [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 241

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 50/159 (31%), Gaps = 32/159 (20%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
            E   L    KP G +       G  ++ + L + F R+  V RLD NT G+L+L     
Sbjct: 13  HEDAALLAVDKPAGRLVIPGREGGEPSLREELEARFGRLWVVHRLDRNTSGVLVLARTAA 72

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDMQVTLDTQ 182
             R L L     +  + Y     G    ++     +   +KG                  
Sbjct: 73  AHRALNLAFDRGEPRKRYLALVRGVPPAEQRIEVAIAPARKG------RMRPAAPDDPRG 126

Query: 183 KGSNAWVT--------------VGLRE-----GKNREIK 202
           K S   V               + L E     G+  +I+
Sbjct: 127 KPSATVVRRLEAYPSHPLGGGPLALVEALPETGRTHQIR 165


>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 = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLRKAER 72
            L    R
Sbjct: 61 EKLPFVSR 68


>gi|329297204|ref|ZP_08254540.1| 23S rRNA pseudouridylate synthase C [Plautia stali symbiont]
          Length = 319

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 77/244 (31%), Gaps = 58/244 (23%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMST 57
           I  EN   QR+   +       R +++        R++ +  V+VN   ++     +   
Sbjct: 13  ITAENAD-QRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKKRVK-PEYKLEDG 63

Query: 58  DHIEVDGVPLRKAERT---------------------RLWLYHKPIGLVTTHSDPDGRST 96
           D + V  V + + E                        L + +KP G             
Sbjct: 64  DEVRVPPVRVAEREEQAVSPKLDKVAALESCILYEDDYLLVLNKPSGTAVHGGSGLSFGV 123

Query: 97  VFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
           +     L      +  V RLD +T G+LL+       R L   L     L+ Y     G 
Sbjct: 124 IEGLRALRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMLKDYLALVRGD 183

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKN 198
                L +++  + ++ I     +V   + +G  +     + E              G+ 
Sbjct: 184 WP-SHLKVVQAPL-LKNILQSGERVVRVSAEGKPSETRFKVEERFGLATLVKASPVTGRT 241

Query: 199 REIK 202
            +I+
Sbjct: 242 HQIR 245


>gi|293364538|ref|ZP_06611261.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
 gi|291316950|gb|EFE57380.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           oralis ATCC 35037]
          Length = 291

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P   + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G+V+  +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEIARDYWALIEGRVESKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             ++   Q       V   L+ G+  +I+
Sbjct: 203 THISRLKQFPNKTTLVRCKLKTGRTHQIR 231


>gi|281599417|gb|ADA72401.1| Ribosomal large subunit pseudouridine synthase A [Shigella flexneri
           2002017]
          Length = 238

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 34  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 93

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 94  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 147

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 148 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 195


>gi|188575741|ref|YP_001912670.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae PXO99A]
 gi|188520193|gb|ACD58138.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae PXO99A]
          Length = 333

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 57/323 (17%), Positives = 102/323 (31%), Gaps = 53/323 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------------ILL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 19  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQVQVV 78

Query: 48  ERAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIF 105
                +    D            E  ++ +  KP GLV      +PDG            
Sbjct: 79  LETQTHAAPQDI-----ALSVLYEDEQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDPA 133

Query: 106 ----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG-------- 151
                R   V RLD +T G+++L         L  +L +    R Y     G        
Sbjct: 134 LASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGTA 193

Query: 152 --QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFN 209
              +D+   + LK  +   G          +  +   A +   L  G+  +I+       
Sbjct: 194 NAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHLK 252

Query: 210 WKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSS 264
             +    L    YG   L  L  G+T E+  ++    R+ L    L+        P+ +S
Sbjct: 253 SPIVGDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLQFLHPVSGEPVRAS 306

Query: 265 ETLVRDRPNIISEVPDDFTRMKK 287
             +  D   +++ + +D  R  +
Sbjct: 307 APVPADLQRLMTALREDSARAAE 329


>gi|163755956|ref|ZP_02163073.1| hypothetical protein KAOT1_11066 [Kordia algicida OT-1]
 gi|161324127|gb|EDP95459.1| hypothetical protein KAOT1_11066 [Kordia algicida OT-1]
          Length = 300

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/140 (18%), Positives = 50/140 (35%), Gaps = 26/140 (18%)

Query: 39  RVKVNGILLERAAVNVMSTDHIEVD-GVPLRKA----------ERTRLWLYHKPIGLVTT 87
           R+ +N  +    A  +   D IE+     + K           E   + + +KP G  T 
Sbjct: 43  RILINNKIATT-ATFISENDVIEIYAEETIVKKIFKLVISVIFEDDEIAIINKPAGFPTN 101

Query: 88  HSDPDGRSTVFDNLP---------SIFSRVISVGRLDINTEGLLLL--TNDGGLARVLEL 136
               +   T+ + LP                 V RLD  T G+L++  T    ++   + 
Sbjct: 102 G---NYFKTIENALPHNLKPSNSIDALPFPKPVHRLDNPTSGILIIAKTKSAQISLYQQF 158

Query: 137 PSTQWLRVYRVRFHGQVDQD 156
              +  + Y+    G+ D++
Sbjct: 159 EQQEISKTYQAIVIGKTDKE 178


>gi|120599252|ref|YP_963826.1| RluA family pseudouridine synthase [Shewanella sp. W3-18-1]
 gi|146292674|ref|YP_001183098.1| RluA family pseudouridine synthase [Shewanella putrefaciens CN-32]
 gi|120559345|gb|ABM25272.1| ribosomal large subunit pseudouridine synthase C [Shewanella sp.
           W3-18-1]
 gi|145564364|gb|ABP75299.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           putrefaciens CN-32]
          Length = 330

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 33/241 (13%), Positives = 73/241 (30%), Gaps = 50/241 (20%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + E+   QR+   +  A     +  + R++ +  V+VN   ++     +   D + +  
Sbjct: 25  TIDEDHFEQRIDNFLMTALKGVPKSMIYRIVRKGEVRVNKKRIK-PEYKLQMGDIVRIPP 83

Query: 65  VPLRK----------------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
           V + +                       E   L + +KP G+            +     
Sbjct: 84  VRVAESDNRTAPSANLSKVSQLEDRILHEDNHLIVLNKPAGIAVHGGSGVDYGVIEALRS 143

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK- 157
           L      +  V RLD +T G+LL+       + L       +  + Y     G+      
Sbjct: 144 LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLALVKGEWSAQDK 203

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREI 201
                L K I ++       ++     +G  +     + +              G+  +I
Sbjct: 204 VVKQPLLK-ITLKSGE----RIVRVNAEGKPSETRFKIMQRYQGCTLVKASPVTGRTHQI 258

Query: 202 K 202
           +
Sbjct: 259 R 259


>gi|304409811|ref|ZP_07391431.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|307304167|ref|ZP_07583920.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
 gi|304352329|gb|EFM16727.1| pseudouridine synthase, RluA family [Shewanella baltica OS183]
 gi|306913065|gb|EFN43488.1| pseudouridine synthase, RluA family [Shewanella baltica BA175]
          Length = 319

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 62/212 (29%), Gaps = 47/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + +  V + +                       
Sbjct: 42  RIVRKGEVRVNKKRIK-PEYKLQIGDIVRIPPVRVAEPDNRTAPSPNLSKVSQLEDRILH 100

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 101 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 160

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              + L       +  + Y     G+       +      I ++       ++     +G
Sbjct: 161 SALKHLHDQLRYKKMQKDYLALVKGEWSAQDKAVKQPLLKITLKSGE----RIVRVNAEG 216

Query: 185 SNAWVTVGLRE--------------GKNREIK 202
             +     + +              G+  +I+
Sbjct: 217 KPSETRFKIMQRYQGCTLVKASPVTGRTHQIR 248


>gi|229084380|ref|ZP_04216660.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
 gi|228698920|gb|EEL51625.1| Pseudouridine synthase [Bacillus cereus Rock3-44]
          Length = 307

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 26/152 (17%), Positives = 56/152 (36%), Gaps = 20/152 (13%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLL 124
           E   + + +KP  + T  S+  G  T+ + +           +V  + RLD +T G ++ 
Sbjct: 90  EDDHVLIVNKPAHMDTHPSNKGGTGTLANLVAFHLQMQGVETKVRHIHRLDKDTTGGVVF 149

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVD------QDKL-----NLLKKGIVIQGIC 171
              G    ++   L      R Y     G+V        + +     +  ++ +  +G  
Sbjct: 150 AKHGIAGVIMDRLLMERNIKRTYLALVEGKVRKKQGIIDEAIGRDRHHATRRRVSQKGDR 209

Query: 172 YGDM-QVTLDTQKGSNAWVTVGLREGKNREIK 202
                ++    +K     VT+ L  G+  +I+
Sbjct: 210 AVTHYKIEKYFKKQDVTLVTLQLETGRTHQIR 241


>gi|153000233|ref|YP_001365914.1| RluA family pseudouridine synthase [Shewanella baltica OS185]
 gi|151364851|gb|ABS07851.1| pseudouridine synthase, RluA family [Shewanella baltica OS185]
          Length = 329

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 62/212 (29%), Gaps = 47/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + +  V + +                       
Sbjct: 52  RIVRKGEVRVNKKRIK-PEYKLQIGDIVRIPPVRVAEPDNRTAPSPNLSKVSQLEDRILH 110

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 111 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 170

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              + L       +  + Y     G+       +      I ++       ++     +G
Sbjct: 171 SALKHLHDQLRYKKMQKDYLALVKGEWSAQDKAVKQPLLKITLKSGE----RIVRVNAEG 226

Query: 185 SNAWVTVGLRE--------------GKNREIK 202
             +     + +              G+  +I+
Sbjct: 227 KPSETRFKIMQRYQGCTLVKASPVTGRTHQIR 258


>gi|116327749|ref|YP_797469.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116120493|gb|ABJ78536.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 277

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 27/141 (19%), Positives = 51/141 (36%), Gaps = 24/141 (17%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT---NDGGLARVL 134
           KP G+    +    R    D L    S   + +V RLD++T GL+ L    +    A  +
Sbjct: 22  KPPGIPVHATKDSKRENFADRLQEQLSLEYLRTVNRLDLDTSGLVFLCKNPDKNKEADRI 81

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV--- 191
              S+   ++Y     G V+++      +   I+       +V     K    ++T+   
Sbjct: 82  LKSSS---KIYLCVADGIVEEEH---FTETCYIKDGNKKVRKVFSGGDKAVTEFLTLKRN 135

Query: 192 ----------GLREGKNREIK 202
                      L  G+  +I+
Sbjct: 136 LKDHYSVLLAKLHTGRRHQIR 156


>gi|331269447|ref|YP_004395939.1| hemolysin A [Clostridium botulinum BKT015925]
 gi|329125997|gb|AEB75942.1| hemolysin A [Clostridium botulinum BKT015925]
          Length = 270

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 28/69 (40%), Gaps = 1/69 (1%)

Query: 10 NFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          N   +R+  ++    I  SR + +  I + ++ VNG  +++    V     IE  G  + 
Sbjct: 3  NVKSERLDVLLVEKNIFESREKAKIAIMEGKIFVNGQRVDKCGQKVKVDSGIEFKGEVMP 62

Query: 69 KAERTRLWL 77
             R    L
Sbjct: 63 YVSRGGYKL 71


>gi|293369136|ref|ZP_06615730.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
 gi|292635719|gb|EFF54217.1| pseudouridine synthase, RluA family [Bacteroides ovatus SD CMC 3f]
          Length = 612

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 24/129 (18%), Positives = 53/129 (41%), Gaps = 8/129 (6%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTND 127
           E   L + +KP G+++     + R +V+  L   +      + V RLD+ T GLLL+   
Sbjct: 350 EDEWLLVVNKPAGMLSVPGKAEDRDSVYHRLKKKYPEATGPMIVHRLDMATSGLLLVAKT 409

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHGQV--DQDKLNLL-KKGIVIQGICYGDMQVTLDTQ 182
             + + L+    +    + Y     G +   + ++  + +K I+I        +     +
Sbjct: 410 KEVHQDLQAQFANRSIKKRYVAVLDGAIIKTEKEIKPIAEKAILIAKETVLTKKTAKAER 469

Query: 183 KGSNAWVTV 191
            G+   + +
Sbjct: 470 TGNTGRIEL 478


>gi|253577230|ref|ZP_04854549.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
 gi|251843344|gb|EES71373.1| pseudouridine synthase [Paenibacillus sp. oral taxon 786 str. D14]
          Length = 321

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 40/230 (17%), Positives = 82/230 (35%), Gaps = 41/230 (17%)

Query: 16  VSKVIARAGIASRREVERM-IAQQRVKVNGILLERAAVNVMSTDHIEVD----------G 64
           + +   R GI SR+ + R+ + ++ V +NG  +   +V V + D + V            
Sbjct: 26  LQR---RMGI-SRKLLSRIKLTERGVMLNGERVY-ISVPVKAGDTVSVSLEKETSTDILP 80

Query: 65  VPLRK---AERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS------RVISVGRLD 115
            P+      E   L + +K  GL+   +      T+ + +   +       R   V RLD
Sbjct: 81  EPIPFDIVYEDEALLIVNKAAGLIVHPTHGHYTGTLANGVVYYWQEKGEKFRFRPVHRLD 140

Query: 116 INTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRF-----------HGQVDQDKLNLLK 162
             T GL+ +  +  + + +   L + +  + Y                G +D+D     +
Sbjct: 141 QETSGLIAIAKNAYVHQHISEQLIAGEVTKKYTALVHGCPAVPEGTIDGPIDRDPAEPHR 200

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWK 211
           + +   G         +    G  A V + L  G+  +I+  +       
Sbjct: 201 RIVTPSGYPSLT-YYKVAEAYGDGARVELRLGTGRTHQIRVHMT-SIGHP 248


>gi|154252611|ref|YP_001413435.1| RluA family pseudouridine synthase [Parvibaculum lavamentivorans
           DS-1]
 gi|154156561|gb|ABS63778.1| pseudouridine synthase, RluA family [Parvibaculum lavamentivorans
           DS-1]
          Length = 482

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 81/265 (30%), Gaps = 74/265 (27%)

Query: 15  RVSKVIARA----GIA------SRREVERMIAQQRVKVN---G--ILLERAAVNVMSTDH 59
           R+ K +  A    G        SR  + ++I Q +V      G   LL   +  V + + 
Sbjct: 147 RLDKYLTEALGDKGEGDAPATLSRARMRQLIEQGQVSREEKAGAPKLLTDPSYRVKAGER 206

Query: 60  IEVD----------GVPLRKA---ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF- 105
           + V           G  +      E   L +  KP GLV   +  +   T+ + L +   
Sbjct: 207 LSVSVPPPTPAKPAGQAIPLEIVYEDADLIVVMKPAGLVVHPAPGNPDMTLVNALVAHCG 266

Query: 106 ---------SRVISVGRLDINTEGLLLL--TN---------------DGGLARVLELPST 139
                     R   V RLD  T GL+++  T+               DG L R     + 
Sbjct: 267 ETLSGIGGEKRPGIVHRLDKETSGLMVVAKTDRAHQGLSAQFAAHGRDGKLTRAYTALTW 326

Query: 140 QWLRVYRVRFHGQVDQDKLN------LLKKGIVIQGICYGDM------QVTLDTQKGSNA 187
              +       G VD +          +   +  +G   G         V  D   G  A
Sbjct: 327 GVPQT----RKGTVDANIARSSHNRSKMAT-VRDRGEETGGRIAITHYTVKTDYADGLVA 381

Query: 188 WVTVGLREGKNREIK-KVFEFFNWK 211
            V   L  G+  +I+  +       
Sbjct: 382 EVECRLETGRTHQIRVHMT-ALGHP 405


>gi|119470572|ref|ZP_01613275.1| pseudouridylate synthase [Alteromonadales bacterium TW-7]
 gi|119446273|gb|EAW27550.1| pseudouridylate synthase [Alteromonadales bacterium TW-7]
          Length = 209

 Score = 50.2 bits (119), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/155 (18%), Positives = 61/155 (39%), Gaps = 18/155 (11%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L + +KP  L+T    DP    ++ + +  +F     V RLD+ T G+L L  +    R 
Sbjct: 14  LLIVNKPSELLTVPGKDPKHADSLINRVNRVFPTARIVHRLDMATSGILCLAMNKAAHRH 73

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
           L +     +  + Y  R  G+++Q+     L L+       K+ +  +          + 
Sbjct: 74  LSMQFQDRETAKRYIARVFGKLEQNNGSVDLPLICDWPNRPKQMVDHENGKPSLTHFKVL 133

Query: 181 TQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
            +  S   V +  +  G++ +++  +       + 
Sbjct: 134 ERDESATRVELTPIT-GRSHQLRVHML-SLGHPIL 166


>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 = 49.8 bits (118), Expect = 6e-04,   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|315267102|gb|ADT93955.1| pseudouridine synthase, RluA family [Shewanella baltica OS678]
          Length = 319

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 62/212 (29%), Gaps = 47/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + +  V + +                       
Sbjct: 42  RIVRKGEVRVNKKRIK-PEYKLQIGDIVRIPPVRVAEPDNRTAPSPNLSKVSQLEDRILH 100

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 101 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 160

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              + L       +  + Y     G+       +      I ++       ++     +G
Sbjct: 161 SALKHLHDQLRYKKMQKDYLALVKGEWSAQDKAVKQPLLKITLKSGE----RIVRVNAEG 216

Query: 185 SNAWVTVGLRE--------------GKNREIK 202
             +     + +              G+  +I+
Sbjct: 217 KPSETRFKIMQRYQGCTLVKASPVTGRTHQIR 248


>gi|229548625|ref|ZP_04437350.1| pseudouridylate synthase RluD [Enterococcus faecalis ATCC 29200]
 gi|257420942|ref|ZP_05597932.1| pseudouridine synthase [Enterococcus faecalis X98]
 gi|229306256|gb|EEN72252.1| pseudouridylate synthase RluD [Enterococcus faecalis ATCC 29200]
 gi|257162766|gb|EEU92726.1| pseudouridine synthase [Enterococcus faecalis X98]
          Length = 287

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 + T   +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVQTLSNNQTAVTCVLETGRTHQIR 235


>gi|124009089|ref|ZP_01693772.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
 gi|123985303|gb|EAY25223.1| ribosomal large subunit pseudouridine synthase C [Microscilla
           marina ATCC 23134]
          Length = 238

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/153 (17%), Positives = 52/153 (33%), Gaps = 19/153 (12%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLPSIFSRVISVGRLDINTEGLL 122
             L   E     + +KP  + +T  D   +G+  +               RLD  T G+L
Sbjct: 7   KDLIVFEDEDYLIINKPPHM-STLDDRASEGKDNIIGMAKDYLESAQVCHRLDKETSGIL 65

Query: 123 LLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLD 180
            +  +    R L +     Q  +VY     G   Q+  + L    ++     G +++ L 
Sbjct: 66  AIAKNPEAYRHLAIQFEKRQVNKVYHAVIGGI--QEYKDTLVDRAILPN-RTGTVKIDLK 122

Query: 181 TQKGSN--AWVTV----GLRE-----GKNREIK 202
            +        + +     L E     G+  +I+
Sbjct: 123 GKPAQTYFKTLKIYKAHTLIEARPVTGRMHQIR 155


>gi|160874866|ref|YP_001554182.1| RluA family pseudouridine synthase [Shewanella baltica OS195]
 gi|160860388|gb|ABX48922.1| pseudouridine synthase, RluA family [Shewanella baltica OS195]
          Length = 329

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 62/212 (29%), Gaps = 47/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + +  V + +                       
Sbjct: 52  RIVRKGEVRVNKKRIK-PEYKLQIGDIVRIPPVRVAEPDNRTAPSPNLSKVSQLEDRILH 110

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 111 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 170

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              + L       +  + Y     G+       +      I ++       ++     +G
Sbjct: 171 SALKHLHDQLRYKKMQKDYLALVKGEWSAQDKAVKQPLLKITLKSGE----RIVRVNAEG 226

Query: 185 SNAWVTVGLRE--------------GKNREIK 202
             +     + +              G+  +I+
Sbjct: 227 KPSETRFKIMQRYQGCTLVKASPVTGRTHQIR 258


>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 = 49.8 bits (118), Expect = 6e-04,   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|170726386|ref|YP_001760412.1| RluA family pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169811733|gb|ACA86317.1| pseudouridine synthase, RluA family [Shewanella woodyi ATCC 51908]
          Length = 319

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/214 (16%), Positives = 64/214 (29%), Gaps = 51/214 (23%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + V  V + +                       
Sbjct: 42  RIVRKGEVRVNKKRIK-PEYKLQDGDIVRVPPVRVSEKDERPGPSANLSKVSQLEERILF 100

Query: 71  ERTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP GL          G      +L      +    RLD +T G+LL+    
Sbjct: 101 EDKHLIVLNKPAGLAVHGGSGVDFGIIEAMRSLRPTQKFLELAHRLDKDTSGVLLIAKKR 160

Query: 129 GLARVLELPS--TQWLRVYRVRFHGQVD--QDKLNL------LKKG-----IVIQGICYG 173
              R L       +  + Y+    G        +        LK G     +  +G    
Sbjct: 161 SALRHLHDQLRFKKMQKDYQALVKGTWQARDKAIKAPLLKLTLKSGERIVRVNQEGKECE 220

Query: 174 DMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
                L   +GS       L +     G+  +I+
Sbjct: 221 TRFKILQRYQGS------TLVQASPVTGRTHQIR 248


>gi|86135800|ref|ZP_01054379.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           MED193]
 gi|85826674|gb|EAQ46870.1| ribosomal large subunit pseudouridine synthase C [Roseobacter sp.
           MED193]
          Length = 348

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 38/200 (19%), Positives = 68/200 (34%), Gaps = 50/200 (25%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
            V E    QR+ + +       RR         +E+M  +  ++++G  ++ A   V + 
Sbjct: 8   TVAEADDDQRIDRWL-------RRLFPHVNQGRIEKMCRKGELRLDGGRVK-ANTRVAAG 59

Query: 58  DHIEV---------------------DGVPLRK---AERTRLWLYHKPIGLVT-----TH 88
             + V                     D   +R     +   + + +KP GL       T 
Sbjct: 60  QVVRVPPLAESDLKPAAPRVARISETDAKMIRGCVIYKDDDVIVLNKPAGLAVQGGSGTT 119

Query: 89  SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
              DG +           R+  V RLD +T G+L+L  +   A+ L          ++Y 
Sbjct: 120 KHVDGLADALRFDAEEKPRL--VHRLDKDTSGVLVLARNRLAAKSLTAAFRHRNTRKIYW 177

Query: 147 VRFHGQVDQDKLNLLKKGIV 166
               G      L  +K G+V
Sbjct: 178 ALVAGVPTP-YLGEIKAGLV 196


>gi|187934581|ref|YP_001884790.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722734|gb|ACD23955.1| pseudouridine synthase, RluA family [Clostridium botulinum B str.
           Eklund 17B]
          Length = 298

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 41/222 (18%), Positives = 78/222 (35%), Gaps = 49/222 (22%)

Query: 33  RMI----AQQRVKVNGILLERAAVNVMSTDHIEVD-----GVPLRKA--------ERTRL 75
           R+I      QR+ VN   +      + + D I++D        +           E   +
Sbjct: 30  RLIRSASKDQRIYVNNSAVR-MNYMIKNGDIIKIDLNRNESQNINPEKIDLDIVYEDEDV 88

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGG 129
            + +K   ++   +      T+ + +   F        V  V RLD+NT GL+++  +  
Sbjct: 89  LVINKQPFIIVHPTKNFQSGTLANGILYYFQETNQNCIVRLVSRLDMNTSGLIIIAKNQF 148

Query: 130 LARVLE-LPSTQWLRVYRVRFHGQVDQDKLNLLKKG-IVI-----QGICYGDMQVTLDTQ 182
               L      +  + Y    HG +++      K+G I +     +GI YG M+V  +  
Sbjct: 149 SHSRLSKDMKEKLQKRYLAIVHGNLEE------KEGTIDLPIYKPEGIEYGSMRVVDERG 202

Query: 183 KGSNAWVTVG-------LRE-----GKNREIKKVFEFFNWKV 212
           + S     V        L E     G+  +I+         +
Sbjct: 203 QRSITHYKVIESFEGGDLVECLLETGRTHQIRVHLSHLGHPI 244


>gi|149194110|ref|ZP_01871208.1| Pseudouridine synthase [Caminibacter mediatlanticus TB-2]
 gi|149136063|gb|EDM24541.1| Pseudouridine synthase [Caminibacter mediatlanticus TB-2]
          Length = 252

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 31/210 (14%), Positives = 68/210 (32%), Gaps = 29/210 (13%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLE--RAAVNVMSTDHIEVDGVPLRKAERTRLW 76
           ++A+    S R  + +I +  V  +   ++  R  + V +   IE    P    E   L 
Sbjct: 9   LLAKQEGISNRAAKELIDRGLVYTHDRKIKIARGLLPVNTRFKIEKIPNPKVIFEDNNLL 68

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +  KP  + +       +  +               RLD  T G+L+LT +    +    
Sbjct: 69  VIDKPPYITSEEISKRFKYPLL-------------HRLDKETSGILVLTKNEDFRKKAIE 115

Query: 137 P--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN-------- 186
              +    + Y     G V +         + I+       +V+ D ++           
Sbjct: 116 EFKNKNVYKEYLAWVSGIVAEPMKIDFPIKV-IKTKSGAFAKVSSDGEEAITEIEPILAF 174

Query: 187 ---AWVTVGLREGKNREIKKVFEFFNWKVN 213
              + +   +  GK  +I+   +  +  + 
Sbjct: 175 RTKSKIKAIIHTGKTHQIRAHLKAIDHPII 204


>gi|120610952|ref|YP_970630.1| tRNA pseudouridine synthase C [Acidovorax citrulli AAC00-1]
 gi|120589416|gb|ABM32856.1| tRNA pseudouridine synthase C [Acidovorax citrulli AAC00-1]
          Length = 277

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/162 (17%), Positives = 47/162 (29%), Gaps = 25/162 (15%)

Query: 75  LWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP G +   +  D      V   L      RV  V RLD  T G+L++      A
Sbjct: 21  LVAVYKPAGWLVHRTGLDAGETRFVMQALRDQLGRRVYPVHRLDKGTCGVLVMGLHAEAA 80

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQ----------VTL 179
           R L       +  + Y     G         +   +                       L
Sbjct: 81  RALSQAFEQHRVDKRYLALVRGHAPDRV--QVDHALRPDDAPPDAAVQPARTALRCLARL 138

Query: 180 DTQKGSNAWV---TVGLRE-----GKNREIKKVFEFFNWKVN 213
           +  + S+A        L E     G+  +I++  +     + 
Sbjct: 139 ELPEASDARFATTRASLVEALPETGRRHQIRRHLKHIAHPIL 180


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 2/66 (3%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  VI R G   SR E  +++      VNG  ++  +  V   D+I V     + +E+ 
Sbjct: 99  RLDNVIYRLGYGQSRAEARQLVTHGHFLVNGRKVDIPSFKVSVNDNITVSDKS-KSSEKF 157

Query: 74  RLWLYH 79
           + +  +
Sbjct: 158 KTFAEN 163


>gi|229154871|ref|ZP_04282985.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 4342]
 gi|228628429|gb|EEK85142.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           ATCC 4342]
          Length = 292

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 41/267 (15%), Positives = 86/267 (32%), Gaps = 50/267 (18%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV-------------DGVPL-RKAERTRLWLYHKPIG 83
             ++VNG         + + + + V             + +PL    E   + + +K   
Sbjct: 36  GAIEVNGQYA-SVRHQLQAGEELRVFFPVEERSEGMIAEDIPLCIVYEDDAVLVINKEAN 94

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE-- 135
           + T  S      +V + L S + +      V  V RLD +T GL+L+  +      L   
Sbjct: 95  MSTIPSREHPAGSVANALLSHYDKQHLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLLSK 153

Query: 136 -LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK 183
                   R Y    HG            + +   +++++ +  +G         +D+  
Sbjct: 154 QHQQKAVKRTYEAIVHGEMVEREGTIDAPIGRKSDSIIERTVCEEGQRAVTHFRVIDSAN 213

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILR- 242
                V++ L  G+  +I+         +               L  G   E+ ++ L  
Sbjct: 214 HKTH-VSLELDTGRTHQIRVHMAHIGHPLLG-----------DNLYGGKRDEMKRQALHS 261

Query: 243 -EQLGPHLLEEAQVNLDAPIYSSETLV 268
                 H + E +++    I +    V
Sbjct: 262 TSLTFYHPILEKEMSFTTTIPNDMQAV 288


>gi|260589549|ref|ZP_05855462.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|331082975|ref|ZP_08332095.1| hypothetical protein HMPREF0992_01019 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540117|gb|EEX20686.1| ribosomal large subunit pseudouridine synthase D [Blautia hansenii
           DSM 20583]
 gi|330399970|gb|EGG79628.1| hypothetical protein HMPREF0992_01019 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 294

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 34/183 (18%), Positives = 63/183 (34%), Gaps = 23/183 (12%)

Query: 41  KVNGILLERAAVNVMSTDHIEVDGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           KVN I+  R      S   + V  +PL    E   + L +KP  +    S  +  +T+ +
Sbjct: 56  KVNDIVTIRLLEEAPSEHIVPVA-LPLDIVYEDEDILLVNKPADMPVHPSINNYDNTLAN 114

Query: 100 NLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +   +           + RLD +T GLL++  +   A +L     + +  R Y     G
Sbjct: 115 GIAHYYQVQGETFVFRCINRLDRDTTGLLIIAKNALSASILSNQMKAREIHRTYLAVVFG 174

Query: 152 QVDQDK-------LNLLKKGIV-----IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNR 199
              ++               I      I G         +   K   + + + L  G+  
Sbjct: 175 IPKKEADTITAPIARKENSAIERCVDFINGERAVT-NYQVVASKEDYSLLKLSLETGRTH 233

Query: 200 EIK 202
           +I+
Sbjct: 234 QIR 236


>gi|148273032|ref|YP_001222593.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830962|emb|CAN01907.1| putative pseudouridine synthase [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
          Length = 305

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 75/240 (31%), Gaps = 41/240 (17%)

Query: 1   MKDKNI-VQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNV----- 54
           M+ + I V +    QRV   +AR    SR     +     V  +G    ++   V     
Sbjct: 1   MEHRTIPVPDGLDGQRVDAGLARLLGFSRSFAAEVAEAGGVTQDGREAGKSDRLVGGSVL 60

Query: 55  ----MSTDHIEVDGVPLRKAE------RTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
                      +  VPL   +         + +  KP+G+    S      TV   L   
Sbjct: 61  AVSWQPKQEPTI--VPLAVPDLGIVHDDDDIVVIDKPVGVAAHPSVGWTGPTVLGALAAA 118

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQV 153
                      R   V RLD  T GL+++         L+      +  +VY     G  
Sbjct: 119 GFRLSTSGAEERQGIVHRLDAGTSGLMVVAKTERAYTELKRQFHDREVEKVYHAVVQGHP 178

Query: 154 DQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +   G        TL+  + + A + V L  G+  +I+
Sbjct: 179 DPLAGTIDAPIGRHPRSDWKFAVTADGKPSVTHYETLEAFRRA-ALLEVHLETGRTHQIR 237


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 35/252 (13%), Positives = 78/252 (30%), Gaps = 49/252 (19%)

Query: 5   NIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV- 62
             + E    QR+   + R+     RR + +++   +V+VN   +  A+  +   D + + 
Sbjct: 27  RQIDETAESQRIDNFLIRSLKGIPRRHIYQLLRSGQVRVNSKRI-DASYRLQLGDKVRIP 85

Query: 63  ----DGVPLRKA------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
                  P+               +   L +  KP G+            V + L     
Sbjct: 86  PVIRSVKPVSSQGVYRTDRFNILYQDDHLLVIDKPAGIAVHGGSGISHG-VIEQLRGQHP 144

Query: 107 RVIS---VGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLL 161
                  V RLD  T G+LLL         L     +    + Y     G+  ++ +  +
Sbjct: 145 DWKFLELVHRLDRETSGILLLARKRQSLLELHRQIREGTVEKHYLTLVRGKW-KNSVQNV 203

Query: 162 KKGIVIQGICYGDMQVTL---------DTQKGSNAWVTV------------GLREGKNRE 200
           +  + +        +  +         D  + ++   T+             L+ G+  +
Sbjct: 204 R--LPLNKYLTAAGERRVAVAAGRNDQDKAQQAHTLFTLQKAWEDFSLLDAELKTGRTHQ 261

Query: 201 IKKVFEFFNWKV 212
           I+       + +
Sbjct: 262 IRVHLAHLGFPI 273


>gi|323453198|gb|EGB09070.1| hypothetical protein AURANDRAFT_53496 [Aureococcus anophagefferens]
          Length = 430

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 40/186 (21%), Positives = 58/186 (31%), Gaps = 16/186 (8%)

Query: 31  VERMIAQQRVKVNGI------LLERAAVNVMSTDHIE--VDGVPLRKAE-RTRLWLYHKP 81
            E + A  R+ VNG       +L+   V V      E  V G P+       R+    KP
Sbjct: 124 AEAL-ADGRILVNGELCGDDLVLKNGDVLVHRAHRHEPPVRGGPIAVVGLDARVLAVDKP 182

Query: 82  IGLVTTHSDPDGRSTVFD-NLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--S 138
            G V  H             L   F+    V RLD  T GL+LL      A  L     +
Sbjct: 183 -GTVPMHPCGSYHYNALSSLLAEDFTPRSFVHRLDRLTSGLVLLARSAEAATELCDCIGA 241

Query: 139 TQWLRVYRVRFHGQVDQDKLNLLK--KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREG 196
            +  + Y  R  G+  +      +                  L       + V    R G
Sbjct: 242 GRARKTYVARVAGRFPERAPAATRGPDAARPDEDASRTRFRLLHRHADGTSTVECHPRTG 301

Query: 197 KNREIK 202
           +  +I+
Sbjct: 302 RTHQIR 307


>gi|315170755|gb|EFU14772.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1342]
          Length = 274

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 15  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 73

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P   +T+ +++ +  +        V RLD  T G ++   +
Sbjct: 74  DEHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 133

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 134 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 192

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 193 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 222


>gi|217973818|ref|YP_002358569.1| RluA family pseudouridine synthase [Shewanella baltica OS223]
 gi|217498953|gb|ACK47146.1| pseudouridine synthase, RluA family [Shewanella baltica OS223]
          Length = 319

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 62/212 (29%), Gaps = 47/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + +  V + +                       
Sbjct: 42  RIVRKGEVRVNKKRIK-PEYKLQIGDIVRIPPVRVAEPDNRTAPSPNLSKVSQLEDRILH 100

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 101 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 160

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              + L       +  + Y     G+       +      I ++       ++     +G
Sbjct: 161 SALKHLHDQLRYKKMQKDYLALVKGEWSAQDKAVKQPLLKITLKSGE----RIVRVNAEG 216

Query: 185 SNAWVTVGLRE--------------GKNREIK 202
             +     + +              G+  +I+
Sbjct: 217 KPSETRFKIMQRYQGCTLVKASPVTGRTHQIR 248


>gi|212637049|ref|YP_002313574.1| pseudouridylate synthase [Shewanella piezotolerans WP3]
 gi|212558533|gb|ACJ30987.1| Pseudouridylate synthase [Shewanella piezotolerans WP3]
          Length = 225

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 25/163 (15%), Positives = 57/163 (34%), Gaps = 34/163 (20%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL----TNDGG 129
           + + +KP GL++    DP    + +  + + +     V RLD+ T G++++    + +  
Sbjct: 23  IMVLNKPSGLLSVPGRDPAHNDSTYSRVLAQYPEAKIVHRLDMATSGVIVVALLRSAESE 82

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDMQVT------- 178
           L R       +  + Y  R  G V  D       G V    I        Q         
Sbjct: 83  LKRQF--RDRETAKTYYARVAGHVKAD------SGTVNLPLICDWPNRPKQKVDHQIGKA 134

Query: 179 ------LDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                 + ++   +  V +  +  G++ +++  +       + 
Sbjct: 135 SQTHYDVVSRAKRSTLVKLTPIT-GRSHQLRVHMM-ALGHPIL 175


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/66 (19%), Positives = 25/66 (37%), Gaps = 1/66 (1%)

Query: 14 QRVSKVIARAGI-ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ + +   G   +R   +  I +  V V+G  + + +  +     + V    L  A R
Sbjct: 1  MRIDQYLVEKGYFTTRTRAQDAIKKGCVSVDGKTIMKNSFVIEEGKEVTVFQEELVLASR 60

Query: 73 TRLWLY 78
              LY
Sbjct: 61 AGFKLY 66


>gi|126173940|ref|YP_001050089.1| RluA family pseudouridine synthase [Shewanella baltica OS155]
 gi|125997145|gb|ABN61220.1| ribosomal large subunit pseudouridine synthase C [Shewanella
           baltica OS155]
          Length = 329

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/212 (12%), Positives = 62/212 (29%), Gaps = 47/212 (22%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA---------------------- 70
           R++ +  V+VN   ++     +   D + +  V + +                       
Sbjct: 52  RIVRKGEVRVNKKRIK-PEYKLQIGDIVRIPPVRVAEPDNRTAPSPNLSKVSQLEDRILH 110

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDG 128
           E   L + +KP G+            +     L      +  V RLD +T G+LL+    
Sbjct: 111 EDNHLIVLNKPAGIAVHGGSGVDYGVIEALRSLRPQQKFLELVHRLDKDTSGVLLVAKKR 170

Query: 129 GLARVLELP--STQWLRVYRVRFHGQVD--QDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
              + L       +  + Y     G+       +      I ++       ++     +G
Sbjct: 171 SALKHLHDQLRYKKMQKDYLALVKGEWSAQDKAVKQPLLKITLKSGE----RIVRVNAEG 226

Query: 185 SNAWVTVGLRE--------------GKNREIK 202
             +     + +              G+  +I+
Sbjct: 227 KPSETRFKIMQRYQGCTLVKASPVTGRTHQIR 258


>gi|319425978|gb|ADV54052.1| pseudouridine synthase, RluA family [Shewanella putrefaciens 200]
          Length = 330

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 33/241 (13%), Positives = 73/241 (30%), Gaps = 50/241 (20%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + E+   QR+   +  A     +  + R++ +  V+VN   ++     +   D + +  
Sbjct: 25  TIDEDHFEQRIDNFLMTALKGVPKSMIYRIVRKGEVRVNKKRIK-PEYKLQMGDIVRIPP 83

Query: 65  VPLRK----------------------AERTRLWLYHKPIGLVTTHSDPDGRSTVFDN-- 100
           V + +                       E   L + +KP G+            +     
Sbjct: 84  VRVAESDNRTAPSANLSKVSQLEDRILHEDNHLIVLNKPAGIAVHGGSGVDYGVIEALRS 143

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDK- 157
           L      +  V RLD +T G+LL+       + L       +  + Y     G+      
Sbjct: 144 LRPQQKFLELVHRLDKDTSGVLLVAKKRSALKHLHDQLRYKKMQKDYLALVKGEWSAQDK 203

Query: 158 --LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREI 201
                L K I ++       ++     +G  +     + +              G+  +I
Sbjct: 204 VVKQPLLK-ITLKSGE----RIVRVNAEGKPSETRFKIMQRYQGCTLVKASPVTGRTHQI 258

Query: 202 K 202
           +
Sbjct: 259 R 259


>gi|71911569|ref|YP_283119.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
 gi|71854351|gb|AAZ52374.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS5005]
          Length = 333

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 36/205 (17%), Positives = 68/205 (33%), Gaps = 32/205 (15%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 66  RKIRHFLRTKKHVLINGHSVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 125

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG---G 129
             + + +KP G+ T  +DP   + +             V RLD  T G +L         
Sbjct: 126 EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 185

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVT 178
           +   L        R Y    HG +D  ++           +  K+ +          +VT
Sbjct: 186 ILNRLL-EKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVT 244

Query: 179 LDTQKGSN-AWVTVGLREGKNREIK 202
           L        + +T  L+ G+  +I+
Sbjct: 245 LVKNFHKTASLLTCQLQTGRTHQIR 269


>gi|311104735|ref|YP_003977588.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           xylosoxidans A8]
 gi|310759424|gb|ADP14873.1| ribosomal large subunit pseudouridine synthase C [Achromobacter
           xylosoxidans A8]
          Length = 325

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 71/236 (30%), Gaps = 59/236 (25%)

Query: 12  TPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMSTDHIEV 62
             QR+   +AR         +        + I    V++N G     A   V   D + +
Sbjct: 33  AGQRLDNFLARL-------CKGVPKTHIYKAIRGGEVRINKGR--TSADYRVAEGDVVRI 83

Query: 63  DGVPLRKAERTR---------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
             + L    + R               L +  KP G+        G S V   +      
Sbjct: 84  PPLRLPDPGKPRPVPGAEFPVVFEDEALLVVDKPAGVAV-----HGGSGVSFGVIEQLRA 138

Query: 108 VIS-------VGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQD 156
                     V RLD  T GLL++         L   L   +  + Y     G    D+ 
Sbjct: 139 ARPGAKFLELVHRLDRETSGLLMVAKKRSALLALHAMLREGKGDKHYLALVEGDWVNDRQ 198

Query: 157 KLNL-LKKGIVIQGICYGDMQ---------VTLDTQKGSNAWVTVGLREGKNREIK 202
            + L L K     G     +          VTL  + G  + V   LR G+  +I+
Sbjct: 199 HIKLGLSKWTTQSGERRVKVDPDGQSAHTIVTLKQRLGGYSLVDAELRTGRTHQIR 254


>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 = 49.8 bits (118), Expect = 6e-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  ++++ + + VNG ++   +  V + D I V
Sbjct: 97  RLDNVVYRLGFGSTRAEARQLVSHKAITVNGQVVNIPSYQVKAGDIIAV 145


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 2/100 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V     IEV        + 
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKHVDIPSYMVKPGQKIEVKEKSKNNPQV 157

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISV 111
            R        G+V     D + +  +F   P     VI +
Sbjct: 158 VRAIDLTAQTGIVPWVDVDKEKKFGIFTRFPQREEVVIPI 197


>gi|237748406|ref|ZP_04578886.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes OXCC13]
 gi|229379768|gb|EEO29859.1| ribosomal large subunit pseudouridine synthase C [Oxalobacter
           formigenes OXCC13]
          Length = 339

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 76/241 (31%), Gaps = 58/241 (24%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMST 57
            V EN   QR+   +        R  +        R++    V+VN   +      +   
Sbjct: 32  TVTENDDGQRIDNFLF-------RTCKGVPKSHIYRILRSGEVRVNKKRI-DQTYRLQEG 83

Query: 58  DHIEVDGVPLRKAERTRL--------------WLYHKPIGLVTTHSDPDGRSTVFDNLPS 103
           D I +  + + + E   +               + +KP G V  H        V + L +
Sbjct: 84  DTIRIPPIKVAEREEKHVPGASFDILYEDDSILVINKPAG-VAVHGGSGVSYGVIEQLRA 142

Query: 104 IFSR---VISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKL 158
                  +  V RLD  T G+L+L         L     +    + Y+    G       
Sbjct: 143 ARPNARFLELVHRLDKETSGILVLAKKRSALVKLHEQIREGSIDKRYQALVKGDWKNQ-- 200

Query: 159 NLLKKGIVIQGICY----GDMQVTLDTQKGSNAWV--------TVGLRE-----GKNREI 201
              ++ + +  + Y    G+ +V +D    ++  +           L E     G+  +I
Sbjct: 201 ---RQHVKLPLLKYHTADGERRVRVDAGGLASHTIFNVLKRFPEFTLLEAELKTGRTHQI 257

Query: 202 K 202
           +
Sbjct: 258 R 258


>gi|326407645|gb|ADZ64716.1| ribosomal large subunit pseudouridine synthase D [Lactococcus
           lactis subsp. lactis CV56]
          Length = 288

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 33/189 (17%), Positives = 58/189 (30%), Gaps = 29/189 (15%)

Query: 42  VNGILLERAAVNVMSTDHIE--VDGVPLRK--------------AERTRLWLYHKPIGLV 85
           VN  L+    + V + D I    D                     E   L + +KP G+ 
Sbjct: 42  VNNKLINENQL-VHAGDKITLIFDNEDFSNLSLKFGSANLADILYEDEHLIVVNKPEGMK 100

Query: 86  TTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLR 143
              +  D  +       +I   V  V RLD  T G +L   +  +  +L       +  R
Sbjct: 101 AHGNTADELALQNHVAAAINQEVFVVHRLDQATSGAVLFAKNQFVLPILGKMFEGNKIHR 160

Query: 144 VYRVRFHGQVDQDKLNLLK----------KGIVIQGICYGDMQVTLDTQKGSNAWVTVGL 193
            Y     G   +++  + +          K I+          V +  +      V   L
Sbjct: 161 EYLALVKGHFPENQFTIDRAIGQNRHDKNKRILSAKGQKAVTHVEIIKKFTDKTLVKCTL 220

Query: 194 REGKNREIK 202
             G+  +I+
Sbjct: 221 DTGRTHQIR 229


>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 = 49.8 bits (118), Expect = 6e-04,   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|256959811|ref|ZP_05563982.1| pseudouridine synthase [Enterococcus faecalis Merz96]
 gi|256950307|gb|EEU66939.1| pseudouridine synthase [Enterococcus faecalis Merz96]
          Length = 287

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATRVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 235


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M +  I+  +    R+  ++ + G+A SR   +R+I   R++V+  ++   +  V     
Sbjct: 1  MDNDKII--DMAKVRLDILLVQRGLAESRTVAQRLILAGRIRVSNEIVTEPSRRVEEDVP 58

Query: 60 IEVD 63
          + +D
Sbjct: 59 LNID 62


>gi|91209118|ref|YP_539104.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UTI89]
 gi|117622346|ref|YP_851259.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli APEC O1]
 gi|218556997|ref|YP_002389910.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli S88]
 gi|237704202|ref|ZP_04534683.1| ribosomal large subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|91070692|gb|ABE05573.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           UTI89]
 gi|115511470|gb|ABI99544.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           APEC O1]
 gi|218363766|emb|CAR01427.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli S88]
 gi|222031890|emb|CAP74628.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           LF82]
 gi|226902114|gb|EEH88373.1| ribosomal large subunit pseudouridine synthase A [Escherichia sp.
           3_2_53FAA]
 gi|294491670|gb|ADE90426.1| pseudouridine synthase, RluA family [Escherichia coli IHE3034]
 gi|307629632|gb|ADN73936.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UM146]
 gi|312944664|gb|ADR25491.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli O83:H1
           str. NRG 857C]
 gi|315285114|gb|EFU44559.1| pseudouridine synthase A [Escherichia coli MS 110-3]
 gi|323950944|gb|EGB46821.1| RNA pseudouridylate synthase [Escherichia coli H252]
 gi|323955254|gb|EGB51027.1| RNA pseudouridylate synthase [Escherichia coli H263]
          Length = 219

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/174 (14%), Positives = 60/174 (34%), Gaps = 31/174 (17%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           D   +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G+
Sbjct: 11  DPWLVVLYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGV 70

Query: 122 LLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM 175
           +++       R L+    +    + Y  R  G           +G+V    I        
Sbjct: 71  IVVALTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPK 124

Query: 176 -QVTLDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +V  +T K +     V               +  G++ +++  +       + 
Sbjct: 125 QKVCYETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/70 (25%), Positives = 30/70 (42%), Gaps = 7/70 (10%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG-------VPL 67
           R+  ++A A  +SR ++   I   +V VNG L+      +   D I V G         L
Sbjct: 189 RLDSLLALAFSSSRTKLVPYIENGKVFVNGKLITSNGYQIKQDDIISVRGLGRFQYKEML 248

Query: 68  RKAERTRLWL 77
            + +R R  +
Sbjct: 249 SQTKRGRYLV 258


>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 = 49.8 bits (118), Expect = 6e-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   +R+E  +++  + V VNG  +   +  V   D IE+
Sbjct: 88  RLDNVLFRLGFGRTRKECRQIVDHKHVLVNGKTVNIPSYRVSVGDVIEI 136


>gi|315156668|gb|EFU00685.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0043]
          Length = 283

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 + T   +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQTLSNNQTAVTCVLETGRTHQIR 231


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 35/202 (17%), Positives = 54/202 (26%), Gaps = 26/202 (12%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLW----------LYHKPIGLVTT 87
            R+ VN   +      V   D IE  G                      +  KP  +   
Sbjct: 35  GRIWVNCNQMTNVNYIVQHNDSIEHIGHRHEHPILDHYIRVIDNDNNIIVVDKPASMPVH 94

Query: 88  HSDPDGRSTVFDNLPSI--FSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWL 142
                   TV   L        +  V RLD  T G+LL   +      L         W 
Sbjct: 95  PCGRYCVHTVLGMLREQRGLRDLRVVHRLDRTTSGVLLFARNSETDTKLKKMLRVGEVWH 154

Query: 143 RVYRVRFHGQVDQDKLNL---------LKKGIV--IQGICYGDMQVTLDTQKGSNAWVTV 191
           + Y  +  G    DK  +         L  GI            +       G  + V  
Sbjct: 155 KEYLCKVEGVFPADKEIICDRPIGPLVLSMGIQCIRDDGKCARSRFWRLWTDGQTSIVRC 214

Query: 192 GLREGKNREIKKVFEFFNWKVN 213
            L  G+  +I+   ++  + + 
Sbjct: 215 MLETGRTHQIRVHLQYLGYPIV 236


>gi|260171398|ref|ZP_05757810.1| ribosomal large subunit pseudouridine synthase A [Bacteroides sp.
           D2]
 gi|315919711|ref|ZP_07915951.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313693586|gb|EFS30421.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 561

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/109 (22%), Positives = 42/109 (38%), Gaps = 8/109 (7%)

Query: 51  AVNVMST---DHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR 107
            + V      + I  D       E   L + +KP G+++     + R +V+  L   +  
Sbjct: 330 GLKVDENPLLNSIHEDEELEIVYEDEWLVVVNKPAGMLSVPGKEEDRDSVYHRLKKKYPD 389

Query: 108 ---VISVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHG 151
               + V RLD+ T GLLL+     + + L+    S    + Y     G
Sbjct: 390 ATGPMIVHRLDMATSGLLLVAKTKEVHQHLQAQFASRSIKKRYVAVLDG 438


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++   G+A SR + + MI +  V VN    ++A        +IE+ G  L+   R
Sbjct: 3  ERLDVLLVNRGLAPSREKAKTMIMEGNVFVNNNREDKAGSTFPDDCNIEIHGKTLQYVSR 62


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLRKAER 72
            L    R
Sbjct: 61 EKLPFVSR 68


>gi|58581220|ref|YP_200236.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae KACC10331]
 gi|58425814|gb|AAW74851.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae KACC10331]
          Length = 335

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 59/324 (18%), Positives = 104/324 (32%), Gaps = 55/324 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------------ILL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 21  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQVQVV 80

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSI 104
                +    D       PL    E  ++ +  KP GLV      +PDG           
Sbjct: 81  LETQTHAAPQDI------PLSVLYEDEQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDP 134

Query: 105 F----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
                 R   V RLD +T G+++L         L  +L +    R Y     G       
Sbjct: 135 ALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGT 194

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D+   + LK  +   G          +  +   A +   L  G+  +I+      
Sbjct: 195 ANAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHL 253

Query: 209 NWKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYS 263
              +    L    YG   L  L  G+T E+  ++    R+ L    L+        P+ +
Sbjct: 254 KSPIVGDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLQFLHPVSGEPVRA 307

Query: 264 SETLVRDRPNIISEVPDDFTRMKK 287
           S  +  D   +++ + +D  R  +
Sbjct: 308 SAPVPADLQRLMTALREDSARAAE 331


>gi|323446696|gb|EGB02765.1| hypothetical protein AURANDRAFT_34908 [Aureococcus anophagefferens]
          Length = 237

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/147 (19%), Positives = 49/147 (33%), Gaps = 15/147 (10%)

Query: 79  HKPIGLVTTH-SDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLARVLEL 136
           +KP G+      D   R  V   L   F R V    RLD  T G LL   DG  A     
Sbjct: 4   NKPAGISVHRNKDTGRRRVVTTQLQRQFRRKVFPAHRLDHRTSGALLFGFDGPTAGKAHD 63

Query: 137 PSTQWLRVYRVRFHG--QVDQDKLN-LLKKGIVIQGICYGDMQVT---LDTQKGSNAWVT 190
                 + Y     G     +   + +++K +        D +     L +Q+     + 
Sbjct: 64  ALAAGTKEYLCLLRGGDWPGEGGADVVVEKPVKGDDGAPRDARTVFRYLASQEEPRCTLC 123

Query: 191 V----GLREGKNREIKKVFEFFNWKVN 213
           +        G+  +I++  +  +  V 
Sbjct: 124 IAAPAT---GRPHQIRRHAQHLSMPVI 147


>gi|306830382|ref|ZP_07463552.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325977346|ref|YP_004287062.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
 gi|304427407|gb|EFM30509.1| ribosomal large subunit pseudouridine synthase [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325177274|emb|CBZ47318.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           gallolyticus subsp. gallolyticus ATCC BAA-2069]
          Length = 286

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 23/150 (15%), Positives = 53/150 (35%), Gaps = 23/150 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG-- 128
           +   L + +KP G+ T  ++P+  + +      +      + RLD+ T G ++   +   
Sbjct: 86  QDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYVGQTCYVIHRLDMETSGAVMFAKNPFV 145

Query: 129 -GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +   L   +    R Y     G+ +     + +  I   G    D +  +  +K    
Sbjct: 146 LPIINRLL-ENKDIAREYWALVQGKFEPKH-QVFQDKI---GRDRHDRRKRVVDRKNGQT 200

Query: 188 WVTVG---------------LREGKNREIK 202
            +T+                L+ G+  +I+
Sbjct: 201 ALTIVDRLKVFPNGTLVKCRLKTGRTHQIR 230


>gi|152996325|ref|YP_001341160.1| RluA family pseudouridine synthase [Marinomonas sp. MWYL1]
 gi|150837249|gb|ABR71225.1| pseudouridine synthase, RluA family [Marinomonas sp. MWYL1]
          Length = 323

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 35/236 (14%), Positives = 75/236 (31%), Gaps = 41/236 (17%)

Query: 6   IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            + +N T QR+   +        + ++  ++ +  ++VN     +    + + D + +  
Sbjct: 18  TIDDNNTGQRIDNFLVTFLKGVPKGKIYNLLRKGEIRVNKKR-TKPDYRLQNEDVVRIAP 76

Query: 65  VPLRKA--------------------ERTRLWLYHKPIGLVTTHSDP--DGRSTVFDNLP 102
           + +                       E   L + +KP GL          G   V   + 
Sbjct: 77  IVIAPESDKPVLSDRLKSEIESRIVYEDKGLIVINKPSGLAVHGGSGLSFGLVEVIRQMR 136

Query: 103 SIFSRVISVGRLDINTEGLLLLTNDGGLARVL---ELPSTQWLRVYRVRFHGQVDQDKLN 159
            +   +  V RLD +T GL+++     + + L           + Y    +G   + KL 
Sbjct: 137 PLEKFIELVHRLDRDTSGLIMVAKKRAVLKELHTALREKEGVQKTYLALVYGSWPKRKLQ 196

Query: 160 --------LLKKG-----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                    L+ G     +   G      +  L  Q    + V      G+  +I+
Sbjct: 197 VNAPLLKNELQSGERVVRVHTDGKESLT-RFKLVRQFEGYSLVECEPVTGRTHQIR 251


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 30/68 (44%), Gaps = 1/68 (1%)

Query: 6  IVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          + ++    +R+  ++   GIA SR + +R I    V +    +++A   V  + +I   G
Sbjct: 1  MAEKKEKKERLDVLLVEQGIAESREKAKRYIMAGMVFIGEKRVDKAGEKVPVSSNIIFRG 60

Query: 65 VPLRKAER 72
            L    R
Sbjct: 61 EKLPFVSR 68


>gi|307544580|ref|YP_003897059.1| 23S rRNA pseudouridylate synthase C [Halomonas elongata DSM 2581]
 gi|307216604|emb|CBV41874.1| 23S rRNA pseudouridylate synthase C [Halomonas elongata DSM 2581]
          Length = 315

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 61/329 (18%), Positives = 100/329 (30%), Gaps = 75/329 (22%)

Query: 7   VQENFTPQRVSKVIA-RAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           V E    QRV   +  R   A R  + R++ +  V+VN   ++ A   + + D + +  +
Sbjct: 12  VTEGQAGQRVDNFLMTRLKGAPRSLIYRIVRKGEVRVNKKRVK-ADSRLATGDVVRIPPL 70

Query: 66  PLRKAERTR--------------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF 105
            L   E  R                      + +KP GL        G S V   L    
Sbjct: 71  KLAPREAVREVSDNLRNLLAGSVLLEGRDWLVLNKPSGLAV-----HGGSGVKIGLIEAL 125

Query: 106 SRVIS-------VGRLDINTEGLLLLTNDGGLARVLELPSTQWL--RVYRVRFHGQVDQ- 155
            +V         V RLD +T G LLL         L     +    + Y     G+    
Sbjct: 126 RQVREDLDFLELVHRLDRDTSGCLLLAKSRTALLTLNTALKRHEMTKRYLALVAGRWPAR 185

Query: 156 -----DKLNLLKKG-------IVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKN 198
                 +L+    G       +   G          +T  G+       L E     G+ 
Sbjct: 186 RDFVSARLDRFDAGNGERRVRVDANGKVARTRFAVRETFAGA------TLMEAEPVTGRT 239

Query: 199 REIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLD 258
            +I+         +            LG    GS RE  +   R  L    L  +++   
Sbjct: 240 HQIRVHAAHAGHPL------------LGDDKYGS-REGQRLAARWDLSRLFLHASELTFP 286

Query: 259 APIYSSETLVRDRPNIISEVPDDFTRMKK 287
            P  +S   V+ R  +   +     R ++
Sbjct: 287 EP--TSGKPVKIRAPLGESLDAVLARARQ 313


>gi|291542721|emb|CBL15831.1| pseudouridine synthase, RluA family [Ruminococcus bromii L2-63]
          Length = 291

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 27/188 (14%), Positives = 59/188 (31%), Gaps = 29/188 (15%)

Query: 69  KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLL 122
           + E     + +KP  +           T+ + +    S+        ++ RLD +T GL+
Sbjct: 83  RYEDEHFLVVNKPHSMPVHPVKQHQSDTLANIVSYYCSQNGKPFVFRAINRLDKDTSGLV 142

Query: 123 LLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-------KLNLLKKGIVI--QGICYG 173
           L+  +   A  +     +  +VY     G+++ +        L    K + I        
Sbjct: 143 LIAKNRFTANAV---KNKTHKVYYALCEGEINIEGIVDKPMDLRDDSKMVRIVRDDGMKA 199

Query: 174 DMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGST 233
                          + + L  G+  +I+    +              P     L  G  
Sbjct: 200 VTHYKPLVATKDFTLLELWLETGRTHQIRCHMAYLGH-----------PLMGDDLYGGKL 248

Query: 234 REVSKKIL 241
            ++S++ L
Sbjct: 249 DKISRQAL 256


>gi|255716616|ref|XP_002554589.1| KLTH0F08866p [Lachancea thermotolerans]
 gi|238935972|emb|CAR24152.1| KLTH0F08866p [Lachancea thermotolerans]
          Length = 234

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 45/151 (29%), Gaps = 29/151 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDP--------DGRSTVFDNLPSIFS----RVISVGRLDINT 118
           E     + +KP G+     D              + + L S  S        V RLD N 
Sbjct: 12  EAKNYVIANKPPGVFCQPPDRNVWYNAQYKEPPILLELLKSQASTRAAEWRPVHRLDTNV 71

Query: 119 EGLLLLTNDGGLARVLEL-------PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGIC 171
            G +L+  +   A +             +  R Y     G    +   L   G++ +   
Sbjct: 72  TGGVLVAKNKNAAAMFSRHLKKGGNHGYKLTRRYVALVEG----NTAELPDTGVISENGR 127

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
               +      K     + + L  GK  +I+
Sbjct: 128 LSKFK------KAGLHVLVLQLCTGKKHQIR 152


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 8/78 (10%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M D+N        QR+ +++   G  ASR      + +  V++ G ++ +A   +     
Sbjct: 1  MSDQN-------SQRLDQLLVSRGLFASRSRARDAVQRGTVRIAGQVVTKAGALIGDDAA 53

Query: 60 IEVDGVPLRKAERTRLWL 77
          IE+D        R  L L
Sbjct: 54 IEIDDPAQDYVSRAALKL 71


>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 = 49.8 bits (118), Expect = 6e-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|293395440|ref|ZP_06639724.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
 gi|291422124|gb|EFE95369.1| ribosomal large subunit pseudouridine synthase A [Serratia
           odorifera DSM 4582]
          Length = 284

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 75/244 (30%), Gaps = 57/244 (23%)

Query: 58  DHIEVDGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDI 116
           D IE+        +  +L L  KP GL++ +  +     +V   L  IF     V RLD 
Sbjct: 67  DRIEI------LYQDEQLVLIDKPAGLLSLSGKNAQNIDSVHHRLVQIFPGCTLVHRLDF 120

Query: 117 NTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD 174
            T GL+L+  +  +   L    +Q    + Y     G ++ +      +G++   I    
Sbjct: 121 GTSGLMLIARNKAINAALCQQFSQRTVSKEYHALLCGHLEHN------EGVIDAAIAKDP 174

Query: 175 M--------------------------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
                                          + +      V +    G+  +++   +  
Sbjct: 175 ALFPLMSICSIHGKPARSRYQVVERGYHAVAEQRPVPVTRVRLTPETGRTHQLRIHCQQL 234

Query: 209 NWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLV 268
              +       YG    G LL G+          EQ    +L  +++    P+       
Sbjct: 235 GHPILGCD--LYG----GRLLPGT----------EQTPRLMLHASELQFVHPVSQRRITA 278

Query: 269 RDRP 272
           R   
Sbjct: 279 RQAS 282


>gi|255033891|ref|YP_003084512.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254946647|gb|ACT91347.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 228

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/156 (18%), Positives = 57/156 (36%), Gaps = 18/156 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF--DNLPSIFS-RVISVGRLDINTEGLLLLTNDGGLA 131
           L   +KP GL+   S     + VF    L    S +V    RLD  T G+LL   +  + 
Sbjct: 13  LVAINKPNGLLVHRSPIASDADVFAVQLLRDQLSQKVYPAHRLDRKTSGVLLFALNENVN 72

Query: 132 RVLEL--PSTQWLRVYRVRFHGQ-VDQDKLN-LLKK--GIVIQGI----CYGDMQVTLDT 181
             ++      +  + Y     G   D+ +++  LK+  G+    +         +V    
Sbjct: 73  SEMQGKFMEGEITKTYHAIVRGHTADRGEIDYPLKRDDGVTQDAVTHFETLARAEVPFAL 132

Query: 182 QKGSNAWVTVG----LREGKNREIKKVFEFFNWKVN 213
            K + +  ++     L  G+  +++K        + 
Sbjct: 133 GKHATSRYSLVQLNPLT-GRMHQLRKHMAHIMHPII 167


>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 = 49.8 bits (118), Expect = 6e-04,   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|295401674|ref|ZP_06811641.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111991|ref|YP_003990307.1| pseudouridine synthase [Geobacillus sp. Y4.1MC1]
 gi|294976294|gb|EFG51905.1| pseudouridine synthase, RluA family [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311217092|gb|ADP75696.1| pseudouridine synthase, RluA family [Geobacillus sp. Y4.1MC1]
          Length = 300

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 37/222 (16%), Positives = 76/222 (34%), Gaps = 33/222 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP  + T  S      T+ + L   + +      +  V RLD +T GL+L+
Sbjct: 88  EDEHVIVVNKPPFMATIPSREHPGGTLANALLYHYEKQQLTSTIHVVTRLDRDTSGLVLI 147

Query: 125 TNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDK--LNL---------LKKGIVIQGIC 171
                +  +L       +  R Y    HG+V +D+  ++          + + +   G  
Sbjct: 148 AKHRHIHHLLSTLQKQGKVARRYEAICHGRVSKDEGTIDAPIARKSDSIIAREVREDGQR 207

Query: 172 YGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAG 231
                  L   +     +++ L  G+  +I+                   P     L  G
Sbjct: 208 AVTHFRVLQRFRDYTH-LSLQLETGRTHQIRVHLAHIGH-----------PLAGDELYGG 255

Query: 232 STREVSKKIL--REQLGPHLLEEAQVNLDAPIYSSETLVRDR 271
           S   + ++ L  +E    H L++       P+      + +R
Sbjct: 256 SRNAIDRQALHSKELSFFHPLKKQAYTFSCPLPDDMQRLIER 297


>gi|253579056|ref|ZP_04856327.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849999|gb|EES77958.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 299

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 29/190 (15%), Positives = 67/190 (35%), Gaps = 31/190 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLL 124
           E   + + +KP  +    S  +  +T+ + +   F+          + RLD +T G L+L
Sbjct: 86  EDEDILVINKPADMPVHPSAGNYENTLANGIAWYFAEKGEDFVYRCINRLDRDTTGALIL 145

Query: 125 TNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ-----DKLNLLKKGIVIQGICYGDMQV 177
             +   A +L +   +   LR Y     G +         +  ++  ++ + + +G  + 
Sbjct: 146 AKNPLSAAILSVQMKKRQILRTYLALVDGLLPDSGTINAPIARMEGSVITREVNFGTGES 205

Query: 178 TL-----DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYG-PFQLGTLLAG 231
            +            +   + L  G+  +I+      + K         G P     L   
Sbjct: 206 AITHYERLAAGKEYSLAELHLETGRTHQIR-----VHMKY-------IGHPLPGDYLYNP 253

Query: 232 STREVSKKIL 241
             R ++++ L
Sbjct: 254 DYRRINRQPL 263


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 4/63 (6%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVM---STDHIEVDGVPLRK 69
          +R+ K++ + G   +R   ++ I    V+V+G    +A   V        + V G  +  
Sbjct: 6  ERLDKMLVKLGFFDTRERAKKAIMAGLVRVDGRAHTKAGDQVSVTLEKHQVTVKGDAIPF 65

Query: 70 AER 72
            R
Sbjct: 66 VSR 68


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 4/79 (5%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+   + R G+A SR    +++    V ++G ++ + A  V     IEV    +   + 
Sbjct: 5  IRIDSELVRRGLARSRTHAAQLVTDGHVTLDGAVVTKPARQVNPAQAIEV---VIPTGDD 61

Query: 73 TRLWLYHKPIGLVTTHSDP 91
                HK  G +   ++ 
Sbjct: 62 YVSRGAHKLAGALDALTER 80


>gi|317486123|ref|ZP_07944968.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
 gi|316922608|gb|EFV43849.1| RNA pseudouridylate synthase [Bilophila wadsworthia 3_1_6]
          Length = 339

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 33/152 (21%), Positives = 57/152 (37%), Gaps = 22/152 (14%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV----DGVPLRKAERTRL 75
           +A  G+ +RR   R+  +  V VNG       + + +   I +    +G  + +   + +
Sbjct: 51  LADLGLRARR---RLCDRSLVLVNGKPGI-PGLKLRAGQEIIILPDPEGAAIPEDAPSLV 106

Query: 76  W------LYHKPIGLVTT----HSDPDGRSTVFDNLPSIFSRVIS--VGRLDINTEGLLL 123
           +        +KP G+ T        P   + + D LPS      S  + RLD  T GL+L
Sbjct: 107 YKDGGIAALYKPAGMHTAALAGSLSPSLETLLGDLLPSEEEGYASRLLNRLDAPTSGLVL 166

Query: 124 --LTNDGGLARVLELPSTQWLRVYRVRFHGQV 153
              T+ G              ++Y     GQ 
Sbjct: 167 ASCTDGGERRWYRAERIGNTDKLYLALIEGQP 198


>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 = 49.8 bits (118), Expect = 6e-04,   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|295103716|emb|CBL01260.1| Uncharacterized conserved protein [Faecalibacterium prausnitzii
          SL3/3]
          Length = 71

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 3  DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K ++   F   ++  ++  AG+  +  E + ++    VKVNG +         + D IE
Sbjct: 2  QKILIHTEF--IKLDALLKFAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDIIE 59

Query: 62 VDGVPLRKAE 71
          +DG  +   +
Sbjct: 60 LDGQSVEIGQ 69


>gi|222151653|ref|YP_002560809.1| tyrosyl-tRNA synthetase [Macrococcus caseolyticus JCSC5402]
 gi|254783616|sp|B9E7E5|SYY_MACCJ RecName: Full=Tyrosyl-tRNA synthetase; AltName: Full=Tyrosine--tRNA
           ligase; Short=TyrRS
 gi|222120778|dbj|BAH18113.1| tyrosyl-tRNA synthetase [Macrococcus caseolyticus JCSC5402]
          Length = 417

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 4   KNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           K++ Q   T   + +++  AGI+ S+R+    I    + +NG  ++  A  +++TD IE 
Sbjct: 341 KDVPQAKVTTTNLVELLIEAGISPSKRQAREDITNGAISINGEKVQDVAYEIVATDKIED 400

Query: 63  DGVPLRKAERTRLWLYH 79
           +   +R+ ++    + H
Sbjct: 401 EFTIIRRGKKKYFMIIH 417


>gi|293384999|ref|ZP_06630833.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|293389269|ref|ZP_06633731.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|312905988|ref|ZP_07765001.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|312909334|ref|ZP_07768190.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
 gi|291077677|gb|EFE15041.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis R712]
 gi|291081433|gb|EFE18396.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Enterococcus faecalis S613]
 gi|310627983|gb|EFQ11266.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           512]
 gi|311290358|gb|EFQ68914.1| pseudouridine synthase, RluA family [Enterococcus faecalis DAPTO
           516]
          Length = 283

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATRVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>gi|289615384|emb|CBI57785.1| unnamed protein product [Sordaria macrospora]
          Length = 476

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 45/138 (32%), Gaps = 20/138 (14%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEVDGVPLRKA----------ERTRLWLYHKPIGLVTT 87
             V VNG  +      + + D I                    E   L + +KP G+   
Sbjct: 107 GLVVVNGKAV-GPDYVLKNGDLISHTTHRHEPPTTAEPIGVIHEDDDLIVINKPSGVPVH 165

Query: 88  HSDPDGRSTVFDNL-----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ-- 140
            +     ++V + +     P    R     RLD  T G++ L  +   A  L    +Q  
Sbjct: 166 PAGRYNYNSVVEIIKSQRGPDFLPR--PCNRLDRLTSGIMFLAKNQRAAERLVAQISQRS 223

Query: 141 WLRVYRVRFHGQVDQDKL 158
             + Y  R  G+    ++
Sbjct: 224 VRKEYIARVVGRFPDGEV 241


>gi|317010619|gb|ADU84366.1| putative ribosomal pseudouridine synthase [Helicobacter pylori
           SouthAfrica7]
          Length = 293

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 38/209 (18%), Positives = 69/209 (33%), Gaps = 43/209 (20%)

Query: 26  ASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKAERTRLWLYHK 80
            S +E +R + +QR+K N  ++ ++ +       I        G  + + +   +  + K
Sbjct: 26  CSLKESQRHLDKQRLKQNQQIVRKSQIIQGVVSLIYFKPNEKQGKLVFETKDFGV--FDK 83

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL--ELP 137
           P  + T         ++ D + S F        RLD  T GL+L       A+ L     
Sbjct: 84  PPQVYTHPKGYFYHESLLDCIQSHFGKNAHPAHRLDYETSGLVLAGKTLQSAKDLKALFM 143

Query: 138 STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ---------KGSNAW 188
             +  + Y    HG VD+         I+I         +  D +         K S   
Sbjct: 144 QKKVQKTYLALVHGLVDES--------IIIDKPILTPENIQKDLRIRSQISPLGKPSTTL 195

Query: 189 VT--------------VG-LREGKNREIK 202
           V               +  L  G+  +I+
Sbjct: 196 VEPLSYNSFLDVSLLKITPLT-GRTHQIR 223


>gi|257086040|ref|ZP_05580401.1| pseudouridine synthase [Enterococcus faecalis D6]
 gi|256994070|gb|EEU81372.1| pseudouridine synthase [Enterococcus faecalis D6]
          Length = 287

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 73/210 (34%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 235


>gi|255066777|ref|ZP_05318632.1| RNA pseudouridine synthase [Neisseria sicca ATCC 29256]
 gi|255048852|gb|EET44316.1| RNA pseudouridine synthase [Neisseria sicca ATCC 29256]
          Length = 309

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/109 (16%), Positives = 38/109 (34%), Gaps = 12/109 (11%)

Query: 106 SRVISVGRLDINTEGLLLLTNDGGLA--RVLELPSTQWLRVYRV----RFHGQVDQDKLN 159
           + +  V RLD +T G++LL+++                 + Y      R       D ++
Sbjct: 144 ADITPVHRLDKDTAGVMLLSHNPATRRDYQTMFQEKSVRKTYHAVAPTRTDLVYPLDVVS 203

Query: 160 LLKKGIVI------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + +G         +G       V L   +G  +   +    GK  +++
Sbjct: 204 RMVRGERFFTTQETEGEPNAHTTVELLENRGEFSLYRLTPHTGKKHQLR 252


>gi|240047291|ref|YP_002960679.1| Ribosomal large subunit pseudouridine synthase [Mycoplasma
           conjunctivae HRC/581]
 gi|239984863|emb|CAT04854.1| Ribosomal large subunit pseudouridine synthase [Mycoplasma
           conjunctivae]
          Length = 284

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/156 (15%), Positives = 54/156 (34%), Gaps = 36/156 (23%)

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLELPSTQWLRVYRVRFHGQVDQD-KLNLLKKGIVIQ 168
            +GRLD +T G+++   +   A  +      +++ Y  +    + +   + L  K    +
Sbjct: 129 HIGRLDKDTTGIVIYAKNYQTALEMNKKQHFFVKRYVFKSDIDLKEKVDVKLWIK----K 184

Query: 169 GICYGDMQVTLDTQKGSNAWVTVG------------LREGKNREIKKVFEFFNWKV---- 212
                 M+V+   +K  N+ + +             L+ GK  +I+       + +    
Sbjct: 185 NDDLKKMEVS--QEKTQNSQLAITSLFLIGNNKIAQLQTGKKHQIRLTLSHLGYPIYGDQ 242

Query: 213 ---------NRLIRISYGPFQLGTLLAGSTREVSKK 239
                      L        QL  L  G+ + ++ K
Sbjct: 243 KYSSFKLMPMFLHCF---FLQLNNLE-GNLQYLNNK 274


>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 = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 31/70 (44%), Gaps = 3/70 (4%)

Query: 3  DKNIVQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           K ++   F   ++  ++  AG+  +  E + ++    VKVNG +         + D IE
Sbjct: 2  QKILIHTEF--IKLDALLKFAGLCETGGEAKELVQGGAVKVNGEVCTMRGKKCRAGDVIE 59

Query: 62 VDGVPLRKAE 71
          +DG  +   +
Sbjct: 60 LDGQSVEIGQ 69


>gi|187918668|ref|YP_001884235.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
 gi|119861516|gb|AAX17311.1| tRNA pseudouridine synthase A [Borrelia hermsii DAH]
          Length = 320

 Score = 49.8 bits (118), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 34/166 (20%), Positives = 58/166 (34%), Gaps = 17/166 (10%)

Query: 54  VMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPD-----GRSTVFDNLPSIFSRV 108
           V   D I  D       E   L + +K  G +                + +NL S+  + 
Sbjct: 86  VKDEDAILRDVKRRIVYEDEDLLVINKRRGALVHGDKYSLGALINSYLLDENLESLSFKP 145

Query: 109 ISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVD----------QD 156
            SV RLD NT GL++   +   AR+L    +     + Y     G++           +D
Sbjct: 146 SSVHRLDRNTSGLIIFAKNIDSARILSRAFSSGIVTKKYLALLDGEIKKPLTYRNFLYRD 205

Query: 157 KLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           ++      +  +G C     V       S+    V +R G   +I+
Sbjct: 206 RIARKTFVVNDEGRCNAITDVKPILVSKSSTLAEVSIRTGFTHQIR 251


>gi|296102896|ref|YP_003613042.1| 23S rRNA pseudouridylate synthase C [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295057355|gb|ADF62093.1| 23S rRNA pseudouridylate synthase C [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 306

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 80/243 (32%), Gaps = 57/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + ++   QR+   +       R +++        R++ +  V+VN   ++     + + D
Sbjct: 4   IADDEAGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKKRVK-PEYKLEAGD 55

Query: 59  HIEVDGVPLRKAERTRL---------------------WLYHKPIGLVTTHSDPDGRSTV 97
            + +  V + + E   +                      + +KP G             +
Sbjct: 56  EVRIPPVRVAEREEEVVSPKLQKVAALSDVILYEDDHILVLNKPSGTAVHGGSGLSFGVI 115

Query: 98  FDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                L      +  V RLD +T G+LL+       R L   L      + Y     GQ 
Sbjct: 116 EGLRALRPEARFLELVHRLDRDTSGVLLVAKKRSALRSLHEQLREKGMQKDYLALVRGQW 175

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNR 199
            Q  + +++  + ++ I     ++   +Q+G  +     + E              G+  
Sbjct: 176 -QSHVKVVQAPL-LKNILQSGERIVRVSQEGKPSETRFKVEERYEFATLVRCSPVTGRTH 233

Query: 200 EIK 202
           +I+
Sbjct: 234 QIR 236


>gi|293390568|ref|ZP_06634902.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951102|gb|EFE01221.1| ribosomal large subunit pseudouridine synthase C [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 319

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 81/249 (32%), Gaps = 49/249 (19%)

Query: 1   MKDKNI--------VQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-------- 43
           M +K I        V ++   QR+   + AR     +  + R++ +  V+VN        
Sbjct: 1   MSEKTINPSVQFLTVSDDEAGQRLDNFLLARLKGVPKSLIYRIVRKGEVRVNKGRSKPEY 60

Query: 44  ----GILLERAAVNVMSTDHIEVDGVPLRKA--------ERTRLWLYHKPIGLVTTHSDP 91
                 ++    V V       +     + A        E   L + +KP G+       
Sbjct: 61  KLRADDVVRIPPVRVAEKAQATISNKLTKVAQLEQHIIFEDNYLLVLNKPSGIAVHGGSG 120

Query: 92  DGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRV 147
                +     L      +  V RLD +T G+LL+       R L   L      + Y  
Sbjct: 121 LDFGVIEALRALRPAACFLELVHRLDRDTSGILLVAKKRSALRNLHEQLREKTVQKDYLA 180

Query: 148 RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------ 195
              GQ  Q    +++  + ++    G  ++   +++G  +     + E            
Sbjct: 181 LVRGQW-QSHCKVVQAPL-LKNELAGGERIVKVSEQGKPSETRFSVEERYTNATLIKASP 238

Query: 196 --GKNREIK 202
             G+  +I+
Sbjct: 239 VTGRTHQIR 247


>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 = 49.8 bits (118), Expect = 7e-04,   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 RLDKALSDLTELSRSLANEQIKSGQVLVNGQ-VKKAKYTVQEGDVVTY 57


>gi|315173986|gb|EFU18003.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1346]
          Length = 283

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 39/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G   R     E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATRVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DDHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 231


>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 = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +I R G A +RRE  +++  + V VNG  +   + +V   D IE+
Sbjct: 105 RLDNIIFRLGFARTRREARQIVDHKHVLVNGKCVNIPSYSVKPGDKIEI 153


>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 = 49.8 bits (118), Expect = 7e-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|291276435|ref|YP_003516207.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
 gi|290963629|emb|CBG39461.1| putative ribosomal pseudouridine synthase [Helicobacter mustelae
           12198]
          Length = 284

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/218 (15%), Positives = 85/218 (38%), Gaps = 29/218 (13%)

Query: 22  RAGIASRREVERMIAQQRVKV-NGILLERAAV---NVMSTDHIEVDGVPLRKAERTRLWL 77
                S +E +R+I ++R++  +G +++++ V    V+  D    +G            +
Sbjct: 22  NCLHYSSKETQRIIDKRRLRYPDGRVIQKSEVICGRVL-LDEFVPNGALRAIFVHEDFAV 80

Query: 78  YHKPIGLVTTHSDPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTND--GGLARVL 134
           + KP  L+T        +++ D++   F  +   V RLD  T G++L++ +    +A   
Sbjct: 81  FAKPHNLLTHPKGRFLHASLCDSIKMQFGMQANPVHRLDFETSGVVLISRNKRAEIALKT 140

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI--QGICYGDMQVTLDTQ---------- 182
                +  ++YR    G ++ +    ++  I++  +     D+ +               
Sbjct: 141 LFERGEVRKIYRALVEGIIEHE--RCIESRILLPKKEDKSKDLGIKCQIHASGKDSITII 198

Query: 183 -----KGSNAWVTVG-LREGKNREIKKVFEFFNWKVNR 214
                +G+   + +  L  G+  +I+        K+  
Sbjct: 199 RPLEVRGNQTLLEIEPLT-GRTHQIRLHLASIGHKIVN 235


>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 = 49.8 bits (118), Expect = 7e-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|303277917|ref|XP_003058252.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226460909|gb|EEH58203.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 508

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/173 (13%), Positives = 48/173 (27%), Gaps = 38/173 (21%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSD----PDGRSTVFDNLPSIFSRVIS-----------V 111
           +   E        KP G++T  +          T+ D     F                V
Sbjct: 253 VVVYEDDHFAAVSKPAGILTHPTGGASVDKRSVTLVDLALDAFGDEHVSALNGADARGIV 312

Query: 112 GRLDINTEGLLLLTNDGGLARVLELPST---QWLRVYRVRFHGQV-------------DQ 155
            RLD  T G++++     +A  L + +    +  + Y     G               + 
Sbjct: 313 HRLDKPTTGVMVIA-KTDVAHALLVTAWYQRKVQKTYWAIVEGVPGRRRPKRRGDAEGED 371

Query: 156 DKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------AWVTVGLREGKNREIK 202
            +      G+V         +      +  N      + V V    G+  +++
Sbjct: 372 AETEDHLFGVVDAPADGRPAKSDWKVLEIFNLPDATCSLVEVTPHTGRKHQVR 424


>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 = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 10/56 (17%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 8  QENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          Q     +R+ K++   G+  +R + + +I    V VN   +++    + +  +I +
Sbjct: 5  QSTPKKERIDKLLVDKGLVETREKAQALIMSGVVFVNNQKIDKPGTKIPTDANIHI 60


>gi|148264981|ref|YP_001231687.1| RluA family pseudouridine synthase [Geobacter uraniireducens Rf4]
 gi|146398481|gb|ABQ27114.1| pseudouridine synthase, RluA family [Geobacter uraniireducens Rf4]
          Length = 296

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 37/218 (16%), Positives = 77/218 (35%), Gaps = 30/218 (13%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP-----LRKA--------ERTRLWLY 78
            +++    + VNG         +   D + +         LRKA        E   + ++
Sbjct: 32  RKLLTAGHLAVNGTPGVS-GTILRLGDTVTLKESSKTSAFLRKARPELDILHEDQWIMIF 90

Query: 79  HKPIGLVTTHSDPDGRSTVFDNLPSIFS-------RVISVGRLDINTEGLLLLTNDGGLA 131
           +K  GL   H+       + D    + +       ++  V RLD  T G ++L      A
Sbjct: 91  NKAPGLPMHHAAEVDERNLVDLGTKLLAGRDGGSVKLRPVNRLDRGTSGAVILAKSSMAA 150

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +    +      ++Y     G++ +D +      + ++G    + +  +   +    +V
Sbjct: 151 AMFGRLIMDEGLGKLYLALVEGELAEDGVIS----VPLEG-KEAETRYRVLFHRSDCTFV 205

Query: 190 TVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGT 227
            V    G+  +I++ F+F      R  R  YG   L  
Sbjct: 206 AVYPVTGRMHQIRQHFKFIGHP-IRGDR-RYGGQPLPG 241


>gi|327534269|gb|AEA93103.1| ribosomal large subunit pseudouridine synthase [Enterococcus
           faecalis OG1RF]
          Length = 283

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P   +T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>gi|282881959|ref|ZP_06290604.1| RluA family pseudouridine synthase [Peptoniphilus lacrimalis 315-B]
 gi|281298234|gb|EFA90685.1| RluA family pseudouridine synthase [Peptoniphilus lacrimalis 315-B]
          Length = 316

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/256 (14%), Positives = 78/256 (30%), Gaps = 71/256 (27%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRREVERM------------IAQQRVKVNGILLERA 50
            K I+  N + QR+ + +           ++             + ++ +KV+G      
Sbjct: 2   RKVIIGPNDSDQRLDRFL-----------KKYFEKAPLSFIYKNLRKKNIKVDGKKA-SP 49

Query: 51  AVNVMSTDHIE--VDGVPLRKAERTRLW-----------------LYHKPIGLVTTHSDP 91
              +     I   +    + K ++ +L                  L  KP+ ++T +   
Sbjct: 50  EDLIKEGQEISLFISDETIEKYKKDKLARNSQKFPQILYEDDNICLMKKPLNMLTHNDKN 109

Query: 92  DGRSTVFDNLPSIF-------------SRVISVGRLDINTEGLLLLTNDGGLARVLELPS 138
             +  + D                    R     RLD NT G+LL   +    R +    
Sbjct: 110 FYQDNMVDRFIDYLIFKEEYSPREENTFRPSICNRLDRNTSGILLGAKNAETLREINKAI 169

Query: 139 TQ--WLRVYRVRFHGQV----------DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN 186
            +    + Y     G+V          ++   N+++K    +        +      G  
Sbjct: 170 KERLVDKFYLTIVKGKVQKPFEINIKLEKTDKNIMRKSSQGKDSLTKFFPL---ISNGEY 226

Query: 187 AWVTVGLREGKNREIK 202
           + + V L  G+  +I+
Sbjct: 227 SLLKVKLITGRTHQIR 242


>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 = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 2/100 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V     IEV        + 
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKRVDIPSYMVKPGQKIEVKEKSKNNPQV 157

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISV 111
            R        G+V     D + +  +F   P     VI +
Sbjct: 158 IRAIDLTSQTGIVPWVDVDKEKKFGIFTRFPQREEVVIPI 197


>gi|170768656|ref|ZP_02903109.1| pseudouridine synthase, RluA family [Escherichia albertii TW07627]
 gi|170122760|gb|EDS91691.1| pseudouridine synthase, RluA family [Escherichia albertii TW07627]
          Length = 219

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 + L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAEQELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>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 (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 1/57 (1%)

Query: 11 FTPQRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVP 66
             QR+  ++    +  SR++ +R+I    VKV   ++++    V +   IEV   P
Sbjct: 1  MAKQRLDLLLVERKLCESRQQAQRVIRAGEVKVKQQIVDKPGTLVPADVDIEVQAKP 57


>gi|116331588|ref|YP_801306.1| pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116125277|gb|ABJ76548.1| Pseudouridylate synthase [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 277

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/141 (19%), Positives = 51/141 (36%), Gaps = 24/141 (17%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFS--RVISVGRLDINTEGLLLLT---NDGGLARVL 134
           KP G+    +    R    D L    S   + +V RLD++T GL+ L    +    A  +
Sbjct: 22  KPPGIPVHATKDSKRENFADRLQEQLSLEYLRTVNRLDLDTSGLVFLCKNPDKNKEADRI 81

Query: 135 ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV--- 191
              S+   ++Y     G V+++      +   I+       +V     K    ++T+   
Sbjct: 82  LKSSS---KIYLCVADGIVEEEH---FTETCYIKDGNKKVRKVFSGGDKAVTEFLTLKRN 135

Query: 192 ----------GLREGKNREIK 202
                      L  G+  +I+
Sbjct: 136 LKDHYSVLLAKLHTGRRHQIR 156


>gi|22127552|ref|NP_670975.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           KIM 10]
 gi|45443414|ref|NP_994953.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51594989|ref|YP_069180.1| 23S rRNA pseudouridylate 746 synthase [Yersinia pseudotuberculosis
           IP 32953]
 gi|108810081|ref|YP_653997.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|108810536|ref|YP_646303.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|145600392|ref|YP_001164468.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|150260466|ref|ZP_01917194.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|153948334|ref|YP_001402394.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|162419457|ref|YP_001605342.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165928068|ref|ZP_02223900.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165937798|ref|ZP_02226359.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166008924|ref|ZP_02229822.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166211832|ref|ZP_02237867.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167401530|ref|ZP_02307024.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167421997|ref|ZP_02313750.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167426100|ref|ZP_02317853.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167467289|ref|ZP_02331993.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           FV-1]
 gi|170025783|ref|YP_001722288.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186893990|ref|YP_001871102.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|218927695|ref|YP_002345570.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|229836920|ref|ZP_04457085.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|229840385|ref|ZP_04460544.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229842465|ref|ZP_04462620.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229900724|ref|ZP_04515848.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|270487905|ref|ZP_06204979.1| pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294502592|ref|YP_003566654.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|34395807|sp|Q8ZIK1|RLUA_YERPE RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|21960656|gb|AAM87226.1|AE013971_2 hypothetical protein y3678 [Yersinia pestis KIM 10]
 gi|45438283|gb|AAS63830.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Microtus str. 91001]
 gi|51588271|emb|CAH19878.1| 23S rRNA pseudouridylate 746 synthase [Yersinia pseudotuberculosis
           IP 32953]
 gi|108774184|gb|ABG16703.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|108781994|gb|ABG16052.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Antiqua]
 gi|115346306|emb|CAL19177.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CO92]
 gi|145212088|gb|ABP41495.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides F]
 gi|149289874|gb|EDM39951.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           CA88-4125]
 gi|152959829|gb|ABS47290.1| ribosomal large subunit pseudouridine synthase A [Yersinia
           pseudotuberculosis IP 31758]
 gi|162352272|gb|ABX86220.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Angola]
 gi|165914210|gb|EDR32826.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165919929|gb|EDR37230.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165992263|gb|EDR44564.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166206578|gb|EDR51058.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166960134|gb|EDR56155.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167048912|gb|EDR60320.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167055023|gb|EDR64823.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|169752317|gb|ACA69835.1| pseudouridine synthase [Yersinia pseudotuberculosis YPIII]
 gi|186697016|gb|ACC87645.1| pseudouridine synthase [Yersinia pseudotuberculosis PB1/+]
 gi|229682063|gb|EEO78155.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Nepal516]
 gi|229690775|gb|EEO82829.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229696751|gb|EEO86798.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229705863|gb|EEO91872.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Pestoides A]
 gi|262360622|gb|ACY57343.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           D106004]
 gi|262364568|gb|ACY61125.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           D182038]
 gi|270336409|gb|EFA47186.1| pseudouridine synthase A [Yersinia pestis KIM D27]
 gi|294353051|gb|ADE63392.1| ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           Z176003]
 gi|320016868|gb|ADW00440.1| Ribosomal large subunit pseudouridine synthase A [Yersinia pestis
           biovar Medievalis str. Harbin 35]
          Length = 206

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/170 (16%), Positives = 63/170 (37%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++     P+ + +V   + + F    SV RLD+ T G++++ 
Sbjct: 2   IVLYQDKHIMVVNKPSGLLSVPGRAPENKDSVMTRVQNDFPTAESVHRLDMATSGVIVVA 61

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G + QD      +G++    I         +V 
Sbjct: 62  LTKAAERELKRQFREREPKKTYIARVWGHLAQD------EGLIDLPLICDWPNRPKQKVC 115

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 116 YETGKSAQTEYQVISRDDDGSTRVKLSPIT-GRSHQLRVHML-AMGHPIL 163


>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 = 49.8 bits (118), Expect = 7e-04,   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|300865112|ref|ZP_07109937.1| Pseudouridine synthase [Oscillatoria sp. PCC 6506]
 gi|300336883|emb|CBN55087.1| Pseudouridine synthase [Oscillatoria sp. PCC 6506]
          Length = 562

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/172 (20%), Positives = 60/172 (34%), Gaps = 19/172 (11%)

Query: 49  RAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFS- 106
                  + D +E + + +   E   L   +KP GL++      D + +V   L  +   
Sbjct: 338 DMGTYRQNFDILEAENLQIIY-EDEWLIAVNKPSGLLSVPGRYRDRQDSVLSRLRQLLPD 396

Query: 107 --RVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQDKLNLLK 162
              +I V RLD+ T G++LL     + R L          +VY     G V  D    + 
Sbjct: 397 GMNIIPVHRLDLETSGIMLLARSLPIYRELSSQFQHKLVKKVYEAVLSGNVVNDYCGEIS 456

Query: 163 KGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE------------GKNREIK 202
             +          QV ++  K S     V  RE            G+  +I+
Sbjct: 457 LPLWGNPEHRPYQQVDIERGKPSLTRFQVIAREGEYTRVEFMPLTGRTHQIR 508


>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 = 49.8 bits (118), Expect = 7e-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|170725279|ref|YP_001759305.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
 gi|169810626|gb|ACA85210.1| pseudouridine synthase [Shewanella woodyi ATCC 51908]
          Length = 225

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/164 (14%), Positives = 61/164 (37%), Gaps = 28/164 (17%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++    DP  R +++  + + +     V RLD+ T G+++L     
Sbjct: 19  QDKDILVVNKPSGLLSVPGRDPAHRDSIYARVLAEYPNAQVVHRLDMATSGIIVLALRRN 78

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI--------QGICYGDMQV-- 177
             + L+      +  + Y  R  G +  D        + +        +     D +V  
Sbjct: 79  AEKELKRQFRERETKKTYYARVAGHIRSDSGK-----VELPLICDWPNRPKQKVDHKVGK 133

Query: 178 ------TLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                  + ++   +  V +  +  G++ +++  +       + 
Sbjct: 134 PSLTHYEVISRAKRSTLVKLTPIT-GRSHQLRVHML-AIGHPIL 175


>gi|319941266|ref|ZP_08015597.1| hypothetical protein HMPREF9464_00816 [Sutterella wadsworthensis
           3_1_45B]
 gi|319805187|gb|EFW02010.1| hypothetical protein HMPREF9464_00816 [Sutterella wadsworthensis
           3_1_45B]
          Length = 457

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 29/157 (18%), Positives = 60/157 (38%), Gaps = 21/157 (13%)

Query: 66  PLRKAERTRLWLYH-------KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINT 118
           P+ ++ R R+ L H       KP GL++        + +        + + +V RLD++T
Sbjct: 240 PVTQSLRPRILLEHRDFIAVFKPSGLLSVPGTGGLPNALTIASEMTGTSLTAVHRLDMDT 299

Query: 119 EGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDK-----------LNLLKKGI 165
            G+LL   T +G  + +      +  + YR    G +  +            L+ L++  
Sbjct: 300 SGILLYGKTPEGIRSLMAAFREGRVEKRYRAILEGTLTAECGLIDFPITTHPLDRLRQIA 359

Query: 166 VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            + G         L  + G      + L  G+  +++
Sbjct: 360 ALGGRPARTQWRRLSEKNGRTLVDFLPLT-GRTHQLR 395


>gi|319955825|ref|YP_004167088.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
 gi|319418229|gb|ADV45339.1| pseudouridine synthase [Nitratifractor salsuginis DSM 16511]
          Length = 324

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/199 (17%), Positives = 70/199 (35%), Gaps = 31/199 (15%)

Query: 30  EVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL-----WLYHKPIGL 84
           E +R+I + R+   G  L   +  +     + V   P  +     +     +L+ KP G+
Sbjct: 30  EAQRIIDRGRLLCRGETLPDKSARISGEVEV-VYFEPQSRGNAPIVTTPDFYLFDKPSGV 88

Query: 85  VTTHSDPDGRSTVFDNLPSIF----SRVISVGRLDINTEGLLLLTNDGGLARVLEL--PS 138
           +     P   +T +  L  +         +V R+D  T GLLL +      R L+     
Sbjct: 89  LV---HPKKMTTPYSMLDEVRFHGGQHANAVHRIDKETSGLLLASRHKESERFLKGAFER 145

Query: 139 TQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVI--QGIC--YGDMQVTLDTQK 183
               + YR    G++++           +     K  + I  +G       + +  D ++
Sbjct: 146 KAIQKSYRAWATGRIEEPFSVDAPIILNNDYGPTKHKVFIHREGKRAYTTFLPIQYD-ER 204

Query: 184 GSNAWVTVGLREGKNREIK 202
                +      G+  +I+
Sbjct: 205 LDATLLECIPHTGRTHQIR 223


>gi|315586335|gb|ADU40716.1| pseudouridine synthase D [Helicobacter pylori 35A]
          Length = 293

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 49/164 (29%), Gaps = 36/164 (21%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           ++ KP  + T         ++ D + S F        RLD  T GL+L       A+ L 
Sbjct: 80  VFDKPPQVYTHPKGYFYHESLLDCIQSHFGKNAHPAHRLDYETSGLVLAGKTLQSAKDLK 139

Query: 135 -ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------- 186
                 +  + Y    HG VD+         IVI         +  D +  S        
Sbjct: 140 ALFMQKKVKKTYLALVHGLVDRS--------IVIDKPILTPQNIQKDLRIKSKISPLGKP 191

Query: 187 ----------------AWVTVG-LREGKNREIKKVFEFFNWKVN 213
                           + + +  +  G+  +I+        ++ 
Sbjct: 192 STTLVEPLSYNPFLDISLLKITPIT-GRTHQIRLHLSSVGHRIV 234


>gi|258647905|ref|ZP_05735374.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella tannerae ATCC 51259]
 gi|260851740|gb|EEX71609.1| ribosomal large subunit pseudouridine synthase family protein
           [Prevotella tannerae ATCC 51259]
          Length = 245

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/188 (12%), Positives = 54/188 (28%), Gaps = 37/188 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFD----NLPSIFSRVISV-----GRLDINTEGL 121
           E   + + +K  G +    D  G  TV D     L   +++  +V      RLD    G+
Sbjct: 12  EDNHIIIVNKQAGEIIQG-DKTGDRTVADEIKAYLKEKYNKPGAVFLGIPHRLDRPVSGV 70

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV-------------DQDKLNLLKKGIV 166
            +          L       +  + Y+     +              ++ +         
Sbjct: 71  SIFARTSKALARLNEMFRKGEIEKTYQAIVIHEPQIASGTLVHWLTRNEKQNKAYAHKAP 130

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
            +      +   ++ +      + V L+ G++ +I+         +             G
Sbjct: 131 QKNAKKAILDYKVEAKSDRYWLINVQLQTGRHHQIRCQLAAIGCPIK------------G 178

Query: 227 TLLAGSTR 234
            L  G+ R
Sbjct: 179 DLKYGAPR 186


>gi|196005647|ref|XP_002112690.1| hypothetical protein TRIADDRAFT_25933 [Trichoplax adhaerens]
 gi|190584731|gb|EDV24800.1| hypothetical protein TRIADDRAFT_25933 [Trichoplax adhaerens]
          Length = 247

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 12/106 (11%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS---------RVISVGRLDINTEGLLLLT 125
             + +KP  +    ++ D + TV   L  +               V RLD  T GLL + 
Sbjct: 19  YVIINKPFDMHINSNEEDVKPTVATQLAELLPTLVDKSICFGFRFVNRLDYATSGLLCIA 78

Query: 126 NDGGLAR--VLELPSTQWLRVYRVRFHGQVDQDKLNLL-KKGIVIQ 168
            D   A        +    + Y     G + +D  ++L +K I + 
Sbjct: 79  FDKRAANMARKLFEANHVSKKYLALVRGILSRDNGDILVRKAIGLD 124


>gi|170079422|ref|YP_001736060.1| ribosomal large chain pseudouridine synthase A [Synechococcus sp.
           PCC 7002]
 gi|169887091|gb|ACB00805.1| ribosomal large chain pseudouridine synthase A [Synechococcus sp.
           PCC 7002]
          Length = 538

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 29/161 (18%), Positives = 56/161 (34%), Gaps = 21/161 (13%)

Query: 58  DHIEVDGVPLRK-AERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLD 115
           D + +  +PL    E   L   HKP GL +          + F  L   +  +  V RLD
Sbjct: 330 DILTIPEIPLEIIYEDHSLIAIHKPAGLPSIPGRSSQTYDSAFSRLRRDYQDIFLVHRLD 389

Query: 116 INTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QG 169
            +T G+LL   +    + L+      +  + Y         ++K+   +  I +      
Sbjct: 390 QDTSGILLFAKNAETQQDLQTQFRRRKIHKEYEALL-----EEKIQRPEGMITLPLWADP 444

Query: 170 ICYGDMQVTLDTQKGSNAWV------TVGLR--EGKNREIK 202
                 +V     K S  +        + L+   G+  +++
Sbjct: 445 GDRPRQKVDAQRGKPSETYFVKLDSHRLKLKPITGRTHQLR 485


>gi|149376750|ref|ZP_01894508.1| 23S rRNA pseudouridylate synthase C [Marinobacter algicola DG893]
 gi|149358989|gb|EDM47455.1| 23S rRNA pseudouridylate synthase C [Marinobacter algicola DG893]
          Length = 313

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 86/241 (35%), Gaps = 46/241 (19%)

Query: 3   DKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHI 60
            K +V E+   QRV   + A+     R  + R+I +  V+VN G +  +    + + D +
Sbjct: 2   RKVVVDEDNHGQRVDNYLMAQIRDVPRSIIYRIIRKGEVRVNKGRV--KPDTRLNTGDEV 59

Query: 61  EVDGVPLRKAERT----------------------RLWLYHKPIGLVTTHSD--PDGRST 96
            +   P+ + E+                       ++ + +KP G+          G   
Sbjct: 60  RI--PPVTRKEKPAQVVPGSRVQGVMQSAVVFENDQMLVVNKPSGIAVHGGSGLDFGLIE 117

Query: 97  VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVD 154
           V          +  V RLD +T GL+++       R L  EL   +  + Y     G   
Sbjct: 118 VLRAARPEARFLELVHRLDRDTSGLVMVAKKRSALRYLQDELRHKRIRKHYHALVAGDWP 177

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTL-DTQKGSNAWVTV-------GLRE-----GKNREI 201
              +  + + ++   +  G+ +V + D  K S     V        L E     G+  +I
Sbjct: 178 GS-VKKVSEPLLRFELGSGERRVRVDDAGKDSLTRFRVLESFSGYTLVEASPVTGRTHQI 236

Query: 202 K 202
           +
Sbjct: 237 R 237


>gi|71904404|ref|YP_281207.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94991334|ref|YP_599434.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94995246|ref|YP_603344.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|209560185|ref|YP_002286657.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
 gi|71803499|gb|AAX72852.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS6180]
 gi|94544842|gb|ABF34890.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10270]
 gi|94548754|gb|ABF38800.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10750]
 gi|209541386|gb|ACI61962.1| Putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes NZ131]
          Length = 333

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 69/204 (33%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 66  RKIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 125

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 126 EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 185

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 186 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 245

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +   L+ G+  +I+
Sbjct: 246 VKNFHKTASLLNCQLQTGRTHQIR 269


>gi|25012059|ref|NP_736454.1| hypothetical protein gbs2021 [Streptococcus agalactiae NEM316]
 gi|24413602|emb|CAD47680.1| Unknown [Streptococcus agalactiae NEM316]
          Length = 270

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 37/207 (17%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIE--VDGV-------PLRKAE------- 71
           R++   +  ++ V +N   +      V   D I    D         PL +AE       
Sbjct: 4   RKIRHFLRVKKHVLINNEFI-NWQTVVQENDTITLIFDDEDYPTKKIPLGRAELIDCLYE 62

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
              L + +KP G+ T  + P+  + +             V RLD+ T G +L   +  + 
Sbjct: 63  DEHLIIVNKPEGMKTHGNQPNEIALLNHVSAYSGQTCYVVHRLDMETSGAVLFAKNPFIL 122

Query: 132 RVLE--LPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG----- 184
            ++   L   +  R Y     G+       +L+    I    +   +  +D++ G     
Sbjct: 123 PLINQRLERKEIWREYWALVEGKFSPKH-QVLRD--KIGRNRHDRRKRIIDSKNGQHAMT 179

Query: 185 ---------SNAWVTVGLREGKNREIK 202
                    +++ +   L  G+  +I+
Sbjct: 180 IIDVLKYIQNSSLIKCRLETGRTHQIR 206


>gi|148239908|ref|YP_001225295.1| ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 7803]
 gi|147848447|emb|CAK23998.1| Ribosomal large subunit pseudouridine synthase A [Synechococcus sp.
           WH 7803]
          Length = 197

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 28/148 (18%), Positives = 53/148 (35%), Gaps = 15/148 (10%)

Query: 80  KPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVL--EL 136
           KP GL+         R ++   L      +  V RLD +T GL+LL  D    RVL    
Sbjct: 6   KPAGLLCQPGLGVHQRDSLISRLQHACPDLRLVHRLDRDTSGLVLLAKDADTQRVLGALF 65

Query: 137 PSTQWLRVYRVRFHGQVD------QDKLNLLKK-----GIVIQGICYGDMQVTLDTQKGS 185
            + +  ++Y     G +          L  L +     G+   G     +   L   + +
Sbjct: 66  AARRVGKLYLADVQGSMGAVSGRIDLPLARLNRQPPTYGVHPDGKACLTLWRRLQRME-T 124

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWKVN 213
              + +  R G++ +++      +  + 
Sbjct: 125 RTRLWLCPRTGRSHQLRAHLAALHHPII 152


>gi|294794416|ref|ZP_06759552.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
 gi|294454746|gb|EFG23119.1| ribosomal large subunit pseudouridine synthase D [Veillonella sp.
           3_1_44]
          Length = 300

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/142 (17%), Positives = 50/142 (35%), Gaps = 18/142 (12%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLR-----KAERTRLWLYHK 80
           ++  ++ + +NG         +   D I       ++D  P+        E T L +  K
Sbjct: 13  KLFEEKLIHINGHKAT-PKDAIYEGDEIWIAMAKEKIDHDPIEMDLRILYEDTDLLIVDK 71

Query: 81  PIGLVTTHSDPDGRST-VFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG--GLARVLE 135
           P G+     D    +  V           +V  + RLD +T G +++   G        +
Sbjct: 72  PSGVTVNSKDQVSLANGVAHYFKEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQSIYQQQ 131

Query: 136 LPSTQWLRVYRVRFHGQVDQDK 157
           +    + + Y     G V+ D+
Sbjct: 132 MDDNTFEKWYMATVEGIVEADE 153


>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 = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 15 RVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
          R+ K++   G + SR + + +I   +V V G  +++    +   + +EV
Sbjct: 3  RLDKLLFERGLVDSREKAQALIMAGQVFVEGRRVDKPGTRLKGDERVEV 51


>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 (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 11/49 (22%), Positives = 24/49 (48%), Gaps = 4/49 (8%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLR 68
          ++ AG     E +  I + +V VNG +  R    +++ D +  +G  ++
Sbjct: 27 MSNAGG----EAKHFIEEGQVTVNGEVETRKRKKIIAGDIVSFNGESVQ 71


>gi|307132626|ref|YP_003884642.1| Ribosomal large subunit pseudouridine synthase A [Dickeya dadantii
           3937]
 gi|306530155|gb|ADN00086.1| Ribosomal large subunit pseudouridine synthase A [Dickeya dadantii
           3937]
          Length = 235

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 26/160 (16%), Positives = 60/160 (37%), Gaps = 19/160 (11%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++      + + ++   + + F    SV RLD+ T G++++     
Sbjct: 35  QDQHIMVVNKPSGLLSVPGRAEEHKDSIMTRIQADFPAAESVHRLDMATSGVMVVALTKA 94

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKL-----------NLLKKGIVIQ-GICYGDM 175
             R L+    +    + Y  R  G ++QD             N  K+ +  + G      
Sbjct: 95  AERELKRQFREREPKKSYIARVWGHLEQDDGLVDLPLICDWPNRPKQKVCFEQGKPAQTG 154

Query: 176 QVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
            V L         V +  +  G++ +++  +       + 
Sbjct: 155 YVVLSRDSDGTTRVKLMPIT-GRSHQLRVHML-ALGHPIL 192


>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 = 49.8 bits (118), Expect = 7e-04,   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|297519884|ref|ZP_06938270.1| 23S rRNA pseudouridylate synthase C [Escherichia coli OP50]
          Length = 319

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/243 (14%), Positives = 79/243 (32%), Gaps = 57/243 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           +  +   QR+   +       R +++        R++ +  V+VN   ++     + + D
Sbjct: 13  ITADEAGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKKRIK-PEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT---------------------RLWLYHKPIGLVTTHSDPDGRSTV 97
            + +  V + + E                        + + +KP G             +
Sbjct: 65  EVRIPPVRVAEREEEAVSPHLQKVAALADVILYEDDHILVLNKPSGTAVHGGSGLSFGVI 124

Query: 98  FDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                L      +  V RLD +T G+LL+T      R L   L      + Y     GQ 
Sbjct: 125 EGLRALRPEARFLELVHRLDRDTSGVLLVTKKRSALRSLHEQLREKGMQKDYLALVRGQW 184

Query: 154 DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNR 199
            Q  +  ++  + ++ I     ++   +Q+G  +     + E              G+  
Sbjct: 185 -QSHVKSVQAPL-LKNILQSGERIVRVSQEGKPSETRFKVEERYAFATLVRCSPVTGRTH 242

Query: 200 EIK 202
           +I+
Sbjct: 243 QIR 245


>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 = 49.8 bits (118), Expect = 7e-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|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 = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 6/67 (8%)

Query: 14 QRVSKVIARAGIASRRE-VERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           R+ K +  +GI  RR   +R+I    VK+NG L +++   V   D IEVD         
Sbjct: 1  MRLDKFLKESGIIKRRTLAQRIIQAGYVKINGKLAKQSD-PVKVDDMIEVD----TPVAY 55

Query: 73 TRLWLYH 79
          TR  + +
Sbjct: 56 TRYVVIN 62


>gi|15805985|ref|NP_294685.1| ribosomal large subunit pseudouridine synthase A [Deinococcus
           radiodurans R1]
 gi|6458684|gb|AAF10535.1|AE001948_4 ribosomal large subunit pseudouridine synthase, Rlu family
           [Deinococcus radiodurans R1]
          Length = 257

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 32/170 (18%), Positives = 55/170 (32%), Gaps = 26/170 (15%)

Query: 65  VPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS-----RVISVGRLDINTE 119
            P    E    ++ HKP   +T       R  V D L  + +      +    RLD  T 
Sbjct: 21  KPRIIVEHPDFYVVHKPALWLT--HPVRARVDVPDLLTFMQAETGETDLAPPHRLDRETS 78

Query: 120 GLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQV--DQDKLN--------------LL 161
           G  LLT D   AR       +    + Y    HG+   D+  L+               +
Sbjct: 79  GAQLLTRDSDAARTFFTLFKTHLVGKTYLAIVHGEPEWDRRTLDAPLGDLGLGGANKIQI 138

Query: 162 KKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           ++ +V  G         +  ++  +A +    R G+  +I+         
Sbjct: 139 RQAVVPDGKPAVT-DFRVVGRRAGHALIECYPRSGRLHQIRAHLAHLGLP 187


>gi|332673190|gb|AEE70007.1| pseudouridine synthase D [Helicobacter pylori 83]
          Length = 293

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 50/164 (30%), Gaps = 36/164 (21%)

Query: 77  LYHKPIGLVTTHSDPDGRSTVFDNLPSIF-SRVISVGRLDINTEGLLLLTNDGGLARVL- 134
           ++ KP  + T         ++ D + S F        RLD  T GL+L+      A+ L 
Sbjct: 80  VFDKPPQVYTHPKGYFYHESLLDCIQSHFGKNAHPAHRLDYETSGLVLVGKTLQSAKDLK 139

Query: 135 -ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSN------- 186
                 +  + Y    HG VD+         IVI         +  D +  S        
Sbjct: 140 TLFMQKKVKKTYLALVHGLVDRS--------IVIDKPILTPQNIQKDLRIKSKISPLGKP 191

Query: 187 ----------------AWVTVG-LREGKNREIKKVFEFFNWKVN 213
                           + + +  +  G+  +I+        ++ 
Sbjct: 192 STTLVEPLSYNPFLDISLLKITPIT-GRTHQIRLHLSSVGHRIV 234


>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 = 49.8 bits (118), Expect = 7e-04,   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|315025718|gb|EFT37650.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2137]
          Length = 283

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 73/210 (34%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQALSNNQTAVTCVLETGRTHQIR 231


>gi|282877802|ref|ZP_06286615.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
 gi|281300118|gb|EFA92474.1| pseudouridine synthase, RluA family [Prevotella buccalis ATCC
           35310]
          Length = 295

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 75/210 (35%), Gaps = 40/210 (19%)

Query: 27  SRREVERMIAQQRVKVNGILLE------RAAVNV---MSTDHIEVDGVPLR-KAERTRLW 76
           S+ +++  +A + + VNG  +        A + +    S  +I      L+   E   L 
Sbjct: 33  SKSKIKATLAGKGIIVNGKCITQFDYPLEAGMKIAVSKSKKNINFKNRYLKIVYEDRYLV 92

Query: 77  LYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRV--ISVGRLDINTEGLLLLTNDGGLA 131
           +  K +G+++    HS  + +  + D   +   +     V RLD  T GL++   D    
Sbjct: 93  VIEKHVGILSMAAGHSSLNVKRVLDDYFRNSKQKCTAHVVHRLDRETSGLMIYAKDMATE 152

Query: 132 RVLELPSTQW--LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
           + LE         R Y     G+++ D      +G++   +      VT  +   +    
Sbjct: 153 QELEHNWHDIVYDRRYVAVVSGEMEDD------EGVITSWLKDNKAYVTYSSPVDNGGKF 206

Query: 190 TVG------------LRE-----GKNREIK 202
            +             L E     G+  +I+
Sbjct: 207 AITHFHTLDRTTEHSLVEYRLETGRKNQIR 236


>gi|269140174|ref|YP_003296875.1| 23S rRNA pseudouridine synthase D [Edwardsiella tarda EIB202]
 gi|267985835|gb|ACY85664.1| 23S rRNA pseudouridine synthase D [Edwardsiella tarda EIB202]
 gi|304560007|gb|ADM42671.1| Ribosomal large subunit pseudouridine synthase D [Edwardsiella
           tarda FL6-60]
          Length = 280

 Score = 49.8 bits (118), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 35/206 (16%), Positives = 67/206 (32%), Gaps = 44/206 (21%)

Query: 43  NGILLERAAVNVMSTDHIEVD------------GVPLR-KAERTRLWLYHKPIGLVTTHS 89
           NG+++ +    V+  +HI +D             + L    E   + + +KP  LV    
Sbjct: 2   NGVIINKPKEKVLGGEHIAIDALIEEENRWEAQDIALDIVYEDEDILVINKPRDLVVHPG 61

Query: 90  DPDGRSTVFDNLPSIFSRVI------SVGRLDINTEGLLLLTNDGGLARVL--ELPSTQW 141
             +   TV + L   + ++        V RLD +T GL+++         L   L   + 
Sbjct: 62  AGNPDGTVLNALLHYYPQIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLREI 121

Query: 142 LRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVT----------------LDTQKGS 185
            R Y     G +          G V + I     + T                +     +
Sbjct: 122 TREYEAVAIGTMT-------AGGTVREPIARHPTKRTHMSVHPMGKPAVTHYRIMEHFRA 174

Query: 186 NAWVTVGLREGKNREIKKVFEFFNWK 211
           +  + + L  G+  +I+      N  
Sbjct: 175 HTRLRLRLETGRTHQIRVHMAHINHP 200


>gi|223043737|ref|ZP_03613780.1| YlmH protein [Staphylococcus capitis SK14]
 gi|222442834|gb|EEE48936.1| YlmH protein [Staphylococcus capitis SK14]
          Length = 262

 Score = 49.4 bits (117), Expect = 7e-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: 176 KIQSTTVSAMRLDVVLKDMIHKSRNIAKQLIEKKRVKVNHTIIDTPDFQLEQNDLLSIQG 235


>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 = 49.4 bits (117), Expect = 7e-04,   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|149203330|ref|ZP_01880300.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
 gi|149143163|gb|EDM31202.1| Pseudouridine synthase, RluD [Roseovarius sp. TM1035]
          Length = 347

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 39/273 (14%), Positives = 76/273 (27%), Gaps = 72/273 (26%)

Query: 3   DKNIVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNV 54
              IV  +   QR+ + +       RR        ++E+M  +  ++V+G  ++  A  +
Sbjct: 5   QTRIVGPDDGDQRLDRWV-------RRLFPHVGQVQIEKMCRKGELRVDGGRVK-PATRL 56

Query: 55  MSTDHIEV------DGVP------LRKAERT-----------RLWLYHKPIGLVTTHSDP 91
                + +      D  P      +  A+              +   +KP GL       
Sbjct: 57  EVGQSVRIPPLPDTDERPTGALARISPADAKMIQSCVIYRDDHIIALNKPPGLPVQGGSK 116

Query: 92  DGRSTVFDNLPSIFS-----RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRV 144
             R    D L          +   V RLD +T G+LLL      A+ L          ++
Sbjct: 117 QLRHV--DGLAEALRFGAEDKPRLVHRLDKDTSGVLLLARTREAAKGLTAAFRHRNTRKI 174

Query: 145 YRVRFHGQVDQDK-------LNLLKKGIVIQGIC--------------YGDMQ---VTLD 180
           Y     G             +     G   +G                          ++
Sbjct: 175 YWAAVAGVPTPRMGTIRFGLVKAPGHGAKGEGEKMLCLHPRDIDATPGAKPATTDYAVIE 234

Query: 181 TQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 AW+ +    G+  +++         + 
Sbjct: 235 AAGARTAWMALIPVTGRTHQLRAHMAEIGHPIV 267


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

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 23/146 (15%), Positives = 47/146 (32%), Gaps = 26/146 (17%)

Query: 31  VERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVP----------------LRK 69
           +E+++   +++V+G   +     + +   + V      G P                L  
Sbjct: 34  IEKLLRTGQIRVDGGRAK-GNQRLSAGQSVRVPPMPDAGEPREQGSITRQDAQFARSLVI 92

Query: 70  AERTRLWLYHKPIGLVTTH--SDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
            E  ++   +KP GL              +         +   V RLD +T G+L++   
Sbjct: 93  YEDKQMIALNKPPGLAVQGGSKVTMHLDHLLQAFGKGDQKPRLVHRLDKDTSGVLVVAKT 152

Query: 128 GGLARVLEL--PSTQWLRVYRVRFHG 151
              A+ L     +    + Y     G
Sbjct: 153 AQSAKRLARLFQTRDVKKTYWAICLG 178


>gi|332874770|ref|ZP_08442640.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
 gi|332737031|gb|EGJ67988.1| pseudouridine synthase A [Acinetobacter baumannii 6014059]
          Length = 196

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/116 (20%), Positives = 43/116 (37%), Gaps = 16/116 (13%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARV 133
            + HKP  +++     D   +V   L +I  R + + RLD +T G+L+   +  G  A  
Sbjct: 1   MVIHKPSDILSVPGKGDLHDSVLTRLVAIEPRTLLIHRLDRDTSGILVFGLSKRGQSAIA 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 61  RQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVVYDPSRPPLHIV 102


>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 = 49.4 bits (117), Expect = 7e-04,   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|84623138|ref|YP_450510.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
 gi|84367078|dbj|BAE68236.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           oryzae pv. oryzae MAFF 311018]
          Length = 331

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 59/324 (18%), Positives = 104/324 (32%), Gaps = 55/324 (16%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNG-----------------ILL 47
           IV +N   +R   V+A      SR  +   I      ++G                  ++
Sbjct: 17  IVPDNAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGAMARPRDTLRGGESVQVQVV 76

Query: 48  ERAAVNVMSTDHIEVDGVPLRK-AERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSI 104
                +    D       PL    E  ++ +  KP GLV      +PDG           
Sbjct: 77  LETQTHAAPQDI------PLSVLYEDEQVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDP 130

Query: 105 F----SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG------- 151
                 R   V RLD +T G+++L         L  +L +    R Y     G       
Sbjct: 131 ALASVPRAGVVHRLDKDTSGVMVLARTVQAQTALVEQLSARDVHRQYLAVVVGALVSGGT 190

Query: 152 ---QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
               +D+   + LK  +   G          +  +   A +   L  G+  +I+      
Sbjct: 191 ANAPIDRHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHL 249

Query: 209 NWKVNR--LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYS 263
              +    L    YG   L  L  G+T E+  ++    R+ L    L+        P+ +
Sbjct: 250 KSPIVGDPL----YGG-ALK-LPKGATDELVHELRTFKRQALHAETLQFLHPVSGEPVRA 303

Query: 264 SETLVRDRPNIISEVPDDFTRMKK 287
           S  +  D   +++ + +D  R  +
Sbjct: 304 SAPVPADLQRLMTALREDSARAAE 327


>gi|307195434|gb|EFN77320.1| RNA pseudouridylate synthase domain-containing protein 2
           [Harpegnathos saltator]
          Length = 357

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/237 (15%), Positives = 87/237 (36%), Gaps = 25/237 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + +KP  +          +TV   L   +    + ++ RLD  T G+LL       AR
Sbjct: 5   VVVVNKPASIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGILLFGRTPKKAR 64

Query: 133 VLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------- 183
            +E    + Q  + Y  R  G+  ++++ +  + I +     G  +V+   +        
Sbjct: 65  QMEHQIRNRQVHKQYVCRVEGEFPEEEV-ICSEPIEVVSYKIGVCKVSDKGKDCVTRFKR 123

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNR--L-IRISYGPFQLGTLLAGSTREV 236
               G ++ V    + G+  +I+   ++  + V    L   + +GP +      G     
Sbjct: 124 LSYNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVFGPHKGKGGNIGK---- 179

Query: 237 SKKIL-REQLGPHLLEE-AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNSSQ 291
           + + L ++ +  H  E    ++ D+ +   +  +     ++    D       ++  
Sbjct: 180 TDEELVKDLISIHNAENWLGMDGDSEMSLFKPKLEMEERMLGSANDKDGSSPSSTPG 236


>gi|300862110|ref|ZP_07108190.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|300848635|gb|EFK76392.1| pseudouridine synthase, RluA family [Enterococcus faecalis TUSoD
           Ef11]
 gi|315031415|gb|EFT43347.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0017]
 gi|315144507|gb|EFT88523.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX2141]
          Length = 283

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 74/210 (35%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P   +T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETNTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGNSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVQVLSNNQTAVTCVLETGRTHQIR 231


>gi|118580263|ref|YP_901513.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
 gi|118502973|gb|ABK99455.1| pseudouridine synthase [Pelobacter propionicus DSM 2379]
          Length = 238

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 48/260 (18%), Positives = 82/260 (31%), Gaps = 67/260 (25%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL--------PSIFSRVISVGRLDINTEGLL 122
           E   + +  KP GL+T  +  D   TV   L        P   +RV  V RLD  T G+L
Sbjct: 16  EDRDIIIIEKPCGLLTIGTGRDKTRTVHSILNDYVRKGDPRSRNRVYIVHRLDRETSGIL 75

Query: 123 LLTNDGGLARVLELPST--QWLRVYRVRFHGQVDQDKLNLLKKGIV-------------- 166
           +L      A  + L     +  + Y    HG +       LK G +              
Sbjct: 76  ILA--KSEANKIYLQEHWQETDKHYVAVVHGTL------ALKSGTISSYLAENSAMRVYS 127

Query: 167 ---IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPF 223
                       +  +  +    + + + L  G+  +I+                     
Sbjct: 128 TTDQAQGKLSHTEYVVMKENRGLSLLAIHLLTGRKHQIR--------------------V 167

Query: 224 QL---GTLLAGSTREVSKKILREQLGPHLLEEAQVNLDAPIYSSETLVRDRPNIISEVPD 280
            L   G  + G ++  + +  R  L  H      +    P+         R  I + +PD
Sbjct: 168 HLSEGGNAVVGDSKYGTDRYARANLALH---ARSLTFTHPVSGR------RMAIETGIPD 218

Query: 281 DFTRMKKNSSQKNGLSKQKK 300
            FTR+  + S      K ++
Sbjct: 219 YFTRLVGSISPNESTDKSRE 238


>gi|293417934|ref|ZP_06660556.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B185]
 gi|291430652|gb|EFF03650.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B185]
          Length = 219

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYATDNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|190572297|ref|YP_001970142.1| putative tRNA pseudouridine synthase C [Stenotrophomonas
           maltophilia K279a]
 gi|190010219|emb|CAQ43827.1| putative tRNA pseudouridine synthase C [Stenotrophomonas
           maltophilia K279a]
          Length = 246

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 34/154 (22%), Positives = 53/154 (34%), Gaps = 25/154 (16%)

Query: 72  RTRLWLYHKPIGLVTTHSD--PDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDG 128
             RL + +KP GL+   S         + D L     R +  V RLD  T G LLL  D 
Sbjct: 24  DERLAVVNKPAGLMVHDSKLARGEDDFLADRLREQLGRPIFLVHRLDRATSGCLLLAFDR 83

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD--MQVTLDTQKG 184
             A  L   L   + L+ Y     G   +      +    + G            D Q+ 
Sbjct: 84  ETASALGKALMGGEVLKDYLTVCRGWPAE---LAWQVDHDLDGGPGKPVKKPAVTDFQRL 140

Query: 185 SNAWVTVGLRE---------------GKNREIKK 203
           +   ++V + E               G+ R+I++
Sbjct: 141 ATGELSVPVGEFTRSRYALLRCQPQTGRFRQIRR 174


>gi|126642499|ref|YP_001085483.1| putative ribosomal large subunit pseudouridine synthase
           A(RluA-like) [Acinetobacter baumannii ATCC 17978]
          Length = 196

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 24/116 (20%), Positives = 43/116 (37%), Gaps = 16/116 (13%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARV 133
            + HKP  +++     D   +V   L +I  R + + RLD +T G+L+   +  G  A  
Sbjct: 1   MVIHKPSDILSVPGKGDLHDSVLTRLVAIEPRTLLIHRLDRDTSGILVFGLSKRGQSAIA 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 61  RQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVVYDPSRPPLHIV 102


>gi|158320638|ref|YP_001513145.1| hemolysin A [Alkaliphilus oremlandii OhILAs]
 gi|158140837|gb|ABW19149.1| hemolysin A [Alkaliphilus oremlandii OhILAs]
          Length = 268

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 24/60 (40%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  V+   G   SR + +  I    V V+   +++    V    ++ V G  +    R
Sbjct: 5  ERLDVVLVEKGFFDSREKAKGAIMAGIVFVDNEKIDKPGTKVKKNGNVVVKGNLIPYVSR 64


>gi|307543955|ref|YP_003896434.1| tRNA pseudouridine synthase C [Halomonas elongata DSM 2581]
 gi|307215979|emb|CBV41249.1| tRNA pseudouridine synthase C [Halomonas elongata DSM 2581]
          Length = 256

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 33/182 (18%), Positives = 64/182 (35%), Gaps = 33/182 (18%)

Query: 74  RLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
            L   HKP G++   S     +    +      I  RV  V RLD  T GL++   D  +
Sbjct: 13  HLIAVHKPAGMLVHRSALARGERHFLLQTLRDQIGQRVYPVHRLDRPTSGLMVFALDPEV 72

Query: 131 ARVLEL--PSTQWLRVYRVRFHGQ-VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
           A  L     + +  + Y     GQ  + ++L+       ++       +  +  ++    
Sbjct: 73  AGRLADAFATQRVAKRYLAVVRGQGPEAERLDY-----ALRDEDGRRPKAEMPAREART- 126

Query: 188 WVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQLGP 247
                       E++++ +     V R+ R     + L        R ++ +  R Q+  
Sbjct: 127 ------------EVRRL-DSVELPV-RVDRYPSARYSLM-----EARPLTGR--RHQIRR 165

Query: 248 HL 249
           HL
Sbjct: 166 HL 167


>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 = 49.4 bits (117), Expect = 8e-04,   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|317122830|ref|YP_004102833.1| pseudouridine synthase [Thermaerobacter marianensis DSM 12885]
 gi|315592810|gb|ADU52106.1| pseudouridine synthase [Thermaerobacter marianensis DSM 12885]
          Length = 414

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 27/120 (22%), Positives = 41/120 (34%), Gaps = 21/120 (17%)

Query: 53  NVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV---- 108
            V   D + V        E   + + +KP G++ TH D     T+   +    +R     
Sbjct: 124 RVPELDPVIV-------YEDDHVLVVNKPAGML-THGDGHAEWTLLAWVRDQLARRGTLP 175

Query: 109 -------ISVGRLDINTEGLLLL--TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLN 159
                      RLD NT GL+    T  G       L S Q ++ Y     G+  +  L 
Sbjct: 176 AGALFQPSPAHRLDRNTSGLVAFGKTRHGAARLAEALRSGQAIKEYLAVVRGRPPEGLLQ 235


>gi|258544489|ref|ZP_05704723.1| tRNA pseudouridine synthase C [Cardiobacterium hominis ATCC 15826]
 gi|258520224|gb|EEV89083.1| tRNA pseudouridine synthase C [Cardiobacterium hominis ATCC 15826]
          Length = 244

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 62/193 (32%), Gaps = 39/193 (20%)

Query: 72  RTRLWLYHKPIGLVTTHS--DPDGRSTVFDNLPSIFS-RVISVGRLDINTEGLLLLTNDG 128
              L   +KP GL+   S  +     TV   L      +     RLD  T G+LLL  D 
Sbjct: 10  DAHLIAVNKPAGLLVHRSPLERYADETVLQILQEQTGLKGYPAHRLDRPTSGVLLLALDP 69

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDMQVTLDT 181
             AR+L   +   +  + Y     G + +       L  L   +  +            T
Sbjct: 70  TTARLLGELIAQQRLEKTYHAIVRGWLAETGEIDYPLAYLPDKMADRNRQREKPPQEALT 129

Query: 182 Q---------------KGSNAWVTV-GLR--EGKNREIKKVFEFFNWKVN--------RL 215
           +               K   +  ++  LR  +G+  ++++  +     +         R 
Sbjct: 130 RYRCLARSELPFASDGKHPTSRYSLAELRPLQGRKHQLRRHLKHIFHPIIGDTTHGDNRQ 189

Query: 216 IRI---SYGPFQL 225
            R+    YG  +L
Sbjct: 190 NRVLGERYGALRL 202


>gi|149911608|ref|ZP_01900220.1| ribosomal large subunit pseudouridine synthase C [Moritella sp.
           PE36]
 gi|149805329|gb|EDM65342.1| ribosomal large subunit pseudouridine synthase C [Moritella sp.
           PE36]
          Length = 317

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 81/252 (32%), Gaps = 73/252 (28%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVN-GILLERAAVNVMS 56
            + E++  QR+   +       R +++        R+I +  V+VN G +  +    +  
Sbjct: 13  TITEDYQGQRIDNFL-------RTKLKGVPKSMIYRIIRKGEVRVNKGRI--KPEYKLQP 63

Query: 57  TDHIEVDGVPLRKAE---------------------RTRLWLYHKPIGLVTTHSDPDGRS 95
            D + +  V + + E                        L + +KP G+        G S
Sbjct: 64  EDIVRIPPVRVSETEAISPSANLDSVRALESQIIYEDDYLIVINKPSGMAV-----HGGS 118

Query: 96  TVFDNLPSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYR 146
            +   L      +         V RLD +T G LL+       + L   L      + Y+
Sbjct: 119 GLSFGLIEGLRAIRPDSRFLELVHRLDRDTSGCLLVAKKRSTLKALHEQLRLKTMRKDYQ 178

Query: 147 VRFHGQVDQDKL---NLLKKGIVIQGICYGDMQVTLDTQ-KGSNAWVTV-------GLRE 195
               G   +        L K  V  G       V +D++ K S    ++        L +
Sbjct: 179 ALVAGAWPRSSRIVNAPLLKNTVSSGERL----VRVDSEGKESQTRFSIIQRYEHGTLVQ 234

Query: 196 -----GKNREIK 202
                G+  +I+
Sbjct: 235 ASPITGRTHQIR 246


>gi|324998566|ref|ZP_08119678.1| hemolysin A [Pseudonocardia sp. P1]
          Length = 274

 Score = 49.4 bits (117), Expect = 8e-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|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 = 49.4 bits (117), Expect = 8e-04,   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|149176956|ref|ZP_01855565.1| choline sulfatase [Planctomyces maris DSM 8797]
 gi|148844211|gb|EDL58565.1| choline sulfatase [Planctomyces maris DSM 8797]
          Length = 549

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/67 (19%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 2   KDKNIVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
              ++V E+  P R+ + +  +A + +    + +I    V VNG++  R    +   D +
Sbjct: 475 SSNDMVSEDRAPIRLDQFLKFQAAVGTGGHAKVVIQGGEVTVNGVVETRRRKQLAPGDIV 534

Query: 61  EVDGVPL 67
              G   
Sbjct: 535 GYAGEEW 541


>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 = 49.4 bits (117), Expect = 8e-04,   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    ++++ +RV VNG L+   + +V   D + +
Sbjct: 98  RLDNVIYRMGFAVTRPAARQLVSHRRVLVNGKLVNLPSYHVKPGDVVAL 146


>gi|332762292|gb|EGJ92559.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           2747-71]
 gi|332768845|gb|EGJ99024.1| 23S rRNA/tRNA pseudouridine synthase [Shigella flexneri 2930-71]
          Length = 219

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 FETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|329121404|ref|ZP_08250029.1| pseudouridylate synthase [Dialister micraerophilus DSM 19965]
 gi|327469694|gb|EGF15161.1| pseudouridylate synthase [Dialister micraerophilus DSM 19965]
          Length = 303

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 37/252 (14%), Positives = 78/252 (30%), Gaps = 49/252 (19%)

Query: 1   MKDKNIVQENFTPQRVSKVIARAGIASRREVERM--------IAQQRVKVNGILLERAAV 52
           MK+  I  +    +R+   I        +E E++        + + ++KVNG   E    
Sbjct: 1   MKEYKITPDK-NGKRLDNYI--------KEKEKIPHFIFIKSLKKNKIKVNGKK-ESGNY 50

Query: 53  NVMSTDHIEVDGVPLRKA-----------ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL 101
            + + D I        K            E   + +  K  G++   +      T+ D +
Sbjct: 51  KLKTGDIITSYIENKNKNEKEKIHFSINYEDENIIIVEKEAGILCNDTTNKEEKTLHDEI 110

Query: 102 PSIFSRV-----ISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVD 154
                         V R+D+NT GL++   +     +L+         + Y     G + 
Sbjct: 111 NEYLKEKNEPEAYPVHRIDLNTTGLVIFAKNMHARAILDRAIKERNIKKYYLCVTTGTMK 170

Query: 155 QD--------KLNLLKKGIVI-----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREI 201
           +           +     + I     +G     M       +   + V   L  G+  +I
Sbjct: 171 KKSGKLEHQLFKDAKNNKVYIYEKPCKGSKTATMNYKCLKTENGLSLVECELITGRTHQI 230

Query: 202 KKVFEFFNWKVN 213
           +    +  + + 
Sbjct: 231 RSQLSYIGYPIL 242


>gi|26245982|ref|NP_752021.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli CFT073]
 gi|227885043|ref|ZP_04002848.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|300981032|ref|ZP_07175309.1| pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|301048442|ref|ZP_07195469.1| pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|331661098|ref|ZP_08362030.1| pseudouridine synthase A [Escherichia coli TA206]
 gi|331681442|ref|ZP_08382079.1| pseudouridine synthase A [Escherichia coli H299]
 gi|34395780|sp|Q8FL93|RLUA_ECOL6 RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|26106379|gb|AAN78565.1|AE016755_65 Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           CFT073]
 gi|227837872|gb|EEJ48338.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 83972]
 gi|300299735|gb|EFJ56120.1| pseudouridine synthase A [Escherichia coli MS 185-1]
 gi|300409068|gb|EFJ92606.1| pseudouridine synthase A [Escherichia coli MS 45-1]
 gi|307551903|gb|ADN44678.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           ABU 83972]
 gi|315293367|gb|EFU52719.1| pseudouridine synthase A [Escherichia coli MS 153-1]
 gi|315298424|gb|EFU57679.1| pseudouridine synthase A [Escherichia coli MS 16-3]
 gi|331052140|gb|EGI24179.1| pseudouridine synthase A [Escherichia coli TA206]
 gi|331081663|gb|EGI52824.1| pseudouridine synthase A [Escherichia coli H299]
          Length = 219

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VVLYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|307702537|ref|ZP_07639490.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
 gi|307623883|gb|EFO02867.1| pseudouridine synthase, RluA family protein [Streptococcus oralis
           ATCC 35037]
          Length = 278

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P   + +      +      V RLD+ T GL+L   +
Sbjct: 70  EVYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 129

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G+V+  +L           +  K+ +  +   Y +
Sbjct: 130 PFILPILNRLLEKKEIARDYWALIEGRVESKELVFRDKIGRDRHDRRKRIVDAKNGQYAE 189

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             ++   Q       V   L+ G+  +I+
Sbjct: 190 THISRLKQFPNKTTLVRCKLKTGRTHQIR 218


>gi|255037507|ref|YP_003088128.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
 gi|254950263|gb|ACT94963.1| pseudouridine synthase [Dyadobacter fermentans DSM 18053]
          Length = 255

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 29/168 (17%), Positives = 53/168 (31%), Gaps = 27/168 (16%)

Query: 51  AVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRS-TVFDNLPSIFSRVI 109
            + +   D I          E     + +KP  L T       R  +V          + 
Sbjct: 15  KMKINFKDIIIF--------EDEDFLVVNKPPHLATLDERTADRGGSVLRLAKEYNPELQ 66

Query: 110 SVGRLDINTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLN------LL 161
           +  RLD  T G L    +    R L +     +  + Y    +G  D + ++       L
Sbjct: 67  AAHRLDKETSGALAFAKNPAAYRHLAMQFEHREVTKRYHAVVNGIHDLEGISVYLPILPL 126

Query: 162 KKG--IVIQGICYGDMQVTLDTQKGSNAWVTVGLRE-----GKNREIK 202
           K G  + I      + +   +T +    +    L E     G+  +I+
Sbjct: 127 KNGTAVKIDRADGKEAETIFNTLQVYRGY---TLVECIPITGRMHQIR 171


>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 = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 34/81 (41%), Gaps = 8/81 (9%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++ +  +A SR + + +I    V V+G   ++A         IEV G  L+   R
Sbjct: 3  ERLDVLLVQRNLAPSREKAKALIMSGIVYVDGQKEDKAGTQFDEAAAIEVRGSTLKYVSR 62

Query: 73 TRLWLYH-------KPIGLVT 86
            L L         +P G V 
Sbjct: 63 GGLKLEKAMTHFGVEPAGKVC 83


>gi|58039270|ref|YP_191234.1| ribosomal large subunit pseudouridine synthase A [Gluconobacter
           oxydans 621H]
 gi|58001684|gb|AAW60578.1| Ribosomal large subunit pseudouridine synthase A [Gluconobacter
           oxydans 621H]
          Length = 265

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 32/159 (20%), Positives = 50/159 (31%), Gaps = 19/159 (11%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL----TN 126
           E  R  + +KP GL          S     LP          RLD +T G LL+    T 
Sbjct: 51  ETPRFLILYKPAGLAVHPGPSTQDSVETRLLPHPRGGPWLAHRLDADTSGCLLVARRKTA 110

Query: 127 DGGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLLKK----G----IVIQGICYGD 174
                +  +       ++Y     G + QD       LL++    G    +  +G     
Sbjct: 111 LIEAQKAFQERQAH--KLYWAVVVGDLPQDSGEIDAPLLRQSDASGWRMVVDAKGDEART 168

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               L   KG   WV + L  G+  + +         + 
Sbjct: 169 RWRVLGRSKGL-CWVELELLTGRTHQARIHCAELGTPIL 206


>gi|295093660|emb|CBK82751.1| SSU ribosomal protein S4P [Coprococcus sp. ART55/1]
          Length = 197

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  +I R G A +RRE  +++  + V VNG  +   + +V   D IE+
Sbjct: 88  RLDNIIFRLGFARTRREARQIVDHKHVLVNGKCVNIPSYSVKPGDKIEI 136


>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 = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 69/209 (33%), Gaps = 39/209 (18%)

Query: 42  VNGILLERAAVNVMSTDHIEVDGVPLRKAERTR-------------LWLYHK-------P 81
           VN   ++  +  +   D IE+D       E                  +  K       P
Sbjct: 38  VNNSFVK-PSFKLSEGDEIEIDDSLFHVPELKAEDMELKIVYENDDYAIIDKDSNVIVHP 96

Query: 82  IGLVTTHSDPDG--RSTVFDNLPSIFSRVIS--VGRLDINTEGLLLL--TNDGGLARVLE 135
            G + T +  +G      +D L  I        V RLD +T GL+ +  TN+        
Sbjct: 97  AGKIITGTLVNGLLGRYGYDGLSHIGGDDRPGIVHRLDKDTTGLIAITKTNEAYKYFKKM 156

Query: 136 LPSTQWLRVYRVRFHGQVDQDK--LNLL-------KKGIVIQGICYGDMQ-VTLDTQKGS 185
             + +  + Y     G  D+ K  ++         ++ + ++      +    + ++   
Sbjct: 157 FETRKVDKYYYAIVFGNFDKKKGTIDNFMDRDVHNRRKMAVRNTGRRAVSHYEVISEVEG 216

Query: 186 NAWVTVGLREGKNREIK-KVFEFFNWKVN 213
            + V + +  G+  +I+  +    N  + 
Sbjct: 217 FSLVRIKIETGRTHQIRVHMT-HINHPIL 244


>gi|224532575|ref|ZP_03673198.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi WI91-23]
 gi|224512518|gb|EEF82896.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi WI91-23]
          Length = 326

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   VKREFTVKENAL--RLDLYLSGNFEVFTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHI--EVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I  E D             +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEESSQIDCLRPSNIPIAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--E--------- 195
               G  +      ++  I           V+ D  K +     + L   E         
Sbjct: 178 AIVKGNFN-SFFGSIESFIDRDKHNRKKFSVSKDRGKKALTEYRLLLNFGEYSLLALKPK 236

Query: 196 -GKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>gi|209963797|ref|YP_002296712.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
 gi|209957263|gb|ACI97899.1| RNA pseudouridine synthase, putative [Rhodospirillum centenum SW]
          Length = 242

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 36/148 (24%), Positives = 51/148 (34%), Gaps = 24/148 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDN---LPSI-FSRVIS---VGRLDINTEGLLLLTND 127
           + +  KP GL        G  TV      LP I F R        RLD +T G L+L  D
Sbjct: 19  VLILDKPHGLPV----HYGTKTVEHLEQYLPWIAFEREEPPRLAHRLDKDTSGCLVLARD 74

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQD----KLNLLK-------KGIVIQGICYGD 174
             +A  L          + Y     G+   D     L LLK       K +V        
Sbjct: 75  AEVAARLGRLFLHGHVGKTYWAVVLGRPRGDAGRIDLPLLKVHIPGCSKVVVDPDGKPAL 134

Query: 175 MQVTLDTQKGSNAWVTVGLREGKNREIK 202
               L    G  +W+ +  R G+  +++
Sbjct: 135 TDWRLLATDGRLSWLELTPRTGRMHQLR 162


>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 = 49.4 bits (117), Expect = 8e-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: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 192


>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 = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 26/56 (46%)

Query: 5   NIVQENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
            +V+ +    R+  ++A A  ASR  +  +I   +V VNG L+      V   D I
Sbjct: 183 ELVRGSVASVRLDSLLALAFGASRSSLVGLIEGGKVFVNGRLITSNGYKVKENDLI 238


>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 = 49.4 bits (117), Expect = 8e-04,   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|317047700|ref|YP_004115348.1| RluA family pseudouridine synthase [Pantoea sp. At-9b]
 gi|316949317|gb|ADU68792.1| pseudouridine synthase, RluA family [Pantoea sp. At-9b]
          Length = 318

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 76/244 (31%), Gaps = 58/244 (23%)

Query: 6   IVQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMST 57
           I  EN   QR+   +       R +++        R++ +  V+VN   ++     +   
Sbjct: 13  ITAEN-AGQRIDNFL-------RTQLKGVPKSMIYRILRKGEVRVNKKRIK-PEYKLEEG 63

Query: 58  DHIEVDGVPLRKAERT---------------------RLWLYHKPIGLVTTHSDPDGRST 96
           D I +  V + + E                        L + +KP G             
Sbjct: 64  DEIRIPPVRVAEREEQAVSPKLEKVASLADAILYEDDYLLVLNKPSGTAVHGGSGLSFGV 123

Query: 97  VFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQ 152
           +     L      +  V RLD +T G+LL+       R L   L      + Y     G 
Sbjct: 124 IEGLRALRPEARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKGMQKDYLALVRGD 183

Query: 153 VDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKN 198
                L +++  + ++ I     +V   + +G  +     + E              G+ 
Sbjct: 184 WP-SHLKVVQAPL-LKNILQSGERVVRVSAEGKPSETRFKVEERFGFATLVKASPVTGRT 241

Query: 199 REIK 202
            +I+
Sbjct: 242 HQIR 245


>gi|256964482|ref|ZP_05568653.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
 gi|256954978|gb|EEU71610.1| pseudouridine synthase [Enterococcus faecalis HIP11704]
          Length = 287

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 73/210 (34%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 28  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 86

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 87  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 146

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 147 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 205

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 206 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 235


>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 = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 11 FTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
             +R+  ++ R G +ASR     +I    V+V GI++ +A   V     I +
Sbjct: 1  MGKERLDTMLVRRGLVASRERARALILAGEVEVGGIIVSKAGTRVAEEAEIAL 53


>gi|34497273|ref|NP_901488.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
 gi|34103129|gb|AAQ59492.1| pseudouridine synthase [Chromobacterium violaceum ATCC 12472]
          Length = 312

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 75/240 (31%), Gaps = 56/240 (23%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V      QR+   + R      +  + R++    V+VN G +   A+  V + D + +  
Sbjct: 14  VDAEDAGQRLDNYLQRLLKGVPKSHIYRILRSGEVRVNKGRV--DASYRVAAGDMLRI-- 69

Query: 65  VPLRKAERTR----------------LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV 108
            P+R AER                  L +  KP G+        G S V   +     R 
Sbjct: 70  PPIRVAERAEKTVPAATFPVVYEDDALLVIDKPAGVAV-----HGGSGVSFGVIEQLRRA 124

Query: 109 IS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLN 159
                    V RLD  T GLL+L         L          + Y     G   ++ + 
Sbjct: 125 HPEWRYLELVHRLDRETSGLLMLAKKRSALTRLHDMMRDNVPDKRYLALATGHWPEN-VK 183

Query: 160 LLKKGIVIQGICYGDMQVTLDTQKGSNAWV------------TVGLRE-----GKNREIK 202
            +K  + +      D +  +   +G +                  L E     G+  +I+
Sbjct: 184 QVK--LPLYKFHTPDGERRVKIAEGDDGQYAHTNFSIQQRYTEFTLVEAHLRTGRTHQIR 241


>gi|322376158|ref|ZP_08050666.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
 gi|321278840|gb|EFX55885.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus sp. C300]
          Length = 291

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/149 (18%), Positives = 56/149 (37%), Gaps = 14/149 (9%)

Query: 68  RKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTND 127
              +   L + +KP G+ T  + P   + +      +      V RLD+ T GL+L   +
Sbjct: 83  EVYQDQHLIIVNKPEGMKTHGNQPGEIALLNHVSAYVGQTCYVVHRLDMETSGLVLFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGD 174
             +  +L   L   +  R Y     G+V+  +L           +  K+ +  +   Y +
Sbjct: 143 PFILPILNRLLEKKEIARDYWALIEGRVESKELVFRDKIGRDRHDRRKRIVDTKNGQYAE 202

Query: 175 MQVTLDTQ-KGSNAWVTVGLREGKNREIK 202
             ++   Q       V   L+ G+  +I+
Sbjct: 203 THISRLKQFPNKTTLVRCKLKTGRTHQIR 231


>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 = 49.4 bits (117), Expect = 8e-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: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 192


>gi|15675829|ref|NP_270003.1| hypothetical protein SPy_2063 [Streptococcus pyogenes M1 GAS]
 gi|13623058|gb|AAK34724.1| conserved hypothetical protein [Streptococcus pyogenes M1 GAS]
          Length = 272

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 70/204 (34%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 5   RKIRHFLRTKKHVLINGHSVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 65  EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 124

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 125 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 184

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +T  L+ G+  +I+
Sbjct: 185 VKNFHKTASLLTCQLQTGRTHQIR 208


>gi|312149435|gb|ADQ29506.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi N40]
          Length = 326

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   VKREFTVKENAL--RLDLYLSGNFEVFTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHI--EVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I  E D             +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEESSQIDCLRPSNIPIAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--E--------- 195
               G  +      ++  I           V+ D  K +     + L   E         
Sbjct: 178 AIVKGNFN-SFFGSIESFIDRDKHNRKKFSVSKDRGKKALTEYRLLLNFGEYSLLALKPK 236

Query: 196 -GKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>gi|257060968|ref|YP_003138856.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
 gi|256591134|gb|ACV02021.1| pseudouridine synthase [Cyanothece sp. PCC 8802]
          Length = 551

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 29/155 (18%), Positives = 54/155 (34%), Gaps = 29/155 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSR---VISVGRLDINTEGLLLLTN 126
           E   +    KP GL++      +   +V   L +       + +V RLD +T G+LLL  
Sbjct: 349 EDQWIIAIDKPSGLLSVPGRYFETFDSVLTRLQNSLPDAQELRTVHRLDQDTSGILLLAR 408

Query: 127 DGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGD-----MQVTL 179
           D    R L       +  ++Y     G V      ++ +G++   +          +V  
Sbjct: 409 DRYTHRHLSQQFAQRKVEKIYEAILAGSV------MMNEGVIQLPLWGDPNNRPYQKVDW 462

Query: 180 DTQKGSNAWVTVGLRE------------GKNREIK 202
           +  K S     V   +            G+  +I+
Sbjct: 463 ELGKPSITQFKVITTQENLTRIQFIPLTGRTHQIR 497


>gi|254487090|ref|ZP_05100295.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           GAI101]
 gi|214043959|gb|EEB84597.1| ribosomal large subunit pseudouridine synthase A [Roseobacter sp.
           GAI101]
          Length = 215

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/162 (16%), Positives = 57/162 (35%), Gaps = 16/162 (9%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL- 124
           +   E   + L  KP GL++     P     +   + ++F   + V RLD +T G+++  
Sbjct: 13  VILHEDAEVLLVDKPAGLLSVPGKGPHLADCLIARVQAVFPDALLVHRLDRDTSGVMIFA 72

Query: 125 -TNDGGLARVLELPSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICY 172
            T        L+       + Y  R  G   ++     L L+        + +  +    
Sbjct: 73  LTPYAQRHLGLQFEKRMTRKTYVARVWGVPTENSGTIDLPLIVDWPNRPLQMVCHETGKS 132

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
                 L   +G  A V +  + G++ +++  +       + 
Sbjct: 133 AQTDWRLLKNEGDTARVRLSPKTGRSHQLRVHML-SLGHPIL 173


>gi|261405374|ref|YP_003241615.1| RluA family pseudouridine synthase [Paenibacillus sp. Y412MC10]
 gi|261281837|gb|ACX63808.1| pseudouridine synthase, RluA family [Paenibacillus sp. Y412MC10]
          Length = 302

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 27/153 (17%), Positives = 60/153 (39%), Gaps = 24/153 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNL-------PSIFSRVISVGRLDINTEGLLL 123
           E     + +KP G +  H D + R T  +++         I + V  + RLD +T G +L
Sbjct: 87  EDDFCLVVNKPAG-LAVHPDNESRETTLNHVVAAYYEAEGIHAAVRHIHRLDKDTTGPVL 145

Query: 124 LTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL------------KKGIVIQG 169
              +      L   +   + +R+Y     G+V Q+ L  +            ++ + + G
Sbjct: 146 YAKNEYAQLKLDEAMREKKIVRMYAAIVQGRVSQE-LKRIDLPIGKDRYHASRRRVSLTG 204

Query: 170 ICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                  ++ +    + + + + L  G+  +I+
Sbjct: 205 QAAITHILSAEAYPKA-SLLHIRLETGRTHQIR 236


>gi|24111502|ref|NP_706012.1| hypothetical protein SF0053 [Shigella flexneri 2a str. 301]
 gi|24050255|gb|AAN41719.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301]
          Length = 228

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 34  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 93

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 94  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 147

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 148 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 195


>gi|331645166|ref|ZP_08346277.1| pseudouridine synthase A [Escherichia coli M605]
 gi|331045923|gb|EGI18042.1| pseudouridine synthase A [Escherichia coli M605]
          Length = 219

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 60/170 (35%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +     + + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGYPIL 176


>gi|254563644|ref|YP_003070739.1| hemolysin [Methylobacterium extorquens DM4]
 gi|254270922|emb|CAX26927.1| hemolysin [Methylobacterium extorquens DM4]
          Length = 250

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 11 FTPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           T +R+   + +   G   SR +    I    V  +G L+ R +  V  +  IE
Sbjct: 1  MTGERLRADRFLVERGHFRSRAQARAAIEAGLVSADGRLVTRPSDLVEPSARIE 54


>gi|240141133|ref|YP_002965613.1| hemolysin [Methylobacterium extorquens AM1]
 gi|240011110|gb|ACS42336.1| hemolysin [Methylobacterium extorquens AM1]
          Length = 250

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 3/54 (5%)

Query: 11 FTPQRV--SKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIE 61
           T +R+   + +   G   SR +    I    V  +G L+ R +  V  +  IE
Sbjct: 1  MTGERLRADRFLVERGHFRSRAQARAAIEAGLVSADGRLVTRPSDLVEPSARIE 54


>gi|218249610|ref|YP_002374552.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi ZS7]
 gi|226321152|ref|ZP_03796693.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 29805]
 gi|218164798|gb|ACK74859.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi ZS7]
 gi|226233444|gb|EEH32184.1| ribosomal large subunit pseudouridine synthase D [Borrelia
           burgdorferi 29805]
          Length = 326

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   VKREFTVKENAL--RLDLYLSGNFEVFTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHI--EVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I  E D             +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEESSQIDCLRPSNIPIAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--E--------- 195
               G  +      ++  I           V+ D  K +     + L   E         
Sbjct: 178 AIVKGNFN-SFFGSIESFIDRDKHNRKKFSVSKDRGKKALTEYRLLLNFGEYSLLALKPK 236

Query: 196 -GKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>gi|332359530|gb|EGJ37349.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK1056]
          Length = 226

 Score = 49.4 bits (117), Expect = 8e-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: 117 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 173


>gi|225028953|ref|ZP_03718145.1| hypothetical protein EUBHAL_03243 [Eubacterium hallii DSM 3353]
 gi|224953728|gb|EEG34937.1| hypothetical protein EUBHAL_03243 [Eubacterium hallii DSM 3353]
          Length = 306

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 23/168 (13%), Positives = 55/168 (32%), Gaps = 27/168 (16%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF----------SRVISVGRLDINTEG 120
           E   L    KP G+V+  S      ++ + + + F          S +  +GRLD  T G
Sbjct: 88  EDEDLIFVDKPAGIVSHPSKGHLSDSMINGVQAYFENEGREKNERSNIHLIGRLDKETSG 147

Query: 121 LLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQVDQ--------DKLNLLKKGIVI--- 167
           +L +  +   A  +     +   ++ Y     G   +        +++   + G  +   
Sbjct: 148 ILGIAKNSVTAERMIKQRQRGILIKEYYALVKGNPPEEGILEIPMEEMRDARDGDKLKMK 207

Query: 168 ----QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
               +          +  +    + V++ +  G+  +I+         
Sbjct: 208 VGKSENAKTAKTFFQVVKRFEKFSLVSLVIETGRTHQIRFHMASIGCP 255


>gi|163814113|ref|ZP_02205505.1| hypothetical protein COPEUT_00266 [Coprococcus eutactus ATCC 27759]
 gi|158450562|gb|EDP27557.1| hypothetical protein COPEUT_00266 [Coprococcus eutactus ATCC 27759]
          Length = 334

 Score = 49.4 bits (117), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 48/274 (17%), Positives = 86/274 (31%), Gaps = 74/274 (27%)

Query: 6   IVQENFTPQRVSK----VIARAGIASRREVERMIAQQRVKVNG------ILLERAAVN-- 53
           ++ +N   QR++K     + +A       V RMI ++ +K+NG       ++    V   
Sbjct: 5   VISKNEAGQRLNKLVMKYLNKAPS---SFVYRMIRKKNIKLNGGKAVGNEIVYVGDVIQL 61

Query: 54  ---VMSTDHIEVDG------------VPLRKAERTRLWLYHKPIGLVT---THSDPDGRS 95
                + D    D              P        + + +KP+G+++   +  D     
Sbjct: 62  YLADDTIDSFRDDNIQTAASGSQKKFKPEIIYHDHNVLIVNKPVGVLSQKASKDDYSINE 121

Query: 96  TVFDNLPSIFS---------RVISVGRLDINTEGLLLL----TNDGGLARVLELPSTQWL 142
           +V D L              +     RLD NT GL+L       +  L+R++        
Sbjct: 122 SVLDYLLDNGYITSEQLRTYKPSICNRLDRNTSGLVLCGVSLMGNQELSRII--RERNID 179

Query: 143 RVYRVRFHGQVD--QDKLNLL-----------KKGI----------VIQGICYGDMQVTL 179
           + Y     G +   QD    L           + G+            + I      V  
Sbjct: 180 KYYYTIVKGHIKSVQDVTAYLVKDEKKNTVIVRDGVDEIKQDSGKNEFEKIHTIFEPV-- 237

Query: 180 DTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
               G    V V L  GK  +I+       + + 
Sbjct: 238 -RSNGKYTEVKVKLITGKTHQIRAQLSHMGYPIV 270


>gi|313638581|gb|EFS03722.1| ribosomal large subunit pseudouridine synthase D [Listeria
           seeligeri FSL S4-171]
          Length = 207

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 35/207 (16%), Positives = 72/207 (34%), Gaps = 33/207 (15%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGG 129
            + +KP G+ +  S      +V + +   +      S +  V RLD  T GL+L+  +  
Sbjct: 1   LIINKPAGIASIPSQYHPSGSVANFVKGHYETQGLTSAIHIVTRLDRETSGLMLIAKNRF 60

Query: 130 LARVLE--LPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQ 176
               L   L      R Y+    G            + +  ++++++ +  +G       
Sbjct: 61  AHARLSTFLQQGLLKRSYQAFVSGELAEQVGSIEAPIGRKAVSIMERVVTPEGKYAKTNY 120

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
             L   +  +  V + L  G+  +I+  F +    +        G      +  G T  +
Sbjct: 121 QVLARYQAFDH-VAIQLETGRTHQIRVHFSYIGHPL-------IG----DDMYGGDTDLL 168

Query: 237 SKKILR--EQLGPHLLEEAQVNLDAPI 261
            ++ L        H L E  +  D P+
Sbjct: 169 KRQALHSCHLHLIHPLTEEYLAFDLPL 195


>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 = 49.4 bits (117), Expect = 9e-04,   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|94989396|ref|YP_597497.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94993288|ref|YP_601387.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
 gi|94542904|gb|ABF32953.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS9429]
 gi|94546796|gb|ABF36843.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS2096]
          Length = 333

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 69/204 (33%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 66  RKIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 125

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 126 EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 185

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 186 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 245

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +   L+ G+  +I+
Sbjct: 246 VKNFHKTASLLNCQLQTGRTHQIR 269


>gi|313143038|ref|ZP_07805231.1| hemolysin [Helicobacter cinaedi CCUG 18818]
 gi|313128069|gb|EFR45686.1| hemolysin [Helicobacter cinaedi CCUG 18818]
          Length = 234

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 27 SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
          SR + +  I    VKVNG ++++ +  +   D + VD   L
Sbjct: 7  SRTKAKEAIESGCVKVNGAVVKKGSFLLEKDDEVGVDSKDL 47


>gi|325265762|ref|ZP_08132449.1| RNA pseudouridine synthase [Kingella denitrificans ATCC 33394]
 gi|324982745|gb|EGC18370.1| RNA pseudouridine synthase [Kingella denitrificans ATCC 33394]
          Length = 309

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 20/130 (15%), Positives = 42/130 (32%), Gaps = 16/130 (12%)

Query: 99  DNLPSIFSRVISVGRLDINTEGLLLLTNDG--GLARVLELPSTQWLRVYRV----RFHGQ 152
           D      + +  V RLD +T G++LL+++     A           + Y      R    
Sbjct: 137 DLQHLNVADITPVHRLDKDTAGVMLLSHNPASRAAYQQMFAEKTVQKTYHALAPTRLDLP 196

Query: 153 VDQDKLNLLKKG------IVIQGICYGDMQVTLDTQKGSNAWVTVG-LREGKNREIK-KV 204
                 + L +G        + G      ++ L    G  +   +  L  GK  +++  +
Sbjct: 197 YPLTVQSRLVRGESFFLTQEVDGTPNAQTEIRLLEMHGDVSLYELKPLT-GKKHQLRVHM 255

Query: 205 FEFFNWKVNR 214
            +     +  
Sbjct: 256 MK-LGMPLLN 264


>gi|307272491|ref|ZP_07553744.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
 gi|306510776|gb|EFM79793.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0855]
          Length = 283

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 73/210 (34%), Gaps = 38/210 (18%)

Query: 29  REVERMIA-QQRVKVNGILLERAAVNVMSTDHIEV-----D--------GVPLRKA---E 71
           R+V   +  ++ VK+NG         V + D + +     D        G         E
Sbjct: 24  RKVRHFLRTRKNVKINGETAA-FHFPVQAGDCVTLTFEETDYVRPTIHLGEATHVKVLYE 82

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLLLLTND 127
              L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G ++   +
Sbjct: 83  DEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAIVFAKN 142

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VIQGICY 172
             +  +L   L + Q  R Y+    G  +Q +   + + I               +G   
Sbjct: 143 PFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQKGDSA 201

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
                 +     +   VT  L  G+  +I+
Sbjct: 202 ITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>gi|194015109|ref|ZP_03053726.1| YhcT [Bacillus pumilus ATCC 7061]
 gi|194014135|gb|EDW23700.1| YhcT [Bacillus pumilus ATCC 7061]
          Length = 302

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 39/202 (19%), Positives = 67/202 (33%), Gaps = 34/202 (16%)

Query: 34  MIAQQRVKVNGILLERAAVNVMSTDHIEVD-------------GVPLRKAERTRLWLYHK 80
            +  Q+V++N      AA  V   D I +D             G      E   L +  K
Sbjct: 39  WMEHQKVRLNQKPAHHAA-KVSQGDQIIIDLFETEESDVTPEYGELEVLFEDEHLLIVQK 97

Query: 81  PIGLVTTHSDPDGRSTVFDNLPSIF------SRVISVGRLDINTEGLLLLTNDGGLARVL 134
           P G  T  ++     T+ + +   F       RV  + RLD +T G ++          L
Sbjct: 98  PAGRPTHPNEQGQTGTLANLVAFHFQANGEEKRVRHIHRLDQDTSGTVIFAKHRLAHAAL 157

Query: 135 --ELPSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLD- 180
              L      R Y     G            + +DK + +++ I   G         +D 
Sbjct: 158 DQMLSKKTIKRTYIAIAEGLFKKKKGTIDAAIGRDKHHAVRRRISPNGQKAVTHFQVMDM 217

Query: 181 TQKGSNAWVTVGLREGKNREIK 202
            ++     V + L  G+  +I+
Sbjct: 218 NKRLQLTAVKLQLETGRTHQIR 239


>gi|42522740|ref|NP_968120.1| methyltransferase [Bdellovibrio bacteriovorus HD100]
 gi|39573936|emb|CAE79113.1| methyltransferase [Bdellovibrio bacteriovorus HD100]
          Length = 521

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 22/133 (16%), Positives = 40/133 (30%), Gaps = 10/133 (7%)

Query: 80  KPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLEL--P 137
           K  GL T   +   R  V      +  ++ +V RLD  T G L+      +A  L     
Sbjct: 20  KIAGLNTHTPEYGQRGCVEIYEEELDRKLYTVHRLDKATSGALVFATSSEIAAQLTQAFE 79

Query: 138 STQWLRVYRVRFHGQVD------QDKLNLLKKGIVIQGICYGDMQ--VTLDTQKGSNAWV 189
             +  + Y      ++       +  +   K   V +     + +         G     
Sbjct: 80  QHKVEKKYLFLTDKKIARTEFTYESFIQKEKNVFVSRDTQEPNSKTSFKWVKALGPYQLW 139

Query: 190 TVGLREGKNREIK 202
                 GK  +I+
Sbjct: 140 EAVPHTGKPHQIR 152


>gi|229132101|ref|ZP_04260962.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST196]
 gi|228651369|gb|EEL07343.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           BDRD-ST196]
          Length = 292

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 66/209 (31%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHI-------------EVDGVPL-RKAERTRLWLYHKP 81
               ++VNG         + + + +             EV+ +PL    E   + + +K 
Sbjct: 34  RGGAIEVNGQH-TSVRHKLQAGEELQIFFPVEERSEGMEVEEIPLCIVYEDDAVLVINKE 92

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + T  S      ++ + L   + +      V  V RLD +T GL+L+  +      L 
Sbjct: 93  ANMSTIPSREHPSGSIANALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLL 151

Query: 136 ---LPSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                     R Y    HG + ++          K + + +  V +          +   
Sbjct: 152 SKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKADSIIERTVCEDGQRAVTHFRVMES 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 V + L  G+  +I+    +    
Sbjct: 212 SSDKTHVALELETGRTHQIRVHMAYIGHP 240


>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 = 49.4 bits (117), Expect = 9e-04,   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|42522902|ref|NP_968282.1| pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
 gi|39574098|emb|CAE79275.1| Pseudouridine synthase Rlu family protein [Bdellovibrio
           bacteriovorus HD100]
          Length = 239

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 48/151 (31%), Gaps = 23/151 (15%)

Query: 75  LWLYHKPIGLVTTHSD------PDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG 128
            +   KP G      +      P  R  ++         V  V RLD  T G++L     
Sbjct: 16  FFAIDKPSGFFVHPPELSPYPVPKERICLWHLRKMFRKDVFPVHRLDAPTSGIVLFAMSR 75

Query: 129 GLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL----KKG---IVIQGICYGDMQVTL 179
             AR L       +  + Y     G V       L     +G   +  Q +     QV L
Sbjct: 76  QDARELNFLFAERRMHKTYHAVVRGFVPASGSIDLPLEVDEGQSIVEAQTVFRSLAQVEL 135

Query: 180 D---TQKGSNAWVTVG----LREGKNREIKK 203
                +K   +  ++     +  G+  +I++
Sbjct: 136 PYAVGKKYPTSRYSLVQAHPVT-GRWHQIRR 165


>gi|127511717|ref|YP_001092914.1| pseudouridylate synthase [Shewanella loihica PV-4]
 gi|126637012|gb|ABO22655.1| ribosomal large subunit pseudouridine synthase A [Shewanella
           loihica PV-4]
          Length = 225

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/162 (15%), Positives = 60/162 (37%), Gaps = 22/162 (13%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL---- 124
            E   + + +KP GL++    DP    +V+  +         V RLD+ T G++++    
Sbjct: 18  HEDKDILVVNKPSGLLSVPGRDPAYYDSVYTRVLRDHPNAQIVHRLDMATSGIIVVALRR 77

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYG 173
           + +  L R      T   ++Y  R  G +  ++            N  K+ +  Q     
Sbjct: 78  SAERELKRQFRDRETH--KIYYARVAGHLKAEQGSVDYPLICDWPNRPKQKVDHQIGKAS 135

Query: 174 DMQVTLDTQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
                + ++   +  V +  +  G++ +++  +       + 
Sbjct: 136 KTLFEVISRAKRSTLVKLTPIT-GRSHQLRVHMM-AIGHPIL 175


>gi|114564164|ref|YP_751678.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
 gi|114335457|gb|ABI72839.1| pseudouridine synthase [Shewanella frigidimarina NCIMB 400]
          Length = 219

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 33/190 (17%), Positives = 63/190 (33%), Gaps = 33/190 (17%)

Query: 63  DGVPLRKAERTRLWLYHKPIGLVT-THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
           DG      +   L L +KP GL++ +  +P  + +V   L   +     V RLD  T G+
Sbjct: 10  DGNIEVLYQDEHLLLINKPTGLLSLSGKNPLNKDSVHHRLVQDYPSATLVHRLDFGTSGI 69

Query: 122 LLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDK------LNLLKKGIVIQGICY 172
           +L+  +  +   L     Q     + Y    +G + +        +        +  IC 
Sbjct: 70  MLVALN-KVINGLLTKQFQLRTVSKTYTAVLYGDLVEQHGDIELPIAKDSDNFPLMKICQ 128

Query: 173 GDMQ-------VTLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKVNRLIRISYGPFQ 224
              +       V    Q+  +  VT   +  G+  +++            +  +  G   
Sbjct: 129 QTGKPAHSQYQVIERHQQRLSTRVTFTPIT-GRTHQLR------------IHSLQIGHPI 175

Query: 225 LG-TLLAGST 233
           LG  L     
Sbjct: 176 LGCDLYRNEY 185


>gi|319775341|ref|YP_004137829.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
 gi|317449932|emb|CBY86144.1| ribosomal large subunit pseudouridine synthase A [Haemophilus
           influenzae F3047]
          Length = 219

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 22/150 (14%), Positives = 49/150 (32%), Gaps = 15/150 (10%)

Query: 79  HKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP 137
           +KP GL++   + P    +V   +   F       RLD+ T G+++        R L+  
Sbjct: 27  NKPSGLLSVPGNQPQYYDSVMSRVKEKFGFCEPAHRLDMATSGIIVFALSKAADRELKRQ 86

Query: 138 --STQWLRVYRVRFHGQVDQDKLNLLKKGI---------VIQ---GICYGDMQVTLDTQK 183
               +  + Y+    G ++ D   +    I          +    G         L    
Sbjct: 87  FREREPEKHYQAIVWGHLENDYGEVNLPMICDWENRPRQRLDFVLGKRAVTKFEVLARLP 146

Query: 184 GSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            ++  V +    G++ +++         + 
Sbjct: 147 NNSTRVKLTPVTGRSHQLRLHMLALGHPIL 176


>gi|167391242|ref|XP_001739694.1| ribosomal pseudouridine synthase [Entamoeba dispar SAW760]
 gi|165896535|gb|EDR23920.1| ribosomal pseudouridine synthase, putative [Entamoeba dispar
           SAW760]
          Length = 378

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 26/164 (15%), Positives = 54/164 (32%), Gaps = 24/164 (14%)

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNL--PSIFSRVISVGRLDINTEGLLLLTNDGGL 130
               + +KP G+    +    ++ + + L     FS +  V RLD NT G+LL       
Sbjct: 111 PEFLVINKPSGIPVHPTGRYNQNCILNILLNEHHFSHLKPVYRLDKNTSGVLLFAKTKKF 170

Query: 131 ARVLEL----------PSTQWLRVYRVRFHGQVDQDK-----LNLLKKGIVIQGICYGDM 175
           A   +             +   ++Y  R  G           L+L++ G   Q     D 
Sbjct: 171 ASSFQSFLKEKSSVFSSPSSLQKIYLARVVGYFPDFIEVNLPLHLIRFGTESQNSICEDG 230

Query: 176 -------QVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKV 212
                  +     +  + + +      G+  +++   +  N  +
Sbjct: 231 VEAKSSFKRLFFDKDSNTSVIECIPHTGRTHQLRLHLKAINHPI 274


>gi|149182747|ref|ZP_01861212.1| hypothetical protein BSG1_15258 [Bacillus sp. SG-1]
 gi|148849561|gb|EDL63746.1| hypothetical protein BSG1_15258 [Bacillus sp. SG-1]
          Length = 294

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 31/198 (15%), Positives = 70/198 (35%), Gaps = 35/198 (17%)

Query: 38  QRVKVNGILLERAAVNVMSTDHIEV--------------DGVPLRKAERTRLWLYHKPIG 83
            ++ V+G  +      +   +H+ V              D +     E   L + +KP  
Sbjct: 41  GKISVDGQEVT-VRYVLQEGNHLTVIFPPEPKSPTLKPEDILLHIIYEDKDLLVINKPSN 99

Query: 84  LVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLELP 137
           + T  S      ++ + +   + R      +  V RLD +T GL+L+     +  ++ L 
Sbjct: 100 MSTIPSREHPDGSLANAVYGYYRRREIDSAIHIVTRLDRDTSGLVLIAKHRHIHHLMSLQ 159

Query: 138 STQ--WLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG 184
             +    R Y     G            + + + +++++ +   G         +  Q G
Sbjct: 160 QKKREIKRSYEAFAEGLFSVREGKINEPIGRKETSIIEREVRSDG-KTAVTHYKVIGQYG 218

Query: 185 SNAWVTVGLREGKNREIK 202
             A + + L  G+  +I+
Sbjct: 219 GFAHIGLVLETGRTHQIR 236


>gi|89900510|ref|YP_522981.1| pseudouridine synthase RluD [Rhodoferax ferrireducens T118]
 gi|89345247|gb|ABD69450.1| Pseudouridine synthase, RluD [Rhodoferax ferrireducens T118]
          Length = 346

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 41/256 (16%), Positives = 80/256 (31%), Gaps = 67/256 (26%)

Query: 7   VQENFTPQRVSKVIARAGIA-SRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVDG 64
           V E+   QR+   + R      +  V R+I    V+VN G     A   + + D + +  
Sbjct: 21  VDEDAAGQRLDNFLMRHLKGVPKTHVYRIIRSGEVRVNKGR--ASADARLAAGDTVRLPP 78

Query: 65  VPLRKA-------------------------ERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
           + + +                          E  +L +  KP G+        G S V  
Sbjct: 79  LRISERVAEKAEAMTQAMAHGAPARDFPILFEDEQLLVIDKPAGVAV-----HGGSGVSF 133

Query: 100 NLPSIFSRVIS-------VGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
            +                V RLD +T G+LL+         L+      +  + Y     
Sbjct: 134 GVIEQLRMARPEAKFLELVHRLDRDTSGILLIAKKRSALTRLQSQFRERETGKTYLALVA 193

Query: 151 G--QVDQDKLNLLKKGIVIQGIC----YGDMQVTLDTQKGSN------------------ 186
           G    ++  L+      ++ G       G+ +V + ++   N                  
Sbjct: 194 GHWPANRKVLDKPLYKYLLPGKDGSAGEGERRVKVVSRDDPNGMPSVTLVKVRETTATSF 253

Query: 187 AWVTVGLREGKNREIK 202
             + V ++ G+  +I+
Sbjct: 254 TLLEVTIKTGRTHQIR 269


>gi|315127724|ref|YP_004069727.1| pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
 gi|315016238|gb|ADT69576.1| pseudouridylate synthase [Pseudoalteromonas sp. SM9913]
          Length = 209

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 60/155 (38%), Gaps = 18/155 (11%)

Query: 75  LWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
           L + +KP  L+T    DP    ++ + +  +F     V RLD+ T G+L L  +    R 
Sbjct: 14  LLIVNKPSELLTVPGKDPKHADSLINRVNRVFPSAKIVHRLDMATSGILCLAMNKAAHRH 73

Query: 134 LEL--PSTQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQVTLD 180
           L +     +  + Y  R +GQ++ +     L L+       K+ +             + 
Sbjct: 74  LSMQFQERETAKRYIARVYGQLETETGSVDLPLICDWPNRPKQMVDHDNGKPSLTHFKVL 133

Query: 181 TQKGSNAWVTVG-LREGKNREIK-KVFEFFNWKVN 213
            ++     V +  +  G++ +++  +       + 
Sbjct: 134 EREAQATRVELTPIT-GRSHQLRVHML-SLGHPIL 166


>gi|331661428|ref|ZP_08362352.1| pseudouridine synthase A [Escherichia coli TA143]
 gi|331061343|gb|EGI33306.1| pseudouridine synthase A [Escherichia coli TA143]
          Length = 219

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+      +  + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFRERKPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|254418198|ref|ZP_05031922.1| hemolysin A [Brevundimonas sp. BAL3]
 gi|196184375|gb|EDX79351.1| hemolysin A [Brevundimonas sp. BAL3]
          Length = 241

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 2/52 (3%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHI-EVD 63
           R+ +++   G+A SR   +  I    V V+G   +  +  V +   I  VD
Sbjct: 1  MRLDQLLVTRGLAESRARAKAAIEAGGVTVDGTPAKSGSQTVGANAEIGYVD 52


>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 = 49.4 bits (117), Expect = 9e-04,   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|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 = 49.4 bits (117), Expect = 9e-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|312886597|ref|ZP_07746205.1| pseudouridine synthase [Mucilaginibacter paludis DSM 18603]
 gi|311301000|gb|EFQ78061.1| pseudouridine synthase [Mucilaginibacter paludis DSM 18603]
          Length = 239

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 24/148 (16%), Positives = 50/148 (33%), Gaps = 21/148 (14%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGL 130
           E   + + +KP  + +      G   +     + ++      RLD  T G L++  +   
Sbjct: 13  ENPDIIVVNKPPFISSLDEREGGEINMLRLAKNYWADAQICHRLDKETSGALIIAKNPEA 72

Query: 131 AR--VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAW 188
            R   ++    +  ++Y     G    + L      I +  +  G   VT+  Q+G  A 
Sbjct: 73  YRFVSIQFEKRRVRKIYHAIIEGTHVFEDLQ-----IDLPILNAGKGNVTISRQEGKRAE 127

Query: 189 VTV---------GLRE-----GKNREIK 202
                        L +     G+  +I+
Sbjct: 128 THFQSLKYFKHYTLVQCRPVTGRMHQIR 155


>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 = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 14 QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGV 65
           ++ + +   GI S   + + MI    VKVNG +  R    +  TD + V G 
Sbjct: 2  IKLDQFLKLLGIGSTGGQAKLMIIDGDVKVNGTVETRRGRKLAPTDIVTVTGK 54


>gi|229056939|ref|ZP_04196335.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH603]
 gi|228720467|gb|EEL72040.1| Uncharacterized RNA pseudouridine synthase yjbO [Bacillus cereus
           AH603]
          Length = 292

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 32/209 (15%), Positives = 66/209 (31%), Gaps = 35/209 (16%)

Query: 36  AQQRVKVNGILLERAAVNVMSTDHI-------------EVDGVPL-RKAERTRLWLYHKP 81
               ++VNG         + + + +             EV+ +PL    E   + + +K 
Sbjct: 34  RGGAIEVNGQH-TSVRHKLQAGEELQIFFPVEERSEGMEVEEIPLCIVYEDDAVLVINKE 92

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSR------VISVGRLDINTEGLLLLTNDGGLARVLE 135
             + T  S      ++ + L   + +      V  V RLD +T GL+L+  +      L 
Sbjct: 93  ANMSTIPSREHPSGSIANALLYHYDKQNLASTVHIVTRLDRDTSGLMLIAKN-RFVHHLL 151

Query: 136 ---LPSTQWLRVYRVRFHGQVDQD----------KLNLLKKGIVIQGICYGDMQVTLDTQ 182
                     R Y    HG + ++          K + + +  V +          +   
Sbjct: 152 SKQHQQKGVKRTYEAIVHGTILEEVGTIDAPIGRKADSIIERTVCEDGQRAVTHFRVMES 211

Query: 183 KGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                 V + L  G+  +I+    +    
Sbjct: 212 SSDKTHVALELETGRTHQIRVHMAYIGHP 240


>gi|254517296|ref|ZP_05129353.1| tRNA pseudouridine synthase C [gamma proteobacterium NOR5-3]
 gi|219674134|gb|EED30503.1| tRNA pseudouridine synthase C [gamma proteobacterium NOR5-3]
          Length = 248

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 31/166 (18%), Positives = 48/166 (28%), Gaps = 27/166 (16%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVF---DNLPSIFSRVISVGRLDINTEGLLLLTNDGGLA 131
           L +  KP GL+   S  D   T F        +   V  V RLD  T GLL+      +A
Sbjct: 15  LVVIDKPPGLLVHRSKIDRHETQFALQMLRDQLGQHVFPVHRLDKPTSGLLIFALSSEVA 74

Query: 132 RVLEL--PSTQWLRVYRVRFHGQVDQ----DKLNLLKKGIVIQGICYGD----------- 174
            +L     +    + Y     G   Q    D     K   ++      D           
Sbjct: 75  TLLSEQFENRAVAKRYLAVVRGYCPQGGEIDHALTEKHDRIVDKRARADKAPQEALTHYR 134

Query: 175 --MQVTLDTQKGSNAWVTVGLRE-----GKNREIKKVFEFFNWKVN 213
              QV               L E     G+  ++++  +     + 
Sbjct: 135 TLAQVEWPEAVDRYPQARYSLVELRPQTGRKHQLRRHMKHIGHPII 180


>gi|83647350|ref|YP_435785.1| 23S RNA-specific pseudouridylate synthases-like protein [Hahella
           chejuensis KCTC 2396]
 gi|83635393|gb|ABC31360.1| Pseudouridylate synthases, 23S RNA-specific [Hahella chejuensis
           KCTC 2396]
          Length = 224

 Score = 49.4 bits (117), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 24/163 (14%), Positives = 56/163 (34%), Gaps = 26/163 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E   + + +KP G++T+         +V+  +         V RLD+ T G+L+L     
Sbjct: 20  EDKDIIVVNKPSGILTSPGRGAHLYDSVWSRVKEKHPLSHVVHRLDLATSGVLVLALRRK 79

Query: 130 LARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVI----QGICYGDMQVTLDTQK 183
             + L+      +  + Y  +  G + +D+       + +            +V  +  K
Sbjct: 80  AEKELKRQFMQREVRKTYVAKVWGVIKEDQGE-----VDLPLICDWPNRPKQKVCFEHGK 134

Query: 184 GSNAWVTV-------GLRE-----GKNREIK-KVFEFFNWKVN 213
            +     V        L E     G++ +++  +       + 
Sbjct: 135 PAVTGYRVLAREENATLVELYPITGRSHQLRVHML-SLGHPIL 176


>gi|319744574|gb|EFV96927.1| S4 domain-containing protein YlmH [Streptococcus agalactiae ATCC
           13813]
          Length = 262

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+ K++A     SR +  ++I   +VKVN  ++ R +  ++  D I V G
Sbjct: 185 RLDKILATILKISRTQSTKLIEADKVKVNYAIVNRVSEQLVEGDLISVRG 234


>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 = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/50 (30%), Positives = 27/50 (54%)

Query: 15  RVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
           R+ K++A     SR +  ++I   +VKVN  ++ R +  ++  D I V G
Sbjct: 185 RLDKILATILKISRTQSTKLIEADKVKVNYAIVNRVSEQLVEGDLISVRG 234


>gi|300928645|ref|ZP_07144164.1| pseudouridine synthase A [Escherichia coli MS 187-1]
 gi|300463314|gb|EFK26807.1| pseudouridine synthase A [Escherichia coli MS 187-1]
          Length = 219

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>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 = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 2/90 (2%)

Query: 15  RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERT 73
           R+  +  R+G+A +RRE  +++    + VNG  ++  +  V   D IEV           
Sbjct: 88  RLDNIAFRSGLARTRREARQIVTHGHLTVNGKQVDIPSYKVSEGDVIEVREKSRSNTLFK 147

Query: 74  RLWLYHKPIGLVT-THSDPDGRSTVFDNLP 102
            +   +   G+V    SD +      D  P
Sbjct: 148 TIKETNATFGVVEWLSSDLENLKVTVDRFP 177


>gi|216264271|ref|ZP_03436263.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 156a]
 gi|215980744|gb|EEC21551.1| ribosomal large subunit pseudouridine synthase D (rRNA-uridine
           isomerase D) [Borrelia burgdorferi 156a]
          Length = 326

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   VKREFTVKENAL--RLDLYLSGNFEVFTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHI--EVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I  E D             +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEESSQIDCLRPSNIPIAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--E--------- 195
               G  +      ++  I           V+ D  K +     + L   E         
Sbjct: 178 AIVKGNFN-SFFGSIESFIDRDKHNRKKFSVSKDRGKKALTEYRLLLNFGEYSLLALKPK 236

Query: 196 -GKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>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 = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          QR+  +I   G+A SR   + +I   +V V+ +  ++A   +    +I V G  +    R
Sbjct: 5  QRLDTLITELGLAPSRTRAQALILSGQVLVDDVPQDKAGAMISPEANITVRGQDMPYVSR 64


>gi|333010548|gb|EGK29981.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           VA-6]
          Length = 219

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARAVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|291336629|gb|ADD96175.1| hypothetical protein [uncultured organism MedDCM-OCT-S05-C185]
          Length = 74

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/41 (51%), Positives = 30/41 (73%)

Query: 205 FEFFNWKVNRLIRISYGPFQLGTLLAGSTREVSKKILREQL 245
            +  + +VNRLIR+++GPFQLG L AG+  EV +  L+EQL
Sbjct: 1   MDSIDLQVNRLIRVAFGPFQLGNLSAGAVEEVPENKLKEQL 41


>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 = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           R+  V+ R GIAS RR+  + +    + VNG  +  A   V   D I V
Sbjct: 96  RLDNVVFRLGIASTRRQARQFVRHGHILVNGKRVNIAGYRVKQGDTIAV 144


>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 = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 42/100 (42%), Gaps = 2/100 (2%)

Query: 14  QRVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
           QR+  V+ R G A+ RR   +++    + VNG  ++  +  V + + IEV        + 
Sbjct: 98  QRLDNVVYRMGFATTRRFARQLVTHGHILVNGKKVDIPSYRVTAGEKIEVAEKSKTNPQI 157

Query: 73  TRLWLYHKPIGLVTTHS-DPDGRSTVFDNLPSIFSRVISV 111
            R        G+V     + D +  +F  +P     VI V
Sbjct: 158 VRAIELTNQTGIVAWVDVEKDKKYGIFTRIPEREEVVIPV 197


>gi|50915102|ref|YP_061074.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|56808190|ref|ZP_00365968.1| COG0564: Pseudouridylate synthases, 23S RNA-specific [Streptococcus
           pyogenes M49 591]
 gi|306826523|ref|ZP_07459832.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
 gi|50904176|gb|AAT87891.1| Ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes MGAS10394]
 gi|304431250|gb|EFM34250.1| ribosomal large subunit pseudouridine synthase D [Streptococcus
           pyogenes ATCC 10782]
          Length = 303

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 69/204 (33%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 36  RKIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 95

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 96  EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 155

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 156 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 215

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +   L+ G+  +I+
Sbjct: 216 VKNFHKTASLLNCQLQTGRTHQIR 239


>gi|226355886|ref|YP_002785626.1| ribosomal large subunit pseudouridine synthase Rlu family
           [Deinococcus deserti VCD115]
 gi|226317876|gb|ACO45872.1| putative Ribosomal large subunit pseudouridine synthase, Rlu family
           [Deinococcus deserti VCD115]
          Length = 252

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/171 (18%), Positives = 54/171 (31%), Gaps = 26/171 (15%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSI-----FSRVISVGRLDINT 118
           G P    E    ++ HKP   +T       R  V D L  +        +    RLD  T
Sbjct: 11  GKPRVIVEHPDFYVVHKPALWLT--HPVRARIDVPDVLTYMQTETGEPDLAPPHRLDRET 68

Query: 119 EGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQD--KLNL-------------- 160
            G  +L+ D   AR       +    + Y    HG    +   L+               
Sbjct: 69  SGAQILSRDSDAARRFFTLFKTHLVGKTYLAIVHGNPTWERYTLDAPLGDLGLGGANRVT 128

Query: 161 LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
           +++ +V  G         +D + G ++ +    R G+  +I+         
Sbjct: 129 IRQAVVPDGRAAVTDFQVVDRRAG-HSLIEAYPRSGRLHQIRAHLHHLGLP 178


>gi|19746943|ref|NP_608079.1| hypothetical protein spyM18_2124 [Streptococcus pyogenes MGAS8232]
 gi|28896670|ref|NP_803020.1| hypothetical protein SPs1758 [Streptococcus pyogenes SSI-1]
 gi|19749193|gb|AAL98578.1| conserved hypothetical protein [Streptococcus pyogenes MGAS8232]
 gi|28811924|dbj|BAC64853.1| conserved hypothetical protein [Streptococcus pyogenes SSI-1]
          Length = 272

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 69/204 (33%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 5   RKIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 65  EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 124

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 125 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 184

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +   L+ G+  +I+
Sbjct: 185 VKNFHKTASLLNCQLQTGRTHQIR 208


>gi|323171216|gb|EFZ56864.1| RNA pseudouridylate synthase family protein [Escherichia coli
           LT-68]
          Length = 219

 Score = 49.4 bits (117), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|332879235|ref|ZP_08446932.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
 gi|332682655|gb|EGJ55555.1| pseudouridine synthase, RluA family [Capnocytophaga sp. oral taxon
           329 str. F0087]
          Length = 320

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/226 (14%), Positives = 73/226 (32%), Gaps = 28/226 (12%)

Query: 16  VSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV-----DGVPLRKA 70
           +  ++      SR + + ++    + V+   + +    +     + V     +     K 
Sbjct: 33  LDFIMESMKGISRNKAKDILTGHGITVDRKSVSQYNYELRPGMVVRVSKHKRNNELKNKY 92

Query: 71  ERTRL-----WLYHKPIGLVT--THSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEG 120
            +         +  K  G+++    +      TV D   +          V RLD +T G
Sbjct: 93  VKIVYEDKDLIVIEKSAGILSMPAVTQQFSIKTVLDEYFTRRHFKCTAHVVHRLDRDTSG 152

Query: 121 LLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQDK------LNLLKKGIVI----- 167
           L++   +  + R+LE    +    R Y     G+++++       L   K  +       
Sbjct: 153 LMMYAKNIEVQRILEEHWQEIVTDRRYVAVVSGKMEKEGGTISSWLKDNKAYVTYSSPTD 212

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
            G  Y          +   + V + L  G+  +I+   +     V 
Sbjct: 213 NGGKYAVTHFHTLDARERYSLVELKLETGRKNQIRVHMQDIGHPVV 258


>gi|315655527|ref|ZP_07908426.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii ATCC 51333]
 gi|315490182|gb|EFU79808.1| ribosomal large subunit pseudouridine synthase D [Mobiluncus
           curtisii ATCC 51333]
          Length = 304

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/228 (14%), Positives = 67/228 (29%), Gaps = 38/228 (16%)

Query: 20  IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMST--------------DHIEVDGV 65
           ++R    SR +   ++    V  +G  L+++   V+                +   VD +
Sbjct: 20  LSRLLGLSRAKAGALLESGAVIQDGETLKKSDQLVVGNLLEIDIPEPTGYVPEVTRVDNL 79

Query: 66  PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLP---------SIFSRVISVGRLDI 116
            +  A+   L +  KP G+           TV   L              R   V RLD 
Sbjct: 80  GILYADDD-LVVVDKPAGVAAHTGPGWEGPTVVGALRAAGIRVSTSGPVEREGIVHRLDA 138

Query: 117 NTEGLLLLTNDGGLARVLELP--STQWLRVYRV-----------RFHGQVDQDKLNLLKK 163
            T G +++         L+      +  ++Y                  + +      K 
Sbjct: 139 GTSGAMVVAKSELAYGKLKNEFRYHRVEKIYTALATGGVKPPVGTIDAPIGRAPGREFKM 198

Query: 164 GIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
            +V  G         ++   G+   + V L  G+  +I+         
Sbjct: 199 AVVSGGKPAVTHYDVIEELPGAT-LLKVQLETGRTHQIRVHLAAIGHP 245


>gi|299769211|ref|YP_003731237.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. DR1]
 gi|298699299|gb|ADI89864.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter sp. DR1]
          Length = 212

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/117 (19%), Positives = 43/117 (36%), Gaps = 16/117 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLAR 132
             + HKP  +++     D   +V   L +I  + + + RLD +T G+L+   +  G  A 
Sbjct: 16  FMVIHKPSDILSVPGKGDLHDSVLTRLVAIEPKTLLIHRLDRDTSGILVFGLSKRGQSAI 75

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 76  ARQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVIYDPSRPPLHIV 118


>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 = 49.0 bits (116), 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  S R E  ++++ + V VNG ++  AA  V  +D + +
Sbjct: 97  RLDNVVYRMGFGSTRSEARQLVSHRAVLVNGQVVNIAAYQVQPSDVVSI 145


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 34/85 (40%), Gaps = 10/85 (11%)

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--------PLRKAERTRLWL 77
            V G          + K ER R+ L
Sbjct: 231 SVRGKGRLEVGEVAVTKKERYRIQL 255


>gi|21911297|ref|NP_665565.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
 gi|21905511|gb|AAM80368.1| putative ribosomal large subunit pseudouridine synthase
           [Streptococcus pyogenes MGAS315]
          Length = 282

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 69/204 (33%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 15  RKIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 74

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 75  EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 134

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 135 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 194

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +   L+ G+  +I+
Sbjct: 195 VKNFHKTASLLNCQLQTGRTHQIR 218


>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 = 49.0 bits (116), Expect = 0.001,   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|332857041|ref|ZP_08436347.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332869978|ref|ZP_08438954.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
 gi|332726856|gb|EGJ58370.1| pseudouridine synthase A [Acinetobacter baumannii 6013150]
 gi|332732478|gb|EGJ63729.1| pseudouridine synthase A [Acinetobacter baumannii 6013113]
          Length = 190

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 24/116 (20%), Positives = 43/116 (37%), Gaps = 16/116 (13%)

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLARV 133
            + HKP  +++     D   +V   L +I  R + + RLD +T G+L+   +  G  A  
Sbjct: 1   MVIHKPSDILSVPGKGDLHDSVLTRLVAIEPRTLLIHRLDRDTSGILVFGLSKRGQSAIA 60

Query: 134 LELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
            +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 61  RQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVVYDPSRPPLHIV 102


>gi|255534329|ref|YP_003094700.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
 gi|255340525|gb|ACU06638.1| Ribosomal large subunit pseudouridine synthase D [Flavobacteriaceae
           bacterium 3519-10]
          Length = 233

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/188 (15%), Positives = 58/188 (30%), Gaps = 37/188 (19%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSR---------VISVGRLDINTEGL 121
           E   L + +K  G +    D  G +++ D +     +         +  V R+D  T GL
Sbjct: 16  EDNHLLVINKKAGQLVQG-DKTGDASLLDLIKDFIKKRDNKAGNVFLGLVHRIDRPTSGL 74

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLL----------KKGIVIQG 169
           ++          L     + +  + Y      +V      LL          K  + I+ 
Sbjct: 75  VIYAKTSKALTRLTQMVKNREIKKTYWAVVPKEVIPHSARLLHYLQKNEKTNKSTVFIKP 134

Query: 170 ICYGDMQV---TLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLG 226
                  V   T+     +   + + L  G++ +I+         +             G
Sbjct: 135 TENAKESVLNYTVIKTLDNFQLLEIDLETGRHHQIRAQLSKIGVPIK------------G 182

Query: 227 TLLAGSTR 234
            L  G++R
Sbjct: 183 DLKYGASR 190


>gi|224373533|ref|YP_002607905.1| ribosomal pseudouridine synthase [Nautilia profundicola AmH]
 gi|223589983|gb|ACM93719.1| ribosomal pseudouridine synthase [Nautilia profundicola AmH]
          Length = 253

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/216 (12%), Positives = 63/216 (29%), Gaps = 41/216 (18%)

Query: 19  VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRLWLY 78
           ++A+    S R  + +I +  V       +   + +            L    + ++  +
Sbjct: 8   LLAKQEGISNRAAKELIDRGLVF-----AKDKKIKIARG--------LLPINTKFKVLKF 54

Query: 79  HKPIGLVTTHSDP-----DGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARV 133
            KP  +     D      D    +     +       + RLD  T G+L+L  +    + 
Sbjct: 55  PKPKKI---FEDKNLLAVDKPPYITSEEIAKNFGYELLHRLDKETSGVLILVKNDEFKKK 111

Query: 134 LELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTV 191
                      + Y     G V       +K  + I+ I      +   ++ G +A   +
Sbjct: 112 AIEEFKKQNVYKEYITWVSGIV----AEPMKIDLPIKVIKTKSGALAKISKDGEDAVTEI 167

Query: 192 --------------GLREGKNREIKKVFEFFNWKVN 213
                          +  G+  +I+   +     + 
Sbjct: 168 EPILAFRTKSKVKAVIHTGRTHQIRAHLKAVEHPIL 203


>gi|157960566|ref|YP_001500600.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
 gi|157845566|gb|ABV86065.1| pseudouridine synthase [Shewanella pealeana ATCC 700345]
          Length = 225

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/168 (16%), Positives = 56/168 (33%), Gaps = 34/168 (20%)

Query: 70  AERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL---- 124
            +   + + +KP GL++    DP    + +  + + F     V RLD+ T G++++    
Sbjct: 18  HQDKDIMVVNKPSGLLSVPGRDPAHADSTYTRVLAEFPHAKIVHRLDMATSGVIVVALLR 77

Query: 125 TNDGGLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVTL 179
           + +  L R       +  + Y  R  G V Q        G +    I         +V  
Sbjct: 78  SAESELKRQF--RDRETQKTYYARVAGHVKQ------SHGTINLPLICDWPNRPKQKVDH 129

Query: 180 DTQKGSNAWVTVG-------------LREGKNREIK-KVFEFFNWKVN 213
              K S     V              +  G++ +++  +       + 
Sbjct: 130 KIGKPSQTHYEVISYGKRSTLVKLTPIT-GRSHQLRVHMM-ALGHPIL 175


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/54 (25%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 15  RVSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPL 67
           R+  V+ R G  S R E  ++++ + + VNG  +   +  V   D + V    L
Sbjct: 97  RLDNVVYRMGFGSTRSESRQLVSHKAISVNGKTVNIPSYQVRPGDVVAVREKSL 150


>gi|307289628|ref|ZP_07569572.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|306499442|gb|EFM68815.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX0109]
 gi|315164544|gb|EFU08561.1| pseudouridine synthase, RluA family [Enterococcus faecalis TX1302]
          Length = 283

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 37/215 (17%), Positives = 74/215 (34%), Gaps = 48/215 (22%)

Query: 29  REVERMIA-QQRVKVNGILLE---------------------RAAVNVMSTDHIEVDGVP 66
           R+V   +  ++ VK+NG                         R  +++    H++V    
Sbjct: 24  RKVRHFLRTRKNVKINGETAAFHFPVQAGDYVTLTFEETDYVRPTIHLGEATHVKV---- 79

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRV----ISVGRLDINTEGLL 122
               E   L + +KP G+ T  + P    T+ +++ +  +        V RLD  T G +
Sbjct: 80  --LYEDEHLMIVNKPYGIKTHPNQPQETDTLLNHVAAYLAEKNQVPYVVHRLDKETSGAI 137

Query: 123 LLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGI-------------VI 167
           +   +  +  +L   L + Q  R Y+    G  +Q +   + + I               
Sbjct: 138 VFAKNPFVLPILGRLLETKQIYRQYQAIVAGHFNQKE-QTINQPIGRDRHDRRKRRIDPQ 196

Query: 168 QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           +G         +     +   VT  L  G+  +I+
Sbjct: 197 KGDSAITHVQVVKALSNNQTAVTCVLETGRTHQIR 231


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 29/65 (44%), Gaps = 8/65 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M D+N        QR+ +++   G  ASR      + +  VK+ G ++ +A     +   
Sbjct: 1  MSDQNT-------QRLDQLLVSLGLFASRSRARDAVQRGTVKIGGQVVTKAGALFGADAA 53

Query: 60 IEVDG 64
          IE+D 
Sbjct: 54 IEIDD 58


>gi|254580497|ref|XP_002496234.1| ZYRO0C13684p [Zygosaccharomyces rouxii]
 gi|238939125|emb|CAR27301.1| ZYRO0C13684p [Zygosaccharomyces rouxii]
          Length = 398

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 39/107 (36%), Gaps = 11/107 (10%)

Query: 50  AAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVI 109
             + V   D +          E   L + +KP G+    +    ++T+ + L       +
Sbjct: 106 PGIKVAGFDIVH---------ENDNLLVLNKPSGIPIHPTGQFYQNTITEILKRHGKTAL 156

Query: 110 SVGRLDINTEGLLLLTNDGGLAR--VLELPSTQWLRVYRVRFHGQVD 154
              RLD  T GLL++  +   A    L++      + Y  R  G+  
Sbjct: 157 PCYRLDKLTSGLLIMAKNTETAGGIQLKIRDHDMSKYYLARVKGKFP 203


>gi|144898737|emb|CAM75601.1| Pseudouridylate synthase [Magnetospirillum gryphiswaldense MSR-1]
          Length = 226

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/156 (21%), Positives = 51/156 (32%), Gaps = 20/156 (12%)

Query: 75  LWLYHKPIG--LVTTHSDPDGRSTVFDNLPSIFSR-VISVGRLDINTEGLLLLTNDGGLA 131
           + +  KP G  +    + PD      D L   +S       RLD +T G LLL       
Sbjct: 17  VIVLDKPAGLAVHAGPNSPDHLELYLDALKFGWSMAPRLAHRLDRDTSGCLLLGRHDKSI 76

Query: 132 RVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLK-------KG---IVIQ--GICYGDMQV 177
           + L       +  + Y    HG   +D   +         KG   I+I   G        
Sbjct: 77  KRLGKMFMQGRVEKAYWTVVHGTPPEDTGEISAPIHKVTGKGGWRIIIDAAGQPAVTRWR 136

Query: 178 TLDTQKGSNAWVTVG-LREGKNREIKKVFEFFNWKV 212
            L    G  +W+    L  G+  +I+   +     V
Sbjct: 137 VLGRGDGL-SWIECTPLT-GRTHQIRVHMKHLGCPV 170


>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 = 49.0 bits (116), Expect = 0.001,   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|296140324|ref|YP_003647567.1| pseudouridine synthase [Tsukamurella paurometabola DSM 20162]
 gi|296028458|gb|ADG79228.1| pseudouridine synthase, RluA family [Tsukamurella paurometabola DSM
           20162]
          Length = 308

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 79/250 (31%), Gaps = 39/250 (15%)

Query: 1   MKDKNIVQ--ENFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLER--------- 49
           M++   +   +     RV   +AR    SR  V  + A+  V ++G  + +         
Sbjct: 1   MRESRTMPVPDGLDGLRVDAGVARLLGLSRTVVSELAAEGSVTLDGAPVGKSDKLRAGAL 60

Query: 50  AAVNVMSTDH-IEVDGVPLRKAERTR----LWLYHKPIGLVTTHSDPDGRSTVFDNL--- 101
             V +      +E+   P+           + +  KP+G+    S      TV   L   
Sbjct: 61  LDVTLPEPARPLEIVAEPVPGMNILYSDDDIVVVDKPVGVAAHASVGWTGPTVIGGLAAA 120

Query: 102 ------PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ--WLRVYRVRFHGQV 153
                      R   V RLD+ T G++ +        VL+    Q    + Y     G  
Sbjct: 121 GFRISTSGAPERQGIVHRLDVGTSGVMAVAVSERAYTVLKRAFKQRTVDKRYHALVQGHP 180

Query: 154 DQ--DKLNL---------LKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           D     ++           K  +   G        T++  + +   + V L  G+  +I+
Sbjct: 181 DPMSGTIDAPIGRHRSSDWKFAVTKDGKPSITHYDTIEAFQAAT-LLDVHLETGRTHQIR 239

Query: 203 KVFEFFNWKV 212
             F   +   
Sbjct: 240 VHFAALHHPC 249


>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 = 49.0 bits (116), Expect = 0.001,   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|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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 22/52 (42%), Gaps = 1/52 (1%)

Query: 14 QRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
          +R+  ++   G   SR      I    V VNG+ +++    +     IEV G
Sbjct: 5  ERLDILLHSRGCFPSRERARSAIMAGVVFVNGVRVDKPGTKLDPHADIEVRG 56


>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 = 49.0 bits (116), Expect = 0.001,   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|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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 16  VSKVIARAGIAS-RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR 74
           +  V+ +A IAS +RE    I Q  +++NG  ++     V ST  I  +   +++ +R  
Sbjct: 344 LD-VLVQAKIASSKREAREWIKQGSIQINGERIKDCEFIVSSTHAITTNKTIIKRGKRNY 402

Query: 75  LWL 77
             +
Sbjct: 403 YVI 405


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 34/84 (40%), Gaps = 4/84 (4%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           +K     +EN   Q   R+  V+ R G A +RR   ++++   V VNG  ++  +  V  
Sbjct: 82  VKQSGDTRENLVAQVERRLDNVVYRLGFAINRRAARQLVSHGHVLVNGKKVDIPSYQVRP 141

Query: 57  TDHIEVDGVPLRKAERTRLWLYHK 80
            D I +           +    +K
Sbjct: 142 GDVISIKEGSRTIEPIKQAIELNK 165


>gi|94497522|ref|ZP_01304091.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58]
 gi|94422939|gb|EAT07971.1| Pseudouridine synthase, RluD [Sphingomonas sp. SKA58]
          Length = 317

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 72/239 (30%), Gaps = 46/239 (19%)

Query: 15  RVSKVIARAG-IASRREVERMIAQQRVK---VNGILLERAAVNVMSTDHIEV-------- 62
           R+ + +A      SR  ++ +I   +V    V G +    ++ V       +        
Sbjct: 20  RLDRALADLLPDLSRERLKTLIGDGQVHSAPV-GRI--SGSMKVAEGQRFTITLPPPVPL 76

Query: 63  ----DGVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS----------R 107
                 +PL    E   L +  KP GLV   +  +   T+ + L    +          R
Sbjct: 77  DTVAQDIPLTIVHEDADLLVVDKPAGLVVHPAAGNLDGTLVNALLHHCAGQLSGIGGVAR 136

Query: 108 VISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHGQV------------ 153
              V R+D +T GLL++         L          R Y    +G              
Sbjct: 137 PGIVHRIDKDTSGLLVVAKTDRAHEGLARQFKDHSIERAYAAITYGIPVPPAGTVDSWIG 196

Query: 154 -DQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWK 211
                   +      +G        TLD  +G+ A V   L  G+  +++         
Sbjct: 197 RSDADRKKMAVHREGRGKHAVTHYRTLDRLRGA-ALVECRLETGRTHQVRVHMAHIGHP 254


>gi|71892188|ref|YP_277920.1| ribosomal large subunit (23S) pseudouridine synthase C [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
 gi|71796294|gb|AAZ41045.1| ribosomal large subunit (23S) pseudouridine synthase C [Candidatus
           Blochmannia pennsylvanicus str. BPEN]
          Length = 338

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 38/252 (15%), Positives = 83/252 (32%), Gaps = 55/252 (21%)

Query: 1   MKDKNI------VQENFTPQRVSKVIAR-AGIASRREVERMIAQQRVKVNGILLE---RA 50
           MK+ +I      +  N + QR+   +     +A +  + ++I    +++N   ++   + 
Sbjct: 1   MKEHDINVHFIRISSNSSGQRIDNFLYTYLKVAPKSMIYKIIRTGAIRINKKRIKFQYKL 60

Query: 51  AV----NVMSTDHIEVDG------------VPLRKAERTRLWLYHKPIGLVTTHSDPDGR 94
            +     +     I+++               +   E   L   +KP G+          
Sbjct: 61  QIGDLLRIPPIRGIKINRFNMKYMEEVAFLQNIIIYEDDYLLALNKPTGVAAHGGSGLKF 120

Query: 95  STVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPS---TQWLRVYRVRF 149
             +     L      +  V RLD  T G+LL+      A V            + Y    
Sbjct: 121 GVIEGLRALRPKAQFLELVHRLDRETSGVLLVA-KRRTALVYLHEQLRLQNMKKEYLALV 179

Query: 150 HGQVDQDK----LNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE---------- 195
           HG+ + +     + L KK  ++         V +D++ G  +     ++E          
Sbjct: 180 HGRWNVNLQIVSVPLFKKNTLLN----SSRVVYIDSENGKFSTTHFQIKEYFDNVATFLA 235

Query: 196 -----GKNREIK 202
                G+  +I+
Sbjct: 236 IKPITGRTHQIR 247


>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 (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/71 (28%), Positives = 36/71 (50%), Gaps = 1/71 (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  RLWLYHKPIGL 84
            L   +KP+ L
Sbjct: 148 ALAENYKPLNL 158


>gi|139474518|ref|YP_001129234.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
 gi|134272765|emb|CAM31038.1| RNA pseudouridylate synthase [Streptococcus pyogenes str. Manfredo]
          Length = 272

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/204 (17%), Positives = 69/204 (33%), Gaps = 30/204 (14%)

Query: 29  REVERMIA-QQRVKVNGILLE-----RAAVNVMST-------DHIEVDGVPLRKA---ER 72
           R++   +  ++ V +NG  +      +    V          + I V G   +     E 
Sbjct: 5   RKIRHFLRTKKHVLINGHPVNWQSCVKYGDQVKLFFDHEDYPEKIIVMGQAEKVTCLYED 64

Query: 73  TRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR 132
             + + +KP G+ T  +DP   + +             V RLD  T G +L      +  
Sbjct: 65  EHIIIVNKPEGMKTHGNDPTELALLNHVSAYTGQTCYVVHRLDKETSGAILFAKTPFILP 124

Query: 133 VL--ELPSTQWLRVYRVRFHGQVDQDKL-----------NLLKKGIVIQGICYGDMQVTL 179
           +L   L      R Y    HG +D  ++           +  K+ +          +VTL
Sbjct: 125 ILNRLLEKRDIHREYLALVHGSLDSPRVTYHHPIGRHRHDRRKRVVDPINGKKAITEVTL 184

Query: 180 DTQKGSN-AWVTVGLREGKNREIK 202
                   + +   L+ G+  +I+
Sbjct: 185 VKNFHKTASLLNCQLQTGRTHQIR 208


>gi|153823924|ref|ZP_01976591.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
 gi|126518556|gb|EAZ75779.1| ribosomal large subunit pseudouridine synthase C [Vibrio cholerae
           B33]
          Length = 224

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/185 (16%), Positives = 58/185 (31%), Gaps = 43/185 (23%)

Query: 7   VQENFTPQRVSKVIARAGIASRREVE--------RMIAQQRVKVNGILLERAAVNVMSTD 58
           + E+   QR+   +       R +++        R++ +  V+VN   ++ A   + + D
Sbjct: 13  IDEDMAGQRIDNFL-------RNQLKNIPKSVVYRILRKGEVRVNKKRVK-AEYKLEAGD 64

Query: 59  HIEVDGVPLRKAERT-----------------------RLWLYHKPIGLVTTHSDPDGRS 95
            + V  V +   E                          L + +KP G            
Sbjct: 65  VVRVPPVTVEVKENEPAPPSTKLSKVAELEHCIVYEDDHLLILNKPSGTAVHGGSGLHFG 124

Query: 96  TVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFHG 151
            +     L      +  V R+D +T G+LL+       R L+         + Y     G
Sbjct: 125 AIEALRALRPQARFLELVHRIDRDTSGILLVAKKRSALRHLQAQFREKTVQKYYYALVMG 184

Query: 152 QVDQD 156
             D +
Sbjct: 185 HWDAE 189


>gi|327481320|gb|AEA84630.1| ribosomal large subunit pseudouridine synthase C [Pseudomonas
           stutzeri DSM 4166]
          Length = 317

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 37/211 (17%), Positives = 65/211 (30%), Gaps = 46/211 (21%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEV---------DGVPLRK-----------AE 71
           R++ +  V+VN G +  +    + + D + V         +  PL +            E
Sbjct: 43  RILRKGEVRVNKGRI--KPEYKLQAGDLVRVPPLRLAERDEPEPLAQGLLERLESAIVYE 100

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 101 DKALIVLNKPAGIAVHGGSGLSYGVIEALRQLRPDAKELELVHRLDRDTSGLLMVAKKRS 160

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQDKLN--------LLKKG-----IVIQGICYGD 174
           + R L          + Y     G+ D  K           L+ G     +   G     
Sbjct: 161 MLRHLHQALRGDGVDKRYMALVRGRWDTSKKQVSAPLLKNTLRSGERMVEVTEDGKEALT 220

Query: 175 MQVTLDTQKGSNAWVT---VGLREGKNREIK 202
           +   L         V    V    G+  +I+
Sbjct: 221 LFRVLRRFGDFATLVEAKPVT---GRTHQIR 248


>gi|326566216|gb|EGE16368.1| RluA family pseudouridine synthase [Moraxella catarrhalis 103P14B1]
          Length = 382

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/177 (17%), Positives = 58/177 (32%), Gaps = 26/177 (14%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDG 64
            V  N   QRV   + AR     R  + ++I    +++NG   + A   +   D + V  
Sbjct: 64  TVTNNQDGQRVDNFLLARLKGLPRSHLYKLIRSDEIRINGKRCK-AHDKLYMGDVVRVAP 122

Query: 65  VPLRKAERTRL-------------------WLYHKPIGLVTTHSDPDGRSTV-FDNLPSI 104
           + L   E   +                    + +KP G+       +    +    L   
Sbjct: 123 IRLSVREAPIISEELAKGLLERIIFEDDGLIVLNKPHGMAVHGGSGESFGIIEAMRLAMG 182

Query: 105 FSRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQ---WLRVYRVRFHGQVDQDKL 158
              +  + R+D +T GLLL+         +     +     + Y     G V  D++
Sbjct: 183 KKYLELIHRIDKDTSGLLLIA-KKRSTLKILQEQFRTKTIHKQYLCLVMGHVQADEM 238


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MKDKNIVQENFTP-QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST- 57
          M +++I  +  TP  R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +  
Sbjct: 1  MTEQHI--DPVTPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGH 58

Query: 58 DHIEVD 63
            + VD
Sbjct: 59 SELAVD 64


>gi|297380156|gb|ADI35043.1| Ribosomal large subunit pseudouridine synthase D [Helicobacter
           pylori v225d]
          Length = 242

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 73/235 (31%), Gaps = 38/235 (16%)

Query: 18  KVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVD--GVPLRKAERTRL 75
           K+++     S ++ + +I    V V    L  A   +    H  V     P    E   +
Sbjct: 6   KILSVQENISHKKAKALIDLGLVSVGEKKLMVARKELPKNTHFSVQKVEKPSVIFEDENI 65

Query: 76  WLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLAR--- 132
               KP  + +           +D + S F   + + RLD  T G++LL  +        
Sbjct: 66  LALFKPPFIES-----------YDLV-SFFKGWVLLHRLDKETSGVILLVKENSEFHLKA 113

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKG-------- 184
                     + Y     G ++++    +   I+         +++   Q+         
Sbjct: 114 KKAFKDRAVKKEYLALAQGIIEEE--QEINAPILTIKTTKAFSKISKKGQEAVTIIAPLK 171

Query: 185 ---SNAWVTVGLREGKNREIKKVFEFFNWKVNRLIRISYGPFQLGTLLAGSTREV 236
                  +   ++ G+  +I+   +  N  +        G   L     GS + +
Sbjct: 172 IINKKTLLKARIKTGRTHQIRVHLKHINHPI-------IGD-TLYNNEPGSAKRL 218


>gi|238021958|ref|ZP_04602384.1| hypothetical protein GCWU000324_01863 [Kingella oralis ATCC 51147]
 gi|237866572|gb|EEP67614.1| hypothetical protein GCWU000324_01863 [Kingella oralis ATCC 51147]
          Length = 305

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 62/182 (34%), Gaps = 25/182 (13%)

Query: 46  LLERAAVNVMSTDHIEVDGVPLRKAERTRLWLYH------KPIGLVTTHSDPDGRSTVFD 99
           +L +A   +     I  D  P    +   LWL +      KP  L  T S      T+  
Sbjct: 67  VLYQAGEKIFYYREISRDAEPRIPFDEKILWLDNDLIVVDKPHFLPVTPSGRFLHETLLT 126

Query: 100 NLPSIF-------SRVISVGRLDINTEGLLLLTNDG--GLARVLELPSTQWLRVYRVRFH 150
            L           + +  + RLD +T G++L +++     A     PS    + Y     
Sbjct: 127 RLRLHPDLQYLNTADITPLHRLDKDTAGVMLFSHNPATRAAYHTLFPSHAIQKTYHALAP 186

Query: 151 GQVDQDKLNLLKKGI----------VIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNRE 200
            ++D     +++  +             G    + +V L   +G  +   +    GK  +
Sbjct: 187 TRLDLAYPLIVRTRLVPSEPFFLMREAAGEANAETRVRLLEPRGEASLYELQPVTGKKHQ 246

Query: 201 IK 202
           ++
Sbjct: 247 LR 248


>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 = 49.0 bits (116), 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+  +  R G A SRR+  +++    V+VNG  +   +  V   D I++
Sbjct: 100 RLDNIAFRLGFATSRRQARQIVRHGHVEVNGRKVNIPSFQVKVGDEIKI 148


>gi|332095345|gb|EGJ00368.1| RNA pseudouridylate synthase family protein [Shigella boydii
           5216-82]
          Length = 219

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|302387565|ref|YP_003823387.1| hemolysin A [Clostridium saccharolyticum WM1]
 gi|302198193|gb|ADL05764.1| hemolysin A [Clostridium saccharolyticum WM1]
          Length = 288

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 1/60 (1%)

Query: 14 QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +R+  ++ + G+A SR + + +I    V V+G   ++A        +IEV G  LR   R
Sbjct: 3  ERLDVLLVKLGLAESREKAKAVIMSGIVYVDGEKEDKAGTTFEENANIEVRGNTLRYVSR 62


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MKDKNIVQENFTP-QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST- 57
          M +++I  +  TP  R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +  
Sbjct: 1  MTEQHI--DPATPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGH 58

Query: 58 DHIEVD 63
            + VD
Sbjct: 59 SELAVD 64


>gi|283850858|ref|ZP_06368144.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
 gi|283573781|gb|EFC21755.1| pseudouridine synthase [Desulfovibrio sp. FW1012B]
          Length = 313

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/175 (19%), Positives = 59/175 (33%), Gaps = 27/175 (15%)

Query: 28  RREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTR------------- 74
           RR   R+IA   V V+G L    A  V + + +   G    + E                
Sbjct: 42  RR---RLIAAGAVLVDGQL-RGPAYRVRTGEILA--GQIPARPEGAFTAADVPVLVQTGD 95

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISV--GRLDINTEGLLLL--TNDGGL 130
                KP GL +      G  ++ D LP++F    ++   RLD  T G++ +  T   G 
Sbjct: 96  FAAVSKPAGLHSAAIAHGGGQSLDDLLPALFPDRAAILLSRLDRLTSGIVAVALTPGAGT 155

Query: 131 ARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGS 185
                  + Q  + Y    HG +    +   +    +        +V   ++   
Sbjct: 156 RYRDLEDAGQVAKDYLAVVHGVIADPFVVDFR----LDTADRAKTRVRFKSEPDP 206


>gi|237736831|ref|ZP_04567312.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
 gi|229420693|gb|EEO35740.1| tRNA pseudouridine synthase A [Fusobacterium mortiferum ATCC 9817]
          Length = 292

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 34/255 (13%), Positives = 77/255 (30%), Gaps = 56/255 (21%)

Query: 6   IVQENFTPQRVSKVIARAGIASRR--------EVERMIAQQRVKVNGILLERAAVNVMST 57
           ++ + +   R+ K +       R+        E+ + I   ++KVNG   +     +   
Sbjct: 4   LIDKEYEDVRLDKFL-------RKKLPDMALTEIFKCIRVGKIKVNGKKSKE-NYRLQLN 55

Query: 58  DHIEV------------------------DGVPLRKAERTRLWLYHKPIGLVTTHSDPDG 93
           D +++                                E  R+ + +K   +V  H     
Sbjct: 56  DVVKLFFVVESKECDKNNNINKINSEKFEKIKKYIVYEDDRVLILNKKANMV-MHKGSGH 114

Query: 94  RSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRF 149
              V + L           V R+D  T GL++      + R L       +  + Y +  
Sbjct: 115 EYGVSEILKEYLNNPNFNFVNRIDKATSGLVVGAKSLVVTRELSEEIRERKVDKKYYILV 174

Query: 150 HGQVDQ------DKLNLLK-KGIVIQGICYGDMQ----VTLDTQKGSNAWVTVGLREGKN 198
            G+V +        L  L+ K + ++    G  +      +     +   +   L  G+ 
Sbjct: 175 EGKVKRREFQIKSYLKKLEDKVVELEQYEEGAKESLSFFKVVEYGKNCTLLEGTLGSGRT 234

Query: 199 REIKKVFEFFNWKVN 213
            +++         + 
Sbjct: 235 HQLRVQLASMGNPII 249


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 15 RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          R+  ++   G   SR   ++ I    V V+    ++A   V    +IEV G P+    R
Sbjct: 4  RIDLLLVEQGHFESRERAKKAIMAGLVFVDNQRCDKAGTEVKEDCNIEVKGNPIPYVSR 62


>gi|213622553|ref|ZP_03375336.1| 16S rRNA pseudouridylate synthase A [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 38

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 6/36 (16%), Positives = 16/36 (44%)

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFF 208
            D+      +  +   V + + EG+  ++K++F   
Sbjct: 3   KDLTKPATLEVITPVQVRLTISEGRYHQVKRMFAAV 38


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MKDKNIVQENFTP-QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST- 57
          M +++I  +  TP  R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +  
Sbjct: 24 MTEQHI--DPATPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGH 81

Query: 58 DHIEVD 63
            + VD
Sbjct: 82 SELAVD 87


>gi|16128052|ref|NP_414600.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           MG1655]
 gi|30061623|ref|NP_835794.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella flexneri 2a str.
           2457T]
 gi|74310675|ref|YP_309094.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sonnei Ss046]
 gi|82542662|ref|YP_406609.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella boydii Sb227]
 gi|82775462|ref|YP_401809.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella dysenteriae Sd197]
 gi|89106942|ref|AP_000722.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           W3110]
 gi|110640270|ref|YP_667998.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 536]
 gi|110804122|ref|YP_687642.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella flexneri 5 str.
           8401]
 gi|157159461|ref|YP_001461228.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli E24377A]
 gi|157159527|ref|YP_001456845.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli HS]
 gi|170021586|ref|YP_001726540.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli ATCC 8739]
 gi|170079719|ref|YP_001729039.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170679993|ref|YP_001742177.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli SMS-3-5]
 gi|188492494|ref|ZP_02999764.1| pseudouridine synthase, RluA family [Escherichia coli 53638]
 gi|191174210|ref|ZP_03035721.1| pseudouridine synthase, RluA family [Escherichia coli F11]
 gi|193065885|ref|ZP_03046946.1| pseudouridine synthase, RluA family [Escherichia coli E22]
 gi|193070842|ref|ZP_03051775.1| pseudouridine synthase, RluA family [Escherichia coli E110019]
 gi|194429362|ref|ZP_03061887.1| pseudouridine synthase, RluA family [Escherichia coli B171]
 gi|209917249|ref|YP_002291333.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli SE11]
 gi|218547506|ref|YP_002381297.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia fergusonii ATCC
           35469]
 gi|218552641|ref|YP_002385554.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli IAI1]
 gi|218687934|ref|YP_002396146.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli ED1a]
 gi|218693528|ref|YP_002401195.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli 55989]
 gi|218698480|ref|YP_002406109.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli IAI39]
 gi|218703318|ref|YP_002410837.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli UMN026]
 gi|238899461|ref|YP_002925257.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BW2952]
 gi|253774912|ref|YP_003037743.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254037473|ref|ZP_04871550.1| pseudouridine synthase for 23S rRNA and tRNA [Escherichia sp.
           1_1_43]
 gi|254160181|ref|YP_003043289.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B str.
           REL606]
 gi|256020104|ref|ZP_05433969.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|256025373|ref|ZP_05439238.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia sp. 4_1_40B]
 gi|260842293|ref|YP_003220071.1| pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|293403132|ref|ZP_06647229.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1412]
 gi|293408151|ref|ZP_06651991.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|293476720|ref|ZP_06665128.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|297517418|ref|ZP_06935804.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli OP50]
 gi|298378660|ref|ZP_06988544.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1302]
 gi|300816093|ref|ZP_07096316.1| pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300821939|ref|ZP_07102083.1| pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300900916|ref|ZP_07119052.1| pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300905460|ref|ZP_07123226.1| pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300919609|ref|ZP_07136101.1| pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300923165|ref|ZP_07139223.1| pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300939473|ref|ZP_07154135.1| pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300948662|ref|ZP_07162745.1| pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300956988|ref|ZP_07169239.1| pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300984199|ref|ZP_07176927.1| pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|301024876|ref|ZP_07188512.1| pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|301026173|ref|ZP_07189644.1| pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|301305052|ref|ZP_07211153.1| pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|301330173|ref|ZP_07222835.1| pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|301648375|ref|ZP_07248112.1| pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|306815344|ref|ZP_07449493.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|307136660|ref|ZP_07496016.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli H736]
 gi|307311490|ref|ZP_07591132.1| pseudouridine synthase [Escherichia coli W]
 gi|309796045|ref|ZP_07690457.1| pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|312970151|ref|ZP_07784333.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|331640509|ref|ZP_08341657.1| pseudouridine synthase A [Escherichia coli H736]
 gi|331650951|ref|ZP_08351979.1| pseudouridine synthase A [Escherichia coli M718]
 gi|331666293|ref|ZP_08367174.1| pseudouridine synthase A [Escherichia coli TA271]
 gi|331680629|ref|ZP_08381288.1| pseudouridine synthase A [Escherichia coli H591]
 gi|332281257|ref|ZP_08393670.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|76363883|sp|P0AA37|RLUA_ECOLI RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|92090791|sp|P0AA38|RLUA_SHIFL RecName: Full=Ribosomal large subunit pseudouridine synthase A;
           AltName: Full=rRNA pseudouridylate synthase A; AltName:
           Full=rRNA-uridine isomerase A
 gi|1786244|gb|AAC73169.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           MG1655]
 gi|30039865|gb|AAP15599.1| hypothetical protein S0055 [Shigella flexneri 2a str. 2457T]
 gi|73854152|gb|AAZ86859.1| conserved hypothetical protein [Shigella sonnei Ss046]
 gi|81239610|gb|ABB60320.1| conserved hypothetical protein [Shigella dysenteriae Sd197]
 gi|81244073|gb|ABB64781.1| conserved hypothetical protein [Shigella boydii Sb227]
 gi|85674306|dbj|BAE76039.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K12 substr.
           W3110]
 gi|110341862|gb|ABG68099.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           536]
 gi|110613670|gb|ABF02337.1| conserved hypothetical protein [Shigella flexneri 5 str. 8401]
 gi|157065207|gb|ABV04462.1| pseudouridine synthase, RluA family [Escherichia coli HS]
 gi|157081491|gb|ABV21199.1| pseudouridine synthase, RluA family [Escherichia coli E24377A]
 gi|169756514|gb|ACA79213.1| pseudouridine synthase [Escherichia coli ATCC 8739]
 gi|169887554|gb|ACB01261.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli str. K-12 substr.
           DH10B]
 gi|170517711|gb|ACB15889.1| pseudouridine synthase, RluA family [Escherichia coli SMS-3-5]
 gi|188487693|gb|EDU62796.1| pseudouridine synthase, RluA family [Escherichia coli 53638]
 gi|190905495|gb|EDV65123.1| pseudouridine synthase, RluA family [Escherichia coli F11]
 gi|192926472|gb|EDV81105.1| pseudouridine synthase, RluA family [Escherichia coli E22]
 gi|192955872|gb|EDV86342.1| pseudouridine synthase, RluA family [Escherichia coli E110019]
 gi|194412582|gb|EDX28879.1| pseudouridine synthase, RluA family [Escherichia coli B171]
 gi|209910508|dbj|BAG75582.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           SE11]
 gi|218350260|emb|CAU95943.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli 55989]
 gi|218355047|emb|CAQ87653.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia fergusonii ATCC 35469]
 gi|218359409|emb|CAQ96948.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli IAI1]
 gi|218368466|emb|CAR16202.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli IAI39]
 gi|218425498|emb|CAR06280.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli ED1a]
 gi|218430415|emb|CAR11282.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli UMN026]
 gi|226840579|gb|EEH72581.1| pseudouridine synthase for 23S rRNA and tRNA [Escherichia sp.
           1_1_43]
 gi|238863331|gb|ACR65329.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BW2952]
 gi|242375895|emb|CAQ30576.1| 23S rRNA and tRNA pseudouridine synthase [Escherichia coli
           BL21(DE3)]
 gi|253325956|gb|ACT30558.1| pseudouridine synthase [Escherichia coli 'BL21-Gold(DE3)pLysS AG']
 gi|253972082|gb|ACT37753.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli B str. REL606]
 gi|253976291|gb|ACT41961.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli BL21(DE3)]
 gi|257757440|dbj|BAI28937.1| pseudouridine synthase [Escherichia coli O103:H2 str. 12009]
 gi|281177273|dbj|BAI53603.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           SE15]
 gi|284919840|emb|CBG32895.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           042]
 gi|291321173|gb|EFE60615.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           B088]
 gi|291430047|gb|EFF03061.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1412]
 gi|291472402|gb|EFF14884.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli B354]
 gi|298280994|gb|EFI22495.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           FVEC1302]
 gi|299880242|gb|EFI88453.1| pseudouridine synthase A [Escherichia coli MS 196-1]
 gi|300306729|gb|EFJ61249.1| pseudouridine synthase A [Escherichia coli MS 200-1]
 gi|300316231|gb|EFJ66015.1| pseudouridine synthase A [Escherichia coli MS 175-1]
 gi|300355628|gb|EFJ71498.1| pseudouridine synthase A [Escherichia coli MS 198-1]
 gi|300395642|gb|EFJ79180.1| pseudouridine synthase A [Escherichia coli MS 69-1]
 gi|300402676|gb|EFJ86214.1| pseudouridine synthase A [Escherichia coli MS 84-1]
 gi|300413355|gb|EFJ96665.1| pseudouridine synthase A [Escherichia coli MS 115-1]
 gi|300420558|gb|EFK03869.1| pseudouridine synthase A [Escherichia coli MS 182-1]
 gi|300451839|gb|EFK15459.1| pseudouridine synthase A [Escherichia coli MS 116-1]
 gi|300455694|gb|EFK19187.1| pseudouridine synthase A [Escherichia coli MS 21-1]
 gi|300525539|gb|EFK46608.1| pseudouridine synthase A [Escherichia coli MS 119-7]
 gi|300531300|gb|EFK52362.1| pseudouridine synthase A [Escherichia coli MS 107-1]
 gi|300839659|gb|EFK67419.1| pseudouridine synthase A [Escherichia coli MS 124-1]
 gi|300843813|gb|EFK71573.1| pseudouridine synthase A [Escherichia coli MS 78-1]
 gi|301073563|gb|EFK88369.1| pseudouridine synthase A [Escherichia coli MS 146-1]
 gi|305851006|gb|EFM51461.1| 23S rRNA/tRNA pseudouridine synthase A [Escherichia coli NC101]
 gi|306908469|gb|EFN38967.1| pseudouridine synthase [Escherichia coli W]
 gi|308120287|gb|EFO57549.1| pseudouridine synthase A [Escherichia coli MS 145-7]
 gi|309700270|emb|CBI99558.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           ETEC H10407]
 gi|310337649|gb|EFQ02760.1| RNA pseudouridylate synthase family protein [Escherichia coli
           1827-70]
 gi|313646565|gb|EFS11026.1| RNA pseudouridylate synthase family protein [Shigella flexneri 2a
           str. 2457T]
 gi|315059282|gb|ADT73609.1| pseudouridine synthase for 23S rRNA (position 746) and
           tRNAphe(position 32) [Escherichia coli W]
 gi|315255668|gb|EFU35636.1| pseudouridine synthase A [Escherichia coli MS 85-1]
 gi|315616165|gb|EFU96784.1| RNA pseudouridylate synthase family protein [Escherichia coli 3431]
 gi|320179617|gb|EFW54566.1| Ribosomal large subunit pseudouridine synthase A [Shigella boydii
           ATCC 9905]
 gi|320200424|gb|EFW75010.1| Ribosomal large subunit pseudouridine synthase A [Escherichia coli
           EC4100B]
 gi|323160072|gb|EFZ46034.1| RNA pseudouridylate synthase family protein [Escherichia coli
           E128010]
 gi|323166108|gb|EFZ51887.1| RNA pseudouridylate synthase family protein [Shigella sonnei 53G]
 gi|323380161|gb|ADX52429.1| pseudouridine synthase [Escherichia coli KO11]
 gi|323935111|gb|EGB31478.1| RNA pseudouridylate synthase [Escherichia coli E1520]
 gi|323939843|gb|EGB36044.1| RNA pseudouridylate synthase [Escherichia coli E482]
 gi|323945687|gb|EGB41735.1| RNA pseudouridylate synthase [Escherichia coli H120]
 gi|323960005|gb|EGB55651.1| RNA pseudouridylate synthase [Escherichia coli H489]
 gi|323964843|gb|EGB60310.1| RNA pseudouridylate synthase [Escherichia coli M863]
 gi|323975775|gb|EGB70871.1| RNA pseudouridylate synthase [Escherichia coli TW10509]
 gi|324008404|gb|EGB77623.1| pseudouridine synthase A [Escherichia coli MS 57-2]
 gi|324012314|gb|EGB81533.1| pseudouridine synthase A [Escherichia coli MS 60-1]
 gi|324017675|gb|EGB86894.1| pseudouridine synthase A [Escherichia coli MS 117-3]
 gi|324112541|gb|EGC06518.1| RNA pseudouridylate synthase [Escherichia fergusonii B253]
 gi|325495982|gb|EGC93841.1| pseudouridine synthase [Escherichia fergusonii ECD227]
 gi|327255037|gb|EGE66640.1| RNA pseudouridylate synthase family protein [Escherichia coli
           STEC_7v]
 gi|330909906|gb|EGH38416.1| ribosomal large subunit pseudouridine synthase A [Escherichia coli
           AA86]
 gi|331040255|gb|EGI12462.1| pseudouridine synthase A [Escherichia coli H736]
 gi|331051405|gb|EGI23454.1| pseudouridine synthase A [Escherichia coli M718]
 gi|331066504|gb|EGI38381.1| pseudouridine synthase A [Escherichia coli TA271]
 gi|331072092|gb|EGI43428.1| pseudouridine synthase A [Escherichia coli H591]
 gi|332098910|gb|EGJ03861.1| RNA pseudouridylate synthase family protein [Shigella boydii
           3594-74]
 gi|332103609|gb|EGJ06955.1| 23S rRNA/tRNA pseudouridine synthase A [Shigella sp. D9]
 gi|332341388|gb|AEE54722.1| pseudouridine synthase RluA [Escherichia coli UMNK88]
 gi|332762617|gb|EGJ92882.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           4343-70]
 gi|332764899|gb|EGJ95127.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-671]
 gi|333009190|gb|EGK28646.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-218]
 gi|333011440|gb|EGK30854.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-272]
 gi|333021679|gb|EGK40928.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-227]
 gi|333022430|gb|EGK41668.1| RNA pseudouridylate synthase family protein [Shigella flexneri
           K-304]
          Length = 219

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>gi|284008559|emb|CBA75113.1| ribosomal large subunit pseudouridine synthase A [Arsenophonus
           nasoniae]
          Length = 215

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/147 (14%), Positives = 59/147 (40%), Gaps = 16/147 (10%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++      + + ++   + + F    SV RLD+ T G++++  +  
Sbjct: 16  QDQHIIVVNKPSGLLSVPGKAVEHKDSIMTRVQADFPTAESVHRLDMATSGIMVVALNKT 75

Query: 130 LARVLELP--STQWLRVYRVRFHGQVDQD----KLNLL-------KKGIVIQGICYGDMQ 176
             + L+      +  ++Y+ R  G +        L L+       K+ +          +
Sbjct: 76  AEKELKRQFREREPEKIYQARVWGHITNKKGLIDLPLICDWPNRPKQKVCFTTGKPAQTK 135

Query: 177 VTLDTQKGSNAWVTVG-LREGKNREIK 202
             +   +     V +  +  G++ +++
Sbjct: 136 YKVLAYEEQTTLVKLIPIT-GRSHQLR 161


>gi|227891498|ref|ZP_04009303.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
 gi|227866645|gb|EEJ74066.1| ribosomal large subunit pseudouridine synthase D [Lactobacillus
           salivarius ATCC 11741]
          Length = 296

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 37/229 (16%), Positives = 71/229 (31%), Gaps = 37/229 (16%)

Query: 8   QENFTPQRVSKVIARAGIASRREVERMIA-QQRVKVNGILLERAAVNV------------ 54
           +E+     + K +   G+ S R +  +     +V V+G      ++ V            
Sbjct: 7   KESDEKMTLKKFLKNKGV-SHRTLSSLKKGNGKVLVDGKK-RSLSIEVGKGKITLILPPE 64

Query: 55  MSTDHIEVDGVPLRKAERTRLWLY-HKPIGLVTT-----HSDPDGRSTVFDNLPSIFSRV 108
            S +++++   PL        WL   KP  L +       +D       F         +
Sbjct: 65  KSDENVKISKEPLDIIYEDSNWLVVDKPPLLSSVPGPSNRTDTLVNRVKFHLWQQKSKDL 124

Query: 109 IS--VGRLDINTEGLLLLTNDGGLARVLEL---PSTQWLRVYRVRFHGQVDQDK------ 157
           +   + RLD +T GL+L+      A+ L           + Y     G + +        
Sbjct: 125 VPHVITRLDRDTSGLVLVAKH-RFAQGLINKQVEEHSIDKRYLAVVEGIIAEKHGIIDKP 183

Query: 158 LNLLKKG----IVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
           L   + G    +   G          +        V   L  G+  +I+
Sbjct: 184 LGPRENGIGQMVTDTGKIAKTEYWVREYLGDKATLVECKLHTGRTHQIR 232


>gi|225552312|ref|ZP_03773252.1| ribosomal large subunit pseudouridine synthase D [Borrelia sp. SV1]
 gi|225371310|gb|EEH00740.1| ribosomal large subunit pseudouridine synthase D [Borrelia sp. SV1]
          Length = 326

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 83/248 (33%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   LKREFTVKENAL--RLDLYLSGNFEVFTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHI--EVDGV-------------PLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I  E D                +   E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEESSQVDCLRPSNIPIVIIYEDSNVIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRTNKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--E--------- 195
               G  +      ++  I           V+ D  K +     + L   E         
Sbjct: 178 AIVKGNFN-SFFGSIESFIDRDKHNRKKFSVSKDRGKKALTEYRLLLNFGEYSLLALKPK 236

Query: 196 -GKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 8/65 (12%)

Query: 1  MKDKNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDH 59
          M D+N        QR+ +++   G  ASR      + +  V++ G ++ +A     +   
Sbjct: 1  MSDQNT-------QRLDQLLVSLGLFASRSRARDAVQRGTVRIGGQVVTKAGALFSADAA 53

Query: 60 IEVDG 64
          IE+D 
Sbjct: 54 IEIDD 58


>gi|328870665|gb|EGG19038.1| hypothetical protein DFA_02281 [Dictyostelium fasciculatum]
          Length = 579

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 70/197 (35%), Gaps = 32/197 (16%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHI-------EVDGVPLRK---AERTRLWLYHKPIGL 84
           IA  ++ VN  L   A   + S D         E+D + L     AE     +  KP  +
Sbjct: 176 IAMGKILVND-LPTTADYVIKSGDTFKHIVHRHEIDVLALEPTLIAETLDYLVVDKPPSI 234

Query: 85  VTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
               + P   +++   L   F  + +++  RLD  T G+++L  +   +  L        
Sbjct: 235 PVHPAGPYRHNSLTFLLARQFGYTNLLACHRLDRLTSGVVVLAKNSTASGRLGKVFKKGD 294

Query: 141 WLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVG-------- 192
             ++Y  +  G     +  ++ K I++     G + V     K S  +  +         
Sbjct: 295 IDKIYLAKVKGMFPYLEETMVAKPIMVLNEITG-LGVEDARGKPSTTFFKLAHYNKESDT 353

Query: 193 -------LREGKNREIK 202
                  +  G+  +I+
Sbjct: 354 SIIWCRPIT-GRGHQIR 369


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

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 90/248 (36%), Gaps = 58/248 (23%)

Query: 7   VQENFTPQRVSK----VIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           V+ +    R+ +         G      +++++   +++V+G  ++   V ++    I V
Sbjct: 9   VEADENGMRLDRWFKVYYPDVGFG---YLQKLLRSGQIRVDGGRVKN-DVRLVMGQSIRV 64

Query: 63  DGVPLRKA-------------------------ERTRLWLYHKPIGLVTTHSDPDGRST- 96
             + + K                          E +++++++KP GL         R   
Sbjct: 65  PPLLIDKEDSFPVINKIVCGQDNDIILKDMLLYEDSKIFVFNKPAGLAVQGGSGLTRHVD 124

Query: 97  ----VFDNLPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYRVRFH 150
               V+ N      R+  V R+D  T G+L++    G A+ L     + +  + Y     
Sbjct: 125 SMLEVWRNKKGEKPRL--VHRIDRETSGVLVVARSRGAAQALTAAFRTRETKKTYWALVR 182

Query: 151 GQV--DQDKLNL-LKKGIVIQGICYGDMQVT-------------LDTQKGSNAWVTVGLR 194
           G     QDK++  + + I  QG      +               LDT+  + +W+ +   
Sbjct: 183 GVPRKKQDKISTWMVREITAQGDKMRVCERRQPDSNHAVSYYRVLDTRGKALSWLEMEPY 242

Query: 195 EGKNREIK 202
            G+  +++
Sbjct: 243 TGRTHQLR 250


>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 = 49.0 bits (116), 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+  ++ R G AS RR+  +++    V VNG  + + + N+   D +E+
Sbjct: 99  RLDNIVFRMGFASSRRQARQLVNHGHVLVNGRRVNKPSFNLRVGDIVEI 147


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 30/66 (45%), Gaps = 4/66 (6%)

Query: 1   MKDKNIVQENFTPQ---RVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMS 56
           MK   I  +N       R+  V+ R G A +R+E  + +    + VNG  ++  +  V +
Sbjct: 71  MKRDGIAGDNLMSILETRLDNVVFRLGFARTRKEARQTVRHGHITVNGRRVDIPSYQVKA 130

Query: 57  TDHIEV 62
            D + V
Sbjct: 131 GDVVAV 136


>gi|226943601|ref|YP_002798674.1| Pseudouridine synthase, RluC [Azotobacter vinelandii DJ]
 gi|226718528|gb|ACO77699.1| Pseudouridine synthase, RluC [Azotobacter vinelandii DJ]
          Length = 278

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/209 (17%), Positives = 67/209 (32%), Gaps = 42/209 (20%)

Query: 33  RMIAQQRVKVN-GILLERAAVNVMSTDHIEV-------DGVPLRKA-------------E 71
           R++ +  V+VN G +  +    + + D + V          P+  A             E
Sbjct: 4   RILRKGEVRVNKGRI--KPEYKLQAGDLVRVPPLRLAERDEPVPLAQGLLERLEAAIVHE 61

Query: 72  RTRLWLYHKPIGLVTTHSDPDGRSTVFDN--LPSIFSRVISVGRLDINTEGLLLLTNDGG 129
              L + +KP G+            +     L      +  V RLD +T GLL++     
Sbjct: 62  DKSLIVLNKPAGIAVHGGSGLSHGVIEALRQLRPEARDLELVHRLDRDTSGLLMIAKKRS 121

Query: 130 LARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQ-KGSN 186
           + R L   L      + Y     G         +   +    +  G+  V +D + + + 
Sbjct: 122 MLRHLHEALRGDGVDKRYLALVRGAWP-SARKQVSAPLQKNTLRSGERMVEVDEEGREAL 180

Query: 187 AWVTV--------GLRE-----GKNREIK 202
               V         L E     G+  +I+
Sbjct: 181 TLFRVLRRFGDFATLVEAKPVTGRTHQIR 209


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MKDKNIVQENFTP-QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST- 57
          M +++I  +  TP  R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +  
Sbjct: 1  MTEQHI--DPATPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGH 58

Query: 58 DHIEVD 63
            + VD
Sbjct: 59 SELAVD 64


>gi|1665844|emb|CAA70352.1| yfiI [Borrelia burgdorferi]
          Length = 309

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 85/248 (34%), Gaps = 53/248 (21%)

Query: 1   MKDKNIVQENFTPQRVSKVIA-RAGIASRREVERMIAQQRV----KVNGILLE-RAAVNV 54
           +K +  V+EN    R+   ++    + +R +    I ++ V    K NG  L+ + +  V
Sbjct: 4   VKREFTVKENAL--RLDLYLSGNFEVFTRSQ----IKRRNVEAFKKSNGKFLKIKLSKPV 57

Query: 55  MSTDHI--EVD------------GVPLRK-AERTRLWLYHKPIGLVTTHSDPDGRSTVFD 99
              D I  E D             +P+    E + + + +KP G+++         TV +
Sbjct: 58  FKDDEILIEFDEESSQIDCLRPSNIPIAIIYEDSNVIVLNKPQGILSHPGISHWDDTVVN 117

Query: 100 NLPSIFS-----------RVISVGRLDINTEGLLLLTNDGGLARVLELP--STQWLRVYR 146
            L                R   V RLD +T G+L+   +    R L       +  +VY 
Sbjct: 118 FLLYHIKSLKINFNEEKIRPGIVHRLDKDTSGVLICAKNISTLRFLAQQFKDKRINKVYI 177

Query: 147 VRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLR--E--------- 195
               G  +      ++  I           V+ D  K +     + L   E         
Sbjct: 178 AIVKGNFN-SFFGSIESFIDRDKHNRKKFSVSKDRGKKALTEYRLLLNFGEYSLLALKPK 236

Query: 196 -GKNREIK 202
            G+  +++
Sbjct: 237 TGRTHQLR 244


>gi|332365060|gb|EGJ42825.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK355]
          Length = 245

 Score = 49.0 bits (116), 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: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVTPGQVISVREKSLKVP 192


>gi|262278251|ref|ZP_06056036.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
 gi|262258602|gb|EEY77335.1| conserved hypothetical protein [Acinetobacter calcoaceticus
           RUH2202]
          Length = 212

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/117 (19%), Positives = 43/117 (36%), Gaps = 16/117 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLAR 132
             + HKP  +++     D   +V   L +I  + + + RLD +T G+L+   +  G  A 
Sbjct: 16  FMVIHKPSDILSVPGKGDLHDSVLTRLVAIEPKTLLIHRLDRDTSGILVFGLSKRGQSAI 75

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 76  ARQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVIYDPSRPPLHIV 118


>gi|229496851|ref|ZP_04390560.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           endodontalis ATCC 35406]
 gi|229316262|gb|EEN82186.1| ribosomal large subunit pseudouridine synthase D [Porphyromonas
           endodontalis ATCC 35406]
          Length = 359

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 36/181 (19%), Positives = 64/181 (35%), Gaps = 28/181 (15%)

Query: 4   KNIVQENFTPQRVSKVIARAG-IASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEV 62
           + +V +  TP R+ K +      +SR  ++       + V G    ++   V   D I +
Sbjct: 34  RIVVDKGQTPLRIDKFLVDKLEHSSRHRIQLAAEAGYLFV-GETPIKSNYKVRPGDVITL 92

Query: 63  -------------DGVPLRKA-ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--- 105
                        + +PL    E   L + +KP G+V    + +   T+ + L   F   
Sbjct: 93  RLARPPHERGIVAEDIPLEVVYEDNDLLVVNKPAGMVVHPGNGNYTGTLVNALAYYFRDD 152

Query: 106 -------SRVISVGRLDINTEGLLLLTNDGGLARVLELPSTQW--LRVYRVRFHGQVDQD 156
                    V  V R+D +T GLL++         L     +    R YR    G   + 
Sbjct: 153 PKYDANDPNVGLVHRIDKDTSGLLVVAKRPEAKTALGKQFFEKTSERSYRALVWGAFKES 212

Query: 157 K 157
           +
Sbjct: 213 E 213


>gi|15602857|ref|NP_245929.1| 23S rRNA pseudouridylate synthase C [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|20139710|sp|Q9CM51|RLUC_PASMU RecName: Full=Ribosomal large subunit pseudouridine synthase C;
           AltName: Full=rRNA pseudouridylate synthase C; AltName:
           Full=rRNA-uridine isomerase C
 gi|12721319|gb|AAK03076.1| RluC [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 326

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 80/238 (33%), Gaps = 45/238 (18%)

Query: 6   IVQENFTPQRVSKVI-ARAGIASRREVERMIAQQRVKVN-GILLERAAVNVMSTDHIEVD 63
            + E+   QR+   + A+     +  + R++ +  V+VN G +  +    + + D + V 
Sbjct: 18  TISEDEAGQRIDNYLLAKLKGVPKSLIYRILRKGEVRVNKGRI--KPEYKLQANDIVRVP 75

Query: 64  GVPLRKAERTRL---------------------WLYHKPIGLVTTHSDPDGRSTVFDN-- 100
            V + + E   +                      + +KP G+            +     
Sbjct: 76  PVRVSEKEHAPISTKLNKVSQLEKQILFEDECLLVLNKPSGIAVHGGSGLSFGVIEALRT 135

Query: 101 LPSIFSRVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQVDQDKL 158
           L      +  V RLD +T G+LL+       R L   L      + Y     GQ  Q   
Sbjct: 136 LRPDARFLELVHRLDRDTSGILLVAKKRSALRSLHEQLREKTVQKDYLALVRGQW-QSHC 194

Query: 159 NLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLRE--------------GKNREIK 202
            ++K  + ++       ++   +++G  +     + E              G+  +I+
Sbjct: 195 KVVKAPL-LKNELSSGERIVRVSEQGKPSETRFSIEERYEYATLVKASPVTGRTHQIR 251


>gi|260063065|ref|YP_003196145.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
 gi|88784634|gb|EAR15804.1| ribosomal large subunit pseudouridine synthase D [Robiginitalea
           biformata HTCC2501]
          Length = 236

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/174 (13%), Positives = 45/174 (25%), Gaps = 25/174 (14%)

Query: 64  GVPLRKAERTRLWLYHKPIGLVTTHS---DPDGRSTVFDNLPSIFSR-----VISVGRLD 115
           G  +   E   L    K  G +       D     TV D +   + +     +  V RLD
Sbjct: 9   GNLMVLYEDNHLIAVSKRAGDIVQGDKTGDTPLPETVKDYIAHKYQKPGKVFLGVVHRLD 68

Query: 116 INTEGLLLLTNDGGLARVLEL--PSTQWLRVYRVRFHGQVDQDKLNLLKKGIV------- 166
             T G+++          +          + Y     G    +    L   +        
Sbjct: 69  RPTTGVIVFARTSKALSRMNRLFAEGGTRKTYWALV-GTPPPETAGRLVHWLERNQKQNK 127

Query: 167 -------IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                  + G     +   L         + + L  G++ +I+         + 
Sbjct: 128 SYARAKEVPGSKQAILNYRLLGSLDRYHLLEIDLETGRHHQIRAQLAAIGSPIK 181


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 23/51 (45%)

Query: 10  NFTPQRVSKVIARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHI 60
             +  R+  +I+ A   SR++ ++++    VKVN   +E         D +
Sbjct: 83  TVSSMRLDVIISNAHHISRQKAKQLVVAGLVKVNWKTVENPDFECEEEDVL 133


>gi|327392692|dbj|BAK10114.1| ribosomal large subunit pseudouridine synthase A RluA [Pantoea
           ananatis AJ13355]
          Length = 217

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/166 (16%), Positives = 59/166 (35%), Gaps = 31/166 (18%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           +   + + +KP GL++      + + +V   +   +    SV RLD+ T G++++     
Sbjct: 17  QDAHIMVVNKPSGLLSVPGRLDEHKDSVMTRIQRDYPEAESVHRLDMATSGVIVVALTKA 76

Query: 130 LARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVTLDTQ 182
             R L+    +    + Y  R  G   Q+      KG+V    I         +V  DT 
Sbjct: 77  AERELKRQFREREPAKTYVARVWGHPAQE------KGMVDLPLICDWPNRPKQKVCFDTG 130

Query: 183 KGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
           K +     V               +  G++ +++  +       + 
Sbjct: 131 KSAQTDYQVVEYGDDNSARVALKPIT-GRSHQLRVHML-ALGHPIL 174


>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 = 49.0 bits (116), Expect = 0.001,   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|288904349|ref|YP_003429570.1| ribosomal large subunit pseudouridine synthase, RluD subfamily
           [Streptococcus gallolyticus UCN34]
 gi|288731074|emb|CBI12620.1| putative ribosomal large subunit pseudouridine synthase, RluD
           subfamily [Streptococcus gallolyticus UCN34]
          Length = 286

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/150 (15%), Positives = 52/150 (34%), Gaps = 23/150 (15%)

Query: 71  ERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDG-- 128
           +   L + +KP G+ T  ++P+  + +      +      + RLD+ T G  +   +   
Sbjct: 86  QDEHLIIVNKPEGMKTHGNEPNEIALLNHVSAYVGQTCYVIHRLDMETSGAAMFAKNPFV 145

Query: 129 -GLARVLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNA 187
             +   L   +    R Y     G+ +     + +  I   G    D +  +  +K    
Sbjct: 146 LPIINRLL-ENKDIAREYWALVQGKFEPKH-QVFQDKI---GRDRHDRRKRVVDRKNGQT 200

Query: 188 WVTVG---------------LREGKNREIK 202
            +T+                L+ G+  +I+
Sbjct: 201 ALTIVDRLKVFPNGTLVKCRLKTGRTHQIR 230


>gi|262369409|ref|ZP_06062737.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           johnsonii SH046]
 gi|262315477|gb|EEY96516.1| ribosomal large subunit pseudouridine synthase D [Acinetobacter
           johnsonii SH046]
          Length = 350

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 37/175 (21%), Positives = 68/175 (38%), Gaps = 35/175 (20%)

Query: 7   VQENFTPQRVSKVIARAGIAS---RREVERMIAQQRVKVNGILLE--------------- 48
           + E +  QR+ +V   A I S   R ++++ + +  + VNG  ++               
Sbjct: 43  LDETYLGQRIDQV--AATIWSEFSREKLKQWLKEGHLLVNGNSVKPKYKCEGFELLTLEV 100

Query: 49  --RAAVNVMSTDHIEVDGVPLRKAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFS 106
              A    +  D I +D       E   + + +KP+G+V      +   T+ + L   + 
Sbjct: 101 ELEAQTRSLPED-IPLD----IVYEDDDIIVVNKPVGMVVHPGAGNSSGTLVNALLHHYP 155

Query: 107 ------RVISVGRLDINTEGLLLLTNDGGLARVLE--LPSTQWLRVYRVRFHGQV 153
                 R   V R+D +T GLL++  +      L   L      RVY +  +G V
Sbjct: 156 KSAELTRAGLVHRIDKDTSGLLVVAKNLEAQFSLSKQLAKKTVYRVYDLIVYGNV 210


>gi|260853270|ref|YP_003227161.1| pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|260866210|ref|YP_003232612.1| pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|257751919|dbj|BAI23421.1| pseudouridine synthase [Escherichia coli O26:H11 str. 11368]
 gi|257762566|dbj|BAI34061.1| pseudouridine synthase [Escherichia coli O111:H- str. 11128]
 gi|323157880|gb|EFZ43983.1| RNA pseudouridylate synthase family protein [Escherichia coli
           EPECa14]
 gi|323176365|gb|EFZ61957.1| RNA pseudouridylate synthase family protein [Escherichia coli 1180]
 gi|324118408|gb|EGC12302.1| RNA pseudouridylate synthase [Escherichia coli E1167]
          Length = 219

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 15  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 74

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 75  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 128

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 129 YETGKPAQTEYEVVEYVADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 176


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 29/67 (43%), Gaps = 2/67 (2%)

Query: 14  QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
            R+  V+ R G   SR E  +++      +NG  ++  +  V + D I V     +  E+
Sbjct: 98  MRLDNVVFRLGYGNSRTEARQLVTHGHFLINGKKVDIPSYQVSANDVITVCDKS-KATEK 156

Query: 73  TRLWLYH 79
            + +  +
Sbjct: 157 FKTFAEN 163


>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 = 49.0 bits (116), Expect = 0.001,   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|21232518|ref|NP_638435.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66767398|ref|YP_242160.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. 8004]
 gi|34395783|sp|Q8P682|RLUD_XANCP RecName: Full=Ribosomal large subunit pseudouridine synthase D;
           AltName: Full=rRNA pseudouridylate synthase D; AltName:
           Full=rRNA-uridine isomerase D
 gi|21114309|gb|AAM42359.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. ATCC 33913]
 gi|66572730|gb|AAY48140.1| ribosomal large subunit pseudouridine synthase D [Xanthomonas
           campestris pv. campestris str. 8004]
          Length = 331

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 60/322 (18%), Positives = 107/322 (33%), Gaps = 43/322 (13%)

Query: 6   IVQENFTPQRVSKVIARA-GIASRREVERMIAQQRVKVNGILLE-RAAVNVMSTDHIEV- 62
           +V ++   +R   V+A      SR  +   I      ++G     R  +    T  ++V 
Sbjct: 17  VVPDSAAGRRFDAVLAELFPEFSRSRLSEWIKSGDALLDGETARPRDTLRGGETVQVQVV 76

Query: 63  ---------DGVPLRK-AERTRLWLYHKPIGLVTT--HSDPDGRSTVFDNLPSIF----S 106
                      +PL    E   + +  KP GLV      +PDG                 
Sbjct: 77  LETQTHAAPQDIPLNVLYEDDHVLVIDKPAGLVVHPGAGNPDGTLVNALLFRDPNLAAVP 136

Query: 107 RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQWLRVYRVRFHG----------QVD 154
           R   V RLD +T G++++         L  +L +    R Y     G           +D
Sbjct: 137 RAGVVHRLDKDTSGVMVVARTLQAQTALVEQLSARDVHRQYLAVVVGALVSGGTADAPID 196

Query: 155 QDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVNR 214
           +   + LK  +   G          +  +   A +   L  G+  +I+         +  
Sbjct: 197 RHPRDRLKMAVRDDGRDAVTHYRLRERFRAHTA-LECRLETGRTHQIRVHMAHLKSPIVG 255

Query: 215 --LIRISYGPFQLGTLLAGSTREVSKKI---LREQLGPHLLEEAQVNLDAPIYSSETLVR 269
             L    YG   L  L  G+T  +  ++    R+ L    LE        PI +S  +  
Sbjct: 256 DPL----YGG-ALK-LPKGATDTLVAELRGFKRQALHAETLEFLHPVSGEPIRASAPVPE 309

Query: 270 DRPNIISEVPDDFTRMKKNSSQ 291
           D   ++S + +D  R  + + +
Sbjct: 310 DLQRLMSALREDSARAAELARR 331


>gi|269798687|ref|YP_003312587.1| pseudouridine synthase [Veillonella parvula DSM 2008]
 gi|269095316|gb|ACZ25307.1| pseudouridine synthase [Veillonella parvula DSM 2008]
          Length = 372

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 22/148 (14%), Positives = 47/148 (31%), Gaps = 30/148 (20%)

Query: 33  RMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAERTRL----------------- 75
           ++  ++ + +NG             D I VD        + ++                 
Sbjct: 85  KLFEEKLIHINGHKAT-------PKDAISVDDEIWIAMAKEKIDHDPIEMDLSVLYEDED 137

Query: 76  -WLYHKPIGLVTTHSDPDGRST-VFDNLPSI--FSRVISVGRLDINTEGLLLLTNDG--G 129
            ++  KP G+     D    +  V           +V  + RLD +T G +++   G   
Sbjct: 138 LFIVDKPSGVTVNSKDRLSLANGVAHYFKEHGIKRKVRFLNRLDRDTTGCIVIAKSGLAQ 197

Query: 130 LARVLELPSTQWLRVYRVRFHGQVDQDK 157
                ++    + + Y     G V+ D+
Sbjct: 198 SLYQQQMDDNTFEKWYMATVEGIVEADE 225


>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 (116), 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|332024709|gb|EGI64898.1| RNA pseudouridylate synthase domain-containing protein 2
           [Acromyrmex echinatior]
          Length = 335

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 87/235 (37%), Gaps = 25/235 (10%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTNDGGLAR 132
           + + +KP  +          +TV   L   +    + ++ RLD  T G+LL       AR
Sbjct: 5   VVVVNKPASIPVHPCGRYRHNTVVFILAKEYNLKNLRTIHRLDRLTSGILLFGRTPKKAR 64

Query: 133 VLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQK------- 183
            +E    + Q  + Y  R  G+  ++++ +  + I +     G  +V+   +        
Sbjct: 65  QMEHQIRNRQVHKQYVCRVEGEFPEEEV-ICSEPIEVVSYKIGVCKVSEKGKDCVTRFKR 123

Query: 184 ----GSNAWVTVGLREGKNREIKKVFEFFNWKVNR--L-IRISYGPFQLGTLLAGSTREV 236
               G ++ V    + G+  +I+   ++  + V    L   + +GP +      G     
Sbjct: 124 LSYNGKSSVVLCKPQTGRMHQIRVHLQYLGYPVVNDPLYNHVVFGPHKGKGGNIGK---- 179

Query: 237 SKKIL-REQLGPHLLEE-AQVNLDAPIYSSETLVRDRPNIISEVPDDFTRMKKNS 289
           + + L R+ +  H  E    ++ D+ +   +  +     ++    D       +S
Sbjct: 180 TDEELVRDLISIHNAENWLGMDGDSDMSLFKPKLELEERMLGSGNDKDNGSSPSS 234


>gi|324989545|gb|EGC21491.1| 30S ribosomal protein S4 [Streptococcus sanguinis SK353]
          Length = 245

 Score = 49.0 bits (116), 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: 136 RLDNVVYRLGLATTRRQARQFVNHGHILVDGKRVDIPSYRVNPGQVISVREKSLKVP 192


>gi|146302439|ref|YP_001197030.1| pseudouridine synthase [Flavobacterium johnsoniae UW101]
 gi|146156857|gb|ABQ07711.1| ribosomal large subunit pseudouridine synthase D [Flavobacterium
           johnsoniae UW101]
          Length = 229

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/167 (8%), Positives = 49/167 (29%), Gaps = 23/167 (13%)

Query: 70  AERTRLWLYHKPIGLVTTHSDPDGRS---TVFDNLPSIFSR-----VISVGRLDINTEGL 121
            E   + + +K +G +        +     V + +   +++     +  + RLD  T G+
Sbjct: 14  HEDNHIIVVNKRVGDIVQGDKTGDKPLSDIVKEYIKDKYNKPGDVFLGVIHRLDRPTTGI 73

Query: 122 LLLTNDGGLARVL--ELPSTQWLRVYRVRFHGQVDQDKLNLL-------------KKGIV 166
           ++          +     + +  + Y      +  +    L+                  
Sbjct: 74  VVFARTSKALSRMNELFSNRETKKTYWAVVKNKPVEAAAKLVHYLKRNEKNNTSKAHLKE 133

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
           +       +   +  +  +   + + L  G++ +I+         + 
Sbjct: 134 VPDSKLASLDYKIIKELQNYTALEINLHTGRHHQIRAQLSAIGSPIK 180


>gi|325122993|gb|ADY82516.1| dual specificity pseudouridine synthase for 23S rRNA and tRNAphe
           modification [Acinetobacter calcoaceticus PHEA-2]
          Length = 212

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/117 (19%), Positives = 43/117 (36%), Gaps = 16/117 (13%)

Query: 75  LWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLL--TNDGGLAR 132
             + HKP  +++     D   +V   L +I  + + + RLD +T G+L+   +  G  A 
Sbjct: 16  FMVIHKPSDILSVPGKGDLHDSVLTRLVAIEPKTLLIHRLDRDTSGILVFGLSKRGQSAI 75

Query: 133 VLELPSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWV 189
             +    Q  ++Y     G               ++G    D+ V  D  +     V
Sbjct: 76  ARQFQDRQTSKIYEALVAGH--------------LEGEGTVDIPVIYDPSRPPLHIV 118


>gi|289450514|ref|YP_003475442.1| putative rRNA pseudouridylate synthase C [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
 gi|289185061|gb|ADC91486.1| putative rRNA pseudouridylate synthase C [Clostridiales genomosp.
           BVAB3 str. UPII9-5]
          Length = 327

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 32/178 (17%), Positives = 55/178 (30%), Gaps = 35/178 (19%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIF--SRVISVGRLDINTEGLLLLTND 127
           E   + L +KP GL      +    ST+ + L + +    +    RLD NT GL+L+  +
Sbjct: 89  EDKNIILINKPQGLTVHPGKNTPPHSTLIEKLRADYNDENLTLCHRLDRNTGGLVLVAKN 148

Query: 128 GGLARVL--ELPSTQWLRVYRVRFHGQVD------------QDKLNLL------KKGIVI 167
                 +   L   Q ++ YR    G  D              +LN           + I
Sbjct: 149 KVTLGKINEALAEQQVIKRYRCLVRGIPDIGRDVYISDGDSMHELNAFWEKPANSDEVFI 208

Query: 168 QGICYGD------------MQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 D            +   L       + + V L  G+  +I+         + 
Sbjct: 209 HDEQQADDLPICTRYRVLHIFTALAADGEPISELEVELVTGRTHQIRAHLAHIGHPIL 266


>gi|148555622|ref|YP_001263204.1| ribosomal large subunit pseudouridine synthase C [Sphingomonas
           wittichii RW1]
 gi|148500812|gb|ABQ69066.1| ribosomal large subunit pseudouridine synthase C [Sphingomonas
           wittichii RW1]
          Length = 368

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 49/172 (28%), Gaps = 28/172 (16%)

Query: 65  VPLRKAERTRLWLYHKPIGLVT---THSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGL 121
             L   +  +  + +KP GL T   T +D      +        SR   V RLD +T G+
Sbjct: 100 RSLVIHQDRQAIVINKPPGLATQGGTKTDIHVDRLLDALQFDAESRPKLVHRLDKDTSGV 159

Query: 122 LLLTNDGGLARVLELP--STQWLRVYRVRFHGQVDQDKLNLLKKGIVI------------ 167
           LLL      A        S    +VY     G    D        I +            
Sbjct: 160 LLLARTSRAAAHFAKAFSSRTARKVYWAIATGVPSIDD-----GMIELPIAKQPGTGGEK 214

Query: 168 ------QGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +G         ++       WV +    G+  +++         + 
Sbjct: 215 MHVDEKEGSPARTRYRVIERAGNRACWVELQPHTGRTHQLRVHLAAIGHPIV 266


>gi|59713667|ref|YP_206442.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
 gi|59481915|gb|AAW87554.1| ribosomal large subunit pseudouridine synthase A [Vibrio fischeri
           ES114]
          Length = 576

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/156 (16%), Positives = 55/156 (35%), Gaps = 18/156 (11%)

Query: 64  GVPLR-KAERTRLWLYHKPIGLVTTHSDPDGRSTVFDNLPSIFSRVIS---VGRLDINTE 119
           G  L    E   L + +KP+  ++  S      +V   + + +        V RLD++T 
Sbjct: 370 GKELEIVYEDDVLVIVNKPVEFLSV-SGKYISDSVHARIQARYPNATGPLIVHRLDMSTS 428

Query: 120 GLLLLTNDGGLARVLELP--STQWLRVYRVRFHG-----------QVDQDKLNLLKKGIV 166
           GLL+LT      + ++         + Y     G            +  D  +  ++ + 
Sbjct: 429 GLLVLTLTAESNKQVQKQFIERTVEKRYTALLEGNIETDNGTINLPLTGDMEDRPRQMVN 488

Query: 167 IQGICYGDMQVTLDTQKGSNAWVTVGLREGKNREIK 202
            +     +    +  Q+G    V +    G+  +++
Sbjct: 489 HKSGRKAETHYQVIAQEGKRTKVHLYPHTGRTHQLR 524


>gi|56461324|ref|YP_156605.1| pseudouridylate synthase Rlu family protein [Idiomarina loihiensis
           L2TR]
 gi|56180334|gb|AAV83056.1| Predicted pseudouridylate synthase, Rlu family [Idiomarina
           loihiensis L2TR]
          Length = 218

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/158 (14%), Positives = 55/158 (34%), Gaps = 16/158 (10%)

Query: 71  ERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLTNDGG 129
           E ++L +  K  GL++     P+ + +V+  +  +   +  V RLD+ T G+LLL     
Sbjct: 19  EDSQLLVVDKQSGLLSVPGKRPEHKDSVYTRVQRVHPEIRVVHRLDMATSGVLLLAKTKA 78

Query: 130 LARVLEL--PSTQWLRVYRVRFHG-----------QVDQDKLNLLKKGIVIQGICYGDMQ 176
               L     +    + Y  +  G            +  D  N  ++ +           
Sbjct: 79  AQSHLNRQFQNRTTRKRYIAQVWGKPPALQGEIELPLSCDWPNRPRQHMDFFTGKPSTTL 138

Query: 177 VTLDTQKGSNAWVTVGLREGKNREIK-KVFEFFNWKVN 213
             +       + V +    G++ +++  + +     + 
Sbjct: 139 YRVTAFDKGCSRVELTPHTGRSHQLRVHM-QAIGCPIL 175


>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 = 49.0 bits (116), Expect = 0.001,   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  ++++ + V VNGI+    +  V + D + +
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAVTVNGIVANIPSQQVKAGDVVAI 146


>gi|85075514|ref|XP_955780.1| hypothetical protein NCU03846 [Neurospora crassa OR74A]
 gi|28916789|gb|EAA26544.1| hypothetical protein NCU03846 [Neurospora crassa OR74A]
          Length = 473

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/141 (20%), Positives = 49/141 (34%), Gaps = 20/141 (14%)

Query: 35  IAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLRK-AERTRLWLYHKPIGL 84
           +    V VNG  +      + + D I          V   P+R   E   L + +KP G+
Sbjct: 104 VETGLVVVNGKAV-GPEHVLKNGDLISHTTHRHEPPVTAEPIRVIHEDNDLIVINKPSGV 162

Query: 85  VTTHSDPDGRSTVFDNL-----PSIFSRVISVGRLDINTEGLLLLTNDGGLARVLELPST 139
               +     ++V + +     P    R     RLD  T G++ L      A  L    +
Sbjct: 163 PVHPAGRYNYNSVVEIIKSERGPGFLPR--PCNRLDRLTSGIMFLAKSQHAAERLVAQIS 220

Query: 140 Q--WLRVYRVRFHGQVDQDKL 158
           Q    + Y  R  G+    ++
Sbjct: 221 QRSVRKEYIARVVGRFPDGEV 241


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)

Query: 20 IARAGIASRREVERMIAQQRVKVNGILLERAAVNVMSTDHIEVDGVPLRKAER 72
          +A  GI      + MI+   V VNG +  R    +   D + V+G  ++   +
Sbjct: 27 LAEDGI----HAKEMISDGIVTVNGQVDTRRGAQIRPGDVVCVNGECVKVTAQ 75


>gi|255263975|ref|ZP_05343317.1| ribosomal large subunit pseudouridine synthase A [Thalassiobium sp.
           R2A62]
 gi|255106310|gb|EET48984.1| ribosomal large subunit pseudouridine synthase A [Thalassiobium sp.
           R2A62]
          Length = 215

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 53/161 (32%), Gaps = 14/161 (8%)

Query: 67  LRKAERTRLWLYHKPIGLVTTHSDPDG-RSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   E   + L  KP GL++     +     +   L + F   + V RLD +T G+++  
Sbjct: 13  VILHEDHEVILVDKPEGLLSVPGKGEHLADCLLTRLQAAFPTALLVHRLDRDTSGVMIFA 72

Query: 126 NDGGLARVLEL--PSTQWLRVYRVRFHGQVDQ-----------DKLNLLKKGIVIQGICY 172
                 R L L        + Y  R  G +             D  N  ++ I  +    
Sbjct: 73  ATRHAQRHLGLQFEKRHTKKTYVARVWGDLQPKEGTVDQPIIVDWENRPRQKICAETGRA 132

Query: 173 GDMQVTLDTQKGSNAWVTVGLREGKNREIKKVFEFFNWKVN 213
                 +    G+   V +  + G++ +++         + 
Sbjct: 133 AQTDWRVVRGDGAETRVRLMPKTGRSHQLRLHMLHLGHPIL 173


>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 = 49.0 bits (116), 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++    ++ V + D I V
Sbjct: 98  RLDNVVYRMGFGSTRAEARQLVSHKAITVNGVVANIPSLQVKAGDVIAV 146


>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 = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 5/66 (7%)

Query: 1  MKDKNIVQENFTP-QRVSKVIARAGIA-SRREVERMIAQQRVKVNGILLERAAVNVMST- 57
          M +++I  +  TP  R+  ++  +G+  SR + +R+I    V+V+G  + + +  V +  
Sbjct: 1  MTEQHI--DPATPLDRLDMMLVASGLVESRAKAQRLIKAGHVRVDGETITKPSFMVKAGH 58

Query: 58 DHIEVD 63
            + VD
Sbjct: 59 SELAVD 64


>gi|309787283|ref|ZP_07681895.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|308924861|gb|EFP70356.1| RNA pseudouridylate synthase family protein [Shigella dysenteriae
           1617]
 gi|323181753|gb|EFZ67166.1| RNA pseudouridylate synthase family protein [Escherichia coli 1357]
          Length = 217

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/170 (14%), Positives = 59/170 (34%), Gaps = 31/170 (18%)

Query: 67  LRKAERTRLWLYHKPIGLVTT-HSDPDGRSTVFDNLPSIFSRVISVGRLDINTEGLLLLT 125
           +   +   + + +KP GL++      + + +V   +   + +  SV RLD+ T G++++ 
Sbjct: 13  VILYQDDHIMVVNKPSGLLSVPGRLEEHKDSVMTRIQRDYPQAESVHRLDMATSGVIVVA 72

Query: 126 NDGGLARVLELPSTQWL--RVYRVRFHGQVDQDKLNLLKKGIV----IQGICYGDM-QVT 178
                 R L+    +    + Y  R  G           +G+V    I         +V 
Sbjct: 73  LTKAAERELKRQFREREPKKQYVARVWGHPSP------AEGLVDLPLICDWPNRPKQKVC 126

Query: 179 LDTQKGSNAWVTVG--------------LREGKNREIK-KVFEFFNWKVN 213
            +T K +     V               +  G++ +++  +       + 
Sbjct: 127 YETGKPAQTEYEVVEYAADNTARVVLKPIT-GRSHQLRVHML-ALGHPIL 174


>gi|296104263|ref|YP_003614409.1| 23S rRNA pseudouridine synthase D [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295058722|gb|ADF63460.1| 23S rRNA pseudouridine synthase D [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 282

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 30/192 (15%), Positives = 62/192 (32%), Gaps = 32/192 (16%)

Query: 42  VNGILLERAAVNVMSTDHIEVD------------GVPLR-KAERTRLWLYHKPIGLVTTH 88
           VNG + ++    V+  + + ++             +PL    E   + + +KP  LV   
Sbjct: 3   VNGKVWDKPKEKVLGGEAVAINAEIEEEIRFEPQDIPLDIVYEDDDILVINKPRDLVVHP 62

Query: 89  SDPDGRSTVFDNLPSIFS------RVISVGRLDINTEGLLLLTNDGGLARVL--ELPSTQ 140
              +   TV + L   +       R   V RLD +T GL+++         L   L   +
Sbjct: 63  GAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTVPAQTRLVESLQLRE 122

Query: 141 WLRVYRV----------RFHGQVDQDKLNLLKKGIVIQGICYGDMQVTLDTQKGSNAWVT 190
             R Y                 + +         +   G         ++  +  +  + 
Sbjct: 123 ITREYEAVAIGHMTAGGTVDEPISRHPTKRTHMSVHPMGKPAVTHYRIMEHFRI-HTRLR 181

Query: 191 VGLREGKNREIK 202
           + L  G+  +I+
Sbjct: 182 LRLETGRTHQIR 193


>gi|302497041|ref|XP_003010521.1| hypothetical protein ARB_03222 [Arthroderma benhamiae CBS 112371]
 gi|291174064|gb|EFE29881.1| hypothetical protein ARB_03222 [Arthroderma benhamiae CBS 112371]
          Length = 482

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/153 (16%), Positives = 50/153 (32%), Gaps = 24/153 (15%)

Query: 32  ERMIAQQRVKVNGILLERAAVNVMSTDHIE---------VDGVPLR-KAERTRLWLYHKP 81
           +  I   R+ ++G +   A   + +   I          V   P++   E   + +  KP
Sbjct: 45  KAAIDGGRITIDGKVAT-ADSIINNGQVISHTLHRHEPPVTSRPIKIIHEDEDIIVIDKP 103

Query: 82  IGLVTTHSDPDGRSTVFDNLPSIFSRVI---SVGRLDINTEGLLLLTNDGGLARVL--EL 136
            G+    +     +++ + + S            RLD  T G++ L      A  +   L
Sbjct: 104 AGIPVHPAGRYNYNSIIEIMRSERGLGWIPYPCNRLDRLTSGIMFLGKHPKAAEQMAQSL 163

Query: 137 PSTQWLRVYRVRFHGQVDQDKLNLLKKGIVIQG 169
            S    + Y  R  G            G+V+  
Sbjct: 164 RSRTLRKEYIARVKGYFPD--------GVVLCD 188


  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
   0.310    0.161    0.475 

Lambda     K      H
   0.267   0.0493    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,874,111,025
Number of Sequences: 14124377
Number of extensions: 343073444
Number of successful extensions: 1014413
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 13650
Number of HSP's successfully gapped in prelim test: 11723
Number of HSP's that attempted gapping in prelim test: 948167
Number of HSP's gapped (non-prelim): 41729
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 (20.9 bits)
S2: 82 (35.9 bits)